cross_match line1copies consensus -M /home/asmit/Matrices/25p41g.matrix -gap_init -25 -gap_ext -5 -minscore 200 -minmatch 6 -alignments -bandwidth 50 -word_raw 
cross_match version 0.990329

Run date:time  070622:091104
Query file(s):  line1copies
Subject file(s):   LINE1-consensus
Presumed sequence type: DNA

Pairwise comparison algorithm: banded Smith-Waterman

Score matrix /home/asmit/Matrices/25p41g.matrix
    A   R   G   C   Y   T   K   M   S   W   N   X   Z
A   8   1  -6 -13 -14 -15 -11  -2 -10  -3  -1  -7   3
R   2   2   1 -13 -13 -14  -6  -5  -5  -5  -1  -7   3
G  -2   3  10 -13 -13 -13  -1  -8  -1  -8  -1  -7   3
C -13 -13 -13  10   3  -2  -8  -1  -1  -8  -1  -7   3
Y -14 -13 -13   1   2   2  -5  -6  -5  -5  -1  -7   3
T -15 -14 -13  -6   1   8  -2 -11 -10  -3  -1  -7   3
K  -9  -5  -1  -9  -6  -2  -1  -9  -5  -5  -1  -7   3
M  -2  -6  -9  -1  -5  -9  -9  -1  -5  -5  -1  -7   3
S  -8  -4  -1  -1  -4  -8  -4  -4  -1  -8  -1  -7   3
W  -3  -6 -10 -10  -6  -3  -6  -6 -10  -3  -1  -7   3
N  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -1  -7   3
X  -7  -7  -7  -7  -7  -7  -7  -7  -7  -7  -7  -7   3
Z   3   3   3   3   3   3   3   3   3   3   3   3   3

Gap penalties: gap_init: -25, gap_ext: -5, ins_gap_ext: -5, del_gap_ext: -5, 
Using complexity-adjusted scores. Assumed background frequencies:
 A: 0.295  R: 0.000  G: 0.205  C: 0.205  Y: 0.000  T: 0.295  K: 0.000  M: 0.000  S: 0.000  W: 0.000  N: 0.000  X: 0.000  Z: 0.000  

minmatch: 6, maxmatch: 6, max_group_size: 20, minscore: 200, bandwidth: 50, indexwordsize: 6
vector_bound: 0
word_raw: 1
masklevel: 80

Sequence file: line1copies    10316 entries
Residue counts:
  A    10358744
  C    5055934
  G    4679265
  N     1000
  T    6056986
  a    5476638
  c    2645750
  g    2452660
  n        1
  t    3114352
Total  39841330

NO QUALITY FILE line1copies.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15.
Maximal single base matches (low complexity regions):
chr1_32606_35329   Z   Score: 8172   Residues:     1 -  2724
chr1_409965_411589.rev   Z   Score: 4875   Residues:     1 -  1625
chr1_412092_418759.rev   Z   Score: 20004   Residues:     1 -  6668
chr1_428953_431249   Z   Score: 6891   Residues:     1 -  2297
chr1_638935_641231.rev   Z   Score: 6891   Residues:     1 -  2297
chr1_651643_657327   Z   Score: 17055   Residues:     1 -  5685
chr1_657831_659454   Z   Score: 4872   Residues:     1 -  1624
chr1_774474_776152.rev   Z   Score: 5037   Residues:     1 -  1679
chr1_1068782_1074868.rev   Z   Score: 18261   Residues:     1 -  6087
chr1_1161545_1168186.rev   A   Score:  218   Residues:  2440 -  2648
chr1_1161545_1168186.rev   A   Score:  201   Residues:  6022 -  6054
chr1_1161545_1168186.rev   Z   Score: 19926   Residues:     1 -  6642
chr1_1913354_1918211   A   Score:  374   Residues:  2780 -  2866
chr1_1913354_1918211   A   Score:  257   Residues:  2554 -  2656
chr1_1913354_1918211   Z   Score: 14574   Residues:     1 -  4858
chr1_2026908_2030462.rev   Z   Score: 10665   Residues:     1 -  3555
chr1_2223365_2225536.rev   A   Score:  257   Residues:  1379 -  1422
chr1_2223365_2225536.rev   Z   Score: 6516   Residues:     1 -  2172
chr1_2327428_2329808.rev   Z   Score: 7143   Residues:     1 -  2381
chr1_2333140_2335535   T   Score:  243   Residues:  1114 -  1150
chr1_2333140_2335535   Z   Score: 7188   Residues:     1 -  2396
chr1_2561987_2565911   A   Score:  216   Residues:  1471 -  1509
chr1_2561987_2565911   Z   Score: 11775   Residues:     1 -  3925
chr1_3801045_3803517   Z   Score: 7419   Residues:     1 -  2473
chr1_3999551_4002503.rev   A   Score:  208   Residues:  1569 -  1602
chr1_3999551_4002503.rev   Z   Score: 8859   Residues:     1 -  2953
chr1_4005338_4010309   A   Score:  235   Residues:  4880 -  4918
chr1_4005338_4010309   Z   Score: 14916   Residues:     1 -  4972
chr1_4159825_4162726.rev   Z   Score: 8706   Residues:     1 -  2902
chr1_4165684_4170572   A   Score:  222   Residues:   849 -   877
chr1_4165684_4170572   Z   Score: 14667   Residues:     1 -  4889
chr1_4208772_4210862.rev   Z   Score: 6273   Residues:     1 -  2091
chr1_4213784_4218602.rev   A   Score:  241   Residues:  3764 -  3837
chr1_4213784_4218602.rev   Z   Score: 14457   Residues:     1 -  4819
chr1_4256714_4261723.rev   A   Score:  232   Residues:  4111 -  4139
chr1_4256714_4261723.rev   Z   Score: 15030   Residues:     1 -  5010
chr1_4361481_4364201   Z   Score: 8160   Residues:     1 -  2720
chr1_4508226_4510434   Z   Score: 6627   Residues:     1 -  2209
chr1_4547502_4551741.rev   A   Score:  269   Residues:   166 -   209
chr1_4547502_4551741.rev   Z   Score: 12720   Residues:     1 -  4240
chr1_4779303_4785987   Z   Score: 20055   Residues:     1 -  6685
chr1_4831446_4838170.rev   A   Score:  206   Residues:  3630 -  3656
chr1_4831446_4838170.rev   Z   Score: 20175   Residues:     1 -  6725
chr1_4963683_4966954   Y   Score:  237   Residues:  2959 -  3115
chr1_4963683_4966954   T   Score:  856   Residues:  2959 -  3115
chr1_4963683_4966954   Z   Score: 9816   Residues:     1 -  3272
chr1_5024790_5027025   Z   Score: 6708   Residues:     1 -  2236
chr1_5182233_5184870   A   Score:  397   Residues:   263 -   512
chr1_5182233_5184870   G   Score:  290   Residues:   342 -   484
chr1_5182233_5184870   Z   Score: 7914   Residues:     1 -  2638
chr1_5199520_5201339   Z   Score: 5460   Residues:     1 -  1820
chr1_5217487_5220079.rev   Z   Score: 7779   Residues:     1 -  2593
chr1_5540578_5545544   Z   Score: 14901   Residues:     1 -  4967
chr1_5618913_5621354   Z   Score: 7326   Residues:     1 -  2442
chr1_5755380_5758182.rev   Z   Score: 8409   Residues:     1 -  2803
chr1_5948331_5949968   Z   Score: 4914   Residues:     1 -  1638
chr1_6799104_6801278.rev   Z   Score: 6525   Residues:     1 -  2175
chr1_6894333_6896447   Z   Score: 6345   Residues:     1 -  2115
chr1_6926571_6928863.rev   Z   Score: 6879   Residues:     1 -  2293
chr1_6940404_6942895.rev   A   Score:  232   Residues:  2362 -  2403
chr1_6940404_6942895.rev   Z   Score: 7476   Residues:     1 -  2492
chr1_7124589_7127091.rev   Z   Score: 7509   Residues:     1 -  2503
chr1_7160386_7165917.rev   Z   Score: 16596   Residues:     1 -  5532
chr1_7173041_7177672   Z   Score: 13896   Residues:     1 -  4632
chr1_7195485_7200515.rev   A   Score:  306   Residues:  1344 -  1385
chr1_7195485_7200515.rev   A   Score:  203   Residues:  2343 -  2389
chr1_7195485_7200515.rev   Z   Score: 15093   Residues:     1 -  5031
chr1_7234665_7237030   Z   Score: 7098   Residues:     1 -  2366
chr1_7299741_7304098.rev   A   Score:  240   Residues:   457 -   486
chr1_7299741_7304098.rev   Z   Score: 13074   Residues:     1 -  4358
chr1_7388267_7393432.rev   Z   Score: 15498   Residues:     1 -  5166
chr1_7406336_7412748.rev   Z   Score: 19239   Residues:     1 -  6413
chr1_7516074_7519494.rev   Z   Score: 10263   Residues:     1 -  3421
chr1_7768961_7770927.rev   A   Score:  205   Residues:  1238 -  1285
chr1_7768961_7770927.rev   Z   Score: 5901   Residues:     1 -  1967
chr1_7872547_7877651   G   Score:  213   Residues:  2186 -  2218
chr1_7872547_7877651   Z   Score: 15312   Residues:     1 -  5104
chr1_8380759_8382526   Z   Score: 5304   Residues:     1 -  1768
chr1_8392854_8395038.rev   Z   Score: 6555   Residues:     1 -  2185
chr1_8480612_8484412   A   Score:  272   Residues:   470 -   508
chr1_8480612_8484412   Z   Score: 11403   Residues:     1 -  3801
chr1_8687914_8690815   A   Score:  216   Residues:  1999 -  2025
chr1_8687914_8690815   Z   Score: 8706   Residues:     1 -  2902
chr1_11078202_11081367.rev   Z   Score: 9498   Residues:     1 -  3166
chr1_11154626_11161328   A   Score:  244   Residues:  4032 -  4096
chr1_11154626_11161328   Z   Score: 20109   Residues:     1 -  6703
chr1_12405904_12407877   Z   Score: 5922   Residues:     1 -  1974
chr1_12691507_12693704.rev   Z   Score: 6594   Residues:     1 -  2198
chr1_12725098_12728971.rev   Z   Score: 11622   Residues:     1 -  3874
chr1_12744071_12749000   A   Score:  234   Residues:  2699 -  2773
chr1_12744071_12749000   A   Score:  216   Residues:  1359 -  1478
chr1_12744071_12749000   Z   Score: 14790   Residues:     1 -  4930
chr1_13623904_13625853   Z   Score: 5850   Residues:     1 -  1950
chr1_13663366_13665360.rev   Z   Score: 5985   Residues:     1 -  1995
chr1_13747071_13749646.rev   Z   Score: 7728   Residues:     1 -  2576
chr1_13909201_13910790.rev   A   Score:  476   Residues:   285 -   430
chr1_13909201_13910790.rev   R   Score:  255   Residues:   285 -   425
chr1_13909201_13910790.rev   G   Score:  270   Residues:  1265 -  1331
chr1_13909201_13910790.rev   G   Score:  234   Residues:   298 -   402
chr1_13909201_13910790.rev   Z   Score: 4770   Residues:     1 -  1590
chr1_13912443_13915173.rev   Z   Score: 8193   Residues:     1 -  2731
chr1_13951724_13954681.rev   Z   Score: 8874   Residues:     1 -  2958
chr1_13990910_13992757.rev   Z   Score: 5544   Residues:     1 -  1848
chr1_14008256_14010861.rev   A   Score:  216   Residues:  1998 -  2037
chr1_14008256_14010861.rev   Z   Score: 7818   Residues:     1 -  2606
chr1_14068267_14074563   A   Score:  258   Residues:  2881 -  2928
chr1_14068267_14074563   Z   Score: 18891   Residues:     1 -  6297
chr1_14074648_14076432   Z   Score: 5355   Residues:     1 -  1785
chr1_14100526_14102589.rev   Z   Score: 6192   Residues:     1 -  2064
chr1_14157295_14160473.rev   Z   Score: 9537   Residues:     1 -  3179
chr1_14224245_14229177.rev   A   Score:  241   Residues:   438 -   497
chr1_14224245_14229177.rev   A   Score:  204   Residues:  2377 -  2429
chr1_14224245_14229177.rev   Z   Score: 14799   Residues:     1 -  4933
chr1_14296291_14298607   A   Score:  211   Residues:  1553 -  1602
chr1_14296291_14298607   Z   Score: 6951   Residues:     1 -  2317
chr1_14427481_14434141.rev   Z   Score: 19983   Residues:     1 -  6661
chr1_14454372_14460643.rev   Z   Score: 18816   Residues:     1 -  6272
chr1_14473713_14475985   Z   Score: 6819   Residues:     1 -  2273
chr1_14715222_14717608.rev   A   Score:  200   Residues:  1781 -  1805
chr1_14715222_14717608.rev   Z   Score: 7161   Residues:     1 -  2387
chr1_15334355_15337480.rev   A   Score:  232   Residues:  2141 -  2177
chr1_15334355_15337480.rev   Z   Score: 9378   Residues:     1 -  3126
chr1_16854773_16857246.rev   Z   Score: 7422   Residues:     1 -  2474
chr1_17882497_17884717.rev   A   Score:  220   Residues:   471 -   500
chr1_17882497_17884717.rev   Z   Score: 6663   Residues:     1 -  2221
chr1_17892345_17894304.rev   Z   Score: 5880   Residues:     1 -  1960
chr1_17942525_17944653.rev   A   Score:  233   Residues:  1481 -  1517
chr1_17942525_17944653.rev   Z   Score: 6387   Residues:     1 -  2129
chr1_17968977_17973044   Y   Score:  284   Residues:   272 -   459
chr1_17968977_17973044   T   Score:  938   Residues:   269 -   458
chr1_17968977_17973044   Z   Score: 12204   Residues:     1 -  4068
chr1_18414498_18416117.rev   Z   Score: 4860   Residues:     1 -  1620
chr1_18441551_18443135   Z   Score: 4755   Residues:     1 -  1585
chr1_18590067_18592069   Z   Score: 6009   Residues:     1 -  2003
chr1_18659693_18661918.rev   A   Score:  220   Residues:  1464 -  1509
chr1_18659693_18661918.rev   Z   Score: 6678   Residues:     1 -  2226
chr1_19053908_19056041   A   Score:  663   Residues:     3 -   147
chr1_19053908_19056041   R   Score:  201   Residues:     1 -   127
chr1_19053908_19056041   Z   Score: 6402   Residues:     1 -  2134
chr1_19372883_19374987.rev   A   Score:  216   Residues:  1482 -  1513
chr1_19372883_19374987.rev   Z   Score: 6315   Residues:     1 -  2105
chr1_19908013_19912577   A   Score:  304   Residues:  2460 -  2540
chr1_19908013_19912577   A   Score:  253   Residues:   819 -   968
chr1_19908013_19912577   A   Score:  203   Residues:   156 -   200
chr1_19908013_19912577   T   Score:  410   Residues:  2040 -  2129
chr1_19908013_19912577   Z   Score: 13695   Residues:     1 -  4565
chr1_19971141_19975214.rev   A   Score:  242   Residues:   352 -   385
chr1_19971141_19975214.rev   A   Score:  227   Residues:  2482 -  2512
chr1_19971141_19975214.rev   Z   Score: 12222   Residues:     1 -  4074
chr1_20090219_20093624.rev   Z   Score: 10218   Residues:     1 -  3406
chr1_20494778_20497764   A   Score:  227   Residues:   266 -   329
chr1_20494778_20497764   Z   Score: 8961   Residues:     1 -  2987
chr1_20825022_20827468   Z   Score: 7341   Residues:     1 -  2447
chr1_21028530_21032091   Z   Score: 10686   Residues:     1 -  3562
chr1_21097221_21099397   Z   Score: 6531   Residues:     1 -  2177
chr1_21147816_21149802   Z   Score: 5961   Residues:     1 -  1987
chr1_21519201_21520865.rev   Z   Score: 4995   Residues:     1 -  1665
chr1_21755677_21758834.rev   Z   Score: 9474   Residues:     1 -  3158
chr1_21842802_21845677   A   Score:  296   Residues:  1919 -  1969
chr1_21842802_21845677   A   Score:  204   Residues:  2252 -  2279
chr1_21842802_21845677   Z   Score: 8628   Residues:     1 -  2876
chr1_22155732_22158021.rev   A   Score:  216   Residues:  1864 -  1898
chr1_22155732_22158021.rev   Z   Score: 6870   Residues:     1 -  2290
chr1_22264400_22267212.rev   A   Score:  228   Residues:  1892 -  1964
chr1_22264400_22267212.rev   Z   Score: 8439   Residues:     1 -  2813
chr1_22270608_22273157.rev   Z   Score: 7650   Residues:     1 -  2550
chr1_22379228_22381551   Z   Score: 6969   Residues:     1 -  2323
chr1_22505500_22507165.rev   Z   Score: 4998   Residues:     1 -  1666
chr1_22510074_22513374.rev   A   Score:  347   Residues:    82 -   172
chr1_22510074_22513374.rev   Z   Score: 9903   Residues:     1 -  3301
chr1_22554840_22557724.rev   Z   Score: 8655   Residues:     1 -  2885
chr1_22676313_22678159   Z   Score: 5541   Residues:     1 -  1847
chr1_23017124_23021999   A   Score:  212   Residues:  1418 -  1446
chr1_23017124_23021999   Z   Score: 14628   Residues:     1 -  4876
chr1_23094366_23096083.rev   A   Score:  234   Residues:  1614 -  1646
chr1_23094366_23096083.rev   Z   Score: 5154   Residues:     1 -  1718
chr1_24016218_24020107.rev   A   Score:  223   Residues:   494 -   560
chr1_24016218_24020107.rev   Z   Score: 11670   Residues:     1 -  3890
chr1_24061978_24064359.rev   A   Score:  242   Residues:   439 -   477
chr1_24061978_24064359.rev   Z   Score: 7146   Residues:     1 -  2382
chr1_24340814_24347501.rev   Z   Score: 20061   Residues:     1 -  6687
chr1_24469542_24472129   Z   Score: 7764   Residues:     1 -  2588
chr1_24685267_24689121.rev   Z   Score: 11565   Residues:     1 -  3855
chr1_24952763_24956461.rev   Z   Score: 11097   Residues:     1 -  3699
chr1_25228424_25231151   Z   Score: 8181   Residues:     1 -  2727
chr1_25231794_25234883   Z   Score: 9270   Residues:     1 -  3090
chr1_25636450_25639425.rev   A   Score:  301   Residues:  1473 -  1564
chr1_25636450_25639425.rev   A   Score:  204   Residues:  2414 -  2465
chr1_25636450_25639425.rev   Z   Score: 8928   Residues:     1 -  2976
chr1_25639491_25644948.rev   Z   Score: 16374   Residues:     1 -  5458
chr1_25730258_25733029.rev   Z   Score: 8316   Residues:     1 -  2772
chr1_25974692_25977167   A   Score:  260   Residues:  1759 -  1828
chr1_25974692_25977167   Z   Score: 7428   Residues:     1 -  2476
chr1_26665047_26667544   A   Score:  233   Residues:  1890 -  1927
chr1_26665047_26667544   Z   Score: 7494   Residues:     1 -  2498
chr1_27322568_27324638   Z   Score: 6213   Residues:     1 -  2071
chr1_27663139_27665086.rev   A   Score:  216   Residues:  1340 -  1371
chr1_27663139_27665086.rev   Z   Score: 5844   Residues:     1 -  1948
chr1_28175197_28178522   A   Score:  301   Residues:   860 -   903
chr1_28175197_28178522   T   Score:  240   Residues:  3090 -  3119
chr1_28175197_28178522   Z   Score: 9978   Residues:     1 -  3326
chr1_28391844_28397776.rev   Z   Score: 17799   Residues:     1 -  5933
chr1_28398373_28400413   Z   Score: 6123   Residues:     1 -  2041
chr1_29083793_29087055.rev   Z   Score: 9789   Residues:     1 -  3263
chr1_29440951_29444109.rev   A   Score:  228   Residues:   457 -   492
chr1_29440951_29444109.rev   Z   Score: 9477   Residues:     1 -  3159
chr1_29520385_29525691.rev   A   Score:  212   Residues:  4886 -  4914
chr1_29520385_29525691.rev   Z   Score: 15921   Residues:     1 -  5307
chr1_29547428_29551953.rev   Z   Score: 13578   Residues:     1 -  4526
chr1_29567079_29570925.rev   Z   Score: 11541   Residues:     1 -  3847
chr1_29729515_29731850   Z   Score: 7008   Residues:     1 -  2336
chr1_29756400_29759477.rev   Z   Score: 9234   Residues:     1 -  3078
chr1_29800420_29804175.rev   A   Score:  200   Residues:  1014 -  1130
chr1_29800420_29804175.rev   Z   Score: 11268   Residues:     1 -  3756
chr1_29955216_29960187.rev   Z   Score: 14916   Residues:     1 -  4972
chr1_30014863_30018609   Z   Score: 11241   Residues:     1 -  3747
chr1_30119285_30121072.rev   Z   Score: 5364   Residues:     1 -  1788
chr1_30138095_30140458   Z   Score: 7092   Residues:     1 -  2364
chr1_30161616_30164657.rev   Z   Score: 9126   Residues:     1 -  3042
chr1_30166968_30169431   Z   Score: 7392   Residues:     1 -  2464
chr1_30300243_30302169   Z   Score: 5781   Residues:     1 -  1927
chr1_30485245_30487635.rev   Z   Score: 7173   Residues:     1 -  2391
chr1_30570890_30575091   Z   Score: 12606   Residues:     1 -  4202
chr1_30575341_30577868   Z   Score: 7584   Residues:     1 -  2528
chr1_30579932_30585814   Z   Score: 17649   Residues:     1 -  5883
chr1_30595779_30602162.rev   Z   Score: 19152   Residues:     1 -  6384
chr1_30634830_30641247   Z   Score: 19254   Residues:     1 -  6418
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chr1_50073951_50076563   Z   Score: 7839   Residues:     1 -  2613
chr1_50078290_50080633   Z   Score: 7032   Residues:     1 -  2344
chr1_50092301_50098694   Z   Score: 19182   Residues:     1 -  6394
chr1_50099462_50101877   Z   Score: 7248   Residues:     1 -  2416
chr1_50118061_50121268   Z   Score: 9624   Residues:     1 -  3208
chr1_50122206_50127809   Z   Score: 16812   Residues:     1 -  5604
chr1_50147046_50148980   Z   Score: 5805   Residues:     1 -  1935
chr1_50173576_50178517   Z   Score: 14826   Residues:     1 -  4942
chr1_50184541_50189488   Z   Score: 14844   Residues:     1 -  4948
chr1_50192867_50194838   Z   Score: 5916   Residues:     1 -  1972
chr1_50515463_50518157.rev   Z   Score: 8085   Residues:     1 -  2695
chr1_50536903_50543028   Z   Score: 18378   Residues:     1 -  6126
chr1_50551054_50554404   Z   Score: 10053   Residues:     1 -  3351
chr1_50584778_50588301   A   Score:  272   Residues:  1191 -  1224
chr1_50584778_50588301   A   Score:  226   Residues:    69 -   100
chr1_50584778_50588301   Z   Score: 10569   Residues:     1 -  3523
chr1_50659950_50661729.rev   Z   Score: 5340   Residues:     1 -  1780
chr1_50675070_50677116   T   Score:  214   Residues:   162 -   189
chr1_50675070_50677116   Z   Score: 6141   Residues:     1 -  2047
chr1_50701340_50703545.rev   Z   Score: 6618   Residues:     1 -  2206
chr1_50792808_50798467.rev   Z   Score: 16980   Residues:     1 -  5660
chr1_50870014_50871622.rev   Z   Score: 4827   Residues:     1 -  1609
chr1_50944457_50949722   A   Score:  220   Residues:     2 -    48
chr1_50944457_50949722   Z   Score: 15798   Residues:     1 -  5266
chr1_50960245_50963733   A   Score:  309   Residues:  3059 -  3120
chr1_50960245_50963733   Z   Score: 10467   Residues:     1 -  3489
chr1_50984929_50990678   Z   Score: 17250   Residues:     1 -  5750
chr1_50993315_50995353.rev   A   Score:  252   Residues:  1440 -  1486
chr1_50993315_50995353.rev   Z   Score: 6117   Residues:     1 -  2039
chr1_51005034_51007226   T   Score:  232   Residues:   912 -   945
chr1_51005034_51007226   Z   Score: 6579   Residues:     1 -  2193
chr1_51036096_51038703   Z   Score: 7824   Residues:     1 -  2608
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chr1_51082826_51089206.rev   Z   Score: 19143   Residues:     1 -  6381
chr1_51100035_51103744   A   Score:  380   Residues:   117 -   181
chr1_51100035_51103744   A   Score:  209   Residues:   477 -   514
chr1_51100035_51103744   Z   Score: 11130   Residues:     1 -  3710
chr1_51174320_51177482   Z   Score: 9489   Residues:     1 -  3163
chr1_51192282_51195616   A   Score:  419   Residues:   327 -   495
chr1_51192282_51195616   R   Score:  260   Residues:   327 -   462
chr1_51192282_51195616   G   Score:  321   Residues:   344 -   459
chr1_51192282_51195616   Z   Score: 10005   Residues:     1 -  3335
chr1_51309297_51315350   A   Score:  201   Residues:     8 -    57
chr1_51309297_51315350   Z   Score: 18162   Residues:     1 -  6054
chr1_51557864_51563519   T   Score:  286   Residues:  4106 -  4147
chr1_51557864_51563519   Z   Score: 16968   Residues:     1 -  5656
chr1_51563641_51568919   Z   Score: 15837   Residues:     1 -  5279
chr1_51679619_51682863   Z   Score: 9735   Residues:     1 -  3245
chr1_51956395_51958322   Z   Score: 5784   Residues:     1 -  1928
chr1_52307285_52309697   Z   Score: 7239   Residues:     1 -  2413
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chr1_52377125_52379548.rev   Z   Score: 7272   Residues:     1 -  2424
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chr1_52426588_52430149.rev   Z   Score: 10686   Residues:     1 -  3562
chr1_52630631_52633148   Z   Score: 7554   Residues:     1 -  2518
chr1_52676203_52679557   Z   Score: 10065   Residues:     1 -  3355
chr1_52719553_52723785   A   Score:  204   Residues:  4099 -  4129
chr1_52719553_52723785   Z   Score: 12699   Residues:     1 -  4233
chr1_52831477_52833498   A   Score:  216   Residues:  1669 -  1695
chr1_52831477_52833498   Z   Score: 6066   Residues:     1 -  2022
chr1_53181856_53188232   Z   Score: 19131   Residues:     1 -  6377
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chr1_53430082_53431702   Z   Score: 4863   Residues:     1 -  1621
chr1_53531526_53533692.rev   Z   Score: 6501   Residues:     1 -  2167
chr1_53670566_53673549.rev   Z   Score: 8952   Residues:     1 -  2984
chr1_53746689_53749364   T   Score:  212   Residues:  1071 -  1134
chr1_53746689_53749364   Z   Score: 8028   Residues:     1 -  2676
chr1_53824218_53826464   A   Score:  711   Residues:   286 -   498
chr1_53824218_53826464   R   Score:  392   Residues:   286 -   498
chr1_53824218_53826464   G   Score:  360   Residues:   303 -   482
chr1_53824218_53826464   Z   Score: 6741   Residues:     1 -  2247
chr1_53989748_53995096   Z   Score: 16047   Residues:     1 -  5349
chr1_54172468_54176461   A   Score:  204   Residues:  1925 -  1979
chr1_54172468_54176461   Z   Score: 11982   Residues:     1 -  3994
chr1_54620898_54627606.rev   Z   Score: 20127   Residues:     1 -  6709
chr1_54904137_54906095   Z   Score: 5877   Residues:     1 -  1959
chr1_55293374_55297008   A   Score:  261   Residues:   559 -   697
chr1_55293374_55297008   A   Score:  214   Residues:  2063 -  2090
chr1_55293374_55297008   A   Score:  213   Residues:  1002 -  1034
chr1_55293374_55297008   Z   Score: 10905   Residues:     1 -  3635
chr1_55339795_55341707   Z   Score: 5739   Residues:     1 -  1913
chr1_55361112_55366790   A   Score:  273   Residues:  5547 -  5592
chr1_55361112_55366790   Z   Score: 17037   Residues:     1 -  5679
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chr1_55444025_55449384.rev   A   Score:  305   Residues:  2118 -  2208
chr1_55444025_55449384.rev   Z   Score: 16080   Residues:     1 -  5360
chr1_55567847_55573726.rev   Z   Score: 17640   Residues:     1 -  5880
chr1_55592201_55594161.rev   Z   Score: 5883   Residues:     1 -  1961
chr1_55633340_55635307   Z   Score: 5904   Residues:     1 -  1968
chr1_55739775_55746163.rev   Z   Score: 19167   Residues:     1 -  6389
chr1_55773787_55778546.rev   A   Score:  208   Residues:   336 -   441
chr1_55773787_55778546.rev   Z   Score: 14280   Residues:     1 -  4760
chr1_55837791_55840044.rev   Z   Score: 6762   Residues:     1 -  2254
chr1_55857565_55860385.rev   Z   Score: 8463   Residues:     1 -  2821
chr1_55976144_55978485.rev   A   Score:  280   Residues:  1648 -  1687
chr1_55976144_55978485.rev   A   Score:  200   Residues:  1340 -  1364
chr1_55976144_55978485.rev   Z   Score: 7026   Residues:     1 -  2342
chr1_55985592_55989707   A   Score:  206   Residues:    15 -    41
chr1_55985592_55989707   Z   Score: 12348   Residues:     1 -  4116
chr1_56017846_56019642.rev   Z   Score: 5391   Residues:     1 -  1797
chr1_56188691_56194411   Z   Score: 17163   Residues:     1 -  5721
chr1_56287269_56290772   T   Score:  209   Residues:  1492 -  1532
chr1_56287269_56290772   Z   Score: 10512   Residues:     1 -  3504
chr1_56304093_56305954   Z   Score: 5586   Residues:     1 -  1862
chr1_56341680_56343830.rev   Z   Score: 6453   Residues:     1 -  2151
chr1_56521373_56526246   A   Score:  270   Residues:  3720 -  3759
chr1_56521373_56526246   Z   Score: 14622   Residues:     1 -  4874
chr1_56908879_56911402   Z   Score: 7572   Residues:     1 -  2524
chr1_57560721_57562346   Z   Score: 4878   Residues:     1 -  1626
chr1_57606430_57608451.rev   Z   Score: 6063   Residues:     1 -  2021
chr1_57610149_57612100   Z   Score: 5856   Residues:     1 -  1952
chr1_57740507_57746882   Z   Score: 19128   Residues:     1 -  6376
chr1_57861259_57866519   A   Score:  264   Residues:  4027 -  4068
chr1_57861259_57866519   Z   Score: 15783   Residues:     1 -  5261
chr1_57892129_57895151   A   Score:  234   Residues:  2807 -  2853
chr1_57892129_57895151   Z   Score: 9066   Residues:     1 -  3022
chr1_57949952_57952986.rev   Z   Score: 9105   Residues:     1 -  3035
chr1_57964109_57966114   Z   Score: 6018   Residues:     1 -  2006
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chr1_58446967_58453225.rev   Z   Score: 18777   Residues:     1 -  6259
chr1_58551123_58557399.rev   Z   Score: 18831   Residues:     1 -  6277
chr1_58666156_58672873   T   Score:  254   Residues:  2330 -  2362
chr1_58666156_58672873   Z   Score: 20154   Residues:     1 -  6718
chr1_58686570_58690355   A   Score:  255   Residues:   717 -   829
chr1_58686570_58690355   Z   Score: 11358   Residues:     1 -  3786
chr1_58734765_58738089   Z   Score: 9975   Residues:     1 -  3325
chr1_58777918_58782479.rev   Z   Score: 13686   Residues:     1 -  4562
chr1_59091591_59094789   Z   Score: 9597   Residues:     1 -  3199
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chr1_59135322_59141724   Z   Score: 19209   Residues:     1 -  6403
chr1_59276748_59279028   Z   Score: 6843   Residues:     1 -  2281
chr1_59353028_59354661.rev   Z   Score: 4902   Residues:     1 -  1634
chr1_59428017_59434403   Z   Score: 19161   Residues:     1 -  6387
chr1_59434880_59436659   Z   Score: 5340   Residues:     1 -  1780
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chr1_59477470_59480560.rev   Z   Score: 9273   Residues:     1 -  3091
chr1_59512957_59515130.rev   Z   Score: 6522   Residues:     1 -  2174
chr1_59546117_59552508   Z   Score: 19176   Residues:     1 -  6392
chr1_59639304_59644960   T   Score:  252   Residues:   157 -   230
chr1_59639304_59644960   Z   Score: 16971   Residues:     1 -  5657
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chr1_59710316_59718216   Z   Score: 23703   Residues:     1 -  7901
chr1_59763997_59770389   Z   Score: 19179   Residues:     1 -  6393
chr1_59787730_59794101   Z   Score: 19113   Residues:     1 -  6371
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chr1_59969255_59974050   Z   Score: 14388   Residues:     1 -  4796
chr1_59978860_59980566   T   Score:  326   Residues:   236 -   358
chr1_59978860_59980566   Z   Score: 5121   Residues:     1 -  1707
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chr1_60110853_60112810   Z   Score: 5874   Residues:     1 -  1958
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chr1_60272276_60274807.rev   Z   Score: 7596   Residues:     1 -  2532
chr1_60301057_60302762   A   Score:  320   Residues:  1275 -  1322
chr1_60301057_60302762   Z   Score: 5118   Residues:     1 -  1706
chr1_60365625_60370765   Z   Score: 15423   Residues:     1 -  5141
chr1_60490298_60492595   Z   Score: 6894   Residues:     1 -  2298
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chr1_60636954_60639027   A   Score:  242   Residues:  1266 -  1323
chr1_60636954_60639027   Z   Score: 6222   Residues:     1 -  2074
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chr1_60663839_60665646   Z   Score: 5424   Residues:     1 -  1808
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chr1_60805948_60807775.rev   Z   Score: 5484   Residues:     1 -  1828
chr1_60817206_60823478   Z   Score: 18819   Residues:     1 -  6273
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chr1_60886809_60891053   G   Score:  228   Residues:   397 -   462
chr1_60886809_60891053   Z   Score: 12735   Residues:     1 -  4245
chr1_60950484_60960416   Z   Score: 29799   Residues:     1 -  9933
chr1_61004602_61006540.rev   Z   Score: 5817   Residues:     1 -  1939
chr1_61210663_61213479.rev   Z   Score: 8451   Residues:     1 -  2817
chr1_61284631_61286849.rev   Z   Score: 6657   Residues:     1 -  2219
chr1_61654836_61656855   A   Score:  209   Residues:  1698 -  1751
chr1_61654836_61656855   T   Score:  247   Residues:  1781 -  1816
chr1_61654836_61656855   Z   Score: 6060   Residues:     1 -  2020
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chr1_61719903_61724222.rev   A   Score:  205   Residues:  1464 -  1592
chr1_61719903_61724222.rev   Z   Score: 12960   Residues:     1 -  4320
chr1_61751326_61757474.rev   Z   Score: 18447   Residues:     1 -  6149
chr1_62007304_62009778   Z   Score: 7425   Residues:     1 -  2475
chr1_62120336_62126668   Z   Score: 18999   Residues:     1 -  6333
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chr1_62239987_62242462.rev   A   Score:  208   Residues:  2255 -  2280
chr1_62239987_62242462.rev   Z   Score: 7428   Residues:     1 -  2476
chr1_62594994_62597187.rev   Z   Score: 6582   Residues:     1 -  2194
chr1_62696036_62702322   Z   Score: 18861   Residues:     1 -  6287
chr1_62740862_62745149   A   Score:  329   Residues:   690 -   734
chr1_62740862_62745149   Z   Score: 12864   Residues:     1 -  4288
chr1_62803019_62807185   Z   Score: 12501   Residues:     1 -  4167
chr1_62850962_62853680   G   Score:  313   Residues:   617 -   707
chr1_62850962_62853680   Z   Score: 8157   Residues:     1 -  2719
chr1_62855597_62857751   Z   Score: 6462   Residues:     1 -  2154
chr1_62877347_62883590.rev   Z   Score: 18732   Residues:     1 -  6244
chr1_62917090_62921377   Z   Score: 12864   Residues:     1 -  4288
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chr1_63047691_63050047.rev   Z   Score: 7071   Residues:     1 -  2357
chr1_63217238_63218879   Z   Score: 4926   Residues:     1 -  1642
chr1_63408849_63410758.rev   Z   Score: 5730   Residues:     1 -  1910
chr1_63411522_63413968.rev   Z   Score: 7341   Residues:     1 -  2447
chr1_63561435_63566203.rev   A   Score:  317   Residues:  3296 -  3396
chr1_63561435_63566203.rev   A   Score:  275   Residues:   954 -   995
chr1_63561435_63566203.rev   Z   Score: 14307   Residues:     1 -  4769
chr1_63607838_63610666.rev   Z   Score: 8487   Residues:     1 -  2829
chr1_63638081_63640768.rev   T   Score:  208   Residues:  1799 -  1824
chr1_63638081_63640768.rev   Z   Score: 8064   Residues:     1 -  2688
chr1_63691667_63693699.rev   T   Score:  238   Residues:   153 -   183
chr1_63691667_63693699.rev   T   Score:  223   Residues:  1032 -  1064
chr1_63691667_63693699.rev   Z   Score: 6099   Residues:     1 -  2033
chr1_63719900_63721611.rev   Z   Score: 5136   Residues:     1 -  1712
chr1_63756991_63763791.rev   A   Score:  202   Residues:   587 -   683
chr1_63756991_63763791.rev   Z   Score: 20403   Residues:     1 -  6801
chr1_64233963_64237457.rev   Z   Score: 10485   Residues:     1 -  3495
chr1_64450631_64457038   Z   Score: 19224   Residues:     1 -  6408
chr1_64537591_64539705   Z   Score: 6345   Residues:     1 -  2115
chr1_64939261_64941602   Z   Score: 7026   Residues:     1 -  2342
chr1_64971804_64975511.rev   Z   Score: 11124   Residues:     1 -  3708
chr1_65300118_65303223.rev   Z   Score: 9318   Residues:     1 -  3106
chr1_65428352_65430326.rev   Z   Score: 5925   Residues:     1 -  1975
chr1_65550734_65555406.rev   Z   Score: 14019   Residues:     1 -  4673
chr1_65628232_65634513.rev   Z   Score: 18846   Residues:     1 -  6282
chr1_65639954_65646374.rev   Z   Score: 19263   Residues:     1 -  6421
chr1_65685145_65687673.rev   Z   Score: 7587   Residues:     1 -  2529
chr1_65722762_65729174.rev   Z   Score: 19239   Residues:     1 -  6413
chr1_65736505_65742780.rev   Z   Score: 18828   Residues:     1 -  6276
chr1_65766374_65768398.rev   Z   Score: 6075   Residues:     1 -  2025
chr1_65828893_65835567   Z   Score: 20025   Residues:     1 -  6675
chr1_65838770_65843771.rev   A   Score: 1074   Residues:  3842 -  4034
chr1_65838770_65843771.rev   R   Score:  287   Residues:  3842 -  4034
chr1_65838770_65843771.rev   Z   Score: 15006   Residues:     1 -  5002
chr1_65892850_65895202.rev   Z   Score: 7059   Residues:     1 -  2353
chr1_65915822_65922306.rev   A   Score:  238   Residues:  4700 -  4743
chr1_65915822_65922306.rev   Z   Score: 19455   Residues:     1 -  6485
chr1_65942588_65947814   A   Score:  218   Residues:  1639 -  1759
chr1_65942588_65947814   Z   Score: 15681   Residues:     1 -  5227
chr1_65957646_65961064   A   Score:  204   Residues:   562 -   724
chr1_65957646_65961064   Z   Score: 10257   Residues:     1 -  3419
chr1_66027749_66030493.rev   Z   Score: 8235   Residues:     1 -  2745
chr1_66038002_66042233.rev   Z   Score: 12696   Residues:     1 -  4232
chr1_66064923_66067627.rev   A   Score:  978   Residues:  2487 -  2705
chr1_66064923_66067627.rev   R   Score:  336   Residues:  2487 -  2705
chr1_66064923_66067627.rev   Z   Score: 8115   Residues:     1 -  2705
chr1_66071358_66072979   Z   Score: 4866   Residues:     1 -  1622
chr1_66119981_66122673.rev   Z   Score: 8079   Residues:     1 -  2693
chr1_66326427_66328529.rev   Z   Score: 6309   Residues:     1 -  2103
chr1_66342655_66345150   Z   Score: 7488   Residues:     1 -  2496
chr1_66362796_66369190.rev   Z   Score: 19185   Residues:     1 -  6395
chr1_66498822_66500775   Z   Score: 5862   Residues:     1 -  1954
chr1_66658128_66664404   Z   Score: 18831   Residues:     1 -  6277
chr1_66744462_66746866.rev   Z   Score: 7215   Residues:     1 -  2405
chr1_66957347_66963777   Z   Score: 19293   Residues:     1 -  6431
chr1_66967811_66969957   Z   Score: 6441   Residues:     1 -  2147
chr1_67020490_67022130.rev   C   Score:  222   Residues:  1178 -  1215
chr1_67020490_67022130.rev   Z   Score: 4923   Residues:     1 -  1641
chr1_67056984_67062964.rev   A   Score:  228   Residues:  2061 -  2091
chr1_67056984_67062964.rev   Z   Score: 17943   Residues:     1 -  5981
chr1_67071493_67073383.rev   Z   Score: 5673   Residues:     1 -  1891
chr1_67076562_67079316.rev   Z   Score: 8265   Residues:     1 -  2755
chr1_67079519_67082136.rev   Z   Score: 7854   Residues:     1 -  2618
chr1_67143996_67146214.rev   Z   Score: 6657   Residues:     1 -  2219
chr1_67200619_67205633.rev   Z   Score: 15045   Residues:     1 -  5015
chr1_67210686_67212313.rev   Z   Score: 4884   Residues:     1 -  1628
chr1_67256848_67263119.rev   Z   Score: 18816   Residues:     1 -  6272
chr1_67328410_67334631.rev   Z   Score: 18666   Residues:     1 -  6222
chr1_67354573_67360980.rev   Z   Score: 19224   Residues:     1 -  6408
chr1_67421265_67426943.rev   Z   Score: 17037   Residues:     1 -  5679
chr1_67779290_67781556   Z   Score: 6801   Residues:     1 -  2267
chr1_67831999_67833728.rev   Z   Score: 5190   Residues:     1 -  1730
chr1_67983788_67987895   A   Score:  263   Residues:  1342 -  1448
chr1_67983788_67987895   Z   Score: 12324   Residues:     1 -  4108
chr1_68079031_68083371.rev   Z   Score: 13023   Residues:     1 -  4341
chr1_68170550_68173252   Z   Score: 8109   Residues:     1 -  2703
chr1_68174518_68178803.rev   A   Score:  257   Residues:   517 -   631
chr1_68174518_68178803.rev   Z   Score: 12858   Residues:     1 -  4286
chr1_68181079_68187420.rev   A   Score:  217   Residues:   429 -   489
chr1_68181079_68187420.rev   Z   Score: 19026   Residues:     1 -  6342
chr1_68236428_68241834   Z   Score: 16221   Residues:     1 -  5407
chr1_68251994_68255656.rev   Z   Score: 10989   Residues:     1 -  3663
chr1_68265549_68271909.rev   A   Score:  256   Residues:  2771 -  2807
chr1_68265549_68271909.rev   Z   Score: 19083   Residues:     1 -  6361
chr1_68272439_68276246.rev   Z   Score: 11424   Residues:     1 -  3808
chr1_68512387_68515060.rev   A   Score:  343   Residues:   125 -   182
chr1_68512387_68515060.rev   A   Score:  205   Residues:  1636 -  1667
chr1_68512387_68515060.rev   Z   Score: 8022   Residues:     1 -  2674
chr1_68667897_68669626   Z   Score: 5190   Residues:     1 -  1730
chr1_68677950_68682123   Z   Score: 12522   Residues:     1 -  4174
chr1_68725610_68731340   Z   Score: 17193   Residues:     1 -  5731
chr1_68755771_68758297   Z   Score: 7581   Residues:     1 -  2527
chr1_68837328_68839165   Z   Score: 5514   Residues:     1 -  1838
chr1_68843225_68844862.rev   A   Score:  230   Residues:    21 -    50
chr1_68843225_68844862.rev   Z   Score: 4914   Residues:     1 -  1638
chr1_68859454_68865840.rev   Z   Score: 19161   Residues:     1 -  6387
chr1_68896404_68898228   Z   Score: 5475   Residues:     1 -  1825
chr1_68912065_68918340.rev   Z   Score: 18828   Residues:     1 -  6276
chr1_68937606_68942710   T   Score:  206   Residues:   809 -   835
chr1_68937606_68942710   Z   Score: 15315   Residues:     1 -  5105
chr1_69017393_69021682.rev   Z   Score: 12870   Residues:     1 -  4290
chr1_69028731_69030396.rev   Z   Score: 4998   Residues:     1 -  1666
chr1_69047550_69049482   T   Score:  257   Residues:   229 -   281
chr1_69047550_69049482   Z   Score: 5799   Residues:     1 -  1933
chr1_69053737_69060009.rev   Z   Score: 18819   Residues:     1 -  6273
chr1_69100691_69106964   Z   Score: 18822   Residues:     1 -  6274
chr1_69164861_69169418   A   Score:  200   Residues:  3816 -  3840
chr1_69164861_69169418   T   Score:  214   Residues:   169 -   196
chr1_69164861_69169418   Z   Score: 13674   Residues:     1 -  4558
chr1_69186818_69190980.rev   Z   Score: 12489   Residues:     1 -  4163
chr1_69243641_69249685.rev   Z   Score: 18135   Residues:     1 -  6045
chr1_69274481_69280872.rev   Z   Score: 19176   Residues:     1 -  6392
chr1_69292427_69298715.rev   Z   Score: 18867   Residues:     1 -  6289
chr1_69329761_69334538.rev   Z   Score: 14334   Residues:     1 -  4778
chr1_69484379_69490226.rev   A   Score:  201   Residues:  2181 -  2218
chr1_69484379_69490226.rev   Z   Score: 17544   Residues:     1 -  5848
chr1_69521394_69523107.rev   Z   Score: 5142   Residues:     1 -  1714
chr1_69545926_69551325.rev   Z   Score: 16200   Residues:     1 -  5400
chr1_69556944_69559315.rev   Z   Score: 7116   Residues:     1 -  2372
chr1_69567403_69573794.rev   A   Score:  266   Residues:   439 -   496
chr1_69567403_69573794.rev   Z   Score: 19176   Residues:     1 -  6392
chr1_69633794_69635586.rev   Z   Score: 5379   Residues:     1 -  1793
chr1_69667288_69669123   Z   Score: 5508   Residues:     1 -  1836
chr1_69801479_69803221.rev   Z   Score: 5229   Residues:     1 -  1743
chr1_69841763_69846044.rev   Z   Score: 12846   Residues:     1 -  4282
chr1_70060569_70066847.rev   Z   Score: 18837   Residues:     1 -  6279
chr1_70083213_70089552.rev   Z   Score: 19020   Residues:     1 -  6340
chr1_70100763_70107156.rev   Z   Score: 19182   Residues:     1 -  6394
chr1_70121968_70124533.rev   Z   Score: 7698   Residues:     1 -  2566
chr1_70145458_70150733   T   Score:  220   Residues:  1045 -  1082
chr1_70145458_70150733   Z   Score: 15828   Residues:     1 -  5276
chr1_70262102_70263693.rev   Z   Score: 4776   Residues:     1 -  1592
chr1_70346679_70349798   Z   Score: 9360   Residues:     1 -  3120
chr1_70370281_70373662   Z   Score: 10146   Residues:     1 -  3382
chr1_70646039_70652400   Z   Score: 19086   Residues:     1 -  6362
chr1_70773072_70779482.rev   Z   Score: 19233   Residues:     1 -  6411
chr1_70798110_70800179.rev   Z   Score: 6210   Residues:     1 -  2070
chr1_70839507_70841510.rev   Z   Score: 6012   Residues:     1 -  2004
chr1_70900084_70905842.rev   A   Score:  262   Residues:   783 -   828
chr1_70900084_70905842.rev   Z   Score: 17277   Residues:     1 -  5759
chr1_70917968_70922913.rev   Z   Score: 14838   Residues:     1 -  4946
chr1_70945672_70950930.rev   Z   Score: 15777   Residues:     1 -  5259
chr1_70970916_70973505   A   Score:  204   Residues:  1721 -  1755
chr1_70970916_70973505   Z   Score: 7770   Residues:     1 -  2590
chr1_71030935_71032577   Z   Score: 4929   Residues:     1 -  1643
chr1_71053394_71059330.rev   T   Score:  204   Residues:   913 -   940
chr1_71053394_71059330.rev   Z   Score: 17811   Residues:     1 -  5937
chr1_71312359_71313965   Z   Score: 4821   Residues:     1 -  1607
chr1_71320886_71327406.rev   Z   Score: 19563   Residues:     1 -  6521
chr1_71393124_71398782   Z   Score: 16977   Residues:     1 -  5659
chr1_71494159_71496239   Z   Score: 6243   Residues:     1 -  2081
chr1_71533462_71535358.rev   Z   Score: 5691   Residues:     1 -  1897
chr1_71563856_71568766   Z   Score: 14733   Residues:     1 -  4911
chr1_71690903_71697194   Z   Score: 18876   Residues:     1 -  6292
chr1_71971392_71973176   Z   Score: 5355   Residues:     1 -  1785
chr1_71989853_71993872.rev   Z   Score: 12060   Residues:     1 -  4020
chr1_72065408_72071687   Z   Score: 18840   Residues:     1 -  6280
chr1_72356007_72358926   Z   Score: 8760   Residues:     1 -  2920
chr1_72392130_72393824   Z   Score: 5085   Residues:     1 -  1695
chr1_72468406_72470972.rev   Z   Score: 7701   Residues:     1 -  2567
chr1_72532504_72535132.rev   Z   Score: 7887   Residues:     1 -  2629
chr1_72560439_72562470   Z   Score: 6096   Residues:     1 -  2032
chr1_72597988_72600389   Z   Score: 7206   Residues:     1 -  2402
chr1_72629887_72634251   Z   Score: 13092   Residues:     1 -  4364
chr1_72798194_72801482.rev   Z   Score: 9867   Residues:     1 -  3289
chr1_72890736_72893128.rev   Z   Score: 7179   Residues:     1 -  2393
chr1_72900382_72902972.rev   Z   Score: 7773   Residues:     1 -  2591
chr1_73008220_73013877   A   Score:  223   Residues:  2252 -  2312
chr1_73008220_73013877   Z   Score: 16974   Residues:     1 -  5658
chr1_73075973_73082545   Z   Score: 19719   Residues:     1 -  6573
chr1_73110133_73112533   Z   Score: 7203   Residues:     1 -  2401
chr1_73129625_73132220.rev   T   Score:  234   Residues:    24 -    81
chr1_73129625_73132220.rev   Z   Score: 7788   Residues:     1 -  2596
chr1_73179569_73181325   Z   Score: 5271   Residues:     1 -  1757
chr1_73204744_73206527   Z   Score: 5352   Residues:     1 -  1784
chr1_73223916_73228850   Z   Score: 14805   Residues:     1 -  4935
chr1_73229307_73231233   A   Score:  276   Residues:  1188 -  1224
chr1_73229307_73231233   Z   Score: 5781   Residues:     1 -  1927
chr1_73253081_73255726   Z   Score: 7938   Residues:     1 -  2646
chr1_73259592_73263938.rev   Z   Score: 13041   Residues:     1 -  4347
chr1_73316447_73320877.rev   Z   Score: 13293   Residues:     1 -  4431
chr1_73331445_73335815   Z   Score: 13113   Residues:     1 -  4371
chr1_73373082_73375351   A   Score:  215   Residues:   833 -   864
chr1_73373082_73375351   Z   Score: 6807   Residues:     1 -  2269
chr1_73383598_73388839   Z   Score: 15726   Residues:     1 -  5242
chr1_73418687_73423637   A   Score:  297   Residues:  4327 -  4382
chr1_73418687_73423637   Z   Score: 14853   Residues:     1 -  4951
chr1_73440530_73445647   A   Score:  204   Residues:  2828 -  2860
chr1_73440530_73445647   Z   Score: 15354   Residues:     1 -  5118
chr1_73499349_73503599.rev   Z   Score: 12753   Residues:     1 -  4251
chr1_73664256_73666858.rev   Z   Score: 7809   Residues:     1 -  2603
chr1_73685763_73687905   Z   Score: 6429   Residues:     1 -  2143
chr1_73709770_73712313.rev   Z   Score: 7632   Residues:     1 -  2544
chr1_73738967_73740642   Z   Score: 5028   Residues:     1 -  1676
chr1_73744167_73746708   Z   Score: 7626   Residues:     1 -  2542
chr1_73755774_73759775   Z   Score: 12006   Residues:     1 -  4002
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chr1_73836799_73839375   Z   Score: 7731   Residues:     1 -  2577
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chr1_74025949_74027948.rev   Z   Score: 6000   Residues:     1 -  2000
chr1_74155310_74157163.rev   Z   Score: 5562   Residues:     1 -  1854
chr1_74234350_74236187   Z   Score: 5514   Residues:     1 -  1838
chr1_74265674_74267279   Z   Score: 4818   Residues:     1 -  1606
chr1_74274326_74279525   Z   Score: 15600   Residues:     1 -  5200
chr1_74301323_74303223.rev   Z   Score: 5703   Residues:     1 -  1901
chr1_74341198_74343463.rev   Z   Score: 6798   Residues:     1 -  2266
chr1_74347129_74351592.rev   Z   Score: 13392   Residues:     1 -  4464
chr1_74403077_74407288   Z   Score: 12636   Residues:     1 -  4212
chr1_74524957_74530493.rev   Z   Score: 16611   Residues:     1 -  5537
chr1_74618961_74625726   T   Score:  219   Residues:  3946 -  3979
chr1_74618961_74625726   T   Score:  210   Residues:  4343 -  4372
chr1_74618961_74625726   Z   Score: 20298   Residues:     1 -  6766
chr1_74709891_74711528   Z   Score: 4914   Residues:     1 -  1638
chr1_74731223_74736036   Z   Score: 14442   Residues:     1 -  4814
chr1_75054326_75060608   Z   Score: 18849   Residues:     1 -  6283
chr1_75093648_75099224.rev   Z   Score: 16731   Residues:     1 -  5577
chr1_75101750_75107517   Z   Score: 17304   Residues:     1 -  5768
chr1_75107696_75110215   Z   Score: 7560   Residues:     1 -  2520
chr1_75164859_75170081   Z   Score: 15669   Residues:     1 -  5223
chr1_75204847_75211802   Z   Score: 20868   Residues:     1 -  6956
chr1_75236292_75238243   Z   Score: 5856   Residues:     1 -  1952
chr1_75284817_75291093.rev   Z   Score: 18831   Residues:     1 -  6277
chr1_75335346_75337321.rev   Z   Score: 5928   Residues:     1 -  1976
chr1_75353629_75360036.rev   Z   Score: 19224   Residues:     1 -  6408
chr1_75393912_75395585.rev   Z   Score: 5022   Residues:     1 -  1674
chr1_75437584_75441598   Z   Score: 12045   Residues:     1 -  4015
chr1_75449275_75452218.rev   Z   Score: 8832   Residues:     1 -  2944
chr1_75460455_75464714.rev   Z   Score: 12780   Residues:     1 -  4260
chr1_75537125_75541537.rev   Z   Score: 13239   Residues:     1 -  4413
chr1_75560665_75565678   Z   Score: 15042   Residues:     1 -  5014
chr1_75566008_75570620   Z   Score: 13839   Residues:     1 -  4613
chr1_75579602_75586329   Z   Score: 20184   Residues:     1 -  6728
chr1_75629013_75633975   Z   Score: 14889   Residues:     1 -  4963
chr1_75641748_75646287   A   Score:  284   Residues:   180 -   239
chr1_75641748_75646287   A   Score:  215   Residues:  1427 -  1654
chr1_75641748_75646287   A   Score:  210   Residues:  2614 -  2643
chr1_75641748_75646287   Z   Score: 13620   Residues:     1 -  4540
chr1_75653468_75659872   Z   Score: 19215   Residues:     1 -  6405
chr1_75673264_75675099   Z   Score: 5508   Residues:     1 -  1836
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chr1_75682818_75685102.rev   Z   Score: 6855   Residues:     1 -  2285
chr1_75781004_75783296.rev   A   Score:  228   Residues:  1779 -  1848
chr1_75781004_75783296.rev   Z   Score: 6879   Residues:     1 -  2293
chr1_75834042_75839963   A   Score:  737   Residues:  2966 -  3155
chr1_75834042_75839963   A   Score:  224   Residues:  5052 -  5079
chr1_75834042_75839963   R   Score:  333   Residues:  2966 -  3157
chr1_75834042_75839963   G   Score:  286   Residues:  3081 -  3194
chr1_75834042_75839963   Z   Score: 17766   Residues:     1 -  5922
chr1_75840717_75844084   A   Score:  241   Residues:  1910 -  1967
chr1_75840717_75844084   Z   Score: 10104   Residues:     1 -  3368
chr1_75854957_75861223   Z   Score: 18801   Residues:     1 -  6267
chr1_75874846_75881127   Z   Score: 18846   Residues:     1 -  6282
chr1_75892179_75894278   Z   Score: 6300   Residues:     1 -  2100
chr1_75933033_75935673   Z   Score: 7923   Residues:     1 -  2641
chr1_75954803_75961203   Z   Score: 19203   Residues:     1 -  6401
chr1_76006032_76012397   Z   Score: 19098   Residues:     1 -  6366
chr1_76034246_76040622.rev   Z   Score: 19131   Residues:     1 -  6377
chr1_76080003_76084564.rev   A   Score:  222   Residues:  2329 -  2362
chr1_76080003_76084564.rev   Z   Score: 13686   Residues:     1 -  4562
chr1_76119178_76121402.rev   Z   Score: 6675   Residues:     1 -  2225
chr1_76123676_76125941   Z   Score: 6798   Residues:     1 -  2266
chr1_76163311_76164939.rev   A   Score:  240   Residues:  1551 -  1590
chr1_76163311_76164939.rev   Z   Score: 4887   Residues:     1 -  1629
chr1_76275731_76277543.rev   Z   Score: 5439   Residues:     1 -  1813
chr1_76342975_76348224.rev   Z   Score: 15750   Residues:     1 -  5250
chr1_76420411_76424796.rev   Z   Score: 13158   Residues:     1 -  4386
chr1_76576184_76578562.rev   Z   Score: 7137   Residues:     1 -  2379
chr1_76627542_76632984.rev   Z   Score: 16329   Residues:     1 -  5443
chr1_76660682_76666244.rev   Z   Score: 16689   Residues:     1 -  5563
chr1_76690109_76694306.rev   Z   Score: 12594   Residues:     1 -  4198
chr1_76733832_76735596.rev   Z   Score: 5295   Residues:     1 -  1765
chr1_76737201_76738799   Z   Score: 4797   Residues:     1 -  1599
chr1_76837933_76839907   Z   Score: 5925   Residues:     1 -  1975
chr1_76909854_76912929.rev   Z   Score: 9228   Residues:     1 -  3076
chr1_77023911_77027661.rev   Z   Score: 11253   Residues:     1 -  3751
chr1_77079324_77081502   Z   Score: 6537   Residues:     1 -  2179
chr1_77142569_77147251.rev   Z   Score: 14046   Residues:     1 -  4682
chr1_77158230_77164631   Z   Score: 19206   Residues:     1 -  6402
chr1_77177448_77183721.rev   Z   Score: 18822   Residues:     1 -  6274
chr1_77246987_77248687.rev   Z   Score: 5103   Residues:     1 -  1701
chr1_77326424_77330990   A   Score:  247   Residues:  1772 -  1845
chr1_77326424_77330990   A   Score:  242   Residues:  3939 -  3984
chr1_77326424_77330990   Z   Score: 13701   Residues:     1 -  4567
chr1_77426845_77431133   Z   Score: 12867   Residues:     1 -  4289
chr1_77486941_77489208.rev   Z   Score: 6804   Residues:     1 -  2268
chr1_77622586_77624901.rev   Z   Score: 6945   Residues:     1 -  2315
chr1_77786230_77790407   Z   Score: 12534   Residues:     1 -  4178
chr1_77964513_77967394.rev   Z   Score: 8646   Residues:     1 -  2882
chr1_78073984_78077125   Z   Score: 9426   Residues:     1 -  3142
chr1_78086928_78091708   Z   Score: 14343   Residues:     1 -  4781
chr1_78264275_78266203   Z   Score: 5787   Residues:     1 -  1929
chr1_78363918_78370812.rev   Z   Score: 20685   Residues:     1 -  6895
chr1_78380318_78387034   A   Score:  368   Residues:  3094 -  3156
chr1_78380318_78387034   Z   Score: 20151   Residues:     1 -  6717
chr1_78437584_78440779   Z   Score: 9588   Residues:     1 -  3196
chr1_78487261_78493635   Z   Score: 19125   Residues:     1 -  6375
chr1_78558568_78560246.rev   Z   Score: 5037   Residues:     1 -  1679
chr1_78637448_78641650.rev   Z   Score: 12609   Residues:     1 -  4203
chr1_78725622_78727894   Z   Score: 6819   Residues:     1 -  2273
chr1_78731808_78736909   Z   Score: 15306   Residues:     1 -  5102
chr1_78751835_78753659.rev   A   Score:  248   Residues:   648 -   686
chr1_78751835_78753659.rev   Z   Score: 5475   Residues:     1 -  1825
chr1_78784906_78791187   Z   Score: 18846   Residues:     1 -  6282
chr1_78792999_78794968   Z   Score: 5910   Residues:     1 -  1970
chr1_78884689_78888026   Z   Score: 10014   Residues:     1 -  3338
chr1_78968507_78971107   Z   Score: 7803   Residues:     1 -  2601
chr1_79023401_79029680.rev   Z   Score: 18840   Residues:     1 -  6280
chr1_79108239_79113021   Z   Score: 14349   Residues:     1 -  4783
chr1_79235929_79239466   Z   Score: 10614   Residues:     1 -  3538
chr1_79345908_79348530   Z   Score: 7869   Residues:     1 -  2623
chr1_79425410_79426987.rev   Z   Score: 4734   Residues:     1 -  1578
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chr1_79571291_79573010   Z   Score: 5160   Residues:     1 -  1720
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chr1_155843633_155845601.rev   Z   Score: 5904   Residues:     1 -  1968
chr1_155889936_155893181   Z   Score: 9738   Residues:     1 -  3246
chr1_155941601_155943457.rev   Z   Score: 5571   Residues:     1 -  1857
chr1_156024475_156028966.rev   Z   Score: 13476   Residues:     1 -  4492
chr1_156051678_156057315   Z   Score: 16914   Residues:     1 -  5638
chr1_156106000_156113323   A   Score:  218   Residues:   431 -   466
chr1_156106000_156113323   Z   Score: 21972   Residues:     1 -  7324
chr1_156182583_156186888   Z   Score: 12918   Residues:     1 -  4306
chr1_156197195_156203705.rev   Z   Score: 19533   Residues:     1 -  6511
chr1_156235317_156241587   Z   Score: 18813   Residues:     1 -  6271
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chr1_156303351_156307854.rev   Z   Score: 13512   Residues:     1 -  4504
chr1_156349646_156351961   Z   Score: 6948   Residues:     1 -  2316
chr1_156352065_156358467.rev   Z   Score: 19209   Residues:     1 -  6403
chr1_156386126_156392516   Z   Score: 19173   Residues:     1 -  6391
chr1_156398445_156405197   A   Score:  223   Residues:  3105 -  3145
chr1_156398445_156405197   Z   Score: 20259   Residues:     1 -  6753
chr1_156418650_156420397.rev   A   Score:  228   Residues:    92 -   187
chr1_156418650_156420397.rev   Z   Score: 5244   Residues:     1 -  1748
chr1_156512813_156519186   Z   Score: 19122   Residues:     1 -  6374
chr1_156749079_156751666.rev   Z   Score: 7764   Residues:     1 -  2588
chr1_157081991_157087267   Z   Score: 15831   Residues:     1 -  5277
chr1_157167727_157174393.rev   Z   Score: 20001   Residues:     1 -  6667
chr1_157226209_157227794.rev   T   Score:  222   Residues:  1159 -  1187
chr1_157226209_157227794.rev   Z   Score: 4758   Residues:     1 -  1586
chr1_157248017_157250375.rev   A   Score:  206   Residues:  1234 -  1260
chr1_157248017_157250375.rev   Z   Score: 7077   Residues:     1 -  2359
chr1_157258419_157264814.rev   Z   Score: 19188   Residues:     1 -  6396
chr1_157281179_157283072.rev   Z   Score: 5682   Residues:     1 -  1894
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chr1_157306774_157313210.rev   Z   Score: 19311   Residues:     1 -  6437
chr1_157340469_157346364   Z   Score: 17688   Residues:     1 -  5896
chr1_157654087_157657564.rev   Z   Score: 10434   Residues:     1 -  3478
chr1_158393808_158404113   Z   Score: 30918   Residues:     1 - 10306
chr1_158798116_158800456.rev   A   Score:  241   Residues:   886 -   924
chr1_158798116_158800456.rev   Z   Score: 7023   Residues:     1 -  2341
chr1_158800523_158807412.rev   Z   Score: 20670   Residues:     1 -  6890
chr1_159004376_159006415.rev   Z   Score: 6120   Residues:     1 -  2040
chr1_159129286_159132248   T   Score:  248   Residues:   922 -   952
chr1_159129286_159132248   Z   Score: 8889   Residues:     1 -  2963
chr1_159181659_159183674   Z   Score: 6048   Residues:     1 -  2016
chr1_159211991_159214033.rev   A   Score:  296   Residues:  1379 -  1420
chr1_159211991_159214033.rev   A   Score:  244   Residues:  1907 -  1980
chr1_159211991_159214033.rev   Z   Score: 6129   Residues:     1 -  2043
chr1_159380834_159382539.rev   Z   Score: 5118   Residues:     1 -  1706
chr1_159446040_159453356   Z   Score: 21951   Residues:     1 -  7317
chr1_159508673_159513327.rev   Z   Score: 13965   Residues:     1 -  4655
chr1_159527329_159529006.rev   Z   Score: 5034   Residues:     1 -  1678
chr1_159566556_159569287   Z   Score: 8196   Residues:     1 -  2732
chr1_159696570_159698177   Z   Score: 4824   Residues:     1 -  1608
chr1_159713172_159715613.rev   Z   Score: 7326   Residues:     1 -  2442
chr1_159716649_159720251.rev   Z   Score: 10806   Residues:     1 -  3602
chr1_159788709_159790787.rev   Z   Score: 6237   Residues:     1 -  2079
chr1_159973151_159974842.rev   A   Score:  337   Residues:  1332 -  1443
chr1_159973151_159974842.rev   Z   Score: 5076   Residues:     1 -  1692
chr1_159982625_159984295   Z   Score: 5013   Residues:     1 -  1671
chr1_160195922_160197793   Z   Score: 5616   Residues:     1 -  1872
chr1_160227056_160229955   Z   Score: 8700   Residues:     1 -  2900
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chr1_160267450_160270345.rev   Z   Score: 8688   Residues:     1 -  2896
chr1_160341659_160347929.rev   Z   Score: 18813   Residues:     1 -  6271
chr1_160383063_160385415   Z   Score: 7059   Residues:     1 -  2353
chr1_160415077_160416727.rev   Z   Score: 4953   Residues:     1 -  1651
chr1_160440065_160444289.rev   A   Score:  250   Residues:  1451 -  1662
chr1_160440065_160444289.rev   Z   Score: 12675   Residues:     1 -  4225
chr1_160451378_160457653.rev   Z   Score: 18828   Residues:     1 -  6276
chr1_160460734_160465113   Z   Score: 13140   Residues:     1 -  4380
chr1_160484003_160486212   Z   Score: 6630   Residues:     1 -  2210
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chr1_160515711_160517568.rev   Z   Score: 5574   Residues:     1 -  1858
chr1_160549567_160551493.rev   Z   Score: 5781   Residues:     1 -  1927
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chr1_160603436_160608327.rev   Z   Score: 14676   Residues:     1 -  4892
chr1_160609965_160611599   Z   Score: 4905   Residues:     1 -  1635
chr1_160665600_160670392   Z   Score: 14379   Residues:     1 -  4793
chr1_160701009_160704282   Z   Score: 9822   Residues:     1 -  3274
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chr1_160867674_160872735   Z   Score: 15186   Residues:     1 -  5062
chr1_160916417_160922830   Z   Score: 19242   Residues:     1 -  6414
chr1_160923079_160925333   Z   Score: 6765   Residues:     1 -  2255
chr1_160966450_160968409   Z   Score: 5880   Residues:     1 -  1960
chr1_160974453_160976635   Z   Score: 6549   Residues:     1 -  2183
chr1_160977733_160981237   A   Score:  205   Residues:   696 -   769
chr1_160977733_160981237   Z   Score: 10515   Residues:     1 -  3505
chr1_161052688_161057049   A   Score:  203   Residues:  1532 -  1601
chr1_161052688_161057049   R   Score:  213   Residues:  2558 -  2660
chr1_161052688_161057049   G   Score:  478   Residues:  2559 -  2660
chr1_161052688_161057049   Z   Score: 13086   Residues:     1 -  4362
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chr1_161159599_161165896   Z   Score: 18894   Residues:     1 -  6298
chr1_161642860_161649052.rev   A   Score:  241   Residues:  1945 -  1987
chr1_161642860_161649052.rev   A   Score:  213   Residues:  1412 -  1567
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chr1_161703476_161706797   Z   Score: 9966   Residues:     1 -  3322
chr1_161785361_161791753   Z   Score: 19179   Residues:     1 -  6393
chr1_161797159_161801633   Z   Score: 13425   Residues:     1 -  4475
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chr1_161804376_161811101.rev   Z   Score: 20175   Residues:     1 -  6725
chr1_162219575_162221815.rev   Z   Score: 6723   Residues:     1 -  2241
chr1_162276430_162278376   Z   Score: 5841   Residues:     1 -  1947
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chr1_162499769_162505370   Z   Score: 16806   Residues:     1 -  5602
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chr1_162677741_162682854.rev   Z   Score: 15342   Residues:     1 -  5114
chr1_162702636_162708900.rev   Z   Score: 18795   Residues:     1 -  6265
chr1_162800600_162807012   Z   Score: 19239   Residues:     1 -  6413
chr1_162912372_162915128.rev   Z   Score: 8271   Residues:     1 -  2757
chr1_162922019_162926365.rev   Z   Score: 13041   Residues:     1 -  4347
chr1_162928801_162934407.rev   Z   Score: 16821   Residues:     1 -  5607
chr1_162944201_162950479.rev   Z   Score: 18837   Residues:     1 -  6279
chr1_162978104_162980733.rev   Z   Score: 7890   Residues:     1 -  2630
chr1_163009981_163018422.rev   A   Score:  208   Residues:  7452 -  7482
chr1_163009981_163018422.rev   Z   Score: 25326   Residues:     1 -  8442
chr1_163100911_163103160.rev   G   Score:  210   Residues:  1239 -  1299
chr1_163100911_163103160.rev   Z   Score: 6750   Residues:     1 -  2250
chr1_163112445_163118833.rev   Z   Score: 19167   Residues:     1 -  6389
chr1_163124603_163130747.rev   Z   Score: 18435   Residues:     1 -  6145
chr1_163139647_163142403.rev   Z   Score: 8271   Residues:     1 -  2757
chr1_163199298_163201265   Z   Score: 5904   Residues:     1 -  1968
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chr1_163315983_163319195.rev   Z   Score: 9639   Residues:     1 -  3213
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chr1_163341747_163346441   Z   Score: 14085   Residues:     1 -  4695
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chr1_163431794_163437068   Z   Score: 15825   Residues:     1 -  5275
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chr1_163452781_163457092   Z   Score: 12936   Residues:     1 -  4312
chr1_163479711_163486686.rev   A   Score:  315   Residues:  2593 -  2668
chr1_163479711_163486686.rev   A   Score:  262   Residues:  3212 -  3245
chr1_163479711_163486686.rev   Z   Score: 20928   Residues:     1 -  6976
chr1_163500191_163504311.rev   Z   Score: 12363   Residues:     1 -  4121
chr1_163724684_163728209   Z   Score: 10578   Residues:     1 -  3526
chr1_163738253_163739896.rev   Z   Score: 4932   Residues:     1 -  1644
chr1_163992836_163996075   A   Score:  228   Residues:  2225 -  2258
chr1_163992836_163996075   Z   Score: 9720   Residues:     1 -  3240
chr1_164055182_164057027.rev   Z   Score: 5538   Residues:     1 -  1846
chr1_164060333_164063267.rev   Z   Score: 8805   Residues:     1 -  2935
chr1_164085019_164087402   Z   Score: 7152   Residues:     1 -  2384
chr1_164107727_164109535   Z   Score: 5427   Residues:     1 -  1809
chr1_164585962_164591359.rev   T   Score:  240   Residues:  1555 -  1589
chr1_164585962_164591359.rev   Z   Score: 16194   Residues:     1 -  5398
chr1_164644957_164649536.rev   Z   Score: 13740   Residues:     1 -  4580
chr1_164658282_164659956.rev   Z   Score: 5025   Residues:     1 -  1675
chr1_164660027_164661680.rev   Z   Score: 4962   Residues:     1 -  1654
chr1_164856468_164861370.rev   A   Score:  290   Residues:  3232 -  3283
chr1_164856468_164861370.rev   A   Score:  272   Residues:  4278 -  4311
chr1_164856468_164861370.rev   T   Score:  216   Residues:  1854 -  1880
chr1_164856468_164861370.rev   Z   Score: 14709   Residues:     1 -  4903
chr1_165050011_165056275.rev   Z   Score: 18795   Residues:     1 -  6265
chr1_165219621_165221190.rev   Z   Score: 4710   Residues:     1 -  1570
chr1_165240149_165241876   Z   Score: 5184   Residues:     1 -  1728
chr1_165246954_165251346   Z   Score: 13179   Residues:     1 -  4393
chr1_165260107_165261742   Z   Score: 4908   Residues:     1 -  1636
chr1_165379430_165385174.rev   Z   Score: 17235   Residues:     1 -  5745
chr1_165450443_165452283.rev   Z   Score: 5523   Residues:     1 -  1841
chr1_165496713_165498854.rev   Z   Score: 6426   Residues:     1 -  2142
chr1_165585157_165587481.rev   Z   Score: 6975   Residues:     1 -  2325
chr1_165628272_165631334   Z   Score: 9189   Residues:     1 -  3063
chr1_165688815_165691708   Z   Score: 8682   Residues:     1 -  2894
chr1_165693788_165700417.rev   A   Score:  240   Residues:  3067 -  3121
chr1_165693788_165700417.rev   Z   Score: 19890   Residues:     1 -  6630
chr1_165738566_165742837   Z   Score: 12816   Residues:     1 -  4272
chr1_165897893_165899511   Z   Score: 4857   Residues:     1 -  1619
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chr1_165948631_165958987.rev   Z   Score: 31071   Residues:     1 - 10357
chr1_165963488_165969595   Z   Score: 18324   Residues:     1 -  6108
chr1_165974613_165985758.rev   T   Score:  230   Residues:  9356 -  9385
chr1_165974613_165985758.rev   Z   Score: 33438   Residues:     1 - 11146
chr1_166051696_166055208   T   Score:  282   Residues:   161 -   217
chr1_166051696_166055208   Z   Score: 10539   Residues:     1 -  3513
chr1_166101088_166107454   Z   Score: 19101   Residues:     1 -  6367
chr1_166108023_166114676   Z   Score: 19962   Residues:     1 -  6654
chr1_166132992_166135601   Z   Score: 7827   Residues:     1 -  2609
chr1_166232228_166235052   Z   Score: 8475   Residues:     1 -  2825
chr1_166336055_166338849   Z   Score: 8385   Residues:     1 -  2795
chr1_166349813_166352025   Z   Score: 6639   Residues:     1 -  2213
chr1_166372735_166374358   Z   Score: 4872   Residues:     1 -  1624
chr1_166413131_166416187   Z   Score: 9171   Residues:     1 -  3057
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chr1_166539810_166542677.rev   Z   Score: 8604   Residues:     1 -  2868
chr1_166729991_166731632   Z   Score: 4926   Residues:     1 -  1642
chr1_166748837_166755555   Z   Score: 20157   Residues:     1 -  6719
chr1_166790223_166796500.rev   Z   Score: 18834   Residues:     1 -  6278
chr1_166803963_166808247.rev   Z   Score: 12855   Residues:     1 -  4285
chr1_166808528_166815081.rev   Z   Score: 19662   Residues:     1 -  6554
chr1_166823859_166825858.rev   Z   Score: 6000   Residues:     1 -  2000
chr1_166841229_166842820.rev   Z   Score: 4776   Residues:     1 -  1592
chr1_166886583_166892626.rev   Z   Score: 18132   Residues:     1 -  6044
chr1_166893086_166896463.rev   Z   Score: 10134   Residues:     1 -  3378
chr1_166979938_166984246   Z   Score: 12927   Residues:     1 -  4309
chr1_167062341_167066577.rev   A   Score:  207   Residues:  2061 -  2101
chr1_167062341_167066577.rev   Z   Score: 12711   Residues:     1 -  4237
chr1_167080126_167084382.rev   Z   Score: 12771   Residues:     1 -  4257
chr1_167100172_167102513   Z   Score: 7026   Residues:     1 -  2342
chr1_167126470_167133132   Z   Score: 19989   Residues:     1 -  6663
chr1_167140698_167143513   Z   Score: 8448   Residues:     1 -  2816
chr1_167152796_167159829.rev   T   Score:  208   Residues:  2670 -  2700
chr1_167152796_167159829.rev   Z   Score: 21102   Residues:     1 -  7034
chr1_167164185_167170582   Z   Score: 19194   Residues:     1 -  6398
chr1_167269732_167275924   Z   Score: 18579   Residues:     1 -  6193
chr1_167309285_167316280.rev   Z   Score: 20988   Residues:     1 -  6996
chr1_167498640_167500454   Z   Score: 5445   Residues:     1 -  1815
chr1_167511054_167517472   Z   Score: 19257   Residues:     1 -  6419
chr1_167569908_167571554   Z   Score: 4941   Residues:     1 -  1647
chr1_167655077_167658943.rev   A   Score:  278   Residues:  1536 -  1580
chr1_167655077_167658943.rev   A   Score:  228   Residues:   320 -   358
chr1_167655077_167658943.rev   Z   Score: 11601   Residues:     1 -  3867
chr1_167728104_167733304.rev   Z   Score: 15603   Residues:     1 -  5201
chr1_167743036_167747609.rev   A   Score:  409   Residues:  1793 -  1904
chr1_167743036_167747609.rev   Z   Score: 13722   Residues:     1 -  4574
chr1_167754488_167756063   Z   Score: 4728   Residues:     1 -  1576
chr1_167758294_167762415   Z   Score: 12366   Residues:     1 -  4122
chr1_167794514_167796471.rev   A   Score:  206   Residues:  1822 -  1848
chr1_167794514_167796471.rev   Z   Score: 5874   Residues:     1 -  1958
chr1_167938282_167944024   Z   Score: 17229   Residues:     1 -  5743
chr1_168059518_168066552   Z   Score: 21105   Residues:     1 -  7035
chr1_168073884_168080123   Z   Score: 18720   Residues:     1 -  6240
chr1_168107113_168112970   Z   Score: 17574   Residues:     1 -  5858
chr1_168145353_168147790   Z   Score: 7314   Residues:     1 -  2438
chr1_168152193_168153892.rev   Z   Score: 5100   Residues:     1 -  1700
chr1_168204371_168206946.rev   Z   Score: 7728   Residues:     1 -  2576
chr1_168251513_168257852.rev   Z   Score: 19020   Residues:     1 -  6340
chr1_168389883_168397718.rev   Z   Score: 23508   Residues:     1 -  7836
chr1_168420973_168423964   Z   Score: 8976   Residues:     1 -  2992
chr1_168561349_168563288   Z   Score: 5820   Residues:     1 -  1940
chr1_168595685_168597979.rev   Z   Score: 6885   Residues:     1 -  2295
chr1_168623563_168628033.rev   Z   Score: 13413   Residues:     1 -  4471
chr1_168708252_168709853.rev   Z   Score: 4806   Residues:     1 -  1602
chr1_168714846_168719530.rev   Z   Score: 14055   Residues:     1 -  4685
chr1_168724815_168732110   Z   Score: 21888   Residues:     1 -  7296
chr1_168736674_168738348   Z   Score: 5025   Residues:     1 -  1675
chr1_168756127_168762406   Z   Score: 18840   Residues:     1 -  6280
chr1_168775367_168778767.rev   Z   Score: 10203   Residues:     1 -  3401
chr1_168896966_168901941.rev   Z   Score: 14928   Residues:     1 -  4976
chr1_168932329_168936555   Z   Score: 12681   Residues:     1 -  4227
chr1_169004039_169008583   Z   Score: 13635   Residues:     1 -  4545
chr1_169014544_169020940   Z   Score: 19191   Residues:     1 -  6397
chr1_169041275_169043310   Z   Score: 6108   Residues:     1 -  2036
chr1_169131919_169138296   Z   Score: 19134   Residues:     1 -  6378
chr1_169158340_169160749   Z   Score: 7230   Residues:     1 -  2410
chr1_169292328_169298716.rev   Z   Score: 19167   Residues:     1 -  6389
chr1_169482932_169487144.rev   Z   Score: 12639   Residues:     1 -  4213
chr1_169492481_169496063.rev   Z   Score: 10749   Residues:     1 -  3583
chr1_169568995_169570921   Z   Score: 5781   Residues:     1 -  1927
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chrX_12541543_12544170   Z   Score: 7884   Residues:     1 -  2628
chrX_12611059_12612777.rev   Z   Score: 5157   Residues:     1 -  1719
chrX_12626838_12633479.rev   Z   Score: 19926   Residues:     1 -  6642
chrX_12636326_12642717.rev   Z   Score: 19176   Residues:     1 -  6392
chrX_12910346_12916742.rev   Z   Score: 19191   Residues:     1 -  6397
chrX_13132601_13134510.rev   Z   Score: 5730   Residues:     1 -  1910
chrX_13501909_13508604   Z   Score: 20088   Residues:     1 -  6696
chrX_13620964_13622571.rev   Z   Score: 4824   Residues:     1 -  1608
chrX_13881972_13885502.rev   Z   Score: 10593   Residues:     1 -  3531
chrX_13933514_13935231.rev   Z   Score: 5154   Residues:     1 -  1718
chrX_13945505_13949792.rev   Z   Score: 12864   Residues:     1 -  4288
chrX_13965662_13971622.rev   Z   Score: 17883   Residues:     1 -  5961
chrX_13978722_13985271.rev   Z   Score: 19650   Residues:     1 -  6550
chrX_14054669_14057177   Z   Score: 7527   Residues:     1 -  2509
chrX_14064638_14067322.rev   Z   Score: 8055   Residues:     1 -  2685
chrX_14124822_14128583   Z   Score: 11286   Residues:     1 -  3762
chrX_14235902_14242281.rev   Z   Score: 19140   Residues:     1 -  6380
chrX_14344449_14347802   A   Score:  250   Residues:  2023 -  2057
chrX_14344449_14347802   Z   Score: 10062   Residues:     1 -  3354
chrX_14364819_14367623.rev   Z   Score: 8415   Residues:     1 -  2805
chrX_14399391_14403976.rev   Z   Score: 13758   Residues:     1 -  4586
chrX_14460581_14467218.rev   Z   Score: 19914   Residues:     1 -  6638
chrX_14544727_14550418.rev   Z   Score: 17076   Residues:     1 -  5692
chrX_14586474_14592861   Z   Score: 19164   Residues:     1 -  6388
chrX_14682513_14685410   Z   Score: 8694   Residues:     1 -  2898
chrX_14747025_14749142.rev   Z   Score: 6354   Residues:     1 -  2118
chrX_14776614_14778313   Z   Score: 5100   Residues:     1 -  1700
chrX_14844103_14846030   Z   Score: 5784   Residues:     1 -  1928
chrX_14865701_14872088   Z   Score: 19164   Residues:     1 -  6388
chrX_14960790_14963114.rev   Z   Score: 6975   Residues:     1 -  2325
chrX_15412687_15414239   Z   Score: 4659   Residues:     1 -  1553
chrX_15505382_15507252.rev   A   Score:  221   Residues:   816 -   861
chrX_15505382_15507252.rev   Z   Score: 5613   Residues:     1 -  1871
chrX_15701329_15702933.rev   Z   Score: 4815   Residues:     1 -  1605
chrX_16008708_16015136.rev   Z   Score: 19287   Residues:     1 -  6429
chrX_16051310_16055917.rev   A   Score:  234   Residues:  1785 -  1910
chrX_16051310_16055917.rev   Z   Score: 13824   Residues:     1 -  4608
chrX_16098926_16105331   Z   Score: 19218   Residues:     1 -  6406
chrX_16117408_16120555.rev   Z   Score: 9444   Residues:     1 -  3148
chrX_16137357_16143748   Z   Score: 19176   Residues:     1 -  6392
chrX_16274637_16281025   Z   Score: 19167   Residues:     1 -  6389
chrX_16736963_16740182   Z   Score: 9660   Residues:     1 -  3220
chrX_16765902_16767972   Z   Score: 6213   Residues:     1 -  2071
chrX_16861927_16863905.rev   Z   Score: 5937   Residues:     1 -  1979
chrX_16867409_16869391.rev   Z   Score: 5949   Residues:     1 -  1983
chrX_16919086_16920897   Z   Score: 5436   Residues:     1 -  1812
chrX_16967443_16969629   Z   Score: 6561   Residues:     1 -  2187
chrX_17008052_17012929.rev   Z   Score: 14634   Residues:     1 -  4878
chrX_17034496_17039065   Z   Score: 13710   Residues:     1 -  4570
chrX_17079843_17084420.rev   Z   Score: 13734   Residues:     1 -  4578
chrX_17120512_17126792.rev   Z   Score: 18843   Residues:     1 -  6281
chrX_17177101_17180374   Z   Score: 9822   Residues:     1 -  3274
chrX_17346697_17353109.rev   Z   Score: 19239   Residues:     1 -  6413
chrX_17441227_17443921.rev   A   Score:  224   Residues:   800 -   827
chrX_17441227_17443921.rev   Z   Score: 8085   Residues:     1 -  2695
chrX_17476241_17478383   A   Score:  218   Residues:  1978 -  2008
chrX_17476241_17478383   Z   Score: 6429   Residues:     1 -  2143
chrX_17559405_17565666.rev   Z   Score: 18786   Residues:     1 -  6262
chrX_17667538_17670634   A   Score:  247   Residues:     2 -    99
chrX_17667538_17670634   Z   Score: 9291   Residues:     1 -  3097
chrX_17869565_17871477.rev   Z   Score: 5739   Residues:     1 -  1913
chrX_17883503_17888442   Z   Score: 14820   Residues:     1 -  4940
chrX_18057110_18062938   Z   Score: 17487   Residues:     1 -  5829
chrX_18073831_18077889   Z   Score: 12177   Residues:     1 -  4059
chrX_18415954_18417698   Z   Score: 5235   Residues:     1 -  1745
chrX_18512154_18518534.rev   Z   Score: 19143   Residues:     1 -  6381
chrX_18528215_18532272.rev   Z   Score: 12174   Residues:     1 -  4058
chrX_18567472_18571901.rev   Z   Score: 13287   Residues:     1 -  4429
chrX_18588713_18594165.rev   A   Score:  337   Residues:   475 -   629
chrX_18588713_18594165.rev   Z   Score: 16359   Residues:     1 -  5453
chrX_18919944_18926223   Z   Score: 18840   Residues:     1 -  6280
chrX_18998151_19000035.rev   Z   Score: 5655   Residues:     1 -  1885
chrX_19044737_19050139   Z   Score: 16209   Residues:     1 -  5403
chrX_19051394_19057782.rev   Z   Score: 19167   Residues:     1 -  6389
chrX_19074139_19076220.rev   A   Score:  238   Residues:   430 -   465
chrX_19074139_19076220.rev   Z   Score: 6246   Residues:     1 -  2082
chrX_19194341_19200714   Z   Score: 19122   Residues:     1 -  6374
chrX_19593539_19598997.rev   Z   Score: 16377   Residues:     1 -  5459
chrX_19718297_19724571.rev   Z   Score: 18825   Residues:     1 -  6275
chrX_20026830_20028451.rev   Z   Score: 4863   Residues:     1 -  1621
chrX_20052880_20057229   Z   Score: 13050   Residues:     1 -  4350
chrX_20147947_20150449.rev   Z   Score: 7509   Residues:     1 -  2503
chrX_20320946_20323905.rev   Z   Score: 8880   Residues:     1 -  2960
chrX_20474413_20476828   Z   Score: 7248   Residues:     1 -  2416
chrX_20527903_20532109.rev   Z   Score: 12621   Residues:     1 -  4207
chrX_20548650_20554849   Z   Score: 18600   Residues:     1 -  6200
chrX_20556614_20559820   A   Score:  270   Residues:  2487 -  2526
chrX_20556614_20559820   Z   Score: 9621   Residues:     1 -  3207
chrX_20597327_20598972.rev   Z   Score: 4938   Residues:     1 -  1646
chrX_20611178_20612777.rev   Z   Score: 4800   Residues:     1 -  1600
chrX_20613064_20616353.rev   Z   Score: 9870   Residues:     1 -  3290
chrX_20622719_20629151   Z   Score: 19296   Residues:     1 -  6432
chrX_20652496_20658254   A   Score:  240   Residues:  3368 -  3397
chrX_20652496_20658254   Z   Score: 17277   Residues:     1 -  5759
chrX_20677788_20683215.rev   Z   Score: 16284   Residues:     1 -  5428
chrX_20700021_20701740.rev   Z   Score: 5160   Residues:     1 -  1720
chrX_20712264_20716153.rev   A   Score:  211   Residues:  1109 -  1229
chrX_20712264_20716153.rev   Z   Score: 11670   Residues:     1 -  3890
chrX_20759701_20765145   Z   Score: 16335   Residues:     1 -  5445
chrX_20809302_20811107   Z   Score: 5418   Residues:     1 -  1806
chrX_20834375_20835965.rev   Z   Score: 4773   Residues:     1 -  1591
chrX_20844310_20845900.rev   Z   Score: 4773   Residues:     1 -  1591
chrX_20877257_20879876   Z   Score: 7860   Residues:     1 -  2620
chrX_20996646_21002735.rev   Z   Score: 18270   Residues:     1 -  6090
chrX_21065119_21067322.rev   Z   Score: 6612   Residues:     1 -  2204
chrX_21099986_21102489.rev   A   Score:  324   Residues:  1893 -  1945
chrX_21099986_21102489.rev   Z   Score: 7512   Residues:     1 -  2504
chrX_21113818_21123245   Z   Score: 28284   Residues:     1 -  9428
chrX_21126536_21132312   Z   Score: 17331   Residues:     1 -  5777
chrX_21191597_21196217.rev   A   Score:  201   Residues:   432 -   502
chrX_21191597_21196217.rev   Z   Score: 13863   Residues:     1 -  4621
chrX_21311964_21317481.rev   A   Score:  287   Residues:  2759 -  2904
chrX_21311964_21317481.rev   Z   Score: 16554   Residues:     1 -  5518
chrX_21322763_21328603   Z   Score: 17523   Residues:     1 -  5841
chrX_21542564_21544700.rev   Z   Score: 6411   Residues:     1 -  2137
chrX_21549521_21553848   A   Score:  270   Residues:  2550 -  2589
chrX_21549521_21553848   Z   Score: 12984   Residues:     1 -  4328
chrX_21777470_21783860.rev   Z   Score: 19173   Residues:     1 -  6391
chrX_21786698_21788817   Z   Score: 6360   Residues:     1 -  2120
chrX_21859734_21864279.rev   Z   Score: 13638   Residues:     1 -  4546
chrX_22006770_22013006.rev   A   Score:  270   Residues:  4972 -  5006
chrX_22006770_22013006.rev   A   Score:  262   Residues:  2593 -  2643
chrX_22006770_22013006.rev   Z   Score: 18711   Residues:     1 -  6237
chrX_22019868_22021963   Z   Score: 6288   Residues:     1 -  2096
chrX_22086308_22088810.rev   Z   Score: 7509   Residues:     1 -  2503
chrX_22170899_22172822   Z   Score: 5772   Residues:     1 -  1924
chrX_22235948_22237818   Z   Score: 5613   Residues:     1 -  1871
chrX_22280746_22282561.rev   Z   Score: 5448   Residues:     1 -  1816
chrX_22305216_22308604   Z   Score: 10167   Residues:     1 -  3389
chrX_22376143_22378106.rev   Z   Score: 5892   Residues:     1 -  1964
chrX_22386463_22392854   Z   Score: 19176   Residues:     1 -  6392
chrX_22454126_22460499   Z   Score: 19122   Residues:     1 -  6374
chrX_22478287_22480020.rev   Z   Score: 5202   Residues:     1 -  1734
chrX_22491566_22493364   A   Score:  451   Residues:   775 -   905
chrX_22491566_22493364   R   Score:  206   Residues:   778 -   912
chrX_22491566_22493364   Z   Score: 5397   Residues:     1 -  1799
chrX_22555490_22557431.rev   Z   Score: 5826   Residues:     1 -  1942
chrX_22568007_22572759   Z   Score: 14259   Residues:     1 -  4753
chrX_22597603_22600727.rev   Z   Score: 9375   Residues:     1 -  3125
chrX_22608469_22610095.rev   Z   Score: 4881   Residues:     1 -  1627
chrX_22643651_22650378   Z   Score: 20184   Residues:     1 -  6728
chrX_22650901_22653532   Z   Score: 7896   Residues:     1 -  2632
chrX_22678239_22680366.rev   Z   Score: 6384   Residues:     1 -  2128
chrX_22767059_22770195.rev   Z   Score: 9411   Residues:     1 -  3137
chrX_22805976_22808119.rev   A   Score:  225   Residues:   129 -   160
chrX_22805976_22808119.rev   Z   Score: 6432   Residues:     1 -  2144
chrX_22846393_22852110   Z   Score: 17154   Residues:     1 -  5718
chrX_22873307_22877728   Z   Score: 13266   Residues:     1 -  4422
chrX_23019868_23022068   Z   Score: 6603   Residues:     1 -  2201
chrX_23030241_23032158   Z   Score: 5754   Residues:     1 -  1918
chrX_23033506_23039570   A   Score:  358   Residues:  2639 -  2689
chrX_23033506_23039570   Z   Score: 18195   Residues:     1 -  6065
chrX_23042557_23044472.rev   Z   Score: 5748   Residues:     1 -  1916
chrX_23135684_23142059.rev   Z   Score: 19128   Residues:     1 -  6376
chrX_23201324_23203687.rev   Z   Score: 7092   Residues:     1 -  2364
chrX_23264289_23266579   A   Score:  207   Residues:  1008 -  1041
chrX_23264289_23266579   Z   Score: 6873   Residues:     1 -  2291
chrX_23304880_23309101   Z   Score: 12663   Residues:     1 -  4221
chrX_23320123_23324647   A   Score:  237   Residues:   371 -   485
chrX_23320123_23324647   Z   Score: 13575   Residues:     1 -  4525
chrX_23338680_23345067.rev   Z   Score: 19164   Residues:     1 -  6388
chrX_23735804_23737936.rev   Z   Score: 6399   Residues:     1 -  2133
chrX_23872475_23875676.rev   A   Score:  206   Residues:  1390 -  1440
chrX_23872475_23875676.rev   A   Score:  203   Residues:   472 -   504
chrX_23872475_23875676.rev   Z   Score: 9606   Residues:     1 -  3202
chrX_23884074_23886652.rev   Z   Score: 7737   Residues:     1 -  2579
chrX_24000578_24002696.rev   Z   Score: 6357   Residues:     1 -  2119
chrX_24134969_24136729   Z   Score: 5283   Residues:     1 -  1761
chrX_24160858_24162604.rev   Z   Score: 5241   Residues:     1 -  1747
chrX_24181656_24183807.rev   Z   Score: 6456   Residues:     1 -  2152
chrX_24377922_24379983   Z   Score: 6186   Residues:     1 -  2062
chrX_24563681_24566107.rev   A   Score:  216   Residues:  1627 -  1653
chrX_24563681_24566107.rev   Z   Score: 7281   Residues:     1 -  2427
chrX_24634021_24635908.rev   Z   Score: 5664   Residues:     1 -  1888
chrX_24689217_24690891   Z   Score: 5025   Residues:     1 -  1675
chrX_24865587_24874620.rev   A   Score:  226   Residues:  6308 -  6339
chrX_24865587_24874620.rev   T   Score:  302   Residues:  7388 -  7483
chrX_24865587_24874620.rev   Z   Score: 27102   Residues:     1 -  9034
chrX_24895169_24901435.rev   Z   Score: 18801   Residues:     1 -  6267
chrX_24926261_24928938.rev   Z   Score: 8034   Residues:     1 -  2678
chrX_25105943_25111725   Z   Score: 17349   Residues:     1 -  5783
chrX_25138264_25142905.rev   Z   Score: 13926   Residues:     1 -  4642
chrX_25186043_25192457.rev   Z   Score: 19245   Residues:     1 -  6415
chrX_25194427_25202661.rev   Z   Score: 24705   Residues:     1 -  8235
chrX_25343839_25348090.rev   Z   Score: 12756   Residues:     1 -  4252
chrX_25405041_25407041.rev   Z   Score: 6003   Residues:     1 -  2001
chrX_25412887_25417475   Z   Score: 13767   Residues:     1 -  4589
chrX_25577043_25581381.rev   Z   Score: 13017   Residues:     1 -  4339
chrX_25598491_25600984   Z   Score: 7482   Residues:     1 -  2494
chrX_25608703_25611432.rev   Z   Score: 8190   Residues:     1 -  2730
chrX_25618995_25620860.rev   Z   Score: 5598   Residues:     1 -  1866
chrX_25689075_25691122.rev   Z   Score: 6144   Residues:     1 -  2048
chrX_25712421_25717357   Z   Score: 14811   Residues:     1 -  4937
chrX_25720874_25725389   A   Score:  218   Residues:  1917 -  1947
chrX_25720874_25725389   Z   Score: 13548   Residues:     1 -  4516
chrX_25747145_25752323   Z   Score: 15537   Residues:     1 -  5179
chrX_25754687_25760424   Z   Score: 17214   Residues:     1 -  5738
chrX_25765989_25767913   Z   Score: 5775   Residues:     1 -  1925
chrX_25781509_25783118   Z   Score: 4830   Residues:     1 -  1610
chrX_25817726_25819445   Z   Score: 5160   Residues:     1 -  1720
chrX_25954569_25963879   Z   Score: 27933   Residues:     1 -  9311
chrX_25978959_25981649   A   Score:  486   Residues:  1773 -  1931
chrX_25978959_25981649   Z   Score: 8073   Residues:     1 -  2691
chrX_26059333_26065685.rev   Z   Score: 19059   Residues:     1 -  6353
chrX_26092443_26098720.rev   Z   Score: 18834   Residues:     1 -  6278
chrX_26111286_26117638   Z   Score: 19059   Residues:     1 -  6353
chrX_26120390_26122801.rev   Z   Score: 7233   Residues:     1 -  2411
chrX_26144820_26146606.rev   Z   Score: 5361   Residues:     1 -  1787
chrX_26255399_26257497   Z   Score: 6297   Residues:     1 -  2099
chrX_26371556_26373351   Z   Score: 5385   Residues:     1 -  1795
chrX_26436357_26438673   Z   Score: 6951   Residues:     1 -  2317
chrX_26507413_26511912.rev   Z   Score: 13500   Residues:     1 -  4500
chrX_26614040_26616151.rev   A   Score:  217   Residues:   484 -   518
chrX_26614040_26616151.rev   Z   Score: 6333   Residues:     1 -  2111
chrX_26624881_26626452.rev   Z   Score: 4716   Residues:     1 -  1572
chrX_26723891_26727565.rev   A   Score:  332   Residues:  2423 -  2476
chrX_26723891_26727565.rev   Z   Score: 11025   Residues:     1 -  3675
chrX_26800304_26801942.rev   Z   Score: 4917   Residues:     1 -  1639
chrX_26961358_26962884   Z   Score: 4581   Residues:     1 -  1527
chrX_27076503_27083196   Z   Score: 20082   Residues:     1 -  6694
chrX_27108887_27110543   Z   Score: 4971   Residues:     1 -  1657
chrX_27146176_27147902   Z   Score: 5181   Residues:     1 -  1727
chrX_27151927_27155158   Z   Score: 9696   Residues:     1 -  3232
chrX_27271969_27273815.rev   Z   Score: 5541   Residues:     1 -  1847
chrX_27280369_27282052.rev   Z   Score: 5052   Residues:     1 -  1684
chrX_27289560_27292074   A   Score:  259   Residues:   994 -  1028
chrX_27289560_27292074   Z   Score: 7545   Residues:     1 -  2515
chrX_27406243_27408536.rev   A   Score:  580   Residues:  1237 -  1361
chrX_27406243_27408536.rev   R   Score:  212   Residues:  1236 -  1361
chrX_27406243_27408536.rev   Z   Score: 6882   Residues:     1 -  2294
chrX_27426835_27429600.rev   Z   Score: 8298   Residues:     1 -  2766
chrX_27496683_27499515.rev   Z   Score: 8499   Residues:     1 -  2833
chrX_27510557_27512163.rev   Z   Score: 4821   Residues:     1 -  1607
chrX_27535860_27542241   Z   Score: 19146   Residues:     1 -  6382
chrX_27580353_27582226.rev   Z   Score: 5622   Residues:     1 -  1874
chrX_27800000_27804802.rev   T   Score:  207   Residues:   525 -   555
chrX_27800000_27804802.rev   Z   Score: 14409   Residues:     1 -  4803
chrX_27839031_27841198.rev   Z   Score: 6504   Residues:     1 -  2168
chrX_27856977_27859220   A   Score:  280   Residues:  2063 -  2097
chrX_27856977_27859220   Z   Score: 6732   Residues:     1 -  2244
chrX_27913273_27917591.rev   A   Score:  205   Residues:   536 -   652
chrX_27913273_27917591.rev   Z   Score: 12957   Residues:     1 -  4319
chrX_27924409_27930956.rev   Z   Score: 19644   Residues:     1 -  6548
chrX_27970154_27971750.rev   Z   Score: 4791   Residues:     1 -  1597
chrX_27984066_27990313   Z   Score: 18744   Residues:     1 -  6248
chrX_28108989_28110930.rev   A   Score:  218   Residues:  1709 -  1790
chrX_28108989_28110930.rev   Z   Score: 5826   Residues:     1 -  1942
chrX_28140117_28146495.rev   Z   Score: 19137   Residues:     1 -  6379
chrX_28456464_28459552.rev   Z   Score: 9267   Residues:     1 -  3089
chrX_28498619_28503056.rev   Z   Score: 13314   Residues:     1 -  4438
chrX_28726964_28728930.rev   Z   Score: 5901   Residues:     1 -  1967
chrX_29066187_29068171.rev   Z   Score: 5955   Residues:     1 -  1985
chrX_29149451_29152557.rev   A   Score:  316   Residues:   892 -   987
chrX_29149451_29152557.rev   A   Score:  227   Residues:   472 -   515
chrX_29149451_29152557.rev   Z   Score: 9321   Residues:     1 -  3107
chrX_29303667_29306183   T   Score:  246   Residues:  1432 -  1463
chrX_29303667_29306183   Z   Score: 7551   Residues:     1 -  2517
chrX_29316217_29319459   Z   Score: 9729   Residues:     1 -  3243
chrX_29372765_29377343.rev   A   Score:  207   Residues:  1511 -  1591
chrX_29372765_29377343.rev   Z   Score: 13737   Residues:     1 -  4579
chrX_29425056_29429309   Z   Score: 12762   Residues:     1 -  4254
chrX_29486244_29488824.rev   Z   Score: 7743   Residues:     1 -  2581
chrX_29759758_29766159.rev   Z   Score: 19206   Residues:     1 -  6402
chrX_29812590_29814498.rev   Z   Score: 5727   Residues:     1 -  1909
chrX_29832063_29836343.rev   Z   Score: 12843   Residues:     1 -  4281
chrX_29857131_29859409.rev   Z   Score: 6837   Residues:     1 -  2279
chrX_29860191_29863413.rev   A   Score:  439   Residues:  2275 -  2410
chrX_29860191_29863413.rev   A   Score:  237   Residues:   359 -   429
chrX_29860191_29863413.rev   Z   Score: 9669   Residues:     1 -  3223
chrX_30100269_30104209.rev   Z   Score: 11823   Residues:     1 -  3941
chrX_30126440_30128399   A   Score:  297   Residues:    90 -   232
chrX_30126440_30128399   Z   Score: 5880   Residues:     1 -  1960
chrX_30238550_30240722.rev   Z   Score: 6519   Residues:     1 -  2173
chrX_30255522_30257749   Z   Score: 6684   Residues:     1 -  2228
chrX_30312854_30316646   Z   Score: 11379   Residues:     1 -  3793
chrX_30393240_30394848   Z   Score: 4827   Residues:     1 -  1609
chrX_30527981_30531005.rev   A   Score:  315   Residues:  1119 -  1177
chrX_30527981_30531005.rev   T   Score:  220   Residues:  2854 -  2888
chrX_30527981_30531005.rev   Z   Score: 9075   Residues:     1 -  3025
chrX_30545791_30550906.rev   Z   Score: 15348   Residues:     1 -  5116
chrX_30552941_30556435.rev   Z   Score: 10485   Residues:     1 -  3495
chrX_30614739_30617822.rev   Z   Score: 9252   Residues:     1 -  3084
chrX_30850520_30852425.rev   Z   Score: 5718   Residues:     1 -  1906
chrX_30855341_30861737.rev   Z   Score: 19191   Residues:     1 -  6397
chrX_31243212_31249010.rev   Z   Score: 17397   Residues:     1 -  5799
chrX_31343143_31345917.rev   Z   Score: 8325   Residues:     1 -  2775
chrX_31468680_31472889   Z   Score: 12630   Residues:     1 -  4210
chrX_31620741_31623099.rev   Z   Score: 7077   Residues:     1 -  2359
chrX_31833485_31836770   A   Score:  202   Residues:   680 -   738
chrX_31833485_31836770   Z   Score: 9858   Residues:     1 -  3286
chrX_32151330_32153095.rev   Z   Score: 5298   Residues:     1 -  1766
chrX_32175967_32177766   Z   Score: 5400   Residues:     1 -  1800
chrX_32202966_32204664   Z   Score: 5097   Residues:     1 -  1699
chrX_32327545_32331100   Z   Score: 10668   Residues:     1 -  3556
chrX_32332841_32334499   Z   Score: 4977   Residues:     1 -  1659
chrX_32380294_32384079   Z   Score: 11358   Residues:     1 -  3786
chrX_32394604_32396254   Z   Score: 4953   Residues:     1 -  1651
chrX_32498728_32500494.rev   Z   Score: 5301   Residues:     1 -  1767
chrX_32508173_32514451   Z   Score: 18834   Residues:     1 -  6278
chrX_32542331_32544911.rev   Z   Score: 7743   Residues:     1 -  2581
chrX_32568979_32574138   Z   Score: 15480   Residues:     1 -  5160
chrX_32717706_32719327   Z   Score: 4866   Residues:     1 -  1622
chrX_32992276_32994526.rev   Z   Score: 6753   Residues:     1 -  2251
chrX_32998784_33004257   Z   Score: 16422   Residues:     1 -  5474
chrX_33006244_33008234.rev   Z   Score: 5973   Residues:     1 -  1991
chrX_33044037_33046832   Z   Score: 8388   Residues:     1 -  2796
chrX_33057083_33059482.rev   Z   Score: 7200   Residues:     1 -  2400
chrX_33119203_33125031   Z   Score: 17487   Residues:     1 -  5829
chrX_33170050_33173398   Z   Score: 10047   Residues:     1 -  3349
chrX_33194609_33199532   Z   Score: 14772   Residues:     1 -  4924
chrX_33213671_33218635   A   Score:  294   Residues:  4328 -  4382
chrX_33213671_33218635   Z   Score: 14895   Residues:     1 -  4965
chrX_33245437_33249132.rev   A   Score:  216   Residues:  2660 -  2686
chrX_33245437_33249132.rev   Z   Score: 11088   Residues:     1 -  3696
chrX_33255201_33260117   Z   Score: 14751   Residues:     1 -  4917
chrX_33271107_33273215.rev   Z   Score: 6327   Residues:     1 -  2109
chrX_33324318_33331594   Z   Score: 21831   Residues:     1 -  7277
chrX_33334753_33336971.rev   Z   Score: 6657   Residues:     1 -  2219
chrX_33344279_33349791.rev   A   Score:  332   Residues:  4663 -  4734
chrX_33344279_33349791.rev   Z   Score: 16539   Residues:     1 -  5513
chrX_33349932_33354531.rev   A   Score:  374   Residues:   213 -   358
chrX_33349932_33354531.rev   Z   Score: 13800   Residues:     1 -  4600
chrX_33412279_33414180.rev   Z   Score: 5706   Residues:     1 -  1902
chrX_33417246_33419564   Z   Score: 6957   Residues:     1 -  2319
chrX_33438258_33441709   Z   Score: 10356   Residues:     1 -  3452
chrX_33459069_33464849.rev   Z   Score: 17343   Residues:     1 -  5781
chrX_33520604_33522233.rev   Z   Score: 4890   Residues:     1 -  1630
chrX_33528178_33532173.rev   Z   Score: 11988   Residues:     1 -  3996
chrX_33533009_33536881.rev   Z   Score: 11619   Residues:     1 -  3873
chrX_33551235_33555338.rev   Z   Score: 12312   Residues:     1 -  4104
chrX_33563153_33565024.rev   Z   Score: 5616   Residues:     1 -  1872
chrX_33567545_33572457.rev   Z   Score: 14739   Residues:     1 -  4913
chrX_33592535_33594876.rev   Z   Score: 7026   Residues:     1 -  2342
chrX_33601786_33607626.rev   Z   Score: 17523   Residues:     1 -  5841
chrX_33610617_33612777.rev   T   Score:  222   Residues:   796 -   824
chrX_33610617_33612777.rev   Z   Score: 6483   Residues:     1 -  2161
chrX_33680160_33682353   Z   Score: 6582   Residues:     1 -  2194
chrX_33722679_33724536   Z   Score: 5574   Residues:     1 -  1858
chrX_33725871_33729489   Z   Score: 10857   Residues:     1 -  3619
chrX_33819595_33821668   Z   Score: 6222   Residues:     1 -  2074
chrX_33892988_33895598   T   Score:  303   Residues:   794 -   847
chrX_33892988_33895598   Z   Score: 7833   Residues:     1 -  2611
chrX_33909757_33911902.rev   Z   Score: 6438   Residues:     1 -  2146
chrX_33931353_33935306.rev   Z   Score: 11862   Residues:     1 -  3954
chrX_33990457_33993459   Z   Score: 9009   Residues:     1 -  3003
chrX_34051820_34053451.rev   Z   Score: 4893   Residues:     1 -  1631
chrX_34178028_34179885   Z   Score: 5574   Residues:     1 -  1858
chrX_34187467_34189631   Z   Score: 6495   Residues:     1 -  2165
chrX_34192465_34198694   Z   Score: 18690   Residues:     1 -  6230
chrX_34220552_34222488   Z   Score: 5811   Residues:     1 -  1937
chrX_34253565_34258944.rev   Z   Score: 16140   Residues:     1 -  5380
chrX_34311817_34313402.rev   Z   Score: 4758   Residues:     1 -  1586
chrX_34374166_34379563.rev   Z   Score: 16194   Residues:     1 -  5398
chrX_34380593_34382239   Z   Score: 4941   Residues:     1 -  1647
chrX_34600030_34602997   Z   Score: 8904   Residues:     1 -  2968
chrX_34607736_34610212   Z   Score: 7431   Residues:     1 -  2477
chrX_34612399_34614590.rev   Z   Score: 6576   Residues:     1 -  2192
chrX_34622896_34624631.rev   Z   Score: 5208   Residues:     1 -  1736
chrX_34644730_34650231   Z   Score: 16506   Residues:     1 -  5502
chrX_34681763_34683556   Z   Score: 5382   Residues:     1 -  1794
chrX_34687076_34690371.rev   Z   Score: 9888   Residues:     1 -  3296
chrX_34718104_34720901   A   Score:  228   Residues:  1314 -  1352
chrX_34718104_34720901   Z   Score: 8391   Residues:     1 -  2797
chrX_34726901_34730953   Z   Score: 12159   Residues:     1 -  4053
chrX_34756424_34761775   Z   Score: 16056   Residues:     1 -  5352
chrX_34797191_34799031.rev   A   Score:  222   Residues:   273 -   332
chrX_34797191_34799031.rev   Z   Score: 5523   Residues:     1 -  1841
chrX_34884915_34887435   Z   Score: 7563   Residues:     1 -  2521
chrX_34910544_34915825.rev   Z   Score: 15846   Residues:     1 -  5282
chrX_34970320_34972811.rev   Z   Score: 7476   Residues:     1 -  2492
chrX_35032407_35034084   Z   Score: 5034   Residues:     1 -  1678
chrX_35060755_35062447   Z   Score: 5079   Residues:     1 -  1693
chrX_35084043_35086354   Z   Score: 6936   Residues:     1 -  2312
chrX_35147161_35150174.rev   Z   Score: 9042   Residues:     1 -  3014
chrX_35188810_35190495   A   Score:  202   Residues:   455 -   483
chrX_35188810_35190495   Z   Score: 5058   Residues:     1 -  1686
chrX_35227846_35231005.rev   Z   Score: 9480   Residues:     1 -  3160
chrX_35301714_35303711.rev   Z   Score: 5994   Residues:     1 -  1998
chrX_35354090_35356683   Z   Score: 7782   Residues:     1 -  2594
chrX_35373485_35376429   Z   Score: 8835   Residues:     1 -  2945
chrX_35397407_35399366   Z   Score: 5880   Residues:     1 -  1960
chrX_35408428_35415091.rev   Z   Score: 19992   Residues:     1 -  6664
chrX_35505662_35511102.rev   Z   Score: 16323   Residues:     1 -  5441
chrX_35525199_35526816.rev   Z   Score: 4854   Residues:     1 -  1618
chrX_35534952_35536849.rev   Z   Score: 5694   Residues:     1 -  1898
chrX_35647824_35650836.rev   Z   Score: 9039   Residues:     1 -  3013
chrX_35682603_35684928.rev   Z   Score: 6978   Residues:     1 -  2326
chrX_35705681_35709477.rev   Z   Score: 11391   Residues:     1 -  3797
chrX_35759541_35766339.rev   Z   Score: 20397   Residues:     1 -  6799
chrX_35853763_35855942.rev   A   Score:  320   Residues:   947 -   986
chrX_35853763_35855942.rev   Z   Score: 6540   Residues:     1 -  2180
chrX_35887136_35892767.rev   Z   Score: 16896   Residues:     1 -  5632
chrX_35894777_35899661.rev   A   Score:  212   Residues:   422 -   490
chrX_35894777_35899661.rev   Z   Score: 14655   Residues:     1 -  4885
chrX_35911175_35913256   A   Score:  326   Residues:   398 -   452
chrX_35911175_35913256   Z   Score: 6246   Residues:     1 -  2082
chrX_35948322_35954598.rev   Z   Score: 18831   Residues:     1 -  6277
chrX_36007635_36014039.rev   Z   Score: 19215   Residues:     1 -  6405
chrX_36020599_36024594   Z   Score: 11988   Residues:     1 -  3996
chrX_36227617_36230359   A   Score:  287   Residues:   555 -   604
chrX_36227617_36230359   Z   Score: 8229   Residues:     1 -  2743
chrX_36232746_36237972   Z   Score: 15681   Residues:     1 -  5227
chrX_36243186_36249142.rev   Z   Score: 17871   Residues:     1 -  5957
chrX_36272192_36273992.rev   Z   Score: 5403   Residues:     1 -  1801
chrX_36274477_36276143   Z   Score: 5001   Residues:     1 -  1667
chrX_36298921_36300759.rev   Z   Score: 5517   Residues:     1 -  1839
chrX_36309726_36312802.rev   Z   Score: 9231   Residues:     1 -  3077
chrX_36325624_36327240.rev   Z   Score: 4851   Residues:     1 -  1617
chrX_36337196_36339117.rev   A   Score: 1058   Residues:   213 -   466
chrX_36337196_36339117.rev   R   Score:  428   Residues:   221 -   466
chrX_36337196_36339117.rev   Z   Score: 5766   Residues:     1 -  1922
chrX_36398667_36400851.rev   Z   Score: 6552   Residues:     1 -  2184
chrX_36402992_36405243.rev   Z   Score: 6756   Residues:     1 -  2252
chrX_36411499_36414097.rev   Z   Score: 7797   Residues:     1 -  2599
chrX_36442382_36446412.rev   A   Score:  287   Residues:  3060 -  3108
chrX_36442382_36446412.rev   Z   Score: 12093   Residues:     1 -  4031
chrX_36448771_36450760.rev   Z   Score: 5970   Residues:     1 -  1990
chrX_36478179_36484564.rev   Z   Score: 19158   Residues:     1 -  6386
chrX_36518475_36520314.rev   Z   Score: 5520   Residues:     1 -  1840
chrX_36574085_36575881   Z   Score: 5391   Residues:     1 -  1797
chrX_36587368_36589228   T   Score:  224   Residues:   138 -   170
chrX_36587368_36589228   Z   Score: 5583   Residues:     1 -  1861
chrX_36611307_36612953   Z   Score: 4941   Residues:     1 -  1647
chrX_36651077_36653238   Z   Score: 6486   Residues:     1 -  2162
chrX_36667450_36671663   A   Score:  219   Residues:   365 -   482
chrX_36667450_36671663   Z   Score: 12642   Residues:     1 -  4214
chrX_36784280_36786436   Z   Score: 6471   Residues:     1 -  2157
chrX_36850430_36853081   Z   Score: 7956   Residues:     1 -  2652
chrX_36937813_36942073   A   Score:  225   Residues:  1425 -  1549
chrX_36937813_36942073   Z   Score: 12783   Residues:     1 -  4261
chrX_36958249_36960308.rev   Z   Score: 6180   Residues:     1 -  2060
chrX_36972947_36976672.rev   Z   Score: 11178   Residues:     1 -  3726
chrX_37012988_37018838   Z   Score: 17553   Residues:     1 -  5851
chrX_37197481_37203881.rev   Z   Score: 19203   Residues:     1 -  6401
chrX_37244146_37250539.rev   Z   Score: 19182   Residues:     1 -  6394
chrX_37339260_37340877   Z   Score: 4854   Residues:     1 -  1618
chrX_37354233_37358483   Z   Score: 12753   Residues:     1 -  4251
chrX_37383578_37389979   Z   Score: 19206   Residues:     1 -  6402
chrX_37712251_37714426   Z   Score: 6528   Residues:     1 -  2176
chrX_37730651_37732306.rev   T   Score:  222   Residues:  1326 -  1354
chrX_37730651_37732306.rev   Z   Score: 4968   Residues:     1 -  1656
chrX_37856138_37858975   Z   Score: 8514   Residues:     1 -  2838
chrX_38033209_38035701.rev   Z   Score: 7476   Residues:     1 -  2492
chrX_38062273_38065015.rev   Z   Score: 8229   Residues:     1 -  2743
chrX_38165359_38167174.rev   Z   Score: 5448   Residues:     1 -  1816
chrX_38219635_38222248   Z   Score: 7842   Residues:     1 -  2614
chrX_38357341_38359230.rev   Z   Score: 5670   Residues:     1 -  1890
chrX_38443140_38445861   Z   Score: 8166   Residues:     1 -  2722
chrX_38490591_38492974.rev   Z   Score: 7152   Residues:     1 -  2384
chrX_38636822_38638498.rev   Z   Score: 5031   Residues:     1 -  1677
chrX_38639562_38643735.rev   Z   Score: 12522   Residues:     1 -  4174
chrX_38692844_38697146.rev   Z   Score: 12909   Residues:     1 -  4303
chrX_38700132_38710806   T   Score:  260   Residues:  5993 -  6032
chrX_38700132_38710806   Z   Score: 32025   Residues:     1 - 10675
chrX_38715480_38717689.rev   Z   Score: 6630   Residues:     1 -  2210
chrX_38718025_38720788   Z   Score: 8292   Residues:     1 -  2764
chrX_38796089_38802468.rev   Z   Score: 19140   Residues:     1 -  6380
chrX_38886833_38897128.rev   G   Score:  219   Residues:  4743 -  4806
chrX_38886833_38897128.rev   T   Score:  266   Residues:  2593 -  2655
chrX_38886833_38897128.rev   Z   Score: 30888   Residues:     1 - 10296
chrX_38960897_38966011   Z   Score: 15345   Residues:     1 -  5115
chrX_38966669_38970842.rev   Z   Score: 12522   Residues:     1 -  4174
chrX_39156837_39163792   A   Score:  202   Residues:  4416 -  4447
chrX_39156837_39163792   Z   Score: 20868   Residues:     1 -  6956
chrX_39221895_39223667   Z   Score: 5319   Residues:     1 -  1773
chrX_40056771_40058982   A   Score:  316   Residues:  1566 -  1612
chrX_40056771_40058982   Z   Score: 6636   Residues:     1 -  2212
chrX_40366837_40370228.rev   Z   Score: 10176   Residues:     1 -  3392
chrX_40400532_40402825.rev   Z   Score: 6882   Residues:     1 -  2294
chrX_40410444_40416144   Z   Score: 17103   Residues:     1 -  5701
chrX_40503116_40505182.rev   Z   Score: 6201   Residues:     1 -  2067
chrX_40570965_40573982   Z   Score: 9054   Residues:     1 -  3018
chrX_40665320_40667465   Z   Score: 6438   Residues:     1 -  2146
chrX_40697294_40699545.rev   Z   Score: 6756   Residues:     1 -  2252
chrX_40793489_40795610.rev   A   Score:  246   Residues:  1991 -  2022
chrX_40793489_40795610.rev   Z   Score: 6366   Residues:     1 -  2122
chrX_41042450_41044310.rev   Z   Score: 5583   Residues:     1 -  1861
chrX_41104188_41106429   Z   Score: 6726   Residues:     1 -  2242
chrX_41423593_41430011   Z   Score: 19257   Residues:     1 -  6419
chrX_41434238_41437330   Z   Score: 9279   Residues:     1 -  3093
chrX_41456307_41461754.rev   Z   Score: 16344   Residues:     1 -  5448
chrX_41619307_41625584   Z   Score: 18834   Residues:     1 -  6278
chrX_41748345_41750513.rev   Z   Score: 6507   Residues:     1 -  2169
chrX_41772501_41777349.rev   Z   Score: 14547   Residues:     1 -  4849
chrX_41817923_41824190.rev   Z   Score: 18804   Residues:     1 -  6268
chrX_41837894_41842453.rev   A   Score:  245   Residues:  1365 -  1422
chrX_41837894_41842453.rev   Z   Score: 13680   Residues:     1 -  4560
chrX_41922804_41927736   A   Score:  217   Residues:   991 -  1029
chrX_41922804_41927736   A   Score:  214   Residues:  4362 -  4389
chrX_41922804_41927736   Z   Score: 14799   Residues:     1 -  4933
chrX_41948080_41951314.rev   A   Score:  314   Residues:    91 -   133
chrX_41948080_41951314.rev   A   Score:  206   Residues:   498 -   629
chrX_41948080_41951314.rev   Z   Score: 9705   Residues:     1 -  3235
chrX_42023462_42029484.rev   Z   Score: 18069   Residues:     1 -  6023
chrX_42040617_42044310.rev   Z   Score: 11082   Residues:     1 -  3694
chrX_42051172_42056132   Z   Score: 14883   Residues:     1 -  4961
chrX_42062811_42064811   Z   Score: 6003   Residues:     1 -  2001
chrX_42121740_42128427   A   Score:  216   Residues:  3093 -  3128
chrX_42121740_42128427   Z   Score: 20064   Residues:     1 -  6688
chrX_42204690_42211066   Z   Score: 19131   Residues:     1 -  6377
chrX_42269586_42275634   A   Score:  200   Residues:  3247 -  3373
chrX_42269586_42275634   Z   Score: 18147   Residues:     1 -  6049
chrX_42348996_42350987   Z   Score: 5976   Residues:     1 -  1992
chrX_42426438_42432959.rev   Z   Score: 19566   Residues:     1 -  6522
chrX_42503374_42509624   Z   Score: 18753   Residues:     1 -  6251
chrX_42539041_42543295   A   Score:  261   Residues:  1438 -  1556
chrX_42539041_42543295   Z   Score: 12765   Residues:     1 -  4255
chrX_42660819_42665068.rev   Z   Score: 12750   Residues:     1 -  4250
chrX_42688105_42691212.rev   Z   Score: 9324   Residues:     1 -  3108
chrX_42776008_42778764   Z   Score: 8271   Residues:     1 -  2757
chrX_42813565_42817040.rev   Z   Score: 10428   Residues:     1 -  3476
chrX_42827079_42832490   Z   Score: 16236   Residues:     1 -  5412
chrX_42834160_42836143.rev   Z   Score: 5952   Residues:     1 -  1984
chrX_42843865_42847016   Z   Score: 9456   Residues:     1 -  3152
chrX_42875543_42877277.rev   Z   Score: 5205   Residues:     1 -  1735
chrX_42895580_42901094.rev   Z   Score: 16545   Residues:     1 -  5515
chrX_42921955_42927793.rev   Z   Score: 17517   Residues:     1 -  5839
chrX_42936255_42940573.rev   Z   Score: 12957   Residues:     1 -  4319
chrX_42960410_42964127.rev   Z   Score: 11154   Residues:     1 -  3718
chrX_43025069_43029336.rev   A   Score:  287   Residues:  2502 -  2587
chrX_43025069_43029336.rev   Z   Score: 12804   Residues:     1 -  4268
chrX_43043597_43045256.rev   Z   Score: 4980   Residues:     1 -  1660
chrX_43103127_43108744   A   Score:  336   Residues:  3317 -  3358
chrX_43103127_43108744   T   Score:  206   Residues:  3996 -  4022
chrX_43103127_43108744   Z   Score: 16854   Residues:     1 -  5618
chrX_43286195_43292598.rev   Z   Score: 19212   Residues:     1 -  6404
chrX_43318926_43321872   Z   Score: 8841   Residues:     1 -  2947
chrX_43337442_43343949.rev   Z   Score: 19524   Residues:     1 -  6508
chrX_43503455_43505355.rev   Z   Score: 5703   Residues:     1 -  1901
chrX_43537650_43543385.rev   Z   Score: 17208   Residues:     1 -  5736
chrX_43621404_43623995   Z   Score: 7776   Residues:     1 -  2592
chrX_43666622_43669807.rev   Z   Score: 9558   Residues:     1 -  3186
chrX_43691755_43694315   Z   Score: 7683   Residues:     1 -  2561
chrX_43745709_43747531.rev   Z   Score: 5469   Residues:     1 -  1823
chrX_43821266_43823909   Z   Score: 7932   Residues:     1 -  2644
chrX_43824300_43827067   Z   Score: 8304   Residues:     1 -  2768
chrX_43867828_43874538   Z   Score: 20133   Residues:     1 -  6711
chrX_43969868_43971625   Z   Score: 5274   Residues:     1 -  1758
chrX_44018964_44023596.rev   A   Score:  223   Residues:     7 -    39
chrX_44018964_44023596.rev   A   Score:  211   Residues:  3991 -  4036
chrX_44018964_44023596.rev   Z   Score: 13899   Residues:     1 -  4633
chrX_44111364_44113164.rev   A   Score:  304   Residues:   474 -   516
chrX_44111364_44113164.rev   T   Score:  250   Residues:  1346 -  1380
chrX_44111364_44113164.rev   Z   Score: 5403   Residues:     1 -  1801
chrX_44354035_44355721.rev   Z   Score: 5061   Residues:     1 -  1687
chrX_44452082_44454603   A   Score:  200   Residues:   989 -  1013
chrX_44452082_44454603   Z   Score: 7566   Residues:     1 -  2522
chrX_44505632_44507543.rev   A   Score:  216   Residues:  1376 -  1402
chrX_44505632_44507543.rev   Z   Score: 5736   Residues:     1 -  1912
chrX_44599161_44605547.rev   Z   Score: 19161   Residues:     1 -  6387
chrX_44737716_44741959.rev   Z   Score: 12732   Residues:     1 -  4244
chrX_44830211_44836097   A   Score:  222   Residues:  2177 -  2205
chrX_44830211_44836097   Z   Score: 17661   Residues:     1 -  5887
chrX_44837755_44839314.rev   Z   Score: 4680   Residues:     1 -  1560
chrX_44859366_44862495.rev   Z   Score: 9390   Residues:     1 -  3130
chrX_44864746_44866693.rev   Z   Score: 5844   Residues:     1 -  1948
chrX_44882995_44884716.rev   Z   Score: 5166   Residues:     1 -  1722
chrX_44989128_44993449   A   Score:  224   Residues:  2047 -  2079
chrX_44989128_44993449   Z   Score: 12966   Residues:     1 -  4322
chrX_45003007_45008134.rev   Z   Score: 15384   Residues:     1 -  5128
chrX_45073217_45077933.rev   Z   Score: 14151   Residues:     1 -  4717
chrX_45078385_45081177.rev   Z   Score: 8379   Residues:     1 -  2793
chrX_45107736_45111673.rev   Z   Score: 11814   Residues:     1 -  3938
chrX_45150027_45154430   A   Score:  209   Residues:   860 -   910
chrX_45150027_45154430   Z   Score: 13212   Residues:     1 -  4404
chrX_45164452_45166639   Z   Score: 6564   Residues:     1 -  2188
chrX_45173548_45177216.rev   Z   Score: 11007   Residues:     1 -  3669
chrX_45200643_45202615.rev   Z   Score: 5919   Residues:     1 -  1973
chrX_45221282_45225759.rev   Z   Score: 13434   Residues:     1 -  4478
chrX_45227915_45229734   Z   Score: 5460   Residues:     1 -  1820
chrX_45231287_45235236.rev   Z   Score: 11850   Residues:     1 -  3950
chrX_45241165_45243116.rev   Z   Score: 5856   Residues:     1 -  1952
chrX_45251659_45255503   Z   Score: 11535   Residues:     1 -  3845
chrX_45306226_45308220   Z   Score: 5985   Residues:     1 -  1995
chrX_45533064_45535671.rev   Z   Score: 7824   Residues:     1 -  2608
chrX_45578533_45583721.rev   Z   Score: 15567   Residues:     1 -  5189
chrX_45614257_45620677.rev   Z   Score: 19263   Residues:     1 -  6421
chrX_45662348_45666983   Z   Score: 13908   Residues:     1 -  4636
chrX_45667974_45674638.rev   A   Score:  210   Residues:  4348 -  4382
chrX_45667974_45674638.rev   Z   Score: 19995   Residues:     1 -  6665
chrX_45690496_45696919.rev   Z   Score: 19272   Residues:     1 -  6424
chrX_45702018_45708714   Z   Score: 20091   Residues:     1 -  6697
chrX_45716627_45725445   Z   Score: 26457   Residues:     1 -  8819
chrX_45737656_45739506.rev   Z   Score: 5553   Residues:     1 -  1851
chrX_45789486_45793804.rev   Z   Score: 12957   Residues:     1 -  4319
chrX_45951401_45955085   Z   Score: 11055   Residues:     1 -  3685
chrX_45961746_45965299   A   Score:  283   Residues:   422 -   567
chrX_45961746_45965299   Z   Score: 10662   Residues:     1 -  3554
chrX_46025830_46032227.rev   Z   Score: 19194   Residues:     1 -  6398
chrX_46095528_46102698.rev   Z   Score: 21513   Residues:     1 -  7171
chrX_46138320_46143560   A   Score:  234   Residues:  2055 -  2087
chrX_46138320_46143560   Z   Score: 15723   Residues:     1 -  5241
chrX_46253572_46256984   Z   Score: 10239   Residues:     1 -  3413
chrX_46270547_46276821   T   Score:  324   Residues:    97 -   144
chrX_46270547_46276821   Z   Score: 18825   Residues:     1 -  6275
chrX_46355866_46358234   Z   Score: 7107   Residues:     1 -  2369
chrX_46379321_46382439   Z   Score: 9357   Residues:     1 -  3119
chrX_46523252_46526029   Z   Score: 8334   Residues:     1 -  2778
chrX_46774665_46776662   Z   Score: 5994   Residues:     1 -  1998
chrX_46992971_46996301.rev   Z   Score: 9990   Residues:     1 -  3330
chrX_47399576_47405850.rev   Z   Score: 18825   Residues:     1 -  6275
chrX_47512467_47516017.rev   Z   Score: 10653   Residues:     1 -  3551
chrX_47541043_47544310.rev   Z   Score: 9804   Residues:     1 -  3268
chrX_47598755_47600335   Z   Score: 4743   Residues:     1 -  1581
chrX_47638781_47641403.rev   A   Score:  265   Residues:  1194 -  1267
chrX_47638781_47641403.rev   Z   Score: 7869   Residues:     1 -  2623
chrX_47676214_47678141   Z   Score: 5784   Residues:     1 -  1928
chrX_47765888_47767890   Z   Score: 6009   Residues:     1 -  2003
chrX_47815437_47817461.rev   Z   Score: 6075   Residues:     1 -  2025
chrX_47856602_47858615   Z   Score: 6042   Residues:     1 -  2014
chrX_47862443_47864485.rev   Z   Score: 6129   Residues:     1 -  2043
chrX_47898605_47900650.rev   Z   Score: 6138   Residues:     1 -  2046
chrX_47926152_47928176.rev   Z   Score: 6075   Residues:     1 -  2025
chrX_47976910_47979252.rev   Z   Score: 7029   Residues:     1 -  2343
chrX_47989241_47991375.rev   Z   Score: 6405   Residues:     1 -  2135
chrX_47992028_47994082   Z   Score: 6165   Residues:     1 -  2055
chrX_48031648_48033703.rev   Z   Score: 6168   Residues:     1 -  2056
chrX_48034357_48036520   Z   Score: 6492   Residues:     1 -  2164
chrX_48058422_48060431   Z   Score: 6030   Residues:     1 -  2010
chrX_48392033_48395924   A   Score:  623   Residues:  3775 -  3892
chrX_48392033_48395924   A   Score:  204   Residues:  3325 -  3352
chrX_48392033_48395924   Z   Score: 11676   Residues:     1 -  3892
chrX_48483257_48488536   A   Score:  208   Residues:  1213 -  1243
chrX_48483257_48488536   Z   Score: 15840   Residues:     1 -  5280
chrX_49088167_49094560.rev   A   Score:  216   Residues:   280 -   315
chrX_49088167_49094560.rev   Z   Score: 19182   Residues:     1 -  6394
chrX_49108586_49110227.rev   Z   Score: 4926   Residues:     1 -  1642
chrX_49149873_49152513.rev   A   Score:  217   Residues:   756 -   823
chrX_49149873_49152513.rev   Z   Score: 7923   Residues:     1 -  2641
chrX_49238368_49240446.rev   Z   Score: 6237   Residues:     1 -  2079
chrX_49362967_49367507.rev   A   Score:  585   Residues:  4425 -  4541
chrX_49362967_49367507.rev   A   Score:  232   Residues:  3994 -  4027
chrX_49362967_49367507.rev   Z   Score: 13623   Residues:     1 -  4541
chrX_49405336_49407195   Z   Score: 5580   Residues:     1 -  1860
chrX_49487374_49493650.rev   A   Score:  219   Residues:   269 -   441
chrX_49487374_49493650.rev   Z   Score: 18831   Residues:     1 -  6277
chrX_49517608_49520837.rev   Z   Score: 9690   Residues:     1 -  3230
chrX_49527337_49533616   Z   Score: 18840   Residues:     1 -  6280
chrX_49587283_49589088   Z   Score: 5418   Residues:     1 -  1806
chrX_49872416_49878815.rev   Z   Score: 19200   Residues:     1 -  6400
chrX_49879072_49883785.rev   A   Score:  274   Residues:  1955 -  1992
chrX_49879072_49883785.rev   Z   Score: 14142   Residues:     1 -  4714
chrX_49892732_49897137.rev   Z   Score: 13218   Residues:     1 -  4406
chrX_50134555_50139670   Z   Score: 15348   Residues:     1 -  5116
chrX_50149818_50152283.rev   Z   Score: 7398   Residues:     1 -  2466
chrX_50165571_50168636.rev   A   Score:  386   Residues:   867 -   933
chrX_50165571_50168636.rev   Z   Score: 9198   Residues:     1 -  3066
chrX_50231544_50234124.rev   Z   Score: 7743   Residues:     1 -  2581
chrX_50307912_50312261   Z   Score: 13050   Residues:     1 -  4350
chrX_50332278_50335585.rev   Z   Score: 9924   Residues:     1 -  3308
chrX_50358644_50361559   Z   Score: 8748   Residues:     1 -  2916
chrX_50364192_50369261   T   Score:  216   Residues:  3422 -  3448
chrX_50364192_50369261   Z   Score: 15210   Residues:     1 -  5070
chrX_50431783_50434670.rev   A   Score:  285   Residues:   153 -   260
chrX_50431783_50434670.rev   Z   Score: 8664   Residues:     1 -  2888
chrX_50466610_50471779   Z   Score: 15510   Residues:     1 -  5170
chrX_50495911_50499507   Z   Score: 10791   Residues:     1 -  3597
chrX_50512686_50516164.rev   Z   Score: 10437   Residues:     1 -  3479
chrX_50551681_50553916.rev   Z   Score: 6708   Residues:     1 -  2236
chrX_50588946_50595338.rev   Z   Score: 19179   Residues:     1 -  6393
chrX_50645279_50649765   Z   Score: 13461   Residues:     1 -  4487
chrX_50688514_50693497   Z   Score: 14952   Residues:     1 -  4984
chrX_50775115_50777214   Z   Score: 6300   Residues:     1 -  2100
chrX_50812578_50818074   Z   Score: 16491   Residues:     1 -  5497
chrX_50837491_50843809   Z   Score: 18957   Residues:     1 -  6319
chrX_50845477_50847854   Z   Score: 7134   Residues:     1 -  2378
chrX_50937311_50943450   Z   Score: 18420   Residues:     1 -  6140
chrX_50947620_50950806   Z   Score: 9561   Residues:     1 -  3187
chrX_51003588_51009987.rev   Z   Score: 19200   Residues:     1 -  6400
chrX_51088457_51094732.rev   Z   Score: 18828   Residues:     1 -  6276
chrX_51107712_51113982.rev   Z   Score: 18813   Residues:     1 -  6271
chrX_51114183_51120327.rev   Z   Score: 18435   Residues:     1 -  6145
chrX_51122911_51125565.rev   A   Score:  727   Residues:   248 -   459
chrX_51122911_51125565.rev   R   Score:  321   Residues:   255 -   461
chrX_51122911_51125565.rev   G   Score:  213   Residues:   276 -   345
chrX_51122911_51125565.rev   Z   Score: 7965   Residues:     1 -  2655
chrX_51126510_51131439.rev   Z   Score: 14790   Residues:     1 -  4930
chrX_51152365_51157446   Z   Score: 15246   Residues:     1 -  5082
chrX_51158693_51162694.rev   A   Score:  273   Residues:  1580 -  1652
chrX_51158693_51162694.rev   Z   Score: 12006   Residues:     1 -  4002
chrX_51164089_51167060   Z   Score: 8916   Residues:     1 -  2972
chrX_51198530_51204906   Z   Score: 19131   Residues:     1 -  6377
chrX_51206667_51211446.rev   Z   Score: 14340   Residues:     1 -  4780
chrX_51220350_51226492   Z   Score: 18429   Residues:     1 -  6143
chrX_51231706_51234156.rev   Z   Score: 7353   Residues:     1 -  2451
chrX_51263394_51265963.rev   A   Score:  229   Residues:  1645 -  1736
chrX_51263394_51265963.rev   Z   Score: 7710   Residues:     1 -  2570
chrX_51269669_51271797   Z   Score: 6387   Residues:     1 -  2129
chrX_51332495_51335324   Z   Score: 8490   Residues:     1 -  2830
chrX_51382834_51384622.rev   Z   Score: 5367   Residues:     1 -  1789
chrX_51395188_51400288.rev   Z   Score: 15303   Residues:     1 -  5101
chrX_51439363_51441819.rev   Z   Score: 7371   Residues:     1 -  2457
chrX_51462145_51465021   A   Score:  216   Residues:  1043 -  1101
chrX_51462145_51465021   Z   Score: 8631   Residues:     1 -  2877
chrX_51484602_51486569.rev   Z   Score: 5904   Residues:     1 -  1968
chrX_51510402_51515061   Z   Score: 13980   Residues:     1 -  4660
chrX_51535749_51540529.rev   Z   Score: 14343   Residues:     1 -  4781
chrX_51544713_51548671   Z   Score: 11877   Residues:     1 -  3959
chrX_51567686_51577854.rev   Z   Score: 30507   Residues:     1 - 10169
chrX_51584122_51585984.rev   Z   Score: 5589   Residues:     1 -  1863
chrX_51596815_51603216.rev   Z   Score: 19206   Residues:     1 -  6402
chrX_51620488_51623917   Z   Score: 10290   Residues:     1 -  3430
chrX_51648229_51652349.rev   Z   Score: 12363   Residues:     1 -  4121
chrX_51659616_51665184.rev   Z   Score: 16707   Residues:     1 -  5569
chrX_51666145_51669087   Z   Score: 8829   Residues:     1 -  2943
chrX_51676956_51683381.rev   Z   Score: 19278   Residues:     1 -  6426
chrX_51686755_51693150   Z   Score: 19188   Residues:     1 -  6396
chrX_51694782_51701194   Z   Score: 19239   Residues:     1 -  6413
chrX_51703618_51709420   Z   Score: 17409   Residues:     1 -  5803
chrX_51734361_51741946   Z   Score: 22758   Residues:     1 -  7586
chrX_51746410_51752810   Z   Score: 19203   Residues:     1 -  6401
chrX_51754010_51758130   Z   Score: 12363   Residues:     1 -  4121
chrX_51782473_51785902.rev   Z   Score: 10290   Residues:     1 -  3430
chrX_51797769_51806198   Z   Score: 25290   Residues:     1 -  8430
chrX_51865002_51866848.rev   Z   Score: 5541   Residues:     1 -  1847
chrX_51867466_51873862   Z   Score: 19191   Residues:     1 -  6397
chrX_51882824_51884546   Z   Score: 5169   Residues:     1 -  1723
chrX_51908535_51911045.rev   Z   Score: 7533   Residues:     1 -  2511
chrX_51969519_51973890.rev   Z   Score: 13116   Residues:     1 -  4372
chrX_52018544_52020926.rev   Z   Score: 7149   Residues:     1 -  2383
chrX_52064904_52066761.rev   A   Score:  292   Residues:   134 -   220
chrX_52064904_52066761.rev   Z   Score: 5574   Residues:     1 -  1858
chrX_52098455_52100312   A   Score:  300   Residues:   131 -   218
chrX_52098455_52100312   Z   Score: 5574   Residues:     1 -  1858
chrX_52144290_52146672   Z   Score: 7149   Residues:     1 -  2383
chrX_52190540_52195697   Z   Score: 15474   Residues:     1 -  5158
chrX_52341484_52343866.rev   Z   Score: 7149   Residues:     1 -  2383
chrX_52387844_52389701.rev   A   Score:  284   Residues:   134 -   219
chrX_52387844_52389701.rev   Z   Score: 5571   Residues:     1 -  1857
chrX_52421427_52423284   A   Score:  292   Residues:   132 -   218
chrX_52421427_52423284   Z   Score: 5574   Residues:     1 -  1858
chrX_52434321_52436178   A   Score:  292   Residues:   132 -   218
chrX_52434321_52436178   Z   Score: 5574   Residues:     1 -  1858
chrX_52526597_52528636.rev   Z   Score: 6120   Residues:     1 -  2040
chrX_52570753_52572777.rev   Z   Score: 6075   Residues:     1 -  2025
chrX_52623750_52626109.rev   Z   Score: 7080   Residues:     1 -  2360
chrX_52639094_52640915   Z   Score: 5466   Residues:     1 -  1822
chrX_52656489_52658849   Z   Score: 7083   Residues:     1 -  2361
chrX_52748592_52750392   T   Score:  206   Residues:    22 -    48
chrX_52748592_52750392   Z   Score: 5403   Residues:     1 -  1801
chrX_52755788_52762230.rev   A   Score:  234   Residues:  2796 -  2861
chrX_52755788_52762230.rev   Z   Score: 19329   Residues:     1 -  6443
chrX_52789316_52793621   Z   Score: 12918   Residues:     1 -  4306
chrX_52794886_52797580.rev   Z   Score: 8085   Residues:     1 -  2695
chrX_52882495_52885189   Z   Score: 8085   Residues:     1 -  2695
chrX_52925644_52928812   A   Score:  312   Residues:  1799 -  1837
chrX_52925644_52928812   A   Score:  288   Residues:  1325 -  1385
chrX_52925644_52928812   Z   Score: 9507   Residues:     1 -  3169
chrX_53017083_53020421.rev   A   Score:  222   Residues:  2345 -  2373
chrX_53017083_53020421.rev   Z   Score: 10017   Residues:     1 -  3339
chrX_53084535_53087895   Z   Score: 10083   Residues:     1 -  3361
chrX_53186498_53191479.rev   A   Score:  382   Residues:  1250 -  1303
chrX_53186498_53191479.rev   A   Score:  238   Residues:  4799 -  4829
chrX_53186498_53191479.rev   Z   Score: 14946   Residues:     1 -  4982
chrX_53515090_53516854   Z   Score: 5295   Residues:     1 -  1765
chrX_53601221_53602810.rev   Z   Score: 4770   Residues:     1 -  1590
chrX_53649682_53651964.rev   Z   Score: 6849   Residues:     1 -  2283
chrX_53654252_53655869.rev   A   Score:  208   Residues:   147 -   177
chrX_53654252_53655869.rev   Z   Score: 4854   Residues:     1 -  1618
chrX_53688067_53690068.rev   Z   Score: 6006   Residues:     1 -  2002
chrX_53692382_53698790   Z   Score: 19227   Residues:     1 -  6409
chrX_53742898_53748481.rev   A   Score:  358   Residues:   226 -   276
chrX_53742898_53748481.rev   A   Score:  266   Residues:  2815 -  2851
chrX_53742898_53748481.rev   A   Score:  224   Residues:  1929 -  1956
chrX_53742898_53748481.rev   Z   Score: 16752   Residues:     1 -  5584
chrX_53784785_53786616.rev   Z   Score: 5496   Residues:     1 -  1832
chrX_53797866_53803742   A   Score:  210   Residues:   459 -   496
chrX_53797866_53803742   Z   Score: 17631   Residues:     1 -  5877
chrX_53877883_53884277   A   Score:  252   Residues:  3893 -  3926
chrX_53877883_53884277   Z   Score: 19185   Residues:     1 -  6395
chrX_53915581_53917615   Z   Score: 6105   Residues:     1 -  2035
chrX_54007525_54009893.rev   Z   Score: 7107   Residues:     1 -  2369
chrX_54013792_54016765   Z   Score: 8922   Residues:     1 -  2974
chrX_54028420_54034698.rev   Z   Score: 18837   Residues:     1 -  6279
chrX_54150949_54153524   A   Score:  206   Residues:  1926 -  1952
chrX_54150949_54153524   Z   Score: 7728   Residues:     1 -  2576
chrX_54248486_54250701   Z   Score: 6645   Residues:     1 -  2215
chrX_54499262_54504587.rev   Z   Score: 15978   Residues:     1 -  5326
chrX_54518060_54523190.rev   Z   Score: 15393   Residues:     1 -  5131
chrX_54531112_54534248.rev   A   Score:  274   Residues:   341 -   378
chrX_54531112_54534248.rev   A   Score:  224   Residues:  2495 -  2522
chrX_54531112_54534248.rev   Z   Score: 9411   Residues:     1 -  3137
chrX_54572751_54574573.rev   Z   Score: 5469   Residues:     1 -  1823
chrX_54584277_54586536   Z   Score: 6780   Residues:     1 -  2260
chrX_54587411_54589104.rev   Z   Score: 5082   Residues:     1 -  1694
chrX_54593485_54596111.rev   A   Score:  980   Residues:   991 -  1205
chrX_54593485_54596111.rev   R   Score:  363   Residues:   991 -  1205
chrX_54593485_54596111.rev   Z   Score: 7881   Residues:     1 -  2627
chrX_54626084_54630755.rev   Z   Score: 14016   Residues:     1 -  4672
chrX_54641169_54645743.rev   Z   Score: 13725   Residues:     1 -  4575
chrX_54692076_54694556   Z   Score: 7443   Residues:     1 -  2481
chrX_54737531_54739283.rev   Z   Score: 5259   Residues:     1 -  1753
chrX_54763637_54772593.rev   Z   Score: 26871   Residues:     1 -  8957
chrX_54820838_54822484   Z   Score: 4941   Residues:     1 -  1647
chrX_54826472_54828950   Z   Score: 7437   Residues:     1 -  2479
chrX_54847329_54851608   Z   Score: 12840   Residues:     1 -  4280
chrX_54877474_54886340   Z   Score: 26601   Residues:     1 -  8867
chrX_54956623_54962894.rev   Z   Score: 18816   Residues:     1 -  6272
chrX_54971306_54975516.rev   Z   Score: 12633   Residues:     1 -  4211
chrX_54976757_54982612.rev   Z   Score: 17568   Residues:     1 -  5856
chrX_55144949_55147352.rev   Z   Score: 7212   Residues:     1 -  2404
chrX_55161256_55164896   Z   Score: 10923   Residues:     1 -  3641
chrX_55203293_55213744.rev   Z   Score: 31356   Residues:     1 - 10452
chrX_55223577_55226760.rev   Z   Score: 9552   Residues:     1 -  3184
chrX_55227539_55232074.rev   Z   Score: 13608   Residues:     1 -  4536
chrX_55257878_55261156.rev   T   Score:  214   Residues:  2404 -  2431
chrX_55257878_55261156.rev   Z   Score: 9837   Residues:     1 -  3279
chrX_55266086_55271922   Z   Score: 17511   Residues:     1 -  5837
chrX_55305469_55311886   Z   Score: 19254   Residues:     1 -  6418
chrX_55335471_55341883   Z   Score: 19239   Residues:     1 -  6413
chrX_55345262_55349517   Z   Score: 12768   Residues:     1 -  4256
chrX_55352198_55358618   A   Score:  313   Residues:  2792 -  2847
chrX_55352198_55358618   Z   Score: 19263   Residues:     1 -  6421
chrX_55441914_55444527.rev   Z   Score: 7842   Residues:     1 -  2614
chrX_55475769_55481875   Z   Score: 18321   Residues:     1 -  6107
chrX_55485306_55487170   Z   Score: 5595   Residues:     1 -  1865
chrX_55495909_55498984   Z   Score: 9228   Residues:     1 -  3076
chrX_55510237_55516044.rev   Z   Score: 17424   Residues:     1 -  5808
chrX_55536194_55540964   Z   Score: 14313   Residues:     1 -  4771
chrX_55578036_55597137.rev   Z   Score: 57306   Residues:     1 - 19102
chrX_55611085_55617792   Z   Score: 20124   Residues:     1 -  6708
chrX_55678620_55685002.rev   Z   Score: 19149   Residues:     1 -  6383
chrX_55688264_55690189   Z   Score: 5778   Residues:     1 -  1926
chrX_55715756_55722136.rev   Z   Score: 19143   Residues:     1 -  6381
chrX_55729344_55733533.rev   Z   Score: 12570   Residues:     1 -  4190
chrX_55737531_55742445   Z   Score: 14745   Residues:     1 -  4915
chrX_55755465_55761871.rev   Z   Score: 19221   Residues:     1 -  6407
chrX_55787876_55793657   Z   Score: 17346   Residues:     1 -  5782
chrX_55838077_55842848.rev   Z   Score: 14316   Residues:     1 -  4772
chrX_55845346_55851732   Z   Score: 19161   Residues:     1 -  6387
chrX_55865613_55867659.rev   Z   Score: 6141   Residues:     1 -  2047
chrX_55877196_55883559   Z   Score: 19092   Residues:     1 -  6364
chrX_55900809_55906493.rev   Z   Score: 17055   Residues:     1 -  5685
chrX_55942714_55944451.rev   A   Score:  223   Residues:   225 -   256
chrX_55942714_55944451.rev   Z   Score: 5211   Residues:     1 -  1737
chrX_55947916_55954159.rev   A   Score:  328   Residues:  3866 -  3906
chrX_55947916_55954159.rev   Z   Score: 18732   Residues:     1 -  6244
chrX_55956974_55963234.rev   Z   Score: 18783   Residues:     1 -  6261
chrX_55983003_55985315.rev   Z   Score: 6939   Residues:     1 -  2313
chrX_55985846_55991300.rev   Z   Score: 16365   Residues:     1 -  5455
chrX_56001032_56002703.rev   Z   Score: 5016   Residues:     1 -  1672
chrX_56010655_56012683.rev   Z   Score: 6087   Residues:     1 -  2029
chrX_56040565_56049968   A   Score:  291   Residues:  6632 -  6701
chrX_56040565_56049968   A   Score:  286   Residues:  1498 -  1614
chrX_56040565_56049968   Z   Score: 28212   Residues:     1 -  9404
chrX_56066595_56071256.rev   Z   Score: 13986   Residues:     1 -  4662
chrX_56072300_56074056.rev   Z   Score: 5271   Residues:     1 -  1757
chrX_56081811_56109451   Z   Score: 82920   Residues:     1 - 27640
chrX_56183227_56186074.rev   Z   Score: 8544   Residues:     1 -  2848
chrX_56201468_56206301   Z   Score: 14499   Residues:     1 -  4833
chrX_56234666_56239528.rev   Z   Score: 14589   Residues:     1 -  4863
chrX_56245351_56251743.rev   Z   Score: 19179   Residues:     1 -  6393
chrX_56253542_56257639   Z   Score: 12294   Residues:     1 -  4098
chrX_56262323_56268726.rev   Z   Score: 19212   Residues:     1 -  6404
chrX_56269296_56271046   Z   Score: 5253   Residues:     1 -  1751
chrX_56272140_56276420.rev   Z   Score: 12843   Residues:     1 -  4281
chrX_56282986_56285482   Z   Score: 7491   Residues:     1 -  2497
chrX_56298186_56304847.rev   A   Score:  208   Residues:  2692 -  2717
chrX_56298186_56304847.rev   Z   Score: 19986   Residues:     1 -  6662
chrX_56322028_56324408.rev   Z   Score: 7143   Residues:     1 -  2381
chrX_56333762_56340162.rev   Z   Score: 19203   Residues:     1 -  6401
chrX_56340905_56351353   Z   Score: 31347   Residues:     1 - 10449
chrX_56362586_56371202.rev   T   Score:  291   Residues:  8243 -  8336
chrX_56362586_56371202.rev   Z   Score: 25851   Residues:     1 -  8617
chrX_56380648_56382380.rev   Z   Score: 5199   Residues:     1 -  1733
chrX_56399219_56405546.rev   Z   Score: 18984   Residues:     1 -  6328
chrX_56410206_56413184   Z   Score: 8937   Residues:     1 -  2979
chrX_56419346_56423322   Z   Score: 11931   Residues:     1 -  3977
chrX_56450235_56454463   Z   Score: 12687   Residues:     1 -  4229
chrX_56485923_56491172.rev   Z   Score: 15750   Residues:     1 -  5250
chrX_56491228_56497626.rev   Z   Score: 19197   Residues:     1 -  6399
chrX_56501383_56508081.rev   Z   Score: 20097   Residues:     1 -  6699
chrX_56513710_56515513   Z   Score: 5412   Residues:     1 -  1804
chrX_56532941_56535271   T   Score:  251   Residues:     3 -    71
chrX_56532941_56535271   Z   Score: 6993   Residues:     1 -  2331
chrX_56539280_56551368   Z   Score: 36267   Residues:     1 - 12089
chrX_56558475_56564305.rev   Z   Score: 17493   Residues:     1 -  5831
chrX_56582657_56589065   Z   Score: 19227   Residues:     1 -  6409
chrX_56592367_56599013.rev   A   Score:  217   Residues:  5953 -  5983
chrX_56592367_56599013.rev   Z   Score: 19941   Residues:     1 -  6647
chrX_56599760_56601462   A   Score:  240   Residues:  1560 -  1594
chrX_56599760_56601462   Z   Score: 5109   Residues:     1 -  1703
chrX_56604839_56611118   Z   Score: 18840   Residues:     1 -  6280
chrX_56615148_56620968.rev   A   Score:  311   Residues:  3208 -  3255
chrX_56615148_56620968.rev   Z   Score: 17463   Residues:     1 -  5821
chrX_56623798_56628537   Z   Score: 14220   Residues:     1 -  4740
chrX_56629322_56635047   A   Score:  662   Residues:  3070 -  3188
chrX_56629322_56635047   A   Score:  200   Residues:  2109 -  2231
chrX_56629322_56635047   Z   Score: 17178   Residues:     1 -  5726
chrX_56715525_56722169.rev   Z   Score: 19935   Residues:     1 -  6645
chrX_56727523_56729727   Z   Score: 6615   Residues:     1 -  2205
chrX_56737075_56739528.rev   Z   Score: 7362   Residues:     1 -  2454
chrX_56755402_56762509   Z   Score: 21324   Residues:     1 -  7108
chrX_56777957_56784341   Z   Score: 19155   Residues:     1 -  6385
chrX_56802886_56809275   Z   Score: 19170   Residues:     1 -  6390
chrX_56816548_56823063.rev   Z   Score: 19548   Residues:     1 -  6516
chrX_56847601_56852370.rev   Z   Score: 14310   Residues:     1 -  4770
chrX_56858446_56863064.rev   Z   Score: 13857   Residues:     1 -  4619
chrX_56864526_56869734   A   Score:  483   Residues:  2371 -  2471
chrX_56864526_56869734   A   Score:  205   Residues:  2080 -  2110
chrX_56864526_56869734   A   Score:  269   Residues:  2881 -  2929
chrX_56864526_56869734   Z   Score: 15627   Residues:     1 -  5209
chrX_56905527_56907224.rev   A   Score:  244   Residues:   465 -   497
chrX_56905527_56907224.rev   Z   Score: 5094   Residues:     1 -  1698
chrX_56910288_56912138.rev   Z   Score: 5553   Residues:     1 -  1851
chrX_56913411_56915493.rev   Z   Score: 6249   Residues:     1 -  2083
chrX_56917450_56919964.rev   Z   Score: 7545   Residues:     1 -  2515
chrX_56920688_56924571.rev   Z   Score: 11652   Residues:     1 -  3884
chrX_56924915_56926569.rev   A   Score:  211   Residues:  1224 -  1260
chrX_56924915_56926569.rev   Z   Score: 4965   Residues:     1 -  1655
chrX_56931811_56940585.rev   Z   Score: 26325   Residues:     1 -  8775
chrX_56955205_56958798   Z   Score: 10782   Residues:     1 -  3594
chrX_56962464_56966702.rev   Z   Score: 12717   Residues:     1 -  4239
chrX_56988631_56991111   Z   Score: 7443   Residues:     1 -  2481
chrX_57003301_57009967   Z   Score: 20001   Residues:     1 -  6667
chrX_57047781_57050340.rev   Z   Score: 7680   Residues:     1 -  2560
chrX_57054266_57057699.rev   Z   Score: 10302   Residues:     1 -  3434
chrX_57067555_57073840.rev   Z   Score: 18858   Residues:     1 -  6286
chrX_57087885_57092423   Z   Score: 13617   Residues:     1 -  4539
chrX_57100194_57102607.rev   Z   Score: 7242   Residues:     1 -  2414
chrX_57104312_57106719.rev   Z   Score: 7224   Residues:     1 -  2408
chrX_57125982_57128876.rev   Z   Score: 8685   Residues:     1 -  2895
chrX_57166660_57168629   Z   Score: 5910   Residues:     1 -  1970
chrX_57171370_57174397   Z   Score: 9084   Residues:     1 -  3028
chrX_57184364_57188820   Z   Score: 13371   Residues:     1 -  4457
chrX_57204441_57210826   Z   Score: 19158   Residues:     1 -  6386
chrX_57222145_57230383   Z   Score: 24717   Residues:     1 -  8239
chrX_57232539_57238304.rev   Z   Score: 17298   Residues:     1 -  5766
chrX_57245498_57249615   Z   Score: 12354   Residues:     1 -  4118
chrX_57252326_57256554.rev   G   Score:  210   Residues:  1888 -  1932
chrX_57252326_57256554.rev   Z   Score: 12687   Residues:     1 -  4229
chrX_57259455_57263813   A   Score:  202   Residues:  3487 -  3524
chrX_57259455_57263813   Z   Score: 13077   Residues:     1 -  4359
chrX_57282432_57284970.rev   Z   Score: 7617   Residues:     1 -  2539
chrX_57285861_57287996.rev   Z   Score: 6408   Residues:     1 -  2136
chrX_57300029_57302317.rev   Z   Score: 6867   Residues:     1 -  2289
chrX_57321929_57330962.rev   Z   Score: 27102   Residues:     1 -  9034
chrX_57334130_57339403   Z   Score: 15822   Residues:     1 -  5274
chrX_57348307_57354672.rev   Z   Score: 19098   Residues:     1 -  6366
chrX_57410711_57417094   Z   Score: 19152   Residues:     1 -  6384
chrX_57420622_57425672.rev   Z   Score: 15153   Residues:     1 -  5051
chrX_57430799_57435136.rev   Z   Score: 13014   Residues:     1 -  4338
chrX_57452274_57462071   A   Score:  206   Residues:  6676 -  6798
chrX_57452274_57462071   A   Score:  200   Residues:  3969 -  3993
chrX_57452274_57462071   Z   Score: 29394   Residues:     1 -  9798
chrX_57468238_57472734   Z   Score: 13491   Residues:     1 -  4497
chrX_57497922_57499836   Z   Score: 5745   Residues:     1 -  1915
chrX_57519541_57529073   A   Score:  253   Residues:  5885 -  5963
chrX_57519541_57529073   Z   Score: 28599   Residues:     1 -  9533
chrX_57532524_57544620   Z   Score: 36291   Residues:     1 - 12097
chrX_57571281_57574406   Z   Score: 9378   Residues:     1 -  3126
chrX_57592106_57599614   Z   Score: 22527   Residues:     1 -  7509
chrX_57601166_57603264   Z   Score: 6297   Residues:     1 -  2099
chrX_57604250_57606130   Z   Score: 5643   Residues:     1 -  1881
chrX_57617484_57623858   Z   Score: 19125   Residues:     1 -  6375
chrX_57629828_57633284.rev   Z   Score: 10371   Residues:     1 -  3457
chrX_57653646_57659466   Z   Score: 17463   Residues:     1 -  5821
chrX_57668098_57669802   Z   Score: 5115   Residues:     1 -  1705
chrX_57705684_57707878.rev   A   Score:  204   Residues:  2076 -  2111
chrX_57705684_57707878.rev   Z   Score: 6585   Residues:     1 -  2195
chrX_57714741_57726523.rev   A   Score:  311   Residues:  2923 -  2974
chrX_57714741_57726523.rev   Z   Score: 35349   Residues:     1 - 11783
chrX_57748279_57750441.rev   Z   Score: 6489   Residues:     1 -  2163
chrX_57750741_57757439   Z   Score: 20097   Residues:     1 -  6699
chrX_57764509_57772003   Z   Score: 22485   Residues:     1 -  7495
chrX_57772149_57778509   Z   Score: 19083   Residues:     1 -  6361
chrX_57787882_57789817   Z   Score: 5808   Residues:     1 -  1936
chrX_57802817_57807792   A   Score:  266   Residues:  2172 -  2298
chrX_57802817_57807792   Z   Score: 14928   Residues:     1 -  4976
chrX_57851847_57856823.rev   Z   Score: 14931   Residues:     1 -  4977
chrX_57870927_57873228.rev   Z   Score: 6906   Residues:     1 -  2302
chrX_57879243_57882341.rev   Z   Score: 9297   Residues:     1 -  3099
chrX_57902426_57907668.rev   Z   Score: 15729   Residues:     1 -  5243
chrX_57911375_57917618   Z   Score: 18732   Residues:     1 -  6244
chrX_57918266_57921342.rev   Z   Score: 9231   Residues:     1 -  3077
chrX_57927628_57932604   A   Score:  216   Residues:  2536 -  2562
chrX_57927628_57932604   Z   Score: 14931   Residues:     1 -  4977
chrX_57932625_57934337   Z   Score: 5139   Residues:     1 -  1713
chrX_57944938_57946977   Z   Score: 6120   Residues:     1 -  2040
chrX_57969843_57971473.rev   Z   Score: 4893   Residues:     1 -  1631
chrX_58001379_58003783   Z   Score: 7215   Residues:     1 -  2405
chrX_58017053_58023456   Z   Score: 19212   Residues:     1 -  6404
chrX_58069259_58070871   Z   Score: 4839   Residues:     1 -  1613
chrX_58306183_58310991   Z   Score: 14427   Residues:     1 -  4809
chrX_61519095_61525365   Z   Score: 18813   Residues:     1 -  6271
chrX_61557428_61563843   Z   Score: 19248   Residues:     1 -  6416
chrX_61744580_61750584   A   Score:  222   Residues:  2356 -  2432
chrX_61744580_61750584   Z   Score: 18015   Residues:     1 -  6005
chrX_61823715_61827987   Z   Score: 12819   Residues:     1 -  4273
chrX_61832736_61835371   Z   Score: 7908   Residues:     1 -  2636
chrX_61837717_61839985   Z   Score: 6807   Residues:     1 -  2269
chrX_61889811_61896480   Z   Score: 20010   Residues:     1 -  6670
chrX_61897198_61899326.rev   Z   Score: 6387   Residues:     1 -  2129
chrX_61900678_61902795.rev   Z   Score: 6354   Residues:     1 -  2118
chrX_61904019_61910106.rev   Z   Score: 18264   Residues:     1 -  6088
chrX_61920708_61924448   Z   Score: 11223   Residues:     1 -  3741
chrX_61948936_61953964   Z   Score: 15087   Residues:     1 -  5029
chrX_61963461_61965533.rev   Z   Score: 6219   Residues:     1 -  2073
chrX_61967663_61969817.rev   Z   Score: 6465   Residues:     1 -  2155
chrX_61970296_61976019   A   Score:  747   Residues:     2 -   137
chrX_61970296_61976019   Z   Score: 17172   Residues:     1 -  5724
chrX_61978649_61985970.rev   Z   Score: 21966   Residues:     1 -  7322
chrX_62007544_62010031.rev   Z   Score: 7464   Residues:     1 -  2488
chrX_62026625_62033184.rev   Z   Score: 19680   Residues:     1 -  6560
chrX_62053699_62057435.rev   Z   Score: 11211   Residues:     1 -  3737
chrX_62094998_62101718   Z   Score: 20163   Residues:     1 -  6721
chrX_62104915_62116522   Z   Score: 34824   Residues:     1 - 11608
chrX_62118826_62123281   Z   Score: 13368   Residues:     1 -  4456
chrX_62150158_62157599   Z   Score: 22326   Residues:     1 -  7442
chrX_62173842_62175911   Z   Score: 6210   Residues:     1 -  2070
chrX_62208427_62210460.rev   Z   Score: 6102   Residues:     1 -  2034
chrX_62226738_62234179.rev   Z   Score: 22326   Residues:     1 -  7442
chrX_62252927_62256139   Z   Score: 9639   Residues:     1 -  3213
chrX_62264226_62270327.rev   Z   Score: 18306   Residues:     1 -  6102
chrX_62289151_62299293   Z   Score: 30429   Residues:     1 - 10143
chrX_62303974_62309894.rev   A   Score:  208   Residues:  2305 -  2335
chrX_62303974_62309894.rev   Z   Score: 17763   Residues:     1 -  5921
chrX_62309966_62312601   Z   Score: 7905   Residues:     1 -  2635
chrX_62373629_62375850   Z   Score: 6666   Residues:     1 -  2222
chrX_62390724_62395180.rev   Z   Score: 13371   Residues:     1 -  4457
chrX_62397810_62400057.rev   Z   Score: 6744   Residues:     1 -  2248
chrX_62409044_62410696.rev   Z   Score: 4959   Residues:     1 -  1653
chrX_62447616_62449386.rev   Z   Score: 5313   Residues:     1 -  1771
chrX_62449611_62455883.rev   Z   Score: 18819   Residues:     1 -  6273
chrX_62480427_62488917   A   Score:  201   Residues:  7261 -  7289
chrX_62480427_62488917   Z   Score: 25473   Residues:     1 -  8491
chrX_62494493_62500901   Z   Score: 19224   Residues:     1 -  6408
chrX_62521558_62527927   Z   Score: 19110   Residues:     1 -  6370
chrX_62534419_62539201   A   Score:  247   Residues:  1822 -  1869
chrX_62534419_62539201   A   Score:  209   Residues:  1428 -  1532
chrX_62534419_62539201   Z   Score: 14346   Residues:     1 -  4782
chrX_62544654_62550150   Z   Score: 16491   Residues:     1 -  5497
chrX_62571390_62574477   A   Score:  225   Residues:   423 -   454
chrX_62571390_62574477   Z   Score: 9264   Residues:     1 -  3088
chrX_62594010_62595936.rev   Z   Score: 5781   Residues:     1 -  1927
chrX_62600346_62602898.rev   Z   Score: 7659   Residues:     1 -  2553
chrX_62653718_62655312   Z   Score: 4785   Residues:     1 -  1595
chrX_62683700_62687680   A   Score:  208   Residues:   868 -   984
chrX_62683700_62687680   Z   Score: 11943   Residues:     1 -  3981
chrX_62691809_62695871   Z   Score: 12189   Residues:     1 -  4063
chrX_62712469_62715433   Z   Score: 8895   Residues:     1 -  2965
chrX_62799888_62806562   Z   Score: 20025   Residues:     1 -  6675
chrX_62824600_62827559.rev   Z   Score: 8880   Residues:     1 -  2960
chrX_62829235_62831240.rev   Z   Score: 6018   Residues:     1 -  2006
chrX_62841044_62847439   Z   Score: 19188   Residues:     1 -  6396
chrX_62863527_62869864.rev   Z   Score: 19014   Residues:     1 -  6338
chrX_62878180_62880903   Z   Score: 8172   Residues:     1 -  2724
chrX_62888301_62893964   A   Score:  205   Residues:  3560 -  3598
chrX_62888301_62893964   Z   Score: 16992   Residues:     1 -  5664
chrX_62896414_62900949   Z   Score: 13608   Residues:     1 -  4536
chrX_62938980_62945819   Z   Score: 20520   Residues:     1 -  6840
chrX_62951358_62955548.rev   A   Score:  692   Residues:  2221 -  2362
chrX_62951358_62955548.rev   R   Score:  205   Residues:  2221 -  2349
chrX_62951358_62955548.rev   Z   Score: 12573   Residues:     1 -  4191
chrX_62955606_62958902   Z   Score: 9891   Residues:     1 -  3297
chrX_62975379_62977281   Z   Score: 5709   Residues:     1 -  1903
chrX_62989330_62994015   Z   Score: 14058   Residues:     1 -  4686
chrX_63016408_63022687.rev   Z   Score: 18840   Residues:     1 -  6280
chrX_63051335_63055954   Z   Score: 13860   Residues:     1 -  4620
chrX_63060655_63066738.rev   Z   Score: 18252   Residues:     1 -  6084
chrX_63068682_63072267.rev   Z   Score: 10758   Residues:     1 -  3586
chrX_63082013_63094412   Z   Score: 37200   Residues:     1 - 12400
chrX_63109577_63119432.rev   Z   Score: 29568   Residues:     1 -  9856
chrX_63120069_63126362.rev   Z   Score: 18882   Residues:     1 -  6294
chrX_63130868_63133237   Z   Score: 7110   Residues:     1 -  2370
chrX_63135031_63141308.rev   Z   Score: 18834   Residues:     1 -  6278
chrX_63156301_63160995   Z   Score: 14085   Residues:     1 -  4695
chrX_63170072_63173373.rev   Z   Score: 9906   Residues:     1 -  3302
chrX_63240373_63243013.rev   Z   Score: 7923   Residues:     1 -  2641
chrX_63245870_63250870.rev   A   Score:  217   Residues:  2186 -  2269
chrX_63245870_63250870.rev   Z   Score: 15003   Residues:     1 -  5001
chrX_63255497_63261776.rev   Z   Score: 18840   Residues:     1 -  6280
chrX_63282719_63291680   A   Score:  400   Residues:  8182 -  8231
chrX_63282719_63291680   Z   Score: 26886   Residues:     1 -  8962
chrX_63299733_63305992.rev   Z   Score: 18780   Residues:     1 -  6260
chrX_63309434_63311445.rev   Z   Score: 6036   Residues:     1 -  2012
chrX_63328175_63330840   Z   Score: 7998   Residues:     1 -  2666
chrX_63366024_63372422   Z   Score: 19197   Residues:     1 -  6399
chrX_63414058_63419316.rev   Z   Score: 15777   Residues:     1 -  5259
chrX_63422264_63423936.rev   Z   Score: 5019   Residues:     1 -  1673
chrX_63460750_63465529.rev   Z   Score: 14340   Residues:     1 -  4780
chrX_63481522_63487918.rev   Z   Score: 19191   Residues:     1 -  6397
chrX_63500363_63511369   Z   Score: 33021   Residues:     1 - 11007
chrX_63533840_63535969.rev   Z   Score: 6390   Residues:     1 -  2130
chrX_63546965_63553334.rev   Z   Score: 19110   Residues:     1 -  6370
chrX_63604598_63611013.rev   A   Score:  239   Residues:  2800 -  2842
chrX_63604598_63611013.rev   Z   Score: 19248   Residues:     1 -  6416
chrX_63615912_63619980.rev   Z   Score: 12207   Residues:     1 -  4069
chrX_63640140_63644171.rev   A   Score:  211   Residues:   985 -  1100
chrX_63640140_63644171.rev   Z   Score: 12096   Residues:     1 -  4032
chrX_63646449_63648497   Z   Score: 6147   Residues:     1 -  2049
chrX_63672776_63676327   Z   Score: 10656   Residues:     1 -  3552
chrX_63676684_63680518   Z   Score: 11505   Residues:     1 -  3835
chrX_63693119_63699388.rev   Z   Score: 18810   Residues:     1 -  6270
chrX_63702412_63709917.rev   Z   Score: 22518   Residues:     1 -  7506
chrX_63716870_63721988   A   Score:  238   Residues:  1306 -  1381
chrX_63716870_63721988   A   Score:  213   Residues:  2319 -  2437
chrX_63716870_63721988   Z   Score: 15357   Residues:     1 -  5119
chrX_63730436_63736240.rev   Z   Score: 17415   Residues:     1 -  5805
chrX_63747615_63752237.rev   Z   Score: 13869   Residues:     1 -  4623
chrX_63762215_63767208.rev   Z   Score: 14982   Residues:     1 -  4994
chrX_63773181_63777970.rev   Z   Score: 14370   Residues:     1 -  4790
chrX_63780368_63783151.rev   Z   Score: 8349   Residues:     1 -  2783
chrX_63810807_63822587   A   Score:  280   Residues:   397 -   480
chrX_63810807_63822587   Z   Score: 35343   Residues:     1 - 11781
chrX_63829946_63832457.rev   Z   Score: 7536   Residues:     1 -  2512
chrX_63835415_63839270.rev   Z   Score: 11568   Residues:     1 -  3856
chrX_63841769_63845903.rev   A   Score:  250   Residues:  1307 -  1434
chrX_63841769_63845903.rev   Z   Score: 12405   Residues:     1 -  4135
chrX_63878874_63881245   Z   Score: 7116   Residues:     1 -  2372
chrX_63910559_63916416   A   Score:  225   Residues:  5038 -  5089
chrX_63910559_63916416   Z   Score: 17574   Residues:     1 -  5858
chrX_63942561_63949376.rev   A   Score:  236   Residues:  2319 -  2350
chrX_63942561_63949376.rev   Z   Score: 20448   Residues:     1 -  6816
chrX_63965421_63967071   Z   Score: 4953   Residues:     1 -  1651
chrX_63967508_63969608   A   Score:  208   Residues:  1331 -  1365
chrX_63967508_63969608   Z   Score: 6303   Residues:     1 -  2101
chrX_63989229_63993188   Z   Score: 11880   Residues:     1 -  3960
chrX_64051328_64053265.rev   Z   Score: 5814   Residues:     1 -  1938
chrX_64056260_64062625.rev   Z   Score: 19098   Residues:     1 -  6366
chrX_64064319_64070135.rev   Z   Score: 17451   Residues:     1 -  5817
chrX_64083676_64087919   Z   Score: 12732   Residues:     1 -  4244
chrX_64112458_64114867.rev   Z   Score: 7230   Residues:     1 -  2410
chrX_64141241_64144738.rev   A   Score:  207   Residues:   745 -   817
chrX_64141241_64144738.rev   Z   Score: 10494   Residues:     1 -  3498
chrX_64160924_64167323.rev   Z   Score: 19200   Residues:     1 -  6400
chrX_64169197_64177289.rev   Z   Score: 24279   Residues:     1 -  8093
chrX_64191949_64193808.rev   Z   Score: 5580   Residues:     1 -  1860
chrX_64207794_64210318   Z   Score: 7575   Residues:     1 -  2525
chrX_64222731_64233197   Z   Score: 31401   Residues:     1 - 10467
chrX_64238702_64244490.rev   Z   Score: 17367   Residues:     1 -  5789
chrX_64247417_64250550   A   Score:  222   Residues:   212 -   240
chrX_64247417_64250550   Z   Score: 9402   Residues:     1 -  3134
chrX_64251234_64253340.rev   Z   Score: 6321   Residues:     1 -  2107
chrX_64289165_64293643   Z   Score: 13437   Residues:     1 -  4479
chrX_64306097_64308465   Z   Score: 7107   Residues:     1 -  2369
chrX_64343095_64348364   Z   Score: 15810   Residues:     1 -  5270
chrX_64349272_64355129   Z   Score: 17574   Residues:     1 -  5858
chrX_64396352_64402843   Z   Score: 19476   Residues:     1 -  6492
chrX_64415446_64417489.rev   Z   Score: 6132   Residues:     1 -  2044
chrX_64426619_64432553.rev   Z   Score: 17805   Residues:     1 -  5935
chrX_64439898_64441852.rev   Z   Score: 5865   Residues:     1 -  1955
chrX_64474575_64477027.rev   A   Score:  211   Residues:  1699 -  1748
chrX_64474575_64477027.rev   Z   Score: 7359   Residues:     1 -  2453
chrX_64617856_64624135.rev   Z   Score: 18840   Residues:     1 -  6280
chrX_64664415_64666744   Z   Score: 6990   Residues:     1 -  2330
chrX_64756057_64757899   T   Score:  230   Residues:   183 -   217
chrX_64756057_64757899   Z   Score: 5529   Residues:     1 -  1843
chrX_64762525_64768640.rev   A   Score:  226   Residues:  5366 -  5399
chrX_64762525_64768640.rev   Z   Score: 18348   Residues:     1 -  6116
chrX_64769361_64773991.rev   Z   Score: 13893   Residues:     1 -  4631
chrX_64779006_64784109   Z   Score: 15312   Residues:     1 -  5104
chrX_64812797_64821131   Z   Score: 25005   Residues:     1 -  8335
chrX_64853813_64860153.rev   Z   Score: 19023   Residues:     1 -  6341
chrX_64869497_64871824   Z   Score: 6984   Residues:     1 -  2328
chrX_64878439_64880583.rev   Z   Score: 6435   Residues:     1 -  2145
chrX_64917681_64921083.rev   A   Score:  268   Residues:   594 -   717
chrX_64917681_64921083.rev   Z   Score: 10209   Residues:     1 -  3403
chrX_64945277_64949888.rev   Z   Score: 13836   Residues:     1 -  4612
chrX_65091107_65095647.rev   A   Score:  228   Residues:  3130 -  3160
chrX_65091107_65095647.rev   Z   Score: 13623   Residues:     1 -  4541
chrX_65096677_65099636   Z   Score: 8880   Residues:     1 -  2960
chrX_65105407_65111802.rev   Z   Score: 19188   Residues:     1 -  6396
chrX_65122530_65131040.rev   C   Score:  205   Residues:  5747 -  5775
chrX_65122530_65131040.rev   Z   Score: 25533   Residues:     1 -  8511
chrX_65183813_65190091.rev   Z   Score: 18837   Residues:     1 -  6279
chrX_65214457_65216369.rev   Z   Score: 5739   Residues:     1 -  1913
chrX_65228665_65232150   Z   Score: 10458   Residues:     1 -  3486
chrX_65237325_65239238.rev   Z   Score: 5742   Residues:     1 -  1914
chrX_65244115_65246136   Z   Score: 6066   Residues:     1 -  2022
chrX_65255003_65256729   Z   Score: 5181   Residues:     1 -  1727
chrX_65271339_65273161   Z   Score: 5469   Residues:     1 -  1823
chrX_65274023_65278815   Z   Score: 14379   Residues:     1 -  4793
chrX_65322826_65327506   Z   Score: 14043   Residues:     1 -  4681
chrX_65335122_65339642.rev   Z   Score: 13563   Residues:     1 -  4521
chrX_65349649_65356480   A   Score:  231   Residues:  5299 -  5385
chrX_65349649_65356480   Z   Score: 20496   Residues:     1 -  6832
chrX_65358297_65361631   Z   Score: 10005   Residues:     1 -  3335
chrX_65401883_65407518.rev   Z   Score: 16908   Residues:     1 -  5636
chrX_65420895_65427509.rev   Z   Score: 19845   Residues:     1 -  6615
chrX_65456205_65462606   Z   Score: 19206   Residues:     1 -  6402
chrX_65491268_65498314   A   Score:  281   Residues:  2569 -  2607
chrX_65491268_65498314   A   Score:  209   Residues:  3434 -  3472
chrX_65491268_65498314   Z   Score: 21141   Residues:     1 -  7047
chrX_65511301_65516889.rev   Z   Score: 16767   Residues:     1 -  5589
chrX_65524300_65527214.rev   Z   Score: 8745   Residues:     1 -  2915
chrX_65528057_65531573   Z   Score: 10551   Residues:     1 -  3517
chrX_65549477_65551152   Z   Score: 5028   Residues:     1 -  1676
chrX_65555861_65562634   Z   Score: 20322   Residues:     1 -  6774
chrX_65591167_65596077.rev   Z   Score: 14733   Residues:     1 -  4911
chrX_65629618_65633963   G   Score:  394   Residues:    13 -   104
chrX_65629618_65633963   Z   Score: 13038   Residues:     1 -  4346
chrX_65647946_65653716.rev   A   Score:  209   Residues:   242 -   289
chrX_65647946_65653716.rev   Z   Score: 17313   Residues:     1 -  5771
chrX_65656889_65660719   Z   Score: 11493   Residues:     1 -  3831
chrX_65672646_65675574.rev   Z   Score: 8787   Residues:     1 -  2929
chrX_65683564_65686056.rev   Z   Score: 7479   Residues:     1 -  2493
chrX_65690104_65693808.rev   Z   Score: 11115   Residues:     1 -  3705
chrX_65702820_65704501.rev   Z   Score: 5043   Residues:     1 -  1681
chrX_65720662_65727360   Z   Score: 20097   Residues:     1 -  6699
chrX_65738800_65742325.rev   A   Score:  225   Residues:   486 -   668
chrX_65738800_65742325.rev   Z   Score: 10578   Residues:     1 -  3526
chrX_65757851_65759754.rev   Z   Score: 5712   Residues:     1 -  1904
chrX_65764165_65770082.rev   Z   Score: 17754   Residues:     1 -  5918
chrX_65773181_65777803.rev   A   Score:  260   Residues:  2065 -  2104
chrX_65773181_65777803.rev   A   Score:  242   Residues:   379 -   486
chrX_65773181_65777803.rev   G   Score:  262   Residues:   403 -   457
chrX_65773181_65777803.rev   Z   Score: 13869   Residues:     1 -  4623
chrX_65785501_65787422   Z   Score: 5766   Residues:     1 -  1922
chrX_65792155_65798531.rev   Z   Score: 19131   Residues:     1 -  6377
chrX_65813752_65815848.rev   A   Score:  222   Residues:   255 -   383
chrX_65813752_65815848.rev   Z   Score: 6291   Residues:     1 -  2097
chrX_65840834_65846579   Z   Score: 17238   Residues:     1 -  5746
chrX_65849344_65850912   Z   Score: 4707   Residues:     1 -  1569
chrX_65923376_65925284.rev   Z   Score: 5727   Residues:     1 -  1909
chrX_65927965_65934237.rev   Z   Score: 18819   Residues:     1 -  6273
chrX_65935631_65940963.rev   Z   Score: 15999   Residues:     1 -  5333
chrX_65945156_65951429   Z   Score: 18822   Residues:     1 -  6274
chrX_65955230_65958414   Z   Score: 9555   Residues:     1 -  3185
chrX_65979266_65981789   Z   Score: 7572   Residues:     1 -  2524
chrX_65993594_65995298.rev   Z   Score: 5115   Residues:     1 -  1705
chrX_66013772_66017642   Z   Score: 11613   Residues:     1 -  3871
chrX_66025241_66027528.rev   Z   Score: 6864   Residues:     1 -  2288
chrX_66028541_66034942   Z   Score: 19206   Residues:     1 -  6402
chrX_66063121_66069497.rev   Z   Score: 19131   Residues:     1 -  6377
chrX_66071342_66076724   Z   Score: 16149   Residues:     1 -  5383
chrX_66086274_66090520.rev   Z   Score: 12741   Residues:     1 -  4247
chrX_66147897_66149720.rev   Z   Score: 5472   Residues:     1 -  1824
chrX_66163871_66169970   A   Score:  215   Residues:  1556 -  1681
chrX_66163871_66169970   Z   Score: 18300   Residues:     1 -  6100
chrX_66175459_66177333   Z   Score: 5625   Residues:     1 -  1875
chrX_66189574_66193808.rev   Z   Score: 12705   Residues:     1 -  4235
chrX_66223351_66225316   Z   Score: 5898   Residues:     1 -  1966
chrX_66226094_66229627   Z   Score: 10602   Residues:     1 -  3534
chrX_66237264_66243170   Z   Score: 17721   Residues:     1 -  5907
chrX_66252293_66260913   Z   Score: 25863   Residues:     1 -  8621
chrX_66265332_66269566.rev   A   Score:  214   Residues:   402 -   493
chrX_66265332_66269566.rev   Z   Score: 12705   Residues:     1 -  4235
chrX_66269648_66275181   Z   Score: 16602   Residues:     1 -  5534
chrX_66282719_66286620   Z   Score: 11706   Residues:     1 -  3902
chrX_66311753_66318358.rev   A   Score:  275   Residues:  4335 -  4385
chrX_66311753_66318358.rev   Z   Score: 19818   Residues:     1 -  6606
chrX_66324430_66330126.rev   Z   Score: 17091   Residues:     1 -  5697
chrX_66332144_66333733   Z   Score: 4770   Residues:     1 -  1590
chrX_66359812_66367607   Z   Score: 23388   Residues:     1 -  7796
chrX_66388927_66394997   Z   Score: 18213   Residues:     1 -  6071
chrX_66396784_66398952.rev   Z   Score: 6507   Residues:     1 -  2169
chrX_66407292_66409870   Z   Score: 7737   Residues:     1 -  2579
chrX_66415419_66418582.rev   Z   Score: 9492   Residues:     1 -  3164
chrX_66424489_66431186.rev   Z   Score: 20094   Residues:     1 -  6698
chrX_66459448_66465228   Z   Score: 17343   Residues:     1 -  5781
chrX_66490697_66497121   Z   Score: 19275   Residues:     1 -  6425
chrX_66508028_66510355.rev   Z   Score: 6984   Residues:     1 -  2328
chrX_66516878_66521095   Z   Score: 12654   Residues:     1 -  4218
chrX_66555156_66557272.rev   Z   Score: 6351   Residues:     1 -  2117
chrX_66629745_66636024.rev   Z   Score: 18840   Residues:     1 -  6280
chrX_66662329_66668615.rev   Z   Score: 18861   Residues:     1 -  6287
chrX_66682070_66683758.rev   Z   Score: 5067   Residues:     1 -  1689
chrX_66706760_66713139.rev   Z   Score: 19140   Residues:     1 -  6380
chrX_66742079_66744073.rev   Z   Score: 5985   Residues:     1 -  1995
chrX_66797635_66799866   A   Score:  217   Residues:   347 -   392
chrX_66797635_66799866   Z   Score: 6696   Residues:     1 -  2232
chrX_66800951_66802680   Z   Score: 5190   Residues:     1 -  1730
chrX_66832940_66838689   Z   Score: 17250   Residues:     1 -  5750
chrX_66878443_66881095   Z   Score: 7959   Residues:     1 -  2653
chrX_66887062_66893454.rev   Z   Score: 19179   Residues:     1 -  6393
chrX_66944892_66951301   Z   Score: 19227   Residues:     1 -  6409
chrX_66970796_66973201   Z   Score: 7215   Residues:     1 -  2405
chrX_66986197_66991785   Z   Score: 16767   Residues:     1 -  5589
chrX_66997665_67003429.rev   A   Score:  465   Residues:  4066 -  4185
chrX_66997665_67003429.rev   Z   Score: 17295   Residues:     1 -  5765
chrX_67077668_67079592   Z   Score: 5775   Residues:     1 -  1925
chrX_67096043_67097957.rev   Z   Score: 5745   Residues:     1 -  1915
chrX_67122689_67124729   Z   Score: 6123   Residues:     1 -  2041
chrX_67168950_67170620   Z   Score: 5013   Residues:     1 -  1671
chrX_67219279_67225553   Z   Score: 18825   Residues:     1 -  6275
chrX_67227116_67233538   Z   Score: 19269   Residues:     1 -  6423
chrX_67266907_67273363   Z   Score: 19371   Residues:     1 -  6457
chrX_67283210_67285185   Z   Score: 5928   Residues:     1 -  1976
chrX_67527602_67534283.rev   Z   Score: 20046   Residues:     1 -  6682
chrX_67553010_67554698.rev   Z   Score: 5067   Residues:     1 -  1689
chrX_67562891_67568116.rev   Z   Score: 15678   Residues:     1 -  5226
chrX_67579387_67583076.rev   Z   Score: 11070   Residues:     1 -  3690
chrX_67604638_67613047   Z   Score: 25230   Residues:     1 -  8410
chrX_67619844_67622045.rev   Z   Score: 6606   Residues:     1 -  2202
chrX_67623322_67627868.rev   A   Score:  201   Residues:   868 -   900
chrX_67623322_67627868.rev   Z   Score: 13641   Residues:     1 -  4547
chrX_67628431_67630372.rev   Z   Score: 5826   Residues:     1 -  1942
chrX_67738614_67745015   Z   Score: 19206   Residues:     1 -  6402
chrX_67778649_67784449   Z   Score: 17403   Residues:     1 -  5801
chrX_67807863_67809516   Z   Score: 4962   Residues:     1 -  1654
chrX_67813414_67816161   Z   Score: 8244   Residues:     1 -  2748
chrX_67816240_67821339   A   Score:  252   Residues:   929 -   962
chrX_67816240_67821339   Z   Score: 15300   Residues:     1 -  5100
chrX_67960328_67962367   A   Score:  250   Residues:   470 -   504
chrX_67960328_67962367   Z   Score: 6120   Residues:     1 -  2040
chrX_67962648_67965122.rev   Z   Score: 7425   Residues:     1 -  2475
chrX_67965963_67970846.rev   Z   Score: 14652   Residues:     1 -  4884
chrX_67971286_67976020   T   Score:  220   Residues:   887 -   921
chrX_67971286_67976020   Z   Score: 14205   Residues:     1 -  4735
chrX_68008715_68011988.rev   Z   Score: 9822   Residues:     1 -  3274
chrX_68041237_68044154.rev   Z   Score: 8754   Residues:     1 -  2918
chrX_68044717_68048302.rev   A   Score:  292   Residues:  1003 -  1062
chrX_68044717_68048302.rev   Z   Score: 10758   Residues:     1 -  3586
chrX_68055465_68057663   T   Score:  317   Residues:   198 -   290
chrX_68055465_68057663   Z   Score: 6597   Residues:     1 -  2199
chrX_68246323_68248282.rev   Z   Score: 5880   Residues:     1 -  1960
chrX_68345822_68349336.rev   Z   Score: 10545   Residues:     1 -  3515
chrX_68353122_68359511   Z   Score: 19170   Residues:     1 -  6390
chrX_68439736_68445708.rev   A   Score:  240   Residues:  3346 -  3393
chrX_68439736_68445708.rev   Z   Score: 17919   Residues:     1 -  5973
chrX_68450736_68457004   Z   Score: 18807   Residues:     1 -  6269
chrX_68461655_68465533.rev   Z   Score: 11637   Residues:     1 -  3879
chrX_68475473_68482309   Z   Score: 20511   Residues:     1 -  6837
chrX_68489678_68491527.rev   Z   Score: 5550   Residues:     1 -  1850
chrX_68595901_68598057   Z   Score: 6471   Residues:     1 -  2157
chrX_68598219_68599946   Z   Score: 5184   Residues:     1 -  1728
chrX_68600377_68602128   Z   Score: 5256   Residues:     1 -  1752
chrX_68624830_68626669.rev   A   Score:  252   Residues:   125 -   201
chrX_68624830_68626669.rev   Z   Score: 5520   Residues:     1 -  1840
chrX_68627794_68629441   Z   Score: 4944   Residues:     1 -  1648
chrX_68659615_68661853.rev   Z   Score: 6717   Residues:     1 -  2239
chrX_68667428_68672673.rev   A   Score:  240   Residues:  2675 -  2716
chrX_68667428_68672673.rev   Z   Score: 15738   Residues:     1 -  5246
chrX_68679945_68686213.rev   Z   Score: 18807   Residues:     1 -  6269
chrX_68716533_68722639.rev   Z   Score: 18321   Residues:     1 -  6107
chrX_68753139_68759551.rev   Z   Score: 19236   Residues:     1 -  6412
chrX_68770316_68772090.rev   Z   Score: 5325   Residues:     1 -  1775
chrX_68786408_68792683.rev   Z   Score: 18828   Residues:     1 -  6276
chrX_68818420_68824013   Z   Score: 16782   Residues:     1 -  5594
chrX_68825813_68830173.rev   Z   Score: 13083   Residues:     1 -  4361
chrX_68874730_68879255   A   Score:  211   Residues:  1499 -  1584
chrX_68874730_68879255   Z   Score: 13578   Residues:     1 -  4526
chrX_68879822_68881427.rev   Z   Score: 4818   Residues:     1 -  1606
chrX_68926277_68931125.rev   Z   Score: 14547   Residues:     1 -  4849
chrX_68940730_68945169.rev   Z   Score: 13320   Residues:     1 -  4440
chrX_69017231_69022475   Z   Score: 15735   Residues:     1 -  5245
chrX_69102477_69106877   Z   Score: 13203   Residues:     1 -  4401
chrX_69194940_69198523   Z   Score: 10752   Residues:     1 -  3584
chrX_69208774_69210646   Z   Score: 5619   Residues:     1 -  1873
chrX_69213525_69219910.rev   Z   Score: 19158   Residues:     1 -  6386
chrX_69366362_69372768.rev   Z   Score: 19221   Residues:     1 -  6407
chrX_69391017_69393977.rev   Z   Score: 8883   Residues:     1 -  2961
chrX_69518243_69524642.rev   Z   Score: 19200   Residues:     1 -  6400
chrX_69559205_69562190   Z   Score: 8958   Residues:     1 -  2986
chrX_69567527_69573929.rev   Z   Score: 19209   Residues:     1 -  6403
chrX_69586305_69589956   Z   Score: 10956   Residues:     1 -  3652
chrX_69599462_69601646   Z   Score: 6555   Residues:     1 -  2185
chrX_69604574_69607292   Z   Score: 8157   Residues:     1 -  2719
chrX_69641274_69647554   Z   Score: 18843   Residues:     1 -  6281
chrX_69647624_69650009   A   Score:  212   Residues:   160 -   216
chrX_69647624_69650009   Z   Score: 7158   Residues:     1 -  2386
chrX_69661055_69662835   Z   Score: 5343   Residues:     1 -  1781
chrX_69713911_69720299.rev   Z   Score: 19167   Residues:     1 -  6389
chrX_69730550_69736937   Z   Score: 19164   Residues:     1 -  6388
chrX_69757988_69764392   Z   Score: 19215   Residues:     1 -  6405
chrX_69776585_69778929   Z   Score: 7035   Residues:     1 -  2345
chrX_69782719_69789101   Z   Score: 19146   Residues:     1 -  6382
chrX_69821227_69824663   Z   Score: 10311   Residues:     1 -  3437
chrX_69840870_69847244   Z   Score: 19125   Residues:     1 -  6375
chrX_69865497_69871659   A   Score:  218   Residues:  2116 -  2146
chrX_69865497_69871659   Z   Score: 18489   Residues:     1 -  6163
chrX_69892596_69899651   Z   Score: 21165   Residues:     1 -  7055
chrX_69921095_69923316.rev   A   Score:  358   Residues:  1063 -  1146
chrX_69921095_69923316.rev   Z   Score: 6666   Residues:     1 -  2222
chrX_69941082_69947482.rev   Z   Score: 19203   Residues:     1 -  6401
chrX_69956974_69960784   A   Score:  253   Residues:   468 -   505
chrX_69956974_69960784   Z   Score: 11433   Residues:     1 -  3811
chrX_69994316_69998770.rev   Z   Score: 13365   Residues:     1 -  4455
chrX_70036599_70038855   A   Score:  356   Residues:   377 -   448
chrX_70036599_70038855   Z   Score: 6771   Residues:     1 -  2257
chrX_70277623_70280749.rev   T   Score:  261   Residues:  1638 -  1686
chrX_70277623_70280749.rev   Z   Score: 9381   Residues:     1 -  3127
chrX_70444788_70447049.rev   Z   Score: 6786   Residues:     1 -  2262
chrX_70736752_70738948.rev   Z   Score: 6591   Residues:     1 -  2197
chrX_70819077_70825457   Z   Score: 19143   Residues:     1 -  6381
chrX_70832044_70838729   Z   Score: 20058   Residues:     1 -  6686
chrX_70841049_70847435.rev   Z   Score: 19161   Residues:     1 -  6387
chrX_70888035_70889931.rev   Z   Score: 5691   Residues:     1 -  1897
chrX_70900194_70906582.rev   A   Score:  225   Residues:   307 -   337
chrX_70900194_70906582.rev   Z   Score: 19167   Residues:     1 -  6389
chrX_70933496_70935290.rev   Z   Score: 5385   Residues:     1 -  1795
chrX_70962486_70964744.rev   A   Score:  355   Residues:   377 -   519
chrX_70962486_70964744.rev   G   Score:  293   Residues:   413 -   474
chrX_70962486_70964744.rev   Z   Score: 6777   Residues:     1 -  2259
chrX_71018112_71019933.rev   Z   Score: 5466   Residues:     1 -  1822
chrX_71120594_71123977.rev   Z   Score: 10152   Residues:     1 -  3384
chrX_71419498_71421815   Z   Score: 6954   Residues:     1 -  2318
chrX_71442965_71449317   Z   Score: 19059   Residues:     1 -  6353
chrX_71473979_71476067.rev   Z   Score: 6267   Residues:     1 -  2089
chrX_71501650_71505402   Z   Score: 11259   Residues:     1 -  3753
chrX_71519550_71521397.rev   Z   Score: 5544   Residues:     1 -  1848
chrX_71534993_71536770.rev   A   Score:  200   Residues:  1627 -  1651
chrX_71534993_71536770.rev   Z   Score: 5334   Residues:     1 -  1778
chrX_71587826_71594192   Z   Score: 19101   Residues:     1 -  6367
chrX_71749086_71750778.rev   Z   Score: 5079   Residues:     1 -  1693
chrX_71797840_71802179.rev   A   Score:  230   Residues:  1131 -  1233
chrX_71797840_71802179.rev   Z   Score: 13020   Residues:     1 -  4340
chrX_71818510_71822422.rev   Z   Score: 11739   Residues:     1 -  3913
chrX_71828322_71830173.rev   Z   Score: 5556   Residues:     1 -  1852
chrX_71891776_71898224   Z   Score: 19347   Residues:     1 -  6449
chrX_71904124_71908030   Z   Score: 11721   Residues:     1 -  3907
chrX_71924359_71928693   A   Score:  222   Residues:  1129 -  1230
chrX_71924359_71928693   Z   Score: 13005   Residues:     1 -  4335
chrX_71975758_71977449   Z   Score: 5076   Residues:     1 -  1692
chrX_71983075_71989504   A   Score:  406   Residues:  2798 -  2857
chrX_71983075_71989504   Z   Score: 19290   Residues:     1 -  6430
chrX_71991726_71993732   Z   Score: 6021   Residues:     1 -  2007
chrX_72020455_72023542.rev   Z   Score: 9264   Residues:     1 -  3088
chrX_72034795_72041196.rev   Z   Score: 19206   Residues:     1 -  6402
chrX_72055497_72061112   Z   Score: 16848   Residues:     1 -  5616
chrX_72062024_72068432   Z   Score: 19227   Residues:     1 -  6409
chrX_72076563_72078221.rev   Z   Score: 4977   Residues:     1 -  1659
chrX_72097046_72102898.rev   Z   Score: 17559   Residues:     1 -  5853
chrX_72108503_72114782   Z   Score: 18840   Residues:     1 -  6280
chrX_72119270_72125548   Z   Score: 18837   Residues:     1 -  6279
chrX_72147410_72151660.rev   A   Score:  224   Residues:   418 -   488
chrX_72147410_72151660.rev   Z   Score: 12753   Residues:     1 -  4251
chrX_72166620_72168809.rev   Z   Score: 6570   Residues:     1 -  2190
chrX_72187258_72193365   Z   Score: 18324   Residues:     1 -  6108
chrX_72232202_72238336   Z   Score: 18405   Residues:     1 -  6135
chrX_72242141_72244329.rev   Z   Score: 6567   Residues:     1 -  2189
chrX_72246748_72253290   A   Score:  212   Residues:   415 -   485
chrX_72246748_72253290   Z   Score: 19629   Residues:     1 -  6543
chrX_72272138_72277243   A   Score:  802   Residues:  3219 -  3390
chrX_72272138_72277243   R   Score:  250   Residues:  3228 -  3390
chrX_72272138_72277243   Z   Score: 15318   Residues:     1 -  5106
chrX_72283735_72290114   Z   Score: 19140   Residues:     1 -  6380
chrX_72302738_72309025.rev   Z   Score: 18864   Residues:     1 -  6288
chrX_72316649_72320402   Z   Score: 11262   Residues:     1 -  3754
chrX_72328442_72330173.rev   Z   Score: 5196   Residues:     1 -  1732
chrX_72338869_72340686   Z   Score: 5454   Residues:     1 -  1818
chrX_72348998_72351437.rev   Z   Score: 7320   Residues:     1 -  2440
chrX_72363973_72368571.rev   Z   Score: 13797   Residues:     1 -  4599
chrX_72377593_72389619   Z   Score: 36081   Residues:     1 - 12027
chrX_72403434_72410091   Z   Score: 19974   Residues:     1 -  6658
chrX_72425107_72430029   Z   Score: 14769   Residues:     1 -  4923
chrX_72431730_72438108.rev   Z   Score: 19137   Residues:     1 -  6379
chrX_72465589_72469764.rev   Z   Score: 12528   Residues:     1 -  4176
chrX_72479359_72485990.rev   Z   Score: 19896   Residues:     1 -  6632
chrX_72495145_72501925.rev   Z   Score: 20343   Residues:     1 -  6781
chrX_72513372_72519678   Z   Score: 18921   Residues:     1 -  6307
chrX_72543831_72553697   A   Score:  288   Residues:  1777 -  1825
chrX_72543831_72553697   Z   Score: 29601   Residues:     1 -  9867
chrX_72575060_72578314.rev   Z   Score: 9765   Residues:     1 -  3255
chrX_72601440_72604147.rev   Z   Score: 8124   Residues:     1 -  2708
chrX_72604628_72611310.rev   Z   Score: 20049   Residues:     1 -  6683
chrX_72631432_72635835.rev   A   Score:  202   Residues:   195 -   226
chrX_72631432_72635835.rev   Z   Score: 13212   Residues:     1 -  4404
chrX_72648018_72650171.rev   Z   Score: 6462   Residues:     1 -  2154
chrX_72650384_72655997   Z   Score: 16842   Residues:     1 -  5614
chrX_72658418_72662225.rev   A   Score:  248   Residues:  1092 -  1122
chrX_72658418_72662225.rev   Z   Score: 11424   Residues:     1 -  3808
chrX_72674876_72681243.rev   Z   Score: 19104   Residues:     1 -  6368
chrX_72695152_72703853   Z   Score: 26106   Residues:     1 -  8702
chrX_72704312_72710154   Z   Score: 17529   Residues:     1 -  5843
chrX_72736062_72738908.rev   Z   Score: 8541   Residues:     1 -  2847
chrX_72746190_72752916.rev   A   Score:  205   Residues:   393 -   486
chrX_72746190_72752916.rev   Z   Score: 20181   Residues:     1 -  6727
chrX_72758563_72761525.rev   Z   Score: 8889   Residues:     1 -  2963
chrX_72773859_72779195   Z   Score: 16011   Residues:     1 -  5337
chrX_72889496_72893905   Z   Score: 13230   Residues:     1 -  4410
chrX_72910307_72913452.rev   A   Score:  208   Residues:  1275 -  1327
chrX_72910307_72913452.rev   Z   Score: 9438   Residues:     1 -  3146
chrX_72938852_72942228   A   Score:  274   Residues:  2412 -  2495
chrX_72938852_72942228   A   Score:  243   Residues:  2093 -  2129
chrX_72938852_72942228   Z   Score: 10131   Residues:     1 -  3377
chrX_72955554_72958524   Z   Score: 8913   Residues:     1 -  2971
chrX_72960976_72964433.rev   Z   Score: 10374   Residues:     1 -  3458
chrX_72974867_72976493.rev   Z   Score: 4881   Residues:     1 -  1627
chrX_73004689_73009434   Z   Score: 14238   Residues:     1 -  4746
chrX_73021858_73026141   Z   Score: 12852   Residues:     1 -  4284
chrX_73028331_73030156   Z   Score: 5478   Residues:     1 -  1826
chrX_73037050_73043431.rev   A   Score:  265   Residues:   457 -   505
chrX_73037050_73043431.rev   Z   Score: 19146   Residues:     1 -  6382
chrX_73043710_73050338.rev   Z   Score: 19887   Residues:     1 -  6629
chrX_73070688_73072559.rev   Z   Score: 5616   Residues:     1 -  1872
chrX_73075108_73081861.rev   Z   Score: 20262   Residues:     1 -  6754
chrX_73177313_73181150   Z   Score: 11514   Residues:     1 -  3838
chrX_73199621_73201911.rev   Z   Score: 6873   Residues:     1 -  2291
chrX_73212317_73214263   Z   Score: 5841   Residues:     1 -  1947
chrX_73231240_73233623   Z   Score: 7152   Residues:     1 -  2384
chrX_73471932_73476016.rev   Z   Score: 12255   Residues:     1 -  4085
chrX_73477587_73483987.rev   Z   Score: 19203   Residues:     1 -  6401
chrX_73563666_73573423   A   Score:  367   Residues:  9472 -  9540
chrX_73563666_73573423   A   Score:  244   Residues:   937 -  1001
chrX_73563666_73573423   G   Score:  221   Residues:  8983 -  9049
chrX_73563666_73573423   T   Score:  405   Residues:  7044 -  7119
chrX_73563666_73573423   Z   Score: 29274   Residues:     1 -  9758
chrX_73640462_73645439   A   Score:  215   Residues:  2186 -  2291
chrX_73640462_73645439   Z   Score: 14934   Residues:     1 -  4978
chrX_73690438_73693808.rev   Z   Score: 10113   Residues:     1 -  3371
chrX_73698071_73704474   Z   Score: 19212   Residues:     1 -  6404
chrX_73715063_73720693   A   Score:  212   Residues:   336 -   379
chrX_73715063_73720693   Z   Score: 16893   Residues:     1 -  5631
chrX_73792082_73798356.rev   Z   Score: 18825   Residues:     1 -  6275
chrX_73820226_73822220   Z   Score: 5985   Residues:     1 -  1995
chrX_73832158_73836952.rev   Z   Score: 14385   Residues:     1 -  4795
chrX_73842522_73847736.rev   Z   Score: 15645   Residues:     1 -  5215
chrX_73863401_73874080   Z   Score: 32040   Residues:     1 - 10680
chrX_73876099_73882371.rev   Z   Score: 18819   Residues:     1 -  6273
chrX_73884518_73890914   Z   Score: 19191   Residues:     1 -  6397
chrX_73940653_73945094.rev   Z   Score: 13326   Residues:     1 -  4442
chrX_73945784_73947855.rev   Z   Score: 6216   Residues:     1 -  2072
chrX_73962395_73965088   Z   Score: 8082   Residues:     1 -  2694
chrX_73997141_74003524.rev   Z   Score: 19152   Residues:     1 -  6384
chrX_74029971_74032258.rev   Z   Score: 6864   Residues:     1 -  2288
chrX_74092149_74096179   A   Score:  241   Residues:   315 -   389
chrX_74092149_74096179   Z   Score: 12093   Residues:     1 -  4031
chrX_74106603_74109726   T   Score:  304   Residues:   301 -   338
chrX_74106603_74109726   Z   Score: 9372   Residues:     1 -  3124
chrX_74125127_74127150.rev   Z   Score: 6072   Residues:     1 -  2024
chrX_74135654_74140646   Z   Score: 14979   Residues:     1 -  4993
chrX_74186130_74192399.rev   Z   Score: 18810   Residues:     1 -  6270
chrX_74237264_74244692   Z   Score: 22287   Residues:     1 -  7429
chrX_74249494_74255809   Z   Score: 18948   Residues:     1 -  6316
chrX_74282399_74284718.rev   Z   Score: 6960   Residues:     1 -  2320
chrX_74310945_74323013.rev   A   Score:  208   Residues:  8977 -  9002
chrX_74310945_74323013.rev   Z   Score: 36207   Residues:     1 - 12069
chrX_74403692_74407994   A   Score:  218   Residues:   420 -   450
chrX_74403692_74407994   Z   Score: 12909   Residues:     1 -  4303
chrX_74420914_74423572   Z   Score: 7977   Residues:     1 -  2659
chrX_74494003_74502892   A   Score:  224   Residues:  5782 -  5900
chrX_74494003_74502892   Z   Score: 26670   Residues:     1 -  8890
chrX_74528860_74532142.rev   Z   Score: 9849   Residues:     1 -  3283
chrX_74556527_74570659.rev   A   Score:  310   Residues: 12625 - 12704
chrX_74556527_74570659.rev   Z   Score: 42399   Residues:     1 - 14133
chrX_74575442_74579520.rev   A   Score:  217   Residues:  1449 -  1575
chrX_74575442_74579520.rev   Z   Score: 12237   Residues:     1 -  4079
chrX_74588885_74595119   Z   Score: 18705   Residues:     1 -  6235
chrX_74599611_74602898.rev   Z   Score: 9864   Residues:     1 -  3288
chrX_74615520_74617624.rev   Z   Score: 6315   Residues:     1 -  2105
chrX_74618756_74625143   Z   Score: 19164   Residues:     1 -  6388
chrX_74629175_74633767.rev   Z   Score: 13779   Residues:     1 -  4593
chrX_74664780_74667209.rev   Z   Score: 7290   Residues:     1 -  2430
chrX_74729634_74736305.rev   Z   Score: 20016   Residues:     1 -  6672
chrX_74792234_74794145.rev   Z   Score: 5736   Residues:     1 -  1912
chrX_74796555_74802148.rev   Z   Score: 16782   Residues:     1 -  5594
chrX_74807914_74814293.rev   Z   Score: 19140   Residues:     1 -  6380
chrX_74816814_74822934   Z   Score: 18363   Residues:     1 -  6121
chrX_74836371_74842228.rev   Z   Score: 17574   Residues:     1 -  5858
chrX_74842825_74846644.rev   A   Score:  238   Residues:   392 -   427
chrX_74842825_74846644.rev   Z   Score: 11460   Residues:     1 -  3820
chrX_74866355_74869291.rev   Z   Score: 8811   Residues:     1 -  2937
chrX_74878774_74884909.rev   A   Score:  213   Residues:     2 -   101
chrX_74878774_74884909.rev   Z   Score: 18408   Residues:     1 -  6136
chrX_74897064_74899501.rev   Z   Score: 7311   Residues:     1 -  2437
chrX_74926385_74928282   Z   Score: 5694   Residues:     1 -  1898
chrX_74941182_74943204.rev   Z   Score: 6069   Residues:     1 -  2023
chrX_74945651_74949938.rev   Z   Score: 12864   Residues:     1 -  4288
chrX_74954528_74958812.rev   Z   Score: 12855   Residues:     1 -  4285
chrX_74974386_74976985   Z   Score: 7800   Residues:     1 -  2600
chrX_74977280_74983500.rev   A   Score:  326   Residues:  3551 -  3603
chrX_74977280_74983500.rev   Z   Score: 18663   Residues:     1 -  6221
chrX_75001865_75011195.rev   A   Score:  228   Residues:  5247 -  5302
chrX_75001865_75011195.rev   Z   Score: 27993   Residues:     1 -  9331
chrX_75018817_75023067   Z   Score: 12753   Residues:     1 -  4251
chrX_75036318_75043084.rev   Z   Score: 20301   Residues:     1 -  6767
chrX_75049557_75055949.rev   Z   Score: 19179   Residues:     1 -  6393
chrX_75057246_75059428.rev   Z   Score: 6549   Residues:     1 -  2183
chrX_75070818_75077092   Z   Score: 18825   Residues:     1 -  6275
chrX_75081649_75086699.rev   Z   Score: 15153   Residues:     1 -  5051
chrX_75092025_75099331.rev   A   Score:  213   Residues:  3831 -  3862
chrX_75092025_75099331.rev   Z   Score: 21921   Residues:     1 -  7307
chrX_75101783_75105822.rev   Z   Score: 12120   Residues:     1 -  4040
chrX_75116969_75121563   A   Score:  246   Residues:  1477 -  1560
chrX_75116969_75121563   Z   Score: 13785   Residues:     1 -  4595
chrX_75129710_75136206   Z   Score: 19491   Residues:     1 -  6497
chrX_75161065_75167775   Z   Score: 20133   Residues:     1 -  6711
chrX_75189411_75191640.rev   Z   Score: 6690   Residues:     1 -  2230
chrX_75191939_75193807.rev   Z   Score: 5607   Residues:     1 -  1869
chrX_75194719_75200625.rev   Z   Score: 17721   Residues:     1 -  5907
chrX_75211862_75217580   Z   Score: 17157   Residues:     1 -  5719
chrX_75237266_75242665   A   Score:  224   Residues:  1802 -  1837
chrX_75237266_75242665   Z   Score: 16200   Residues:     1 -  5400
chrX_75258720_75276280   T   Score:  232   Residues:  6024 -  6062
chrX_75258720_75276280   Z   Score: 52683   Residues:     1 - 17561
chrX_75285551_75290109.rev   A   Score:  217   Residues:   335 -   496
chrX_75285551_75290109.rev   Z   Score: 13677   Residues:     1 -  4559
chrX_75290597_75304075.rev   Z   Score: 40437   Residues:     1 - 13479
chrX_75314327_75320709.rev   A   Score:  217   Residues:  3547 -  3665
chrX_75314327_75320709.rev   Z   Score: 19149   Residues:     1 -  6383
chrX_75326137_75330173.rev   Z   Score: 12111   Residues:     1 -  4037
chrX_75331603_75333394   Z   Score: 5376   Residues:     1 -  1792
chrX_75338791_75342058   Z   Score: 9804   Residues:     1 -  3268
chrX_75361019_75362631.rev   Z   Score: 4839   Residues:     1 -  1613
chrX_75376897_75382179.rev   Z   Score: 15849   Residues:     1 -  5283
chrX_75382569_75388686   A   Score:  215   Residues:  1650 -  1765
chrX_75382569_75388686   Z   Score: 18354   Residues:     1 -  6118
chrX_75391593_75400186.rev   Z   Score: 25782   Residues:     1 -  8594
chrX_75419084_75423744   Z   Score: 13983   Residues:     1 -  4661
chrX_75440311_75445023.rev   A   Score:  248   Residues:   433 -   513
chrX_75440311_75445023.rev   Z   Score: 14139   Residues:     1 -  4713
chrX_75446171_75450398.rev   Z   Score: 12684   Residues:     1 -  4228
chrX_75451636_75453958.rev   Z   Score: 6969   Residues:     1 -  2323
chrX_75458744_75463473   Z   Score: 14190   Residues:     1 -  4730
chrX_75465176_75469509.rev   A   Score:  232   Residues:  1469 -  1591
chrX_75465176_75469509.rev   Z   Score: 13002   Residues:     1 -  4334
chrX_75474411_75480233   Z   Score: 17469   Residues:     1 -  5823
chrX_75483199_75487121.rev   Z   Score: 11769   Residues:     1 -  3923
chrX_75495826_75501625   Z   Score: 17400   Residues:     1 -  5800
chrX_75502418_75505600.rev   Z   Score: 9549   Residues:     1 -  3183
chrX_75525182_75531609.rev   Z   Score: 19284   Residues:     1 -  6428
chrX_75545936_75551359.rev   A   Score:  209   Residues:  1774 -  1838
chrX_75545936_75551359.rev   Z   Score: 16272   Residues:     1 -  5424
chrX_75562158_75568563   Z   Score: 19218   Residues:     1 -  6406
chrX_75570639_75577050   Z   Score: 19236   Residues:     1 -  6412
chrX_75581171_75587574.rev   Z   Score: 19212   Residues:     1 -  6404
chrX_75588895_75595483.rev   Z   Score: 19767   Residues:     1 -  6589
chrX_75600440_75602898.rev   Z   Score: 7377   Residues:     1 -  2459
chrX_75611299_75615809   A   Score:  212   Residues:   803 -   831
chrX_75611299_75615809   Z   Score: 13533   Residues:     1 -  4511
chrX_75622052_75626845   A   Score:  216   Residues:   477 -   531
chrX_75622052_75626845   Z   Score: 14382   Residues:     1 -  4794
chrX_75634374_75642224.rev   Z   Score: 23553   Residues:     1 -  7851
chrX_75654198_75656514.rev   Z   Score: 6951   Residues:     1 -  2317
chrX_75663624_75670013.rev   Z   Score: 19170   Residues:     1 -  6390
chrX_75686703_75689700.rev   Z   Score: 8994   Residues:     1 -  2998
chrX_75702302_75709314   A   Score:  242   Residues:   420 -   485
chrX_75702302_75709314   Z   Score: 21039   Residues:     1 -  7013
chrX_75723389_75736147   A   Score:  310   Residues: 10110 - 10162
chrX_75723389_75736147   A   Score:  268   Residues:  9657 -  9751
chrX_75723389_75736147   Z   Score: 38277   Residues:     1 - 12759
chrX_75745200_75750155   Z   Score: 14868   Residues:     1 -  4956
chrX_75758215_75767582   A   Score:  255   Residues:  4435 -  4521
chrX_75758215_75767582   Z   Score: 28104   Residues:     1 -  9368
chrX_75775496_75777398   Z   Score: 5709   Residues:     1 -  1903
chrX_75789584_75791802   Z   Score: 6657   Residues:     1 -  2219
chrX_75809500_75811972   Z   Score: 7419   Residues:     1 -  2473
chrX_75812080_75816213   A   Score:  232   Residues:   416 -   492
chrX_75812080_75816213   Z   Score: 12402   Residues:     1 -  4134
chrX_75843255_75850573   Z   Score: 21957   Residues:     1 -  7319
chrX_75873629_75876011   Z   Score: 7149   Residues:     1 -  2383
chrX_75884829_75895189   Z   Score: 31083   Residues:     1 - 10361
chrX_75895989_75899117   Z   Score: 9387   Residues:     1 -  3129
chrX_75911680_75918511   A   Score:  295   Residues:  4786 -  4835
chrX_75911680_75918511   Z   Score: 20496   Residues:     1 -  6832
chrX_75926982_75933378   Z   Score: 19191   Residues:     1 -  6397
chrX_75953019_75959172   Z   Score: 18462   Residues:     1 -  6154
chrX_75981224_75987625   T   Score:  585   Residues:     1 -   442
chrX_75981224_75987625   Z   Score: 19206   Residues:     1 -  6402
chrX_76039559_76046563   Z   Score: 21015   Residues:     1 -  7005
chrX_76048839_76056809   Z   Score: 23913   Residues:     1 -  7971
chrX_76091879_76098266   Z   Score: 19164   Residues:     1 -  6388
chrX_76108099_76112637   Z   Score: 13617   Residues:     1 -  4539
chrX_76135376_76141775.rev   Z   Score: 19200   Residues:     1 -  6400
chrX_76173210_76175447   Z   Score: 6714   Residues:     1 -  2238
chrX_76187118_76193512   Z   Score: 19185   Residues:     1 -  6395
chrX_76194892_76198937.rev   Z   Score: 12138   Residues:     1 -  4046
chrX_76200115_76203055.rev   Z   Score: 8823   Residues:     1 -  2941
chrX_76229993_76234202   A   Score:  245   Residues:  1453 -  1493
chrX_76229993_76234202   A   Score:  242   Residues:   431 -   527
chrX_76229993_76234202   Z   Score: 12630   Residues:     1 -  4210
chrX_76240365_76245256   A   Score:  244   Residues:   157 -   218
chrX_76240365_76245256   Z   Score: 14676   Residues:     1 -  4892
chrX_76246911_76253189   Z   Score: 18837   Residues:     1 -  6279
chrX_76270799_76277006   Z   Score: 18624   Residues:     1 -  6208
chrX_76285163_76291854   Z   Score: 20076   Residues:     1 -  6692
chrX_76307358_76313471   Z   Score: 18342   Residues:     1 -  6114
chrX_76321534_76329370   Z   Score: 23511   Residues:     1 -  7837
chrX_76329705_76335617.rev   Z   Score: 17739   Residues:     1 -  5913
chrX_76336599_76342995   Z   Score: 19191   Residues:     1 -  6397
chrX_76350378_76356556   Z   Score: 18537   Residues:     1 -  6179
chrX_76370894_76373134   Z   Score: 6723   Residues:     1 -  2241
chrX_76379904_76384156   Z   Score: 12759   Residues:     1 -  4253
chrX_76388489_76392729   A   Score:  443   Residues:   335 -   498
chrX_76388489_76392729   A   Score:  211   Residues:  2007 -  2055
chrX_76388489_76392729   Z   Score: 12723   Residues:     1 -  4241
chrX_76392830_76399497   Z   Score: 20004   Residues:     1 -  6668
chrX_76409491_76416409.rev   Z   Score: 20757   Residues:     1 -  6919
chrX_76526275_76529132.rev   Z   Score: 8574   Residues:     1 -  2858
chrX_76531786_76538168   A   Score:  206   Residues:   108 -   178
chrX_76531786_76538168   Z   Score: 19149   Residues:     1 -  6383
chrX_76543905_76550583   A   Score:  204   Residues:  4622 -  4653
chrX_76543905_76550583   Z   Score: 20037   Residues:     1 -  6679
chrX_76555924_76562091   Z   Score: 18504   Residues:     1 -  6168
chrX_76574758_76577143   A   Score:  223   Residues:   181 -   212
chrX_76574758_76577143   Z   Score: 7158   Residues:     1 -  2386
chrX_76577367_76581537   Z   Score: 12513   Residues:     1 -  4171
chrX_76600705_76605344   Z   Score: 13920   Residues:     1 -  4640
chrX_76628368_76633079   A   Score:  270   Residues:  1349 -  1439
chrX_76628368_76633079   A   Score:  208   Residues:   344 -   485
chrX_76628368_76633079   Z   Score: 14136   Residues:     1 -  4712
chrX_76642319_76647176   A   Score:  398   Residues:  1691 -  1951
chrX_76642319_76647176   Z   Score: 14574   Residues:     1 -  4858
chrX_76767019_76769972   Z   Score: 8862   Residues:     1 -  2954
chrX_76782068_76784724   Z   Score: 7971   Residues:     1 -  2657
chrX_76852254_76854956   A   Score:  213   Residues:  1185 -  1225
chrX_76852254_76854956   A   Score:  200   Residues:   836 -   876
chrX_76852254_76854956   T   Score:  270   Residues:  1340 -  1379
chrX_76852254_76854956   Z   Score: 8109   Residues:     1 -  2703
chrX_76856717_76858840   T   Score:  266   Residues:  1843 -  1897
chrX_76856717_76858840   Z   Score: 6372   Residues:     1 -  2124
chrX_76870046_76872320.rev   Z   Score: 6825   Residues:     1 -  2275
chrX_77138253_77143672.rev   Z   Score: 16260   Residues:     1 -  5420
chrX_77207089_77213575.rev   Z   Score: 19461   Residues:     1 -  6487
chrX_77214336_77220171.rev   Z   Score: 17508   Residues:     1 -  5836
chrX_77245740_77256394   A   Score:  206   Residues:   341 -   375
chrX_77245740_77256394   Z   Score: 31965   Residues:     1 - 10655
chrX_77266690_77269927   Z   Score: 9714   Residues:     1 -  3238
chrX_77271986_77274809.rev   A   Score:  238   Residues:   136 -   193
chrX_77271986_77274809.rev   Z   Score: 8472   Residues:     1 -  2824
chrX_77279540_77281972.rev   Z   Score: 7299   Residues:     1 -  2433
chrX_77283954_77286162   A   Score:  240   Residues:   662 -   691
chrX_77283954_77286162   A   Score:  210   Residues:   969 -  1027
chrX_77283954_77286162   Z   Score: 6627   Residues:     1 -  2209
chrX_77339501_77341505   Z   Score: 6015   Residues:     1 -  2005
chrX_77350856_77361037.rev   Z   Score: 30546   Residues:     1 - 10182
chrX_77372617_77374867   Z   Score: 6753   Residues:     1 -  2251
chrX_77397668_77402644.rev   Z   Score: 14931   Residues:     1 -  4977
chrX_77403949_77408669   Z   Score: 14163   Residues:     1 -  4721
chrX_77421696_77423410   Z   Score: 5145   Residues:     1 -  1715
chrX_77430276_77435327.rev   Z   Score: 15156   Residues:     1 -  5052
chrX_77452826_77456222   Z   Score: 10191   Residues:     1 -  3397
chrX_77457017_77461241   Z   Score: 12675   Residues:     1 -  4225
chrX_77463888_77469469   Z   Score: 16746   Residues:     1 -  5582
chrX_77471005_77476172   Z   Score: 15504   Residues:     1 -  5168
chrX_77477810_77481263   Z   Score: 10362   Residues:     1 -  3454
chrX_77504739_77510337.rev   Z   Score: 16797   Residues:     1 -  5599
chrX_77521638_77526194.rev   Z   Score: 13671   Residues:     1 -  4557
chrX_77528117_77538020.rev   Z   Score: 29712   Residues:     1 -  9904
chrX_77570756_77575052   Z   Score: 12891   Residues:     1 -  4297
chrX_77601539_77606894.rev   Z   Score: 16068   Residues:     1 -  5356
chrX_77619714_77625464.rev   Z   Score: 17253   Residues:     1 -  5751
chrX_77627940_77629659.rev   Z   Score: 5160   Residues:     1 -  1720
chrX_77648469_77652555.rev   A   Score:  230   Residues:  1292 -  1413
chrX_77648469_77652555.rev   Z   Score: 12261   Residues:     1 -  4087
chrX_77661577_77663513   Z   Score: 5811   Residues:     1 -  1937
chrX_77675258_77679418.rev   A   Score:  225   Residues:  1601 -  1660
chrX_77675258_77679418.rev   Z   Score: 12483   Residues:     1 -  4161
chrX_77697546_77700601.rev   A   Score:  209   Residues:  1837 -  1870
chrX_77697546_77700601.rev   Z   Score: 9165   Residues:     1 -  3055
chrX_77705714_77710682   Z   Score: 14907   Residues:     1 -  4969
chrX_77738141_77740156   Z   Score: 6048   Residues:     1 -  2016
chrX_77781493_77783221   Z   Score: 5187   Residues:     1 -  1729
chrX_77791878_77796130.rev   Z   Score: 12759   Residues:     1 -  4253
chrX_77821243_77823185.rev   Z   Score: 5829   Residues:     1 -  1943
chrX_77835787_77840318.rev   Z   Score: 13596   Residues:     1 -  4532
chrX_77878376_77881127   A   Score:  226   Residues:  1186 -  1217
chrX_77878376_77881127   Z   Score: 8256   Residues:     1 -  2752
chrX_77906322_77908516   Z   Score: 6585   Residues:     1 -  2195
chrX_77925778_77928222.rev   Z   Score: 7335   Residues:     1 -  2445
chrX_77936594_77942434   Z   Score: 17523   Residues:     1 -  5841
chrX_77954717_77959012.rev   Z   Score: 12888   Residues:     1 -  4296
chrX_77966007_77971943.rev   Z   Score: 17811   Residues:     1 -  5937
chrX_77986499_77988285   Z   Score: 5361   Residues:     1 -  1787
chrX_77997559_77999417.rev   Z   Score: 5577   Residues:     1 -  1859
chrX_78035851_78040777.rev   A   Score:  201   Residues:  3704 -  3732
chrX_78035851_78040777.rev   Z   Score: 14781   Residues:     1 -  4927
chrX_78064520_78066810   Z   Score: 6873   Residues:     1 -  2291
chrX_78069318_78076010.rev   Z   Score: 20079   Residues:     1 -  6693
chrX_78077386_78079804   Z   Score: 7257   Residues:     1 -  2419
chrX_78082021_78086189   Z   Score: 12507   Residues:     1 -  4169
chrX_78086429_78088140   Z   Score: 5136   Residues:     1 -  1712
chrX_78088487_78094868.rev   Z   Score: 19146   Residues:     1 -  6382
chrX_78100163_78102247.rev   A   Score:  279   Residues:   305 -   360
chrX_78100163_78102247.rev   Z   Score: 6255   Residues:     1 -  2085
chrX_78106472_78108845   Z   Score: 7122   Residues:     1 -  2374
chrX_78122717_78126861.rev   A   Score:  344   Residues:  1127 -  1179
chrX_78122717_78126861.rev   A   Score:  246   Residues:  3845 -  3876
chrX_78122717_78126861.rev   Z   Score: 12435   Residues:     1 -  4145
chrX_78133151_78139085   A   Score:  330   Residues:  2835 -  2884
chrX_78133151_78139085   Z   Score: 17805   Residues:     1 -  5935
chrX_78188642_78190306   Z   Score: 4995   Residues:     1 -  1665
chrX_78251549_78253369.rev   Z   Score: 5463   Residues:     1 -  1821
chrX_78257707_78265963   A   Score:  550   Residues:  4337 -  4406
chrX_78257707_78265963   A   Score:  203   Residues:  5500 -  5620
chrX_78257707_78265963   Z   Score: 24771   Residues:     1 -  8257
chrX_78267600_78273975.rev   Z   Score: 19128   Residues:     1 -  6376
chrX_78276376_78281620.rev   A   Score:  228   Residues:  1576 -  1615
chrX_78276376_78281620.rev   Z   Score: 15735   Residues:     1 -  5245
chrX_78287880_78292145.rev   Z   Score: 12798   Residues:     1 -  4266
chrX_78316205_78318075   Z   Score: 5613   Residues:     1 -  1871
chrX_78361323_78367297   Z   Score: 17925   Residues:     1 -  5975
chrX_78373091_78377108   Z   Score: 12054   Residues:     1 -  4018
chrX_78389573_78394836.rev   Z   Score: 15792   Residues:     1 -  5264
chrX_78405465_78410014   Z   Score: 13650   Residues:     1 -  4550
chrX_78441843_78447622   Z   Score: 17340   Residues:     1 -  5780
chrX_78490069_78492233.rev   Z   Score: 6495   Residues:     1 -  2165
chrX_78495791_78499211   Z   Score: 10263   Residues:     1 -  3421
chrX_78504088_78506926.rev   Z   Score: 8517   Residues:     1 -  2839
chrX_78539936_78543833.rev   Z   Score: 11694   Residues:     1 -  3898
chrX_78554994_78561678   Z   Score: 20055   Residues:     1 -  6685
chrX_78626107_78632183.rev   Z   Score: 18231   Residues:     1 -  6077
chrX_78646063_78647702.rev   Z   Score: 4920   Residues:     1 -  1640
chrX_78668111_78672960   Z   Score: 14550   Residues:     1 -  4850
chrX_78696685_78700963.rev   A   Score:  221   Residues:  1182 -  1231
chrX_78696685_78700963.rev   Z   Score: 12837   Residues:     1 -  4279
chrX_78707120_78710799.rev   Z   Score: 11040   Residues:     1 -  3680
chrX_78721104_78724149.rev   Z   Score: 9138   Residues:     1 -  3046
chrX_78726228_78730062   Z   Score: 11505   Residues:     1 -  3835
chrX_78745440_78747614.rev   Z   Score: 6525   Residues:     1 -  2175
chrX_78752910_78759881.rev   A   Score:  256   Residues:  4317 -  4416
chrX_78752910_78759881.rev   Z   Score: 20916   Residues:     1 -  6972
chrX_78793997_78798259   Z   Score: 12789   Residues:     1 -  4263
chrX_78818914_78822221.rev   Z   Score: 9924   Residues:     1 -  3308
chrX_78827490_78836841.rev   Z   Score: 28056   Residues:     1 -  9352
chrX_78861162_78865684.rev   Z   Score: 13569   Residues:     1 -  4523
chrX_78874900_78879432.rev   Z   Score: 13599   Residues:     1 -  4533
chrX_78926489_78928862.rev   Z   Score: 7122   Residues:     1 -  2374
chrX_78929935_78935362   A   Score:  255   Residues:  1550 -  1597
chrX_78929935_78935362   Z   Score: 16284   Residues:     1 -  5428
chrX_78935385_78937230.rev   Z   Score: 5538   Residues:     1 -  1846
chrX_78958589_78960246   Z   Score: 4974   Residues:     1 -  1658
chrX_78963888_78966442   Z   Score: 7665   Residues:     1 -  2555
chrX_78977137_78980471.rev   A   Score:  205   Residues:   520 -   645
chrX_78977137_78980471.rev   Z   Score: 10005   Residues:     1 -  3335
chrX_78987942_78994218   Z   Score: 18831   Residues:     1 -  6277
chrX_79028377_79032961.rev   Z   Score: 13755   Residues:     1 -  4585
chrX_79054794_79057310   Z   Score: 7551   Residues:     1 -  2517
chrX_79057565_79059285   Z   Score: 5163   Residues:     1 -  1721
chrX_79070362_79072590.rev   Z   Score: 6687   Residues:     1 -  2229
chrX_79103014_79104776.rev   Z   Score: 5289   Residues:     1 -  1763
chrX_79121033_79128833.rev   Z   Score: 23403   Residues:     1 -  7801
chrX_79129339_79132906.rev   Z   Score: 10704   Residues:     1 -  3568
chrX_79187156_79190853.rev   Z   Score: 11094   Residues:     1 -  3698
chrX_79213196_79219602.rev   Z   Score: 19221   Residues:     1 -  6407
chrX_79235268_79237104.rev   Z   Score: 5511   Residues:     1 -  1837
chrX_79253745_79255521.rev   Z   Score: 5331   Residues:     1 -  1777
chrX_79255880_79259540.rev   Z   Score: 10983   Residues:     1 -  3661
chrX_79263656_79267554.rev   Z   Score: 11697   Residues:     1 -  3899
chrX_79334580_79341279   Z   Score: 20100   Residues:     1 -  6700
chrX_79347688_79349749   Z   Score: 6186   Residues:     1 -  2062
chrX_79362263_79366513.rev   A   Score:  237   Residues:  1464 -  1582
chrX_79362263_79366513.rev   Z   Score: 12753   Residues:     1 -  4251
chrX_79380423_79386981   Z   Score: 19677   Residues:     1 -  6559
chrX_79408574_79415273.rev   T   Score:  231   Residues:   885 -   922
chrX_79408574_79415273.rev   Z   Score: 20100   Residues:     1 -  6700
chrX_79459312_79460985.rev   C   Score:  236   Residues:  1356 -  1437
chrX_79459312_79460985.rev   Z   Score: 5022   Residues:     1 -  1674
chrX_79466386_79472649   Z   Score: 18792   Residues:     1 -  6264
chrX_79523334_79530108   Z   Score: 20325   Residues:     1 -  6775
chrX_79551581_79553750.rev   Z   Score: 6510   Residues:     1 -  2170
chrX_79560945_79562625   Z   Score: 5043   Residues:     1 -  1681
chrX_79563561_79567763   A   Score:  234   Residues:   314 -   367
chrX_79563561_79567763   Z   Score: 12609   Residues:     1 -  4203
chrX_79567781_79570043   Z   Score: 6789   Residues:     1 -  2263
chrX_79604555_79609529   Z   Score: 14925   Residues:     1 -  4975
chrX_79627203_79631565.rev   Z   Score: 13089   Residues:     1 -  4363
chrX_79642761_79647702.rev   Z   Score: 14826   Residues:     1 -  4942
chrX_79657876_79660745.rev   Z   Score: 8610   Residues:     1 -  2870
chrX_79679069_79684861.rev   A   Score:  279   Residues:  3118 -  3211
chrX_79679069_79684861.rev   Z   Score: 17379   Residues:     1 -  5793
chrX_79699969_79705126   A   Score:  235   Residues:  4350 -  4396
chrX_79699969_79705126   Z   Score: 15474   Residues:     1 -  5158
chrX_79711740_79718122   Z   Score: 19149   Residues:     1 -  6383
chrX_79722585_79726303.rev   A   Score:  215   Residues:   629 -   736
chrX_79722585_79726303.rev   Z   Score: 11157   Residues:     1 -  3719
chrX_79813797_79817300.rev   Z   Score: 10512   Residues:     1 -  3504
chrX_79824645_79827071   Z   Score: 7281   Residues:     1 -  2427
chrX_79884118_79889857.rev   Z   Score: 17220   Residues:     1 -  5740
chrX_79896899_79901514   Z   Score: 13848   Residues:     1 -  4616
chrX_79924321_79927219.rev   A   Score:  248   Residues:  1675 -  1722
chrX_79924321_79927219.rev   Z   Score: 8697   Residues:     1 -  2899
chrX_79930294_79932051.rev   T   Score:  214   Residues:   171 -   198
chrX_79930294_79932051.rev   Z   Score: 5271   Residues:     1 -  1757
chrX_79949505_79955896.rev   Z   Score: 19176   Residues:     1 -  6392
chrX_79966959_79974264   A   Score:  319   Residues:  3654 -  3706
chrX_79966959_79974264   Z   Score: 21918   Residues:     1 -  7306
chrX_79977008_79979859   Z   Score: 8556   Residues:     1 -  2852
chrX_79984716_79987433.rev   Z   Score: 8154   Residues:     1 -  2718
chrX_79997714_80004093   Z   Score: 19140   Residues:     1 -  6380
chrX_80020763_80025499.rev   Z   Score: 14211   Residues:     1 -  4737
chrX_80038675_80044950.rev   A   Score:  276   Residues:   355 -   435
chrX_80038675_80044950.rev   Z   Score: 18828   Residues:     1 -  6276
chrX_80054793_80058841   Z   Score: 12147   Residues:     1 -  4049
chrX_80068010_80071373.rev   Z   Score: 10092   Residues:     1 -  3364
chrX_80085184_80087397   Z   Score: 6642   Residues:     1 -  2214
chrX_80087979_80094377   Z   Score: 19197   Residues:     1 -  6399
chrX_80098283_80102159   Z   Score: 11631   Residues:     1 -  3877
chrX_80104193_80106774.rev   A   Score:  325   Residues:  1565 -  1618
chrX_80104193_80106774.rev   Z   Score: 7746   Residues:     1 -  2582
chrX_80141229_80143986   Z   Score: 8274   Residues:     1 -  2758
chrX_80145706_80156746   A   Score:  228   Residues:  5979 -  6021
chrX_80145706_80156746   A   Score:  214   Residues:  8012 -  8046
chrX_80145706_80156746   Z   Score: 33123   Residues:     1 - 11041
chrX_80161927_80167184.rev   Z   Score: 15774   Residues:     1 -  5258
chrX_80172533_80174771   Z   Score: 6717   Residues:     1 -  2239
chrX_80204523_80216923   A   Score:  217   Residues:  7690 -  7809
chrX_80204523_80216923   A   Score:  200   Residues:   312 -   380
chrX_80204523_80216923   Z   Score: 37203   Residues:     1 - 12401
chrX_80254979_80256653   Z   Score: 5025   Residues:     1 -  1675
chrX_80307210_80310362.rev   Z   Score: 9459   Residues:     1 -  3153
chrX_80327092_80329521.rev   Z   Score: 7290   Residues:     1 -  2430
chrX_80364689_80368960.rev   Z   Score: 12816   Residues:     1 -  4272
chrX_80372286_80374977.rev   Z   Score: 8076   Residues:     1 -  2692
chrX_80392056_80394233.rev   Z   Score: 6534   Residues:     1 -  2178
chrX_80401776_80408050.rev   Z   Score: 18825   Residues:     1 -  6275
chrX_80418772_80420432.rev   Z   Score: 4983   Residues:     1 -  1661
chrX_80440555_80442271.rev   Z   Score: 5151   Residues:     1 -  1717
chrX_80444146_80447549.rev   Z   Score: 10212   Residues:     1 -  3404
chrX_80496089_80498902.rev   Z   Score: 8442   Residues:     1 -  2814
chrX_80502343_80505013.rev   A   Score:  501   Residues:  1175 -  1283
chrX_80502343_80505013.rev   A   Score:  249   Residues:   303 -   404
chrX_80502343_80505013.rev   Z   Score: 8013   Residues:     1 -  2671
chrX_80511080_80516783   Z   Score: 17112   Residues:     1 -  5704
chrX_80519955_80522159.rev   Z   Score: 6615   Residues:     1 -  2205
chrX_80523461_80526192.rev   Z   Score: 8196   Residues:     1 -  2732
chrX_80531372_80537730.rev   Z   Score: 19077   Residues:     1 -  6359
chrX_80541544_80545471   Z   Score: 11784   Residues:     1 -  3928
chrX_80563997_80567926   Z   Score: 11790   Residues:     1 -  3930
chrX_80586037_80594617.rev   A   Score:  230   Residues:  3351 -  3389
chrX_80586037_80594617.rev   Z   Score: 25743   Residues:     1 -  8581
chrX_80613159_80618271.rev   Z   Score: 15339   Residues:     1 -  5113
chrX_80631570_80635766   Z   Score: 12591   Residues:     1 -  4197
chrX_80640433_80645462   A   Score:  200   Residues:  1252 -  1294
chrX_80640433_80645462   Z   Score: 15090   Residues:     1 -  5030
chrX_80672974_80675128.rev   Z   Score: 6465   Residues:     1 -  2155
chrX_80701113_80709169.rev   Z   Score: 24171   Residues:     1 -  8057
chrX_80783460_80785138   Z   Score: 5037   Residues:     1 -  1679
chrX_80802025_80810704   Z   Score: 26040   Residues:     1 -  8680
chrX_80845544_80848216.rev   Z   Score: 8019   Residues:     1 -  2673
chrX_80853267_80858612   Z   Score: 16038   Residues:     1 -  5346
chrX_80860187_80862490.rev   Z   Score: 6912   Residues:     1 -  2304
chrX_80866147_80867880.rev   Z   Score: 5202   Residues:     1 -  1734
chrX_80887488_80890096   A   Score:  244   Residues:  2004 -  2041
chrX_80887488_80890096   Z   Score: 7827   Residues:     1 -  2609
chrX_80902298_80908576   Z   Score: 18837   Residues:     1 -  6279
chrX_80922243_80923847   Z   Score: 4815   Residues:     1 -  1605
chrX_80943724_80947973.rev   Z   Score: 12750   Residues:     1 -  4250
chrX_80964320_80968445.rev   Z   Score: 12378   Residues:     1 -  4126
chrX_80975495_80977462   Z   Score: 5904   Residues:     1 -  1968
chrX_81001482_81007773   Z   Score: 18876   Residues:     1 -  6292
chrX_81026174_81028040   Z   Score: 5601   Residues:     1 -  1867
chrX_81066161_81071993.rev   Z   Score: 17499   Residues:     1 -  5833
chrX_81087423_81092476   Z   Score: 15162   Residues:     1 -  5054
chrX_81098268_81100550   Z   Score: 6849   Residues:     1 -  2283
chrX_81101200_81103888.rev   A   Score:  316   Residues:   124 -   288
chrX_81101200_81103888.rev   Z   Score: 8067   Residues:     1 -  2689
chrX_81110134_81114254   A   Score:  220   Residues:  2368 -  2437
chrX_81110134_81114254   Z   Score: 12363   Residues:     1 -  4121
chrX_81122194_81127596   T   Score:  392   Residues:    70 -   153
chrX_81122194_81127596   Z   Score: 16209   Residues:     1 -  5403
chrX_81154635_81162486.rev   Z   Score: 23556   Residues:     1 -  7852
chrX_81172248_81174769.rev   Z   Score: 7566   Residues:     1 -  2522
chrX_81198150_81200561   Z   Score: 7236   Residues:     1 -  2412
chrX_81210817_81215373   Z   Score: 13671   Residues:     1 -  4557
chrX_81218357_81220171.rev   Z   Score: 5445   Residues:     1 -  1815
chrX_81239057_81241065.rev   Z   Score: 6027   Residues:     1 -  2009
chrX_81245771_81249599.rev   Z   Score: 11487   Residues:     1 -  3829
chrX_81259725_81263921.rev   Z   Score: 12591   Residues:     1 -  4197
chrX_81274981_81280168.rev   Z   Score: 15564   Residues:     1 -  5188
chrX_81282112_81284067.rev   Z   Score: 5868   Residues:     1 -  1956
chrX_81286337_81288511.rev   Z   Score: 6525   Residues:     1 -  2175
chrX_81311725_81313390.rev   Z   Score: 4998   Residues:     1 -  1666
chrX_81315828_81319914.rev   Z   Score: 12261   Residues:     1 -  4087
chrX_81331295_81333177.rev   Z   Score: 5649   Residues:     1 -  1883
chrX_81344553_81346522   Z   Score: 5910   Residues:     1 -  1970
chrX_81359660_81365102   A   Score:  220   Residues:  4402 -  4444
chrX_81359660_81365102   Z   Score: 16329   Residues:     1 -  5443
chrX_81383095_81390214   Z   Score: 21360   Residues:     1 -  7120
chrX_81413671_81416889   Z   Score: 9657   Residues:     1 -  3219
chrX_81449389_81455564   Z   Score: 18528   Residues:     1 -  6176
chrX_81466554_81470749.rev   A   Score:  324   Residues:   385 -   475
chrX_81466554_81470749.rev   Z   Score: 12588   Residues:     1 -  4196
chrX_81480085_81484373   Z   Score: 12867   Residues:     1 -  4289
chrX_81495068_81501672   A   Score:  215   Residues:   509 -   591
chrX_81495068_81501672   Z   Score: 19815   Residues:     1 -  6605
chrX_81529272_81533484.rev   Z   Score: 12639   Residues:     1 -  4213
chrX_81533933_81538772.rev   Z   Score: 14520   Residues:     1 -  4840
chrX_81548990_81552306   Z   Score: 9951   Residues:     1 -  3317
chrX_81559118_81564075.rev   Z   Score: 14874   Residues:     1 -  4958
chrX_81605245_81608116   Z   Score: 8616   Residues:     1 -  2872
chrX_81608382_81614666.rev   Z   Score: 18855   Residues:     1 -  6285
chrX_81625624_81628342.rev   Z   Score: 8157   Residues:     1 -  2719
chrX_81628619_81630504.rev   Z   Score: 5658   Residues:     1 -  1886
chrX_81663654_81667046   Z   Score: 10179   Residues:     1 -  3393
chrX_81686062_81688928   Z   Score: 8601   Residues:     1 -  2867
chrX_81691174_81693729   Z   Score: 7668   Residues:     1 -  2556
chrX_81743873_81746001.rev   Z   Score: 6384   Residues:     1 -  2128
chrX_81830795_81835123.rev   A   Score:  255   Residues:  1505 -  1608
chrX_81830795_81835123.rev   Z   Score: 12987   Residues:     1 -  4329
chrX_81848930_81855357   Z   Score: 19284   Residues:     1 -  6428
chrX_81864192_81870593.rev   Z   Score: 19206   Residues:     1 -  6402
chrX_81872527_81874334   Z   Score: 5424   Residues:     1 -  1808
chrX_81917133_81920137   Z   Score: 9015   Residues:     1 -  3005
chrX_81940852_81946642   Z   Score: 17373   Residues:     1 -  5791
chrX_81961724_81965337   Z   Score: 10842   Residues:     1 -  3614
chrX_81967436_81969230   Z   Score: 5385   Residues:     1 -  1795
chrX_81973178_81975654   Z   Score: 7431   Residues:     1 -  2477
chrX_81979914_81983056.rev   Z   Score: 9429   Residues:     1 -  3143
chrX_82002298_82004950.rev   A   Score:  398   Residues:  2471 -  2526
chrX_82002298_82004950.rev   Z   Score: 7959   Residues:     1 -  2653
chrX_82009338_82011600   Z   Score: 6789   Residues:     1 -  2263
chrX_82024803_82027045.rev   A   Score:  761   Residues:   365 -   523
chrX_82024803_82027045.rev   R   Score:  254   Residues:   369 -   524
chrX_82024803_82027045.rev   Z   Score: 6729   Residues:     1 -  2243
chrX_82037418_82040525   Z   Score: 9324   Residues:     1 -  3108
chrX_82085485_82089628   Z   Score: 12432   Residues:     1 -  4144
chrX_82104887_82107336.rev   Z   Score: 7350   Residues:     1 -  2450
chrX_82121011_82127290.rev   Z   Score: 18840   Residues:     1 -  6280
chrX_82158305_82161821   Z   Score: 10551   Residues:     1 -  3517
chrX_82191158_82195998   A   Score:  247   Residues:  3417 -  3471
chrX_82191158_82195998   A   Score:  203   Residues:  1877 -  1974
chrX_82191158_82195998   Z   Score: 14523   Residues:     1 -  4841
chrX_82200282_82204818   Z   Score: 13611   Residues:     1 -  4537
chrX_82218178_82221020.rev   Z   Score: 8529   Residues:     1 -  2843
chrX_82229835_82232478.rev   Z   Score: 7932   Residues:     1 -  2644
chrX_82286537_82292270.rev   A   Score:  258   Residues:  4458 -  4493
chrX_82286537_82292270.rev   Z   Score: 17202   Residues:     1 -  5734
chrX_82294385_82302915   A   Score:  241   Residues:  6272 -  6326
chrX_82294385_82302915   A   Score:  233   Residues:  2417 -  2459
chrX_82294385_82302915   Z   Score: 25593   Residues:     1 -  8531
chrX_82315833_82317742   Z   Score: 5730   Residues:     1 -  1910
chrX_82321576_82327723   A   Score:  223   Residues:  5545 -  5589
chrX_82321576_82327723   Z   Score: 18444   Residues:     1 -  6148
chrX_82328773_82330817   A   Score:  215   Residues:   897 -   928
chrX_82328773_82330817   Z   Score: 6135   Residues:     1 -  2045
chrX_82346951_82353326   Z   Score: 19128   Residues:     1 -  6376
chrX_82430016_82434141.rev   Z   Score: 12378   Residues:     1 -  4126
chrX_82448520_82450337   Z   Score: 5454   Residues:     1 -  1818
chrX_82458140_82464758   Z   Score: 19857   Residues:     1 -  6619
chrX_82467789_82474104   A   Score:  288   Residues:    60 -   197
chrX_82467789_82474104   G   Score:  266   Residues:    87 -   167
chrX_82467789_82474104   Z   Score: 18948   Residues:     1 -  6316
chrX_82535839_82539405   Z   Score: 10701   Residues:     1 -  3567
chrX_82603050_82609323   Z   Score: 18822   Residues:     1 -  6274
chrX_82623165_82628902.rev   Z   Score: 17214   Residues:     1 -  5738
chrX_82645704_82651376   A   Score:  230   Residues:  2147 -  2208
chrX_82645704_82651376   Z   Score: 17019   Residues:     1 -  5673
chrX_82694524_82697506.rev   Z   Score: 8949   Residues:     1 -  2983
chrX_82702158_82705740.rev   Z   Score: 10749   Residues:     1 -  3583
chrX_82710971_82717401.rev   Z   Score: 19290   Residues:     1 -  6430
chrX_82722143_82727802.rev   Z   Score: 16980   Residues:     1 -  5660
chrX_82729391_82738299   T   Score:  224   Residues:  4974 -  5043
chrX_82729391_82738299   Z   Score: 26727   Residues:     1 -  8909
chrX_82744330_82751011.rev   Z   Score: 20046   Residues:     1 -  6682
chrX_82759387_82761078.rev   Z   Score: 5076   Residues:     1 -  1692
chrX_82761147_82764617.rev   A   Score:  276   Residues:  2832 -  2877
chrX_82761147_82764617.rev   Z   Score: 10413   Residues:     1 -  3471
chrX_82764736_82769510.rev   A   Score:  352   Residues:   333 -   376
chrX_82764736_82769510.rev   Z   Score: 14325   Residues:     1 -  4775
chrX_82779993_82783794.rev   A   Score:  336   Residues:   331 -   372
chrX_82779993_82783794.rev   Z   Score: 11406   Residues:     1 -  3802
chrX_82801340_82805593   Z   Score: 12762   Residues:     1 -  4254
chrX_82811154_82817552   Z   Score: 19197   Residues:     1 -  6399
chrX_82844061_82847207   Z   Score: 9441   Residues:     1 -  3147
chrX_82850876_82855103   Z   Score: 12684   Residues:     1 -  4228
chrX_82866921_82870737.rev   Z   Score: 11451   Residues:     1 -  3817
chrX_82882101_82886447   Z   Score: 13041   Residues:     1 -  4347
chrX_82900514_82904983   Z   Score: 13410   Residues:     1 -  4470
chrX_82951874_82953956.rev   Z   Score: 6249   Residues:     1 -  2083
chrX_82993194_82995336   Z   Score: 6429   Residues:     1 -  2143
chrX_82996252_83004756.rev   A   Score:  283   Residues:  8194 -  8240
chrX_82996252_83004756.rev   A   Score:  217   Residues:  4837 -  4867
chrX_82996252_83004756.rev   Z   Score: 25515   Residues:     1 -  8505
chrX_83010305_83013827   Z   Score: 10569   Residues:     1 -  3523
chrX_83016331_83022414   Z   Score: 18252   Residues:     1 -  6084
chrX_83030132_83034875   Z   Score: 14232   Residues:     1 -  4744
chrX_83046693_83051600   Z   Score: 14724   Residues:     1 -  4908
chrX_83098462_83100463.rev   Z   Score: 6006   Residues:     1 -  2002
chrX_83109724_83111414.rev   A   Score:  218   Residues:    57 -   124
chrX_83109724_83111414.rev   Z   Score: 5073   Residues:     1 -  1691
chrX_83144626_83147693.rev   Z   Score: 9204   Residues:     1 -  3068
chrX_83171799_83177018   Z   Score: 15660   Residues:     1 -  5220
chrX_83186657_83190909   Z   Score: 12759   Residues:     1 -  4253
chrX_83203983_83206088   Z   Score: 6318   Residues:     1 -  2106
chrX_83254447_83258080.rev   Z   Score: 10902   Residues:     1 -  3634
chrX_83259195_83261139   A   Score:  251   Residues:  1283 -  1325
chrX_83259195_83261139   Z   Score: 5835   Residues:     1 -  1945
chrX_83340589_83343332.rev   Z   Score: 8232   Residues:     1 -  2744
chrX_83345218_83348975.rev   Z   Score: 11274   Residues:     1 -  3758
chrX_83349884_83354076.rev   A   Score:  231   Residues:  1440 -  1630
chrX_83349884_83354076.rev   Z   Score: 12579   Residues:     1 -  4193
chrX_83373198_83377401   Z   Score: 12609   Residues:     1 -  4203
chrX_83439435_83443759   Z   Score: 12975   Residues:     1 -  4325
chrX_83444953_83450294.rev   A   Score:  306   Residues:  3912 -  3979
chrX_83444953_83450294.rev   Z   Score: 16026   Residues:     1 -  5342
chrX_83452354_83456667.rev   Z   Score: 12942   Residues:     1 -  4314
chrX_83458789_83463121   Z   Score: 12999   Residues:     1 -  4333
chrX_83468448_83470643.rev   Z   Score: 6588   Residues:     1 -  2196
chrX_83482218_83486879   A   Score:  212   Residues:  2400 -  2453
chrX_83482218_83486879   Z   Score: 13986   Residues:     1 -  4662
chrX_83493606_83496889.rev   Z   Score: 9852   Residues:     1 -  3284
chrX_83519639_83523582   A   Score:  222   Residues:   956 -   989
chrX_83519639_83523582   Z   Score: 11832   Residues:     1 -  3944
chrX_83616196_83622591   Z   Score: 19188   Residues:     1 -  6396
chrX_83632400_83638596   A   Score:  243   Residues:  2527 -  2608
chrX_83632400_83638596   Z   Score: 18591   Residues:     1 -  6197
chrX_83639434_83643524.rev   Z   Score: 12273   Residues:     1 -  4091
chrX_83652726_83658589   Z   Score: 17592   Residues:     1 -  5864
chrX_83662466_83668436.rev   Z   Score: 17913   Residues:     1 -  5971
chrX_83681972_83683608.rev   Z   Score: 4911   Residues:     1 -  1637
chrX_83685339_83689575.rev   A   Score:  204   Residues:  1412 -  1532
chrX_83685339_83689575.rev   Z   Score: 12711   Residues:     1 -  4237
chrX_83696309_83701902   A   Score:  209   Residues:  2825 -  2907
chrX_83696309_83701902   Z   Score: 16782   Residues:     1 -  5594
chrX_83711585_83716110.rev   Z   Score: 13578   Residues:     1 -  4526
chrX_83724823_83728375.rev   Z   Score: 10659   Residues:     1 -  3553
chrX_83731918_83736184   Z   Score: 12801   Residues:     1 -  4267
chrX_83785830_83790945.rev   A   Score:  234   Residues:     2 -    58
chrX_83785830_83790945.rev   Z   Score: 15348   Residues:     1 -  5116
chrX_83846904_83849381.rev   Z   Score: 7434   Residues:     1 -  2478
chrX_83853278_83857745   Z   Score: 13404   Residues:     1 -  4468
chrX_83861497_83863732.rev   Z   Score: 6708   Residues:     1 -  2236
chrX_83865187_83867124.rev   Z   Score: 5814   Residues:     1 -  1938
chrX_83940229_83942483.rev   Z   Score: 6765   Residues:     1 -  2255
chrX_83976646_83980520   A   Score:  338   Residues:   872 -  1010
chrX_83976646_83980520   A   Score:  282   Residues:  2400 -  2443
chrX_83976646_83980520   Z   Score: 11625   Residues:     1 -  3875
chrX_83982174_83987784.rev   Z   Score: 16833   Residues:     1 -  5611
chrX_84026761_84032835.rev   Z   Score: 18225   Residues:     1 -  6075
chrX_84071748_84076003.rev   Z   Score: 12768   Residues:     1 -  4256
chrX_84095861_84098344.rev   Z   Score: 7452   Residues:     1 -  2484
chrX_84119475_84127254.rev   Z   Score: 23340   Residues:     1 -  7780
chrX_84138495_84144171.rev   Z   Score: 17031   Residues:     1 -  5677
chrX_84158603_84163097   Z   Score: 13485   Residues:     1 -  4495
chrX_84189049_84193157.rev   Z   Score: 12327   Residues:     1 -  4109
chrX_84207489_84213879   Z   Score: 19173   Residues:     1 -  6391
chrX_84226417_84228188   Z   Score: 5316   Residues:     1 -  1772
chrX_84290317_84292486   Z   Score: 6510   Residues:     1 -  2170
chrX_84295491_84299619   Z   Score: 12387   Residues:     1 -  4129
chrX_84299886_84301864   Z   Score: 5937   Residues:     1 -  1979
chrX_84319312_84321969.rev   Z   Score: 7974   Residues:     1 -  2658
chrX_84372579_84374977.rev   Z   Score: 7197   Residues:     1 -  2399
chrX_84397210_84398876.rev   Z   Score: 5001   Residues:     1 -  1667
chrX_84421628_84427030.rev   Z   Score: 16209   Residues:     1 -  5403
chrX_84455843_84457879.rev   T   Score:  250   Residues:   996 -  1042
chrX_84455843_84457879.rev   Z   Score: 6111   Residues:     1 -  2037
chrX_84457909_84462547.rev   T   Score:  244   Residues:  2719 -  2751
chrX_84457909_84462547.rev   Z   Score: 13917   Residues:     1 -  4639
chrX_84463415_84465657.rev   Z   Score: 6729   Residues:     1 -  2243
chrX_84480528_84489512.rev   Z   Score: 26955   Residues:     1 -  8985
chrX_84526077_84534055.rev   Z   Score: 23937   Residues:     1 -  7979
chrX_84544635_84550399.rev   A   Score:  214   Residues:  1673 -  1705
chrX_84544635_84550399.rev   Z   Score: 17295   Residues:     1 -  5765
chrX_84589864_84598715   A   Score:  661   Residues:  6572 -  6689
chrX_84589864_84598715   Z   Score: 26556   Residues:     1 -  8852
chrX_84606242_84608229.rev   A   Score:  221   Residues:   547 -   620
chrX_84606242_84608229.rev   Z   Score: 5964   Residues:     1 -  1988
chrX_84612516_84616677.rev   Z   Score: 12486   Residues:     1 -  4162
chrX_84616809_84622634.rev   Z   Score: 17478   Residues:     1 -  5826
chrX_84625048_84629817.rev   A   Score:  215   Residues:  3555 -  3590
chrX_84625048_84629817.rev   Z   Score: 14310   Residues:     1 -  4770
chrX_84645703_84650201   Z   Score: 13494   Residues:     1 -  4498
chrX_84656224_84660794   Z   Score: 13713   Residues:     1 -  4571
chrX_84673919_84680932.rev   Z   Score: 21042   Residues:     1 -  7014
chrX_84697584_84702588.rev   Z   Score: 15015   Residues:     1 -  5005
chrX_84703948_84709397   A   Score:  253   Residues:  3695 -  3738
chrX_84703948_84709397   Z   Score: 16350   Residues:     1 -  5450
chrX_84714027_84720319.rev   Z   Score: 18879   Residues:     1 -  6293
chrX_84729039_84732037.rev   Z   Score: 8997   Residues:     1 -  2999
chrX_84749721_84751757   Z   Score: 6111   Residues:     1 -  2037
chrX_84754581_84760362.rev   Z   Score: 17346   Residues:     1 -  5782
chrX_84774732_84779717.rev   Z   Score: 14958   Residues:     1 -  4986
chrX_84789930_84795336.rev   Z   Score: 16221   Residues:     1 -  5407
chrX_84800350_84806349   Z   Score: 18000   Residues:     1 -  6000
chrX_84808539_84819517.rev   A   Score:  217   Residues:  8141 -  8196
chrX_84808539_84819517.rev   Z   Score: 32937   Residues:     1 - 10979
chrX_84828293_84834684.rev   Z   Score: 19176   Residues:     1 -  6392
chrX_84852663_84857844.rev   Z   Score: 15546   Residues:     1 -  5182
chrX_84883386_84888491   Z   Score: 15318   Residues:     1 -  5106
chrX_85034571_85036752   Z   Score: 6546   Residues:     1 -  2182
chrX_85063084_85069317   Z   Score: 18702   Residues:     1 -  6234
chrX_85147924_85150889   Z   Score: 8898   Residues:     1 -  2966
chrX_85166829_85171647   A   Score:  208   Residues:  3398 -  3459
chrX_85166829_85171647   Z   Score: 14457   Residues:     1 -  4819
chrX_85174719_85180997.rev   A   Score:  201   Residues:   396 -   481
chrX_85174719_85180997.rev   Z   Score: 18837   Residues:     1 -  6279
chrX_85226230_85230190.rev   Z   Score: 11883   Residues:     1 -  3961
chrX_85256572_85262345   A   Score:  288   Residues:  1269 -  1313
chrX_85256572_85262345   Z   Score: 17322   Residues:     1 -  5774
chrX_85306626_85311110   Z   Score: 13455   Residues:     1 -  4485
chrX_85350821_85357073.rev   Z   Score: 18759   Residues:     1 -  6253
chrX_85416430_85418321.rev   Z   Score: 5676   Residues:     1 -  1892
chrX_85456787_85465091   Z   Score: 24915   Residues:     1 -  8305
chrX_85502905_85506452.rev   Z   Score: 10644   Residues:     1 -  3548
chrX_85507694_85510337.rev   Z   Score: 7932   Residues:     1 -  2644
chrX_85534764_85539342.rev   Z   Score: 13737   Residues:     1 -  4579
chrX_85577984_85583149.rev   Z   Score: 15498   Residues:     1 -  5166
chrX_85648282_85650798.rev   Z   Score: 7551   Residues:     1 -  2517
chrX_85652112_85658925.rev   A   Score:  208   Residues:  4335 -  4383
chrX_85652112_85658925.rev   Z   Score: 20442   Residues:     1 -  6814
chrX_85677168_85679177.rev   Z   Score: 6030   Residues:     1 -  2010
chrX_85693324_85700317   A   Score:  325   Residues:  5024 -  5074
chrX_85693324_85700317   A   Score:  200   Residues:   893 -   991
chrX_85693324_85700317   Z   Score: 20982   Residues:     1 -  6994
chrX_85701882_85706960   Z   Score: 15237   Residues:     1 -  5079
chrX_85762680_85766317   Z   Score: 10914   Residues:     1 -  3638
chrX_85767191_85771448   Z   Score: 12774   Residues:     1 -  4258
chrX_85778897_85781127.rev   A   Score:  312   Residues:    24 -    67
chrX_85778897_85781127.rev   Z   Score: 6693   Residues:     1 -  2231
chrX_85807154_85812041.rev   Z   Score: 14664   Residues:     1 -  4888
chrX_85815817_85818784.rev   Z   Score: 8904   Residues:     1 -  2968
chrX_85825629_85827629.rev   A   Score:  280   Residues:   756 -   807
chrX_85825629_85827629.rev   Z   Score: 6003   Residues:     1 -  2001
chrX_85908959_85910725.rev   Z   Score: 5301   Residues:     1 -  1767
chrX_85910845_85913613.rev   Z   Score: 8307   Residues:     1 -  2769
chrX_85918436_85922096   Z   Score: 10983   Residues:     1 -  3661
chrX_85938984_85943264.rev   Z   Score: 12843   Residues:     1 -  4281
chrX_85955414_85957199.rev   Z   Score: 5358   Residues:     1 -  1786
chrX_85992084_85996881.rev   Z   Score: 14394   Residues:     1 -  4798
chrX_86013192_86015644   Z   Score: 7359   Residues:     1 -  2453
chrX_86016958_86019136.rev   Z   Score: 6537   Residues:     1 -  2179
chrX_86028377_86036550   Z   Score: 24522   Residues:     1 -  8174
chrX_86072163_86077167   Z   Score: 15015   Residues:     1 -  5005
chrX_86092620_86094260.rev   A   Score:  200   Residues:   450 -   504
chrX_86092620_86094260.rev   Z   Score: 4923   Residues:     1 -  1641
chrX_86114914_86118726   T   Score:  217   Residues:  1673 -  1824
chrX_86114914_86118726   Z   Score: 11439   Residues:     1 -  3813
chrX_86119161_86120870   Z   Score: 5130   Residues:     1 -  1710
chrX_86139214_86141241.rev   Z   Score: 6084   Residues:     1 -  2028
chrX_86145703_86148866   Z   Score: 9492   Residues:     1 -  3164
chrX_86154476_86159480.rev   Z   Score: 15015   Residues:     1 -  5005
chrX_86171217_86172933   Z   Score: 5151   Residues:     1 -  1717
chrX_86176955_86183235   Z   Score: 18843   Residues:     1 -  6281
chrX_86191381_86195434   Z   Score: 12162   Residues:     1 -  4054
chrX_86196281_86200749   Z   Score: 13407   Residues:     1 -  4469
chrX_86202138_86203757.rev   Z   Score: 4860   Residues:     1 -  1620
chrX_86212134_86215586.rev   Z   Score: 10359   Residues:     1 -  3453
chrX_86256174_86258395   Z   Score: 6666   Residues:     1 -  2222
chrX_86274818_86277109.rev   Z   Score: 6876   Residues:     1 -  2292
chrX_86307455_86309603.rev   Z   Score: 6447   Residues:     1 -  2149
chrX_86315007_86320674   A   Score:  227   Residues:  2468 -  2515
chrX_86315007_86320674   Z   Score: 17004   Residues:     1 -  5668
chrX_86322932_86324625   Z   Score: 5082   Residues:     1 -  1694
chrX_86355189_86358570.rev   Z   Score: 10146   Residues:     1 -  3382
chrX_86363109_86366703.rev   A   Score:  322   Residues:  1225 -  1273
chrX_86363109_86366703.rev   Z   Score: 10785   Residues:     1 -  3595
chrX_86390677_86392589   Z   Score: 5739   Residues:     1 -  1913
chrX_86395194_86397247.rev   Z   Score: 6162   Residues:     1 -  2054
chrX_86406934_86409058.rev   Z   Score: 6375   Residues:     1 -  2125
chrX_86420473_86424931   Z   Score: 13377   Residues:     1 -  4459
chrX_86425817_86427607   Z   Score: 5373   Residues:     1 -  1791
chrX_86476967_86479736.rev   A   Score:  303   Residues:  1164 -  1231
chrX_86476967_86479736.rev   Z   Score: 8310   Residues:     1 -  2770
chrX_86497933_86502531.rev   Z   Score: 13797   Residues:     1 -  4599
chrX_86504523_86510337.rev   Z   Score: 17445   Residues:     1 -  5815
chrX_86516097_86520943   Z   Score: 14541   Residues:     1 -  4847
chrX_86530009_86533651   Z   Score: 10926   Residues:     1 -  3642
chrX_86609519_86613950   A   Score:  224   Residues:   454 -   527
chrX_86609519_86613950   Z   Score: 13296   Residues:     1 -  4432
chrX_86628868_86630875   T   Score:  328   Residues:   645 -   690
chrX_86628868_86630875   Z   Score: 6024   Residues:     1 -  2008
chrX_86646400_86650716   A   Score:  325   Residues:  3528 -  3623
chrX_86646400_86650716   Z   Score: 12951   Residues:     1 -  4317
chrX_86665173_86667983.rev   A   Score:  227   Residues:  2382 -  2417
chrX_86665173_86667983.rev   Z   Score: 8433   Residues:     1 -  2811
chrX_86818915_86823711.rev   Z   Score: 14391   Residues:     1 -  4797
chrX_86838765_86845456   Z   Score: 20076   Residues:     1 -  6692
chrX_86860377_86862733.rev   Z   Score: 7071   Residues:     1 -  2357
chrX_86882053_86888316   Z   Score: 18792   Residues:     1 -  6264
chrX_86889342_86895319.rev   Z   Score: 17934   Residues:     1 -  5978
chrX_86940467_86945049.rev   Z   Score: 13749   Residues:     1 -  4583
chrX_86978423_86980482   Z   Score: 6180   Residues:     1 -  2060
chrX_87014063_87021630   Z   Score: 22704   Residues:     1 -  7568
chrX_87023012_87027636   A   Score:  201   Residues:  2243 -  2358
chrX_87023012_87027636   Z   Score: 13875   Residues:     1 -  4625
chrX_87038131_87042421   Z   Score: 12873   Residues:     1 -  4291
chrX_87083823_87085869   Z   Score: 6141   Residues:     1 -  2047
chrX_87102288_87106826   A   Score:  227   Residues:  1954 -  1996
chrX_87102288_87106826   A   Score:  213   Residues:  1415 -  1540
chrX_87102288_87106826   Z   Score: 13617   Residues:     1 -  4539
chrX_87116415_87118163   Z   Score: 5247   Residues:     1 -  1749
chrX_87135454_87137512   Z   Score: 6177   Residues:     1 -  2059
chrX_87146895_87151406.rev   Z   Score: 13536   Residues:     1 -  4512
chrX_87181658_87184837   Z   Score: 9540   Residues:     1 -  3180
chrX_87243026_87246073.rev   A   Score:  248   Residues:  2399 -  2447
chrX_87243026_87246073.rev   Z   Score: 9144   Residues:     1 -  3048
chrX_87251009_87260233   A   Score:  228   Residues:  2440 -  2470
chrX_87251009_87260233   A   Score:  206   Residues:  1443 -  1554
chrX_87251009_87260233   Z   Score: 27675   Residues:     1 -  9225
chrX_87268532_87274812   Z   Score: 18843   Residues:     1 -  6281
chrX_87284627_87286846.rev   Z   Score: 6660   Residues:     1 -  2220
chrX_87292638_87294581   Z   Score: 5832   Residues:     1 -  1944
chrX_87307448_87310924.rev   Z   Score: 10431   Residues:     1 -  3477
chrX_87321214_87324652.rev   Z   Score: 10317   Residues:     1 -  3439
chrX_87350263_87352213   Z   Score: 5853   Residues:     1 -  1951
chrX_87364224_87366032.rev   Z   Score: 5427   Residues:     1 -  1809
chrX_87369364_87371485.rev   Z   Score: 6366   Residues:     1 -  2122
chrX_87372979_87375393   Z   Score: 7245   Residues:     1 -  2415
chrX_87385236_87387805.rev   Z   Score: 7710   Residues:     1 -  2570
chrX_87416399_87419714   Z   Score: 9948   Residues:     1 -  3316
chrX_87420059_87421736   Z   Score: 5034   Residues:     1 -  1678
chrX_87446509_87451522   A   Score:  320   Residues:   243 -   282
chrX_87446509_87451522   A   Score:  219   Residues:  2173 -  2305
chrX_87446509_87451522   Z   Score: 15042   Residues:     1 -  5014
chrX_87552160_87556368.rev   A   Score:  307   Residues:    20 -    99
chrX_87552160_87556368.rev   A   Score:  210   Residues:  1210 -  1302
chrX_87552160_87556368.rev   Z   Score: 12627   Residues:     1 -  4209
chrX_87580844_87584532   Z   Score: 11067   Residues:     1 -  3689
chrX_87604589_87606325   Z   Score: 5211   Residues:     1 -  1737
chrX_87607780_87609405.rev   Z   Score: 4878   Residues:     1 -  1626
chrX_87639344_87641889   Z   Score: 7638   Residues:     1 -  2546
chrX_87646594_87651674   Z   Score: 15243   Residues:     1 -  5081
chrX_87655013_87656922   Z   Score: 5730   Residues:     1 -  1910
chrX_87671003_87672828   Z   Score: 5478   Residues:     1 -  1826
chrX_87672919_87674524   Z   Score: 4818   Residues:     1 -  1606
chrX_87675985_87681063   T   Score:  290   Residues:  2548 -  2587
chrX_87675985_87681063   Z   Score: 15237   Residues:     1 -  5079
chrX_87686604_87691721   Z   Score: 15354   Residues:     1 -  5118
chrX_87692988_87697237   A   Score:  217   Residues:  1472 -  1546
chrX_87692988_87697237   Z   Score: 12750   Residues:     1 -  4250
chrX_87714925_87716947   A   Score:  270   Residues:   169 -   259
chrX_87714925_87716947   Z   Score: 6069   Residues:     1 -  2023
chrX_87724774_87727209.rev   A   Score:  243   Residues:  1220 -  1268
chrX_87724774_87727209.rev   Z   Score: 7308   Residues:     1 -  2436
chrX_87781318_87784067.rev   Z   Score: 8250   Residues:     1 -  2750
chrX_87827743_87830848   Z   Score: 9318   Residues:     1 -  3106
chrX_87838801_87841955.rev   Z   Score: 9465   Residues:     1 -  3155
chrX_87842812_87849208.rev   Z   Score: 19191   Residues:     1 -  6397
chrX_87861056_87866717   Z   Score: 16986   Residues:     1 -  5662
chrX_87867364_87869471   Z   Score: 6324   Residues:     1 -  2108
chrX_87872838_87874769.rev   Z   Score: 5796   Residues:     1 -  1932
chrX_87879193_87881013.rev   Z   Score: 5463   Residues:     1 -  1821
chrX_87918243_87920432.rev   Z   Score: 6570   Residues:     1 -  2190
chrX_87936105_87938246.rev   Z   Score: 6426   Residues:     1 -  2142
chrX_87951229_87952816.rev   Z   Score: 4764   Residues:     1 -  1588
chrX_87958270_87964237   Z   Score: 17904   Residues:     1 -  5968
chrX_88026769_88034495   Z   Score: 23181   Residues:     1 -  7727
chrX_88079201_88081248   Z   Score: 6144   Residues:     1 -  2048
chrX_88087846_88091312.rev   Z   Score: 10401   Residues:     1 -  3467
chrX_88101907_88105829.rev   Z   Score: 11769   Residues:     1 -  3923
chrX_88182650_88188079.rev   A   Score:  272   Residues:  4677 -  4710
chrX_88182650_88188079.rev   Z   Score: 16290   Residues:     1 -  5430
chrX_88190036_88193157.rev   A   Score:  214   Residues:  1990 -  2039
chrX_88190036_88193157.rev   Z   Score: 9366   Residues:     1 -  3122
chrX_88219192_88225211.rev   Z   Score: 18060   Residues:     1 -  6020
chrX_88228107_88232474   A   Score:  210   Residues:  1460 -  1584
chrX_88228107_88232474   Z   Score: 13104   Residues:     1 -  4368
chrX_88289379_88291571   Z   Score: 6579   Residues:     1 -  2193
chrX_88305780_88308080.rev   A   Score:  240   Residues:  1267 -  1305
chrX_88305780_88308080.rev   Z   Score: 6903   Residues:     1 -  2301
chrX_88310574_88312591.rev   Z   Score: 6054   Residues:     1 -  2018
chrX_88325756_88328078.rev   Z   Score: 6969   Residues:     1 -  2323
chrX_88339292_88344286   Z   Score: 14985   Residues:     1 -  4995
chrX_88353274_88359550   Z   Score: 18831   Residues:     1 -  6277
chrX_88381730_88386090   Z   Score: 13083   Residues:     1 -  4361
chrX_88396016_88399116   Z   Score: 9303   Residues:     1 -  3101
chrX_88405899_88411359.rev   A   Score:  227   Residues:  3693 -  3740
chrX_88405899_88411359.rev   Z   Score: 16383   Residues:     1 -  5461
chrX_88431291_88433960   Z   Score: 8010   Residues:     1 -  2670
chrX_88455522_88459773.rev   Z   Score: 12756   Residues:     1 -  4252
chrX_88467475_88469266.rev   Z   Score: 5376   Residues:     1 -  1792
chrX_88474555_88476559   Z   Score: 6015   Residues:     1 -  2005
chrX_88490736_88493107.rev   Z   Score: 7116   Residues:     1 -  2372
chrX_88510262_88511981.rev   Z   Score: 5160   Residues:     1 -  1720
chrX_88553819_88556792.rev   Z   Score: 8922   Residues:     1 -  2974
chrX_88580930_88585847.rev   Z   Score: 14754   Residues:     1 -  4918
chrX_88669267_88671275   Z   Score: 6027   Residues:     1 -  2009
chrX_88687693_88692267.rev   A   Score:  242   Residues:  1715 -  1840
chrX_88687693_88692267.rev   Z   Score: 13725   Residues:     1 -  4575
chrX_88701185_88706524   A   Score:  220   Residues:  1974 -  2139
chrX_88701185_88706524   Z   Score: 16020   Residues:     1 -  5340
chrX_88722652_88726266.rev   Z   Score: 10845   Residues:     1 -  3615
chrX_88736613_88741219   Z   Score: 13821   Residues:     1 -  4607
chrX_88749365_88753936.rev   Z   Score: 13716   Residues:     1 -  4572
chrX_88785094_88789713.rev   A   Score:  570   Residues:  1406 -  1490
chrX_88785094_88789713.rev   T   Score:  207   Residues:   728 -   771
chrX_88785094_88789713.rev   Z   Score: 13860   Residues:     1 -  4620
chrX_88808552_88812183.rev   A   Score:  218   Residues:  2104 -  2159
chrX_88808552_88812183.rev   Z   Score: 10896   Residues:     1 -  3632
chrX_88841654_88845871   Z   Score: 12654   Residues:     1 -  4218
chrX_88882030_88884925.rev   Z   Score: 8688   Residues:     1 -  2896
chrX_88946730_88949753.rev   Z   Score: 9072   Residues:     1 -  3024
chrX_88963890_88967356   Z   Score: 10401   Residues:     1 -  3467
chrX_88968683_88970880   Z   Score: 6594   Residues:     1 -  2198
chrX_88992892_88999842.rev   Z   Score: 20853   Residues:     1 -  6951
chrX_89060387_89062566.rev   Z   Score: 6540   Residues:     1 -  2180
chrX_89063409_89068177.rev   Z   Score: 14307   Residues:     1 -  4769
chrX_89071851_89077066.rev   Z   Score: 15648   Residues:     1 -  5216
chrX_89083354_89087801   Z   Score: 13341   Residues:     1 -  4447
chrX_89128911_89134837.rev   A   Score:  240   Residues:  4311 -  4340
chrX_89128911_89134837.rev   Z   Score: 17781   Residues:     1 -  5927
chrX_89161883_89167687.rev   Z   Score: 17415   Residues:     1 -  5805
chrX_89177557_89179210   Z   Score: 4962   Residues:     1 -  1654
chrX_89275312_89277028   Z   Score: 5151   Residues:     1 -  1717
chrX_89308513_89319759   Z   Score: 33741   Residues:     1 - 11247
chrX_89388764_89395050   Z   Score: 18861   Residues:     1 -  6287
chrX_89423961_89429302.rev   A   Score:  216   Residues:  3917 -  3943
chrX_89423961_89429302.rev   T   Score:  220   Residues:   349 -   399
chrX_89423961_89429302.rev   Z   Score: 16026   Residues:     1 -  5342
chrX_89467336_89470312.rev   Z   Score: 8931   Residues:     1 -  2977
chrX_89470566_89474814.rev   A   Score:  234   Residues:  1388 -  1534
chrX_89470566_89474814.rev   Z   Score: 12747   Residues:     1 -  4249
chrX_89483323_89489473   Z   Score: 18453   Residues:     1 -  6151
chrX_89523428_89525760.rev   Z   Score: 6999   Residues:     1 -  2333
chrX_89569751_89575413   A   Score:  276   Residues:  3152 -  3227
chrX_89569751_89575413   Z   Score: 16989   Residues:     1 -  5663
chrX_89576158_89580406   A   Score:  202   Residues:  3101 -  3141
chrX_89576158_89580406   Z   Score: 12747   Residues:     1 -  4249
chrX_89604358_89608868   A   Score:  298   Residues:  1618 -  1658
chrX_89604358_89608868   Z   Score: 13533   Residues:     1 -  4511
chrX_89609734_89614553   A   Score:  273   Residues:  2004 -  2130
chrX_89609734_89614553   Z   Score: 14460   Residues:     1 -  4820
chrX_89649916_89652040.rev   Z   Score: 6375   Residues:     1 -  2125
chrX_89654437_89658860.rev   Z   Score: 13272   Residues:     1 -  4424
chrX_89675281_89678807.rev   A   Score:  236   Residues:   820 -   943
chrX_89675281_89678807.rev   Z   Score: 10581   Residues:     1 -  3527
chrX_89694851_89699779   Z   Score: 14787   Residues:     1 -  4929
chrX_89717610_89721800.rev   Z   Score: 12573   Residues:     1 -  4191
chrX_89786681_89789935   Z   Score: 9765   Residues:     1 -  3255
chrX_89798546_89804299   A   Score:  218   Residues:  2930 -  3040
chrX_89798546_89804299   Z   Score: 17262   Residues:     1 -  5754
chrX_89809742_89813643   Z   Score: 11706   Residues:     1 -  3902
chrX_89814657_89817369   Z   Score: 8139   Residues:     1 -  2713
chrX_89877488_89879068.rev   Z   Score: 4743   Residues:     1 -  1581
chrX_89896875_89903265   Z   Score: 19173   Residues:     1 -  6391
chrX_89904190_89908425.rev   Z   Score: 12708   Residues:     1 -  4236
chrX_89926215_89935052   Z   Score: 26514   Residues:     1 -  8838
chrX_89938873_89944136.rev   Z   Score: 15792   Residues:     1 -  5264
chrX_89958394_89962606.rev   A   Score:  217   Residues:  1442 -  1556
chrX_89958394_89962606.rev   Z   Score: 12639   Residues:     1 -  4213
chrX_89974057_89975686.rev   Z   Score: 4890   Residues:     1 -  1630
chrX_90044744_90050556   C   Score:  208   Residues:  5494 -  5549
chrX_90044744_90050556   Z   Score: 17439   Residues:     1 -  5813
chrX_90050873_90053239.rev   Z   Score: 7101   Residues:     1 -  2367
chrX_90084785_90087083   Z   Score: 6897   Residues:     1 -  2299
chrX_90095179_90102245.rev   Z   Score: 21201   Residues:     1 -  7067
chrX_90105084_90106890   Z   Score: 5421   Residues:     1 -  1807
chrX_90128198_90132968   Z   Score: 14313   Residues:     1 -  4771
chrX_90133616_90135476   Z   Score: 5583   Residues:     1 -  1861
chrX_90165280_90169864.rev   A   Score:  201   Residues:  1056 -  1084
chrX_90165280_90169864.rev   Z   Score: 13755   Residues:     1 -  4585
chrX_90215491_90219317   Z   Score: 11481   Residues:     1 -  3827
chrX_90230302_90234682.rev   A   Score:  212   Residues:  2109 -  2162
chrX_90230302_90234682.rev   Z   Score: 13143   Residues:     1 -  4381
chrX_90248795_90256503   A   Score:  233   Residues:  2177 -  2218
chrX_90248795_90256503   Z   Score: 23127   Residues:     1 -  7709
chrX_90280780_90283169   Z   Score: 7170   Residues:     1 -  2390
chrX_90299805_90304546.rev   T   Score:  513   Residues:  3645 -  3745
chrX_90299805_90304546.rev   Z   Score: 14226   Residues:     1 -  4742
chrX_90355889_90362866   A   Score:  204   Residues:  5850 -  5881
chrX_90355889_90362866   Z   Score: 20934   Residues:     1 -  6978
chrX_90381856_90385611   Z   Score: 11268   Residues:     1 -  3756
chrX_90415648_90417267   Z   Score: 4860   Residues:     1 -  1620
chrX_90429489_90432991.rev   A   Score:  200   Residues:   786 -   897
chrX_90429489_90432991.rev   Z   Score: 10509   Residues:     1 -  3503
chrX_90446179_90450451   A   Score:  218   Residues:  1454 -  1573
chrX_90446179_90450451   Z   Score: 12816   Residues:     1 -  4272
chrX_90464694_90468391   Z   Score: 11094   Residues:     1 -  3698
chrX_90470259_90474868   A   Score:  249   Residues:   281 -   319
chrX_90470259_90474868   Z   Score: 13830   Residues:     1 -  4610
chrX_90492669_90494488.rev   Z   Score: 5460   Residues:     1 -  1820
chrX_90510318_90512174   Z   Score: 5571   Residues:     1 -  1857
chrX_90528603_90530621.rev   T   Score:  271   Residues:    70 -   189
chrX_90528603_90530621.rev   Z   Score: 6057   Residues:     1 -  2019
chrX_90561950_90566822   Z   Score: 14619   Residues:     1 -  4873
chrX_90568291_90571718   Z   Score: 10284   Residues:     1 -  3428
chrX_90589927_90594686.rev   Z   Score: 14280   Residues:     1 -  4760
chrX_90600761_90605955   A   Score:  248   Residues:   471 -   511
chrX_90600761_90605955   Z   Score: 15585   Residues:     1 -  5195
chrX_90643333_90646378.rev   Z   Score: 9138   Residues:     1 -  3046
chrX_90648626_90652886   Z   Score: 12783   Residues:     1 -  4261
chrX_90679272_90683595.rev   Z   Score: 12972   Residues:     1 -  4324
chrX_90691158_90694145   Z   Score: 8964   Residues:     1 -  2988
chrX_90704632_90706622.rev   Z   Score: 5973   Residues:     1 -  1991
chrX_90747118_90752743   Z   Score: 16878   Residues:     1 -  5626
chrX_90765598_90767464   Z   Score: 5601   Residues:     1 -  1867
chrX_90778482_90783145   Z   Score: 13992   Residues:     1 -  4664
chrX_90789200_90795001.rev   Z   Score: 17403   Residues:     1 -  5801
chrX_90813445_90819720   Z   Score: 18828   Residues:     1 -  6276
chrX_90881067_90887346.rev   Z   Score: 18840   Residues:     1 -  6280
chrX_90919864_90922993.rev   Z   Score: 9390   Residues:     1 -  3130
chrX_91020692_91022683.rev   Z   Score: 5976   Residues:     1 -  1992
chrX_91032843_91034532.rev   Z   Score: 5070   Residues:     1 -  1690
chrX_91055543_91058173.rev   T   Score:  233   Residues:  1779 -  1815
chrX_91055543_91058173.rev   Z   Score: 7893   Residues:     1 -  2631
chrX_91061973_91066869.rev   A   Score:  202   Residues:  4242 -  4270
chrX_91061973_91066869.rev   A   Score:  201   Residues:   934 -   993
chrX_91061973_91066869.rev   Z   Score: 14691   Residues:     1 -  4897
chrX_91121725_91124177.rev   Z   Score: 7359   Residues:     1 -  2453
chrX_91126255_91131138.rev   Z   Score: 14652   Residues:     1 -  4884
chrX_91275706_91282104   Z   Score: 19197   Residues:     1 -  6399
chrX_91303509_91305278.rev   Z   Score: 5310   Residues:     1 -  1770
chrX_91366596_91370539   Z   Score: 11832   Residues:     1 -  3944
chrX_91423026_91425807.rev   Z   Score: 8346   Residues:     1 -  2782
chrX_91503901_91507053.rev   A   Score:  200   Residues:   694 -   718
chrX_91503901_91507053.rev   Z   Score: 9459   Residues:     1 -  3153
chrX_91521663_91523580   Z   Score: 5754   Residues:     1 -  1918
chrX_91532504_91534746.rev   Z   Score: 6729   Residues:     1 -  2243
chrX_91565525_91569092.rev   A   Score:  316   Residues:  2774 -  2863
chrX_91565525_91569092.rev   A   Score:  277   Residues:  1712 -  1774
chrX_91565525_91569092.rev   Z   Score: 10704   Residues:     1 -  3568
chrX_91657074_91660105   Z   Score: 9096   Residues:     1 -  3032
chrX_91665996_91668576   A   Score:  206   Residues:  1381 -  1407
chrX_91665996_91668576   Z   Score: 7743   Residues:     1 -  2581
chrX_91670992_91675526.rev   Z   Score: 13605   Residues:     1 -  4535
chrX_91709111_91710975   Z   Score: 5595   Residues:     1 -  1865
chrX_91732596_91734646   Z   Score: 6153   Residues:     1 -  2051
chrX_91776588_91782566   A   Score:  281   Residues:  2401 -  2475
chrX_91776588_91782566   Z   Score: 17937   Residues:     1 -  5979
chrX_91794809_91796541   Z   Score: 5199   Residues:     1 -  1733
chrX_91806435_91810869.rev   Z   Score: 13305   Residues:     1 -  4435
chrX_91835083_91840426   A   Score:  207   Residues:  2538 -  2762
chrX_91835083_91840426   Z   Score: 16032   Residues:     1 -  5344
chrX_91841232_91843731   Z   Score: 7500   Residues:     1 -  2500
chrX_91856828_91863705   A   Score:  279   Residues:  5331 -  5390
chrX_91856828_91863705   A   Score:  241   Residues:   291 -   496
chrX_91856828_91863705   A   Score:  203   Residues:  3715 -  3782
chrX_91856828_91863705   R   Score:  333   Residues:   298 -   457
chrX_91856828_91863705   G   Score:  672   Residues:   314 -   452
chrX_91856828_91863705   Z   Score: 20634   Residues:     1 -  6878
chrX_91875331_91877573   Z   Score: 6729   Residues:     1 -  2243
chrX_91993713_91995663   Z   Score: 5853   Residues:     1 -  1951
chrX_92004623_92008769.rev   Z   Score: 12441   Residues:     1 -  4147
chrX_92030321_92034465.rev   Z   Score: 12435   Residues:     1 -  4145
chrX_92062979_92071844.rev   Z   Score: 26598   Residues:     1 -  8866
chrX_92089282_92090895   T   Score:  213   Residues:  1171 -  1217
chrX_92089282_92090895   Z   Score: 4842   Residues:     1 -  1614
chrX_92111533_92114659.rev   A   Score:  211   Residues:    46 -   159
chrX_92111533_92114659.rev   Z   Score: 9381   Residues:     1 -  3127
chrX_92120883_92127227   Z   Score: 19035   Residues:     1 -  6345
chrX_92134523_92138788   Z   Score: 12798   Residues:     1 -  4266
chrX_92144925_92147700.rev   Z   Score: 8328   Residues:     1 -  2776
chrX_92165172_92169528.rev   Z   Score: 13071   Residues:     1 -  4357
chrX_92177842_92180013   Z   Score: 6516   Residues:     1 -  2172
chrX_92190595_92192588.rev   Z   Score: 5982   Residues:     1 -  1994
chrX_92193389_92197572   Z   Score: 12552   Residues:     1 -  4184
chrX_92219338_92221070.rev   Z   Score: 5199   Residues:     1 -  1733
chrX_92230193_92234308   A   Score:  202   Residues:   417 -   491
chrX_92230193_92234308   Z   Score: 12348   Residues:     1 -  4116
chrX_92254243_92259184   Z   Score: 14826   Residues:     1 -  4942
chrX_92267297_92270345   Z   Score: 9147   Residues:     1 -  3049
chrX_92300606_92305657   Z   Score: 15156   Residues:     1 -  5052
chrX_92357315_92363110   Z   Score: 17388   Residues:     1 -  5796
chrX_92383986_92385839   Z   Score: 5562   Residues:     1 -  1854
chrX_92419110_92421374   Z   Score: 6795   Residues:     1 -  2265
chrX_92427328_92432337.rev   Z   Score: 15030   Residues:     1 -  5010
chrX_92501214_92505065   Z   Score: 11556   Residues:     1 -  3852
chrX_92509881_92513937.rev   Z   Score: 12171   Residues:     1 -  4057
chrX_92530652_92535606   A   Score:  222   Residues:  3191 -  3249
chrX_92530652_92535606   Z   Score: 14865   Residues:     1 -  4955
chrX_92554865_92564013   A   Score:  310   Residues:  2441 -  2480
chrX_92554865_92564013   Z   Score: 27447   Residues:     1 -  9149
chrX_92568180_92571494   A   Score:  291   Residues:  2214 -  2375
chrX_92568180_92571494   Z   Score: 9945   Residues:     1 -  3315
chrX_92606811_92609142   A   Score:  215   Residues:   545 -   589
chrX_92606811_92609142   Z   Score: 6996   Residues:     1 -  2332
chrX_92629775_92631567.rev   Z   Score: 5379   Residues:     1 -  1793
chrX_92660512_92662517   Z   Score: 6018   Residues:     1 -  2006
chrX_92691158_92694376   Z   Score: 9657   Residues:     1 -  3219
chrX_92700879_92702971   A   Score:  240   Residues:  1769 -  1798
chrX_92700879_92702971   T   Score:  208   Residues:    93 -   127
chrX_92700879_92702971   Z   Score: 6279   Residues:     1 -  2093
chrX_92707681_92710122   Z   Score: 7326   Residues:     1 -  2442
chrX_92723294_92727507   A   Score:  231   Residues:   611 -   652
chrX_92723294_92727507   Z   Score: 12642   Residues:     1 -  4214
chrX_92738767_92740457.rev   Z   Score: 5073   Residues:     1 -  1691
chrX_92744410_92746023.rev   Z   Score: 4842   Residues:     1 -  1614
chrX_92751612_92753509.rev   Z   Score: 5694   Residues:     1 -  1898
chrX_92795194_92799454.rev   Z   Score: 12783   Residues:     1 -  4261
chrX_92898818_92900821.rev   Z   Score: 6012   Residues:     1 -  2004
chrX_92901750_92903773.rev   Z   Score: 6072   Residues:     1 -  2024
chrX_92944580_92948799.rev   Z   Score: 12660   Residues:     1 -  4220
chrX_92975252_92977519   Z   Score: 6804   Residues:     1 -  2268
chrX_92978924_92980975   Z   Score: 6156   Residues:     1 -  2052
chrX_92995311_92996933.rev   Z   Score: 4869   Residues:     1 -  1623
chrX_93000386_93006795   Z   Score: 19230   Residues:     1 -  6410
chrX_93011903_93015183.rev   Z   Score: 9843   Residues:     1 -  3281
chrX_93057884_93062657.rev   A   Score:  202   Residues:  2626 -  2694
chrX_93057884_93062657.rev   Z   Score: 14322   Residues:     1 -  4774
chrX_93097335_93099136.rev   Z   Score: 5406   Residues:     1 -  1802
chrX_93138554_93140145   Z   Score: 4776   Residues:     1 -  1592
chrX_93209613_93213058   Z   Score: 10338   Residues:     1 -  3446
chrX_93216425_93218724.rev   Z   Score: 6900   Residues:     1 -  2300
chrX_93319427_93324903   A   Score:  253   Residues:  2536 -  2665
chrX_93319427_93324903   Z   Score: 16431   Residues:     1 -  5477
chrX_93327523_93329706   Z   Score: 6552   Residues:     1 -  2184
chrX_93341116_93345301.rev   A   Score:  246   Residues:  2931 -  2984
chrX_93341116_93345301.rev   A   Score:  233   Residues:  1345 -  1436
chrX_93341116_93345301.rev   Z   Score: 12555   Residues:     1 -  4185
chrX_93358068_93362394.rev   A   Score:  219   Residues:  2051 -  2085
chrX_93358068_93362394.rev   A   Score:  218   Residues:  1458 -  1570
chrX_93358068_93362394.rev   Z   Score: 12981   Residues:     1 -  4327
chrX_93433164_93434802   Z   Score: 4917   Residues:     1 -  1639
chrX_93455125_93459085.rev   A   Score:  356   Residues:   462 -   550
chrX_93455125_93459085.rev   A   Score:  201   Residues:  1752 -  1785
chrX_93455125_93459085.rev   Z   Score: 11883   Residues:     1 -  3961
chrX_93525843_93528120   Z   Score: 6834   Residues:     1 -  2278
chrX_93541926_93546589.rev   A   Score:  352   Residues:  2203 -  2246
chrX_93541926_93546589.rev   A   Score:  205   Residues:  4309 -  4340
chrX_93541926_93546589.rev   Z   Score: 13992   Residues:     1 -  4664
chrX_93566526_93568207   Z   Score: 5046   Residues:     1 -  1682
chrX_93586024_93587951   Z   Score: 5781   Residues:     1 -  1927
chrX_93622076_93626208.rev   Z   Score: 12399   Residues:     1 -  4133
chrX_93641791_93646197   A   Score:  257   Residues:   439 -   506
chrX_93641791_93646197   T   Score:  208   Residues:  1188 -  1213
chrX_93641791_93646197   Z   Score: 13221   Residues:     1 -  4407
chrX_93655157_93656919   Z   Score: 5289   Residues:     1 -  1763
chrX_93668316_93672552.rev   Z   Score: 12711   Residues:     1 -  4237
chrX_93709093_93711319.rev   Z   Score: 6681   Residues:     1 -  2227
chrX_93730806_93733374.rev   A   Score:  262   Residues:  1353 -  1386
chrX_93730806_93733374.rev   Z   Score: 7707   Residues:     1 -  2569
chrX_93741840_93745123.rev   A   Score:  269   Residues:  2241 -  2285
chrX_93741840_93745123.rev   Z   Score: 9852   Residues:     1 -  3284
chrX_93772289_93776211   Z   Score: 11769   Residues:     1 -  3923
chrX_93809485_93811728.rev   Z   Score: 6732   Residues:     1 -  2244
chrX_93824978_93829522.rev   Z   Score: 13635   Residues:     1 -  4545
chrX_93857779_93862341.rev   Z   Score: 13689   Residues:     1 -  4563
chrX_93900595_93907300.rev   Z   Score: 20118   Residues:     1 -  6706
chrX_93918433_93921129   Z   Score: 8091   Residues:     1 -  2697
chrX_93923020_93931142   Z   Score: 24369   Residues:     1 -  8123
chrX_93943165_93947745.rev   A   Score:  338   Residues:  2465 -  2510
chrX_93943165_93947745.rev   A   Score:  257   Residues:  1844 -  1964
chrX_93943165_93947745.rev   Z   Score: 13743   Residues:     1 -  4581
chrX_93957383_93962683.rev   Z   Score: 15903   Residues:     1 -  5301
chrX_93984698_93987735   A   Score:  819   Residues:  2026 -  2179
chrX_93984698_93987735   R   Score:  217   Residues:  2026 -  2179
chrX_93984698_93987735   Z   Score: 9114   Residues:     1 -  3038
chrX_94003832_94009694   A   Score:  222   Residues:  2193 -  2263
chrX_94003832_94009694   Z   Score: 17589   Residues:     1 -  5863
chrX_94033358_94038595.rev   Z   Score: 15714   Residues:     1 -  5238
chrX_94045403_94047715   Z   Score: 6939   Residues:     1 -  2313
chrX_94048586_94052811   A   Score:  272   Residues:  4009 -  4071
chrX_94048586_94052811   Z   Score: 12678   Residues:     1 -  4226
chrX_94054293_94056292.rev   Z   Score: 6000   Residues:     1 -  2000
chrX_94062804_94064682   Z   Score: 5637   Residues:     1 -  1879
chrX_94067041_94071316.rev   Z   Score: 12828   Residues:     1 -  4276
chrX_94098067_94099798.rev   Z   Score: 5196   Residues:     1 -  1732
chrX_94140983_94144794   A   Score:  322   Residues:   321 -   402
chrX_94140983_94144794   Z   Score: 11436   Residues:     1 -  3812
chrX_94152632_94155578   Z   Score: 8841   Residues:     1 -  2947
chrX_94174733_94180836.rev   A   Score:  335   Residues:  3846 -  3905
chrX_94174733_94180836.rev   Z   Score: 18312   Residues:     1 -  6104
chrX_94182588_94184618   Z   Score: 6093   Residues:     1 -  2031
chrX_94188975_94190997   Z   Score: 6069   Residues:     1 -  2023
chrX_94218489_94224505   Z   Score: 18051   Residues:     1 -  6017
chrX_94246426_94250429.rev   Z   Score: 12012   Residues:     1 -  4004
chrX_94252496_94257860.rev   Z   Score: 16095   Residues:     1 -  5365
chrX_94259188_94264169.rev   Z   Score: 14946   Residues:     1 -  4982
chrX_94286860_94291733   Z   Score: 14622   Residues:     1 -  4874
chrX_94302969_94307199   Z   Score: 12693   Residues:     1 -  4231
chrX_94313382_94317681.rev   A   Score:  221   Residues:  3010 -  3071
chrX_94313382_94317681.rev   Z   Score: 12900   Residues:     1 -  4300
chrX_94335759_94341102   Z   Score: 16032   Residues:     1 -  5344
chrX_94365757_94368699   Z   Score: 8829   Residues:     1 -  2943
chrX_94374814_94379018.rev   A   Score:  200   Residues:  1441 -  1527
chrX_94374814_94379018.rev   Z   Score: 12615   Residues:     1 -  4205
chrX_94395780_94401413   Z   Score: 16902   Residues:     1 -  5634
chrX_94431267_94437993   Z   Score: 20181   Residues:     1 -  6727
chrX_94446122_94449745.rev   A   Score:  276   Residues:  2072 -  2108
chrX_94446122_94449745.rev   Z   Score: 10872   Residues:     1 -  3624
chrX_94459636_94463649   A   Score:  264   Residues:   426 -   468
chrX_94459636_94463649   Z   Score: 12042   Residues:     1 -  4014
chrX_94466382_94468231   Z   Score: 5550   Residues:     1 -  1850
chrX_94511343_94513607.rev   Z   Score: 6795   Residues:     1 -  2265
chrX_94526660_94528363.rev   Z   Score: 5112   Residues:     1 -  1704
chrX_94537271_94540087   Z   Score: 8451   Residues:     1 -  2817
chrX_94586188_94590264   Z   Score: 12231   Residues:     1 -  4077
chrX_94602055_94604087   Z   Score: 6099   Residues:     1 -  2033
chrX_94605287_94611548.rev   Z   Score: 18786   Residues:     1 -  6262
chrX_94624291_94630581   Z   Score: 18873   Residues:     1 -  6291
chrX_94639238_94641392.rev   T   Score:  284   Residues:   550 -   587
chrX_94639238_94641392.rev   Z   Score: 6465   Residues:     1 -  2155
chrX_94661286_94665415   A   Score:  352   Residues:  1976 -  2124
chrX_94661286_94665415   Z   Score: 12390   Residues:     1 -  4130
chrX_94674346_94681046.rev   Z   Score: 20103   Residues:     1 -  6701
chrX_94761247_94762847.rev   Z   Score: 4803   Residues:     1 -  1601
chrX_94816727_94818491.rev   Z   Score: 5295   Residues:     1 -  1765
chrX_94891237_94896289.rev   Z   Score: 15159   Residues:     1 -  5053
chrX_94928809_94934667   Z   Score: 17577   Residues:     1 -  5859
chrX_94997108_95001422.rev   Z   Score: 12945   Residues:     1 -  4315
chrX_95042206_95046474.rev   Z   Score: 12807   Residues:     1 -  4269
chrX_95119208_95125486.rev   Z   Score: 18837   Residues:     1 -  6279
chrX_95137355_95143804   Z   Score: 19350   Residues:     1 -  6450
chrX_95149435_95154727   Z   Score: 15879   Residues:     1 -  5293
chrX_95202776_95205292   Z   Score: 7551   Residues:     1 -  2517
chrX_95205559_95207797   A   Score:  200   Residues:  1456 -  1480
chrX_95205559_95207797   Z   Score: 6717   Residues:     1 -  2239
chrX_95259471_95261918   Z   Score: 7344   Residues:     1 -  2448
chrX_95265348_95269845   Z   Score: 13494   Residues:     1 -  4498
chrX_95274859_95281567   Z   Score: 20127   Residues:     1 -  6709
chrX_95315606_95320018.rev   Z   Score: 13239   Residues:     1 -  4413
chrX_95330036_95336415   Z   Score: 19140   Residues:     1 -  6380
chrX_95336423_95341170   A   Score:  228   Residues:  1961 -  2066
chrX_95336423_95341170   Z   Score: 14244   Residues:     1 -  4748
chrX_95341260_95342925   Z   Score: 4998   Residues:     1 -  1666
chrX_95343389_95345959   Z   Score: 7713   Residues:     1 -  2571
chrX_95367199_95370823   Z   Score: 10875   Residues:     1 -  3625
chrX_95406764_95412535.rev   Z   Score: 17316   Residues:     1 -  5772
chrX_95539308_95541303   Z   Score: 5988   Residues:     1 -  1996
chrX_95547388_95553464   Z   Score: 18231   Residues:     1 -  6077
chrX_95562721_95564533.rev   C   Score:  217   Residues:     3 -    66
chrX_95562721_95564533.rev   Z   Score: 5439   Residues:     1 -  1813
chrX_95588624_95590765   Z   Score: 6426   Residues:     1 -  2142
chrX_95645705_95650996   Z   Score: 15876   Residues:     1 -  5292
chrX_95658285_95664677   Z   Score: 19179   Residues:     1 -  6393
chrX_95691864_95693952   Z   Score: 6267   Residues:     1 -  2089
chrX_95717318_95723356   A   Score:  228   Residues:  3203 -  3246
chrX_95717318_95723356   Z   Score: 18117   Residues:     1 -  6039
chrX_95779674_95781499.rev   Z   Score: 5478   Residues:     1 -  1826
chrX_95870913_95874977.rev   Z   Score: 12195   Residues:     1 -  4065
chrX_96020024_96022884.rev   Z   Score: 8583   Residues:     1 -  2861
chrX_96028806_96032613.rev   Z   Score: 11424   Residues:     1 -  3808
chrX_96260572_96267212   Z   Score: 19923   Residues:     1 -  6641
chrX_96470049_96476758   Z   Score: 20130   Residues:     1 -  6710
chrX_96548510_96553387.rev   Z   Score: 14634   Residues:     1 -  4878
chrX_96570904_96577169.rev   Z   Score: 18798   Residues:     1 -  6266
chrX_96639566_96645832.rev   Z   Score: 18801   Residues:     1 -  6267
chrX_96736463_96738600.rev   A   Score:  208   Residues:   882 -   907
chrX_96736463_96738600.rev   Z   Score: 6414   Residues:     1 -  2138
chrX_96771087_96773574   Z   Score: 7464   Residues:     1 -  2488
chrX_96845939_96847994   A   Score:  220   Residues:   349 -   378
chrX_96845939_96847994   Z   Score: 6168   Residues:     1 -  2056
chrX_96859306_96865680.rev   Z   Score: 19125   Residues:     1 -  6375
chrX_96948669_96951369.rev   T   Score:  214   Residues:  2480 -  2507
chrX_96948669_96951369.rev   Z   Score: 8103   Residues:     1 -  2701
chrX_96975610_96988099   Z   Score: 37470   Residues:     1 - 12490
chrX_97070237_97074771.rev   Z   Score: 13605   Residues:     1 -  4535
chrX_97104779_97111452.rev   Z   Score: 20022   Residues:     1 -  6674
chrX_97112664_97116938.rev   Z   Score: 12825   Residues:     1 -  4275
chrX_97138712_97140350.rev   Z   Score: 4917   Residues:     1 -  1639
chrX_97183692_97190679   Z   Score: 20964   Residues:     1 -  6988
chrX_97292203_97295569   Z   Score: 10101   Residues:     1 -  3367
chrX_97296255_97302940.rev   Z   Score: 20058   Residues:     1 -  6686
chrX_97316064_97320064   Z   Score: 12003   Residues:     1 -  4001
chrX_97327556_97332935   Z   Score: 16140   Residues:     1 -  5380
chrX_97360987_97367255   Z   Score: 18807   Residues:     1 -  6269
chrX_97382485_97385591   Z   Score: 9321   Residues:     1 -  3107
chrX_97400580_97405187.rev   Z   Score: 13824   Residues:     1 -  4608
chrX_97485721_97492000.rev   Z   Score: 18840   Residues:     1 -  6280
chrX_97502426_97506698   Z   Score: 12819   Residues:     1 -  4273
chrX_97520673_97522832.rev   Z   Score: 6480   Residues:     1 -  2160
chrX_97595998_97600719   Z   Score: 14166   Residues:     1 -  4722
chrX_97621485_97627260.rev   Z   Score: 17328   Residues:     1 -  5776
chrX_97627633_97630496.rev   Z   Score: 8592   Residues:     1 -  2864
chrX_97674676_97680371.rev   Z   Score: 17088   Residues:     1 -  5696
chrX_97700306_97703072   Z   Score: 8301   Residues:     1 -  2767
chrX_97744809_97746757.rev   Z   Score: 5847   Residues:     1 -  1949
chrX_97748890_97761211.rev   Z   Score: 36966   Residues:     1 - 12322
chrX_97806504_97811022.rev   Z   Score: 13557   Residues:     1 -  4519
chrX_97822547_97824625   Z   Score: 6237   Residues:     1 -  2079
chrX_97851323_97853160   Z   Score: 5514   Residues:     1 -  1838
chrX_97903239_97907436.rev   Z   Score: 12594   Residues:     1 -  4198
chrX_97931388_97937240.rev   A   Score:  210   Residues:   495 -   545
chrX_97931388_97937240.rev   Z   Score: 17559   Residues:     1 -  5853
chrX_97942112_97947816   Z   Score: 17115   Residues:     1 -  5705
chrX_98035100_98039353   A   Score:  216   Residues:  1403 -  1585
chrX_98035100_98039353   Z   Score: 12762   Residues:     1 -  4254
chrX_98086489_98088582.rev   Z   Score: 6282   Residues:     1 -  2094
chrX_98104043_98108304.rev   A   Score:  204   Residues:  1456 -  1558
chrX_98104043_98108304.rev   Z   Score: 12786   Residues:     1 -  4262
chrX_98147173_98152887   Z   Score: 17145   Residues:     1 -  5715
chrX_98169012_98170999   Z   Score: 5964   Residues:     1 -  1988
chrX_98214758_98219739   Z   Score: 14946   Residues:     1 -  4982
chrX_98235696_98238550   Z   Score: 8565   Residues:     1 -  2855
chrX_98255690_98260187.rev   A   Score:  259   Residues:  1225 -  1313
chrX_98255690_98260187.rev   A   Score:  232   Residues:  2908 -  2945
chrX_98255690_98260187.rev   Z   Score: 13494   Residues:     1 -  4498
chrX_98263371_98267607.rev   Z   Score: 12711   Residues:     1 -  4237
chrX_98287551_98289200   Z   Score: 4950   Residues:     1 -  1650
chrX_98295277_98301656   Z   Score: 19140   Residues:     1 -  6380
chrX_98307333_98310023   Z   Score: 8073   Residues:     1 -  2691
chrX_98327740_98329522.rev   Z   Score: 5349   Residues:     1 -  1783
chrX_98337328_98341479   Z   Score: 12456   Residues:     1 -  4152
chrX_98396438_98399482.rev   Z   Score: 9135   Residues:     1 -  3045
chrX_98402126_98406338.rev   Z   Score: 12639   Residues:     1 -  4213
chrX_98449900_98454145.rev   A   Score:  256   Residues:   347 -   487
chrX_98449900_98454145.rev   Z   Score: 12738   Residues:     1 -  4246
chrX_98463178_98465522   Z   Score: 7035   Residues:     1 -  2345
chrX_98503003_98505739   Z   Score: 8211   Residues:     1 -  2737
chrX_98525335_98527398.rev   Z   Score: 6192   Residues:     1 -  2064
chrX_98539735_98541987   Z   Score: 6759   Residues:     1 -  2253
chrX_98543580_98548689   T   Score:  285   Residues:  2600 -  2709
chrX_98543580_98548689   Z   Score: 15330   Residues:     1 -  5110
chrX_98554848_98556484.rev   Z   Score: 4911   Residues:     1 -  1637
chrX_98561279_98562931   Z   Score: 4959   Residues:     1 -  1653
chrX_98571406_98580778   Z   Score: 28119   Residues:     1 -  9373
chrX_98583045_98588535   Z   Score: 16473   Residues:     1 -  5491
chrX_98605604_98609826   Z   Score: 12669   Residues:     1 -  4223
chrX_98619964_98623796   Z   Score: 11499   Residues:     1 -  3833
chrX_98639698_98643828.rev   Z   Score: 12393   Residues:     1 -  4131
chrX_98655384_98660387.rev   Z   Score: 15012   Residues:     1 -  5004
chrX_98688408_98690634   Z   Score: 6681   Residues:     1 -  2227
chrX_98694126_98698161   Z   Score: 12108   Residues:     1 -  4036
chrX_98699934_98701911   Z   Score: 5934   Residues:     1 -  1978
chrX_98726094_98728469.rev   A   Score:  290   Residues:  1443 -  1516
chrX_98726094_98728469.rev   C   Score:  219   Residues:   278 -   309
chrX_98726094_98728469.rev   Z   Score: 7128   Residues:     1 -  2376
chrX_98735665_98737756.rev   Z   Score: 6276   Residues:     1 -  2092
chrX_98787230_98789052.rev   Z   Score: 5469   Residues:     1 -  1823
chrX_98824512_98831590   A   Score:  224   Residues:   420 -   485
chrX_98824512_98831590   Z   Score: 21237   Residues:     1 -  7079
chrX_98833375_98837576.rev   A   Score:  218   Residues:   432 -   499
chrX_98833375_98837576.rev   Z   Score: 12606   Residues:     1 -  4202
chrX_98846598_98848321.rev   Z   Score: 5172   Residues:     1 -  1724
chrX_98848770_98854083.rev   A   Score:  208   Residues:  3577 -  3635
chrX_98848770_98854083.rev   Z   Score: 15942   Residues:     1 -  5314
chrX_98866200_98872242   Z   Score: 18129   Residues:     1 -  6043
chrX_98930361_98934534   Z   Score: 12522   Residues:     1 -  4174
chrX_98941792_98947535   Z   Score: 17232   Residues:     1 -  5744
chrX_98962889_98965086   Z   Score: 6594   Residues:     1 -  2198
chrX_99111428_99117818   Z   Score: 19173   Residues:     1 -  6391
chrX_99153510_99158937   Z   Score: 16284   Residues:     1 -  5428
chrX_99195581_99201860   Z   Score: 18840   Residues:     1 -  6280
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chrX_107158121_107160772.rev   Z   Score: 7956   Residues:     1 -  2652
chrX_107327523_107332283   Z   Score: 14283   Residues:     1 -  4761
chrX_107381477_107383089.rev   Z   Score: 4839   Residues:     1 -  1613
chrX_107435346_107441850.rev   Z   Score: 19515   Residues:     1 -  6505
chrX_107543795_107545447   Z   Score: 4959   Residues:     1 -  1653
chrX_107555817_107559436   A   Score:  268   Residues:   786 -   838
chrX_107555817_107559436   A   Score:  229   Residues:  2116 -  2150
chrX_107555817_107559436   Z   Score: 10860   Residues:     1 -  3620
chrX_107562363_107564032.rev   Z   Score: 5010   Residues:     1 -  1670
chrX_107571414_107574224.rev   Z   Score: 8433   Residues:     1 -  2811
chrX_107578410_107583825   A   Score:  284   Residues:  5099 -  5156
chrX_107578410_107583825   Z   Score: 16248   Residues:     1 -  5416
chrX_107591734_107598130.rev   Z   Score: 19191   Residues:     1 -  6397
chrX_107601342_107603383   Z   Score: 6126   Residues:     1 -  2042
chrX_107660391_107663567   Z   Score: 9531   Residues:     1 -  3177
chrX_107685516_107689673   Z   Score: 12474   Residues:     1 -  4158
chrX_107705636_107709790.rev   Z   Score: 12465   Residues:     1 -  4155
chrX_107713075_107714695   Z   Score: 4863   Residues:     1 -  1621
chrX_107754495_107757622.rev   Z   Score: 9384   Residues:     1 -  3128
chrX_107800291_107805416   Z   Score: 15378   Residues:     1 -  5126
chrX_107810600_107815241.rev   Z   Score: 13926   Residues:     1 -  4642
chrX_107815246_107818555.rev   T   Score:  207   Residues:   382 -   438
chrX_107815246_107818555.rev   Z   Score: 9930   Residues:     1 -  3310
chrX_107829056_107831886.rev   Z   Score: 8493   Residues:     1 -  2831
chrX_107836775_107841462.rev   Z   Score: 14064   Residues:     1 -  4688
chrX_107868861_107874977.rev   Z   Score: 18351   Residues:     1 -  6117
chrX_107875145_107877170   Z   Score: 6078   Residues:     1 -  2026
chrX_107900609_107907110   T   Score:  304   Residues:  3793 -  3830
chrX_107900609_107907110   Z   Score: 19506   Residues:     1 -  6502
chrX_107936061_107939314   Z   Score: 9762   Residues:     1 -  3254
chrX_107952769_107958922   Z   Score: 18462   Residues:     1 -  6154
chrX_107973901_107979169.rev   Z   Score: 15807   Residues:     1 -  5269
chrX_107980831_107987187.rev   T   Score:  202   Residues:  1064 -  1104
chrX_107980831_107987187.rev   Z   Score: 19071   Residues:     1 -  6357
chrX_107988050_107994703.rev   Z   Score: 19962   Residues:     1 -  6654
chrX_107997096_107999186.rev   Z   Score: 6273   Residues:     1 -  2091
chrX_108023612_108026402   Z   Score: 8373   Residues:     1 -  2791
chrX_108032579_108036741.rev   Z   Score: 12489   Residues:     1 -  4163
chrX_108059279_108065962   A   Score:  238   Residues:  5932 -  5962
chrX_108059279_108065962   Z   Score: 20052   Residues:     1 -  6684
chrX_108068946_108075347.rev   T   Score:  212   Residues:   365 -   424
chrX_108068946_108075347.rev   Z   Score: 19206   Residues:     1 -  6402
chrX_108103466_108107917   Z   Score: 13356   Residues:     1 -  4452
chrX_108110242_108115011   A   Score:  210   Residues:  3344 -  3395
chrX_108110242_108115011   Z   Score: 14310   Residues:     1 -  4770
chrX_108116269_108127459.rev   Z   Score: 33573   Residues:     1 - 11191
chrX_108132960_108139589.rev   Z   Score: 19890   Residues:     1 -  6630
chrX_108146166_108150369.rev   Z   Score: 12612   Residues:     1 -  4204
chrX_108162183_108168456   Z   Score: 18822   Residues:     1 -  6274
chrX_108188952_108192301   T   Score:  227   Residues:  1376 -  1420
chrX_108188952_108192301   Z   Score: 10047   Residues:     1 -  3349
chrX_108193976_108198556   Z   Score: 13743   Residues:     1 -  4581
chrX_108240590_108247253   Z   Score: 19992   Residues:     1 -  6664
chrX_108252294_108258776.rev   A   Score:  202   Residues:  2233 -  2265
chrX_108252294_108258776.rev   Z   Score: 19449   Residues:     1 -  6483
chrX_108292616_108302942.rev   Z   Score: 30981   Residues:     1 - 10327
chrX_108307570_108311797.rev   Z   Score: 12684   Residues:     1 -  4228
chrX_108337796_108342011.rev   Z   Score: 12648   Residues:     1 -  4216
chrX_108364494_108369614.rev   Z   Score: 15363   Residues:     1 -  5121
chrX_108379439_108385843.rev   Z   Score: 19215   Residues:     1 -  6405
chrX_108558155_108562398   A   Score:  225   Residues:  1463 -  1575
chrX_108558155_108562398   Z   Score: 12732   Residues:     1 -  4244
chrX_108569350_108574885   Z   Score: 16608   Residues:     1 -  5536
chrX_108633086_108637846   A   Score:  290   Residues:  1459 -  1513
chrX_108633086_108637846   Z   Score: 14283   Residues:     1 -  4761
chrX_108652829_108658680   Z   Score: 17556   Residues:     1 -  5852
chrX_108693541_108699812   Z   Score: 18816   Residues:     1 -  6272
chrX_108803427_108808059   Z   Score: 13899   Residues:     1 -  4633
chrX_108816298_108820102   A   Score: 1197   Residues:    28 -   322
chrX_108816298_108820102   R   Score:  511   Residues:    28 -   323
chrX_108816298_108820102   G   Score:  307   Residues:   179 -   291
chrX_108816298_108820102   Z   Score: 11415   Residues:     1 -  3805
chrX_108945091_108951502.rev   Z   Score: 19236   Residues:     1 -  6412
chrX_109017529_109022873.rev   A   Score:  216   Residues:  1434 -  1583
chrX_109017529_109022873.rev   Z   Score: 16035   Residues:     1 -  5345
chrX_109123083_109128056.rev   Z   Score: 14922   Residues:     1 -  4974
chrX_109131730_109133583.rev   Z   Score: 5562   Residues:     1 -  1854
chrX_109140333_109146685.rev   Z   Score: 19059   Residues:     1 -  6353
chrX_109147622_109152306.rev   A   Score:  305   Residues:  1858 -  1960
chrX_109147622_109152306.rev   A   Score:  209   Residues:   952 -  1052
chrX_109147622_109152306.rev   A   Score:  200   Residues:  4121 -  4158
chrX_109147622_109152306.rev   Z   Score: 14055   Residues:     1 -  4685
chrX_109171554_109173211.rev   Z   Score: 4974   Residues:     1 -  1658
chrX_109234416_109237348   Z   Score: 8799   Residues:     1 -  2933
chrX_109282068_109285115   A   Score:  304   Residues:   195 -   322
chrX_109282068_109285115   Z   Score: 9144   Residues:     1 -  3048
chrX_109399169_109401861   Z   Score: 8079   Residues:     1 -  2693
chrX_109527578_109529849.rev   Z   Score: 6816   Residues:     1 -  2272
chrX_109534117_109540027.rev   Z   Score: 17733   Residues:     1 -  5911
chrX_109554794_109557310   Z   Score: 7551   Residues:     1 -  2517
chrX_109577263_109579122   Z   Score: 5580   Residues:     1 -  1860
chrX_109614082_109615904.rev   Z   Score: 5469   Residues:     1 -  1823
chrX_109654702_109663842   Z   Score: 27423   Residues:     1 -  9141
chrX_109665680_109669949.rev   Z   Score: 12810   Residues:     1 -  4270
chrX_109674891_109681589   Z   Score: 20097   Residues:     1 -  6699
chrX_109689633_109693157.rev   Z   Score: 10575   Residues:     1 -  3525
chrX_109700947_109702931   A   Score:  254   Residues:  1011 -  1048
chrX_109700947_109702931   Z   Score: 5955   Residues:     1 -  1985
chrX_109705779_109712173   Z   Score: 19185   Residues:     1 -  6395
chrX_109756144_109757928   Z   Score: 5355   Residues:     1 -  1785
chrX_109812875_109815553.rev   Z   Score: 8037   Residues:     1 -  2679
chrX_109826478_109829519.rev   Z   Score: 9126   Residues:     1 -  3042
chrX_109866379_109872646.rev   Z   Score: 18804   Residues:     1 -  6268
chrX_109875178_109879331   Z   Score: 12462   Residues:     1 -  4154
chrX_109916647_109918707   Z   Score: 6183   Residues:     1 -  2061
chrX_109948019_109954335.rev   A   Score:  206   Residues:  2748 -  2818
chrX_109948019_109954335.rev   Z   Score: 18951   Residues:     1 -  6317
chrX_110065863_110069682   A   Score:  332   Residues:   226 -   347
chrX_110065863_110069682   A   Score:  216   Residues:  3201 -  3232
chrX_110065863_110069682   R   Score:  225   Residues:   226 -   344
chrX_110065863_110069682   G   Score:  306   Residues:   236 -   328
chrX_110065863_110069682   Z   Score: 11460   Residues:     1 -  3820
chrX_110107309_110110502.rev   Z   Score: 9582   Residues:     1 -  3194
chrX_110284371_110286236   Z   Score: 5598   Residues:     1 -  1866
chrX_110389388_110395527   Z   Score: 18420   Residues:     1 -  6140
chrX_110428826_110430641.rev   Z   Score: 5448   Residues:     1 -  1816
chrX_110497985_110500939   Z   Score: 8865   Residues:     1 -  2955
chrX_110533249_110535541.rev   Z   Score: 6879   Residues:     1 -  2293
chrX_110588619_110591269   Z   Score: 7953   Residues:     1 -  2651
chrX_110638323_110644600.rev   Z   Score: 18834   Residues:     1 -  6278
chrX_110651541_110654779.rev   Z   Score: 9717   Residues:     1 -  3239
chrX_110683199_110684845   Z   Score: 4941   Residues:     1 -  1647
chrX_110797387_110799336.rev   Z   Score: 5850   Residues:     1 -  1950
chrX_110833329_110839693   Z   Score: 19095   Residues:     1 -  6365
chrX_110850516_110852274.rev   Z   Score: 5277   Residues:     1 -  1759
chrX_111011712_111018109   Z   Score: 19194   Residues:     1 -  6398
chrX_111024811_111027750   Z   Score: 8820   Residues:     1 -  2940
chrX_111027957_111029604   Z   Score: 4944   Residues:     1 -  1648
chrX_111042526_111048033.rev   Z   Score: 16524   Residues:     1 -  5508
chrX_111081744_111084395.rev   A   Score:  213   Residues:   687 -   736
chrX_111081744_111084395.rev   Z   Score: 7956   Residues:     1 -  2652
chrX_111101250_111102849.rev   Z   Score: 4800   Residues:     1 -  1600
chrX_111175256_111178971   Z   Score: 11148   Residues:     1 -  3716
chrX_111185341_111187135   Z   Score: 5385   Residues:     1 -  1795
chrX_111251890_111254926.rev   Z   Score: 9111   Residues:     1 -  3037
chrX_111290317_111296724.rev   Z   Score: 19224   Residues:     1 -  6408
chrX_111373828_111381292   Z   Score: 22395   Residues:     1 -  7465
chrX_111435981_111441069.rev   Z   Score: 15267   Residues:     1 -  5089
chrX_111458740_111462989   Z   Score: 12750   Residues:     1 -  4250
chrX_111474553_111476240.rev   Z   Score: 5064   Residues:     1 -  1688
chrX_111510686_111517098   Z   Score: 19239   Residues:     1 -  6413
chrX_111531437_111533259.rev   Z   Score: 5469   Residues:     1 -  1823
chrX_111535360_111538281.rev   A   Score:  207   Residues:  1375 -  1413
chrX_111535360_111538281.rev   Z   Score: 8766   Residues:     1 -  2922
chrX_111554793_111557186   Z   Score: 7182   Residues:     1 -  2394
chrX_111604916_111610726   A   Score:  222   Residues:  5047 -  5095
chrX_111604916_111610726   A   Score:  204   Residues:  4539 -  4583
chrX_111604916_111610726   Z   Score: 17433   Residues:     1 -  5811
chrX_111616235_111618646.rev   Z   Score: 7236   Residues:     1 -  2412
chrX_111638997_111645402   Z   Score: 19218   Residues:     1 -  6406
chrX_111645703_111648605   Z   Score: 8709   Residues:     1 -  2903
chrX_111704874_111708418   A   Score:  271   Residues:  2924 -  2962
chrX_111704874_111708418   A   Score:  212   Residues:  2398 -  2442
chrX_111704874_111708418   Z   Score: 10635   Residues:     1 -  3545
chrX_111722873_111724570   Z   Score: 5094   Residues:     1 -  1698
chrX_111743984_111748013.rev   Z   Score: 12090   Residues:     1 -  4030
chrX_111749974_111752748.rev   Z   Score: 8325   Residues:     1 -  2775
chrX_111756482_111759794.rev   Z   Score: 9939   Residues:     1 -  3313
chrX_111767483_111773761   Z   Score: 18837   Residues:     1 -  6279
chrX_111964007_111965885.rev   Z   Score: 5637   Residues:     1 -  1879
chrX_112077569_112079871.rev   Z   Score: 6909   Residues:     1 -  2303
chrX_112113981_112119026.rev   A   Score:  238   Residues:   374 -   499
chrX_112113981_112119026.rev   A   Score:  205   Residues:  1516 -  1546
chrX_112113981_112119026.rev   Z   Score: 15138   Residues:     1 -  5046
chrX_112125055_112127600   Z   Score: 7638   Residues:     1 -  2546
chrX_112138145_112143171   Z   Score: 15081   Residues:     1 -  5027
chrX_112148093_112152977.rev   A   Score:  274   Residues:   472 -   509
chrX_112148093_112152977.rev   Z   Score: 14655   Residues:     1 -  4885
chrX_112163345_112164932   Z   Score: 4764   Residues:     1 -  1588
chrX_112191334_112193157.rev   Z   Score: 5472   Residues:     1 -  1824
chrX_112210285_112211998.rev   Z   Score: 5142   Residues:     1 -  1714
chrX_112240081_112242112   Z   Score: 6096   Residues:     1 -  2032
chrX_112246773_112252555.rev   Z   Score: 17349   Residues:     1 -  5783
chrX_112256235_112262548.rev   Z   Score: 18942   Residues:     1 -  6314
chrX_112283778_112287180.rev   Z   Score: 10209   Residues:     1 -  3403
chrX_112296197_112300020.rev   Z   Score: 11472   Residues:     1 -  3824
chrX_112305538_112309888.rev   Z   Score: 13053   Residues:     1 -  4351
chrX_112368920_112373310   A   Score:  225   Residues:   380 -   497
chrX_112368920_112373310   Z   Score: 13173   Residues:     1 -  4391
chrX_112382416_112384076.rev   Z   Score: 4983   Residues:     1 -  1661
chrX_112387448_112393725.rev   Z   Score: 18834   Residues:     1 -  6278
chrX_112409991_112412392.rev   Z   Score: 7206   Residues:     1 -  2402
chrX_112421282_112424565.rev   A   Score:  314   Residues:   885 -   927
chrX_112421282_112424565.rev   Z   Score: 9852   Residues:     1 -  3284
chrX_112430087_112432523   Z   Score: 7311   Residues:     1 -  2437
chrX_112435030_112440414.rev   Z   Score: 16155   Residues:     1 -  5385
chrX_112480831_112485053   Z   Score: 12669   Residues:     1 -  4223
chrX_112491398_112500619   A   Score:  261   Residues:  1053 -  1179
chrX_112491398_112500619   Z   Score: 27666   Residues:     1 -  9222
chrX_112524551_112534571   Z   Score: 30063   Residues:     1 - 10021
chrX_112589409_112591957   Z   Score: 7647   Residues:     1 -  2549
chrX_112648561_112652782   Z   Score: 12666   Residues:     1 -  4222
chrX_112672827_112675678.rev   Z   Score: 8556   Residues:     1 -  2852
chrX_112688737_112690872.rev   Z   Score: 6408   Residues:     1 -  2136
chrX_112726920_112729373.rev   Z   Score: 7362   Residues:     1 -  2454
chrX_112741293_112747963.rev   Z   Score: 20013   Residues:     1 -  6671
chrX_112762817_112765082.rev   Z   Score: 6798   Residues:     1 -  2266
chrX_112778970_112784067.rev   Z   Score: 15294   Residues:     1 -  5098
chrX_112868481_112876945   T   Score:  310   Residues:  3880 -  3927
chrX_112868481_112876945   Z   Score: 25395   Residues:     1 -  8465
chrX_112907049_112913130.rev   Z   Score: 18246   Residues:     1 -  6082
chrX_112972896_112976757.rev   A   Score:  281   Residues:   326 -   487
chrX_112972896_112976757.rev   Z   Score: 11586   Residues:     1 -  3862
chrX_112980635_112982228.rev   Z   Score: 4782   Residues:     1 -  1594
chrX_113016354_113018691   Z   Score: 7014   Residues:     1 -  2338
chrX_113057781_113060835.rev   T   Score:  280   Residues:  1696 -  1735
chrX_113057781_113060835.rev   Z   Score: 9165   Residues:     1 -  3055
chrX_113138041_113142589   A   Score:  219   Residues:  1914 -  1970
chrX_113138041_113142589   Z   Score: 13647   Residues:     1 -  4549
chrX_113171058_113177727.rev   Z   Score: 20010   Residues:     1 -  6670
chrX_113194307_113196421   Z   Score: 6345   Residues:     1 -  2115
chrX_113231650_113238338   A   Score:  211   Residues:  3101 -  3142
chrX_113231650_113238338   Z   Score: 20067   Residues:     1 -  6689
chrX_113242502_113244444   Z   Score: 5829   Residues:     1 -  1943
chrX_113292545_113295656   Z   Score: 9336   Residues:     1 -  3112
chrX_113310507_113312637   Z   Score: 6393   Residues:     1 -  2131
chrX_113430897_113433007   Z   Score: 6333   Residues:     1 -  2111
chrX_113499363_113501721.rev   Z   Score: 7077   Residues:     1 -  2359
chrX_113559726_113565181   Z   Score: 16368   Residues:     1 -  5456
chrX_113577831_113582064   Z   Score: 12702   Residues:     1 -  4234
chrX_113600421_113602077   Z   Score: 4971   Residues:     1 -  1657
chrX_113628794_113632816   A   Score:  242   Residues:   472 -   535
chrX_113628794_113632816   Z   Score: 12069   Residues:     1 -  4023
chrX_113757473_113763865   Z   Score: 19179   Residues:     1 -  6393
chrX_113778157_113784420.rev   Z   Score: 18792   Residues:     1 -  6264
chrX_113803015_113807047   A   Score:  262   Residues:  3859 -  3892
chrX_113803015_113807047   A   Score:  230   Residues:  1389 -  1428
chrX_113803015_113807047   Z   Score: 12099   Residues:     1 -  4033
chrX_113810364_113813723   Z   Score: 10080   Residues:     1 -  3360
chrX_113888492_113891148.rev   Z   Score: 7971   Residues:     1 -  2657
chrX_113914541_113918623.rev   Z   Score: 12249   Residues:     1 -  4083
chrX_113918776_113920642.rev   Z   Score: 5601   Residues:     1 -  1867
chrX_113938155_113941685.rev   Z   Score: 10593   Residues:     1 -  3531
chrX_113949445_113951984   Z   Score: 7620   Residues:     1 -  2540
chrX_113994741_114001667.rev   A   Score:  232   Residues:  6185 -  6213
chrX_113994741_114001667.rev   Z   Score: 20781   Residues:     1 -  6927
chrX_114025672_114027640   Z   Score: 5907   Residues:     1 -  1969
chrX_114029040_114030735   Z   Score: 5088   Residues:     1 -  1696
chrX_114045952_114047679   Z   Score: 5184   Residues:     1 -  1728
chrX_114138232_114144654.rev   Z   Score: 19269   Residues:     1 -  6423
chrX_114151239_114155562   A   Score:  201   Residues:  1119 -  1230
chrX_114151239_114155562   Z   Score: 12972   Residues:     1 -  4324
chrX_114156693_114161675   Z   Score: 14949   Residues:     1 -  4983
chrX_114171821_114174000   A   Score:  234   Residues:   148 -   261
chrX_114171821_114174000   Z   Score: 6540   Residues:     1 -  2180
chrX_114279118_114281627   Z   Score: 7530   Residues:     1 -  2510
chrX_114299346_114301243.rev   Z   Score: 5694   Residues:     1 -  1898
chrX_114308259_114309941   Z   Score: 5049   Residues:     1 -  1683
chrX_114367518_114369131.rev   Z   Score: 4842   Residues:     1 -  1614
chrX_114636450_114638390.rev   Z   Score: 5823   Residues:     1 -  1941
chrX_114851938_114854669   Z   Score: 8196   Residues:     1 -  2732
chrX_114857508_114861844.rev   Z   Score: 13011   Residues:     1 -  4337
chrX_114890477_114894761   Z   Score: 12855   Residues:     1 -  4285
chrX_114957972_114967996   Z   Score: 30075   Residues:     1 - 10025
chrX_114976167_114978273   Z   Score: 6321   Residues:     1 -  2107
chrX_115007277_115013216.rev   Z   Score: 17820   Residues:     1 -  5940
chrX_115016044_115020683   Z   Score: 13920   Residues:     1 -  4640
chrX_115026088_115028116   Z   Score: 6087   Residues:     1 -  2029
chrX_115039127_115041194.rev   Z   Score: 6204   Residues:     1 -  2068
chrX_115042270_115044138.rev   T   Score:  215   Residues:    13 -    87
chrX_115042270_115044138.rev   Z   Score: 5607   Residues:     1 -  1869
chrX_115045506_115047984.rev   Z   Score: 7437   Residues:     1 -  2479
chrX_115063837_115071991   Z   Score: 24465   Residues:     1 -  8155
chrX_115101837_115108241   Z   Score: 19215   Residues:     1 -  6405
chrX_115135711_115138470   Z   Score: 8280   Residues:     1 -  2760
chrX_115142349_115144348.rev   Z   Score: 6000   Residues:     1 -  2000
chrX_115148448_115155446   Z   Score: 20997   Residues:     1 -  6999
chrX_115243692_115248084.rev   A   Score:  206   Residues:  1400 -  1520
chrX_115243692_115248084.rev   Z   Score: 13179   Residues:     1 -  4393
chrX_115253789_115256707   Z   Score: 8757   Residues:     1 -  2919
chrX_115279377_115283090   Z   Score: 11142   Residues:     1 -  3714
chrX_115339918_115341828.rev   Z   Score: 5733   Residues:     1 -  1911
chrX_115357794_115359416   A   Score:  232   Residues:   884 -   929
chrX_115357794_115359416   Z   Score: 4869   Residues:     1 -  1623
chrX_115408459_115412486.rev   Z   Score: 12084   Residues:     1 -  4028
chrX_115425110_115431201   A   Score:  272   Residues:  5250 -  5321
chrX_115425110_115431201   A   Score:  248   Residues:   458 -   511
chrX_115425110_115431201   Z   Score: 18273   Residues:     1 -  6091
chrX_115438085_115440149.rev   A   Score:  255   Residues:   152 -   267
chrX_115438085_115440149.rev   Z   Score: 6195   Residues:     1 -  2065
chrX_115443888_115445523.rev   Z   Score: 4908   Residues:     1 -  1636
chrX_115452667_115455767.rev   Z   Score: 9303   Residues:     1 -  3101
chrX_115457899_115461166.rev   Z   Score: 9804   Residues:     1 -  3268
chrX_115483834_115489582.rev   Z   Score: 17247   Residues:     1 -  5749
chrX_115527633_115530069   Z   Score: 7311   Residues:     1 -  2437
chrX_115565063_115569652.rev   A   Score:  254   Residues:  1788 -  1903
chrX_115565063_115569652.rev   T   Score:  216   Residues:   723 -   749
chrX_115565063_115569652.rev   Z   Score: 13770   Residues:     1 -  4590
chrX_115589798_115591456.rev   Z   Score: 4977   Residues:     1 -  1659
chrX_115613326_115617422.rev   Z   Score: 12291   Residues:     1 -  4097
chrX_115618220_115622470.rev   A   Score:  233   Residues:  1859 -  1899
chrX_115618220_115622470.rev   Z   Score: 12753   Residues:     1 -  4251
chrX_115623846_115629587.rev   Z   Score: 17226   Residues:     1 -  5742
chrX_115630144_115634952   Z   Score: 14427   Residues:     1 -  4809
chrX_115658696_115660720.rev   Z   Score: 6075   Residues:     1 -  2025
chrX_115675196_115677090   Z   Score: 5685   Residues:     1 -  1895
chrX_115682229_115684650.rev   Z   Score: 7266   Residues:     1 -  2422
chrX_115687877_115691162   Z   Score: 9858   Residues:     1 -  3286
chrX_115712835_115715668.rev   Z   Score: 8502   Residues:     1 -  2834
chrX_115715944_115720132.rev   Z   Score: 12567   Residues:     1 -  4189
chrX_115737835_115739971   Z   Score: 6411   Residues:     1 -  2137
chrX_115770496_115772619.rev   Z   Score: 6372   Residues:     1 -  2124
chrX_115792491_115796604.rev   Z   Score: 12342   Residues:     1 -  4114
chrX_115802325_115806579.rev   A   Score:  441   Residues:  3488 -  3561
chrX_115802325_115806579.rev   T   Score:  229   Residues:   228 -   270
chrX_115802325_115806579.rev   Z   Score: 12765   Residues:     1 -  4255
chrX_115857381_115863636.rev   Z   Score: 18768   Residues:     1 -  6256
chrX_115870179_115871874   Z   Score: 5088   Residues:     1 -  1696
chrX_115880931_115887185.rev   Z   Score: 18765   Residues:     1 -  6255
chrX_115895235_115897336   Z   Score: 6306   Residues:     1 -  2102
chrX_115939600_115943794.rev   A   Score:  236   Residues:  1001 -  1036
chrX_115939600_115943794.rev   T   Score:  228   Residues:    31 -    64
chrX_115939600_115943794.rev   Z   Score: 12585   Residues:     1 -  4195
chrX_115957036_115958902   Z   Score: 5601   Residues:     1 -  1867
chrX_115962950_115967165   A   Score:  220   Residues:   417 -   485
chrX_115962950_115967165   Z   Score: 12648   Residues:     1 -  4216
chrX_116026653_116030074   Z   Score: 10266   Residues:     1 -  3422
chrX_116059481_116061127.rev   Z   Score: 4941   Residues:     1 -  1647
chrX_116064600_116066774.rev   Z   Score: 6525   Residues:     1 -  2175
chrX_116168385_116172810.rev   Z   Score: 13278   Residues:     1 -  4426
chrX_116176037_116182414   Z   Score: 19134   Residues:     1 -  6378
chrX_116183420_116190099   Z   Score: 20040   Residues:     1 -  6680
chrX_116213850_116216181.rev   Z   Score: 6996   Residues:     1 -  2332
chrX_116268703_116272894.rev   Z   Score: 12576   Residues:     1 -  4192
chrX_116275157_116279031   Z   Score: 11625   Residues:     1 -  3875
chrX_116325496_116330770   Z   Score: 15825   Residues:     1 -  5275
chrX_116332034_116333857.rev   Z   Score: 5472   Residues:     1 -  1824
chrX_116358500_116365171   Z   Score: 20016   Residues:     1 -  6672
chrX_116378297_116383862.rev   Z   Score: 16698   Residues:     1 -  5566
chrX_116413857_116419088   A   Score:  200   Residues:   192 -   216
chrX_116413857_116419088   Z   Score: 15696   Residues:     1 -  5232
chrX_116419297_116421705   Z   Score: 7227   Residues:     1 -  2409
chrX_116471037_116477396   Z   Score: 19080   Residues:     1 -  6360
chrX_116492781_116498567.rev   Z   Score: 17361   Residues:     1 -  5787
chrX_116505426_116511096   Z   Score: 17013   Residues:     1 -  5671
chrX_116532801_116539905.rev   Z   Score: 21315   Residues:     1 -  7105
chrX_116590903_116596742   Z   Score: 17520   Residues:     1 -  5840
chrX_116608499_116610533.rev   Z   Score: 6105   Residues:     1 -  2035
chrX_116613605_116617864   Z   Score: 12780   Residues:     1 -  4260
chrX_116656053_116657707   Z   Score: 4965   Residues:     1 -  1655
chrX_116673274_116679676.rev   Z   Score: 19209   Residues:     1 -  6403
chrX_116725338_116731442   Z   Score: 18315   Residues:     1 -  6105
chrX_116731929_116736388   Z   Score: 13380   Residues:     1 -  4460
chrX_116737323_116742945.rev   Z   Score: 16869   Residues:     1 -  5623
chrX_116743544_116749937.rev   Z   Score: 19182   Residues:     1 -  6394
chrX_116790094_116800210   A   Score:  204   Residues:  7263 -  7408
chrX_116790094_116800210   Z   Score: 30351   Residues:     1 - 10117
chrX_116924393_116926303.rev   Z   Score: 5733   Residues:     1 -  1911
chrX_116934602_116936748.rev   Z   Score: 6441   Residues:     1 -  2147
chrX_116947075_116953350   Z   Score: 18828   Residues:     1 -  6276
chrX_116957212_116961828   A   Score:  218   Residues:  4005 -  4035
chrX_116957212_116961828   A   Score:  204   Residues:  1463 -  1687
chrX_116957212_116961828   Z   Score: 13851   Residues:     1 -  4617
chrX_117009313_117014672   Z   Score: 16080   Residues:     1 -  5360
chrX_117053039_117055180.rev   Z   Score: 6426   Residues:     1 -  2142
chrX_117157052_117163463   Z   Score: 19236   Residues:     1 -  6412
chrX_117582318_117584797.rev   Z   Score: 7440   Residues:     1 -  2480
chrX_117606560_117610248.rev   Z   Score: 11067   Residues:     1 -  3689
chrX_117648734_117650608.rev   Z   Score: 5625   Residues:     1 -  1875
chrX_117730906_117733786.rev   A   Score:  216   Residues:  1227 -  1258
chrX_117730906_117733786.rev   Z   Score: 8643   Residues:     1 -  2881
chrX_117821640_117827753.rev   A   Score:  310   Residues:  3173 -  3216
chrX_117821640_117827753.rev   Z   Score: 18342   Residues:     1 -  6114
chrX_117871764_117877303   A   Score:  228   Residues:  3996 -  4031
chrX_117871764_117877303   A   Score:  208   Residues:  2583 -  2613
chrX_117871764_117877303   Z   Score: 16620   Residues:     1 -  5540
chrX_118025397_118028926   Z   Score: 10590   Residues:     1 -  3530
chrX_118097934_118099625   Z   Score: 5076   Residues:     1 -  1692
chrX_118208803_118211515.rev   T   Score:  444   Residues:  2390 -  2472
chrX_118208803_118211515.rev   Z   Score: 8139   Residues:     1 -  2713
chrX_118213572_118216231.rev   Z   Score: 7980   Residues:     1 -  2660
chrX_118351566_118357838.rev   Z   Score: 18819   Residues:     1 -  6273
chrX_118424733_118427019.rev   A   Score:  235   Residues:  2213 -  2256
chrX_118424733_118427019.rev   Z   Score: 6861   Residues:     1 -  2287
chrX_118443942_118446143.rev   Z   Score: 6606   Residues:     1 -  2202
chrX_118630051_118635748   Z   Score: 17094   Residues:     1 -  5698
chrX_118866709_118873796.rev   A   Score:  246   Residues:  3109 -  3231
chrX_118866709_118873796.rev   A   Score:  211   Residues:   190 -   373
chrX_118866709_118873796.rev   Z   Score: 21264   Residues:     1 -  7088
chrX_118942961_118944853   Z   Score: 5679   Residues:     1 -  1893
chrX_118962502_118968865.rev   Z   Score: 19092   Residues:     1 -  6364
chrX_119057149_119058808.rev   A   Score:  251   Residues:   421 -   504
chrX_119057149_119058808.rev   Z   Score: 4980   Residues:     1 -  1660
chrX_119099069_119105445   Z   Score: 19131   Residues:     1 -  6377
chrX_119239063_119242946.rev   A   Score:  238   Residues:   162 -   272
chrX_119239063_119242946.rev   Z   Score: 11652   Residues:     1 -  3884
chrX_119259473_119265895   Z   Score: 19269   Residues:     1 -  6423
chrX_119301052_119307445.rev   Z   Score: 19182   Residues:     1 -  6394
chrX_119434929_119437609   Z   Score: 8043   Residues:     1 -  2681
chrX_119502989_119504785   Z   Score: 5391   Residues:     1 -  1797
chrX_119613322_119618373   Z   Score: 15156   Residues:     1 -  5052
chrX_119743057_119749750.rev   Z   Score: 20082   Residues:     1 -  6694
chrX_119759976_119764849.rev   Z   Score: 14622   Residues:     1 -  4874
chrX_119899031_119901254   Z   Score: 6672   Residues:     1 -  2224
chrX_119917265_119921467.rev   Z   Score: 12609   Residues:     1 -  4203
chrX_119929713_119934035.rev   Z   Score: 12969   Residues:     1 -  4323
chrX_120059581_120062705.rev   Z   Score: 9375   Residues:     1 -  3125
chrX_120127299_120129133.rev   Z   Score: 5505   Residues:     1 -  1835
chrX_120135708_120140186   Z   Score: 13437   Residues:     1 -  4479
chrX_120158512_120160339.rev   Z   Score: 5484   Residues:     1 -  1828
chrX_120216715_120220530   Z   Score: 11448   Residues:     1 -  3816
chrX_120320301_120324859.rev   A   Score:  252   Residues:   379 -   487
chrX_120320301_120324859.rev   Z   Score: 13677   Residues:     1 -  4559
chrX_120331579_120333725.rev   Z   Score: 6441   Residues:     1 -  2147
chrX_120350606_120356559.rev   A   Score:  262   Residues:  1533 -  1633
chrX_120350606_120356559.rev   A   Score:  242   Residues:  1992 -  2065
chrX_120350606_120356559.rev   Z   Score: 17862   Residues:     1 -  5954
chrX_120360755_120364022.rev   Z   Score: 9804   Residues:     1 -  3268
chrX_120390844_120397250.rev   Z   Score: 19221   Residues:     1 -  6407
chrX_120412010_120416224   A   Score:  202   Residues:   420 -   478
chrX_120412010_120416224   Z   Score: 12645   Residues:     1 -  4215
chrX_120431750_120434287   Z   Score: 7614   Residues:     1 -  2538
chrX_120486460_120489247   Z   Score: 8364   Residues:     1 -  2788
chrX_120546382_120549219.rev   Z   Score: 8514   Residues:     1 -  2838
chrX_120553621_120557787.rev   Z   Score: 12501   Residues:     1 -  4167
chrX_120559821_120561910.rev   A   Score:  212   Residues:   322 -   429
chrX_120559821_120561910.rev   Z   Score: 6270   Residues:     1 -  2090
chrX_120623301_120625161   Z   Score: 5583   Residues:     1 -  1861
chrX_120630211_120637629.rev   A   Score:  320   Residues:  7285 -  7324
chrX_120630211_120637629.rev   Z   Score: 22257   Residues:     1 -  7419
chrX_120656785_120662632.rev   Z   Score: 17544   Residues:     1 -  5848
chrX_120669928_120674608.rev   Z   Score: 14043   Residues:     1 -  4681
chrX_120683231_120686339   A   Score:  294   Residues:   466 -   512
chrX_120683231_120686339   Z   Score: 9327   Residues:     1 -  3109
chrX_120736245_120742657   Z   Score: 19239   Residues:     1 -  6413
chrX_120760204_120762019.rev   Z   Score: 5448   Residues:     1 -  1816
chrX_120782547_120787558   Z   Score: 15036   Residues:     1 -  5012
chrX_120809147_120811320   Z   Score: 6522   Residues:     1 -  2174
chrX_120840079_120842509   Z   Score: 7293   Residues:     1 -  2431
chrX_120857680_120863751.rev   Z   Score: 18213   Residues:     1 -  6071
chrX_120896311_120902126.rev   A   Score:  201   Residues:  4595 -  4623
chrX_120896311_120902126.rev   Z   Score: 17448   Residues:     1 -  5816
chrX_120922768_120926678   A   Score:  247   Residues:  1067 -  1143
chrX_120922768_120926678   Z   Score: 11733   Residues:     1 -  3911
chrX_120998889_121005312   Z   Score: 19272   Residues:     1 -  6424
chrX_121013885_121015506   Z   Score: 4866   Residues:     1 -  1622
chrX_121023033_121025079   Z   Score: 6141   Residues:     1 -  2047
chrX_121027197_121029138   Z   Score: 5826   Residues:     1 -  1942
chrX_121090985_121095517.rev   Z   Score: 13599   Residues:     1 -  4533
chrX_121120032_121124406.rev   A   Score:  287   Residues:    20 -    59
chrX_121120032_121124406.rev   Z   Score: 13125   Residues:     1 -  4375
chrX_121135830_121138773.rev   Z   Score: 8832   Residues:     1 -  2944
chrX_121146388_121148080   Z   Score: 5079   Residues:     1 -  1693
chrX_121153894_121160065.rev   A   Score:  212   Residues:  3928 -  3969
chrX_121153894_121160065.rev   Z   Score: 18516   Residues:     1 -  6172
chrX_121186053_121190196   Z   Score: 12432   Residues:     1 -  4144
chrX_121212680_121215834   Z   Score: 9465   Residues:     1 -  3155
chrX_121217399_121222803.rev   Z   Score: 16215   Residues:     1 -  5405
chrX_121226863_121229750   Z   Score: 8664   Residues:     1 -  2888
chrX_121230896_121236939.rev   A   Score:  236   Residues:  2795 -  2833
chrX_121230896_121236939.rev   A   Score:  208   Residues:  1182 -  1287
chrX_121230896_121236939.rev   Z   Score: 18132   Residues:     1 -  6044
chrX_121248579_121251074.rev   Z   Score: 7488   Residues:     1 -  2496
chrX_121288877_121290558.rev   Z   Score: 5046   Residues:     1 -  1682
chrX_121293402_121297067.rev   A   Score:  207   Residues:  3530 -  3570
chrX_121293402_121297067.rev   Z   Score: 10998   Residues:     1 -  3666
chrX_121342225_121345486   Z   Score: 9786   Residues:     1 -  3262
chrX_121352113_121358249   T   Score:  213   Residues:  3938 -  3976
chrX_121352113_121358249   Z   Score: 18411   Residues:     1 -  6137
chrX_121363171_121365314.rev   Z   Score: 6432   Residues:     1 -  2144
chrX_121372577_121377801   Z   Score: 15672   Residues:     1 -  5224
chrX_121394056_121395795   Z   Score: 5220   Residues:     1 -  1740
chrX_121398424_121400744   Z   Score: 6963   Residues:     1 -  2321
chrX_121418957_121424577   Z   Score: 16863   Residues:     1 -  5621
chrX_121455915_121457954   Z   Score: 6120   Residues:     1 -  2040
chrX_121459795_121463227   Z   Score: 10299   Residues:     1 -  3433
chrX_121475502_121481326.rev   A   Score:  249   Residues:  2256 -  2290
chrX_121475502_121481326.rev   Z   Score: 17475   Residues:     1 -  5825
chrX_121489926_121494247.rev   A   Score:  229   Residues:  1433 -  1554
chrX_121489926_121494247.rev   Z   Score: 12966   Residues:     1 -  4322
chrX_121508682_121510337   Z   Score: 4968   Residues:     1 -  1656
chrX_121532819_121537805   Z   Score: 14961   Residues:     1 -  4987
chrX_121546557_121548818   Z   Score: 6786   Residues:     1 -  2262
chrX_121564402_121569987   Z   Score: 16758   Residues:     1 -  5586
chrX_121570751_121573537   A   Score:  242   Residues:  1137 -  1296
chrX_121570751_121573537   A   Score:  222   Residues:  2166 -  2199
chrX_121570751_121573537   Z   Score: 8361   Residues:     1 -  2787
chrX_121588426_121591038   Z   Score: 7839   Residues:     1 -  2613
chrX_121619422_121621343   Z   Score: 5766   Residues:     1 -  1922
chrX_121623568_121628400   Z   Score: 14499   Residues:     1 -  4833
chrX_121665490_121667212   Z   Score: 5169   Residues:     1 -  1723
chrX_121780017_121783665.rev   Z   Score: 10947   Residues:     1 -  3649
chrX_121792814_121797568   Z   Score: 14265   Residues:     1 -  4755
chrX_121812328_121814284.rev   Z   Score: 5871   Residues:     1 -  1957
chrX_121869300_121871145   Z   Score: 5538   Residues:     1 -  1846
chrX_121880019_121885284   Z   Score: 15798   Residues:     1 -  5266
chrX_121981680_121987039   Z   Score: 16080   Residues:     1 -  5360
chrX_122008981_122010899   Z   Score: 5757   Residues:     1 -  1919
chrX_122021701_122024029.rev   Z   Score: 6987   Residues:     1 -  2329
chrX_122141839_122148563   A   Score:  225   Residues:  3110 -  3149
chrX_122141839_122148563   Z   Score: 20175   Residues:     1 -  6725
chrX_122245080_122249951.rev   Z   Score: 14613   Residues:     1 -  4871
chrX_122366201_122368071   Z   Score: 5613   Residues:     1 -  1871
chrX_122382642_122384437.rev   Z   Score: 5388   Residues:     1 -  1796
chrX_122388662_122395426.rev   Z   Score: 20295   Residues:     1 -  6765
chrX_122432098_122439097   A   Score:  261   Residues:  3792 -  3834
chrX_122432098_122439097   Z   Score: 21000   Residues:     1 -  7000
chrX_122445330_122447737.rev   Z   Score: 7224   Residues:     1 -  2408
chrX_122506901_122513561   Z   Score: 19983   Residues:     1 -  6661
chrX_122576923_122579180   Z   Score: 6774   Residues:     1 -  2258
chrX_122964047_122970222.rev   Z   Score: 18528   Residues:     1 -  6176
chrX_123080394_123083185.rev   Z   Score: 8376   Residues:     1 -  2792
chrX_123174157_123178774   T   Score:  356   Residues:  2698 -  2754
chrX_123174157_123178774   Z   Score: 13854   Residues:     1 -  4618
chrX_123268198_123270664   Z   Score: 7401   Residues:     1 -  2467
chrX_123441456_123447836   Z   Score: 19143   Residues:     1 -  6381
chrX_123518209_123520518   Z   Score: 6930   Residues:     1 -  2310
chrX_123545373_123547680   T   Score:  378   Residues:  2204 -  2304
chrX_123545373_123547680   Z   Score: 6924   Residues:     1 -  2308
chrX_123611128_123617527.rev   Z   Score: 19200   Residues:     1 -  6400
chrX_123724529_123728774   Z   Score: 12738   Residues:     1 -  4246
chrX_123865306_123871482   Z   Score: 18531   Residues:     1 -  6177
chrX_123909739_123911990   Z   Score: 6756   Residues:     1 -  2252
chrX_123972330_123976526   Z   Score: 12591   Residues:     1 -  4197
chrX_124073125_124074827.rev   Z   Score: 5109   Residues:     1 -  1703
chrX_124104867_124106582   Z   Score: 5148   Residues:     1 -  1716
chrX_124129246_124132049.rev   Z   Score: 8412   Residues:     1 -  2804
chrX_124206738_124208614   Z   Score: 5631   Residues:     1 -  1877
chrX_124300044_124301815.rev   Z   Score: 5316   Residues:     1 -  1772
chrX_124303992_124309858   Z   Score: 17601   Residues:     1 -  5867
chrX_124357969_124362221.rev   A   Score:  228   Residues:   341 -   487
chrX_124357969_124362221.rev   Z   Score: 12759   Residues:     1 -  4253
chrX_124369995_124375071.rev   Z   Score: 15231   Residues:     1 -  5077
chrX_124385712_124389902.rev   Z   Score: 12573   Residues:     1 -  4191
chrX_124396339_124401311   Z   Score: 14919   Residues:     1 -  4973
chrX_124406172_124408001.rev   Z   Score: 5487   Residues:     1 -  1829
chrX_124409152_124410803   Z   Score: 4956   Residues:     1 -  1652
chrX_124434162_124437203   Z   Score: 9126   Residues:     1 -  3042
chrX_124468730_124475000.rev   A   Score:  270   Residues:     1 -   119
chrX_124468730_124475000.rev   Z   Score: 18813   Residues:     1 -  6271
chrX_124488800_124493747   A   Score:  214   Residues:  2117 -  2244
chrX_124488800_124493747   Z   Score: 14844   Residues:     1 -  4948
chrX_124507351_124508988.rev   Z   Score: 4914   Residues:     1 -  1638
chrX_124510255_124513851.rev   A   Score:  332   Residues:   301 -   349
chrX_124510255_124513851.rev   Z   Score: 10788   Residues:     1 -  3596
chrX_124524070_124528986   Z   Score: 14751   Residues:     1 -  4917
chrX_124536717_124538319.rev   Z   Score: 4809   Residues:     1 -  1603
chrX_124559486_124561127.rev   Z   Score: 4926   Residues:     1 -  1642
chrX_124570545_124572304   Z   Score: 5280   Residues:     1 -  1760
chrX_124584457_124586630.rev   Z   Score: 6522   Residues:     1 -  2174
chrX_124639692_124641668.rev   Z   Score: 5931   Residues:     1 -  1977
chrX_124655936_124658233   Z   Score: 6894   Residues:     1 -  2298
chrX_124678071_124685647.rev   A   Score:  225   Residues:  6368 -  6399
chrX_124678071_124685647.rev   Z   Score: 22731   Residues:     1 -  7577
chrX_124697878_124704281   Z   Score: 19212   Residues:     1 -  6404
chrX_124705771_124708367.rev   Z   Score: 7791   Residues:     1 -  2597
chrX_124713380_124715457.rev   Z   Score: 6234   Residues:     1 -  2078
chrX_124720796_124726216   Z   Score: 16263   Residues:     1 -  5421
chrX_124746177_124749334.rev   Z   Score: 9474   Residues:     1 -  3158
chrX_124749377_124753655.rev   A   Score:  209   Residues:  1501 -  1578
chrX_124749377_124753655.rev   Z   Score: 12837   Residues:     1 -  4279
chrX_124777137_124782939.rev   Z   Score: 17409   Residues:     1 -  5803
chrX_124787136_124789490.rev   Z   Score: 7065   Residues:     1 -  2355
chrX_124825475_124827559.rev   Z   Score: 6255   Residues:     1 -  2085
chrX_124867233_124872372   Z   Score: 15420   Residues:     1 -  5140
chrX_124872604_124876883.rev   Z   Score: 12840   Residues:     1 -  4280
chrX_124883563_124885284.rev   A   Score:  346   Residues:     1 -    74
chrX_124883563_124885284.rev   Z   Score: 5166   Residues:     1 -  1722
chrX_124922768_124928451   Z   Score: 17049   Residues:     1 -  5683
chrX_124963895_124970155.rev   Z   Score: 18783   Residues:     1 -  6261
chrX_124976853_124978852.rev   Z   Score: 6000   Residues:     1 -  2000
chrX_124986797_124989896.rev   A   Score:  202   Residues:    57 -   140
chrX_124986797_124989896.rev   Z   Score: 9300   Residues:     1 -  3100
chrX_125004737_125010546.rev   Z   Score: 17430   Residues:     1 -  5810
chrX_125044989_125051270.rev   Z   Score: 18846   Residues:     1 -  6282
chrX_125089228_125095445.rev   Z   Score: 18654   Residues:     1 -  6218
chrX_125111796_125115374.rev   Z   Score: 10737   Residues:     1 -  3579
chrX_125152272_125153992   Z   Score: 5163   Residues:     1 -  1721
chrX_125170286_125172184.rev   Z   Score: 5697   Residues:     1 -  1899
chrX_125182594_125188343   Z   Score: 17250   Residues:     1 -  5750
chrX_125190749_125192743.rev   Z   Score: 5985   Residues:     1 -  1995
chrX_125221976_125223928.rev   Z   Score: 5859   Residues:     1 -  1953
chrX_125229187_125232209   Z   Score: 9069   Residues:     1 -  3023
chrX_125242169_125248544   Z   Score: 19128   Residues:     1 -  6376
chrX_125277862_125282843.rev   Z   Score: 14946   Residues:     1 -  4982
chrX_125293922_125296365   A   Score: 1245   Residues:   233 -   528
chrX_125293922_125296365   R   Score:  398   Residues:   233 -   502
chrX_125293922_125296365   Z   Score: 7332   Residues:     1 -  2444
chrX_125300437_125304361.rev   Z   Score: 11775   Residues:     1 -  3925
chrX_125319679_125324556   Z   Score: 14634   Residues:     1 -  4878
chrX_125360160_125361916.rev   Z   Score: 5271   Residues:     1 -  1757
chrX_125363349_125366404.rev   Z   Score: 9168   Residues:     1 -  3056
chrX_125399404_125401446   Z   Score: 6129   Residues:     1 -  2043
chrX_125449305_125451686.rev   Z   Score: 7146   Residues:     1 -  2382
chrX_125461443_125465472   A   Score:  282   Residues:  3296 -  3352
chrX_125461443_125465472   Z   Score: 12090   Residues:     1 -  4030
chrX_125485834_125487908.rev   Z   Score: 6225   Residues:     1 -  2075
chrX_125502762_125504556   Z   Score: 5385   Residues:     1 -  1795
chrX_125529941_125537523   C   Score:  243   Residues:  2747 -  2836
chrX_125529941_125537523   T   Score:  222   Residues:   222 -   288
chrX_125529941_125537523   Z   Score: 22749   Residues:     1 -  7583
chrX_125632334_125636337   A   Score:  246   Residues:  2474 -  2521
chrX_125632334_125636337   Z   Score: 12012   Residues:     1 -  4004
chrX_125667993_125671926.rev   Z   Score: 11802   Residues:     1 -  3934
chrX_125697384_125701843   A   Score:  200   Residues:   428 -   485
chrX_125697384_125701843   Z   Score: 13380   Residues:     1 -  4460
chrX_125711129_125715117.rev   Z   Score: 11967   Residues:     1 -  3989
chrX_125716815_125721064   A   Score:  234   Residues:   420 -   485
chrX_125716815_125721064   A   Score:  207   Residues:  1435 -  1568
chrX_125716815_125721064   Z   Score: 12750   Residues:     1 -  4250
chrX_125731062_125735747.rev   Z   Score: 14058   Residues:     1 -  4686
chrX_125760511_125765897   Z   Score: 16161   Residues:     1 -  5387
chrX_125766135_125770050   Z   Score: 11748   Residues:     1 -  3916
chrX_125783767_125787498.rev   Z   Score: 11196   Residues:     1 -  3732
chrX_125789915_125793324.rev   Z   Score: 10230   Residues:     1 -  3410
chrX_125805798_125812155   A   Score:  221   Residues:  2819 -  2860
chrX_125805798_125812155   Z   Score: 19074   Residues:     1 -  6358
chrX_125828133_125829873   Z   Score: 5223   Residues:     1 -  1741
chrX_125878371_125882052   A   Score:  208   Residues:  1411 -  1445
chrX_125878371_125882052   Z   Score: 11046   Residues:     1 -  3682
chrX_125893225_125895998   Z   Score: 8322   Residues:     1 -  2774
chrX_125905482_125909883.rev   Z   Score: 13206   Residues:     1 -  4402
chrX_125910593_125916970.rev   Z   Score: 19134   Residues:     1 -  6378
chrX_125930699_125932508.rev   Z   Score: 5430   Residues:     1 -  1810
chrX_125938564_125940270   Z   Score: 5121   Residues:     1 -  1707
chrX_125941137_125943151   A   Score:  208   Residues:   897 -   955
chrX_125941137_125943151   Z   Score: 6042   Residues:     1 -  2014
chrX_125961270_125967318   Z   Score: 18147   Residues:     1 -  6049
chrX_125968223_125971576   Z   Score: 10062   Residues:     1 -  3354
chrX_125976468_125983989   Z   Score: 22566   Residues:     1 -  7522
chrX_126009333_126011415.rev   Z   Score: 6249   Residues:     1 -  2083
chrX_126021513_126023437.rev   Z   Score: 5775   Residues:     1 -  1925
chrX_126060891_126066545   Z   Score: 16965   Residues:     1 -  5655
chrX_126073749_126079171   Z   Score: 16269   Residues:     1 -  5423
chrX_126079720_126083927.rev   Z   Score: 12624   Residues:     1 -  4208
chrX_126110233_126116510.rev   Z   Score: 18834   Residues:     1 -  6278
chrX_126164549_126171218   A   Score:  215   Residues:  3064 -  3103
chrX_126164549_126171218   Z   Score: 20010   Residues:     1 -  6670
chrX_126196181_126200504.rev   A   Score:  610   Residues:  2487 -  2618
chrX_126196181_126200504.rev   Z   Score: 12972   Residues:     1 -  4324
chrX_126200817_126204306   Z   Score: 10470   Residues:     1 -  3490
chrX_126221242_126227520   Z   Score: 18837   Residues:     1 -  6279
chrX_126233716_126238622   A   Score:  224   Residues:  3171 -  3226
chrX_126233716_126238622   Z   Score: 14721   Residues:     1 -  4907
chrX_126239846_126241852.rev   Z   Score: 6021   Residues:     1 -  2007
chrX_126322598_126324595   Z   Score: 5994   Residues:     1 -  1998
chrX_126333079_126338138   Z   Score: 15180   Residues:     1 -  5060
chrX_126340232_126343506.rev   Z   Score: 9825   Residues:     1 -  3275
chrX_126355003_126359072   A   Score:  242   Residues:  1711 -  1752
chrX_126355003_126359072   Z   Score: 12210   Residues:     1 -  4070
chrX_126376701_126378623.rev   Z   Score: 5769   Residues:     1 -  1923
chrX_126379206_126384927   Z   Score: 17166   Residues:     1 -  5722
chrX_126398402_126403017.rev   A   Score:  209   Residues:   418 -   486
chrX_126398402_126403017.rev   Z   Score: 13848   Residues:     1 -  4616
chrX_126421198_126423231.rev   Z   Score: 6102   Residues:     1 -  2034
chrX_126511628_126514053   Z   Score: 7278   Residues:     1 -  2426
chrX_126577620_126580457   Z   Score: 8514   Residues:     1 -  2838
chrX_126596913_126599402   Z   Score: 7470   Residues:     1 -  2490
chrX_126625710_126630239   A   Score:  231   Residues:  4402 -  4451
chrX_126625710_126630239   Z   Score: 13590   Residues:     1 -  4530
chrX_126639197_126642403.rev   A   Score:  244   Residues:   473 -   505
chrX_126639197_126642403.rev   Z   Score: 9621   Residues:     1 -  3207
chrX_126642685_126646934.rev   Z   Score: 12750   Residues:     1 -  4250
chrX_126650038_126654187   Z   Score: 12450   Residues:     1 -  4150
chrX_126676358_126681651   A   Score:  253   Residues:  3352 -  3397
chrX_126676358_126681651   Z   Score: 15879   Residues:     1 -  5293
chrX_126682046_126685392   A   Score:  207   Residues:   296 -   325
chrX_126682046_126685392   Z   Score: 10041   Residues:     1 -  3347
chrX_126695542_126697313   Z   Score: 5316   Residues:     1 -  1772
chrX_126702169_126703840   Z   Score: 5016   Residues:     1 -  1672
chrX_126722240_126724489   Z   Score: 6750   Residues:     1 -  2250
chrX_126727202_126729265   Z   Score: 6192   Residues:     1 -  2064
chrX_126769615_126772778   Z   Score: 9492   Residues:     1 -  3164
chrX_126811729_126816126.rev   Z   Score: 13194   Residues:     1 -  4398
chrX_126819305_126823657.rev   Z   Score: 13059   Residues:     1 -  4353
chrX_126838412_126840286   Z   Score: 5625   Residues:     1 -  1875
chrX_126843557_126847397.rev   Z   Score: 11523   Residues:     1 -  3841
chrX_126867085_126868710.rev   Z   Score: 4878   Residues:     1 -  1626
chrX_126880239_126883538   Z   Score: 9900   Residues:     1 -  3300
chrX_126901418_126906336.rev   Z   Score: 14757   Residues:     1 -  4919
chrX_126911896_126913933.rev   A   Score:  261   Residues:   475 -   555
chrX_126911896_126913933.rev   Z   Score: 6114   Residues:     1 -  2038
chrX_126918842_126923827   Z   Score: 14958   Residues:     1 -  4986
chrX_126930234_126938275   A   Score:  263   Residues:  4652 -  4702
chrX_126930234_126938275   Z   Score: 24126   Residues:     1 -  8042
chrX_126968569_126970221.rev   Z   Score: 4959   Residues:     1 -  1653
chrX_126982951_126986671   Z   Score: 11163   Residues:     1 -  3721
chrX_127007494_127013069   Z   Score: 16728   Residues:     1 -  5576
chrX_127016963_127021542.rev   A   Score:  274   Residues:  2367 -  2404
chrX_127016963_127021542.rev   Z   Score: 13740   Residues:     1 -  4580
chrX_127037319_127043085   Z   Score: 17301   Residues:     1 -  5767
chrX_127059128_127064349   Z   Score: 15666   Residues:     1 -  5222
chrX_127068012_127074023   A   Score:  238   Residues:  3798 -  3841
chrX_127068012_127074023   Z   Score: 18036   Residues:     1 -  6012
chrX_127134909_127136683   Z   Score: 5325   Residues:     1 -  1775
chrX_127148828_127151367   Z   Score: 7620   Residues:     1 -  2540
chrX_127154709_127157257   A   Score:  513   Residues:   391 -   509
chrX_127154709_127157257   A   Score:  261   Residues:   983 -  1025
chrX_127154709_127157257   Z   Score: 7647   Residues:     1 -  2549
chrX_127158857_127163746   A   Score:  205   Residues:  3878 -  3917
chrX_127158857_127163746   Z   Score: 14670   Residues:     1 -  4890
chrX_127186957_127192000.rev   A   Score:  345   Residues:  3663 -  3713
chrX_127186957_127192000.rev   Z   Score: 15132   Residues:     1 -  5044
chrX_127237965_127242198   Z   Score: 12702   Residues:     1 -  4234
chrX_127244211_127249209   Z   Score: 14997   Residues:     1 -  4999
chrX_127272201_127275100.rev   Z   Score: 8700   Residues:     1 -  2900
chrX_127369279_127372617   A   Score:  326   Residues:  1390 -  1441
chrX_127369279_127372617   Z   Score: 10017   Residues:     1 -  3339
chrX_127384975_127390414   A   Score:  251   Residues:  5015 -  5070
chrX_127384975_127390414   Z   Score: 16320   Residues:     1 -  5440
chrX_127397066_127403211.rev   Z   Score: 18438   Residues:     1 -  6146
chrX_127450875_127457199.rev   Z   Score: 18975   Residues:     1 -  6325
chrX_127528800_127535529.rev   Z   Score: 20190   Residues:     1 -  6730
chrX_127591751_127598155   Z   Score: 19215   Residues:     1 -  6405
chrX_127632326_127636680.rev   Z   Score: 13065   Residues:     1 -  4355
chrX_127641668_127647935   Z   Score: 18804   Residues:     1 -  6268
chrX_127651368_127655974   Z   Score: 13821   Residues:     1 -  4607
chrX_127775559_127777487   Z   Score: 5787   Residues:     1 -  1929
chrX_127846657_127850892.rev   A   Score:  241   Residues:  1444 -  1563
chrX_127846657_127850892.rev   Z   Score: 12708   Residues:     1 -  4236
chrX_127876303_127878970.rev   Z   Score: 8004   Residues:     1 -  2668
chrX_127903350_127909659   Z   Score: 18930   Residues:     1 -  6310
chrX_128017794_128020239.rev   Z   Score: 7338   Residues:     1 -  2446
chrX_128032280_128036556.rev   Z   Score: 12831   Residues:     1 -  4277
chrX_128064466_128068757.rev   Z   Score: 12876   Residues:     1 -  4292
chrX_128099874_128106265   Z   Score: 19176   Residues:     1 -  6392
chrX_128109998_128114258.rev   Z   Score: 12783   Residues:     1 -  4261
chrX_128137217_128140120.rev   Z   Score: 8712   Residues:     1 -  2904
chrX_128150038_128153359   Z   Score: 9966   Residues:     1 -  3322
chrX_128196068_128202331   Z   Score: 18792   Residues:     1 -  6264
chrX_128211220_128217225   Z   Score: 18018   Residues:     1 -  6006
chrX_128239301_128242268   A   Score:  256   Residues:   976 -  1012
chrX_128239301_128242268   Z   Score: 8904   Residues:     1 -  2968
chrX_128247210_128252184   Z   Score: 14925   Residues:     1 -  4975
chrX_128268215_128270583   A   Score:  272   Residues:  1942 -  1991
chrX_128268215_128270583   Z   Score: 7107   Residues:     1 -  2369
chrX_128282599_128286730.rev   Z   Score: 12396   Residues:     1 -  4132
chrX_128312367_128314878   Z   Score: 7536   Residues:     1 -  2512
chrX_128483224_128486167   Z   Score: 8832   Residues:     1 -  2944
chrX_128622108_128624362   Z   Score: 6765   Residues:     1 -  2255
chrX_128666859_128668989   Z   Score: 6393   Residues:     1 -  2131
chrX_128713410_128719372.rev   Z   Score: 17889   Residues:     1 -  5963
chrX_129161377_129163687.rev   Z   Score: 6933   Residues:     1 -  2311
chrX_129168317_129170851.rev   Z   Score: 7602   Residues:     1 -  2534
chrX_129172980_129174972.rev   Z   Score: 5979   Residues:     1 -  1993
chrX_129297599_129301222.rev   Z   Score: 10872   Residues:     1 -  3624
chrX_129307270_129313662.rev   Z   Score: 19179   Residues:     1 -  6393
chrX_129377313_129382664   Z   Score: 16056   Residues:     1 -  5352
chrX_129427429_129433670.rev   Z   Score: 18726   Residues:     1 -  6242
chrX_129437668_129439298   A   Score:  366   Residues:    78 -   136
chrX_129437668_129439298   Z   Score: 4893   Residues:     1 -  1631
chrX_129590573_129593294   Z   Score: 8166   Residues:     1 -  2722
chrX_129617824_129623164.rev   T   Score:  306   Residues:  2830 -  2871
chrX_129617824_129623164.rev   T   Score:  216   Residues:  4053 -  4079
chrX_129617824_129623164.rev   Z   Score: 16023   Residues:     1 -  5341
chrX_129672469_129679145   Z   Score: 20031   Residues:     1 -  6677
chrX_129794090_129797515   Z   Score: 10278   Residues:     1 -  3426
chrX_129812068_129816090.rev   T   Score:  214   Residues:   159 -   186
chrX_129812068_129816090.rev   Z   Score: 12069   Residues:     1 -  4023
chrX_129817941_129824215   Z   Score: 18825   Residues:     1 -  6275
chrX_129878459_129882815.rev   Z   Score: 13071   Residues:     1 -  4357
chrX_129964911_129970222.rev   Z   Score: 15936   Residues:     1 -  5312
chrX_129982975_129989252.rev   Z   Score: 18834   Residues:     1 -  6278
chrX_129993486_129995103.rev   Z   Score: 4854   Residues:     1 -  1618
chrX_130001038_130003149   Z   Score: 6336   Residues:     1 -  2112
chrX_130012032_130014672.rev   Z   Score: 7923   Residues:     1 -  2641
chrX_130041475_130043115.rev   Z   Score: 4923   Residues:     1 -  1641
chrX_130105303_130111583.rev   Z   Score: 18843   Residues:     1 -  6281
chrX_130169003_130170781   Z   Score: 5337   Residues:     1 -  1779
chrX_130194712_130196546.rev   T   Score:  380   Residues:   303 -   405
chrX_130194712_130196546.rev   Z   Score: 5505   Residues:     1 -  1835
chrX_130209669_130211933   A   Score:  227   Residues:   440 -   546
chrX_130209669_130211933   Z   Score: 6795   Residues:     1 -  2265
chrX_130238096_130242947.rev   Z   Score: 14556   Residues:     1 -  4852
chrX_130286993_130293673   Z   Score: 20043   Residues:     1 -  6681
chrX_130383500_130389889   Z   Score: 19170   Residues:     1 -  6390
chrX_130428185_130430551.rev   Z   Score: 7098   Residues:     1 -  2366
chrX_130437690_130443988   Z   Score: 18897   Residues:     1 -  6299
chrX_130461005_130463296.rev   Z   Score: 6876   Residues:     1 -  2292
chrX_130498640_130501142   Z   Score: 7509   Residues:     1 -  2503
chrX_130508175_130510214.rev   A   Score:  219   Residues:   274 -   356
chrX_130508175_130510214.rev   Z   Score: 6120   Residues:     1 -  2040
chrX_130512265_130514662.rev   Z   Score: 7194   Residues:     1 -  2398
chrX_130523001_130529283   Z   Score: 18849   Residues:     1 -  6283
chrX_130728726_130730560   Z   Score: 5505   Residues:     1 -  1835
chrX_130780335_130782370   Z   Score: 6108   Residues:     1 -  2036
chrX_130811981_130814781.rev   Z   Score: 8403   Residues:     1 -  2801
chrX_130825917_130828812   A   Score:  280   Residues:   236 -   328
chrX_130825917_130828812   Z   Score: 8688   Residues:     1 -  2896
chrX_130848557_130854964   T   Score:  200   Residues:   180 -   216
chrX_130848557_130854964   Z   Score: 19224   Residues:     1 -  6408
chrX_130946648_130949806   A   Score:  238   Residues:  1473 -  1508
chrX_130946648_130949806   Z   Score: 9477   Residues:     1 -  3159
chrX_130991874_130998071   T   Score:  212   Residues:   229 -   260
chrX_130991874_130998071   Z   Score: 18594   Residues:     1 -  6198
chrX_131015959_131022221.rev   Z   Score: 18789   Residues:     1 -  6263
chrX_131090492_131093975.rev   Z   Score: 10452   Residues:     1 -  3484
chrX_131103850_131106582.rev   Z   Score: 8199   Residues:     1 -  2733
chrX_131134025_131137721.rev   A   Score:  205   Residues:   907 -  1029
chrX_131134025_131137721.rev   Z   Score: 11091   Residues:     1 -  3697
chrX_131139100_131140743.rev   Z   Score: 4932   Residues:     1 -  1644
chrX_131144283_131150680.rev   Z   Score: 19194   Residues:     1 -  6398
chrX_131370141_131371778   Z   Score: 4914   Residues:     1 -  1638
chrX_131394549_131399278.rev   A   Score:  247   Residues:  4273 -  4435
chrX_131394549_131399278.rev   T   Score:  385   Residues:  3295 -  3356
chrX_131394549_131399278.rev   T   Score:  303   Residues:  3660 -  3740
chrX_131394549_131399278.rev   Z   Score: 14190   Residues:     1 -  4730
chrX_131415409_131417033.rev   Z   Score: 4875   Residues:     1 -  1625
chrX_131722971_131731248   Z   Score: 24834   Residues:     1 -  8278
chrX_131740441_131742947.rev   Z   Score: 7521   Residues:     1 -  2507
chrX_131796797_131800753   A   Score:  226   Residues:   928 -   969
chrX_131796797_131800753   Z   Score: 11871   Residues:     1 -  3957
chrX_131868722_131875130   Z   Score: 19227   Residues:     1 -  6409
chrX_131895977_131902708.rev   Z   Score: 20196   Residues:     1 -  6732
chrX_131922768_131927184   Z   Score: 13251   Residues:     1 -  4417
chrX_131968215_131975829   Z   Score: 22845   Residues:     1 -  7615
chrX_132017814_132025901   Z   Score: 24261   Residues:     1 -  8087
chrX_132137745_132144417   Z   Score: 20019   Residues:     1 -  6673
chrX_132376837_132378660.rev   Z   Score: 5472   Residues:     1 -  1824
chrX_132480228_132486624   Z   Score: 19191   Residues:     1 -  6397
chrX_132592508_132596186   A   Score:  356   Residues:  1587 -  1663
chrX_132592508_132596186   Z   Score: 11037   Residues:     1 -  3679
chrX_132618136_132620094   Z   Score: 5877   Residues:     1 -  1959
chrX_132787733_132789347.rev   Z   Score: 4845   Residues:     1 -  1615
chrX_132903961_132910356.rev   Z   Score: 19188   Residues:     1 -  6396
chrX_132916436_132922824.rev   A   Score:  283   Residues:  1894 -  1963
chrX_132916436_132922824.rev   Z   Score: 19167   Residues:     1 -  6389
chrX_132938541_132944903   Z   Score: 19089   Residues:     1 -  6363
chrX_132971121_132973043.rev   Z   Score: 5769   Residues:     1 -  1923
chrX_132976230_132982629   Z   Score: 19200   Residues:     1 -  6400
chrX_133070459_133072883   Z   Score: 7275   Residues:     1 -  2425
chrX_133137284_133139357.rev   A   Score:  308   Residues:  1137 -  1243
chrX_133137284_133139357.rev   A   Score:  242   Residues:   724 -   770
chrX_133137284_133139357.rev   Z   Score: 6222   Residues:     1 -  2074
chrX_133161033_133165593   A   Score:  202   Residues:  1440 -  1566
chrX_133161033_133165593   Z   Score: 13683   Residues:     1 -  4561
chrX_133183803_133188496.rev   A   Score:  290   Residues:  4334 -  4406
chrX_133183803_133188496.rev   Z   Score: 14082   Residues:     1 -  4694
chrX_133267599_133269476.rev   Z   Score: 5634   Residues:     1 -  1878
chrX_133450950_133455951.rev   A   Score:  231   Residues:  1475 -  1581
chrX_133450950_133455951.rev   A   Score:  200   Residues:  3661 -  3699
chrX_133450950_133455951.rev   Z   Score: 15003   Residues:     1 -  5001
chrX_133474379_133476825.rev   A   Score:  225   Residues:   285 -   325
chrX_133474379_133476825.rev   Z   Score: 7341   Residues:     1 -  2447
chrX_133568118_133570291   Z   Score: 6522   Residues:     1 -  2174
chrX_133614685_133616981.rev   A   Score:  344   Residues:  1553 -  1620
chrX_133614685_133616981.rev   Z   Score: 6891   Residues:     1 -  2297
chrX_133617000_133619082   Z   Score: 6249   Residues:     1 -  2083
chrX_133701131_133704527.rev   A   Score:  207   Residues:  1394 -  1423
chrX_133701131_133704527.rev   Z   Score: 10191   Residues:     1 -  3397
chrX_133839566_133841494.rev   Z   Score: 5787   Residues:     1 -  1929
chrX_133884521_133887499   Z   Score: 8937   Residues:     1 -  2979
chrX_133929138_133930804   Z   Score: 5001   Residues:     1 -  1667
chrX_133966050_133970217.rev   Z   Score: 12504   Residues:     1 -  4168
chrX_134023498_134027793   A   Score:  223   Residues:  1984 -  2025
chrX_134023498_134027793   Z   Score: 12888   Residues:     1 -  4296
chrX_134046754_134051048   Z   Score: 12885   Residues:     1 -  4295
chrX_134062612_134067900.rev   Z   Score: 15867   Residues:     1 -  5289
chrX_134117513_134123914.rev   Z   Score: 19206   Residues:     1 -  6402
chrX_134125220_134129473   Z   Score: 12762   Residues:     1 -  4254
chrX_134136192_134142893.rev   Z   Score: 20106   Residues:     1 -  6702
chrX_134158331_134160074.rev   Z   Score: 5232   Residues:     1 -  1744
chrX_134171700_134175895.rev   Z   Score: 12588   Residues:     1 -  4196
chrX_134215371_134217439.rev   Z   Score: 6207   Residues:     1 -  2069
chrX_134268792_134270472   Z   Score: 5043   Residues:     1 -  1681
chrX_134276087_134278586   Z   Score: 7500   Residues:     1 -  2500
chrX_134316517_134318942.rev   Z   Score: 7278   Residues:     1 -  2426
chrX_134519007_134525398.rev   Z   Score: 19176   Residues:     1 -  6392
chrX_134575162_134578158.rev   Z   Score: 8991   Residues:     1 -  2997
chrX_134650038_134652531   Z   Score: 7482   Residues:     1 -  2494
chrX_134743786_134750042.rev   Z   Score: 18771   Residues:     1 -  6257
chrX_134755006_134758030   Z   Score: 9075   Residues:     1 -  3025
chrX_134762323_134764695   Z   Score: 7119   Residues:     1 -  2373
chrX_134915751_134919318.rev   A   Score:  213   Residues:  2863 -  2902
chrX_134915751_134919318.rev   T   Score:  424   Residues:  1651 -  1713
chrX_134915751_134919318.rev   Z   Score: 10704   Residues:     1 -  3568
chrX_135181966_135187490.rev   A   Score:  506   Residues:   170 -   417
chrX_135181966_135187490.rev   A   Score:  314   Residues:  2603 -  2670
chrX_135181966_135187490.rev   R   Score:  266   Residues:   170 -   392
chrX_135181966_135187490.rev   G   Score:  333   Residues:   230 -   392
chrX_135181966_135187490.rev   Z   Score: 16575   Residues:     1 -  5525
chrX_135248200_135254480.rev   Z   Score: 18843   Residues:     1 -  6281
chrX_135266607_135269650.rev   Z   Score: 9132   Residues:     1 -  3044
chrX_135643557_135645958.rev   Z   Score: 7206   Residues:     1 -  2402
chrX_135706713_135709262.rev   Z   Score: 7650   Residues:     1 -  2550
chrX_135775420_135778316.rev   Z   Score: 8691   Residues:     1 -  2897
chrX_135785051_135788402.rev   Z   Score: 10056   Residues:     1 -  3352
chrX_135792970_135795053.rev   Z   Score: 6252   Residues:     1 -  2084
chrX_135882654_135889048.rev   Z   Score: 19185   Residues:     1 -  6395
chrX_135920900_135922490.rev   Z   Score: 4773   Residues:     1 -  1591
chrX_135929598_135935976   Z   Score: 19137   Residues:     1 -  6379
chrX_135937184_135943051   A   Score:  320   Residues:  3462 -  3501
chrX_135937184_135943051   Z   Score: 17601   Residues:     1 -  5867
chrX_135943942_135947367   A   Score:  206   Residues:  2769 -  2795
chrX_135943942_135947367   Z   Score: 10278   Residues:     1 -  3426
chrX_135962547_135965294   A   Score:  209   Residues:  1225 -  1266
chrX_135962547_135965294   A   Score:  207   Residues:   800 -   854
chrX_135962547_135965294   Z   Score: 8244   Residues:     1 -  2748
chrX_136054754_136057787   Z   Score: 9102   Residues:     1 -  3034
chrX_136105883_136107773   A   Score:  280   Residues:  1695 -  1734
chrX_136105883_136107773   Z   Score: 5673   Residues:     1 -  1891
chrX_136190198_136192996   Z   Score: 8397   Residues:     1 -  2799
chrX_136199696_136201305   Z   Score: 4830   Residues:     1 -  1610
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chrX_136201394_136206090.rev   Z   Score: 14091   Residues:     1 -  4697
chrX_136470045_136472873.rev   A   Score:  890   Residues:   819 -  1003
chrX_136470045_136472873.rev   R   Score:  309   Residues:   819 -  1005
chrX_136470045_136472873.rev   Z   Score: 8487   Residues:     1 -  2829
chrX_136479297_136485689   Z   Score: 19179   Residues:     1 -  6393
chrX_136520566_136524191.rev   Z   Score: 10878   Residues:     1 -  3626
chrX_136598921_136605891   A   Score:  242   Residues:  4115 -  4193
chrX_136598921_136605891   Z   Score: 20913   Residues:     1 -  6971
chrX_136639858_136644434.rev   A   Score:  234   Residues:  3284 -  3316
chrX_136639858_136644434.rev   Z   Score: 13731   Residues:     1 -  4577
chrX_136742772_136745005   A   Score:  228   Residues:   681 -   715
chrX_136742772_136745005   Z   Score: 6702   Residues:     1 -  2234
chrX_136759195_136763344.rev   Z   Score: 12450   Residues:     1 -  4150
chrX_136766866_136773261   Z   Score: 19188   Residues:     1 -  6396
chrX_136778163_136784557   Z   Score: 19185   Residues:     1 -  6395
chrX_136835114_136840055   Z   Score: 14826   Residues:     1 -  4942
chrX_136880618_136886988   Z   Score: 19113   Residues:     1 -  6371
chrX_136892855_136899857   A   Score:  272   Residues:   942 -   980
chrX_136892855_136899857   Z   Score: 21009   Residues:     1 -  7003
chrX_136909332_136918879   Z   Score: 28644   Residues:     1 -  9548
chrX_136927065_136928771.rev   Z   Score: 5121   Residues:     1 -  1707
chrX_136975947_136977882.rev   Z   Score: 5808   Residues:     1 -  1936
chrX_137002940_137005032.rev   Z   Score: 6279   Residues:     1 -  2093
chrX_137005487_137011864   Z   Score: 19134   Residues:     1 -  6378
chrX_137037922_137044312   Z   Score: 19173   Residues:     1 -  6391
chrX_137085020_137089335.rev   Z   Score: 12948   Residues:     1 -  4316
chrX_137124318_137128966.rev   A   Score:  234   Residues:  1822 -  1908
chrX_137124318_137128966.rev   Z   Score: 13947   Residues:     1 -  4649
chrX_137191639_137196577   Z   Score: 14817   Residues:     1 -  4939
chrX_137244791_137247183.rev   Z   Score: 7179   Residues:     1 -  2393
chrX_137263023_137269419   Z   Score: 19191   Residues:     1 -  6397
chrX_137271383_137276787   Z   Score: 16215   Residues:     1 -  5405
chrX_137317062_137318971   Z   Score: 5730   Residues:     1 -  1910
chrX_137337233_137339299.rev   Z   Score: 6201   Residues:     1 -  2067
chrX_137342485_137344367   Z   Score: 5649   Residues:     1 -  1883
chrX_137402800_137404394   Z   Score: 4785   Residues:     1 -  1595
chrX_137412885_137416510.rev   Z   Score: 10878   Residues:     1 -  3626
chrX_137430587_137433277   Z   Score: 8073   Residues:     1 -  2691
chrX_137585490_137591758   Z   Score: 18807   Residues:     1 -  6269
chrX_137603993_137606582.rev   Z   Score: 7770   Residues:     1 -  2590
chrX_137614520_137619038   Z   Score: 13557   Residues:     1 -  4519
chrX_137621250_137624427   A   Score:  205   Residues:  2205 -  2242
chrX_137621250_137624427   Z   Score: 9534   Residues:     1 -  3178
chrX_137639594_137645205.rev   Z   Score: 16836   Residues:     1 -  5612
chrX_137658670_137661155   Z   Score: 7458   Residues:     1 -  2486
chrX_137803246_137809783   Z   Score: 19614   Residues:     1 -  6538
chrX_137816963_137821285   A   Score:  260   Residues:  2066 -  2113
chrX_137816963_137821285   Z   Score: 12969   Residues:     1 -  4323
chrX_137860687_137863487.rev   A   Score:  200   Residues:  1665 -  1689
chrX_137860687_137863487.rev   Z   Score: 8403   Residues:     1 -  2801
chrX_137869003_137870907.rev   Z   Score: 5715   Residues:     1 -  1905
chrX_137874962_137877020.rev   Z   Score: 6177   Residues:     1 -  2059
chrX_137968223_137970985   Z   Score: 8289   Residues:     1 -  2763
chrX_137981335_137985807.rev   A   Score:  201   Residues:  1631 -  1746
chrX_137981335_137985807.rev   Z   Score: 13419   Residues:     1 -  4473
chrX_138066731_138073107   A   Score:  207   Residues:   321 -   356
chrX_138066731_138073107   Z   Score: 19131   Residues:     1 -  6377
chrX_138134693_138139014   Z   Score: 12966   Residues:     1 -  4322
chrX_138156453_138160692.rev   Z   Score: 12720   Residues:     1 -  4240
chrX_138178716_138181088.rev   Z   Score: 7119   Residues:     1 -  2373
chrX_138242876_138249267   Z   Score: 19176   Residues:     1 -  6392
chrX_138331858_138337127   Z   Score: 15810   Residues:     1 -  5270
chrX_138427583_138431179   Z   Score: 10791   Residues:     1 -  3597
chrX_138461571_138464175.rev   Z   Score: 7815   Residues:     1 -  2605
chrX_138478244_138484634.rev   Z   Score: 19173   Residues:     1 -  6391
chrX_138490530_138492419   Z   Score: 5670   Residues:     1 -  1890
chrX_138511187_138514155   A   Score:  213   Residues:   225 -   324
chrX_138511187_138514155   Z   Score: 8907   Residues:     1 -  2969
chrX_138723907_138725781   A   Score:  222   Residues:  1728 -  1756
chrX_138723907_138725781   Z   Score: 5625   Residues:     1 -  1875
chrX_138765793_138772503   Z   Score: 20133   Residues:     1 -  6711
chrX_138796935_138803342.rev   Z   Score: 19224   Residues:     1 -  6408
chrX_138831975_138833728.rev   A   Score:  250   Residues:   410 -   449
chrX_138831975_138833728.rev   Z   Score: 5262   Residues:     1 -  1754
chrX_138922151_138924762.rev   Z   Score: 7836   Residues:     1 -  2612
chrX_138939546_138942951.rev   Z   Score: 10215   Residues:     1 -  3405
chrX_138959397_138961460.rev   Z   Score: 6192   Residues:     1 -  2064
chrX_139046240_139050440.rev   Z   Score: 12603   Residues:     1 -  4201
chrX_139074767_139081533.rev   Z   Score: 20301   Residues:     1 -  6767
chrX_139084871_139089131.rev   Z   Score: 12783   Residues:     1 -  4261
chrX_139115626_139119701   Z   Score: 12225   Residues:     1 -  4075
chrX_139173459_139175340   Z   Score: 5646   Residues:     1 -  1882
chrX_139200629_139205040   A   Score:  232   Residues:  1986 -  2014
chrX_139200629_139205040   Z   Score: 13236   Residues:     1 -  4412
chrX_139205779_139210110   Z   Score: 12996   Residues:     1 -  4332
chrX_139361806_139364132   Z   Score: 6981   Residues:     1 -  2327
chrX_139372872_139377782.rev   Z   Score: 14733   Residues:     1 -  4911
chrX_139413537_139415934.rev   Z   Score: 7194   Residues:     1 -  2398
chrX_139440108_139446520   Z   Score: 19239   Residues:     1 -  6413
chrX_139596889_139599543.rev   Z   Score: 7965   Residues:     1 -  2655
chrX_139616597_139621203.rev   Z   Score: 13821   Residues:     1 -  4607
chrX_139681228_139683155   Z   Score: 5784   Residues:     1 -  1928
chrX_139690960_139694671   A   Score:  206   Residues:  1484 -  1510
chrX_139690960_139694671   Z   Score: 11136   Residues:     1 -  3712
chrX_139863517_139869704   Z   Score: 18564   Residues:     1 -  6188
chrX_139982428_139986620   Z   Score: 12579   Residues:     1 -  4193
chrX_140005164_140011305.rev   Z   Score: 18426   Residues:     1 -  6142
chrX_140104347_140106582.rev   Z   Score: 6708   Residues:     1 -  2236
chrX_140149009_140151064   Z   Score: 6168   Residues:     1 -  2056
chrX_140185265_140191208   A   Score:  212   Residues:  3320 -  3367
chrX_140185265_140191208   Z   Score: 17832   Residues:     1 -  5944
chrX_140199269_140204121   Z   Score: 14559   Residues:     1 -  4853
chrX_140204989_140207153.rev   Z   Score: 6495   Residues:     1 -  2165
chrX_140213072_140215011.rev   Z   Score: 5820   Residues:     1 -  1940
chrX_140237838_140241522   A   Score:  275   Residues:   361 -   406
chrX_140237838_140241522   Z   Score: 11055   Residues:     1 -  3685
chrX_140261509_140267336   Z   Score: 17484   Residues:     1 -  5828
chrX_140350975_140357162.rev   Z   Score: 18564   Residues:     1 -  6188
chrX_140469579_140472077   Z   Score: 7497   Residues:     1 -  2499
chrX_140558776_140561127.rev   Z   Score: 7056   Residues:     1 -  2352
chrX_140612791_140617777.rev   Z   Score: 14961   Residues:     1 -  4987
chrX_140621643_140626181.rev   Z   Score: 13617   Residues:     1 -  4539
chrX_140661013_140663456   Z   Score: 7332   Residues:     1 -  2444
chrX_140674029_140675999   Z   Score: 5913   Residues:     1 -  1971
chrX_140686468_140688414   Z   Score: 5841   Residues:     1 -  1947
chrX_140738624_140742867.rev   Z   Score: 12732   Residues:     1 -  4244
chrX_140759486_140764029.rev   Z   Score: 13632   Residues:     1 -  4544
chrX_140789790_140794070.rev   A   Score:  278   Residues:   288 -   328
chrX_140789790_140794070.rev   Z   Score: 12843   Residues:     1 -  4281
chrX_140821579_140825058.rev   Z   Score: 10440   Residues:     1 -  3480
chrX_140825597_140829216.rev   A   Score:  296   Residues:   946 -   982
chrX_140825597_140829216.rev   A   Score:  274   Residues:  2912 -  2949
chrX_140825597_140829216.rev   Z   Score: 10860   Residues:     1 -  3620
chrX_140873047_140877479.rev   Z   Score: 13299   Residues:     1 -  4433
chrX_140945303_140948096.rev   Z   Score: 8382   Residues:     1 -  2794
chrX_140951752_140956344   Z   Score: 13779   Residues:     1 -  4593
chrX_140966276_140969770.rev   Z   Score: 10485   Residues:     1 -  3495
chrX_140983945_140985658   Z   Score: 5142   Residues:     1 -  1714
chrX_141059130_141061219   Z   Score: 6270   Residues:     1 -  2090
chrX_141150930_141157209   Z   Score: 18840   Residues:     1 -  6280
chrX_141199150_141205428.rev   Z   Score: 18837   Residues:     1 -  6279
chrX_141223726_141228461   A   Score:  210   Residues:   417 -   484
chrX_141223726_141228461   Z   Score: 14208   Residues:     1 -  4736
chrX_141247969_141250440   Z   Score: 7416   Residues:     1 -  2472
chrX_141281144_141283089   Z   Score: 5838   Residues:     1 -  1946
chrX_141290656_141296927   Z   Score: 18816   Residues:     1 -  6272
chrX_141312247_141316320   Z   Score: 12222   Residues:     1 -  4074
chrX_141352865_141354869.rev   Z   Score: 6015   Residues:     1 -  2005
chrX_141375871_141379304.rev   A   Score:  249   Residues:   713 -   776
chrX_141375871_141379304.rev   Z   Score: 10302   Residues:     1 -  3434
chrX_141385273_141388074   Z   Score: 8406   Residues:     1 -  2802
chrX_141441383_141444443.rev   Z   Score: 9183   Residues:     1 -  3061
chrX_141478003_141479613.rev   A   Score:  232   Residues:   117 -   265
chrX_141478003_141479613.rev   Z   Score: 4833   Residues:     1 -  1611
chrX_141512159_141514144.rev   Z   Score: 5958   Residues:     1 -  1986
chrX_141519973_141521863   Z   Score: 5673   Residues:     1 -  1891
chrX_141529381_141531134   Z   Score: 5262   Residues:     1 -  1754
chrX_141570222_141573779.rev   Z   Score: 10674   Residues:     1 -  3558
chrX_141577394_141584483.rev   Z   Score: 21270   Residues:     1 -  7090
chrX_141603831_141609263.rev   Z   Score: 16299   Residues:     1 -  5433
chrX_141624149_141626515   Z   Score: 7101   Residues:     1 -  2367
chrX_141653617_141655234.rev   Z   Score: 4854   Residues:     1 -  1618
chrX_141781756_141788985   Z   Score: 21690   Residues:     1 -  7230
chrX_141795287_141796990   Z   Score: 5112   Residues:     1 -  1704
chrX_141831858_141834508   Z   Score: 7953   Residues:     1 -  2651
chrX_141859318_141863503.rev   Z   Score: 12558   Residues:     1 -  4186
chrX_141874103_141876660.rev   A   Score:  225   Residues:  1678 -  1748
chrX_141874103_141876660.rev   Z   Score: 7674   Residues:     1 -  2558
chrX_141956244_141964945   T   Score:  200   Residues:  3745 -  3769
chrX_141956244_141964945   Z   Score: 26106   Residues:     1 -  8702
chrX_142011058_142014667.rev   Z   Score: 10830   Residues:     1 -  3610
chrX_142226063_142230338.rev   Z   Score: 12828   Residues:     1 -  4276
chrX_142337006_142341250.rev   Z   Score: 12735   Residues:     1 -  4245
chrX_142351932_142357902   Z   Score: 17913   Residues:     1 -  5971
chrX_142377314_142380527   A   Score:  281   Residues:   168 -   237
chrX_142377314_142380527   Z   Score: 9642   Residues:     1 -  3214
chrX_142412104_142415214   Z   Score: 9333   Residues:     1 -  3111
chrX_142470046_142471791   Z   Score: 5238   Residues:     1 -  1746
chrX_142571163_142577510.rev   Z   Score: 19044   Residues:     1 -  6348
chrX_142687889_142689574.rev   A   Score:  207   Residues:  1466 -  1500
chrX_142687889_142689574.rev   Z   Score: 5058   Residues:     1 -  1686
chrX_142704876_142708208.rev   A   Score:  220   Residues:   807 -   841
chrX_142704876_142708208.rev   Z   Score: 9999   Residues:     1 -  3333
chrX_142731675_142735992   Z   Score: 12954   Residues:     1 -  4318
chrX_142741567_142743268.rev   Z   Score: 5106   Residues:     1 -  1702
chrX_142759009_142760934   Z   Score: 5778   Residues:     1 -  1926
chrX_142766470_142774878.rev   Z   Score: 25227   Residues:     1 -  8409
chrX_142779002_142780623.rev   Z   Score: 4866   Residues:     1 -  1622
chrX_142803311_142805363   Z   Score: 6159   Residues:     1 -  2053
chrX_142832229_142834148   Z   Score: 5760   Residues:     1 -  1920
chrX_142857111_142862236   A   Score:  219   Residues:  4997 -  5038
chrX_142857111_142862236   Z   Score: 15378   Residues:     1 -  5126
chrX_142869895_142875290   Z   Score: 16188   Residues:     1 -  5396
chrX_142903257_142904926   Z   Score: 5010   Residues:     1 -  1670
chrX_142913959_142919496   Z   Score: 16614   Residues:     1 -  5538
chrX_142968229_142973699   Z   Score: 16413   Residues:     1 -  5471
chrX_143033509_143035344.rev   Z   Score: 5508   Residues:     1 -  1836
chrX_143067458_143069138.rev   Z   Score: 5043   Residues:     1 -  1681
chrX_143090744_143094828.rev   Z   Score: 12255   Residues:     1 -  4085
chrX_143123395_143126491   Z   Score: 9291   Residues:     1 -  3097
chrX_143207871_143210802   Z   Score: 8796   Residues:     1 -  2932
chrX_143305907_143309819.rev   Z   Score: 11739   Residues:     1 -  3913
chrX_143367467_143371712.rev   Z   Score: 12738   Residues:     1 -  4246
chrX_143429610_143431828   Z   Score: 6657   Residues:     1 -  2219
chrX_143538163_143544760.rev   A   Score:  308   Residues:  2033 -  2073
chrX_143538163_143544760.rev   Z   Score: 19794   Residues:     1 -  6598
chrX_143592285_143595300.rev   Z   Score: 9048   Residues:     1 -  3016
chrX_143599947_143604160   Z   Score: 12642   Residues:     1 -  4214
chrX_143606233_143607839   Z   Score: 4821   Residues:     1 -  1607
chrX_143616625_143618372   Z   Score: 5244   Residues:     1 -  1748
chrX_143641803_143643628   Z   Score: 5478   Residues:     1 -  1826
chrX_143655183_143660150.rev   Z   Score: 14904   Residues:     1 -  4968
chrX_143671469_143673591   Z   Score: 6369   Residues:     1 -  2123
chrX_143717539_143721664.rev   Z   Score: 12378   Residues:     1 -  4126
chrX_143742233_143746784   Z   Score: 13656   Residues:     1 -  4552
chrX_143779908_143786843.rev   A   Score:  397   Residues:  6111 -  6276
chrX_143779908_143786843.rev   Z   Score: 20808   Residues:     1 -  6936
chrX_143803202_143806457   Z   Score: 9768   Residues:     1 -  3256
chrX_143807823_143810817   Z   Score: 8985   Residues:     1 -  2995
chrX_143835353_143841668   Z   Score: 18948   Residues:     1 -  6316
chrX_143921841_143923465   Z   Score: 4875   Residues:     1 -  1625
chrX_143993539_143997985   Z   Score: 13341   Residues:     1 -  4447
chrX_144053604_144058624   Z   Score: 15063   Residues:     1 -  5021
chrX_144087019_144092546.rev   Z   Score: 16584   Residues:     1 -  5528
chrX_144135613_144137445   Z   Score: 5499   Residues:     1 -  1833
chrX_144139497_144141346   Z   Score: 5550   Residues:     1 -  1850
chrX_144173841_144180575.rev   Z   Score: 20205   Residues:     1 -  6735
chrX_144187439_144191136   Z   Score: 11094   Residues:     1 -  3698
chrX_144228660_144230780   Z   Score: 6363   Residues:     1 -  2121
chrX_144342851_144348164   Z   Score: 15942   Residues:     1 -  5314
chrX_144348573_144350532.rev   Z   Score: 5880   Residues:     1 -  1960
chrX_144421860_144423609.rev   Z   Score: 5250   Residues:     1 -  1750
chrX_144427596_144431219   Z   Score: 10872   Residues:     1 -  3624
chrX_144442388_144444483   Z   Score: 6288   Residues:     1 -  2096
chrX_144456343_144459178.rev   Z   Score: 8508   Residues:     1 -  2836
chrX_144489640_144493855   Z   Score: 12648   Residues:     1 -  4216
chrX_144549217_144551100   Z   Score: 5652   Residues:     1 -  1884
chrX_144570111_144574845   A   Score:  241   Residues:   414 -   501
chrX_144570111_144574845   A   Score:  200   Residues:    32 -    56
chrX_144570111_144574845   Z   Score: 14205   Residues:     1 -  4735
chrX_144654335_144659708.rev   Z   Score: 16122   Residues:     1 -  5374
chrX_144675666_144680381.rev   Z   Score: 14148   Residues:     1 -  4716
chrX_144681019_144685243.rev   Z   Score: 12675   Residues:     1 -  4225
chrX_144704656_144706528   Z   Score: 5619   Residues:     1 -  1873
chrX_144742572_144744409   Z   Score: 5514   Residues:     1 -  1838
chrX_144752121_144755989   Z   Score: 11607   Residues:     1 -  3869
chrX_144799202_144800961   Z   Score: 5280   Residues:     1 -  1760
chrX_144903719_144912157   Z   Score: 25317   Residues:     1 -  8439
chrX_144919815_144921662.rev   Z   Score: 5544   Residues:     1 -  1848
chrX_144997104_145000463.rev   A   Score:  207   Residues:  2216 -  2305
chrX_144997104_145000463.rev   Z   Score: 10080   Residues:     1 -  3360
chrX_145015245_145021657.rev   T   Score:  228   Residues:    94 -   129
chrX_145015245_145021657.rev   Z   Score: 19239   Residues:     1 -  6413
chrX_145040030_145041932   Z   Score: 5709   Residues:     1 -  1903
chrX_145060711_145065506.rev   Z   Score: 14388   Residues:     1 -  4796
chrX_145080185_145082104.rev   Z   Score: 5760   Residues:     1 -  1920
chrX_145109096_145111891   Z   Score: 8388   Residues:     1 -  2796
chrX_145175679_145180065.rev   A   Score:  231   Residues:   422 -   490
chrX_145175679_145180065.rev   Z   Score: 13161   Residues:     1 -  4387
chrX_145243456_145248422   Z   Score: 14901   Residues:     1 -  4967
chrX_145270343_145272259.rev   Z   Score: 5751   Residues:     1 -  1917
chrX_145277788_145284957   A   Score:  234   Residues:  2544 -  2581
chrX_145277788_145284957   Z   Score: 21510   Residues:     1 -  7170
chrX_145301545_145306091.rev   A   Score:  202   Residues:  3430 -  3478
chrX_145301545_145306091.rev   Z   Score: 13641   Residues:     1 -  4547
chrX_145307837_145310168   Z   Score: 6996   Residues:     1 -  2332
chrX_145381494_145385818.rev   A   Score:  215   Residues:   417 -   475
chrX_145381494_145385818.rev   Z   Score: 12975   Residues:     1 -  4325
chrX_145389908_145391738.rev   Z   Score: 5493   Residues:     1 -  1831
chrX_145421585_145423312   Z   Score: 5184   Residues:     1 -  1728
chrX_145469801_145474084.rev   Z   Score: 12852   Residues:     1 -  4284
chrX_145591734_145593940   Z   Score: 6621   Residues:     1 -  2207
chrX_145604703_145606909.rev   Z   Score: 6621   Residues:     1 -  2207
chrX_145631467_145633330   Z   Score: 5592   Residues:     1 -  1864
chrX_145722676_145727338.rev   A   Score:  304   Residues:  2636 -  2697
chrX_145722676_145727338.rev   A   Score:  209   Residues:   386 -   465
chrX_145722676_145727338.rev   A   Score:  212   Residues:  3255 -  3283
chrX_145722676_145727338.rev   G   Score:  218   Residues:   399 -   463
chrX_145722676_145727338.rev   Z   Score: 13989   Residues:     1 -  4663
chrX_145790115_145793702.rev   Z   Score: 10764   Residues:     1 -  3588
chrX_145795357_145799173.rev   Z   Score: 11451   Residues:     1 -  3817
chrX_145799891_145802755   Z   Score: 8595   Residues:     1 -  2865
chrX_145812519_145814143.rev   Z   Score: 4875   Residues:     1 -  1625
chrX_145823885_145825739.rev   Z   Score: 5565   Residues:     1 -  1855
chrX_145833468_145835989   A   Score:  602   Residues:  1516 -  1664
chrX_145833468_145835989   R   Score:  267   Residues:  1516 -  1664
chrX_145833468_145835989   G   Score:  202   Residues:  1533 -  1621
chrX_145833468_145835989   Z   Score: 7566   Residues:     1 -  2522
chrX_145898730_145901708   Z   Score: 8937   Residues:     1 -  2979
chrX_145921703_145924243   Z   Score: 7623   Residues:     1 -  2541
chrX_145929330_145935725.rev   Z   Score: 19188   Residues:     1 -  6396
chrX_145946806_145951071.rev   Z   Score: 12798   Residues:     1 -  4266
chrX_145989642_145993255   Z   Score: 10842   Residues:     1 -  3614
chrX_146142337_146144439   Z   Score: 6309   Residues:     1 -  2103
chrX_146157881_146163147.rev   A   Score:  336   Residues:   753 -   794
chrX_146157881_146163147.rev   Z   Score: 15801   Residues:     1 -  5267
chrX_146193064_146196392   A   Score:  277   Residues:  2680 -  2732
chrX_146193064_146196392   Z   Score: 9987   Residues:     1 -  3329
chrX_146247840_146249501   Z   Score: 4983   Residues:     1 -  1661
chrX_146267330_146271468.rev   Z   Score: 12417   Residues:     1 -  4139
chrX_146303249_146304962.rev   Z   Score: 5142   Residues:     1 -  1714
chrX_146307820_146310535   Z   Score: 8148   Residues:     1 -  2716
chrX_146364723_146367846   Z   Score: 9372   Residues:     1 -  3124
chrX_146374794_146377357   Z   Score: 7692   Residues:     1 -  2564
chrX_146378833_146380786   Z   Score: 5862   Residues:     1 -  1954
chrX_146444185_146446578   Z   Score: 7182   Residues:     1 -  2394
chrX_146449833_146451667.rev   Z   Score: 5505   Residues:     1 -  1835
chrX_146459823_146461500   Z   Score: 5034   Residues:     1 -  1678
chrX_146463894_146465793   Z   Score: 5700   Residues:     1 -  1900
chrX_146470285_146475140   A   Score:  236   Residues:  1470 -  1505
chrX_146470285_146475140   A   Score:  200   Residues:  2299 -  2328
chrX_146470285_146475140   Z   Score: 14568   Residues:     1 -  4856
chrX_146481701_146483485   Z   Score: 5355   Residues:     1 -  1785
chrX_146486099_146488397   A   Score:  280   Residues:  1691 -  1725
chrX_146486099_146488397   Z   Score: 6897   Residues:     1 -  2299
chrX_146498764_146500970.rev   Z   Score: 6621   Residues:     1 -  2207
chrX_146555065_146557394.rev   Z   Score: 6990   Residues:     1 -  2330
chrX_146605642_146612378   Z   Score: 20211   Residues:     1 -  6737
chrX_146639554_146641330.rev   Z   Score: 5331   Residues:     1 -  1777
chrX_146656603_146660892   Z   Score: 12870   Residues:     1 -  4290
chrX_146692070_146694719   Z   Score: 7950   Residues:     1 -  2650
chrX_146754414_146762046   Z   Score: 22899   Residues:     1 -  7633
chrX_146770054_146778008.rev   Z   Score: 23865   Residues:     1 -  7955
chrX_146845032_146846865.rev   Z   Score: 5502   Residues:     1 -  1834
chrX_146910784_146917041.rev   Z   Score: 18774   Residues:     1 -  6258
chrX_146925348_146926974   Z   Score: 4881   Residues:     1 -  1627
chrX_146963462_146970068.rev   Z   Score: 19821   Residues:     1 -  6607
chrX_147060948_147066686   Z   Score: 17217   Residues:     1 -  5739
chrX_147087068_147093430.rev   Z   Score: 19089   Residues:     1 -  6363
chrX_147112818_147119169.rev   Z   Score: 19056   Residues:     1 -  6352
chrX_147127767_147132104   A   Score:  616   Residues:  1981 -  2120
chrX_147127767_147132104   R   Score:  203   Residues:  1981 -  2120
chrX_147127767_147132104   Z   Score: 13014   Residues:     1 -  4338
chrX_147134227_147140602.rev   Z   Score: 19128   Residues:     1 -  6376
chrX_147176502_147180780   A   Score:  227   Residues:   150 -   180
chrX_147176502_147180780   A   Score:  202   Residues:  3008 -  3040
chrX_147176502_147180780   Z   Score: 12837   Residues:     1 -  4279
chrX_147182753_147184715.rev   Z   Score: 5889   Residues:     1 -  1963
chrX_147522939_147527235.rev   Z   Score: 12891   Residues:     1 -  4297
chrX_147606001_147607852.rev   Z   Score: 5556   Residues:     1 -  1852
chrX_147808832_147810945   Z   Score: 6342   Residues:     1 -  2114
chrX_147870559_147873608   Z   Score: 9150   Residues:     1 -  3050
chrX_147899037_147903457   Z   Score: 13263   Residues:     1 -  4421
chrX_147939718_147944411.rev   Z   Score: 14082   Residues:     1 -  4694
chrX_147949291_147954148   Z   Score: 14574   Residues:     1 -  4858
chrX_147965446_147972732   Z   Score: 21861   Residues:     1 -  7287
chrX_147979411_147983862   Z   Score: 13356   Residues:     1 -  4452
chrX_148022619_148025761   Z   Score: 9429   Residues:     1 -  3143
chrX_148027372_148029272   Z   Score: 5703   Residues:     1 -  1901
chrX_148029852_148032457.rev   Z   Score: 7818   Residues:     1 -  2606
chrX_148120616_148126881   Z   Score: 18798   Residues:     1 -  6266
chrX_148178721_148180363   Z   Score: 4929   Residues:     1 -  1643
chrX_148202716_148204347   Z   Score: 4896   Residues:     1 -  1632
chrX_148212366_148216657   Z   Score: 12876   Residues:     1 -  4292
chrX_148216832_148218458   Z   Score: 4881   Residues:     1 -  1627
chrX_148222645_148228892   Z   Score: 18744   Residues:     1 -  6248
chrX_148303831_148308882   A   Score:  266   Residues:  2600 -  2641
chrX_148303831_148308882   Z   Score: 15156   Residues:     1 -  5052
chrX_148361855_148364660   Z   Score: 8418   Residues:     1 -  2806
chrX_148403545_148405333   Z   Score: 5367   Residues:     1 -  1789
chrX_148579359_148582164.rev   Z   Score: 8418   Residues:     1 -  2806
chrX_148601265_148603691   Z   Score: 7281   Residues:     1 -  2427
chrX_148646373_148652019   Z   Score: 16941   Residues:     1 -  5647
chrX_148676787_148679673   Z   Score: 8661   Residues:     1 -  2887
chrX_148857616_148859420.rev   Z   Score: 5415   Residues:     1 -  1805
chrX_148867942_148869692   Z   Score: 5253   Residues:     1 -  1751
chrX_148905172_148910923.rev   Z   Score: 17256   Residues:     1 -  5752
chrX_148960450_148965557   Z   Score: 15324   Residues:     1 -  5108
chrX_148967759_148969428.rev   Z   Score: 5010   Residues:     1 -  1670
chrX_149047909_149049532.rev   Z   Score: 4872   Residues:     1 -  1624
chrX_149125941_149128314   Z   Score: 7122   Residues:     1 -  2374
chrX_149130151_149132511   Z   Score: 7083   Residues:     1 -  2361
chrX_149218620_149221973.rev   A   Score:  336   Residues:   217 -   273
chrX_149218620_149221973.rev   A   Score:  232   Residues:  2372 -  2425
chrX_149218620_149221973.rev   Z   Score: 10062   Residues:     1 -  3354
chrX_149232024_149236007.rev   A   Score:  224   Residues:   995 -  1022
chrX_149232024_149236007.rev   A   Score:  213   Residues:  3014 -  3046
chrX_149232024_149236007.rev   Z   Score: 11952   Residues:     1 -  3984
chrX_149268237_149276208.rev   A   Score:  338   Residues:  7335 -  7393
chrX_149268237_149276208.rev   Z   Score: 23916   Residues:     1 -  7972
chrX_149277425_149279398.rev   Z   Score: 5922   Residues:     1 -  1974
chrX_149545084_149547035   Z   Score: 5856   Residues:     1 -  1952
chrX_149592107_149593856.rev   Z   Score: 5250   Residues:     1 -  1750
chrX_149829893_149832924   Z   Score: 9096   Residues:     1 -  3032
chrX_149901807_149904121.rev   Z   Score: 6945   Residues:     1 -  2315
chrX_149945226_149950983.rev   A   Score:  325   Residues:  3329 -  3380
chrX_149945226_149950983.rev   A   Score:  208   Residues:  1104 -  1139
chrX_149945226_149950983.rev   Z   Score: 17274   Residues:     1 -  5758
chrX_149988258_149989941.rev   Z   Score: 5052   Residues:     1 -  1684
chrX_150025113_150026737.rev   Z   Score: 4875   Residues:     1 -  1625
chrX_150038373_150044784   Z   Score: 19236   Residues:     1 -  6412
chrX_150045660_150048723.rev   Z   Score: 9192   Residues:     1 -  3064
chrX_150054332_150056059.rev   Z   Score: 5184   Residues:     1 -  1728
chrX_150090969_150097758   A   Score:  215   Residues:  3076 -  3115
chrX_150090969_150097758   Z   Score: 20370   Residues:     1 -  6790
chrX_150124152_150127323.rev   A   Score: 1336   Residues:  2059 -  2325
chrX_150124152_150127323.rev   R   Score:  433   Residues:  2057 -  2325
chrX_150124152_150127323.rev   Z   Score: 9516   Residues:     1 -  3172
chrX_150129808_150133005.rev   Z   Score: 9594   Residues:     1 -  3198
chrX_150158775_150161082.rev   Z   Score: 6924   Residues:     1 -  2308
chrX_150168861_150175139   Z   Score: 18837   Residues:     1 -  6279
chrX_150239338_150241640.rev   Z   Score: 6909   Residues:     1 -  2303
chrX_150289188_150292816.rev   Z   Score: 10887   Residues:     1 -  3629
chrX_150294111_150297059.rev   Z   Score: 8847   Residues:     1 -  2949
chrX_150308618_150313212.rev   Z   Score: 13785   Residues:     1 -  4595
chrX_150319466_150321914   Z   Score: 7347   Residues:     1 -  2449
chrX_150332560_150335215.rev   Z   Score: 7968   Residues:     1 -  2656
chrX_150337627_150341428   Z   Score: 11406   Residues:     1 -  3802
chrX_150381069_150383317.rev   Z   Score: 6747   Residues:     1 -  2249
chrX_150624739_150626645   Z   Score: 5721   Residues:     1 -  1907
chrX_150671694_150674645   Z   Score: 8856   Residues:     1 -  2952
chrX_150675222_150681343   Z   Score: 18366   Residues:     1 -  6122
chrX_150684218_150685962   Z   Score: 5235   Residues:     1 -  1745
chrX_150688114_150689789   Z   Score: 5028   Residues:     1 -  1676
chrX_150746326_150747910   Z   Score: 4755   Residues:     1 -  1585
chrX_150777103_150779051.rev   Z   Score: 5844   Residues:     1 -  1948
chrX_150838990_150840983.rev   Z   Score: 5982   Residues:     1 -  1994
chrX_150850142_150851868   Z   Score: 5181   Residues:     1 -  1727
chrX_150889543_150894558   Z   Score: 15048   Residues:     1 -  5016
chrX_150896898_150899562   Z   Score: 7995   Residues:     1 -  2665
chrX_150900354_150902278   Z   Score: 5775   Residues:     1 -  1925
chrX_150902849_150905358.rev   Z   Score: 7530   Residues:     1 -  2510
chrX_150915734_150917767.rev   Z   Score: 6102   Residues:     1 -  2034
chrX_150929752_150931408   Z   Score: 4971   Residues:     1 -  1657
chrX_150962758_150964355.rev   A   Score:  222   Residues:   190 -   315
chrX_150962758_150964355.rev   R   Score:  250   Residues:   188 -   315
chrX_150962758_150964355.rev   G   Score:  446   Residues:   188 -   313
chrX_150962758_150964355.rev   Z   Score: 4794   Residues:     1 -  1598
chrX_150982216_150985439.rev   Z   Score: 9672   Residues:     1 -  3224
chrX_151075286_151077589.rev   Z   Score: 6912   Residues:     1 -  2304
chrX_151128804_151135368.rev   Z   Score: 19695   Residues:     1 -  6565
chrX_151142604_151144524.rev   Z   Score: 5763   Residues:     1 -  1921
chrX_151147631_151152432   Z   Score: 14406   Residues:     1 -  4802
chrX_151166500_151169650   Z   Score: 9453   Residues:     1 -  3151
chrX_151195918_151199367.rev   Z   Score: 10350   Residues:     1 -  3450
chrX_151212599_151214565.rev   A   Score:  282   Residues:  1168 -  1206
chrX_151212599_151214565.rev   Z   Score: 5901   Residues:     1 -  1967
chrX_151222927_151224538   Z   Score: 4836   Residues:     1 -  1612
chrX_151273001_151277755   Z   Score: 14265   Residues:     1 -  4755
chrX_151300994_151303402   Z   Score: 7227   Residues:     1 -  2409
chrX_151304348_151306459   Z   Score: 6336   Residues:     1 -  2112
chrX_151308626_151314891   Z   Score: 18798   Residues:     1 -  6266
chrX_151320943_151322750   Z   Score: 5424   Residues:     1 -  1808
chrX_151356694_151359258   A   Score:  202   Residues:  1877 -  1912
chrX_151356694_151359258   Z   Score: 7695   Residues:     1 -  2565
chrX_151361867_151364424   Z   Score: 7674   Residues:     1 -  2558
chrX_151383066_151389338   Z   Score: 18819   Residues:     1 -  6273
chrX_151420455_151426845   Z   Score: 19173   Residues:     1 -  6391
chrX_151431719_151434125.rev   Z   Score: 7221   Residues:     1 -  2407
chrX_151502252_151504815.rev   Z   Score: 7692   Residues:     1 -  2564
chrX_151513763_151518107.rev   Z   Score: 13035   Residues:     1 -  4345
chrX_151532739_151534330   A   Score:  237   Residues:  1173 -  1208
chrX_151532739_151534330   Z   Score: 4776   Residues:     1 -  1592
chrX_151548404_151550003   A   Score:  256   Residues:   235 -   311
chrX_151548404_151550003   Z   Score: 4800   Residues:     1 -  1600
chrX_151577473_151579054.rev   Z   Score: 4746   Residues:     1 -  1582
chrX_151596614_151598213.rev   A   Score:  256   Residues:   237 -   313
chrX_151596614_151598213.rev   Z   Score: 4800   Residues:     1 -  1600
chrX_151612270_151613864.rev   A   Score:  237   Residues:  1174 -  1209
chrX_151612270_151613864.rev   Z   Score: 4785   Residues:     1 -  1595
chrX_151631508_151633167.rev   Z   Score: 4980   Residues:     1 -  1660
chrX_151674665_151681050.rev   Z   Score: 19158   Residues:     1 -  6386
chrX_152116408_152118018.rev   Z   Score: 4833   Residues:     1 -  1611
chrX_152403236_152404894.rev   Z   Score: 4977   Residues:     1 -  1659
chrX_152540401_152543875   A   Score:  202   Residues:  1007 -  1040
chrX_152540401_152543875   Z   Score: 10425   Residues:     1 -  3475
chrX_153457362_153462830.rev   Z   Score: 16407   Residues:     1 -  5469
chrX_153478212_153481216   A   Score:  215   Residues:   960 -   995
chrX_153478212_153481216   Z   Score: 9015   Residues:     1 -  3005
chrX_153482922_153484898   Z   Score: 5931   Residues:     1 -  1977
chrX_153493120_153495300   Z   Score: 6543   Residues:     1 -  2181
chrX_153499485_153501101   Z   Score: 4848   Residues:     1 -  1616
chrX_153546743_153549032   A   Score:  241   Residues:  1164 -  1197
chrX_153546743_153549032   Z   Score: 6870   Residues:     1 -  2290
chrX_153588818_153590509   Z   Score: 5076   Residues:     1 -  1692
chrX_153597951_153599574   G   Score:  256   Residues:   460 -   494
chrX_153597951_153599574   Z   Score: 4872   Residues:     1 -  1624
chrX_153635025_153641412.rev   Z   Score: 19164   Residues:     1 -  6388
chrX_153643139_153645249.rev   Z   Score: 6333   Residues:     1 -  2111
chrX_153659925_153666701   Z   Score: 20328   Residues:     1 -  6776
chrX_153672963_153675988   Z   Score: 9078   Residues:     1 -  3026
chrX_153703431_153705166.rev   Z   Score: 5208   Residues:     1 -  1736
chrX_153733556_153739776   A   Score:  220   Residues:  5648 -  5677
chrX_153733556_153739776   Z   Score: 18663   Residues:     1 -  6221
chrX_153763753_153768890.rev   A   Score:  330   Residues:  4180 -  4233
chrX_153763753_153768890.rev   Z   Score: 15414   Residues:     1 -  5138
chrX_153803729_153808401   Z   Score: 14016   Residues:     1 -  4672
chrX_153811441_153813228   Z   Score: 5364   Residues:     1 -  1788
chrX_153827742_153829760.rev   Z   Score: 6057   Residues:     1 -  2019
chrX_153830576_153832596.rev   Z   Score: 6063   Residues:     1 -  2021
chrX_153888057_153889894   Z   Score: 5514   Residues:     1 -  1838
chrX_153900127_153903101.rev   Z   Score: 8922   Residues:     1 -  2974
chrX_153904113_153906358   T   Score:  218   Residues:   978 -  1012
chrX_153904113_153906358   Z   Score: 6738   Residues:     1 -  2246
chrX_153912735_153914739   Z   Score: 6015   Residues:     1 -  2005
chrX_153916959_153918533   Z   Score: 4725   Residues:     1 -  1575
chrX_153942057_153946341.rev   Z   Score: 12855   Residues:     1 -  4285
chrX_153949648_153955812.rev   Z   Score: 18495   Residues:     1 -  6165
chrX_153981949_153987323.rev   T   Score:  206   Residues:  1541 -  1571
chrX_153981949_153987323.rev   Z   Score: 16125   Residues:     1 -  5375
chrX_153989108_153995502   Z   Score: 19185   Residues:     1 -  6395
chrX_154059118_154063536.rev   Z   Score: 13257   Residues:     1 -  4419
chrX_154092845_154099118.rev   Z   Score: 18822   Residues:     1 -  6274
chrX_154111782_154118539   Z   Score: 20274   Residues:     1 -  6758
chrX_154130075_154133081.rev   Z   Score: 9021   Residues:     1 -  3007
chrX_154133365_154135412.rev   Z   Score: 6144   Residues:     1 -  2048
chrX_154146867_154152633   Z   Score: 17301   Residues:     1 -  5767
chrX_154170117_154173099   Z   Score: 8949   Residues:     1 -  2983
chrX_154185683_154188788   Z   Score: 9318   Residues:     1 -  3106
chrX_154199442_154205098   Z   Score: 16971   Residues:     1 -  5657
chrX_154214840_154221241   Z   Score: 19206   Residues:     1 -  6402
chrX_154254333_154257315.rev   Z   Score: 8949   Residues:     1 -  2983
chrX_154274985_154280765.rev   Z   Score: 17343   Residues:     1 -  5781
chrX_154294540_154297546   Z   Score: 9021   Residues:     1 -  3007
chrX_154309634_154315913.rev   Z   Score: 18840   Residues:     1 -  6280
chrX_154360719_154367109   Z   Score: 19173   Residues:     1 -  6391
chrX_154368469_154371131   Z   Score: 7989   Residues:     1 -  2663
chrX_154371728_154374116   Z   Score: 7167   Residues:     1 -  2389
chrX_154377156_154382608   Z   Score: 16359   Residues:     1 -  5453
chrX_154398099_154402680   Z   Score: 13746   Residues:     1 -  4582
chrX_154411660_154413302.rev   Z   Score: 4929   Residues:     1 -  1643
chrX_154445833_154447668.rev   Z   Score: 5508   Residues:     1 -  1836
chrX_154457070_154459023   Z   Score: 5862   Residues:     1 -  1954
chrX_154502282_154506564.rev   A   Score:  252   Residues:  1464 -  1596
chrX_154502282_154506564.rev   Z   Score: 12849   Residues:     1 -  4283
chrX_154516400_154522689.rev   Z   Score: 18870   Residues:     1 -  6290
chrX_154546712_154548827.rev   Z   Score: 6348   Residues:     1 -  2116
chrX_154600844_154608090   Z   Score: 21741   Residues:     1 -  7247
chrX_154698034_154703458.rev   C   Score:  241   Residues:  1500 -  1576
chrX_154698034_154703458.rev   Z   Score: 16275   Residues:     1 -  5425
chrX_154705994_154712630.rev   Z   Score: 19911   Residues:     1 -  6637
chrX_154724330_154730691.rev   Z   Score: 19086   Residues:     1 -  6362
chr20_32931_38007   Z   Score: 15231   Residues:     1 -  5077
chr20_40777_43316.rev   A   Score:  274   Residues:  1647 -  1684
chr20_40777_43316.rev   Z   Score: 7620   Residues:     1 -  2540
chr20_58106_64382   Z   Score: 18831   Residues:     1 -  6277
chr20_111361_115972   Z   Score: 13836   Residues:     1 -  4612
chr20_340385_342510.rev   Z   Score: 6378   Residues:     1 -  2126
chr20_448389_450460   Z   Score: 6216   Residues:     1 -  2072
chr20_1025365_1027494.rev   Z   Score: 6390   Residues:     1 -  2130
chr20_1028149_1030958.rev   Z   Score: 8430   Residues:     1 -  2810
chr20_1039640_1041317   Z   Score: 5034   Residues:     1 -  1678
chr20_1067343_1073327   A   Score:  210   Residues:   126 -   179
chr20_1067343_1073327   Z   Score: 17955   Residues:     1 -  5985
chr20_1144919_1151713   Y   Score:  235   Residues:  5070 -  5222
chr20_1144919_1151713   T   Score:  816   Residues:  5071 -  5222
chr20_1144919_1151713   Z   Score: 20385   Residues:     1 -  6795
chr20_1274334_1281831.rev   A   Score:  575   Residues:   842 -  1042
chr20_1274334_1281831.rev   R   Score:  365   Residues:   841 -  1045
chr20_1274334_1281831.rev   G   Score:  408   Residues:   863 -  1048
chr20_1274334_1281831.rev   Z   Score: 22494   Residues:     1 -  7498
chr20_1359524_1362240.rev   Z   Score: 8151   Residues:     1 -  2717
chr20_1412165_1417469   T   Score:  252   Residues:  2526 -  2571
chr20_1412165_1417469   Z   Score: 15915   Residues:     1 -  5305
chr20_1469535_1475356.rev   Z   Score: 17466   Residues:     1 -  5822
chr20_1512067_1514638   Z   Score: 7716   Residues:     1 -  2572
chr20_1567518_1573239.rev   Z   Score: 17166   Residues:     1 -  5722
chr20_1631333_1633896   Z   Score: 7692   Residues:     1 -  2564
chr20_1720716_1722401   Z   Score: 5055   Residues:     1 -  1685
chr20_1945226_1947736   Z   Score: 7533   Residues:     1 -  2511
chr20_2004082_2005749   Z   Score: 5004   Residues:     1 -  1668
chr20_2084379_2087952   Z   Score: 10722   Residues:     1 -  3574
chr20_2192596_2199006   Z   Score: 19233   Residues:     1 -  6411
chr20_2283236_2284890   Z   Score: 4965   Residues:     1 -  1655
chr20_2349681_2354824.rev   Z   Score: 15432   Residues:     1 -  5144
chr20_2387797_2390271.rev   Z   Score: 7425   Residues:     1 -  2475
chr20_2401998_2403994.rev   Z   Score: 5991   Residues:     1 -  1997
chr20_2416053_2417646.rev   Z   Score: 4782   Residues:     1 -  1594
chr20_2428972_2435352   Z   Score: 19143   Residues:     1 -  6381
chr20_2439929_2442524   Z   Score: 7788   Residues:     1 -  2596
chr20_2479363_2484817.rev   Z   Score: 16365   Residues:     1 -  5455
chr20_2498059_2500557   Z   Score: 7497   Residues:     1 -  2499
chr20_2755219_2758122   Z   Score: 8712   Residues:     1 -  2904
chr20_2843513_2846413.rev   Z   Score: 8703   Residues:     1 -  2901
chr20_2889532_2891371.rev   Z   Score: 5520   Residues:     1 -  1840
chr20_2898604_2900482.rev   Z   Score: 5637   Residues:     1 -  1879
chr20_2927171_2929537   Z   Score: 7101   Residues:     1 -  2367
chr20_2989495_2992043   A   Score:  222   Residues:   837 -   888
chr20_2989495_2992043   Z   Score: 7647   Residues:     1 -  2549
chr20_3312838_3316019   Z   Score: 9546   Residues:     1 -  3182
chr20_3450635_3456482   Z   Score: 17544   Residues:     1 -  5848
chr20_3515137_3517399.rev   Z   Score: 6789   Residues:     1 -  2263
chr20_3757768_3760758.rev   A   Score:  214   Residues:   858 -   885
chr20_3757768_3760758.rev   Z   Score: 8973   Residues:     1 -  2991
chr20_3843058_3845416.rev   Z   Score: 7077   Residues:     1 -  2359
chr20_3958270_3961008.rev   Z   Score: 8217   Residues:     1 -  2739
chr20_4212622_4219028.rev   Z   Score: 19221   Residues:     1 -  6407
chr20_4316641_4320199   Z   Score: 10677   Residues:     1 -  3559
chr20_4324862_4327537   Z   Score: 8028   Residues:     1 -  2676
chr20_4388210_4389929.rev   Z   Score: 5160   Residues:     1 -  1720
chr20_4424702_4431106.rev   Z   Score: 19215   Residues:     1 -  6405
chr20_4456405_4459536   Z   Score: 9396   Residues:     1 -  3132
chr20_4464236_4467171   Z   Score: 8808   Residues:     1 -  2936
chr20_4485860_4488201   Z   Score: 7023   Residues:     1 -  2341
chr20_4547906_4554919.rev   Z   Score: 21042   Residues:     1 -  7014
chr20_4587262_4588880   Z   Score: 4857   Residues:     1 -  1619
chr20_4682063_4686994.rev   A   Score:  470   Residues:  3139 -  3223
chr20_4682063_4686994.rev   A   Score:  214   Residues:   900 -   927
chr20_4682063_4686994.rev   Z   Score: 14796   Residues:     1 -  4932
chr20_4770929_4772821.rev   Z   Score: 5679   Residues:     1 -  1893
chr20_5164659_5171316.rev   Z   Score: 19974   Residues:     1 -  6658
chr20_5174190_5179179.rev   A   Score:  200   Residues:  2135 -  2255
chr20_5174190_5179179.rev   Z   Score: 14970   Residues:     1 -  4990
chr20_5186003_5187615   Z   Score: 4839   Residues:     1 -  1613
chr20_5212786_5217358   A   Score:  229   Residues:  2032 -  2074
chr20_5212786_5217358   Z   Score: 13719   Residues:     1 -  4573
chr20_5267739_5272230   Z   Score: 13476   Residues:     1 -  4492
chr20_5313040_5317685   Z   Score: 13938   Residues:     1 -  4646
chr20_5322791_5324979   Z   Score: 6567   Residues:     1 -  2189
chr20_5348987_5350915   Z   Score: 5787   Residues:     1 -  1929
chr20_5386009_5392973.rev   Z   Score: 20895   Residues:     1 -  6965
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chr20_45130616_45132856   Z   Score: 6723   Residues:     1 -  2241
chr20_45143826_45147198   A   Score:  306   Residues:     1 -    52
chr20_45143826_45147198   Z   Score: 10119   Residues:     1 -  3373
chr20_45165750_45167737.rev   Z   Score: 5964   Residues:     1 -  1988
chr20_45873772_45876019   Z   Score: 6744   Residues:     1 -  2248
chr20_46057569_46060443.rev   A   Score:  234   Residues:  1630 -  1694
chr20_46057569_46060443.rev   Z   Score: 8625   Residues:     1 -  2875
chr20_46194095_46196603.rev   Z   Score: 7527   Residues:     1 -  2509
chr20_46763334_46764972   A   Score:  209   Residues:   470 -   506
chr20_46763334_46764972   Z   Score: 4917   Residues:     1 -  1639
chr20_46827645_46829698   Z   Score: 6162   Residues:     1 -  2054
chr20_47027172_47033571.rev   Z   Score: 19200   Residues:     1 -  6400
chr20_47157150_47159557   A   Score:  232   Residues:  1237 -  1265
chr20_47157150_47159557   Z   Score: 7224   Residues:     1 -  2408
chr20_47537292_47539019.rev   Z   Score: 5184   Residues:     1 -  1728
chr20_48385432_48387145   Z   Score: 5142   Residues:     1 -  1714
chr20_48858053_48860586.rev   Z   Score: 7602   Residues:     1 -  2534
chr20_49199518_49203136   A   Score:  214   Residues:   471 -   498
chr20_49199518_49203136   Z   Score: 10857   Residues:     1 -  3619
chr20_50555213_50559429   Z   Score: 12651   Residues:     1 -  4217
chr20_50592398_50599128   Z   Score: 20193   Residues:     1 -  6731
chr20_50605142_50609274.rev   Z   Score: 12399   Residues:     1 -  4133
chr20_51505758_51512012.rev   Z   Score: 18765   Residues:     1 -  6255
chr20_51522091_51528369   Z   Score: 18837   Residues:     1 -  6279
chr20_51553298_51559570   A   Score:  323   Residues:   340 -   487
chr20_51553298_51559570   R   Score:  302   Residues:   340 -   487
chr20_51553298_51559570   G   Score:  491   Residues:   346 -   486
chr20_51553298_51559570   Z   Score: 18819   Residues:     1 -  6273
chr20_52058870_52061946   Z   Score: 9231   Residues:     1 -  3077
chr20_52289489_52293849   Z   Score: 13083   Residues:     1 -  4361
chr20_52385325_52387769   Z   Score: 7335   Residues:     1 -  2445
chr20_52419487_52421541.rev   Z   Score: 6165   Residues:     1 -  2055
chr20_52441350_52445492.rev   Z   Score: 12429   Residues:     1 -  4143
chr20_52464978_52467716.rev   Z   Score: 8217   Residues:     1 -  2739
chr20_52474415_52476129   Z   Score: 5145   Residues:     1 -  1715
chr20_52616418_52618370.rev   Z   Score: 5859   Residues:     1 -  1953
chr20_52630058_52634260.rev   Z   Score: 12609   Residues:     1 -  4203
chr20_52834550_52843281.rev   Z   Score: 26196   Residues:     1 -  8732
chr20_52932365_52937016.rev   Z   Score: 13956   Residues:     1 -  4652
chr20_53111415_53117484.rev   T   Score:  216   Residues:  3157 -  3183
chr20_53111415_53117484.rev   Z   Score: 18210   Residues:     1 -  6070
chr20_53270503_53276919.rev   Z   Score: 19251   Residues:     1 -  6417
chr20_53284791_53287503.rev   Z   Score: 8139   Residues:     1 -  2713
chr20_53294116_53298798   Z   Score: 14049   Residues:     1 -  4683
chr20_53347391_53349720   Z   Score: 6990   Residues:     1 -  2330
chr20_53355318_53361074   Z   Score: 17271   Residues:     1 -  5757
chr20_53385342_53387269.rev   Z   Score: 5784   Residues:     1 -  1928
chr20_53415010_53417434   Z   Score: 7275   Residues:     1 -  2425
chr20_53452229_53455890.rev   A   Score:  213   Residues:   830 -   931
chr20_53452229_53455890.rev   Z   Score: 10986   Residues:     1 -  3662
chr20_53459255_53463715   A   Score:  236   Residues:  3397 -  3459
chr20_53459255_53463715   T   Score:  209   Residues:  1884 -  1917
chr20_53459255_53463715   Z   Score: 13383   Residues:     1 -  4461
chr20_53513513_53515124.rev   Z   Score: 4836   Residues:     1 -  1612
chr20_53542688_53552861   T   Score:  254   Residues:  4879 -  4915
chr20_53542688_53552861   Z   Score: 30522   Residues:     1 - 10174
chr20_53569497_53573323.rev   Z   Score: 11481   Residues:     1 -  3827
chr20_53856461_53859419   Z   Score: 8877   Residues:     1 -  2959
chr20_53867530_53873732   Z   Score: 18609   Residues:     1 -  6203
chr20_53874779_53880078   Z   Score: 15900   Residues:     1 -  5300
chr20_53908944_53915362.rev   Z   Score: 19257   Residues:     1 -  6419
chr20_54061820_54064263   Z   Score: 7332   Residues:     1 -  2444
chr20_54072839_54075249   A   Score:  214   Residues:    73 -   143
chr20_54072839_54075249   Z   Score: 7233   Residues:     1 -  2411
chr20_54088016_54091018.rev   Z   Score: 9009   Residues:     1 -  3003
chr20_54290752_54292556   Z   Score: 5415   Residues:     1 -  1805
chr20_54328008_54330080   Z   Score: 6219   Residues:     1 -  2073
chr20_54516596_54518212   Z   Score: 4851   Residues:     1 -  1617
chr20_54778429_54780800.rev   T   Score:  224   Residues:  1643 -  1675
chr20_54778429_54780800.rev   Z   Score: 7116   Residues:     1 -  2372
chr20_55085623_55088595.rev   Z   Score: 8919   Residues:     1 -  2973
chr20_55497093_55499708   A   Score:  228   Residues:  1812 -  1842
chr20_55497093_55499708   A   Score:  222   Residues:  2493 -  2556
chr20_55497093_55499708   Z   Score: 7848   Residues:     1 -  2616
chr20_55649310_55651768   Z   Score: 7377   Residues:     1 -  2459
chr20_55783955_55785772.rev   Z   Score: 5454   Residues:     1 -  1818
chr20_55866500_55868693.rev   Z   Score: 6582   Residues:     1 -  2194
chr20_55894784_55897069.rev   Z   Score: 6858   Residues:     1 -  2286
chr20_56130152_56132430   Z   Score: 6837   Residues:     1 -  2279
chr20_56260434_56262658   A   Score:  204   Residues:   380 -   407
chr20_56260434_56262658   Z   Score: 6675   Residues:     1 -  2225
chr20_56534763_56537384.rev   Z   Score: 7866   Residues:     1 -  2622
chr20_56739649_56744387   Z   Score: 14217   Residues:     1 -  4739
chr20_56745440_56748546   Z   Score: 9321   Residues:     1 -  3107
chr20_56976940_56979226   Z   Score: 6861   Residues:     1 -  2287
chr20_57169967_57172290.rev   Z   Score: 6972   Residues:     1 -  2324
chr20_57175134_57178406.rev   Z   Score: 9819   Residues:     1 -  3273
chr20_57536700_57539543   Z   Score: 8532   Residues:     1 -  2844
chr20_57540478_57546753.rev   Z   Score: 18828   Residues:     1 -  6276
chr20_57555996_57559488   Z   Score: 10479   Residues:     1 -  3493
chr20_57601204_57603446.rev   Z   Score: 6729   Residues:     1 -  2243
chr20_57721957_57724681.rev   Z   Score: 8175   Residues:     1 -  2725
chr20_57866871_57870519.rev   Z   Score: 10947   Residues:     1 -  3649
chr20_57913958_57915860   Z   Score: 5709   Residues:     1 -  1903
chr20_57936256_57938113   Z   Score: 5574   Residues:     1 -  1858
chr20_57988169_57990526.rev   Z   Score: 7074   Residues:     1 -  2358
chr20_58023333_58027567.rev   A   Score:  321   Residues:   382 -   461
chr20_58023333_58027567.rev   Z   Score: 12705   Residues:     1 -  4235
chr20_58136276_58137961   Z   Score: 5058   Residues:     1 -  1686
chr20_58204145_58208504.rev   Z   Score: 13080   Residues:     1 -  4360
chr20_58226512_58228130.rev   Z   Score: 4857   Residues:     1 -  1619
chr20_58390272_58393723   Z   Score: 10356   Residues:     1 -  3452
chr20_58423047_58427294.rev   Z   Score: 12744   Residues:     1 -  4248
chr20_58447397_58449507.rev   Z   Score: 6333   Residues:     1 -  2111
chr20_58467883_58471210   Z   Score: 9984   Residues:     1 -  3328
chr20_58552450_58556981.rev   Z   Score: 13596   Residues:     1 -  4532
chr20_58616490_58618198   Z   Score: 5127   Residues:     1 -  1709
chr20_58711416_58714097.rev   A   Score:  667   Residues:  2549 -  2682
chr20_58711416_58714097.rev   Z   Score: 8046   Residues:     1 -  2682
chr20_58730542_58732150   Z   Score: 4827   Residues:     1 -  1609
chr20_58747178_58750215.rev   A   Score:  232   Residues:  2614 -  2642
chr20_58747178_58750215.rev   Z   Score: 9114   Residues:     1 -  3038
chr20_58987452_58989413   Z   Score: 5886   Residues:     1 -  1962
chr20_59025843_59027577   Z   Score: 5205   Residues:     1 -  1735
chr20_59151900_59154078.rev   Z   Score: 6537   Residues:     1 -  2179
chr20_59559668_59561328   Z   Score: 4983   Residues:     1 -  1661
chr20_59963032_59965259   Z   Score: 6684   Residues:     1 -  2228
chr20_60030874_60033911   A   Score:  310   Residues:  1326 -  1370
chr20_60030874_60033911   Z   Score: 9114   Residues:     1 -  3038
chr20_60042213_60044893   Z   Score: 8043   Residues:     1 -  2681
chr20_60046436_60048862   Z   Score: 7281   Residues:     1 -  2427
chr20_60847825_60852002   Z   Score: 12534   Residues:     1 -  4178
chr20_60858158_60859984.rev   Z   Score: 5481   Residues:     1 -  1827
chr20_61139944_61142941.rev   Z   Score: 8994   Residues:     1 -  2998
chr20_61210015_61212965.rev   Z   Score: 8853   Residues:     1 -  2951
chr20_61611445_61613702.rev   A   Score:  209   Residues:   972 -  1026
chr20_61611445_61613702.rev   A   Score:  201   Residues:   472 -   500
chr20_61611445_61613702.rev   Z   Score: 6774   Residues:     1 -  2258
chr20_62284904_62286961.rev   Z   Score: 6174   Residues:     1 -  2058
chr20_62433612_62435964.rev   Z   Score: 7059   Residues:     1 -  2353

3064 24.63 1.07 3.85  chr1_32606_35329     1298  2231 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_32606_3532   1298 TAGAAAGCTATCTCATGTTAATAGATTAGAAAAAGTAATATTGTTAAGAT 1347
                          i     v    i      v  i    i   i vv               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_32606_3532   1348 GTCCTCACTACTTAAAGCAATTTATAGATCTAATGCATTTATTGCAATCT 1397
                          v vvi   v ii   vii  i  i    ii  i   ---------   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA---------ATCC 91

  chr1_32606_3532   1398 CT-TCAAAATCCCAAAGGTATTTTTGACAGAAATAAAAAAAA-AATTCTA 1445
                           -           ivv iv     vi       vi v  iv-i  i   
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr1_32606_3532   1446 AAATATGCATGAAACCACAAAAGACTGTGAATAGCTAAAGCAATCTTGAG 1495
                             viii   i  vii   ii   ivv       i   i         i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_32606_3532   1496 CAAGATGAACAACACTGGAAGCATCACACTACCTTATTTCAAAATCTACT 1545
                         v    v      vii    i vv       v  iv         ii    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_32606_3532   1546 ACAAAGCTATAGTGATCAAAGCAACATGATACTGTCATAAAAACACACAG 1595
                                  i   i     ii  iii  i     v     ii i v   v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_32606_3532   1596 ATAAACCTATGGAATGGAATAAAGAGCACAGAAATAAGTCCACACATTTA 1645
                            i i v       i    vi    iv         ii   i       
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_32606_3532   1646 CATTCAATTGATTTTCAACAACAATGTCAAGAAGA--CAATGGGGAAAAG 1693
                         iiv             i    vii  i     vv --           ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_32606_3532   1694 ACAATCTCTTCAATAAATGATGCTGGAAAAACTATATATCCACATGCAGA 1743
                          i i   i     i     i      i v    iv   ?         i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_32606_3532   1744 AGAATGCAGTTGAATCCTGATTTCATACCATATGCAAAATTCAACTGGAA 1793
                               v     i i  iv ii   i       i     v i    vi  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_32606_3532   1794 ATGGATTAAATAC--AAATTTAAAACATGAAATGGTATAACTATTAGAAC 1841
                               i ? v  --    v   i vv i   ivi  v    v      v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_32606_3532   1842 AAAACATAGAAAATATTCTTCCTGACATTGGTTTGGGCCATCATTTTTCT 1891
                                  i?ivv v     v    v    v  i   v  vi   i iv
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_32606_3532   1892 GATATGACTCTAAAAGCACAGGCAAAAAAAGAAAAAATAGACAAATGAGA 1941
                                 v i         i    v               i    vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_32606_3532   1942 CT--ATGCCAAATTAAAAAATTTCTAACAACAAAAGAAACGATCAATAGA 1989
                           --  - v          v   ivvi vv    i  v  v     v i 
  L1M4_orf2#LINE/    642 CTTCAT-CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_32606_3532   1990 GTGAAAAAGATAACCTCTTGAATGGGAGAAA-TATTTGCAAACTACTCAT 2038
                                -  i    iviv            -          ii ivi  
  L1M4_orf2#LINE/    691 GTGAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_32606_3532   2039 CCAACCGGGGATTGATATCCAGAATATACAAGTAACACAAATATGTCAAA 2088
                          ii ivi    i vi             i  iv   v ------- i --
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC-------TTA-- 780

  chr1_32606_3532   2089 AGTAAAATAAATAAATAAATAAATAAATAAATAAATTAAATAAATTATTT 2138
                         -------i  v v     -    v i i      vii  --------  ?
  L1M4_orf2#LINE/    781 -------CAACTCAATAA-TAAAAAGACAAATAACCCAA--------TTW 814

  chr1_32606_3532   2139 AAAAATCGGCAGAGGACAGGAATAGACATTTCTCAGGAGACAACATACAA 2188
                               v    i    ivv               vii   vi i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_32606_3532   2189 AGGGCCA-CAGATACATCAAAAAATGCTCAACATCACTATTTGT 2231
                          v     -i iii    v    i             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.29 (46 / 14)  


2392 23.39 4.74 1.68  chr1_409965_411589.rev      500  1153 (472)    L1M4_orf2#LINE/L1      235   908 (0)  

  chr1_409965_411    500 ACATATCACAAAACCATAGTAATCAAAACAATATGACACTTGCACAAAAA 549
                           v  ii     i i i         i   i i  ii   v   i  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_409965_411    550 CAGACACATTGACCAGGGGAACAGAATAAGGAGCCCAGAAATAAACTCAT 599
                         i     i  v  i  iv    i     vii   i            i   
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_409965_411    600 GCATTTATGACCAATAAATTTTTGACAAAGGTGCCCAGAAAACGTAATGA 649
                         i        ii    vi     i     i      v   vv ivi    i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_409965_411    650 AGAATAGACATTTGTTTCAATAAATGGTGTTAAGAAAACTAGATATCCAC 699
                         i   vii i v iv      i        i ii  v    i    ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_409965_411    700 ATGCAGAAGAACACGAATGTGTATGGTGTGTATCCTTATCTCACACCATA 749
                              i     i--   ---  -   ----- i  i  i           
  L1M4_orf2#LINE/    435 ATGCAAAAGAAT--GAA---GT-TGG-----ACCCCTACCTCACACCATA 473

  chr1_409965_411    750 CACAAAAATCAATTCAAAATGGATTAAAGGTTTAAACATAA-------AA 792
                         i        i  i           i ?  iii    ii   -------  
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_409965_411    793 CTGTAAAACTACTAGATGAAAACATAGGGGAAAAGTTCCACAATGTTGGT 842
                           i       vi    v           ? v   vi i iii iv    v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_409965_411    843 TTGGTCAAAGATTTCTTGGATATCACCCCCAAAGCACAGGCAACAAAAGC 892
                           i v   v i      i     v  v  v        i          v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_409965_411    893 AAAAATATATG----GGATTGCATCAAACTAAAAAGCTTCTGCACAGCAA 938
                                v  i----   i v       v v    i   i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_409965_411    939 AGGAAAC----AATATGGTGAAGAGACAACCTACAAGTTGTGAGAAAATA 984
                             v  ----  v vi     i        i   iiv  v         
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_409965_411    985 TTTGCAGAGCATACATCTGATGAAAGGCTAATCTCCA-AATATATAAGGG 1033
                               i v    i       i ii i  vi v    -         i i
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_409965_411   1034 ACTC----AACTCAATATCAAGAAAACAAATAACCAAGTCAAAAAATGGG 1079
                             ----         vi  i  i          v i i?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_409965_411   1080 CAA-GGTCCTAAATAGACATTTCTCAAAAAAA---ATACAAATGACTAA- 1124
                            -  vii i              v   i  ---         i i  -
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_409965_411   1125 -----CATAAAAAAA-GTTTGTCATCCTAATTATC 1153
                         -----   i    i - i iiv    v????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (103 / 46)
Gap_init rate = 0.02 (13 / 674), avg. gap size = 3.23 (42 / 13)  


3013 27.57 1.22 0.66  chr1_412092_418759.rev     5275  6177 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_412092_418   5275 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5324
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_412092_418   5325 GGACATACTGCCCAAAGTT--TTTATAGACTCAATGCTGTCCCCATCAAG 5372
                           vv     v      -  -- i  i   i    i  vi    i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_412092_418   5373 CTACCA-CTGACTTTGTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTT 5419
                         v v   -   v    -  ii     -   -- v  i  - iii    v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTT-TTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chr1_412092_418   5420 CATATGGAACCAAAAATGAGCCCGCAGAGCTAGGACAGTCCTAAGCAAGT 5469
                                  viiv  iv  v  v v v   i ii   i  i i iv   v
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_412092_418   5470 AGAACAAATCTGGAGGCATCACGCTGTCTGACTTCGAACTATACTACAAG 5519
                                 vi      vv    i  vi ii i   i  viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_412092_418   5520 TCTTCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATGTAGA 5569
                         v  v      i   i    ii         i iv ii i   i  i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_412092_418   5570 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACT 5619
                         i        i    iv   ivii         vv   i    i  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_412092_418   5620 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAACGATTCC 5669
                          vi    i  i     ivv  v   i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_412092_418   5670 CTTTTTAATAAATGGTGTTGGGAAAACCGGCTAGCCATATGCAGAAAACT 5719
                              i  i        i     v   i  v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_412092_418   5720 GAAACTGGATCCCTTTCTTACACTTTACACAAAAATTAACTCACGATGTA 5769
                            ii    i    vi  i    iv  i               vi   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_412092_418   5770 TTAAAGACTTAAACATAAGATCTAAAACCATAAAAAACCCTAGAAGAAAA 5819
                          i ?    i    ii     v       i      v-i i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chr1_412092_418   5820 CCTAGGCA-ATACCATTCAGTACATAGGCATGGACAAAAACTTCATGACT 5868
                          v    ?i- v i -   ivv  v v  vv i i   viii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_412092_418   5869 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5918
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_412092_418   5919 AATTAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5968
                         v  i   v v  i i  ii  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_412092_418   5969 ACAGGCAACCTACAGAATGGGTGAAAATTTTTGCAATCTATCCATCTGAC 6018
                          v  i     i          v      v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_412092_418   6019 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAATTTA-CAAGAA 6067
                           i  i  vi          v  i        ivv    i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_412092_418   6068 AATAACAAACAAACCCATC----AGTGGGTGAAGGATATGAACTGACATT 6113
                           vi     i  v  v  i---- i    ii      v    iv      
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_412092_418   6114 TCTCTAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCA 6163
                             i        i  vi viii     i  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_412092_418   6164 TCATCACTGGTCAT 6177
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


3351 25.11 2.02 0.22  chr1_428953_431249      913  1804 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_428953_431    913 TGGAAAGATATATCATGTTCATGGATTGGAAAAAGTAATATGTTTGAAAT 962
                                    vi                  i vv      vv  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_428953_431    963 GTCCATACTATCCAAAGTGATGTACATATTGAATGCAATCTCTATCAAAA 1012
                          v v     vi     v    v    v   v  i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_428953_431   1013 TTCCTATGACATTTTCCCACAGAAATAGAAAAAC-AACTCTCAAATCTGT 1061
                          i  viivi v    ii-i       v  v  i -i ii  v    iii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_428953_431   1062 ATGGAATCACAAAAAACTCTGAAAAGCCAAAATAATCTTGATCGAAAAAA 1111
                               vii   iii  i v   v        i        vvi i  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_428953_431   1112 GCAAGGCAGGAGATATCACATTACCTGACTTCAAATTATACTACATAGCT 1161
                         i   i iv    ivv     i v  ii i      viv       v    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_428953_431   1162 ATAGCAATCGAAACACCATGGTACTGGCATAAACGCAGACACATAGACCA 1211
                          i  i    i i   vii              ivii     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_428953_431   1212 ATTACACAGAATAAAGAGCCCATAAATAAATCTACATATT-ATAGTCAAT 1260
                           viv i     vi    i   v       i i i i   -  i      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_428953_431   1261 TGACTTTCAACAAAGGTGCCAGGAACACACA-TGGGGAAAGAACAGTCTC 1309
                            i    i    i       i  v  iv  -           i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_428953_431   1310 TTCAAAAAATGGTGTTGAGAAAACTGAATGTCCACA------AGATTGAT 1353
                              v        i  i  v     i  i?     ------   v   v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_428953_431   1354 CTTAGGCCCTTATTTCATACCATATAAAAATATAAATTCAAAATAAGTTA 1403
                         v  i i   i  ii   i        v   v  v  i       iii i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_428953_431   1404 --GACTTAAATGTAAGACCTAGCACTATAGAACTCCTGGAAGAAAACAGG 1451
                         --   i           v   iv      i     i i          vi
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_428953_431   1452 GGAATAA--CTCCAAGACATTGGTCTGGGCAATAATATTTTATGATATGA 1499
                           ?i   --  i iv   v    vi i      ii v i   -       
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GATATGA 598

  chr1_428953_431   1500 CTCTAAA-GCACAGGCAAGAAAAGCAACAAAACACAAATGGAATAGCATC 1548
                          v i   -     i    v     v  v  v v i    v i ivv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_428953_431   1549 AACCTAAAAAGCTTCTGCACAGCAAAAGAAA--GTCAACAGAGTGAAGTG 1596
                           vv v    i   i  ii vv    i  v --i    v i      iv 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_428953_431   1597 ATAACCTACAAAATGGGAGAAATTATCTGCAAACTATACATTTGATAAGA 1646
                          i    i   i           v   i      ii   i  i       i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_428953_431   1647 GGCTAATGTCCAAAATATCTTAGGAACTCAAACAACACAATAATAAGAAA 1696
                          i  vi i    i     v v i      vv     v         i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_428953_431   1697 ACAAGGAACCCTAATGAAAAATTGACAAAGGATCTAAATAGACATTTCTC 1746
                             iv     v v ?      v i        i i              
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_428953_431   1747 AAAAGAAGACATACAAATGGCCAACAGATATATAAAAA--TGCTAATTAT 1794
                         v        i              i iii i  i    --    v vi  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_428953_431   1795 CACTGATCAT 1804
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.63 (137 / 84)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


3413 24.66 2.02 0.22  chr1_638935_641231.rev      915  1806 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_638935_641    915 TGGAAAGATATCTCATGTTCATGGATTGGAAAAAGTAATATGTTTGAAAT 964
                                     i                  i vv      vv  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_638935_641    965 GTCCATACTATCCAAAGTGATGTACATATTGAATGCAATCTCTATCAAAA 1014
                          v v     vi     v    v    v   v  i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_638935_641   1015 TTCCTATGACATTTTCCCACAGAAATAGAAAAAC-AACTCTCAAATCTGT 1063
                          i  viivi v    ii-i       v  v  i -i ii  v    iii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_638935_641   1064 ATGGAATCACAAAAAACTCTGAAAAGCCAAAATAATCTTGATCAAAAAAA 1113
                               vii   iii  i v   v        i        vv  i  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_638935_641   1114 GCAAGGCAGGAGATATCACATTACCTGACTTCAAATTATACTACATAGCT 1163
                         i   i iv    ivv     i v  ii i      viv       v    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_638935_641   1164 ATAGCAATCGAAACACCATGGTACTGGCATAAACGCAGACACATAGACCA 1213
                          i  i    i i   vii              ivii     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_638935_641   1214 ATTACACAGAATAAAGAGCCCATAAATAAATCTACATATT-ATAGTCAAT 1262
                           viv i     vi    i   v       i i i i   -  i      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_638935_641   1263 TGACTTTCAACAAAGGTGCCAGGAACACACA-TGGGGAAAGAACAGTCTC 1311
                            i    i    i       i  v  iv  -           i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_638935_641   1312 TTCAAAAAATGGTGTTGAGAAAACTGAATGTCCACA------AGATTGAT 1355
                              v        i  i  v     i  i?     ------   v   v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_638935_641   1356 ATTAGGCCCTTATTTCATACCATATAAAAATATAAACTCAAAATAAGTTA 1405
                         i  i i   i  ii   i        v   v  v          iii i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_638935_641   1406 --GACTTAAATGTAAGACCTAGCACTATAGAACTCCTAGAAGAAAACAGG 1453
                         --   i           v   iv      i     i            vi
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_638935_641   1454 GGAATAA--CTCCAAGACATTGGTCTGGGCAATAATATTTTATGATATGA 1501
                           ?i   --  i iv   v    vi i      ii v i   -       
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GATATGA 598

  chr1_638935_641   1502 CTCTAAA-GCACAGGCAAGAAAAGCAACAAAACACAAATGGAATAGCATC 1550
                          v i   -     i    v     v  v  v v i    v i ivv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_638935_641   1551 AACCTAAAAAGCTTCTGCACAGCAAAAGAAA--GTCAACAGAGTGAAGTG 1598
                           vv v    i   i  ii vv    i  v --i    v i      iv 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_638935_641   1599 ATAACCTACAAAATGGGAGAAATTATCTGCAAACTATACATTTGATAAGA 1648
                          i    i   i           v   i      ii   i  i       i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_638935_641   1649 GGCTAATGTCCAAAATATCTTAGGAACTCAAACAACACAATAATAAGAAA 1698
                          i  vi i    i     v v i      vv     v         i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_638935_641   1699 ACAAGGAACCCTAATGAAAAATTGACAAAGGATCTAAATAGACATTTCTC 1748
                             iv     v v ?      v i        i i              
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_638935_641   1749 AAAAGAAGACATACAAATGGCCAACAGATATATAAAAA--TGCTAATTAT 1796
                         v        i              i iii i  i    --    v vi  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_638935_641   1797 CACTGATCAT 1806
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.65 (135 / 82)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


3022 27.46 1.22 0.66  chr1_651643_657327     4290  5192 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_651643_657   4290 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4339
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_651643_657   4340 GGACATACTGCCCAAAGTT--TTTATAGACTCAATGCTATCCCCATCAAG 4387
                           vv     v      -  -- i  i   i    i  v     i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_651643_657   4388 CTACCA-CTGACTTTGTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTT 4434
                         v v   -   v    -  ii     -   -- v  i  - iii    v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTT-TTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chr1_651643_657   4435 CATATGGAACCAAAAATGAGCCCGCAGAGCTAGGACAGTCCTAAGCAAGT 4484
                                  viiv  iv  v  v v v   i ii   i  i i iv   v
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_651643_657   4485 AGAACAAATCTGGAGGCATCACGCTGTCTGACTTCGAACTATACTACAAG 4534
                                 vi      vv    i  vi ii i   i  viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_651643_657   4535 TCTTCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATGTAGA 4584
                         v  v      i   i    ii         i iv ii i   i  i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_651643_657   4585 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACT 4634
                         i        i    iv   ivii         vv   i    i  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_651643_657   4635 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAACGATTCC 4684
                          vi    i  i     ivv  v   i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_651643_657   4685 CTTTTTAATAAATGGTGTTGGGAAAACCGGCTAGCCATATGCAGAAAACT 4734
                              i  i        i     v   i  v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_651643_657   4735 GAAACTGGATCCCTTTCTTACACTTTACACAAAAATTAACTCACGATGTA 4784
                            ii    i    vi  i    iv  i               vi   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_651643_657   4785 TTAAAGACTTAAACATAAGATCTAAAACCATAAAAAACCCTAGAAGAAAA 4834
                          i ?    i    ii     v       i      v-i i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chr1_651643_657   4835 CCTAGGCA-ATACCATTCAGTACATAGGCATGGACAAAAACTTCATGACT 4883
                          v    ?i- v i -   ivv  v v  vv i i   viii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_651643_657   4884 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4933
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_651643_657   4934 AATTAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTATCATCAGAGTGA 4983
                         v  i   v v  i i  ii  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_651643_657   4984 ACAGGCAACCTACAGAATGGGTGAAAATTTTTGCAATCTATCCATCTGAC 5033
                          v  i     i          v      v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_651643_657   5034 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAATTTA-CAAGAA 5082
                           i  i  vi          v  i        ivv    i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_651643_657   5083 AATAACAAACAAACCCATC----AGTGGGTGAAGGATATGAACTGACATT 5128
                           vi     i  v  v  i---- i    ii      v    iv      
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_651643_657   5129 TCTCTAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCA 5178
                             i        i  vi viii     i  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_651643_657   5179 TCATCACTGGTCAT 5192
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


2400 23.39 4.74 1.68  chr1_657831_659454      497  1150 (474)    L1M4_orf2#LINE/L1      235   908 (0)  

  chr1_657831_659    497 ACGTATCACAAAACCATAGTAATCAAAACAATATGACACTTGCACAAAAA 546
                           v  ii     i i i         i   i i  ii   v   i  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_657831_659    547 CAGACACATTGACCAGGGGAACAGAATAAGGAGCCCAGAAATAAACTCAT 596
                         i     i  v  i  iv    i     vii   i            i   
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_657831_659    597 GCATTTATGACCAATAAATTTTTGACAAAGGTGCCCAGAAAACGTAATGA 646
                         i        ii    vi     i     i      v   vv ivi    i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_657831_659    647 AGAATAGACATTTGTTTCAATAAATGGTGTTAAGAAAACTAGATATCCAC 696
                         i   vii i v iv      i        i ii  v    i    ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_657831_659    697 ATGCAGAAGAACACGAATGTGTATGGTGTGTATCCTTATCTCACACCATA 746
                              i     i--   ---  -   ----- i  i  i           
  L1M4_orf2#LINE/    435 ATGCAAAAGAAT--GAA---GT-TGG-----ACCCCTACCTCACACCATA 473

  chr1_657831_659    747 CACAAAAATCAATTCAAAATGGATTAAAGGTTTAAACATAA-------AA 789
                         i        i  i           i ?  iii    ii   -------  
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_657831_659    790 CTGTAAAACTACTAGATGAAAACATAGGGGAAAAGTTCCACAATGTTGGT 839
                           i       vi    v           ? v   vi i iii iv    v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_657831_659    840 TTGGTCAAAGATTTCTTGGATATCACCCCCAAAGCACAGGCAACAAAAGC 889
                           i v   v i      i     v  v  v        i          v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_657831_659    890 AAAAATATATG----GGATTGCATCAAACTAAAAAGCTTCTGCACAGCAA 935
                                v  i----   i v       v v    i   i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_657831_659    936 AGGAAAC----AATATGGTGAAGAGACAACCTACAAGTTGTGAGAAAATA 981
                             v  ----  v vi     i        i   iiv  v         
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_657831_659    982 TTTGCAGAGCATACATCTGATGAAAGGCTAATCTCCA-AATATATAAGGG 1030
                               i v    i       i ii i  vi v    -         i i
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_657831_659   1031 ACTC----AACTCAATATCAAGAAAACAAATAACCAAGTCAAAAAATGGG 1076
                             ----         vi  i  i          v i i?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_657831_659   1077 CAA-GGTCCTAAATAGACATTTCTCAAAAAAA---ATACAAATGACTAA- 1121
                            -  vii i              v   i  ---         i i  -
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_657831_659   1122 -----CATAAAAAAA-GTTTGTCATCCTAATTATC 1150
                         -----   i    i - i iiv    v????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (103 / 46)
Gap_init rate = 0.02 (13 / 674), avg. gap size = 3.23 (42 / 13)  


2305 27.11 1.04 0.30  chr1_774474_776152.rev      504  1178 (501)    L1M4_orf2#LINE/L1      215   894 (14)  

  chr1_774474_776    504 TCATACTACCTGACTTCAGACTATATTACAAGGCTACAGTAACCAAAACA 553
                            i   v  ii i    i viv  i     i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_774474_776    554 GCATGATACTGGCACCAAAACAGATATATAGACCAATGGAACAGAACAGA 603
                          ii  i        iv ii i   i       i        i    iv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_774474_776    604 GGCCTCAGAAATAACGCCACACATCTACAACCATCTGATCTTTCACAAAC 653
                          ivii         vv   i    i  iiii  vi    i  iv    iv
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_774474_776    654 CTGAGAAAAACAAGCAATGGGGAAAGGGTTCCCTATTTAATAAATGGTGT 703
                         v  vv  i v  vv            ii vvi  v  i  i        i
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_774474_776    704 TGGGAAAACTGGCTAGCCATATGCAAAAAACTGAAACTGGACCACTTCCT 753
                              v      v  ?   i        i v    ii      v  v   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_774474_776    754 TACACCTTTATACAAAAATTAACTCAAGATGGATTAAAGACTTAAACATA 803
                         i     v -                  i      i ?    i    ii  
  L1M4_orf2#LINE/    465 CACACCAT-ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_774474_776    804 AGACCTAAAACCATAAAAACCCTACAAGAAAAGCTAGGCA-ATACCATTC 852
                            v       i      vi i  v       vv    ?i- v i -   
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC 562

  chr1_774474_776    853 AGGACATAGGCACGGGCAAAGACTTGATGTCTAAAACACCGAAAGCAATG 902
                         iv   v v  vvii     v ii  vv ivv  vi     i      vvi
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_774474_776    903 GCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTT 952
                                   vv     v  i    v   ii v  i   v v  i i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_774474_776    953 CTGCATAGCAAAAGAAACTATCATCAGAGCGAAGAGGCAACCTACAGAAT 1002
                         i  iiivv    i  v       vv i  i   i  i     i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_774474_776   1003 GGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAACATCCAGA 1052
                                   v       vii  vi      i  i  i  vii       
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_774474_776   1053 ATCTACAAAGAACTTAAACAAATTTACAAGAAAAAAACAA----CCCCAT 1098
                           v  i        ivv    v iv i  v     i    ----   v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_774474_776   1099 CAAAAAGTGGGTAAAGGATATGAACAGACACTTCTCAAAAGAAGAAATTT 1148
                         i?    i    i       v    i     i     v        v  vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_774474_776   1149 ATGCAGCCAACAA--ACATGAAAAAAAGCTCA 1178
                          viii     i  --         i v     
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.42 (105 / 74)
Gap_init rate = 0.01 (5 / 680), avg. gap size = 1.80 (9 / 5)  


1486 23.45 12.43 4.80  chr1_1068782_1074868.rev     4302  4864 (1223)    L1M4_orf2#LINE/L1       95   700 (208)  

  chr1_1068782_10   4302 TCAAAATCGCAGCAGGCTTTTTTGTAGGAATTGACACAATGAGTCTAAAA 4351
                                 v    v v        i  i        viv   vi      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_1068782_10   4352 T------GGAAACACATGTGACCTGGAATTGCCAAAGCAATT-------- 4387
                          ------     ii  v v    ii    v      i    i--------
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_1068782_10   4388 ---AATCAAAGT-GGAG--CTGATACGTGCCCTGATTTCAAAGTTTCTAT 4431
                         ---i v      -    --  v i  v --  ii        ii  -- -
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTT--CCCAATTTCAAAACTT--A- 239

  chr1_1068782_10   4432 TCTACTTACAGCTTCAGTAATCCAGTCAGCCGCAGTGTCCCTG----AAG 4477
                         -    -- v    v        v  v   i----   viv   ----   
  L1M4_orf2#LINE/    240 -CTAC--AAAGCTACAGTAATCAAGACAGT----GTGGTACTGGCATAAG 282

  chr1_1068782_10   4478 AATAGACACACAGGTGAGTGGAACAGAATAGAAAGACTGGAAATAGACCC 4527
                         i       i i  i v i     i     v  i  v ii      i    
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_1068782_10   4528 -CACCTCTATAGTCCATTGATTTTCAATGAAGATGTCAACGTAATTCCAC 4576
                         -i  v i   i   v          i ii i i  i   viiv    v i
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_1068782_10   4577 ATGGAAAGAAAAGTCTTTTTAGCAACTGTT---------------TATAC 4611
                         iv        v        i i   v  v ---------------  ?v 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_1068782_10   4612 ATAAGGAAAGAAATGACGCTTGACCTGCATTTCAC--CATACACAAAGGT 4659
                          i v v   ii     v i v    ivi ii    --    i     ii 
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_1068782_10   4660 -GACTCAGAATG-----------------CAAAAGCTAAAACTGTAACAC 4691
                         -i     i    -----------------i  i          i   v  
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_1068782_10   4692 TTCTGGAAGAAAGCA-----GTAAATCTTAGTGACCATGAGGTCAAGGCA 4736
                          ii i       i  -----         v      v  i v --     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT--AGGCA 580

  chr1_1068782_10   4737 GAGATTTCTTAG----GACATAAAAAACAAGAACCACAAAAGGAAAAATG 4782
                         iv i        ----    iv    i  vi i v       i      i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_1068782_10   4783 GATGCATTCAATTTTATTAAAAATTTCATTAAAATTAAAAACATTTGCTC 4832
                            i-----    -------ii i     i            v    iv 
  L1M4_orf2#LINE/    631 GATA-----AATT-------GGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_1068782_10   4833 TTCAAAAGATGTCCAT-AAAAAAATGATAAGAC 4864
                               i  ii- i  -  i   i   v     
  L1M4_orf2#LINE/    669 TTCAAAGGACA-CTATCAAGAAAGTGAAAAGAC 700

Transitions / transversions = 1.79 (84 / 47)
Gap_init rate = 0.04 (22 / 606), avg. gap size = 4.41 (97 / 22)  

 297 20.27 0.00 1.35  chr1_1068782_1074868.rev     5150  5223 (864)    L1M4_orf2#LINE/L1      685   757 (151)  

  chr1_1068782_10   5150 AAAAAAGATGATAAGACAAACCACAGGATGGAAGAAAATATTTGCAATAC 5199
                           i    -   v       v      i    i               vv 
  L1M4_orf2#LINE/    685 AAGAAAG-TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_1068782_10   5200 ATAAGTCTGATGAAGAATATGTGT 5223
                            vi      i i i iv   i 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTAT 757

Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1)  

 473 15.53 1.94 1.94  chr1_1068782_1074868.rev     5494  5596 (491)    L1M4_orf2#LINE/L1      806   908 (0)  

  chr1_1068782_10   5494 ACCCAATTAAACAAAATGGGCAGAAGATGTGAGTAGGCACTTC-AGAAAG 5542
                                 ?  --         i i   v   i   i  i   -vv    
  L1M4_orf2#LINE/    806 ACCCAATTWAA--AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_1068782_10   5543 AAGATATATAAGTGGCTAATAAACACATGGAAAGATGC-CATCATTAGTC 5591
                                 i  i    i     i      i        -  v   i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_1068782_10   5592 TTCAG 5596
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.03 (3 / 103), avg. gap size = 1.33 (4 / 3)  


 541 17.17 5.05 0.00  chr1_1161545_1168186.rev     4077  4175 (2467)    L1M4_orf2#LINE/L1        1   104 (804)  

  chr1_1161545_11   4077 TGGAAAGACATCCTATATTCATGGATCGGAAGACTAAATATTGTTAAGAT 4126
                                 i    i  i         i        v              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_1161545_11   4127 GCCACTGCTACG-----TGACTTACAGATTCAATGCAATGCCTATTAAAA 4171
                          v  v i  v v-----   ii           i     v     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_1161545_11   4172 TTTC 4175
                          ii 
  L1M4_orf2#LINE/    101 TCCC 104

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.01 (1 / 104), avg. gap size = 5.00 (5 / 1)  

2578 15.83 1.80 2.81  chr1_1161545_1168186.rev     4476  4974 (1668)    L1M4_orf2#LINE/L1       97   590 (318)  

  chr1_1161545_11   4476 AAAATTTCA-TTGGACTTTTTCCCCAGAAATGGAAAAGCCAATCTTAAAA 4524
                              ii  -i  -- i    iiv       v  v    ii   i     
  L1M4_orf2#LINE/     97 AAAATCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_1161545_11   4525 TTCATATGGAATTGTGGAATTGTAAGGGGCCCCTGAATAGCCAAAATAAT 4574
                                    -------  - i     i   v-            i   
  L1M4_orf2#LINE/    145 TTCATATGGAA-------AT-GCAAGGGACCCA-GAATAGCCAAAACAAT 185

  chr1_1161545_11   4575 CTTGAAAAAGAACAATA---TTGAAAGACTCACATATCCCAATTTCAGGA 4621
                                     v  i ---   i i        iv           ii 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_1161545_11   4622 CTTACTACAAAGCTACAGCAATCAAAACCATGTGGTACTGGCATAAAGAC 4671
                                           i      i  vi                i  i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_1161545_11   4672 AGACATATACACTAATGGAATGGAACTGAGAGTCCAAAAATAAACACTTG 4721
                                  v ii        i   i          i        v v i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_1161545_11   4722 CAGCTCTGGTCAATTGGTTTTTGATACTA-TGCCAGGACCATTCCATGGG 4770
                           vi v          i    i  i vvi-     i        v     
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_1161545_11   4771 GGAAAGAATAGTCTCTTCAACAAATGGTGCTGGGATAACTGGATAGCCAC 4820
                          -            i                    i         ?    
  L1M4_orf2#LINE/    386 G-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_1161545_11   4821 ATGCAAGAGAATGCTGTTGGATCCCTAACTCACACCATACACAAAAATTA 4870
                               i      vv      i     v           i          
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_1161545_11   4871 ACTGAAAATGGATCCAAGACCTAAATATAAGAGCTAAAACTATACCATT- 4919
                            v          v?          i                 vv i -
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_1161545_11   4920 TTAGAAAGAAACATAAGTGTAA-TTTTCAC--TCTGCTGGATTTGGCAAT 4966
                               ii       i ?    - i   ii--i  --   i  v      
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT--TGGGTTAGGCAAT 582

  chr1_1161545_11   4967 TTTTTTTT 4974
                         vv   i  
  L1M4_orf2#LINE/    583 GGTTTCTT 590

Transitions / transversions = 2.04 (51 / 25)
Gap_init rate = 0.02 (12 / 494), avg. gap size = 1.92 (23 / 12)  

1074 17.54 3.51 1.32  chr1_1161545_1168186.rev     5512  5739 (903)    L1M4_orf2#LINE/L1      547   779 (129)  

  chr1_1161545_11   5512 ACAGGCGTGAGTCACCGC-ACCT--GGC---ACAATGGATTTTTAGATAT 5555
                          i   ?  i i  vi  i-    --  i---i      v  i        
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_1161545_11   5556 GATACTAAAAGCATGAGTAACCAAAGGAAAAAAATGGATAAACTGGATTT 5605
                           i  i       ii  i   v    --       i      i    i  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAG--AAAAAATAGATAAATTGGACTT 644

  chr1_1161545_11   5606 CATCAAAACTAAAAGCTTTTGTGGT-CAAAGGACATTATCAAGAAAGTGA 5654
                                 i     i        v -         i              
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_1161545_11   5655 AAAGACAGCC-ACAATATTCCAGAAAAATATTGGCAAATCATATGTCTGA 5703
                                i  -   iv  vvv      -    v           i     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGA 743

  chr1_1161545_11   5704 TAAAGGCCTAGTGTTTAGAATATGTAAAGAACTTTT 5739
                            i  v  v  i ii       i         i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

Transitions / transversions = 2.55 (28 / 11)
Gap_init rate = 0.03 (7 / 233), avg. gap size = 1.57 (11 / 7)  

 351 25.53 2.13 0.00  chr1_1161545_1168186.rev     6072  6165 (477)    L1M4_orf2#LINE/L1      813   908 (0)  

  chr1_1161545_11   6072 TAAAGAACAGCCACAGCGTTTGAATAGACATTTCTCTAAAGAATATACAT 6121
                          ?  i  ii v  v  vi                  i      v   i i
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_1161545_11   6122 AGCTGGCCAGTGAACACATGAA--GTTATTTGTCATTAGCAAAATG 6165
                          iv      i i i        -- v ii iiv   i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.01 (1 / 96), avg. gap size = 2.00 (2 / 1)  


 369 18.56 1.03 4.12  chr1_1913354_1918211      492   588 (4270)  C L1M4_orf2#LINE/L1   (0)   908   815  

C chr1_1913354_19    588 AAAAATGGGCAAAAGACT-GAACAGATGCTTCACCAGAGAAGATACGTAC 540
                                      i  i -   i   iii   v   i        iii v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

C chr1_1913354_19    539 GTGGATGAGAAATTCGCACATGAAAAGACGCTCAACATCATTAAACAT 492
                         i   vii v  ----             i           ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAA----GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.50 (14 / 4)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 2.50 (5 / 2)  

1086 27.45 4.48 1.40  chr1_1913354_1918211      886  1242 (3616)  C L1M4_orf2#LINE/L1   (79)   829   462  

C chr1_1913354_19   1242 CCTCACACTGTAAACAAAAGTTA-CTCAAAATAGATGATGTACCTAAAAG 1194
                                 ii  v      i   -        i   v ?iv       v 
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

C chr1_1913354_19   1193 TTAAGCCTAAAAATATAAAATTCCCCCCCGAAAAAAACACAGGAGAGAAT 1144
                          v iiv      v       i  iiv---   i      i   ? vi   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTA---GAAGAAAACATAGGNGTAAAT 558

C chr1_1913354_19   1143 GT--GTGGCCCTAGGTGAGGCAAAGGTTTTTCTTAGACATAACATTGAAA 1096
                         v --   i  i i   v      v     --      i  i   iii   
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTT--CTTAGATATGACACCAAAA 606

C chr1_1913354_19   1095 TTATG-GCCCCTGGTTTAAAAATTG-TAAACTGGACTTCGCCAAAACCAA 1048
                         vi ii-  vv viivvv      v -    i        ii     ii  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

C chr1_1913354_19   1047 GAACATCTGCTTTTTGAAAGACGCTGTTAAGAGACTGCAGAGATAAGCCA 998
                         i   v i  ivi  ii  i   i  i i    i v  v i   i  v   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

C chr1_1913354_19    997 CAGACTGGCGGAAAGCATTAGCAAATCACAAATCCGATAAAAAATTTGTG 948
                             v   vi    ii   v        i v   i     iii i    i
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

C chr1_1913354_19    947 TCCAAAATATGTAA----TTTTCAAATCTCAAT--TGGAAA-----ATAA 909
                             i     i   ----i i i v v      -- ii   -----    
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

C chr1_1913354_19    908 CCCAGTCAAAAAATGGGCAAAAG 886
                             i i?             i 
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 2.06 (64 / 31)
Gap_init rate = 0.02 (9 / 368), avg. gap size = 2.33 (21 / 9)  

1335 24.03 7.49 0.52  chr1_1913354_1918211     1615  2001 (2857)  C L1M4_orf2#LINE/L1   (470)   438    25  

C chr1_1913354_19   2001 ATTGGAACACTTCAC-----TAAAATGTGAATA-TCCCAGAACTAA-CTA 1959
                                v    v i-----   i   vv    -    vi  i i -   
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

C chr1_1913354_19   1958 TGGAT-CAATGCAATTCCAACCAAAATTCCAGGAAGATTTTTTAATGGAA 1910
                         ii   -   i     i  v i      i    vvivv      i-ii   
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG-CAGAA 123

C chr1_1913354_19   1909 ATTGACAAGGTGATTATAACGTTTATATGGAAAACCAGAGGACCTAGAGT 1860
                                  v    iv   vi  i         vv  ii     i   i 
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

C chr1_1913354_19   1859 GACCAAAACAATTTTGAAAAA-----ACAAATTTCAAGGACTTACACTAC 1815
                         ii          i        -----     v  vi      i     v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

C chr1_1913354_19   1814 CTGATTTCAAGA-TTACTATGAAG-TACAGTAA-CAAGACAGTGTGGT-- 1770
                          ii       i -      ii   -        -              --
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

C chr1_1913354_19   1769 -GGT----GAACAGAGATAGAGACCCAACGGAACAA----GAGAATCCAA 1729
                         -  i---- i i   v   v   i -  i    i i----    i    i
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATC-AATGGAATAGAATTGAGAGTCCAG 322

C chr1_1913354_19   1728 AAATAGAC--ACACAATTATAGTCAACTGGTTTTGAACAGAGGTGCAAAA 1681
                              i  -- i   v    i     i  i    vi   ii     v  i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

C chr1_1913354_19   1680 GTAATTGCTTGGAGAAAGAACAGTCTTTTCAACAAGTGAGGCCATAACAA 1631
                         iiv   vvv   i       i              i  iv  iivi    
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

C chr1_1913354_19   1630 TTGGATAAACATAAGC 1615
                         i      ?v  i v  
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGC 438

Transitions / transversions = 1.97 (61 / 31)
Gap_init rate = 0.03 (14 / 414), avg. gap size = 2.21 (31 / 14)  

1147 23.75 1.17 5.87  chr1_1913354_1918211     3201  3541 (1317)    L1M4_orf2#LINE/L1       31   355 (553)  

  chr1_1913354_19   3201 AGCCTCAATACTGTTAAGATGTCAGTTCTCCCCAAATTGATCTATAGATT 3250
                           v  i    i          v  i v                 i     
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chr1_1913354_19   3251 CAATGCTATGCCAATCAGATTCATGCTA--TGCTTTTTTGGTAGAAATAA 3298
                            i  v  v  v    i v  --- i --   i     v i      vi
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATC---CCAGCTGCCTTTTTTGCAGAAATTG 127

  chr1_1913354_19   3299 AAAAGCTGATTCTACAGTTTATGTGGAAATGTAAAGGACCTAAACTATCC 3348
                          v        i   v i  i  i        i  i     i i v  ---
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA--- 174

  chr1_1913354_19   3349 TGAGGCCCTAATGCAAATATTGTGGAAAAAAAAGAACAAAGTTGGGTGAC 3398
                         ----   vv  i---   v   ---     i              iv   
  L1M4_orf2#LINE/    175 ----GCCAAAAC---AATCTTG---AAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_1913354_19   3399 TTACACTACCTGGCTTCAAGGCTTTGTCTGAGTCCATGATAACCAAGACA 3448
                          i     v  iiii     ii   vv vii iv i iii   i       
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_1913354_19   3449 ATG--GCTCTGGCATAAGAATAATTAAATGGATCAATTAATCAGAAAAAA 3496
                         i  -- iv          i   ivi v  i       vi vi    vvi 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_1913354_19   3497 GAGGCGAGAACTATATAAGCTCATGCTTATATGGTCAATTGACTT 3541
                            v v    ----    i i   i v v             i  
  L1M4_orf2#LINE/    315 GAGTCCAGAA----ATAAACCCATACATTTATGGTCAATTGATTT 355

Transitions / transversions = 1.53 (49 / 32)
Gap_init rate = 0.02 (7 / 325), avg. gap size = 3.43 (24 / 7)  

 476 31.68 12.40 4.01  chr1_1913354_1918211     3842  4365 (493)    L1M4_orf2#LINE/L1      341   908 (0)  

  chr1_1913354_19   3842 ATGGTCAATTGATTTTTGACACGGACAACGAATGGATCGAATGGG-ATAG 3890
                                         i    v  iiiv i ivvv  iv      - v  
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_1913354_19   3891 CAGAGTCC-----AC---TTGTGCCGTG------GAATACACAAACACGC 3926
                         v v    i-----  --- v    i v ------ i   ?v  --  i  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA--CATGC 438

  chr1_1913354_19   3927 ACCAGGGGAAATGAGCCTCAGCCCTGACTTC-CACCACAAGCAGGAGTGA 3975
                          vv  ----     ivi vii   iv  i  -     i vi  ii i v 
  L1M4_orf2#LINE/    439 AAAAG----AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_1913354_19   3976 ATTTGAGGTGGATCATACACCTCAACACAAAAGCGA----TGT------- 4014
                          i ii ii       ? v    v  iii  i   v ---- i -------
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_1913354_19   4015 -----------CCTATG------TCTTTATGACCCTGGAGGAGAAAAAAA 4047
                         ----------- v  v ------    ii     i   ivv  iv  vii
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_1913354_19   4048 TTGCCTAAAAAT--CATAAAAA--ACAAATTCCAATAGAAATGACTGGTA 4093
                           v i  i v  --  iv    --    iivv   v     vi iv i  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_1913354_19   4094 AATATGCAAAGACT-----GGACTGAAGAACTTT---GATTTGAGAAAAG 4135
                            -  ----    -----ii v v  i      --- v  i---   i 
  L1M4_orf2#LINE/    635 AAT-TG----GACTTCATCAAAATTAAAAACTTTTGTGCTTC---AAAGG 676

  chr1_1913354_19   4136 ACGTCATAAAGGGAGAGGAAGGCCCAGCCACAGACTCGGAGGCAGCACCT 4185
                           iii  v   ii  v i  i v v v       v v    iv ii ii 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_1913354_19   4186 GCAA--CATTCCTCAGGGAGGAGGGCTGGAATCTGGG-TGCATGAAGAGC 4232
                             --   viv  v iv i -  i  v v   ii i- ii  i    i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAG-GGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_1913354_19   4233 TCCTATGAATGAATGAGAAGAAGACAGACAATCCCAC--AGAA--GAACA 4278
                           i  ii v v   i v  i      i i  i  v i-- i  -- ii  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_1913354_19   4279 AGGGATAGCCTTAAACAGAGATGTCACACCAAAGAAGATA--CAACTTGT 4326
                          i    ----  i  i   v  v  v --           --   v v i
  L1M4_orf2#LINE/    826 AAGGAT----TTGAATAGACATTTCTC--CAAAGAAGATATACAAATGGC 869

  chr1_1913354_19   4327 AAATGGGCCCAGGGAAAGACACGCAATCTCACTGGTGAT 4365
                         v   ii  v  v i     ii v   iv   ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (97 / 67)
Gap_init rate = 0.04 (25 / 568), avg. gap size = 3.44 (86 / 25)  


3832 20.26 3.06 0.24  chr1_2026908_2030462.rev     1868  2716 (839)    L1M4_orf2#LINE/L1        3   875 (33)  

  chr1_2026908_20   1868 GAAACACACTTCA-GTTCATGGATTGGAAGTCTTCATACTGTTAAGATGT 1916
                             v i iii  -                v   v   i          v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_2026908_20   1917 CAGCACTACCCAAAGTGATCTACAGAGCCAATGCAATCCCTGCAAAAATC 1966
                           ii   v      v           vi   i         iiv      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_2026908_20   1967 ACAATAATGTTTTTTGCAGAAATAGAAAAGCCTGTCCTAAAATTCATCTG 2016
                         v  iiviiv              v  v    ivi             v  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_2026908_20   2017 GAATCTCAGGGGACCC--------CAAAACAATCTTGAAAAGGAAGAACA 2058
                            viv  i       --------                 i        
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_2026908_20   2059 AAGCTGGAGGGCTCACACTTCCTGATTTCAAAACTTCCTACAAAGCTACA 2108
                            i      i           ii            v             
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_2026908_20   2109 GTGATCAAAACAGTGTGGCACTGGCTCAAAGAGAGACACAGAGACCAATG 2158
                           i     i         i      vi  i  v     i v   i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_2026908_20   2159 GACTAGAA--GAGACTCCACAAATGAACCCTCCCATATATGGTGAAACGA 2206
                           v     --    v    v    i     viv   v      v  vi  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_2026908_20   2207 TTTTCAACAAGGGTGCCAATGCAGTCCAATGGGGA-------GTCTTTTC 2249
                              i             vi vi i         -------        
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_2026908_20   2250 ACCAA-TGGTGCTAAGAAAACTGGACCTCCACATGCAAAGGAATGAAGTT 2298
                          v   -       ii  v       iv?           i          
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_2026908_20   2299 AGATGCTTACCTTACACCACATACAAAAATTAACTCAGGAT-AATCCATG 2347
                         i  iv i     i      i                 ii  -i   v?v 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_2026908_20   2348 ACCTAAACATAAAACCTAAAATTATAAAATCCTTAGATGAAAGAGAAGGG 2397
                                ii   i v      i       ii      v    iviv   ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_2026908_20   2398 GAAAAGCTTCACAACATTCGATTTGGCAGTGATTTCTTGGATGTGACACC 2447
                          v   v    iii  v  v i  v    i  i      i   i       
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_2026908_20   2448 AAATACACAGGCAACAAAAGAAAAAAACATTAAGCAGGATTTCAGGAAAA 2497
                            vi    i                vviv   iiv   i    vv    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_2026908_20   2498 TTTTAAAACTTT-GTCCATCAAAAGGCACTATCAACAAAGTAAAAAAACA 2546
                           -v        -  v v     i i         v     i    i   
  L1M4_orf2#LINE/    653 TT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_2026908_20   2547 ACCCACAAAGCAGGAGAAGATATTTGCTAATCATATATCTGCTACGGGAT 2596
                                i iii      i        v             v  v    i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_2026908_20   2597 TAACATCCAGGACA----GAGAACTAGTAACACTCACCAACAAAAAAACC 2642
                          vii      i i ----i      vv  vv     vi  i     i  -
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC- 800

  chr1_2026908_20   2643 AAACAACCCA-TTCAAAAATGGACACAGGACGCGAAAAGACATTTCACCA 2691
                            i      -  ?        i  v    ivi   v         v   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_2026908_20   2692 AAGAAGACACAGAAATGGCCAACAA 2716
                                i i v          i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAA 875

Transitions / transversions = 1.37 (97 / 71)
Gap_init rate = 0.01 (11 / 873), avg. gap size = 2.55 (28 / 11)  

 258 13.56 0.00 0.00  chr1_2026908_2030462.rev     3006  3064 (491)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_2026908_20   3006 AAAAAAAAAAAAGAAATGGCCAACAGGCACATGAAAAAATGCTCAACATC 3055
                            i  i v v v          i i           i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_2026908_20   3056 ACTTATCAC 3064
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


1599 27.58 10.32 1.60  chr1_2223365_2225536.rev      533  1094 (1078)    L1M4_orf2#LINE/L1       18   628 (280)  

  chr1_2223365_22    533 TCCGTTGGTCGGAAAACTCCCGATTGTTAAGAT------ATTCCC--AAT 574
                          i i v i i    i   ivvv           ------ i    --   
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr1_2223365_22    575 TTATCTATGGACTCAATACAATCCCAATCAAAATTTCCCAGAAATG---- 620
                          v     ii  i    ii       v        --     v--  ----
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAAT--CCCAGC--TGCCTT 113

  chr1_2223365_22    621 -TTCACAGAAATTGACAAACTGATTCTAAAATTCATATGGAAAAGTGGAA 669
                         -  ii             i     i                  v iiiii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_2223365_22    670 GATCCCGAATAGCTGTAACAGCTCTGAAAAAGTG---CAGGGTTAGAGCG 716
                           i  v       iiv    iiii        vi---  ii   i   vi
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_2223365_22    717 CGAATATCACCTGACCTCAACAATTATTTCAAAGCTACAATAATCCAAAA 766
                          vv i iiv  ii ii    v v   i v          i     -  i 
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC-AAGA 262

  chr1_2223365_22    767 CAGCATGGCGTTGATGTAAAAAGATAAACAAGTGGATCAACTGAATA--- 813
                            ii   iii  -- i v  i    i   vi i      iv     ---
  L1M4_orf2#LINE/    263 CAGTGTGGTACTG--GCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_2223365_22    814 -----------------------CACATCTGCA--CAGCTGATTTCTGAC 838
                         -----------------------i    i iii--  ii      ii   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr1_2223365_22    839 AAAGGCACAAAGACAATCCAGTAGAGAAC---TAATCTTTACAACAAACT 885
                           i  ii v     v  i  i i i   v---  i     v       iv
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_2223365_22    886 CCACTGAAACATCTGAACA-CCTTAGGCAAAGAAATGAACTCAGGTCCAC 934
                         vii   ii   v   i i -  vi v     ii      v ii ii  vi
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_2223365_22    935 ACCTTGCATTGCACACAAAAATTAACTCAAAATGGATCACAGACCTAAAT 984
                             ii  iiii i                         ?          
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_2223365_22    985 ATACAACTTAAAGCTACAAAATTTCTAGAA-----TACAGGAGATAATCT 1029
                         i  vi vi    i   i    i ii     -----i i   ? vv     
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_2223365_22   1030 CTGTGACCTTGAGTTAGGGACAAAG--TTCCCAGCTAGGAAACCGAA-GT 1076
                         ii         i      --   v --   ii  v  v  v   i  - i
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGG--CAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_2223365_22   1077 CCAAAC--CAAAAGAACAAA 1094
                         v   i --        v   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAA 628

Transitions / transversions = 2.64 (111 / 42)
Gap_init rate = 0.03 (17 / 611), avg. gap size = 3.94 (67 / 17)  

 642 28.81 4.41 0.68  chr1_2223365_2225536.rev     1389  1683 (489)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr1_2223365_22   1389 AAAAAAAAAAAAAGAAAAAGAACAAACTGAAAAATTGGATCCCATAAAAA 1438
                             iv v  iv iv       v   iv  v        iii   v    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_2223365_22   1439 TTTTGCAGTTCTACTCTTCAAAAAACACCGTTCAGAAAA-GGAAAG---- 1483
                           vviv v  i iiv       ii    ii iv     i- i    ----
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_2223365_22   1484 -CCATGGACAGGGACAAAGTCTACGTAAGGCGCAAATGTGAAAAGGGACT 1532
                         -   ii  vv    v   i v vi i  iv ii v  v   v        
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_2223365_22   1533 TGCATCCAGAATACGTAAAGA--TCTCACGAGTCAACAGTAAAACAACAA 1580
                           i          ii      --   i  i v    i i     vi    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_2223365_22   1581 A---CCCAGTCTAAAATAACTGGCAAAA-ATCAGAAGGGACATTTCACCA 1626
                          ---    i i?    -- iv      i-  iv   vi        v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAA--ATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_2223365_22   1627 AAGAAGACATATGG-TGGCAAATACGCACAAGAGAAGCCACTCTACGTTC 1675
                                i   iii-    v    v     v  i   vii   v  i iv
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_2223365_22   1676 TCAACGAT 1683
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.40 (49 / 35)
Gap_init rate = 0.02 (7 / 306), avg. gap size = 2.14 (15 / 7)  


 203 14.63 0.00 0.00  chr1_2327428_2329808.rev      463   503 (1878)  C L1M4_orf2#LINE/L1   (0)   908   868  

C chr1_2327428_23    503 GCCAAAAAACACATGAAGAAATGCTTACCATCACTGGCTAT 463
                              v  i        i i     i v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (4 / 2)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  

3110 27.26 1.58 0.57  chr1_2327428_2329808.rev      999  1882 (499)    L1M4_orf2#LINE/L1        1   893 (15)  

  chr1_2327428_23    999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1048
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_2327428_23   1049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1098
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_2327428_23   1099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1146
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_2327428_23   1147 TATGGCACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 1196
                              v viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_2327428_23   1197 AACAAAGCTGGAGGTATCATGCTACCTGACTTCAAACTATACTACAAGGC 1246
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_2327428_23   1247 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGATC 1296
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_2327428_23   1297 AATGGAACAGAGC--AGAGCCCTCAGAAATAACGCTGCGTATCTACAACT 1344
                                i   ii--    i  --        vv iiiii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_2327428_23   1345 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1394
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_2327428_23   1395 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1444
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_2327428_23   1445 GAAACTAGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1494
                            ii i  i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_2327428_23   1495 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1544
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_2327428_23   1545 CTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1594
                         v    ?v v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_2327428_23   1595 AACACCGAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1644
                         i     i      vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_2327428_23   1645 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAGACTACCATCAGAGTGAAC 1694
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_2327428_23   1695 AGGCAACCCACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 1744
                           i         i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_2327428_23   1745 AGGGCTAATATCCAGAATCTACAATGAACTC----AAATTTACAAGAAAA 1790
                         i  i  vi          v  i  v      ----  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_2327428_23   1791 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 1836
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_2327428_23   1837 TCAAAAGAAGACATTTA--TGCACCAAAAAACACATGAAAAAATGTTC 1882
                           v        i  vi --  -i    v  i          i   i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATG-GCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (9 / 893), avg. gap size = 2.11 (19 / 9)  


2811 23.48 3.48 3.85  chr1_2333140_2335535      307  1111 (1285)    L1M4_orf2#LINE/L1        1   802 (106)  

  chr1_2333140_23    307 TGGAGAGATGCTTCTGTGTTCATGAGATGGAGGCCTCAGTGTTGGTAAGA 356
                             i    i- i ii        iiv    i v  i i i   v     
  L1M4_orf2#LINE/      1 TGGAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_2333140_23    357 TTTCA----TCTGGACATTC-TCTCCAGAGGGGTTCAACGCA-CCTCCAT 400
                          vv  ----  ivv v   v-   v    ----         -i i i  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGA----TTCAACGCAATCCCTAT 95

  chr1_2333140_23    401 CAACATTCCAGCAGCCTTCTTTTGTTGTTGTTGCAGAAGTTGGCAAACTG 450
                            v  i     v     i   ----------      i   i   i   
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTT----------GCAGAAATTGACAAGCTG 135

  chr1_2333140_23    451 ATCTTAAAATTTTATACAGAAATGTAAAGGTCCCAGCAGAGTCAAGATCA 500
                            i       i-   ii      i  i  v     v v  i   i iv 
  L1M4_orf2#LINE/    136 ATCCTAAAATTC-ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_2333140_23    501 TTTTGAAAAGGAAAAACAAAACTGGAGGACTC------TCCAATTGGAAA 544
                          i       i   i      ii          ------i      vv   
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_2333140_23    545 ACGTGCTA-AAAGCAACAAGAATCCAGATAGCGTGGCCCTGGCATAGACT 593
                           v i   -     v   iv    v   i  i    iv        ----
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA---- 280

  chr1_2333140_23    594 GAGGATAAATCAGGATAGACAGATCAGTGGAGCAGA-CGGGGGGTCCAGG 642
                         -      ------  i v i      i    ii   -iv i i      i
  L1M4_orf2#LINE/    281 -AGGATA------GACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_2333140_23    643 CATCAACCCTGACTCTTAGGGCTGACTGATTTTCAACCAAGGTGCCAGGG 692
                         v  v     vv  vi   v  iii i        i  v i       i i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_2333140_23    693 CAACTCAACGGCAAAAGGACGGTGTTCTCAACAAATGATGCTGGGATGAT 742
                          v i    i  vi    i ii  v  i          i        ii i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_2333140_23    743 TGAACATCCCCATGAAGAAAAGATGAATTTAGAACTTTATCTTTT-CCAT 791
                           i i ?  v    v i  i -     v  i  v ii  i  ivi-    
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGA-ATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_2333140_23    792 A---AAAAAT-AACTCACACTGGATCCCAGGCCTAAATGTAAGAGCTAGA 837
                          ---      -      v v      v?  i                 i 
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_2333140_23    838 ACTATAAGAGTTCTGGAGGGATAC----GAGAAAATCTTTGTGAAACTTG 883
                                i v ii i  i i v  ---- ? v       i    v-    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC-CTTG 571

  chr1_2333140_23    884 GGTTAGGCAAAGAATTCTTAAATACGGTACCAAAACTATGCTCCATAAAA 933
                                   v iv      i   i ii       vi iivv v i    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_2333140_23    934 GAAAAAATGGACAAACTGGACTTCAGCAAAATGAAAAACTTTTGCTGTTC 983
                                 i  i   i         v      v           -  i i
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTT 670

  chr1_2333140_23    984 CAAAG-ATAGCATTAGGCAAATGAAAAGATGAGCCGTAGG-TGGACGGAA 1031
                              - i vi  i i v  i        ii v  ii  i-   i-i   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG-AGAA 719

  chr1_2333140_23   1032 AGCATTTGCAAAG-ACATATCTGATAAAGGACTTATATCCGCAATAGGTA 1080
                          ii         v- i           i      i     iv    vi  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_2333140_23   1081 AAGAACTCT-ATAGCTAAA-AATAAGAAGACAA 1111
                                  - i i  v  -     i       
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAA 802

Transitions / transversions = 2.00 (124 / 62)
Gap_init rate = 0.03 (25 / 802), avg. gap size = 2.36 (59 / 25)  

 463 21.05 0.00 2.63  chr1_2333140_2335535     1790  1903 (493)    L1M4_orf2#LINE/L1      798   908 (0)  

  chr1_2333140_23   1790 GACTGATAGTCTAATTTTTAAAAAATGGGTACAATATTTGAATAGACATT 1839
                            vi   ii i    ?---         i v iv               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTW---AAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_2333140_23   1840 TCTCCAAAGAAGATAAACAAACAGCCAATCAACACAGCGAGAGCCACTCA 1889
                                        v     ii      v i    vvi i  vii    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_2333140_23   1890 TCGTCATCACTCGT 1903
                         v i   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.01 (1 / 111), avg. gap size = 3.00 (3 / 1)  


1268 25.85 12.51 6.32  chr1_2561987_2565911     2579  3433 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_2561987_25   2579 TGGAAGCATATATCATGTTCATGGATTGGAAGACTCAGCATTGCAAAG-T 2627
                              iv    vi                      i ii    iv   - 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_2561987_25   2628 -------CTCCCCAAATTGATAGAGAGATTCAAAGTGATCCCTATCAAAT 2670
                         -------              vv v        v ii            v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_2561987_25   2671 TTCTAGCAGAGTTTTCTTTTTGTGTGTGTGCGTGTATGCAAATGGA-AGG 2719
                          i i   v -----i      -----------  i - -    v  - i 
  L1M4_orf2#LINE/    101 TCCCAGCTG-----CCTTTTT-----------TGCA-G-AAATTGACAAG 132

  chr1_2561987_25   2720 CAGATTTTAAGTTTTATGTGAAAATGCAAAGGACTGAGAATTATCAAGAC 2769
                          v   ii   iv  i  i  i        i    iv     vii   i  
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr1_2561987_25   2770 ACTCTTGAA------GAACAAAGTTGAAATATATACTCTATTGACTATCA 2813
                          v       ------           i iv ivi  v  viiv v v   
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_2561987_25   2814 AGAC--ATTATAAAGCTGAAGGAGT---GATGGTG--GTAGGGGTTATCA 2856
                          i  -- i  i      iv  v i ---  ii   --   vv  i-  v 
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC-ATAA 281

  chr1_2561987_25   2857 CTTGGATAGATAAAGAGACCAGTGGGGCAAAA--GAGAGTCCAGAAATAT 2904
                         ---       i v v   i  i   iii i  --               v
  L1M4_orf2#LINE/    282 ---GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_2561987_25   2905 ACATATGGGCCCACGCATAGACACACAGGAACACCTGATTTATAACACAG 2954
                           --------   ii   vv i------ iv  vi      vii   ---
  L1M4_orf2#LINE/    329 AC--------CCATACATTTAT------GGTCAATTGATTTTCGACA--- 361

  chr1_2561987_25   2955 AAGGCACCAAGACCA------GGGGCTCACAGGGGGCTCTTTTTAATAAA 2998
                          i  ii         ------    --- v  iiviv      i  i   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGG---AAAGAATAGTCTTTTCAACAAA 408

  chr1_2561987_25   2999 TGGTGCTGA-ATGACTGGAAATCCATA------AGAAAGAAAC--AATTC 3039
                                 i- ii      v ?   i ------    v   ii--i ii 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_2561987_25   3040 CTACATCTCACTGTCCAT-TAAAAAAATCAACTCACAGTAGATTGTAGAC 3088
                             --     v--    -  v      i      v i i   ii?    
  L1M4_orf2#LINE/    459 CTAC--CTCACA--CCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_2561987_25   3089 CTAA--GCAA-ACCTGAGGGTAGGCAAAGAGTTCTTTAGCAGAACACA-A 3134
                             -- i  - v  i iiv  --i   i--i    -  v    v   - 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTA--TAAAA--CTCTT-AGAAGAAAACATA 549

  chr1_2561987_25   3135 AGAATA---CT----AACCACGAAGAAG-------------AGATCTG-C 3163
                         i ?i  ---  ----i   vi iivv  -------------    v  - 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_2561987_25   3164 ACACATTTGC-TAAGC--CAA-------------TAAATTGGAC--CAT- 3194
                           -  vvv  -i    --   -------------          --   -
  L1M4_orf2#LINE/    600 AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_2561987_25   3195 ----TTAATAGCCTCCATTGAAACAAAGAA-ACCCTTATGAGAGTAAAAA 3239
                         ----    v i i iii - vvv     i -  iv i v  i   i    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGT-GCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_2561987_25   3240 AGCAAGCTGCCCAGTGGG-GAGAACATTTGTACA-CATA-AGCTGACCAA 3286
                         ii   v ii vv i    -  i  i     i v -    - v    iv i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_2561987_25   3287 GGAGTCACATCTAAAATAGGTAA----CTCCAAGAA-TCAATCAGAGAAA 3331
                            v iii   i i    vi   ----   iv v  -     v v i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_2561987_25   3332 GA----TCGCCCGATAGAACAAATGGGCAA--GACTCAAACAGACGTTCC 3375
                           ---- vi   i  v?  -          --  i ii  i    i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_2561987_25   3376 ACAAAAGGGAATG-GCAT-TGGCCAATTG--ACAGGAGATGGCGTTTAAC 3421
                         v v    iii  i-i  v-        vi--   v  i v ii i i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_2561987_25   3422 CTCCTCCGCCCT 3433
                         v  v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (135 / 82)
Gap_init rate = 0.06 (54 / 908), avg. gap size = 2.98 (161 / 54)  


3402 13.45 3.62 19.39  chr1_3801045_3803517      903  1980 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_3801045_38    903 TGGATTAACATCCCATGTTCATGGATTGGAAAACTTAACATTGTTAAGAT 952
                             vvi i                      i      i           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_3801045_38    953 GGTGGGACTCCCCAAACTGACCTACAAATTCAACACAATCCCTATGAAAA 1002
                           iiiv          i   i     i       i          v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_3801045_38   1003 TTCCAGCTGGTTTCATTGTAGAAATTGACATGCTGATTCTAATCCACAGT 1052
                          i       vi  iv   i           v      i    ----- i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA-----AAT 145

  chr1_3801045_38   1053 TCATATGGAATTGCAAGAGACCCAGAATAGCCAAAACGACTGTGAAAAAG 1102
                                   v      i                   i iiv        
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_3801045_38   1103 AAGAT---AGTAGGAGGACCCACATATTCTGATTTCAAAACTTAGTACAA 1149
                             v---   v       i    iv i ii             v     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_3801045_38   1150 AGCCACAGTAATCAAGAC----TGACACTGGTACAAGGACAGATATATAG 1195
                            i              ----  ii     i i     i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_3801045_38   1196 ATCAATGGAATAGAACAGAGCACCCAGAAAT----CTATGTATCTGTGGT 1241
                                        iv   vii        ---- i  ii  i i    
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_3801045_38   1242 CA---------------GGATGCCAGGACCATTCAACGGAGGGGGAAGAG 1276
                           ---------------  i     i          i  ---  i    i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG---GGAAAGAA 392

  chr1_3801045_38   1277 TAGTATCTTCAACAGATAGTGCTGGGACAACTGTATATTCACATACAAAA 1326
                             v i       i  i               v   ?i     i     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_3801045_38   1327 GAATGAAGTTGGACTCTTAGCTGGTACCTTATACAAAAAGTA---CAA-- 1371
                                       i i  v  vii   v          v  ---   --
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_3801045_38   1372 TAAATGAAAGACCTAAATGTAAAAGTTAAAAATATAAAGCCCTTAGAAGA 1421
                          ii  v ?              i  i     v      i i         
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_3801045_38   1422 AAACATAGCGATAAGTCCTCATCGCCTTGGATTTGGCAAAAGATTCTTAG 1471
                                 v?i   i  i  i vi      i  v     vi v       
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_3801045_38   1472 ATTTGACACCAAAAACATGAGCAGCAGAAGAAAAAACAGATAAATTGGGC 1521
                           v           i  ii    i  i         i           i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_3801045_38   1522 TTCATCAACATTAAGAACTCTGGCCCGGGCACGGTGGCTCAAGCCTGTAA 1571
                                 v     i    i v -----------  vi    --------
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTG-----------TGCTTCAA-------- 673

  chr1_3801045_38   1572 TCCCAGCACTTTGGGAGGCCGAGACGGGCAGATCACTTGAGGTCAGGAGT 1621
                         --------------------------------------------    --
  L1M4_orf2#LINE/    674 --------------------------------------------AGGA-- 677

  chr1_3801045_38   1622 TGAGACAAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACA 1671
                         -------------------------------------i    --------
  L1M4_orf2#LINE/    678 -------------------------------------CACTA-------- 682

  chr1_3801045_38   1672 AAAATTAGCCGGGCGTGGTGGCAGGCGCCTGTAATTCCAGCTACTCAGGA 1721
                         --------------------------------------------   ---
  L1M4_orf2#LINE/    683 --------------------------------------------TCA--- 685

  chr1_3801045_38   1722 GGCTGAGGCAGGAGAATTGCTTGAACCGGGGAGGTGGAGGCTGCAGTGAA 1771
                         ------------    ----------------------------      
  L1M4_orf2#LINE/    686 ------------AGAA----------------------------AGTGAA 695

  chr1_3801045_38   1772 C-GACAGCCCACAGAATAGGACAAAATAGTTGCCAATCATGTATCTAATA 1820
                         v-    i          i   v      v    v      i     i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_3801045_38   1821 CGGGACTTGCATC-AGAATATATAAAGAATCCTTATAACTTAATAGTAAA 1869
                         v        i   -               ii    i    i    i    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_3801045_38   1870 AAGA----TAACCCAATT-AAACATGGGCAAAGGTTCTGAAAAGAAAGAA 1914
                             ----          -   v           v i    v   v ---
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA--- 842

  chr1_3801045_38   1915 ATGTCTCCAAGGAAGATATTCAAGTGGTCG-TAAGCACAGGAAAAGGTGC 1963
                         - v       i        v   i   i i-        v      i   
  L1M4_orf2#LINE/    843 -TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_3801045_38   1964 TTGAGATCATCAGTCGT 1980
                          ii v    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (97 / 45)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 12.40 (248 / 20)  


2029 26.15 10.06 3.20  chr1_3999551_4002503.rev     1618  2462 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_3999551_40   1618 AGACATAACATGCTCATGGCTTGGAAGA-TTCATGTAGTAAAGATATCAA 1666
                            i  vv    i      v        -  v  i v  v     iv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_3999551_40   1667 TCTTCCCCAAATGGATCTATAAATTTAATTCAATTCCCA-CAAAAATCCA 1715
                          vi         v      i i   i  iv    i  i -     vi   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_3999551_40   1716 GTAGGATTTTT-GAAGACATAGACAAACTGGT--TAAAA----------- 1751
                          iv vv     - v   v  v     i   i --     -----------
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_3999551_40   1752 ----AAGGAACT-AGAGTAGCTAAGACAAATCTGAAAAGGAAAATGGAAA 1796
                         ----    i  i-   i    i  i    vii      i   i vvi  i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_3999551_40   1797 CAGGAAGAATCACCCTACAGATATTT--AGGCTTAATGGGCTTCA--GCT 1842
                         iv   i  v    v  v vv -    -- ii    -----  v  --   
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCA-ATTTCAAAACTTA-----CTACAAAGCT 249

  chr1_3999551_40   1843 ACAGTAGTCAAGACTGGGTGGTATTAGCAGTGGGCCA-ACACGGAGATCA 1891
                               i       v v      i i   vvi  vi -   iiv      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_3999551_40   1892 ATGTAACAGGA--------------------CCACACAAGTACAACTCAC 1921
                            v  i  i --------------------   i   vv  iiiiiv i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_3999551_40   1922 TGACTTTTCACAAAGGTACACATG-CAAATCAATAATGAAAGG-TGGTCT 1969
                            i   iv    i   i -  v - v v     iiv     i- i    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_3999551_40   1970 TTTCAACAAATGGTATTGGTCATCCATAGGCAAAACACACACGCACACAC 2019
                                       ii   --iv v iv  - v ? -    i   v ---
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGG--GACAACTGG-ATAKC-CACATGCAAA--- 441

  chr1_3999551_40   2020 AGACACACACACACCTTAACCTACACCTCACTTT-TATACAAAAATTAAC 2068
                            ----- iiv vi vi   ivi       vii-               
  L1M4_orf2#LINE/    442 AGA-----ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_3999551_40   2069 TCAAA-TGGATCAAAAATCTAAATGGAAAATGGGAAA-TGTAAA-CTTTT 2115
                              -       ? i i       v  i vvvi   - i    -  i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_3999551_40   2116 AGAAGAAGACATAGGAGACAATTTTTACCACTTAGGTTTAGGCAAAGAGT 2165
                                i       ? vv   i  iiiv  i v  v        v iv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_3999551_40   2166 TCTTAGCCATGACACCAAAAGCATGATTCATAAAACAAAACAAAAAAAAA 2215
                               vi               i--------  i   v v  i      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCAC--------AAGCAACAAAAGAAAAAA 628

  chr1_3999551_40   2216 AAGACAAATTAAATTTTGGCAAAATTCAAAACGTTTTCTCTTCCAAAGAC 2265
                         v   i     ii i  iiv       v     v   viv    v  i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_3999551_40   2266 ACCATTAGAAGAATGAA-----------------GAGAGAAAATATGCAT 2298
                           i  i ii i i    ----------------- i          viii
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_3999551_40   2299 AAATCACATATCCAAAAAAAGCCTTATATTGAGAATATATAAAGAACTCT 2348
                               i     ii v  ii v   i   iv                   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_3999551_40   2349 CAATACTCAACAA---------------CTCAATTTTACA-TGGTCAAAA 2382
                         i vv      i  --------------- i     ?v v -   v    i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_3999551_40   2383 GGCTTAAACAGGTGCTTCACCAAAGAGGTTGTGTGGATGGCAAATAAGCA 2432
                          ii  i  i  iiii   v       i v i iiii     v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_3999551_40   2433 CAGGAAATGAAGTTCAACACCATTACTAAT 2462
                           v    v  v i      i  ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (129 / 88)
Gap_init rate = 0.03 (28 / 903), avg. gap size = 4.00 (112 / 28)  


3184 26.72 1.00 0.33  chr1_4005338_4010309     3578  4479 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_4005338_40   3578 TGGAAACACATCCCACGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3627
                               v i      i i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4005338_40   3628 GATCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAAA 3677
                          iiv     v  v   vii       i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_4005338_40   3678 TACCACCATCGCTCTTCACAGAACTAGAAAAAA-AATCCTAAAAATCATA 3726
                          v   v vv vi i  ii     v v  v  iv-i         v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_4005338_40   3727 TAGAA---CAAAAAGAGCCTGCATAGTCAAGGTAAGACTAAGCAAGAAGA 3773
                          i   --- -  ii  v  v v    i   iii  vvi i iv       
  L1M4_orf2#LINE/    151 TGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_4005338_40   3774 ACAAATCTGAAGGCATCACATTACTTGACTTCAAACTATGCTATAAGACC 3823
                              vi  i   vv     i v iii i      viv i   i  ii i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_4005338_40   3824 ATACTCACCAAGACAGCATGGTACTGGTACAAAAATAAGCACATAGACCA 3873
                          i v v i        ii         i i  ii   ii  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_4005338_40   3874 ATGGAACAGAATAGAGAACCCAGAAA-AAAGCTAAATGCTTACAGCCAAA 3922
                               i     v    ii       -   v i v iii   ii i   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_4005338_40   3923 TGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTA 3972
                             i  i     i vviv   i v   vv i         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_4005338_40   3973 TTCAACAAATGGTGCTGGGATAATTGGCAAGCTACATGTAGAAGAATGAA 4022
                                             i  i   vv ? i     i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_4005338_40   4023 ACTGGATCTTCATCTCTCACCTTTTACAAAAATTGACTTAAGGTGGATGA 4072
                         ii    i iii i   v    v v          i   i  ii     v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_4005338_40   4073 AAGACTTAAATCTAAGACCTGAAACCATAAAGATTCTAGAAGATAACATT 4122
                         ?    i     v     v  i    i     iv ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_4005338_40   4123 GGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTTATGACCAAGAA 4172
                           ?iv  vi    vv   v    v        v ii  iv iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_4005338_40   4173 CCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGAACTTAATTA 4222
                         v         v v         iv   i   i   i  v i    v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_4005338_40   4223 AACTAAAAAGCTTCTGCACAGCAAAAGAAATGATCAGCAGAGTAAACAGA 4272
                           v v    i   i  ii vv    i  v iv    iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_4005338_40   4273 CAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAGAGG 4322
                                    i           v  ii   vii   i      i ii  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_4005338_40   4323 ACTAATATCCAGAATCTCTACAAAGAACTC----AAATCAGCAAGAAAAA 4368
                            vi          --v  i         ----  v   ii  v     
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAAT--ATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_4005338_40   4369 AACAAACAATCCCATCAAAAAGTGGGCTAGGGACATGAATAGACAATTCT 4418
                         i     i  i  v  i?    i     v i   iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_4005338_40   4419 CAAAAGAAGATATACAAATGGGCAACAAGCATATAGAAAAATGCTCAGTA 4468
                          v                   v   i     i  ii   i       ii 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_4005338_40   4469 TCACCAATTAT 4479
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


 296 22.03 0.00 0.00  chr1_4159825_4162726.rev     1364  1422 (1480)    L1M4_orf2#LINE/L1        1    59 (849)  

  chr1_4159825_41   1364 TGGGAAGTTACTCCATGTTCATGAACAGGAAGGCTCTATATTGTCAAGGT 1413
                            i   v  ii           i iv     i  iv       i   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4159825_41   1414 GTCAATACT 1422
                          v       
  L1M4_orf2#LINE/     51 GGCAATACT 59

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  

2619 24.23 2.73 6.26  chr1_4159825_4162726.rev     1534  2412 (490)    L1M4_orf2#LINE/L1       61   908 (0)  

  chr1_4159825_41   1534 CCCAACTTTATCTCTAGAT-CAATGCAATCCCAATCAAAATGCCAGCAAG 1582
                              v  v    vi    -   i        v        v     viv
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr1_4159825_41   1583 TTATTTTGTGGTTATCAAAAAATTAATTCTAAAGTTTATACAGAGAGGCA 1632
                         i v     ii vv  ii v  ii i  i     i  i   ii  i v   
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr1_4159825_41   1633 AGAGATCCAGATTAGCCAACACAATATTGAAGGAAAACACTGTTTTATGA 1682
                           i  i     v       v     v     -------------------
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAA------------------- 191

  chr1_4159825_41   1683 TAAACTCATAAACAAAGAGAACAAAAGAACAAAAAGTCAGAAGACTGACA 1732
                         -------------     -------        --  ii  i    v   
  L1M4_orf2#LINE/    192 -------------AAAGA-------AGAACAAA--GTTGGAGGACTCACA 219

  chr1_4159825_41   1733 GTATCTAACTTCAAGATATACTATTAATACAAAGCTACAGTCATTAAGAC 1782
                         v vi i  i     i iv     ------            v  i     
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTA------CAAAGCTACAGTAATCAAGAC 263

  chr1_4159825_41   1783 AGTACAGTAT---CAAAAGAACAAGCAAACAGATCAATGGAACAGAGTGG 1829
                            iii   i---  v   i i ii  v i            i   i v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_4159825_41   1830 AAAGCCCAGA-------CTATATAAATATAGTCAATTGAACTTTGACAAA 1872
                          i  i     ------- i   i vv   i         vi  i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_4159825_41   1873 TAAGCAAAGACAATACAACAGAGCAAAGATAGTCTTTTCATCAAACGTTG 1922
                         viv  v     v  v   ii i v  ii            v    i v  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_4159825_41   1923 C------AACTGGACATCCACACACAAAGAAAAAAATGAATCTAGACACT 1966
                          ------       i ?     ii    ---- i      vi i   v i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAA----AGAATGAAGTTGGACCCC 459

  chr1_4159825_41   1967 GGCCTTACACCCTTCACAAAAAATTAACTCAAAATGGATCATAGATGTAA 2016
                         vi   i     v vi       -                  ?   iv   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_4159825_41   2017 ATGTGAAATTCAAAGCTATTAAACTTCTAGAAGGTAACATAGGAAAGAAT 2066
                             i i vii   i    v     ii      iv        ?ivi   
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_4159825_41   2067 CTAGATGACTTTGC-CTATGTTACTATTTT---GACAAAACATTAAAAGC 2112
                           vvi    i   v-i  v iv ivi   i---  i vi   ii      
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_4159825_41   2113 AAGATTCATGAAAGAAATAATCGATAAGCTAGACTTGATTAAAATTTAAA 2162
                          vi viv ii       v   v     ii i     v  i      v   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_4159825_41   2163 ACTTCTCTGC---AAAAGAGACTGCCAAGTCAGTGAGAAGACAAACCGTA 2209
                             i v   ---   i  v   ii    vv     i       v  ii 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_4159825_41   2210 GACTGGGAGAAAATATTTGCAGAAGGCCTGTCTGATAAAGGAGTATTATT 2259
                           v                  i vviiv i        i   v vv   i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_4159825_41   2260 CAAAATATACAAAGACTTCTTAAAACTCAACAATAATAAAAAAAAACCAA 2309
                           i      i     vi     v       i     -   i v   i-  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAA-AAAGACAAAT-AA 806

  chr1_4159825_41   2310 CCTGATTTTAAAAATGAACAAAATATCTGAATGGACACCTCATCAAAGAA 2359
                           ii   ?-       ii    iv  i     i    ii  vi       
  L1M4_orf2#LINE/    807 CCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_4159825_41   2360 GATATGCAGATAACAAATAAGTATATGAAGAGATGTTCAGCATCGTATGT 2409
                              i  i  ii v      i i     i     i   i    i?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_4159825_41   2410 CGT 2412
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.75 (133 / 76)
Gap_init rate = 0.02 (16 / 848), avg. gap size = 4.94 (79 / 16)  


1084 22.03 1.32 0.00  chr1_4165684_4170572        1   227 (4662)  C L1M4_orf2#LINE/L1   (364)   544   315  

C chr1_4165684_41    227 GAGGCTAAAGATAGGACCCCACATTTATGTTCATTTAATTTT-GGCAAGA 179
                            v i i i   iiv  vi         v   v  i     - i    i
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

C chr1_4165684_41    178 GTATCAAGGCCATTTTATGGTTAAAGACTAATCTTTTCAACAAATGGTGC 129
                           ii    i     iv    vv     v  i                   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

C chr1_4165684_41    128 TAGAAAAACTGTATATTCCCATGCAAGAGAATAAAATTGGACCCCTACCT 79
                          i i v     v   ?i v       i     i  i              
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

C chr1_4165684_41     78 CATATCATATGCAAAA-TTAACTTGAA-TAGATCAAAGACATAAATGTAA 31
                           i i     i     -      ii  - i     ?    v         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

C chr1_4165684_41     30 GAACTAAAGTTATGATTCTTCTAGGAGAAA 1
                           i     ii   i vv  ii   i     
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAA 544

Transitions / transversions = 2.20 (33 / 15)
Gap_init rate = 0.01 (3 / 230), avg. gap size = 1.00 (3 / 3)  

2999 25.98 0.65 1.96  chr1_4165684_4170572     3477  4396 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_4165684_41   3477 TGGAAACACATCCCATGCTCATGAAG-GGTAGAATCAATATTGTGAAAAT 3525
                               v i        i     i v-  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4165684_41   3526 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 3575
                          i v     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_4165684_41   3576 TACCAACATCACTCTTCACAGAACTAGAAAAAC-AATCCTAAAATTCACA 3624
                          v   i vv vi i  ii     v v  v  i -i             i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_4165684_41   3625 TGGAAC--CAAAAAACAGCCCTCATAGCCAAAGCAAGACTAAGCAAAAAG 3672
                              v--   iii  --  vvv         i   vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_4165684_41   3673 AACAAATCTGGAGGCATGGCATTACCTGACTTCAAACTATACTATTGAAT 3722
                               vi      vv vi  i v  ii i      viv     i-----
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC----- 243

  chr1_4165684_41   3723 ATAAGGCCATAGTCCCCAAAACAGCATGGTACTGGTATAAACATAGGTGG 3772
                         --  i  i i   vvi   i    ii         i    iv    iiiv
  L1M4_orf2#LINE/    244 --AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_4165684_41   3773 ATACACCAGTGCAACAGAATACAGAACCCAGAAATGAAGCCAAATACTTA 3822
                            v i  i  v  i     vv   ii        i  v   v i i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_4165684_41   3823 CAGCCACATGGTCTTCAACAAAGCAAATAAAAGCATAAAGTGAGAAAAGG 3872
                         ii i  vv  i i   i    i vvivi  i v   vv i  i i    i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_4165684_41   3873 ATACTCTGTTCAACAAATGGTGCTGGGATAATTTTCAAACCACATGTAGA 3922
                            v   v                    i  i vvvv ?       i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_4165684_41   3923 AGAATGAAACTGGATCTTTATCTCTCACCTTATAAAAAAATCAACTCAAG 3972
                                 ii    i ii  i   v    v    v      i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_4165684_41   3973 ATGAATCAAAGACCTAAATCTAAG-GCCAGGAATCATAAACATTCT-AAA 4020
                            i    ?          v    -  i i-  ii     - i   - i 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAA-AACTATAAA-ACTCTTAGA 539

  chr1_4165684_41   4021 AGAAAACATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGAGTTCA 4070
                                  v  ?iv  vi    vv   v    v        v iv   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_4165684_41   4071 TGAGCAAGAACCCAGAAGCAAATGCAACAAAAACAAAGATAAATAGATGG 4120
                          iiii v  vv   i     v v         iv   i   i   i  v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_4165684_41   4121 AACTTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATTGGCAG 4170
                         i    v  i   v v    i   i  ii vv    i  v iv  iiiv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_4165684_41   4171 AGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTTGCAAACTATGCAT 4220
                            i  v              i           v        ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_4165684_41   4221 CTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTCAAACAAATCCAT 4270
                             i  i  i  vi          v  i  i      vv    v  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_4165684_41   4271 AGGAAAAATAACAAAAACAAATAATTCCATCAAAAAGTGGGCTAAGGACA 4320
                          ------    -   i        ii v  i?    i     v     iv
  L1M4_orf2#LINE/    790 A------ATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_4165684_41   4321 TCAATACACAATTCTCAAAAGAAGACATACAAATGGCCAACAAACATATG 4370
                          v    v   v     v        i              i  i  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_4165684_41   4371 GAAAAATGCTCAACATCACTAGTCAT 4396
                         i   i             ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.18 (24 / 11)  


 954 26.78 17.52 3.31  chr1_4208772_4210862.rev      509  1113 (978)    L1M4_orf2#LINE/L1        6   696 (212)  

  chr1_4208772_42    509 AGACAGACTAAGTTGATGATTAAGAAGACTAAATATTGTCAAGATGATAA 558
                            i vv i v   v   iv vi       v        i      ii  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_4208772_42    559 T---TCTCAAATAG-TCTGCACATTTA---CAATCCTAATCAAAAATCCA 601
                          ---i i     v -   i  v   i ---      iv       -   v
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCC 104

  chr1_4208772_42    602 AGCAACCTTT---GTGAAAATTAATAAGTGGGTTCTAAAATTTATTTTAA 648
                            vi     --- iii     i i   iv i i        i  v --i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT--G 152

  chr1_4208772_42    649 AAAATGAAATGGGAA--AGAATAGCCAAGATAATCTTGCCAAAAAA---T 693
                         i     v  -    v--           i i       vv   i  ---i
  L1M4_orf2#LINE/    153 GAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_4208772_42    694 AAAACTGGAATGTTT-CTCTATCAGATATTAAGG-TTGCTGTAAAGCCAC 741
                            ii    ivii i- v  vi vi  v i  ii-  i  ii     i  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_4208772_42    742 AGTAACTAAAACAATGGAGTACCA-CGTCAAGGAGAGAGAAATGGATGAA 790
                              ii  i   i  vi    ii- i -     v   v v  i   v  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATCAA 300

  chr1_4208772_42    791 TGGAACACACGAGAGAGTCCAAAAAATGACCCCCATACAC--ACGGCCAC 838
                              i v vvv         i   - i v   -     i-- i  i  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAA-TAAACCC-ATACATTTATGGTCAA 348

  chr1_4208772_42    839 GTGAGTT-------------------------ATGGG------------- 850
                         v   v  -------------------------     -------------
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_4208772_42    851 --TCA-------GTG----------TGGA---CC-CATTTAGGAAAAC-A 876
                         --   -------   ----------    ---  -   vi ii i  i- 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_4208772_42    877 AGTATCTTGACCCTTGCCTCACAC--TACAGAATAATCAATTCCCTATGG 924
                            --- v     i i        --  i v  v   i  i  vvv    
  L1M4_orf2#LINE/    449 AGT---TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_4208772_42    925 ATTATAGCTCTAAATACCAAAGGTAAAATAACAATGTATCTGAAAGAAAA 974
                           i ?  vi      iiv i  v     iv i  viivii ii       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_4208772_42    975 CATAAGAG--AATCT----AATCTTGGGATGGATAAAGATTTCTTAAA-A 1017
                             i ? --     ----i i      v i ii  v i       i - 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_4208772_42   1018 CAAAACT----GC-CGACCAA--AAAGAAAAATAAAGATACGGTGGACTT 1060
                         ii v  i----  - i v   --         - v     viv       
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTT 644

  chr1_4208772_42   1061 CAT------TAAGAAGTTCTGTTAGTTCTGATTATCAAAAGAC--CATTA 1102
                            ------   i  v  i   -- i -------     i   --i  i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGT--GCT-------TCAAAGGACACTATCA 685

  chr1_4208772_42   1103 AGAGATTAAAA 1113
                            i v i   
  L1M4_orf2#LINE/    686 AGAAAGTGAAA 696

Transitions / transversions = 1.76 (102 / 58)
Gap_init rate = 0.05 (36 / 691), avg. gap size = 3.50 (126 / 36)  

 453 24.34 4.42 4.42  chr1_4208772_4210862.rev     1397  1622 (469)    L1M4_orf2#LINE/L1      683   908 (0)  

  chr1_4208772_42   1397 TCAAAAAAAAAAAAAAAATCCAAGCCACAGAGTGGGGGAAGCTACTTGCT 1446
                             i   ivi    i ---   v       i    i   iv  i    v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGA---CAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_4208772_42   1447 ATACACACATCTAACAATGTACTCATTTCCAGAATATATAAAGAACCCCT 1496
                          vv  i i    i i  v v   ii v                   i i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_4208772_42   1497 A-AACATGAGCAAGAAAAAGGCAATT---TTA--TAGAAAATTGACAAAA 1540
                          -   - v ii  v      i   v ---ii -- ?i     v i    i
  L1M4_orf2#LINE/    780 ACAAC-TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_4208772_42   1541 GCTTTGAAGAGGCACTTCAACATGAGGCAGACACACA--TGGCAAATAA- 1587
                          v      v  i  i   vv  -- i v   i i   --    v     -
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCA--AAGAAGATATACAAATGGCCAATAAG 876

  chr1_4208772_42   1588 -ATATAATACAGTTGATCATATTCATTAGTCAGGAA 1622
                         - i  i - v  v  v   - --   i ????????
  L1M4_orf2#LINE/    877 CACATGA-AAAGATGCTCA-A--CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (32 / 22)
Gap_init rate = 0.05 (11 / 226), avg. gap size = 1.82 (20 / 11)  


1328 26.05 7.91 0.93  chr1_4213784_4218602.rev      660  1089 (3730)    L1M4_orf2#LINE/L1        1   460 (448)  

  chr1_4213784_42    660 TGGAGAGATATTCCATATTCATAGATAGGAAGACTCAATATCATTAAGAT 709
                             i      i    i     i   v        i     ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4213784_42    710 GTCACTTCTTTT-AAATTTGTC-ACA------ACTTGATCC--AT--AGA 747
                          v  v v  iii-     vi  -   ------  vii    --  -- i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_4213784_42    748 TTC--ACTGCAATT-----AGAAAT---------GATCCTAAATCTCATA 781
                          i --i    vv  -----      ---------         vi     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_4213784_42    782 TGGAAAGGCAAAGA--CTAGAGTAGCTAATATAATACTGAAGGATAAGAA 829
                               v    i i-- i   i    i  v i   vi    ii v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_4213784_42    830 CAAAGTTGGAGGACTGACACTACTCAACTTTAGCTCTTAGCATAAACTGA 879
                                        v     v i   i  i ivv    vi i   viv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_4213784_42    880 CAGTTATCA---CAGCATGACACTGGCAAAAGAATAGACAAATAGATCAA 926
                             v    ---   ii  ii       v   i       v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_4213784_42    927 TGGAACAGAATAAAAAACCCAGAAATAGACCTACACAAATACAATCAACC 976
                              i     vi i ii         i   i i   vv  iii    ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_4213784_42    977 GGTGTTTGATAAAGAAGCAAAGACAATTTGATGGAGCATACATTGTATTT 1026
                          i v  i  i  i iv  v     v   ii    i v viv  v  v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_4213784_42   1027 TCAAGAAATGGTGCTGG-ACACATACACCCTCCCAAGACTAAACCAGGAA 1075
                             v            -   vv iv iv?i v  v --i   --  i v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG--CAAA--AGAAT 446

  chr1_4213784_42   1076 GAAGTTGAATCTCT 1089
                                i i i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCT 460

Transitions / transversions = 1.58 (68 / 43)
Gap_init rate = 0.03 (13 / 460), avg. gap size = 2.92 (38 / 13)  

3153 26.74 1.22 0.88  chr1_4213784_4218602.rev     2137  3041 (1778)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_4213784_42   2137 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2186
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4213784_42   2187 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2236
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_4213784_42   2237 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 2284
                          v    ivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_4213784_42   2285 ACATGGACCAAA---AAAGAGCCCACA-TCGCCAAGTCAATCCTAAGCCA 2330
                          i     ---  ---  i ii    v - v     iv     i i ivv 
  L1M4_orf2#LINE/    148 ATATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_4213784_42   2331 AAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACA 2380
                         i          i      vv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_4213784_42   2381 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 2430
                          i          i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_4213784_42   2431 GATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTAC 2478
                                    i    i--    i  --        vv   i i  i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chr1_4213784_42   2479 AACTATCTGATATTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGA 2528
                         iiii vi    v  i     ivv  vv  i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_4213784_42   2529 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 2578
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_4213784_42   2579 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 2628
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_4213784_42   2629 TGGATTAAAGACTTAAACATCAGACCTAAAACCATAAAAACCCTAGAAGA 2678
                              i ?    i    ii v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_4213784_42   2679 AAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 2728
                             v    ?i v viv   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_4213784_42   2729 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 2778
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_4213784_42   2779 CTAATTAAACTAAAGAGCTTCTGCACAGCAGAAGAAAGTACCACCAGAGT 2828
                         i v  i   v v  i i   i  ii vv  i i  v v  i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_4213784_42   2829 GAACAGGCAACCTACAAAATGGGAGAAAATTTTCAC---CTACTCATCTG 2875
                            v  i     i   i             v  ii ---ii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_4213784_42   2876 ACAAAGAGCTAATATCCAGAATCCACAATGAACTCAAACAAATTTACAAG 2925
                          i  i ii  vi          vi i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_4213784_42   2926 AAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACA 2975
                              i     i     v  i?    i     i     iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_4213784_42   2976 CTTCTCAAGGGAAGACATTCATGCAGCCAAAAAACACATGAAAAAATGCT 3025
                         i     v ii     i  v  viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_4213784_42   3026 CACCATCACTGGCCAT 3041
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (146 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  

1711 25.35 2.41 0.60  chr1_4213784_4218602.rev     3832  4328 (491)    L1M4_orf2#LINE/L1      403   908 (0)  

  chr1_4213784_42   3832 AAGAAATGGTGCTGGAACAATTGAACATGTACATGTCAAAAAA--AATCT 3879
                           v            i    i  i i ?vi     iv   i  --  vi 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_4213784_42   3880 AGACAACAGAACTTATGCCTTTCACAAAAATTAATTTAAAATGGAGCATA 3929
                         i   vv -v v  i ii  v vi           i i        v  ? 
  L1M4_orf2#LINE/    453 GGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_4213784_42   3930 CACATAAATGTAACATTCAAAACTATAAA-CTCCTAGAAGATAACACAGA 3978
                         v  v         v vii           -   i       v    i  i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_4213784_42   3979 AGAAAATCTAGATGACTTTGTGTTTGAGGTCA--GTTT-TTAGATACAAC 4025
                         ? v      vvi    i   v   --   iv --    -       ii  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTT--AGGCAATGGTTTCTTAGATATGAC 599

  chr1_4213784_42   4026 ACCAAAAGTGCAACCTATGCAAGAAAAAATTGATAAGTTGGACTTTATTA 4075
                                 ii   v v iiv          v     i        i  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_4213784_42   4076 AAATTAAAACCCTCTGCTCTGCAAAAGACACTATTA-GAGAATGAAAAGA 4124
                                  v i i  iv  v    i        i -  i i        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_4213784_42   4125 CAAGCCACAGG-TGGGAGAATATATTTGCAAA--ACTTATCTGATAAAGA 4171
                            v      i-        v           -- iv          i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_4213784_42   4172 GCCGTTAGCCAAAATGCACAAAGAATTCTTAAAACTCAACAGTTAAAAAA 4221
                         i ivv  v   i   ii i      i     v       i i v    i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_4213784_42   4222 TGAACAGCCTGATTTAGCAGTGGGCCAA--ATTCTAACAGACACAGCACT 4269
                         ii  i i  ii   ? iv i     v  --   iv  i     ivv v i
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_4213784_42   4270 GAGGAAGATACACAGATGAAAATTAAACATATGGAAACATATTCAGCATC 4319
                         i i       i   i   ivv v   i  i   i   v  ii   i    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_4213784_42   4320 ATATCTTAT 4328
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.65 (76 / 46)
Gap_init rate = 0.02 (10 / 506), avg. gap size = 1.50 (15 / 10)  

 611 26.09 7.07 7.07  chr1_4213784_4218602.rev     4424  4791 (28)    L1M4_orf2#LINE/L1      480   847 (61)  

  chr1_4213784_42   4424 AATTAACTTGATATTGATCCAAAAC-TCAATGTAA-ACCTAAAATTACAA 4471
                                 ii v  v    v? i  - v       - v      i  i  
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_4213784_42   4472 A-CTTTCCGAA-----CACGGAAGAAAATCTTTATCAACTCGTCATAGGC 4515
                          -  i iv   -----  ii i? v       ii v v  i vvv     
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_4213784_42   4516 AAAGATTTCT--GATATAAGATGCAAAAACACATAAGTCATAGAAGATAA 4563
                           v i     --     i v i-     i    --  iv i i    -  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACAC-CAAAAGCACA--AGCAACAAAAGA-AA 625

  chr1_4213784_42   4564 AAAT-GATAAATTGGACTT-ATTCCAATTCAAA-TTTCTGCTCCTCAAAA 4610
                             -              -  ivv    v   -i  i  iv i     i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_4213784_42   4611 AATATTATTGAGGAAAGGAAAATACAAGAAGTAATCTGGGCAGGG-GGGG 4659
                         i i i   ii  i  iv     v    -------i ii--   ii-   i
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAA-------CCCA--CAGAATGGGA 716

  chr1_4213784_42   4660 GA------TCACAATACATATATCTAACAAAGGATTTGAATCGTGTGTGT 4703
                           ------ ii   vv         i i  i   i   v   vv vi i 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_4213784_42   4704 GTGTGTGTGTGTGTGTGA--TCTCACAACTCAATA-TGAAAAGA-AAATC 4749
                         i ivi-----------  --   i           - i      -    -
  L1M4_orf2#LINE/    767 ATAAA-----------GAACTCTTACAACTCAATAATAAAAAGACAAAT- 804

  chr1_4213784_42   4750 AAATTT--TTAAAAATTGAGTACAAAATTAGAATAAATATGTCT 4791
                         -  iii--  ?    v  i i v ii   v     i i  v   
  L1M4_orf2#LINE/    805 -AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

Transitions / transversions = 1.91 (61 / 32)
Gap_init rate = 0.06 (21 / 368), avg. gap size = 2.48 (52 / 21)  


2211 24.02 2.42 11.50  chr1_4256714_4261723.rev     3535  4525 (485)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_4256714_42   3535 ACATTCCATACTCATGGCTAGAAAGAATCAATATTGCTTAAATGCGCA-T 3583
                          i  i    ii      v v i    v i       i v i   -   - 
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG-GCAAT 56

  chr1_4256714_42   3584 ACTGCCCAAAGCAATTCATAGATTCAATGTTATTCCTATCTAACTAACAT 3633
                            v      vii  ii i        i iv  i      v  v vv  v
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_4256714_42   3634 CAACATTTTTCACAGAATTAGAAATAACT-ATTCTAAAATTTATACGGAA 3682
                          vi v     ii     v v  v - i  -  i        i   i    
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATATGGAA 155

  chr1_4256714_42   3683 CCATAAAAGTGTCAGAATAGCCAAGGCAATCCTAAGGAAAAATAACAAAG 3732
                         viii  ii vvi            ii     i i ii  i  v       
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_4256714_42   3733 CTGGAGACATCACACTACCCAACTTCAAACTATGCTATAATGCTACAGTA 3782
                         i     ivv       v     i      viv i   i  v         
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_4256714_42   3783 ACCAAAACAGCATGCC-CTGGTACAAAAACAGACACATAGACCAATATAA 3831
                          i   i    ii  vi-    i i  ii i     i     i    iv  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_4256714_42   3832 CAGGTTAGAGAACCCAGAAATAAAGCCACACACCTACAACCATCTGATCT 3881
                         i  iv v    ii           v   i   ii  iiii  vi    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_4256714_42   3882 TTGACAAAGTCTACAAAAATAAGCAATGAGGAAAGGACTCCCTATTCAAT 3931
                          i     i vivv   i vi vv     i      i ivvi  v     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_4256714_42   3932 AAATGTTGCTGCAGTAACTGGCTATCCATGTGCAGAAGATTGAAACTGG- 3980
                              v     viii      v  ?   ii    i    v    ii   -
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_4256714_42   3981 CCCCTTCCTCTCACCA----CAAAAATCAAGTGGTGGATTAAAGTGGATT 4026
                              v    v     ----       i  v -------i   i     i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACT-------CAAAATGGATC 498

  chr1_4256714_42   4027 AAAGATTTAAATTTAAAACTCAAGAGGCGGAGCTTGCAGTGAGCCCAGGC 4076
                          ?   ii     v   -------------     ----------------
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAA-------------GAGCT---------------- 519

  chr1_4256714_42   4077 CATGCCACCGCACTCCAGAGCGAAACTCCATCTCAAAAAAAAAAAAAAAA 4126
                         --------------------------------------------------
  L1M4_orf2#LINE/    520 -------------------------------------------------- 519

  chr1_4256714_42   4127 AAAAAAAAAAAAACTCAAACTATGAAAACCCTAGAAGAAAACCTAGG--- 4173
                         ---------      ------  i   vi i           v    ---
  L1M4_orf2#LINE/    520 ---------AAAACT------ATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_4256714_42   4174 AAAT----GTCATTCTGGACATAGGTACTGGGAAAGATTTTCATGACGAA 4219
                             ----  v iii   ii-    i v   -------    v iivv v
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGT-TAGGCAATGG-------TTTCTTAGATAT 596

  chr1_4256714_42   4220 GATACCAACAGCAATTACAACAAAAACAAATACTGACAAATGGGACCTAA 4269
                           i     v    vvvi        iv   v iv  i    v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_4256714_42   4270 TTAAACTAAAGAGCTTCTACACA-AAAAAGAAACTAGCAACAGAGTAAAC 4318
                          i   v v  i i   i iii v-v   i  v    v   v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_4256714_42   4319 AGACACCTTACAGAATTGGAGAAAATACTTGCAAACTATGCATCTGACAA 4368
                              v ii       v          i       ii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_4256714_42   4369 AGGTCTAATATCCAGAACCTATAAGTAACTT----AAATCAACAAGCAAA 4414
                         i  v  vi         iv     iv    i----  v    i  -i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAA 795

  chr1_4256714_42   4415 AAAACAAATAATCCCATTAAAAAATGGACAAAGGACATGAACAGACAGTT 4464
                           i        i  v   ?        i       iv    i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_4256714_42   4465 CTCAAAAGAAAA----CACATGCAGCCAACAAGCATATGAAAAAATGTTT 4510
                            v      i ----  v   --     i     i       i   i i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTC 893

  chr1_4256714_42   4511 AATCTTAGAGAAATA 4525
                           iv i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (147 / 88)
Gap_init rate = 0.02 (20 / 901), avg. gap size = 6.90 (138 / 20)  


2977 25.64 1.66 2.54  chr1_4361481_4364201     1324  2228 (492)    L1M4_orf2#LINE/L1       12   908 (0)  

  chr1_4361481_43   1324 CCCGTG--CATAGATAGAAAGACTCCATATCATCAAGACATCAGTTCTTT 1371
                            i  --   i   v i      iv    ii i    iiv  i v  ii
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chr1_4361481_43   1372 CTACCTTGATCCATAGAGTCAATGCAATCCCAATCAAAAGCCCA-CAAGT 1420
                          i vv      i i   v    i        v       v    - vivi
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr1_4361481_43   1421 TATTTTGTAGATATCAGCAAACTGATTCCAAAGTTTATATGGAGAGGAAA 1470
                          v     i   v  iii   i     i i   i  i       i v v  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_4361481_43   1471 AAGACCCAGAATAGCCACCCCAATATTAAAGGAGAAAAACAAAGTCAGAG 1520
                         ii               vvv    v  i  ii    i        ii   
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_4361481_43   1521 AACTGAAATTACCTGACTTCAAGATTTACTGTGAAGCTGAAATAATCAAG 1570
                         i   v v i v  ii i     i i     iii     iv i        
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_4361481_43   1571 ATAGTGTGGTCCTAGTGAAAGAATAGACAAATAGATCACTAGAACAGAAA 1620
                          i        v  i iiv   i       v        v i   i    v
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_4361481_43   1621 AGAAAGCTGAGAAACCATCCCACATAAATATAGTCAAGTGATCTTTGACA 1670
                         v  i  iiv     iv v    i i vv   i     v    i  i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_4361481_43   1671 AAGGAGCAAAGTTAA---AATGACCAAGCAAAGATATAATCTTTTCAACA 1717
                          i  v  v   viv ---    i---- v     -   i           
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGG----GGAAAGA-ATAGTCTTTTCAACA 406

  chr1_4361481_43   1718 AATGATACAGGAATAATTGGAAATCTATGTGCAAAATAATGAAACTAGAA 1767
                             i i v  i i  i    v ? i ii       v      ii i  v
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_4361481_43   1768 ACAGACTGTACACACTTCACAAAAATTAACTCAAAATGAACTATAGTCCC 1817
                         v vv  ivi    vv vi                    i ii ?  v  i
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_4361481_43   1818 AAATATAGAATGC-AAAACTATAAAACTCTTGGAAGATAATATAGGAGAA 1866
                             i  ii -  -                 i     v  i     ? v 
  L1M4_orf2#LINE/    507 AAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_4361481_43   1867 AATCTAAATGATCTTGGATATGGTGATGACTTTTGAAATA---CACCAAA 1913
                              vvi   i     i vv  ii   ii  i v i   ---       
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_4361481_43   1914 TGCATAATCCATGAAA-AAATAATTGATAAGGTAGACTTTATTAAAATTA 1962
                         v   i  v v ii   -   v   v     iv i     i  i       
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_4361481_43   1963 AAAACT---GTGCCTATAAAGACA-TGTCAGGAGAATGAGAAGACAAGCC 2008
                               ---    i vv  i    - i   i  i i   i       v  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_4361481_43   2009 ACAGACTGGGATAAAATATTTGCAAAAGACACGTCTGATAAAAGATGTTT 2058
                              v     v              vv i ii        ii  iv v 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_4361481_43   2059 ATCCAAAATGTGCAAAGAACTCTTAATACTCAACAATAAGAAAATGAGAA 2108
                              i   i ii            vv      i     i  i i---- 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC----A 801

  chr1_4361481_43   2109 AATGAACAACACCTTATGTAAAAAAAAAAAAAAAGCCAAAGACCTTAACA 2158
                            ----   -  --------  vv?     vii  v  i  ii v  i 
  L1M4_orf2#LINE/    802 AAT----AAC-CC--------AATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_4361481_43   2159 GATACTTCACCACAGAAGGTATACAGAAGGCAAGTAAGCATATGCAAAGA 2208
                           i i   v   v     i      i v   v i      i   v     
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_4361481_43   2209 TGTCCAACATCATATGTCAT 2228
                           ii        ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (142 / 86)
Gap_init rate = 0.02 (15 / 897), avg. gap size = 2.53 (38 / 15)  


 396 31.01 7.59 7.17  chr1_4508226_4510434       36   509 (1700)    L1M4_orf2#LINE/L1      244   719 (189)  

  chr1_4508226_45     36 AAAGCCATAGTAG--GAAACAGCA--GTATTAGTA-AAAGACTGAC---- 76
                              i i    i--i i    ii--   i i i -  i  iv   ----
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_4508226_45     77 ---TGAATTGGACACAGT-----GCCCAGAAACAGATCCATGCATGTGTG 118
                         --- v   v i i v i ----- i       i i i    i   v i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_4508226_45    119 AAAAATTAAAATATGAGAAAGATGTTA---CTGTGGGTCAATGGTAGAAC 165
                         ivv    i vv vi  v  i i  ii --- ii ---       vii  v
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCAT---TCAATGGGGAAAG 390

  chr1_4508226_45    166 AATGGATTCATCAATAAGTGGAGGTGGAACATTTGATTGTTCTTATAGGA 215
                            i vi iv    i  i   v v   i   vi  iv i?i -- i v v
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC--ACATGC 438

  chr1_4508226_45    216 AACAGAATACAGTTAGGTCCCGATCTCATTATCTCATGCCACATTCAATA 265
                           v     iv    i ii   --------  i    ii   i  v   v 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCC--------TACCTCACACCATATACAAAA 480

  chr1_4508226_45    266 TTCAATTCTAGTTGTGT-AAAGCCCTAAATGAGAAAAGCAAAATAATTTA 314
                         v i  i  v iv  vi - ?  v        -v  i   v   - v v  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATG-TAAGAGCTAAA-ACTATA 528

  chr1_4508226_45    315 AA---TTTAGAAAAAAATTATGGGACTACCTTTAATGTTTCACAACA--G 359
                           ---i      i    i-  i  ?v  -----   -i   iii  v-- 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAAC-ATAGGNGTA-----AAT-CTTCGTGACCTTG 571

  chr1_4508226_45    360 GGATATATA-----TTTTTAAAGAAGAC--TAATAAGGCAAAAACCACAG 402
                           v  vii -----  i   i v v   --i  -- i   v  i v   i
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAA--AAGCACAAGCAACAA 619

  chr1_4508226_45    403 AAGAAATAATTGCTAAATACAAGTACATTAAA-TTAAGAAAGAAAAAAAC 451
                               v   v v     vvi v v   i   -    ---------    
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA---------AAAC 660

  chr1_4508226_45    452 TTTTTGGTAACAGGAGATACTATTTTAGAAA-TGCAAAAGTAGCC-ACAG 499
                             vv ivv  iii  i     iv-     -  v   iii i  -    
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCA-AGAAAGTGAAAAGACAACCCACAG 709

  chr1_4508226_45    500 GTCAGGACAA 509
                         ivii   v  
  L1M4_orf2#LINE/    710 AATGGGAGAA 719

Transitions / transversions = 1.53 (87 / 57)
Gap_init rate = 0.05 (25 / 476), avg. gap size = 2.80 (70 / 25)  

3270 18.00 10.10 4.65  chr1_4508226_4510434      864  1724 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_4508226_45    864 TGGAAAGATATCATGTGACCATCGATTGGAAGTCTCTGTAGTG--AAGAT 911
                                     vii  vi   v         v  ivi  v  --     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4508226_45    912 GGCAA-ACTTCCTAAGCTGATCTATGATCTGCAGATTCCACACAACCACT 960
                              -   i  i  ii       -------       v  i   i v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTA-------CAGATTCAACGCAATCCCT 93

  chr1_4508226_45    961 ACCAAAACACTAAGTGGCATTGATTGATTGATTGATTGATTGATTGATTG 1010
                          i     iv i - iv  v  ----------------------  --   
  L1M4_orf2#LINE/     94 ATCAAAATCCCA-GCTGCCTT----------------------TT--TTG 118

  chr1_4508226_45   1011 TAGAGATTGACAAGGTAATCCTAAAATTCATATGAAAATTCAAGGAAATC 1060
                         i   i         v i                 i    v     i vi 
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr1_4508226_45   1061 AGAATAGCCAAAGCAATCTAGAAAAG------------------------ 1086
                                     i      v     i------------------------
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_4508226_45   1087 ---------TTTCAAAACTTACTACAAAGCTGCAAGAATTAAGACTGTGT 1127
                         ---------                      i  iv   i     v    
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_4508226_45   1128 GGCACTGGCATACA-ATAGACACA--GATCAATGGAAGAGTACTGAAAGT 1174
                           i         vi-       i --           v  v i   i   
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_4508226_45   1175 TCAGAAATAAACTCAAGCGTTTATGGTGAATTGATTTTCAATAAGAGTGC 1224
                         i           i  vi i        v           i i   i    
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_4508226_45   1225 CAAAGCAAATCAATTGAGGACATAATAGTCTTTTTAACTAACAACGCTGA 1274
                            ii v v     - i   v v           i   v  iiii    i
  L1M4_orf2#LINE/    369 CAAGACCATTCAAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_4508226_45   1275 TACAACTGGTTATCTACACACAAAAGAATGAAGTTGGATGCATACCTCAC 1324
                         v        v  ? i   ii                  iv v        
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_4508226_45   1325 ACCATATACAAAAAATAACTCAAAATGGATCAAAGGCCTAAATGTAAGAG 1374
                                       v                 ?  i              
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_4508226_45   1375 CTAAAATGAGAAAGTCGTTAGAGGAAAATATAGGCATA---------GAT 1415
                               iv v   iiiv     i     i     ?i  ---------  i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_4508226_45   1416 CTTGGATTAGGCAATGGTTTCTTA-------------AAGTATAAGCAAC 1452
                              i                  -------------   i i       
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_4508226_45   1453 AAAATTAACAA---ATAAATTGGAGCTTACCAAAATTAACAAATTTCATG 1499
                             vv  v  ---          vi i i         v  v   ii  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_4508226_45   1500 TTTCATGTTTTGAAAGA----ATAAAGA----GAAAAGATGGCCCAGAGA 1541
                         i    -------  i  ----  v    ----       iii    v   
  L1M4_orf2#LINE/    668 CTTCA-------AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_4508226_45   1542 TAGTGAAAAAAACTTT--AAATCTAATATCTGATAAAGTTATAGTATTCA 1589
                         vv v  i    vv   --     vv           i vvv v    i  
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_4508226_45   1590 GTATATATACAGAACTC--ATGGTTCAACAATAAAAAGACAAATA----- 1632
                          v       v       -- iiii    i                -----
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_4508226_45   1633 -T-----AATGAGCAAGGGATTCAAATGGACATTTCTTCAAAGAAGATAT 1676
                         - -----    i    i     ii   i         i            
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_4508226_45   1677 GCAAATGGTCAATCAGTACATGAAAAGATGCTTGATCTCCTTACTCAT 1724
                         i       i    v  i               ii iv  v????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (93 / 59)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 6.35 (127 / 20)  


2903 26.68 1.10 0.99  chr1_4547502_4551741.rev     2843  3749 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_4547502_45   2843 TGGAAAAACATTCCATCCTCGTACATAGGAAGAATCAATATCATGAAAAT 2892
                               i i  i    vi  i iv  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4547502_45   2893 GACCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 2942
                          i v     v      v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_4547502_45   2943 TACCATTGACATTCTTCACAGAATTAGAACAAACT-ACTTTAAATTTCAT 2991
                          v   vivi v  i  ii     v v  -   i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr1_4547502_45   2992 ATGGAA-TCCAAGAAGACCCTGTATGGCAAAAACAATTCTAAGCAAAAAG 3040
                               - v    i-     v v  i  v        ii i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_4547502_45   3041 AACAAAGACGGAGGCATCAAGCTACCTGACTTCGAACTATACTACAAGGC 3090
                                vi     vv   vi  v  ii i   i  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_4547502_45   3091 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACACATAGATC 3140
                                 i   i    ii         i iv ii i     i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_4547502_45   3141 AATGGAACAGAACAGAGACCTCAGAAATAACACTACACATCTACAATTAT 3190
                                i    iv    vii         vv i i    i  iii i v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_4547502_45   3191 CTAATATTCAACAAACTTGACACAAACAGGCAATGTGGAAAGGATCTCCT 3240
                         i i  v   i    ivv  v  vi v  vv     v      i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_4547502_45   3241 ATTCAATAAATAGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTAA 3290
                         v     i    i         v      v  ?   i     i  i v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_4547502_45   3291 AACTCGACCCCTTCCTTACACCTTATAGAAAAATTAACTCACGTTGGATT 3340
                          ii v       v   i     v    v             viv     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_4547502_45   3341 AAAGACCTAAATGTAAAACCCAAAACCATAAAAACCCTAGAATAAAACCT 3390
                          ?              i v i     i      vi i     v     v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_4547502_45   3391 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAAAAAA 3439
                            ?i- v i -   iv   v v  vv i     v ii   v -- i v 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT--AGATA 595

  chr1_4547502_45   3440 TGCC-CCAAA----CAATTGCAACAAAAGCCAAAATTGACAAATGAGATC 3484
                           v -     ----   --          vv     v  i    vi  ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_4547502_45   3485 CAATTAAACTAAAGAGCTTCTGAACAGCAAAAGAAAGTATCATCAGAGTG 3534
                         iv  i   v v  i i   i  vi vv    i  v v     vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_4547502_45   3535 AACAGACAACCTACAGAATGGGAGAAATTTTTCTGCAATCTACCCATCTG 3584
                           v        i               v v  -     vii ivi     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATT-TGCAAATCATATATCTG 742

  chr1_4547502_45   3585 ACAAAAGTCTAGTATCTAGAATTTACAAGGAACTTAAACAAATTTACAAG 3634
                          i  ii v  v     i     v  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_4547502_45   3635 AAAAAAAGCAAACAACCCCATCAAAAAGTGGGCAAAGGATAAGAACAGGC 3684
                              i -    i     v  i?    i            vv   i  i 
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_4547502_45   3685 ACTTCTC-AAAAAAGATGTTTAAGCAGCCAG-AAACATATGAAAAAAAGC 3732
                          i     -   i     i vi  iii    i-  i  i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_4547502_45   3733 TCAACATTACTGATCAT 3749
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.36 (19 / 14)  


3316 25.96 2.82 0.34  chr1_4779303_4785987      888  1773 (4912)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_4779303_47    888 TGGAGAACCAGTCCATGTTCATGGATAGAAAGACTCAATGTTGTCAAGAT 937
                             i ivi vi              v i      i   i    i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4779303_47    938 GTCAGTTCTCCCCAACTTGATCTATAGATTCAATGCAATTCCGATCAAAA 987
                          v  i v        v        i        i     i  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_4779303_47    988 TTCCAGGAAGTTATTTTGAGGATATTGACAAACTGATTCTAAAGTCTATA 1037
                          i    vvivi v     vi  v        i     i     i ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_4779303_47   1038 TGGAAAGGCAAAAGGCCACAAAGC-GCCTCCACATTATTGAA---GAAGA 1083
                               v    ii i  -  i ii-   vvv   v v     ---     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_4779303_47   1084 ACGAAACTGAAAGAATGACACCACCCAACTTCAAGACTTACTGTAAAACT 1133
                           i  ii  i i  v v    iv     i     i       ii   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_4779303_47   1134 ACAATAATCAAGACAATGTGGTATTGGTGAAAGAACTGACAAAAAGATCA 1183
                            i           i       i   iiv   i iv    v v      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_4779303_47   1184 GTGGACCACC-TAGAGAG-CCAGAAGTAGACTCACATAAATATAGTCAGC 1231
                         i    vi vv- v     -      i  i  i  i i vv   i    ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_4779303_47   1232 TGATCTTTGTCAGAGGCACAAAGAAAATACAGTGGAGAAAAGAGAGCCTT 1281
                             i  i v  ii  ii v    vv  v  i   i    ii v  i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_4779303_47   1282 TTTAATAAATGATGCTGGAACAACTGGACATTCATAGGCAAAAATATAAC 1331
                           i  i     i      i         i ?i  i v      iv  i v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_4779303_47   1332 TCTAGACACAAACCTTACAT-GTTTACAAAGGTTAACTCAAAATG----- 1375
                         vi i   v vv    i   i-i v      ii             -----
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_4779303_47   1376 ------------TAGGATTTAAAACTATAAAATTCCTAGAAAACAGTATA 1413
                         ------------  i  vi             i  i     i v ii   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_4779303_47   1414 GAAGAAAATCTATGTGACCTAGAGTTTGGTAATGATTTTTTTAGATACAA 1463
                          i? v      vi       v i   v  i    i   i  -     ii 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chr1_4779303_47   1464 TACCGCAGGCCTGATACATAAATGAAAGAACTCACAACCTGGATCTCCAC 1513
                         i   iv i  vii vvv i   v    i  ivv i  vi    -  i  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA-CTTCAT 647

  chr1_4779303_47   1514 CAAAATTAAAAATTTCTGCTCTGTGAAAGACACTGTCAAGAGAATAAAAA 1563
                                     i  i  iv  vii  i      i      i i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_4779303_47   1564 GATAAGCCACAAGCTGGGTGAAAATATTTGCAAAAGACACATCTGATAAA 1613
                           i  v     iiv    v               vv i i         i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_4779303_47   1614 GGACTGTTATTCAAAATATACAAAGAAATCTTGAAACTCAACAATAAGAA 1663
                              vv   i  i      i      v    iv       i     i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_4779303_47   1664 AATAAACAACTCAATTTAAAAATGGGCCAAAGACTTTAGCAAACACCTCA 1713
                         i i   i   i     ?          v  i  i  v ii i   ii  v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_4779303_47   1714 CCAATGAAGATATACAGATGGCAAATA-GAATATGAAAGTATTCTCCACA 1762
                             v           i     v    - v i      iv  v   v   
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_4779303_47   1763 TCGTAAGCCAT 1773
                           i????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.80 (146 / 81)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.80 (28 / 10)  

2802 23.29 6.05 2.40  chr1_4779303_4785987     5318  6193 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_4779303_47   5318 TGGAGAGAAATATCTTGTTCAAAGATTGAAAGACTCAATATT---AAGAT 5364
                             i   v  vi v      vi     i      i      ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4779303_47   5365 GTTAATTCCTCCCACATTGATC-AAAAATTTGACATAACCCCATTCAAAA 5413
                          vi   v ii    v       - v i   ii  ii  i   vv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_4779303_47   5414 TCCCAGC-ACACTTCTTAAAAAAAT-AACAAACTGATTCTAAAATTTAC- 5460
                                -i vi  i  iv i    -i    i     i        i i-
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_4779303_47   5461 TGGAAATGCAAAGAAAACCTAGAATAGACAAAAAAAATTTTTTTAATAGA 5510
                                    i i --  i       v     v  -- i  vv  v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAA--TCTTGAAAAAGA 196

  chr1_4779303_47   5511 ATAGCAACATAGGAGG-CTTGCTGCTTCTTCATTTCAACACGAATTATAA 5559
                          v i   vi v     -  ii -i    iiv       v  vv i  i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_4779303_47   5560 AGCCACAGTAATCACGACAGTGTGGTATGGGCATAAGGATAGACACATAA 5609
                            i          v            iv                i   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_4779303_47   5610 GTCAATGGAACAGCACAGAGA-TCTACGAAATAAGTTCACACTTCAATGG 5658
                         i         i  v iv    -  i -       iii  i  v iv    
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATGG 344

  chr1_4779303_47   5659 TCAATTAATGTTCAGTAAAGGTGTCAAGGTAATTTAATGGGGAAATGATA 5708
                               i  v   iii  i    i    iiv   i          vi   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_4779303_47   5709 GTCTTT-CAA-AAATGGTCCAGAGGTAA-TGAACACCCATATACAAAAAA 5755
                               -   -       v v i ii  -  i i ?   i  i     i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_4779303_47   5756 AAAAGAACTTTCATTTTTATCTTACACCATATGTAAAAATTAACTTGGAA 5805
                          v--   v  vv iiii  i  i         ii           iii  
  L1M4_orf2#LINE/    445 AT--GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_4779303_47   5806 TAGATCTTAGATTTAAATGTAAAAGCTAAAACTATAAA-CTTGTAGAATA 5854
                          i    v?   ii         i               -  iv     v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_4779303_47   5855 AAATATAGAAG-ACATCTTCATGACCTTGAGGTAAGCAAAGATTTTATGG 5903
                            i    i? - v      i        i v  i    v i   iv i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_4779303_47   5904 ----GATACAAAAAGAACAAAGCACAAAAGAAAAAAT-TATAAATTGGAC 5948
                         ----  i  v     v    ivv              -v           
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_4779303_47   5949 TTCATTCAACATCAAAAACTTTGACTTTTCAAAAAAAAAATCAGTAAGAA 5998
                              -   v  i         viivi      ii v --ii vi     
  L1M4_orf2#LINE/    643 TTCAT-CAAAATTAAAAACTTTTGTGCTTCAAAGGACA--CTATCAAGAA 689

  chr1_4779303_47   5999 AAT--AAAGCCAAATCATCACTGACTAGGGGAAAATATCCACAA--TATA 6044
                          i --    v   vi  -  --  v i  i        iii   --i   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCA-CA--GAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_4779303_47   6045 CATTCCGGACAAAGAACACGTATCCAGAATATTTAGAGAATCC------- 6087
                         i  -- v  i  i i  vi             v  i    ii -------
  L1M4_orf2#LINE/    737 TAT--CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_4779303_47   6088 -----AATAAAATTAGACAAACAACTCAATTTTTAAAATGTGCAGAACAA 6132
                         -----       --       i   i     ?v-      v   i iv v
  L1M4_orf2#LINE/    785 TCAATAATAAAA--AGACAAATAACCCAATTWA-AAAATGGGCAAAGGAT 831

  chr1_4779303_47   6133 TTGGATG--CATC----------------ACAATGATGACAAATAAACAC 6164
                            i  i--   i----------------    --   i v     i   
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAA--ATGGCCAATAAGCAC 879

  chr1_4779303_47   6165 ATGAAAAGGCACTCAGCATCCTCAGTCAT 6193
                                 iii    i    v????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (132 / 68)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 2.31 (74 / 32)  


3073 27.86 0.55 0.55  chr1_4831446_4838170.rev     5327  6234 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_4831446_48   5327 TGGAAGAACATTCCATGCTCATGGATAGGATGAATCAGTATCATGAAAAT 5376
                              ii i  i     i        v   v  v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4831446_48   5377 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5426
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_4831446_48   5427 TACCAATGAGTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5474
                          v   iivivi  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_4831446_48   5475 TATGGAATCAAAAAAGAGCCTGCATTGACAAGACAATCCTAAGCCAAAAG 5524
                                viiv  ii  v  v v  v v   i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_4831446_48   5525 AACATAGCTGGAGGCATCACGCCACCTGACTTCAAACTGTACTACAAGGC 5574
                             v  i      vv    i iv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_4831446_48   5575 TACAGACACCAAAACAGCATGGTATTGGTACCAAAACAGAGATACAGACC 5624
                              vv i   i    ii     i   i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_4831446_48   5625 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5672
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_4831446_48   5673 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5722
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_4831446_48   5723 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5772
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_4831446_48   5773 GAAACTGGATCTGTTCCTTACACCTTATACAAAAATTAATTAAAGATGGA 5822
                            ii    i iv v   i     v              i v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_4831446_48   5823 TTAAAGACTTATATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5872
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_4831446_48   5873 TTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTG 5921
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_4831446_48   5922 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5971
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_4831446_48   5972 ATTAAACTAAAGAGCTTATGCACAGCAAAAGAAACTACCTTCAGAGTGAA 6021
                           i   v v  i i   v  ii vv    i  v    i vvv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_4831446_48   6022 CAGGCAACCTACAAAATGGGAGAAAATTTTCACGACCTACTCATCTGACA 6071
                         v  i     i   i             v  ii i vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_4831446_48   6072 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 6121
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_4831446_48   6122 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 6171
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_4831446_48   6172 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 6221
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_4831446_48   6222 CATCACTGGTCAT 6234
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (146 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1050 28.39 8.59 0.52  chr1_4963683_4966954     1435  1818 (1454)    L1M4_orf2#LINE/L1        1   415 (493)  

  chr1_4963683_49   1435 TGGAAAGACATACAGTATTCATAGATTTAAAAACTCA-CATAGTAAATAT 1483
                                 i  v vi i     i    vi  i   i -i  v  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_4963683_49   1484 GTTAATTTTCCCTTAATTGAGATACAGTTTTAGCACAAATTGTATCAAAG 1533
                          vi   vi    iv      vv     v  i i i   viiv       i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_4963683_49   1534 TATCAGCAAATATTTTTGTAGATATAGATGAGATTATTCTAAATGTTATA 1583
                          vi    viviv      i   v  v  ii  v v  i     vv i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_4963683_49   1584 ----------AAGGACCTAGAATCACTAAAAAACAATTTTGAAAAAGAAG 1623
                         ---------- i     i     vi i    --    i            
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAA--CAATCTTGAAAAAGAAG 198

  chr1_4963683_49   1624 A---------------TC----TATCCAATTTAGAGAC--ATTATATAGC 1652
                          ---------------  ---- vi       vi i  -- i  i v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_4963683_49   1653 TATGGTAATCTAGAATGGATGATCTTGGCAGATGGACAGGCTTATAGAT- 1701
                           ii      v   vv vi  i vi     v v   i  i v       -
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_4963683_49   1702 AATGGAACAGAACAGAGAACCCAAAAATAGATTTACACAAATATTCTCAA 1751
                                i    iv    ii   i     i iii i   vv   vv    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_4963683_49   1752 TTGATTTTTGACTAAGGTGCAAAAGTAAGTCAATGGAAGAAAGATAGACT 1801
                                 i   v i     v  iiiv v       iii  ii    v  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_4963683_49   1802 TTTCAACCAATGGTGCT 1818
                                v         
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCT 415

Transitions / transversions = 1.32 (62 / 47)
Gap_init rate = 0.02 (7 / 415), avg. gap size = 5.00 (35 / 7)  

1447 25.67 4.11 1.85  chr1_4963683_4966954     2293  2779 (493)    L1M4_orf2#LINE/L1      411   908 (0)  

  chr1_4963683_49   2293 GTGCTGGAGTGAGTGAGTGTTCATATTCAATAAAATAAACCTCAAACTAA 2342
                                iiii v  ii i?i  i  v   v i   i  vi vi v ivv
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_4963683_49   2343 GGCTCACCCCTTATACAAAAATTCACCAAAAATGGACTATGGAACTAAAT 2392
                         iv     v  v            v  iv        ii ?i  v      
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_4963683_49   2393 ATAAAATATAAAACTAGAAAACTTTTAGAA-AAAACAATGGAAAAAATCT 2441
                         i   i vv        v      i      -      vv  ?iv      
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_4963683_49   2442 TCTGGATCTAAGGT-AGACAAAGATTTCCTAGACTTGGCACCAAAAGCAT 2490
                           vv  i  vi   -  i   v i    i    iv  i           i
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_4963683_49   2491 GATCTATAAATGGAAACATAAAT---TTGG-CTTCATCAAACTTAAAATC 2536
                         i v v i   v i   v   i  ---    -          v      v 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_4963683_49   2537 TTTTGCCCTGTGAAG-ACAAGAGCCTGTTAAGAGGATAAAAATGCAAGCT 2585
                              iv  vii   -   -----  i i    iii i    vi   v i
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACA-----CTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_4963683_49   2586 ATAGACTGGCAGAAAATATCTGCAAACCACATATCTGACAAAGGATTATT 2635
                          i   v   v         i      i  i        i  i   i vv 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_4963683_49   2636 ATCTAGAATATATAAACAAAACTTTCCAAATTCAACAATAGGAAAAAAAA 2685
                            i            --i    i ivv  i    i    --    i v 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAA--GAACTCTTACAACTCAATAATA--AAAAGACA 801

  chr1_4963683_49   2686 AACAATCCAATTAGAAAGTGAGTTAATGACATAAAGGGACATTTCACCAA 2735
                           i  i      ?i   i  i iv  v  iv i  vi        v    
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_4963683_49   2736 AGAAAATAAACAACTG-TCAA----CACATG--------TTCAACATCAT 2772
                             i   v    v  -i   ----      --------i         ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_4963683_49   2773 TAACTTC 2779
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.47 (72 / 49)
Gap_init rate = 0.02 (11 / 498), avg. gap size = 2.64 (29 / 11)  


2692 26.16 4.06 1.69  chr1_5024790_5027025      858  1744 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_5024790_50    858 TGGAAATACATCCCATGCTCATAGATTGGAAGAATCCATATCGCGAAACT 907
                               v i        i    i          v iv    i iv  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_5024790_50    908 GACTATACTGTCCAAAGCAACCTACAGATTCAATGCAATTCCTATCAAAA 957
                          i v     vi     vii i            i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_5024790_50    958 TATCAACATCATTTTTCACAGAAGTAGAAAAGA-AATTGCAAAGTAAATA 1006
                          vi  i vv v     ii     i v  v   v-i  ivi   i vv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_5024790_50   1007 TGGAAC--CAAAAAACAGCCTGAACAGTCAAAACAATCCTAAGCAAAAAG 1054
                              v--   iii  --  v   i  i          i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_5024790_50   1055 AGCAAATCTGGGGGCATCACATTACCTGACTTCAAA--TTACAGTACAAG 1102
                          i    vi   i  vv     i v  ii i      --    --     i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAA 246

  chr1_5024790_50   1103 TTTATAGTAACCAAAACAGCATGGTAATAGTATAAAAGTAAATAGATAGA 1152
                         vi  i     i   i    ii     v i i    iii  i i v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_5024790_50   1153 CAAATGGAACAGAATAGAGAACCTAGAAATGCAGGCAAATACTAACAACC 1202
                         iv       i     v    ii i      iv vv  v i i v iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_5024790_50   1203 AAGTAAGTGATCCTTGACAAAGCATGCAAAAAC-AT-AAATTGGGGGAAA 1250
                           - ---    ii i     i -i   v  i  -  -v   --       
  L1M4_orf2#LINE/    347 AA-T---TGATTTTCGACAAGG-GTGCCAAGACCATTCAAT--GGGGAAA 389

  chr1_5024790_50   1251 GGACA-TCTTATTTAATAAATGGTGCTGGGAGAATTGGATAACCACATGT 1299
                          i i -    -  i  i              v  i      ?       i
  L1M4_orf2#LINE/    390 GAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_5024790_50   1300 AGAAGAGTGAAACTAGATCCTTGTCTCTCACCATATACAAAACTTAACTC 1349
                          i    i    ii i  i  i ii   v              v       
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_5024790_50   1350 AGGATGAATTAAAGACTTAAATCTAAGCCCTGAAACCATAAAAATTCTAG 1399
                          ii   i  i ?    i     v    vv  i    i      v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_5024790_50   1400 AAGAAAACCTAGGTAAGACTCCCC-TGTACATTGACATAGACAAAAATTT 1448
                                 v    ?ivi v  ii -  -  v   ivv   i   vii   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTT 587

  chr1_5024790_50   1449 TATGACTAAAACCCCAAAAGGAAATGCAACAAAA--ATTAATAAATAAAT 1496
                         iv iiv  vi  v       v v v         -- vv    i      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_5024790_50   1497 GAGATCTAATTAAATCTAAAAACTTCTGCACAGCAAAATAAATAATCATC 1546
                         vi  ii v  i   vi         i  ii vv    iv v iv    vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_5024790_50   1547 AGAGTGAA-----------CAGA-----------TACTTCC---TCTATG 1571
                          i      -----------    -----------  i  v ---  -  i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATA 736

  chr1_5024790_50   1572 CATCTGACAAAACACTTATATCCAGAATCTATGAGAAACTCAAGCAAATA 1621
                         i      i  iiv    i          v   i ii     vvi   v v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_5024790_50   1622 AGCAAGAAAAAAACCAAATAATCTCATTTAAAAGTGGACCAGTGACGTGA 1671
                          ii  v     i  -      i iv   ?    i   i v iv  iv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_5024790_50   1672 ATAGACATTTCTCAAAAGAAGATGTACAAATGGCCAATAAACATATGAAA 1721
                                      v         i                i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_5024790_50   1722 AAGTGCTCAACATCGCTAATCAT 1744
                          ii           i????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (145 / 83)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.43 (51 / 21)  


1835 28.38 10.72 0.73  chr1_5182233_5184870     1326  2146 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_5182233_51   1326 AGATATCC-ATG-----GGACTGGA-GACTTGACATTGTTAAGAT--TAA 1366
                                 -   -----   i    -     i i           --i  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_5182233_51   1367 TTCTCTCAAAATTTCCCTATAGCTCCAACTTAATCACAATCTAAATTCCG 1416
                          v   i v     vvi   i  v i    vi    v v   v    i  i
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_5182233_51   1417 GCAGGCATTTATGTAAGACTTGATGAGCTGAATCTAAAATTTTTATGAAA 1466
                           v v v   v  i ii v    ii      vi        iv    i  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_5182233_51   1467 ATGTAAAGGAACTAGAATAGCCAAAACAATGTTGAAGACAAAGAATAAAA 1516
                            i  i   v i                 v     i vi     i   i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_5182233_51   1517 TGAAAATATTTAGAATACCTGATTCCAA-------------GTTA----- 1548
                          vii iv i i v v v  ii   i   ------------- i  -----
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_5182233_51   1549 ---------GTTTGGTATTGACATAAGAATAGACATACAGATTTGTTGAA 1589
                         ---------  v     i  i      i         i    ivi v   
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_5182233_51   1590 CAAAAT-----AT--AGAACTAGACCTACAAATATATGGCCAATTAATAT 1632
                         i i   -----i --    v  i   i i v  v     i     i  v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_5182233_51   1633 TCATAAAAAATGTCAAGGTAATTCAATGGGGAAACAATA-TCTATTTGAT 1681
                           ivv  iii  i    iiv              v    -   v  ii i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_5182233_51   1682 AAAAGGTTCTAAAATATCCAGATAGTCATACTATGAAATA-TGAATTTTG 1730
                            v   v  iii i v ii    ?i  i - iii   v -    v  v 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGAATGAAGTTGG 454

  chr1_5182233_51   1731 ATCTCTACTTCATACATTACACAAAATTTAATTTGAAATGGGCAATAGGC 1780
                          i i    i   i  vv  i      v    i ii      iiv ?  i 
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_5182233_51   1781 CCAAATATAAAACTTAATACTATAAAGCTTCTAGAAAAAAAT-TGTGAAA 1829
                          i    i   i vi   v        i  ii     i    i- iv ?iv
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_5182233_51   1830 AAATATTTTGTGATTTAGGGATGGGCAACATTTTCTTAGAAAGGACATGG 1879
                             -i  i    ii v   v i     iiv         v v    ivi
  L1M4_orf2#LINE/    555 AAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_5182233_51   1880 AAAGCA---ATAACTTTAAAAAAA---GATAATTTTGACTGCATCAATAG 1923
                               ---ii   vvv i     ---     v  v    v      - i
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA-AA 652

  chr1_5182233_51   1924 TTCAAA---TTTCTGCTCATAAAAAGAATCAATGAATAAAATGAA----T 1966
                           v   ---   v    -- v   i  vv v  v  v   i    ----i
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCT--TCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_5182233_51   1967 AAGCCATAGGAAAAGAAAAA----TGGCA--TTATACAACTGATAA---- 2006
                           v   i  i vii  i   ---- v   -- i   i v       ----
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_5182233_51   2007 CCCCTA--CAG------TAGTGG-----TAGAAGTTCAACACTTAAAAAA 2043
                          iiv  --   ------  iv i-----  v  -i    i v v    i 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAAAAGA 799

  chr1_5182233_51   2044 AAAATGA----ATTTAGAA--GAGACAAGCCTTTGAACAAACATGTCATA 2087
                         v    i ----   ? i  -- i vv   vv      i i    v  viv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_5182233_51   2088 CATGAAGGTAAATGAATAATCAATAAGCAGATGGAAAAGTGCTCAACATC 2137
                         v v    i  v ii   iii         v   i   ii           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_5182233_51   2138 GTTAGCTAT 2146
                         i????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.03 (28 / 903), avg. gap size = 3.36 (94 / 28)  


1314 31.86 7.82 1.98  chr1_5199520_5201339      500  1356 (464)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_5199520_52    500 GGAAAGCAATATGTCCACGTTCATAG-TAGGAAAACTCAACATCGAAAAG 548
                               --    -i   i      i - v    i   i  i  i vv   
  L1M4_orf2#LINE/      2 GGAAAG--ATAT-CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_5199520_52    549 CTGAAGGTCCTCCCTAAATTGATCTATTGATGCCATGTATTTCTGAACCA 598
                         v  ivii v     i           iv   v v i i v i iv v v 
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_5199520_52    599 ACTTCTAATAGGGATTCTATG--GATCTTGACAAATTGATTTAAAAATTT 646
                          v i i ii-v vv  i v  --  vv       ii    iiv      i
  L1M4_orf2#LINE/     99 AATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_5199520_52    647 ATGTAGACATGCAAAAGACCAAGAA------AAACAGT---AAAGATGAA 687
                           i i  v      ii    v    ------     i ---i  i v   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_5199520_52    688 GAATAGAAT-GAAACACTGTCAGTACCAGATCTCAATGCTTACCATAAAA 736
                            i i i - i iv   vv  v v  vi  i    vi     i i   i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_5199520_52    737 CAACAGTAA----GACAATGTCGTATTGCCATAGAAGTTGATAAATTGGC 782
                          v       ----    i   v   i  v    iiii v  i v  v ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_5199520_52    783 CAAATATAAAGTAAAC---AGAGCCCAGAATTAGAC--ACACACTAA--- 824
                            --- ii i  i v---    i      v  i  -- i   i v ---
  L1M4_orf2#LINE/    298 CAA---TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_5199520_52    825 --AA---------GAAAGAGGTGACTGTACCGAGTGATGGGTAAAGAG-G 862
                         --  ---------  v ii    v viv   ivvii     v     i-i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_5199520_52    863 GACTTTTTGATAAATAGTACTGGCACAGTTGGTTATCCATATTTTTAAAA 912
                          v     ii i    i  i    v   ii   v  ?   i  viv-   i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAG 443

  chr1_5199520_52    913 AGTGAAATAGGCTATCCACCTTCCATTAAATACAACA-TTAATTTCAAAT 961
                          i    i v  vivi i    iv  ii v      v -    i iv    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_5199520_52    962 AAATTTGAAACTACAAGTAAAAAAGC-AAAACTCAAAAATGTTTAAAAGA 1010
                         ii  iv? i  i-i  i iv  i   -      vv    ivi   i    
  L1M4_orf2#LINE/    494 GGATCAWAGACC-TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_5199520_52   1011 AAATATAGACAGATATCTTTCTGAGCTTGAAATAGGGAAGGAGCTCATAA 1060
                            i    i?iv v     iv   v    iiv    v  v ivi  v  i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_5199520_52   1061 ACA-GA-ACCAAAAAATTAAACATTTAAAAAAAAATT-------TTGG-C 1100
                          i -  -       ivvi  i  viv   i     v -------    - 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_5199520_52   1101 TGCATTGCAATCAAAA-CTTGTATTTTGCAAAACACACTAT--------- 1140
                          v   iiv   i    -   v i vi v    iv       ---------
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_5199520_52   1141 --ACAGACAACTAA-AAAAGGGAAGAAGATATTTTCGATACATATAACTA 1187
                         -- v       iv - i  v  i    i      v i vv      v  -
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT- 741

  chr1_5199520_52   1188 AAAATGAAAAGAGGATTTACTATTTAGAAAACATACAGAGGTCCTTTAAA 1237
                         -----  v   -   i  i-   ii    v i   v   iv  i vi  v
  L1M4_orf2#LINE/    742 -----GATAAG-GGACTTG-TATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_5199520_52   1238 TCAGTAAGCAAAAAAGAAATGAACCAATAGTAAAATGTGTAATGGATGTG 1287
                            i   vv    i v    i v     v?v      v i  v    v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_5199520_52   1288 AACTGCCACTACCCAGAAGTGGAAATACATAT--TCCATAGACAAGTGA- 1334
                           iv v  i v i vi   vi  v     v  --i v   ii  vi   -
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_5199520_52   1335 --GATAACAGACCTCATTAGAAAT 1356
                         --   ivivi  v   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (151 / 118)
Gap_init rate = 0.03 (31 / 907), avg. gap size = 2.71 (84 / 31)  


3497 17.86 2.75 0.96  chr1_5217487_5220079.rev      890  1617 (976)    L1M4_orf2#LINE/L1        1   741 (167)  

  chr1_5217487_52    890 TGGAAAGACATCCCATGTTCATGAATTGGAAGACTTAATGTTGTTAAGAT 939
                                 i              i               i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_5217487_52    940 -----TAC---CCAAAGCAA-CTACAGAGTCAATACAATTTCTATCATAA 980
                         -----   ---     vii -       v    ii    ii      v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_5217487_52    981 TTCCAACAACCTTTTTTTGAAGAAGTGGA-AAGCTGATCCACAAATGCAT 1029
                          i   i vi        - v    i v  -          vv    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_5217487_52   1030 GTGGAACTTCAAAAG-CCCA-AGTA--CAAAACCATATTGAATAAAAAAA 1075
                         i     v v   ii -    - i  --      v  v     --   i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--AAAGAA 197

  chr1_5217487_52   1076 GAACAAAGTTTGAGGACTCACATTTTCTAATTTCAAAACCTACTACAAAC 1125
                                   v           i  i i           i         v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_5217487_52   1126 ATATGCTAATCAATACAGTATGGTATTGACATAAAGATTGACAAATGGAC 1175
                         v  iiv       v     i     i  i     i   v    v  i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_5217487_52   1176 TAATAGAATAAAATCAAGAGTCTAGAAATAAACCCATATATCTATGGCCA 1225
                         i   i     i   ii      i               i  i     i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_5217487_52   1226 ATATAATTTTGAACAAAAGCACCAAGACTATTCAATGGGGAAAGGAATAA 1275
                           - i     vi    ii ii       i               -    i
  L1M4_orf2#LINE/    348 AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAG 395

  chr1_5217487_52   1276 TTTCTTCAGCATGTGGTACTGGAATAAC--AATAGCCACATGCAAAAAAA 1323
                          i i    i  vi    i    i i   --i   ?            i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_5217487_52   1324 ATGAAGTTGAACCTCTACCTCACAGTATCTACAAAAAGTAAATCATAAAG 1373
                         -        i   i          vi  v        v   v   v  v 
  L1M4_orf2#LINE/    446 -TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_5217487_52   1374 AATCAGTGACTTAAATACAAGAACCAGACCT-TGGA-TTCTTAGATGAAA 1421
                         i    ?v   i     ii    i i i v  - ii -i       v    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_5217487_52   1422 ACA--GGGGTAAATCTTTATGACCTTGGCTTTGACACTGGATTCTTAGAT 1469
                            --  ?         ii         v  v i  v   v         
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_5217487_52   1470 ATAACACCAAAAGCATAAGCAACAACAACAACAAATAGATAAATTGGACT 1519
                           i            i         -  v  v                  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAA-AAGAAAAAATAGATAAATTGGACT 643

  chr1_5217487_52   1520 TTACTAAAATTAAAACCTTTTGTACATTAAAGAACATTATCAAGAAAGTG 1569
                          i ii          v       i v i    i   i             
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_5217487_52   1570 AAAAGATGACTGAAAGAATGGGAGAAAATATTTGAAAATCATAAATCT 1617
                               ii  iv v                    v        v    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

Transitions / transversions = 1.95 (84 / 43)
Gap_init rate = 0.02 (17 / 741), avg. gap size = 1.59 (27 / 17)  

 830 17.44 0.00 6.15  chr1_5217487_5220079.rev     1920  2114 (479)    L1M4_orf2#LINE/L1      726   908 (0)  

  chr1_5217487_52   1920 TGCAAATCATAAATCTGATAAAGGCCTAGTATCCAGAATATTTAAATAAC 1969
                                    v         i  v  v             v    v   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_5217487_52   1970 TCCTACAACTCAACAACAACAACAACAACAAAAAGACAAACAGCCTAATT 2019
                           i          i  i  ------------         i i  i    
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAA------------AAAGACAAATAACCCAATT 813

  chr1_5217487_52   2020 AAAAGGCGAGTAAATGATTTCAATAGACATTTCTCTAAAGAAAATATACA 2069
                         ?   iii i i   v     v              i      i       
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_5217487_52   2070 AATGGGCAATATACATATGGAAAGACATGCAATGCCATTGTTCAT 2114
                              v     vi  i   i     iiiv   iii  ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.30 (23 / 10)
Gap_init rate = 0.01 (1 / 183), avg. gap size = 12.00 (12 / 1)  


4400 16.19 2.33 1.88  chr1_5540578_5545544     3574  4475 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_5540578_55   3574 GGAACACATCTCGTATTTATGGATTTGAAGTCTTAACATTGTTAAGATGT 3623
                          i  v i   i i i  i       v    v     i            v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_5540578_55   3624 CAGTACTACCCAAAGTGACCTACAGATTCAACATAATCCCTATCAGCGTC 3673
                           i    v      v   i             ii           ivi  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_5540578_55   3674 T-AGATGATGCTTTCTGCAGAAATAGAAAACCCCATCCTAAAATTAAAAT 3722
                         i-  v  vi-i   i         v  v  v iv           v v  
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_5540578_55   3723 GGAATCTCTAGGGACCCTGAATAGCCAAAATAATCTTGAAAAATAAGAG- 3771
                             viv v        v            i            v    i-
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_5540578_55   3772 AAAGCTGGAGGACTTACATTTCCTGTTTTCAAAACCTATTACAAAGCTAC 3821
                             i         i   i    iiv         i  i           
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_5540578_55   3822 AGTCATCAAAATAATGTGGTACTGGCATAAAGACAGACATATAGA-CAA- 3869
                            v     i i i                i  i           -   -
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_5540578_55   3870 ---ATAGAATAGAGAGCCCAGAAATAAACGCTCACATATATGATGAAATG 3916
                         ---       v     i            v vi    v    i v  v  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_5540578_55   3917 ATATTTTACAAGGATGCCAAGACCATCCAATGGGGAAAGGATGGTCTATT 3966
                           v  iv      i            i            i  i    v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_5540578_55   3967 CAACAAATGGTGTTGGTAAAACTGGATATTCACATGCGAAAGAATGAAGT 4016
                                     i   v v         ?i       i            
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_5540578_55   4017 TGGACCCTTACCTATAACCATATACAAACAATAGCTTAAAATGG-TCTAA 4065
                                i     vvv            v v  i  i       -  v? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_5540578_55   4066 GACCTAAATGTAAGACCTGAAAATACAAAACTCTTAGAAGGAAACA--GG 4113
                                        v  i   v  i              i     --  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_5540578_55   4114 GGAAAAGCTTCACAACATTGGATTTGGCAGTGATTTCTTGGATATGACAC 4163
                         ? v   v    iii  v    i  v    i  i      i          
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_5540578_55   4164 CAAAGGCACAGGCAACAAAAGAAAAAAAATAGACAAATTGAACTTCAT-- 4211
                             i     i                --    i      i       --
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAAATTGGACTTCATCA 649

  chr1_5540578_55   4212 -----AAAAAATTTTGTACATCAAACGACAGTATCAACAAAGTAAAAAAA 4256
                         -----     v      i v     v    v      v     i    i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_5540578_55   4257 AAAACAACTCATAGAATGGGAGAAAATATTTGAAAATCATATATCTGATA 4306
                         ----    i  i                    v                 
  L1M4_orf2#LINE/    700 ----CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_5540578_55   4307 AAGGATCAATATACAGAATATA--GAGAGCTCCTAAAACTCAACAAAAAC 4354
                          i   iivi   v         --i   i   i  v       i  v  -
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA- 794

  chr1_5540578_55   4355 ACAACAACAAAAACAAAAAAACCTAACTCAAAAATGAGCTAAGGACTTGA 4404
                         --------   i     v  -  i  i ?       i  v     i    
  L1M4_orf2#LINE/    795 --------AAAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_5540578_55   4405 GTAAACATTTATCCAAAGAAGATATACAAATGGCCAATAAACACATAAAA 4454
                         i  i      v                             i     i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_5540578_55   4455 A--TGCTCAACATCCCTAATCAT 4475
                          --           v????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (83 / 59)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 2.71 (38 / 14)  


2640 23.03 5.32 5.44  chr1_5618913_5621354     1086  1949 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_5618913_56   1086 AAGGTGACAGCTTTCCCCAGGG-GTTCTATAGATTCAAGGCAATCCCATT 1134
                            i  i  iivi      iiv- v    i        v        vv 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_5618913_56   1135 CAAAATGACAGCAAGCTTTTTATGTAGAAATTGACAAACTGATTCTAAAA 1184
                               vv    viv      -  i            i     i      
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_5618913_56   1185 TTCATATGGAAATGCATGCTAAGGACC-AAAATAGCCAAAACCGTGTTGA 1233
                                         ---- i     - i            vi v    
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCA----AGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_5618913_56   1234 GAAAGAA--------CTAG--------------CTGATGTCAAGACTTAT 1261
                         i      --------i i -------------- ii  v    i     i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_5618913_56   1262 TGTAAAGCTATGGCAATCTTGACAGTATAGCACTGATATCAGCATCAATA 1311
                          ii       ii i    vv      i i i    ii  v  v  vi i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_5618913_56   1312 AAT-GATCAATGGAATAAAA--GAGAGTTCAGAAATAGACCCACACATAT 1358
                         v  -             i  --      i        i     i    v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_5618913_56   1359 ATGGATAACTTGTGGGCTTTTTTTTTACAAAGGTGCAAAGACAATTTAAT 1408
                             vi  -   v-------    iv    i     v     v   i   
  L1M4_orf2#LINE/    341 ATGGTCAA-TTGA-------TTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_5618913_56   1409 AGATAAAGGATAATCTTTTCAACAAATGATACTGAAATGATTGCTTACCC 1458
                         i iv    i   i               i i   ii ii i  vv  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_5618913_56   1459 ACATGCAAGACAAAATAACCTTCAATCCATACCTTGCACAGCCTATAAAA 1508
                                 i --i   i vv  vi i  v     ii   viiv  i    
  L1M4_orf2#LINE/    433 ACATGCAAAA--GAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_5618913_56   1509 ATTAACTCAAAATAGGTCTCAGTTCTAAATATAAAACCTAAAAGCATAAA 1558
                                      i i  v?  vi      i   i v      vi     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_5618913_56   1559 ACCAT------AAAATTCCTAGCAAGAAGGCTTTGTGACCTTAAGGTGGG 1602
                           iv ------    -- v   v?iv  iv   i        ii v i  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAA--CATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_5618913_56   1603 CAAATATTTTTT-GATTTGACACCAAAATCACAATTCATAAAGAAACAAA 1651
                            vvi   i  -   v           v     viv i   ii  v   
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_5618913_56   1652 TTGATAAATTGGATTTCACCAAAATGTAAAGCTTCTGTTCTTTGAAAGAT 1701
                          v           i    i      vv   i   i   v   ii  i  i
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_5618913_56   1702 GCTGTGAATAAAATGAAAAGACGAGCTGCAGTCTAAGAAATTACAGTTGC 1751
                         i  i v  v   i         i v ii   vv ii  i vv i v    
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_5618913_56   1752 AATGTGTCAAAGACCTCGTTAGATAGGTCAGATATTAGACACAGGCCTTG 1801
                           ------------------------i   v    iv  i vi  v    
  L1M4_orf2#LINE/    729 AA------------------------ATCATATATCTGATAAGGGACTTG 754

  chr1_5618913_56   1802 TCTCCAGAATATATAAGAAGAA----TATA-CTT-----TCAAAA-ATAA 1840
                          v              --    ----  i -  i----- v    - i  
  L1M4_orf2#LINE/    755 TATCCAGAATATATAA--AGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_5618913_56   1841 ATGACCCGACTTTTTAAAACTGGA-ACAATATTTGAAGTGATACTTCACC 1889
                           i    i ---  ?    v   i- v iv       vv  i i   v  
  L1M4_orf2#LINE/    803 ATAACCCAA---TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_5618913_56   1890 AAAAAAGATGTCCCAATGGCAAATAAGCACATGAAAAGATGCTGGAGCAT 1939
                            i     i v v      v                      vi -   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA-CAT 898

  chr1_5618913_56   1940 CATTAGTCAC 1949
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (116 / 79)
Gap_init rate = 0.03 (23 / 863), avg. gap size = 4.04 (93 / 23)  


2945 25.48 4.08 2.72  chr1_5755380_5758182.rev     1422  2304 (499)    L1M4_orf2#LINE/L1        1   895 (13)  

  chr1_5755380_57   1422 TGGAGAAATATATTTTGTTCATTTACTGGAAGGCTCAACATAGTAAAGAT 1471
                             i i    viiv       vv i      i  i  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_5755380_57   1472 GTCATTTTCCCCTAAATTGATGCACTAGTTTAACCCAATTCCTATCAAAA 1521
                          v  v vii   i        vi  vii  i   v    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_5755380_57   1522 TCTCAGCAAGATTTTTTTTTTGTAAATATGAACAAGACT-ATTCTAAAAT 1570
                           i    ---- vii       i i v  vi     -  -  i       
  L1M4_orf2#LINE/    101 TCCCAGC----TGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAAT 145

  chr1_5755380_57   1571 TTATTTGGAAAGACAAGAGGACTT-GAATAGCTAAAACAAATTTGAAAAA 1619
                          i  v      vi    -    ii-       i       vi        
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_5755380_57   1620 GAAGAATAAAGTGGAAGGAGTCAATCTATATGATTTCAAGACTTATTATA 1669
                               i     v i    v   vv  vivii       i     i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_5755380_57   1670 TCGCTGTCATGATCAACATTGTGTTGCAGTGGTG-AAGGAAAGACATACA 1718
                         vv   iivi i     v iv    v i v   ii-     v       i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_5755380_57   1719 GATCGAT--------------AACCCAGACACAGACTTGCACAAATATGC 1754
                             i  -------------- ii     v i i  iiii   vv    v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_5755380_57   1755 CCAACGGATTT--GGCAAATGTACAAAAGCAATTCAATGGGTAAAAGATA 1802
                         i   iv     -- i   iv  i v  ii v          v   ii   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_5755380_57   1803 GCCTTT-CAGCAAATGGTGCCAGAGCAATTAGCCATTCATAAGGCAAAC- 1850
                          i    -  i          ii ii   i i vi ?i  i -v     v-
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAG 443

  chr1_5755380_57   1851 ----AAGTTGAACCTTGAACAAAATCTCACACCTTATGCAAAAATTAGCT 1896
                         ----      i   iiv ------i        v   i         i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTA------CCTCACACCATATACAAAAATTAACT 487

  chr1_5755380_57   1897 AAAAATGGATCATGAACCTAGATGTAA--------ACTATGAAACT--TA 1936
                         v           ?ii     i      --------     i     --  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_5755380_57   1937 GGAAAAAACCTAGGACAAAAGCTTTGAGATATAGGGCCAGGCAAAGAGCT 1986
                          i i     v    ?vv   v   i v  iv v   ii      v ivi 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_5755380_57   1987 CTTAGACTTTGTTTCAAGAAGCATAATCCATAAAAGGAAAAATGGACTAG 2036
                               - v  viv v i     i  v v i     i      i  iv i
  L1M4_orf2#LINE/    588 CTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_5755380_57   2037 TTGGGCTTCATCAAAAT-AAAAACTTTTTCTCAGCAAAAGACCCAGTTAA 2085
                             i            -          viv vv    i   v vi i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_5755380_57   2086 GAAGCTGAAAATATAAATTACAGAGTGGGAAAGAATATTTGCAAACCACG 2135
                            iv      v i  vii     i     i i            i  ii
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_5755380_57   2136 TATTTGACAAAGGAGTAGTATCTAGAATATATAAAGAATGCTCAAAATTC 2185
                            i   i  i   v v     i               iv  i v  i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_5755380_57   2186 AATAGTAAAAAAGCAAGTCATTCAACTAGAACATGGCATGAATGAGTGAA 2235
                             i      ii   i v ii   i ?i  ---------    i i-  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAA---------AATGGGC-AA 826

  chr1_5755380_57   2236 AAGGCATGAACAGACATTTCCCCAAGGAAGATATACAGATGGCAAATAAA 2285
                          i iiv    i         i    i           i     v     i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_5755380_57   2286 CACATGAAAAGATGTTCAA 2304
                                       i    
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.80 (142 / 79)
Gap_init rate = 0.02 (18 / 895), avg. gap size = 3.33 (60 / 18)  


2231 22.64 0.93 6.20  chr1_5948331_5949968      501  1145 (493)    L1M4_orf2#LINE/L1      298   908 (0)  

  chr1_5948331_59    501 CAATGGAACAGAATAGAGATTCCAGAAATAAATTCATGCCACCTACAGCT 550
                                 i     v    v            ii   i - ii  ii ii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC-ATTTATGGTC 346

  chr1_5948331_59    551 GACTGATTTTTAA-AGAGGTGCCAAGAACACGCACTGGGGAAAAGGCAGT 599
                         i i       ii - ii          v  iv  v        iiii   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_5948331_59    600 CTCTTCAATAAATGGTGCTGGACAAACTGGACACCCACATGCAGAAGAAT 649
                           i     i            ivv       i ?         i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_5948331_59    650 GAGATGAGACGCCCTACCTCTCTCCATATATAAAAGTCAACTCAAAATAG 699
                           ii vi   -         v v       i    i i          i 
  L1M4_orf2#LINE/    447 GAAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_5948331_59    700 ATTGAAGACTTAAATGTAAAACCTGAAACTATGAAACTACTAGAAGAAAA 749
                           ii?    i         i v  i       i     vi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_5948331_59    750 C---GGAAGAAGTGCTTCGTAACACTGGGCTGAGTAAGGATTTTTTTAAG 796
                          ---  ?iv  i -      i  vi    ----------------   i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGG----------------TTAGG 578

  chr1_5948331_59    797 TAACATTGGGCTGTGAAAGGATTTTTTTAAATAAAACCGTAAAAGCACAG 846
                         i  ---   -------------   i   i   vi  vvi         i
  L1M4_orf2#LINE/    579 CAA---TGG-------------TTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_5948331_59    847 GCAACAAAAGCAAAAAGAAACAAAT-GGATTATATCAAAATAAAAAGGTC 895
                                   v     v i i    -   i vi        v    iv i
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_5948331_59    896 TTACACAATAAAGTAAACAATTAACCGAGTGAAGAGATAACCTGCACAAT 945
                           iii vvi    v v  v  i  vvi      i   i    ii  v   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_5948331_59    946 GGGAGAAAATATTTGTAAACTATATATCTAACAAGGGGTTAATATCCAGA 995
                                        i   ii        i i     ii vi        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_5948331_59    996 ATACATAAGGAATTTAAGCAACTCAACAGAAAAAAAAAAAAACTAGTAGC 1045
                            i    i   i ivvi        i iv     i v   -----  i 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA-----TAAC 807

  chr1_5948331_59   1046 TTGATTTTAAAATGGGCAAAAGGCCTTAACAGACATTTCTCAAAAGAAGA 1095
                         iii   ?v            i iii v  i           v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_5948331_59   1096 CGTTCGAATA-CCTGTAGGCACAGGAAACGATGCTCAGCCTCACTAGTCA 1144
                         ii v i   i-  vi  i     v    v        i v   ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_5948331_59   1145 T 1145
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.30 (99 / 43)
Gap_init rate = 0.02 (11 / 611), avg. gap size = 4.18 (46 / 11)  


3555 15.05 1.19 2.09  chr1_6799104_6801278.rev      488  1158 (1017)    L1M4_orf2#LINE/L1       45   709 (199)  

  chr1_6799104_68    488 TAAAATG--AATTTAAACTCCCCAAATAGATCCTCAGATTGAATATAATC 535
                            i   --   ----           v    iv      v  iii    
  L1M4_orf2#LINE/     45 TAAGATGGCAAT----ACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chr1_6799104_68    536 CCCATTATA-TCTCAGTTGTCTCTTCTGTGGAAACTAACAAGCTGATCCT 584
                           i  i v -  i   i  i  i  i  ii    i i             
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr1_6799104_68    585 AATATTCATACGGAAATACAAGGGAGCTAGCACAGCCAAAACAATCTTGA 634
                           v       i      i       v i  v i                 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_6799104_68    635 AAAAGAAGAACAGAGTTAAAGGACTGACAGTTCCTGATTTCAAAACTTAC 684
                                     i    ii      v   v    ii              
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_6799104_68    685 TACAAAGCTACAG-AATCAAGACATTGTGGTAATGGCACAAAGATAGACA 733
                                      -          v       v     i  i        
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_6799104_68    734 TATAGATCAATGGAATAGAATCAAGACTCTAAAAATAAACCCACAGATTT 783
                                              ii   v  i i           i v    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_6799104_68    784 ATAGTCAGTTGATTTTCAACAAGGGTGCCAAGACACTTCAGTGAGGAAAG 833
                           i    i         i                vv    i  i      
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_6799104_68    834 AATGGTCTTTTCAACAAATGG-GCTAGGACAACTGAATATCCACATGCAA 882
                            i                 -   i         i   ?          
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_6799104_68    883 AAAAATGAAGCTGGAAGCCTACCTCACACTGTGTACAAAAATTAACTGAA 932
                           i       i    vv            ii i              v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_6799104_68    933 GATCTATCAGAGAACTAAATGTCAGAGCTAAAACTACAGAACTCTAACAA 982
                         i  vv    ?   v        v             i i      v v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_6799104_68    983 AAAAACACAGGTGTAAACCTTCACGACCTTGGATATGACAATGGTTTCTT 1032
                         i      i   ?     i    ii        i vv i            
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_6799104_68   1033 AT-TATGATACCAAAAGCATAAGTGACCAAAAAAAAAAACAAAAAAACAG 1081
                          v-     i          i   ----   v    i   -----   i  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAG----CAACAAAAGAAA-----AAATAG 631

  chr1_6799104_68   1082 ATAAATGGGACACAATCAAATTTAAAA-CTTCTGTTCTTCAAAGGACACT 1130
                               v    viv      v      -   i   v              
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_6799104_68   1131 ATCAAGAAAGT-AAAGGCCAGCACAGCAG 1158
                                    -   i v  i v  -   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCA-CAG 709

Transitions / transversions = 1.80 (63 / 35)
Gap_init rate = 0.02 (11 / 665), avg. gap size = 2.00 (22 / 11)  

 963 12.11 4.30 10.94  chr1_6799104_6801278.rev     1429  1684 (491)    L1M4_orf2#LINE/L1      670   908 (0)  

  chr1_6799104_68   1429 TCAAAAAACA--------AAAGCGAAAAGACAACCCACACAGAATCAGAG 1470
                              ii   --------    i                --    vi   
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA--GAATGGGAG 717

  chr1_6799104_68   1471 AAAAATCACATATCACATGTCAATCATACATTTG-AAATCACATATCTGA 1519
                             ------------------------i     -      i        
  L1M4_orf2#LINE/    718 AAAA------------------------TATTTGCAAATCATATATCTGA 743

  chr1_6799104_68   1520 TAAGGGACTGATATCTAGAACACATATAAAGAATTCCTACAACTGAACAG 1569
                                  vi    i    i --         i  i       v  i i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATA--TATAAAGAACTCTTACAACTCAATAA 791

  chr1_6799104_68   1570 CAAAAATTCAATTGACTCAATTCAAAAATGGA-AGAGGATTTGAATAGAC 1618
                         i     vv   v i  i     ?        i- i               
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_6799104_68   1619 ATTTGTC-AAAGCAGACATACAAATGGCTAATAAGCTCATGAACAGATGC 1667
                             v  -    v   i           i       v      v      
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_6799104_68   1668 TCAACATCATTAGTCAC 1684
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.03 (7 / 239), avg. gap size = 5.57 (39 / 7)  


3170 23.44 8.97 0.36  chr1_6894333_6896447      790  1625 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_6894333_68    790 TGGAGGGCTATACCATGT------ATTGAAAGACTAAATA--GT-AAGAT 830
                             ii v   v      ------    i      v    --  -     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_6894333_68    831 GTCTGTTTTCCCTAAATTGATTTATGAATTCCGTGCCATCCTACTCAAAA 880
                          v vi vi    i        i  iii    vii  v    ivv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_6894333_68    881 TC----------------------TAGATAAACTAATTGCAAGGTTTTTA 908
                           ---------------------- v  i  i  i  ivi  ii  iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_6894333_68    909 TGGAAATGCAAAAGATCTAGAAAGACCAAAGCAGCTTTGAAAAAGAG--- 955
                                    ii  i i    vii     i  iii          i---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_6894333_68    956 CAAAGCTAGGAGAT--AG----CCTGATTTCAAGACTTCCTGTAATGCTA 999
                              i i ii  i-- v----  ii       i    v  ii  v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_6894333_68   1000 CAGTAATCAAGACAGTGTGGTATTG-CAAAAAGATGGACATATAAATCAA 1048
                                               i  -  v  i   i        i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_6894333_68   1049 TGGAACCAAATAGGGAATCCAGAAACAGATCCACACATAGATGCTCAATT 1098
                              ivi   v i  i        i i i   i    vv   v      
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_6894333_68   1099 GGTTTTTGACAGAGGTGCAAAGGGAATTCAATGGAGAAAGGATAGTCTTT 1148
                          i    i    ii     v   ivv         i     i         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_6894333_68   1149 TCAACAGATTGTAATGGAACAACTGGACATTCATGTGCAAATAAAATGAA 1198
                               i  v  iv   i         i ?i  ii      - i      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-AGAATGAA 449

  chr1_6894333_68   1199 CCTCAACCCATACCCCATACTGTATATAAAAATTAACTCAAAGTGGATCA 1248
                         vi vi    v    i  i  ii    i               i       
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_6894333_68   1249 TAGACCTAAGT-------TTAAATCTATAAGCCTTCTGGAAGAAAACATG 1291
                         ?        i -------i    v      iv  ii i           i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_6894333_68   1292 GGAGAAAGTTTTCATGACCTTGGGTTAG-CAGTGATTTATTAGATATGGC 1340
                           ? v  i i   i              -  i  i   v         i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_6894333_68   1341 ACCAATTGTGCAATCCATAAGAGACAAAACA------TCAGACTTCCTAG 1384
                              vv ii   v v i  i   v    i ------ ii      v vi
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_6894333_68   1385 AAATTAAAAAATCCTGTTCTTCAAAAGGTACTGTTTAGATAATGAAAAAA 1434
                                   v ii   v       i ii   i iv   v i      i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_6894333_68   1435 CAAGCCACAGACTGGGAGGAACC-TTTGTAAAACATACGTCTAATAAGGG 1483
                            v       v      i  vi-    i   v    ii   i       
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_6894333_68   1484 A------TCCATAATGTATGAAGAACTTTAAAACCTT-----TAAAAACT 1522
                          ------    v   i   i       i v v v  i-----      vv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_6894333_68   1523 TTAAAACAACCCAATTTAAAAATGGGCAAGAGAGTTCTCTAGACATCTT- 1571
                         i--   i         ?            ii  v  vvv       i i-
  L1M4_orf2#LINE/    800 C--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_6894333_68   1572 ------AGGATACACAGATGGCAACTAAGCACATGAAGA-ATGTTCAACA 1614
                         ------ i    i   i     v v            i -   i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_6894333_68   1615 GCGTTATTCAT 1625
                         v i????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.05 (129 / 63)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.33 (78 / 18)  


1770 20.59 3.78 5.46  chr1_6926571_6928863.rev      502   977 (1316)    L1M4_orf2#LINE/L1       86   553 (355)  

  chr1_6926571_69    502 CAATCCCAATCAAAATCCCAGCAGGCTTTGTGCTGGAAACTGACA-GCCA 550
                                v              v v    v vvii    i     -  ii
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chr1_6926571_69    551 ATTCTAAAATCCATATGGAAATGCAAAGGACCTCGAGTGGCCAGAACAA- 599
                           i       i               i     iv  i i    i     -
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_6926571_69    600 CTTGAACAAGAA---TAAAGTTGCAGAGCTAACACGACTTAGATTCACAG 646
                               v     ---i       v  ii  v    --------   v  -
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC--------TTCCCA- 226

  chr1_6926571_69    647 GATTTCAAGACTTGTTATACAGCCACACTAGTCAAGACAGTGGGGTATTG 696
                         -       i    ii  i v   i   v  i           v    i  
  L1M4_orf2#LINE/    227 -ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_6926571_69    697 GCTTAAAGACAGACCACCGGATCAATT-AACAGAACTGAG--TCCAGAAA 743
                           v   i  i    vvvii       v-  i    i    --        
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_6926571_69    744 TAGACCTTCATATATATGGATAAATGATTTCTTACAAAGGGGCAAAATGC 793
                           i   ivi i  v     vi  v      iiv    i  v  v  i-i 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG-AC 374

  chr1_6926571_69    794 AATTCAGTGGAGAAAGAGGAGTCTTTTCCACAAATAGTGCTGAAATAATT 843
                         v     i   i      iv         v      i      ii i  i 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_6926571_69    844 GGATGTCTACGTGCAAAAAAAAAAAAAATGAAAAACGAACCTCAACCCAT 893
                             i? i  i       i  -------    i-------i vi    v 
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAA-------TGAAG-------TTGGACCCCT 460

  chr1_6926571_69    894 ACCTCACACCATATGCT----TTAACTGAAAATAGACTATAGGCCTAAAT 939
                                       i v----      v     i  ii ?  i       
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_6926571_69    940 TT------TAAAATCTATAAAATTCTGAGACGAAAACATAGGAG 977
                         v ------     -        i   v   v           ? 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACATAGGNG 553

Transitions / transversions = 1.64 (59 / 36)
Gap_init rate = 0.03 (13 / 468), avg. gap size = 3.38 (44 / 13)  

 235 21.67 0.00 3.33  chr1_6926571_6928863.rev     1255  1314 (979)    L1M4_orf2#LINE/L1      537   594 (314)  

  chr1_6926571_69   1255 AGAAACGAAAACACAGGAGAAAATATTTGTGACTTTGCATTAGCTAAAGA 1304
                             --       i   ? v    v  i     i   vi    vi  v i
  L1M4_orf2#LINE/    537 AGAA--GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_6926571_69   1305 TTGCTTAGAT 1314
                           v       
  L1M4_orf2#LINE/    585 TTTCTTAGAT 594

Transitions / transversions = 1.00 (6 / 6)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 2.00 (2 / 1)  

1189 17.91 5.07 5.67  chr1_6926571_6928863.rev     1468  1802 (491)    L1M4_orf2#LINE/L1      576   908 (0)  

  chr1_6926571_69   1468 AGATGATGATTGCTTAGATACAACACCATGAGCATGATCCCTAAAAACAG 1517
                           iii   i  v        ii      vi    ii v ------    i
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC------AACAA 619

  chr1_6926571_69   1518 AAAAAAAAAAGATTTAAAAAAACTG-ACATTATCATAATTAA---CTTCT 1563
                           i      -----  i v   i  -  v i    v      ---   i 
  L1M4_orf2#LINE/    620 AAGAAAAAA-----TAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_6926571_69   1564 GTTCTTCAAAAGATACTGTTAAGAGGATGAAAAGACAAATCACAGACTGG 1613
                           v       i  i   i i    iii           vi      v   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_6926571_69   1614 AAGAAAATCTCTGCAAAGCATATATCTGATAAAGAACTT-TATCTAGAAT 1662
                         i       v i      v              i i    -    i     
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_6926571_69   1663 ATATATAAAGAACTCTCAAAAC--AATAATAAGAACACAG----CCCGAC 1706
                              --         i v   --        i  v   i----   i -
  L1M4_orf2#LINE/    765 ATATA--AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA- 811

  chr1_6926571_69   1707 TTTTTTAAA---GGACAAAAGATTTGAATAGACACTTCACTAAAGAAGAT 1753
                         ---  ?   ---  i    i              i   v i         
  L1M4_orf2#LINE/    812 ---TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_6926571_69   1754 ACATGGGTATGGC---TAAATGCAGGTAAAGATGCTCAACATCATTATTT 1800
                          i iii--     ---   iii  v v                 ??????
  L1M4_orf2#LINE/    859 ATACAA--ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_6926571_69   1801 AC 1802
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.69 (43 / 16)
Gap_init rate = 0.04 (12 / 333), avg. gap size = 3.00 (36 / 12)  


3948 15.13 2.52 0.28  chr1_6940404_6942895.rev     1288  2001 (491)    L1M4_orf2#LINE/L1      179   908 (0)  

  chr1_6940404_69   1288 AAACAATTTTGAAAAAGCGAAAAGAAGTTGGAAGACTCATAGTTCTCAAT 1337
                                i         vii  vi        i      i v   i    
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_6940404_69   1338 TTCAAAACTTACTACCAAGCTATAGTAATCATGACAGTGTGGTACGGGCA 1387
                                        v      i        v             v    
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_6940404_69   1388 TAAGGGTGGACATACAGATCACTG-CACAGAGATAGAGAGTTCAGAAGTT 1436
                              i i      i      v  -v i   -  v      i     i v
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGA-ATTGAGAGTCCAGAAATA 327

  chr1_6940404_69   1437 AACCCTCACACTTATGGCCAATTGATTTACAAAAAGGATACCAAGATAAT 1486
                              vi   i      i          v i v    i i      iv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_6940404_69   1487 TCAATGGGGGAAAATAGAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 1536
                                  i  i - v                                 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_6940404_69   1537 ATGTCCACATGCAAAAGAATGGAGTTAGATCCCTCCCTCACACTGTATAC 1586
                           i?                 i    i  i    v        ii     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_6940404_69   1587 AAAAATTAACTCAAAATAAATCAAAGACCTAAGCGTCAGAGCTACAGCTA 1636
                                          ii    ?        ii  v       v i   
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_6940404_69   1637 CAAAACTCTTAGACAAAAACATAGAAGTAAATCTTTATGACCTTGGATTA 1686
                         i            vi         i?         ii         i   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_6940404_69   1687 AGCAATGGTTTCTTAGTTATAACACCAAAAGCACAAACAGCAAAAGAAAA 1736
                         i               v   i               i  i          
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_6940404_69   1737 ACTA----AACGGAACATCATCAAAATGTAAAACTTTTGTGCTTCAAAGG 1782
                          v  ----  iv i  v          vv                     
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_6940404_69   1783 ACACGGTGAAGGAAGTGAAAAGACAACCCATAGAACAGGACAAAATATTT 1832
                             vi v   i                  i    ii   v         
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_6940404_69   1833 GCAAATCCTATCTCTGACAAGGGATCTGTACCTAGAATATATAAAGAACT 1882
                                v   v     i      ii    i i                 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_6940404_69   1883 CTCACAACACAATGATAAAAAGACAAATA---CTATTTTAAAATTGGCAA 1929
                           i     v    i               --- v   ?v     v     
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_6940404_69   1930 AGAATCT-AACAGACATTTCCCCAAAGAAGATACACAAAT---------A 1969
                           i  i -  i         i            i      ---------i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_6940404_69   1970 TATATAAAAAGATATGCAACATCATTAATCAT 2001
                         i i  i       iiv        ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (69 / 35)
Gap_init rate = 0.01 (7 / 730), avg. gap size = 2.86 (20 / 7)  


 774 16.85 2.17 5.43  chr1_7124589_7127091.rev      502   685 (1818)    L1M4_orf2#LINE/L1       34   211 (697)  

  chr1_7124589_71    502 CTTAATATTATTAAGATGTCAATTCTCCCCAAATTCACCTATACATTCAA 551
                                  i        v    v           v i   i v      
  L1M4_orf2#LINE/     34 CTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAA 83

  chr1_7124589_71    552 AGCAATCCTAATTAAAATCCTATCAGGCTTGTT-GCAGAAATTGATAAGC 600
                         v       iv  i       i v v v   v  -           i    
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC 133

  chr1_7124589_71    601 TGATGTTAAAATTTCTAAAATGTATATGGAAATGAAAAATGACTTAGAAA 650
                             ---------i       vi           v  ii-   ii    v
  L1M4_orf2#LINE/    134 TGAT---------CCTAAAATTCATATGGAAATGCAAGG-GACCCAGAAT 173

  chr1_7124589_71    651 AGCCAAAATAATTGTGAAAATGAA---CAAAATTGGAG 685
                                 i   iv      v   ---    i      
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

Transitions / transversions = 1.07 (16 / 15)
Gap_init rate = 0.02 (4 / 178), avg. gap size = 3.50 (14 / 4)  

1555 24.33 3.23 7.41  chr1_7124589_7127091.rev      994  1519 (984)    L1M4_orf2#LINE/L1      201   704 (204)  

  chr1_7124589_71    994 CAAAATTGGAATATGTACACC-CCTGATTTGAATACATGTTGTAAAGCTA 1042
                             i     iv ivi    i-  ii    v  v  v ii ii       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_7124589_71   1043 TATTAAT-AA---AGTATGATATTGGCATAAGTAGAGACATACGGAAAAA 1088
                         i v    -  ---   i  i  i         v v       ii  vv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_7124589_71   1089 TGAAACAGGATAGAAAGTTTAGGAAAAGACTCACACATACATGGTGAATT 1138
                           i  i  i  v  i   ii  i  v i  i  i    vi     v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_7124589_71   1139 GGTTTTCAGTGAAGGGGCCAAGGCAATTCAATGGAAAAAGAATAATCATT 1188
                          i     iiii i  v      i v         ii        i  v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_7124589_71   1189 TCAACAAATAGTGCAGGAATAATCAGGTAGCCACA-GCAAGAAAAAAAAA 1237
                                  i    v  i i  iii i  ?     -    ----------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA---------- 440

  chr1_7124589_71   1238 AAAAAAAGAAAAGACGATCCTTGACCCTCATCTCACACCACACATAAAAA 1287
                         -  i  v   i--------i v     ii i         i i i     
  L1M4_orf2#LINE/    441 -AAGAATGAAG--------TTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_7124589_71   1288 CTAACTTGAAACT-ATGATAGACCTGACTATAAGAGGTAA--CTACTAAA 1334
                         i     ii   iv-  v ?      i v i      v   --   -    
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA-TAAA 530

  chr1_7124589_71   1335 CTTCTT----GTAAACCTAGGAGAAAATCTTAATGATCTTGGATTTGACA 1380
                         vi    ---- v    v    ? v       vi   i     i  v i  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_7124589_71   1381 AGGATTTCTTCCTTTATTAACTTCTTAAATATGATGCCAAAAGCATGAAC 1430
                          v i      ---------------- i      ii         ii i 
  L1M4_orf2#LINE/    581 ATGGTTTCTT----------------AGATATGACACCAAAAGCACAAGC 614

  chr1_7124589_71   1431 CAT----GAAAAAATAGTCAACAAATTTTACTTCACCGAAATTTAAAACC 1476
                         v i----          --- i     vv      i i     v     i
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAG---ATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_7124589_71   1477 TTTTCTCTTCAAATGACGCTGTTATAAAAATGAAAAGGCGGCC 1519
                            viv       v   i  i i vi   i       i ii  
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

Transitions / transversions = 2.21 (86 / 39)
Gap_init rate = 0.03 (13 / 504), avg. gap size = 4.31 (56 / 13)  

 515 22.73 6.82 5.00  chr1_7124589_7127091.rev     1805  2024 (479)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_7124589_71   1805 AAGAAAA-GAAAAGGCAAGGAACAAACTC--AGAAAATATCTGTAAAATA 1851
                               i-      i   vvv   i v v--         i  i   vi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_7124589_71   1852 TATATCCAACAAAGAATTCATATCTAAAATATGCAAAGAACTTTTACAAC 1901
                               ii i  i i i ii    i i     ii        i       
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_7124589_71   1902 TCAGTAATAGGAATACA--T--TCCAATTTTTTAAAGA--GGCAAAAGAT 1945
                            i     ii  v   -- --i      ?---   i --      i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTW---AAAAATGGGCAAAGGAT 831

  chr1_7124589_71   1946 TGGAATATGTACTTCATTGCAGAAGAGAGATATATGGATAGCAAACAGAC 1995
                          v     vii i   -- v  -    -       iii  i  v  i ii 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTC--TCCA-AAGA-AGATATACAAATGGCCAATAAGC 877

  chr1_7124589_71   1996 AAACAGTTGGAGAGAT------TATCAGCTCTTGA 2024
                          --  --  i i    ------i    ????????
  L1M4_orf2#LINE/    878 A--CA--TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.45 (38 / 11)
Gap_init rate = 0.05 (12 / 224), avg. gap size = 2.17 (26 / 12)  


 524 25.61 11.42 10.44  chr1_7160386_7165917.rev     3869  4481 (1051)    L1M4_orf2#LINE/L1       29   647 (261)  

  chr1_7160386_71   3869 GAAGACTCAATATCCTAAATAGGTCAATTCTCACCAAACTGA----CAGA 3914
                                i     iv v  v v v    v   v     i   ----    
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chr1_7160386_71   3915 TTTAATGTAATTCCAATCAAAATCTC-----CCCATAGGAATTTGAGGAT 3959
                           i  i i   i  v         i -----  iv -----    vi  v
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT-----TTTGCAGAA 123

  chr1_7160386_71   3960 TTTGACAAGATTATCTTCCGTAATGTTCAT---GAAACAGCAAAGG-CCA 4005
                         v        v v   i ----  vi     ---    i-    i  -  v
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCT----AAAATTCATATGGAAAT-GCAAGGGACCC 168

  chr1_7160386_71   4006 AGAATAGGTGAAATGCAGAACATATATATAGTGGTAGGAGGGAGAGGAGA 4055
                                v-------  i    ---  v --  -- ii i i   iv i 
  L1M4_orf2#LINE/    169 AGAATAGC-------CAAAACA---ATCT--TG--AAAAAGAAGAACAAA 204

  chr1_7160386_71   4056 ATGTGA----TCA-ACCACC---TGTGAAGACTTATTTCCAAGCTACAGT 4097
                         i vv  ----   -  iv  --- v v  i     i v v          
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_7160386_71   4098 GAACTACAGCAACTGAACTGATGGTGTG---CTGAGACAAGAATAGACAA 4144
                         i -- ----   -------  ii     ---   iv i   i       v
  L1M4_orf2#LINE/    255 AA--T----CAA-------GACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_7160386_71   4145 ACTGACGACTACAGTG--ATGGCATAAGGGGCCCAGAAACAGATCTACGC 4192
                          iv  i-----  i  --  i v  vii i i       i i i i ii 
  L1M4_orf2#LINE/    292 ATAGAT-----CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_7160386_71   4193 ACAGGCAGCTACTTGACATAAGACAGGAATCATCTATGGACAGACTTGAC 4242
                          ivviii ii v    iv vv    i ii v-- i -----    ---- 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTG--CCA-----AGAC----C 375

  chr1_7160386_71   4243 ATATGCACATCACTGGGGAAAGGAT-GACTCATC--CAA----TGCATGG 4285
                           -------   v         i  - v  iv  --   ----   -   
  L1M4_orf2#LINE/    376 AT-------TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC-TGG 417

  chr1_7160386_71   4286 GACACCTC--TTTCCAACACGGAAAAAAAGGAGAATT---TTCCTAC--- 4327
                             v  v-- v?   -  i v    i  v  - i  ---ii     ---
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCA-CATGCAAAAGAATGA-AGTTGGACCCCTACCTC 465

  chr1_7160386_71   4328 ---------ACAAAA-TGAATTTTAGATAGATTA-AAACTTGGATGTGAA 4366
                         ---------      - v  i iv i  i   i - i  i ii    i i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_7160386_71   4367 AGCCAAACC----AAACTCCTAAACTA---TTTAGAAGATAATATTTATG 4409
                            i   v ----      i  i vv ---iv   i? vv   v  ii  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_7160386_71   4410 ------GATTAGGATAAAGATTTAGTAAACAAGA-ACAAGAAGCACTAAC 4452
                         ------ i     -i  v i   vv  i i v  -  v i      v i 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGG-CAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_7160386_71   4453 A-TAAAAAATAAAAT---TAAATTAAACTGCAT 4481
                          -i    i v     ---      ii   v   
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

Transitions / transversions = 1.46 (92 / 63)
Gap_init rate = 0.07 (42 / 619), avg. gap size = 3.19 (134 / 42)  

 360 25.00 11.40 4.41  chr1_7160386_7165917.rev     4770  5041 (491)    L1M4_orf2#LINE/L1      618   908 (0)  

  chr1_7160386_71   4770 AAAAAAAAAAA-----AAA----ACTGCATCAAAACTAAGAATTTCTACC 4810
                             i      -----   ----   v        i   i  i  i iiv
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_7160386_71   4811 CACCAA--GACACCATTAGGAACACTTTCTTAAAAG------TATCAAAA 4852
                          vi   --     i  i i   vi----- v     ------i -  i  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAG-----TGAAAAGACAACCCA-CAGAA 711

  chr1_7160386_71   4853 TGA-AGAAAACAGTTGTAATGCATAGAGCAAACTCAAGATCAGGGTCTAG 4901
                           i-      i v   i  vv    v v vi ivvii  iiv vi  i  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_7160386_71   4902 AAAATATTAAGAATCCCTGCAAATCAATCAATAACTAAAAGACAGACAAT 4951
                           v    v     ii i i   v     -     ---       i i  i
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAAT-AATAA---AAAGACAAATAAC 807

  chr1_7160386_71   4952 CCAAT---------AGCAA-GGAAAAGAATGGGCAATTCAC---AGAAGA 4988
                              ---------i    -   vvv    i i  v   v ---      
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_7160386_71   4989 AACCCAAATGGCCAATAACCCTCTATGAGAAGAAGCTCAGCCTCACTGTA 5038
                         v iv              v vi--    i    v     i v   ?????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCAC--ATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_7160386_71   5039 GCA 5041
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.34 (39 / 29)
Gap_init rate = 0.04 (13 / 291), avg. gap size = 3.31 (43 / 13)  


 966 34.46 3.01 1.13  chr1_7173041_7177672     3012  3542 (1090)    L1M4_orf2#LINE/L1        1   541 (367)  

  chr1_7173041_71   3012 TAGAAAGACATCCCTTGATTTTGGATGGATTGATTTAACATCATAAAAA- 3060
                          i      i     v  v iv     v ivv  i    i  ii v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_7173041_71   3061 ---AGTTTGTCCCAAGTTAATTTATGAATTTAACATAATCCCAGAGAAAG 3107
                         --- i vivi     i  i  i  iii   i   ii      vivv   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_7173041_71   3108 TATCAGTAAGTTTTTTTATGGAGCTACACAA-CTGATACTTAAGTTCATA 3156
                          vi   ivivi      iii  iv vv    -     v  v  i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_7173041_71   3157 TGAAAAGACAAAC-ATGCAG--TAACCACGATAACCCTGCAAATTAAGAA 3203
                           i   vi   iv- iv   --  i   vi i  i i  v   vv     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_7173041_71   3204 CTAC-TGGGAGGAATAGCTCTACCAAACATTAAAATGAACTATAAAGCCT 3252
                          v v- v      v vi v  v  v  iv i    ivv    i     iv
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_7173041_71   3253 CTATAATTAAAACAGTATGGTGAAATTGATGCATGAATATTCAAAATAG- 3301
                          vi    i  i     i    --- i  iiii v i   vv  v -   -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGT---ACTGGCATAAGGATAGACATA-TAGA 296

  chr1_7173041_71   3302 -CAGTAGAATTGAATAGAAAGTCTTGAAATAGACCC-CAAGTTCATATGG 3349
                         -  i i    v    v  i    iv      i    -i vi  --     
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGG 344

  chr1_7173041_71   3350 AAATTTAGTATATGACAAAGGTGGTATCTCAAATCACTGGAGCAGAGATT 3399
                         vv v  ii v vi     i    vi vvv v v   v   i v iii  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_7173041_71   3400 ACCTTTTCAATACATTGTTCCGGGATGACCAGGCAGCCTT-TGGAAGAAG 3448
                         ii        i v  v  v i    ii  ii ii ?  vi-  v  i ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_7173041_71   3449 ATAAAATTA-ATGCATAAGTTCCAGTATACACAAGAAA-AACTCCAAATG 3496
                           i  i  i- iv v  vv iv  vi   i    i  v-     v     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_7173041_71   3497 GATTG-AGATCTAAATATAAAAGGTGAAATCATAAAAGTACTAGAAG 3542
                            ii-   i      i   i  v i   ii      v vi      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

Transitions / transversions = 1.33 (104 / 78)
Gap_init rate = 0.03 (14 / 541), avg. gap size = 1.57 (22 / 14)  

 561 26.96 12.17 1.74  chr1_7173041_7177672     3795  4139 (493)    L1M4_orf2#LINE/L1      528   908 (0)  

  chr1_7173041_71   3795 AAAACACT-AGAAGAAAACATGGGTG-AGCTTTTCTGTAACAT-GGATGT 3841
                              v  -            i  ? - iv i   -  i  v -  i - 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGGGT-T 575

  chr1_7173041_71   3842 AAGAAAAGGTTTTCTAACAATGACTCAAAATCCAGATGTAGTTAAAGAAA 3891
                          i v  v     ii  ivv     v v   vv  v v i iiv       
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_7173041_71   3892 AGATTGACAAGTTTGATTACA--AAAGTCCA---------TGAT---AAG 3927
                          i  v  i  i  v  i v  --   i iv ---------  v ---   
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_7173041_71   3928 CACA--GTCAAAA---TGCAAATGAC--TTTGTAG-----GAGAAGGTAT 3965
                         v   --i    i ---  v   -   --iiiii  -----     ii   
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAA-GACAACCCACAGAATGGGAGAAAATAT 724

  chr1_7173041_71   3966 TTGCAG--CATATATCAGAAGTAAAGGGTTAATATCCCTGATATGTAAAG 4013
                              i--        v  --   i  ii vi     vvi    i     
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGA--TAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_7173041_71   4014 AGCTGTTA----TCATTGAGGAAGGGGTA-----CTTGATAGAAAAAATG 4054
                          i  v   ----   v i vi  ii ii ----- iii  -v?       
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT-TWAAAAATG 821

  chr1_7173041_71   4055 GGCACAAGACATGAA-AGATAATTC-ACATCAAGGATATACAAATGTCCT 4102
                             v i  iv    -   i v   -v  vvi i            v  v
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_7173041_71   4103 TTAAACAAACGAAAAGATGTTCAACATCACTCATAAT 4139
                         v   i  v i         i         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (52 / 39)
Gap_init rate = 0.05 (20 / 381), avg. gap size = 2.40 (48 / 20)  


 843 24.75 6.64 6.04  chr1_7195485_7200515.rev       75   571 (4460)    L1M4_orf2#LINE/L1      232   731 (177)  

  chr1_7195485_72     75 AAAA--TACTACAAAGCCTTCATAATTAAAACAGTGTA-TACTGGTGTAT 121
                             --           ivivi    i  i       i-      ii  v
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_7195485_72    122 GAGTTGACAGA--GA--AGTGGAGTAGAA--GA-AGTCCAGATATGC-CC 163
                          ii v    v --  -- i    i     --  -        v  iv-  
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_7195485_72    164 CAACCACATTT--GGAAACTCAGTATACGATAAAGGTGGCCTCTAAAA-- 209
                           --i      --  vv v iii v v   i  i    ---- i  i --
  L1M4_orf2#LINE/    332 CA--TACATTTATGGTCAATTGATTTTCGACAAGGGTG----CCAAGACC 375

  chr1_7195485_72    210 --TTACTGGAGAAAACAGATGTTTTTAAATAAATGCTGCTGGAACAACTG 257
                         -- i v   i    iv v vvi    v  i     v      i       
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_7195485_72    258 AATAACAAT-TTTAAAA-AATTAAGT----CCAGTATCTCCTACCAAGCA 301
                         i   ? v i- vi    -   v    ----  vv  i   vi    vii 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_7195485_72    302 CAAGAATGAATTCTAAATGAATCAAAGAT-TAAATGTAAGAAAAAAAATG 350
                            i   v  i  v     i    ?   i-           iv----- i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-----TA 520

  chr1_7195485_72    351 AAACCATACGAGTACTAGAAGAAAAT-TGGGT-TAATTTCTTTTTGATCT 398
                             i   vi v vi          i- i  ?-   v -   iv   i  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCT 569

  chr1_7195485_72    399 -GGATGTAGGAAGAGGTTTTCTTAC-TATGACTCAAAAATACACACACAG 446
                         -  i -    v iv     -    v-      v v    -i    vi  i
  L1M4_orf2#LINE/    570 TGGGT-TAGGCAATGGTTT-CTTAGATATGACACCAAAA-GCACAAGCAA 616

  chr1_7195485_72    447 TAAAAGAAAAGATTGATGAACAGGACTACA-CAGAAATAAAAAGTTTT-- 493
                         i         i  v   i  iv     v  -  i  v      v    --
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_7195485_72    494 --TTCACAGAAGACACATCTGATATTCAAAGACACAAAAAGGTTGAAAGT 541
                         --    v  --     ------   -   ii viii     ii---  vi
  L1M4_orf2#LINE/    667 GCTTCAAAG--GACAC------TAT-CAAGAAAGTGAAAAGAC---AACC 704

  chr1_7195485_72    542 AAAAGCATGAAAATAAATATGTCATGCAAA 571
                         v v  v   ii iv      - --      
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATAT-T--TGCAAA 731

Transitions / transversions = 1.31 (68 / 52)
Gap_init rate = 0.06 (32 / 500), avg. gap size = 1.97 (63 / 32)  

4578 16.96 1.87 1.87  chr1_7195485_7200515.rev     3658  4565 (466)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_7195485_72   3658 TGGAAAAAC-TTCAATGTTCATGGGTCAGAAAACTTAACATCGTTAAGAT 3706
                               i i- i v          i ii   i      i  i        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_7195485_72   3707 ATCAGTACTCTCCAAACTGCTCTACAGAGTCAATTCAATCTCTGTGAGAA 3756
                         iv  i     i     i  v        v    iv     i  i v i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_7195485_72   3757 TTCCAGCTGACTTCTTTGTAGATATTGTCAAGCTGATTCTAAAATTCATA 3806
                          i       v   i    i   v    v         i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_7195485_72   3807 TGAAACTGTAAGAGACACAGAATAGCCAAAACAATACTAAGAAA--AGAA 3854
                           i  v  i   i   v                  vi i i   --    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_7195485_72   3855 CAAAGTAGGAGGATTCACACTTTCTGAATTCAAAATTTACTACAAAGCAA 3904
                               v      i        i ii v       i            v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_7195485_72   3905 TGGTAATCAAGACAATGTGGTACTAGCACAAAGG-AGACGTACAGATCAA 3953
                         ii            i         i   i  i i-    i  i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_7195485_72   3954 TAGAATAGAAATGACAGCCTAGAAATAAACCCATACAGCTGTCATCAATT 4003
                          i        v   v  i i                 vi i vi      
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_7195485_72   4004 GACTTTTGACAATGGCACCAAAACCATTCAACTGGGAAAAAAATAGTCTT 4053
                           i   i     v  ii    i         -    i   i         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTT 399

  chr1_7195485_72   4054 TTCAACAAATGAAGCTGGGACAACTAGCTAGTCACATGCAAAAGAATGAA 4103
                                    iv            i v  ?i                  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_7195485_72   4104 ATTGAATCCTTATCTCACACCATATACAAAAATAAACTCAAAACAGATGG 4153
                         i   i i  i  i                    v         ----   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA----TGG 495

  chr1_7195485_72   4154 ATCAAAGAGCTAAATGAAAGAGTTAAAACTA--AAATTCTTAAAAGAAAA 4201
                             ?   v       v     i        --   i     i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_7195485_72   4202 CATAGGTATAAACATTCACGGCCTTGGATT-GGCAAAGCATTTTTTAGAT 4250
                               ?i    iv   ii i      i  -     v -i   i      
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTAGAT 594

  chr1_7195485_72   4251 ATGACATCAAAAGCATGAACAACAAAATAAAAAATAGACACATGGGGCTT 4300
                               i        ii i        v          i v  v  i   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_7195485_72   4301 CTTCAGAACACAGAACTTTTGTGCTTCAAAGGACACCA--AAAAAATTGA 4348
                          v   i  ivv i                       i --  i   v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_7195485_72   4349 AACTGTGGA--------AGAATAGGATAAAATATTTGCAAATTATATATC 4390
                           ----i  --------     i   v               i       
  L1M4_orf2#LINE/    695 AA----AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_7195485_72   4391 TGATAAAGAACTTATGTCTAGAATATATAAAGAACTCTTACAACTTAATA 4440
                               i i    i i  i                          i    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_7195485_72   4441 ATAAAAAGGACAGGTAACCCAATTTAAAAATAGGCAAAGCCTCTGAATAG 4490
                                 -   ii          ?      i       vv i       
  L1M4_orf2#LINE/    791 ATAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_7195485_72   4491 ACATTTCTCTAAGGAAGAAATACAAATGGAAAATATACAAATATACACAC 4540
                                  i  i     v          vv    vi  ------  iiv
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA------CATGA 883

  chr1_7195485_72   4541 AAAGACACTTGATATTATTAGCTAT 4565
                              ii  ii i  i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.57 (108 / 42)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.62 (34 / 13)  


3740 18.42 3.84 4.28  chr1_7234665_7237030      962  1873 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_7234665_72    962 TAGAAAGACATTCCATGTTCTGCAATTGGAAGTGGTTGGAAGACTCAATA 1011
                          i      i  i        ----  -   -----          i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTC----AT-GGA-----TTGGAAGACTTAATA 40

  chr1_7234665_72   1012 TTGTTAAGATGGCAATTCTCTCAAAATTGATTTCTAGATTCAGTACAACT 1061
                                         v   i v        i vi       iii   ii
  L1M4_orf2#LINE/     41 TTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chr1_7234665_72   1062 CCAATTAAAATTCTAGCAGCCTTTTTTCCTCAGAAATTGTCAAGCTAACC 1111
                           v  i     i i   v         v --        v      i i 
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGC--AGAAATTGACAAGCTGATC 138

  chr1_7234665_72   1112 CTAAAATATATATGGAAATACAAAGGACTTAAAATAGCCAAAACAGTTTT 1161
                                vi          i   i    ii i             i i  
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_7234665_72   1162 GAAAAAGAAGAACAAAGTTGGAGGACTTATAGTCCCGGATTTCAAAACTT 1211
                                                    i i v i  vi            
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_7234665_72   1212 ATTATAAAGCTGCTACAATCAAGATAG-ATAGTATTGGCATAAAAATAGA 1260
                          i  i      i vii        i  -i i   i        ii     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_7234665_72   1261 CA---------ATGGAACAGAAGAGAAAGTTCAGAAATAAAATCATATGT 1301
                           ---------      i    vv  i   i          vi    ii 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_7234665_72   1302 TTATGGTCAATTTATTTTCAACAAAGGTGCAAAAGCAATTCAGTGGAGTT 1351
                                     v      i    i     v  ii v     i   ----
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG---- 384

  chr1_7234665_72   1352 GGGGGTGGAGAAAATAGGCTGTTTAAATTTAAAAAATGGTGCTGGGACAA 1401
                         ------   i i     v  -   v  i-----                 
  L1M4_orf2#LINE/    385 ------GGAAAGAATAGTCT-TTTCAAC-----AAATGGTGCTGGGACAA 422

  chr1_7234665_72   1402 TTGGATATTCA-GTG-ACAAAAATAAACTTG-ACCTTTATCTCACACCAT 1448
                         i      ?i  -i  - v  i   i  v   -   ii  i          
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_7234665_72   1449 ATGCAAAAATTCACTCAAAATGGATCAT-GACCTAAATGCAAGAGCTAAA 1497
                           i        v               ?-          i          
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_7234665_72   1498 GATATAAAAGATATAGAAGAAGACATAAG---ACATGTTTATTACCTTGG 1544
                         iv       vviv        i     i --- v  v  ii v       
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_7234665_72   1545 GTTCGGCAAAGCACCCTTAGAT--GAGACTAA--GTACTATTCATAAAAG 1590
                            v     v vvii       --  v  i  -- i  v viv i     
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_7234665_72   1591 AAAAAATTGATAAATTGGAACTTACCAAAGGGGAAAATTTTTACTCTTTT 1640
                                v           vi i i    ivvi    i    iiv   iv
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_7234665_72   1641 AAAGAAACCATCAAGCCATTAAG-GAAAAGAGGGACAAGTTATGGATTGG 1689
                           i  v  i      -- --   -       ----   vii ii  v   
  L1M4_orf2#LINE/    673 AAGGACACTATCAAG--A--AAGTGAAAAGA----CAACCCACAGAATGG 714

  chr1_7234665_72   1690 GAGAAAGTATTTGCAAATCATATGTCTGATAAAGGACTTGTATCTAGATT 1739
                               i                i        i           i   --
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA-- 762

  chr1_7234665_72   1740 ATATGTAAAGAGCTCTTAAAACTCAAAAAACAAGAAGGCAA----CTCAA 1785
                             i      i      v       v  -i  i   i   ---- i   
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAA 811

  chr1_7234665_72   1786 TT-AAAAATAGGCAAGAGATTCAAATAGA------TTCAATG--TCTATC 1826
                           -      i     ii    ii      ------ i   v --vv   v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_7234665_72   1827 TGAATGGCTAACAAGGACATGAAAAGGTACTCAACATCATTAGTTAT 1873
                         ii      i  i   v          i i          ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (113 / 53)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.85 (74 / 26)  

 332 33.49 5.96 2.29  chr1_7234665_7237030     2080  2297 (69)  C L1M4_orf2#LINE/L1   (289)   619   394  

C chr1_7234665_72   2297 AGT-TTTTCA-TAAGTGAAATTGGGGGACCTAGA-AGGCACATGGAAAAT 2251
                            -      -i  i  ivii    iv v  i  - ?v      v    v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

C chr1_7234665_72   2250 ACCAAAATGGGTTTACCCCT----CACATCATACAGCAGCACTGATGCTA 2205
                          vii  i v  ---      ----    i    i vv iv i i iv v 
  L1M4_orf2#LINE/    444 AATGAAGTTGG---ACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

C chr1_7234665_72   2204 AACAG-TCAGAGATTTCAATGTAATAAATAAAATCATAC--CTACCCTAC 2158
                           ii -   ?   ii v       v iv     ii   v--  -- i  v
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT--CTTAG 538

C chr1_7234665_72   2157 AAGAAAATACAGGTGAATTTCTCTATAACCTGAAAGTGGAGAAAACTTTC 2108
                                i i   ? v vv   iii i    viiiv i iv  viv    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

C chr1_7234665_72   2107 TTAACCATGAT--TGAAAACCCA-GCAACAA 2080
                            ivi    i--ii   i v  -       
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAA 619

Transitions / transversions = 1.50 (42 / 28)
Gap_init rate = 0.04 (10 / 226), avg. gap size = 1.80 (18 / 10)  


2265 26.60 6.04 2.67  chr1_7299741_7304098.rev     3008  3868 (490)    L1M4_orf2#LINE/L1       19   908 (0)  

  chr1_7299741_73   3008 TCACATATTGGAAAACTCAGCATAGGAAAGGTTTCCAGTTTCCCCCAAAG 3057
                            iiv       i   i ii  v vv   i vv - i vii       v
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGC-AATACTCCCCAAAT 67

  chr1_7299741_73   3058 TGATCTATAGATGTAACACTATATCAATAAAAATTTCAGCAGGATTCTTT 3107
                                i    vi   i v  vi v  v     ii    v --iii   
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG--CCTTTT 115

  chr1_7299741_73   3108 TTGTAACTATAGACATACTGATTCAAAAATGTATACTGAAAGGCAAAGTA 3157
                            i ivv  v    vi     i v     vi   iv    v    i v 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_7299741_73   3158 ATTAGTATAGCCAAAACAATTTCTTAAAAGAAAACTAAATTTTGGGAAAT 3207
                         vii  v              i ivv       i vi   v  v i i v 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_7299741_73   3208 TTGACTAACCAATTTGAAGACCTA-TATAGACCTACAGTAATGAAAACAA 3256
                         ivv   vv       v  i  i  -  i i v          v  i   i
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_7299741_73   3257 TGTGGTATTGGTG-ATGTGATAGGCACAAAAATGAATAGAACACAA--GA 3303
                                i   ii- v -     i  i v i  v   i   i v  --  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAG-GATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_7299741_73   3304 GACATAATAGAAATAAACTC-CACAAATACAGACAATTGATTTTTGACAA 3352
                           -i v-i          i -i   vv  ii v           i     
  L1M4_orf2#LINE/    315 GA-GTC-CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_7299741_73   3353 AGGTGCAAAGGCAAATTCAATGGAGAAG--ATTTTTTTTTCAATAAGTGG 3400
                         i     v   i v -        i   i--  vv i       i  i   
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_7299741_73   3401 TATTAGAACAATAAGACATCTAAATGCAAACAAAAACAAAAAAACAGAGA 3450
                          ii i i    ivi  i ? i v       -- i  ii  i-----vv i
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAA--AGAATGAAG-----TTGG 454

  chr1_7299741_73   3451 ACCCTCAACCTAAGCCTCACACATTAGACAAAAGTTAGCTCAGAATGGAT 3500
                             -----   --        vv  v      i   i    i       
  L1M4_orf2#LINE/    455 ACCC-----CTA--CCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_7299741_73   3501 CCTAGCTCTAAGTGCAATATGTAAAATCATACACTTTTTAAAAGCGAACA 3550
                          v?  vi    i  i  v vv     ii   v vi i   i   vi    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_7299741_73   3551 TAGGAGAAAATATCTGTGACCTGGAGTTAAGCAAATATTTGCTAGACATA 3600
                             ? v    v ii       v i    i    vvi   vi    i  i
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_7299741_73   3601 AAACCAAAAACAGAATCCATAAAAGAAACAATCGCTAAATAGGACTTCAA 3650
                          v       i  v  v v i        v   v v     v        v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_7299741_73   3651 CGAAATTGTAAAACTTTT---CTTCTAGGAGACACTTTTCAGATAATGAA 3697
                          i     i-         ---    v i -      v iv   v i    
  L1M4_orf2#LINE/    648 CAAAATTA-AAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGAA 695

  chr1_7299741_73   3698 CAGACAAGTTACAGACTAGTTAAAAATATTGGCAAATCACATATCTGA-- 3745
                         v      vii     v i vvi        v        i        --
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_7299741_73   3746 --------------------------------------CTCAACAGCAAG 3757
                         --------------------------------------     i ii  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_7299741_73   3758 CAAACAAACAACCCAAT-AAATAATGGACAAAA-ATTTGGACAGATACTT 3805
                         v i     i        -?  v     i    i-     i i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_7299741_73   3806 CACTTAAGAGGATACAGAAATGGAAAATAAGCCCATGCAAAGTTGTTCAA 3855
                          v iv    i    i v      vv       v    v    v  i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_7299741_73   3856 CATCGTTAACCAT 3868
                             i????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (125 / 100)
Gap_init rate = 0.02 (21 / 890), avg. gap size = 3.57 (75 / 21)  


2012 26.85 1.30 0.93  chr1_7388267_7393432.rev     3386  3925 (1241)    L1M4_orf2#LINE/L1        1   542 (366)  

  chr1_7388267_73   3386 TGAAAAGATATCCCATATTCATGGATTGGAAGAATTGATATTGTTAAAAT 3435
                           i             i                v  i          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_7388267_73   3436 GTTCACATTACCCAAATCAATCTATAGGTTTGATGCAACCTGTATCAAAA 3485
                          viv i i v       ii     i  i  ii i    i iv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_7388267_73   3486 TACCAATAACATTGTTCATAGAAACAGATAAAACAATCAGGAAATTCATA 3535
                          v   iivi v  v  iii     iv  i  ivii   vvi         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_7388267_73   3536 TGGAACCATAAAAGACTCTGAATAGTGAAATCAATTTTGAGTAAAATGAA 3585
                              viii  ii   i v      iv   v    i    iv  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_7388267_73   3586 TAAAGCCAGAGGGTCCATCACATTACCTACCTTCAAAATATACAACAAAG 3635
                         i    iii    ii---     i v  i vi       iv   v      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGAC---TCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_7388267_73   3636 CTATAATAATCAAAACAGCATGGCACCACCATAAACACAGACATATAGAC 3685
                            i i       i    ii   i  iiv     iv i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_7388267_73   3686 GAATGGAACAGAATAGAGAACACAGAAATAAATCTGTGTACTTACAGGGA 3735
                         v       i     v    iiv          i ii ii i   ii vv 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_7388267_73   3736 ACCAATTTTCAACAAAGGCAACAATAATACACACTGGGGAAAGGGCAGTC 3785
                          iii      i    i  iiv   v vi iv  v         iii    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_7388267_73   3786 TTTTCAGTAAGTTTTGCTGGGAAAACTGGACATCTACATGCATAACAATG 3835
                               ii  i vv        v       i ? i       v  v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_7388267_73   3836 AAATTAGAGCC-TATCTCTCACCATACAAAAAAA------CAAAATGGAT 3878
                           i  i  v  -  i   v       i v     ------          
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_7388267_73   3879 TAAATATTCTTATATGTAAGAACTGAAACAATAAAACTACTAGAAGA 3925
                         i ? v -- i  v        i  i    v        vi       
  L1M4_orf2#LINE/    498 CAWAGA--CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

Transitions / transversions = 2.04 (96 / 47)
Gap_init rate = 0.01 (4 / 542), avg. gap size = 3.00 (12 / 4)  

1601 20.95 0.27 1.33  chr1_7388267_7393432.rev     4299  4675 (491)    L1M4_orf2#LINE/L1      536   908 (0)  

  chr1_7388267_73   4299 TACAAGAAAATATAGGGG-AAATGCTTCATGATATTGGTCTGGGTAAGGA 4347
                           v       i     ? -    -    i   iv    vi i  i  v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_7388267_73   4348 TTTTTTAAAAATAATACCTCAAAAGCATAGGCAACAAAAGGAACAATAGA 4397
                            i   i v  i i   --       i i          i  v      
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_7388267_73   4398 CAAATGGGATTACATCAAATTTAAAAAGCTTCTGCACAGCAAAGGAAACA 4447
                         i    v   i v       v       -   i  ii vv       v  v
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT 681

  chr1_7388267_73   4448 ATAAACAGAGTGAAAAGACAAGCTGCAGAATAGGAGAAAATATTTGCAAA 4497
                           v  v i             v ii      i                  
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_7388267_73   4498 CTGTGTATCTGACAAGGGCTTAATATCCAGAATGTATAAGGAACTCAAAT 4547
                         iii i       i     vi vi          i     i      vv i
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_7388267_73   4548 AACTCAGTAGCAAGAAAACAAATAATCTGATTAAAAAGTGGGCAAAAAAC 4597
                               i  ii  i  i        i ii   ?    i        ii i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_7388267_73   4598 CTGAATAGACATTTCTCAAAAGACAGCATACAAATGGTCAACAAGTACAT 4647
                         i                v     viii          i   i   i    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_7388267_73   4648 TTTAAAAATGCTCAACATCACTAATCAT 4675
                         -vv   i             ????????
  L1M4_orf2#LINE/    882 -GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (53 / 24)
Gap_init rate = 0.01 (5 / 373), avg. gap size = 1.20 (6 / 5)  


3244 26.55 1.00 0.55  chr1_7406336_7412748.rev     5019  5922 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_7406336_74   5019 TGGAAGAACATTCCATGCTCATGGGTTGGAAGAATCAATATCGTGAAAAT 5068
                              ii i  i     i      i        v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_7406336_74   5069 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5118
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_7406336_74   5119 TACCAATGGCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5166
                          v   iiv  i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_7406336_74   5167 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCTTAAGCCAAAAG 5216
                                viiv  ii  v  v v  vi    iv       i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_7406336_74   5217 AACAAAGGCGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5266
                                vi     vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_7406336_74   5267 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5316
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_7406336_74   5317 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATGTCTACAACT 5364
                                i    i--    i  --        vv iii ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_7406336_74   5365 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5414
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_7406336_74   5415 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5464
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_7406336_74   5465 GAAACTGGATCCCTTCCTTACACCTTAAACAAAAATTAATTCAAGATGGA 5514
                            ii    i    v   i     v  v           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_7406336_74   5515 TTAAAGACTTACATGTTAGACCTAAAAGCATAAAAACCCTAGAAGAAAAC 5564
                          i ?    i  v    v   v      vi      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_7406336_74   5565 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5613
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_7406336_74   5614 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTC 5663
                         vi            vvi          vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_7406336_74   5664 ATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5713
                           i   v v  i ii  i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_7406336_74   5714 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5763
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_7406336_74   5764 AAGGGCTAATAACCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5813
                          i  i  vi  v       v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_7406336_74   5814 AAAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5859
                           i    ----   v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_7406336_74   5860 CTCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAACAATGCTCAC 5909
                            v           vi viii     v  i         vi       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_7406336_74   5910 CATCACTGGCCAC 5922
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


 849 25.08 2.82 8.15  chr1_7516074_7519494.rev     1678  1996 (1425)    L1M4_orf2#LINE/L1        3   304 (604)  

  chr1_7516074_75   1678 GAGACACATACCTTTTTCATGGATTGGAAGACCCAACCTAGTGAAGATGT 1727
                           i v i  v  v v                 ii  iv v  v      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_7516074_75   1728 CAATTCTCTTCCGATTTATCTATAGGTTTAATACAATTCCTATCAAAACT 1777
                             v   ii vi   v     i  i  i  ii    i          ii
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_7516074_75   1778 GCAGCAATATTTCGGATAGTCATGGACAA--TGTATCCTATAATTTATAT 1825
                         v    viiv   ivvii  vv  v     --  -      v    i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCATAT 151

  chr1_7516074_75   1826 GGAAAGGCACAGGGCTTAGAATAGATACCAATATTAGAATAGAATAGCTA 1875
                              v   -    ------------   ----------i        i 
  L1M4_orf2#LINE/    152 GGAAATGCA-AGGG------------ACC----------CAGAATAGCCA 178

  chr1_7516074_75   1876 AAACAGGCTTGACAGAGAAGAATAAA--TA-AGAACCCACTCTACCTGAT 1922
                              iv     v i       i   -- i-  i  i   v  v  ii  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_7516074_75   1923 ACTGAGGATTAATACAGAGTTATAGCAATCAAGTCAGTGTGATGTCAG-- 1970
                         viii iiv   v    i  i  i  i       v       i iiii --
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_7516074_75   1971 --AGGAGAGACAGTCATATATTAATAGA 1996
                         --    v     --i   v  i   i  
  L1M4_orf2#LINE/    279 TAAGGATAGACA--TATAGATCAATGGA 304

Transitions / transversions = 1.58 (49 / 31)
Gap_init rate = 0.03 (9 / 302), avg. gap size = 3.89 (35 / 9)  

1737 23.44 4.78 6.70  chr1_7516074_7519494.rev     2304  2930 (491)    L1M4_orf2#LINE/L1      294   908 (0)  

  chr1_7516074_75   2304 AGATCAACAGAACAGAATACAGAACCCAGAAATAGCCCCA-ACAAACACA 2352
                                ii   i     vv   ii         iv    -   vvi ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_7516074_75   2353 CTCAACTTATTTTTGACAAAGGCACAAAAGCAATTAAATGGAGGAAGGAT 2402
                         v    i v     i     i  ii v  ii v   v     i i   i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_7516074_75   2403 AAACTTTTCAACAAATGGTATTGGAGCAATTGGATATCCACAGGCCAAAA 2452
                          iv                ii   ii   i      ?     v  -----
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC----- 438

  chr1_7516074_75   2453 CCAAAACAAAACACAAAAAACCAAACCCCAGAAACAAAAGGAACCTCGAC 2502
                         --------------    i ------------------ v   vi v   
  L1M4_orf2#LINE/    439 --------------AAAAGA------------------ATGAAGTTGGAC 456

  chr1_7516074_75   2503 CTAAACCTTATGCTTTAAACAAAAGTGAACTAAGAATGAATTACGGACTT 2552
                          ivv    i ii iv  v      i v    v i    i  i ?i   i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_7516074_75   2553 AAATGTAA-------AATTATAATACTTGTAGAA--AAACACAAGAGAAA 2593
                                 -------  i     v   iv     --     i i ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_7516074_75   2594 GTATTTGGGATCTAGGACTGGGCAA------CTTAG------TCCTAAAA 2631
                         i v  i v  i  v  ii i     ------     ------iv i    
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_7516074_75   2632 GCATGGTCCATAAATGGAAAA-T-GCTAAAACTGGACCTCATCAACATTA 2679
                            iiiv v i   v i    - - v    -i     i       v    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAA-TTGGACTTCATCAAAATTA 655

  chr1_7516074_75   2680 AAAACTTTTGTTCTACAAAAGCTCATT-TGGAGAAGATGAAAAAGCAAGC 2728
                                    v  v    i v-  i - vi    ii      ii   v 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGA-CACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_7516074_75   2729 TACAGACTGGGAGAAAATATTTGCAAATCACATAGTCAGCAAAGGACTCG 2778
                         i     v                       i   viiiii  i     i 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_7516074_75   2779 TACTGAGAATATAATAACAAACTCTCAAAATTCAACAGTAAAAA--CAAG 2826
                           iiv        -   vi      i v  i    i i      --   i
  L1M4_orf2#LINE/    755 TATCCAGAATATA-TAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_7516074_75   2827 CAATTCCATTAGAAAACGGGCAAAAGAC--ACATAGAGATATCTCGGCAA 2874
                         i  ii v   ?i    i       i  i--iv     v  v    --   
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC--CAA 851

  chr1_7516074_75   2875 AGATGATATACAGATGGCATGTAAGCACCTGAAA-GATGCTTAACATCAC 2923
                            v        i     vvi       v     -      i       ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_7516074_75   2924 TAGCCTT 2930
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.80 (92 / 51)
Gap_init rate = 0.03 (17 / 615), avg. gap size = 4.24 (72 / 17)  


 405 16.67 0.00 0.00  chr1_7768961_7770927.rev      434   499 (1468)    L1M4_orf2#LINE/L1        1    66 (842)  

  chr1_7768961_77    434 TGGGAAAACATCCTATGTTCACACACTGGAAGACTTAATATTGCTAAGAG 483
                            i  i i    i       iiv i                 i     v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_7768961_77    484 GGCAGTACTCCCCAAA 499
                             i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA 66

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.00 (0 / 0)  

2669 14.51 3.52 0.22  chr1_7768961_7770927.rev      502   956 (1011)    L1M4_orf2#LINE/L1      218   687 (221)  

  chr1_7768961_77    502 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAAACAGTG 551
                                                                    i      
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_7768961_77    552 TGATACTGGCATAAGGACAAACATATAGACTGATGGAATAGAACTGAGAG 601
                           i              i i         iii           i      
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_7768961_77    602 TCTAGAAGTCAACCTAAGCATCTATGGCCAATTGATTTTTGACAAGAGTG 651
                           i    i v    i vi   i     i           i      i   
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_7768961_77    652 CGAAGGCCATCCAAC-----------AGTCTTTTCAATAAACAGTGCTGG 690
                          v   i    i   i-----------           i   ii       
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_7768961_77    691 GCCAATTGAAGAGCCAACATGCAAAAGAATGAAGTTGAATCCCCACCTCA 740
                          v   i  i v ?   -                    i i   i      
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCA-CATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_7768961_77    741 CCCTATATACAAAAAGTAACTCAAAATGGATCAATAATCTAAGTGTAAGA 790
                          v i           v                 ?vi i    i       
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_7768961_77    791 GCTAAAGCCATAAAACTCTTAGAAGAAAACATAAGGGTAAATCTTCATTA 840
                               i i                        i ?          i v 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_7768961_77    841 CTTTGGATTTGACTGTGGATTCTTA--TAT---ACCAAAATCAAGAACAA 885
                          i    i  v i vi   v      --   ---       v  vi i   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_7768961_77    886 CAAAAGGAAAAACAGATACATTGGACTTCATAAAAATTAAAAACTTTTGT 935
                               i     i     v            v                  
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_7768961_77    936 GCATCAAAGAACATTATCAGG 956
                           v      i   i     i 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAG 687

Transitions / transversions = 2.71 (46 / 17)
Gap_init rate = 0.01 (4 / 470), avg. gap size = 4.25 (17 / 4)  

1088  9.86 8.92 2.35  chr1_7768961_7770927.rev     1264  1476 (491)    L1M4_orf2#LINE/L1      682   908 (0)  

  chr1_7768961_77   1264 ATAAAAAAAATGTAAAAGACAAGCCACAGAATGGGAGAAAGTATTTGCAA 1313
                           v  i   i  -         v                 i         
  L1M4_orf2#LINE/    682 ATCAAGAAAGTG-AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_7768961_77   1314 ATCACATGTCTGATAAAGAAAGATTTAATATCCAGAATACATAAAAAACT 1363
                             i  i        i ---  i  -i           i     i    
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGG---GACTT-GTATCCAGAATATATAAAGAACT 776

  chr1_7768961_77   1364 CTCACAACTCAA--------------ACAACCCAATTAAAAAATGGGCAA 1399
                           i         -------------- i         ?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_7768961_77   1400 AG--CCTGAACAGACATTTCTTCAAAGA---CATACAAATGGCCAATAAG 1444
                           --ii    i          i      ---i                  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_7768961_77   1445 CACATGAAAAGATGCTTAACATCACTAATCAT 1476
                                         i       ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 9.00 (18 / 2)
Gap_init rate = 0.03 (6 / 227), avg. gap size = 4.00 (24 / 6)  


1875 17.78 2.11 25.95  chr1_7872547_7877651     3428  4614 (490)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr1_7872547_78   3428 AAGATGTCTCATGTTCATGGATCAGAAGAATTAATATTGTTAAAATGACC 3477
                              i  i             ii     v             i   i v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_7872547_78   3478 ATACTCCCCAAAGCAATCTATATATTCAATGCAATCCCTATCAAAATGC- 3526
                                     vii     i v      i                 v -
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_7872547_78   3527 AATGACATTCTTCACAGAAAAAGAAAAAGCAGCCCTAAAATTCGTATGGG 3576
                          iivi v  i  ii      vv  v  iviiii          i     i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_7872547_78   3577 ACCACAAAG-ATCCTGAATAGCCAAAGCAATGCTGAGCAAAAAGAACAAA 3625
                          vii   i - i  v           i    vi   iv  i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_7872547_78   3626 GTTAAAGGCATCATATTACCTGACTTCAAAACATCCTATAAAGTTA--GT 3673
                            ii   vv   i i v  ii i        v v   i    i  --  
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_7872547_78   3674 AACCAAAACAGCATGGTATTGGTATAAAAATAGACACATAGACCAATGGA 3723
                           i   i    ii     i   i    ii       i     i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_7872547_78   3724 AAAGCACAGAAAACCCAGAAATAAATCCGTATATTCACAGCAAATGGATT 3773
                          v  v iv  i ii           i  i  i   i ii iv   v    
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_7872547_78   3774 TTCAACAAAAGCACCAAGAACAGACACTGGGTAAAAGACATCCTCTTCAA 3823
                            i    ii ii      v  -----------------------     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCA-----------------------TTCAA 381

  chr1_7872547_78   3824 TAAATGGTGTCCAGGCGTGGTGGCATATGTGTGTAACCCCAACACTTTGG 3873
                          -------------------------------------------------
  L1M4_orf2#LINE/    382 T------------------------------------------------- 382

  chr1_7872547_78   3874 GAGGCCAAGGTGGGAGTATTGCTTGGGCCCTGGAGATCAAGACAAGCCTG 3923
                         -------------------------------  i  --    --------
  L1M4_orf2#LINE/    383 -------------------------------GGGGA--AAGA-------- 391

  chr1_7872547_78   3924 GGCAACAAAGGGAGACGCCATCTCTACAAACACTTTAAAAATTAGCTGAG 3973
                         --------------------------------------------------
  L1M4_orf2#LINE/    392 -------------------------------------------------- 391

  chr1_7872547_78   3974 TGTGGTGGATAGTGCCTGTAGTTCCAGCTACTTGGGAGGCTTAGGTGGAA 4023
                         --------     -------------------------------------
  L1M4_orf2#LINE/    392 --------ATAGT------------------------------------- 396

  chr1_7872547_78   4024 GTATTGCTTGAGCCCAGGAAGTCAAGGCTGCAGTGAACTATGATAGTGCC 4073
                         ------   -----------------------------------------
  L1M4_orf2#LINE/    397 ------CTT----------------------------------------- 399

  chr1_7872547_78   4074 ACTGCACTCCAGCCTGGGCAACAGAGTGAGTTCCTGACTCTAAATAAATA 4123
                         ------------------------------   -----------------
  L1M4_orf2#LINE/    400 ------------------------------TTC----------------- 402

  chr1_7872547_78   4124 AATAAATAGTGCTGGAGGAACTGAGTATCTATATGCAGAATAATTAAACT 4173
                           i    i       iiv     ii  ? i i     i  v   v  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_7872547_78   4174 AGATGTGTATCTCTCCCCATATACAAAAATCAACTTAAAATGGATTAAAG 4223
                         i  iviv  i   v v              i    i         i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_7872547_78   4224 ACTTAAATGT------TAAGAC---------CTTAGAAGAAAACATAGGG 4258
                           i       ------   i  ---------                  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_7872547_78   4259 G-AAATGCTTCAGGACATCAGTCTTGGCA--GATTTTATGGCTAAGACCT 4305
                          -    -    iv   v ii vi v    -- i   iv i v  v   vi
  L1M4_orf2#LINE/    553 GTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_7872547_78   4306 CAAAAGCATAGGCAACAAAAACAAAAATAGACAAATGGGACTATATTGAA 4355
                                 i i         iv         i    v     vi  ii  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_7872547_78   4356 CT--AAAACTCTGCTGCACAGCAAAGAAAACAATCAACAGCATGAAGAGA 4403
                         v --      i --  ii vv     i v  v     v ivi    i   
  L1M4_orf2#LINE/    652 ATTAAAAACTTT--TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_7872547_78   4404 CAACCTAGAGAATGTAAGAAAATATTTGCAAGCTATTCATCCAACAAAGG 4453
                              i v      vi               iii  vi   ii i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_7872547_78   4454 ACTAATATCCAGACTATACATGGAACGCAAACAACTCAACAG-AAAACAA 4502
                            vi        v    i vi    v vv         i i-    vi 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_7872547_78   4503 CAACACATCATATGATTAAACAGTGGGCAAGTGATTTGAATAGACCTTTC 4552
                            ---  v ivii   ?  v i       iv             v    
  L1M4_orf2#LINE/    800 CAA---ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_7872547_78   4553 TCAAAAGAAGACATACAAATGGCCAAGAGATATATGAAAAAATGTTCAAC 4602
                           v        i              v iii i       i   i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_7872547_78   4603 ATTGCTGATCAT 4614
                           ii????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (139 / 68)
Gap_init rate = 0.02 (19 / 904), avg. gap size = 17.53 (333 / 19)  


 371 22.14 7.14 1.43  chr1_8380759_8382526      126   265 (1503)    L1M4_orf2#LINE/L1      761   908 (0)  

  chr1_8380759_83    126 GAATATCTA--GAACTCTTACAAATGAAAAAGAAAAGGACAA----TCCA 169
                               v  --            v v  v  v    i     ----i   
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_8380759_83    170 -TTGAAAAATAAGCAAAAGACTTACACAGGC---CCTTCATGAAAAAGAA 215
                         -  ?      ii     i  i  iv i  i ---i  i  --  i    v
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA--AAGAAGAT 858

  chr1_8380759_83    216 ACACAAACAGCCAATAAACTCATTATAGGATGCCCAATATGATTAGTAAC 265
                          i     ii        i v   v v i     i   i  v ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (19 / 11)
Gap_init rate = 0.03 (5 / 148), avg. gap size = 2.40 (12 / 5)  

1288 27.35 10.97 3.61  chr1_8380759_8382526      503  1277 (491)    L1M4_orf2#LINE/L1       77   908 (0)  

  chr1_8380759_83    503 GATTCAACACTATCTCATTCAAAATCCCAGCTGGTTAGTTTGTGGAACAA 552
                                 i v   i vv               vi vv    ii   vvv
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

  chr1_8380759_83    553 GACAAGCTGATTTTAAAAATTTTAAAGAAGAATAAAGTGCC---ACTAAT 599
                                    ii     v iv  vi   ivii  i vi  --- v  ii
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr1_8380759_83    600 CAAGACACTCTTGAAAAACAAGAA-AAAGGTAGGGGACCTGCTAAGT--- 645
                            i   v          v     -    v i i    iii -- v ---
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC--ACTTCC 224

  chr1_8380759_83    646 CAACTATCAACAATTATCCTAAAGCTA----------GACAGTGAAGCAC 685
                            i -    v v   iivi       ----------       vi i  
  L1M4_orf2#LINE/    225 CAATT-TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_8380759_83    686 TGG------AATAGACAGAGAGACCAACAGAACAAAAC----AGCTTAGA 725
                            ------i       v v   i   ii   i i  i----  iii   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_8380759_83    726 AACAGATTCACACTCTTATGGAAATTTCACTTT-GACATAGCTGGCAACA 774
                           i i ii  i  vi      vv v  v i   -    vi v  v   v 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_8380759_83    775 CAAATCAGTGGAGAAAAGGCTGGACTTCTCCAGAGATGACACTGGGACAC 824
                          v v   i   i    - iv i v   i  v v i   iii        v
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_8380759_83    825 CTGGTGATGTAT-TACAGAAACAAGTAAATCTGGTCTCTTTCTTTATGC- 872
                             vv ?vi i- i  i  i-- i i  vi   v i i v i i ii -
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAG--AATGAAGTTGGACCCCTACCTCACACC 470

  chr1_8380759_83    873 -TACACAA----TCAC-CAAACCCACGGACTAAGAACTTAAATACGAAAA 916
                         -  i    ---- v  -    --- i   ii ?ii  i     ii-  i 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAA---ATGGATCAWAGACCTAAATGT-AAGA 516

  chr1_8380759_83    917 GC-AAAATTATAAAACTTTTAGAAAACAGTAAGTATAGGAGACTGCCTAA 965
                           -    i         i      i ----  ii     ? vvvii  vv
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGA----AAACATAGGNGTAAATCTTC 562

  chr1_8380759_83    966 ATGACC-------AAGAGA-GATTTCTAACAAATAAAAGCTCAAAGTATA 1007
                         i     ------- i vi - i     v v v  i v - iv    i i 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA-CCAAAAGCACA 611

  chr1_8380759_83   1008 AAGGCTGATACATTTAAGGAGAGAG--GATAAA----A--TCGTTAAAAT 1049
                          --  -- -   ---  i  i i i--      ---- --  i i     
  L1M4_orf2#LINE/    612 A--GC--A-ACA---AAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_8380759_83   1050 TAACAACATATTAATCTTTAAC---CA--ATCATAAAAAGTGTGAAAAGA 1094
                            v   v -  ivv   i  v---  --    - i      --      
  L1M4_orf2#LINE/    654 TAAAAACTT-TTGTGCTTCAAAGGACACTATCA-AGAAAGTG--AAAAGA 699

  chr1_8380759_83   1095 TAAGCCACAA---GCCAGAAGGTATTTGCAACACACATTATTTAAGATGA 1141
                         i  v     i--- vv    ii         vv  i  -  i i v v i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGG 748

  chr1_8380759_83   1142 G-----TATCTAGAA-----------CTCTTACAAATC--TAG-AAAAAG 1172
                          -----    i    -----------         v  --  i-      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_8380759_83   1173 ACAA----TCAAATTGAAAAGTAAGCAAAAGATTTATATAGGCCCTTC-A 1217
                             ----i v    ?    i ii     i     iv    i vi   -v
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_8380759_83   1218 TAAAGAGGAAACACAAATAGCCAATAAACTCATTAAAGGATGCTCAATAT 1267
                         i     i  v i      i        i v   v   i         i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_8380759_83   1268 GACTGGAAAC 1277
                         v ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.60 (128 / 80)
Gap_init rate = 0.05 (42 / 832), avg. gap size = 2.69 (113 / 42)  


 521 28.67 21.12 2.66  chr1_8392854_8395038.rev      960  1674 (511)    L1M4_orf2#LINE/L1        1   847 (61)  

  chr1_8392854_83    960 TGGAGAGATGATGCGCCGATGTTAATGGA--AAAAGTACTCTGCATTATA 1007
                             i    -  ---  v     v     --ii   -   ivii   i v
  L1M4_orf2#LINE/      1 TGGAAAGAT-AT---CCCATGTTCATGGATTGGAAG-ACTTAATATTGTT 45

  chr1_8392854_83   1008 AAGATCCCCTTACTCTCTCA-TTG--CTATA---TCA------TTTCAAT 1045
                              vv vv     i iv -   --   i ---   ------ ii v  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_8392854_83   1046 CAAAACTTTAACAGGATTTTTTTGTGGAA-----CCAGCAGA--CTGA-- 1086
                              iiii i -v vi       ii   ----- v   v  --  i --
  L1M4_orf2#LINE/     96 CAAAATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_8392854_83   1087 TTTGTGTGGTAGAATAAAGGTCCAAGAATAGCAAGAA-AAT--TGAGTAA 1133
                           ii i   v ivii  i  v  v        v i  -   --   iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_8392854_83   1134 GAA--ACAAGGAAGATAGGCTTTATAC-----AAATGAGATAAGACTTGT 1176
                            --    i vv i-   vi i i  -----  v v---i  i    ii
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGG-AGGACTCACACTTCCCAATTT---CAAAACTTAC 240

  chr1_8392854_83   1177 ---AAAGTTAGAGTAATTAAGACCTGGTGGTATTGATGCAAA-ATAGAGA 1222
                         ---    i  v      i     vvv      i  iiii  i-     v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_8392854_83   1223 CGT----CAGTGTAATGG----GGG----CAGAA--------------CT 1246
                         ii ----  i  v   i ---- i ----     --------------i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_8392854_83   1247 ATG------TGATATCCG-----------------------TGGGGAACT 1267
                            ------    v i  -----------------------       vv
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_8392854_83   1268 AACCAATTATTCAGTAAATGGT-TTGGGACCAATGGGCTTAGCTGGCATA 1316
                           ivivi v    ii       -i      v v   i--  ? ---  i 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA--TAKC---CACA 435

  chr1_8392854_83   1317 TGGGAACAAAATAAAATAAGATTGTAACTTT----CAGATA----AGTTA 1358
                           vi  - i   i  i vi  iiviv  i i----  v   ---- i   
  L1M4_orf2#LINE/    436 TGCAAA-AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_8392854_83   1359 A---------------AG--CCA---GGAAAAAC-AAGACTTTAAAACTG 1387
                          ---------------  -- i --- v  i i -  i   v       v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_8392854_83   1388 T---AAGAAAA--TAGA---ACATTTTAATGTTCCCTGAGT-AGGGAAGG 1428
                          ---       --   i--- v  i  vi  v-  i  i  -   v  v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGA-CCTTGGGTTAGGCAATG 583

  chr1_8392854_83   1429 GTTTATAAGAAATAGTACAAAAAGTACAACTCA-AAAAGTAAATGATA-A 1476
                             v v   v  iii  v     i    viv -     v   -i   - 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGA 632

  chr1_8392854_83   1477 TATATTTATCTATATTAAGACTTAAAAAGTCT-GTGTTTTATAGGAAACC 1525
                           v   viv  vi  i  i -       v i -   i  i v    v  i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_8392854_83   1526 AT----AAAGTGAGAAAA-AAGTGACAGACTGAGAGAAGATATTTATAA- 1569
                           ----       i  i -  viv     v  i     i      ii  -
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_8392854_83   1570 ---CATAACTG------GATTAGTATCTAGAATGCATGAAGAACTTGTAG 1610
                         ---i   v   ------  i v     i     ii  i       iv  v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_8392854_83   1611 AAATCTATAATAGACA--CAAGCAGTTCAATAGAAAAATGGGTGAAAGAT 1658
                           v  v      i v --   ii iii    v?         ii  i   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_8392854_83   1659 GAGAACAGGTAGTTTT 1674
                         vv   i  ii v  i 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCT 847

Transitions / transversions = 1.54 (123 / 80)
Gap_init rate = 0.06 (51 / 847), avg. gap size = 3.33 (170 / 51)  


 518 24.56 1.75 0.00  chr1_8480612_8484412     1839  1952 (1849)    L1M4_orf2#LINE/L1        1   116 (792)  

  chr1_8480612_84   1839 TAGAGAAATATC--GTATTTATGGATTAGAAGATCCAATATTGTTAGGAT 1886
                          i  i i     --i i  i       i     iii          i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_8480612_84   1887 GTCAGTATTTCCCAAACTGATCCATAAATTCAATAGAATCCCAATTAAAA 1936
                          v  i  i i      i     i i i      iiv      v  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_8480612_84   1937 TTCCATCAGACTTTTT 1952
                          i   v v v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT 116

Transitions / transversions = 3.67 (22 / 6)
Gap_init rate = 0.01 (1 / 116), avg. gap size = 2.00 (2 / 1)  

 999 29.26 10.79 0.24  chr1_8480612_8484412     2275  2691 (1110)    L1M4_orf2#LINE/L1      120   580 (328)  

  chr1_8480612_84   2275 AGAAACTGGAAGGCTGATTCTAAAATTTACATGGAAATGGAAATTACCTC 2324
                              i  iv i      i        i i         v  ivv   iv
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_8480612_84   2325 AAATAGCCAAAGCAATCTTTAAAATCACATTTAAAGCAGAAAGAC----A 2370
                         i          i       v    vv vivvi    iv i i   ---- 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_8480612_84   2371 CC-CCTGAGGTCAAGACTTCCTATATAGCTACAGTATTCAAAACACAGAG 2419
                          i-  ii vv    i    v   i v          v    i   vv v 
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_8480612_84   2420 GCCCTA--ATAA-------C-----GATCAATGAGACAGAAT--AGAATC 2453
                          iv  i--    ------- -----        ii i     --   i  
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_8480612_84   2454 CAGAAAAAGATCCAAACATAAAAAAGCAGCTGATTTTCAATAACAATGTC 2503
                               v i i   v    vv viiv  ii        i i  vii  i 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_8480612_84   2504 AAGGCAGTCAAATGAGAAAAG-----TTTTTCCAACCAATATTGTTCAAA 2548
                            i vi iv    i i    ----- i   i    v   iv  i vii 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_8480612_84   2549 CAACAGG-TATCTGTGTGGAAGAAAATCAATTTTCACTCCATAATTAACG 2597
                             v  -  ? iiii  v  i i   v  v  vv  i  -  vi v  i
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC-TACCTCACA 468

  chr1_8480612_84   2598 C-AT-CACAA-------TTCAAAATGAATCAAAGACCTAAATGTAAGAA- 2637
                          -  -i    -------i        i    ?                i-
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_8480612_84   2638 -------GTAAAACTTCTAGAATAAAGCACAGAAACAA-TCTTTGTAATC 2679
                         -------i       ii     v   i  i  i?ii  -    i  i i 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_8480612_84   2680 TTGGAGTAATCA 2691
                             iv  iv  
  L1M4_orf2#LINE/    569 TTGGGTTAGGCA 580

Transitions / transversions = 1.70 (75 / 44)
Gap_init rate = 0.03 (14 / 461), avg. gap size = 3.29 (46 / 14)  

 453 26.01 7.62 1.35  chr1_8480612_8484412     3090  3312 (489)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr1_8480612_84   3090 AAAAAATTTTTTTAAAAGAATGAAAAAA--AGTCATGGTATGGGACAAA- 3136
                            ii ivi v i  i i i      i -- vi  ii v      v   -
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_8480612_84   3137 TAATTCCCAATACATATATC----AAAGGACTTCTACCTGAAATATTAAC 3182
                           v  v v   -        ----  i      v  i iii     -- i
  L1M4_orf2#LINE/    722 TATTTGCAAAT-CATATATCTGATAAGGGACTTGTATCCAGAATAT--AT 768

  chr1_8480612_84   3183 AAACAATCCTTATAACTAAATTGTAAAA---CAAATT------TTTTTAA 3223
                            v  ii    i    v   vi     ---     v------  ?vv  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_8480612_84   3224 GTAAACAAACTATTTGAACAGAGGCTTCACAAAAAAAGATAAACAAATGG 3273
                         i iii    vv       i   vii   v v   i      v        
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_8480612_84   3274 GCAATAAA-ACAGGAAAAGATGCTCAACCCTATTAAATTA 3312
                         v      i-   v               vii ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (33 / 24)
Gap_init rate = 0.03 (8 / 237), avg. gap size = 2.50 (20 / 8)  


2078 28.72 2.80 1.03  chr1_8687914_8690815     1200  1878 (1024)    L1M4_orf2#LINE/L1        1   691 (217)  

  chr1_8687914_86   1200 TGGAAAAACATTTGATGCTCATAGATTGGAAGA------ATCATTAAAAT 1243
                               i i  iiv   i    i          ------  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_8687914_86   1244 GACCACACTTTCCTAAGCAATCTACAGATTTAATGCTATTCCTATCAAAC 1293
                          i v i   ii  v  vii           i  i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_8687914_86   1294 TACTAA-TGTCATTTTTCACAGAATTAAACAAAGTAATTCTAAAATTCAT 1342
                          v i i-  i -     ii     v vi    iv i  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_8687914_86   1343 ATGAAACCAAAAAAAGTACCCA-AAGAGCCAAAGAAATCCTAAGGGGGGG 1391
                            i  -- viv  i v     -  v       iv    i i iiii ii
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_8687914_86   1392 GGGGGAATGCTGGCAGCATCACATTATCCAACTTCAAGCTATACTATAAG 1441
                          iivi  - i   vi vv     i vi    i     iviv     i  i
  L1M4_orf2#LINE/    198 GAACAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_8687914_86   1442 GCTACGGTAATCAAAACAGGAGGGTACAGGTACAAAAACAGACACATAGA 1491
                              i        i    viv     v  i i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_8687914_86   1492 CCAATGAAACAGAATAGAGAACCTACAAATAAAGTCATAAACCTACAGCC 1541
                         i     i  i     v    ii i v       vi    v ii  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_8687914_86   1542 ATCTGATCTTTGACAATGCTGACAAAAACAAGCAATGGGTAAAGGACTGC 1591
                          vi    i  i     v v  v   i v  vv       v    i iv i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_8687914_86   1592 CTATTCAAAAAATGGTGCTGGGATAGCTAGCTAGCCATATGCAGAA---- 1637
                           v     v              i i  i v  ?   i     i  ----
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_8687914_86   1638 ----CTGGACCGCTACCTTTTCCCATATATAAACATCAACTCAAGGTGGA 1683
                         ----i      v      iviv       i   v  i       ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_8687914_86   1684 TTAAATATTTAAATGCAAGACCACAAACTGTAAAAATCCCAGAAGAAAAC 1733
                          i ? v ii      i    v vv     i     v  ii          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_8687914_86   1734 CTAAAAA-ACACCATTCCGACCCTTGGCTTTAGGAAATAATTTAT--GAC 1780
                         v  ii?i- v i v ivi    i v  --     v   ii   v --  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGA- 593

  chr1_8687914_86   1781 TAAGTCCTCAAAAGCAACTGCAACAAAAACAAAAATTGACAACTGGGACC 1830
                           v v vi        vvv         iv      v  i  v v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_8687914_86   1831 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAAAG 1878
                          v  i   v v  i i   i  ii vv    i  v        v    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

Transitions / transversions = 1.59 (118 / 74)
Gap_init rate = 0.02 (11 / 691), avg. gap size = 2.36 (26 / 11)  

 851 23.40 0.85 0.00  chr1_8687914_8690815     2175  2409 (493)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr1_8687914_86   2175 AAACAAAACTGTCAACAAAGTAAACAGACAACCTACAAAATAGCAGAAAA 2224
                            vi v   i    v     i  v        i   i   i v      
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_8687914_86   2225 TATTTAAATATCATGCATCTGACAAAGGTCTAATACCCAGAATCTATAAG 2274
                              iv v     ii      i  i  v  vi  i       v     i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_8687914_86   2275 GAACTTTAACAATACAACAAGCAGAAAACAAATAACCCCATTACAAACTA 2324
                              i v    iv   i  vv i  i           v   ?v   v i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_8687914_86   2325 AGCAAAAGGCATTAACAGACATTCCTCAAAAGAAGACATACAAGTGGCCA 2374
                         i     i iiv v  i       i   v        i      i      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_8687914_86   2375 ACAA--ATATGATAAAATGTTTAACATCATTCATCAT 2409
                          i  -- i    v  i   i i       ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (33 / 21)
Gap_init rate = 0.00 (1 / 237), avg. gap size = 2.00 (2 / 1)  


3172 26.68 0.99 0.88  chr1_11078202_11081367.rev     1769  2675 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_11078202_1   1769 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1818
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_11078202_1   1819 GGCCATACTGTCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 1868
                            v     vi    iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_11078202_1   1869 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTAGTT-TAAAGTTCA 1916
                          v   iivi i  i  ii     -   -- v  i  ii i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_11078202_1   1917 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 1966
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_11078202_1   1967 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2016
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_11078202_1   2017 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2066
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_11078202_1   2067 AATAGAACAGAAC--AGAGCCCTCAGAAATAACGCCATATATCTACAACT 2114
                            i   i    i--    i  --        vv     i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_11078202_1   2115 ATCTGATCTTTGACAAACCTGACAAAAAACAAGCAATGGGGAAAGGATTC 2164
                          vi    i  i     ivv  v   i v-  vv            i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAG 395

  chr1_11078202_1   2165 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2214
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_11078202_1   2215 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 2264
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_11078202_1   2265 ATTAAAGACTTAACAACGTTAGACCTAAAACCATAAAAACCCTAGAAGGA 2314
                           i ?    i   -- i  v   v       i      vi i      i 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAA--ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_11078202_1   2315 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 2363
                            v    ?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_11078202_1   2364 CTAAGACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACCAATGGGAT 2413
                         v  v             vvi          vv i   v  iv   v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_11078202_1   2414 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 2463
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_11078202_1   2464 GAACAGGCAACCCACAAAATGGGAGAAAATCTTCGCAACCTACTCATCTG 2513
                            v  i         i             v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_11078202_1   2514 ACAAAGGGCTAATTTGCAGAATCTACAATGAACTCAAACAAATTTACAAG 2563
                          i  i  i  vi v v      v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_11078202_1   2564 AAAAA----AATAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACA 2609
                              ----        v  i?    i    ii     iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_11078202_1   2610 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCT 2659
                         i     v        i  vi viii     v  i        i i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_11078202_1   2660 CACCATCACTGGCCAT 2675
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


3222 26.16 0.99 0.77  chr1_11154626_11161328     5305  6210 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_11154626_1   5305 TAGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5354
                          i   ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_11154626_1   5355 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5404
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_11154626_1   5405 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5452
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_11154626_1   5453 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGACAATCCTAAGCCAAAAG 5502
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_11154626_1   5503 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAATTATACTACAAGGC 5552
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_11154626_1   5553 TACAGTAACCAA-ACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5601
                                 i   -    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_11154626_1   5602 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAATC 5649
                                i    i--    i  --        vv   i    i  iii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_11154626_1   5650 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGGAAGGATTCC 5699
                          vi    i  i     ivv  v   i v  vv        i   i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_11154626_1   5700 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAATCT 5749
                           v  i  i              v      v  ?   i   i i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_11154626_1   5750 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATCAATTCAAGATGGA 5799
                            ii    i    v   i   i v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_11154626_1   5800 TTAAAGACTTAACAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5849
                          i ?    i   -- i  v   v       i      vi i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAA--ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_11154626_1   5850 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCACGTC 5898
                           v    ?i- v i -   iv   v v  vv i     v ii   viivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_11154626_1   5899 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5948
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_11154626_1   5949 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTG 5998
                          v  i   v v  i i   i  ii vv    i  v  i i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_11154626_1   5999 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTAA 6048
                           v  i     i                 v       vii ivi    i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_11154626_1   6049 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 6098
                         i  i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_11154626_1   6099 AAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGAGATGAACAGACAC 6148
                             iv    i     v  i?    i           vv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_11154626_1   6149 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 6198
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_11154626_1   6199 A---TCACTGGCCAT 6210
                          ---   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2500 28.36 3.92 2.13  chr1_12405904_12407877      590  1481 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_12405904_1    590 TGAAGGGACATACCATGTCGATAAGTTGGAAGATTCGGTA-----AAGTT 634
                           i ii  i  v      iv  iii        i iii  -----   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_12405904_1    635 GTCGTTGCTCCTCAAATTGATCTGTAGATTCAGTACAGTCCTGATGAAAA 684
                          v iv i    i           ii       iii  i   iv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_12405904_1    685 TTCCAGCAGTTTTTTTGGAAGCAAATTGACAAGCTGATTCTAAAATTTCT 734
                          i     v ii     v v  -                i        iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG-AAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_12405904_1    735 CTGCAGTTGAAAAGCGCAAAGAGCAGCTAAGGTAACCCTGGAGAAAAAGT 784
                         v  v iv  v  i vi vv   ii   i  iii  i i  i i  i   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_12405904_1    785 ACAAAGTTGGGGAGAGCTTACACTATTCGATTTCAGAAATTATTACAAGA 834
                                   --  ii  i     vii i      i  v   i     ii
  L1M4_orf2#LINE/    200 ACAAAGTTGG--AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_12405904_1    835 CTACAGTAATTAAGACAGTGTGGCATTAGTAGAAAG---------CAGAG 875
                                   i            i i i i v  i ---------i   v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_12405904_1    876 CAAAGTGAAACAGAAGAGAGAATCCAGAAATGGATGTATA-AT--ACCAT 922
                            --  i  i    vv    i         ii ivi   -  -- ivi 
  L1M4_orf2#LINE/    298 CAA--TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_12405904_1    923 CACGTGACTTTTGACAGCATTTATGCCA-TAC--TGCGGTAGTGGAACGG 969
                           vv   i   i    ivi---i     -v  -- v ii i -    v i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG---GTGCCAAGACCATTCAATGG-GGAAAGA 391

  chr1_12405904_1    970 ATGACCTTTTCAGTAAATATTACT----TAGTTCAATATTTATCAG-AAA 1014
                           iii       ii    iv i  ----i ii vi   ?ii ivv -   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_12405904_1   1015 AAAATGAATCTTGGCCACTCCCTCCTACCGTACATAAAAATAAATTCTAG 1064
                          i      vi v i  v  v    vi   i  i i      v  i  v i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_12405904_1   1065 GTGGAGCATAAATAAAATCTAGGTGTGAAGAG-TAAAACAATAAAACTTG 1113
                         i    v  ? i i-----   ii   -     -      v        iv
  L1M4_orf2#LINE/    492 ATGGATCAWAGAC-----CTAAATGT-AAGAGCTAAAACTATAAAACTCT 535

  chr1_12405904_1   1114 TATAAGTAAACGT---GGTAATATCTTTATGACCTTGGTGTAGACAAAAA 1160
                           v   v    i ---?    -     ii         vv   i   vii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_12405904_1   1161 TTTCTTAACCAGGACACAGAAAGCTCTTACCATATAAGAAAATATTGATA 1210
                                ivi v     vi     v vvi v i v       v  v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_12405904_1   1211 AGGCAGATTTCCTTAAAATTAAGACTGTCTGATCATTAAAAGACACCATT 1260
                          ivii  i   v i        i viv i  vv v i   i     i  i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_12405904_1   1261 TAAAGAGTAGTAAGATAAGTCACAGAATGGAAGAAGATATTTGCAACACA 1310
                         v i i   iiv    i  vi          i    i          vv  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_12405904_1   1311 TCTGTTCAACAGAGGACTTGGTATACAGAATATATAA-GAACTCCTACAA 1359
                          v i iii i ii       -   v            -      i     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_12405904_1   1360 AGCAGTAAGAAATAAAAAACATGAACTCACTACAAAAATGAGCAAAATAC 1409
                         vv  i   v   -  i v v  -   i  v v?       i     iv i
  L1M4_orf2#LINE/    784 CTCAATAATAAA-AAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_12405904_1   1410 TTCAATAAGCACTTCAC--AAAAAGATATCCAAATGGCTTAT--GCAT-T 1454
                           v    ii  i   v --  i       v        iv  --   i- 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_12405904_1   1455 TAAAAGTTGCTTAATCTCACTTCTCAA 1481
                         v     v    i  iv   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (158 / 91)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.16 (54 / 25)  


 733 27.88 17.31 1.60  chr1_12691507_12693704.rev      643   954 (1244)    L1M4_orf2#LINE/L1        6   366 (542)  

  chr1_12691507_1    643 AGA-ATACTATTCTCATAGACTGGAAGACTTGATAGTGA-AAAATATAAA 690
                            -  v i  vi    i  i          i   v  v-  i  ivv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_12691507_1    691 TTCTCCCCAATTTGATCTTTTAATTTAATTCATTCCCAATCAAAATTTTA 740
                          v        v       vivi   i  iv  v    v        iii 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_12691507_1    741 TCTGCTTTTTTTTTTTGCAGAAATTGACAAGTTTA-CTTAAAATATATGT 789
                         v    i      ----               i v - i      vi  i 
  L1M4_orf2#LINE/    106 GCTGCCTTTTTT----GCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_12691507_1    790 GGAAATGCAAAGAACC---------------------------------- 805
                                   i i   ----------------------------------
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_12691507_1    806 --------AAGATTTACACTATCAGATGTTAAAA-TTATTGGAAGGCTAC 846
                         -------- i  i i     vi vi  v i    -   i iv  i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_12691507_1    847 TATAATTAA-ACAGTACACTATCAGTGCAAGTGTAG-----CAAACCAGT 890
                         vi    i  -     iiiv  iii iii   vi   -----i i i  i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_12691507_1    891 GTAGCAGAA--GAGGAATCCAGAAACTAATTCACACATACATGGCCACCT 938
                          v ii    --   - i        iv  ii  i    vi    i  vi 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_12691507_1    939 GATTTATGACAAAGAT 954
                              vi     i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGT 366

Transitions / transversions = 2.11 (59 / 28)
Gap_init rate = 0.03 (10 / 361), avg. gap size = 5.90 (59 / 10)  

 211 26.61 1.61 12.10  chr1_12691507_12693704.rev     1063  1186 (1012)    L1M4_orf2#LINE/L1      577   687 (221)  

  chr1_12691507_1   1063 GATAAAGATTTCTTAAGGA--AAACTAAAAGCACTAACCGTAAATGCCAG 1110
                          ii  v i       iiv -- v  i        v i vii   ----  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA----AG 622

  chr1_12691507_1   1111 AGAGCAGGGGAGAGAAGGATAAACTGGACCATATTAAGATTGAGAACTTC 1160
                          i --------- i vi      i     ivi  i  i   i i     i
  L1M4_orf2#LINE/    623 AAA---------AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_12691507_1   1161 TCTGTTCATCAAAAGATACCATGAAG 1186
                          v  i --     i  i  i  v   
  L1M4_orf2#LINE/    664 TGTGCT--TCAAAGGACACTATCAAG 687

Transitions / transversions = 2.67 (24 / 9)
Gap_init rate = 0.04 (4 / 111), avg. gap size = 4.25 (17 / 4)  

 509 23.58 4.88 8.54  chr1_12691507_12693704.rev     1511  1756 (442)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr1_12691507_1   1511 AGAAGATACCATGAAGAGAGGAAAAAGACAACCTGTAGAGTGGGA--AGA 1558
                          i i  i  i  v    i  vi           iii   i     -- i 
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_12691507_1   1559 TATTTGCAATACAATACCTATTTCCAACAAGTGAAACACATTCAAAACAT 1608
                                  ----  - v   v  ii i   v  vviii  i  i  i  
  L1M4_orf2#LINE/    722 TATTTGCAA----AT-CATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_12691507_1   1609 ATAAAGAACTCCTACAA------AGCAAAAAGACTGAAAATGTAATAGAA 1652
                                    i     ------ ii        vi v  ivi   v?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_12691507_1   1653 AAATGAGCAAAT-ATTTGAAGAGGCCCTTTACAAAAGAGAATATGCAACA 1701
                              i     v-       v  i vi  iv v     ii    i   --
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA-- 864

  chr1_12691507_1   1702 CACATGTGTCAAATGTGGCCAATACACACAGGACAA--T-TTCAATTTCA 1748
                         --------------i         vi    v  v  -- -i    iv   
  L1M4_orf2#LINE/    865 --------------ATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_12691507_1   1749 TTAGTCAT 1756
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.85 (37 / 20)
Gap_init rate = 0.03 (8 / 237), avg. gap size = 4.12 (33 / 8)  


2892 28.57 0.78 0.22  chr1_12725098_12728971.rev     2481  3383 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_12725098_1   2481 TAGAAA-ACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 2529
                          i    - i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_12725098_1   2530 GGCCATACAGCCCCAAGTAATGTATAGATTCAATGCTATTCCCATCAAGC 2579
                            v    vv   v  v i  v  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_12725098_1   2580 TACCATTGACTTCCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 2628
                          v   vivi i ii  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_12725098_1   2629 ATGGAACCAAAAAGGAGCCCATATATCCAAGACAATCCTAAGCAAAAAGA 2678
                               viiv  i   v  viv   v    i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_12725098_1   2679 ACAAAGCTGGAGGCATGATGCTATCTGACTTCAAACTATACTACAAGGCT 2728
                               i      vv v ii  vi ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_12725098_1   2729 ACAATAACCAAAACAGCATGATACTGGTACCAAAACAGACATGAAGACCA 2778
                            i   i   i    ii  i      i iv ii i      iv   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_12725098_1   2779 ATGGAACAGAACAGAGGCCTCAGCAATAACACCACATGTCTACAACCATC 2828
                               i    iv   ivii   v     vv   i ii i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_12725098_1   2829 TGATCTTTGACAAACCTGACAAACACAAGCAACGGGGAAAGGATTCCCTA 2878
                             i  i     ivv  v   ivv  vv   i        i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_12725098_1   2879 TTTAATCAATGGTGTTGGGGAAGCTGGCTAGCCATATGCAGAAAACTGAA 2928
                           i  iv       i    iv i    v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_12725098_1   2929 ACTGGACCCCTTCCTTACACCTTATACAAAAACTAACTCAAGATGAATTA 2978
                         ii         v   i     v          i        i   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_12725098_1   2979 AAGACTTAAACATGAGACCTAAAACCATAAAAACCCTAAAAGAAAACCTA 3028
                         ?    i    ii i   v       i      vi i  i        v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_12725098_1   3029 GGCA-ATACCATTCAGGACACAGGCATGGGCAAAGACTTCATGACTAAAA 3077
                           ?i- v i -   iv   viv  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_12725098_1   3078 TACCAAAAGCAATTGCAACGAAAGCCAAAATTGACAAATGGGATCTAATT 3127
                         i          vvv     i    vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_12725098_1   3128 AAACTAAAGAGCTTCTGCTCAGCAAAAGAAACGATCATCAGAGTGAACAG 3177
                            v v  i i   i  iv vv    i  v  v    vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_12725098_1   3178 GCAACCTACAGAATGCGAGAAAA-ATTTGCAATCTCTCCATCTGACAAAG 3226
                         i     i        v       -        viiv vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_12725098_1   3227 GTCTAATATCCACACTCCACAAGGAACTTAAACAAATTTACAAGAAAAAA 3276
                          v  vi      v v vi i  i     ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_12725098_1   3277 ACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCTC 3326
                              i     v  i?    i    ii      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_12725098_1   3327 AAAAGAAAACAT-TACGTGGCCAACAA--ACATGAAAAAAAGCTCACCAT 3373
                         v      i i  -i vi       i  --         i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_12725098_1   3374 CACTGGTCAT 3383
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (148 / 106)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


3647 15.05 1.32 15.90  chr1_12744071_12749000     3375  4437 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_12744071_1   3375 TGGAATGACACCCTGTGTTCATGGAT-GGAAGACTTAATATTGTTAAGAT 3423
                              v  i i  ii           -                       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_12744071_1   3424 ATCAATACTACACAAAGCTATCTACAGATTCAATGCAATCATTATCAAAA 3473
                         iv       v v    viv              i      vi        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_12744071_1   3474 CCCCAGTAAAGGTTTTTTTTTTTTGCAGACAT--AAAATCC-ATCCTAAA 3520
                         i     i------- vii           v  -- v  v i-        
  L1M4_orf2#LINE/    101 TCCCAGC-------TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_12744071_1   3521 ATTCATATAAAATCTCAAGAGACTCCAAATGGCCAAAACAATCTTGAAAA 3570
                                 ii  viv    i   i vi   i                   
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_12744071_1   3571 A-AAGAACAAAATTGGAAGACTCACATGTCTCAGTTTCAAAACTTACTA- 3618
                          -         i     i        iv  i  i               -
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_12744071_1   3619 AAAGCTACAGTAATCAAGACAGTGTGATACTGGCATACAGATAGATACAT 3668
                                                   i          vi      i i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_12744071_1   3669 AGACCTATAGAACAAAAGAGAGAGCCTAGAAATAAACATTTGTATATACG 3718
                            i v  i   i i  vv     i i          viv ii  v  i 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_12744071_1   3719 GTCAAATGACTCTTGACGAGGATGCTAAACCTGTTCAATGGGGGAAAGGA 3768
                              v   i i i   i   i   i  iv ii          -    i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAA 392

  chr1_12744071_1   3769 CAATTTCTTCAATAAATGGTGTTCAGTAAAGTGGATATCTAGGTGCGAAA 3818
                         i i i i     i        i vi vv  v      ? i vi   i   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_12744071_1   3819 AAATAAAGTTAGACCCTTCCCTAATTCCATATACAAAACTGAACTCAAAG 3868
                         i   i     i     i v   v iv            v v        i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_12744071_1   3869 TGGATCAGAGACCTGGATG--AGACCTAAAACTACAAAACTCTTAGAAGA 3916
                                ?      ii   --   v         i               
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_12744071_1   3917 AAACATAGGGGGCTGGGTGTGGTGACTCATGCCAGTAATCCCAGCACTTT 3966
                                  ? ------------------------   ------------
  L1M4_orf2#LINE/    543 AAACATAGGNG------------------------TAA------------ 556

  chr1_12744071_1   3967 GAGAGTCTGAGGCAGGAGGACTGCTTGAGGAAAGGAGTTCAAGACCAGCC 4016
                         --------------------------------------------------
  L1M4_orf2#LINE/    557 -------------------------------------------------- 556

  chr1_12744071_1   4017 TAGGCGACACAGCAAGAACTTATCTCTCTCTTTTTTTTTAATTAAATAAA 4066
                         ---------------------    -------------------------
  L1M4_orf2#LINE/    557 ---------------------ATCT------------------------- 560

  chr1_12744071_1   4067 AAAAGAAGAAAACATCGGGGAAAATTCTCATGACATTGGCTTTAGCAAGA 4116
                         ---------------------------  i    v    v  vi    vi
  L1M4_orf2#LINE/    561 ---------------------------TCGTGACCTTGGGTTAGGCAATG 583

  chr1_12744071_1   4117 ATTTCTT-GATGTGACACCAAAAGCACAGGCAACACAAGAAAAAAATAAT 4165
                         i      -   i                i      v         vvi  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_12744071_1   4166 AAACTGGACGTCATCAAAACAAAAAACTTT-GTGCCTCAAAGGACACTAA 4214
                            i     v         iv         -    i             v
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_12744071_1   4215 CAACAGAGT-AAATGACAACCAATGGAGTAGGAGAGAATATTTGCAAATC 4263
                            v i   -   v       v ii  i i     i              
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_12744071_1   4264 ATATATCTGATAAGGGACTAATATCCAGAATATGTAAAGGACTTCTATAA 4313
                                            vi            i     i   ii  i  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_12744071_1   4314 CTCAACAATAGCCAAAGACAAGCAACCTGATTAAAAAATGA-CAAAGGAG 4362
                              i    i--        ii    ii   ?       i-       v
  L1M4_orf2#LINE/    784 CTCAATAATAA--AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_12744071_1   4363 CTGAATAGGTATTTCTCCAAAGAAGATGTACAAATGGCCAATAAACACAT 4412
                         i       ii                 i                i     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_12744071_1   4413 --AAACATAGTCAACCTCACTGATTAT 4437
                         --   v  iv     v   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (103 / 53)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 10.76 (183 / 17)  


 215 32.41 1.85 5.56  chr1_13623904_13625853      465   572 (1378)    L1M4_orf2#LINE/L1      199   302 (606)  

  chr1_13623904_1    465 AACAAA--TGGAAATATTATTTTTGCCTAATCTCACATCAAGACTTATGA 512
                               --    iivv i ivi  -  i   i   ----- i     iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTT-CCCAATTTCA-----AAACTTACTA 242

  chr1_13623904_1    513 TGAAGTTATGGTAAGTAAAACAGTATGATATTGATGCAGTTACAGACATA 562
                         ii   i  ii    vi  i     i  i  i  iiii ivv i       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_13623904_1    563 ATAATCAATG 572
                         vvi       
  L1M4_orf2#LINE/    293 TAGATCAATG 302

Transitions / transversions = 2.89 (26 / 9)
Gap_init rate = 0.03 (3 / 104), avg. gap size = 2.67 (8 / 3)  

 997 29.25 6.60 3.21  chr1_13623904_13625853      928  1457 (493)    L1M4_orf2#LINE/L1      361   908 (0)  

  chr1_13623904_1    928 AAGGGGAGCTATATCAGTTCCATGAGTAAAAGAT-GTACTATGAAAC--- 973
                              viv v v i  -   v   i v   ii  -  -  v vv   ---
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGT-CTTTTCAACAAA 408

  chr1_13623904_1    974 TAATCTTGAGATAAATGGTTAGCCACCTGGGGTGGGGATGGGGGTGATTG 1023
                          ii vi  i  i  v   v  ?    v  vii-ii i   ii ----   
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAA-AAGAATGAAG----TTG 453

  chr1_13623904_1   1024 AACCCTTACCTGACACCACATACAAAA-TCAATTTCGAGTGGATTAACAA 1072
                         i    i     v      i        - i  i ivi i     i ?vi 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_13623904_1   1073 CTTAAAAGTAGGACATAAAAGTTTAAAACT-TCATAATAAAATATGAAAG 1121
                          i    v   i  vv     v v       - i v  v    i  iii? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_13623904_1   1122 AATATTTTTGTGACCTAGAGATAAGGTAAGAGTTTTTTA----------- 1160
                         v v  i  i       v i v  -  i  vi    i   -----------
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATATGACACC 602

  chr1_13623904_1   1161 -----CACGACT--TAAAAGAAAAACTTGGCACATTGAGTTACATTAAAA 1203
                         -----   i vi--i          v v ii v    iii v   i    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_13623904_1   1204 TTAACCATTTCTGTTCATCAAAAGATACCATAAAGAAACTGAAAA-ACAA 1252
                             vv i  i   v v     i  i  i  v      v      -    
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_13623904_1   1253 GTCATAAATTGGGGGTA--TATTTGCATA-CACATAACCACGAATAAGTG 1299
                         vi  i i v    i v --        v -  i   v ii---     v 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG---ATAAGGG 749

  chr1_13623904_1   1300 GCAGCATATAAAGGATATAGACATGTATTAACTTTGACAAATCAATAATA 1349
                         i -vii   vv  i     v v - ----    i v    v         
  L1M4_orf2#LINE/    750 AC-TTGTATCCAGAATATATAAA-G----AACTCTTACAACTCAATAATA 793

  chr1_13623904_1   1350 AAAAGACAG----TCTAGGAACAAAACGGACAAAAGATATGAGCAGACCT 1395
                                 i----i i ivv?v    i  i    i   v   ii    v 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_13623904_1   1396 TTC---AATGAGAAAATGCATATGGTGGATAAACATATGGAACGATAACC 1442
                            ---  v  ii v  i  v    ivi    i  i   i  v   ivi 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_13623904_1   1443 AATCTCACTAGTAGT 1457
                           iv   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (86 / 65)
Gap_init rate = 0.04 (20 / 548), avg. gap size = 2.60 (52 / 20)  


1103 14.35 11.48 0.00  chr1_13663366_13665360.rev      502   710 (1285)    L1M4_orf2#LINE/L1      169   401 (507)  

  chr1_13663366_1    502 AGAATCACCAAAGCAATCTTGGTAAA----AACAAAGT----AGACTCAT 543
                              vi     i        iv   ----        ----i      i
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_13663366_1    544 ACTTCC--ATTTCAAAACTTACTACAAAGCTGCAGTAATCAAGACGGTGC 591
                               --                       i             i   i
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_13663366_1    592 --TACTGGTAGGAGGATAGACATATAGATCAAT---------TTAA---T 627
                         --      i vi                     ---------  i --- 
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_13663366_1    628 CCAGAATTAAACCTATACATTTATGGGTAATTGATTTTTGACAGAGGTGC 677
                               v      i            vi          i    ii     
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_13663366_1    678 CAAGATTCTTCAGCGAAGAAAGAATCATCTTTT 710
                              iiv    ii ii        vi      
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

Transitions / transversions = 3.29 (23 / 7)
Gap_init rate = 0.03 (6 / 233), avg. gap size = 4.00 (24 / 6)  

1926 18.05 8.92 3.04  chr1_13663366_13665360.rev     1012  1504 (491)    L1M4_orf2#LINE/L1      387   908 (0)  

  chr1_13663366_1   1012 AAAAAATCATCTTTTCAACAAATGGTACCTTGACCACTGGATACCCACAT 1061
                            i   vi                 i ivv   v        ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_13663366_1   1062 GCAAAAGAATGGAGTTGGGCCTCTACTTCATAGCCCACACAAAAATGAAC 1111
                                    i      i  i    i   i v vi i        v   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_13663366_1   1112 TCTAAATGAATCAAAGACCCAAATATCAGAGCTAAAACTGTAA------- 1154
                           v     i    ?     i    i v            i   -------
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_13663366_1   1155 --------------GAGTAAATCGCTGTAAGCTTGGACTAGGCAACAGCT 1190
                         -------------- ?       vii  i v     ii       ii i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_13663366_1   1191 TCCTAGAT--GACGCCAACAGTACAAGCAACAAAACA-----CAGATACA 1233
                           i     --   i    v  i             v -----i     v 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_13663366_1   1234 TTTAACTTTACCAAAATTTTAAAC------GCTATTCAATGGTTGCTATC 1277
                           vi    i i       vv    ------   --    v  vii     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTATC 684

  chr1_13663366_1   1278 AAGAAATTGAAAAGACAACCCAGTCCAAAGGATGGGAGAAAA-GTCTGCA 1326
                               v               ---  i --           -i i    
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCA---CAGA--ATGGGAGAAAATATTTGCA 729

  chr1_13663366_1   1327 ATTCATATATTT---AAGGGTCTAATATCTAGAATATATAAAGGAGGCTT 1373
                          v        i ---     v  vi    i             i vv   
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_13663366_1   1374 TCAA-TCAACAATATAAAGTTAGCAAAGGATTTAACTCAACTTTAG--TG 1420
                         v   -    i    v    ---i    -----    i   i ?v i--  
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAG---ACAAA-----TAACCCAATTWAAAAATG 821

  chr1_13663366_1   1421 AGCAAAGGATTTAAACAAACATATCTCCAAAGA---TACACAATTGGCGA 1467
                         i           i  i i    v          ---  i    v    v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_13663366_1   1468 AGAAGTGCATAAAAAGATGCTCAGCATCACTAATCAT 1504
                          v   ii   i            i     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (53 / 32)
Gap_init rate = 0.03 (14 / 522), avg. gap size = 4.21 (59 / 14)  


1150 15.20 2.94 0.00  chr1_13747071_13749646.rev      496   699 (1877)    L1M4_orf2#LINE/L1      259   468 (440)  

  chr1_13747071_1    496 AAAAAAGTGTGATGGTGGCATAGGAACAGACATGCA--TCAGTGGAATAG 543
                           i v      i iv       i i i      ii --   i        
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_13747071_1    544 AATCCAGAGACTGGAAATAAACCCATACAGTTATGGTCAATTGATTTTTG 593
                            iv    v ii                v                  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_13747071_1    594 ACA---TTGCCAAGAAAATTCAATGGGGAAAGAATAATCTTTTCAACAAA 640
                            ---v        vv                   i             
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_13747071_1    641 TGGTGCTGGAACAACTGCATAGCCACATGCAAAA-AGTGAGGTTGGACCC 689
                                  i       v   ?            - i   i         
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_13747071_1    690 CCAACTGATA 699
                          i v  v i 
  L1M4_orf2#LINE/    459 CTACCTCACA 468

Transitions / transversions = 1.73 (19 / 11)
Gap_init rate = 0.01 (3 / 210), avg. gap size = 2.00 (6 / 3)  

 856 15.30 6.01 0.55  chr1_13747071_13749646.rev     1366  1548 (1028)    L1M4_orf2#LINE/L1      477   669 (239)  

  chr1_13747071_1   1366 AAAAATTAACTCAAAAT---------ACTTAAATGTAAGAGATAAAACCA 1406
                                          ---------  i            v      i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_13747071_1   1407 TAGAACTTGTAGAAGAAAACAGAGGAGTAAATCTCTATAGCATTTGGT-A 1455
                           i    iv            v   ?        iii ii v  v   - 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_13747071_1   1456 GGCAATGGTGTCTTAGATGTGATAACAAAAGCAAAAACAACTAAAGAAAA 1505
                                  v        i   i v        v  i    v        
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_13747071_1   1506 AAACAAATAACTCGAACTTCATCAAAATTAAAAACTCTTG-GCT 1548
                           -i i    v i i                     i   -   
  L1M4_orf2#LINE/    627 AA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.02 (4 / 193), avg. gap size = 3.00 (12 / 4)  

1396 13.95 0.78 0.00  chr1_13747071_13749646.rev     1828  2085 (491)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr1_13747071_1   1828 AAAATTAAAA-CTCCTGTGCATCAAAGGACATTATTAAGAAAGTACAAAG 1876
                                   -  ii     v          i   i        iv    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_13747071_1   1877 -CAACCCAGACAATGGGAGAAAATATTTATAAATCATATATCTGATAAGG 1925
                         -       v v                 ii                    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_13747071_1   1926 GTCCGATCTCCAGAATATATAAAGAACTGTTACAAATCAACAATAAAAAG 1975
                          v ivi v                    v      v    i         
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_13747071_1   1976 AATAATAGCCCCATTTTTAAAGGGGCCAAGGATTTGTATAGACATTTCTC 2025
                          vv    i   v   ?vv   v    v         v             
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_13747071_1   2026 CAAAGAAGATATACAAATGACTAATAAACCCATGAAAAGATGTTCAATTT 2075
                                            i i     i v            i    iv 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_13747071_1   2076 CATTTGTCTT 2085
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 0.84 (16 / 19)
Gap_init rate = 0.01 (2 / 260), avg. gap size = 1.00 (2 / 2)  


1563 25.44 5.70 6.58  chr1_13909201_13910790.rev      426  1109 (481)    L1M4_orf2#LINE/L1      231   908 (0)  

  chr1_13909201_1    426 CAAGACTTATTTTATAGCCACGGTAATTAAGACTGCATGATATGGGCATA 475
                            i     i vi v   i  i     i     v ii  i  iv      
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_13909201_1    476 CAGTCAATTTCCAAGTGCCATAAGA-AGGCAAA-AGAAAAGACAATCTAT 523
                         --------------------- i  -  i  v -   --------  v  
  L1M4_orf2#LINE/    281 ---------------------AGGATAGACATATAGA--------TCAAT 301

  chr1_13909201_1    524 GAAACAGGATAGGGAATACAGAAATAGACCCACCCACACATATATGCCCA 573
                          i  i  i  v i  i v        i     i----    v    vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCAT----ACATTTATGGTCA 347

  chr1_13909201_1    574 ACTGATTTTTGACAAGA-TGC-AAAAGCATTTCAATGGAGGAAACATGGC 621
                          i       i      i-   -  i v    -      i i  iv  i i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAGT 396

  chr1_13909201_1    622 CTTTTTGACAAATGATGCTGGAGTAAGTGGATATTTATAGGTTAAAAAAA 671
                              ii       i      iii  v      ?ii i v i-    i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-AAAAGAA 445

  chr1_13909201_1    672 AAAAAC--AACCTTGACCTAAGTCTTACACATTACACAAAA-TTAATTCA 718
                         vi  ii--i   ----    --i  i    vv  i      -    i   
  L1M4_orf2#LINE/    446 TGAAGTTGGACC----CCTA--CCTCACACCATATACAAAAATTAACTCA 489

  chr1_13909201_1    719 ACATGGATCATAGGCTTAAATGTAA-------AACTATAAA--TCATGTA 759
                          v        ?  i i         -------         --  v iv 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_13909201_1    760 AAAAAA-ATAGGA--AAACCCTAG-GGC--TGGG---GGAATTGAT---- 796
                          i    -     ?--   i i v - i --    ---  v v  i ----
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_13909201_1    797 -AGACA--ACACCAAACGCATGATCCATAAAAGCATAAATTGATGAATCA 843
                         -   i --        v   ii v v i     v v    v   i   ii
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_13909201_1    844 GATTTCATCAAAATTCAAAATGTTTG--CTTTATGAAAAACCCTGCTAAA 891
                           i            v    iv    --   i --  ii  v  iii  i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAG 687

  chr1_13909201_1    892 AAGATAAAAAGACAGGCTGTAGACTAGAAACATATATATATACAAACCAC 941
                           ii i        iv iii   v i i iv v    - - i    i  i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT-T-TGCAAATCAT 735

  chr1_13909201_1    942 ATAGCCAACAAACAACTGATATGCAGACTATATAAAGAATTCTCAAAACC 991
                            v ii i  ivi   vi   v    v           i   i v   i
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_13909201_1    992 CAACAGTGAGAAAACAA----TTCAATCAAAACGTGGGCAAAA-ACATGA 1036
                            i i i i  i    ----ii    i?   vi        i- iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_13909201_1   1037 GCAGATATTTTACTGAGAAGGAGATACAGATGACAAATAATCACATGAAA 1086
                         ii   i    iv ii ii i  v     i   i v     v         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_13909201_1   1087 AGATGTGTACCCTTAGCCATGAA 1109
                              ivi v v i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (119 / 51)
Gap_init rate = 0.04 (28 / 678), avg. gap size = 3.00 (84 / 28)  


2811 27.46 3.39 0.79  chr1_13912443_13915173.rev     1356  2240 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_13912443_1   1356 TGAAAAAGCATTCCGTGCTCATAGATAGGAAGAATCAATATAATAAAAAT 1405
                           i   iii  i  i  i    i   v      v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_13912443_1   1406 GGCCATACTCCCCAAAGCAATTTACAGGTTCGATGCTATTCCTATCAAAC 1455
                            v            vii  i     i   i i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_13912443_1   1456 TACCAATGACATTCTTCACAGAATTAGAAAAAAAAAATTTAAAAATTCAT 1505
                          v   iivi v  i  ii     v v  v  ivvi vii     -     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCAT 149

  chr1_13912443_1   1506 ATGGAATCAAAAAAGAGCCTGAATAACCAACGCAATTCTAAGCAAAAAGA 1555
                               viiv  ii  v  v     i    vi    ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_13912443_1   1556 ACAAAGCTGGAGGCATCATGTTACCTGACTTCAAATTATACTACAGGGCT 1605
                               i      vv   iii v  ii i      viv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_13912443_1   1606 ACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCA 1655
                                i   i    ii         i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_13912443_1   1656 TTGGAAGAGAATATAAAGCCCAGAAATAATGTTGTACACCTACAACCATC 1705
                         v     v     vv i  i          vviii    ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_13912443_1   1706 TGTTGTTCAACAAAGCTGACA---------------GAAACAGGACTCCT 1740
                           v v   i    i v  v  ---------------    v iv v  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_13912443_1   1741 CCATCAATAAATGGTGCAGTGATAACTGGCTAGCCATATGCAGAATATTG 1790
                         i--    i         v v  i      v  ?   i     i  v v  
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_13912443_1   1791 AAGCTGGACACCTACCTAACACCACATACAAAAATCCACTCAAGATGGGT 1840
                            i     v       v      i          iv      i    i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_13912443_1   1841 TAAAAACTTAAATATAAAACTTAAAACTATAAGAACCTTGGCAGATAATC 1890
                         i ? i  i     i   i vi           i vi   i v   v  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_13912443_1   1891 TAGG---AAATACCATTCTGGACACAGGACTTGGCAAAGATTTCACAACA 1937
                             ---    -- -   vv   viv  ii v     v i    vi ivv
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_13912443_1   1938 AAAATGCCAAAAGCAATTGCAAGAAAAACAAAAGTTGACAAATGGAATCT 1987
                          vi ii         vvv    v    iv    i v  i    v i ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_13912443_1   1988 AATTAAGCTGAAAACCTTCTACACAGCAAAAGAAACTGTCAACAGAATAA 2037
                         v  i  iv v    v   i iii vv    i  v   i    v i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_13912443_1   2038 ACAGACATCCTAAAGAATGGGAGAAAATATTTGCAAACTATGCATCTGAC 2087
                          v     v  i v                        ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_13912443_1   2088 AAAGATCTAATATCCAGAATCTATAAGGAACT--TA---------AACAA 2126
                           i iv  vi          v     i     --  ---------  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_13912443_1   2127 ATTTACAA-CAGCCCCATTAAAAAGTGGGAAAAGGACATGAACAGACATT 2175
                          vvv    -i i   v   ?    i    v      iv    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_13912443_1   2176 TTTCAAAAGAAGATATACATGTAGCCAATAAGCATATTAAAAAAATGCTT 2225
                          i  v              vi i           i  -i    i     i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-GAAAAGATGCTC 893

  chr1_13912443_1   2226 GACATCACTAATCAT 2240
                         i      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.70 (37 / 10)  


 828 28.72 12.55 2.34  chr1_13951724_13954681.rev     1006  1475 (1483)    L1M4_orf2#LINE/L1       19   536 (372)  

  chr1_13951724_1   1006 TCATAG-TTTGATGACTCAATGTTGTAAAAACTTCAATTCTCCC-AAATT 1053
                             i -  v  v    i   i    v  i ivv    v     -     
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chr1_13951724_1   1054 AATCTACACATTTAAT-CAG-----ATCAAAATTTAAGCAGA-TTTTCTG 1096
                         i       v   i  i-  i-----        iiv   v v-    i  
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG 118

  chr1_13951724_1   1097 TAAACATTGACAAGATGATTCTAGAATTTAACTGGAAAGGCAAAGGGCC- 1145
                         i i v         v    i   i    i vv      v    i  i  -
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr1_13951724_1   1146 --AAAAGC--------TCTTGGTGAAGGCCACCAGAAATGAAG-ACTTGT 1184
                         --  v   --------     ivi   ivv v  i iv  i  -   iii
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_13951724_1   1185 TCCACCAGATGCTCCAGACAGATAATTAAGCTTCAGTAGTTAGGAGAGCA 1234
                         v iv  vi  -i  v i  vv iv iv     v     i i i  v  ii
  L1M4_orf2#LINE/    219 ACTTCCCAAT-TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_13951724_1   1235 TGGTATTGGGCTAAGAATACACAGAGAGATCAAT--AATGAGAATAAAGT 1282
                              i   vv    i   v   v v        --   -     vi  v
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT-AGAATTGAGA 316

  chr1_13951724_1   1283 GTCCAGAAGCTGACTCA------------CTATTGCATT-------AGGA 1313
                                 iivi  i  ------------ v    -   -------   i
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTG-ATTTTCGACAAGGG 365

  chr1_13951724_1   1314 ---CAACACCAT-CACTGCAGGGCAGCGGAGATGCTT-------AATGGC 1352
                         ---   v     -  v  --   v i- i v vv   -------     i
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATG--GGGAAA-GAATAGTCTTTTCAACAAATGGT 412

  chr1_13951724_1   1353 GGTCAATCAAGTGGAAATTCATATGGAGAAAAAAAGTGAAAGTTGACCTC 1402
                          v viiv   v    v ?i  i   v i  i  ---    iv v    i 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAA---TGAAGTTGGACCCC 459

  chr1_13951724_1   1403 CACTTTACACCATAGATGGAAGTGAGTT--ACATGCAGATTGTAGATTTC 1450
                         i  i i        v iii  i v ii -- v   --   ii?   ii v
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATG--GATCAWAGACCTA 507

  chr1_13951724_1   1451 AATGTGAAATC-AAAAC---AAAACTTTT 1475
                              i i v -     ---      i  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTT 536

Transitions / transversions = 1.25 (74 / 59)
Gap_init rate = 0.05 (24 / 518), avg. gap size = 2.92 (70 / 24)  

 312 27.67 11.07 7.11  chr1_13951724_13954681.rev     1815  2067 (891)    L1M4_orf2#LINE/L1      563   825 (83)  

  chr1_13951724_1   1815 GTAACGGTGGGC-GGGCAATA-CTTCTTAAACGAGACACAAAAAGCACCA 1862
                           i  vv    i-i      i-i      i iiv     v        v 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_13951724_1   1863 ACCATTAGGGAAAAGATTGATAAATTAGAT---ATCAAAGTTAAGAACTT 1909
                         i v iv ii     i  v        i  i---      i    i     
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_13951724_1   1910 -----CTCC------CATT-TCT-----GTGACTAGTCTTTCTACTCTCT 1942
                         -----  i ------  i -  v-----    vv  v v----  i v v
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA----ACCCACA 708

  chr1_13951724_1   1943 TATTATTGTCTCTTGATGAAAGAAAGAAATGTGTAACACCTATAACCAAG 1992
                         v -------------   ii     - v  v  i  vv v    v ii v
  L1M4_orf2#LINE/    709 GA-------------ATGGGAGAAA-ATATTTGCAAATCATATATCTGAT 744

  chr1_13951724_1   1993 AAAAGATTCATATTCTCATTATAGAAAGAACTCCCCCAAATCAATAA--- 2039
                           ii  i ii   i vv v    v         iiv   v       ---
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_13951724_1   2040 ---GGCAAAAAACTCAGTTAAAACATAGACA 2067
                         --- i    v   i  i  ?   v  i i  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 1.23 (38 / 31)
Gap_init rate = 0.04 (11 / 263), avg. gap size = 4.18 (46 / 11)  

 222 25.95 6.11 4.58  chr1_13951724_13954681.rev     2347  2477 (481)    L1M4_orf2#LINE/L1      776   908 (0)  

  chr1_13951724_1   2347 TCTTAAAAAACAA--ACAAACAAACAAACAAACAAAAAAACAAAAGTAGA 2394
                              v  vv   -- i   v i     i  v v  vv? --   i i i
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA--AAAATGGG 823

  chr1_13951724_1   2395 CAGGAAACTTGGACAAGCATTTCACAAACGAGGGTATTTAAATGGCCAAT 2444
                           iiii i   i i ii      v v  v  i i   vi           
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_13951724_1   2445 A------TGAAAAGATGTTCACCCCCCATTATTCATCGG 2477
                          ------          i   v ----  i ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAAC----ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (20 / 13)
Gap_init rate = 0.03 (4 / 133), avg. gap size = 3.50 (14 / 4)  


 425 23.86 10.15 5.08  chr1_13990910_13992757.rev      502   698 (1150)    L1M4_orf2#LINE/L1      195   401 (507)  

  chr1_13990910_1    502 GAAG--CAAAGCTGGAGGACTTACACTCTTGAATAGTAAACCTGATACCC 549
                             --     i         i     iiiv   vvi   v  --   iv
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT--TACTA 242

  chr1_13990910_1    550 CAAAG------TAATTAAAACAGTATGGTGTGAGTACA-GGACAGGTAAA 592
                              ------    i  i     i    iivi i i -   i  ii v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_13990910_1    593 CACATCAA-AGAACAGAAT--AGAGTCCA-AAACAGACCACATATAGG-A 637
                         i v     -i   i     --        -   i i   -    i vv- 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC-CATACATTTA 341

  chr1_13990910_1    638 TGGACACTTGATTCATGGCAAA------AAGAGCACTTCAGAACATGGGA 681
                            v  v      ivi i   i------    v  -    ----     i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCA----ATGGGG 386

  chr1_13990910_1    682 CAGAAAAATAACCTTTT 698
                         --i  i    ii     
  L1M4_orf2#LINE/    387 --AAAGAATAGTCTTTT 401

Transitions / transversions = 2.36 (33 / 14)
Gap_init rate = 0.06 (13 / 207), avg. gap size = 2.31 (30 / 13)  

 897 27.34 19.46 0.00  chr1_13990910_13992757.rev      944  1349 (499)    L1M4_orf2#LINE/L1      389   873 (35)  

  chr1_13990910_1    944 AAAATAACCTTTTTAATAAATGGCTCTGGGTCAATAGGATATTCATACAG 993
                          i    ii     i  i      iv     v   iv     ?i  i iiv
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_13990910_1    994 AAAAGGAAGAATCATGACCCCTAACTCACACCATACACAAAAATTAATTT 1043
                              i v   vivv        v           i           i i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_13990910_1   1044 CAGGTAGATTTTAGATCCAAATATAAAAGGTTAA-CAATAAAGCTTCTAA 1092
                         v ii i   iv?   i i    i   i  v v  - v     i  ii  i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_13990910_1   1093 AAGATAACATAGGC-----------------TGGGT---GTGGTGGCCT- 1121
                             v        ?-----------------     --- iii   ii -
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_13990910_1   1122 ------ATGA-----------------------GAAATATTA-ATATTGT 1141
                         ------    -----------------------    v v  -   vvv 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_13990910_1   1142 GGACTACATCAAAATTGGAAGTTTCTGCTCATCAA----CAATGTCA-GA 1186
                              v          ii  ii  i  iv v    ----  v i   -  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_13990910_1   1187 GGGTGAAAAGGCAAGCCACA---------------TCCACCATCCATATG 1221
                         ii        i   v     --------------- iii v vi     i
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_13990910_1   1222 CCCCA-AAG--ACTGGCATGCACACTATATATA-AACTTTTAAAATTTAA 1267
                         i iv -   --   v i  v  v v      v -    i   v  i i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_13990910_1   1268 TAAGGAAAACACAGATAACCCAATACAGAAATGGACAAAAGCCTTGAACA 1317
                            vi    v   i          v? i      i    i vi     i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_13990910_1   1318 AACA---CTTGACAACAGATGTCCAAATGGCCAAT 1349
                         i   ---  iv v iv    i v            
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

Transitions / transversions = 1.55 (65 / 42)
Gap_init rate = 0.03 (13 / 485), avg. gap size = 6.08 (79 / 13)  


2822 25.63 0.96 1.56  chr1_14008256_14010861.rev      884  1718 (888)    L1M4_orf2#LINE/L1        2   831 (77)  

  chr1_14008256_1    884 GAAAAAAACTTCCATGCTCATGGATTGGAAGAATCAATATTTTTAAAATG 933
                          i   i vv i     i               v i      v    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_14008256_1    934 ACCATACTGCCCAAAGCAATCTACAGATTCAATGCGATTTCTATTAAATT 983
                         i v     v      vii              i  i  ii    i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_14008256_1    984 ATCAAC-ATCATTTTT-CATATTTCAATTAGAAAAAACAATCCTGAAATT 1031
                         vi  i -ii v     -  v ----    -  v  ivii     i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGA----AATT-GACAAGCTGATCCTAAAATT 146

  chr1_14008256_1   1032 CACATGGAACCAAAAAAGAGTCTGAATAGCCAAAATACTCCTAAGCAAAA 1081
                           i      viiv  ii  vi v            i v  i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_14008256_1   1082 ATAACAAAACTGGAGACATCACATTATCTAACTTCAAATTATACTATAAT 1131
                          v      ii     ivv     i vi i  i      viv     i  v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_14008256_1   1132 GATACTACAAGTTTATAACAGCATGGTACTGGCATAAAAATAGAAACATA 1181
                          v   vii  -- i vi    ii              ii     v i   
  L1M4_orf2#LINE/    247 GCTACAGTAA--TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_14008256_1   1182 GGTCAATTGAACAGAATAGAGAACCCAGAAATACAGCCACATACCTACAA 1231
                          i     v   i     v    ii         v v   i i ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_14008256_1   1232 CCAGCTGATCTTTAACAAAGTCAACAAAAATATACACTGAGGAAAGA-CA 1280
                         i  ii    i  ii    i viiv   i vi  v  v  i       -i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_14008256_1   1281 CCCTATTCAATAAATGGTGCTAGGAAAATTGGTTAGCCATTTACAAAAGA 1330
                         vi  v     i          i   v  i   v  ?   iv i       
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_14008256_1   1331 ATAAAACTGGACCCATATCTCTCACTATACACAAAAATTAACTCAAGATG 1380
                           i  ii       v  i   v   i   i                i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_14008256_1   1381 GATTAAAGACTTAAATATAAGACCTGAAACTCTAAAAATCCTTGAAGAAA 1430
                            i ?    i     i     v  i     v     v  i v       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_14008256_1   1431 ACCTAGGA--AAATCTCTTCTGGACATTGGTATAGGCCAAAGAA--CTTA 1476
                           v    ?--      --  vv   v    vv     -  v iv--    
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCT--TCGTGACCTTGGGTTAGGC-AATGGTTTCTTA 591

  chr1_14008256_1   1477 CGACTAAGTCCTCAAAAGCAAATGCAACGAAAACAAAAATAAACAAATGA 1526
                         -  -  v v vi        v v     i   iv       i i    vi
  L1M4_orf2#LINE/    592 -GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_14008256_1   1527 GACTTAATTAAA-CTAAAAGCTTCTGCATAGCAAAAGAAATAATCAACAG 1575
                              v  i   -i     i   i  iiivv    i  v iv     v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_14008256_1   1576 AGTAAACAGACAACCTATGCAATGGGAGAAAATATTTGCAAACTATGCAT 1625
                            i  v        i iiv                      ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_14008256_1   1626 CTGACAAAGTACTAATATCCAGGATCTACAAGGAACTCAAACAACTCATC 1675
                             i  i v   vi       i  v  i  i      vv        vi
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_14008256_1   1676 AAGGAAAACAACAAATAACACCATTAAAAAGTGGGCAAAGGAT 1718
                           vi    -i         v v   ?    i            
  L1M4_orf2#LINE/    790 AATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.56 (128 / 82)
Gap_init rate = 0.02 (14 / 830), avg. gap size = 1.50 (21 / 14)  

 377 20.31 5.47 0.00  chr1_14008256_14010861.rev     1988  2115 (491)    L1M4_orf2#LINE/L1      774   908 (0)  

  chr1_14008256_1   1988 ACTC---CATTTCAAAAAAAAAAAAACAAAAGAA--AA--AAAAAGTGGG 2030
                             ---  vi    v  v     i     vi v--  --?    i    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_14008256_1   2031 GAAAAAACATGAATGGACATTTTTCAAAAGAAGATATACAAGTGGCCAAA 2080
                         v   ii iv     i       i  v               i       v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_14008256_1   2081 AAACATACATAAAAATGCTCAACATCACTAATCAT 2115
                           i  i iiv   i             ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.02 (3 / 135), avg. gap size = 2.33 (7 / 3)  


3079 26.66 1.11 0.66  chr1_14068267_14074563     4901  5804 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_14068267_1   4901 TAAAAAAACATTTCATCCTCATGGATAGGAAGAATAAATATCATGAAAAT 4950
                          ii   i i  ii   vi        v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_14068267_1   4951 GGCCATACTGCCCAAAGGAATTTTTAAATTCAATGTTATTCCTATCAAAC 5000
                            v     v      vvi  i vi i      i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_14068267_1   5001 TACCATTGACATTCTTCACA-AAATTAGAAAAAACT-ACTTTAAATTTCA 5048
                          v   vivi v  i  ii  -     i-- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_14068267_1   5049 TATGGAA-T-CAAAGAAGACCCCATATAGCCAAGACAATCCTAGGCAAAA 5096
                                - -   i --     viv        i      i iiiv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_14068267_1   5097 AGAACAAAGCTTGAGGCATCACGCTACCTGACTTCAAACTATACTGCAAG 5146
                                  i v    vv    i  v  ii i      viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_14068267_1   5147 GCTACAGTAACCAAAACAGCATGGCACTTGTACCAAAACAGACATATAGA 5196
                                   i   i    ii   i   v i iv ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_14068267_1   5197 CCAATGGAACAGGACAGAGACCTCAGAAATAACACCATACATCTACAACC 5246
                         i        i  i iv    vii         vv        i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_14068267_1   5247 ATCTGATCTTCGACAAACCTGATAAAA--AG-CAATGGGGAAAGGATCTC 5293
                          vi    i        ivv  vi  i -- v-            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_14068267_1   5294 CTATTCAATAAATGGTGCTCAGAAAACTGGCTAGCCATATGCAGAAAACT 5343
                           v     i          vi  v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_14068267_1   5344 GAAACTGGACCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGGA 5393
                            ii         v   i i   v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_14068267_1   5394 TTAAAGACTTAAATGTAAAACCCCAAACCATAAAATCCCTAAAAGAAAAC 5443
                          i ?    i         i v iv    i      ii i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_14068267_1   5444 CTAGACAGTA--CCATTCAGGACACAGACATGGGCAATGACCTCATAATC 5491
                         v   i?-   --i -   iv   viv ivv i       iii  v  ivi
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_14068267_1   5492 AAAATGCCAAAAGCAATTGCAACAAAAGCCAAAATTGGCAAATGGGATCT 5541
                          vi ii         vvv          vv     v ii    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_14068267_1   5542 AATTAAACTAAAGAACTTCTGCACAACAAAAGAAACTATTATCAGAGTGA 5591
                         v  i   v v  i     i  ii vv    i  v     i vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_14068267_1   5592 ACAGGCAACCTACAGAATGGGAAAAAATTTTTGCAATCTACCCATCTGAC 5641
                          v  i     i           i     v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_14068267_1   5642 AAAGGTCTAATATCCAGAATATACAAGGAACTTAAAGAAATTTACAAGAA 5691
                           i  v  vi             i  i     ivv v  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_14068267_1   5692 AAAT-CAAACAACCCAGTCAAAAAGTGGGCAAAGGACATGAACAGACCGT 5740
                            v-    i      i i?    i           iv    i    vv 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_14068267_1   5741 TCTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTCA 5790
                             v        i  vi vi       i  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_14068267_1   5791 ACATCACTGATTGA 5804
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


1508 27.36 4.79 5.30  chr1_14074648_14076432      500  1292 (493)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr1_14074648_1    500 AGAAAATTACAAGTTGAACCTAAAATGTATGTGGAAATGCAAGATGCTAG 549
                              v v     i   v        vi  i            ------ 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG------G 163

  chr1_14074648_1    550 GACTTGTCAAGGCAATCTAGCCAGCACTTACACTTTTATATAGAAAGAAG 599
                            ---- v  --   --     i- ---   v i  i--- i       
  L1M4_orf2#LINE/    164 GAC----CCAG--AAT--AGCCAA-A---ACAATCTTG---AAAAAGAAG 198

  chr1_14074648_1    600 TGAAAATAGATGAAGGACTTAGACTACTAGATACCAATTCCTATTTAAAA 649
                         --  v v  v  i      i v   v ivi  vi   vv i  i vv   
  L1M4_orf2#LINE/    199 --AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_14074648_1    650 AC-ATAGTAAT-AAGA--GTATAATACTGACACACGGATGGACAAAGACA 695
                         i - i      -    --  i ii     i  i v    i    --v i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA--TATA 294

  chr1_14074648_1    696 GACCA-TAAAA-AGA---GAAAGTCCAGAAATATACCCACAAATATACAG 740
                           i  - ii  -   ---  i            v     i v  v  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_14074648_1    741 TCATTTGATTT---GTAAGA---CCACACACTGCAGTGTGGTGGTGAAAT 784
                            v       ---ii   i---   - v  --  v -iii   v    v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCA-AGAC--CATT-CAATGGGGAAAG 390

  chr1_14074648_1    785 TATTTTTATTTCAATAAATGCTGCCAAGTTAACTGGCTATTTATATGAAA 834
                         v  vv iv      i     v   iii vi      v  ?ii i   v  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_14074648_1    835 AAAGATGACAGGTGCATGGTAGACCTAATTGTGAAAGCAAAAGCAAGC-A 883
                           ii    -  v  v ivvi-v    v ivviiv vi     iiv i -v
  L1M4_orf2#LINE/    441 AAGAATGA-AGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTC 488

  chr1_14074648_1    884 AAAACAAAACAGAAAC--------AAAACCAGAAACCA-AAAACCCTCCT 924
                             iii v  ? i  --------  i v vi    i -     i  -- 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT--T 536

  chr1_14074648_1    925 AGAAGAAAATGTAGGAGAGCAGATTTATGATTTTGAGGCAGTCAACATTG 974
                                  ii    ? viv vv  ii   ii   i vi  v   iiv v
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_14074648_1    975 TTTTAAATGAGAT-CCAGAAAGCTCTAACCATAACGAAAAAAGGAACTGG 1023
                          i   i  iv  i-   -     v v i ---   i   i  ii  iv i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCA-AAAGCACAAGC---AACAAAAGAAAAAATAGA 632

  chr1_14074648_1   1024 TAAATAGGACTACATTAAAATTGAGAGCTTCTGTTCTTCAACAGATACTA 1073
                              v     v   i      i i i   i   v      vi  i    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_14074648_1   1074 TTAAGGGAGTTAAAAGGCAGTTCATGGAATGGAAAAAGACATTTGCAA-- 1121
                          i   ii   v     i  iii  ii      i i  i i        --
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_14074648_1   1122 --TATATTTGACAAAAGACTCATTTACATAATATATAAAGG-CCCTTACA 1168
                         --     i   i  ii    ii v v  v           i- i      
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_14074648_1   1169 AATCAATAATAAGAAAGCAGGCAATTTAATAGAAAAAATGGGCAAAGGGT 1218
                          v          i  ii  iii  iii   -v?               i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGAT 831

  chr1_14074648_1   1219 TTTAGCATTCACCTCCCAAAAGAGGATATCTAAACTGCCCAAAAA----- 1263
                           v ii vv  ii  i v     i     vi   -  v    v  -----
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACA 880

  chr1_14074648_1   1264 --AAAAGCAAATGTCCAACGTCATTAGAAAT 1292
                         --     ---   ii    i   ????????
  L1M4_orf2#LINE/    881 TGAAAAG---ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (134 / 79)
Gap_init rate = 0.04 (35 / 789), avg. gap size = 2.29 (80 / 35)  


3249 26.65 0.55 0.55  chr1_14100526_14102589.rev      666  1573 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_14100526_1    666 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 715
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_14100526_1    716 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 765
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_14100526_1    766 TACCAA-TGACTTTCTT-CAAAGAATTGGAAAAAACT-ACTTTAAAGTTC 812
                          v   i-  v    i  -  i -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_14100526_1    813 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGGCAATCCTAAGCCAAAA 862
                                 viiv  ii  v  v v  v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_14100526_1    863 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 912
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_14100526_1    913 CTACAGTAACCGAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 962
                                  i i i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_14100526_1    963 CAATGCAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAAC 1010
                              v  i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_14100526_1   1011 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTT 1060
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_14100526_1   1061 CCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCGTATGTAGAAAGC 1110
                         i  v  i  i        i     v      v  ?  ii   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_14100526_1   1111 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCGAGATGG 1160
                             ii    i    v   i     v           i  i  i i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_14100526_1   1161 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1210
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_14100526_1   1211 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 1260
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_14100526_1   1261 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 1310
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_14100526_1   1311 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1360
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_14100526_1   1361 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 1410
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_14100526_1   1411 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1460
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_14100526_1   1461 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 1510
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_14100526_1   1511 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1560
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_14100526_1   1561 CATCACTGGCCAT 1573
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1783 20.43 12.86 7.57  chr1_14157295_14160473.rev     1531  2230 (949)    L1M4_orf2#LINE/L1        1   737 (171)  

  chr1_14157295_1   1531 TGGAGAGATACATCATATGCTCATTGACTAGAAGATTCACTATGATGATG 1580
                             i     --  vi   i    v  i i     i i v   vi v v 
  L1M4_orf2#LINE/      1 TGGAAAGATA--TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_14157295_1   1581 ATGGTGACG-TCC----------------GTTC-------TCCCTAGTCA 1606
                             ii ii-   ----------------i   -------      -   
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCA 97

  chr1_14157295_1   1607 AATTCCCAGCAAGCTGTTTTTG-AAAAATTCACAA------CCTAA---T 1646
                           v       v-  iv      - i     v    ------     --- 
  L1M4_orf2#LINE/     98 AAATCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_14157295_1   1647 GATA--GAAACACAAAGGACTTAGAATAGCAAAAACAATTTTTAAAAAGA 1694
                         v   --    ii   i    ii        v        i  v       
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_14157295_1   1695 A----AAAGTTGGAGGCCTTACAATTATTTGATTTCAAGA--TATTATAA 1738
                          ----           v  i   v  -iiii       i --  i  i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAA 245

  chr1_14157295_1   1739 AGCTGAAGATATCAAGACTGTGTAGCATTTGCATAA-------------- 1774
                             iv  vv        v    i i i v      --------------
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_14157295_1   1775 --CAAC---ACAGAAGACAGTGTCTACAAATTGACCCACGCATACATGGT 1819
                         --   i--- i    vvv  v   i v    vi     ii   vi     
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_14157295_1   1820 CAATTAAATTTCAACAAAGATGTCAAGACAATTCAATGGAGAAAAGATAA 1869
                              i v    i    i i  i      v         i    ii   i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_14157295_1   1870 TCTTTTAAATAAATTATCCTCGAACAATTGGATATCCGTAT--------- 1910
                               v  i    vi v  v i    i      ?  ii  ---------
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_14157295_1   1911 -----CTAGACCCTTCCCTCATACTATGTACAAAAATTAACTCCAAATGG 1955
                         -----i i     i v     i  i  i               v      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_14157295_1   1956 ATCATAGACCTAAATGTAAAAGCTAAA-TTATAAAACTTCTAGAAAAAAA 2004
                             ?              i       -i         ii     i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_14157295_1   2005 --TAGGAGAAAATATTAATT-CTTTGAGTACAGCAAAGTCTACTTAAATA 2051
                         --    ? v    v  vi v- i   i  -------------------  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGT-------------------TA 576

  chr1_14157295_1   2052 GGCAAAGATTATTTATGTCTTTAGAACTTA-AAAACTTAAAGTTCTTTAG 2100
                              v i  -------    -   ---  -i v  iv    iv ----i
  L1M4_orf2#LINE/    577 GGCAATGGTT-------TCTT-AGA---TATGACACCAAAAGCAC----A 611

  chr1_14157295_1   2101 AGTAAATGTGAAATATAAAAGAAACAATTGATAAATTTAAC---ATCAAA 2147
                           i  ----------i        v   v        vi  ---      
  L1M4_orf2#LINE/    612 AGCAA----------CAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_14157295_1   2148 ATTAAAACCTTTTAATATTTGA---GATACTGATAAGAAAATGAAAAGGC 2194
                                v     i- ii  v ---  i   ivi      i       i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_14157295_1   2195 AAACCATAGACTGGGAGAACCAAATACCTAC----CATAT 2230
                           v   i   v        ---    ii i ----     
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAA---AATATTTGCAAATCATAT 737

Transitions / transversions = 1.75 (89 / 51)
Gap_init rate = 0.04 (31 / 737), avg. gap size = 4.61 (143 / 31)  

 647 22.42 0.90 5.38  chr1_14157295_14160473.rev     2466  2688 (491)    L1M4_orf2#LINE/L1      696   908 (0)  

  chr1_14157295_1   2466 AAAATAAACCAAACCAAACCAAAATAAAATATTTGCAAGATGTATATTTG 2515
                           i i  v   ---  i viiii v             ivii     i  
  L1M4_orf2#LINE/    696 AAGACAACCCA---CAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_14157295_1   2516 ATAAGAGATTTGCGTCCAAAATATATGAAGAACTCCTAAAACTCAATTGT 2565
                              i  i   ii    i       i        i  v        vi 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_14157295_1   2566 ATGAAATCAAAATATCCAAC--AAATATGAGCAAGGGATTTGAACAGACA 2613
                          vi  iv    vv i    i--   v   i    i         i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_14157295_1   2614 TCTCACCAAAGTATATTTAAGAGGATGGCAAATAAGAATATGAGGGCCAA 2663
                          i  v      v v  v  vi --     v      v i    i------
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAA--ATGGCCAATAAGCACATGAA------ 884

  chr1_14157295_1   2664 TAAGATGCTGAACAACAATAATCAT 2688
                         -        v    v  ????????
  L1M4_orf2#LINE/    885 -AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (30 / 20)
Gap_init rate = 0.02 (4 / 213), avg. gap size = 3.50 (14 / 4)  


1364 25.68 0.60 0.00  chr1_14224245_14229177.rev     3227  3557 (1376)    L1M4_orf2#LINE/L1        1   333 (575)  

  chr1_14224245_1   3227 TGGAAAGATATTTCATGTTCATGGATTGGAAGAATCGATATTATTAAAAT 3276
                                    ii                    v ii     i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_14224245_1   3277 CCCCACACTACTCACAGCAATCTACAGGT-CAATGCAATCCCTATCAGAA 3325
                         vv v i   v i  v vii        i -   i             i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_14224245_1   3326 TACTAATGGCATTCTTCACATAAGTAGAAAAAA-AATCCTAAAATTTATA 3374
                          v i iiv  v  i  ii  v  i v  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_14224245_1   3375 TGTAACCACAAAAGACCCAGAATGGCCAAAACTATTATAAGCAAAAAGAA 3424
                           v  vii   ii          i        v  iv i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_14224245_1   3425 CAAAACTGGAGGAATAACATTACCTGACTTTAAATTATACTACAGACCTA 3474
                             ii       v v   i v  ii i  i   viv       i v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_14224245_1   3475 CAGTAACCAAAATGGTATGGTCCTGGCATAAAAACAGACCTGTAGACCAG 3524
                               i   i ii  i    v         ii i    v i    i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_14224245_1   3525 TGGAACAGAATAGAGAACCCAGAAACAAATCCA 3557
                              i     v    ii       i   i   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

Transitions / transversions = 2.04 (57 / 28)
Gap_init rate = 0.01 (2 / 333), avg. gap size = 1.00 (2 / 2)  

1747 25.50 2.73 1.64  chr1_14224245_14229177.rev     3896  4444 (489)    L1M4_orf2#LINE/L1      354   908 (0)  

  chr1_14224245_1   3896 TTTTGACAAAGGTGCCAATAACATACACTGAGAAAAAGACA--------- 3936
                            i     i        v v   v  v  i i   ii i ---------
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_14224245_1   3937 -TAAATGAAGCTGGGAAAGTTGGATATCCAAATGCGAAAGAATGAAACTA 3985
                         -i     iv       v ii      ?   v    i          ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_14224245_1   3986 GATCCCTATCTCTCAACATATACGAAAATGGAATCAAAATG-ATTAAAGA 4034
                           i     i   v  v       i     vi v        -  i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_14224245_1   4035 CTTAAATCTAA-ACCTCATACTGTGAAACTACTAAAAGAAAACATTGGGG 4083
                          i     v   - v  v v   i i     vi  i          v  ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_14224245_1   4084 GAAACTCTCCAGAGCATTGATCTGGGCAAAAATTTCTTGAATGAT-ACCC 4132
                         v   -   i ivii v   ivi i     vii      ii  -  -  v 
  L1M4_orf2#LINE/    554 TAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACAC 601

  chr1_14224245_1   4133 CACAAGCATAGGCAGCCAAAGCAAATATGGACATATGTGAACA-CATCAA 4181
                           v     i i   i v    v   v  i  i v  -  i  v-      
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT-TGGACTTCATCAA 650

  chr1_14224245_1   4182 A-TTAAAAAGCTTCTGCACGGCAAAGGAAACAATTAACAAAGTGACAAGA 4230
                          -       -   i  ii vv       v  v  i  v       v    
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_14224245_1   4231 CAACTCCCAAATATTGGGAGACGATATTTACAAACTACCCATCTGACAAG 4280
                             i v  i -  -      vi      i    ii ivi      i   
  L1M4_orf2#LINE/    700 CAACCCACAGA-AT-GGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_14224245_1   4281 GGATTCATAATTAGATTTTATAAGAAGTTCAAACAACTCTGTAGGAAAAA 4330
                            i ii  vii   v v     ii ii  vv       vi  iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_14224245_1   4331 TATCTAATAATCTGATTTTTAAGTGGGCGAAAGATCTAAATAGACATTTC 4380
                         v - v     i ii   ?vv  i     i  i   i i            
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_14224245_1   4381 TCAATTAAAAAAACTTACCAATGGCAAACAGGTATATGAAAAGATGCTCA 4430
                           v --  i  i iv   v      v  i i i i               
  L1M4_orf2#LINE/    847 TCCA--AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_14224245_1   4431 ACATTCTTGATCAT 4444
                             iv????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (82 / 54)
Gap_init rate = 0.03 (14 / 555), avg. gap size = 1.71 (24 / 14)  


2494 25.59 3.32 6.10  chr1_14296291_14298607      904  1837 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_14296291_1    904 TGGAAAAACATTCCATGGTCATGGATAGAAAGAATCAATATCATGAAAAT 953
                               i i  i     v        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_14296291_1    954 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATCCTTTTCAAAC 1003
                            v     v      vii  i           i  v    i v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_14296291_1   1004 TACCAATGACATTTTTCACAAAATTAGAAAAA--AATTCTAAAATTCATT 1051
                          v   iivi v     ii  i  v v  v  i--i  i           v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_14296291_1   1052 TGAAACAAAAAAATAAGCCTGAATAGCCAAAGCAAGCCTAAGCAAAAAGA 1101
                           i  - viv  ivi v  v           i   v i i iv  i    
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_14296291_1   1102 ACA------GAGGCATCATACTACCTTACTTCAAACTATATTACAGGG-T 1144
                            ------    vv   i   v  iv i      viv  i    ii - 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_14296291_1   1145 ATAGTAACTAAAACAGTATG-TCCTGGTGCAGAAAACAGACACATAGGCC 1193
                          i     ii  i     i  - v    iii - ii i     i    ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATA-AGGATAGACATATAGATC 298

  chr1_14296291_1   1194 AATGGAA--------------CAGTAGTAAAGC--TACATTCCTACAAGT 1227
                                --------------   v i    v --      --  iiivi
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTC 346

  chr1_14296291_1   1228 ATCTAATCCTTGATAAAGCCAATAATAACGAGCAATGGGGAAAGGAAT-G 1276
                          vi i  ii i  i  i viivi  v v ivv            -   - 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAG 395

  chr1_14296291_1   1277 CCTATTCAATAAGTGGTACTGGAATAATTGGCCAGCCATATGCAGA-GAA 1325
                         i  v     i  i    i    i i  i   vi ?   i     i -   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_14296291_1   1326 TATTGAAACTGGACCC-TGCATTTCACCATATGCAAAATTTAACTCAAGA 1374
                          ---   ii       - i v iv        i     v         i 
  L1M4_orf2#LINE/    446 T---GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_14296291_1   1375 TGGATTAAGGACTTAAGTGTGAAACCTAAAACTGTAAAAACCCTGGAAGA 1424
                              i ?i   i   i   i i v        i     vi i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_14296291_1   1425 CAACCTAGGAATTACCATTTGAGACACAGGCCTTGGTGAAGACTTCAT-G 1473
                         v   v    ?i v viv  i v   viv  vi v  ii v ii   v - 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_14296291_1   1474 ATGAAGACTCCAAAAGCAATTGCAACAAAAACAAAAATTGACCA-TAGGA 1522
                           - v   v         vvv         iv      v  iv - v   
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_14296291_1   1523 CCTAATCAAACTAAAGAGCTTCTGCACAGCAAAAAACAAAAAAACAAAAC 1572
                          i v      v v  i i   i  ii vv    ii   ------------
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA------------ 679

  chr1_14296291_1   1573 AACAAACAACAAAACAAAACAAACAAAAAACCACCCTATCAACAGAGTAA 1622
                         -----------------------------------       v i   i 
  L1M4_orf2#LINE/    680 -----------------------------------CTATCAAGAAAGTGA 694

  chr1_14296291_1   1623 ACAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCTGAC 1672
                          v        i                          ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_14296291_1   1673 GAAGGTCGAATATCCAGAATCTATAAGGAACTTAAGCAAATTAACAAGCA 1722
                         i i  v vvi          v     i     ivvi   v i  i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_14296291_1   1723 AAACCCAAACAATCTCGTTAAAAAATGGGCAAAGGACATGAACAGACACT 1772
                            vv    i  i ivi  ?                iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_14296291_1   1773 TCTCAAAAGAAGACATACATGTGGCCAACAAGCATATGAAAAAAATTTTC 1822
                             v        i     vi       i     i       i - vi  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chr1_14296291_1   1823 AATATCACTAATCAT 1837
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 4.63 (88 / 19)  


3329 26.22 0.88 0.44  chr1_14427481_14434141.rev     5267  6170 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_14427481_1   5267 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5316
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_14427481_1   5317 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCTATCAAGC 5366
                            v     v      v i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_14427481_1   5367 CACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTCTAAATTTCAT 5415
                         iv   vivi i  i  ii     v v  v  i-  - ii     v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_14427481_1   5416 ATGGAACCAAAAAAGAGCCCGTATAGTCAAGACAATCCTAAGCAAAAAGA 5465
                               viiv  ii  v  v v    i   i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_14427481_1   5466 ACAAAGCTGGAGGTATCCTGCTACCTGACTTCAAACTATACTACAAGGCT 5515
                               i      vv  vii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_14427481_1   5516 ACAGTAACCAAAACAGCATGGTACCAGTACCCAAACAGATATATAGACCA 5565
                                i   i    ii      ii i ivvii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_14427481_1   5566 ATGGAACAGAACAGAGGACTCAGAAATAACGCCACACATCCACAACCATC 5615
                               i    iv   iiii         vv   i    ii iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_14427481_1   5616 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5665
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_14427481_1   5666 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 5715
                           i  i        i     v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_14427481_1   5716 ACTGGACCCCTTCCTTACACCTTATACAAAAAATAACTCAAGATGGATTA 5765
                         ii         v   i     v          v        i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_14427481_1   5766 AAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAATCTA 5815
                         ?    i       v   v       i      vi i          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_14427481_1   5816 GGC---AATCCCATTCAGGACCTAGGCATGGGCAAAAACTTCATGACTAA 5862
                           ?---    ---   iv     v  vv i     viii   v iiv  v
  L1M4_orf2#LINE/    550 GGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_14427481_1   5863 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5912
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_14427481_1   5913 TTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTATCATCAGAGTGAAC 5962
                          i   v v  i i   i  ii vvi   i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_14427481_1   5963 AGGCAGCCTACAGAATGAAAGAAAATTTTTACAACCTATCAATCTGACAA 6012
                           i  i  i        ii       v   i   vii  vv      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_14427481_1   6013 AGGGCTAATATCCAGAATCTACAAGGAACTCAAACAAATTTACAAGAGAA 6062
                         i  i  vi          v  i  i      vv    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_14427481_1   6063 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 6108
                          i    ----   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_14427481_1   6109 TCAAAAGAAGACATTTATGAGGCCAACAAACACATGAAAAAAAGCTCGTC 6158
                           v        i  vi viv      i  i          i v    iv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_14427481_1   6159 ATCACTGGTCAT 6170
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.40 (12 / 5)  


2065 24.28 1.44 0.00  chr1_14454372_14460643.rev        4   489 (5783)  C L1M4_orf2#LINE/L1   (280)   628   136  

C chr1_14454372_1    489 ATTCTAAACTTCATATGGAACCACAAAAGACCCTGAATAGCCAAGGCTAT 440
                           i     v           vii   ii     v          ii v  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

C chr1_14454372_1    439 CCTAAACAAAAAGAACAAAACTGGAGGAATCACATTACTTGACTTTAAAA 390
                          i i  v  i         ii       v     i v iii i  i    
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

C chr1_14454372_1    389 TATACTACAGAGTTATAGTAGCCAAAACAGTACAGTACTGGCATAAAAAT 340
                         iv       i  i  i    ii   i     iii            ii  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

C chr1_14454372_1    339 AGACACATAGATCAGTGGAACAGA-----GAACCCAGAGATAAATAGATA 295
                              i        i     i   -----  ii     i     ivv   
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

C chr1_14454372_1    294 CATCTATGATGAGCTCATTTTTGACAAACATGCCAAGAGCATACACTGGG 245
                            i    i v ii v     i     ivi        v   v  v    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

C chr1_14454372_1    244 AAAAAAA--GTCTCTTCAATAAATGATGCAGGGAAAACTGGATATCCATA 197
                         i   i  --    i     i     i   v    v         ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

C chr1_14454372_1    196 TGCAGAAGAATGAAACTAGACCCCTATCTCTAAAAATATACAAAAATCAA 147
                             i         ii i        i   vv vv            i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

C chr1_14454372_1    146 ATCAAGAAGAATTACAGACTTAAATATAAGACCTAAAACTATGATACTAC 97
                         v    i v i  i ?    i     i     v          i v   vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

C chr1_14454372_1     96 TAAAAGAAAACATTAGGGAAACTCTCCAGGACATTGGACTGGGCAAAGAT 47
                           i          vi ? v  v   i iv   v    ii i     v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

C chr1_14454372_1     46 TTCTTGAGTAATATCCCACAAGCACAGGCAACCAAAGCAAAAA 4
                              iii  vv iv   v       i     v    v     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

Transitions / transversions = 1.95 (76 / 39)
Gap_init rate = 0.00 (2 / 493), avg. gap size = 3.50 (7 / 2)  

3236 27.24 0.78 0.22  chr1_14454372_14460643.rev     4879  5781 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_14454372_1   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4928
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_14454372_1   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_14454372_1   4979 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5027
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_14454372_1   5028 TGGAATCAAAAAAGAGCCCATATAGCCAAGTCAATCCTAAGCCAAAAGAA 5077
                              viiv  ii  v  viv        iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_14454372_1   5078 CAAAGGCGGAGGCATCACAGTACCTGACTTCAAACTATACTACAAGGCTA 5127
                              vi     vv     v v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_14454372_1   5128 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGAGAGATCAA 5177
                               i   i    ii         i iv ii i   v v v       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_14454372_1   5178 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT 5225
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_14454372_1   5226 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5275
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_14454372_1   5276 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5325
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_14454372_1   5326 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5375
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_14454372_1   5376 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5425
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_14454372_1   5426 AGGCTTTACCATTCAGGATGTAGGCATGGGCAAGGACTTCATATCTAAAA 5475
                            ?v v viv   iv  iv v  vv i     v ii   v  vv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_14454372_1   5476 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5525
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_14454372_1   5526 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5575
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_14454372_1   5576 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 5625
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_14454372_1   5626 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAGGAAAAAA 5675
                          i  vi          v  i  v      vv    v iv i iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_14454372_1   5676 ACAA----CCCCATCAAAAAGTGGATGAAGGATATGAACAGACACTTCTC 5721
                             ----   v  i?    i   iii      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_14454372_1   5722 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAACAATGCTCACCAT 5771
                         v        i  vi viii     v  i         vi       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_14454372_1   5772 CACTGGCCAT 5781
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (141 / 101)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.25 (9 / 4)  


 351 33.13 4.64 4.64  chr1_14473713_14475985      580   902 (1371)    L1M4_orf2#LINE/L1        1   323 (585)  

  chr1_14473713_1    580 TAGGAATATATATTATATTGTTTCATGGGAAAACTGAATATCTAAATGTC 629
                          i i  v    vii  i  vv vv  v    i   v     -----   i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-----TGTT 45

  chr1_14473713_1    630 ATAAATATAAAATA-TCCCCAAATTAACTTATAAATGTCAATATG-TTAT 677
                          - i  i-iv    -          i ii  i i  -    iiii- ivi
  L1M4_orf2#LINE/     46 A-AGATG-GCAATACTCCCCAAATTGATCTACAGAT-TCAACGCAATCCC 92

  chr1_14473713_1    678 AATCAAAGTCCTGACAAAATATTTTTAAATGAAACTAGACAAACTGATTC 727
                         v      i   iii vivv -     iv -    i -     i     i 
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCT-TTTTTGCA-GAAATT-GACAAGCTGATCC 139

  chr1_14473713_1    728 TGAAAATCACACAGAAGAGTAAACATCGAAGAGTTGCTAAATAAGTTGTG 777
                          i   v   i ii   iv i  iviv vv   i v  i   vv i iv  
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_14473713_1    778 AAAAAGAACAAAAAAG---AAGAACCTGCTCT-ATCAGTTACCAAGACTA 823
                                 v  v    ---i  i  iii v  -vi  i  -i   i   v
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT-TCAAAACTT 238

  chr1_14473713_1    824 ACC------CTATTATAATGAAAAC--TATGACACTGGTGAAGAAATAGG 865
                           i------   ivi    v  i  -- i  ii     iiv iii    i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_14473713_1    866 TTAATAGATCGATGAAGGAGAAT-AAAAATCTCACAGA 902
                         ivv       i   i iv     -i i i  ---    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTC---CAGA 323

Transitions / transversions = 1.97 (71 / 36)
Gap_init rate = 0.05 (16 / 323), avg. gap size = 1.88 (30 / 16)  

 844 22.86 10.00 6.94  chr1_14473713_14475985     1291  1780 (493)    L1M4_orf2#LINE/L1      404   908 (0)  

  chr1_14473713_1   1291 ACAAATGGTGCTGGGAGAATTAGCT--TTGTATGTAAGAAAAAAATGAAA 1338
                                         v  i i v --iiii   i  ---  i      i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA---AAGAATGAAG 450

  chr1_14473713_1   1339 GTACATCCTTACTTCACACCATACTCAAAAATTAAAACAGA-TGGATCA- 1386
                         v iv i  i   i          iv          vv  i -       -
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_14473713_1   1387 AAACCTAGATGCAAAAAG-AAAACTTTAAATCTATTAGAAGAAAATGT-- 1433
                          i     i   i  i iv-      v    v  v           ii --
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_14473713_1   1434 --------CTTTGAAGCTTCAGGCTCAGCCAAGAGTTCTTAGTAAAGATC 1475
                         --------   i vii i ii  i vi  v v iv       vv v  --
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-- 598

  chr1_14473713_1   1476 CCTTTACTCCCCAAACGAAAAAAAAATCAGCAAAAGAAACATTA-ATAT- 1523
                         -------- v     v v v  i----  i         v v  -   v-
  L1M4_orf2#LINE/    599 --------CACCAAAAGCACAAG----CAACAAAAGAAAAAATAGATAAA 636

  chr1_14473713_1   1524 TTGG--TTCATTTCAATTTTATAAGCCTTTTGTG---------------- 1555
                             --     --   vv   -  iv        ----------------
  L1M4_orf2#LINE/    637 TTGGACTTCAT--CAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_14473713_1   1556 -AACAAAATTGAAAGACAAACCACAGACTCGAAGTAGGTATTTGCAA--C 1602
                         -  v   i vi        v       v v i  v ii         -- 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_14473713_1   1603 ATATAACTGA------ATTAGTATCTAGAATATATAAAGAATTTT--CAA 1644
                              v    ------ i v     i               i i --   
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_14473713_1   1645 CATCAATAAGAAAAGGACAAAGAACCAACAACAAAAGAACCACACTAACA 1694
                          -       v    i      v    --   iv?  i  ivi-----i  
  L1M4_orf2#LINE/    784 C-TCAATAATAAAAAGACAAATAACC--CAATTWAAAAATGG-----GCA 825

  chr1_14473713_1   1695 AA--ATCAAAATAGAGAAATG-ACAGAAAAGAAATATGAAATGGCCAGTC 1741
                           --  ivi      v vv v-v  i i    v   i-         i -
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC-AAATGGCCAAT- 873

  chr1_14473713_1   1742 TAGAACCCATGGGAGGAGAGCCTCAACCTCACTCACAGT 1780
                         --i i v    ii --   vv      v   ????????
  L1M4_orf2#LINE/    874 --AAGCACATGAAA--AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.13 (59 / 52)
Gap_init rate = 0.05 (25 / 505), avg. gap size = 3.32 (83 / 25)  


2737 26.77 1.77 1.01  chr1_14715222_14717608.rev      358  1149 (1238)    L1M4_orf2#LINE/L1        1   798 (110)  

  chr1_14715222_1    358 TGGAAAACTATCCCCTGTTTATGGATAGGAAGAGTTAATATCATTAAAAT 407
                               iv      v    i      v      v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_14715222_1    408 GTCCATACTGCCCAAAGCAATTTACAGATTCAATGCTGTTCCTATCAAAC 457
                          v v     v      vii  i           i  vi i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_14715222_1    458 TACCACCAACATTCTTCATAGAACTAGAAAAAACT-ATTTTAGAATTCAT 506
                          v   v vi v  i  iii    v v  v  i-  -  ii  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_14715222_1    507 ATGGAACCAAAAAAGAACCCAAATAGCCAAGGCAACTTCAAGCAAAAAGA 556
                               viiv  ii  v  vi         ii   ii ii iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_14715222_1    557 ACAAAGCTGGAGGCATCATGTTACCTGACTTCAAACTATACTACAAGGCT 606
                               i      vv   iii v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_14715222_1    607 ACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGGTACACAGACCA 656
                                i   i    ii         i i  ii i  ii i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_14715222_1    657 ATGGAACAGAATAGAGAGCCCAGAAATAAGGCTGCACACCCAAGACCACC 706
                               i     v     i          iv iii   iii v ii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_14715222_1    707 CAATCTTCAACAAAACTAACAAAAGTA----ATGGGGAAAAGACTCCCGA 752
                         ii  i   i    iiv iv   i vi ----         ii ivvi vv
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_14715222_1    753 TTCAATAAATGGTGCTGGGGTAACTGGCATATGACTATATGCAGAAGATT 802
                              i             ii      -   ?-- i i     i    v 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGG-ATAK--CCACATGCAAAAGAAT 446

  chr1_14715222_1    803 GAAATTGGACCCCTTCCTTACACCATATACACAAATTAACTGAAGACAGA 852
                            i          v   i            v         v  i ii  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_14715222_1    853 TTAAAGACTTACATGTAAAATCCACAACTATAAAAATCCTGAAAGACAAC 902
                          i ?    i  v      i v i v          v  i ii    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_14715222_1    903 TTAGGCA-ACACCATTCTAGACAAAAGAACAGGCAACGATTTCACGACAA 951
                         v    ?i- v i -   vv   vvvi ivi      i i    viiivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_14715222_1    952 AGACACCAAAAGCAATCA--CAACAAAAGCAAAAATTGACAAATGGGATT 999
                         v             --  --         v      v  i    v   i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_14715222_1   1000 T------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGGGT 1043
                          ------       i -   i  ii vv    i  v        v ii  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_14715222_1   1044 AAACAGACAACCTATAGAATGGGAGAAAATATTTGCAAACCATGCATCTG 1093
                         i  v        i i                        i   ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_14715222_1   1094 ATAAAGGTCTAATGTCCAGCATCTATAAGGAACTTAAACAAATTTACAAG 1143
                             i  v  vi i     v  v     i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_14715222_1   1144 AGAAGG 1149
                          i  i 
  L1M4_orf2#LINE/    793 AAAAAG 798

Transitions / transversions = 1.75 (133 / 76)
Gap_init rate = 0.01 (11 / 798), avg. gap size = 2.00 (22 / 11)  

 392 17.83 7.75 0.78  chr1_14715222_14717608.rev     1768  1896 (491)    L1M4_orf2#LINE/L1      771   908 (0)  

  chr1_14715222_1   1768 AAAACTC---CATCTCAAAAAAAAAAAAAAAAAAAA-------AAAAAGT 1807
                          i     ---  v     v  v     i v   v  -------?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_14715222_1   1808 GGGCAAAGGACATGAATAGACATTTTTCAAAAGAAGACACACATGTGGCC 1857
                                   iv             i  v        i i   vi     
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_14715222_1   1858 AAGAAGAATATGAAAAAAAAGCTCAATATCACTGAGCAT 1896
                           v   v i       i v-      i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (11 / 11)
Gap_init rate = 0.02 (3 / 138), avg. gap size = 3.67 (11 / 3)  


2678 13.24 0.73 27.44  chr1_15334355_15337480.rev     1397  2635 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_15334355_1   1397 TGGAAAGACAACCCATGTTCAAGAATTGGAAGACCTAATATTGTTTAGAA 1446
                                 i v          v i          i          v   -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr1_15334355_1   1447 CATCAATACTACCCAAGC-AACCTACAGATTTAATGCAATCTTTATCAAA 1495
                         iiv       v     ii-i i         i  i      ii       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_15334355_1   1496 ATTCCAATGGTGTTCTTTTTTCCCAGAAATAGAAAATTTTATTCTAAAAT 1545
                           i   -- v  -- i     iv       v  v  vi v  i       
  L1M4_orf2#LINE/    100 ATCCCA--GCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_15334355_1   1546 TTATATGGA--TTCTCAAAGGAACCCTGAAGAGCCAAAACAATCTTGAAA 1593
                          i       -- v ---    i    v   v                   
  L1M4_orf2#LINE/    146 TCATATGGAAATGC---AAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_15334355_1   1594 AAGAAGAACA--GTTGGAAGTGTCATACTTCCTGGTTTCAAAAGTTATTA 1641
                                   --      i vv   i      iii        v   i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_15334355_1   1642 AAAAGATAGGGTAATCAAAACACTGTGGGCTTAGCATTTATGCCAGACAC 1691
                         v    v  vi        i   v     vvi i    v- v vi     i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA-AGGATAGACAT 291

  chr1_15334355_1   1692 ATAGA-CAGTGAAACAGATTAGAAAGCCCCCATATAAACCTTTGCATATA 1740
                              -  i  i  i   v v  i  i  vv v       iv i   v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_15334355_1   1741 TGGTCAAATGATTTTCGACAAGGGTGTCAATACCATTCAATGGTGGAAAG 1790
                                v                  i   v            -      
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAG 390

  chr1_15334355_1   1791 GACAGTCTTTTCAACAAATGATGCTGGGAAAACTGGATATCCACATGTAT 1840
                         i i                 i        v         ?       i -
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA- 439

  chr1_15334355_1   1841 TAGTAAAAGAATGAAACTAGGCTGGGCACAGTGGCTCACGCCTGTAATCC 1890
                         --------------------------------------------------
  L1M4_orf2#LINE/    440 -------------------------------------------------- 439

  chr1_15334355_1   1891 CAGCACTTTGGGAGGCTGAGGCGGGCAGATCACGAGGTCAGGAGATCAAG 1940
                         --------------------------------------------------
  L1M4_orf2#LINE/    440 -------------------------------------------------- 439

  chr1_15334355_1   1941 ACCATCTGGGCTAACACAATGAAACCCCGCCTCTACTAAAAATACAAAAA 1990
                         --------------------------------------------------
  L1M4_orf2#LINE/    440 -------------------------------------------------- 439

  chr1_15334355_1   1991 ATTAGTTGGGCGTGGTGGCAGGTGCCTGTAGTCCCAGCTACTTGGGAGGC 2040
                         --------------------------------------------------
  L1M4_orf2#LINE/    440 -------------------------------------------------- 439

  chr1_15334355_1   2041 TGAGGCAGGAGAATGGCATGAACCCGTGAGGCGGAGCTTGCAGTGAGCCG 2090
                         --------------------------------------------------
  L1M4_orf2#LINE/    440 -------------------------------------------------- 439

  chr1_15334355_1   2091 AGATTGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACGCTGTCTC 2140
                         --------------------------------------------------
  L1M4_orf2#LINE/    440 -------------------------------------------------- 439

  chr1_15334355_1   2141 AGACAAAAAAAAAAAAAAAAAAAAAAAAAGAATAAAACTGGACCCTTAAC 2190
                         --------------------------       i  ii       i  v 
  L1M4_orf2#LINE/    440 --------------------------AAAGAATGAAGTTGGACCCCTACC 463

  chr1_15334355_1   2191 TTACACCATAAACAAAAATTAGTTCAAAATGGATCAAAGACCTAAACATA 2240
                          i        v          ii             ?         ii  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_15334355_1   2241 AGAGCTAACACTATAAAACCCTTAAAAGAAAACATAGAAGAAAAGCTTCC 2290
                                 v          i    i            i? v   v    v
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_15334355_1   2291 GGACAATAGATTTGACAGTTATTTCTTGGCAATGACACCAAGAACACAGG 2340
                         v   vv i i  v i  i vi      i vv          i i    i 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_15334355_1   2341 CAACAAAAGTAAAAATAGATAAACTGGAATACATTAACATTAAAA-CTTC 2389
                                  v             i    v v   i  v       -   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_15334355_1   2390 TATATATCAAAGGATACACTCAACACAGTGAAAAGGCAACCTACGGAATG 2439
                          i iiv        i  vv    v v         i     i  i     
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_15334355_1   2440 GAAGAAAATATTTACAAATCACATATCTGAAAAAGGGTTAATCTCCATGA 2489
                          i           i       i        v  i  ii vi v    vi 
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_15334355_1   2490 TATATAAAGAACCCC-ACAACTCAACAGTAACAAAACAAAAATAACCCTA 2538
                                     i i-         i i   v  i     --      v 
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA--TAACCCAA 811

  chr1_15334355_1   2539 TTAAAAAATGTGCAAAGGATTTGAATGGAC-TTTCTCCAAAGAAGATACA 2587
                           ?       v               i   -                 i 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_15334355_1   2588 CAAATGGCCAACAAGTATATGAGAAGAATGCTCAAGATCACAAATCAT 2635
                                    i   i i    i    -       v    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (94 / 66)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 21.81 (349 / 16)  


2677 25.82 3.05 4.14  chr1_16854773_16857246.rev     1066  1983 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_16854773_1   1066 TGAAGAAGCATTACAAATTCATGAATCAGAAGACTCAACA--GTAAAGAT 1113
                           i i iii  iv  vi      i  ii       i  i --  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_16854773_1   1114 GTCAATTCTCCCCATCTTGATATATGGGT-CAATATAACTGCAAACAAAA 1162
                          v    v       vv     v  ii i -   iii  iiv v v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_16854773_1   1163 TCCCAGCAATATTATT-GCATAGATCTAGACAAGATTATCCTAAA-TGTA 1210
                                viiv  v  -   v i  i--      v v        - vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr1_16854773_1   1211 TATAAAATGGCAGAGAAACTAGAATAGCTAAAACAATTTTGAAAAAGAAA 1260
                            ii  vv   ii i v i        i        i           i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_16854773_1   1261 AATGAAATGGGATAGATT-AGTCTACCTAATGTCAAGATTTACTGTATAG 1309
                           ii  i v   -i  i - vv  v  i   v    i i     ii v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGA-GGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_16854773_1   1310 CTACAGTGATCAAGGCTACATGCTATTAGTGAAGGGATAGATACACAGAC 1359
                                i      i viii  v  i i iiv i       i i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_16854773_1   1360 CAGTGGAA----GTTAA-----TAGAAATAGGCCCACGCAAAATTT---- 1396
                           i     ----i  i -----i       ii    ii  ---   ----
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA---TTTATGG 344

  chr1_16854773_1   1397 CCAACTGACTTTAGATAAGGGTACAAAGGCAATTCAATGGAGGAAAGATA 1446
                         i   i   i   v  i      i v   i v         i i  ii   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_16854773_1   1447 CCCTTTTCAACAAATGGTATGGAAGCAA-TCGATATTCATAAGCAAAAAA 1495
                         vi                iiv iii   - v    ?i  i v      i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_16854773_1   1496 TAAATAAA--TAAACCTCAATCTAGTCTCACGCTTCATGCAGAAATTAAC 1543
                         ---  i  -- ii   i ----  -i     i ivi  i  i        
  L1M4_orf2#LINE/    445 ---ATGAAGTTGGACCCC----TA-CCTCACACCATATACAAAAATTAAC 486

  chr1_16854773_1   1544 TCCAAATTGATCATGGATTTACATGTAAAACATAAAACGATAAAACTTAT 1593
                           v    v     ?i  ii  v      i vv      v        iv 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_16854773_1   1594 AGAGAAAAA---AAGAGAAAATATTTGAAAGCTAGGGCCAGGCAAGGAAT 1640
                            ii    --- i ? v    v  i vi v  v   ii      v iv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_16854773_1   1641 TCTTAGACTTGATGCCAAAAGCATGAGCCATAAGAGGAAAAATGGTTAAA 1690
                                iv   ii         ii   v i  i  i      i v    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_16854773_1   1691 TTAGACTTCATCAAAGTTAAACA--TTTGCTCTATGAAAGACCCTGTTAA 1738
                           i            i     v --    iv  vii  i   v  i i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_16854773_1   1739 GAGGATGAAAAGTCAAGCTACAGACTGGGAGAAAATACTTGCAAACTGCC 1788
                           iii       v   v i     v            i       iiiiv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_16854773_1   1789 TATCTGACAAAGGACTAGTATGTAGAATATAGAAAGAACTCTCAAAACTC 1838
                                i  i     v    vi        v          i v     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_16854773_1   1839 CACAGTAAAAAAAATAAAAAATAAATAAATAAGAATTTTTAAATTTGAAG 1888
                         ---------  v        i--- i      ------iiv    ?i  -
  L1M4_orf2#LINE/    787 ---------AATAATAAAAAG---ACAAATAA------CCCAATTWAAA- 817

  chr1_16854773_1   1889 AAATGAG-AAAAGACATGAAGAGATATTTAACTGAAGAGGAAAATATACA 1937
                         -    i -   i  iv    v   i    vv ii    --- i       
  L1M4_orf2#LINE/    818 -AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA---AGATATACA 863

  chr1_16854773_1   1938 GGTGGCAAATAAGCATATGAAGAGGTAATTTAAAATCATTAGCCAT 1983
                         ii    v        i     i  i i-i i  v    ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATG-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (158 / 75)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.64 (66 / 25)  


 990 22.71 3.30 5.49  chr1_17882497_17884717.rev      502   774 (1447)    L1M4_orf2#LINE/L1        6   272 (636)  

  chr1_17882497_1    502 AGATATGCTATGTTCACAGATTAGACAATTCAATATCATTAAAATGTCAT 551
                               v i       ii    i  vi i i     ii    i   v  v
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_17882497_1    552 TTCTACCTAAGCTGCTTTATAGATTCAATCCTAATCAAAATCTCAGAATC 601
                          v  v  i  ii  v i  i        iv -    vv-- v   i    
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGC-AATCCC--TATCAAAATC 102

  chr1_17882497_1    602 CCAGCAGGATTACCGTT-----AGATATCAACAAGTTGATTCTAAAGTGT 646
                              ----- i  v  -----   v  ii     i    i     i vi
  L1M4_orf2#LINE/    103 CCAGC-----TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_17882497_1    647 ATATGGTAAGGCAAAGGAATCAGAATAGCCAAAACAATTTCTAAAA---- 692
                               v  v    i   vi                  i iv    ----
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_17882497_1    693 GAACAAAGTTGGAAGACTCACACTATCTGATTTCAAGGCCCACTATAAGT 742
                                      i          vi ii       ii ii    i  iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_17882497_1    743 TTATAATAATCAAGATAGAGCTGGGTGTGGTA 774
                         i  i i         i  -------       
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAG-------TGTGGTA 272

Transitions / transversions = 2.10 (42 / 20)
Gap_init rate = 0.02 (6 / 267), avg. gap size = 4.00 (24 / 6)  

2290 22.71 1.77 3.69  chr1_17882497_17884717.rev     1053  1730 (491)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr1_17882497_1   1053 AAAACC-CAGTCATCAAGACAATGTGACATTGGTAAAAGCACAGTCACAT 1101
                            i i-    v         i    ii i   i v   v i  v  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_17882497_1   1102 GGATCAGTAGAAAAGAACAGAGTGTCCAAGAATAGACTCACACAAATCTA 1151
                         i     i i   v    iv   v     ii    i  i  i   vv v i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_17882497_1   1152 ATCAATTGATTTT-GACAAAGGTACAAGGACAATTCCGTGATGAAAAGAT 1200
                         i            -     i   i v i   v    vi  iv    ii  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_17882497_1   1201 AGTCTTTTCAACAAATGGTGCTGGAAAAACTGGACTTCTCCGTGTAAAAA 1250
                                                 i v       iv? iv i  i    i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_17882497_1   1251 TAAT-AACCTCGACTCATTCCTCAC-TTGTTTACAAAAAACATAATTAAC 1298
                         -   -  vi v   i v v      -iii v        ------     
  L1M4_orf2#LINE/    444 -AATGAAGTTGGACCCCTACCTCACACCATATACAAAAA------TTAAC 486

  chr1_17882497_1   1299 TCAAAATGGATCATGTAAAATATAGATATAAAACAGAAAATTATAAAACT 1348
                                      ?--- i iv  i  i   i vvv    i         
  L1M4_orf2#LINE/    487 TCAAAATGGATCAW---AGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_17882497_1   1349 TCT-GCAAAAAACATAAGA--ACATCTGTGTGACCTTAGATCTAAGAACA 1395
                         ii - v i        i ?-- v    vi        i i -  i v - 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCA-A 581

  chr1_17882497_1   1396 TCTAAGTTTCTTAGGTACAACATCAAAAGCACCACTCATAAAAGAAAAAG 1445
                          ---i         i  ii   i         v viv i          i
  L1M4_orf2#LINE/    582 T---GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_17882497_1   1446 TTAATATCCTGGACTTCACCAAAATTTTAAAATTCTGCTCTTTGAAAGAC 1495
                          vi   vvi         i       vv   v  i  iv   ii  i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_17882497_1   1496 ACTATCAAGAGAATGAAAATGAAAAGCCAAAGACTGGGAGAAACTATTTG 1545
                                   i i      -  v  v   v   v         v      
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAA-GACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_17882497_1   1546 CAAGTCACACATCACACATCTGCTAAAGGACTTGTATCCAGAATATATAA 1595
                            -------    i i     v   i                       
  L1M4_orf2#LINE/    728 CAA-------ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_17882497_1   1596 AGACCAACTAATAA-TCAATAATAAGAAAGCAAACAACTCACTTCCAAAG 1644
                            v v-  v i  -          i  ii    i   i  v  ?-   i
  L1M4_orf2#LINE/    771 AGAACT-CTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAA 818

  chr1_17882497_1   1645 ATGGGCCAAAGATTT---TC-ACACTTCATCAAATAAGCTACACAGACGG 1690
                               v  i     --- v-   i   vi    v   v  i   i i  
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_17882497_1   1691 TAAGTAAGCACACTGAAAGATGCTAAATGTCATTAGTCAC 1730
                         iv i        ivi         v  ii   ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (92 / 58)
Gap_init rate = 0.03 (19 / 665), avg. gap size = 1.95 (37 / 19)  


 320 20.78 0.00 5.19  chr1_17892345_17894304.rev      502   578 (1382)    L1M4_orf2#LINE/L1      218   290 (618)  

  chr1_17892345_1    502 CACTACCTGATGTTCAGACTTACTCAAAAGCTACAGTAGCCAAGACAATG 551
                             v  ii  v iv i       vv            ii       i  
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_17892345_1    552 TGGGAGGTACTGGTAAAAGAATAGTCA 578
                            ----      i v   i    v  
  L1M4_orf2#LINE/    268 TGG----TACTGGCATAAGGATAGACA 290

Transitions / transversions = 1.29 (9 / 7)
Gap_init rate = 0.01 (1 / 73), avg. gap size = 4.00 (4 / 1)  

1856 22.18 8.74 3.36  chr1_17892345_17894304.rev      875  1469 (491)    L1M4_orf2#LINE/L1      282   908 (0)  

  chr1_17892345_1    875 GAATAGTCACAAACATAGATCCATGGAACAGAA-----AGTCCAGAAATA 919
                          i    --   --i       v      i    -----            
  L1M4_orf2#LINE/    282 GGATAG--ACA--TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_17892345_1    920 GGCCCACACACAAAAAAAGTGTCATTTGCTCTTTGACAAGGTCGA-AAAA 968
                         ii    i   ivv vi----    v   v i  i       vi v-  i 
  L1M4_orf2#LINE/    328 AACCCATACATTTATG----GTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_17892345_1    969 TAATTAAATGGAGAAAGGACAGTCTTTACAACAAATAGCAA-AGAACAAT 1017
                         iv   v     i     i i       v        i iiv-i i    i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_17892345_1   1018 TGGATGTCCATATACCAAAAAAAGAACCTTAGCCCATACCTCACACCTTA 1067
                              i?   i  i v   i  v   vi vii   v           v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_17892345_1   1068 CA-AAAAATTAACTTAAAATGGATCACAGAAATAAATGTAAAACCTGAAA 1116
                         i -           i           ?   vv         i v  i   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_17892345_1   1117 CCATAAGACTTCTAAAAGAACACCTAGGAG-AAACC---ACGA------- 1155
                          i    i   ii  i     v  v    ? -   i ---ii  -------
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_17892345_1   1156 --AGGCAAAGTTTCCTTAGA----ACATTAGAAGTCTGACCCACAAAAGA 1199
                         --      v v  i      ----   ii i   ivii v v        
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_17892345_1   1200 ACAAATTGATAAACTGGATTTCATCACATTTAGGAACTTTTGTCCTTCCA 1249
                          v    v      i    i       v v   ii         v    v 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_17892345_1   1250 AAGACGCTATTTACTACAAAGAGAATGAAAAGACAAGCCATAGACTGGGA 1299
                          i   i    i-------    i i           v   i   v     
  L1M4_orf2#LINE/    674 AGGACACTATC-------AAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_17892345_1   1300 GAAAATACTTACAAATCATATATTTAATA-------------CAGAA--- 1333
                                i  i            i i   -------------     ---
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_17892345_1   1334 --------CTCTCAAAACCCAGTAATAG---GAGAAACAAGCCAATTTTT 1372
                         --------    i v   i  i     i---  v   i  v      ?vv
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_17892345_1   1373 TTTTTTAATGGGCAAAAGCTTTGAAGAATCACTTCACCAAAGAAGATAGA 1422
                         v-----          i v      v iv  i   v            v 
  L1M4_orf2#LINE/    817 A-----AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_17892345_1   1423 TGGATGGCACATAAACACATGAAAAGGTATTCAGCATTATTACTCAT 1469
                         iii     vv    i           i ii   i   i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (79 / 49)
Gap_init rate = 0.03 (16 / 627), avg. gap size = 4.50 (72 / 16)  


3152 22.56 1.38 0.83  chr1_17942525_17944653.rev      471  1197 (932)    L1M4_orf2#LINE/L1       48   778 (130)  

  chr1_17942525_1    471 GATGGCGTGACACCCTTAAGGTTG--CAAAAGA--CACTGCCATCCTTAC 516
                               ivv  v   iv  --   -- v v   --  vi  v    i  i
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_17942525_1    517 AAAGATCCCTGTGGGCTTCTTTTTAGAAATTAACAAGCAGATCCCAAAAT 566
                         v  i     v iv v   i   vi       i      v     i     
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_17942525_1    567 TTATATGGAAATGCTAAAGAGGTAGAACAGCAAAAACAATTCTGAAAGAC 616
                          i            v ii  vvi    i   v        ii     i v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_17942525_1    617 AA---CAGAATGAAAGAACGTATACTACCTGATTTCGAAACTTACTATAA 663
                           ---  i i vii  i  vi i   v  ii     i          i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_17942525_1    664 AGCCACACAAATCAAGATAGTGTGGTATTGCCACAAAGATAGGCACACAG 713
                            i   vv        i         i  v  i  i     i  i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_17942525_1    714 ACCAACAGAATGGAATTAAGAGTCTAGAAATAAATCCTTACATTTATGGC 763
                          i   ii    i     i      i         i  v           i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_17942525_1    764 TAATTGATTTTCAACAAAGGTCCTAAGAC-ATTCCAGTGGAGAAACAATC 812
                         i           i    i   v i     -    - i   i    v   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTC-AATGGGGAAAGAATA 394

  chr1_17942525_1    813 ATCTTTTCAACAATTGGTGCCAGGATAATTGGATATTCACATGTTAAAAA 862
                         i            v      ii   i  i      ?i      iv   i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_17942525_1    863 TATCAA-TTGATACCTTTACCTTATACCATACACAAAAATCAACTCAAAA 911
                         -  v  -   i-   ii     i i      i        i         
  L1M4_orf2#LINE/    445 -ATGAAGTTGG-ACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_17942525_1    912 CAGATCCTAGGCCTGAAAGTTAGAACTAAAACTCTAAATATTTTAGAAGA 961
                         ii    v?  i   i  v  v   i        v    vv i        
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_17942525_1    962 AAACATAGGAAAAAAAATTTTATAACCTTGGGTTGGACAAAGAATTATTA 1011
                                  ?iv   v-i  ii i          i i   v iv  v   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_17942525_1   1012 TATATGACAGCAATAGCATGATCGATGTAAAGAAAAATTGATAAATTGGA 1061
                         v        v   v    ii v i iiv  ii      v           
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_17942525_1   1062 CTTCATCAAAATTAACCACTTTCACACTTTAGAAGATACCATTAAGAGAA 1111
                                        vv     iiii   i i i  i  i  i    i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_17942525_1   1112 TAAAAAGAAAAGCCACAGACTGGGAGAAAATATT-GCAAATCATATATCT 1160
                          i      v  v       v              -               
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_17942525_1   1161 GATTGTGGGCTTGTATCCAGACTATATAAAGAACTTT 1197
                            viv  i            v             i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

Transitions / transversions = 1.82 (104 / 57)
Gap_init rate = 0.02 (11 / 731), avg. gap size = 1.45 (16 / 11)  

 455 19.38 8.53 0.00  chr1_17942525_17944653.rev     1512  1640 (489)    L1M4_orf2#LINE/L1      769   908 (0)  

  chr1_17942525_1   1512 AAAAAACTTTGATAACTTAGTAATAA---GACAAAAAATCCAAT------ 1552
                            i    i v i    i i      ---      v  i     ------
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_17942525_1   1553 --AGGCAAAAGATTTCAATACATATTTCATTAAAGATAATATACAAACAG 1600
                         --i      i     v    v i     vii     vi         ii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_17942525_1   1601 CAAACAAGCACATGAGAAAATGCTCAACATAATTAATCAT 1640
                          v  i          i  i           v ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (17 / 8)
Gap_init rate = 0.01 (2 / 140), avg. gap size = 5.50 (11 / 2)  


2759 22.70 5.73 3.71  chr1_17968977_17973044     2686  3575 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_17968977_1   2686 TGGAAAAACATTGCATGCTCATGGATTGGAAGAATTAATATCATTAAGGT 2735
                               i i  iv    i               v       ii     i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_17968977_1   2736 GTACACATTGCCCAAAGCAATCTACAGATTCAATGCTATTCCTATCAATT 2785
                          vvv i i v      vii              i  v  i        vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_17968977_1   2786 TGCCAACATCATTTTTCACAGAAA---ACA---TG-TTCTAGAATTCATT 2828
                          v   i vv v     ii      ---   ---  - i   i       v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_17968977_1   2829 TGGAACTAAAATTAAAAAAAAAAACCA-AATAGCCAAGACAATCCTAAGC 2877
                              -----  ---iv  iii v   -         i      i i iv
  L1M4_orf2#LINE/    151 TGGAA-----AT---GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_17968977_1   2878 AAAAAGAATAAAGCTGGAGACATTACATTACCTGACTTCAAACTATACTA 2927
                           i     i    i     ivv i   i v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_17968977_1   2928 CAAGGCTACAGTAACCAAAACAGCATTGTGCTGGTA-AAAAATAGGCAT- 2975
                            i          i   i    ii v  i    i -  ii    i   -
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_17968977_1   2976 TG--TC--TGGAACAGAATGGAGACCTCTGAAATAAAGTCGCACATGTAC 3021
                          i--  --     i     v    vii v        vi ii    v  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_17968977_1   3022 AACCAACTGATATTTGACGAAGTCAACAAGAACAAACAATGAGGAAAAGA 3071
                         iii   i    v  i   i i viiv     v  vv     i     i--
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-- 390

  chr1_17968977_1   3072 GGAAAAAGTACCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAACCAT 3121
                         ---  v   ---  v  i  i        i     v      v  ?   i
  L1M4_orf2#LINE/    391 ---AATAGT---CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_17968977_1   3122 ATGCAGAAGAATGAAACTGGATCCTTATTGCTCATCATATACAAAA---- 3167
                              i         ii    i  i  iiv v  i           ----
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_17968977_1   3168 -CTCAAGATGGATTAAAAACTTAA-TGTAAGACCTCAAACTATAAAAATC 3215
                         -     i      i ? i  i   -       v  v           v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_17968977_1   3216 CTAGAAGAAAACCTAGA---AAATGCTCTTCTAGACATTGGCTTAGACAA 3262
                         i           v   i---    ---    vv   v    v    i   
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA 581

  chr1_17968977_1   3263 AGAACTTATGTTAAA---GACCCCAAAAACAAATGTGACAAAATTAAAAA 3309
                         v i--  - v   i ---   v      i  v v ii      vv     
  L1M4_orf2#LINE/    582 TGG--TT-TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_17968977_1   3310 TAGACAAATGGGACTT-----AAACTAAAGA-----GCACAGCAAAAACA 3349
                             i    v      -----   i    i ----- ii vv    ii--
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG-- 676

  chr1_17968977_1   3350 AAAAACAAAAAGCTATCAA-----TAAACAAACAACCTAAATAATGGGAG 3394
                         ----   -----       ----- i  v i      i v v        
  L1M4_orf2#LINE/    677 ----ACA-----CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_17968977_1   3395 AAA-TATTTGCGAACTATGCATCCAACAAAGGTTTAGTATCCAGAATCTA 3443
                            -       i  ii  ii   ii i  i  vi v           v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_17968977_1   3444 TAGGAAATG-----AAATCAGCAAGAAAAAGA--ATTAGCTCAATTAAAA 3486
                           iii  iv-----  v   ii  v       -- v  i i     ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_17968977_1   3487 AATGGGCAAAGGACATTAACAGACACTTCTCAAAAGAAGACATATAAGCA 3536
                                      iv v  i     i     v        i   i  iii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_17968977_1   3537 GCCAATAA--ACATAAAAAAATGCTCAACATCACTAATCAT 3575
                                 --    i    i             ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (127 / 72)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.00 (84 / 28)  


3241 17.36 1.11 0.32  chr1_18414498_18416117.rev      502  1129 (491)    L1M4_orf2#LINE/L1      276   908 (0)  

  chr1_18414498_1    502 GCACAGGGATAGACATATAGAGCAGTGAAACAGAATGGAGAGTCTGGAAA 551
                            i i               v  i  i  i     v       ii    
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_18414498_1    552 TAAACTCGCACTTTCACAGTCAATTGATTTTCGACAAGGATGCCAAGATA 601
                              i ii  v  i ii                     i        iv
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_18414498_1    602 ATTCAATGGGGATAGAATAGTGTGTTCGACAAATGGTGCTGGGACAACCA 651
                                     v        v v   i                    ii
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_18414498_1    652 GACATCCACATGCAAATGA-TGAAGTTGGACCCCTCCCTCACACCATATA 700
                           i ?           v  -               v              
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_18414498_1    701 TAAAAATAAACTTGAAATGCATCATCAACTTAACTGTAAGAGCTAAAACT 750
                         i      v    ii     v    ?vi  i   v                
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_18414498_1    751 ATACAAACTCCTAGAAGAGAAATACAGGAGTAAGT---TGTGAGATTGAG 797
                            -      i       -   i i   ?    i ---i    vv   i 
  L1M4_orf2#LINE/    526 ATA-AAACTCTTAGAAGA-AAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_18414498_1    798 TTAGGCAAAGCCTCCTTAAATA-GACACGAAAAGCACAAGTGACAAAAGA 846
                                 v vi i    i   -     v           ii        
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_18414498_1    847 AAAAATAGATAAACTGGATTTCATTGACATTAAAACATTTTGTCCTTCAA 896
                                      i    i     ii v       vv      v      
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_18414498_1    897 AGGACACCATGGAGAAAGTAAAAAGACAATCTACACAATGGGAGAAAA-A 945
                                i  vi       i         i i   v            - 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_18414498_1    946 TATGCAGATGATACACCTGATAAGGGACTTACATGTAGGTCAGATAGAGA 995
                          v    i  v   i i              ii  vi  ivi v   i   
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_18414498_1    996 ACTCTTACAACTCAATCATAAAAAGAAAAATAAGGCCATT-GAAAATGAC 1044
                                         v         v      vv v   -i      iv
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_18414498_1   1045 CAAAGGCTCTGAGTAGATGTTTCTCCAAAGAAGATGTCCAAATGGCCAAG 1094
                               v i   i    ii                i v           v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_18414498_1   1095 AAGCACAGGAAAGGACGTACAGTGTCATTGGCCCT 1129
                                v    i  i iv  iii   ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (66 / 40)
Gap_init rate = 0.01 (7 / 633), avg. gap size = 1.29 (9 / 7)  


1547 25.80 8.43 2.87  chr1_18441551_18443135      500  1092 (493)    L1M4_orf2#LINE/L1      283   908 (0)  

  chr1_18441551_1    500 GGTAGACAAATAGATTGACAAAACAGGAT--AGAGTCCAGAAATAGATCT 547
                          i      v      ii iii  i  i  --              i i i
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_18441551_1    548 ACATACACAGAGTTCATTGATTTTTGCCAAAGACCCCCAAGGCGGTTCAA 597
                          i i ivi vi  iv         i v   i iiv  -   i vi     
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC-AAGACCATTCAA 381

  chr1_18441551_1    598 TCAGGAAAGAGAAGTTCTCTTAAAAAATGACCCTGAAACAAATGAATAGG 647
                          vi       iv   ii i i  v     iiv   ii    v  i   ?v
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_18441551_1    648 CATAAGGAAAA-ATTAAACCTGGACCCCTGCCTCGCAC-ACACACAAAAA 695
                           i v v    - v i  vi         i    i   - i i       
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_18441551_1    696 TTAATTTGAAATGAATCATAGATTTAAAAGTAGAAGTCAGCATCATGAAG 745
                             i ii     i    ?   ii    v   ii  ii iv ii  i  i
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_18441551_1    746 CCTCTAGAACAAAACATAG-------CCTTTGTGATATTTGTGT--AACA 786
                          iii     v         -------i   i    i-i   v  --ii  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCA 580

  chr1_18441551_1    787 AAGGTTTCTTAAA-GTGGTCAC--AAAATAAAAACTAAATAAAAACTAAA 833
                          v         i -i  i-   --   ii v  i --  i    i--   
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGA-CACCAAAAGCACAAGC--AACAAAAG--AAA 625

  chr1_18441551_1    834 TGATAAATTGAATTTGGTAAATTGGACTTAATCAAAAATTAAATCTTCTG 883
                         ----    v  ------            v       v v   v   i  
  L1M4_orf2#LINE/    626 ----AAATAGA------TAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_18441551_1    884 CTCTTACAAAGATATCCTTGAGAAAAAAGAAAAGCAAACTATAGAATGAG 933
                         iv   vv  i  i iiv ii     ivii   ii   v i i      i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_18441551_1    934 AGAAAATACTCTCAATACATATATCTGACAAAGCATTTGTAACCAGAATA 983
                                 i iv   vv           i  i v i     v        
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_18441551_1    984 TATAAAGAACTATGACAAATCAATAATGAAA-GAC---TA-CCCAATTT- 1027
                                    v v    v        i   -   ---  -       ?-
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_18441551_1   1028 ---------------TTTAAA-------------AAAGAAAATATACAAA 1049
                         ---------------   i  -------------      i         
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_18441551_1   1050 TGGCTAATAAACATGTAAAAACCTACACTACATTATTAGTTAT 1092
                             i     i  ii i    vv i v v    i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.26 (104 / 46)
Gap_init rate = 0.03 (19 / 626), avg. gap size = 3.53 (67 / 19)  


4294 15.54 5.41 0.92  chr1_18590067_18592069      642  1510 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_18590067_1    642 TGGCAAAACATCTCATGTTCATGGACTGAAATACTTAATATTGTTAAATT 691
                            v  i i   i            i  i  v               iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_18590067_1    692 GGCAATACTTTCCAAACTGATCTACAGAATCAAAACAATTCCTATTCCAA 741
                                  ii     i           v    vi    i     ivv  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_18590067_1    742 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGGTCCTACAATCCATA 791
                                                            i     v   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_18590067_1    792 TGAAAATACCAGAGATCCCAAATAGCCAAAACAACCTTAATAAATAAGAA 841
                           i    i v  i  i  vi              i   i v   v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_18590067_1    842 CAAAGTTGAGGGACTCAACTTTCCCAATTTCAATGCTTACTACAAAGCTA 891
                                 ii       vvi             vi               
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_18590067_1    892 CAGTAATCAAGACAG------ACT--TATAAAAACAGACACATCAATCAA 933
                                        ------   --i    ii i     i  vi     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_18590067_1    934 TGGAACAGAATTCAGAGTTCAGAAATAAAC------ATCTATAGTCAATT 977
                              i      v     i           ------  i   i       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_18590067_1    978 GAGTTTTGAAAAGGATGCCAAGATAATTCAATGGAGAA-TATTAGTCTTT 1026
                           v   i  v    i        iv         i   -v v        
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_18590067_1   1027 TCAACATATGGCGCT----TAA-----TATTCACATGTAAAAAAAATGAA 1067
                               v    i   ----i  -----  ?i      i    i  -    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAA 449

  chr1_18590067_1   1068 TTTGGATTCC--------ACCATATA-AAAAATTAACTCAAAAGTGG-TC 1107
                         v     ii  --------        -                -   -  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGATC 498

  chr1_18590067_1   1108 AAAGGCCTAAGTGTAAAATCTAAAACTATGAAACACTTAGAAAAAAA--T 1155
                          ?  i     i     i v          i    v       i    -- 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_18590067_1   1156 AAGTGTAAAACTTTTATGACCTTGGATTAGGCAATGGTTTACTTATATGC 1205
                          i ?     v   i-i         i              -    --- -
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTT-CTTA---G- 592

  chr1_18590067_1   1206 ATATCACATCTAAAGCATAG--------AAAAAAAATACATAAATTCGAC 1247
                             v   i v      i i-------- i        v       v   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_18590067_1   1248 TTCATAAAAATTAAAA-CTTTTGTGCATCAAAGGACAGCATCAAAAAAAT 1296
                              v          -         v          vi     i   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_18590067_1   1297 GTAAAGACAATCTGCAGAATAGGAGACTATATTTTCAAATCATACAGCTG 1346
                          v        i ii      i     vv      v         i v   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_18590067_1   1347 ATAAGGAACTTATGTACAGA-CATATAAAGAACTCTTACTACTCAACAGT 1395
                               i    i i v    -i                 v      i i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_18590067_1   1396 AAAAAGACAAATGACCAGACTTTTTAATCAA-AAAAGATTTGCATAGATG 1444
                                     i   vi i ?vvv   vii-   i      v     ii
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_18590067_1   1445 TTTCTCTAAAGGAGATATACAAGTGGCCAATAAGCACATGAAAAGATGCT 1494
                               i    i          i                           
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_18590067_1   1495 CAACATCATAGTCATA 1510
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (84 / 47)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.75 (55 / 20)  


 680 30.63 12.55 3.51  chr1_18659693_18661918.rev      335   876 (1350)    L1M4_orf2#LINE/L1       54   644 (264)  

  chr1_18659693_1    335 AATTCTCTCTCAGCTAATTGATAAATATACTTTGATTCTGATAAAAAATA 384
                            v   i iv ii i  iv i i  vi vivii  i iv  v    ---
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA--- 100

  chr1_18659693_1    385 TCCACAG------TTTTTGTTGAA--TGAGGCATGCTTATCCTAAAGTTC 426
                            -   ------      iv   --   --  v   v        i   
  L1M4_orf2#LINE/    101 TCC-CAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTC 147

  chr1_18659693_1    427 GTATGAAAAATTAA-----CCAGTAGGCATAGACAGGAAAATTCTGGAAA 471
                         i    i   vvi  -----    - ---    v  ii v   -  v    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAG-A---ATAGCCAAAACAAT-CTTGAAA 192

  chr1_18659693_1    472 AAGAGGGTGCTCGGGGGAAGGACCAAC-----CCA-----------TATT 505
                             i i-i vvi vv i     iv  -----   -----------  i 
  L1M4_orf2#LINE/    193 AAGAAGA-ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_18659693_1    506 ATGAAGCCTCAATCATTAAAACAATGTGGTTTTGACCCGTGAATAGTCAA 555
                          ii    iv  i v  i  i   i      vi  i viiv i    v  v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_18659693_1    556 GCAGA-CAATAAAATAAAA--GAAAACTCAGAAATAGGCC--TACATTAA 600
                         ii   -    ii    i  --  i iii        ii  --      v 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_18659693_1    601 ATGGACAGTTAGT-------AAGGTTACCA-TACCA---AACCAGCAAAG 639
                         -   v  i  ii -------    v i   -v    ---  ivi v    
  L1M4_orf2#LINE/    342 -TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_18659693_1    640 AAAAGCTGAATTATTTAATAAACGGTGTTGG-ACAACTGGAAAGACACCT 688
                           v  ii---  -  i  i   i    i   -         v ?v   v 
  L1M4_orf2#LINE/    391 AATAGTC---TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_18659693_1    689 GGAAAAAAA---ATCTGGATTTCTACTTTATATT-TA-----AAATAAAT 729
                          v    i  --- vi    iii    i i i ii-  -----    v  i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_18659693_1    730 GTTGAAGGAATCAAAAATTTAAGTGTGAAAA-TGAAGCT-TAAACATTTT 777
                         vivi  v i    ? i ii   i   i i i- i  i  -    vv i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_18659693_1    778 AGAAGGAAACATCAGAGAGTTTCTTTATGACTTTTAAATGAGG----GAC 823
                              i      vi ? vivv    ii    i  -iii v   ---- ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTT-GGGTTAGGCAATGGT 585

  chr1_18659693_1    824 TTTCTAATTATGACTCAGAAATCTAGAAGCTATTAAA-----AATGGATA 868
                           ii  iv      v vi   v - v    v iv   -----   i    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_18659693_1    869 ATTT--ACTT 876
                          v  --    
  L1M4_orf2#LINE/    635 AATTGGACTT 644

Transitions / transversions = 1.76 (104 / 59)
Gap_init rate = 0.05 (32 / 591), avg. gap size = 2.72 (87 / 32)  


1030 29.08 6.22 5.38  chr1_19053908_19056041      500  1094 (1040)    L1M4_orf2#LINE/L1       63   662 (246)  

  chr1_19053908_1    500 CAAATTAATTTAT-TATTCAATGCAGCTCCAAATTAAACCCCAACAAGGT 548
                               i  i  i-v      i   iii  v viv   i    i --v i
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC--TGC 110

  chr1_19053908_1    549 GTTCATGGCATA---TGACAATCTCTTTCTATAATTTA----GAA--GCA 589
                         v  iv v   v ---      v  vv i   v    i ----   --   
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr1_19053908_1    590 AAGGGTCAAAAGGAGCCAAGACATTCCTGAAGAAGAATAGCAAGGAGTAG 639
                          i  ii v i iv      i   v  i    i     v i   i -----
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG----- 205

  chr1_19053908_1    640 GGCTTGGTCTACCAGGTCTCAAGAGAACATAAAGTGATAATT--AAGACT 687
                         ---    ------   v    ------  i---v vvi    --  i   
  L1M4_orf2#LINE/    206 ---TTGG------AGGACTCA------CAC---TTCCCAATTTCAAAACT 237

  chr1_19053908_1    688 TGCTTTAAAGCACTTGTGATCAAGATAGTGTGGAATTGGCCCAGGGATAG 737
                          i  vi     vviv  i       i       v i    vi i      
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_19053908_1    738 ACACATAGA-CAGTGAATGAGACTAGAGAGTCCAGAAGCAGACTCAAGAA 786
                            i     -  i  i vv   v v            ii i  i  viv 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_19053908_1    787 TAAATGA-AAATGTGATCTGTA-----GATGACATGGTTTTGCAAAATAA 830
                          vv   i-v   -    i vii----- i  v  v iiiv v   -- ii
  L1M4_orf2#LINE/    338 TTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGG 384

  chr1_19053908_1    831 GGTAAAATATGAACTATTCAATAAACATAGCTTATGTAGTTACTTATCCA 880
                           v  i -  iiv  v     i   iivv   vivii ii ivv  ?   
  L1M4_orf2#LINE/    385 GGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_19053908_1    881 TATGGAAAAAAACTGAAATTGTATCCTT--CTC------TATACAAAA-T 921
                         i   v    i  -    i   v i  i --   ------         - 
  L1M4_orf2#LINE/    434 CATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_19053908_1    922 CAATTCCAGATGGATTAAAGTCTTAAATGCA-----TAAGGC---ACAAC 963
                         i  i  v i      i ?  v i      i -----   ii --- v   
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_19053908_1    964 TTTTAGAAGAAAATAAAGGAA-AAGTACTTCTGTAACCTCAGGGGAAGGA 1012
                          i           i v   ?i-  i -    -  i    ii  vv i v 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAAT-CTTC-GTGACCTTGGGTTAGGCA 580

  chr1_19053908_1   1013 GGAATTTCTTTTAAAGGACACAAAAAGCACAAATAATAAAGGAAAGTATC 1062
                         ivii      vv v v     v          ii  i   i    iv  v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_19053908_1   1063 AACAAACTCTACTACATTAAAAATAAGAACTT 1094
                         i i   i vv   v   i    v   i     
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTT 662

Transitions / transversions = 1.39 (99 / 71)
Gap_init rate = 0.04 (25 / 600), avg. gap size = 2.76 (69 / 25)  

 341 24.22 6.64 4.69  chr1_19053908_19056041     1391  1646 (488)    L1M4_orf2#LINE/L1      648   908 (0)  

  chr1_19053908_1   1391 CAAAA--AATAACTTCTGT---TCACACACACAAAAACACCATCTAGAAA 1435
                              --  v     i   ---   -------  ii    i   v     
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCA-------AAGGACACTATCAAGAAA 690

  chr1_19053908_1   1436 ATGAAAAGACAAGTCACAGGTTGGGAAATGATACTTAGAATGCATATAAT 1485
                         i           vi     iv     i vi   i  iv  vv      vi
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_19053908_1   1486 TTACCTAAG--ATTAGGATA-AGAATATGTAAAATGCTCCTGAAGAATCA 1532
                          v --    -- i v v  v-       i    ivi   i iv - v   
  L1M4_orf2#LINE/    741 TGA--TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCA 787

  chr1_19053908_1   1533 ATA-CAAAAA---AAGCAACACAAAAGAAAAA-GGACTAAAAACATAGCT 1577
                            -i     ---  ii   v   vv?     -  i v  ii iv iiv 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_19053908_1   1578 AGAC-CTTGTGGAGACAAGGAA-ACAAGTATTGCCAATAA--ACATGAAA 1623
                             -i  v vv i v   iv -    --  v        --        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAA--ATGGCCAATAAGCACATGAAA 885

  chr1_19053908_1   1624 AGATGCCCAAGCTCATTAGAAAT 1646
                               i   vv   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.03 (31 / 30)
Gap_init rate = 0.05 (14 / 261), avg. gap size = 2.07 (29 / 14)  


2898 17.22 9.04 2.15  chr1_19372883_19374987.rev      502  1198 (907)    L1M4_orf2#LINE/L1       66   810 (98)  

  chr1_19372883_1    502 ATTGATCAAAAGATTTGATATAATTCCTATTAT--TCCCAGCTGACTTTT 549
                                v v     ii iii   i     i v--         v     
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_19372883_1    550 TCTTAATACTGAAATTGACAAACTAATCCTAAAGCTCATATGGAAATTCA 599
                          ----- i v           i  i        ii            v  
  L1M4_orf2#LINE/    116 T-----TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr1_19372883_1    600 AGGGACCCAGGAGAACCAAAACAGTCTTGAAAAACA----CATAGTTGGA 645
                                   i v i        i          v ----  v       
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_19372883_1    646 GGACTTATACTTTCTGATTTCAAAACTTACTACAAAGCTACAGTAATAAA 695
                              i i    i ii                               v  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr1_19372883_1    696 GACAATG--GTTCTGGCATAAGAATAGA------G--CAACTGAACAGAA 735
                             i  --  v          i     ------ --   iv   i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_19372883_1    736 CTGAGAGTCCAGAAATAAACTCTTACTGATTT-TAG--AGTTGAGT---G 779
                         i                   i v   --    - i -- i    v --- 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATAC--ATTTATGGTCAATTGATTTTCG 358

  chr1_19372883_1    780 ACAAC----TCAATAGGGACAGTTCAATAGGGAAAAGAATCATCTT--CA 823
                             v----i   ----   vi      i      -    vi    --  
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAA----GACCATTCAATGGGGAAA-GAATAGTCTTTTCA 403

  chr1_19372883_1    824 CCAA------------CATCCAGATGTCCTGCTGTGAAAGAGTGAAGTTG 861
                         v   ------------  v ii   i?  vvv  ii     i        
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_19372883_1    862 GACCCCTTCCCCATACCATAAACAAAAAATTAACTC-----GAATCACC- 905
                                v  i  i      v       -       ----- i    ?v-
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAG 502

  chr1_19372883_1    906 ATCTAAATGTATAAGGTAAA-CTATAAAACTCTTAGAAGAAAATACTTGA 954
                          i         vi  v    -                      i ivv ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_19372883_1    955 GTCAAGT----GTGACTTTGGATTAGGCAGTGGTTTCTTAGATGTTGACA 1000
                           -  i ----     i    i       i             i -    
  L1M4_orf2#LINE/    553 GT-AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-GACA 600

  chr1_19372883_1   1001 CCAAAAGCACACGTGGCAAAAGAAAAAGTA----AAGTCAACACCATCAA 1046
                                    v iii           i  ----  v vi  vi      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_19372883_1   1047 AGATGAAAGTGTTCGTGCTTCAGGGAACACTATCAAGAAAGTGAAAAGAC 1096
                          iv i   iiv  i        ii i                        
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_19372883_1   1097 AACCCA-AGAATGGGATAGTAT-TTTGCAAATCACATATCTGTTAAGAAT 1144
                               -         v iv  -           i       v    iiv
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_19372883_1   1145 CTTGTATCTATTCTAGCTATAGGACTCTTACAACTTAATAA----AAGAG 1190
                                 i vvv  vv  v  i            i     ----    v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_19372883_1   1191 AAA--ACCCA 1198
                            --     
  L1M4_orf2#LINE/    801 AAATAACCCA 810

Transitions / transversions = 1.54 (71 / 46)
Gap_init rate = 0.04 (27 / 745), avg. gap size = 2.89 (78 / 27)  

 486 19.47 1.77 0.00  chr1_19372883_19374987.rev     1502  1614 (491)    L1M4_orf2#LINE/L1      794   908 (0)  

  chr1_19372883_1   1502 AAAAGAAAGAAATCCCAATTAAACAATGGGCAAATTATTGGAATAGACCT 1551
                               v i v v       ?  v          vv   v        v 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_19372883_1   1552 TTTTCCAGAG--GGCATACAGGTGGTCAGTAACCACATGGAAAGCTGCTC 1599
                           i    i  -- ii     ii   i  i   v      i    v     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_19372883_1   1600 AAAATCAGTACTTAT 1614
                           v    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 0.91 (10 / 11)
Gap_init rate = 0.01 (1 / 115), avg. gap size = 2.00 (2 / 1)  


3474 15.77 3.68 1.38  chr1_19908013_19912577     2883  3535 (1030)    L1M4_orf2#LINE/L1        1   668 (240)  

  chr1_19908013_1   2883 TGGAAAGATATCCTATGTTTATGGATTGTAAGATTTAATATTGTTAAAAT 2932
                                      i     i        v    i             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_19908013_1   2933 ATCCACACACCCCAAATTAATCTACCAATTTAATGCAATTCCTATGGAAA 2982
                         iv v i  v         i      vi   i  i     i     vi   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_19908013_1   2983 ACCTAACTGGCTTTATTTTTGCAGAAATTGACAAGTTAATCTTAAAATTT 3032
                         v  i i   v    ---                  i i   i       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT---TTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_19908013_1   3033 ATATGGAAATTCAAGGGATCCAGAATAGGAAAAAACAATTTCGAAAAAGA 3082
                                   v       i         vv    -    i i        
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGA 196

  chr1_19908013_1   3083 AGAATAAAATAGGAGAACTCACACTTCCCAATTTCAAAACTTACCACAAG 3132
                             i   i v    i                            i    -
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA- 245

  chr1_19908013_1   3133 GAGCTGTAGTAGTCAAGACCATGAGGCACTGGTATAAGAATAGATGTATA 3182
                         -    ii    i       vi  v  i     i     i     ii    
  L1M4_orf2#LINE/    246 -AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_19908013_1   3183 GATTAACTGAATAGAGTTGGAAGCCCAGAAATAAACTCATACATTT---G 3229
                            i  iv       i   ii  i            i         --- 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_19908013_1   3230 TCAATTGATTTTCAACAGTGATGCTAACACAATTCAATGAGGGAAAGAAT 3279
                                      i   iv i   i  v  v        -          
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAAT 393

  chr1_19908013_1   3280 AGTCTTTTCAACAAATGGTGCTGGAATAGCTGGATATCCACATTTAGAAG 3329
                                                 i i i       ?      vi i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_19908013_1   3330 AAAGAAGTTGGAC---------ATA--ATTTAACAAAATTAGCTCAAAAT 3368
                           v          --------- i --  v  vv       i        
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_19908013_1   3369 GGACCAAAGACCTAAATGTAAGAGCTAAAAGTGTAACATTCTTAGAAGAA 3418
                            i  ?                       v i   v i           
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_19908013_1   3419 AACATAGGTGCAAATCTTTATGACCTTGGAATAATCAGTGGCTACTTAGA 3468
                                 ? i       ii         iv  iv  i   i v      
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_19908013_1   3469 TGTCACACACAAAGCACAAGCAACTGAAAAAAAAAT----------GACT 3508
                          i v    vv              vi  i       ----------    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_19908013_1   3509 TCATCAAGATTAAAAATGTTTTTGGGC 3535
                                i        i--     v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAAC--TTTTGTGC 668

Transitions / transversions = 2.03 (67 / 33)
Gap_init rate = 0.01 (9 / 668), avg. gap size = 3.67 (33 / 9)  

1174 14.23 6.32 0.40  chr1_19908013_19912577     3812  4064 (501)    L1M4_orf2#LINE/L1      624   891 (17)  

  chr1_19908013_1   3812 AAAAATAAATAAATT----------AAAA--AAAAAGTTT-ATGCTCCAA 3848
                                i       ----------    --     v   -i    i   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_19908013_1   3849 AGG-CACGATCACAAAAGTGAAAAAAAAAACCCACAGAATGAAAGAAAAT 3897
                            -   v    vi          i v  -           ii       
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAA-CCCACAGAATGGGAGAAAAT 722

  chr1_19908013_1   3898 ATTTGCAAATTCTATAACTGA-AAGAGTCTAGTATCCAGAATATATAATA 3946
                                   iv    v    -   i v  v                 vi
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_19908013_1   3947 AACTCTTACAATTTAACAGTAAAA-TACAAATAGCTCAATTTAAAAATGG 3995
                                    i i  i i     -v       i i     ?        
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_19908013_1   3996 GCAAAGAATTTGAACAGACATTTCTCCCAAGAAGATATGTAAAGGACCAA 4045
                               i       i            v          ii   v i    
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_19908013_1   4046 TAAGCAGGTGAAAAGATGC 4064
                               vi           
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGC 891

Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.03 (7 / 268), avg. gap size = 2.43 (17 / 7)  


 808 17.59 6.02 1.85  chr1_19971141_19975214.rev      665   880 (3194)    L1M4_orf2#LINE/L1      684   908 (0)  

  chr1_19971141_1    665 CAAGAGAATCAACAAAAAACTACTGCA-AACCAAAAAAATTACA-GCAAA 712
                              i i v  v i v   -- ii  -  ivii i   v  iv-     
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAAC--CCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_19971141_1    713 TCATATACCTGGGTAAGAATCTAGCATCTAGAATATATTAAAAAACTCTT 762
                                i   i-    iiv  v i   i         -   i       
  L1M4_orf2#LINE/    732 TCATATATCTGA-TAAGGGACTTGTATCCAGAATATAT-AAAGAACTCTT 779

  chr1_19971141_1    763 ACAACTCAA------AAAGGCAGA--ACCCAATTAAAAAATAGGCAAAAG 804
                                  ------    i  i --        ?      i      i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_19971141_1    805 ACTTGAATAGACATTTTTCCAAAGA---TATACAAATGGCCGAAAACCAC 851
                          i              i        ---             i v  v   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_19971141_1    852 ATGAAAAGATGTTCAATGTCATTAGCTAT 880
                                    i    ii   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.70 (27 / 10)
Gap_init rate = 0.04 (8 / 225), avg. gap size = 2.12 (17 / 8)  

 332 31.31 9.34 5.30  chr1_19971141_19975214.rev     2509  2904 (1170)    L1M4_orf2#LINE/L1       97   508 (400)  

  chr1_19971141_1   2509 AAAACCTCAATAGGATTTCCTTTG---AACTAGACACATTGATTCTAACA 2555
                             i i  iiv vv   --    ---  v v    vii    i    v 
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTT--TTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_19971141_1   2556 TTCATTTTGTTTTTTTTAAA----AAAGAC--AACATA--TAAGGAAA-C 2596
                              v v --------   ---- ii   -- iv   --i  iiv  - 
  L1M4_orf2#LINE/    145 TTCATATGG--------AAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_19971141_1   2597 TTATAAAAAGAAAATTAATTATGAGT--GAAAAATC---CTACCAGATTT 2641
                           i-        i vi  -----   --  ii v  ---  v  vi    
  L1M4_orf2#LINE/    187 TTG-AAAAAGAAGAACAA-----AGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_19971141_1   2642 TAAAATATAC--CAA--CTA---------AAACAATGAGGCATCAACATG 2678
                         i    iv   --   --   --------- i   i  v  i iiii   i
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_19971141_1   2679 TGAACAGGGA----GATCAGTGGACCAGAACCAAATGTCTAGGAATAGAC 2724
                         v i i  iv ----     i    vi    iii iv   i  i    i  
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_19971141_1   2725 CCAAATACATATGGGAATTTAGTATATGGAAAGAAAGTGGCATTTTAAAT 2774
                            v i iv     vv v  ii v vi iv   i--   v  vvviv v 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGG--GTGCCAAGACCATT 378

  chr1_19971141_1   2775 CAGTGGAGAAAAGAT-GTATAATTAATCAATGGT-TTGGGTACAACTAGG 2822
                           i   i    ii  -  v vv i  iv      -i    -      i i
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG-ACAACTGGA 427

  chr1_19971141_1   2823 TAATCACAAGGGAAATA-TAAAGTTGGATCCATAGCCTCCTACCCTTATT 2871
                           ?i    v vi   v - i        i  v  -    vi   v -  v
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTA-CCTCACACCAT-ATA 475

  chr1_19971141_1   2872 TCAATATAAATTTCAGATGAAGCCAAGATTTAA 2904
                         iv  v  v  i iv i   i v v?   ii   
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

Transitions / transversions = 1.35 (70 / 52)
Gap_init rate = 0.05 (22 / 412), avg. gap size = 2.64 (58 / 22)  

 457 30.57 6.22 1.81  chr1_19971141_19975214.rev     3206  3591 (483)    L1M4_orf2#LINE/L1      506   908 (0)  

  chr1_19971141_1   3206 TAAATAAATAAAGTGAAACTATGAAAGTACTATTCTAAACTATGGGAG-A 3254
                              iv vi iv i       i   v vi  vvvv   vi  i  ? - 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_19971141_1   3255 ATTCTTTTTAACCTCAGAGTGGGAAAGACTTTCCCAGTTATGAC-CCAAA 3303
                          v    iv i    ii iv i  v  viv    ii  v      -     
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_19971141_1   3304 ATC-CAAAGGGCATATAAGAAAATCGTAACAAATTTAACTATGTAAAAAT 3352
                          v -   ivii  v vi i     v -- i     vi   vii v     
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAG--ATAAATTGGACTTCATCAAAAT 653

  chr1_19971141_1   3353 CTAAAATTCTTTCATAGCAAAGACCACAG--GAGAAAGAACAAAAAGACA 3400
                         iv    i i  viiivv     iv   vi--i      --ii        
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG--TGAAAAGACA 701

  chr1_19971141_1   3401 AATGACAGAGTGCGAAAAACTATTTGCAACTCATATCACAGACAGAGG-C 3449
                          viv     i  v  i   v         v      vv v  i ii  - 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_19971141_1   3450 TAATTTCCCTAATACATAAAAAGCTCCC-CAA---AATCATTAA--GACA 3493
                          vi v   vv    i     i i   ii-   ---   v  v  --    
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_19971141_1   3494 A----CTTAATAGGAAAAAAATGGAGAAAGAAAATGAATAC-CATTT--- 3535
                          ---- ii   v---?        iv    i vv      v-     ---
  L1M4_orf2#LINE/    802 AATAACCCAATT---WAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_19971141_1   3536 -ACAAAAAATAGAAATATGTCT--TAAACACAGGAAAAGATGCATAA-AT 3581
                         - v i  i   v v v   v i--   i    v          vi  -  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_19971141_1   3582 AAGAGAAATG 3591
                         v ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.00 (58 / 58)
Gap_init rate = 0.04 (16 / 403), avg. gap size = 1.94 (31 / 16)  


1072 18.08 0.46 25.50  chr1_20090219_20093624.rev     1552  2198 (1208)    L1M4_orf2#LINE/L1        4   488 (420)  

  chr1_20090219_2   1552 AAAGACATCTCATGTTCATGGATTGGAAGAATTGATACTGTGAAAATGAC 1601
                              i   i                    v  i   i   v  i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_20090219_2   1602 CACACTACCAAAAATTATCTACAGATTCAATAAAATGCCTATCAAAATAC 1651
                         v i   v  v   v v              iiv   v           v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_20090219_2   1652 CAACTGCATTCTTCACAGAAATAGAAAAAA-AATACTAAAGATTT-TATG 1699
                           i    v  i  ii       v  v  iv-i  v     -   i-    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA-ATTCATATG 152

  chr1_20090219_2   1700 GAACCACAAATGACCCTGAATAGTCAAATCAATTCTCAGCTAAAAGAACA 1749
                            vii   iv     v      i    v    ii v ivv i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_20090219_2   1750 AGGCTAGAGGCATCACACCACCAAATGTCAAAATATACTACAAACCTATA 1799
                          i i i    vv      iv  v   v      iv         v   i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_20090219_2   1800 TTAACCAAAACAGTGTGGTGGCTAGGTACAGTAGTTCATGCCTGTAATTT 1849
                         v   i   i          -------------------------------
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGT------------------------------- 271

  chr1_20090219_2   1850 CAGCACTTTGAAAGGCTGAGATAGGAGGATTTCTTATGGCCAGGAGTTCA 1899
                         --------------------------------------------------
  L1M4_orf2#LINE/    272 -------------------------------------------------- 271

  chr1_20090219_2   1900 AGATCAGCCTGGGCAACAAAGAGAGACACCATCTCTGCCAAAAATAAAAA 1949
                         --------------------------------------------------
  L1M4_orf2#LINE/    272 -------------------------------------------------- 271

  chr1_20090219_2   1950 TAAATTTAAAAATAAAACAGGACAGTACTGGCATGAAATCAGACATATAG 1999
                         --------------------------        i iivi          
  L1M4_orf2#LINE/    272 --------------------------ACTGGCATAAGGATAGACATATAG 295

  chr1_20090219_2   2000 AGCATTGAAACAGATTAGATAACACAGAAATAAATCCATGTATTTACAGC 2049
                          v  v  i  i   v v  v iiv          i    ii     ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_20090219_2   2050 CTATTCATTTTCAACATAGCCACAAAGACCATTCA-TGGAGGAAGTGACA 2098
                          v   v      i   vi vii v           -   i i   -i i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATA 394

  chr1_20090219_2   2099 GTCTCTCCAATAAAGGGTGCTGGGAAAACTGAATATCCATATGCAGGCAA 2148
                             i i   i   v          v     i   ?   i     -----
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA----- 439

  chr1_20090219_2   2149 AAAAAAAAAAAACTAGACCACTATCTCTCACTGTATAAAAAAATCAACTC 2198
                         -   i  vi  ii i    v   i   v   ii    v      i     
  L1M4_orf2#LINE/    440 -AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

Transitions / transversions = 1.42 (68 / 48)
Gap_init rate = 0.01 (7 / 485), avg. gap size = 24.00 (168 / 7)  

1136 24.76 6.01 1.20  chr1_20090219_20093624.rev     2500  2915 (491)    L1M4_orf2#LINE/L1      473   908 (0)  

  chr1_20090219_2   2500 ATAAATAAACAAACTCTAAATGGATTAAAGATTTAAACATAAGACTCCGA 2549
                            v v   iv     v        i ?   ii    ii     viivi 
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_20090219_2   2550 ACCATGGAAGTACAAGAAAAAAAACATAATAGGAGGAACAGTTTAGGACA 2599
                           i  ii  v viv    i    -    ---  ? v  vvv  iiv   v
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAA-CATA---GGNGTAAATCTTCGTGACC 568

  chr1_20090219_2   2600 CTGATCTGGACAAAGGTATTATGGAGA--ACACTTCAAAGCACAAGCA-C 2646
                         i  ivi i i   v   v iv i  v --    i-v            - 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACC-AAAAGCACAAGCAAC 617

  chr1_20090219_2   2647 AAAAACAAAAATAGACAAATGGTATTACATTAAACTAAAAGCCTTCTGTA 2696
                             iv         i    v v i v   i   v v   iv   i   i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_20090219_2   2697 TAGCAAAGGAAACAAACA-GAA--TGAAGAGACAACCTGAAGAATGGGAG 2743
                         ivv       v  v v  -   --    i        iiv          
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_20090219_2   2744 AAAATATTTGAAAACTATTCATCTGACAAGGGATTAATA-CTAGAATATA 2792
                                   v   ii  vi      i      i vi  - i        
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_20090219_2   2793 CAAGGAACTAAAACAACTCAA--------------ATAATCCAATTTTAA 2828
                         i  i     vvv         --------------    i      ?v  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_20090219_2   2829 AATGGGCAAATGACT-GAATAGACATCTCTCAAAAGAAGACATGCAGATG 2877
                                   v  i -          i    v        i  i  i   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_20090219_2   2878 CCCAA---GTCTGTGAAAAAATGCTCAATATCACTAATCAT 2915
                         v    --- ivii      i        i    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (55 / 45)
Gap_init rate = 0.03 (11 / 436), avg. gap size = 2.73 (30 / 11)  


5019 15.13 1.22 0.56  chr1_20494778_20497764     1596  2494 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_20494778_2   1596 AAAGATGTCCTATGTTCATGGATTACCAAACTCA-TATTGTTGATATAAG 1644
                               i   i             ivv i   i -       i v  iiv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_20494778_2   1645 CATACTCCCCACACTGACCTATAGATTCAATGCAATGCCTATCAATGCAA 1694
                         v          v i   i   i        i     v        ---  
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA---AA 100

  chr1_20494778_2   1695 TCCCAATGGCATTTTTTGTAGAAATGAAAATTCCAATCCCAAAATTTATA 1744
                              iiv  v       i      vi v vv ii    i      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_20494778_2   1745 TATAATTGCAAGGAACACCAAATAGTCAAAACAATCTTGAAAAAGAAAAA 1794
                          iv  v       i  v vi     i                     i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_20494778_2   1795 CAAAATTTGAGGAATCACATTTCCCAATTTTAAAACTTAATACAAAGCTA 1844
                             i  v     v     i          i        v          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_20494778_2   1845 TAAAAGTCAAAACAGTGTAGTACTGGCATAAGGACAGACACATAGGTCAA 1894
                         i iv i    i       i               i     i    i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_20494778_2   1895 TGGAATAGAATTAAGGGTCCAGAAATAAAGCCATACAGCTATGGTCATTT 1944
                                     i  i             v       vi        v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_20494778_2   1945 GATTTTTGACAAGGATGCCAAGACCATTCAATGGAGAAAGAATAGTCTCA 1994
                               i       i                   i             iv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_20494778_2   1995 TCAATAAATGATGCTGGGG-AACTGGATAGCCTCATGAAAAAGAATCACG 2043
                             i     i       i-         ?  v    v        v v 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_20494778_2   2044 TTTGACCCTTAACTTACACCATACACAAAAAGTTAACTCAAAATGGATCA 2093
                           v     i  v  i        i       -                  
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCA 499

  chr1_20494778_2   2094 AAGATCTAAATGTAAGAGCCAAAATTATAAAGCTCTTAGAAGAAAACAGA 2143
                         ?   i              i    i      i                v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_20494778_2   2144 GCGATAAATCTTCATGACCTTGGATTTGGCCATGGGTTCTTGTATGTGAC 2193
                          v?i         i         i  v   v    v     iv  i    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_20494778_2   2194 ACCAAAAGCACAAGCAACAAAAGAAAAAAATAGATAAGTTGAACTTCATC 2243
                                                      -       i   i        
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATC 648

  chr1_20494778_2   2244 AAAATTTAAAACTTTTGTGCTTCCAAAGATACAATTGAGATAGTGAAAAG 2293
                               v                v  i  i  v  ii   v         
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_20494778_2   2294 AAAACCCACAAAATAGGAGAAAATGTTTGCAAATCATATGTCTGACAGGG 2343
                          v        i   i         i              i     i i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_20494778_2   2344 GACTTGTAT-------ATAGAAGGAACTCTTACAAGTCA-TAATAAAAAG 2385
                                  -------   v  i            v   -          
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_20494778_2   2386 CCAAGTAATCCAAATTAAAAATGGGCAAAGGACCTGGATAGACATTTCTC 2435
                         v   i   i    v ?                ii  i             
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_20494778_2   2436 CAAAGAAGATGTACCTATGGCTAA-AAATACATGAAAATATAATCAGCAT 2484
                                   i   vv     i  -  ii         v  iv   i   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_20494778_2   2485 CATTAGCCAT 2494
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.64 (82 / 50)
Gap_init rate = 0.01 (8 / 905), avg. gap size = 2.00 (16 / 8)  


3099 18.17 12.80 2.44  chr1_20825022_20827468     1135  1954 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_20825022_2   1135 AAAGAGACCTC-TGTGTCATGGATTGGAAAACTCAACGTTGTT--GACAG 1181
                              v i i -   -             i   i  ii     --  ii 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGT-TCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_20825022_2   1182 TGAGTCTCCCCAAATTGATCTATAGGTTCAAGGCAATTCCTACCAAAACT 1231
                         ii vv                 i  i     v     i    i     ii
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_20825022_2   1232 CCAGCTGTTTTTTTGGTTTTTTTTTTTTGGCAGAAATGGACAA------- 1274
                                ii     -------------  -       v     -------
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTT-------------TG-CAGAAATTGACAAGCTGATC 138

  chr1_20825022_2   1275 ------TTTGTATGGAACTGTACAGGACCCGGCATAGTCAAAACATTCCT 1318
                         ------  ii       v  i vi      i v    i       v  i 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_20825022_2   1319 GAAAAAG----------TTAGAGGGCTTATAATTCCAAATTTCAAAATTC 1358
                                ----------  i    i  i i v    v          i i
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_20825022_2   1359 ACTATAAAGCTACAGTCAGTAAGACAGTGCAGTATTAGCATGAAGGATAC 1408
                             i           v vi         ii   i i    -       v
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAG 287

  chr1_20825022_2   1409 ACCTACAGAACAA---AAGAGAACTCAGAATCCGGAAATAAACCCTTATA 1455
                           v  i   v   ---  v    i v   i   i           v  i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_20825022_2   1456 TTTATGGTCAATTGATTTTC-ATAAGA-TGCTACGGCAATTCAATAGGGA 1503
                                             - i   i-   i v i v       i    
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_20825022_2   1504 AGGGACAGTCTTTTCAATAAAAGGTGCTGGAATAATCACACACCCACATG 1553
                          i i i           i   v        i i  iiiv i ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_20825022_2   1554 CAAAAAGATAAA-TTATACCCTTACCTCTCACTATAAACAAAA------- 1595
                              ii  i  -  iv    i      v   i   v      -------
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_20825022_2   1596 CAATATAGATCACAGACCTAAATGTAGGAGCCAAAATTATAAAACTCTTA 1645
                            v  i     ?             i    i    i             
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_20825022_2   1646 -----AAACGTACGAGTAAATTTTCATTACCTTTAATTAGGCAATG-TTT 1689
                         -----    i  v ?      i   i v     vii          -   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_20825022_2   1690 CTTAGATA--ACCATAAAACTGCAAAAGCAATTT--TTAAAAAT-GATAA 1734
                                 --  vvi    --   v      ivv--vv      -     
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAA--GCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_20825022_2   1735 ATAGGACTTCATCAAAA--AGTAAAC------GCTTCAAAAGATACTACT 1776
                           v              -- i-    ------        i  i    ii
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_20825022_2   1777 GAGAAAGT------------CACAGAATAGGAGAAAA--------AATC- 1805
                         i       ------------        i        --------    -
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_20825022_2   1806 ------TGAT--GAGACTTTATGTCTAGAGTA-AT---GAATTCTTGT-- 1841
                         ------    -- i     -i i  i   i  -  ---   i    ii--
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTT-GTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_20825022_2   1842 -----TAACGAATAACCAAC---CCCCTTTTAAAAATGGGCAAAAGATTT 1883
                         -----   ii  v iv   v---   vv  ?             i     
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_20825022_2   1884 GAATAAACATTTCACTACAGACAATAAACAAATGGCCT-TAAGCACA--- 1929
                              i       v i v   vi   v          v-        ---
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_20825022_2   1930 AGAGATGCTCAACATCAGTAATTAT 1954
                          i               ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (97 / 48)
Gap_init rate = 0.04 (33 / 905), avg. gap size = 3.79 (125 / 33)  


2450 24.01 5.86 3.49  chr1_21028530_21032091     2183  3069 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_21028530_2   2183 TGGAAATGCATCCCATAATCATAGACTGGAAGAATCAATGTTGTGAAAAT 2232
                               vii       iv    i  i       v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_21028530_2   2233 GGCCATACTACTAAAAGCAATCTACAGATTCAATGTAATTCTCATCAAAA 2282
                            v     v iv   vii              i i   i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_21028530_2   2283 TACCAAC-G----TTTCACAGAATCAGAAAAAAAAATCCTAAAATTCATA 2327
                          v   i - ----   ii     viv  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_21028530_2   2328 TGGAACCAAAAAAGGG-CCCA-AGTAGCCAAAGCAATCCTAGGCAAAAAG 2375
                              -- viv     -    - i        i     i iiiv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_21028530_2   2376 GAGAAATCTGGGGGCATCACAATT----ACTTCAAA--TCA-TACAAGGT 2418
                         i v   vi   i  vv     v  ---- i      -- i -     i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_21028530_2   2419 TATAGTTAACAAAACAGCGTAGTACTGGTATAAAAGTAGGCAAATA-ACT 2467
                           i   v v   i    i  i       i    iii   i  v   - ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_21028530_2   2468 AATGGAACAGAATACAGAACCCAGAAGTAAAGCCAAGAAAGTACAGCCAA 2517
                                i     vv   ii      i    v   viv vv  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_21028530_2   2518 CTGATCTTCAACAAAGCATATAAAAAC-ATAAATTGAGGAATAGACACCC 2566
                         i    i   i    i -i iiv  i  -  vv v  i    vii i vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_21028530_2   2567 TATTTAACAAATGGTGCTGGCAAAACTGGCAAACCTCATGTAAAAGAATG 2616
                          v  i               v v      vv ?  v    i         
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_21028530_2   2617 AAAC--GATCCCTATTTCTCACCTTGTACAAAAGTCAACTCAAGATAGAT 2664
                           ii--  i     ii  v    v i       i i       i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_21028530_2   2665 CAAAGACTTAAATATAAGACCTGAAACTGTAAAAATTCTAGAAGATAACA 2714
                           ?    i     i     v  i     i     v ii       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_21028530_2   2715 TTGGAAAAAACTCTTCTAGACATCAGCCCAGGCAAATAATTCATGAG-TA 2763
                          v  ?iv   -     vv   v ii vii      - ii  iv v  -  
  L1M4_orf2#LINE/    548 TAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATA 595

  chr1_21028530_2   2764 AGACCCCAAA-GCAAATGCAACAAAAACGCAAATAAATA----GAACCTA 2808
                         v   v     -   v v         iviv     i   ---- i  i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_21028530_2   2809 ATTAAACTAAAAACCTTTTGCACAGCAAAAGAAAC----AATAGAGTAAA 2854
                           i   v v    v      ii vv    i  v  ----  v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_21028530_2   2855 AAGACAACCCATAGA----GA---------TGCAAACTACACATCTGATG 2891
                                    i   ----  ---------      ii i i       i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_21028530_2   2892 AAGGA-----------AATCTACAAGGAACTCAAACAAATCAGCAATAAT 2930
                          i   -----------   v  i  i      vv    v   --------
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-------- 787

  chr1_21028530_2   2931 AATAATAATAATAATAATAATAATAATAATAATAATCCCATCAAAAAGTG 2980
                         -------------       v  -i i  --    i  v  i?    i  
  L1M4_orf2#LINE/    788 -------------ATAATAAAAA-GACAA--ATAACCCAATTWAAAAATG 821

  chr1_21028530_2   2981 GGCAAAGGACATGAATAGACATTTCTCAAAAAAAGATACATAAATTGGCC 3030
                                  iv                v   i      i i    -    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT-GGCC 870

  chr1_21028530_2   3031 TACAAACAACATGAAAGCATGCTTAACATCACTAATGAT 3069
                         v i  i  -       iv     i       ????????
  L1M4_orf2#LINE/    871 AATAAGCA-CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (128 / 81)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.19 (83 / 26)  


2895 21.70 2.80 2.13  chr1_21097221_21099397      495  1245 (932)    L1M4_orf2#LINE/L1        4   759 (149)  

  chr1_21097221_2    495 AAAATTATCCCCTGTTCATGAACTGGAAGATTTAATATTGTTAATATACC 544
                            iv      v        i i       i             v  iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_21097221_2    545 AATACAACCCAAAGTGACTTACAGATTCAATGCAATCTCTATCAAAATCC 594
                              vv      v   ii           i      i            
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_21097221_2    595 CAATGGTGTGTTCTACAAAAACAGAAAAACTCCCCATCCTGATATTCATA 644
                           iiv iv v  i i  i   iv  v  i  v---     i v       
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTG---ATCCTAAAATTCATA 150

  chr1_21097221_2    645 TGTATTCTCAAGGAAGTCTGGATAGCCAAAACAATAGCTGAAAA----GA 690
                           v vviv     i vi v i              v-i      ----  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAAGAAGA 199

  chr1_21097221_2    691 AAAAAGCTGGAGGCCTCACAATTCCAGATTTCAAAATT----ACAAATCT 736
                          v    i      v      v    vi         i ----     v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_21097221_2    737 GCAAAAATGAAAA--GTGCAGTACTGGTGTAAAAATAAACCAAAAGTAAT 784
                         i  iv   v  i --   ii       ii   ii   i  -----i  --
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC-----ATA-- 292

  chr1_21097221_2    785 TAGA--AATGGGAAAAAAT----GGCCCAGAAATAAACCCACAAATATAT 828
                             --     i v i   ----i i               i v  v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_21097221_2    829 GTTCAAACGATTTTTGAAAAGGGTACCAAAACCATTCAATGGGGAAAGGA 878
                          v    vi      i  v      i    i                  i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_21097221_2    879 CA---TTTTCAACAAATGGTTCTGGGAGAAATTAGATATACATATGCAAA 925
                         i ---               v      v  -i i    ?v  i       
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAA 441

  chr1_21097221_2    926 AGAATGAAGTTAGACCCTCACTTAACACCAAATACAAAAATTAAGTCAAA 975
                                    i     ii  i v      v             v     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_21097221_2    976 ATAGATTA-AGACCAAAATGTAAGAGCTAAAAGTAAAAAAATCTGAGAAG 1024
                           i   i -     v                 v  v    v   v     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_21097221_2   1025 AAATCAGAGAGAAAACGCTCTGAAACACTGGATTTGGCAATGACTTCTTA 1074
                            v  v  i?iv  vv  ii vi  vi   i  v       ii      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_21097221_2   1075 GATACAATACCAAAGGCAGAAGCAAAAAAAAAAAAAAGTAGACAACTTGG 1124
                             ii i      i   v      v    i      -    i  v    
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGG 640

  chr1_21097221_2   1125 GCAT-ATTAACAATTTAAAATTTTTGTGCATCGAAAGATATTACACCAAG 1173
                         i v -  i  -    v    i        v  i  i  i i  i--    
  L1M4_orf2#LINE/    641 ACTTCATCAA-AATTAAAAACTTTTGTGCTTCAAAGGACACTAT--CAAG 687

  chr1_21097221_2   1174 AGAGTCAAGAGGCAACCTACAGAAGAAGAGAAAATATTTGTAAACTGTAC 1223
                          i   v  i  i     i      vii             i   iii  i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_21097221_2   1224 ACCTGTTAAAAAGTTAATATCC 1245
                          i   v   iiiii vi     
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCC 759

Transitions / transversions = 1.56 (98 / 63)
Gap_init rate = 0.02 (16 / 756), avg. gap size = 2.31 (37 / 16)  

 606 18.18 1.30 1.30  chr1_21097221_21099397     1539  1692 (485)    L1M4_orf2#LINE/L1      755   908 (0)  

  chr1_21097221_2   1539 TATCCTGAATATATA--GAACTCCTAAAACTCAATCACAAAAAAGCAAAC 1586
                              v         --      i  v        v i     ii    i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_21097221_2   1587 AATCAGATTCAGAAATGGGCAAAGGACACGAATAGACATTTCTATTAAAA 1636
                           i vi   ? i              ivi              viv  i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_21097221_2   1637 AGACATACACAAATGGCCAACAAGCCCATGAAAATATGCTAATCCTAAGG 1686
                            i     --         i    v        v     v v v v ??
  L1M4_orf2#LINE/    855 AGATATACA--AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_21097221_2   1687 AAATAC 1692
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.08 (14 / 13)
Gap_init rate = 0.01 (2 / 154), avg. gap size = 2.00 (4 / 2)  


1824 25.83 3.31 2.83  chr1_21147816_21149802      479  1113 (874)    L1M4_orf2#LINE/L1      188   825 (83)  

  chr1_21147816_2    479 TAAAAATAAAAAATAAAAAAATAGAGACATGATACTACCTAACTTCAAAA 528
                          i    vi  i  i   iv-- i   ivv v i   v  i  i       
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGT--TGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_21147816_2    529 TATGCTGCACAGCTACAGTAACCAAAACAGCATGATACTGGACTAA---- 574
                         iv i  i  v           i   i    ii  i      vv   ----
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_21147816_2    575 AAACATA--GACCAATGGAAGACAACAGAGAATCAAGAAACAAATCCATT 622
                          i     --  i        v v  iv    i  v     i   i    v
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_21147816_2    623 TATTTATAGCCAATTCATTTTTT-TAAGGGTGCCAAGAATATACACAGGA 671
                         i      i i     v     iv-i             vi  v  vv  i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_21147816_2    672 GAAAGGACAGTCTCCTCAATCAACAGTGCTGGGAAAACTGGATATCTACA 721
                              i i     ii    iv  ii         v         ? i   
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_21147816_2    722 TGCAGAGAAATGAAACTAGATCCCTATCTCTAACCATATACCAAAATCAA 771
                             i ii      ii i  i     i   vv         v     i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_21147816_2    772 ACCAAAATGGACTAAATATTTAAATGTTAAGATCTGAAACCATGAAACGA 821
                         vi         ii ? v ii       -    v  i    i  i    vv
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTC 534

  chr1_21147816_2    822 ATACAAGAAAACACCAAGG-AAATGCTTCAGAACATTGGTCTGAAAAAAG 870
                         v  v         ivii? -    -    ivi  v    vi iiiv  v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_21147816_2    871 ATTTTTCTTTTGGGTAAAAT-CTAAAAAGAGAA-----AAAAGCAAAACT 914
                         i   i ---- i i  vi i- i    iv v  -----     v    v 
  L1M4_orf2#LINE/    584 GTTTCT----TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_21147816_2    915 AGAGAAGTGGGATTATATCCAA-TTAAAAAGTTTC-TGCAAATTTAA-GG 961
                            v  i v   i vi   v  -       v   i-   ---  i  -  
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC---TTCAAAGG 676

  chr1_21147816_2    962 AAACAGTCAACAGAGTAAAGAGACAACTTACAGAACGGGAGAAAATATAT 1011
                          v  vi    v i   i  i       ii      i            v 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_21147816_2   1012 GCAAACTATACATTTGACAATTGATTAACAGCCAAACTATATAAGAAAC- 1060
                              ii   i  i   i  vv  i vii v   i v       ii   -
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_21147816_2   1061 ---ACAACTCAACAGCAAAAAGAAAAGAAGAAAAAAATCCAATTTAAAAA 1107
                         ---         i ii       v  ------- v  i      ?     
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAA-------ATAACCCAATTWAAAAA 819

  chr1_21147816_2   1108 TGGGCA 1113
                               
  L1M4_orf2#LINE/    820 TGGGCA 825

Transitions / transversions = 1.67 (100 / 60)
Gap_init rate = 0.03 (16 / 638), avg. gap size = 2.44 (39 / 16)  

 431 15.74 7.41 0.00  chr1_21147816_21149802     1387  1494 (493)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr1_21147816_2   1387 AAAAAAAAAAAGAA-------AAAAAAAGGACAAATGATCTAAACAGACA 1429
                              i v   v  -------?     v  i    v   i i  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_21147816_2   1430 TTTCTCAAAAGAAGATATACAAATGGCTGACAAGTATATGAAAAG-TGCT 1478
                               v                    ii i   i i        -    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_21147816_2   1479 CAATATCACTGATCAT 1494
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.20 (11 / 5)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 4.00 (8 / 2)  


1855 26.09 5.25 2.70  chr1_21519201_21520865.rev      508  1174 (491)    L1M4_orf2#LINE/L1      225   908 (0)  

  chr1_21519201_2    508 CAACTTCAGGACTTAC-ATTAAGCTACAGTAACCCAAATAGTGTGAAGTT 556
                            i    ii      - iv            i v i i      ivii 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_21519201_2    557 GGTGAAAAGAGAAAACACACACAAATAGATTCGTGGAAAAGGAATACAGA 606
                           iiv  i  v i -------  v      ivi     v  -   vv   
  L1M4_orf2#LINE/    275 GGCATAAGGATAGA-------CATATAGATCAATGGAATAG-AATTGAGA 316

  chr1_21519201_2    607 GCCCAGAAACAGGCC--TACAG--ACAGTCCACTGATCGTCCATGAAGGT 652
                          i       i ii  --    v-- ii   v i    iv  v ii i   
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_21519201_2    653 TTAGAGACAATTTAAAACAGCAAAGACAGCCTTTCCAACTAGTGGTGCTA 702
                         vivi    v   i  vivi v  ii i  i    i    v i       i
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_21519201_2    703 GAACAGCTGGACAAACACATGCAAAAAAAAAAAATAATAATAAATCCAGG 752
                          i   i     i ?v           i  vi  i ----- ii i  vvi
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGT-----TGGACCCCTA 461

  chr1_21519201_2    753 TATGCATGTTATACCC-----TTTAT--AAAATAAATCTTACATGTAAAT 795
                         iv -  iiii   iv -----  v i--     ii   v? v iv     
  L1M4_orf2#LINE/    462 CCT-CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_21519201_2    796 GTAAGATGC-AAAACCATAAGAATCCTAGGAGATAACATAAGAGAAAATC 844
                               -  -     i    i v  i   i   v      i ? v     
  L1M4_orf2#LINE/    511 GTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_21519201_2    845 TTGGGGATCTTGGGTTGGATGATGGCTTCTTAGATACAAAACCAAAAGCA 894
                           v v  i        i iii    i          ii v          
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_21519201_2    895 CAATCTACTAATGAAAAAA--ATTAAGTTGAGCCTCATTAAAATTAAAAA 942
                            v v  v  v       --iv   i   ii i    i           
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_21519201_2    943 CTTCTGCTCTGTGAAAGACACTGTCAAGAGAATGGAAAAAGCAAGTCACA 992
                            i  iv  vii  i      i      i i  i   i -   vi    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA-CAACCCACA 708

  chr1_21519201_2    993 GACTGGCAGAAAATATTTACAAA--ATA-ATCTGATGGAAAAACTGCTGT 1039
                           v   v           i    --   -       i- iii   vv i 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATA-AGGGACTTGTAT 757

  chr1_21519201_2   1040 CCAAAATATATGAAGAATTCTGAGAACTAAACAACACAAAGA-AAA---- 1084
                            i       i     i   v v    v  i  i v     -   ----
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_21519201_2   1085 -------AAAAATAGGTGAAAGATCTGAA----CACCTCATTAA-TAAGA 1122
                         -------      i  ii  i   i    ----  ii  vii  -v    
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_21519201_2   1123 TATACAGATGGCAAATATGCATATGAAAAAGACACTCAAAATCATTTGTC 1172
                               i     v    v   i       -  ii     v    ??????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZ 906

  chr1_21519201_2   1173 GT 1174
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.95 (113 / 58)
Gap_init rate = 0.03 (21 / 684), avg. gap size = 2.52 (53 / 21)  


2874 24.21 11.49 0.49  chr1_21755677_21758834.rev     1850  2667 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_21755677_2   1850 TGGAAAGATATCCTGTGCTCATGGATCAGAAGAATTAATATTGTTAAAAT 1899
                                      ii  i        ii     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_21755677_2   1900 GACCATATTACCCAAAATAACCTGCAGATTAAATGCAATTCCTATCAAAA 1949
                          i v   i v      v i i  i      v  i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_21755677_2   1950 TACCAATGACATTCCTCACAGAAATAGAAAAACACAATCCTAAAATTCAT 1999
                          v   iivi v  ii ii       v  v  i -ii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_21755677_2   2000 ATGGAACCACAAAAGACCCTGAATAGCCAAATCAATCCTCAGCAAAAAGA 2049
                               vii   ii     v           v     i v iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_21755677_2   2050 ACAAAGCTGGAGGCATCATGCTACCTGGTTTCAAAATATACTACAAAGCT 2099
                               i      vv   ii  v  iii        iv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_21755677_2   2100 ATGGTAACCTAAACAGCATGGTATTGGTATAAA-------ACATAGGACA 2142
                          ii    i v i    ii     i   i    i------- i    iv  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_21755677_2   2143 ATGGAACAGAATAAAGAACCCAAAAATAAATTCACGTATTTACAGCCAAC 2192
                               i     vi   ii   i       ii  iii     ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_21755677_2   2193 TAATTTATGACAAAGGCACCAAGAACATACACTGGGGAAAGGGCACCCTC 2242
                          i    vi     i  ii      v   v  v         iii vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_21755677_2   2243 TTCACTAGATTTTGCTGGGAAAACTGGATATCGATATGCAGAAAAATGAG 2292
                             vi i  vv        v         ? v i     i  i     i
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_21755677_2   2293 ACTAGACCTCTGTCTCTCACTATATATTAAAATCAACTCAAAATGGATTA 2342
                         ii i    i  ii   v   i     iv     i              i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_21755677_2   2343 AAGACTTAAATGTAAGACTTGAAACTATGAAATTGCTAGAATTCAATATG 2392
                         ?    i           vi i       i   i vi     vvv  i  i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_21755677_2   2393 GGGG-AAATGCTGTCA-AACATTGGTCTAGACAGAGATTT--TAGCTGAG 2438
                           ? -    -  -  i-i  v    vi   i  iv i   --   v iv 
  L1M4_orf2#LINE/    550 GGNGTAAAT-CT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_21755677_2   2439 ACCTCAAA-GCACAGGGAACAAAACCAAAAATAACCAAAT-GGACTATAT 2486
                           vi    -     i v       vv       ivi    -     vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_21755677_2   2487 TAAACTAAAAAGCTTCTGCACAGCAAAGGAAATAATCTGCAGAGTTGAAG 2536
                         i   v v    i   i  ii vv       v iv   viv i   -   i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT-GAAA 696

  chr1_21755677_2   2537 AGACAACCTGTAGAATGGGAGAAAATAT-----AATC------------- 2568
                                 iii                 -----    -------------
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_21755677_2   2569 --------------------------------------TCA--------- 2571
                         --------------------------------------   ---------
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_21755677_2   2572 ---------------TTAAACAGTAGGCAACGGACCTGAACAGACATTTC 2606
                         ---------------  ?  v i i     v   ii    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_21755677_2   2607 TCAAAAGAAGACATAAACATGGCCAATAGGTGTATGAAA-GATGCTCAGC 2655
                           v        i   v v          i iii      -        i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_21755677_2   2656 ATCACTAATCAT 2667
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (131 / 63)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 7.00 (98 / 14)  


 299 27.92 7.17 8.30  chr1_21842802_21845677      934  1198 (1678)    L1M4_orf2#LINE/L1      321   582 (326)  

  chr1_21842802_2    934 AAAAATAAACCCAAGTAAATATGGGAATTTGCCATGTAATAAAGGTG--- 980
                          i           vii vv     vv v   viv vii i  i    ---
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_21842802_2    981 -GATT-TTTAACTGGTGAGGAAAAAGACTGAATTGTTCAATAAATGGT-T 1027
                         -  ii-  i  ----  i     --  v iivi v     i       -i
  L1M4_orf2#LINE/    371 AGACCATTCAA----TGGGGAAA--GAATAGTCTTTTCAACAAATGGTGC 414

  chr1_21842802_2   1028 TAAGACAAGTGAGTAGCCATTTGGTAAAAGGCAAAATAAAATATTGATGG 1077
                          ii     v  ii  ?   iv  -i     ----   i  i -----   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATG-CAAAAG----AATGAAGT-----TGG 454

  chr1_21842802_2   1078 ATCCCTACCTCAATCCATA------AATCAAATTAAATT--AT-AAAAAC 1118
                          i          vv     ------   i  v i   v --  - ? i  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_21842802_2   1119 ATAAAGGTTGCATAAAAGT--AAACCATCAG--TACTAAAACACAACATG 1164
                         v    ---  --   i  i--    i  v i-- vi  i  v v     i
  L1M4_orf2#LINE/    505 CTAAA---TG--TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_21842802_2   1165 AGTGAATATTTTTATAACCTCAGAATTGGGAAAT 1198
                         i ? v v  i  ii i    ii i-  i  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGG-TTAGGCAAT 582

Transitions / transversions = 1.73 (45 / 26)
Gap_init rate = 0.06 (16 / 262), avg. gap size = 2.56 (41 / 16)  


1467 17.72 12.66 0.00  chr1_22155732_22158021.rev      658   973 (1317)    L1M4_orf2#LINE/L1        1   356 (552)  

  chr1_22155732_2    658 TGGAAACACATCCCACATTCATGAACTGGAAGACTTAATATTGTTGACAT 707
                               v i      ii      i i                   i v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_22155732_2    708 GTCAACATTATCCAAAGCAACCTACAGACTCAATGCAATCCCTATCAAAA 757
                          v   i i vi     vii i       i    i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_22155732_2    758 TCCCAAC---------------AAGGGATAG--TAATCTTGAAA------ 784
                              i ---------------  vv  i i-- i   i i   ------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_22155732_2    785 --------CAAGGGAC----AATAGACAAAATAATCTTGAAAAAGAA--- 819
                         --------        ----     v     i               ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_22155732_2    820 TAAAGCTGAAGCACTCCCATTTCCTGATTTCAAAACTTACTACAAGGCTA 869
                         i    i  i  v    v  i    ii                   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_22155732_2    870 CAATAATCAAAACAGTGCGGTATTGGCATAGGGA--GATATATAAGACAA 917
                           i       i      i    i       i   --  i     iiv   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_22155732_2    918 TGGAATAGACTAGAGAACCCAGAAATAAACCCTTACATATGTGGGCAAAT 967
                                  v v    ii              v     v i   v   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_22155732_2    968 GATTTT 973
                               
  L1M4_orf2#LINE/    351 GATTTT 356

Transitions / transversions = 2.29 (39 / 17)
Gap_init rate = 0.02 (6 / 356), avg. gap size = 6.67 (40 / 6)  

1892 19.58 9.40 1.15  chr1_22155732_22158021.rev     1279  1799 (491)    L1M4_orf2#LINE/L1      345   908 (0)  

  chr1_22155732_2   1279 TCAAATAATTTTTGATAAGGGTGCCAAGACCATTCAGTGGTAAAAGGA-- 1326
                             v i     i  i                    i   vi    i --
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_22155732_2   1327 --CTCTTCAATAAATGGTGCTGAGAAAATGACATATTCACAAGCAAAAGA 1374
                         --  i     i           i  v  iviv   ?i    v        
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_22155732_2   1375 -CAAAGATGAAACCTTACCTAATACTATATACTAAAATTAACTCAAAATG 1423
                         -ii   v  i v  i     v i  i      v                 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_22155732_2   1424 GATAAAAGGTCTAAATGTTAGACCTAAAACTTTAAAACTCCCAGAA---A 1470
                            v ?  ii        v   v        v        ii    --- 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_22155732_2   1471 ACATAGGGCAAAAGATTCAGG----TGGACTTGGCAATAATTTGTTTGGA 1516
                                ?vv   vv   iv ----   ii v      ii   -i  i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-CTTAGA 593

  chr1_22155732_2   1517 TATCACACCAAAC-CAC------CAAAA-----AATAGACAAA-----CT 1549
                            v        v-   ------     -----      i   -----  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_22155732_2   1550 TCATGAAGCTGTGAAAA-TTTTATACATCAGAAAATAGTATCAACAGAAT 1598
                             v  iv - i    -    i i v   i ii i v      v i i 
  L1M4_orf2#LINE/    644 TCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_22155732_2   1599 AAAAACGCAACCCACAAAATAGGAAAAAATATATGCAAATCGTGTATGTG 1648
                         i    vi         i   i   i       v        i i   v  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_22155732_2   1649 ATAAGAGATTAATACCCGGAATCTACAAAGAACTCCTAAAACTTACCC-C 1697
                              i  i vi  i  i    v  i         i  v    i viv-i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_22155732_2   1698 AAAAAAA-AAAT--CCCAATTCAAAAATGGGCAAAGAACTTGATTAAACA 1744
                              i -    --       ?              i i    v  i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_22155732_2   1745 GACCTTTCTCCAAAGA---TATATAAATGGCCA-TAAG-----------A 1779
                         ----            ---    i         -    ----------- 
  L1M4_orf2#LINE/    843 ----TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_22155732_2   1780 TGCTCAACATCACTAATCAT 1799
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (62 / 36)
Gap_init rate = 0.03 (18 / 564), avg. gap size = 3.06 (55 / 18)  


 430 19.34 0.41 20.58  chr1_22264400_22267212.rev      502   744 (2069)    L1M4_orf2#LINE/L1       22   215 (693)  

  chr1_22264400_2    502 TGGATCAGAAGATTCCCTATTATAAAGATGTCAATTCTCCTCATATTGAT 551
                              ii     i ivv    i v      v    v    i  v      
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGAT 71

  chr1_22264400_2    552 GTGGAAATTCAGTGAAATTATGATTTAAAATCCCATAAGTGTGTGTGTGT 601
                         v iv i     ii v   iviv  i-         ---------------
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATCCCTATC-AAAATCCCA--------------- 105

  chr1_22264400_2    602 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGACAGAGAGAGAGACAGA 651
                         ------------------ i-  iv v v -  -------------    
  L1M4_orf2#LINE/    106 ------------------GC-TGCCTTTTT-TG-------------CAGA 122

  chr1_22264400_2    652 AAGGTGTCAAGATGATTCTAAAATTTGTTTGGAAATGCAAAACACCAAGA 701
                           v-  v    v    i        ii v           iiv   v   
  L1M4_orf2#LINE/    123 AAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr1_22264400_2    702 ATATCCAAGTCAAACTTGAAAATGAAGAACAA-GCTAGAGGACT 744
                            v    iv   v        v         - i i       
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

Transitions / transversions = 0.96 (23 / 24)
Gap_init rate = 0.04 (7 / 194), avg. gap size = 7.29 (51 / 7)  

1238 27.86 7.21 2.00  chr1_22264400_22267212.rev     1107  1605 (1208)    L1M4_orf2#LINE/L1      259   783 (125)  

  chr1_22264400_2   1107 AAGGCATTGTAATATTGGTGTAAGGATAGACAGACCCATCAAT----TAG 1152
                            i  v   ii  i   ii            v ivv      ----   
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_22264400_2   1153 CTTAGGGAGTCCAGGAACAACCCCACAC--CTGTGAT-ACCGGATGCATG 1199
                         vv v i        i  i  v    i  --i i  i - viv   vivi 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_22264400_2   1200 ACAAAGGTG---ATACTGCACTGCAGTGTGGGAAGCAAAATCTTTTCAGT 1246
                             i    --- v  --  i -  i  v  i   v v i        ii
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGAC--CATT-CAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_22264400_2   1247 AAAGGAT-------CAACTAGGTGTCCCCA--CAAGGAAA--AAGCCTTG 1285
                            v i -------     i i i?  v  --   iii  --   i- v 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT-TGG 454

  chr1_22264400_2   1286 ACCTCTACTTCACAAACCATGCACAAAG-TTA-TTCCAGATAAACTGTCT 1333
                            i    i     --    ii     i-   -i  v i  ii iii?vv
  L1M4_orf2#LINE/    455 ACCCCTACCTCACA--CCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_22264400_2   1334 GTCTAAATGTGAAAGATAAA--TA-AAAGCTTCTA------AGCATAAGA 1374
                         ii        i i  v    --  -   i  ii  ------ i    i ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_22264400_2   1375 GAATAGCTTCATGACCTCTGGGCT-GGCAAAAGTTTCTTAAACAGAAAAC 1423
                          v v v    i      -    i -     vi        i i vi v  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_22264400_2   1424 TGAAAGCACCAACCATAAAAGAAAATAATGGATACATTTAGCAGC-TTAA 1472
                         ii       v i v i         -   i    v   vii vv - i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAA 650

  chr1_22264400_2   1473 GGTTTAGAACTTCCGTTCACTGAAAGACTCCCCTAAGTGAGTAGAAAGAC 1522
                         ii  v i     ii  v viii  i   v ivii   vi   ii      
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_22264400_2   1523 AAGCTAATGAGTGGGAGAAAAATATTTG-AAATCCATACATCTGACAAAG 1571
                           v i vv  i          -      -     -   i      i  i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAA-TATTTGCAAATC-ATATATCTGATAAGG 748

  chr1_22264400_2   1572 AACCTATGTCCAGAATATATAAAGAATTCT-ACAA 1605
                         i  i i i                  i   -    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

Transitions / transversions = 2.09 (92 / 44)
Gap_init rate = 0.05 (24 / 525), avg. gap size = 1.92 (46 / 24)  


3484 22.33 2.78 1.89  chr1_22270608_22273157.rev     1161  2060 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_22270608_2   1161 TAAAAAGATATTCCATATTCATGAATTGGAAGAATCAATATGATTAAGAG 1210
                          ii        i    i      i         v i     vi      v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_22270608_2   1211 GTCAGCTTCTTCCCAATTTGCTCTATATATACATGCAATGCAATGTTAAT 1260
                          v  i- v  i     v   v    i v  --- -   i     viiv  
  L1M4_orf2#LINE/     51 GGCAA-TACTCCCCAAATTGATCTACAGAT---T-CAACGCAATCCCTAT 95

  chr1_22270608_2   1261 GAAAATCCCAGC-AAGTTACTTGTGGATATTGACAAACTGATTCTAAAAT 1309
                         v           -ivv  vi   ii  v        i     i       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_22270608_2   1310 ATATATGGAAAGACAAAAGATCCAGAATAGCCAATACGATACTGAA---T 1356
                         vi         vi   ii  i             v  i  vi    ---v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_22270608_2   1357 GAGAACCAAGTCAGAGGCCTGGCACTACCTGGCTTTAGA-CTTACTAGAA 1405
                         i     v    ii    v  vi    v  iiii  i i -       v  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_22270608_2   1406 AGCTACAGTAGTCAAGATAGCATGGCACTGGCA--AGGAGAAAACACATA 1453
                                   i      i  ii   i       --    v i -  i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA-CATATA 294

  chr1_22270608_2   1454 AATCTATAGACCAGAAGAGACAGCCCCAAAATTTAACCCACTCAAATATA 1503
                         i   v  i  vi    vv  v  i  vi    v-      iv  vv   i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATA-AACCCATACATTTATG 343

  chr1_22270608_2   1504 GTTATCTTATAGTTGACAAAGGCGCAAAGGCAATTCAATGGAGAAAGGAT 1553
                           i vi v  vv i     i  i  v   i v         i     i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_22270608_2   1554 AGTCTTTTCAACAAACGGTGCCGGGACAACTGGACATCCACATGCAAAAA 1603
                                        i     i            i ?            i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_22270608_2   1604 TAAAATTTTAAAAAATCTAGACACAGACCTTACACCTTTCACAAAAACTA 1653
                         ---   -----i  i - i   v vv    i     v vi       i  
  L1M4_orf2#LINE/    444 ---AAT-----GAAGT-TGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_22270608_2   1654 ACTCAAACTGGATCATAGACCTAAGTGTAAAATAGAAAACTATAAAGCTC 1703
                                v       ?        i     i vvv           i   
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_22270608_2   1704 CTAGAAAATAAAACAGGAGAAAAATCTAAGTGAGTTTGGGTTTGGCAATG 1753
                         i     i v  v i   ? v   -   vv    vi       v       
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_22270608_2   1754 AGTTTTTAGATACAGCACCAAAAGCATGACCTCTGAATGAAAAATGTGAT 1803
                         iv  i       iii           ii v vvii  v      vvv   
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_22270608_2   1804 AAGCTGGACTTCATTAAAATTAAAAATTTCTGTTCTGTGAAAGACATCAT 1853
                           ii          i           i  i   v  vii  i    ii  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_22270608_2   1854 TAAGAGAATAAAAAG-----CCACAGACTGAAAGAAAATATTTGCAATAC 1898
                         i    i i i     -----       v  ii               vv 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_22270608_2   1899 ATGTATCTCATAAAGGATTTGTATCCAAAATATACAAAGAACTCTGA-AG 1947
                           i     v    i   i         i      i          v - i
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_22270608_2   1948 TTCTATAAGAAAAA-------AATCCCATTTAAAAATTGA-AAAAGATCT 1989
                         i  v    v     -------  i  v   ?      v i-   i   i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_22270608_2   1990 GAA----CACCTTACCAAAGAAGATACACAAATGGCAAATAAGCATATGA 2035
                            ----  ii iv            i         v        i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_22270608_2   2036 AAAGATGTTCAACATCGTATGTTGT 2060
                                i        i????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (118 / 79)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.33 (42 / 18)  


3581 22.38 2.76 2.65  chr1_22379228_22381551      928  1834 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_22379228_2    928 TGGAGAGGTATACTATGTTCATGAGTTAGAAGACTCAACATTGTTAAGAT 977
                             i  i   v i         ii  i       i  i           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_22379228_2    978 GTCAGCTCTCCCCAGATTAACCCATAGAGTCAATGTAATCCA-ATCAAAA 1026
                          v  iiv       i   i i i i   v    i i     v-       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_22379228_2   1027 TCCCAGT---CTTTTGTGTA-AGACTGATAAGCTGATTCTAAGAGTTGCA 1072
                               i---     v  i - i i   i        i    i v iii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_22379228_2   1073 TG-AAATGCAAAGGACCTAGAATAGTCAAAGCAACCCTGAAAAACCG--- 1118
                           -        i     i       i    i   i i       -- ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA--GAAG 198

  chr1_22379228_2   1119 --TGAAGTGGGAGGACTTAACACTCCCTGATATCAAGACTTAGCATAAAG 1166
                         --ii    v        i -    i  ii  v    i     vi i    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_22379228_2   1167 CTACAGTAACCAACACTGTGTGGCATGGGCTTAATGATAGACACATAGAT 1216
                                  i   v  v      i iv   v   v        i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_22379228_2   1217 CAATGGAATACAAAAGGAAATCCAGAAATAGATACACATGTGTATGGACA 1266
                                   v  vv ii i          i iv  i ii v     v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_22379228_2   1267 ACTGATGTTTGACAAAGATGCAAATGCAATTCAGTGGAGAAAGAACAGTT 1316
                          i    v  i     i i   v  vi v     i   i       i   i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_22379228_2   1317 TTTTTATGGAATGGTGCTGAAACAATTGAATATCTACTTGCAAAAACAAA 1366
                             i vvi          ii    i  i   ? i  v       i--  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG--AA 445

  chr1_22379228_2   1367 GAAAGAAAGACCTATCTATACTTTATACTATATTTTAAAAATGAGCTCAA 1416
                         vi   vvi    i--   -- i i i  i    vi-      v i     
  L1M4_orf2#LINE/    446 TGAAGTTGGACCC--CTA--CCTCACACCATATAC-AAAAATTAACTCAA 490

  chr1_22379228_2   1417 AATGGATCATAGATCTAAATGTAAAATCTAAATCTATGAAATTCCTAGAA 1466
                                  ?   i          i v     v    i   i  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_22379228_2   1467 GAAAACGTTGGAGAAAATCCTTATGACCTTGGGTTAGGCAAATATTTCTT 1516
                               i v  ? v     i ii                  vvi      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_22379228_2   1517 AGCTGCAACACCGAAAGCATGGCTCATAAAAGAGG---TGGATAAATTGG 1563
                           v iii     i      iiiviv i      ii--- i          
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_22379228_2   1564 ACTTTATTAAAAATTAAAAAAACCCACTTGTACTATTCAAAAGACAATGT 1613
                             i  i    -       ---- vi    i  --     i    v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAA-TTAAAAA----CTTTTGTGCT--TCAAAGGACACTAT 683

  chr1_22379228_2   1614 TAAGAGAATGAAAATACAAGCCACATAATAGGAGGAAATTTTTTCAAATC 1663
                         i    i i      v    v     v   i    i    v   v      
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_22379228_2   1664 CTGTATCTGATAAAGGACTTATATCCAAAATACGTAAGGAACTCTCAAAA 1713
                         v i          i      i      i    ii   i       i v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_22379228_2   1714 ACTCAA--ATAAGAGAGCG-----CCCAACTTATTTTTTTAAATGGGCGA 1756
                         -     --    i iii i-----     i ? v------        i 
  L1M4_orf2#LINE/    784 -CTCAATAATAAAAAGACAAATAACCCAATTWAA------AAATGGGCAA 826

  chr1_22379228_2   1757 --GATTTGAA--GTCATTTCACCAAATCACATATTCGGATGGTAAATAAT 1802
                         --        -- v      v     vv v    v ii    iv     v
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_22379228_2   1803 CATGTGAAAAGATGTTTGATAGAAAACATGTC 1834
                           ii          i ii i vv ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (137 / 62)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.33 (49 / 21)  


 627 30.91 13.44 2.96  chr1_22505500_22507165.rev      435  1178 (488)    L1M4_orf2#LINE/L1       87   908 (0)  

  chr1_22505500_2    435 AACTCCCAGCAAACATACCAAC-ACGTTTTTTTCTGAAACTGGAGAAGCT 483
                           ii  i v    -  v   i -i v      v v    i  - v     
  L1M4_orf2#LINE/     87 AATCCCTATCAAA-ATCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCT 134

  chr1_22505500_2    484 GACTATCAAGTTCAAATGGAAAAACAAG--------------CAA--CAA 517
                           iiv v  i    v       vi    --------------   --   
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_22505500_2    518 ------------AGAATG----TGGAGAGCCAGCCCTGCCAGATATTAAA 551
                         ------------    ii----     ii ivi v  v  vi  v i   
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_22505500_2    552 CTATATTTTAAAGCTTCAACAGTTAAAATAGTGAATAATTAGCACATCAA 601
                         viv  i vi      v  ii i i  i i    vivv i i   i vvi 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_22505500_2    602 CAGACA----AACCAATAGAACAAAAA-GAAAGTCCAGAAATACACCAAG 646
                         i     ----i i    i   i i  v-  i            v   v v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_22505500_2    647 ATACATACAGAAATTTAGTTTATGCTAAAGATG--------------TGA 682
                          i iv  ii vv v  ii   vi vi  i i  --------------  i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_22505500_2    683 AGTAAAGATAAACTTTATAATTAAAAGTTG--GGGATAACTGGGTAATAA 730
                         i v  ii   iv    vi  i-   v v  --    i      i  ?iv 
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAAC-AAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_22505500_2    731 TTTGAAAAAGAA----GTTTTATCTATACCTCACATCTTATGCTAGGATA 776
                         iv  v       ----   vv i iv         i v   i v ii  v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_22505500_2    777 AAC-CATAAAAAGATCAAAGACTTAAAGCTAA-----AAAATTGTAGACA 820
                            -  -   vi     ?    i    vv   -----    i i  ----
  L1M4_orf2#LINE/    484 AACTCA-AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA---- 528

  chr1_22505500_2    821 TTAAAGTACCAGGAAAAAAT----GGGCAATTTCTTTATAACCCTGAGGT 866
                         --   v vii  i i    i---- ? i  v -   ii i   i  i v 
  L1M4_orf2#LINE/    529 --AAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTT 575

  chr1_22505500_2    867 -GGCAAAGA---CCTA-AT-TGA-GTCAAATTCCCAAAACCATAAAAGAA 909
                         -     v i--- i  -  -   -ii    vv v   i- v i       
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG-CAACAAAAGAA 624

  chr1_22505500_2    910 AAGATTGATAAATTCAA--TCA-CA-----------TTTTAT-----AAA 940
                           i  v        vi --   -  -----------    i -----   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_22505500_2    941 --AT-CCATAAATAAAGTCTAAACGCAAATAACAACCTGGGAAAATACAT 987
                         -- i- i  v  v     vv   vi   viv   ivv     i  v i  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_22505500_2    988 TTGAAACTCATATTACAGACAAAGGATTCATTTTCCTAATATATGAAGAG 1037
                            v  v      vv v  i  i   i ii v i vv       i    i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_22505500_2   1038 CTTCTAGAAATTCACAAGAACAAGACCAAAAATCTTCAAAATCTTAGAAA 1087
                           ii  v  v iv i  v  v     v  v  i --   ----  ?-   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACC--CAA----TTW-AAA 817

  chr1_22505500_2   1088 AATGAGCAGAG-ACACAAAGAAGCAGTTAATACATATGAAAGGCACGAAA 1136
                             i   i  - ivii  v ii  v  v- v  v --i   ii iiv  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTC-TCCAAA--GAAGATATACAA 864

  chr1_22505500_2   1137 ATGACTTATAAATACTCAAAAAGATGCTCGA--TTAATTCATAG 1178
                            i iv    ii  vii           i -- i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (130 / 96)
Gap_init rate = 0.05 (38 / 822), avg. gap size = 3.21 (122 / 38)  


3497 19.25 4.72 1.61  chr1_22510074_22513374.rev     1603  2407 (894)    L1M4_orf2#LINE/L1        1   830 (78)  

  chr1_22510074_2   1603 TGGAAACACGTCCCATGTTAATGGATTGGAAGGCTTAGTATTGCTAAGAT 1652
                               v ii         v            i    i     i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_22510074_2   1653 GTTAATATTACCAAAAGCTATCTATGGATTCAATACAA----------AA 1692
                          vi    i v  v   viv     ii       ii   ----------  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_22510074_2   1693 CACCAATGACATTTTTTGCAAGAATAGAAAAAGAACACATTCTAACATTT 1742
                         iv   iivi v         ii   v  v  i--- vv  i    v   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr1_22510074_2   1743 ATATGGAATAT-TAATGGTCTCCAAATAGCCAAAACAATCTTAAAAAAGA 1791
                                 -  -i  v  v i vi                  i       
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_22510074_2   1792 A---CAATGCTGGAGGACTCATGCTTCCTCATTTCAAAACTTACTACAGA 1838
                          ---   v i           ii     iv                  i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_22510074_2   1839 GCTACAGTAATCAAAACAGTGTGGTACTGGCATAAAGAAAGACACAAACA 1888
                                       i                    i  v     i v v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_22510074_2   1889 CTAATGGAGTAGAATAAAGAGCTTAGAAATAAATGTTCCCCATA----TA 1934
                         ii      i      vi    iii         -----      ----  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAA-----CCCATACATTTA 341

  chr1_22510074_2   1935 TGGTCAAATAATTTTTGACAAAGACACCAAGGCCATTCAATGAGGAAAGA 1984
                                v i     i     i iii     i          i       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_22510074_2   1985 ATAGTTTCTTTTCAGCAAATGGTGCTGGGAAAACT--------ACATATG 2026
                              --       i               v    --------    iii
  L1M4_orf2#LINE/    392 ATAGT--CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_22510074_2   2027 AAAGAATAAAGTTGGACCCTTATTTAACACCGTATACAAAAATTAATTCA 2076
                                i           i  ii v     i              i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_22510074_2   2077 AAATGAATTGAACACATAAATGTAAGACCTAAA-CTATAAAACTCTTAGA 2125
                              i  ii? v  v           v     -                
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_22510074_2   2126 AGAAAACATGAAGCA-AAAGCTTTGCAACATTGATTT-GGTAATGGTTTC 2173
                                  - i ?i-   v   i ii  v   iv  -  i         
  L1M4_orf2#LINE/    540 AGAAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_22510074_2   2174 TTGAATATGATGGCAAAGGCACAGACAATAAAAGAAAAAATGGACAAATT 2223
                           ii      iiv    i     ii   i            i  i     
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_22510074_2   2224 GGACTTCACAAAATATTAAAAA-TTTTGTGCATGAAAAAA----ATAAAC 2268
                                 iv   -        -        v v   ii ----  v  v
  L1M4_orf2#LINE/    639 GGACTTCATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_22510074_2   2269 ATAGTAATAGGGAAACCCATGGAATGAAAGAAAACATTTATAAATCATAT 2318
                          v   i v i iv      ii     ii      i    ii         
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_22510074_2   2319 ATCAGATAAAGGCTTAATATCTGTAACATACAGAGAACTCTTAAAACTCA 2368
                            v     i  vi vi    iiv  i   i i          v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_22510074_2   2369 ACAACAAAAA--TAAGT--CCCAATTTAAAAATAGGCAAAAGA 2407
                          i  i     --i  i --       ?      i      i  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 2.23 (105 / 47)
Gap_init rate = 0.02 (18 / 830), avg. gap size = 2.83 (51 / 18)  

 495  8.11 10.81 3.60  chr1_22510074_22513374.rev     2700  2810 (491)    L1M4_orf2#LINE/L1      790   908 (0)  

  chr1_22510074_2   2700 AATAAATAAATAAATAA---AATGAAATAAAAAATGGGCAAAAGA----- 2741
                               v i i      ---   ---- ?             i  -----
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAAT----TWAAAAATGGGCAAAGGATTTGA 835

  chr1_22510074_2   2742 ----ATATTTCTCTAAAGAAGATACACAAATGGCCAATAAGCACATGAAA 2787
                         ---- i       i          i                         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_22510074_2   2788 AGATGCTCAACATTAATAATCAT 2810
                                      i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 7.00 (7 / 1)
Gap_init rate = 0.03 (3 / 119), avg. gap size = 5.33 (16 / 3)  


 218 21.54 3.08 4.62  chr1_22554840_22557724.rev     1627  1691 (1194)    L1M4_orf2#LINE/L1        1    64 (844)  

  chr1_22554840_2   1627 TGGAGAGATATCCCATGTTGTTAGATAGAAATATTCAATATT-TTCAGA- 1674
                             i              vv i   v i  v i i      -  v   -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_22554840_2   1675 GACTCAGATCTTCCCCA 1691
                          i ---i  vi      
  L1M4_orf2#LINE/     51 GGC---AATACTCCCCA 64

Transitions / transversions = 1.33 (8 / 6)
Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.67 (5 / 3)  

2564 22.51 6.55 0.85  chr1_22554840_22557724.rev     1695  2396 (489)    L1M4_orf2#LINE/L1      167   908 (0)  

  chr1_22554840_2   1695 CCAAAATAGCTAACTCAATATTGAAGGAGAAGACTGAAGTTGGAGGACTG 1744
                            i      i  vv    v     ii      vii             v
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr1_22554840_2   1745 ATAAT----GACTTCAACATTTACTATTTTAAAGCTACAATAATGAAGAC 1790
                          i v ----i i     v i      i---         i    v     
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTAC---AAAGCTACAGTAATCAAGAC 263

  chr1_22554840_2   1791 AATGTGGTATTGGTGAAAGAATAGACAAGTAGACCAGTGGAACAGAACAG 1840
                          i       i   iiv   i       vi    i  i     i    iv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_22554840_2   1841 AAAGCCCAGAAACAGACCCACACAAATATAGTCAATTCATCTTTGACAAA 1890
                          i  i       i i     i   vv   i       v  i  i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_22554840_2   1891 GGAGCAAAGGCACTAAAATGAAGCAAAGAGTA-TCTTTTCAACAAGTGAT 1939
                           v  v   i vv vv    ii -     i  -            i  i 
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_22554840_2   1940 GCTGGAACCAACTGGACATTCACATACGAAAAAATGAATCTAGACATAGA 1989
                              i  -       i ?i     i i   i      vi i   vivv 
  L1M4_orf2#LINE/    413 GCTGGGAC-AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_22554840_2   1990 CCTTACACCCTTCACAAAAATTAACTTAAAATACATCAGAGACCTATATG 2039
                            i     v vi             i     iv    ?       v   
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_22554840_2   2040 TAAAATACAAAATTATAA--TTCCTAGAAGTTAACATAGGAGAAAA-CTT 2086
                            i vvi    i     --i  i      vv        ? v   -   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_22554840_2   2087 AGTTGACTTTGGCTATGGCAGT--CTTTTTAGGTACAACACCAAAGGCAC 2134
                         v  -   i    v vv    i --i  i    i  ii        i    
  L1M4_orf2#LINE/    562 CGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_22554840_2   2135 AATCCATGACAGAAA-------TAAATTTTGCTCCATGAAA--------- 2168
                           v v ii v     -------      vvi  i   v   ---------
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_22554840_2   2169 ---------------GACAATGTCAAAAGAATGAAAAGACAAGCCACAGA 2203
                         ---------------    v i    i i i           v       
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_22554840_2   2204 CTGGGAGAAAATATTTGCAAAAAACACACCTGATAAAAGACTATTATCCA 2253
                         v                    vv i i i       ii    vv      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_22554840_2   2254 AAATACACAAAGAACTCTCAAAACTCAACAATAAGAAAACAA----CCCA 2299
                         i    i i          i v       i     i  i    ----    
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_22554840_2   2300 ATTAAAAAATAG-CAGAAGACCTGAACAGACACCTCATCAAAGAAGATAT 2348
                            ?      i -  i i  ii    i     ii  vi            
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_22554840_2   2349 GCAGATGACAAATAAGCAAATGAAAAGATGTTGTACATGGTATGTCTT 2396
                         i  i   i v        v           i vv    vi????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (97 / 57)
Gap_init rate = 0.02 (13 / 742), avg. gap size = 4.00 (52 / 13)  


1315 27.66 10.40 4.49  chr1_22676313_22678159      509  1354 (493)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr1_22676313_2    509 CCATGTTCATGGATGAGGAGCCTCACCGCCACAACGCTGGC--TACGCCC 556
                                       vi i  v  i viiiiiiv v v    --   v   
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_22676313_2    557 TTCCAATTTAATCTATACATTTTAT----TTCCAATAACAATTGCAGTGG 602
                         ---   v  i     i v   iv i---- i  v  v v   iv   iv 
  L1M4_orf2#LINE/     63 ---CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_22676313_2    603 GGTTTTCCTGGCA--ACTTGACAGAGTCATCCCCAAATGTACATGGAATA 650
                         vv    -- v   -- v      iiv v    iv    vi i      vv
  L1M4_orf2#LINE/    110 CCTTTT--TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_22676313_2    651 ATAAAGAACCCAGAATAGCCAAGACAATTTTGAAAAAGAAAGAGGAAGAG 700
                         ii  i i               i     i           ii vi   vv
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_22676313_2    701 GAAGGGAACCTCACCCTATCAGGTATCAATAGGCACTGTGGAGCTCTAAT 750
                          i   i---     v  vi vii v    v vvi   iiii    vi i 
  L1M4_orf2#LINE/    208 GGAGGA---CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_22676313_2    751 AATTAAAATAGTGTGAT-TTGGTCCCAGGAATAGACCAACAGAT-AATAG 798
                            i  i i      i -i   - vi i i      vv i    -   i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGG-CATAAGGATAGACATATAGATCAATGG 303

  chr1_22676313_2    799 AACAGAGAAT--AATGCCTAGGGGAAGATCAAAATATATA-GG------- 838
                           i   --  -- iv i i  iiiv i i v v i  v  -  -------
  L1M4_orf2#LINE/    304 AATAGA--ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_22676313_2    839 ----------AGAGTGT-GAGACAGGACAAAGGGTAAA--ATGGTCTTGT 875
                         ----------  i   i-i    vivv   v   v   --  i     v 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_22676313_2    876 TAACAGATGATGTTGA-ACAATGGAATACCCCTACTGGAAAACA-TAAAA 923
                         i    i   i  i  i-    iv i   ?  vi -  v    v - i  i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGAATGAAG 450

  chr1_22676313_2    924 TTGGATCCCTGC-TCACACCACTCACAAAA-TAAGTTCCAGGTTGGTTAA 971
                              i    i -        ivi      - v ii  v ii v i i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_22676313_2    972 AGTCCTAAATGTGAAGAG--AACACTATAAAACTTTTTAAAAGAAAACAG 1019
                           v         -     --  v           i  - i         v
  L1M4_orf2#LINE/    501 AGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTT-AGAAGAAAACAT 548

  chr1_22676313_2   1020 AGGAAAGTAA--CTTTATGATCTTAGAGTAGA-AAC-------TAAACAA 1059
                            ?--    --   ii   i   i iv   i-  i-------  i i v
  L1M4_orf2#LINE/    549 AGGN--GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_22676313_2   1060 AACACAAAAAGCATAAATGATTTTTAAAG------T-GATAAAT----CT 1098
                         i    v       i  iii iv---    ------ -       ----  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACA---AAAGAAAAAATAGATAAATTGGACT 643

  chr1_22676313_2   1099 T-ACTACAATTAAGAGCTTCT---CTTT----GACA-------AAAGATG 1133
                          - ii v      i i   i ---   i----    -------i  ii  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_22676313_2   1134 AATAGATTTGTTAAAGCCACTAGCTGGGAGAAGGTATTTGCAGCCCGTAT 1183
                           v   i------  v    viiv        ii        ivi i   
  L1M4_orf2#LINE/    694 AAAAGAC------AACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_22676313_2   1184 A---AGCAAGAGACAATTAGTTTCCAAAAGAATTTTTTAAAAAACCTCTA 1230
                          ---iii   i   --  -  v    i  v ---- v    i   iii  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGAC--TT-GTATCCAGAATA----TATAAAGAACTCTTA 780

  chr1_22676313_2   1231 GAGAATCAATC-TACCAAAACATTCCAGAGC--AATAGGAAAATGGGCAA 1277
                         v - v     v-  vv  i   ---v v i --   v?i           
  L1M4_orf2#LINE/    781 CA-ACTCAATAATAAAAAGACA---AATAACCCAATTWAAAAATGGGCAA 826

  chr1_22676313_2   1278 AAAATGTGAATAAATA-----CCAGAGGAAGAAATTTGAAAGGCCAAACA 1322
                          ii  v      i i -----   i  -    v  vii  v      -i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAG-AAGATATACAAATGGCCAA-TA 874

  chr1_22676313_2   1323 AG-ATAT-AAAAGAGTCTCAACATCACTAGTAAA 1354
                           - i  -      vv          ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (142 / 88)
Gap_init rate = 0.05 (49 / 896), avg. gap size = 2.57 (126 / 49)  


1184 19.79 3.12 10.68  chr1_23017124_23021999     1874  2257 (2619)    L1M4_orf2#LINE/L1        3   357 (551)  

  chr1_23017124_2   1874 GAGAGATATATTGTGTTCATGAATTAGAAGACTCAA-------AAGATGC 1916
                           i      viii        i   i       i  -------      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_23017124_2   1917 GAGT-CTTCTCAAATTGATATTCAGATTTAATAAAATTTCTATCAAAATC 1965
                         v i -  i i         v v      i  iiv   ii           
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_23017124_2   1966 CCAGCATGCTATTTTGTAGTAGATGTAGACAAGAT--TTCTATAACATTT 2013
                              -   i-    v - i   vi v      v -- i   -  -   i
  L1M4_orf2#LINE/    103 CCAGC-TGCC-TTTTTT-GCAGAAATTGACAAGCTGATCCTA-AA-ATTC 147

  chr1_23017124_2   2014 GTATGGAAA-GCAAAGGACCTATAATAGCTAAAACAATTTTGAAAAAGAA 2062
                         i        -    i     i v      i        i           
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_23017124_2   2063 GGATAAAGTGGGAGAAATCAGTCTACCCAGTTTATAACTTCAAGATTTA- 2111
                          i i     v    i v   vv  v    i   -------   i i   -
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTT-------CAAAACTTAC 240

  chr1_23017124_2   2112 TATACAGCTATAGTGATCAAGACTATGCTGTATTGGAAGGAACGCATTCA 2161
                           i v     i   i        vi  iv   i   --------   ---
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG--------CAT--- 279

  chr1_23017124_2   2162 AACCACAGCACCTGGTTGAGGGATAGACACATAGTTCAGTAAAATAGGAT 2211
                         ------------------ i         i    v   i ii     i  
  L1M4_orf2#LINE/    280 ------------------AAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_23017124_2   2212 AAAGAACCCAGGAATAGTCCCACACAAATATGCCCAACTGATTTTC 2257
                         vi   ii    i    iv    i   vv    vi   i        
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

Transitions / transversions = 2.04 (51 / 25)
Gap_init rate = 0.04 (13 / 355), avg. gap size = 4.08 (53 / 13)  

 807 28.24 1.18 0.39  chr1_23017124_23021999     3057  3311 (1565)    L1M4_orf2#LINE/L1      383   639 (269)  

  chr1_23017124_2   3057 GAGGAAAG-ATAGCCATTTCAATAAATGATGCTGGAATAACAGGACACCC 3105
                          i      -    i v      i     i      i i   v   i ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_23017124_2   3106 ATGGGCAAAAACATGAACCCCAACTTAAACCTCACACCTTAATACAAAA- 3154
                          iiv      iv     viivi  iivv          v  -       -
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA-TACAAAAA 481

  chr1_23017124_2   3155 TTAACTCAAAATAGATCACAAACTTAAATCTAAAACACATAATGAT-AGA 3203
                                     i     ? i  i     v   i vvi v  iv  - i 
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_23017124_2   3204 CTTTTAAAAAACACCATAGAAGAAAATCTCTGGGATCTAGGGCTAGGCAA 3253
                           i   i  i v v     i? v      ii v  i  v   i       
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_23017124_2   3254 AGAGTTTGCAGACTTAAGACCAAAAGCATGATCCATAAGAGAAAAAGTTG 3303
                         v iv  ivi   iv i v          ii v v i  i       i v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_23017124_2   3304 ACAAAGTG 3311
                          i   v  
  L1M4_orf2#LINE/    632 ATAAATTG 639

Transitions / transversions = 1.46 (41 / 28)
Gap_init rate = 0.02 (4 / 257), avg. gap size = 1.00 (4 / 4)  

 997 19.39 6.46 2.28  chr1_23017124_23021999     4121  4383 (493)    L1M4_orf2#LINE/L1      635   908 (0)  

  chr1_23017124_2   4121 AATTGGACTTGATCAAAATTTTAAATTTTTGCTCTGCAGAAGAC----CC 4166
                                   v         vv   i     iv  v  i i   ----i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_23017124_2   4167 AAGAGGATGAAAAGACAAGCTACAGAAT---AGAAAAGATTTTCAAACTT 4213
                             iii           v i       ---      v    v    - i
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TC 733

  chr1_23017124_2   4214 AGGTACCTGACAAAGGACTGGTTTCTGGAATGTATAAAGAACCCTCAAAA 4263
                          vi  i    i  i     v  v  ii    i          i  i v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_23017124_2   4264 CTCAACAAGTTTTTAAAAA--------ATCCAATTAGAAAATGGGCAAAA 4305
                              i  -----      -------- i      ?i            i
  L1M4_orf2#LINE/    784 CTCAATAA-----TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_23017124_2   4306 GACATAAAGAGATATTTCACTGAAGAGGATATACAGATGGCAAAAAAGCA 4355
                           iv i  v   i     v ii    i        i     v  v     
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_23017124_2   4356 TATAAAAA--TGTTCAACATCATTAGCTAT 4383
                         i  i    --  i         ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (33 / 17)
Gap_init rate = 0.02 (6 / 274), avg. gap size = 3.83 (23 / 6)  


3300 13.64 18.18 1.24  chr1_23094366_23096083.rev      502  1227 (491)    L1M4_orf2#LINE/L1       60   908 (0)  

  chr1_23094366_2    502 CCCCAAACTTACAATCTGCAGATTCAACACAATCACAATCAGAATCCCAG 551
                                i ---i    i          i     v v    i        
  L1M4_orf2#LINE/     60 CCCCAAATT---GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_23094366_2    552 CAGCCCTTTTTGCAGAAACTGACAAGCTGGTCCTAAAATTCATATGGAAA 601
                          v   i            i          i                    
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_23094366_2    602 TGCAAAGCATTCAGAACAGCCAAAATAATCTTGCAAAAGAAGAACAAAGT 651
                              i v ii     i        i       v                
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_23094366_2    652 TG-AGGA---ACACTTCCTAATTTCAAAATTTATTATGAAACTAAAGTAA 697
                           -    ---        i          i   i  ii  i   v     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_23094366_2    698 TCAGGATAGTGTGGTACTGGAATGGACGGAAATATATAATAGATCAATGG 747
                            i  i             v  -- v   v v i   -           
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATA-TAGATCAATGG 303

  chr1_23094366_2    748 AATAGAGTTGAGAGTCCAGAAATAAACTCTTAGATTTATAGTTAAT---- 793
                               i                    i v  v      i  i   ----
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_23094366_2    794 ---CAATGAGGGTGCCAA--CTATTCGCTGAGAGAAAGAATAGTCTT--C 836
                         --- i ii          -- i    iv  i -              -- 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTTTTC 402

  chr1_23094366_2    837 AATAAACTGTGCTGGGACAAC-----------ATGCAAAATAATGAAACT 875
                           i   iv             -----------        v      ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_23094366_2    876 GAACCCCTACCTCACACCATATACAAAAATTAACTGAGAAAAGATCATCG 925
                          i                                 v i  vi     ?v 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_23094366_2    926 ACATAAATGCAAGAGCTAAAACTAAAAAACTCTTAGAAGAAAACATAGGA 975
                           v      i              v                        ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_23094366_2    976 GTAAATCCTCGTGACATTGGATAAGGCAATGGTTTATTAGATATAACACC 1025
                                i       v    i v            v        i     
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_23094366_2   1026 AGAAGTAAAGGGAGCAAAAGAA--------TAAATTGGATCTCATCAAAA 1067
                          i   i v i v i        --------         ii         
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_23094366_2   1068 TCACAAATTT---------------------------------------- 1077
                          i v   i  ----------------------------------------
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_23094366_2   1078 CC------------------------------------------------ 1079
                           ------------------------------------------------
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_23094366_2   1080 -GTAACCAGAATATGTAAAGAACTCTTACTAGAAAATGATGAA--GACAA 1126
                         -   v         i              v vvv   i  i  --     
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_23094366_2   1127 ----CTCAATTTTTAAAAATGAGCCAAGGATTTGAATAGTCATTTC---A 1169
                         ---- i     ?--       i  v              v      --- 
  L1M4_orf2#LINE/    803 ATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_23094366_2   1170 ACAAAAATATAAAAATGGCTAATAAACACATGAAAAGATGCCCAACATCA 1219
                          vi  i     v       i     i               i        
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_23094366_2   1220 TTAGTCAT 1227
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.74 (61 / 35)
Gap_init rate = 0.02 (17 / 849), avg. gap size = 8.29 (141 / 17)  


3484 17.36 2.08 0.45  chr1_24016218_24020107.rev     1899  2572 (1318)    L1M4_orf2#LINE/L1        1   685 (223)  

  chr1_24016218_2   1899 TGGAAAGACATC--------ATAGATTAGAGAAGACTTAATATTGTTAAG 1940
                                 i   --------  i    i  --                  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGA--AGACTTAATATTGTTAAG 48

  chr1_24016218_2   1941 ATGTCAATACTATTCAAAACATTCTATAGATTCAATGCAATCCCTATCAA 1990
                            v       vii    viiv    i        i              
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_24016218_2   1991 AATCCCAAC---ATTTTTTACAGAAATAGAAAAATCCACCCTAAAATTCA 2037
                                i ---v      i       v  v  iiiv i           
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_24016218_2   2038 TAAGGAATTTCAAGAGACCTTGAATAGCCAAATCAACCTTTAAAAAGAAG 2087
                           v    v v    i    iv           v   i   v         
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_24016218_2   2088 ACCAAAATTGGACATCCCACATTTCCTGATTTCAAAACTCACTACAAAGC 2137
                          v    i     viv i    i    ii           i          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_24016218_2   2138 TACAGTAATTAAAATAGTATGGTACTGGCATAAAGACAGACATATAGACC 2187
                                  i  i i   i              i  i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_24016218_2   2188 AATAGCACAGAATAAAGAGCCCAGAAATAAGCCCTCACATACATGGTATA 2237
                            i v i     vi    i          i   vi    vi     vv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_24016218_2   2238 ATAATTTTTGTCAAAGATGCCAAAATCATTCAATGGAGAAAGGACAATCT 2287
                         v i     i v   i i      i i          i     i i i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_24016218_2   2288 TTTCAACAAATGGGGCTAGGAAAACTGGAT-GTAAAATACCAAAGAATGA 2336
                                      v   i   v        -?iv v  i v         
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_24016218_2   2337 AGTTAGACCCTTACCTAACATCATATGTGAAAATTAACTCAAAATGGATC 2386
                             i     i     v   i     iii                     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_24016218_2   2387 AAAGACCTAAATGTAAGAGATAAAACTATAAAACT--TAAAAGAAAACAT 2434
                          ?                 v               --  i          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_24016218_2   2435 AGGGCAAAAGCTTCATGACATTGGATTTGGCAATAATTTCTTGGATTATA 2484
                            ?vv   v    i    v    i  v      ii      i   -  i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr1_24016218_2   2485 GCACCAAAGGCACAGGTAACAAAAGAAAAAATGGACAAATGGGACTACAT 2534
                         i       i     i i               i  i    v     v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_24016218_2   2535 GAAAATCAAAAACTTTTGTGCATCAAAGAACACTATCA 2572
                         v     i              v      i         
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

Transitions / transversions = 1.78 (73 / 41)
Gap_init rate = 0.01 (6 / 685), avg. gap size = 2.83 (17 / 6)  

 658 17.11 3.95 0.66  chr1_24016218_24020107.rev     2859  3010 (880)    L1M4_orf2#LINE/L1      672   828 (80)  

  chr1_24016218_2   2859 AAAGGACATTATCAAACAGAGGGAAGAGGAAAATTATGGAATGAGAGAAA 2908
                                 i      i- i  v   i  iv  vii ii     i      
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAG-AAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_24016218_2   2909 ACATTTGCAAATCATATATCTGATAAGGGAGTAATATCCAGAATTTATAA 2958
                          i                            v vi          v     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_24016218_2   2959 ATAGCTCCTAAAACTCAACAA----AAGA--AATAAACTAATTCAAAAAT 3002
                          v i   i  v       i  ----    --     v i    ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_24016218_2   3003 GGGCAAAG 3010
                                 
  L1M4_orf2#LINE/    821 GGGCAAAG 828

Transitions / transversions = 1.78 (16 / 9)
Gap_init rate = 0.02 (3 / 157), avg. gap size = 2.33 (7 / 3)  

 513 12.24 1.02 0.00  chr1_24016218_24020107.rev     3302  3399 (491)    L1M4_orf2#LINE/L1      810   908 (0)  

  chr1_24016218_2   3302 AATAAAGAAAAGTGCAAAGGGCTTGAATGGACGTTTATCCAAAGAAGATA 3351
                            v? i   v v       ii      i   i   v             
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_24016218_2   3352 TACAAATG-CCAATAAGCACATGAAAAGATGCTCAATAACACTAATCAT 3399
                                 -                           i v  ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (6 / 5)
Gap_init rate = 0.01 (1 / 99), avg. gap size = 1.00 (1 / 1)  


1260 29.95 0.80 0.00  chr1_24061978_24064359.rev      504   877 (1505)    L1M4_orf2#LINE/L1      112   488 (420)  

  chr1_24061978_2    504 TTCTTCACAGAACTAGAAAAAA-AATTCTAAAATTCGTGTGGAACCA-AA 551
                           i  ii     v v  v  iv-i  i         i i     vii-  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_24061978_2    552 AAGACCCCATATAGGCAAAACAGAACTAAGCAACAAGAACGAATCTGGAG 601
                         ii     viv    v       ivvi i iv  v      i  vi     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_24061978_2    602 GCATCACTGTACCTGATTTCAAACTATACTACAAGGCCATACTCACCAAA 651
                          vv    vv v  ii        viv        i  i i v v i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_24061978_2    652 ACCACATGATACTGGTATAAAAATAGGCACATAGACCAATGGAACAGAAT 701
                           viii  i      i    ii    i  i     i        i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_24061978_2    702 AGAGAACACATAAATAAACTCAAATACTTACAGCCAACCGATCTTCAACA 751
                         v    iiv  v        i  v i i   ii i   ii   i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_24061978_2    752 AAGCAAACAAAATCATAAAGTAGGGAAAGGACACCCTTTTCAACAA-TGG 800
                          i vviv   i i   vv i i       i i vi           -   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_24061978_2    801 TGCTGGGGTAATTGGCTGTCCACTTGTAGGAGAATGAGACTGGATCCTCA 850
                                ii  i   v i?    v  i ii       iii    i  ii 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_24061978_2    851 TCTCTCACCTTATACAAAAATCAACTC 877
                         i   v    v           i     
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTC 488

Transitions / transversions = 2.00 (74 / 37)
Gap_init rate = 0.01 (3 / 377), avg. gap size = 1.00 (3 / 3)  

1070 27.75 2.02 0.00  chr1_24061978_24064359.rev     1163  1508 (874)    L1M4_orf2#LINE/L1      477   829 (79)  

  chr1_24061978_2   1163 AAAAATCAACTCAAGATGGATTAAGGACTTAAATCTAAGACTTGAAACTA 1212
                               i       i      i ?i   i     v     vi i      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_24061978_2   1213 TAAAAATTCTAGAAGATAACATTGGAAAAGCCCTTCTAGACATTGGCTTA 1262
                              v ii       v     v  ?iv ivi    vv   v    v   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_24061978_2   1263 GACAAT---TTCATGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAA 1309
                          i    ---   v iivi v  vv         v v    i    iv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_24061978_2   1310 GATAAACAGCTGGGACTTAATTAAACTAAAGAGTTTGTGCACAGCAAAAG 1359
                         i   i i iv v      v  i   v v  i ii  v  ii vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_24061978_2   1360 GAACAGTCAGCAGAGTAAATAGACAACCCATAGAATGGGAGAAAATCTTC 1409
                         iv  vi   iv i   i  v          i               v  i
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_24061978_2   1410 ACTAACTATACATCTGACAAAGGACTAATATCCAGAATCTACAACAAACT 1459
                         i v  ii   i      i  i     vi          v  i  vi    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_24061978_2   1460 CAAACAAATCAGCAAGAAAAAAACAA----TCCCATCAAAAAGTGGGCTA 1505
                          vv    v   ii  v     i    ----i  v  i?    i     v 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_24061978_2   1506 AGG 1508
                            
  L1M4_orf2#LINE/    827 AGG 829

Transitions / transversions = 1.21 (51 / 42)
Gap_init rate = 0.01 (2 / 353), avg. gap size = 3.50 (7 / 2)  

 426 15.79 0.00 1.05  chr1_24061978_24064359.rev     1797  1891 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_24061978_2   1797 AAAAATGGTCTAAGGACACAAATAGACAATTCTTAAAAGAAGATACACAA 1846
                                 v v     ivii        v    iv          i    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_24061978_2   1847 ATGGTCAATAAACATTATGAAAAAATGTTCAACATCACTAATGAT 1891
                             i      i  i-       i   i         ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCAC-ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


3127 26.46 0.99 0.88  chr1_24340814_24347501.rev     5292  6198 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_24340814_2   5292 TGGAAAAAGATTCCATGCTCATGGATAGGAAGAACCAATATTGTGAAAAT 5341
                               i v  i     i        v      vii        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_24340814_2   5342 GGCCATACTGCCCAAAGTAATTTGTAGATTCAATGCTATCCCTATCAAAC 5391
                            v     v      v i  i ii        i  v            v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_24340814_2   5392 TACCATTGACTTTCTTCACAGAA-TTAAAAAAAACT-ACTTTAAATTTCA 5439
                          v   vivi i  i  ii     -  i v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_24340814_2   5440 TATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAA-AAG 5488
                                viiv  ii  v  viv        i      i i iv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_24340814_2   5489 AACAAAGCTGGAGGCATAATGCTACCTGACTTCAAACTATACTACAAAGC 5538
                                i      vv v ii  v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_24340814_2   5539 TACAGTAGCCAAAACAGCATGGTACTGGTACCAAAACAGATACACAGACA 5588
                                ii   i    ii         i iv ii i   i i i   iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_24340814_2   5589 AATGAAACAGAGCAGAGGCTTCAGGAATAATGCCACACATCTACAACCAT 5638
                             i  i   iiv   iv i   i     vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_24340814_2   5639 CTGATCTTTGACATATCTGACAAAAACAAGCAATGGGGAAAGAATTCCCT 5688
                         i    i  i    vivv  v   i v  vv               vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_24340814_2   5689 ATTTAATAAATAGTATTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5738
                         v  i  i    i  ii     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_24340814_2   5739 AACTGGACCCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGATT 5788
                          ii         v   i    iv                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_24340814_2   5789 AAAGACTTAAATGTAAGACTTAAAACCATAAAAACCCTGGGAGAAAATCT 5838
                          ?    i           vi      i      vi i i i      iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_24340814_2   5839 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTAATGACTAAA 5887
                            ?i- v i -   iv   v v  vv i     v ii  vv iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_24340814_2   5888 ACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATAGGATCTAAT 5937
                                     vvi      i   vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_24340814_2   5938 TAAA-TGAAATAACTTCTGCACAGCAAAAGAAACTATCATCAGAGTAAAC 5986
                         i   - v   -     i  ii vv    i  v       vv i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_24340814_2   5987 AGGCAACCTAAAGAATGGGAGAAAATTTTTGCAATCCATCCATCTGACGA 6036
                           i     i v               v       vi   vi      ii 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_24340814_2   6037 AGGGCTAATATCCAGAATTTACAAGGAACTTAAACAAATGTACAAGAA-- 6084
                         i  i  vi          v  i  i     ivv    v ---   v  --
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATA 793

  chr1_24340814_2   6085 AAAAAACAAACAACCCCATCAAAAGGTGGGCAAAGGATATGAACAGACAC 6134
                             i     i     v  i?   ii            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_24340814_2   6135 TTCTCAAAAGAAGACATTTATGCAGTCAACAA--ACATGAAAAAAAAGCT 6182
                              v        i  vi viii i   i  --         i v-   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCT 892

  chr1_24340814_2   6183 CATCATTGCTGGTCAT 6198
                           v   ii????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


 238 23.38 1.30 2.60  chr1_24469542_24472129      426   502 (2086)  C L1M4_orf2#LINE/L1   (0)   908   833  

C chr1_24469542_2    502 TAAACAGTTACTTCACCAAAAAAAAGATATACAGAGGGAAAATA-GCATA 454
                          i  i  vi i   v     i  --        i v  vv    -   i 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAA--GATATACAAATGGCCAATAAGCACA 880

C chr1_24469542_2    453 TGAAGGACTGCTTAGCATCATTAGTCAT 426
                             iiiv    i i     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.50 (3 / 2)  

 390 26.09 0.00 2.90  chr1_24469542_24472129     1114  1251 (1337)    L1M4_orf2#LINE/L1       20   153 (755)  

  chr1_24469542_2   1114 CATGGATTAGAGAAGTTAATATTTATTGTAAAGATGTAAATTATCCTTAA 1163
                                 i  ii v        ----  v      vv   vv   ii  
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATT----GTTAAGATGGCAATACTCCCCAA 65

  chr1_24469542_2   1164 ATTGATTTCTAGAATCAATGCAATCCAAATTAAAATGAGAGTAGAGTTTT 1213
                               i vi   v    i       vv  i     vvv  iv vv    
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_24469542_2   1214 TTTAAGACATTAATAAGCTGATTGTAAAATTTGTATAG 1251
                           vv   v   i i        iv       ii   i 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

Transitions / transversions = 0.80 (16 / 20)
Gap_init rate = 0.01 (1 / 134), avg. gap size = 4.00 (4 / 1)  

1514 24.49 11.90 6.98  chr1_24469542_24472129     1365  2095 (493)    L1M4_orf2#LINE/L1      142   908 (0)  

  chr1_24469542_2   1365 AAATTTATATGGAAATGCACTGGGGTCAAGAATAGCCAGCATAAAC---- 1410
                              i             v-   ii v          iv i  v ----
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_24469542_2   1411 -AAAGAAGTACAAAGTTGAAGGGCTTATGCTAC------TAAAGAGTTAT 1453
                         -       v         i   i  i ii  v ------ v  i v   i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_24469542_2   1454 TATAAAGTTACAGTAATTAGGACAGTATGATATTTGAACA-GAATAAATA 1502
                           i    i         i i      i  i  i v v i - i   i i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_24469542_2   1503 -----ATCAA-GAAGCAGAGCTG------------------CATATGCCT 1528
                         -----     - i ii   ii  ------------------    iiii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_24469542_2   1529 --GGACACTTGATTTATGACAAAGGTAGCAACAGCAATACAGAGTAGTAG 1576
                         --  v  v       vi     i   iv   v v  v ------i i i 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT------CAATGG 384

  chr1_24469542_2   1577 AGAATGAGCAGCCTTT-CAATAAATGGTGCTGGGTCAAC----------- 1614
                         i   v  ii  i    -   i             v    -----------
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_24469542_2   1615 ATGGAAAACAACAGACTCGGGCATCTTCCTCA----AT---CAAAAAC-A 1656
                            v    v  iii v i  i vi  v     ----  ---      i- 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_24469542_2   1657 ATTTCAAGTGAATTGTAGATCTAGATGTAAAAGGTAAAATAATAGAGTTT 1706
                          i iv  i  i  ii?   i   i      i  v     iv   i ii i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_24469542_2   1707 CTAGAAGAAA--------------CT-----ATCTTGGGATGGGCAAAGA 1737
                         i         --------------  ----- i      v i     v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_24469542_2   1738 TTTCTTAAGTATTA-ATAAAATAGACATGTACACTAAACATAAAGAGACT 1786
                                ii   v - iv   viv   v i -  v   ---i  i i iv
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCA-ACAAAA---GAAAAAATA 630

  chr1_24469542_2   1787 GATAAATTGGGCTATATTAAAATCAAGAGTTTCTGTGTCTTA--GCACAT 1834
                                   i  vi  i     i  i ii  i    ii i -- v   i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_24469542_2   1835 TGTTAAGAGAGTGAAAAGGAAAGTCCCAGGATAAGGGATGACATTTAC-- 1882
                          i i    i         iv  vi v   i  ii i  vi i    i --
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_24469542_2   1883 --C-TACAGCTAACAAATGACTTGTTTCTAGAATAAAGAATCCCTATAAA 1929
                         -- -  i v  i i  iv       v  i      ---------      
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATA---------TATAAA 771

  chr1_24469542_2   1930 TAAGAAAAGGACAGAATGGTTTAAAGAACTCCTATAAATAAAAAAAAGAA 1979
                         -------------------------      i  i  v v  v  v -  
  L1M4_orf2#LINE/    772 -------------------------GAACTCTTACAACTCAATAATA-AA 795

  chr1_24469542_2   1980 AAGACAAGACAAGACCCAGCAGAAGAAAATGGGCAAAAAAGTTGAACAGT 2029
                                - i  --    iiv?  --           ii v     i  v
  L1M4_orf2#LINE/    796 AAGACAA-ATAA--CCCAATTWAA--AAATGGGCAAAGGATTTGAATAGA 840

  chr1_24469542_2   2030 CACTTCTCCAAAGAGAATATCCAAAAGGCCAGTCA--ACATGAAAAAGTG 2077
                           i           ii    v    v     i v --         ii  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_24469542_2   2078 CTCAATCTCATTGATCTC 2095
                              iv   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (121 / 56)
Gap_init rate = 0.04 (29 / 767), avg. gap size = 4.76 (138 / 29)  


 729 29.59 9.44 2.30  chr1_24685267_24689121.rev      125   516 (3339)    L1M4_orf2#LINE/L1      304   723 (185)  

  chr1_24685267_2    125 AATAAAATT-----TCTACAGAAA-----CTACACATATACAGTCACTCA 164
                             i    -----  --      ----- i i    v  ii    v ii
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_24685267_2    165 ATTCATGATAAGGTGATGCTATAGTAACA--CA---GGAAAAGAATAATC 209
                            ivi  i    --i   i -  - v  --  ---  i        i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGG--GTGCCA-AG-ACCATTCAATGGGGAAAGAATAGTC 397

  chr1_24685267_2    210 TTCTTGACAAATGATTCTTAGTTAATCAGATATCTATATG--GAAGAAAG 257
                           i ii       i v  vi vi  iii    ? i i   --i     v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_24685267_2    258 GAATATTGACCCC-ACCTCCCAC-ACATGGCAAAATCAATTTCAGACACA 305
                         i i - v      -     v   - i  ivv     i  i iv i iiv 
  L1M4_orf2#LINE/    448 AAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_24685267_2    306 TCACATATCCAGATACAAAAAGTAAAACAATGTGACTTTTAAAAGAAAAC 355
                            ? v i i i  ii  i iv      v  ivi   i   i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_24685267_2    356 ATAGAAGAAAA--------ATCTTTAGGTAGGCAATGATTTCTTAAGCAG 397
                             i? v   -------- i   vi v         i       iii v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_24685267_2    398 AATACAAAGAGCACTAATTATAAAGGAAAACATTGATAA---------CA 438
                         i i  v  i     v iiv i   i     v  v     ---------  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_24685267_2    439 TTTAGATTAAAAATGTATTTTCCCTAAAAGAAACCATTAAGAGATATAAA 488
                          iv i        iv v v v iii   i  v  i  i    i -i i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA-GTGAA 695

  chr1_24685267_2    489 AAGGCAGAC-ACCGAATAGAAAAATAATA 516
                            i  iv -  v    i i i  -    
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAA-AATA 723

Transitions / transversions = 2.23 (78 / 35)
Gap_init rate = 0.04 (17 / 420), avg. gap size = 2.71 (46 / 17)  

1060 15.14 0.54 0.54  chr1_24685267_24689121.rev     1750  1934 (1921)    L1M4_orf2#LINE/L1        4   188 (720)  

  chr1_24685267_2   1750 AAAAATACATCCATGTTCATGGAACAAAAGACTTAATGTTATTAAAACGG 1799
                            i   i-i             viii          i  i    i i  
  L1M4_orf2#LINE/      4 AAAGATAT-CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_24685267_2   1800 CAATACTACCCAATTTGATCTACAAATTCAACTTAATTTCTATCAAAATC 1849
                                v     v          i       vi   ii           
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_24685267_2   1850 CCAGCTGCCATTTTTGCA-AAATTGACAAGCTGATACTAAAATTCATACA 1898
                                  v        -                v            ii
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_24685267_2   1899 GAGATACAAGAAACCTAGAATAGCCAAAATAATCTT 1934
                           i  i    ii   i             i      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

Transitions / transversions = 3.67 (22 / 6)
Gap_init rate = 0.01 (2 / 185), avg. gap size = 1.00 (2 / 2)  

2305 13.84 2.19 12.39  chr1_24685267_24689121.rev     2233  2781 (1074)    L1M4_orf2#LINE/L1      176   668 (240)  

  chr1_24685267_2   2233 CCAAAATAATCTTGAACAAGGAAAACAAAGAGGGAGGACAGGAAAAAGTT 2282
                               i         v   i i       ------------------  
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAG------------------TT 207

  chr1_24685267_2   2283 TGAGGACTCACACTTCCTGATTTCCAAACTTATTATAAA----------T 2322
                         v                ii     v       i  i   ---------- 
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_24685267_2   2323 CAACACAGTGTGATAATGGTAGAAGAATAGAAATATAGATCA-TGGAACA 2371
                            v        i  v   i v   i     v          -     i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_24685267_2   2372 GAATTCAGAGTCCAGGTATAAACCCTCCTATTTATGGTCAACTGTTTTTT 2421
                              v         iv        vivi            i  v    i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_24685267_2   2422 GACTAGAGTACCAAGATAATTCAATGGGAAAA-AATAGTCTTTTCAACAT 2470
                            v  i  i      iv          i   -                v
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_24685267_2   2471 ACGGTGCTGGGAGAAGTGAATATCTACATGCAAAAGGATAAAGCTGGTCC 2520
                          i          v  v  i   ? i           i  i   i   v  
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_24685267_2   2521 CCTATCTCATACCATATATAAAAATTAACTCAATAACTTGGTCCTCAGTT 2570
                             i    i        i              -----------------
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAA----------------- 490

  chr1_24685267_2   2571 TGATCAGAATAAAAAGAAAAAAATTAACTCAAAATGGATCATAGACCAAA 2620
                         --------------------------------         ?     v  
  L1M4_orf2#LINE/    491 --------------------------------AATGGATCAWAGACCTAA 508

  chr1_24685267_2   2621 TTTTAAGAGCTAAAACTAGAAAACACTTACAAGAAAACATGGGAGTAAAC 2670
                         v v               v     v    v          i  ?     i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_24685267_2   2671 CTTCATTACTTTGGATCAGGCAATGATTTCTGAGATATGAAATCAAAAGC 2720
                             i v  i    i i        i     v        v i       
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_24685267_2   2721 ACAAGTGACAAAAGACAAAAATAGATGAATTGGGCTTTGTCAAAATTAAA 2770
                              ii        -          i      i   ii           
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_24685267_2   2771 AATGTTTGGGC 2781
                           iv    v  
  L1M4_orf2#LINE/    658 AACTTTTGTGC 668

Transitions / transversions = 1.52 (44 / 29)
Gap_init rate = 0.01 (6 / 493), avg. gap size = 13.33 (80 / 6)  

1279 13.77 1.31 3.28  chr1_24685267_24689121.rev     3060  3364 (491)    L1M4_orf2#LINE/L1      610   908 (0)  

  chr1_24685267_2   3060 CAAAAAAAAAAAAAAAAAATAATAATAATAATAA---TAATAATAATTTA 3106
                            iv  v    i        i--    - v ii--- v  v v    v 
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAG--ATAA-ATTGGACTTCATCAAAATTAA 656

  chr1_24685267_2   3107 AAACATTTGTGCTGCAAAGGACATCACCAAGAAAGTGAAGAAAAGACAAC 3156
                             v        v         ii i            ---        
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA---AAGACAAC 703

  chr1_24685267_2   3157 CCACAGAACAGGAGAAAATGTTTGCAAATTATATATCTTATAAGGGACTT 3206
                                 ii         i         i        v           
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_24685267_2   3207 GTATCCAGAATATAGAAAGAATTCTTACAAGTCAA-AACAACAAAAATCA 3255
                                       v      i        v    -  i  -   i -  
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AAAGA-CA 801

  chr1_24685267_2   3256 AATAACCCAATTTAAAAATGAGCAAAGAAGTTGCAATAGACATTTCTTCA 3305
                                     ?       i      i v   -             i  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTG-AATAGACATTTCTCCA 850

  chr1_24685267_2   3306 AAAATGATATAAAAATCACCAATCTGTACATGAAAAAGATGTTCAATATC 3355
                           i v      v    vi     vv i         -    i    i   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAACATC 899

  chr1_24685267_2   3356 ATTCACTAG 3364
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.28 (23 / 18)
Gap_init rate = 0.03 (9 / 299), avg. gap size = 1.56 (14 / 9)  


2882 22.36 1.64 8.51  chr1_24952763_24956461.rev     2234  3208 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_24952763_2   2234 TAAAGAGATATTCCATATTCACAGATAGGAAGATTCAAAATTGTCATGAT 2283
                          ii i      i    i    ii   v      i i  v     i v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_24952763_2   2284 ATAAGTTTTCCCCAACCTGATCTATAGATTCAGTGCAATCCCAATCAAAA 2333
                         ivv i vi       vi       i       ii        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_24952763_2   2334 TCCCAGCATGT-TATTTTGTGGATATTGAAAAA-TGATTCTAAAGTTTAT 2381
                                -  i- v     ii  v     v  i-    i     i  i  
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_24952763_2   2382 ATGAAGAGGGAAAGA--TCAAAATAATCAACACAATACTGAG---GAAGA 2426
                            i i v v  i i--i  i    ii   v     vi   i---     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_24952763_2   2427 ACAAAGTTGGAGGACAGACACTACCTGACTTCAAGACTTACTAGCTATAG 2476
                                        vv     v  ii i     i        -------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA------- 242

  chr1_24952763_2   2477 TAGTCTTCAAGACTTAAAGCTATAGTAATCTTCAAGACTTAAAGCTATAC 2526
                         --------------i       i       --------------------
  L1M4_orf2#LINE/    243 --------------CAAAGCTACAGTAATC-------------------- 258

  chr1_24952763_2   2527 TAATCAAGACAGTGTGGTATTGGCAAAAGAATAAACAAGTAGATTAATA- 2575
                         -----              i     v   i   i   vi     i   i-
  L1M4_orf2#LINE/    259 -----AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_24952763_2   2576 AACAGAATAGAGAGCCCA-ACATAGGCCCACATAAATGTAGTCAACTAAT 2624
                           i     v     i   - v   ii    i i vv i i     i i  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_24952763_2   2625 CTTTGACAAAGAAGCAAAGACAATGCAATAGAGCAAAGACAGTCTTTTCA 2674
                         i  i     i iv  v     v  v    i i v  ii i          
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_24952763_2   2675 AAATATCATGCAAAAATCCATCTTTTAAAAAATATGAATAACTGGACATC 2724
                          v v  vi   --------------------- i- i i       i ? 
  L1M4_orf2#LINE/    404 ACAAATGGTGC---------------------TG-GGACAACTGGATAKC 431

  chr1_24952763_2   2725 CATATACCAAAAAAACTGAATTTAGACACAGACATTATACATTCCACAAA 2774
                           i  i -    i  -    v  i   v vv  v i i  vv vi     
  L1M4_orf2#LINE/    432 CACATGC-AAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_24952763_2   2775 AGTTAACTCAAAGTACCTCATAAATCTAAAT-TAAAAATGC-AAAACTGT 2822
                          i          i ivv   ? i i      -   i --  -      i 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA--GCTAAAACTAT 527

  chr1_24952763_2   2823 AAAACTCTTGAGAAGACAACATAGGAAAAAGTCTAGATGACCTTAGGTAT 2872
                                  -      v        ?iv  i   vvi       i   vv
  L1M4_orf2#LINE/    528 AAAACTCTT-AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_24952763_2   2873 GGTGATGACTTGTCAGGTATAACACCGAAAGCATTATTGCTGAAATAAAC 2922
                           ii   ii  v i  i   i     i      iv viivii   v   v
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_24952763_2   2923 AATGAATGAGCTGGAATTCATTAAAAAAATTTTTTAAACTTCTGTTTTGT 2972
                            ii  i ii    v     i    -----  vv      i   vi vi
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAA-----TTAAAAACTTTTGTGCTTC 671

  chr1_24952763_2   2973 GAAAGCCAATGTCAAGGGAATAACCAGACATGCAACAAACTGGGAGAAAA 3022
                         i  i v  v i     ii i i vv     vv v   i v          
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_24952763_2   3023 TATTTGCAAAAGACATGTTTGATAAGAGACAGTTGT--CCAAAATATACA 3070
                                   vv i  i i       i   --    --   i      i 
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGAC--TTGTATCCAGAATATATA 769

  chr1_24952763_2   3071 AAGAACTCTTAAAGCTCTCAATAAGAAAAA---AAACAACCCAATTAAAA 3117
                                    v i   --     v     ---   i         ?   
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTC--AATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_24952763_2   3118 AATGGGCCATGTACCTTAATAGACACCTCACCAAAAAAGATATACAGATG 3167
                                v v v ii v        ii  v     i          i   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_24952763_2   3168 TCAAATAAGCATAAGAAAAGATACTCTACATCACATGTTAT 3208
                         v v        i v        i   v      ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (134 / 80)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.50 (99 / 22)  


 360 27.36 10.10 4.89  chr1_25228424_25231151      684   990 (1737)    L1M4_orf2#LINE/L1        3   325 (583)  

  chr1_25228424_2    684 GAAAGATA--CCAT---CA---ATCAAAAGACACAACAAAATAAACACAA 725
                                 --    ---  ---  iii     vi  i vvi v  v iii
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_25228424_2    726 CAGTTTTCCCTCCACTGCTCTATAAATTCAGTTTAATTCCATTCAATTCC 775
                           i vi    ivv i  v    i i     ---------- iv    i  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCA----------ACGCAATCCC 92

  chr1_25228424_2    776 AAT-AAAACCCCAAGCAGTATTTATTTTGTAGAACATT--CAGCCTAATT 822
                         v  -    i    -  v iv   --    i    -   --  iv  i  i
  L1M4_orf2#LINE/     93 TATCAAAATCCCA-GCTGCCTTT--TTTGCAGAA-ATTGACAAGCTGATC 138

  chr1_25228424_2    823 GTACAAT--ATATGC-----CACAGTAC--AAAACA-CAAAAATA--CTT 860
                         v  v   --     v-----  vi v  -- i  i - v    i --   
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_25228424_2    861 CAAAA-GAGAAACAAAAT---GGGATTTGTCTTTAAAAATATCAAAGATT 906
                         v    -  ii      i ---i   i iiivi  vvv   v     iv  
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_25228424_2    907 ATTTTAAAGCTGTTAATTATTAAGACAATGAAATACTGTCATG-GGATAG 955
                          i vi      ii- i v  i      i  vii     v   i-      
  L1M4_orf2#LINE/    239 ACTACAAAGCTAC-AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_25228424_2    956 AAAAATTGATCAATAGAA-AGAAT--AGAGGCTAGAAA 990
                          v v  v       i   -     --    v i     
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

Transitions / transversions = 1.40 (49 / 35)
Gap_init rate = 0.06 (20 / 323), avg. gap size = 2.30 (46 / 20)  

 522 27.17 9.84 1.97  chr1_25228424_25231151     1353  1606 (1121)    L1M4_orf2#LINE/L1      380   653 (255)  

  chr1_25228424_2   1353 AATGAGAAAAGGATGGGTTCCTCAA-AGATGGCTGC-AAGACAATTGGTT 1400
                             i i    i  i vi ii    - i    -   -ii     i   v 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGG-TGCTGGGACAACTGGAT 428

  chr1_25228424_2   1401 ATATGTAGGGGAAAGAGGTGACATTAGATCCTTACCTCACACCATACACT 1450
                          ?viii v vi     i-   vi  i  i  i              i  v
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_25228424_2   1451 GAAATGAG-TCAAAGGTAGATTAAGGACTTAAA-----------AAACT- 1487
                         i    v i-     i- i   i ?i   i    -----------     -
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAA-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_25228424_2   1488 ------TTTTAGTAGACAAAAGAGAA-TAATTTTTTATGACTTTGGGGTA 1530
                         ------ i    v   v  v v  i?-   v i  ii    i     v  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_25228424_2   1531 GGAGAAGGACTTCTTAAACAAGAGAT-AAAAGAACTTACCACAAATGAAA 1579
                           v-  v ii      i i v  v i-     v  vvi v     v    
  L1M4_orf2#LINE/    577 GGC-AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_25228424_2   1580 AGAAT-GATAAAATTGA-TTCATTAAAAT 1606
                          -   -      v v  -     i     
  L1M4_orf2#LINE/    626 A-AATAGATAAATTGGACTTCATCAAAAT 653

Transitions / transversions = 1.64 (41 / 25)
Gap_init rate = 0.05 (14 / 274), avg. gap size = 2.14 (30 / 14)  

 296 28.77 14.61 0.91  chr1_25228424_25231151     2017  2235 (492)    L1M4_orf2#LINE/L1      660   908 (0)  

  chr1_25228424_2   2017 CTTTTAT----CAAAATGCATTATAAACAAAATGAGCAAACAAGCCACAA 2062
                              i ----    ivi  i   v  v   i   iv i    v     i
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_25228424_2   2063 ACTGGGGAAAGACATTTACCACCCGTA-ATCAGATTA---AC----ATCT 2104
                          v    ii  i i    i v vi i  -   v   v ---  ----   i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_25228424_2   2105 G--ATATA----GAACTCTTATAAACCAAGAAGTAAAAAATAAAACAATC 2148
                         i--     ----         i  vi   v  -      ivv   i  i 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAACC 808

  chr1_25228424_2   2149 TAAT------------AGAAGACTTAAAGCAAGCAGTTCACAGAAGAGAA 2186
                         i   ------------ i i  i  i  -i ii  v   v vi    ii 
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAA-TAGACATTTCTCCAAAGAAGA 857

  chr1_25228424_2   2187 AACCCAAATAACTAATAG--ACATGTAAAGACATCCAACCTCATTAGTAT 2234
                         v iv     ii i    i--     v     iiii    v   ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_25228424_2   2235 T 2235
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.00 (42 / 21)
Gap_init rate = 0.04 (10 / 249), avg. gap size = 3.40 (34 / 10)  


2648 23.70 3.50 3.89  chr1_25231794_25234883     1509  2280 (810)    L1M4_orf2#LINE/L1        1   769 (139)  

  chr1_25231794_2   1509 TGGAGAGATAGTCCATGTTCATGGAAT--ATGA------ACTGGAGAGAT 1550
                             i     vi             v -- v  ------ i  vvi    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_25231794_2   1551 GCCAGT---TCTCAACTTGATCTATAGATTCAATACAATCTCAATCAAAA 1597
                          v  i ---i i   v        i        ii     i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_25231794_2   1598 TCCTGAC-AATTATTTTGTAGATAGTGACAAACTGAT-------TTTATA 1639
                            iii -ivi v     i   v v      i     -------  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_25231794_2   1640 TGGAGTGGCATATAACCCAGAATACCCAACACAACAATGAAAGAGAG--- 1686
                             ivv   vivi          v    v    ivv     i   i---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_25231794_2   1687 CAAAGTTAGAGGACTAACACTATTCAACTTCAATACTCACTATAGAGCTA 1736
                                i       v     vii   i     v   i    i i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_25231794_2   1737 CAGTAATCAAGACAGTGTTGCACTGGCAAAAGGGGAAGCAAATAGATCAA 1786
                                           v i       v    iv ii  v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_25231794_2   1787 TAGAGCATAATAGATAATCCAGAAATAGACCCACATAAATATAGTCAACT 1836
                          i  ii v   v  v i          i     i i vv   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_25231794_2   1837 GATCTTTGACAAAGG-ACCATGGGCAATACAGTGGACCAAAAATAGTTTT 1885
                            i  i     i  -i   -i i v  v  i   ivv  i      i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_25231794_2   1886 TTAATCAACAGAAACTATTTTGTTGATTAAAAATGGTGTAAGAATAGCTG 1935
                           ---     ---------------------       ivi i i i   
  L1M4_orf2#LINE/    400 TT---CAACA---------------------AATGGTGCTGGGACAACTG 425

  chr1_25231794_2   1936 GACATTCACATACGAAAAAAATGAATCTAGACACAGACTTTACACCTTTC 1985
                           i ?i     i -    i      vi i   v vv  i i     v vi
  L1M4_orf2#LINE/    426 GATAKCCACATGC-AAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_25231794_2   1986 ACAAAAATTAACTCAAAATGAATCAGAGACCTAAATGTAAA--CCACAAC 2033
                                             i    ?              i-- i v   
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_25231794_2   2034 ATTATAAGATTCCTGGAAGATAATATAGGAGAAAAACTAGTTAGCCCTGT 2083
                         --     i i  i i     v  i     ? v   v  vvv ii  i  v
  L1M4_orf2#LINE/    525 --TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_25231794_2   2084 GTGAGGCAATGATATTTTAGATACAACATCAAAGGCAAAATCCATGAAAG 2133
                           v        i v i       ii   i    i   v  v v ii    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_25231794_2   2134 AAATAATTCATAAGCTGGACTTCACTAAAATTAAAACCATCTGCTCTGGG 2183
                            v   vv    ii         ii          v v i  iv  vvi
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_25231794_2   2184 AAAAACGTTGCCAAGAGAATGAGAAAACAAGCCACAGAATGGGAGAAAGT 2233
                           ii  ii ii     i i   i  i    v                 i 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_25231794_2   2234 ATTTGCAAAAGTCATAT--CCAATAAAATACTGTTATCCAAAATATACA 2280
                                  --      -- ii    iiv   vv      i      i 
  L1M4_orf2#LINE/    723 ATTTGCAAA--TCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

Transitions / transversions = 1.65 (112 / 68)
Gap_init rate = 0.02 (15 / 769), avg. gap size = 3.80 (57 / 15)  

 618 19.61 0.00 2.61  chr1_25231794_25234883     2445  2597 (493)    L1M4_orf2#LINE/L1      760   908 (0)  

  chr1_25231794_2   2445 AAAAAATACAAATAACTCATAAAATTCAACAATAAGAAAATGAACAACCT 2494
                          i  v   i   v     v  v  i    i     i  i ii  i    i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_25231794_2   2495 GATTAAAAAATGGGCAAAAGACCTGAACAGACCCTTCCTTCACTAAAGAT 2544
                         i   ?             i  ii    i    vi   i---- i     v
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT----CCAAAGAA 855

  chr1_25231794_2   2545 GATATACAGATGGCAAATAAGTATATGAAAAGATGCTCAATATCATATAT 2594
                                 i     v      i i                i    ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_25231794_2   2595 CAT 2597
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 3.14 (22 / 7)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 4.00 (4 / 1)  


 368 22.34 12.77 0.00  chr1_25636450_25639425.rev      647   740 (2236)    L1M4_orf2#LINE/L1        3   108 (800)  

  chr1_25636450_2    647 GACAGATA--CCACATTCATAGAATGAAAGACCCAATACTGTTAAGATAA 694
                           v     --   ii     i  v  i     ii    i         ii
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_25636450_2    695 CAAT----------TTGATCTATGGATTCAAGTCAAACTCAGTCAAAATC 734
                             ----------        ii       vv   v i vi        
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_25636450_2    735 TCAGTT 740
                         i   i 
  L1M4_orf2#LINE/    103 CCAGCT 108

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.02 (2 / 106), avg. gap size = 6.00 (12 / 2)  

 703 24.58 1.12 2.23  chr1_25636450_25639425.rev     1040  1218 (1758)    L1M4_orf2#LINE/L1      101   277 (631)  

  chr1_25636450_2   1040 TCCCAGCAAGATTTTTCATGGAAAGTGACAAATTTGTTCTCAAATGTATA 1089
                                vivv     iiii    v      ii vi i  v    vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_25636450_2   1090 CAGACATGCAAAGGAACTACAATGGCCAAAGCAATTTTGAAAAAGAAGAT 1139
                         ii  v      i   v i v   i      i    i             v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_25636450_2   1140 CAAAGATGGAGGAATCACACTACCTGTTTTCAAGACTGACTTACTATGAG 1189
                              v       v       v  iiv      i   ----     ii i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT----TACTACAAA 246

  chr1_25636450_2   1190 GCTATAGCA-TCAAGAAAGCATGG-ATTGGC 1218
                             i  i -      v  ii   - i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGC 277

Transitions / transversions = 1.75 (28 / 16)
Gap_init rate = 0.02 (3 / 177), avg. gap size = 2.00 (6 / 3)  

1767 24.26 4.89 2.62  chr1_25636450_25639425.rev     1560  2132 (844)    L1M4_orf2#LINE/L1      292   877 (31)  

  chr1_25636450_2   1560 ATAAATCACTAGAGTGGAA----AAATCCAGAAACAAAACCATATTGTAT 1605
                            i    v i  i i   ----i i        i   v     i-i v 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC-ATTT 340

  chr1_25636450_2   1606 ATAGTCAATTAGTT--CAGCGAAGGCATCAAAGCAATTCAGCAGGGAAAG 1653
                           i       ii  -- ii i i  iii   ii v     iii       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_25636450_2   1654 GAAAGTTTTTTTCAACAAATAGTGATAA-ACAACTGGACATCTAAATAGC 1702
                         i v   i    -        i   v ii-         i ? i v  ivv
  L1M4_orf2#LINE/    391 AATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_25636450_2   1703 AAATAGTGAACTTTAACTCCTACCTTACATTATATACAAAAATTAACTTG 1752
                            v i    v  vi  i       i   ii                 ii
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_25636450_2   1753 AAGTCAATGAAAGACCTAAATGTAAATACTGAAATGATCAAGCTTCTGGA 1802
                           i vi  v ?              ivi  i   iv  v  i  ii i  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_25636450_2   1803 ATTAAA---------AAATATTCATAACCTGGGGT-AGGCAAAGTTTTTT 1842
                          vv   ---------    v   i i    v    -      v v   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_25636450_2   1843 TTAAACTA-GATACAGAAAGCAC--TCATCAAAAGGAAAATACTGATACA 1889
                          - i -  -  i  vi       --v  v      i    - iv    v 
  L1M4_orf2#LINE/    590 T-AGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAA 636

  chr1_25636450_2   1890 CTGGCCTTTATAAAAATTAAAA-CTTCTGCTCTTTGAGTGACACCATTAA 1938
                         i   v   i  v          -   i  iv   ii iv     i  i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_25636450_2   1939 GAAAATGAAAAGACAAACCATAGACTGGGAACAAACATTTATAATACATA 1988
                             i           v   i   v     iv   i    ii  vv    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_25636450_2   1989 TATCTGTTAAAGAACTTGTATCTAGAATATATGAAGCATTCTTGCAATTC 2038
                               v   i i         i         i   v i    i   i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_25636450_2   2039 AATAAGACAGTAAATAGACCAGTTTTTGAC---ATTAAAAAA-GAACAAA 2084
                              -----    v    v i ----i  ---   ?     - ii    
  L1M4_orf2#LINE/    787 AATAA-----TAAAAAGACAAAT----AACCCAATTWAAAAATGGGCAAA 827

  chr1_25636450_2   2085 AGTTTTAAACAGACATTTAT---AAGAGAGATACAGAAACAGCAAATAAA 2131
                         i v   i  i        v ---    -     i v   ii  v     i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAG 876

  chr1_25636450_2   2132 C 2132
                          
  L1M4_orf2#LINE/    877 C 877

Transitions / transversions = 2.02 (91 / 45)
Gap_init rate = 0.03 (19 / 586), avg. gap size = 2.26 (43 / 19)  


2574 26.90 1.69 1.93  chr1_25639491_25644948.rev     3763  4591 (867)    L1M4_orf2#LINE/L1        1   827 (81)  

  chr1_25639491_2   3763 TGGAAACACATCCCATGCTCATGGATTAGAAGAATCAGTATTGTGAAAAT 3812
                               v i        i         i     v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_25639491_2   3813 GACCATACTGCCCAAAGCAATCTACAGATTCAATGCAATCCCAAACAAAA 3862
                          i v     v      vii              i        v v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_25639491_2   3863 TAACAACATCATTGTTCACAGAATTAGAAAAAATAATCCTAAAATTAATA 3912
                          vv  i vv v  v  ii     v v  v  iv i           v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_25639491_2   3913 TGAAATTTTTAAAAAGAGCCTGAATGGCCAAAGCAAACCTAAGCAAAAAC 3962
                           i  v vi--  ii  v  v    i      i   v i i iv  i  v
  L1M4_orf2#LINE/    151 TGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_25639491_2   3963 AACAAATCTAGAGGTATCACATTACCAGACTTCAAATTGTACCACAAGGC 4012
                               vi i    vv     i v  vi i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_25639491_2   4013 TATAGTTACCAAAACAGAATGGTACTGATATAAAAGTAGGCACATAGACC 4062
                           i   v i   i    vi        ii    iii   i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_25639491_2   4063 CATGGAAAAGAATAGAGAACCCATAGATAAAGCCAAATATTTACAACCAA 4112
                         v      v     v    ii   v i     v   v i     iiii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_25639491_2   4113 CGGATCTTTGATGAAGCATATAAAAATATTTATTTTTTAAATAGGGTAAA 4162
                         iv   i  i  i-   vi iiv  i i---i   i----   i   -   
  L1M4_orf2#LINE/    349 TTGATTTTCGAC-AAGGGTGCCAAGAC---CATTC----AATGGGG-AAA 389

  chr1_25639491_2   4163 GGGCACCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACACATA 4212
                          iii vi  v  i  i              v      v  ?     iii 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_25639491_2   4213 GAGGAATGAAACTGGATCCCTATCTCTCATCTTATACAAAAAA-AACTCA 4261
                         i i       ii    i     i   v  i v          v-      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_25639491_2   4262 GGATGAGTCAACGACTTAAATCTAAGACCTGAAACCATAAGAATTCT--A 4309
                         ii   ii   ?v   i     v     v  i    i    -  i   --i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAG 538

  chr1_25639491_2   4310 AAGATAACATCAGAAAAACTCTTCTGGACATTGGCCTAGGCAAAGACTTC 4359
                             v     vi ?iv  v     vv   v    vi       v ii   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_25639491_2   4360 ATGACTAAGACCCCAAAAGCGAATGCAATAAAAACAAAAATAGATCAATA 4409
                         v iiv  v   v        iv v    i    iv          ---- 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT----A 634

  chr1_25639491_2   4410 AATGGGATCTCGTTAAACTAAAAAGTTTCTGCACAGCAAAAGTAATAATC 4459
                            v   ii  i i   v v    ii  i  ii vv    i vv iv   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_25639491_2   4460 ATCAGAGTAAAAAGACAATGCACATAATGGGAGAAAATATTTGCATACTA 4509
                          vv i   i         iv    v                    v ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_25639491_2   4510 TATATCCAACAAAGAACTAGTGTCTAAAAACCACAAGAAACTC----AAA 4555
                               ii i  i i   v  i  i i  vvi i  ii     ----  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_25639491_2   4556 TCAGAAAAAAAAA---AAAT----CAATTAAAAAGTGGGCAAA 4591
                            iv  v     ---    ----     ?    i        
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

Transitions / transversions = 1.46 (130 / 89)
Gap_init rate = 0.01 (12 / 827), avg. gap size = 2.50 (30 / 12)  

 449 14.95 1.87 0.93  chr1_25639491_25644948.rev     4861  4967 (491)    L1M4_orf2#LINE/L1      801   908 (0)  

  chr1_25639491_2   4861 AAATAAATTAATTAATTAAGTAGGCAAATGACATGAATAGACATTTCTC- 4909
                               vii    ? v-  i i      v  iv                -
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_25639491_2   4910 AAAAAAGATACACAAATGGCCAAGAAACATATGAAAA-ATGCTCTACATC 4958
                            i      i            v  i  i       -      v     
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_25639491_2   4959 ACTAATCAT 4967
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.03 (3 / 108), avg. gap size = 1.00 (3 / 3)  


3506 13.76 3.58 14.19  chr1_25730258_25733029.rev      962  1884 (888)    L1M4_orf2#LINE/L1        1   825 (83)  

  chr1_25730258_2    962 TGGAAAGACATTTCATATTCATGAACCGGAAAACTTAGTATTATTAAAAT 1011
                                 i  ii   i      i ii    i     i    i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_25730258_2   1012 GGCAATATTCCTCAAATTGATCTATAAATTCAGTGTAATCCCTATCAAAA 1061
                                i   i            i i     ii i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_25730258_2   1062 TCCCAACTGGCTTTTTCGCAGAAGTTGACAAGCTGATCCCAAAATTAATA 1111
                              i   v      i      i               i      v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_25730258_2   1112 TGGAAACTGAGATTACACCTGTAATCGCAGCACTCTGGGGGGCTAAGAAT 1161
                               --------------------------------------------
  L1M4_orf2#LINE/    151 TGGAAA-------------------------------------------- 156

  chr1_25730258_2   1162 GAAGGATTGCTTGAAGCTAGGAGTTTGAGACAAGCCTGGGCAGCACAGCA 1211
                         -------   ----------------------------------------
  L1M4_orf2#LINE/    157 -------TGC---------------------------------------- 159

  chr1_25730258_2   1212 AGAACCTTGTAAAAAAAATTCATATGGAAATAAATATAAGGGACCCAGAA 1261
                         -------------------------------------             
  L1M4_orf2#LINE/    160 -------------------------------------AAGGGACCCAGAA 172

  chr1_25730258_2   1262 TAGGCCAAACAACCTTGAAAAAGAA---CAAAGATGGAGTACTCACATTT 1308
                            v v      i            ---     v     v       i  
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_25730258_2   1309 CGTG-TTTTAAAA---ACTACAAAGCTACAATAATCAAGACAGTGTGATA 1354
                          vii-   i    ---              i                i  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_25730258_2   1355 CTGGCATAAAAATAGACATA--GATCAATGAAAT-----CGAGAGTCCAG 1397
                                  ii         --        i   -----i          
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_25730258_2   1398 AAATAATACCTGATAC---TATGCTCAACTAAGTTTTGACAAGGATGCTA 1444
                               -   i-    ---    v    i i v   i       i   i 
  L1M4_orf2#LINE/    323 AAATAA-ACCC-ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_25730258_2   1445 AGACAACTCAATCGGAAAAGAACAGTCTTTTCAAAAAATTGTGCTGGAAC 1494
                             v i     v  i      i           v    v       i  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_25730258_2   1495 AATTGGATATCCACATGCAAAAGAATGAAGCTGGAGTCCTACCTCACACC 1544
                           i      ?                    i    vi             
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_25730258_2   1545 ACAACCCCAAATAAACTCGAAATGAGTCATGG-CCTAAAAGTAATAGCTA 1593
                          i vv vv    v     i     ii   ?i -      v    v     
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_25730258_2   1594 AAACTATAACACTTCTAGAAGAAAACACAGGAATTA-TGTTCATGACCTT 1642
                                  v   ii            i   ?i v - v   i       
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_25730258_2   1643 GGGTAAGGCAATGGATTCTTAGA-----CGTCAAAAGTACAAGTAACAAA 1687
                             v         v        ----- ii      i     i      
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_25730258_2   1688 AGAAAAAAATCGATACACTGGACTACATCAAA-CTAAAAACTTTGGTGCT 1736
                                 - v    v i      v       -i          v     
  L1M4_orf2#LINE/    621 AGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_25730258_2   1737 GAAAACTATTCCATCAAGAAAGAGAAAAGATAACCCACAGAATGGAAGAG 1786
                         vv   vv iv i          v       i              i   i
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_25730258_2   1787 AATACTTGCAAATCATATGTCCCATAGAGAACTGGTATCCAGAACAAACG 1836
                             i             i  iv   ii i   v          i v ii
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_25730258_2   1837 GAGAACTTCTACAGCTCAACAATAAA--------CTACCCAATTAAAATA 1878
                         i      ii    i     i      --------iv        ?   v 
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_25730258_2   1879 TGGGCA 1884
                               
  L1M4_orf2#LINE/    820 TGGGCA 825

Transitions / transversions = 2.00 (82 / 41)
Gap_init rate = 0.02 (16 / 825), avg. gap size = 10.25 (164 / 16)  

 382 16.46 0.00 0.00  chr1_25730258_25733029.rev     2203  2281 (491)    L1M4_orf2#LINE/L1      830   908 (0)  

  chr1_25730258_2   2203 ATTTGAATATACATTTCTCTAAAGACAACACACAAAGGATGAAAAAGCAC 2252
                                  v         i     vi i i     v iiv  v      
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_25730258_2   2253 ATGAAAAGATGTTTAACATCATTAGACAT 2281
                                    i i       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.00 (0 / 0)  


2645 24.47 3.59 0.80  chr1_25974692_25977167      722  1473 (1003)    L1M4_orf2#LINE/L1        2   774 (134)  

  chr1_25974692_2    722 GAAAAAACATCCCACACTCATGGAATGGAAGAATCAATGTTGTTAAAAAT 771
                          i   i i      iii       v       v i   i       i - 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-T 50

  chr1_25974692_2    772 GACCATAATGCTCAAAGCAATTTACAGATTCAACGCAATTCCTATTAAAC 821
                          i v   v v i    vii  i                 i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_25974692_2    822 TACCAAC-GCCATTTTTTACAGAATTAGAAAAAAAG-TCCTCAAATTCAT 869
                          v   i -   -      i     v v  v  ivv -    v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_25974692_2    870 ATGGAACCAAAAAAGAGCC----T-GTCAAAGCAACCTTAAGCAAAAAGA 914
                               viiv  ii  v  ---- - i    i   i   i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_25974692_2    915 ACAAAGCTGGAGGCATCACATGACCCAACTTCAAATTATACTACAAGGTT 964
                               i      vv     ivv     i      viv        i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_25974692_2    965 ATAGTAACCAAAAGAGCATGTTACTTGTATAAACACAGAAAAATAGATAA 1014
                          i     i   i v  ii  v    v i    iv i   v v      v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_25974692_2   1015 ATGAAACAGAATAGAGAACCCAGAAATAAAGCCCCCATAC--CTACAACC 1062
                            i  i     v    ii           ---       --i  iiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAA---CCCATACATTTATGGTC 346

  chr1_25974692_2   1063 AACTGATCTTTGTCAAAGTCAACAAAAATATATACATGGGGAAAAGATAC 1112
                           i    i  i v   i viiv   i vi  vi -         ii   v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAGAATAG 395

  chr1_25974692_2   1113 CCTATTCAACAAATGGTGCTGGAAAAATTGGATAGCCATATGAAGAAGAA 1162
                         i  v                  i v  i      ?   i   v i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_25974692_2   1163 TGAAACAGGACCCATATCTCTCAGCATATATAAAAATTAACTCAAGATGG 1212
                             iiv      v  i   v  v      i              i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_25974692_2   1213 ATTAAAGACTTAAACATAAGACTTGAAACTATAAAAATCCTAGAAGAAAA 1262
                           i ?    i    ii     vi i           v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_25974692_2   1263 ----------ACTCTTCTGGACATTGGCTCACGCAAAGAATTC------- 1295
                         ---------- v     vv   v    v i v    v iv   -------
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_25974692_2   1296 -GTCCTTAAAAGCAAATGCAACAAAACCAAAAACAGACAAATGAGACTGA 1344
                         - v vii       v v         vv     i   i    vi    vv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_25974692_2   1345 ATTAAACTAAAAAGCTTATGTACCACAAAAGAAACAATCAACAGAGTAAA 1394
                           i   v v    i   v   i iv    i  v  v     v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_25974692_2   1395 TAGACAACCTACAGAATGGAAGAAAATATTTCTGAACTATATATCCAACA 1444
                         v        i         i           vii  ii       ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_25974692_2   1445 AAGGGCTAATATCCAGAATCTATAAGGAA 1473
                          i  i  vi          v     i   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAA 774

Transitions / transversions = 1.43 (107 / 75)
Gap_init rate = 0.01 (11 / 773), avg. gap size = 3.00 (33 / 11)  

 367 17.00 0.00 6.00  chr1_25974692_25977167     1884  1983 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_25974692_2   1884 AAAAGTGGACAAAGGACATGAATAGACATTTTTTTCAAAAGAAGACATAC 1933
                             i   i       iv             i -- v        i    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCT--CCAAAGAAGATATAC 862

  chr1_25974692_2   1934 AAGTGTCCCACAAACATATTTAAAAAAAAAAGTTCAACATCACTAACCGT 1983
                           i  v  v i  i  i  ----i    i v i         ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACAT----GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 3.00 (6 / 2)  


 556 19.44 2.78 0.00  chr1_26665047_26667544      500   607 (1891)    L1M4_orf2#LINE/L1      276   386 (522)  

  chr1_26665047_2    500 GCATAAAGACAGATGT---GACCAATGGAATAGAATAGAGAGCCCAGAAA 546
                               i  i   ii ---  i              v     i       
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_26665047_2    547 TAAACTCTCAAGTATATGATTAAATGATTTTCAACAAGGGTATCAAGATC 596
                              i vi vi v    i i  v        i        ii     i 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_26665047_2    597 ATTTAATGGGG 607
                            i       
  L1M4_orf2#LINE/    376 ATTCAATGGGG 386

Transitions / transversions = 3.20 (16 / 5)
Gap_init rate = 0.01 (1 / 111), avg. gap size = 3.00 (3 / 1)  

1257 17.05 5.43 0.78  chr1_26665047_26667544      869  1126 (1372)    L1M4_orf2#LINE/L1      370   639 (269)  

  chr1_26665047_2    869 AAAATCATTTCATAGGGGAAAGAACAGTCTTTTTAACAAATGGTGTTGGG 918
                           i i    iv  -          i        i           i    
  L1M4_orf2#LINE/    370 AAGACCATTCAAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_26665047_2    919 AAAATTGGATATCCATAAGCAAAAGA-----------CTCTTACTTTACA 957
                          v  i      ?   i v        ----------- i i   i i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_26665047_2    958 TTGAATACAAAA-TGAACTCAAAATGGGTCAAAGATCTAA-TATCATAGT 1005
                         iiiv        - v            i   ?   i    - i v v  i
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_26665047_2   1006 TAAAATTAGAAAATTCTCAGAAGAAAACATAGGAGAAAAGCTTCATGACA 1055
                              i  v    i   i               ? v   v    i    v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_26665047_2   1056 TTGGATTTGGCAATGATT-CTTGAATATGACACCAAAAGCATAGGCAACA 1104
                             i  v       i  -   ii                 i i      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_26665047_2   1105 AAAGAAAAAAATAGATAAATTG 1126
                                   -           
  L1M4_orf2#LINE/    619 AAAGAAAAAA-TAGATAAATTG 639

Transitions / transversions = 2.42 (29 / 12)
Gap_init rate = 0.02 (6 / 270), avg. gap size = 2.67 (16 / 6)  

 895 17.87 1.45 0.97  chr1_26665047_26667544     1401  1607 (891)    L1M4_orf2#LINE/L1      618   825 (83)  

  chr1_26665047_2   1401 AAAAGAAAAAAATAAATAAATTGAACTATATCAAAATTTAAAACTTGTGT 1450
                              -        i        i   vi         v       v   
  L1M4_orf2#LINE/    618 AAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_26665047_2   1451 GCATCAAAGAACACTGTCAACAAAGTAAAAAGGCCACACACAGAATGGGA 1500
                           v      i     i    v     i     i v  v            
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_26665047_2   1501 GAAAATATTTGAATATCATATATATGATAAAAGATTGATATCCAGAACAC 1550
                                    v v         v      ii  i vi         i i
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_26665047_2   1551 ATGATGAACTCCTAGAACTCACTGACTGAAAAACAAA---CCCAACTAAA 1597
                           i v      i  v      v i ivi   i     ---     i ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_26665047_2   1598 AAAATGGACA 1607
                            -   i  
  L1M4_orf2#LINE/    817 AAA-TGGGCA 825

Transitions / transversions = 1.40 (21 / 15)
Gap_init rate = 0.01 (3 / 208), avg. gap size = 1.67 (5 / 3)  

 449 12.61 5.88 0.84  chr1_26665047_26667544     1887  2005 (493)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_26665047_2   1887 CTCAAAAAAAAAAAAAAAAAAAA---AA---AAAAAAGGACGAAGGATTT 1930
                              v  v     i v   v  ---  ---     v  i i        
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_26665047_2   1931 GAATAGATATTTCTCCAAAGAAGCTATACAGATGGCCAATAATTTACATG 1980
                                i               v      i           vi-     
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC-ACATG 882

  chr1_26665047_2   1981 AAT-GATGCTAAACATCAGTAAATGT 2005
                           v-      v       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.67 (6 / 9)
Gap_init rate = 0.03 (4 / 125), avg. gap size = 2.00 (8 / 4)  


2058 21.14 2.31 8.18  chr1_27322568_27324638      500  1147 (924)    L1M4_orf2#LINE/L1      161   770 (138)  

  chr1_27322568_2    500 AAAGACCCAGAATAACCAACATAATACTT----ACGAAAAACAAATTCAG 545
                          ii           i    v i   -   ---- v   i      v ii 
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_27322568_2    546 AGGATTAACACT-CCTGACTTCAAGACTTACTATCAAGCTACAATAATCA 594
                             i v     -  ii i     i        iv        i      
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_27322568_2    595 AGACAGTGTGGTACTGGCAAAAGAATAGACAAATAGGCCAATGGAACA-A 643
                                            v   i       v    ii        i - 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_27322568_2    644 ATAGAGAACCCAGGAATAGACACACACAAATACAGTCAGCTGATCTTTGA 693
                           v    ii    i    i  v  i   vv  ii    ii    i  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_27322568_2    694 CAAGGCAGTAAAGTCAATTCAATGGAGAAACGATAGTCTTATCAACAAAC 743
                              vv iv   v v         i    vi        v        i
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_27322568_2    744 AGTGATGGAACAACTGGACATCCATATGCAAAAAAAAAAATCTAAACACT 793
                         i   v   i         i ?   i        i  vi  vi ii  v i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_27322568_2    794 GACCTAACACTGTTTACAAAAGTTAACTCAAAATAGATGACAGACCTCCT 843
                         v    v    ii v       i            i   v ?      ---
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT--- 506

  chr1_27322568_2    844 AAATTTAAAATACAAAACTATGAAACTTCTAGAAGATAACATAGGAAAAA 893
                             v   i vvi        i     ii       v        ?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_27322568_2    894 AATCCAACTTGATCTATAGCTTTAACATAATCCGAGTTGCAGTCCCAGCC 943
                          -----------   ------- -- i i i ------------------
  L1M4_orf2#LINE/    557 A-----------TCT-------T--CGTGACC------------------ 568

  chr1_27322568_2    944 ACTTATTTTGTTGGATTTGGCAATGAGTTTTTAGATACAACACCAAAACC 993
                         ----------    i  v       iv  i       ii         v 
  L1M4_orf2#LINE/    569 ----------TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_27322568_2    994 TCAATCCATGAAAGAAAAAAATTGGCAAGTTGGACTTCATTAAAATAAAA 1043
                         v   v v ii          - v ii  i           i     v   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_27322568_2   1044 AATTTCTCAGTT---AAAGACACAGTGGAGAGAATGAAAAGAAAAGCCAA 1090
                           i  i vv i ---  i     vi vi   i i        v  v   v
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_27322568_2   1091 GGACTGGGAGACA-TATTTGTAAAACACA-----GATAAAGGATTTGTAT 1134
                         i  v       v -      i   v  i -----     i   i      
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_27322568_2   1135 TCGAAATACACAA 1147
                         i ii    i i  
  L1M4_orf2#LINE/    758 CCAGAATATATAA 770

Transitions / transversions = 1.73 (85 / 49)
Gap_init rate = 0.02 (13 / 610), avg. gap size = 5.23 (68 / 13)  

 502 21.37 6.11 0.00  chr1_27322568_27324638     1448  1578 (493)    L1M4_orf2#LINE/L1      770   908 (0)  

  chr1_27322568_2   1448 AAGAACTCTTAAAACTCAACAATATGGAAACAA----CCCAATTTCAAAA 1493
                                    v       i    vii i    ----       ?v    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_27322568_2   1494 TGGGCAAAAGATCCAAA----CACCACACCAAAGATGATTTACAGGTGAC 1539
                                 i   iii  ----  iiv v       v   v    ii  i 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_27322568_2   1540 TAGTAAGCATATGAAAAGATTTTTAACATTATGTCATCA 1578
                         i i      i          vi i     i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (19 / 8)
Gap_init rate = 0.01 (2 / 139), avg. gap size = 4.00 (8 / 2)  


 926 29.68 4.64 4.27  chr1_27663139_27665086.rev      473  1011 (937)    L1M4_orf2#LINE/L1      223   763 (145)  

  chr1_27663139_2    473 CTCGGTCTCAAAAC--AAAACAAAACAAAAAATAATAATTAAAACCACTT 520
                          i ii i       -- vv     i v ----i i    i  i  viiv 
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTA----CAGTAATCAAGACAGTGT 268

  chr1_27663139_2    521 GGT-TTGGTTCAGGAAGAGACAAACAGACCAATGGACTAGAATAGAAAGT 569
                            -i   ivi i i v     v i   i       v      v  i   
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_27663139_2    570 CCAGAAATAGACCTA---ATTGCACGCGAGAATTTAGTATTTGATAAAGG 616
                                  i   i ---   -i i - vv    v v -  i  i  i  
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATT-TATG-GTCAATTGATT-TTCGACAAGGG 365

  chr1_27663139_2    617 TGTC-----CTCTCAAAGTGGAAA--ATGGACTCTTTAATAAATGGTGTT 659
                           i ----- vi    v v     --  i v  i  i  i        i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_27663139_2    660 GGGACACCTAGGTAGCCAACTAGGAAAAAA-AAAATTAGATCCGTGCCTC 708
                               v  i i  ?   vv ivi   i  -i  i  i  i  v i    
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_27663139_2    709 ACACTGAGCACCAGGATGAGCTCCCAAGGGATAAAATATTTAAATGTTTG 758
                             iivii  v ii  v i   vv  v    v ? v ii       ---
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT--- 512

  chr1_27663139_2    759 AAAAATCAAAATAAAACCGTAAAGGCACTAGAGGAAAACATGGGAG--AA 806
                         -  i v ----      ii    ivivi    i        i  ? --  
  L1M4_orf2#LINE/    513 -AAGAGC----TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_27663139_2    807 TGT--ATAATCTCATAGTGGAGAA-AGTTT---AACCATGACTCAAAAAT 850
                          v --i i i  iiviv i iv  -i    --- ivi     v v    v
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_27663139_2    851 CAAAAAGCTGTAAAAAGAAAAGATTGATAAAGTCAACTATATAAAAATCA 900
                           v  -  vii    -     i  v      v vi   vi  v     i 
  L1M4_orf2#LINE/    608 CACAA-GCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_27663139_2    901 AAAACTTCTG--CATGGAAAAACACTATAAATCAACGCATAAGACAAATG 948
                                i  -- v vi  ii       v  vv  vvv v       viv
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_27663139_2    949 ACAATCTGGGGGAAA-TATTTACAACTCTAATCACAGACAAGGGAACATC 997
                            ivv    i    -     i   v  vv  vv v  i      ---- 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA----C 751

  chr1_27663139_2    998 TCGCTTATTTAGAA 1011
                          i --   ii    
  L1M4_orf2#LINE/    752 TTG--TATCCAGAA 763

Transitions / transversions = 1.31 (89 / 68)
Gap_init rate = 0.04 (22 / 541), avg. gap size = 2.18 (48 / 22)  


2704 18.79 1.95 1.42  chr1_28175197_28178522     1285  1848 (1478)    L1M4_orf2#LINE/L1        1   567 (341)  

  chr1_28175197_2   1285 TGGAAAGACATCCCAAGTTCATGGATTGGAAGACTTAATATTATTAAAAT 1334
                                 i      v                          i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_28175197_2   1335 GTCCATACCACCCAAAGTGATCTACAGGTTCAATGCCATTC-TACCAAAA 1383
                          v v    iv      v          i     i  v  i -  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_28175197_2   1384 TCCCAG-TGTAATTTTTACAGAAATTTTTTAAAAATTG----TAAAATTC 1428
                               -  ivv     i        v--- v  ii  ----        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_28175197_2   1429 ATATGAAACCTCAAAGGACAACAAATAGTCAAAACAATCTTGAGAAAGAA 1478
                              i  viv   i    vvvi     i              i      
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_28175197_2   1479 GAACAAAACTGAAAGAC----AACTCCTGATTTCAAAACATATTACAAAG 1524
                                ii  i i   ---- vi   ii          v  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_28175197_2   1525 CTACAATAATCAAAATGGTTTGG-ACTGGCATAAAGACAGACACATAGAT 1573
                              i       i ii  v   -          i  i     i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_28175197_2   1574 CAATGGGACAGAATAGAGAGACCCAAAATAAACCCTCACATACATAGTCA 1623
                               i i     v     v  vi          vi    vi  i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_28175197_2   1624 AATAATCTTTGACAAGAGGACCATGATTACACAATGGGGAAAGAATAGTC 1673
                          v i  i  i      i vi   v  ii iv                   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_28175197_2   1674 CCTTCAACGAAAAGTGCTGGGAAAGATGGATATCCACATGCAGAAGAATG 1723
                         ii      i  vi         v iv      ?         i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_28175197_2   1724 AAGATGGGCTCTTATCTTACACCATATATTATACAAAAATTAACTTAAAA 1773
                            v   i i i  i  i          -----            i    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATA-----CAAAAATTAACTCAAAA 492

  chr1_28175197_2   1774 TGGATTAAAGACCTAAACATAAGACCTGAAACTATAAAACTCCTCAAAGA 1823
                              i ?         ii     v  i              i vi    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_28175197_2   1824 AAACATAGGATAAAAGCTTCTTGGC 1848
                                  ?vv   v    v  i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGAC 567

Transitions / transversions = 1.78 (66 / 37)
Gap_init rate = 0.01 (7 / 567), avg. gap size = 2.71 (19 / 7)  

1135 20.74 4.83 4.26  chr1_28175197_28178522     2482  2833 (493)    L1M4_orf2#LINE/L1      555   908 (0)  

  chr1_28175197_2   2482 AAAGCCTCATGACATTGGAATGGGTCATAATTTCCTGGATATGACACCAA 2531
                            v i  i    v    iv i  iv  ii    i i             
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_28175197_2   2532 AAGCACAGGCAACGAAAGCACAAATAAACTATTT----TTTGGCAAACTT 2577
                                i     i    v v     i iv v  ----  iiv    v  
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_28175197_2   2578 TAAATAATCTCCATGAAGCAAAGGAAAACAATCAGCAGAGTGGAAAGGCA 2627
                         -   -  ii iii  vvv       v - v    iv i    i    i  
  L1M4_orf2#LINE/    655 -AAA-AACTTTTGTGCTTCAAAGGACA-CTATCAAGAAAGTGAAAAGACA 701

  chr1_28175197_2   2628 ACCTGTGGA-TGGGAGAAAAGGCAACCTTTCGGATGGAACCAGATATCAG 2676
                            iiii  -          --i ----  i v ---  i  v     v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAA--TA----TTTGCA---AATCATATATCTG 742

  chr1_28175197_2   2677 ATAAGGGGTT---------AATATGCA--GAACTCCTACAACTCAGTAAC 2715
                                ii ---------     ii --      i         i   i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_28175197_2   2716 AACAATAACAAAAAATTCAATTTAAAAAATGGGCAAAGAACCTGAATAGA 2765
                           v  -i     v  ii     ?     -         i ii        
  L1M4_orf2#LINE/    793 AAAAA-GACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGA 840

  chr1_28175197_2   2766 CATTTCTCCAAAGACGATATACCAATGACCA-TAAACATGTGAAAAGATG 2814
                                       v       v    i   -   i  ii          
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_28175197_2   2815 GCTCAATATCACTGATCAT 2833
                         -     i    ????????
  L1M4_orf2#LINE/    891 -CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (49 / 23)
Gap_init rate = 0.04 (14 / 354), avg. gap size = 2.29 (32 / 14)  


1224 29.53 3.72 0.99  chr1_28391844_28397776.rev     3626  4028 (1905)    L1M4_orf2#LINE/L1        1   414 (494)  

  chr1_28391844_2   3626 TGGAAAAACGTCCCATGCCTATGGATAGGAAGAATCAATATTGTTAAAAG 3675
                               i ii       iii      v      v i           i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_28391844_2   3676 GGCCGCACTGCTCTAAGAAATGTATAGATTCCATGCCATTCCTATTAAAA 3725
                            vii   v i v  vvi  v  i      v i  v  i     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_28391844_2   3726 TACTATTGACATTCTTCATAAAACTAGAAAAAAAAATTATTTTAAAATTC 3775
                          v i vivi v  i  iii i  v v  v  ---iv v  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA---GCTGATCCTAAAATTC 147

  chr1_28391844_2   3776 ATATGGAA-----------CCAAAAGAGCCAAGGAAATCCTAAGCAAAAA 3814
                                 -----------   i  v      iiv    i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_28391844_2   3815 GAACAAAGCTGGAGGCATCATGCTATCCAACATCAAACTATACCACAGGG 3864
                                 i      vv   ii  vi    iv     viv   i   ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_28391844_2   3865 CTACAGTAACCAATACAGCATGGTACTGGTACAAAAAAAGACACATAGAC 3914
                                  i   v    ii         i i  ii v     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_28391844_2   3915 CAATAGAACAGAATGGAGAACTCAGAAATAAAGGCCACACACCTACAAGT 3964
                             i   i     v    iii          -v   i   ii  iiivi
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTC 346

  chr1_28391844_2   3965 ATCTGATCTTTGATAAGCCAGACAAAAATAGGCAATGAGGAA----TTCC 4010
                          vi    i  i  i   vvv v   i vi vv     i    ---- vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_28391844_2   4011 CCATTCAATAAATGGTGC 4028
                          iv     i         
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGC 414

Transitions / transversions = 1.64 (74 / 45)
Gap_init rate = 0.01 (4 / 414), avg. gap size = 4.75 (19 / 4)  

 626 28.04 2.65 0.53  chr1_28391844_28397776.rev     4334  4522 (1411)    L1M4_orf2#LINE/L1      403   595 (313)  

  chr1_28391844_2   4334 AATAAACAGTGCTGGGATAACTGGCTAGT---ATGCAGAAGATTGAAAAT 4380
                           i   ii         i      v  ?i---     i    v    iv 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_28391844_2   4381 GGATCCCTTCCTTACTCTATATACAAAAATTAACCTAAGACAGATTAAAG 4430
                            i    v   i  v i                ii  i ii   i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_28391844_2   4431 ACTTAAATGTAAAACCCGAAACTACAAAAACCCTGGAAGACAAGCTAGGC 4480
                           i         i v ii      i    vi i i     v  vv    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_28391844_2   4481 A-ATACCATTCTGGACATAAAAATGGGCAAAAATTTCAT-GATA 4522
                         i- v i -   vv   v viiiv i     vii    v -    
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

Transitions / transversions = 1.78 (32 / 18)
Gap_init rate = 0.02 (4 / 193), avg. gap size = 1.50 (6 / 4)  

 771 24.45 2.62 0.87  chr1_28391844_28397776.rev     4830  5058 (875)    L1M4_orf2#LINE/L1      597   829 (79)  

  chr1_28391844_2   4830 GACACCAAAAGCAATTACTACAAAAGCAAAAATTGATAAATGGGGTCT-- 4877
                                      vvvi v       v      v       v  iii --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_28391844_2   4878 ----AATTAAAGAGCTCCTGCACAGAAAAGGAAACTATCAACAGGGTGAA 4923
                         ----       i -  ii  ii vvv      v        v ii     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_28391844_2   4924 CAAACAACCTACAGAATGGGAGAAAATTTTTGCAAACTATGCATCTGACA 4973
                         v i      i                 v        ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_28391844_2   4974 AAGGTCTAATATCCAGCATCTACAAGGAACTTAAACAAATTTGTAAGAAG 5023
                          i  v  vi       v  v  i  i     ivv    v ivi   v  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_28391844_2   5024 AAAACTAAACAACCCCATTAAAGAGTAGGCAAAGG 5058
                           i  -   i     v   ?  i i i        
  L1M4_orf2#LINE/    796 AAGAC-AAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.29 (31 / 24)
Gap_init rate = 0.01 (3 / 233), avg. gap size = 2.67 (8 / 3)  

 409 17.20 1.08 0.00  chr1_28391844_28397776.rev     5350  5442 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_28391844_2   5350 AAAAGTCGGCAAAGGACATGAACTGACATTTTTCAAAAGAAGACATACAT 5399
                             i v         iv    iv       i  v        i     v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_28391844_2   5400 ACAGCCAACAATCATATGAAAAAA-GCTCAACATCACTGACCAT 5442
                          ii     i  v  i       i -           ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


1375 24.50 2.56 1.42  chr1_28398373_28400413      498   848 (1193)    L1M4_orf2#LINE/L1      134   488 (420)  

  chr1_28398373_2    498 TAATCTTAAAATTTGTATGGAACACAAAAAGG-CTCTGAATAGTCAAAGC 546
                          i   i       ii       - iiv  i  - i v      i    i 
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr1_28398373_2    547 AATTTTGAGCTAAAAGAATAAAGCCAGAGGCATCATACTGTCTTATTTCA 596
                            i    ivv i     i    iii    vv   i   vi iv      
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_28398373_2    597 AAATATGCGACAAAACTGAAGTAA----AACAGCGTGGATCTGCCATAAA 642
                            iv i v     i  iv     ----i    i    vv   v     i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_28398373_2    643 AA--GACATA--GACAAATTGAATAGACTAGGGAATCCAGAAATAAGTCC 688
                         i --      --  iv   v       v v i  i           ii  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_28398373_2    689 ACGTAGGTATGGTCAATTGATTTTCGACAAAGATGCCAAGAACACACAGT 738
                          iii vv                       i i        v  iv  i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_28398373_2    739 GGGGAAAGGACAATCAGTGTCTTCAGTAAATGATGTTGGGTAAAGTGGAT 788
                                 i i i  ---- i    ii     i  i    vv  v     
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTC----TTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_28398373_2    789 ATCCACATGCAGAAGAATGAAATTAGATCCATGTCTCTCACCATCTTAAA 838
                          ?         i         i  i  i  v ii   v      v vv  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_28398373_2    839 AAATCAACTC 848
                             i     
  L1M4_orf2#LINE/    479 AAATTAACTC 488

Transitions / transversions = 1.83 (55 / 30)
Gap_init rate = 0.02 (6 / 355), avg. gap size = 2.33 (14 / 6)  

1631 22.30 6.21 0.46  chr1_28398373_28400413     1114  1548 (493)    L1M4_orf2#LINE/L1      449   908 (0)  

  chr1_28398373_2   1114 AGCCAGACTCC-ATCTCAAA------AAAAAAATCAACTCAAAATGGATT 1156
                           iii   i  - i    v ------ v      i              i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_28398373_2   1157 TAAAGACTTAAATGTAAGACCTGAAACTGTAAAACTACTAGAAGCAAACA 1206
                         - ?    i           v  i     i       vi      v     
  L1M4_orf2#LINE/    499 -AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_28398373_2   1207 CAAGAG-AAAGCTTCATGAC-TTGGTCTGGGCAATGATTTTTTGATTATG 1254
                         i i ? -   v    i    -    vi i       i   i  iiv    
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_28398373_2   1255 ACCCCAAAAGCACAGGCAACAAAAAGCAAAAATAGTCAAAGGGGATTACA 1304
                           v           i         - v        vi   vv   i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCA 646

  chr1_28398373_2   1305 TCAAACTCAAAAGCTTCCGCACAGCAAGGGAAAC----AACAGAATGAAG 1350
                              v i    i   ii ii vv   i   v  ----  v i i    i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_28398373_2   1351 AGACAACGTATAGAATGGGAGAAAATATTTGTAAACTATATGTATGATTA 1400
                                vi i                    i   ii    i v    v 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_28398373_2   1401 GAGGTTAATAGGAAAAGT-TATGAGGAACTC------------AACAGCA 1437
                          i ii vi  vvv i i -   i i      ------------  i iv 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_28398373_2   1438 AGG-AAACAATCCCATTTTAAAATGGGCAAAAGATCTGAATAGACATTTC 1486
                           i-   i  i  v   ?v            i   i              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_28398373_2   1487 TCAAAAGAAGACCTATAAATGGCCAACAAGTATATGAAAAAATGTTCAGT 1536
                           v        iv  i          i   i i       i   i   ii
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_28398373_2   1537 ATCACTAATCCT 1548
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (63 / 31)
Gap_init rate = 0.02 (10 / 460), avg. gap size = 2.90 (29 / 10)  


3377 15.98 3.04 1.98  chr1_29083793_29087055.rev     1581  2237 (1026)    L1M4_orf2#LINE/L1        2   665 (243)  

  chr1_29083793_2   1581 GGAAAAA-ATCCCATGTTCATAGATTAGAAGACTTCACGTTGTTAAGATG 1629
                              i -             i    i        v ii           
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_29083793_2   1630 GCAATATTCCC-AAATTAATCTACAGATTCAGTGCAGTAGACATCAAAAT 1678
                               i    -     i             ii   i vvvi        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_29083793_2   1679 CCCAACTACCTTTTCCACAAAAATGGACAAAACTGATGCTAAAATTCATA 1728
                             i  i      iii  i    v     i-     v            
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr1_29083793_2   1729 TGGAAATACAAGGGATAGCCAGAACAGCCAAAACAATGTTGAAAAATAAG 1778
                                i       i--      i            v        v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_29083793_2   1779 ACCACAGTTAGAGGACTCACACTTACCAATTTCAAAGCTTACCACAAACC 1828
                          v  v    i              v           i     i     v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_29083793_2   1829 TACAGTAATCAAGACAATGTGGTACCAGCATAAGGATAAACACGTAGATC 1878
                                         i        ii           i   ii      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_29083793_2   1879 AACGGAATGGAACTGAGAGTCCAGAAATAAACTCATACATCTATATCCAG 1928
                           i     i   i                   i       i   ivi  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_29083793_2   1929 TTGGTTG-CAACAAGGGTGCCAAGACAATTCAATGGAGGAAAGGAAAGTC 1977
                            i  v- i                v         -      i v    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTC 397

  chr1_29083793_2   1978 CTTTCAACATATAATGCTGGGACAACTGGACATCTACCTGCAAGTGAGTG 2027
                         i        v  ii                i ? i  v     iv  i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_29083793_2   2028 AATCCAGACAGACCCCTGTCTCACCTCATATAAAAAATTTAATTTGAAAT 2077
                           ---- vii       ii     vi      v    v    i ii    
  L1M4_orf2#LINE/    448 AA----GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_29083793_2   2078 GGATCAAAGATATGAATGTAAGAGCTAA---CATAAAATTCCTAGAAGAA 2124
                               ?   iv i              ---i      i  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_29083793_2   2125 AAGATAAGACGTAAATTTCCATGATTTTGATTTAGGCAATGATTTCTTAC 2174
                           v   i ?-      i i i   ii   iv          i       v
  L1M4_orf2#LINE/    544 AACATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_29083793_2   2175 ATATGATACCAAAA--ACAACCAA---------AAATTTTTTTATAAATT 2213
                               i       --    v   ---------    vv----       
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG----ATAAATT 638

  chr1_29083793_2   2214 GGACTTCA---AAATTCAAAACTTATG 2237
                                 ---     v       v  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 2.19 (70 / 32)
Gap_init rate = 0.02 (13 / 664), avg. gap size = 2.54 (33 / 13)  

1008 17.65 13.33 0.00  chr1_29083793_29087055.rev     2518  2772 (491)    L1M4_orf2#LINE/L1      620   908 (0)  

  chr1_29083793_2   2518 AAAAAAAAATAAATAAAT-----------------AAAAACTTTTGTGCT 2550
                           i        i      -----------------               
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_29083793_2   2551 TTAAA--ATGC-GTCAGAAAAGTGGAAATACAGCCTAAACAACAGGAGAA 2597
                          i   -- ii -i   ii      i   v   i  i v v  ii      
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_29083793_2   2598 A---TTTGCAAATTATATGCCTGATAAAGGTTTAGTCTATGGAATGCATA 2644
                          ---         i    ii       i  vi v  v vii    ii   
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_29083793_2   2645 AAGTACTCTCACAATTCAA--------AGACAAATAACACAATGTAAA-- 2684
                            v     i    i    --------           v    v?   --
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_29083793_2   2685 TGAGCAAAGTACTTGAACAGACATTTCACAAGAGAAGATACACAAATGGC 2734
                           i      v i     i         v v i        i         
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_29083793_2   2735 CAATA-GCACATGAAAAGGTGTTCAACATCATTAGTCAT 2772
                              -            i  i         ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (31 / 13)
Gap_init rate = 0.02 (7 / 289), avg. gap size = 4.86 (34 / 7)  


 331 24.09 9.49 0.73  chr1_29440951_29444109.rev     1490  1626 (1533)    L1M4_orf2#LINE/L1        2   150 (758)  

  chr1_29440951_2   1490 GGCAATATAAATCACTTTCATGGGTGGAAAGAC--AAT-TTCATAAGATG 1536
                           v  v   vvi  iv       i v i     --   -  vv       
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_29440951_2   1537 GCGATTCTTCC-AAATTGATCTATAAATTCAATACAAAACC-ATCCAA-- 1582
                           i  v  i  -           i i      ii   vv  -   v  --
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_29440951_2   1583 CAAAG------TTTTTCAAGAAACTTAAAGAGATGACTCTAAAATTTATA 1626
                          vv  ------     vv     -  i vi  v   ii        i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCATA 150

Transitions / transversions = 0.83 (15 / 18)
Gap_init rate = 0.05 (7 / 149), avg. gap size = 2.00 (14 / 7)  

1359 29.78 5.62 1.69  chr1_29440951_29444109.rev     1957  2668 (491)    L1M4_orf2#LINE/L1      169   908 (0)  

  chr1_29440951_2   1957 AAAATAGCCAAGACATCCTTGAT---GAAGCACAAAGTTGGCACAGCTT- 2002
                          i         i   vi     v---    v          - vii  i-
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG-AGGACTCA 217

  chr1_29440951_2   2003 CATGTTTCAGATATCAAGACTTA----AATAGCCTCGATAATTA-GACCG 2047
                           iv ii  -  v    i     ----  -   iv ii    i -   v 
  L1M4_orf2#LINE/    218 CACTTCCCA-ATTTCAAAACTTACTACAA-AGCTACAGTAATCAAGACAG 265

  chr1_29440951_2   2048 TGTGGT-------TAGGAATCAACCAAACCAACCAATGAAAGA-AACAGG 2089
                               -------  i i  vi  - v ivi i     i  v -  iv i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGAC-ATATAGATCAATGGAATAGAATTGA 314

  chr1_29440951_2   2090 GAACTGAAAAATGA-TCTACTTATCTGTAG--AAATGGGGTGTGCGAGAA 2136
                           iiiv i    i -i i ivi  i i i --  v  i-- v v   v  
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA--TTTTCGACAA 362

  chr1_29440951_2   2137 AGATGGCACTGCAAATCAGCAGGGAAAGCGTGAACTAT--AATAAATGAT 2184
                         i i  v  vvi v v   iii       vi iiv  v --  i     i 
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_29440951_2   2185 GCTGGGACAG-TGGCTTATCACCATGGAAAA-AATAAAAT-----CCTTA 2227
                                  i-   v v?i   -   v    -   i  i -----  i  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCAC-ATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_29440951_2   2228 ACTTATACCACCACACACAAAAATCAATTCCAGATGGAT-AAAGATTTAA 2276
                         v  i ---     i i        i  i  v i      - ?   ii   
  L1M4_orf2#LINE/    462 CCTCA---CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_29440951_2   2277 ATATAAAATGTAAAATGTTATAAGTTCTAGAAAAAAAGCA-AAAAATA-- 2323
                           i   i vv     ivv  v  v ii     i    -  - ii?i  --
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGTAAA 557

  chr1_29440951_2   2324 -TTTTATAACTTTGGAT-AGGGAAAACTTCTTTAAAAA--ACACAAAAAG 2369
                         -i  ii i  i    i -   v  viv  ii   i v --    v     
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_29440951_2   2370 TAGAAATCACAAAGAAAAAGACTGATGAATTTAAATACA-CAAAAATAAA 2418
                         i v  iiv     ii    i iv   i    vi v v  -     v    
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_29440951_2   2419 AATCTTCTGTTCATCCAAAGACACTATAAATAACCTAGGAAGATAAGCCA 2468
                           -   i   v v  v  i        v  v  vv iii    i  v   
  L1M4_orf2#LINE/    658 AA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_29440951_2   2469 CAAATTGGGAGGAGATATTTGCAATTCACAAGT--GACAAATGATTATTA 2516
                           i v      i i          v   i vi --  i  iv  i vv  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_29440951_2   2517 TCCTAAATATATAAAGAACTCCTAAAAACCACTAAGAAAGCAACAGAAAA 2566
                            vi                i  v  vi  v   v   ivi   i v  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_29440951_2   2567 CCCAATAGAAAATTAGGTGAAAGACATGAACAGGCATTTCATGGAAAAAG 2616
                               v?    v i  ii  i  iv    i  i      vivi  i   
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_29440951_2   2617 AGACCTGAATGGCCATTGATGACTTGAAAATACGTTCAACTTCATTAGTC 2666
                          v ivii        v i vv  v      v i i     v   ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_29440951_2   2667 AT 2668
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.48 (124 / 84)
Gap_init rate = 0.04 (28 / 740), avg. gap size = 1.86 (52 / 28)  


3091 24.73 4.08 0.60  chr1_29520385_29525691.rev     3976  4808 (499)    L1M4_orf2#LINE/L1        1   862 (46)  

  chr1_29520385_2   3976 TGGAAAGATATTGCATGCTCATGGATTAGAAAAATTAATATTGTTAAAAT 4025
                                    iv    i         i   i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_29520385_2   4026 GACAAAACTACCTAAAGCAATTTGTAGATTCAGTGCAATCCCTATCAAAA 4075
                          i   v   v  i   vii  i ii       ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_29520385_2   4076 TACCAAGGACATTCTTCACAGAAATAAAAAAA---ATCCTAAAATTTGTA 4122
                          v   ivvi v  i  ii       vi v  i---           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_29520385_2   4123 TGGAACCACAAAAGACCCTGAATAGCCAAAGCAATCTTAAGCAAAAATAC 4172
                              vii   ii     v           i       i iv  i  v v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_29520385_2   4173 CAAAGCTGGAGACATCACACTACCTGACTTCAAAATATACTGCAAAGCTA 4222
                              i     ivv       v  ii i       iv    i        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_29520385_2   4223 TTGTAA-CAAAATAAGCATGGTACTGGCATAAAAACAGGCACATAGACCA 4271
                         iv    -   i i - ii              ii i  i  i     i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACA-GTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_29520385_2   4272 ACAGAACAAAATTAAGAAGCCAGATATAAACCCACACACTTATAGCTGAC 4321
                          ii   i i    i   iv     v         i   i    i iii i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_29520385_2   4322 TCATTTTCAACAAAGGTGCCAAGAACATTCAGTGGGGAAAGGA--GTCTC 4369
                          v      i    i          v      i         i --    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_29520385_2   4370 TTCAATAAA-------------ACGGGATAACCATATGCAGAAGGATGAA 4406
                              i   -------------  v     ?   i     i   i     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_29520385_2   4407 GCTATACCCCTATTTCTCACCATTCCCAAAAATCAAATCAAAATGGATTA 4456
                          i iv       ii  v      viv       i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_29520385_2   4457 AAGACTTAAATCTAAGACCTGAAACTATGAAACCACCAGAAGAAAACA-- 4504
                         ?    i     v     v  i       i    ivii           --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_29520385_2   4505 ---------CTCTAGGACATTGGTCTGAGCAAAGAATTTTTGTGTAAGAT 4545
                         ---------  iiiv   v    vi ii    v iv  i  ivi  v  i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_29520385_2   4546 CTCAAACACACAGGCAACCAAAGCAAAAATAGACAAAT-GGATTACATCA 4594
                         vi    vi    i     v    v         i    -   i v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_29520385_2   4595 AGCTAAAAAGCTTCTGCGCAGCAAAGAAAACAATCAACAAAATGAAGAGA 4644
                          iv v    i   i  i  vv     i v  v     v   i    i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_29520385_2   4645 TAACCCACAGAATAAGAGAAAACACGTGCAAACTATTCATTTGACAAGGG 4694
                         i            ii       i iv      ii  vi  i   i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_29520385_2   4695 ATTAATA-ACAGAATATATAAGGAGCTCAAACAACTCAATAGCTAAACAA 4743
                          i vi  -v            i  i   vv           i-    v i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAG 798

  chr1_29520385_2   4744 ATAAATAATCTGATTTTAATTTTA--AAAGAATCAGAGTCTTCTTTTTGT 4791
                          i      i ii   ?v  vv vi--    i  iv  i vvv v   ---
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT--- 845

  chr1_29520385_2   4792 CTTAAAAGAAGACATAC 4808
                           iv        i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATAC 862

Transitions / transversions = 1.90 (133 / 70)
Gap_init rate = 0.01 (11 / 862), avg. gap size = 3.55 (39 / 11)  

 354 10.17 0.00 0.00  chr1_29520385_29525691.rev     4907  4965 (342)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_29520385_2   4907 AAAGAAGACATACAAATGGCCAGTAGGTATATGAAAAAATGCTCAACATC 4956
                                 i             i  i i i       i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_29520385_2   4957 ACTAAACTT 4965
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.00 (6 / 0)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


3198 26.63 0.99 0.66  chr1_29547428_29551953.rev     3131  4035 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_29547428_2   3131 TGGAAGAACATTCCATGCTCGTGGACAGGAAGAATCAATATCATGAAAAT 3180
                              ii i  i     i  i    iv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_29547428_2   3181 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3230
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_29547428_2   3231 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3278
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_29547428_2   3279 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCGAAAAG 3328
                                viiv  ii  v  v v  v     iv     i i ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_29547428_2   3329 AACATACCTG----ACTTCACGCTACCTGACTTCAAACTATACTACAAGG 3374
                             v vi  ----   -   i  v  ii i      viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACT-CACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_29547428_2   3375 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 3424
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_29547428_2   3425 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 3472
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_29547428_2   3473 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 3522
                         i vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_29547428_2   3523 CCTATTTAATAAACAGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3572
                         i  v  i  i   ii         v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_29547428_2   3573 TGAAAGTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 3622
                             iv    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_29547428_2   3623 ATTAAAGACTTAAATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAG 3672
                           i ?    i       v   v       i      vi i         i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_29547428_2   3673 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 3721
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_29547428_2   3722 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3771
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_29547428_2   3772 AATTAAACTAAAGAGCTTCTGCACAGCTAAAGAAACTACCATCAGAGTGA 3821
                         v  i   v v  i i   i  ii vv v  i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_29547428_2   3822 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 3871
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_29547428_2   3872 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 3921
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_29547428_2   3922 AAAAACAAACAACCCCATCAAAAATTGGGCAAAGGATATGAACAGACACT 3971
                            i     i     v  i?    v            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_29547428_2   3972 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGTTCA 4021
                             v        i  vi viii     i ii          i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_29547428_2   4022 TCATCACTGGCCAT 4035
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


 244 26.32 0.00 0.00  chr1_29567079_29570925.rev     2152  2208 (1639)    L1M4_orf2#LINE/L1        2    58 (850)  

  chr1_29567079_2   2152 GGAAAGATATCTCACGCTTAGGAATCAGAAGAATTAATATCATTAAAAAG 2201
                                    i  i i i v i  ii     v       ii    i v 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_29567079_2   2202 GCCACAC 2208
                           v i  
  L1M4_orf2#LINE/     52 GCAATAC 58

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.00 (0 / 0)  

3057 25.15 1.86 1.40  chr1_29567079_29570925.rev     2498  3356 (491)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_29567079_2   2498 AAAAAAGCCATACTGTTCAAAGCAATCTACAGATTCAATGCAATCCCTAT 2547
                           i vi  v     vii    vii              i           
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_29567079_2   2548 CAAAATATCAAGGTCATTTTTCACAGAATTAGAAGAAATAATCTTGAAAT 2597
                               vi  ivvv v     ii     v v  vi iv i   i i    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_29567079_2   2598 TCAAATGGAACCAAAAAAAGAGCCCAC--TAGCCAAAGCAATCCTGAGCA 2645
                            v      -- viv  i ii    v--        i     i   -- 
  L1M4_orf2#LINE/    146 TCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--A 191

  chr1_29567079_2   2646 AAAGGGGAA-AAATCTGGAG--CTACCACACTACCTGACTTCAAAACACA 2692
                             ii   -   vi     --  --      v  ii i        vi 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACT--CACACTTCCCAATTTCAAAACTTA 239

  chr1_29567079_2   2693 TTACAAGGCTATAGTAACCAAAACAGCATGGTATTGGTATGAAAATAGAC 2742
                         i     i    i     i   i    ii     i   i  i ii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_29567079_2   2743 ACACAGACCAATGGAACAAAAT----AGTTCAGAAATAAATCCACATATT 2788
                          i i   i        i i   ----   i          i   i i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_29567079_2   2789 TGCAGGCAACTGATTTTTAATAAAGGTGCCAAGAACATACACTGGGGAAA 2838
                          iii v   i       ii i  i          v   v  v        
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_29567079_2   2839 GGACGCCCTCTTTAATAAATGTTACAGGGA-AATTGGATATCCATATGCA 2887
                          i iivi  i  i  i     v i v    -  i      ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_29567079_2   2888 AAAGAATGAGACTAGATTCCCTATCTCTCCCCATATACAAAAGTCAACTT 2937
                                  iii i  i-     i   v v            i i    i
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_29567079_2   2938 AAGATAGATTAAAGACTTAAATGTAAGACCCGAAGCTATTCAACTGCTAG 2987
                           i  i   i ?    i           v ii  i    vv    vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_29567079_2   2988 AAAAGAAAACATGTGGAAAACACTTCAAGACATTGTTTTAGTCAAAGATT 3037
                           --        iv ?iv  vv    iv   v   vv    v   v i  
  L1M4_orf2#LINE/    539 AA--GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_29567079_2   3038 TCTTAT-TAAGACCTCAAAAGCACAGACAACTATAACAAAAATAAACAAA 3086
                              v-  v   vi          ii    v v iv       i i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_29567079_2   3087 TGAGACTATATTAAACTAAAAAGCTTCTTCACAGCAAAGGAAACAATTGA 3136
                          vi    vi  i   v v    i   i vii vv       v  v  ii 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_29567079_2   3137 CAGACTGAAGAGCTAACCCG-----TTGAAGAAAATATTTGCAAATTATT 3181
                         v i v    i  vi     i----- v i                 i  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_29567079_2   3182 CACCCAACAAAAGACTAATATCTAGAATTTACAAAGAACTCGAACAACTC 3231
                         i i ii i  ii    vi    i     v  i         vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_29567079_2   3232 AACAATAAAAAAAAAGCAAATAATTCCATTAAAAAGTGGGTGAAGGACAT 3281
                           i        i ---       ii v   ?    i    ii     iv 
  L1M4_orf2#LINE/    787 AATAATAAAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_29567079_2   3282 GAGCAGATATTTCTCAAAATAAGACATACAAATGGCCAACGTGAATATTT 3331
                           ii   i       v   v    i              iiv v i  vv
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_29567079_2   3332 AAAAATGCTCAACAGCACTAGTCAT 3356
                            i          v  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (136 / 76)
Gap_init rate = 0.02 (13 / 863), avg. gap size = 2.15 (28 / 13)  


2270 22.92 11.94 2.41  chr1_29729515_29731850     1016  1844 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_29729515_2   1016 TGGAGAAATAAATATTATCCATGGGCCACATGATTTAATATTGATAAAAT 1065
                             i i   vvivv i i     iiiiv v  i         v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_29729515_2   1066 GGTCAATTCTCCCCAAATTGATAACTA--GGTTCAAGTCAATCCCAACCA 1113
                           -    v              --   -- i     vv       v i  
  L1M4_orf2#LINE/     51 GG-CAATACTCCCCAAATTGAT--CTACAGATTCAACGCAATCCCTATCA 97

  chr1_29729515_2   1114 AAAGTACAAGAGGCTTTTGATTTACCAGCTGAAATTTACAAACTCATAA- 1162
                            - v v  vv  i   --   ----  v      v    i  v  vv-
  L1M4_orf2#LINE/     98 AAA-TCCCAGCTGCCTTT--TTT----GCAGAAATTGACAAGCTGATCCT 140

  chr1_29729515_2   1163 AAAATTCATATGGAAATGCAAAAGACCTAGCATAGCAAAATAGAAAACTT 1212
                                              ii    i  v     v   --- v  ii 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA---ACAATCT 187

  chr1_29729515_2   1213 TGAAAAAGA-GAAAAAAAT----------ATAGTTGGCA---TCA----- 1243
                                  -   v   i ---------- i v  vv  ---   -----
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_29729515_2   1244 -------------------TCAAAACAAGGCGGTGTTGGCATAAATGTGA 1274
                         -------------------    i   iv i   ii        ivi ii
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_29729515_2   1275 ACAAAAAGATTTATATGGAACAGAATAGAGTGTTCAGAAATAGACCCATT 1324
                            v v    i- -      i     v   v  i        i      v
  L1M4_orf2#LINE/    288 ACATATAGATC-A-ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_29729515_2   1325 CATATAAGAACAACTGATTTCTGACAAAAGTGCAAAGGCCATT---TGCG 1371
                            v  v iv   i      ii     ii    v   i     ---  v 
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_29729515_2   1372 GAGAG------CTTTTCCAACAAATGATGCTGGCACAATTGGATGTTCAT 1415
                           i  ------      -        i      v    i     i?i  i
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTC-AACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_29729515_2   1416 ATGCAAAAAAGGAGAGCGTTCATTCATACCTTACACAATATA--AAAATT 1463
                                 i ivii  i- vv ii v     i    v     --      
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_29729515_2   1464 ----TAAAGTGGATCATAGACTTAAAAATAAATCCTAAAATTATAAAACT 1509
                         ----i   i       ?    i    vi   ivv      i         
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_29729515_2   1510 -TAAGAAGAAAACAGAGGAAAAAATCTTTGTTACCTTGGATTAGTCAAGG 1558
                         - v           v   ?iv       i  v       i    v   v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_29729515_2   1559 ATTTCTCAAATATAACACCAAAAGCATGACT--CATAAGACA---TTGAT 1603
                         i     i i    i            ii vi--  v    v --- v   
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_29729515_2   1604 AAATTTGGTTTTATAAAAATTAAAAA----TGTTTTTTGAAAGACACTGC 1649
                              v ii  i  v           ----   vi  ii  i      ii
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_29729515_2   1650 TAAGACAATTAAAATACAAGCCATAGATTGGGAGAA--TATTCTCAAAGC 1697
                         i    v i v    v    v   i   v        --    iv    v 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_29729515_2   1698 ATATATCTGATAAAATATTTACATCTAGGGCATGTAAATAACTCCCAAAA 1747
                                      iiv i  ii   i  iii  i    v     ii v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_29729515_2   1748 C-----------AAGCCA------CCAAT-AAAAAACAGGCAAAGGATTC 1779
                          -----------   v  ------     -?     ii           i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_29729515_2   1780 ------ACATATC----AAGAAGACATGTGAACG-TAAAGATGTCCAACA 1818
                         ------    v  ----       i  iii  i -iv  v v i---   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC---ACA 880

  chr1_29729515_2   1819 TGAA--GATGCTGGACATCTTTAGTCAT 1844
                             --      vi     v????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (108 / 78)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.61 (119 / 33)  


2455 22.59 8.40 5.45  chr1_29756400_29759477.rev     1709  2589 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_29756400_2   1709 GAAGAGATATTCCATGCTCATGGATTGAAAGACTCAATATT--------- 1749
                          i i      i     i          i      i      ---------
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_29756400_2   1750 -CAATTTTTTCCAACTTGATACATAGACTCTATGCAATAACAATCAAAAT 1798
                         -    vi ii    v     vi i   i  v i     vv v        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_29756400_2   1799 ----GCTACTAAAATATTTTATAAATATTGACAAACTGATTTTAAA-TTT 1843
                         ----   i i---- v    ii i v        i     ii    -  i
  L1M4_orf2#LINE/    102 CCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_29756400_2   1844 ATATAGAAAGGCAAATACGTATTTGCCTTTCTATATTGTATTGACTAGAA 1893
                             i    v    i---------------------- v i--- i    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAG----------------------GGAC---CCAGAA 172

  chr1_29756400_2   1894 TAGCCAATACAATACTGAAAAAGAACAAC---GTTGGAGGACTCACACAA 1940
                                v     vi          v   ---                vv
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_29756400_2   1941 TCCATTATCAAGACTAACTATAAAGCTACAGTAAACAAAACAGTG----- 1985
                         i   v v    i   v    i             v   i      -----
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_29756400_2   1986 -------AAAATTAGACACACAGATCAAGAGACCAGAATAGAGAGCCCAG 2028
                         -------  iiv      i i       vi  vi     v     i    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_29756400_2   2029 AAATAGACCCACACAAATATAATCAACTGGTTTTTTTACAAAGGAG--AA 2076
                              i     i   vv   ii    i  i    iv-    i  v --  
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCG-ACAAGGGTGCCAA 371

  chr1_29756400_2   2077 AAGCAATTAA------------------------AAATGGTGCTTAAACA 2102
                         i v  v i  ------------------------          vii   
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_29756400_2   2103 ATTGGACTTCCATATGCAAAAACAAAAGAAAACAAAAAAAAGAACCTAGG 2152
                          i    iv?   i        i----------------  v   vi i i
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAG----------------AATGAAGTTGGA 455

  chr1_29756400_2   2153 CACAGACCTTACATCTTTCACATAAATTCATTCAAAATTGGTGACAAATC 2202
                          v vv    i   i v vi   v     v i       v i v ? i i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_29756400_2   2203 TAAATATAAAATGC-AAAACAATAAAATTCCTAGAAGAAAATGTAGGAAG 2251
                              i   i -  -     v      i  i          ii    ?iv
  L1M4_orf2#LINE/    506 TAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_29756400_2   2252 AAATCTAGATGACCTTGGATTTTGCAATAAGTTTATAGTTACAACACCAA 2301
                               vvi         i  vv     iiv  iv   v  ii       
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_29756400_2   2302 AAGCATGAT--ACATGGGGGAAAACTGACAAGTTG-AGTTTATTAAAATT 2348
                              ii v--   vii ii    iv  i  i   - v  i  i      
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_29756400_2   2349 AAAAGCTTCTTCTG-TAAGAAAGACAC-ATTTTAAAAATGAAAATATAAG 2396
                             i   -  v  - vvi  i     -  ivvi   i      v i  v
  L1M4_orf2#LINE/    655 AAAAACTT-TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_29756400_2   2397 GCAGAGACTGACAGAACACATTTGAAAAACACATATCTGGTAAAAGATTT 2446
                         v  v   v  iv    v i     v   v  i       i   ii  i  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_29756400_2   2447 GTATCCAAAATATATGAAGAACTCTTAAAATTCAATAATAAAAAAACAA- 2495
                                i       i           v  i             i    -
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_29756400_2   2496 ---CCTAATTTAAAAAGGAGCAAAAGATCTGAACAGACTCTTCACAAAAA 2542
                         ---  i    ?     v i     i   i    i    vi   v v   i
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_29756400_2   2543 AAGGTA--------GCAACTAAGCACCTGAAAAAATGCTCAACATAATTT 2584
                            i  --------  v v       v      i           v ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_29756400_2   2585 GTCAT 2589
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.47 (116 / 79)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 5.81 (122 / 21)  


4033 17.76 4.73 0.23  chr1_29800420_29804175.rev     2399  3265 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_29800420_2   2399 GAAAAATATTCCATGTTCATGGATAAGAAGACTTAACATTGTTAAGATGT 2448
                             i    i              vi          i            v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_29800420_2   2449 CAATACTACCCAAAACAATCTACATATTCAATGCAACTCATATCAGAATT 2498
                                v      vii       v      i    ii v     i   i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_29800420_2   2499 CCAATGATGTGTTTTT--CAGAAATAGAAAAACTCATCCTAAAATTCATA 2546
                            -- v  iv     --       v  v  i  v               
  L1M4_orf2#LINE/    103 CCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_29800420_2   2547 CGGAATCTTAAGGGACCCC-AATAGCCAAAACAATCTTGAAAAAGAA--- 2592
                         i    vivi         v-                           ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_29800420_2   2593 CAAATTTGGAAGACT-ACA--------------AATGTACTACAAAACTA 2627
                             v     i    -   --------------  iv         i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_29800420_2   2628 CAGTAATCAAAACAGTATGGTAATGGTATAAAGACAGAAATATAGACCA- 2676
                                   i     i     v   i    i  i   v       i  -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_29800420_2   2677 TGGAGTAGAATGGAGAGCCCAGAAGTAAACCCTCACATACATGGTCAAAC 2726
                             i      v     i      i       vi    vi        vi
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_29800420_2   2727 GATTTTTGATAAGGGCACTAAGACCACTCAGTGGCAAAAGAACAGTCTT- 2775
                               i  i     ii i       i   i   vi      i      -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_29800420_2   2776 -CAACACATGGTGCTAGAAAAACTGGATATCCACATGAAAAAGAATGAAG 2824
                         -     v        i i v         ?       v            
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_29800420_2   2825 TTGGACCCACACTTAACACCATATACATAAATTAACTCAAAACAGATTAA 2874
                                 vi  i v            v              ii   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_29800420_2   2875 AGACCTAAATATAAGACTCAAAACAATATAACTCTTAGAAGAAAACATAT 2924
                                   i     vii     v   v                    v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_29800420_2   2925 GGCAAAATCTTCATGACATCAGATTTGACAATGATTTCTTGAATATGACA 2974
                          ?vv        i    v ii i  v i     i      ii        
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_29800420_2   2975 GCAAAGGCACAAGCAATATACAAAGAAATAGACAGATTAAACTTCATAAA 3024
                         v    i          i v vi  i       i i   ii       v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_29800420_2   3025 AATTTAGAA-TTTTCTGCATTAAAAGATACTGTCAACAGAGTAAAAAG-C 3072
                             v i  -    v   v i   i  i   i    v i   i     - 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_29800420_2   3073 AACCCGTAAAATGGGGGAAAATATT-GCAAAT----TATTTTATAAGGGA 3117
                              ii i      i         -      ----   i v        
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_29800420_2   3118 TTAATATCCAGAATATACAGAGAACTCCTAAAATGCAACAACAA-----C 3162
                         i vi             i i       i  v  iv   i  i  ----- 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_29800420_2   3163 AAA-AACTGGATTCAAAAATGGGCAAATTGCTTAAATAGAGACTTCTC-A 3210
                            -   ivi   ?             vvii  i      v i     - 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_29800420_2   3211 AAAAA---ATTCAAATAGCCAATAAGCAAATAAAAAGATGCTCAACATCA 3257
                           i  ---  v     i           v  i                  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_29800420_2   3258 TTAATCAT 3265
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.73 (95 / 55)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 2.69 (43 / 16)  


1380 26.75 7.58 1.60  chr1_29955216_29960187.rev        1   501 (4471)    L1M4_orf2#LINE/L1      245   775 (133)  

  chr1_29955216_2      1 AAGCTACAGTAATTAAGACAATGTAATACTGGCAAAAAGAAAGGCATATT 50
                                      i      i   ii        v  i  v  i     -
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT- 293

  chr1_29955216_2     51 ACATCAATGGAACAGGGTAGACAATCCAGAAATAAACTCATACAAATACA 100
                          v          i  ii v  v i             i      vv  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_29955216_2    101 ACCACTTCATCTTTGGCAAAGATACAAAAGCAATTCAATGGAGAAAGGAT 150
                         ii  v  v  i  i i   i i i v  ii v         i     i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_29955216_2    151 AATTTTTTT--TAAATGGTATTATAAAAATTGGTCATCCATAAACAATCA 198
                          i i    i--i       ii ivi v  i   vi ?   i vi   vvi
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_29955216_2    199 AACAAAATAACCTTGACTTAAACTTCACATTTTATACAAGA-CTAACTCA 247
                           ii  i ---- v   iivv  i     iiv       i -i       
  L1M4_orf2#LINE/    444 AATGAAGT----TGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_29955216_2    248 AAAATAGATTACAGA--TAAAGACAGAAAGCATAAAACTATACAATTTTT 295
                            - i   i ?   --    vii - i   -          v  i i  
  L1M4_orf2#LINE/    490 AAA-TGGATCAWAGACCTAAATGTA-AGAGC-TAAAACTATAAAACTCTT 536

  chr1_29955216_2    296 AGAATACAATGTCAG----ATTCTTAGTGAACTC---------------T 326
                             v v  ii vi ---- v    v    v  i--------------- 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_29955216_2    327 TC--------ACCACCAAAAGCATAGTCCATAAAATTAAAAACTGATAAA 368
                           --------iv           i iv v i    vv     iv      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_29955216_2    369 TTGGATGTCATCAAAAGTTAAAATTTTTGTTCTGCCAAAGAC--TATCAA 416
                              iv         v v    i      v  v v  i   --      
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_29955216_2    417 GACAATGAA--GATAAGCTA--GAGTGGAAGAAAATATTTGCAAACAACA 462
                           v i    --  i  v i --  i   i                iv i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_29955216_2    463 TATACAACAAAGAATTTGTACGCGAACTGTATAAGGAAC 501
                            vii i  i i i     iv ii v i     i    
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

Transitions / transversions = 1.81 (85 / 47)
Gap_init rate = 0.03 (14 / 531), avg. gap size = 3.29 (46 / 14)  

2300 25.00 1.45 2.47  chr1_29955216_29960187.rev      502  1189 (3783)    L1M4_orf2#LINE/L1      228   908 (0)  

  chr1_29955216_2    502 TCTCAAAACTCAGCAATAAGAAAACAAATAATTAAAAT-GTGGGGAAAGA 550
                          i        i - v i  iivv   i-    i  i i-   v  -----
  L1M4_orf2#LINE/    228 TTTCAAAACTTA-CTACAAAGCTACAG-TAATCAAGACAGTGTGG----- 270

  chr1_29955216_2    551 TATCTGA-AGAATGATAGACATACAGATCAATGGAACAGGCCAGAGAACT 599
                           -   i- v  v          i            i  iviv    iii
  L1M4_orf2#LINE/    271 TA-CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_29955216_2    600 CAGAAATAAACCTACAAAAATATGACCAACTGATTTTTGACAAGGGTACA 649
                                     i i v vv    ii   i       i         i v
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_29955216_2    650 AAAGTAATTCAATGAAGAAAAAATAGCCCTTTCAACAAATGTTGTTGAAA 699
                           iiiv        ii    i     i i            v  i  ii 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_29955216_2    700 CAATTGAACATTCATAGGCCAAAAAAAAAAAAAAAGAACTTCATGCTAAG 749
                            i  i i ?i  i v  --    i  vi  ivv i  ii ----  --
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGC--AAAAGAATGAAGTTGGACCCC----TA-- 461

  chr1_29955216_2    750 TCTCATATGTTATACAAAA-TTAACTGAAAATGATTCATGGGCTTAAGTG 798
                         i    i ivv         -      v      iv   ?i i i   i  
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_29955216_2    799 TAAAATACAAAGCTATAAAAGTTTTAGAACATAACATAGGGAAAAAATCT 848
                            i vvi   i        v i      v v        ?iv   -   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCT 560

  chr1_29955216_2    849 TCACAATCTAGGGCTAGGCA--GAGTTCTCAGACTTGAGACCAAGAGTAC 896
                           iii i  v   i      -- iv    i   iv   v     i  i  
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_29955216_2    897 AATTTGTAAAGGGAAAATTTGATGAATTGGATTTCATCAAAATTAAAAAC 946
                           vivii   i i    v v   i       i                  
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_29955216_2    947 TCTTGTTCTTCAAAAGACTTCATCGAAATGATGAAAAGACAAACTACAGA 996
                          i    v       i   vii   i i vii           v i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_29955216_2    997 GGAGGATAAAATATTTGCAAAACACATATCCAACAAAGGACTAATGTCTA 1046
                         ivi   v              v  i     ii i  i     vi i  i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_29955216_2   1047 GAATATATAAAGAACTCCCAAAACTCTACAGTTAAA---TAAACAATTCA 1093
                                          ii v     v i i v   ---i   i  ii  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_29955216_2   1094 ATTAGAAAACGGGCAAAAGATATGAAGAGATGTTTTATGAAAGCA--TAG 1141
                            ?i    i       i   v    v   ii   iviv    v --  v
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_29955216_2   1142 ACAGATGGCAAATAAGCACATGGAAAGATGCTCAACAGGACTGGATAT 1189
                            i     v            i              vv ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (112 / 56)
Gap_init rate = 0.02 (14 / 681), avg. gap size = 1.93 (27 / 14)  

1605 16.74 2.15 27.92  chr1_29955216_29960187.rev     3281  4487 (485)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr1_29955216_2   3281 CCGTATTCTTGG-TTGGGAGACTCCATATTGTAAATATGTCAATTTTTCC 3329
                           i i   v   -    i     iv       v  v   v    vi -  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT-CC 61

  chr1_29955216_2   3330 CCAAATTGATCAATAGATTCAATGCAATCACAGGCAAAATCCCCATAGTC 3379
                                    v i        i      v viv         viiv i 
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr1_29955216_2   3380 TTTTTTTTTTCAATAGAAATTGACAAATTTATTCTAAAATTCCTATGGAT 3429
                               ------ii            ii v  i         v      v
  L1M4_orf2#LINE/    112 TTTTTT------GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_29955216_2   3430 ATGCAAAGGACCTAGA-TGGCCAAAA---------AGAAGAAGAA-AAAA 3468
                               i     i   - i       --------- i        -   i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_29955216_2   3469 TTAGAGGTCTAACACTATCTGATTTCAAGACTTCTTATAAAACTTCAAAA 3518
                           i    v  v     vi ii       i    vi  i   i  v  iv 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_29955216_2   3519 ATTAAGGTAGTGTGGTGTTGATGGAAAGATAGTCAAATTAAGCAAAGGAA 3568
                           i   ii        ii  iiiv  i     v  v  vi v   v    
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_29955216_2   3569 CAGAAT--AGAGTCTAGAAATAGACCCACACAT--AGAGACAACTGATTT 3614
                         i     --      i       i     i    -- vi v   i      
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_29955216_2   3615 TTGATAAAGGTGCAAAGACAATTCACTGGGAAAA-AATAGTCTTTTCAAC 3663
                          i  i  i     v     v     v    i   -               
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_29955216_2   3664 AA-TTATGCTGAAGCAACCGGATGTCTATGTGCAAAAATATGAATCTTGG 3712
                           - vi     iii    i    i? i ii       ----    -----
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA----GAAT----- 446

  chr1_29955216_2   3713 CCAGGCACTTTGGCTAACACATGTAATCCTAGCACTTTTGGAGGCTGAGA 3762
                         --------------------------------------------------
  L1M4_orf2#LINE/    447 -------------------------------------------------- 446

  chr1_29955216_2   3763 TGGGAAGATTTCTTGAGCCAAGGAGTTCAATACCAGCCTGAGCAACATGG 3812
                         ---    -------------------------------------------
  L1M4_orf2#LINE/    447 ---GAAG------------------------------------------- 450

  chr1_29955216_2   3813 CAAAACCCTGTCTGTACCAAAAAAAAAAAAAACCACACACACACACACAA 3862
                         --------------------------------------------------
  L1M4_orf2#LINE/    451 -------------------------------------------------- 450

  chr1_29955216_2   3863 AAATTGGCCCAGCCTGGTGGCATGCACCTGTAGTCCCAGCTACTTGGTAG 3912
                         -------------------------------------------    ---
  L1M4_orf2#LINE/    451 -------------------------------------------TTGG--- 454

  chr1_29955216_2   3913 GCAGAGGTGGGAGGATCACTGGAGCCCAGAAGGTCAAGGTTGCAGTGAGC 3962
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chr1_29955216_2   3963 CATGATCACACCACTGCACTTCGACCTGGGTGACAGAATGACACCCTGTC 4012
                         ------------------------------------------    i---
  L1M4_orf2#LINE/    455 ------------------------------------------ACCCC--- 459

  chr1_29955216_2   4013 AAAAAAATAATGAAAAGAATCTTGATTCATACCTCCCACCATTTACAAAA 4062
                         -----------------------------      v      v       
  L1M4_orf2#LINE/    460 -----------------------------TACCTCACACCATATACAAAA 480

  chr1_29955216_2   4063 ATTAACTCCAAATTTATTATAGGACTAAATACAAAACCTAAAACCATGAA 4112
                                 v    vv  i ?  iv      ii  i v       i  i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_29955216_2   4113 ACTTCTAGAAAAAAAC-CATGAGAAAATATATGTGACCTTGGGTTAAGCA 4161
                            ii     i     -i v ? v    v vi              i   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_29955216_2   4162 AAGGTTTGCTAAATGCAACACCAAGAGCACAACCA-TACAAGAAAAAATT 4210
                          v     vi  i  iii       i       v  -i v          v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_29955216_2   4211 AAAGAATTGGACTCAATCAAAATTTAAAACTTCTGCTCTTCAAAAAA-AC 4259
                         i vi         iv         v       i  iv       ii -  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_29955216_2   4260 AA-AAGGAGAGAGAGAGAGAGAAAAGCCACAGACTGGGAGAAAATACTCA 4308
                         v -v i  i  v  i ---   v  v       v            i ii
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAA---AGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_29955216_2   4309 CAAACCATATATTTAATAAAGGCCTTGTATTCATAATATGTACA-AATTT 4357
                             i       i i    i  v       i  v     i  v -  i i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_29955216_2   4358 TGAAAACTCAATAATGAGAAGAATAGCAATTCAAT-AAAAAGTGACCAAA 4406
                          v v           i i    vv ii  ii    -?    i  iv    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_29955216_2   4407 G-ATTTGAACAGAAACTTTACTAAAAAATACA-ACAAAGAAGACAAGTAA 4454
                          -       i   v i  iv i   i  v i -     v-- i v i   
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT--GGCCAATAA 875

  chr1_29955216_2   4455 GTAGACGAAAAGACATTCATTGTCATTAGACAT 4487
                          i v i       iii   vii   ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (124 / 74)
Gap_init rate = 0.03 (25 / 896), avg. gap size = 14.52 (363 / 25)  


1226 21.15 3.82 18.16  chr1_30014863_30018609     1825  2661 (1086)    L1M4_orf2#LINE/L1      173   889 (19)  

  chr1_30014863_3   1825 TAACTAAGACAATGTTAAAAAA--AGAATAAAGTGGGAAAA-TCACTATA 1871
                           i i  i     v  i     --    i     v   ii -    --- 
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC---A 219

  chr1_30014863_3   1872 CTTGACA-TT---AGGCTTACTGTATACCTAGGGTAATCAAGGCAGCATG 1917
                            vv  -  --- ii      ii v v   vi         i   ii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_30014863_3   1918 GTGTCGG--TGAACATATACACAAATATCAGTGAAACAAAATAGAGAACC 1965
                           iii  -- i iv   v   i v v    i  i  i i   v    ii 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_30014863_3   1966 CAGATATAGACCCATGCATATATATCCAACTGATTTCTGACAAAAGTACA 2015
                             v   i      i   v   ivi   i      ii     ii  i v
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_30014863_3   2016 AAAATAATTCAATAAGAAACATAGTTTTCTGGGTGAGGAGGCATGCACCT 2065
                           i iv       ii i  -------------------------------
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAA------------------------------- 388

  chr1_30014863_3   2066 GTGGTCTCAGCTACTCCGAGTCAGCCATGATTGCACCACTGCACTCCAGC 2115
                         --------------------------------------------------
  L1M4_orf2#LINE/    389 -------------------------------------------------- 388

  chr1_30014863_3   2116 CTGGGCGACAGAGTGAGGCTGTGTCTCAAAAGAAGGAAGAAAGTTTTTTA 2165
                         ---------   i ---------------------------   i    v
  L1M4_orf2#LINE/    389 ---------AGAAT---------------------------AGTCTTTTC 402

  chr1_30014863_3   2166 AACAAATGGTGCTGGAGAAATTGGACATCAATAAGCCAAATAGGTAAA-- 2213
                                        iiv  i    i ? v i v  v   v i- i  --
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGT 451

  chr1_30014863_3   2214 CAAACCTCAACCTAA-ACCTCTAATGGATCCA----TTAACTCAAAATGG 2258
                         iii   i v    v -   ----  --  v  ----              
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACC----AT--ATACAAAAATTAACTCAAAATGG 495

  chr1_30014863_3   2259 ATCACAGACTTAAATGTGAAACATAAAACTATAAAAGTTTTAGGAAAAAA 2308
                             ?    i       i i vv             v i    i i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_30014863_3   2309 AATAGAAGAAAATCCTCTGGACCTAGGACCAGGTGAAAAGGTCAAAAAGA 2358
                         v    i? v     i  vv     v  iii   i--  v   ivvvv   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC--AATGGTTTCTTAGA 593

  chr1_30014863_3   2359 TTTGACATCAAAAGAACAATCCATAAAAGGAAAATTTGATAAACTGGACA 2408
                          v     i      v    v v i     i    v v      i     v
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_30014863_3   2409 TCATCAAT-TTAAAAACTTTTACTCTGCAAAAGAT-TGGTGGAAAGGATT 2456
                                v-            iiv  v    i  i-ivi vi i iii v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_30014863_3   2457 AAAAGACAAACCTCTGACTGGGAGAAAGTATTTGCAAAGCACTCATCTGA 2506
                                  v  v v  v         i          v  ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_30014863_3   2507 CAAAGGGCTTTTATCTAACCTGTAAATAGAATTCTCAAAACTCAAGAGTG 2556
                         i  i  i   v    i ivv i  v v    i   i v       v i -
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT- 792

  chr1_30014863_3   2557 TAAAAAAAAATAATAATAATCCAAATAAATCTAGTTTTAAAAA-GGGTGA 2605
                         ---     i i  --    i    -----------  ?     -   ii 
  L1M4_orf2#LINE/    793 ---AAAAAGACAA--ATAACCCAA-----------TTWAAAAATGGGCAA 826

  chr1_30014863_3   2606 AGGGCATTGAG-AGAC-T---------GAA--TATACAAATGGACAATGG 2642
                            ii-    i-    - ---------   --           v    --
  L1M4_orf2#LINE/    827 AGGAT-TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT-- 873

  chr1_30014863_3   2643 CCAGGCCATATGTAAAAAT 2661
                         -- i  - i   v   i  
  L1M4_orf2#LINE/    874 --AAGC-ACATGAAAAGAT 889

Transitions / transversions = 1.58 (106 / 67)
Gap_init rate = 0.04 (28 / 717), avg. gap size = 6.57 (184 / 28)  

 255 10.64 0.00 0.00  chr1_30014863_30018609     3208  3254 (493)    L1M4_orf2#LINE/L1      862   908 (0)  

  chr1_30014863_3   3208 CAGATGAAAAATAAGCACATGAAAAGATGTTCAACATCATCAGCCAT 3254
                           i   ivv                    i         ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (3 / 2)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.00 (0 / 0)  


2519 24.28 8.76 1.25  chr1_30119285_30121072.rev      502  1300 (488)    L1M4_orf2#LINE/L1       50   908 (0)  

  chr1_30119285_3    502 TGTCAGTTTCCCCCTAATTGTTCTATAGATTCACTTCAATCTCAATCAGA 551
                           v  i vii    v     v    i       viv     i v    i 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_30119285_3    552 AACCCAGCAGTCTGCTTTGCAGAAATTGAGAAAAACTG-TTCTAATATCT 600
                          v      v i  vi              v  i--   - i    v  ii
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr1_30119285_3    601 ATATGTAAATGTAAG--ACCTAGAATAGCTAAGACAATTTT-AAACACAA 647
                              v     i   --   i        i  i     i  -   v v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_30119285_3    648 GAACAAAGTTGAAAGACTAACAGTACTTAATTTCAAGATTTATTCTAAAA 697
                                    i i    v   v v ii        i i   i vi   i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_30119285_3    698 CTGCATTA-TCAAGACAATGTGCTATTGGCATCAAGAAT-GACAAATAGA 745
                           i  v  -        i    v  i      -   i  -    v     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGA 296

  chr1_30119285_3    746 CCAGTGAAATAGAAT--AGAGTCCAGAAAGAGACCCACACATATACAGAC 793
                         i  i  i        --            v i     i    v  ii v 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_30119285_3    794 ACCTGATTTTTTACAATGAAGTAAAAATAATTCTGTTCAAAAGAGATAGG 843
                          vi       iv    v iv iv  i iv    vi vvii  iii    -
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG- 395

  chr1_30119285_3    844 GCTTTTTTTCAACAACTGGCTCTGGGACCATTGGATATCCATATTCCAAC 893
                         --- i          v   iv       v i      ?   i  v v  v
  L1M4_orf2#LINE/    396 ---TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_30119285_3    894 AAACAAAGATGGACTT-TGTTCCACAC----------------------- 919
                         i  ii   v     ii- iiii     -----------------------
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_30119285_3    920 -------------TAAATGTAAAACCTAAAACCATAAAGCATCT--GAGG 954
                         -------------         i v       i     i -   --  i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAG 541

  chr1_30119285_3    955 AAAGCACAGTAGAAAAACTTTTATGAGATTGGTTTAAGCAAAGATTTCTT 1004
                            i  i  v? v   v   i-i   vv    v   i    v i      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_30119285_3   1005 AGATATAACATCAAAAACACAATTCATAAAGGAACAAACTGATAAAACAG 1054
                               i   i     i     viv i   i   v   iv      vii 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_30119285_3   1055 A--TCATCAAAAT-AAAAATGTCTGCTCTTTGAAAGATACTTTTAAAGAG 1101
                          --          -     iv i  iv   ii  i  i   v i  -  i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA-GAA 689

  chr1_30119285_3   1102 AATGGAAAGATAAGCCACAGACTGAAAGAAAACGTTTGTAAATCACATGT 1151
                          i  i     i  v       v  ii      ii    i      i  i 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_30119285_3   1152 CTGCTAAAAGACATGTATTCATA-TATATAAA------TCAAAACCTGAT 1194
                            v   ii   v     i  v -        ------ i v   iii  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_30119285_3   1195 A-TAAGAAAACAGA-----CAATTTAAA----GGCAAAAGCTTTCAACAA 1234
                          -   i  i   i -----     ?   ----      i v   v  i i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_30119285_3   1235 ATAT--CATCAAAGT-GATATATGGATGGCAAATAAGCCCATGAAAATAT 1281
                          i  -- vi     v-      iii     v       v        v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_30119285_3   1282 GCTCAACAACTATAGTCAT 1300
                                 v v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (119 / 72)
Gap_init rate = 0.03 (24 / 859), avg. gap size = 3.33 (80 / 24)  


3160 26.36 1.44 0.89  chr1_30138095_30140458      969  1871 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_30138095_3    969 TGGAAGGACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 1018
                              i  i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_30138095_3   1019 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCACCAAGC 1068
                            v     v     iv i  i  i        i  v     i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_30138095_3   1069 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 1116
                          v   iivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_30138095_3   1117 TATGGAACCAAAAAAAGAGCCCACATT-GCCAAGTCAATCCTAAGCCAAA 1165
                                -- viv  i ii    v v -     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_30138095_3   1166 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 1215
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_30138095_3   1216 GTTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 1265
                          i        i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_30138095_3   1266 CCACTGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATACCTAAAA 1313
                         i  v     i    i--    i  --        vv   i i ii  vii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_30138095_3   1314 CTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 1363
                         ii vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_30138095_3   1364 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 1413
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_30138095_3   1414 CTGAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAGGATG 1463
                         v    ii    i    v   i     v     v        i   ii   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_30138095_3   1464 GATTAAAGATTTAAATGTTAGACCTAAAAACCATAAAAACCCTAGAAGAA 1513
                            i ?   ii       v   v      - i      vi i        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAA 543

  chr1_30138095_3   1514 AACCTAGGCA-ATACCATTCAGGATATAGGCATGGGCAAGGACTTCATGT 1562
                            v    ?i- v i -   iv  iv v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_30138095_3   1563 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 1612
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_30138095_3   1613 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 1662
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_30138095_3   1663 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATTTG 1712
                            v  i     i                 v       vii ivi  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_30138095_3   1713 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAG 1762
                          i  i  i  vi          v  i         vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_30138095_3   1763 AAAAAAACAAACAACCCCATCAACAAGTGGACGAAGGATATGAACAGACA 1812
                              i     i     v  i? v  i   i i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_30138095_3   1813 CTTCTCAAAAGAAGACATTTA--TG-----CAGACACATGAAAAAATGCT 1855
                         i     v        i  vi --  -----i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_30138095_3   1856 CATCATCACTGGCCAT 1871
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


1619 21.52 1.82 0.00  chr1_30161616_30164657.rev      923  1252 (1790)    L1M4_orf2#LINE/L1        1   336 (572)  

  chr1_30161616_3    923 TGAAAAAACATTCCATATATGTGTATTAGAAAACTCAATATTGTTAAGAT 972
                           i   i i  i    i vii  v   i   i   i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_30161616_3    973 GGCGATACTTTC-AAATTGATCTGTTGATTAACTACAATCTCTGTTAGCA 1021
                            i     ii -          iiv    v vii     i  i i iv 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_30161616_3   1022 TCTCAGCTGACTTCTTTGTAACAATTAACAAGCTGATCCTAGAATACATG 1071
                           i      v   i    i iv    i              i   v   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_30161616_3   1072 TGGAATTGCAAGTGGCCCAGAGTAGCCAAAACAATCTTGGAAAAGAGGAA 1121
                              v      v i      i                 i      i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_30161616_3   1122 CAA-GCAGGAGAACTGACATTTTCTGATGTTAAAACTTATTACATTACAA 1170
                            - iv    i   v   i  i ii  v i        i    vvi v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_30161616_3   1171 TGGTAATAAAGACAGCATGGAACTGGCATAAGAA----CATATAGATTAA 1216
                         ii     v       ii   v           i ----         i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_30161616_3   1217 TGGAAGAGAATTGAGAATCCAGCAATAAACTGATAC 1252
                              v          i     v       iv    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

Transitions / transversions = 2.23 (49 / 22)
Gap_init rate = 0.01 (3 / 336), avg. gap size = 2.00 (6 / 3)  

2027 17.08 2.32 11.61  chr1_30161616_30164657.rev     1609  2211 (831)    L1M4_orf2#LINE/L1      325   871 (37)  

  chr1_30161616_3   1609 ATAAACCCATGTGTCTATAGTCAACTAATTTCTGACAAGCATGCTGAGAA 1658
                                   iii i   i     i i    ii      vi   ii   v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_30161616_3   1659 AAATCAATGGGGAAAAGAACTGT-TTTCCAACAAATGGTACTATGACAAC 1707
                         v v            -   iv  -   i           i  iv      
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_30161616_3   1708 TGGATAGCCATCTGCAAAGGAATGAAGTTGAACTTGTACCCTAGGCTATA 1757
                               ?   iv      i           i  iiv    ii vi i   
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_30161616_3   1758 TATGAAAAATAATTCAAAATGGCTCACGCAT---AAT-TAAGAGCTAAAC 1803
                           ii    v   i         v   ?iv i---   -           v
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_30161616_3   1804 CTATACAACTCTTAGAAGAATACATACAGGTAAATCCACATGACCTCAGA 1853
                              v              v     vi?       iv i      ii i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_30161616_3   1854 TTTGGCAATGAATTCTTAGATATGACACCTAAAGCATGAGTTATTAAAGC 1903
                           v       iv                 v      ii  iv iv    v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_30161616_3   1904 AAAA-TAGGTAAAC--AACTCAATAAAAATTAAAAACATTTGTACATCAA 1950
                             -   i    i--i   iv  v            v     i v    
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_30161616_3   1951 GGGATACTGCCAAGAAACTTAAAAGACAAGCCAAAGACTGGGGCAATGTG 2000
                         i   i   ii       v v         v   v   v    iv  vi i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_30161616_3   2001 TTTGCTAAATGTATATCTTATGTGTTTGCTAAACATATATCTATGACAGA 2050
                              -    -----------------------         ------  
  L1M4_orf2#LINE/    724 TTTGC-AAAT-----------------------CATATATCT------GA 743

  chr1_30161616_3   2051 TATATATATATATTATATATATATATGACAGATTTGCTAAACATATGTCT 2100
                           ------------------------- vi  i   --------- i  -
  L1M4_orf2#LINE/    744 TA-------------------------AGGGACTTG---------TATC- 758

  chr1_30161616_3   2101 AGGACAGATTATATAAA-AACTCTTATAACTCAACAATAAAAATACAAAT 2149
                         ----    v        -        i       i        v      
  L1M4_orf2#LINE/    759 ----CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_30161616_3   2150 AATTCAATT--AAAATGGGCAAAGGATTTGAATATATATTTATCCAAAGA 2197
                           ii     --                       v i    v        
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_30161616_3   2198 AGATATACA---GGCCA 2211
                                  ---     
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCA 871

Transitions / transversions = 1.56 (61 / 39)
Gap_init rate = 0.03 (15 / 547), avg. gap size = 5.60 (84 / 15)  

 330 11.86 0.00 0.00  chr1_30161616_30164657.rev     2493  2551 (491)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_30161616_3   2493 AAAAAAGATATACAAATAGCCAGTAAGCACATGAATAGGTGCCCCACATC 2542
                            i             i    i            v  i   i v     
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_30161616_3   2543 ATTAGTCAT 2551
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


4206 19.26 1.75 2.41  chr1_30166968_30169431     1058  1971 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_30166968_3   1058 TGGAAAGATACCCCATGTTCATAGATAGGAATGCTTAACATTGTTTAGAT 1107
                                   i           i   v    vi     i      v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_30166968_3   1108 GTCAATGCTGCTCAACTTGATCTACAGATTTAATGCAATCCCCAACCAAA 1157
                          v    i  v i   v              i  i        i v v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_30166968_3   1158 TCCTAATGATTAAGTGATTTTTTTTTTTTTGTCGAAATAGAAAAACTCAT 1207
                            i ii-------  ------ii       iv     v  v  i  v  
  L1M4_orf2#LINE/    101 TCCCAGC-------TG------CCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chr1_30166968_3   1208 CCTGAAATTTGTGTGGAATCTCAAGGAACTCCAAATAGCCAAAAACAATC 1257
                            i     ii i     viv     i  i vi           -     
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATC 186

  chr1_30166968_3   1258 TTGAAAAAGAAGAATGAAGCTGGAAGTCTCACACTTTCTGATTTCAAAAA 1307
                                       ii   i    i v         i ii         -
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA- 235

  chr1_30166968_3   1308 CTTATTACAAAGTTACAGTAATAAAAACAGTGTGGTTTTGGCAAAAAGAC 1357
                             i       i         v  i          vi     v  i  i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_30166968_3   1358 AGACATAGAGGCCAATGATGTACAACAGAGGGCCTAGAAATAAGCCCTCA 1407
                                v  ii     ivi  v  iv   i i i        i   vi 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_30166968_3   1408 CATATATGGTTAAATGATTT-CAACAATAGTGCCAAGACCATTCAATGAG 1456
                            v      i  v      - i    vi                   i 
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_30166968_3   1457 GAAAGGACAACCTTTTCAACAAATGGCATTGGGAAAACTGGATATCCACA 1506
                              i i ii               iii     v         ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_30166968_3   1507 TGCAAAATAATTAAGTAGGACTCTTATCTTATACTGTATATAAAAATTAA 1556
                                v   v    v    i i  i  i i  ii    i         
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_30166968_3   1557 TTTAACATGGACCAAAGACTGAAATGTAAGAGCTAAAACTGTAAAACCCT 1606
                         i i  v     i  ?    iv                   i      i  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_30166968_3   1607 TAGAAAAAAATACAGGGAAAAATCTTTATGACATTGGATTTGGCAATGAC 1656
                              i    i i   ?iv       ii    v    i  v       ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_30166968_3   1657 TTCTTGGAAAGGACACCAACAACATAGATGAAAAATGGAAAAAAATA-AT 1705
                              i  v v        v i  i iiii v   v --        -  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG--AAAAAATAGAT 633

  chr1_30166968_3   1706 ACATTTAGCCTCATTTTTCCA---TTAAAATCTTTTGTGTATCAAAGGAC 1752
                          v   vii i    -----  ---      v        iv         
  L1M4_orf2#LINE/    634 AAATTGGACTTCAT-----CAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_30166968_3   1753 ACAATCAACAAAGTAAAAAGGCAATCCACAGAATGGAAGGAAATATTTGC 1802
                           v     v     i     i   i           i  i          
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_30166968_3   1803 AAATTA-ATTTCTGATATGGGAATAATATCCAGATTACATAAAGAACACC 1851
                             i -  v       v    v vi        v  i         v i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_30166968_3   1852 TACAATTCAACAATAGCAA--CAA------CA--TTAAAAATGAGCAAAG 1891
                              i    i    iv  --   ------  -- ?       i      
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_30166968_3   1892 GACTTAAATATACTTTTCCCCAAATAAGATATATGAGTGGTTAATAAGCA 1941
                           i  i    v  v    i     v        ii i   ii        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_30166968_3   1942 CATGAAAAAAGGCTCAACATCACTATCACT 1971
                                 i v           ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (114 / 58)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.92 (38 / 13)  


 859 31.00 13.63 4.22  chr1_30300243_30302169      606  1434 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_30300243_3    606 GGAGAGATATACCCTGCTAATCGGTAGGAAGGACTAATATTCTAAAGATG 655
                            i      v  v  i v  v i v     ivi       v v      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_30300243_3    656 TCAATTATCCCCATGCTAATCCATAAACACAATACAATAATAATTTTTTA 705
                         v    vv      vii i   i i i iv   ii    v----ii v i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC----CCTATCA 97

  chr1_30300243_3    706 AAATCCCAACAGAACTTCAAGT-GAACATGATAGGCTGATTCAAAAGTTT 754
                                 i v vvi  ivv i-   vv   i i      i v   i  i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_30300243_3    755 -----------CCAGGGA-------------AAATAATTTTGAA------ 774
                         ----------- v     -------------   i   i     ------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_30300243_3    775 GGGCAA----GGACAACTTACCTTTCCCAACACCAAGATTTATGATTAAG 820
                          ii   ----   vi   i  vi       ivi   i i   iv iv   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_30300243_3    821 TTCTAGCATTTTCGATTGTGGTTGTTAGCGTTGTACAAGG-TAAA----T 865
                         i vi  i v ivv  iv   --  v  vi -- i i    -  i ---- 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTG--TGGTACTG--GCATAAGGATAGACATAT 293

  chr1_30300243_3    866 AGGCCACTGGA--------GAAA--CCAGACACAGACTCAGATGGACACA 905
                           ii  v    --------  i --     v i i  i  v iivvi ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_30300243_3    906 GAAACTCCAC--ATATGTGGGGGAGGTGCTGCAAAGAGGA------GGGG 947
                          ----  v i--  v vi iviii     i---    vv ------    
  L1M4_orf2#LINE/    344 G----TCAATTGATTTTCGACAAGGGTGCC---AAGACCATTCAATGGGG 386

  chr1_30300243_3    948 AGAGG-TGGATGACTCAACAAATAGCGCTAGGA-AATTGG----CTAGAT 991
                          i  i- i vivvi         i i   i   -  i   ---- i v  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_30300243_3    992 GTTGAGGG--GGGGTAAAAT-------TCACATCTTACATAGAAAATAAC 1032
                          ivi i i-- ii  vii i-------     i v  i i i   v    
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_30300243_3   1033 TGTATAAAGTGAAACTCTACTGCAGAAAACCAAG---AAAAAATAAAACT 1079
                          ---i   i  i --  ------ ? i v i  i---  i iv       
  L1M4_orf2#LINE/    487 T---CAAAATGGA--TC------AWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_30300243_3   1080 TTAAAACAATTAGAA-AAATTA-AGAAAAAAATCTTTATGACCATGAAGT 1127
                         v      vv      -   vi -  i?iv       ii     v  iiv 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_30300243_3   1128 GGAAAGTAATTTTTTACATAAAACACACAAAAGCACAAACTGTTAAGGGA 1177
                         i iv i ii   i   v   vi    -           i viiv  i i 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACAC-CAAAAGCACAAGCAACAAAAGAA 624

  chr1_30300243_3   1178 GAGATTGATCAAATTG-ACTACA-----GTGGAACGCTTTTCTATGATAA 1221
                         i i  v   -      -   v  -----i vi  vi     v iivvi  
  L1M4_orf2#LINE/    625 AAAATAGAT-AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_30300243_3   1222 AAGATACCATAATGAAAGTTTTTTAAAAAGGCAAGACACGGACTAGAAAA 1271
                          i  i  i  v v      -----i     i   vv   i  v i i i 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGT-----GAAAAGACAACCCACAGAATGGGAGA 718

  chr1_30300243_3   1272 AGATATTGGCCATGCATATAATCAATAAAGAACTATCCTTCAGAATATGT 1321
                          i     v  v vv      viii    i i   vviv i        i 
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_30300243_3   1322 AAAGAATTCCTA-AACATTATT--TAAAAATGACAAACTGCCCAACAGAA 1368
                               i  i  -   - i v --      -      ivi     iv?  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAAC-TCAATAATAAAAA-GACAAATAACCCAATTWAA 816

  chr1_30300243_3   1369 AAATGTACA-----------------------CAGAGAAAACATGCA--T 1393
                              vi  -----------------------  i    i i  i  -- 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_30300243_3   1394 GGCCAATAATCAAAAGAGAC-ATGTTCAACGTTACTAGAAAC 1434
                                  v  v v  i v-   i     i i ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (157 / 97)
Gap_init rate = 0.04 (39 / 907), avg. gap size = 3.79 (148 / 39)  


 465 22.38 7.62 7.14  chr1_30485245_30487635.rev      650   859 (1532)    L1M4_orf2#LINE/L1        4   214 (694)  

  chr1_30485245_3    650 AAACATATTGCAT--TCGTGGATTAAAAGATTCAATATTATTAACATGTC 697
                            v    iv   --  i      ii    i i      i    v   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_30485245_3    698 AATCCTACCCCAAGTGACCAATAAATTTGACACACATGCACA-CAAAACC 746
                            v  v   v  v   i v i i   ii  i  -  v vi -     i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCA-ATCCCTATCAAAATC 102

  chr1_30485245_3    747 CCAAGCAGGATTTTTTTTTTTTTTTTGGTATAAATCACCAAGCTAGTTCT 796
                            -  v ----------ii       -i v    iiv      ii i  
  L1M4_orf2#LINE/    103 CCA-GCTG----------CCTTTTTTG-CAGAAATTGACAAGCTGATCCT 140

  chr1_30485245_3    797 AAAATTACACAT--AAATGCAATAAAACTACACTAGCCAAAACATTCATT 844
                               -  i  --        vii v i v v           v  -  
  L1M4_orf2#LINE/    141 AAAATT-CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-TT 188

  chr1_30485245_3    845 -------AATAAC----TTGGAGGAC 859
                         -------  v   ----         
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGAC 214

Transitions / transversions = 1.35 (27 / 20)
Gap_init rate = 0.05 (11 / 211), avg. gap size = 2.82 (31 / 11)  

1386 22.10 7.95 11.05  chr1_30485245_30487635.rev     1159  1900 (491)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr1_30485245_3   1159 AAATAAATAAATAAACTTGGAGGACATATAATACCTGACTTCAAGACT-- 1206
                            v i vi  i   v         vi i v v  ii i     i   --
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_30485245_3   1207 --ATGCAGGTATGATAATCAAGGCAAAGT-----------AAGAAGAGAC 1243
                         -- iiv  v  iii        i  iv  -----------   i v    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_30485245_3   1244 AAGTGGATTAATGGAACAGAGTAGAGAGGCACCAAGTAGACCCACACATA 1293
                          vi i   i       i   i v     v vvv  i  i     i    v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_30485245_3   1294 TAT-----ATTG----TC--TAAGA---CTAAGATATTTCAGTGGGGGAA 1329
                            -----    ----  --i   i--- i    ivv    i     -  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AA 388

  chr1_30485245_3   1330 AGGACTGTCTTTTCAATAAATGGTGCTGTAACAGCTGAATATCCACATGG 1379
                           i iv          i           vi   i   i   ?       v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_30485245_3   1380 AAAAATTTTACATTTAGACCCTTACCTCACACCTTACATAGAAATGAATT 1429
                             ivv v - v  i     i           v  i i i    v  i 
  L1M4_orf2#LINE/    439 AAAAGAATGA-AGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_30485245_3   1430 TGACATAAAACATAGACCTAAACATAAAAACTAAAG--ATAA-------- 1469
                         ii v  ii v  ?         ii   i i     i--    --------
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_30485245_3   1470 GAGAAAAATATTGAATATATATCTTCATAATTTGGAAGTAGATCAAGATT 1519
                           ii    i  v i?-i  v      i i ii v iiv   iiv v i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_30485245_3   1520 TCTTAAGACACTCACAT-AAAAGCAGTAACCATGATTACCATGAAAGAAA 1568
                              -  i - v   i-       -i  v  -------- ii       
  L1M4_orf2#LINE/    587 TCTTA-GATA-TGACACCAAAAGCA-CAAGCA--------ACAAAAGAAA 625

  chr1_30485245_3   1569 AAACCATAAACAATACTAATTTGGACTT-ATCAACAT--AAAAGTTTTCT 1615
                            ---  i ------   v        -     v  --    v    v 
  L1M4_orf2#LINE/    626 AAA---TAGA------TAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_30485245_3   1616 GCTTTTCAAATGATATCATTAAAGAACCTAGCGCCTATTATATCAAGTGT 1665
                             --    v  i i------------------------       ---
  L1M4_orf2#LINE/    667 GCTT--CAAAGGACAC------------------------TATCAAG--- 687

  chr1_30485245_3   1666 ATAATGTATTATACACTTGAAAATTTTTTTAAAAAGAAAATGTAAACCAC 1715
                         -------------------   i ------i      v  i-----    
  L1M4_orf2#LINE/    688 -------------------AAAGT------GAAAAGACAAC-----CCAC 707

  chr1_30485245_3   1716 AAATTTGGA-AAAATAGCCATAACACATATATCTGACAAAGGACTTGTAC 1764
                          i v v   -      viiii  vv           i  i         i
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_30485245_3   1765 CCAGAATATGTAAAGAATCCCTACAAGTTAATCATGAAAAGA-AAA--AC 1811
                                  i       ii i     v i   v  i      -   --  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_30485245_3   1812 TCAAT--AAAACTGGGCAAAATATTTCAACATACACTGCACATTAGAAGA 1859
                         i    --    v        iv    v  i v   i v v vvv      
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_30485245_3   1860 GATACAAA----------ACACGTGAAAAACTGCTCAACATTATTAGTCA 1899
                         v       ----------i   i      iv          i ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_30485245_3   1900 G 1900
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.60 (99 / 62)
Gap_init rate = 0.04 (30 / 719), avg. gap size = 4.70 (141 / 30)  


3393 23.42 3.38 1.13  chr1_30570890_30575091     2824  3711 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_30570890_3   2824 TGAAAAGTTATCCCATGCTCATGGATTGAAAGAATTAAT--TGTTAAAAT 2871
                           i    v         i          i    v     --      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_30570890_3   2872 GTCAATACTATTCAAAGTGATCTACAAACTCATTGCAATCACTACCAAAA 2921
                          v       vii    v         i i   vi      v   i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_30570890_3   2922 TACCAATAACATTCTTCACAGAAATAGAAAAA--AATTACTAAAATTTGT 2969
                          v   iivi v  i  ii       v  v  i--i  i-        ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-CTAAAATTCAT 149

  chr1_30570890_3   2970 AAAGGACCACAAAAGACTCCAAATAACCAAAGCAATCGTAAGAAA-AAGA 3018
                          vi i vii   ii   i vi    i     i     v i i   -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_30570890_3   3019 ACAAAGCTGGAGGCATCAC-CTACCTGACTTCCAAATATACTACAAAGCC 3067
                               i      vv    -  v  ii i   v   iv           i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_30570890_3   3068 ATAGTAACCTAAACAGCATGGTACTGGCAGGAAATCAGACACATAAGACT 3117
                          i     i v i    ii           vi iivi     i   -  ii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA-GATC 298

  chr1_30570890_3   3118 GATGGAACAGAATAGAGAACCCAGATATAAGTCCATGAATTTATAGCCAA 3167
                         i      i     v    ii     v    ii    iv      i i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_30570890_3   3168 CTCATTTCTGACAAAGGGATCAAGAACATACTA-GAGGAAAGGACAGTCT 3216
                         i v    ii     i  vii     v   v v - i      i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_30570890_3   3217 TTTCAATAAATGGTGCTAGGAAAACTAGATAA------GCA---GAATGA 3257
                               i          i   v    i    ?------   ---      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_30570890_3   3258 ATCTAGACCCCTACCTCTCACCACATACAAAAATCAGATCAAAATGGATT 3307
                          vi i            v     i          i iv           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_30570890_3   3308 AAAGACTTAAATCTAAGACCTGAAACTATGAAATTATGAGAGGAAAACAC 3357
                          ?    i     v     v  i       i   i v v   i       i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_30570890_3   3358 TGGGG-AAAT-------ACTTTAGGAAAATTTGGGCAA-GTTTTTTTGGG 3398
                         v  ? -    -------  i  i  -----  i     - v   i  i i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGG-----TTAGGCAATGGTTTCTTAGA 593

  chr1_30570890_3   3399 TAAGACCTTAAAAACACAGGCAACAAAAGCAAAAATAAACAAATGGGATT 3448
                           v   vii    i    i          v       i i    v   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_30570890_3   3449 CCTTCAGGCTAAAAAGCTTATATACAGCAAAGGGAACAATTGACAAAGTG 3498
                         i v   iiv v    i   v i i vv      iv  v  ii v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_30570890_3   3499 AAGAGACAACCTACAGAGTAGGAGAAGATATTTGCAAACTGTCCATCCAA 3548
                           i        i     i i      i           iii vi   ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_30570890_3   3549 CAAGGGGCTAATAACCAGAATACATAAGGAACTCAAACAACTCAACAG-- 3596
                         i     i  vi  v        i    i      vv         i i--
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_30570890_3   3597 AAAAAATAAA---CGCGATTTTAAAATGGGCAAAAGATGTAAATAGAGAT 3643
                             i i   --- v i   ?v            i   v i      v  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_30570890_3   3644 TTCTCAAAAAAAGACATACAAATGGCCAACAGACATATGAAAAAGAAATG 3693
                              v   i    i              i ii  i       i---   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG---ATG 890

  chr1_30570890_3   3694 GTCAACATTGCTAATCGT 3711
                         v       ii????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (138 / 66)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.50 (40 / 16)  


4547 15.22 2.97 0.92  chr1_30575341_30577868     1162  2035 (493)    L1M4_orf2#LINE/L1       17   908 (0)  

  chr1_30575341_3   1162 GTTTATGGATCAGAAGACTTAATATTGTTAAGATGGCAATATACTGCAAG 1211
                            i      ii                             iv iv   i
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chr1_30575341_3   1212 TTGATTTACAGATTCAGTGGAATCCTTATCACAATCC-AGCTGCGATTTT 1260
                              i          ii v     i     v     -      -v    
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC-CTTTT 115

  chr1_30575341_3   1261 TTGCAGAAATTGACAAGCTTATTCTAAAATTCATAAGGAAACTCAAAAGA 1310
                                            v  i            v     iv   ii  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_30575341_3   1311 TCCAGAATACCCAAAACAATGTCAAAAAAAGAAGACCAAAGTTGAAAGAC 1360
                         i        v          v ii     -     v        i i   
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAA-GAAGAACAAAGTTGGAGGAC 214

  chr1_30575341_3   1361 TCA--------------------TACTACAAAGCTACAGAAATCAAAATA 1390
                            --------------------                v      i i 
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_30575341_3   1391 CTGTGGTTATTTGCACAAGGATAAAGATA--GATCAATGGAATAGAATTG 1438
                         v      - i v   i       i v   --                   
  L1M4_orf2#LINE/    265 GTGTGGT-ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_30575341_3   1439 ACAGTCAAAATATAAACCATTACCCTTATGTCCAGTGAATTTTCAACAAG 1488
                          v    v i v       vv   vi     vi  i vi      i     
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_30575341_3   1489 GATGCCAAGACAATACAATGAGACACAGAATACTCTTTTCAACAAATAGT 1538
                          i         v  v     i iv -      v              i  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAA-AGAATAGTCTTTTCAACAAATGGT 412

  chr1_30575341_3   1539 GCTGGAACAATTAGGTATCCATACACAAAAGAATGAAGTTGTACCCCTAT 1588
                              i    i i i  ?   i ii                v       i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_30575341_3   1589 TTCACACCATACACAAAAAAATACTCAAAATATATCATAGGCCTCCATGT 1638
                         i          i       vvv         iv    ?  i   vv    
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_30575341_3   1639 AAAAGTTAAAGCTATAAAACTCTTATAAGTAAACATAGGCATAAATCATC 1688
                           i  i    i              v   v         ?i      v  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_30575341_3   1689 ATGACCCTGGATTAGGCAGTAGTTT-TTAGATATGAC-CCTAAAGCACA- 1735
                         i     i   i       i i    -           -  v        -
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_30575341_3   1736 GCAAAAAAAGAAAAAGTAGATAAATTGGGATTCATCAAAATTAAGAACAT 1785
                             v          i            iv              i   v 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_30575341_3   1786 TTGTGCCTCAAAGGACATCATCAAGAAAGTGAAAATACAACCCACAGAAT 1835
                               i          ii                v              
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_30575341_3   1836 AGGATAAAATTTGTGCAAATCATATATCTGATAGGTAACTGAAATAAATA 1885
                         i   v     v v                    i vi   ---- iv  v
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT----TGTATC 758

  chr1_30575341_3   1886 TAGAATATATAAAGAAATCTCACAACTCAACAATAAGTAGACAAGCCACC 1935
                         i               v   i         i     iv      iiv   
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_30575341_3   1936 CAATCTATAAAAGGGCAAAGGATATGAATAGGCATTTCTCCAAAGAATAT 1985
                             i? v   v           v       i               v  
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_30575341_3   1986 ACACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCATTACTCAT 2035
                          i                                        ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (74 / 55)
Gap_init rate = 0.01 (11 / 892), avg. gap size = 3.09 (34 / 11)  


3364 26.87 0.33 0.33  chr1_30579932_30585814     4483  5390 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_30579932_3   4483 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4532
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_30579932_3   4533 GGCCATACTCCTCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4582
                            v       i   iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_30579932_3   4583 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 4631
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_30579932_3   4632 ATGGAACCAAAAGAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAGA 4681
                               viiv   i  v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_30579932_3   4682 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 4731
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_30579932_3   4732 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATTGATCA 4781
                                i   i    ii         i iv ii i   v    v     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_30579932_3   4782 ATGGAACAGAAC--AGGGCCCTCAGAAATAACGCCGCATATCTACAACTA 4829
                               i    i--  i i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_30579932_3   4830 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 4879
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_30579932_3   4880 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4929
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_30579932_3   4930 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 4979
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_30579932_3   4980 TAAAGAGTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACG 5029
                         i ?   vi    i  v   v       i      vi i           i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_30579932_3   5030 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5079
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_30579932_3   5080 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5129
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_30579932_3   5130 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5179
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_30579932_3   5180 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5229
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_30579932_3   5230 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5279
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_30579932_3   5280 AACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCT 5329
                         i     i     v  i?    i    ii     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_30579932_3   5330 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5379
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_30579932_3   5380 TCACTGGCCAT 5390
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3235 25.66 1.21 1.21  chr1_30595779_30602162.rev     4986  5893 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_30595779_3   4986 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5035
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_30595779_3   5036 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5085
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_30595779_3   5086 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5133
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_30595779_3   5134 TATGGAGCCTAAAAAGAGCCCACATT-GCCAAGTCAATCCTAAGCCAAAA 5182
                               iv- iv  i ii    v v -     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_30595779_3   5183 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACAATACTACAAGG 5232
                                 i      vv   ii  v  ii i      vvv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_30595779_3   5233 CTAGAGTAACTAAAACAGCTTGGTACTGGTACCAAAACAGAGATATAGAC 5282
                            v     ii  i    iv         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_30595779_3   5283 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5330
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_30595779_3   5331 CATCTGATCTTTGACAAACCTATCAAAAATAAGAAATGGGGAAAGATTC- 5379
                           vi    i  i     ivv ii   i vi vvv            v v-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_30595779_3   5380 CCTATTTAATGAATAGTGCTGGGAAAACTGGCTAGCCATAATGTAGAAAG 5429
                         i  v  i  ii   i         v      v  ?   i -  i i  ii
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGA 444

  chr1_30595779_3   5430 CTGAAACTGGATCCCTTCCTCACACCTTCTACTAAAATTAATTCAAGATG 5479
                         v    ii    i    v         v v   v        i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_30595779_3   5480 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5529
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_30595779_3   5530 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGGC 5578
                           v    ?i- v i -   iv   v v  vv i     v ii   v i v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_30595779_3   5579 TAAAACACCAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGGGATC 5628
                           vi            vvi          iv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_30595779_3   5629 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTACCATCAGAGTG 5678
                          v  i   v v  i i   i  ii vv    i  v i  i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_30595779_3   5679 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5728
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_30595779_3   5729 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 5778
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_30595779_3   5779 AAAAAACAAACAACCCCATCAAAAAGTAGGTGAAGGATATGAACAGACAC 5828
                             i     i     v  i?    i i  ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_30595779_3   5829 TTCTCAAAAGAAGACCTTTATGCA----GCCAACAGACACATGAAAAAAT 5874
                              v        ----   i  ----     i ii          i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_30595779_3   5875 GCTCATCATCACTGGCCAT 5893
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


3279 26.65 0.55 0.55  chr1_30634830_30641247     5018  5925 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_30634830_3   5018 TGGAAGAACATTCCATGCTCATGAGTAGGAAGAATCAATATCATGAAAAT 5067
                              ii i  i     i     ii v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_30634830_3   5068 GGCCATACTGCCCAAGGTAATTTATACGTTGAACGCCATCTCCATCAAGG 5117
                            v     v     iv i  i  i vi  v     v   i i     ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_30634830_3   5118 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5165
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_30634830_3   5166 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5215
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_30634830_3   5216 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5265
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_30634830_3   5266 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATACAGATC 5315
                                 i   i    ii  i      i iv ii i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_30634830_3   5316 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 5363
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_30634830_3   5364 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5413
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_30634830_3   5414 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAACCATATGTAGAAAGCT 5463
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_30634830_3   5464 GAAACTGGATCCCTTCCTCACACCTTATACAAAAATCAATTCAAGATGGA 5513
                            ii    i    v         v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_30634830_3   5514 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5563
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_30634830_3   5564 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGGCTA 5612
                         v    ?i- v i -   iv   v v  vv i     v ii   v i v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_30634830_3   5613 AAACACCAAAAGCGATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5662
                         vi           ivvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_30634830_3   5663 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5712
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_30634830_3   5713 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5762
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_30634830_3   5763 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5812
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_30634830_3   5813 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5862
                           i     i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_30634830_3   5863 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5912
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_30634830_3   5913 CATCACTGGCCAT 5925
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (147 / 91)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 439 17.78 1.11 0.00  chr1_30670417_30672501.rev      503   592 (1492)    L1M4_orf2#LINE/L1      112   202 (706)  

  chr1_30670417_3    503 TTTTTTGTAGAAATTGAGAAGCAGATTCTAAA-TGCACATGGAAATTCAA 551
                                i         v    v   i     - v  i        v   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_30670417_3    552 AGGACCTATAAAAGCCAAAGCAACTTTGTAAAAGAAGTACA 592
                         i     i v  v       i   ii   v        v   
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

Transitions / transversions = 1.00 (8 / 8)
Gap_init rate = 0.01 (1 / 91), avg. gap size = 1.00 (1 / 1)  

2094 23.48 7.25 2.90  chr1_30670417_30672501.rev      896  1585 (499)    L1M4_orf2#LINE/L1      174   893 (15)  

  chr1_30670417_3    896 AGCCAAAACGAACA-AAAAAAGAAGTACA---------GATTCAG--TCC 933
                                  i v v-i         v   ---------  i   v-- i 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr1_30670417_3    934 CCAATTTTGAA-----TTATAAAGTTACAGCAATCAAAGCAG-GAGATAT 977
                                ii  -----i  i    i     i      ii   - v i  i
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_30670417_3    978 TGGCGTCAAGATAAA----TAGATCAGTGAAACAGTA--GAGGGTCTAGA 1021
                             i v i    i ----       i  i  i  v --   i   i   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_30670417_3   1022 AATAAACTTATGTAAAGATTTA----CAAGTGATTTTTGACCACAGCATG 1067
                                ii  ---- v     ----   v       i   v vi iiiv
  L1M4_orf2#LINE/    324 AATAAACCCAT----ACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_30670417_3   1068 AAGGCAATTCAGGAGAGTAAGAATAGTCTCCTCAACAAATGGTGGAGGAA 1117
                            i v     ivi i v           ii             vv  i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_30670417_3   1118 CAACTGGATAGTCATAAAACAAAGCAAACAAACAAAAAGGAAACTTTGAT 1167
                                   ?i  ----------  vi    -- i  v   i-  v  i
  L1M4_orf2#LINE/    420 CAACTGGATAKCCA----------CATGCAAA--AGAATGAAG-TTGGAC 456

  chr1_30670417_3   1168 CCCTACCTTGTACCATATACAAAAATTGACTGGAAATGTATGATAGATCT 1217
                                 iii                i   vi     v  v ?   i  
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_30670417_3   1218 AAATGTAAAATTTAAAACTACAAAACAACTT-GAAGACAACATAGAAA-A 1265
                                 i vi        i     v-   -     v       i?i- 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNGTA 555

  chr1_30670417_3   1266 AATTTT-ACAGCCTTATTTTAGATCAAGATTGCTTCAATGTGGCAGAAAA 1314
                            i  -iiii    ivv    iiv v i  v   vi  i  i  vv   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_30670417_3   1315 AGTATGATCCATAAAAGAACAAAAT-GATAAGTTGGACGTCATCAAAAGA 1363
                           i ii v v i       -     -     i      v         vv
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAA-AAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_30670417_3   1364 AAAAAACCATTGCTCTTTAAAAGACTCCGATAGGAGAATGAAAAGAGAAG 1413
                              - iv   iv   i   i   v iivi i  i i        v  v
  L1M4_orf2#LINE/    655 AAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_30670417_3   1414 ACACAACCTAGGGGAAGATATTTGCAAGGCATATATTTAGTAAAGGACTT 1463
                         v    ivv i  i   i          iv       i ii   i      
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_30670417_3   1464 TTATCCAGAATATACAAAGA-TTCTCAAAACTCAGTAA-AAAA------- 1504
                         v             i     -i   i v      i   -    -------
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_30670417_3   1505 ---CCCAAC-AAAAAATAG-CAAAAGACCTGAACAGACACTTTATCACAG 1549
                         ---     i-?      i -    i  ii    i     i  ivi  v  
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_30670417_3   1550 AAGATATACAGATGAC----AAACAAATGAAAAGATGCTC 1585
                                   i   i ----  i  v              
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.93 (104 / 54)
Gap_init rate = 0.03 (25 / 720), avg. gap size = 2.80 (70 / 25)  


3052 26.05 1.17 0.47  chr1_30723489_30727916.rev     3076  3931 (497)    L1M4_orf2#LINE/L1        1   862 (46)  

  chr1_30723489_3   3076 TGGAAGAACATTCCATGCTCATGGATAGGATGAATCAATATTGTGAAAAT 3125
                              ii i  i     i        v   v  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_30723489_3   3126 GGACATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCTGTCAAGC 3175
                           vv     v      v i  i  i        i  v      i    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_30723489_3   3176 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTC 3222
                          v   -   v    i  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_30723489_3   3223 ATATGGAGCCAAAAAAGAGCCTGCATGGCCAAGACAATCCTAAGCAAAAA 3272
                                iviiv  ii  v  v v  i     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_30723489_3   3273 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 3322
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_30723489_3   3323 CTACGGTAACCAAAACAGCACGGTACTGGTACCAAAACAGATATATAAAC 3372
                             i    i   i    iii        i iv ii i   i     i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_30723489_3   3373 CAATGGAACCGAACAGATGCCTCAAAAATAACACCACACATCTACAATCA 3422
                                 iv   iv  vivii  i      vv   i    i  iii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_30723489_3   3423 TCTGATCTTTGGCAAATCTGACAAAAACAAGCAGTGGGAAAAGGATTCCC 3472
                         vi    i  i i   ivv  v   i v  vv  i    i    i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_30723489_3   3473 TATTTAATAAATGGTGCTGGGAAAACCAGCTAGCCATATGCAGAAAGCTG 3522
                          v  i  i              v   ii v  ?   i     i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_30723489_3   3523 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 3572
                           ii    i    v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_30723489_3   3573 TAAAGACTTAAATGTAAGACCTAACACCATAAAACCCT-AGAAGAAAACC 3621
                         i ?    i           v    v  i       i  -          v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_30723489_3   3622 TAGGCA-ATACCATTCAGGACGTAGGCATGAGCAAAGACTTCATGACTAA 3670
                             ?i- v i -   iv   v v  vv ii    v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_30723489_3   3671 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 3720
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_30723489_3   3721 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 3770
                          i   v v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_30723489_3   3771 AGACAACCTACAGAATGGGAGAAAAGTTTTGCAATCTACTCATTTGACAA 3820
                                 i                vv       vii ivi  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_30723489_3   3821 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATGTACAATTAAA 3870
                         i  i  vi          v  i        ivv    v vv i   v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_30723489_3   3871 A---AAA-AACCCA-TCAAAAAGCGGCCAAAGGATATGAATAGACACTTC 3915
                          ---   -      - i?    ii  v        v          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_30723489_3   3916 TCAAAATAAAAAATAC 3931
                           v   v  i v    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATAC 862

Transitions / transversions = 1.41 (128 / 91)
Gap_init rate = 0.01 (11 / 862), avg. gap size = 1.27 (14 / 11)  


3796 20.38 3.02 1.68  chr1_30732634_30736525     2507  3399 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_30732634_3   2507 AAAGATATCCCATGTTAATGGATTGAAAAAGTTAACAGTGTTTAATTTTT 2556
                                         v        i  i v    i v    v iv vvi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_30732634_3   2557 CATACTACCCAATGCAACCTACAGATTTAAGGCATTGAGATCTATCAAAA 2606
                         v     v     vvii i         i  v   --- vvi         
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCA---ATCCCTATCAAAA 100

  chr1_30732634_3   2607 TTTCAATGGCATTTTTTTTGCAGAAATTGAAAAA--AATTCTTAAGATTA 2654
                          ii  iiv  --i                 v  i--i  i  -  i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAATTC 147

  chr1_30732634_3   2655 ATATGGAAACCCAAGAAATCCTGAATAGCCAAAACCATCTTGAAAA---- 2700
                                  iv    ii i  v             v          ----
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_30732634_3   2701 -------GTTGGAGGCCTTATGTTTCCTAATTTTAGAAAATATTACAAAG 2743
                         -------        v  i iii    i     i i  vv  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_30732634_3   2744 TTACAATAATCAAAAGAGTGTACTACTGGCATAAACACAGACAAATAGAC 2793
                         i    i       i v     iv           iv i     v     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_30732634_3   2794 CAATGGAACAGAATAGAAAACACAGAAATAAACCCTTACATATATAATCA 2843
                                 i     v  i iiv             v     v   ii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_30732634_3   2844 AATGATCTTCAATAAGATT-CCAAGTCCACTCAATAAGAAAAGAACAATC 2892
                          v    i   i i   iv -     v   i     ii i      i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_30732634_3   2893 TTTTCAAAAAATGGTGCTGGGAAAGCTGTATAACATCATGCAAAAGAATA 2942
                                v              v i   v   ? vv             i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_30732634_3   2943 AAGTTGGACCTTTACCATATACCACATGCAAAAATTAACTCTAAATGGAT 2992
                                   ii    vi i    i  i             v        
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_30732634_3   2993 TAAAGAGCTAAACATAAGACCTAAAAACTATAACGTTCCTAGAAGAAAAC 3042
                         i ?   v     ii     v      -      vii  i           
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAAC 546

  chr1_30732634_3   3043 G--GGGGGAAACCT-CATGGCATTGGTTTTGGCAATGACTTATTGGATAT 3089
                         i--  ? v   i  - i  i v    v  v       ii  v  i     
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_30732634_3   3090 GACACAAAAAGCACAAACAACAGAAGCAAAAATAGATGAATAGGACTATA 3139
                              v          i     i   v          i   v     vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_30732634_3   3140 TCAAAGTTTAAAACTTCTGTACACCAAAGAAAATGATCAATAGAGTAAAA 3189
                              i  v       i   i vi     i v iv     v i   i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_30732634_3   3190 AGGCAACCTATAGAATGGGAGAAACCATTTGCAAATCATATATCTGATAA 3239
                           i     i i             vi                        
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_30732634_3   3240 AAGGTTAAGATCCAGAATAT--------TTTTTAAAACTCTCTAACAGTA 3281
                         ii ii viv           --------i i   v     ---  i i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC---AATAATA 793

  chr1_30732634_3   3282 AAAAAAAAAA-AATTTTAAACAATTAGAAAATGGTCAAAGGACTTGAATA 3330
                             i v   -  ii-----     ?i       v       i       
  L1M4_orf2#LINE/    794 AAAAGACAAATAACC-----CAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_30732634_3   3331 GACATTTCTGCAAGGAAGATATACAAATGGCCAACA-GCATATGAAACGA 3379
                                  v   i                    i -   i      v  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_30732634_3   3380 TGTTCAGTGTCACTAATCAT 3399
                           i   iii   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (112 / 66)
Gap_init rate = 0.02 (14 / 905), avg. gap size = 3.00 (42 / 14)  


 858 18.56 1.20 2.99  chr1_31352339_31355787     1099  1265 (2184)    L1M4_orf2#LINE/L1        4   167 (741)  

  chr1_31352339_3   1099 AAAGAAGACCCAAATTTATGGATTGGGAGACTTGATATTGTTAAAATGGT 1148
                              viv    vi  i         i      i          i    i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_31352339_3   1149 AATACTTCCCAAATTGATCTACAGATTCAATGCA--CTCTATCAAAATTC 1196
                               i                       i   -- i          i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_31352339_3   1197 CAACTACCTTTTTTTTTTTTCAGGAATGTATAAGTTGGCCTTAAAATTCA 1246
                           i  i        -----v   i   vv i   i  ii i         
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTT-----GCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_31352339_3   1247 TATGGAAATATGTGGAATC 1265
                                  iiiv  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACC 167

Transitions / transversions = 3.43 (24 / 7)
Gap_init rate = 0.01 (2 / 164), avg. gap size = 3.50 (7 / 2)  

2515 14.45 2.10 0.70  chr1_31352339_31355787     1577  2005 (1444)    L1M4_orf2#LINE/L1      156   590 (318)  

  chr1_31352339_3   1577 ATATATGGAGTTCA-AATAAC-AAAATAATCTTGAAAAAGAA---CAAAG 1621
                           ii v  iiii  -    i -    i               ---     
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_31352339_3   1622 TTTGAGGACTCATACTTCCTGATTTCAAAACTTACAATGACAAAGTTACA 1671
                           v         i      ii              -- -      i    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--T-ACAAAGCTACA 252

  chr1_31352339_3   1672 GTTATCAAGACAGTGTGGTACTAGCATAAGGATAGACATACAGATAAATG 1721
                           v                   i                 i    v    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_31352339_3   1722 GAACAGACT----AGTCCCAAACCAAATCCATACATCTATTGTCAATTGA 1767
                            i   v ----     vi  vi   i        i   v         
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_31352339_3   1768 TTTTCAACAAGGGTGCCAAGACTATTCAATGGAGAAAGCATAGTTTTTTC 1817
                              i                i         i     v     i     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_31352339_3   1818 AACAAATGTTGCTGGGACAACTGGATACTCACATGCAAAAGAATAAAGGT 1867
                                 v                  ?i               i   v 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_31352339_3   1868 GCACTCCTTCCTCACACCATATACAAAAATTAACTGAAAATGGGTCAAAA 1917
                          v  i   v                          v       i   ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_31352339_3   1918 ACCTAAATGTAAGAGCCAAAACTATAAGATCCTTGGAAGGAACCATAGGT 1967
                                         i          i ii   i    i  v      ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_31352339_3   1968 ATAAATCTGTATTACTCTGGATTAGGTAATAGTTTCTT 2005
                         i       vii v  ii   i     i   i       
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 2.47 (42 / 17)
Gap_init rate = 0.01 (6 / 435), avg. gap size = 2.00 (12 / 6)  

 204 16.28 0.00 0.00  chr1_31352339_31355787     2659  2701 (748)    L1M4_orf2#LINE/L1      655   697 (211)  

  chr1_31352339_3   2659 AAAAACATTAGTATATCAAAGGGTACTATCAAGAAAGTGAAAA 2701
                               v  v  iiv       ii                   
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

Transitions / transversions = 1.33 (4 / 3)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.00 (0 / 0)  

1027 17.19 1.36 0.00  chr1_31352339_31355787     2737  2957 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_31352339_3   2737 AAGAAAGTGAGAAGTCAACCCATACAATATGAGACAATGTTTGCCAATCA 2786
                                   i   v       i v   iv    v   i     v     
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_31352339_3   2787 TACATCTAATAAGTGTCCAAAATCCAGGATATATAAAGAACTTTTGCAAT 2836
                           i    i     v v iviv      i              i  i   i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_31352339_3   2837 TCACCAGTAAATAGATAAATAACCCAATT-AAAAATGGAAAAAGGATTTG 2885
                            vi i    v   i             -        iv          
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_31352339_3   2886 CAAAGA-ATTTCTCCAAAGAAGGTATACAAGTGGCTGATAAGCACAAAAA 2934
                         v v   -               i       i    ii         vi  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_31352339_3   2935 AATATGCTCAAAAT-AGTCATTTG 2957
                           v        v  - ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (21 / 17)
Gap_init rate = 0.01 (3 / 224), avg. gap size = 1.00 (3 / 3)  


3466 14.83 5.11 12.78  chr1_31494563_31496832.rev      802  1779 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_31494563_3    802 AGATATCCAATTTTCATGGATTGGAAGATTTAATACAGTTGAAATGTCCA 851
                                 v  v                i      iv   i i   v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_31494563_3    852 TACTATCCAAAGCAATCTACAGATTAAATGCAATCTCTATCAGAAT---- 897
                             vi     vii           v  i      i      i   ----
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_31494563_3    898 ----------TTGCAAAAATATAAAAATCT-ATCTTAAAATTCATATGAA 936
                         ----------     i    - i v  v  -   i             i 
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_31494563_3    937 ATCTTTCAAAGGACCCCAAATAGCCCAAACAATCTTGAAAAAGAA---CA 983
                          v-- v   i      vi       v                   ---  
  L1M4_orf2#LINE/    155 AA--TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_31494563_3    984 AAGCTGGAGGATCCACAATTCCCAACTTCAAAGCTTACTAAAAAGCTACA 1033
                            i       ii    v       i      i       v         
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_31494563_3   1034 GTAGTCAAAACAGTGTGGTACTGACATAA----AGACATATAGACCAGTG 1079
                            i    i              i     ----           i  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_31494563_3   1080 --ATAGAAT---------------AAATCCTCACTTATTTGGTCAAATGA 1112
                         --       ---------------   i  vi  v v v       v   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_31494563_3   1113 TTTTCAACAGGGG--CCAAGACCATTCAGTGGGGAAAAGGACAGTCTTTT 1160
                              i   i   --             i        - i i        
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTT 401

  chr1_31494563_3   1161 CAACCTATGGTGTTTTAAAAACTAGAGATCTACATGCAAAGAAATT---T 1207
                             vv      i vvi v    i  v ? i         ii   v--- 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_31494563_3   1208 TGGACCCTTTCTGTACACCATATACAAAAATAAACTCAAAATGGATCAAA 1257
                                i v ivi                 v                ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_31494563_3   1258 GACCTAAACGTAAGAGCTAAAGCTACAAAACTCTTAGAA--AAATATAAG 1305
                                 i            i   i             --   i   i 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_31494563_3   1306 GGAAAAGCTTCATGACATTGGATTTGGCAATGATTTCTTGAGTATGACAT 1355
                         ? v   v    i    v    i  v       i      iii       i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_31494563_3   1356 TAAAAGCATCAGCAATAAGAGAAAAAA-AGGTAAGTTTAACTTAACCAAG 1404
                         i       iv     i  i        -  i   i  vi    v i   i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_31494563_3   1405 ATTAAAATTTTTTTGTGCAATGAATACTATCATGAACATACTCAACATTA 1454
                                vi    -    --------------------------------
  L1M4_orf2#LINE/    652 ATTAAAAACTTTT-GTGC-------------------------------- 668

  chr1_31494563_3   1455 CTGAACTGTACACTTAAAAATAGTTAAGATGGTAAATGTTATATGTTCTT 1504
                         --------------------------------------------------
  L1M4_orf2#LINE/    669 -------------------------------------------------- 668

  chr1_31494563_3   1505 TACCACTATTTTAAAAAGTCTAAATCTGATAGGGAAAAAAGGGACACTAT 1554
                         ---------  i   --------------------------         
  L1M4_orf2#LINE/    669 ---------TTCAAA--------------------------GGACACTAT 683

  chr1_31494563_3   1555 CAACAGAGTAAAAAAACAATCCACAGATTAGAAGAAAGTATTTGCAAACC 1604
                            v i   i    i    i       v i i     i          i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_31494563_3   1605 ATATATCTGAT--GGGATTGATATCCAGAACATATAAAAAATTCCTACAT 1652
                                    --    i vi         i       i  i  i    v
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_31494563_3   1653 ATCAACAACAACAACA-AAATAAACAAGCTTATGCAAAATAGGCAAAGAA 1701
                         v    i  i  v  v -      v v ii ? ---     i       i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWA---AAAATGGGCAAAGGA 830

  chr1_31494563_3   1702 CTTAAATAGCCATTTCTCCAAAGAAAATATACATATGGCCAATAAGCACA 1751
                         i  i     v               i       v                
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_31494563_3   1752 TGAAAAGATATTCAATATCACTAATCAT 1779
                                  ii    i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (91 / 50)
Gap_init rate = 0.02 (19 / 903), avg. gap size = 9.21 (175 / 19)  


2586 26.49 3.96 1.36  chr1_32028230_32030780      856  1663 (888)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr1_32028230_3    856 TGGAAAAATATTACATGCTCATGGATTGGAAGAATCAGTATCTTTAAAAT 905
                               i    iv    i               v i i   iv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_32028230_3    906 GGCCATACTGCCCAAAGCAATTTACATATTTAACACTATTCCTATCAAAC 955
                            v     v      vii  i    v   i   i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_32028230_3    956 TACCAA-TGTCATTTTTCACAGAATCAGAAAAAACT-ATTCTAAAATTCA 1003
                          v   i-  i -     ii     viv  v  i-  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_32028230_3   1004 CATACAACCAAAAAAGAGCCCAAATAGCCAAAACAATCCCAAGCAAAAAA 1053
                         i  iv  viiv  ii  v  vi                iii ----    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA----AAAA 194

  chr1_32028230_3   1054 AAAAAAAAAAGCCAGAGACATCACACTATCTGACTTCAAACTATACTATA 1103
                         i  i  v    iii   ivv       vi ii i      viv     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_32028230_3   1104 AGGCTAGAGTAAATAAAACAGTATGGTACTGGTACAAAAACAGATGCATA 1153
                          i    v     vi  i     i         i i  ii i   iii   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_32028230_3   1154 GACCAGTGGAACAGAATAGAGAACCCAGAAATAAAGCCATACACCTACAA 1203
                           i  i     i     v    ii           v       ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_32028230_3   1204 CCATCTGATCTTCGACA-GAGTAGACAAAAACAAGCAATGGAGAATGGGC 1252
                         i  vi    i       - i  - v   i v  vv      i   v iii
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_32028230_3   1253 TCCCTATTCAATAAATGGTGCTTGGATCACTGGCTAGCCATATACAGAAG 1302
                         vvi  v     i          v   iv     v  ?   i  i  i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_32028230_3   1303 AATGAAACTGAAACCCCATCTTTCACCATATACAAAAATCGACTCAAGAT 1352
                               ii  i v   i i  iv                ii      i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_32028230_3   1353 AGATTAAAGATTTAAATGTAAGACCTCAAACTATAAAA-TCCTAGAAGAA 1401
                         i   i ?   ii           v  v           -  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_32028230_3   1402 AACCCAGG---AAATATCCTTCTCAACATCAGCCTTGGCAAAGAATTTTT 1448
                            vi   ---    ---    vii  v ii vi v     v iv  i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_32028230_3   1449 GGCTAAGTCCTCACAAGCAATTGCAACAAAAACAAAAATTGGCAAGTGGA 1498
                         i v  v v vi  v     vvv         iv      v ii  i v i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_32028230_3   1499 ACCTAATTAAACTAAGGAGGTTCTGCCCAGCAAAAGAAACTTACAACA-- 1546
                           i v  i   v v ii iv  i  iv vv    i  v   vv   v --
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_32028230_3   1547 -------GACAACTTACAAAATGGGAGAAAATATTCGCAAACTATGCATC 1589
                         -------      ii   i                i     ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_32028230_3   1590 CAACAAA-------TATCCAGAATCTGTAAGGAACTT---------AACA 1623
                         ii i  i-------          v i   i     i---------  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_32028230_3   1624 AGCAAAAAACAAATAACCCCACTAAAAAAATGGGCAAAGG 1663
                          vv    i           v i ?     -          
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGG 829

Transitions / transversions = 1.74 (134 / 77)
Gap_init rate = 0.02 (14 / 829), avg. gap size = 3.07 (43 / 14)  

 390 18.10 7.76 0.00  chr1_32028230_32030780     1943  2058 (493)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_32028230_3   1943 CTCAAAAAAAAAAA---AAATAA----ATAAAGAGGGGGGCAAAGGACAT 1985
                              v  v     ---      ----  v? i iiv          iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_32028230_3   1986 GAATAGGTACTTCTCAAAAGAAGACATACAAGTGGCCAACAA--ACATGA 2033
                               ii i     v        i      i       i  --      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_32028230_3   2034 AAAATTGCTCATCACCACTAATCAT 2058
                            iv      v  i  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (12 / 8)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 3.00 (9 / 3)  


1713 23.00 4.79 7.83  chr1_32703405_32706759.rev     1510  2135 (1220)    L1M4_orf2#LINE/L1        1   607 (301)  

  chr1_32703405_3   1510 TGGAAAGATAAGCCATGCAGATGAATTAGAAGA---AACA--GTTAATAT 1554
                                   vv     ivv   i   i     ---  i --     v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_32703405_3   1555 GTCAATTCTATTCAAGTGGACGTACAGGATTAATGTAATCCCAA-CAAAA 1603
                          v    v  vii   i v  iv     iv i  i i      v -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_32703405_3   1604 TCCAAGCAAATTTATCTCTGTAGAAAGTATCAAGCTGCTTCTAAAATTTA 1653
                            v   vivi  --i i  i     v iv       v i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_32703405_3   1654 AA-GGGAATTCAGTGGACCTAAAATAGCCAAAACAATTTTGAAAAAGAAG 1702
                         v -  i   v  iv     i i               i            
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_32703405_3   1703 AGGAAAA---GGGAACTTAACCTACGTAATTACAAGACTTACTATAA--C 1747
                          iv   i--- i i   i vv  v vi    v   i        i  -- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_32703405_3   1748 TATGGTAACCAAGATAGTGTATTATTGGCAGTAAGACAGGCACATAGATC 1797
                           ii    i     i     iv  i     vv i  i  i  i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_32703405_3   1798 AATGGAATAGA-------GTCCAGAAATAGACACATGAATATATTATCAA 1840
                                    -------           i  v   iv  v   vi    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_32703405_3   1841 TTGATTTTTTAGTCAGGTTTACTTTATCAATTGGCTTTTGACAAAGATAT 1890
                                 i------------------------------     i i ii
  L1M4_orf2#LINE/    349 TTGATTTTC------------------------------GACAAGGGTGC 368

  chr1_32703405_3   1891 CACAGTCACTGAATGGGGAAAGGTTCATGTTTTCAAACAAATGGTGCCAG 1940
                           viii  i v           iv vi v       -          ii 
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA-CAAATGGTGCTGG 417

  chr1_32703405_3   1941 AACAACTGGATATCCAT-TAGAGAAGAAAAAACAATCTTGATTCTTACTT 1989
                         i           ?   i- iv i     vi  --i - v  ii i   i 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAA--GT-TGGACCCCTACCT 464

  chr1_32703405_3   1990 TACACAACATACAAATTTTCATTTGACAAGGATCATAGA---AAAAGTTC 2036
                         i    v i       vv  v i ii v v      ?   ---   v  --
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-- 512

  chr1_32703405_3   2037 ATAGAAAAACATCATGGTAAAAGC-TAAA--TTTCAGAAGAAAACAAAGG 2083
                         ----  i i -------     vi-    -- i i           v   
  L1M4_orf2#LINE/    513 ----AAGAGC-------TAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_32703405_3   2084 AGAAAGTCTTTGGGACCTTGGGGTGGACAAAGATTTCTTAA----GACAC 2129
                         ? v  i    i v         v i i   v i       i----     
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_32703405_3   2130 AAAAAG 2135
                         v     
  L1M4_orf2#LINE/    602 CAAAAG 607

Transitions / transversions = 1.52 (85 / 56)
Gap_init rate = 0.03 (19 / 607), avg. gap size = 4.16 (79 / 19)  

 204 27.38 14.29 0.00  chr1_32703405_32706759.rev     2290  2373 (982)    L1M4_orf2#LINE/L1      603   698 (210)  

  chr1_32703405_3   2290 AATAGCATGAACTATAA--GAAAAAGTTGACAAAT--GGCTTTATCAAAA 2335
                           v    ii i v i  --      i v  i    -- i   i       
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_32703405_3   2336 TT--------CTGCTCTTTTAAAGATACCATTAAGGAAAGGAAAAG 2373
                           --------i  iv   iv  i  i  i  i   i  iv      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

Transitions / transversions = 2.83 (17 / 6)
Gap_init rate = 0.03 (3 / 96), avg. gap size = 4.00 (12 / 3)  

 569 17.17 15.15 2.02  chr1_32703405_32706759.rev     2675  2872 (483)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_32703405_3   2675 AAAAAAG-GAAAGGAAAACCAGACCACAAACCAGGATAAAATATTTGCAG 2723
                           i    -    i  v    ----    i vii   v            i
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACC----CACAGAATGGGAGAAAATATTTGCAA 730

  chr1_32703405_3   2724 TATATATATCTGACAAAAGAGTTGTACCCAGAATACATAAAGAACTC--- 2770
                         vvi          i  ii  v     i        i           ---
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_32703405_3   2771 ------AACACTAG---GACAAAAAACCCA---------CGGGCAAATGA 2802
                         ------  i v  i---      v      ---------i       v  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_32703405_3   2803 TTTGAACAGACACTTCATAATAGAAAACAAACAAA------ATAAGCACA 2846
                               i     i   viv v    i i v     ------         
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_32703405_3   2847 TGAAAAGATG-TCA-CTTCAGGGAAATG 2872
                                   -   - v   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (20 / 14)
Gap_init rate = 0.04 (8 / 224), avg. gap size = 4.25 (34 / 8)  


 555 23.33 30.00 3.33  chr1_32974980_32978482.rev     1190  1519 (1984)    L1M4_orf2#LINE/L1       45   462 (446)  

  chr1_32974980_3   1190 TAAAATGTTAATTCTCTCTCAGTTTTATTTATTTATATAGACTCAATACA 1239
                            i   vi   v   i iv -----   v  i  i --  i    ii  
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAA-----ATTGATCTACA--GATTCAACGCA 87

  chr1_32974980_3   1240 ATCCCAATGGAAATCCCACCAAGCCTT-----AAGAAATTGATACGCTAA 1284
                              v  vi        v v-     -----v         i v   i 
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr1_32974980_3   1285 TTCTAAAATTTATATGGAAATGCAAAGAATCTACAAAAGCCAACACAAC- 1333
                          i        i              i i i i v  v      v    i-
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_32974980_3   1334 -TGAAAAATAAGAACA---CTAGTGGA---ACAC------ATT---AGTC 1367
                         -       v       ---i i v   ---    ------   --- iv 
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_32974980_3   1368 TTTTT------TT-------TC--------------CTGG---------A 1381
                           vi ------i -------  --------------    --------- 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_32974980_3   1382 AACCT---GATT------------TT-----TCTAGAGACAAA------- 1404
                         i  v ---   i------------  -----  i   i i   -------
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_32974980_3   1405 -------------TGATTTTTGACAAAGGTACAAAGGCAATTCAATGCAG 1441
                         -------------       i     i   i v   i v        vi 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_32974980_3   1442 AATGGACAGTCTTTTCAATAAATGGTAAAGAAGCAATTGAATATCCATGT 1491
                           v i i           i       ivv iii   i  i   ?   ii 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_32974980_3   1492 GCCAAGAAAAT-AAGCCTTACATTCCCAC 1519
                           -  i i   -   --  iv ii  i  
  L1M4_orf2#LINE/    437 GC-AAAAGAATGAAG--TTGGACCCCTAC 462

Transitions / transversions = 2.04 (51 / 25)
Gap_init rate = 0.05 (20 / 418), avg. gap size = 5.50 (110 / 20)  

 591 25.31 1.23 1.23  chr1_32974980_32978482.rev     1868  2029 (1474)    L1M4_orf2#LINE/L1      451   612 (296)  

  chr1_32974980_3   1868 TTTAATCCATATCTTGCACTACATACAGAA-TAAATTTTAAAAGGATCAT 1916
                           vi i  v  i  ii   i i     i  - v  i iv   v      ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_32974980_3   1917 AGATCTAAATGTAATCCCTAAAGCTATAAAACCTCTAGAAAAAAACATAG 1966
                            i          vvv     i         iii     i         
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_32974980_3   1967 GAGAAAATTTTTGTGGCCTTTTCTTTTAAGCAAAGATTTCTTAGATACCA 2016
                          ? v    i  i   i    vvv  -- i    v i           iv 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTT--AGGCAATGGTTTCTTAGATATGA 598

  chr1_32974980_3   2017 CAT-GAAAGCATAA 2029
                           i-i      i  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAA 612

Transitions / transversions = 1.79 (25 / 14)
Gap_init rate = 0.02 (3 / 162), avg. gap size = 1.33 (4 / 3)  

 629 22.22 4.17 3.24  chr1_32974980_32978482.rev     2393  2608 (895)    L1M4_orf2#LINE/L1      596   813 (95)  

  chr1_32974980_3   2393 TGACTACCAAGAAAAATAAATAA-ATAAATAAAAATAAACAAACTT-ACT 2440
                             -     -  iv i  ii  - v  iv       i i   i v-   
  L1M4_orf2#LINE/    596 TGAC-ACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_32974980_3   2441 TCATCAAAACTAAGAA-TTATGTTCTTTAGAAGACACT--TATGGGAATG 2487
                                  i   i  -  v   v   i i i      --i v ii i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_32974980_3   2488 AAAAGACAAGGCATATACTGGGAGAAAATATTTCCAAATTACTTATCTGG 2537
                                  vv  i v v               v     i iv      i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_32974980_3   2538 CAAAGAAACTTGCATTTGGAACATGTATTTAAAGAACTCTCGAAACTCAG 2587
                         i  i i -    i  iii   ----   v           iiv      i
  L1M4_orf2#LINE/    744 TAAGGGA-CTTGTATCCAGAA----TATATAAAGAACTCTTACAACTCAA 788

  chr1_32974980_3   2588 TAATAAGAA----AATAATCCAATT 2608
                               i  ----     i      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATT 813

Transitions / transversions = 2.20 (33 / 15)
Gap_init rate = 0.04 (9 / 218), avg. gap size = 1.78 (16 / 9)  

 445 13.13 10.10 1.01  chr1_32974980_32978482.rev     2914  3012 (491)    L1M4_orf2#LINE/L1      801   908 (0)  

  chr1_32974980_3   2914 AAATAATCCAATTTTTTAAATGAGCAAAAAAT----------ACTTCACC 2953
                               i      ?vv-     i     ii  ---------- i   v  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_32974980_3   2954 AAAGAAGATATACAGGTGGCAAATAAGCACATGAAAAGATGCTCAACATT 3003
                                       ii    v                            i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_32974980_3   3004 ATTACTCAT 3012
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.02 (2 / 108), avg. gap size = 5.50 (11 / 2)  


 706 11.93 0.92 0.00  chr1_33042853_33045582      813   921 (1809)    L1M4_orf2#LINE/L1        1   110 (798)  

  chr1_33042853_3    813 TAGAAAGACATCCTAAGTTCATAAATTGGAAGACTTAATATCATTAAGAT 862
                          i      i    i v      ii                 ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_33042853_3    863 GGCAATTCTCCC-AAATTGATCTACAGATTCAATATAATCCCTATCAAAA 911
                               v     -                    iii              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_33042853_3    912 TCCAAGCTGC 921
                            v      
  L1M4_orf2#LINE/    101 TCCCAGCTGC 110

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.01 (1 / 110), avg. gap size = 1.00 (1 / 1)  

1266 15.58 1.30 0.43  chr1_33042853_33045582     1088  1318 (1412)    L1M4_orf2#LINE/L1       97   329 (579)  

  chr1_33042853_3   1088 AAAATAAAAACTGCCTTTTTTTGCAGAAATTGGTAAACTGATCCT-AAAT 1136
                              vvv i     -                ii  i        -    
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_33042853_3   1137 TTATATGGAAATACAGAAGATACAGAATAATCAAAACAATCCTGAGAAAG 1186
                          i          i  iii  iv       ii          i   i    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_33042853_3   1187 AAAATAAAAGTTGAAGAACTCACACTTCCCAATTCTAA--CTTACAATAA 1234
                           i vv       i  i                 ii  --     v i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_33042853_3   1235 AGTTAAAATAATCAAGACAATGTGGTACTGACATAAGGATGGACATATGG 1284
                           i  v i           i          i         i       i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_33042853_3   1285 ATCAATGGAATAGAACTGAGAGTCCAAAAATAAA 1318
                                        i          i       
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

Transitions / transversions = 3.50 (28 / 8)
Gap_init rate = 0.01 (3 / 233), avg. gap size = 1.33 (4 / 3)  

3012 15.83 2.16 0.18  chr1_33042853_33045582     1682  2237 (493)    L1M4_orf2#LINE/L1      342   908 (0)  

  chr1_33042853_3   1682 TGGTTAACTGAGTTTTGACAAGGATGCCAAGATGATTCAAGGGAGAAATA 1731
                             i  i   v   i       i        iv      v  i    v 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_33042853_3   1732 ATAGTCTTT-CAACAAATGGAGCTGGGACAATTGGGTATCC-CATGCAAA 1779
                                  -          v          i   i  ?  -        
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_33042853_3   1780 AGGATGAAGCTGGACCCCTAACTCATACTATGTACAAAAATACACTCAAA 1829
                           i      i          v    i  i  i         vv       
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_33042853_3   1830 CTGAATCAAAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTTTAAG 1879
                         v  i    ?                                    vv   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_33042853_3   1880 AAAACATAGACGTAAGTCTTTGTGACCTTGGATCAGACAATGATTTCTTA 1929
                                  i?    i    i          i i  i     i       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_33042853_3   1930 CTTATGACACTAAAAGCACAAGCAACCAAAGAAAAA-TAGGTAATTATGA 1978
                         vv        i               v         -   i   v vv  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_33042853_3   1979 TTTCTTTGAAATTAAAAACTTTTGCGCTTCAAAGGACACTATCAGGAAAG 2028
                         i   v ii                i                   i     
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_33042853_3   2029 TAAAAAGATAACCCATCA---------AAAATATTTGCAAGTCATACATC 2069
                          i      i      -  ---------             i     i   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCA-CAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_33042853_3   2070 TGATAGACATCTAGTATCCAAAATACACAAAAAAGTCTTACGATTCAACA 2119
                              iiviv  v       i    i i   i  v      i i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_33042853_3   2120 ACAAAAGGACAAATAACCCAACTGAAAAAGAGGCAAAAGATTTTAATAAA 2169
                          i    i              i ?     vi      i     v    i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_33042853_3   2170 CATTTATCCAAACAAGAAACATAGATGGCTAAGAAGTATAGGAAAAGATG 2219
                              v      v    v i i i     i  v   i i v         
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_33042853_3   2220 CTCAATATCATTCGTCGA 2237
                              i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (55 / 29)
Gap_init rate = 0.01 (5 / 567), avg. gap size = 2.60 (13 / 5)  


2968 25.73 3.27 0.79  chr1_33337916_33347088.rev     3817  4702 (4471)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_33337916_3   3817 TGGAAGAACATTCCATGCTCATGGATAGGAAAAATCAATATCGTGAAAAT 3866
                              ii i  i     i        v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_33337916_3   3867 GGCCATACTGCACAAGGTAATTTATAGTTTCAATGCTATCCCCATCAAGC 3916
                            v     v v   iv i  i  i  v     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_33337916_3   3917 TACCA-CTGATTTTCTTTACAGAA-TTGGAAAAAAACGACTTTAAATTTC 3964
                          v   -   vi   -   i     -   -- v  ivi  iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_33337916_3   3965 ATATGGAACAAAAAAAGAGCCCACAG-AGCCAAGACGATTCTAAGCAAAA 4013
                                 - viv  i ii    v i-      i  i  ii i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_33337916_3   4014 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCTAAACTACAAG 4063
                                  i      vv    i  v  ii i     ivivv       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_33337916_3   4064 GCTACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGATATATAGA 4113
                                   i   i    ii i       i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_33337916_3   4114 TCAATGGAACAGAACAGAG-GCCACAGAAATAA-----CACGTCTACAAC 4157
                                  i    iv   - i -         -----i  i i  iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chr1_33337916_3   4158 CATCTGATATTTGACAAACCCCACAAAAACAAACAATGGGGAAAGGATGC 4207
                           vi    v  i     ivvivv   i v  vv            i  iv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_33337916_3   4208 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 4257
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_33337916_3   4258 TGAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGG 4307
                             ii    i    v   i    iv                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_33337916_3   4308 ATTAAAGAC------GTAA-------AACCATAAAAACCCTAGAAGAAAA 4344
                           i ?    ------    -------   i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_33337916_3   4345 CCTAGGCA-ATACCATTAAAGACATAGGCATGGGCAAAGACTTCATGACT 4393
                          v    ?i- v i -  viv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_33337916_3   4394 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGAGGACT 4443
                          vi            vvi          vv        i    v-     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT-GGACT 643

  chr1_33337916_3   4444 -AGTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 4492
                         -vi i   v v  i i   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_33337916_3   4493 AACAGGCAATCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGA 4542
                           v  i   i i                 v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_33337916_3   4543 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTATAAGA 4592
                         i  i  i  vi          v  i        ivv    v iv    v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_33337916_3   4593 AAAA---AAACAACCCCATCAAAAAGTG--CAAAGGATATGAACAGACAC 4637
                             ---   i     v  i?    i  --        v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_33337916_3   4638 TTCTTAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTC 4687
                             iv        i  vi viii     i ii  i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_33337916_3   4688 ATCATCACTGGTTAT 4702
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  

 705 15.68 1.10 32.13  chr1_33337916_33347088.rev     5549  6460 (2713)  C L1M4_orf2#LINE/L1   (0)   908   280  

C chr1_33337916_3   6460 AAAGATAGACAAATAGATCAATAGAACAGAGTACAGATTCCAAATATAGA 6411
                           i        v          i   i   i vv   v    i v   i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

C chr1_33337916_3   6410 CCCGTGTTTATATAGTCAACTGATTTTTGACAAAGATGTGCAGGCCATTC 6361
                            i iiv v   i     i       i     i i  ivv  i      
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

C chr1_33337916_3   6360 ATTTGAGAAAAGATAATCTTTTAAAACAAATAATATTGGAAAAATTATAT 6311
                          v v i    ii   i      v  -     ii ii   i v  i iv  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAA-CAAATGGTGCTGGGACAACTGGAT 428

C chr1_33337916_3   6310 ATTCATGTGCAAATGCAAAAACAAAACAAAAATAAAACTTGAGCCATAAC 6261
                          ?i  ii      --------------- i   i  ii v  v  v  - 
  L1M4_orf2#LINE/    429 AKCCACATGCAAA---------------AGAATGAAGTTGGACCCCTA-C 462

C chr1_33337916_3   6260 TTCAAATGTATCATAGAAAATTAGCATATAAAAATGTTTGACATCATTAA 6211
                         i   ----i i    -----------  i      --- i  --------
  L1M4_orf2#LINE/    463 CTCA----CACCATA-----------TACAAAAAT---TAAC-------- 486

C chr1_33337916_3   6210 TCATTAAGGAGATGCAAATGAAAACTACAATAAGATACTACCATGCACCT 6161
                            ------------     ------------------------------
  L1M4_orf2#LINE/    487 TCA------------AAATG------------------------------ 494

C chr1_33337916_3   6160 GTTGATTTTAGATCTTTCCTGCTTAAGTGTACAACATAAAAATATAAAAC 6111
                         ---   iv?   i  ---------  i    vi vv     v        
  L1M4_orf2#LINE/    495 ---GATCAWAGACCT---------AAATGTAAGAGCTAAAACTATAAAAC 532

C chr1_33337916_3   6110 TTCTAGAAGAAAACATATAAGATAATTTTATGGGCCTTGAGTTGGGCAAA 6061
                          ii              vi? vv   i  vvv i     i   i     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

C chr1_33337916_3   6060 GATTTATTGGACATAATACCAAAA-CAAAAAAAAAATGACTACAACAAAC 6012
                          i   v  i  i  i i       -  v  i-----------       -
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAG-----------CAACAAA- 620

C chr1_33337916_3   6011 AAGAAAAAATTGATAAACTGGATTTCATCGAAGTTAAGAAAATTTGTAAT 5962
                         -         v      i    i      i  i    i  vv     iv 
  L1M4_orf2#LINE/    621 -AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

C chr1_33337916_3   5961 TCAAAAGAATCTATTATAGCTAAGCATGGTGATATGAACCTGTAGTCTCA 5912
                              i  ------------------------------------------
  L1M4_orf2#LINE/    670 TCAAAGGA------------------------------------------ 677

C chr1_33337916_3   5911 GTTACTCATGAAGCTGAGATGGGAGGATCACTTGAGCCCAGGAATTTGAG 5862
                         ----------------------------    ------------------
  L1M4_orf2#LINE/    678 ----------------------------CACT------------------ 681

C chr1_33337916_3   5861 GCTGCAGTGTGTTATGATTGCACCTGTGAATAACTACTGTACTCTAGCCT 5812
                         --------------------------------------------------
  L1M4_orf2#LINE/    682 -------------------------------------------------- 681

C chr1_33337916_3   5811 GGCCAACACAGTGAGACCCCATCTGTAAAAAGAGAAAAAAATACTATTAT 5762
                         --------------------   -----------  i   i --------
  L1M4_orf2#LINE/    682 --------------------ATC-----------AAGAAAGT-------- 692

C chr1_33337916_3   5761 AAAAACGAAAAGACAAGCCACAGACTGGGGAAAAATATTTGCATATCACA 5712
                         ------          v       v    ii            v    i 
  L1M4_orf2#LINE/    693 ------GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

C chr1_33337916_3   5711 TATCTGATAAAGGACTTGTAACTAGAATGTATAAAGAACTCTGAAAACTC 5662
                                   i         v i     i             v v     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

C chr1_33337916_3   5661 AATAATAGTAAAACACACATCTC--TCCCAAAATGGGCAAAAAACTTT-- 5616
                                iv  i   v i v i -- i?v            ii i  v--
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

C chr1_33337916_3   5615 CAGACACTT----AAATAATATATGCAGATGGAAAATTAGTATAT-AAAA 5571
                         i     i  ----   v  v    i  i    vv   v  i i  -    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

C chr1_33337916_3   5570 TATGTTCGACATCATTAATCAT 5549
                         v   i  i      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (87 / 52)
Gap_init rate = 0.03 (21 / 629), avg. gap size = 14.43 (303 / 21)  

 495 22.79 5.15 0.74  chr1_33337916_33347088.rev     6765  6900 (2273)  C L1M4_orf2#LINE/L1   (613)   295   154  

C chr1_33337916_3   6900 AAATGCAAAGGATCTAAAATAGAAAAAAATAACTTTGAAAAAAAAGAAGA 6851
                                 i   i i i     vv    -i  ii        i     v 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACA 202

C chr1_33337916_3   6850 AAGTTGAAGGACTTAT--TT---GACTTTATGAC--ATTATAAAGCTACA 6808
                               i      i i--  ---i i  i vi  -- i  i         
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

C chr1_33337916_3   6807 GTAGTCAAGATATTTTGGTATTGGTATCAAGATAGACAAACAG 6765
                            i      i v v     i   i  v i        v i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 2.88 (23 / 8)
Gap_init rate = 0.03 (4 / 142), avg. gap size = 2.00 (8 / 4)  

 504 23.60 2.25 9.55  chr1_33337916_33347088.rev     7196  7373 (1800)  C L1M4_orf2#LINE/L1   (743)   165     1  

C chr1_33337916_3   7373 TGGGAAGATATACCATGTTCTTAGATTAGAAGACTCAATACTGCTAAGAT 7324
                            i       v        v i    i       i    i  i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_33337916_3   7323 GTCAACTCTCTCAAAATTCATCTATATATTTAAGAGAATCCTAATGCAAA 7274
                          v   iv   i v     v     i v   i  viv     iv  vv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_33337916_3   7273 TCCTGTGTGTTTTTGTGTGTGTGTGTGTGTATTTACA--AATGGATGAGC 7226
                            iivv  ii   -----------------   i  --   v  ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-----------------TTTGCAGAAATTGACAAGC 133

C chr1_33337916_3   7225 TAATTTTAAAATTC-TA-AAAAATGCAGAGAA 7196
                          i  ii        -  -ii       ii i 
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGA 165

Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.02 (4 / 165), avg. gap size = 5.25 (21 / 4)  

3628 22.74 2.21 1.99  chr1_33337916_33347088.rev     7777  8682 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_33337916_3   7777 TGGAAAGACATCCTATGTTCATGGATTAGAA---TTAATATTGTTAAAAT 7823
                                 i    i             i   ---             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_33337916_3   7824 GTTCATACTACTGAATTCCATATACAGGTTTATTCCAATCCCTATGAAAG 7873
                          viv     v iv  v iv  v     i  i viv          v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_33337916_3   7874 TTTCAATGGCATTCTTTACAGAAATAGGAAAAGC-AATTCTAAAATTTGT 7922
                          ii  iiv  v  i   i       -v  v    -i  i        ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_33337916_3   7923 ATGGAACCACAAAAGACCACAAGTAGCCAAAGCAATTTAGAGAAAGAAAA 7972
                               vii   ii    vvi i        i    i v  i      i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_33337916_3   7973 ACAAAGTTGAAGGCATCACATTTCCTGATTTTTAATTATATTATAAAGGT 8022
                                  i   vv     i    ii    iv  viv  i  i    v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_33337916_3   8023 ATGGTAATCAAAACAGTATAGTACTGACATAAAAGACAGACACATAGACA 8072
                          ii        i     i i      i     i-  i     i     iv
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATATAGATC 298

  chr1_33337916_3   8073 AATGGAACAGAATAGAGAGCCCAGAAATAAACTCAGTCATATATGGTCAA 8122
                                i     v     i            i  vv   v         
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_33337916_3   8123 CTAATTTTTGACAAGGGTACCAAGAAGACATAATGGGGAAAAGACAGCCT 8172
                         i i     i         i      vv ivi          ii i  i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_33337916_3   8173 CTTCAATAGATGGTGCTGAAA-AACTAGATTTCCACATGCCAAAAAATGT 8221
                         i     i i         ii -    i   v?        v   i    -
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG- 447

  chr1_33337916_3   8222 GGAAACTGGACTCTTATATTATAC---AGAAAAAAATCAACTCAAAATGG 8268
                         --  ii     i i  iv i i  --- v v      i            
  L1M4_orf2#LINE/    448 --AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_33337916_3   8269 ACAAAGGACCTAAATATAAGAACCAAAACCATAAAATTTCTAAAAGAAAA 8318
                          iv ?i         i     i i     i      i ii  i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_33337916_3   8319 CACAGAGGAAAAGCTCCTTGACTTTGGCCTTGGTAATAATTTTCTGGATA 8368
                           i  i? v   v  i v    i    vi v  i   ii   ii i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_33337916_3   8369 TCACACAAAAAGCTCAGGCTATAAAAGCAAAAATAAATAAATGGGACTAC 8418
                          v    v      v  i  v i     v       i      v     v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_33337916_3   8419 ATCAAACCAAAGAGCTTCTTCACAGCAGGGGAAACAGTCAGTAAAAGGAA 8468
                               viv  i i   i vii vv  ii   v  vi   iv   iv   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_33337916_3   8469 AAGGCAGCATACAAAATGGGAGAAAATGTTTGCAAACCGTACATCTGATA 8518
                            i  i vi   i             i        i i  i        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_33337916_3   8519 -----------TCCAAAATATATAAGAAACTCAAACAATTCAATAGCAAG 8557
                         -----------    i         ii     vv    i      -----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA----- 790

  chr1_33337916_3   8558 AAACAATAGCAAGAAAACAAATAACCCAATTAAAAAATGCGCAAAGGACT 8607
                         -----   --- i  i               ?       v        i 
  L1M4_orf2#LINE/    791 -----ATA---AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_33337916_3   8608 -GAAAAGACATTTCTTCAAAGAAGACATTAAAATGGTCAATACGTGTATG 8656
                         -   v          i         i  vv      i     v iii   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_33337916_3   8657 AAAAGGTGTTCAACATCACTAATCAT 8682
                              i  i         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (135 / 67)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.45 (38 / 11)  


2984 25.95 2.35 0.78  chr1_33582847_33586310     2078  2971 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_33582847_3   2078 TGGAAACACATCCCATGCACATGGATGGGTAGAATCCATATTCTGAAAAT 2127
                               v i        iv       v  v   v iv     v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_33582847_3   2128 GACCATATTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATAAAAA 2177
                          i v   i v  v   vii       i      i     i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_33582847_3   2178 GATCACCATCATTCTTCACAGAATTAGAAAAAACAACCCCAAAATTCATA 2227
                         vvi  v vv v  i  ii     v v  v  ivii i  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_33582847_3   2228 TAGAAC--CAAAAGAGTCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 2275
                          i   v--   ii  vi viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_33582847_3   2276 CAAATCTGGAGGCATCACATTACTAAACTTCAAACTATACTATAAGGCCA 2325
                             vi      vv     i v iv  i      viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_33582847_3   2326 TAGTCACCAAAACAGCATCATACTGGTATAAAAATAGGCA-------CAA 2368
                         i   v i   i    ii vi      i    ii    i  -------   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_33582847_3   2369 AGAAATAAA--------CCCAGAAATAAAGCCAAATACTTACAGCCAACT 2410
                         v i    i --------i           v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_33582847_3   2411 GATCTTCGACAAAGCAAACAAAAGCATAAAGTGAGGAAAGGACAGCCTAT 2460
                            i        i vviv   i v   vv i  i      i i  i  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_33582847_3   2461 TCAACAAACAGTGCTGGGATAATTGGCAAGCCACACGTAGAAGAATGAAG 2510
                                 ii         i  i   vv ?     i i i          
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_33582847_3   2511 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCGAAGTGCATCAA 2560
                         i    i  ii i   v    v           i     i  i  v    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_33582847_3   2561 AGACTTAAATCTAAGACCTGAAACCATAAAAATTCTGGAAGATAACATTG 2610
                             i     v     v  i    i      v ii i     v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_33582847_3   2611 GAG-AAATCTTCTAGACGTTTTGGCTTAGGCAAAGACTTC--AGGACCAA 2657
                          ? -        vv   --i    v        v ii   --  i--i v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGAC--CTTGGGTTAGGCAATGGTTTCTTAGA--TAT 596

  chr1_33582847_3   2658 GAACCCAAAAGCAAATGCAACGAAAACAAAGATAAATAGATGGGACTTAA 2707
                           vv         v v     i   iv   i   i   i  v      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_33582847_3   2708 TTAAACTGAAAAGCTTCTGCACAGCCAAACAAATAATCAGCAGAGTAAAC 2757
                          i   v v    i   i  ii vv v  iv v iv    iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_33582847_3   2758 AGACAACCCACAGAGTGAGAGAAAATCTTTGCAGACTATGCATCTGACAA 2807
                                       i  i        v      i ii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_33582847_3   2808 AAGACTAATATCTATAATCTACAAGAAACTCAAACAAATCGGCAAGAA-A 2856
                         ii    vi    i v   v  i  ii     vv    v  ---  v  - 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC---AATAATA 793

  chr1_33582847_3   2857 AAAAAACAAACAATCCCATCAAAAAGTGGGCTTAGGACATGAATAGTCAA 2906
                             i     i  i  v  i?    i     vv    iv       v  v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_33582847_3   2907 TTCTCCAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTC 2956
                                                      i  i  i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_33582847_3   2957 AACATCACTAATGAT 2971
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.11 (28 / 9)  


 522 28.37 2.84 0.00  chr1_33617011_33621092.rev     2548  2688 (1394)    L1M4_orf2#LINE/L1        1   145 (763)  

  chr1_33617011_3   2548 TGGAACAATATTCCATGTTCACAGATAGAAAGGCTCACTGTAGTCAAGAT 2597
                              vi    i         ii   v i   i  i v i v  i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_33617011_3   2598 GTCAGCTTTTCCCAATTTGATCTACAGATTCAACAC----CCAATCAAAA 2643
                          v  iivi i     v                  i ----  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_33617011_3   2644 TCACAGAAATTTATCTTGTGGATATCAACAAACTGACTGTAAAGT 2688
                           v   vviii v i   ii  v  ii    i    iiv    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

Transitions / transversions = 1.86 (26 / 14)
Gap_init rate = 0.01 (1 / 145), avg. gap size = 4.00 (4 / 1)  

2558 24.66 3.77 0.54  chr1_33617011_33621092.rev     2852  3593 (489)    L1M4_orf2#LINE/L1      143   908 (0)  

  chr1_33617011_3   2852 AGTTTATATGAAGAAGCAAAG-ACCTGGAATAACCAACTCAATATTGAAG 2900
                          i  i     i i v    i -   ii     i    vv    v     i
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_33617011_3   2901 GAGAAGGAAAAAAATCAAAGAAATGACACA-CCTGACTTCAAGATTTACT 2949
                         i     -  v   i iii  i v v    v-  ii i     i i     
  L1M4_orf2#LINE/    193 AAGAAG-AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_33617011_3   2950 ATAAA-CTATAGTAATCAAGACAGTGTGGTATTGGCAAAAGAATAAAGC- 2997
                          i   -   i                     i     v   i   i - -
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA-CA 290

  chr1_33617011_3   2998 ----GATCAATGGAACAGAATAGAGACCCCAGAAATAGTCCCACATAAAG 3043
                         ----           i     v    vi         iv    i i vvv
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_33617011_3   3044 ATAGTCGACTGAACTTTGATAAACGAGCAAAGGTAATACAGTGAAGCAAA 3093
                           i   i i   vi  i  i  iv v  v   iiv  v  i  ii v  i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_33617011_3   3094 TATA---TTTTCAACAAATGATACTAA---AACTGGACATCCACATGAAA 3137
                         v   ---             i i  ii---       i ?       v  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_33617011_3   3138 AAAAAAAAAA----GCTTCTATCCTAT-CCTT-CACAAAAATCAACTCAA 3181
                           i  vi  i----i ii   i ii i-  v -i        i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_33617011_3   3182 AATGGATCACAGACCTTAACGTTAAAATGAAAAACTATAAAATTCCTA-- 3229
                                  ?      v  i  v i iiv    -        i  i  --
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGA 539

  chr1_33617011_3   3230 ---AAATATAGGAGAAAA-CTGAGATAATGTCAGGTATAGCAATGACTTT 3275
                         ---   i     ? v   -  vv - i iv ii   vvi      ii  i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_33617011_3   3276 TCAGATACAAAATCAAAGGCATAATCCATGAAAGAAATAATTGATAAGCT 3325
                          i     ii v i    i   i  v v ii       v   v     ii 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_33617011_3   3326 GGACTTCGTTAAAATTAAAAAATACTGCTCTATGAAAGATACTGTCAAGA 3375
                                i i           v vi  iv  vii  i  i   i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_33617011_3   3376 GAATGAGAAGACAAGCCACAGACTGGGAGAATATATTTGCAAAACACATA 3425
                         i i   i       v       v        v           v  i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_33617011_3   3426 TCTGATAAAGGACCGTTACCCCGAACATACAAAGAACTCTTAAAACTCAA 3475
                                 i    ivv  i  v   i   i            v       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_33617011_3   3476 GAGTAAGAAGACAAACAACCCAATTTAAAAATGGGCAA--GACTTTAACA 3523
                         v i   i        i         ?            --  i  v  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_33617011_3   3524 GTCACCACACCAAAGAAAATATACAGATGGCAAGTAAACATATGAAAACA 3573
                          v  iiv v        i       i     v i   i  i       v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_33617011_3   3574 TGTATAACATGGTAGGTTAT 3593
                           ivi     vi????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (118 / 61)
Gap_init rate = 0.02 (16 / 766), avg. gap size = 2.00 (32 / 16)  


1174 17.49 2.69 0.45  chr1_33663568_33665193       19   241 (1385)    L1M4_orf2#LINE/L1        1   228 (680)  

  chr1_33663568_3     19 TGGAAAGACATCACATGTTCATGGTTTGGAAACCTTAATATTGTTCAGAT 68
                                 i   v           v      iv            v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_33663568_3     69 GGCAATACTCCCCAAATTGATCTACAGGTTCAATGCAATTTCTGCCAAAA 118
                                                    i     i     ii  ii     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_33663568_3    119 TTCCAGCTCTCTAGTTTGCAGAAATTGACAAGCCAATCTTAAAATCTGTA 168
                          i      vi  vv                   ii   i      iii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_33663568_3    169 TAGAAA--CAAAAGGCAAAACAATAGGCAAA-CAGTCTTAAAAAAGAA-- 213
                          i    --   ii i vv i-     v    -  i    i        --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAG-AATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_33663568_3    214 -CAAAGTTGGATAATTGATACGTCCCAAT 241
                         -          vi i v i  v       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAAT 228

Transitions / transversions = 2.00 (26 / 13)
Gap_init rate = 0.02 (4 / 228), avg. gap size = 1.75 (7 / 4)  

3270 17.19 4.68 0.30  chr1_33663568_33665193      490  1152 (474)    L1M4_orf2#LINE/L1      217   908 (0)  

  chr1_33663568_3    490 ACACTTGCCAATTTGAAAACCTACTACAAAGCTAAAGTAATCAGGGCTGG 539
                               v       v     i             v        i i v v
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr1_33663568_3    540 GTGGTAATGGCATAAAGAGAGTCATAGAGATCAATGGAATAGAATAGAGA 589
                               v        i  v  v    v                  v    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr1_33663568_3    590 ATCCAGATATAAACTCATACATTTATGGTCAAATGATTTTTGACGGGAGT 639
                         i      v      i                 v       i   ii i  
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_33663568_3    640 GTCAAGACAATTCAACAGGGAAAGAATAGTCTTGCCAACAAATGGTGCTG 689
                          i      v      ii                vi               
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_33663568_3    690 GAACAACTGGATAGCCACATAAAAAAGAATGAGTTTGGATTCTAACCTAA 739
                          i           ?      iv          iv     ii iv    v 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_33663568_3    740 TATCATA---AAAAATTAATTCAAAATGGATCAAAGACATAAATCTAAGA 786
                         i i    ---         i             ?    v     v     
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_33663568_3    787 AGTAAAACTAGAAAACTCTAAGAATAAAACATAGGCATAAATCTTTGTGA 836
                         iv        v        v    v          ?i        i    
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_33663568_3    837 CCTTGGAT---GTATCACAGTTTCTTAGATATGACAACAAAAGCATATGC 883
                               i --- i -- ii                 v        i v  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCA--ATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_33663568_3    884 AACCCCC---AAAATAGAAAAGTTAGATTTTATCAAAATTAAAGACACTG 930
                            vvvv---        v  i  i  i  i            i  vi v
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_33663568_3    931 GTGCTTCAGAGAACACCAACAAGAGAGCGAAAAGACACCCCGTGAAATGG 980
                                 i  i    i v     i  i         v   iiii     
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_33663568_3    981 GAAAAAAT--TTGCAAATCATGTACCTTATAAAGGCCTTGTATTTTAGAT 1028
                           i     --           i  i  v    i  v       iivii  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_33663568_3   1029 AGAGAAAGAACACTTTCAACTCAACAATAAAAAGATAAGT----CAGT-A 1073
                          v v       v   v        i          i  i ----  i -?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_33663568_3   1074 AAAAATGGACAAAGGATTTGAATAGACATTTCTCTAAGGAAGACATACA- 1122
                                 i                         i  i     i     -
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_33663568_3   1123 --------------CATAAAAAAGTGCTGAGCACCATTAGCCAT 1152
                         --------------   i    ii    v i  i  ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (67 / 43)
Gap_init rate = 0.01 (8 / 692), avg. gap size = 4.12 (33 / 8)  

1255 22.26 0.32 1.29  chr1_33663568_33665193     1178  1487 (139)    L1M4_orf2#LINE/L1      602   908 (0)  

  chr1_33663568_3   1178 CAATGATACAGGCAACAAAAGCAAAAGTAGACAAATGAGATTACATCAAA 1227
                            viii   i          v    i    i    vi  i v       
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_33663568_3   1228 CTGAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAGAGTGAAGAGGCA 1277
                         v v    i   i  ii vv       v  v     v i      i  i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_33663568_3   1278 ACCTGTGGAATGGGAGAAATTGTTTGCAAACCACACATCTGGTAAGAGAT 1327
                            iiii            v i        i  i i     i    i  i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_33663568_3   1328 TAACATCTAAGGAACATATAGAAGGAACTAAAACAACTCGATAGCAAGAA 1377
                          vii   i --   i     i --     vvv       i   ii  i  
  L1M4_orf2#LINE/    752 TTGTATCCA--GAATATATAAA--GAACTCTTACAACTCAATAATAAAAA 797

  chr1_33663568_3   1378 AATAGATAACCTGATTTAAAAACAGGCAAAGGACCTGAATAGACATTTCT 1427
                         i i i      ii   ?     ii         ii               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_33663568_3   1428 GAAAAGAAGACATACAAATGGCCAACAGGTATATGAAAA-ATGCTCAGCA 1476
                         vv        i              i i i i       -       i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_33663568_3   1477 TCACTAACCAT 1487
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.78 (50 / 18)
Gap_init rate = 0.01 (3 / 307), avg. gap size = 1.67 (5 / 3)  


3148 26.79 0.55 0.66  chr1_33806191_33812565     4976  5882 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_33806191_3   4976 GAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATG 5025
                               -i  i     i      i v      v i        v  i   
  L1M4_orf2#LINE/      3 GAAAGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_33806191_3   5026 GCCATACTGCCCAACGTAATTTATAGATTCAATGCCATCCCCATTAAGCT 5075
                           v     v     vv i  i  i        i  v     i  i  iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_33806191_3   5076 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 5123
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr1_33806191_3   5124 ATGGCATCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGA 5173
                             v viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_33806191_3   5174 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5223
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_33806191_3   5224 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5273
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_33806191_3   5274 ATAGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATTTACAACCA 5321
                           i   i    i--    i  --        vv   i i     iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_33806191_3   5322 CCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5371
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_33806191_3   5372 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5421
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_33806191_3   5422 AAACTGGATCACTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5471
                           ii    i v  v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_33806191_3   5472 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5521
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_33806191_3   5522 TAGGCA-ATACCATGCAGGACATAGGCATGGGCAAGGACTTCATCTCTAA 5570
                             ?i- v i - v iv   v v  vv i     v ii   v vvv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_33806191_3   5571 AACACCAAAAGCAATGGGAACAAAAGCCAAAATTGACAAATGGGATCTAA 5620
                         i            vvi v        vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_33806191_3   5621 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACGAACATCAGAGTGAAC 5670
                          i   v v  i i   i  ii vv    i  v  v v  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_33806191_3   5671 AGGCAACCTACAGAATGGGAGAAAATTTTGGCAACCTACTCATCTGACAA 5720
                           i     i                 v  v    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_33806191_3   5721 AGGGCTAACATCCAGAATCTACAGTGAACTCAAACAAATTTACAAGAAAA 5770
                         i  i  vii         v  i iv      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_33806191_3   5771 AAACAAACAACCCCATCAAAAAGTGGGCAACGGATATGAACAGATACTTC 5820
                          i     i     v  i?    i       v    v    i   i i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_33806191_3   5821 TCAAAAGAAGACATTTATGCAGTCAAAAAACACATGAAAAAATGCTCATC 5870
                           v        i  vi viii i   v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_33806191_3   5871 ATCACTGGCCAT 5882
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (135 / 104)
Gap_init rate = 0.01 (8 / 906), avg. gap size = 1.38 (11 / 8)  


3241 26.43 0.55 0.55  chr1_33963715_33970107     4993  5900 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_33963715_3   4993 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5042
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_33963715_3   5043 GGCCATACTGCCCAAGGTAATTTATAGACTCAATGCCATCCCCATGAAGC 5092
                            v     v     iv i  i  i   i    i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_33963715_3   5093 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5139
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_33963715_3   5140 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAATCAATCCTAAGCCAAAA 5189
                                 viiv  ii  v  v v  v      v     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_33963715_3   5190 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAAGG 5239
                                 i      vv    i  v  ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_33963715_3   5240 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5289
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_33963715_3   5290 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5337
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_33963715_3   5338 TATCTGATCTTCGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5387
                         i vi    i        ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_33963715_3   5388 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5437
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_33963715_3   5438 TGAAACTGGATCACTTCCTTACACCTTATACAAAAATCAATCCAAGATGG 5487
                             ii    i v  v   i     v           i  ii   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_33963715_3   5488 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5537
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_33963715_3   5538 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5587
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_33963715_3   5588 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5637
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_33963715_3   5638 ATTAAACTAAAGAGCTTCTGCACAGCAAAACAAACTACCATCAGAGTGAA 5687
                           i   v v  i i   i  ii vv    iv v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_33963715_3   5688 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5737
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_33963715_3   5738 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5787
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_33963715_3   5788 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5837
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_33963715_3   5838 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAACTGCTCAC 5887
                            v        i  vi viii     v  i          iv      v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_33963715_3   5888 CATCACTGGCCAT 5900
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 582 32.57 6.86 3.81  chr1_34021925_34024516      900  1424 (1168)    L1M4_orf2#LINE/L1        4   544 (364)  

  chr1_34021925_3    900 AGAGGCATACCATCGTCCA-GGATAGGAATATTTA---CTGTAAAAATTT 945
                          i  ii  v    -  i  -    v    v i   ---i   v  i  vv
  L1M4_orf2#LINE/      4 AAAGATATCCCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_34021925_3    946 TAATTCTCTCCAAATCAATCTACAAATTCAGTGAAATTTCAACGAAAGTC 995
                         i   v   i      ii       i     ii v   ii v iv   i  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_34021925_3    996 ACAG-TGAAATTTCTTTGGGGGAAATCTGAAAAATTTACTCTAAAATTCA 1044
                         v   -  ---ii i   v vi     -   v  ii v ii          
  L1M4_orf2#LINE/    103 CCAGCTG---CCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chr1_34021925_3   1045 TCTGGAAAAGTAAACGCACAACAATTGTCAACAAATATTTTCAAAGTAAT 1094
                          v      v i  iv vv v v   v i   v v -  i  v   --  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACA-ATCTTGAAA--AAG 195

  chr1_34021925_3   1095 AATAATGAAG---GAGGTCT-----TTTCTGGGTAGAAAACAAAAATTAT 1136
                           v  ii   ---    v  -----  i iiiv vv     -----   i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC-----TTAC 240

  chr1_34021925_3   1137 TACAAAGCTATGGCAAAATTCAA-ATGATACAATTATGACACAGAAATAG 1185
                                   ii i  ---    - iii iiii vv  i  i iii    
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAA---TCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_34021925_3   1186 ATTAACAGAGAAATAAAATAGAAGAAAAAGTCCAGTTGTAGAACCATGAA 1235
                          ivv i   vv   ii       vvi i       vvi  i v    iv 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_34021925_3   1236 TAGA-GCTGAACTCAGTTT-----ATGATGAAAGGACTATTTCAAATCAG 1279
                          vv - v v  i v v   ----- v i  vv i   i   -   vvvi 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGG 386

  chr1_34021925_3   1280 AAAGGACAGGTTT----------GGAGTT-----AATTCATTATTCATTT 1314
                             i i  vi  ----------  v i -----  i viv  ?i  iv 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_34021925_3   1315 ATAACTAAAATAAAGCTAGATCTATAGCTCAAACCTCGTACAAAAATATA 1364
                         ii  v- i   i   i i  i iv  v    v   vii         -  
  L1M4_orf2#LINE/    437 GCAAA-AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TA 484

  chr1_34021925_3   1365 ATTCACA-CAGATTAAATAGCTAAATGTAAAATATAAAAATTCTGAGAGT 1413
                          i   v -ii   i ? v v          i vv     -i v i i v 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACT 533

  chr1_34021925_3   1414 TCCAGAATAAA 1424
                         iii    v   
  L1M4_orf2#LINE/    534 CTTAGAAGAAA 544

Transitions / transversions = 1.28 (95 / 74)
Gap_init rate = 0.04 (22 / 541), avg. gap size = 2.55 (56 / 22)  

 366 26.32 8.50 2.83  chr1_34021925_34024516     1867  2113 (479)    L1M4_orf2#LINE/L1      648   908 (0)  

  chr1_34021925_3   1867 CAAAAT--AAAACTT--ATGCTGTGAGAGACAACA--AAGTAAGGCTAAA 1910
                               --       --i    vii ii    vi --   -  i iv   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAA 696

  chr1_34021925_3   1911 AGACATGCTACTGATTGATAAAACCTTTTTACAA--CATATAT-TGATTT 1957
                              vv i  v  v  iv i  vv v   i   --       -    --
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT-- 744

  chr1_34021925_3   1958 TAAT--ACATGT--TAAAAATATACAAAGAGCTCCTATAAATGAATAGGA 2003
                         -  v--  v   --iv i      i     i   i  i  v v    iv 
  L1M4_orf2#LINE/    745 -AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_34021925_3   2004 AAAACAAACATGACCTGATAGAAAAATGGGTAGAGAATATGAACAGGCA- 2052
                             v v v  i   ii  v?         i i  i  v    i  i  -
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_34021925_3   2053 --ATCCAGAAAA----TAAAAGTGACCA-TGGACATATGAAGAGATTACT 2095
                         --v    i i  ----  v  i  i   - iii  i     i    -i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCT 892

  chr1_34021925_3   2096 AACTACACTAATAATTGG 2113
                         v --   ii ????????
  L1M4_orf2#LINE/    893 CA--ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (39 / 25)
Gap_init rate = 0.05 (14 / 261), avg. gap size = 2.00 (28 / 14)  


3193 24.76 1.06 1.30  chr1_34058987_34060825.rev      502  1349 (490)    L1M4_orf2#LINE/L1       63   908 (0)  

  chr1_34058987_3    502 CAAAGCAACCTACAGATTCAATGTAATCTGTATCAAAATACCCG-TGTCA 550
                             vii i            i i    iv         v  v -  i -
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC- 111

  chr1_34058987_3    551 TTTTTCACAGAAATAGAAAAAACAATCCTAAAATTCATAAGGAACAACAA 600
                              ii       v  v  ivii               v    vvi   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_34058987_3    601 AAAAGCCTGAAAAGCCAAAGCAATCTTGAGCAAAAAGAACAAAGCTGGAA 650
                         iii v  v   v       i         iv  i          i    i
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_34058987_3    651 GCATCATTCTACCTGGCTTCAAAATATATTACAAGGCTATAATAACCAAA 700
                          vv   iv  v  iiii       iv  i     i    i i   i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_34058987_3    701 ACAGGATGGTATTAGTATAAAAACAGACACA--GACCAATGAAACAGAAT 748
                             vi     i i i    ii i     i --  i     i  i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_34058987_3    749 AGAGAGTCCAGAAATAAATTCATATACTTACAGCCAACTGATTTTCAGCA 798
                         v                 ii    i i   ii i   i        ii  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_34058987_3    799 AAGGCACCAAGAACATGCATTAGGGGAAGGACGCTTGCTTCAATA----G 844
                          i  ii      v   v  v i   i   i iiv ivi     i ---- 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_34058987_3    845 TGCTGGGAAAACTGGATAACCATATGCAGAAAAATGAAACTAAACACCCA 894
                                 v         ?   i     i  i      ii ii  v  i 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_34058987_3    895 TCTCTCACCATATACAAAAATCAACTTAAAATGAATTAGAGACCTAAACT 944
                         i   v                i    i      i  i ?         iv
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_34058987_3    945 TAAGACCCCAAACTATAAAACTACTGGAAGAAAACTTAGGGG--AGTTAT 992
                              v iv             vi i         v    ? -- i i--
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-- 559

  chr1_34058987_3    993 TCCAGGAGATTGGTCTAGGCAAAGATTTTATGGCTAAGACCTCAAAAGCA 1042
                          i iv  vv    vi       v i   iv i v  v   vi        
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_34058987_3   1043 CAGGCAACAAAAACACAAATAGACAAATGGGACTATATTAAACTAAAAAG 1092
                           i         iv v       i    v     vi  i   v v    i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_34058987_3   1093 CTTCTACACAGAAAAAGAAACCATCAACAAAGTGAAAAGACGACCTGTTA 1142
                            i iii vvv   i  v  i     v             i   iiivi
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_34058987_3   1143 AAGACGAGAAAATATTTGCAAGCTATTCATCTGAGAGGGGACTAATGTCC 1192
                           viv                iii  vi      v i      vi i   
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_34058987_3   1193 AGAATGTACAAGTAACTCAAACAACTCAACAGCAAAAAAATAATAATAAT 1242
                              i  i  iv     vv         i ii     i i  -----  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA-----AT 804

  chr1_34058987_3   1243 AACAATCCCATTAAAAAGTGAGCTAAGGACATGAATAGACATTTTTCAAA 1292
                            ---  v   ?    i  i  v     iv             i  v  
  L1M4_orf2#LINE/    805 AAC---CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_34058987_3   1293 AGAAGACATTAAAATGGCAAACAGGTATATGAAAAAATGTTCAACATCTC 1342
                               i  vv       v  i i i i       i   i        v?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_34058987_3   1343 TGATCAT 1349
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.90 (135 / 71)
Gap_init rate = 0.01 (8 / 846), avg. gap size = 2.50 (20 / 8)  


3336 26.10 0.55 0.55  chr1_34226589_34232868     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_34226589_3   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_34226589_3   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_34226589_3   4980 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5026
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_34226589_3   5027 ATATGAAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5076
                              i  viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_34226589_3   5077 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACCACAAGG 5126
                                 i      vv       v  ii i      viv   i    i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_34226589_3   5127 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5176
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_34226589_3   5177 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5224
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_34226589_3   5225 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5274
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_34226589_3   5275 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5324
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_34226589_3   5325 TGAAAGTGGATCCCTTCTTTACACCTTATACAAAAATCAATTCAAGATGG 5374
                             iv    i    v i i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_34226589_3   5375 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5424
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_34226589_3   5425 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5474
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_34226589_3   5475 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5524
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_34226589_3   5525 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5574
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_34226589_3   5575 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5624
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_34226589_3   5625 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTGACAAGAAA 5674
                          i  i  vi          v  i  v      vv    v ii i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_34226589_3   5675 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5724
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_34226589_3   5725 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5774
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_34226589_3   5775 CATCACTGGCCAT 5787
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


4257 20.94 1.34 0.22  chr1_34250277_34254874     3208  4105 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_34250277_3   3208 TGGAAAGACATTCCATGTCCATGAGTTGGAAGACTTAATGTTGTTAAAAT 3257
                                 i  i      i    ii              i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_34250277_3   3258 GCTCATATTTTCCCAAAGTGATCTTCAGGTTCGATGCAATCCCTATCAAA 3307
                          viv   i i-      v      v   i   i i               
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_34250277_3   3308 ACCCCAATGGCACATTTTGCAGAAATAGAAAAAGCCATTCTAATATTTAT 3357
                          i    iiv  viv            v  v  iviv  i    v   i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_34250277_3   3358 ATGGAATCTTAAAGGACCCCAAATAGCCAAAACAAATCTGAGAAAGAAAA 3407
                               vivi  i      vi              vii   i      i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_34250277_3   3408 ACAAAGCTGAAGGCCCCACACTTCCTAATTTCAAAACACATTGCAAAGCT 3457
                               i  i   v i         i           vi i i       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_34250277_3   3458 ACAGTAATCAAAACAGTATAGCATTGGACTAAAGAAAGACAAATAGACCA 3507
                                    i     i i i i   vv   i  v     v     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_34250277_3   3508 GTGAAACAGAATAGAAACCTCAGAAATAAA----TATATT----GTCAAA 3549
                         i  i  i     v  i vii          ----  i   ----     v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_34250277_3   3550 TGGTCTTTGACAAGGGTGTCAAACCTACAAAATGGGGAAAGAATGGCCTC 3599
                           i i  i          i   iv i ivv              i i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_34250277_3   3600 TTTAACAAATGTTGTTGGGAAAACTGGATATCTACATGCAGAAGAATAAA 3649
                           i        v  i     v         ? i       i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_34250277_3   3650 GTTGGACCCTTACCATATACCATATATAAAAATTAACTCAAAATGGAATA 3699
                                  i    vi i        i                    vi 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_34250277_3   3700 -AGATCTAAAAGCAAGACCTGAAACTATAAAATTCCTAGAAGAAAACATA 3748
                         -   i     v i    v  i           i  i              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_34250277_3   3749 AAAGGAAAGCTTTATGACATTGGATTTGGCAAAGATTTCTTGGATATGAC 3798
                         ii? v   v   ii    v    i  v     v i      i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_34250277_3   3799 AACACAAGCACAGGCAACAAAAGCAAAAATAGACAAACGAAACTACATCA 3848
                          v  v       i          v         i   ivii   v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_34250277_3   3849 AACTTAAGAACTTCTGTGCAGCAAAGGAAATAGTCAACAGAATGGAAAGG 3898
                           v    i     i     vv       v ivi    v i i  i    i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_34250277_3   3899 CAACCTAAGAAATGGGAGAAAATATTTGCAAACCATATTATCTGGTGAGT 3948
                              i vii                      i     -     i i  v
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGG 748

  chr1_34250277_3   3949 GGCT---ATACAGAATATACAGAGAACTCCTCTAACTCAACAATAACTGA 3995
                          i  ---  v         i i       i vi       i     vvii
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_34250277_3   3996 ATGAATAATCTGATTTTAAAATGAGCAAAGGACTTTAATAGACATTTCCC 4045
                          ii     i ii   ?v      i        i  v            i 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_34250277_3   4046 CAAAGAAGATAGACAAATGGCTGACAAACATATGAAATTATGTTCAACAT 4095
                                    v         ii i  i  i      vv   i       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_34250277_3   4096 TACTAACCAT 4105
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.03 (124 / 61)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.33 (14 / 6)  


3189 26.35 0.88 0.77  chr1_34384936_34391213     4879  5785 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_34384936_3   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAGGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v   i  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_34384936_3   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_34384936_3   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_34384936_3   5027 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_34384936_3   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_34384936_3   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_34384936_3   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAGCGCCGCATATCTACAACT 5224
                                i    i--    i  --       ivv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_34384936_3   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_34384936_3   5275 CTATTTAATAAATGGTGCTGGAA-AACTGGCTAGCCATATGTAGAAAGCT 5323
                           v  i  i            i -      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_34384936_3   5324 GAAACTGGATCCCTTCTTTACACCTTATACAAAAATCAATTCAAGATGGA 5373
                            ii    i    v i i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_34384936_3   5374 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_34384936_3   5424 CTAGAGA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5472
                         v   i?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_34384936_3   5473 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGCGATCTA 5522
                         vi            vvi          vv     v  i    vv  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_34384936_3   5523 ATTAAACTAAAGAGCTTCTGCGCAGCAAAAGAAACTACCATCAGAGTGAA 5572
                           i   v v  i i   i  i  vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_34384936_3   5573 CAGGCAACCTACAAAATGGGAGAAAAT-TTT-CAGAACCTACTCATCTGA 5620
                         v  i     i   i             -   -  i v v  i--      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chr1_34384936_3   5621 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTGACAAGA 5670
                         i  i  i  vi          v  i  v      vv    v ii i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_34384936_3   5671 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACCA 5720
                             i     i     v  i?    i     i     iv    i    vv
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_34384936_3   5721 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5770
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_34384936_3   5771 ATCATCACTGGACAT 5785
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2776 25.59 3.24 1.79  chr1_34441145_34446461     3930  4824 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_34441145_3   3930 TGGAAAAACATTCCAAGTTTACGTATAGGA-GAATCAATATTATTAAAAT 3978
                               i i  i   v   i i v  v   -  v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_34441145_3   3979 GGCCTTAGAACCCAAAACAACTTACAGATTCAGTGACATTTCTATCAAAC 4028
                            vv  vvv      vii ii          ii vv  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_34441145_3   4029 TACCAA-TGCCATTTTTCACAGAATTAGAAAAACCTATTCTAAAATTCAT 4077
                          v   i-    -     ii     v v  v  i iv  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_34441145_3   4078 ATGGAA-TCCAAAAAGAGCCCA-AATAGCCAAAAGTATCTTAAGCAAAAA 4125
                               - v   i-- ii    -           vv     i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_34441145_3   4126 GAACAAAGCCAAAGGCATCACACTACCCAACTTCAATCCGTACTACAAGG 4175
                                 iiii   vv       v     i     vv v        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_34441145_3   4176 CTACAGTAACCAAAACAGGATGGTACTGGTACAAAAGACGACCCTTATAC 4225
                                  i   i    vi         i i  iiivv   viv  v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_34441145_3   4226 TAACGGAACAGTTTAAAGAACCCAGAAATGAAGCTGCACTCTTAACAACC 4275
                         i  i    i  vv vi   ii        i  v iii  vi   -iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTC 346

  chr1_34441145_3   4276 ATCTGATCTTTGATAAAGTCAACAATAACAAGCAATGGGGAAAGGA--GT 4323
                          vi    i  i  i  i viiv   v v  vv            i --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_34441145_3   4324 CCGAATTTATTAAATGGCGCTGGGATAATGGGCTATGTACATGTGGGAGA 4373
                          iv--  i vi      i       i  iv  v  ?vi     iiii   
  L1M4_orf2#LINE/    397 CTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_34441145_3   4374 TTGAAACTGGACCCCTTCCTTTCACCATATACAAAAATCAACTCAAAATA 4423
                         v    ii         v   iv                i          i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_34441145_3   4424 GATAGAAGGCATAAATATAAGTCCTAAAATAATTGTTTTAAA--TCCTAG 4471
                            vi?  i v     i    vv      iv  ------   --  i   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTAT------AAAACTCTTAG 538

  chr1_34441145_3   4472 AAGAAAATCTAAGAA-ATATCATTTTG-GACATGGGCTTTGGCAA----- 4514
                                iv  i ?i- v   --  i -   v v  v  v     -----
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_34441145_3   4515 ----AGATGAAGTCTCCAAAAGCAAGTACAACACAAACAAAAATAGACAG 4560
                         ----    - v v v         vivi     v  iv         i i
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_34441145_3   4561 GTGAGACCTAA-CTAAATTAAAGAGCTCTGCAGAGCAAATGATACTATCA 4609
                         i vi   i v - v        i vi i  iivvv    v  i       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_34441145_3   4610 ACAGAGTAAACAGACAACCTACAGAATGGGAGAACATATTCACAAACTAT 4659
                          v i   i  v        i              v     ii    ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_34441145_3   4660 GTATCCGATGAAGGTTCTAATATCCAGAATCTATAAGGAACTT----GAA 4705
                         i    i   -    vv  vi          v     i     i----i v
  L1M4_orf2#LINE/    736 ATATCTGAT-AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_34441145_3   4706 TCAGTAAGCAAAAAACAA----CCCCATT-AAAAATGTGAAAAGGACATG 4750
                            i   vv    i    ----   v   -       v v      iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_34441145_3   4751 AACAGACACTTCTCAAAAGAAGATATATATATGGCCAACAAGTATATGAA 4800
                           i     i     v            i v        i   i i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_34441145_3   4801 AAAATGCTCAAGATCACTAATCAT 4824
                           i        v    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (129 / 97)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.14 (45 / 21)  


3230 23.85 4.82 1.03  chr1_34676457_34678302      494  1365 (481)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_34676457_3    494 AAAAAT-TATCATGGTTCATGGGTAAGAAGACTCAATATTGTTAAAGTGT 542
                            i  - vi    -       i vi       i           ii  v
  L1M4_orf2#LINE/      4 AAAGATATCCCATG-TTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_34676457_3    543 CAGCTCTTCCCAACTTAATCTATAGATTCAACACAATCCCAATGAAAACC 592
                           iiv  i     v  i     i         i       v  v    i 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_34676457_3    593 CCAGCAAGTTATTTTGCAGATATCAATGGACTGATTCTAAA--------G 634
                              vivi v         v  ii iiii     i     -------- 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_34676457_3    635 GGAGC-CAAAAGACCCAAGATAACCAAAACAATATTGAAGGAGAAAAATA 683
                          i ii-   ii      ii   i          v     ii    i  i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_34676457_3    684 AAGC-AGAGGACTGACACTACTTAACTTAAAGACTTACTATAAAGCAATA 732
                            i-i       v     v ii  i  v  i        i     v i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_34676457_3    733 GTGATCAAGACAATGTGGTATTGGTGAACGACTAGACA----GACTAATG 778
                           i         i       i   iiv v iv      ----  ii    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_34676457_3    779 GAACAGAACAGATAGATCCA--------CCTAAACAC----AGTCAACTG 816
                            i    iv  v  -    --------  i v   i----i     i  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAG-TCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_34676457_3    817 ATCTTTAACAAAGAAGCAAAGGCAACTCAATGGAGAAAAGACAGTCTTCT 866
                           i  ii    i iv  v   i v i       i    ii i      i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_34676457_3    867 CAACAAATGATGCCTGAACAACTGGATATCCACATGCAAAAAGCTGAATT 916
                                  i   iv i           ?            iiv    v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_34676457_3    917 TTGACACAGATCTTATATCTTTCACAAAAGTTAACTCAAAATGAAACACA 966
                          v   v vv i  i i i v vi      i             i v  ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_34676457_3    967 GACCTAAATGTAAAAGACAAAACTATAAAACACCTGGAAAATAACATAGG 1016
                                      i  vi             v i i   i v        
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_34676457_3   1017 AGAAAGACTAGATGACCTTGGGCTTCACAATGACCATTTAGGTACAACA- 1065
                         ? v  iv  vvi          i vvi     iiivi    i  ii   -
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_34676457_3   1066 -AAACAGTATAATCATTGAAAGAAAAAAAAAAAAGATCAGTTGGACTTCA 1114
                         -   -  i i  v  vii          v ----   v i          
  L1M4_orf2#LINE/    602 CAAA-AGCACAAGCAACAAAAGAAAAAATA----GATAAATTGGACTTCA 646

  chr1_34676457_3   1115 CTAAAGTTAAAAACTTCTAATTGA--CAAAAGACACTGTTAAGAGACTGA 1162
                         ii   i          i i--  v--    i      i i    i v   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTG--TGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_34676457_3   1163 AAAGATAAGCCACAGACTGGGTGAAAACATTTGCAAAACACATATCTGAT 1212
                              i  v       v    v     i         v  i         
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_34676457_3   1213 AAAGTAATTGCGTGTAAAATATGCAAAGAACATTTAAAACTCAACAATGA 1262
                           i v v   ii vi i     ii       vi   v       i   i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_34676457_3   1263 GGAAAGAACTACCCCAATTAAAAAATGGGCAAACAATCTGAATAGACACC 1312
                         ii i v  v  v       ?             vi  i          ii
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_34676457_3   1313 TCACCAAAGAAGATATATAAGTGATAAATAAGC-----------TGTTCA 1351
                           v              i  i  iiv       -----------  i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_34676457_3   1352 TTATCACATATCAT 1365
                         vi    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (137 / 67)
Gap_init rate = 0.02 (15 / 905), avg. gap size = 3.40 (51 / 15)  


3281 26.87 0.44 0.44  chr1_34701019_34707299.rev     4883  5790 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_34701019_3   4883 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4932
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_34701019_3   4933 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4982
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_34701019_3   4983 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5030
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_34701019_3   5031 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5080
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_34701019_3   5081 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5130
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_34701019_3   5131 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5180
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_34701019_3   5181 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5228
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_34701019_3   5229 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5278
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_34701019_3   5279 CTATTTAATAAATGGTGGTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5328
                           v  i  i        v     v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_34701019_3   5329 GAAAGTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5378
                            iv    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_34701019_3   5379 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5428
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_34701019_3   5429 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5478
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_34701019_3   5479 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5528
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_34701019_3   5529 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5578
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_34701019_3   5579 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5628
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_34701019_3   5629 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5678
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_34701019_3   5679 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5728
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_34701019_3   5729 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5778
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_34701019_3   5779 ATCACTGGCCAT 5790
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2129 22.32 10.44 5.68  chr1_34951370_34953904      998  1754 (781)    L1M4_orf2#LINE/L1        1   793 (115)  

  chr1_34951370_3    998 TGGAGAGACATGCTATACTCATGGATTGGAAGATTCAACATAGTAAAGAT 1047
                             i   i  v i  ii               i i  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_34951370_3   1048 GATAATTTCCCCCAAATT-----ACAGAATTAACGCAATTCCTTTCAAAA 1092
                          ii   vii         -----     v i        i   v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_34951370_3   1093 CCCCAGCAAGTCTTTTTATACATAGA--GACAAGTTCGTCCTAAAATT-A 1139
                         i      v- i      - i  v i --      i vi          - 
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_34951370_3   1140 TATGGAAAGGCAAAGGAACTAGAATAGCTAGTAAAAACA--TTGGGGAAA 1187
                                 v    i   v i        i ----     --i v ii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCA----AAACAATCTTGAAAAA 194

  chr1_34951370_3   1188 AAAGAATATAGTGCGAGAAATCAGTCAACCCAATTTCGAGACTTATTACA 1237
                         i     i v   vv   i v   vv vv         i i     i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_34951370_3   1238 TAGCTACA-TAATCAGAGCCACATGGTAC---CATGCAGTGACAGACACA 1283
                         v       -      iii viii      ---   i-  -  i     i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA-AG-GATAGACATA 292

  chr1_34951370_3   1284 T----CAGTGGAACAGAATAGAGACTTCAGAAATAGACACACATAAATAT 1329
                          ----  i     i     v    v i        i  v  i i vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_34951370_3   1330 TCCCAACTAATTTTTGAGAAAAG---CAA-----CTCAATGAGGAAAGAT 1371
                         vvi   i i     i  v  ii ---   -----i      i       v
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_34951370_3   1372 AAGTCTTTTCAACAAGCAGTGCTGTAGCAATTGAGCATTCATACACAAAT 1421
                         v              iii      vii   i  iii ?i  i ii    -
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA- 441

  chr1_34951370_3   1422 AATAATAATAATAATAATAATAATAATAATAATGCACTTCAACCTAAGTC 1471
                         ------------------- v   i - i --  v  i----    --i 
  L1M4_orf2#LINE/    442 -------------------AGAATGA-AGT--TGGACC----CCTA--CC 463

  chr1_34951370_3   1472 TCACACCTTATACA----------CAG--TGGATCATGGACTTAAATGTA 1509
                                v      ----------  i--       ?i   i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_34951370_3   1510 A-------AATCATAAAATTTT-----------ATAAATG-AAATC--CA 1538
                          -------  ii      i i -----------   ii? -     -- i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_34951370_3   1539 -------GGGCTAGGCAAAAAATG--TTCTTAGGCTTCACACTAAAAGCA 1579
                         -------   i       ----  --       iiv v    i       
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAA----TGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_34951370_3   1580 ---------AAAGGAAAAACTGATGAATCAAACTTCATCAAAATTAAAAA 1620
                         ---------    i     iv   i   iii                   
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_34951370_3   1621 ATGT-GTGCTTTGTGAAAGACCCTGTTAAAAGGATAAAAAGATAAGCTGC 1669
                         v v -      ii--  i   v  i i  i iii i      i  v ii 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCA--AAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_34951370_3   1670 GGAG-AGAACAAAATATTTGCAAACCATATATCCACCAAAGGACTAGTAT 1718
                         i  i-i i v              i        iivi  i     v    
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_34951370_3   1719 CTAGAATATATAAAGAACCCTCAAAACTCAACAGTA 1754
                          i                i  i v       i i  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

Transitions / transversions = 2.53 (119 / 47)
Gap_init rate = 0.04 (32 / 793), avg. gap size = 3.81 (122 / 32)  

 535 18.46 0.00 2.31  chr1_34951370_34953904     1913  2042 (493)    L1M4_orf2#LINE/L1      782   908 (0)  

  chr1_34951370_3   1913 AACTCAACAGTAAAAAAAATCCAAACAATCCAATTAATACATGGGCAAAA 1962
                                i i      i ---    i  i      ? v v         i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_34951370_3   1963 GATGTGAAGAGACATTTTACTGAAGAAGATATACAGATGGCAAATAAGAA 2012
                            v    v        iv ii             i     v      v 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_34951370_3   2013 CTTGAGAATATACCCAACATTATAAGCCAT 2042
                          v   i  v  i i      i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.01 (1 / 127), avg. gap size = 3.00 (3 / 1)  


3597 23.45 1.44 1.00  chr1_35203535_35207855.rev     2927  3830 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_35203535_3   2927 TGGAAAGATATCCCATATTCACAAATTGGAAGAATTGATATTGTTGAAAT 2976
                                         i    iii         v  i        i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_35203535_3   2977 CCCCACACTACCCAAAGCAATCTATAGATTTAATGCAATCTCTACAAAAA 3026
                         vv v i   v      vii     i     i  i      i   iv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_35203535_3   3027 TACCAATGACATTATTCACAGAAATATAAAAAAC-AATCTAAAAATTCAA 3075
                          v   iivi v  v  ii       - i v  i -i   iv        v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_35203535_3   3076 ATGGAACCACAAACAACTCCAAATTGCTAAAGCAATCCTGAGCAAAAAGA 3125
                               vii   ivi  i vi   v  i   i     i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_35203535_3   3126 ACAAAGCTGGAAGCATTATTCTATCAGACTTCAAAATATACTATCAAGCT 3175
                               i    i vv i iv  vi vi i       iv     iv     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_35203535_3   3176 ATAGTAACCAAAACAGCATGGTACTGGCACAAACACACACACATAGACCA 3225
                          i     i   i    ii           i  iv i v   i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_35203535_3   3226 ATAGAACAGAACAGAAAGCCCAGAAATAAAGTCATGCACCTACAGCTAAC 3275
                           i   i    iv  i  i           vi   i  ii  ii ii  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_35203535_3   3276 TGATTTTCAACAAAGGTGCCAAGAGCACACATTGGGTAAAAGACAGTTTC 3325
                                 i    i          v  iv  v    v   ii i   i i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_35203535_3   3326 TTCAATAAACAATGCTGGGAAAATTGGATATGCATATGCACAAGAATGAA 3375
                              i   iii        v  i      ?v  i     v         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_35203535_3   3376 GCTAGACTCCTACCTCTCACCATATACAAAATTCAATTCAAAATGAATTA 3425
                          i i   i        v              v i  i        i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_35203535_3   3426 AAGACTTAAATGTAAAACCTGAAACCATTAAATTACTAGAAGAAAACACA 3475
                         ?    i         i v  i    i  v   i vi            i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_35203535_3   3476 GGGA-AAATGCTTAATAACATTGGACTGGGCAAT--TTTTTTAAAAAAAT 3522
                           ?i-    -   vi i  v    ii i      --   i   i ---- 
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA----T 594

  chr1_35203535_3   3523 AAGTCCTCAAAAGCACAGGCAACAAAAACAAAAATAGACAAATGGAACTA 3572
                          v v vi          i         iv         i    v i   v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_35203535_3   3573 CATCAAACTAAAAAGTTTTTGTGCAGCAAAGGAAAC----AATAGAGTGA 3618
                                v v    ii        vv       v  ----  v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_35203535_3   3619 AGAAAGACAATCTATAGAATGGGAGAAAATATTTGCAAACTATACATCTG 3668
                          --       i i i                        ii   i     
  L1M4_orf2#LINE/    695 A--AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_35203535_3   3669 ACAAAAGGTTAATATCCAGAATATATAAGGAAGTT----AACTCAACAAC 3714
                          i  ii ii vi                i   v i----       i  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_35203535_3   3715 AAAAAAACAGATAATCTGATTTTAAAATGGACAAGATAACTT-AAGAGAC 3763
                              i   i    i ii   ?v       i   - vi i  -  v    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAA-AGGATTTGAATAGAC 841

  chr1_35203535_3   3764 ATTTCTCAAAAGAATTAATTCAAATGGCCAACAGGTACACGAAAAAATAC 3813
                                v      vvv  v           i i i   i     i  i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_35203535_3   3814 TCAACATCACATATCAG 3830
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (142 / 66)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


 603 29.72 10.68 6.58  chr1_35472916_35475466.rev      548  1109 (1442)    L1M4_orf2#LINE/L1        4   588 (320)  

  chr1_35472916_3    548 AAAGACATACCAAGTTCATGGATAGAAAGAC-----------ACAATGCC 586
                              i  v   v          v i     ----------- vi   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_35472916_3    587 ACTTCTCTCTCAGTTGATCTACACATTCATGATAATTAAATAAAATTCCC 636
                          v v   i iv i          v     ---------- iiv   i  i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCA----------ACGCAATCCCT 93

  chr1_35472916_3    637 A-AAAAATTTTTGTTATTTGATTTTGTTCTGTCAGAAACTTCCCAAGATA 685
                          -v     iiiv i iii --    ----  -      -  vv    v i
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCT--TTTT----TG-CAGAAA-TTGACAAGCTG 135

  chr1_35472916_3    686 TTTCTAA--------TGTAAA--CAGGGG--CAAGAATAGGCAAAACATT 723
                         v i    --------  v   --  i   -- v       v       v 
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_35472916_3    724 CCTGAAGAA-------AAATTTTCAGGG---ATGTGTCCCATCAGATTAT 763
                          i    i  -------   v  vv   i--- iiiv     ----   - 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA----ATT-T 230

  chr1_35472916_3    764 TAAGAATTATTACACAGCT-CATTCATTAGAACACCTTGGTACTGTCACA 812
                         i  i v   i    v    -  v v  i ii   viv        v  i 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_35472916_3    813 GGAATAAACAAACAAACAGTCCAAGAAAACATTAACTGAGAATGTGGGGA 862
                         i i   i   v i i i----   vii  i v-  i     i vii ii 
  L1M4_orf2#LINE/    281 AGGATAGACATATAGAT----CAATGGAATAG-AATTGAGAGTCCAGAAA 325

  chr1_35472916_3    863 --AATGCCTACAGATGTAGTTA-TAGA-----GA-AACTTTGC--AG--- 898
                         --  iv v    vv i i  i - v  -----  -  vvv   --  ---
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_35472916_3    899 -CTTACTGGAGAAAGGAGGTAGTATTT--GATAGATGCTGGTGAGTAAGG 945
                         -i i v   i     i --    v   --i i i   v  v  i ----i
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAA--TAGTCTTTTCAACAAATGGTGCTGGG----A 419

  chr1_35472916_3    946 TAATTTATTAGCCTTAT--AATAGTAAATAAAATTAGTTCCCTACTCCAC 993
                         i  i viv  ?  vi  --  v  --   i  i  i vi      ii   
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAG--AATGAAGTTGGACCCCTACCTCAC 467

  chr1_35472916_3    994 ACCATATA-AAAAATTAGTGTAGGGTAATTCA-AAAGCTACACGTGAAAG 1041
                                 -        iivi iii iiv   - i v   v i  i i  
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_35472916_3   1042 GCAAAATCAATAAAGATTTTAGGAAATAATATACAGTCATCCCTCCATAT 1091
                         vi    - v     iv i    i i v  i   vi?vi vvi  i i iv
  L1M4_orf2#LINE/    518 CTAAAA-CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_35472916_3   1092 CCATGGG----GCACTAGTTCC 1109
                           v    ----   v i   i 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTC 588

Transitions / transversions = 1.46 (98 / 67)
Gap_init rate = 0.05 (32 / 585), avg. gap size = 3.03 (97 / 32)  

 513 25.07 8.75 6.41  chr1_35472916_35475466.rev     1724  2066 (485)    L1M4_orf2#LINE/L1      558   908 (0)  

  chr1_35472916_3   1724 TCTTCCTGATCTCAGCCCAGGAAATT-TTTCCTAAATAAAATGGGGGTTA 1772
                              v   i  ii vii   v   v-    i  i   ---  iviviv 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA---TGACACCAA 604

  chr1_35472916_3   1773 AAATATAAACCATAAAGGAAAAGACTGATAAATTTATTATCGTTCAACTA 1822
                           ii i  i v i   i     i iv        ------- ---i   v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATT-------G---GACTT 644

  chr1_35472916_3   1823 CATTAAAATCAATTAACTTCTGCATATGCAAAGATTTTATGAAGACA-T- 1870
                            i     i  v-     i  iiiv vv  i  ivi   v    v - -
  L1M4_orf2#LINE/    645 CATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_35472916_3   1871 AAGAGAT--------GAATGAGA-AGTTTATTCGCACCATC-TATAACTG 1910
                           i   i--------     i  - ivv    i   v-   -    v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTG 742

  chr1_35472916_3   1911 GTAAG---TTTATTGTTCAGAACATTTAGAGAATGCCTACAATTCAATAA 1957
                         i    ---i  i -i i     i  v  i    iv i     i       
  L1M4_orf2#LINE/    743 ATAAGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_35472916_3   1958 GAAAAAAACTAATAGC---------AAGTGGGTAATAGATTTAACGTAAC 1998
                         v     i  v    i ---------  i    i  vi     i ---- i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA----AT 837

  chr1_35472916_3   1999 AGGCATTTC-ACAAAAAAAAT-TAAAAATACCCAATAA--ATGTGAAAA- 2043
                           i      -v    i  i  -  v    iv       -- ii      -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_35472916_3   2044 ATGTTCAACTACTCATTAACAAG 2066
                            i     - -   ????????
  L1M4_orf2#LINE/    888 ATGCTCAAC-A-TCAZZZZZZZZ 908

Transitions / transversions = 1.97 (57 / 29)
Gap_init rate = 0.06 (21 / 351), avg. gap size = 2.48 (52 / 21)  


 523 27.43 6.29 0.57  chr1_35476736_35479243.rev      497   671 (1837)    L1M4_orf2#LINE/L1        4   188 (720)  

  chr1_35476736_3    497 AGAAATATTCCATGCTTATGAA----AAGACTATATATACTTAAGGTGTT 542
                          i i    i     i i   i ----      vv    vv     i  vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_35476736_3    543 AATTTTCCCCCAAATTAATCTAGAGATTTAATGTAACTCC----AAAGTC 588
                            vi     -     i     v     i  i i  ii  ----   i  
  L1M4_orf2#LINE/     54 AATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_35476736_3    589 TCTGTGGATTATTCT--AGAAATTTACACATTGACTCTAAAATGTATGTG 636
                         i v iv vi v  i --       v   vii   ii       vi  i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_35476736_3    637 TAACTACAAGAGACAT-GAAAAGCCAAAACAATTTT 671
                         v  v i    i   vi-   v            i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

Transitions / transversions = 1.67 (30 / 18)
Gap_init rate = 0.03 (5 / 185), avg. gap size = 2.40 (12 / 5)  

1354 24.28 10.02 2.00  chr1_35476736_35479243.rev      978  1426 (1082)    L1M4_orf2#LINE/L1      235   719 (189)  

  chr1_35476736_3    978 ATTTAATATAAAGCTAAATTAACCAAGACAGTGTGATATTGGCCTAAGGA 1027
                          i   v  i       v v   i            i  i    v      
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_35476736_3   1028 TAAACATACGGATTTGTGGAATAGAA----AAGTCCAAAAATAGACTCAA 1073
                           i     ii   ivi          ----i      i     i  i  v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_35476736_3   1074 AAACATT---GGTCAAATGACTTCCCACAAAAGTGCCAAGGTAAATCAAT 1120
                          --    ---      v   i  i v    ii        iiv v     
  L1M4_orf2#LINE/    335 A--CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_35476736_3   1121 CCAAAAAAAA-AATCTT--CAATAAATGTTACTGATACAACTGGACATCC 1167
                         vvii   i  - i    --   i     v i   iv         i ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_35476736_3   1168 ATATACAAAAAGAT------------TTATTTTACACTACATACAGAAA- 1204
                          i  i     ii  ------------i  ii i    i i     i   -
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_35476736_3   1205 ---CTTGAAATGGATCATCAACTTAAGCATAAAAGCTAAGCCTAAACTAT 1251
                         ---  ii          ?vi  i   iii   i      -----      
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA-----AACTAT 527

  chr1_35476736_3   1252 AAGGTTTCTAGAAAAAAA-GCAAGTACAAATTTTCATGATCTTATGATAG 1300
                           iii ii     i    -ii i ?ii    i   i   i   iv v   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_35476736_3   1301 A------TTTCTTAGA----ACAC----AGCATAGACCATAAAA-ATATA 1335
                         i------         ----    ----    i ii v i    - v v 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_35476736_3   1336 ATAATAAAATTGGGCTTCATCAATATTAAAAA--TTTGTGCTTTTCAAAG 1383
                            ivv       i         v        --         --     
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAG 675

  chr1_35476736_3   1384 AACACCAACAATACAAC-AAAAGGCAATCCAAAGAACAGATGAA 1426
                         i    i v   v v ii-     i   i   v    ii iv   
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

Transitions / transversions = 2.79 (78 / 28)
Gap_init rate = 0.03 (16 / 485), avg. gap size = 3.38 (54 / 16)  

 402 21.48 4.44 0.74  chr1_35476736_35479243.rev     1883  2017 (491)    L1M4_orf2#LINE/L1      769   908 (0)  

  chr1_35476736_3   1883 AAAGGATCCTTACAACTTCATAAAAAGAAGACAAACAA----ATTTTAAG 1928
                             i ii         iv    v  i        i  ----   ?v  i
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_35476736_3   1929 ATGGACAAA-AATTCAAACATACACTTCACAAAACAACATTTAGGAAAGG 1977
                             i    -i   ii  i v   i   v v   v  v  v  vi  v  
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_35476736_3   1978 CCAATAAGTACTCTGAAAA-ATGCTCAACACCATTGGTTAC 2017
                                 i  -v      -          i  ????????
  L1M4_orf2#LINE/    869 CCAATAAGCAC-ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (16 / 12)
Gap_init rate = 0.03 (4 / 140), avg. gap size = 1.75 (7 / 4)  


2764 23.09 8.58 3.83  chr1_35535576_35539152.rev     2225  3086 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_35535576_3   2225 AGACTATTCCATGTTTCCAAATTAGAAGACTCAACATTCCTAAAATGTCA 2274
                            -   i       iviii   i       i  i   vi   i   v  
  L1M4_orf2#LINE/      6 AGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_35535576_3   2275 ATTCTCTCC--------CTCTGGATTCAGGACAGCCCCAACTGAAATTCT 2316
                           v   i  --------  vii      ivi  ii   v iii    i i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_35535576_3   2317 AGCAGCCTTTTTTTTTTTTTTTTTTTTAAAGAAATTGACAAGTTGATTCC 2366
                            v         vi--------------             i    i i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGC--------------AGAAATTGACAAGCTGATCCT 140

  chr1_35535576_3   2367 AAAATGTATATAGACATGCAAATGAC----------------AAGTTT-- 2398
                              vi    i  v      iv   ----------------  vi  --
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_35535576_3   2399 --AAGAAGAACAAAGCTGGAAGATTTACACT-CTTAATTTCCAGGCTCAC 2445
                         --             i    i  i i     - ii      v ii  i  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_35535576_3   2446 TGTAAAATCACAGTAATCAGGACAGT-TGGTACTGGTATAAAAATAGACA 2494
                          ii   iii          i      -         i    ii       
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_35535576_3   2495 TATAAGTCAATAGAACAGAATAGAAAGTTTCAGAAACAGACTGATAGATA 2544
                             ii     i   i     v  i   i-      i i  iv   ----
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATA---- 335

  chr1_35535576_3   2545 CATATATG----ATTGACTTTTAACAGAGTTGCCAATGTAATTCAATGGG 2590
                            v    ----     i   ii   ii v      viiv          
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_35535576_3   2591 GAATGAATAGTCTTTTT--CAAGGGCAGTGCTGGAACAACTGGATGTCCA 2638
                            v            i--   iv --       i          i?   
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATG--GTGCTGGGACAACTGGATAKCCA 433

  chr1_35535576_3   2639 TATTCAAAA-AATGAACCTTGACCCTTGTCTCAACTCATATATAAAAATT 2687
                         i  v     -      vi v     i ii    vvi      i       
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_35535576_3   2688 ACCTCAAAATAGATCACAAAC------ATAAAAGTTAAAACTATAAAACT 2731
                          v        i     ? i  ------i   i  i               
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_35535576_3   2732 TCTAGAAGAAAATGTAAGAGAATGTCTTAGTTACTATGAGTTAGGCAAAA 2781
                         ii          ii  i ? v vi    v  v  iv  i         vi
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_35535576_3   2782 ATTT-TTAGATGAGGTATTAAAAAGCACAATCCATAAAATAACAAATTGA 2830
                         i   -      iv ii ii    -      v v i    v  v    v  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_35535576_3   2831 TAAAAGGGACTTCCTCAAAATCAAAA---TCTGCTACT--------CATC 2869
                             vv       v       i    --- i  - i  --------  ii
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACT 681

  chr1_35535576_3   2870 ATTAAGAAAATAAAAAGG-AAGTAACAAAATAGGACCAAACGTT-G---- 2913
                           i      i i     i-  viv   i   i   vv   ii  - ----
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_35535576_3   2914 ------ATTTGATAAAGAAATTATGTCCACAGTA----AAGAATACTTAC 2953
                         ------  i      i i v  i i    v i  ----     iv     
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_35535576_3   2954 AACTCAGCAAGATAA---CAACCAACCCAACAAAAAAATGAAAAAAATGT 3000
                               ii  v v  ---   vi       iv?       i---------
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG--------- 822

  chr1_35535576_3   3001 GCGAAAACTGTGAATAAACACTTTACCAAAGAAGACACATGAATGGCAAA 3050
                           i  iiv v      i   i  iv          i i ii      v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_35535576_3   3051 TACATATATGAAAAGATGCTTAACATCATTAATCAT 3086
                           vii i             i       ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (136 / 59)
Gap_init rate = 0.03 (25 / 903), avg. gap size = 4.28 (107 / 25)  


1039 20.42 8.65 2.77  chr1_35543719_35547714.rev     1279  1567 (2429)    L1M4_orf2#LINE/L1        3   308 (600)  

  chr1_35543719_3   1279 GAAAGACATCCTGTAGTCACAGATCAGAAGATTTAATGATGTTAAAATGG 1328
                               i    ii iv   ii   ii     i     iv      i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_35543719_3   1329 CAATATTCTCCAAATCAATTTATAGATTCACTGCAATCA-TATCAAAATC 1377
                              i  i      ii  i  i       vi      v-          
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_35543719_3   1378 C-AATGACCTTTTTCTGCAGAAATGGAAAAACCCATTCTAAAATTGACAT 1426
                          - iivi       -         v  v  i iv  i        v i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_35543719_3   1427 AGAATTTCAAAGGACCTTGAAGAGCCCAAAGAATTTTGAG------GAAC 1470
                         i   v v   i     iv   v    v   v   i    i------    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_35543719_3   1471 --------------CACATTTCCTGATTTCAAAACTTAATACAAAGCTAT 1506
                         --------------    i    ii             v          i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_35543719_3   1507 AATGTAAGTTGCAAAAC--TGTG-TACTGCCCTAAAAATAGCCATCTATA 1553
                          --    -- -   i  --    -     v v   ii    v   --   
  L1M4_orf2#LINE/    252 A--GTAA--T-CAAGACAGTGTGGTACTGGCATAAGGATAGACAT--ATA 294

  chr1_35543719_3   1554 GAAAAATGGATTAG 1567
                           vv      v   
  L1M4_orf2#LINE/    295 GATCAATGGAATAG 308

Transitions / transversions = 1.68 (37 / 22)
Gap_init rate = 0.04 (11 / 306), avg. gap size = 3.00 (33 / 11)  

1603 16.75 1.29 6.70  chr1_35543719_35547714.rev     1846  2233 (1763)    L1M4_orf2#LINE/L1      299   665 (243)  

  chr1_35543719_3   1846 AATGGATTATAACTGAGAGTCCA-AATTAAACCCATCTATATTTGGTCAA 1894
                               v  v  i          -  v         vi  v v       
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_35543719_3   1895 AAGATTTTCTACAATGGTATCAAGCCCATACAATGGGTAAAGAACAGTCT 1944
                         vv       v    v   ii    v    v       v      i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_35543719_3   1945 CTTCAACAAATGGTGCTGAGAGAACTGGATAACCACATACAAAAGAATGA 1994
                         i                 i  v         ?      i           
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_35543719_3   1995 AGGTAGACC--TAGCTCATACCAGATACAAAAATTAACTCAAAATAAATG 2042
                           v i    --  v    i    v                     ii  v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_35543719_3   2043 AACGACCTAAATATAAGAGCTAAAATCATAAAACTCTCTGAAGAAAAGA- 2091
                          ?v         i            ii          iv        v -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_35543719_3   2092 -GGATTAAATCTTCATGCCCTTGAATGTGGCAGTAGATTCCTAGATATAA 2140
                         -  ?v         i  v     ii vv    i i v   i       i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_35543719_3   2141 CACCAGGAGCACAGGCAATAAAAAGAAAAGAGAAAGGAAAAGAAAAGGAA 2190
                              ii      i    i    ------------------     ----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAA------------------GAAAA---- 626

  chr1_35543719_3   2191 GAACAAAAAAGAAACTGAACTTCATTAAAATAAAAAAAATTTG 2233
                         ----  v i v   i  i       i     v     vv    
  L1M4_orf2#LINE/    627 ----AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.00 (31 / 31)
Gap_init rate = 0.01 (5 / 367), avg. gap size = 6.20 (31 / 5)  

 699 16.16 3.49 7.86  chr1_35543719_35547714.rev     2516  2744 (1252)    L1M4_orf2#LINE/L1      621   839 (69)  

  chr1_35543719_3   2516 AAAATAAATAAATAAATTAA--TTAATAAACAGATAAATAAATAAATAAA 2563
                          i  v     i       ii--  v  ---  ---    ---    -  v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCAT---CA---AAAT---TAAA-AAC 660

  chr1_35543719_3   2564 TATATATTTGTCATTCAAAGTACACTACACCAAGAGAGTGAAAAGAAAAT 2613
                          -----     vv       v      i--     i          v  i
  L1M4_orf2#LINE/    661 T-----TTTGTGCTTCAAAGGACACTAT--CAAGAAAGTGAAAAGACAAC 703

  chr1_35543719_3   2614 CCAGAGAATGGGAGAAGATATTTGCAAATCACATATCTGATAAAAGTTTA 2663
                            v            i              i           ii vi v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_35543719_3   2664 ATATCTAGAATATATATAG--TTTCTACAACACAATGACAAAAAGACAA- 2710
                         i    i          v  --i ii      v    i i          -
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_35543719_3   2711 ---TTCAATTAAAAATTAGGCAAAGGACTTGATATAG 2744
                         ---ii     ?    v i         i    -    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGA-ATAG 839

Transitions / transversions = 1.77 (23 / 13)
Gap_init rate = 0.05 (10 / 219), avg. gap size = 2.60 (26 / 10)  

 433 15.85 0.00 0.00  chr1_35543719_35547714.rev     3424  3505 (491)    L1M4_orf2#LINE/L1      827   908 (0)  

  chr1_35543719_3   3424 AGGACTTAAATAGACATTTCTCCAAAGAAGGTATACACATGGTCAAAAAG 3473
                             i  i                      i      v    i   v   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_35543719_3   3474 TACACAAAAAGATTCCCAATGTCATTAGGAAA 3505
                         i   ii       v i   ii   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.00 (0 / 0)  


2751 23.54 4.87 0.84  chr1_35617194_35618901.rev      500  1217 (490)    L1M4_orf2#LINE/L1      162   908 (0)  

  chr1_35617194_3    500 GGGATCTAGAATGATCAAAATGATTTTGAAAAAGAACAATAGAGTTGGAG 549
                             i i     iii     ii  i           v  i i        
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_35617194_3    550 GACTTAAACTATCTAGCTAGAAGACTTACTGTATAGCCACAGTAATCAAG 599
                             i v   vi i ii vv  i       ii v   i            
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_35617194_3    600 GCAGTG--GTATTGGTATAAAACTAGAT---TAAGTTAATGGAACATAAT 644
                         i     --   i   i    iiv    i---  ii i       i v   
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_35617194_3    645 ATAGAGTCCAGAAATAGACCCACACCTATATGGTCCATTGAT-------- 686
                         vv              i     i  v v       v      --------
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_35617194_3    687 ---GTGCCAGTGCAGTTCAGTGGGGAAGGGATAATCTTTTCAACAAATGG 733
                         ---      ivi vi    i       i i   i                
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_35617194_3    734 TGCTAGAACAATTAGATAATGATATGTAAAAACATGAACCTTGACCCTTA 783
                             i i    i i    ?iv i   i    iv     vi v     i  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_35617194_3    784 CCTC------TAGAGGAAAATCAACTCAAAACGGATCATAGATCTCAATT 827
                             ------  v vi     i         i      ?   i  v   v
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_35617194_3    828 TAAGAGTAAAAGCTATAAAACTTATGGAAGAGAACCCAGGAGAACATTTT 877
                               iv   i          iv i     i   vi   ? v v  i  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_35617194_3    878 TGTGATCTTGCTTT-GGCAAAGATTTCTTAGCCATGTCACTGAAAGCATG 926
                         i    i    vv  -     v i        vi   v   ii      ii
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_35617194_3    927 AACTGTAAAAGAAACAAAT-GATAAATTGGAGCTTATCAAAATTACAAAT 975
                          i vii        -    -           vi i          v   i
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_35617194_3    976 TTTTGTTAATGAAAAGCTAACACTAACAAAA---CGAAAAAGGAAGATAC 1022
                               vvv v   i ---      v   i ---i     iiv  vvi  
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGG---ACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_35617194_3   1023 AGACTG--AGAAAACATTTGCAAATTATATGTCTGACAAAGGACTCATTT 1070
                            v  --      i          i    i     i  i     ii v 
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_35617194_3   1071 ATAGAA---ATAAATGAGCTCTTGTAACTTGAT--TAGAAA-ACTAGTAA 1114
                         vi    ---     -  i     ii    ii  --  i   -  v i   
  L1M4_orf2#LINE/    758 CCAGAATATATAAA-GAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_35617194_3   1115 CCCATTTTAAAAAGCAGGCAAAAGATTGGAACAGATAGTCCACCAAAGAG 1164
                             v  ?     -ii      i    v   i   i v i v       i
  L1M4_orf2#LINE/    807 CCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_35617194_3   1165 GTTATACAGGTGTCCGATAAATACATAAAAAGATGTTCAATGTCGCTAAT 1214
                          v      ii  v  i    ii    i        i    ii  i?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_35617194_3   1215 CAC 1217
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.06 (111 / 54)
Gap_init rate = 0.02 (15 / 747), avg. gap size = 2.73 (41 / 15)  


3072 25.68 0.98 1.75  chr1_35648582_35653173     3185  4099 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_35648582_3   3185 TGGAAAAACATGCCATGCTCATGAATAGGAAGAATCAATATCATTAAAAT 3234
                               i i  v     i     i  v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_35648582_3   3235 GGTCATACTACCCAAATCAATTTACAGACTCAATGCTATACCTATCAAAC 3284
                           iv     v       ii  i      i    i  v  v         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_35648582_3   3285 TACCAATGACATTCTTCACAGAACTAGAAAAAAAACT-ATTTTAAAATTC 3333
                          v   iivi v  i  ii     v v  v  i---  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr1_35648582_3   3334 ATTATGGAACTAAAAAAGAGCCCAAATAGCCCATACAATGCTAAGCCAAA 3383
                           -      v iv  ii  v  vi       v v     vi i ivv i 
  L1M4_orf2#LINE/    148 AT-ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_35648582_3   3384 AGACCAAAGCTGGTGGTAC-CACGTTACCCGACTTCTAACTATACTACAG 3432
                            v     i   v  -  -   ii v   i i   v  viv       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_35648582_3   3433 GGCTACAGCAACCAAAACAGCATGGTAATGGTACAAAAATTGGCACATAG 3482
                         i       i  i   i    ii     v   i i  ii  v i  i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_35648582_3   3483 ACCAACGGAACAGAATAGAGAGCCCAGAAACAAAGCCACACACCTACGAA 3532
                          i   i    i     v     i       i   v   i   ii  i iv
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_35648582_3   3533 CATCTGAGTTTTGACAAAGCTGACAAAAACAAGCAATGAGGAAAAGACAC 3582
                           vi   v   i     i v  v   i v  vv     i     ii i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_35648582_3   3583 CTTACTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGAT 3632
                         ii vi    i              i      v  ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_35648582_3   3633 TAAAGCTGGACCCCTTCCTTATACCATATACAAAAATCAAATCAAGATGG 3682
                          i   i         v   i i               i  v    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_35648582_3   3683 ATTAAAGACCTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGACAA 3732
                           i ?              i v i            vi i i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_35648582_3   3733 CGACAACCTAGGCAATACCATCCTAGGAACATAGAAACAGACAAAGATTT 3782
                          i------    ?i-  v-   i v vi  v v iivi  i   v i   
  L1M4_orf2#LINE/    546 CA------TAGGNG-TAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_35648582_3   3783 CAT-GATAAAGACACCAAAAGCAATCA--CAACAAAAGCCAAAATTGACA 3829
                          v -    v-             --  --         vv     v  i 
  L1M4_orf2#LINE/    588 CTTAGATAT-GACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATA 634

  chr1_35648582_3   3830 AATGGGATCTAATTAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTATC 3879
                            v   ii v  i   v    i i   i  ii vv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_35648582_3   3880 AACAGAGTAAAGAGACAATCTACAGAATGGGAGAAAATACTTGCAAACTA 3929
                           v i   i  i      i i                  i       ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_35648582_3   3930 TGCATCTGACAAAAGTCTAATATCCAGCATTTATAAGGAAGCTAAACAAA 3979
                          ii      i  ii v  vi       v  v     i   viivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_35648582_3   3980 TTTACAAGAGAAAAACAAC---CTCAAT-AAAAAGTGGGCAAAGGACATT 4025
                          iv i  v i   i    v--- i    -?    i           iv v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_35648582_3   4026 AACACACACTTTTCAAAAGAAGACATACAGGCAACCAATAAGCATATTTT 4075
                           i v   i  i  v        i     iiiii          i  vvv
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_35648582_3   4076 AAAAAGTTCAATATCACTGATCAT 4099
                           i v i    i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (143 / 88)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.79 (25 / 14)  


 289 18.75 1.56 0.00  chr1_35659795_35661450.rev        6    69 (1587)    L1M4_orf2#LINE/L1      171   235 (673)  

  chr1_35659795_3      6 AATAACCAAAGCAAT-TTGAACAAAAAGAATAAAGCAGGAGGCATCACAC 54
                             i     i    -     v  i     i    iv     vv      
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr1_35659795_3     55 TTCCTGACTTCAAAA 69
                             ii i       
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAA 235

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1)  

2407 23.95 3.31 2.71  chr1_35659795_35661450.rev      502  1165 (491)    L1M4_orf2#LINE/L1      241   908 (0)  

  chr1_35659795_3    502 TATAAAATTCTAGTAACCAAAACAACAGACAGCATGGTATTGGTATAAAA 551
                           i   ii vi     i   -------     ii     i   i    ii
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAA-------GACAGTGTGGTACTGGCATAAGG 283

  chr1_35659795_3    552 ACAGACAGTCACATAGACTAATGGGACAGAACAGAGAACTCAGAAATAAA 601
                          i     ----i     ii     i i    iv    iii          
  L1M4_orf2#LINE/    284 ATAGACA----TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_35659795_3    602 CCCACGTATTAATAGCCAATTGATTTTTGACAGAGGTGCCAAGGACACAC 651
                             iii   v  i i           i    ii         iv  iv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_35659795_3    652 ATTGGGGAAAGGATA-TCTTGTTCAACAAATGGTCCTGGGAAAACTGGAT 700
                          v         i   -    -             v      v        
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_35659795_3    701 ACTCATACACAGAAGAATGAAACTAGAGCCCCTGTCTGTCATCATATACA 750
                          ?i  i ii  i         ii i  -     ii  vv  i        
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGA-CCCCTACCTCACACCATATACA 477

  chr1_35659795_3    751 AAAATCAACTCAAAATGGATTAAAGACTTAAATGTGAGACCCAGAACTGT 800
                              i              i ?    i       i   v i i    i 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_35659795_3    801 AAAACTACTGGGAAGAAACATAGGGGAAACACTCTAGCATATTGGTCTAG 850
                               vi i i ii         ? v  vv  iiivv iv    vi   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_35659795_3    851 GCAAAGATTTTATGGCTAAGACCCTAAAAGCACAGGCTGCAAAACCAAAA 900
                             v i   iv i v  v   v i         i  vi     vv    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_35659795_3    901 ATAGACAAATGGGATTATGTTAAGCTAAAAAGCTTCTGCACAGCAAATGA 950
                              i    v   i vii i  iv v    i   i  ii vv    v  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_35659795_3    951 AAC----AACAAAGTGAAGAGAGAACCCGTTGAATGGGAGAAAATATTTG 996
                         v  ----  v        i   v     iiv                   
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_35659795_3    997 CAAAATATCTGTCTGGTGACAAGGGACTAATATCCATAATACACAA---- 1042
                             vi  v i    i ---        vi      v    i i  ----
  L1M4_orf2#LINE/    728 CAAATCATATATCTGAT---AAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_35659795_3   1043 TTCCAACAACTCAACAGCAAAAAACCCTACATAGCCCCATTAAAAAGTGG 1092
                         i  iv         i ii     iv -- v   i   v   ?    i   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGAC--AAATAACCCAATTWAAAAATGG 822

  chr1_35659795_3   1093 GCAAAGGATCTACATA--------TCCA-----GACATAAAAATGATTAA 1129
                                  i iv   --------    -----  i   v     iii  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_35659795_3   1130 CAGATATGTGAAAAAATGTTCAACATCACTAATTAT 1165
                         i iii ii      i   i         ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.23 (107 / 48)
Gap_init rate = 0.02 (11 / 668), avg. gap size = 3.64 (40 / 11)  


 722 12.15 0.00 0.00  chr1_35932236_35937027     2338  2444 (2348)    L1M4_orf2#LINE/L1        1   107 (801)  

  chr1_35932236_3   2338 TGGAAAGATATCCTGTGTTCATGAATTGCAATACTTAATATTGTTAAGAT 2387
                                      ii        i    v  v                  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_35932236_3   2388 GGCAATACTCCCCAAATTGACTTACAGATTCAATGTAATTCATATCAAAA 2437
                                             ii           i i   i v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_35932236_3   2438 TTCCAAC 2444
                          i   i 
  L1M4_orf2#LINE/    101 TCCCAGC 107

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.00 (0 / 0)  

1708 12.36 0.39 0.00  chr1_35932236_35937027     2827  3085 (1707)    L1M4_orf2#LINE/L1       98   357 (551)  

  chr1_35932236_3   2827 AAGTTCCAACTGCCTTTCTTGCAGAAATGGACAAGCATATCCTAAAATTC 2876
                           i i   i        i          v       vv            
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_35932236_3   2877 ATATGGAAATGCAAGGGACCCAGAATAGCCACAACAATCTTGAAAAAGAA 2926
                                                        v                  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_35932236_3   2927 GAACAAAGTTGGATGACTTGCACTTCCTGATTTCAAAATTTACTACAAAG 2976
                                      v    ii       ii         i           
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_35932236_3   2977 TTACAGTAATTGAGGCAATGTGATACTGGCATAAGGATAGACATA-AGAT 3025
                         i         ii  i  i    i                      -    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_35932236_3   3026 TGACGGGATAGAATTAACAGTCTAGAAATAAACCCTTACATGTATAGTCA 3075
                         ii i  i        i v    i            v     v   i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_35932236_3   3076 ACTGACTTTC 3085
                          i   i    
  L1M4_orf2#LINE/    348 ATTGATTTTC 357

Transitions / transversions = 3.00 (24 / 8)
Gap_init rate = 0.00 (1 / 260), avg. gap size = 1.00 (1 / 1)  

2613 13.51 3.89 8.45  chr1_35932236_35937027     3708  4299 (493)    L1M4_orf2#LINE/L1      344   908 (0)  

  chr1_35932236_3   3708 GTCAACTAATTTTCAACAAGGGTGCCA-GACCATTCATTAGGGGAAAGAA 3756
                              i i      i            -         v -          
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAA 392

  chr1_35932236_3   3757 TAGTCTTTTCAACAAATGGTGCTTGGACAACTCAGTATTCATATACAAAA 3806
                                                v        vii  ?i  i  i     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_35932236_3   3807 GAATGATTTTGAACCCCTACATCATGCTGTATACAAAAGTTAACTCAAAA 3856
                               vv   i        v   ii ii         i           
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_35932236_3   3857 TGGGCCAAAGACCCAAATGTAAGAGCTAAAACTA--AAACTGTTAGAAGA 3904
                            ii  ?     i                    --     v        
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_35932236_3   3905 CAACATAGGAATAAATCTTCATGATCATGGATTAGA------TTTCTTAG 3948
                         v        ?i         i   i v   i    i------        
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_35932236_3   3949 ATAATAACAA-AAAAGCACAAGAAACCAAAGAAAAAA---ATAAACTGGA 3994
                            - i   v-           v   v          ---     i    
  L1M4_orf2#LINE/    593 ATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_35932236_3   3995 CTTCATCTACATGAGAAACTTTTGTACTTCAAAGAACACCATTAAAAAAG 4044
                                v v  v i          i        i    i  i  i    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_35932236_3   4045 TGAAATAGTTCAGTGTGCAGGAAGGAACGTTAAAAACAAAAAGAGGAAAG 4094
                              ---------------------------- i    -----------
  L1M4_orf2#LINE/    692 TGAAA----------------------------AGACAA----------- 702

  chr1_35932236_3   4095 TGAAATATCCAGCAGAACGTAGGAAAGT-TTTGCAAATCAC----CTGAT 4139
                         -------i   -     i vii    i -           i----     
  L1M4_orf2#LINE/    703 -------CCCA-CAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_35932236_3   4140 AAGGGACTGGTATCAAGGATGTATAAAGGACTCCTGCAGCTCAATAACAA 4189
                                 v     v  i  i       i    i i  i        i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_35932236_3   4190 AAGAGATAAATTATCCAATTTTTAAAAGGACAGAAGATTTGAATAGACAT 4239
                           -   i    v i      ?vv   v  i  i i               
  L1M4_orf2#LINE/    795 AA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_35932236_3   4240 TTCTCCAAAGAAGACATACAAATGGCCAGTAAGTACATGG-----TGTTC 4284
                                       i             i    i     i-----  i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_35932236_3   4285 AACATCATTAGTACT 4299
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.45 (54 / 22)
Gap_init rate = 0.02 (14 / 565), avg. gap size = 5.21 (73 / 14)  


 317 22.68 7.22 1.03  chr1_36128485_36132024     1070  1166 (2374)    L1M4_orf2#LINE/L1       16   118 (790)  

  chr1_36128485_3   1070 TGTTCTTGGACCAGAAGTCTCAA-ATTGTTAAGAATTTCATTCTCCCCAA 1118
                              v    iii    v  i  -          vvviv  v        
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_36128485_3   1119 ATTGATCTATAAACTCAATACAAT----A--GAAATCCCATCAGGCTTAC 1162
                                  i i i    ii    ---- --i        v v v   -i
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT-T 114

  chr1_36128485_3   1163 TTTG 1166
                             
  L1M4_orf2#LINE/    115 TTTG 118

Transitions / transversions = 1.20 (12 / 10)
Gap_init rate = 0.04 (4 / 103), avg. gap size = 2.00 (8 / 4)  

1014 26.97 8.99 3.60  chr1_36128485_36132024     1453  1897 (1643)    L1M4_orf2#LINE/L1      122   590 (318)  

  chr1_36128485_3   1453 AAATTGTCAAGCTGATTCTAAGATTTATATGCTGGTACAAAGAACTTAAC 1502
                               v         i    i   i     vvii i   i i  ii --
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA-- 169

  chr1_36128485_3   1503 ATTTCTATTTTGAAGAGCCAAAA-AATCTTTTAAA-GAAGAACGAAGTTG 1550
                         -----------   v        -      vv   -       i      
  L1M4_orf2#LINE/    170 -----------GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_36128485_3   1551 GTGGATTTATACTACCTGTGTTCAAGACGTGCTATAAAACTACTGAAATC 1600
                          v   i i i   v  iivv     i  v i   i   i    v v    
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_36128485_3   1601 AAAACAGTG--ATACTGGGGTAAAGATTGTCA----GGTTA-CAGAATAG 1643
                           i      --i      vi   i   v v  ---- i i -ii      
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_36128485_3   1644 --CTA-----CCAGAA-TAGACCCACTA-ATGTA--GCTGGTTGATTTTT 1682
                         --i i-----      -  i     -  -  v  -- iiii        i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCA-TACATTTATGGTCAATTGATTTTC 357

  chr1_36128485_3   1683 GGCAAAGGGCCCAACATAATAGAATGCCAAAAAGGTTAGTCTTCTCAGTA 1732
                          i   i  vv    v iv  vv    v-ii    iv       i   ii 
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACA 406

  chr1_36128485_3   1733 AATGATGT---AACAACTGGGTATTTGTAT-TAAAAAAATTA--T----C 1772
                             i  i---i        i  ?iiii  -i    i   v -- ---- 
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_36128485_3   1773 CTCTACTTAACAGCACACAGAAAATTTAATTCAGAGTTTATC-----CCA 1817
                          i    i v   v  i i v    v    i   i i vv   -----  v
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_36128485_3   1818 GGATA-AAACATTAAAACTGGTAAATTTCC---AAGACAAAAT-GGGGAA 1862
                         ii  i-  ivii       i-    vi  i---    v  v  -  ? v 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTA-TAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_36128485_3   1863 AATATTCATGATCTTGGACGAGGCAAAGATTTTTT 1897
                            v   i   i     iiv      v i   i  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.88 (77 / 41)
Gap_init rate = 0.05 (22 / 469), avg. gap size = 2.55 (56 / 22)  

 239 28.17 2.82 0.00  chr1_36128485_36132024     2199  2269 (1271)    L1M4_orf2#LINE/L1      632   704 (204)  

  chr1_36128485_3   2199 ATAAATTGAAAACCATTGCAATTAAAAGCTTCT--CCTTTTGAGAACACC 2246
                                 i vvi   iiv        i   i --v   ivi  i    i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_36128485_3   2247 ATTAAGAAAATGACAAGGCAGCC 2269
                           i      i   v   i  i  
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACC 704

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.01 (1 / 73), avg. gap size = 2.00 (2 / 1)  

 222 26.96 4.35 0.87  chr1_36128485_36132024     2541  2655 (885)    L1M4_orf2#LINE/L1      685   803 (105)  

  chr1_36128485_3   2541 AAAAAAATGAAAACACAAGCTACCGC-TGAGAAAACACATTTGCAAAACG 2589
                           i   i      v    v i  v v-  i  i  v i         v i
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_36128485_3   2590 TA-ACAGAACAACG--CTTAGGTCCAGAATATATGAA-AATTGTACATAA 2635
                           - ivvi i  v --   ivi            i  -  i v -i i  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAA 783

  chr1_36128485_3   2636 CTCAGTAAGAAATAGAAAAA 2655
                             i   v   v   v   
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAA 803

Transitions / transversions = 1.21 (17 / 14)
Gap_init rate = 0.04 (5 / 119), avg. gap size = 1.20 (6 / 5)  

 210 21.31 0.00 3.28  chr1_36128485_36132024     2988  3048 (492)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_36128485_3   2988 AAAAAAATTATATGTGAATGGCCAGTGAGCCCTTGAGAAGATGCAGAACA 3037
                            i  i--    iii        i i   v v   i       vv    
  L1M4_orf2#LINE/    850 AAAGAAG--ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_36128485_3   3038 TCGTTGGCCGT 3048
                           i????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 2.00 (2 / 1)  


1449 28.71 11.88 1.61  chr1_36632096_36635825.rev     2432  3239 (491)    L1M4_orf2#LINE/L1       18   908 (0)  

  chr1_36632096_3   2432 TTCATGAATAAGGAGACTCAGTATT-TGGATATATCTATTTCCTCTAAAT 2480
                               i  vi i     i i    - vi v  iv v  vii i i    
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr1_36632096_3   2481 TGATCTATAAAATCAATGCAACTCCAATCAAAATCACAACAGAATTTGT- 2529
                                i i v    i    ii  v         v  i v vv   v -
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr1_36632096_3   2530 GTGGATCCTGACAAGCTAATTCTAAAATACCTTAGGGAGA-GCAAAGGCA 2578
                          ii  vvi         i  i       -i v  v   i -    i  vv
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAAT-TCATATGGAAATGCAAGGGAC 166

  chr1_36632096_3   2579 CAAGAATAGGCAAAAC-----TGGGGA-GAAAAACAAGGTGGGATAGCAT 2622
                          v       v      -----  iii -   i     i  v   vii vi
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr1_36632096_3   2623 GCCCTATCAGATATCAAGACTTAT---AAATGTAATGTAATTGAGACAGA 2669
                         i v  vi vi  v    i     i---   vv  vv     ii      v
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr1_36632096_3   2670 ATGAGATTGACACAGGGAT-GATGAAGTAGACCAATGGAATAGAATGAAG 2718
                         i  iv i  i  i i    -  iiv -    i              vi  
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATA-TAGATCAATGGAATAGAATTGAG 315

  chr1_36632096_3   2719 AGCCTCAAAATGAGCC-ACAAATATATGG-AAATGTGATATATGACACAG 2766
                           i ivi    i i  - i v  v     -v   -    v vi    -  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAAT-TGATTTTCGACA-AG 363

  chr1_36632096_3   2767 AGGTAGCACTGCAGA----TCACTGGGGAAGGGAAGAG-CTATTCAATAA 2811
                         -   iv  ----   ----   v       i -  v  -  v     i  
  L1M4_orf2#LINE/    364 -GGTGCCA----AGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAA 407

  chr1_36632096_3   2812 ATGA-ATTG------TTCAATATCTACACAGAAAAGCATAAAATCGAATC 2854
                            i-ii  ------i vi   ? i   iiv     v  i  i i i i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_36632096_3   2855 CATTCACCAAATCATA-AGTGATATCTATTCCAGGTGGATTCAAAAC--A 2901
                          v v vi  v i    - vvi v  iv i  v ii     iv? i  -- 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_36632096_3   2902 AACAGGAAAGGCAAAACTTTTAAACTCATAAAAGAAAATATAGAAGAATA 2951
                           iivi i  vi      v v      v  i       i    i? v v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_36632096_3   2952 TCTTTATGACCTCAGAATAGGAAAGGCTTTCTTCAACAAGATA--AAAAG 2999
                             ii      ii iv    v  v v      vi i v  i --     
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_36632096_3   3000 TACCAACCATAAA-GAATATATTCATAAACTCAATTACATTAAAACTAAG 3048
                         i  v i v i   -   v v  vv     i vi i v   i    i   i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_36632096_3   3049 CAATTTTCTCTGTCAA--GACATAATAAAGAAAATGAAAAGGCAAGCCAC 3096
                         v v    v viv    --    iv  v      i       i   v    
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_36632096_3   3097 CAACTGGGAGTAGTTATTTGCAA--CATACA------------------- 3125
                         vi v      v iv         --    i -------------------
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_36632096_3   3126 -----------------------CAGCT------------GACAG----C 3136
                         -----------------------  i  ------------    i---- 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_36632096_3   3137 CCAGCTGAAAACATGAGCAAAAGACATGAACAAGAGCATTTCTCAGAAGC 3186
                            ii ?    -   i     i  iv    i -  -        vi   v
  L1M4_orf2#LINE/    808 CCAATTWAAAA-ATGGGCAAAGGATTTGAATA-GA-CATTTCTCCAAAGA 854

  chr1_36632096_3   3187 GGG-ACACAAAAGACCAATCAACACATGAAAAGAAGATCAACTTCATTAA 3235
                         i i- i     v i     v i            v v     v   ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_36632096_3   3236 TAAT 3239
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.28 (128 / 100)
Gap_init rate = 0.04 (33 / 891), avg. gap size = 3.30 (109 / 33)  


 285 37.31 2.07 1.04  chr1_36766075_36770599.rev     1624  1816 (2709)    L1M4_orf2#LINE/L1      131   325 (583)  

  chr1_36766075_3   1624 AGGTAAGTTTGAAGTTCATATTTAAAAACAAGAAAATGAAAAAATAGCCA 1673
                           v i vii i  i       vv   vi    ii viv i  --      
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA--TAGCCA 178

  chr1_36766075_3   1674 GGAAAATTCTGAAAAGTAATGA--GAG--GGGAGACTAGCCCTATCAGAT 1719
                         ii v   ii      iv  vi --i  --  ii    vi v  vi vi  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_36766075_3   1720 ATTTAAACTTATTATAGATCTGCAATAATTTGAATAGTATGGTAGTAAGT 1769
                         v iv       i  i i v  i  i    ivii i   i     v iivv
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_36766075_3   1770 TGTGAGCAGACAAATATGTCAATGGAACAAAACAAAAAGCACAGAAA 1816
                          iv iii     v   vi         i i  ivi i  iv      
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

Transitions / transversions = 1.77 (46 / 26)
Gap_init rate = 0.02 (3 / 195), avg. gap size = 2.00 (6 / 3)  

 337 12.90 0.00 0.00  chr1_36766075_36770599.rev     1852  1913 (2612)    L1M4_orf2#LINE/L1      847   908 (0)  

  chr1_36766075_3   1852 TCAAAAGAAGATATACAAATGGTCAATGGGTATATGAAAAAATTCTCAAC 1901
                           v                   i    ii i i       i  v      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_36766075_3   1902 ATCACTAATCAT 1913
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.00 (0 / 0)  

 261 33.33 0.68 8.16  chr1_36766075_36770599.rev     3126  3272 (1253)    L1M4_orf2#LINE/L1      378   513 (395)  

  chr1_36766075_3   3126 TCATTGAAGAGAAGATGAACTATTCAAT-CATGTTATTAGGACAACGGGG 3174
                            v  ii  i ii  iiv  v     i-v   v ii i       v  i
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_36766075_3   3175 CAGCCATTGACAAAAAAATTAAAATTAGGTCCATTTCTCACCCTTTATAC 3224
                         i ?   ivvi     i   -i  i  i ii  v vi     v iv     
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAAT-GAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_36766075_3   3225 CAAGATAAATGCCAGATGAATTTGTTTAAATTCAAGGATTTAAATATA 3272
                         v  i  v  iv v i   i  -----------  ?i  ii     i  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGAT-----------CAWAGACCTAAATGTA 513

Transitions / transversions = 1.94 (31 / 16)
Gap_init rate = 0.02 (3 / 136), avg. gap size = 4.33 (13 / 3)  

 470 26.94 8.89 4.72  chr1_36766075_36770599.rev     3675  4034 (491)    L1M4_orf2#LINE/L1      534   908 (0)  

  chr1_36766075_3   3675 CCTAGAAGAAACCAT--GAGGAAGTTTTTAAAAATAATCTTCATGTGAG- 3721
                          i         v   -- ? v  i i  ii---- i i   vi-  v  -
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCG----TGACCTTGG-GTTAGG 578

  chr1_36766075_3   3722 -AA-GGC--CTTTGACAAGACACC-----CAGAAGCCAAAAAAATAAAAG 3762
                         -  -  i--   v  i v      -----  v    v v    iv    i
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_36766075_3   3763 CGCTGCTAAATGTGTATAT-ATAAAAATAGAAAATCTCCTCATGG--CAG 3809
                         ii-- v     -  v iv -  v     vi    ii -- ii  v--  i
  L1M4_orf2#LINE/    629 TA--GATAAAT-TGGACTTCATCAAAATTAAAAACTT--TTGTGCTTCAA 673

  chr1_36766075_3   3810 AAATCACCATTAGCAAAGTCAAAAGACAAC----AAACCAAGAGAAA-TA 3854
                          iiv   i  i iv     v          ---- i viii      -  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_36766075_3   3855 TCTGGTGCTTATCACA-----GATAAAGGGTTCATTTCCCACTTGTGTAA 3899
                          i  --- vv    i -----     i  ii ii v   vivv i i   
  L1M4_orf2#LINE/    724 TTTG---CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_36766075_3   3900 AAACGTCTTACAATTCTATTGAGAAAAAGACCAGTAACACAGTAGAAAAA 3949
                          i vv        i  v  -i v        v i    v  i -v?    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAAT-AATAAAAAGACAAATAACCCAAT-TWAAAA 818

  chr1_36766075_3   3950 ATGAACAAAG-ATATGAA--AATAGTTCCCAGCAAAGAAAATAGATA--- 3993
                            ii     -  v    --i i v   i --       i   v i ---
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTC--CAAAGAAGATATACAAAT 866

  chr1_36766075_3   3994 GGTCT-TGAACATTTGAAAAGATGCTCAACCTCACCTCTAAG 4034
                           i v- i i  iv                v   ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (56 / 39)
Gap_init rate = 0.06 (23 / 375), avg. gap size = 2.13 (49 / 23)  


1510 14.44 4.44 1.11  chr1_36847464_36849535      500   769 (1303)    L1M4_orf2#LINE/L1      123   401 (507)  

  chr1_36847464_3    500 AATGGACAAACTGATCCTAAAACTCCTATGGAAATGCAAGGGACTCCAG- 548
                            v     i            i  v                  -    -
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC-CCAGA 171

  chr1_36847464_3    549 GTAGCCAAAAACAATCTTAAGAAAGAA---CAAAGCTGGAGAGCTCACAG 595
                         i         -       i i      ---     i     ii      v
  L1M4_orf2#LINE/    172 ATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr1_36847464_3    596 TTCCTGATTTTAAAATTTACTACAAAGACATAATAATCAAAATGATGTGG 645
                             ii    i    i           vi i i       i iii     
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr1_36847464_3    646 TACTAGCACAAGGACAGACACATAGATCAATAGAATAGGATTGAGAGTCC 695
                             i   i     i     i          i      i           
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_36847464_3    696 AGAAGCAACCCCATACATCTGTG--------ATTTTTGACAAGGGTGACA 737
                             ii  v         i i  --------     i          v  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_36847464_3    738 AAATCACTCAATGGGGGAAAGAATAGTCTTTT 769
                          i i  i         -               
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGG-AAAGAATAGTCTTTT 401

Transitions / transversions = 5.50 (33 / 6)
Gap_init rate = 0.02 (6 / 279), avg. gap size = 2.50 (15 / 6)  

2876 14.73 1.16 0.19  chr1_36847464_36849535     1064  1579 (493)    L1M4_orf2#LINE/L1      388   908 (0)  

  chr1_36847464_3   1064 AAGAATAGTCTTTTTAATAAATAGTGTTGGGACAATTGATTATTCACGTG 1113
                                       i  i    i   i        i  iv  ?i   i  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_36847464_3   1114 CAAAAGAACAAATTTGGACCCTTACCTCCCACCATATAAAAAAGTGAATT 1163
                                 ii  v        i      v         v    i v  i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_36847464_3   1164 CAAAATG---CAAAGACCTAACTGTAAGAGCTAAAACTATAAAAACTCTT 1210
                                ---  ?        v                      -     
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTT 536

  chr1_36847464_3   1211 AGAAGGAAACAAAAGTATAAATCTTAGT-ATCTTGGATTAGGCAACAGTT 1259
                              i     v i ?i        v  - i     i        ii   
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_36847464_3   1260 CCTTAATTATAACACCAAAACCACAAGCAGCAAAGGAAAAACTAGATAAA 1309
                         i    iv   i         v        i    i      v        
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_36847464_3   1310 CTG-ACTTCAACAAA-TTAAGAATGTTTGTCTATCAAGGGATACTATCAA 1357
                         i  -      v    -    i  iv     viv    i   i        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_36847464_3   1358 GAGAGTAAATAAACAACCTACAGAATGGGAGAATATATTTGCAAATTATA 1407
                           i   i  v i      i              v            i   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_36847464_3   1408 TATCTGACAAGAGTCTAGTATCCAGAATATGTAAAGAACTATTACAACTC 1457
                                i   i v  v             i         v         
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_36847464_3   1458 AACAACAAAAAGACAAACAACCCAATTTAAAAATGGGTGAAGGATTTGAA 1507
                           i  i           i         ?         ii           
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_36847464_3   1508 TAGACATCTTTCCAAAGAAGATTTACAAATGGCCAATACACACATGAGAA 1557
                                i i            v               vi       i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_36847464_3   1558 AATGATCAACATCATTAGTCAT 1579
                         i   v         ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (49 / 23)
Gap_init rate = 0.01 (5 / 521), avg. gap size = 1.40 (7 / 5)  


 726 31.17 7.49 6.03  chr1_37025536_37028641     1720  2614 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_37025536_3   1720 TGAAGAGACATGGTGTGTTTCTGAAT-GGTAAAGTTCACGT-GTAGAGGT 1767
                           i i   i  vvii    iv  i  -  v i v  v ii -  vi  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_37025536_3   1768 GTCAGT-TTTTCCAAATTAATTT-----TTCAGTTTAATTCCAATCAGAA 1811
                          v  i -i ii       i  i -----    iivi   i  v    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_37025536_3   1812 TCATGAAAGGATTTTTCTTTTCC------TGATAAAATGACTCTAAAATG 1855
                           vii---- v vii i    v ------   i  iv   ii       v
  L1M4_orf2#LINE/    101 TCCCA----GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_37025536_3   1856 TATCTGGAAGACTAAACATGAACT---AATGACCAAAACATGTTTTAAAA 1902
                         i  v     ivvi  i--- i  i---   ii        vvi  v    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAG---GGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_37025536_3   1903 AGAA--------TGAGAGGTAATTCGTACTGCCAGATTTTAAAATATATC 1944
                             -------- vi    -- i  ii   v  vi    i    iv  ii
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGG--ACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_37025536_3   1945 ATTAAGCCA-AATAATTAAATTCATGTTCTAATAGCATATGAAAACACAG 1993
                          iv    i - i    i  ivivi   vv  v i     v i v v   v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_37025536_3   1994 ATAGATCAAAGGAACAGGAT-AAAAGCTCCCATAAAGAGACTCAAGTAGA 2042
                                  v    i  i  -i i  i--   v   v i  i  vii vv
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGT--CCAGAAATAAACCCATACATT 339

  chr1_37025536_3   2043 GATAAGTATTTAAAACATGAGAAAGATGGCTAGTTCCAATCAGTAAGTAA 2092
                         v  iivi v  i vvivi  v  i i  v v  v-   v   i ii v  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAA 388

  chr1_37025536_3   2093 ATGAAT----TATTCATTAACTG-TGCTGTGACAATTATTCAATTATTTG 2137
                          -    ---- v    vi  v  -     v     i ivvi ?ii iv  
  L1M4_orf2#LINE/    389 A-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_37025536_3   2138 GAAGAAATTTAAGTTAGAATTCAATCTTA----ATCTA---AAATAAATT 2180
                         v  i i v v     i  vii v i  i ----  v  ---    v  i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_37025536_3   2181 CCAGATAAATTAAAGATTAATGGCAAATGGGTAAGGGGAGGAGCAGAAAA 2230
                          v i  ii  i ?   ii-----i     --    ------   vi   -
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACC-----TAAATG--TAAG------AGCTAAAA- 523

  chr1_37025536_3   2231 AATACTATAAAAGTACCAAAAAAGAAAATATAGGTGAATATTTT-ACAAT 2279
                         ----        v -- vv i       i     ? v v  i  -iii i
  L1M4_orf2#LINE/    524 ----CTATAAAACT--CTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_37025536_3   2280 ATTGGGT-AGAGGA-GGTCTTTCTAAGCCTT----TCAAAAACATCAGAA 2323
                         v      -  ivi -   --    v  viv ----i     i  iv  v 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGT--TTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_37025536_3   2324 ACCATAAAAGAAAGTTTGATAG------CTCCACAAAAATAACATAAAAC 2367
                           v v i  i   -- v    i------  i  iv     v ---     
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAA--TAGATAAATTGGACTTCATCAAAATTA---AAAAC 660

  chr1_37025536_3   2368 TTCTACCCATTAAAA---ACCATAAACAAAATTAAATTACAAAC-ACAAA 2413
                           i iiv v i   i---  i  v  v   i v   vv    v -   i 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_37025536_3   2414 CTTGAAATAAATATTTGTAA--CATATGTGGGAGCATAAAGATGGAAGCT 2461
                         v v i iv         i  --     i vv  ---   ----  i -  
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGA---TAA----GGGA-CT 752

  chr1_37025536_3   2462 CTTATTT------TATAAAAAGCTCTTA-AATTCTACAA--AAAGGACGA 2502
                         iv   ii------      i i      -  i  v i  --   i   i 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_37025536_3   2503 ATACTCCCATAGAAAAATGTGCAAAGGACGAGTATGAACCTTTAACAAAA 2552
                            vi  v  v?       v        ivv v  ii  v   vv v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_37025536_3   2553 GAAAAGAAAATAATACAAAGGGGCTATTAATGTATGAAGAAGTGTGCAAC 2602
                            i -----  -      v  v v  v iiii     i ii  iv    
  L1M4_orf2#LINE/    853 GAAGA-----TA-TACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_37025536_3   2603 TTCCCTAATAAT 2614
                         v  v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (155 / 120)
Gap_init rate = 0.05 (43 / 908), avg. gap size = 2.81 (121 / 43)  


 421 17.50 1.25 0.00  chr1_37033921_37038424        2    81 (4423)    L1M4_orf2#LINE/L1      688   768 (140)  

  chr1_37033921_3      2 AGAGTAAAATG-CAACCTATAGAATGCGAGAAGATATTTGCAAATCATAC 50
                          i   i   v -     i i      v     i                i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_37033921_3     51 ACCTGATAAGGAATTAATATCCAGAACATAT 81
                          i         i i vi         i    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATAT 768

Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.01 (1 / 81), avg. gap size = 1.00 (1 / 1)  

2619 24.56 4.97 0.29  chr1_37033921_37038424     2867  3550 (954)    L1M4_orf2#LINE/L1        1   716 (192)  

  chr1_37033921_3   2867 TGGAGAGACCTTCAATGTTCATGGATAAGAAAAGTCAATTATTTTCAAGA 2916
                             i   iv i v            vi   i v i   -   v i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT-ATTGTTAAGA 49

  chr1_37033921_3   2917 TGTGAGTTTTTCCCAAATTGATTTATAGATACAGTGCAATCCCAATCAAA 2966
                           vv i vi i           i  i    v  ii        v      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_37033921_3   2967 ATCTCAGCAAGTTATTTTGTGGCTATTGACAAATTGATTCTAAAGTGTAC 3016
                            i    vivi v     ii vv        ii    i     i vi i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_37033921_3   3017 ATAGAGAGGCAAAAGACC-AGAATAATCAACACAATATTGAAGGAGAAGA 3065
                           i  i v    ii    -      ii   v     v     ii      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_37033921_3   3066 ACAACATTGGGAGATCAACACGGCTCAACTTCAAGACTTGCTATAAAGCT 3115
                             vi    ii  iiv    vv i   i     i    i   i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_37033921_3   3116 ATAGTAATCAAGACAGCATGATGTTGGCATATAGACAGACAAATAGATCA 3165
                          i              ii  i ii       vi  i     v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_37033921_3   3166 TTGGAACAGAATGGAGAATTCAGATGCAGACCCACATAAATAAAGTCGAC 3215
                         v     i     v    i i    vii i     i i vv  vi   i i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_37033921_3   3216 CGATCTTTGACAAGGGAGCAAAGGCAATACGGTGGAGAAAAGAAAGACTT 3265
                         i   i  i        v  v   i v  v ii   i    ii v  v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_37033921_3   3266 TTCAACAAAAGG-GCTAGAACAACTGGACATCCACATGCAAAAAA--GAA 3312
                                  v  -   i i         i ?            i --   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_37033921_3   3313 TCTAGACACAGACCTTACACCCTTCACAAAAATGAACTCAAAGTGTATCA 3362
                         vi i   v vv    i     v vi        v        i  v    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_37033921_3   3363 GAGACCTCAATGTACAATGC-AAAACTATAAA----TT------------ 3395
                         ?      v      vi -  -           ----  ------------
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_37033921_3   3396 --GC-CAAA----------CTTGGGTTTGGCAATGGCTTTTTAGATATAA 3432
                         -- ?-i   ----------        v        i  i        i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_37033921_3   3433 TACCAAAGGCACGACCCATGAAAGAAATAATTGATAAGCTGGACTACATT 3482
                         i      i    i v v ii       v   v     ii      v   i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_37033921_3   3483 AAAATTAAAATTTTCTGCTCTGCAAAAGACACAGTAAAGAGAATGAAAAA 3532
                                   vi  i  iv  v    i     vi v    i i      i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_37033921_3   3533 TGAAGCCACTGACTGGGA 3550
                         vv  v    v  v     
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGA 716

Transitions / transversions = 1.58 (101 / 64)
Gap_init rate = 0.01 (10 / 716), avg. gap size = 3.60 (36 / 10)  

 486 22.22 10.46 0.00  chr1_37033921_37038424     3859  4011 (493)    L1M4_orf2#LINE/L1      740   908 (0)  

  chr1_37033921_3   3859 CTGATGATGGACTATTATCCAACATATGCAAACCACTTTTAAAATTCAAC 3908
                              i v     vv      iv    ii   vv   i   v  i    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_37033921_3   3909 AATAAGAAAACAAACAACCTTATTAAAAAGTGGGCCAA----------AG 3948
                              i  i     i    iv   ?    i     v  ----------  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_37033921_3   3949 AC----CTTAACAGAATATATACAGATGGAAAATAAGCATATGAA--GAT 3992
                           ----  iv v    v       i    vv        i     --   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_37033921_3   3993 ACTCCATATTATATGTCAT 4011
                         i   v i  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (18 / 15)
Gap_init rate = 0.02 (3 / 169), avg. gap size = 5.33 (16 / 3)  


4614 15.10 1.86 2.52  chr1_37296857_37301433.rev     3175  4088 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_37296857_3   3175 TGGAAAGACATTTCATATTCATGG-TCAGAAG-CTT-----TGTTAAGCT 3217
                                 i  ii   i       - ii    -   -----       v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_37296857_3   3218 GGAAATACTCCCCAGATTGATCCACAGATTAAATGCAATCCCTGTTAGAA 3267
                           v           i       i       v  i         i i i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_37296857_3   3268 TACAAGCTGACTTCTTTGTAGAAATTCACAAGCTAATTCTAAAGTTCATA 3317
                          v v     v   i    i       v       i  i     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_37296857_3   3318 TG-AAATGTAAAGGGACCCAGAATGACCAAAATAATCTTGAAAGGCAATA 3366
                           -     i  -            ii      i          iiv  v 
  L1M4_orf2#LINE/    151 TGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_37296857_3   3367 ACAAAGTATGAGTACTCTTACTGCTTGATATCAAAACTTACTACAAAAAA 3416
                                vv   v    vi   v iii  v                 ivv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_37296857_3   3417 AAAAAAAAAAACCCGGTAATCAAGACAGTACAGGGCTGGCATAAGGATAG 3466
                          ------------ i              iii vi               
  L1M4_orf2#LINE/    250 A------------CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_37296857_3   3467 ACATGTATATCAATAGAATGGAATTGAG--TTGATAGATTAAACCCATAC 3514
                             i  v      i    i        -- iv v i  -          
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT-AAACCCATAC 336

  chr1_37296857_3   3515 ATCTATGGCCAACTGATTATTAACAAGGTTGCCAAGACAATTCAATGAAG 3564
                           i     i   i     v ii      v         v        i- 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-G 385

  chr1_37296857_3   3565 GAAAGAATAGTCTT--CAACAAATGATGCTGG-ACA-CTGTATAGCCACT 3610
                                       --         i      -   -   v   ?    v
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_37296857_3   3611 TGCCAAAAAGAAAGAAGT-AGAACCCTACCTCACATCATATACAAAAATC 3659
                            --       v     -i  v            i             i
  L1M4_orf2#LINE/    436 TGC--AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_37296857_3   3660 AGCTAAAAATGGATCAAAGATCTAAACATAGGAGCTAAAACTATAACACT 3709
                          i  v           ?   i     ii  i               v   
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_37296857_3   3710 TGTAGAAGAAAATGCAGGAGAAAATCTTTATAACCTTGGATTGGACAATG 3759
                         iv          iii   ? v       ii i       i  i i     
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_37296857_3   3760 GATTCTTAGATTTGGCGCTAAAAGCACAAGTGACAAAACAAACAAAAAAT 3809
                          v         v  i i i           ii      v   ----    
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA----AAAT 629

  chr1_37296857_3   3810 AGACAAACTGGACTTCATCAAAATTAAAA-CTTTCATGCTTCAAACGACA 3858
                            i   i                     -    ii         v    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_37296857_3   3859 CCATCAAGAAAGTGAAAAGACAAATCCA-AAAATGGGAGAAAATATATGC 3907
                          i                     -i   - i               v   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAA-CCCACAGAATGGGAGAAAATATTTGC 728

  chr1_37296857_3   3908 AAATTATATATCTGATAAGGGTATTGTTTTCAGGATATATAAAGAACTCT 3957
                             i                vv    v i   i                
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_37296857_3   3958 TACAACTCAATAATAAAAAGGAAAGTAACTCAGTTTTTAAAATGGGCAAA 4007
                                             iv  i    i  i  ?v-            
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAA 827

  chr1_37296857_3   4008 TAATTTGAACAGAAATTTCTCCAAAGAAGATATACAATTGTCCAATAACC 4057
                         vi       i   v                       v  v       v 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_37296857_3   4058 ACATGAAAAGATGCTTAATATAATCAGTCAT 4088
                                        i  i  v ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (86 / 48)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.11 (40 / 19)  


3238 21.93 6.61 1.28  chr1_37333262_37337426     2811  3672 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_37333262_3   2811 TAGAAAGACAGCCCATGTTCATGGATTAGAAAGATTAATGTTGTTAA-AT 2859
                          i      i v                i   iiv     i       -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_37333262_3   2860 ATCCATGCTACCCAAAGTGACCTATAGATTCAATGCAATCCTTATCAAAA 2909
                         iv v  i  v      v   i   i        i       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_37333262_3   2910 TTGCAATGGCATTCTTCACAGAAATGGGGGAA--AATCCTAAAATTCACT 2957
                          iv  iiv  v  i  ii       v ivi i--i             iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_37333262_3   2958 TGGAACCAGAAAATAGTCTAAATAGTCACAGCAATCTTTAGAGCAAGAAG 3007
                              viiv  iiv vi vi     i  v i       --  iv      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--GAAAAAGAAG 198

  chr1_37333262_3   3008 AACAAAGCTGGAACA-TCACACTCCCTAATTTCAAAGTATATTACAAAGC 3056
                                i    iv -       i  i         iiv  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_37333262_3   3057 TACAGTAATAAAAACAATATGGTACTGGAATATAAACAAACATA--GACC 3104
                                  v  i   i i         v   vii i i     --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_37333262_3   3105 AATATGAAATAGAATAGAAAGCCCAGAAATAAATCCATGCATTTAC---- 3150
                            -- i        v  i  i           i    i      i----
  L1M4_orf2#LINE/    299 AAT--GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_37333262_3   3151 ---------------AGAGTGCCAATGACACA--CAAT----AAAGAA-- 3177
                         ---------------  i       -   -  --    ----      --
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAA-GAC-CATTCAATGGGGAAAGAATA 394

  chr1_37333262_3   3178 GTATCTCAAATAAATGGGGTTGGGAAAATTGGATATACATGTGCAGAAGA 3227
                           v i iv  i      v i     v  i      ?v  ii    i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_37333262_3   3228 ATAAAATTGGACAT-TATCTCATACCACATGCCAGAAATAGATCAACTTG 3276
                           i  i      vi-  i    i    i  i - i    ----i    ii
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATAC-AAAAAT----TAACTCA 489

  chr1_37333262_3   3277 AAATGGATTAAAAACTTATATGTAAGACCTGAAACTATAAAACTACTGAA 3326
                                 i ? i  i  v        v  i             vi ii 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_37333262_3   3327 AGAAAACATAGAGAAAACGCTTACTGACGTTGTTCTGAACAATGATTTTT 3376
                                    i?iv  vv   vv    v   vvi iii     i   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_37333262_3   3377 TGGATTTCACTCCAAAAGCACAGGCAATAAAAGCAAAACTTGACAAGTGG 3426
                          i   v v  v           i    i     v    v v  i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_37333262_3   3427 GATTGCATCAAA-CTAAATACATCTGCACAATGAAGGAAACAAT--AGAG 3473
                           i v       -i    v  v i  ii vvii     v  v  --   i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_37333262_3   3474 AG----AAGACA-CCTAT-GAATGGGAGACAATATTCGCAAACCATATAT 3517
                           ----      -  i i-          v      i     i       
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_37333262_3   3518 CTGATAAAG----TGT----------TATAAGGAACTCATACGACTCAAG 3553
                                i ----   ----------     i      v   i      v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_37333262_3   3554 AGGAAAAAAGCAAATAACCCAATTTGAAAATGGGCAAAGGACCTAAATAG 3603
                          iv     ii              ?i               ii i     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_37333262_3   3604 ATATTTCTCAAAAGAAGATATAAAAATGGTTAATAGATATATGAAAAGAT 3653
                          i       v            v      ii    iii i          
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_37333262_3   3654 GCTCAACGTCACTAATCAA 3672
                                i   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (123 / 62)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.09 (68 / 22)  


1370 26.62 1.62 2.78  chr1_37342224_37348009       11   442 (5344)    L1M4_orf2#LINE/L1       93   519 (389)  

  chr1_37342224_3     11 TATCAAAATTCCAAGGTCATTTTTTACAGAAATAGAAAAAATAATATTAA 60
                                  i   ivvv v      i       v  v  iv i  vi   
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr1_37342224_3     61 A-TTTGTATGGGACCAGAAAAGACCATGAATAACGAAAGCAATACTGAGC 109
                          -  ii     i viiv  ii    vv     i v   i    vi   iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_37342224_3    110 AAAAAGAACAAAGCTGGAGGCATCACACTCCCTAATTTCAAAATAGATTA 159
                           i          i      vv       i  i          ivv i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_37342224_3    160 AAAAGCTATTGTAATCAAAACAGCATAATTTAAAAATA--ATAAAAACAG 207
                         v       iv        i    ii ii ----- v i--    ii i  
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGT-----ACTGGCATAAGGATAG 287

  chr1_37342224_3    208 ATACATTGACCAATTAAACAGGATAGAAAGCACAGAAGTAGTCCCAAGTA 257
                          i i  v  i    vi  i  i  v  i  iv     i  iv    vii 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_37342224_3    258 TTTTCAGTCAATTGGCTTTTGACAAAGGTGCCAAGAACA--CAATTGGAA 305
                            vii        ii   i     i          v  --    v  --
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-- 385

  chr1_37342224_3    306 GAGAAAGGACAGTATCTTCAATAAATGGTGCTGGAAAAACTGAATATACA 355
                         --     i i   v i     i            i v     i   ?v  
  L1M4_orf2#LINE/    386 --GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_37342224_3    356 CATGCAGAGGAATGAAAATGCACTCATATCTCACCCTTTATACAAGAATC 405
                               i i       iv  v  i v  i     v iv       i   i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_37342224_3    406 AATTCAGA--GGAGCCAAGATGGCCGAATAGGAACAGCT 442
                           i   i --   v v?   i-- ii   - v  v    
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGAC--CTAAAT-GTAAGAGCT 519

Transitions / transversions = 1.63 (70 / 43)
Gap_init rate = 0.02 (8 / 427), avg. gap size = 2.38 (19 / 8)  

3210 27.06 0.55 0.66  chr1_37342224_37348009     4385  5293 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_37342224_3   4385 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4434
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_37342224_3   4435 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 4484
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_37342224_3   4485 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 4532
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_37342224_3   4533 TATGGAATCAAAAAAGAGCCCACGTCGCCAAGTCAATCCTAAGCCAAAAG 4582
                                viiv  ii  v  vivi v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_37342224_3   4583 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4632
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_37342224_3   4633 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4682
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_37342224_3   4683 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAGCT 4730
                                i    i--    i  --        vv iii i  i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_37342224_3   4731 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4780
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_37342224_3   4781 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4830
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_37342224_3   4831 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4880
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_37342224_3   4881 TTAAAGACTTAAACATTAGACCTAAAACCATAGAAACCCTAGAAGAAAAC 4930
                          i ?    i    ii v   v       i   i  vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_37342224_3   4931 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4980
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_37342224_3   4981 AACATCAAAAGCA-ATGTCAACAAAAGCCAAAATTGACAAATGGGATCTA 5029
                         i   i        - v -         vv     v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_37342224_3   5030 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAAAGTGAA 5079
                           i   v v  i i   i  ii vv    i  v    i  vv        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_37342224_3   5080 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5129
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_37342224_3   5130 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5179
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_37342224_3   5180 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5229
                           i -    i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_37342224_3   5230 TCTCAAAAGAAGACATCTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5279
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_37342224_3   5280 TCATCACTGGCCAT 5293
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3718 21.53 1.75 2.51  chr1_37364490_37366550.rev      658  1572 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_37364490_3    658 TGAAAAGATATCCCATGTTCATGGATTGGCATAATTAATAGTGTTAAAAT 707
                           i                          v v v      v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_37364490_3    708 GTCCATACTATTCAAAGTGATCTACAGATTCAATGCAATCCCCATCAAAA 757
                          v v     vii    v                i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_37364490_3    758 TCC-AGTGACATTTTTCACAGAAATAGAAAAA--AAACCTGAAATTTATA 804
                            -  ivi v     ii       v  v  i--i v   i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_37364490_3    805 TAAAACCACAAAG-ACACTGAATAGCTAAAGCAATTGTGAGAAAAAAGAA 853
                          ii  vii   i -  v v       i   i    iv   i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_37364490_3    854 CAAAACTGGAGGTATCACACTACCTAGTTTCAAATTATATTACAAAGTTA 903
                             ii      vv       v  i i       viv  i       i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_37364490_3    904 TAGTAATTCAAACAGCATAGTATTGGCATAAAAATGAACATATAGACCAA 953
                         i      iv i    ii i   i        ii  ii         i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_37364490_3    954 TGGAACAGAGTAAATAGCCCAGAAATAAATTCATTCATTTA--GTCAGTT 1001
                              i   i vi v  i           ii   v      --    i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_37364490_3   1002 GATCTTCAACAAAAGTGCCAGGAACACACAATGGGAAAAGGACGGTTTCT 1051
                            i   i    ii      i  v  iv       i    i ii  i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_37364490_3   1052 TCAATGAACGGTGTTGGGAAAACTAGATAGCCAAATGCAGAAGAATGAA- 1100
                             ii  i    i     v    i    ?   v     i         -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_37364490_3   1101 TTGGACTTTTATCTCACATCATACACAAAAACCAACTCAAA-TGGATTAA 1149
                               iii  i      i    i       ii        -     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_37364490_3   1150 GGACTTAAATATAAGACCTAAAAG-GTAAAACTACTAGAAGAAAACATAG 1198
                         i   i     i     v      v-i       vi               
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_37364490_3   1199 AGAAAAAGCTTTATGACATTGGTCTGGGCAATGATTTTTTTTTTTTTTTT 1248
                         i?iv   v   ii    v    vi i       i   i  vvv v ----
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT---- 596

  chr1_37364490_3   1249 GACCCTAAAAGCACAGGCAACAAAAGCAAACATAGACAAACGGGATTGCA 1298
                            v i         i          v   v     i   iv   i v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_37364490_3   1299 TCAAACTGAAATCCTTATGTGCAGCAAAGGAAACAATCAGTAGAGAGGAG 1348
                              v v   vv   v     vv       v  v    iv i  v i i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_37364490_3   1349 ATACAACCTAAGGAATGATAGAATATATACGCAAATCATGTATCTGATA- 1397
                          v      i vi     iv    v    vi         i         -
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_37364490_3   1398 --TACATGTATCCAGATATATATATTCTAACAAAATATATAAGGAAATTA 1445
                         --v  v          ------------------        i   v iv
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGA------------------ATATATAAAGAACTCT 778

  chr1_37364490_3   1446 TACAACTCAATAGCAAAAAAAAAAAC--CCTAATTTAAAAATGGGCAAAA 1493
                                     ii     i v   i--  i    ?             i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_37364490_3   1494 GACTTAAATAGCTATTTCTCAAAAGAAGACATACAAATGGCCAACAGGTA 1543
                           i  i     vi       v        i              i i i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_37364490_3   1544 ATATGAAAAAA--ATCAACATTGCTAATCAT 1572
                         -i       i --v       ii????????
  L1M4_orf2#LINE/    879 -CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (123 / 70)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.00 (39 / 13)  


3278 26.51 0.55 0.66  chr1_37509968_37516391.rev     5025  5933 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_37509968_3   5025 TGGAAGAACATCC-ATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5073
                              ii i    -   i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_37509968_3   5074 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5123
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_37509968_3   5124 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTCTAAAGTTCA 5171
                          v   iivi i  i  ii     -   -- v  i  -  i     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_37509968_3   5172 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAAG 5221
                                viiv  ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_37509968_3   5222 AATAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5271
                           i    i i    vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_37509968_3   5272 TACAGTAACCAAAACAGCATGATACTGGCACCAAAACAGATACATAGACC 5321
                                 i   i    ii  i        iv ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_37509968_3   5322 AATGGAACAGGACAGAGGCCTCAGAAATAACACTACACATCTACAACCAT 5371
                                i  i iv   ivii         vv i i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_37509968_3   5372 CTGATCTTTGACAAACCTGACAAAAACAAGATATGGGGAAATGATTCCCT 5421
                         i    i  i     ivv  v   i v  vvvv         vi  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_37509968_3   5422 ATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATCTGTAGAAAGCTGA 5471
                         v  i  i              v      v  ?   iv  i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_37509968_3   5472 AACTGCATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5521
                          ii  v i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_37509968_3   5522 AAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAGCCT 5571
                          ?   ii       v   v       i      vi i         i v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_37509968_3   5572 AGGCA-ATATCATTAAGGACATAGGCATGAGCAAGGACTTCATGACTAAA 5620
                            ?i- v   -  viv   v v  vv ii    v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_37509968_3   5621 ACACCAAAAGCAAAGGCAACAAAAGCCAAAATAGACAAATGGGATCTAAT 5670
                                     v i          vv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_37509968_3   5671 TAAACTAAAGAGCTTCTGTATGGCAAAAGAAACTACCATCAGAGTGAACA 5720
                         i   v v  i i   i   iivv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_37509968_3   5721 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5770
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_37509968_3   5771 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA-AA 5819
                           i  vi          v  i        ivv    v ---   v  -  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAA 794

  chr1_37509968_3   5820 AAAAACAAAAAAACCCATCCAAAAGTGGGCGAAGGATATGAACAGACACT 5869
                            i     v  v  v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_37509968_3   5870 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTTA 5919
                             v        i  vi viii     i ii          i     i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_37509968_3   5920 TCATCACTGGTCAT 5933
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (145 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


 392 21.01 5.88 4.20  chr1_37683192_37686007      815   933 (1883)    L1M4_orf2#LINE/L1        2   122 (786)  

  chr1_37683192_3    815 GGGGAGATACACAATGTTCATGGATTAGAAGATTTAACATAGTAAAAA-G 863
                           ii     iv v             i     i    i  v  v  i - 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_37683192_3    864 TCAATTATTGCCCCCAAA-----CGCCAG-TTTAACACAAATCCTATCAA 907
                         v    - i --       ----- vv   -  i   i   vi        
  L1M4_orf2#LINE/     52 GCAAT-ACT--CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_37683192_3    908 AATCCTAGCAAGACTTTTCTTTCAGA 933
                              i   --vi i   i  v    
  L1M4_orf2#LINE/     99 AATCCCAGC--TGCCTTTTTTGCAGA 122

Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.05 (6 / 121), avg. gap size = 2.00 (12 / 6)  

1993 25.67 4.91 2.52  chr1_37683192_37686007     1212  1924 (892)    L1M4_orf2#LINE/L1      102   831 (77)  

  chr1_37683192_3   1212 CCCAG--ACTTTTT----AAAAATAGAGGCAAGATTGTTCTAAAACTTAC 1255
                              --i i    ---- i    v  --    v vi i      i i i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCAT 149

  chr1_37683192_3   1256 ATGGATGAA---AAAAGAAGCTGAATAGCTAAAGCAATTTTTATAAAGAA 1302
                              --  ---  ii  vv v       i   i    i  v v      
  L1M4_orf2#LINE/    150 ATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_37683192_3   1303 GACTACAATGGGAAAAATCAGTCCATACAATTTCAAGACTTATTATATAG 1352
                           vi v i v   ii v   vv iviv         i     i  i v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_37683192_3   1353 CTATAGTAATCAAGACTGTGTGGTATTGGCAGAGTGACAGACAC-T-GAC 1400
                            i            v        i     v iv  i     i- -  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_37683192_3   1401 AAATGAAACAGAACAGAGATTCCAGAAATAGACCCACACAAATATGCCCA 1450
                         v    i  i    iv    v          i     i   vv    vi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_37683192_3   1451 ACTGATTTTTGACAAAAGAGCAAAAGTAATTCATTGGAGGAAAGATGGTC 1500
                          i       i     ii v  v  iiiv     v   i i  ii  i   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_37683192_3   1501 TTTTCAACAAATGGTGTTGATGCAAGTGGACATTCATAGGCAAAAAAAAC 1550
                                         i  ivi   v    i ?i  i v      i  vv
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_37683192_3   1551 AAA---AAC---------AAAACAAA-ACAAAA-------CAAAACAAAA 1580
                           i---i  --------- v v  v -      -------     iii v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_37683192_3   1581 CAAAAACCCTGAAACCCTGAAAAGAAACTGAAAGCAGATCATGGACTTTT 1630
                           ? i   i--   ---  v  i-- i  i   vi v ----ii   i  
  L1M4_orf2#LINE/    498 CAWAGACCT--AAA---TGTAAG--AGCTAAAACTATA----AAACTCTT 536

  chr1_37683192_3   1631 AAGAAAAAAAATTTAGGAGAAAATTTCAGAGATCTAGGGCTAGGCAAAAA 1680
                          i--  i    iv    ? v    i iv v  i  v   i       vii
  L1M4_orf2#LINE/    537 AG--AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_37683192_3   1681 GTTCTTAGCCATGACATCAAAAGCACAATCCATAAAAGGAAAAACAGATA 1730
                         v       vi      i           v v i     i     i     
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_37683192_3   1731 AGCTGGACTTCATTGAAATTAAAAACTTTTGCTCTGAGATAAACCCTGTT 1780
                          ii          ii                iv  vvi vii  v  i i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_37683192_3   1781 AAGAAAATGAA--GACAGCT-ACAGACTGGGAAAAAATATTTGTAAACCA 1827
                               i    --    i i-     v     i          i   i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_37683192_3   1828 TTTATCCC-CAAAGGGCTAGTATCCACAATATAAAAAGAATTCTTAAACA 1876
                          v    iv-i  i  i  v       v      v      i     v - 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-A 783

  chr1_37683192_3   1877 CTAAACAGTAAAAAAGCAAATAATAGTATTAGAAAACAGGCAAAAGAT 1924
                           v  i i      ii       ivvv   ?i    ii      i   
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.63 (111 / 68)
Gap_init rate = 0.03 (20 / 730), avg. gap size = 2.65 (53 / 20)  

 276 23.77 4.10 1.64  chr1_37683192_37686007     2207  2328 (488)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_37683192_3   2207 CTCAAAAAATAAAAAATAAAAAATAAAA--AATAAACAGGCAAAAGACAT 2254
                              v  vv    i i   v  ivv  --? v   ii      i  iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_37683192_3   2255 GA---GACATTGCACCTGAGAAGATACATATAGATGGCAAATAAGCACAT 2301
                           ---      v v  vi        --  i i     v           
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATA--TACAAATGGCCAATAAGCACAT 881

  chr1_37683192_3   2302 GAAAAGACGTCCAAGGCCAGGTGCAGT 2328
                                i ii   vii  ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (15 / 13)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 2.33 (7 / 3)  


2650 17.03 2.08 18.28  chr1_37871599_37873685      129  1091 (996)    L1M4_orf2#LINE/L1        1   807 (101)  

  chr1_37871599_3    129 TGGAAAGGCATCCTGTGTTCATGGAATAGAACACTTAATACTGTTAAAAT 178
                                ii    ii          v i   v        i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_37871599_3    179 GTCTCTACTACCAAAAGTGATCTACAGATTTAATGCAATCC-TATCAAAA 227
                          v vv    v  v   v             i  i       -        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_37871599_3    228 TCCCAG--GCATTTTTTGCAGAAATAGAAAAAAC-ATCCTAAAATTCATA 274
                               --  v              v  v  ivi-               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_37871599_3    275 TGGAATCTAAAAGGACCATGAATAGTCAACACAATCATGGGAAGGAAAAA 324
                              vivv  i     vv      i   v      v  ii  i   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_37871599_3    325 TAAAGGTGGGCCAGAGGCAGTGGCTCACACCTGTAATCCCAGCACTTTGA 374
                         i    -----------------------------------------   -
  L1M4_orf2#LINE/    201 CAAAG-----------------------------------------TTG- 208

  chr1_37871599_3    375 GAGGCCAAGGTGAGAGAATCACTTGAGGCCAGCATTTTGAGACCAGCCTG 424
                         -------------   i --------------------------------
  L1M4_orf2#LINE/    209 -------------GAGGA-------------------------------- 213

  chr1_37871599_3    425 GGCAACACAGTGAGACTCCATCATTTACAAAAACCAACCAACAACAAAAC 474
                         --------------------------------------------------
  L1M4_orf2#LINE/    214 -------------------------------------------------- 213

  chr1_37871599_3    475 CTACACACACACACACTCACACACAAAAGGTAGAGTCCTCACACTTCCTT 524
                         -------------------------------------           iv
  L1M4_orf2#LINE/    214 -------------------------------------CTCACACTTCCCA 226

  chr1_37871599_3    525 ACTTCAAAACATATTTCAAAGCTACAGTAATCAAAGCAATATGGTAC--- 571
                          i        v  i v                  ii  i i      ---
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr1_37871599_3    572 ---------AGACATATAGACCAATGAAACAGAATACAGAGCCCAGAAAT 612
                         ---------           i     i  i     vv    i        
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_37871599_3    613 AACTCCTCTCCATGTATGGTCAAATGATCTCCCACAAGGGTACCAAGGTT 662
                           vi  -v v   v         v    i i v        i     iii
  L1M4_orf2#LINE/    327 AAACCC-ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_37871599_3    663 ATGCTATGCAGAAAGGATAGTCTCTTCACCAAATGGCACTGAGAAAAGTG 712
                           v v   vi     i       i    v       ii   i  v  v  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_37871599_3    713 GATATCCACCTGCAAATGAATGAAGTTGGACCCTCACCTAAAATCATATG 762
                             ?    v      v                ii    v v i     i
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_37871599_3    763 CAAAAAATGAACTCAAAGTGGATTAAAGACCTAAATGTAGGATCTGAAAT 812
                               - v        i     i ?             i  v  i   i
  L1M4_orf2#LINE/    476 CAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_37871599_3    813 GATAAAACTCCTAGAAGAAAACACAGGGGAAAAGATTCATGACACTGGAT 862
                         v         i            i   ? v   vv   i    vi   i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_37871599_3    863 TCAGCAATGATTTCTTGGATATGACACCAAAAGCACAGGCAGCAAAAACG 912
                          vi      i      i                    i   i     ivi
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_37871599_3    913 AAAATAGACAAATGAGACTACATCAAACTTTAAAACTTCTGCAGGGCAAA 962
                                 i    vi    v       v  v       i  iivvv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_37871599_3    963 GGCAACAATAATCAGAGTGAAAAAGCAGTCTTTGAAATGGGAGAAAATGC 1012
                           vv  v  v vv i        ii  ii iviii             ii
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_37871599_3   1013 TTGCTAACCATTTATCT---AAGGGGTTAATATCCAGAATGTATAAAGAA 1059
                             v  i   v     ---     ii vi          i         
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_37871599_3   1060 TGTCTAGAACTCAACAACAAAGAC-CAAATAAC 1091
                         ivii  v       i  i   i v-        
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAAC 807

Transitions / transversions = 1.33 (92 / 69)
Gap_init rate = 0.01 (11 / 807), avg. gap size = 17.82 (196 / 11)  

 201 12.50 0.00 0.00  chr1_37871599_37873685     1220  1251 (836)    L1M4_orf2#LINE/L1      832   863 (45)  

  chr1_37871599_3   1220 TTGAGTAGACATTTCTTCAAAAAAGATATATA 1251
                             i           i    i        i 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.00 (4 / 0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.00 (0 / 0)  

 353 12.50 4.55 3.41  chr1_37871599_37873685     1507  1594 (493)    L1M4_orf2#LINE/L1      820   908 (0)  

  chr1_37871599_3   1507 TGGGCAACAGAGT-GA---GACTCTGTCTCAAAAAAAAAGATATACAAAA 1552
                                vi  v -  ---   vi -    v   i  --          v
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATT-TCTCCAAAGAA--GATATACAAAT 866

  chr1_37871599_3   1553 GGCCAAGAAGCACATGAAAAGATGCTTAATATCATTAATCAT 1594
                               v                   i  i    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.83 (5 / 6)
Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.75 (7 / 4)  


1887 21.30 3.85 3.85  chr1_38412054_38414662.rev      955  1447 (1162)    L1M4_orf2#LINE/L1        3   495 (413)  

  chr1_38412054_3    955 GAAAGACATATTGTGTACATGGATTGGAAGA----ATACTGTTAAGATGT 1000
                               i  viii   v              ----   i          v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_38412054_3   1001 CAGTTCTCCCCAAACTGATCTATTGATTCAGTTCAATGCCTATCAAAATC 1050
                           i v         i       iv      iiv    v            
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_38412054_3   1051 CCAGAAGAAAATTTTGTAGAAATCAACAAGCAGATCCTAAACTTTGTATG 1100
                             vv vvvv     i      ii      v         v  ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_38412054_3   1101 GAAAAACAAAGAAATTATAATAGCCAAAACAACTTTGAAAAAGAAGAACA 1150
                             vi   i i vii v              ii                
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_38412054_3   1151 AAGTCAGAGAAATCACACTACCTGACGTTAAGACTTACTATAAAGCAAGA 1200
                             ii   i v       v  ii iv i  i        i     v v 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_38412054_3   1201 GTAATCAAGA---TGTGGTGTTGGCAAAAAGA--GA------GATCAATA 1239
                                   ---      ii     v  i  --  ------       i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_38412054_3   1240 GAATAGAAC--AGTGTCCAGCAATAGACTCCTATATACATGGTTAATTGA 1287
                                 i--  v      v    i  i v  i  vi     i      
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_38412054_3   1288 TTTTTGACAAAGGTGAGAAGGCAATTCAATGACAAAAGAACAGTCGTTTA 1337
                             i     i    vv   i v        ivi      i    v   v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_38412054_3   1338 AACAA-TAGTTCTGGAATAATTGTACATAAATATGCAAAAAATAGAAAAG 1386
                              - i  v    i i  i  v i ?vv i        i --------
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-------- 444

  chr1_38412054_3   1387 AAAGTTTAAAAATAAAATTG-ATCCACACCATGTACCATACATAAAAATT 1435
                         -----------  i  i   - i  vi   viii      i i       
  L1M4_orf2#LINE/    445 -----------ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_38412054_3   1436 AACACAAAATGG 1447
                            v        
  L1M4_orf2#LINE/    484 AACTCAAAATGG 495

Transitions / transversions = 1.54 (63 / 41)
Gap_init rate = 0.02 (8 / 493), avg. gap size = 4.75 (38 / 8)  

 928 20.30 15.74 4.06  chr1_38412054_38414662.rev     1725  2118 (491)    L1M4_orf2#LINE/L1      469   908 (0)  

  chr1_38412054_3   1725 CCAGAAAAAAAAATTAACACAAAATAGATCATAGGCCT------------ 1762
                            v v v          v      i     ?  i   ------------
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_38412054_3   1763 ------CATAAAACTTTTAGA-GAATA-AGAAGGGTGG------GGGAGC 1798
                         ------i        i     -   v - v i ?  ii------ v  - 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA-C 567

  chr1_38412054_3   1799 TTTGGACTAGGAAAAGCTTTCATAGACATGAAACTAAAAATATGATCCAT 1848
                         i    ii    v  v v    v    i    v  i    ii ii v v i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_38412054_3   1849 AAAAGAAAAAATTCATAA-CTGAACTTCAATAAAATT---------TG-- 1886
                                     vv    -i  i      vi      ---------  --
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_38412054_3   1887 -----AAAGACACTGCTAAGAA--TGAAGAGGGAAACCATAGATGGAGAG 1929
                         -----  i      iii     --    i  iv  v   i   vv i   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_38412054_3   1930 AAAAATATTTGCAAAGCAGACATCTGATAA-------------AGAATAT 1966
                             -          v  v i         -------------       
  L1M4_orf2#LINE/    718 AAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_38412054_3   1967 GTAAAGAATTCTTAAAACTCAGTAATAAAAAAAGAAA--AC--AACTTAA 2012
                         i       i     v      i         i v   --  --  i ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_38412054_3   2013 AAATGGGTAACAGTTTTGAACAGACACTTCTCCGAATAATATATAGATGC 2062
                                i  vi v      i     i      i  v  v     -----
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA----- 861

  chr1_38412054_3   2063 CAAAAACAACAACAACAACAACAACATATAAAAAGATGTTCAACATTATT 2112
                             -----iii --   i  --i  i  i        i       i ??
  L1M4_orf2#LINE/    862 CAAA-----TGGC--CAATAA--GCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_38412054_3   2113 AGTCAC 2118
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.66 (48 / 29)
Gap_init rate = 0.04 (17 / 440), avg. gap size = 4.59 (78 / 17)  


2706 22.80 1.12 5.82  chr1_38446017_38447833      519  1325 (492)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr1_38446017_3    519 TAAAATTCACATGGAACCAAAAAAGAGCCCAAAGC-GCCAAAGCAATCCT 567
                                  i      viiv  ii  -    i ii-      i     i 
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTT 188

  chr1_38446017_3    568 AAGCAAAAAGAACAAAGCTGCAGACATCACATTACCTGACTTTAAACTAT 617
                         i iv  i          i  v  ivv     i v  ii i  i   viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_38446017_3    618 ACCTCAAGGCCACAGTAACCAAAACAGCATGGTACTAGTATAAAAACAGA 667
                           iv   i  i       i   i    ii       i i    ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_38446017_3    668 CACATAGGTCAATGGAACATAATAGAGAACCGAGAAATAAAGCCACATAT 717
                           i    i         i v   v    ii v         v   -----
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA----- 333

  chr1_38446017_3    718 CTGCTTTCCACAGTTACTGAACTAATTTACATTCTCACCAGCCATCTGAT 767
                         --------------   -------     ii--------- i  vi    
  L1M4_orf2#LINE/    334 --------------TAC-------ATTTATG---------GTCAATTGAT 353

  chr1_38446017_3    768 CTTCAACAAAGTTGACAAAAATAAACAATGGGGAAAGCATTCCCTATTCA 817
                         i   i    i v  v   i vi vv            v  vvi  v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_38446017_3    818 ATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGAATGAAACTG 867
                          i              i      v  ?   i     i         ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_38446017_3    868 GACCCCTACCTTTCACCATATACAAAAATTAACTCAAAAGTTGATTGGAT 917
                                    iv                          ------     
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAA------TGGAT 497

  chr1_38446017_3    918 TA-AGACTTAAATGTAAGACTTAAAACTTTAAAAATTCTAAAAGAAAAAA 966
                         i -    i           vi       v     v ii  i       v 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_38446017_3    967 TCTAGG---AAATACCCTTCTGGACACTGGCCTTGGCAAAGGATTTATGA 1013
                          --   ---    ---    vv   vi   vi v     v  v  iv ii
  L1M4_orf2#LINE/    548 T--AGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_38446017_3   1014 ATAAGTCCTCAAAAGCAATTGCAACAAAAAGAAGAATTGGCAAGTGGGAC 1063
                            v v vi        vvv         ii  i   v ii  i v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_38446017_3   1064 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAATATCAACAGAAT 1113
                         i v  i   v v  i i   i  ii vv    i  v v      v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_38446017_3   1114 AAAAAGCCAACCTACAGAATGGGAGAAAATATTTACAAACTATGCATCCA 1163
                         i     v     i                     i    ii  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_38446017_3   1164 ATAAAGATCTAATATCCAGAATCTATAAGGAACTTC----ATTCAACAAG 1209
                             i iv  vi          v     i     ii---- i    i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_38446017_3   1210 CAAAAAATAAGTAACCCCCTTAAGAAGTGGGCAAAGGACATGAACAGATA 1259
                         v    i i  i      vv  ? i  i           iv    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_38446017_3   1260 CTTCTCAAAAGAAGACATACAAGTGGCCAACAAATATATGAAAAAATGTT 1309
                         i     v        i      i       i  ii i       i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_38446017_3   1310 CAACATCGCTAATCAT 1325
                                i????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (118 / 64)
Gap_init rate = 0.01 (11 / 769), avg. gap size = 5.09 (56 / 11)  


2065 23.53 5.88 1.47  chr1_38448993_38453782.rev     2585  3196 (1594)    L1M4_orf2#LINE/L1        1   639 (269)  

  chr1_38448993_3   2585 TGGAGAGACATTTCATGTTCATAAATAGCAAGACTCAGAATTGCTAAGAT 2634
                             i   i  ii         ii  v v      i iv    i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_38448993_3   2635 GTCAATTGTTTCCAGATTGATC----AAT----CTCAGTCTCAATCAAGA 2676
                          v    vv ii   i       ----i  ---- v  i  i v     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_38448993_3   2677 TCCCAGAAAGGTATTTTGTGGATATCAACAAACTGATTCTAAAGTGTATA 2726
                               vvivv v     ii  v  ii    i     i     i vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_38448993_3   2727 TGGAAAAGCAAAAGACTCAGAAAAGCCAA--CA--CTTGAA---GAAGAA 2769
                               v    ii   i     v      --  --      ---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_38448993_3   2770 CAAACTTGGGGGACTGACACTACGCAATCTGAAAACTTACTATAAGTTTA 2819
                             v    i     v     v v    i v           i  ivi  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_38448993_3   2820 AATTAATCAAGATAGTATGGTATTGACAAAAGAGT-GACTCATAGATCAA 2868
                         v v         i   i     i  i  v   ii -   vi         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_38448993_3   2869 TGGGAAAGAATAGGAAGCTCAGAAATAAATCCACACAAACATAGTCAACT 2918
                            i v     v ii  ii          i   i   vvi  i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_38448993_3   2919 GATCTTTGA-AA--------AGACTAT-CAAAGGG-------TAGTCCTT 2951
                            i  i  -  --------    i  -   v   -------     i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_38448993_3   2952 TCAA-AAATGGTGCTGGAACAATTGGATTTCCAAATGAAAAAAAAAAAGA 3000
                             -            i    i     v?   v   v    i  v--  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT--GA 448

  chr1_38448993_3   3001 ATCTAGATTCAGACCTTAAACCTTTCAGAAAAATTAACTCAAAATGGAGC 3050
                          vi i  ii vv    i v   v vi v                    v 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_38448993_3   3051 ACAAACCTAAATATAAAATGC-AATATTATAAAA-TGTTAGAAGAAAACA 3098
                          ? i        i   i -  -  v i       - v             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_38448993_3   3099 TAAGACATAATTTAAGTGACATTGTGTTTGACAATGACATTTTAGATACC 3148
                           i ?vvv   i vv     v   v   v i     iiv i       iv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_38448993_3   3149 ACCCCAAAAGTACAATCTATGTGACAGTGGAAAAACACACATGAACTG 3196
                           v       i    ----- ii   ivi      - i v  i  i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA-----GCAACAAAAGAAAAA-ATAGATAAATTG 639

Transitions / transversions = 1.39 (82 / 59)
Gap_init rate = 0.03 (17 / 639), avg. gap size = 2.65 (45 / 17)  

1034 21.48 3.87 1.41  chr1_38448993_38453782.rev     4016  4299 (491)    L1M4_orf2#LINE/L1      618   908 (0)  

  chr1_38448993_3   4016 AAGGAAAAAAATGGACACATTGAACTTTATTAAAATTAAAA-TTTTTGCT 4064
                           iii       i  i v    i    i  i          -i     iv
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_38448993_3   4065 CTGTGAAAGATACAGTTAAGAGAATTAAAAGACAAGCCACAGACTGGGAG 4114
                           vii  i  i  vi i    i i v         v       v      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_38448993_3   4115 AAAATATTTGCAAAACGCGTA--------GTAGCTGTACATCCAAAATAT 4156
                                       v iii  -------- vii  - ii     i     
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACT-TGTATCCAGAATAT 766

  chr1_38448993_3   4157 ACATAAAAAAACTCTTAAAACTTAACAATAAGAAAACAAACAACCTAATT 4206
                          i ---  i        v    i  i     i  i     i    i    
  L1M4_orf2#LINE/    767 ATA---AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_38448993_3   4207 -AAATATTGGCAAAG-ATGTGAACAGACACCCCACCAAAGAAGATATGCA 4254
                         -   v  v       -  v    i     iii v             i  
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_38448993_3   4255 AATGAAAAATAAGCCTATGAAAATATGTTCAACTTCATTTGTCAT 4299
                             ivv       vi       v   i     v   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (42 / 19)
Gap_init rate = 0.02 (6 / 291), avg. gap size = 2.50 (15 / 6)  


2977 26.47 1.78 0.78  chr1_38538974_38543867     3503  4401 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_38538974_3   3503 TGGAAACACATCCCCTGCTCATGGATGGGTAGAATCAACATTGTGAAAAT 3552
                               v i     v  i        v  v   v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_38538974_3   3553 GATCATACTGCCAAAAGCAATCTACATATTCAATGCAGTTCCCATCAAAA 3602
                          iiv     v  v   vii       v      i   i i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_38538974_3   3603 TACCACCATCGTTCTTCACAGAGCTAGAAAAA--AATTCCTAACATTTTT 3650
                          v   v vv v  i  ii    iv v  v  i--i  -     v   iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chr1_38538974_3   3651 ATGGAACCA-AAATGATCCTGCATAGGCAAAGTAAGACTAAGCAAAAAGA 3699
                               vii-  iv  i  v v    v    ii  vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_38538974_3   3700 ACAAATCTGGAGGCATCGCATTACTGGACTTCAAACTATACTATTAGGCC 3749
                              vi      vv  i  i v ivi i      viv     iv i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_38538974_3   3750 ATTATCTCCAAAACAGCATGGTACTGGTGTAAAAATAGGCACACAGACCA 3799
                          ivi vvi   i    ii         ii   ii    i  i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_38538974_3   3800 ATGGAACAGAATAGAGAACCCAGAAATAATGCCAAATACTTGCAGCCAAC 3849
                               i     v    ii          vv   v i i  iii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_38538974_3   3850 TGATCTTCGACAAAGCAAGCAAAAACATAAAGTGGGGAAAGAACACCCTA 3899
                             i        i vviv   i v   vv i           i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_38538974_3   3900 TTCAACAAATGGTGCTGGGATAACTAGCAAGCCACATGTAGAAGAATGAA 3949
                                             i    i vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_38538974_3   3950 ACTGGAACCTCT-TCTCTCACTTTATACAAAAATCAACTCAAGATGAATC 3998
                         ii    -  i  -i   v   iv           i       i   i   
  L1M4_orf2#LINE/    450 GTTGGA-CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_38538974_3   3999 AAAGATTTAAATCTAAGACCTGAAACCATAAAAATTATAGAAGACGACAT 4048
                          ?   ii     v     v  i    i      v iv       vi    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_38538974_3   4049 CAGAAAAACCCTTCTAGACATTGGCTAAGTCAAAGAGTTCATGACCTAGA 4098
                         vi ?iv  vi    vv   v    v v  v   v iv   -----i    
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-----TTAGA 593

  chr1_38538974_3   4099 -ATG----CAAAAGCAAATGCAACAAAACAAAGA-TAAATAGTTGGGACT 4142
                         -   ----        v v         v   i -  i   iv v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_38538974_3   4143 TAATTAAACTAAAAAGCTTCTGCACAGTAAAGGAAACAATCAGGAGAGTA 4192
                          v  i   v v    i   i  ii vvi      v  v    i  i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_38538974_3   4193 AACAGACAACCCACAGGGTGGGAGAGAATCTTCATAATCTATACATCTGA 4242
                           v             ii       i   v  iii  vii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_38538974_3   4243 CAAAGGACTAATATCCAGAATCTCCAAGGAATTC----AAATAAATCATC 4288
                         i  i     vi          v vi  i   i  ----  v v   v  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_38538974_3   4289 AAGAAAAAAATATCCCA-TCAAAAGGTGGGCTAAGAACAAGAATAGACAA 4337
                           i i v     v    - i?   ii     v   i ivv         v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_38538974_3   4338 TTCTCAAAAGAAGATATACAAATGGTCAACAAACATATGAAAA-ATACTC 4386
                              v                   i   i  i  i       -  i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_38538974_3   4387 AACATCACTAATGTT 4401
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (133 / 101)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


1463 18.03 1.04 25.28  chr1_38545648_38547797      500  1658 (492)    L1M4_orf2#LINE/L1       31   908 (0)  

  chr1_38545648_3    500 AGACTCAATATTTTTGTCAT--CAGTTCTTCCCAAATTGATCTACATGTT 547
                              i      v  ivv  --  i v  i                vi  
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chr1_38545648_3    548 TAATGGTATCCCATTCAAAATCAAAGCAGGCATTTTTGTAGAAATTGCCA 597
                         i  i vv     vv        vv   v v v      i        v  
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA 130

  chr1_38545648_3    598 AGCTGATTCTAAAATATGTATAGAAATTCAAAGGGCCTGAAATATCCAAA 647
                                i       vii   i     v   i  i  iii    v     
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr1_38545648_3    648 ATAATCTCAAAAAA--AGAACAAAGTTAGAAAATTTATTCTACCTGATTT 695
                          i     ii     --           i  ii i i iv  v  ii    
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_38545648_3    696 TAAAACTTACTATAAAGCTGCAGTAAATCTGAAAC--TGTTATATTGCCA 743
                         i           i      i      -  -i i  --   vi  i  v  
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAA-TC-AAGACAGTGTGGTACTGGCA 278

  chr1_38545648_3    744 TAAAGGTAGACATAAAAATCAGTAGATCAGAATAGTGAGTCCATAAAAAG 793
                            i i        v i    i i  vi     v v       v   v i
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_38545648_3    794 GCCCACATAATATGCCAACTAAAGTCACCAAAAGTAATTTTATTTGAAAA 843
                         i    i i v --------  vi    --------------   ------
  L1M4_orf2#LINE/    329 ACCCATACATT--------TATGGTCA--------------ATT------ 350

  chr1_38545648_3    844 AGATAATCTTTTCAACAAAGGATGCTAAAACAATTGGCTATTCATGTGGA 893
                         -   -----    i    i  -   i  i  -------i     -i   i
  L1M4_orf2#LINE/    351 -GAT-----TTTCGACAAGGG-TGCCAAGAC-------CATTCA-ATGGG 385

  chr1_38545648_3    894 GAAAAATGAACCTCAACCTCCATATCATACCACCTCCAAAAATTAATTTA 943
                             i --------------------   --ii  -----------   v
  L1M4_orf2#LINE/    386 GAAAGA--------------------ATA--GTCT-----------TTTC 402

  chr1_38545648_3    944 AAGCCAGGCGCAATGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCAG 993
                           --  -----     --------  i-------------     --  -
  L1M4_orf2#LINE/    403 AA--CA-----AATGG--------TGC-------------TGGGA--CA- 421

  chr1_38545648_3    994 AGGTGGGTGGATCACTTGAGCCCAGGAGTTTGAGACCACCTGGCCAACAT 1043
                         -------------   --------   ------------- i?   -   
  L1M4_orf2#LINE/    422 -------------ACT--------GGA-------------TAKCCA-CAT 436

  chr1_38545648_3   1044 GGTGAAACCCCCTCTCTACTAAAAATACAAAAAAACTAGCCAAGTGTGGT 1093
                          --------------------------     i  i--------------
  L1M4_orf2#LINE/    437 G--------------------------CAAAAGAAT-------------- 446

  chr1_38545648_3   1094 GGTGGGTGCATGTAATCCCAGCTACTCGGCAGGCAGAAGAATTGCTTGAA 1143
                         -----------------------------------    ------   i 
  L1M4_orf2#LINE/    447 -----------------------------------GAAG------TTGGA 455

  chr1_38545648_3   1144 CCTGGGAGGCAGAGGTGGCAGTGAGGCAAGATCACACTACCGCACTCCAG 1193
                           i---------------------------------     v   -----
  L1M4_orf2#LINE/    456 CCC---------------------------------CTACCTCAC----- 467

  chr1_38545648_3   1194 CCTGGGTGACAGAGTGAGACCCTGTCTCAAAAGAAAAAAAAATAATTTGA 1243
                         ------------------   v i --------- v     v   i ii 
  L1M4_orf2#LINE/    468 ------------------ACCATAT---------ACAAAAATTAACTCAA 490

  chr1_38545648_3   1244 GATGAAGCATAAACCTAAATAAAAAAGCTAAAACTATAAAGTTTCTAGAA 1293
                         i   i v  ? i        iv  i               ii ii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_38545648_3   1294 GAAAACAGAAGAGAGTATCTTTGCATCTTAAGGGCAAGCAA-AATTTCTT 1342
                                v i ? viv     i iiv i vi  vi i    -ii      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_38545648_3   1343 AGCCAAGATTCTAAA-GCACTAACCATAAGAGAAAAAAACCTGATATGCT 1391
                           vi v  iv i   -    v i v i  i        --iv    vii 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAAATT 638

  chr1_38545648_3   1392 GGACTTCAT-AAAATATAAAACTTCCATTCTTCCAAAAATAACATTAATA 1440
                                  -     vv       iii v    v  ii i vi  i  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_38545648_3   1441 AAAT-AAAAGGCAAGCCACAGCCTGCTAGAAG-TATTTGCCATACATAAA 1488
                           i -     i   v      vv  vv    i-       v vv    v 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_38545648_3   1489 CCTGAAAAAGAAATTTTATCCAAAATGTATAATGAATTCCTATAATTCAA 1538
                         i    v  i i v  v      i   i     v   i  i  i  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_38545648_3   1539 TAATGAAAAAACTAAATAATCCAAT-AAAAAGTGAGCAAAAGATTTATAC 1587
                             i    i  -      i     -?    i  i     i     iv i
  L1M4_orf2#LINE/    789 TAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_38545648_3   1588 AGACTCATCATAAAAGAAGATACATGAATGGCCACTAAGCACATGAAAAG 1637
                             viv  viv          i ii        v               
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_38545648_3   1638 ATGCTCAACGTCCCTGGTCAT 1658
                                  i  v????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (129 / 76)
Gap_init rate = 0.04 (38 / 878), avg. gap size = 8.03 (305 / 38)  


3753 16.67 3.31 1.32  chr1_38606704_38608450      499  1254 (493)    L1M4_orf2#LINE/L1      138   908 (0)  

  chr1_38606704_3    499 CCTAAAATTCATATGGAA-TGTCAAGAGACCCCAGATAACCAAAACAATC 547
                                           -  -    i     vii   i           
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_38606704_3    548 TTGGAAAAGGA---CAAACTTAGAGATCTCACACTTCCTGATTTCAAAAC 594
                            i     i ---    v  i   iv           ii          
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_38606704_3    595 CTACTGCAAAGCTACAGTAATCAAAATAATGTGGTACTGGCATAAAGATA 644
                         i    i                  i i i                i    
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_38606704_3    645 GACATATTAGCCAAGGGAATAGAC-----AGCCCAGAAATAAACCCTCAC 689
                                viii   v        v-----  i              vi  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_38606704_3    690 TTATATTGTCAAATGATTTTCAGCAAGGGCATCAAGACCATTCAATGGGA 739
                         v v   v     v        ii      iii                 i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_38606704_3    740 AAAGAACAGTTTTTTCAACAAATGATTGTGAG-TATCTTGCTTTGGATAT 788
                               i   i             i vv  i -i v  ------     ?
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT------GGATAK 430

  chr1_38606704_3    789 CTGCATACAAGAAAATGAAGTTGGACCATTACTTTACATCATATACAAAA 838
                          ii   i   i i              vi   i i   i           
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_38606704_3    839 ATTAACTCAAAATGGACCCAAAACCTAAATGTAAGGGCTAAAACTATGAA 888
                                         i v? i             i           i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_38606704_3    889 ACTCTTAGAAAAAAAAACACAGGGGAAAAGCTTTATGACAT-AAGCTATG 937
                                   i    --  i   ? v   v   ii    v -ii i  - 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAA--CATAGGNGTAAATCTTCGTGACCTTGGGTTA-G 577

  chr1_38606704_3    938 GCAATTATTTCTTCACTATGATGCTGAA-GCACAGGCAACAAAAGAAAAT 986
                              vi      viv     ii ii  -     i              v
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_38606704_3    987 GTAAATAAATTGACCTTCATCAAAATGTAAAACTTCTGTGCATGAAAGGA 1036
                         i  i        iv            vv       i     v v      
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_38606704_3   1037 CACAACCAATAGAGTAAAACGATAACACACAGAATGGGAAAAAATATTTG 1086
                            v i   v i   i   v  i   v            i          
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_38606704_3   1087 CAAATTATATTTCTGATAAGGAGTTACTATCCAGAATATATAACTAAACC 1136
                              i    v          iii vv                vv  vi 
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_38606704_3   1137 --ACAACC-------AAAAACCCAA----CCTGATTAAAAAATGGGCAAA 1173
                         --     i-------     vv   ----  ii   ?             
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_38606704_3   1174 GGATTTGACTAAACATTTCTCTAAAGAAGATACACAAATGGTCAATAAGC 1223
                                 v  i         i          i        i        
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_38606704_3   1224 ACATGAAAGGATGCTCAACATCACTAATCAT 1254
                                 i              ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (81 / 41)
Gap_init rate = 0.02 (13 / 771), avg. gap size = 2.69 (35 / 13)  


3277 26.39 1.11 0.44  chr1_38764169_38770620.rev     5061  5962 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_38764169_3   5061 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATACCATGAAAAT 5110
                              ii i  i     i        v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_38764169_3   5111 GGCCGTACTGCCCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 5160
                            vi    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_38764169_3   5161 TACCAATGACTTTCTTCCCAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5208
                          v   iivi i  i  iv     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_38764169_3   5209 GATGGAACCAAAAAAGAGCCCGCATTGTCAAGACAATCCTAAGCAAAAAG 5258
                         v      viiv  ii  v  v v  v i   i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_38764169_3   5259 AACAAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGGC 5308
                                i      vv   i   v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_38764169_3   5309 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5358
                           i     i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_38764169_3   5359 AATGAAACAGAGCAGAG-GTCTCAGAAATAATGCCACGCATTTACAACC- 5406
                             i  i   iiv   -   -         vv   ii      iiii -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chr1_38764169_3   5407 --TGATCTTTGACAAACCTGACAAAAACAAGCAACGGGGAAAGGATTCCC 5454
                         --    i  i     ivv  v   i v  vv   i        i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_38764169_3   5455 TATTTAATAAATGGTTCTGGGAAAACTGGCTAGCCACATGTAGAAAGCTG 5504
                          v  i  i       v      v      v  ?       i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_38764169_3   5505 AAACTCGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAGATGGAT 5554
                           ii v  i    v   i     v    i         i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_38764169_3   5555 TAAAGACTTAAGTGTTAGACCTAAAACCATAAAATCCCTAGAAGAAAACC 5604
                         i ?    i   i   v   v       i      ii i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_38764169_3   5605 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5653
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_38764169_3   5654 AACACCAAAAGCAATAGCAACAAAAGCCAAAATAGACAAATGGGATTTAA 5703
                         i            vv           vv        i    v   i  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_38764169_3   5704 TTAAACTAAAGAGGTTCTGCATGGCAAAAGAAACTACCATCAGAGTGAAT 5753
                          i   v v  i iv  i  iiivv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_38764169_3   5754 AGGCAACCTACATAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 5803
                           i     i   v             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_38764169_3   5804 AGGGCTAA-ATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5852
                         i  i  vi-         v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_38764169_3   5853 AAACAAACAACCCCGTCAAAAAGTGGGCAAAGGATATGAACAGACATTTC 5902
                          i     i     vi i?    i            v    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_38764169_3   5903 TCAAAAGAAGACATCTATGCAGCCAACAG--ACATGAAAAAATGCTCATC 5950
                           v        i  vi viii     i i--         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_38764169_3   5951 ATCGTTGGTCAT 5962
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (144 / 90)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


 646 32.56 14.50 1.89  chr1_38817118_38819579.rev      838  1313 (1149)    L1M4_orf2#LINE/L1        1   536 (372)  

  chr1_38817118_3    838 TGGATAGATG----ATGTTCTTGGAC-AAAATACCCTGTATTATAAAGAT 882
                             v    i----      v    i-ii  v  iivi    i v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_38817118_3    883 G-TAA-ATTCCCCAAACAAGACTTTTGATTCAATATAATTCCAATTAGAT 930
                          -i  - i        iviiv  viv       iii   i  v  i i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_38817118_3    931 TTACAACAGAGTT------GGAACTTGACAAGGTAATTCT------TATA 968
                          iv  i v vv  ------i   v        v i  i  ------i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_38817118_3    969 TAGTATAACAAGGG----------GCCAAGATCCTCTTAAAGAATAAGAA 1008
                          i v vvi      ----------     i ivv    i  i  v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_38817118_3   1009 GAAGCTGGGGGGATTTTCATCCACCAGATAACAAGGCTTATCATAAAGCT 1058
                         v  iv v  i   i iv  iiiv   -  vv   ii    ii i      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCT 249

  chr1_38817118_3   1059 GTAGTAATTAGG-----GTGGT-----------GAT---CA-----ATGA 1084
                         ii      i i -----     -----------   ---  -----  v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_38817118_3   1085 ATAGGACAGAAGAAAGAGCCCAGAAACAAATT-ATGTGTGTCTGGAAACT 1133
                           i i i    vvi    i       i   ii-  iii v v   vv v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_38817118_3   1134 TGATTCTTAATGAGG-------------TAGATGGGGAAGGAATGGAATA 1170
                              i ii ii   ------------- vi        i    i vv v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_38817118_3   1171 GTCAATTGATAGTGCTGGGAAAATTAGTTATCTATACCGAAAAAAAAAAA 1220
                         v    ivi  i         v  i i v  ? i i i-------iv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-------GCAAAA 442

  chr1_38817118_3   1221 AAAGGAATTTGG-TTCTTACCTCATGATC-TACACAAAGATAATTTTCAT 1268
                         i  v   v    -ii i       i- i -  i     i  v vi iv v
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCAC-ACCATATACAAAAATTAACTCAAA 491

  chr1_38817118_3   1269 GTGAGTTAAAAAACTAAAAATAATGGGAAAAACTAGAAAACTTTT 1313
                         i  ii i ? i v     vi   vi vv       v      i  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

Transitions / transversions = 1.59 (94 / 59)
Gap_init rate = 0.03 (18 / 536), avg. gap size = 4.33 (78 / 18)  

 803 27.53 10.11 1.12  chr1_38817118_38819579.rev     1616  1971 (491)    L1M4_orf2#LINE/L1      521   908 (0)  

  chr1_38817118_3   1616 AACCTAGAAAACTTTTATGACACAATATGTGAGCATACCTTCATAACCTT 1665
                           v   v      i   vi v v  i  iv ? i v i    i i     
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_38817118_3   1666 G----AGGTCATG-------AAACATG----------CACA--CTATAAA 1692
                          ----   iv   ------- i i   ----------    -- v i   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_38817118_3   1693 GAAAAAGTTCAATAAATTTGACCCTATTAGAATTAAGAACTT--GTTCCT 1740
                         ii    iv vi       v   iii  i i      i     --  v i 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_38817118_3   1741 CCCAAGACACTGT----AGAGTGAAAAGACAAGCCACACCCTAGGAGGAG 1786
                          vv i      i ---- i             v     vvv i    i i
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_38817118_3   1787 ATATTTGTAA--CATATATAATCAACTAAGGATTAATATCCAGAATATAT 1834
                                i  --       --iii iv i   i vi              
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATAT--CTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_38817118_3   1835 AAAGAA---TGAC--CGCAAATGTGTAAGTACAATATATTTGTAATAAAA 1879
                               --- v  -- v   vvi iv  iv    -   vii-i   v?  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAA-ATAACC-CAATTWAA 816

  chr1_38817118_3   1880 TAGTGGGCAAAAGACATATGCAGGTATTTTACAGAAGAGGAAACACAAAT 1929
                         v i        i  iv ivii  ii    iv vi    i  v i      
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_38817118_3   1930 GGGGAAGAAACACATGAAAAGATGCTCAATTTCACTGACAAT 1971
                           vv  v  i                   iv   ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (57 / 39)
Gap_init rate = 0.03 (12 / 388), avg. gap size = 3.33 (40 / 12)  


 502 29.10 6.88 5.03  chr1_38824152_38827148        1   378 (2619)  C L1M4_orf2#LINE/L1   (17)   891   507  

C chr1_38824152_3    378 AAATGTAAAAATTAAAACTTTAGGATTACTGAAAGAAAATATCTGGGAAA 329
                                 i ii       v  ii i vi ii       i  vv ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

C chr1_38824152_3    328 TTATCTTTAT-ACCTTTTATAACTTAGTAGTA-TGGAAGTCTTCTCCAAG 281
                         --     ii -     ----iiv    -- i -   ----i    i- ii
  L1M4_orf2#LINE/    557 --ATCTTCGTGACCTT----GGGTTAG--GCAATGG----TTTCTT-AGA 593

C chr1_38824152_3    280 TGTGACCCCAAAAGCAGAAACCATAAATAAAAAAGTTATTAGATTATACT 231
                          i    v         v  i v i   vi     i viv  i   iv   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

C chr1_38824152_3    230 ACATAAAAATTGTAAA--TTGATATTCTAAAGA----TGTCATAAACAT- 188
                         v   v      iv   --  vi ii ii    i---- i   vi  vi -
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

C chr1_38824152_3    187 ---AGACTAATTACCAC----TGATAAAAAATGTATGCAA--CATATATG 147
                         ---    -  i--    ----  iv i     i v     --       -
  L1M4_orf2#LINE/    694 AAAAGAC-AAC--CCACAGAATGGGAGAAAATATTTGCAAATCATATAT- 739

C chr1_38824152_3    146 ATAGATAAAGGATT---ATTTATAATATATGAAGAGTTCACATACATCAA 100
                         -iv     i   i ---  ii v       i    ii  vi i vv    
  L1M4_orf2#LINE/    740 -CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

C chr1_38824152_3     99 TAGGAAAAATTAGAACAATCTC-TTAAATAAACGGGCAAAAGGCATGAAC 51
                           iv     vvvi  i  i iv-  ?  -   i       i iiv    i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAAT 837

C chr1_38824152_3     50 AAGTAGTTT----AAAAAGAAATACAAATATCTAACAAAAGTATGAAAAG 5
                          iii v  i----  i    v        iv i  i  ivii        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

C chr1_38824152_3      4 ATGC 1
                             
  L1M4_orf2#LINE/    888 ATGC 891

Transitions / transversions = 2.00 (72 / 36)
Gap_init rate = 0.05 (19 / 385), avg. gap size = 2.37 (45 / 19)  

 748 22.75 7.11 2.37  chr1_38824152_38827148     1051  1261 (1736)    L1M4_orf2#LINE/L1        1   221 (687)  

  chr1_38824152_3   1051 TGGAGAGTTACACCATATGCATAGATTAGAAGATTCAGCATTGTTAA-AT 1099
                             i  v  iv    i v   i    i     i i ii        -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_38824152_3   1100 GTCTGTTCTCCCCAAATCAATCTATAAATTC----CAATC------AAAA 1139
                          v vi v          ii     i i    ----     ------    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_38824152_3   1140 TCCTAGAGAGGTTTTTTTTTTGTATAAATTGGTAAACTGACTTTAAAACT 1189
                            i  ----v vii       i v      ii  i    iii     i 
  L1M4_orf2#LINE/    101 TCCCAG----CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_38824152_3   1190 AA-ATGAAAATGCAAAGAATACAGACTAGCTCAAGGAAATCT-GAAAAA- 1236
                         v -   i        i i iv    v    -   iiv     -      -
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGC-CAAAACAATCTTGAAAAAG 195

  chr1_38824152_3   1237 -AGAACAAAATTGGAGGATCTACACT 1261
                         -        i        iii     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACT 221

Transitions / transversions = 2.69 (35 / 13)
Gap_init rate = 0.04 (8 / 221), avg. gap size = 2.50 (20 / 8)  

2296 23.80 1.31 3.48  chr1_38824152_38827148     1816  2504 (493)    L1M4_orf2#LINE/L1      235   908 (0)  

  chr1_38824152_3   1816 ACTGTACTATGAAGCTACAGTATGATGATGTTACAGAATTACACAGGCAT 1865
                            -     ii           --  v v --    vi vii  v     
  L1M4_orf2#LINE/    235 ACT-TACTACAAAGCTACAGTA--ATCAAG--ACAGTGTGGTACTGGCAT 279

  chr1_38824152_3   1866 AAGGGTAAAAATGTAGATCAATGGAAGAGACTAGAGAGTCCAGAAAGAGG 1915
                             i  i v  i             v   v v             v ii
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_38824152_3   1916 CCAACATATACATGGCCAATTGATTTTTAATAACATAGGCACCAGCATAA 1965
                           v i i  vi    i           ii i  ---i  ii   iv iv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAA---GGGTGCCAAGACCA 376

  chr1_38824152_3   1966 TTCAATGGGGAAGGGGTAATGATTTTTTAA-AAATAGGGCTAGAACAACT 2014
                                     i ii  i --i    i  -    i v   i i      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGT--CTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_38824152_3   2015 GGATTGTCATATGAAAGAAAAGTAAACTCAATCCCCGTCTCACACCATAC 2064
                             v?i  i   v  i i  vv  ii vi i   iii           i
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_38824152_3   2065 ACAAATATTGATTTGAAATCAGTCATAGACATAAACATAAAACCTAAAAC 2114
                              v   i i ii    vii   ?    v    ii   i v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_38824152_3   2115 TATAAAATTTCTAGAAGAAATAATAGAAAAAAGAACCCTTTGTAGTTTGG 2164
                                i ii         vv    i?iv  i---i   i  iiii v 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAA---TCTTCGTGACCTTG 571

  chr1_38824152_3   2165 GGTTAGACAAGAATTTCTTTGATA-GACA---AAAGTATTAGTCATAAAA 2210
                               i   vii      v    -    ---    i iv  iv i    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_38824152_3   2211 GAAAAAATTAATAAACTAGACTTCATCAAAATAAAACACTTCTGCTCTCT 2260
                                 vi     i i              v   v    i  iv  ii
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_38824152_3   2261 AAAAGACATAATCAA-AAAGTGAAAAGGCAAGTCACAAATTGGGAGAAAA 2309
                            i    iv     -           i   vi    i v          
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_38824152_3   2310 TATGTGCATCACATATATCTGTCAAGAAGCATGCATAAAAAAGCCAGAAT 2359
                            v    vvv          vi   iii v  i  -------       
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTAT-------CCAGAAT 764

  chr1_38824152_3   2360 ACAAAAAGAACTCTTATTACTCAATAAGAAAAAGACAAAACACTCAATTT 2409
                          i v            iv         v           vv  i     ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_38824152_3   2410 TTTAAATGGGCAAA--ATTTGAATGG-TGCTTTATGAAAGAAGCTATACA 2456
                         vv-           --        i -iii  iviv       v      
  L1M4_orf2#LINE/    815 AA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_38824152_3   2457 AAAAGGTCAATAAACTCAAGAAAAAAAATGTTCAACAACATGAGTCAC 2504
                           v-  i      i v  v     i --  i      v  ????????
  L1M4_orf2#LINE/    864 AAT-GGCCAATAAGCACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (101 / 59)
Gap_init rate = 0.02 (16 / 674), avg. gap size = 2.06 (33 / 16)  


3070 15.59 7.87 1.26  chr1_38939589_38941215      500  1134 (493)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr1_38939589_3    500 AAAACCTACTGCAAAGCTGCAATGGTCA-GACAGTGTGGCACTAGCATAA 548
                              i    i       i  i ii   -          i   i      
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_38939589_3    549 GGACAGACACATAGATCAGTGGAAGAGATTTGAGAGTCCAGAAGTAAATC 598
                            i     i        i     v   v              i    i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_38939589_3    599 CTTAACGTGTATGGTCAATTAATTTT-GACAAAGTTGCCAAAATAATTCA 647
                          v  - i v           i     -     i v      i iv     
  L1M4_orf2#LINE/    332 CATA-CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_38939589_3    648 ATGGGGAAAGACTACTCTTTTAAACAAACGGTGCTGCGACAACAGGACAG 697
                                    v  v      v      i       v      v   i ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_38939589_3    698 CCACAT------------------------------CATCCTATACAACA 717
                               ------------------------------  i v       v 
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_38939589_3    718 ATTAACTCAAAATGGATCAAGGACCTAAATGTAAGAGCTAGAACTATAGA 767
                                            ?i                   i       i 
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_38939589_3    768 TCTCTTGGAAAAAAACACGAGAGTAAATCTTTGTGACCTTTGGTTAGGCA 817
                         v     i   i      iii ?         i        v         
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_38939589_3    818 GTGGTTTCTTAGATGTGACAGCAAAAGCACACGCACACACAAAAAGAAGA 867
                         i             i     v          v   ---      ii  i 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCA---ACAAAAGAAAAA 627

  chr1_38939589_3    868 CAAGA-AAA----ACTACATCAAAATTTAAAATTTGTGTGCTGCAAAAAA 912
                         vv   -   ----   v          v    i  v      v    ii 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_38939589_3    913 GTTTA-------AGTGAAAAGATCACCTCCAAAATGGTGAAAAAAAAAAC 955
                         vvi  -------          iv   iv  i     ---i i    v i
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG---GAGAAAATAT 724

  chr1_38939589_3    956 TTGCAAATCATATATCTAGTAAGAGGCTTATATCCAGAATATATAAAGAA 1005
                                          ii    i i   i                    
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_38939589_3   1006 TTCTTACAACTCAATAATAA---GACAAATAACTAAATTTTTACATGGGG 1052
                         i                   ---          iv    ?vv v     v
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_38939589_3   1053 AAAAT-TTTAAATAGATATTTCTCTGAA--AGATACCATAAATGGCCCAT 1099
                            iv-   i      i       ii  --     i- i        v  
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT-ACAAATGGCCAAT 873

  chr1_38939589_3   1100 AAACACATGAAAAGATGCTCAACATCATTAACCGT 1134
                           i                        ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (60 / 35)
Gap_init rate = 0.02 (13 / 677), avg. gap size = 4.46 (58 / 13)  


1400 27.70 7.82 1.06  chr1_39041033_39043397      522   994 (1371)    L1M4_orf2#LINE/L1       16   520 (388)  

  chr1_39041033_3    522 TGTTCATACATTGAAACACTCAATATAGAAAATATATCAGTTCTCCCCAA 571
                                iv    i  v   i     v vv  v  iv  i v        
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_39041033_3    572 ATTGATGTACAGATTTAAGGCAACTCCTATCAAAATTCCAGCAAGAATTT 621
                               v        i  v    ii           i     vivvv   
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_39041033_3    622 CTATAGCTATAAACAGAATTATTCTAACGCTTATATGGAAAGGCAAAGGA 671
                         i ii  vv  vi   iiv v  i    vii i         v    i   
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_39041033_3    672 ATTAAAACAGCTA---CAATTTTCAAAATGAAGAATAAAATGGGAGGAAT 718
                         vii i  i   i ---    i  v    v      i   i v      v 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_39041033_3    719 CA----TTCTGATTTCAAAACTTATTATATAGCTACAGTAATCAAGCCTA 764
                           ---- i ii             i  i v                v vi
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_39041033_3    765 TGTAGTTTTGGTGGAGGGATAGACATAGAGATTGATAGAATAAAA---AG 811
                            i  vi   iiv i           v    ii  i     i  ---  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_39041033_3    812 AACCCAGAA-TAGCCCCCACAAAACTATAGGCAACTGATTTTTTATAATG 860
                          ii      -  iv   - i v vi   i v   i       iv i  v 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCC-ATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_39041033_3    861 GTGTAAAAGCAATTCAACAAAGGAGGAAAAAT--TCCTTTCAACGAATTA 908
                            iv  ii v      i---  i i  i   --  i       i   vi
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAAT---GGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_39041033_3    909 TTCTAGCATAATTGGATATCTTCAGGCCAAACAAACAAAA-------CAA 951
                          v  i v i  i      ? iv  v  v   -i  ii  i------- vv
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAAGTTGGACCCCT 460

  chr1_39041033_3    952 ACCTCA-----------------AACTCAAAATGGGTTGCATATTTAAAA 984
                               -----------------            i ii? v ii    v
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_39041033_3    985 GTAAAGGCCA 994
                             ii  i 
  L1M4_orf2#LINE/    511 GTAAGAGCTA 520

Transitions / transversions = 1.58 (79 / 50)
Gap_init rate = 0.02 (10 / 505), avg. gap size = 4.20 (42 / 10)  

1270 24.32 5.71 0.74  chr1_39041033_39043397     1471  1873 (492)    L1M4_orf2#LINE/L1      486   908 (0)  

  chr1_39041033_3   1471 CTAAAAGTGAA-CAAACAAATAAATGTAA-AGCATAAAGCTATAA--TTT 1516
                           v   i  i -  ? v vv         -   -    i      --i i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTC 534

  chr1_39041033_3   1517 TTAGAAGATAACATTGGAAAAAATCCTCAGGACCTAAGGTTCAGTGAAAG 1566
                                 v     v  ?iv     i  iv     vi    vi i-  v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC-AATG 583

  chr1_39041033_3   1567 GTTTTTAAGACATAACCCCAAAAGTACCATTCATAAATGGAAAAATTGAT 1616
                             i v   i  i  v       i  v viv i   v i      v   
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_39041033_3   1617 --GTTAGACTTCATCAAAATTTAAAATTCATGTTCTCTGAAAGACCTTGG 1664
                         --i  i               v    i iv   v  iii  i   vi iv
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_39041033_3   1665 TAAGAGGATAAAAAGACAAGCTACAGACTGGGTGAAAATATTTATAAACT 1714
                         i    iii i         v i     v    v          ii   ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_39041033_3   1715 ACATATTCAGCTAAGGG-CTAGCATCTAGAATATATAAAGAACCCTCAAA 1763
                          i    - v v      -  v i   i                i  i v 
  L1M4_orf2#LINE/    734 ATATAT-CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_39041033_3   1764 ATTCAACAGTTAAAAAA----------AGTTAGAAAATGGGCAAAAAACA 1803
                          i    i i v    i ---------- i  ?i            ii iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_39041033_3   1804 TAAAGAGACATTTCACTAAAGAAGATA----GATGACAGATAAGCACATA 1849
                          i  v         v i          ----i   i vi          i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_39041033_3   1850 AAAAGATATTCAACA--ATGCATCTC 1873
                                ii      -- ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (60 / 35)
Gap_init rate = 0.03 (11 / 423), avg. gap size = 2.36 (26 / 11)  


 995 24.84 0.65 5.48  chr1_39153721_39156106.rev      653   962 (1424)    L1M4_orf2#LINE/L1        1   295 (613)  

  chr1_39153721_3    653 TGGAAACACATCCCATGTTCATGGATGGGTAGAAATCAATATTGTGAAAA 702
                               v i                 v  v   -v i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA-CTTAATATTGTTAAGA 49

  chr1_39153721_3    703 TGACCATACTGCCAAAAGCAATCTACAAATTCAACGCAATCCCCATCAAA 752
                           i v     v  v   vii       i               i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_39153721_3    753 ATACCA-CCACCATTCTTCACAGAATTAGAAAAAACAATTCTAAAAAAAA 801
                           v   - ii  -  i  ii     v v  v  ivii  i      ----
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAA---- 144

  chr1_39153721_3    802 AAATTATAAAATTTATATGGAACCAAAAAAGAGCTTGCATAGCCAAAGCA 851
                         -----------  i        viiv  ii  v iv v         i  
  L1M4_orf2#LINE/    145 -----------TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr1_39153721_3    852 AGGCTAAGCAAAAAGAACAAATCTGGAGGCATCACATTACCTGATTTTAA 901
                          vvi i iv  i         vi      vv     i v  ii    i  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_39153721_3    902 ACTATACTATAAGGCCATAGTCA-CAAAACAGCATAGTACTGATATAAAA 950
                          viv     i  i  i i   v -   i    ii i      ii    ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_39153721_3    951 ATAGGCACATAG 962
                             i  i    
  L1M4_orf2#LINE/    284 ATAGACATATAG 295

Transitions / transversions = 1.66 (48 / 29)
Gap_init rate = 0.02 (5 / 295), avg. gap size = 3.80 (19 / 5)  

2009 25.92 3.53 1.38  chr1_39153721_39156106.rev     1244  1895 (491)    L1M4_orf2#LINE/L1      243   908 (0)  

  chr1_39153721_3   1244 CAAAATAATAATAATAATAATAATAATAATAATAAAATAAATAAATAGGC 1293
                             iiv i i    v vi i i i- ii  v iiv    i--i    i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTG-TGGTACTGGCATAAG--GATAGAC 289

  chr1_39153721_3   1294 ACATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATATT 1343
                          i     i        i     v    ii               v i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_39153721_3   1344 TACACCCAACTGATCTTTGACAAAGCAAACAAAAACATAAAGTGAGGAAA 1393
                           iivi   i    i  i     i vviv   i v   vv i  i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_39153721_3   1394 GGACA-CCTTTTCAACAAATGGTGCCTGGACAATTGGCTAGCCATGTGTA 1442
                          i i -i                  iv      i   v  ?   ii  i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_39153721_3   1443 GGAGAATGAAACTGGATCCTCATCTCTCACCTTAAATAAAAATCAACTCA 1492
                         ii        ii    i  ii i   v    v  v i      i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_39153721_3   1493 AGATGGATTAAGGACTTAAATCTAAGACCTGAAACTATAAAAAGTCTAGA 1542
                          i      i ?i   i     v     v  i           vvii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_39153721_3   1543 AAATAACTTAG---------------ACATTGGCTTAGGCAAGAATTTCA 1577
                          i v   v   ---------------  v    v        vii    v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_39153721_3   1578 TGACGAAGAAGCCAAAAGCAAATGCAATAAAAACAAAGACAAATAGTTGG 1627
                          iivv v  vi         v v    i    iv   i i i   iv v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_39153721_3   1628 GACTTAATTAAACTAAAGAGATTTTGCATGGCAAAAGTAACAGCCAGCAG 1677
                              v  i   v v  i iv     iiivv    i vv  vii  iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_39153721_3   1678 AGTAAACAGACAACCCACAGAGTGAGAGAAAATCTTCACAA-TC-TATAT 1725
                            i  v              i  i        v  ii   -  -     
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_39153721_3   1726 CTGACAAAGGATTAATATCCAGAATCTATAACAAAAACAAACTCAAACAA 1775
                             i  i   i vi          v     -- i   ----  vv    
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAA--AGAAC----TCTTACAA 783

  chr1_39153721_3   1776 ATCAGTAAGAAAAAAA-----AATCCCATCAAAAAGTGGGCTAAGGACAT 1820
                         v   i   v     i -----  i  v  i?    i     v     iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_39153721_3   1821 GAATACACAATTCTCAAAAGAAGATATACAAATGACCAACAAACATATTT 1870
                              v   v     v                  i    i  i  i  vv
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_39153721_3   1871 AAAAAAGCTCAACATCACTAATGAT 1895
                            i v           ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (101 / 65)
Gap_init rate = 0.01 (9 / 666), avg. gap size = 3.56 (32 / 9)  


3586  8.44 0.71 30.21  chr1_39315629_39317874      500  1767 (479)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr1_39315629_3    500 ACGTTCATGCATTGGAAGACTTAATATTGTTAAGATGGCAGCACTCCCCA 549
                          i       v                              ii        
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_39315629_3    550 AACTGATCTATAGATTCAATGCAATCCCTGTCAGAATCCCAGTGGGGTTT 599
                           i       i        i         i   i        --------
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG-------- 106

  chr1_39315629_3    600 TTTCTTCTTCTTTCTTCTCCTCCTCCTCCTCTTCCTCTTATTCTTCGTCT 649
                         ------------------------------------------------  
  L1M4_orf2#LINE/    107 ------------------------------------------------CT 108

  chr1_39315629_3    650 TCCTCTTCCTCCTCCTCCTCTTCTTCCAGAAATTGGCAAGCTGCTCCTGA 699
                         v   i  ----------------  v         i       v    i 
  L1M4_orf2#LINE/    109 GCCTTTT----------------TTGCAGAAATTGACAAGCTGATCCTAA 142

  chr1_39315629_3    700 AATTCATGTGAAAATGCAAGGGACCCAGAATAGTCAAAACAATCTTGAAA 749
                                i  i                      i                
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_39315629_3    750 AAGAA---CAAAATTGGAGGACTCACACTTCCAGATTTGAAAACTTACTA 796
                              ---    i                   vi    v           
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_39315629_3    797 CAAAGCTACAGTAATTAAGACAGGATGGTACTGGCATAGGGATAGACATA 846
                                        i       vi             i           
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_39315629_3    847 TAGATCAATGGAATAGAATTGAGAGTCTAAAAATAAACCCTTACATTTAT 896
                                                    i i          v         
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_39315629_3    897 GGTAAATTGATTTGTGATAAAGGTGCCAAGACAATTCAATGTAGAAAGAA 946
                            v         vi  i  i           v        vi       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_39315629_3    947 TTGTCTTTTCAACAAATTATACTGGGACAACTGGATATCCATATACAAAA 996
                          v               vi i                ?   i  i     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_39315629_3    997 GAATGAAATTGGCCAGGCGTTGTGGCTCACGCCCATAATCCCAGCACTTT 1046
                                i    --------------------------------------
  L1M4_orf2#LINE/    443 GAATGAAGTTGG-------------------------------------- 454

  chr1_39315629_3   1047 AGCAGGCAGAGGTAGGTGGATCACGAGATCAGGAGTTCGAGACCAGCCTG 1096
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chr1_39315629_3   1097 GCCAACATTGTGAAACCCCATTTCTACTAAAAATACAAAAATTAGCTGGA 1146
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chr1_39315629_3   1147 TGTGGTGGCGGGCACCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGA 1196
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chr1_39315629_3   1197 GAATCGCTTGAACCCGGGAGGCAGAGGTTGCAGTGAGCTGAGATGACGCC 1246
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chr1_39315629_3   1247 ATTGCACTCCAGCCTGGGCAACAGAGCAAGACTCCACCTTAAAAAAAAAA 1296
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chr1_39315629_3   1297 AAAAAAAGAATTTAAACCCTGACCTCACACAACATATAAAACTTAACTCA 1346
                         ---------------    iv         v i   i    v        
  L1M4_orf2#LINE/    455 ---------------ACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_39315629_3   1347 AAGTGGAACATAGACCTACATATAAGAGCTAAAATTACAAAACTATTAGA 1396
                           i    v  ?       v  i            i  i      v     
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_39315629_3   1397 AGAAAACTTAGGGGTAAATCTTTGTGACCTTGGATTAGGTAGTGGTTTCT 1446
                                v    ?         i          i     i i        
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_39315629_3   1447 TGTAGCTAACACTGAAAGTATACACAAAAAAGAAAAAAATAGAGAAATTA 1496
                          iv vv i    ii    i i vi   v   ii          v     i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_39315629_3   1497 TACTTGATCAAAATGTAAAACCTTTGTGCTTCAAAGGACACTACCTAGAA 1546
                         v    v        vv     i                     i v    
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_39315629_3   1547 AATGAA--GACACCTCACAGAATGGGAGAAAATATTTGCAAATCATATAT 1594
                          i    --    v i                                   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_39315629_3   1595 CTAATAAGGGACTTATATCCAAAATATATAAAGAATTCTTTGAACTCAAC 1644
                           i           i      i             i    vv       i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_39315629_3   1645 AGTAAAAAGA-AAA---CCCAATAAAAAAATGGGCAAAGGATTTATATAG 1690
                          i        -   ---      v?                   iv    
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_39315629_3   1691 CCATTTCTTCAAAGAAGATATACAAATGGCTAATAAGCACATGAAAAGAT 1740
                         v       i                     i                   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_39315629_3   1741 GCTTAGATGCTTAACATCATTAGTTAT 1767
                            i --------      ????????
  L1M4_orf2#LINE/    890 GCTCA--------ACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (65 / 38)
Gap_init rate = 0.01 (8 / 894), avg. gap size = 49.00 (392 / 8)  


 351 34.41 6.07 1.62  chr1_39498531_39502606.rev     1625  1871 (2205)    L1M4_orf2#LINE/L1       74   331 (577)  

  chr1_39498531_3   1625 ATACATTTAGTGTGACCCACATAAAAAT----GCTAACTTCTCT--AGAA 1668
                          i v   i ii ii i  vi  v     ----   iv   i i --    
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAA 123

  chr1_39498531_3   1669 -CTAATGAAGGTGATTCCTAAATTCACATAGAAAAATAAATGTGCAACTA 1717
                         -i i i-   v    i iv       i  i    vii  iv vv v vv 
  L1M4_orf2#LINE/    124 ATTGAC-AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr1_39498531_3   1718 CACCTATGAAAAACTTTGAAAGAAAAAAATTGAG---GAGGACTAGCTCT 1764
                         i v i -i  v  ii      i i  i  ivi  ---       vi v  
  L1M4_orf2#LINE/    173 TAGCCA-AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_39498531_3   1765 CTACCACACATTAAAATATACCATAAAGCCTCTATAATTAAAATAGTATG 1814
                         - v   - iv i    iv   i i     iv vi    i  i i   i  
  L1M4_orf2#LINE/    222 -TCCCA-ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_39498531_3   1815 CT-CTGGTACATGAATGGAAACAC----CAGCAAAACAGAATAGAAAATC 1859
                         v -    i i v i  i  v i i----  iiii  i     v  i i  
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_39498531_3   1860 CAGAAATAGGCC 1871
                                 ii  
  L1M4_orf2#LINE/    320 CAGAAATAAACC 331

Transitions / transversions = 2.15 (58 / 27)
Gap_init rate = 0.04 (10 / 258), avg. gap size = 1.90 (19 / 10)  

 206 30.90 11.80 2.25  chr1_39498531_39502606.rev     2819  2996 (1080)    L1M4_orf2#LINE/L1      417   611 (297)  

  chr1_39498531_3   2819 GAACAACTAGATAGACATA-ACAGAAAAAGGTAACATGATTCATACTTCA 2867
                          i      i    ?v  i -i  i  i  v v iivv  ii v   i   
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_39498531_3   2868 ------------GAATAAGCTTAAATTGT-TAAAAGATTCAAATGTAAAA 2904
                         ------------i   v i  i   v  v- v ?   iii        i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_39498531_3   2905 A--AAAATTAAAACAAGTTTTAGAATAAAGCAT--GAATAAATTTTTTCA 2950
                         i--    i  v  -  v i      v   i   -- ?i     i  -- i
  L1M4_orf2#LINE/    517 GCTAAAACTATAA-AACTCTTAGAAGAAAACATAGGNGTAAATCTT--CG 563

  chr1_39498531_3   2951 TAACCT-GGGTGTGACAAAAATCTTTCAAACTATGAC--TAAAAATACA 2996
                          i    -    vv i   vii i i i i -      --i    ii   
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACA 611

Transitions / transversions = 2.25 (36 / 16)
Gap_init rate = 0.05 (10 / 195), avg. gap size = 2.50 (25 / 10)  


 427 18.18 7.07 0.00  chr1_39668212_39670673      264   362 (2100)    L1M4_orf2#LINE/L1      676   781 (127)  

  chr1_39668212_3    264 GACCCTGTCTAAAAAA--AAAAAAAAA-----AGAATGAGAGAAACTATT 306
                            v  i  v i   i--    i v  -----      i      v    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_39668212_3    307 TGCAAATTATACATCTGATAAGAGACCTGTATCTAAAATATTTAAAGAAT 356
                                i   i          i   i      i i     v       i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_39668212_3    357 TCTGAC 362
                            v  
  L1M4_orf2#LINE/    776 TCTTAC 781

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.02 (2 / 106), avg. gap size = 3.50 (7 / 2)  

3239 19.15 5.85 0.44  chr1_39668212_39670673      548  1231 (1231)    L1M4_orf2#LINE/L1        1   721 (187)  

  chr1_39668212_3    548 TGAAAAGATATCCTGTGTTCATGGATCAGAAGACTTAATATTGTTAAGAT 597
                           i          ii           ii                      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_39668212_3    598 GATGATACTCCT-AAATT---CTTCACATTCAGTGCAATCTGTATTAAAA 643
                          iii       i-     ---  v  v     ii      iv   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_39668212_3    644 TCCTAGCTGGCTTTTTTCATACGAGTTGATAAGCTTATCCCAAAATTCTT 693
                            i     v       -ii vi i    i     v    i       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_39668212_3    694 A-AGAAATGTAAGAGACTCAGGATAACCAAAACAATCTTGAAAG-GAAAA 741
                          -i      i   i   i   i   i                 i-   i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_39668212_3    742 ACAAAGTTGGAGGACTCGCATTTCCAGAATTAAAAATTTACTACAAAGCT 791
                                          i  i    vi v  v    i             
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_39668212_3    792 ATGGAATTTAAGACACAGTAGTAATGGCCTAATAACAGACATACAGATCA 841
                          ii v v i      vv  i   v    v   vi i       i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_39668212_3    842 ACAAAATATAATTTAGAATCCAGAAG-AAACCCTTACATTTATGGTCAAC 890
                          iii    v    v   i       i-      v               i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_39668212_3    891 T-ATATTCACCAAGGATACCAAGACAATTAAACAGGAAAAAAACTAGCCT 939
                          -  v   iv     i i       v   v  ii  i   i  -   i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCT 398

  chr1_39668212_3    940 TTTCAACAAATGGTGCTAGGACGACTGAAAATCCACATGTAAAAGAGTAA 989
                                          i    i    i v ?       i      i i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_39668212_3    990 CGCTGGACCACTTTCCTCACACTATACACAAAAATTAACTTCAAATGGAG 1039
                         v i      - i v        i   i             iv       v
  L1M4_orf2#LINE/    449 AGTTGGACC-CCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_39668212_3   1040 TAAAGACTTCAGTGTAAGAGAGAAAACCATAAAATACTTAATAGAAAGTG 1089
                         i ?    i v i        vv     i      iv    iv     iii
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_39668212_3   1090 TAGGAGTAAATCTTCATAATC--------------------------ACT 1113
                             ?          i i i -------------------------- iv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_39668212_3   1114 ACACCAAAAGTACAAGTGACAAAAAAA------GATAAATTAGACTTTAT 1157
                                   i     ii      i  ------        i     i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_39668212_3   1158 CAAAATTAAAATATTTTGTGCTTCAAACGACGCCATCAAAAAAGTGAAAA 1207
                                    vv              v   i i     i          
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_39668212_3   1208 GACAACCTATAGAATGAAAGAAAA 1231
                                i i      ii      
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAA 721

Transitions / transversions = 2.37 (90 / 38)
Gap_init rate = 0.02 (11 / 721), avg. gap size = 3.91 (43 / 11)  

 759 12.35 3.09 3.70  chr1_39668212_39670673     1808  1969 (493)    L1M4_orf2#LINE/L1      748   908 (0)  

  chr1_39668212_3   1808 GAACCTGTCTCAAAAAACAAAAAACA-AAAGAATTCTTAC---TCAACAA 1853
                          i  i   v  ------  i  v i -      i      ---    i  
  L1M4_orf2#LINE/    748 GGACTTGTATC------CAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_39668212_3   1854 TAGAAAGACAAATAATCCAATT-AAAAATTGGTAAAGGGTCTGAAGAGAC 1902
                           i            i      -      v  i     i i    v    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_39668212_3   1903 ATTTTTCCAAAGAAGATATAGAGAAGGCCAATAAACACATGAAAAGATGC 1952
                             i               v i v         i               
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_39668212_3   1953 TCAACATCATTAACTAG 1969
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.02 (4 / 161), avg. gap size = 2.75 (11 / 4)  


1057 31.95 0.78 0.52  chr1_40244889_40248970     2392  2776 (1306)    L1M4_orf2#LINE/L1        1   386 (522)  

  chr1_40244889_4   2392 TGGGAAAATATTCC-TGCTCATGAACTGGAAGAATCGACATCATTAAAAT 2440
                            i  i    i  -  i     i i       v ii i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_40244889_4   2441 GGCAATACTGCCCAAAGCAATCTACAAGTTCAATACTATTCCTATCAAAC 2490
                                  v      vii       ii     ii v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_40244889_4   2491 CACCAACATCATTTCTCACAGAA-TTGGAAAAAAACTTCTAAAATGCATG 2539
                         iv   i vv v   i ii     -   iv  ivviv i       v   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_40244889_4   2540 AGGAATCGAAAAAGAGCCAGAATCACCAGAGCAATCCTTAGCAAAAATAA 2589
                         v    vi v  ii  v       vi   i i     i v iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_40244889_4   2590 AAACGTCAGAGACATCTCATTAGACAACTTCGAA-CTTATGCTACAAGGC 2638
                         v  v  ii   ivv  v  i vvv   i   i  -    --      i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGC 248

  chr1_40244889_4   2639 TAGAGTAACCAAGATAGCATGGTATGGGTACAAATACAGTCACATAAACC 2688
                           v     i     i  ii     iv  i i  iv i  v  i   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_40244889_4   2689 AAGGAAACAGAATAGAGAACTCAAAAATTAAACCACACATGTACAACTAT 2738
                           v i  i     v    iii  i    v  v   i    v  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_40244889_4   2739 CTGATCTTGGACAAAATCGACAAAAATAAGCAATGAGG 2776
                         i    i  v     iivi v   i vi vv     i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

Transitions / transversions = 1.67 (77 / 46)
Gap_init rate = 0.01 (4 / 386), avg. gap size = 1.25 (5 / 4)  

2032 23.33 2.10 0.76  chr1_40244889_40248970     3067  3589 (493)    L1M4_orf2#LINE/L1      379   908 (0)  

  chr1_40244889_4   3067 CAATGGGGAAAAGACTCCCTATTTAATAAATGGTGTTGGGATAACTGGCT 3116
                                    ii ivvi  v  i  i        i     i      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_40244889_4   3117 ATCTGTATGCAGAAGAAGGAAATCGAACCCCTACCTATCACCATATATAA 3166
                          ? iii     i     v   i i i          vv         i  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_40244889_4   3167 AAATTAACTCAAGATGGATTAAGGACTTAAATGTAAAACCTAAAACTATA 3216
                                     i      i ?i   i         i v           
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_40244889_4   3217 AAAATCCTGGAAGAAAACCTAGG---AAATACCCTTCTTGATATTGGCCT 3263
                            v  i i         v    ---    ---    v   iv    vi 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTT 575

  chr1_40244889_4   3264 TGGCAAATAATTTAT-GGCTAAGTTCTCAAAAGCAATTGCAACAAGAGCA 3312
                         v     - ii   v -i v  v vivi        vvv       i  v 
  L1M4_orf2#LINE/    576 AGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_40244889_4   3313 AAAATTGACAAGTGGGACCTAATTCAACGAAAGAGCTTCTGCATAGCAAG 3362
                              v  i  i v    i v  iv  vvv  i i   i  iiivv   i
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_40244889_4   3363 AGAAACTATCAAAGGAGTAAACAGACAACCTACAGAATGGGAGAAAATAT 3412
                         i  v        iii   i  v        i                   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_40244889_4   3413 TCACAAACCATGAATTCAACAAAGGTCTACTATCTAAAATGTATAAGGAA 3462
                          ii    i   iv  iii i  i  v  vv    i i   i     i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_40244889_4   3463 CTT----AAATCAATAAGCAAAA-ACAAATAACTCCATTAAAAAGTAGGC 3507
                           i----  v       vv    -         i v   ?    i i   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_40244889_4   3508 AAAGGACATGAACAGAC--TTCTCAAAAAAAGACTTACAAATGGCCAATG 3555
                               iv    i    --     v   i    iv              i
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_40244889_4   3556 AACATATGAAAAAATGCTCATCATCACTAACCAT 3589
                          i  i       i       v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (73 / 46)
Gap_init rate = 0.01 (7 / 530), avg. gap size = 2.14 (15 / 7)  


3948 16.01 1.82 9.83  chr1_40249079_40251301      744  1730 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_40249079_4    744 TGAAAAGACATCCCATGTTCATGAATCCAAAGATTTAATATTAT-AAGAT 792
                           i     i              i  ivi    i        i -     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_40249079_4    793 GTCAATACTATCCAAAGAGATCAACAGATTGAATGCAATTCCTATCACAA 842
                          v       vi     vv    v       v  i     i       v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_40249079_4    843 TCCCAAG-GACTTTTTTGCATAAAT----AAA--------AAAACTCATA 879
                              iv- v          v    ----  i--------    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_40249079_4    880 TGGAATCTCAAAGGATCCTGGATAACCAAGACAATCCTGAAATGGAAGAA 929
                              viv   i   i  v i   i    i      i     vi      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_40249079_4    930 CAAAGCTGGAAGACTCACAGTTCCTGATTTCAAAACTGACTACAAAGCTA 979
                              i    i        v    ii           v            
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_40249079_4    980 CAGTAATTAAAACAGTGTAGTGGTACTGGCATAAAGATAGATATATGTAC 1029
                                i  i       ---             i      i    ----
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGT---GGTACTGGCATAAGGATAGACATAT---- 293

  chr1_40249079_4   1030 AACTATATATGTATATGTACATAAAATATGTACAACTATGATATTTCCAT 1079
                         --------------------------------------------------
  L1M4_orf2#LINE/    294 -------------------------------------------------- 293

  chr1_40249079_4   1080 AAATTTTATAATAATTTAGTTTTTTAAAAGATTGATATAGACCAATGGGA 1129
                         --------------------------------------   i      i 
  L1M4_orf2#LINE/    294 --------------------------------------AGATCAATGGAA 305

  chr1_40249079_4   1130 TAGCATAGCAAATCTAGAAATAAATCCTTGCATATATGTTCAAATAATTG 1179
                            v  v vi i  i         i  v i   v    v    v i   -
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT- 354

  chr1_40249079_4   1180 TTTTACAAAGGTGCCAAGACCATTCAATGGGGAAAAGACAGTCTTTTCAA 1229
                           iv    i                          ii i           
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_40249079_4   1230 CAAATAGTTTTAGGAAAACTAAATATTCACACACAAAAGAATGAAGTTGG 1279
                              i  vi i   v    ii   ?i    ii                 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_40249079_4   1280 ATCCTTATTTAACACTATATACAAAAATTAACTCAAAATGGATTTATGAC 1329
                          i  i  ii v    i                           iv?v   
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_40249079_4   1330 CTAAATGTAATA-CTTAAATTATAAAATTCTTAGAAGAAAACATAGGA-C 1377
                                   v -  v   i       i                   ?-i
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_40249079_4   1378 AAAACTTCACAACATTGGATTTGGCAATAATTTCTTGGATATGACACCAA 1427
                            v    iii  v    i  v      ii      i             
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_40249079_4   1428 AAACAAAAGCAACCAAATAAAATATAGACAAATTGGATTTCATGAAAATT 1477
                           i  v       v   v    v     i        i     v      
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_40249079_4   1478 AAAATATTTTGCACAGCAAATGACACTATTAACAGAGTAAAAAAGGCAAC 1527
                             vv     ii vv    v        i  v i   i    - i    
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GACAAC 703

  chr1_40249079_4   1528 TTACAGAATGGGAGACCTTTTTTGCAAATTATATATCTAGTAAGGGATTA 1577
                         ii             vvv v         i        ii       i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_40249079_4   1578 ATATTCAGAATATATAGAGAATCTCTAAAACTCAGCAA-AAGAAG-CAAA 1625
                         i   i           i    iiii  v      ii  -  i   -    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_40249079_4   1626 CAAAGCAATTCAAAAATGGGCAAAGGACTTGAATAGACATTTCTGTAAAG 1675
                         i  vv     ?                i                vi    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_40249079_4   1676 AAGATATACAAATGGCAGATAAGTAGATTAAAAGATGCTCAACATCACTA 1725
                                         vi     i v  v                  ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_40249079_4   1726 ATCCT 1730
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.66 (96 / 58)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 9.58 (115 / 12)  


2365 19.22 1.49 3.92  chr1_40271020_40273405      504  1039 (1347)    L1M4_orf2#LINE/L1      114   636 (272)  

  chr1_40271020_4    504 TTTTATAGAAAT-----ATCC-ATCCTAAAATTTATGTGAAATTTCAAGA 547
                             ii      ----- v i-           i  i  i  v v    i
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_40271020_4    548 GACCCTGAATGGTCAAAACAATCTTTAAAAAGAAAAACAAAGTTGTAGGT 597
                              v    i i            v        i          v   v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_40271020_4    598 TTTACATTTTCTGATTTTGAAACTTTTAATGAAGCCAGAGTCACTAAAAC 647
                         i i   i  i ii    ii      viv ii    i v   v ii  i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_40271020_4    648 AGTGTGCTCTTGGCATAAAGACAGACATATAGACCAATGGAGTAGAAAT- 696
                               v vi        i  i           i       i     v -
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_40271020_4    697 AGAGCCCAGAAATAAACCCTCCTATATATGATCAAATGACTTTTGGCAAG 746
                             i              vivi  v    i    v   i   i i    
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_40271020_4    747 GGTGCCAGGTATATTCAACTGGGAAAGGACAGTCTTTTCAAGAAATAGTT 796
                                i vvi      iv       i i           v    i  v
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_40271020_4    797 TTGGGAAAACTGGATATCCACATATAAATGAATAAAGTTAAAACCCTACC 846
                         i     v         ?      ii   v    i     ii v       
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_40271020_4    847 TTATACCATATACAGTAATTAATTCGAAGACCTAAAATAATTAGATCAAA 896
                          i i          iv      i  --------     i----     ? 
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTC--------AAAATG----GATCAWA 501

  chr1_40271020_4    897 GACCTCAA-ATAAGAGCTAAAACTATAAAACTTTTAAAAGAAAACATAAC 945
                              v  -i                      i   i           --
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA-- 549

  chr1_40271020_4    946 GTTGTTTATAACGATTGTTCATAACGTTGGATTTAGCAGTGATTTCTTGA 995
                          v?  ----  --  i-   i i  v    i  vi   i  i      ii
  L1M4_orf2#LINE/    550 GGNGT----AA--ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_40271020_4    996 ATATGACACCAAAAGCACAGGCAACAAAAGTGAAAATAGATAAA 1039
                                            i          vi            
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

Transitions / transversions = 2.12 (68 / 32)
Gap_init rate = 0.02 (10 / 523), avg. gap size = 2.90 (29 / 10)  

 704 16.33 10.20 0.00  chr1_40271020_40273405     1349  1495 (891)    L1M4_orf2#LINE/L1      666   827 (81)  

  chr1_40271020_4   1349 TGCTCTAAAGGACACAATCAGG---GTAAAAAGGCAACCCACAGAATGAG 1395
                             ii         v    i ---  i     i              i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_40271020_4   1396 AGAAAATAATTGCA-CTCCTATATCTGATAAGGGGTTAATATCCAGAATA 1444
                                 v     -v  v               ii vi           
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_40271020_4   1445 TACAGAGAGTTCTCACAGC-----------AAAACAAACAACCCAATTAA 1483
                           i i   ii   i   i -----------  i     i         ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_40271020_4   1484 AAATTGGGCAAA 1495
                            v        
  L1M4_orf2#LINE/    816 AAAATGGGCAAA 827

Transitions / transversions = 2.83 (17 / 6)
Gap_init rate = 0.02 (3 / 162), avg. gap size = 5.00 (15 / 3)  

 477 13.79 6.03 0.00  chr1_40271020_40273405     1778  1893 (493)    L1M4_orf2#LINE/L1      786   908 (0)  

  chr1_40271020_4   1778 CAAAAA-AAAAAAACAAAAAA---AAC--AAAAA-GGGCAAAGAGCTTGA 1820
                            v  -     i     v  ---  i--     -        iii    
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_40271020_4   1821 ATAGTTATTTCTCCAAAGAAGATATGCACATGGCCAAAAAGCACATGCAA 1870
                             vi                   i  v        v         v  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_40271020_4   1871 AGATGTTTGACATCACTAATCAT 1893
                              i ii      ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.03 (4 / 123), avg. gap size = 1.75 (7 / 4)  


 458 21.71 2.33 4.65  chr1_40314909_40316837.rev      496   624 (1305)    L1M4_orf2#LINE/L1      277   402 (506)  

  chr1_40314909_4    496 CATAAA---AGACACACAGAACAATGGAATCTAACAGAAAGCCAAGAAAT 542
                              i---     i i   v         vv  iv  i  i v      
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_40314909_4    543 AAATCCTTGTATATGTGGTCAAATGAAAATGATTTTCACCTAGGATGCCA 592
                            i  v ii  v i       - -----        iv v   i     
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAA-T-----TGATTTTCGACAAGGGTGCCA 370

  chr1_40314909_4    593 AGACCATTCAAAGGGAAAAAGACAGCATTTTC 624
                                    v   i   ii i  iv     
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

Transitions / transversions = 1.55 (17 / 11)
Gap_init rate = 0.02 (3 / 126), avg. gap size = 3.00 (9 / 3)  

2352 18.76 2.32 0.39  chr1_40314909_40316837.rev      922  1438 (491)    L1M4_orf2#LINE/L1      382   908 (0)  

  chr1_40314909_4    922 TGGCCAAAG-ACAGCCTTTTCATTCAACAATGTTAGGAAAACCAAATATT 970
                            vv    - i  i       viv  iii  i i   v   iii   ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_40314909_4    971 CACATACAATAGACTGAAGCTGGA-CCTTACCTTACACCATATACATAAA 1019
                              i   v   v     i    -  i     i            v   
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_40314909_4   1020 CCAACTTGAAATGGATCAAAGATCTAAACATATGAACTAAAATGATAAAA 1069
                         ii    ii          ?   i     ii  v  i      iv      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_40314909_4   1070 CT-TCAGGAGAAAACATAG--ATAAATAGCTTCATTACATTGGATTTGGC 1116
                           - i  i           --i     --    i v  v    i  v   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGC 579

  chr1_40314909_4   1117 AACTATTTTTTGACTATGATACCAAAAGCACAAGCAACACAA----AAAT 1162
                           ivi   i  iiv     i                   v  ----    
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_40314909_4   1163 ATATAAACTGGACTTCATCAAAATTAAAAACTTCTGTGCATCAAAGGACA 1212
                          v     i                         i     v          
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_40314909_4   1213 CTATCAAGAGAGTAAAAAGGAAACCCATAAAATGGGAGAAAATA-CAGCA 1261
                                  i   i     iv      i i              -iv   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_40314909_4   1262 AATCTTATATCTGTTGATGGATTAATATCTA-AACACATAAAGACCTCCT 1310
                             v        v i v   i vi    i -  i i       v   i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_40314909_4   1311 AAAACTCAACAACACAAA-ACAAACAAGCCAATTAAAAATTGGGCAGAAG 1359
                          v       i  i v   -     i  v      ?    v      i i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_40314909_4   1360 ACTTGAAAAGACATTTCTCCAAGGAAGACATACAAATGGCCAATAAGCAC 1409
                          i     v              i     i                     
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_40314909_4   1410 ATGAAAAGATATGAAACACCACTAATTAG 1438
                                   iivv    i  ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (62 / 32)
Gap_init rate = 0.02 (9 / 527), avg. gap size = 1.56 (14 / 9)  


 622 21.86 26.51 3.26  chr1_40463030_40465318.rev      695  1124 (1165)    L1M4_orf2#LINE/L1        1   530 (378)  

  chr1_40463030_4    695 TAGAGAGATCTACCATGTCCATGAATTGGAAGACTCAATATAGTAAAGA- 743
                          i  i    v v      i    i           i     v  v    -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_40463030_4    744 ----ATGCC-----AGTTGAACTACAGGTTTAACACAATTCCTATCAAAA 784
                         ----  i i----- i    v      i  i   i    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_40463030_4    785 ATCAAGACAAGATTTTTTTTGTAAACACAGACAAGGTTTTTCTAAAATTT 834
                         vi v  vii---ii       i i v iv      v vv i        i
  L1M4_orf2#LINE/    101 TCCCAGCTG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_40463030_4    835 ATATAGGAAGGCAAAAAGGAACTAGAATATCTAAAAC---C----AAAAG 877
                             i i  v    i--   v i      v i     --- ----     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_40463030_4    878 AATAAACAAAA---AAGAAT-----------AATT--AAAA--------A 903
                           -i      i---i  i i-----------    --    -------- 
  L1M4_orf2#LINE/    196 AA-GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_40463030_4    904 AAG----AATA-TCTAAAGCCAGT-------TGGAA-AATGATAAA---- 936
                            ---- i  -  --   v    -------   v -  v    i ----
  L1M4_orf2#LINE/    245 AAGCTACAGTAATC--AAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_40463030_4    937 -------GTGGGA--------GGAATC---------ACC--TACCTTGA- 959
                         -------i   i --------i  i  ---------   --   v  v -
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_40463030_4    960 GATCCATCTA----CCACTAGGAT-------CCATTTAAACTG----AAA 994
                          i  v  iv ---- v  v   i -------     i  --  ----  i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAG 390

  chr1_40463030_4    995 AATAATTT--------AGTGAT--TGAAGGATAATTGGATATCCATAGGC 1034
                             i i -------- i  i --  --   i  i      ?   i v  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTG--GGACAACTGGATAKCCACATGC 438

  chr1_40463030_4   1035 AAAAAAATGAACCATGG-CATAAACCTCATATTTTATACAAAATTTACCT 1083
                             i      vi-   - vivv      i iiv         v   v  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_40463030_4   1084 CAAAA-GGATCATA-ATTCAAATGTAA-AGCGTAAAACTATAAA 1124
                              -      ? - iii        -   -            
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAA 530

Transitions / transversions = 1.79 (59 / 33)
Gap_init rate = 0.06 (34 / 530), avg. gap size = 3.76 (128 / 34)  

1113 20.94 10.19 2.48  chr1_40463030_40465318.rev     1436  1798 (491)    L1M4_orf2#LINE/L1      518   908 (0)  

  chr1_40463030_4   1436 CTAAAACTATAAA-TTATTA-----AGACA---GAGAACATCTGCTGGAC 1476
                                      -i v   ----- i   --- ? v v    v vv   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_40463030_4   1477 GTAGGGCTCAGCAA--GTT-CTTAGACATGATACCAAAACCA-AAATATG 1522
                         v v   i vi    --   -      i    i       v  -  ii -i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA-A 616

  chr1_40463030_4   1523 TAAAAGAAAAAAATCAATACATTGAACTTCATCAAGATTAAAATCTTTTG 1572
                         i           - vi   v    i          i       v      
  L1M4_orf2#LINE/    617 CAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_40463030_4   1573 CTTTGC--CAAAGGCCTGATT-TTAAAAGTATAAAAAGCCAAGTTACAGA 1619
                         ---   --      v -- i - i  i ivi i     v   vii     
  L1M4_orf2#LINE/    666 ---TGCTTCAAAGGAC--ACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_40463030_4   1620 ATAGGAGAAAATACTTGCAAACTATACGTCTAACAAAGGACTCATATCTA 1669
                           i          i       ii   ii   i i  i     ii    i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_40463030_4   1670 GAATATATAAAGAAGTC---------------------GCAAATGCATCC 1698
                                       v  ---------------------i     i- i  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA-ACCC 809

  chr1_40463030_4   1699 AATTAGAAAATAGGCAAAAGACATAAACAGACATTTCAAACAAAGAGGAT 1748
                             ?i     i      i  iv i  i         vv-      i   
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC-CAAAGAAGAT 858

  chr1_40463030_4   1749 ATACAGATGGGAAATAAGCACTTGTAAAGATGTTTAGTATTAATAGCCAT 1798
                              i    vv         v  v       i i ii  i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (49 / 25)
Gap_init rate = 0.04 (15 / 391), avg. gap size = 3.07 (46 / 15)  


3274 26.98 0.44 0.44  chr1_40499888_40505382     4095  5002 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_40499888_4   4095 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4144
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_40499888_4   4145 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4194
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_40499888_4   4195 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4242
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_40499888_4   4243 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 4292
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_40499888_4   4293 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTTTACTACAAGGC 4342
                                i      vv       v  ii i      vi         i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_40499888_4   4343 TACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4392
                             i   i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_40499888_4   4393 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 4440
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_40499888_4   4441 GTCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 4490
                         ivi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_40499888_4   4491 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4540
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_40499888_4   4541 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4590
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_40499888_4   4591 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4640
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_40499888_4   4641 CTAGGCATTACCATTCAGAACATAGGCATGGGCAAGGACTTCATGTCCAA 4690
                         v    ?i v viv   ivi  v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_40499888_4   4691 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 4740
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_40499888_4   4741 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4790
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_40499888_4   4791 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4840
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_40499888_4   4841 AGGGCTAATATCCAGAATCTACAATGAACTCAACCAAATTTACAAGAAAA 4890
                         i  i  vi          v  i  v      vvv   v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_40499888_4   4891 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 4940
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_40499888_4   4941 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 4990
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_40499888_4   4991 ATCACTGGCCAT 5002
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1869 17.82 1.67 26.06  chr1_40658943_40661326      691  1891 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_40658943_4    691 TGGAAAGACATTACATGCTCGTGGGTCAGAA---TTAATATTGT-AAAAT 736
                                 i  iv    i  i   i ii   ---          -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_40658943_4    737 GACCATACTACCTAAGGCAATCTACAGATTCAGTGCAATCCCTATCAGAA 786
                          i v     v  i  ivii             ii             i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_40658943_4    787 TATCAATGACATCCTTCACAGAAATAGAAAAA-TG-TCTTAAAATTTGTA 834
                          vi  iivi v ii  ii       v  v  i-  -  i       ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_40658943_4    835 GGGAGCCACACAAGACCCCAAATAGCCAAAGCAATCCTGAGCAGAAAGAA 884
                         v   ivii  vii     vi          i     i   iv ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_40658943_4    885 CAAAGCCAGAAGAATCACACTACCTAACTTCACAATATAGTACAAAGCTG 934
                              iii  i  v       v  i  i    v  iv  v         i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_40658943_4    935 TAGTAACCAAAACAGCCTTGTACTGGCATAAAAACAGACACATAAATCAA 984
                         i     i   i    iv v            ii i     i   i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_40658943_4    985 TGCAACAGAATAGAGAAACCAGGAATTAATC-ACATATCTACAGCCAACT 1033
                           v  i     v    iv    i   v  i - i i  i  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_40658943_4   1034 AATTTTTGGCAAATGTGCCAAGAACACTTTTTGGGGACAGAGCAGTCTCT 1083
                         i     i i   iv         v  i ivv      v   ii     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_40658943_4   1084 TCAACAAATGCTGCTGAGAAAAT--GATATCAATATGTCGAAGAATGAAA 1131
                                   v     i  v  i--    ? v i   ivi         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_40658943_4   1132 CTAGACTCTCATCTTTCACCCTATAAAAAAATCAACTCAAGGCCAGGCGC 1181
                         i i   ------------     i--------------------------
  L1M4_orf2#LINE/    451 TTGGAC------------CCCTAC-------------------------- 462

  chr1_40658943_4   1182 GGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCAGAGGTGGGCAGA 1231
                         -----     ----------------------------------------
  L1M4_orf2#LINE/    463 -----CTCAC---------------------------------------- 467

  chr1_40658943_4   1232 TCACGAGGTCAGGAGACTGAGACCATCCTGGCTAACACGGTGAAACCCCA 1281
                         ---------------------     ------------------------
  L1M4_orf2#LINE/    468 ---------------------ACCAT------------------------ 472

  chr1_40658943_4   1282 TCTCTACTAAAAATACAAAAAATTAGCTGGGCATGGTGGCTGGCGCCTGT 1331
                         ------------         -----------------------------
  L1M4_orf2#LINE/    473 ------------ATACAAAAA----------------------------- 481

  chr1_40658943_4   1332 AGTCTCAGCTACTCGGGAGGCTGTTTGGCAGGAAAATGGCATGAACCCAG 1381
                         --------------------------------------------------
  L1M4_orf2#LINE/    482 -------------------------------------------------- 481

  chr1_40658943_4   1382 GAGGCGGAGCTTGCAGTGAGCCGAGATCACACCACTGCACTCCAGCCTGG 1431
                         --------------------------------------------------
  L1M4_orf2#LINE/    482 -------------------------------------------------- 481

  chr1_40658943_4   1432 GCAACAGAGCCAGACTCCGTCTCAAAAAAAAAAAAAAAAAAATCAACTCA 1481
                         ------------------------------------------ i      
  L1M4_orf2#LINE/    482 ------------------------------------------TTAACTCA 489

  chr1_40658943_4   1482 AAATGGATTAAAGACCTAAATATAAGACCTGAAACTATAAAACTACTAGA 1531
                                 i ?          i     v  i             vi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_40658943_4   1532 ATAAAACATAGAGG-AAATGTTTCAGACTATTGGTCTAGGGAAATATTTT 1580
                          v         i? -    v  ivv   i-    vi    v  vvi   i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTC 588

  chr1_40658943_4   1581 ATGAATAAGACCTCAGAAGCACAGACAACAAAAGCAAAAAATAAACAAAT 1630
                         v ii   v   vi  i       ii         -        i i    
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAAT 637

  chr1_40658943_4   1631 GGTATTATACCAAACTAAAAAGCTTCCGTGCAGCAAAGGGAAC----AAC 1676
                         v v i vi i    v v    i   ii    vv      iv  ----  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_40658943_4   1677 AGAACGAAAAGACAACCTGCAGAATGGGATAAAATATTTGCAAACCATTC 1726
                          i ii            ii          v              i   vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_40658943_4   1727 ATTCAACAAGGAATTCATATCCAGAATATACAAGGAACTCAAATGTCTCA 1776
                           iii i    i i ii             i  i      vv iiv    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_40658943_4   1777 ACAGCAAAAAAATGAACAATGCAATT-AAAAGTGGGAAAATGATCTG--- 1822
                          i ii     i ii  i  iv     -    i    v   v   i  ---
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_40658943_4   1823 -GACATTTCTCAAAAGAAGACATACAAATGGCCAAAAAATATATGAAAA- 1870
                         -          v        i              v  ii i       -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_40658943_4   1871 ATGTTCAACATCACTTAATCA 1891
                            i         ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.20 (145 / 66)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 18.50 (333 / 18)  


 563 26.06 16.97 4.70  chr1_41219458_41222837     2228  2887 (493)    L1M4_orf2#LINE/L1      168   908 (0)  

  chr1_41219458_4   2228 CAGAA--ACCATAACAATAACTAAGAAAACAACAGAATGTGAGAGCTGAG 2275
                              --i   v      --  vii    v  --   i--- i  i  ii
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAAT--CTTGAAAAAGAA--GAAC---AAAGTTGGA 210

  chr1_41219458_4   2276 GGAATTAGCCTTAGCAGACATTAAAA-----TACAAAGCTTCTATTATGA 2320
                            v i vv   vv  - iv i    -----         v vi v  v 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_41219458_4   2321 AAAC--TGTGGTACTGGTACACCAATGGACAGGCACACCAATGGAATAGA 2368
                          i  --           i i vvi  i    vii v i            
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_41219458_4   2369 AA-AACAGACCC-AACTATACACATAAATCT--GG------GATAT--GA 2406
                          v-i v  v  v-  v  v  v    v  i --  ------   v --  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_41219458_4   2407 TAAAAG---CAGTATC--TCAAATTACTAGGGCAAAGATGAAGACATT-- 2449
                         i  ii ---  iv i --    ----- i   v  ii  --  v v  --
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAA-----TGGGGAAAGAAT--AGTCTTTTC 402

  chr1_41219458_4   2450 AATAAATGATAGTGGAACAA-TGGATGGCCAC-TGGAAAAACACAAA-TT 2496
                           i     i iv   i    -     i?    -  v    iv ii  -  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_41219458_4   2497 AGATCTATTTCTCACACCAAATACAAGAATAAATTCCAAATGGATCAGAG 2546
                         i  i iv vi         v      i   v  i  v          ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_41219458_4   2547 ATGTAACAATAAAAAAGA-AAAACAATATATAAGTACTAGAGGAAAATAT 2595
                          iv   --  iv  i  v-     --    v  v vi    i     i  
  L1M4_orf2#LINE/    503 ACCTAA--ATGTAAGAGCTAAAAC--TATAAAACTCTTAGAAGAAAACAT 548

  chr1_41219458_4   2596 AGGTG--AATT-------CCT--------ATAATG--------------- 2613
                            ? --   i-------   --------ii    ---------------
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_41219458_4   2614 -------------------------AAAGGTTAATAAATTTAACT--AT- 2635
                         -------------------------   ii vi       vi   --  -
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_41219458_4   2636 AAAATTAAAA-CTTTTG-----CATGAGAAACAAATGAAAAACTACCATA 2679
                                   -      -----  vii  v  v vii i   v i-- v 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG--AAA 696

  chr1_41219458_4   2680 AG-CAAAGTACAAATTGGGAGAAAATATTTACGA--TATATGTTACAATA 2726
                           -   vvi   i v               i i --i    i i-ii   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC-TGATA 745

  chr1_41219458_4   2727 AAAGGG---TGTATCTA--ACATACAAAGGACTTTTAAAATTGAGAGGAA 2771
                          --   ---      i -- i   i    i   i   v  i v iviiv 
  L1M4_orf2#LINE/    746 A--GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_41219458_4   2772 AAAAGACCTATAATCACACGGGTAAATGAGCAAAAGA----AAT-GACAA 2816
                                vv    i vv iv?iv     i     i  ----   -    v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_41219458_4   2817 CCTGTAAAAGAAAAAAAAAAGATA-AAATGGCACCCTAGACATATGAAAA 2865
                         iiiviv      i ------v   -       - vv  ii  i       
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGA------TATACAAATGGC-CAATAAGCACATGAAAA 886

  chr1_41219458_4   2866 GATGTTAAACTTCACTCATAAA 2887
                             i v   v   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (95 / 73)
Gap_init rate = 0.06 (43 / 741), avg. gap size = 3.33 (143 / 43)  


 312 17.05 5.68 4.55  chr1_41279117_41282753.rev      753   840 (2797)    L1M4_orf2#LINE/L1      820   908 (0)  

  chr1_41279117_4    753 TGGGTCGAAAGATTTAGAACAAACA-----CCAAGGAAAATGTATACAGG 797
                             - i  i     -   i i   -----    i   i  i  i v v 
  L1M4_orf2#LINE/    820 TGGG-CAAAGGATTT-GAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_41279117_4    798 GCAAATAAGTACATGAATAGAGATGCTCAATACCATTATTTCA 840
                           v      i       --i          i i  ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAA--AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.04 (4 / 89), avg. gap size = 2.25 (9 / 4)  

 401 22.86 3.81 1.90  chr1_41279117_41282753.rev     1091  1195 (2442)    L1M4_orf2#LINE/L1      623   729 (179)  

  chr1_41279117_4   1091 AAAAAATAGAG----TGGACTTTGTCAAAATTAAGAACTTCTGCTCTTCA 1136
                                   v----       ii          i     i  iv     
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_41279117_4   1137 AAAGATACTGGTAAGAGAACAAAAATACAGGTCACAGACTATGAGAGAAT 1186
                           i  i   ivi    i iii    v   ivi      v iv    i   
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_41279117_4   1187 AGTTTTGCA 1195
                          --      
  L1M4_orf2#LINE/    723 A--TTTGCA 729

Transitions / transversions = 2.43 (17 / 7)
Gap_init rate = 0.02 (2 / 107), avg. gap size = 3.00 (6 / 2)  

4334 15.49 5.49 0.49  chr1_41279117_41282753.rev     2334  3153 (484)    L1M4_orf2#LINE/L1       48   908 (0)  

  chr1_41279117_4   2334 GACAGCATTATTTTCCAAATTGATCTGTAGATTCAACACAATCTCTGTCA 2383
                           ii   v  i ii            ii         i     i  i   
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_41279117_4   2384 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAATTCATTCTAAAATTC 2433
                                                           ii v  i         
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_41279117_4   2434 TTA--------CAAGAGACCCAGAATAGCCATAGCAATCTTGAAAAGAGA 2475
                         v  --------    i               v i            iii 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_41279117_4   2476 GAACAAAGCTGAAGGATTCACATTTCCTGATTTCAAAACTTACTACAAAG 2525
                                 i  i    i     i    ii                     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_41279117_4   2526 CTACAGTACTTAAGACATAATGGTTCTGGCAGGAAAATAGACATATAGAT 2575
                                 v i      vvi    v      vi ii              
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_41279117_4   2576 CCATGAATTAAAATTGAGAGTACAGAAATTGACCCATCAATTTATGATCG 2625
                          v   i v  i          v       vi      vv       i  i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_41279117_4   2626 ATCGATTTTTGACAAGGGTACCAAGACAGTTCAGTGGG-----------T 2664
                           i      i         i       vi    i    -----------i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_41279117_4   2665 TTTTCAACAACTGGTGCAGGTACAGCTGGTTATCCACATAAAAAAAAGTG 2714
                                   v      v  v   i    v  ?      iv    i i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_41279117_4   2715 AAGTTGGACTC-TACCTCTATGCCATATACAAAAATTAACTTCAAGTGGA 2763
                                  i -      - ii                   iv  i    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTC-ACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_41279117_4   2764 TCATGGACCTAAATGTAAGAGTTAAAACTGCAAAACTCTTTAAAGAAAAC 2813
                            ?i                i       ii         vi        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_41279117_4   2814 ATAGAAGGAAATCTTCATGACCTTGGATTAGATA--------TTA----T 2851
                             i? v        i         i    ii --------   ---- 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_41279117_4   2852 AACACCAAAAACATAAACAACAAAAGAAAAAATAGATAATTTAAACTTCA 2901
                         i         i  i  i                      v  ii      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_41279117_4   2902 TCAAAATTAAAAGATTTT-TGTTTCCA----CACCATCAGGAAAGTGAAA 2946
                                     iv    -  i   v ----   i    i          
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_41279117_4   2947 AGAACAACCCACACAATGGGAGAAAATATTTGAGAATTATATATCTGGTA 2996
                            -         v                  vi   i         i  
  L1M4_orf2#LINE/    697 AGA-CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_41279117_4   2997 AAGGACTTGTATCCAGAATATAGAAAGAACTCTTAAAACTCGGAAATTAA 3046
                          i                    v            v     iiv   v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_41279117_4   3047 AAGACAA----CATGATTTTAAAATGGACAAAGAATTTGAATAGATATTT 3092
                                ---- vii   ?v       i     i           i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_41279117_4   3093 CTCCAAATA---TATACAAATGACCAGTTAGGCACATTAAA-GATACTCA 3138
                                v ---          i   i - i      v   -   i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAAT-AAGCACATGAAAAGATGCTCA 894

  chr1_41279117_4   3139 GTAGTCATTAGAGAA 3153
                         ii -   ????????
  L1M4_orf2#LINE/    895 ACA-TCAZZZZZZZZ 908

Transitions / transversions = 2.32 (86 / 37)
Gap_init rate = 0.02 (14 / 861), avg. gap size = 3.50 (49 / 14)  


3086 27.86 0.55 0.55  chr1_41310530_41316875     4946  5853 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_41310530_4   4946 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4995
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_41310530_4   4996 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCAACAAGC 5045
                            v     v     iv i  i  i        i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_41310530_4   5046 TACCAATGACTTTCTCCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5093
                          v   iivi i  i iii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_41310530_4   5094 CATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5143
                         i      viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_41310530_4   5144 AACAAAGCTAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5193
                                i i    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_41310530_4   5194 TACAGTAACCAAAACAGCATGGTAGTGATACCAAAACAGAGGTATAGACC 5243
                                 i   i    ii     v  ii iv ii i   vi      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_41310530_4   5244 AATGGAACAGAAT--AGAGCCCTCAGAAATAACGCCGCATATCTACAACC 5291
                                i     --    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_41310530_4   5292 ATCTGATCTTTGGCAAATCTGACAAAAATAAGAAATGGGGAAACGATTCC 5341
                          vi    i  i i   ivv  v   i vi vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_41310530_4   5342 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5391
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_41310530_4   5392 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5441
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_41310530_4   5442 TTAAAGACTTAAATGTTAGACCTAAACCCATAAAAACCCTAGAAGAAAAC 5491
                          i ?    i       v   v     v i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_41310530_4   5492 CTAGGCA-ATACCATTCGGGACACAGGCATGGGCTAGGACTTCATGTCTA 5540
                         v    ?i- v i -    v   viv  vv i   v v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_41310530_4   5541 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5590
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_41310530_4   5591 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5640
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_41310530_4   5641 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTCACA 5690
                         v  i     i                 v       vii ivi    v i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_41310530_4   5691 AAGGGTTAGTATCCAGAATCAACAATGAACTCAAACAAATTTACAAGAAA 5740
                          i  ii v           vv i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_41310530_4   5741 AAAACACACAACCCCATCAAAAAGTGGGCCAAGGATATGAACAGACACTT 5790
                           i   v i     v  i?    i     v      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_41310530_4   5791 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAGAAATGCTCAT 5840
                            v        i  vi viii     i ii        i i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_41310530_4   5841 CATCACTGGCCAT 5853
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


4013 17.75 4.61 2.58  chr1_41329571_41332223     1271  2160 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_41329571_4   1271 TGAAAAGATACTCTGTTCTGTGTTCATGGACTGAAAGACT-AATATTGTT 1319
                           i       ----- i ii          i  i      -         
  L1M4_orf2#LINE/      1 TGGAAAGATA-----TCCCATGTTCATGGATTGGAAGACTTAATATTGTT 45

  chr1_41329571_4   1320 AAGATGGCAATACTATCCAAAGCAATCTACAGATTCAACGCAATCCCTAT 1369
                                       vi     vii                          
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_41329571_4   1370 CAAAATCCAAACGGCATTTTT-GCACAAATAGAAAAAGTTG-TCCTAAAA 1417
                                 v i v  v     -   v    v  v  - i  -        
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAA 144

  chr1_41329571_4   1418 TTCACAAAGAATCTTAAAGGATTCCAAATAGCTCAAACAATCTTGAAAAA 1467
                             i vi   vivi  i   ii vi      iv                
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_41329571_4   1468 -AAGAACAAAGTTAGAAAACTTACACTTTCTAATTCCAGAATGTACTACA 1516
                         -            i  ii   i      i i    i  i  iv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_41329571_4   1517 AAGCTACAGTAATCAAAATAGTACAGTATTGGCATAAGGATAGATAAGCA 1566
                                         i i   iii   i               i vii 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_41329571_4   1567 GACCAATGTAATAGAACAGAGAGCTCAAAAATAG---------------- 1600
                           i     v       iv     ii  i     i----------------
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_41329571_4   1601 ----TTAATTTTCAATAAAAGTCCCAAGACCATTTAATGGGAAAAGGACA 1646
                         ----  i      i i  ii  v           i      i    i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_41329571_4   1647 --CTCTTCAACAAACAGGTCTGGGAAAACTGAATATCCAGATGCAGGAGA 1694
                         --  i         ii vv      v     i   ?   v     ii   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_41329571_4   1695 ATGAAGTTGAATACTTACCTTATACCATATACAAAAAAATTAACTCAAAA 1744
                                  i iv i     i i              --           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAA 492

  chr1_41329571_4   1745 TTTATCAATGACCTAAATAAATGTAAGAGCTAAAACTATAAAACTCTTAG 1794
                          vv    ?v         ----                            
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAAT----GTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_41329571_4   1795 AAGAAAACATAGGGGAAAATCTTTAACATTTTAGATTTGGCAATGACT-A 1843
                                      ? v       iivv ii  i i  v       ii -v
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_41329571_4   1844 TAGGATATGACAGATAAAACACAGGCAACAAAACAGAAAACAGATAAACT 1893
                          vi         vvv   i    i         v i    i       i 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_41329571_4   1894 GGACTTCACCAAAATGAAAAACTGTTGTGCATCAAAAGATCCTATCATCA 1943
                                 i      v       v      v     i  iv      vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_41329571_4   1944 GAGTGAAAAGACAGTCCACAGAATCGGAGACAATACTTGCAAATCATGTT 1993
                         i            ii         v     v    i           i v
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_41329571_4   1994 TGTAGTCTG----TCGATATCCAAAATATACACGGAACCCCTATAATTCA 2039
                          v ii vv ---- i -      i      i vi    i i  i  i   
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_41329571_4   2040 ACAACAAGAAGAACTAAAAACCTAAACAACCCAATTCAAAAATGGGCAAA 2089
                          i  i  i    ----------i   i         ?             
  L1M4_orf2#LINE/    788 ATAATAAAAAGA----------CAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_41329571_4   2090 ----------AGACAATTCTCCAAAGAAGATATACAGATGGCCAATAACC 2129
                         ----------     v                    i           v 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_41329571_4   2130 ACATGAAAAGATGCTCAGCATCAATAATCAC 2160
                                          i     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (103 / 51)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.27 (64 / 15)  


3134 26.04 2.82 0.45  chr1_41385915_41391765.rev     4475  5361 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_41385915_4   4475 TGGAAAAACATTCCATGCTTATGGATAGGAAGAATCAGTATCATTAAAAT 4524
                               i i  i     i i      v      v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_41385915_4   4525 GGCTATATTGCCCAAAGCAACTTACAGATTTAGTGCCATTCCTATCAAAC 4574
                            v   i v      vii ii        i ii  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_41385915_4   4575 TACTGACAACATTCTTCACAGAACTAGAAAAAAAATATTTTAAAATTTAT 4624
                          v iii vi v  i  ii     v v  v  ivvi-  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chr1_41385915_4   4625 ATGGAACCAAAAAAGAACCCAAATAGCCAAGGCAATCCTAAGCAAAAAGA 4674
                               viiv  ii  v  vi         ii     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_41385915_4   4675 ACAAAGCTGGAGGAATCACATTACTCAACTTCAAACTATACTACAAGGCT 4724
                               i       v     i v i   i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_41385915_4   4725 ACAGTGGCCAAAACAGCATGGTACTGATACAAAAACAGGCACATAGCCCA 4774
                              iii   i    ii        ii i  ii i  i  i    vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_41385915_4   4775 ATGGAACAGAACAGAGATCCCAGAAATGAGGCTGCACATCTACAACCATC 4824
                               i    iv    vi        i iv iii    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_41385915_4   4825 TGATCTTCGACAAAGCTGACAAAAGCA----ATGGGGAAAAGACTCCCTA 4870
                             i        i v  v   i v  ----         ii ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_41385915_4   4871 TTCAATAAATGGTGCTGGGACAACTAGCTAGCCATATGCAGAAGATTGAA 4920
                              i                   i v  ?   i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_41385915_4   4921 GCTGGACCCCTTCCTCACACCATATATGAAAATCAACTCAAGATGAACTA 4970
                          i         v              ii     i       i   i ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_41385915_4   4971 AAGACATAAATGTAAAATTCAAAACTAGAAAAACCCTAGAAGACAACCTA 5020
                         ?    v         i vii       v    vi i       v   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_41385915_4   5021 GACA-ATACCATCCTGGATGTAGGAACAGGCAAAGATTTCACAACAAAGA 5069
                          i?i- v i v  v  - iv v  ivi      v i    vi ivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_41385915_4   5070 CATTGAAAGCAATTGCAACAAAAGCAAAAATGGACAAATGGAACCTAATT 5119
                           iii      vvv          v      i  i    v i  i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_41385915_4   5120 AAACATAAGAGCTTCTGCACAGCAAAAGAAACTATCGACA---------G 5160
                            vv   i i   i  ii vv    i  v      i v --------- 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_41385915_4   5161 ACAACCTAAAGAATGAGAGAAAATATTTGCAAACTATGCTTCTGACAAAG 5210
                               i v      i                 ii  iiv     i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_41385915_4   5211 GTCTAATATCCAGCATGTATAAAGAACT--TA-AATTTA----TAAAA-G 5252
                          v  vi       v  i           --  -  i i ----     - 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_41385915_4   5253 AAAAACAACCCCATTAAAAAGTGGGTAAAAGACATGAACAGACACTTCTC 5302
                          v   i     v   ?    i    i   i  iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_41385915_4   5303 AAAAGAAGAAATA---ATGCAGCCAACAAGCATATGAAAACAAGCTCAAT 5349
                         v        v   ---   --     i     i       v v      i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_41385915_4   5350 ATCGCTGATCAT 5361
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (148 / 79)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.64 (29 / 11)  


3868 14.87 1.97 1.71  chr1_41690642_41692388.rev      497  1256 (491)    L1M4_orf2#LINE/L1      147   908 (0)  

  chr1_41690642_4    497 CAGATGAAGA-GCAAGGGACCTTGAACCACCAAAACAATCTTGCAAGAGG 545
                           v   i i -          iv   ivi              v  i  i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_41690642_4    546 A---CAATGTTGCAGCTCTCACACTTCCTGATTTCAAAACTTACTACAAA 592
                          ---   v    v  vv           ii                    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_41690642_4    593 AATACAGTAATTGAAACAGTGTGGTACTGACACAAG-ACAGAAATATAGT 641
                         iv         ii i              i  i   - i   v      v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_41690642_4    642 TCAGTGGAATACAACAGAGAGCCCAGAAATAAACCC-TAGCAAATATGGT 690
                            i       v  iv     i              -  -  vv      
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGT 345

  chr1_41690642_4    691 CAAATGATTTTCAGCAAGGTTGCCAAGGCTATTCAATGGGGAAAGAA-AG 739
                            v        ii     v       i i                 -  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_41690642_4    740 TCTTTCCAAGGAATGATGCAAAAGCA---GAATATCCACATGCAAAAGG- 785
                              i   vi    i   viiii  --- i   ?             i-
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_41690642_4    786 TGAAGTTGGACTCATACCTTACACCATATACAGAAATGAACTCAAAATGG 835
                                    i v     i            i    v            
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_41690642_4    836 ATCAAAGACCTAAAGGTGAGAGCTAAAACTATAATAAAACTCTTAGGAGA 885
                             ?         v  i                ---         i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA---AACTCTTAGAAGA 542

  chr1_41690642_4    886 AAACATAAGGGAAGAACTTCATGAAATTGGATTTGGCAATGATTTCTTGG 935
                                i ? v i v    i   vv    i  v       i      i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_41690642_4    936 ATACAACACCAA--GCATAGGCAACAAAAGAAAAAATAGATAAGTTTGGA 983
                            ii       --   i i                       i  -   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT-GGA 641

  chr1_41690642_4    984 CTTCATCAAAATTTAAAACTTTTATTCATTAAAGGACACTATCAACAGAA 1033
                                      v         i v v i               v i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_41690642_4   1034 TGAAAAGGCAACCCTGGGAATGGGAGAAAATATTTGCAAATCATATATTT 1083
                                i      vvi                               i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_41690642_4   1084 GATAAGGG-CTTGATATCCAGAATATGTAAAGAACTCCTACAACTCAACA 1132
                                 -    -            i          i          i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_41690642_4   1133 ACAACAACCTCAATCCAAA-AACCCAATTTTAAAAATAGCCAAAAAGCAT 1181
                          i  v  ----i --    -         ?-      i v    iiiiv 
  L1M4_orf2#LINE/    791 ATAAAAA----GA--CAAATAACCCAATTW-AAAAATGGGCAAAGGATTT 833

  chr1_41690642_4   1182 GAATGGACATTTCTCCAAACAAGATATACAAATGGCCAATCATCACATGA 1231
                             i              v                    v v       
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_41690642_4   1232 AAAGACATTCAACCTCACTAATCAT 1256
                              iii     v   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (69 / 40)
Gap_init rate = 0.02 (17 / 762), avg. gap size = 1.65 (28 / 17)  


2332 25.00 2.86 4.82  chr1_41889243_41890998      496  1263 (493)    L1M4_orf2#LINE/L1      156   908 (0)  

  chr1_41889243_4    496 ATGCCAAAGGAACCAGAACA-CTGAAACAATTTTGAAAAAAGAAAAATAA 544
                             -  i   v      i - ii       i        -   i  i  
  L1M4_orf2#LINE/    156 ATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA-GAAGAACAA 203

  chr1_41889243_4    545 GGTGAGAAGCATCACTTTACCTGATGTTAAGAC--ATGATATAGCTACAG 592
                         i  vi  i vv    vi v  ii  v i  i  -- iv i v        
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_41889243_4    593 TAATCAAGAATGTGTGGTATTGGCA---GGACAGATACATAGGTCACTGG 639
                                  vv        i     ---   i   i i    i   v   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_41889243_4    640 AAACAAATAGCGAACCCAGAAATAGTTCCACATGGCTACAGCCAACCGAG 689
                           vvi   v v  ii         ivi   i iivi  ii i   ii  v
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_41889243_4    690 TTTGGACAAAGGCAAAAAAGCAATTCAATGAAGGAAGCATAGTTTTTTTT 739
                            v     i  iivv  ii v        ii i   v     i    i-
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC- 402

  chr1_41889243_4    740 TAACAAGCGGTGCTAGAAATATTAGCTATCCATAAGGAAAACA------- 782
                         -     ii      i i vv i i v  ?   i v v    v -------
  L1M4_orf2#LINE/    403 -AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_41889243_4    783 TGGACCTCAATGCAAACCTTCCACTTTATACAAAATTTCATCCAAAAGAG 832
                               i -- ----    iv   iv         v  v ii     vi 
  L1M4_orf2#LINE/    452 TGGACCCC--T----ACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_41889243_4    833 GTAATAGATTTAAACATAAAATGC-AAAACCATAAAACATTCAGA-GATA 880
                         i v ?   ii    ii   i -  -     i       vi i   -  v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_41889243_4    881 ACACAGGAGAAGATTTTCAGGACCTAGAGCCCAGTGAAGAGTCTTTAGGT 930
                            i   ? v i  i   iv     v i iivi ii v iv ii    i 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_41889243_4    931 GTGATATCAAAAGCACAATCCATAAAAGAAAAAA--AATCCACAAAATTG 978
                         i   i i           v v i           --i  -----      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT-----AAATTG 639

  chr1_41889243_4    979 AATTTCATCAAAATTAAAAACT-----GCTTCGCATAAGACCCTGTTAAG 1023
                         i i                   -----     -- v i   v  i i   
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTC--AAAGGACACTATCAAG 687

  chr1_41889243_4   1024 AGAATGAAAAGGCAAGCTATGGACTAGGAGAAGATATCTGCAAACAACAA 1073
                          i i       i   v i ii  v i      i    i      iv i v
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_41889243_4   1074 ATCTGACAAAGGACTCATATCTAGAACATACAAAGAACTCTCAAAACACA 1123
                               i  i     ii    i    i   i          i v   ---
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC--- 784

  chr1_41889243_4   1124 GCAGTCAAAAAAAAAAAAACACCCAAAACAATAAACAATCTAATTAGAAA 1173
                         ----    v  v     i   ------------  i  i i    ?i   
  L1M4_orf2#LINE/    785 ----TCAATAATAAAAAGACA------------AATAACCCAATTWAAAA 818

  chr1_41889243_4   1174 ATGGGCTAAAGACATGAATGAACACTTCACCGAAGAGGATATACAGATGG 1223
                               v  i  iv     ii   i   v  i    i        i    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_41889243_4   1224 CAAATAAGCACGTAAAAAGATGTTCAATGTCATTAGCCAT 1263
                          v         i i        i    ii   ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.19 (129 / 59)
Gap_init rate = 0.02 (18 / 753), avg. gap size = 3.28 (59 / 18)  


2677 21.14 5.71 1.29  chr1_42065140_42066831.rev      502  1201 (491)    L1M4_orf2#LINE/L1      178   908 (0)  

  chr1_42065140_4    502 AAAACAAATCTGAAAAAGCA---CAAAGTTGGAGGACTCAGACAGTACCC 548
                                vii        v ---                 v  -- v   
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC--TTCCC 225

  chr1_42065140_4    549 AATTTTGAGACTTGTTACAAAGTTATAATAATCAAGGAAGTGTAGTGTTG 598
                              ii i    ii       i  i i        iv     i  ii  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_42065140_4    599 ACAAAATGATAGATACAATAATCAGTGGAACAGAGTTGAGAGCCCAGAGG 648
                         i  v  v      i i vvi    i     i   i       i     ii
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_42065140_4    649 TAGACCCACACAAATATAATCACCTCATTTTTGACAAGGGTG--AAGA-- 694
                           i     i   vv   ii   vi v     i          --    --
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_42065140_4    695 ----AATG--------ATAGTCTTTTCAACAAATGGTGTTGGAACAGTTG 732
                         ----    --------                      i   i   ii  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_42065140_4    733 GATATCTATATGCAAGAAAGAAAATGAACCTCAACACTTACCTCACACCT 782
                             ? i i      --     --    vi vi  v i           v
  L1M4_orf2#LINE/    426 GATAKCCACATGCAA--AAGAA--TGAAGTTGGACCCCTACCTCACACCA 471

  chr1_42065140_4    783 TA---AAAAAC-AACTGAGAAAAAGATCATAGATCTAAATGTAAAAGATG 828
                           ---     i-    v -   vi     ?   i          i  v i
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCA-AAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_42065140_4    829 AAACTACAATACATCTAGAAAAAAAATCACAGGAGAAAAT----ATGACC 874
                               i  v  vii     i    --  i   ? v    ----i     
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATCTTCGTGACC 568

  chr1_42065140_4    875 TTTGGTTTGGCAAAGAGTTTTTAGATACAACATTAAAAGCACAATCAATA 924
                           v    v     v iv  i       ii   ii          v   i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_42065140_4    925 AAAGAAACATTA-ATGAATTGAACTT----GAAAT-AAAAA-TTTTGCTC 967
                                v v  -  i     i    ----i    -     -     iv 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_42065140_4    968 TGTGAAAGACAATGTTAAGGGAATAAAAAGACAAGCCACAGATTGTGAGA 1017
                          vii  i    v i i   ii i i         v       v  v    
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_42065140_4   1018 AAATATTTGCAA-TCATATATGTAATGAAGGACTTGTATCCAGAATATAT 1066
                                     -        v i  i i                     
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_42065140_4   1067 AAAGAACTTTCA-AGCTT--CAGCAAGAAAGTAAACAACTCTAT-AAAAA 1112
                                 i i - i  i--i ii  i  iii   i   i v  -?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_42065140_4   1113 ATGGGCAAAATATTTGAACATATGTTTTACCAAAGAAAGCATATGA-TGG 1161
                                  iv       i v ii   iv        iii   ii -   
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_42065140_4   1162 CAAATAAGCATATGAAGAGACACTTAACATTATTTTTAAT 1201
                          v        i     i   ii  i     i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.43 (102 / 42)
Gap_init rate = 0.03 (21 / 731), avg. gap size = 2.33 (49 / 21)  


2835 27.22 1.67 0.78  chr1_42098376_42105225     5461  6360 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_42098376_4   5461 TGGAAAAACATTCCATGTTCATGGATAGGAAGAATCAATATCGTGAAAAT 5510
                               i i  i              v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_42098376_4   5511 GGCCATATTGCCCAAAGTAATTTACAGATTCCATGCTATTCCCATTAAAC 5560
                            v   i v      v i  i         v i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_42098376_4   5561 TACCATTGACATTCTTCTTAGAATTAGAGAAAACT-ATTTCAAAATCCAT 5609
                          v   vivi v  i  ivi    v v  v  i-  -  iii     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_42098376_4   5610 ATGGAACCAAAAAAGAGCCTATATAGCCAAGACAATCCTAAGCAGAAAGA 5659
                               viiv  ii  v  viv        i      i i iv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_42098376_4   5660 ACAAAACTGGAGACATCATGCTACCTGAGTTCAAACTATACTACAAGGCT 5709
                              ii     ivv   ii  v  ii v      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_42098376_4   5710 ACAGTAACCAAAACATCATGATACTGGTACAAA-ATAGACACATAGACCA 5758
                                i   i   vii  i      i i  i-       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_42098376_4   5759 ATGGAACAGAACAGAGAACTCAGAAATAAGACCACACACCTACAACCATC 5808
                               i    iv    iii         iv   i   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_42098376_4   5809 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGACAGAAT-TTCCT 5857
                             i  i     ivv  v   i v  vv         v     -v  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_42098376_4   5858 ATTAATAAATGGTGCTAGGAGAACCGGCTAGTCATATGAAGAAAATTGAA 5907
                         v i  i          i   v   i  v  ?i  i   v i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_42098376_4   5908 ACTGGACCCACT-CCTTATACCTTATACAAAAATTAGCTCAAGACGAATT 5956
                         ii       -  -   i i   v             i     i i i  i
  L1M4_orf2#LINE/    450 GTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_42098376_4   5957 AAACGCTTACATGTAAAACTCAAAACTATAAAAATTCTAGAAGAAAATCT 6006
                          ? vi i  v      i vii            v ii          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_42098376_4   6007 AGG---AAATACCATTCAGGACACAGGCATGAGCAAAGATTTCAT-GATG 6052
                            ---    -- -   iv   viv  vv ii    v i    v -   -
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr1_42098376_4   6053 AAAACATCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGCGATCT 6102
                          vi   i        vvv          v      v  i    vv  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_42098376_4   6103 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTTTCATCAGAGCAG 6152
                         v  i   v v  i i   i  ii vv    i  v i v   vv i  iii
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_42098376_4   6153 ACAGACAATCTAAAGAATGGGAGAAAA-ATGTTGCAATTTATCCAACTGA 6201
                          v      i i v              -  -      v i  vi v    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATAT-TTGCAAATCATATATCTGA 743

  chr1_42098376_4   6202 CCAAGGTCTAATATCCAGAATCTACAAGGAAGTTGAATAAATTTACAAGC 6251
                         iv i  v  vi          v  i  i   v ivv i  v iv i  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_42098376_4   6252 AAAAAACAA----CCCCATTAAAAAGTGGGCAAAGGACATGAACAGACAC 6297
                             i    ----   v   ?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_42098376_4   6298 TTCTCAAAAGAAGACATTTATGTGGCCAACAAGCA--TGAAAAAAAGCTC 6345
                              v        i  vi vi       i     --      i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_42098376_4   6346 AACAAGAGAAATACA 6360
                             vv ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.47 (22 / 15)  


 799 25.51 3.40 3.06  chr1_42152304_42155784.rev     1634  1927 (1554)    L1M4_orf2#LINE/L1        1   295 (613)  

  chr1_42152304_4   1634 TGGAAAGATATACCATGTTCATAGAATGGATGACTCAATATTGTGAAGAT 1683
                                    v          i  v    v    i        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_42152304_4   1684 GTCAACTTTCCTTAAATTAATTTGTATATT--ATACAAGCCAT-TCAAAA 1730
                          v   ivi   ii     i  i ii v   -- ii   v  v -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_42152304_4   1731 TTCTAGCAGGCTTTTTAAATG--GATATCAACAAACTGAATATAAAATCT 1778
                          i i   v v      ---  --  v  ii    i    viv      ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT---TGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_42152304_4   1779 GCATGGAAAAGAAAAGGGCC--GAGTTAAGCCATCACAATAATTAAGAAT 1826
                         ii       v v  i  i  --  i --     vv     vv v  i  v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAAT--AGCCAAAACAATCTTGAAAAAG 195

  chr1_42152304_4   1827 ATGAAGGAGGCTGAGATAACTTATGGCACCAAATATTTAGAA-TTATTAT 1875
                          v   vi i i  -  vi   i iiviv  v   -  i i  -   i  i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTG-GAGGACTCACACTTCCCAAT-TTCAAAACTTACTAC 243

  chr1_42152304_4   1876 AAAGCTATTGTAATTAAGTCAATGTGGCATCTGTGC-TAAA-ATAGACAA 1923
                                iv     i   v  i     i -   -  -   i-       v
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTA-CTG-GCATAAGGATAGACAT 291

  chr1_42152304_4   1924 ATGG 1927
                           i 
  L1M4_orf2#LINE/    292 ATAG 295

Transitions / transversions = 1.42 (44 / 31)
Gap_init rate = 0.04 (13 / 295), avg. gap size = 1.46 (19 / 13)  

1219 29.67 11.90 0.00  chr1_42152304_42155784.rev     2453  2998 (483)    L1M4_orf2#LINE/L1      298   908 (0)  

  chr1_42152304_4   2453 CAATGGAACAGATTAGAGAATTTAGAAAGAGATCTTTA----TATGATCA 2498
                                 i   v v    i ii     v i i iv  ----    i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_42152304_4   2499 CTTGATTTATGACAAAGTTGACACTAAAATACAGTAGAGAAAGGAT-GTC 2547
                         v       vi     i v  v  vv vv  v  i i i     i  -   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_42152304_4   2548 TTTTCAATAAATAGTGCTGACTCAATTTAGTATCCATACGGGAAAAAAAG 2597
                                i    i      ivv   i vii  ?   i i vi   i  v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_42152304_4   2598 AA--------TCTTCCTCAAGCCATTCACAAATATCAATTCTAGCTGCAT 2639
                           --------i  v     vi    vi     v  i  i  v iv  v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_42152304_4   2640 TGTAGGTCTATATATATTAGGTAAGACAATAAAGCTCTTAAAAGAAAACA 2689
                         ii?  ii   v  i  vv  v   i  v     i      i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_42152304_4   2690 TAAGAGAATATCTGTATATCCTTAGAATAGCCAAACATTTCTTAAACATT 2739
                           i ? v v    vii iv    i iv   v   vvi       i i  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_42152304_4   2740 ACAC-AGAAGGACTAACTATAAAGGAAAATATTGATAAACTAGATTAAAC 2788
                             - i   v  v i v i   i     v  v      i i  i vv i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_42152304_4   2789 TAAACTCAAGAAATTCTGATCATCAAAAGATACTATTAAGGGAATGAAAG 2838
                         i   v i  i  v  i  vv v     i  i     i   ii i     i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_42152304_4   2839 AGCAAGCC-CAGAGTAGGAGAAGATACT---------------------- 2865
                         ii   v  -    i i      i   i ----------------------
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_42152304_4   2866 -------------------ATAAATAACT---ACAAATCAATATGAGAAA 2893
                         -------------------     v    ---    v      vv i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_42152304_4   2894 GGCAAGTAACCCAAAAGAAAAGTGGACAAAAAGCTTGAAAAAACACTT-T 2942
                          i   i        vv?    i   i    iiii     v i   i  - 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_42152304_4   2943 ACACAGAGAATGTTCAAATGGCTTACAAATATGTTAAAAGTT-----ATA 2987
                         v  v   ii  i v        iv i  ii ii v     v ----- i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_42152304_4   2988 TCAATTGCATT 2998
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (93 / 65)
Gap_init rate = 0.01 (9 / 611), avg. gap size = 7.22 (65 / 9)  


3132 26.64 0.77 1.21  chr1_42188314_42190390.rev      705  1616 (461)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_42188314_4    705 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAGT 754
                               i    i     i        v      v i i   ii v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_42188314_4    755 GGTCATACTACCCAAAGTAATTTATAGACTCAATGCTATTCCCATTAAAC 804
                           iv     v      v i  i  i   i    i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_42188314_4    805 TACCATTGACATTCTTCATAGAATTAGAAAAACT-ATTTTAAAATTCATA 853
                          v   vivi v  i  iii    v v  v  i  -  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_42188314_4    854 TGGAACCAAAAAAGAGCTTGTATAGTCAAGACAATCCTAAGAAAAAAGAA 903
                              viiv  ii  v iv v    i   i      i i i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_42188314_4    904 CAAAGCTGGAGGTATCACATTACCCAAGTTCAAACTATACTACAAGGCTA 953
                              i      vv     i v     v      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_42188314_4    954 CAGTAACCAAAACATCATGGTACTGGTACAAAAATAGACACACAGACCAA 1003
                               i   i   vii         i i  ii       i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_42188314_4   1004 TGGAACAGAATAGAGAACTCAGAAATAAGACCACATGCTTGCAACCATCT 1053
                              i     v    iii         iv   i iii  iiiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_42188314_4   1054 GATCTTTGATAAACCTGACCAAAACAAG-CAATGGGGAAAGG-TATTTTT 1101
                            i  i  i  ivv  -    i  v v-            i-  v ---
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGT--- 396

  chr1_42188314_4   1102 ACCTTTTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAA 1151
                         --     i  i              v      v  ?   i     i  i 
  L1M4_orf2#LINE/    397 --CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_42188314_4   1152 TTAAAATTGGACCCATTCTTTACACTTTATACAAAAACCAACTCAAGATG 1201
                         v i  i        v v i i    iv          ii       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_42188314_4   1202 GATTAAAGATTTAAATGTAAAACCCAAAACCATAAAAACCCTAGATGAAA 1251
                            i ?   ii         i v i     i      vi i    v    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_42188314_4   1252 ATCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTCAT-GA 1299
                          iv    ?i- v i -   iv   v v  vv i     v i    v -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_42188314_4   1300 TGAAAACACCAAAAGCAATTGTAACAAAAGCAAAAATTGACAAATGGGAC 1349
                          - vi            vvv i        v      v  i    v    
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_42188314_4   1350 TTAATTAAACTAAAGAGCTTCTGCACAGGAAAAGAAACTATCATTGGAGT 1399
                           v  i   v v  i i   i  ii vvv   i  v       vvii   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_42188314_4   1400 GAACAGACAACCTACAGAATGGGAGAAAAAGTGTGCCATCTATCCATTTG 1449
                            v        i                vi v   v vii  vi  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_42188314_4   1450 ACAAAGATCTAATATCCAGATTCTACAAGGAACTTAAACAAATTTACAAG 1499
                          i  i iv  vi        v v  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_42188314_4   1500 AATAAAACAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACA 1549
                           v  i     i     v   ?    i           iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_42188314_4   1550 CTTCTCAAAAGAAGACATTCATGCAGTCA-TGATCGT-TGCAGAAATGCA 1597
                         i     v        i  v  viii i  - i v ii-  v i i    -
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC- 891

  chr1_42188314_4   1598 AATTAAAACCATGATGAAA 1616
                         -- i  v i  ????????
  L1M4_orf2#LINE/    892 --TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


3070 26.23 1.90 0.56  chr1_42196677_42199886     1822  2717 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_42196677_4   1822 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 1871
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_42196677_4   1872 GCCA-TACTGCCCAAGGTAATTTATAGATTCAAGGCCATCCCCATCAAGC 1920
                          v  -    v     iv i  i  i        v  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_42196677_4   1921 TACCAATGACTTTCTTCATAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 1969
                          v   iivi i  i  iii    v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_42196677_4   1970 ATGGAACCAAAAAAGAGCCTGCATTGCCAAGTGAATCCTAAGCCAAAAGA 2019
                               viiv  ii  v  v v  v     ivv    i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_42196677_4   2020 ACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGGCT 2069
                               i      vv    v  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_42196677_4   2070 ACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGATCA 2119
                                i   i    ii    i    i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_42196677_4   2120 ATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCA 2167
                               i    i--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_42196677_4   2168 TCTGATATTTGACAAACCTGACAAAAGCAAGAAATGGGGAAAGGATTCCC 2217
                         vi    v  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_42196677_4   2218 TATTTAATAAATGATGCTGGGAAAACTGACTAGTCATATATAGAAAGCTG 2267
                          v  i  i     i        v     iv  ?i  i  ii i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_42196677_4   2268 AAACTGGATCCCTTCCTTACACCTTATACAGAAATTAATTCAAGATGTAT 2317
                           ii    i    v   i     v      i       i    i   v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_42196677_4   2318 TAAAGACTTAAACGTTAGACCTAAAATCATAAAAACCCTAGAAGAAAACC 2367
                         i ?    i    i  v   v      ii      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_42196677_4   2368 GAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 2416
                         v   ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_42196677_4   2417 AACACCAAAAGCAATAGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 2466
                         i            vv           vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_42196677_4   2467 TCAAACTAAAGAACTTCTGCGCAGCAAAAGAAACTACCATCAGGGTGAAC 2516
                              v v  i     i  i  vv    i  v    i  vv ii     v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_42196677_4   2517 AGGCAACCTACAGAATGGGAGAAAATTTTTACAA-TCAACCCATCTGACA 2565
                           i     i                 v   i   -   -ivi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGATA 745

  chr1_42196677_4   2566 AAGGGCTAATATCCAGAAC-T-TAAACAAAT-TTACAAG--------AAA 2604
                          i  i  vi         i- -    v  v -      v--------   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_42196677_4   2605 AAATCAAACAACCCCATCGAAAAGTGGGCAAAGGGTATGAACAGACACTT 2654
                           iv    i     v  i?    i          i v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_42196677_4   2655 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 2704
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_42196677_4   2705 CATCACTGGCCAT 2717
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


 542 23.89 11.11 1.67  chr1_42200691_42203280      962  1141 (1449)    L1M4_orf2#LINE/L1        2   198 (710)  

  chr1_42200691_4    962 GGAAAGACATAACGTGTTCAAGG-TTGATGAAGACTTTATATGGTGGAGG 1010
                                i  vv i      v  -   --        v    v  vi  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTG--GAAGACTTAATATTGTTAAGA 49

  chr1_42200691_4   1011 TGGTACTTCTTTCCAAAATAATCTA-AAATTGAACACAATTGCAATCAAA 1059
                            i v v  ii     v i     - i   v   i    iv v      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_42200691_4   1060 ATTCCAAC------------AGAAA-----AAGCCGATCCCGAAATTCAT 1092
                           i   i ------------     -----    i     ii        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_42200691_4   1093 TTAGGAAAGCAAAGAGAGTCA-AATAACTGGGATAGTTTTGAAAAAGAAG 1141
                         v i i  v    i -  vi  -    i iiii i i i            
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

Transitions / transversions = 1.87 (28 / 15)
Gap_init rate = 0.04 (7 / 197), avg. gap size = 3.29 (23 / 7)  

 857 28.92 10.11 4.56  chr1_42200691_42203280     1436  2137 (453)    L1M4_orf2#LINE/L1      168   908 (0)  

  chr1_42200691_4   1436 CAAAACAA--AAAACAAAC---AAACAAACAAACAAAAAAGGTTGGGAGG 1480
                           i  i i--       v ---   v i vi      ----     ii i
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA----GTTGGAGGA 213

  chr1_42200691_4   1481 CTCACA-TACCAGATAGTT---AGGTTATCTCAAC-CCATAATAATGAAG 1525
                               - v  vi  --  --- iv   iiv   v- i i i    v   
  L1M4_orf2#LINE/    214 CTCACACTTCCCAAT--TTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_42200691_4   1526 ACAATGTGAAATTGGCTTAGAGAAGGATGAAGACATCAATGGAGCAGGAT 1575
                            i    iv i    v  ii  vi  iiv v v         ii  i  
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_42200691_4   1576 AGAGAGTGTAGAAATGGACTGATA------TGAAAACTTGATCTATGACA 1619
                         v      vi      ii  iv   ------  ivv v     i vi    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_42200691_4   1620 GAGG---CAGCACTATAACTAGTGCAGAAAGGATGGGCTGTTTAATAATT 1666
                         ii  ---  iv  i  --ii i  vi     i  i v  v  i  i  v 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCAT--TCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_42200691_4   1667 TATGCTGTGACA------TAACCAAAAGGAAAA-ATTAAAATTCAATCCT 1709
                         vi     v    ------  ?   v v v    - v i  i  vi i  i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_42200691_4   1710 TAACTCACATTATATA---AAATAAATCTTAAGTAGATTAAAGATTTAA- 1755
                           v      ii     ---    v  iiiv  i i   i ?   ii   -
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_42200691_4   1756 TATGAGAATTAAAACTACAAGATT-TCAATAGAAAATATAGAAGAATATC 1804
                          i i   ii        i  i i - i iv      i    i? v v   
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_42200691_4   1805 TTTATGGTTGTAGAGAAATAATATCGTTTAAAAAATAAGATTCCTTACAT 1854
                           ii  iiiv i i-------------   iiv   -- i  i    v  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGG-------------TTAGGCAAT--GGTTTCTTAGAT 594

  chr1_42200691_4   1855 GAGAAGCAGAAAGTACAA--AACATAAGGTAAACGATTGATAGATCTG-- 1900
                         iv  vi vi    i    --    v   --   vi  v    i  iv --
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAG--AAAAAATAGATAAATTGGAC 642

  chr1_42200691_4   1901 -TCATTTAAATTAA-----TGTATGCCTAACCAAAG----CTATCATGAA 1940
                         -    iv       ----- v i   i ---     ----      v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTT---CAAAGGACACTATCAAGAA 689

  chr1_42200691_4   1941 CAGGTTAAAGACAA-------GATAG-AGGAAACATTTGTAATGCACACA 1982
                         -  vvv        -------i  i -  i   i     i  vv  i i 
  L1M4_orf2#LINE/    690 -AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_42200691_4   1983 GCTGACAAAGCACTAGTGTCTA-AATTCACACAGAGCT---ACAATTTGA 2028
                         v    i  i v   v  i  i -   vi i v   i  ---    i ii 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_42200691_4   2029 TAAGAAAAAAATACATAA--------GAAAATGAACAAATCACATAAACA 2070
                            v     i i v    --------i      ii    vv iv i  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_42200691_4   2071 GACAACTCACAGAAGAAGAGTAAACTTAAA---CCA-TAAATCAATGAAA 2116
                             vi  v vi       -  v  --   ---   -   iivv      
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGA-TATAC--AAATGGCCAATAAGCACATGAAA 885

  chr1_42200691_4   2117 A-ATTTTGAGCA-CACTGGGAAT 2137
                          -  vi v i  -  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (124 / 76)
Gap_init rate = 0.05 (35 / 741), avg. gap size = 2.94 (103 / 35)  


3049 25.43 5.02 1.48  chr1_42205673_42213955.rev     3130  4006 (4277)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_42205673_4   3130 TGGAAAGATATCCCATGCTCATGGATCAAAAAGCT-AGTAATGTTAAAAT 3178
                                          i        iii  ii  - i  v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_42205673_4   3179 GATTGTGCTGCCCAAAGCAATCTACAGATTCAATGCAATTTGTATGAAAA 3228
                          iivi i  v      vii              i     iiv   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_42205673_4   3229 CACCAATGACATTTTTCATGGAAATAGAAAAAAACAACTG----TAAAAT 3274
                         iv   iivi v     iiii     v  v  i-----   ----      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAAT 145

  chr1_42205673_4   3275 TAGTATGGAACAAAAAGAGATCCA---------AAGCAATCTTGAGCAA- 3314
                          vi       vviv   i  i   ---------  i         iv  -
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_42205673_4   3315 AAGAACAAAGCCAGAGGCATCACCCTGCCTGACTTCAATA--TATTGCAA 3362
                                   iii    vv    v  v  ii i     v --  i i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_42205673_4   3363 GGCTATGATAACCAAAACAGCATGGTATTGGTATAGAAACACACACAGAG 3412
                         i    iii   i   i    ii     i   i   iii i v   i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_42205673_4   3413 ACCAATAGAGCAGAATAGAGAACCCAGAAATAAATCCATGTATTTACAGC 3462
                          i    i  ii     v    ii           i    ii     ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_42205673_4   3463 CAATTGATTTTTGACAAAGACTCCAAGAACATACATTGGAGAAATGACAA 3512
                                    i     i iiv      v   v  v   i    vi i i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_42205673_4   3513 CCTCTTCCATAAGTAGTGCTGGTAAAACTGGGTATTTATATGCAGAAGAG 3562
                         i  i   v i  i i       v v      i  ?ii i     i    i
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_42205673_4   3563 TGAAACTAGACTCCTGTCTCTCAC-ATGTACAAAAATCAACTCCAGATGG 3611
                             ii i   i   ii   v   -  i         i     v i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_42205673_4   3612 ATTAAAGACGTAAATGTAAGACCCCAAACTACATATCTACTA-------A 3654
                           i ?    v           v iv      i v v  vi  ------- 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_42205673_4   3655 CATGGGG--AACACTCCAAGACATTGGGCTAGGCAAAGGTTTTATGGCTG 3702
                            i  ?--  vv  i iv   v     i       v     iv i v i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_42205673_4   3703 AGACCTCAAAAGCACAGGCAACAAACACCAAAATAGACAAATGGGACTAT 3752
                         v   vi          i        vivv        i    v     vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_42205673_4   3753 GTT----TTTTGCAGAGGTTTTACCTTTCTGCAAAGGAAACAATCAACAG 3798
                         i i----  ---v i iv    i--- v  v       v  v     v i
  L1M4_orf2#LINE/    646 ATCAAAATT---AAAAACTTTTG---TGCTTCAAAGGACACTATCAAGAA 689

  chr1_42205673_4   3799 ACTGAA--GACAACCTGTTGAATGGGAGAAAATATTC-----------AT 3835
                          v    --       iiiv                 i-----------  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_42205673_4   3836 CCAACAAGGGACTAATATCTAGAATATACAAGGAACTCAAGCAGCTCAAC 3885
                          ii i        vi    i        i  i      vvi  i     i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_42205673_4   3886 AGCAAAAACACCAAATAGTTCCATTATAAAGTGGGCAAAGGATCTGAACA 3935
                          ii     v  -     iii v   ?v   i            i    i 
  L1M4_orf2#LINE/    790 AATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_42205673_4   3936 GACATTTCGCAAAAGAAGACTTGCAAATGGCCAGCAGGAATATGAAAAAA 3985
                                 v v        iv i          ii i v i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_42205673_4   3986 ATGCTCAACATCAGTAATCAT 4006
                         -            ????????
  L1M4_orf2#LINE/    889 -TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (146 / 73)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.56 (57 / 16)  

3733 23.22 0.77 1.31  chr1_42205673_42213955.rev     6880  7792 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_42205673_4   6880 TGGAGAAATATTTCATGTTCCTGAATAGGAAGACTCAATATTGTCAAGAT 6929
                             i i    ii       v  i  v        i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_42205673_4   6930 GTCAGTTCTTCCCAATTTGATCTATAGATTCAACACAATCCAAATCAGAA 6979
                          v  i v  i     v        i         i      vv    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_42205673_4   6980 -----ACTGCCAAGTTGTACTGTGGGCGTCAACAAACTGATTCTAAAGTT 7024
                         -----i     ---  v -i  ii ivi ii    i     i     i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC---TTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_42205673_4   7025 TATGTGGAGAGGCAAGAGACCCAGAATAGCCAACTCAATACTAAAGGAGA 7074
                         i  i    i v     i                vv    vi i  ii   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_42205673_4   7075 AGAACAAAGTTGGAGGACTGACACCATCTGACTTCAGGACTTAACTATAA 7124
                                            v    ivi ii i    ii     -   i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAA 245

  chr1_42205673_4   7125 AGCTACAGTAATGAAGACAGTGTGGTGC-GGTGAAGGAATAGGTA-ACAG 7172
                                     v             i -  iiv i i    ii - i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_42205673_4   7173 ATCAATGGAACGGAAGAGAGAGCCCAGAAATAGACCCATATAAATATAGT 7222
                                   ii   vv     i         i       i vv   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_42205673_4   7223 CAAGTGATTTTTGACAAAGGAGCAAAGGCAATACAATGAGGTAAAGGTAG 7272
                            v       i     i  v  v   i v  v     i  v  iii   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_42205673_4   7273 TTTTTTCAACAAATGGTGCTGGAACAACTGGACATCAATATGCAAAAAAA 7322
                          i                    i         i ? v i        i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_42205673_4   7323 AAAAAAAATCTAGTCACAGACATTACACTCTTCACAAAAACTAAATCAAA 7372
                         vi  i----i i v v vv  v i    iv vi       i   v     
  L1M4_orf2#LINE/    446 TGAAG----TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_42205673_4   7373 ATGGATCATAGACCTAAATGTAATAAGTGAAACTATAAAACCCCTAGAGA 7422
                                 ?              v iv i            i i    ii
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_42205673_4   7423 ATAACACTGGAGAAAACCTAGATTGTCTTGACTATGGCAATAATGTTTTA 7472
                          v    iv  ? v   i  vvi vii    iv vv      ii v i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_42205673_4   7473 GATATAACACCAAAGGCACAATCCAAGAAAGAAGTAATTGTTAAGCTGGA 7522
                              i        i      v v vi      iv   v v   ii    
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_42205673_4   7523 CTTCATGAGAATAAAAAAAAAATGTTCTGCAAAAGACAATTTCAAGAAAA 7572
                               v i   v     vvvv   v  v    i    v v        i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_42205673_4   7573 TCAGAAGGCAAGCCACAGACTGGGAGAAAATGTTTGCAAAAGACATATCT 7622
                          v i   i   v       v           i        vv i      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_42205673_4   7623 GCTAAAAGACTGTTATTCAAAATATACAAAGAGTATTTAAAATTCAACAA 7672
                          v   ii    vv   i  i      i     iivi   v  i    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_42205673_4   7673 TAAGAAAACAAACAACTCAATTAAAAAAAAATGGGCCAAAGACCTGAACA 7722
                            i  i     i   i     ?     ---     v  i  ii    i 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAA---TGGGCAAAGGATTTGAATA 838

  chr1_42205673_4   7723 GATGCCTCACCAAAGAAGATATACAGATAGCACATAAGCATATGCAAAGA 7772
                           iiii  v                i  i  vv       i   v     
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_42205673_4   7773 TGTTCTACATCATATGTCAT 7792
                           i  v      ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (127 / 81)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  


 764 31.44 3.88 8.45  chr1_42258166_42260425      498  1219 (1041)    L1M4_orf2#LINE/L1        1   689 (219)  

  chr1_42258166_4    498 TAGAAGTGATATACTATGTGCATGGATTG-AAGACTACATATTTTAAAGA 546
                          i   i-     v i    v         -      vv     v v    
  L1M4_orf2#LINE/      1 TGGAAA-GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_42258166_4    547 CATCAATTATTACCAAACCAATTTGTAGATTTATTGCAATCCCCA-AAAA 595
                         iiv    vv iv     iii  i ii     i vi        i -v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_42258166_4    596 ATACCAA-TGGGTTAACTCTG-------TGACAATATATTTCTAAAAACT 637
                           v   i-  vv  --i i  -------      vv iv i      vii
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_42258166_4    638 ATTTGGAAATCTCAAGTG-CCAAAAGTAGGTATGTTATTCTT---ATAGA 683
                           v       v-    v -  v i i   vi vivi v    --- v   
  L1M4_orf2#LINE/    148 ATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_42258166_4    684 AAGACAAAGGTTAAGAAA--GTGCTTTATGAGTGATCAAGATTTCTTATA 731
                          ii      v vi  i v--iii   ivii v --    i i  vi  i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATT--TCAAAACTTACTACA 244

  chr1_42258166_4    732 ACAATACAGTAATTATGAGAGTGTGGTAATAGTGCAAAATTTTAAAAATA 781
                          viv         i v  v         v i iii  iiv vv v v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_42258166_4    782 AAACAATGGAATAGAATAGAGAGTCCAGAAATGTGTGTGTGTATGTGTGT 831
                         i v              v              i--------- -------
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATA---------A------- 328

  chr1_42258166_4    832 GTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTATGTCTGTGTAGACAACT 881
                         --------------------------ii ii  ii i i  -- v   i 
  L1M4_orf2#LINE/    329 --------------------------ACCCATACATTTATG--GTCAATT 350

  chr1_42258166_4    882 GGTTAATGATAAAGGTGACATTGCAGAGAATT----GGAGAAAGAAAAAC 927
                          i  vvi  i  i    v  ----   vv   ----  i       v ii
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGAAAGAATAGT 396

  chr1_42258166_4    928 TTTTAAAATAAACAATATGGAGTTAATTGAATACTCATATAGAAAAATAA 977
                         i   vv  i   iii iiv i vi  i  i   ?i  i  - v    v  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAA 445

  chr1_42258166_4    978 CCAAACTCAATCCCTACCTCATAACCATATACAAATATGAGTTTCAGATG 1027
                         iv  ii vi i          i -           v  v ii iv i   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACA-CCATATACAAAAATTAACTCAAAATG 494

  chr1_42258166_4   1028 GACTGTATATATAGATGTGAATGGC---AACAATAAAGCTTTTAAAAGTG 1074
                           iii? v iv  i    -  vi  ---   v     i  i   i   vi
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_42258166_4   1075 AATATGGGGG-ATAGCTTTACAATATTGGGGTAAAGAAAAATCTTCATAA 1123
                           i  i  ? - v v   iiii iv     v  iiv  vii -   v  i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAG 592

  chr1_42258166_4   1124 ACTGGATATAAAAAG-ATTAACCGTAAAGAAAAAACTACA---ATTCAAT 1169
                          ivv  i iv     - iv i vii   ii     v  v ---   vi i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_42258166_4   1170 GACATAAATATTAGGAATATCTCCTCATCCTCAAAATATACCATTAAGAA 1219
                         vv   v  v    ii  ---  ii vvv i     iv i  i  i     
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA---CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

Transitions / transversions = 1.43 (132 / 92)
Gap_init rate = 0.04 (25 / 689), avg. gap size = 3.56 (89 / 25)  

 613 19.83 6.03 5.60  chr1_42258166_42260425     1536  1767 (493)    L1M4_orf2#LINE/L1      676   908 (0)  

  chr1_42258166_4   1536 GATACCATTAAGAGAGTGAGAAGATAAGCCACTGGGTGG-AGAAAATGTT 1584
                           i  i  i    i     i    i  v    v ii   -       i  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_42258166_4   1585 TGCAAA-AATATAACTGACAAAGGGCTTGTATCCAGAACAT--------- 1624
                               -v     v    i  i  i             i  ---------
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_42258166_4   1625 --TTACAAATCAATAATAAAAATAGAAAAGTGAAATAGAAACAGTAAAAT 1672
                         --      v             --  v  i --------   --iv  v 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAA--GACAAAT--------AAC--CCAATT 813

  chr1_42258166_4   1673 AGAAATACAGACAAAAGAATTAAATAGGCACACCACAAAAGAAGAAAAAG 1722
                         ?i   - ii i    i  v  i     i  ivi v v        v v v
  L1M4_orf2#LINE/    814 WAAAA-ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_42258166_4   1723 AAATGGGCAACA-GCATACAAAAAGATACTCAACATCATTCGTGAT 1767
                               v   i -   i ii       i          ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (29 / 16)
Gap_init rate = 0.03 (8 / 233), avg. gap size = 3.38 (27 / 8)  


1987 17.31 7.05 19.17  chr1_42293117_42295909.rev      972  1936 (857)    L1M4_orf2#LINE/L1        1   848 (60)  

  chr1_42293117_4    972 TGGAAAGGTATTCCATATTCATGGATTGGAAGAATTAATATTTTTAAAGT 1021
                                i   i    i                v        v    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_42293117_4   1022 GTTTATACTATCCAGAATGATCCACAGATTTAATGCAATCCCTATCAAAA 1071
                          viv     vi   i v     i       i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_42293117_4   1072 TTCCAATTACATTTTTTCACAGAAATAGGAAAAACAATCCTAAA-TTC-- 1118
                          i   ii i v      -i       v iv  ivii        -   --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_42293117_4   1119 ----------------CCCA-AATAGCCAAAGCAATGTTGAGCAAAAAAG 1151
                         ----------------    -          i    v    i-   i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAG 198

  chr1_42293117_4   1152 AA-AAAGCTGGAAGCATCACACTACTTGATCTCAAAATCTACTACAGAGC 1200
                           -    i    i vv       v iii  i      ii       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_42293117_4   1201 TGTAG-------AACAGCATAGTACTGGCACAAAG-CAGACAACGAGACT 1242
                          ii  -------i    ii i         i  i -i     vvv   ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_42293117_4   1243 AATGGAACAGAATAGAGAGAGCCCAGAAATAAATCTACACATTTACAATC 1292
                                i     v     --i           i i i       iii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAG--TCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_42293117_4   1293 ---TGATCTTTGACAAAAGTGCCAAGATCACACAATGGGGAAAGGACAGT 1339
                         ---    i  i     ii         i  iv            i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_42293117_4   1340 CTCTTCAATAAATGGTATTGGGACA--------------TGCAGAAAAAT 1375
                           i     i       ii       --------------    i  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_42293117_4   1376 GAAATTAGACACTTATCTAACCTCATGTACAAAAATTAACTCAAAATGGA 1425
                            i  i   v i  i  v  vi   i                       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_42293117_4   1426 TTAAAGTCTTAAGACCTGAAACTGTAAAGCTACTGGAAGAAGGCAGGAGC 1475
                          i ?  -------    i  --     i----------------------
  L1M4_orf2#LINE/    497 TCAWAG-------ACCTAAA--TGTAAG---------------------- 515

  chr1_42293117_4   1476 AGTGGTGAATGCCTGTAGTCCCAGCTACTCGGAAGCTTGAGGCAAGAGGA 1525
                         ----------------------     -----  i  -------------
  L1M4_orf2#LINE/    516 ----------------------AGCTA-----AAACT------------- 525

  chr1_42293117_4   1526 TCACTGGAGCCCAGGAATTTGAGGCCAGCCTACACAACACAGTGAGACCC 1575
                         ----------------  --------------------------------
  L1M4_orf2#LINE/    526 ----------------AT-------------------------------- 527

  chr1_42293117_4   1576 TGCCAAAAACAAACAAACAAACACCAAAACCCAAAACAAAACAAAGTAAC 1625
                         -------------------------     i -------------- ---
  L1M4_orf2#LINE/    528 -------------------------AAAACTC--------------T--- 535

  chr1_42293117_4   1626 AACAACAACAAAAAATGTACCAGAGGAAACATAGAGGAAAA-CTTCTTGA 1674
                         --------i i  i -----------        i? v   -    v   
  L1M4_orf2#LINE/    536 --------TAGAAGA-----------AAACATAGGNGTAAATCTTCGTGA 566

  chr1_42293117_4   1675 CATTGGTCTTGGCAAAGATTTCTCGCCTATGATCCCAAAACCACAGGCAA 1724
                          v    vi v     v i     iivv     iv      v    i    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_42293117_4   1725 CAAAACCAAAAATAGACAAAAAGGAGTGCAGCAAA-TTAAACTGCTTCTG 1773
                              vv         i   vv   v v  v    -     v-i   i  
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTG 665

  chr1_42293117_4   1774 -----CACAGG-------TAAGGAA-TGAAAAGA--ATCTATAGAATGAG 1808
                         -----  v   -------i   i  -        -- i i i      i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_42293117_4   1809 ACAAAATATTT-CAAATGAAACATATGCTAGTGGATTAATATCCGAAATC 1857
                          v         -     v v i  v  v  iv   i vi     ii   v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_42293117_4   1858 CATACAGAATTCAAACAACTCAATAGCAAGAAAACAA----CCCAATTTA 1903
                         i   v    i  vv           ii  i  i    ----       ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_42293117_4   1904 AAAACAGGCAAAGCAACTGAATAGACATTTCTC 1936
                             ii       v vi                
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

Transitions / transversions = 2.04 (110 / 54)
Gap_init rate = 0.03 (29 / 848), avg. gap size = 8.72 (253 / 29)  

 337 17.14 0.00 0.00  chr1_42293117_42295909.rev     2233  2302 (491)    L1M4_orf2#LINE/L1      839   908 (0)  

  chr1_42293117_4   2233 GACATTTTTCAAAAGAAGACATACAAAAGGCAAGGAGGTATATGAGAAGG 2282
                                i  v        i       v   v iv i i i    i   i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_42293117_4   2283 TGCTCAACATCACTAATCAA 2302
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.00 (0 / 0)  


2364 27.64 7.08 1.63  chr1_42430363_42434889.rev     3176  4036 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_42430363_4   3176 TGGCAAAACATTTTGTGCTGTTGGATTGGAAGAATCAATATCACAAAAAT 3225
                            v  i i  iiii  i vv            v i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_42430363_4   3226 GACCATACTATTCAAAGCAATCTACAGATTCAATGAAATTCCTTTCAAAT 3275
                          i v     vii    vii              i v   i   v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_42430363_4   3276 TACTAACATCAGTTTTCACAGAATTAGAAAAACAG-CACTGGAGTGCATA 3324
                          v i i vv vv    ii     v v  v  i v -iv  ii i v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_42430363_4   3325 TGGAATCAAAAAAGCACTCAG-----CCAGAGCGATCCTAAGCAAAAGGA 3369
                              viiv  ii -  i   -----   i i i   i i iv  i i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_42430363_4   3370 ACAAATTCAGAGGCATCAGATTGCCTGACTTCAAATTATACTACAAGGCT 3419
                              v ii    vv   v i v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_42430363_4   3420 ATAGTAACTAAAGCAGCATGATAGTGGTACAAAAATATGCATAGAGATCA 3469
                          i     ii  ii   ii  i  v   i i  ii   vi    v      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_42430363_4   3470 GTGGAACAGAATAGAGAGCCTAGAAATAAAGCCACATACCTACAACCAAC 3519
                         i     i     v     i i         v   i i ii  iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_42430363_4   3520 TGATCTTTGACAAAGTTGATGAAAATAAACAGTGGAGAAAGGACATTAAC 3569
                             i  i     i v  vii i vi vv  i   i     ------  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG------AAT 393

  chr1_42430363_4   3570 ACTCTATTCAATAGATGGTGCTGGGATA-TTGGCTAGCCATATGCAAAAG 3618
                          v   v     i i            i -i   v  ?   i         
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_42430363_4   3619 AAGGAAACTGGACCCTTGTGTCTCACCATGTATGAAAATTAACTCAGGAC 3668
                           v   ii       i iiv  v      i  ii            ii -
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA- 492

  chr1_42430363_4   3669 GGATGGATTAAAGACTTGAACATAAGACCTTAAACTATAAAAGTCCTAGA 3718
                         ---     i ?    i i  ii     v  v           v  i    
  L1M4_orf2#LINE/    493 ---TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_42430363_4   3719 AGAAAACTTAGGAAGAACTCTT-G-GATGTTGGCCTAGGCGAAGAATT-- 3764
                                v    ?iv  v    - -  iv    vi     i v iv  --
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_42430363_4   3765 ----TATGA----GGAAG--------ACAAAA------ATAGACAAATGA 3792
                         ----     ----ii   --------      ------     i    vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_42430363_4   3793 GACTTAATTAAACT--AAAGCTTC---ACAGCAAAAGAAATACTCAACAG 3837
                              v  i   v --   i   i---i vv    i  v ivv    v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_42430363_4   3838 ATTAAA----CAGCCTATAGAATGGGAGAAAATGTTTGCAAATGAT-TAC 3882
                          v i  ----  i  i i               i         v  -  -
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA- 738

  chr1_42430363_4   3883 TTTCAGAAAGGATGAACATC-AGAATCTACACGGAACTCT--------AA 3923
                          i v v  i   ivvii   -     v  i vi       --------  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_42430363_4   3924 TAACGGGGAAA-AAACAGCTTCTTTTAAAAACTAGGCAGAGGACATGA-- 3970
                            iiiii i -   i i iivv  ?     - i    i    iv   --
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAAT 837

  chr1_42430363_4   3971 -GACATTTCTT----GAAGAAATACAAGTG-CCAACAAACACTTGAAAAA 4014
                         -         i----     v      i  -    i  i   v      i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_42430363_4   4015 AATACTCAACATTACTAATCAT 4036
                          - i        i ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (154 / 80)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.00 (75 / 25)  


2432 17.84 3.35 2.23  chr1_42541044_42543005.rev      499  1036 (926)    L1M4_orf2#LINE/L1      224   767 (141)  

  chr1_42541044_4    499 CCAATCTCAAAACTTACTATAAAGTTACAGTAATCAAGACAGTGTGGC-T 547
                              i             i    i                      i-i
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_42541044_4    548 TGGCATA----TAGAACTATA--TCAAAAGAATAAAATTGAGAACCCAGA 591
                                ----    vv    --    vi     i        ii     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_42541044_4    592 AATCAACCTTCACGCACATGGTGAGCTGATTTTTGACAAGGGTTCTAACA 641
                            v    ivi  iivi     v ii       i         v i  v 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_42541044_4    642 GCTTTTAGTGGGGGAATGAACAGGCTCTTCAACAAATGGTACTGGGAAAA 691
                         v v  i i     i  -   i  v  i             i      v  
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_42541044_4    692 CTGGATATCCACATTCAAAAGAATCAAGTTGAACCCCTACCTCATACCAT 741
                                ?      v         v      i            i     
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_42541044_4    742 ACATAAAAATTAACTCAAAATGTATCAAAGACTCAAAGGTAAGGGCTAAA 791
                          i i                  v    ?    ii   v     i      
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_42541044_4    792 ACTATGAAGCTTTTAGAAGGCAACATAAATGTAAGTCTGTGTGGCTTTGG 841
                              i  i  i       iv      ii?    i   vi   i i    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_42541044_4    842 ATTAGGCAA-G----CACAAA-ATGACATCAAAAGCATATGGAAACAAAA 885
                         i        - ---- vi i -      i        i -i v       
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA-AGCAACAAAA 621

  chr1_42541044_4    886 --AAAAATAGACAAGTTAGACTTTACCAAAATAAAAAACTTTTGTGCATC 933
                         --         i  i  i     i i      v              v  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_42541044_4    934 AAAG-ATACTATATCAAGAAA-TGAAAAGACAACCTATGGGAATGTGA-A 980
                             - i     --       -             i ii -    v  - 
  L1M4_orf2#LINE/    672 AAAGGACACTAT--CAAGAAAGTGAAAAGACAACCCACAG-AATGGGAGA 718

  chr1_42541044_4    981 AAACATGTTCAAACATGTTGTTATATATCTAATAAGGATTTAGAATCTAC 1030
                            i  v v    ------- i        i      ivi v v   i v
  L1M4_orf2#LINE/    719 AAATATTTGCAAA-------TCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_42541044_4   1031 ATTATA 1036
                          v    
  L1M4_orf2#LINE/    762 AATATA 767

Transitions / transversions = 2.00 (62 / 31)
Gap_init rate = 0.03 (15 / 544), avg. gap size = 2.00 (30 / 15)  

 780 14.47 0.66 0.00  chr1_42541044_42543005.rev     1320  1471 (491)    L1M4_orf2#LINE/L1      756   908 (0)  

  chr1_42541044_4   1320 ATCTACATTATACAA-GAACCCTTCAAACTCGACAATAAAAAGATTAAAA 1368
                            i v v    i  -    i   vv     i i          iv  v 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_42541044_4   1369 ACCCAGTTAAAAAGTGGGCAAAGGATATGAAAAAACATTCCTCCAAAGAA 1418
                              i  ?    i            v    v i     i          
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_42541044_4   1419 GATACACAAATGGCCAACAAGCACATGAAAAGATGTTCAACATCATTAGT 1468
                             i            i                 i         ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_42541044_4   1469 CTT 1471
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.01 (1 / 153), avg. gap size = 1.00 (1 / 1)  


2505 16.69 3.37 10.10  chr1_42651132_42653223.rev      346  1058 (1034)    L1M4_orf2#LINE/L1        1   665 (243)  

  chr1_42651132_4    346 TGGAAAGACATTC-ATGTTCATG-ATTGGAAAACT----ATTGTTACAAT 389
                                 i  i -         -       i   ----       vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_42651132_4    390 GTAAATACTATCCAAAGCTATCTACAGATTCAATATAATCCCTATCAAAA 439
                          vv      vi     viv              iii              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_42651132_4    440 TTCCAACAATATTTTTTGCAGAAATAAAACAATCC-ATCCTAAAATTTGT 488
                          i   i viiv              vi -   v i-           ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr1_42651132_4    489 ACAGA---GCCTAAAGGGACCCCAAACAGCCACAACAATCTTGAAAAAGA 535
                          ii  ---  ---         vi  i     v                 
  L1M4_orf2#LINE/    150 ATGGAAATGC---AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_42651132_4    536 AAAACAAAAGTTGGAGGACTCACACTTTCTGATTTCAAAACTTACTACAA 585
                          i      -                  i ii                   
  L1M4_orf2#LINE/    197 AGAACAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_42651132_4    586 AGCTGCAGTGTTCAAAACAGTGTCATAATTGAATAAAGACAAATATATAG 635
                             i    iv    i       vi  v v v    i  i i i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_42651132_4    636 ACCAAGGGAATACAATAGACATCCCAGAAACAAACTCTCGCATATTTGAT 685
                          i   v      v   v  v vi       i    i -------------
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC------------- 332

  chr1_42651132_4    686 CTTGCATATTTGATATTTAAATGTTTGGTAGAACGAAGCCATCAAGTCTA 735
                         -----   i-----     ------    -------------   -----
  L1M4_orf2#LINE/    333 -----ATAC-----ATTTA------TGGT-------------CAA----- 348

  chr1_42651132_4    736 GGGCTTTTCTTTGTTGAATGATTTTCAACAAGAGTGCAAAGAC-----GA 780
                         -------------    ----     i     i    v     -----i 
  L1M4_orf2#LINE/    349 -------------TTGA----TTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_42651132_4    781 TGGAGGAAAGAA-AGTTTTCT-AGTAAATGGTGATAAAACAAC-----AT 823
                            -        -   i  i - ii        v iii     ----- ?
  L1M4_orf2#LINE/    382 TGG-GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_42651132_4    824 CCACATG-AAAAAAACTAAGTTAGACACTTACCTTACACTATTCACAAAA 872
                                -    i  iv     i   v i     i    i  vi      
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_42651132_4    873 ATTAATTCAAAAAGGATAAAAAGACCTAAACACAAGAGCTAAAACTGTAA 922
                              i      v    v ? -        iii             i   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWA-GACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_42651132_4    923 AATTCTTTTGCAGAAAACTTAGGGGGAACTCTCCATGACTATGGATTTGG 972
                           i    v- v       v    ? v  v   i i    iv   i  v  
  L1M4_orf2#LINE/    530 AACTCTTA-GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_42651132_4    973 CAATGATTTCTTGGATATGACATCAAAGACACAGGCAACAAAAGAAAAAT 1022
                              i      i         i    ii    i               v
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_42651132_4   1023 TTAA-AAACTGTATTGCATAAAAACTAAAAACTTTTG 1058
                          vi -   i  v i v   v    i            
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.83 (75 / 41)
Gap_init rate = 0.03 (23 / 665), avg. gap size = 4.17 (96 / 23)  

 956 16.45 3.46 0.87  chr1_42651132_42653223.rev     1371  1601 (491)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr1_42651132_4   1371 AAATAACACTGTCAACAAAGTAGAAAGGCAACCTACAAAGTAGGAGAAAA 1420
                            vi     i    v     ii    i     i   i i i        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_42651132_4   1421 TATTTGCAAATCATGTATCTGATAAGGAATATTAACATCTAGAATATACA 1470
                                       i            i i-  i-i   i        i 
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGAC-TTG-TATCCAGAATATATA 769

  chr1_42651132_4   1471 GAGAACT-TTAAAACTTA-TAAGAAAAAC-CAAA---CCTAATTCAATAA 1514
                         i      -   v    i -   v     v-    ---  i    ?  v  
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_42651132_4   1515 TGAGGAAATAATTT-AATAGATATTTCTCCAAAGAAGATAAACAAATGAC 1563
                           i v   vi    -      i                  v       i 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_42651132_4   1564 TAATAAACACCTCAAAAGATGCT-AACATTAATAATCAC 1601
                         i     i   v v          -     i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.36 (26 / 11)
Gap_init rate = 0.03 (8 / 237), avg. gap size = 1.25 (10 / 8)  


3665 23.07 0.99 0.99  chr1_42757247_42761640.rev     2998  3903 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_42757247_4   2998 GAAAGATATTCCATGTTCTTGGATTGGAAGAATCAATATTGTTAAAATGT 3047
                                  i        v            v i           i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_42757247_4   3048 CCATATTACCAAAAGCAATCTACAGATTCAATGCAATCCCTACCAAAATA 3097
                          v   i v  v   vii              i          i      v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_42757247_4   3098 CCAATGACATTCTTCACAGAAATAGAAAAAACT-ATCCTAAAATTTATAT 3146
                            iivi v  i  ii       v  v  i-  -           i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr1_42757247_4   3147 GAAACCACAAAGGACCCAGAATAGCCAAAGACA-TCCTAAGCATAAAGAA 3195
                          i  vii   i                  -   -  i i iv vi     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGAA 200

  chr1_42757247_4   3196 CAAAACTGGAGAAATCACATTACGTGCCTTCAAATTATAC-ACAGAGCTA 3244
                             ii     i v     i v viivi      viv   -   i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_42757247_4   3245 TGATAACCAAAATGGTATAGTACTGGCATAAAAATAGACACATAGACCAA 3294
                         iii   i   i ii  i i            ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_42757247_4   3295 TAGAACAGAATAGAGAACCCAGAAACAAATCCACACACCTACAGTGAACT 3344
                          i   i     v    ii       i   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_42757247_4   3345 CATTTT-GACAAAGGTGCCAAGAACATACACCAGGGAAAAGATAGTCTCT 3393
                         v     -     i          v   v  vii      ii       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_42757247_4   3394 TCAATAAATGGTGCTGGGAAAACTGGATGTCCATATGCAGAAGAATAAAA 3443
                             i              v        i?   i     i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_42757247_4   3444 CTAGATCCCTATCTCTCACTGTATACAAAAATCAAATCAAAATTGATTAA 3493
                         i i  i     i   v   ii           i  v       v   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_42757247_4   3494 GGACTTAAATCTAAGACCTCAAAGTGTAAGAGTACTATAAGAAAACACTG 3543
                         i   i     v     v  v   v i   i v vi  v         iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_42757247_4   3544 GGGAAATTCTCCAGGATATTGGTCTGTGAGAAAAT---TTCTTGAGTAAT 3590
                          ? v  v   i iv  iv    ---  v  iv   ---     iii  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGG---GTTAGGCAATGGTTTCTTAGATATG 597

  chr1_42757247_4   3591 ACCCCACAAGTGCAGGCAACCAAAGCAAAAATGGACAAATGGAATCACAT 3640
                           v   v   ii  i     v    v      i  i    v i iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_42757247_4   3641 CAAG-TTAAAAAAAATCTTCTGCACAGCAAAGGAAACAATCAACAAAGTG 3689
                            i-       ----   i  ii vv       v  v     v      
  L1M4_orf2#LINE/    648 CAAAATTAAAAA----CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_42757247_4   3690 AAGTGACAACCCATGGAATAGG-GAAAATATTTGCAAAATGCCCATCTGA 3738
                           iv         ii    i  -               viiivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_42757247_4   3739 CAAGGGTTTAATAACCAGAATATATAAGGAACTCAAACAACTATGTAGGA 3788
                         i     vi vi  v             i      vv      vvi  iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_42757247_4   3789 AAAAATCCAATAATCTGATTTTAAAATGGTCAAAATATTTGAATAGACAT 3838
                             iv v     i ii   ?v       v    iv              
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_42757247_4   3839 TTCTGAAAAGAAAACATACAAATGGCAAACAGGCATATGAAAAGGTGCTC 3888
                             vv      i i           v  i i   i        i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_42757247_4   3889 AACATCATTGATTAT 3903
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (128 / 77)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.64 (18 / 11)  


 998 23.97 1.24 0.41  chr1_42781398_42786755     3325  3566 (1792)    L1M4_orf2#LINE/L1        1   244 (664)  

  chr1_42781398_4   3325 TGAAAAGATATTA-ATGTTCATGAATCGAAAGAATTAATATTGCTAAAAT 3373
                           i        iv-         i  i i    v         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_42781398_4   3374 GCCCATACCACCCAAAGCAATCTATAGGTTCAGTGCAATACCTATCAAAA 3423
                          v v    iv      vii     i  i    ii     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_42781398_4   3424 TTCCAA-TGTCATTTTTCGTAGAAATAGAAAAAACAGTCCTAAAATTCAT 3472
                          i   i-  i -     i i      v  v  iviii             
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_42781398_4   3473 GTGGAACTACAAAACCCCCA-AATAGCCAAGGCAATATTCAGCAGAAAGA 3521
                         i     v i   iivv    -         ii    v  v iv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_42781398_4   3522 ACAAAGCTGGAGGCCTCATACTACCTGATTTCAAACTATATTACA 3566
                               i      v    i   v  ii        viv  i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

Transitions / transversions = 1.90 (38 / 20)
Gap_init rate = 0.02 (4 / 244), avg. gap size = 1.00 (4 / 4)  

 413 24.11 3.57 0.89  chr1_42781398_42786755     3910  4021 (1337)    L1M4_orf2#LINE/L1      242   356 (552)  

  chr1_42781398_4   3910 ACAGAACTACAGTAATTAAAACAACATGGGACTGGCATTAAAACAGACAC 3959
                            i i          i  i   iii   v        v ii i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_42781398_4   3960 ATTGACAAAATGAAACAGCATAGAGAGCTTAAAAACAAACCCACACATTT 4009
                           v  i-v    i  i  v  v     iii i   i       i      
  L1M4_orf2#LINE/    292 ATAGAT-CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_42781398_4   4010 A----AAATTGATTTT 4021
                          ----v          
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTT 356

Transitions / transversions = 2.86 (20 / 7)
Gap_init rate = 0.02 (2 / 115), avg. gap size = 2.50 (5 / 2)  

2064 23.25 2.10 2.62  chr1_42781398_42786755     4294  4865 (493)    L1M4_orf2#LINE/L1      340   908 (0)  

  chr1_42781398_4   4294 TACAGTCAGTTAATTTTTTGACAAAGGATG--AAAATGA--CATTGAGAA 4339
                           ii    i  i     i-     i  -  --  i iv --  v  i i 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTC-GACAAGGG-TGCCAAGACCATTCAATGGGGA 387

  chr1_42781398_4   4340 AAGGACAGTCCCTTCAACAAAACGGTATTGAGAAAACTGGATATCTATGT 4389
                            i i    ii         -i   ii  i  v         ? i ii 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_42781398_4   4390 GCAGAAGAATGAAAGTGGACCGTTACCTAACACCACATTAAAAAATCAAC 4439
                            i         iv      vi     v      i  vv      i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_42781398_4   4440 TCCAAATGGATTAAAGACTTAAAGACAAGACCTGAAATTGTAAAACTACT 4489
                           v        i ?    i    vii    v  i   i i       vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_42781398_4   4490 AGAAGAACACTACATAGGGGAAAAACTACATGATATTGACCTGGACAACA 4539
                                - --       ? v   v  v i   iv   ivi i i   ii
  L1M4_orf2#LINE/    537 AGAAGAA-A--ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_42781398_4   4540 ATTTTTCCAATGTGACACGAAAAGCTCAGGGAACAAAAACAAACATATAC 4589
                         i   i ivi  i      v      v  i v       iv   v   v i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_42781398_4   4590 AAATGGGATGGGATTATATCAAACTAAAAAGCTTCTGCACAGCAAAAGAA 4639
                             v   i----  -i      v v    i   i  ii vv    i  v
  L1M4_orf2#LINE/    634 AAATTGGAC----TT-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_42781398_4   4640 ACAATTAACAGAGTGAAGAGGCAACCTATGGATTGGGAGAAAATATCTGT 4689
                           v  i  v i      i  i     i ii  v             i  i
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_42781398_4   4690 AAGCTACACATCTGATAAGGGATTAATATCCAAAATATATAAGGA--TCT 4737
                           iii i i             i vi      i         i  --   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_42781398_4   4738 --CAACTCAATAGCAAGAACACAA----CCCAATTAAAAAGTAGGCAAAG 4781
                         --          ii  i  v    ----       ?    i i       
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_42781398_4   4782 GGCCTGAATAGACATTTCTCAAAAAAAGACATACAAATGGACAACAGATA 4831
                          iii                v   i    i          v   i iii 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_42781398_4   4832 TATGAAAAAAAAAAAGCTCAACATCATGAATCGT 4865
                         i       i v----           ????????
  L1M4_orf2#LINE/    879 CATGAAAAGAT----GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.39 (91 / 38)
Gap_init rate = 0.02 (13 / 569), avg. gap size = 2.08 (27 / 13)  


 855 22.73 3.72 2.89  chr1_42842233_42848790.rev     4323  4564 (1994)    L1M4_orf2#LINE/L1        6   249 (659)  

  chr1_42842233_4   4323 AGACATCACATTCTCATGGATCAGAA---TTAATACTGTTAA-----CAA 4364
                            i   v   vi        ii   ---      i      -----   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_42842233_4   4365 TACTGCCCAAAACAATCTATAGATTCAATGCAATCTCTATCAAAATACCA 4414
                             v      vii     i        i      i          v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_42842233_4   4415 A-TGTCATTTTACATAGAATTAGAAAAAACAATCCTAAAATTCATACGGA 4463
                         i-  i v    -iii    v v  v  ivii               i   
  L1M4_orf2#LINE/    106 GCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_42842233_4   4464 ACCACAAAAGAGCCTGAATAGCCAAAGTAATCCTGAACAACAACAAAAAA 4513
                          vii   ii  v  v           ii    i    ----  -- i  i
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA----AA--AGAAG 198

  chr1_42842233_4   4514 AACAAAGCTGGAGGCATCACATTACTTGACTTCAAAATATATTAGAAGGC 4563
                                i      vv     i v iii i       iv  i  v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_42842233_4   4564 T 4564
                          
  L1M4_orf2#LINE/    249 T 249

Transitions / transversions = 2.06 (37 / 18)
Gap_init rate = 0.02 (6 / 244), avg. gap size = 2.67 (16 / 6)  

 864 26.47 2.94 0.00  chr1_42842233_42848790.rev     4930  5133 (1425)    L1M4_orf2#LINE/L1      244   453 (455)  

  chr1_42842233_4   4930 AAGGCTATAGTACCAAAAACAGCAAGGTATTGGTATAAAAACAGACACAC 4979
                           i    i    viv  i    iiv    i   i    ii i     i i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_42842233_4   4980 AGACCAATGGTACAGAATAGAAAACCCAGAAATAAATCCACATCTTTACA 5029
                            i      v i     v  i ii           i   i iv    ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_42842233_4   5030 GCCAACTGACTTTTGATAAAGGTGCCAAGAATATGCACTGGAGAAAGGAC 5079
                          i   i   i   i  i  i          vi  v  v   i     i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_42842233_4   5080 ACCCTCTTCAATAAATGGTGCTAAGAAAATTGGATATCCATA------AG 5123
                          vi  i     i          ii  v  i      ?   i ------  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_42842233_4   5124 AATGAAACTG 5133
                               ii  
  L1M4_orf2#LINE/    444 AATGAAGTTG 453

Transitions / transversions = 3.82 (42 / 11)
Gap_init rate = 0.00 (1 / 210), avg. gap size = 6.00 (6 / 1)  

 327 17.53 21.65 3.09  chr1_42842233_42848790.rev     5429  5525 (1033)    L1M4_orf2#LINE/L1      439   553 (355)  

  chr1_42842233_4   5429 AAAAGAATGAAACTGGTCCCTTATCTCTTCCTATATACAA-------CTC 5471
                                    ii   v   i  i   viv i        -------   
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_42842233_4   5472 AAGATGGATTAAAGACTTAAA--------------CTATAAAAACTATTC 5507
                           i      i ?    i    --------------        -  v  v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTA 537

  chr1_42842233_4   5508 GAAAAAAAATCATAGGGG 5525
                            i    --      ? 
  L1M4_orf2#LINE/    538 GAAGAAAA--CATAGGNG 553

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.03 (4 / 115), avg. gap size = 6.00 (24 / 4)  

 785 23.45 11.07 1.30  chr1_42842233_42848790.rev     5761  6067 (491)    L1M4_orf2#LINE/L1      572   908 (0)  

  chr1_42842233_4   5761 GGTTCCAGGCAAAGATGTCATGACTAAGGATGCAAAAGCACAACTGTAAT 5810
                             --      v i v  v iiv  v ivvv           -- i  i
  L1M4_orf2#LINE/    572 GGTT--AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GCAAC 617

  chr1_42842233_4   5811 AAAT------ATAGACAAATGCGATCATATTAAACTAAAAAGCTTCTATA 5854
                            v------     i    vv  iivi  i   v v    i   i i i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_42842233_4   5855 CAACAAGGGGAA--A-CAACAGAGTGAAGAGAAAACTTACTGAATGGGAG 5901
                          vv   i  iv -- -   v i      i   v   ii  v         
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_42842233_4   5902 AAAATATGT-CAA---------CT--TAA--------TGTCCAGAGTATA 5931
                                v -   ---------  --   -------- i      i    
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_42842233_4   5932 CAAGGAACTCAAATAAC-----AATAAAAAAACAAATAATCCCATTAAAA 5976
                         i  i      vv i   -----        i        i  v   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_42842233_4   5977 AGTGGGCTAAGGACATGAATAGACATTTCTCACATGAAAATATTCAAGCA 6026
                          i     v     iv                vv v   i    v   iii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_42842233_4   6027 GCCAACAGATACCTGGAAAAATGCTCAACATCACTAGACAT 6067
                              i iii  v  i   i             ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (40 / 31)
Gap_init rate = 0.03 (10 / 337), avg. gap size = 3.80 (38 / 10)  


3256 25.11 1.33 0.88  chr1_43006939_43009836.rev     1504  2407 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_43006939_4   1504 TGGAAAATCATTTCATGCTCATGGATAGGAAGAACCAACATTGTTAAAAT 1553
                               ivi  ii    i        v      vii  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_43006939_4   1554 GGCCATACTGCCCAAAGCAATTTACAGATTCAACACTGTTCCTATCAAAC 1603
                            v     v      vii  i            i vi i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_43006939_4   1604 TACCAATGACATTCTTCATAGAATTAGAAAAAACT-ATTCTAAAATTCAT 1652
                          v   iivi v  i  iii    v v  v  i-  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_43006939_4   1653 GTGGAACTTAAAAAAACAGCCTGAATAGACAAAGGAATCCTAAGCAAAAA 1702
                         i     v vv  iii  --  v      v    iv    i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_43006939_4   1703 GAACAAAGCTGGAGGCATGACACATTACCCAACTTCAAACTATGTTACAA 1752
                                 i      vv --    i v     i      viv ii     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACT--CACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_43006939_4   1753 GGCTACAGTAATCAAAACAGTATGGTACTGGTACAAAAACAGACACATAA 1802
                         i              i     i         i i  ii i     i   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_43006939_4   1803 CCCAATAGAACAGAATAGAGAGCCCAGAAATAAAGCTGTACACCTATAAC 1852
                         vi    i   i     v     i           v ii    ii   iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_43006939_4   1853 CATCTGATCTTTGAGAAAATCAACAAAAACAAGCAAAGAGGAAAGGACTC 1902
                           vi    i  i  v  iiviiv   i v  vv   v i      i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_43006939_4   1903 CCTATTCAATAAGTAGTACTGGGATAACTGGCTAGCCATATGCAGAAGAT 1952
                         i  v     i  i i  i      i      v  ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_43006939_4   1953 TGAAACTGGAACCTT-CCTTACACTATATACAAAAATCAACCCAAGATGG 2001
                             ii    v  i -   i    i            i   i   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_43006939_4   2002 ATTAGAGACTTAAATGTAAAACCTAAAACTATAAAAATCCTTGAAGAAAA 2051
                           i ?    i         i v              v  i v        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_43006939_4   2052 CCTAGG---AAATACCATTCTGGACATAGGCCCTGGCAAAGATTTCAT-G 2097
                          v    ---    -- -   vv   v v  viiv     v i    v - 
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_43006939_4   2098 AAAAGATGCCAAAAGCAATTGTGACAAAAACAAAAATTGACAAATGGGAC 2147
                          v v  ii         vvv ii      iv      v  i    v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_43006939_4   2148 TTAATTAAACTAAAGAGCTGCCACACACCAAAAGAAACTATCAATAGAAT 2197
                           v  i   v v  i i  viiiii vi    i  v        v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_43006939_4   2198 AAACAGACAACCCACAGGATGGAATAAAATATTTTCAAACTATGCATCTG 2247
                         i  v             i    i v         v    ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_43006939_4   2248 ACAAAGGTCTAATATCCAGAATCCATAAGGAACTTAAACAAATTAACAAG 2297
                          i  i  v  vi          vi    i     ivv    v i  i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_43006939_4   2298 CAAAAAACAA----TCCCATTAAAAAGTGGGAAAAGGACATGAACAGACA 2343
                         v    i    ----i  v   ?    i    v      iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_43006939_4   2344 CTTC--AAAAGAAGACATACACGTGGCCAACAAGCATATGAAAAAATGCT 2391
                         i   --v        i     vi       i     i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_43006939_4   2392 CAACATCACGAATTAT 2407
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


3036 27.27 1.00 0.33  chr1_43029288_43033576.rev     2897  3798 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_43029288_4   2897 TGGAAACATATCCCATGCTCATGGATGGGTAGAATAAATATTGTGAAAAT 2946
                               v          i        v  v   v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_43029288_4   2947 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTGCCT-TCAAA 2995
                          i v     v  v   vii       i      i     i-   -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC-CCTATCAAA 99

  chr1_43029288_4   2996 ATACCACCATCATTCTTCACAGAA-TT-ATAAAAAAATTCTAAAATTCAT 3043
                           v   v vv v  i  ii     -  - i  ivvi  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_43029288_4   3044 ATGGAACCAATAAAGAGCCCA-CATAGCCAAAGCAAGACTAAGCAAAAAG 3092
                               vi-ii  i ii    -v         i   vvi i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_43029288_4   3093 AACAAATCTGGAGGCATCACACTACCTGATTTCAGACTATACTATAAGGC 3142
                               vi      vv       v  ii      i viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_43029288_4   3143 CATAGTCACCAAAACAGCATAGTACTAGTATAAAAATAGGCACATAGACC 3192
                         i i   v i   i    ii i     i i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_43029288_4   3193 AATGGAACAGAATAGAGAACCCAAAAATAAACCAA-ATACTTACAGCCAA 3241
                                i     v    ii   i         v - i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_43029288_4   3242 CTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAGGGACACCCT 3291
                         i    i   i    i vviv   i v   vv i       i i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_43029288_4   3292 TTTCAACACATGGCACCAGGATAATTGGCTAGCCACAAGTAGGAGAATGA 3341
                                 v    ii ii   i  i   v  ?     v i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_43029288_4   3342 AACTGGATCCTCATCTCTCACCTTAAACCAAAATCAACCCACGAAGGATT 3391
                          ii    i  ii i   v    v  v  v     i   i  vi v    i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_43029288_4   3392 AAGGACTTAAATCTAAGACCTGACACTAGAAAAATACTAGAAGATAACAC 3441
                          ?i   i     v     v  i v    v    v vi       v    i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_43029288_4   3442 TGGAAAAACCCTTCTAGACATTGGCTTAAG----GATTTCATGACCAAGA 3487
                         v  ?iv  vi    vv   v    v   i ---- i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_43029288_4   3488 ACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGAACTTAATT 3537
                         vv         v v    i    iv   i   i   iv v i    v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_43029288_4   3538 AAACTAAGGAGCTTTTGCATGGCAAAAGGAATGGTCAGTAGAATAAACAG 3587
                            v v ii i      iiivv    i iv ivi   iv i i i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_43029288_4   3588 ACAACCCACAGAGTGGGAAAAAATCTTCACAATTTATGCATTTGACAAAG 3637
                                     i     i     v  ii   v i  ii  i   i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_43029288_4   3638 GACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGCAAGAAATAA 3687
                             vi          v  i  v      vv    v   ii  v   -  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AA 797

  chr1_43029288_4   3688 AACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGATAATTCT 3737
                         i     i  i  v  i?    i     v     iv        i v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_43029288_4   3738 CAAAAGAAGATATACAAATACCCAACAAACATATGAAAAAATGCTTGACA 3787
                          v                 iv    i  i  i       i     ii   
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_43029288_4   3788 TCACTAATGAT 3798
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


 555 22.17 4.25 9.43  chr1_43247804_43255780.rev      298   509 (7468)    L1M4_orf2#LINE/L1       13   213 (695)  

  chr1_43247804_4    298 CCATGTTCATAGATTGGAAGATATAATATTGTTAAGAAGTCAATATTACC 347
                                   i          iv              v v     i v  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_43247804_4    348 AAAAGGGATCTACAGATTTGACATAATGTCTATCAAAATCTCAA-TGATT 396
                         v   vv            ii  ii   vi           i  i-  vi 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_43247804_4    397 TCTTTTTAGAAATTAAAAAATTACCTGGGCAATGATTCTATGAAAAAAAA 446
                          i   vi       i v  ---------  --    i   -------   
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAA---------GC--TGATCCTA-------AAA 144

  chr1_43247804_4    447 TCCACGTCAAACTAAGATAAAATCTCAAGGGACAAAACAATC-------- 488
                          i  ii vi  v ivi vii vi vv  vi v          --------
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_43247804_4    489 GAAAAACAAAGTCGGGGAGGA 509
                            i        i  --    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGG--AGGA 213

Transitions / transversions = 1.35 (27 / 20)
Gap_init rate = 0.03 (6 / 201), avg. gap size = 4.83 (29 / 6)  

3228 26.65 0.55 0.55  chr1_43247804_43255780.rev     4858  5765 (2212)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_43247804_4   4858 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4907
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_43247804_4   4908 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4957
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_43247804_4   4958 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTC 5004
                          v   i-       i  -i     -   -- v  i  - iii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_43247804_4   5005 ATATGGAACCAAAAAAGAGCCCGCATTACCAAGTCAATCCTAAGCCAAAA 5054
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_43247804_4   5055 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5104
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_43247804_4   5105 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5154
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_43247804_4   5155 CAATGGGACAGAAC--AGAGCCCTCAGAAACAACGCCGCATATCTACAAC 5202
                               i i    i--    i  --     i  vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_43247804_4   5203 TATCTGATCTTTGACAAACCTGAAAAAAACAAGCAATGGGGAAAGGATTC 5252
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_43247804_4   5253 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5302
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_43247804_4   5303 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5352
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_43247804_4   5353 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCCAGAAGAAAA 5402
                           i ?    i    i  v   v       i      vi ii         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_43247804_4   5403 CCGAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5452
                          vv   ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_43247804_4   5453 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5502
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_43247804_4   5503 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5552
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_43247804_4   5553 CAGGCAACCTAAAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5602
                         v  i     i v i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_43247804_4   5603 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5652
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_43247804_4   5653 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5702
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_43247804_4   5703 CTCAAAAGAAGACATTTATGCATCCAAAAAACACATGAAAAAATGCTCAT 5752
                            v        i  vi viiiv    v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_43247804_4   5753 CCTCACTGGCCAT 5765
                          v   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

3066 17.26 4.56 0.00  chr1_43247804_43255780.rev     6485  7098 (879)    L1M4_orf2#LINE/L1      189   830 (78)  

  chr1_43247804_4   6485 GAAAAAGAAAAACAAAGTCAGAGG--TC-----TCTTGATTTCAAAACTT 6527
                                  i        ii    --  -----  iii            
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_43247804_4   6528 ACTATAAAGCCACAGTAATAAAAACAGTGTGGTACTGGCATAAAGATAAA 6577
                             i     i        v  i                    i    i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_43247804_4   6578 CATAAAGACCAATGGAATAGACTGGAGAGCCCAAAAATAAACCTCTA--- 6624
                             v   i            v v     i   i         iv  ---
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_43247804_4   6625 -TGTGGTCAAATGATGTTTGACAAGGGTGTCAGTACCATTAAATAGGAAA 6673
                         - i       v    v  i          i  iv      v   i  i  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_43247804_4   6674 AGAACAGTCTTTTCTGCAAATGGTGGTGTGAAAACTGGATATCTACATGC 6723
                             i         vi         v  v  v         ? i      
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_43247804_4   6724 AAAAGAATGAAGTTGGACC------TTAAACCACATACAAAAAGTAACCC 6767
                                            ------ i v    i         v    i 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_43247804_4   6768 AAAATGGATCACAGACCTAAACGTAAGACCTAAAACTATAAAATGTGTAG 6817
                                    ?         i      v              iviv   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_43247804_4   6818 AAGAAAACATAAGGGGAAG-CTTCATGACATTGGATTTGGCAGTGATTTC 6866
                                    i ? v  i-    i    v    i  v    i  i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_43247804_4   6867 TTGAATATTACACCAAAAGCACAGGCAACAAAATAAAATATAGATCACTT 6916
                           ii    v              i         v    v      v v  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_43247804_4   6917 GGACTACATCAAAATTTAAAATTCCTGTGCCTCAAAAGTCACAAGAAACA 6966
                              v          v    i ii     i     i v   v vv  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_43247804_4   6967 GAGTGAAAGGGTAACCAATTGAATGAGTGAATATATTCGCAAATCATATA 7016
                         i       i ii    v iv     i v   v     i            
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_43247804_4   7017 TCTGAAAAGGGGTTAATATCCAGAATGTATAAAGAATTTCTACAAC--AA 7064
                              v     ii vi          i         i ii      --  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_43247804_4   7065 CAGCAAAAA--C------TCCAATTTAAAAATGAGCAAAGGA 7098
                         i ii     -- ------i      ?       i        
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.62 (63 / 39)
Gap_init rate = 0.01 (8 / 642), avg. gap size = 3.50 (28 / 8)  

 603  8.51 0.00 0.00  chr1_43247804_43255780.rev     7394  7487 (490)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_43247804_4   7394 AAAAATGGGCAAAGGATATGACTAGACATTTTTCTAAAGAAGATATACAA 7443
                                          v   v         i  i               
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_43247804_4   7444 ATGGCTAATAAACACATGAAGAGATGCTCAACATCCCTAACCAC 7487
                              i     i        i              v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


4665 15.50 4.36 0.11  chr1_43322792_43328655.rev     4503  5373 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_43322792_4   4503 TGGAAA-ATATCTCATGCTCAAGAATTGGAAGGCTTAGTATTGTTAAGAT 4551
                               -     i    i   v i        i    i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_43322792_4   4552 GGCAACACTCCCCACATTGATCTATAAATTCAATGCAATCCCGGTGAGGA 4601
                              i        v         i i      i        vi v ii 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_43322792_4   4602 TCCCAGATGGCTTCTT-GTAGAAATTGAAAAGCTGACTGTAAAATCCATA 4650
                               v  v   i  - i         v       iiv      i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_43322792_4   4651 TGGAATTGCAAGGGACACAGACTACCCAAAACAATCTTGATAAAGTAGAC 4700
                              v          v    v  v               v    v   v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_43322792_4   4701 TACATTTGCAAGATTCACAATTCCCAATTTTAAAGTTTGCTACAAAGCAG 4750
                         i v v   v i  i     v          i   ii  i         vi
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_43322792_4   4751 CAGTAATCAAGACAGTGTGGTACTGGCATAAAGATAGACA----GATCAA 4796
                                                        i        ----      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_43322792_4   4797 TGGAACAGAATTGGAAGTCCTGAAACAAACCCATGT-------GTCAACT 4839
                              i       ii     v    i        ii-------     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_43322792_4   4840 GATTTCCAACAAGA-TGCCAAGACTACTCAATGGAGAAAGACTAGCCTTT 4888
                              i i     i-         i i       i      v   i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_43322792_4   4889 TCAACAAATGATGCTGTGACGACTGGATATCTACATGCCAAAGAATGAAG 4938
                                   i     v   i        ? i      v           
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_43322792_4   4939 TTGGACCCCTATACCATCCCATATACTCAAATGAATTCAAAACGGATTAA 4988
                                    ivi  iv        vv    v  i      i    i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_43322792_4   4989 AGACCTAGATGTAAGAGCTAGCACTATGAAACTCTTAGAAGAAA-TACAG 5037
                                i            iv     i                -i i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_43322792_4   5038 AGGTAAATCTTCATGGCCTC-----AGGCATTGGCTTCTTAAATATAACA 5082
                         i?          i  i   i-----     v   i      i    i   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_43322792_4   5083 TGGAAAGCACAACCAACAAAAGAAAAA-TAGATAAATTCAATTTCATCAA 5131
                         ivi         v              -          vi i        
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_43322792_4   5132 AATTGAAAACTT-----CATCAAAAGACAACATCAAAAAAGTGAAAAGAC 5176
                             i       ----- v     i    vi     i             
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_43322792_4   5177 AACCCACAGAATGGGACATAGTATTTGCAAATCACATATCTGATAAAGGA 5226
                                         v v i             i           i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_43322792_4   5227 CTTATATCTAGAAT-TATAAATAACTGTTACAACTCAATAATAAAAAGAC 5275
                            i    i     -      v    v                       
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_43322792_4   5276 ATATGACTCAATTTTTTAAATGGGCAAAAAATCTGAATAGACATTTCTTC 5325
                          v  i  i     ?vv-           ii  i               i 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_43322792_4   5326 AAAGAAGAATTAGAAAT------T-----CTTGAAAAGACGTTCATCATT 5364
                                 vv  v    ------ ----- v        i i   v   i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_43322792_4   5365 AATCACCAG 5373
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.73 (83 / 48)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.00 (39 / 13)  


 823 15.32 0.00 0.00  chr1_43459373_43462969     1606  1729 (1868)    L1M4_orf2#LINE/L1       10   133 (775)  

  chr1_43459373_4   1606 ATCTCATGTCCATGAATTGGAAGGCTTAATATTGGTAAGATGATAATACT 1655
                            i     i    i        i          v       ii      
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_43459373_4   1656 TCCCAAATTGGTCTATAGATTCAATGCAGTCCCTATCAGAATCTCAGCTG 1705
                         i         i    i        i   i         i    i      
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_43459373_4   1706 GCTTCTTTGTAGAAATTGGCAAAC 1729
                         v   i    i        i   i 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGC 133

Transitions / transversions = 8.50 (17 / 2)
Gap_init rate = 0.00 (0 / 124), avg. gap size = 0.00 (0 / 0)  

4095 14.69 3.74 1.80  chr1_43459373_43462969     2332  3107 (490)    L1M4_orf2#LINE/L1      118   908 (0)  

  chr1_43459373_4   2332 GCCGAAATTGGCAAAC--ATTTTTAA-TTCATATGGCATTGCAAGAGACC 2378
                           v       i   i --  ii v  -         v v      i    
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr1_43459373_4   2379 CAGCCAAAATAGCCAAAACAATCTTGAAACAGAGGAATGAAGTTGGAGGA 2428
                            ----                      v   i   ii           
  L1M4_orf2#LINE/    168 CAG----AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_43459373_4   2429 CTCACATTGCCAGATTTCAAAAGTTACTACAAAGCAACAAAAATCAAGAC 2478
                               i v  vi         v            v   iv         
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_43459373_4   2479 GGTGTGGTACTGGCATAAGGAGAGACATATGAGATCAATCAAACAGAACT 2528
                         i                    v        -        vi  i    i 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATAT-AGATCAATGGAATAGAATT 312

  chr1_43459373_4   2529 GAGAATCCAG-----------------TATGGTCAACTGATTTTCAACAG 2561
                             i     -----------------         i        i   i
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_43459373_4   2562 AGGCGCCAAGGCCATTTAATGGGGAAAGAATAGTCTT--CAACAAATGGT 2609
                         i  i      i     i                    --           
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_43459373_4   2610 GCTGGGACAATTGGATAGCCACATGCAAAAGAATGAATTTGGACTCCTAC 2659
                                   i      ?                   v      i     
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_43459373_4   2660 CCAAACACCACATACAAAAATTAACTCAAAGTGGGTCAAATACCTAAATA 2709
                          iv -     i                   i   i   ? v        i
  L1M4_orf2#LINE/    463 CTCA-CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_43459373_4   2710 TTAGAACCAAAATTATAAAGCCCTTA-AAGAAAGCATAGAAGTAAATCAT 2758
                          v   i i    i      i i    -      i     i?       v 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_43459373_4   2759 AATTACCTCAGATTTGGCAGTGGATTTTTAGATATGACAGCAAAGATATG 2808
                         vi v    ii i  v    i   v  i            v    iii ii
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_43459373_4   2809 GGTAACAAAATCAAAAATACATAAGTTAGAATTCATCAAAATTGAAAACT 2858
                         i i       vv       v    i  i  v            i      
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_43459373_4   2859 TTTGTGCATCAAAGGACACTATCAGGAAGGTGAAAA------CCACAGAA 2902
                                v                i   i       ------        
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_43459373_4   2903 TAGAAGAAAACACTTGCAAGTCACATATCCTGTAAGAGACTTGTATCTAG 2952
                          i i      i i      i   i     ivi    i          i  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_43459373_4   2953 AATATATTAATACAAAGAAGTCTTATAACTCAATAGTAAAGTGACAGATA 3002
                                ------      v     i         i    iv    i   
  L1M4_orf2#LINE/    762 AATATAT------AAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_43459373_4   3003 ACCCAGTATCTTTTAATGGACAAAGGCTCTGAATAGACATTTCTCCAAAG 3052
                              --  i?vvv     i      v i                     
  L1M4_orf2#LINE/    806 ACCCA--ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_43459373_4   3053 AAGATAAACAAATGGCCAATAAGCACATGAAAAGATGTTCAACAGGATGA 3102
                               v                              i      vv ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_43459373_4   3103 GTCAT 3107
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.97 (73 / 37)
Gap_init rate = 0.01 (11 / 791), avg. gap size = 3.91 (43 / 11)  


3723 12.24 3.16 16.35  chr1_43619760_43625625.rev     4035  4982 (884)    L1M4_orf2#LINE/L1        1   823 (85)  

  chr1_43619760_4   4035 TAGAAAAAC-TTCTGTTTTCTTAAGTTGGAAGACTTAATATTGTTGAGAT 4083
                          i    i i- i ii v   v iii                    i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_43619760_4   4084 GGCAATATTCTCCAAATTGATATACAGATTTAATGCAATTTATATCAAAA 4133
                                i  i          v        i  i     iiv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_43619760_4   4134 TTTCAAATACCTCTTTTGCAGAAATTGACAAGATGATCCTAAAAGTCATA 4183
                          ii  iv i   i                   v           v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_43619760_4   4184 TGAAAATGCAAAGGATCCAGAAGGGCCAATATAATCCTGAAAAGGAA--- 4230
                           i        i   i      vi     v i    i      i   ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_43619760_4   4231 CAAAGTTGGAGGACTCCCACTTTCTGATTTTCAAAACTTACTGTAAAACT 4280
                                         v     i ii    -           ii   i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTT-CAAAACTTACTACAAAGCT 249

  chr1_43619760_4   4281 ACAGTAATTAAGACAGTGTAGTACTGGCAAAAGGACAGCCATATAGGTCA 4330
                                 i          i         v     i  v       i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_43619760_4   4331 ATGGAATAAAAGTAAGACTC--------------------TATGGTTAAT 4360
                                 i  v i   v  --------------------      i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_43619760_4   4361 TGATTTTCAACAAGGATGCCAAGACCATGCAATGAAGAAAAGAACAAAAT 4410
                                 i      i            v     ii    i---------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG--------- 390

  chr1_43619760_4   4411 AACAATCTTTTCAACAAATAATAGTAGGACA-CTGGATATCCACATGCAA 4459
                           i i              ii iv i     -       ?          
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_43619760_4   4460 GGGAATGAATTTGGACCCCTAACTCACACCGTGTACAAAAAACTAACTCA 4509
                         ii       v           v        i i        -i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCA 489

  chr1_43619760_4   4510 GAATGGATCAAAGATTTTTTTTTTTTTTTGGGATAAGTTCTCACTATGTT 4559
                         i         ?   ------------------------------------
  L1M4_orf2#LINE/    490 AAATGGATCAWAGA------------------------------------ 503

  chr1_43619760_4   4560 GCCCAGACTGTTCTTGAACTCCTGGGCTCATGCGATCCTCCCACCTTGGC 4609
                         --------------------------------------------------
  L1M4_orf2#LINE/    504 -------------------------------------------------- 503

  chr1_43619760_4   4610 CTCCCAAATTGCTGGGATTATAGGCATGAGCCACAGTGCCCCCACAGCCA 4659
                         --  i    --------------------------  -------------
  L1M4_orf2#LINE/    504 --CCTAAAT--------------------------GT------------- 512

  chr1_43619760_4   4660 GATCAAAGATCTTAAGAGCTAAAACTATAAAGCCCTTGGAAGAAAATATA 4709
                         -------------                  i i   i        i   
  L1M4_orf2#LINE/    513 -------------AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_43619760_4   4710 GGGCTAAATCTTCATGACTTTGGATTAGGTAATAGTTTCTTAGGTACGAC 4759
                           ?v         i    i    i     i   i         i  i   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_43619760_4   4760 ACCTAAAGCACAAGCAATTAAAGAAAAAAATAGATAAATTAGACTTCA-- 4807
                            v             iv          -          i       --
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATC 648

  chr1_43619760_4   4808 -AATTTAAAAACCTTTGTGCATCAAAGGACACTCACAGGAAAATGAAAAG 4856
                         -  v        i       v            vv  i    i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_43619760_4   4857 ACAACCCACAGAATGAGAGAAAATATTTGTAATTTATATATCTGACAAGT 4906
                                        i             i  v i          i   v
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_43619760_4   4907 AACTTGTATCTAGAATAGA--AAGAACTCCTACAATTCAATAATTAAAAA 4954
                         i         i      v --        i     i        ---   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT---AAA 795

  chr1_43619760_4   4955 AAGACAAATAACCCAATTTTAAAATGGG 4982
                                           ?v        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGG 823

Transitions / transversions = 2.86 (83 / 29)
Gap_init rate = 0.02 (14 / 823), avg. gap size = 13.21 (185 / 14)  

 498 17.02 0.00 0.00  chr1_43619760_43625625.rev     5282  5375 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_43619760_4   5282 AAAAAAAGGCAAAGGATCTGAATAAGTATTTCTCCAAAGTAGGTTTGCAA 5331
                              vi          i      iii            v  i v i   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_43619760_4   5332 ATGGCCAATAAGCACACGAAAATATGCTTGATGTCATTAGTCAT 5375
                                         i     v     ii ii   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (12 / 4)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


 221 16.67 8.33 3.33  chr1_43891054_43893348      553   612 (1683)    L1M4_orf2#LINE/L1        3    65 (843)  

  chr1_43891054_4    553 GAAATCGACATACCATGTTCATGGGTCAGAAGACCTATTAATGTTACTA- 601
                             --  i  v            i ii      i  v  v     vv -
  L1M4_orf2#LINE/      3 GAAA--GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_43891054_4    602 ---AAT-CTCCCCAA 612
                         ---   -        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA 65

Transitions / transversions = 1.00 (5 / 5)
Gap_init rate = 0.05 (3 / 63), avg. gap size = 2.33 (7 / 3)  

2636 19.12 5.17 9.67  chr1_43891054_43893348      914  1802 (493)    L1M4_orf2#LINE/L1       60   908 (0)  

  chr1_43891054_4    914 CCCCAATGTGTTTTA-AAATGCAGCACATTCTCTCAATCAAAATCCCAGA 962
                               vv  v i  - i  v  i i  v  i  --             -
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCT--ATCAAAATCCCAG- 106

  chr1_43891054_4    963 AGGCTTGGGTTTTTTTGTCTTTAAAAAATTTTTGCTTTGGTAGAAATTGA 1012
                         --------------i  i    --------     ------         
  L1M4_orf2#LINE/    107 --------------CTGCCTTT--------TTTGC------AGAAATTGA 128

  chr1_43891054_4   1013 -AAACTGATTTTAAAACTTATATAGAAATATA-GAGATTCAAGAATAGTC 1060
                         -  i     ii     i i    i     ii - i  ii  -      i 
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA-GAATAGCC 177

  chr1_43891054_4   1061 AAACCA-TTTTGAAAAAGAA---CAAAGTTGGAGGGTTTACATTACCTGC 1106
                            v  - i           ---            ii i   i v  iiv
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_43891054_4   1107 TTTCAAAACTTATCATAAAGCCAGCAGCAATCAAGATAGAGTGGTACTGG 1156
                                     ii i     i -   i        i  v          
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTA-CAGTAATCAAGACAGTGTGGTACTGG 276

  chr1_43891054_4   1157 TATAAAGATAGATATATAGATCAATGAGACAGAAAACAGAGCCCAGAAAT 1206
                         i    i      i             ii i    vvv    i        
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_43891054_4   1207 AGACCCACACATATATGGCCGATTGATTTTTCACAAAGGGGCCCAGGCAA 1256
                          i     i    v     i i         iv    i  v   v  i v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_43891054_4   1257 TTCAAAGGAGAAAGTATAGTCTTTTCAATAACTGGTTGC----ACAA--- 1299
                              v  i     v             i  v    -  ----    ---
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT-GCTGGGACAACTG 425

  chr1_43891054_4   1300 AA-----ACAAACAAAAGAAC--ACT--GATTCTTATTTCTCACCATGTA 1340
                         i -----   vi        i-- v --  ii i  ii  v      i  
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_43891054_4   1341 CAAAA-TTAACTTGAAATGGATCATGCAACCTAAACAGAAGAGCTAAGAC 1389
                              -      ii          ?i-i       iiv         i  
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWA-GACCTAAATGTAAGAGCTAAAAC 524

  chr1_43891054_4   1390 TAAAAAACGCATAGAACAAAATATAGGAGAGAAATGTTAGTGATTTTGAG 1439
                           v     v v     v    i     ? -v    v  v    ii   i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGG 573

  chr1_43891054_4   1440 TTTGGTAAAGATTTCTTAAATAGGGCAG-AAAAGCATAA----------A 1478
                           v  i  v i       i   v i  v-       i  ---------- 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_43891054_4   1479 AAAAA-----ACATTGAACTTTATCAAAAGTAAAAACTTTTGCTCTTTAA 1523
                              ----- v    i    i       v            iv   i  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_43891054_4   1524 ACAACACTGTTACAAATATTTAAAGGCAAGCCACAGCCTGGGAGAAAATA 1573
                          vi     i i vi  vi vv    i   v      vv            
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_43891054_4   1574 TT-GTGAAACATCTAC--AACAAAGGTCTTGTACTTTACTGTTGTACTTT 1620
                           - ii  v   v  i--i i  i  v      -----------------
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTA----------------- 756

  chr1_43891054_4   1621 ACTAAGTCAATAAAAAGTCAAAACAAAGTCAATACAAGACAAAGGTCTTG 1670
                         ------  ----------  i  i -------  i  -----  iv  --
  L1M4_orf2#LINE/    757 ------TC----------CAGAATA-------TATAA-----AGAACT-- 776

  chr1_43891054_4   1671 TACCTTACTATTCAGTAATAAGTAGACAAAGAGCC--AGCTAAAAATAAA 1718
                         ---     v i   i      iv       v i  -- vi?      iii
  L1M4_orf2#LINE/    777 ---CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_43891054_4   1719 CAAAG-ATATGTATAGACACTTCACCAAAGTAGACATACACATGGCAAGT 1767
                              -  v  v       i   v      v   i     v     v i 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_43891054_4   1768 AAGCACTTGAAAAGATTCTCAGCATCAAATTAGTA 1802
                               v         v    i     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (105 / 62)
Gap_init rate = 0.04 (32 / 849), avg. gap size = 4.12 (132 / 32)  


2969 23.56 3.93 2.54  chr1_43960075_43963923     2498  3363 (486)    L1M4_orf2#LINE/L1       31   908 (0)  

  chr1_43960075_4   2498 AGCCTCAGTATTGTTAAGATGTCAATTCTCTAC---TTGATCTATAAATT 2544
                           v  i i             v    v   iv ---        i i   
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chr1_43960075_4   2545 CAATGTAATCAGAATCAAAATTGCAGCAAGTCATTTTT-CGAATATCAAC 2593
                            i i    vvv        iv    v- i v     - ii v  ii  
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCT-GCCTTTTTTGCAGAAATTGAC 129

  chr1_43960075_4   2594 AA-CTTACGTTAAAATTTATATGGAAAGGCAGAAGACCCAGAAT--CTA- 2639
                           -  v ivi       i         v   iii          -- i -
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr1_43960075_4   2640 -------CTGATGAAGAAGAAGAAAGTTGGAAGATTGACAGTACCTGACT 2682
                         -------i   vi        v         i  i v   v v  ii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_43960075_4   2683 CCAGA-CCTACAATAAAGCTATCAAGATACAATCAAGATAGCGTAGTATT 2731
                         i  i - i   v i       i--  ---i        i  i  i   i 
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTAC--AG---TAATCAAGACAGTGTGGTACT 274

  chr1_43960075_4   2732 GGCAAAAGAATAGACAAATAGATCAATAGAATAGGATAGAGATCCCATAA 2781
                             v   i       v          i      i  v    vi   v  
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_43960075_4   2782 ATTGACCCACACAAATATAGTCTGTTGATCTCTGACAAAGGAACAAAGGC 2831
                           vi     i   vv   i   vi     i ii     i  vi v   i 
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_43960075_4   2832 AATTCAATGGAAAAAGGATAATTTTTTCAATAAATGATACTGGAATAATT 2881
                         v         ii    i   i i       i     i i    i i  i 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_43960075_4   2882 AGATATCTGTATGTACAAA-------TTAATCATTCACCTTGTACCTTTC 2924
                         i    ? iii   i v  i-------  iiv viii    iii   v vi
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_43960075_4   2925 ACAAAAATTAACTCAAAATGGAACCTAAATAGAC-TAAATGCAAAACCTG 2973
                                               v ---- ?    -      i  i v  i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATC----AWAGACCTAAATGTAAGAGCTA 520

  chr1_43960075_4   2974 AAACTATAATAAACTTCTGGAAGGTAACATAGA---AAATTTATGTGATT 3020
                                  --    ii i    iv       i---    i vi    ii
  L1M4_orf2#LINE/    521 AAACTATAA--AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_43960075_4   3021 TTGGGTTTGGTAATGAGTTTTTAGATATAAAACCAAAAGCAAAATTCAGA 3070
                                v  i    iv  i        i v          v  viv v 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_43960075_4   3071 AAAGAAAAATCAG-TACGTTG-ATTTTATTAAACTCCAAAACTTGTACTC 3118
                                  vi  -  vi   - i  i  i   v iv       v iiv 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_43960075_4   3119 TGTGAAGTTCACTGTTAAGTGAATGAAAAAACAAGCCACAAACTGGG-GA 3167
                          vii   vv    i i   vi i      i    v     i v    -  
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_43960075_4   3168 AAAAATT-GCAAA-CACATACCTGATTAAGGACTTGTATTCAGAATATAC 3215
                            v   -     -  i   i     v i          i         i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_43960075_4   3216 AAAGAACTCTTAAAACTCAACATTAAGAAAACAACCAACCCAATTAAAAA 3265
                                     v       i v   i  i    vi         ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_43960075_4   3266 AATGGGCAAAAGAACCAAAAAGACACCCTTTCCAGATGGTCAAAAAAGAT 3315
                          -        i  viii  v     ---    i------i    i     
  L1M4_orf2#LINE/    819 A-TGGGCAAAGGATTTGAATAGACA---TTTCT------CCAAAGAAGAT 858

  chr1_43960075_4   3316 ATGCAGATGGA-AATAAGCATATGAAAAGATGTTTG-CATTATATGTCAT 3363
                           i  i    v-        i           i ii-   i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (133 / 68)
Gap_init rate = 0.03 (24 / 878), avg. gap size = 2.33 (56 / 24)  


 370 26.06 11.52 1.82  chr1_44228385_44231643.rev        1   165 (3094)    L1M4_orf2#LINE/L1      599   779 (129)  

  chr1_44228385_4      1 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 50
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_44228385_4     51 AAACTAAAGAGCTTCTG------AA----------CAGGAAAAGAAACAG 84
                            v v  i i   i  ------  ----------  i    ivi  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_44228385_4     85 GCAACCTACAGAATGGGAGAACTTTTTTGCAATCTATCCATCTGACAAAA 134
                         i     i              vv v       vii  vi      i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_44228385_4    135 -ATTTATTTAATTTAAAA-AT-TAAAAAAATTTT 165
                         - i  i ---  ii i  -  -    i  v i  
  L1M4_orf2#LINE/    749 GACTTGT---ATCCAGAATATATAAAGAACTCTT 779

Transitions / transversions = 1.53 (26 / 17)
Gap_init rate = 0.03 (6 / 181), avg. gap size = 3.67 (22 / 6)  

 565 15.38 0.96 0.00  chr1_44228385_44231643.rev     1214  1317 (1942)    L1M4_orf2#LINE/L1        1   105 (803)  

  chr1_44228385_4   1214 TGGAAAGATATTCCATGTTCATGGATTGG-AGAATCAATATTGGTAAAAT 1262
                                    i                 -   v i       v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_44228385_4   1263 GTTTATACTACCCAAAAAAATCTACGGATTAAATGCAATCCCTATCAAAA 1312
                          viv     v      vvi      i    v  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_44228385_4   1313 TACCA 1317
                          v   
  L1M4_orf2#LINE/    101 TCCCA 105

Transitions / transversions = 0.78 (7 / 9)
Gap_init rate = 0.01 (1 / 105), avg. gap size = 1.00 (1 / 1)  

2774 25.69 0.79 0.79  chr1_44228385_44231643.rev     1999  2761 (498)    L1M4_orf2#LINE/L1      112   874 (34)  

  chr1_44228385_4   1999 TTTTTCACAAAACTAGAAAAAAATATTCTAAAATGTGTATGGAACCACAA 2048
                              ii  i  v v  v  ivvv  i       vii       vii   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_44228385_4   2049 AAGACATAGAACAGTAAAAGCCATCCTGAGCAAAAAGAACAAAGCTGGAA 2098
                         ii   vi    i  iv   i v   i   iv  i          i    i
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_44228385_4   2099 GCATCACATTACCTGACTTCAAATTATACTACAGAATTATGGTAACCAAA 2148
                          vv     i v  ii i      viv       i ii  ii    i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_44228385_4   2149 ACAGCATGGTACTGGCAATAAAAACAGACACATTGCCCAGTGGAACAGAA 2198
                             ii           -   ii i     i  v vi  i     i    
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_44228385_4   2199 TAGAGAACCCAGAAATAAAATTAATGCATTTACAGTCAACTCATTTTTGA 2248
                          v    ii           vii - i      ii     i v     i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCA-TACATTTATGGTCAATTGATTTTCGA 359

  chr1_44228385_4   2249 CAAAGGTGCTAAAAACATACATTGGGGAGAGGATAGTATTGTCAATAAAT 2298
                            i     i  i v   v  v      i  i     v  v    i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_44228385_4   2299 GGTGCTGGGGAAAATGGATAGCCATAGTCA---GAATGAAAGCAGACCCC 2345
                                  iv  v      ?   i vv  ---       ivii      
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_44228385_4   2346 TATCCCTCATCATACACAAAAATCAAATCAAAATGGATTAAAAACTTAAA 2395
                           i i v  i    i        i  v           i ? i  i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_44228385_4   2396 CCTAAGACCGGAAACTATGAAACCACTAAAAGAAAACATTGGAGAAACTC 2445
                         iv     v vi       i    ivi  i          v  ? v  v  
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_44228385_4   2446 TCTAGGACACTGGTCT-GGCAAAGATTTCTTGACTAAGACCACAAAAGCA 2494
                          iiiv   vi   vi -     v i      iiv  v   vv        
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_44228385_4   2495 CAAGGCAACCAAAGAAAAA-TGGAAAAACAGGATCACATCAAGCTAAAAA 2543
                             -    v         - i  v   iv   iiv      iv v    
  L1M4_orf2#LINE/    610 CAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_44228385_4   2544 GCTTCTGCACAGCAGAGGAAACAATTAACAAAGAAAAGAGACAACCCATG 2593
                         i   i  ii vv  i    v  v  i  v    vi  i          ii
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_44228385_4   2594 GAATGGGGGAAAATATTTGCAAACTACCCATCTGACAAGGGATTAATAAT 2643
                                i               ii ivi      i      i vi  vi
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_44228385_4   2644 C-GAATACATAAGGAGTTCAAGCAACTCAATAGGAAAAAAAAAACAAATA 2692
                          -     i    i  ii  vvi          --- v     i       
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATA---ATAAAAAGACAAATA 805

  chr1_44228385_4   2693 ACCTGTGTTTAAAATGGGCAAAAGATTTGAATACACATTTCTCAAAAGAA 2742
                            iivv ?v            i          v         v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_44228385_4   2743 GACATACTAATGGTCAACA 2761
                           i    v     i   i 
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATA 874

Transitions / transversions = 1.63 (119 / 73)
Gap_init rate = 0.01 (8 / 763), avg. gap size = 1.50 (12 / 8)  


 389 24.02 18.34 6.11  chr1_44585639_44587522.rev      502   730 (1154)    L1M4_orf2#LINE/L1      228   484 (424)  

  chr1_44585639_4    502 TTTTAAAAATT-CTATAATGCTACAATAATCACAACAGTGTGGTGTTTGC 550
                            i    v  -   i  v      i      vi          ii v  
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_44585639_4    551 ACACAAATGGACCAAAAATAAAAAAATCCAAGGAGTAGAAC--AGAATTC 598
                          i vii  i   -----   v i --  v v   i     i--   i i 
  L1M4_orf2#LINE/    278 ATAAGGATAGAC-----ATATAGA--TCAATGGAATAGAATTGAGAGTCC 320

  chr1_44585639_4    599 AGAAGCAAACCCATG----TACAGCC---TGGCATTTT----AAA----- 632
                             ii        i----  ii i ---  --     ----  i-----
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTG--ATTTTCGACAAGGGTGC 368

  chr1_44585639_4    633 ---------TCAGTAGGAAAAGGATGATGGACTATTTAA----TTGTGTT 669
                         ---------   i i  i    i  ii ---  v  i  ---- v   i 
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGT---CTTTTCAACAAATGGTGCT 415

  chr1_44585639_4    670 GGGACTACTGGAAATTCTC-T---------TAAAGTTATAAACCTAATTC 709
                              v      v ?i v - --------- i     iv vv    vi  
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_44585639_4    710 ACACTACATACTATCAAATTA 730
                             i i    v --      
  L1M4_orf2#LINE/    466 ACACCATATACAA--AAATTA 484

Transitions / transversions = 2.00 (36 / 18)
Gap_init rate = 0.05 (14 / 257), avg. gap size = 4.00 (56 / 14)  

 225 26.55 9.45 2.18  chr1_44585639_44587522.rev     1119  1393 (491)    L1M4_orf2#LINE/L1      614   908 (0)  

  chr1_44585639_4   1119 CAAAAAAAAATAAAATA---AAATCAAAAATAAAAAAGAATTAAAACCTT 1165
                            v    i v      ---    iii vv v vv  -        v   
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA-AATTAAAAACTT 662

  chr1_44585639_4   1166 ATGTATGATTTAA--GACAATGT-----AAAT--AAAGACCAGCAATAGA 1206
                         v   -- v  i  --    v i -----  i --      v v v i   
  L1M4_orf2#LINE/    663 TTGT--GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_44585639_4   1207 CCAGGAAAAAATATTTGCAACACATATCACAGAGAAAGAATTAATATC-A 1255
                         vii   i             vv     vv v  v  i i i vi    - 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_44585639_4   1256 TAATGTAATGGAGAGAACCTTCA-AACTAAA-AAGAATAAGACAA----T 1299
                         v   i  - -- i     ii i -    v  -  v  v       ----i
  L1M4_orf2#LINE/    761 GAATATA-T--AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_44585639_4   1300 CTAATAGAGAAAAAGACAA----TATAAACAGGCAATTCAC---AGAACA 1342
                          i   v? i   vi i   ---- v i  i  i  v   v ---    v 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_44585639_4   1343 AATAGAAATAATCAATAAATATATGAAAGCATGCTCAATTTCATTAGTAG 1392
                         v   v    iii      ii i      iv        iv   ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_44585639_4   1393 C 1393
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.00 (36 / 36)
Gap_init rate = 0.05 (14 / 295), avg. gap size = 2.29 (32 / 14)  


1793 24.70 7.11 0.59  chr1_45158230_45162616.rev     2392  2897 (1490)    L1M4_orf2#LINE/L1        4   542 (366)  

  chr1_45158230_4   2392 AGAAATGGTCCATGTTCATGGATAATAAGA----ATGTGTATTAGGAGGT 2437
                          i i  ivi              viv    ----  i - i   i  v v
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-TGTTAAGATGG 52

  chr1_45158230_4   2438 TAGTTCTTCCCAATGTGATCTATAGATTTAACACAATCCCAATCAAAATC 2487
                         i i v  i     vv       i     i   i       v         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_45158230_4   2488 CCAGCAATTTATTTTGTGCATATCAACAAACCCTTTCTAAACTTTGTGTG 2537
                              viii v     iiv v  ii    i ivv i     v  ii i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_45158230_4   2538 GAAAAACGAAAGACCTAGAATAGCCAACATAATATTGAA------GAACA 2581
                             vi i ii    i           v i   v     ------     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_45158230_4   2582 A-GTCAGAGGCCTGACACTACCCAATGGAAACACTTACTATAA---TAT- 2626
                          -  ii    v  v     v      vvv  v        i  ---  i-
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_45158230_4   2627 -TAATCAAGACAGTGTGGTACTGTTG-AAAAACTGAGAAACAGATCAATG 2674
                         -                      vii-  ii iv  v v i         
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_45158230_4   2675 GAACAAAATTAAAAGCTCAGAAATAGACTCACACAAATATAGTCAACTGA 2724
                            i i    i i  ii        i  i  i   vv   i     i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_45158230_4   2725 T-------------ACTGAGA------AAGGAGCAAAAGATTGTCTTTTC 2755
                          -------------i ii   ------  v i v   ii  v        
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_45158230_4   2756 AACAAATGGTGCTAGAAAATCTGGACATTCACATGCAAAAAGAAATTAAT 2805
                                      i i v v     i ?i           i--   v  v
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG--AATGAAG 450

  chr1_45158230_4   2806 ATAGACACTGACCTTAGACCTTTCACAAAAATTAACTCAAAATGGATCAT 2855
                         v i   v iv    i v   v vi                         ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_45158230_4   2856 AGACCTAAAGGTAAAACACAAAACTATAAAATTTCTAGAGGA 2897
                                  v    i vvi            i ii    i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

Transitions / transversions = 1.56 (75 / 48)
Gap_init rate = 0.02 (10 / 539), avg. gap size = 3.90 (39 / 10)  

 533 21.48 2.22 0.74  chr1_45158230_45162616.rev     3204  3338 (1049)    L1M4_orf2#LINE/L1      526   662 (246)  

  chr1_45158230_4   3204 ATAATAATTC-TAGAGGATAATCTAGGAGAAAATCTAGGTGATTTGGGGT 3252
                             -  i  -    i  v  iv    ? v      vv    ii v    
  L1M4_orf2#LINE/    526 ATAA-AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_45158230_4   3253 TTGACAATGACTTTTTAGATACAACACCAAAAGCACAATCA-TGAAAGAA 3301
                          v i     ii  i       ii               v  -ii      
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_45158230_4   3302 AAAATGAGTA-GTTGGAATTCATTAAAATTCAAAACTT 3338
                              iii  -i     v     i      v       
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.03 (4 / 137), avg. gap size = 1.00 (4 / 4)  

 869 17.98 4.82 0.88  chr1_45158230_45162616.rev     3672  3899 (488)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr1_45158230_4   3672 AAAGAAAAACTGTTAAGAAAACAAAAAGACAAGC-AGAGACTGGGAGAAA 3720
                             i v -  i i      iii         v - v   v         
  L1M4_orf2#LINE/    672 AAAGGACA-CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_45158230_4   3721 AATATTTGAAAA--A---ATCTGATAAAGGACTTATATCCCAAATATACA 3765
                          -      v   -- ---         i      i     vi      i 
  L1M4_orf2#LINE/    721 A-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_45158230_4   3766 AAAAACTCTTAAAACTCAACAATAAGAAAACAA----CCCAATTTTAAAA 3811
                           i        v       i     i  i    ----       ?v    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_45158230_4   3812 TGGGCTAAAGATCTGGAGAGACACCTCACCAAAGAAGATACACAGATATC 3861
                              v  i   i  i v     ii  v            i   i  iv 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_45158230_4   3862 AAACAAGCATATGAAATAATGCTCAAC-TTATATGTCAT 3899
                         v  i     i      vi         - i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (26 / 14)
Gap_init rate = 0.03 (7 / 237), avg. gap size = 1.86 (13 / 7)  


3562 22.62 2.33 1.66  chr1_45206442_45210995.rev     3162  4063 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_45206442_4   3162 TGGAAAGATATTCCATGTTCATGGATTGGAAAAATCAATATTGTTAAAAT 3211
                                    i                   i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_45206442_4   3212 ATTCATACTACTCAA-----TCTACAGATTCAATGTAATCCCTATCAAAA 3256
                         iviv     v i   -----             i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_45206442_4   3257 TACCAATGACATTCTTCACAGAAATAGAAAACACAATTCTAAAATTGTTT 3306
                          v   iivi v  i  ii       v  v  vvii  i        ----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT---- 146

  chr1_45206442_4   3307 TTTGCTATGTGAAACCACAAAAGACCTGGAATAACCAAAGCTATCCTAAG 3356
                         -----i  i  i  vii   ii    ii     i     i v   i i i
  L1M4_orf2#LINE/    147 -----CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_45206442_4   3357 CAAAAAGAACAAAACTGGAG---TTATTACTT---GACTTCACATTATAC 3400
                         v  i         ii     --- i i-    ---i i    v viv   
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTTAC 240

  chr1_45206442_4   3401 TACAGAGCTATAGTAACCAAAATAGCATGGTACTGTCATAAA-ATAGACA 3449
                             i     i     i   i i  ii        v     i-       
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_45206442_4   3450 CACAGACCAATGGAACAGAATAGAAAACCTAGAAACAAATCCACACACGT 3499
                         i i   i        i     v  i ii i     i   i   i   iv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_45206442_4   3500 ACACTGAACTCATTTGTTACAAAGGTGCCAAGAACATACACTGGGGAAAA 3549
                          iiv v  i v    viv    i          v   v  v        i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_45206442_4   3550 GACAGTTTTTTCAATAAATGGATGCTAGGA-AACTGGATATCCATATGCA 3598
                         i i   i       i      -    i   -         ?   i     
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGG-TGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_45206442_4   3599 GAAGAAATGAAACTAGACCCCTATCTCTAGCCATATACAAAAATCAGATA 3648
                         i     -    ii i        i   vvi              i iv v
  L1M4_orf2#LINE/    440 AAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_45206442_4   3649 AAAATGGATTAAAGACTTAAATCTAAGACCTGAAACTATGAAACTACTAC 3698
                                  i ?    i     v     v  i       i     vi  v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_45206442_4   3699 AAGAAAACATTGGGGAAACTCTCTAGGACACTGGACTGGGCAAAGATTTC 3748
                                   v  ? v  v   iiiv   vi   ii i     v i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_45206442_4   3749 TTGAGTAATAAC-CCACAAGCACAGGCAACCAAAGCAAAAATGGATAAAT 3797
                           iii  - i  -   v       i     v    v      i       
  L1M4_orf2#LINE/    589 TTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_45206442_4   3798 GGGATCACATCAAG-TTAAAAAGCTTCTGTACAG-AAAGGAAATAATTGA 3845
                         v   iiv      i-       -   i   i vv-      v iv  ii 
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_45206442_4   3846 CAAAGTGAAGAGACAAACCACAGAATGGGAGAAAATATTAGCAAACTACC 3895
                         v        i      v                      v     ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_45206442_4   3896 CATCTGACAAGG-ACTTAATAACAAGAATATATAAGGAGCTT----AATT 3940
                         i      i    -    i-  v v           i  i  i----  i 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_45206442_4   3941 CAATAGGAAAAAATCTAATAATCTGATGTTAAAATGGGCAATAGATCTGA 3990
                              iv     iv v     i ii  v?v           vi   i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_45206442_4   3991 ACAGACATTTCTCAAAAGACGACATACAAGTGGCAAATGAGTATATGAAA 4040
                          i           v     v  i      i    v   i  i i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_45206442_4   4041 AGGTACTCAATATCATTTGTCAT 4063
                           i i     i    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (134 / 66)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


1723 21.40 1.67 17.21  chr1_45276521_45280339     2252  3326 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_45276521_4   2252 TAGAGAGATATACTGTGTTCACAGATTG-AAGACTCAATATAGTGAAGAT 2300
                          i  i      v ii      ii     -      i     v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_45276521_4   2301 TTCAATTTTCCTAAACTTGATATATAGGTTTAATGCAATATCAGTCAAAA 2350
                         vv    vi   iv  v     v  i  i  i  i     vi vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_45276521_4   2351 TCTCAGATA----TTTTA-AAATATAGACAAGCTAATTTTAAAATTTATA 2395
                           i   v i----    i- i v  v        i  ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_45276521_4   2396 CAGAAAGCCAAAGGAACTGGAAGAGCTAAAATAATTCTGAAAGGGAAGAA 2445
                         ii    vv   i   v ii   v   i    i   ii     ii      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_45276521_4   2446 TAAAGTTAGAGGAATCAAATG----AACTTTAAGAAATACTATAAAGCAG 2491
                         i      i     v   v iv----  i  i  i vv     i     --
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC-- 248

  chr1_45276521_4   2492 CCAGGCATGGTGGTTCAAGCCTGTAATCCCAGCACTTTGGGAGGCTGAGG 2541
                         ------------- v  -----      vvii  v v   v --   -- 
  L1M4_orf2#LINE/    249 -------------TACA-----GTAATCAAGACAGTGTGGTA--CTG--G 276

  chr1_45276521_4   2542 CAGGAGGATCATTTGAGGCCAGGAGTTCGAGACCAGCAAGGTCAGTATCA 2591
                           vi     ------  i ---- -- vv   i  iiiiii -  v  ii
  L1M4_orf2#LINE/    277 CATAAGGAT------AGAC----A--TATAGATCAATGGAAT-AGAATTG 313

  chr1_45276521_4   2592 CGAGATCTTGTCTCTAGAAAAAAAAAAAAAGAAAAAATTGCCAGCCATG- 2640
                         v   --------  i     v   v---------------   vv   v-
  L1M4_orf2#LINE/    314 AGAG--------TCCAGAAATAAAC---------------CCATACATTT 340

  chr1_45276521_4   2641 ATGGTGCACAACTGTTGTGTCCCAGCTCCTTGGGAGGTTGAGACAGGAGG 2690
                              ---   i  v v --------  -------------    i i -
  L1M4_orf2#LINE/    341 ATGGT---CAATTGATTT--------TC-------------GACAAGGG- 365

  chr1_45276521_4   2691 TTTGCTTGAGCCCAGGAGTTTGAGGCTGCAAGTGAGCTATGATCGTGCTA 2740
                         --   i-i  v   ----  ii v vv v   -- ---  ii  v vii 
  L1M4_orf2#LINE/    366 --TGCC-AAGACCA----TTCAATGGGGAAAG--A---ATAGTCTTTTCA 403

  chr1_45276521_4   2741 CTGGACTCTAG-GCTGG-ACAACAGCGTGAGACCCTGTCTCCACACAAAT 2788
                         viii --- i -     -     ----  -  ----- v?     -----
  L1M4_orf2#LINE/    404 ACAAA---TGGTGCTGGGACAAC----TG-GA-----TAKCCACA----- 435

  chr1_45276521_4   2789 ATGGCCAATCGATTTTGCAAAAGAAATAAAATCAATTCAATGAAGCGAGG 2838
                         ---------------          ---------------     iv-  
  L1M4_orf2#LINE/    436 ---------------TGCAAAAGAA---------------TGAAGTT-GG 454

  chr1_45276521_4   2839 ACAGTCTTTTCAATATATAGGACTGGACACTGAACACTAAACATTGAACA 2888
                           --- ii ------------  ivv    iiv i  -   v   -   -
  L1M4_orf2#LINE/    455 AC---CCCT------------ACCTCACACCATATAC-AAAAATT-AAC- 486

  chr1_45276521_4   2889 TCAATAAGCAAAATGAATAAACAAACCTCAATCTAAACCTCACATTTTGT 2938
                             -------    i  v ?- i    v   v   ------------ v
  L1M4_orf2#LINE/    487 TCAA-------AATGGATCAW-AGACCTAAATGTAA------------GA 516

  chr1_45276521_4   2939 ACAAAAATGTTTAAACTGTTTAGAATAAAACACAGCAGGATATCTTTGTG 2988
                         i v    ivv v     -i      v      i  v? v v     i   
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_45276521_4   2989 ACCTGGGATTAGGCAAAGAGTTTTTATACATGTAACCAAAAGCAGACTCC 3038
                             v  i        v iv  i   v i   vv          v vv v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_45276521_4   3039 ATAAAAGAAGAAACTGGTAAGTTGGATTTCATTAACATTAAAAACTCTTG 3088
                          i       i   iv i   i     i     i  v          i   
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_45276521_4   3089 CTCTGACAAAGACACTATTAAAATATTGAAGAAACAAGCCACAGACTGGG 3138
                         iv  vvv  i        i  i v v    i i    v       v    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_45276521_4   3139 AGAAAATATTTGCAAGACACATATCCAATAAAGGACTTGCATCTAGGATA 3188
                                        iv  i     ii    i       i   i  i   
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_45276521_4   3189 GAAAACGAACTCTAAAAACTCAA-AATAAGAATATGAACAAGTCAATTTA 3237
                         v v  v       v v       -     i  v ii  i  vi     ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_45276521_4   3238 AAAATAGGCAAAAGATGTG----GGTACTACTCTGAAGAGAATATACAAA 3283
                              i      i   v  ---- ii i v   ii    ii         
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_45276521_4   3284 TGGCAAATAAGTACATGAAAAAATGTTCAGCATCATTAGCTCT 3326
                             v      i         i   i   i     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (128 / 98)
Gap_init rate = 0.05 (43 / 908), avg. gap size = 4.72 (203 / 43)  


3206 26.48 0.66 0.88  chr1_45296614_45303001     4986  5895 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_45296614_4   4986 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATAAATATTGTGAAAAT 5035
                              ii i  i     i        v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_45296614_4   5036 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCACCATCAAGC 5085
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_45296614_4   5086 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5133
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_45296614_4   5134 GACGGAACCAAAAAAAGAGCCC-GCATTGCCAAGTCAATCCTAAGCCAAA 5182
                         v i    -- viv  i ii   - v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_45296614_4   5183 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 5232
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_45296614_4   5233 GCTACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGA 5282
                                   i   i i  ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_45296614_4   5283 CCCATGGAACAGAAC--AGAGCCCTCGGAAATAATACCACACATCTACAA 5330
                         i v      i    i--    i  --i       vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_45296614_4   5331 CCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5380
                         i  vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_45296614_4   5381 CCCTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5430
                         vi  v  i  i   i          v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_45296614_4   5431 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAACTAATTCAAGATG 5480
                         v    ii    i    v   i     v          i   i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_45296614_4   5481 GATTAAAGACTTAAATGTTAGACCCAAAACCATAAAAACCCTAGAAGAAA 5530
                            i ?    i       v   v i     i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_45296614_4   5531 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5579
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_45296614_4   5580 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5629
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_45296614_4   5630 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGGGTG 5679
                          v  i   v v  i i   i  ii vv    i  v    i  vv ii   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_45296614_4   5680 AACAGGCAACCTACAGAATGAGAGAAAATTTTTGCAATCTACCCATCTGA 5729
                           v  i     i        i        v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_45296614_4   5730 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 5779
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_45296614_4   5780 AAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACTGACA 5829
                             i -    i     v  i?    i     i      v    iv    
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_45296614_4   5830 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCT 5879
                         i     v        i  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_45296614_4   5880 CATCATCACTGGCCAT 5895
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


 277 20.37 0.00 0.00  chr1_45314210_45320928      217   270 (6449)    L1M4_orf2#LINE/L1        1    54 (854)  

  chr1_45314210_4    217 TGGGGAGACATCCCATGTTCATGGATCAGAAGATGAGATGTTGTTATGAT 266
                            ii   i                 ii     ivvi  i      v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_45314210_4    267 GGCA 270
                             
  L1M4_orf2#LINE/     51 GGCA 54

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.00 (0 / 0)  

3293 27.06 0.22 0.33  chr1_45314210_45320928     5318  6226 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_45314210_4   5318 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5367
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_45314210_4   5368 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5417
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_45314210_4   5418 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5465
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_45314210_4   5466 TATGGAACCAAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCCAAAAG 5515
                                viiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_45314210_4   5516 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5565
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_45314210_4   5566 TACAGTAACCAAAACAGAATGGTACTGGTACCAAAACAGAGATATAGATC 5615
                                 i   i    vi         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_45314210_4   5616 AATGGAACAGAACAGAGGCCTCAGAAATAACGCCGCATATCTACAACTAT 5665
                                i    iv   ivii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_45314210_4   5666 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5715
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_45314210_4   5716 ATTTAATAAACGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5765
                         v  i  i   i i        v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_45314210_4   5766 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5815
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_45314210_4   5816 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5865
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_45314210_4   5866 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5915
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_45314210_4   5916 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5965
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_45314210_4   5966 AAACGAAAGAGCTTCTGCACAGCAAAAGAAACTACGATCAGAGTGAACAG 6015
                            vvv  i i   i  ii vv    i  v    iv vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_45314210_4   6016 GCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAG 6065
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_45314210_4   6066 GGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAA 6115
                          i  vi          v  i         vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_45314210_4   6116 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 6165
                          -    i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_45314210_4   6166 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 6215
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_45314210_4   6216 TCACTGGCCAT 6226
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.25 (5 / 4)  


4257 14.50 4.18 1.86  chr1_45321280_45323119      486  1347 (493)    L1M4_orf2#LINE/L1       27   908 (0)  

  chr1_45321280_4    486 TAGAACACT-AATA-----GAGATGCCAAAACTTCC-AAACTGATCTACG 528
                          i   v   -    -----i     v   v   i  -   i        i
  L1M4_orf2#LINE/     27 TGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACA 76

  chr1_45321280_4    529 GATTCGATACAATCGCTTTCAAAATCCCAACTAGATTTTTTTTTGCAAAA 578
                              i ii     v  v           i  i---ii         i  
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTG---CCTTTTTTGCAGAA 123

  chr1_45321280_4    579 A---ATAAACTGATACTAAAATTCATAGGGAAACTCAAGGGAATGAGAAT 625
                          --- i  i     v            v     iv       viv     
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chr1_45321280_4    626 AGCCAAAACAATCTTGAAAAAGAAGAATAAAGTTGGAGGACTCACACTTT 675
                                                    i                     i
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr1_45321280_4    676 GCAATTTCAAAACTTACTA--GAGCAAGAGTAATAAAGACAATGTGATAC 723
                         v                  --i   v v      v      i    i   
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_45321280_4    724 TAACATAAGGATAGACATAAAGATCAATGGAATAGAATTGAGAGTCCTGA 773
                          ii                v                           v  
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_45321280_4    774 AATAAACTCAT----TTATGGTTAACTGGCTTTCAACA-GCATGTCAAGA 818
                                i   ----       i  i  ii    i   - vi  i     
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_45321280_4    819 TCATTCAATGGAGAAAGACTAGTCATTTCACCAAATAATGCTGGAAAAAA 868
                         i          i      v     v     v     ii      i v  v
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_45321280_4    869 TGGATATCCATAT-TAAAAAAA---AGTTGAAGCCCCT-TCTGACATCA- 912
                               ?   i  -i    i  ---     i -     -i  v   i  -
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGA-CCCCTACCTCACACCAT 472

  chr1_45321280_4    913 ---CAAAAGTCAACTCAAAATGAAACATAAAACAAAATATAAGAGCTAAA 959
                         ---     i i           i v  ? i v v    i           
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_45321280_4    960 ACTAGAAAACACTTAGAAGAAAACATGGTAGTAAATCTTCTTGATCTTGG 1009
                             v     v               i v?          v   i     
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_45321280_4   1010 GTTAGGCAATGGTTTCTTAGCTATACTATCAAAAGAAAGAAAGAAAGAAA 1059
                                             v   ivi i      v v--   v  v   
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC--AAGCAACAAA 620

  chr1_45321280_4   1060 AAAGCAACCGAGAAAAAAAATAAATTGTACTTCATCAAAATTTAACACTT 1109
                          --------  i    v i        v              v  v    
  L1M4_orf2#LINE/    621 A--------GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_45321280_4   1110 TTGTGCTTCAAAGGACACTATCAAGAGAGTTAA--GACACCTCACAAAAT 1157
                                                   i   v  --    v i    i   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_45321280_4   1158 GGGAAAATATATTTGCAAATCACATATCTGATAACGGACTAGTATCTAGA 1207
                             i  v              i           v     v     i   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_45321280_4   1208 ATGAATAAGGAACTGTCACAACTTAAGAATAAAAA-------AATCCAAT 1250
                           iv    i     v i      i  v        -------  i     
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_45321280_4   1251 TTAAAAATGGGCAAAGGATCTGAATAAACATTTTTTTCCAAAGAAGTTAT 1300
                          ?                 i      i      i --         v   
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCT--CCAAAGAAGATAT 860

  chr1_45321280_4   1301 ACAAATGACCAATACACACATGAAAAGAT-CTCAACATCATTAGTCAC 1347
                                i      vi             -          ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (71 / 50)
Gap_init rate = 0.02 (19 / 882), avg. gap size = 2.74 (52 / 19)  


 882 25.63 2.53 5.05  chr1_45367996_45373752      966  1242 (4515)    L1M4_orf2#LINE/L1        1   270 (638)  

  chr1_45367996_4    966 TGGAGAAATATAACAGGTTCATGGGTCAGAAGACTCAGTCTTGTTAAGGT 1015
                             i i    vv  v        i ii       i i v        i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_45367996_4   1016 GTCAATTCTCCCCAAATTTATCTGTAGATTCAAT-CAGGT--TAGGCAGG 1062
                          v    v           v    ii        i-  ivi--  v-  ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-CAAA 99

  chr1_45367996_4   1063 TTTTTTGTTTTTGTTTTTAAGTAGAAATTGACAAGCAGTTTCTTAAATGT 1112
                         v iiiv i viiv     -- i              v v i  v    vi
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_45367996_4   1113 ATATGAGAATGCAAAGGACCTAGAATCTAAATGCAAAGGACTAAACAACC 1162
                              ii       i     i     -----------i v v      i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAAT-----------AGCCAAAACAATC 186

  chr1_45367996_4   1163 CTGAAAGGGAA--ACAA-GCTAGAGGACTCATACTACCTGACTTCAAGAC 1209
                         i     ii   --    - i i         i   v  ii i     i  
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_45367996_4   1210 CTATTATAAAACGATAGCA-TTAAGACTGTAGGG 1242
                         i  i  i   i v i  i - i     v  iv  
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

Transitions / transversions = 2.09 (48 / 23)
Gap_init rate = 0.03 (8 / 270), avg. gap size = 2.62 (21 / 8)  

 335 22.99 4.60 0.00  chr1_45367996_45373752     1555  1641 (4116)    L1M4_orf2#LINE/L1      255   345 (563)  

  chr1_45367996_4   1555 AAACAAAAC-TTATGGT---GGCATAAGGATAGACATATGGACCATTGGA 1600
                           v   i  -v i    ---                   i  i  v    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_45367996_4   1601 ACTGAATAGAGAACCTATAAATAAACTCACGTATATATGAT 1641
                          iv    v    ii i v        i  iii  v    i 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 2.00 (4 / 2)  

 808 26.26 11.78 0.34  chr1_45367996_45373752     4449  4745 (1012)    L1M4_orf2#LINE/L1      369   699 (209)  

  chr1_45367996_4   4449 CAAAGCAATCTAACAGAAAAGGGAAAGCCTTTT-AACAAATAGTGCTAGA 4497
                            ii v  ii  ii ii  i i v  i     -       i     i i
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_45367996_4   4498 ATAGATGAATATCCATA----AAAAAATGATCCTCAACTCCTACCTCACA 4543
                          i iv  i   ?   i ----   i     vvi vi  i           
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_45367996_4   4544 CCATATACAAAAATTAATTCA---TG------ACACCTAAATGTAAAACC 4584
                                          i   ---  ------ v            i v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_45367996_4   4585 TAAAACTA--AAGCCTTTGGTGGGGGAGAAAGGAG---------G----C 4619
                                 --  i ii  i vi iii v v   ? --------- ---- 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_45367996_4   4620 TTGGGAGTAGACAA-ATTTTCTTAAATATGACATGGAAAGCA---ATAAT 4665
                              -v   i   -iv       i        ivi      ---ii  i
  L1M4_orf2#LINE/    569 TTGGG-TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_45367996_4   4666 AATTTTTAAAGTA-ATAAGTTAGACTTCATCAAAATTAAAA-CTTCTATT 4713
                           vvvvv   i  -    i  i                   -   i i v
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_45367996_4   4714 CATCAAAAAATATCATTAAGAAAATAATAGGA 4745
                          v     ii i ii  i      i i v i  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

Transitions / transversions = 2.45 (54 / 22)
Gap_init rate = 0.04 (12 / 331), avg. gap size = 3.00 (36 / 12)  

 641 19.31 11.39 0.50  chr1_45367996_45373752     5063  5264 (493)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_45367996_4   5063 AAGAAAATAATAGGCAAAACCACAAACTGGAAGAATATATCCACAAAACA 5112
                               i i v i vv  v     i v   i    v    iii    v  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_45367996_4   5113 TATATTTGACAAGGGACTTGTATTCAAAATATACAAAGAA---TTAC--- 5156
                              i   i             i  i      i      ---    ---
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_45367996_4   5157 -------TAAAA---TTAATA------TTAATAAATAGGCAAAATATTTG 5190
                         -------     ---iv    ------  ? v    i      iv     
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_45367996_4   5191 AACAGACACTTC-ACAAAGCAAGATATATGAAAGGCCAATATGAACAAGA 5239
                           i     i   -v     -        ii  v        v v   v  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_45367996_4   5240 AAAAGTGCTCAACCTCATTACTCAC 5264
                            ii        v   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (22 / 16)
Gap_init rate = 0.03 (6 / 224), avg. gap size = 4.00 (24 / 6)  


 626 25.86 0.57 2.87  chr1_45377085_45379131      480   653 (1394)    L1M4_orf2#LINE/L1      125   294 (614)  

  chr1_45377085_4    480 TTAACAAAATCTCTGGGCACAAAATTCATATGGAACCAAAAAAGAGCCCA 529
                           i    i----   iv vi               viiv  ii  v  vi
  L1M4_orf2#LINE/    125 TTGACAAG----CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr1_45377085_4    530 AATAGCCAAACCAATCCTGAGCAAAAAGAACAAAACTGGAGGCAC-CATG 578
                                   v     i   iv  i         ii      -  -  ii
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-ACTCACA 219

  chr1_45377085_4    579 CTATCTGACTTCAAAATATATTACAAGGTTATAGTAACCAAAACAGCATG 628
                           vi ii i       iv  i     i i  i     i   i    ii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_45377085_4    629 GCATTGGTATAAAAACAGACATATA 653
                          i i   i    ii i         
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATA 294

Transitions / transversions = 3.50 (35 / 10)
Gap_init rate = 0.02 (3 / 170), avg. gap size = 2.00 (6 / 3)  

2338 23.85 4.28 0.33  chr1_45377085_45379131      949  1556 (491)    L1M4_orf2#LINE/L1      277   908 (0)  

  chr1_45377085_4    949 CAAAAAAGCAGACATATAGACAAATGAAACAGAATAGAGAACCCAGAAAT 998
                           v  iiii           iv    i  i     v    ii        
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_45377085_4    999 AAATGCATATGTTTGCAGCCAATTGATTTTTGA-AAAGGTGCCAAGAATA 1047
                            iv    ii   iii i           i  -  i          vi 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_45377085_4   1048 TACATTGGGGAAAAGGACACCCTTTTCAATAAATGGTGCTGGGA------ 1091
                          v  v        - i i vi        i              ------
  L1M4_orf2#LINE/    377 TTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_45377085_4   1092 ----------------AAAATGAAACTGGACCCCTCTGTCTTACCATATA 1125
                         ---------------- i      ii         viv  vi        
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_45377085_4   1126 CAAAAATCAACTCAAAATGGATTAAAGGCTTAAACA-GAGACCTGAAACT 1174
                                i              i ?  i i    ii-i   v  i     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_45377085_4   1175 AGAAAACTACTAGAATAAAATATAGGAGAAACACTTCAGAATGTTGGTTT 1224
                          v      vi     v    i     ? v  vv    ivi iv    v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_45377085_4   1225 AGACAAAGATTTTATAGCTAAGACCTCAGAAGTACAGATAATAAGAACAG 1274
                           i   v i   iv   v  v   vi  i   i   iii  i  i iv i
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_45377085_4   1275 AAATAGACAAATAGGACTATATTGAACTAAAAAGCTTCTGTACAGCAAAG 1324
                                i    v     vi  ii  v v    i   i   i vv     
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_45377085_4   1325 GAAACAATCAACAGAGTGAAGAGACAACTTGTTGAATGGGAGAAATATAT 1374
                           v  v     v i      i       iiiiv            -    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA-ATAT 724

  chr1_45377085_4   1375 CTGCAAACTATTCGTTTGCTAAGGGACTAATATCTAGAATATACAAGGAA 1424
                         i      ii  vii i  v         vi    i        i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_45377085_4   1425 TTGAAACAACTCAACAGCAAAAA-ACAAATAATCCCATTAAAAAGTGAGC 1473
                         i vvv         i ii     -        i  v   ?    i  i  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_45377085_4   1474 AAAGGATCTAAACAGACATTTCTTAAAAGAAAACATA-AAATGACCAACA 1522
                                i i  i          iv      i i   -     i    i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_45377085_4   1523 GGCATATGAAAAAATGCTCAACATTGCTAATCAT 1556
                         i   i       i           ii????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (97 / 45)
Gap_init rate = 0.01 (7 / 632), avg. gap size = 4.00 (28 / 7)  


3399 26.24 0.44 0.33  chr1_45418831_45425224     4996  5902 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_45418831_4   4996 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5045
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_45418831_4   5046 AGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                         i  v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_45418831_4   5096 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5142
                          v   -   v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_45418831_4   5143 ATATGGAACCAAAAAGAGCCC-GCATTGCCAAGTCAATCGTAAGCCAAAA 5191
                                 viiv  i ii   - v  v     iv     v i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_45418831_4   5192 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5241
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_45418831_4   5242 CTACAGTAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGATATAGAC 5291
                                  i   i    i          i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_45418831_4   5292 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCGCATATCTACAACTA 5341
                                 i    iv   ivii         vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_45418831_4   5342 TCTGATCTTTGACAAACCTGAAAAAAACAAGCAATGGGGAAAGGATTCCC 5391
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_45418831_4   5392 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGAAAGCTG 5441
                          v  i  i              v      v  ?  ii   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_45418831_4   5442 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5491
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_45418831_4   5492 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5541
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_45418831_4   5542 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5591
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_45418831_4   5592 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGATTTAAT 5641
                                     vvi          vv     v       v   i  v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_45418831_4   5642 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGGCAGAGTGAACA 5691
                         i   v v  i i   i  ii vv    i  v    i iiv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_45418831_4   5692 GGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5741
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_45418831_4   5742 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5791
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_45418831_4   5792 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATGGACACTTCT 5841
                         i     i     v  i?    i            v     i    i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_45418831_4   5842 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5891
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_45418831_4   5892 TCTCTGGCCAT 5902
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


 275 23.44 0.00 0.00  chr1_45558966_45562124     1525  1588 (1571)    L1M4_orf2#LINE/L1        1    64 (844)  

  chr1_45558966_4   1525 TGGAAAGATATTCCATGTTCATGAATTGCAACAATCGGTATTTTTAAAAT 1574
                                    i           i    v  v v iii    v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_45558966_4   1575 TCCCATACTACTCA 1588
                         vv v     v i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCA 64

Transitions / transversions = 0.88 (7 / 8)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.00 (0 / 0)  

 270 25.68 1.35 0.00  chr1_45558966_45562124     1589  1662 (1497)    L1M4_orf2#LINE/L1      135   209 (699)  

  chr1_45558966_4   1589 GATACTAAACTTTCTATGGAATCACAA-AGACCCAGAATCGCCAAAGCCA 1637
                            v     v  iv       vii   -i          v      i v 
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_45558966_4   1638 TCCTGAGGAAAAGAAAAAAAGCTGG 1662
                           i   ii  i ii  v    i   
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGG 209

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1)  

2593 24.05 2.25 1.27  chr1_45558966_45562124     1956  2666 (493)    L1M4_orf2#LINE/L1      191   908 (0)  

  chr1_45558966_4   1956 AAAAAAAGAAAGAAACTGGAGGAATCACATTACCTGATT-CAAATTATAC 2004
                             i     vi  ii       v     i v  ii   -    viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_45558966_4   2005 CACAGAGCTATTGTAACCAAAATAACATGGTATTGGCATAAAAACAGAAA 2054
                         i   i     iv    i   i i iii     i        ii i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_45558966_4   2055 CATAGACCAATGGAACAGAATAGAGAATCCAATAACAAATCCATAAATCT 2104
                         i     i        i     v    i    iv  i   i     v  i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_45558966_4   2105 ACAATAAACTCTCATTTTCAACAAAAGTACCAAGAACATACATTGGGGAA 2154
                          iii v  i v--      i    ii  i      v   v  v       
  L1M4_orf2#LINE/    341 ATGGTCAATTG--ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_45558966_4   2155 AGGACAGTCTCTTCAACAAATAGTGCTGGGAAAACTGTATAGTTACATGC 2204
                           i i     i          i         v     v   ?ii      
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_45558966_4   2205 AGAAGAATGAAACTAGACTCCTATCTCTAGCCATATGCAAAAATCTAA-T 2253
                          i         ii i   i    i   vvi      i       -   - 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAACT 487

  chr1_45558966_4   2254 CAAAATGGATTAAAGATTTCGATCTAGGACCTCAAACTATGAAACTACTA 2303
                                   i ?   ii vi  v  i  v  v       i     vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_45558966_4   2304 CAAGAAAACATCGGGGGAAACTCTCC----CATTGGTCT--GCAAAGATT 2347
                         v          v  ? v   -   i ---- v    vi --    v i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_45558966_4   2348 GCTCGAGTAATACTCCAAAAGCACAGGCAACTAAAGCAAAAATGGACAAA 2397
                         v  iiii  vv  v           i     v    v      i  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_45558966_4   2398 TGGGATCACATCCGG-TTAAAAAGCTTCTGCACAGCAAATGAAAC----- 2441
                          v   iiv    vii-       -   i  ii vv    v  v  -----
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_45558966_4   2442 --AAAGTGAAGAGTCAATCCATGGAATGGGAGAAAATATTTGCAAAATAT 2489
                         --        i  v   i   ii                       vi  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_45558966_4   2490 CCATCTGACAAAGGATTAATAACCAGAATATATAAGAAGTTCAAACAACT 2539
                         vi      i  i   i vi  v             ii ii  vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_45558966_4   2540 CTATAGGAAAAAAAAATCTAACAATCAGATTTTTTAAATGGGCAAAAGAT 2589
                          v   iv     i v ---  i  i vi   ?vv-           i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACA---AATAACCCAATTWAA-AAATGGGCAAAGGAT 831

  chr1_45558966_4   2590 CTGAACAGACATTTCTCAAAAGAAGACATACGAACAGCAAACAGGTATAT 2639
                         i    i           v        i    i  ii  v  i i i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_45558966_4   2640 GTAAAGGTATTCAACATCACTGATCAT 2666
                          v    i ii         ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (108 / 59)
Gap_init rate = 0.02 (12 / 718), avg. gap size = 2.08 (25 / 12)  


 565 17.92 0.00 0.94  chr1_45568842_45573056.rev     1087  1192 (3023)    L1M4_orf2#LINE/L1        1   105 (803)  

  chr1_45568842_4   1087 TAGAAAGATATCTTATGCTCATGGATTGGAAGAATTAATATTGTTAAAAC 1136
                          i          ii   i               v             i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_45568842_4   1137 GACCATGCTACCCAAAAACAATCTACAGATTCAGTGAAATCCCTATCAAG 1186
                          i v  i  v      -vii             ii v            i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_45568842_4   1187 ATACCA 1192
                           v   
  L1M4_orf2#LINE/    100 ATCCCA 105

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.01 (1 / 105), avg. gap size = 1.00 (1 / 1)  

1286 25.66 5.82 2.12  chr1_45568842_45573056.rev     2113  2490 (1725)    L1M4_orf2#LINE/L1       97   488 (420)  

  chr1_45568842_4   2113 AAGATACCAA-TGTCATTTTTCACAGAAATAGAAAAAGCAGTCCTAAAAT 2161
                           i  v   i-  i -     ii       v  v  iviii         
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_45568842_4   2162 TTTGTATGGAAACAAAAAAGAGACC--AAATAGCCAAAGCAGTCCTGAGC 2209
                          i-i        iiv  -- i    --i          i  i  i   iv
  L1M4_orf2#LINE/    146 TC-ATATGGAAATGCAA--GGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_45568842_4   2210 AAAAAGAACAAAGCTGGAGGCATCATACTACCTGACTTCAATATATATTA 2259
                           i          i      vv   i   v  ii i     v iv  i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_45568842_4   2260 CAAGGCTATACTGAGCACAACAGCATGATATTTGTATAA--ATCAGACAC 2307
                            i    i v i v  vi    ii  i  i v i    --  -     i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACAT 291

  chr1_45568842_4   2308 ATAGACCAATGGAACAGAAT---------------AAATCCACGTGTTTA 2342
                              i        i     ---------------   i   iiii    
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_45568842_4   2343 CAGCCAACTGATTTTCAACAAAGGTACCAAGAACGTACACTGGGGACAAG 2392
                         ii i   i        i    i   i      v i v  v      v ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_45568842_4   2393 ACACTTTCTTGAATAAATGGTGCTGAGA--ACATGGTATATTATATATGC 2440
                          i v i i  v  i           i  --  -   -   ?i-i i    
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAAC-TGG-ATAKC-CACATGC 438

  chr1_45568842_4   2441 AGAAGAATGAAACTGGATCTCCATCTCTTACTATATACAAAAGTCAAATC 2490
                          i         ii    i i i i   vi  i          i i  v  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

Transitions / transversions = 3.17 (73 / 23)
Gap_init rate = 0.03 (12 / 392), avg. gap size = 2.50 (30 / 12)  

 318 25.00 5.36 0.00  chr1_45568842_45573056.rev     2518  2629 (1586)    L1M4_orf2#LINE/L1      437   554 (354)  

  chr1_45568842_4   2518 GCAAAAGAGTGA-----GA-CTCTGTCTCAAATAATAAAATAAAATAAAA 2561
                                 i   -----  - i  ii    v iv   v vv     v  v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_45568842_4   2562 TAAAGATAATTTAAAGACTTAAATGTAAAACCCCAAACTACAAAACTACT 2611
                          v  i  iiv i ?    i         i v iv      i      vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_45568842_4   2612 AGAAGAAAACATAGGGGT 2629
                                        ?  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGT 554

Transitions / transversions = 1.17 (14 / 12)
Gap_init rate = 0.02 (2 / 118), avg. gap size = 3.00 (6 / 2)  

1089 23.32 2.33 5.96  chr1_45568842_45573056.rev     3339  3724 (491)    L1M4_orf2#LINE/L1      537   908 (0)  

  chr1_45568842_4   3339 AAAAGTAAACAGAGG---AAACACTTCAAGACATTGGTCTAGGCAAAGAT 3385
                          i   v     v   ---   i-    iv   v    vi       v i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_45568842_4   3386 TTTATGGCAAAGACCTCAAAAGTATAGGCAGCAAAACCAAAAATCGACAA 3435
                           iv i vv v   vi      i i i   i     vv      v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_45568842_4   3436 ATGGGACTATATTAGACTAAAAATCTTCTGCACAGCAAAGGAAAC----A 3481
                           v     vi  i i v v    v   i  ii vv       v  ---- 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_45568842_4   3482 ATAGAGTGAAGAGACAACCTTTTGAATGGGAGGAAATACTCGTAAACTAT 3531
                          v i      i        iviv         i     i i i   ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_45568842_4   3532 TTATCCAAAAAGGGGCTAATATTTGGAATATACAAGGAACTCAAACAACT 3581
                         v    ii v     i  vi   iii       i  i      vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_45568842_4   3582 CAACAGTAAAAA-ATAAAAAACCATCTCTCCCTACCCCGAAAATCCCATT 3630
                            i i      - i   v    ---------------------- v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACC----------------------CAATT 813

  chr1_45568842_4   3631 TAAAAATGGGCAAAGGACATGAACAGAAATTTCTTGAAAGAAAACATAGG 3680
                         ?                iv    i   v      iv      i i   vi
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_45568842_4   3681 AATGGTCAACAGGTATACGAAAA-ATGCTCAACATCATAAAAAAT 3724
                              i   i i i i i     -             ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (53 / 36)
Gap_init rate = 0.02 (6 / 372), avg. gap size = 5.33 (32 / 6)  


3880 22.92 0.66 0.11  chr1_45706232_45708273.rev      649  1551 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_45706232_4    649 TGGAAAGATATTCCATGTTCATGAATTGGAAGAATCAATATTGTTAAAAT 698
                                    i           i         v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_45706232_4    699 GTCCATACTACTGAAAGCAATCTACAGATTCAATGCAATCACTATCAAAA 748
                          v v     v iv   vii              i      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_45706232_4    749 TATCAATGACATTCTTTACAGAAATGGAAAAGACAATCATAAAATTTATA 798
                          vi  iivi v  i   i       v  v   vii   v       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_45706232_4    799 TGGAACCACAAAAGACCCAGAATAGCCAAAGCTATACTAAGCAAAAAGAA 848
                              vii   ii                 i v  vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_45706232_4    849 CAAAACTGAAGGAATCACATTATCTTACTTCAAATTTTGTTACAGAGCTA 898
                             ii  i    v     i vi iv i      vi  ii    i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_45706232_4    899 TAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACATATAGACCAA 948
                         i     i   i    ii              ii i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_45706232_4    949 TGGAACAGAATAGAGGACTCAGAAACAAATCCACACACCTGCAGTGAACT 998
                              i     v   iiii      i   i   i   ii iii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_45706232_4    999 CATTGTCAACAAACGTGCCAAGAACACATACTGGGGAAAAGACAGTCTCT 1048
                         v   v  i    iv         v  ivi v        ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_45706232_4   1049 TCAATAAATGGTGCTGGGAAAACAGGATATCCATATGCAGAAGAATGAAA 1098
                             i              v   v     ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_45706232_4   1099 CTAGACCCCTATCTCTCACCATATACAAAAATTAAATCAAAATGAATTAA 1148
                         i i        i   v                   v        i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_45706232_4   1149 AGACTTAAATCTAAGACCTCGAAATATGAAACAACTGCAAGAAAACACCG 1198
                             i     v     v  vi  v   i    vvi iv         iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_45706232_4   1199 GAGAAACTCTCCAGGACATTGATCTGTGTAAAAATTTCTTGAGTAATACC 1248
                          ? v  v   i iv   v   ivi iv i  vii      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_45706232_4   1249 CCACAAGCACAGGCAACCAAAGTAAAAATGGACAAATGGGATCACATC-T 1297
                            v       i     v    v      i  i    v   iiv    -v
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_45706232_4   1298 AGTTAAAAAGCTTCTGTACAGCAAAGGAAACAATCATTAAAGTGAAGAGA 1347
                          i       -   i   i vv       v  v    vv        i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_45706232_4   1348 TAACCCACAGAATGGGAGAAAATATTTGCAAACTATCTCTCTGACAAAGG 1397
                         i                               ii  v v     i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_45706232_4   1398 ATTAATAACCAGAGTATATAAGGAAGTCAAACAACTCTATGGGAAAAA-- 1445
                          i vi  v     i       i   v  vv       v  iiv     --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_45706232_4   1446 -ATATAATCCAGT--GAAAATACACAAAACATTTGAATAGACATTTCTCA 1492
                         - v    i   i --i     ivi    iv                   v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_45706232_4   1493 AAAGAAGACATACAAATGGAAAACAGGCATATGAAAAGGTGCTCAACATC 1542
                                 i          vv  i i   i        i           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_45706232_4   1543 ACGGATCAT 1551
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.58 (125 / 79)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.75 (7 / 4)  


2114 22.47 5.70 2.37  chr1_45735202_45736825.rev      502  1133 (491)    L1M4_orf2#LINE/L1      256   908 (0)  

  chr1_45735202_4    502 ATTAAGACAATGTAGTATTGGCATAAAGAAAACCAAATGGATCAA----A 547
                           i      i   i   i        i  v iv  v  i      ---- 
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_45735202_4    548 TAGAACACAGAGTACAAAAACAGATCCATGCATATATGACTGACTGAAAT 597
                              ivv     v  i   i i i    i   v    iiii i   v- 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT-T 354

  chr1_45735202_4    598 TTTGAAAAAGGTACCAAGGCAATGCAATGAGGAATGGATAATCT----AA 643
                           i  v  i   i     i v  v     i    v i   i   ----  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_45735202_4    644 CAAATGGTGCTGGAGTAATTATAAATCCACATGCAATAAAGTGAACCTCA 693
                                      iii  i iv v ?          v i i    vi vi
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_45735202_4    694 ACTGTTATCTCATATCTCATACAAAAATTAATCTGCAATGGATCATAGGC 743
                           ivi  i    i i vi             iiiiv         ?  i 
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_45735202_4    744 TTTCTAAATATAAGATTTAAA-CCATAAAGTTTCTACAAGAAAATACAGG 792
                         ---      i     vi    - i     ii ii  v       i i   
  L1M4_orf2#LINE/    505 ---CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_45735202_4    793 ATAAAATCTTAGTGACTTTGGCTTTGGCAAAGACTTCTTGAATATGAAAG 842
                         ?vv       v     i    v  v     v ii     ii      v v
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_45735202_4    843 AAAAAGCACAAACTATTAACAAGAGGAAAAAAAATCAATAAACTAGACAC 892
                         v          i ----     i  ---       vi     i i   vi
  L1M4_orf2#LINE/    602 CAAAAGCACAAGC----AACAAAAG---AAAAAATAGATAAATTGGACTT 644

  chr1_45735202_4    893 ACCACTAAAATGAAAAACTT--G-GTTTTGAAAGACACTGTTATAAAAAC 939
                         --  ii     v        -- - i  ii  i      i i - i   v
  L1M4_orf2#LINE/    645 --CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA-AGAAAG 691

  chr1_45735202_4    940 AAAAAAGGCAGGCCCA---ACTGGGAGAAAATATATGCAAA----ACTTC 982
                         vi     i  i-    --- v             v      ---- iv  
  L1M4_orf2#LINE/    692 TGAAAAGACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_45735202_4    983 TGATAAAGGACTTG-------AATATATAAAGAACTCTTAGAACGTAGTA 1025
                               i       -------                   v   vi i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_45735202_4   1026 ATAAAAA-----ACAATCCAAT-AAAAAGGGGGCGAAAGATTTTAACAAA 1069
                                ----- i  i     -?    iv    i  i     v  i i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_45735202_4   1070 CATGTCATCAAAGA---TACACAGATGGCAAATAAGCACATGAAAAGATG 1116
                            v  vi      ---  i   i     v                    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_45735202_4   1117 C-CAACATTATTGCTCAC 1133
                          -      i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (92 / 46)
Gap_init rate = 0.03 (19 / 653), avg. gap size = 2.68 (51 / 19)  


 295 28.68 5.43 1.55  chr1_45804495_45807765.rev     1019  1147 (2124)    L1M4_orf2#LINE/L1       13   146 (762)  

  chr1_45804495_4   1019 CCGTGCTCATGATTTGGAAGATTTA---TTATGAAGATGTCAGTTCTCCC 1065
                           i  i     iv        i   ---  i v      v  i v     
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_45804495_4   1066 -ATTTTGATCTA--GATTTATTGCCATTCCAAGCAATGTCATAGCAATAT 1112
                         - vv        --    i vi  v  i  v v   vi  vi   viiv 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_45804495_4   1113 TTTCCCCCTTAAATTTGACA-GTTGTTTTTAAAATT 1147
                            iiv v--i  v      - i  v ii       
  L1M4_orf2#LINE/    113 TTTTTGCA--GAAATTGACAAGCTGATCCTAAAATT 146

Transitions / transversions = 1.06 (19 / 18)
Gap_init rate = 0.04 (5 / 134), avg. gap size = 1.80 (9 / 5)  

 835 30.54 13.39 0.89  chr1_45804495_45807765.rev     2213  2772 (499)    L1M4_orf2#LINE/L1      259   888 (20)  

  chr1_45804495_4   2213 AAGACA-TATGGTAGTAGTGTAGAAATATGTAAATAAGCCAATGGAACAT 2261
                               - i     v i ii  iii   vii v   iii        i v
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_45804495_4   2262 AA------ATTTGGAAGCAGTTGCATACATATATAG--AAACAATTTATG 2303
                           ------i iii   ii iviv       v   i --  vii    vi 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_45804495_4   2304 ATAGAGCTGGCTGTATAAATCAGTGGAAAAAGAATA--CTT--------- 2342
                          i ii v  v viv iv v   i   ii        --   ---------
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_45804495_4   2343 -----CTGGGACAGTTTTTTTTTCATATGGAAAAGAATGAAATTGGACCT 2387
                         -----        ii vvv v?i  i   v           i       i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_45804495_4   2388 GGGTCTCATACCGTATACAAA--TCATTTCCAACTG-ATTG------TAA 2428
                         vvii    i   i        -- i vi  v  v  -  ii------   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_45804495_4   2429 ATGTGAAAGACAAAACT-TAAAACTA--AGAAGTCAATATAGG--TAAAT 2473
                             i i  vi      -       v--     vv  i     --     
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_45804495_4   2474 TGTTTG-GACCTTGGAGAAG--AACTGTTAC--AAACAAGACAC-AGAAA 2517
                         i-  i -        ivv  --  iv   v -- i i v     - i  i
  L1M4_orf2#LINE/    559 C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_45804495_4   2518 TGTGAATCATAAAGGAAATGACCAGCAGCTTTGATTGCATCTAAATTAAG 2567
                         iiii iiv i   i    vi iviii iv  v  i v    v       i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_45804495_4   2568 AACGT--GTGCTCATCAA--GACATGGGAAAGAAAATCAAAAGATAACCC 2613
                            v --     --    --    ivivv      i v      i     
  L1M4_orf2#LINE/    658 AACTTTTGTGCT--TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_45804495_4   2614 ATGAAGTGGAAAAAGGTATTTGCAACTCATATAATC--ATA--GGATTCG 2659
                          iii i   i i  ii         v       -  --   --   i i 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATA-TCTGATAAGGGACTTG 754

  chr1_45804495_4   2660 TATCTG--ATTTATT-----CTCTTGCA--TTAATAA------GATCAAC 2694
                             ii--  v   v-----     i  -- i     ------  iv  i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_45804495_4   2695 AACCAAAA-GAAGAATGG-TAAAAA----GAATAGGTATC-CTATAAAAA 2737
                             v  v-?  i     -i   ii----      ii  i-  vi   i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_45804495_4   2738 GGGAAGTACAAAGACCTGATAAATAGATTAAAAGA 2772
                         i iv -      viv ii    ii v  v      
  L1M4_orf2#LINE/    855 AGATA-TACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.91 (111 / 58)
Gap_init rate = 0.05 (31 / 630), avg. gap size = 2.58 (80 / 31)  


2392 22.97 0.45 5.71  chr1_45968537_45971543.rev     1262  1927 (1080)    L1M4_orf2#LINE/L1        1   631 (277)  

  chr1_45968537_4   1262 TGGAAAGACATCTCACATCTCATGTTCATGGATTGGAAGAACCAGTAACA 1311
                                 i   i  -------                  -------- v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCA-------TGTTCATGGATTGGAAGA--------CT 35

  chr1_45968537_4   1312 TAAAAATGATCATACAACCAATAATGTCAAAATGATCATACTACCAAAAG 1361
                            ------------------  v   i  i   iiv     v  v   -
  L1M4_orf2#LINE/     36 TAA------------------TATTGTTAAGATGGCAATACTCCCCAAA- 66

  chr1_45968537_4   1362 CTG-TCTATAGATTCAATGCAATCCCTATCAAAATACCAGTGACATTCTT 1410
                         i  -    i        i                 v    ivi v  i  
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTT 116

  chr1_45968537_4   1411 CTCAGAATGTTTCACAGAAAAAAATCCTAAAATTCATATGGAACTACAGA 1460
                         iv     v--  v   -- ivvi                    v i  ii
  L1M4_orf2#LINE/    117 TGCAGAAA--TTGACA--AGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr1_45968537_4   1461 AAACTCCTAATAGCCAAAGCAATCCTGAGCAAAAAGAACAAAGTGGGATG 1510
                         ii  i vv          i     i   iv  i           v   v 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr1_45968537_4   1511 CATCACACTACCTGACTTCAAAATATACTACAAGGCTATAGTAACTAAAA 1560
                         vv       v  ii i       iv        i    i     ii  i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_45968537_4   1561 CAGCATAGTACTGACCTAAAAATGGATATATACACCTATGGAATGGAATA 1610
                            ii i      i v   ii  i  i     v i v       i    v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_45968537_4   1611 GAGAACGC-GAAATAAATCCATGTATTTACAGCCAACTGATTTTTGACTA 1659
                             iiv -        i    ii     ii i   i       i   v 
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_45968537_4   1660 AGGCACCAAGAACATTCATTGGAGGAAGTAAAGTCTCTTCAATAAATG-T 1708
                         i  ii      v      v   i i   v v     i     i     - 
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_45968537_4   1709 ACTAGGAAAACTGGATATCTGTATGCTGTAGAATGAAACCAGACCTTTAT 1758
                         i  i   v         ? iii    viv        iiii    ii  i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_45968537_4   1759 CTCTCACAATATACAAAAATCAACTCAAAATGGACTAAAGACTTAAATGT 1808
                            v   v            i             ii ?    i       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_45968537_4   1809 AAGACCTGAAACTATGAAACTACTAAAAGAAAGTATAAAAGAAACACTCC 1858
                             v  i       i     vi  i      ii   ii? v  vv  i 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_45968537_4   1859 AAAACATGGGACTGGGCAAAGATTTTATAGATAATACCTCACAAGCACAA 1908
                         ivi  v v  ii i     v i   iv      vv  vi  v        
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_45968537_4   1909 GCAACAAACTCAAAAATAG 1927
                                 vvv        
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAG 631

Transitions / transversions = 1.73 (95 / 55)
Gap_init rate = 0.01 (9 / 631), avg. gap size = 4.56 (41 / 9)  

 991 20.33 2.62 2.30  chr1_45968537_45971543.rev     2212  2516 (491)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr1_45968537_4   2212 AAAAAAAGAAGCAAAAATAGACAAAAGGGATTA-TT--ACTATATCAAA- 2257
                             iv v      v  v   v    vi   v -  --   vi      -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_45968537_4   2258 CTAAAATCTTCTCCACAGCAAAGGAAACTATCAACAGAGTGAAGAGACAA 2307
                         i     v   i vii vv       v        v i      i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_45968537_4   2308 CCAGTAGAATGGGAGAAAATATTTTCAAA--ATATTAATCTGGCAAAGGA 2355
                           vii                   v    --    --     ii  i   
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGATAAGGGA 750

  chr1_45968537_4   2356 TTAATA-CCACGAATATACAAGGAACTCAAACAATTCAACAGCAAAAACA 2404
                         i vi  -   -       i  i      vv    i    i ii     v 
  L1M4_orf2#LINE/    751 CTTGTATCCA-GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_45968537_4   2405 CCCAAAGAATCCAATTTTTTTAAATGGGCAAATGAGTTGAATAGACATCT 2454
                          --   v  i      ?vv--           v  v            i 
  L1M4_orf2#LINE/    800 C--AAATAACCCAATTWAA--AAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_45968537_4   2455 CTC-AAATGAGACATACAAATGGCCAGCAGGTATATAAAAGAACGCTCAA 2503
                            -   vi   i             ii i i i  i   ii i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_45968537_4   2504 CATCACTAATCAC 2516
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (35 / 26)
Gap_init rate = 0.03 (10 / 306), avg. gap size = 1.50 (15 / 10)  


2932 24.24 2.72 4.13  chr1_46027395_46029906.rev     1103  2022 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_46027395_4   1103 GGAAAAAAATTTCATGCTCATGGATTAGAAGAATCAATACTGTTGAAACA 1152
                              i v  ii    i         i     v i    i    i i ii
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_46027395_4   1153 GCCATACTGTCCAAATCAATCTACAGATTCAGCATAATTCTTATCAAACT 1202
                           v     vi      ii             i ii   i i       v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_46027395_4   1203 ACCAA-TGTCATTTTTCACAGAACTAGAAAGAACT-ATTCTAAAATTTAC 1250
                         v   i-  i -     ii     v v  v - i  -  i        i i
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr1_46027395_4   1251 ATGAAACCAAAAAAGAGCTCAAATAGCCAAAACAATCCTAAGCAAAAAGA 1300
                            i  viiv  ii  v ivi                i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_46027395_4   1301 ACAAAGCTGCAGGGATTACATTACCCAGCTTCAGACTATACTATAAGGCT 1350
                               i  v   iv i   i v    ii    i viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_46027395_4   1351 ACAGTGTTTAAAAAAAAAAAAAAAAAAAAGCATAGTACTGGTACAAAAGC 1400
                              --------------  vv  i v  ii i       i i  iiii
  L1M4_orf2#LINE/    250 ACAGT--------------AATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_46027395_4   1401 AGACACATAGACCTATAGAACAGAATAGAGAACCCAGAAATAAAGCCACA 1450
                              i     i v  i   i     v    ii           v   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_46027395_4   1451 CACCTACAATCTTCTGATCTTTAGCAAAGTCAACAAAAATAAGCAATGGG 1500
                           ii  iii  vvi    i  iii   i viiv   i vi vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_46027395_4   1501 GAGAGGAC--TCTATTCAATAAATAGTGCTGGGATAGCTGGCTAGGCACA 1548
                           i  i i--   v     i    i         i i    v  ?v    
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_46027395_4   1549 TGCAGAAGAATGAAACTGGAACCCTACCTTTCACCACATACAAAAATTAA 1598
                             i         ii    v        iv     i             
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_46027395_4   1599 CTCAAGATGGATTAAAGATTTAAATGTAAGACCTCAAACTGTAAGAATCC 1648
                              i      i ?   ii           v  v     i   i v  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_46027395_4   1649 TAGGGAAAAAACAAACAAACAAACTAGGAA-ACACCATTCCAGACACTGA 1697
                            i- i      -----------    ?i- v i -   -- ----   
  L1M4_orf2#LINE/    536 TAGA-AGAAAACA-----------TAGGNGTAAATC-TTC--G----TGA 566

  chr1_46027395_4   1698 CCTTGGG--AAACAAT------TTATGAC-TGAGTCCTCAAAAGCAATTG 1738
                                -- ii    ------   -  i-   -- vi        vvv 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTA-GATATGA--CACCAAAAGCACAAG 613

  chr1_46027395_4   1739 CAACAAAAACAAAAATTGTCAAGTGGGACCTAATTAGACTAAAGAGTTTC 1788
                                 iv      v vi  i v    i v  i i v v  i ii  i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_46027395_4   1789 TGCACAGCAAAAGAAACAATCAGTAGAGTTAA----CAGCCTACAGAATG 1834
                           ii vv    i  v  v    iv i   v  ----  i  i        
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_46027395_4   1835 GGAGAAAATATTTGCAAACTATGCATCTGACAAAGGTCTAATATCTAGAC 1884
                                           ii  ii      i  i  v  vi    i   v
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_46027395_4   1885 TCTATAAAGAACTTAAACAATTAAACAAGCAAAAAACAA----CCCCATC 1930
                          v           ivv    i v  i  vv    i    ----   v  i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_46027395_4   1931 ACAAAATGGGCAAAAGACATGAACAGACACTTCTCAAAAGAAGATATACA 1980
                         ?v            i  iv    i     i     v              
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_46027395_4   1981 GGCAGCCAACAA--ACATGAAAACATGCTCCACAT-ACTAACCAT 2022
                         iiii     i  --         v      v    - ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (146 / 73)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 3.00 (63 / 21)  


2819 26.00 4.33 0.80  chr1_46077957_46081938.rev     2616  3492 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_46077957_4   2616 TGGAAAAACATCCTATGATCATGGATAGGAAGAATCAATATCGTGAAAAT 2665
                               i i    i   v        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_46077957_4   2666 GACTACACTGCCCAAA------------------GCAATTTTAATCAAAT 2697
                          i v i   v      ------------------     iiiv      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_46077957_4   2698 TACCAA-TGTCGTTTTTCACAGAATCAGAAAAAACCATTCCAAAATTCAT 2746
                          v   i-  i -     ii     viv  v  iviv  i i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_46077957_4   2747 ATGGAAC--CAAAGAAGAGCCCACA-TAGTAAAAGCAATCGTAAGCAAAA 2793
                               v--   i i ---    v -   iv   i     v i iv  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_46077957_4   2794 ATAACAAAGCTGGAAGCATCACACTACTCGACTTCAAATTATACTACAAG 2843
                          v       i    i vv       v i i i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_46077957_4   2844 GCTATAGTCACCAAAACATCATGGTACTGGTACAAAAACAGACACACAGC 2893
                             i   v i   i   vii         i i  ii i     i i  v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_46077957_4   2894 TCAATGAAATAAAACAGAGAACCCAGAAGTCAATCCATACACCTACAGTA 2943
                               i    i  iv    ii      i v  i       ii  ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_46077957_4   2944 AAGTGATCTTCAACAAAGTTGACCACAATAATCAATGGGGAAAGGACACT 2993
                           v    i   i    i v  v v v vi v             i i v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_46077957_4   2994 CCATTCAATGAATGGTGCTGGGAAAATTGGCTAGCCATATGCAGAAGAAT 3043
                          iv     ii             v  i   v  ?   i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_46077957_4   3044 GAAACTGGACCCCTATCTCTCACCATATATAAAAATTAACACATGATGGA 3093
                            ii          i   v         i          v  vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_46077957_4   3094 TTAAAAATTTAAATTTAAGACCTGAAACTATAAAAACCCTAAAAGAATAC 3143
                          i ? i ii     v     v  i           vi i  i     v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_46077957_4   3144 CTAGGAAAAACTCTTATGGACATTGGCCTAGGCAAATAATTTAT--GACT 3191
                         v    ?iv  v    vvv   v    vi       - ii   v --  - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA-T 594

  chr1_46077957_4   3192 AAGACCTCAAAAACAAATATGACCAAAACGAAAATGGACAAATGAGACTT 3241
                          v   vi     i  v viii  v   ivi     i  i    vi     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_46077957_4   3242 AATTAAACTAAAGAGCTTCTGTACAGCACAAGAAACAATCAACAGAATAA 3291
                         v  i   v v  i i   i   i vv  v i  v  v     v i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_46077957_4   3292 AAAGACAACCCATAGAATGGGAGAAAATATCTGCCAACTACGCATCCAAC 3341
                                     i                 i   v  ii iii   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_46077957_4   3342 AAAGGACTAATATCCAGAATCTATAAGGAACTT----AAATCG-TAAGAA 3386
                           i     vi          v     i     i----  v  i-   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_46077957_4   3387 AAAAACAAATAAATCTGCTAAAAAGTAGGCAATAGAAACGAACAGACA-- 3434
                            i        vi vii ?    i i     vi  vvi   i     --
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_46077957_4   3435 ---CAAAAGAAGA----CAAGTGACCAACAAACTCATGAAAAAAATATCC 3477
                         --- v        ----   i  i    i  i v        i - iii 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chr1_46077957_4   3478 AACATCGGCCGGGCG 3492
                               i????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.21 (45 / 14)  


 542 22.13 1.64 0.82  chr1_46116006_46119995.rev     2348  2469 (1521)    L1M4_orf2#LINE/L1       17   139 (769)  

  chr1_46116006_4   2348 GTTCTTGGATTAGAA--CTCAGTGTTGTTGAGATGGCAATTCTCCCTCAA 2395
                             v      i   --  i i i     i          v     -   
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC-CAA 65

  chr1_46116006_4   2396 ACTGATGTATAAATTCAAAGTAATCATTATCAAAATGCCAGCAAGGTCTT 2445
                          i    v  i i      v i    vi         v     vivv i  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_46116006_4   2446 TTGTAGAAATTGAAAAATTGGGCC 2469
                            i         v  ii  iv  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCC 139

Transitions / transversions = 1.45 (16 / 11)
Gap_init rate = 0.02 (2 / 123), avg. gap size = 1.50 (3 / 2)  

2504 22.22 7.99 1.08  chr1_46116006_46119995.rev     2767  3504 (486)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr1_46116006_4   2767 AAAAATTGAAAAATTGATCCTCATACTTATATAGCAACACAAAGCACCCA 2816
                          i       v  ii       v v i i    i v  ii   i v     
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_46116006_4   2817 AAACACATAAAATAATTTTGAAAAAGAA---CAAAGTTGGAGGAATTATA 2863
                         i  i vvi    i   i           ---             v i i 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_46116006_4   2864 CCACCTGATTTCAAAACTTAGTATAAAGCCACATTAAACAAAGATAGTGT 2913
                          iv  ii             v  i     i   v   v   -  i     
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA-GACAGTGT 268

  chr1_46116006_4   2914 GGAATTAGCACAAGGATAGGCATATAGATTAATGGAAGGCAAGAGAGAGT 2963
                           v i i   i        i         i       viv  vv      
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_46116006_4   2964 CCAGAAATAAACTGTTAACACTTGTGGTCAATTGACTT-CAACAAAGGTG 3012
                                     ivv  -  i  i           i  - i    i    
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATA-CATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_46116006_4   3013 TCAAGAGGATTCAATAGTAGAAGGATACCCTTTCCAGCGAATTCTGCTAG 3062
                         i     vv       i vii   i   vi    i  i i   vv    i 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_46116006_4   3063 AAAAATTGGACAGTCACACACACAC--AT----TTG-------ACCTCAT 3099
                         i v  i    i ?i    ii  v v--  ----   -------      i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_46116006_4   3100 ACCATACATAAATATTAACTCAAA-TGGATCATAAACCTAAATTTAGGAG 3148
                               i i   v           -       ? i        v  i   
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_46116006_4   3149 TAGAAAATGTAAAACTTCTGGAAGAAAATGGAAAAAAAAAAC------AG 3192
                         ivi   v i       ii i        iiv ii?iv   v ------ v
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_46116006_4   3193 CTTGGGTTAGGCAAGTAAGTTCTTAGATA-----CCAAAAGCATGATCAA 3237
                                       - iiv          -----         ii v   
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_46116006_4   3238 TAAAA-----AATAAA-AAATT-------ATCAA---------TTTTTGC 3265
                         i    -----    i -     -------     ---------i     i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_46116006_4   3266 ATTTCAAACGACACCATCCAAATACATGGAAAGA--ACCACCATAGACAG 3313
                         ii      v     i   v i - vi  i     --   --  i   vv 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGA-AAGTGAAAAGACAACC--CACAGAATG 713

  chr1_46116006_4   3314 GGAGAAAATAATTGCAAATCATATAGCTAATAAAGGGCTTGTATCTAGAA 3363
                                   v              v  i    i  i        i    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_46116006_4   3364 CATACAAAGAACTC--AAGGCTCAATATTTAAAAAAAAAACGAACAGATT 3411
                         i   i         -- vii       v v    i v   i-   vv v 
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT-AACCCAAT 812

  chr1_46116006_4   3412 TTTTAAATGAACAAAAATATTTGATCAGACATTCCACCAAAAAAGATATA 3461
                          ?vv     ii    ii-      vi       i v     i        
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGG-ATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_46116006_4   3462 CAAATGGCTAACAATGAGAT---AAGATGCTCAG-ATCATTACCCAT 3504
                                 i  i  vv v  ---          i-    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (101 / 59)
Gap_init rate = 0.03 (23 / 789), avg. gap size = 2.91 (67 / 23)  


2386 23.60 3.55 4.09  chr1_46167486_46170068.rev      861  1593 (990)    L1M4_orf2#LINE/L1       14   742 (166)  

  chr1_46167486_4    861 CATGATCATAA--TGGAAGACTCAATATGACTAAAATGTTAATTATAAGC 908
                             v    ii--         i     vii   i   vi   vv vvv 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr1_46167486_4    909 AATTTGATCTACGGATTAAATGCAATCCCAATCAAAATCCAAGCAAGTTA 958
                           v         i    v  i        v          v   vivi v
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr1_46167486_4    959 GTTTGTGAATATTGACAAATTGATTCTAAAGTTTACATGGAAAGGCAAAA 1008
                         v    iii v        ii    i     i  i i       v    ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_46167486_4   1009 TAACCTAAACAACCAATACAATACTGAA---GAAGAATAAGGTTAGAGGA 1055
                         v v  vi  i i    v     vi    ---      i  i   i     
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_46167486_4   1056 CTGATATTACCTGACCTCAAGACTCACTATAAAGCTATAGTGATCAAGAC 1105
                           v i i v  ii ii    i   i    i       i   i        
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_46167486_4   1106 AACATGGT---GG---AAGAACAGATACATAAATCAGCAGAACAAAGCAG 1149
                          iii    ---  ---   i i   i i   i    iii   i i iiv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_46167486_4   1150 AGACTCCACAAACAGACCCATACAAATATAGTCAACTGATATATGACAAA 1199
                            v    v   i i         vv   i     i    v vi     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_46167486_4   1200 GGAGCACTGGCAATTCAATGAAGAAAATATA-TATTCTCATTGACGAATG 1248
                           v  vvv i v        ii    iv   - v  i   ---  i    
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA---ACAAATG 410

  chr1_46167486_4   1249 GTGCTGGAACAACTGAATGTTCATATGCAAAAAAATGAATCTAGA----T 1294
                                i       i  i?i  i        i      vi i  ---- 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_46167486_4   1295 AC---A-ACCTTTTACAAAAATTAACTCAAAATGGGTCATGAAAATGATC 1340
                           --- -   v v                      i   ?----------
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW---------- 500

  chr1_46167486_4   1341 CGAATGTAAGATTTACCTAAATGTAAAAACAAAAAACGATAAAACTTGTA 1390
                         --------   ----           i i v    - v        iv  
  L1M4_orf2#LINE/    501 --------AGA----CCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTA 537

  chr1_46167486_4   1391 TATGATAACATAGGACAAAATCTAGGTGACCTTGGGTTTGGCGATGAATT 1440
                         v v  v        ?vv      vv             v   i   iv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_46167486_4   1441 TTTAGGATATGAAACCAAAAGCA-AAACCATGAAAAAAAACATTAATAAG 1489
                         i    -      v          -  i v ii   i    v  vi    i
  L1M4_orf2#LINE/    588 CTTAG-ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_46167486_4   1490 CTAGACTGCATTAAAATTAAGAACTTCTG-----CAAAAGATACTGTTAA 1534
                         i i    v   i        i     i  -----    i  i   i i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_46167486_4   1535 GAGAATGAAAAAGACAGACCATAGACTAGGAGGAAATATCTGTAAAAAAC 1584
                           i i      -    iv   i   v i    i      i  i   v-- 
  L1M4_orf2#LINE/    687 GAAAGTGAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAAT--C 733

  chr1_46167486_4   1585 ACATACTTG 1593
                          i   ii  
  L1M4_orf2#LINE/    734 ATATATCTG 742

Transitions / transversions = 1.74 (108 / 62)
Gap_init rate = 0.02 (17 / 729), avg. gap size = 3.29 (56 / 17)  

 562 20.21 10.36 2.07  chr1_46167486_46170068.rev     1900  2092 (491)    L1M4_orf2#LINE/L1      700   908 (0)  

  chr1_46167486_4   1900 CAACCCCCAAAACAAAACAAAAC-----CAAAAACCCACATACTTGATAA 1944
                               v  i  iiii v    i-----    ---i  i   ii      
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAA---TCATATATCTGATAA 746

  chr1_46167486_4   1945 AAGAC---------AAATGTGTAAAGAACTCTTAAATCTCAACAAGAAAA 1985
                         ii   ---------i   i i             v v     i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_46167486_4   1986 ---CAAACAACCCAATTTTAAAAATGAGCAAAAGATCTGAACAGCCACCT 2032
                         ---    i         ?-       i     i   i    i  v  ii 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_46167486_4   2033 CACCAAAGA---TATACAGATAGCAAACAAGTATATAAAAAGATTCTCAA 2079
                          v       ---      i  i  v  i   i i  i       v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_46167486_4   2080 CATCATTTGGCAT 2092
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 3.22 (29 / 9)
Gap_init rate = 0.03 (6 / 209), avg. gap size = 4.00 (24 / 6)  


3103 27.72 1.22 0.55  chr1_46191789_46195771     2589  3490 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_46191789_4   2589 TGGAAGAGCATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2638
                              iiii  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_46191789_4   2639 GGCCATACTGCCCAAGGTAATTTTTATAGATTCAACACCATCCCCATCAA 2688
                            v     v     iv i  i -- i         i v     i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCT--ACAGATTCAACGCAATCCCTATCAA 98

  chr1_46191789_4   2689 GCTACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTC 2737
                         iv v   iivi i  i  ii     v v  v  i-  - iii    i   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr1_46191789_4   2738 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 2787
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_46191789_4   2788 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 2837
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_46191789_4   2838 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 2887
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_46191789_4   2888 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAAC 2935
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_46191789_4   2936 TATCTGATCTTTGACAAACCTGAGAAAAATAAGCAATGGGGAAAGGATTC 2985
                         i vi    i  i     ivv  vv  i vi vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_46191789_4   2986 CCTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGTAGAAAGC 3035
                         i  v  i  i           i  v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_46191789_4   3036 TGAAATTGGATCCCTTCCGTACACCTTATATAAAAATTAATTCAAGATGG 3085
                             i     i    v  vi     v    i         i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_46191789_4   3086 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3135
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_46191789_4   3136 CCTAGGCATTACCATTCAGGACATAGGCTTGGGCAAGGACTTCATGTCTA 3185
                          v    ?i v viv   iv   v v  v  i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_46191789_4   3186 AAGCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3235
                         vii           vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_46191789_4   3236 ATTAAACGAAAGAGCTGCTGCACAGCAAAAGAAACTACCATCAGAGGGAA 3285
                           i   vvv  i i  vi  ii vv    i  v    i  vv i  v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_46191789_4   3286 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 3335
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_46191789_4   3336 AAGGGCTAATATCCAGAATCTACAATGAACTC----AAATTTACAAGAAA 3381
                          i  i  vi          v  i  v      ----  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_46191789_4   3382 AAAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAGCAGACACTT 3427
                           i    ----   v  i?    i     i     iv   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_46191789_4   3428 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 3477
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_46191789_4   3478 CATCACTGGCCAT 3490
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


1242 27.14 17.93 1.66  chr1_46943161_46944949.rev      518  1298 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_46943161_4    518 TGGGGAAATATACCAAATCCATGGATGAGAAGACTCAGTATCACAAAGGT 567
                            ii i    v   vi i       vi       i i   iiiv   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_46943161_4    568 GGCACTTCTTCCTAAAGTAATCCATAATTTCAATGCCATTCCAAACAAAA 617
                             v v  i  i   v i   i i iv     i  v  i  v v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_46943161_4    618 TAGTAACAGGAATTTTTGTGGGACTTACTGAGCTGGTCCTAAAATTCTTA 667
                          vvi i v vvv      ii i v  ivii     i           v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_46943161_4    668 TGGAAGAATAAATGGCTAAGTATAGCCAGAAGAA-CTGGAAAAAGAGTAA 716
                              ivii  iv i iv  v       i  v  -  v        iv  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_46943161_4    717 --GAGT----GAACTTGC-CTTCATAGGGATATCAAGACTT--TTCAAAG 757
                         --i   ---- i   ii -    vi ---  v    i    -- v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCA---ATTTCAAAACTTACTACAAAG 247

  chr1_46943161_4    758 CTATAATAATATTTAGA-AGTGTGGTAATGTCA----------------- 789
                            i i    --iv   -         v  v  -----------------
  L1M4_orf2#LINE/    248 CTACAGTAAT--CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_46943161_4    790 --CAATGGAACAGAA---AGA--CTA-------------ACAT-----GT 814
                         --        i    ---   -- i -------------    -----  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_46943161_4    815 TAAAACTTCATGTAAGATGAAAGTATCATTACAAATCAGTGTGAATAAAT 864
                         i  ---  v  v vv  ii ii  ii  vv  v v   i  v i v i v
  L1M4_orf2#LINE/    346 CAA---TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_46943161_4    865 TAAGTATT---AATAGATGATGCTATAACTATTGACTATCCACATGAAAA 911
                           -  v  ---  i i   i    ivi  v i  iv  ?       v   
  L1M4_orf2#LINE/    393 TA-GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_46943161_4    912 TGAGGAAAATTAGATCTCT----CATATCATACTTAAAAATT----CCAA 953
                         v  ivi  i  i  i i  ----  i i    ivi       ---- v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_46943161_4    954 ATGGATTAAAGACCTAAACATTAATTTGTTAAAGCTTTAAAACTTTTA-- 1001
                               i ?         ii v iv-- i    i  v       i   --
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGA--GCTAAAACTATAAAACTCTTAGA 539

  chr1_46943161_4   1002 ---AACCATAAGGGAAAA--------A--TTGA----------------- 1021
                         ---  v    i ? v   -------- --   i-----------------
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_46943161_4   1022 TATATCTGAT--CAGAA-----------------AAAAATGGATAAATTT 1052
                           v  v   i--  i  -----------------      i        v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_46943161_4   1053 TACCACATTAAAATTTGAAATTTGTGTATGACAAAAGGTATTTAATAAGC 1102
                         v  iv   i      vi   i  v   iivv    i ii i - vi   v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGA 688

  chr1_46943161_4   1103 AAGATTGAAAGACAAGTCACAGACTGA-ATCAGATATTTAAAAAGCATAT 1151
                            - vi        vi      v  i- vv i      iv   v     
  L1M4_orf2#LINE/    689 AAG-TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_46943161_4   1152 A-------AG-------CATCCAAAATATATAAAGA---TTTACAAAT-A 1183
                          -------  -------i     i            ---i      v - 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_46943161_4   1184 ATAAGCAAAAGACAAACATACCAATTAAGAAATGGGCAAAAAACATAAAA 1233
                             vv          i vv      ? i           ii iv i  v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_46943161_4   1234 AGGCAATT-TATAAATGAAATAT-CAA-TGGCCAA-AA--ACATGGAGAA 1277
                           i  v  - vi   vi i    -   -       -  --     i i i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_46943161_4   1278 ATGTTTAACCTCACTAGAAAT 1298
                            i i   v   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (121 / 87)
Gap_init rate = 0.04 (37 / 908), avg. gap size = 4.14 (153 / 37)  


2006 27.27 0.39 0.39  chr1_46954289_46960163.rev     2890  3406 (2469)    L1M4_orf2#LINE/L1        1   517 (391)  

  chr1_46954289_4   2890 TGGAAACACGTTTCACACTCATGGATGGGTAGAATCAATATTGTGAAAAT 2939
                               v ii ii  iii        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_46954289_4   2940 GACTATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCTCATCAAAA 2989
                          i v     v  v   vii       i      i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_46954289_4   2990 TACTACCATCATTCTTCACAGAGTTAGAAAAAAAAATTCTAAAATTCATA 3039
                          v i v vv v  i  ii    iv v  v  ivvi  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_46954289_4   3040 TAGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 3089
                          i   viiv  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_46954289_4   3090 CAAATCTGGACGCATCACACTACCTGATTTCAAACTGTACTATAAGGCCA 3139
                             vi    v vv       v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_46954289_4   3140 TAGTCACCAAAACAGCATGGTACTGGTGTAAAAATAGGCACACAGACCAA 3189
                         i   v i   i    ii         ii   ii    i  i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_46954289_4   3190 TGGAACAGAATAGAGAGCCCAGAAATAAACCCAAATACTTACAGCCAACT 3239
                              i     v     i               v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_46954289_4   3240 GATCTTTGACAAGAAAACAAAAAC--TTAAAGTGAGGGAAGGACACCCTT 3287
                            i  i      iivi v  i  --  v  -  i  i   i i vi   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTT 399

  chr1_46954289_4   3288 TTCAATAAATGATGCTGGGATAATTGGCTAGCCACATGTAAGAGAATGAA 3337
                              i     i        i  i   v  ?       i  i        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_46954289_4   3338 ACTGGATCCTCATCTCTTACCTTATACAAAAATCAACTCAAGATGGATTA 3387
                         ii    i  ii i   vi   v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_46954289_4   3388 AGGACTTAAACCTAATGAG 3406
                         ?i   i    iv   -   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAA-GAG 517

Transitions / transversions = 2.09 (94 / 45)
Gap_init rate = 0.01 (3 / 517), avg. gap size = 1.33 (4 / 3)  

1224 27.46 0.25 0.25  chr1_46954289_46960163.rev     4988  5384 (491)    L1M4_orf2#LINE/L1      512   908 (0)  

  chr1_46954289_4   4988 TAAGACTTGAAACTATAAAAATTCTAGAAGATAACATTGGAAAAACCCTT 5037
                              vi i           v ii       v     v  ?iv  vi   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_46954289_4   5038 CTAAACAATGACCTAGGCAAGGATTTCATGACCAAAAACCCAAAAGCAAT 5087
                          vvi  vv  ivi       v i    v iivi vi vv         vv
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_46954289_4   5088 TGCAATAAAAACAAAGATAAATAGCTGGGACCTAATTAAACTAAAGAGCT 5137
                         v    i    iv   i   i   iv v    i v  i   v v  i i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_46954289_4   5138 TTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAATAGACAACCCACAGAG 5187
                             ii vv    i iv  vi   iv i   i  v              i
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_46954289_4   5188 TGGGAGGAAATCTTCACAATCTGTATGTCTGACAAAGGACTAACATCGAG 5237
                               i    v  ii   viii   i     i  i     vii   v  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_46954289_4   5238 AATCTACAATGAACTGAAACAAGTCAGTAAGAAAAAAAACAATCAATCCC 5287
                            v  i  v     vvv    v   i   v     i -   vi  i  v
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCA 810

  chr1_46954289_4   5288 ATCAAAAAGTGGGCTAAGGACATGAATAGATAGTTCTCAAAAGAAGATAT 5337
                           i?    i     v     iv        i v     v           
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_46954289_4   5338 ACAAATGAC-AACAAACATATGAAAAAATGCTCAACATTACTAATGAT 5384
                                i -  i  i  i       i           i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (58 / 49)
Gap_init rate = 0.01 (2 / 397), avg. gap size = 1.00 (2 / 2)  


3188 26.93 0.77 0.55  chr1_47003081_47009498.rev     5022  5927 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47003081_4   5022 TAGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5071
                          i   ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47003081_4   5072 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCGTCCCCATCAAGC 5121
                            v     vi    iv i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47003081_4   5122 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 5169
                          v   iivi i  i  ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_47003081_4   5170 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5219
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_47003081_4   5220 AATAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5269
                           i    i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_47003081_4   5270 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5319
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_47003081_4   5320 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCATACATCTACAACC 5367
                                i    i--    i  --        vv        i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_47003081_4   5368 ATCTGATCTTTGACAAACCTGACAAAAACAAAAAATGCGGAAAAGATTCC 5417
                          vi    i  i     ivv  v   i v  vvv    v     ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_47003081_4   5418 CTATTTAATAAATGGTGCTGGGAAAACCGGCTAGCCATATGTAGAAAGCT 5467
                           v  i  i              v   i  v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_47003081_4   5468 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5517
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_47003081_4   5518 TTAAAGACTTAAATGTTAGGCCTAAAACCATAAAAACCCTAGAAGAAAAG 5567
                          i ?    i       v  iv       i      vi i          v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_47003081_4   5568 CTAGGCA-ATACCATTAAGAACATAGGCATGGGCAAAGATTTCATGACTA 5616
                         v    ?i- v i v iiv  v v i  i- i     v i    v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr1_47003081_4   5617 AAATACTAAAAGCAATGGCAACAAA-GCCAAAATTGACAAATGGGATCTA 5665
                         vi i  i       vvi        - vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_47003081_4   5666 ATTAAACAAAAGAGCTTCTGCACACCAAAAGAAACTACCATCAGAGTGAA 5715
                           i   vvv  i i   i  ii vi    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_47003081_4   5716 CAGGCAACCTACAGAATGGGAGAAAATTTGTGCAATCTACCCATCTGACA 5765
                         v  i     i                 v v     vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_47003081_4   5766 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5815
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_47003081_4   5816 AAATCAAACAACCCCATC-AAAAGTAGGCGAAGGATATGAATAGACACTT 5864
                           iv    i     v  i-    i i   i      v          i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_47003081_4   5865 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5914
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_47003081_4   5915 CATCACTGGCCAT 5927
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2842 25.41 6.26 0.93  chr1_47017722_47020230.rev     1158  2019 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47017722_4   1158 TGGGAAAACATTTCATGCTCATGAATTGGTAGCATCAAAATTGTTAAAAT 1207
                            i  i i  ii    i     i     v  vv i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47017722_4   1208 GACCGTACTTCCCAAAGCAATCTACAGATTCAGTGCTATTCCTATCAAG- 1256
                          i vi    i      vii             ii  v  i        i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47017722_4   1257 --CCAGCAATGTCCTTTTTCACAGAA---------------CTA------ 1283
                         --     --  -       ii     ---------------   ------
  L1M4_orf2#LINE/    101 TCCCAGC--TG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_47017722_4   1284 ----GGAAA---AAAAGAGCCTGAATAATCAAAGCAATCCTAAGCAAAAA 1326
                         ----     ---  ii  v  v     ii    i     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_47017722_4   1327 GAACAAAGCCAGAGGCATCACATTACCCA-CTTCAAACTACACTACAAGT 1375
                                 iii    vv     i v    -i      vivi       iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_47017722_4   1376 CTACAGTAGCCAAAATAGCATGGTACTGGTACAAA-ATAAACACATATAC 1424
                                 ii   i i  ii         i i  i-   i   i   v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_47017722_4   1425 CAATGGAACAGAATAGAGAGCCCAGAAATAAAGCCATACACCTGCAACCT 1474
                                 i     v     i           v       ii iiiii v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_47017722_4   1475 TCTGGTCTTCAACAAGCTTGACAAAATAAG-CAATGGGGAAA-AAGACTC 1522
                         vi  i i   i     vv  v   i iv v-           -  v v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_47017722_4   1523 TGTATCCATTAAATTGTGCTGGGATAACTGGCTATCTATATGCTGAAGAA 1572
                          - - i  vi    v         i      v  ? i i    vi     
  L1M4_orf2#LINE/    398 T-T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_47017722_4   1573 TGAAACTGGGCCCTT----TA------ATACAAAAAATAACTCAAGATGG 1612
                             ii   i   i ----i ------         v        i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_47017722_4   1613 ATTAAAGACTTAAATGTAAGACCTCAAACTATAACAATTCT-AGAAGAAA 1661
                           i ?    i           v  v         -  i   -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAA 544

  chr1_47017722_4   1662 ACCTAGACAATAACCTTCTCCATTTCAGCCCTGGCAAAGAATTTATGGCT 1711
                           v   i?ivv  i    viv ii ii viiv     v iv  iv i v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_47017722_4   1712 AAGTCCCCAAAAGCGATTGTGACAAAAACAAAAATTGATAAGTAGGACCT 1761
                          v v v        ivvv ii      iv      v     i v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_47017722_4   1762 AAGCAAACTAAAGAGCTTCTGCGCAGCAAGAGAAACTATCAAGAGAGTAA 1811
                         v v    v v  i i   i  i  vv   ii  v          i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_47017722_4   1812 ACAGACAACCTGCAGAATGGGAGAAAATATTTGCAAACCATGCATCCGAC 1861
                          v        ii                         i   ii   i  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_47017722_4   1862 AGAGGTCTAATATCCAGAATCTATAAGGAGTTTAAACAAATCAACAAGCA 1911
                          ii  v  vi          v     i  ii ivv    v    i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_47017722_4   1912 AAAAGCAAAGAACTCCACGAAAAAGTGGGCA-------TGTAT-GTCTTC 1953
                            ii    v   i v iv?    i      -------  v  - v v -
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT- 843

  chr1_47017722_4   1954 TTTTCTAAAGAAGACATACATGTGGCCAACAAGCATATAAAAAAAAAGCT 2003
                           i  i        i     vi       i     i  i    i v-   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCT 892

  chr1_47017722_4   2004 CAATATCGCGGATCAT 2019
                            i   i????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (136 / 79)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.10 (62 / 20)  


 751 28.23 0.96 0.96  chr1_47023323_47030080     5054  5262 (1496)    L1M4_orf2#LINE/L1        1   209 (699)  

  chr1_47023323_4   5054 TGGAAGAACATTCCATGCTCATGAGTAGGAAGAATCAATATCGTGAAAAT 5103
                              ii i  i     i     ii v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47023323_4   5104 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5153
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47023323_4   5154 TACCAATGACTTTCTTCACAGAA-TTGGAAAGAACT-ACTTTAAATTTCA 5201
                          v   iivi i  i  ii     -   iv   --  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_47023323_4   5202 TATGGAACCAAAAAAGAGCCTACATTGCCAAGACAATCCCAAGCAAAAAG 5251
                                viiv  ii  v  viv  v     i      iii iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_47023323_4   5252 AACAAAGCTGG 5262
                                i   
  L1M4_orf2#LINE/    199 AACAAAGTTGG 209

Transitions / transversions = 2.11 (40 / 19)
Gap_init rate = 0.01 (3 / 209), avg. gap size = 1.33 (4 / 3)  

2591 25.07 2.56 0.94  chr1_47023323_47030080     5524  6265 (493)    L1M4_orf2#LINE/L1      155   908 (0)  

  chr1_47023323_4   5524 AGTGCAAGAATGTGTCTCAAAAAAA--AAAAAAA----AAAAAAAAAGAA 5567
                          i      i---- v i  i  v i--    v  ----i     i     
  L1M4_orf2#LINE/    155 AATGCAAGG----GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_47023323_4   5568 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5617
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_47023323_4   5618 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5667
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_47023323_4   5668 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCATACATCTACAACCAT 5715
                              i    i--    i  --        vv        i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_47023323_4   5716 CTGATCCT-GACAAAAA---CAAGA------AATAGGGAAAGCATTCCCT 5755
                         i    ii -     iii---     ------   i       v  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_47023323_4   5756 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCTGA 5805
                         v  i  i              v      v  ?       i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_47023323_4   5806 AACTGGATCCCTTCCTTACACCTTATACAAAAATTATTTCAAGATGGATT 5855
                          ii    i    v   i     v             vi    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_47023323_4   5856 AAAGACTCAAATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAACCT 5905
                          ?    ii      v   v  i    i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_47023323_4   5906 AGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCATGACTAAA 5954
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_47023323_4   5955 ACACCAAAAGCAATGGCAACACAAGCCAAAATTGACAAATGGGATCTAAT 6004
                                     vvi      v   vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_47023323_4   6005 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 6054
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_47023323_4   6055 GGCAACCTACAGAATGGGAGAAAATTTGTGCAATCTACTCATCTGACAAA 6104
                          i     i                 v v     vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_47023323_4   6105 GGGCTAGTATCCAGAATCTACAAAGAACTTAAACAAATTTATAATAAAAA 6154
                           i  v           v  i        ivv    v iv          
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_47023323_4   6155 ATCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 6204
                         iv    i     v  i?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_47023323_4   6205 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCG 6254
                          v        i  vi viii     i ii          i       v i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_47023323_4   6255 TCACTGGCCAT 6265
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.60 (112 / 70)
Gap_init rate = 0.01 (10 / 754), avg. gap size = 2.60 (26 / 10)  


 476 32.09 4.65 3.26  chr1_47046010_47048531      665   879 (1643)    L1M4_orf2#LINE/L1        1   218 (690)  

  chr1_47046010_4    665 TGGGAAAGCATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 714
                            i  iii  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47046010_4    715 GGCCATGTTGCTCAAAGCAATTTATGGATTCAATGCTGTTCCCATTAAAC 764
                            v  ii v i    vii  i  ii       i  vi i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47046010_4    765 TACTATTGAGATTCTTCATAGAATTAGAAAAA--ACTTTTAAAATTCATA 812
                          v i vivivv  i  iii    v v  v  i--iv ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_47046010_4    813 TGGGGCTGGGTGCAGTGG-CTCATGCCTGTAATCCCAACACT-TTG---- 856
                            ii----i    iv  - i  vi---i  ii vv    v -   ----
  L1M4_orf2#LINE/    151 TGGAA----ATGCAAGGGACCCAGA---ATAGCCAAAACAATCTTGAAAA 193

  chr1_47046010_4    857 -GAAGGCCAAGGTGGGAGGA-TCAC 879
                         -    iv   i  v      -    
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCAC 218

Transitions / transversions = 1.88 (45 / 24)
Gap_init rate = 0.03 (7 / 218), avg. gap size = 2.43 (17 / 7)  

1298 21.26 3.77 18.72  chr1_47046010_47048531     1127  2029 (493)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_47046010_4   1127 AACACTCACATGGAACCCAAAAAGAGCCTGAGTAGCCAAGACAATCCTAA 1176
                           v i   i      vivv  ii  v  v  i       i      i --
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT-- 188

  chr1_47046010_4   1177 GAAAACAAACAAACAAACAAACCAAAGCTGGAGGCCTC------------ 1214
                              vi  v  ----------     i      v   ------------
  L1M4_orf2#LINE/    189 GAAAAAGAAGAA----------CAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_47046010_4   1215 TTCAAA--TTATTCCACAAGACTACAGTAACTAAAAAAGCATGGTACTGG 1262
                               --   i --    ii         ii  i v  ii         
  L1M4_orf2#LINE/    229 TTCAAAACTTACT--ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr1_47046010_4   1263 TACAAGAACAGACACAGAGACCAATGGAACAGAATAGGGAACCCACAAAT 1312
                         i i   i i     i v   i        i     v i  ii   v    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_47046010_4   1313 AAGACTGCACACCTACAATCATCTGATCTTCAGCCAAGTCAACAATAACA 1362
                           iv iii   ii  iii   vi    i   ii v i viiv   v v  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_47046010_4   1363 AGCAATGGAAAAAGGATTCCCTATTTAATAAACCATGCTGGGAGAACTGG 1412
                         vv      ii    i  vvi  v  i  i   ivi        v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_47046010_4   1413 GTAGTCATATGGAAAAAA-------TGGAAACTT-CCTTACATTATGTGC 1454
                         i  ?i  i   v    i -------    vv i -   i   ii  i i 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_47046010_4   1455 AAAAATCAACTCAAGATGGATTAAAGAACCCAAAACTATGAAAACTCCAG 1504
                               i       i      i ?   -  i   -- i i i i  ----
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGA-CCTAAA--TGTAAGAGCT---- 519

  chr1_47046010_4   1505 ACAAAAATCTAGGCAATACCATTCAGGACATAGGACACCGGGGCCTGTTG 1554
                         ---    -   --i  v  iv  --------  i ---------------
  L1M4_orf2#LINE/    520 ---AAAA-CTA--TAAAACTCTT--------AGAA--------------- 540

  chr1_47046010_4   1555 TGAGGTGGGGGGAGTGGGGAGGGATAGCATTAGGAGATATACCTAATGTT 1604
                         ----------------------  v i   -   ? ---  ---   v  
  L1M4_orf2#LINE/    541 ----------------------GAAAACAT-AGGNG---TA---AATCTT 561

  chr1_47046010_4   1605 AAATGACGAGTTACTGGGTGCAGCACACCAACATGGCACATGTATACATA 1654
                         vi-    ---i --     vvi   -------    i-------------
  L1M4_orf2#LINE/    562 CG-TGAC---CT--TGGGTTAGGCA-------ATGGT------------- 585

  chr1_47046010_4   1655 TGTAACTAACCTGCACGTTGTGCACATGTACCCTAAAACTTAAAGTATAA 1704
                         -----------------  -------------------    i -   --
  L1M4_orf2#LINE/    586 -----------------TT-------------------CTTAGA-TAT-- 596

  chr1_47046010_4   1705 TAATAAAAAAATTAAAAAAAAAAGACGCCAAAAGCAATTGCAACAAAAGC 1754
                         -----------------------   i         vvv          v
  L1M4_orf2#LINE/    597 -----------------------GACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_47046010_4   1755 AGAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTCTGCACAAC 1804
                          i    v  i    v   ii v  i   v v  i i   i v   vi-- 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--C 671

  chr1_47046010_4   1805 AAAAGAAACTATTATCAGCATGAATAGACAACCTACAGAATAGGAGAAAA 1854
                            i  v     i vv ivi    v        i       i        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_47046010_4   1855 TTTTTGCAATCTATCCATTTGACAAAGGCCTAATATCCAGCATCTACAAG 1904
                          v       vii  vi  i   i  i  v  vi       v  v  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_47046010_4   1905 GAATT--TA-AATTTAC-------AAGAAAAACAACTCCATTAAAAAGGA 1944
                            i --  -  i i v-------    v   i   i v   ?    ivi
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_47046010_4   1945 GGCAAAGGACATGGATAAATATTTCTCAAAGGAAGACATACATGTGGCCA 1994
                                  iv  i   i i       v  i     i     vi      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_47046010_4   1995 AAAAACACATGAAAAA--GCTCAACATCAGTAATCAT 2029
                          v  i          i--           ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (120 / 68)
Gap_init rate = 0.04 (30 / 768), avg. gap size = 6.77 (203 / 30)  


2930 25.75 1.89 1.11  chr1_47092113_47095614.rev     2111  3011 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47092113_4   2111 TGGAAACACATCCCATGTTCATGGATGGGTAGAATCAATGTTGCAAAAGT 2160
                               v i                 v  v   v i   i   iv  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47092113_4   2161 GACCATACTGCCAAAAGCAACCTACAAATTCAATGTGATTCCCATCAAAA 2210
                          i v     v  v   vii i     i      i ii  i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47092113_4   2211 TACCA-CCACCATTCTTCACAGAACTAGAAAAA-TAACCCTAAAATTCAT 2258
                          v   - ii  -  i  ii     v v  v  i- i i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_47092113_4   2259 ATGGAACCAAAAAAGGCCCCACATAGCCAAAGCAAGACTAAGCAAAAAGA 2308
                               viiv  ii i   viv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_47092113_4   2309 ACAAATCTAGAGGCATCACA-TTACCAACTTCAAACTATACTATACTATA 2357
                              vi i    vv     -  v    i      ----   -     i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACT-TACTACA 244

  chr1_47092113_4   2358 AGGGTGTAGTCACCAAAACACCA-GGTACTGGTATAAAAATAGGCACATA 2406
                          i v ii   v i   i   vii-        i    ii    i  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_47092113_4   2407 GACTAATGGAATAGAATAAAGAACCCAGAAAAAAACCCAAATGCTTACAG 2456
                           ii             vi   ii       v       v iii   ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_47092113_4   2457 CCAACTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGAAAAGGATA 2506
                         i   i    i   i    i vviv   i v   vv i    i    i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_47092113_4   2507 CCCTATTCTACAAATGATGCTGGGATAATCGGCAAGCCACATGTAAAAGA 2556
                         vi  v   v       i        i  ii  vv ?       i      
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_47092113_4   2557 ATGAAACTGGATCCTCATCTCTCACCTTAAACAAAAATCAACTCAAGATG 2606
                              ii    i  ii i   v    v  v        i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_47092113_4   2607 GATCAAAGACTTAAATCCAAGACCTGAAACCGTAAAGATTCTAGAAGATA 2656
                              ?    i     vi    v  i    ii    iv ii       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_47092113_4   2657 ACATCAGAAAAACCCTTCCAGACATTGGCTTAGGCAACGACTTTATGACC 2706
                             vi ?iv  vi    vv   v    v        i ii  iv iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_47092113_4   2707 AAGAACCCAAAAGCAAATGCAACAAAAAGACAAATAGGTG----GGATTT 2752
                          v  vv         v v         ii v      i i----   i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_47092113_4   2753 AATTAAACTAAAAAGATTCTGCACAGCAAAAGAAATAATCAACAGAGTTA 2802
                         v  i   v v    iv  i  ii vv    i  v iv     v i   v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_47092113_4   2803 ACAGACAATCCACAAAGTGAGAGAATATCTTCACAA-TCTATATATATCC 2851
                          v      i     i i  i     v  v  ii   -  ---       i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC---ATATATCT 741

  chr1_47092113_4   2852 AACAAAGGACTAATATCCAGAATCTACAAATAACTAAAACAAACCAGCAG 2901
                         i i  i     vi          v  i   v    vvv    vi  ii i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_47092113_4   2902 GAAAAA---AAAT--CCCA--TCAAAAAGGGATATAAGGAAT-GAATAGA 2943
                         v     ---    --    -- ?     v  ii -     v -       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCA-AAGGATTTGAATAGA 840

  chr1_47092113_4   2944 CAGTTCTCAAAAGAAGATATACAAATGGTCAACAAGCATATGGAAAAATA 2993
                           v     v                   i   i     i   i   i  i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_47092113_4   2994 CTCAACATCACTAATTAT 3011
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (140 / 88)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.80 (27 / 15)  


2950 25.05 1.53 2.61  chr1_47148868_47153110.rev     2835  3752 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47148868_4   2835 TAGGAAAACATTCCAAGCTCATGGATATGGA-GAATCAATATCGTTAAAA 2883
                          i i  i i  i   v i        -    -  v i     i     i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-TGGAAGACTTAATATTGTTAAGA 49

  chr1_47148868_4   2884 TGGTCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAA 2933
                            iv     v      vii  i           i  v  i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_47148868_4   2934 CTACTAACAACATTTTTT-CACAATTAGAAACAACC--ACTCTAAAATTC 2980
                         v v i i vi v      -  v  v v  --   v -- ii         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTC 147

  chr1_47148868_4   2981 ATTTGGAACCACAAAAGAGCCCAG--TAGCCAAAGATATCCTAAGCAAAA 3028
                           v     vii   ii  -     --        ivv   i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_47148868_4   3029 AGAACAA-GCTGGAGGCATCACACTACCTGACTTTAAAATATACTGCAAA 3077
                                - i      vv       v  ii i  i    iv    i    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_47148868_4   3078 GCTACAGTAACTAAAACAGCATTGTACTGACACAAAAGCAGAAACATAGA 3127
                                   ii  i    ii v      i  i  iiii   v i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_47148868_4   3128 CCAATGGAACAGAATAGATAAGTGAGTAATAAAGCCTCACACCTACAACC 3177
                         i        i     v  v iviv  v      v  vi   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_47148868_4   3178 ATGTGATCTTCGACAAAGCCAACCAAAACAAG-CAATGGGGAAAAGGACC 3226
                          vv    i        i vii-    i  v v-           - i iv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAA-GAATA 394

  chr1_47148868_4   3227 CTCTATTCAATAGATAGTGCTGAGACAACTGGCTAGCCATGTGTAGAAGA 3276
                         v   v     i i  i      i         v  ?   ii  i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_47148868_4   3277 TTTAAACTGGACCCCTGTTTTTCATCATATACAAAACTCAACTCAAGGTG 3326
                         v v  ii         iii iv  i           v i       ii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_47148868_4   3327 GATTAAATATATAAATGTAAGATATGAAACTATAAAAACTCT-GGAAGAA 3375
                            i ? v iv           vv i           -    -i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chr1_47148868_4   3376 AACCTAGAATATAATACCATTTTGGCCATAGGCCCTGGCAAATAATTTAT 3425
                            v   i?-i   - i v iv  i  v i  iiv-     - ii   v 
  L1M4_orf2#LINE/    544 AACATAGGN-GTAA-ATCTTCGTGACCTTGGGTTA-GGCAA-TGGTTTCT 589

  chr1_47148868_4   3426 --GATGAAGACTCTAAAAGCAATTGCAACAAAAACAAAAATTGACAAATG 3473
                         --   - v   v i       vvv         iv      v  i    v
  L1M4_orf2#LINE/    590 TAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_47148868_4   3474 GGATCTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATTATCAACA 3523
                            ii v  i   v v    i   i  ii vv    i  v i      v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_47148868_4   3524 GAGTACATGGACAGTCTACAGAATAGGAGAAAATATTTGCAAGGTATGCA 3573
                         i   iv vi    ii i       i                 ivi  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_47148868_4   3574 TTTGACAGAGGTCTAATATCCAGAATCTATAGCAAGCTTAAATTAACAAG 3623
                          i   i ii  v  vi          v    ivi i  i---   -   v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC---TTA-CAAC 784

  chr1_47148868_4   3624 CCAAAAAACAAAACAAAACAAAAAAACCAACCCCATTAAAAAATCAGCAA 3673
                         i   v  -i    -- i     -----i     v   ?      vi    
  L1M4_orf2#LINE/    785 TCAATAA-TAAAA--AGACAAA-----TAACCCAATTWAAAAATGGGCAA 826

  chr1_47148868_4   3674 AGGATTTGAACAGACACTTCTCAAAAGAAGATATACATGTGGCCAAGAAA 3723
                                   i     i     v              vi       v  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_47148868_4   3724 ---ATGAAAAAATACTCAATATCACTAACTAT 3752
                         ---       i  i     i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (142 / 84)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 1.52 (38 / 25)  


3044 27.00 0.66 0.99  chr1_47153172_47159585     5011  5921 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47153172_4   5011 TGGAAGAGCATTCCATGCTCATGGATAGGAAAAATCAATATCGTGAAAAT 5060
                              iiii  i     i        v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47153172_4   5061 GGCCATACTGCCCAAGGTGTAATTTATAGATTCAATGCCATCCCCATCAA 5110
                            v     v     iv  --  i  i        i  v     i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_47153172_4   5111 GCTACCAATGACTTTCTTCACAGAATTAGAAAAAGCT-ACTTTAAAGTTC 5159
                         iv v   iivi i  i  ii     v v  v  -   - iii    i   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTC 147

  chr1_47153172_4   5160 ATATGGAACCAAAAAAGAGCCCATATTGCCAAGACAATACTTAGCAAA-A 5208
                                 viiv  ii  v  viv  v     i     -   iiv   - 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGA 196

  chr1_47153172_4   5209 AGAACAAAGCTGGAGACATCATACTACCTGACTTCAAACTATACTACAAG 5258
                                  i     ivv   i   v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_47153172_4   5259 GCTACAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5308
                                   v   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_47153172_4   5309 TCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACA-CC 5357
                                  i    iv   ivii         vv   i    i  ii-i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_47153172_4   5358 ATCTGATCTTTGCCAAACCTGACAAAAGCAAGAAATGGGGAAAGGATTCC 5407
                          vi    i  i v   ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_47153172_4   5408 CTATTTAAAAATAAATGGTGCTGGGAAAACTGCCTAGCCATATGTAGAAA 5457
                           v  i  ---i              v     vv  ?   i   i i  i
  L1M4_orf2#LINE/    397 CTTTTCAA---CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_47153172_4   5458 GCTGAAACTGGATCCCTTCCTTGCACCTTATACAAAATTTAATTCAAGAT 5507
                         iv    ii    i    v   ii    v         v    i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_47153172_4   5508 GGATTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCTTAGAAGAA 5557
                             i ?    i     i v   v       i      vi          
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_47153172_4   5558 AACCTAGGCA-ATACCATTCAGAACATAGGCACGGGTAAGGACTTCATGA 5606
                            v    ?i- v i -   ivi  v v  vvii  i  v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_47153172_4   5607 CTAAAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGAT 5656
                         v  vi            vvi      i   vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_47153172_4   5657 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5706
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_47153172_4   5707 GAACAGGCCACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTA 5756
                            v  i v   i                 v       vii ivi    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_47153172_4   5757 ACAAGGG-CTAATATCCAGAATCTACAAAGAACATAAACAAATTTACAAG 5805
                          i     -  vi          v  i       vivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_47153172_4   5806 AAAAAAATCAGACACTCCA-TCAAAAAGTGGGCAAAGGATATGAACAGAC 5854
                              i -  i i vi   - i?    i            v    i    
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_47153172_4   5855 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAAAGC 5904
                          i     v        i  vi viii     v ii          i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_47153172_4   5905 TCATCATCACTGGTCAT 5921
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


3119 27.70 0.55 0.33  chr1_47164859_47168503     2247  3152 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47164859_4   2247 TGGAAGAACATTCCATACTCATGGATAGGAAGAATCAATATCATGAAAAT 2296
                              ii i  i    ii        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47164859_4   2297 GGACATACTGCCCAAAGTAATTTATAGATTCAATACTATCCCCATCAAGC 2346
                           vv     v      v i  i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47164859_4   2347 TACCATTGACTTTCTTCACAGAATTAGAAAAAGCT-ACTTTAAATTTCAT 2395
                          v   vivi i  i  ii     v v - v     - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr1_47164859_4   2396 ATGGAACCAAAAAAGAGCCCACATAGACAAGACAATCATAAGCAAAAAGA 2445
                               viiv  ii  v  viv    v   i      v i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_47164859_4   2446 GCAAAGCTGGAGGCATCACACTATTTGACTTCAAACTGTACTACAAGGCT 2495
                         i     i      vv       viiii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_47164859_4   2496 ACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGATATATAGACCA 2545
                                i   i    ii i       i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_47164859_4   2546 ATGGAACAGAATAGAGACCTCAGAAATAACACCACATATCTACAACCCAT 2595
                               i     v    vii         vv   i i  i  iiii v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_47164859_4   2596 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT--TCC 2643
                         -    i  i     ivv  v   i v  vvv           i  --  i
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_47164859_4   2644 CTT-AATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCTGA 2692
                         i  -  i              v      v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_47164859_4   2693 AACTGGATCCCTTCCTTACACTTTATACAAAAATTAATGCAAGATGGATT 2742
                          ii    i    v   i    iv              iv   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_47164859_4   2743 AAAGACTTAAATGTAAAACCCCAAACCATAAAAACTCT-AGAAGAAAACC 2791
                          ?    i         i v iv    i      -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr1_47164859_4   2792 TAGGCAATAGCTTTCAGGATATAGGCATGGGCAAAGGCCTCATGACTAAA 2841
                             ?ivv iii   iv  iv v  vv i     v  ii  v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_47164859_4   2842 ACACCAAAAGCAATGGCAACAAAAGCCAAAAGTGACAAATGGAATCTAGT 2891
                                     vvi          vv    vv  i    v i ii vi 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_47164859_4   2892 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 2941
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_47164859_4   2942 AGCATCCTACAGAATGGGAGAAAATTTTTGCAATCTGTCCATCTGACAAA 2991
                         ii  v  i                 v       viii vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_47164859_4   2992 GGGCCAATATCCAGAATCTACAAAGAACATAAACAAATTTACAAGAAAAA 3041
                           i ivi          v  i       vivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_47164859_4   3042 AACAAACAACCCCACCAAAAAGTGGGTGAAGGATATGAACAGACATTTGT 3091
                         i     i     v ii?    i    ii      v    i        v 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_47164859_4   3092 CAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCATCA 3141
                          v        i  vi viii     i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_47164859_4   3142 TCAGTGGCCCT 3152
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


3037 27.75 0.77 0.77  chr1_47183639_47190012     4974  5881 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47183639_4   4974 TGGACTAACATTCCATGCTCACGGGTAGGAAGAATCAATATCGTGAAAAT 5023
                             vvi i  i     i   i  i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47183639_4   5024 GGCTATACTGCCCATGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5073
                            v     v    viv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47183639_4   5074 TACCAATGACTTTCTTCACAGAATTAGAAAATACT-ACTTTAAAGTTCAT 5122
                          v   iivi i  i  ii     v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_47183639_4   5123 AGAGAAC--CAAAAAACAGCCCGCATTGCCAAGACAACCCTAAGCCAAAA 5170
                          vi   v--   iii  --  v v  v     i    i i i ivv i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_47183639_4   5171 GAACAAAGCTGGAGGCATAATGCTATCTGACTTCAAGCTATACTACAAGG 5220
                                 i      vv v ii  vi ii i     iviv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_47183639_4   5221 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5270
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_47183639_4   5271 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACATC 5318
                                 i    i--    i  --        vv   i    i  iivi
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_47183639_4   5319 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5368
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_47183639_4   5369 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5418
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_47183639_4   5419 TGAAACTGGATCTCTTCCTTACACTTTATACAAAAATTAATTCAAGATGG 5468
                             ii    i i  v   i    iv              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_47183639_4   5469 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5518
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_47183639_4   5519 CCTAGGCA-ATACCATTCA-GAACATAGGTATGGGCAAGGACTTTATGAC 5566
                          v    ?i- v i -   i-  v v i   - i     v ii  iv iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGA 593

  chr1_47183639_4   5567 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGTGATC 5616
                           vi            vvi          vv     v  i    vv  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_47183639_4   5617 TAATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGACTG 5666
                          v  i   v v  i ii  i  ii vv    i  v    i  vv i v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_47183639_4   5667 AACAGGCAACCTACAGAATGGGAAAAAATTTTTACAATCTACCCATCTGG 5716
                           v  i     i           i     v   i   vii ivi     i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_47183639_4   5717 CAAATGGCTAATATCCAGAATCTACAAAGAACTTAAATAAATTTACAAGA 5766
                         i  iv i  vi          v  i        ivv i  v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_47183639_4   5767 AAAAATCAAACAACCCCATCAAAAAGTGGACAAAGGATACGAACAGACAC 5816
                             iv    i     v  i?    i   i        vi   i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_47183639_4   5817 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAGATGCTC 5866
                              v        i  vi viii     v ii                 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_47183639_4   5867 ATCATCACTGGCCAT 5881
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (151 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


3262 25.14 2.59 0.68  chr1_47218726_47220643.rev      541  1427 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr1_47218726_4    541 AAAATACCCTGTGTTCATTAATTGGAAGCATTAATACTGTTAAAATATCC 590
                           i   i  ii       vi        vv      i      i  iv v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_47218726_4    591 ATACTACCCAAA----------GATTCAATGCAATCTCCATCAAAATTCC 630
                              v      ----------       i      i i        i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_47218726_4    631 AATGGCATTATTCACAGTAATCGAAAAAAAAAAAAAGCCCTAAAATTCGT 680
                          iiv  v  v  ii   v   i  v  ivvi -----i          i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-----TCCTAAAATTCAT 149

  chr1_47218726_4    681 ATGGAA-TA-AAAAAACTCA-AATAGCCAAAGCAATTTTGAGCAAAAAGA 727
                               - i-  iii  i  -          i    i    iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_47218726_4    728 GCAAAGCTGGAGGCATCATACTACCTGATCT-GAAATTGACTACAGAGCT 776
                         i     i      vv   i   v  ii  i -i   i v      i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_47218726_4    777 CTAGTCACCAAAACAGCATAGAGCTTCTAAAAAAAGAGACATATAAACTA 826
                         vi   v i   i    ii i vi  vvi v  ii v         i ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_47218726_4    827 ATAAAACAGGATAAAGAGTCCAGAAATACACCCACACATTTATTGTCAAC 876
                           ii  i  i  vi              v     i        v     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_47218726_4    877 TGATCT---ACAAAGGTTCCAGTAACATACAGTGGTGAAAGGGCAGTATC 923
                             i ---    i   v   iv v   v  i   v     iii   v i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_47218726_4    924 TTCAATAAATGGTGTTGAGAAAACTGGATATGCACTAGTAGAAGAATAAA 973
                              i        i  i  v         ?v   vv i i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_47218726_4    974 AGTGGACCTTTATCTCACTCCATATACAAAAATCAACTAAAAATGGATTA 1023
                         iv      ii  i     v              i    v         i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_47218726_4   1024 AAGATTTAAACATATGACCTGAAACTATAAAACTACTAGAAAAAAACATA 1073
                         ?   ii    ii  v  v  i             vi     i        
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_47218726_4   1074 GAGA-AAAGCTTCTTGATATTATTCTTGGCAATGATTTTTTGGATACAAC 1122
                          i?i-   v    v   iv  ivvi v       i   i  i    ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_47218726_4   1123 TCTGGAAGTATAGTCAACAGAAGAAAAAATAGATAAAT-GGTTTTGCAGC 1171
                         v iii   i i iv     i                  -  vi  -  v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATC 648

  chr1_47218726_4   1172 AAACTAAAAAGCTTCTGCACAACAAAGGAAACAATCAACATAGTGAAGAG 1221
                            v v    i   i  ii vv       v  v     v v      i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_47218726_4   1222 ACAACTTAAAGGATGGGAGAACATGTCTGCAAATGATACATCTGATAAGG 1271
                              ii v  i         v  i i       v   i           
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_47218726_4   1272 GGTTAATATTCAAAATATATGAGGAACTCACACAATTCAAAAGCAAGAAA 1321
                          ii vi   i  i       i i      vi    i    v ii  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_47218726_4   1322 ACAAATAACTAGATTTAAAAATGAG-AAAAACCTAAAATA-ACATTCCTA 1369
                                  ivi   ?       i -   iivi vi    -     i  v
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_47218726_4   1370 CAAAGAAGACATG--AATGGCCAGCAGGTATTTAAAACAATGCTCAACAT 1417
                                  i  i--        ii i i iv i   vi           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_47218726_4   1418 CACTAATCAT 1427
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.96 (145 / 74)
Gap_init rate = 0.01 (13 / 904), avg. gap size = 2.23 (29 / 13)  


3083 27.42 0.77 0.77  chr1_47230861_47235508.rev     3250  4157 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47230861_4   3250 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3299
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47230861_4   3300 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3349
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47230861_4   3350 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3397
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_47230861_4   3398 TATGGAACCAAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCCAAAAG 3447
                                viiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_47230861_4   3448 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAGACTATACTACAAGGC 3497
                                i      vv   ii  v  ii i    i viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_47230861_4   3498 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3547
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_47230861_4   3548 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 3595
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_47230861_4   3596 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACAATTCC 3645
                          vi    i  i     ivv  v   i v  vvv          v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_47230861_4   3646 CTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3695
                           v  i  i   i          v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_47230861_4   3696 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3745
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_47230861_4   3746 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3795
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_47230861_4   3796 CTAGGC---AATGCCATTCAGGACATAAGCATGGGCAAGGACTTCATGTC 3842
                         v    ?---   -- -   iv   v vi vv i     v ii   v ivv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_47230861_4   3843 TAAAAAACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 3892
                           vi v          vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_47230861_4   3893 TAATTAAACGAAAGAGCTTCTGCACAGCAAAACAAACTACCATCACACTG 3942
                          v  i   vvv  i i   i  ii vv    iv v    i  vv v v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_47230861_4   3943 AATGGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 3992
                           vi i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_47230861_4   3993 CAAAGGCCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 4042
                         i  i  v  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_47230861_4   4043 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAGCAGAGAC 4092
                             i     i     v  i?    i     i      v   ii   v i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_47230861_4   4093 TTCTCAAAAGAGGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 4142
                              v     i  i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_47230861_4   4143 ATCATCACTGGCCAT 4157
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2734 24.03 4.87 4.32  chr1_47296487_47299027     1148  2050 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47296487_4   1148 TGGGAAAATATTTCATGCTCATGAATTGGTAGCATCAAAATTGTTAAAAT 1197
                            i  i    ii    i     i     v  vv i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47296487_4   1198 GACCATACTTCCCAAAGCAATCTACAGATTCAATGCTATTCCTATCAAG- 1246
                          i v     i      vii              i  v  i        i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47296487_4   1247 --CCAGCAATGTCCTTTTTCACAGAA---------------CTA------ 1273
                         --     --  -       ii     ---------------   ------
  L1M4_orf2#LINE/    101 TCCCAGC--TG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_47296487_4   1274 ----GGAAAAAAAAGAG--CCTGAATAATCAAAGCAATCCTAAGCAAAAA 1317
                         ----     viv   i --  v     ii    i     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_47296487_4   1318 GAACAAAGCCAGAGGCATCACATTACCCA-CTTCAAACTACACTACAAGG 1366
                                 iii    vv     i v    -i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_47296487_4   1367 CTACAGTAGCCAAAATAGCATGGTACTGGTACAAA-ATAAACACATATAC 1415
                                 ii   i i  ii         i i  i-   i   i   v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_47296487_4   1416 CAATGGAACAGAATAGAGAGCCCAGAAATAAAGCCATACACCTGCAACCT 1465
                                 i     v     i           v       ii iiiii v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_47296487_4   1466 TCTGATCTTCAACAAGCTTGACAAAATAAG-CAATGGGGAAA-AAGACTC 1513
                         vi    i   i     vv  v   i iv v-           -  v v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_47296487_4   1514 TGTATCCATTAAATTGTGCTGGGATAACTGGCTATCTATATGCTGAAGAA 1563
                          - - i  vi    v         i      v  ? i i    vi     
  L1M4_orf2#LINE/    398 T-T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_47296487_4   1564 TGAAACTGGACCCCATCTATATGCTGAAGAATGAAACTGGTCCCTTTATA 1613
                             ii        -----  i-  v -------------- v iv    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCC-----TAC-CTCA--------------CACCATATA 475

  chr1_47296487_4   1614 CAAAAATTAACTCAAGAGGGATTAAAGACTTAAATGTAAGACCTCAAACT 1663
                                        i v    i ?    i           v  v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_47296487_4   1664 ATAACAATTCT-AGAAGAAAACCTAGGAAATAACCTTCTCCATTTCAGCC 1712
                             -  i   -          v    ?ivv  i    viv ii ii vi
  L1M4_orf2#LINE/    526 ATAA-AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_47296487_4   1713 CTGGCAAAGAATTTATGGCTAAGTCCCCAAAAGCAATTGTGACAAAAACA 1762
                         iv     v iv  iv i v  v v v         vvv ii      iv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_47296487_4   1763 AAAATTGATAAGTAGGACCTAAGCAAACTAAAGAAAGAGCTTCTGCACAG 1812
                              v     i v    i v v    v v  i  ----   i  ii vv
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA----CTTTTGTGCTT 670

  chr1_47296487_4   1813 CAAGAGAAACTACCAAGAGAGTAAACAGACAACCTGCAGAATGAGAGAAA 1862
                            ii  v    i     i   i  v        ii       i      
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_47296487_4   1863 ATATTTGCAAACCATGCATCCGACAGAGGTCTAATATCCAGAATCTATAA 1912
                                    i   ii   i  i ii  v  vi          v     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_47296487_4   1913 GGAGTTTAAACAAATCAAGAAGCAAAAAGCAAAGAACTCCATGAAAAAGT 1962
                         i  ii ivv    v    v  vv    ii    v   i v  v?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_47296487_4   1963 GGACA-------TGCAT-GTCTTTTTTTCTAAAGAAGAAAGAAGACACAC 2004
                           i  -------  v  - v v   i i --------        i i  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCC--------AAAGAAGATATAC 862

  chr1_47296487_4   2005 ATGTGGCCAACAAGCATATAAAAAAAAAGCTCAATA-CACTGATCAT 2050
                          vi       i     i  i    i v-      i -  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (130 / 83)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.61 (83 / 23)  


3226 25.88 1.32 1.32  chr1_47346679_47349507     1430  2337 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47346679_4   1430 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1479
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47346679_4   1480 GGCCATACTGCCCAAGGTAATTTATAGATTCAATACCATCCCCATCAAGC 1529
                            v     v     iv i  i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47346679_4   1530 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1577
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_47346679_4   1578 TATGGAAC--CAAAAAACAGCCCACATTGCCAAGTCAATCCTAAGCCAAA 1625
                                v--   iii  --  viv  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_47346679_4   1626 AGAATAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 1675
                             i    i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_47346679_4   1676 GCTGTAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 1725
                            ii i   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_47346679_4   1726 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAA 1773
                         i        i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_47346679_4   1774 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 1823
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_47346679_4   1824 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 1873
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_47346679_4   1874 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 1923
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_47346679_4   1924 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAAAAGAAA 1973
                            i ?    i    i  v   v       i      vi i  i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_47346679_4   1974 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTC---AA 2019
                           v    ?i- v i -   iv   v v  vv i     v ii   ---i 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_47346679_4   2020 TGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGG 2069
                          i ----i            vvi          vv     v  i    v 
  L1M4_orf2#LINE/    594 TAT----GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_47346679_4   2070 GATCTTATTAAA-TGAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCA 2118
                           ii i  i   - v   i -   i  ii vv    i  v    i  vv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_47346679_4   2119 GAGTGAAAAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCA 2168
                         i         i     i   i             v       vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_47346679_4   2169 TCTGACAAAGTGCT-ATATCCAGAATCTACAATGAACTCAAACAAATTTA 2217
                              i  i vi  -i          v  i  v      vv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_47346679_4   2218 CAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACA 2267
                         i  v     i     i     v  i?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_47346679_4   2268 GACACTTCTCAAAAGAAGACATTTAGGCAGCCAACAGACACATGAAAAAA 2317
                             i     v        i  vi iiii     i ii          i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_47346679_4   2318 TGCTCATCATCCCTGGCCAT 2337
                               v    v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (148 / 83)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.71 (24 / 14)  


3595 23.28 3.16 0.56  chr1_47379829_47381855      650  1534 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47379829_4    650 TGGAAAGACATCTTATGCTCATGGATTGGAAGAATTAATATTGTTAAAAT 699
                                 i   ii   i               v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47379829_4    700 GACAATAGTAATTGAAAGTAATTTATACATTCAATGCAATCCCTATCAAA 749
                          i     v vvii-   v i  i  i v      i               
  L1M4_orf2#LINE/     51 GGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_47379829_4    750 ATACCAAGATA--TTTTTCACAGAAATAAAAAAA---ATC-TAAAATTCA 793
                           v   - v i--     ii       vi v  i---   -         
  L1M4_orf2#LINE/    100 ATCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_47379829_4    794 TATGGGACCAAAAAAGAGCCCAAACAGCCAAAGCAATCCTAAGCAAAAAG 843
                              i viiv  ii  v  vi  i       i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_47379829_4    844 AACAAAGCTGGAGACATTACACTACTTGGCTTTAAAATATATTACAAAGC 893
                                i     ivv i     v iiiii  i    iv  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_47379829_4    894 TATAGCAACCAAAACTGTGTGGTATTGGTATAAAAATACGTACATAGACC 943
                           i  i  i   i  v        i   i    ii   vii i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_47379829_4    944 AATGGAACAGAACAGAGAAACCAGAAATAAATTCATATATTTATAGTCAC 993
                                i    iv    iv           ii    i      i    v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_47379829_4    994 CTGATTTTCAACAAGGATGCCAGGAACCTACATTGGGAAAAGGATACCCT 1043
                         i        i      i     i  v v v  v    i    i   vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_47379829_4   1044 CTTCAATAAATGGTGCTGGGGAAATTGGACATCTATATTCAGAAGAATGA 1093
                         i     i             iv  i    i ? i i  v  i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_47379829_4   1094 GATTGTACTCCTATCTCTCACCATATACAAAAATCAACTCACGATGGATT 1143
                         ii   v  i    i   v                i      vi      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_47379829_4   1144 AAAGACTGAAATGTAAGGCCTAGAACTGCAAAAGTACTGGAAGAAAACAT 1193
                          ?    iv         iv   i    ii    v vi i           
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_47379829_4   1194 AGGAGAAACACTTCAGGTTGATC--GATCTAGGCAAAGACTTTATGGCTA 1241
                            ? v  vv    i---   i -- ivi       v ii  iv i v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCG---TGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_47379829_4   1242 AGATCCCAAAAGAACAGGCAATTAAAACAAAAATAGGTAAATGGGACTAT 1291
                         v  iv       v   i    iv   iv        i     v     vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_47379829_4   1292 ATTAAACTTGAAAGCTT-----ATCCACAGAAAA-----AAAAGAGTGAA 1331
                           i   v  i   i   -----v i  v  i v -----  i i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_47379829_4   1332 GAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTAGTCATTTAACA 1381
                         i        i                          ii vvi  i i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_47379829_4   1382 AGGAACT-ATATCCAGAATATACAA-GAA--------ACTCAGGAGCAAA 1421
                            i   -i             i  -   --------     iv ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_47379829_4   1422 ACAAGAAACAATATCATTAAAAAGTGGGCAAAGGATCTGAATAGACATTT 1471
                          vi v   i  iviv   ?    i            i             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_47379829_4   1472 CTCAAAAGAAGATATACTAACGGCCAACAGGCATATGAAAGAACGTTCAA 1521
                            v             v  i      i i   i      ii i i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_47379829_4   1522 CATCACTAATCAT 1534
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (137 / 65)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.75 (33 / 12)  


1415 29.21 6.85 3.25  chr1_47787283_47791339      871  1702 (2355)    L1M4_orf2#LINE/L1        1   862 (46)  

  chr1_47787283_4    871 TGGAAAGA----CCATGTTTTTGGCTAGGAAGACTCAACATCATAAAGAT 916
                                 ----       iv   v v        i  i  ii v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47787283_4    917 GTCAATTCTCCGTGAGTTAATTTCTAAATTTAATGTGAGCTCAAT-AAAA 965
                          v    v    vii i  i  i vi i   i  i ii v i v  -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47787283_4    966 TATCAGCAGTTTTATTTTTTAGCCA--GACAAGCTGATTCTAAAGTTCAT 1013
                          vi    v ii  -    vi  vv --           i     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_47787283_4   1014 GTGAAAA---AAAAAA---AGAA--ACAAAAACATTCA-GAAAAACTCTG 1054
                         i  i   ---  iii ---    --i v      v  v-      ---- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA----G 195

  chr1_47787283_4   1055 AAGAGTACTATCAGGGGACTAGCTCTACCAGATATTAAAACATAATA--- 1101
                             ii vvi ii i     vi v  v  vi  v i     v  v  ---
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_47787283_4   1102 -GTCTCAGTAACTGAAACAGTGAGGAACTGATGCATGAATAGCAAGACAG 1150
                         - iiv      iii i      v  v    iiii v i    vv v i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_47787283_4   1151 GCCGATCAACTATAATAGAAAGTCCAGAAATAGAAGTTACTACACATATG 1200
                         ii i  vi v  v   v  i            -  vii -    iv    
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATA-AACCCA-TACATTTATG 343

  chr1_47787283_4   1201 GGAGCTTAGTATATGAAAAAAACTGGCTTCTAAGA----TCAGTGGGAGA 1246
                          vviv  ii v vi  v  -----  v v i    ----   i    -  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAA-----GGGTGCCAAGACCATTCAATGGG-GA 387

  chr1_47787283_4   1247 AATGATTAA-CTGTTCAATAAATGTGGTTGGGGTCATTGGTTGGCCATGT 1295
                           -  v  i-  v     i     vv i    iiv i   v i?   ii 
  L1M4_orf2#LINE/    388 AA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_47787283_4   1296 GGAAAAAAAATAAAGTTAGATTCATACCTAGCACCATACACCAGGATAAC 1345
                          v    i  - i     i  ii v     vi       i  v ii  v v
  L1M4_orf2#LINE/    437 GCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_47787283_4   1346 TTCCAAATGGATCAAAGATTGAAAAACCAGAA-TAATGCCACAATATGCT 1394
                         i  v          ?   iiv   viiv   i-   vi i i  v iv  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_47787283_4   1395 -AGAAGAAAACTT--GAGAAAATCCTTTTGTAATCTTGGGATCAGAAA-G 1440
                         -          v -- ? v     --  i  i i      v vi v  - 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATG 583

  chr1_47787283_4   1441 ATCTTTCAAATTATGAC-CTAAAATAGAGAAG--ACCTTAGAGAAAAAAA 1487
                         i i i i i  -     - i    -iv v   --  ----- i  i    
  L1M4_orf2#LINE/    584 GTTTCTTAGAT-ATGACACCAAAA-GCACAAGCAAC-----AAAAGAAAA 626

  chr1_47787283_4   1488 AATAGAAAAGTTACACTACATTAAGG----AAATCTTTATGC--CAAA-- 1529
                               v  i  iv   v   i  ii----   ii   i   --    --
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_47787283_4   1530 ATAC-------AAAGCCAAA-GATAACTTA---ATTGGGAAAGAATATTT 1568
                          i  -------    iv   -  i   ii --- v     i i       
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_47787283_4   1569 GATACTCATTTCATCAGA--AGG--TTAATCTCCCTAATTTATAAAGTGG 1614
                          vv v    v -   v  --   --i vi v   vv   v       viv
  L1M4_orf2#LINE/    727 GCAAATCATAT-ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_47787283_4   1615 TCATAGAAACCAATGAGATAAAGAATCAAG-AACTCAATAGAAAAATTGG 1663
                           v  v  vi    i v v     --   i-   i    v?      v  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGG 823

  chr1_47787283_4   1664 CAAAGGATATGATCAAGTGGTTCACAGAAAAAGTTCTAC 1702
                                 v   vi iiiiv   v vi  i   v v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

Transitions / transversions = 1.28 (134 / 105)
Gap_init rate = 0.05 (39 / 862), avg. gap size = 2.15 (84 / 39)  

 276 29.20 3.65 1.46  chr1_47787283_47791339     2342  2478 (1579)    L1M4_orf2#LINE/L1      230   369 (539)  

  chr1_47787283_4   2342 TTAAATACTT-TTAAAAATCT-CATAAATGAAAACATT-TGATACTTGGT 2388
                          i   -    -i  v   v  -  vv   v  i   v -  i    -  i
  L1M4_orf2#LINE/    230 TCAAA-ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT-GGC 277

  chr1_47787283_4   2389 ACAGGATTAAATAAATAGAGCAACAGATAAGAATAGAGAGCCTAAAAACA 2438
                          i i iv  i i v     v   ii  vv     v     i i i   i 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_47787283_4   2439 GACCCCTACCCCTATGGAAAATT--TTTACATCAGGGGTCCC 2478
                         i    v   vii     vv    --   v iv  i    v  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

Transitions / transversions = 1.11 (21 / 19)
Gap_init rate = 0.04 (6 / 140), avg. gap size = 1.17 (7 / 6)  

 732 29.86 3.39 2.49  chr1_47787283_47791339     3115  3556 (501)    L1M4_orf2#LINE/L1      440   885 (23)  

  chr1_47787283_4   3115 AAAAAGTAAAATTGTTCTGCTAACTCTCACTTTATGCAAAAATTAATTCT 3164
                            i i i  i   vv iv   v   v   iv   i          i  -
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC- 488

  chr1_47787283_4   3165 AGAATCAAT-ATGGAAGAATATGGAAAACCAAAAAC-ATAACAGTTTCAG 3212
                          i   vi  - ?i  vvv v   v  i v v     -    v v i i  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_47787283_4   3213 ATAAAAACCTAGGAGAATATCTTTCTGACCTCAGG---------GATTTC 3253
                          vi     v    ? v v     iv      ii  --------- i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_47787283_4   3254 TTAAACAGTTTACAAAAAAACCAGAAACAAGTATGGGAAAACATGGATAG 3303
                            i i -- v   vv    v  v  i   -i vii     v  i    i
  L1M4_orf2#LINE/    589 TTAGATA--TGACACCAAAAGCACAAGCAA-CAAAAGAAAAAATAGATAA 635

  chr1_47787283_4   3304 ATTTGACTACATTAAAATTCAAATGTTTATATGCATCAAAAGACAAAGAC 3353
                            v    v   i      v   vv   - i   v     i    -----
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACA----- 679

  chr1_47787283_4   3354 ACTACAAACAATGTAAAAAGAGAAGTTACAGACTAGGAGAGGATATATGC 3403
                         -   iv  v  v  i      v  vii     v i     ii    v   
  L1M4_orf2#LINE/    680 -CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_47787283_4   3404 AACACATTTCACAAAAAAGTGATGAGTATGCAGAATACATAAA-AAGACC 3452
                           vv   v vv vi v   v  ivv    v       i     -  vv i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_47787283_4   3453 TACAAATCAAT--TAGATATGCAAAGAACCTA-CAGAAAAATAGCCAAAA 3499
                              v     --  i v vi    v    i -iv?      i v    i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_47787283_4   3500 TATGCCAAGAGTCAATTCACAGAAGAGAAAACCTGAATGGCCAATACATA 3549
                         v  viv  v  v  v   v vi    ii v ivii           vii 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_47787283_4   3550 TTTGAAA 3556
                         iv     
  L1M4_orf2#LINE/    879 CATGAAA 885

Transitions / transversions = 0.79 (57 / 72)
Gap_init rate = 0.02 (11 / 446), avg. gap size = 2.36 (26 / 11)  


1918 28.30 5.75 3.38  chr1_47847361_47849435.rev      702  1588 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_47847361_4    702 TGGAAGGACATAACAAATTCACGTATTAAAA-ACTCAGTGTTGCAAAGAT 750
                              i  i  vv  vi    i v   ii  -   i i i   iv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_47847361_4    751 ATCAGTTCTCCTCAATTTGATCTATAGAGTCAATGGAATTTTAATAAAAT 800
                         iv  i v    i   v        i   v    i v   iiiv  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_47847361_4    801 TCCCAGCAATTGC----TTTATGAAAGTTCACAAGCTGATTCTAAAATT- 845
                                ---   ----   iiii  i  v          i        -
  L1M4_orf2#LINE/    101 TCCCAGC---TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_47847361_4    846 ACATAGAA-TGCAAAGAGCTAAAAACATCCAAGATTCA--CTTCAGGAAG 892
                          i  i   -     i ii iv i  i v    i --  --   v ii   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAA--CAATCTTGAAAAAG 195

  chr1_47847361_4    893 AATAGTAAGATTAGAAGACTTATTCTGTGGA--TACAAAAATGTATTACA 940
                           v ii  ii  i  i    i iv  vivv -- v     v -  i    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACA 244

  chr1_47847361_4    941 AAGAGACAGTACCCTACAGAAATTATTTTGCTAATTGGCCACAAGGATAG 990
                            vv      vi -----  ivi v v  v  -i    - i        
  L1M4_orf2#LINE/    245 AAGCTACAGTAATC-----AAGACAGTGTGGTA-CTGGC-ATAAGGATAG 287

  chr1_47847361_4    991 GGAAATAGATCAACAGAACAAA-------GTTCAGAAA--GACTCGTGCT 1031
                         iv v         ii   i i -------  i      --i  i i i v
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_47847361_4   1032 TATATGGGGGCTT--CTTTAAAGAGAAAGATGACACCACAGATCATT--- 1076
                          v     vviv  --i   v--  v  i i  ---   -   i    ---
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTC--GACAAGGGTG---CCA-AGACCATTCAA 381

  chr1_47847361_4   1077 -AGAGAAAGAATGAACTTTTTCACGAATGGTACTCAGTCAAATGTGTATA 1125
                         -i i        iiv     iv  i      i  vi v   v  vi  ?v
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_47847361_4   1126 -ATATGCAGGGAGGGAGGGGATTAAAACCGATTCCTTCCTCACACCATAC 1174
                         - i     i-- i i v iii  i-----  ii   v            i
  L1M4_orf2#LINE/    432 CACATGCAA--AAGAATGAAGTTG-----GACCCCTACCTCACACCATAT 474

  chr1_47847361_4   1175 A---AAATCAATTAAAAACAAATTATAGATCTAAA-GTGAAA-CAAGAAG 1219
                          ---    i  i v    iii  i ?   i     -  i i - v i  -
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA- 523

  chr1_47847361_4   1220 CAATAAA----------GACAACATAGAAGAATATCATCATGAACTAGGC 1259
                          v     ----------  v       i? v v   v  i   v  v  v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_47847361_4   1260 ATAGGGAAAGATTTCTTAAAGAGGACAC-AAAAGTTCTAGTCATAAATAG 1308
                         v    v  v i       i v v     -     iv v  iv i   -  
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA-AG 622

  chr1_47847361_4   1309 AAAGCTTTAATGAATTGGATTACATTAAAATCCAGAACTTCTGTTCATTA 1358
                            ivv vi  i       i v   i     iv i     i   v v i 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_47847361_4   1359 TAAGACTTGATTAAGAGAGCAAAAAGGCAAGCTAAAGAGTGGAAGAAGAT 1408
                         v i   viv  i    i  ii     i   v i v   i   i    i  
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_47847361_4   1409 ATCTGCAA--CATGTATAACTGACAAAGAAATTG-ATTCAGAATATTTAA 1455
                           i     --   i   --    i  i i v   -  i        v   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATAT--CTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_47847361_4   1456 AGAATTCTAGTAGC-CAACAAGAAAAGGGTGAA----CCAATTAAAAAGT 1500
                             i   vii i -   i  v    i iii  ----      ?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_47847361_4   1501 TAAAAAGAGATTTCAAAAGCCAACTCACAGAAGAGGAAATCCAAATGGTC 1550
                         viiv  ii     v  v  v  vi  v vi    i  v  v       i 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_47847361_4   1551 AATAAATATATGAAAAGGTATTCAACCTTATTGGTCCT 1588
                              ii i        i ii     v i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (153 / 94)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 2.38 (81 / 34)  


3021 23.03 3.68 5.51  chr1_48038608_48041707     1684  2608 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_48038608_4   1684 TGGAGAGATATTCCATGTTCATAGATAGGAAGAC--AATATTTTCAAGAT 1731
                             i      i          i   v       --      v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_48038608_4   1732 GTCAGGTCTTCCCAACTCAATCTACATATTCAACACAATCCTAATCAAAA 1781
                          v  ivv  i     v ii       v       i      iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_48038608_4   1782 TCCCACCAAGTTATTTTGTGTCTATCAACAAACTGATTCTAAAGTTTATA 1831
                              v vivi v     iivvv  ii    i     i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_48038608_4   1832 TGGAGAGGCAAAAGACT--GGATAGTGAACACAATATTAAAGGAGAAGAA 1879
                             i v    ii   i-- i    iv  v     v  i  ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_48038608_4   1880 CAAAGTTAAAGGAATGACAGTACTCAATT-CAAGACTTATTATAAAGCTA 1928
                                ii    v v   v v i     -   i     i  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_48038608_4   1929 TAATCATCAAGACAGTGTGGTGTTGGTGAAAGAAAAGACAAATAGATCAA 1978
                         i i v                ii   iiv   i v     v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_48038608_4   1979 ATGCAACAGAAAAGGGTGCCCAGAAATAGACTCACATAAATGTAGTCAAC 2028
                         -  v  i    vv i v i         i  i  i i vv i i     i
  L1M4_orf2#LINE/    301 -TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_48038608_4   2029 TAATCTTTGACACAGGCACTATGGCT-------------------GCCTT 2059
                          i  i  i    vi  ii i v i i------------------- i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_48038608_4   2060 TTCAACAAATAGTGCTTGAACAAATGGTCATTCACATGTAAAATAATGAA 2109
                                   i     v i    v   vi ?i      i    v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_48038608_4   2110 TCTAGGCACAGACCTTACACTCTTCACAAAAATTAAGACAAAATGAATCA 2159
                         vi i i v vv    i    iv vi           vv       i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_48038608_4   2160 CAGCCCTAAATGTAAAACACGAAACTATGAAACTCCTAGAAGGTAACATA 2209
                         ?  v           i vvii       i      i      iv      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_48038608_4   2210 GAAGAAAATCTAGATGGCTTTCAGTTTGGTGGTGACTTTTTAGATAGGAC 2259
                          i? v      vvi  i i  vi   v  iii  ii  i       v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_48038608_4   2260 ACCAAA-GCATGATCCATGAAAGAAAGAATTGATAAGCTGGACTTTATTA 2308
                               -   ii v v ii       i   v     ii       i  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_48038608_4   2309 AAATAAAAAA--TCTGCTCTGTGAAGGATACTGCCAAGAGAATGAAAAGA 2356
                             v     -- i  iv  vii     i   ii     i i        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_48038608_4   2357 TAAGCT-CAGATTGGGAGAAAATATTTGCAAAAGACTGATAAATATAAAT 2405
                         i  v i-    v                    ------------------
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAA------------------ 731

  chr1_48038608_4   2406 ATATATATATATATAGGATAACTGGATAATTGGATATATCCTATATAATT 2455
                         --- -i      v --     v-   i--   ----     --- v   -
  L1M4_orf2#LINE/    732 ---T-CATATATCT--GATAAG-GGAC--TTG----TATCC---AGAAT- 764

  chr1_48038608_4   2456 TTATATATATATATATATATATAATCTCTTAAAACTCAACAATAAGAAAA 2505
                         --------------     v v  -      v       i     i  i 
  L1M4_orf2#LINE/    765 --------------ATATAAAGAA-CTCTTACAACTCAATAATAAAAAGA 799

  chr1_48038608_4   2506 CAA----CCTGATTAAAAGATGGGCCAAAGACCTTAATAGACTACTCACC 2551
                            ----  ii   ?   i      v  i  ii v       vvi  v  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_48038608_4   2552 AAAGAA--TGTACAGATGACAAGTAAGTATATAAAAAGATGCTCCACATC 2599
                               -- i    i   i v i    i i  i           v     
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_48038608_4   2600 CTATGTCAT 2608
                         v????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.65 (130 / 79)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 4.47 (85 / 19)  


3158 27.15 0.66 0.66  chr1_48133429_48139816     4990  5895 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_48133429_4   4990 GAAGAACATTCCACGCTCATGGATAGGAAGAATCAATATCGTGAAAATGG 5039
                            ii i  i   i i        v      v i     i  v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_48133429_4   5040 CCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 5089
                          v     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_48133429_4   5090 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 5137
                            iivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr1_48133429_4   5138 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTGAGCCAAAAGAA 5187
                              viiv  ii  v  v v  v     iv     i   ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_48133429_4   5188 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5237
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_48133429_4   5238 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACCAA 5287
                               i   i    ii         i iv ii i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_48133429_4   5288 TGCAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACCAT 5335
                           v  i    i--    i  --        vv  ii i  i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_48133429_4   5336 CTGACCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5385
                         i   ii  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_48133429_4   5386 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5435
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_48133429_4   5436 AACTGGATCTCTTCCTTACACCTTATACAAAAATTGATTCAAGATGGATT 5485
                          ii    i i  v   i     v            i i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_48133429_4   5486 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5535
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_48133429_4   5536 A--CGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5583
                          --? i  - i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_48133429_4   5584 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACCAATGGGATCTAA 5633
                         i            vvi          vv     v  iv   v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_48133429_4   5634 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCACCAGAGTGAAC 5683
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_48133429_4   5684 AGGCAACCTACAGAATCGGAGAAAATTTTTACAATCTACCCATCTGACAC 5733
                           i     i       v         v   i   vii ivi      i v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_48133429_4   5734 AGGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAGAAAA 5783
                         i  i  vi          v  i   v    ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_48133429_4   5784 AATCAAACAACCCCTTCAAAAAGTGGGCAAAGGATATGAGCAGACACTTC 5833
                          iv    i     vv i?    i            v   ii     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_48133429_4   5834 TCAAAAGAAGATATTTATGCAACCAACAGACATGTGAAAAAATGCTCATC 5883
                           v           vi viiii    i ii  ii      i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_48133429_4   5884 ATCACTGGCCAT 5895
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (8 / 906), avg. gap size = 1.50 (12 / 8)  


 392 30.95 4.76 3.87  chr1_48192131_48194691.rev      667  1002 (1559)    L1M4_orf2#LINE/L1        1   339 (569)  

  chr1_48192131_4    667 TAGAGAGACATTCC-TGTGCATG-ATTGAGCTGACTTAATATTAAAAACA 714
                          i  i   i  i  -   v    -    - vv           ivv  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTG-GAAGACTTAATATTGTTAAGA 49

  chr1_48192131_4    715 TGCCCCTTCTCCA-AAATCAATATAAACATATAATATGAAGCCAATCAAA 763
                           v vv v    v-    ii  v  v v  vi  iiii vv  v      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_48192131_4    764 ATATCAGTTGA-TTTCTTG-AGGATGCAATACACTTACTCTAAAATGTAC 811
                           vi   i  v-   i   -  i vvii i vi  v ii       vi i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_48192131_4    812 ACGGAGGAATTCAAATGGAGTTAACCTAAAAATGTTAAA----TCGTAAT 857
                          i   --   v   i-   -----  i i  vv ii   ----  v i v
  L1M4_orf2#LINE/    150 ATGGA--AATGCAAG-GGA-----CCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_48192131_4    858 AAAGAAAAAAGAAAAGAAGAAAACCTCACTCTTCCAGATATCAACA--TG 905
                               i  v--    vv i iiv     v     vi  v    v -- i
  L1M4_orf2#LINE/    192 AAAGAAGAAC--AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_48192131_4    906 CTACAAAAGCAAGATAATAAACACACTGTAATAATGGCC----AATA-AC 950
                                ivi vii    v  v   v   ii  v    v----i   -  
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_48192131_4    951 AGATAGAGTCACTGTCACAGAACAGAGAGCCACAGAGACACATCCTCACA 1000
                          v     -   v  vv i    iv     i -    i i v i  vi   
  L1M4_orf2#LINE/    290 ATATAGA-TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACA 337

  chr1_48192131_4   1001 CT 1002
                         i 
  L1M4_orf2#LINE/    338 TT 339

Transitions / transversions = 1.00 (52 / 52)
Gap_init rate = 0.05 (16 / 339), avg. gap size = 1.81 (29 / 16)  

 476 28.84 3.00 9.93  chr1_48192131_48194691.rev     1537  2070 (491)    L1M4_orf2#LINE/L1      412   908 (0)  

  chr1_48192131_4   1537 TGTTGGAA-AATTAGTTCACCATATGTAGAAGAGGAAAACTGGATCTCTT 1585
                           i   i -  i i v v?   i   i i    ivi  ii    i i  -
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT- 460

  chr1_48192131_4   1586 ACTTAATATCATATACAAAAGTGATATT--ATATGGATTAAAAACACAAA 1633
                           i v i i           i v - i -- v      i ? i  vi   
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTA-ACTCAAAATGGATCAWAGACCTAAA 509

  chr1_48192131_4   1634 TGTGAAAGAAAAAATAAAGTTATCAGAAGAATGATAAAGTTAATAGAAGA 1683
                            -----  i iv    ii   ------------   ii vv       
  L1M4_orf2#LINE/    510 TGT-----AAGAGCTAAAACTAT------------AAAACTCTTAGAAGA 542

  chr1_48192131_4   1684 TCTAAAAAATTTAAAGTTAATAGAATACGTTGAAGTTTATCTTTATGAC- 1732
                         ------   iv  ii?v   ------------------     ii    -
  L1M4_orf2#LINE/    543 ------AAACATAGGNGTAA------------------ATCTTCGTGACC 568

  chr1_48192131_4   1733 TTAGATATGAGGAATAATTTCACACAAAAAACATTAAAAGCACAAACAAT 1782
                           i i - ii v   ii    vi v v vi   ii          i   i
  L1M4_orf2#LINE/    569 TTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_48192131_4   1783 GTGGGAAAAGATAAATA--TT--ACTCCATTATATTTTTAGAAGATTTCT 1828
                         ivii     i   i   --  --   i   i v v  ---i  i i  i 
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT---AAAAACTTTT 664

  chr1_48192131_4   1829 ATCCAATGAAGGGCTCTATGGAGAAAATAAATAAATAAA--ATA-AATAA 1875
                         i v vvii    i v    vi     i i  v i i  v-- i -   ii
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_48192131_4   1876 TAGAAGGTATTCGCAACATCTGAAAT-TGGCACGGGATTAACATTGAAAA 1924
                         v    ii    i    -   vv v  -  ii v    i vii  iv i  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAA-ATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_48192131_4   1925 GATACAAA-AACTGCTACGAATCAACAAGAAAAAGAGAAA-AGCC--ATG 1970
                         v   i   -    vi   i v    i  v       v   - i  --  v
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_48192131_4   1971 AGAAAAGTGAGCAAAGGATATTTGTGCATAGGTAATTTTAAAAAGAGGAA 2020
                         ?i    -  i         --   --v    ii v  i vv     i  v
  L1M4_orf2#LINE/    814 WAAAAA-TGGGCAAAGGAT--TTG--AATAGACATTTCTCCAAAGAAGAT 858

  chr1_48192131_4   2021 ACTCAAAAAGAGGAAAAGTATTAGGAGAGTTGCTCAAAATTATTAGTAGC 2070
                          iv    vi vvi v   i ivv i i  v       v  i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (96 / 54)
Gap_init rate = 0.05 (23 / 497), avg. gap size = 3.00 (69 / 23)  


3229 23.76 3.49 1.91  chr1_48264471_48267544.rev     1697  2584 (490)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr1_48264471_4   1697 GACATTCTTTGTTTGTGGATCAGAAAACTCACCATGGTTAAGATTTTACT 1746
                           i  i iv    ii     ii   i   i vi  v        vvi v 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_48264471_4   1747 TCTCCCCAAATTGATCTATACATTCA-TGCATTCCACATCAAAATCCCAG 1795
                         v                 i v     -i   v   vi             
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_48264471_4   1796 CAGGCTTATG-GCATAAATTGATAAGTTGATTCTAAAATTCATGTGATCA 1844
                          v v   v v-   v       i   i    i           i  ivv 
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_48264471_4   1845 TAAAAAAGACCTAGAATAACTAAAACGGTTCTGAAAAAGAA---CAATGT 1891
                          iv  ii    i      i i     ii ii          ---   v  
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_48264471_4   1892 TGATAGGA-TAACTCTACCTGATTTCAAGACTTATTATAAAG------TA 1934
                           i-    - v  v  v  ii       i     i  i    ------  
  L1M4_orf2#LINE/    207 TGG-AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_48264471_4   1935 ATCAA---AGTGTGACATTAGAATCAAACTAGACAAATAGATCAATGGAA 1981
                              ---      ii i i v  v iiv      v              
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_48264471_4   1982 CAGAATACAGAGTCCATAAATGGATCCACACACATATGGACAACTGATGT 2031
                         i     vv        v    ii i   i   iv     v   i    v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_48264471_4   2032 TTGACAAAGATTTAAAAGCAATTCAAGGAAGGAAGGACAGTGTTTTCAAT 2081
                          i     i i viv  ii v      v ii i   i i   v       i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_48264471_4   2082 AAATGTTGTTAACACAGCTGGATGTATGTAAGCAAACAAAACAAAACAGA 2131
                              v  i iiv   i      i?viii v     -----------   
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-----------AGA 444

  chr1_48264471_4   2132 AAGAGAGGGTCCAATTCATAATTCACACTGTATATAAAAAATTAACTCAA 2181
                          v  i---  ivi ii v  vi      ii    i     -         
  L1M4_orf2#LINE/    445 ATGAA---GTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAA 490

  chr1_48264471_4   2182 ACTAAGTTATAGATCTAAATGTAAATCATACATTTATAACATTTTTTGGA 2231
                          v iii i ?   i          ivvv  v vi     v i i  v i 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_48264471_4   2232 GAAAA------------TCTTTGTGACCACAGGATAGGCAA-AGTCTTTT 2268
                              ------------    i      vii  v       -i  i i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_48264471_4   2269 AGATTCAACATCAAA-GTACAATCCATAAGAGAAAATTTTGATAAATTGG 2317
                             vii   i    - i    v v i  i      vv v          
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_48264471_4   2318 ACATTATCAAAATTTAAAACTTC-ATACTTCAAAAGACACTATTAAGAAA 2366
                           v i         v       i-i i       i        i      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_48264471_4   2367 ATGAAAAGACAAGCTACAGAATGGGTCAAAATATTTGCAGAGCATATATT 2416
                         i           v i          vv            i v       i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_48264471_4   2417 TGGCAAAGGACTTGTATTCAAAATCTATAACGAACTCTCA-AATTCAATA 2465
                           ii  i          i  i   v     v       i -  i      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_48264471_4   2466 AAAAGAAAACAAGCAATCCAATAAAAAAAATAGACAAAATATTTGAAGAG 2515
                          v  i  i    ii  i     v?     - i i    iv       v  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAG 839

  chr1_48264471_4   2516 ACATTTTACCAAAGAATATATATGCATGGCAAATAAGCGCATGAAAAGGT 2565
                               iv        v     iiv     v       i         i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_48264471_4   2566 GCTCATCATCCTTAGCAAT 2584
                              v    v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (129 / 79)
Gap_init rate = 0.02 (16 / 902), avg. gap size = 3.00 (48 / 16)  


2580 25.33 3.60 1.07  chr1_48303725_48305447      481  1230 (493)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr1_48303725_4    481 TAAAGCATTGATGTGAAAAAATTAAAGAAGATCT-GAGTAGCCAAAGCAA 529
                             --   v  i  i   --- iv iii  i i-  i        i   
  L1M4_orf2#LINE/    140 TAAA--ATTCATATGGAAA---TGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_48303725_4    530 TATTTAGCAAGATAAA---AGCTG----ACATCACACTCCCTGATTTCAA 572
                          v  v iv    vi  ---  i  ----  -       i  ii       
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAA 233

  chr1_48303725_4    573 AA-----TATAAAGATACAATAATTAAAACAGTATGGTACCACCATAAAA 617
                           -----  i    v    i    i  i     i      iiv     ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_48303725_4    618 ACAGAACATATAGACCAGTGGAACAGAATAGAGACCCCAGAAGTAAATTT 667
                          i   -        i  i     i     v    vi      i    iii
  L1M4_orf2#LINE/    284 ATAGA-CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_48303725_4    668 ACACATTTACTATCAACTGATGTTTGATAATGATGCCAATAAAAA-CAAT 716
                          i       ivi    i    v  i  i  v i      v vv v-    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_48303725_4    717 GTGAAATGGAGAGACTCTTCAAAAAATGATGTTGGAAAAACT--ATTCCT 764
                          v i  v i v  v  i     v     i  i   i v    --  v? i
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_48303725_4    765 GCATGTAGCATAAGTAAATTGGACCTTTATCTCTCATCATGTACAAAGAT 814
                         i    i iv v  vv  i       ii  i   v  i   i      i  
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_48303725_4    815 GAACTAAAAATGGATTAAAGGCTTAAATGTAAGAACCGAAACCATAATAC 864
                         v    v         i ?  i i           i ii    i    v  
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_48303725_4    865 CGCTAGAAGATACTATAGGAAAAAGCCTTT-TGACATTGGTCTGGGCAAT 913
                         ivi       v vi     ?iv  ii   i-    v    vi i      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_48303725_4    914 GATTTTTTAGA-ATGACATCAAACACAAAAGCAACGAAAGCAAAGATAAG 962
                          i   i     -      i    vi  v       i    v   i   ii
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_48303725_4    963 TAA----GGCTACATCAAA-TTAAGAAGCTTCTGCGCAGCAAAGGAAATA 1007
                            ---- i  v       -    i  -   i  i  vv       v iv
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT 681

  chr1_48303725_4   1008 ATCAAA----TGAAAAGTCAATGTATGGAATGGAAGAAAATATTTGCAAG 1053
                              i----       v   ivi ii      i               i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_48303725_4   1054 TCACATTTCTAATAAGGGATTCGTATTCAAAATATATAAGGAACTCATTC 1103
                            i  v   i        i i    i  i         i      v v 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_48303725_4   1104 AACTCAAGAGCAGAATGCCAAAACACTCAATTAAAAAACGAGTAAAGAGC 1153
                                v ii i  v v    vv  i     ?     i i i    iii
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_48303725_4   1154 CTGAATTTATATTTTTCAAAAGAAGACATGCAATTGGCTAAGAGGCGTAT 1203
                         i     vv i    i  v        i  i   v    i  v i  ii  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_48303725_4   1204 GAAAAAGTTCTCAATACCACTAATCAT 1230
                              ii v     i i  ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (124 / 62)
Gap_init rate = 0.02 (16 / 769), avg. gap size = 2.19 (35 / 16)  


3013 26.52 1.10 0.77  chr1_48310805_48316084.rev     3885  4789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_48310805_4   3885 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCACAAAAAT 3934
                               i i  i     i        v      v i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_48310805_4   3935 GGCCATACTGCCCAAAGTAATTTATAAATTCGGCATTATCCCCAATAAGC 3984
                            v     v      v i  i  i i    ii iiv     i vi  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_48310805_4   3985 TACCATTGACATTCTTCACAGAATTAGAAAAATCTAATT-TAAATTTCAT 4033
                          v   vivi v  i  ii     v v  v  i-  i  i-    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_48310805_4   4034 ACAGAACTTGAAAAGAGCCCACA-TAGCCAAGACAATCCTAAGCAAAAAG 4082
                          ii   v - v  i ii    v -       i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_48310805_4   4083 AAGAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTAAACTACAAGGC 4132
                           v    i      vv    i  v  ii i      vivv       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_48310805_4   4133 AACAGTAGGCAAAACACCATGGTACTGGTACCAAAACAGATATATAGACC 4182
                         v      iv   i   vii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_48310805_4   4183 AATGGAACAGA--TCAGAGGCCTCAGAAATAACACTACACATTTACAACC 4230
                                i   -- v    v  --        vv i i       iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_48310805_4   4231 ATCTGATCTTTTACAACC-TGACAAAAACAAGCAATGGGGAAAGGATTCC 4279
                          vi    i  iv    vv-  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_48310805_4   4280 CTGTTTAATAAATTATGTTCAGAAAACTGGCTAGCCATATGCAGAAAACT 4329
                           v  i  i    vi  i vi  v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_48310805_4   4330 GAAACTGGACCCCTTCCTTACACCTTATACAAAAACTAACTCAAGATGGA 4379
                            ii         v   i     v          i        i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_48310805_4   4380 TTAAAGACTTAAATGTAAGATCTAAAACCATAACCACCCT-AGAAGAAAA 4428
                          i ?    i           v       i    v-  i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chr1_48310805_4   4429 CCTAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAAGACTTCATGAA 4476
                          v    ?-   --i -   iv   v v  vv i     v ii   v ii 
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_48310805_4   4477 TAAGACACCAAAAGCAATGGCAACAAAAACCGAAATTGACAAATGGGATC 4526
                           v             vvi         ivvi    v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_48310805_4   4527 TAATTCAACTAAAGAGCTTCTGCATGGCAAAAGAAACTATCATCAGAGTG 4576
                          v  iv  v v  i i   i  iiivv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_48310805_4   4577 AACAGGCAACCTACAGAATGAGAGAAAATTTTTGCAATCTATCCATCTGA 4626
                           v  i     i        i        v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_48310805_4   4627 CAAAAGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 4676
                         i  ii i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_48310805_4   4677 AAAAAA--AATAACCCCATCAAAAGATGGACAAAGGATATGAACAAACAC 4724
                             i --        v  i?   i    i        v    i i   i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_48310805_4   4725 TTCTCAAAAGAAGACATCCATGCAGCCAACAAACATATGAAAAAAAACTC 4774
                              v        i  v  viii     i  i  i       i vi   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_48310805_4   4775 ATCATCACTTGTCAT 4789
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.31 (17 / 13)  


2868 26.94 1.80 1.35  chr1_48321252_48326290     3660  4546 (493)    L1M4_orf2#LINE/L1       18   908 (0)  

  chr1_48321252_4   3660 TCCATGCGATAGGAAGAATCAATATAATTAAAGTGGCTATACTGCCCAA- 3708
                          i    -   v      v i     vi    ii    v     v     -
  L1M4_orf2#LINE/     18 TTCATG-GATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chr1_48321252_4   3709 -TGAAATGTACAGATTCAATGCAATTTTCATCAAAACACCATCATTATTC 3757
                         -   -- v           i     iiii       iv   v vviv  i
  L1M4_orf2#LINE/     67 TTGA--TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr1_48321252_4   3758 TTCACAGAGCTAGAAAAAAATATTTTAAAATCCGTATGGA--TTCAAAAA 3805
                           ii    iv v  v  ivvv  ii      i i      -- v   iii
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_48321252_4   3806 AGAGCCCA-ATTGGCCAAGGCAATCCTAAGCAACAAGAACAAAACTGGAG 3854
                          ---    - v i     ii     i i iv  v         ii     
  L1M4_orf2#LINE/    165 A---CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_48321252_4   3855 GCATTATATTACCTGACTTCAAACTATACTATAAGGCTACAGTAACCAAA 3904
                          vv i i i v  ii i      viv     i  i          i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_48321252_4   3905 ACAACGTAGTACTGCTATAAAAACAGGTATATAGACCAATAGAACAGAAA 3954
                            ii  i      vi    ii i  ii       i    i   i    v
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_48321252_4   3955 AAATAGCCCAGAAGTAATGTTACACATCTGTGATCATCCTGATCTTCAAC 4004
                         vi v  i      i   vvii i    i i  i   -vi    i   i  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCA-ATTGATTTTCGAC 360

  chr1_48321252_4   4005 AAAACTGATAAAAGCAAGCAATGAGGAAAAGAAT--CCTTATTCAATAAA 4052
                           iiv  vi  i v  vv     i     -    --i   -     i   
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTT-TTCAACAAA 408

  chr1_48321252_4   4053 TGGTGCTAGAATAACTGGCTAGCCATATGCAGAAGATTGAAGCTGGACTC 4102
                                i i i      v  ?   i     i    v     i     i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_48321252_4   4103 CTTCTTTATGCCATATACAAAATTCAACTCAAGATAGATTAAAGACTTAA 4152
                           v i i ii            v i       i  i   i ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_48321252_4   4153 GTGTAAAATCCAAAATTATAAAAACCCCAGAAGACAACCTAGGCACTACC 4202
                         i     i v i    i       vi ii      v   v    ?iiv --
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-- 556

  chr1_48321252_4   4203 ATCCT-G-GACACTGGAGAAGGCACAGATTTCATGACAAAGACACCAAAA 4250
                            i - -   vi   ivv     vv i    v iivv v          
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_48321252_4   4251 GCAATTGCAACAAAAGCAATAATTTATAAGTAGGATCTAATTAAACTTAG 4300
                            vvv          v  v   vv    i v   ii v  i   v   i
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_48321252_4   4301 GAGCTTCTGCTCAGCAAAAGAAACTATCAACAGAGTGAAGAGACAACCTA 4350
                         i i   i  iv vv    i  v        v i      i        i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_48321252_4   4351 CAGAATGAGAGAAAATATTTGCAAGCTATGCATCTAACAAAGGTCTACTA 4400
                                i                iii  ii    i i  i  v  vv  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_48321252_4   4401 TGCAGTGTCTATAAAGAACTTAAACAAATTTACAAGAGAAAAACAACCAA 4450
                          v   vi v           ivv    v iv i  v i   i    vi  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_48321252_4   4451 CTCAATTAAAAAGTGGGGAAAGGACATG------TACTTCTCAAAAGAAG 4494
                          i     ?    i    v      iv  ------i i     v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_48321252_4   4495 -CATACATGTGACTAACAAGCATATGAAAAAAAAGCTCAATATCACTAAG 4543
                         -i     vi  i i  i     i       i v-      i    ?????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACATCAZZZZZ 905

  chr1_48321252_4   4544 TTT 4546
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.67 (147 / 88)
Gap_init rate = 0.02 (16 / 891), avg. gap size = 1.75 (28 / 16)  


 440 25.00 0.00 0.00  chr1_48327318_48333597        1    92 (6188)  C L1M4_orf2#LINE/L1   (816)    92     1  

C chr1_48327318_4     92 TGGAAAGAAATCTCATGCTCATGGACTAGAAGAATTAATCTTGTTAAAAT 43
                                 v   i    i       i i     v     v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_48327318_4     42 GACCATACTGCCCAAAGCAATGTATGAATTTGGTGCAATTCC 1
                          i v     v      vii  v  iii   iiii     i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.00 (0 / 0)  

3219 27.42 0.44 0.44  chr1_48327318_48333597     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_48327318_4   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_48327318_4   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_48327318_4   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_48327318_4   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_48327318_4   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_48327318_4   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_48327318_4   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5225
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_48327318_4   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_48327318_4   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_48327318_4   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_48327318_4   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_48327318_4   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_48327318_4   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACCAATGGGATCTAA 5525
                         i            vvi          vv     v  iv   v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_48327318_4   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_48327318_4   5576 AGGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5625
                           i     i   iv            v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_48327318_4   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_48327318_4   5676 AAACAAACAACCCCATCAAATAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?  v i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_48327318_4   5726 TCAAAAGAAGACGTTTATGCAGCCAAAAAATACATGAAAAAATGCTCATC 5775
                           v        ii vi viii     v  ii         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_48327318_4   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2772 19.77 4.13 1.99  chr1_48333854_48335543      499  1201 (489)    L1M4_orf2#LINE/L1      191   908 (0)  

  chr1_48333854_4    499 AAAAGAAGAACAAAGCCAGAAGACTCACACTTTCTAATTCCAGA-CCTAC 547
                                        iii  i           i i    i  i - i   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_48333854_4    548 TACAAAGCTACAGTAATCAAAACAGTGTGATACTGACATAGAAAAAGAAA 597
                                             i        i     i    iii v   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_48333854_4    598 CATAGACCATTGGAATATAAT--AGAGCCCAGAAATAAACCTTTACAAA- 644
                         i     i  v       v   --    i             iv    vv-
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_48333854_4    645 ATGGTTAAAGAATCTTTGACATGGGTGTTAAGAGCGTTCACTGGGAAAAG 694
                              i  vvi  i  i    v     ii    v i    v    i    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_48333854_4    695 GAGAGTCATTTCAATAAATGATTCTGGAAAAACTGGATATCCACATG--- 741
                         i v    v      i     i v    i v         ?       ---
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_48333854_4    742 AAGAATGAAGTTGGACCCTTATATAATACCATATTCAAAAATTAACAGAA 791
                                           i  iv v i       v           vv  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_48333854_4    792 AGTAGATCAAAAGCATACA-GTAAGA-C-----------AATTCTTAAAA 828
                          i i     ? ii v  v -      - -----------  i     i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_48333854_4    829 GAAAACATAGGATAAAAGCTTCTTGAC-TTGGATTTAGTGATGATTTCTT 877
                                    ?vv   v    v    -    i  vi ii   i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_48333854_4    878 TAACATGAAACCAAAAGCACAA-CAATGAAAGAAATAATAAACATTCAGA 926
                         vi i    v             -   ii       v    i i ----- 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA-----A 635

  chr1_48333854_4    927 TATTGGACTGCTTGAAAAATTCTTTAAA-----TTGTGCCTCAAAAAGTC 971
                         -        v v v    -----     -----      i     i- v 
  L1M4_orf2#LINE/    636 -ATTGGACTTCATCAAAA-----TTAAAAACTTTTGTGCTTCAAAG-GAC 678

  chr1_48333854_4    972 ATCATTCACCAAGTAAAAATGCAACC-ACACAATAGGAGAAATTATTTGA 1020
                          ii  iv vv    i    vi     -   v   i       v      v
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_48333854_4   1021 AAATCTTACATCTGATAAGGAATTAATATCCAGAATATGTTGAGAAATCT 1070
                              v  i           i i vi            i vi    v   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_48333854_4   1071 GAAAAGTCAACAACAAAA-GACCCACAACCCTTTTCAAAAATGAGCACAT 1119
                         v v  v    i  i    -   vv i     vv  ?       i   v v
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_48333854_4   1120 GAATTGAATAGACATTTCTCCAAAGAATATATGTAAGCAGCCAATAGGTA 1169
                           v                        v    ii  iii       i i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_48333854_4   1170 CATGAAAAGATGCCCAATATGCCAATCATTAG 1201
                                      i   i  --  ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACAT--CAZZZZZZZZ 908

Transitions / transversions = 1.37 (78 / 57)
Gap_init rate = 0.02 (17 / 718), avg. gap size = 2.53 (43 / 17)  


3133 27.31 0.55 0.55  chr1_48345275_48348678.rev     2006  2913 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_48345275_4   2006 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAACATCATGAAAAT 2055
                               i i  i     i        v      v i  i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_48345275_4   2056 GGCCATACTGCTTAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 2105
                            v     v ii   v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_48345275_4   2106 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 2153
                          v   -   v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_48345275_4   2154 TATGGAACCAAAAAAGAGCCTATGTAGCCAAGGCAATCCTAAGCAAAAAG 2203
                                viiv  ii  v  vivi       ii     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_48345275_4   2204 AACAAACCTGGAGGCATCATTCAACCTGACTTCAAACTACACTACAAGGC 2253
                               vi      vv   iv vv  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_48345275_4   2254 TACAGTAACCCAAACAGCATGGTACTG--ATAACCAAACAGATATATTGA 2301
                                 i v i    ii        --    --ii i   i    v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAA--GGATAGACATATAGA 296

  chr1_48345275_4   2302 CCAATGGAACAGAACACAGGCCTCAGAAATAACTCCACACATCTACAACC 2351
                         i        i    ivv  ivii         vi   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_48345275_4   2352 ATCTGATCTTTGGCAAACCTGACAAAAACATGCAATAGGGAAAGGATCCC 2401
                          vi    i  i i   ivv  v   i v   v    i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_48345275_4   2402 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATACAGAACACT 2451
                           v  i  i        i     v      v  ?   i  i  i  v v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_48345275_4   2452 GAAACTGGACCCCTTCCTTATACCTTACACAAAAATTAACTCAAGATGGA 2501
                            ii         v   i i   v  i                i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_48345275_4   2502 TTAAAAACTTAAATGTAAGACCTAAAACCATGAAAACCCCAGAAGAAAAC 2551
                          i ? i  i           v       i  i   vi ii          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_48345275_4   2552 CTAGGCA-ATACCATTCAGGACATAGGCACGGGCAAAGACTTCATGACTA 2600
                         v    ?i- v i -   iv   v v  vvii     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_48345275_4   2601 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2650
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_48345275_4   2651 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCCAAGTGAA 2700
                           i   v v  i i   i  ii vv    i  v       vvv       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_48345275_4   2701 CAGGCAACCTACAGAATGGGAGAACATTTTTGCAATATGTGCATCTGACA 2750
                         v  i     i              v  v       vvii ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_48345275_4   2751 AAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAA 2800
                          i  i  vi          v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_48345275_4   2801 AGAACAAACAACCCCATCAAAAAGTGGGGAAAAGATATGAACAGATGTTT 2850
                          ii     i     v  i?    i    v   i   v    i   ii   
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_48345275_4   2851 CTCAAAAGAAGACATTTATGTGGCCAACACACATATGAAAAAAAGCTCAT 2900
                            v        i  vi vi       i vi  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_48345275_4   2901 TATCACTGGTCAT 2913
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


3569 20.39 0.00 0.00  chr1_48395924_48397631.rev      502  1217 (491)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr1_48395924_4    502 AAGAAGAACAAAGTTGGAGGTTTCATGCATCCTGATTTCAAAACTCACTA 551
                                             vi   ii v   ii           i    
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_48395924_4    552 CAAAGCTACAGTAGTGAAAGCAGTGTGGTAGTGGCATAAAGACAATCATA 601
                                      i v  ii          v        i  i iv    
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_48395924_4    602 TAAACCAATGGAATAGAACAGAGAGCCCAGAAATAAAGTCTCACAGTTAC 651
                           i i             iv     i           vi vi   v   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_48395924_4    652 AGTCAAATGATTCTTGACAAGAGTGTGAAGACCACTCAGTGGAAAAATGA 701
                         i     v     i i      i   iv       i   i   ii   vi 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_48395924_4    702 CAGCATTTTCAACAAATGATGCTGAGAAAATGGAATATTCCTATGCCAAA 751
                         i  iv             i     i  v  iv i   ?i vi    v   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_48395924_4    752 GAAAGAAGTTGGACCCTTACATTGCACCATATATGAAAATTAACTCAAGA 801
                            v            i   v ii         ii             i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_48395924_4    802 TGGATTGAAGACTTAAATGCAAGAGCTAAGAAAATAAAGCTCTTAGAAGA 851
                              ii?    i      i         i vv     i           
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_48395924_4    852 AAACATAGGGTAAAATCTTCATGTTGTTGGACTTGGAGATAATTTCTTGG 901
                                  ?vv        i  viv    ii v  vi  ii      i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_48395924_4    902 TGATGATGCCAAAATCACAGGCAATAAAGGAAAAAATAAATAAACTGAAC 951
                         vv    ii      v    i    i   i         i     i  i  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_48395924_4    952 TTCGTCAAAATTAAAAACTTCTGAGCATCAAAGGACACTATCAACAGAGT 1001
                            i                i  v  v                 v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_48395924_4   1002 GAAAAGGCAACCGATGGAATGGGAGAAAATATTTACAAATCATACATCTG 1051
                               i     v ii                  i         i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_48395924_4   1052 ATAAGGGATTAGTACCTATAATATATGAAGAATTCCAGTAAATCAACACA 1101
                                 i v   i i v       i     i  ivii  v    i vv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_48395924_4   1102 AATGAAACTAACAATCCTACTCAAAAATAAGCAAAGGAGTTGAATAGACA 1151
                           vi i  v  i  i  v i ?      ii        v           
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_48395924_4   1152 ATTCTCCAAAGAAGTTATACAGGTGGCCAAAATGCATATGAAAAGATGTT 1201
                         v             v      ii       v v   i           i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_48395924_4   1202 CAACACCACTAATCAT 1217
                              i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (94 / 48)
Gap_init rate = 0.00 (0 / 716), avg. gap size = 0.00 (0 / 0)  


3162 26.90 0.77 0.66  chr1_48454387_48460788     5003  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_48454387_4   5003 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5052
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_48454387_4   5053 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5102
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_48454387_4   5103 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACTA--CTTAAAGTTCA 5149
                          v   iivi i  i  iii    -   -- v  i  i-- i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_48454387_4   5150 TAAGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 5199
                           v    viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_48454387_4   5200 AGCAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGT 5249
                          i     i      vv       v  ii i      viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_48454387_4   5250 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATATATC 5299
                                 i   i    ii         i iv ii i   v     v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_48454387_4   5300 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACGTATCTACAACT 5347
                                i    i--    i  --        vv   iii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_48454387_4   5348 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5397
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_48454387_4   5398 CTATTTAATAGATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5447
                           v  i  i i            v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_48454387_4   5448 GAAACTGGATCTCTTCCTTACACCTTTTACAAAAATTAATTCAAGATGGA 5497
                            ii    i i  v   i     v v            i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_48454387_4   5498 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5547
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_48454387_4   5548 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGATTTCATGTCTAA 5597
                         v    ?i v viv   iv   v v  vv i     v i    v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_48454387_4   5598 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5647
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_48454387_4   5648 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAAC 5697
                          i   v v  i i   i  ii vv    i  v    i  vv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_48454387_4   5698 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAGAA 5747
                           i     i   i             v  ii   vii ivi      v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_48454387_4   5748 AGGGGCTAATATCCAGAATCTACAATGAACTCAAACAAACTTA-CAAGAA 5796
                         -   i  vi          v  i  v      vv    -  i -i  v  
  L1M4_orf2#LINE/    747 -GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAA 794

  chr1_48454387_4   5797 AAAAACAAACAACCCCATC-AAAAATGGGCAAAGGACATGAACAGACACT 5845
                            i     i     v  i-                iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_48454387_4   5846 TCTCAAAAGAAGACATTTATGCAGCCACAAAACACATGAAAAAATGCTCA 5895
                             v        i  vi viii    vv  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_48454387_4   5896 CCATCACTGGCCAT 5909
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


3147 26.58 1.22 0.66  chr1_48488781_48495132     4957  5859 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_48488781_4   4957 TGGAAGAACATTCCATGCTCACGGGTAGGAAGAATCAATATCATGAAAAT 5006
                              ii i  i     i   i  i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_48488781_4   5007 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCAACCCCATCAAGC 5056
                            v     v     iv i  i           i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_48488781_4   5057 TACCAGTGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5104
                          v    ivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_48488781_4   5105 TATGGAAACAAAAAGGAGCCCGCATTACCAAGTCAATTCTAAGCCAAAAG 5154
                                 iiv  i   v  v v  vi    iv    ii i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_48488781_4   5155 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5204
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_48488781_4   5205 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5254
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_48488781_4   5255 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5302
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_48488781_4   5303 ATCTGATCTTTGACAAACGTGACAAAAACAAAAAATGGGGAAAGGATTCC 5352
                          vi    i  i     iv   v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_48488781_4   5353 CTATTTAATAAATAGTGCTGGGAAAACTGGCTAGCCATATTTAGAAAGCT 5402
                           v  i  i    i         v      v  ?   i  vi i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_48488781_4   5403 GAAACTGGATCCCTTCCT-ACACCTTATACAAAAATTAATTCAAGATGGA 5451
                            ii    i    v   -     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_48488781_4   5452 TTAAAGACTTACTTGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5501
                          i ?    i  vv   v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_48488781_4   5502 CTAGGCA-ATACCATTCAGGACATAGGCATGAGCAAGGACTTCATGTCTA 5550
                         v    ?i- v i -   iv   v v  vv ii    v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_48488781_4   5551 AAACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5600
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_48488781_4   5601 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5650
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_48488781_4   5651 CAGGCAACCCACAGAATGGGAGAAAATTTTTGCAATCTACTA-ATCTGAC 5699
                         v  i                       v       vii -  -      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGAT 744

  chr1_48488781_4   5700 AAAGGGCTAATATCTAGAATCTGCAATGAACTAAAACAAATTTACAAGAA 5749
                           i  i  vi    i     v ii  v     vvv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_48488781_4   5750 AAAAACAA----CCCCATCAAAAAGTGTGCAAAGGATATGAACAGACACT 5795
                            i    ----   v  i?    i  v         v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_48488781_4   5796 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5845
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_48488781_4   5846 TCATCACTGGCCAT 5859
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


2573 25.22 3.44 2.56  chr1_48503367_48505449      691  1590 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_48503367_4    691 TGGAAAAACATCCCATGCTCATGGTGCATTAGGA---TCAGTTATGTTAA 737
                               i i        i      ---   i i --- i i vv      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGG---ATTGGAAGACTTAATATTGTTAA 47

  chr1_48503367_4    738 AATGACCATACTACCCAAAGCAATCTACAGATTCAACACAATTCCTATCC 787
                         i   i v     v      vii               i    i      v
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_48503367_4    788 AATTACCAACATCATTTTTTAAAGAATTAGAAAAAATAATCCTAAAGTTC 837
                           v v   i vv v      iv    v v  v  iv i        i   
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_48503367_4    838 ATATGAAACAAAAAAAAAAAAAAAGAAAAAGCCTGAATAGCTAAAGCAAT 887
                              i  ---------- viv   ii v--  v       i   i    
  L1M4_orf2#LINE/    148 ATATGGAA----------ATGCAAGGGAC--CCAGAATAGCCAAAACAAT 185

  chr1_48503367_4    888 CCTAAGTAAAAAGGACAAATCTGGAAGCATCACATTATATAGCTTTAA-- 935
                          i i iv  i   i     vi    i vv     i vivi ii  i  --
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_48503367_4    936 CTTATATTACAAAACTATAGTAACTAAAACAGCATGGTACTAGAAGAAAA 985
                             i--      i   i     ii  i    ii       i v v  ii
  L1M4_orf2#LINE/    236 CTTAC--TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_48503367_4    986 ACAGACACATA-ATCAATGGAATAGAATAGATAACCCAGAAATAAAGCCA 1034
                          i     i   -                v  v ii           v   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_48503367_4   1035 CATACCCACAATTAACTAATGTT-GACAAAAA---CAAA------CAATG 1074
                         i i iii iii i  i i  v  -     iii---   i------     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_48503367_4   1075 GGGAAAGGACACCTTATTCAATGAATAGCGCTGGGAGAATTAGCTAGCCA 1124
                                i i vii v     ii   i i       v  i i v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_48503367_4   1125 TATGCAAAAT--TAAACTCGGACCCTTATCTCTCACCATACACAGTAATT 1172
                         i        v-- i  v i      i  i   v       i   iv    
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_48503367_4   1173 AATTCATGATATATTAAAGACTTAAATGTAATACCTGAAACTATAAAAAG 1222
                           i   vi  iv  i ?    i         v v  i           vv
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_48503367_4   1223 CCTGGAAGAAAACCTAGGGAAAAACTCTACTGAATATTGGCCTAGACAA- 1271
                          i i         v    ?iv   -   v vvi iv    vi   i   -
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_48503367_4   1272 -ACAACTTACGACAAAAACCCCAAAAGCAAATGCAACAAAAACAAAAATA 1320
                         -iivv    -  i vi - v         v v         iv       
  L1M4_orf2#LINE/    583 GGTTTCTTA-GATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_48503367_4   1321 GACAAATAGGACTT-----AAACTATAAAGGTTCTGTACAACAAAATATA 1365
                           i    v      -----   i  -   iv  i   i vv    iv i 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACA 679

  chr1_48503367_4   1366 TAATCAACATAGTAAACAGACAACTTACATAGTAGGAGAAAATATTTGCA 1415
                         iv     v v   i  v       ii   v i i                
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_48503367_4   1416 AACTATGTCTTTGACAAAGGACTAGAATCCACAAGTAACTCAAACAACTC 1465
                           ii  i v i   i  i     v v     v  -  vv -   v     
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAA-TATAT-AAAGAACTC 777

  chr1_48503367_4   1466 CCACA-CACACTAA-AAAAAGAAAAA----CCAATAAAAAACCAGGCAAA 1509
                         ii   - v  v   -       v   ----     v?    vii      
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_48503367_4   1510 GGACCTGAACAGTCATTCCTCAAAAGAAGAAATAAAAGCGGCTAACAAAC 1559
                            ii    i  v    i   v        v   v  ii   i  i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_48503367_4   1560 ACACAAAAAAATGCTCAACATCACTAATCAT 1590
                            ii    i             ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (137 / 86)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.45 (54 / 22)  


2660 26.08 2.21 1.88  chr1_48508290_48514234     4548  5452 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_48508290_4   4548 TGGAAGAAAATTCCATGCTCATGGATAGGAAGAATAAATATCATTAAAAT 4597
                              ii v  i     i        v      v v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_48508290_4   4598 GACCATACTGCTCAATGCAATTTACAGATTCAATGCTATTCCTATCAAAC 4647
                          i v     v i   vvii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_48508290_4   4648 TACCAATGAAAATTTT--CAAATAATTAGAAAAAACT-ATTCTAAAATTC 4694
                          v   iivivvv    --  i -    i-- v  i  -  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_48508290_4   4695 ATATGGAACAAAAAAAGAACCTGAAAAGCCAAGGCAATCCTAGGCAAAAA 4744
                                 vviv  ii  v  v   v      ii     i i--------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-------- 189

  chr1_48508290_4   4745 AAAAAGAAAAA-AAAGCTGGAGGAATCACATTGCCTGACCTCAAACCATA 4793
                                 i  -    i       v     i v  ii ii     v v  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_48508290_4   4794 CTACAAGGCTAGAGTAACCAAAATACCATGGTACTCATACAAAAGTAGAC 4843
                               i    v     i   i i vii       vii i  iii     
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_48508290_4   4844 ACATAGGCCAATAGAACAGAAGAGAGAGCCAAGAAATAAAGCCACTCACC 4893
                          i    ii    i   i    vv     i v         v   iv  ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_48508290_4   4894 TACAGCCATCTGATCTTTGACAAAGCTGACAACAACAAGCAATGGGGAAA 4943
                           ii i  vi    i  i     i v  v   v v  vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_48508290_4   4944 GGACTCCCTACTCAATAAATAGTGCTGGAATAACTGGCTAGC----TG-- 4987
                          i ivvi  vi    i    i       i i      v  ? ----  --
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_48508290_4   4988 -AAGATTGAAACTGGACCACTTCCTTAAAACATATGCAAAAATCAACATA 5036
                         -    v    ii      v  v   i v v     i       i   vi 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_48508290_4   5037 AGATTGATTAAAGACCTAAATGTAAACCCTGTAACTGTAAAAACTCT-GG 5085
                          i  v   i ?              ivv  iv    i     -    -i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAG 538

  chr1_48508290_4   5086 AAGATAACCTAGGCA-ATACCATTTTTGACATAGGAATAGGCAAAGATCT 5134
                             v   v    ?i- v i -  iv    v v  iv       v i i 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_48508290_4   5135 CATGACAGAAAATGTCCAAAGCAATTGCAACAAAAGCAAAAAT-GACAAA 5183
                          - v v v vi iii v      vvv          v      -  i   
  L1M4_orf2#LINE/    588 C-TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_48508290_4   5184 TGGCGCCTAATTAAA-TGAAAGAGGTTTTGCACAGCAAAAGAAACTATTA 5232
                          v vi i v  i   - v   i v-     ii vv    i  v     i 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCA 685

  chr1_48508290_4   5233 ACAAAGTAAACAGACAACTTACAGAATGGAAGAAACATATCTGTAAACGA 5282
                          v     i  v       ii         i     -    i  i   iv 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA-ATATTTGCAAATCA 734

  chr1_48508290_4   5283 TACATATGACAAAGATCTAACATCTAGAATCTACAGGGAACT--TA-AAC 5329
                           i  v   i  i iv  vii   i     v  i ii     --  -   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_48508290_4   5330 ACA-TAAGCAAAAAATGAACAATCCCATTAAAAAGTGGGCAAAGGACATG 5378
                         v  -   vv    i ii  i  i  v   ?    i           iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_48508290_4   5379 AACAGACACTTTTGAAAAGAAGGCATACAA-TGCACCAAAAAGCATATGA 5427
                           i     i  i vv       ii      -  -i    v     i    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATG-GCCAATAAGCACATGA 883

  chr1_48508290_4   5428 AAAAATGTACAATATCACTAATCAT 5452
                            i   iv   i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (136 / 96)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.68 (37 / 22)  


1788 21.86 14.37 5.43  chr1_48527375_48530181.rev     1492  2319 (488)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr1_48527375_4   1492 GACATATCATGTTCATGGACAGGAGGATTCAATATT-------TG--AAT 1532
                           i  vi            iv   i  i i      -------  --   
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_48527375_4   1533 ----CTCAATTTGATGTCTAGATTTTATGCAATCTTAATCAAAATTCCAG 1578
                         ---- i   v     v vi     iv i      iiv        i    
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_48527375_4   1579 CACATG--TTTTTAGTAGATATTGACAAGCTTATTCAACAATGTGTATG- 1625
                          ---  --     v i   v           v  i v v   vii    -
  L1M4_orf2#LINE/    107 C---TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_48527375_4   1626 AAAGGCAAAGAAACTTGAAAAATCAAAACGATCT-GAAACA----AACAA 1670
                            v    i i v iv   v ii      i    -    v ----     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_48527375_4   1671 AGCTGGAGGACTCAC--TGCCTAATTTTAAGATTTTTGCAATAAAGC-AC 1717
                           i            -- v  i     i  i i  --i v i     -  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTT--ACTACAAAGCTAC 251

  chr1_48527375_4   1718 AGTAATGAAGATTGTGTTATATTGATTAAATTATGGACACATGTATCAAA 1767
                               v    iv    vi  i  iivv  vv  i    i  iv     v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_48527375_4   1768 GGAATAGAATAAAGATTCCAGAAATAGACCCACGTAAATACTGTCAACTG 1817
                                   vi   v          i     iii vv  iv     i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_48527375_4   1818 ATTTT-GACAAAAGTGTAAAGCCAATTAAATGTCGACTTTGTTTTTG--T 1864
                              -     ii   iv   v v   v    vv  vv-------- -- 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA--------GAAT 393

  chr1_48527375_4   1865 TATCTTTTAAACAAATGGT--T-------CTAGATTTTT---TTTAAAAG 1902
                         vi      v          -- -------  i   v?ii--- vi     
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_48527375_4   1903 ------------CCCCT------TGGCGTGTA---------ATTCAAAAT 1925
                         ------------     ------iiv i i  --------- i       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_48527375_4   1926 AGATCATAGATCTTCAATGTAA-------AACTGTAAAACTTCTAGAGGA 1968
                         i     ?   i  -v       -------    i       ii    i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCT-AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_48527375_4   1969 AAACATAGTAGAAAATCTGTGTAAT-TTAATTTCGGCAATGAGTTTTTA- 2016
                                 v? v      vi  i i-  iiv  v       iv  i   -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_48527375_4   2017 -TATGATAGCAA--GCACAA-CATCCATAAAGTTAAAAAAACTGATAAAT 2062
                         -     i v   --      -  --- i   i--i      iv       
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCA---ACAAAA--GAAAAAATAGATAAAT 637

  chr1_48527375_4   2063 TGGATTT------AATT---------TGCTCTGTGGAAGTCACTATTAAG 2097
                             i  ------    ---------  iv  viii i v      i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_48527375_4   2098 AGAAAGAAAAAAGG--CCACAAGTTGGATGAAAATATTTTAAAATCACAT 2145
                          i iv     i vi--     iiv   iv          vv      i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_48527375_4   2146 ATATGAGTTA--GGACTTGTATCCAGAGTTAGGAAAAAAAAAAAAGAAAG 2193
                           v   --  --               i ------------- v v    
  L1M4_orf2#LINE/    738 ATCTGA--TAAGGGACTTGTATCCAGAAT-------------ATATAAAG 772

  chr1_48527375_4   2194 AAAAGCACAAAACAACTATCCAAACTTAACAAAAAAAATAAATAACCAAA 2243
                           --- v vv -     ---   ---   i     i -i        v  
  L1M4_orf2#LINE/    773 AA---CTCTTA-CAACT---CAA---TAATAAAAAGA-CAAATAACCCAA 811

  chr1_48527375_4   2244 TTAAATAATGGGCAAAAGATCTGAACAGGCACTTCACCAAA--AGA---- 2287
                           ?  v          i   i    i  i  i   v     --   ----
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_48527375_4   2288 --------------ACACATTAAAACATGCTCAAC-TCATAATGGAA 2319
                         --------------i     v    v         -   ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (101 / 76)
Gap_init rate = 0.05 (42 / 902), avg. gap size = 3.90 (164 / 42)  


3008 27.10 1.33 0.88  chr1_48541746_48548121.rev     4983  5886 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_48541746_4   4983 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5032
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_48541746_4   5033 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCCACCCCCATCAAGC 5082
                            v     v      v i  i           i  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_48541746_4   5083 TGCTAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5130
                          v i iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_48541746_4   5131 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5180
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_48541746_4   5181 AACAAACCCGGAGGCAC-CACGCTACCTGACTTCAAACTATACTACAAGG 5229
                               vii     -  -   i  v  ii i      viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_48541746_4   5230 CTACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGAT 5279
                                  i   i    ii        vi iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_48541746_4   5280 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGACGCATA--TCTACA 5325
                                 i    i--    i  --        --  v    -- i  ii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAA--ACCCATACATTTATG 343

  chr1_48541746_4   5326 ACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT 5375
                         iii vi    i  i     ivv  vv  i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_48541746_4   5376 TCCCTATTTAATAAAGGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5425
                         vvi  v  i  i   v          v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_48541746_4   5426 GCTGAAACTGGATCCTTTCCTTACACCTTATACAAAAACTAATTCACGAT 5475
                         iv    ii    i  i v   i     v          i   i   vi  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_48541746_4   5476 GGATTAAAGACTTACATGTAAGACCTAAAACCATAAAAACCCTAGAAGAA 5525
                             i ?    i  v        v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_48541746_4   5526 AACCTAGGCA-ATACCATTCAGGACATGGGCATGGGCAAGGACTTCATGT 5574
                            v    ?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_48541746_4   5575 CTAAAACACCAAAAGCGGTGGCAACAAAAGCCACAATTGACAAATGGAAT 5624
                         v  vi           ivvi          vv v   v  i    v i i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_48541746_4   5625 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5674
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_48541746_4   5675 GAACAGGCAACCTACAAAATGGGTGAAAATTTTCGCAACCTACTCATCTG 5724
                            v  i     i   i      v      v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_48541746_4   5725 CCAAAGGGCTAACATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 5774
                         vi  i  i  vii         v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_48541746_4   5775 AAAAAAACAA----CCCCATCAAAAAGTTGGCAAAGGATATGAACAGACA 5820
                              i    ----   v  i?    i v          v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_48541746_4   5821 TGTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 5870
                          v    v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_48541746_4   5871 CATCATCCCTGGCCAT 5886
                           v    v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


1370 25.77 0.84 1.12  chr1_48602688_48604383        4   360 (1336)  C L1M4_orf2#LINE/L1   (267)   641   286  

C chr1_48602688_4    360 AGACACATAGACCAGTGGAACAGAATCAGAGAACCCAGAAACAAATCCAT 311
                              i     i  i     i     i-    ii       i   i    
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATT-GAGAGTCCAGAAATAAACCCAT 334

C chr1_48602688_4    310 ACACCTACAGTGAACTCATTTTTGACAGAGGTGTCAAAAACATAACACTG 261
                            ii  ii  v  i v     i    ii    i   i v   v-  v  
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATG 383

C chr1_48602688_4    260 GGGAAAGA-TAGTCTCTTTAATAAATAGTACTGGAGAAACTGGGTATCTA 212
                                 -      i  i  i    i  i    iiv      i  ? i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

C chr1_48602688_4    211 TATGCAAAAGAGTGAAACTAGTTCCCTATCTCTCACCATATACAAAAACC 162
                         i          i    ii i vi     i   v               ii
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

C chr1_48602688_4    161 AAACCAAAATGTATTGAAGACTTAAATCTAAGACCTCAAATTATGAAACT 112
                           vi       v  ii?    i     v     v  v   i   i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

C chr1_48602688_4    111 ACTACAGGAAAACATTGGGGAAAGTCTCCAGTA--CATGGGTCAGGGCAA 64
                         vi  v i        v  ? v  i   i -  i-- v     i   -   
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGG-CAA 581

C chr1_48602688_4     63 AGACTTCTTGAGCACTACCCCTCAAGCACAGGTAACCAAAGTAAATGTGG 14
                         v ii     iiii iv  v  vv       i i   v    v   vi i 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

C chr1_48602688_4     13 ACAACTGGGA 4
                          i  v v   
  L1M4_orf2#LINE/    632 ATAAATTGGA 641

Transitions / transversions = 2.18 (61 / 28)
Gap_init rate = 0.02 (6 / 356), avg. gap size = 1.17 (7 / 6)  

1306 25.60 5.73 7.07  chr1_48602688_48604383      500  1249 (447)    L1M4_orf2#LINE/L1      169   908 (0)  

  chr1_48602688_4    500 AGACTAGCTAAGGCAATCTTCAAAAAGAAGAATAAACTTGGAGG-CTTAA 548
                            v    i  ii       v           i   v       -  i v
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_48602688_4    549 ACTACCAGATAGCAAAACTTA------AGCTACAGTAATTAAGAAAGTAT 592
                            v  vi  vv         ------            i    v   i 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_48602688_4    593 AATATTTATGCAAGGATGGACAAACAGACCCAAGAAACAGAAC--AGAAT 640
                         ii  i viiii      i    v i   i v v i  i    i--   i 
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_48602688_4    641 CTAGAAAAAAGTTCCACATGCCTACATGTGCCCTAGCAGGCACTTAATTT 690
                          i     v  ii-   ------     v i--- i i---  v  i    
  L1M4_orf2#LINE/    319 CCAGAAATAAAC-CCA------TACATTTA---TGGT---CAATTGATTT 355

  chr1_48602688_4    691 ATGACAAAA-TA--AACACTATGAAGCAATGGGAATA----AGTCTTTTC 733
                         vi     ii- i--  v  i  v---       i v ----         
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATT---CAATGGGGAAAGAATAGTCTTTTC 402

  chr1_48602688_4    734 AACAAATCGTATTGTT-TAATTAGAGATT-ATATATGAATAAAACAAATT 781
                                v  ii  vv-i  i i  v ?i- i  iii  vi  vv  i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_48602688_4    782 TTATCCCTACTTTATACTATATATAAAAATTAAATCCAGGTGGACTATAA 831
                         vv i      i i i  i     i         v  v ii    ii ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_48602688_4    832 ATCAAAATGTAAAAGGTAAAA----AAAATGCTTCTTGAAGATTATGTAG 877
                          i v        i  v     ----    --  ii v     vv ii   
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAA--CTCTTAGAAGAAAACATAG 550

  chr1_48602688_4    878 AATGATATTTTCATAAC--TGGTGTAAGCAAAGATTTCTTTAAAATGAAA 925
                         i?vv v  i   i i  --   vv  i    v i      vi v    v 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_48602688_4    926 --AAAAA-ACAAGCAGTAGGCACAAAGGAAAATATTAATAAATCAAACTA 972
                         --    i-       ------     i     v  vi      iii   v
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCA------ACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_48602688_4    973 CATTACTAAGTCAGATTGTGTTAAAAATAACTTGCTCATCAAAAGA-AC- 1020
                            i ------- i   -----     iv-i   iv v     i  -  -
  L1M4_orf2#LINE/    645 CATCA-------AAATT-----AAAAACT-TTTGTGCTTCAAAGGACACT 681

  chr1_48602688_4   1021 ---AAGAATCGCTAATGGATTAAAAATGTAAGCCACAGAGTGGGACAAGA 1067
                         ---     ----- i  -----    vii  v       i     v  i 
  L1M4_orf2#LINE/    682 ATCAAGAA-----AGTG-----AAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_48602688_4   1068 TACTTG-AAA-CATATAACTGGCAAATGGCTTGTAATGAGAAAATGTAGG 1115
                           i   -   -      v   ii  iv i      viv    v  i  ii
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_48602688_4   1116 GAATTCCTACAAATTAATAAGAACAGAACAAACAACCCAATGGAAAAACG 1165
                            i  i     v i     v  v ii     i        v?     i 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_48602688_4   1166 GGCAAAAGAC------AGGCACTTCAC--AAGGAGAAGGAAGAGTGTATC 1207
                               i  i------  i  i   v --   i   viv vi i  -ii 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG-GCC 870

  chr1_48602688_4   1208 TA-AAGGACCTGGAAAGATAATCCCTAAACAGCCAATACACAC 1249
                         v -   v  v  i      iv  ----    -i  ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTC----AACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.65 (117 / 71)
Gap_init rate = 0.05 (34 / 740), avg. gap size = 2.82 (96 / 34)  


3079 24.59 2.34 1.41  chr1_49015302_49017128      481  1334 (493)    L1M4_orf2#LINE/L1       47   908 (0)  

  chr1_49015302_4    481 AGATGAAAAGCAATGAATAACTACCCAAAGCAATCTACAGAT-CAGTGCA 529
                              ----     -----   v      vii          -  ii   
  L1M4_orf2#LINE/     47 AGATG----GCAAT-----ACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chr1_49015302_4    530 ATCCCTATAAAAATACCAATGAAATTCAACACAGAAATAGAAAAAAGC-A 578
                                 v     v   iivivv  ivvii       v  v  --  -i
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTG 135

  chr1_49015302_4    579 ATCCTAAAATTTTTCTGGAACCACAAAAGACCCAGAATAGCTAATAAGTT 628
                                    iv v     vii   ii             i  v viv 
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_49015302_4    629 CCTGAGCAA-AAGCACAAAGCTGGAGGCATCACATTACCTGACATCAAAG 677
                          i   iv  -   v      i      vv     i v  ii iv     i
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_49015302_4    678 TATACTATAAAGCTGTATTAACCCAAACAGCATGATACTAGCATAAAAAC 727
                         iv     i      ii v   i v i    ii  i    i      ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_49015302_4    728 AGACATATAGACCAGTAGAACAGAATAGAAAACCCAGAAATAAATCCACG 777
                                    i  i i   i     v  i ii           i   ii
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_49015302_4    778 TATTTA--ATTAACTCATTTTTGACAAAGGCATCAAGAACAAACATTGGA 825
                         i     --i i  i v     i     i  iii     v  vv  v   i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_49015302_4    826 GAAAGGAAAAGCTCTTTAGTAAATG-TGCTGGGAAAGCTGGGTATCCATA 874
                              i v iv  i  i ii     -        v i    i  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_49015302_4    875 TGCAGGAGAATAAAACTAGACCCCTATCTCTCACCATATATAAAAATCAA 924
                             ii     i  ii i        i   v         i      i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_49015302_4    925 ATAAAAATAGGTTAAAGATGTAAATGTATTACCTGCAACCATGAAACTAC 974
                         v v     i i i ?   iv        vv v  iv   i  i     vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_49015302_4    975 TAGAAGAAAACGTTGGGA-AAATGCTTTAGGACATTGGTCTAGGCAAAGA 1023
                                    i v  ?i-    -   iiv   v    vi       v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_49015302_4   1024 TTTCTTGAGTAAGACATCAAAAGTACAGACAATCAAAGCAAAAATCGACA 1073
                               iii  v    i      i   ii   iv    v      v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_49015302_4   1074 AATGGGATTACATGAAGCTAAAAAGCTTTTATACACCAAAGGAAACAATC 1123
                            v   i v   v  iv v    i     i i vi       v  v   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_49015302_4   1124 AACAAAGTGAAGAGACAAACTACAGAGTGGGGGAAAATATTTGCAAACAA 1173
                           v        i      v i     i    i               iv 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_49015302_4   1174 TTCAATTTACAAAGGATTAATAACCAGAATATATAAGGAACTC----AAC 1219
                          vi vi v i  i   i vi  v             i      ----   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_49015302_4   1220 TCAATAGCAAGAAAACAA----TCTGATTTAAAAATGGGCAAAAGATCTG 1265
                               ii  i  i    ----i ii   ?             i   i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_49015302_4   1266 AATAGCAATTTCTGAAAAGAAGACATACAAATGGCCAACAGGTATA---- 1311
                              vv      vv        i              i i i i ----
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_49015302_4   1312 -AAATGCTCAACATCACTAATTAT 1334
                         - i             ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (133 / 73)
Gap_init rate = 0.02 (13 / 862), avg. gap size = 2.46 (32 / 13)  


 984 27.98 8.27 4.13  chr1_49040769_49042382      500  1128 (486)    L1M4_orf2#LINE/L1      254   908 (0)  

  chr1_49040769_4    500 TAAATAAGACAATGTTGAATCGATGCAGAATTAAGCGTGGTAGGCCAATG 549
                            vi      i   v v ii iiii iiiv  ii i i-   ii     
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGATCAATG 302

  chr1_49040769_4    550 CAATAGTATCGAGAA---GAAAATAGATTT-TGTAT--ATAGTAAAATTG 593
                         v     v  i    i---ii     i iii- ii  --  i  v  -   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA-TTG 351

  chr1_49040769_4    594 ATAGATGACAGATGTGT---AATTACT-AATGGGTAGAAATATAGACTAG 639
                           vvvi    iiv   i---i ii i -      --    ----  v   
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGG--GAAA----GAATAG 395

  chr1_49040769_4    640 TGGTTT------ATGGTGCTGAGACAATGGGTTATCCATACACACACAAA 683
                          vv   ------         i     iv  v  ?   ----  ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA----CATGCAAA 441

  chr1_49040769_4    684 AAAATAAA-TT-----CCTATTTCA-----TATACAAAGATCAGTCCTAA 722
                          i   i  -  -----    ii   -----        i  i iii v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_49040769_4    723 ATGAGACAAGTAAAGACCCAAGTGTGACA--CAAAACTTGAGAAATTTTA 770
                            i---- vi ?     i  i   i v --i      vv i  v i   
  L1M4_orf2#LINE/    492 ATGG----ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_49040769_4    771 GAAGTAAATACAGGAG--AAT----ACGATATTTAGATAGGGAG-GATTT 813
                             v   i i   ? --   ----ii  iv  vi v    v i- i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_49040769_4    814 CTTAAATAAGCCAC-AAAAGTA-AAGCCTATAAAACAAGAGATCGATAAA 861
                             i   v v   -     i -    v- i    v  i i  v      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCA-ACAAAAGAAAAAATAGATAAA 636

  chr1_49040769_4    862 TTCAACTACATAAAAAAATTTTTTAAAACCTCGCATATATCAAAACACAT 911
                           vi   v   v    ------      v  ivii iiv     iv   i
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAA------TTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_49040769_4    912 CATGGAAAAAATTTAAAAATACAAGCCATAGTCTGGGAGAAGACGTTTGC 961
                         i  vi i   i --i    v    v   i  vv        i ii     
  L1M4_orf2#LINE/    681 TATCAAGAAAGT--GAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_49040769_4    962 AATGTATATAAGTGACACAGTACTGATACTCAGAACA-ATAAA---CTCC 1007
                           vvi     vv   i vi v   vi  ii     i -     ---   i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_49040769_4   1008 TAAAAATCAATAA-AAAGAGACAA----CCCAAT-AGAATACAGATAAAG 1051
                           v  v       -   i      ----      -?i  v ii ii    
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_49040769_4   1052 GATATGAAAAATCAATTCAC---AGAAGAAAC-CAAAGTGGACAATAAAG 1097
                            v    v iv  v   v ---      v i-    -   v      iv
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGC 877

  chr1_49040769_4   1098 ATATAAAAAGATGCCCTATCTCATTAGTAAT 1128
                          i  i         i v iv   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (108 / 64)
Gap_init rate = 0.05 (32 / 655), avg. gap size = 2.44 (78 / 32)  


2279 23.03 3.59 4.83  chr1_49074917_49076996.rev      471  1195 (885)    L1M4_orf2#LINE/L1      110   825 (83)  

  chr1_49074917_4    471 CCCTTTTTGTGGATCAAAC--ACAAAGGGCATCATTCTAAAATATATATG 518
                           i      ii  ---  i--    ---  - v  i       vi     
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGA---AATTGACAA---GC-TGATCCTAAAATTCATATG 152

  chr1_49074917_4    519 GAACCGTAAAAGCCCCA-AATAGCCAAAGCAACCCTGAGCAAAAAGAACA 567
                            vi i  ii v    -          i   i i   iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_49074917_4    568 AGGCTGGAAGCATCACACTACCAGACTTCAAAATTTACTACAAAGCTCTA 617
                          i i    i vv       v  vi i       i             vi 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_49074917_4    618 ATACCTAAAACAACATGGTACTGGCATAAAAAAAAAATAAGCACATAGAC 667
                         i  vii  i   iii              ii -----  ii  i     i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGA-----TAGACATATAGAT 297

  chr1_49074917_4    668 CAATGAAACAGAATAGAGAATCCGGA--------TATAC---------CA 700
                              i  i     v    i   i  --------i    ---------  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_49074917_4    701 ACTCATCTTTAACAAAGGTGCCAAGAACATACAATGAGGAAAGGATGGTC 750
                          i v  i  ii    i          v   v     i      i  i   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_49074917_4    751 TTTTCAATAAATGGTGTGGGGAAAGCTAGATAACTATATGCAGAAGAATG 800
                                i        iv    v i  i    ? i i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_49074917_4    801 AAACAAGATTCCTCTCTCTCACCATACACAAAAATCAAATCAAAATGGAT 850
                           iivi  ii   vi   v       i        i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_49074917_4    851 TAAAGGCTTAAATCTAAGACCTGAAACTATGAAACT---AGAAGAACACA 897
                         i ?  i i     v     v  i       i     ---       v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_49074917_4    898 CTGGGG-AAGTGCTCCAGGACCTTGGTCTGGGCAAAAGATTTTCTTTGTA 946
                         iv  ? -  i -  i iv        vi i     vi --      v - 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGG--TTTCTTAG-A 593

  chr1_49074917_4    947 TAAGACCTCAAAAGCACAGACAACAAA-GCAAAAACAGACAAATGAGATT 995
                           v   vi          ii       - v     i   i    vi  i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_49074917_4    996 ACATTAAGCTAAAAAGTTTCTGCACAGCAAAGGAAACACTCAACATAGTG 1045
                         v   i  iv v    ii  i  ii vv       v  vv    v v    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_49074917_4   1046 GGAGAGACAACCCACAGAATGGGAGAAAACATTTTTAAACTATCCATCCG 1095
                         ii -                         i    vi   ii  vi   i 
  L1M4_orf2#LINE/    694 AAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_49074917_4   1096 ACAAGGGATTAATGACCAGAACAAAGAGACTAAACAATTTAAGCCAAAAA 1145
                          i      i vi iv      i v -----    v  i ---- iv v  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATA-----TAAAGAACT----CTTACAA 783

  chr1_49074917_4   1146 CAAAACAAACAAACAAAAAAACAAA-AGCCAAATAATCAAAAAAGTGGGC 1194
                          vv  i  -----i     i     - i  ---i   i?     -     
  L1M4_orf2#LINE/    784 CTCAATAA-----TAAAAAGACAAATAACC---CAATTWAAAAA-TGGGC 824

  chr1_49074917_4   1195 A 1195
                          
  L1M4_orf2#LINE/    825 A 825

Transitions / transversions = 2.08 (110 / 53)
Gap_init rate = 0.03 (21 / 716), avg. gap size = 2.90 (61 / 21)  

 421 18.58 6.19 0.00  chr1_49074917_49076996.rev     1477  1589 (491)    L1M4_orf2#LINE/L1      789   908 (0)  

  chr1_49074917_4   1477 TAAAAAAAAAAAAAAAAA-------AAAAAGTGGGCAAAAGATCCGAACA 1519
                            v     i v   v  -------?    i        i   ii   i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_49074917_4   1520 GACATTTCTTAAAGGAAGACATAAAAATGGCCAACAGGTATATGAAAAAA 1569
                                  iv  i     i   v          i i i i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_49074917_4   1570 TGCTCAACATTACTAATCAT 1589
                                   i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (15 / 5)
Gap_init rate = 0.01 (1 / 120), avg. gap size = 7.00 (7 / 1)  


3069 21.86 4.45 1.40  chr1_49077545_49079323      500  1286 (493)    L1M4_orf2#LINE/L1       98   908 (0)  

  chr1_49077545_4    500 AAATCCTAGCAGGCTTTGTTATAAAAAT-GTCATACTAATTCTGAAATTC 548
                               i   v v    v  ii i    - v  vi  i  i  i      
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_49077545_4    549 ATATGAAAATGCAAAGGACCTAGAATACCCAAAATAACTTTGAGAAAGAA 598
                              i        i     i      v      i  ii    i      
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_49077545_4    599 ---CAAAGTTGATGTACTGACACTACCTGATTTAAAGACTTATTATAAAC 645
                         ---        iv v   v     v  ii    v  i     i  i   v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_49077545_4    646 CTACAGTAATCAAGACAGTGTGGT-TTGGTTTTAGCATA---AT-TAGAT 690
                                                 -i   iv v  v   ---  -     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_49077545_4    691 CCATAAAACAGAAC--AGAGTCCAGAAATAGACCCACACATATATAGACA 738
                          v  ii  i    i--              i     i    v   i v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_49077545_4    739 ACCAGTTTTCAACAAAGATTTGAAAGCAATTCAGTGGAGAAAAAAACAGT 788
                          iiii     i    i i viv  ii v     i   i    i  -i   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGT 396

  chr1_49077545_4    789 TTTTTCAACAAATGGAACTGAAACAATTGGTTATCCATATGGGGGAAAAT 838
                         i              vi   ii    i   v  ?   i   viii i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_49077545_4    839 AAGAATTTTGATCCATACCTCACACCACATATGTAAATTCATTCAAAATG 888
                         --   v  v  i  v            i   iiv     v i        
  L1M4_orf2#LINE/    447 --GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_49077545_4    889 GCACATAGTCCTAAATGTAAAACCTGAAACTCTAAAATTCT-GGAAGAAA 937
                          vv  ?  v           i v  i     v     i   -i       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_49077545_4    938 ACATAGGAGAAGACCTTCATAACCTTAGATTAGGGAAAGATTTCTTAGAG 987
                                ? v i i    i i     i i     v  v i         v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_49077545_4    988 ACAACACCAAAAGCATGATCCATAAAAGAG--------CAAATTG----- 1024
                          ii            ii v v i      i--------i      -----
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_49077545_4   1025 -ATCAAAATTTCAAAACTTCTA--ATTGAAAGAAC--TGTTAAGAGAATT 1069
                         -         -v       i i--v  v    i  -- i i    i i v
  L1M4_orf2#LINE/    645 CATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_49077545_4   1070 AAAAGACAAACCATAGATTAGGAGAAAATATTTGCAAATAATATATCTGA 1119
                                  v   i   v i                   v          
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_49077545_4   1120 TAAAGGGCTTGAATCTAGAATATGTATATAAAAACTCT-AAAATGAAATA 1168
                            i  i    v   i       i  ---  i      - v  ivv    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATA---AAGAACTCTTACAACTCAATA 790

  chr1_49077545_4   1169 ATAAAAA---AAGCAACCTAATTTTAGTAAAAGCGGGCAAAAGATCTGAA 1215
                                ---  ii    i    ?----    ii       i   i    
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTW----AAAAATGGGCAAAGGATTTGAA 836

  chr1_49077545_4   1216 CAGATGCTTTACTGAAGGAGATGTATAGATGGTAAATAAGCACATAAGAA 1265
                         i   iii  iv ii   i    i  i i    iv           i i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_49077545_4   1266 -AGGCTCAATATCATTAGTCAT 1286
                         - v      i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (114 / 54)
Gap_init rate = 0.02 (19 / 811), avg. gap size = 2.42 (46 / 19)  


3369 25.33 0.77 0.77  chr1_49183205_49189484     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49183205_4   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49183205_4   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATGCCCATCAAGC 4979
                            v     v     iv i  i           i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49183205_4   4980 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5026
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_49183205_4   5027 ATATGGAACCAAAAAAGAGCTCGCATCGCCAAGTCAATCCTAAGCCAAAA 5076
                                 viiv  ii  v iv v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_49183205_4   5077 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5126
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_49183205_4   5127 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5176
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_49183205_4   5177 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5224
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_49183205_4   5225 TATCTGATCTTTGACAAACCTGAGAAAAATAAGCAATGGGGAAAGGATTC 5274
                         i vi    i  i     ivv  vv  i vi vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_49183205_4   5275 CCTATTTAATAAATGGTGCTGGGAAAACTAGCTAGCCATATGTAGAAAGC 5324
                         i  v  i  i              v    i v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_49183205_4   5325 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5374
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_49183205_4   5375 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAA 5423
                           i ?    i    i  v   v       i      -    -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr1_49183205_4   5424 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCCTGTC 5472
                           v    ?i- v i -   iv   v v  vv i     v ii   i ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_49183205_4   5473 TAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATC 5522
                           vi            vvi           v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_49183205_4   5523 TAATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTG 5572
                          v  i   v v  i i   i   i vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_49183205_4   5573 AACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 5622
                           v  i     i   i             v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_49183205_4   5623 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5672
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_49183205_4   5673 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACAC 5722
                             i     i     v  i?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_49183205_4   5723 TTCTCAAAAGAAGATATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5772
                              v           vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_49183205_4   5773 ACCATCACTGGCCAT 5787
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3030 26.87 0.66 0.66  chr1_49246174_49252715.rev     5144  6051 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49246174_4   5144 TGGAAGAACATTCCATGCTTATGTATAGAAAGAATCAATATCGTGAAAAT 5193
                              ii i  i     i i   v  v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49246174_4   5194 GGCTATACTGCCCATAGTAATTTATAGATTCAATGCTATCACCATCAGGC 5243
                            v     v    v v i  i  i        i  v   v i    iiv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49246174_4   5244 TACCA-CTGACTTTCTTCACAGAATTAGAAAACACT-ACTTGAAAGTTCA 5291
                          v   -   v    i  -i     v v  v  -i  - iiiv   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr1_49246174_4   5292 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAACAAG 5341
                                viiv  ii  v  viv        i      i i iv  v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_49246174_4   5342 AACACAGCTGGAGGTGTCACGCTACCTGACTTCAAACTATACTACAAGGC 5391
                             v  i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_49246174_4   5392 TACAGTAACCAAAACAGCATAGTATTGGTACCACAACAGATACATAGACC 5441
                                 i   i    ii i   i   i iv vi i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_49246174_4   5442 AATGGAACAGAACAGAGGCCCTCAGAAAAAAACACCACACATCTACAACC 5491
                                i    iv   ivi -      v    -   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAAC-CCATACATTTATGGTC 346

  chr1_49246174_4   5492 ATCTGATCTTTGACACAC-TGACAAAACAAG-CAAGGGGGAAAGGATTCC 5539
                          vi    i  i    viv-  v   i  v v-   v        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_49246174_4   5540 CTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATAAGCAGAAAGCT 5589
                           v  i  i  i           v      v  ?   i v   i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_49246174_4   5590 GAAACTGGATCCCTTCCTTACACCTTATATAAAAATTAACTCAAGATGGA 5639
                            ii    i    v   i     v    i              i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_49246174_4   5640 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTT-GAAGAAAT 5688
                          i ?    i           v       i      - i   -       v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_49246174_4   5689 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGCTT 5737
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_49246174_4   5738 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 5787
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_49246174_4   5788 AATTAAACAAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGA 5837
                         v  i   vvv  i i   i  ii vv    i  v    i  vv i v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_49246174_4   5838 ATAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTAGCCATCTGAC 5887
                          v  i     i                 v       vii vvi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_49246174_4   5888 AAAGGGCTAATATACAGAATCTACAAAGAACCTAAACAAATTTACAAGAA 5937
                           i  i  vi   v      v  i       iivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_49246174_4   5938 AAAAACAAACAACCCCATCAAGAAGTGGGCAAATTATATGAACAGACACT 5987
                            i     i     v  i? i  i        vv  v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_49246174_4   5988 TCTCAAAAGAAGACATTTATGCAGCCAACAGAAACATGAAAAAATGCTCA 6037
                             v        i  vi viii     i iiv         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_49246174_4   6038 TCATCACTGGTCAT 6051
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (138 / 102)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.00 (12 / 12)  


3202 26.60 0.77 0.55  chr1_49294164_49300534.rev     4975  5880 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49294164_4   4975 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATACAGTGAAGAT 5024
                              ii    i     i        v      v i    iv  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49294164_4   5025 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5074
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49294164_4   5075 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5123
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_49294164_4   5124 ATGGAACCAAAAAAGAGCCCATATTGCCAAGACAATCCTAAGCAAAAAGA 5173
                               viiv  ii  v  viv  v     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_49294164_4   5174 ACAAAGCTGGAGGCATCACGCTACTTGACTTCAAACTATACTACAAGGCT 5223
                               i      vv    i  v iii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_49294164_4   5224 ACAGTAACCAAAATAGCATGGTAGTAGTACCAAAACAGATATATAGACTA 5273
                                i   i i  ii     v i i iv ii i   i       ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_49294164_4   5274 ATGCAACAGAA--AAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5321
                            v  i    --i    v  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_49294164_4   5322 TCTGATCTTTGAGAAACCTGACAAAAACAAGCAGTGGGGAAAGGATTCCC 5371
                         vi    i  i  v  ivv  v   i v  vv  i         i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_49294164_4   5372 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5421
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_49294164_4   5422 AAACTGGATCCCCTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5471
                           ii    i   iv   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_49294164_4   5472 TGAAGACTTAAATGTTAGATCGAAAACCATAAAAACCCTAGAAGAACACC 5521
                         ii?    i       v   v v     i      vi i        v  v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_49294164_4   5522 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAA-GGTCTTCATGACTA 5569
                             ?i- v i -   iv   v v  vv i     -   -   v iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATA 595

  chr1_49294164_4   5570 AAACACCAAAAGCAATGGCAACAAAAGCTAAAATAGACAAATGGGATCTA 5619
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_49294164_4   5620 ATTAAACTAAAGAGCTTCTGCACAGCCAGAGAAACTTCCATCAGAGTGAA 5669
                           i   v v  i i   i  ii vv v ii  v   vi  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_49294164_4   5670 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAAACTACCAATCTGACA 5719
                         v  i     i                 v        ii ivv      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_49294164_4   5720 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGGAA 5769
                          i  i  vi          v  i         vv    v iv i  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_49294164_4   5770 AAAA-AAA-AACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5817
                           i -   -     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_49294164_4   5818 CTCAAAAGAAGACATTTATGCAGACAACAGACACATGAAAAAATGCTCAT 5867
                            v        i  vi viii v   i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_49294164_4   5868 CATCACTGGTCAT 5880
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.20 (12 / 10)  


2420 25.46 7.03 2.42  chr1_49305426_49307306      521  1388 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49305426_4    521 TGAAGAGATACATTATGC-CATATATTGGAAGGTTAAATATTATTATGCT 569
                           i i     ivii   i-   iv        ii v      i   v v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49305426_4    570 ATCAATTATCCTAAAATTAACCTATAAGTTAAATATAATCCC-------- 611
                         iv    vv   iv     i i   i ii  v  iii      --------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49305426_4    612 ----------------------AATTGATAAATTTACTCTGTAATTTATA 639
                         ----------------------      i  ii v ii  iv    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_49305426_4    640 TAGCAATGCAAAGAAACTAGAATAGCTACAACTATTATGAAAAA------ 683
                          i v       i i v i        i v   v  iv       ------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_49305426_4    684 CAAGGTTGGAGAGCCTATACTACCTGATTTTAAGAGTTTTTATAAAGCTA 733
                            i       ii ii i   v  ii    i  i v  vi  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_49305426_4    734 AAATAATCAAGAATGTGCAAAATTGGTCTAAGGATTGGCATATAGATCGA 783
                         v i         vv   iiiv i   iv       v i          i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_49305426_4    784 TGGAACAGAGTCGAG--CTCAGAAATAGAATACAAACAGAAATAGAAACA 831
                              i   i i   --ii        -  iv  v   v--- -------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATA-AACCCATACAT---T------- 339

  chr1_49305426_4    832 GAATGTGGTCAATTGATTTTTGACAAAACAGCCAAAATAACTTAATAAGG 881
                         --- i               i     iivv     i iv i i   ii  
  L1M4_orf2#LINE/    340 ---TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_49305426_4    882 AAAGGATTGTTCCTTCAACCGATGATGCTAGAACAACTGGATATCCA-AT 930
                             i  v  iii      vi   i    i i           ?   -  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_49305426_4    931 GGAAAA-AATAAACCTGGACAATAATATCATACCATATGCAAAAATGAAC 979
                          v    -   i  vi     vviv iv   i       i       v   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_49305426_4    980 TTAAAATGAACTATAAATATAAATGTAAAAAAGCTAAA-CTGTAAAATTT 1028
                          i      i ii ? i iv         i --      -  i     i i
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGA--GCTAAAACTATAAAACTC 534

  chr1_49305426_4   1029 CTGGAAGAACACATAGGAAACAAATTTT--TGACCAAAGGTTTGGCAAAG 1076
                         i i      v       ?i-i    i  --     vvi    v     v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_49305426_4   1077 ATTTTTTAAATAGGATACAGAAAGCATAAACCTTAAAAGAAGATAATATG 1126
                         i   i   i   v  i  vi      i  i vvi       i -    - 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATA-G 631

  chr1_49305426_4   1127 ATAAAAATGGACTATATAAAAATTAAATATGTCTGATTTTTGAAAAAA-- 1174
                              v-      vi  v         v iv i  - vi  v   ii --
  L1M4_orf2#LINE/    632 ATAAAT-TGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACA 679

  chr1_49305426_4   1175 --ATTCAGAAAATGCAAAATAAAGCCACA---TAGAAAAAAAT--TAATA 1217
                         --  iv     i  v   ivv  v     --- i i i     -- vii 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_49305426_4   1218 AATCATATACGTGATAAAAGACTTGTATCTAGAAAATATAAAGAACTCAT 1267
                                  iv      ii          i    v             v 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_49305426_4   1268 ACAATTCACTAGTAA---GATAA-TAG---AATCAGAAAATGGGCAAAAG 1310
                             i   v  i   ---  i  -  i---   i?i            i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_49305426_4   1311 ATTTAAATAGACATTTTAACAAAACCCACAAACAAATGGACAAAAAGCTC 1360
                             i           ivv    ivvv i v        v   v    v 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_49305426_4   1361 ATGAAAA-ATGCTTACTATCATCAGGCAC 1388
                                -     i vi    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.42 (82 / 24)  


3155 19.76 3.38 0.27  chr1_49379478_49381208      500  1238 (493)    L1M4_orf2#LINE/L1      147   908 (0)  

  chr1_49379478_4    500 CATATAGAATAT-CAAAGAACCTCAAATGATCAAAACCATCTTGAAAAAG 548
                              i   -  -   i i   ivi   iii      v            
  L1M4_orf2#LINE/    147 CATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_49379478_4    549 AGGAGCAAAGCTGGAGACCTCACACTTCCTGAGTGAAAAACATACTACAA 598
                          i  i     i     iv           ii v vv     v        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_49379478_4    599 AGCTACAGTAATCAAAGAGGTATGGTACTGGCATCAAGACAGACATGTAG 648
                                        iivi  i            v i  i      i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_49379478_4    649 ACCA-TGAAACAGAATAGAGAGCCAAAAAATAAACCTTCACATATATGGT 697
                          i  -  i  i     v     i v i         ivi    v      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_49379478_4    698 CAAT-GATCTTTGACAAGTGTGCCAAGTCTGCACAGTGGGGAAAGAATAG 746
                             -   i  i      v        v iiiv  i              
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_49379478_4    747 CTTCTTCAACAATTGGTATTGGGAAAATTGGATATCCACATTGAAAAAAA 796
                         ii i        v    ii     v  i      ?      vv    i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_49379478_4    797 TG------GAACCTTATCTTAAA------ACAAAAAGAAACTCAAAATGG 834
                           ------  v  i  i  i v ------       vv            
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_49379478_4    835 GATAAAGACCTAAATATAAGACCTTAAACTATAAAACTCATAGAAGAAT- 883
                         ivi ?          i     v  v              v        v-
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_49379478_4    884 --CAGTAGAAAAGCTTTAT-ACATTGCCATAGGCAATGCTTTCTTGGATA 930
                         --i  v? v   v   ii -  v   vvv         v      i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_49379478_4    931 TGACATCAAAAGCACA-GCAAAAAAAGCAAAAATAGACAAATGAGACAAC 979
                              i          -    v     v         i    vi   vv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_49379478_4    980 ATCAAAGATTAAAA-CTATTACACAGCAAAAGAAACAACCAACAGAGTGA 1028
                               -       -  v  iii vv    i  v  v i   v i     
  L1M4_orf2#LINE/    646 ATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_49379478_4   1029 AAAGGCAACCTACAGAATGAGAGAAAATATTTGTGAACAAAATATC-AAT 1077
                             i     i        i             ii  iv v     -i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_49379478_4   1078 GAGGGGTTAATATCCAGAATATATAAAGAACTCCTACAAATCAAAAACAA 1127
                         i    ii vi                       i     v    v  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_49379478_4   1128 AA---CAAATAATCTGATTTTAAAATGGGAAAAAGAGTTGAACAGACATT 1174
                           ---       i ii   ?v        v   i  v     i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_49379478_4   1175 TCTTTAAAGTAGATATAGAAATGGCCAGCAAGCATATAAAAAGATGCTCA 1224
                            ii    v       v         ii     i  i            
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_49379478_4   1225 ACATCACTAATCAT 1238
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (84 / 58)
Gap_init rate = 0.02 (13 / 762), avg. gap size = 2.08 (27 / 13)  


3158 27.46 1.00 0.44  chr1_49437584_49440759     1781  2683 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49437584_4   1781 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1830
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49437584_4   1831 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1880
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49437584_4   1881 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1928
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_49437584_4   1929 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 1978
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_49437584_4   1979 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 2028
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_49437584_4   2029 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2078
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_49437584_4   2079 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 2126
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_49437584_4   2127 GTCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2176
                         ivi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_49437584_4   2177 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2226
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_49437584_4   2227 GAAACTGGATACCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 2276
                            ii    iv   v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_49437584_4   2277 TTAAAGACTTAAACTTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2326
                          i ?    i    iv v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_49437584_4   2327 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2376
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_49437584_4   2377 AACACT----TCATG-GCGACAAAAGACAAAATTGACAAATGGGATCTAA 2421
                         i    i----v  ii-  i        v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_49437584_4   2422 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCTTCACAGTGAAC 2471
                          i   v v  i i   i  ii vv    i  v    i vvv v      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_49437584_4   2472 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 2521
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_49437584_4   2522 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2571
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_49437584_4   2572 AAACAAACAACCCCATCAAAAAGTGGGCAAAGTATATGAACAGACACTTC 2621
                          i     i     v  i?    i         v  v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_49437584_4   2622 TCAAAAGAAGATATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 2671
                           v           vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_49437584_4   2672 ATCACTGGCCAT 2683
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


1822 24.95 4.92 1.28  chr1_49480600_49482519.rev      502  1050 (870)    L1M4_orf2#LINE/L1      292   860 (48)  

  chr1_49480600_4    502 ATAGACCAATGGAACAGAATAGAGATCTCAGAAATAAGACTGCACATCTG 551
                              i        i     v    vii         iv iii    i i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_49480600_4    552 CAACCATCTGATCTTCGACAAAA----CAAG------CAATGGGGAAAGG 591
                         iiii  vi    i        ii----    ------            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_49480600_4    592 ATTCCCTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGCAGA 641
                           vvi  v  i  i              v     iv  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_49480600_4    642 AAATTGAAACTGGACTCCTTCCTTACACCTTATACAAAAATTAACTCAAG 691
                          i v    ii     i   v   i     v                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_49480600_4    692 ATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAG 741
                               i ?    i         i v i            vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_49480600_4    742 AAAATCTAGGCA-ATACCATGCAGGACATAGACACACACA--GATTTC-- 786
                             iv    ?i- v i - v iv   v v ivvi vi  -- i    --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_49480600_4    787 ----ATGACAAAAATGTCAAAAGCAATGGCAACAAAAGCAAAAATTGACA 832
                         ----      ------i        vvi          v      v  i 
  L1M4_orf2#LINE/    591 AGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_49480600_4    833 AGTGGGGTTTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATC 882
                          i v  ii  v  i   v v  i i   i  ii vv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_49480600_4    883 ACCAGAGTGAACAGGCAACCTACAGAATCAGAGAAAATTTTTGCAATCTA 932
                          vv i      v  i     i       vi        v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_49480600_4    933 TCAATCTGACAAAGGCCTAATTCCCAGAATCTAGAAGGAACT--TA-AAT 979
                          vv      i  i  v  vi vi       v  v  i     --  -  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_49480600_4    980 TTA-CGAGAAAAAACCAA----CCCCATTAAAAAGCAGGCAAAGGACATG 1024
                          i -ii v     iv   ----   v   ?    iii         iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_49480600_4   1025 AACAGACACTTCTCAAAAGAAGACAT 1050
                           i     i     v        i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.56 (81 / 52)
Gap_init rate = 0.02 (11 / 569), avg. gap size = 3.09 (34 / 11)  


2422 25.89 2.81 0.15  chr1_49492176_49493836      501  1176 (485)    L1M4_orf2#LINE/L1      215   908 (0)  

  chr1_49492176_4    501 TCACACTACCTGACTTCAGACTACACTACAAGACTACAGTAACCAAACCA 550
                                v  ii i    i vivi       ii         i   iv  
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_49492176_4    551 GCATGGTACTGGTACCAAAACAGATATATAGACCAATGGAACAGAACAGA 600
                          ii         i iv ii i   i       i        i    iv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_49492176_4    601 GGCCTCAGAAATACAACCAT--------------CTGATCTTTGACAAAC 636
                          ivii        v v    --------------i    i  i     iv
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_49492176_4    637 CTGACAAAAACAAGCAATGGGGAAAGCTTTGCCTATTTAATAAATGGTGT 686
                         v  v   i v  vv            vv v i  v  i  i        i
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_49492176_4    687 TGGGAAAACTGGCTAGCCATATGTAGAAAACTGAAACTGGACCCCTTCCT 736
                              v      v  ?   i   i i  i v    ii         v   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_49492176_4    737 TACACCTTATACAAAAATTAACTCAAGATGGATTAAAGAGTTAAATGTAA 786
                         i     v                   i      i ?   vi         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_49492176_4    787 GATCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ACACCATTCA 835
                           v       i      vi i           v    ?i- v i -   i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCG 563

  chr1_49492176_4    836 GGACATAGGCATGGGCAAAGACTTCATGAATAAAACACCAAAAGCAATGG 885
                         v   v v  vv i     v ii   v ii   vi            vvi 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_49492176_4    886 CAACAGAAGCCAAAATTGACAAATGGGATCTAGTTAAACTAAAGAGCTTC 935
                              i   vv     v  i    v   ii vi i   v v  i i   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_49492176_4    936 TGCACAGCAAAACAAACTATCATCAGAGTGAACAGGCAACCTACAGAATG 985
                           ii vv    iv v       vv i      v  i     i        
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_49492176_4    986 GGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCTAGAA 1035
                                  v       vii  vi      i  i  i  vi    i    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_49492176_4   1036 TCTACAAAGAACTTAAACAAATTTACAAGAAAAAAACAA----CCCCATC 1081
                          v  i        ivv    v iv i  v     i    ----   v  i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_49492176_4   1082 AAAAAGTGCGCAAAGTATATGAACAGACATTTCTCAAAAGAAGACATTTA 1131
                         ?    i  v      v  v    i           v        i  vi 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_49492176_4   1132 TGCGGCCAACAAACATATGGAAAAAAGCTTTAATTCATTTCTGAT 1176
                         vii      i  i  i   i   i v   iv vv   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (97 / 74)
Gap_init rate = 0.01 (4 / 694), avg. gap size = 5.00 (20 / 4)  


2496 22.48 2.64 2.64  chr1_49560172_49562847      670  1314 (1362)    L1M4_orf2#LINE/L1        3   647 (261)  

  chr1_49560172_4    670 GAAAAATGTCCCATGTTCATGGATTGGAAAACTTAATATTACTAAAATGT 719
                             i  i                     i          ii   i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG- 51

  chr1_49560172_4    720 CTGTACTACTCAAAGTGACCTACAGATTTATCTACAGATTCAATGCAATC 769
                         -- i v     -------  --  i   v              i      
  L1M4_orf2#LINE/     52 --GCAATACTC-------CC--CAAATTGATCTACAGATTCAACGCAATC 90

  chr1_49560172_4    770 ATTGTGATCACAATGACATTTTTCATTATTTTGCAGAAAT--ACAAAGAA 817
                         vi ---    v   vv  vi vi -  -            --    ivvi
  L1M4_orf2#LINE/     91 CCT---ATCAAAATCCCAGCTGCC-TT-TTTTGCAGAAATTGACAAGCTG 135

  chr1_49560172_4    818 AACCTAAAATTCATATAATATCTCATAAGACT--GAATGGCCAAAATAAT 865
                          v              iiv viv  vii   i--    i       i   
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_49560172_4    866 CTTGAGGAAAAAAAACATAGTTAAAAGCCTGACACTTTCTGAATTCAAA- 914
                              ii  i  i    v    ii i v  v      i ii v      -
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_49560172_4    915 CATATTACAAAACTACAGTGATGAACACAGTATGATACTAGCATAAAGAC 964
                          v  i      i       i  v  v     i  i    i      i  i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_49560172_4    965 AGACATTTAGAAAAATGGGACAGGATAGAGAGCCCCAAAATAAACCCTCA 1014
                               v    vv     i i  i  v     i  vi          vi 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_49560172_4   1015 CATATATGGTCAACTGGCTTT-GACATGAGTGTCAAGGCTGCACAATGGG 1063
                            v         i  ii   -    v i   i    i iiiv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_49560172_4   1064 GAAAGTACAGTTTCTTCAATTACTGGTGTTGAGAAAACTGTATATCCACA 1113
                              v i   i i     iv v     i  i  v     v   ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_49560172_4   1114 TGTAAAAAAATGAGATTGGACACTTATGTCACACTATATCCAAAAATTAA 1163
                           i    i     ii      v i  iv      i    v          
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_49560172_4   1164 CTCAAAATGAATTAAAGATCTAAATGTAAGATCTGAAACTATAAAACTCC 1213
                                  i  i ?   i            v  i              i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_49560172_4   1214 TAGAA---AACATACAGGAAAAGTTTAATAATATTGTATTCAGCAGCGAT 1260
                              ---      vi? v   vi  vi i iv   vi  vi   ii i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_49560172_4   1261 TTCT-------GGCACAGATAACAAAAGCAA-AAAAGAAAAAATAAACAA 1302
                             ------- i   vi v i  v      -             i i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_49560172_4   1303 ATGAGACTGTAT 1314
                           vi    vi  
  L1M4_orf2#LINE/    636 ATTGGACTTCAT 647

Transitions / transversions = 1.73 (90 / 52)
Gap_init rate = 0.02 (13 / 645), avg. gap size = 2.62 (34 / 13)  

 593 21.50 8.88 2.34  chr1_49560172_49562847     1616  1829 (847)    L1M4_orf2#LINE/L1      641   868 (40)  

  chr1_49560172_4   1616 ACTATATCAAATTTTAAAACTTCTGCACAGCAAAGGAAACAATCAATGGA 1665
                            vi      v  v       i  ii vv       v  v     vii 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_49560172_4   1666 GTAAAAAAGGCAACCAATGGAATGGCAGAAAATGTTTGCAAACCATATAT 1715
                           i    - i     v ii      v       i        i       
  L1M4_orf2#LINE/    691 GTGAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_49560172_4   1716 CTAATATGGAATTAATATACAGAGCATATTTTTAAAAA--TCTTAAAACT 1763
                           i   v  i i vi   v    ii    ----   i --     v    
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATAT----AAAGAACTCTTACAACT 785

  chr1_49560172_4   1764 CAATGATAAAAA-----AT--TCGGATTCAAAAAT----------TCGGA 1796
                             i       -----  --i vi   ?      ---------- iv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_49560172_4   1797 AGAGACAATTGTGAAAAGAAGATATAAAAATGG 1829
                          v     v  v vv            v      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGG 868

Transitions / transversions = 1.05 (23 / 22)
Gap_init rate = 0.03 (6 / 228), avg. gap size = 4.00 (24 / 6)  


3295 22.80 0.95 4.67  chr1_49576791_49581599.rev     3379  4321 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49576791_4   3379 TGGAAAGATATTCCATGTTTATGAATTGGAAAGATCACTATTTTTAAAAT 3428
                                    i       i   i       iiv i v    v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49576791_4   3429 GTTTATACTCTCCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 3478
                          viv      i     vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49576791_4   3479 TACCAATGACATTTTTCACTGAAATAGAAAAAAAATTCCTAAAATGTATA 3528
                          v   iivi v     ii v     v  v  ivviv         vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_49576791_4   3529 TGGATCAG-AAAAGACCCAGAATAGCCAAAGCCATCCTCAGCAAAAAGAA 3577
                             vvv -  ii                 i v   i v iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_49576791_4   3578 CAAAACTGGAGGAATCACATTACCTGACTTCAGATTATGCTACAGAGCTA 3627
                             ii       v     i v  ii i    i viv i     i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_49576791_4   3628 CAGTAACCAAAACAGCATGGTACTGGCATAAAAACAAACATAATAGACCA 3677
                               i   i    ii              ii i i     -    i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGATCA 299

  chr1_49576791_4   3678 GTGGAACATAATAGAGAACCCAGAAACAAATCCACATACCTATGGTTAAT 3727
                         i     i v   v    ii       i   i   i i ii      i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_49576791_4   3728 TCATTTTTGACAAAGTTGCCAAGAACATACACTGGGGAAAACACAGTCTC 3777
                          v     i     i v        v   v  v        iv i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_49576791_4   3778 TTCAATAAGTGGTGTGGGGGAAAGTGGATATTCATATGCAGAAGAATGAA 3827
                              i  i     iv   iv  v      ?i  i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_49576791_4   3828 ACTAGAATCTCACCATATCTCACCAGTCTCATCATATATGGTGACCTATG 3877
                         ii i  ---- v  -  i     ---------------------------
  L1M4_orf2#LINE/    450 GTTGGA----CCCC-TACCTCAC--------------------------- 467

  chr1_49576791_4   3878 CTTCACCATATACAAAAATCAAATCAAAATGGATTAAAGACTTAAATCTA 3927
                         ----               i  v           i ?    i     v  
  L1M4_orf2#LINE/    468 ----ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_49576791_4   3928 AGACCTCAAATCATGAAACTACTACAAGAAAAAATCGG-GTAAACTCTCC 3976
                            v  v   ii  i     vi  v       v  v  -     -   i 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTC 562

  chr1_49576791_4   3977 AGGACATTGGACTGGAGA---GTTTCTTGAGTAATTCCCCACAGGCACAG 4023
                         iv   v    ii i iv ---       iii  vvv v   v i     i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_49576791_4   4024 ACAACCAAAGCAAAAATGGACAAATGAGATCACACCAAG-TTAAAATCCT 4072
                         i    v    v      i  i    vi  iiv  i   i-      -v  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA-ACT 661

  chr1_49576791_4   4073 TCTGTACAACAAAGAAAACAATAAACAAAGTGAAGAGACAACCCAGATAA 4122
                          i   i vv     i v  v  v  v        i          v v  
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_49576791_4   4123 TGAGAGAAGATATTTTTCAACTACCCATCTGACAAGGGATTAATAACCAG 4172
                           i     i      viv  ii ivi      i      i vi  v    
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_49576791_4   4173 AATATAAAAGGAGCTCAAACAACTCTGTAGGAAAGAAAAAG-CTAATACC 4221
                               v  i  i   vv       vi  ---- v      - v    v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATA----ATAAAAAGACAAATAAC 807

  chr1_49576791_4   4222 GTGATT-AAAAATGGACAGAAGACCTGAATAGACATTTCTGAAAAGAAGA 4270
                         vii   -        i  i i  ii               vv        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_49576791_4   4271 CATACAAGTGGAAAA-AAGTTATATGAAAAGATGCTCAACACTGCTGATT 4319
                         i      i   vv  -   i- i                  iii??????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGC-ACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_49576791_4   4320 AT 4321
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.54 (129 / 84)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.53 (53 / 15)  


2357 26.90 2.40 0.93  chr1_49620222_49621910.rev      451  1201 (488)    L1M4_orf2#LINE/L1      147   908 (0)  

  chr1_49620222_4    451 CAGATATAAATAAAATGGAGTCTTAAAACAATACAAAGGATCTCCAAAAT 500
                           v  iv    iv  v   -- ii i  i iivv   vi    iv    v
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_49620222_4    501 GAAAGAACAAGGCTGGAGG-CTCACATTACCTGACTTCAAAATATATTAT 549
                            -      i i      -      i v  ii i       iv  i  i
  L1M4_orf2#LINE/    195 GAA-GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_49620222_4    550 AAGATTATTGTATTGAAAAGAGCGTGGTATTAGTATAAAAATAGGCACAT 599
                           iii  iv   v v  i v  i      i i i    ii    i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_49620222_4    600 AGATCAATGGAACAGAATTGAAAACTCAGAAATGAAGCCACAGATGTACA 649
                                     i        i iii       i  v   i v  v  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_49620222_4    650 GCCAATTGAACTATGACAAAA---CACAAGAGCTTATAATGGGGAAAGGA 696
                          i       vi vi     ii--- -     v v vi           i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAA 392

  chr1_49620222_4    697 CACCTTCTTCAATAAGTGTTGCCAGAAAAATTGGATAGCCACATGCAGAA 746
                         i vii i     i  i  v   ii i v  i      ?         i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_49620222_4    747 GAATAAAACTGGGCTCCTATTTGTCACCATATA-AAAAATCAACTGAAAA 795
                             i  ii   i i    ii vv         -      i    v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_49620222_4    796 TTGCTTAAAGACTTAAAAGTAAGATCTGAAATTATAAAAATATT-GAAGA 844
                          v v i ?    i    v      v  i   i       v v  -     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_49620222_4    845 ACATCTAGAGA-AAACTTTCCTGGACATTGATCTAGGCAAATAATTTGTG 893
                          v iv   i?i-   ii   v  -  v   ivi       - ii   v v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAA-TGGTTTCTT 590

  chr1_49620222_4    894 ACAAA-GACCTCAAAA-CACAGACAGCAAAAATGAAAATAGGCAAATGTG 941
                          v v -   vi     -    ii  i     ivi       ii    vv 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_49620222_4    942 ACTTAATTATA-TTAAAAAGCTTCTTCACAACAAAAGAAAT----AACAG 986
                             v  i v -       -   i vii vv    i  v i----  v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_49620222_4    987 ATTGAAGAGACAACTTGCTGAACAGGAGAAAATATTTGCAAATGAT---- 1032
                          v    i       iii v   ii                   v  ----
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_49620222_4   1033 CTGATAAAGGACTAATATCCAGAATATACAAGGAACTCAAGCAATTCAAC 1082
                                i     vi             i  i      vvi   i    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_49620222_4   1083 AGGAAAAAAGTAAATAATCTCATTAAAAAGTGGACAAAGGATGTGAATAG 1132
                          iv     iii      i iv   ?    i   i        v       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_49620222_4   1133 ACATCTCTCAAAAGAAAACACACAAACAGCCAACAGTTACATTAATAAAT 1182
                             i    v      i i i     ii     i ivi    v  v i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_49620222_4   1183 GATCATCACTAATTGTTAG 1201
                          v   v  ii ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (128 / 70)
Gap_init rate = 0.02 (16 / 762), avg. gap size = 1.56 (25 / 16)  


2716 27.60 3.17 0.45  chr1_49634517_49638822.rev     2932  3815 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49634517_4   2932 TGGAAACACATTCCATGCTAATTGATGGGTACAATCAATATTGTGAAAGA 2981
                               v i  i     i v  v   v  v v v i        v  iiv
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49634517_4   2982 GACCATACTGCCAAAAGCAATCTACA-ATTCAATGCAATTTCCATCAAAA 3030
                          i v     v  v   vii       -      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49634517_4   3031 TTCTACCATCATTATTCACAGAACCCGTAAAAAC-AATCCTAAAATTCAT 3079
                          i i v vv v  v  ii     vii - v  i -i              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr1_49634517_4   3080 ATGGA---GCCAAAAAC---GA---GCCAAAAACAAGACTAAGCAAAAAG 3120
                              ---  v iii  ---  ---       -   vvi i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAG 198

  chr1_49634517_4   3121 AACAAATCTGGAGGCATCACTTTACCTGACTTCAC--CCTAAACTATAAG 3168
                               vi      vv    vi v  ii i    v-- i  --   i  i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAA 246

  chr1_49634517_4   3169 GTCATAGTCACCAAAACAGCATGGTAGAGGTATAAAAATAGGCACACAGA 3218
                          ii i   v i   i    ii     vv  i    ii    i  i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_49634517_4   3219 TCAATGGTACAGAACAGAGAAGCCAGAAATAAAACCAAATACTTACCGTC 3268
                                v i    iv    iv           v   v i i   iv   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_49634517_4   3269 AATTTATCTTTGGTAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACC 3318
                             v  i  i ii  i vviv   i v   vv i         i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_49634517_4   3319 CTATTCAACAAACGGTGCTGGGATAATTGGCAAGCCACTTG-AGAAGAAT 3367
                           v         i          i  i   vv ?    v  - i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_49634517_4   3368 GAAACTGGATCCTTATGTCTCACCTTGTACAAAAATAAACTAAAGATGGA 3417
                            ii    i  i  iv  v    v i         v    v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_49634517_4   3418 TCAAAGACTTAAATCTAAGACCTGAAACTATAAAAATTTTGGAAGATAGC 3467
                            ?    i     v     v  i           v i  i     v i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_49634517_4   3468 ATCAGAAAAACCCTTCTAGACAGTGACTTAGGCAAAGATTTTGTGACCAA 3517
                           vi ?iv  vi    vv   vv  iv        v i   iv iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_49634517_4   3518 GAACCCAAAAGCAAATGCAACAAAAACAAAGATAAAAAGATGGAACCGAG 3567
                           vv         v v         iv   i   i v i  v i  ivvi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_49634517_4   3568 TTAAACTTAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTTAAC 3617
                          i   v      i   i  ii vv    i  v iv    iv i   v  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_49634517_4   3618 AGACAACTCACAGAGTGGGAGAAAATGTTCACAGTCTGTACATCCAACAA 3667
                                i      i           i  ii  iviii  i   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_49634517_4   3668 AGGGCTAATATCCAGAATATACATAGAATTCAAACAAATCAGCAAGAACA 3717
                         i  i  vi             i v    i  vv    v   ii  v  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_49634517_4   3718 A---AAACAATC-----------TGGGCTGAGATAATGAATAGACAATTC 3753
                          ---   i  i -----------     vi  ivvv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_49634517_4   3754 TCAAAAGAAGATATACAAATGGTTAATGAGCATATGGAAAAATGCTCAAC 3803
                           v                   ii   i    i   i   i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_49634517_4   3804 CTCATCAATTAT 3815
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (137 / 104)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.67 (32 / 12)  


2773 26.82 3.03 1.12  chr1_49650587_49654975.rev     3008  3898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49650587_4   3008 TGGAAAAACATTCCACATACATAGGTTGGAAGAACCAATATCATTAAAAT 3057
                               i i  i   ii v   i i        vii     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49650587_4   3058 GTTCATACTGCCCAAAGCAATCTACAGATTCAATGCTATTTCTATCCAAT 3107
                          viv     v      vii              i  v  ii     v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49650587_4   3108 TACCAA-TGTCATTTTTTCACATAATTAGAAAAAATGATCATAAAGTTCA 3156
                          v   i-  i v     v  v -    -  v  iv     v    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATT-GACAAGCTGATCCTAAAATTCA 148

  chr1_49650587_4   3157 TATGGAACTAAAAGAG-CCCA-AATAGCGAAGGAAGTCCTAAGCAAAAAG 3204
                                v iv   i -    -      v  iiv i  i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_49650587_4   3205 AATAAAGCTGGAATCATCATGTTACCTGACTTCAAACTATGCTACAAGGC 3254
                           i    i    ivvv   iii v  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_49650587_4   3255 TGCAGTAAACAAAATGACATGGTACTGGTACAAATGTAGACACA--GATC 3302
                          i      v   i iiiii         i i  ivi      i --    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_49650587_4   3303 AACATAACTGAATAGAGACCTCTGAAATAAACCTGCCCACATACAGCCAA 3352
                           iiv  iv    v    vii v          iiiv  iv  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_49650587_4   3353 CTGATATTCAACAAAGTTTACAAAAATAAACAACTGGGAAAGGATACCCT 3402
                         i    v   i    i v vv   i vi vv   iv       i   vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_49650587_4   3403 ATTCAGCAAGTGCTTCTGGGAAAACTGGCTAACCACATACAGCAGAGTGA 3452
                         v    i   i  v v      v      v  ?      i  iv   i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_49650587_4   3453 AATTGGACCCTTGCCTTTCACTACATACAAAAATTAACTAAAAATGGATT 3502
                          i        i i   iv   i i               v         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_49650587_4   3503 AAAGACTAATGTGTAAAACCTAAAACTATAAAAATACTAGAAGAAAATCC 3552
                          ?    iv vi     i v              v vi          ivi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_49650587_4   3553 AGGAAATACTCTTCTAGACATTGATCTATGCAAAGA--------ATATGA 3594
                            ?ivv v     vv   v   ivi  v    v i--------      
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_49650587_4   3595 CTAAATCCTTAAAAGCAATAGCAACAAAGACAAAAATTGACAAGTGGGAC 3644
                          --- i ---       vv         iiv      v  i  i v    
  L1M4_orf2#LINE/    599 C---ACC---AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_49650587_4   3645 CTAATTAAACTAAACAGTGTCTTCACAGCAAAATAAACTATCAAGAGAGC 3694
                         i v  i   v v  v iiv i vii vv    iv v          i  i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_49650587_4   3695 AAACAGACAACCTACAGAATAAGAAAAATTTTATTTGCAAA--------C 3736
                         i  v        i       ii  i   v --         -------- 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAAT--ATTTGCAAATCATATATC 740

  chr1_49650587_4   3737 TGACAGAGGTCTAGTATCCAGAATCTATAAGGAACTT----AAATCAACA 3782
                            i ii  v  v           v     i     i----  v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_49650587_4   3783 AGCAAAAACCAAACATCTCTATTAAAAAATAGGCAAAGGACATGAGCAGA 3832
                          vv    iv    i v i v   ?      i         iv   ii   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_49650587_4   3833 CACTTCTCAGAAGAAGACATACAAGTAGTCAACAA--ACATGAAAAAATG 3880
                           i     vi       i      i i i   i  --         i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_49650587_4   3881 CTCAACCTCACTAATCAT 3898
                               v   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.85 (37 / 13)  


3010 27.10 0.88 0.77  chr1_49677319_49679412.rev      700  1603 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_49677319_4    700 AAATACATTTCATGCTCGTGGATGGATAGAATTAATATTGTGAAAATGAT 749
                            v i  ii    i  i     v iv   v          v  i   ii
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_49677319_4    750 CATACTGGCAAAAGCAGTGTGCAAATTCAGTGCACCTTTCATCAAAATAC 799
                         v     vv v   viii v i  i     ii   viiiii        v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_49677319_4    800 CATC-ATCATTTTTACAGAACTAGATAA-CTGAATCCTAAAATTCATATG 847
                           v -ii v     i     v v  i  -    -                
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATATG 152

  chr1_49677319_4    848 GAATTAAAAACAGCCC-GCTTTTCCAAAGGAAGACTAAGCAAAAAGAACA 896
                            v iv  ivii   - vv vv     iv  vvi i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_49677319_4    897 AATCTGGTGGCATCACATTATTCTACTTCAAACTATACCTCAAGGCAATA 946
                           vi   v  vv     i vii v i      viv   iv   i  v i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_49677319_4    947 GTTACCAAAACAGCATGGTACTGGTATAAAAACAGGCATATAGACCAATG 996
                           v i   i    ii         i    ii i  i        i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_49677319_4    997 GAACAGAATAGAGAACCCAGAAATAAAACAA-ATACTTATAGTCAACTGA 1045
                            i     v    ii           v v - i i    i     i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_49677319_4   1046 TCTTTGACAAAGTGAATAAAAACATAAAGTGGGGAAAGGACATTCTATTC 1095
                          i  i     i vvivi  i v   vv i         i i v   v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_49677319_4   1096 AACAAAGGGTTCTAGGATAATTGTCAAGACACGTGTAGAAGAATAAAAGT 1145
                               v   v  i   i  i  vvv ?v   i  i i      i  iv 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_49677319_4   1146 TGATCCTCGTCTCTCACCTTATACAAAAACCAACTCAAGGTGAGTCAAAA 1195
                         v  i  iiii   v    v          ii       ii  ii   ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_49677319_4   1196 ACTTAAATCTAAGATGTGAAACTATAAAAATTCTAGAAGATAACATCAGA 1245
                           i     v     vv i           v ii       v     vi ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_49677319_4   1246 AAAATTCTTCTTGACATTGGCTTAGGCA--GAGTTCATGAACAAAAACCC 1293
                         iv  v     v    v    v       -- iv   v ii i vi vv  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_49677319_4   1294 AAAAGCAAATGCAAAAAAAAAAAAGATAAATAGATGGGACCTAATTAAAC 1343
                                v v    v    i    i   i   i  v    i v  i   -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA- 651

  chr1_49677319_4   1344 TAAAAATAAAAAGCTTCTGCACAGCAAAATAAATAATCAGCAGAGT--AA 1391
                         -----  v    i   i  ii vv    iv v iv    iv i   --  
  L1M4_orf2#LINE/    652 -----ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_49677319_4   1392 AGACAACCCACAGAGTGGCAGAAAATGTTTGCAAACTATGCATCCAACAA 1441
                                       i   v       i        ii  ii   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_49677319_4   1442 AGGACTAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAAGAAGA 1491
                         i     vi          v  i  i      vv    v   ii  v  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_49677319_4   1492 AAACAAATAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTC 1541
                          i        i  v  i?    i     v     iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_49677319_4   1542 TCAAAAGAAGATATACAAATGGCTAACAAACATATGAAAAAATGCTCACC 1591
                           v                    i  i  i  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_49677319_4   1592 ATCACTAATAAT 1603
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (140 / 101)
Gap_init rate = 0.01 (8 / 905), avg. gap size = 1.88 (15 / 8)  


2624 26.45 0.28 0.28  chr1_49687526_49689243.rev      502  1227 (491)    L1M4_orf2#LINE/L1      183   908 (0)  

  chr1_49687526_4    502 AATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCA 551
                             i i ivv i          i      vv       v  ii i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_49687526_4    552 AACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAA 601
                           viv        i          i   i    ii         i iv i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_49687526_4    602 AACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACG 649
                         i i   v                i    i--    i  --        vv
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAAC 330

  chr1_49687526_4    650 CCGCATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCA 699
                           ii i  i  iiiii vi    i  i     ivv  vv  i v  vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_49687526_4    700 ATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAG 749
                                   i  vvi  v  i  i              v      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_49687526_4    750 CCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAA 799
                            i   i i  iiv    ii    i    v   i     v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_49687526_4    800 ATCAATTCAAGTTGGATTAAAGACTTAAACATTAGACCTAAAACCATAAA 849
                           i  i    iv     i ?    i    ii v   v       i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_49687526_4    850 AACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCA 899
                          vi i           v    ?i v viv   iv   v v  vv i    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_49687526_4    900 AGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACCAAAGACAAAATT 949
                          v ii   v ivvi vi            vvi     v     v     v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_49687526_4    950 GACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAC 999
                           i    v   ii v  i   v v  i i   i  ii vv    i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_49687526_4   1000 TACCATCAGAGTGAACAGGCAACCTACAACATGGGAGAAAATTTTTGCAA 1049
                           i  vv i      v  i     i   iv            v       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_49687526_4   1050 CCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAA 1099
                         vii ivi      i  i  i  vi          v  i  v      vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_49687526_4   1100 CAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGA 1149
                            v iv i  v     i     i     v  i?    i           
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_49687526_4   1150 CATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACA 1199
                         iv    i     i     v        i  vi viii     v  i    
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_49687526_4   1200 TGAAAAAATGCTCACCATCACTGGCCAT 1227
                               i       v     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (109 / 79)
Gap_init rate = 0.00 (2 / 726), avg. gap size = 2.00 (4 / 2)  


 908 27.12 1.63 2.29  chr1_49713668_49715754      510   815 (1272)    L1M4_orf2#LINE/L1       72   375 (533)  

  chr1_49713668_4    510 CTACAAATTCAATGTCAATCC-TATCAAAGAAAATACCAACATCATCTTT 558
                              i      i -      -       ----  v   i vv v i   
  L1M4_orf2#LINE/     72 CTACAGATTCAACG-CAATCCCTATCAAA----ATCCCAGCTGCCTTTTT 116

  chr1_49713668_4    559 CACAGAATTAGAAAAAACAACCCTAAAATTCATACGGTACCAACAAAAG- 607
                         ii     v v  v  ivii i             i  v vii-   ii -
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG-CAAGGGA 165

  chr1_49713668_4    608 CCCA--ATAGACAAAGCAATCCTAAGCAAAAAGAATGAAGCTGGAGGCAT 655
                             --    v    i     i i iv  i     ii   i      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_49713668_4    656 CATATTATGTAACTTCAAATTATATTACAAGGCTATAGTAA-CAAAATAG 704
                           i i vivi  i      viv  i     i    i     -   i i  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_49713668_4    705 CATGGTATTGGTATAAAAATACACACATTGATTAATGAAACAGAATAGAG 754
                         ii     i   i    ii   v   i  v   i    i  i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_49713668_4    755 AACCCAGAAATAAAGCCACATATTTACATCCAACTGATCTTTTAAAAAGA 804
                          ii           v   i i     iivi   i    i  iv v  i i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_49713668_4    805 TGACAGAAACC 815
                           v  - i   
  L1M4_orf2#LINE/    366 TGCCA-AGACC 375

Transitions / transversions = 2.19 (57 / 26)
Gap_init rate = 0.03 (8 / 304), avg. gap size = 1.50 (12 / 8)  

1652 24.05 2.35 3.25  chr1_49713668_49715754     1042  1594 (493)    L1M4_orf2#LINE/L1      361   908 (0)  

  chr1_49713668_4   1042 AAAGTTGACAGAAACAT---ATGCCAGGCAAAGGACA--CCTTAGTCAAT 1086
                           i v  v  ii v   ---   ---  v    i i -- i  --    i
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATG---GGGAAAGAATAGTCTTT--TCAAC 405

  chr1_49713668_4   1087 AAACTGTGCTGGGAAAATTGGCTACCTATATGCAGAAGAATGGAACTGGA 1136
                            iv         v  i   v  ? i i     i       i ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_49713668_4   1137 CCCCTATCTCTCACCGTATATAAAAATAAACTCAAGATGGAATAAAGACT 1186
                               i   v    i    i      v       i     vi ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_49713668_4   1187 TAAATGTAAGACCTGAGTCTATAAAAATACTAGACAAAAATCTAGGGA-A 1235
                                    v  i iv        v vi    vi    iv    ?i- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_49713668_4   1236 TCTCTTCTGGACATTGGTCTAGGCAAACAATTTATCACGA-A-GATCTCA 1283
                         vv     vv   v    vi       -iii   v i -  - -  ivi  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA-GATATGACACCA 603

  chr1_49713668_4   1284 AAAACACAGGCAACAAAACAAAAA-TAGACAAATGATAGTTAACTAAACT 1332
                            i    i         v     -    i    viv v  v ii   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_49713668_4   1333 AAAAAAACTTCTGCTCAGCAAAAGAAAT----AACAGAGTGAACAGACAG 1378
                         v     -   i  iv vv    i  v i----  v i      v     i
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_49713668_4   1379 CCCACTGAATGAGAGAAAACATTTGCAAACTATGCATCTCACAGGGGACT 1428
                              v     i       i         ii  ii    v i i      
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_49713668_4   1429 AATATCCAGACTTTACAAGGAACTCAAACAACTCAATAACAACAACAAAC 1478
                         vi        v v  i  i      vv            i  ----   v
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA----AAAG 798

  chr1_49713668_4   1479 AATCAAGTAATTCCATTAAAAAGTGGGAAAGGGACACGAATATTTTATGC 1528
                          --   i   ii v   ?    i    v  i   ivi     v--- iii
  L1M4_orf2#LINE/    799 A--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG---ACAT 843

  chr1_49713668_4   1529 CTTTCAAAAGAAGGCACAAAACTGGCCAATAAGCATAAGAAAAAAATGTT 1578
                         i i  v       ii i v  v             i v     i -  i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr1_49713668_4   1579 CAACATCACTAATCAT 1594
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (76 / 53)
Gap_init rate = 0.03 (16 / 548), avg. gap size = 1.94 (31 / 16)  


3106 26.14 1.11 0.44  chr1_49723953_49729292.rev     3953  4851 (489)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_49723953_4   3953 AAATACATTTCATGCTCAAGGATGGGTAGAATCAATATTGTGAAAATGAC 4002
                            v i  ii    i   v    v  v   v i        v  i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_49723953_4   4003 CATACTGCCAAAAGGGATCTACAAATTCAACGCTATCCCCATCAAA-TAC 4051
                         v     v  v   vv        i         v     i      - v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_49723953_4   4052 CACCATCATTCTTTACAGAATTAGAAAAAGCAATTCTAAAATTCATATGG 4101
                           v vv v  i   i     v v  v  ivii  i               
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_49723953_4   4102 AACCAAAGAAGGGGCCC-GCATAGCCAAAGCAAGACTAAGCAAAAAGAAC 4150
                           -- viv     i   - v         i   vvi i iv  i      
  L1M4_orf2#LINE/    154 AA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_49723953_4   4151 AAATCTGGAAGCATCACACTACCTGATTTCAAACTATGCTATAAGGCCAT 4200
                            vi    i vv       v  ii        viv i   i  i  i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_49723953_4   4201 AGTCACCAAAACATCCTGGTACTGCTATAAAAATAGGTACATAGGCCAAT 4250
                            v i   i   viv        vi    ii    ii i    ii    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_49723953_4   4251 GGAACAGAATAGAGATCCCAGAAATAAACCCAAATACTTACAGCCAACTG 4300
                             i     v    vi               v i i   ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_49723953_4   4301 ATCTTTGACAAAGCAAACAAAAACATAAAGTGAGGAAAGGACAGCCTTTT 4350
                           i  i     i vviv   i v   vv i  i      i i  i     
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_49723953_4   4351 CAACAAATAGTGCTGGTATAATTGGCTAGCCACATGTAGGAGAATGAAAC 4400
                                 i       v i  i   v  ?       i ii        ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_49723953_4   4401 TGGATCCTCATCTCTCACCTTATTAAAAAATCAACACAAGATGGATTAAG 4450
                             i  ii i   v    v   vv      i   v   i      i ?i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_49723953_4   4451 GA-TTAAATCTAAGACATGAAACTATGAAAATTATAGAGGATAACATTGG 4499
                           -i     v     vv i       i   v iv    i  v     v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_49723953_4   4500 AAAAACTCTTCTAGACATTGGCTTAGGGAAGGATTTCATGACCAAG-CAC 4548
                         ?iv  v     vv   v    v     v  v i    v iivi v -  -
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA- 600

  chr1_49723953_4   4549 CCAGAAGCAAATGCAATAAAGACAAAGATAAA--AGTTGGGACTTAATTA 4596
                            i     v v    i   iiv   i   i -- i    -    v  i 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG-ACTTCATCA 649

  chr1_49723953_4   4597 AACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAAAGTAAGCAAA 4646
                           v v  i i      ii vv    i iv  vi   iv     i iv i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_49723953_4   4647 CAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGG 4696
                                    i           v  ii   vii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_49723953_4   4697 ACTCATACCCAGAATCTACAACTAACTCAAACAAATCAATAAGAAAAAAA 4746
                            ii  i       v  i  vv     vv    v       v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_49723953_4   4747 CAA----TCCCATCAAAAACGGGGCTAAGCACATTAATAGACAGTTCTCA 4792
                            ----i  v  i?    vv    v   v iv v        v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_49723953_4   4793 AAAAAAGATATACAAATGGCTAATAAGCATATGAAACAATGCACAATATG 4842
                            i                i        i      vi    v   i  v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_49723953_4   4843 ACTAATGAT 4851
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.22 (127 / 104)
Gap_init rate = 0.01 (9 / 905), avg. gap size = 1.56 (14 / 9)  


3152 27.09 0.55 0.55  chr1_49739251_49745639.rev     4991  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49739251_4   4991 TGGAAGAACATTCCATGCTCATGAGTAGGAAGAATCAATATCATGAAAAT 5040
                              ii i  i     i     ii v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49739251_4   5041 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5090
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49739251_4   5091 TGCCAATGACTTTCTTCACAGAATTGGAAATAACT-ACTTTAAAGTCCAT 5139
                          v   iivi i  i  ii     v v  v - i  - iii    i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr1_49739251_4   5140 ATGGAATCAACAAAGAGCCCACATT-GCCAAGTCAATCCTAAGCCAAAAG 5188
                               vii-   i ii    v v -     iv     i i ivv i   
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_49739251_4   5189 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5238
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_49739251_4   5239 CACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5288
                         i       i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_49739251_4   5289 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCATATATCTACAAAT 5336
                                i    i--    i  --        vv     i  i  iiivi
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_49739251_4   5337 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAAGGGGGAAAGGATTCC 5386
                          vi    i  i     ivv  v   i v  vv   v        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_49739251_4   5387 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAAGCAGAAAGCT 5436
                           v  i  i              v      v  ?   i v   i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_49739251_4   5437 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5486
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_49739251_4   5487 TTAAAGACTTACATGTTAGACCTCAAACCATAAAAACCCTAGAAGAAAAC 5536
                          i ?    i  v    v   v  v    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_49739251_4   5537 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTATA 5585
                         v    ?i- v i -   iv   v v  vv i     v ii   v iv   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_49739251_4   5586 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5635
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_49739251_4   5636 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 5685
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_49739251_4   5686 CAGGCAACCTACAGAATGGGAGAAGATTTTTGCAACCTACTTATCTGACA 5735
                         v  i     i              i  v       vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_49739251_4   5736 GAGGGCTAATATCCAGAATCTACAATGAACTCAAACACATTTACAAGAAA 5785
                         ii  i  vi          v  i  v      vv   vv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_49739251_4   5786 AAAACAAACAACCACATTAAAAAGTCGGCGAAGGATATGAACCCACACTT 5835
                           i     i    vv   ?    i v   i      v    ivv   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_49739251_4   5836 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACCTGAAAAAATGCTCAT 5885
                            v        i  vi viii     v  i   v      i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_49739251_4   5886 CATCACTGGCCAT 5898
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (141 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


2531 27.38 1.42 2.30  chr1_49747521_49750757.rev     1834  2746 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_49747521_4   1834 AAAGGCATCTTCTGGTGATGTACCTGAAGAATTAATGTAGTTAA-AGGAT 1882
                             ii   iiv  v v   v iiv     v     i v     - v ii
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_49747521_4   1883 TATACTGCTCAAAGAAATCTACAGATTCAATACAATCTTTCTCATAATAC 1932
                         v     v i    vvi              ii     ii v   v   v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_49747521_4   1933 AAACACCGTCTTTCACAGAATTAGAAAAAAAAAAAGGCCTAAAATACATA 1982
                         v i vv v i   ii     v v  v  ivvi ---v        v    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA---TCCTAAAATTCATA 150

  chr1_49747521_4   1983 TGGTACTATGAAAGAG-CCCA-AATAAACAAAGCAATCCTAGGCAAAAAG 2030
                            v --   v   i -    -    iv    i     i iiiv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_49747521_4   2031 AATGAAGCTAGAGGCATCATATTATGTGACTTCAAATTATATTGCAAGGC 2080
                           ii   i i    vv   i i vivii i      viv  i i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_49747521_4   2081 TATAGTAAT-AAAACAGCATGGTAATGGTATAAAAACAGACACATAGATC 2129
                           i      -  i    ii     v   i    ii i     i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_49747521_4   2130 AATGAAACAGAATAGAGAACCCAGAAATAAAGCCACTTATCTACAGCCAA 2179
                             i  i     v    ii           v   ivi  i  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_49747521_4   2180 CTGATCTTTGAAAAAGTTGACAAAAACTTACACTGGGAAAAGGACACCCT 2229
                         i    i  i  v  i v  v   i v v v  v    i    i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_49747521_4   2230 AGTAAATCAATGGTACTGGGAAGATTGCCTAGCCATAGACAGAAGAATGA 2279
                         vv v  iv      i      vi i  vv  ?   i vi  i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_49747521_4   2280 ACCTGGATCCTTATCTCTCATCATATATAAAAATAAACTCAAGATGAATT 2329
                          vi    i  i  i   v  i      i      v       i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_49747521_4   2330 AAATGCTTAAATGTAAGACATGAATCTATAAAAATACTAGACGAAAATCT 2379
                          ? vi i           vv i  v        v vi    v     iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_49747521_4   2380 AGGGA-ACCTCTTCTGGACATTGGTCTAGGCAAACAATATAT--GACTAA 2426
                            ?i- vv     vv   v    vi       -iii v v --  -  v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA-TAT 596

  chr1_49747521_4   2427 GACTTCAAAAACACAGGCAACAAAACAAAAA-TAGATAAATGAGACTTAA 2475
                            vi     i    i         v     -         vi     v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_49747521_4   2476 TTTAACTAAAAAGCTTCTGCACAGCAAAATAAATAATCAACATAGTGAA- 2524
                          iv  v v    i   i  ii vv    iv v iv     v v      -
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_49747521_4   2525 -GACTGCCTACAGAATAGGAAAAAACATTTGGAAATAATGCATCTAACAG 2573
                         -   vi  i       i   i    i     v    v  ii    i i i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_49747521_4   2574 AGGATTAATACCCAGACTTTACAAGGAAGTCAAAAAACC--ACAACAAAA 2621
                         i   i vi  i     v v  i  i   v  vv v   i-- i  i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_49747521_4   2622 CTCCCAAATGATCCAATTAAAAAGTGGGCAAAGGACATATTTTTAATGTT 2671
                         vvv -    i i      ?    i           -----   v   ---
  L1M4_orf2#LINE/    797 AGAC-AAATAACCCAATTWAAAAATGGGCAAAGGA-----TTTGAAT--- 837

  chr1_49747521_4   2672 TATGCAGACATTTTTAAAAAGAAGATATGCATATGGCCAAGAAGCA-ATT 2720
                         -----        i vv           i  v        v     -  v
  L1M4_orf2#LINE/    838 -----AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_49747521_4   2721 TTAGCATGCTGAACATCACTAATCAT 2746
                         vv iv     v       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (133 / 113)
Gap_init rate = 0.02 (17 / 905), avg. gap size = 2.00 (34 / 17)  


2176 30.30 1.12 1.00  chr1_49768682_49770841      500  1301 (859)    L1M4_orf2#LINE/L1       39   841 (67)  

  chr1_49768682_4    500 TATCGTTAAAATGACCATACTGCA-AAAGCAATTTATTAATTCAATGCTA 548
                            i     i   i v     v v-   vii  i  ivi      i  v 
  L1M4_orf2#LINE/     39 TATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAA 88

  chr1_49768682_4    549 TTCCTATCAAACTACCAATGACATTCTTCACAGAACAAGAAAAAACT-AT 597
                          i         v v   iivi v  i  ii     - vvi v  i  -  
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGAT 137

  chr1_49768682_4    598 TTTAAAATTGATATGGAACCAAAAAAGAGTTCAAATAGCCAAGGCAATTC 647
                         ii       v        viiv  ii  viivi         ii    ii
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_49768682_4    648 TAAGCAAAAATAACAAAGCCAGAAGAATCACTCTACTTGACTTCAAACTA 697
                          i iv  i  v       iii  i  v    v  v iii i      viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_49768682_4    698 TACTACAGGGCTACTGAAACCAAAACAGCATAATACTCGTACAAAAACAG 747
                                ii     v v  i   i    ii ii    v i i  ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_49768682_4    748 ATACATAGACCAATGGAACAAAATAAGGAGCCTACAAATAAGGCTGCACA 797
                          i i     i        i i   vii   i i v      iv iii   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_49768682_4    798 CCTACAACCATCTGATCTTCAAAAAAGTTTACAAAAACAAGGAATGGAGA 847
                         ii  iiii  vi    i   i v  i v vv   i v  vvv     i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_49768682_4    848 AAGGG--GTCCCTATTCAATAAATGGTCCTAGAATAACTGGCTAGCCATA 895
                            ii--   -- v     i       v  i i i      v  ?   i 
  L1M4_orf2#LINE/    388 AAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_49768682_4    896 TGCAGAAGATTGAAAATCAATTCCTTCCTTACACCATATACAAAAATCAA 945
                             i    v    iv vi ii   v   i                 i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_49768682_4    946 CTCAAGATGGATTAAAGACTTAAATGTAAAACATAAAACTATAAAAACCC 995
                              i      i ?    i         i vv             vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_49768682_4    996 TGGAAGAAAACCTAAA---AAATACCATTCTGGACATAGGCCCTGGCAAC 1042
                          i         v  ii---    -- -   vv   v v  viiv     i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAAT 582

  chr1_49768682_4   1043 AATTTCAT-GATGAAGACTCCAAAAGCAATTGCAACAAAAACAAAAATTG 1091
                         ii    v -   - v   v         vvv         iv      v 
  L1M4_orf2#LINE/    583 GGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_49768682_4   1092 ACAAATGGGATCTAATTAAA-CTAAGGGCTTCTTCACAGCAAAATAAACT 1140
                          i    v   ii v  i   -i   iii   i vii vv    iv v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_49768682_4   1141 GCCAATAGAATAAACAGACAACCTACAGAATGGAAGAAAATATTTGCAAA 1190
                         ii   v i i i  v        i         i                
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_49768682_4   1191 CTATGCACTCAACAAAAATCTAACATCCAGAATCTCCAAGGAACTTAAAC 1240
                         ii  ii iiii i  iiiv  vii         v vi  i     ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_49768682_4   1241 AAATCAAATAAGCAAAAAACAAACAACTCTATTAAAAAATAGGCAAAAAA 1290
                           v    -   vv    i     i   i v   ?      i      ii 
  L1M4_orf2#LINE/    782 AACTCAA-TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_49768682_4   1291 CATGAACAGGC 1301
                         iv    i  i 
  L1M4_orf2#LINE/    831 TTTGAATAGAC 841

Transitions / transversions = 1.82 (155 / 85)
Gap_init rate = 0.01 (12 / 803), avg. gap size = 1.42 (17 / 12)  

 280 14.67 4.00 2.67  chr1_49768682_49770841     1593  1667 (493)    L1M4_orf2#LINE/L1      833   908 (0)  

  chr1_49768682_4   1593 TGAACAAACACTTCTGAAAAGAAGAGTATACATGTG---AACAAGCATAT 1639
                             i i   i    vv        -      vi  ---  i     i  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGA-TATACAAATGGCCAATAAGCACAT 881

  chr1_49768682_4   1640 GGAAAAAATACTCAACATCATTAGTCAT 1667
                          -    i  i          ????????
  L1M4_orf2#LINE/    882 G-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.04 (3 / 76), avg. gap size = 1.67 (5 / 3)  


3107 26.19 0.99 0.66  chr1_49795571_49798571     1604  2508 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49795571_4   1604 TGGAAAAACATTCCATTCTCATTGATAGGAAGAATCAATATCGTGAAAAT 1653
                               i i  i    vi    v   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49795571_4   1654 GGCCATAGTGCCCAAAGTAATTTATAGATTCAATGCTATCTCCATCAAGC 1703
                            v   v v      v i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49795571_4   1704 TACCATTGACTTTCTTCACAGAATTAGAGAATACTA--CTTTAAATTACA 1751
                          v   vivi i  i  ii     v v  v  -i  i-- i v     -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATT-CA 148

  chr1_49795571_4   1752 TATGGAACCAAAAAAGAGTCTGTATAGCGAAGACAATCCTAAGCTAAAAA 1801
                                viiv  ii  vi v v     v  i      i i iv-  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGAA 197

  chr1_49795571_4   1802 AAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATATTAAAAGA 1851
                         i       i      vv       v  ii i      viv  i  v  ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_49795571_4   1852 CTACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGATGTATAGAT 1901
                                  i v i    ii         i iv ii i   ii       
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_49795571_4   1902 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 1951
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_49795571_4   1952 TCTGATCTGCGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 2001
                         vi    i v      ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_49795571_4   2002 TATTTAATAAATGGTTTTGGGAAAACTGACTAGCCACATGCAGAAAACTG 2051
                          v  i  i       vi     v     iv  ?         i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_49795571_4   2052 AAACTGGACCCCTTCCCTACATCTTATACAAAAATTAATTCAAGATGGGT 2101
                           ii         v  ii   i v              i    i    i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_49795571_4   2102 TAGAGACTTAAACCTAAGACCTAAAACCATAAAAACCCTAGAAGAACACC 2151
                         i ?    i    iv     v       i      vi i        v  v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_49795571_4   2152 TAGGCA-ATACCATTCAGGACATAAGCATGGGCAAAGACTTCATTACTAA 2200
                             ?i- v i -   iv   v vi vv i     v ii   v viv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_49795571_4   2201 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGAAAAATGGGATCTAA 2250
                         i            vvi          vv        v    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_49795571_4   2251 TTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTATTACTAGAGTGAAC 2300
                          i   v v  i i   i iii vv    i  v     i vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_49795571_4   2301 AGGCAACCTGCAGAATGGGAGAAAA-ATCTTGCAATCTATCCATCTGACA 2349
                           i     ii               -  -      vii  vi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATAT-TTGCAAATCATATATCTGATA 745

  chr1_49795571_4   2350 AAGGGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTA-CAAGAAA 2395
                          i  i  vi          v  i        --  -  i i -i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_49795571_4   2396 AAAACAAACCACCCCATC-AAAAATGGGCAAAGGATATGAACAGACATTT 2444
                           i     iv    v  i-                 v    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_49795571_4   2445 CTCAAAAGAAGACATTCATGTGGCCAACAAACATATGAAAAAAAAGCTCA 2494
                            v        i  v  vi       i  i  i       i v-     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCA 894

  chr1_49795571_4   2495 TCATCACTGGTCAT 2508
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.15 (15 / 13)  


3016 27.09 0.88 0.88  chr1_49915039_49921506     5068  5975 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49915039_4   5068 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5117
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49915039_4   5118 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5167
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49915039_4   5168 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5215
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_49915039_4   5216 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5265
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_49915039_4   5266 AACAAAGCTGGAAGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5315
                                i    i vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_49915039_4   5316 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 5365
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_49915039_4   5366 AATGGAACAGAAC--AGAGCCCTCGGAAATAATGCCACATATCTACAA-C 5412
                                i    i--    i  --i       vv   i i  i  iii- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_49915039_4   5413 AATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5462
                            -    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_49915039_4   5463 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATTTAGAAAGC 5512
                         i  v  i  i              v      v  ?   i  vi i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_49915039_4   5513 TGAAACCGGATCCCTCTCTTACACTTTATACAAAAATTAATTCAAGATG- 5561
                             iii   i    vi  i    iv              i    i   -
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_49915039_4   5562 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAAAAAA 5611
                           i ?    i       v   v       i      vi i     i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_49915039_4   5612 CCTA--CGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5659
                          v  --? i  - i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_49915039_4   5660 TAAAACACCAAAAGCAATGACAACAAAAGACAAAATTGACAAATGGGATC 5709
                           vi            vvii          v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_49915039_4   5710 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCTTCAGACTG 5759
                          v  i   v v  i i   i  ii vv    i  v    i vvv i v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_49915039_4   5760 AACAGTCAAACCTACAGAATGGGAGAAGATTTTTGCAATCTACTCATCTG 5809
                           v  v   -  i              i  v       vii ivi     
  L1M4_orf2#LINE/    694 AAAAGACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_49915039_4   5810 ACAAAGGGCTAACATCCGGAATCTACAATTAACTCAAACACATTTACAAG 5859
                          i  i  i  vii    i    v  i  vv     vv   vv iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_49915039_4   5860 AAAAAAACAAACAACCCCAACAAAAACTGGGCAAAGGATATGAACAGACA 5909
                              i     i     v vi?    v            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_49915039_4   5910 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCT 5959
                         i     v        i  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_49915039_4   5960 CATCATCACTAGCCAT 5975
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


2153 26.62 4.37 2.11  chr1_49939517_49941593.rev      479  1188 (889)    L1M4_orf2#LINE/L1      101   826 (82)  

  chr1_49939517_4    479 TCTCAGCCATCTTAGACTGGAACAAGTGAAAAAAATAATCTTAAAATTTA 528
                           i    iii   v--i v v v  i vi v  iv i   i       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT--TTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_49939517_4    529 TATGGAAAGGCACAGTACCTTGGACAGT-GAAGTAGTCCTGAGCAGAGAG 577
                                 v   vi v   iv i i  i-i  ii i  i   iv iii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_49939517_4    578 AACAAAGCTGGGGGAATCACACTACCTGACTTTAAAATACACTGCAAGGC 627
                                i   i   v       v  ii i  i    ivi   i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_49939517_4    628 TGTAGTAACTAACACAGCATGGGACTGGCATAAAATCTGACATC--AACC 675
                          ii     ii  v    ii   v          iiviv     v--i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_49939517_4    676 AGTGGAACAGAAGCAAGAGTCTAGAAATAAATTACACACTCCTATAACCA 725
                          i     i    vii      i         ii-  i  vii   iii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACC-CATACATTTATGGTCA 347

  chr1_49939517_4    726 ACTGATTTTTGACAAAGGTGCCAGGAACACACATTGGGAAAAGA-CAATC 774
                          i       i     i       i  v  iv  v    i     -i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_49939517_4    775 T---------ATGGAGCAGGGAAAATTAGATAACTATATGCAGAAGAATG 815
                          ---------    v  v    v  i i    ? i i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_49939517_4    816 TGAGTAGACTCCTAACTCTCATCATATACAAAACATCAAATCAAAATGGA 865
                         viiv i   i    v   v  i           -  i  v          
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATGGA 496

  chr1_49939517_4    866 TTAAAAACTTAAATATAAAACTTGAAACTATAATATGAAAGTACTAGAAG 915
                          i ? i  i     i   i vi i         -----  v vi      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAA-----AACTCTTAGAAG 541

  chr1_49939517_4    916 AAAACA--GGAG-AAATACTTTATGACGCTGGGCTGGGCAAGGATTTTTT 962
                               --  ? -    -   ii    vi    i i     v i   i  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_49939517_4    963 AAATAAGGCCTCGAAAGTACAGAAAACAAAAGCAAAAATAGACAAATGGG 1012
                          i   v i vi i    i   iiv        v         i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_49939517_4   1013 GATTATATCTAACTGAAAAGCTT----GCT-CAGAGAGGGAAGCAGTTAA 1057
                         - i vi   v  v v    i   ----   -  i  ---  vi vi i  
  L1M4_orf2#LINE/    641 -ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG---GACACTATCAA 686

  chr1_49939517_4   1058 CAAAGTGAAAAGATAACTTACAGAATGGGAGAAAACATTTGCA------- 1100
                         v            i   ii                i       -------
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_49939517_4   1101 --TGGGAGAAGGATTTAATAAACAGACTATATAAAGAATTTAAACAACTC 1148
                         -- vv  v    ivi vi  vv    v           i ivv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_49939517_4   1149 AACAATGAAAA-ACAAATAACTGGATAAGAAAATTGAGCAA 1188
                           i   i    -         ivi  v?i     - i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAAT-GGGCAA 826

Transitions / transversions = 1.98 (123 / 62)
Gap_init rate = 0.02 (18 / 726), avg. gap size = 2.56 (46 / 18)  

 363 21.37 6.84 0.00  chr1_49939517_49941593.rev     1470  1586 (491)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_49939517_4   1470 CTCAAAAA-AAAAAAAAAAAGAA-------GAAAATTGAGAAGAAAACCT 1511
                              v  -     i v   v  -------?    v  i v i ii ii 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_49939517_4   1512 TAATAGACATTTCTCTAAAACAGACATACAAATGGCCAACAGGTACATGA 1561
                         v              i   iv   i              i i i      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_49939517_4   1562 AAAAATATTCAGCATCACTAATCAT 1586
                            i  ii   i     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.43 (17 / 7)
Gap_init rate = 0.02 (2 / 125), avg. gap size = 4.00 (8 / 2)  


3426 17.49 10.45 3.87  chr1_49958038_49963043     3664  4515 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_49958038_4   3664 TGTAAAGATATCTCATGGTCATAGATCAAAAGTCTTAATATT---AAGAT 3710
                           v         i    v    i   iii   v         ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_49958038_4   3711 GGCAGTACTCCTGAGATTGATC--------------AATCCCAAACACAA 3746
                             i      iv i       --------------      v v  v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_49958038_4   3747 TTACAGCTGCTATTCTTGCAGAAATTGGCAATTTTGTTCAAAACTTTATA 3796
                          iv       iv  i            i   vi vi i v   v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_49958038_4   3797 TAGAAATGCAAGGGACTCAGAACAGTCAGAATAACCTTGCAAAAGAAGAA 3846
                          i              i     i  i  i  i  i    v          
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_49958038_4   3847 CAAAGTTGCATGTTGCACCCTTCCCTATTTCAAAACTTGTTTCAAAGCTA 3896
                                 v v viv   v      v            ii v        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_49958038_4   3897 CAGTAATCAATACAATATGGTACTGACATAAGAATAGACATCTATATCAA 3946
                                   v   i i        i      i        v  v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_49958038_4   3947 TGGAATAGAACTGAGAGTCCAGAAATAAATCCTTACATTTATGGTCAATT 3996
                                   i                  i  v                 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_49958038_4   3997 GATTTTTGACACAGGTGCCAAGACCATTTGATAGAGAAAACA-AGTCTCT 4045
                               i    vi               ii  i i    iv -     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_49958038_4   4046 TCAATGAACTATACTGAAA-AACTGGATATCTACTCACAAAATTATGCAG 4094
                             ii  ivi i   ii -         ? i  ----------     -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCAC----------ATGCA- 439

  chr1_49958038_4   4095 TTGGAACCCTTCCTCAAACCACAAATGATGGAGTTAGACCCCTTTCTCAA 4144
                         ----------------------   vi   i    i       vi    v
  L1M4_orf2#LINE/    440 ----------------------AAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_49958038_4   4145 ACCACACACTAAAATGAACTCAAAACAGATCAAACATCTAAATGTAAGAG 4194
                             i i  v     v         ii     ? v i             
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_49958038_4   4195 CTAAAACTA----------ATAAGAAAACATAGGTGCAAGTCTTCATGAT 4234
                                  ---------- v             ? i  i     i   i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_49958038_4   4235 CTCGGATCAGGCAATAATTTTTCA-ATGTCACACCAATAGCACAAGTAAC 4283
                           i  i i       ii   i i -  i v       v        i   
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_49958038_4   4284 AAAATTTAAAAACGATAAATTTGACTTCATCCAAATT--------CTGTG 4325
                             vvv    vv        v         v     --------i    
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_49958038_4   4326 CAACAAGTGATACTATGAAGAAAATGAAAACACAAGCCACAGAATAGGA- 4374
                          vv   iv  i     v      i      v    v         i   -
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_49958038_4   4375 -AAATAATTTTAAA-----------------GACTTATATCCAGCACATA 4406
                         -     v  vi   -----------------     i       v i   
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_49958038_4   4407 TAAAGAACTCTTACAGTT-AATAATAAAAAGATAAATGACCCAAT-AAAA 4454
                                        ii -             i    i       -?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_49958038_4   4455 AAT-----------------------------AAAAAATATATACAAATG 4475
                            -----------------------------   i  v           
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_49958038_4   4476 GAAAACAAATACATTAAAAGATATTCAACA-CAATTAGTGA 4515
                          vv  i  ii    v       ii      -  ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (88 / 57)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 8.13 (122 / 15)  


2395 25.58 3.07 6.81  chr1_50023837_50026221      647  1557 (828)    L1M4_orf2#LINE/L1        1   877 (31)  

  chr1_50023837_5    647 TGAAAAAACATCCCATACTCATGGAGCAGAAGAATTAATACTGTTAAAGT 696
                           i   i i       ii       vii     v      i      ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50023837_5    697 GATCACACTGCCCAAAGCAAGCTACAGATTCAATGCAATCCCTCTCAAAA 746
                          iiv i   v      vii v            i         v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50023837_5    747 TACTGACATTATTTTTAACAGAACTAGATAAAGCAATCCTAAAATTCATA 796
                          v iii vviv     vi     v v  i  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_50023837_5    797 TTGTACC-CAAAGGAGCCCAAATAGCCAAAGCAGTTCTAAGCAAAAACAA 845
                          v v vi-   i   v  vi          i  i ii i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_50023837_5    846 CAAAGCTGGAGATATCAAATTATCTGGCATCAAATTACACATACTACAAG 895
                              i     ivv   v i vi iiiiv     ----  v        i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACTTACTACAAA 246

  chr1_50023837_5    896 GCTTTATTAACCAAAACAGCATGGTACTGGTTTAAAAATAGACAATTAAC 945
                            vi v   i   i    ii         iv   ii       vv  i-
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG- 295

  chr1_50023837_5    946 ATCAATTAAA--GAATAGAGAACCCAGAAATAAAGCCACCTATCTCCAGC 993
                               vi  --    v    ii           v   ivi  i vii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_50023837_5    994 CAACT--------ACA-------------CATACATTGGGAAGAGGACAT 1022
                            i --------   -------------   v  v    i i  i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_50023837_5   1023 TGTTTTCAATAAGTGGTACTGGTAATATTGGATTGCCACCTGCAGAAGAA 1072
                          v       i  i    i    v vv i     v?    v    i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_50023837_5   1073 TGAAACTAGACTCCTATCTCTTGGCATACACAAAAATCAACTCAAGATGG 1122
                             ii i   i    i   viiv    i        i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_50023837_5   1123 ATTAAAGACTTAAATGTAAGACCTAAAACTATAAAAATACTATAAGAAAA 1172
                           i ?    i           v              v vi  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_50023837_5   1173 ACTATGGAAACCTCTTTTGGACATTGGTCTAGGCAAATAATTCATGACTA 1222
                         vv  v ?iv vv    ivv   v    vi       vviv   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_50023837_5   1223 AGGCCTCAAAAGTATAAGCAACACAAACAAAAATAGATCTATGGGACTTA 1272
                         v i vi      i i        v  iv          vv  v      v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_50023837_5   1273 ATTAAACTAAAAAGCTTCCACACAGCAAAAGAAATAATCAACACAATGAA 1322
                           i   v v    i   iiiii vv    i  v iv     v v i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_50023837_5   1323 CAGACAACATGCAGAATTGGGAGAAAATATCTGCACACTATACATCGGAC 1372
                         v       vii      -            i    v ii   i   v  i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAAT-GGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_50023837_5   1373 AGGGGACTAATATCCAAATTTTATCCAATTTTTACAAAAATGTCACAAAA 1422
                          i      --------------------------------   -------
  L1M4_orf2#LINE/    745 AAGGGACT--------------------------------TGT------- 755

  chr1_50023837_5   1423 AAGTAGATATCCAAATATCCAAAATTTATAAGGAACTCAAACAAC--AAC 1470
                         ----------------     i   v     i      vv     --  i
  L1M4_orf2#LINE/    756 ----------------ATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_50023837_5   1471 CACAACAAAATCAATAACCCCATT--AAAATAAGCAAAGGACATGAATAA 1518
                         v i  v  i iv        v   --     ii        iv      i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_50023837_5   1519 ATATTTTTTAAAAAAGAACATTACAAATGGCAAATAAAC 1557
                          i    i iv   i ii i  -         v     i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATAT-ACAAATGGCCAATAAGC 877

Transitions / transversions = 1.35 (132 / 98)
Gap_init rate = 0.01 (12 / 877), avg. gap size = 7.50 (90 / 12)  


2831 24.16 3.37 2.47  chr1_50032355_50036320     2584  3473 (493)    L1M4_orf2#LINE/L1       11   908 (0)  

  chr1_50032355_5   2584 TCCCATGCTCATGGATTAGAAGAAT-AGCATTGTTAAAATGACCATACCA 2632
                                i         i     v - ii        i   i v    iv
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chr1_50032355_5   2633 CCCAAAGCAATCTACAGAGCCAATGTAATCCCTTTCAAAATAC-AATGAC 2681
                               vii         vi   i i       v       v - iivi 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr1_50032355_5   2682 TTTCTTCACAGAAATAGAGAAAATAATCAATCCTAAAATTGACATGGAAA 2731
                         i  i  ii       v  v  iv i   ----        v i       
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATC----CTAAAATTCATATGGAAA 156

  chr1_50032355_5   2732 CACAAATACCCCA-AATAGCCAA--CAACATTGAGCAAACAGAACAAACA 2778
                         ii   iviv    -         --   iv    iv  iv        vv
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_50032355_5   2779 TGGAGTCATCACACTACCATACTTCATATGCCAAAAC-----AAAAAGCC 2823
                              vvv       v  ------  -  vi      ----- v     i
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCC------CA-ATTTCAAAACTTACTACAAAGCT 249

  chr1_50032355_5   2824 ATAATAGTCAAAATAACACAGTGTTAGTAAATAAACAGATACATAGACCC 2873
                          i i  i    i i iiiii  ii i i v vii i   i i     i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_50032355_5   2874 ATGGAAGAGAATAAAAAACCAAAAAGTAATTTCATGTATTTACAGACAAA 2923
                               v     vi i ii v i  i   vii   ii     ii v   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_50032355_5   2924 TAATTTTTAACAAA--TGCACAGAGAGAACATACACTGGGGAAAGGACAG 2971
                          i     ii    i--   -  ---   v   v  v         i i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGC-CA---AGACCATTCAATGGGGAAAGAATAG 395

  chr1_50032355_5   2972 TCTCTTTAATAAATGGTGCTGTGAAAACTGAATATCCACATGCAGAAGAA 3021
                            i  i  i           v  v     i   ?         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_50032355_5   3022 TGAAACTAGACCCC-ATCTCTCACCATATACAAAAATCAACTCAATGTGA 3070
                             ii i      - i   v                i       vi  i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_50032355_5   3071 ATTATGGACTTAAATATAAGAACTGAAACTATAAAACTATTAGAAGAAA- 3119
                           i ?i   i     i     i  i             v          -
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_50032355_5   3120 CA-----------CTTCAGTAGA--TTGGTCTAGGCAAAGATTTAATGGC 3156
                           -----------    -  -  --    vi       v i   vv i v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTC-GT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_50032355_5   3157 TAAGACATCAAAAGCACAGGCAACAGAAACAAAAATAGACCAATGGGACT 3206
                           v    i          i      i  iv         iv   v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_50032355_5   3207 -AATTGAACTAAAAAGCTTCTGCACAGTGAAGGAAACAATCAACAAAATG 3255
                         -v  ii  v v    i   i  ii vvii     v  v     v   i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_50032355_5   3256 ATTAGACAATCTTTAGAATAAAAGAAAATATTTGCAAATTATTTACCCAA 3305
                          vv      i ivi     iii                 i  v  i ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_50032355_5   3306 --AGGGACTAACTCTCTAGAATATACAAAGAACTCAAAAAACTCAACAAC 3353
                         --       vi- v  i        i         vv v       i  i
  L1M4_orf2#LINE/    744 TAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_50032355_5   3354 AACAAAAAAATAAAATATCCTCATTAAAAAGTGGACAGCAGAAATGACCA 3403
                           ---   i i   -  v  iv   ?    i   i  ivi  vv   vi 
  L1M4_orf2#LINE/    793 AA---AAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_50032355_5   3404 GATATTTCTCAAAAGGAGACATACAAATGTCCCCAAAACATATGAAAAAA 3453
                           i       v    i   i         v  vvv  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_50032355_5   3454 TGCTCAACATCACTAATCAT 3473
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (133 / 79)
Gap_init rate = 0.02 (22 / 898), avg. gap size = 2.36 (52 / 22)  


2354 22.97 2.70 1.05  chr1_50040229_50041885      499  1164 (493)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr1_50040229_5    499 AAAATTATACTACAAAACTACAGTAAGCAAAACAGCATGGTACTGACATA 548
                             i -         i         v   i    ii        i    
  L1M4_orf2#LINE/    232 AAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_50040229_5    549 AAAACAGACACATATACCAATGGAACAAAATAGAGCACACAGAAACAAAC 598
                          ii i     i   v i        i i   v   viiv      i    
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_50040229_5    599 ----ACATGTACAGTGAACCCATTTTTGACAAAGGTGCCAAGAACATACA 644
                         ----    v  ii  v  iiv     i     i          v   v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_50040229_5    645 CTCAGGAAAGGACAGTCTCTTCAATAAATGGTGCTGGGAAAACAGGATAT 694
                         v vi      i i     i     i              v   v     ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_50040229_5    695 CCATATGGAAAA---TGAATCTAGACCCCTATCTCTCACCATATACAAAA 741
                            i   v    ---    vi i        i   v              
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_50040229_5    742 AATCAAATCAAAATTGGTTAAATACCT-----TAAGACTTCAAACTATGA 786
                          - i  v       v i i ? v    -----     vi v       i 
  L1M4_orf2#LINE/    481 A-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_50040229_5    787 AACTACTACAAAAACACATTGGAAAAAATCACCAGGACATTGGTCTGGCC 836
                             vi  v  i  v    v  ?iv     vi iv   v    vi i v 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_50040229_5    837 AAAGATTTCTTCAGCAATGTC-CTACAAACACAGACAACCAAAGCAACAA 885
                           v i      -  vv   v - i v  i    ii    v    v  v  
  L1M4_orf2#LINE/    580 AATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_50040229_5    886 TGAACAAAT--GACATCACATACAGTTAAAAAGATTCTGCACAGCAAAGG 933
                          ii i    --   v   i-i v i       v-  i  ii vv      
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCAT-CAAAATTAAAAAC-TTTTGTGCTTCAAAGG 676

  chr1_50040229_5    934 ATTCAATCAACAAAGTGAAGAGACAACCCACAGAATGTGAGAAAATATTT 983
                          iv v     v        i                 v            
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_50040229_5    984 GTAGAAAT--TTCATCTGACAAATAATTAATAACAAGAATATATAAGGAG 1031
                          i --   -- vi      i  ivi i vi  v v           i  i
  L1M4_orf2#LINE/    727 GCA--AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_50040229_5   1032 CTCAAATAACCCTATAAGAAAATTTCTAATAATCTAATCAAAAGATGGGC 1081
                            vv i   i v    v    vvv v     i i   i?   i      
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_50040229_5   1082 AAAG-ATTTGAATAGGCATTTTGGAAAAGAAGACATAAAAATGGCAAACA 1130
                             -          i     ivvv        i   v       v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_50040229_5   1131 GGCATATGAAAAGGTGTTCAACATCACTGATCAT 1164
                         i   i        i  i         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (82 / 67)
Gap_init rate = 0.02 (13 / 677), avg. gap size = 1.92 (25 / 13)  


3220 27.31 0.44 0.44  chr1_50053100_50060960.rev      733  1640 (6221)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50053100_5    733 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 782
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50053100_5    783 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 832
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50053100_5    833 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 880
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_50053100_5    881 TATGGCACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 930
                              v viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_50053100_5    931 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 980
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_50053100_5    981 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1030
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_50053100_5   1031 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1078
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_50053100_5   1079 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1128
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_50053100_5   1129 CTATTTAATAAATGGTGCTTGGAAAACTGGCTAGCCATATGTAGAAAGCT 1178
                           v  i  i          v   v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_50053100_5   1179 GAAACTGGATCCCTTCCTTACACCTTATATGAAAATCAATTCAAGATGGA 1228
                            ii    i    v   i     v    ii     i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_50053100_5   1229 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1278
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_50053100_5   1279 CTAGGTATTACCATTCAGGACATAGGCACAGGCAAGGACTTCATGTCCAA 1328
                         v    ?i v viv   iv   v v  vvi      v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_50053100_5   1329 AACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAA 1378
                         i            vvi     v    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_50053100_5   1379 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1428
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_50053100_5   1429 AGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 1478
                           i         i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_50053100_5   1479 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 1528
                         i  i  vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_50053100_5   1529 AAACAAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGACACTTC 1578
                          i     i     v  i?    i     i i   iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_50053100_5   1579 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 1628
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_50053100_5   1629 ATCACTGGCCAT 1640
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

3252 27.20 0.44 0.44  chr1_50053100_50060960.rev     6463  7370 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50053100_5   6463 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 6512
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50053100_5   6513 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 6562
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50053100_5   6563 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6610
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_50053100_5   6611 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 6660
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_50053100_5   6661 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6710
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_50053100_5   6711 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 6760
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_50053100_5   6761 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATACCTACAACT 6808
                                i    i--    i  --        vv   i i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_50053100_5   6809 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 6858
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_50053100_5   6859 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6908
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_50053100_5   6909 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 6958
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_50053100_5   6959 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 7008
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_50053100_5   7009 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 7058
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_50053100_5   7059 AACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAA 7108
                         i            vvi     v    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_50053100_5   7109 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAAC 7158
                          i   v v  i i   i  ii vv    i  v    i ivv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_50053100_5   7159 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 7208
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_50053100_5   7209 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 7258
                         i  i  vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_50053100_5   7259 AAACAAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGACACTTC 7308
                          i     i     v  i?    i     i i   iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_50053100_5   7309 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 7358
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_50053100_5   7359 ATCACTGGCCAT 7370
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2985 25.33 1.64 2.51  chr1_50073951_50076563     1210  2125 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50073951_5   1210 TGGAAAAATATTACAAGTTCATGCATTGGAAGAATCAATATTATTAAAAT 1259
                               i    iv  v       v         v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50073951_5   1260 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTGTCAAAA 1309
                          v v     v      vii              i         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50073951_5   1310 TAT-AATGACATTCTTCACAAACATATAAAAAA--AATCCTAAAATTTCT 1356
                          vi- iivi v  i  ii  i v  - i v  i--i           iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_50073951_5   1357 ATGGAGCCACAAAAGACTCAGAAGACCCAAAGCTATCCTAAGTAAAAAGA 1406
                              ivii   ii   i     v v     i v   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_50073951_5   1407 ACAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCG 1456
                              ii       v     i v  ii i      viv       i   v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_50073951_5   1457 ATAGTAACTCAAACAGCATGATAATAGCATAAAAAACAGCATGATAATAG 1506
                          i     iiv i    ii  i  v i      i---------    i--i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAG---------GATAG--A 288

  chr1_50073951_5   1507 CATAAAACATAGAAAAATGGAGCAGAATAGACAACCCAGAAATAAATCCA 1556
                             -----    vv      ii     v  v ii           i   
  L1M4_orf2#LINE/    289 CATA-----TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_50073951_5   1557 TACATCTACAAGGAACTCACTTTCAACAAAGATGCAAAGAACATACATTA 1606
                              i  iiivv  i v i    i    i i   v    v   v  v i
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_50073951_5   1607 GGGAAAGGACAGTCTGTTCAATAAATGGTA-------AACTGGATATCCA 1649
                                i i     v     i       i-------         ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_50073951_5   1650 CATGCAGAAGAATGAAACTATACACCTCTTTTTTTCCATGTACAAAAATC 1699
                               i         ii iv  v   vii iviv    i         i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_50073951_5   1700 AAATCAAAATGGATTAAACACTTAAATCTAAGACTTTGAAATTATGAACC 1749
                           v           i ? v  i     v     vi -i   i   i  v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAAC 532

  chr1_50073951_5   1750 TCC-ACCAGAAA-CACTGGGGAAACTCTCCAGAACATTGGACTGGACAAA 1797
                           i- vv     -  iv  ? v  v   i ivi  v    ii i i   v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_50073951_5   1798 GATTTCTTGAGCAATACCCCACAAGAACAGGTAACCAAAGCAAAAATGAA 1847
                          i      iiii vv  v   v   v   i i   v    v      ii 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_50073951_5   1848 CAAATGGGATCACATCAAG-TTAAAAAGTCTCTGCACAGCAAACGAAATA 1896
                         i    v   iiv      i-       v i -  ii vv    v  v iv
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACT 681

  chr1_50073951_5   1897 ATCAACAAAGTGAAGAGATAACCCACTAAATGGGAGAAAATATTTGCAAA 1946
                              v        i   i       vi                      
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_50073951_5   1947 TTACCCACGTGAAAAGGGATTAATAATCAGAATGTAGAAAGAGCTCC-AA 1995
                          i ivi iv   v      i vi  vi      i  v     i   i- v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_50073951_5   1996 AACTCTACAGGGGGAAAAAGAGCTAGTAATTCAATTTAAAAATGGGCAAA 2045
                              v i iv---       - v i   ii     ?             
  L1M4_orf2#LINE/    782 AACTCAATAAT---AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_50073951_5   2046 AGGCCTGAATAGACATT-CTCAAAAGAAGACATACAAATGACAAGTAGGC 2094
                         i iii            -   v        i         i v i  i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_50073951_5   2095 ATAAGAAAAGGTGCTCAAATTCATTGATCAT 2125
                          i v      i       vv   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (140 / 88)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.38 (38 / 16)  


2823 26.76 2.23 1.00  chr1_50078290_50080633      955  1851 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50078290_5    955 TGGAAAAACATTCCATGCTCATGGAAAGGAGGAATCAATATGGTTAAAAT 1004
                               i i  i     i       vv   i  v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50078290_5   1005 GACAATACTGACCAAAGCAATTTACAGATTCAATGTTATTCCTATCAA-- 1052
                          i       vv     vii  i           i iv  i        --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50078290_5   1053 -TCTAGCAATGACATTATTCACAGAATGAGAAAAACT-ATCTCAAAATTC 1100
                         -i i   --  v v  -  ii     vvv  v  i  -   ii       
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_50078290_5   1101 ATATGGAACCAAAAAAGAATCCAAATAGCCAAGGCAATCCTATGCAAAAA 1150
                                 viiv  ii  vi vi         ii     i iviv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_50078290_5   1151 GAACAAAGCTGGAGGCATCACATTATCCAACTTCAAACTATATTTCAAGG 1200
                                 i      vv     i vi    i      viv  i v   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_50078290_5   1201 CCACAGTAACCAAAACAGCACTGTACTGGTACAAAAACAGACACATAGAC 1250
                          i       i   i    iiiv       i i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_50078290_5   1251 CAAAGGAACAGAATACAGAACCCAGAAATAATCCCTCATACTTACAGCCA 1300
                            v    i     vv   ii          v   vi i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_50078290_5   1301 TCTGATCCTTGACAAACTTGACAAA--CATAAACAACAAGGAAAGGACTC 1348
                         vi    ii i     ivv  v   i--   v--   iii      i ivv
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATT--CAATGGGGAAAGAATAG 395

  chr1_50078290_5   1349 CCTTTTCAATAAGTGGTGCTGTGATAACTGGCTAGCCATATTCAGAAGAC 1398
                         i        i  i        v  i      v  ?   i  v  i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_50078290_5   1399 TGAAACTGGACCCCTTCCTTACACCAAATGCAAAAATTAACACAAGATGG 1448
                             ii         v   i      v  i           v   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_50078290_5   1449 ATCAAAGACTTAAATATAAAA-CCAAAACTATAAAAACCCTGGGAAATAA 1497
                             ?    i     i   i - i            - i  vi   iv  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr1_50078290_5   1498 AC-TAGG---AAATACCATTCTGGACACAGAACCTGACAAGGATTTCATG 1543
                           -    ---    -- -   vv   viv iiiiv i   v i    v i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_50078290_5   1544 ACAAAGATGCCAAAAGAAACTGCAACAAAACCAAAAATTAACAAGTGGTG 1593
                         ivv v  ii       v vvv         vv      vi i  i v vi
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_50078290_5   1594 CCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAA-- 1641
                          i v  i   v v  i i   i  ii vv    i  v        v  --
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_50078290_5   1642 TCA---GAGAACCTAGAGAATGGAAGAAAATACTTGTAAACTATGCATCT 1688
                          v ---  v    i v       i        i   i   ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_50078290_5   1689 GACAAAAGTCTGATATCCAGAATCTATAAGGACCTTAAAGAAATTCACAA 1738
                           i  ii v  vi          v     i  v  ivv v  v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_50078290_5   1739 GCAAAATACAAACAACCCCATTAAAAACTGGGCAAAGGATATGAA----C 1784
                         vv    v     i     v   ?    v            v    ---- 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_50078290_5   1785 ACTTTTCAAAAGAATACATACATGCAGCCTACAAGCATATGAAAAAATGC 1834
                          i  i  v      v i     viii   v i     i       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_50078290_5   1835 TCAACATTACTAATCAT 1851
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.93 (29 / 15)  


3355 25.96 0.55 0.66  chr1_50092301_50098694     4993  5901 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50092301_5   4993 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5042
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50092301_5   5043 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5092
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50092301_5   5093 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5140
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_50092301_5   5141 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5190
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_50092301_5   5191 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5240
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_50092301_5   5241 TACAGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGAGATATAGATC 5290
                                 i   i    ii     v   i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_50092301_5   5291 AATGGAACAGAAC--AGAGTCCTCAGAAATAATACCACACATCTACAACT 5338
                                i    i--       --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_50092301_5   5339 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5388
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_50092301_5   5389 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5438
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_50092301_5   5439 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGA 5488
                            ii    i    v   i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_50092301_5   5489 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAGAC 5538
                          i ?    i  v    v   v       i      vi i        i  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_50092301_5   5539 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5587
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_50092301_5   5588 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5637
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_50092301_5   5638 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAA 5687
                           i   v v  i i   i  ii vv    i  v    i  vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_50092301_5   5688 CAGGCCACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5737
                         v  i v   i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_50092301_5   5738 AAGGGCTAATATCCAGAATCTATAAAGAACTCGAACAAATTTACAAGAAA 5787
                          i  i  vi          v            vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_50092301_5   5788 AGAAATAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5837
                          - i i   i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    796 A-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_50092301_5   5838 TCTCAAAAGAAAACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5887
                             v      i i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_50092301_5   5888 TCATCACTGGCCAT 5901
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2627 26.02 2.65 2.54  chr1_50099462_50101877     1057  1963 (453)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50099462_5   1057 TGGAAAAGCATTACATGCTCATGGATAGGAAGAATCAATATTTTTAAAAT 1106
                               iii  iv    i        v      v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50099462_5   1107 GGCAATACTGCCCAAAGCAATTTATAGATTTGATGCTATTCCTATTAAAT 1156
                                  v      vii  i  i     ii i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50099462_5   1157 TAGCATTGAGATTCTTCACAGGTGAACTAGAAAAAAAACT--TTTTAAAA 1204
                          vv  vivivv  i  ii   i--  i i---- v  i  -- ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA--AATTG----ACAAGCTGATCCTAAAA 144

  chr1_50099462_5   1205 TTCTTAGGGAACCAAAAAAAGAGCTC-GAATAGCCAAGACAATCCTAAGC 1253
                            v  v    -- viv  i ii i -          i      i i iv
  L1M4_orf2#LINE/    145 TTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_50099462_5   1254 AAAAACAACAAAGCTGGAGGCATCACGCTACTCGACTTCAAACAATCCTA 1303
                           i  v       i      vv    i  v i i i      vvv v   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_50099462_5   1304 CAGAGCTACAGTTACCAAAACAGCATG-TATTGGTACAAAAACAGACACA 1352
                           i         v i   i    ii  -  i   i i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_50099462_5   1353 TAGTCCAATGGAACAAAATAGAAA-CCAAGAAATAAGACTGCAAACAA-- 1399
                            vi        i i   v  i -i v        -  i-  v   v--
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA-ACC-CATACATTT 340

  chr1_50099462_5   1400 ACAACTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAG 1449
                          iiiii vi    i  i     ivv  v   i v  vv            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_50099462_5   1450 GACACCCTGTTCAATAAATGGTGCCGGGATAACTGGTTAGCCATATGCAG 1499
                         i i vi  v     i         i    i      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_50099462_5   1500 AAGGCTGAAACTGGATCCCTTCCTTTTACCAAATACAAAAACCAACTCAA 1549
                            iv    ii    i    v   ivi    v         ii       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_50099462_5   1550 GATGAATTAAAGACTTAAATGTAAAACCTAAAACTATAAAATCCCTAGAA 1599
                         i   i  i ?    i         i v              ii i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_50099462_5   1600 GAAAACCTAGGAAATACCATTTTAAACAAATGCCCT-------GGCAAAG 1642
                               v    ?i-  v-  i  --- i--  v   -------     v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNG-TAA-ATCTT---CG--TGACCTTGGGTTAGGCAATG 583

  chr1_50099462_5   1643 ATTT----GATGATGA----AGATGTGATGATGGTGACAAAATAAAAAAA 1684
                         i   ----   -    ---- i v i- ii -- ii      v      v
  L1M4_orf2#LINE/    584 GTTTCTTAGAT-ATGACACCAAAAGC-ACAA--GCAACAAAAGAAAAAAT 629

  chr1_50099462_5   1685 AAATAAGTGTGACCTAAGTAAACTAAAGAGCTTCTGCACAGCAAAAGAAA 1734
                          i    i vv   i v vi   v v  i i   i  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_50099462_5   1735 CGATCAACAGAGTAATCAGAAAACCTACAGAATGGGAGAAAAATTTTGCA 1784
                          v     v i   i vv   v    i                vv      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_50099462_5   1785 AACTATGCATTTGACTAAGGTCTAATATCAAGAATCTATAAGGAACTTAA 1834
                           ii  ii  i   iv i  v  vi    v     v     i     ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_50099462_5   1835 ACAAA-CATATAAGAAAAAACAAAATAACCCCATTAAAAAGTGGGCAAGG 1883
                             v-  -    v     ivv         v   ?    i       i 
  L1M4_orf2#LINE/    780 ACAACTCA-ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_50099462_5   1884 GACATGAACAGACACTTCTCAAAAGAACACATACAAGTGAACA-CAATTA 1932
                           iv    i     i     v      v i      i  iv  -i  vi 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_50099462_5   1933 TATGAAAAAAAAGCTAAACATCCCTGTTCAC 1963
                         i       i v-   v      v????????
  L1M4_orf2#LINE/    879 CATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (140 / 92)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.96 (47 / 24)  


2958 24.91 4.57 1.83  chr1_50118061_50121268     1841  2715 (493)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr1_50118061_5   1841 ACCTCATGTCGATAGACCGGGAAAATTAATATTGCCAAAATGTCCATACT 1890
                          i i     iv  i  ii  i i v         ii  i   v v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_50118061_5   1891 AAACAAAGCAATCTATGAATTCAAAGCAACCCCTATGAAAATTACAATGA 1940
                         vvv    vii     iii      v    i      v     iv  iivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_50118061_5   1941 CATTTTTCACAAGAATAGAAAAAACAATCCTAAAATTCTTATGGAACCAC 1990
                          v     ii  ii   v  v  ivii            v       vii 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_50118061_5   1991 ATAAGACATCAAATAGCCAAAGCAAACTTGAGCGAAAA-AACAAAG--GG 2037
                          vii   vivi          i   v     ivi i  -       --  
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_50118061_5   2038 AAGGCATTACACTACCTGATTTCAAAACATATGATAAACCTGTAGTAATC 2087
                          i i - i     v  ii          v  iv i   v  ii       
  L1M4_orf2#LINE/    210 AGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_50118061_5   2088 AAG-CAACATGGCACTAGCATAAAAATAGACATATAGACCAACAAGACAG 2136
                            -  iii   i   i      ii             i   iiii i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_50118061_5   2137 AA--AACATCCCAGAAATAAATCCACATATTTACTATCAACTGATGTTCA 2184
                           --i v vi           i   i i     ivi    i    v   i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_50118061_5   2185 ACAAAGGTGTCAAGAACATACCATAATAAAATAACAGTTTCTTCAATAAA 2234
                             i    i     v   v v  iivi   v  i   i i     i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_50118061_5   2235 TAGTGTTGGAAAGATTGTCTATCCACATGCAAAAGAATGAAATTGTATCC 2284
                          i   i   i vi i  vv  ?                   i   v i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_50118061_5   2285 CTTGTACC--ATAC-GTACACAAAAATCAACTCAAAATGAATTAAAGACT 2331
                           ---   -- i  -i  i        i           i  i ?    i
  L1M4_orf2#LINE/    459 CT---ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_50118061_5   2332 TAAACATACAATGTGAAACTGTAAAAC------AATAAAACATAGAGGGA 2375
                             ii  vi vv i     i      ------  v         i? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_50118061_5   2376 AAGCTTCTTGACCTTAGTCTGAGTAATGAATTTTTGTACATGGTATCAAA 2425
                           v    v       i vi ii i    iv  i  iv i   ii i    
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_50118061_5   2426 AGCACAGACAACAAAAGCAAAAAATAGACAAATGGGATTGTATCAAA--- 2472
                               ii         -          i    v   i vi      ---
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_50118061_5   2473 ---------------TCAAAAAA----ATCAACTGAGTGACGAGACAACC 2503
                         ---------------     ii ----     vvi     vi        
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_50118061_5   2504 TATAGAATACAAGCAAATATTTGCAAACCATATATCTGATAAGAGGTTAA 2553
                         i i     ivi  v             i               i ii vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_50118061_5   2554 TATACAAAATACATAGGCAACTCAAATAATTCAATATCAATCAATAAATA 2603
                            v  i    i   iiv     vv i  i      -------     v 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATA-------ATAAAAA 797

  chr1_50118061_5   2604 GA--AATAACC-ATTTTCAAAATGAGCCAAGGACCTGAATAGACATTTCT 2650
                           --       - v  ?v      i  v     ii               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_50118061_5   2651 CTAAAGAAGTCATTCAAATGACCAGCAGGCAGGTATATAAAAAGGTGCTC 2700
                          i       vi  v      i   ii i   ----i  i     i     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCA----CATGAAAAGATGCTC 893

  chr1_50118061_5   2701 AACATCACTAATCAT 2715
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (146 / 68)
Gap_init rate = 0.02 (16 / 899), avg. gap size = 3.50 (56 / 16)  


2683 26.00 2.38 4.01  chr1_50122206_50127809     4189  5111 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50122206_5   4189 TGGAAGCACATCCTATGTTCATGGATGGGTAGAATAAATATTGTGAAAAT 4238
                              iv i    i            v  v   v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50122206_5   4239 GACCATACTGCCAAAAGCAATGTACAAATTCAGTGCAATTCCCATCAAAA 4288
                          i v     v  v   vii  v    i     ii     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50122206_5   4289 TATCACCATCATTTTTCACGGAACTAGAAAAAACAATTCTAAAATTCATA 4338
                          vi  v vv v     ii i   v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_50122206_5   4339 TGGAGCCAAAAACGAGCCCACCA-AGTCAAAGCAAGACTAACCAAAAAGA 4387
                             iviiv  iv  -    vv -  i    i   vvi i vv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_50122206_5   4388 ACAAATCTAGAGGCATCACATTACACATTAGAATAATTTCAAA--TTATT 4435
                              vi i    vv     i v v  --------        --   --
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCA--------ATTTCAAAACTTA-- 239

  chr1_50122206_5   4436 CTATAAGGCCATAGTCACCAAAACAGCATAGTACTGGTATAAAAATAGGC 4485
                            i  i  i i   v i   i    ii i       i    ii    i 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_50122206_5   4486 ACATAGACCAATGGAACATAATAGTGAACCCAGAAATAAACCCAAATACT 4535
                          i     i        i v   v v  ii               v i i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_50122206_5   4536 TACAG------GATCTTTGACAAAGCAGACAAAAACATAAAGTGGGGAAA 4579
                           ii ------   i  i     i vv v   i v   vv i        
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_50122206_5   4580 GGACACCCTATTCAACAAACAGTGCTGGGATAATTGGCTAGCCACATGTA 4629
                          i i vi  v         ii         i  i   v  ?       i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_50122206_5   4630 GGAGAATGAAACTGGATCCTCATCTCTCATCTTATACAAAAAAATCATCT 4679
                         ii        ii    i  ii i   ------- i  -------------
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTC-------ACAC------------- 469

  chr1_50122206_5   4680 CTCATCTTATACAAAAATCAACTCAAGAAGGATCAAGGACCTAAATCTAA 4729
                         --   ---          i       i v      ?i         v   
  L1M4_orf2#LINE/    470 --CAT---ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_50122206_5   4730 GACTTGAAACTATAAAAATTCTAAAAAATAACATCAGAAACACCCTTCTA 4779
                           vi i           v ii  i  i v     vi ?ivv vi    vv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_50122206_5   4780 GACATTGGCTTAGGCAAGGATTTCATGACCAAGAACCCAAAAGCAATTGC 4829
                            v    v        v i    v iivi v  vv         vvv  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_50122206_5   4830 AATAAAAACAAAGATAAATAG-CTGGACTT------AATTAAAGAGCTTT 4872
                           i    iv   i   i   i-i       ------       i -    
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTT 663

  chr1_50122206_5   4873 TCCATGGCAAAAGGAACAGTCAGCAGAGTAAACAGAATGCT------GTG 4916
                          viiivv    i iv  vi   iv i   i  v   vvi i------i  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_50122206_5   4917 GGAGAAAATCTTCACAATCTGTACATCTGAGAAAGGACTAATATCCAGAA 4966
                                  v  ii   viii  i      v  i     vi         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_50122206_5   4967 TCTACAACAAACACAAACAAATTAGCAAGAAAAAAACAAACAATCCCATC 5016
                          v  i  vi   v vv    v i ii  v     i     i  i  v  i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_50122206_5   5017 AAAAGGTGGACTAAGGACATGAATAGACAGTTATCAAAAGAAGATATACA 5066
                         ?   ii   i v     iv          v  v  v              
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_50122206_5   5067 ACTGGCCAACAAACATATGGAAAAATGCTTAACATCACTAATGAT 5111
                          v       i  i  i   i   i     i       ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.54 (59 / 13)  


2713 22.69 0.45 1.34  chr1_50147046_50148980      500  1169 (766)    L1M4_orf2#LINE/L1      245   908 (0)  

  chr1_50147046_5    500 AAGCTGTCATAGTCAAAACAGTATGGTTACTGGCATAAAAACACAGACAC 549
                              iivi  i    i     i    -          ii i --    i
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGT-ACTGGCATAAGGATA--GACAT 291

  chr1_50147046_5    550 ATAGACCAATAGAACAGAACAGAGAACCCAGAAATAAACACACACATAAA 599
                              i    i   i    iv    ii            v  i    vv 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_50147046_5    600 CGGT-AATTCATCTTTGACAAGCGTACCAAGAATACATGATGGGGAAAGA 648
                         i   -    v  i  i      v  i      vi ivii           
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_50147046_5    649 GTAGTCTCTTCAATAGATAGTGTTGAGAAAATTGGATATCCACATGCAAA 698
                         i      i     i i  i   i  i  v  i      ?           
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_50147046_5    699 AGAATGAAATTGGACCCTTATCTTACACCATACACAAAAATTAATCCAAA 748
                                 i        i  i  i        i           ii    
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_50147046_5    749 AGTGGAGTAAAGACTTAAATGTAAGACCTGAAACCATAAATTACCAAGAA 798
                          -    vi ?    i           v  i    i     viv iv    
  L1M4_orf2#LINE/    492 A-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_50147046_5    799 GAAAACATAAGGGAAAAGCTTCTTGCCACTGGTCTTGACAATGATTTCTT 848
                                  i ? v   v    v  v vi   vi v i     i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_50147046_5    849 GGATCTGACACCAAAAACATGAGCAACAAAAGGAAAAATAGACAAATAGG 898
                         i   v           i  ii           i         i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_50147046_5    899 ACTATAT-AAAACCAAAAAGCTCCTGAACAGCAAAGGAAATATTCAACAG 947
                            vi  -    ii     -  ii  vi vv       v ivv    v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_50147046_5    948 AATGAAAAGGCAACCTATGGCATAGGAAAAAATATTTGCAAACCAAATAT 997
                          i       i     i ii v  i   i              i  v    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_50147046_5    998 CTGACAAAGGATTAATATC-AAAATATATAAATAATGGCTACAACTCAAT 1046
                             i  i   i vi    - i          v  ivvi           
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_50147046_5   1047 AGCGAAAAAACAAATAATCCCATTTAAAAGTGAGCAAAGGAAATGAATAA 1096
                          iii    i        i  v   ?    i  i        vv      i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_50147046_5   1097 CCATTTTGCCAAAGAAGACATCCAAATAGGTAACAGGTATAAGAATCGGT 1146
                         v     iv          i  v     i vi  i i i i v   vv i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_50147046_5   1147 GCCTGGCCAACATGGTGAAACCC 1169
                           ----i      vi????????
  L1M4_orf2#LINE/    890 GC----TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (99 / 49)
Gap_init rate = 0.01 (8 / 664), avg. gap size = 1.50 (12 / 8)  


2600 27.74 2.13 0.78  chr1_50173576_50178517     3562  4455 (487)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_50173576_5   3562 GAAATACATCCCGTGCTCATGGATGCATAGAATCAATACTGCAAAACTGA 3611
                             v i     i  i        vviv   v i    i  iv  iv  i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_50173576_5   3612 CCATAGTGCCAAAAACTATCTACAAATTCAATGCAATTCATATCAAAATA 3661
                          v   v v  v   viv       i      i     i v         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_50173576_5   3662 CCACCATCATTCTTCACAAAACTAGAAAAAACAATCCTAAAATTCACATG 3711
                            v vv v  i  ii  i  v v  v  ivii             i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_50173576_5   3712 GAACCAAAAAGAGCCTACC-TAGCCAAAGCAAGACTAAACAACAACAACA 3760
                            viiv  i ii  i vv-        i   vvi i  v  v  v    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_50173576_5   3761 AAAATCTGGAGGTATCTTAGTACCCAACCTCAAACTATATCATAAGGC-- 3808
                           i--i      vv  vi v v     ii     viv  ii i  i  --
  L1M4_orf2#LINE/    203 AAG--TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_50173576_5   3809 -------CAAAACAGCATGGTACTGATATAAAAATAGGTATACAGACCAG 3851
                         -------   i    ii        ii    ii    ii   i   i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_50173576_5   3852 TGGAACAGAATAGGGAACCCAGAAATAAATCCATATACATATAGCCAACT 3901
                              i     v i  ii           i     i iv   i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_50173576_5   3902 AATCTTTGACAAAGCAAACAAAAACATAAAGTAGAGAGAGGACA-CCTAT 3950
                         i  i  i     i vviv   i v   vv i i i  i  i i -i  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_50173576_5   3951 TCAACAAATAGTGCTGGGATAATTCGCAAGCCACATGTAGAAGAATGAAA 4000
                                  i         i  i v vv ?       i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_50173576_5   4001 CTGGATCCTCATCTCTCACCCTATACAAAAACCAACT-AAGATGGATCAA 4049
                         i    i  ii i   v    v          ii    -  i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_50173576_5   4050 ATACTTAAATCTAAGACCTAAAACCATAAAAATTCTAGAAGATAACATCA 4099
                          v  i     v     v       i      v ii       v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_50173576_5   4100 GAAAAACCCTTCTAGACATTGGCTTAGACAAAGACCTCAT-GACCAAGGA 4148
                          ?iv  vi    vv   v    v    i   v iii  v -  i-- v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGA 598

  chr1_50173576_5   4149 T-CCAAAAGCAAATGCAACAAAAACAAAGATAAAAATAGAA-GGACTTAA 4196
                         i-         v v         iv   i   i --  i v-      v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGA--TAAATTGGACTTCA 646

  chr1_50173576_5   4197 T-GAAACTAAAAATCTTTGGCACAGCAAAAGAAATAATCAGCAGACTAAA 4245
                          -i   i      -    v ii vv    i  v iv    iv i v i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_50173576_5   4246 CAGACAACCCACAAAGTGAGAGAAAATATTTGTAATCTATACAGCTGGCA 4295
                         v            i i  i             i  vii   i v   ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_50173576_5   4296 AAGGACTAATATCCAGAATCTACAAGGAACTAAAACAAATCAGCAAGAAA 4345
                          i     vi          v  i  i     vvv    v   ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_50173576_5   4346 A---CAAACAACCCCATCAAAAAGTGGGCTAAGGACATGAACAGACAATT 4392
                          ---    i     v  i?    i     v     iv    i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_50173576_5   4393 ATCAAAAGAAGATATACATACCACCAATGAACATATGGAAAAATGTTCAG 4442
                         v  v              v ivi     i i  i   i   i   i   i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_50173576_5   4443 TGTCACTAATGAG 4455
                         ii   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 2.00 (26 / 13)  


2783 23.39 0.60 9.38  chr1_50184541_50189488     3464  4455 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_50184541_5   3464 AAAAAAATTCAACATTCATGGATTGGAAGAATCAATATTGTTAAAATGTT 3513
                            i v  i v ii                v i           i   vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_50184541_5   3514 CATACTATCCAAAGCAATCTACAGATTCA-TGCAATCTCTATCAAAATAT 3562
                         v     vi     vii             -i      i          vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_50184541_5   3563 CAATGAGATTCTTCACAGAAATAGAAAAAATAATCCCAAAATTTGTAAGG 3612
                           iivivv  i  ii       v  v  iv i    i      ii  v  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_50184541_5   3613 AACCACAAACACACACACACACACACACACACACAACAGAGCCAAAGCTA 3662
                           vii   ivi-------------------  v  iv v       i v 
  L1M4_orf2#LINE/    154 AAATGCAAGGG-------------------ACCCAGAATAGCCAAAACAA 184

  chr1_50184541_5   3663 TCCTAAAGCAAAAAAACAAAACAAAACTGGAGGA-TCACATTACCTGATT 3711
                           i i  --   i  i---      ii       -     i v  ii   
  L1M4_orf2#LINE/    185 TCTTGAA--AAAGAAG---AACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_50184541_5   3712 -CAAATTATATGATAGAGCTATAGTAACCAAAATAGCATGGTACTGGCAT 3760
                         -    viv  iv i i     i     i   i i  ii            
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_50184541_5   3761 AAAAACAGACACATAGACCAATGGGACAGAATAGAGAACCCAGAAACAAA 3810
                           ii i     i     i      i i     v    ii       i   
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_50184541_5   3811 TCCACACACATACAATGAAATCATTTTCAACAAAGGTGCCAAGAACATAC 3860
                         i   i   iv  iii v  v v      i    i          v   v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_50184541_5   3861 ACTGGGGAAAGGACAGTCTCTTCAGTAAATGGTGCTAGGAAAACTGAATA 3910
                          v         i i     i    ii          i   v     i   
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_50184541_5   3911 TTTATATGCAGAAAAATAAAACTAGACCTCTATCTCTTGCCACATACAAC 3960
                         ?ii i     i  i   i  ii i    i   i   vii   i      v
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_50184541_5   3961 AATCAAATCAAAATAGATTCAAGACTTAAATCTAAGAAATCAAACTATAA 4010
                            i  v       i   iv?    i     v     iv v         
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_50184541_5   4011 AACTACTACAAGAAAACATTGGGGATATTCTCCAGGACATTGGACTGGGC 4060
                             vi  v          v  ? vv v   i iv   v    ii i   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_50184541_5   4061 AAAGATTCCTGGAGCAGTATCTCACAAGCTCA-GCAACCAAAGCAAAAAT 4109
                           v i  i  viiii vv ivi  v    v  -     v    v      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_50184541_5   4110 GGACAAATGGGATCACATCAAG-TTAAAAAGCATCTGCAAAGCAAAGGAT 4158
                         i  i    v   iiv      i-       - v i  iivvv       i
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chr1_50184541_5   4159 ACAATCAACAAATTTAAGAGACATCTCACAGAAAGGGAGAAAATATTTAC 4208
                           v     v   v v  i     v i       v              i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_50184541_5   4209 AAACTACCCATAACACAGAGAAGGAATTCAGAATCCTATCAGATAAATTT 4258
                            i----    ------------------------    v     i---
  L1M4_orf2#LINE/    729 AAAT----CATA------------------------TATCTGATAAG--- 747

  chr1_50184541_5   4259 AACAAAAAGATTTGTTAAATTTGTTAATTTGTTAAAGAGATTAATAACAA 4308
                         -------i  i    ----------------------------  -- v 
  L1M4_orf2#LINE/    748 -------GGACTTGT----------------------------AT--CCA 760

  chr1_50184541_5   4309 GAATATATAAGGAGCTCAAACAACTCTATAGGAAAAAAGTCAGTAATCTG 4358
                                   i  i   vv       v   iv     iiiv i   i ii
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_50184541_5   4359 ATC-AAAAATGGGCAAAATATTTGAATAGATATTTTTTAAAAGAAGAAAT 4407
                           i-             iv           i    i iv        v  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_50184541_5   4408 CAAAATGGCAAACAGGCATACGAAAAGGTGTTTGACATCATTGATCAT 4455
                         vv       v  i i   i i      i  i ii      ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (146 / 83)
Gap_init rate = 0.02 (15 / 905), avg. gap size = 6.60 (99 / 15)  


1652 27.41 5.58 1.18  chr1_50192867_50194838      514  1104 (868)    L1M4_orf2#LINE/L1      174   790 (118)  

  chr1_50192867_5    514 AGCAAAAACAAAC------AAAAAAAACAAAGCCAGAGGCATCACATTAC 557
                            v       v ------  i  i       iii    vv     i v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr1_50192867_5    558 CTGACTTCAAACTATACTACAACACTACAGTAACTAAAACAGCATGGTAC 607
                          ii i      viv        vi         ii  i    ii      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_50192867_5    608 TAGTACAAAAACAGACACAAAGACCCATGGAACAGAACAGAGGAAGCAGA 657
                          i i i  ii i     i v   i v      i    iv   iivv    
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_50192867_5    658 AATAAAGCTGCACATCTACAACTATCTGATCTTCAACAAAGTAGACAAAA 707
                               v iii    i  iiiii vi    i   i    i vv v   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_50192867_5    708 ACAAGCAATAGGGAAATGACTCCCTATTCAATAAACAGTGCTGGGATAAC 757
                         v  vv    i      vi ivvi  v     i   ii         i   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_50192867_5    758 TGGCTAGTCACATGAAGAAGATTGAAA-------------------CATA 788
                            v  ?i      v i    v    i-------------------    
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_50192867_5    789 TACAAAAATCAACTCAAGATGGATTAATGACTTAAATGTAAAAACTAAAA 838
                                  i       i      i ?v   i         i i      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_50192867_5    839 CTGTAAAAACCCTA-AAGAAAACTTGGG---AAATACCATTTTGCACATA 884
                           i     vi i  -        v i  ---    -- v iv  -  v v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTG-ACCTT 570

  chr1_50192867_5    885 GGCCCTGGCAAAGATTT----GATGATGGAGACATGAAAAGCAACTGCAA 930
                           viiv     v i   ----   -   ---   iv       vvv    
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGAT-ATG---ACACCAAAAGCACAAGCAA 616

  chr1_50192867_5    931 CAAAAACAAAAATTGACAAGTGTGACCTAATTAAACTAAAGAGCTTCTGC 980
                              iv      v  i  i vv   i v  i   v v  i i   i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_50192867_5    981 ACAGCAAAAGAAACTATCAACAGAGTAATCAGACAACCTACAGAATGGGA 1030
                         i vv    i  v        v i   i vv        i           
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_50192867_5   1031 GAAAACTTTTGCAAACTATGCATTCAACTAAGGTCTAATATCCAGAATCT 1080
                              iv        ii  ii  iii iv i  v  vi          v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_50192867_5   1081 ATAAGGAACTTAAACAAATTAACA 1104
                             i     ivv    v i  i 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATA 790

Transitions / transversions = 1.54 (97 / 63)
Gap_init rate = 0.01 (9 / 617), avg. gap size = 4.44 (40 / 9)  

 286 15.84 20.79 0.00  chr1_50192867_50194838     1391  1491 (481)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr1_50192867_5   1391 AATAATAAATAAA--AATAA------TAAAAAGCGGGCAAAGGAGATGAA 1432
                                  v i --     ------ ?    ii          vv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_50192867_5   1433 CAGGCAGTTCTC---AGAAGACATATATGTGGCCAACAAGCA-------- 1471
                         i  i  v     ---      i   i vi       i     --------
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_50192867_5   1472 -ATGCTCAGCA-CACACATACA 1491
                         -       i  -  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.04 (5 / 122), avg. gap size = 4.20 (21 / 5)  

 225  7.32 2.44 0.00  chr1_50192867_50194838     1495  1535 (437)    L1M4_orf2#LINE/L1      867   908 (0)  

  chr1_50192867_5   1495 GGCCAACAAGCATATGATAA-ATGCTCAACATCACTAATTAT 1535
                               i     i    v  -             ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (2 / 1)
Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1)  


3247 24.22 1.67 2.34  chr1_50515463_50518157.rev     1331  2226 (469)    L1M4_orf2#LINE/L1        1   890 (18)  

  chr1_50515463_5   1331 TGGAGATATATTCCATGTTCATGGATAGACAGACTCAATACTATCTATTT 1380
                             i v    i              v iv     i    i i iv vv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50515463_5   1381 GACAGTTCTTCCTAACTTGATCTATAGATTCAATACAATCCCAGTGAAAA 1430
                          i  i v  i  i  v        i        ii       vi v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50515463_5   1431 TCCCAGCAAGTTATTTTGTAGATATCGACAAACTGATTCTAAAGTTTATA 1480
                                vivi v     i   v  i     i     i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_50515463_5   1481 TGGAGAGGCAAATCACCTAGGATAGCCAACACAACATTGAAGGAGATGAA 1530
                             i v    ivv   i  i        v    iv     ii   v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_50515463_5   1531 CAAATTTAAAGGATTGGCATTACATGGCTTCGAAACTTACTACAAAGCCA 1580
                             v  ii    i vi  i v viiii   i                i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_50515463_5   1581 CAGTAATCAAGATGGTGTGGTATTGGCA-AA--ATAGACAAATAGATCAT 1627
                                     ii        i     -  --       v        v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_50515463_5   1628 TGGAACAGAACAGAGAGCCCCAAAATAGAATCATATAAATATGGTCAACT 1677
                              i    iv     i  vi     i vi    i vv         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_50515463_5   1678 GAACTTTGACAAAGGAGCAAAGGCAATACGATGGAGAAAAGACAGTCTTT 1727
                           vi  i     i  v  v   i v  v i    i    ii i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_50515463_5   1728 TCAACAAAAGGTGCTAGAACAACTGAAGCTTCACATGGCAAAAAACCGA- 1776
                                 v      i i       i vv?i      -     i vi  -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAATGAA 449

  chr1_50515463_5   1777 -TCGAGATATAGACCTTAAACCTT-T-CAAAAATTAGCTCATTTTTGTTA 1823
                         - i -  ivivv    i v   v - -         i    ---------
  L1M4_orf2#LINE/    450 GTTG-GACCCCTACCTCACACCATATACAAAAATTAACTCA--------- 489

  chr1_50515463_5   1824 ATTTTGTGAAAGGATCATAAATTTAAATGTAAAA--TAAAAATAACAAAA 1871
                         -------i  v      ? i ii         i --     v  -i    
  L1M4_orf2#LINE/    490 -------AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA-TAAAA 531

  chr1_50515463_5   1872 CTCCTAGAAGATAGCATAGGAGAACATCTAGATGCTCTTGGGTATGGCAA 1921
                            i       v i      ? v v    vvi  vi       vv     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_50515463_5   1922 TGATGTTTAAGATAAAACACCAAAGACAAGATCCATGAAAGAAATAATTG 1971
                           i v i v     vi        ii  vi v v ii       v   v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_50515463_5   1972 ACAGGCTGGACTTCATCAAAATTTAAAACTTCTGCTCTGTGAAAGACACC 2021
                          i iii                 v       i  iv  vii  i     i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_50515463_5   2022 TTCAAGAGAAT---AAGACAAACCACAAACTGAGAGAAAATATTTGCAAA 2068
                         v      i i ---       v     i v  i                 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_50515463_5   2069 AGATACATTAAATAAAGGACTGTTATCCAAAATACACAAAGAACTCTTAA 2118
                         vv   i  ivi    i     vv      i    i i            v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_50515463_5   2119 AACGCAACAGTAAGAAAATGAACAACCCTATTTTAAAAATGGGCAAAAGA 2168
                            v   i i   i  i ii  i     v   ?-             i  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGA 830

  chr1_50515463_5   2169 CCTGAACACATACTTCACTAAAAAAGATGC-CAAGTGGGGAATGAAGGA- 2216
                         ii    i v i i   v i   i     ii-   i   vv   -   v -
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCAC 879

  chr1_50515463_5   2217 -TGAATAGGTG 2226
                         -    v  i  
  L1M4_orf2#LINE/    880 ATGAAAAGATG 890

Transitions / transversions = 1.57 (130 / 83)
Gap_init rate = 0.02 (15 / 890), avg. gap size = 2.40 (36 / 15)  


2820 26.93 1.32 1.10  chr1_50536903_50543028     4728  5633 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50536903_5   4728 TGAAAAAACATTTCATTCTCATGGATAGGAAGAATCAATGTCATGGAAAT 4777
                           i   i i  ii   vi        v      v i   i ii vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50536903_5   4778 AAACATACTGCCCAAAGTAATTTACAGATTCAATGCTATTCCCATCAAAC 4827
                         iivv     v      v i  i           i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50536903_5   4828 TACCA-CTGACACTCTTCACAGAATTAGAAAAAACT-ACTTTAAAATTCA 4875
                          v   -   v -i i  ii     v v  v  i-  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_50536903_5   4876 TATGGAACCAAAAAAGGG-CCCATA-TAGCCAAGACAATCCTAAGCAAAA 4923
                                -- viv     -    v -       i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_50536903_5   4924 AGAACAAAACTGGAGGCATCACACTACCTGACTTCAAACTATACTATAAG 4973
                                 ii      vv       v  ii i      viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_50536903_5   4974 GCTACAGTAACCAAAACAACACGGTACTGGTACCAAAACAGACACATAGA 5023
                                   i   i   iiii        i iv ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_50536903_5   5024 CCAATGAAACAGAATAGAGACCTCAGAAATAAGACCACACATCTACAACT 5073
                         i     i  i     v    vii         iv   i    i  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_50536903_5   5074 ACCTGATCTTCGACAAACCTGACAAAAATCAG-CAATTGAAAAGGATTA- 5121
                          vi    i        ivv  v   i -i  v-    v ii  i  v  -
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAG 395

  chr1_50536903_5   5122 CCTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGCAGAAAAC 5171
                         i  v  i  i           i  v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_50536903_5   5172 --AAATTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGG 5219
                         --  i     i    v   i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_50536903_5   5220 ATTAAAGACTTAAATGTAAAACTCAAAACTGTAAAAACTCT-AGAAGAAA 5268
                           i ?    i         i vii      i     -    -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr1_50536903_5   5269 ATCTAGATAATACTATTCAGTACATAAGCATGGGCAAAGACTTTAT-GAT 5317
                          iv   i?ivv v v   ivv  v vi vv i     v ii  iv -   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_50536903_5   5318 GAAATCACCAAAA--ACAATTGCAACAAAAGCTAAAATTAACAAATGGGA 5365
                         ivi -        --    --          vv     vi i    v   
  L1M4_orf2#LINE/    595 ATGA-CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_50536903_5   5366 TCTAATTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTATCATCAGAG 5415
                         ii v  i   v v  v i   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_50536903_5   5416 TGCACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACCCATCT 5465
                           v v  i     i   i             v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_50536903_5   5466 GACAAAGGTCTAATATCCAGAATTTACAATGAACTTAAACAAATTTAGAA 5515
                           i  i  v  vi          v  i  v     ivv    -i i iv 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATA 790

  chr1_50536903_5   5516 GAAAAAAGAAAAGCAATCCCTTCAAAAAGTGGGCAAAGGACATGAAAAGA 5565
                         iv       v  ii  i  vv i?    i           iv    v   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_50536903_5   5566 CACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACGTATTTTAAAAAG 5615
                           i     v        i  vi viii     i  i ii  vvv  i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_50536903_5   5616 CTCAACATCACTGATCAT 5633
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.22 (22 / 18)  


2665 26.64 1.97 2.84  chr1_50551054_50554404     1943  2858 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50551054_5   1943 TGGAAACACATCCCATGCTTGTG---TGAAA---------TTGTGAAAAT 1980
                               v i        i ii  ---  i  ---------    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50551054_5   1981 CACCATACTGCCAAAAGCAATCTGTAAATTCTTTGCAATTCACATCAAAA 2030
                         vi v     v  v   vii    ii i    vvi     i vi       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50551054_5   2031 TACCACCATTATTCTTCACAGAACTAGAAAAAA-AATCCTAAAATTCAAA 2079
                          v   v vviv  i  ii     v v  v  iv-i             v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_50551054_5   2080 TGGAACCAAAAAAAGAACCT-GCACAGCCAAAGCAAGACTAAACAAAAAG 2128
                              -- viv  i i   i- v i       i   vvi i  v  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_50551054_5   2129 AACTAATCTGGATGCAC-CACATTACCCAACTTCAAACTATAGTATAAGG 2177
                            v  vi    v -  -    i v     i      viv  v  i  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_50551054_5   2178 CCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGAC 2227
                          i i   v i   i    ii         i    ii    i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_50551054_5   2228 CAATGGAGCAGAAAAGAGAACCTAGAAATAAAGCCAAATACTTAGAATCA 2277
                                ii    vv    ii i         v   v i i   vii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_50551054_5   2278 ACTGATCTTCAACAAAGCAAACAAAAACATAAAATAGGGAAAGGGCACCC 2327
                          i    i   i    i vviv   i v   vv   i       iii vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_50551054_5   2328 TATTCAACAAAATGATGCTGGGATAAGTGGCAAGCCATATGTAGAAGAAT 2377
                          v         -  i        i  v   vv ?   i   i i      
  L1M4_orf2#LINE/    398 TTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_50551054_5   2378 GAAACCAGATCCTCATCTCTCACCCTATACAAAAATCAACTCAAGATGGA 2427
                            iiii  i  ii i   v    v           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_50551054_5   2428 TCAAAGACTTAAATCTAAGACCTGAAATCATAAAAATTCTAGAAGACAGC 2477
                            ?    i     v     v  i   ii      v ii       v i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_50551054_5   2478 TT---TGAAAACCCCTTCTAGACATTGGCTTGGGCAAGGACTTCATGACC 2524
                         v ---? v   i --   vv   v    v  i     v ii   v iivi
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_50551054_5   2525 AAGAACCCAAAAGCAAACACAACAAAAACAAAGATAAATAGAAGGAACTT 2574
                          v  vv         v vi        iv   i   i   i vv i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_50551054_5   2575 AATTAAACTAAAAAGGTTCTGCACAGAAAAAGAAATAATCAGCAGAGTAG 2624
                         v  i   v v    iv  i  ii vvv   i  v iv    --   i---
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--AGAA--- 689

  chr1_50551054_5   2625 ACAGACAACCCGCAGAGTAGACAGACAACCCACAGAGTGGGAGAAAATCT 2674
                         ---------------   ii v              i           v 
  L1M4_orf2#LINE/    690 ---------------AGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_50551054_5   2675 TCACAATCTATACATCTGACAAAGGACTAATATCCAGGGTCTACAAGGAA 2724
                          ii   vii   i      i  i     vi       ii v  i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_50551054_5   2725 CTCAAACAAATGAGCAAGAGAAAAACAAACAATCCCATCAAAAAGTGGGC 2774
                            vv    v v ii  v i   i     i  i  v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_50551054_5   2775 TAAGGACATGAATAGACAATTCTCAAAAGAATATGTACAAATGGTCAACA 2824
                         v     iv          v     v      v  i         i   i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_50551054_5   2825 AACATATGAAAACGTGCTCAACATCACTAATGAT 2858
                          i  i       vi            ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.67 (44 / 12)  


3727 12.43 1.51 20.87  chr1_50584778_50588301     1906  3031 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50584778_5   1906 TAGAAAGACATCCCATGTTCCTGGAT-GAAAGACTTAATATTGTTAAGAT 1954
                          i      i           v     - i                     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50584778_5   1955 GGTAATACTTCTCAAGTTGATCTACAAATTTAATGCTATTCACATCAGT- 2003
                           i      i i   i          i   i  i  v  i vi    iv-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50584778_5   2004 TTCCAGCTAACTACTTTGTAGAAATTGACAGGCTGATTCTAAAATTTATA 2053
                          i      iv  vi    i           i      i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_50584778_5   2054 TGGAAATTCAAGGGACACTGTGTAGTCAAAACAATCTTGGAAAAGAAG-- 2101
                                v        v v vi   i             i        --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_50584778_5   2102 -----TTGGAAGACTCATACTTCCCAATTTCAAA-CTTACTACAAAGATA 2145
                         -----     i      i                -            v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_50584778_5   2146 CAGTAATTGATACAGTGTGGTACTGGTATAAAGATAGGTATATAAATCAA 2195
                                ii v               i    i     ii     i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_50584778_5   2196 TAGAATA-AACTGAGAGTTCAGAAATAAGCCCTCACATTTATGGTTAATT 2244
                          i     -  i       i         i   vi           i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_50584778_5   2245 GAGGGATTCTTTTCATTTAGGTTTTTTGTTTTCTTTCATTGTCAAAGCTC 2294
                           --------------------------     -----------------
  L1M4_orf2#LINE/    351 GA--------------------------TTTTC----------------- 357

  chr1_50584778_5   2295 TTCTCAGGGTTAACTGAGTTTTGACAAGGGTCCCAAGACAATTCAATGGG 2344
                         ----------------------         v       v          
  L1M4_orf2#LINE/    358 ----------------------GACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_50584778_5   2345 GAAAGAATAATCTTTCTTTTTAAAATCTTTGTACTTTTAATTTTTGTGGG 2394
                                  -----------------------------------------
  L1M4_orf2#LINE/    386 GAAAGAATA----------------------------------------- 394

  chr1_50584778_5   2395 TACATATCAGGTATATATTTATTTGGTATGTGAGATATTTTGATACAGAC 2444
                         --------------------------------------------------
  L1M4_orf2#LINE/    395 -------------------------------------------------- 394

  chr1_50584778_5   2445 ATGCAATGTGTAATAATCACATCATGGGAAGTGGAGTATCTATCCCTTCA 2494
                         --------------------------------------------------
  L1M4_orf2#LINE/    395 -------------------------------------------------- 394

  chr1_50584778_5   2495 GGCATTTATCCTTTGAGGTATAGTCTTTTCAACAAATAATGCTGGGACCG 2544
                         ----------------------               ii         vi
  L1M4_orf2#LINE/    395 ----------------------GTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_50584778_5   2545 TTGGATATTCACATGTAAAAGAATGAATTAAGATAA-TATCTCATAC-AT 2592
                         i      ?i      i           v vi  ivv-  i    i  -  
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_50584778_5   2593 ATGCAAAAATTAACTAAAAATGAATTAAAAACTTACATATAAGAGCTAAA 2642
                           i            v      i  i ? i  i  v  i           
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_50584778_5   2643 ACTATAAAACTCTTTGAAGAAGAAAATCTAGATGTAAATCTTCATGACCT 2692
                                       ---         iv   i?          i      
  L1M4_orf2#LINE/    523 ACTATAAAACTCTT---AGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr1_50584778_5   2693 TGGTCTAGGTAGTGGCTTCTTAGATGTAATACAAAAAATACAAACTACAA 2742
                            vi    i i   i         i i i  v    ii    i v    
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_50584778_5   2743 AAGAAAAAAAAAACAGATGAACTGGACTTCATCAAAACTCAAAACTTTTG 2792
                                  ----i    i  i               i v          
  L1M4_orf2#LINE/    620 AAGAAAAAA----TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_50584778_5   2793 TGTTACAAAAGACACCACCAAGAAAGTGAAAAGACAAACCACAGAATGGA 2842
                           i v    i     i i                   v           i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_50584778_5   2843 AGAAAATACTTGTAAGTCATCTAACTGATAAGAGGCTTGTATCTAGAAGA 2892
                                 i   i  i    v  v        i i        i    v 
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_50584778_5   2893 TATAAATAAATTTTACGATTCAGTAGTAAAAAAA-AAATA---CAATTTC 2938
                               v  v i    i i   i  i      i -     ---     ?v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_50584778_5   2939 AAAGTAGTCAAATGACTTGAATAGACATTTTTCCAAAGAAGATACACAAG 2988
                            i i v    v  i              i             i    i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_50584778_5   2989 TGGCCAGAAAACACATGAAAAGATGTTCAACATTATTAATTGT 3031
                               iv  i              i       i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.58 (98 / 38)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 18.00 (252 / 14)  


2754 20.96 7.83 3.79  chr1_50659950_50661729.rev      500  1291 (489)    L1M4_orf2#LINE/L1       85   908 (0)  

  chr1_50659950_5    500 GTAATTCTAATCAAATATCT--ACAAGATTTTCTATAGAGATTGATAAAC 547
                          i   i iv      -   i--i vivv    i ii   i     i  i 
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAA-ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC 133

  chr1_50659950_5    548 TGATTCTTAAATTTATATGAAAAAGCAATAGAACTGGAATAGTCTAAACA 597
                             i  v     i     i   v    vi  v ii      i v     
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr1_50659950_5    598 ATTTTGAAAAAGAA-AACAAAGTTGGACG--------TTACTAGAGTGCA 638
                           i           -            v --------  v i - v v  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTCA 232

  chr1_50659950_5    639 GGACTTACTA-----------TAATCAAGACATAGTGGTATTTACAAAAA 677
                         ii        -----------           vv      i vi  v  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_50659950_5    678 AAAATGGACCCATGAATCAATGGA------------GTCCAGAAATAGAC 715
                         i -- i   vi  ii         ------------           i  
  L1M4_orf2#LINE/    283 GA--TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_50659950_5    716 CCACACATATATGGTCAATTGATTTTCAACAGAGATACAAAGGCAATTCA 765
                            i    v                  i   ii i i v   i v     
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_50659950_5    766 ATGGGGAAAGGATAGTCTTTTCAACACATGATGCTGCAACAATTGAATAT 815
                                   i               v   i     vi    i  i   ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_50659950_5    816 TTATATCCAAAAAAAATCCCATAGAAAACCAGTTTTAAAATGCTTCAATT 865
                         ii i  v     i  -------------------- i  i --- vi ii
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAA--------------------TGAAGT---TGGACC 457

  chr1_50659950_5    866 CATATATTGCATCACAAGCAAAAATTAACTCAAAATGGGTAATAGACCTA 915
                          v  iv ii  i  i vi                    i v ?       
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_50659950_5    916 AATGTAAAATCTAAAACTATTCAAGTCCCAGAAGAAAACGTAGGAGAAAA 965
                                i v          vv  v  ii          i    ? v   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_50659950_5    966 TCTTCATGACCTTGAGTCAGGCAAAGATTTCTTAGATCTGACACCAAAGA 1015
                              i        i  i      v i          v          ii
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_50659950_5   1016 CACAACCTATAAAATAACAAATATGTAAATTAGACTTTATCAAGATTAGA 1065
                              v v i    v  v     vi      i     i     i    i 
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_50659950_5   1066 AACTT--GTACTATTTATAAAATACTGCTAGGAAATTGAAAAAACAAGCC 1113
                              --  i  -- i v ii i   iii i    v      i    v  
  L1M4_orf2#LINE/    658 AACTTTTGTGCT--TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_50659950_5   1114 ACAGACAAGGGGAAAAT----------CATATATCTGATG---------- 1143
                              vvi  i      ----------            i----------
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_50659950_5   1144 -TCCAGAATACAAAAAGAACTCTCAAAACTCAATAATAAGAAAGCAA--- 1189
                         -         i v          i v             i  ii   ---
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_50659950_5   1190 -CCCAAGTATTAAAATGAGCAAAATATTTAAA-AGACACTTCATCAAAGA 1237
                         -     v ?v-      i     iv    i  -     i   vi      
  L1M4_orf2#LINE/    806 ACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_50659950_5   1238 AAATATACAGAAGGCAAATAAGTGCATCAAAATATGCTCAAAATTTTTAG 1287
                          i       i v   v      ii   v    v        v  iv????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_50659950_5   1288 CCGT 1291
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.79 (104 / 58)
Gap_init rate = 0.02 (17 / 824), avg. gap size = 5.41 (92 / 17)  


3183 19.46 4.12 0.43  chr1_50675070_50677116      500  1203 (844)    L1M4_orf2#LINE/L1      100   829 (79)  

  chr1_50675070_5    500 ATCTCAA-TGCCATTTTTTACAGAAACAGAAAAACCCATCATAAAATGCA 548
                            i  i-    -      i      iv  v  i iv   v      v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_50675070_5    549 TACAGAATCTCAAGGGACCCCTAATAATCAAAACAATCTTCAAAAGTAA- 597
                           ii   viv          vv    ii            v    iv  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_50675070_5    598 --CAAAGTTGAAAGAGTCACTTTTCCTGATTTCAAAACTTACTATAAAGC 645
                         --        i i  v    vi    ii                i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_50675070_5    646 TACAGTAATTGAAAC--CGTGGTAGTGGCATAATGATAGACATATAGAAA 693
                                  ii i  --i      v        v              vv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_50675070_5    694 AATGAAATAGAACAGAAAGCCCAGAAAGAAATCCTCACATATATGTTGGA 743
                             i       iv  i  i       v   i  vi    v    v vi 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_50675070_5    744 TTGATCTTCAACAAGGGTGGCAAGACCATTCAATGAGGAAAGAACAGTCT 793
                              i   i         v               i        i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_50675070_5    794 CCTCAACAAATGATGTTAGGAAAGCTGGATATCCACATGCAAAAGAATAA 843
                         ii          i  i i   v i       ?                i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_50675070_5    844 AGCTGGACCCTCATCATACCTCATATTAAAAAAAAAGCTTAAAATGAATC 893
                           i       ii i vi  vi     vv     vv i  i      i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_50675070_5    894 AAAGACTCAAATTTAAGAGCTAAAACCATAACATTCTTAGATAAAAACAT 943
                          ?    ii    v             i    v i       vi       
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_50675070_5    944 AGGTGAAAATCTTCATGACCATGGATTAGGCAATGATTTCTTTAGTACGT 993
                            ? v        i     v   i          i      vii  i v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_50675070_5    994 CATTGAAAGCATAA-----AAAGAAAAAAACAGAGAAATTACACTTCATC 1038
                           iii      i  -----   ii      i   v     iv        
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_50675070_5   1039 AAAATTAAA--CCTTT----TTCA-------CT--CAAGAGAGTGGAAAG 1073
                                  -- i   ----    -------  --     i    i    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_50675070_5   1074 ATAATCCACAGAATGGAAGAAAATATTTGCA---CGTGATGTCTGATAAA 1120
                          i  i           i              --- i -  i        i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-ATATCTGATAAG 747

  chr1_50675070_5   1121 GGATTACTATCCAGAATATATAATAAACTCCAACAACTAAACAACAAAGA 1170
                            i vv                vi     iv      v  i  i   i 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_50675070_5   1171 AACTAAACAAGCTAATTAAAAAATGGTCAAAGG 1203
                         i  -   i  v i    ?        v      
  L1M4_orf2#LINE/    798 GAC-AAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.83 (86 / 47)
Gap_init rate = 0.02 (12 / 730), avg. gap size = 2.67 (32 / 12)  

 324 18.18 1.52 0.00  chr1_50675070_50677116     1489  1554 (493)    L1M4_orf2#LINE/L1      816   882 (26)  

  chr1_50675070_5   1489 AAAAAAGTCAAAGGACTTGAATAGACATTT-TCCAGAGAAGATGTATAAA 1537
                             vi v       i              -    i       i  i   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_50675070_5   1538 TGGCCAGTACAGGCATG 1554
                               i  vivi    
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATG 882

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1)  


 484 29.61 1.32 0.66  chr1_50701340_50703545.rev      516   667 (1539)    L1M4_orf2#LINE/L1        1   153 (755)  

  chr1_50701340_5    516 TGGAAAAACATTTCATGCTCAAAGGTAAGAAGAATCAATATTGTTAAAAT 565
                               i i  ii    i   vi i vi     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50701340_5    566 GGCCATACTGCCCAAAGCAATTTATAGATTCAGTGTTATTCCTATTAAAC 615
                            v     v      vii  i  i       ii iv  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50701340_5    616 TACCATTGAGATTCTTCACAGAACTAGAAAAA--AACTTTTAAAATACAT 663
                          v   vivivv  i  ii     v v  v  i--i - ii      v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_50701340_5    664 ATGG 667
                             
  L1M4_orf2#LINE/    150 ATGG 153

Transitions / transversions = 1.65 (28 / 17)
Gap_init rate = 0.01 (2 / 153), avg. gap size = 1.50 (3 / 2)  

2488 26.25 2.77 1.45  chr1_50701340_50703545.rev      958  1715 (491)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_50701340_5    958 AAAATTCATATGGGACCAAAAAAAAGAGCCTGAATAGCCAAAGTAATCCT 1007
                                      i -- viv  ii  v  v           ii    i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_50701340_5   1008 AAGCAAAAATAACAAAGATGGAGGGATTATGCTACTTGACTTCAAACTAT 1057
                         i iv  i  v       v      iv i ii  v iii i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_50701340_5   1058 ACTACAGGGTTGCAGTACCCAAAATAACATGGTACTGGTACAAAAACAGA 1107
                               ii i i     vi   i i iii         i i  ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_50701340_5   1108 CACATAGACCAATGGAACAGAATAGAAAACTCAGAAATAAGACCGCACAC 1157
                           i     i        i     v  i iii         iv  ii   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_50701340_5   1158 CTACAACTATCTGATGTTTGACAAAGCTGACAAAAACAAGCAATGGGTTA 1207
                         i  iiiii vi    v  i     i v  v   i v  vv       vv 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_50701340_5   1208 AGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGGCTCACCATATGC 1257
                           i ivvi  v     i              i      v v?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_50701340_5   1258 AGAAGATTGAAACCGGACTCTTTCCTTACACCATATACAAAAATTAACTC 1307
                          i    v    iii    i i v   i                       
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_50701340_5   1308 AAGATAGATTGAAGACTTAAATGGAAAACCCAAAACTATAAAAACCCTAG 1357
                           i  i   ii?    i      v  i v i            vi i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_50701340_5   1358 AAGACAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGCCTT 1406
                             v   v    ?i- v i -   iv   v v  vv i     v vi  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_50701340_5   1407 C------ATGACAAAAATGCCAAAAGCAATAGCAACAAAAGCAAAAATTG 1450
                          ------      ------         vv           v      v 
  L1M4_orf2#LINE/    588 CTTAGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_50701340_5   1451 ACAAATGGGATCTAATTAAACTAAATACCTTCTGCAGAGCAAAACACAC- 1499
                          i    v   ii v  i   v v  v v   i  iivvv    iv    -
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_50701340_5   1500 ATCAGCAGAGTAAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAAA 1549
                             iv i   i  v        i                 v        
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_50701340_5   1550 CTGTACATCTGACAGAGGTCTAATATCCAGCATTTATAAGGAACT--TA- 1596
                         iii  i      i ii  v  vi       v  v     i     --  -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_50701340_5   1597 AATTTACAAATAA---------CAACCCCATTAAGAAGTGGCCAAAGGGC 1637
                           i i vv     ---------i     v   ? i  i   v      ii
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_50701340_5   1638 ACGAACAGACACTTTTCAAAAGAAGACATACATGTGGTCAACAATTATAT 1687
                         vi   i     i  i  v        i     vi   i   i  vi i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_50701340_5   1688 GAATAAAAAT-CACAGCATCACAGGTCAT 1715
                            --  i  - v  i     ????????
  L1M4_orf2#LINE/    882 GAA--AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (122 / 73)
Gap_init rate = 0.01 (11 / 768), avg. gap size = 2.91 (32 / 11)  

 474 12.79 1.16 0.00  chr1_50701340_50703545.rev     2121  2206 (0)    L1M4_orf2#LINE/L1      685   771 (137)  

  chr1_50701340_5   2121 AAAAAAG-AATGAGATAACCCACAGAATGGAAGAAAATATTTGCAAATCA 2169
                           i    -i vi   i              i                   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_50701340_5   2170 TATATCTGATAAGGGTTTAATATCCAGAATATATTAA 2206
                                        vi vi              v  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1)  


2349 28.41 4.77 1.59  chr1_50792808_50798467.rev     4290  5169 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50792808_5   4290 TGGAAAAACAATTCATAGTCATGCATTGGAAGAATCAGTATCATTAAAAT 4339
                               i i vii   iv     v         v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50792808_5   4340 GGCCACAGTGACAAAGGCAACATACAGATTCTGTGTTATTCCGATCAAAC 4389
                            v i v vv v  ivii iv         vii iv  i  v      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50792808_5   4390 TACCAATGTTAC--TTTTCACTAAACTAGAAACAAA--AATTCTAAAATT 4435
                          v   -- i i --    ii vi  v v  --   i--i  i        
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATT 146

  chr1_50792808_5   4436 AATATGGAACCTAGAAAGAGCCT-GAATACCCAAAGCAATACTAAGCTGA 4484
                         v        v- iv  i ii  i-     v     i    vi i ivvii
  L1M4_orf2#LINE/    147 CATATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_50792808_5   4485 AAGAACAAAATGGGA---------CTTC---------AAACTAAAGTGTA 4516
                                  i v   ---------    ---------     v v- ii 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC-TACA 244

  chr1_50792808_5   4517 AGGCTACAGTAACCAAAATAGCATGGTATTGATACAAAAACAGACACATA 4566
                          i          i   i i  ii     i  ii i  ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_50792808_5   4567 GACCAATGGAACAGAATAGAAGACTCAGAAATAAAGTCACTTACCTACAA 4616
                           i        i     v  iiiii          vi  ivi ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_50792808_5   4617 CCATCTGATTTTTGACAAGGCCAACAAAACAAG-CAATGTGGAAAGGACT 4665
                         i  vi       i       viiv   i  v v-     v      i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_50792808_5   4666 CCCTTTTCAATAAATG-TGCTGGGATAACTGGCTAGCCATATGCAAAGGA 4714
                         vi        i     -        i      v  ?   i       i  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_50792808_5   4715 ATGGAACTAGGCACCTTAAATTTTATA--ATATACAAAAATTATCTCAAG 4762
                            i ii i i v   --- ii i i --              v     i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCT---ACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_50792808_5   4763 ATGGATTAAAGATTTAAATGTAAAACCTCAAACTATAAAAATCCCAGAAG 4812
                               i ?   ii         i v  v           v  ii     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_50792808_5   4813 AAAACGTGGG---AAATACCCTTCTCAATAAGGGCCTTGGCAAAGATTTT 4859
                              i i  ---    ---    vii ivvv  vi v     v i   i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_50792808_5   4860 TTTGGCTTAGTCCCCAAAAACAGTTGCAACAAAAACAAAAATTGACAAGT 4909
                           v iiv - v v      i  vvv         iv      v  i  i 
  L1M4_orf2#LINE/    589 TTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_50792808_5   4910 AGGACCTAATTAAACTAAAGAGCATCTGCACAGAAAAATAAACTATTGAC 4959
                         v    i v  i   v v  i i v i  ii vvv   iv v     ii v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_50792808_5   4960 GGAGT-AAATGACA---TACAGAATGGGAGAAAATACTTTCAAACTCTAC 5005
                         ii   -   v    ---i                  i  v    iiv  i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_50792808_5   5006 ATCCAACAAAAATTCTATATCCAAAAATCTGTAAGGAACTGAAACAA--- 5052
                            ii i  iiivii i      i  - v i   i     vvv    ---
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAA-TATATAAAGAACTCTTACAACTC 786

  chr1_50792808_5   5053 ----ACAAGCAGA-AAACAAGCCCATTAAAAAATGGATAAAGGATATAAA 5097
                         ---- i  iv   -   i  v  v   ?        ii       v i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_50792808_5   5098 CAGACATTTCTCAAAAGAAGACATATAAGCAGCTAACAAACATATGAAAA 5147
                         i           v        i   i  iii  i  i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_50792808_5   5148 AATGCTAATCATCAGAGGAATG 5169
                         i     v v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (159 / 88)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.67 (56 / 21)  


3000 16.43 6.60 0.81  chr1_50870014_50871622.rev      499  1119 (490)    L1M4_orf2#LINE/L1      252   908 (0)  

  chr1_50870014_5    499 AGTA-TTAAGAC--TGTGGAACCAGCATAAGGACAGACAGATAGATCAGT 545
                             - i     --     v  ii         i     v        i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_50870014_5    546 GCACTAGAATTGAGAACCTAGAAAGAAACCCTTACATTTATGGTCAATTA 595
                          v v           ii i     v      v                 i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_50870014_5    596 ATTTTCAGCAAGATTACCAAGA-------------AAA----------TT 622
                               ii    iv i      -------------   ----------  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_50870014_5    623 CAACATATGGTGCTGGGACAACTAGATATCTACATGCACAAGAATGAAAC 672
                              v                 i    ? i       v         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_50870014_5    673 TGGACTGTTCCCTCACACCAGACAGAAAGAAAAATTAACTTAAA-----T 717
                              ivi v          v i v   ----        i   ----- 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAA----AATTAACTCAAAATGGAT 497

  chr1_50870014_5    718 CACAGATCCAAATCTAAGACTTAAAACTATAAACCTCATAGAAGAAAACA 767
                           ?   i i    v     vi            v   v            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_50870014_5    768 --GGAAAAATTTTTCGTGGTTTTTGGGTTAGGTAATGGTTTCTCAGTTAG 815
                         --  ?iv  v i      iii  -        i          i  v  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTT-GGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_50870014_5    816 GACACTAAAACTACAAACAA-----GGAAAAATAGGTTATTTGAACTTCA 860
                              i    vi    i   ----- i        i v v   i      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_50870014_5    861 TCAAAATTAAAAACTTTAGTGCCTCAGAGGGCATCATCAGTAAAATGACA 910
                                          v    i   i   i  ii    iv   i   v 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_50870014_5    911 TGACAATTTAAAGAATGGAAGAAAATATTTCCAAATTGTATAT-TGATAA 959
                         v     iii v       i           v     ii     -      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_50870014_5    960 GAGACTTGTATCTAGGATATATGAAGAACTCTTACAACTCAATAATAAAA 1009
                          i          i  i      i                           
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_50870014_5   1010 AGACAAATAATCTAATT-GAAAATTGGCAAAG-ATCTGAATAGACATTTC 1057
                                   i i    -i     v       -  i              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_50870014_5   1058 TCAGGAGAAGATATGCAAACAGCCAATAAGCAAATGAAAAGTTGCCCAAC 1107
                           vii         i    ii           v        v   i    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_50870014_5   1108 ATCTTTAGTCAT 1119
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (64 / 35)
Gap_init rate = 0.02 (12 / 657), avg. gap size = 3.83 (46 / 12)  


2870 25.46 2.18 3.37  chr1_50944457_50949722     3855  4773 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50944457_5   3855 TGAAAAAACATTTCATGCTCA---ATAGGAAGCATGAATATTATGAAAAT 3901
                           i   i i  ii    i   ---  v     vv v      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50944457_5   3902 GGCCATACTGCCCAGAGCAATTTACAGATTCAATGCTATTTCTACCAAAC 3951
                            v     v    i vii  i           i  v  ii   i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50944457_5   3952 TACCAAGGACATTCTTCACACAATTAGAAAAGACT-ATTTTAAAATTCAT 4000
                          v   ivvi v  i  ii  v  v v  v   -  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_50944457_5   4001 ATGGAACCAAAAAGGAGCCTGAATAGCCAAGATAATCCTAAGCAAAAAGA 4050
                               viiv  i   v  v          i i    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_50944457_5   4051 ACCTAAGCAGAAAGCTGGAGGCAC-CACATTACCCAACTTCAAACTATAC 4099
                           --------    i      -  -    i v     i      viv   
  L1M4_orf2#LINE/    200 AC--------AAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_50944457_5   4100 TACAAGGCTGCAGTAACCATAACAGCACGTTACTGGTATAAAAACAGACA 4149
                              i   i      i  vi    iii v      i    ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_50944457_5   4150 CACAGACTCATGGAATGGA-----GAGCCCAGAAATAATGCTGCACATCT 4194
                         i i   iiv       i  -----   i          vv iii    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_50944457_5   4195 ACAACCATCTGATCTTCGACAAAGTTGACAAAAACA---AATGGGGAAAG 4241
                          iiii  vi    i        i v  v   i v  ---           
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_50944457_5   4242 GCTC-CCTATTCAATAAATGGTGTTGGGGTAGCTGGTTAGTCATATGCAG 4290
                         iv v-i  v     i        i    ii i    v  ?i  i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_50944457_5   4291 AAGACTGAAACTGGACCCCTTCCTTACAGCATATACAAAAATCAACTTAA 4340
                             v    ii         v   i   v             i    i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_50944457_5   4341 GATGGATTAAAGACTCAAATGTAAAACCTAAAACTACAAAAACCCTAGAA 4390
                         i      i ?    ii        i v         i    vi i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_50944457_5   4391 GACAACCTAGAAG-ATACCATTCTGGACATAGGCCCTGGCAAAGATTTCA 4439
                           v   v   i? - v i -   vv   v v  viiv     v i    v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_50944457_5   4440 TAACAAAGACATCAAAAGCAATTCCAATAAAAACAAAAATTGACAAATGA 4489
                           ivv v    i        vvvv   i    iv      v  i    vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_50944457_5   4490 GACCCAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAG 4539
                            iiv  i   v v  i i   i  ii vv    i  v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_50944457_5   4540 AGTAATCACACAACCTACAGAATGGGAGAAAATATTTGCAACCTACAGAA 4589
                            i vv v      i                         -------- 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA--------A 731

  chr1_50944457_5   4590 TGGGAGGAGATATTTGCATCCAATAAAGGTCTAATATCCAGAATCTATAA 4639
                          v-------    ----   ii    i  v  vi          v     
  L1M4_orf2#LINE/    732 TC-------ATAT----ATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_50944457_5   4640 GAAACTT----AAATTAATGAGCAAAAAACAAACAACCCCATTAAAAAGT 4685
                         ii    i----  v i   i vv    i     i     v   ?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_50944457_5   4686 AGGCAAAGGACACGATCAGATACTTTTTGAAAGAAGCCATATATTTGGCC 4735
                         i         ivi  vi   i i  i iv       vi   i vv     
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_50944457_5   4736 AAAAAAGCATACACAAA-ATGCTTAGTATCACTAATTAT 4773
                           v  -   i iiv   -     i ii    ????????
  L1M4_orf2#LINE/    871 AATAA-GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.00 (51 / 17)  


3306 19.22 1.90 11.01  chr1_50960245_50963733     1998  2996 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_50960245_5   1998 TGGAAAAGCTTCCCATGGTCATGGACTGAAAAATTTAACATTGTTAAAAT 2047
                               iiiv       v       i  i  i i    i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_50960245_5   2048 GTCCATACTATCCAAAGTGATCTGCAGATTCAATGCAATCTCTATCAAAA 2097
                          v v     vi     v      i         i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_50960245_5   2098 GCCCAATGGTATTTTTTGCAGAAAT-AAGGAAATAATCCTAAATATCATA 2146
                         v    iiv iv              -i vi iv i        vv     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_50960245_5   2147 AGTAACCACAAGGAACTC--------CAAACACAATTGTGAGAAAGAAGA 2188
                         v v  vii     i  i --------    -     iv   i        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGA 199

  chr1_50960245_5   2189 ACAAAGCTGGAGGCCTCCTACTTCCTAACTCCAAAACATATTACAAAGCT 2238
                               i      v   vi      i  i i      v  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_50960245_5   2239 AGAGTAATTAGATCAGTTTGTTAGTGGCATAAAGACAGACACACCAACTA 2288
                          v      i iiv    v  v  v        i  i     i ivi ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_50960245_5   2289 ATAGAACAAAACTGAAATCCCAAAAATAAACCCACACGTATACAGTCAAA 2338
                           i   i i  i   i vi   i           i  i v  ii     v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_50960245_5   2339 TGATCTTTGACTAGAGTGCCAAGACCCCACAATGTGGAAAGGATAGTTTC 2388
                             i  i   v  i           viv     v      i     i i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_50960245_5   2389 TTCAAAAAATGGTACTGGGAAAACTGGATATCCACATGCAAAAGAAC--- 2435
                              v       i      v         ?               i---
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_50960245_5   2436 -TTGGAACCTCATAACCTCATAACATACACAAACATCATCTCATGGTATT 2484
                         -     v  ii ---     i v    i     v  i v    vii ---
  L1M4_orf2#LINE/    450 GTTGGACCCCTA---CCTCACACCATATACAAAAATTAACTCAAAAT--- 493

  chr1_50960245_5   2485 GTGTGAATTAAAGACATAAACATAAGACTTGAAACTATACGAGCAAAGAC 2534
                         ---- i  i ?    v    ii     -----------------------
  L1M4_orf2#LINE/    494 ----GGATCAWAGACCTAAATGTAAGA----------------------- 516

  chr1_50960245_5   2535 CTTGCTACTGTCCTCCAGCCTGGGTGACAGAGCAAGACCCTATCTCAAAA 2584
                         ---    -------------------------------------------
  L1M4_orf2#LINE/    517 ---GCTA------------------------------------------- 520

  chr1_50960245_5   2585 AAAAAAAAAAAAAAAAAAAGACTTGAAACTATAAAACTTGTAGAAGAAAG 2634
                         -------------------------             iv         i
  L1M4_orf2#LINE/    521 -------------------------AAACTATAAAACTCTTAGAAGAAAA 545

  chr1_50960245_5   2635 CAGAAGAGAGGAAATGCTTTATAACACTGATCTTGGCAATGGTTTTTTGG 2684
                           v i ? --v    -   ii i  vi  ivi v           i  i 
  L1M4_orf2#LINE/    546 CATAGGNG--TAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_50960245_5   2685 AAATGACTCCAAAAGCAGAGGCAATGAAAGAAAAAATAGACAAGTGGGAC 2734
                          v     v         v i    ii              i  i v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_50960245_5   2735 TTTATCAAA-TTAAAAAGCTTCTGCACAGAAAAGTAAAC----AACAGAG 2779
                           i      -       -   i  ii vvv    v v  ----  v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_50960245_5   2780 TAAAAAGGCAACCTACAGAATGAGAGGAAACATGTGTGAACCATATATCT 2829
                          i     i     i        i   i   i  v  ii  i         
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_50960245_5   2830 AATAAGGGGTTAAAATACAAAATACAGAAA-AACTTCTATAACTCAACAA 2878
                         i       ii viv  v  i    i v   -    ii  i       i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_50960245_5   2879 TAAAATATCAAATAACCCATTTAAAAAAATGGACAAAGGACTTGAATAGA 2928
                              viv           v  ?     -   i       i         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGA 840

  chr1_50960245_5   2929 CATTTCTCCAAAAAAGACATACAAATGGCCAACAGGTATATGAAAAGATA 2978
                                     i    i              i i i i          i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_50960245_5   2979 CTCAACATCACTAATCAG 2996
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (123 / 65)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 8.60 (129 / 15)  


2675 26.20 2.17 3.59  chr1_50984929_50990678     4338  5257 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_50984929_5   4338 GAAAAAACATTTCATGCTCATCAATAGGAAGAATCAATATTGTGAAAATG 4387
                          i   i i  ii    i    vi  v      v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_50984929_5   4388 GCCACACTGCCTAAAGCAATTTACAGATTCAGTGCTATTCGTATCAAACT 4437
                           v i   v  i   vii  i          ii  v  i v       v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_50984929_5   4438 ACCAAGGACATTCTTCACATAATTAGAAAAGACT-ATTTTAAAATTCATA 4486
                         v   ivvi v  i  ii  v  v v  v   -  -  ii           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr1_50984929_5   4487 TGGAACCAAAAAGGAGCCTGAGTAGCCAAGACAATCCTAAGCAAAAAGAG 4536
                              viiv  i   v  v  i       i      i i iv  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_50984929_5   4537 CCTAAGCAAAAAACTGGAGGCAC-CACATTACCTGACTTCAAACTATACC 4585
                          --------   ii      -  -    i v  ii i      viv   i
  L1M4_orf2#LINE/    201 C--------AAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_50984929_5   4586 ATAAAGCTGCAGTAACCATTACAGCATGGTACTGATACAA----AAACAC 4631
                          i      i      i  vv    ii        ii i  ---- i   i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_50984929_5   4632 ATAGACCCATGGAACAGAATAGAGAGCCAAGAAACAATGCCACACTCCAA 4681
                              i v      i     v     i v     i  vv   i  viiv 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_50984929_5   4682 CAACCACCAGATCTTTGATAAAGGTAACAAAAATAAGCAATGGGGAAAGG 4731
                         iiii  viv   i  i  i  i   iv   i vi vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_50984929_5   4732 ACTCCCTGTTCAATAAATGGTGTTGGGGTAGCTGGTTAGTCATATACAGA 4781
                          ivvi  v     i        i    ii i    v  ?i  i  i  i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_50984929_5   4782 AGACTGAAACTGGGCCCCTTCCATACAGCATATACAAAAATCAACTCAAG 4831
                            v    ii   i     v  vi   v             i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_50984929_5   4832 ATGAATTAAAGACTCAAATGTAAAACCTAAAAC-------CTC---AAAG 4871
                            i  i ?    ii        i v       -------   ---i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_50984929_5   4872 ATAACCTAGGAG-ATACCATTCTGGACCTAAGTCCTGGCAAAGATTTCAT 4920
                          v   v    ? - v i -   vv     vi viiv     v i    v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_50984929_5   4921 -GACAAACACGCCAAAAGCAACTGCAACAAAAACAAAAAAT-GACCAATG 4968
                         -  i vi-  i         vvv         i-       -  iv   v
  L1M4_orf2#LINE/    591 AGATATG-ACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATT 638

  chr1_50984929_5   4969 AGACAT-ATTTAAACTAGAGAGCTTCTGCACAGCAAAAGAAACTATTAAC 5017
                         i   v -  iv   i  i i -   i  ii vv    i  v     i  v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_50984929_5   5018 AGAGTAATCACACAACCAATGGAATGGGAGAAAATATTTGCAACCTACAG 5067
                          i   i vv v      v ii                      -------
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA------- 730

  chr1_50984929_5   5068 AATGGGAGAAGATATACGTATCCAAAAAAGGTCTAATATCCAGAATCTAT 5117
                         -  ---------i   --    ii v  i  v  vi          v   
  L1M4_orf2#LINE/    731 -AT---------CATA--TATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_50984929_5   5118 AAGAAACTTAAACAACTTAATGAGCAAAAAACAAACAACCCCATTAAAAA 5167
                           ii    ivv      i   i vv    i     i     v   ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_50984929_5   5168 GTGGGCAAATGACATGATCAAACACTTTTCAAAAGAAGACATACATGCAG 5217
                         i        v  iv   vi i   i  i  v        i     viii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_50984929_5   5218 CCAGAAAGCATACGAAAAAATGCTCAATATCACTAATCAT 5257
                            iv     i i     i        i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (146 / 91)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 2.79 (53 / 19)  


1898 27.08 1.97 2.12  chr1_50993315_50995353.rev      500  1160 (879)    L1M4_orf2#LINE/L1      170   829 (79)  

  chr1_50993315_5    500 GAATAGCCAAAGCCATCCTGAGCAAAAAGAACAAAGTTGGAGGCATCACA 549
                                    i v   i   iv  i                 vv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_50993315_5    550 TTACCCGACTTCAAAATATACTGTAAGACTAAAGTAACCGTAACGCCATG 599
                         i v   i i       iv    ii  ii   v     i ivi  ivii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_50993315_5    600 GTACTAGTACAAAAACAGACACATAGACCTAGGGAGCAGAGTGAAGAACC 649
                              i i i  ii i     i     i v v   ii   i vi   ii 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_50993315_5    650 CAGAAATAATGCTGCACACCTACAGCCATCTAATCTTCAACCAGT-TAAC 698
                                  vv iii   ii  ii i  vi i  i   i  v  v- iv 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_50993315_5    699 AAAAATAAGCAACGAAGAAAGGAC--TCCTTAGTCAATAAATGGTGCTAG 746
                           i vi vv   i ii     i i--  i  --    i          i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGG 417

  chr1_50993315_5    747 GATAGCTGGTTAGCCGTATTCAGAAAAAAATGAAAGTAGACCCCTACCAT 796
                           i i    v  ?  ii  v  --   i      iv i          vi
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCA--AAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_50993315_5    797 TCACCATACACAAAAACTAAATTAGGATGGATGAAAGAATTAAATGTAAG 846
                         v       i       i   v i ii      v ?   vi          
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_50993315_5    847 ACCCCAAACTATAAGAATCT-AGAAGAAAACCTAGG---AAATGCCATTC 892
                          v iv         i v   -          v    ---    -- -   
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTC 562

  chr1_50993315_5    893 TAAACATCGGTCTTGGCAAAGAATTAT--GACTAAGTCCTCAAAAGCATT 940
                         vvi  v i  vi v     v iv  v --  -  v v vi        iv
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACA 611

  chr1_50993315_5    941 TGCAACCGAAACAAAAATTGACAAGTGAAACCTAATTAAACTAAAGAGCT 990
                         v     vi  iv      v  i  i vii  i v  i   v v  i i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_50993315_5    991 TCTGCCGAGCAAAAGAAGCTATCAATATAGTAAACAAACAACCTACAGAA 1040
                          i  ivvvv    i  vi       v v   i  v i      i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_50993315_5   1041 TGGGAGAAAAATATTCGCAA--CATATGCACCTGACAAAGGCCTAATATC 1088
                                   -    i    --     -- i    i  i  v  vi    
  L1M4_orf2#LINE/    712 TGGGAGAAAA-TATTTGCAAATCATAT--ATCTGATAAGGGACTTGTATC 758

  chr1_50993315_5   1089 CAGGATTTACAAAGGACT-TAAAAATTTGAACAAGCTAAAAA-ACAAATA 1136
                            i  v  i    i   - v v  i i-  i  --      -       
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTC-AATAA--TAAAAAGACAAATA 805

  chr1_50993315_5   1137 GCCCCGTTAAAAAGTGGGCAAAAG 1160
                         i   vi  ?    i        i 
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.63 (109 / 67)
Gap_init rate = 0.03 (17 / 660), avg. gap size = 1.59 (27 / 17)  


1036 27.69 6.15 3.08  chr1_51005034_51007226      529   918 (1275)    L1M4_orf2#LINE/L1        1   402 (506)  

  chr1_51005034_5    529 TGGAAGGATATTCTATGTTCATAGATTTGAAGACTTTATACTGTAAATAT 578
                              i     i i        i    v        v   i   v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_51005034_5    579 GTTAATTCTTCCCAGATTCATCTTCAAATCTGATATGATCTCAATTACAA 628
                          vi   v  i    i   v    v  i  iii iiii   i v  i v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_51005034_5    629 TCCTGGA-ATATTTTTTGAGGAAATTGATAACTTGACTGTAAA-TATATG 676
                            ii v-iiv       vi        i  vi   iiv    - vi  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_51005034_5    677 TGAAGATACAAAGACCCAAGAATATCCAAGACCATCTTAGTAAAGAA--- 723
                           i i  i   i iv  v      v    i  v     iiv      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_51005034_5    724 -AAAGTTCAAAGACCTACACTACCAGGTTATCAAGACTT-TTA------- 764
                         -      vi i   ii     v  vii  -    i    -i  -------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATT-TCAAAACTTACTACAAAGCT 249

  chr1_51005034_5    765 ---ATAAATAAAACAGGGTAGTACTGA-ATGAAGCAAGTATAGACAAATA 810
                         ---i   vi  i    v  i      i-  -----   v       v   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCAT-----AAGGATAGACATATA 294

  chr1_51005034_5    811 AACAAATATAAAAGACTAGAGAATTCAGAAACAGTCCCATACAGGTAGGA 860
                         i iv   iv  v   v v    i i      i iv        vv  v i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_51005034_5    861 ATACTTGATTTATGACAAAGATGGCACTGCAGAGA------AGTAGGGAA 904
                         vi v       vi     i i  v  ------   ------ i i     
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCA------AGACCATTCAATGGGGAA 388

  chr1_51005034_5    905 AAAAGGGTCTTTTC 918
                          i  vi        
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTC 402

Transitions / transversions = 1.57 (66 / 42)
Gap_init rate = 0.02 (10 / 402), avg. gap size = 3.60 (36 / 10)  

 928 27.80 7.20 3.00  chr1_51005034_51007226     1228  1727 (466)    L1M4_orf2#LINE/L1      388   908 (0)  

  chr1_51005034_5   1228 AAGAAGGGTCTTTTCAATAAATGATGGT----TAAATGGATACCC-CATG 1272
                              vi          i     i  v ----i  v      ?  -    
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_51005034_5   1273 -AGAAAAACAAAAC-AAACTTCAGGCTCTCTTATACCA-ACACAAAA-TT 1318
                         - i  i  ii  ii-ii  ii ---- vi  i i    - i      -  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCC----TACCTCACACCATATACAAAAATT 483

  chr1_51005034_5   1319 AACTTTCGATAAATTAC-GACATTAAATATAAAAGGTAAAA--ACAATGC 1365
                             ivvi  ii  i ?-   -i     i   i  v     -- i  vi 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGAC-CTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_51005034_5   1366 TTCTAAAAGAAA-CGCAGGAAAACATCTTCATGAGCTGAAGGTGGACA-- 1412
                          ii  i      - ii   ?iv v      i   v  vii v i i  --
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_51005034_5   1413 GGTTTCTTTGAAAACAGGAT-CCAAAAGAACAAAATCAATAAAGGAAAGA 1461
                                 --- i i v  i-       v    i--   i   i    i 
  L1M4_orf2#LINE/    583 GGTTTCTT---AGATATGACACCAAAAGCACAAG--CAACAAAAGAAAAA 627

  chr1_51005034_5   1462 ATA----AACTGAACTACACTAAAATTAGTTATTCTTGCTTATTAAAG-- 1505
                            ----  i  i   v  ii       ivv i i   iviv i    --
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_51005034_5   1506 -ACTCATTAAAAGGGCAAAAACACAAGCCACAGAATAGATGATGATCTCT 1554
                         -   -  i  i ii ii    v    v         i iv  vi  v i 
  L1M4_orf2#LINE/    678 CACT-ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_51005034_5   1555 GCAA--CACACA----ACAAAAAGCTTCTATCCAGAAAATATAAAAAACT 1598
                             --  i i ---- i  iiii   v         v       i    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_51005034_5   1599 CTTGTAAATCAACAGGAAAAAGACACACAGTTCAACAGAAAA----GAAA 1644
                            ii  v    i iv         v i iii   iv?    ---- v  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_51005034_5   1645 AAGATTTGAATAGGCA---CTCACAAGACAGCATCCCCAAATGGCTATTA 1691
                          i           i  ---   vv    -  -  viv        i v  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGA-AG-ATATACAAATGGCCAATA 874

  chr1_51005034_5   1692 ATAATCTGGGAAGTATAATTTAAAACCACAATGAAA 1727
                          vv iv  ii   -  i-i i  v i  ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAG-ATG-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (94 / 41)
Gap_init rate = 0.05 (26 / 521), avg. gap size = 1.96 (51 / 26)  


2849 26.03 2.11 1.45  chr1_51036096_51038703     1217  2115 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_51036096_5   1217 AAAAACATTCCATGCTCACAGGTTGGAAGAATCAATATCATTAAAATGGC 1266
                            i i  i     i   ii i        v i     ii    i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_51036096_5   1267 CACACTGCCCAATGCAATCCAGAGATTCAATGCTATTCCTATCAAACTAC 1316
                         v i   v     vvii   i v        i  v  i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_51036096_5   1317 CAA-TG--TTATTTGTCACAAACTAGAAAA--AA--CTAAAATTCATATG 1359
                           i-  --  v    -  v   i iiv  i--i --              
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_51036096_5   1360 GAATCAAAAAAGAGCCCAAATAGCCAAAGTAATCCTAAGCAAAAAGAACA 1409
                            viiv  ii  v  vi          ii    i i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_51036096_5   1410 AAGCTGGAGGCATCACATTATCCAACTTCAAACTATACTGTAAGGATACA 1459
                            i      vv     i vi    i      viv    ii  i v    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_51036096_5   1460 ATAATCAAAACAGCATGGAATCGATACAAAAACAGACATAAACACTCATG 1509
                         i       i    ii   v ii ii i  ii i       v v iiv   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_51036096_5   1510 GAACAGAATAGAGAACCCAGAAATAAAGCTGCTTGCACAACTACAGCCAT 1559
                            i     v    ii           ---- iiii   vi  ii i  v
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAA----CCCATACATTTATGGTCAA 348

  chr1_51036096_5   1560 TTGATCTTCAACAAAGCCTACAAAAATAAGCAATAGGGAAAGGACTGCCT 1609
                              i   i    i vivv   i vi vv    i       i iv i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_51036096_5   1610 ATTGAATAAACAAACAGTGCTGGGATAGCTGGCTACCCATGTACAGAAGA 1659
                         -  --- v      ii         i i    v  ?   ii i  i    
  L1M4_orf2#LINE/    399 -TT---TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_51036096_5   1660 ATGACACTAGACCCCTACTTTTCACCATACACAAAAATTAACTCAGGATG 1709
                             vii i         i iv       i               ii   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_51036096_5   1710 GATTAAAGATTTAAATGTAAGACCTCAAACTATAAGAATCT-AGAAGAAA 1758
                            i ?   ii           v  v         i v   -        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_51036096_5   1759 ACCTAAG---AAATGCCATTCTGGACATCAATCTTGGCAAAGAATTTACT 1805
                           v  i ---    -- -   vv   v iiivi v     v i-   vi 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGG-TTTCTT 590

  chr1_51036096_5   1806 AC-TAAGTTATCAAAATCAACTGCAACCAAAACCAAAATTGACAAGTTAG 1854
                          v-  v vi i     v  vvv     v   ivv     v  i  i  i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_51036096_5   1855 ACCTAATTATACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGG 1904
                           i v  i v v v  i i   i  ii vv    i  v        v ii
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_51036096_5   1905 GTAAACATACAACCTACAGAATAGGATAAAATATTCACAAACTACACATG 1954
                           i  v v      i       i   v        ii    ii i i  v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_51036096_5   1955 TGACAAGAT-CTAATATCCAGAATCTATAAGCAACTT----AAATCAACA 1999
                            i   iv-  vi          v     iv    i----  v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_51036096_5   2000 AGCAAAAGACAAGTAACCCCATTAAAAAATGGGCAAAGGACATGAACAGA 2049
                          vv         i      v   ?                iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_51036096_5   2050 CACTTCTCAAAAGAAGACGTACACATGGCCAACAA--ACATGAAAAAATG 2097
                           i     v        ii    v        i  --         i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_51036096_5   2098 TTCCACATCACCAATCAC 2115
                         i  v      ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (144 / 87)
Gap_init rate = 0.02 (17 / 905), avg. gap size = 1.88 (32 / 17)  


3074 27.18 1.22 0.88  chr1_51064324_51070686.rev     4968  5872 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_51064324_5   4968 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5017
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_51064324_5   5018 GGCCATACTGCCCAAGGTAATTCATAGATTCAATGCCATCCCCATCAAGC 5067
                            v     v     iv i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_51064324_5   5068 TACCAATGACTTTCTTCACAGAATTGGAGAAAACT-ACTTTAAAGTTCAT 5116
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_51064324_5   5117 ATGGAACCAAAAAAGAGCCTGCCTTGCCAAGACAATCCTAAGCCAAAAGA 5166
                               viiv  ii  v  v vv v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_51064324_5   5167 ACAAAGCTGGAGGCATCATGTTACCTGACTT-GAAACTATACTGCAAAGC 5215
                               i      vv   iii v  ii i  -i     -    i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr1_51064324_5   5216 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5265
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_51064324_5   5266 AATGGAACAGAAC--AGAGCCCTCCA-AAATAATGCCACACATCTACAAC 5312
                                i    i--    ---    -      vv   i    i  iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAG---TCCAGAAATAAACCCATACATTTATGGT 345

  chr1_51064324_5   5313 CATCTGATCTTTGACAAACCTGATAAAAACAAGAAATGGGGAAAGGATTC 5362
                           vi    i  i     ivv  vi  i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_51064324_5   5363 CCTGTTTAATAATTGGTGCTGGGAAAACCGGCTAGCCATATGTAGAAAGC 5412
                         i  v  i  i  v           v   i  v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_51064324_5   5413 TGAAACTGGATCCCTTCCTTACACCTTCTACAAAAATTAATTCAAAGATG 5462
                             ii    i    v   i     v v            i     -   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA-ATG 494

  chr1_51064324_5   5463 GATTAAAGACTTAATTATTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5512
                            i ?    i   v i v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_51064324_5   5513 ATGTAGGCA-ATACCATTCA-GGCTATAGGCATGGGCAAGGACTTCATGT 5560
                          ii    ?i- v i -   i- i iv i  i- i     v ii   v iv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAG 592

  chr1_51064324_5   5561 CTAAAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGAT 5610
                         v  vi            vvi     v    vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_51064324_5   5611 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5660
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_51064324_5   5661 GAACAGGCAACCTACCGAATGGGAGAAAATTTTTTCAATCTACTCATCTG 5710
                            v  i     i  v              v   v   vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_51064324_5   5711 ACAAAGGGCTAATATCCAGAACCTACAAAGAACTCAAACAAAT---TTAC 5757
                          i  i  i  vi         iv  i         vv    v --- v i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_51064324_5   5758 AAGAAAACAA-CAACCCCATCAACAAGTGGGCGAAGGATGTGAACAGGTA 5806
                           i  i    -i     v  i? v  i     i      v    i  ii 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_51064324_5   5807 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCT 5856
                         i     v        i  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_51064324_5   5857 CATCATCACTGGCCAT 5872
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (150 / 92)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.36 (19 / 14)  


3128 27.77 0.77 0.33  chr1_51082826_51089206.rev     4987  5890 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_51082826_5   4987 TGGAAGAACATTCCATGCTTATGGATAGGAAGAATCAACATTGTGAAAAT 5036
                              ii i  i     i i      v      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_51082826_5   5037 GGCCATACTGCCCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 5086
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_51082826_5   5087 CACCAATGACTTTCTTCACAGAATTGGAAAAAAGAACTTTAAAGTTCATA 5136
                         iv   iivi i  i  ii     v v  v  ivvi iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_51082826_5   5137 TGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATAGTAAGCCAAAAGAA 5186
                              viiv  ii  v  v v  v     i     vv i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_51082826_5   5187 CAAAGCTGGAGGCATCACGTTACCTGACTTCAAACTATACTACAAAGCTA 5236
                              i      vv    ii v  ii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_51082826_5   5237 CAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGACCAA 5286
                           i   i   i    ii         i iv ii i   v  i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_51082826_5   5287 TGGAATACAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCAT 5334
                                v  i--    i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_51082826_5   5335 CTGATCTTTGACAAACCTGATAAAAACAAGAAATGGGGAAAGGATTCCCT 5384
                         i    i  i     ivv  vi  i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_51082826_5   5385 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5434
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_51082826_5   5435 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGATT 5484
                          ii    i    v   i     v              i    ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_51082826_5   5485 AAAGACTCAAATGTTAGACGTAAAACCATAAAAACCCTAGAAGAAAACGT 5534
                          ?    ii      v   vv      i      vi i           i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_51082826_5   5535 AGGCA-ATACCATTCAGGACTTAGGCATGGGCAAGGACTTCATGACTAAA 5583
                            ?i- v i -   iv   i v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_51082826_5   5584 ACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAACGGGATCTAAT 5633
                                     vvi     v    vv     v  i   iv   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_51082826_5   5634 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTGAACA 5683
                         i   v v  i i   i  ii vv    i  v   ii  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_51082826_5   5684 GGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACCCATCTGACAAA 5733
                          i     i                vv       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_51082826_5   5734 GGGCTAATATCCAGAATCTACAAAGAACT--TA-AACATATTTACAAGAA 5780
                           i  vi          v  i        --  -   vi v v i  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_51082826_5   5781 AA-AATCAACCCCATCAAAAAGTGGGTGAAGGATATTAACAGACACTTCT 5829
                         i -  vi     v  i?    i    ii      v v  i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_51082826_5   5830 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5879
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_51082826_5   5880 TCACTGGCCAT 5890
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 966 25.55 6.93 0.36  chr1_51100035_51103744     2086  2359 (1351)    L1M4_orf2#LINE/L1        4   295 (613)  

  chr1_51100035_5   2086 AAAGGCATCCCATACTCATTGATTAGAAGAATTAATATTGTTAAAATGAC 2135
                             ii       ii    v    i     v             i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_51100035_5   2136 CATACTACCCAAAGCAATCTACAGGTACAGCATCATCTCTAT-AAAATAC 2184
                         v     v      vii        i v  i iiv   i    -     v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_51100035_5   2185 CAAGGACATTCTTTACAGAAATAGAAAAAGCAATCCTTAAGTTCATATAG 2234
                           ivvi v  i   i       v  v  ivii     v  i       i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_51100035_5   2235 AAGCACAATAGACCCTGAATAGCCAAAGCAATAATCAGAAAAAAAGAACA 2284
                           iii   vi     v           i    -v iii    i       
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAACA 202

  chr1_51100035_5   2285 AAGCTG------------------ACTTCAAAATATACAGCAGAGCTATA 2316
                            i  ------------------ i       iv   vi  i     i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_51100035_5   2317 GTAACCAAAACAGCATAGTATTGGTATAATAAAAGATACATAG 2359
                             i   i    ii i   i   i    vi v   i i    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 2.18 (48 / 22)
Gap_init rate = 0.01 (3 / 292), avg. gap size = 6.67 (20 / 3)  

1517 25.82 10.55 1.82  chr1_51100035_51103744     2659  3208 (502)    L1M4_orf2#LINE/L1      281   878 (30)  

  chr1_51100035_5   2659 AAAACAGATACATAGACCAACAGAACAGAGAACCTTGAAATTAAAAATAT 2708
                          ii i   i i     i   ii   i   i----    i v vv i ---
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAA----TTGAGAGTCCAGA--- 323

  chr1_51100035_5   2709 TAATAAATCCACATATTTTTAGCCAACTGATACTCAGCAAAAGTGCTAAG 2758
                         -      i   i i    v i i   i    vi  ii   ii    i   
  L1M4_orf2#LINE/    324 -AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_51100035_5   2759 AATACACATTGGGAAAACAACAGTCTCTTCAATAAATGGTGCTAAGAAAA 2808
                          vi iv  v    i   v  i     i     i          ii  v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_51100035_5   2809 ATGGATAGTCATATGCAGAGGAATGAAACTAGACCCCTATCTATCACTAC 2858
                         v      ?i  i     i i       ii i        i  vv   i i
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_51100035_5   2859 ATACAAAAATTAACTCAAAATGGATTAAAGACTTAAATGTAAGACTCAAA 2908
                                                  i ?    i           vii   
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_51100035_5   2909 ACTATAAAACT-----------GC-TGGGTG-GAATC------AC----- 2934
                                    -----------i - i  ? -i    ------  -----
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_51100035_5   2935 GTCAGG-------------------ACA---AAAACACAGACAACAAGA- 2961
                           i   -------------------   ---   i    ii      i -
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_51100035_5   2962 -----ATAGACAAATGGGACTGTACTAAACTAAAAGGCTTCTCCACGGTA 3006
                         -----     i    v     vi ii   v v   ii   i vii vvi 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_51100035_5   3007 AAAGAAACAATCAACACAGTTAAGAGATAACCTGTAGA-TAGGA--AAAT 3053
                           i  v  v     v v   v  i   i    iii   - i   --    
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_51100035_5   3054 ACTTACAAATCGTTTGACTAACAAAGAACTAACAACCAGAATATACAAGG 3103
                          i  i      i v iv  i i  i i   vii v          i  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_51100035_5   3104 AATTC--A-AACTTAGCACCAAAAAAAAAAAAATCCCACTACTACAAAGT 3150
                           i  -- -    i ii vi     i v   v v    -- i ?v   i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCA--ATTWAAAAAT 820

  chr1_51100035_5   3151 GGGTCAAAGATCTGAACAGACATTTCTCAAACGAAGACATAGAAATGGCC 3200
                            iv  i   i    i           v  v     i   v        
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_51100035_5   3201 AACAAATA 3208
                           i  ii 
  L1M4_orf2#LINE/    871 AATAAGCA 878

Transitions / transversions = 2.54 (99 / 39)
Gap_init rate = 0.03 (15 / 598), avg. gap size = 4.53 (68 / 15)  


2995 23.00 1.94 1.69  chr1_51174320_51177482     1185  2010 (1153)    L1M4_orf2#LINE/L1       15   842 (66)  

  chr1_51174320_5   1185 ATGTTAATGGAGTGGAAGAATCAAT---GTTAAAATGTCCATACTACCCA 1231
                              v     v       v i   ---     i   v v     v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_51174320_5   1232 AAGAAAGCTACAGATTCAATGCAATCCCTATCTAAATACCAATAACATTC 1281
                           vvi v            i            v    v   iivi v  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr1_51174320_5   1282 TTCACAGAAATGGAAAAAAAAATCCTAAAATTTATATAGAACAACAAAG- 1330
                           ii       v  v  ivvi           i    i   vvi   i -
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_51174320_5   1331 ACCCAGAATAGC-AAA----TCTTAGGATAAAGCAAAAAGAACAAAACTG 1375
                                     -   ----    --  v    ----         ii  
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTT--GAAAAAG----AAGAACAAAGTTG 208

  chr1_51174320_5   1376 GAGGAATCACATTACCTGACTT-AAAATTATACCACAGAAATATAGTAAT 1424
                              v     i v  ii i  -    i -   i   i iv  i      
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAAT 257

  chr1_51174320_5   1425 CAAAACAACACGGTACGGGCAGAAAAACAGACACAATAGACCAATGGAAC 1474
                            i   iiii     v    v  ii i     i -    i        i
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGATCAATGGAAT 306

  chr1_51174320_5   1475 AGAATAGAGAACCCAGAAATATATTCACACACCTACAGTGAACTCATTTT 1524
                              v    ii         v ii  i   ii  ii  v  i v     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_51174320_5   1525 TGACAAAGGTGCTAAGAACATACATTGGTGAAAGGACAATCTCTTAAATA 1574
                         i     i     i    v   v  v   v     i i i   i  v  i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_51174320_5   1575 AATGGTGCTGGGAAAATTGGACCTCTATCTGCAGA-GAATAAAACTAGAC 1623
                                      v  i    iv? i iv    i -    i  ii i   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_51174320_5   1624 CCCTATCTCTCACGATATACAAAACTCAAATGAAAATGAATTAGAGACTT 1673
                              i   v   v          v i  v v      i  i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_51174320_5   1674 AAATCTAAGACCTCGAACTATGAAACTACTAAAAGAAAAGTTGGGGG-AA 1722
                             v     v  vi      i     vi  i       vv i  ? -  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_51174320_5   1723 CTCTCCAAGACATTGGTCTGAGCAAAGTATTTCTTGAGTA--ATACCCAA 1770
                         v   i iv   v    vi ii    v -i      iii  -- i   -- 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTAGATATGACACC--A 603

  chr1_51174320_5   1771 AAAGCACAGGCAGCCAAAGCAAAAATGGACAAATGGGACCACATCACA-T 1819
                                 i   i v    v      i  i    v    iv     v - 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_51174320_5   1820 GAAAAAGCTTCTGCACACCAAAGGGAACAATCAACAAAGTGAAGAGACAA 1869
                         v     -   i  ii vi      iv  v     v        i      
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_51174320_5   1870 CCCAAAGAATGGGAGAAAATATTTGCAAACTATCCATCTGACAAGGGGAT 1919
                             v                        ii  vi      i     - i
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG-AC 751

  chr1_51174320_5   1920 TAATAACTGGAATATATAAGGAGCTCAAACAACTCTATAGGAAAAAAATT 1969
                          vi  v ii          i  i   vv       v   iv     i iv
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_51174320_5   1970 TAATAATCCAATT-AAAAATGGACAAAATAGTTGAATAGCCA 2010
                         -     i      -        i    iv v        v  
  L1M4_orf2#LINE/    802 -AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

Transitions / transversions = 1.49 (112 / 75)
Gap_init rate = 0.02 (19 / 828), avg. gap size = 1.58 (30 / 19)  

 201 21.54 4.62 1.54  chr1_51174320_51177482     2277  2341 (822)    L1M4_orf2#LINE/L1      805   871 (37)  

  chr1_51174320_5   2277 AACTCCATCTCAAAAAAAAAAAAAAAAGTTGAATAGACATTTCTCAAGAG 2326
                            i v  - ?     viiiv   ii v                 v i  
  L1M4_orf2#LINE/    805 AACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_51174320_5   2327 AAGACATACA---GGCCA 2341
                             i     ---     
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCA 871

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.03 (2 / 67), avg. gap size = 2.00 (4 / 2)  


1627 26.91 11.62 1.59  chr1_51192282_51195616     1750  2377 (958)    L1M4_orf2#LINE/L1        1   691 (217)  

  chr1_51192282_5   1750 TAAAAAGATAATTTATGTTAATGGA--GGAAAAAACCTTAATAATAATAA 1797
                          ii       viii     v     --    i ---       v iv   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA---CTTAATATTGTTAA 47

  chr1_51192282_5   1798 GATGCCAAT-TTCCCACAACTTTATCTATATATTAAATGCAATCCGAATC 1846
                             v    -i    -   v  v     i v   v  i       vv   
  L1M4_orf2#LINE/     48 GATGGCAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_51192282_5   1847 AAAATTCCAG--GTTTGAACTTTGTGGAAATTGACAAGCTGATTCTAAAA 1894
                              i    -- ii v--i    ii                 i      
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_51192282_5   1895 TTTATATGCAAATGTAAAGGACCTAGGATAGCCAAGATAATCTTGACAAA 1944
                           i     v     i  i     i  i        i i        v   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_51192282_5   1945 GAA---CAAG----------------------ATTTTAAGACTTACTATA 1969
                            ---   i----------------------    i  i        i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_51192282_5   1970 AAGTTAGAGTGATTA-----TTGTGGTATTGGCACAA------------- 2001
                            i  v   i  i -----v       i     i  -------------
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_51192282_5   2002 ---TAATGGTGCAGAATAGGGACTTCAGAAATAGATTCACACATGTACAG 2048
                         ---i     vii     v i  v i        i ii  i    v  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_51192282_5   2049 TCACCTGATTTACAATGAAATTGT---AACTGTAATTAA-GTAGAAAAAA 2094
                            vi      v i ii iiv  i---i  ii -- i  - vi    i  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAA 392

  chr1_51192282_5   2095 T--TTTTTTAAACAAATGTTGCTAG-ACAATTGAATACCTGTATGAGAAA 2141
                          -- i    v        v    i -    i  i   ? iii   vi   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_51192282_5   2142 CAACAAAACTTAACCTCTAACTCATACCATCCATAAGAGT--AGTTGAGA 2189
                         v  ii  ii vi   i   v    i     vi i  i i -- v ii i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_51192282_5   2190 TGAATCACGAATCTAAATATGAAGAC-AAAACAATAAAGTTTATGGAGGA 2238
                           i    ?ii i      i i iii -     v     ii iv i  i  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_51192282_5   2239 AAAACATAGAAGAATATCTTTATGACTTTGTTGTAGACAAAGATTAATCA 2288
                            -     i? v v     ii    i   vvv   i   v i  vv i 
  L1M4_orf2#LINE/    543 AAA-CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_51192282_5   2289 G----GATACAAATAAACACTAACTGTAAGATAAAAATTA-ATAAATTGA 2333
                          ----  i  v  -  i   v i vii  i v     v  -        i
  L1M4_orf2#LINE/    592 GATATGACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_51192282_5   2334 GCTTCAT------TAAGAGCTTTAATTCATCAAAA-ACACCAGTAAGAAG 2376
                         i      ------   i i    vi v v     i-    i vi     i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_51192282_5   2377 G 2377
                          
  L1M4_orf2#LINE/    691 G 691

Transitions / transversions = 2.25 (115 / 51)
Gap_init rate = 0.03 (23 / 691), avg. gap size = 3.61 (83 / 23)  

 323 20.49 8.78 7.32  chr1_51192282_51195616     2630  2834 (501)    L1M4_orf2#LINE/L1      671   878 (30)  

  chr1_51192282_5   2630 CAAAAAACCAGCAGTAAGAGAGTGAAAAGGAAGGCAACA--ACGCAGAGA 2677
                             ii  - vi vi    i         iv iv v   -- i -i    
  L1M4_orf2#LINE/    671 CAAAGGAC-ACTATCAAGAAAGTGAAAAGACAACCCACAGAATG-GGAGA 718

  chr1_51192282_5   2678 AGAGATTCA-AAATACATACAT---ATAACCTTTG---TTTGTATCCTGA 2720
                          i v   ii-    -    i  ---    ----- ---i        v  
  L1M4_orf2#LINE/    719 AAATATTTGCAAAT-CATATATCTGATAA-----GGGACTTGTATCCAGA 762

  chr1_51192282_5   2721 GTTTATACAGAATTCCTACAAATAAGATAA-AAGAAAACATTTTTTAAAC 2769
                         i v    v    i  i     v v -    -  i  i   vv ----   
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCA-ATAATAAAAAGACAAAT----AAC 807

  chr1_51192282_5   2770 ---ATT--AAAATGGACAAAAGAATTGAACAGG---TCCTCCTAACAGAA 2811
                         ---   --       i    i  v     i  i--- i    -  -    
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC-AA-AGAA 855

  chr1_51192282_5   2812 GATATTCAAGTGACCAATAAGTA 2834
                              v   i  i        i 
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCA 878

Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.08 (16 / 208), avg. gap size = 2.06 (33 / 16)  


2617 24.31 0.60 10.52  chr1_51309297_51315350     4567  5574 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_51309297_5   4567 TGGAAAAACCTTCCATGCTCATGGATAGGAAGAATCAATATTGTTTAAAT 4616
                               i iv i     i        v      v i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_51309297_5   4617 GGCCATACTGCCCAAAACAATTTATAGATTCAATGCTATTCCTATTAAAC 4666
                            v     v      vii  i  i        i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_51309297_5   4667 TATTATTGACATTCTTCATAGAACTAGAAAAAAAATCATTTTATTTTATT 4716
                          vii vivi v  i  iii    v v  v  i------------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG------------------ 132

  chr1_51309297_5   4717 ATTTCTATTTTGATCTTGATTTTTTTTTTTTTTGAGATGGAGTCTTGCTC 4766
                         ---------i     i i vv  i---------- v     ---------
  L1M4_orf2#LINE/    133 ---------CTGATCCTAAAATTC----------ATATGGA--------- 154

  chr1_51309297_5   4767 TGTCACCCAGGCTGGAGTGCAGTGGTGTGATCTCAGCTCACTGAAACAAA 4816
                         --------------- i    -----------------------------
  L1M4_orf2#LINE/    155 ---------------AATGCA----------------------------- 160

  chr1_51309297_5   4817 AAAGAGCCTGAGTAGCCAAGGAAATCCTAAGCAAAAAGAACAAAGCTGGC 4866
                          ii  v  v  i       iiv    i i iv  i          i   v
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_51309297_5   4867 GGCATCACACTGCTGCACTTCAAACTGTGCTATAGAGTTACAGTAGCCAA 4916
                           vv       v ivv i      viv i   i i  i       ii   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr1_51309297_5   4917 AACAGCTACTGTTTTGTACTGGTACAAAAACAGACGCATAGATCAACGGA 4966
                         i    ----   v--       i i  ii i    ii         i   
  L1M4_orf2#LINE/    261 GACAG----TGTG--GTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_51309297_5   4967 ACAGAATACAGAACCCAGAAATAAGGCCACACACCTACAATGATCTGATC 5016
                          i     vv   ii          iv   i   ii  iii v vi    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_51309297_5   5017 TTTGGCAAACCTGACAAAAACAAGCAATGGGGGAAGAATTCCCTATTCAG 5066
                           i i   ivv  v   i v  vv        i      vvi  v    i
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_51309297_5   5067 TAAATGGTGTTGGGATAACTGGCTAACCATATGCAGAAGACTGAAACTGG 5116
                         i        i     i      v  ?   i     i    v    ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_51309297_5   5117 ACCCCTTCCTTATATCATGTACAAAAATTAACTCAAGACGGATTAAAGAC 5166
                               v   i i i   i                 i i    i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_51309297_5   5167 TTAAATGTAAA---TAAAACCCAAATGTATAAAAACCCTGGAAGACCACC 5213
                         i         i---      -------       vi i i     vv  v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAAC-------TATAAAACTCTTAGAAGAAAACA 547

  chr1_51309297_5   5214 TAGGCA-ATACCATTCTGGACATAGAAATGGGCAAAGATTTCAT-GATGA 5261
                             ?i- v i -   vv   v v iiv i     v i    v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr1_51309297_5   5262 AGACACCAATAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTA 5311
                         v        v    vvv          v      v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_51309297_5   5312 ATTTAACTAAAGAGCTTCTGCACAGCAAAAGAAATTATCAACAGAGTAAA 5361
                           iv  v v  i i   i  ii vv    i  v i      v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_51309297_5   5362 CAAAAAACCTACA-AATGGGAGAAAATTTTTGCAAACCATGCATCTGACA 5410
                         v i v    i   -             v        i   ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_51309297_5   5411 AAGGTCTAATATCCAGCATCTGTCAGGAACTTCAACAAATTTACAAGAAA 5460
                          i  v  vi       v  v i v i     iiv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_51309297_5   5461 AAAACAAGCAGCCCCATTAAAAAGTGAGGAAAGGACATGAACAGACACTT 5510
                           i    ii i   v   ?    i  i v      iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_51309297_5   5511 TTCAAAAGAAGACATGCATGTGGCCATGAATCATATGAAAAAAAAGTTCA 5560
                         i  v        i  i  vi      vv  v  i       i v- i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCA 894

  chr1_51309297_5   5561 ATATCACTGATCAT 5574
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 8.00 (112 / 14)  


 983 16.67 0.52 2.60  chr1_51557864_51563519     3918  4109 (1547)    L1M4_orf2#LINE/L1        1   188 (720)  

  chr1_51557864_5   3918 TGGAAAGACATCCCATGTTCACAGATTAGAAGACTTAATATTTTTAAGTT 3967
                                 i            ii    i              v     v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_51557864_5   3968 GGTAATATTACCCAAAGATATCTACAGATTCAATGCAATCCCTATCAAAA 4017
                           i    i v      vvv              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_51557864_5   4018 ATCCTAATGACTTTTTCTTTTGGCAGAAATAGAAAAATTCATCCTAAAAT 4067
                         -   i iivi i    i ----        v  v  ii v          
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTTTTTT----GCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_51557864_5   4068 TCATATGGAATCTCAAGGAACCT-GAATAGCCAAAGCAGTCTT 4109
                                   viv     i   i-           i  i    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

Transitions / transversions = 1.67 (20 / 12)
Gap_init rate = 0.02 (3 / 188), avg. gap size = 2.00 (6 / 3)  

3286 17.45 5.15 0.29  chr1_51557864_51563519     4466  5164 (492)    L1M4_orf2#LINE/L1      176   908 (0)  

  chr1_51557864_5   4466 CCAAAGCAGTCTTAAAAAGGAACAACAAAGTTGGTAG--TCAAACTTTCT 4513
                              i  i    i    i   v           vi --   v    i i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr1_51557864_5   4514 GATTTCAAATCTTATTTCAAAGCTATAGTAATTAAAACAGTGAGGAACTG 4563
                         i        v    i v        i      i  i      v  v    
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_51557864_5   4564 -CATAAATACAAACCATATAGATCAATGGAACAGAATACAGAATCCAGAA 4612
                         -     iv i i  -                i     vv   i       
  L1M4_orf2#LINE/    276 GCATAAGGATAGAC-ATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_51557864_5   4613 ATAAACCCTCACATATATGGTCAAATGATTTTCAAGAAACGTGCCAAGAA 4662
                                 vi    v         v        i v  iv         v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_51557864_5   4663 CAAACAATGGAAAAAGGACGGTCTTCACAAGAAAAGATGATGGGAAAACT 4712
                           vv      ii    i ii     iv   v   v i  v     v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_51557864_5   4713 GAATATCCACATGCAAATGAATGAAGTTGGACTCTTACCTCACACAATAT 4762
                          i   ?           v              i i          v    
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_51557864_5   4763 ACAAAAATTAACTCAAAATGGATTAAATACCTAAATGTAAGAGCTAAAAC 4812
                                                i ? v                      
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_51557864_5   4813 TATAAAACTT------------ATCGGGG-AAATGCTTCCTGATATTGGA 4849
                                  i------------  v  ? -    -    v   iv    i
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGG 573

  chr1_51557864_5   4850 TTTAGCAACGCTTTCTTGGTTATAACACTAAAAGCAAAGGCAACAACA-A 4898
                           vi    i v      i v   i    i       v i       v - 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_51557864_5   4899 CACAATAGATAAAATGAGCTACATCAAAATTAAAAACTTTTGTTCACCAA 4948
                         v v          v  ii  v                      v vi   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_51557864_5   4949 CGGACAGTACTAACAGAATGAAAAGGTAACCCACAGGATGGGAGAAAATA 4998
                         v     v  ii  v i i       ii         i             
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_51557864_5   4999 TTTGCAAATCATTTATCTGATAAGGGGTTAATATCTAGGATATATAAAAA 5048
                                     v             ii vi    i  i         i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_51557864_5   5049 ATTC----AAC----------AAAAACAA----CCTGATTTAGAAATGGG 5080
                          i  ----   ----------   i    ----  ii   ? i       
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_51557864_5   5081 CAGAGGACTTGAATAGGTATTTCTCCATAGAAGATATACAAATAGCCAAT 5130
                           i    i        ii         v               i      
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_51557864_5   5131 AAGCATATAAAAAAAGGCACTACAT-ACTAATCAT 5164
                              i  i    i v  v v    - ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (69 / 49)
Gap_init rate = 0.02 (11 / 733), avg. gap size = 3.45 (38 / 11)  


3263 26.93 0.66 0.44  chr1_51563641_51568919     3881  4786 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_51563641_5   3881 TGGAAGAACATTCCATGTTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3930
                              ii i  i            i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_51563641_5   3931 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3980
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_51563641_5   3981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTCA 4028
                          v   iivi i  i  ii     -   -- v  i  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_51563641_5   4029 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 4078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_51563641_5   4079 AACAAAGCTGGCAGCATCAAA-TACCTGACTTCAAACTATACTACAAGGC 4127
                                i   vi vv   v - v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_51563641_5   4128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_51563641_5   4178 AATGGAACAGAAC--AGAGCCCTTAGAAATAACGCCGCATATCTACAACT 4225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_51563641_5   4226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGAGGAAAGGATTCC 4275
                          vi    i  i     ivv  vv  i v  vv     i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_51563641_5   4276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_51563641_5   4326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4375
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_51563641_5   4376 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4425
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_51563641_5   4426 CTAGGCATCACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_51563641_5   4476 AACACCAAAAGCAATGACAACAGAAGCCAAAATTGACAAATGGGATCTCA 4525
                         i            vvii     i   vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_51563641_5   4526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_51563641_5   4576 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 4625
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_51563641_5   4626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_51563641_5   4676 AAA-AAACAACCCCATCAAAAAGTGGATGAAGGATATGAACAGACACTTC 4724
                          i -   i     v  i?    i   iii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_51563641_5   4725 TCCAAAGAAGACATTTATGCAGCCAACAGACACGTGAAAAAATGCTCATC 4774
                                    i  vi viii     i ii   i      i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_51563641_5   4775 ATCACTGGCCAT 4786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1087 18.50 4.00 0.00  chr1_51679619_51682863     1230  1429 (1816)    L1M4_orf2#LINE/L1        2   209 (699)  

  chr1_51679619_5   1230 GGAAAAACATCCCACGTTCATAGATCAGAAGACCT-----TGTTAAGAT- 1273
                              i i      i      i   ii      i -----         -
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_51679619_5   1274 --AATACTCCCCAAACTAATCTATAGATTCAATGCAATTTATATGAGAAT 1321
                         --             i i     i        i     iiv   v i   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_51679619_5   1322 TCCAACTGACTGTTTTGTAGAAACTGGCAAGCTGATTCTGAAATTCAGAT 1371
                         i   i   v  v     i     i  i         i  i       v  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_51679619_5   1372 AGAATTGCAAGGAATCCGGAATAGCCGAAACAATCTTGAAAGAAAAAAGC 1421
                         i   v       i i  i        i              i i  i i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_51679619_5   1422 AAAGTAGG 1429
                              v  
  L1M4_orf2#LINE/    202 AAAGTTGG 209

Transitions / transversions = 4.29 (30 / 7)
Gap_init rate = 0.01 (2 / 208), avg. gap size = 4.00 (8 / 2)  

2363 14.55 3.23 3.64  chr1_51679619_51682863     1704  2198 (1047)    L1M4_orf2#LINE/L1      170   662 (246)  

  chr1_51679619_5   1704 GAACAACAACAAAA-AAT---AAAAAATAAAAAAGCAAAGTTAGAGGACT 1749
                            i i --     -   ---i     v  i  --       i       
  L1M4_orf2#LINE/    170 GAATAGC--CAAAACAATCTTGAAAAAGAAGAA--CAAAGTTGGAGGACT 215

  chr1_51679619_5   1750 AACACATCCCAATTTCAAAATGTATTACAAAACAACAATACTCAAGACAG 1799
                         v    v              iv  i      i v   i  v         
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_51679619_5   1800 TGTTGTACTG-CACAGG-----ACATATAGATCAATGGAACAGAATTAAG 1843
                            v      -  i i -----                  i      i  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_51679619_5   1844 ---TCAGAACTAAATC-ATACATCTATGGTTAACTGATTATTGACAAGAG 1889
                         ---i     v    i -      i      i  i     v i      i 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_51679619_5   1890 TGCCAAGATCATTCAATGTGGAAAGAATAGCCTTTTCAACAAATGATGCT 1939
                                 i         v           i              i    
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_51679619_5   1940 GGAATACCATGTCACAAGCAAAAGATATCCACTAGCAAAAAAATGAAGTT 1989
                           i i v -  ------------    ?    vv      i         
  L1M4_orf2#LINE/    416 GGGACAAC-TG------------GATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_51679619_5   1990 GGACCTTTACCTCACACCATATATAAAAATCAACTTGAAATAGATCAAGG 2039
                              ii                i      i    ii    i     ?i 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_51679619_5   2040 ACCTAGATATAATAGCTAAAACTATAAAACTCTTAAAAGAAAACACAGGG 2089
                              i  i   v                      i         i   ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_51679619_5   2090 ATAAATCTTCATGACCTTAGATTTGCCAAAAGACTC--AGCTATGTCACC 2137
                         i         i       i i  v v   vi vi  --  v    v    
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_51679619_5   2138 AAAAGCACAAGCAACAAAAGAAAAATATATATAAATTAGACTTTATAAAA 2187
                                                  -   v       i     i  v   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAA 651

  chr1_51679619_5   2188 ATTATAAACTT 2198
                             v      
  L1M4_orf2#LINE/    652 ATTAAAAACTT 662

Transitions / transversions = 2.00 (46 / 23)
Gap_init rate = 0.02 (12 / 493), avg. gap size = 2.83 (34 / 12)  

1260 14.07 7.04 0.74  chr1_51679619_51682863     2483  2752 (493)    L1M4_orf2#LINE/L1      622   908 (0)  

  chr1_51679619_5   2483 GAAAACA-AAATAAATTAAAATT-----AAATTAAAAACTTCAAAGTACT 2526
                              v - i       ii v  -----             iv--  i  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT--GTGCT 669

  chr1_51679619_5   2527 TCAAAGAACACCATCAAGAAAAT--------AATCCATGAAATGGGAGAA 2568
                               i    i         i --------  i   iii          
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_51679619_5   2569 AATATATGCAAACCACGTATCTAATAAGG-ACTTCTATCTAGAATACATA 2617
                              v      i  ii     i      -    v    i      i   
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_51679619_5   2618 AAGAATTCTTACAACTCAATAATAAAAAGACAA----CTCAATTTTAAAA 2663
                              i                           ---- i     ?v    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_51679619_5   2664 CAGGCAAAGAATATAAATAGACATTTCTCTAAAGAAGACATACAAATGGC 2713
                         ii       i  v i              i        i           
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_51679619_5   2714 TAATAAGCACATAAAAAGATGCTTGACATCATTAATCAT 2752
                         i           i          ii      ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.29 (30 / 7)
Gap_init rate = 0.02 (6 / 287), avg. gap size = 3.50 (21 / 6)  


1850 23.43 3.32 2.97  chr1_51956395_51958322      501  1072 (856)    L1M4_orf2#LINE/L1      286   859 (49)  

  chr1_51956395_5    501 AGGCACATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAA 550
                           i  i     i        i     v    ii           v   v 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_51956395_5    551 ----TACAGCCAACTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGG 596
                         ----  ii i   i    i  i     i vviv   i v   vv i    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_51956395_5    597 AAAAGGACACCCTTCTCAACAAATGGTGCTGGGATAACTAGCAAGCCACA 646
                         i    i i vi   i                   i    i vv ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_51956395_5    647 TGTAGAAGAATGAAATTGGATCCACATCACTCACCTTATACAAAAATCAA 696
                           i i         i     i  vi i v v    v           i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_51956395_5    697 CTCAACATATATCAGAGACTTAAATCTAAGACCTAAAATCATAAAAATTC 746
                              v  iv    ?    i     v     v      ii      v ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_51956395_5    747 TAGAAGATAACATTGGA--AAAACTTCTGGACATTGGCCTAGGCAAAGAC 794
                                v     v  ?--   v    vv   v    vi       v ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_51956395_5    795 TTTAT-GACCAATAAT-CCAAAAGTGAATGCAACAAAG------ATAAAT 836
                           iv -  i--  i i-       iiv v        i------   i  
  L1M4_orf2#LINE/    586 TTCTTAGAT--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_51956395_5    837 AGATGGAACTTAGTCAAA-TTAAAAAGTTTCTGCACAGCAAAAGAAAT-- 883
                          i  v i    vi     -       v   -  ii vv    i  v i--
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTA 682

  chr1_51956395_5    884 --AACAGAGTAAACAGACAACCCAGAGAGTAGGAGAAAATATTCGCAAAC 931
                         --  v i   i  v          v   i i            i     i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_51956395_5    932 TATGCATCTGGCAAAGGACTAATATCCAGAATCTACAAGGAACTCAAACA 981
                         i  ii     ii  i     vi          v  i  i      vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_51956395_5    982 GATCAGGAAGAAAAAAAAACAAAAACAAAAACAAATAATCCCATCAAAAA 1031
                         iv   iv  v     i --------------       i  v  i?    
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGA--------------CAAATAACCCAATTWAAAA 818

  chr1_51956395_5   1032 GTGGGCTAAGGACATGAATAGACAATTATCAAAAGAAGATA 1072
                         i     v     iv          v  v  v          
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

Transitions / transversions = 1.41 (76 / 54)
Gap_init rate = 0.02 (10 / 574), avg. gap size = 3.60 (36 / 10)  


3112 26.79 1.67 0.33  chr1_52307285_52309697     1025  1920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_52307285_5   1025 TGGAAAAACATTCCAGGCTCATGGATAGGAAGAATCAATATCATGAAAAT 1074
                               i i  i   v i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_52307285_5   1075 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 1124
                            v     v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_52307285_5   1125 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAAACGACTTGAAATTTCA 1173
                          v   -   v    i  -i     v v  v  iv-i  iiiv   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chr1_52307285_5   1174 TATGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAG 1223
                                viiv  ii  v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_52307285_5   1224 AACAAAGCTGGAGGCATGACGCTACCTGACGTCAAACTATACTACAAGGC 1273
                                i      vv v  i  v  ii iv     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_52307285_5   1274 TACAGTAACTAAAACTGCAAAGTATTGGTACCAAAACAGATACATAGACC 1323
                                 ii  i  v iivi   i   i iv ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_52307285_5   1324 AATGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACAACCAT 1373
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_52307285_5   1374 CTGATCTTTGACAAACCTGATAAAAACAAGCAATGGGGAAAGGATTCCCT 1423
                         i    i  i     ivv  vi  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_52307285_5   1424 ATTTAATAAATGGTGTTGGAAAAACTTGCTAGCCATATGCAGAAAACTGA 1473
                         v  i  i        i   i v    v v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_52307285_5   1474 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCGAGATGGATT 1523
                          ii         v   i     v                 i i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_52307285_5   1524 AAAGGCTTAAACGTAAGATCTAAAAC-ATAAAAATCCTAGAAGAAAACCT 1572
                          ?  i i    i      v       -      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_52307285_5   1573 AGGCA-ATACCATTCAAGACATAGGCATAGGCAAAGACTTCATGACTAAA 1621
                            ?i- v i -   iv   v v  vv       v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_52307285_5   1622 ACACCAAAAGGAAAGGCAACAAAAGCCAGAATTGACAAATGGGATCTAAT 1671
                                   v v i          vv i   v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_52307285_5   1672 TAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAGTGAACA 1721
                         i   v v  i i   i  iiivv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_52307285_5   1722 GGAAATCTACAGAATGGGAGAAAATTTTTGCAA-TTATCCATCTGACAAA 1770
                          iv  i i                 v       - i  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_52307285_5   1771 GGGCTAATATCCAGAATCTACAAGGAACTTGAACAAATT--TA------- 1811
                           i  vi          v  i  i     ivv    v i--  -------
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_52307285_5   1812 --CAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 1859
                         --    i     v  i?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_52307285_5   1860 CAAAATAAGACATTTATGTGGACAACAAACATATGAAAAAAAGCTCATCA 1909
                          v   v    i  vi vi   v   i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_52307285_5   1910 TCACTACTCAT 1920
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


3167 27.64 0.44 0.44  chr1_52348944_52355334.rev     4993  5900 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_52348944_5   4993 TGGAAGAACATTCCATGCTCATGGGTAGGAACAATCAATACCGTGAAAAT 5042
                              ii i  i     i      i v    v v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_52348944_5   5043 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5092
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_52348944_5   5093 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5140
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_52348944_5   5141 TAAGGAACCAAAAAAGAGCCCGAATCACCAAGTCAATCCTAAGCCAAAAG 5190
                           v    viiv  ii  v  v    vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_52348944_5   5191 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5240
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_52348944_5   5241 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAATAGAGATATAGATC 5290
                                 i   i    ii         i iv ii     v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_52348944_5   5291 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5338
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_52348944_5   5339 ATCTGATCTTTGACAAATCTGAGATAAACAAGCAATGGGGAAAGGATTCC 5388
                          vi    i  i     ivv  vv vi v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_52348944_5   5389 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5438
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_52348944_5   5439 GAAACTGGATCCCTTCCTTACATCTTATAAAAAATTTAATTCAAGATGGA 5488
                            ii    i    v   i   i v    v    v    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_52348944_5   5489 CTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5538
                         ii ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_52348944_5   5539 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5588
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_52348944_5   5589 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5638
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_52348944_5   5639 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5688
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_52348944_5   5689 AGGCAACCTACAAAATGGAAGAAAATTTTCGCAACCTACTCATCTGACAA 5738
                           i     i   i     i       v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_52348944_5   5739 AGAGCTAATATCCAGAATCTACAATGAACACAAACAAATTTACAAGAAAA 5788
                         i ii  vi          v  i  v    v vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_52348944_5   5789 AAACAAACAACCCCATCAAAAAGCAGGCAAAGGATATGAACAGACACTTC 5838
                          i     i     v  i?    iii          v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_52348944_5   5839 TCAAAAGAAGACATTTATGTAGCCAAAAGACACATGAAAAAATGCTCATC 5888
                           v        i  vi vi i     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_52348944_5   5889 ATCACTGGCCAT 5900
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2289 24.92 3.87 0.93  chr1_52377125_52379548.rev      725  1370 (1054)    L1M4_orf2#LINE/L1        1   665 (243)  

  chr1_52377125_5    725 TGAAAAGATATTCCATGTTCACGAACAGAAAGACTTAATATTGTCAAGAT 774
                           i        i         i i iv i               i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_52377125_5    775 GTCATTTCTTCCTGACTTGATCTACAGATTCAACACAATCCCAGTCAAAA 824
                          v  v v  i  ii v                  i       vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_52377125_5    825 TCCCAGAAAGTTATTTTATAAACATTGACAAATTGATCCTAAAATTTATA 874
                               vvivi v    ii i v        ii             i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_52377125_5    875 TGGAG--GAGAAAGACCCAGAATAACCAACACATTATTGACAGAGAAGAA 922
                             i-- vi ii           i    v   v v    v i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_52377125_5    923 CAAAGTTAGAAGCCTAACACTACCCTACTTCAAGATATACT--------- 963
                                i  i v  v     v   v i     i iv    ---------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_52377125_5    964 --GTAATCAAGACAGTGTCAAATTGGT-----GATAGACAAATAAATCTA 1006
                         --                viv i   i-----        v   i   v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_52377125_5   1007 TAAAACAGAATAGAGAGGCCAGAAAAAGACACACACAAATATAGTCAGCT 1056
                          ii  i     v     v       v i  v  i   vv   i    ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_52377125_5   1057 GATCTTTGACAAAAAAGCAAAAGCAATACAATGGATCAGAGATAGTATTT 1106
                            i  i     iiiv  v  ii v  v      ivv iii     v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_52377125_5   1107 TTA-CAAATGGTACTGG---AACTAGACATCCAACATATAAAAAAAGATA 1152
                          i -        i    ---    i  i ?   -   ii    i  -- i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCA-CATGCAAAAGAA--TG 447

  chr1_52377125_5   1153 AATCTAGACACAGACCCCTATACCTTTCACAGGAGTTAACTCAAAATGAA 1202
                           vi i   v vv   i - i   v vi   ii i             i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTC-ACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_52377125_5   1203 TCAGAAAACTAAATATAAAACACAAAACTATTAAACTGCTAGAAGATAAC 1252
                            ? i v      i   i vvi        v     vi       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_52377125_5   1253 AGTAGA---AAATCTAGATGACCTTTGATTTGGCAATGACTTTTTAGACA 1299
                          -   i---      vvi       v i  v       ii  i     i 
  L1M4_orf2#LINE/    547 A-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_52377125_5   1300 CAATACCAAAGGAATGATCTATGAAAACAAGAATTGATAAGGTGCACCTT 1349
                         ii i      i v ii v v ii   iv  i   v     iv  v  -  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC-TT 644

  chr1_52377125_5   1350 CACTAAAATTAAAAATTTCTG 1370
                           ii           i  i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.61 (98 / 61)
Gap_init rate = 0.02 (11 / 665), avg. gap size = 2.82 (31 / 11)  

 964 21.92 1.54 0.38  chr1_52377125_52379548.rev     1674  1933 (491)    L1M4_orf2#LINE/L1      646   908 (0)  

  chr1_52377125_5   1674 ATAAAAAATAAAAA-TTCTGCTCTGCAAATGACACTGTTAAGAGGATGAA 1722
                           v    v      -  i  iv  v    v      i i    iii    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_52377125_5   1723 AAGACAAGCCACAGACTGGGAGAACATACTTGAAAAAGATTTATCTGATA 1772
                                v       v        v   i   v   vv  v         
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_52377125_5   1773 AAGGTCTATTATCCAAAATGTACAAAGAACTTTTAAAAC--AATAATAAA 1820
                          i  v  vv      i   i  i        i   v   --         
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_52377125_5   1821 AAAAAAAA-AACTGGATCAAAAAACAGGCCAAAGACCTGTACAGACACTT 1869
                           i v   -   ivi  i?     ii   v  i  ii  v i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_52377125_5   1870 CACCAAAGAAGGTACACAGATGGCAAACAGGCATTATGATAAGATACTCC 1919
                          v         i  i   i     v  i i   -i    v     i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCA-CATGAAAAGATGCTCA 894

  chr1_52377125_5   1920 ACATTATTTGTTAT 1933
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (32 / 24)
Gap_init rate = 0.02 (4 / 263), avg. gap size = 1.25 (5 / 4)  


3876 18.81 4.82 0.69  chr1_52426588_52430149.rev     2200  3071 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_52426588_5   2200 TGGAAAAACATTCCATGTTCATGGACTAGAAGGCTTA---TTATTAAGAT 2246
                               i i  i             i i    i    ---  i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_52426588_5   2247 GTCAACAATGCCCATAGTGATCTACAGATTCAACGCAATCTCTATCAAAA 2296
                          v   i v v    v v                       i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_52426588_5   2297 CCCTAACCATGTTTTCTGCAGAAACAGAAAAATCCATTCTCAAATTCAAA 2346
                         i  i i iiiv    i        iv  v  iiiv  i  v       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_52426588_5   2347 TTGAATCTCAAGGGATCCAGAATAGCCAAAATAATCCTGACAAACTACAA 2396
                          v   viv       i               i    i   v   vv v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_52426588_5   2397 CC---CCAGAGGACTCACATTCCATGTTTTCAAAACTTACTATGAAGCTA 2443
                          v---iii           i i viiv               ii      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_52426588_5   2444 TGGTAATCAAAACCATGTGGTACTGACATTAAAGACAGACATAAAGACCA 2493
                         ii        i  vi          i   -  i  i       v   i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATCA 299

  chr1_52426588_5   2494 ATGGAATAGAA--AAAAGCCCAGAAATAAACTCTCACTTATATGGTCCAG 2541
                                    --i i  i            i vi  v v       v v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_52426588_5   2542 TTAGTTTTGACAAGAGTGCCAAAACCATTCCATAGGAACAGAACAGTCTT 2591
                          v v   i      i       i       v  i  i v    i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_52426588_5   2592 TCCAACAAATGATACTGAGAAAACCAGATATCCACATTCAAAAGAATAAA 2641
                          i         i i   i  v   ii    ?      v         i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_52426588_5   2642 ACTA-------AGCTAATACTATACACAAAAAATTAACTCAAAATGGATA 2684
                         ii i------- v  v i  i   i       -                v
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATC 498

  chr1_52426588_5   2685 AAAGACCTAAACGCAAGCACTAAAACTGCAAAACACTTAGAAGACAACAT 2734
                          ?         i i   vi        ii     v         v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_52426588_5   2735 AAGGGAAAGACTTCATGACATCAAATTTGGAGATGATTTCTTTGATATGA 2784
                          i ? v  iv    i    v iiii  v  vi   i      v       
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_52426588_5   2785 CACCAAAAGCACAGGCAACAAAAGAAAA--TG--TAAGTTGGAGTTCATC 2830
                                      i              -- i--   i     v      
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_52426588_5   2831 AAAATTAAAAACTTTGGTGCATCAAAGGACA------ACAGAATGAAAA- 2873
                                        v    v          ------ v i i      -
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_52426588_5   2874 ---ACCCA-AGAATAAGAGAAAATATCTGCAAATCATTTATGTGATAGGA 2919
                         ---     -     ii          i          v   v     i i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_52426588_5   2920 GACT-GAATT----ATATATAAAGAGCTCT-AAAACTCAACAACAGAAA- 2962
                             - v  i----           i    - v       i  i i   -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_52426588_5   2963 ACA--CAACCCAATTTAAAAATGGGCAAAAGACCTGAATAGACATTTCTC 3010
                            --i         ?             i  ii                
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_52426588_5   3011 CAAAGATTTTTAATATAGA---GACCAGTAAGTACATGAAAAGAGGCTCA 3057
                               v----i     v --- i   i    i           v     
  L1M4_orf2#LINE/    849 CAAAGAA----GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_52426588_5   3058 ACATCACTAACCAT 3071
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (103 / 57)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.67 (48 / 18)  


3158 24.49 3.71 1.69  chr1_52630631_52633148     1151  2040 (478)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_52630631_5   1151 TGGAGAGATATTCCATTATAATTGACAGGAAGACTCAAAATTGTCAAGAT 1200
                             i      i    vv v  v  iv        i  v     i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_52630631_5   1201 GTCAGTTCTTCCCTACTTGGTCTCCAGATTCAATTCAATCCCAATCAAAA 1250
                          v  i v  i   v v   i   v         iv       v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_52630631_5   1251 TTCTAGCAAGTCATTTTGTGGATATAGACAAACTGATTCTAAAGTTTACA 1300
                          i i   viviiv     ii  v  v     i     i     i  i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_52630631_5   1301 TAGAGAGGCAAAAGACTCAGAATAGCTAACACAATATTGAAGGAGAAGAA 1350
                          i  i v    ii   i         i  v     v     ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_52630631_5   1351 CAAAGCTGCAAGACTGATGCAACCCAACCTCAAGAGTTATTATAACACTA 1400
                              i  v i    v ii vv     ii    i v   i  i  vi   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_52630631_5   1401 CTATAAATAAGAGAGTATGGCATTGGTGAAATAATAAA----TAAATCAA 1446
                          vi   vi    v   i   i i   iiv  vi   i ----  i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_52630631_5   1447 TGCAACAG--TGGAGGGCCCAAAAGTATATAAATATAGTACATAAATATA 1494
                           v  i  -- v   i i   i  ----     ivi -     v--   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAA----ATAAACCCA-TACATT--TATG 343

  chr1_52630631_5   1495 GTCAACTGATCCTTGACAAAGGAGCAAAGACAATACAGTGGAGAAATAAT 1544
                              i    ii i     i  v  v     v  v  i   i    v   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_52630631_5   1545 ATTCTTTTCAACAAATGGTATTGAAACAAATGAACATCCACACGCAAAAC 1594
                          v                 ii  ii    v  i i ?     i      v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_52630631_5   1595 AATGAATCTAGGCATAGACCTTATACCGTTCACAAAAATTAACTCTAAAT 1644
                               vi i i vivv    i i   i vi              v    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_52630631_5   1645 GGCTCACAGGCCTAAATGTAAAA----------TAAAACTCCTGGAAGAA 1684
                           v   ?  i           i ----------        i i      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_52630631_5   1685 AACACAAGAGAAAATCTGTATGACCTTGAGTATAGTGATATCTTTTTAGA 1734
                             i i ? v      vii        i  vvi ii  ivi  i     
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_52630631_5   1735 CACAACACCAAAGGCAAGAGCTATGAAAGAAATAATTGACAAGATGGACT 1784
                         i ii        i   vi   v ii       v   v  i  iv      
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_52630631_5   1785 TTACTAAAATTAAAATTTTCTGCTCTGCAAAAGACAACGTCAAGGGAATG 1834
                          i ii          vi  i  iv  v    i    vii     ii i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_52630631_5   1835 AAAAAACAAGCCACAGACATGG-AGAACATAGTTGCAAAACACACATCTG 1883
                             i    v       -    -    v   v       v  i i     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGA-ATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_52630631_5   1884 ATAAAGGACTATTATTCAAAATACACAAAGAACTCCTTA-AACTCAACAG 1932
                             i     vv   i  i    i i         -   -       i i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTC-TTACAACTCAATAA 791

  chr1_52630631_5   1933 TAAGAA----AATAACCTGTTTAAAAAAATGGACCAAAGA---------- 1968
                            i  ----       iiv  ?     -   i v  i  ----------
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGA 840

  chr1_52630631_5   1969 -ACCTCACCAAAGAAGACATATGAATGGCAAAATAAGCATATGAAAAGAT 2017
                         - ii  v          i   ii      v  -      i          
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGAT 889

  chr1_52630631_5   2018 TTCCGCATAATGTCATCAGGGAG 2040
                         ----  vi  ii   ????????
  L1M4_orf2#LINE/    890 ----GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (138 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.20 (48 / 15)  


 615 25.16 2.58 0.00  chr1_52676203_52679557      454   608 (2747)    L1M4_orf2#LINE/L1      112   270 (638)  

  chr1_52676203_5    454 TTTTTCACAGAAATATAAAGATCAATCCTAAA-TGTACACAGACTCTCAA 502
                              ii       vv v iiiii        - vi i ii  vviv   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_52676203_5    503 AGGACCCCAAATAGCCAAAACGATCCTGACAAAGAA---CAAAGCTGGAG 549
                         i      vi            i   i   v      ---     i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_52676203_5    550 GATTCACACTTACTGGCTGCAAAACGTACTACAAAGCTATAGTAATCAAA 599
                           i        v iiii v      v             i         i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_52676203_5    600 ACAACATGG 608
                            iii   
  L1M4_orf2#LINE/    262 ACAGTGTGG 270

Transitions / transversions = 2.25 (27 / 12)
Gap_init rate = 0.01 (2 / 159), avg. gap size = 2.00 (4 / 2)  

 209 20.00 0.00 0.00  chr1_52676203_52679557     1240  1284 (2071)    L1M4_orf2#LINE/L1      278   322 (586)  

  chr1_52676203_5   1240 ATAAAGACAGACATGTAGACCAATGGAATCAAACAGAGAGCCCAG 1284
                             i  i      i    i         vi  iv     i    
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.00 (0 / 0)  

1315 14.73 0.00 0.45  chr1_52676203_52679557     1618  1841 (1514)    L1M4_orf2#LINE/L1      304   526 (382)  

  chr1_52676203_5   1618 AAAAGAACAGAGTGCCCAGAAATAAACCCTGGCATGTATGGTCTAATGAT 1667
                           v    iv   v i              vvi   v       v v    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_52676203_5   1668 TTTTGACAAGGGTGCCAAGAACACTCAATGGGGAAAGGACAGTTTTTTCA 1717
                            i                v  i             i i   i      
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_52676203_5   1718 ACAAATGTTGCTGGGAAAACTGAATATCTACATGTAAAAGAATGAAGCTG 1767
                                v        v     i   ? i     i            i  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_52676203_5   1768 GACTCTGACCTTAGATCATATACAAAAATTAACTCAAAATGGATCAAAGA 1817
                            i iv    i v i                              ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_52676203_5   1818 CCTAAATGTCAGAAACTAAAACTA 1841
                                  v   -i         
  L1M4_orf2#LINE/    504 CCTAAATGTAAGA-GCTAAAACTA 526

Transitions / transversions = 1.21 (17 / 14)
Gap_init rate = 0.00 (1 / 223), avg. gap size = 1.00 (1 / 1)  

1875 16.19 2.09 0.26  chr1_52676203_52679557     2480  2862 (493)    L1M4_orf2#LINE/L1      519   908 (0)  

  chr1_52676203_5   2480 TAAAATCATAGAACTCCTAGAAAAAAACAGAAG-GTAAGT-TTCATGACA 2527
                              ii   i     i     i      v i -    i -   i    v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_52676203_5   2528 TTGGATTTGGCAATGATTTCTTGAATATGACACAAAAGACATAGGCAACA 2577
                             i  v       i      ii         v   ii  i i      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_52676203_5   2578 AAAGTAAAAGCAGATAAATTAGACTGGA-CGAAATTTAGAACTTTTGTTC 2626
                             v    ii         i    vv - i     v i         v 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_52676203_5   2627 ATCAAAAGACACTACTGACAGAGTAAAAAGACAACCCACAAAATGGAAGA 2676
                         v     i       iii v i   i               i     i   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_52676203_5   2677 ACATATTTGC-AATCATGTATCTAATAAGGGATTAATATCCAGAATATAT 2725
                          v        -      i     i        i vi              
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_52676203_5   2726 AAATAATCCCTTA-AACTCAACAATAAGAAAACAAACAACCCAATTCAAA 2774
                            v  - i    -       i     i  i     i         ?   
  L1M4_orf2#LINE/    769 AAAGAA-CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_52676203_5   2775 AGTGAACAAAGGATTTGAATAGACATTTCTCCAAAGA---TATACAAATG 2821
                          i  ii                               ---          
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_52676203_5   2822 CCAAATAAGTACATGAAAAGATGCTAAATACCACTAATCAT 2862
                         v v      i               v  i i  ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.59 (44 / 17)
Gap_init rate = 0.02 (7 / 390), avg. gap size = 1.29 (9 / 7)  


1097 18.07 1.68 3.36  chr1_52719553_52723785     1923  2160 (2073)    L1M4_orf2#LINE/L1       34   267 (641)  

  chr1_52719553_5   1923 CTTACTGTTGTTAAAATGTCCACACTACCCAAAGCAATCTAAACATTTAA 1972
                             v i       i   v v i   v      vii     v v   i  
  L1M4_orf2#LINE/     34 CTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAA 83

  chr1_52719553_5   1973 TGCAATCCCTATCAAAATTCCAATGACATTTTTTGCAGAAAT--ACCAAA 2020
                         i                 i   iivi v              --  --  
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC--AA 131

  chr1_52719553_5   2021 ATCAATCCTAAAATTCACATGGAATCTCAAGAGACCCCAAATAGCCAAAA 2070
                         iiii             i      viv    i     vi           
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_52719553_5   2071 --GTCTTGACAAAGAAAAACAAAAGTGGAGGACTCATACTTCCTAGTCGC 2118
                         --i      v      i      iv           i      i i iv 
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_52719553_5   2119 AAAACTTACTACAAAGCTACAATAATCAGGCTGGGCACAGTG 2160
                                              i      i ------      
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAG------ACAGTG 267

Transitions / transversions = 1.87 (28 / 15)
Gap_init rate = 0.02 (4 / 234), avg. gap size = 3.00 (12 / 4)  

1785 18.69 3.90 6.57  chr1_52719553_52723785     2419  2905 (1328)    L1M4_orf2#LINE/L1      223   696 (212)  

  chr1_52719553_5   2419 CTCCATTTCAAAAAAAAA-AAAAAGCTACAGTAATCAAAATAGTATGGTA 2467
                          i v         vvv v- v                 i i   i     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_52719553_5   2468 TTAGTATAAATACATACAGACAGACCAATGGAATCAAAC--AGA--CCAG 2513
                         i i i    iv i v   v i   i         vi  i--   --    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_52719553_5   2514 AAATAAACCCTCACATATGTGGTCAAATAATTTTTAACAAGGATGACAAA 2563
                                   vi    v i       v i     ii      i  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_52719553_5   2564 GCCATTCAATAGGGAAAGGACAGTCTTTTCAGCAAATGGCGCTGGGAAAA 2613
                         i         i       i i          i       i       v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_52719553_5   2614 CTGGTAATCCATCTGCAAAAGATTGAATTTTGACC-------------AT 2650
                             vv ?   iv         v    v  v    -------------  
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_52719553_5   2651 AAACAAAAATTAACTCAAAATGGATCAAAGACCTAAGAAACCTAAACTTG 2700
                          v                         ?        i-----------  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA-----------TG 511

  chr1_52719553_5   2701 TAACTATAAAACCATAACTAAGAAACATAAAACTATAAGGCTCTTAGACG 2750
                            -------------------i i -           ii        v 
  L1M4_orf2#LINE/    512 TAA-------------------GAGC-TAAAACTATAAAACTCTTAGAAG 541

  chr1_52719553_5   2751 AAAACAAAAGGGAAAAGCTTCATGACACTGGAGTT-GGCAATTATTTGTT 2799
                               v i ? v   v    i    -  v i   -      vi   v  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTT 590

  chr1_52719553_5   2800 GAGTATGACACCAAAGGCACGGGCAACAAAAGAAAAAATGGACAAACTAG 2849
                         iii            i    ii                 i  i   i i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_52719553_5   2850 ACTGGCTGAAAATTTAAAACTTTTGTTAATCAAAAGACACTATCAACTGA 2899
                            vvv v      v           vvv     i           vvi 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_52719553_5   2900 GTAAAA 2905
                           i   
  L1M4_orf2#LINE/    691 GTGAAA 696

Transitions / transversions = 1.26 (49 / 39)
Gap_init rate = 0.02 (9 / 474), avg. gap size = 5.67 (51 / 9)  

 985 15.32 5.11 5.11  chr1_52719553_52723785     3506  3740 (493)    L1M4_orf2#LINE/L1      674   908 (0)  

  chr1_52719553_5   3506 AAGACTCTGTCTCAAAAAAAAAAAAAAAAGTAACCCCACAGAACAGAATG 3555
                          i   v  i  ----  i   ivi    iii     ------        
  L1M4_orf2#LINE/    674 AGGACACTATC----AAGAAAGTGAAAAGACAACCC------ACAGAATG 713

  chr1_52719553_5   3556 GAAGAAAATATTTATAAATCATGTATCTGATAAGGGACTAATATCCAGAA 3605
                          i           ii       i                vi         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_52719553_5   3606 TATATAG----------CAACTCCAAAAAATGAACAAA-AAATGACCTGA 3644
                               i----------      --  v   i  v i -    i   ii 
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTC--AATAATAAAAAGACAAATAACCCAA 811

  chr1_52719553_5   3645 TTTGAAAATGGGCAAAGGGCTGGCATAGACATTTCTCCAAAGAAGATATA 3694
                           ?i              ii v v                          
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_52719553_5   3695 CAGACGGCCA-CAAGCACGTGAAAAGATGCTGAATATCACTAATCAT 3740
                           i i     -i      i            v  i    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.38 (27 / 8)
Gap_init rate = 0.03 (6 / 235), avg. gap size = 4.00 (24 / 6)  


1832 23.37 6.05 3.92  chr1_52831477_52833498      491  1102 (920)    L1M4_orf2#LINE/L1      122   746 (162)  

  chr1_52831477_5    491 AGATAGATAAGCTAATTCTCAAATTTATATATAGAGAGACAAAGGAACTA 540
                          i  v  i     i  i  v     i    i--  i vi   i   v i 
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATG--GAAATGCAAGGGACCCA 169

  chr1_52831477_5    541 GAATAGCTAAAGTAATACTGAAAAAGAATAATGAAGTTGGAGGAAATCAC 590
                                i   ii   vi          v  ii           v-    
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC-TCAC 218

  chr1_52831477_5    591 ACTACTCAATTTTAAGACTTATTGTATAGCAACAATAATAAACAGTAAGG 640
                            v i      i  i     i ii v   v   i    v  --------
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA-------- 260

  chr1_52831477_5    641 AGGATAGTGTGGTATTGGAGGAGGGACAGACACATGCATAGATCAA---A 687
                         --  i         i   viv i   i     i  ----       --- 
  L1M4_orf2#LINE/    261 --GACAGTGTGGTACTGGCATAAGGATAGACATAT----AGATCAATGGA 304

  chr1_52831477_5    688 ATA----TG---GTCCAGAAGTAGACTGACATCAT--AAGGTTGTCCAAC 728
                            ----  ---        i  i  iv i -   -- v   ----   i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGT----CAAT 349

  chr1_52831477_5    729 AGATTTTTGATGAAGGTGCAAAATCAATTCAACTGGGGAAGA-TAGTCTT 777
                         v      i  ii i     v  iv v      iv   i    -       
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_52831477_5    778 TTCAATAAATGGTGTTAAAACAACTAAACTTCCATAAGTAAAA-AATAAA 826
                              i        i iii      ii iv?   i v i    -   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_52831477_5    827 CCTTTACCTAGATCTCACACCTTGTACAAAAATTATCTCAAAA------- 869
                         vi vv   ivv i        v i           v       -------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_52831477_5    870 AAGATCTAAATGTAAACCAA--AAAACTCTAACACTTTTAGAAGAAAACA 917
                         ?   i          i-- i--      v   v   i             
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAG--AGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_52831477_5    918 --GGGAAAAATCTTCATGACATGCGGTTATGCAAAGAATTCTTAAACAAG 965
                         --  ?iv        i    v vv     v    v iv      i i v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_52831477_5    966 ACATCAAAAGCACAAT--ACATTTTAAAAAA--GATAAGCCAGTATTCAT 1011
                            i           v--   vvvv      --     iiii vv     
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_52831477_5   1012 CAAAGTTCAAAATTTTAATGCTGTGAAAGATCCTGTTAAGAGGATGAAAA 1061
                             i  v    i   vi    vii  i  iv  i i    iii      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_52831477_5   1062 GGCAAGCCTCAGACTGG-AGAATATATT-------CACATATTTGACAA 1102
                          i   v  v    v   -    v     -------  i    i   i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

Transitions / transversions = 1.59 (86 / 54)
Gap_init rate = 0.03 (20 / 625), avg. gap size = 3.05 (61 / 20)  

 376 21.88 1.04 1.04  chr1_52831477_52833498     1426  1521 (501)    L1M4_orf2#LINE/L1      759   854 (54)  

  chr1_52831477_5   1426 CAAAATATATAAAGAACACCCTA-AACTCAACATTAAGAAAACAAATGAT 1474
                           i              -i i  -       i v   i  i      i i
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAAC-TCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_52831477_5   1475 CCCATTAGAAAATGAGCAGAAGACTTGAACAGACACTTCATTAAAGA 1521
                           v   ?i      i   i i  i     i     i   vii     
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

Transitions / transversions = 5.67 (17 / 3)
Gap_init rate = 0.02 (2 / 96), avg. gap size = 1.00 (2 / 2)  

 290 20.00 0.00 0.00  chr1_52831477_52833498     1856  1920 (102)    L1M4_orf2#LINE/L1      844   908 (0)  

  chr1_52831477_5   1856 TTTTTGAAAAAGGATATATAGGTGGCAAATAGGCACATGAAAATATGTTC 1905
                           i iv   i i      i ii    v    i           v   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_52831477_5   1906 AACTTCATTAGTCAT 1920
                            v   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.00 (0 / 0)  


3256 26.65 0.66 0.66  chr1_53181856_53188232     4977  5884 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_53181856_5   4977 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATGAATATCGTGAAAAT 5026
                              ii i  i     i      i v      v v     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_53181856_5   5027 GGCCGTACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGT 5076
                            vi    v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_53181856_5   5077 TACCAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTAA 5124
                          v   iivi    i  ii     -   -- v  i  - iii    i  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_53181856_5   5125 TATGAAACCAAAAAAGAGGCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5174
                             i  viiv  ii  vv v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_53181856_5   5175 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5224
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_53181856_5   5225 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGACC 5274
                                 i   i    ii         i  v ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_53181856_5   5275 AATGGAACAGAAC--AGAGCCCTGAGAAATAATACCACACATCTACAACC 5322
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_53181856_5   5323 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGGAAGGATTCC 5372
                          vi    i  i     ivv  v   i v  vvv       i   i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_53181856_5   5373 CTATTTAGTAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5422
                           v  i ii   i          v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_53181856_5   5423 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5472
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_53181856_5   5473 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5522
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_53181856_5   5523 CTAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGACT 5570
                         v    ?i- v i -   i- i  v i  i- i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr1_53181856_5   5571 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5620
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_53181856_5   5621 AATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAC 5670
                         v  i   v v  i i   i  ii vv    i  v    i  vv i   iv
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_53181856_5   5671 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACCTATCTGAG 5720
                          v  i     i                 v       vii iv       v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_53181856_5   5721 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5770
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_53181856_5   5771 AAAATCAAACAACCCCATCAAAAAGCGGGAGAAGGATATGAACAGACACT 5820
                            iv    i     v  i?    ii   vi      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_53181856_5   5821 CCTCAAAAGAAGATATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5870
                         i   v           vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_53181856_5   5871 TCATCACTGGCCAT 5884
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (146 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


 820 26.52 22.82 3.43  chr1_53408370_53409919.rev      313  1070 (480)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_53408370_5    313 AAATATGTATCGTTTTTGTGGATGGCAAGATTCAGTATCATAAAGATGTC 362
                            v  i vi i v  ii     v v    i i i   ii v      v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_53408370_5    363 AGTTTTCAACAAAGTAATTTATAAATTCACTCTTAATTCAAATAAAAATC 412
                          i vi  vv    v i  i  i i     v- vi   i vv  v      
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAAATC 102

  chr1_53408370_5    413 GCAGTAGGATTTTTTTCCCTTTAGAATCAAATAGAATGAGCATTAAATTC 462
                         v   iv vv      v -----    vivi i iiv   v v v      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGC-----AGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_53408370_5    463 AT--GGAAAATCAGAGG--CAAGAGTAGCCAAAATAAT------------ 496
                           --     vv  ii  -- v   i         i   ------------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_53408370_5    497 --AC-----TGGA---------------AATTTC--------TTACAAAG 516
                         --  -----    ---------------      --------i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_53408370_5    517 CTGTGGTCATT--TGTAGTATGATATTGCCTCGGGAATTGACAGCTAAAC 564
                           iii  v  i--vii   i  i  i  v viii i  v    vv  i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_53408370_5    565 CAATGGAACAGAATAGAGAGCCCAGAAACCAACCTATGAATATATGGAAA 614
                                 i     v     i       iv    i  iv  v     vv 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_53408370_5    615 CTTAGAAAAGTGTGCTACAGAGGTG----GACTTTCACATT-AATGGGAA 659
                         v  -  ---- v v v   ii    ----   -----    -      i 
  L1M4_orf2#LINE/    348 ATT-GA----TTTTCGACAAGGGTGCCAAGAC-----CATTCAATGGGGA 387

  chr1_53408370_5    660 AAGAACGAATTATTTAACAAATTGTACCAGGACAGCTG-------ACA-- 700
                              iiivi v  i       v  i ii     i   -------   --
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_53408370_5    701 -------ATGTATTTATGGA---------------ATAT-------TT-- 719
                         -------   v v  --   ---------------    -------  --
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTT--GGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_53408370_5    720 -TTAAAATTAGGCCATAGA----AAT----------------CAAAAATT 748
                         - i     -i ii  ?   ----   ----------------i    v i
  L1M4_orf2#LINE/    486 CTCAAAAT-GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_53408370_5    749 TTA-AACAGAATATAGACTTGTATTATTTC-------TGGGT-AGAGAAG 789
                            -  v i  i    i?v iv  i--   -------     -  iv  v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAAT 582

  chr1_53408370_5    790 GAGTTTTTAAA----ACTCCTTAAG-------------GGGTAAGATTGG 822
                          iv  i   i ----  v  vv   -------------i iv  i  v i
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_53408370_5    823 TAAATTTGACTTC-------TTTACAACTT--AGGTTTGACAAAAGA--- 860
                               v      -------  v v     --iv i  --    i  ---
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACAC 680

  chr1_53408370_5    861 TGGCAAGATAAAGTTGAAAGATAAGCCATAGACTGGAAGAAGTTATCTGC 910
                          iv     --    vi     i  v   i   v   i    iv   i   
  L1M4_orf2#LINE/    681 TATCAAGA--AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_53408370_5    911 AAAACATAAAACTGGCAAGAGTTCTCCATCCAGAATATATAAAGAA---T 957
                            v    v v   ii   i vii vi                   --- 
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_53408370_5    958 TACAAAT---TAATAAAAAGAC---TGTCCCG-TGGCAGAATGTGCAAAG 1000
                              v ---            --- iv   i- v?v i    v      
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_53408370_5   1001 GTTATGAATAGATAACTTAC-----AAGATCAAACAAGTGGCTAATA--- 1042
                          v v        i vi iv -----     - v    i    i    ---
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGAT-ATACAAATGGCCAATAAGC 877

  chr1_53408370_5   1043 ---TGAAAAGATTTACGGCTTCATTTGTAAA 1070
                         ---         viv ii v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (107 / 91)
Gap_init rate = 0.05 (41 / 905), avg. gap size = 4.85 (199 / 41)  


 799 31.85 12.30 2.77  chr1_53430082_53431702      300  1128 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_53430082_5    300 TGAAATAAATAGGCCACATTTCTGGATGGGAAGCTTTAATATAATAAAAA 349
                           i  - i   vv   ii  iv     v     vi       vi v  i 
  L1M4_orf2#LINE/      1 TGGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_53430082_5    350 -GGTATATTCTCCTCACATAAACTCATATATCTAAAACAATCTTGATAAA 398
                         -  i -  v    i  v  vi iii i v  ii  vi     iiv  v  
  L1M4_orf2#LINE/     50 TGGCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_53430082_5    399 AACTTCA-CCAAAATTTTTATAGAA-TTGATAAGATTATTCTGAAGTTCA 446
                           iii  - iivvv     ii    -    i   v v  i  i  i    
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_53430082_5    447 CCTAGAAG----AGAAACT--GAATA---AAAATAGC--TGA----GAAG 481
                         iv i   i----  ii  i--     ---    i ii--   ----    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_53430082_5    482 AT----GTTGTGAG-------------------CATAACATATCATGAAG 508
                          v----    -   -------------------  v   v  ii ii   
  L1M4_orf2#LINE/    199 AACAAAGTTG-GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_53430082_5    509 TTGTGCTAAT------AGTATG---------TAGGAATA----TATAAAT 539
                         i iiiv    ------   i  ---------  i i   ----    i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_53430082_5    540 CAGTGAAGGAAAATAAACTGCTTAGACGCAAATCAAAGTACGTATGGG-A 588
                           i  i iv i   vi vv iii   vii   i v vii iv     v- 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_53430082_5    589 GGTAGTTTATAATAAAGATGACGTG-CAAGTCA--GGAGAGAAGTATGGA 635
                         iv ii   vii i  i i  v iv - v v   --  i  -   v  i v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATAGT 396

  chr1_53430082_5    636 TTATTCAATGA-TGGTTTTGGGGAAACTAGACAGGTATATAGAGAAAAAA 684
                         i v     ii -    vi    iv    i  i ?vi i  iv i  i  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_53430082_5    685 ACAGTTAAATCTCTACCTCATACGATACTCTAAAATTTAAATTCCAAATA 734
                         iv    ii i i        i  v   iv v      --  i  v    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATT--AACTCAAAATG 494

  chr1_53430082_5    735 GATTAATATCCTAATACTAAAA---AAAAGTTTAAAG----TAGAAAAGA 777
                            i ?viv     vvv   i ---    v v    i----     i --
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA-- 542

  chr1_53430082_5    778 AAAACATCAGGAG-ATATTTTAATAAGTTAGAGTGAGGC--TGGCCTTCT 824
                         -      -   ? - v  i  vi i vi v i  v    --   i-    
  L1M4_orf2#LINE/    543 -AAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCT 589

  chr1_53430082_5    825 TAAGCAAGACACAAAACCCAGAAATCTTAAAAGA-----TTGACAAATCT 869
                           iii v     v   vv  v  iivvi      ----- v  i    iv
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_53430082_5    870 GAT--------ACTTAAAAGTTTCATATTTATGCATGGCAAAAGATACCA 911
                           i-------- v      ii  -----  i   v --    i  i  i 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTT-----TTGTGCTT--CAAAGGACACTA 682

  chr1_53430082_5    912 TAAACAAACTTTAAAACCAAATGTCAGACTGGAAGAAAATATTTGTAA-- 959
                          v  v   v vv   iv   vivv    v   i            i  --
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_53430082_5    960 CATATATTT--TAAAGGTTTAATATTTGTCATGTATAAATATTTCT-ATA 1006
                                i --   i  vi vi   iiivv  i      v vi   - i 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_53430082_5   1007 A----ATAAGAAAAAGATAG-----CCAATAGAAAAATAAGAAAAGACTG 1047
                          ----    v       i i-----     v?      ii v    iv v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_53430082_5   1048 TGAGTGGGCGATTCATAACAGATAAAATATAAGTAAAGGGGCTGATAAGC 1097
                            i i i iv   vi--  i v  i     --i   v  - ii      
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTC--CAAAGAAGATATA--CAAATGG-CCAATAAGC 877

  chr1_53430082_5   1098 TTACGAAAATATACTCTACCTCACAGGGAAA 1128
                         vi i     v  i   v  v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (156 / 104)
Gap_init rate = 0.05 (41 / 908), avg. gap size = 3.05 (125 / 41)  


2063 25.12 5.65 1.10  chr1_53531526_53533692.rev      502  1138 (1029)    L1M4_orf2#LINE/L1       29   694 (214)  

  chr1_53531526_5    502 GAAGACTTGATATGGTTAAGATGTCCATTCTCCCCAAAATGACCTATCGA 551
                                 i    v         v v  v         v   i   iv  
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chr1_53531526_5    552 TTCAACACAATCCCTATTATAGTAAGAGTAGGCCCTTTTAAAGAAGTAGA 601
                               i          i v i vvv  iv v ii    iv    i v  
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chr1_53531526_5    602 CAAGTTGATCTGAAAATTTACGTGAGAATTTAAGC-ATCCAGAATAGCTA 650
                             i     iv      i ii  ii   vi   v- i          i 
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr1_53531526_5    651 AAACAATCTTGAAAATGAAGAACAA-GTTTGAAGA---ACACTGCCTGAC 696
                                        v         -   v  i  ---     v  ii i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_53531526_5    697 TTAACGACTTACTATAAAGCTACAGTAATCAAGACAATGTGATATCAATG 746
                           v vi        i                     i    i  iiiiii
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_53531526_5    747 TAAGCATATGCAAATAGAACAAAGGAACAGAACGTAAAATTCAGAAATAG 796
                             v   vi  v     v   v    i    ivv i i i        i
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_53531526_5    797 ATCTCATGTAT--ATGGT----TGAGTTTCAACCAAAGGACCAAAACAAT 840
                          i -   ii  --     ----   v    i  v ii vi    i  v  
  L1M4_orf2#LINE/    329 ACC-CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_53531526_5    841 TTACCGGGGAAGGAAC-TTCTTTTTGAACAAATGGTGTTGGAACAACTGT 889
                          i vi      i   i-v      i-           i   i       v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTC-AACAAATGGTGCTGGGACAACTGG 426

  chr1_53531526_5    890 ATATCGACATGGGAAA--ATG---TTAAAGTCCTTATCTCACTCCAAACA 934
                            ? v     vi   --   ---  ii -i  i  i     v   v i 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGA-CCCCTACCTCACACCATATA 475

  chr1_53531526_5    935 CAAACATTAATTTATA-TGGATCGTAGAAATAAATGAAAAAGCCATAATC 983
                             v     i i v -      i?   vv      v  i   i v  ii
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_53531526_5    984 ATAAAATTTCTAGGTAAAAA-ATAGA---ATGTTTTTGGGACGCTGAGGT 1029
                               i ii   ivi    -    i--- vi i  i v   vi  i v 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_53531526_5   1030 AAGCAAAGATTTCTTAGAAGTCAGGACAT-AAAA---TAACCA-TAAAAG 1074
                          i    v i         ---i v    i-    ---i  v  -i     
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGA---TATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_53531526_5   1075 AAAACAATTTATAAATT--------TTGAAATTAGACACTTCTGC-CATC 1115
                             -   vv       -------- ii      i v    i  i- v  
  L1M4_orf2#LINE/    623 AAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_53531526_5   1116 AAAAGACATCATTGAAAAAATGA 1138
                            i    ii  ii i   i   
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGA 694

Transitions / transversions = 1.72 (100 / 58)
Gap_init rate = 0.03 (21 / 666), avg. gap size = 2.05 (43 / 21)  

 789 18.00 1.20 12.00  chr1_53531526_53533692.rev     1427  1676 (491)    L1M4_orf2#LINE/L1      686   908 (0)  

  chr1_53531526_5   1427 AGAGAATGAATAGGTGAGTTACAGATTGGTAGAAAATATTCACAAAACAT 1476
                            i i    v  iii vii     v   v          ii    v   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_53531526_5   1477 AAATACGTGTATGTCTGTGTGTGTGTGTGTGTGAGACAAAGGACTGGTAT 1526
                          ---------- i    ------------------ i  i     v    
  L1M4_orf2#LINE/    736 A----------TATCTG------------------ATAAGGGACTTGTAT 757

  chr1_53531526_5   1527 CCAGGATATATCAAGTACTCCTACAACTCAATAATTAAAAAGATAAACAA 1576
                             i      v   v    i              -       i   i  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAAAAGACAAATAA 806

  chr1_53531526_5   1577 CCTAATTTTTAAGTTAGGCCAAAGATTTTCATGGACA---CTTCACAAAA 1623
                           i    ?vv  i -i   v  i     vv  i    ---  i  v i  
  L1M4_orf2#LINE/    807 CCCAATTWAAAAAT-GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_53531526_5   1624 GTTATGCAAATGGCCAATAGGCAAATGAAGAAATGCTCAACACCATTAGT 1673
                          v   i             i   v     i i          i  ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_53531526_5   1674 CAT 1676
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.75 (28 / 16)
Gap_init rate = 0.02 (5 / 223), avg. gap size = 6.60 (33 / 5)  


2991 12.14 6.54 22.04  chr1_53670566_53673549.rev     1423  2493 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_53670566_5   1423 AATGACAGCCCATGTTCATCAATTAGGAGACTTAGTATTATTAGGATAGT 1472
                           v  i v           vi   i i       i    i   i   i i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_53670566_5   1473 AGTATTCCCCAGTTTGATCTACAGATTCAGCACAATCCCTCTCAAAGTCC 1522
                          i  i      iv                i i        v     i   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_53670566_5   1523 CAGATGGATTTTGTGCAGAAATTGACAATCTGATCATGACATTCATATGG 1572
                            v  vv    v               v      v i v          
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_53670566_5   1573 AAATTCAAAGGACCCCGAATAGCCAAGACAATCTACAAAAAGAAGAACAA 1622
                             v   i      v          i       vv              
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_53670566_5   1623 AGTTGGAGAACTCACACTTCCCAATTTCAAAACTTACTTTAAAGCT---- 1668
                                 i                             vi      ----
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_53670566_5   1669 -----------------TATAGGCATAAAGAAAGACCTGTAG-------G 1694
                         -----------------  iv       i  v    v i   ------- 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_53670566_5   1695 AATAGAATTGAGAGTTCAGAAACAAACCTTCACATTTATGGTCAATTGAT 1744
                                        i      i     ivi                   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_53670566_5   1745 TTTTAAT--GAGTGCCAAGATAATTAAATGGAGAAAGAATAGTCTTTTCA 1792
                            ii i-- i         iv   v     i                  
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_53670566_5   1793 ACATATGGGTACTGGGACAACTGGATATCCCCATGCAAAAGAATGAAGTG 1842
                            v    - i                ?  v                  v
  L1M4_orf2#LINE/    404 ACAAATGG-TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_53670566_5   1843 GGATCCCTACCTCATATTATATGTAAAAATATGCTCAAAGTGGACCAAAG 1892
                            i          i ii    ii      vvi      i    i  ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_53670566_5   1893 ACCTAAAT--AAAAATTAAAACTATAAAACTAAGAAAAAAAATAAGAGTG 1940
                                 --  i ii               -------------------
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACT------------------- 533

  chr1_53670566_5   1941 AATATTTGTGCCAGCCTGGGCAACATGGCAAAACCCCGTCTCTACAAAGA 1990
                         ----i  ----------------------------------------   
  L1M4_orf2#LINE/    534 ----CTT----------------------------------------AGA 539

  chr1_53670566_5   1991 ATATAAAAATTAGCCAGGCGTGGTGGTGTGCGCCTATAGTCCCAGCTACT 2040
                          ---i    i-------------------------    -----------
  L1M4_orf2#LINE/    540 A---GAAAAC-------------------------ATAG----------- 550

  chr1_53670566_5   2041 TGGGAGGCTGAGTGGGAGGATTGCTTGAGCCCGGGAGGTCAAGGCTGCAG 2090
                         --------------------------------------------------
  L1M4_orf2#LINE/    551 -------------------------------------------------- 550

  chr1_53670566_5   2091 TGGGCCAAAATCGTGCCAGCGCACTCCAGCCTGGGTAACAGAGTGAGACC 2140
                         -------------------------------- ?    ------------
  L1M4_orf2#LINE/    551 --------------------------------GNGTAA------------ 556

  chr1_53670566_5   2141 CTGTTTCACACGAAGAAAGAAAAAAAGAAAAAGAAAAACATCTTTGTGCC 2190
                         ---------------------------------------     i   v 
  L1M4_orf2#LINE/    557 ---------------------------------------ATCTTCGTGAC 567

  chr1_53670566_5   2191 CTTGGATTAGGCATTGATTTCTTAAATATAACTCCAAAAGCACCACCACC 2240
                              i       v  i       i    i  v          v v  v 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_53670566_5   2241 AACAACAAA----GATAAACTGAATTCCATTAAAATTAAATTTTTTTGTA 2286
                           v iv   ----      i  i i i   i         vvi      i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_53670566_5   2287 CT-AAAAGGACATCATCAAAAAAGTGAAAAGACAATCCACAGAATGGGAG 2335
                           -v        ii     i               i              
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_53670566_5   2336 AAAATATACGTAA--CATATATCAGATAAGGGAATTATAGCCGGAATATA 2383
                                vi i  --        v         v  i  v  i       
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_53670566_5   2384 TTAAGAACTTTTACATCTCAGTAATAAAAGGACAA----CCCAAT----- 2424
                          v       i     v    i        i     ----      -----
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_53670566_5   2425 ----GTTGAAAGA-------AGA----------AAGATGATTTACAAATG 2453
                         ---- vii  i  -------   ----------    v   v        
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_53670566_5   2454 GCAAATA-GCACATGAAAAGATGCTCAGCGTCATGAACCAT 2493
                           v    -                   i i   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (78 / 49)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 16.11 (306 / 19)  


 238 24.41 0.79 11.81  chr1_53746689_53749364      946  1072 (1604)    L1M4_orf2#LINE/L1       14   126 (782)  

  chr1_53746689_5    946 CATGTTTATGAACAATAAGAATTAATAATCATATAAAGA-GGTCCTATTC 994
                               i   i iviv    v      - -- i v    -  ivv  i  
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATA-T--TGTTAAGATGGCAATACTC 60

  chr1_53746689_5    995 CCGTTCCCCCCAACCAAATTGATCTATAGAGTAAATGGAATTCCAATCAA 1044
                           ------------            i   v v  i v   i  v     
  L1M4_orf2#LINE/     61 CC------------CAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_53746689_5   1045 AATCTAATCAAGGTTTTCCATAGAAATT 1072
                             iv v vivv    iiii       
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATT 126

Transitions / transversions = 1.07 (16 / 15)
Gap_init rate = 0.04 (4 / 113), avg. gap size = 4.00 (16 / 4)  

1270 25.33 11.35 6.60  chr1_53746689_53749364     1426  2183 (493)    L1M4_orf2#LINE/L1      115   908 (0)  

  chr1_53746689_5   1426 TTCGTGGAAATTTTAAAGTTGATTCCAAAATACACATATGGAAGAGCAAA 1475
                           i ii      vvv   i    i i     v  --       iv    i
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCA--TATGGAAATGCAAG 162

  chr1_53746689_5   1476 GT-CCAAGAAAAGCCAAGGAACA--CT---AAAACAAGACTGGGGTGGGA 1519
                          v-  v    v      --    --  ---    v    viiii  v   
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAA--AACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_53746689_5   1520 AATAGCGGGGATGGACTTTTCTACTAGATACTAGCAAAAACTTTTTATGA 1569
                         --------   ivv  vi   -- i iv v -----       vi  ii 
  L1M4_orf2#LINE/    211 --------GGACTCACACTTC--CCAATTTC-----AAAACTTACTACAA 245

  chr1_53746689_5   1570 AACTATGGTAATTAATGTGCTGTGGTATTGGTGCAGGGGTAGAAAAACTC 1619
                          i   ii     i  viiiv       i   iii i  i    v v ivv
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_53746689_5   1620 AGTAATAGAACAGAAGTG----CCCAGAAATAGGCTCATAGATATACAG- 1664
                          vi   i   i    v  ----i         ii i    v  v  ii -
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_53746689_5   1665 -AGTCTCTGATATATGACA-GAGTGGCACTACAGATCACTGGATTTGCAG 1712
                         - i ---    v vi    - i   v  ----   i  i ----------
  L1M4_orf2#LINE/    346 CAAT---TGATTTTCGACAAGGGTGCCA----AGACCATT---------- 378

  chr1_53746689_5   1713 ATCACTAGTAAAAAGATAGGCAATCCAACAAACGGCTCCCAGAATAGCTG 1762
                         --  v i vi   ii    v vv i       i  - v ii i i i   
  L1M4_orf2#LINE/    379 --CAATGGGGAAAGAATAGTCTTTTCAACAAATGG-TGCTGGGACAACTG 425

  chr1_53746689_5   1763 GATATCCAGCTGGAAACAAATCAAACTGGATTCCTACCTCATACCATATA 1812
                             ?   vv  v   vi   v  ii    ii         i        
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_53746689_5   1813 CT----CTAATTCCAA-TGGATTAAAAA--TAAATGTGAAAG-TAAAAAT 1854
                          v----i   i  v  -     i ? i --       i i  -     v 
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_53746689_5   1855 GTAAAATAAGCCCTCCCATTATCAGAGGATTTA--------TCT--GTAG 1894
                         i     ------   ---   vv   ii iv  --------   --  ii
  L1M4_orf2#LINE/    526 ATAAAA------CTC---TTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_53746689_5   1895 CATTAAGGTAGAGAAGGACATTTTAC-TGCAGACAC-AAAAATACAAACA 1942
                          v  ii v   iv  v iiv i   v- ii-     -    ii    i  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCA 615

  chr1_53746689_5   1943 ATAAAAGGAAAGATTGATAAATTCCACT-CATGAAAATGAAAAGCTTCTA 1991
                          i     i   i  v        vv   -   v     v    i   i i
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_53746689_5   1992 --CTAAAAAAAAATACCATCAGGAAAGTGAA--GCTAAGTCACAAA---- 2033
                         --  vv   ii -i  i    i         -- vi  vi    i ----
  L1M4_orf2#LINE/    666 TGCTTCAAAGGA-CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_53746689_5   2034 -------------------------CTGA---------------CAGAAA 2043
                         -------------------------    ---------------     v
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_53746689_5   2044 ATATCAAGAATTCCTATAAATCAATAAGAAAAAGACAAACAACC-AATAG 2092
                             v     i  i  i  v       v           i    -   v?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_53746689_5   2093 AAAAATGGGCAGAGGACGTGAAAGGAC-TTTTACAGAAGAGGAAACACAA 2141
                                    i    iv    vi   -   iv vi    i  v i    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_53746689_5   2142 ATGGCCTATAAAC-TGTGAAAAG-TGCTCAACCTCATTAGTAAT 2183
                               v    i -ii       -        v   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (115 / 74)
Gap_init rate = 0.05 (36 / 794), avg. gap size = 3.78 (136 / 36)  


1695 25.14 10.27 7.30  chr1_53824218_53826464      621  1360 (887)    L1M4_orf2#LINE/L1       58   819 (89)  

  chr1_53824218_5    621 CTTCCCAAATTTATCTAGAGATTCAGTGCAATCCAAATCAAAATCCCAGC 670
                           i        v     v       ii       vv              
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr1_53824218_5    671 AGGTTCTTTTTGTCTGTGGAAATTACCAAGCTGGTTCTAAAATTTATATT 720
                         v --i      ---  ii      iv       i i        i    v
  L1M4_orf2#LINE/    108 TG--CCTTTTT---TGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_53824218_5    721 AAAATTCAAACAGCCAAGAATAGCCAGGGTGATCCTGAA------GAATA 764
                         i    v   ivii  v          iiiii   i    ------   i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_53824218_5    765 AGGT---AG---------------ATATCAAGACTTATTATAAAGCTACA 796
                          i  ---  ---------------  v    i     i  i         
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_53824218_5    797 GTAATTAA-----TGTGAAACTGGCACAAAGATAAACAAATAGGCTAATG 841
                              i  -----    iv       i  i    i   v    iii    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_53824218_5    842 GAACAGAACAGAGAATCCAGAAATAGAGCCAT----TTAT--TTAATTGA 885
                            i    iv    i          i v    ----    -- i      
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_53824218_5    886 TTTATGGTAAAGGTG-----GCCCTTCAGAAAAGTGGGGGAAGGACAACG 930
                            vi ii  i    -----i  v    i-----     i   i i iiv
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAA-----TGGGGAAAGAATAGTC 397

  chr1_53824218_5    931 TGGTCAATAGAAGCTGCTGGCTCAATCGGATTTCTATACAATGTCGGAAA 980
                          vv    i i v v      vv   ii    v? i i ---  - ii  i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA---TG-CAAAAG 443

  chr1_53824218_5    981 AAAGAAACTTGACACCTTCTGCACACCAAACATAAAAACCAAATCCAGAG 1030
                           v   ii v   v   v iv       v i i     ii  --------
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA-------- 485

  chr1_53824218_5   1031 AGCCTCCTCGTATTTAGATGGACTATACATCTAAATACTAAATGTAAAAC 1080
                         ------   i----- i     ii ? v i      -------    i -
  L1M4_orf2#LINE/    486 ------CTCA-----AAATGGATCAWAGACCTAAAT-------GTAAGA- 516

  chr1_53824218_5   1081 AGCCAAG-CTTCAAAAATAAGCTTGTAAAAGAAAATTGTATAGGAGACTA 1129
                         -  i  i-  vi    -----  iv  i       i---     ? vvv 
  L1M4_orf2#LINE/    517 -GCTAAAACTATAAAA-----CTCTTAGAAGAAAAC---ATAGGNGTAAA 557

  chr1_53824218_5   1130 TTTTCACAAT-TTGAGATAAATTCACAAAGATTTCTTAAACAGGAC-TCA 1177
                          i   iii i-   i v  ii----   v i       i i v   -i  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGG----CAATGGTTTCTTAGATATGACACCA 603

  chr1_53824218_5   1178 GAAGCACTAACCATAAAAGTAAAGATGAATAAACTAGATTATTTTGAAAT 1227
                         i      v i v i     v   i  ii     i i  i viv ii    
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_53824218_5   1228 GGAGAGTTTCTACTCATCAAAAGACATCATTAAGAGAGAAAAAGGGCAAG 1277
                         vi i ii  i iiv v     i    ii  i    i  vi   i i   v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_53824218_5   1278 CCACA-----------------------TC---TAACTAACAAAGGGCTT 1301
                              -----------------------  ---  v  i i  i  i   
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_53824218_5   1302 GGATCTAGAATACATGAAGATCTTCTACA---CGA----AAAAAGGCAAA 1344
                          v   i      i  i    v  ii    --- i ----      i    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_53824218_5   1345 CAACTCAATTAAAAAA 1360
                         i   i     ?     
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAA 819

Transitions / transversions = 2.43 (129 / 53)
Gap_init rate = 0.03 (26 / 762), avg. gap size = 5.00 (130 / 26)  

 339 17.59 15.74 0.00  chr1_53824218_53826464     1647  1754 (493)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_53824218_5   1647 CTCAA----AAAAAAATAAA------AATTAAAAAA-------AAGACTT 1679
                              ----     i i   ------    ?     ------- i  i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_53824218_5   1680 GAATAGGCACTTTACAAAAGAGAATATTCAAATGGTCAAAAAATATATGA 1729
                               i  i  iv v     ii    v       i   v  ii i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_53824218_5   1730 AATGATGCTCAACATCATTAATCGC 1754
                           v              ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 5.67 (17 / 3)  


3038 25.45 0.21 4.33  chr1_53989748_53995096     3910  4856 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_53989748_5   3910 TGGAAACACATCCCATGCTCATGGATGGGTAA--TTAATATTATGAAAAT 3957
                               v i        i        v  v i--        i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_53989748_5   3958 GACCATACTGCCAAAAGCAATCTAAAAATTCAACACAATCCCCATCAGAA 4007
                          i v     v  v   vii     v i       i       i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_53989748_5   4008 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTTAAATTCATA 4057
                          v   v vv v  i  ii     v v  v  ivii  i  v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_53989748_5   4058 TGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAGGCAAAAAGAA 4107
                              viiv  ii  v  viv         i   vvi iiiv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_53989748_5   4108 CAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAAGCCA 4157
                             vi      vv       v  ii        viv     i     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_53989748_5   4158 TAGTCACCAAAACAGAGCGGTACTGGTGTGAAAATACGCACATAGACCAA 4207
                         i   v i   i    v i        ii i ii   vi  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_53989748_5   4208 TGGAGCAGGATAGAGAACCCAGAAATAAACCCAAATACTTTCAGCCAACT 4257
                             ii  i  v    ii               v i i  vii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_53989748_5   4258 GATCTTCGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTTT 4307
                            i        i vviv   i v   vv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_53989748_5   4308 TCAACAAATGATGCTGGGATAATTGGCTAGCCACATGTAGAAGAATGAAA 4357
                                   i        i  i   v  ?       i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_53989748_5   4358 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTAA 4407
                         i    i  ii i   v    v           i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_53989748_5   4408 GGACTTAAACCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACATTG 4457
                         i   i    iv     v  i    i      v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_53989748_5   4458 AAAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCACGACCAAAAG 4507
                         i?iv   i -   vv   v    v        v i    viiivi vi v
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_53989748_5   4508 CCCAAAAGCAAATGCAATAAAAACAACGATAAATAGCTGGGACCTAATTA 4557
                         v         v v    i    iv  vi   i   iv v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_53989748_5   4558 AACTAAAGAGCTTTTGCATGGGGAAACAAAAAACAAAAAAAAAAAAAACA 4607
                           v v  i i      iiivv-----    ii   vv vv  i   ----
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTT-----CAAAGGACACTATCAAGAAA---- 690

  chr1_53989748_5   4608 GCAAAGTAAGCAGACAACCCACAGAGTGGGAGAAAATCTTTACAATCTAT 4657
                         -----  i iv              i           v   i   vii  
  L1M4_orf2#LINE/    691 -----GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_53989748_5   4658 ACATGTGACAAAGGACTAATATCTGGAATCTACAACAAACTCAAACAAAT 4707
                          i  v   i  i     vi    ii    v  i  vi     vv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_53989748_5   4708 CAGTAAGAAAAAAAACAAACAATCCCATCAAAAAGTGGGCTAAGGACATG 4757
                           i   v     i -    i  i  v  i?    i     v     iv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_53989748_5   4758 AATAGACAATTCTTAAAAGAAGATATACAAATAGTCAATGACATAGAAAA 4807
                                 v    iv                 i i    i ---------
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA--------- 875

  chr1_53989748_5   4808 TGACAAATGGCAAATGACATATGAAAAAATGCTCAATATCACTAATGAT 4856
                         ----------------i  i       i        i    ????????
  L1M4_orf2#LINE/    876 ----------------GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 7.17 (43 / 6)  


 983 17.80 8.71 3.03  chr1_54172468_54176461      488   751 (3243)    L1M4_orf2#LINE/L1      244   522 (386)  

  chr1_54172468_5    488 AAAGCCTACA--AA--AAGACAGTGTGGTATTGGCAACAAAATAGACAAA 533
                              -    --  --              i     vv ii       v 
  L1M4_orf2#LINE/    244 AAAGC-TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_54172468_5    534 TAGGTCAATGGAACA-AAT--AGA--CCAA---------CATACAT--AT 567
                            i         i -   --   --   i---------       --  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_54172468_5    568 GGATTACTT-ATTTTTGACAAAGATGCAAAAGCAATTAAATAGAGAGAGG 616
                           - i v  -     i     i i   v  ii v   v   i i  i  i
  L1M4_orf2#LINE/    343 GG-TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_54172468_5    617 ATTGTCTTTTCAACAAATAGTGCTGGGATAATTGGAT-TTTATGTGCAAA 665
                           v               i         i  i     -?ii ii      
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_54172468_5    666 GCAAAAAAAGGAATGTTG-ATTTATTCCTTATACCATATACAAAAATTAA 714
                         ----- i  v   -    - iiiv v   i i                  
  L1M4_orf2#LINE/    442 -----AGAATGAA-GTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_54172468_5    715 CTCAAAATGGATTATAGACCTAATTATAAAACCTAAA 751
                                     i ?        v i   i v     
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

Transitions / transversions = 2.46 (32 / 13)
Gap_init rate = 0.05 (14 / 279), avg. gap size = 2.21 (31 / 14)  

 993 20.72 2.39 1.59  chr1_54172468_54176461     1049  1299 (2695)    L1M4_orf2#LINE/L1      508   760 (148)  

  chr1_54172468_5   1049 AATGAAAAACCTAAAATTATAAGCCTGCTAGAAGAACACAGAGGATAAAA 1098
                             v  i v      i     iv  vi        v   v   ?vv   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_54172468_5   1099 TTCTTGTGATCTTGAGTTACGCAATGACTCCT-AAATAT---ACCAAAAG 1144
                          ii i    i    i    v      ii i  - i    ---        
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_54172468_5   1145 ATCATGAGCCATAAAAGAAAAATATTGATCAATTGGACTTCACCAAAATA 1194
                         --  ii   v i          -  v   v            i      v
  L1M4_orf2#LINE/    608 --CACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAATT 654

  chr1_54172468_5   1195 AAAAAACTCCTGCTCTTTAAAAGGCACTATTAAAAGAATGAAAAGACAAG 1244
                              -  ii  iv   i   i i      i  i i i           v
  L1M4_orf2#LINE/    655 AAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_54172468_5   1245 CCACAGACTAGAAGAAA-TAGT-GTAAATCATATATCTGATAAAGAACAT 1292
                                v i i     -  v - i                  i i  v 
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_54172468_5   1293 GTATTCA 1299
                             i  
  L1M4_orf2#LINE/    754 GTATCCA 760

Transitions / transversions = 1.83 (33 / 18)
Gap_init rate = 0.03 (7 / 253), avg. gap size = 1.43 (10 / 7)  

2278 26.04 1.23 0.77  chr1_54172468_54176461     1983  2631 (1363)    L1M4_orf2#LINE/L1      257   908 (0)  

  chr1_54172468_5   1983 TCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGACCAATGGAAC 2032
                             i    ii         i  v ii i   v       i        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_54172468_5   2033 AGAACGGAGCCCTCAGAAATAACACCACAGATCTACAACCATTTGATCTT 2082
                             iv   vvii         vv   i v  i  iiii  v     i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_54172468_5   2083 TGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATA 2132
                         i     ivv  v   i v  vvv           i  vvi  v  i  i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_54172468_5   2133 AATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGAAT 2182
                                      v      v  ?   i   i i  iiv    ii  i i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_54172468_5   2183 CCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTT 2232
                             v   i i   v              i    i      i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_54172468_5   2233 AAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-AT 2281
                               v   v       i      vi i           v    ?i- v
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_54172468_5   2282 ACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAAACACTAAA 2331
                          i -   iv   v v  vv i     v ii   v iiv  vi    i   
  L1M4_orf2#LINE/    557 ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_54172468_5   2332 AGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT------AATTA 2375
                             vvi          vv     v  i    v   ii ------     
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_54172468_5   2376 AAGAGCTTCTGCACAGCAGAAGAAATTACCATCAGAGTGAACAGGCAACC 2425
                           i -   i  ii vv  i i  v i  i  vv i      v  i     
  L1M4_orf2#LINE/    656 AAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_54172468_5   2426 TACAGAATGGGAGAAAATGTTTGCAATCTACCCATCTGACAAAGGGCCAA 2475
                         i                 i       vii ivi      i  i  i ivi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_54172468_5   2476 TATCCAAAATCTACAAAGAACTTAAACAAATTTACAATAAAAAAAACCAA 2525
                               i   v  i        ivv    v iv i        i --   
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CAA 802

  chr1_54172468_5   2526 ACAACCGCAAC-AAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAGA 2574
                          i    -   i-?    i            v    i     i     vi 
  L1M4_orf2#LINE/    803 ATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_54172468_5   2575 AGAAGACATTTATGCAGCCAACAGACACAGGAAAAAATACTCATCATCAC 2624
                               i  vi viii     i ii    v     i  i    v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_54172468_5   2625 TGGTCAT 2631
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.58 (101 / 64)
Gap_init rate = 0.01 (7 / 652), avg. gap size = 1.86 (13 / 7)  

 556 20.89 3.80 1.90  chr1_54172468_54176461     3344  3501 (493)    L1M4_orf2#LINE/L1      748   908 (0)  

  chr1_54172468_5   3344 GAACTTAAAGTATTAAAAA-----AAAAAACTCTCAAAATGCAATAATGA 3388
                          i    ---    iv i  -----   i      i v  iv       i 
  L1M4_orf2#LINE/    748 GGACTT---GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_54172468_5   3389 AAAAACAAGCCATCTAATAATAAAATGGGCAAAAGATCCGAACAGACCCT 3438
                            i    iiv i i   v?v            i   ii   i    vi 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_54172468_5   3439 TCACCAAAGAAAATATATGGATGGCAAATAAGCACATGAAAAGACGCCCA 3488
                           v        i     iii     v                  i  i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_54172468_5   3489 A-ATCATTAGTCAT 3501
                          -    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.56 (23 / 9)
Gap_init rate = 0.02 (3 / 161), avg. gap size = 3.00 (9 / 3)  


2126 26.35 0.72 0.90  chr1_54620898_54627606.rev     4998  5551 (1158)    L1M4_orf2#LINE/L1        1   553 (355)  

  chr1_54620898_5   4998 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATAGTGAAAAA 5047
                              ii i  i     i        v      v i i   v  v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr1_54620898_5   5048 TGGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAG 5097
                             v     v     iv i  i  i        i  v     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_54620898_5   5098 CTACCAATGACTTTTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5145
                         v v   iivi i     ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_54620898_5   5146 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAA 5195
                                 viiv  ii  v  v v  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_54620898_5   5196 GAACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTACATCACAAGG 5245
                                 i      vv   vi  v  ii i      vivi ii    i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_54620898_5   5246 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5295
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_54620898_5   5296 CAATGGAACAGAAC--AGAGTCCTCAGAAATGATACCACACGTCTACAAC 5343
                                 i    i--       --      i vv   i  i i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_54620898_5   5344 CATCTGATCTTTGACAAACCTGACAAAAACAGGAAATGGGGAAAGGATTC 5393
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_54620898_5   5394 CCCATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5443
                         i iv  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_54620898_5   5444 TGAAACTGGATCCTTTCCTTACACCTTAAACAAAAATTAATTCAAGATGG 5493
                             ii    i  i v   i     v  v           i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_54620898_5   5494 ATTACAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5543
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_54620898_5   5544 CCTAGGTG 5551
                          v    ? 
  L1M4_orf2#LINE/    546 CATAGGNG 553

Transitions / transversions = 1.80 (92 / 51)
Gap_init rate = 0.01 (6 / 553), avg. gap size = 1.50 (9 / 6)  

1217 24.86 0.81 0.81  chr1_54620898_54627606.rev     5849  6218 (491)    L1M4_orf2#LINE/L1      539   908 (0)  

  chr1_54620898_5   5849 AAGAAAACCTAGGCA-ATACCACTCA-GGCCATAGGCATGGGCAAGGACT 5896
                                 v    ?i- v i -i  i- i  v i  i- i     v ii 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTT 586

  chr1_54620898_5   5897 TCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAA 5946
                           v iiv  vi            vvi          vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_54620898_5   5947 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCAT 5996
                          v   ii v  i   v v  i i   i  ii vv       v    i  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_54620898_5   5997 CAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACC 6046
                         v i      v  i     i   i             v       vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_54620898_5   6047 TATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATT 6096
                                i  i  i  vi          v  i        ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_54620898_5   6097 TACAAGAAAAAATTCAAACAACCCCATC-AAAAAGGGGCAAAGGATATGA 6145
                         v i  v     iv-    i     v  i-     v           v   
  L1M4_orf2#LINE/    787 AATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_54620898_5   6146 ACAGACATTTCTCAAAAGAAGACATTTATGTAGCCAACAGACACATGAAA 6195
                          i           v        i  vi vi i     i ii         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_54620898_5   6196 AAATGCTCATCATCACTGGCCAT 6218
                          i       v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (51 / 40)
Gap_init rate = 0.02 (6 / 370), avg. gap size = 1.00 (6 / 6)  


 440 18.60 3.49 0.00  chr1_54904137_54906095      252   337 (1622)    L1M4_orf2#LINE/L1        1    89 (819)  

  chr1_54904137_5    252 TAGGAAGACATCCCATGTTCATAGATTAGA--TCTTAATATTGTTA-GAT 298
                          i i    i             i    i  --v             -   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_54904137_5    299 GGCAATACTCCCAAAATTAGTGTATCAATTCAGTGTAAT 337
                                     v     ii v  ivi     ii i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

Transitions / transversions = 3.00 (12 / 4)
Gap_init rate = 0.02 (2 / 89), avg. gap size = 1.50 (3 / 2)  

3142 12.69 4.85 19.20  chr1_54904137_54906095      498  1466 (493)    L1M4_orf2#LINE/L1       79   908 (0)  

  chr1_54904137_5    498 TTCAGTGCAATCTGTATCAAAAGTCCAATTGGCTTCTCTGCAGAAATGGA 547
                             ii      iv        vi   ii  v   i i         v  
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chr1_54904137_5    548 CAGGCTGATCATAATATTCACATAGAAATTCAAGGGACTCTGAATGACCA 597
                           i       v   v     i  i     v        i v    ii   
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr1_54904137_5    598 A--CAATCATGAAAGACAAAAAAAAAAAAAAAACAAAATTGGAAGACTCA 645
                          --     v     -----------  i  i      i     i      
  L1M4_orf2#LINE/    179 AAACAATCTTGAAA-----------AAGAAGAACAAAGTTGGAGGACTCA 217

  chr1_54904137_5    646 CACTTCCCAATTTCAAAACATACGACAGAGCTACAGTAATCAAGGCATTG 695
                                            v   v   i                i  v  
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_54904137_5    696 TGGTACTGGCATAACAATAGACATATAGGTCAATGTAATAAAATTTAGAG 745
                                       vi            i      v    i    v    
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_54904137_5    746 CTCAGAAATAAGCCCTCACATTTATGGGGAATTTATTTTCAACAAGTGTG 795
                         ii         i   vi          vv    v      i     v   
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_54904137_5    796 CCAAGACCATTCAATAGGGAGG---TAATCTTTTCAACAAAGGATAGTGG 842
                                        i    ii---  i             v i iv   
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_54904137_5    843 GACAACTGGATATTCACATGTGGGAGAATGAAGCTAGAACTTTACCTCAT 892
                                     ?i      iiii         i i  v ii       i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_54904137_5    893 ACTATATAAAAAAGTTA-CCCAAAGTAGATCAAATACCCAAATGTAAGAG 941
                           i     v    i   - i    i i     ? v   i           
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_54904137_5    942 CTAAGACTATACAACTCTTAAAAGAAAACATAGATATGAATCTTCATGAA 991
                             i      v        i            i?i i       i   v
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_54904137_5    992 CTTGG--------------------ATATGACAC--AAAGCACAAGCAAC 1019
                              --------------------         --              
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_54904137_5   1020 AAAAGGAAAAGTAGATTGATTGCACTTCATCAAAAGTAAAAACTTTT-TG 1068
                              i    i     vi    v            v           -  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_54904137_5   1069 CTTCAAAGGATACCATCAAAAAAATGAAAAGATAAATGTGAAGAAAAAAG 1118
                                   i  i     i   i        i  ---------------
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA--------------- 702

  chr1_54904137_5   1119 TGAAAAGGGGCCAGATGCAGTGGCTCACACCTGTAATCCTAGCATTTTGG 1168
                         --------------------------------------------------
  L1M4_orf2#LINE/    703 -------------------------------------------------- 702

  chr1_54904137_5   1169 GAGGCCAGGGCAGGAGGACCACTTGAGGCCAGGAATTCGAGACCAACCTG 1218
                         --------------------------------------------------
  L1M4_orf2#LINE/    703 -------------------------------------------------- 702

  chr1_54904137_5   1219 GGCAACAAAGTGAGACCTCATCTCTACAAAAAAAAAAAAAAAAAAAAAAG 1268
                         --------------------------------------------------
  L1M4_orf2#LINE/    703 -------------------------------------------------- 702

  chr1_54904137_5   1269 TGAAAAAGCCCACAGAATGGAAGACAATATTGGTAAGTCATA-------- 1310
                         --------            i   v      v i  i     --------
  L1M4_orf2#LINE/    703 --------CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_54904137_5   1311 -AGGGACTTTTATCTACAACATATAAACAACTCTTATCATCTCAATAA-- 1357
                         -        v    i v  i       v        -  v        --
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATA 793

  chr1_54904137_5   1358 ----GACAGGTAACTCAGTTTTTTAAATGAGGAAAGGATGTGAATAGACA 1403
                         ----    ii    i  i  ?vv-     i v       v          
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACA 842

  chr1_54904137_5   1404 CTTCTCCAAAGA---CACACAAATGGCCAAAAAGCACATGAAAAGATGTT 1450
                         i           ---i i            v                 i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_54904137_5   1451 CAACATCATTAATAAT 1466
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (78 / 41)
Gap_init rate = 0.02 (13 / 830), avg. gap size = 17.92 (233 / 13)  


3490 19.35 10.40 0.60  chr1_55293374_55297008     2316  3142 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_55293374_5   2316 TAAAAAGACATCTTGTGTTCAAGGATTGAAAGACAAAATCTTGTTAAGAT 2365
                          ii     i   iii      v      i     vv   v          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_55293374_5   2366 GTCATTACTATTCAAAGTCACCTACAGGTTCAATGAAATCTCTATGAAAA 2415
                          v  v    vii    v v i      i     i v    i    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_55293374_5   2416 TCCCAAAGACATTT---GCAAAAATAGAAAAACCCATTCTAAAATTCACA 2462
                              ivvi v   ---   i    v  v  i iv  i          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_55293374_5   2463 TGGAC-T--------CTCCAAGTAGCCAAATCAATCCTGAAAAAGAGGAA 2503
                             v- -------- i vi i        v     i         i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_55293374_5   2504 TAAGGCTGAAAGACTCATACTTCCTGATTTTAAG-CTTAGTACAATACTA 2552
                         i  i i  i i      i      ii    i  i-    v     vi   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_55293374_5   2553 CAGTAATCAAAACAGTCTTATACTGGTAAAAAGACAGACATACAGACCAA 2602
                                   i     v vi      i v  i  i       i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_55293374_5   2603 TGCAATAGAAATATAGAACTCAAAAATA--------------TGGTC--C 2636
                           v       v i-   iii  i     --------------     --i
  L1M4_orf2#LINE/    301 TGGAATAGAATTG-AGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_55293374_5   2637 TGATTTTCATCAAGGGCACCAAAACCATTCAATGGGGAAAGGATAGTATT 2686
                                 iv      ii    i                  i     v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_55293374_5   2687 TTTAAAAAGGGGCACTGGGAAAACTGGATATTCACATGGAGAAAAACGAA 2736
                           i  v  iv  ii      v         ?i      v i  i  i   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_55293374_5   2737 GTCAGACCCTTACCTTACACCATAATGCAAAACTAAACTCAAAATGGATG 2786
                           ii     i     i        - i     v v              v
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATA-TACAAAAATTAACTCAAAATGGATC 498

  chr1_55293374_5   2787 AAACACCTAAATGTAAGAACTAAAACTATAAAACCTTTAGAAGAAAACA- 2835
                          ? v              i               ii             -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_55293374_5   2836 --GGGAAAA-CTTTGTGACACAGGATTTGGCCATAATTTCCTGGCTATGA 2882
                         -- ? v   -   i     viv  i  v   v  ii    i i v     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_55293374_5   2883 CAGCAAAAAACACAGGTAACTAAAGAGAAAATACATA------------- 2919
                           v     i-    i i   v     i      v   -------------
  L1M4_orf2#LINE/    599 CACCAAAAG-CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_55293374_5   2920 -----------------------CACAGGACACCATCAAGAGAGCTAAAA 2946
                         -----------------------  v       i       i  iv    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_55293374_5   2947 GACAACCCACAGATTGGGAGAAAATATCTGCATATCATATCATCTGATAA 2996
                                      v             i    v       -         
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAA 746

  chr1_55293374_5   2997 GGGATCAATATTCAGGATATATAAAGAATTCC-ACAAC------------ 3033
                             iivi   i   i            i  i-     ------------
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_55293374_5   3034 ----AAATAATCCAATTTAAAAATGAGCAAAGGTCTTAAAATAGATGTTT 3079
                         ----      i      ?       i       vi  i  -    ii   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA-TAGACATTT 845

  chr1_55293374_5   3080 CTCCAAAGAAGATATACGAATGGCCAACATGCACATGATGAGACGCTCAA 3129
                                          i         i v        vi   i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_55293374_5   3130 CATCAGTCATCAA 3142
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (102 / 54)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 5.69 (91 / 16)  


 854 31.61 9.64 2.94  chr1_55339795_55341707      575  1425 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_55339795_5    575 TGGGGAGACA--CCATGTTTCTAAATGGAAAAGACC-ATTATTGTAAAAA 621
                            ii   i --       iv ii  v i  -   i- v      v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAA-GACTTAATATTGTTAAGA 49

  chr1_55339795_5    622 CATCAATTCTCTCTGCACTGACCTATAAATTTAATGCAATTCCAAACACG 671
                         iiv    v   i iiv i   i   i i   i  i     i  v v  vi
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_55339795_5    672 ATCTCAGTAGAATTTTCTACAGCAGAACCTGACAGGTTGACTACACCCAG 721
                            i   iv vv    i ---      vi     i i   i----  i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT---GCAGAAATTGACAAGCTGAT----CCTAA 142

  chr1_55339795_5    722 AA--CAT-TAAAAATAT--GGAAAC---AATAA--AAAATTTTTTTAGAA 761
                           --   - ii    ii--  i v ---    i--    ivv i  ii  
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_55339795_5    762 AAGAATGATA---CTGGGCAGAAGTGACACTACCAGTAAT----GAAC-- 802
                              vi i ---i   --  i v v     v  --i   ----i   --
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGG--AGGACTCACACTTCC--CAATTTCAAAACTT 238

  chr1_55339795_5    803 ---ACAATGTTGCAACAGTACAGAAA---TGA-ACCAA-ATAATGAATGA 844
                         ---    v i i  ii i vv   v ---  i-  iii-    - i  ii
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA-GGATAG 287

  chr1_55339795_5    845 ATTAATAAATGACTGGAACAGAG------GTCCAGAAACAAATCCATTGG 888
                          ivv   i  v v     i   i------         i   i    --i
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT--A 335

  chr1_55339795_5    889 CAC--ACGGGCCTTTGATATT--ATTAAGCCAGCAACTACAAATAATAAG 934
                           i-- i  v vv     v  -- iv i viiv   vvv  vvi   ii 
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_55339795_5    935 GAAAAGAGAGATTATTCAACAGAGGAT-CTAACAACAATTGGCTACCTAT 983
                             ii v  vi v       i v i -  ii-i    i   v  ? i i
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGG-GACAACTGGATAKCCAC 434

  chr1_55339795_5    984 TTGGAAGAAAATAAAATTAAATCCCTATCTTTTCAAATATACAAAAATAA 1033
                         v  v  i i   i  i  ii i     i  ivivvv            v 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_55339795_5   1034 ATTCTAAATGAATTCAAGGACTAAGTTAAAAAAATAAAAATATGAAAGTA 1083
                          i  v     i  iv?  iv    i vv  i iv     v   i   v v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_55339795_5   1084 TAAAAAGAAAAAATA----TA--TTTTTATAAACTTGAGGTGGGAGAACA 1127
                          v i       v   ----  -- i  ii i v    i v i  vi vvi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_55339795_5   1128 TTATCTAAGCAAGTTAGAAAACTTTTAAGACACCAAGGAAAAA------- 1170
                           vii  iii v vi vv   vvivi   vv  v  i      -------
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_55339795_5   1171 --TTTGACTACGTAAAAGTCTGAAACTTCTATATAGCAAAAGATACCATC 1218
                         --  v    v i v   i ivi      i i iivv    i  i  i   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_55339795_5   1219 AATAAAAATGAAAAGA--AGCAAAATACTAGGAGAAAAGATTTACAAAT- 1265
                           -i   i        -- v v v v v i        v    i     -
  L1M4_orf2#LINE/    685 AA-GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_55339795_5   1266 ATGCAAAATA---GATACAGCATTGATAAGCTTAATATAAAAATAATTCC 1312
                           -----   ---    vi v i vi  vv vv      v   v  i  i
  L1M4_orf2#LINE/    734 AT-----ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_55339795_5   1313 TA-AA---AAT--TAACAAAACACGTCACCCAA--------------AGA 1342
                           -  ---   --   v  i   vi v      -------------- ii
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_55339795_5   1343 GACCTAAATAAACTAGGTCAATTCACAGAAGAAATACAAATAACCAATAA 1392
                           ii i    i  - vv  -- i  v      v        ii       
  L1M4_orf2#LINE/    829 GATTTGAATAGAC-ATTTC--TCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_55339795_5   1393 TCATATGACAAAATGCTCAAGTTCACAAGAAAT 1425
                         v  i    v  i        vv   ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (155 / 112)
Gap_init rate = 0.04 (39 / 908), avg. gap size = 2.74 (107 / 39)  


3142 15.91 15.66 4.07  chr1_55361112_55366790     4377  5187 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_55361112_5   4377 AAAGACATCCTATGTTCATAGATTGGAA--CTTAAAACTGTTAAGATAAC 4424
                              i    i        i        --     v i         ii 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_55361112_5   4425 AATATTCCCCAAATTGGTCTACAAATTGAACACAATCCGCATCAAAATTC 4474
                             i           i      i   v   i      vi        i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_55361112_5   4475 CAGCTAGTTTCTTTGCAAAAAACGACAATCTAACTTTAAAATTTA----- 4519
                              ivi  i      i   vi     v  i iii       i -----
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_55361112_5   4520 -----CAAGGAACCCTGAATAGTCAAAACAA----------------CAA 4548
                         -----     i    v      i        ----------------   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_55361112_5   4549 AGTTCAAGAATTCACATTTCCCATTTTCAAAACTTACTACAGCGCTATAG 4598
                             vi  i i     i      v                 iv    i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_55361112_5   4599 TAATCAAGACAATCTGGTACTGGCATAATGA-----------ATCAATGG 4637
                                    i v              v  -----------        
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_55361112_5   4638 AATATAATGGAGATTTCATAAATAATACCTG-GTATTTATGGTCAATTAA 4686
                             v   v    v i  v      -   ii-ii              i 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCAATTGA 352

  chr1_55361112_5   4687 TTTTTCAGCAAGAGTCACGAGACAACTTAATCTTTCACAAAGACAAAAAA 4736
                             - ii    i  ---------------------i v     v ----
  L1M4_orf2#LINE/    353 TTTT-CGACAAGGGT---------------------GCCAAGACCA---- 376

  chr1_55361112_5   4737 GTAATCCAATGGAGGAAGGACAGTCTTTTCAACAAATGGTGCTGAGACAA 4786
                         ---- i      i i   i i                       i     
  L1M4_orf2#LINE/    377 ----TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_55361112_5   4787 CTGAATATACACAAGCAAAAGAATGAAAT--GACCCC-ACCTCAAGCCAC 4833
                            i   ?v    v             i --      -      vi   i
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_55361112_5   4834 ATACAAAAACTAACTCAA-------------------TGTAA-------- 4856
                                  i        -------------------     --------
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_55361112_5   4857 -----------------------CGCAAGACTAAATATTCATGACCTTGG 4883
                         ----------------------- ii i ?v     v   i         
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_55361112_5   4884 ATTAGGTAATTATTTCTTGGA----------AAAGCAAAAGCAACAAA-G 4922
                         i     i   vi      i  ----------      v          - 
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_55361112_5   4923 AAAAAATAAA---------CTTCATCAAAAATAAAAATTTTTGTGCATCA 4963
                                 i ---------           v      i        v   
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_55361112_5   4964 AAAGTCACCATTAAGAAAGTGAAAAAAAGAATCTACAGAATGAGAAACAG 5013
                           i v   i  i             i v-  i i        i  i v i
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGAC-AACCCACAGAATGGGAGAAAA 721

  chr1_55361112_5   5014 TATTTGCAAATCATAGATCTGATAAAAGATTTGCATATAGAATACAAAAA 5063
                                        v         ii  i   i  vi      i v   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_55361112_5   5064 AAAAACCTTACAACTCAATAA---AAAGACAAATAACCTAAT-AAAAAAT 5109
                         i  v-i               ---              i   -?      
  L1M4_orf2#LINE/    772 GAAC-TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_55361112_5   5110 GGGCAAAAGATTTGAATAAATGTTTCTCCAAAAAAGATA--CAAGCGGTT 5157
                                i          i ii          i      --   ii  ii
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_55361112_5   5158 ------CACA--AAAAGATGCTAAGCATCTTCAGGAAA 5187
                         ------    --          v i    v????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (90 / 36)
Gap_init rate = 0.03 (23 / 905), avg. gap size = 6.96 (160 / 23)  


2185 24.02 14.87 1.40  chr1_55444025_55449384.rev     4085  4871 (489)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr1_55444025_5   4085 TGTTCATGGATTGAAAGAGTCAAAAGAGTGAAGATGTCAATTCTCCCCAA 4134
                                      i    v i  v vv  v      v    v        
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_55444025_5   4135 ATTGATCTATAAGTTTAATGTGATCCTTCTCTAAATTCTGGCAATACTTT 4184
                                  i ii  i  i ii    i v  v    i ii  -- i i  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC--TGCCTT 113

  chr1_55444025_5   4185 TTT---AGATATAAAGAAGTGTATTCTAAATTTTAGATGAAAAAGCAAAG 4231
                            ---   v  vi v   ivv  i     v  i v   i   v    i 
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_55444025_5   4232 AAACTACAATAGCCAAAACAATTTTGAAAAAGAAGAA--AAATGAGAAGA 4279
                         i v i v               i              --  i vi  i  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_55444025_5   4280 ATCAGACCACCTGCTTTCAACACTTAGTCTATAGCTATAGTAATCAAGAT 4329
                         v   v  iv  iiv      v     v vi v     i           i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_55444025_5   4330 ----TGATATTGGTGGAATTGGTGGTGATCTACATAGATCAGTGGAACAG 4375
                         ----  i  i   iiv  -----  vv vvi i        i     i  
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAA-----GGATAGACATATAGATCAATGGAATAG 308

  chr1_55444025_5   4376 AATAGAGAA-CTAATAAAAGACCCATGCAAATATGCCCAAATG------- 4417
                            v    i- i iv  v i      i  vv    vi   v  -------
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_55444025_5   4418 ----------CAAAACCATCCAATGGAGAAA---TAGCCTTTTCGACAAA 4454
                         ----------   i     i      i    ---   i      i     
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_55444025_5   4455 TGATGCTGGAATAACTGAATACCCAGAAGGAGGGAAAGTTAACTTCAACC 4504
                           i      i i     i   ?   v v v iiii  - v  v  vi   
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACC 457

  chr1_55444025_5   4505 TAAGTCTGACATCTTATACAAAAATTAACTCAAAATGGATTATGGACTTT 4554
                         ivvii  v   i v                          i ?i   i v
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_55444025_5   4555 AATGTAAGA-------CTATAACACTTTTAGAAAAAAA------------ 4585
                                  -------      v   i      i    ------------
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_55444025_5   4586 --------AC--------------------------TAT----------- 4590
                         --------  --------------------------   -----------
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_55444025_5   4591 ----------AAAATAAAAAATGGATAAAATGGACTTCATCAATATAAAA 4630
                         ----------    v       i      v             v  v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_55444025_5   4631 AATTTT---GCTCCATGAAAAACCCTGTTAAGAG-GAGAAAAGACAAACT 4676
                           i   ---   i  --  ii  v  i i    i- v          v i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCA--AAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_55444025_5   4677 AGAGACTGAAAAAACATATTTGCAAACCACATATCAAACAAG-------T 4719
                          v   v  ii i  v           i  i     vi i   ------- 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_55444025_5   4720 AGGTAGAATATATAAACATCACTCAAAATTTAAC--TTAAAAAACAAACA 4767
                          vvi            v v v  i v  i i  i-- v    i     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_55444025_5   4768 ATCCAATTAGAAAATGGGAAAAAAGACGTGTAGAGGCATTTCACGAAGGA 4817
                          i      ?i        v   i-  iv  v v  i      v v  i  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAG-GATTTGAATAGACATTTCTCCAAAGA 854

  chr1_55444025_5   4818 GGATACACAGATGATAAATAAGCACATGAAAAGATGGTTAATATTGTCAG 4867
                         i    i   i   iiv                    v i  i  ii????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_55444025_5   4868 CCAG 4871
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.38 (108 / 78)
Gap_init rate = 0.02 (19 / 893), avg. gap size = 6.74 (128 / 19)  


3149 24.16 2.12 1.00  chr1_55567847_55573726.rev     4492  5389 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_55567847_5   4492 TGGAAACACATCCTATGTTCATGGATTAGAAGAATCAATATCATGAAAAT 4541
                               v i    i             i     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_55567847_5   4542 GACCATCCTGCCAAAAGCAATGCCTACAGATTCAATGCAATTCTTATCAA 4591
                          i v  v  v  v   vii  --            i     i i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT--CTACAGATTCAACGCAATCCCTATCAA 98

  chr1_55567847_5   4592 AATACCAACATCATTTTTCACAGAAATAGGAAAAA-AATCCTAAAATTCA 4640
                            v   i vv v     ii       v iv  iv-i             
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_55567847_5   4641 TATGGAACCAAAAAAGGGCCCCA--ATAGCCAAAGCAATCTGAAGCAAAG 4688
                                -- viv     v    --         i      vi iv  ii
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_55567847_5   4689 AGAACAAATCTGGAAGCATCACATTACCTGACTTCAATTTATACTACAAG 4738
                                 vi    i vv     i v  ii i     vviv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_55567847_5   4739 GCTATAGAGTTACCAAAACAGCATGGTCCTGGTATAAATGTAGACACATA 4788
                             i  -- v i   i    ii    v    i    ivi      i   
  L1M4_orf2#LINE/    247 GCTACAG--TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_55567847_5   4789 GACCAATGAAACTGAATGGAGAACCCAGAAATAAAGCCAAA----TACAA 4834
                           i     i  iv    v    ii           v   v ----  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_55567847_5   4835 CCAATTGATCTTTGACACAG-CACACAAAAACATAAACTGAGGAAAGGAT 4883
                         i        i  i    vi -ii -   i v   vv v  i      i  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAAT 393

  chr1_55567847_5   4884 -GCCATATTTAATAAATGGTGCTGGGAAAACTGGATAGCTACATGTAGAA 4932
                         - i v -  i  i              v         ? i     i i  
  L1M4_orf2#LINE/    394 AGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_55567847_5   4933 GAACGAAACTGGATCCCTATCTCTCACCTTATATAAAAATCAACTCAAGA 4982
                            i   ii    i     i   v    v    i      i       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_55567847_5   4983 TGGATTGAAGACTTAAATCTAAGACTTGAAACCATAAAAATTCTGGAAGA 5032
                              ii?    i     v     vi i    i      v ii i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_55567847_5   5033 TAATCTAGGAAAAACTATTCTGGACATGGGCCTAGGCAAAGAATTTATGA 5082
                         v  iv    ?iv  v v   vv   v v  vi       v iv  iv ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_55567847_5   5083 CTAAGACGCCAAAAGCA-AATTAACAAAATCAAAAATAAATAAATGGGAC 5131
                         v  v   i         -  vi       vv       i      v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_55567847_5   5132 ATAATTAAACTAAAAAGCTTCTGTACAGCAAAAGAAATAATCATCAGGGT 5181
                         v v  i   v v    i   i   i vv    i  v iv    vv ii  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_55567847_5   5182 AAACAGACAACCCACAGAATTGGGAGGAAATATTTTCAAACTATTCATTC 5231
                         i  v                -     i        v    ii  vi  ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAAT-GGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_55567847_5   5232 CACAAAGGACTAATATTCAGAATCTACAAGGAACTCAAACAAATCAG--- 5278
                         v i  i     vi   i      v  i  i      vv    v   i---
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_55567847_5   5279 -AAAAAAA-AAAT--CCCA--CCAAAAGTGGGCAAATAACATGAATAAAC 5322
                         -     i -    --    --i?    i        vi iv      i  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_55567847_5   5323 ATTTCTCAAAAGAAGATATACAGATGGAAAATAAACAAATGAAAAAATGC 5372
                                v              i    vv     i  v       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_55567847_5   5373 TCAACATCACTAATCAT 5389
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (123 / 90)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.75 (28 / 16)  


2860 27.39 0.67 0.56  chr1_55592201_55594161.rev      573  1470 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr1_55592201_5    573 ACCTCATGCTCATTGATGGGTAAAAC-CAATATTGTGAAAATGACCATAC 621
                          i i    i    v   v  -  i  -i        v  i   i v    
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGG-AAGACTTAATATTGTTAAGATGGCAATAC 58

  chr1_55592201_5    622 TGCCGAAAGCAATCTACAAATTTAATGTAATTCCCATCAAAATACCACCA 671
                          v  v   vii       i   i  i i   i  i        v   v v
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr1_55592201_5    672 TCATTCTTCACAGAACCAGAAAAAACAATTCTAAAATTCATATGGAACCA 721
                         v v  i  ii     viv  v  ivii  i                 vii
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr1_55592201_5    722 AAAAAGGGCCCGCATAGCCAAAGAAAGACTAAGCAAAAGGAACAAATCTG 771
                         v  ii iv  v v         iv  vvi i iv  i i       vi  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_55592201_5    772 GAGACATCACATTACCTGACTTCAAACTATACTATGAGGCCATCGTCACT 821
                            ivv     i v  ii i      viv     ii i  i iv  v ii
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_55592201_5    822 AAAACAGCATGGTACTGGTATAAAAATAGGTACATATAAACCAACAGAAC 871
                           i    ii         i    ii    --       i i   ii   i
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAG--ACATATAGATCAATGGAAT 306

  chr1_55592201_5    872 AGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAACTGATCTT 921
                              v    ii               v i i   ii i   i    i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_55592201_5    922 CAACAAAG-CACACAAAAACATAAAGTGGGGAAAGGATACCCTATTCAAC 970
                          i    i -ii -   i v   vv i         i   vi  v      
  L1M4_orf2#LINE/    357 CGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_55592201_5    971 AAATTTGTGCTGGGATAATTGGCAAGCCACATGAAGAAGAATAAAACTGG 1020
                             -v         i  i   vv ?       v i      i  ii   
  L1M4_orf2#LINE/    406 AAAT-GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_55592201_5   1021 ATCCTCATCTCTCACTTTATACAAAAATCAACTCAAGATGGATCAAGGAG 1070
                          i  ii i   v   iv           i       i        ?i  v
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_55592201_5   1071 TTAAACCTAAGACCTGAAGTTATAAAAATTCTGGAAGATAACACCAGAAA 1120
                         i    iv     v  i  ii       v ii i     v    ivi ?iv
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_55592201_5   1121 AACCCTTGAAGACATTGGCTTAGGCAA-AACCTCATGACCAAGAACCCAA 1169
                           vi   viv   v    v        -iiii  v iivi v  vv    
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_55592201_5   1170 AAGCAAATGAAACAAAACAAAGA-TAAATAAATGAGACATAATTAAACTA 1218
                              v v v       v   i -  i      vi   v v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_55592201_5   1219 AAAAGCTTCTGCACAGCAAAAGAAACAATCAGCAGCGTAAACAGACAACC 1268
                             i   i  ii vv    i  v  v    iv iv  i  v        
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_55592201_5   1269 CACCAAATGGGAGAAAATCTTCACCATCTGTAGATCAAACAAAGGACTAA 1318
                            vi             v  ii v viii  v   vi i  i     vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_55592201_5   1319 TATCCAGAGTCTACAAGGAACTCAAACAAATCAGCAAGAAAAAAA-AAA- 1366
                                 i v  i  i      vv    v   ii  v     i -   -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_55592201_5   1367 AATCCCATCAAAAATTGGGCTAAGGACATGAATAGACAATTCTCAAAAGA 1416
                           i  v  i?    v     v     iv          v     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_55592201_5   1417 AGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCACTAA 1466
                                           i  i  i       i             ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_55592201_5   1467 TGAT 1470
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (10 / 899), avg. gap size = 1.10 (11 / 10)  


 753 24.40 0.00 0.48  chr1_55633340_55635307      251   459 (1509)  C L1M4_orf2#LINE/L1   (0)   908   701  

C chr1_55633340_5    459 AACCTAGAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAGGG 410
                             i v               v       vii ivi      i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

C chr1_55633340_5    409 CTAACATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAAAT 360
                           vii         v  i        ivv    v iv i  v     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA- 799

C chr1_55633340_5    359 CAAACAACCCCATCAAAAAGTGGGCAAAAGATATGAACACACACTTCTCA 310
                             i     v  i?    i        i   v    i v   i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

C chr1_55633340_5    309 AAATAAGACATTTATGCAGCCAACAGACACATGAAAAAATGTTCATCATC 260
                            v    i  vi viii     i ii          i   i   v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

C chr1_55633340_5    259 ACTGGCCAT 251
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.63 (31 / 19)
Gap_init rate = 0.00 (1 / 208), avg. gap size = 1.00 (1 / 1)  

1128 25.46 12.20 0.27  chr1_55633340_55635307      500   876 (1092)    L1M4_orf2#LINE/L1      249   670 (238)  

  chr1_55633340_5    500 TGCAGTAATCAAGATAGAGTGCTATTGGTATAGAGGCAGAAATTTAGATT 549
                          i            i  v   v  i   i   ii ii   v  v     i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_55633340_5    550 AATGAAACAG---TAA-AGTCCA-ACAGAGACCAAAAAATATAGGGTCAG 594
                             i  i  --- i -      - v v i   v v v  v  v     i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_55633340_5    595 TTGCTTTTTGACCAACGTGCCAAGGTAATCCAATGGGGAAAGGACTGCAT 644
                            v    i   v iv        iiv  i            i iv iv 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_55633340_5    645 TTACAACAAATGGTGCTGG---AACCAGGTATCCATTTGAAAAAATATGA 691
                           v                ---   ii i  ?   iv  v    iv    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_55633340_5    692 ACCTTGACTCTTAGCCCATGTCACATA--AAAATTAACTGGAAATTGGTC 739
                          vi v   i i  v i  iii  i   --          vi    v i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_55633340_5    740 AGAGATCTAAATGTAAAAGCTAAAACTATAAAA----TA----------- 774
                          ?   i          i                ----  -----------
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_55633340_5    775 ------------TTATGATTTTGG---AAATAA-AATTTCTTAG----GA 804
                         ------------ ii   ii    --- iii  -ii        ----  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_55633340_5    805 CAT-AGAATCATGAATCACAAAAGAAAATAGTTGATACATGTTATTTCAT 853
                           i- i  v  ii iiv           - i v    v  vvv i     
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCAT 647

  chr1_55633340_5    854 CAAAAGTAAAAATTTCTGCTCTT 876
                              v      i  i  iv   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTT 670

Transitions / transversions = 1.69 (59 / 35)
Gap_init rate = 0.03 (12 / 422), avg. gap size = 3.92 (47 / 12)  

 539 20.56 2.09 11.50  chr1_55633340_55635307     1189  1475 (493)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr1_55633340_5   1189 AAAATTAAAAATTTCTGCTCTTCAAAGTAAAATGTTAAGAAAAT-AAAAC 1237
                                    i  i  iv        v v v i i      i -    v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_55633340_5   1238 CCAGGCCATAGT-TGAGAGAAAGTATTTATAATAGAT-GTATACCTTTTA 1285
                         v  iv   i  v-  i      i     ii  ---  -i    i  vv  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAA---ATCATATATCTGATA 745

  chr1_55633340_5   1286 AAG-ACTAGTAACAAGAATATATAAA-AACCTTTACTTGATGTTCTTGTG 1333
                          i -   v   v v            -   ii    --------------
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTAC-------------- 781

  chr1_55633340_5   1334 ATACTGAAAAAAGTAAAGAACTTCATCAGTCAGTCAAACAGTCCAGT-GA 1382
                          -   v  v  --    i ------------- v    i ii   i -? 
  L1M4_orf2#LINE/    782 A-ACTCAATAA--TAAAAA-------------GACAAATAACCCAATTWA 815

  chr1_55633340_5   1383 AAAACAGGAAAGAGATTTGAATAGCTACTACACAAATGAAGATAAACAAT 1432
                             ii  v  ii           vi i v v v  v       v    v
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_55633340_5   1433 GGGCCAATAAGCACATGAAAATATGTCCTACATTATTAGTCAG 1475
                         v                    v   ii v    i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (31 / 27)
Gap_init rate = 0.04 (11 / 260), avg. gap size = 3.55 (39 / 11)  


3088 26.78 1.44 0.56  chr1_55739775_55746163.rev     4999  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_55739775_5   4999 TGGAAGACCATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAGT 5048
                              iivi  i     i        v      v i     i  v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_55739775_5   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCATGC 5098
                            v     v     iv i  i  i        i  v     i    viv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_55739775_5   5099 TACCAATGACTTTCTTCCCAGAA-TTGGAAAAAGCT-ATTTTAAAGTTCA 5146
                          v   iivi i  i  iv     -   -- v     -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_55739775_5   5147 TATGGAACCAAAAAAGAGCTCGCATTGCCAAGACAATCCTAAGCCAAAAG 5196
                                viiv  ii  v iv v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_55739775_5   5197 AA--AAGCTGGAGGCATCACGCTACCTAACTTCAAACTATACTACAAGGC 5244
                           --   i      vv    i  v  i  i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_55739775_5   5245 TATAGTAACCAAAATAACATGGTACTGGGACCAAAACAGAGATATAGACC 5294
                           i     i   i i iii         v iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_55739775_5   5295 AATGGAACCGAAC--ATAATATCAGAAATAATATCATACATCTACACCCA 5342
                                iv   i-- v i -i         vvi       i  iivi  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGT-CCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_55739775_5   5343 TCCGATCTTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCCC 5392
                         vii   i  i     ivv  v   i vv vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_55739775_5   5393 TACTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5442
                          vi i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_55739775_5   5443 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGAT 5492
                           ii    i    v   i     v              i    ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_55739775_5   5493 TAAAGACTTACAGGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5542
                         i ?    i  v v  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_55739775_5   5543 TAGGCA-ATACCATTCAGGACATAGGCATAGGCAAGGACTTCATGTTTAA 5591
                             ?i- v i -   iv   v v  vv       v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_55739775_5   5592 AACACCAAAAGCAATGGCAACAACAGCCAAAATTGACAAATGGGATCT-- 5639
                         i            vvi       v  vv     v  i    v   ii --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_55739775_5   5640 ----AATTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTAAA 5685
                         ----       i -   i  ii vv    i  v  i i  vv i   i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_55739775_5   5686 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5735
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_55739775_5   5736 AAGGGCTAATATCCAAAATCTACAATGAACTCAAACAAATTTACAAGAAA 5785
                          i  i  vi      i   v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_55739775_5   5786 AAAACAAACAACCCCATCAAAAAGTGGGCCAAGGATATGAACAGACACTT 5835
                           i     i     v  i?    i     v      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_55739775_5   5836 CTCAAAAGAAGACATTTATGCGGCCAAAAAACACATGAAAAAATGCTCAT 5885
                            v        i  vi vii      v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_55739775_5   5886 CATCACTGGCCAT 5898
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (136 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


2665 22.98 6.60 3.30  chr1_55773787_55778546.rev     1638  2516 (2244)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_55773787_5   1638 TGAAAAGCTAAATATATCTTGTTCAGCATTTAGAAGACTCACTATTGTTA 1687
                           i    ----    vi v      vviv  i       i v        
  L1M4_orf2#LINE/      1 TGGAAAG----ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chr1_55773787_5   1688 AGAGAGCAACACTCCCCAT-TTAGCCTATTGATTCAACACAATCCCAACC 1736
                            vi    i        v-  iii   iv        i       v i 
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_55773787_5   1737 AAAATTCCAGCATGTATTTTTTG-AGAAATTAACAGGCT--TTCTAAAAT 1783
                              i     -  iv       -       i   i   -- i       
  L1M4_orf2#LINE/     97 AAAATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_55773787_5   1784 TCACAGGAAAATGGAAAGGATCTAGCATAATTAAAACAATTTCAATAAAG 1833
                            i v i     v  i   i i  v   iii        i ii v    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_55773787_5   1834 AAGAA---AGTTGTAACACTATCACTACCTGCTTTCA-------TTATAA 1873
                              ---     v iv   vv    v  iiv     -------i  i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_55773787_5   1874 AAGTATAGTCATCAAGACAGTGTGATTATTATTGAT-TA--GACAAATAT 1920
                          iv  i   v              i ---- i  ii-  --  i i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGT----ACTGGCATAAGGATAGACAT 291

  chr1_55773787_5   1921 CAAATAGATTAATGGAATGAAATAGAGAATACTGAAATAGACTCA--CAT 1968
                         ---      i        ii   v    i v v      i  i  --   
  L1M4_orf2#LINE/    292 ---ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_55773787_5   1969 TATATAGACAACGGATTTTTGACAAAGA-ATAAATGGCAATTCCATGGAG 2017
                          -   i v   iv      i     i i-iiv  - i v    v    i 
  L1M4_orf2#LINE/    339 T-TATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGG 386

  chr1_55773787_5   2018 AAAAGACAGTCTTTTTAAAAAATGGTGCTGAAACAATTAGATATTCATAA 2067
                            ii i        i  v           ii    i i    ?i  i v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_55773787_5   2068 GCAAAAAAA--ACCTTTTGTTTATACCTCATTTCATATAGAAAAATATAC 2115
                               i  -- vv  vviiiiv       ivi      v      vv  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_55773787_5   2116 TCAAACATAGATCAGATGAAAACCTAA-TGTAAAATCTAAA-CCATAAAA 2163
                              -  i     ----? i      -     i v     - i      
  L1M4_orf2#LINE/    487 TCAAA-ATGGATCA----WAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_55773787_5   2164 CTTTTAGAAAACCAACATGAGGAAAAATCTGTGTAGCCCTTGGATCAGGC 2213
                           i      i v-     ii ?iv      vi  - v      i i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAA-AACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGC 579

  chr1_55773787_5   2214 AAAGATTTCCTAGATATGATACCACAATCATGATCCATAAAAGAAAAAAA 2263
                           v i    i         i    v  v  ii v v i           v
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_55773787_5   2264 AGAATAAATT------TAT-------AAAGAC----------------AC 2284
                            -      ------i  -------   i  ----------------  
  L1M4_orf2#LINE/    630 AGA-TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_55773787_5   2285 ACTGTTAAAAGAATGAAAAGACT-----CGGACTGAGGGAAAATATTCAC 2329
                            i i  i i i         v----- i  v  i i         ii 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_55773787_5   2330 AAAGCACAAATCCGATAAAGACCTTGTATCTGGAATATACAAAGAACACT 2379
                            v  i v   i     i iv        ii       i       v  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_55773787_5   2380 CAAAATTCAATATTAAGAAAACAAAAAGCCCAATTTTAAACATTGCAAAA 2429
                         i v  i      v   i  i     v i       ?-   v  v vv   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAA 827

  chr1_55773787_5   2430 TGATTTGAACATACACTGCACAAAAGAAAATATTAATATATGTATAGCTA 2479
                         v        i v   i v v v      i    -- i v   ----  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATAT--ACAAATG----GCCA 871

  chr1_55773787_5   2480 ATAAGCAAATTAAAAGATATTCAACATCATAGTCATT 2516
                                v  v       ii         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (124 / 74)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.90 (87 / 30)  

3359 24.34 0.88 1.64  chr1_55773787_55778546.rev     3358  4269 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_55773787_5   3358 AAAGATATCCCATACACATAGATTGGAAGAATTAATATTGTTAAAATATC 3407
                                      iiv   i          v             i  iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_55773787_5   3408 TATACTTCCCAAAAC-ATCTATAAGATTCAATGCAATTCCTATCAAAATA 3456
                         v     i      vi-     i -       i     i           v
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACA-GATTCAACGCAATCCCTATCAAAATC 102

  chr1_55773787_5   3457 CAAATAACATTCTTCACAGAAATAGAAAAA-TAATCCTAAATTTTGTATG 3505
                          v iivi v  i  ii       v  v  i- i        v  ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_55773787_5   3506 GAACCACAAAAGACCCCAATTAGCTAACACAATCCTGAGCAAAAAGAACA 3555
                            vii   ii     vi v    i  v      i   iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_55773787_5   3556 AAGCTGGAGGCATCACACTACCTAATTTCAAAATATCCTACCAAGCTATA 3605
                            i      vv       v  i          iv v    v      i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_55773787_5   3606 GTAACCAAAACAGCATGGTACTAGCATAAAAGTAGACACA--GATCAGTG 3653
                             i   i    ii       i      iii      i --     i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_55773787_5   3654 GAACAGAACAGAGAACCCAGAAATAAATCCATGCACTTAATAGTCAACTC 3703
                            i    iv    ii           i    i  i   - i     i v
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAATTG 351

  chr1_55773787_5   3704 ATTTTTGACAAAGTTGCCAAGAACATACACTGAGGAAAGGACAGTCTCTT 3753
                              i     i v        v   v  v  i      i i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_55773787_5   3754 -AATAAATAGTGTTGGGAAAACGGTAAGA-ATCAATACGCAGAA-AATGA 3800
                         -  i    i   i     v   v ---  - ? v i i   i  -     
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTG---GATAKCCACATGCAAAAGAATGA 448

  chr1_55773787_5   3801 AACTAGACCCCCATCTTTCACCATATACAAAAATCAACTCAACATGGATT 3850
                          ii i      i i  iv                i       v      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_55773787_5   3851 AAGCATTTAAATGGAAGATCTGAAACCACTGAAAACTGAAATTACTAAAA 3900
                          ?iv ii      v    v  i    i -------- i   i vi  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTA--------TAAAACTCTTAGAA 540

  chr1_55773787_5   3901 GAAAACATTGGGG-AAACATTACAGGATATTGGTCTGGGCAAAGATTTTT 3949
                                 v  ? -   iv  - iv  iv    vi i     v i   i 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_55773787_5   3950 TGAAAAAGACCTCAAAAGCACAGGTGACCAAAGCAAAATTAGACAAATGG 3999
                          ii v v   vi          i ii  v    v    v    i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_55773787_5   4000 GATTACATCAACCTAAAAAGTTTCTGCACAGCAAAGAAAACAAACAACAA 4049
                           i v      vv v    ii  i  ii vv     i v  v v   v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_55773787_5   4050 CGTGAAGAGGCAACCTACAAAAAAGGAGAAAATATTTGCAAACTACCCAT 4099
                         v     i  i     i   i  vi                  ii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_55773787_5   4100 CTGACAATGGATTAATAACCAGAACATGTAAGAAACTCAAACAATTCAAC 4149
                             i  v   i vi  v      i  i   ii     vv    i    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_55773787_5   4150 AGCAAAAAAAAAAAAAAATCTGATTTAAAAATGAGCAGAAGACCTGAATA 4199
                          ii     i v   v  -i ii   ?       i   i i  ii      
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_55773787_5   4200 GATGTTTCTCAAAAGTAGACATACAAATGGCAAAAAGGTTTATTAAAAAG 4249
                           ii      v    v   i           v  v i ivi  v    ii
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_55773787_5   4250 TGTTCAAAATCATTGACCAT 4269
                           i    v    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (140 / 78)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 1.77 (23 / 13)  


2712 25.74 0.83 2.49  chr1_55837791_55840044.rev      527  1369 (885)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr1_55837791_5    527 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 576
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_55837791_5    577 AACCATACTGCCCAAAGCAATCTACAGATTCAATGCAATTCCCATCAAAC 626
                         ii v     v      vii              i     i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_55837791_5    627 TACCATC-G--TTCATCACAGAACTAGAAAAAATAATCTTAAAATGCATA 673
                          v   v - --  iv ii     v v  v  iv i   i      v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_55837791_5    674 TGGAACCACAAAAGCACCCACA-TAGCCAAAGCAAGACTAAGCAGAAAGA 722
                              vii   ii -     v -        i   vvi i iv ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_55837791_5    723 ACAAATTTGGAGGCATCACATTATTTGACTTCAAATTATACTACAAGGCT 772
                              v       vv     i viiii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_55837791_5    773 ATACTTACCAAAACAGCATGGTACTGGTATTAAAATGGGCACATAGACCA 822
                          i v v i   i    ii         i  v ii  i i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_55837791_5    823 ATGGAACAGAATAGAGAACCCAGAAATAAAGTGAAATACTTACAGACAAC 872
                               i     v    ii           viv v i i   ii v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_55837791_5    873 TGATCTTCAACAAAGCATACAAAAAC-ATAAACTGGGGAAAGGACGCCCT 921
                             i   i    i -i i v  i  -  vv v         i iivi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_55837791_5    922 ATTCAATAAATGGTTCTAGGAAAAGTGGCAAGCCACTTGTAGAAGAATGA 971
                         v     i       v  i   v  v   vv ?    v  i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_55837791_5    972 AACTGTAGAAGAATGAAACTGGAACCTCATCTCTCACCTTATACAAAAAT 1021
                          ---  -------------    v  ii i   v    v           
  L1M4_orf2#LINE/    449 A---GT-------------TGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_55837791_5   1022 CAACTCAAGACAGATCAAAGACTTAAATCTGAGACCTGAAACCATACAAA 1071
                         i       i ii     ?    i     v i   v  i    i   -   
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAA 531

  chr1_55837791_5   1072 TTCT-AGAAGATAACAT-TGAATAAACTGTTCTAGACATTGGGTTAGGCA 1119
                         i   -      v     -v ?i    - v   vv   v            
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCA 580

  chr1_55837791_5   1120 AAGAATTTATGACTAAAACCCAAAAAGCAAATGCAACGAAAACAAAAATA 1169
                          v iv  iv iiv  vi  v v       v v     i   iv       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_55837791_5   1170 AATAAATTATACCCAATTAATCTAAAAATCTTCTGCACAGCAAAAGGAAT 1219
                         i       iv  iiv  i  vv v    v   i  ii vv    i iv i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_55837791_5   1220 TATCAGCAGAGTAAACAGACAACCCACATAGTGGGAGAAAACATTAACAA 1269
                              iv i   i  v            v i          i   vi   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_55837791_5   1270 ACTATCCACCTGACAAAGGACTAATATCCAGAATGTGTAAGAAACTCAAA 1319
                          ii  vi i    i  i     vi          i i   ii     vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_55837791_5   1320 CAAATCAGCAAGAAAAAAAACAAATAACCTCATTAAACAGTGGGCAAAGG 1369
                            v   ii  v     i -         iv   ?  v i          
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.37 (123 / 90)
Gap_init rate = 0.02 (13 / 829), avg. gap size = 2.15 (28 / 13)  

 411 15.79 9.65 0.00  chr1_55837791_55840044.rev     1650  1763 (491)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_55837791_5   1650 CTCAAAAAAAAAAAAAAAAA-----------AAAAGTGGACAAAGGACAT 1688
                              v  v     i v   -----------    i   i       iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_55837791_5   1689 GAATAGATAATTCTCAAAAGAAGATATACAAACAGCCAACAAACATATGA 1738
                                i v     v                ii     i  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_55837791_5   1739 AAAAATGCTCAACATTACTAATTAT 1763
                            i           i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.01 (1 / 125), avg. gap size = 11.00 (11 / 1)  


1042 25.52 27.45 0.96  chr1_55857565_55860385.rev      502  1124 (1697)    L1M4_orf2#LINE/L1      121   908 (0)  

  chr1_55857565_5    502 GAAATCAATGAGC-GATGCTAAAATGTATATAAAAATGCAAAC-AGCCAA 549
                              ii ii   -   v       vi    ii        iv- v   i
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr1_55857565_5    550 ACCAAACAAATATAACTTGGAAAAGGAAGAATAAACTTGGAGTATTTACT 599
                          vi iv    - i  ii v     i      i   v      v i i  v
  L1M4_orf2#LINE/    171 AATAGCCAAA-ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_55857565_5    600 CT-------------ACATATTCTAAATCTACATTAAATAAAACAAGTGT 636
                           -------------  v  i vi   v     v   vi  i   -    
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA-GTGT 268

  chr1_55857565_5    637 GGTTCTGGTGCAGTAATAGACAAACAG-CCAATGGAAGAAAAATT----- 680
                            v    iii ivi       v i  -i        v i  -  -----
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA-TTGAGAG 317

  chr1_55857565_5    681 TCCAAAAACAGATATATACATATATGGTCATATGATTTATATCAAAGATG 730
                             i   i i ivi      v        vv      viiv   i i  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_55857565_5    731 -----ACTAT----------------AGT--------------GTACTGG 745
                         -----  i  ----------------   --------------  i    
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_55857565_5    746 GAAAAC-------CC-------------TGGTGTT--------------- 760
                           v   -------  -------------  iv   ---------------
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_55857565_5    761 ------TTTAATAATT---------TG--TC------CTGAAT------- 780
                         ------ vi  v    ---------  --  ------  i   -------
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_55857565_5    781 -------TATAGGAC--------------ATAGG----------CATG-- 797
                         -------    ii  --------------     ---------- i  --
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_55857565_5    798 ---------GACAAGGACTTCATGACTAAAACACCAAAAGCAATGGCAAC 838
                         --------- i   v ii   v iiv  vi            vvi     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_55857565_5    839 AAAAGCCAAAATTGACAAATGAGATCTAATTAAACTAAAGAGCTTCTACA 888
                              vv     v  i    vi  ii v  i   v v  i i   i iii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_55857565_5    889 CAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACATACAGAATGGGAG 938
                          vv    i  v    i  vv i      v  i    vi            
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_55857565_5    939 AAAACTTTTACAATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTA 988
                             iv   i   vii  vi      i  i  i  vi          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_55857565_5    989 CAAAGAACTCAAACAAATTTACAAGAAAAAAACAA----CCCCATCAAAA 1034
                         i         vv    v iv i  v     i    ----   v  i?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_55857565_5   1035 AGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGAATCTGTGCA- 1083
                          i            v    i     i     v        --- i i  -
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA---TATACAA 864

  chr1_55857565_5   1084 ---GCCAACAGACACATGAAAAAATGTTCCTCATCATCACTGGC 1124
                         ---     i ii          i   i  vv     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (94 / 64)
Gap_init rate = 0.03 (24 / 788), avg. gap size = 7.38 (177 / 24)  

 686 30.02 10.35 2.28  chr1_55857565_55860385.rev     1848  2330 (491)    L1M4_orf2#LINE/L1      387   908 (0)  

  chr1_55857565_5   1848 AAAGTATAATAATTAAAAAAAATTGTCCAGAATTAATTGAATACTAATAC 1897
                             v   i vv  vv  v    v  v v iivi  i  i   ?iv i i
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_55857565_5   1898 AGAGAAAAATAAA-------CCTT---TCACA--------AAAAATTCAA 1929
                         iv i  i   i  -------  i ---     --------       -  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AA 485

  chr1_55857565_5   1930 TCCCAGATGGATTGTAGACGTAA-TGCGATAAGTAAAAA-ATAAAGCCTC 1977
                         ii v i      ii?    v   -  ii v iv     v-     i iii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_55857565_5   1978 TGGAAGATAACCTACAATCGTA--TATTTATGACCTTGAGGTAGGTACAT 2025
                          i     v   -- i iv?   -- v  ii        i v    i -  
  L1M4_orf2#LINE/    536 TAGAAGAAAAC--ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-AT 582

  chr1_55857565_5   2026 ATTTCCTTA-ATAGAACAC--AATACACTAACCATAAAGGA-----TGCA 2067
                         iv  i    -   vi    --  vi   v i v i   i  ----- iv 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_55857565_5   2068 TATATATGACTTTAGTAA---TAACAACATTTTTCTGTGCATTGAAAGTT 2114
                           v  vv     i vi  ---   v   ----  i     v ii  i vi
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAAC----TTTTGTGCTTCAAAGGAC 678

  chr1_55857565_5   2115 ACCGTTAAGACAGTGAAAAGACAA---A-AAAGTAGGGAGAGATATTT-- 2158
                           ii i    v             --- - i i i  iii i      --
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_55857565_5   2159 AAACTACACCTATCCAACAAAAGATTTATAATAAAAA-AT-TAAAGGATT 2206
                            ii i --    ii i  ii  i  i  viv i  -  -     i i 
  L1M4_orf2#LINE/    729 AAATCATA--TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_55857565_5   2207 CCTATAAATCAATAAGAATAGGACACATAGCACAATTTTTAAGTCAGTGA 2256
                          i  i  v       v  v i    v   i v     ?vv  i vi i- 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC-A 825

  chr1_55857565_5   2257 AAAGACTTAAAGAAGCATATCATGAAAGAGGATGTTCAAATGGCCATTA- 2305
                           i  i  i  v ii   v  viv     i   i v          v  -
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_55857565_5   2306 GCACACG--------TTCAACATTAGTAGCCAT 2330
                              i --------i       i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (90 / 51)
Gap_init rate = 0.04 (23 / 522), avg. gap size = 2.65 (61 / 23)  


2044 27.49 4.61 0.74  chr1_55976144_55978485.rev      690  1362 (980)    L1M4_orf2#LINE/L1        1   699 (209)  

  chr1_55976144_5    690 TGGAAAAATATTTCATGCTCACAGATTAGAAGAATTAATA--GTTAAAAT 737
                               i    ii    i   ii    i     v      --     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_55976144_5    738 GGCCATGCTGTCCAAAGCAACTTACAGATTCAACAAAATCCCTATCAAAA 787
                            v  i  vi     vii ii            iv              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_55976144_5    788 TATCAATGACGGTTTCCAGAGAATTAGAAAAACCAATCCTAAAATTCCCC 837
                          vi  iivi vv   iiiv    v v  v  i ii            viv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_55976144_5    838 TGGACTCAAAAACAGCTCA-AATAGCCAAAGCAATCCTAAGCAGAAAGAA 886
                             vviiv  ivii i  -          i     i i iv ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_55976144_5    887 CAAAGCCAGAGGCATCACATTGCCCAACTTCACACTATACTATAAAACTA 936
                              iii    vv     i v     i    v viv     i   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_55976144_5    937 CAGTAATCAAAACAGCATGGTTCTTGTACAAA---AGACACATAAACCAG 983
                                   i    ii    v  v i i  i---     i   i i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_55976144_5    984 TTGACCAGAATAGAGAACCTAGAAATAAACCCACATACTTACTGCCACCT 1033
                          v  vi     v    ii i             i i i   iv i  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_55976144_5   1034 GGTATTTGACAAAA---TCAAAA--A--CAATGCAGGAAAGGACTCCCTA 1076
                          i v  i     ii---i   i -- --     -i      i ivvi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTT 399

  chr1_55976144_5   1077 TTTGGTAAATGGTTCTGGGAAAACTGGCTAGCCATATGACAAAGAATGAA 1126
                           iiii       v      v      v  ?   i   vv          
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_55976144_5   1127 ACTGGACCCCTACCTCTCACTGTATACAAAAATCAACTTAAGATGGATCA 1176
                         ii              v   ii           i    i  i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_55976144_5   1177 GAGATTTAA-CACAAGACCTCAAACTATAAA--TCCTGGGAGAAAACCTA 1223
                         ?   ii   -iii    v  v          --  i i i       v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_55976144_5   1224 GG---AAATGCCCTTCTCAACATAGGCTTTGGCAAAGAATTTATGACTAT 1270
                           ---    ---    vii  v v  v  v     v iv  iv iiv   
  L1M4_orf2#LINE/    550 GGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_55976144_5   1271 GTCCCCAAAAGCAATTGCAACAAAACAAAAATTGG-CAAGTGGGACCT-- 1317
                          v v         vvv         v     v i -i  i v    i --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_55976144_5   1318 ----AATTAAAGACCTTCTGCACAGCAAAAAAAA-----AAAAAAAAAAA 1358
                         ----       i  i  -  ii vv    ii v -----  i   ivi  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_55976144_5   1359 AAAA 1362
                           i 
  L1M4_orf2#LINE/    696 AAGA 699

Transitions / transversions = 1.73 (116 / 67)
Gap_init rate = 0.02 (15 / 699), avg. gap size = 2.40 (36 / 15)  

 451 24.24 13.94 0.61  chr1_55976144_55978485.rev     1680  1844 (498)    L1M4_orf2#LINE/L1      672   858 (50)  

  chr1_55976144_5   1680 AAAAGAAATTACCAACAGAGTAAA----CAGCCTACAAAATAGGAGAAAA 1725
                            i  v i  i   v i   i  ----  i  i   i   i        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_55976144_5   1726 TATT--CAAACTATGCATTTGACAAAGGTCTAATATCCAGAATCTACAAG 1773
                             --    ii  ii  i   i  i  v  vi          v  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_55976144_5   1774 GAACT---------------TAAACA-ACAAACA-TCTAGTCAAAAATAT 1806
                              ---------------    v -     i -i i i i?    -  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA-AT 820

  chr1_55976144_5   1807 GAGCAAAGGACATGAACAGATGCTTCTCAAAAGAAAAT 1844
                          i        iv    i   iii     v      i  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

Transitions / transversions = 3.88 (31 / 8)
Gap_init rate = 0.03 (6 / 187), avg. gap size = 4.00 (24 / 6)  


3241 24.55 3.03 1.23  chr1_55985592_55989707     2732  3623 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_55985592_5   2732 TGGCAAAATACTC--TGTGCATGGATTTCAAGAATCAATA--GTTAAAAT 2777
                            v  i   ii --   v        vv    v i    --     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_55985592_5   2778 GTCCATACTTCCCAAAGCAATCTACAGATTCAATTCAATCCCTATCAAAA 2827
                          v v     i      vii              iv               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_55985592_5   2828 TACCAATGACATTCTTCATGAAAAAAGAAAAAAAATTCCTAAGATTTATG 2877
                          v   iivi v  i  iiiii   vv  v  ivviv      i   i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_55985592_5   2878 TGGAATCACAAAAGGCCCAGAATAGCCAAAGCTATCATAAGCAAAAAGGA 2927
                              vii   ii i               i v   v i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_55985592_5   2928 CAAAACTGGAGGAACCGCATTACTTGACTTCAAAATTATACCACAGAGTT 2977
                             ii       vi i  i v iii i       i -   i   i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr1_55985592_5   2978 -TAGTAAACAAAACAGCATGGTAGTGGCATAAAAACAGACACATAGACCA 3026
                         -i     v   i    ii     v        ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_55985592_5   3027 ATGGATCGGAATAGAGAGCCCAGAAACAATTCTACACACCTATGGTAAAC 3076
                              vii    v     i       i  vi i i   ii      v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_55985592_5   3077 TCATTTTTGATAAAGGTGCCAAGAATATATCCTGGGGAAAAGACAGTCTC 3126
                          v     i  i  i          vi  vivv        ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_55985592_5   3127 TTCGATAAATGGTGCTGGGAAAACTGGATATCCATATGCAAAATAATGGA 3176
                            i i              v         ?   i        v    i 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_55985592_5   3177 ACTAGACCCCTATCTCTCACCATATACAAAAATCAAATCAAAATGGGTTA 3226
                         ii i        i   v                i  v         i i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_55985592_5   3227 CATACTTAAATCTAAGACCTCAGACTATGAAACTCCTACAGACTATGAAA 3276
                         ? v  i     v     v  v i     i      i  v i-----    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA-----GAAA 544

  chr1_55985592_5   3277 ACACTGGGGAAAATCTCCAGGACACTGG-TCAGGGCAAAGACTTCTTGAG 3325
                            iv  ? v      i iv   vi   - i   -   v ii     iii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTAGA 593

  chr1_55985592_5   3326 CACTATCCCACAAAGCACAGACAACCAA-GCAAACATGGACAAATGGGAT 3374
                         i iv iv   -        ii    v  - v   v  i  i    v   i
  L1M4_orf2#LINE/    594 TATGACACCA-AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_55985592_5   3375 CACATTAAG-TTAAAAAGCTTCTGCATAGCAAATGATACAATCAA---AG 3420
                         iv   i  i-       -   i  iiivv    v  i  v     ---  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_55985592_5   3421 TAAAGAGACAACCCACAGAATGAGAAAATATAGTTGCAAACTAC-TACTC 3469
                          i  i                 i  i  v   v       ii i-  -  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA-TC 740

  chr1_55985592_5   3470 TGACAAGAGATTAATAACCAAGATATATAAGGAATTC--A-AACTC--TA 3514
                            i   i  i vi  v   ii        i   i  -- -     --  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_55985592_5   3515 GAAAAAAAGC---TAATCTGATCAGAAGATGGGCAAAAGATTTGAATTAG 3561
                         iv     ii ---   i ii  i?i  i         i         -  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT-AG 839

  chr1_55985592_5   3562 ACATTTCTCAAAAGA-------CAAATGTCAAACAGGCATAGAAAAAGGT 3604
                                  v     -------      v v  i i   i vi     i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_55985592_5   3605 GCTCAACATCATTGATTAG 3623
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (146 / 69)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.90 (38 / 20)  


1409 27.11 16.77 2.27  chr1_56017846_56019642.rev      532  1324 (473)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_56017846_5    532 TGGAGAGAGAGACCATGCTCATTCATCGAAAGACTCAACATT---AAGTT 578
                             i   v vv     i    vv  i i      i  i   ---   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_56017846_5    579 CTCAGTTCTCCCCAAAGTGACCTATGAATTCTATGCAATCTCAGTCATAC 628
                         vv  i v         v   i   iii    v i      i vi   v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_56017846_5    629 TCCT--CTAGGCTCTTTAAGTAAAAATAAATATGCTTATTTAAAAATGCA 676
                            i--  --  ii   vv i i    vi i v   v  iiv     v  
  L1M4_orf2#LINE/    101 TCCCAGCT--GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_56017846_5    677 CATGGAAATCCAAAGGACCTAAAATATCCAAAACAATCTTAAAA------ 720
                         i        v   i     i i    v             i   ------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_56017846_5    721 --C----TTGGA---CTCA-ACT----GAGTTCAAGTCTTACTATAAATC 756
                         -- ----     ---    -   ----i v     iv       i   v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_56017846_5    757 TGTTGTGATCAGGATAGTGTGGCACTGACATAAGAATAAACA----GGTC 802
                          iiv  i    i  i       i    i      i   i   ---- i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_56017846_5    803 AA---------------AGTTAAGACATTCGTCCGTAC-TTAATGGTAAC 836
                           ---------------   iv   v  vvii  i   -  v     v v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_56017846_5    837 TTTATATCTTTGTCAAAAGT--------CAT------------------- 859
                           v  --i  i v   ii  --------   -------------------
  L1M4_orf2#LINE/    349 TTGAT--TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_56017846_5    860 CTTTTTAGTAAGTGGTGCTGGAAATCATCAGACATCCACTTAGAAAA-AA 908
                              i ii  i         i -iv iii  i ?    v iv    -  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGA-CAACTGGATAKCCACATGCAAAAGAA 445

  chr1_56017846_5    909 TAAACCTCAACCCCCACCCCATGTCACATCGTACAGAAAACTTAGTTCCA 958
                          i  vi vi     i   -----     i i  i v    v   ii  v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACC-----TCACACCATATACAAAAATTAACTCAA 490

  chr1_56017846_5    959 GATGGATTATACAACTAAAC-------TTAAAATTACAATGCATCT---- 997
                         i      i ? v v     i-------i     i  i  vi -   ----
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGA 539

  chr1_56017846_5    998 AGAAAACCTAAG-----ATCTTTAC-ACTTGGAGATAGGAAGGATTGTTT 1041
                                v  i -----     iii-  i v i v    v --  v    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA--ATGGTTT 587

  chr1_56017846_5   1042 TTT-----TAA----AAAAGGATAA----CAGAATGAAATCCTATAAAAA 1078
                         i  ----- i ----     v i  ----  i  -    vvv  v v   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAA 636

  chr1_56017846_5   1079 TACAACA-CATCAAAATCGGACATTCT----CACCAAAAAAGATCATTAA 1123
                          vvi  v-         iii v i i ---- vi    ii v ii  i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_56017846_5   1124 GAAAAT----AGTCATGGTATAAATCAGGAGAAAATATTTACCAAACGTA 1169
                             i ----  v  vvvi i i vii             i v  v i  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_56017846_5   1170 TGTCTGACAAAGAACTCATATCCAGAACACCAAAATAAATTCCCA-AATT 1218
                          i     i  i i   ii         i ivv   -i  i  ii -  i 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAA-GAACTCTTACAACT 785

  chr1_56017846_5   1219 TAACAATAAAAAGACAG----CTCAA------ACTCAGCAAAATATTTGA 1258
                         i  i            i---- i   ------ v vi     iv      
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_56017846_5   1259 ATGGAGACTTCTC-AAAGACAGCCACAGAAATAGCCAGT--------GAA 1299
                           i  v i     -     -  vi i v    i    i --------   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_56017846_5   1300 GTGAT-CTCCACATGGCAGAAGAGAA 1324
                         iv   -   v    --  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACAT--CAZZZZZZZZ 908

Transitions / transversions = 1.63 (132 / 81)
Gap_init rate = 0.04 (39 / 908), avg. gap size = 3.87 (151 / 39)  


2944 26.30 3.39 0.90  chr1_56188691_56194411     4343  5228 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_56188691_5   4343 TGGAAGAACATCCCATGCTCATGGATAGGGAGAATCAATATTATTGAAAG 4392
                              ii i        i        v  i   v i      i  i i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_56188691_5   4393 GGCCATGCTGCCCAAAGCAATGTACAGATTTAATGCTATTCCTATCAAAC 4442
                            v  i  v      vii  v        i  i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_56188691_5   4443 TACAAATGACATTCTTCACAAAGCTAGAAAAAAACT-ATTTTAAAATTCA 4491
                          v v iivi v  i  ii  i iv v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_56188691_5   4492 TATGGGACCGAAAAACAGCCTGAATGGCCAAGGTAATCCTAAGCGAAAAG 4541
                              i vi v  iiv v  v    i     iii    i i ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_56188691_5   4542 TA-AAGGGTGGAGTCATCACATTACCCAACTGCAAACCATACGACTGGGC 4590
                         v -  i v     vvv     i v     i v    v v   v  vii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_56188691_5   4591 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACGTGGACC 4640
                                 i   i    ii         i i  ii i     ii i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_56188691_5   4641 AATGGAACAGAATAGAGAGCCCAGAAACAAGGCCACACACCTATAGCCAT 4690
                                i     v     i       i  iv   i   ii   i i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_56188691_5   4691 CTGATTTTTGACTAAAATGACAAAAACAAGCAATGGGGAAAGGATTCCCT 4740
                         i       i   v iii  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_56188691_5   4741 ATTTAATAAATGGTGTGGGGATAACTGGCTAGCCATACGCAAAAGATTGA 4790
                         v  i  i        iv    i      v  ?   i i        v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_56188691_5   4791 AGCTAGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGATT 4840
                           i i       v   i                 i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_56188691_5   4841 AAAGACTTAAATATAAAACCCAAAACTATAAAAACCCTGTAAGACAACCT 4890
                          ?    i     i   i v i            vi i iv    v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_56188691_5   4891 AAGCA-ATACC------ATCCTGGACATAGG-AACAGC------------ 4920
                          i ?i- v i ------ i i   ii-    -  ii i------------
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chr1_56188691_5   4921 ACAAAAAAAGCAATCA--CAACAAAAGCAAAAATTGACAAATGAGATCTA 4968
                            vv       --  --         v      v  i    vi  ii v
  L1M4_orf2#LINE/    598 ACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_56188691_5   4969 ATTAAGCTTAAGAGCATCCTGCACAGCAAAAGAAACTATCAACAGAGTAA 5018
                           i  iv    i i - ii  ii vv    i  v        v i   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_56188691_5   5019 ACAGACAACCTACAGAATGGGAGAAAATATCTGCGAAGTATGCATCTGTC 5068
                          v        i                   i   i  vi  ii     vi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_56188691_5   5069 AAAGGTCTACTATCCAGCATCTATAAGAAACTTAGACAA----ATTTTCA 5114
                           i  v  vv       v  v     ii    ivv    ----  vv v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_56188691_5   5115 AGAGAAAAACAACTCCACTGAAAAGTGG-CAAAGTACATGAACAGACACA 5163
                          i   v   i   i v i ?    i   -     v iv    i     i-
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT- 843

  chr1_56188691_5   5164 CTTTTCAAAAAAAGATATACATGTGGCCAACA-GCATATGAAAAAAAGCT 5212
                         -  i  v   i          vi       i -   i       i v   
  L1M4_orf2#LINE/    844 -TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_56188691_5   5213 CAATATCACGATCATT 5228
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (144 / 85)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.53 (38 / 15)  


2698 28.57 0.22 1.20  chr1_56287269_56290772      492  1408 (2096)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_56287269_5   1408 TGGAAATATATCCTATAGTCATGGATAGGTAGGTAGAATAAATATTGTAA 1359
                               v      i  iv        v  - ---   v v        v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGG-A---AGACTTAATATTGTTA 46

C chr1_56287269_5   1358 AAATGACCATACCGCCAAAACCAATCTGCAAATTCAATGCAATTCTCATC 1309
                          i   i v    iv  v   iii    i  i      i     i ii   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

C chr1_56287269_5   1308 AAAATACCATCATCAGTCTTCATAGAACTAGAAAAATCAATCTTAAAATT 1259
                              v   v vv vv i  iii    v v  v  iiii   i       
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

C chr1_56287269_5   1258 CACGTGGAACCAAAAAAGAGCTTGCATAGCCAAATCCAGACTAAACAAAA 1209
                           ii     viiv  ii  v iv v         v v vvi i  v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

C chr1_56287269_5   1208 AGAACAAATCTGGAAGCATCACATTACCAAACTTCAAACCATACTACAAG 1159
                                 vi    i vv     i v  v  i      v v        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

C chr1_56287269_5   1158 GCTATCATTAGCAAAACAGCATGATGCTGGCATAAAAACAATCATGTAGA 1109
                             ivi v v   i    ii  i i         ii i iv   i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chr1_56287269_5   1108 CCAATGGAGCAGAATAGAGAAACCAGAAATAAAGCCAAATGCTTATAGCC 1059
                         i       ii     v    iv           v   v iii    i i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

C chr1_56287269_5   1058 AACTGATTTTTAACAAAGCAAACAAATACATAAAGCAGGGAAGAGGACA- 1010
                           i       ii    i vviv   ivv   vv iii     -  i i -
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAATAG 395

C chr1_56287269_5   1009 TCTTATTCAACAAATTCGAGTGCTGGACTAATTGGCAAATCACATGTAGA 960
                             -          ---i       ivi  i   vv ?i      i i 
  L1M4_orf2#LINE/    396 TCTT-TTCAACAAAT---GGTGCTGGGACAACTGGATAKCCACATGCAAA 441

C chr1_56287269_5    959 AGAATGAAACTGGATTCTCATCTCTCAGCTTACACAAAAATCAACTTGAG 910
                                 ii    ii ii i   v  v v  i        i    ii i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

C chr1_56287269_5    909 ATGGATCAAAGACTTAAATGTAAGACCTGAAACCATAAAAATTCTACAAT 860
                                 ?    i           v  i    i      v ii  v  v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

C chr1_56287269_5    859 ATAACATCAAAA-AACTTTTCTAGATATTGGCTTAGGCAAAGGGCTCATG 811
                          v     vii?i-  v i   vv  iv    v        v  vi  v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

C chr1_56287269_5    810 ACCAAGAACCCAAAAGCAAATGGAACAAAAACAAAGATAAATAGATAAAA 761
                         ivi v  vv         v v v       iv   i   i   i  vii 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

C chr1_56287269_5    760 CTTAATTAAATGTAAAAGATTATGCAGAGCAAAATAAATAATCATCAGAG 711
                            v  i   vv     iv  v  iivvv    iv v iv    vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

C chr1_56287269_5    710 TTAACAGACAACCCACAGAGTGGGAGAAAATCTTTGCAAACTATGCATCC 661
                          v  v              i           v        ii  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

C chr1_56287269_5    660 AACAAAGGACTAAATATTCAGAATCTACAAGGAACTCAAACAAATTAGCA 611
                         i i  i     vi-   i      v  i  i      vv    v i ii 
  L1M4_orf2#LINE/    742 GATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

C chr1_56287269_5    610 AGAAAACAATAAATAATCCCATCAACACGTGGGCTAAGGACATGAATAGG 561
                          v    vi i      i  v  i? v vi     v     iv       i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

C chr1_56287269_5    560 TAATTCTCAAAAGAAGATACACAAATGACCAACAAACATATGAAAAAAAA 511
                         i v     v          i       i    i  i  i       i vi
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

C chr1_56287269_5    510 TCTTAACATCACTGATTAT 492
                         -  i       ????????
  L1M4_orf2#LINE/    891 -CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (148 / 110)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  

2924 26.69 1.54 0.71  chr1_56287269_56290772     2161  3003 (501)    L1M4_orf2#LINE/L1        4   853 (55)  

  chr1_56287269_5   2161 AAAAAAATTCCATGATCATGGATTGGAAGAATCGATATAGTTAAAATGGC 2210
                            i v  i     v               v ii    v     i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_56287269_5   2211 CATAGTGCCCAGAGCAATTTATAGATTTAATACTATTCTTATCAAAATAC 2260
                         v   v v    i vii  i  i     i  ii v  i i         v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_56287269_5   2261 CAACATTATTTTTCACAGAACTAGAAAAAAACT-ACTCTAAAATTCATTT 2309
                           i vviv     ii     v v  v  i--  - ii           v 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATAT 151

  chr1_56287269_5   2310 GGAATAAAAAAAGAGCCTGAATAGCTAAA----TCCTAAGCAAAAAGAAC 2355
                             vviv  ii  v  v       i   ----  i i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_56287269_5   2356 AAAGCCAGAGGTAC-CACATTGCCTGACTTCAAACTATACTGTAAGGTTA 2404
                             iii    -  -    i v  ii i      viv    ii  i i  
  L1M4_orf2#LINE/    202 AAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_56287269_5   2405 CAGTAATCAAAACAGCATGGTACTGGTAT---GGTACAAAAACAGATCAG 2451
                                   i    ii         i  --- i  v v v i      i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_56287269_5   2452 TAGAACAGAATTGTGAACCCAGAAATAAACCCACACACCAACAACCATCT 2501
                          i   i       v  ii               i   iiv iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_56287269_5   2502 GGTCTTTGACAAAAACAACAAAAATAAGCAATGTGAAATGGACTGTCTAT 2551
                          i i  i     iiiiiv   i vi vv     v i  v i iv    v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_56287269_5   2552 TCAATAAATGGTGCTGGGAAAATTGTCTAGCCATATGCAGAAGAATGAAA 2601
                             i              v  i  vv  ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_56287269_5   2602 CTGGACCCCTACCTCTCAACGTATATGAAAATTAATTTAAGATGGATTAA 2651
                         i              v  v i    ii        i i  i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_56287269_5   2652 AGATTTAAATGTAAGACCTGAAACTATAAAAATCATAGAAGAAAACCTAG 2701
                            ii           v  i           v  v           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_56287269_5   2702 G---AAATACCCTTGTTAATGTTGGCTTTGGCAATAAATTTATGGCTAAG 2748
                          ---    -- i i  -i iv    v  v      iiv  iv i v  v 
  L1M4_orf2#LINE/    551 GNGTAAAT--CTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_56287269_5   2749 TGACCAAAAGCAATTGCAACGAAA-ACAAAATTGACAAATATGACCTAAT 2797
                         vv          vvv     i   - v     v  i    vv   i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_56287269_5   2798 TAAACAAAAGAGCTTCTGCACAGCAAAAGAAATTATCAACAGGGTAAACA 2847
                         i   vvv  i i   i  ii vv    i  v i      v ii  i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_56287269_5   2848 GACAACCTACAGAATGGGAGAATACACTTGCAAACTATGCCTCTGACAAA 2897
                                i              v i i       ii  iiv     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_56287269_5   2898 AGTCTAATATCTAGACTCTACAGGGAACTTAAACAAATCAACAAGCAAAA 2947
                         i v  vi    i   v v  i ii     ivv    v    i  vv    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_56287269_5   2948 AACAAACAATCCAATTGAAAAATGGGCAAAGGACATGAATAGACACTTTT 2997
                         i     i  i      ?                iv          i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_56287269_5   2998 CAAAAG 3003
                          v    
  L1M4_orf2#LINE/    848 CCAAAG 853

Transitions / transversions = 1.55 (135 / 87)
Gap_init rate = 0.01 (10 / 850), avg. gap size = 1.90 (19 / 10)  


2783 26.44 2.30 1.38  chr1_56304093_56305954      500  1369 (493)    L1M4_orf2#LINE/L1       31   908 (0)  

  chr1_56304093_5    500 AGAATCAATATAGTTAAAATGTCCATACTGCCCAAAGCAAACTACAGACT 549
                            v i     v     i   v v     v      vii v       i 
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chr1_56304093_5    550 CAATGCTATTCCTATCAAATTACCAATATCATTTTTCACAGCACTAGAAA 599
                            i  v  i         v v   iivv v     ii   v v v  v 
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA 130

  chr1_56304093_5    600 AAATTATCCTAAAATTTATATAGAACCAAAAAAGAGCCCAAATAGCCCAA 649
                          iv v           i    i   viiv  ii  v  vi       v  
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr1_56304093_5    650 GGATTCCTAGGTGAAAA-AACAAAGCTGGAGCCATCGCACTAGCCAACTT 698
                         iv v  i iiivi i  -       i     vvv  i    vv    i  
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_56304093_5    699 CAAACTACACTTGAAGGCTACAGTAA-CACAAACAGTATGGTACTGGTAT 747
                             vivi   vv  i          -  - i     i         i  
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCA-AGACAGTGTGGTACTGGCAT 279

  chr1_56304093_5    748 AAAAATAGACACATAGACCAATGGAGCAGAATAGAGAGCCCAGAAATAAA 797
                           ii       i     i       ii     v     i           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_56304093_5    798 GCCACACACCTACAATCAACTGATCTTTAACAAAGTCGGCACAAATAAGC 847
                         v   i   ii  iii    i    i  ii    i vi v  vi vi vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_56304093_5    848 AACAGGGAAAGGAC--TCCTTATTCAATGAATGGTTCTGGAAAAATTGAC 895
                           ii       i i--  i  --    ii      v    i v  i  iv
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_56304093_5    896 TAACCATATGCAGAAGAATGAAATTGGACACTTACCTCTTACCATATACA 945
                           ?   i     i         i      v i      vi          
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_56304093_5    946 AAAATTAACTCAGGATGAATTAAAGACTTACATGAGTGACTTCAAACTAT 995
                                     ii   i  i ?    i  v   viv  vi v       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_56304093_5    996 ATAAATCTTAGAAGAAAACCTAGGAAATACTCTT-GTGGACATTGGCCTA 1044
                          v  v              v    ?ivv v    -   -  v    vi  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTA 576

  chr1_56304093_5   1045 GGCAAAGAATT------TATGACTAACTTCTCAAAGCAAATGCAGCAAAA 1088
                              v iv  ------      --  i---v      v v   i     
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGAC--ACC---AAAAGCACAAGCAACAAAA 621

  chr1_56304093_5   1089 ACAAGAATTGACAAATGGGATCTAATTAAAGT-----GCCTCTGCACAGC 1133
                         iv  i   v  i    v   ii v  i   i -----i i i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_56304093_5   1134 AAAAGAAACTATCAACAGAATAAACAGACAACCTACCGAATGGAAGAAAA 1183
                            i  v        v i i i  v        i  v      i      
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_56304093_5   1184 TATTCACACACTATGCATCTGACGAAGGACTAATATCCAGAATCTATAAA 1233
                             ii  v ii  ii      ii i     vi          v      
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_56304093_5   1234 GAAGTTAAACAAATTAACAAGAGAAAAACGA----CCCCATTAAAAAGTG 1279
                            v ivv    v i  i  v i   i  i ----   v   ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_56304093_5   1280 AGCAAAGAACACTAATAGACACTTCTCAAAAGAAAACCTACAAGTGGTCA 1329
                         i      i iviv        i     v      i iv     i   i  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_56304093_5   1330 AAAATTATGTAAAACAAAAGTGCTCAATATCACTGATCAT 1369
                          v  vi ii i   --- ii       i    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAA---AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.01 (13 / 878), avg. gap size = 2.46 (32 / 13)  


2901 24.06 1.93 4.81  chr1_56341680_56343830.rev      726  1660 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_56341680_5    726 TGGAAAAATATTACATGCTCATAGATAGTAAGAATCAATATTGTTAAAAT 775
                               i    iv    i    i   v v    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_56341680_5    776 GTCCATATTGCCCAAAGCAACTTATAGATTCAGTGCTATTCCTAGCAAAC 825
                          v v   i v      vii ii  i       ii  v  i    v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_56341680_5    826 TACCAGTGATATTTTTCACAGAATTAGAAAAAAAAAAAAAACT-ATTCAA 874
                          v    iviiv     ii     v v  v  i---------  -  i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---------CTGATCCTA 141

  chr1_56341680_5    875 AAATCC-TATGGAACTTTTAGAG--CCTGAATAGTGAAAAATAGGTTAAG 921
                             i -       v viv  i --  v      iv    vv vv  i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_56341680_5    922 CAAAAAGAACAAAACTGAAGGCATCACGTTACCTGACTTTAAACCATATT 971
                         v  i         ii  i   vv    ii v  ii i  i   v v  i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_56341680_5    972 ACAGAGTTACAATAACCAAAACATCATAGTACTGGTACAAAAACAGACAC 1021
                            i  i    i   i   i   vii i       i i  ii i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_56341680_5   1022 ATGGACCAATGCAACAGAATAGAGAGCCTAGAAATAAAGCCACACACCTA 1071
                           i  i     v  i     v     i i         v   i   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_56341680_5   1072 CAGTCATCTGATCTTTGACAACATCTACAAAAACAAGCAATGAGAAAAGA 1121
                         ii    vi    i  i     vivivv   i v  vv     i i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_56341680_5   1122 CT--TCCTGTTCAACAAATGGTGCTGAGATAACTGCCTAGCCATATGCAG 1169
                         v --  i -                 i  i     vv  ?   i     i
  L1M4_orf2#LINE/    392 ATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_56341680_5   1170 AAGATTGAAACTGGACCGCCCCCCCCACCCTTTTTTTTTTTTTTTTTTTT 1219
                             v    ii      -  iv  i   ----------------------
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACC-CCTACCTCAC---------------------- 467

  chr1_56341680_5   1220 TTTTACCATATACAAAAACCAACTCAAGATGGATTAAAGACTTAAATGTA 1269
                         ----              ii       i      i ?    i        
  L1M4_orf2#LINE/    468 ----ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_56341680_5   1270 AAACCTAAAACTATAAAAAACCTAGAAGAAATCCTAGGAA-AAACTATTA 1318
                          i v              vv i         v v    ?i-   iiv ii
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_56341680_5   1319 TGGACATAGGTCCTGGCAAAGATTTCATGACAAAGATGCCAAAAGCAATT 1368
                           iv v i   iv-     v i    v iivv v  ii         vvv
  L1M4_orf2#LINE/    564 TGACCTTGGGTTA-GGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_56341680_5   1369 GCAACAAAAAGAAAAATTGACACATGGGACCTAATTAAA-TTAATGAGCT 1417
                                  ii      v  i v  v    i v  i   -    -i i  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA-AAACT 661

  chr1_56341680_5   1418 TCTGTACAGCAAAAGAAACAATCAACAGAGTGAAGAGACAACCTACAGAA 1467
                          i   i vv    i  v  v     v i      i        i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_56341680_5   1468 TGGAAGAAAATATTTTCAAAC--TGCATCTGACAA---ACTTCTAATATC 1512
                            i           v    i-- ii      i  ---    ---i    
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT---GTATC 758

  chr1_56341680_5   1513 TAGAATCTATAAGGAACTTAAACAA---AATAACAAGCAGAAAACAAACA 1559
                         i     v     i     ivv    ---     i  i---  i     i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAA---AAGACAAATA 805

  chr1_56341680_5   1560 ATCCCATTAAAAATTGGGCAAAGGACATGAATAGACACTTTTCAAAAGAA 1609
                          i  v   ?    v           iv          i  i  v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_56341680_5   1610 GACATACACACAGTCAATAAGCA--TGAAAAAATGCTCAACATTACTAAT 1657
                           i     v ii i         --      i           i ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_56341680_5   1658 TAT 1660
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.60 (136 / 85)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.50 (63 / 18)  

 267 17.78 2.22 6.67  chr1_56341680_56343830.rev     1661  1750 (401)    L1M4_orf2#LINE/L1      792   877 (31)  

  chr1_56341680_5   1661 TAAAGAAATCCAAATCAAAACCAAAT--GAAATTGGGCAAAGGGCATGAA 1708
                             i i --     ---    v   --i   v          iiv    
  L1M4_orf2#LINE/    792 TAAAAAGA--CAAAT---AACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_56341680_5   1709 CAGACACTTTTCAAAAGAAGACATACACACAAGCCAATAAGC 1750
                         i     i  i  v        i     v ii-          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATG-GCCAATAAGC 877

Transitions / transversions = 2.20 (11 / 5)
Gap_init rate = 0.05 (4 / 86), avg. gap size = 2.00 (8 / 4)  

 447 14.38 3.42 6.16  chr1_56341680_56343830.rev     1751  1896 (255)    L1M4_orf2#LINE/L1      767   908 (0)  

  chr1_56341680_5   1751 ATGAAAAAATGTT-CAACATCACTAATTATTAAAGAAATCCAAATCAAAA 1799
                           i  i  v v  -    -   v    v --     ----     --  v
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAAC-TCAATAATAA--AAAGA----CAAAT--AAC 807

  chr1_56341680_5   1800 CCAA--AGAAATTGGGCAAAGGACATGAATAGACACTTTTCAAAAGAAGA 1847
                             --?i   v           iv          i  i  v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_56341680_5   1848 CATACACACAGCCAATAAGCA--TGAAAAAATGCTGAACATCACTAATTA 1895
                         i     v ii           --      i     v       ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_56341680_5   1896 T 1896
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.00 (10 / 10)
Gap_init rate = 0.05 (7 / 142), avg. gap size = 2.00 (14 / 7)  


2735 25.27 1.71 4.90  chr1_56521373_56526246     3446  4383 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_56521373_5   3446 TAAAAAAGCATTCCATGCTCAGGGATTGGAGGAATTAATACCATTAAGAT 3495
                          ii   iii  i     i   v        i  v      iii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_56521373_5   3496 GTTTATACTGCCCAAAGCAGTCTATAGATTTAATGCTATTT-TATAAAAT 3544
                          viv     v      viii    i     i  i  v  ii-   v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_56521373_5   3545 TTTCA--T-CATTTTTCACAGAACTAGAAGGAAACT-ATTCTAAAATTTA 3590
                          ii  -- - v     ii     v v  v--  i  -  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chr1_56521373_5   3591 TATGGAATCAAAAAAGAGCCTGAATAGCTAAATCAATCCTAAGCAAAAAT 3640
                                viiv  ii  v  v       i   v     i i iv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_56521373_5   3641 AATAAAGCCAGAAGCATCACATTATCTGACTC--AAACTATACTACAAGA 3688
                           i    iii  i vv     i vi ii i i--     -        ii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_56521373_5   3689 CTACAGTAACCAAAACAGCATGGTAGTGGTTAAAAAAAAAAAAAAAGAAA 3738
                                  i   i    ii     v   i--------------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGC-------------------- 277

  chr1_56521373_5   3739 GAAAGAAAGAAAAAAAAAAGACACATAGACCAATGGAACAGCAT--AGAC 3786
                         ---------- v  ii v     i     i        i  v  --   v
  L1M4_orf2#LINE/    278 ----------ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_56521373_5   3787 TCCTGAAATAAAGCTGCACACTTACAACCAACTGATCGCCAACAAAGTCA 3836
                            v        v iii   i   iiii   i    ivi i    i vii
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_56521373_5   3837 ACAAAAATAAACAGTAGGGAAAGGATATCCTATTAAATAAATAGTGCTGG 3886
                         v   i vi vv  i i       i   vi  v  v  i    i       
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_56521373_5   3887 GAAAAATGGCTAACCATATGCAGAAGAATGAAACTGGACCCCCACCCCCA 3936
                           v  v   v  ?   i     i         ii        i   i --
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC-- 465

  chr1_56521373_5   3937 TCCCACCTCTTACCACATACAAAAATTAACTCAAGCTGGATTAAAGGCTT 3986
                         ----  -----    i                  iv     i ?  i i 
  L1M4_orf2#LINE/    466 ----AC-----ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_56521373_5   3987 AAATGTAAGACTTCAAATTATAAAAATCCTAGAAGAAAACATAGGAAATA 4036
                                   vi v   i       v  i                ?ivv 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_56521373_5   4037 CTCTTCTAGAGATTGGCCTAGGCCAAGAAATTTATGACCAAGTCCTCAAA 4086
                         v     vv  vv    vi     -  viiv  iv iivi v v vi    
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTAGATATGACACCAAA 605

  chr1_56521373_5   4087 ATCAATTGCAACAAAA-AAAAAATC-ACAATTGGGATCTAATTAAA-TGA 4133
                          v  vvv         -       v- i  v v   ii v  i   - v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_56521373_5   4134 GAGAGCTTCTGCACAGCCAAAGAAACTATCAACAGAGTAAACAGACAGCC 4183
                         i i -   i  ii vv v  i  v        v i   i  v     i  
  L1M4_orf2#LINE/    656 AAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_56521373_5   4184 TACAGAATGAAAGAAAATATTCGCAAACTGTGCATCTGACGAAGGTCTAG 4233
                         i        ii          i     iii ii      ii i  v  v 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_56521373_5   4234 TATCCAGAATCTATAGGGAACTTAAACAAATCAACAAGAAAAAAACAAAT 4283
                                   v    ii     ivv    v    i  v     i      
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_56521373_5   4284 AACACCATTAAAAGGTGGGCAAAG----TGAACAGACACTTCTCAAAAGA 4329
                            v v   ?   ii         ----    i     i     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_56521373_5   4330 AGATATACAAGTGGACAGAAAACACATGAAAAAATGTTCAACATAACTGA 4379
                                   i   v  iv  i          i   i       v ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_56521373_5   4380 TCAT 4383
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.62 (144 / 89)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.65 (62 / 17)  


3219 23.96 2.20 1.04  chr1_56908879_56911402     1159  2022 (502)    L1M4_orf2#LINE/L1        1   874 (34)  

  chr1_56908879_5   1159 TGGAAGGACATCTCATGCTCATAGATTGGAAGAATTAATATTGTTAAAAT 1208
                              i  i   i    i    i          v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_56908879_5   1209 GACCATATTACCCAAGGCAATCTACAGATTCAATGCAATCCCCATCAAAA 1258
                          i v   i v     ivii              i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_56908879_5   1259 TACCAA-TGCCTTTCTTCACAGAAATAGAAAACACAATCTTAGAATTTGT 1307
                          v   i-       i  -i       v  v  vvii   i  i    ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_56908879_5   1308 ATGGAATCACAAAAGACCCCAAGTAGCTGAAGCAATTCTGAGCAA-AAGA 1356
                               vii   ii     vi i    ii  i    ii   iv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_56908879_5   1357 ACAAATCTGTATAAAGCACAGTACCAGACTTCAAAACATTCTACAAAGCT 1406
                              vi  v vi vv    v v  vi i        v v          
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_56908879_5   1407 CTAGTAATCAAAACAGCACAGTGTTGGCATAAA-ACAGACACACAAACCA 1455
                         vi         i    iiii  ii        i- i     i i i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_56908879_5   1456 ATGGAACAGAATAGATAACCCAGAAATTAATCCATGTATCTACAGCCAAC 1505
                               i     v  v ii        v  i    ii  i  ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_56908879_5   1506 TGCTTTT-GACAAAAACTCCAAGAACACTCAATGGGGGAAGTACAGTCTT 1554
                           v    -     iiiiv      v  i         i   v i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_56908879_5   1555 TTCAGTAAATGGTGCTAGGAAAACTGGATATCCATATACAGAAGAATAAA 1604
                             ii          i   v         ?   i  i  i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_56908879_5   1605 ACTAGACCCCC-CCACCCACCACTTACACTATACAAAAATCAAACAAAAA 1653
                         ii i      i-  v v     -------           i  viv    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCA-------TATACAAAAATTAACTCAAAA 492

  chr1_56908879_5   1654 TAGATCAAAGACTTAAAATGTAAGGCCCAAACCTCTAAAACTATTAGAAG 1703
                          i     ?    i    -      iv i   v  v       v       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_56908879_5   1704 AAAACA--GGGGAAACACTTCAGGACATTGGTCTAGGAAAAGGTTTTATG 1751
                               --  ? v  vv    iv   v    vi    v  v     iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_56908879_5   1752 ACTAAGACCTCAGTAGCACAAGTAACAAA-GCAAAAATCAACAAATGGGA 1800
                         iv  v   vi  iv        i      - v      vi i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_56908879_5   1801 TTTCAGCAATCTAAAAAGCTTCTGCACAGTAAAAGAAACAATCAACAGAG 1850
                         i    v   vv v    i   i  ii vvi   i  v  v     v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_56908879_5   1851 TGAAAAGACAACTTACAGAATGGAGAAAAATATTCACAAACTATTAATCT 1900
                                     ii         iii        ii    ii  vv    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_56908879_5   1901 GACAGGTGATTAATATCCAGAATATACAAGGAACTCAAACAGC--AA-AA 1947
                           i i v  i vi             i  i      vv   i --  -  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_56908879_5   1948 CAGAAAAAAAAAT---TCAATTAAAAAATGGGCAAA-----TGAACAGAC 1989
                         i i   i v    ---i     ?             -----    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_56908879_5   1990 ATTTCTCAAAAGATGACATTAAAATGACCAATA 2022
                                v     v  i  vv     i      
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.71 (128 / 75)
Gap_init rate = 0.02 (14 / 874), avg. gap size = 2.00 (28 / 14)  


2832 20.82 3.47 0.00  chr1_57560721_57562346      500  1133 (493)    L1M4_orf2#LINE/L1      253   908 (0)  

  chr1_57560721_5    500 GTAATGAAAACAGTGTGGTGCTGGCATAAAGACAGACATAGAGACCAATA 549
                              v  i          i         i  i       v   i    i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_57560721_5    550 GAAGAGAACAGAAAGCCAAGAAATAAAACCTCACATAGAAGGTCAAATGA 599
                            v    iv  i  i v         v  vi    vv v      v   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_57560721_5    600 TTTTTGACAAGGGT--TAA----ATTCAGTGGGGAAAAGACAGTGTCTTT 643
                             i         --i  ----     i        ii i   v i  i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_57560721_5    644 AGCAAACAGTGTTGGGAAAACTGAATATCTAGATGCAAAAGAATGAAATT 693
                          i    ii   i     v     i   ? i v               i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_57560721_5    694 GGACCCTTACCTAACTCCATTTACAAAAATTACCTCAAAATGGCTCAAAG 743
                               i     v  v    v           v          v   ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_57560721_5    744 ACCTAACCATGAAACTTACAACTACAAAACCTTTGAAAGAAAACACAAAG 793
                               vii i i vi  v     i     ii  ii         i ii?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_57560721_5    794 GAAAAGTTTCACAATACTGAATTTAGCAACAATTTTTTGGATATGATACC 843
                          v   vi   iii ivi  ii  vi    iii   i  i       i   
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_57560721_5    844 AAAAGCACAAACAACAAAAGTAAAAATGCGTAAATCACACTATATCAAAA 893
                                   i         v      ivi     iiv   vi       
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_57560721_5    894 TTTAAAACATCTATGCATCAAAGGACATGATCAAAAGAGTAATAAG---- 939
                           v     v i i   v          iv     i i   i v   ----
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_57560721_5    940 ----TGG--TAAGAAAAAATATTTGCAAATCATATATT--ATAAGGGGTT 981
                         ----ii -- ii  i                      i--       ii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_57560721_5    982 AATATCCAGAATATATAAAGTATTCTTACAACTCAACAAGAACAAGACAA 1031
                         vi                  v i             i  v  v       
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_57560721_5   1032 ----CCCAATTTAAAAATGAGCAAAAGACTTGAATGCTCATTTCTCCAAA 1077
                         ----       ?       i     i  i      ivv            
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_57560721_5   1078 GAAGACATACAAATTGCCAACAAGCATTTGAAAAGATGCCCAACATCACC 1127
                              i        v     i     iv           i        ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_57560721_5   1128 AATCAT 1133
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.98 (85 / 43)
Gap_init rate = 0.01 (6 / 656), avg. gap size = 3.67 (22 / 6)  


3513 25.94 0.99 0.77  chr1_57606430_57608451.rev      625  1530 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_57606430_5    625 TAGAAAGCGATCCCATGCTCATGGAGTAGAATAATTAATGTTGCTAAAGT 674
                          i     vv        i       v i   v v     i   i   ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_57606430_5    675 ATCCATACTATCCAAAGCAATTGATAGATTCAATATAATCCCTAT-AAAA 723
                         iv v     vi     vii  iv i        iii         -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_57606430_5    724 TGCTAATTACGTTTTTCACAGAAATAGAAAAAA-AATCCTAGAATGTATA 772
                          v i ii i v     ii       v  v  iv-i      i   vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_57606430_5    773 TGGAACCACAAAAGACTTTGAATATATAAAGCAGTCTTATAAGATAATTA 822
                              vii   ii   iiv     vvi   i  i    iv  i v  vv 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_57606430_5    823 CAAC-CCAGAGGCATCATACTACCTGATTTCAAAGTATATTATAAAGCAA 871
                            v-iii    vv   i   v  ii        iiv  i  i     v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_57606430_5    872 TAGTAATCAAAATAGTATGATACTGGAATGAAAACTGACACATAGACCAA 921
                         i         i i   i  i      v  i ii iv    i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_57606430_5    922 TGAAACAGAATAGAGGGCCTAGGAATAAATTCACCCATATACCATCAACT 971
                           i  i     v   i i i  i      ii  iv   v  ivi    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_57606430_5    972 AATCTTTGGTAAAGTCACCAAG--CATACATAAAGGGGAAAGGATAGTCT 1019
                         i  i  i ii  i vii     --   v  -- v        i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAGAATAGTCT 398

  chr1_57606430_5   1020 TTTCAATAAATGGTGTTGGGAAAACTGCATGTCCACAAGCAAAAGAATGA 1069
                               i        i     v     v  i?     v            
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_57606430_5   1070 AATTGAATCCTTATATTATGCCATATATGAAAATCAACTCAAAATGGATT 1119
                          i   i i  i  iv i ii       ii     i              i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_57606430_5   1120 AACGAC--AGATGGAAGACTTGCAATAATAAAAATCCTAAAAGAAAACAC 1167
                          ?v   -- i   v    vi iv  iv      v  i  i         i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_57606430_5   1168 AGAGGAAAAGCTCCTTGGCATTGGTCTTCACAATGATTTTTTGGATATGG 1217
                           i? v   v  i v  i v    vi vvi     i   i  i      i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_57606430_5   1218 CACCAAAAGCATAGGCAACAAAAGTGAAAGTAGACAGGTGGGGCTACATC 1267
                                    i i          vi   i    i ii v  i  v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_57606430_5   1268 AAACTCAAAA-CTTTTTCATAGCAAAGGAAACCATCAAAAAAATGAAAAG 1316
                            v i    -     viiivv       v  i     i   i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_57606430_5   1317 GCAACCTACAGAATGGGAGAAAATATTTGCAAGCCATGTATCTGATAAGG 1366
                         i     i                         ii   i            
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_57606430_5   1367 GGTTAATACTCAAAATATGTAAGGAATTCATTACAACTCAATAGTAGACA 1416
                          ii vi  ii  i     i   i   i  -             i  i v 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTC-TTACAACTCAATAATAAAAA 797

  chr1_57606430_5   1417 -ACAAACAACCTTATTTTTAAAACGGGCAAAGGACCTGAATGGACTTTTT 1465
                         -     i    iv   ?v-    i          ii     i   v   i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_57606430_5   1466 TTTGTTAAAGAAGGCATATAAATGGCCAGCAGGCATGTAAAAAGTTGCTT 1515
                          ii---       ii   i         ii i   ii i     v    i
  L1M4_orf2#LINE/    847 TCC---AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_57606430_5   1516 AATATCACGAATCAT 1530
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.30 (161 / 70)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


2211 25.21 10.04 1.55  chr1_57610149_57612100      623  1459 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_57610149_5    623 TGGAGAGACATACAATGTTCATGGTTTGAAAAACAT--TATTGATTAGAT 670
                             i   i  v v          v   i  i  v --     v v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_57610149_5    671 GTCACTTCTCCC-AAACTGAAGTATACATTCAGCACAATCCCAATAAAAT 719
                          v  v v     -   i   vv  i v     i i       v  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_57610149_5    720 TCCTAGC-ACACTTTTTGAAAAAACTGACAAGTAAATTAAAAAATATACA 768
                            i   -i vi      v i   i       ivi  ivv     vi i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_57610149_5    769 TGAGAATGCAAAGGGACTTGGAATAGCCAAAACAATCCTGGGAAAGAAGA 818
                           ii       -     iii                 i  ii        
  L1M4_orf2#LINE/    151 TGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_57610149_5    819 ACAAAGTTAGAAGGTTTATCCTACCTGATTTCAAGACTTACTAGAAAGCT 868
                                 i  i ii i iv  v  ii       i        v      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_57610149_5    869 CTAGTAATCAAAACCTTATGGTAATTGGCA-------------------- 898
                         vi         i  vv i     -i     --------------------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTA-CTGGCATAAGGATAGACATATAGATC 298

  chr1_57610149_5    899 AATGAGACAAAATAGAGAATACAGAAATAGATCAATGCA------GTCAC 942
                             ii i i   v    i v        i i v  i  ------    v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_57610149_5    943 TTGATTTTTTTTTGA--AAAGTGACAATGCAGTTCATTGAGGAAAG---- 986
                                 i----  -- ii   v   vi vi    v  i      ----
  L1M4_orf2#LINE/    349 TTGATTTTC----GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_57610149_5    987 -TCTTT--AAAATATGGTACTGAAACAACTGCATAAACATATGGGAAAAA 1033
                         -     --  v v     i   ii       v   ?v  i   vi   i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_57610149_5   1034 ATCAGCATGAAGTTCTTCCTCATAT-GTATATAGAA-------CAAAATA 1075
                           v ivv  i vii  v     i i-i    i i  -------      i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_57610149_5   1076 -----------------TAAAAGCTAAAATGGTAAAAGTTCTGGAAGAGA 1108
                         -----------------   i        ivi     v ii i     i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_57610149_5   1109 ACCTTGGAAAGTGTCTTCATGATTTAGAGGTATGCACAGGTTTCTTAGAG 1158
                           v v  ?ivivi     i   ii v i v  v   vv           v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_57610149_5   1159 AGGAGACAAAAATCACTG--AACATGAGAAAA--T-GCTGAATTGAACTT 1203
                          v  v  v    v   vi--    vi      -- - v i     i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_57610149_5   1204 TATCACAGTTTAGAATATTTGATGAT-CAAAGAAAAC-ATTAAGAAAGTT 1251
                         i    v i  v i  iv    -  v -     i v  -  i        v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_57610149_5   1252 AATGG-TAAACCACAAACTTGGGGAAAATATTCACAACACATATATCTGA 1300
                           vi -i  v     i v v  i         ii   vv           
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_57610149_5   1301 CAAAGGACTTGAATCCAAAAAA-ATAAAGAAATTCTT-CAAATTAATAGT 1348
                         i  i       v     i  v -        -i    -   v i    i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATAAT 792

  chr1_57610149_5   1349 GAAAAGACAA----TCTAATT--AGAATGAACGGAAGACTT---T-GACA 1388
                         i         ----i i    -- i    ii ii i  i  --- -    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_57610149_5   1389 GCTCACCAAAAAAAAAAAAACAAAAAAACTATAAGTAGGTACATGAAGAG 1438
                         vi  v     i  i v v -    viiv v     i ----      i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATA-CAAATGGCCAATAAGCA----CATGAAAAG 887

  chr1_57610149_5   1439 ATGCTCAATATCACTGATCCA 1459
                                 i    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (123 / 86)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 3.23 (97 / 30)  


3107 26.10 1.21 1.21  chr1_57740507_57746882     4976  5883 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_57740507_5   4976 TGGAAGAACATTC-ATGCTCATGGATAGGAAGAATCAATATGGTGAAAAT 5024
                              ii i  i -   i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_57740507_5   5025 GGCCATACTGCCCAAGGTAATTTATAGATTTAATGCCATCCCCATCAAGC 5074
                            v     v     iv i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_57740507_5   5075 TACAAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5122
                          v v iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_57740507_5   5123 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5172
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_57740507_5   5173 AACAAAGCTGGAGGCATCACGCTACCTGACCTCAACCTATACTATAAGGC 5222
                                i      vv    i  v  ii ii    vviv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_57740507_5   5223 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5272
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_57740507_5   5273 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACT 5320
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_57740507_5   5321 ATCTGATCTTTGACAAACCTGACACAAACAAGAAATGGGGAAAGGATTCC 5370
                          vi    i  i     ivv  v  vi v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_57740507_5   5371 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 5420
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_57740507_5   5421 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGAA 5470
                            ii    i    v   i     v              i    i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_57740507_5   5471 TTAAAGACTTAATTGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5520
                          i ?    i   v   v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_57740507_5   5521 CCAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5569
                         vi   ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_57740507_5   5570 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCGA 5619
                         vi            vvi          vv     v  i    v   iivv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_57740507_5   5620 ATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCACCAGAGTGAA 5669
                           i   v v  i i   i  iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_57740507_5   5670 CAGGCAACCTACAGAACGGGAGAAAATTTTTGCAATCTACTCATCTGATA 5719
                         v  i     i      i          v       vii ivi        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_57740507_5   5720 AAGGTCTAATATCCAGAATCTACAAAGAACTCAAACAAACTTA-CAAGAA 5768
                          i  v  vi          v  i         vv    -  i -i  v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAA 794

  chr1_57740507_5   5769 AAAAACAAACAACCTCATCAAAAACCGGGCAAAAGGTATGAACAGACATG 5818
                            i     i    iv  i?    vi       i i v    i      v
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_57740507_5   5819 TCTCAAAAGAAGACTTTTATGCA----GCCAACAGACACATGAAAAAAAT 5864
                             v        ----   i  ----     i ii          i - 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGA-T 889

  chr1_57740507_5   5865 GCTCATCATCACTGGCCAT 5883
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


2781 24.68 1.61 4.18  chr1_57861259_57866519     3837  4768 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_57861259_5   3837 TGGAAAAACACTCCATGCTCATGAATTGGAAGAATTAATATCATTAAAAT 3886
                               i i ii     i     i         v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_57861259_5   3887 GACCATACTGCCCAAAGTAATCTACAGGTTCAGCACTGTTCCTATCAAAC 3936
                          i v     v      v i        i    i i vi i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_57861259_5   3937 TACCAA-TACCATTTTTCACAGAATTAGAAAAATCTATTCTAAAACTCAT 3985
                          v   i- i  -     ii     v v  v  iiiv  i      i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_57861259_5   3986 ATGTAACAACAACAGAAAACCTGAATATCGAAAGTAATCTTAAGAAACAA 4035
                            v  vvi   -- ii v  v     v v   ii      i -------
  L1M4_orf2#LINE/    150 ATGGAAATGCAA--GGGACCCAGAATAGCCAAAACAATCTTGA------- 190

  chr1_57861259_5   4036 AAAAAAAAAAAAAAAAAAGAAAAAAAGAACAAAGCTCTAGGCATCACAAG 4085
                         -------------------    i          i vv   vv     vv
  L1M4_orf2#LINE/    191 -------------------AAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_57861259_5   4086 ACCTAACTTCAAACTATACTAAAAGGCTACAGTAACCAAAATAGCATGGT 4135
                         v  i  i      viv     v  i          i   i i  ii    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_57861259_5   4136 ACTGGTACAAAAACAGACACAAAGACCAATGGAATAGAACAGAGAACCCA 4185
                              i i  ii i     i v   i             iv    ii   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_57861259_5   4186 GAAAAAAAGCTACACATCTACAACCATCTGATCTTTGACAAAGCCAACAA 4235
                             v   v i i    i  iiii  vi    i  i     i viiv   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_57861259_5   4236 AAGTAAGCAATGGGGAAAGGAATC-TCTATTAAATAAATG-TGCTGGGAT 4283
                         i vi vv            -   v-   v  v  i     -        i
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_57861259_5   4284 AACGGGCTAGCCATATGCAGAAGAATGAAACTAGACCCACTACTTTTCAG 4333
                            v  v  ?   i     i         ii i     -    i iv  v
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC-CTACCTCACAC 469

  chr1_57861259_5   4334 CATATACAAAAATTAACTCAAGAT-----AAAAATATAAATGTAAGAAAT 4378
                                              i  ----- ? i iv           iv 
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_57861259_5   4379 CAAATTATAAAAATCCTAGAAGAAAATCTAGG---AAATATCCTTCTCAA 4425
                         v   i       v  i          iv    ---    ---    vii 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGA 566

  chr1_57861259_5   4426 CATTGGCCTTGACAAATAATTT-TTGGCTAAGTGCCCAAAAGCAATTGCA 4474
                          v    vi v i   - ii   -  i v  v vvv         vvv   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_57861259_5   4475 ACGAAACCAAAAAATTGACAAACAGTACCTAATTAAACTGAAGAGCTTCT 4524
                           i   v-       v  i   iv v  i v  i   v v  i i   i 
  L1M4_orf2#LINE/    616 ACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_57861259_5   4525 GCACAGCAAAAGAAACTATCAACAGAATAAACAGACAACCAACAGAATGG 4574
                          ii vv    i  v        v i i i  v        v         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_57861259_5   4575 GAGAAAATACTTGTAAACTACACATCTGACAAAGATCTAATATCCAGATT 4624
                                  i   i   ii i i      i  i iv  vi        v 
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_57861259_5   4625 ATATG--GAATTTAAGGAAATTAATTAGCAAAAGACAA-TCTCCCCCTCC 4671
                             i--   i ivviv  v i   v vv         - vv   vv i-
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT- 813

  chr1_57861259_5   4672 AAAAAAATGGGCAAAGGACATAAACAGACACTTCTCAAAAGAAGACATGC 4721
                         -?                iv i  i     i     v        i  i 
  L1M4_orf2#LINE/    814 -WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_57861259_5   4722 AAGCAGCCAACAAACATTTTAAAAAAATGCTCATCATCACTAATCAT 4768
                           iii     i  i  iv -i    i       v     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACAT-GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (134 / 93)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.00 (54 / 18)  


 554 19.33 0.00 3.36  chr1_57892129_57895151     1364  1482 (1540)    L1M4_orf2#LINE/L1        3   117 (791)  

  chr1_57892129_5   1364 GAAAGATAGGCCACGTTCATGAATTGGGAAAATTAATATTGTTAACAATG 1413
                                 vv   i       i     i i v             -i   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA-GATG 51

  chr1_57892129_5   1414 TCCATATTACCCAAATCAATCTACAGACTCAATGCAATTCCTATCAAAGT 1463
                         v v   i v       ii         i    i     i         i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_57892129_5   1464 ACCAATGACATTCTTTTTT 1482
                         v   iivi ---       
  L1M4_orf2#LINE/    102 CCCAGCTGC---CTTTTTT 117

Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.02 (2 / 115), avg. gap size = 2.00 (4 / 2)  

2702 24.90 2.75 1.83  chr1_57892129_57895151     1765  2527 (495)    L1M4_orf2#LINE/L1      102   871 (37)  

  chr1_57892129_5   1765 CCCAGCCCATGACATTCTTCACAGAAATAGAAATAAAAAG--AACCTTAA 1812
                               ---  v -  i  ii       ----- i v   --i i i   
  L1M4_orf2#LINE/    102 CCCAGC---TGCC-TTTTTTGCAGAAAT-----TGACAAGCTGATCCTAA 142

  chr1_57892129_5   1813 AATTCATGCGAAAATGCAAAAGACCCTGGATAGCCAAAGCAATCTTGAG- 1861
                                ii i        ii     v i         i         i-
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_57892129_5   1862 --GAAAAATAAAGCTGGGGCA-TCATATTACCTGACTTCAAAATATATTA 1908
                         --   i  i    i   i v -   i i v  ii i       iv  i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_57892129_5   1909 CAAAACTATAGTG-CCAAAATAGCAAGCTATTGGCATAAAAACTGAGATA 1957
                             i   i   i-i   i i  iiv v  i        ii iv  v   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_57892129_5   1958 TAGACCAGTGGAACAGTGTACAGAACCCAGAAATAAATCCATGTATTTAT 2007
                             i  i     i  vi vv   ii           i    ii      
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_57892129_5   2008 AGCCAGCTGATTTTTAACAAAGGTGCGAAAATACA--CATTGGGGAAAGG 2055
                         i i  ii       ii    i     v  i i-  --  v         i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGA 391

  chr1_57892129_5   2056 CCAGTCTTGG-AATAAGTGGGGCTGAGAAAACTAGACATCCACATGCAGA 2104
                         vi      vv-  i  i   v    i  v    i  i ?         i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_57892129_5   2105 AGAAAGAA-----AACCTTATCTCTCACCATACACAAAAATCAACTCTAA 2149
                             v   ----- v  i  i   v       i        i     v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_57892129_5   2150 GTGGATTAAAGACTTAAATGTAAAAATCCCAGACTATGAAACTACTAGAA 2199
                         i     i ?    i         i i- iv i     i     vi     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAG-CTAAAACTATAAAACTCTTAGAA 540

  chr1_57892129_5   2200 GAAAACACAGGGG-AAATATTTCATAAAATCAAACAGGGCAAGGATTGTT 2248
                                i   ? -    -i   i i vv iiiiivi     v i  vi 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_57892129_5   2249 AAAATACGACTTCAAAAGCAAAGGCAACAAAAGCAATAATAGACAAATTC 2298
                         v i   i   vi        v i          v  v      i     v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_57892129_5   2299 GATTATATCAAACTAATGAGCTTCTGCACAGCAAAGAAAACAATCAGTAA 2348
                           i vi      v v vi i   i  ii vv     i v  v    iv  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_57892129_5   2349 AGTGAAGAGACCAACCTACAGAATGGGAGAAAGTATCTGCAAGCTATATG 2398
                               i    -    i               i   i     iii    i
  L1M4_orf2#LINE/    690 AGTGAAAAGAC-AACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_57892129_5   2399 TCTGACAGGGG-TTAATACGTAGAATTTATAAGGAACTT---CAACTCAA 2444
                              i i   -i vi  ivi     v     i     i---        
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_57892129_5   2445 TAGCCAAAAAGCAACTAATCAGGTTTAAAA-TGGGGAAAAGACTTAAATA 2493
                           iiv    ii   v   i vii  ?    -    v   i  i  i    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_57892129_5   2494 GACATTTTCCAAAAGAAGACATACAAATGGGCCA 2527
                                ii v        i          -   
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGG-CCA 871

Transitions / transversions = 2.44 (132 / 54)
Gap_init rate = 0.02 (19 / 770), avg. gap size = 1.84 (35 / 19)  


2528 25.37 2.76 6.37  chr1_57949952_57952986.rev     1147  2088 (947)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_57949952_5   1147 TGGGAAGCTTTACCATAATGCTGAATTAGAAAACTCAATATTTTTATGAT 1196
                            i   v v v    iv vv  i   i   i   i      v   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_57949952_5   1197 GTCCATTTTCCCCAGATTAACTCAT-GATTCAAGGAGATCTCAATCAAAA 1245
                          v v  vi      i   i iii i-       v vi   i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_57949952_5   1246 TTACAACAGGGGCTCCCCCCGCCAAAATTTACAATCCTATTCTAAAATTT 1295
                          iv  i ---v  iiiiiii  vi     v    v iv  i        i
  L1M4_orf2#LINE/    101 TCCCAGC---TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_57949952_5   1296 AGATGAAAAATGCAAAAGACCTAAAACAGCCAAAATAATTTTGGAAAAGA 1345
                          v   i   -     ii    i i  i        i   i   i      
  L1M4_orf2#LINE/    148 ATATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_57949952_5   1346 TTAACAAAATTGGAGGACTTACGATACCTTATTTCAAGACTTTTCATAAA 1395
                         vv      i          i  iv v  iv       i    vii i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_57949952_5   1396 ACTACAGTAA-CAACGCATAATAGAATTGATGTAAG------CATATCAT 1438
                         i         -   vi  vvi i v i  iii    ------     viv
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_57949952_5   1439 TAAATGAAACAGAACAGAGATTCCTGAAATAGACCCACACATATATGCTC 1488
                          v    i  i    iv    v   v      i     i    v    v  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_57949952_5   1489 AACTGATTTTCAACAGAGTTGCTAAAACATTTCAATGGGAGAA-AAGACT 1537
                           i        i   ii v   i  i  vv         ii  -  v v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_57949952_5   1538 CTTTTTACCAAATAGTGGTGGAATTGCTGGATATTTATATGAAAAAGAA- 1586
                              i v     i   v   i ivi       ?ii i   v       -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_57949952_5   1587 -AAGTACTAGACCCTCATCGCATATCATACACTTAAATTA-CTTGAAATG 1634
                         -    -- i     ii i v  i i    i  vv      -  ii     
  L1M4_orf2#LINE/    447 GAAGT--TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_57949952_5   1635 GATAGTATACACAAACATAAAGGCTGAAATGATAAAGCTCCTAGAAGAAA 1684
                            vi? v  vi   ii   ii   i   iv     i   i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_57949952_5   1685 ATATATAATCAAATATTCATAACCTTGGGGTAGATACGTATTTCTCAA-- 1732
                          i   vi?vi    v   i i        v   ii vvvi     i i--
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_57949952_5   1733 --GACATATAGATCATAG--AACATAACATGAAAAATACATAAATTTTAC 1778
                         --    ivv i v  i i--    v  v --       v       vv  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGA--AAAAATAGATAAATTGGAC 642

  chr1_57949952_5   1779 TTCACTAGAATTAAAAACTTTTGTTCTTGAAATAAAGACCTTGTTAAGGA 1828
                             ii i                v   v   ---i   vi i i   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAA---GGACACTATCAAGAA 689

  chr1_57949952_5   1829 AATGAAA-GACAAGCCATAGACTTGGAAAAAACATTCACAAAGTGTTTGT 1877
                          i     -     v   i   v v   i    i   ii    vii v i 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_57949952_5   1878 CTGGCAAATAACTGGTATCCAAAGTGTTTGTGTGTACGTGTCTGTGTGTG 1927
                            ii  ivi   v       i i i v ivi- v  ---   -------
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAA-GAAC---TCT------- 778

  chr1_57949952_5   1928 TGTGTGTGTGTGTGTGTGTGTGTATACAACTCAATAACAAGAAGATAAAT 1977
                         ------------------------             i  i    i    
  L1M4_orf2#LINE/    779 ------------------------TACAACTCAATAATAAAAAGACAAAT 804

  chr1_57949952_5   1978 AATCCAATTCAAAA-TGGGCAAAATATTTGAA----CATTTAATTCAAAC 2022
                           i      ?    -        iv       ----     v- i    v
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC-TCCAAAG 853

  chr1_57949952_5   2023 ACATATATATATACACACATGTAATTAGCTAATCAGTACATGAAAAAATG 2072
                          ----- v       -------   -i  i   v  i         i   
  L1M4_orf2#LINE/    854 A-----AGATATACA-------AAT-GGCCAATAAGCACATGAAAAGATG 890

  chr1_57949952_5   2073 CT--ATGTTAATTTCCTG 2088
                           -- ii i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (147 / 88)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.58 (86 / 24)  


2647 24.83 3.66 2.99  chr1_57964109_57966114      612  1513 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_57964109_5    612 TGGAAAGATAAACTGTATTAGTGGACTGGAAAACTCAATAT-ATTAACAT 660
                                   vv ii i  vi    i     i   i     -i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_57964109_5    661 ATCAATTATCCTCAAATTGATCTATAGTTTCAACACAATCCCAGTCAAAA 710
                         iv    vv   i            i  v      i       vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_57964109_5    711 TTCTAGTAGA--TATTTAAAAAAATAAATTGTCCGGCTAATTATAAAATG 758
                          i i  iv v-- v   iv i    ----  v vi   i  iv      v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT----TGACAAGCTGATCCTAAAATT 146

  chr1_57964109_5    759 TATATAAAAATGTAAAT-ATCTAATATGGCCAAATCAATGTTGAAACAGA 807
                         i    ii     i  iv- i i iv  i      v    v      v   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_57964109_5    808 AGAACAAAATTGTAGGAGTTAGAGTATTTGATTTCATGACTTACCATAAA 857
                                 i   v    v i v v viiii      vi      i i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_57964109_5    858 ACTACAGTGGTCAAAGCAGTGCAAAGAGTGTGGCATTGCCATATAAATAG 907
                         i       ii    ii     ---------   i i  v    vii    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTG---------TGGTACTGGCATAAGGATAG 287

  chr1_57964109_5    908 ACAAATACATAAATGGAACAGAAC--AGTGTCCA-AAATAGACCTGCACG 954
                            v   v  v       i    i--  v     -     i   iii  i
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_57964109_5    955 TATAGAATCAATTGATTTTTTTTACCAAG--TACAATGGCAATTTAATGG 1002
                          v  vii            i---iv    -- i v v i v   i     
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTC---GACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_57964109_5   1003 AGAGAGAATAGTTTTTTCAA---ATAGCACTGGAACAATTAGATGCCCAT 1049
                         i  i        i       ---  i ii    i    i i   i?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_57964109_5   1050 TTGCAAAGGAAAAAACATGA----CAAACTCACACAATATACAAAAATTA 1095
                         v      i   vi  vv  i---- v v       v              
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_57964109_5   1096 ATT-AAAAGAGATCACAGACATAAACTAAAAATCTAAGATTATAAAACTT 1144
                          i -    vi     ?    v    ivv  i v    i i         i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_57964109_5   1145 CTAGAAAGAAACATAGGAAAAAAAGTCTTGGTAATCTTGGATTAGGCAAA 1194
                         i     ii         ?iv   --    v  i i     i        v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_57964109_5   1195 AAGGTTTTT---ATAGGACACAAAAAGCATGAACTATAAAATAAAAAAAT 1241
                         --     i ---   v     v       ii i v i    -i       
  L1M4_orf2#LINE/    583 --GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA-GAAAAAAT 629

  chr1_57964109_5   1242 TGATACACTGAATTTCACTAAAATTAAAATCTTCGGCTTTTCAAAAGAAA 1291
                         v    v i  i i    ii          v   iv ivi      i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_57964109_5   1292 CTATTAAGAATATTAAATGGCAAACTACAGCCTGGTAGAAAATGTTTATT 1341
                             i     vi v   v i   v i    vv   v       ----   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT----ATT 725

  chr1_57964109_5   1342 TGCAAAACACACATTTGTTAAAGGACTCGTAAGAAGAATACATAAAAACT 1391
                               v  i i  i  v   i     i   vvv      i     i vi
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_57964109_5   1392 TCCTAAAACTCAATAA------GACAA----CACAATTTTTAAAATGAGG 1431
                           i  v          ------     ---- v     ?v-      i v
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGC 824

  chr1_57964109_5   1432 AAACAATT-AAATATGTACTTCATCAGAAAAAGATG-A-GAATACCAAAT 1478
                            vi   -i    vii i   vi  -  i     i- -i   iv v   
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCA-AAGAAGATATACAAATGGCCAAT 873

  chr1_57964109_5   1479 AAGCCCATGAAAAGATACTCGGTATCATTCATCAT 1513
                             v           i   iii    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (133 / 87)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.50 (60 / 24)  


3214 27.12 0.55 0.44  chr1_58304403_58310678.rev     4879  5785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_58304403_5   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_58304403_5   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_58304403_5   4979 TACCAATGACTTTCTTCACACAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_58304403_5   5027 TATGGAACCAAAAAAGAGCCCGCATAGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v        iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_58304403_5   5077 AACAA-GCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5125
                              - i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_58304403_5   5126 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_58304403_5   5176 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 5223
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_58304403_5   5224 ATGTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5273
                          vv    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_58304403_5   5274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_58304403_5   5324 GAAACTGGATCCGTTCCTTACACCTTATACAAAAATCAGTTCAAGATGGA 5373
                            ii    i  v v   i     v           i ii    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_58304403_5   5374 TGAAAGAGTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          v ?   vi       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_58304403_5   5424 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5473
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_58304403_5   5474 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5523
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_58304403_5   5524 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5573
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_58304403_5   5574 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5623
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_58304403_5   5624 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTGCAGGAAAA 5673
                         i  i  vi          v  i  v      vv    v ivii iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_58304403_5   5674 AAACAAACAACCCCATCAAAAAGTGGGCGAGGAACATGAACAGACACTTC 5723
                          i     i     v  i?    i     i i i iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_58304403_5   5724 TCAAAAGAAGACATTTATGCAGCCAAGAAACACATGAAAAAATGCTCATC 5773
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_58304403_5   5774 ATCACTGGCCAT 5785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2195 20.76 3.79 0.20  chr1_58446967_58453225.rev        1   501 (5758)  C L1M4_orf2#LINE/L1   (50)   858   340  

C chr1_58446967_5    501 TATACTCAAATGATTTTTAACAAAGGTGCCAAGAACACTTAATAAGGAGA 452
                            iv    v       ii    i          v  i i   ii   i 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

C chr1_58446967_5    451 GGACAATCTTTTCCACCAATGATGCTGGGAAAATTGGATGTCCACATATA 402
                          i i i       v  v    i        v  i     i?      ii 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

C chr1_58446967_5    401 AAAAAATAAATTTAGACCTTTATGTGATACTCTATGTAAAAATTAACACA 352
                            i   i  v  i    ii  iv v i  iv   ii          v  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

C chr1_58446967_5    351 AAATGAATCAAAGATGTAAATATAAGACCTAAAACTATAAAACTTTCAAA 302
                              i    ?   iv     i     v                i i i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

C chr1_58446967_5    301 AGAAAACATAGGAGAAGAGCTTCGTGACATTAATTT-GGCAATGATTTCT 253
                                     ? v i v         v  iiv  -       i     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

C chr1_58446967_5    252 TGGATATTACGCCGAAAGAAGAAACAATAAAGGTAAAAACAGGTAAATTG 203
                          i     v  i  i    v v  i   i   i v     i  i       
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

C chr1_58446967_5    202 GACTACATCAAAATTAAAA-CTTCTTTGCACAAAAGGACAAAATCAAAAG 154
                             v              -   i v   viv        vv     i i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

C chr1_58446967_5    153 AGTGAAAAGGCAAACTTT----TGGGAGAAAGTATTCATAAATCATATAT 108
                                  i   v ivi----         i    iii           
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

C chr1_58446967_5    107 CTGATACAGAGTTTAATATTCAGAATATATAAAGAACTCCTGCAACTCAA 58
                               -  i vi vi   i                   i i        
  L1M4_orf2#LINE/    740 CTGATA-AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

C chr1_58446967_5     57 CAACAAAAAAACAAATAA----ATT--------GGCAAAA-ACTTGAATA 21
                         i  i     i        ----   --------      i- i       
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

C chr1_58446967_5     20 GTTATTTCTCCAAAGAATAT 1
                          vi              v  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGAT 858

Transitions / transversions = 2.06 (68 / 33)
Gap_init rate = 0.01 (7 / 519), avg. gap size = 2.86 (20 / 7)  

3252 26.57 0.88 0.77  chr1_58446967_58453225.rev     4862  5768 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_58446967_5   4862 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4911
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_58446967_5   4912 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4961
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_58446967_5   4962 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5009
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_58446967_5   5010 TATGGAACCACAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5059
                                vii   ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_58446967_5   5060 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5109
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_58446967_5   5110 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5159
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_58446967_5   5160 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5207
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_58446967_5   5208 ATGTGATCTTTGACAAA----CCGAGAAAAACAAGCAATGGGGAAAGGAT 5253
                          vv    i  i     i----  ---  i v  vv            i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCC---AAGACCATTCAATGGGGAAAGAAT 393

  chr1_58446967_5   5254 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5303
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_58446967_5   5304 GCTGAAACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAGAT 5353
                         iv    ii    i    v   i     v  i        i  i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_58446967_5   5354 GGATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5403
                             i ?   ii    i  v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_58446967_5   5404 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5453
                            v    ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_58446967_5   5454 CAAAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATC 5503
                         i vi            vvi     v    vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_58446967_5   5504 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5553
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_58446967_5   5554 AACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGA 5603
                           v  i     i   i             v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_58446967_5   5604 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5653
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_58446967_5   5654 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGACAC 5703
                             i     i     v  i?    i     i i   iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_58446967_5   5704 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5753
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_58446967_5   5754 ATCATCACTGGCCAT 5768
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (145 / 92)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.14 (15 / 7)  


3183 26.32 1.10 1.10  chr1_58551123_58557399.rev     4879  5786 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_58551123_5   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAAGATCGTGAAAAT 4928
                              ii i  i     i      i v      v i  v  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_58551123_5   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 4978
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_58551123_5   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_58551123_5   5027 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_58551123_5   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_58551123_5   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_58551123_5   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCTTACCTACAACT 5224
                                i    i--    i  --        ----i ii --    vi 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAA----ACCCA--TACATTT 340

  chr1_58551123_5   5225 ATG------TGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAG 5268
                            ------    i  i     ivv  vv  i v  vv            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_58551123_5   5269 GATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAG 5318
                         i  vvi  v  i  i              v      v  ?   i   i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_58551123_5   5319 AAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAA 5368
                           iiv    ii    i    v   i     v           i  i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_58551123_5   5369 GATGGATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAA 5418
                         i      i ?   ii    i  v   v       i      vi i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_58551123_5   5419 GAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 5468
                               v    ?i v viv   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_58551123_5   5469 GTCCAAAACACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGG 5518
                         ivvi vi         i  vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_58551123_5   5519 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 5568
                          ii v  i   v v  i i   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_58551123_5   5569 GTGAACAGGCAACCTACAACACGGGAGAAAATTTTTGCAACCTACTCATC 5618
                              v  i     i   iv i          v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_58551123_5   5619 TGACAAAGGGCGTATATCCAGAATCTACAATGAACTCAAACAAATTTACA 5668
                            i  i  i v i          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_58551123_5   5669 AGAAAAAAACAAAGAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGA 5718
                          v     i     v     v  i?    i     i     iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_58551123_5   5719 CACTTCTCAAAAGAAGACATTTATGCAGCCAAGAAACACATGAAAAAATG 5768
                           i     v        i  vi viii     v  i          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_58551123_5   5769 CTCACCATCACTGGCCAT 5786
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.50 (20 / 8)  


3271 26.76 0.55 0.55  chr1_58666156_58672873     5318  6225 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_58666156_5   5318 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATGGTGAAAAT 5367
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_58666156_5   5368 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5417
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_58666156_5   5418 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5465
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_58666156_5   5466 TATGGTACCAAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCAAAAAG 5515
                              v viiv  ii  v  vvv  v     iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_58666156_5   5516 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5565
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_58666156_5   5566 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5615
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_58666156_5   5616 ATTGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATGTCTACAACT 5663
                          v     i    i--    i  --        vv   i ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_58666156_5   5664 ATCTGATCTTTGACAAACCTGACAAAAATAAGAAATGGGGAAAGGATTCC 5713
                          vi    i  i     ivv  v   i vi vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_58666156_5   5714 CTCTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5763
                           i  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_58666156_5   5764 GAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGA 5813
                            ii    i    v   i     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_58666156_5   5814 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5863
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_58666156_5   5864 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5912
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_58666156_5   5913 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGATCTA 5962
                         vi            vvi          vv     v       v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_58666156_5   5963 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 6012
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_58666156_5   6013 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCAACTGACA 6062
                         v  i     i                 v       vii ivi v    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_58666156_5   6063 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 6112
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_58666156_5   6113 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 6162
                           i     i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_58666156_5   6163 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 6212
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_58666156_5   6213 CATCACTGGCCAT 6225
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2294 16.24 2.37 25.55  chr1_58686570_58690355     2112  3293 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_58686570_5   2112 TGGAAAGACATCCCATGTTCATGGATTGTAAGACTTAATATCGTTAAAAT 2161
                                 i                   v            i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_58686570_5   2162 ATCCATACCACCCAAGGTGATCTACAGATTCAATGAGATCTCTATGAAAA 2211
                         iv v    iv     iv                i vi   i    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_58686570_5   2212 TCCCATTGGCACTTTTCTTATAGAAACAGAAAAAACGATCCTAAAATTCA 2261
                              -- vii i   i  ii     iv  v  ivi              
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_58686570_5   2262 CATGGAACCACAACTAACCCCAAATCGCCAAAGCAATCTTGAAAAAGAG- 2310
                         i      vii   vvi    vi   v      i               i-
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_58686570_5   2311 --TAAGACTAGAGGCATCATGCTTCCTGATTTCAAAATATATTACAAAGC 2358
                         --i  iii i    vv   ii     ii         iv  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_58686570_5   2359 TACAGTAATTAAAACAGTATAGTATTAGCAGAAAGATAACCGT-TAAATG 2407
                                  i  i     i i   i i   v  i    iv i -  i  v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_58686570_5   2408 AATGGAACAGAAGAGAGAGCCCAAAATTAAGCCCACACAAATACAGATCT 2457
                                i    vv     i   i  v   i    i   ---------- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA----------T 338

  chr1_58686570_5   2458 TTGATGAGGGTACCAAAAATATACAATGGGAGGCCAGGTATGGTGGTTCA 2507
                           -------------------------------------     ------
  L1M4_orf2#LINE/    339 TT-------------------------------------ATGGT------ 345

  chr1_58686570_5   2508 TATCTGTGATCCCAGCAGTTTGGGAGGCTGAGGCACATGGATTGCTTGAG 2557
                         ---------------  i  -------------------    -i i  -
  L1M4_orf2#LINE/    346 ---------------CAATT-------------------GATT-TTCGA- 359

  chr1_58686570_5   2558 ACCAGGAGTCCAAGACCAACCTGGGCAACATGGTGAAACCATCTCTACAA 2607
                         ----------    ------------------------------------
  L1M4_orf2#LINE/    360 ----------CAAG------------------------------------ 363

  chr1_58686570_5   2608 AAAATTAGGCAGGTGTGATGGTACACACCTGTGCACCAAGAGGCTGAGGT 2657
                         -----------    --------------------      ---------
  L1M4_orf2#LINE/    364 -----------GGTG--------------------CCAAGA--------- 373

  chr1_58686570_5   2658 GGGAGGATCACCTGAGCCTGGGAAGTCGAGGCTAGAGTAAGCTGTGATCA 2707
                         --------------------------------------------------
  L1M4_orf2#LINE/    374 -------------------------------------------------- 373

  chr1_58686570_5   2708 CATCACTGCACTCTAGCCTGGGTAACAGAGCAAGACCCTGTCTCAAAAAC 2757
                         --i  i -------------------------------------------
  L1M4_orf2#LINE/    374 --CCATT------------------------------------------- 378

  chr1_58686570_5   2758 GAACACACACACACACACAAACCCCACAATGAGGAAAGAGCAGTCTCTTC 2807
                         --------------------------     i       ii     i   
  L1M4_orf2#LINE/    379 --------------------------CAATGGGGAAAGAATAGTCTTTTC 402

  chr1_58686570_5   2808 AACAAATGGTGCTAGAAAAACTGAATATTCACATGCAAAAGAATGAAACT 2857
                                      i i v     i   ?i                  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_58686570_5   2858 GGACCCTTATCTTACGCTACACACAAAAACCAACTAAAAATGGATTAAAG 2907
                               i  i  i  i i i i       ii    v         i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_58686570_5   2908 ATTTAAACGTAAGACCTAAAACTATAAAACTCCTAGAAGAAAATATAAGG 2957
                          ii    i      v                 i          i   i ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_58686570_5   2958 GAAAAGTTTCATGACTTTGGTCTTGGCAATGATTTTGTGAATATGACACC 3007
                          v   vi   i    i    vi v       i   iv ii          
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_58686570_5   3008 AAAAGCACGGGAAACAAAAGGCAAAAATAGACAGGTGGAACT-------- 3049
                                 ii v        i-         i ii v i   --------
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_58686570_5   3050 ACCAAAAAGCTCTGCACAGCTAAGGAAAC-------AGAGTGAAAGG-CA 3091
                          ii     vi i  ii vv v     v  ------- i       i -  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_58686570_5   3092 ATCTACAGAATGGGAAAAACCATTTGTATACCAAATAACTGATAAACAGT 3141
                          i i           i   vi     i v i  v   v       iviii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_58686570_5   3142 TAATTTCTAAAATATATAAAGAATTTCTACAACTCAATAGCAAAAA---- 3187
                          vi v  i i             i ii            ii     ----
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_58686570_5   3188 ----ACCCAATTTAAAAAATAGGCAAAGGATCTCAATAGACATTTCTTCA 3233
                         ----        ?     - i          i v             i  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_58686570_5   3234 AAAAAGACATTCAAAAGTAGGTAACAAGTATTAGAAAAAATGTTCAATAT 3283
                           i    i  v    -- i vi  i   i ivv     i   i    i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAA--TGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_58686570_5   3284 CACTAATCAT 3293
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.62 (136 / 52)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 16.50 (330 / 20)  


1850 22.37 3.88 5.73  chr1_58734765_58738089     1563  2103 (1222)    L1M4_orf2#LINE/L1        4   534 (374)  

  chr1_58734765_5   1563 AGAGATATTCTGTTATTCATGGATGGGAAGACATAATATTGTCA----GT 1608
                          i      i ii -i         v       v         i ---- v
  L1M4_orf2#LINE/      4 AAAGATATCCCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_58734765_5   1609 CAGTTCTTCCCAACTTGACCTATAGAGTCAATGTAATTTCAATGAAACTC 1658
                           i v  i     v    i   i   v    i i   ii v  v   v  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_58734765_5   1659 TCATCGAGTTATTTTGTGGATATTGCCAAACTAATTCTAAAA-------- 1700
                         i  v vivi v     ii  v    v   i  i  i      --------
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_58734765_5   1701 -----GCAAAGACGCCGGAGTAGCCAAGACAATATT--AAAAGT-GAACA 1742
                         -----    i ivv  i  i       i     v  --     v-     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_58734765_5   1743 AAATTAGAGAACTGACACTACCAGACTTCTAGACTTACTATGAAACTACA 1792
                           i  i   i   v     v  vi i   v i        ii  i     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_58734765_5   1793 GTAATCAAGACAGTGCTGTACTGGCAAAAGAAGAGACAAATAGACCAAAG 1842
                                        iv         v   i v     v     i   v 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_58734765_5   1843 GAACAGAAAAGGGAGTCCGAGTCCAGAATTAGACCCATATAGATATAGTC 1892
                            i    vv i      ------    v  i       i vv   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCC------AGAAATAAACCCATACATTTATGGTC 346

  chr1_58734765_5   1893 AACTCATCTTTGACAAAGAAGCAAAGGTAATACAATGGAGAAAAGATAAT 1942
                           i v  i  i     i iv  v   iiv  v      i    ii   i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_58734765_5   1943 CTTTTCAAAAAATGGTGCTGGAACAACTAGATAGCCACATACCAAAAAAC 1992
                                 v            i      i    ?      i --------
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-------- 438

  chr1_58734765_5   1993 AAACAAACAGAAAAAAAAAAAACGAATCTAGACACAGACCTTACACTCTT 2042
                         ---------------    i  i   vi i   v vv    i    iv v
  L1M4_orf2#LINE/    439 ---------------AAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_58734765_5   2043 CACAAAAATTAACTAAAAATGGATTACGGATGTAAATGTAAAATGC-AAA 2091
                         i             v         i ?i  iv         i -  -   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAA 522

  chr1_58734765_5   2092 ACCAAAAGACTC 2103
                           i v  i    
  L1M4_orf2#LINE/    523 ACTATAAAACTC 534

Transitions / transversions = 1.48 (71 / 48)
Gap_init rate = 0.02 (9 / 531), avg. gap size = 5.78 (52 / 9)  

 990 27.19 0.91 0.91  chr1_58734765_58738089     2502  2832 (493)    L1M4_orf2#LINE/L1      578   908 (0)  

  chr1_58734765_5   2502 GCAATGACTTTTTAAGTGCAACACCAAAGGCATGATCTATGTAAAAAACA 2551
                               ii  i   ii iii        i   ii v v iiv  i   v 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_58734765_5   2552 ATTAATAAAATGGACTTTATTAAAATTAAAATTTTCTGCCCTGAAAAAGA 2601
                           vi     v       i  i          vi  i  iv  vv   i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_58734765_5   2602 TACTGTCAGGAGAGTTAAAAGAAAAGTGACAGACTGGG-GAAAGTATTTG 2650
                         i   i   i  i   v      v  viv     v    -    i      
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_58734765_5   2651 CAAA-AAAATACCTATTTTTAAAATGTTATTCAAAATATGTGAATAACTC 2699
                             -v v   i  iv vvvii v vv   i  i     i i  v     
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_58734765_5   2700 TTAAAACTCAACAACATAAACACACAAAAAAATCTGATT-AAAAATGGGT 2748
                            v       i  i v   v   ---  v  i ii   -         i
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACA---AATAACCCAATTWAAAAATGGGC 824

  chr1_58734765_5   2749 CAAAGACCTTAACAAATATCTCATCAAAGAAGAAATACAGATGATAAATA 2798
                         v  i  ii v  i i i  i  vi         v     i   iiv    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_58734765_5   2799 AGCATATAAAAAGATGCCCTACATCATATGTCAC 2832
                             i  i         i v      ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (55 / 35)
Gap_init rate = 0.01 (4 / 331), avg. gap size = 1.50 (6 / 4)  


3024 25.63 1.76 1.87  chr1_58777918_58782479.rev     3164  4072 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_58777918_5   3164 TGGAAACACGTCCCATGCTCATGGATGGGAAGAATCAATATTGTGAAAAT 3213
                               v ii       i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_58777918_5   3214 GACCATACTGACAAAAGCAATCTACAGATTCAATACAATTCCCATCAAAG 3263
                          i v     vv v   vii              ii    i  i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_58777918_5   3264 TACCATCATCATTCTTCACAGAGCCAGGAAAAACAATCTGAAATTTCATA 3313
                          v   v vv v  i  ii    iviv iv  ivii   iv   v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_58777918_5   3314 TGGAACCAAAAGAAAGACCCGACATAGCCAAAGCAAGACTGAGCAAAAGG 3363
                              viiv   i--     iiv         i   vvi   iv  i i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_58777918_5   3364 AAAAAATCTGGAGGCATCACATTGCTGGACTTCAAGCTATACTACAAGGC 3413
                           v   vi      vv     i v ivi i     iviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_58777918_5   3414 TGTGGTTACCAAAACAGTATGGTACTGGTATAAAAATAGGTACATAGACC 3463
                          iii  v i   i     i         i    ii    ii i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_58777918_5   3464 ATTGGAACAGAATACAGAATGCAGAAATAAAGCCAAATGCTTACAGCCAA 3513
                          v     i     vv   i v          v   v iii   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_58777918_5   3514 CTGATCTTTGACAAAGCAAACAGAAACATAAAATGGGGAAAGGGCACCCT 3563
                         i    i  i     i vviv  ii v   vv           iii vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_58777918_5   3564 ATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGCAGAATAATAA 3613
                         v                    i  i   vv ?         i  v   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_58777918_5   3614 AACTGGATCCTCATTTCTCACCTTATACAAAAATCAGCTCAAGATGGATT 3663
                          ii    i  ii ii  v    v           i i     i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_58777918_5   3664 GAAGACTTAAATCTAAGACCTGAAACCATAAAAATGAT-GAAGATGGCAT 3712
                         i?    i     v     v  i    i      v vv -     vii   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_58777918_5   3713 TGGTAAAACTCTTCCGGATGTTGGCTT-GGCAAAG-------AGATCATG 3754
                         v  ?iv  v     vv  iv    v  -     v -------    -   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr1_58777918_5   3755 ACCAAGAATGCAAAAGCAAATGAAACAAAAACAAAAATAAATAGATAGGA 3804
                           ----- i-        v v v       iv       i   i  v   
  L1M4_orf2#LINE/    598 AC-----AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_58777918_5   3805 TCTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCA-----G 3849
                         ii v  i   v v    i   i  ii vv    i  v iv    ----- 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_58777918_5   3850 CAAACAGACAACCCACTGAATGGGGGAAAATATTTGCAAACTATACATCC 3899
                         ii  v           v       i               ii   i   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_58777918_5   3900 AACAAAGGACTAATATCCAGAATCTACAGGGAACTCAAACAAATCAGCAA 3949
                         i i  i     vi          v  i ii      vv    v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_58777918_5   3950 GAAAGAAAAACAAAAACAAATAACCCCATCAAAAAGTGGACAAATGACAT 3999
                         v   --------  i           v  i?    i   i    v  iv 
  L1M4_orf2#LINE/    792 TAAA--------AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_58777918_5   4000 GAATAGACAATTCTCAAAAGAAAATATACAAATGGCCAACAA--ACAGGA 4047
                                  v     v      i                i  --   v  
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_58777918_5   4048 AAAAATGATCAACATCTTTAATTAT 4072
                            i   v        v????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (133 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.30 (33 / 10)  


2574 23.16 14.57 1.49  chr1_59091591_59094789     1904  2706 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59091591_5   1904 TGGAGAGACGCACCTTATTCATGGATCCAAAGACTCAATATTTTTAAGA- 1952
                             i   iiiv  v i         ivi      i      v      -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59091591_5   1953 GGTAAGTTCCCCCCAGATTGATCTA--GATTCA----------------- 1983
                           i  - v i     i         --      -----------------
  L1M4_orf2#LINE/     51 GGCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_59091591_5   1984 -------------------------------------TTCTAAAACTTAT 1996
                         ------------------------------------- i      i i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_59091591_5   1997 ATAGAAATGTAAAAGACCTTGGACATCCAAAATGACTTTGAAAAAGAACG 2046
                           i      i  ii    iv i i v      ii ii           vi
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_59091591_5   2047 ATA---TTGGAGAGCTAGCAGTACCTGATTTCAAAGTACATTATAAAACT 2093
                          i ---      ii  vi  v v  ii        iivi i  i   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_59091591_5   2094 GCAGTGATCAGAACAATGTAGTATTGATGCAATGATAGACAAACAGATCA 2143
                         i    i    ii   i   i   i  iiii  v        v i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_59091591_5   2144 GTGGAACAGAATATAGAATCAAGAAGTAGATCCATAGATATATGGGCAGC 2193
                         i     i     vv   i  v    i  i i     v  v     v  ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_59091591_5   2194 TGATTTTTGACAAAGATGCAAAGGCAATT--------------TAGTGTT 2229
                                i     i i   v   i v   --------------    v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_59091591_5   2230 TTCAACAAATGGTTCTAGAACAATTGGATAATCTCTATGAAAAAATATTG 2279
                                      v  i i    i      ?i v -   v    iv  - 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCAC-ATGCAAAAGAAT-G 447

  chr1_59091591_5   2280 ATGTTTGACCTATACTT-GCATCACACAAAAACATTAACTAAAAATGGAT 2328
                          v   v    iv   i -i  i  i i v   v       v         
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_59091591_5   2329 CATAGACCCAAGTGTGAAA-CTAAAATTTATAAAACTTCTAGAACAAAAC 2377
                           ?     i  i   i i -      i -        ii     v     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTTAGAAGAAAAC 546

  chr1_59091591_5   2378 ATAAGAGAAAA---------------------CAAAGGTTTCTCACATAC 2406
                            i ? v   ---------------------   v       i v   i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_59091591_5   2407 AATATCAAAAGCATAAAAGGTCCATAAAAGATCAAATTAATAAATTAGAC 2456
                         i i i        i  i---- v i      vv    vi       i   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAG----CAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_59091591_5   2457 TTCATACAAAATTAAAAACTTAT---TTTTGAAAGACACTGTTAAGAGAA 2503
                              -               v ---i  ii  i      i i    i i
  L1M4_orf2#LINE/    643 TTCAT-CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_59091591_5   2504 TGAAAAGACAAGCTACAAACTGGAAGAAAATATGTGTAAAGCATATATCT 2553
                                    v i   i v   i         v  i   v         
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_59091591_5   2554 GATAAAAAGACTTATATAGAGACTATATAAATAATTCTCAAAATGTAGTA 2603
                              ii-     i   vv   v        v  i   i v  ivi i  
  L1M4_orf2#LINE/    742 GATAAGG-GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_59091591_5   2604 ATAAGAAAACAAA-----------------GGGACCAAAAGATCTGAACA 2636
                             i  i     -----------------   --    i   i    i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGG--CAAAGGATTTGAATA 838

  chr1_59091591_5   2637 GGCACTTCACCAAGGGAAATACATGGATGGCAAATAAGCATATGAAAAGA 2686
                          i  i   v    i i i   i iii     v        i         
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_59091591_5   2687 TACTCAGCACCATTAGAGGA 2706
                          i    i  i  ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.39 (129 / 54)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 7.17 (129 / 18)  


2890 25.40 1.51 3.77  chr1_59124194_59126490.rev      878  1806 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59124194_5    878 TGAAAAAATCTTCCATGCTCATGGATTG-AAGAATCTATATGGTTAACAT 926
                           i   i  v i     i          -    v iv    v     v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59124194_5    927 GGCCATACTGCCCAAAGCAATCTACAGATTCAACATTATTCCTATCAAAC 976
                            v     v      vii               iiv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59124194_5    977 TACCAAGACCGTTTTTCACAGAGCTAGAGAAAACTATTCTAAAACTATTT 1026
                          v   ivvv v     ii    iv v  v  i------  i ----- ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG------CTGA-----TCC 139

  chr1_59124194_5   1027 TAAAATTCATATGGAAACAAAAAAGAGCCTGAATAGCCAAAGCAATCTTA 1076
                                          iiv  ii  v  v           i       i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_59124194_5   1077 AGCAA-AAGAACAAAGCCAGAGGCATCACATAATCCAACTTCAAACTATA 1125
                          iv  -          iii    vv     ivvi    i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_59124194_5   1126 CTTTAAGGCTACAGTAGCCAAAACAGCATGATACTGATACAAAAATAGAC 1175
                           vi  i         ii   i    ii  i     ii i  ii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_59124194_5   1176 ACATAAATCAATGAAACAGAATAGAGAACCCAGAAATAAAACTGCACACC 1225
                          i   i       i  i     v    ii           v iii   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_59124194_5   1226 TATAAT-AATCCGATCTTCAATGAAGTTGACAGAAGTAAGCCTTGAGGGA 1274
                            ii -   i-   i   i ii i v  v  ii vi vv vv  -    
  L1M4_orf2#LINE/    340 TATGGTCAATT-GATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGA 387

  chr1_59124194_5   1275 AAGACTC-CCTATTCAGTAAATGCTGCTGGGATAGCTGACTAGTCATATG 1323
                             v v-i  v    ii     v        i i   iv  ?i  i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_59124194_5   1324 CGGAAGAATGAAATTGGGTGCCTACCTTTCATCATATACAAAAATTAACT 1373
                          ii         i    iiv       iv  i                  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_59124194_5   1374 CAAAATGGATTAAAGAT-TAAATGTAAGACCTCAAACTATACAAATCCTA 1422
                                   i ?   i-           v  v        v  v  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_59124194_5   1423 GAAGAAAACCTAGGAA-ACATCATTCTGGATATCGGCCTTGGGAAAGACT 1471
                                  v    ?i- v   -   vv  iv i  vi v  v  v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_59124194_5   1472 TT----ATAAGTCTTCAAAATCGATTGCTACAAAAACAAAATTTGACAAG 1517
                          i----   v v vi     v ivvv  v      iv    v v  i  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_59124194_5   1518 TGGGACCTAATTAAA-TAAAGAGCTTCTACACAGAAAAAGAAACTACCAA 1566
                          v    i v  i   - v  i i   i iii vvv   i  v    i   
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_59124194_5   1567 CAGAGTAAACAGACAACCTACAGGTTTGTTTCCTGGGTATGTTTCCTGGG 1616
                         v i   i  v        i    i--------------   -------  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGA--------------ATG-------GG 715

  chr1_59124194_5   1617 AGAAATTATTCATAGACCATACATCCGACAAAGGTCTAATATCCAGAATC 1666
                              v    iii i i    i   i  i  i  v  vi          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_59124194_5   1667 TATAAGGAACTTAAACAACTAAACAA-GCAAAGACAAATAACTTGATTAA 1715
                              i     ivv      v  i  -iv             iii   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_59124194_5   1716 AAAATGGACAAGAGACATGAACAGACATTTCTCAAAAGAAGACATATAAG 1765
                                i   ii  iv    i           v        i   i  i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_59124194_5   1766 CAGGCAACAA--ACATGAAAAAGTTCTCAAAATCACTAATCAT 1806
                         ii v   i  --         ii v     v    ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (141 / 91)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.88 (49 / 17)  


3194 27.53 0.44 0.44  chr1_59135322_59141724     5003  5910 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59135322_5   5003 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5052
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59135322_5   5053 GGCCATACTGCCCAAGATAATTTATAGATTCAATGCCATCACCATCAAGC 5102
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59135322_5   5103 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5150
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_59135322_5   5151 TATGGAACCAAAAAAGAACCCGTATCGCCAAGTCTATCCTAAGCCAAAAG 5200
                                viiv  ii  v  v v  v     iv v   i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_59135322_5   5201 AACAAAGCTGGAGGCATCACGTTACCTGACTTCAAACTATACTACAAGGC 5250
                                i      vv    ii v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_59135322_5   5251 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5300
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_59135322_5   5301 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 5348
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_59135322_5   5349 CTCTGATCTTTGACAAACCTGAGAAAAACAGGCAATGGGGAAAGGATTCC 5398
                         vvi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_59135322_5   5399 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5448
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_59135322_5   5449 GCAACTGGATCCCTTCCTTACACCTTAAACAAAAATTAATTCAAGATGGA 5498
                          v ii    i    v   i     v  v           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_59135322_5   5499 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5548
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_59135322_5   5549 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5598
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_59135322_5   5599 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5648
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_59135322_5   5649 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGAAC 5698
                          i   v v  i i   i  ii vv    i  v    i  vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_59135322_5   5699 AGGCTACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5748
                           i v   i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_59135322_5   5749 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5798
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_59135322_5   5799 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGGTATGAACAGACACTTC 5848
                          i     i     v  i?    i          i v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_59135322_5   5849 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5898
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_59135322_5   5899 ATCACTGGCCAT 5910
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (145 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 277 32.05 3.21 3.85  chr1_59276748_59279028      595   750 (1531)    L1M4_orf2#LINE/L1        1   155 (753)  

  chr1_59276748_5    595 TAGAAAAATATCTC-TGTTCTTGGTTCAGACATCTCAACATTATCA-GTC 642
                          i    i     i -     v   v ii  viv  i  i   i i - vi
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59276748_5    643 AGCCAGTCTACCCTAAGTTAATTTATTAATTTATTGTAATACTAATAAAA 692
                         i  v vv  -   i  i  i  i  ivi   i vi i   v iv  v   
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_59276748_5    693 ATACAAAAAAGCTG---TTTTTCCTGAAGCTAAACAAGCTGATATTAAAG 739
                           v v ----    ---     v v   ii i -         vi    i
  L1M4_orf2#LINE/    100 ATCCCA----GCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAA 144

  chr1_59276748_5    740 TTTGTACAAAA 750
                           ii  iii  
  L1M4_orf2#LINE/    145 TTCATATGGAA 155

Transitions / transversions = 1.78 (32 / 18)
Gap_init rate = 0.04 (6 / 155), avg. gap size = 1.83 (11 / 6)  

 778 22.93 9.56 10.69  chr1_59276748_59279028     1070  1780 (501)    L1M4_orf2#LINE/L1      169   871 (37)  

  chr1_59276748_5   1070 AGAATG--CAAAAAAATGGCTAGGAAAACACTGAAGGAAATTGCTAGAAG 1117
                              i--     v   --  v i    v v-   vi  i   ------ 
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAAT--CTTGAAAAAGAA-GAACAAAGTTG------G 209

  chr1_59276748_5   1118 AGGGCACTAGCCCTACCAAATATTAAAAC---------ATCTATAG--GT 1156
                            --   vi v  v  v   v i     --------- v   i  --i 
  L1M4_orf2#LINE/    210 AGG--ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_59276748_5   1157 TAAAATAGTGTAACACTGCTATGTGAATAGGCATAC----CAATAGACTA 1202
                         i  i i     iii    vi  iv i    i    i----    i  v  
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_59276748_5   1203 GATTAGGAAGTCCAGAAATAAACCTAACCATATATGAAGTTCAAGAATAT 1252
                           v v ii                ----    i  ----  -------  
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACC----CATACAT----TT-------AT 342

  chr1_59276748_5   1253 AATAAAAGTAATAACTCAGATCATTAGGACAAAAATGGACTTTTTTTCAA 1302
                         ii --------i  i --   --  vv     iii  ---------i   
  L1M4_orf2#LINE/    343 GGT--------CAATT--GAT--TTTCGACAAGGGTG---------CCAA 371

  chr1_59276748_5   1303 -ACTTTTTTTTAATGATCAGAAAAAAATTGACTTTTTAATAAGTGGTATT 1351
                         -  iv  i---    i--- i   i   v v     i  i  i    ii 
  L1M4_orf2#LINE/    372 GACCATTC---AATGG---GGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_59276748_5   1352 GGAACAATTAGA----CATTTG-AAAAATATAAAATTAGATCTATTCCTT 1396
                           i    i i  ----  iv  -    iv  i  i  i  i iv v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_59276748_5   1397 ATACCATAGATAAAAATAAATTCCAAATGCATCAAAGATCTAAATGTAAA 1446
                          i      v i      v  i  v     v    ?   i          i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_59276748_5   1447 A--TAAGTGAATAATACAAGTATTAGAAGAAAACATGGAC--AAATTTCC 1492
                          --   ---  iv   v  v v              i i?--    i i 
  L1M4_orf2#LINE/    516 AGCTAA---AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_59276748_5   1493 TATAAGCT-GACTGTTGAGAAAGGGTTGCT-AACTGTGACGC--AAAGT- 1537
                         -i i v  - i--   ii v  v    v  - iv i    i --    i-
  L1M4_orf2#LINE/    563 -GTGACCTTGG--GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_59276748_5   1538 CAAGATATGATAAAAGAAGAAAATTGATAAATTTGACTACTTAAAAGATT 1587
                             ---ii i       -     v        v    v v v   -   
  L1M4_orf2#LINE/    610 CAAG---CAACAAAAGAA-AAAATAGATAAATTGGACTTCATCAAA-ATT 654

  chr1_59276748_5   1588 CAAAAAACCTTT-TGCATGGCAAA--ATACCAT-AAGCAAAGCCAAAAGA 1633
                         --      i   -   v --    -- i  i  -   -    iv      
  L1M4_orf2#LINE/    655 --AAAAACTTTTGTGCTT--CAAAGGACACTATCAAG-AAAGTGAAAAGA 699

  chr1_59276748_5   1634 CAAATGACAAATTTGGAAAAAGTACTTACAATGCAAATCACA-----GAT 1678
                            viv   i v v   i   i  i  -----        i -----   
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTT-----GCAAATCATATATCTGAT 744

  chr1_59276748_5   1679 AA-----TT---TCTA--ACATATAAAGAGATTTCAAATCTCAAGGGGAA 1718
                           -----  ---  i -- i         iv i i v v     viiv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_59276748_5   1719 AAA--CAAAGATTGTATGTAAAAAA---ACA-------TGAATAGATG-- 1754
                            --    v vivi vv ?     ---i  -------        ii--
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_59276748_5   1755 ---CCAGAGATATATGCATAAATGAGCCA 1780
                         ---   i   - v  ii i     -    
  L1M4_orf2#LINE/    845 TCTCCAAAGA-AGATATACAAATG-GCCA 871

Transitions / transversions = 1.67 (100 / 60)
Gap_init rate = 0.07 (49 / 703), avg. gap size = 2.94 (144 / 49)  


3179 15.19 2.10 19.03  chr1_59353028_59354661.rev       51  1143 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59353028_5     51 TGGAGAGATAGCCTGTGTTTATGGATTGGAAGACTTACTATTATTAAGAC 100
                             i     v  ii    i                 v    i      i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59353028_5    101 GTTGACACTACCCAAAGCAATCTATGGATTAAATGCAATTTATATCAAAA 150
                          vii i   v      vii     ii    v  i     iiv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59353028_5    151 TCTCAATGACATTTTTTGCAGAAATTTTTTGGAT--GTTTTTCCTAAAAA 198
                           i  iivi v               -----  i-- i vv        -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-----GACAAGCTGATCCTAAAA- 144

  chr1_59353028_5    199 TCTGTTCTAAAATGTGTCTGATATCTTGAGGAACCCAGC-TAGTCAAAAT 247
                         ----   ----  i  ---  v  vi-i   i      v-   i     i
  L1M4_orf2#LINE/    145 ----TTC----ATATG---GAAATGC-AAGGGACCCAGAATAGCCAAAAC 182

  chr1_59353028_5    248 AATCTTGAAAAAGAAGAACAAAGTTGGAGGTCTCA-ACTTCCTGATTTCA 296
                                                       v    -      ii      
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_59353028_5    297 AAACTTATGGTAAA-CTATAGTAAAACAGTGAGTGCAGGGGTGGTGGCTC 345
                                ivii   -   i     --------------------------
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAA-------------------------- 256

  chr1_59353028_5    346 ATGCCTGTAGTCCCATCAATGAGGGGGGCTGAGTCAAGAGGATCCCCCAG 395
                         ---------------------------------      -----------
  L1M4_orf2#LINE/    257 ---------------------------------TCAAGA----------- 262

  chr1_59353028_5    396 GAGTTCAAGGCAGCAGTGAGCTATGCTCATGCCACTGCACTCTAGCCTGG 445
                         -------------     -----------------------------   
  L1M4_orf2#LINE/    263 -------------CAGTG-----------------------------TGG 270

  chr1_59353028_5    446 GCAACAGAGCGAGACCTCGTCTCTTAAAAAAATGAACAAACAAAAAGCAC 495
                         --------------------------------------------------
  L1M4_orf2#LINE/    271 -------------------------------------------------- 270

  chr1_59353028_5    496 ATACAAAAAACAGTGATGTACTGGTATAAAAGTATAAAGATAGACATA-- 543
                         ------------------      i    i--------          --
  L1M4_orf2#LINE/    271 ------------------TACTGGCATAAG--------GATAGACATATA 294

  chr1_59353028_5    544 GACAAATGGAATAGAATAGAGAGCCCAGAAGTACACCCTTGCATATATGG 593
                           iv             v     i      i  v    v i   v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_59353028_5    594 TCCAGTGATTTTCAACAAGGGTGTCATGACCAGTCAATGGGGGAAAAGAC 643
                           v v        i         i  v     v         i  i - i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-AT 393

  chr1_59353028_5    644 AATCTGTTCAACAAATAGTATTGGGAAAACTGATTGTCCACATTCAAAAA 693
                          i   v          i  ii     v     iv i?      v     i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_59353028_5    694 AATGAAGCTGGATCCTTACCTTACACCATATTCAAA------CTTAAAAT 737
                                i    i  i     i         v    ------  i     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_59353028_5    738 TGATCAAAGACCTAAACAAAAGAGTTAAAAATATAAAAGTTTTAGAAGAA 787
                         v     ?         iiv     i     v       v i         
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_59353028_5    788 AACATATGAGAAAATGTTCATGACATTGGATTTGGCATTGATTTTTTGGA 837
                               v ? v    v   i    v    i  v    v  i   i  i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_59353028_5    838 TATGACCTCAAAAGCACAA----CAAAAGAAAAAATAGATG--TTAGACT 881
                               vi           ----                 i--  i    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_59353028_5    882 TCATCAAAATTTAAAAACTTTTGTGTGTGAAAGGCCAGTATTAACAGAGT 931
                                    -             iv v     v  v   i  v i   
  L1M4_orf2#LINE/    644 TCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_59353028_5    932 AAAAAGGCAACATATAAGATGGGAAAAAATACTTACAAATCCTATATCAT 981
                         i     i    vi i ii      i      i  i      v      vv
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_59353028_5    982 ATAAAGAACCAATGTCCAGAATATATAAGGAACTCCTACAACTCAGCAAC 1031
                             i i  ivi i              i      i         ii  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_59353028_5   1032 AAAACAACAA----TCCAATTTAAAACTAGGCACAGAACTTGAATAAATA 1077
                             vi    ----i      ?    v i    v  i i       i i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_59353028_5   1078 TTTCTCCAGAGAAGATATTCAAAAAATGAATAAGCACTTAAAAAGATGCT 1127
                                 i         v    viiiv         v i          
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_59353028_5   1128 CAATATCACTAGATGT 1143
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (104 / 58)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 11.00 (231 / 21)  


3179 26.08 1.55 1.22  chr1_59428017_59434403     4990  5894 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59428017_5   4990 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAACAT 5039
                              ii i  i     i      i v      v i     i  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59428017_5   5040 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAG- 5088
                            v     v     iv i  i  i        i  v   i i     i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59428017_5   5089 --CTAGCTACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTA 5134
                         -- i    i  -------  ii ii     -   -- v  i  - iii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-------TTTTTTGCAGAAATTG--ACAAGCTGATCCTA 141

  chr1_59428017_5   5135 AAGTTCATATGGAAGCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAG 5184
                           i           iiiv  ii  v  v v  v     iv     i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_59428017_5   5185 CCAAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACT 5234
                         vv i          i      vv    i  v  ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_59428017_5   5235 ACAA-------GTAACCAAAACAGCATGGTACTGGTACCAAAACAGACAT 5277
                             -------    i   i    ii         i iv ii i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_59428017_5   5278 ATAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATC 5325
                              i        i    i--    i  --        vv   i i  i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATT 339

  chr1_59428017_5   5326 TACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAA 5375
                           iiiii vi    i  i     ivv  vv  i v  vvv          
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_59428017_5   5376 GGATTTCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGA 5425
                          i  vvi  v  i  i              v      v  ?   i   v 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_59428017_5   5426 GAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCA 5475
                         i  iiv    ii    i    v   i     v              i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_59428017_5   5476 AGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGA 5525
                          i      i ?    i       v   v       i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_59428017_5   5526 AGAAAACCTAGGCAATAACATTCAGGACATAGACATGGGCAAGGACTTCA 5575
                                v    ?ivv  iv   iv   v v ivv i     v ii   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_59428017_5   5576 TGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCG 5625
                          ivv  vi            vvi          vv     v  i    i 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_59428017_5   5626 GATCTAATTAAACTAAAGAGCTTCTGGACAGCAAAAGAAAATACCATCAG 5675
                           ii v  i   v v  i i   i  vi vv    i  v v  i  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_59428017_5   5676 AGTGAACAGGCAACTTACAGAATGGGAGAAAATTTTTGCAACCTACTCAT 5725
                               v  i    ii                 v       vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_59428017_5   5726 CTGACAAAGGGCTGATATCCAGAATCTACAAAGAACTCAAACAAATCTAC 5775
                             i  i  i  vi          v  i         vv    v  v i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_59428017_5   5776 AAGAAAAAAACAAACAACCCCATCAACAAGTGGGAGAAGGATATGAACAG 5825
                           v     i     i     v  i? v  i    vi      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_59428017_5   5826 ACATTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAAT 5875
                                  v        i  vi viii     v ii          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_59428017_5   5876 GCTCATCATCACTGGCCAT 5894
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.12 (25 / 8)  


1422 26.40 3.43 10.53  chr1_59434880_59436659      500  1287 (493)    L1M4_orf2#LINE/L1      177   908 (0)  

  chr1_59434880_5    500 CAAAGCAATCTTTTAAAAAAAGACCAAAATTGGA------ATACTTAACA 543
                             i       vv    i    v    i     ------ i    vv  
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr1_59434880_5    544 GATTTCAAGACTTATTATAGAGCTACAGTAATTAAGACAGTGCAGTTTTG 593
                         -       i     i  i i            i         ii  vi  
  L1M4_orf2#LINE/    227 -ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_59434880_5    594 GTATTAAGTTAGAAAAACAGAACAATAAAATAGATTATAGAGTCCAGAAA 643
                          i  v i v    v v i   v    ii      v vv            
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_59434880_5    644 TAGATCCCCACGCATAGGGTCATTTGACTT-----AAAGCTTT----GCA 684
                           i i  vi  iiv  v     v    i  -----  i v vi----i v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_59434880_5    685 ATTCAGTATGAAGAAGACCATCTTTTCAATAAATAATGCAAGTTTTCCTT 734
                              i iv i i ii ivi         i    ii   vi --------
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG-------- 417

  chr1_59434880_5    735 ATTTTCTACATTGACACTCAGTTTACATTTATATTGAATTTATATTGAAT 784
                         ------------    --------------------------- i  i  
  L1M4_orf2#LINE/    418 ------------GACA---------------------------ACTGGAT 428

  chr1_59434880_5    785 ATCAGTGTGGAAAATAAAGGAAGCTTGATCTCTACCTCAGGCCATGCACA 834
                          ? viii  v    -i  v    i v  i i        vi    ii   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAA-GAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_59434880_5    835 AAAATTAATTTGAAGTAGATTAAGAACCAAAATGTGACGTCCGAAGTAAT 884
                                 i ii  i i   i ?ii   v      i viv ii  iiv  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_59434880_5    885 CAAGCTTCTAGCTGAAAATATAGAAGAATATCTTCCTGGCTTTGATATAG 934
                         v  i  ii   vv     i    i? v v      v  i i   ivv   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_59434880_5    935 GTAA-AATGTATTAAATAAGACACAAAAAGAATTTACCCTAAAAGAAAAA 983
                          i  -ii v v   i   v     v     v ivvi vvi          
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_59434880_5    984 AATTATAAAATTGATTTTATTAATGTTGGGAATTTCTGTTTATCAAAAAG 1033
                          vvv     v v  i  i  i  vi  iii  i  i   viv     iii
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_59434880_5   1034 CAA-ATAGGCAAGGCACAGAGTTACAGGTGCAAACAGAGGCTAGAGAAG- 1081
                           v-  ---    ---- i   ---------------------  i   -
  L1M4_orf2#LINE/    678 CACTAT---CAAG----AAAGT---------------------GAAAAGA 699

  chr1_59434880_5   1082 CAACCCAGAGACCCAGGTTGGCATTATTTATAATACATATATCCAACAAA 1131
                                v   vi--  vv iv v     ii  vv        ii i  i
  L1M4_orf2#LINE/    700 CAACCCACAGAAT--GGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_59434880_5   1132 TCACTCATACTCAGAATGTATAAAGAACTCCTTCCAAAATTAAATAACAA 1181
                         vv   ii  ii      i            i v ---  i v     i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTAC---AACTCAATAATAA 794

  chr1_59434880_5   1182 AAACACAA----CCCAATTTTACAA-AGGCAAAATTATCT-AACAGATAT 1225
                            v    ----       ?v v  -i      iv-  i -  i   i  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGG-ATTTGAATAGACAT 843

  chr1_59434880_5   1226 TGCACAAAAGAGGCTGTTCAAATGGTCAA---GCAGATGGAAAGGTGTTC 1272
                          v v v     i v i v       i   ---   v   i    i  i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_59434880_5   1273 AATTTCATTAGCTAT 1287
                           iv   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (122 / 82)
Gap_init rate = 0.03 (20 / 732), avg. gap size = 5.50 (110 / 20)  


2414 23.69 6.67 3.69  chr1_59477470_59480560.rev     1753  2592 (499)    L1M4_orf2#LINE/L1        1   865 (43)  

  chr1_59477470_5   1753 TGAACAGATATACTGTGTCCACGGGTCAGAAGACTTGGTATT--TCAAAT 1800
                           i v      v ii   i  i  i ii        ii    -- v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59477470_5   1801 GTCAATTCTCCCCCCAAATTAATGTATACATTCAATACAATTCCAGTTAA 1850
                          v    v      --     i  v  i v      ii    i  vi i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCC--AAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_59477470_5   1851 AATCTAAATAGGCCTTATTTTG---AAATGGACAAAGTGATTATAAAATT 1897
                             iv ii-v     -     ---    v     iv    iv       
  L1M4_orf2#LINE/     99 AATCCCAGC-TGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_59477470_5   1898 CATATGGAAATA----GAACCTAGAATAATCAAAACAAATTTTAAAAAGA 1943
                                    i---- i   i      ii        vi  v       
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_59477470_5   1944 A---CAAAATTAAAGGACTTATACTACCTGATTTCAGTACTTATTACAAA 1990
                          ---    i  ii      i i   v  ii      iv     i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_59477470_5   1991 GCTGTATTTAT-AAGACTATGTGGTGTTCGCATTAAAATAGACA-AGAGA 2038
                            ii v v  -     vi      ii v    v ii       - v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_59477470_5   2039 TCAACTGAACAAAAT--AAAACACAAAATTGGGCCAATGTATACATGGTA 2086
                             iv   i i   -- i iiv  i  v iii  v  ii  vi     v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_59477470_5   2087 AATTGATTTTTGAACAAAGGTGCAAAGGCAATTCAATGAAGA-----TAG 2131
                                   i  -   i     v   i v        ii  -----   
  L1M4_orf2#LINE/    347 AATTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_59477470_5   2132 GCTTTTCAGCAAACAGTGCTGG---AACTGGATAGCCATATGCAAAAAAA 2178
                         v       i    ii       ---         ?   i        i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_59477470_5   2179 -AAACTTGATTCCATATTTCATGTCCTATACAAAAATTACCTTAAAATG- 2226
                         -i  v   ivi  v  ii   iii v             v  i      -
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_59477470_5   2227 ATCACAGATTTAA-TATAAAACCAAAAATGACAAAACTTCTTTTAAAAA- 2274
                             ?   ii   - i   i v v    iv i      -   vv  i  -
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAA 544

  chr1_59477470_5   2275 ---TAGGAA-GAATATTTGAGACCTTAGGTTAAGCAAAGATATCTTAGAT 2320
                         ---    ?i-i   v  i v      i     i    v i v        
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_59477470_5   2321 AAAACACAAAAAGCATGATCCATTATAATTCAGATTGGTAACATTTATTT 2370
                          vi    v       ii v ------  --  i --i v  ---------
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGC------AA--CAAA--AGAAA--------- 625

  chr1_59477470_5   2371 AACCAAAT-TATAAATTAGACTTCATCAAAATTAAGAACTCT---GCTTT 2416
                         ----    -v       i                 i    i ---    -
  L1M4_orf2#LINE/    626 ----AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT- 670

  chr1_59477470_5   2417 CAAAAGACACTGT--------TGA---GACAAGCATCAAAATA--AGAAA 2453
                             i      i --------   ---     v vv  i   i--     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_59477470_5   2454 ATATCTGCAAGT--TACACGTGATAAAGAACTTATGATAAGAATA----A 2497
                             i     i --  i iv      i i    i iviv      ---- 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_59477470_5   2498 AGAATTCTCAAAGCTCAATAAAAAGAAAATAAAAGGCTCATTTTTTAAAA 2547
                             i   i v i        v  i  i i   vii i  v  ?v-    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAA 819

  chr1_59477470_5   2548 TGGACGAAAGATT-GAATACATACTTTACCTTAGGGGGTATACAAA 2592
                            i i  i    -     v i i  iv  vv  ii i        
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

Transitions / transversions = 1.95 (129 / 66)
Gap_init rate = 0.04 (33 / 865), avg. gap size = 2.64 (87 / 33)  


 453 28.81 1.69 0.00  chr1_59512957_59515130.rev      580   697 (1477)    L1M4_orf2#LINE/L1        1   120 (788)  

  chr1_59512957_5    580 TGGAGAAATATGTCACACTCGTAAAATGGAAAATTCAACATTGTTCAGAT 629
                             i i    vi  iii  i ii v     i i i  i      v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59512957_5    630 GGTAAT-CTCTTCAAATTAACCTACAGATTCTCCACAACTCC-ATTAAAA 677
                           i   -   ii      i i          vv i   ii  -  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59512957_5    678 TCCTAGCAGGTTTTCTAACA 697
                            i   v vi   i vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA 120

Transitions / transversions = 3.25 (26 / 8)
Gap_init rate = 0.02 (2 / 120), avg. gap size = 1.00 (2 / 2)  

2263 21.53 8.55 1.18  chr1_59512957_59515130.rev     1006  1683 (491)    L1M4_orf2#LINE/L1      181   908 (0)  

  chr1_59512957_5   1006 ACAAAATTGAATAGAAAGAAC----TTGGAAAATATATGCTATCTGACTT 1051
                             vv     v ii      ----     ii ivi ii  vi ii i  
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_59512957_5   1052 CAAAACTTACTATAAAACTA--GCATTCCTAAGTTTATGTGGTATTGGTA 1099
                                     i   i   -- i v  --   vivi       i   i 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATC--AAGACAGTGTGGTACTGGCA 278

  chr1_59512957_5   1100 TAAGGATAAATTTATAAATCAATAGAACAGA---GATA--TAAGAAGTAA 1144
                                 i iv    i      i   i   ---  v --iv    i   
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_59512957_5   1145 ACCCAT----TTATGG-CAATTGGCTTT-GGTAAATGTGCCTATATAATT 1188
                               ----      -      ii   - ii  iv     v v iv   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_59512957_5   1189 TAATGGGGGAAAGGACAGACTATTTGACAG-TGATGCTAG---AACTATA 1234
                         i       -    i i  v  v  ii   i-  i    i ---    iv 
  L1M4_orf2#LINE/    379 CAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_59512957_5   1235 TGACTATATGCAAAAAA--GAACTTAGACTCTTACCTCACACCATACACA 1282
                          i? i i        i --   v  i   i i              i   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_59512957_5   1283 AAACTTAACTCAAAACATATCACATCCCTAAATGTAAGA-CTAAAAATAT 1331
                            v           iiv    ? vv             -      v   
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_59512957_5   1332 AAAATGTGTAGAAGAAAACA--GGAGAACATTGTTGCAACCTTGCATTAG 1379
                             iviv            --  ? v v  iv i ii      vi    
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_59512957_5   1380 ATGAAGATTT------TATAA-----AAAGCAAGCAAGACCCACAAAAGA 1418
                         iii v i   ------   i -----      --    -- v        
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCA--CAAG--CAACAAAAGA 623

  chr1_59512957_5   1419 AAAAAT-------TTTGACTTCATCAAAATTTAAAAATCTTTTTCTTCAA 1461
                               -------  v               v    v i  v v      
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_59512957_5   1462 AAGAAACAATTA-GAAAACGAAAAGACAAGCTACAGACTGGAAGAAAATA 1510
                          i  v  v  i -    ii          v i     v   i        
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_59512957_5   1511 TTTGCAAACAACACATCTGATAATATACTTGCATATAAAATATAT----- 1555
                                 iv i i         viv     i  vi i       -----
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_59512957_5   1556 ---TTTAAAACTCAAATAATAAGAGGAAAAACAACCCAATGATAACATTG 1602
                         ---i   v       -      i i  v   i        v?v  v  v 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAA-TAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_59512957_5   1603 GCAAAAGATGTG----GACACTTCTGCAAAGAAAATATACAAATGGCCAA 1648
                              i   v  ----    i    v       i                
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_59512957_5   1649 TGTACACATGAAAAAGTGCTCAA-ATCATTAGTCAC 1683
                          ivi          ii       -    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (88 / 54)
Gap_init rate = 0.03 (24 / 728), avg. gap size = 2.75 (66 / 24)  


3090 27.21 1.00 0.55  chr1_59546117_59552508     4996  5899 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59546117_5   4996 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5045
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59546117_5   5046 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5095
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59546117_5   5096 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_59546117_5   5144 TATGGAACCAAAAAAGAGCCCGCATCCCCAAGTCAATCCTAAGCCAAAAG 5193
                                viiv  ii  v  v v  vv    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_59546117_5   5194 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGTC 5243
                                i      vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_59546117_5   5244 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5293
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_59546117_5   5294 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5341
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_59546117_5   5342 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5391
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_59546117_5   5392 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCA---GGAGAAAGCT 5438
                           v  i  i              v      v  ?   --- v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_59546117_5   5439 GAAACTGGATCCCTTCCTTACACCCTATACAAAAATTAATTCAAGATGGA 5488
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_59546117_5   5489 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAACC 5538
                          i ?    i    i  v   v       i      vi i         v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_59546117_5   5539 -CAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5586
                         -i   ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_59546117_5   5587 AAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCTC 5636
                         vi            vvi          vv i   v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_59546117_5   5637 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5686
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_59546117_5   5687 CAGGCAACCCACAAAATGGCAGAAAATTTTCACAACCTACTCATCTGACA 5736
                         v  i         i     v       v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_59546117_5   5737 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5786
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_59546117_5   5787 AAAACAAGCAACCCCATCAAAAAGTGGGTGCAGGACATGAACAGACACTT 5836
                           i    ii     v  i?    i    iiv    iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_59546117_5   5837 CTCAAAAGAAGACATTTATGCAGCCAGAAACCACATGAAAAAATGCTCAC 5886
                            v        i  vi viii    iv  v          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_59546117_5   5887 CATCACTGGCCAT 5899
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2169 26.76 0.48 0.32  chr1_59639304_59644960      493  1116 (4541)    L1M4_orf2#LINE/L1      284   908 (0)  

  chr1_59639304_5    493 ACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGC 540
                          i   v                i    i--    i  --        vv 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACC 331

  chr1_59639304_5    541 CGCATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGAAA 590
                          ii i  i  iiiii vi    i  i     ivv  vv  i v  vvv  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_59639304_5    591 TGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGC 640
                                  i  vvi  v  i  i              v      v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_59639304_5    641 CATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAG 690
                           i   i i  iiv    ii    i    v   i     v         i
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_59639304_5    691 TTAATTCAAGGTGGATTAAAGACTTAACCGTTAGACCTAAAACCATAAAA 740
                             i    ii     i ?    i   vi  v   v       i      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_59639304_5    741 ACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAA 790
                         vi i           v    ?i v viv   iv   v v  vv i     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_59639304_5    791 GGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTG 840
                         v ii   v ivv  vi            vvi          vv     v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_59639304_5    841 ACAAATGGGATCTCATTAAACTAAAGAGCTTCTGGACAGCAAAAGAAACT 890
                          i    v   ii    i   v v  i i   i  vi vv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_59639304_5    891 ACCATCAGAGTGAACAGGCAACCCACAAAATGGCAGAAAATTTTCGCAAC 940
                          i  vv i      v  i         i     v       v  i    v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_59639304_5    941 CTACTTATCTGACAAGGG-CTAATATCCAGAATCTACAGTGAACTCAAGC 989
                         ii iv       i     -  vi          v  i iv      vvi 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_59639304_5    990 AAATTTACAAGGAAAAAACAAACAACCCCATCAGCAAGTGGGCAAAGGAT 1039
                           v iv i  vi    i     i     v  i?iv  i            
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_59639304_5   1040 ATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAACACACAT 1089
                         v    i     i     v        i  vi viii     v vi     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_59639304_5   1090 GAAAAAATGCTCATCATCACTTGCCAT 1116
                              i       v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (89 / 74)
Gap_init rate = 0.00 (3 / 625), avg. gap size = 1.67 (5 / 3)  

3178 27.12 0.66 0.55  chr1_59639304_59644960     4258  5164 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59639304_5   4258 TGGAAGAACATTGCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4307
                              ii i  iv    i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59639304_5   4308 TGCCATACTGCCCAAGGTAATTTATAGATTCCATGCCATTCCCATCAAGC 4357
                         v  v     v     iv i  i  i      v i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59639304_5   4358 TACCAATGACTTTCTTCACAGAA-CTGAAAAAAACT-ACTTTAAAGTTCA 4405
                          v   iivi i  i  ii     -i   v  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_59639304_5   4406 TATGGAACCAAAAAAGAGCTCACATTGCCAAGACAATCCTAAGCAAAAAG 4455
                                viiv  ii  v iviv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_59639304_5   4456 AA-AAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4504
                           -    i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_59639304_5   4505 TACAGTAACCAAAAGAGCATAGTACTGCTACCAAAACAGAGATATAGACC 4554
                                 i   i v  ii i      vi iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_59639304_5   4555 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 4602
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_59639304_5   4603 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4652
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_59639304_5   4653 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4702
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_59639304_5   4703 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 4752
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_59639304_5   4753 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4802
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_59639304_5   4803 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4851
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_59639304_5   4852 AAACACCAAAAGCAATGGCACCAAAAGCCAAAATTGACAAATGGGATCTC 4901
                         vi            vvi   v      vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_59639304_5   4902 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4951
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_59639304_5   4952 CAGGCAACCTACAGAATGGGAGAAAATTTTCACAACCTGCTCATCTGACA 5001
                         v  i     i                 v  ii   viiiivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_59639304_5   5002 AAGGGCTAGTATCCAGAATGTACAAAGAACTCAAACAACTTTACAAGAAA 5051
                          i  i  v           i  i         vv      iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_59639304_5   5052 AAATAAAACAACCCCATCAAAAAGTGGGCAACGGATATGAACAGACACTT 5101
                           ivv   i     v  i?    i       v    v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_59639304_5   5102 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAACATGCTCAT 5151
                            v        i  vi viii     i ii          v       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_59639304_5   5152 CATCACTGGTCAT 5164
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2413 21.01 1.81 15.09  chr1_59672287_59674433.rev      610  1656 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59672287_5    610 TGGAAAAACATTCCATGCTCATGGAAAGGAGGAATCAATATTATTAAAAT 659
                               i i  i     i       vv   i  v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59672287_5    660 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATTCCCATCAAAC 709
                            v     v      v i  i           i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59672287_5    710 TGCCAATGACATTTTTCACAGAACTAGAAAAAACT-ATTCTAAAATTCAT 758
                          v   iivi v     ii     v v  v  i-  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_59672287_5    759 ATGGAACCAAAAAAGAGCCCGAATAGACAAAGCAATCCTAAGCACAAAGA 808
                               viiv  ii  v  v      v    i     i i iv vi    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_59672287_5    809 ACAAAGCTGGAGGCAC-CACATTACCTGACTTCAAACTATATTCCAAGGC 857
                               i      -  -    i v  ii i      viv  i v   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_59672287_5    858 TACAGTAACTAAAACAGTATGACACTAGTACAATAACAGACACATAGATC 907
                                 ii  i     i  ii   i i i  vi i     i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_59672287_5    908 CATGGAAAAGAATAGAGAGCACAGAAATAAAGCCACACACCTACAA-CAA 956
                         v      v     v     iv          v   i   ii  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_59672287_5    957 TCTGATCTTCAACAAAGTTGACACAAACAAGCAATAAGGAAAGACCCCTC 1006
                          -    i   i    i v  v  vi v  vv    ii       vivv  
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_59672287_5   1007 CCCCCAATTCAATAAATGGTGCTGGGATAACTAG----CCATATGCAGAA 1052
                         ii-----     i              i    i ----   i     i  
  L1M4_orf2#LINE/    398 TT-----TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_59672287_5   1053 GATTGAAACTGGACCCCTTCCTTATACCACATATAAAAATCAATTCAAGA 1102
                           v    ii         v   i i    i   i      i  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_59672287_5   1103 TAGATTAAAGACTTAGATGTAAAACCTAAAACTATAAAAACCCTAGAAGA 1152
                          i   i ?    i  i      i v              vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_59672287_5   1153 AAACCTAGGAAATACAATTAGGTATTATATACCTAATTGTATACCATATA 1202
                             v    ?----------------------------   ---------
  L1M4_orf2#LINE/    543 AAACATAGGN----------------------------GTA--------- 555

  chr1_59672287_5   1203 TAAAAATCATATATAAAATCAATACTCCATATATAAAAATCAATTCAAGA 1252
                         -------------------------------------    --   iv  
  L1M4_orf2#LINE/    556 -------------------------------------AATC--TTCGTGA 566

  chr1_59672287_5   1253 TAGATTAAAGACTTAGATATAAAACCTAAAACTATAAAAACCCTAGAAGA 1302
                         i----------   i i --------------------------------
  L1M4_orf2#LINE/    567 C----------CTTGGGT-------------------------------- 574

  chr1_59672287_5   1303 AAACCTAGGAAATACCATTCTAGACATAGGCTCTGGCTAAGATTTCACGA 1352
                         -----    v   ---------------  i i---  v    ------ 
  L1M4_orf2#LINE/    575 -----TAGGCAAT---------------GGTTT---CTTAGAT------A 595

  chr1_59672287_5   1353 TGAAGATGTCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGGC 1402
                            ---iii        vvv          v      v  i    v  i 
  L1M4_orf2#LINE/    596 TGA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_59672287_5   1403 CTAATTAAACTAAAAAGCTTCCACACAGCAAAAGAAACTATCAATAGAGT 1452
                         i v  i   v v    i   iiiii vv    i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_59672287_5   1453 AAACAGTCAACCTACAGAATAGGAGAAAATATTTGCAAACTATGCATCCA 1502
                         i  v  v     i       i                  ii  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_59672287_5   1503 ACAAAGGATTAATACCCAGAATATTTAAGGAATTTAAGCAAATTAACAA- 1551
                          i  i   i vi  i         v   i   i ivvi   v i  i  -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_59672287_5   1552 ---GCGAAAAATAACCCCATTAAAAAATGGGGAAATAACATGAA----CA 1594
                         ---iv  v         v   ?         v   vi iv    ----  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_59672287_5   1595 CTTTTCAAAAGAAGACATACAA----CCAACAAACATATGAAAAAGTGTT 1640
                         i  i  v        i      ----    i  i  i       ii  i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_59672287_5   1641 AATCATTAGAGAAATC 1656
                         v v   i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (140 / 77)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 8.85 (177 / 20)  


3087 27.80 1.00 0.44  chr1_59710316_59718216     4738  5640 (2261)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59710316_5   4738 TGGAAGAACATTCCATGCTCGTGGATAGGAAGAATCAATATCATGAAAAT 4787
                              ii i  i     i  i     v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59710316_5   4788 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4837
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59710316_5   4838 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 4885
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_59710316_5   4886 TATGGAACCAAAAAGAGCCC-GCATCACCAAGTCAATCCTAAACCAAAAG 4934
                                viiv  i ii   - v  vi    iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_59710316_5   4935 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCTATACTACAAGGG 4984
                                i      vv    i  v  ii i     iviv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_59710316_5   4985 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGATC 5034
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_59710316_5   5035 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5082
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_59710316_5   5083 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5132
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_59710316_5   5133 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5182
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_59710316_5   5183 GAAACTAGATTCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5232
                            ii i  ii   v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_59710316_5   5233 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAATCCTAGAGGAAAAC 5282
                          i ?    i    i  v   v       i      v  i    i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_59710316_5   5283 CTAGGCATTACCATTCAGAACATAGGCATGGGCAAGGACTTCATGTCTAA 5332
                         v    ?i v viv   ivi  v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_59710316_5   5333 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5382
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_59710316_5   5383 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGAAC 5432
                          i   v v  i i   i  ii vv    i  v    i  vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_59710316_5   5433 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTGCTCATCTGACAA 5482
                           i     i   i             v  ii   viiiivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_59710316_5   5483 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACGAGAAAA 5532
                         i  i  vi          v  i  v      vv    v iv ii v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_59710316_5   5533 AAACAA----CCCCATGAAAAAGTGGGCGAGGGACATAAACAGACACTTC 5578
                          i    ----   v  v?    i     i i   iv i  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_59710316_5   5579 TCAAAAGAAGACATTTATGCAGCCAAAACACACATGAAAAAATGCTCACC 5628
                           v        i  vi viii     v vi          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_59710316_5   5629 ATCACTGGCCAT 5640
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  

1913 28.43 5.69 4.68  chr1_59710316_59718216     6516  7412 (489)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_59710316_5   6516 GAGGGATATATGATGTTCATTGATTGGAAAAC--AGTATTATAAATGTGA 6563
                           ii     viv        v        i  -- i    i v  vi  i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_59710316_5   6564 CAGTTTCTTCCCGG-TTGTTCTATAGATTCAGTGTACTTCAGTTCAGCAT 6612
                           i v-  i   ii-   v    i       ii i v i vvv   iv  
  L1M4_orf2#LINE/     53 CAATA-CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_59710316_5   6613 TCTAGCAGATTTGTGTGTAAGAGGATGGAAATTGGTAGAC--ATCCTAAA 6660
                         i i   v vi  v v  i --------       ii ii --        
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCA--------GAAATTGACAAGCTGATCCTAAA 143

  chr1_59710316_5   6661 ACTTAGATGGAAA------GGATC---AATAAT-AAGACAGTCTTGAAAA 6700
                          i i v       ------   i ---    ii-  i   i         
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_59710316_5   6701 AGAA---CAAAGTTGGGAAAACTCCATAATGCCAGATAGCAGAACATATT 6747
                             ---         - ii    - i v v  vi  vv  i   v  i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGG-AGGACTC-ACACTTCCCAATTTCAAAACTTACT 241

  chr1_59710316_5   6748 ACGAAG------TAATTAAGA----ATGGTATTGAGGGAAGGACAGACA- 6786
                           i   ------    i    ----i     i  iviv     i     -
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_59710316_5   6787 ---ACCCAGAGGAAAACAGATTAAGGAGCCCAGAAACAAACTCACACATG 6833
                         ---ivi  iv    v v -   i  -  i       i    i  i    v
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGA-ATTGAG-AGTCCAGAAATAAACCCATACATT 339

  chr1_59710316_5   6834 TATGGACAGTTAATTTGTGGCAAAGATGCCGTTGCCAGAGCTGTAAGGAA 6883
                              v  i  i    vi i   i i    ivvi   v-v vi ii    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAA 388

  chr1_59710316_5   6884 GCAAT-GTATTTTTCAGTGAAATAGTACCCTGCCGATTGGTTATCACTAT 6932
                         iv   -  -i      ii-    i  i ivv v i i   v  ? vvi  
  L1M4_orf2#LINE/    389 AGAATAGT-CTTTTCAAC-AAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_59710316_5   6933 GGCAGAAATTGAATTTTGGCCCTTCTCCTTATACTATGCATACAAATACA 6982
                          vv i i v    v  v i   i v-   i i  i  ii i v    vv 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTA-CCTCACACCATATACAAAAATTAA 485

  chr1_59710316_5   6983 TTCCAAACAGATTAAAAACTTAAGTATGAAATTTAAAAAAATAAAGTTCC 7032
                         i  v   ii   i ? i  i   i i i i vi     vv     ii  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_59710316_5   7033 TAAAAGA---CA-AGG------TCTTCATGACTTTGAGATAGACAAT--T 7070
                           i    ---  -   ------     i    i   i v   i    -- 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_59710316_5   7071 TTCCTAAATAGGACATTAATGTAAGTACAACCA-TAAAGAAAAGGATTGG 7119
                            i  i   v    ii  ---   i    v  -i   ii   ii  v i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAA---AAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_59710316_5   7120 TAAATAAGACTATGTTAAAATAAGAAACTTCTTTTCATCAAAAGCTTCCA 7169
                              vi    vii i     v i      i v v v     i viv i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_59710316_5   7170 TTAAAAGAGTGAAAATGCAAGCCACAAAGTGGAAGGAAATAGTTGCAATG 7219
                          i  i i        vi   v     i i   i  i     v      vv
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_59710316_5   7220 CATATA----ACAAAAGATGTGTATCCAGAGTATGTAAAGAATGTCTACA 7265
                               ---- i  ii  iv          i   i       ivii    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_59710316_5   7266 CATTAATGAGAAAAGAACAATTATTTTGACAGAACAATGGTTAAATGTGT 7315
                         vv i   i v    ii    v  viiii iv?  v     vi   v ---
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG--- 829

  chr1_59710316_5   7316 ATAAATGTGTGCATATATACATTTGAGCAGCTTTGCAGAAAAGAGGATAT 7365
                         ----  v  --- -   v      ------  ii-----     i     
  L1M4_orf2#LINE/    830 ----ATTTG---A-ATAGACATTT------CTCC-----AAAGAAGATAT 860

  chr1_59710316_5   7366 ACAAATGGACAATAAG-ATACGAAAAATTGTCCAGCCTTGTTAGTCAT 7412
                                 v       - i i     iv  ii  i v ii????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (162 / 90)
Gap_init rate = 0.04 (34 / 906), avg. gap size = 2.74 (93 / 34)  


3030 27.94 1.11 0.44  chr1_59763997_59770389     4999  5900 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59763997_5   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 5048
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59763997_5   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59763997_5   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_59763997_5   5147 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5196
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_59763997_5   5197 AACAAA-CTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5245
                               -i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_59763997_5   5246 TACAGTAACCAAAAGAGCATGGTACTGGTAACAAAACAGAGATATAGACC 5295
                                 i   i v  ii         i vv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_59763997_5   5296 AATGTAACAGGAC--AGAGCCCTCAGAAATAACACCGCATATCTATAACT 5343
                             v  i  i i--    i  --        vv  ii i  i   iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_59763997_5   5344 ACCTGATCTTTGACATACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5393
                          vi    i  i    vivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_59763997_5   5394 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5443
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_59763997_5   5444 GAAACTGGATTCCTTCCTTACACCTTATACAAAAGTTAATTCAAGATGGA 5493
                            ii    ii   v   i     v         i    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_59763997_5   5494 TTAAAGACTTAAACGTTCGACCTAAAACCATAAAAACCCTAGAAGAAAAA 5543
                          i ?    i    i  vv  v       i      vi i          v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_59763997_5   5544 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5593
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_59763997_5   5594 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5643
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_59763997_5   5644 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGAAC 5693
                          i   v v  i i   i  ii vv    i  v    i  vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_59763997_5   5694 AGGCAACCTACAAAATGGGTGAAAATTTTCGCAACCTACTCATCTGACAA 5743
                           i     i   i      v      v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_59763997_5   5744 AGGGCTAATATTCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5793
                         i  i  vi   i      v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_59763997_5   5794 AG-----CAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5838
                           -----i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_59763997_5   5839 TCAAAAGAAGACATTTATGCAGCAAAAAAACACATGAAAAAATGCTCACC 5888
                           v        i  vi viii  v  v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_59763997_5   5889 ATCACTGGCCAT 5900
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (144 / 104)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  


3153 27.43 1.00 0.55  chr1_59787730_59794101     4976  5879 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59787730_5   4976 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5025
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59787730_5   5026 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5075
                            v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59787730_5   5076 TACTGATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5123
                          v iiiivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_59787730_5   5124 TATGGAATCAAAAAAGAGCCCATATTGCCAAGTCAATCCTAAGCCAAAAG 5173
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_59787730_5   5174 AACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTATACTACAAGGC 5223
                                i     ivv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_59787730_5   5224 TACAGCAACCAAAACAGCATGGTACTGGTATCATAACAGAGATATAGACC 5273
                              i  i   i    ii         i  v vi i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_59787730_5   5274 AATGAAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5321
                             i  i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_59787730_5   5322 ATCTGATTTTTGACAAATCTGACAAAAGCA----ATGGGGAAAGGATTCC 5367
                          vi       i     ivv  v   i v  ----          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_59787730_5   5368 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5417
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_59787730_5   5418 GAAACTGGATCCCTTCCTTACACCCTATACAAAAATTAATTCAAGATGGA 5467
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_59787730_5   5468 TTAAAGACTTAAATGTTAGACCTACAACCATAAAAACCCTAGAAGAAAAC 5517
                          i ?    i       v   v   v   i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_59787730_5   5518 CCAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5566
                         vi   ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_59787730_5   5567 AAACATCAAAAGCAACGGCAACAAAAGCCAAAATTGACAAATGAGATCTC 5616
                         vi   i        vvi          vv     v  i    vi  ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_59787730_5   5617 ATTAAACTAAAGAGCTTCTGCCCAGCAAAAGAAACTACCATCAGAGTGAA 5666
                           i   v v  i i   i  iv vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_59787730_5   5667 CAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5716
                         v  i  i  i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_59787730_5   5717 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTCACAAGAAT 5766
                          i  i  vi          v  i  v      vv    v iv i  v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_59787730_5   5767 AAAAGAAACAACCCCATCAGCAAGTGGGCGAAAGATATGAACAGACACTT 5816
                           i v   i     v  i?iv  i     i  i   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_59787730_5   5817 CTCAAATGAAGACATTTATGTAGCCAAAAGACACATGAAAAAATGCTCAT 5866
                            v  v     i  vi vi i     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_59787730_5   5867 CATCACTGGCCAT 5879
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3169 27.42 0.44 0.44  chr1_59825693_59831972.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59825693_5   4882 TGGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  ii    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59825693_5   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59825693_5   4982 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_59825693_5   5030 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_59825693_5   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_59825693_5   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAAGAGAGATATAGACC 5179
                                 i   i    ii         i iv ii v   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_59825693_5   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATACCTAAAACT 5227
                                i    i--    i  --        vv  ii i ii  viiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_59825693_5   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_59825693_5   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 5327
                           v  i  i              v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_59825693_5   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_59825693_5   5378 TTAAAGATTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_59825693_5   5428 CTAGGCATGACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5477
                         v    ?i i viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_59825693_5   5478 AACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5527
                         i    v       vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_59825693_5   5528 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGAAC 5577
                          i   v v  i i   i  ii vv    i  v    i  vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_59825693_5   5578 AGGCAACCTACAAAATGGGTGAAAATTTTCGCAACCTACTCATCTGACAA 5627
                           i     i   i      v      v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_59825693_5   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAACCAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vvv   v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_59825693_5   5678 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_59825693_5   5728 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5777
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_59825693_5   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2373 25.84 3.98 2.73  chr1_59901924_59905066.rev     1848  2652 (491)    L1M4_orf2#LINE/L1       94   908 (0)  

  chr1_59901924_5   1848 ATTGAATTTTCAGCGAACTATTTT-TAAGTATCCATAAAATGATTCTAAA 1896
                           ii  v ii    viv  v    -i iiv  iv i  iv    i     
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_59901924_5   1897 ATTTATATGGAAAGGCAAAAGATCTACATTAGTCAACATAATACTAAAGA 1946
                            i         v    ii  i i v v   i   v i   vi i  i 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_59901924_5   1947 AAAAGAACAAAGTCAGTGAACTGACACTACCCAACTTCATGACTTACTGT 1996
                          i           ii v i   v     v     i    vi       ii
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_59901924_5   1997 AAAGCTACAATAATTAAGACAGTGTAAGGTTGGGGAAAGAAAAGACAAAT 2046
                                  i    i          iivii   viv   i v     v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_59901924_5   2047 AGATCAATGGAACCAAGGA--GAGAATCCAGAAATAGACACAAA----TA 2090
                                     i--  i --    i          i  v  v ----  
  L1M4_orf2#LINE/    294 AGATCAATGGAAT--AGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_59901924_5   2091 GAGTCAACTGATTTATTCCTTTTCCAACTCCTTTGACAAAGGAGTAAAGG 2140
                         vi     i      ------------------ i     i  v iv   i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTT------------------TCGACAAGGGTGCCAAGA 373

  chr1_59901924_5   2141 TAATTCAAAGGATATAGTGTAATATTTTCAACAAGTCATGTTTGAAATAT 2190
                         iv      v  iv v  vi  i v          i vi  i v i vv i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_59901924_5   2191 TGTATGTCCACATGCAAAACAATGAATTTAGACAGTGACATTAGACATTC 2240
                           v  i?            v      v  i   vviv  v i v  vv v
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_59901924_5   2241 TGCAAAAATTAACTCAAAGTGGATCACATATGTAATTGTAAAACACAAAA 2290
                          i                i       ? v iv   v     i vvi    
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_59901924_5   2291 CTATAAAACATCTAGAAGATAACA--GGAAAAAATTTAGGTGACCTTGGG 2338
                                  vii       v    --  ?iv    i vv           
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_59901924_5   2339 TTAGGTGATAAGTT--TAGATACAAAACCAAAAGCATAATCCATGAAA-- 2384
                              ii  iiv  --      ii v          i  v v ii   --
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_59901924_5   2385 -AAAATTGATAAGCTGGA--TCACTAAAATTCTAAAACT---GCTCTGCA 2428
                         -     v     ii    --   ii      v-      --- iv  v  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCA 672

  chr1_59901924_5   2429 ACAGACATTTTTAACAGAATGGAAAGACAAGCCACAAACTAGAAGAAAA- 2477
                          vi    i v i  v i i  i        v     i v i i      -
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_59901924_5   2478 ----------CACATATCTGATAAAGAAACTTGTATCT-GAATATACAAA 2516
                         ----------  i           i i -        i-       i   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGA-CTTGTATCCAGAATATATAAA 771

  chr1_59901924_5   2517 GAACTCTTAAAATTCAACAATAAGTAAACAAGCAATGTAGTGAAAAAGTA 2566
                                  v  i    i     iv i    ii  ivi i v?    i i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_59901924_5   2567 AGCAAAATATATGAACATGTGATTCACCAAAGAAGATATATAGATGGCAC 2616
                         i     iv  v    i viiiv   v              i i     vv
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_59901924_5   2617 ATAA-TATATATAAAGACACTCAACATCATTTGCCAT 2652
                             -i i  iv     ii          ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (122 / 82)
Gap_init rate = 0.02 (15 / 815), avg. gap size = 3.60 (54 / 15)  


2720 24.73 7.77 0.82  chr1_59969255_59974050     3455  4303 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_59969255_5   3455 TGAAAAAAAATTCCATGTTTATGGATTGGAATAATTAATATTGTCAAAAT 3504
                           i   i v  i       i           v v          i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_59969255_5   3505 GCCCACATAACCCAAAGCAATGTACAGATTCAATTTAATCCATATCAAAA 3554
                          v v i ivv      vii  v           ivi     v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_59969255_5   3555 TGCCAATGGCATTCTTCATAGAAATGAAAAAAAAAACCCTAAAATTTGTA 3604
                          v   iiv  v  i  iii      vi v  ivvi i         ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_59969255_5   3605 TGAAATCACAAAAGACCCCAAATAGCCAAACTAATTCTGAATAAAAGGAA 3654
                           i  vii   ii     vi          vi   ii    v  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_59969255_5   3655 CAAAGCTGAAGCCATTATAGTTCCTGCTTTCAAATTATAATACAAAGCTA 3704
                              i  i  vvv i i v    iiv       viv  v          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_59969255_5   3705 TACTAACCAAAATAGCATGGTACTAGCATAAAAACAGACAGATAGACCA- 3753
                         i v   i   i i  ii       i      ii i     v     i  -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_59969255_5   3754 TGGCAAAGAACAGAAAACAGAAAAATGAATTAATGTACTTATGGCCCACT 3803
                            v v    iv  i iivv i    i  iiv  ii i      i v i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_59969255_5   3804 GATT---GACAAAGGTGACAAGAATATCCACTGGGGAAAAGATAGACTCT 3850
                             ---     i    v     vi  i  v        ii    v  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_59969255_5   3851 TCAAAAAATGGTGCTGGTAAAACTGGATATCTATATATATCCAGAAGAAT 3900
                             v            v v         ? i i  i----  i      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG----CAAAAGAAT 446

  chr1_59969255_5   3901 AAAATTAGACCCTCTACTTCTCACCATATACAAAAATCAACTTGAAATGG 3950
                         i  i  i     -    i  v                i    ii      
  L1M4_orf2#LINE/    447 GAAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_59969255_5   3951 ATTAAAGACTTAAATGTAAGACACAAAACTATAAAACCACCAGAAAAAAA 4000
                           i ?    i           vvi             ivii    i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_59969255_5   4001 CATAGGAGAAACACTTC-TGA-----------GCAAAGATTTAAT-GATG 4037
                               ? v  vv    -   -----------    v i   vv -   i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_59969255_5   4038 AGACTTCAAGAGCACAGGCAACAAAAGCAAAAAT-GACAAATGGGATTAT 4086
                         v   vi   i      i          v      -  i    v   i vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_59969255_5   4087 ATCAAACTCAAAAGCTTCACTGTAACAAAGGAAACAATCAAGAGAATAAA 4136
                               v i    i   ivv  ivv       v  v       i i i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_59969255_5   4137 GAGGCAA----------GGGA-----------------------TTAATA 4153
                         i  i   ----------    -----------------------i i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_59969255_5   4154 A-----------CCAGAATACAGAAGGAACTCAAACAATTCAACAGCAAA 4192
                          -----------        i v  i      vv    i    i ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_59969255_5   4193 AAAAAAAA-AATCTGATTTAAAAATGGGCAAATGATCAAAATAGACATTT 4241
                           i v   -  i ii   ?             v   ivi           
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_59969255_5   4242 ATTTTTTAAAAAGACATACAAATGGC-AAT--GTATATGCAAAAGTGCTC 4288
                         --i iiv  i    i           -   -- i i   v   ii     
  L1M4_orf2#LINE/    846 --CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_59969255_5   4289 AACATCACAAACCAT 4303
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (130 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.87 (73 / 15)  


 271 32.20 0.85 2.54  chr1_59978860_59980566      390   507 (1200)  C L1M4_orf2#LINE/L1   (711)   197    82 *

C chr1_59978860_5    507 AGCATGATTCTCATTAAATTACCATTGACCTTCTTTACAGAATTAGAAAA 458
                          i iii  i ii  i   v v   vivi    i   i     v v  v  
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

C chr1_59978860_5    457 AACTATCTTAAAATTCATATAGAACAAAAAAAAAGGGCCCA-AATAGCCA 409
                         iviv   i            i   --- viv  i  i    -        
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAA---ATGCAAGGGACCCAGAATAGCCA 178

C chr1_59978860_5    408 AGTCAGTCCTAAGCAAAAA 390
                          iv  i  i i iv  i  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAA 197

Transitions / transversions = 1.92 (25 / 13)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 2.00 (4 / 2)  

2064 26.38 1.08 4.58  chr1_59978860_59980566      472  1214 (493)    L1M4_orf2#LINE/L1      192   908 (0)  

  chr1_59978860_5    472 AAAGAAGGTCAATGGTAATTTAATGAGAATCATGCTACCTGACTTCAAAC 521
                                iv   ---- i  vi --i  v   ii  v  ii i      v
  L1M4_orf2#LINE/    192 AAAGAAGAACAA----AGTTGGA--GGACTCACACTTCCCAATTTCAAAA 235

  chr1_59978860_5    522 TGTACTACAAGGCTACAGTAACCAAAACAGCATGGTACTAGTACAAGAAC 571
                         iv        i          i   i    ii       i i i   i i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_59978860_5    572 AGACACATAGACTAATGAATCAGAATAGAGAAATCAGAAATGAGACCACA 621
                              i     ii    i vi     v    ivi       i iv   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_59978860_5    622 CACCTGCAACCATCTGATCTTTGACAAATCTAACAAAAACAAACAATGGG 671
                           ii iiiii  vi    i  i     ivv iv   i v  vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_59978860_5    672 GAAAGGATCCCCTATTTAATAAATGGTGCTAGGAGAAGTGGCTAGCAGTA 721
                              i  vvi  v  i  i          i   v  v   v  ? vii 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_59978860_5    722 TGCAGAAAATTGAAACTGGACCCCCTCCTTACACCATATACAAAAATTAA 771
                             i  i v    ii        iv   i                    
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_59978860_5    772 CTCAAAATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAATCC 821
                                     i ?    i         i v i            v  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_59978860_5    822 TAGACGACACTCTAGACA-ATACCATTCAGGAC-----GC-AAGCAAAAA 864
                             v  v viv   i?i- v i -   iv   ----- i- i    vii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_59978860_5    865 TTTCACAACAAAAATATCAAAAGCA-ATTCAATAAAAGCAAAAATTGACA 913
                             vi ivv vi i i        - vv   i     v      v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_59978860_5    914 AATGGGATCTAATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATT 963
                            v   ii v  i   v v  i i   i  ii vv    i  v     i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_59978860_5    964 ATCAGAGTGAACAGACAGCCTACAGAATGGGAGAAAAATTTTGCTATCTA 1013
                          vv i      v     i  i                vv     v ----
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA---- 730

  chr1_59978860_5   1014 TCTATCTATCTATCTATCTATCTACCTAACAAAGATCTAATATCCAGAAT 1063
                         ---------------   -  v  i  i i  i iv  vi          
  L1M4_orf2#LINE/    731 ---------------ATC-ATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_59978860_5   1064 CCACAAGTAACTTAAACAAATTTACAAGAAAAAAATAAACAACCCCATTA 1113
                         vi i  iv    ivv    v iv i  v     i i   i     v   ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_59978860_5   1114 AAAAGCGGACATTAAAAAGTGAACATGAACAGATCCTTCTCAAAGGAAGA 1163
                             ii  i  --  ii v -----    i   ivi     v  i     
  L1M4_orf2#LINE/    815 AAAAATGGGCA--AAGGATT-----TGAATAGACATTTCTCCAAAGAAGA 857

  chr1_59978860_5   1164 CATACATACGGCCAACAAACATATGAAAAAAAGCTCAACATCACTGATCA 1213
                         i     v i      i  i  i       i v           ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_59978860_5   1214 T 1214
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.67 (120 / 72)
Gap_init rate = 0.02 (11 / 717), avg. gap size = 3.82 (42 / 11)  


2478 12.74 2.15 27.05  chr1_60027314_60030485.rev     1473  2681 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_60027314_6   1473 TGAAATGATAGCCCACATTCATGGATCAGAAAA-TTAATACTGTTAAG-T 1520
                           i  v    v    ii         ii   i -      i       - 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60027314_6   1521 GGCAACATTTCT-AAATTAATCTATAGAT-CAA-GAAGTTCTTATAAAAA 1567
                              i i i i-     i     i    -   - v i i i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_60027314_6   1568 TCTCAGCTGCCTTTTTTTTGCAAGAATTGACAAGCTGATTTCAAGATTCA 1617
                           i              --   ii               iii  i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_60027314_6   1618 CATGAAAATGCTAGGGAATCAGAATAACAAAAACAGCCTTGAA---GAAG 1664
                         i   i      v     vi       i v      ii      ---    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_60027314_6   1665 AATAAAGTTTGAAAACTCACCCTTTCCAATTTCAAAACTTAACTACAAAA 1714
                           i      v  ii      v   i                -       i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAAAG 247

  chr1_60027314_6   1715 CTACAGTAATCAATAATCAATATATGAGTGTGGTACTAGCATAAGATTAG 1764
                                      v --  --------          i       iv   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGA--CA--------GTGTGGTACTGGCATAAGGATAG 287

  chr1_60027314_6   1765 ACATACAACCCAGTAGTAAACCATTAAAAGACCACAAATAAACCCTTGCA 1814
                              --------   ----------------------------------
  L1M4_orf2#LINE/    288 ACATA--------TAG---------------------------------- 295

  chr1_60027314_6   1815 TTTATGGTCAAACGAATTTTTAAACCTTTTTAATTATTAATGGAGGTTAT 1864
                         -----------------------------------  i      ----  
  L1M4_orf2#LINE/    296 -----------------------------------ATCAATGGA----AT 306

  chr1_60027314_6   1865 TTTCTGAGCAGTTTTAGGTTTTTAGAAAAATTGAGCAGAAAATACAGAGT 1914
                         -------------------------- i       ---------------
  L1M4_orf2#LINE/    307 --------------------------AGAATTGAG--------------- 315

  chr1_60027314_6   1915 TCTTTTACATTCCTCTTACCCTCTTCTCACTCTCAGTCTCCCCTATTATT 1964
                         ----------------------------------    i-----------
  L1M4_orf2#LINE/    316 ----------------------------------AGTCC----------- 320

  chr1_60027314_6   1965 ACTATCTTGCATTTGTGTGGTAATTTGTTAGAATTGATGAGCCAATGCTG 2014
                         -----------------------------    -----------------
  L1M4_orf2#LINE/    321 -----------------------------AGAA----------------- 324

  chr1_60027314_6   2015 ATACACTGTTATTAACTAAAGTCCATCATTTATATTGCAGTTTACTCTTT 2064
                         --------------------------------------------------
  L1M4_orf2#LINE/    325 -------------------------------------------------- 324

  chr1_60027314_6   2065 TTGTTATACACCCTATGGATTTTCACGAATGTATAATGACATGTATACAC 2114
                         -----   v    -------------------------------     i
  L1M4_orf2#LINE/    325 -----ATAAACCC-------------------------------ATACAT 338

  chr1_60027314_6   2115 CATTAAAGTATCATGGCCAAGTGATTTTTAACAAGAATACCAA-ATAATT 2163
                         ---------- i    i   v       ii     ii i    - iv   
  L1M4_orf2#LINE/    339 ----------TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_60027314_6   2164 CGATGTAGTAAGAATAGTTTTATCAACTGGTGGTACTAGTACAACTGGAT 2213
                          i   vi v         i  v     vii    i  i v          
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_60027314_6   2214 ATCAACATACAAAAGAATAAAGCCAGATGCCTACCTCACACCATATAC-- 2261
                          ? v    i         i   iii  iv                   --
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_60027314_6   2262 ---------CAAA-TGGATCACAGAC-TAAATATATGAGCTAAAACCATA 2300
                         ---------    -       ?    -     i  v          i   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_60027314_6   2301 AAACTGTTTAAATGAAAAACACAGG-GTAAATCTTTGT-ACCTTAGGTTA 2348
                              -i   i v     -  i   -         i  -     i     
  L1M4_orf2#LINE/    529 AAACT-CTTAGAAGAAAA-CATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_60027314_6   2349 CACAGTGGTTTTTTTAGAAACATCACCAAAAAAAGACAAGCAACAAAAGG 2398
                         vi  i      i  -   v iiv        iv --             i
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTT-AGATATGACACCAAAAGCA--CAAGCAACAAAAGA 623

  chr1_60027314_6   2399 AAAAACAAGTAACTCTGATCTCATCAAAATGTAATACTTG-GTGCTGCAA 2447
                              i ii   v iv  ii          vv  v    v-     v   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_60027314_6   2448 ACTATATCATCAAGAAAGTGAGATGATAACACACAGAATAGAAAAAAAAA 2497
                          vv i ii             i v  i   v        i i i    v 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_60027314_6   2498 ACTGCAAATCATATACCTGACAAGGAACTTGTATCTAGAATATATAAAAA 2547
                         vi             i    i    i         i            i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_60027314_6   2548 ACTATTCCAACTCAATAATTAAAAAGCATATAACCTAAGTAAAACATTGG 2597
                            v  v            v    ii  v      i  v ?   v  v  
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_60027314_6   2598 CAAAGGATTTGAAGAGACATTTTTCCAAGGAAGATATACAAATGGCTAAT 2647
                                      v        i     i                 i   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_60027314_6   2648 AAGTACAT-AAAAGATGCTCAACAACATTAGTCAG 2681
                            i    -               v  ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (102 / 49)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 11.39 (353 / 31)  


3237 22.16 5.11 1.93  chr1_60110853_60112810      586  1465 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_60110853_6    586 TGGAAAGACATCCCATGTTCATAGATTGAAAGACTTAATATTGTTAAAAT 635
                                 i             i     i                  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60110853_6    636 GTCCATATTACCGAAATTAATTTGCAGATTTAATGTCATCCATATCAAAA 685
                          v v   i v  v     i  i i      i  i iv    v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_60110853_6    686 TCCTCTTGACTTTTCCTTTTTTGCAGAAGAAATTAAAAAAT--ATTCTAA 733
                            i---ii  v--              ---   i v  ii--  i    
  L1M4_orf2#LINE/    101 TCCC---AGCTG--CCTTTTTTGCAGAA---ATTGACAAGCTGATCCTAA 142

  chr1_60110853_6    734 AATTTATATGGACCTACAAAAGACCCTGAAAAAGTGAAACAATTTTGAGA 783
                             i       vv i   ii     v   v ivii       i    i 
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_60110853_6    784 AACAAAAACAAAGCTGCAGG---CACAAAACTTTCCTAATTCCAAAAC-- 828
                           v  i       i  v   ---    ----i    i    i      --
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACA----CTTCCCAATTTCAAAACTT 238

  chr1_60110853_6    829 ATTACAAA-CTACAGTAACCAAATAAATCTGATACTGGCATAAAGACAGA 877
                          i      -         i   ivv i v  i           i  i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_60110853_6    878 CCTAGAGACCAATGAAACAGAATAGACAGCCCAGAAACAAATCCATGCAT 927
                          v  v   i     i  i     v  v  i       i   i    i   
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_60110853_6    928 ATATGAGCAAATGGTCTTCAACAAGGATATCAATACTACATAACGGGGAA 977
                         v    iv   v  i i   i      i ii   v  i ivi  i      
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_60110853_6    978 AGGACAGTCTCTTCAACAA-TGGTG-TGGCAAAACTGTATAACCACATGT 1025
                           i i     i        -     -   v v     v   ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_60110853_6   1026 AAAAGAATGAAATTGAACCCTTATTATATAACACAGACAAAAATAAACTC 1075
                                    i   i    i  iivi i v  i v        v     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_60110853_6   1076 AAAATGGATTAAAAACCTAAACATATGACGTGAAACCCTAAAGCTCCTAG 1125
                                  i ? i       ii  v  vv i    iv    i   i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_60110853_6   1126 AAGAAAACACAGGGGAAAGACTTCATAACAGTGGTCTTAGCAATGATTT- 1174
                                  i   ? v  iv    i i  vv   vi vi      i   -
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_60110853_6   1175 --GGATATAACATCAAAAGCAGAGGCAACAAAAGCAAAAACATACAAGTG 1222
                         --i     i   i        v i          v     i v i  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_60110853_6   1223 AGAAT--ATCAAACT--AAAGCTT-----CTTCA-----------CAACA 1252
                         i  v --      v --   i   -----     -----------   v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_60110853_6   1253 AAG-GAAA---CAATC-----AATGCAGTGAAAATACATGCAAATCGTGT 1293
                            -    ---   i -----    -i v       iv        i i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATG-GGAGAAAATATTTGCAAATCATAT 737

  chr1_60110853_6   1294 ATCTGATAGGGGGTTGATATA-AAAATATGTAAGAAATTCCTACAAATTG 1342
                                 i   ii vi   v- i     i   ii  i  i     v ii
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_60110853_6   1343 ATAGCAAAAAATCCCCAAATAACCTGATTTTAAA-TGGGCAAATGACTTG 1391
                            ii     i---v         ii   ?v   -        v  i   
  L1M4_orf2#LINE/    788 ATAATAAAAAG---ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_60110853_6   1392 AATAGATATTTTACTAAGGAA-ACATACAAGTGGGTGAACAGGTATATGA 1440
                               i    iv i  i   - i      i   vi-  i i i i    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCC-AATAAGCACATGA 883

  chr1_60110853_6   1441 AATGATGCTCAATGTCACTAATCAT 1465
                           v         ii   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (129 / 62)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.58 (62 / 24)  


 812 32.01 4.40 6.49  chr1_60226556_60228960.rev      998  1906 (499)    L1M4_orf2#LINE/L1        1   890 (18)  

  chr1_60226556_6    998 TGGAAAGGCATGCTGTTTTCTTGTACATAAAATGTTAACATCATCAAAAC 1047
                                ii  v ii v   v  v ivvi  ivv    i  ii i  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60226556_6   1048 GTCAATCCTCCCTAGGGTAATTTATAAATTTGTTGGGATTCCAACAAAAA 1097
                          v    v     i iiv i  i  i i   iivi vi  i  v iv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_60226556_6   1098 AATAGTGTTCGGTTTTTATTTTGTTTTGTTTTACAACTAGCCAAATTGAT 1147
                         ----- -ii i i ---iii  -     i--- v  v v v   ii    
  L1M4_orf2#LINE/    101 -----T-CCCAGCT---GCCTT-TTTTGC---AGAAATTGACAAGCTGAT 137

  chr1_60226556_6   1148 TAGCAAGTTAATTTGGAATAACAAACAAGCATGAATAGTCAAGAAAACCC 1197
                         ivvv  i  v  v     vvi   ivi v vv      i   i v  i i
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_60226556_6   1198 TGAAAAGGAGAGCAGCACTATGAATAATGGGTAAGATAC-CATTACCAGA 1246
                               i  ----  v  ----  - i v  - i  iv -  i v  vi 
  L1M4_orf2#LINE/    188 TGAAAAAGA----AGAAC----AA-AGTTGG-AGGACTCACACTTCCCAA 227

  chr1_60226556_6   1247 TATTAAAAC-----AAAAAGTCTCTATATTTAAAATAGTGTGGTTTTGGC 1291
                          v i     ----- v    iiv vi  v i  i i        vi    
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_60226556_6   1292 ACATGAATA--CATGAAAGACCAATGAAATTGAAAAGAAAAATTCAGAAA 1339
                          i v i   --   - v   i     i   v   vv  i i- i      
  L1M4_orf2#LINE/    278 ATAAGGATAGACAT-ATAGATCAATGGAATAGAATTGAGAG-TCCAGAAA 325

  chr1_60226556_6   1340 TAAACCCACTGGCAT--ATTGTTATTTTGTATATGATAAAGGTGACATTG 1387
                                 i--i   --  v  i v  vi v vi  i  i    v  v- 
  L1M4_orf2#LINE/    326 TAAACCCAT--ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA-G 372

  chr1_60226556_6   1388 AAAATT-AATAAGAAACAGATGGACATTTTAATCAGTGACAC----ATTA 1432
                          vv   -   ii i  vii  i v v   i  iv i  iii ---- iv 
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_60226556_6   1433 TTGGATAGCTATA-G-AGAAGTTTTAAGTTGGGTCTATTCCTCATATACC 1480
                         i      ? i i - - i   vv v       ii iv v     i --  
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA--CC 470

  chr1_60226556_6   1481 ATACATACGTAAGATGTACATTAGGATATATTCCAAATACATCAAAGGTT 1530
                            --   --  i -----    ------ i  v    iv    ?  iii
  L1M4_orf2#LINE/    471 ATA--TAC--AAAA-----ATTA------ACTCAAAATGGATCAWAGACC 505

  chr1_60226556_6   1531 TAAGTGTAAAGAAATAAACATATACAAATAGTACAAGTAAACATGAGTG- 1579
                            i     -  iv    vv    v  v vv  v   v      ii ? -
  L1M4_orf2#LINE/    506 TAAATGTAA-GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_60226556_6   1580 ATTTCTTCTATCATCTGGGATAAGGGGAAACTTTCTTAACTGTGACTCAA 1629
                          vv     -i v i  v  i v   vi viv       iv i    v v 
  L1M4_orf2#LINE/    555 AAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_60226556_6   1630 AATGCAGATACAATGAGG---AAAAT-GATAC-TT----TTCACTGAAGG 1670
                           v   v vi   ii ii---     -    v-  ----    iii  --
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA-- 651

  chr1_60226556_6   1671 AGTGATTATTTTCA--CCATAAGGGCCAGACACCTGTAAGCAAAGCATAT 1718
                          v i vv i   ii-- ivi  i  ----    ivvi   -    iiv v
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGG----ACACTATCAAG-AAAGTGAAA 696

  chr1_60226556_6   1719 AAACACCTGACAAAGTAGGAGGAAA-ATCTGCAACTTGCATCACTGACAA 1767
                          i   v iv   i i i    i   -  i     v iii  vv    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_60226556_6   1768 A-----TATATCTCTCATCTATAGAATATTCT----ACTTAA-AATAGAG 1807
                         i----- i    ivvv  v    i iv i   ----   i  -    i -
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA- 795

  chr1_60226556_6   1808 AAGAAAAAGGGTTATACTATTAGAAAAATGGGCAAAATACATGAACAGGC 1857
                             v   --- v iv v   ?-             iv iv    i  i 
  L1M4_orf2#LINE/    796 AAGACAAA---TAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_60226556_6   1858 AGTTCACAGAAAAACAAATGTAAATGTTCCTTAAATATATCAAAAGATG 1906
                          v   v vi  i  v v  ii     vi vv   ii i  v        
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

Transitions / transversions = 1.30 (162 / 125)
Gap_init rate = 0.05 (44 / 890), avg. gap size = 2.25 (99 / 44)  


1250 26.52 6.71 8.44  chr1_60272276_60274807.rev     1118  2041 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_60272276_6   1118 TGGAGGGATATACCATGTTCATGGATTTAACAACTCA-TACTATAAAAAT 1166
                             ii     v               vi vi   i -  i i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60272276_6   1167 GTTAATTTCCCTCAAAATTGATCTATTGATTTCATGCTATCTCACTCAAC 1216
                          vi   vii  i    -        iv    iv i  v   i vv    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_60272276_6   1217 ATCCCCAGCAAAAATTATTAATTTGTTTTGTGAAAAAAAGACCATCTGAT 1266
                              -   --------- ivi  -     i- i   vv   v v     
  L1M4_orf2#LINE/    100 ATCCC-AGC---------TGCCTT-TTTTGC-AGAAATTGACAAGCTGAT 137

  chr1_60272276_6   1267 TCTAAAATTTGTGTTGAAATGCAAAAGGTTAAGAATAGCAAAGACAATTG 1316
                         i        ii i v         ii iiiv        v  i     iv
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_60272276_6   1317 TGAAAAA--AGA-CAATACTGGGAGATTTAC-----CCATGAGTTTTCAA 1358
                                --   -   vii   ii  i i  -----   -- --      
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA--A--TTTCAA 233

  chr1_60272276_6   1359 AACTTG-TGTATGTCTACATTAATTAAGACATTGAAGTATTGGTGTGTTG 1407
                              i- ii viv     v    i      v  vi   i   ii ivv 
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_60272276_6   1408 ATAGATACATA-ATTA---GAACAGAAGAGCGAGTTCAAAAATATA---A 1450
                              i i   -  i ---   i    vv v    i  i     v --- 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_60272276_6   1451 TA----TATGGTCAATTGATTTT-GACAGTTATTTCTCTGAAGTGTAGTT 1495
                           ----                 -    ivvi vi ----   vvi -  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCC----AAGACCA-TT 378

  chr1_60272276_6   1496 TAA-----AAATAATGATCTTTGCAATAAATGCTACTGACTCAATTGGAA 1540
                         i  -----   v   ii     v   i     v i   ivv   i    v
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_60272276_6   1541 ATTATTATTGAAAAATGTAAATCTCAATTGTTTCTGAACAAGAAGCAACA 1590
                          ?ivvi  vv    ivi i  vi vi iivi v ivv   vv vii -  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA-CA 477

  chr1_60272276_6   1591 AAAACTAATTATCAGTGAAATACAGATCTAAATATGAAAATGTAGAACAT 1640
                             i   i vvv i  i vi ?   i      i i i ii-  i   vv
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTA 526

  chr1_60272276_6   1641 TAAAGCTTCTAGAAGAAAACAAAAGAATATACTTTTATGATCTTAGGGTA 1690
                             i  ii            v i ?i  v ii  ii   i   i  v  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_60272276_6   1691 AGAAACACAGATTTATTAAACAATACAAAATCAATAACAGAAATTATAAA 1740
                         i v  i--- i   v   i ---  ii v i   v i  v  iiv i   
  L1M4_orf2#LINE/    577 GGCAAT---GGTTTCTTAGA---TATGACACCAAAAGCACAAGCAACAAA 620

  chr1_60272276_6   1741 TTATATAAAAATTAG-TAACT----CTTATATACCAAAAGAGTATTTAAA 1785
                         ---- v     v   -   v ----   ---i i     ------     
  L1M4_orf2#LINE/    621 ----AGAAAAAATAGATAAATTGGACTT---CATCAAAA------TTAAA 657

  chr1_60272276_6   1786 GAGTGGAAAGTCAAATCAGGGGGCTATGGGTAAGGAAAAAATAAAATAAA 1835
                         -------  v i--- i--- v   vi--------   ii i -------
  L1M4_orf2#LINE/    658 -------AACTT---TT---GTGCTTC--------AAAGGACA------- 679

  chr1_60272276_6   1836 TAATTAATTTAAAAAAG-AAAAAGTCAAGTTACAGAGTAGGAGAATATAT 1884
                         ---i  -- i  i    -i     v   vii     i i      v    
  L1M4_orf2#LINE/    680 ---CTA--TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_60272276_6   1885 TTG-A---CATATATATAGCAAAGAATCCATATCCAGA-T---TAAAAAA 1926
                            - ---       v iii  i i iiii        - ---    i  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_60272276_6   1927 T-----------AATAATAATAAACTACAAAT----CAAG-AAGAAAGAG 1960
                         i-----------        v  i--      ----   v-? i   vi 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAG--ACAAATAACCCAATTWAAAAATGG 822

  chr1_60272276_6   1961 GCACA--ATCAAAATAGGCATTTCAC---AAAAGATGTCCAAATAGCCAA 2005
                            v --  ivi     i      v --- i     i v     i     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_60272276_6   2006 TAAGCATATGAAAAGGTACTCAACTTCATTAAACAT 2041
                               i        i i      v   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (150 / 91)
Gap_init rate = 0.05 (46 / 908), avg. gap size = 3.04 (140 / 46)  


2276 27.18 1.39 0.97  chr1_60301057_60302762      493  1213 (493)    L1M4_orf2#LINE/L1      185   908 (0)  

  chr1_60301057_6    493 TCTTCAAAGAAAAAAGAAAAATGCTTGAGGCATCACATTACCTGACTTCA 542
                             v   --  i     v  v i v    vv     i v  ii i    
  L1M4_orf2#LINE/    185 TCTTGAAA--AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_60301057_6    543 AATTTTACTACAAGGCTATAGTAACCAAAACACCATGGTACTGCTATAAA 592
                           vi         i    i     i   i   vii        vi    i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_60301057_6    593 AATTGTCACATATATAAATGGAACAGAATAGAGAACCCAGAAATAAGGGG 642
                         i  v v  i   v  v       i     v    ii          ivvv
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_60301057_6    643 ACATACCAA----CAACCAATTTTTGAAAAAATCAACAAAAATATACATT 688
                          i i iiv ----   iii     i  v  iiviiv   i vi  v  v 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_60301057_6    689 GGGAAAAGGACACTCAATTCAATAAGTGGTGATGGAAAAATTGAACTGCC 738
                            i    i i v  vv     i  i     v   i v  i  i iv?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_60301057_6    739 TCATGCAGAAGAATAAAACTGGATCCATACCCCTTACCATATACAAAAAC 788
                         v      i      i  ii    i  v    i vi              i
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_60301057_6    789 TAAC-CAAGATAGATTAAAGACCTAAATGTAAGACCTGGAAGCTACAAAA 837
                             -   i  i   i ?                v  ii  -   i    
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAA 531

  chr1_60301057_6    838 ATCCTAGAAGAAAATCTAGGGA-AAACTATTGTGGACACTGGCCTAGGGA 886
                         v  i          iv    ?i-   iiv i   -  vi   vi    v 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCA 580

  chr1_60301057_6    887 A-GGTATTTATGAACAAGTCCTCCAAAGCAAACCCAGCGAAACCAAAAGT 935
                          -   v i - ii i v v vi v      v vv  i i   vv    i 
  L1M4_orf2#LINE/    581 ATGGTTTCT-TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_60301057_6    936 AGACAAATGGGACTTCATTAAA--TGAAAGCTTCTGCACAGCAAAAGAAG 983
                            i    v         i   -- i   i   i  ii vv    i  vi
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_60301057_6    984 TCATCAACTGAGTAAATTGACAACCTACAGAATGGGGATAAGTATTCACA 1033
                         ii     vvi   i  vv       i          iiv  i    ii  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_60301057_6   1034 AATCATGTGTGTGACGAAGGGCTAATATCCAGAATGTAAAAAAAACTCAA 1083
                               i i v   ii i  i  vi          i  v   i     vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_60301057_6   1084 ACAACTCAACAACAACAACAACAAAATAACCTCATTAAAAAGTAGGCAAA 1133
                                  i  i  v  -i     -     iv   ?    i i      
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAA-GACAAA-TAACCCAATTWAAAAATGGGCAAA 827

  chr1_60301057_6   1134 GAACATGG-CAGACATTTTTCAAAAGAAGACATACAAGCAACCAACAAAT 1182
                          i iv  i-i        i  v        i      iiii    i  ii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_60301057_6   1183 ATATGAAAAAATGCTCAACATCACTAATTAT 1213
                          i       i             ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (123 / 69)
Gap_init rate = 0.02 (12 / 724), avg. gap size = 1.42 (17 / 12)  


2152 25.66 3.19 0.18  chr1_60365625_60370765     3382  3946 (1195)    L1M4_orf2#LINE/L1        1   582 (326)  

  chr1_60365625_6   3382 TGGAGAGATATTCCATATTCATGCATAGAAAGACTCAATACTGTCAAGAT 3431
                             i      i    i      v  v i      i    i   i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60365625_6   3432 GTCAGTTCTTCCCAATTTGAT--------TCAATGGAATCTCAATCAAAA 3473
                          v  i v  i     v     --------    i v    i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_60365625_6   3474 TTCCAGCAAGTCACTTTGTGGATAATGACAAACTCATTCCGAAGTTTATA 3523
                          i     viviivi    ii  v v      i  v  i ii  i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_60365625_6   3524 TGAATGGGCAAAAGACATAGAATAGCCAACACAATACTGAAAGAGAAGAA 3573
                           i viv    ii   vi           v     vi     i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_60365625_6   3574 TAAAGTTGGAGGGCTGACACTACTTGACTTCAAAACATACTATAAA-TTA 3622
                         i           i  v     v iii i        v     i   -i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_60365625_6   3623 TAGCAATCAAGACAGTGTAGTATTGGTGAAAGAATTGACAAATAGATCAA 3672
                         i  i              i   i   iiv   i  v    v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_60365625_6   3673 TGAAACAGAATAGAGATCCCTGAAATTGACCCAAA----TATAGTCAACT 3718
                           i  i     v    vi  v     vi     v ----   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_60365625_6   3719 GATCTTTGACAAAGGAGTTAAGGCAATACAATGGAGAAA--ATTTTTTTT 3766
                            i  i     i  v ii   i v  v      i    --  vv i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_60365625_6   3767 TCATCAAATGCCACTGAAACAACTGAACTTCCACATGCAAAAAA--GGAG 3814
                            v      vii   ii       i iv?            i -- i  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_60365625_6   3815 TATAGATACAGATTTTACACCCTTCACAAAAATTAATTCAAAATGTGTGA 3864
                          - i  iv vv ii i     v vi           i        vi v 
  L1M4_orf2#LINE/    451 T-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_60365625_6   3865 CAGGTCTAAA-GTAAAATTAAAAACCATAAGACTCTGAGAAGATAACAAA 3913
                         ?  ii     -    i viv     i    i     v      v    v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_60365625_6   3914 AAAGAAAATCTAAATAATTTGGGGTTTGGCAAT 3946
                         ii? v      vvi i ii v     v      
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

Transitions / transversions = 1.63 (88 / 54)
Gap_init rate = 0.01 (7 / 582), avg. gap size = 2.71 (19 / 7)  

1018 23.23 2.58 2.26  chr1_60365625_60370765     4339  4648 (493)    L1M4_orf2#LINE/L1      598   908 (0)  

  chr1_60365625_6   4339 ACACCAAAGTCATGGTCTATGAAAGAAATAATTGATAAACTGGACTTTAT 4388
                                 iv  iiiv v ii       v   v      i       i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_60365625_6   4389 TAAAATGAAAAATTTCTTCTCTGTGAATGACACTGTCAAGAAGATAAAAT 4438
                         i     v     i  i viv  vii  v      i       ----- i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA-----AGT 692

  chr1_60365625_6   4439 GATAAGCGACAAGCCACAGATTTGGATAAG---TTGGCAAAACACATATG 4485
                           v   --    v       v v   v  i---  v     v  i    v
  L1M4_orf2#LINE/    693 GAAAAG--ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_60365625_6   4486 AGATAAAGAATTGTTATGCAAGATACACTAAGAACTCTTA-AACTCAACA 4534
                         v     i i i vv   v  ii   i iv           -       i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_60365625_6   4535 ATAATAACATGAACAACCTAATTGAAAAATAGGCCAAAGACCT---T-GA 4580
                             v  v ii  i    i    ?      i   v  i  ii --- -  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_60365625_6   4581 CAACTCACCAAAGAAGATACATAGATGGTAAATAAGCATATGAAAAGATG 4630
                           vi  v            i i i    iv        i           
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_60365625_6   4631 CTCCGCATCATATGTCAT 4648
                            vi     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (41 / 30)
Gap_init rate = 0.02 (6 / 311), avg. gap size = 2.50 (15 / 6)  


2685 19.74 3.17 4.76  chr1_60490298_60492595      592  1285 (1013)    L1M4_orf2#LINE/L1        1   683 (225)  

  chr1_60490298_6    592 TGCAAGGATACCCCATGTTCATGGGTTGTTAAGACTTAATATTGTTAAAA 641
                           v  i    i             i   v-                  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGG-AAGACTTAATATTGTTAAGA 49

  chr1_60490298_6    642 TGTCCATACTACCAAAA-------GCAAATTTAATGCCATCCCTATAAAA 684
                           v v     v  v   -------i  i   i  i  v        v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_60490298_6    685 AATCCCAG-TGATTTTTTTTTGCAGAAATAGAAAAATCCATCCAACACTT 733
                          -      -  --ii              v  v  iiiv    v v v  
  L1M4_orf2#LINE/    100 A-TCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_60490298_6    734 CATATTAAATCTCAATGGACCCTAAATAGGCAAGGTAATATTGAAAAAAA 783
                              vi  viv   v      vi     v   iii   v        i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_60490298_6    784 AAAAAGAGCAAAGCTAGAGGTATCACACTTTCTGATCTTAAAACTTACTA 833
                          i  ----     i i    vv        i ii  i i           
  L1M4_orf2#LINE/    197 AGAA----CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_60490298_6    834 CAAGTGTATAGTAATCAAAACAATGTGGTACTGGGATAAAGAAATACATA 883
                            ivv  i         i   i           v    i  v v     
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_60490298_6    884 TAGAAAAATGGAATAGGATAGAAAACTCAGAAATAAATCCTCACA----- 928
                             vv          i  v  i iii          i  vi   -----
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_60490298_6    929 GAT---TTGATTTTTGAGAAGGGTGCCAAAACTACTCAGTGGGGAAAGTT 975
                          i ---        i  v           i  i i   i         --
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-- 390

  chr1_60490298_6    976 TTGAAACTTGGGAAAGTTTGAAGATTTGTCTTTTCAACAAATGGTGCTGG 1025
                         --------------------  v ---                       
  L1M4_orf2#LINE/    391 --------------------AATA---GTCTTTTCAACAAATGGTGCTGG 417

  chr1_60490298_6   1026 GA-AACAAGAGATTCACATGGAAAAAAA-GTGGTTAGATTTTTAGTGAAC 1073
                           -   vi  v ?i      v    i  - vi   i  iiii  vivv  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_60490298_6   1074 ACCATATATAAAAATTAATTCAAAATGCATCAAATACCTAAATATAAG-- 1121
                                 i         i        v    ? v        i    --
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_60490298_6   1122 CTAAAACTATAAAACTCTCAGAAGAAAACATAGAGCAAAAATTTCACAAC 1171
                                           i              i?vv   vi   iii  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_60490298_6   1172 ATTGGATTTGATGATGATTTCTTGGATATGCCATCAAA-GAACAGGAAAT 1220
                         v    i  v iii   i      i      v  i    - v   i v  i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_60490298_6   1221 AAA-GAAAAAATAGACAAATTAGACTTCATGAAAATTAAAAACTTTTGCA 1269
                            -           i     i        v                 ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_60490298_6   1270 CATTAATGGACATTAT 1285
                          v i  v     i   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTAT 683

Transitions / transversions = 1.48 (80 / 54)
Gap_init rate = 0.02 (15 / 683), avg. gap size = 3.67 (55 / 15)  

 898 20.09 7.14 0.89  chr1_60490298_60492595     1582  1805 (493)    L1M4_orf2#LINE/L1      671   908 (0)  

  chr1_60490298_6   1582 CAATGGACACTACTAATAGAGTAAAAAAGCAACCTATGATATGTGAGAAA 1631
                            v        ii  v i   i    ii     i iiiv   v      
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_60490298_6   1632 ATATTTGCAAATCATATATCTGGTAAGGGATT---------AATA-ATGC 1671
                                               i       i ---------    -  iv
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_60490298_6   1672 AGAACTCCTAAAGCTCAACGACAA-----CAACCACAACCTGATTCAAAC 1716
                                i  v i     ii i  -----   -- i    ii   ?   v
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAA--ATAACCCAATTWAAAA 818

  chr1_60490298_6   1717 ATGGACAAAGGATTTCAATAGATATTTCTCTAAAGAAGATACATGAATGA 1766
                             i          v      i       i          i ii    i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_60490298_6   1767 CCAATA-GCACATTTTAAACTGCTTGATATCACTAATAAT 1805
                               -      vvv  iv    ii i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.67 (32 / 12)
Gap_init rate = 0.02 (5 / 238), avg. gap size = 3.60 (18 / 5)  


2882 28.46 2.12 0.78  chr1_60501324_60506522.rev     3813  4708 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_60501324_6   3813 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 3862
                               i i  i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60501324_6   3863 GGCCACACTGCTCAAAGTAATTTATAGATTCAATGCTATCCTCATCAAGC 3912
                            v i   v i    v i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_60501324_6   3913 TACC-GCTGACTTTCTT-CAAAGAATTAGAAAAAAACT-ACTTTAAATTT 3959
                          v  -    v    i  -  i -    i--- v  i  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAGCTGATCCTAAAATT 146

  chr1_60501324_6   3960 CATATGGCACCAAAAAAGAGCCCGTATAGCCATGACAATCCTAAGCAAAA 4009
                                v viiv  ii  v  v v       vi      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_60501324_6   4010 AGATCAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAAG 4059
                            v     i      vv    i  v  ii i      vivi       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_60501324_6   4060 GCTCCAGTAACCAGAACAGCATGGTGCTGGTACCAAAACAGATATATAGA 4109
                            v      i  ii    ii    i    i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_60501324_6   4110 CCAATGGAACAGAATCAAGGCCTCATAAATAACCCCACACGTCTACAACC 4159
                         i        i     ii  ivii  v      v    i  i i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_60501324_6   4160 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAAAAGGGTTCC 4209
                          vi    i  i     ivv  v   i v  vv       i    ii vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_60501324_6   4210 CTATTTAATAAATGATGTTGAGAAAACTGGCTAGCCATATGCAGAAAACT 4259
                           v  i  i     i  i  i  v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_60501324_6   4260 GTAACTGGATCCATTCCTTACACCTTATACAAAAATTAACTCAAGATAGA 4309
                          v ii    i  v v   i     v                   i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_60501324_6   4310 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAAAATAC 4359
                          i ?    i           v       i      vi i     i  v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_60501324_6   4360 CTAGGCA-ATATGATTCAGGACATAGGCATGGGCAAAGACTTCACGACTA 4408
                         v    ?i- v  v-   iv   v v  vv i     v ii   viiiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_60501324_6   4409 AAACACCAAAAGCAATCA--CGACAAAAGCCAAAATTGACAAATGGGATC 4456
                         vi            --  -- i       vv     v  i    v   ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_60501324_6   4457 TAATTAAACTAAAGTGCTTCTGCACAGCAAAAGAAACCATCATCAGAGTG 4506
                          v  i   v v  ivi   i  ii vv    i  v  i    vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_60501324_6   4507 AACAGGCAATGTACAGAATGGGAGAAAATGTTTGCAATCTATCCATTTGG 4556
                           v  i   ivi                 i       vii  vi  i  i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_60501324_6   4557 CAAAAGGCTAATATCTAGAATCTACAAAGAAG----GTAAATTGACAA-- 4600
                         i  ii i  vi    i     v  i      v----ii  v ii i  --
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_60501324_6   4601 -------AAACAACCCCATCAAAATGTGGGTGAAGTATATGAACAGACAC 4643
                         -------   i     v  i?   vi    ii   v  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_60501324_6   4644 TTCTCAAAAGAAGACATTTATGCAACTAGTAAACATATGAAAAAAAGCTC 4693
                              v        i  vi viiii i i   i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_60501324_6   4694 ATCATCACTGGTCAC 4708
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (158 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.36 (26 / 11)  


1464 26.75 0.64 3.61  chr1_60636954_60639027      494   964 (1110)    L1M4_orf2#LINE/L1      160   616 (292)  

  chr1_60636954_6    494 AAAAAACCCTGAACAGCCAAG-CAATCCTGAGCAAAATGAACAAAGCTGG 542
                           iii    v   i      i-     i   iv  i v        i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_60636954_6    543 -GGACAGCATACTACCTGACTTCAAAACACATTACAAGTCTATAGTAATC 591
                         -    -v  i   v  ii i        vi i     iv   i       
  L1M4_orf2#LINE/    210 AGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_60636954_6    592 AAAGAAGCATGGAAGCATGCTATTGGTATAAAAACAAACAGGTAGACCAA 641
                           iiv  ii   --------  i   i    ii i i   vi    i   
  L1M4_orf2#LINE/    259 AAGACAGTGTGG--------TACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_60636954_6    642 TGGAACAGACATTGTCTAGTCAACCCAGAAATAAATCTATGTATTTACAA 691
                              i   -    ---  -- ii           i i  ii     iii
  L1M4_orf2#LINE/    301 TGGAATAGA-ATTG---AG--AGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_60636954_6    692 CCAAA-GATTTTTGACAAAGGAATTAAAAAACATACACTGGGGAAAAAAA 740
                         i   v-      i     i  viii  i v-   v  v        i  -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAA- 392

  chr1_60636954_6    741 CACCCTCTTCAACAAATGGTAGTAGAAAATGTGGACGTCCATATTCAGAA 790
                         i vi  i             iv i i v vv    ii?   i  v  i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_60636954_6    791 AAATAAAACTCAACCTCTATGTCTCAACATATACAAGAATAAACTAAAAA 840
                         i   i  ii vi   i   iv  v  v         i   v    v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_60636954_6    841 TGGATCAAAAATTTAAATGTAAGACCTGAAACTATAAAACTATTAGAAGA 890
                                ? i ii           v  i             v        
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_60636954_6    891 AAATATAGGGAAAACACTCCAAGACATTGGTCCAGAGAACGATTTTATGA 940
                            i     ?iv  vv  i iv   v    vii  iv  i i   iv ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_60636954_6    941 CTACAACCTCAAAAGCACAGGCAA 964
                         v  ii  vi          i    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAA 616

Transitions / transversions = 2.24 (85 / 38)
Gap_init rate = 0.02 (10 / 457), avg. gap size = 2.00 (20 / 10)  

 857 24.00 4.67 2.67  chr1_60636954_60639027     1282  1581 (493)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr1_60636954_6   1282 AAAAAAAGAGGCAGGAAAATCAAAAAGTAGACAAATGAGAAATGAGACTA 1331
                             iv v i   iv    v-     i    i    ------  -    v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAG-AAAAAATAGATAAAT------TG-GACTT 644

  chr1_60636954_6   1332 TATTAAA-CCAAAAGCTTCTGCACAGCAAAGGAAACAATTGACAGAATGA 1380
                         i  i   -ii    i   i  ii vv       v  v  ii v i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_60636954_6   1381 AGAGAAAACTTATTGAATATGAGGAAATATTT----------CATCTGAC 1420
                          i   v   ii iv    iv   i        ----------i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_60636954_6   1421 AAGGGACTAATATCTAGAATATACAGGGAACTCAAACAACTCAACAGCAA 1470
                                 vi    i        i ii      vv         i ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_60636954_6   1471 A--TATTAATAATTCCATTTAAAAGTGATCAA-GGACATTAATAGATATT 1517
                          --v iv     ii v   ?    i  iv   -   iv v      i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_60636954_6   1518 TCTCAAAAGAAGACATACCAAGGGCCAATAGGCATATGTAAAAATGCTTA 1567
                             v        i    v  v        i   i   v   i     i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_60636954_6   1568 ACATCACTAATAAT 1581
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (45 / 26)
Gap_init rate = 0.02 (7 / 306), avg. gap size = 3.14 (22 / 7)  


3152 26.79 0.99 0.88  chr1_60642493_60644831.rev      942  1848 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_60642493_6    942 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 991
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60642493_6    992 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1041
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_60642493_6   1042 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 1090
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_60642493_6   1091 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGA 1140
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_60642493_6   1141 ACAAAGCTGGAGGCATCATGTTACCTGACTTCAAACTATACTACAAGGCT 1190
                               i      vv   iii v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_60642493_6   1191 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 1240
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_60642493_6   1241 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACTA 1288
                               i    i--    i  --        vv  ii i ii  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_60642493_6   1289 TCTGATCTTTGACAAACCTGAGAAAAGCAAGCAATGGGGAAAGGAT--TC 1336
                         vi    i  i     ivv  vv  i v  vv            i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_60642493_6   1337 CCCATATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTCGAAA 1386
                         ---- v  i  i              v      v  ?   i   - i   
  L1M4_orf2#LINE/    398 ----TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAA 442

  chr1_60642493_6   1387 GC-TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGA 1435
                          v-    ii    i    v   i     v           i  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_60642493_6   1436 TGGATTAAAGATTTAAACATTAGACCTAAAACCATAAAAACCCTGGAAGA 1485
                              i ?   ii    ii v   v       i      vi i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_60642493_6   1486 AAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 1535
                             v    ?i v viv   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_60642493_6   1536 CCAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGAT 1585
                         vi vi            vvi           v     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_60642493_6   1586 CTAATTAAACTAAAGAGCTTCTGCGCAGCAAAAGAAACTACCATCAGAGT 1635
                         i v  i   v v  i i   i  i  vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_60642493_6   1636 GAACAGGCAACCTACAAAATGGGAGAGAATTTTCGCAACCTACTCATCTG 1685
                            v  i     i   i         i   v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_60642493_6   1686 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 1735
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_60642493_6   1736 AAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACA 1785
                              i     i     v  i?    i     i     iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_60642493_6   1786 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 1835
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_60642493_6   1836 CA---TCAGAACAAAC 1848
                           ---   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


3582 19.61 2.94 0.86  chr1_60663839_60665646      500  1315 (493)    L1M4_orf2#LINE/L1       76   908 (0)  

  chr1_60663839_6    500 AGATTCAGATAAACCTCTGTCAAAATCCCAGCTGTTATTTTTGCAGAAAT 549
                                ivvv  i i  i               iiv             
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr1_60663839_6    550 TGAAAAGTTAATCTTAAATTTCACATGGAAATGCAAAGGATCCAGAATAA 599
                            v   i i   i    v    i            i   i        i
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr1_60663839_6    600 CCAAAACAAACTGGAAATAGAA--ACTAAGTTGGAGATTTTACACTTCTT 647
                                  v  v    v    --  v         ivi i       ii
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr1_60663839_6    648 GATTTCCAAACTTACTACAAAGCTACAACAATCAAGGCAGTATGGTACCA 697
                         i     v                    ii       i    i      ii
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_60663839_6    698 ACTTAAAGAGATCATATATAGATCAATAGAATAGAACTGAGAGTCCAGAA 747
                         i v   i  v v- i            i        i             
  L1M4_orf2#LINE/    276 GCATAAGGATAG-ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_60663839_6    748 GTAAGCCCTCATATTTATGG-CATATTGCTTTTTAACAAAGGTGTTAAGA 796
                         i   i   vi i        -  -    v    ii    i    ii    
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCA-ATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_60663839_6    797 CAATTCAATGTGGAAAGGATAGTTTTTTGAACAAATGATGCTTGGACAAT 846
                          v        v      i     i    v        i    v      i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_60663839_6    847 TGGATATCTACATTGCAAGA-AATACATTTGTCCCTTTACCTCATACCAT 895
                               ? i    -    i -   iv v   vv  ii       i     
  L1M4_orf2#LINE/    424 TGGATAKCCACAT-GCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_60663839_6    896 GCACAAAAATTAACTCAAAATAGCTCCTAGACCTAAATATATGAGCTAAA 945
                         ii                   i v  v?          i  v        
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_60663839_6    946 ACTATAAACCTACTTA-AAGAAAATATAGGGGCACATTTATGTAATCCTG 994
                                 v  -    -       i     ? i v  i vi  i i i  
  L1M4_orf2#LINE/    523 ACTATAAAACT-CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_60663839_6    995 TGT--AACAAATATTTCTTAGATATGGTATCTAAAATTTAATGAAGAAAA 1042
                         v  --ii   vvi             ii i v   iivi  vv  v    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_60663839_6   1043 GATAAAAATA-ATACATTGGACTTCATTAAAATTAGAAACTTT-GCCCTT 1090
                           -       -   v            i       i       - iv   
  L1M4_orf2#LINE/    622 GA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_60663839_6   1091 AATAAAACACTACCAAGACAATAAAAAAAGACAAGTCATGGATTACAA-- 1138
                         v v ii      i     v i i    --     vi  ii  v ivi --
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAA--GACAACCCACAGAATGGGAGA 718

  chr1_60663839_6   1139 AAATATTTCTAAATTGTATATCCAATAAGGAACTTGTATCCAGAATA--- 1185
                                 vi    ii      ii      i                ---
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_60663839_6   1186 AAATAATTCTTTTAACTCAATAAGAAAA---CAAA----CCAATTTTAAA 1228
                            v  i    vi          v    ---    ----      ?v   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_60663839_6   1229 ATGTG--AAGTGTTTCA-TAAACATTTCACCAAAGAAGCTATATAAATGG 1275
                            v --   vi   v -  i       v         v    i      
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_60663839_6   1276 CAAATAAGCCCGTGAAAAGATGCCCAATAACATTGGGCAT 1315
                          v       v i           i   i v  ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (96 / 60)
Gap_init rate = 0.02 (19 / 833), avg. gap size = 1.63 (31 / 19)  


3264 26.54 0.55 0.55  chr1_60667326_60673590     4865  5772 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_60667326_6   4865 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4914
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60667326_6   4915 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4964
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_60667326_6   4965 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5011
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_60667326_6   5012 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5061
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_60667326_6   5062 GAACAAAGCTGGGGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5111
                                 i   i  vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_60667326_6   5112 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5161
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_60667326_6   5162 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5209
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_60667326_6   5210 TATCTGATCTTTGACAAACCTGAGAAAAACAAGGAATGGGGAAAGGATTC 5259
                         i vi    i  i     ivv  vv  i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_60667326_6   5260 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5309
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_60667326_6   5310 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATAG 5359
                             ii    i    v   i     v           i  i    i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_60667326_6   5360 ATTAAAGACTTAAACGTTAGACCTAAAACCACAAAAACCCTAGAAGAAAA 5409
                           i ?    i    i  v   v       i i    vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_60667326_6   5410 CCTAGGCATTACCATTCAGGGCATAGGCATGGGCAAGGACTTCACGTCTA 5459
                          v    ?i v viv   iv i v v  vv i     v ii   viivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_60667326_6   5460 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5509
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_60667326_6   5510 ATTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5559
                           i   v v  v i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_60667326_6   5560 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5609
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_60667326_6   5610 AAGGGCTAATATCCAGAGTCCACAATGAACTCAAATAAATTTACAAGAAA 5659
                          i  i  vi        i vi i  v      vv i  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_60667326_6   5660 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5709
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_60667326_6   5710 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5759
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_60667326_6   5760 CATCACCGGCCAT 5772
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2251 25.60 5.74 2.39  chr1_60805948_60807775.rev      502  1337 (491)    L1M4_orf2#LINE/L1       45   908 (0)  

  chr1_60805948_6    502 TAAGAAGCCATTTCTCTCAAAAATGATCTAGAGATTCAACTTAATACTGA 551
                              v v  v v   i v   v       v         vi   v iv 
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr1_60805948_6    552 CCAAAATATCATCAGGCTTTTTAAAATAGAGAAATTGATAATAAGATTCT 601
                         i      vi  v v v      ---- iv         i  vvv   i  
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTT----TGCAGAAATTGACAAGCTGATCCT 140

  chr1_60805948_6    602 AGTATTTACAAGAAAATACAAAGGGGCCTAGAACAGCCAAAACAATTTTG 651
                          iv   i i v i    i   -   i  i    i            i   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_60805948_6    652 AAAAAAAA-----ATGTTGGAAGATACACAAT-CCTTATGTCAAGACTAA 695
                              i  ----- v      i  iv    v -  iv  v    i   v 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_60805948_6    696 TTATGAAGCTTCAGTGATCTAGACAGTGTGATATTCTTGTAAGGAGAGCA 745
                         i  ii     v    i   v          i  i vvii      v  vv
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_60805948_6    746 AT-TACATCAGTGAAACAGAGTAGAGAGTCCAGGAATAGATGTACCC-TT 793
                           -  v    i  i  i   i v          i    i ivi iv -  
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_60805948_6    794 TATA-TTAATTCATTTGTAACAAAAGTTGTAAAG--CAATCAATTGGAGA 840
                            i- i    v    vii    ii  - iv   --  v     -  i  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGT-GCCAAGACCATTCAAT-GGGGA 387

  chr1_60805948_6    841 AATGAGAGTCATTTCTGCAAAACCTGCTGGA------GGATGT-----TG 879
                           vi v    v    vi    vvv      i------    i?-----  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_60805948_6    880 TGGGAGAAACAACAGCTTTGACTCTTACCTAACACACTACACAAAAATTA 929
                         iiii    vv  -- -  v   i i     v    vv  i          
  L1M4_orf2#LINE/    438 CAAAAGAATGAA--G-TTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_60805948_6    930 ACTGAAAGTAGACCATAGACCTAAATGTAGCAGTTAAAACTTTAAAACTT 979
                            v   i i  i  ?             iv  i       v       i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_60805948_6    980 CCAGAAGAAAATGTAGAAG-ACATTTTTGCAAATTTGAGGTGGAAAATA- 1027
                         ii         ii   i? - v  i  i ii vi   i v i iv   i-
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_60805948_6   1028 -TTTTTAAATTAGGACTCAAAAAGTTTAAAACCATAAAAGAAAAAAGACA 1076
                         -  i   i  - v   v v     ivi  i- v i           v v 
  L1M4_orf2#LINE/    585 TTTCTTAGAT-ATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGA 632

  chr1_60805948_6   1077 TAA-T----CTTTATCAAAATTAAAAACCAGTGCTCTTTGAAG-ACACC- 1119
                            - ----   i               ivv  iv   ii   -    i-
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_60805948_6   1120 -TAAGAAAATGAAAAGGCAA---GTAAAAGTTGGGA-AAAGTATTAATAA 1164
                         -i      i       i   ---ii i  --     -   i    vii  
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAA--TGGGAGAAAATATTTGCAA 730

  chr1_60805948_6   1165 TAAATATGTCCAGTAAAGGACTTGCATGCAAAACACATAATGAACTTCTA 1214
                         vvv    i  iii   i       i  v  i  i i    v     ii  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_60805948_6   1215 CAA-----TAATAGAGAGACAGACAACTCAA-----AAATAGGCAAAAGT 1254
                            -----     i i     i i   i   -----    i      i v
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_60805948_6   1255 TTTAAGTGTACATGAAGCGTTCATCAAGAAAGATATATAAATG-CCAACA 1303
                            i i iv    ------   vi   ii        i     -    i 
  L1M4_orf2#LINE/    831 TTTGAATAGACAT------TTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_60805948_6   1304 AGAATAAACAAAGATGATCAACATCATTAATCAC 1337
                           v i viv       v         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (127 / 84)
Gap_init rate = 0.03 (29 / 864), avg. gap size = 2.34 (68 / 29)  


3189 27.64 0.44 0.44  chr1_60817206_60823478     4873  5780 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_60817206_6   4873 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4922
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60817206_6   4923 GGCCATACTGCCCAAGGTAATTTACAGATTCAATACCATCCCCATAAAGC 4972
                            v     v     iv i  i           ii v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_60817206_6   4973 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5020
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_60817206_6   5021 TATGGAACCAAAAAAGGGCCCGCATTGCCAAGGCAATCCGAAGCCAAAAG 5070
                                viiv  ii iv  v v  v     ii     ivi ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_60817206_6   5071 AACAAATCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5120
                               vi      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_60817206_6   5121 TACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATATAGATC 5170
                                 i   i    ii     i   i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_60817206_6   5171 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5218
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_60817206_6   5219 ATCTGATCTTTGACAAACCTGAGAAAAATGAGCAATGGGGAAAGGATTCC 5268
                          vi    i  i     ivv  vv  i viivv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_60817206_6   5269 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5318
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_60817206_6   5319 GAAACTGGATCCTTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5368
                            ii    i  i v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_60817206_6   5369 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5418
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_60817206_6   5419 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5468
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_60817206_6   5469 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5518
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_60817206_6   5519 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5568
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_60817206_6   5569 AGGCAACCTACAAAATGGGAGAAAACTTTCGCAACCTACTCATCTGACAA 5618
                           i     i   i            iv  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_60817206_6   5619 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5668
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_60817206_6   5669 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5718
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_60817206_6   5719 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5768
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_60817206_6   5769 ATCACTGGCCAT 5780
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3274 24.86 2.69 1.01  chr1_60886809_60891053     2860  3752 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_60886809_6   2860 TGAAAAGATATTCCATTTACATGGATTAGAAGAATCAATATTGTTAAAAT 2909
                           i        i    v v        i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60886809_6   2910 GTTCATACTATTCAAAGCAATCTATGGGTTAGATGCAATTCCTGTCAAAA 2959
                          viv     vii    vii     ii i  vi i     i   i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_60886809_6   2960 TACCAATGACATTCCTCACAGAAATAGAAAAAAAAAATCCTAAGATTTAT 3009
                          v   iivi v  ii ii       v  v  ivvi -      i   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_60886809_6   3010 GTGGAACCACAAAAGACCTAGAACAGCCAAAGCTAACCTTAGCAAA-AAG 3058
                         i     vii   ii    i    i       i -  i   iiv   -   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AATCTTGAAAAAGAAG 198

  chr1_60886809_6   3059 AACAAAACTGGAGGAATTACATTACCTGACTTCAAATTATATTACAAAGC 3108
                               ii       v i   i v  ii i      viv  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_60886809_6   3109 CATGGCAACCAAAATAGTATGGTACTGGCATAAAAGCAGACACATAGATC 3158
                         i ii i  i   i i   i              iiii     i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_60886809_6   3159 AATGGAACAGAATAGAGAACCCAGAACTAAATCCACACATCTACAATGAA 3208
                                i     v    ii      v    i   i    i  iii v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_60886809_6   3209 CTCATTTTCAACAAAGGTACCAAGAAACTATAATACATTGGGAAAAG--T 3256
                         i v      i    i   i      -- i  -- -  v    i    -- 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGA--CCAT--T-CAATGGGGAAAGAAT 393

  chr1_60886809_6   3257 AGTCTCTTCAATAAATGGTGCTGAGAAAGCTGGATATCCATACGCAGAAG 3306
                              i     i           i  v i       ?   i i   i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_60886809_6   3307 AATGAAACTTGACCCCTATCTCTCGC-ACATACAAAAATAAAATCAAAAT 3355
                               ii v        i   v i - i          v  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_60886809_6   3356 GGATTAAAGACTTAAAT-------CGAAAACTAC--------TGAAATAA 3390
                             i ?    i     ------- v       i-------- ii  v  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_60886809_6   3391 AATATCAGGGAAACTCTCTAGGAC-TTGGAGTGGGCAAAATCATCTTGAG 3439
                           i  vi ? v  v   iiiv   -    iv i     viviv    iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_60886809_6   3440 TAATACCCCACAGGCACAGGCAACCAAA--AAAAATGGACAAATGGGGTC 3487
                           vv  v   v i     i     v   --      i  i    v  iii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_60886809_6   3488 ACATCAAG-TTAAAAAGCTTCTGCACAGCAAAGGAAACAACCAACAAAAT 3536
                         v      i-       -   i  ii vv       v  v i   v   i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_60886809_6   3537 GAAGAGAAAACCCATGGTATGTGAGAAAATATTTGCAAACTACTCATCTG 3586
                            i   v      ii v   v                 ii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_60886809_6   3587 ACAAGGGATTAATAACCAGAATATACAAGGAGCTCAAATAACTCAATAGG 3636
                          i      i vi  v          i  i  i   vv i         iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_60886809_6   3637 AAAAAAATCAAATAATCTGATTTTAAAATAGGCAAAAAATCTGAATAGAC 3686
                              i -       i ii   ?v     i      ii  i         
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_60886809_6   3687 ATTTTACAAAAGAAGAGTTTCAAATGGTTAACAGGTATACGAAAA-AGGC 3735
                             iv v        vv v       ii  i i i i i     - v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_60886809_6   3736 TCAACATCATTAATAAC 3752
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (149 / 69)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.06 (33 / 16)  


3052 26.53 2.01 0.78  chr1_60950484_60960416      492  1388 (8545)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_60950484_6   1388 TGGAAGAACATTCCATGTTCATGGATAGGAAGAATCAATATCGTGACAAT 1339
                              ii i  i              v      v i     i  v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_60950484_6   1338 GGCCATACTGCCCAAGGTAATTTATACATTCAATACCATCCCCATCAAGC 1289
                            v     v     iv i  i  i v      ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_60950484_6   1288 TACCAA-TGATTTTCTT-CAGAGAATTGGAAAAAACT-ACTTTAAAGTTC 1242
                          v   i-  vi   i  -    -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

C chr1_60950484_6   1241 ATATGGAACCAAAGAAGAGCCTGCATTGCTACAACAATCCTAAGCCAAAA 1192
                                 viiv iii  v  v v  v  i v       i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chr1_60950484_6   1191 GAACAAAGCTGGAGGCATCACGCTACATGACTTCAAACTATAATGCAAGG 1142
                                 i      vv    i  v vii i      viv  v i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chr1_60950484_6   1141 CTACAATAATCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGAC 1092
                              i       i i  ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chr1_60950484_6   1091 CAATGGAATAGAAC--AGAGCCATCAGAAATAATGGCACATATCTACCAC 1044
                                      i--    i --         vvv  i i  i  ivii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGT 345

C chr1_60950484_6   1043 TATCTGATCTTTGACAAACCTGACAAAAGCAAGAAATGGGGAAAGGATTC 994
                         i vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

C chr1_60950484_6    993 CCTATTTAATAAATGGTGCTGGAA-AACTGGATAGCCATATGTAGAATGC 945
                         i  v  i  i            i -         ?   i   i i  viv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

C chr1_60950484_6    944 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAACTAATTCAAGATGG 895
                             ii    i    v   i     v          i   i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

C chr1_60950484_6    894 ATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 845
                           i ?    i  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

C chr1_60950484_6    844 CCTAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 797
                          v    ?-   --i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

C chr1_60950484_6    796 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 747
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

C chr1_60950484_6    746 TCATTAAAG-----AGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 702
                             i   i----- i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

C chr1_60950484_6    701 AAAGG-CAACCTACAGAATGGGAGATAATTTTTGCAATCTACTCTTCTGA 653
                            i -     i             v   v       vii iviv     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

C chr1_60950484_6    652 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 603
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

C chr1_60950484_6    602 CAAAAACAA----CCCTATCAACAAGTGGGTGAAGGATATGAACATATGC 557
                         v   i    ----   v  i? v  i    ii      v    i v iii
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

C chr1_60950484_6    556 TTCTCAAAAGAAGACATTTATGCAGCCAAGAGACACATGAAAAGATGCTC 507
                              v        i  vi viii     v ii                 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

C chr1_60950484_6    506 ATCATCACTGGCCAT 492
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.79 (25 / 14)  

3069 26.27 1.66 1.00  chr1_60950484_60960416     8539  9440 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_60950484_6   8539 TGGAAGAACATTCCATGTTCATGGATAGGAAGAATCAATATCGTGACAAT 8588
                              ii i  i              v      v i     i  v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_60950484_6   8589 GGCCATACTGCCCAAGGTAATTTATACATTCAATACCATCCCCATCAAGC 8638
                            v     v     iv i  i  i v      ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_60950484_6   8639 TACCAA-TGATTTTCTT-CAGAGAATTGGAAAAAACT-ACTTTAAAGTTC 8685
                          v   i-  vi   i  -    -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_60950484_6   8686 ATATGGAACTAAAAAAGAGCCCGCATTGCCACAACAATCCTAAGCCAAAA 8735
                                 v iv  ii  v  v v  v    v       i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_60950484_6   8736 TAAGAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATAATACAAGG 8785
                         v  v    i      vv    i  v  ii i      viv  v     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_60950484_6   8786 CTACAGTAACCAAAGCAGCATGCTGCTGGTACCAAAACAGAGATATAGAC 8835
                                  i   ii   ii  v i    i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_60950484_6   8836 CAATGGAACAGAAC--AGAACCCTCAGAAATAATACCACACATCTACAAC 8883
                                 i    i--   ii  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_60950484_6   8884 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGAGAAAGGATTC 8933
                           vi    i  i     ivv  v   i v  vvv     i     i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_60950484_6   8934 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 8983
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_60950484_6   8984 TGGGACTGGATGCCTTCCTTACATCTTACACAAAAATTAATTCAAGATGG 9033
                           iiii    iv   v   i   i v  i           i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_60950484_6   9034 ATTAAAGACTTAAATGTAACACCTAAAACCATAAAAACCCTAGAAGAAAA 9083
                           i ?    i         v v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_60950484_6   9084 CCTAGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCTGTCTA 9132
                          v    ?i- v i -   iv   v v  vv i     v ii    ---  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT---TA 591

  chr1_60950484_6   9133 AA----ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 9178
                         i ----            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_60950484_6   9179 TCTCATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 9228
                         ii    i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_60950484_6   9229 TGAAAGG-CAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCT 9277
                              i -     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_60950484_6   9278 GACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAAGAAGTTTACAA 9327
                           i  i  i  vi          v  i         vv v  v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_60950484_6   9328 GACAAAAACAA----CCCCATCAACAAGTGGGTGAAGGATATGAACAGAC 9373
                         v v   i    ----   v  i? v  i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_60950484_6   9374 ACTTCTCAAAAGAAGACATTTATGCAGCCAAGAGACACATGAAAAAATGC 9423
                          i     v        i  vi viii     v ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_60950484_6   9424 TCATCATCACTGGCCAT 9440
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


2571 18.07 1.85 0.00  chr1_61004602_61006540.rev      502   988 (951)    L1M4_orf2#LINE/L1      254   749 (159)  

  chr1_61004602_6    502 TAATAAAACCAATGTGGTAATACCATAGGGATAGACATATAGATCAGTGG 551
                             v  iv  i       v iv    i                  i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_61004602_6    552 TACAGAATTAAGAGTTTAGGAATAAGCCCATACGCATATGGTCAATTAAT 601
                         v i      i     ii  i     i       iiv           i  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_61004602_6    602 TGTTAGCAAGGGTGCCATGAATACTTAATAGGAAAATAACAGCCTTTTCA 651
                          v iii           v  vi i i   i  i   v  i  i       
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_61004602_6    652 ACAAATGGTGCTGGGACAACTGTGTATCCATGTGAAAAAAAGTGAAATTA 701
                                               vi  ?   ii  v    i i    i  i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_61004602_6    702 AATTCTTACCTAGCACTATATACAAAAATTAAGTCAAAATGGATCAAAGA 751
                         i ii i     vi   i               v             ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_61004602_6    752 CTTAAATGTAGGAGCTGAAACTATACAACTCTTAGAAGAAAACAT-GGAG 800
                          i        i     i        v                   -  ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_61004602_6    801 TAAA-CTCCCTGACCTTGGCTTTGGCACTGATTTCTTAGACATGACACCA 849
                             -  i v         v  v    v  i         i         
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_61004602_6    850 AAAGTATAAGCCATACAAGAAAAAATGGATAAATCTGACTTCGTCAAAAT 899
                             i i    v i v          i       iv      i       
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_61004602_6    900 TAAAAACTTTATTGAATCAAAGGACAATATCAAGACAGTGAGAAGACA-- 947
                                   vv  vv          v        v     i      --
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_61004602_6    948 -----GAATGGAGGAAAATATTTCCAAATAGTATACCTGTTAAGGG 988
                         -----      ii          v     vi    i   v      
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

Transitions / transversions = 1.74 (54 / 31)
Gap_init rate = 0.01 (3 / 496), avg. gap size = 3.00 (9 / 3)  

 730 16.35 3.77 0.63  chr1_61004602_61006540.rev     1290  1448 (491)    L1M4_orf2#LINE/L1      745   908 (0)  

  chr1_61004602_6   1290 AAGGGACAAATATCCATAATATATAAAGAA---TTATAACTCAACAACAA 1336
                                vvi      v             ---   i       i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_61004602_6   1337 AA--GCAAATGTCCCAGTTAAGAAAATGGGGAAAAGGCTTGAATACACAT 1384
                           --i     iv    i  ? -        v   i ii       v    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_61004602_6   1385 TTCTCCAAAGGAGATATCTCAATGGCCA-TGAGCACATGAAAAGATGCTT 1433
                                   i      viv        - i                  i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_61004602_6   1434 GATGTCATTAGTCAT 1448
                         i ii   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (17 / 8)
Gap_init rate = 0.02 (4 / 164), avg. gap size = 1.75 (7 / 4)  


1420 26.86 10.13 3.79  chr1_61210663_61213479.rev     1140  1958 (859)    L1M4_orf2#LINE/L1        1   871 (37)  

  chr1_61210663_6   1140 TAAAAAGGCATATACCGTGTTAAAG--TTGGACAATACAATATTATAAAT 1187
                          ii    --    v  i    v v --     vi ivi      i v  v
  L1M4_orf2#LINE/      1 TGGAAAG--ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_61210663_6   1188 ATGTTCTTTCTCTCCAAAATGATCTATAAGTTTAATGTATTCCCAATGAA 1237
                            vivv v   i     v       i ii  i  i i v    v  v  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_61210663_6   1238 AACCCCAACTGGAATTTTAAAATGGAACTTGGAAAGATTATTCTAAA-TG 1286
                           i    i   vvv    viv --   v   iv   v v  i     - v
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCA--GAAATTGACAAGCTGATCCTAAAATT 146

  chr1_61210663_6   1287 TACATGTTAGTGCAAATGGCCAAGAATAGACAAGGTA--CTTGAT---GA 1331
                         i i   vv i     iv i  v       v   iii --     v---  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_61210663_6   1332 AGAATACTG--GGAGGGTTTGC---TCC--ATTGCA--------TATGAA 1366
                             i vv --     ii ii ---   --   v  --------  ii  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_61210663_6   1367 GACTGCAGAAATCA-----GTGTAGTATTGCCACCTGAATA--CA---AA 1406
                          -  i   v     -----    i   i  v  ivv i   --  --- i
  L1M4_orf2#LINE/    247 G-CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_61210663_6   1407 GTTAA---AATAGGA-----ATTCCAGTAAGAGACCCATGCACATATAG- 1447
                         i i  ---     i ----- v     v  v i      i  iv   i -
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_61210663_6   1448 CACTTGATT-----CAAAG----CGAGATGTTGTTTC-T----AAAGA-- 1481
                           v      -----   i ---- i   i--ii  iv- ----     --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGAC--CATTCAATGGGGAAAGAAT 393

  chr1_61210663_6   1482 -GACTTTTC--CAAA----ACTGGGTCAGTTGGCTATCCTGAT-TAAAAA 1523
                         - v      --    ----i     v  ii   v  ?  vv  -i    i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_61210663_6   1524 AATTAAAT--GACTTACTGCCTCACACCAGACTAAACATAAACAAATTCA 1571
                            v  i --   ii-  i          ---  v   -----   --- 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCC-CTACCTCACACCA---TATACA-----AAA---A 481

  chr1_61210663_6   1572 TTCACTCATTCCAGGTCACTGTAGACCTAAAAGTGAAGGATAAAACAATG 1621
                           v     vvvii i   ---?         v  i ii v      v  i
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCA---WAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_61210663_6   1622 AAGCTTCTAGAAGATAGTATAG-CATAATATATTCACAACCTTGGGATAG 1670
                           i  ii       v ii    -?i   -  v   iii        v   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAG 577

  chr1_61210663_6   1671 GGAAATTTTTCTTAAA-GTGA-ATGAAATGAAGCACAAA-ATCTCAAGAG 1717
                          v  vvv       i -i   - iv   ---       i- v vv    i
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAA---AGCACAAGCAACAAAAGAA 624

  chr1_61210663_6   1718 AAATATTGATGCAGTGGATTACAT-AAAATTAAGAGCTTCTTTTCCTCTG 1766
                            -  v   iv v    i v   -        i i   i v v i  vi
  L1M4_orf2#LINE/    625 AAA-ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_61210663_6   1767 AAGACACCATTCGGAGAGTGTAAAGG-AAGCCATCAAACAGGAGAAGGTA 1815
                          i     i  ivi  i    v    i-  v   ivi  ii      ii  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_61210663_6   1816 TTTGTAAAATACTTAACTGATAAAG--CCTATGTCCAGAATAGATAAAAA 1863
                             i   vi iv  v       i -- i i i         v     i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_61210663_6   1864 TAACTCTTA----TCATTAAAAAAAATACAAAATGACA-AATCTGGTAGA 1908
                         --       ----   v   v     v     - i  v-   i?ii- i 
  L1M4_orf2#LINE/    774 --ACTCTTACAACTCAATAATAAAAAGACAAA-TAACCCAATTWAA-AAA 819

  chr1_61210663_6   1909 CAGGCAAGAGACTTGAACAGGGACTTCGCAAAAGAAGATATTCAA--GGC 1956
                         ii     ii  i     i  iv i   v v           v   --   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_61210663_6   1957 CA 1958
                           
  L1M4_orf2#LINE/    870 CA 871

Transitions / transversions = 1.35 (124 / 92)
Gap_init rate = 0.06 (48 / 871), avg. gap size = 2.38 (114 / 48)  


1324 29.85 7.90 2.44  chr1_61284631_61286849.rev      874  1734 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_61284631_6    874 TGAAGAGACATACCATGTTCATAGATAATAATATTTGATA--GTTAAAAA 921
                           i i   i  v          i   viv  v i  i   --     ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA--- 47

  chr1_61284631_6    922 AAGATGTCAAT-TTCC-----TTTATCTGTAGATTCAATATATTTCTAAA 965
                         --    v    -i   -----  v    ii        iii v i iv v
  L1M4_orf2#LINE/     48 --GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_61284631_6    966 CAAAGTCCCAATAGGATGTTTCACAAAACTTGACAAAGTAATGCCATGAT 1015
                             i     iiv vv v   ii  i  v       iv i  v i vi  
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_61284631_6   1016 ATATATGGAATAGTGAGGGGTAAAGAATAACTAAAA-AATTTATTTCAAA 1064
                         vi        vv ii    iivv      i i    -   i --- v   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT---TGAAA 192

  chr1_61284631_6   1065 AAGAGGTGTGAAATT-------TTGC--TT-----TATCAAGACTCATTA 1100
                             i viii  i  ------- ii --  ----- v    i   i i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_61284631_6   1101 TAAGGGCT-TAGTAAGTGAAAAATTGTGGTGATGGTATAGGG-CAGACAA 1148
                         i  i -  -i     vii i v v      iv   i   i  -i     v
  L1M4_orf2#LINE/    243 CAAAG-CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_61284631_6   1149 GTTGATCAGTGTAACAGAGCAAAGAATCCAAAAACAGACATACACAAATA 1198
                         i v     i  v  i   iivi   i    i   i i  vi i   vv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_61284631_6   1199 TAAAAAATAAAT----GACAGAGGTATCATTTTACATTATT---TGGGGA 1241
                          iivv   vi  ----    ii   ii  ---- v ii   ---      
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGA 387

  chr1_61284631_6   1242 ATAGAGAAAT-TATTCAATAAGTGATAAAGTGAAAACTGTCCATTCATAC 1290
                          -   iv i - v     i  i  i ivv v  v     vvi ?i  i i
  L1M4_orf2#LINE/    388 A-AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_61284631_6   1291 AGAATAAAATGAAATTGGATCCCTACCTCACACCATACACAAA------T 1334
                         iv  v i      i     i                 i     ------i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_61284631_6   1335 TCCGGATGGAATACAAACCTAA-TGTGAGA--TGAACACT-TAAAAGATA 1380
                           vii     vi ? i      -   i   -- i  -   -     vviv
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA-ACTATAAAACTCT 535

  chr1_61284631_6   1381 TACAAAAAATACCATA----TA---CTTC-TAAACTTGGAGTAAAAAAGG 1422
                           v  i   -  -   ----  ---    - i v     iv  iiv  v 
  L1M4_orf2#LINE/    536 TAGAAGAAA-AC-ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_61284631_6   1423 ATATCTTCAACAAGACAA-AAAAGCAATAAC--CATGTGATAAAGATTGA 1469
                         i v    vi i v    v-       vv i --  viv  -   i  v  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGA 632

  chr1_61284631_6   1470 TAAATTTTACTGTATTAAAATTAAGAATTTTTGTTGATCAAAG-ATAACA 1518
                               vv   vi  i        i  i      vvv      - i vi 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_61284631_6   1519 TGAAGAAAATTTTAAAACAAGCCAGAAACTACGAAAATATATTGGCAAA- 1567
                          v      i vvv  i    v   v i v iv  i  v     v     -
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_61284631_6   1568 CGTACA-CTGGCCAAAAATTAGAATGCAGAATCTATAAAGAACTCCTACA 1616
                          i  i -   iiv iii i v v  v      v            i    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_61284631_6   1617 AACCAATAAGTAAACAATAAGCAATAAAATAGAAAAAAATGAATAAATGA 1666
                          vi      vv   vi i  ii  ivv   v--?       iii   v  
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATT--WAAAAATGGGCAAAGGA 830

  chr1_61284631_6   1667 C---AA-AAACATTTATTCCACAG----TA---AAGTGGCTCATACATAT 1705
                         i---  - i      -i    v  ----  ---  i    iv   vii i
  L1M4_orf2#LINE/    831 TTTGAATAGACATTT-CTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_61284631_6   1706 ACAAAAAGATGTTTAGTCTCATTAGTAAT 1734
                          ii        i i iiv   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (151 / 103)
Gap_init rate = 0.04 (39 / 908), avg. gap size = 2.28 (89 / 39)  


3122 21.70 5.04 2.40  chr1_61654836_61656855      686  1519 (501)    L1M4_orf2#LINE/L1        1   856 (52)  

  chr1_61654836_6    686 TGGATAAATACACCATATTCTTGGATTGGAAGAC--AATATTGTTAAGAT 733
                             v i   iv    i   v             --              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_61654836_6    734 GTCAATTCTCTACAAATTGATCTGTAGAGTCAA-GTTGTTCATAATAGAT 782
                          v    v   iv           ii   v    - ivi i v  vi i -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr1_61654836_6    783 ATCTCAGG-GCATTTTTTTGTAGATATCAACAATCTGATTTCAAGATTAA 831
                            i   v-  -i       i   v  ii    v     iii  i   v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_61654836_6    832 TATTTTTAAAAATGCA------CTAGAAAAACCAAAAGATTTTTGAAAGA 875
                            ----ii       ------ i    v i      v v i      i 
  L1M4_orf2#LINE/    149 TAT----GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_61654836_6    876 AAGGAACAAAGTTGGAGCACTCACACTATCTGATTTCAAGTCTTACTATA 925
                         i i              v         vi ii       iv       i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_61654836_6    926 AAACTACAATAATCAAGAAGGTGCAGTATTGGCAAAAGAATACATATATA 975
                           i     i         vi   ii   i     v   i   v i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_61654836_6    976 GATCAATGGAATAGAGC--AGAGTCTAGAAATAGATCCACACAAGTGTAG 1023
                                        ii--      i       i i   i   vv i i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_61654836_6   1024 TCAACTGATTTGTGAAAGGGGTGCAAAGGCAATTCAATGG----AGAATT 1069
                             i      vi  v i      v   i v         ----     v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_61654836_6   1070 GTCTTTTCAACAAATGGTGCTGGAA-AATTGGACATC-ACATGCAAAAAG 1117
                                                i -  i    i ? -          ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_61654836_6   1118 AAGAAAGAGGAGAACAGCCTCTATTCTACTTTATACTTTGTACAAAATTT 1167
                          v   ivv   ------  i   ----- i i i  iv i       v  
  L1M4_orf2#LINE/    445 ATGAAGTTGGA------CCCCTA-----CCTCACACCATATACAAAAATT 483

  chr1_61654836_6   1168 AATTCAAAATGGACCATAGAACTAAATAGAAAACCTAAAATTATAAAACT 1217
                           i          i  ?   v      iv  i v      i         
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_61654836_6   1218 TCTAGAATCAAATATCCTAAAAAGTCTTTGTGACCCTGGGTTGTGC---- 1263
                         ii     vv   i  vvv?iv  i    i      i      iv  ----
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_61654836_6   1264 --TTCTGAGATATAAGAGCAAAAGCATCAAG-------------GAT-GA 1297
                         --    v      i v v        -    -------------i  -  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGA 632

  chr1_61654836_6   1298 TACATTGG-CTTTATTAAAACTAAAGTATTTTTCT-TGTCAAAAGACACT 1345
                           v     -   i  i    i    i- i    v -iv     i      
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACT 681

  chr1_61654836_6   1346 GTTAAGAGATGGAAAAGACAAGTCACAGGCTGAAAAAAAA-ATTTTCAAA 1394
                         i i    i vv          vi     iv  ii i    -    v    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_61654836_6   1395 ACATGTATACAACAAGGAACTTGTATCTAGGATACCTAAAGAACCCTCAA 1444
                         v   i   vii i    i         i  i   iv        i  i v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_61654836_6   1445 ATCTGAACAATAATAAAAACAAACAACCCAATT-AAAAATAAACAAAAGA 1493
                          v  v  i     -   i     i         -      iii    i  
  L1M4_orf2#LINE/    782 AACTCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_61654836_6   1494 TTTGAATAGACACTTTATCAAAGAAG 1519
                                     i  ivi        
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAG 856

Transitions / transversions = 1.83 (115 / 63)
Gap_init rate = 0.03 (23 / 856), avg. gap size = 2.70 (62 / 23)  


 579 26.91 3.61 6.02  chr1_61697438_61699408.rev       77   325 (1646)    L1M4_orf2#LINE/L1        7   249 (659)  

  chr1_61697438_6     77 GATATATCGTGTTCCTGGGTTGAGAGGATTCTTTCAACACAGGAACATGA 126
                              vi i     v   i   -  i  --   --  i i-------  v
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTG-GAAGA--CTT--AATAT-------TGT 44

  chr1_61697438_6    127 TATAAATGTCAGTCCTCCCCAGCATAAACCAGTGATTCAGTGCAACCCCA 176
                           - i   v  i v       ivv i v i vv      ii    i   v
  L1M4_orf2#LINE/     45 TA-AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr1_61697438_6    177 TTTAGAATCCCAGGTAGTTTTT----AGGTAATTGACAAGGTGATTCTAA 222
                         v i i        v ivi    ----  i-          v    i    
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAA 142

  chr1_61697438_6    223 TATTTATACAAAAATACAAATGAT--AAAATTAGCTTAAGAATTTTTGAA 270
                         v   i   iii    i   iv  i-- i   -   iv  iv v i     
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAAT-AGCCAAAACAATCTTGAA 191

  chr1_61697438_6    271 ---GAAGAACAAAGTTTGAGGACTTATATTACTGTATAGTAAAACTCACT 317
                         ---             v       i i i v ivv  vvi      i   
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_61697438_6    318 GTAAAATT 325
                         ii   ii 
  L1M4_orf2#LINE/    242 ACAAAGCT 249

Transitions / transversions = 1.58 (41 / 26)
Gap_init rate = 0.04 (10 / 243), avg. gap size = 2.40 (24 / 10)  

4262 15.79 4.82 3.14  chr1_61697438_61699408.rev      588  1480 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_61697438_6    588 TGAAAAGATATCCCATTGTCATGTATTGCAAAACTTAATATTGTTAAAAT 637
                           i             vv     v    v  i               i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_61697438_6    638 AGCAATACTTCCCAAAATAAACTACAAATTCAACATAATTCCTATGAAAA 687
                         i        i      v i v     i       ii   i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_61697438_6    688 TCTCAGATGGCTTTTCCCCACAGAAATTAACATGCTGACTCTAAAATTCA 737
                           i   v  v     ii--i        i   v     ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_61697438_6    738 CATGGAAAAG-AAAGGACTTCAAATAGACAAAACAGTCTTGAAAAAGAAG 786
                         i       v -  i    iivi     v       i              
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_61697438_6    787 TATGAAGTTGGAGGACTCACATTTTTCAATTTCAAAACTTACTACAAAAC 836
                         v ii                 i  ii                      i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_61697438_6    837 TATAGTAACTAAGACAGTGTGATATTGGCAAAGGGAAAGGCATATAGATC 886
                           i     ii           i  i     v i   v  i          
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_61697438_6    887 AATGGAATAGAATTAAAAGTCCAGACATAAAAATTCTTACTTTTATGGTT 936
                                       i i        v     --ii v   v        i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACATTTATGGTC 346

  chr1_61697438_6    937 CATTGATTTTCAGCAAGAGAGTCAAGACAATTCACTGGGGAAAGG-TAGT 985
                         v          ii    i v i      v     v         i-    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_61697438_6    986 CTTTTCAACAAATG---TTTGTACAACTGGATATCCACA-GCAAAAGAAT 1031
                                       ---i v v           ?     -          
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_61697438_6   1032 GAAGTTAAACTCTCCTACCTCACACCACATACAAAAATTAACTCAACATG 1081
                               ii  i --             i                  v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCC--CTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_61697438_6   1082 CTTTATAG-CCTAAATGTAGAAGCTGAAACTAAAACACTGTTAGAAGGAA 1130
                         vv i ?  -          ii    i      v  v   v       i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_61697438_6   1131 A---AGGAAGTAAAGTTCTATGACCTTAGATTAGGCAACAGTTTCTTAGA 1177
                          ---   ?-     vi iii       i i        ii          
  L1M4_orf2#LINE/    545 ACATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_61697438_6   1178 TGTGACAATAAAAGTACAAATGATAACAGTAAAAATAGCTAAAATCAAAA 1227
                          i     vi     i    iii i  v  v        -----  --   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG-----AT--AAA 636

  chr1_61697438_6   1228 TTAAATAATTTTAAATAGATTAATCAAAATGAAAGACTTTTGTGCTTCAA 1277
                           ii i-------------  v        v   i               
  L1M4_orf2#LINE/    637 TTGGAC-------------TTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_61697438_6   1278 AGGACATTATCACAAAAGTGAAA--------------------------- 1300
                               i     vi         ---------------------------
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_61697438_6   1301 -TTGAAAATCATATATCAAATAAGGAACTGGTACTCAAAATGTATAAAGA 1349
                         -   v            vi      i   v   ii  i   i        
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_61697438_6   1350 ACTCTTACAAGTCAATAATA----GACAAATAATCCAGTTTTTAAAATGG 1395
                                   v         ----         i   i  ?v-       
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGG 822

  chr1_61697438_6   1396 GCAAAGTATTTGACTAGACATTTCTCCTGAGAAGATATAGAAGTGGCCAA 1445
                               v      v             vi          v  i       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_61697438_6   1446 CA-GCACATGAAAAGATTCTCAACCTCATTAGTCAT 1480
                         i -              v      v   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (88 / 49)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.18 (71 / 17)  


3260 26.16 0.77 0.55  chr1_61719903_61724222.rev     2924  3829 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_61719903_6   2924 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATGTTGTGAAAAT 2973
                               v i        i        v  v   v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_61719903_6   2974 GACCATACTGCCAAAAGCAATCTACAAATTCAACACAATCCCCATCAGAA 3023
                          i v     v  v   vii       i       i       i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_61719903_6   3024 TACCA----CCATAATTCTACAGAGAATTAGAAAAAAACAATTCTAAAAT 3069
                          v   ----  v --  i i    -    i-- v  ivii  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT--TTTTGCAGA-AATTG--ACAAGCTGATCCTAAAAT 145

  chr1_61719903_6   3070 TCATGTGGAACCAAAAAAGAGCCCACATAGCCAAAGCAGGACTAAGCAAA 3119
                             i     viiv  ii  v  viv         i  ivvi i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_61719903_6   3120 AAGAACAAATCTGGAGGCATCACACTACATGATTTCAAACTATACTATAA 3169
                                  vi      vv       v vii        viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_61719903_6   3170 GGCCACAGTCACTAAAACAGCATGGCACTGGTATAAAAGTAGGCACATAG 3219
                         i  i     v ii  i    ii   i     i    iii   i  i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_61719903_6   3220 ACCAATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGT 3269
                          i        i     v    ii               v i i   ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_61719903_6   3270 CAACTGATCTTCGACAAAGCGAACAAAAACACGAAGTGGGGAAAGGACAC 3319
                            i    i        i vviv   i v  ivv i         i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_61719903_6   3320 CCTTTTCAACAAATGGTACTGGGATACTTGGCTACCCACCTGTAGGAGAA 3369
                         i                i      i vi   v  ?    v  i ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_61719903_6   3370 TGAAAGTGGATCTTCATCTCTCACCTTATACAAAAATTAACTCAAGATGG 3419
                             iv    i iii i   v    v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_61719903_6   3420 ATTAAGGACTTAAATCTAAGACCTGAAACTATAAAAATTCCAGAAGACAA 3469
                           i ?i   i     v     v  i           v iii      v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_61719903_6   3470 CACTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACTA 3519
                           iv  ?iv  vi    vv   v    v        v i    v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_61719903_6   3520 AGAACCCGAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTA 3569
                         v  vv  i      v v    i    iv   i   i   iv v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_61719903_6   3570 ATTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAA 3619
                           i   v v  i i      iiivv    i iv  vi   iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_61719903_6   3620 CAGGCAACCCACAGAGTGGGTGAAAATCTTCACCGTCTATACATCTGACA 3669
                         v  i           i    v      v  ii vivii   i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_61719903_6   3670 AAGGACTAATATCCCGGATCTACAACAAAATCAAACAAATCAGTAAGAAA 3719
                          i     vi     v i  v  i  vi  v  vv    v   i   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_61719903_6   3720 ATAACAAACAATCCCATC-AAAAATCGGCCAAGGACATGAATAGACCGTT 3768
                          vi     i  i  v  i-      v   v     iv         vv  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_61719903_6   3769 CTCAAAAGAATGTATACAAATGGCCAACAA--ACATGAAAAAATGCTCAG 3816
                            v      vi               i  --         i       i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_61719903_6   3817 CATCACTAATGAT 3829
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3148 27.39 0.55 0.66  chr1_61751326_61757474.rev     4750  5658 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_61751326_6   4750 TGGAAGAATATTCTGTGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4799
                              ii    i ii  i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_61751326_6   4800 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCACCATCAAGC 4849
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_61751326_6   4850 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4897
                          v    ivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_61751326_6   4898 TATGGAAC--CAAAAAACAGCCTGCATTGGCAAGACAATCCTAAGCAAAA 4945
                                v--   iii  --  v v  v v   i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_61751326_6   4946 AGAGCAAAGCTGGAGGTATCACGCTACCTGACTTCAAACTATACTACAAG 4995
                            i     i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_61751326_6   4996 TCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5045
                         v         i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_61751326_6   5046 CCAATGGAAAGGGACAGAGGCCTCAGAAATAACGCCACACATCTACAACC 5095
                         i        vi i iv   ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_61751326_6   5096 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5145
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_61751326_6   5146 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5195
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_61751326_6   5196 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCCAGATGGA 5245
                            ii    i    v   i     v              i  v i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_61751326_6   5246 TTAAAGACTTAAATGTTAGACCTACAACCATAAAAACCCTAGCAGAAAAC 5295
                          i ?    i       v   v   v   i      vi i   v       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_61751326_6   5296 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTTGTGACTA 5344
                         v    ?i- v i -   iv   v v  vv i     v ii  iv iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_61751326_6   5345 AAAACACCAAAAGCAATTACAACGAGAGCCAAAATTGACAAATGGGATCT 5394
                         vi -           vvvi    i i  vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_61751326_6   5395 AATTAAACTAAGAAGCTTCTGCACAGCAAAAGAAAGTACCATCAGAGTGA 5444
                         v  i   v v i  i   i  ii vv    i  v v  i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_61751326_6   5445 ACAGGCAACCTACAGAATGGGAGAAAAGTTTTGCAATCTACCCATCTGAC 5494
                          v  i     i                vv       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_61751326_6   5495 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5544
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_61751326_6   5545 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5594
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_61751326_6   5595 ACTCAAAAGAAGACATTTATGCAACCAACAAACACACGAAAAAATGCTCA 5644
                         v   v        i  vi viiii    i  i    i     i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_61751326_6   5645 TTATCACTGGTCAT 5658
                         vi    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1686 26.95 0.74 5.02  chr1_62007304_62009778      760  1297 (1178)    L1M4_orf2#LINE/L1        1   515 (393)  

  chr1_62007304_6    760 TAGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATAGTGTTAAAGT 809
                          i    i i  i     i        v      v i    v      ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_62007304_6    810 GGCCATACTGCCCAAAGCAATTTATAGATTCAGTGCTATTTCTGTGACAT 859
                            v     v      vii  i  i       ii  v  ii  i v v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_62007304_6    860 TTTTCACCGAATTAGAAAAAAACTATTCTAAAATTTTTCTAAATTT--TA 907
                          i----  ------------ i  iiii ----    v vi  v  --i 
  L1M4_orf2#LINE/    101 TC----CC------------AGCTGCCTT----TTTTGCAGAAATTGACA 130

  chr1_62007304_6    908 AGGAAATTTTTAGAAAAATTTTT-TGGAACCAAAAAAGAGCCCAAATAGC 956
                           vvi  ii ----      iv -     viiv  ii  v  vi      
  L1M4_orf2#LINE/    131 AGCTGATCCT----AAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr1_62007304_6    957 CAAAGCAGTCCTAACCAAAAAGAACAAAGCCAGAGGTATCACACTACCCA 1006
                             i  i  i i vv  i          iii    vv       v    
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr1_62007304_6   1007 ACTTCAAACTATGTAGTACAAGGCTATAGTAATCAAAACAGCATAGTATT 1056
                          i      -- iv  v     i    i         i    ii i   i 
  L1M4_orf2#LINE/    227 ATTTCAAA--ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_62007304_6   1057 GGTACAAAAATAGACACATAGACCAATGGAACAGGTTAAAGAACCTAGAA 1106
                           i i  ii       i     i        i  iv vi   ii i    
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_62007304_6   1107 ATAAAGGTGCACATCTACAAGCATCTGTTGTTTAACAAAGTCAACAATAA 1156
                              vviii    i  iiiv  vi  v v  ii    i viiv   v v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_62007304_6   1157 CAAGCAATGGGGAATGGAC-TTCTTATTTGGAAAATGTTGCTGGGAAAAC 1205
                           vv          v i i-v    -  iiiv     v        v   
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAAC 423

  chr1_62007304_6   1206 TGGCTACCCATATGCCGAAGATTGAAACTGGACCCCTTCCTTTCACCATA 1255
                            v  ?   i    vi    v    ii         v   iv       
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_62007304_6   1256 TACAAAAATCAGCTCAACATGGATTAAAGACTTAAATGTAGG 1297
                                  i i     v      i ?    i        i 
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

Transitions / transversions = 1.75 (91 / 52)
Gap_init rate = 0.02 (9 / 515), avg. gap size = 3.44 (31 / 9)  

1223 23.87 2.26 1.26  chr1_62007304_62009778     1591  1988 (487)    L1M4_orf2#LINE/L1      507   908 (0)  

  chr1_62007304_6   1591 AAAAGTAAAACCTAAAACTATAAAAACCCTGGAAGAAAACCTAGGAACTA 1640
                            v    i v              vi i i         v    ?iiv 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_62007304_6   1641 -CCATTGTGGATATTGGCCTTGGCAAAGATTTCAT-GATGAAGATTTCAA 1688
                         -i v i   - iv    vi v     v i    v -   - v  ivi   
  L1M4_orf2#LINE/    557 ATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAA 604

  chr1_62007304_6   1689 GAGCAATTGCAACAAAAACAAAAATTGACAAGTGGGACTTAATTAAACCA 1738
                         i    vvv         iv      v  i  i v      v  i   viv
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_62007304_6   1739 AAGAACTTTTGCACAGCAAAAGAAACTATCAACAGAGTAAACAGGCAACC 1788
                           i        ii vv    i  v        v i   i  v  i     
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_62007304_6   1789 TACAGACTGAGAGAAAATATTTGCAAACTATGCATCTGACAAAGATCTAA 1838
                         i     v  i                 ii  ii      i  i iv  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_62007304_6   1839 TATCCAAGAATCTATAAAGAACT--TAAAAC--AGCAAGCAAAA-ACAAA 1883
                               -    v           --  v   -- ii  vv    -     
  L1M4_orf2#LINE/    755 TATCCA-GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_62007304_6   1884 CAGCCACCATTAAAAAATGGGCAAAGGACACG--TCGCACACTTCTCAAA 1931
                         i i  - v   ?                ivi -- v -   i     v  
  L1M4_orf2#LINE/    804 TAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAG-ACATTTCTCCAA 851

  chr1_62007304_6   1932 AGAAGACATATACGTGGCCAACCACCATATGAAAAAATGCTTAATAGCAC 1981
                               i   i vi       iv v  i       i     i  i v  ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_62007304_6   1982 TGATCAT 1988
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.21 (51 / 42)
Gap_init rate = 0.03 (11 / 402), avg. gap size = 1.27 (14 / 11)  


3242 27.04 0.55 0.33  chr1_62120336_62126668     4935  5840 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_62120336_6   4935 TGGAAGAACATTCCATGCTCATGGATAGGGAGAATCAATATCACGGAAAT 4984
                              ii i  i     i        v  i   v i     iiivi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_62120336_6   4985 GGCCATACTACCCAAGGTAATTTATAGATTGAATGCCATCCCCATGAGGC 5034
                            v     v     iv i  i  i     v  i  v     i  v iiv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_62120336_6   5035 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5082
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_62120336_6   5083 TATGGAACCAAAAAAGAGCCCGCATTGCCAAAACAATCCTAAGCAAAAAG 5132
                                viiv  ii  v  v v  v            i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_62120336_6   5133 AACAAAGCTGGAGTCATCTCGCTACCTGACTTCAAACTGTACTACAAGGC 5182
                                i     vvv  v i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_62120336_6   5183 TACAGTAACCAAAACAGAATGGTACTGGTACCAAAACAGAGATATAGACC 5232
                                 i   i    vi         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_62120336_6   5233 AATGGAATAGAAGC-AGCCCTCAGAAATAATACCACACATCTACAACCAT 5281
                                     vi-  vvii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_62120336_6   5282 CTGATCTTTGACAAACCTGACAAAAACATGAAATGGGGAAAGGATTCCCT 5331
                         i    i  i     ivv  v   i v   vv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_62120336_6   5332 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5381
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_62120336_6   5382 AACTGGATCCTT-CCTTACACCTTGTACAAAAATTAATTCAAGTTGGATT 5430
                          ii    i  i -   i     v i            i    iv     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_62120336_6   5431 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5480
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_62120336_6   5481 AGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAAA 5529
                            ?i- v i -   iv   v v  vv i i   v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_62120336_6   5530 ACACCAAAAGCAATAGCAACAAAAGCCAAAATTGACAAATGGGATCTCAT 5579
                                     vv           vv     v  i    v   ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_62120336_6   5580 TAAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGAACA 5629
                         i   v v  i i   i iii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_62120336_6   5630 GGCATCCTACAGAATGGGAGAAAATTTTTACAATCTATCCATCTGACAAA 5679
                          i  v  i                 v   i   vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_62120336_6   5680 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5729
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_62120336_6   5730 ATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGGACAGACACTTCT 5779
                         iv    i     v  i?    i            v  i i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_62120336_6   5780 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5829
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_62120336_6   5830 TCACTGGCCAT 5840
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


2458 27.75 2.52 2.41  chr1_62239987_62242462.rev     1116  1987 (489)    L1M4_orf2#LINE/L1        1   873 (35)  

  chr1_62239987_6   1116 TGGAAAAACATTCTATGCTCATGGACTGGATGAATCAATATTGTTAAAAT 1165
                               i i  i i   i       i    v  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_62239987_6   1166 GGCTATACTGCCCAAAGCAATCTATGCATTCAATGCTATTTCTGTCAAAC 1215
                            v     v      vii     iiv      i  v  ii  i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_62239987_6   1216 TACCAATATCACTTTTCACAAAAGTAGGAAAAGCT-ATCCTAAAATCTGT 1264
                          v   iivv vi    ii  i  i -v  v     -          iii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_62239987_6   1265 ATGGCACCAAA---AAAGGGCCTA-AATAGCCAAAGCAATCTTAAGAAAA 1310
                             ----   ---  i  i  i -          i       i -    
  L1M4_orf2#LINE/    150 ATGG----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAA 194

  chr1_62239987_6   1311 AAAAAATGAAGCCAGAGGCATCTCATTATCTGACTTCAAACTATACTATA 1360
                         i  i  ii   iii    vv  v  i vi ii i      viv     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_62239987_6   1361 TAGCTATAATAACTAAAACAGCATGGTACTGGCACAAAAACAGACATGCA 1410
                         v     i i   ii  i    ii           i  ii i      ii 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_62239987_6   1411 GGGCAACAGAACAAAACAGAGAACCCAGAAACAAAGTTGCACACCTACAA 1460
                          iv   ii   i i  iv    ii       i   viiii   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_62239987_6   1461 CCAACTGATCTTTGACAAAGTCAACAAAAATAAGAAATGTGGAAAGGTTC 1510
                         i   i    i  i     i viiv   i vi vvv    v      iv v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_62239987_6   1511 CACATGTCAATAAATTGTGCTGGGATAACCAGCTATCCATTTGCAGAAGA 1560
                         vv v v    i    v         i   ii v  ?   iv    i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_62239987_6   1561 ATTAAACTGGATCCCCTTCTAGTACCATACATAAAAGTTAACTCAAGATG 1610
                           v  ii    i   ivi  vii      i i    i         i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_62239987_6   1611 GATTGAAGACTTAA-T-TAAGACCTAAAAGTATAAAAATCCTAGAAGAAA 1658
                            ii?    i   - -     v      v       v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_62239987_6   1659 ACCTAGG---AAATGCCCTTC-TGTACATCAGCCTTCACAAAGAATTTGT 1704
                           v    ---    ---    -  -  v ii vi vvi   v iv  iv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT---CTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_62239987_6   1705 AACTGAGTGCTCAAAA--ACAATTGCAACCAAAACAAAAATTGACAAGTG 1752
                          iv iv vvvi     --    --     v   iv      v  i  i v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATT 638

  chr1_62239987_6   1753 GGACCTAAT---AATTAAAGAGTTTC-TGCATAGCAAAAGAAACTATTAA 1798
                             i v  ---       i v   i-   v --    i  v     i  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAA 686

  chr1_62239987_6   1799 CAGAGTAAACAGACAACCTACAGAATAGGAGAAAATATTCATAAACTACA 1848
                         v i   i  v        i       i            iii   ii i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_62239987_6   1849 CATCCAACAAAGGTCTAATATCCAGAATCTATAAGGAACTTCAACAAATC 1898
                         i   ii i  i  v  vi          v     i     iiv    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_62239987_6   1899 AACAAGCCAAAAACAA-----CCATATTAAACAGCAGGCAAAGGCAAAGG 1943
                           i  vvv   i    -----   -   ?  v ------ vi        
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCA-ATTWAAAA------ATGGGCAAAGG 829

  chr1_62239987_6   1944 ACAAGAACACACTCTTCTGGAAAGAAGACATACACCTGGACAGT 1987
                          ivv   i v  vi    vv        i     vv   v  i 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

Transitions / transversions = 1.72 (151 / 88)
Gap_init rate = 0.02 (20 / 873), avg. gap size = 2.15 (43 / 20)  

 207 17.74 0.00 4.84  chr1_62239987_62242462.rev     2376  2437 (39)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_62239987_6   2376 AAAGAAGACAACATAGAAGCAGCCAACCAACATATGAAAAAATGCTCAAC 2425
                                 i ---  v  iii     iv i  i       i         
  L1M4_orf2#LINE/    850 AAAGAAGATA---TACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_62239987_6   2426 ATCGATAATCAC 2437
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 3.00 (3 / 1)  


2605 21.04 6.81 1.33  chr1_62594994_62597187.rev      502  1176 (1018)    L1M4_orf2#LINE/L1      122   833 (75)  

  chr1_62594994_6    502 AAATTGACAAGTTGACTCTAAA-TTTACTTGGAAATGCAAAGCAACTCTA 550
                                    i   ii     -  i iv           i -i  i - 
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG-GACCC-A 169

  chr1_62594994_6    551 GAATAGTTAA-----TTCTGAAAAGGAAGTACAATATCAGAGGACTTTCT 595
                               ii  ----- ii      i    v    vi ii       iv v
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_62594994_6    596 CTACTTGATTTCAAAACTCACTATAGAGCTACAGCAATCAAGATTGTGTG 645
                           v iii           i    i i        i        iv     
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_62594994_6    646 GTATTGGTATAAGAATAGACATATAGATTTCTAAAACAAAAT--AGAGTC 693
                            i   i     i              ivv ii  i i   --      
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_62594994_6    694 CAGAAACAGACC--TACATTATTATGGTTAACTGATTTTTAACAAGTGTA 741
                               i i   --      --      i  i       ii     v  i
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATT--TATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_62594994_6    742 CCATGGTAATTCAAAGGAGAAAAAAATAGTCTTTTCAACAAATGGTGCTG 791
                            v iiv      v  i    i  -                        
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAA-TAGTCTTTTCAACAAATGGTGCTG 416

  chr1_62594994_6    792 GAATA-TTGCATATTCAAATTT----GGGT-AACCTCAACTTCTATTTCA 835
                          i i -i  v   ?i  v  vi---- ii -  vi vi  ii   ii   
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_62594994_6    836 CATCACAGGCAAAAATTAA---AATATAAACTA--GAACTAAATGTAGGA 880
                           i  i vi          ---  v  ii ii --  v         i  
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_62594994_6    881 GCTAAAACTATAAAACTTCTTGAAGAAAACGTAGGATAAAATCTTTGTGA 930
                                          ii v         i    ?vv       i    
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_62594994_6    931 ACTCA--TTAGGCAAACATTTCTTAGATA---CACCAAAAGCATGAACCA 975
                         v  ii--        vvi           ---           ii i v 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_62594994_6    976 TGAAGGAAAAAAAAGACAAACTGGAATTCAT------TGAAAATTTTTAC 1019
                         ii  i       v   i   i    v     ------ i    i    ii
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_62594994_6   1020 TTTTCAA--GACATTAATAAAAAAG-GAAAG------CTACAGAATGAGA 1060
                         vi     --    i  vi  i    -    i------ i        i  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_62594994_6   1061 GAAAATATTTGCAAAT---ATATCTGATGAAG-ACTTGTATCCAGAATGT 1106
                                         ---         i i -               i 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_62594994_6   1107 AAAAAGAACTCTTAGAACTTAAGAAAGAAAAAAAAAA-ACTCCGATTTTC 1155
                          v            v    i  v  vi    i v   - vi  i   ?--
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-- 814

  chr1_62594994_6   1156 AAAAAAATGGGCAAAAGACTT 1176
                         --             i  i  
  L1M4_orf2#LINE/    815 --AAAAATGGGCAAAGGATTT 833

Transitions / transversions = 2.66 (101 / 38)
Gap_init rate = 0.03 (23 / 712), avg. gap size = 2.39 (55 / 23)  

 363 15.19 1.27 0.00  chr1_62594994_62597187.rev     1625  1703 (491)    L1M4_orf2#LINE/L1      829   908 (0)  

  chr1_62594994_6   1625 GATTTGAGCAGAAATGTCATTAAAGAA-ATATACAAATGGAACATTAGCA 1673
                                ii   v  v  vii      -            vvv  v    
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_62594994_6   1674 CATGAAAAGATGCTCAGCATCATGAGTCAC 1703
                                         i     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.71 (5 / 7)
Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1)  


2552 25.45 1.65 0.28  chr1_62696036_62702322     1447  2173 (4114)    L1M4_orf2#LINE/L1      172   908 (0)  

  chr1_62696036_6   1447 ATAGCCAAGACAAT---GAGCAAAAAGAACAAAGCTGGAGGCATCACACT 1493
                                 i     ---  iv  i          i      vv       
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_62696036_6   1494 ACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCA-GGT 1542
                         v  ii i      viv        i          i   i    ii-   
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_62696036_6   1543 ACTGGTACCAAAACAGATACATAGACCAAGGGAACAGAACAGAGGCCTCA 1592
                              i iv ii i   i i     i   v    i    iv   ivii  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_62696036_6   1593 GAAATAACACCACACATCTACAACCATCTGATCTTTGACAAACCTGACAA 1642
                                vv   i    i  iiii  vi    i  i     ivv  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_62696036_6   1643 AAACAATCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGTTCGGA-- 1690
                         i v  v             i  vvi  v  i  i        i v   --
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_62696036_6   1691 ACCGCCTAGCCATATGCAGAAAACTGAAACTGGATCCCTTCCTTATACCT 1740
                           i vv  ?   i     i  i v    ii    i    v   i i   v
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_62696036_6   1741 TATACAAAAATTAACTCGAGATGGATTGAAGACTTAAACGTAAGACCTAA 1790
                                          i i      ii?    i    i      v    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_62696036_6   1791 AACCATAAAAACCCTT-GAAGAAAACCTAGGCA-ATACCATTCAGGACAT 1838
                            i      - i   -         v    ?i- v i -   iv   v 
  L1M4_orf2#LINE/    522 AACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT 569

  chr1_62696036_6   1839 AGGCATGGGCAAACACTTCATGACTAAAACACCAAAAGCAATGGCAACAA 1888
                         v  vv i     vvii   v iiv  vi            vvi       
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_62696036_6   1889 AAGCCAAAATTGACAAATGGGATCTAATCAAACTAAAGAGCTTCTGCACA 1938
                            vv     v  i    v   ii v      v v  i i   i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_62696036_6   1939 ACAAATGAAACTATCATCAGAGTGAACAGGCAACCTATAGAATGGGAGAA 1988
                         v    v  v       vv i      v  i     i i            
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_62696036_6   1989 AAATTTTGCAATCTATCCAACTGACAAAGGGCTAATATCCAGAATCTACA 2038
                           vv       vii  vi v    i  i  i  vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_62696036_6   2039 AAGAACTCAAACAAATTTACAAGGAAAAAACAA----CCCCACCAAAAAG 2084
                                 vv    v iv i  vi    i    ----   v ii?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_62696036_6   2085 TGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGAGGC 2134
                                     v    i     i     v        i  vi viv   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_62696036_6   2135 CAACAAACATATGAAAAAAAGCTCATCATCACTGGTCAT 2173
                            i  i  i       i v     v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (105 / 76)
Gap_init rate = 0.01 (8 / 737), avg. gap size = 1.75 (14 / 8)  

 261 23.91 0.00 15.94  chr1_62696036_62702322     4769  4906 (1381)    L1M4_orf2#LINE/L1       78   193 (715)  

  chr1_62696036_6   4769 ATTCAATACAATCTTAACTAAAATTTTAACAGGTTTATTGGTTTTTGTTT 4818
                               ii     iiv ii     iii i ---------------  ii 
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGC---------------TGCCT 112

  chr1_62696036_6   4819 ATTTATTTTAGTGGAACTTTACAAGCTGATTTTCAAATTTATGTAGATAT 4868
                         -----    v ii   v  v          ii v     i  i i  v  
  L1M4_orf2#LINE/    113 -----TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_62696036_6   4869 ACAAAGGGCCAAAAAGTAGCCAAGAAAAATTTTAAAAA 4906
                         i   i  i  v i  -       -  v   i  i    
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAA-TAGCCAA-AACAATCTTGAAAA 193

Transitions / transversions = 3.12 (25 / 8)
Gap_init rate = 0.03 (4 / 116), avg. gap size = 5.50 (22 / 4)  

 230 30.26 4.43 8.49  chr1_62696036_62702322     4959  5229 (1058)    L1M4_orf2#LINE/L1      382   641 (267)  

  chr1_62696036_6   4959 TAGGGAAA--ATATTCTTTT-AATAAACGGTGCTGAAATAATCTGGCATA 5005
                          i      --   v      -  i   i       ii i  -    -   
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA-CTGG-ATA 429

  chr1_62696036_6   5006 ---ATATGCAATATAAATAAATAAATAAATGAACCTGGACTCCCAACTTA 5052
                         --- i      -----------  i--      vi     i  i v  i 
  L1M4_orf2#LINE/    430 KCCACATGCAA-----------AAG--AATGAAGTTGGACCCCTACCTCA 466

  chr1_62696036_6   5053 CACTGTATATAAAAAAATCTATTTCAGGTAGATTTTAATTTTAAAATTAA 5102
                            i--     v      iv i iv ii i   i--- ?--- i vi   
  L1M4_orf2#LINE/    467 CACC--ATATACAAAAATTAACTCAAAATGGATC---AW---AGACCTAA 508

  chr1_62696036_6   5103 ATGTAAAAGGAAGAACAA-AAAATT--TCGAATGTAACACAGA---ATAC 5146
                               i  vv i   v -    i -- v   viv    i  i--- v i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_62696036_6   5147 CTTCAAAATTCTGAAACAGAAAAAAATTCCTTAAATAAGATATAGAAAAT 5196
                             ivi iii  iivi  iv  vii  i    i   v  i ivi   ii
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_62696036_6   5197 ATTAGCTGCAAGACTAAATTTAAGTATATTAAA 5229
                          iv   vi   i vv   vv  ii  v   ii 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

Transitions / transversions = 2.00 (54 / 27)
Gap_init rate = 0.05 (13 / 260), avg. gap size = 2.69 (35 / 13)  

 378 26.91 10.18 1.45  chr1_62696036_62702322     5523  5797 (490)    L1M4_orf2#LINE/L1      610   908 (0)  

  chr1_62696036_6   5523 CAAG--ATAAATAAATAAATAAATAAA---AAGTAAAATAAAATTAGGCA 5567
                             -- i   vi  v     i     ---i v vv vi       iiv 
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_62696036_6   5568 -TTCTA-ACCACCAAATTCACCATTAAATGGGTAAAACAGCAAGCCACAG 5615
                         -  i i-i iv v  ivv   i  i  ivii  i   vii   v      
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_62696036_6   5616 A----GAAGAAATATTTG--AACCACTTATAACTGACAATGGACTTG-AT 5658
                          ----  ii         --  i  --    v    i  v       -  
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCA--TATATCTGATAAGGGACTTGTAT 757

  chr1_62696036_6   5659 CTAGAACATACAAAG---TCCTAAAAATCATTAAACAAAAG-CAAACAAC 5704
                          i    i   i    ---  i  v  v   v   vv     -    i   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_62696036_6   5705 CAAAT-GGAAAACAAGCAAAGAACTC---TAGACA---CTTCAAAAGAGA 5747
                          v   -?i    iii      i i i---      ---  i    ii   
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_62696036_6   5748 GAATCCAAATGGTCAATCATACTTATGGAAAAGTGC---ACACCGCACAA 5794
                         v - v       i    v -i vi   i   ii   ---   i i?????
  L1M4_orf2#LINE/    858 TA-TACAAATGGCCAATAA-GCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_62696036_6   5795 GTC 5797
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.81 (47 / 26)
Gap_init rate = 0.05 (16 / 299), avg. gap size = 2.00 (32 / 16)  


3088 26.44 1.22 0.33  chr1_62740862_62745149     2896  3795 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_62740862_6   2896 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAGTATCAGGAAAAT 2945
                               i i  i     i        v      v i i   iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_62740862_6   2946 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2995
                            v     v      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_62740862_6   2996 TACCA-TTGACTTTCTT-CAGAGAACTGGAAAA---A--CTAAACTTCAC 3038
                          v   -i  v    i  -    -  i  iv  i--- --     v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_62740862_6   3039 ATGGAACCAAAAAAGAGCCCACAG-AGCCAAGACAATCATAAGCAAAAAG 3087
                               viiv  ii  -    v i-      i      v i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_62740862_6   3088 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACGAGGC 3137
                                i      vv       v  ii i      vivi     i i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_62740862_6   3138 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 3187
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_62740862_6   3188 AAGGAAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACAACCAT 3237
                           v i  i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_62740862_6   3238 ATGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 3287
                         v    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_62740862_6   3288 ATTTGATAAATGGTGTTGGGAAAACTGGCTAGTCATATGCAGAACACTGA 3337
                         v  ii i        i     v      v  ?i  i     i  v v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_62740862_6   3338 AACTGGACCCTT-CCTTACACCTTAAACAAAAATTAACTCAGGATGGATT 3386
                          ii       i -   i     v  v               ii      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_62740862_6   3387 AAAAACTTAAACATAAGACCTAACACCATAAAAATCCTAGAAGAAAACCT 3436
                          ? i  i    ii     v    v  i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_62740862_6   3437 AGGCA-ATACCATTCAGGACATAGGCATGAGCAAACACTTCATGTCTAAA 3485
                            ?i- v i -   iv   v v  vv ii    vvii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_62740862_6   3486 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 3535
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_62740862_6   3536 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 3585
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_62740862_6   3586 AGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTATCTATCTGACAAA 3635
                         ii     i   i             v       vii  v       i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_62740862_6   3636 GGGCTAATAACCAGAAC-TACAAAGAACTTAAATAAATTCACAAGAAAAA 3684
                           i  vi  v      i-  i        ivv i  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_62740862_6   3685 AATAAATAATCCCATCAAAAAGTTGGCAAAGGTTATGAACAGACACTTCT 3734
                         i i      i  v  i?    i v        v v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_62740862_6   3735 CAAAAGAAGACATTTATGCAGCCAAGAGACACATGAAAAAATGCTCATCA 3784
                          v        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_62740862_6   3785 TCACTGATCAA 3795
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


1194 17.79 1.98 1.19  chr1_62803019_62807185     2420  2672 (1495)    L1M4_orf2#LINE/L1        3   257 (651)  

  chr1_62803019_6   2420 GAAAAAAATTTCATGTTCATAGATTCAAAGATTTAAAATTGTTAAAATGG 2469
                             i v  ii         i    vi    i    v        i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_62803019_6   2470 CAACAATCTATAAATTGACTTAGAGATTCAATGTCAGCCCTATCAAAATC 2519
                            i v  ivi       ii  v        i iv v             
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_62803019_6   2520 CCAGATGCCTTT-GTGCACAAACTGACA-GCTGGTCCTAAA-TTTATATG 2566
                             v       -v    v   i     -    i       -  i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_62803019_6   2567 GAAATAAAAGAAACCCAAAATTGCCAAAACAAATCTTGAAACAGGATAA- 2615
                              iv   ii     i   v          -        v  i v  -
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAAC 201

  chr1_62803019_6   2616 -AAGCTGGAAGACCCACTCTTCTCAATTTCAAAACTTAGCCTTCAAAGGT 2664
                         -   i    i   i   v    i               --  v     v 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGCT 249

  chr1_62803019_6   2665 AAAGTAAT 2672
                          v      
  L1M4_orf2#LINE/    250 ACAGTAAT 257

Transitions / transversions = 1.37 (26 / 19)
Gap_init rate = 0.02 (6 / 255), avg. gap size = 1.33 (8 / 6)  

2454 15.18 3.99 8.59  chr1_62803019_62807185     3024  3675 (492)    L1M4_orf2#LINE/L1      287   908 (0)  

  chr1_62803019_6   3024 GGCATACAGATCAGTGGAATGGGATGGAGAGTCCAGAAATAAATCC-CAC 3072
                          i    i      i      i i  v                 i  -i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_62803019_6   3073 ATGAATGGTCAATTGACTTTCAATAAGGGATCTAAGAAAATTCAATGGGA 3122
                           vv            i    i i     vv i    vv          i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_62803019_6   3123 AAAGAATAGCCTTTTTAATAAATGGTGCTGAAACAACTGGATATCCACAT 3172
                                  i     i  i           ii           ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_62803019_6   3173 A-AAAAGAATGAAATTGGAC---TACCTCACA--ACATACAAATATTAAC 3216
                         i-           i      ---         -- i       v      
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_62803019_6   3217 TCAAAATGGATTATTATAAACCTAAATGTAACAGCTGAAACTATAAAACT 3266
                                    i ?--- i            v    i             
  L1M4_orf2#LINE/    487 TCAAAATGGATCAW---AGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_62803019_6   3267 CTTACAAGAATACATACAAGTAAATTTT---GAT-TCATATTACATAATG 3312
                             v     v     vi?      i  ---  i- iivi   vii    
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_62803019_6   3313 GTTTCTTAGATAAAACACCAAAAGCACA-GTGACAAAAGAAAAAAATAGA 3361
                                     vi              - ii             -    
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGA 632

  chr1_62803019_6   3362 AAAATGTAACTTCCTCAAAATTTAAAACTTCTGTGCTACGAACAATACCA 3411
                         v    vvi     v        v       i      v i  vi i  i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_62803019_6   3412 TCAAGAAAAGTGAA-------CTCACAGACTAGGAGAAAAT--TTGCTA- 3451
                                 -     ------- i      v i         --    v -
  L1M4_orf2#LINE/    683 TCAAGAAA-GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_62803019_6   3452 TCATATATTAGGCAAGGAATTTGCATCTTGAACATATAAAGAACTCCTAC 3501
                                 iv ii    i i   i   iv   i             i   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_62803019_6   3502 AACTCAATGCCAAGAAGGTTAAAACCCCATTTAAAAAATAGGCATCAACT 3551
                                 --------------  -------      i------------
  L1M4_orf2#LINE/    782 AACTCAAT--------------AA-------TAAAAAG------------ 798

  chr1_62803019_6   3552 ATTAATAAATAATAAAAAGACCAAAGCCATTAAAAAATGAGCAAAGG--T 3599
                         ---- i      i-------    -----  ?       i       -- 
  L1M4_orf2#LINE/    799 ----ACAAATAAC-------CCAA-----TTWAAAAATGGGCAAAGGATT 832

  chr1_62803019_6   3600 TAAAAATACCTATTACTCCAAGAAAGATACACAAATAGCCAATA--CACA 3647
                          i  v v  --   v      ii      i      i       --    
  L1M4_orf2#LINE/    833 TGAATAGAC--ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_62803019_6   3648 CAAAATGATGCTTAATATCGCTAGCTTT 3675
                         ii   v      i  i   i????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (65 / 30)
Gap_init rate = 0.03 (21 / 622), avg. gap size = 3.90 (82 / 21)  


3313 20.57 3.08 2.46  chr1_62850962_62853680     1053  1864 (855)    L1M4_orf2#LINE/L1       13   829 (79)  

  chr1_62850962_6   1053 CCATTTTCATGGATTGGAAGACTCAATATTGTTCAGATGGCAATTCTCCC 1102
                             v                  i         v          v     
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_62850962_6   1103 -AAACTGATCAACAGATTCAGTGCAATCTCTATCAAAATCCCAACAAGAC 1151
                         -   i     v         ii      i              i v- v 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT-GCC 111

  chr1_62850962_6   1152 TTT---GCAGAAACTTGCATACTTTATATAGATATTGGTCCTAAAATGTA 1198
                            ---       i vi  ----------  ---i  i         vi 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACA----------AG---CTGATCCTAAAATTCA 148

  chr1_62850962_6   1199 TATGAAAATGCAAAAAATCCAGAATAGACAAAGCAATTTTGAAAAA--AG 1246
                             i        iii i         v    i    i        --  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_62850962_6   1247 TAAAAAATTGGAGGACCCACACTTACAAATTTCAAATTTTACTTTAAAGC 1296
                         v v   i         i       v v         vi     vi     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_62850962_6   1297 AATGGTAACCAGAACAGCACTGTACTGGTATAAGGATAGACACACAGAGC 1346
                         v ii    i  ii    iiiv       i             i i   v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_62850962_6   1347 AATGAAACAGAACTGAGTATCAAGAAATGAACTCTTACATTTATGATCAA 1396
                             i  i    i    vi  v      i   i v          i    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_62850962_6   1397 CTGATTTTTTTTGACAATGGTGCCAAGGCAATTCAATTGGACAAAAGTAT 1446
                         i       i---     v         i v       v  iv  i i  v
  L1M4_orf2#LINE/    349 TTGATTTTC---GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_62850962_6   1447 TCTTTTCAACA----GTGTTGCAACAATTGAACACCCACACACTAAAGA- 1491
                                    ----   i  vi    i  i i ?     ii v     -
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_62850962_6   1492 TAAATTTAGACCTTTATCTCAAACCATGCATAAAAACTAACGCAAAATGG 1541
                          i  v  i    ii  i    v     ii i     i    v        
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_62850962_6   1542 AACATAAACCTTAATATAATAACTAAAACTATCAAATTTTTAGCAGAA-- 1589
                          v  ? i    v   i   v i          v   i i    v    --
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_62850962_6   1590 CATAGAAAAAAAT--TCATGACAATGGATTAGGCAAAAAGT-CTTAGCTA 1636
                              i?iv    --  i    vv   i        viiv -     v  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_62850962_6   1637 CAACACCAAAATCCTGATGCA-TAAAAGAAAAAAACTGATGAACTGGACT 1685
                         ii         v vii -   -i           -iv   i  i      
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAA-GCAACAAAAGAAAAAA-TAGATAAATTGGACT 643

  chr1_62850962_6   1686 TCATTAAAATTGAAAACCTTTGTGCTTCAAA---CATCACCTAAAAAATG 1732
                             i      i     i             ---  ii i v i   i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_62850962_6   1733 AAAGGACAAGCCAAACAA--GGAGACAATAGTTGTAAATTATATATCTAA 1780
                            i     v   v v  --     v    v   i    i        i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_62850962_6   1781 AGAAGGACTTTTACTCAGAACACATAAAGAACTCCTACAACTCAAAAGCA 1830
                         vi i      v  ii     i i           i          v ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_62850962_6   1831 A---GATAAATAATCCCACTGAAAAATGAATAAGAGG 1864
                          ---  i      i  v i ?       iii  -   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAA-AGG 829

Transitions / transversions = 1.96 (108 / 55)
Gap_init rate = 0.02 (19 / 817), avg. gap size = 2.37 (45 / 19)  

 294 28.57 0.00 0.00  chr1_62850962_62853680     2149  2218 (501)    L1M4_orf2#LINE/L1      817   886 (22)  

  chr1_62850962_6   2149 AAATGAGTAAGAGACCTGAACAGGTATTTCACCAGGGCAGATACGTGAGT 2198
                              i i  ii  ii    i  ii     v   ii v     iiii i 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_62850962_6   2199 GGCTAATAAGCACATAAAAA 2218
                            i           i    
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAA 886

Transitions / transversions = 9.00 (18 / 2)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.00 (0 / 0)  


 478 24.55 3.12 17.37  chr1_62855597_62857751      604  1662 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_62855597_6    604 TGGAGAAATACACTATGGATCATGGATTGGAA-ACTCAATATTATAAGGA 652
                             i i   iv i   v-             -   i      i v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGT-TCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_62855597_6    653 TGTCATTTCTCCCCTGAATTAACATATAGATTCAATGCAATCCCAATCAA 702
                           v  v v      -i    i iv  i        i        v     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_62855597_6    703 A-TTCTA--TGAGTTTTGGGTT-CAGGGAGTTTTGTTTTGTCTTTGGTAG 748
                          - i i --  vv    ---  -   ii --------   v v--i iv 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTT---TTGCAGAAA--------TTGACA--AGCTG 135

  chr1_62855597_6    749 ATTCTAAAATTTACGTGGAAATTCAAAGGGCTAAGAGCAGTCAAGATTTT 798
                           i        i ii       v   i  i iv   ii  i   i ivv 
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_62855597_6    799 TTTTTAAAGGTGGAAGGAGTTACTCTACCAAATGCCAAGACTGATTATAC 848
                         i  vv   i ---   i --------- v  i vvv i    ---i i  
  L1M4_orf2#LINE/    186 CTTGAAAAAG---AAGAA---------CAAAGTTGGAGGACT---CACAC 220

  chr1_62855597_6    849 CTAAGATTATTTATAATTTGTAAAAAAAATACTGTATAACCAGACCAATG 898
                         ---------  ivi     v---    vv    ii v i i v vi   -
  L1M4_orf2#LINE/    221 ---------TTCCCAATTTC---AAAACTTACTACAAAGCTACAGTAAT- 257

  chr1_62855597_6    899 GAACAAAACAGAGATCCCAGAAAAAGACCCACAAATAAGGATATATCATC 948
                         ---   i    v - ---- iv vv i ------         v -   -
  L1M4_orf2#LINE/    258 ---CAAGACAGTG-T----GGTACTGGC------ATAAGGATAGA-CAT- 291

  chr1_62855597_6    949 TACAACAGATAATTTCAATGTACATTTTAAAAATAACTAAAAGAATTG-G 997
                         ---- i    -----     ----------i    -------      - 
  L1M4_orf2#LINE/    292 ----ATAGAT-----CAATG----------GAATA-------GAATTGAG 315

  chr1_62855597_6    998 ATTGTTACACAAGATAAATGCTTGACATGATAGATACCCCATTTACCCTG 1047
                          --  i-  v  -     iv ------------    ---     -----
  L1M4_orf2#LINE/    316 A--GTC-CAGAA-ATAAACCC------------ATAC---ATTTA----- 341

  chr1_62855597_6   1048 ATGTGATTCTTACACATTGATGCCTGTATCAAAATATCTTATGTACCCCA 1097
                         ---  i -----  -      viii - -   ii--------  i  ---
  L1M4_orf2#LINE/    342 ---TGGT-----CA-ATTGATTTTCG-A-CAAGG--------GTGCC--- 369

  chr1_62855597_6   1098 TAAATACATATGCATACTATGTACCCACAAATATTAAAATTAATTTTTTT 1147
                         --  v  -----   v v   vi-----i  ---- i   - i i    i
  L1M4_orf2#LINE/    370 --AAGAC-----CATTCAATGGG-----GAA----AGAAT-AGTCTTTTC 402

  chr1_62855597_6   1148 AATCTACAATAGAGGCGGCAGGGCAGATTAATGGGGAAAGGACAATC-CA 1196
                           i-- -   ---  i vii  i  - i ----------   i ?i -  
  L1M4_orf2#LINE/    403 AAC--A-AAT---GGTGCTGGGACA-ACT----------GGATAKCCACA 435

  chr1_62855597_6   1197 TTTAGAAAAA---AATTAAA-----ATTTCACACCATACACATA--TCAA 1236
                          vi i  i  --- i  ii ----- ii          i   v -- i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_62855597_6   1237 GACAAGGTGGAATATAAACCTAAATAAAAAGGGGGTAACTACAAA-TTCA 1285
                         vv   ii    vi ? i        iv  ii vviv     i   -i  v
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_62855597_6   1286 T----GATAATATGGATGAATATCTTAAT-ATCTCAGGGTAATAAAATAT 1330
                          ----  v  i  i i? v v     vi - i  ii  v  ivv  vvi 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_62855597_6   1331 TTCTTA----CGAC-CCATAAAC-CAATAACCATTAAAAAAGACTGGTAA 1374
                               ----i   -   v  i -   vv v  vv i    i iv i   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_62855597_6   1375 GTTAAACTGCATTAAAACTGAGAACATACAGCTTTCATAAGATTCCATTA 1424
                         i  ii   v   i    i i i   v viivvi    v i  iv i  i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_62855597_6   1425 AAACTATGAAAA-ACAAGCCACAGGGTGGGAAAAGGTATTTGCTACACAT 1473
                          i vvi      -    v      ii     i  ii       v vv   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_62855597_6   1474 ATAATCAATAAACAACTAATACACAGACTGTATGTAAAGTACTCACACAA 1523
                            viii    ivi   vi  iv    --i   i     v    vi    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGA--ATATATAAAGAACTCTTACAA 783

  chr1_62855597_6   1524 AATCAATTCCTAAAAAACCCAAAGGGAAAAAAC--AATGGAGGAGGGGGA 1571
                         v-     ----  v   ----   iv   v   --   v? ii iv   -
  L1M4_orf2#LINE/    784 C-TCAAT----AATAAA----AAGACAAATAACCCAATTWAAAAATGGG- 823

  chr1_62855597_6   1572 TAACAGCAAAATATTTAAATAAGCAATTTACATAAGAAGAAATTCAAATC 1621
                         ------    iv    i    ii  v  iv vv       v  v     v
  L1M4_orf2#LINE/    824 ------CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_62855597_6   1622 ATCAATAAACATACAAAACAGA-GCTCAACCTCATTAGTAAT 1662
                         ii      i  i ii   -   -       v   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAA-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (153 / 103)
Gap_init rate = 0.07 (64 / 908), avg. gap size = 3.39 (217 / 64)  

 652 21.29 1.94 1.94  chr1_62855597_62857751     1996  2150 (4)    L1M4_orf2#LINE/L1        1   155 (753)  

  chr1_62855597_6   1996 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 2045
                              ii    i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_62855597_6   2046 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2095
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_62855597_6   2096 TACCAA-TGACTTTCTT-CAGAGAATTGGAAAAAACT-ACTTTAAAGTTC 2142
                          v   i-  v    i  -    -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_62855597_6   2143 ATGTGGAA 2150
                           i     
  L1M4_orf2#LINE/    148 ATATGGAA 155

Transitions / transversions = 2.00 (22 / 11)
Gap_init rate = 0.03 (5 / 155), avg. gap size = 1.20 (6 / 5)  


3210 26.32 0.88 0.88  chr1_62877347_62883590.rev     4846  5753 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_62877347_6   4846 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4895
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_62877347_6   4896 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4945
                           iv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_62877347_6   4946 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4993
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_62877347_6   4994 TATGGAAC--CAAAGAAGAGCCCACATT-GCCAAGTCAATCCTAAGCCAA 5040
                                v--   i i ---    v v -     iv     i i ivv i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_62877347_6   5041 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAA 5090
                                   i      vv   ii  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_62877347_6   5091 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 5140
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_62877347_6   5141 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACA 5188
                          i        i    i--    i  --        vv  ii i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr1_62877347_6   5189 ACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT 5238
                         iii vi    i  i     ivv  v   i v  vvv           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_62877347_6   5239 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5288
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_62877347_6   5289 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAACTGAATTCAAGAT 5338
                         iv    ii    i    v   i     v         v v  i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_62877347_6   5339 GGATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5388
                             i ?    i  v    v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_62877347_6   5389 AACCTAGACA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 5437
                            v   i?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_62877347_6   5438 CTAAAACAACAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5487
                         v  vi   v        vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_62877347_6   5488 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5537
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_62877347_6   5538 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTG 5587
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_62877347_6   5588 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAGAAG 5637
                          i  i  i  vi          v  i  v      vv    v iv v  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_62877347_6   5638 AAAAAAATAAACAGCCCCATCAAAAACTGGGCAAAGGATATGAACAGACA 5687
                              i i   i i   v  i?    v            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_62877347_6   5688 CTTCTCAAAAGAAGACATTTATGCAGCCAGAAAACACATGAAAAAATGCT 5737
                         i     v        i  vi viii    iv  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_62877347_6   5738 CATCATCACTGGCCAT 5753
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3259 25.89 1.11 0.22  chr1_62917090_62921377     2896  3795 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_62917090_6   2896 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAGTATTGTCAAAAT 2945
                               v i        i        v  v   v i i      i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_62917090_6   2946 GACCATACTGCC-AAATGCAATCTACAAATTCAACACAATCCCCATCAAA 2994
                          i v     v  -    -ii       i       i       i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_62917090_6   2995 ATACCAACATCATTCTTCACAGAGTTAGAAAAAA-AATTCTAAAATTCAT 3043
                           v   i vv v  i  ii    iv v  v  iv-i  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_62917090_6   3044 ATGGAACCAAAAAAGAGCCCCCATAGCCATAGCAAGACTAAGCAAAAGGA 3093
                               viiv  ii  v  vvv       v i   vvi i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_62917090_6   3094 GCAAATCTGGAGGCATCACACTACCTGATTTCAAACTATAATATAAGGTC 3143
                         i    vi      vv       v  ii        viv  v  i  i ii
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_62917090_6   3144 ATTGTCACCAAAACAGCATGGTACTGGTATAAAAATAAGCACGTAGACCA 3193
                          iv  v i   i    ii         i    ii   ii  ii    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_62917090_6   3194 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAAC 3243
                               i     v    ii               v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_62917090_6   3244 TGATATTCAACAAAGCAAACAAAATCATAAAGTGGGGAAAGAACACCCTT 3293
                             v   i    i vviv   i i   vv i           i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_62917090_6   3294 TTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAA 3343
                                             i  i   v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_62917090_6   3344 ACTGCATCCTCATCTCTCACTTTATACAAAAGTCAACTCAAGATGGATTA 3393
                         ii  v i  ii i   v   iv         i i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_62917090_6   3394 AGGACTTAAACCTAAGACGTGAAACTATAATAATTCT-ACAAGATACCAT 3442
                         ?i   i    iv     vv i         -  i   - v    v v   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACAT 548

  chr1_62917090_6   3443 TGGAAAAACCCTTCTAGATATTGGCTTAGGCAAGGATTTCATGACCAAGA 3492
                         v  ?iv  vi    vv  iv    v        v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_62917090_6   3493 ACCCAAAAGCAAACGCAATAAAAACAAAGATAAATAGCTGGGACCTAATT 3542
                         vv         v v    i    iv   i   i   iv v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_62917090_6   3543 AA-TCCAAAGAGATTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAACAG 3591
                           -vii   i vv    iiivv    i iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_62917090_6   3592 ACAACCCACAGAGTGGGAGAAAATCTTCACAA-TC-TATACCTGACAAAG 3639
                                     i           v  ii   -  -    i    i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_62917090_6   3640 GACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGTAAGAAAAAA 3689
                             vi          v  i  v      vv    v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_62917090_6   3690 ACAA----TCCCATCAAAAAGTGGACTAAGAACTTGAATAGACAGTTCTC 3735
                             ----i  v  i?    i   i v   i i           v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_62917090_6   3736 AAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCACCAT 3785
                         v                       i  i  i       i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_62917090_6   3786 CACTAATGAT 3795
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1685 16.00 4.92 0.92  chr1_63047691_63050047.rev      503   827 (1530)    L1M4_orf2#LINE/L1      167   504 (404)  

  chr1_63047691_6    503 CCAGAAATTGCCATG-CAATGTTGAAAAAGAAGAACAGAGCTGAAGGACT 551
                               - v    vi-    v                i  i  i      
  L1M4_orf2#LINE/    167 CCAGAA-TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_63047691_6    552 TACACCTCCCAATTGCAGAATTTATTACAAAGCCAAGGTAATCAAGACAG 601
                         i    i        v  i  i   i        i vi             
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_63047691_6    602 TATCAAACTGGCATGAGGCTAGATA--------AATGGAATAGATTTGAG 643
                          i viv        i   v    i --------           v     
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_63047691_6    644 AGTCTACAAATAAACCCTTATATTTACAGTCAGTTGACTTTCAACAAGGG 693
                             i v          v  i     ii    i    i    i       
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_63047691_6    694 CGACAACACTATTCATTTGTTGAAAAGAGTAGTCTTTTCAACAAATGGTG 743
                         i v   v  i     v v -- i     i                     
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGG--GGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_63047691_6    744 CTTGGACAACTGGACATT-ACATGCAAAAGAATAAA------CACCTACC 786
                           v           i ?i-              i  ------ v      
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_63047691_6    787 TCACACCATATACAAAAATCAACTCAAAATGGATTTAAAAC 827
                                            i              iv? i  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

Transitions / transversions = 1.78 (32 / 18)
Gap_init rate = 0.02 (6 / 338), avg. gap size = 3.17 (19 / 6)  

 890 19.17 2.59 1.04  chr1_63047691_63050047.rev     1158  1350 (1007)    L1M4_orf2#LINE/L1      504   699 (209)  

  chr1_63047691_6   1158 CCTAAATGTAACAGCTAAAACTATAAAACTCTTAGGAGAAAGTATAGGTA 1207
                                    v                       i     ii     ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_63047691_6   1208 TAGACCCCTTTAGGACCTTGAATCAATCAATGGTTTCTCAGATATAACAC 1257
                           i i --  iiv       ii i iv           i      i    
  L1M4_orf2#LINE/    554 TAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_63047691_6   1258 CAAATGCACAAGAAATTAAAAAAA-----CATAAATTAGACTTTATCAAA 1302
                             v       v  iv   i   -----v       i     i      
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_63047691_6   1303 ATTAAAACTTTCAGTAGTTCATAGGATACCATCAACAAAGTAAAAAGA 1350
                                vi  iv  iv    v    i  i     v     i      
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

Transitions / transversions = 2.00 (24 / 12)
Gap_init rate = 0.01 (2 / 196), avg. gap size = 3.50 (7 / 2)  

1021 18.83 2.09 0.42  chr1_63047691_63050047.rev     1628  1866 (491)    L1M4_orf2#LINE/L1      666   908 (0)  

  chr1_63047691_6   1628 TGCCTCAAAAAAAAAAA--AAAAAAGATAAAAAGACAACCTACAGAACAA 1675
                            i     ii v vv --  i    - i           i      iii
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAG-TGAAAAGACAACCCACAGAATGG 714

  chr1_63047691_6   1676 GAGAAAATGCTTGTAAATCATATATCTGATGAAGTACTTGTATCCCAAAT 1725
                                 ii   i                i i v          vi   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_63047691_6   1726 ATGCAAAGAACACTTATAACTCAATAATATAAACACAAATAACCTAAATT 1775
                           ii       v    i            v   v          i  v ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_63047691_6   1776 TAAAATGAGCAAAGATTTTAAATATACATTTTTCCAAAGAAGACATAAAA 1825
                         v      i      iv   i    v      i           i   v  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_63047691_6   1826 GTGGTCAACAAGCATATGGAAAGATA---AACATTATTAGTCAC 1866
                         i   i   i     i   i      i---     i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (31 / 13)
Gap_init rate = 0.01 (3 / 243), avg. gap size = 2.00 (6 / 3)  


3124 14.77 3.54 4.77  chr1_63217238_63218879      500  1149 (493)    L1M4_orf2#LINE/L1      267   908 (0)  

  chr1_63217238_6    500 GTGGTACTGGCATGAGGGCAGACATATAGATCCATGGAATCGAATCGAGA 549
                                      i   ii             v       v    i    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr1_63217238_6    550 GTCCAGAAATAAATCTATACATCTATGGTCAATTGATTTTTGACAAGCAT 599
                                      i i      i                 i      vi 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_63217238_6    600 GCTAAAAAAATTCAATGGAGAAAGAATAGTCTTTTGTCCAAATAATGCTG 649
                           i  i vv         i                vvv     ii     
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_63217238_6    650 GGA-AGCTGGATGTTCTGGTTTTCTAGAATGAAAAAGAATAAATGAAAAA 698
                            - i      i?i ------------------------ v   v    
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCC------------------------ACATGCAAAA 442

  chr1_63217238_6    699 AGAATGAATTTGGACTCTTACCTCACACCATATACAATACAAAAATTAAC 748
                         -       v      i i                   -----        
  L1M4_orf2#LINE/    443 -GAATGAAGTTGGACCCCTACCTCACACCATATACAA-----AAATTAAC 486

  chr1_63217238_6    749 TCAAGATATAGCAAAGACCAAAATGAAAG---------TATAAAACTTTC 789
                             i  iv v  ?     v     v   ---------         i i
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_63217238_6    790 AGAAGGGAAACATAAGTATAAATCTTTGTGACCCTGAGCTAGGCAACAGT 839
                              i-       i ?i        i      i  i i       ii  
  L1M4_orf2#LINE/    537 AGAAGA-AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_63217238_6    840 TTCTTAAACATGGCACCAAACACACAAGCAA----ACAAAAACTGGATAA 885
                               i i   i       vi         ---- v     v i     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_63217238_6    886 -TTGGACTTCATCAAA-TTAAAAACTTTTATG--TCAAAAGACACTATCA 931
                         -               -            i  --     i          
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_63217238_6    932 AGTACTTAAAAGGACAACTCATAGAATGGGAGAAAATATTTGCAAATCAT 981
                           v vv i   i      i  i                            
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_63217238_6    982 ATATCTGATAAGGATCTAGTATTCAGGCTATATAAAGAATCCTTATGATT 1031
                                      iv  v    i   iv           ii    ii i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_63217238_6   1032 CAATAATCAGAAGACAA----CCCTATT-AAAAATGAGCAAAAGATTTGA 1076
                                v i       ----   v   -       i     i       
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_63217238_6   1077 ATAGAGAGTTCTACAAATAAGATGCGTAAATGGCCAATAGGTGCATGAAA 1126
                              v v    v    v     iiii            i ii       
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_63217238_6   1127 AGATGCTAAACATTATGAGTTCT 1149
                                v     i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (62 / 31)
Gap_init rate = 0.02 (12 / 642), avg. gap size = 4.50 (54 / 12)  


3460 24.32 2.51 0.68  chr1_63408849_63410758.rev      540  1415 (495)    L1M4_orf2#LINE/L1        1   892 (16)  

  chr1_63408849_6    540 TGGAAGGGATTCTCCATGTTCATGGACAGGA-GTCTCAATATTGTCAAGA 588
                              i -  vii             iv   - v  i        i    
  L1M4_orf2#LINE/      1 TGGAAAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_63408849_6    589 TGTCTGTTCCTTCCAGCTTGATTTATAGATTCAATGCAATCT-----AAA 633
                           v vi v iii   iv     i  i        i      i-----   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_63408849_6    634 ATGCCTGCAAGTTATTTTGTAGATATTGACCAACTGATTTTAAAGTTCAT 683
                           v  v  vivi v     i   v      v i     ii    i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_63408849_6    684 ATAGAGAGGCAAAAGACCTAGGATATATAACACAATAATGAATTAGAAGA 733
                           i  i v    ii    i  i   vvi  v     vv    vv      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_63408849_6    734 ACAAAGTCAGAGGACTGACACTTCTTGCCTTTAAGACTTACTATAAAGCT 783
                                ii       v       iiivi  i  i        i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_63408849_6    784 ACAGTAACCAGGACAGTGTGGTATTGGTGAAAGAATCGACAAATAGATCA 833
                                i  i            i   iiv   i  v    v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_63408849_6    834 ATG--ACAGAATAGAGGGCCTAGAAATAGACCCCCATAACTACAGTCAAC 881
                            -- i     v   i i i       i    vi i vi  ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_63408849_6    882 TGATCTTTGACAAAGGGGCACAGGTAGTACAATGGAGAAAAAACCATCTT 931
                             i  i     i  v  vv  iivi v      i    i  ivi    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_63408849_6    932 TTCAACAAATGGTGTTGGAACAAGAGGACATCCACATGCAAAAAAATGAA 981
                                       i   i    vv   i ?            i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_63408849_6    982 TCTAGACACAGATTTTACCCCGT-CACAAAAATTAACTCAAAGTGGATTA 1030
                         vi i   v vv ii i  v  i -i                 i     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_63408849_6   1031 TAGATCAAAATGTA-GAACACAAAACTATAAAACTCCTAGAAAATAACAT 1079
                         ?   i v       -  i -i               i     i v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_63408849_6   1080 AGCAGAAAATCTAGATGACTTTGGGCATGGCAATGACTTTTTAAATAAAA 1129
                           v? v      vvi    i     ivv       ii  i   i   vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_63408849_6   1130 CACCGAAGACATAGTCCATGAAAGAATTAATTGATCAGCTAGAGTT-ATT 1178
                             i  ii  i iv v ii      vv   v   v ii i  v  -  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_63408849_6   1179 AAAATTAAAA---TTCCTGCTCTGTGCAAAAGACACTGTCAAGAGAATGA 1225
                                   ---  iv    i----    i      i      i i   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTT----CAAAGGACACTATCAAGAAAGTGA 694

  chr1_63408849_6   1226 GAAGAGAGGCCACAGACAGGAGGAAAATATTTGCAAAAGGCATATCTGAT 1275
                         i    v iv       vv  ii               vvii         
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_63408849_6   1276 ACAGGACTGTTATCCAAAATATACAGATAACTCTTACAAGTCAACAATAA 1325
                          vi     vv      i      i i v           v    i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_63408849_6   1326 GAAAACAA----CCCAATTAAAAAATAGGCCAAAGATGTGAAAAAATACC 1371
                         i  i    ----       ?      i   v  i   v    v i i ii
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_63408849_6   1372 TCACCAAAGAAGGTCTACAGATGGCAAA-AAGCATACAAAA---TGCT 1415
                           v         i v    i     v  -     i ii   ---    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.71 (132 / 77)
Gap_init rate = 0.01 (13 / 892), avg. gap size = 2.15 (28 / 13)  


2455 14.80 1.76 25.84  chr1_63411522_63413968.rev      761  1956 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_63411522_6    761 TGGAAAGACATCCCATATTCATGGATCAGAAGTCTTAATATTGTTAAGAT 810
                                 i       i         ii    v                 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_63411522_6    811 GTCCATACTACCCAAATCAATCTACA-ATTCACTATAATCCTT-TCAAAA 858
                          v v     v       ii       -     viii     i -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_63411522_6    859 TCCCAATGACATTTATTGCAGAAATAGAAAAATTTATCCTAAAATT--TA 906
                              iivi v   v          v  v  ii v           --  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_63411522_6    907 CGGAATCTCAAGGGACCCCAAA-AGCTAAAA-ATTTTTTAAAAAGAA--- 951
                         i    viv          vi  -   i    - v i  v        ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_63411522_6    952 CAAAGTTGGAAGATTCACACTTCCTGATTTCAAAGTATATTACAAAGCCA 1001
                                   i  i          ii        iiv  i        i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_63411522_6   1002 TGGTAATCAAAACAATGTGGTATTGACATAA----AGACAGATGGAACAA 1047
                         ii        i   i       i  i     ----     v  i  v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_63411522_6   1048 TAAAATGGCATAAACAGCCTAGAAATAAACCC-TCCACATAAGGTCAAAT 1096
                          ii   i v  vi v  i i            - v  iv  v      v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_63411522_6   1097 GATCTTTGACAAGAATGTCAAGACCACTCAATGGGGGAAAGGACAGCGTC 1146
                            i  i      ii  i        i         -    i i  iv i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTT 399

  chr1_63411522_6   1147 TTCAACAAATGATGTTGATAAAAGGAGATATTCAAATGCTAAAGAGTGAA 1196
                                    i  i  iv v  vvi    ?i  v    v     i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_63411522_6   1197 ATTAGACCCTTATCTTACATCATATTCAAAAATTAACTCAAAATAGATTA 1246
                         i  i     i  i  i   i     v                  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_63411522_6   1247 AAGACCTAAACATGAGACTCAATACTATAAAATCCCTTGAAGAAGGCCGG 1296
                         ?         ----------------------------------------
  L1M4_orf2#LINE/    500 WAGACCTAAA---------------------------------------- 509

  chr1_63411522_6   1297 GCACAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGG 1346
                         -----------------     ----------------------------
  L1M4_orf2#LINE/    510 -----------------TGTAA---------------------------- 514

  chr1_63411522_6   1347 CAGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTGACCAACATGGAGAA 1396
                         ---------------------------------------------   --
  L1M4_orf2#LINE/    515 ---------------------------------------------GAG-- 517

  chr1_63411522_6   1397 ACCCCGTCTGTACTAAAAATACAAAATTAGCCGGGTATGTTGGCACATGC 1446
                         ------------      v  i    i ----------------------
  L1M4_orf2#LINE/    518 ------------CTAAAACTATAAAACT---------------------- 533

  chr1_63411522_6   1447 CTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGAAGAATCATTTGAACCC 1496
                         --------------------------------------------------
  L1M4_orf2#LINE/    534 -------------------------------------------------- 533

  chr1_63411522_6   1497 GGGAGGTGGAGGTTGCGGTGAGCCAAGATTGCACCATTGCACTCCAGCCT 1546
                         --------------------------------------------------
  L1M4_orf2#LINE/    534 -------------------------------------------------- 533

  chr1_63411522_6   1547 GGGCAACAAGAGCAAAACTCTGTCTTAAAAAAAAAAAATCCCTTGAAGAA 1596
                         -----------------------    -----------------      
  L1M4_orf2#LINE/    534 -----------------------CTTA-----------------GAAGAA 543

  chr1_63411522_6   1597 AACA--GGGGAAAAGTTTTATGACATTGGACTTTGCAACGATCTCTTGGC 1644
                             --  ? v   vi  ii    v    ii vv    i i i    i v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_63411522_6   1645 TATGACAGTGAATGCACA-GTAACTAAAAGCAAAAATAGGCAAATGAGAC 1693
                                vii  v     - i   -     v        ii    vi   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGGAC 642

  chr1_63411522_6   1694 TTCATCAAACTTAAATACTTTTGTGCATAAGAGGACACAATCAACAGAGT 1743
                                  v     v          v v i       v     v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_63411522_6   1744 CAAAGG-CACCCTACAGAATAGGGAGAAAATATTTGCAAATCGTAAACCT 1792
                         v   i -  v  i       -                     i  v i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAAT-GGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_63411522_6   1793 AATAAGGA--TTAAATTCACAATATTTAAAGAATTCCTATGACTCAACAA 1840
                         i      i--  iv  i  v     v       i  i  ii      i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_63411522_6   1841 CAAAAAAGCAAATAAGCTGATTAAAAAATGGA-AAAAGACTTAAATAGAT 1889
                         i     ii       v ii   ?        i-   i  i  i      i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_63411522_6   1890 GTTTCTCCAAAGAGGATGTACAAATTGCCAACAAGCATATGAAAAGATGC 1939
                         i            i   i       v     i     i            
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_63411522_6   1940 TCAACATTACTAATCAT 1956
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (114 / 59)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 15.71 (330 / 21)  


3613 23.15 2.36 0.34  chr1_63561435_63566203.rev     3389  4278 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_63561435_6   3389 TGGGAAAATATTCCATGTTCATGGATTGGAAGAATCAATATCATTAA-AT 3437
                            i  i    i                     v i     ii    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_63561435_6   3438 GTCCATTCTACCCAAAGCAATCTACAGATTCAATGCAATCTCCATCAAAC 3487
                          v v  v  v      vii              i      i i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_63561435_6   3488 TACCAATGATATTCCTCACAGAAATAGAAAAAATAATCCTAAAATTTATA 3537
                          v   iiviiv  ii ii       v  v  iv i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_63561435_6   3538 TGGAACCACAAAAGACCCCAAATAGTCAAAACTATCCTAAGCAAAAAGAA 3587
                              vii   ii     vi     i      v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_63561435_6   3588 CAAAACTGGAGGAATTACATTACACTGACTTCAAT-TTTACTACAGAGCT 3636
                             ii       v i   i v - ii i     v-i        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTC-CCAATTTCAAAACTTACTACAAAGCT 249

  chr1_63561435_6   3637 ACAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGATACCTAGACCA 3686
                                i   i    ii              ii i   i iv    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_63561435_6   3687 -TGGAACAGAATAGAGAACCCAGAAACAAATACACACATCTACAGTGAAC 3735
                         -     i     v    ii       i   iv  i    i  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_63561435_6   3736 TCATTTTTGACAAAGGTGCCAAGAACATACACTGGGGAAAAGAGAGTCTC 3785
                          v     i     i          v   v  v        ii v     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_63561435_6   3786 TT-------TGG----GGGAAAATTGGATATCTATATGCAGAA-AATGAA 3823
                           -------   ----    v  i      ? i i     i  -      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_63561435_6   3824 ACTAAACCCCTATCTCTCATCAGATACAAAAATCAAATCAAAATGGATTA 3873
                         ii ii       i   v  i  v          i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_63561435_6   3874 AAGACTTAAATATACGACCTCACACTATGAAACTGCTCCAAGAAAACACT 3923
                         ?    i     i  v  v  v v     i     vi vv         iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_63561435_6   3924 GGGGAAACTCTCTAGGACATTGGTCTGGGCAAAAATTTCTTGAGTAATAC 3973
                           ? v  v   iiiv   v    vi i     vii      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_63561435_6   3974 TCTACAAGCACAAGCAACCAAAGCAAAAACGGGCAAATGGGA-TCCATGA 4022
                         v i v             v    v     ii ii    v   - i   v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_63561435_6   4023 AGTTTAAAAGCTTCTGCACAGCAAAGGAAGCAATCAACAAAG---ACAGA 4069
                          iv      i   i  ii vv       vi v     v    --- v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_63561435_6   4070 --ACCCACAGAATGGGAGAAAATATGCGCAAACTACCCATCTGACAAGGG 4117
                         --                       vi     ii ivi      i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_63561435_6   4118 ATTAACAACCAGAATATATAAGGAATTCAAGCAACTCAATAGGAAAAAAA 4167
                          i vii v             i   i  vvi          iv     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_63561435_6   4168 ATTAAATAACCCAATTAAAAAATGGGCAAAAGATCTGAATACACATTTTT 4217
                         --i             ?             i   i      v      i 
  L1M4_orf2#LINE/    800 --CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_63561435_6   4218 CAAAAGAAGACATACAAATGGCAAACAGGAATATGAAAAAGTGCTCAACA 4267
                          v        i           v  i i v i       ii         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_63561435_6   4268 TCACTGATGAT 4278
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.77 (129 / 73)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.18 (24 / 11)  


 273 19.30 5.26 0.00  chr1_63607838_63610666.rev     1310  1366 (1463)    L1M4_orf2#LINE/L1        1    60 (848)  

  chr1_63607838_6   1310 TGGAAACACATCCTGTGTTTGTTCATTGGAAGACTAAATATT---AAGAC 1356
                               v i    ii    ii vv           v      ---    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_63607838_6   1357 GGCAATATTC 1366
                                i  
  L1M4_orf2#LINE/     51 GGCAATACTC 60

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 3.00 (3 / 1)  

3891 14.50 9.67 0.64  chr1_63607838_63610666.rev     1553  2338 (491)    L1M4_orf2#LINE/L1       52   908 (0)  

  chr1_63607838_6   1553 GCAATATTCCACAAATTGATATGCAGAATCGACTCAGTCCCTATCAAAAT 1602
                               i   v         v i    v  i  v  i             
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_63607838_6   1603 CTCAGCTGAGTTTTGGGAGAAAACTGATGAACT---TCTAAAAATAATAT 1649
                          i      vv    vv vii   i   ii i  ---i      v v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_63607838_6   1650 GAAAATA-AAGGGATGTAAAATAGATAAAACAATCTTGTAAAAGAA---C 1695
                          i    i-      ivi i     vi            v       --- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_63607838_6   1696 AAAATCAGTGGACTTGCATTTTC-AATTTCAAAACTAACTACAAAGCTAC 1744
                            i ii v     ii  i  i -            v             
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_63607838_6   1745 AGTAAACAAGACAGTATGGCAGTGGCATAAGGATAGACATATAGATCAAT 1794
                              v         i   i v                            
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_63607838_6   1795 GGAACAGAACTGAGATTCCAGAAATAAACCCTTACATTTAAGAACAACTG 1844
                             i    i     v               v        v iv   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_63607838_6   1845 ATTTTCAACAAGAGTGCCAAGACAATTCAATGG----------------- 1877
                               i     i          v         -----------------
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_63607838_6   1878 -AAC---------TGAAATAATTGAATA------------------AAGT 1899
                         -   ---------  ii i  i  i   ------------------    
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_63607838_6   1900 CAGACTCCTACCTCACACCATATACAATA-TTAACTCAAAGCAACTCAAA 1948
                         ii   i                     v -          iiiiv   ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_63607838_6   1949 GGCATAGATTTAA------AAACTATAAAACTCTTAGAAGAAAATACAGG 1992
                          i v  i  v   ------                         i i   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_63607838_6   1993 GGTAAATATTTGTGACCACTGGTTATACAATGGTTTCTTAGATATGACAC 2042
                         ?      v  i      viv     vi                       
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_63607838_6   2043 CAAAAGCACAA----CAAAAGAAAAAAATAGATATACTGGATGTTATCAA 2088
                                    ----            -      v i    iv i     
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAA 650

  chr1_63607838_6   2089 AATCAAAA-CTTTTCTGCTGCAAATGATACCATCAAGAAAGTGAAAAGGC 2137
                            i    -     v    v    v  i  i                 i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_63607838_6   2138 AACACACAGAATGGGAGAGGATATTTGCAAGTTAAATATCTGGTAAGGAA 2187
                            v              ii          i i v       i     i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_63607838_6   2188 CTCATATCAAGAATATATATTAAAAAAACTCTTACAACTCAA------AA 2231
                           ii    v          ----  i                ------  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATA----AAGAACTCTTACAACTCAATAATAAAA 796

  chr1_63607838_6   2232 AGACAA----CCCAGTTTAAAA-TGGGCAAAGGATTTGAATAGGCATTTC 2276
                               ----    i  ?    -                    i      
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_63607838_6   2277 TCCAAAGAAGATATACAAATGGCCGATAAGCACATGAAAAGATGTTCAAC 2326
                                                 i                   i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_63607838_6   2327 ATCATTAGTCAT 2338
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (72 / 39)
Gap_init rate = 0.02 (16 / 857), avg. gap size = 5.06 (81 / 16)  


3989 18.62 1.64 2.58  chr1_63638081_63640768.rev      952  1805 (883)    L1M4_orf2#LINE/L1        2   847 (61)  

  chr1_63638081_6    952 GGAAAGATATTCTGTATTCATGGGCAAGAAGATTTAATATTGTTAAGATG 1001
                                   i ii i       iivi     i                 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_63638081_6   1002 TTAATGCTACTACCCAAAGCAATCTACAGATTCACTGTAATTCCTATATT 1051
                         vi   ---   v      vii             vi i   i     ---
  L1M4_orf2#LINE/     52 GCAAT---ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT--- 95

  chr1_63638081_6   1052 TCTTTTGCAGAATGATTAAACAGCACTTTTTGCAGAAATGGAAAAACCTG 1101
                         -------  i   --iiv i v  vi             v  v  i ivi
  L1M4_orf2#LINE/     96 -------CAAAAT--CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr1_63638081_6   1102 TCCTTAAATTCATATGAAGCTACAGGAGACCCTAAATAGCCAAA-CAATC 1150
                             v           i iv i  i i     vi          -     
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_63638081_6   1151 TTGAAAAAGGA---CAAAGTTGGAAGACTCATATTTCCTGATTTCAAAAC 1197
                                  i ---          i      i i    ii          
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_63638081_6   1198 ATACTACAAAGCTACAGTCATCAAAACAGTATGGCACTGGCGTTAACAGT 1247
                         v                 v     i     i   i      i -  vii 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGAT 285

  chr1_63638081_6   1248 AGCCATAGAGACCAATGGAATAGAATTGGGGGTCCA-AAACAAATGCATA 1296
                           v    v   i                i i     -   i   iv    
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_63638081_6   1297 CATCTATGGCCAGTTGGTTTTTGACAAGGAGGCCAAGTTTATTTAATGGA 1346
                            i     i  i   i    i       iv      vii   i     i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_63638081_6   1347 GAAAGAATAGTCTCTTCAATAAATGTTGCTGGGA-AACAGGATTTCCTTA 1395
                                      i     i     v        -   v    v?  vi 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_63638081_6   1396 CAAAAAAGAATGAAGTTGGATTCCTACCTCACAGCATATGTAAAAATTAA 1445
                         iiv                 ii           v     ii         
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_63638081_6   1446 ATCAAAATGGATCAGTGACCTAAATATAAGGGCTAAAACCATTTATAACT 1495
                         v             ?v         i    i        i  -- v    
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT--AAAACT 533

  chr1_63638081_6   1496 ATCTTAGAGGAAAACATAATGATAAATCTTCATGACCTTGAATTTGTTGA 1545
                         --      i         iv?i         i        ii  v vii 
  L1M4_orf2#LINE/    534 --CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_63638081_6   1546 TAGATTCTTATATAACAACACCAAAAGCACAATGAACAAAAGAAAAAATA 1595
                          i v      v   -ii               vv                
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_63638081_6   1596 ----AATTTGACTTTATCAAAAGTAAAAGCTTTTGTGTTTCAAAGTACAC 1641
                         ----    v     i       v     i        i       v    
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_63638081_6   1642 CATCAAGAAAGTGAAAAGGCAAAGCACAGAATGGGAGAAAATATTTTCAA 1691
                         i                 i   vv                      v   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_63638081_6   1692 ATTATATATCTAATAAGGGTTTAAGGTCCAGAGTAGATCAAGAGCTTCCA 1741
                           i        i       vi vivi      i  v  v    i  iii 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_63638081_6   1742 AAACTCAACAAGAAAAA---AGACAATCCAATTTTAAATATAGGCAAAG- 1787
                         v       i  v     --- i i  i      ?v   -  i       -
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGG 829

  chr1_63638081_6   1788 ACTTGAGTAGATTTTTTT 1805
                          i    i    iv   i 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCT 847

Transitions / transversions = 1.92 (102 / 53)
Gap_init rate = 0.02 (15 / 846), avg. gap size = 2.40 (36 / 15)  

 351 19.51 0.00 0.00  chr1_63638081_63640768.rev     2116  2197 (491)    L1M4_orf2#LINE/L1      827   908 (0)  

  chr1_63638081_6   2116 AGGCCTTGAGTAGATATTTCTTGAAAGAACTTATATAAATTGCCAATAAA 2165
                            vi    i    i      iv      vv    i    v        i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_63638081_6   2166 CACATGAAAATATATTAAATATCATTAGTCAT 2197
                                   v  ii v  i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (9 / 7)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.00 (0 / 0)  


1256 28.30 11.70 1.51  chr1_63691667_63693699.rev      502  1031 (1002)    L1M4_orf2#LINE/L1      112   695 (213)  

  chr1_63691667_6    502 TTTTTT--AGAAATTGA-AAACTGATTTCAAAATTTGTATGGAAAGGCAA 548
                               --         -  i     iii      ii        v    
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_63691667_6    549 GTGACTTGCAGTAGCCAAAACAATTTTGAAAAAAAAGAATGAAGTTGGAG 598
                          v   iiiv i             i        i     ii         
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_63691667_6    599 TATGTACACT----AACT---AGACATGGCATAAAGTGTTGGTAATGAAC 641
                         v ivi     ----  i --- i  v ivi i    ivvii     v  v
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_63691667_6    642 TCAATGTGGTTTGGGCATA----TAGAGAAATAGGTAAATAGAATAGAAT 687
                         v  i      viv      ----    v v    i v   i         
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_63691667_6    688 AGAAAGTCCAGAAATAGACCCA--------------------------CA 711
                         v  i            i     --------------------------  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_63691667_6    712 AAGGTACCAAAGCAGCTCAGTGGGGATAACAGAAGATTTTCTTCC-CAAG 760
                          i   i    ii vii   i      -  --   v v i i   v-   i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGA-AA--GAATAGTCTTTTCAACAAA 408

  chr1_63691667_6    761 TGGTGCTGG--CA------TACCCAGTGGGGAAAAAAACAAAACACCTTG 802
                                  --  ------  ?   -iiv v    i  ii  ii--- v 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCA-CATGCAAAAGAATGAAGT---TGG 454

  chr1_63691667_6    803 ACCTTCACCTTATATTACATACAAAAATTAATTTGAGATACATTTTAGTC 852
                            iii    i i ii i             i ii i  iv  iv?  v 
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_63691667_6    853 CTAAATGTAA-----AAAGG---AAAGTTTCTGGAGGGAAATATTTGAGA 894
                                   -----   iv---   ii ii i  i i   i  vv ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_63691667_6    895 ATATTTTTACAGTCTGAAGT-AGGTGA-AATTTC--AGGCAAGACGCGGA 940
                          v  i  iiiiii  vii  -   ii -ii    --  ii v   i vi 
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_63691667_6    941 AAGCAATAATTATAAAAGAAAAAAT-GATAAATTATGCTTCATCTAACTT 989
                              vv iiv i            -        ivi       v  v  
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_63691667_6    990 TTAAACTTTTGCTCATCAAGAGATACCGTTAAAAAAAGTAAA 1031
                         vv         iv v    ii  i  ii i  i   -  i  
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA-GTGAA 695

Transitions / transversions = 2.20 (101 / 46)
Gap_init rate = 0.03 (20 / 584), avg. gap size = 3.50 (70 / 20)  

 495 25.26 3.09 1.03  chr1_63691667_63693699.rev     1345  1538 (495)    L1M4_orf2#LINE/L1      685   882 (26)  

  chr1_63691667_6   1345 AAAAAAGTAAATTTTCAAACAACTGACTGGGAGAAAGTATGTAACAGAT- 1393
                           i     i  vvvv   v v  v  v         i   v -i  i  -
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATC 733

  chr1_63691667_6   1394 ATATATCAGACAAAGGATTTATATTTAGGATA-AGAAAGAACTCTTACTA 1442
                                v  i  i   i  i   ii  i   - v             v 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_63691667_6   1443 ATCAACAGTAGAAAGACAAA-AATGTTATTAAAATAATGGCCCAAAGATT 1491
                         v    i i  i         -  iviv   ?   -     v v  i    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATT 832

  chr1_63691667_6   1492 TGAACCAATAGTTAATAAAAGAAGATACACAAATGAACCATAA---CATG 1538
                             ivi i v  vviv          i       iv v    ---    
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

Transitions / transversions = 1.00 (24 / 24)
Gap_init rate = 0.03 (6 / 198), avg. gap size = 1.33 (8 / 6)  


3373 18.61 3.33 0.97  chr1_63719900_63721611.rev      502  1221 (491)    L1M4_orf2#LINE/L1      172   908 (0)  

  chr1_63719900_6    502 ATATCCAAAATATTTTGCTGTTGAAAACGAATAAAGCTAGAGGACTCAGA 551
                            v      i v i --  vvi  i v   i    i i         v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCT--TGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_63719900_6    552 CTTTCTGATTTCAAAACTTACTACAAAGATACAGTAATCAAAAGGGTGTG 601
                            i ii                     v            i vi     
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_63719900_6    602 GTACTAGCATGAAAACAGACATACAGAACAATAGAACAGAATGGATAGCC 651
                              i    i ii i       i   v    i   i     v  v  i 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_63719900_6    652 CATAAATAAATCCTTGCCTATATGGTCTAATGATTTTCAAAAAGGGTGCC 701
                           v       i  v i v v       v v        i v         
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_63719900_6    702 AAGATCATTCATTGAGGGCAAGGACAGTCTTTTCAACAAATGAGGCTGGG 751
                             i      v  -   v   i i                 iv      
  L1M4_orf2#LINE/    370 AAGACCATTCAATG-GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_63719900_6    752 AAAACTGAATATCCATCTGCAAAAGAATAAATTTGGGCTCTTATCTTATG 801
                          v     i   ?   iv           i  v    i i i  i  i ii
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_63719900_6    802 CAACACATAAAAATTAACTCAACCTGAA-----GACCTAAATAT----GC 842
                          v i i i              vv  i -----         i ----  
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_63719900_6    843 TAAAATTATAAAACTCTAAGAAGAAAACATAGGGGGAAAGCT----GACG 888
                              i           v               ? v   v  ----   v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_63719900_6    889 CTGGATCTGGCAATGGTTTCTCAGATATGACAACAAAAGCACAAGCAACA 938
                         i   i iv             i          v                 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_63719900_6    939 AT--------CAAATAAATTGGAATTCATCAAAATTAAAAACTTTTGTGC 980
                          v--------i i          v                          
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_63719900_6    981 ATCAAAGGACACTACCAACAGAATGAAAAGGCAATTCATGAAATGGGAGA 1030
                         v             i   v i i       i   ii  iii         
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_63719900_6   1031 AATTATTTGCAAATCACATATCCAAAAAGGGATTAATATATAGAGCATAT 1080
                           v             i     ii v      i vi   vi   ii    
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_63719900_6   1081 AAAGAACTCCTACAATTCAACAACAAAA---CAAACCACCAGATTTTTTA 1127
                                  i     i    i  i    ---    iv   vi   ?vv- 
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA-A 817

  chr1_63719900_6   1128 AATGGGCAAAGGAATCATCAAATGATCACCTCTCTAAAGAAGATATATAG 1177
                                      - -- ii   iiv  ii    i            i i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGA-T--TTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_63719900_6   1178 AAGGCCAATAAGCAAATGAAGAGATGCTCAACATCACTAATCAT 1221
                          v            v     i               ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (83 / 48)
Gap_init rate = 0.01 (10 / 737), avg. gap size = 3.10 (31 / 10)  


3034 24.97 1.39 4.48  chr1_63756991_63763791.rev     5374  6310 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_63756991_6   5374 TGGAGAGCAATACTATGTTCATGAATTGGAAGAGTCAACATAATAAACAT 5423
                             i  vv  v i         i         v i  i  vi v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_63756991_6   5424 GCCAGTTCCCCCCAAAT-GATCAATACAG--TTAACACAATACCAGTTAA 5470
                          v  i v i        -    --     -- i   i    v  vi i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATC--TACAGATTCAACGCAATCCCTATCAA 98

  chr1_63756991_6   5471 AATCCCAGCAGGATTTATTTTTTGTAGATATAAACAAGCCAGTTCTAAAA 5520
                                  v ----iv       i   v  vi      iii i      
  L1M4_orf2#LINE/     99 AATCCCAGCTG----CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_63756991_6   5521 TTTATATGAAAAGGGAAAGAAACTAAAATAGCTAAGATGATTCTGGAAAA 5570
                           i     i   v v  i i v i i      i  i ii  ii  i    
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_63756991_6   5571 GAACAGTACCATTGGGGAAATCATGTTACCTGAATATAAGACTTACAATG 5620
                            v ii vvi    i i v   iii v  ii v vi  i      v ii
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_63756991_6   5621 AAGCTACTGTAATCAGGACAATGTAGTATTAGTGAAGGGAAAGACACATC 5670
                                v       i    i   i   i i iiv i   v     i  v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_63756991_6   5671 GATCAATGGAACAGAAT--AGAGTTCAGAAATAGACTCATGCAAAGATAT 5718
                                    i     --     i        i  i   i  -------
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA------- 337

  chr1_63756991_6   5719 GGTTCTATATGACCAGTGAATTTTTCAACAAAGGTAC-AAGAGCAATTTA 5767
                         --  ---    ii  i vi     - i    i   i -    v  -  i 
  L1M4_orf2#LINE/    338 --TT---TATGGTCAATTGATTTT-CGACAAGGGTGCCAAGACCA-TTCA 380

  chr1_63756991_6   5768 ATGGAGAAAGGATAATCTTTTCAACCGATGATATTGGAATAACTG-ACAT 5816
                             i     i   i          vi   i ii   i i     - i ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_63756991_6   5817 CCATATGAAAAAAAATGGACCTCAACCTAAACCTCAGAACTCATACAAAA 5866
                            i   v    i    i vi vi   ivv      v v vi        
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_63756991_6   5867 ATTAACTCAAAATGCATCACACATATAAATGTATGAAGTAAAACTATACA 5916
                                       v    ? v iv        v  iv          v 
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_63756991_6   5917 ACTTTTAGAAGAAAGCAGAAGAA-AAATCTTTGTGACCTGGGGTTAGACA 5965
                            i          i  v i ?i-       i       v       i  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_63756991_6   5966 ACGACTTCT--AACTTGACACCAAATGCATAATCCATTAAATGAAAAACT 6013
                          i ii    --i iv          v   i  v v iv   vi     iv
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_63756991_6   6014 GATTAATTGGACTTCATCAAAATGTAAAACTTTCACTCTCTATACGATCC 6063
                            v                   vv        iiiv  ii v v  iv 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_63756991_6   6064 AGTTAAGAGAACAAAAAGACTATCTACAGAAGAGAAGAAAATACTTTCAA 6113
                         vi i    i iii       v i i      vi i        i  v   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_63756991_6   6114 ATAACATATCCAATAAAAGGC--ATATCCAGAATTTATAAAGAATCAAAT 6161
                           v i     ii    ii i --i          v         ii----
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT---- 776

  chr1_63756991_6   6162 GGTAAGAAAATGAAACTCAAAACTCAACAGTAAGAAAACAAATAACCTAA 6211
                         ---------------  i v       i i   i  i          i  
  L1M4_orf2#LINE/    777 ---------------CTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_63756991_6   6212 TTTCAAA-TGGGCAAAAGGCTTGAAGAAGCACACCATCAAAAAGTATACT 6260
                           ?v   -        i ii     v ii  ivi vi    i iv   - 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA-T 860

  chr1_63756991_6   6261 ATGTATGCAGATGACAAGCCTATGAAAAGTTGTTCAACATCATTAGCCAT 6310
                          iiv   -- vii i    vi        v  i         ????????
  L1M4_orf2#LINE/    861 ACAAATG--GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (151 / 79)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.06 (55 / 18)  


1185 13.57 0.00 4.07  chr1_64233963_64237457.rev     1775  1995 (1500)    L1M4_orf2#LINE/L1        1   212 (696)  

  chr1_64233963_6   1775 TGGAAAGACATCCCATGTTCATGGATTAGATGACTTAATACTGTTGAGAC 1824
                                 i                  i  v         i    i   i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_64233963_6   1825 AGCAGTACTCCCCAAATTAATCTACAGATTTAATGCCATCCTTATCAATA 1874
                         i   i             i           i  i  v    i      v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_64233963_6   1875 TTCCAGCTGACTTTTTGGTGGCATAAATTAATAAGCTGACCCTAAAATTC 1924
                          i       v      --  -  v     i i       i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT--TG-CAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_64233963_6   1925 ATATGGAAATGCAAAGCACTCAGAATAACAACAACAACAAAAGTCTTGAA 1974
                                       i v  i       i --   -     ---       
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGC--CAA-AACAA---TCTTGAA 191

  chr1_64233963_6   1975 AAAGAACAATATAGAAAGAGG 1995
                               v  i v  vvi    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGG 212

Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.02 (5 / 212), avg. gap size = 1.80 (9 / 5)  

3055 14.87 10.95 1.41  chr1_64233963_64237457.rev     2366  3004 (491)    L1M4_orf2#LINE/L1      209   908 (0)  

  chr1_64233963_6   2366 GAGTACTCATATTTCCTGATTTCAAAACTTACTACAAACCTATAGTAATC 2415
                            v     i i    ii                    v   i       
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_64233963_6   2416 AAGACTATGTAGAACTGA-ATAGGGATAGACACATAGA------------ 2452
                              vi   i v    i-   i         i     ------------
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_64233963_6   2453 -----------------------CACATGTTTA------ATTGGTTT--A 2471
                         -----------------------  i ii    ------    i   --i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_64233963_6   2472 ACA-GAGTGCCAAGACAATTCAATGGGTAAAGAATGGTCTTTTCATCAAA 2520
                            - i          v          v       i         v    
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_64233963_6   2521 TGATATTGGAACAACAGGATATCCACATGCAAAAGAATGAACCTGGACTC 2570
                           i ii   i     v     ?                   vi     i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_64233963_6   2571 CCACCTCACACACTGTATACAAAAATTAATTCAAGATGGACCAAAAACCT 2620
                          i         --ii              i    i     i  ? i    
  L1M4_orf2#LINE/    459 CTACCTCACAC--CATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_64233963_6   2621 AAATGTAAGAGCTAAAACTGTAAATAAAAACTTTTAGGAAAAAAACAGAG 2670
                                            i    -----   i    -  i      v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAA-----ACTCTTAG-AAGAAAACATAG 550

  chr1_64233963_6   2671 GAGTAAATCTTTGTACGCTTGCATCAGGCGATGGTTTT------------ 2708
                          ?         i  ivv    vi i    i       i------------
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_64233963_6   2709 -CAAAATCACAACCAACCAAAGAATGGGTA-ATAAATTGAATGTCATCAA 2756
                         -     v     v    v      viii  -        i iv       
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_64233963_6   2757 AATGAAAAACTTTTGTGTTTCAAAGAACACTATCAAGAAAATGAAAAGAC 2806
                            v             i       i              i         
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_64233963_6   2807 AATCCATAGAATG----AAAATATTTGCAAATCATATATCTAATAAGGG- 2851
                           i   i      ----                        i       -
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_64233963_6   2852 TATATACCCAAAATA----AGTAACTCTTACACCTCAAGAATAAAAAGAC 2897
                         iv i  i   i    ---- iv          v     v           
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_64233963_6   2898 AATTAATTCAATTTAAAAAATGGGTAAAAAGTTTGAACAAACATTTCCCC 2947
                           v   ii     ?     -    i   iii      i i       i  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_64233963_6   2948 AAAGAAAACATA--AATGGCCAATATGCACATGAAAAGATGCTCAACATC 2995
                               i i   --           v                        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_64233963_6   2996 ATGAGTCAT 3004
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.64 (66 / 25)
Gap_init rate = 0.02 (15 / 700), avg. gap size = 5.27 (79 / 15)  


3276 27.09 0.44 0.44  chr1_64450631_64457038     5008  5915 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_64450631_6   5008 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5057
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_64450631_6   5058 GGCTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5107
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_64450631_6   5108 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5155
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_64450631_6   5156 TATGGAATCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5205
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_64450631_6   5206 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5255
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_64450631_6   5256 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGATG 5305
                                 i   i    ii  i      i iv ii i   v        v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_64450631_6   5306 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5353
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_64450631_6   5354 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5403
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_64450631_6   5404 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5453
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_64450631_6   5454 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5503
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_64450631_6   5504 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5553
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_64450631_6   5554 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5603
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_64450631_6   5604 AACACCAAAAGCAACGGCAATGAAAGCCAAAATTGACAAATGGGATCTAA 5653
                         i            vvi    ii    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_64450631_6   5654 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5703
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_64450631_6   5704 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5753
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_64450631_6   5754 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5803
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_64450631_6   5804 AAACAAACAACCCCATCAATAAGTGGGCAAAGGATATGAACAGACACTTC 5853
                          i     i     v  i? v  i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_64450631_6   5854 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5903
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_64450631_6   5904 ATCACTGGCCAT 5915
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


4546 17.08 3.05 0.34  chr1_64537591_64539705      741  1624 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_64537591_6    741 TGGAAAGACAGCCCACATTCATAGACTGGAAAACTTACTAGTGTTAAGAT 790
                                 i v    ii     i  i     i     v  v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_64537591_6    791 GTTACCACTATGCAAAGTGATATACAGATCCAATGCAATCCCTATTAAAA 840
                          vi vi   viv    v    v       i   i           i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_64537591_6    841 TTTCAA-TGATGTTTTTGCAGAAATAGAAAAACCCGTCCTAAAATTCATA 889
                          ii  i-  viv             v  v  i ivi              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_64537591_6    890 TGGCATCTCATGGGACCCCATATAGCCAAAACAACATTGAAAAAAAACAA 939
                            v viv  v       viv             iv        i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_64537591_6    940 TA---TTGG---TCTCACATTTCCCGATTTCAAAACTTTCTGCAGTGCTA 983
                         i ---    ---v      i     i            v  i  iv    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_64537591_6    984 CAATAATCAAAACAGTCTAGTACTGGTATAAAGACAGACATACAGAGCAA 1033
                           i       i     v i       i    i  i       i   v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_64537591_6   1034 TGAAATAGAATAGAAAGCCCAGAAATAAATCCTCCCACTTAAGGTCAAAT 1083
                           i        v  i  i           i  viv  i   v      v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_64537591_6   1084 GATTTTCAACAAGGGGGCCAAGACCATTCAATAGGTAAAGGACAGTCTTT 1133
                                i       v                i  v    i i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_64537591_6   1134 CCAACAAATAGTGTTGGGAAACTTGTATATCCACATGCAAAAGAATGAAG 1183
                         i        i   i     v vi  v   ?                    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_64537591_6   1184 TTGAACCCTTAGTTTCTGCCATATATAAAAAT------------------ 1215
                            i    i  vi ivii       i      ------------------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_64537591_6   1216 -GACCAAAACATAAGAGCTAAAGCTATAAAATTCTTAGAAGAAAACATAG 1264
                         -    v   ii           i        i                  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_64537591_6   1265 GGCAAAACCTTCATTGTATTGGATTTAGCAATGATTTCTTGGATATGAAA 1314
                          ?vv   i    i viiv    i  vi      i      i       v 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_64537591_6   1315 CCAAAAGTACAAGCAACAAAAGAAAAAAATAGATAAATTGGACACTATCA 1364
                                i                    -              vii    
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCA 649

  chr1_64537591_6   1365 AAATTAAAAACTTCTGTGCATCAAAGAATACCATCAACAAGGTAAAAAGG 1414
                                      i     v      i i  i     v  i  i     i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_64537591_6   1415 TAACCCACCAGAATGGGAGAAAATATTTGCAAATCACATATCTGATAAGG 1464
                         i       -                           i             
  L1M4_orf2#LINE/    700 CAACCCAC-AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_64537591_6   1465 GATTAATATCCAGGATATCTAAATAACTTTTACAACTCAACAACAAATAC 1514
                           i vi       i    v    v    i           i  i   v v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_64537591_6   1515 ACAAATAACCCAGTTCAAAAATGAGCAAA-TATTTGAATAGACATTTCTC 1563
                                     i  ?       i     -v                   
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_64537591_6   1564 TAAAGAAGATATGCAAATGGCTAAATAAGCACATGAAAAGATGCTCAACA 1613
                         i           i        i  -                         
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGATGCTCAACA 897

  chr1_64537591_6   1614 TTTCTAATCAT 1624
                          iv????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.64 (92 / 56)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.75 (30 / 8)  


2332 24.66 6.81 1.77  chr1_64939261_64941602      726  1459 (883)    L1M4_orf2#LINE/L1        1   771 (137)  

  chr1_64939261_6    726 TGGAAGAACATTCCACATTTGTGGATTGGAAGACTCAGTATCATTTAGAT 775
                              ii i  i   ii  ii              i i   ii  v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_64939261_6    776 GTCAGTTGTTCCCAAACTGATCTATAGTGTCAATGGAATCCAC-TCAAAA 824
                          v  i vv i      i       i  vv    i v     vi-      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_64939261_6    825 TCCTAGTAGGTTTTTTTTTTAA---TGA-AAACTGATTCTAAAATTTGTA 870
                            i  iv vi      vivi ---   -  i     i        ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_64939261_6    871 CAGAAATGCAAGTGACCTGGAATAGCCAAGATACTTTTGAAAAAAAAAAA 920
                         ii          v    ii          i i v i        i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_64939261_6    921 ---ACTTGGAAGACTTACACTACCAGATTTCAAAGCTTACTATAAAGCTC 967
                         --- v     i    i     v  vi        i       i      v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_64939261_6    968 AAATAATTTGTTCAGTGTGATATTGGTACAGTGACTAGACAAGTACACTA 1017
                         v i    ivivv       i  i   i i iv  -      vi  v ii 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCA 299

  chr1_64939261_6   1018 GTGGGACAGAAT--AGAGTCCAGAAATTAACCCACAGAAT-ATAG----- 1059
                         i   i i     --             v      i v v -  i -----
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_64939261_6   1060 -------CAAC-----------------TCAGTAGTAGAAAGAATAGTCT 1085
                         ------- i  -----------------   i i -i             
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCT 398

  chr1_64939261_6   1086 TTTCAACAGATGATGCTAGGGCAGTTTGATATTCAAAT-CAAAAAAATTG 1134
                                 i   i    i  i  ii v    ?i  v  -     i   - 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT-G 447

  chr1_64939261_6   1135 AACCTTGACCCCTACCTAATACCACTTAGAAATATTCTATTAAGATGGCT 1184
                           vi v           v i    iv  v   v   vvv i  i    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_64939261_6   1185 TATAG-TCTAAATGTAAATGTTAAGACAATAAACATTCC-AGAAGAAAAG 1232
                         i ?  -i          iv i   i  v     - i  i-         v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chr1_64939261_6   1233 ATAGATCAGTG--TCTTCATGACCTTGGGT-AGGTAAAGATTTCTTAAAG 1279
                             i?--  i--     i           -   i  v i       i v
  L1M4_orf2#LINE/    547 ATAGGN--GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_64939261_6   1280 AGGTCACAAAAGGCATTAACCAGAAAAGAAGATATTATATGATAGATGGG 1329
                          v v   v   i   iv i v v       i - --   -    i  v  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAA-A--ATA-GATAAATTGG 640

  chr1_64939261_6   1330 ACTTTGGCAAAATTAATGTCTTCT-TA-TCAAAAAGACATTACTAATAAA 1377
                             iiv         viv   i - i- iv   i    i  ii  v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_64939261_6   1378 -TCAGTAGGCAAACCACAGGCTAGATGAGGATATTTGCAATACCA-ATAT 1425
                         - v iv  i   v      iv i iv  ii          - i  -    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATAT 739

  chr1_64939261_6   1426 TTGACAAAGGAGACTGATATCCAGAATTTATAAA 1459
                         i   i  i   --  vi          v      
  L1M4_orf2#LINE/    740 CTGATAAGGGA--CTTGTATCCAGAATATATAAA 771

Transitions / transversions = 1.78 (114 / 64)
Gap_init rate = 0.04 (27 / 771), avg. gap size = 2.33 (63 / 27)  

 262 22.58 12.90 0.81  chr1_64939261_64941602     1749  1872 (470)    L1M4_orf2#LINE/L1      770   908 (0)  

  chr1_64939261_6   1749 AAAAATTCT-ACGAGTTAATAA--AAAAGA----TAACCCAGTT-AAAAA 1790
                           i  i   -  i v i     --      ----       i  -     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_64939261_6   1791 TAGATGAAAGATTACAACAGGCATTTCACAAAAAAGGAATATCCAAATGG 1840
                          i iii  i    vv  i  i      v v   i i  -   v       
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA-TATACAAATGG 868

  chr1_64939261_6   1841 C--------ATATTAAAAGGTCAGTAATATCATTATAAGT 1872
                          -------- i  v     i vvvi  i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.04 (6 / 139), avg. gap size = 2.83 (17 / 6)  


2858 22.52 7.27 2.42  chr1_64971804_64975511.rev     2352  3217 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_64971804_6   2352 TGAAAAGATATACCATACTTATGGATCAGAAGCCTCAGAATTGTTG---T 2398
                           i        v    ii i      ii    v  i iv      i--- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_64971804_6   2399 G--AATTCTGCCTAAATTAGCATACAAAT-CAACACAATCTCAATCAAAA 2445
                          --   v  v  i     iiiv    i  -    i     i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_64971804_6   2446 TCCCAGCCGACATTTTTCATAGAAATTGGCACTCTGATTCTAAAATTTAT 2495
                                i v -     iii        i  vv     i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_64971804_6   2496 AAGTCAATGCAAAGAACCTGGAATGGCCAAA-CAACTTTGAAAAAGAAGA 2544
                          v vv       i i   ii    i      -   ii             
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_64971804_6   2545 ATAAAGTTGAAGGACTTACACTAACTGATTTCAGGATTTATAACACA--T 2592
                          i       i      i     vv ii      ii i   iv   v -- 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_64971804_6   2593 ATATTTTGGTA-TAGAGACAGTATTGATATAAAGACAGTACTGGTA-AAA 2640
                          i -----   - vi       i ------------i       i -  i
  L1M4_orf2#LINE/    250 ACA-----GTAATCAAGACAGTGT------------GGTACTGGCATAAG 282

  chr1_64971804_6   2641 GACAGACATTTAGGTCAATGAAC--------ACAGTTTAGTTATAGCCTC 2682
                           i      v   i      i v-------- v   ii  vv   iv i 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_64971804_6   2683 ATGCATATATGGTGAACTGATTTTTGGGAAA--TGTCAAAAT-ATTCAAT 2729
                           i   v      v  i       i iv  i--  i   i i-       
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_64971804_6   2730 G---AAACATTA-TCTTTCTAAACAAATGATGCCAGAATAATTGTATAAC 2775
                          ---   v v  -     - v        i   ii i i  i  v   ? 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTT-TCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_64971804_6   2776 TATATGTAAAAAAA-AAATCTGGACTCTTACCTCATACTACAAACTAAAA 2824
                         i i   i    i  -i  vi     i i       i  i i v  v    
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_64971804_6   2825 TTAACTCAAAATAGATCATAGACCTAAATATAGGGATAAAAATTATAAAA 2874
                                     i     ?          i  i iiiv    i       
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_64971804_6   2875 CTTTCTCCAAGAAAACATACAAGAAAATCTTAGAAAACCTGAATTTGGCA 2924
                           i - vv           vi? v       v vi v i  ii  v    
  L1M4_orf2#LINE/    532 CTCT-TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_64971804_6   2925 AAGATTTCTCAAATATGACACAGGAAGTACAAATTATAAAAGAAAAAATA 2974
                          v i     i i         vii   i    iiv i             
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_64971804_6   2975 -ATAAATTGGATTTTGTCAAAAT-AAAAAATTTTGCTCCTCAAAAGACAC 3022
                         -          i  ii       -     v     iv i     i     
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_64971804_6   3023 TGTTAAAAAA------------------------------ATATTTGCAA 3042
                          i i  i   ------------------------------          
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_64971804_6   3043 ACCATATATCCAACAGAGTACTTGTATGTAAAATAAA-AAAACACTCTTA 3091
                          i        ii i ii v        vi i    v -   iv       
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_64971804_6   3092 CAACT---TGATAAGAAGACAAACAACTCAGTTTTTAACACGTGCAAAAT 3138
                              --- i    i        i   i  i  ?v-  v i v     iv
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGG 829

  chr1_64971804_6   3139 ATTTGAAAAGACATATCACCAAAGAAGATATAAAGATGACAAATAAGCAC 3188
                                v      v  v              v i   i v         
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_64971804_6   3189 AATAAAAGAAGCTCAAAATCATTAGTCAA 3217
                          vv      v      v    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (126 / 65)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.50 (84 / 24)  


3273 27.01 0.44 0.33  chr1_65300118_65303223.rev     1709  2615 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65300118_6   1709 TGGAAGAACATTCCATACTCATGGATAGGAAGAATCAATATCATGAAAAT 1758
                              ii i  i    ii        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65300118_6   1759 GGCCATACTGCCCAAACTAATTTATAGATTCAATGCCATCCCCATTAAGC 1808
                            v     v      i i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65300118_6   1809 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1856
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_65300118_6   1857 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAG 1906
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_65300118_6   1907 AACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTATACTACAAGGC 1956
                                i     ivv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_65300118_6   1957 TACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2006
                                 iv  i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_65300118_6   2007 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 2056
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_65300118_6   2057 CTGATTTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 2106
                         i       i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_65300118_6   2107 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTATATGCAGAAAGCTGA 2156
                         v  i  i              v      v  ? i i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_65300118_6   2157 AACTGGGTCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 2206
                          ii   ii    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_65300118_6   2207 AAAGACTTAAATGTTAGACCGAAAACCATAAAAACCCTAGAAGAAAACCT 2256
                          ?    i       v   v v     i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_65300118_6   2257 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 2305
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_65300118_6   2306 ACACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 2355
                                  i  vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_65300118_6   2356 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGGACA 2405
                         i   v v  i i   i  ii vv    i  v  i i  vv i    i v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_65300118_6   2406 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 2455
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_65300118_6   2456 GGGCTAATACCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 2505
                           i  vi  i       v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_65300118_6   2506 ATCAAACAACCCCATCAAAAAGTGG-CAAAGGATATGAACAGATACTTCT 2554
                         iv    i     v  i?    i   -        v    i   i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_65300118_6   2555 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCTTCA 2604
                          v        i  vi viii     i ii          i      vv  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_65300118_6   2605 TCATTGGTCAT 2615
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


1749 24.46 5.70 3.52  chr1_65428352_65430326.rev      502  1098 (877)    L1M4_orf2#LINE/L1      197   806 (102)  

  chr1_65428352_6    502 AAAATAAAATGGGAGGAATCACTCCACCCAAACTTGAAGCCTACTGTAAA 551
                          i  i   i v      v    v iv     vi ii  i i    ii   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_65428352_6    552 GGTACAATT-TCAAAAACCGTGCAGTGTTGGCAGAAAAATAGACACATA- 599
                          v    i v-    i - v   ii  ii     v  ii       i   -
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_65428352_6    600 -TCAACGGAACAGAATAAAGA-CCCAGAAATAGAATGGACCCACGTAAAT 647
                         -    i    i     vi   -i         i -----    iii vv 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-----CCCATACATTT 340

  chr1_65428352_6    648 CTGTCCAACTAATTTTTGACAAAGG-ATCAAAAGCAATTCAGTGG--AAG 694
                         v  vi   i i     i     i  -ii   i v  -    i   --  i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAA 389

  chr1_65428352_6    695 AAATGTGCTTTTTCAACAAATGATGTTGGAGCAATTGGACATCCATAGGA 744
                         i   i- ii             i  i   ii   i    i ?   i v v
  L1M4_orf2#LINE/    390 GAATA-GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_65428352_6    745 AAAAAAAAAAAGAGAGAAAATCCAGGACCCAAACTTCATACCTTATACAA 794
                             i  vi   -------- i--      vv  i   i   v       
  L1M4_orf2#LINE/    439 AAAAGAATGAAG--------TT--GGACCCCTACCTCACACCATATACAA 478

  chr1_65428352_6    795 AAATCAAGTCAAAATGGATTCTAGACTTAAATGTAA-------AACTATA 837
                             i  v           iv?    i         -------       
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_65428352_6    838 AAACT--TAGAAAGAAA--TAGGAGAAAATTTTCTAGT-ACCCAGAGCTA 882
                              --     ii   --    ? v    i   --  -   iv i i  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTC--GTGACCTTGGGTTA 576

  chr1_65428352_6    883 TACAAAGAGTTCTGTGGCT-TGTTACCAAAAGCACAA----TAAGAGGAA 927
                         vi   v iv    - i v -  vi             ----i  i  i  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCT-TAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_65428352_6    928 AAATTGATATGTTGGACCTTATCAAGATTA----TTTTTGCTCTGTGAAA 973
                             v    vi      i i     i    ----i     iv  vii  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_65428352_6    974 GACCCTGTTAAGAAGATGAAAAGACATACTACCAACTGGGC-AAAATACT 1022
                            v  i i     ii          vv i  vi v    v-      i 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_65428352_6   1023 TG-AAACCACATAGCCAACAAAGGA---GTATTTAGAATATGTAAAGAAT 1068
                           -   i  i   v ii i  i   ---    ii       i       i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_65428352_6   1069 TCTCAAAACTCAGCATTAAAAA-ACAAACAA 1098
                            i v      ii v      -     i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAA 806

Transitions / transversions = 2.33 (100 / 43)
Gap_init rate = 0.04 (24 / 610), avg. gap size = 2.29 (55 / 24)  

 230 25.00 11.54 0.00  chr1_65428352_65430326.rev     1383  1486 (489)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr1_65428352_6   1383 AAAAAAAAAAA------AATT--AAAATGTGCAAAAGACATAAACGCATA 1424
                              i v   ------    --      v     i  iv i  iiv i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_65428352_6   1425 TTTCCCTGAAACAGATACATAGAT----AACAAGCATATGAAAAGAAATT 1470
                             i ii  iv     i i i  ----  i     i         vii 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_65428352_6   1471 CAACATTGTTAGCCAT 1486
                               ii????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 3.33 (20 / 6)
Gap_init rate = 0.03 (3 / 116), avg. gap size = 4.00 (12 / 3)  


3216 25.58 1.10 1.10  chr1_65550734_65555406.rev     3276  4182 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_65550734_6   3276 GGAAAGGTATTCCATGCTCATGGATTAGAAGAAATAATATTGTTAAAATG 3325
                               i   i     i         i     vv            i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_65550734_6   3326 GCAATACTACCCAAAGCAATGTACAGATTCAATGCAATCTCTATCAAAAT 3375
                                 v      vii  v           i      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_65550734_6   3376 GCCAATGACATTCTTCACAGAAATAAAAAAA--AACCCCTAAAATGTATG 3423
                         v   iivi v  i  ii       vi v  i--i i  -      vi  i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC-TAAAATTCATA 150

  chr1_65550734_6   3424 TGGAACCACAAAAGACTCCAAATAGCCAAAGCCACCCTGAGCAAAAAGAA 3473
                              vii   ii   i vi          i v i i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_65550734_6   3474 CAAAGTTAGAGGCATCACATCATCTGACTTCAAAGTTTTTTACAAAGCTA 3523
                                i    vv     iivi ii i      ii  vi          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_65550734_6   3524 CCGTAACCAAAACAGCATGGTACTGGCATAAAAACAGGCACATGGACTAA 3573
                          v    i   i    ii              ii i  i  i  i  ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_65550734_6   3574 TGGAACAAAATAGAGAACCCAGATATAAGTCCACGCATTTACCACCAATT 3623
                              i i   v    ii     v    ii   ii      ivii     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_65550734_6   3624 CATCTTTGACAAAGATTCTAAGAACTTACAGTGGG-AGAGGACAGTCTTT 3672
                         v  i  i     i i v i    v v v  i    - i  i i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_65550734_6   3673 TCCATAGATGGTGCTGGGAAAAGTGGGTAACTATATGCAGAAAAATGAAA 3722
                           v i i            v  v   i  ? i i     i  i      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_65550734_6   3723 ATAGACCTATATCTCTAACTATATATAAAAATCAAAT-AAAATTGATTAA 3771
                         v i    iv  i   vv  i     i      i  v -     v   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_65550734_6   3772 AAACTTGAATCCAAAACCCAAAAATATAAAATGACTAGAAGAAAACATTA 3821
                          i  i i   vi  i v i    v       ivvi             vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_65550734_6   3822 GAG-AAATGTTCCAGGACATTGATCTGGACAAAAATTTCTTGTGGAAGAC 3870
                          ? -    v   -iv   v   ivi i i   vii      iviv v   
  L1M4_orf2#LINE/    551 GNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_65550734_6   3871 CTCAAAAGCACACACAACCAAAGCAAAAATACACAATTGGGACTATAT-G 3919
                         vi          vi    v    v       v i  v v     vi  -i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_65550734_6   3920 AAGCTAAACAGCTTCTGCAAAGCAAAGCAAACAATCAACGAAGTGAAGAG 3969
                           ii    - i   i  iivvv     v v  v     vi       i  
  L1M4_orf2#LINE/    650 AAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_65550734_6   3970 ACAACCCACTGAATGGCAGGAAATACTTGTGAACTATTCATTTGACAAGA 4019
                                  v      v  i     i   ii  ii  vi  i   i   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_65550734_6   4020 AATTAATAACCAGAATATATAAGGAGCTCAAACAACTCAACAATAAAAA- 4068
                         i i vi  v             i  i   vv         i        -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_65550734_6   4069 --AAAAAAACAAATTAAAAACTGGGCAAAAGAGTTGAAGAGA-ATTAACA 4115
                         --   v  v v    ?    v        i  v     v   -   ----
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT---- 844

  chr1_65550734_6   4116 GATCTTCCAAAGAAGACATAGAAATGGCATACAGTTATATGAAAAAATGT 4165
                         --   -          i   v       vv i ivi i       i   i
  L1M4_orf2#LINE/    845 --TCT-CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_65550734_6   4166 CCAACATCACTAATCAG 4182
                         i        ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (145 / 83)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 1.67 (20 / 12)  


3136 27.64 0.55 0.55  chr1_65628232_65634513.rev     4884  5791 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65628232_6   4884 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4933
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65628232_6   4934 GGCCATACCGCCCAAGGTAATTTACAGATTCAATGCCATACCCATCAAGC 4983
                            v    iv     iv i  i           i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65628232_6   4984 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5031
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_65628232_6   5032 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5081
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_65628232_6   5082 AACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGGC 5131
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_65628232_6   5132 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGATC 5181
                                 i   i    iii        i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_65628232_6   5182 AGTGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5229
                          i     i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_65628232_6   5230 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5279
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_65628232_6   5280 CTATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5329
                           v  i  i       i      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_65628232_6   5330 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5379
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_65628232_6   5380 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5429
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_65628232_6   5430 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5479
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_65628232_6   5480 AACACCAAGAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5529
                         i       i    vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_65628232_6   5530 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 5579
                          i   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_65628232_6   5580 AGGCAACCTACAAAATGAGAGAAAATTTTCGCAACCTACTCATCTGCCAA 5629
                           i     i   i    i        v  i    vii ivi     vi  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_65628232_6   5630 AGGGCTAATATCCAGAATCTACAATGAACTCAAAGTAATTTA-CAAGAAA 5678
                         i  i  vi          v  i  v      vv -i  i i -i  v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATAAA 795

  chr1_65628232_6   5679 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5728
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_65628232_6   5729 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5778
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_65628232_6   5779 CATCACTGGCCAT 5791
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (151 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3236 25.03 0.75 3.22  chr1_65639954_65646374.rev     5000  5930 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65639954_6   5000 TGGAAGAACATTCCATGTTCATGGAAAGGAAGAATCAATATCATGAAAAT 5049
                              ii i  i             vv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65639954_6   5050 GGCTATACTGCCCAAGGTAATTTATGGATTCAGTGCCATCCCCATCAAGC 5099
                            v     v     iv i  i  ii      ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65639954_6   5100 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTGTAAAGTTC 5146
                          v   -   v    i  -i     -   -- v  i  - iiv    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_65639954_6   5147 GTATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAA 5196
                         i       viiv  ii  v  viv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_65639954_6   5197 GAACAAAGCTGGAGGCATCATGCTATCTGACTTCAAACTATACTACAAGG 5246
                                 i      vv   ii  vi ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_65639954_6   5247 CTACACTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5296
                              v   i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_65639954_6   5297 CAATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATCTACAACCA 5346
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_65639954_6   5347 TCTGATCTTTGACAAACCTGACACAAACAAGCAATGGGGAAACCTGACAC 5396
                         vi    i  i     ivv  v  vi v  vv           --------
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-------- 389

  chr1_65639954_6   5397 AAACAACCAAATAGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAA 5446
                         --------i     -----------i  v  i  i              v
  L1M4_orf2#LINE/    390 --------GAATAG-----------TCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_65639954_6   5447 AACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATTCCTTCCTTACACC 5496
                               v  ?   i   i i  iiv    ii    ii   v   i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_65639954_6   5497 ATATACAAAAATTAACTCAAGATGGATTAAAGACTTAAATGTAAGACCTA 5546
                                             i      i ?    i           v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_65639954_6   5547 ACACCATAAAAACCCTAGAAGAAAACCTAGGTACTACCATTCAGGACATA 5596
                          v  i      vi i           v    ?iiv viv   iv   v v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_65639954_6   5597 GGCATGGGCAAAGATTTCATGACTAAAACACCAAAAGCAATAGCAACAAA 5646
                           vv i     v i    v iiv  vi            vv         
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_65639954_6   5647 AGCCAAAATTGACAAATGGTATCTAATTAAACTAAAGAGCTTCTGTACAG 5696
                           vv     v  i    v v ii v  i   v v  i i   i   i vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_65639954_6   5697 CAAAAGAAACTATCATCAGAGTGAACAGGCAACATATAGAATGGGAGAAA 5746
                             i  v       vv i      v  i    vi i             
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_65639954_6   5747 ATCTTTGCAATCTACCCATCTGACAAAAGGCTAATATCTGGAATCTACAA 5796
                           v       vii ivi      i  ii i  vi    ii    v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_65639954_6   5797 AGAACT--TA-AATTTA-TAAGAAAAAAACAAACAACCCCATCAAAAAGT 5842
                               --  -  i i -   v     i     i     v  i?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_65639954_6   5843 GGGCAAAGGATATAAACAGACATTTCTCAAAAGAAGACATTTATGCAGCC 5892
                                    v i  i           v        i  vi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_65639954_6   5893 AACAGACATATGAAAAAATGCTCATCATCACTGGTCAT 5930
                           i ii  i       i       v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.70 (37 / 10)  


3458 24.83 1.10 0.88  chr1_65685145_65687673.rev     1135  2040 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65685145_6   1135 TGGAAAGATATTGTGCGCTCATGGAGTGGAAGAATTTATATTTTTTAAAC 1184
                                    iviii i       v       v  v     v  v i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65685145_6   1185 ATCCATATTACTCAAAGCAATCTACAGAGTCATTGCAATCCCTACCAAAA 1234
                         iv v   i v i    vii         v   vi          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65685145_6   1235 TGCTAA-TGTCATTCTTCACAGAAATTTTTTAA--AATTCTAAAATTTGT 1281
                          v i i-  i -  i  ii        vviv i--i  i        ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_65685145_6   1282 ATG-AAGTCCAAAAGACCCCAAATAGCCAAAGCAATCTTGACCAGAAAGA 1330
                            -  i v   ii     vi          i         ---i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGA 196

  chr1_65685145_6   1331 AAAGTCAAAGCCAG-GGTCATCACACTATCAGATGTCAAAATATATTACT 1379
                          i i-     iii -  v -       vi vi  v      iv  i   v
  L1M4_orf2#LINE/    197 AGAA-CAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_65685145_6   1380 AAATTATAGTAATCAAAACAACATGGTACTGGCATAAAAACAGACACATA 1429
                           ii  i         i   iii              ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_65685145_6   1430 GACCAACAGAATAGCACAGAGAGCTCAGGAATAAACCTATACATCTACAG 1479
                           i   ii      v iv     ii   i        i      i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_65685145_6   1480 TCAATTGATTTTTGACAAAGATACCAAGCACACACAATGGGGAAAGGACA 1529
                                     i     i i i     vv  iv            i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_65685145_6   1530 -TCTCTTCAATAAATCATATTGTGAAAACTGGATATCCACATGAAGAATA 1578
                         -   i     i    vi ii  v  v         ?       v i  v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_65685145_6   1579 ATCAAAATGTACCATTACCTTATCCCTTATAGAAGATTCAACTCAAAATG 1628
                           v  iv  v   vi     i iv  v    v  i v i           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_65685145_6   1629 GATTAAAGACTTAAACATAGGACCTGAAACTATAAAACTACTAGAAGAAA 1678
                            i ?    i    ii  i  v  i             vi         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_65685145_6   1679 ACCTAGGGA-AAAGTTTCACGACATTGGTCTGGGGAATGATTTCTTGGCT 1727
                           v    ?i-   vi   ii   v    vi i  v    i      i v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_65685145_6   1728 ATAATGCCAAAACCACAGGCAATAAAAGCAAAAATAGACAGATGGGATTG 1777
                           i ii      v    i    i     v         i i  v   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_65685145_6   1778 CGTCAAA-CTAAAAACTCT-GCACAATAAAGGAAAATCTCAAAAGAGTAA 1825
                          i     -i        i - ii vvi      v v v    i i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_65685145_6   1826 AGAAACAACCCATAAACTGGGAAAAAGTATTT-TAAGTTATACATTGGAT 1874
                          i i        i i v     i   i     -i  i i   i  iv   
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_65685145_6   1875 AAGAGGCTAATATCTAAAATACACAAGAAACTCAAACTACTCAATAACAA 1924
                            i i  vi    i i    i i  ii     vv  v         i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_65685145_6   1925 GAAAACAAATAACCCAATGAAAAAACTGGCAAAGAATTTCCATAGACATT 1974
                         i  i              v?     iv       i    vv         
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_65685145_6   1975 TCTCAGGAGAAGACATACAAATGGCCAAGACATACATTTACCAAAATGCT 2024
                             vii      i              v vii    vv --  i     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA--AAGATGCT 892

  chr1_65685145_6   2025 CAACATTTCTAATTAT 2040
                               iv????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (146 / 75)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.29 (18 / 14)  


3279 27.09 0.44 0.44  chr1_65722762_65729174.rev     5015  5922 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65722762_6   5015 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5064
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65722762_6   5065 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCGCATCAAGC 5114
                            v     v     iv i  i  i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65722762_6   5115 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5162
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_65722762_6   5163 CATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5212
                         i      viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_65722762_6   5213 AACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGGC 5262
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_65722762_6   5263 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGATC 5312
                                 i   i    iii        i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_65722762_6   5313 AATGGAATAGAAC--AGAGCCCTCAGAAATAACACTGCATATCTACAACT 5360
                                     i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_65722762_6   5361 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5410
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_65722762_6   5411 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5460
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_65722762_6   5461 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5510
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_65722762_6   5511 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5560
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_65722762_6   5561 CTAGGCATTACCACTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5610
                         v    ?i v vivi  iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_65722762_6   5611 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTCA 5660
                         i            vvi          vv     v  i    vi  ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_65722762_6   5661 TTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGAAC 5710
                          i   v v  i i   i  ii vv v  i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_65722762_6   5711 AGGCAACCTACAAAATGGGAGAAAATTTTCACAAACTACTCATCTGACAA 5760
                           i     i   i             v  ii    ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_65722762_6   5761 AGGGCTAATATCCAGAATCTACAATGAACTCAAACTAATTTACAAGAAGA 5810
                         i  i  vi          v  i  v      vv  v v iv i  v  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_65722762_6   5811 AGACAGACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5860
                              i i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_65722762_6   5861 TCAAAAGAAGACATTTATGTAGCCAAAAGACACATGAAAAAATGCTCACC 5910
                           v        i  vi vi i     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_65722762_6   5911 ATCACTGGCCAT 5922
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3232 27.42 0.44 0.44  chr1_65736505_65742780.rev     4878  5785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65736505_6   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65736505_6   4928 GGCCATACTGCCCAAGGTCATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv v  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65736505_6   4978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 5025
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_65736505_6   5026 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_65736505_6   5076 AACAAAGCTGGAGGCATTACACTACCTGACTTCAAACTGTACTACAAGGC 5125
                                i      vv i     v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_65736505_6   5126 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_65736505_6   5176 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATACCTACAACT 5223
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_65736505_6   5224 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5273
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_65736505_6   5274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 5323
                           v  i  i              v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_65736505_6   5324 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAGATGGA 5373
                            ii    i    v   i     v  i        i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_65736505_6   5374 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_65736505_6   5424 CTAGGCATGACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5473
                         v    ?i i viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_65736505_6   5474 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5523
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_65736505_6   5524 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5573
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_65736505_6   5574 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5623
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_65736505_6   5624 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5673
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_65736505_6   5674 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5723
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_65736505_6   5724 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5773
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_65736505_6   5774 ATCACTGGCCAT 5785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (150 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3219 24.48 1.10 1.21  chr1_65766374_65768398.rev      628  1534 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_65766374_6    628 GAGAGATGTACTGTGCTTATGGGTCAGAAGACTCAATATGGTTAATATGC 677
                           i    i v ii  i i    i ii       i     v     v   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_65766374_6    678 CAGCTCTCCTCAAATTTATCTACAGATTTAATGCAATGCTACTCACAATC 727
                           iiv    i      v           i  i     v ivv   v    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_65766374_6    728 TCAACAGGCTATTTTACACAAATTGACAAGATGAATCTAAAAATTCATAT 777
                         i  i v v  v    i  v           v   vi      -       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCATAT 151

  chr1_65766374_6    778 GGAAATGCAAAGAATCTAGAATAGCCAAAACAACTTTGAAACTGAAGAAC 827
                                   i i i i                ii      vv       
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_65766374_6    828 ATATTTTGAAGAATAACAATACCTAACTTCAAAATGTATTATAAAGCTGC 877
                          v v  v  i  v v   v v  i  i       iv  i  i      i 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_65766374_6    878 AATAATCAGGCCAATGAAGTATTCATGTAAAAACAAAAAAAAGTAAATGA 927
                          i      i v  i  vi   i viii   ii i i v v --  i  v 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA--TAGATCA 299

  chr1_65766374_6    928 ATGGACCAGAAT--AGAGTCTAGAA-TAGACTAACACTTACATGGACAAC 974
                              vi     --      i    -  i  iv i  v vi    v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_65766374_6    975 TGATTTTCTACAAAGGCACAAAAGAAATTCTGTGGAAAAATGATAATCTT 1024
                                 v    i  ii v  iivv    vi   ii   vi   i    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_65766374_6   1025 TCTGATAAATTGTGCTGGAACAATGGAATATCTATATGCAATAAAAGAAA 1074
                          iii i    v       i    iv i   ? i i      ---     v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA---AAGAAT 446

  chr1_65766374_6   1075 AGAACTTTAATCCATACCTCACATCAGATACAAAAATTAATTCCAAATGA 1124
                         -   v  vi i  v         i  v             i  v     i
  L1M4_orf2#LINE/    447 -GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_65766374_6   1125 ATCATAAATCTAAATGTAAAACCTAAAGCTATGAAACTTCTAGAAGAAAA 1174
                             ? i i          i v     i    i     ii          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_65766374_6   1175 CATAAGTAAAAAATTTTGTGACCTTGTGTTAATTAAAAATTTCTTATATA 1224
                             i ?iv   vi  i         v    ivi  vii       v   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_65766374_6   1225 TGACACAAAAAGCATGATCCATAAAAGAACAAACTGATAAATTAGACTTT 1274
                               v       ii v v i       v   iv        i     i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_65766374_6   1275 ATCAAAATTGAAAAGTT--GT-TTTCTGAGAAGCACTATGAAAGATAACA 1321
                                  i    v  --  -i   vi  i -      v  -  v iii
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-CACTATCAA-GAAAGTG 693

  chr1_65766374_6   1322 AAAAGACAAACCATACAC--AGAGAACATATTTGCCAATTATCTATCTGA 1369
                                  v   i v v--i     v        v   i  v       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_65766374_6   1370 TAAAAGATTTGTATACATAAGGTATCTACAATACTCAAAACTAAATAATA 1419
                            ii  i      v  v  vi   vv v  iv  i v    v       
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_65766374_6   1420 ATAATACAAACAACCCAGTTAAAAAGATAGGCAAA--ATGTTACACAGTC 1467
                          v  v     i      i  ?    -  i      --  -  iv i  v 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGGAT-TTGAATAGAC 841

  chr1_65766374_6   1468 ACTTCACCATATAAATCATAGTTATGGCAAATAAGCATATGAAAGGATGC 1517
                          i   v   v v  ivi   vvv     v        i      i     
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_65766374_6   1518 TCAACATCATTAGTCAC 1534
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (124 / 94)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 1.50 (21 / 14)  


3153 27.58 0.44 0.66  chr1_65828893_65835567     5273  6182 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65828893_6   5273 TGGAAGAACATTTCATGCTCATGGATGGAAAGAATCAATATAGTGAAAAT 5322
                              ii i  ii    i        v i    v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65828893_6   5323 GGCCATACTACCCAAAGTAATTTATAGATTCAATGATATTCCCATCAAGC 5372
                            v     v      v i  i  i        i vv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65828893_6   5373 TACCATTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTTA 5421
                          v   vivi i  i  ii     v v  v  i--  - iii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_65828893_6   5422 TATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGTAAGAAG 5471
                                viiv  ii  v  viv        i      i i iv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_65828893_6   5472 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5521
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_65828893_6   5522 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATACATAGACC 5571
                                 i   i    ii         i iv ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_65828893_6   5572 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5621
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_65828893_6   5622 CTGATCTTTGACAAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5671
                         i    i  i     iiv-  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_65828893_6   5672 TGTTTAATAAATGGTGTTGTGAAAACTGGCTAGCCATATGCAGAAAACTG 5721
                          v  i  i        i  v  v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_65828893_6   5722 AAACTGGACGCCTTTCTTACACCTTATACAAAAATTAACTCAAGATGGAT 5771
                           ii     v   vi  i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_65828893_6   5772 GAAAGATTTCAATATAAGACCTAAAACCATAAAAACCCTAGAAGGAAACC 5821
                         v ?   ii v   i     v       i      vi i      i    v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_65828893_6   5822 TAGGCA-ATACCATTCAGGACATAGGCATGGGCTAAGGCTTCATGACTTA 5870
                             ?i- v i -   iv   v v  vv i   v v  i   v iiv vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_65828893_6   5871 AATACCAAAAGCAATGGCAACAAAAGGGAAAATTGATAAATGAGATGTAA 5920
                         i i          vvi          ii     v       vi  iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_65828893_6   5921 TTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAGTGAAC 5970
                          i   v v  i i   i  iiivv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_65828893_6   5971 AGGCAACCTACAGAATGGGA--AAATTTTTGCGATCTTTCCATCTGACGA 6018
                           i     i           --    v     i viiv vi      ii 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_65828893_6   6019 AGGGCTGATACCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 6068
                         i  i  vi  i       v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_65828893_6   6069 AAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGCGATGAATAGACACT 6118
                          i --    i     v  i?    i          vvv          i 
  L1M4_orf2#LINE/    797 AGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_65828893_6   6119 TCTCAAAAGAAGACATTTATGCAGCCACCAGACCCATGAAAAAATGCTCA 6168
                             v        i  vi viii    vi ii v        i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_65828893_6   6169 TCATCACTGGCCAT 6182
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2537 18.80 1.18 18.71  chr1_65838770_65843771.rev     3411  4511 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65838770_6   3411 TGGAAAGACATCCAATGTTTGTGTATTGGACGAATTAATATTACCAAAAT 3460
                                 i    v     ii  v      v  v        iii  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65838770_6   3461 ATCTATGCTAATAAAAG-GATCTATAGATCTAATGCAATTTCTGTGAAAA 3509
                         iv v  i  vviv   v-      i    ii  i     ii  i v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65838770_6   3510 TATCAATGGCATTCTTTATAGAAATAAAAAAG-TG---CTAAAATTCATA 3555
                          vi  iiv  v  i   ii      vi v   -  ---            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_65838770_6   3556 TGGAATCAAAAAAGACATTGAAAAGCCAAATTAATTTTGAGAAAGAAGAA 3605
                              viiv  ii   viv   v       vi   i    i         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_65838770_6   3606 CAAAGCTGGGGGCATCATATTTTTTAATTTCAAAATATATTGCACATCTA 3655
                              i   i  vv   i i  iii          iv  i i  v v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_65838770_6   3656 CAGTAATTGAAGCAGTGTGGTACTGGCATAAAAAGAGACATATACATCAA 3705
                                ii ii                   ii v         v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_65838770_6   3706 TAGAACAGAATAAAGAGCCCA-AAATAAATTCATACAGTTACAGTCAACT 3754
                          i   i     vi    i   -       ii      v   ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_65838770_6   3755 TATCTATGACAAAAGTGCCAGGAACA--CAGATGAAAAAAGAATACTCTC 3802
                         v  i vi     ii      i  v  --  -   iii        v   i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAGAATAGTCTT 399

  chr1_65838770_6   3803 TTCAATAAAAGGTATTGGGAAAACTGGATATCCACATGCAAAAAAGAAAG 3852
                              i   v   ii     v         ?            -------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA------- 442

  chr1_65838770_6   3853 AAAGAAAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGA 3902
                         --------------------------------------------------
  L1M4_orf2#LINE/    443 -------------------------------------------------- 442

  chr1_65838770_6   3903 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAGAGAAAGAAA 3952
                         --------------------------------------------------
  L1M4_orf2#LINE/    443 -------------------------------------------------- 442

  chr1_65838770_6   3953 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGAGAAAGAAAGAAAA 4002
                         ----------------------------   v    --------------
  L1M4_orf2#LINE/    443 ----------------------------GAATGAAG-------------- 450

  chr1_65838770_6   4003 GAAAAGAAAAAAGAAAAGAAAGAGAAAAGAAATTGGACCG-TATGTCACA 4051
                         --------------------------------       v-  iv     
  L1M4_orf2#LINE/    451 --------------------------------TTGGACCCCTACCTCACA 468

  chr1_65838770_6   4052 CCATTTACAATAAAATCATCTCAAAACAGATTAAATACTTAAATGTAAGA 4101
                             v     --    i v       ii   i ? v  i           
  L1M4_orf2#LINE/    469 CCATATACAA--AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_65838770_6   4102 CCTAAAACTATAAAAATACTAGAAGAAAACATAGAGA-AAAGCTTCTTGC 4150
                         v              v vi               i?i-   v    v  v
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_65838770_6   4151 CATTGATCTGGGCAATGGTTTTTTTTTGCATATGATACCAAAATCACAGG 4200
                          v   ivi i           i  ---iv      i       v    i 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTT---AGATATGACACCAAAAGCACAAG 613

  chr1_65838770_6   4201 CAATGAAAGCAAAAATAGATGAGTGGAATTATCTCAAA-TTAAAAAGCCT 4249
                            ii    v          i i v i i viv     -       - i 
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTT 662

  chr1_65838770_6   4250 GTGCACAGCAAAGGTAACAATCAACAGAGTGAAAAGGCAGCCTACAGAAT 4299
                         v  ii vv      vv  v     v i         i  i  i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_65838770_6   4300 GGGAGGAAATACTTGCAAGCCATATATTTAATAAGG-AGTTA-ATTCAAA 4347
                              i     i      ii       i i      - v  i-  i  i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_65838770_6   4348 ATGTAGAGGGAATGCATATAATTAAATGGCAAGAAACAAATAAAGCAAAA 4397
                           i  v ii   iv v  i  i v   -----------      ---  i
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAAT-----------AATAAA---AAG 798

  chr1_65838770_6   4398 ACAAACAAAAAATGCAATTTAAAAATGAGCAAAAGACCTGAATAGACATT 4447
                              i  ----iv     ?       i     i  ii            
  L1M4_orf2#LINE/    799 ACAAATAA----CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_65838770_6   4448 TCTCAAAAGAAAACACACAAATGGCCAACAGGTATATGAAAAGATTCTCA 4497
                             v      i i i            i i i i          v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_65838770_6   4498 GTGTCACTAATGAT 4511
                         iii   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (131 / 72)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 11.53 (219 / 19)  


3375 25.08 0.88 0.99  chr1_65892850_65895202.rev      954  1862 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65892850_6    954 TGAAAAGATATTTCATTTGTATGGATTGGAAAAATCAATATTGTTAAAAT 1003
                           i        ii   v vi           i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65892850_6   1004 GTTCATACTACTCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 1053
                          viv     v i    vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65892850_6   1054 TACCAATGACATTCTTCACAGAAATAGAAAAAAAAAACTCTAAAATTTAT 1103
                          v   iivi v  i  ii       v  v  ivvi v -        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-CTAAAATTCAT 149

  chr1_65892850_6   1104 ATGGAACCAGAAAAGACCCAGAATAGCCAAAGCTATCCTATACAA-AACA 1152
                               viiv  ii                 i v   i iv v  -  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_65892850_6   1153 ACAAAACTGGTGGAATCACATTACCTGCCTTCAAATTATAGTACAGAGCT 1202
                              ii   v   v     i v  iivi      viv  v    i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_65892850_6   1203 A-AGTCACCAAAGCAGCATGGTACTGGCATAAAAACAGACACATGGATAA 1251
                          -   v i   ii   ii              ii i     i  i   v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_65892850_6   1252 ATGGAACAGAATAGAGAACCCAGAAACAAATCCACACACCCACAGTGAAT 1301
                               i     v    ii       i   i   i   iii ii  v   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_65892850_6   1302 TCATTTTTGACAAAAGTGCCAAGAACATACACTGGGTAGAAGACAGTCTC 1351
                          v     i     ii         v   v  v    v i ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_65892850_6   1352 TTCAATAAATGATGCTGGGAAAACTGGATATCCACAGGCAGAAGAATGAA 1401
                              i     i        v         ?     v   i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_65892850_6   1402 ACTAGACCCTTATCCTTCTCTGTATACAAGAATCAAATCAAAATGGACTA 1451
                         ii i     i  i iiv v ii       i   i  v          ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_65892850_6   1452 AAGACTTAACTCTAAGAACTCAAATTATGAAACTACTACAAGAAAACATT 1501
                         ?    i   v v     i  v   i   i     vi  v          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_65892850_6   1502 GAGGAAACTCTCCAGGACATTGGTCTGGGCAAAACTTTCTTGAGTA--AT 1549
                          i? v  v   i iv   v    vi i     viv      iii  -- i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_65892850_6   1550 ACCCAGGCAAGCACAGGCAACCAAAGCAAAAATGGACTAGTGGGATCACA 1599
                            v ---       i     v    v      i  iv i v   iiv  
  L1M4_orf2#LINE/    600 ACCAA---AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_65892850_6   1600 ACAAG-TTAAAAATCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAA 1648
                         v   i-       -   i  ii vv       v  v     v        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_65892850_6   1649 TAGACAACCCACAGAACAGGAGAAAATATTTGCAAACTACCCATATGACA 1698
                         v               ii                  ii ivi  v   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_65892850_6   1699 AGAAATTAATAACCATGTTTTATATAAGGAGCTTAAACAGCCTTAGAGGA 1748
                           ii i vi  v   viv --      i  i  ivv   i iiv v iv 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAAT--ATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_65892850_6   1749 AAAAAAATCTAATAATCTGATTAAACAATAGGCAAAAGATTTGAATATAA 1798
                             i -- v     i ii   ?  v   i      i          v v
  L1M4_orf2#LINE/    794 AAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_65892850_6   1799 ATTTCTC---AAAAAACATACAAATGACCAACAGGCATAAGAAAAGGTGC 1845
                                --- i  i i         i    i i   i v      i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_65892850_6   1846 TCAACATTACTGATCAT 1862
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (140 / 84)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


2917 27.35 1.33 0.78  chr1_65915822_65922306.rev     5092  5994 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65915822_6   5092 TGGAAAAACATTTCACGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5141
                               i i  ii  i i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65915822_6   5142 ATTGGGCCATACTACCCAAAGTAATTCATAGATTCAATGATATTCCCATC 5191
                         ----   v     v      v i  ii i        i vv  i  i   
  L1M4_orf2#LINE/     51 ----GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_65915822_6   5192 AAGCTACCATTGACTTTCTTCACAGAATTAGAAAAAA-AATACTTTAAAT 5240
                           iv v   vivi i  i  ii     v v  v  iv-i  v  --   v
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAA 144

  chr1_65915822_6   5241 TTCACATGGAACCAAAAAAGAGCCCGTATAACCAAGACAATGCTAAGCAA 5290
                             i      viiv  ii  v  v v   i    i     vi i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_65915822_6   5291 AAAGAATAAAGCTGGATGCATCACACTACCTGACTTCAAACTATACCA-A 5339
                         i     i    i    v vv       v  ii i      viv   i - 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_65915822_6   5340 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATA 5389
                          i          i   i    ii         i iv ii i   i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_65915822_6   5390 GACAAATGGAACAGAACAGAGGCCTCAAAAATAACACCACACATCTACAA 5439
                           iv       i    iv   ivii  i      vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_65915822_6   5440 CCATCTGTTGTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGAATT 5489
                         i  vi  v v  i     ivv  v   i v  vv               v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_65915822_6   5490 TTCTATTTAATAAACGGTGTTGG-----CTAG----CCATATGCAGAAAA 5530
                         v   v  i  i   i    i   -----  i ----   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_65915822_6   5531 CTGAAACTAGACCCCTTCTTTACACCTTATACAAAAATTAACTCAAAATG 5580
                         v    ii i       v i i     v                       
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_65915822_6   5581 GATTATAGACTTAAATGTAAGACCTAAAAGCATAAAAACCCTAGAAGAAA 5630
                            i ?    i           v      vi      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_65915822_6   5631 ACCTAGCCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAC 5679
                           v   v?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_65915822_6   5680 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5729
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_65915822_6   5730 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCATCATCAGAGTG 5779
                          v  i   v v  i i   i  ii vv    i  v  i    vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_65915822_6   5780 AACAGGCAACATACAGAATGGGAGAAAATCTTTGCAATCTATCCAACTGA 5829
                           v  i    vi                 v       vii  vi v    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_65915822_6   5830 CAAAGGGCTAATAACCAGAATCTACAAGGGACTTAAACAAATTTACAAGA 5879
                         i  i  i  vi  v       v  i  i i   ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_65915822_6   5880 AAAAAACAAATAACCCCAATAAAAAGTGGGCAAAGGATAGGAACAGACAC 5929
                             i           v v ?    i            vv   i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_65915822_6   5930 TTCTCAAAAGAAGACACTTATGTGGCCAACAAACATATGAAAAAAGGCGC 5979
                              v        i ivi vi       i  i  i       i v  v 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_65915822_6   5980 AGCATCACTGGTCAT 5994
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (140 / 104)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  


4443 16.04 2.90 1.78  chr1_65942588_65947814     3839  4736 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65942588_6   3839 TGGACATACACCACATATTTATGCTTTGGAAAACTCAGTATTGTTAAGAT 3888
                             v v i i v   i  i   vv      i   i i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65942588_6   3889 AGCAATATTCCCCAAAGTGATAAACAGATTTAATGCAATGTCTATTAAAA 3938
                         i      i        v    vv       i  i     vi    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65942588_6   3939 TTCTACCTGTTTTTTTGGCAGAAATTGACAAGCTGATCCTAAAATTCAT- 3987
                          i i v   ii     v                                -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_65942588_6   3988 -GGAAATGCAAGGAACACAGAATAGACAAAATAATCT-GAAATAAAA--- 4032
                         -            i  v        v     i     -    v i  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_65942588_6   4033 CAAAGTTGGAGGACTCACACTTTCCAATTTCAAACCTTACTACAAAGCTA 4082
                                               i           v               
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_65942588_6   4083 CAGTAATCAAGATAGTGTGGCACTGGTGAAAGGATAGAAATATCTATCAA 4132
                                     i       i     iiv         v    vv     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_65942588_6   4133 TGGAATAGGTTTGGGGTTCCAGAACTAACTCCTTTCATTTATGAACAATT 4182
                                 iv   i iv       v   vi  v v        iv     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_65942588_6   4183 TATTTTTTGATAAGGAGGACAAGAC-A---AATGAAGAAAGAATAGTCCC 4228
                         v     i-  i    iv v      - ---    ii            ii
  L1M4_orf2#LINE/    351 GATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_65942588_6   4229 TTCAACAAATGACAGTGGGATAACTATATATCCAC-TGGGACAGAATAAA 4277
                                    iiiv     i    iv   ?    -  vi v     i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_65942588_6   4278 GTTGAACCCCTACCTCACACCATATACAAAAATGAACTCAAAATGGATTA 4327
                             i                            v              i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_65942588_6   4328 GAAATCTAAACATAAGTAAACCTTAACATATAGCTAAAACTATAAAATTG 4377
                         ? i i     ii    ---------------                i v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAG---------------AGCTAAAACTATAAAACTC 534

  chr1_65942588_6   4378 TTAGAAGAAAACC--GGAGTAAACTTTTGTGCCTTTGGATTAG-CAATAA 4424
                                     v--  ?     ii  i   v i    i    -    ii
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_65942588_6   4425 TTTCTCA--CATGACACCAAAAGTATAAATAACAAATGAAAAAATAGATA 4472
                              i --i             i i  ii      v             
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_65942588_6   4473 AATTGGACTTCATAAAAATGAAAAGCTTTTGTGATTCAAAGGAC-TTA-- 4519
                                      v     v    i        v          -i  --
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_65942588_6   4520 AGGAAAGTGAAAAGACAACTCATAGAATGGGAGAAAATATCTTCAAGTCA 4569
                          i                 i  i                 i v   i   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_65942588_6   4570 TAAATTGGCTAAGGAAACTATACATTGAATATATTAAAATCTCTTAAAAC 4619
                           v  iv v     i vi i  iviv        v  i v      v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_65942588_6   4620 TCAACAGTTCAAAAA-----AACTCAATT-AAAAATGGACAAAGGATTTG 4663
                             i i vv   i -----   i     -        i           
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_65942588_6   4664 AATAGACATTT-TCCAAAGGAGATAAACAGATGGCCAATAAGCACAAGAA 4712
                                    -       i     v   i                v   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_65942588_6   4713 AAGATGCTCAACATAATTAGTCTT 4736
                                       v ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (85 / 56)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.62 (42 / 16)  


2761 27.38 0.43 2.16  chr1_65957646_65961064     2003  2926 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_65957646_6   2003 TGGAAACATATCCCATGCTCATGGATGGGTGGAATCAATAATGTAAAAAT 2052
                               v          i        v  vi  v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_65957646_6   2053 GACCATACTGCCAAAAGCAATCTACAAACTCAATGCAATTCCCATCAAAA 2102
                          i v     v  v   vii       i i    i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_65957646_6   2103 TATCATCATTGTTCTCATCATCATCTACCATCACTGAGAAAACAATTCTA 2152
                          vi  v --  iii i------- i i vivv i   v  ivii  i   
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTT-------TTTGCAGAAATTGACAAGCTGATCCTA 141

  chr1_65957646_6   2153 AAATTCATATGGAACCAAAAAAAGAGCCTGCATAGTGAAAGAAAGACCAA 2202
                                       viiv  ii-  v  v v    iv   iv  vviii 
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_65957646_6   2203 GCAAATATAACAAATCAGGAGGCATCACATTACCTGACTTCAAACTCTAC 2252
                         iv  iv v      viv     vv     i v  ii i      vii   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_65957646_6   2253 TATAAGGCTACAGTCACCAAAACATCATGGTACTGGCATAAAAATAGGCA 2302
                           i  i        v i   i   vii              ii    i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_65957646_6   2303 AATAGACTGATGGAACAGAATATAGAACCCAGAAATAAAGCCAAATACTT 2352
                         v     iii      i     vv   ii           v   v i i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_65957646_6   2353 ACAGCCAACTGACCTTTGAGAAGGCAAACAAAAACATAAAGTGGGGGAAT 2402
                          ii i   i   ii  i  v    vviv   i v   vv i     i  -
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA- 389

  chr1_65957646_6   2403 GGACATCCTATTAAACAAATGA-GATGGAATAATTGGCAAGCCACATATA 2451
                          i i vi  v  v        i- v   i i  i   vv ?      ii 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_65957646_6   2452 GAAAAATGAAACTGGAAATGAGGATTTCTCATCTTACACAAAAATCAACT 2501
                         i  i      ii    vviv--v ii  v  i v  i        i    
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCC--TACCTCACACCATATACAAAAATTAACT 487

  chr1_65957646_6   2502 CAAGATGGATCAAAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTA 2551
                            i        ?    i     v     v  i    i      v ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_65957646_6   2552 GAAGATAACATTGGAAAAACCCTTCTAGACACTGGCTTAGGCAAAGACTT 2601
                              v     v  ?iv  vi    vv   vi   v        v ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_65957646_6   2602 CATGACCAAGAACCCAAAAGCAAATGCAATAAAAATGAATATAAATAGAT 2651
                          v iivi v  vv         v v    i    ivi  v   i   i  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_65957646_6   2652 GGGACTTAATTGAACTAAAAAGTTGGTGTGCAGCAAAAGAAATAATCAGC 2701
                         v      v  ii  v v    ii vv     vv    i  v iv    iv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_65957646_6   2702 AGAGTAAACAGACAACC-ACAAAGTGGGAGAAAATCTTTGCAAAGTATGC 2750
                          i   i  v        -   i i           v        vi  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_65957646_6   2751 ATCCGATAAAGAACTAATATCCAGAATCTACAAGGAACTCAAACAAATCA 2800
                            i     i i   vi          v  i  i      vv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_65957646_6   2801 GCAAGAAAAAAAAAACAGACAAACAATCCCATCAAAAAGTAGGCTAAGAA 2850
                         ii  v     -------      i  i  v  i?    i i   v   i 
  L1M4_orf2#LINE/    788 ATAATAAAAA-------GACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_65957646_6   2851 CATGAATAGACAATTCTCAAAAGAAAATATACAAATGGCCAAAAA--ATA 2898
                         iv          v     v      i                v  -- i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_65957646_6   2899 TGAAAAAATGCTCAACATCACTCATTAT 2926
                               i             ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (141 / 108)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  


1895 24.15 4.15 11.38  chr1_66027749_66030493.rev     1307  2246 (499)    L1M4_orf2#LINE/L1        1   872 (36)  

  chr1_66027749_6   1307 TAGAGAAACATACAATGTTCATTAATCATAAGACT-AAGATTGTTCA--C 1353
                          i  i i i  v v        vi  iiv      -  v      v --i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_66027749_6   1354 GTTAGTTCTCTTTAAATTTATCTATAGAGTCAACTTAATCCAAATCAAAA 1403
                          vi i v   iii     v     i   v     vi     vv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_66027749_6   1404 TCTCAGCAAATGC---TTTTGTAAATATTAATTATATGATTCTAACATAT 1450
                           i    ---   ---     i i v   i iv vv    i    v  vi
  L1M4_orf2#LINE/    101 TCCCAGC---TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_66027749_6   1451 ATATAGAAAAAATGTGTATATAAATGCAAAAAAAGAAAAAAATGCTAAAA 1500
                             i    ---------------     iii v---------- i i  
  L1M4_orf2#LINE/    148 ATATGGAAA---------------TGCAAGGGAC----------CCAGAA 172

  chr1_66027749_6   1501 TAGCAAAAACTGTTTTGAAAAAGTA---CATATTGGGAGGACTTAAACTG 1547
                             v     vi i         v ---  v v v        i v   v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_66027749_6   1548 TTGGATGGCAAATTTTACCATAAAGCTGCTGTAATCAAGACAATATGGTA 1597
                         iivi  vv    vi    i i      i v            i i     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_66027749_6   1598 CTGGCATAAGGATAAA-ACATAGGTTCATGAAACAAATTAGAGAATCCAG 1646
                                       i - i    i iv   i  i i v v    i     
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_66027749_6   1647 AAACATATCAA-GCGTATTCGGCCTATTGATTTTTGACA---GCATCTAA 1692
                            i v i v -i i v vi  i v         i    --- iii v i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_66027749_6   1693 ACTAATTCAATGGGAAATAGAA-AGACTTTTTAGCTAATTGTTGCTAGAA 1741
                           i -         i  -    -  v     i i v   v  -   i i 
  L1M4_orf2#LINE/    373 ACCA-TTCAATGGGGAA-AGAATAGTCTTTTCAACAAATGGT-GCTGGGA 419

  chr1_66027749_6   1742 CAATTGAGCATCC-CTTGGGGTAAGGGGAGGACTCATATTCACATACATG 1790
                            i  iii ?  - v  ---i  ii i v  ----- v ----------
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATG---CAAAAGAATGA-----AGT---------- 451

  chr1_66027749_6   1791 TGAACCTCAAGTATTATCTCACTTCATACA-AAAAATTAATCTGAAATGG 1839
                           i   i ------  i     vi    i -         iiii      
  L1M4_orf2#LINE/    452 TGGACCCC------TACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_66027749_6   1840 ATCACAGACCTAAATGTGAAAGCTAATACACTAAAACTTACAGAATAAAA 1889
                             ?            i i      v  vv       ivi    v    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_66027749_6   1890 CATGAAAGAAAATATTTGTTACCT------AGGTAAAGATTTCTTCGATA 1933
                            iii? v    v  i  v    ------   i  v i      v    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_66027749_6   1934 GGAAAG-AAAAGCACAAAGTGTTAAAA----------ATATGTTAGACTT 1972
                         v  v v-          - iivi    ----------   vi  i     
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_66027749_6   1973 TATCAAGTTTTTAAAATTCTGCTCTTTGAAACTCATTGTGAACAAAATGC 2022
                         i     iv  vv   v  i  iv   ii  ivv  i i v  v   i  v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_66027749_6   2023 AAAGGCAAGATACAGACTGAGGGAAAACTTTTGTAA--CATATATTTGG- 2069
                             i   vvi     v  i i     iv    i  --       i  i-
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_66027749_6   2070 --GGGTACACCCACATCTAGAATATATATATATACACACACATGCAAACA 2117
                         --   ---  iiii   i          -----------------  iv 
  L1M4_orf2#LINE/    745 AAGGG---ACTTGTATCCAGAATATATA-----------------AAGAA 774

  chr1_66027749_6   2118 CACATATACACACAAATACACACAAACACACTCTTACTCAGCTATAAGAA 2167
                          v v  i ---------------------------     iiv    i  
  L1M4_orf2#LINE/    775 CTCTTACA---------------------------ACTCAATAATAAAAA 797

  chr1_66027749_6   2168 CACAAACCAATAATTCACTTTTGTAATGGACAAAAGATTTGAACAGAAAC 2217
                         v     ----   ii  v  ?viv     i    i        i   v i
  L1M4_orf2#LINE/    798 GACAAA----TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_66027749_6   2218 TTCTCATAAAAAGATACACAAATGGCCAA 2246
                              vv  i      i            
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAA 872

Transitions / transversions = 1.51 (134 / 89)
Gap_init rate = 0.03 (30 / 872), avg. gap size = 4.87 (146 / 30)  


2899 28.19 0.44 0.44  chr1_66038002_66042233.rev     2834  3741 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_66038002_6   2834 TGGAAAAATATTCCACTCTCATGGATAGGAAAAATCAATATCATGAAAAT 2883
                               i    i   ivi        v    i v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_66038002_6   2884 GGCCTTATGGCCCAAAGTAATTTAGAGATAGAATCCTATTCCCATCAAGC 2933
                            vv  ivv      v i  i  v    vv  iv v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_66038002_6   2934 TACCATTGACCTTCATTGCAGAATTAGAAAAAAACT-ACTTTAAATTTTG 2982
                          v   vivi    iv        v v  v  i--  - iii    v  ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_66038002_6   2983 TATGGAACCAAAAAAGAGCCTGTATAGCTAAGACAATCCTAAGCAAAAAG 3032
                                viiv  ii  v  v v     i  i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_66038002_6   3033 AACAAAGCTAGAGGCATCACACTACCTGACTTCAAA-CTAACTACAAGGC 3081
                                i i    vv       v  ii i      -  v       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_66038002_6   3082 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATAAAGACC 3131
                                 i   i    ii         i iv ii i   i   v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_66038002_6   3132 AGTGGAACAGAAAAGAGACCTCAGAAATAACACCACACATCTACAGCCAT 3181
                          i     i    vv    vii         vv   i    i  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_66038002_6   3182 CTGATCATCAACAAACCTGGCAAAAACAAGCAATGGAGAAAGGATTCTCT 3231
                         i    iv  i    ivv  v   i v  vv      i     i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_66038002_6   3232 ATTTAATAAATGGTGCTGAGAAAACTCACTAGCTGTATGCAGAAGAGAGA 3281
                         v  i  i           i  v    viv  ? iii     i    iv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_66038002_6   3282 AACTGCACTCCTTCCTTATACCTCATACAAAAATTAACTCAAGATGGATT 3331
                          ii  v  i   v   i i   vi                  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_66038002_6   3332 AAAGATTTAAATGTAAAACCCCAAACCATAAAAACCATAGAAGAAAACCT 3381
                          ?   ii         i v iv    i      vi v           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_66038002_6   3382 AGGCA-ATACCGTTCAGGACCTAGGCAAGGGCAAAGACTTCA-AGACTAA 3429
                            ?i- v i -   iv     v  vvvi     v ii   v-   -  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TAT 596

  chr1_66038002_6   3430 AACACCAAAAGCAATTGCAACAAAAGTCAACATTGACAAAAGGGATCTAA 3479
                         i            vvv          vv  v  v  i   vv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_66038002_6   3480 TTAAACTAAAACACTTCTGCACAGCAAAAGAAACTATCATCAGACTGAAC 3529
                          i   v v   v    i  ii vv    i  v       vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_66038002_6   3530 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 3579
                           i     i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_66038002_6   3580 AGGGCTAAGATCCAGAATCTACAAAGAATTTAAACAAATTTACAAGAAAA 3629
                         i  i  viv         v  i      i ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_66038002_6   3630 AAACAAATGTCCCCATCAAAAAGTGGGTGAAGGATATGAACAGACATTTC 3679
                          i      iv   v  i?    i    ii      v    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_66038002_6   3680 TCAAAAGAAGACATTTTTGCAGCCAACAAACATATGAAAAAGAGCTTATC 3729
                           v        i  vivviii     i  i  i       iiv   i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_66038002_6   3730 TTCACTGGTCAT 3741
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (139 / 113)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


2734 27.59 2.39 0.68  chr1_66064923_66067627.rev     1330  2206 (499)    L1M4_orf2#LINE/L1        1   892 (16)  

  chr1_66064923_6   1330 TGGAAAGACATCCCCTGCTCATGAATCAAAAGAAT-AA-ATCATCAAAAT 1377
                                 i     v  i     i  iii    v -  -  ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_66064923_6   1378 AACCATACTGTCCAAAGCAATTTGCAGATTCAATATAATTCCAATCAAAA 1427
                         ii v     vi     vii  i i         iii   i  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_66064923_6   1428 TAGCAA-TGCCATTTTTTCACATAAATAGAAAAAACAATCCTAAAATTCA 1476
                          vv  i-    --     ii  v    v  v  ivii             
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_66064923_6   1477 TGTGTTAACAAAGAAGAGTCTGAACTGCCAAAGCAATCCTAAGCAAAAGA 1526
                          i  vv  iiv iii  vi v   iv      i     i i iv  i ii
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_66064923_6   1527 AACAAAGCTGGAGGCAC-CACATTACCTGACTTCAAAATATATTACAAGA 1575
                                i      -  -    i v  ii i       iv  i     ii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_66064923_6   1576 CTGTCATAACTAAAACAGCATGGTTTTTGTATAAAAACAAACACATACAC 1625
                           iivi   ii  i    ii    vi v i    ii i i   i   v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_66064923_6   1626 CA-CGGGACAAAGTAGCAAACCCAGAAATAAATTCACGTATTTTCAACCA 1674
                           -i  i i i i v vi ii           ii  iii    viiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_66064923_6   1675 AAGGATTTTTGACAAAGGAAGCAAGAATATATATTGGAGAAAGAACATTC 1724
                          vv      i     i  viv     vi  vi v   i       i v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_66064923_6   1725 TCTTCAATAAATGGTGCTAGGAAAATTGG-TCGCCACATGCAGAAGAATG 1773
                          i     i          i   v  i   - v?         i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_66064923_6   1774 AAACTAGACCCCTAACTCTCACCAAATACAAAAATCAACTCAGGGTAGAT 1823
                           ii i        v   v     v          i      iii i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_66064923_6   1824 TAAAGACTTATACATAAGACCTGAAACTATAAAAACTGCTAGAAGAAAAC 1873
                         i ?    i  v ii     v  i           -  vi           
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr1_66064923_6   1874 AAAGGAGAAACACTTCTGGACATAGGTCTAGAAAA-GATTTTATGGCTAA 1922
                          v   ? v  vv    vv   v v  vi   iv  - i   iv i v  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_66064923_6   1923 GACCTCAAAAGCACGGGCAACAAAAACAAAAATAGACAAATGAGACTACA 1972
                            vi         ii         iv         i    vi    v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_66064923_6   1973 GTAAATTTAAAAGTGTCTTCACAGCAAAGGTAACAATCAACTTAGTGAAC 2022
                         vi   v      iiv i vii vv      vv  v     vvv      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_66064923_6   2023 AGACAATCTGTTGACTGGAATAATCTATTTGCAAACTATTCATCTAATAA 2072
                               i iiiv  v   i v  vv          ii  vi    i    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_66064923_6   2073 GAGACTAATATCCAGA-TATAGAAGGAACTCAAACAAGT------TAAAA 2115
                          i    vi        -    v  i      vv    v ------     
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_66064923_6   2116 A---AAAT--CTCA-TTGAAAAATGGGCAA-GCACATAAATTGACATTTC 2158
                          ---    -- i  -  ?            - v iv i   v        
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_66064923_6   2159 TCAAAAGAAGACAGACAAATGGCAAATAGGTATATGAAAATAAGTGCT 2206
                           v        i v         v    i i i       v --    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGCT 892

Transitions / transversions = 1.59 (146 / 92)
Gap_init rate = 0.02 (17 / 892), avg. gap size = 1.59 (27 / 17)  


1329 25.95 15.03 1.27  chr1_66071358_66072979      500  1131 (491)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr1_66071358_6    500 AAAGAAAAAAACAGAGTTAGAGGATTTACACT------------AAGTGA 537
                            i i  i    i    i     i i     ------------  v v 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_66071358_6    538 TT---------------TTAAGACAATATTCTATTGGCATAAGGATAGAC 572
                         i --------------- i      i i vv  i                
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_66071358_6    573 AC--------------TAAGATAGAGAGTCCAGAAATAATTCCATGCCTA 608
                          i--------------  ii  v                vi    i v v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_66071358_6    609 TACCAGCAAGTAATTTTC--TAAG-----TAA-----CTTAAAGAGGAAA 646
                           iviv   v i      --i   -----i  -----i i  v i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_66071358_6    647 AAGGTAGTATTTTCAACAATTAATGTTGGA-----TG-----TTATATGG 686
                         i i-    v          v ii  i   i-----  -----ii i   v
  L1M4_orf2#LINE/    390 GAA-TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_66071358_6    687 GAAA--ATTAATTTGTATAA-TAACTCATGCTATATAAAAAAATTAACTC 733
                         i   --  v  v   v ivv-  v    ii i     v            
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_66071358_6    734 AAAATGAA-CATATAC----ATATGAAACTTAAA--TATATAACTTCTAG 776
                               i -  ? v  ----  i i i vi    --    v    ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_66071358_6    777 AAGGAAATATAGGAACATAATCTATGAAATGATGGGTTGATCAAAGATTT 826
                            i   i     ?ii -     vi vi ivv      iiv   v i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_66071358_6    827 CTTAGA----ACACAAAATGT-CAGACCATATAA-----AATTAATAAAT 866
                               ----    v   v i-  ii v i v  -----   vi      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_66071358_6    867 TGGAAAATTC--TAAACCTAAAAACTTTGCTGTTT-AAAAGACATTGTGC 913
                             v--   --i   vi          vv  i  -   i    i i vv
  L1M4_orf2#LINE/    638 TGGAC--TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_66071358_6    914 AGAAAATAAAACGACATGTCTCAGCCTTGAAGGAAATGTTTACAAAGCAT 963
                              i i   v    vvi v   vv v i  i    i   i    v   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_66071358_6    964 ATATCTTGTAAATAATTTGTTTTCAAAACATGTAAGCAACTCTTACAAAC 1013
                               vi   ivi i    v i  i  i  i   iv           vi
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_66071358_6   1014 CAGTAG---GGAGAAAAATCACCAAAT---AAAATTATGGGGGAAAAG-- 1055
                           i  i---ii   v    v   v   ---     ----   v   i --
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAAT----GGGCAAAGGAT 831

  chr1_66071358_6   1056 TCGAACAT-CATTTCACAAAAGAAAATATATGAATGGAAGATAAACACAT 1104
                          i   i v-      v v      i     ii     vvi    i     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_66071358_6   1105 GAAAAGATGCTCAACATTGTTAGTTCT 1131
                                          ii????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (98 / 64)
Gap_init rate = 0.04 (26 / 719), avg. gap size = 3.96 (103 / 26)  


3508 23.47 3.29 0.34  chr1_66119981_66122673.rev     1321  2202 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_66119981_6   1321 TGGAGAGGGAATCTATGTTCATGGCTTTGAAGAATTCATATTGTTAAAAT 1370
                             i  iv vi i          v  v     v  v          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_66119981_6   1371 GTCCATACTATCCAAAGTGATCTACAAATTCAGTGTAATTTCTATCAAAA 1420
                          v v     vi     v         i     ii i   ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_66119981_6   1421 TTCCAATGGCATTTTTTCACAGAAATAAAATAACCAATTCTAAAATTTGT 1470
                          i   iiv  v      -i       vi vv i ii  i        ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_66119981_6   1471 TTGGAACCATAGAATTCCCTGAATAGCTAAAGCAATCTTAAGCAAAAATA 1520
                         v     viii iiivv   v       i   i       i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_66119981_6   1521 ACAAAGCTGAAGGCAC-CACACTACCTGATTTCAAAATATACCACAAAGC 1569
                               i  i   -  -      v  ii         iv   i       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_66119981_6   1570 AATAATAATCAAAACAGCATGGTGCTGTCATAAAAACAGATACATAGACC 1619
                         v i i       i    ii    i   v     ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_66119981_6   1620 AAAAGAACAGA-----GAGCCCAGAAATAAATCCACACATTAATGGTCAA 1664
                           vi   i   -----   i           i   i     v        
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_66119981_6   1665 TTGATTTTTGACAAAGGAGCTAAGAATACACAATG-----AGAATATTCG 1709
                                 i     i  v  i    vi iv     -----      v  v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_66119981_6   1710 TT--AATAAACGATGTTGGCAAAACTAGATATTCACATTCAAAAGAATGA 1757
                           --  i   i i  i   v v    i    ?i     v           
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_66119981_6   1758 AATTAGACCCTCATCTCATACCATAAACAAAAATCAACTAAAAATTGATT 1807
                          i  i     ii i    i      v        i    v     v   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_66119981_6   1808 TAAGAGTTAAATGTAAGATCTGAAAATGAAAAACTACCAGAAGAAAACAT 1857
                         v?   vi           v  i   v iv      vii            
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_66119981_6   1858 AGGGGAAAAGCTCCATTACACTGGTCTGGGTAATACTTTTTTTAGGTATA 1907
                            ? v   v  i i v  vi   vi i  i   iv   i  -  i   i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chr1_66119981_6   1908 AACCTGAAAGCATGAGCAACAAAAACAAAAATAAACAATTGGGATTATAT 1957
                          vv ii      ii          iv       i i  v v   i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_66119981_6   1958 CAAACTGAAAAGCTTCTGTACAGCCAAGCAAACAATCAACAGAGTAAAGA 2007
                             v v    i   i   i vv v   v v  v     v i   i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_66119981_6   2008 GACAACCTACAAAATGGGAGAAAATATGTGCAAGCCACACAGCTGATAAG 2057
                                i   i               v     ii  i i v        
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_66119981_6   2058 GGATTAATAGCCAAAATATATAAGGAACTCAAACAACTCAATACTAA--- 2104
                            i vi  v   i         i      vv           v   ---
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_66119981_6   2105 ------T-------TTTAAACATGGACAAAAGATCTGAATAGACATTTCT 2141
                         ------ -------  ?   v    i    i   i               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_66119981_6   2142 CAAAAGAAGAAACACAAATGCCCAATAGGTATATGAAAAAACGTTCAACA 2191
                          v        v i       v      i i i       i i i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_66119981_6   2192 TCACTAATCAT 2202
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.64 (126 / 77)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.56 (32 / 9)  


2007 12.81 4.21 28.49  chr1_66326427_66328529.rev      497  1612 (491)    L1M4_orf2#LINE/L1       64   908 (0)  

  chr1_66326427_6    497 AAAACGATCTTCAGAGCCAGTGCAATGCCTGACACAATTCCATTGGCCCT 546
                            vi     v    vi  ii     v   iv  v   i   viv   i 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr1_66326427_6    547 TTTTTTTTCTTTCAGAAATTGAAAAGCTGATTCCAGAATTCTTATGGGGT 596
                             v-------          v        i i i     v     iiv
  L1M4_orf2#LINE/    114 TTTTG-------CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_66326427_6    597 TACAAAGGCCCCTAAATAGCCAACACCATCTTGAAAAAGAA---CAAAGT 643
                          i   i  v   vi         v  v              ---      
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_66326427_6    644 TGTAGGATTTACTATTCCTGATTTCAAAGTCTTA-------GTTATA--- 683
                           v    i i  vv    ii        i-    ------- i  i ---
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAA-CTTACTACAAAGCTACAGTA 255

  chr1_66326427_6    684 ----AGACAGTGTGATACTAGCATAAGGATATACATAGAGATCAATGGAA 729
                         ----          i    i           v     v            
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_66326427_6    730 TGGGAATTGAGAGTCCAGATATAAACTCACACATGTATGGCCAATTAATT 779
                          i -               v      i  i    v     i     i   
  L1M4_orf2#LINE/    306 TAG-AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_66326427_6    780 TTCTACAAGGGTTCCACAACAATTTAATGGGGAAAGAACAGTCTTTTCAA 829
                            v        v   vi  v   i             i           
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_66326427_6    830 CAAATGGTGAGGAGATAACTGGCTACCCACATAACAAAGAATGCAGTTGG 879
                                  vv i  i      v  ?      ivv        v      
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_66326427_6    880 ACTCCTACCTTACAACATATTAAAAAATTATTTCAAAATTTATCAGAGTC 929
                           i       i   v     vv        vi       vv    ?  --
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG-- 502

  chr1_66326427_6    930 CAAACTTTATTTTTCATTTTATTTATCTTATTTTATATATTTTTTGAGAC 979
                         --------------------------------------------------
  L1M4_orf2#LINE/    503 -------------------------------------------------- 502

  chr1_66326427_6    980 AGGGTATTGCTGTGTCACCCAGACTGGAGTGCAGTGGCATAATCATAGCT 1029
                         ----------------   --------------------   --------
  L1M4_orf2#LINE/    503 ----------------ACC--------------------TAA-------- 508

  chr1_66326427_6   1030 TACTGCATCCTCAAACTCCTGGGATCAAGGGATGCTCCTGCCTCCGCCTA 1079
                         -------------------------------   ----------------
  L1M4_orf2#LINE/    509 -------------------------------ATG---------------- 511

  chr1_66326427_6   1080 CTGAGTAGCTAAGACTACAGGCATGTGCCACCACACCTGGATAATTTTTC 1129
                         - i  -      i    i -------------------------------
  L1M4_orf2#LINE/    512 -TAAG-AGCTAAAACTATA------------------------------- 528

  chr1_66326427_6   1130 ACTTTTTTGGAGAGATAGGTCTCACTATGTTGCCCAGGCTGATCTCAAAT 1179
                         ----------------------------------------------   i
  L1M4_orf2#LINE/    529 ----------------------------------------------AAAC 532

  chr1_66326427_6   1180 TCCTGCCTTCAAGCTATCCTCCCATCTTGGCTTCCCAAAGTTCTGGGATT 1229
                           i ----------------------------------------------
  L1M4_orf2#LINE/    533 TCTT---------------------------------------------- 536

  chr1_66326427_6   1230 ACTAGCACCCCAGCACCCCCAAACCTTAAGTTGCAGAAGAAAGCACAGGA 1279
                         ----------------------------------        i  i   ?
  L1M4_orf2#LINE/    537 ----------------------------------AGAAGAAAACATAGGN 552

  chr1_66326427_6   1280 GTAAATTCTCATAACCTTTTGTTAGGTAATGGTTTCTTAGAAGGGACACC 1329
                               ii  i i     vv      i              viv      
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_66326427_6   1330 AACAGCACAAGTGACAAAAGAAAAAA-ATGCAAATTTGACCACATCAAAA 1378
                           v        ii             - vii     v   iv        
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_66326427_6   1379 TTAA-------TGTGCTACAAATGATAATATCAAGGGAGTAAAAAGACAA 1421
                             -------      v    v  i v       ii   i         
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_66326427_6   1422 TCCATAGAATAGGAGAAAATATTTGCAAATTATATAATCAATAATCAGAC 1471
                         i   i     i                   i     viii    --i i-
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA--GGG- 749

  chr1_66326427_6   1472 ATACTTGTGTCCAGAATATATAAA---------TAACTCAATAGTTTAAA 1512
                         --      i               ---------i         i vv   
  L1M4_orf2#LINE/    750 --ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_66326427_6   1513 AATA--TAAT--AATTTAAA--TGGG-----GATTTAGATAGATGTTTCT 1551
                         i i --   i--    ?   --    -----     ii     ii     
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_66326427_6   1552 C-AAAAAAAATATAAACAGATGGCCATTA-GCACATGAAAAGATACTCAC 1599
                          -   i  i     --  i       v  -              i    v
  L1M4_orf2#LINE/    848 CCAAAGAAGATATA--CAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_66326427_6   1600 CATCATCATTCAA 1612
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (84 / 55)
Gap_init rate = 0.03 (25 / 845), avg. gap size = 14.60 (365 / 25)  


3343 17.62 2.72 2.72  chr1_66342655_66345150      804  1501 (995)    L1M4_orf2#LINE/L1        1   698 (210)  

  chr1_66342655_6    804 TAGAAGAACGTCCTATGTTAGTGGATTGGAAGACTCAA-ATT-TTAAGAT 851
                          i   ii ii   i     vi              i  -   -       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_66342655_6    852 GGTATTACTCCCCAGATTCGTTTACAGATTCAAAATAATCCTTATCAAAA 901
                           i v         i   vi i           vii     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_66342655_6    902 TTCCAGTTGCTTTCTTTTTTTTGGAGAAATTGACAAGCTGATCCTAGGAT 951
                          i    i   i  -----     v                      ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-----TTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_66342655_6    952 TCATATGGAAATGCAAGGGACCTATAAAAAACAAATCAAACCTTGAGGGG 1001
                                               i v  v iv    v   -i     ----
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGA---- 190

  chr1_66342655_6   1002 AAAAAAAAAAAAGAAATTGGAGGATTCACACTTTCCAATTTAAAAATTTA 1051
                         -    i  i  vi  i        i        i       v    i   
  L1M4_orf2#LINE/    191 -AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_66342655_6   1052 CTAAAATG-----GTA---------GTATAGTACTGACATAAGG-TAGAC 1086
                            v  v -----   ---------  i i      i       -     
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_66342655_6   1087 ATATACAGATTAATAGAATAGAATTGAGAGGCTAGAAATAAATCTATGCC 1136
                              --   i   i               v i         i i  i v
  L1M4_orf2#LINE/    290 ATATA--GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_66342655_6   1137 TGTATAATCAATCTATTTTTGACCAAGATGCCAAGGCAATTCAATGGGGG 1186
                          v   ii     iv     i   v i i       i v           i
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_66342655_6   1187 AGTGGGGGAATCGCCTTTTCAACAAATAATACAGAGACAACTGGATATCC 1236
                          i-----    v i             ii i v i            ?  
  L1M4_orf2#LINE/    388 AA-----GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_66342655_6   1237 ACATGCAAAAGAATGGAATTGGACTTCTAATTTACTCCATGTACAAAAAC 1286
                                        i i      ii   vi i  v    i        i
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_66342655_6   1287 TAAC-CAAAGTGAATCATAGATCTAAAAGTAAGAGCTAAAAGCATAACAA 1335
                             -    i  i    ?   i     v             vi    v v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_66342655_6   1336 TCTAATAAGAAAACACAGGAGTAAATATTCATGACCTAGGGTTAGTCAAT 1385
                            v v         i   ?      v   i      v       v    
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_66342655_6   1386 GGTTTCTTAGCTATGACACCAATTACATAAATGACAAA-GAAAAAATAGA 1434
                                   v           vvi  i  iii     -           
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_66342655_6   1435 TGAAATGGATTTCATTAAAGTGAAAAACTTTTTGTTCTTCCAAGGACGCT 1484
                          i  v    i     i   i v          -  v    v      i  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACT 681

  chr1_66342655_6   1485 ATTAAAACAGTGAAAGG 1501
                           i  i v       i 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAG 698

Transitions / transversions = 2.00 (80 / 40)
Gap_init rate = 0.02 (13 / 698), avg. gap size = 2.92 (38 / 13)  

1098 15.79 0.00 1.75  chr1_66342655_66345150     1795  2022 (474)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_66342655_6   1795 AAAAAAGTGAAAGGACAACCCACCGAATGGGAGAAAATATTTGTTAATCA 1844
                           i         i          v                   iv     
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_66342655_6   1845 TGTATCTGATAAGGGACATGTTTCTAGAATACACAAAGAATACTTACAAT 1894
                          i               v   v  i      i i      iv       i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_66342655_6   1895 TCAACAACAAAAAGCCACAGACCGTAACTAACAAATGGGCAAAGGATTTG 1944
                             i  i      v  v v v vi  i ? v                  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_66342655_6   1945 AATAGGCATTTCTCCAAAGAAGAAACACAAATGGACAATGATCATATGAA 1994
                              i                 v i        v    i v  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_66342655_6   1995 AGTAGACTGTCATACCATTAGTCATTAG 2022
                          --   -  - vi v   i ????????
  L1M4_orf2#LINE/    885 A--AGA-TG-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (19 / 16)
Gap_init rate = 0.01 (3 / 224), avg. gap size = 1.33 (4 / 3)  


3049 26.97 1.78 1.00  chr1_66362796_66369190.rev     5004  5904 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_66362796_6   5004 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5053
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_66362796_6   5054 GGCCATACTGCCCAAGGTGATTTATAGATTCGATGCTATCTCCATCAAGT 5103
                            v     v     iv    i  i      i i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_66362796_6   5104 TACCAATGACTTTCTTCACTGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5151
                          v   iivi i  i  ii v   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_66362796_6   5152 TATGGAACCAAAAAAGGGCCCGCATCACCAAGTGAATCCTAAGCCAAAAG 5201
                                viiv  ii iv  v v  vi    ivv    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_66362796_6   5202 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAATTATACAATGAGGC 5251
                                i      vv    i  v  ii i      viv   v ii i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_66362796_6   5252 TACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGACC 5301
                                 i   i    ii    i    i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_66362796_6   5302 AATGGAACAGAA---AGAGCCCTCAGAAATAATGCCGCATATCTAAAACT 5348
                                i    ---    i  --        vv  ii i  i  viiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_66362796_6   5349 ATCTGATGTTTGACAAACATGACAAAAACAAGAAATGGGGAAAGGATTCC 5398
                          vi    v  i     ivi  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_66362796_6   5399 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5448
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_66362796_6   5449 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGG 5498
                            ii    i    v   i     v              i    i    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_66362796_6   5499 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAAC 5548
                          i ?    i       v   v       i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_66362796_6   5549 CTAGGC---AATGCCATTCAAGACATAGGCATGGGCAAGGACTTCATATC 5595
                         v    ?---   -- -   iv   v v  vv i     v ii   v  vv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_66362796_6   5596 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5645
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_66362796_6   5646 TAATTAAACTAAAGAGCCTCTGCACAGCAAAAGAAACTACCATCAGAATG 5695
                          v  i   v v  i i i i  ii vv    i  v    i  vv i i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_66362796_6   5696 AAAAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5745
                              i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_66362796_6   5746 CAAAGGGCTAATATCCAGAGTCTACAATGAACTCAAACAAATTTACAAGA 5795
                         i  i  i  vi        i v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_66362796_6   5796 AAAA-----ACAACTCCATCAACCAGTGGGCGAAGAAGAT---AACAGAC 5837
                             ----- i   i v  i? vv i     i   --   ---  i    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAG--GATTTGAATAGAC 841

  chr1_66362796_6   5838 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGC 5887
                          i     v        i  vi viii     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_66362796_6   5888 TCATCATCACTGGCCAT 5904
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.27 (25 / 11)  


3084 26.82 2.01 0.56  chr1_66498822_66500775      568  1462 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_66498822_6    568 TGGAAGAACATTCTACGCTCATGGATAGGAAGAATCAATATCGTGAACAT 617
                              ii i  i i i i        v      v i     i  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_66498822_6    618 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCTATTCCCATCAAGC 667
                            v     v     iv i  i  i       ii  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_66498822_6    668 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGCTC 714
                          v   -   v    i  -i     -   -- v  i  - iii    ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_66498822_6    715 ATATGGAACCAAAAAAGAGCCCGCATGGCCAAGACAATCCTAAGCCAAAA 764
                                 viiv  ii  v  v v  i     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_66498822_6    765 GAACAAAGCTGGAGGCGTTATGCTACCTGACTTCAAACTATACTACAAGG 814
                                 i      vv i ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_66498822_6    815 CTACAGTAACCAAAACAACATGGTACTGGTACCAGAACGCAGATATAGAC 864
                                  i   i   iii         i iv  i iiv v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_66498822_6    865 CACTGGAACAGAAC--AGAGTCCTCAGAAATAACACCACATATCTACAAC 912
                           v     i    i--       --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_66498822_6    913 CT-CTGATCTTTGACAAACTTGACAAAAACAAGCAATGGGGTAATGATTC 961
                          v-i    i  i     ivv  v   i v  vv        v  vi  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_66498822_6    962 CCTATTTAATAAACGGTGCTGGAAAAACTGGCTAGCCATAAGTAGAAAGC 1011
                         i  v  i  i   i        i v      v  ?   i v i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_66498822_6   1012 TGAAACTGGATCCCTTCCTTATACCGTATACAAAAATTAACTCAAGATGG 1061
                             ii    i    v   i i   i                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_66498822_6   1062 ATTAAAGACTTAAATGTAAGATCTAACACCATAAAAACCCTAGAAGAAAA 1111
                           i ?    i           v    v  i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_66498822_6   1112 CCTAGGCAT------TCAGGACATAGGCATGGGCAAAGACTTCATGACTA 1155
                          v    ?i ------  iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_66498822_6   1156 AAACACCAAAAGCAATGGCAACAAATGCCAAAATAGACAAATGGGATCTA 1205
                         vi            vvi        v vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_66498822_6   1206 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 1255
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_66498822_6   1256 CAGGCAACCTACAGATTGGGAGAAAATCTTTGCACTCTACCCATCTGACA 1305
                         v  i     i     v           v      vvii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_66498822_6   1306 AAGGGCTAATATCCGGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 1355
                          i  i  vi     i    v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_66498822_6   1356 AAAACAA----CTCCATCAAAAAGTGGGCAAAGGATATGAACAGACATTT 1401
                           i    ---- i v  i?    i            v    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_66498822_6   1402 CTCAAAAGAAGACATTGATGCAGCCAACAG--ACATGAATAAATGCTCAT 1449
                            v        i  vv viii     i i--       v i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_66498822_6   1450 CATCCCTGGTCAT 1462
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


3189 27.53 0.44 0.44  chr1_66658128_66664404     4877  5784 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_66658128_6   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_66658128_6   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAGTGCCATCCCCATCAAGC 4976
                            v     v     iv i  i          ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_66658128_6   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAGAAACTGCTT-TAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_66658128_6   5025 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_66658128_6   5075 AACAAAGCTGGAGGCATCACACTTCCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv          ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_66658128_6   5125 TACAGTAACCAAAACAGCATGGTACTCTTACCAAAACAGAGATATAGATG 5174
                                 i   i    ii       vvi iv ii i   v        v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_66658128_6   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 5222
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_66658128_6   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_66658128_6   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_66658128_6   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_66658128_6   5373 TTGAAGAATTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          ii?   vi    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_66658128_6   5423 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5472
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_66658128_6   5473 AACACCAAAACTAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5522
                         i         vi vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_66658128_6   5523 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_66658128_6   5573 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5622
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_66658128_6   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5672
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_66658128_6   5673 AAACAAACAACCCCATCAAAAAGTGGGGGAAGGACATGAACAGACACTTC 5722
                          i     i     v  i?    i    vi     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_66658128_6   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTTACC 5772
                           v        i  vi viii     v  i          i     i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_66658128_6   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (145 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3145 27.10 0.66 0.22  chr1_66744462_66746866.rev     1011  1914 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_66744462_6   1011 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 1060
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_66744462_6   1061 GGCCATACTACCCAAAGTAATTAATACATTCAATGCAATTCCCACCAAAC 1110
                            v     v      v i  iv i v      i     i  i i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_66744462_6   1111 TACCATTGACATTCTTCACAGAATCAGAAAAAACTACTTTAAATTCCATA 1160
                          v   vivi v  i  ii     viv  v  iviv iii    v i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_66744462_6   1161 TGGAACCAAAAAAGAGCTCATATAGCCAAGACAATCCTAAGCAAAAAGAA 1210
                              viiv  ii  v iviv        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_66744462_6   1211 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 1260
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_66744462_6   1261 CAGTAACCAAAACAGCATGGTACTGGTACCAAAGCAGACATGTAGACCAA 1310
                               i   i    ii         i iv iiii      i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_66744462_6   1311 GTGAACAGAACAGAGACCGCAGAAATAACACCACACATCTAAAGCCATCT 1360
                         vv   i    iv    viv         vv   i    i  vi i  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_66744462_6   1361 GATCTTCGACAAATGTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 1410
                            i        iv   v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_66744462_6   1411 TTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAA 1460
                          i  i        i     v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_66744462_6   1461 CCAGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAA 1510
                         iii       v   i     v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_66744462_6   1511 AAACTTAAATGTAAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 1560
                          i  i         i v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_66744462_6   1561 GCAATACTATTCAGAACATAGGCATAGGCAAAGATTTCAT-GATGAAAAT 1609
                          ?ivv v v   ivi  v v  vv       v i    v -   - vi i
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGAC 599

  chr1_66744462_6   1610 GCCAAAAGC-CATTGCAACAAAAATGAAAATTGACAAATAGGATCTAATT 1658
                         i        -  -v         ivi     v  i    v   ii v  i
  L1M4_orf2#LINE/    600 ACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_66744462_6   1659 AAACTAAAGATCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGATCAG 1708
                            v v  i v   i  ii vv    i  v       vv i     vv  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_66744462_6   1709 GCAACATACAGAATGGGAGAGCATTTTTGCAATCTACCCATCTGACAAAG 1758
                         i    vi             iv  v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_66744462_6   1759 GTCTAATATTCAGAATCTATAAGGAACTTAAACAAATTTACAAGAAAAAA 1808
                          v  vi   i      v     i     ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_66744462_6   1809 ACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTTTC 1854
                             ----   v  i?    i            v    i     i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_66744462_6   1855 AAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAGAGCTCATCAT 1904
                         v        i  vi viii     i  i  i       iiv     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_66744462_6   1905 CACTGGTCAT 1914
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.34 (138 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3105 27.39 0.55 0.66  chr1_66957347_66963777     5030  5938 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_66957347_6   5030 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5079
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_66957347_6   5080 GCCCATACAGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5129
                          v v    vv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_66957347_6   5130 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5177
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_66957347_6   5178 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5227
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_66957347_6   5228 AACAAAGCCAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5277
                                iii    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_66957347_6   5278 TACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5327
                            i    i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_66957347_6   5328 AATGGAACAGAAC--AGAGCCCTCAGAAACAATGACACATATCTACAACC 5375
                                i    i--    i  --     i  vvv  i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_66957347_6   5376 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATTGGGAAAGGATTCC 5425
                          vi    i  i     ivv  v   i v  vv    v       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_66957347_6   5426 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATAGAGAAAGCT 5475
                           v  i  i              v      v  ?   i  iv i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_66957347_6   5476 GATACTGGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATGTA 5525
                           vii    i  i v   i     v              i    i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_66957347_6   5526 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5575
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_66957347_6   5576 CTAGGCA-ATACCATTCGGGACATAGGCATGGGCAAGGACTTCATGTCTA 5624
                         v    ?i- v i -    v   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_66957347_6   5625 GAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5674
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_66957347_6   5675 ATTGACCTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5724
                           ii vv v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_66957347_6   5725 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5774
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_66957347_6   5775 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5824
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_66957347_6   5825 AAAAACAAACAACCCCATCGAAAAGTGGGCGAAGGATATGAACAGACACT 5874
                           i -    i     v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_66957347_6   5875 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACACGAAAAAATGCTCA 5924
                             v        i  vi viii     v ii    i     i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_66957347_6   5925 TCATCACTGGCCAT 5938
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


 664 33.09 12.10 2.22  chr1_66967811_66969957      850  1659 (488)    L1M4_orf2#LINE/L1       19   908 (0)  

  chr1_66967811_6    850 TTATAAATAGGAATTCTTAACATCAT-AGAATGTAAATGTTTCCTACATT 898
                          i  ii  v    vv     i  ii - ii   vv   ii i  i v   
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chr1_66967811_6    899 --TGTATGTATGTAATGCAACTCAAATCATAATTCCAATGAGTTTTTTTA 946
                         -- v  iiv  vi  i    ii vv    v   i   iiv- ii     -
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT-GCCTTTTT- 116

  chr1_66967811_6    947 GTACAGAA--TAACAA------------ATTCATATGGAAGCATATAAGT 982
                         - i     -- i    ------------            iiii vii v
  L1M4_orf2#LINE/    117 -TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_66967811_6    983 CTCATAATAGTCATAAAAATTATTTCTAGAAAAGCTATAGAGATGGGCAA 1032
                          i  v     i  v  v   i--  vv i  i ivv i i  v   ivi 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATC--TTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_66967811_6   1033 CTTTT-CTTACTAGATATTAAAATTTACCGCAAAGCTACTACAGTCAAAA 1081
                           ivi-   v i -  v i    i    ii         vii i    i 
  L1M4_orf2#LINE/    214 CTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_66967811_6   1082 TAGGATAGAGTTAACCCAGGGAAA-----ATAGATCAGTG-AACAGAATA 1125
                         i  vi i vii ii vi i   v -----        i  -  i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_66967811_6   1126 AACAGACTATAA-TAGTTCAAAGTATA---AAGG--AAACAACATATGAC 1169
                         i v  v i v  -  ivi v --  i --- v  --  vii iv vi   
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAATTGATTTTCGAC 360

  chr1_66967811_6   1170 TAAAGTGACGTGACATTTTTACGGGAAAAAGATAATTCATTTAATAAATG 1219
                         v ii   v iv   vv  iv i   i   ii   i iiv  i  i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_66967811_6   1220 ATGCAGGCAATATTTGCTATCCATCTGGAGAAAATTAAAATTA-ACC--- 1265
                         i   v  v vv i v v  ?   iv  v i  i v i  i  i-   ---
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_66967811_6   1266 ACTTCATGC--TATGCAAAAATAAATGTAGGATGAATTA--GATATGAAT 1311
                           i   ii --   i       v  ivi ii   i  i --  iv i   
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_66967811_6   1312 TCAAAGGATAAA-CAGTAAAATTACTACACTGAAACTTAGGAG-AAGTCT 1359
                         vi  ii v    - vi     i vi  v vvi    v    ? -  i   
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_66967811_6   1360 TGTGCAACCTCACGGAAAGGGA--GATCTTCCTAAGCAAAGCAGGAAATT 1407
                          -i ii    ii-  vv   v -- i -   i  iii vii  vv   vv
  L1M4_orf2#LINE/    561 T-CGTGACCTTG-GGTTAGGCAATGGT-TTCTTAGATATGACACCAAAAG 607

  chr1_66967811_6   1408 CAGAAACTGTGAAAGAAAAA---GACAGA--------CAT---------- 1436
                           v  i viii         ---  i i --------   ----------
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_66967811_6   1437 ------TGTATGTCAAAGGACATCCTAAATGAAGT--AAAGACA--TAAA 1476
                         ------   iiv          iiv v  vi    --       --iv v
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_66967811_6   1477 AGACTAGGAGAAAATATTTTACCTGGAGAGCA---GTC----AAAAAGTT 1519
                            v i             ----- v i v  ---i  ----  iiiii 
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTT-----GCAAATCATATATCTGATAAGGGACT 752

  chr1_66967811_6   1520 AGTATTCTTAATATAAAAAG--CTTTGA-AATTTGATAAGAAAAATACA- 1565
                         v    i vv      v    --  i v -  i ii    v     v   -
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_66967811_6   1566 -TAG--------AAAAATGGGAAAATCATATGGACAGATTAATTTATACA 1606
                         -  i--------         v   vv  v  i i   i--    v v  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC--ATTTCTCCA 850

  chr1_66967811_6   1607 A-GAGAAAATACAAGTGGCCGATAAATACA---AAAGGTGATCA-CTCCA 1651
                          -  ii v      i     i    ii   ---    i  v   - vi  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_66967811_6   1652 TAGTCAAG 1659
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.56 (162 / 104)
Gap_init rate = 0.05 (41 / 890), avg. gap size = 2.83 (116 / 41)  


2122 24.65 5.70 0.62  chr1_67020490_67022130.rev      502  1150 (491)    L1M4_orf2#LINE/L1      227   908 (0)  

  chr1_67020490_6    502 ATTTCAAGACTTAGTATAAAGCTATCGTGGTCAAGACAGCATGCTATTGG 551
                                i     v  i       iv  ii         ii  v  i   
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr1_67020490_6    552 CAAGAGAATAAACAAATATATAGAATAGAACAGAATAGAGAGCCTAGTAA 601
                           vi  i   i   v   v  v-   i   i     v     i i  v  
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATC-AATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_67020490_6    602 TAGATCTGCCAAAATATAGTCAGCTGATCTTTGACAAAAG----AAGAA- 646
                           i i iiivv vv   i    ii    i  i     ii ----    v-
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_67020490_6    647 AGGCAATAGAAAAAAGATAGTCTTT-CAACAAATGGT---------ACTA 686
                          vv    i ii   ii         -           ---------   i
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_67020490_6    687 AATA----------------CGAACCTAGACACAGACTTTACACC-TGTC 719
                         i   ----------------i   vi i   v vv  i i     - i -
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT- 474

  chr1_67020490_6    720 ACAAAAATTAACTCAAA-TGGATCATAGACCTGAATGTAAAATGC-AAAA 767
                                          -       ?      i       i -  -    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAA 523

  chr1_67020490_6    768 CTATAAAACTCCTAGAAGATAACATAGGAGAAACACTAGATGACCTTGGA 817
                                    i       v        ? v  vv  vvi         i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_67020490_6    818 TCTTACAATGACTTTTAAAATACAACACCAAATGCATGATCCATTGAGAG 867
                          ivvi     ii  i v i   ii        v   ii v v i-i i  
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-AAAAG 622

  chr1_67020490_6    868 ACATAATTGATAAGCTGGGCCTCATTAAGATTAAAAACTTCTGCTCTGCA 917
                          v v   v     ii   i i    i  i           i  iv  v  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_67020490_6    918 AAAGACACTGTCAAGAGAATAAGAAGACAAGTCACATACTGA-AGATAAT 966
                           i      i      i i i i       vi    v v  i-   v   
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_67020490_6    967 ATTTTCAAAAGACATTTCTGATACATTACTATTATCCAAAATATACAAAG 1016
                             v    vv i  v       vivv   vv      i      i    
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_67020490_6   1017 AACTCTTAAAACCCAACAATAAGAAAATAAACAACATGATT--AAAATGG 1064
                                 v   i   i     i  i i   i   vii   --       
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_67020490_6   1065 GCAAAAGACCTGAAGAGATACCTCACTGAAGAAAATATACACATGCCAAA 1114
                              i  ii    v   i ii  v ii     i       v   v v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_67020490_6   1115 GTAGCATACAAAAAGATACTCAACATCATATTATTA 1150
                         vv    i ii       i          ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (99 / 59)
Gap_init rate = 0.02 (14 / 682), avg. gap size = 2.93 (41 / 14)  


2158 25.71 6.88 2.47  chr1_67056984_67062964.rev     2331  3100 (2881)    L1M4_orf2#LINE/L1       10   813 (95)  

  chr1_67056984_6   2331 ATTTCATATGCATGCATTGGAACATTCAGTATTGTAAAGATATCAGTTAT 2380
                           ii   i v    v       v i i i      v     iv  i vv 
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_67056984_6   2381 TTGTAATTCGATGTATAGATTCAATCCAATCTTAATCAAAATCCCAGCAA 2430
                         iivi  v i   v  i        iv     iiv              vi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_67056984_6   2431 TCTTTTTTGTAGATATCAGCTAATTTATTCTATAATTTATATTGAAGAAC 2480
                         i        i   v  iii v ii v  i   v    i    v   ivi 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_67056984_6   2481 AGAGGATTTAAAACAGCCAGCCCAACTCTGGAAAAAAAA----AAAGT-G 2525
                          ii   iii i  i     ivv   -   v      i  ----     - 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_67056984_6   2526 AAGGACTCACATTACCTGATTTCAAGCATAAGTATAGAGCTATCACAATC 2575
                         i          i v  ii       ivv v v  i i     ivii    
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_67056984_6   2576 AAGTACA--------CTG--ATAA--ATAAA-----------ATGGAATA 2602
                            -   --------   --    --   i -----------        
  L1M4_orf2#LINE/    259 AAG-ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_67056984_6   2603 CA-----GAGCTCAGAAATAGAACCACACTAATATAATCAACTGATTTTT 2647
                         v -----   ii        i v   i  vvv   ii    i       i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_67056984_6   2648 TACAAAAATACAAAGGCAATTCAATGAAGAAAGAATTCTCTTTTCAATAA 2697
                         v    iii i v   i v        ii        vv         i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_67056984_6   2698 ATGTTGATGGAAAAATTGAACATCCATATGCAAAAAAAAAGAGAGAGAGA 2747
                            v  v   i v  i  i i ?   i        i  vii  v------
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT------ 451

  chr1_67056984_6   2748 GAGAGCATAGACACAGACCTTACATCTTACTCAAAAATTAACTCAAAATG 2797
                         ------- i   v vv    i   i v  iv                   
  L1M4_orf2#LINE/    452 -------TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_67056984_6   2798 GATCATGGGCCTAAAGTTAAAATGC-AAAAGTAAGAAACTTTTTGAA--A 2844
                              ?i i      vv   i -  -    v  vi     i  v   -- 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_67056984_6   2845 AACATCAGGAAAAAATCTGTGTGATCTTGGCTTTGGTAATGGAATTTTAG 2894
                              -   ?iv      vi    i     v  v  i     vv i    
  L1M4_orf2#LINE/    544 AACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_67056984_6   2895 ATA---CACCAAAAGCACAATCCATAAAATTAGAAATTGGTAGAATTGGA 2941
                            ---              v v i    vv i    v i  -       
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA-AATTGGA 641

  chr1_67056984_6   2942 CTTT-------TTAAAAATTTTTGCTTTGTGAAATAAAATGTTAAGTGAA 2984
                            i-------       i     ivi vii  iv v v i i   vi i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_67056984_6   2985 TGATAAGACAAACCACAGGCTGGGAGAAAATTGTTTGCAAATCAAATAGA 3034
                            v       v      iv           -i           v   vv
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAAT-ATTTGCAAATCATATATC 740

  chr1_67056984_6   3035 TCATAACGGACTTTTATCCAAAGTACATATACAATTCATA-AATTTCACA 3083
                          v    v      v      i i  i   v v  i  v  -  i iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_67056984_6   3084 GTAAAAAAA------ACCCAACT 3100
                         i      i ------      i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATT 813

Transitions / transversions = 1.35 (112 / 83)
Gap_init rate = 0.02 (20 / 804), avg. gap size = 3.60 (72 / 20)  

 402 19.81 0.94 2.83  chr1_67056984_67062964.rev     5391  5496 (485)    L1M4_orf2#LINE/L1      805   908 (0)  

  chr1_67056984_6   5391 AACCCAGT-GAAAAATGAACAAAACATAGGAACAAACACTTCATCAAAAA 5439
                               i -?       ii    iv  vv   i i   i   vi    i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_67056984_6   5440 AGATATACAGATGGCATATAATAAGCATATGAAATGATGCTCAGTTTCAT 5489
                                  i     ---i        i      v        iiv   ?
  L1M4_orf2#LINE/    855 AGATATACAAATGGC---CAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_67056984_6   5490 ATGTCAT 5496
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.02 (2 / 104), avg. gap size = 2.00 (4 / 2)  


1013 24.25 20.45 3.15  chr1_67071493_67073383.rev      645  1407 (484)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr1_67071493_6    645 CATATTTGTGCAGAGCAAAAGTCAATATT-TTAAGAT-----TAT--CCT 686
                            i  ii  v vv v  i v i      -       -----  i--  i
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr1_67071493_6    687 AAATTTTGATTTATAGATTCTTTGCAATTTTAATCAAAATCTCAAGTTTT 736
                              --   i  i      vvi     iiiv         i  - i --
  L1M4_orf2#LINE/     64 AAATT--GATCTACAGATTCAACGCAATCCCTATCAAAATCCCA-GCT-- 108

  chr1_67071493_6    737 AAAGTTATTTTTTCCAGAAACTTTTCAAGATAATTCTAAAATTTATATGT 786
                         --- ii-      v      -  vv    v i  i        i     v
  L1M4_orf2#LINE/    109 ---GCC-TTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_67071493_6    787 AAATGCTAAAGGCTAAAAATAGCCAAGACA--CTTGCA---TAAAAACTC 831
                               v ii i iv i         i   --    v ---v  i   vv
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_67071493_6    832 AGT-GGAA-----ACACTTGC---TTTC----CTAGATACCAGGCT---- 864
                            -   i-----      v ---    ----  viv   v i   ----
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_67071493_6    865 TAAT-AAAACA-TATAATATTAGCA-AATTAGAGA-GTCT---TCAA--- 904
                             -  i   - i ii  i i   -  vv v   -i v ---    ---
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_67071493_6    905 -AT-GACCTGAG----CACATATAAACACTTAT-TTTATAATAAATGTGA 947
                         -  -  vi    ----  v v      v v  i-     ii v   -   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT-TGA 352

  chr1_67071493_6    948 ------AC-----TGCAGAG------TAATGGGGAAAGGACAGGATTTTC 980
                         ------  -----   vi  ------i           i i  vv     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_67071493_6    981 AAAAACTCTTGTTGAGACAATTGGATGTTCTTATAAAACAAAAATATA-T 1029
                           v  v vv  i  i     i     i?i vi  iv  -  i   iv - 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA-AAGAATGAAGT 451

  chr1_67071493_6   1030 TGG----CTTTCTTATCCTATATATAAAA-TTAATTCTGGGTATATTATA 1074
                            ----  vi  i iv i     i    -    i  viii iv  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_67071493_6   1075 GACTTAAATATGAAAAGC---AAC--------------------ATATAG 1101
                            i     i -  i   ---   -------------------- i    
  L1M4_orf2#LINE/    502 GACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_67071493_6   1102 GA------CTTCA-------GGGCTGGG-AATGTTTTTTTTAAGGAGATG 1137
                          ?------    i-------   i i  -    v   i  vi viv  ii
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_67071493_6   1138 TCTAAAGCACAATCCATAATGGAAAACAT-GATACAATTG-ACTACGTTA 1185
                         i v         v v i  vi     v  -    -     -   v i i 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA-AATTGGACTTCATCA 649

  chr1_67071493_6   1186 AAAATAA---CTCATATTCATCAAAT-ATACCATAAAGAAAAT--AAAG- 1228
                            v   ---  iv i v v     v- i  i  v      i --    -
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_67071493_6   1229 ----CCACAGAGTGAAAGAAGACATTTGCAGCTCATACAACTGA--AAGG 1272
                         ----       i  ii    i i       iv     i v    -- i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_67071493_6   1273 ACTCATA--CA-----------------TTAC----CAATAATAAAAAAG 1299
                            ii  --  -----------------    ----            ii
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_67071493_6   1300 T------CTCAAT-AAAAATTGTGCAAAGGACTTGAATAGGAAATTCTCC 1342
                         i------ i    -?    v  v        i        - v   i---
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG-ACATTT--- 845

  chr1_67071493_6   1343 CCCTCCAAACGGAAAT-CA-AAATAGG-AATAAATATATAAAAAGA-GTT 1388
                         --       - i i  -i -    i v-     ii i  i      - i 
  L1M4_orf2#LINE/    846 --CTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_67071493_6   1389 CAACTGTATCAATATCTCT 1407
                             ---    ????????
  L1M4_orf2#LINE/    893 CAAC---ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (112 / 69)
Gap_init rate = 0.07 (59 / 895), avg. gap size = 3.05 (180 / 59)  


 774 20.53 1.32 0.00  chr1_67076562_67079316.rev     1063  1213 (1542)    L1M4_orf2#LINE/L1        1   153 (755)  

  chr1_67076562_6   1063 TGGGAAAGTATCCCATGGTCAT-GATCAAAAGACCTACTATTGTTAAGAT 1111
                            i  ii         v    -   iii     i  v            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_67076562_6   1112 CGTTATACTCCCCAAACTGATCTGTAAACTTAACACAATTGTTATCAGAA 1161
                         v iv            i      ii i i i   i    ivi     i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_67076562_6   1162 TTCCAGCTGACTTCTTTCTACAAACTGACAA-CTGATTCTAAAATTCATA 1210
                          i       v   i   vi v   i      -     i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_67076562_6   1211 TGG 1213
                            
  L1M4_orf2#LINE/    151 TGG 153

Transitions / transversions = 2.88 (23 / 8)
Gap_init rate = 0.01 (2 / 153), avg. gap size = 1.00 (2 / 2)  

3072 19.34 6.22 0.00  chr1_67076562_67079316.rev     1551  2274 (481)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr1_67076562_6   1551 TAAAATTCATATGGAATCACAGAGGACCCAGAAGAGCCAAAATCATCCTG 1600
                                         vii  ii          v        iv   i  
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_67076562_6   1601 AAAAAGAG---CAAAGTAGGATGATTCACACTTCGCTGTTTCAAAAGTTA 1647
                                i---      v   v  i         v vi        v   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_67076562_6   1648 C---AAAGCAATAGTAATCAAAATCATGTGTTATTGGCACAAAGATAGAC 1694
                          ---     v i         i ivi    v  i     i  i       
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_67076562_6   1695 ATGTAGATCAATGGGATACAATTGAGAGTTCAGAAATAAACCCATTTACC 1744
                           i           i   v          i               vi ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_67076562_6   1745 TAAAGTCAACTGATTTTTT-TATGATTGCCGAGATCACTCAATGGGGAAA 1793
                           vi     i       iv-i v iv    i   i  i            
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_67076562_6   1794 GGATATTCTGTTGAACAAATTGTTCCAGGATAACTGGATTGCCACCTGGA 1843
                          i   v   v  v       v  v ii   i        v?    v  v 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_67076562_6   1844 AAAGAATGAACTTAGACCCTTACCTCATATTTT---CAAA--CTAATTCA 1888
                                   v  i     i       i iiv ---    --i   i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_67076562_6   1889 AAATTTATTAAAGAC--AGATTTAAGAGCTAAAACTGTAACACTCTTAGA 1936
                             vv  i ?    -- i  v              i   v         
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_67076562_6   1937 AGAAAACATAGGGGTAA--------GACCTTGGATTTGGCATAGGATTCT 1978
                                     ?    --------        i  v    vv  v    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_67076562_6   1979 TACATGTGACACTGAAAGCATACGTAACAAAAGAAAAAGTAGACAAATTT 2028
                           v  i      ii      i v i             i    i     v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_67076562_6   2029 GACCTTATGAAAATTTTTAAATGTT-TGCATCAAAAG-CA-TAT--ACAG 2073
                            i i  v      vvv  v v  -   v     i -  -   -- v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_67076562_6   2074 AGTGAAAAGATAACCCACAGAA--ATAGAAAATATTTGTGAAACATATAT 2121
                                   i           --iv            ii  v       
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_67076562_6   2122 CTGATAAGAG-CTTTTATC----ATATATAAAGAACTCTTACAATTCATT 2166
                                 i -   v    ----                     i   v 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_67076562_6   2167 AATAAA--GACAAATAATT--ATTCA----T---CATACAATCTGAATGC 2205
                               --         ii--   ? ---- ---  v vi  i     iv
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_67076562_6   2206 TCATTTCTCAAGAAAATATATACAAATGATCAAAAAGCATATGAAAATAT 2255
                         v        v i i  v           ii   v     i       v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_67076562_6   2256 GGTGGACGTTGTTAGCCAT 2274
                          v vi  i ii????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (76 / 60)
Gap_init rate = 0.02 (18 / 769), avg. gap size = 2.50 (45 / 18)  


3851 19.75 3.63 0.79  chr1_67079519_67082136.rev     1247  2127 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_67079519_6   1247 GAAAGACATTTCTTGTTCATAGATTGGAAGGCGTAATAGTGTTAGGTTGT 1296
                               i  ii v       i         i v     v     i v  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_67079519_6   1297 CAATACTACCTAAAGTGACTTACAGATTCAATACATTCCCT-CCAAAATC 1345
                                v  i   v   ii           ii  v     -i       
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_67079519_6   1346 CCAGTGATATTTTTT-CAGAAGTAGAAAAACCTATCCTAAAATGTATATG 1394
                             iviiv      -     i v  v  i iv          vi     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_67079519_6   1395 -AAATATCAAGAGATGCA-AATAGCCCAAACAATCTTGAATAAGAAGAAC 1442
                         -    i-    i  iv  -       v             v         
  L1M4_orf2#LINE/    153 GAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_67079519_6   1443 AAAGTTGGAAGTCTCATACTGCCTGATTTTAAAACTTATTACACATCTAT 1492
                                  i v    i   v  ii    i        i    v v   i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_67079519_6   1493 AGTAATCCAAACAGGGTGGTAGTGGAATAAAAACAAACATACGGTATAGA 1542
                                v i    v      v   v    ii i i     -----    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-----TAGA 296

  chr1_67079519_6   1543 CCAATGGAATGGAAT----GGCCCAGAAATAAAATTTCACATATATGGTC 1588
                         i         i    ----i i           viivi    v       
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_67079519_6   1589 AAATGGTTTT-GACAAAGAAGCCAAGATTATGCAATGGAGAAAAGACAGT 1637
                           v  i    -     i iv       ii  v      i    ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_67079519_6   1638 TTTGTCAACAAATCTTGTTGGGACAACTGGATATCCACATGGAAAAGAAT 1687
                         i  v         vv  i               ?       v        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_67079519_6   1688 GAAGTTGGATCCTTACCTTATACCATCTGCAAAAATAAATTCAGAATGGA 1737
                                  i  i     i i     v i       v  i   i      
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_67079519_6   1738 TCAAAGACCCCAA-ATAAGAGCTAACTCTGTAAAATTCCTAGAGGAAAA- 1785
                            ?     iv  -i          vv  i     i  i    i     -
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_67079519_6   1786 -TAGGGA-AAA-------GAAATTA--TTTGCCAACAATTTCTTGCATAT 1824
                         -    ?i-   -------  vv  i--  v v   iii      iv    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_67079519_6   1825 GACAACAAAAGCATATGCAGCTAAAGAAAAAATATATATATTGGACTACA 1874
                             v        i v   i v            v   v        v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_67079519_6   1875 TTAAAATTAGAAATTTCTGTCTATCAAAAGACATTAACAG---AGTGAAA 1921
                          i       i   i  i   viv     i    i  v  i---       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_67079519_6   1922 AAACAACCCACAGGATGGTACAAAATATTTGCAAATTATATATTTGATAA 1971
                          i           i    v v               i      i      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_67079519_6   1972 GATGCTAATAACCAGAATATATAAATAACT---ACAAATTGACAACAAAG 2018
                          ivi  vi  v              v    ---    v ii i  i   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_67079519_6   2019 AAACAG----CCCAATTAAAAGAATGGGCAAATAACTTGATTAGATATTT 2064
                          i   i----       ?   -          vi i    v    i    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_67079519_6   2065 TTACAAAGAAGATGTACAAATAACCAACAAACACAGGAAAAGATACTCAA 2114
                         i v          i       ii    i  i    v        i     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_67079519_6   2115 CATCACTAAACAT 2127
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (105 / 65)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 2.29 (39 / 17)  


3275 23.57 3.03 1.12  chr1_67143996_67146214.rev      868  1758 (461)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_67143996_6    868 TGGAATGATATTCCACATTCATGGATTCAAAGAATCAGTGTTGTTAAAAT 917
                              v     i   ii          vi    v i i i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_67143996_6    918 GTCCATGCTACCAAAAGCAATCTACAGATTCAATGAAATCCTTATCAAAT 967
                          v v  i  v  v   vii              i v     i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_67143996_6    968 TACCAATGACATTCTTCACAGAAATAGAAAAAAAGTTCCTAAAATTTATA 1017
                          v   iivi v  i  ii       v  v  ivv v          i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_67143996_6   1018 TGGAACCACAAAAGACTCAGAATAGCCAAAGCTATCCTAAGCAGAAAGAA 1067
                              vii   ii   i             i v   i i iv ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_67143996_6   1068 CAAAACTGGAGGAATCACATTACCTAACTTCAAATTATACTACAGAGCTA 1117
                             ii       v     i v  i  i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_67143996_6   1118 CAGTAACTAAAACAGCATG-TACTGGCATAAAAATAAGACATACAGA--- 1163
                               ii  i    ii  -           ii   -      i   ---
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGATCA 299

  chr1_67143996_6   1164 -----ACAGAACACAGGACCCAGAAACAAGTCACATAC--CTACAGTGAA 1206
                         ----- i    ivv  iii       i  ii -     --i  ii  v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACC-CATACATTTATGGTCAA 348

  chr1_67143996_6   1207 CTCATTTTTGACAAAGATGCCAAGAATGTACACTGGGAAAAGA-TAGTCT 1255
                         i v     i     i i        vii v  v    i     -      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_67143996_6   1256 CTTCAATAAATGGTGCTGGGA-AACTGGATATCCATATGCAGAAGAATGG 1304
                         i     i              -         ?   i     i       i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_67143996_6   1305 AACTAGACCCCTATATCTTGTCACACACAAAAAC-----CAAAATAGATT 1349
                          ii i        iv  viii  i i       i-----      i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_67143996_6   1350 AAAGACTTACATCTAAGACCTCAAACTATGAAACTACTACAATAAAATAT 1399
                          ?    i  v  v     v  v       i     vi  v  v    i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_67143996_6   1400 TGGGGAAATTCTGCAGGACACTGGACTGAGGGCAAAGACTTCCTGAATAA 1449
                         v  ? v  v   v iv   vi   ii i--     v ii   i ii   v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATAT 596

  chr1_67143996_6   1450 TACCCCACAAGCACAGGCAACCAAAGCAAAAATAGACAAATAGGATCATA 1499
                         v  v   v       i     v    v         i    v   iivi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_67143996_6   1500 TTAAG-TTAACAAGCTTTTGCACAGCAAAGGAAACAATCAACAAAG---- 1544
                          i  i-    -  i      ii vv       v  v     v    ----
  L1M4_orf2#LINE/    647 TCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_67143996_6   1545 -AGACAACCTACAGAATGGGAGAAAATATTTGCAAACTACCCATCTTAGA 1593
                         -        i                          ii ivi    v v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_67143996_6   1594 AGGCACTAATAACTAGAATATATAAGGAGCTCAAACAACTCTATTGAAAA 1643
                            v   vi  v i           i  i   vv       v  viv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_67143996_6   1644 AAGTCTAATAATCTGATTTAAAAATGGGCAAAAGATCTGAAGAGACATTT 1693
                            v v     i ii   ?             i   i    v        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_67143996_6   1694 CTCAAAAGAATACATACAGATGGCAAAAAAAGTGTCCATCAACAGATG-- 1741
                            v      v i     i     v  v  --- iv   v  v     --
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAA---GCACATGAAAAGATGCT 892

  chr1_67143996_6   1742 -AATGCATCAAAACCACA 1758
                         -  --     ????????
  L1M4_orf2#LINE/    893 CAA--CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (124 / 82)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.47 (37 / 15)  


1426 29.37 4.54 0.22  chr1_67200619_67205633.rev     2226  2688 (2327)    L1M4_orf2#LINE/L1        7   489 (419)  

  chr1_67200619_6   2226 GAT-TTTTATGTTTATTAATTAGATGGTTTGATATAATT----TGTCAGT 2270
                            - iii     i  vi   i  v ii  i    vi  ----  v  i 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_67200619_6   2271 TCTTAGCAAATTCATCTATAGATTCAACACCACCCC------AACTCTAT 2314
                         v  ivv      v     i         i v i   ------  ii i -
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA- 105

  chr1_67200619_6   2315 GGGAAGATTTTTGTAGATATTGACAAGCAGATTTTTAAATTTATGTGGAA 2364
                          vvivvv      i   v          v   ii v     i  i     
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_67200619_6   2365 TTGCAAAGGACTTAGTATAGTCAAATCAGTTTTCAAAAATAACAGC---T 2411
                         v     i    ii  v    i    v  i i  v     v  v i ---v
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_67200619_6   2412 TTAGAGGATTTACCCTACTTGATTTCAACACTTCTTATAAAGCTTCAGTA 2461
                           i     i i  v  v iii       v    vi  i      v     
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_67200619_6   2462 ATCAAGACACTGTGATATTGGATTAAGAGTAGACA----GACCAGTGAAA 2507
                                  v    i  i   vv    ii      ----  i  i  i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_67200619_6   2508 CAGAACAGAGAATCTAGAAATAGAAATATAC-CATGTGGGCAATC-ATTT 2555
                         i    iv    i  i       i vvi    -iv i   v    i-    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_67200619_6   2556 TTGTCAAAGGTGTGAAAATAGATCAATGAGGAAAAGATAATGTCTTCAGC 2605
                          i v   i    iv  i iviv      i     ii   i v i    i 
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_67200619_6   2606 AAATGTTGGTAGAACAATTTGACATCTGTATGCAAAATAGTGAACCTTGA 2655
                              v  v i i    i v  i ? iii        v i    vi v  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_67200619_6   2656 CTGTGACCTTGTGGAATATACAAACATTAA-TCA 2688
                          iviv    iiiivv         v     -   
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCA 489

Transitions / transversions = 1.55 (82 / 53)
Gap_init rate = 0.02 (9 / 483), avg. gap size = 2.44 (22 / 9)  

 678 22.86 5.71 0.95  chr1_67200619_67205633.rev     3473  3682 (1333)    L1M4_orf2#LINE/L1      479   698 (210)  

  chr1_67200619_6   3473 AAACTAATGTTAAAA-GGTTCATAGACCTAACTGTAAAAGCTAAAACCAT 3521
                            i   i- i    -  v   ?        v     i         i  
  L1M4_orf2#LINE/    479 AAATTAAC-TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_67200619_6   3522 AAAACT---AGAAGAAAAGATAGGAGAAGATCTT--TGACTTTTGGTTAC 3566
                               ---         v     ? v i     --    i  v     v
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_67200619_6   3567 ACCCAGGTTTCATTAAA----AAGTTATAAGCAAGAATTATAAAAGACAA 3612
                         i vvv      -   i ---- viii v     vi iiv i      v  
  L1M4_orf2#LINE/    578 GCAATGGTTTC-TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_67200619_6   3613 TATTGAT--GTTAGACTACATCAACATTAACATTTTTTGCTCTTCAAAAG 3660
                         v  v   --i  i    v      v     v vi     iv       i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_67200619_6   3661 ACACTATTAAGAAAATGCAAGG 3682
                                i      i  v  i 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAG 698

Transitions / transversions = 1.09 (24 / 22)
Gap_init rate = 0.03 (7 / 220), avg. gap size = 2.00 (14 / 7)  

 386 18.90 2.44 13.41  chr1_67200619_67205633.rev     3981  4144 (871)    L1M4_orf2#LINE/L1      685   830 (78)  

  chr1_67200619_6   3981 AAGAAAATGGAAGG-TGAGTCACAGACTGGGAAAAAATATTTGTATTTTA 4029
                               i  i  i -ii vi      v     i          i -----
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA----- 729

  chr1_67200619_6   4030 TGTATGTGTGTGTATAGCATATGTGTGATTAAGGACTTTTATCTAGAATA 4079
                         --- ---------  --     i v    v i      v    i      
  L1M4_orf2#LINE/    730 ---A---------AT--CATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_67200619_6   4080 TATTTTTAAAAACTCGTGCAGCTCAGTAATAA---GACAAATAATGTGAA 4126
                            v---  i     v i  i    i      ---         ivii v
  L1M4_orf2#LINE/    766 TATA---AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_67200619_6   4127 TAAAAATTTGGCAAAAGA 4144
                          ?    v v      i  
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.73 (19 / 11)
Gap_init rate = 0.04 (6 / 146), avg. gap size = 4.33 (26 / 6)  

 308 17.24 8.05 0.00  chr1_67200619_67205633.rev     4440  4526 (489)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_67200619_6   4440 AAAAATGG-CAAAAGATTTAGACAGACACTTCACCAAAGAAGAAATGCTA 4488
                                 -    i     ii i     i   v          v  i v 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_67200619_6   4489 ATG-TCAA--AG---ATTAAAAGATACTCAATATTGATAGTCTT 4526
                            -i   --  ---  v       i     i  ii????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.75 (7 / 4)  


3072 24.63 5.87 1.38  chr1_67210686_67212313.rev      271  1139 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_67210686_6    271 TGGAAAGCTATTCCATGTTCATGGATTGGAAAAATCAATATTGTTAAAAT 320
                                v   i                   i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_67210686_6    321 GTTCATGCTGCCTGAAGCAATCTACAGATTTAATTCAACCCCTGTCAAAA 370
                          viv  i  v  ii  vii           i  iv   i    i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_67210686_6    371 TACCAGTGAAATTCTTCACAGAAGTAGAAAAAAATATCCTAAAATTTATG 420
                          v    ivivv  i  ii     i v  v  ivvv           i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_67210686_6    421 TGGAACCACAAAAGACCCAGAATAGCCAAAGCCATCCTAAGCAAAGAGAA 470
                              vii   ii                 i v   i i iv  ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_67210686_6    471 CAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCTA 520
                             ii       v     i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_67210686_6    521 TAGTAACCAAAACAGCATGGTACTGTCATAAAAACAGACATATAGATCAG 570
                         i     i   i    ii        v     ii i              i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_67210686_6    571 TGAAATCTATGTGTCTGAAT--AGAACACAGAACTAAATCCATACATCTA 618
                           i   -- -------    --   iiv     v    i        i  
  L1M4_orf2#LINE/    301 TGGAAT--A-------GAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_67210686_6    619 CAGTAAACTAATTTTTGACAATGGTGCCAAGAACATACACTGGGGAAGGG 668
                         ii  v  i i     i     v          v   v  v       i i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_67210686_6    669 ACAGTCTCTTCAGTGTATGGTTCAGGGAAAGCCGGGTGTACATATGCAAA 718
                          i     i    iiiv     v v    v i i  i i?v  i       
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_67210686_6    719 A-AATGACGCTAGATCCCTATCTCCTGCCTTGGACAAAAATCAAATCATA 767
                          -     v i i  i     i   vii  v iv        i  v   v 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_67210686_6    768 ATGGATTAAAGACTTA--TCTAAAACTTCAAAGTATGAAACTAGTAGAAG 815
                               i ?    i  -- v   i vi v   v   i     vv      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_67210686_6    816 AAAATATTGGGGAAACTCTCCAGCATATTGGACTGGGCAAGGATTTCTTA 865
                             i  v  ? v  v   i ivv iv    ii i     v i       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_67210686_6    866 G-TAATACCCCACAAGCACAGACAACCAAAGTAAAAATGGACAGAGGGAA 914
                          -  vv  v   v       ii    v    v      i  i i vv i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_67210686_6    915 TCACATCAAG-TTAAAAAGCTTCTGCACAGTGAAGAAAAC------AACA 957
                         iiv      i-       -   i  ii vvii   i v  ------i v 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_67210686_6    958 GTCAAGAGACAACCCACAGAATGGGAGAAAATATTTGTAAAT-----ATT 1002
                           v  i                               i    -----  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_67210686_6   1003 TGA-------------------------AAA--------ACAGCTCTATA 1019
                            -------------------------   --------   i   v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_67210686_6   1020 GGAAAAAATCTAGTAATCTGATTAAAATAATTGGCAAAAGATCTGAGTAG 1069
                         iv     iv v i   i ii   ?   -   v      i   i   i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAG 839

  chr1_67210686_6   1070 ACATTTCTCAAAAGAAGACATACAGATGGCAAACAGTCATATACAAAAAG 1119
                                  v        i     i     v  i iv  i  i-    ii
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGA 888

  chr1_67210686_6   1120 TGCTAAACATTGTTGATCAT 1139
                             v     ii????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (132 / 78)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.50 (63 / 14)  


3294 26.98 0.44 0.44  chr1_67256848_67263119.rev     4874  5781 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_67256848_6   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4923
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_67256848_6   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4973
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_67256848_6   4974 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5021
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_67256848_6   5022 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5071
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_67256848_6   5072 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5121
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_67256848_6   5122 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5171
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_67256848_6   5172 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5219
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_67256848_6   5220 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5269
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_67256848_6   5270 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5319
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_67256848_6   5320 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5369
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_67256848_6   5370 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5419
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_67256848_6   5420 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5469
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_67256848_6   5470 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5519
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_67256848_6   5520 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5569
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_67256848_6   5570 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5619
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_67256848_6   5620 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5669
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_67256848_6   5670 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5719
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_67256848_6   5720 TCAAAGGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5769
                           v  i     i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_67256848_6   5770 ATCACTGGCCAT 5781
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2906 27.13 0.88 1.53  chr1_67328410_67334631.rev     4818  5731 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_67328410_6   4818 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4867
                               i i  i    vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_67328410_6   4868 AACCATAGTGCCCAAAGTAATTTATAGATTCAAGCCTATTCCCATCCAAC 4917
                         ii v   v v      v i  i  i        vv v  i  i   v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_67328410_6   4918 TACCATTTACATTCTTCGCAGAATTAGAAAAATCTACTTTAAATTTCATA 4967
                          v   vi i v  i  i      v v  v  iiiv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_67328410_6   4968 TGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAGAA 5017
                              viiv  ii  v  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_67328410_6   5018 GAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGCTG 5067
                         v    i      vv       v  ii i      vivi       i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_67328410_6   5068 CAGTAACCAAAACAGCATGCTACTGCTACAAAAACAGTAGACATATAGAC 5117
                               i   i    ii  v     vi i  ii -----------     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-----------TAGAC 289

  chr1_67328410_6   5118 ATACAGACCAATGCAACAGAACAGAGACCTCAGAAACAACACCACATATC 5167
                            i   i     v  i    iv    vii      i  vv   i i  i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_67328410_6   5168 TACAACCATCTGATCTTCGACAAACGTGACAAAAATAAGCAATGGGGAAA 5217
                           iiii  vi    i        iv   v   i vi vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_67328410_6   5218 GGATTCCCTATTTAATAAATGATGCTGGAAAAGCTGGCTAGCCATATACA 5267
                          i  vvi  v  i  i     i      i v i    v  ?   i  i  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_67328410_6   5268 GAAAATTGAAACTGGACCCTTTCCTTACACCTTATATGAAAATTAACTCA 5317
                         i  i v    ii       i v   i     v    ii            
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_67328410_6   5318 AGATGGATTAAAGACTTAAAATATAAAACCTGAAACCATAAAAACCCTAG 5367
                          i      i ?    i    - i   i v  i    i      vi i   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_67328410_6   5368 AAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTT 5416
                                 v    ?i- v i -   iv   v v  vv i     v ii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_67328410_6   5417 CAT-GATGAAAACACCCAAAGCAATTGCAACAAAAGCCAAAATTGACAAA 5465
                          v -   - vi     v      vvv          vv     v  i   
  L1M4_orf2#LINE/    588 CTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_67328410_6   5466 TGGGATCTAATTAAACTAAAGATCTTCTGCACAGCAAAAGAAACTAGCAT 5515
                          v   ii v  i   v v  i v   i  ii vv    i  v    v  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_67328410_6   5516 CAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACC 5565
                         v i      v  i     i                 v       vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_67328410_6   5566 CATCTGACAAAGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATT 5615
                         i      i  i  v  vi          v  i  i     ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_67328410_6   5616 TACAAGAAAAAACCAA----CCCCCTCAAAAAGTGGTCAAAGCATATGAA 5661
                         v i  v     iv   ----   vv i?    i   v     v  v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_67328410_6   5662 CAGACATTTCTCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAA 5709
                         i           v        i  vi viii     i  --         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_67328410_6   5710 AAAGCACATCACCACTGATCTG 5731
                         i v  v  v  i  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (136 / 108)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.75 (22 / 8)  


3117 26.57 1.10 0.99  chr1_67354573_67360980.rev     5011  5917 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_67354573_6   5011 TGGAAGAACATTCCATGCTCATGGGGAGGAAGAATCAATATCGTGAAAAT 5060
                              ii i  i     i      ivv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_67354573_6   5061 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5110
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_67354573_6   5111 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTAGTT-TAAAGGTCA 5158
                          v   iivi i  i  ii     -   -- v  i  ii i-    iv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_67354573_6   5159 TATGGAACCAAACACAAG----CCTGCATCGCCAAGTCAATCCTAAGCCA 5204
                                ---- ii    ----  v v  v     iv     i i ivv 
  L1M4_orf2#LINE/    149 TATGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_67354573_6   5205 AAAGGACAAAGCCGGAGGCATCATGCTACCTGACTTCAAACTATACTACA 5254
                         i   i      ii     vv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_67354573_6   5255 AGGCTACAGTAACAAAAACAGCAGGATACTGGTACCAAAACAGATATATA 5304
                          i          iv  i    iiv i      i iv ii i   i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_67354573_6   5305 GACCAATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAA 5354
                           i        i    iv    vii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_67354573_6   5355 CCATCTGATCTTTGACAAACCTGACAAAAACGAGCAATAGGGAAAGGATT 5404
                         i  vi    i  i     ivv  v   i v ivv    i       i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_67354573_6   5405 CCCTATTTAATAAATTGTGTTGGGA-AACTGGCTAGCCATATGCATAAGG 5453
                         vi  v  i  i    v   i     -      v  ?   i     v   i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_67354573_6   5454 CTGAAACTGGATCCCTTCCTTGCACCTTATACAAAAATTAACTCAAGATG 5503
                         v    ii    i    v   ii    v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_67354573_6   5504 GATTCAATACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAT 5553
                            iv? v  i    ii     v       i      vi i        v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_67354573_6   5554 ACCTAGA--TAATACCATTCAGGACATAGGCATGGGCAAAGACTTCAT-G 5600
                           v   i--   - i -   iv   v v  vv i     v ii   v - 
  L1M4_orf2#LINE/    545 ACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_67354573_6   5601 ATGAAAACACTAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5650
                           - vi    i    i  vvi          vv     v  i    v   
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_67354573_6   5651 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5700
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_67354573_6   5701 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCT 5750
                             v  i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_67354573_6   5751 GACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAA 5800
                           i  i  i  vi          v  i         vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_67354573_6   5801 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCAACAGATATGAACAGAC 5850
                         v     i     i     v  i?    i       vi   v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_67354573_6   5851 ACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGC 5900
                          i     v        i  vi viii     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_67354573_6   5901 TCATCATCACTGGCCAT 5917
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


3039 26.95 0.77 0.88  chr1_67421265_67426943.rev     4280  5188 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_67421265_6   4280 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4329
                               i i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_67421265_6   4330 GGCCATATTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4379
                            v   i v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_67421265_6   4380 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 4427
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_67421265_6   4428 TATGGAATCAAAAAAGAGCCCACATAGCCAAGACAATTCTAAGCAAAAAG 4477
                                viiv  ii  v  viv        i     ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_67421265_6   4478 AACAAACCTGGAGGCATCACGCTATCTGACTTCAAACTATACTACAAGGT 4527
                               vi      vv    i  vi ii i      viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_67421265_6   4528 TACAGTAACAAAAACAGCAGGATACTGGTACCAAAACAGATATATAGACC 4577
                                 iv  i    iiv i      i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_67421265_6   4578 AATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAT 4627
                                i    iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_67421265_6   4628 CTGATCTTTGACAAACCTGACAAAAACGAGCAATAGGGAAAGGATTCCCT 4677
                         i    i  i     ivv  v   i v ivv    i       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_67421265_6   4678 ATTTAATAAATTGTGTTGGGA-AACTGGCTAGCCATATGCATAAGGCTGA 4726
                         v  i  i    v   i     -      v  ?   i     v   iv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_67421265_6   4727 AACTGGATCCCTTCCTTGCACCTTATACAAAAATTAACTCAAGATGGATT 4776
                          ii    i    v   ii    v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_67421265_6   4777 CAATACTTAAACATAAGACCTAATAACCATAAAAAACCTAGAAGAATACC 4826
                         v? v  i    ii     v    -   i      vv i        v  v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAA-AACTATAAAACTCTTAGAAGAAAACA 547

  chr1_67421265_6   4827 TAG--ATAATACCATTCAGGACATAGGCATGGGCAAAGAGTTCAT-GATG 4873
                            --i   - i -   iv   v v  vv i     v iv   v -   -
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr1_67421265_6   4874 AAAACACTAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4923
                          vi    i    i  vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_67421265_6   4924 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAAAGTGA 4973
                         v  i   v v  i i   i  ii vv    i  v       vv       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_67421265_6   4974 ACAGGCAACCTAGAGTATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5023
                          v  i     i v  v            v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_67421265_6   5024 AAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAA 5073
                           i  i  vi          v  i  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_67421265_6   5074 AACAAACAAACCAACCCA-TCAAAAAGTGGGTGAAGGATATGAACAGACA 5122
                           - i     -i      - i?    i    ii      v    i     
  L1M4_orf2#LINE/    795 AA-AGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_67421265_6   5123 CTTCTCAAAAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCT 5172
                         i     v        i  vi vii      i  i  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_67421265_6   5173 CGTCATCACTAGTCAT 5188
                          iv     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.15 (15 / 13)  


3136 22.70 1.62 3.68  chr1_67779290_67781556      884  1808 (459)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_67779290_6    884 GAGAAA-ATCCCATGCTAATGGATTGGAAGAATAAATATCATGAAAATGA 932
                           i i -        i v             v v     ii v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_67779290_6    933 CCATACTGCCCAAAGTGATCTTCAGATTCAATACAATTCCTAACAAAATA 982
                          v     v      v      v         ii    i    v      v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_67779290_6    983 CCAACATAATTTTTCACAGAATTAGA-AATCATAATCCTAAAATTCATAT 1031
                            i vvvv     ii     v v  -  v - i                
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATAT 151

  chr1_67779290_6   1032 GGAACCA-AAAAGAGCCAAAATAACCAAAGCAACCCTAAGCAAAACAAAC 1080
                             vii-  ii  v   i    i     i   i i i --    -----
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAA----- 194

  chr1_67779290_6   1081 AAACAAACAAACAAAAAACAAATCTGGAGGCATCACACTACCAGATTTCA 1130
                         ------------i  i      vi      vv       v  vi      
  L1M4_orf2#LINE/    195 ------------GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_67779290_6   1131 AATTCTACTACAAGGCTATAGTAATCAAAACAGCATGGTACTGGTATAAA 1180
                           vii        i    i         i    ii         i    i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_67779290_6   1181 AGAAGACACATAGA------GAACAGAATAGAGAACCCAGAAATAAAGCC 1224
                         iiv     i     ------   i     v    ii           v  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_67779290_6   1225 AAATACCTACAGCCAACTGATCTTCAACAAAGCAGACAAAAGCATACCCT 1274
                          v i ii  ii i   i    i   i    i vv v   i v   v vv 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_67779290_6   1275 GGAAAAAGGAGACTCTATCCAACAAGGGGTGCTGGGAAAATTGGATAGCC 1324
                           ii    i v v   v i      iv          v  i      ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_67779290_6   1325 ACACACAGAAGAAAGAAACTAGATCCCTATCTCTTGCCATATACAAAAAT 1374
                            ii  i     v   ii i  i     i   vii              
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_67779290_6   1375 TAACTCAAAGTGGATTAAAGACTTAAATGAAAGACCTGAAACCATAAAAA 1424
                                  i     i ?    i      v    v  i    i      v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_67779290_6   1425 TTCTAGAAGGAGAAAACCTGGGAAAAACCCTTCTGGACATTGGCCTAGGC 1474
                          ii      ---     v i  ?iv  vi    vv   v    vi     
  L1M4_orf2#LINE/    533 TCTTAGAAG---AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_67779290_6   1475 AAAGAATTTATGACTAAGACCCCAAAAGCAAATGCAATAAAACAAAAAAT 1524
                           v iv  iv iiv  v   v         v v    i    v       
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_67779290_6   1525 AAATAAATGGGACTTAATTAAAATAAAAAGCTTCAGCACAGCAAAAGAAA 1574
                          i      v      v  i     v    i   iv ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_67779290_6   1575 TAATCAACAGAGTGAATAGACAACCTACAGAATGGGAGAAAATATTTACA 1624
                         iv     v i      v        i                     i  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_67779290_6   1625 AACTATACATCTGAAAAAGGACTAATATTCAGAATCTCTAAGGAACTC-- 1672
                           ii   i      v  i     vi   i      v v   i      --
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_67779290_6   1673 --AAATCAGCAAGAAAAAAAATGAAGAATCCCGTTAAAAAGTGGGCAAAC 1720
                         --  v   ii  v     i -ii  v  i  vi  ?    i        v
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_67779290_6   1721 AACATGAACAGATATTTTTCAAAAGAAGATATACAAATGGCCAACATCAC 1770
                         i iv    i   i    i  v                       ------
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA------ 872

  chr1_67779290_6   1771 TAATTATCAGGGAAA--TGCAAATTAAAATCACCATGAGA 1808
                            vi -  v i   --   --- i  v    ????????
  L1M4_orf2#LINE/    873 TAAGCA-CATGAAAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (120 / 86)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 3.50 (49 / 14)  


2268 21.47 11.41 3.12  chr1_67831999_67833728.rev      504  1239 (491)    L1M4_orf2#LINE/L1      112   908 (0)  

  chr1_67831999_6    504 TTTTTGGTAGAAATTGACCAGCT-----TA---TTCAGATGGAAATACAA 545
                              v i          v    -----  ---    v        i   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_67831999_6    546 AGGACCTAAAATAGTCAAA-TAATTTTGAAAAAGTAAAACAAA------- 587
                         i     i i     i    -i   i         v i      -------
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_67831999_6    588 --CTTACTCTACATGACTCCAAGACTTACT------CTACA--AAT---- 623
                         --  i  v  v vii i i   i       ------     --   ----
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_67831999_6    624 --GTTATGGTATTGGCATAAAGAAACACATAAAGATTAACTGAAAAGAGT 671
                         --iv i     i        i  v v     v    i  iv   v   i 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_67831999_6    672 AGAGA-CGCAGAAATGGGCCCACTCATATATGGTCAATTGATTTTTGACA 720
                         v    -iv       iii    iv   v                 i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_67831999_6    721 TAAGTGCCAAGGTATTTCAATGTGGAAATAATAATTTTTCCAAAAAATAG 770
                         vii        iivv       v     v    i i   i   v    i 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_67831999_6    771 TGTTAAAGCAA-----------------------------TAGGCCCTTA 791
                           i iiii   ----------------------------- i i   i  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_67831999_6    792 ACTTACCCCATACACAAAAATTCACTTGAAATGGGTCATAGACCTAAATA 841
                         v  i  v     i         v   ii      i   ?          i
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_67831999_6    842 TAAAAGCTAAAACTATTAAACTTATAGGA-AAAACAATTTAGCAG---AT 887
                            i            v     iv   i -      ---   v? ---  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA---TAGGNGTAAAT 558

  chr1_67831999_6    888 TATTGGAATAACTTTGAAGTAGGCAAAGATTTTTAAGATGGGATACAAAA 937
                         iv i --- i  i   iiv       v i   i v    iv  i  v   
  L1M4_orf2#LINE/    559 CTTCG---TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_67831999_6    938 AGTCATAA--AAGAAAAAAATTGGTAACACTTAAAAATGTTTAAAAATAA 985
                           -  i  --  v    i  -------------     ivv    -- vi
  L1M4_orf2#LINE/    606 AG-CACAAGCAACAAAAGAA-------------AAAATAGATAAA--TTG 639

  chr1_67831999_6    986 TATTTTA--AAATTTTAAAACATTTGTTCTTTGAAAGACATTGTTAAGAA 1033
                         v i  i --   v  v     v     v   ii  i    i i i     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_67831999_6   1034 AATGGAAAGGCAAACCACAGACTGGGAGAAAAC---TGCGAAACAAATAT 1080
                          i  i    i   v       v          i---   i  v  v    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_67831999_6   1081 TTGATAAAAGACTTGTATCTAGAATATATAAAGAACTCTTACAACT---- 1126
                         i      ii          i                          ----
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_67831999_6   1127 --TAAGAAGACAAA-AATCTAATTTTAAAAATGAGCAAAAGATATGAAAA 1173
                         --   i        -  i i    ?-       i     i   v    v 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATA 838

  chr1_67831999_6   1174 GATACTTTATCAAAGAAAATATATTGATGAC----AAACACATAAAAAGA 1219
                           i i  ivi       i     ivi   i ----  i     i      
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_67831999_6   1220 TATTCGACATTATTAGTTAG 1239
                          ii  i    i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (103 / 52)
Gap_init rate = 0.03 (23 / 797), avg. gap size = 4.65 (107 / 23)  


3052 24.66 3.59 2.02  chr1_67983788_67987895     2724  3615 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_67983788_6   2724 GAAAGAGAGTCCATGTTCACAGACAGGAAAACACAATATTGTCAAGATGT 2773
                               v vi         ii  iv    i  vi        i      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_67983788_6   2774 CAGTTCTCCCTAACTTGACCTATAGATTCAGTGCAATCACAATCAAAATC 2823
                           i v     i  v    i   i       ii      v v         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_67983788_6   2824 TCAGAAAATTATTTTATGGATATAAACAAACTGAATCTAAAGTAT-TACG 2872
                         i   vvivi v    iii  v  vi    i    vi     i vi-  i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_67983788_6   2873 AAGAAGCAAAAGGCCTAGAATAGCCAACTCAATATTGAA------GAACA 2916
                         i i v    ii i  i           vv    v     ------     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_67983788_6   2917 AAGTTGGAGGACTGACACCACTTGATTTCAAGACTTATTATAAAGCTAGA 2966
                                      v    iv iii       i     i  i       v 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_67983788_6   2967 GAAATTAAGGCAGTGTGGTATTAGTAAAGAAACAGACTAACAGGTGAACG 3016
                          v   i   i          i i i v iii i    vv i  i v  i 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_67983788_6   3017 AAACAGAAC--AGATCCTAGAAACAGACCCACATA------GTCACCTGG 3058
                         i  i    i--   vi i     i i     i i ------    vi  i
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_67983788_6   3059 TCTTTGACAAAGAAGCAAAGGTAATACAGTGGAGCAAAAATAGTATTTTC 3108
                          i  i     i iv  v   iiv  v  i   i v  i      v     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_67983788_6   3109 AACAAATAGTGCCAG---AACTGGACATCCACATTCCCTGCCCCCACCAA 3155
                                i    ii ---       i ?      -----  ---------
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACAT-----GC--------- 438

  chr1_67983788_6   3156 AAAAGAAAGAATCTAGACACAGACCT-ATAGCCTTCACAAGAATTAAGTC 3204
                                v   vi i   v vv    - i v v vi    i      v  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_67983788_6   3205 AAAATTGATCACAGAACTAAATGTAAAATACAAAACTAGAAAACTCCTAG 3254
                              v     ?   v          i vvi       v       i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_67983788_6   3255 AAGAAAACATAGGAGAAAATGTAGATGACCAAGGGTATGGCAATGGCTTT 3304
                                      ? v    v vvi     vv    vv        i  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_67983788_6   3305 TTACATACAACACCAAAGGCATGAACCACAAAAGAGAGAATA----AGCT 3350
                            v   ii        i   ii i v        i i    ---- ii 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_67983788_6   3351 ACACTTCATTAAAATGAAAACCTTCTTCTCTGCCAAAGACAATGTCAAGA 3400
                         iv       i     v    v   i viv  v v  i    v i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_67983788_6   3401 GAATGAGAAG-----CCACAGACTGGGAGAAAATATTTGCAGAAGACACT 3445
                         i i   i   -----       v                  i vv i iv
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_67983788_6   3446 TCTGATAAAGGACTGTTATCCAAAATATATATAAAGAACTCTTAAAACTC 3495
                                 i     vv      i        --           v     
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATA--AAGAACTCTTACAACTC 786

  chr1_67983788_6   3496 AAGAATAAGAA----AATAATTTGATTGAAAAATGATCAAAAGTGACCTG 3541
                           v     i  ----     iiii   ?       iv    i -- ii  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG--ATTTG 834

  chr1_67983788_6   3542 AACATATACCTCACCAAAGAAAACATACAGATGGCAAGTAAGTGTCTGAA 3591
                           i v i ii  v        i i     i     v i    iiiv    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_67983788_6   3592 AATAGGTTCAATATTACGTCACTG 3615
                           v v i    i  i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (132 / 84)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 3.85 (50 / 13)  


2973 26.67 1.79 0.45  chr1_68079031_68083371.rev     2955  3850 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68079031_6   2955 TGGAAACACATCCCATGCTCGTGGATGGGTGGAATCAATATTGTAAAAAT 3004
                               v i        i  i     v  vi  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68079031_6   3005 GACCATATTGCCAAAAGCAATCTAAAAATTCAATGCAATTCCCATCAAAA 3054
                          i v   i v  v   vii     v i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68079031_6   3055 TACCACCATCACTCTTTACAGAACTGGAAAAAACAATCCTGAAATTCATA 3104
                          v   v vv vi i   i     v v  v  ivii     i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_68079031_6   3105 TAAAACCAAAAAAGAGCCCGCATAGCCAAAGCAAGACTACGCAAAAAAGA 3154
                          ii  viiv  ii  v  v v         i   v-  vviv   i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGA 199

  chr1_68079031_6   3155 ACAAATCTGGAGGTATCACATTACCTGACTTCAAACTATACTATAAGGCC 3204
                              vi      vv     i v  ii i      viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_68079031_6   3205 AGAGCCATCAAAACAGTATGGTACCGATATAGAAATAGGCACATAGACCA 3254
                          v  iv     i     i      i ii   iii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_68079031_6   3255 GTGGAAAAGAATAGAGAACCCAGAAATAAACTCAAACACTTACAGCCAAC 3304
                         i     v     v    ii            i  v   i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_68079031_6   3305 TGATCTTCAACAAAGCAAACAGAAACATAAAGTGGAGAAAGGAAACCCTA 3354
                             i   i    i vviv  ii v   vv i   i     i v vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_68079031_6   3355 TTCAACAAATGGTGCTGGGATAATTGGCAAGCCAGATGTAGGAGAATGAA 3404
                                             i  i   vv ?   v   i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_68079031_6   3405 ACTGGATCCTCATCTCTCACC-TATACAAAAATCAACTTGAGATGAATCA 3453
                         ii    i  ii i   v    -           i    ii i   i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_68079031_6   3454 AGGACTTAAA-GTC----CTGAAACAATAAAAATTCTAGACGATAACATT 3498
                         ?i   i    -  v----  i    v      v ii    v  v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_68079031_6   3499 GAAA-AAACCCTTGTAAACCTTGGTGTAGGCAAGGATTTCATGACCAAGA 3547
                          i?i-   i i i  i -      vv       v i    v iivi v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGA-CCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_68079031_6   3548 ACCCAAATGCAAATGCAATAAAAACAAGGATAAATAACTGGGAGTTAATT 3597
                         vv     v   v v    i    iv  ii   i    v v   v  v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_68079031_6   3598 AAACTAAAGAGCTTTTGCACAGCAAAAGGGATAGTCAGCAGAGTATACAG 3647
                            v v  i i      ii vv    i iv ivi   iv i   iv v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_68079031_6   3648 AAAACCCACAGAGTGAAA-AAAATTTTTTTACAATCTATATATCTGACAA 3696
                          v          i  ii -     v   vi -    -          i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGATAA 746

  chr1_68079031_6   3697 AAGACTAATATCCAGAATCTACAACGAACTCAAACAAATTACCAAGAAAA 3746
                         ii    vi          v  i  v      vv    v i vi  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_68079031_6   3747 AAA------ACC--ATTAAAAAGTGGGCTAAGGACATGAATAGACAATTC 3788
                          i ------   --   ?    i     v     iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_68079031_6   3789 TCAAAAGAAGTTATACAAATGGCCAACAAACATATGAAAAAATGCTCAAC 3838
                           v       v               i  i  i       i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_68079031_6   3839 ATCACTGATTAT 3850
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


3523 21.35 2.11 6.13  chr1_68170550_68173252     1265  2210 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68170550_6   1265 TGGAAAGATATTTCATGTTCATGAATCAGAAGAATTTATGTTGTTAAAAT 1314
                                    ii          i  ii     v  v  i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68170550_6   1315 GTCCAGACTACCCAAAGTGATCTACAGATGCAATGCAATTATTATCAAGA 1364
                          v v v   v      v            v   i     ivi      i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68170550_6   1365 TTACAATAGCATTTTTCACAGAAATGGAATAATAAATCCTAAAATTTGTG 1414
                          iv  iiv  v     ii       v  vv iivi           ii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_68170550_6   1415 TGGAACCACAAAAGACCTTAAATAGCTAGTGCAACCTTGAGAAAAAAGAA 1464
                              vii   ii    ivi      i ivi   i     i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_68170550_6   1465 CAAAGTGGGAGGTATCACACTCCCTGATTTCAAAATATATTACAAAGCTG 1514
                               v     vv       i  ii         iv  i         i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_68170550_6   1515 TAGTAATCAAAACAGTATGGTAATGAC-T-------------TAGACCAA 1550
                         i         i     i     v  i - -------------    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_68170550_6   1551 TGGAACAGATTAGAGAGCCCCAAAATAAACTCATGTATATATGGTCAACC 1600
                              i   v v     i  vi        i   ii  v         ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_68170550_6   1601 AATCTTTGACAGGTGAACCAATAATACACAATGAGGAAAGGAAAATCTCT 1650
                         i  i  i    i v vi    v vi iv     i      i v i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_68170550_6   1651 TCAATAAGTGGTGTTGAGAAAACTAGATATCCACCTTCAAAGGAATGAAA 1700
                             i  i     i  i  v    i    ?    v v    i       i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_68170550_6   1701 TTGGACCCCTTTTACAAGGCTGTTTTTATTTAAAAGAAAAGAAGAAATTG 1750
                                   ----------------------------------------
  L1M4_orf2#LINE/    451 TTGGACCCCT---------------------------------------- 460

  chr1_68170550_6   1751 GACCCTTGCCTTTCACCATATACAAAAATTAACTCAAAATGGATTAAAGG 1800
                         -------i   iv                               i ?  i
  L1M4_orf2#LINE/    461 -------ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_68170550_6   1801 CTTAATCCATTAATCTTAAAATCTGAAACCATAAA-CTCCCAGAAGAAAA 1849
                          i   -------  v -  i v  i    i     -   ii         
  L1M4_orf2#LINE/    504 CCTAA-------ATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_68170550_6   1850 TATAGGGAAAAACTTTCTTTACATTGGTCTTGGCAGTGATTT-TTGGATA 1898
                         i     ?iv   ii   v v  v    vi v    i  i   -  i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_68170550_6   1899 TGACACCAGCAGCACAGACAACAAAAGAAAAT-TAAACAAGCTGGATTAT 1947
                                 iv      ii             v-  i i  ii    i vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_68170550_6   1948 ATTAAACTAAAAAGCTTTTGCACAGCAAAGGAAACAATCAACAAAATGAA 1997
                           i   v v    i      ii vv       v  v     v   i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_68170550_6   1998 AAGGCAATATATTAGAATGGGAAAAAATATTTGCGAATCATATATCTTAT 2047
                            i   ivi i-         i           i            v  
  L1M4_orf2#LINE/    696 AAGACAACCCAC-AGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_68170550_6   2048 AAGGGACTAATATCCAAAATGTAGAAGGAGCTCAAACAACTCAATAGCAA 2097
                                 vi      i   i  v  i  i   vv           ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_68170550_6   2098 AAACAACCAAAAAACTTAATTAAGAAATGCGCAAAGCATCTAAATAGACA 2147
                            v --    v   ii    ? i     v      v  i i        
  L1M4_orf2#LINE/    795 AAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_68170550_6   2148 TTTTTCCAAAGAAGACCTACCGATGACCAA---GTATATGAAAAAGTGCT 2194
                            i           iv   vi   i    --- i i       ii    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_68170550_6   2195 CAATATCACTAATCAT 2210
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (130 / 68)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 7.09 (78 / 11)  


 649 24.55 4.19 0.60  chr1_68174518_68178803.rev     2117  2283 (2003)    L1M4_orf2#LINE/L1       13   185 (723)  

  chr1_68174518_6   2117 CCGTGTTCATGGACTGGAAAACTGAACAAGATAAAGCTGTCAATTCTCTG 2166
                           i          i     i   v  i vvi v   v  v    v   iv
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_68174518_6   2167 CAAATTGATCTATAGATTTAATGCAATCCTTATAAAAACCCCAACATGG- 2215
                                     i     i  i       i   v    i    i -  v-
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCC 111

  chr1_68174518_6   2216 --TGTTGTAGACA----CAAGCTTATTTTAAAATTTACATAAAAATAAAA 2259
                         -- v   i   v ----      v  ii       i i  ii    iv  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_68174518_6   2260 AGGCCCTAGAACGCCCAAAATAAT 2283
                         i  v  i    iiv      i   
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAAT 185

Transitions / transversions = 1.56 (25 / 16)
Gap_init rate = 0.02 (3 / 173), avg. gap size = 2.67 (8 / 3)  

 786 25.10 6.17 1.65  chr1_68174518_68178803.rev     2661  2903 (1383)    L1M4_orf2#LINE/L1      176   429 (479)  

  chr1_68174518_6   2661 CCAAAATTATTTTGATAAAGAAAATTA----TGAAGAA-TCAGTCTTCTC 2705
                               iv  i    v      i vi ----  i  i -   vv    i 
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr1_68174518_6   2706 CATGTTAAAGCTTAACATATAGCTGCAGTAATCAATA---TGTAGTCCTG 2752
                         v  v i   i    vi i v    i          v ---   i  v   
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_68174518_6   2753 GCAGAA----AGGCACATAGATCAATGAAACAGCATAGAGAATTCAGAAA 2798
                            v  ----  i  i           i  i  v  v    i i      
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_68174518_6   2799 TAGACCCATACAAATATGCTCAACTGATTTTTAACAAAGATTTGAAAGCA 2848
                           i         vv    v    i       ii    i i viv  ii v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_68174518_6   2849 ATTCAATGTAAGAGGGATAGCCTTTTCTACG--TGGAGCAGGAGTGAACA 2896
                                 viii i i    i      v  i--   v  v  i----   
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG----ACA 421

  chr1_68174518_6   2897 A-TGGACA 2903
                          -    i 
  L1M4_orf2#LINE/    422 ACTGGATA 429

Transitions / transversions = 1.54 (37 / 24)
Gap_init rate = 0.03 (7 / 254), avg. gap size = 2.71 (19 / 7)  

1236 26.37 5.07 4.06  chr1_68174518_68178803.rev     3303  3795 (491)    L1M4_orf2#LINE/L1      411   908 (0)  

  chr1_68174518_6   3303 GTATTGGCAAACAAC--AACAACAACA-ACAACAACAACAAAA---AACC 3346
                           ii   --i     --i i ? v   -i   -  v  ii  i---i   
  L1M4_orf2#LINE/    411 GTGCTGG--GACAACTGGATAKCCACATGCAA-AAGAATGAAGTTGGACC 457

  chr1_68174518_6   3347 CCAACCTAAACTCCACACCTTATACAAAGATTAACACAAAATATATCATG 3396
                           v    ------      v        i      v      iv    ?i
  L1M4_orf2#LINE/    458 CCTACCT------CACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_68174518_6   3397 GATTTAAATGAGAAATGC-AAAACTATAAACCTTTTAGAAAGAAACATAG 3445
                           ii      vi i -  -           v  i      ii        
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_68174518_6   3446 GGGAAAATCTTTGGGACCTAGAAATGAGTGAAGAGTCTTCAGATCTGATA 3495
                          ? v       i v     v iiv ii ii v iv ii i    v   i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_68174518_6   3496 CTAAGTGCCTGATCTATTAAAGGAAAAATTAGTGTGTTTTTATCAGCGA- 3544
                          i  iv  vii v v iv    i      vii ivi  ------- -  -
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT-------G-GAC 642

  chr1_68174518_6   3545 -TAATCAAAATTAAAAATTCTTGCTCTACGAACTACCCTACTAAAAGGAT 3593
                         - v              i i   iv  v i  vv  v   ii  i iii 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_68174518_6   3594 -AAAAGACAAATTATGGGCTTGAAGAAAATACTTGTAAATCAC----TTG 3638
                         -         vii ii iv v i        i   i      i----i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_68174518_6   3639 ACAAGT-ATTTCTATCTAGAATATATAAAGAACTCTCAAAACTCAGTACT 3687
                          i   v- i  v    i                   i v      i  v 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_68174518_6   3688 TTAAAAAG--------TCTACTTAGGAATTGGGCAAAT-ACCTAAACAGA 3728
                         --      --------i i v  ?ii  v        v- ii i  i   
  L1M4_orf2#LINE/    793 --AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_68174518_6   3729 CACTTATT-AAAGAAGATGTACGGATGGCTGATAATCATGTGAAAAGATG 3777
                           i  v i-         i   ii     ii    v  ii          
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_68174518_6   3778 TTCAGCATCATTAGTCAT 3795
                         i   i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (86 / 40)
Gap_init rate = 0.04 (18 / 498), avg. gap size = 2.50 (45 / 18)  


2813 26.71 2.54 2.32  chr1_68181079_68187420.rev     4946  5851 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68181079_6   4946 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAAAATCATGAAAAT 4995
                              ii i  i     i        v      v i  v  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68181079_6   4996 GGCTATACCACCCAAGGTAATTTATGGATTCAGTGCCATTCCCCATCAAG 5045
                            v    iv     iv i  i  ii      ii  v  -   i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT-CCCTATCAAA 99

  chr1_68181079_6   5046 CTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTG---TTAAAGTTC 5091
                         v v   iivi i  i  ii     -   -- v  i   ---i    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_68181079_6   5092 ATATGGAATCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAA 5141
                                 viiv  ii  v  v v  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_68181079_6   5142 GAACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGG 5191
                                 i      vv    v  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_68181079_6   5192 CTACAGCAACCAAAACAGCCTGGTAGTGGTACCAAAACAGAGATATAGAC 5241
                               i  i   i    iv     v   i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_68181079_6   5242 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAACA 5291
                                 i    iv   ivii         vv   i    i  iiiv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_68181079_6   5292 TCTGATCTTTGACAAATCTGACAAAAACAAGACTTC----GGGAAAGGAT 5337
                         vi    i  i     ivv  v   i v  ----   ----       i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCA----TTCAATGGGGAAAGAAT 393

  chr1_68181079_6   5338 TCCCTATTTAATAAATCCCTACATATGGCTAACAGGGAAAACTGGGTAGC 5387
                         vvi  v  i  i    ----------  i--i v    v      i  ? 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAAT----------GGT--GCTGGGACAACTGGATAKC 431

  chr1_68181079_6   5388 CATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACATCTTATACAAAAA 5437
                           i   i i  iiv    ii    i    v   i   i v          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_68181079_6   5438 TTAATTCAAGATGGATTGAAGACTTAAATGTTAAACCTAAAACCACAAAA 5487
                             i    i      ii?    i       v i v       i i    
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_68181079_6   5488 ACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATAGGTA 5536
                         vi i           v    ?i- v i -   iv   v v  vv    i 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chr1_68181079_6   5537 AGGACTTCATGACTAAAACACTAAAAGCAATGGCAACAAAAGCCAAAATA 5586
                          v ii   v iiv  vi    i       vvi          vv      
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_68181079_6   5587 GACAAATGGGATCTAATTAAACTAAAGAGCCTCTGTACAGCAAAAGAAAC 5636
                           i    v   ii v  i   v v  i i i i   i vv    i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_68181079_6   5637 TACCATCAGAGCGAACAGGCAACCTACATAATAGGGAGAAAATTTTTGCA 5686
                           i  vv i  i   v  i     i   v   -          v      
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAAT-GGGAGAAAATATTTGCA 729

  chr1_68181079_6   5687 ATCTACCCATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAA 5736
                          vii ivi      i  i  i  vi          v  i        ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_68181079_6   5737 ACAAATTTACAAGAAAAAAACAA----CCCCATCAAAAAGGGGGCAAAGG 5782
                             v iv i  v     i    ----   v  i?    iv         
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_68181079_6   5783 ATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAA---- 5828
                           v    i     i     v        i  vi viii     i  ----
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_68181079_6   5829 -----AAG-TGCTCATCATCACTGGCAAT 5851
                         -----   -      v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.14 (44 / 14)  


2998 24.54 1.74 3.15  chr1_68236428_68241834     4001  4921 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68236428_6   4001 TGGAAAAACATTCCATACTTATGGAT----AGACTCAATATTGTTAAAAT 4046
                               i i  i    ii i      ----     i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68236428_6   4047 GGTCATACTGCCCAAAGCAATTTATAGATTCAATGCTACTTCTATTAAAC 4096
                           iv     v      vii  i  i        i  v iii    i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68236428_6   4097 TACCAATGACATTTTTCACAGAACTAGAAAAAAATTATTTTAAAATTCAC 4146
                          v   iivi v     ii     v v  v  iv- v  ii         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_68236428_6   4147 ATAGAACCCAAAAAGATCTCAAATAGCCAACACAATCCTAAGGAA-AAGA 4195
                           i   vivv  ii  i ivi         v      i i ii  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_68236428_6   4196 ACAAAGCTGGAGGCATTACACTACCCAACTTCAAACTATACTATAGTTGG 4245
                               i      vv i     v     i      ----   --------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACT-------- 237

  chr1_68236428_6   4246 GCAAAAGTATACTATAGGGCTACAGTAAACAAAACAGCATGGTACTGGTA 4295
                         ---------     i ii          v   i    ii         i 
  L1M4_orf2#LINE/    238 ---------TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_68236428_6   4296 CAAACACATACACATAGAACAATGAAACAGAATAGAGAGCCCAGAAATAA 4345
                         i  iv i v   i     v     i  i     v     i          
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_68236428_6   4346 GGCTGCATATCTACAACTATCTGATGTTCAACAAGC-TGACAAAAACAAG 4394
                         iv iii i  i  iiiii vi    v   i     v-  v   i v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_68236428_6   4395 CAATGGGGAAAGAACTCCCTATTTAATAAATGGTGCTTGGATCACTGGCT 4444
                                       ivvi  v  i  i          v   iv     v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_68236428_6   4445 AGCCATATGCAGAAGATTAAAACTAGAATCTTTCCTTATACCATATGCAA 4494
                          ?   i     i    v i  ii i  vi i v   i i       i   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_68236428_6   4495 AAATCAACTCAAGATGGATTAAAGAC--AATTTTAAAATCTAAAACTATA 4542
                             i       i      i ?    --  v v   i v           
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_68236428_6   4543 AAAATCCTGGAAGACAACATAGGCA-ATACCATTCTGGACATAGGGATGG 4591
                            v  i i     v        ?i- v i -   vv   v v   v i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG 577

  chr1_68236428_6   4592 GCAAAGATTTCAT-GATGAAGATGCCAAAAGCAACTCCAACAAAACCAAA 4640
                             v i    v -   - v  ii         vvvv        vv   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_68236428_6   4641 ATT-GACCAATGGGACCAAATTAAACAAAAGAGCTTCTGCACAGCAAAAG 4689
                          v -  iv   v    ivv  i   vvv  i i   i  ii vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_68236428_6   4690 AAACTATCAACAGAGTGAACAGACAACCTACAAAATGGGAAAACATTTTT 4739
                          v        v i      v        i   i       i  v  v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_68236428_6   4740 TGCAAACTATGCATCTGACAAAGGTCTAATATCCAGCTTCTAGAAAGAAC 4789
                         -     ii  ii      i  i  v  vi       vv v  v       
  L1M4_orf2#LINE/    727 -GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_68236428_6   4790 TT----AAATATATAAGAGAAAAACAAACAACCCCACTAAAAAGTGGGCA 4835
                          i----  v vv    v i   i     i     v i ?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_68236428_6   4836 AAGGACATGAATAGACACTTTTC-AAAGAAGATATACTTGTGGCCAATAA 4884
                              iv          i  i  -             vvi          
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_68236428_6   4885 GCATATGAAAAAAAGCTCATCACTGATCATTAGAGAA 4921
                            i       i v     --  --    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCA--AC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (129 / 93)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.65 (45 / 17)  


2713 25.22 3.30 3.30  chr1_68251994_68255656.rev     2265  3172 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68251994_6   2265 TGGAAACACATCTCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2314
                               v i   i    i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68251994_6   2315 GATCATACTGCC---ATT---CTACAAATTCAATGCAATTCCCATCAAAA 2358
                          iiv     v  ---   ---     i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68251994_6   2359 TACCACCATCATTCATCACAGGACTAGAAAAAACAATCCTAAAATTCATA 2408
                          v   v vv v  iv ii   i v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_68251994_6   2409 TGAAACCAAAAAAGAGCCCACATAGCCAAAGAAAGACTAAGCAAAAAGAA 2458
                           i  viiv  ii  v  viv         iv  vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_68251994_6   2459 CAAATCTGGAGGCATTACATTACCTGACTTCAAACTATACTACAGGGCTA 2508
                             vi      vv i   i v  ii i      viv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_68251994_6   2509 CAGTAACCAAAACAGCATGGTACTGATACAAAAACAGACATGTAGACCAC 2558
                               i   i    ii        ii i  ii i      i    i  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_68251994_6   2559 TAGAACAGAATAGAGAGCCCAGAAATAAAGCCAAACACCTACAACCATCT 2608
                          i   i     v     i           v   v   ii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_68251994_6   2609 GAACTTTGACAAACGTCATAAAAACAAGCAATGGAGAAGGGA--GTCC-- 2654
                           vi  i     iv  vvi  i v  vv      i   i i --   i--
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_68251994_6   2655 ----CCATTGGCCCTGGGATAACTAGCTAGCTACATGGAGAAGATTGAAA 2700
                         ---- v v   iv      i    i v  ? i     v i    v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_68251994_6   2701 CTATACCCCTTCCTTATACCACATACAAAAATCAACTCAAGATGGATTAA 2750
                         i iv      v   i i    i          i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_68251994_6   2751 ATACTTCAGTGTAAAACCTAAAACTGTAAAAAATTAAAACCTAAAACTGT 2800
                          v  i v i     i v        i     --i ---- i  i  ----
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA--CT----CTTAGAA---- 540

  chr1_68251994_6   2801 AAAAACTAATA-----AAATCCTTAGGAAATACCAATTTGGACGTATGCC 2845
                         i     --   -----     i iiv  ----  ---    ii-  ----
  L1M4_orf2#LINE/    541 GAAAAC--ATAGGNGTAAATCTTCGTGA----CC---TTGGGT-TA---- 576

  chr1_68251994_6   2846 CTGGCAAAGATTTCAT-GATGAAGATGCCCAAAGCAATTGCAATAAAA-- 2892
                         --     v i    v -   - v  ii  v      vvv    i    --
  L1M4_orf2#LINE/    577 --GGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_68251994_6   2893 AAAAATTGACAAATGTGACCTAATTAGACTAAAGAACTTCTGTACAGCAA 2942
                               v  i    vv   i v  i i v v  i     i   i vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_68251994_6   2943 AAGAAACTGTCAACAGAGTCAACAGACAACTTACTGAATGGGAGAAAATA 2992
                          i  v   i    v i   v  v       ii  v               
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_68251994_6   2993 TTTGCAAACTATGCATTCAACAAAGGTCTAATATCCACAGTCTATAAGGA 3042
                                 ii  ii  iii i  i  v  vi      v i v     i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_68251994_6   3043 ACT--TAAAAAGATTTACAAACAAAAAG-----TAACCTCATTAAAAAAT 3085
                            --  v  ---i i vv  i      -----     iv   ?      
  L1M4_orf2#LINE/    774 ACTCTTACAA---CTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_68251994_6   3086 GGACAAAGGGCATGAACAGACACTTCTCAAAAGA-GATGTACACATGGCC 3134
                           i      iiv    i     i     v     -   i    v      
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_68251994_6   3135 AAAAATCATATGAAAAAATGTTCAACATCACTAATTGT 3172
                           v  v  i       i   i         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (137 / 89)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.00 (60 / 20)  


3149 27.18 0.77 0.44  chr1_68265549_68271909.rev     4966  5870 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68265549_6   4966 TGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATCATGAAAAT 5015
                              ii i  i     i     i  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68265549_6   5016 GGCCATAATGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5065
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68265549_6   5066 TACCAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTTCA 5113
                          v   iivi i  i  ii  -      -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_68265549_6   5114 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAG 5163
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_68265549_6   5164 AACAAAGCTGGAGGCTTCATGCTACCTGACTTCAAA--CTA-TACAAGTC 5210
                                i      vi   ii  v  ii i      --i  -     iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_68265549_6   5211 TACAGTAACCAAAACAGCATGGTACAGGTACCAAAACAGAGATATACACC 5260
                                 i   i    ii      v  i iv ii i   v     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_68265549_6   5261 AACGGAACAGAACAGAG-GTCTCAGAAATAACACCACCCATCTATAACCA 5309
                           i    i    iv   -   -         vv   iv   i   iii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chr1_68265549_6   5310 ACTAATCTTTGACAAACCTGACAAAAACAAGACATGGGGAAAGGATTCCC 5359
                          i i  i  i     ivv  v   i v  vvvv          i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_68265549_6   5360 TATTTAATCAATGGTGCTGGGAAAACTGGCTAGGCATATGTAGAAAGCTG 5409
                          v  i  iv             v      v  ?v  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_68265549_6   5410 AAACTGGATCCCTTTCTTACACCTTATACGAAACTTAATTCAAGATGGAT 5459
                           ii    i    vi  i     v     i   v    i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_68265549_6   5460 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5509
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_68265549_6   5510 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTCCATGACTA-A 5558
                             ?i v viv   iv   v v  vv i     v ii i v iiv  -i
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_68265549_6   5559 ACACTAAAAGCAATGGCAACAAAAGCTAAAATAGATAAATGGGATCTAAT 5608
                             i       vvi          vv             v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_68265549_6   5609 TAAACTAAAGAGTTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAACA 5658
                         i   v v  i ii  i   i vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_68265549_6   5659 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5708
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_68265549_6   5709 GGGCTAATATCTAGAATCTACAAAGAACTTAAACAAATTTAAAAGAAAAA 5758
                           i  vi    i     v  i        ivv    v iv v  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_68265549_6   5759 AATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTT 5808
                         i -    i     v  i?    i            v    i     i  i
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_68265549_6   5809 TCAAAAAAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5858
                           v   i    i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_68265549_6   5859 ATCACTGGTCAT 5870
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.22 (11 / 9)  


1490 28.43 12.88 2.79  chr1_68272439_68276246.rev     2495  3317 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_68272439_6   2495 GAGAAATATCCCATCTTGGTAGAATGAAGAAAGCTT--TAT------GA- 2535
                           i i         v  vi i  v  --   ii   --   ------  -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTG--GAAGACTTAATATTGTTAAGAT 50

  chr1_68272439_6   2536 AACAA-ACTCC----ATT-AT-----------ATGCAATCCCCATTAAAA 2568
                         ii   -     ----   -  ----------- i        i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68272439_6   2569 TCACAGCAGTGTTTTTTAATAAAAAATTCTGAGCAGCTTCTAAAATATAT 2618
                           v    v iv      i-i i   v vvii   v v i       vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_68272439_6   2619 ACAGAAATACAAAGGACTGTAAATAGC----------------------- 2645
                          ii     i   i    ivvi      -----------------------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_68272439_6   2646 ATAAAGCCTAAGGACTTACTCCATCAGATATCAAGACTTATAGGTAATTA 2695
                          i    iivi      i  v ivi vi  v    i     i---  -iv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC---TA-CAA 245

  chr1_68272439_6   2696 AACTACAGTAATTAAGACAGTGTGATATTGATGTAAGGATAGACAAATAG 2745
                          i          i           i  i  iii            v    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_68272439_6   2746 ACTACAGGAA-AGAGTT-----TTCA--AACAGATCCACCCATACTTGGA 2787
                          ii vv    -   i  ----- i  --  i i i   iv   viv   v
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_68272439_6   2788 CATTCGATCTT--GCAAG----CTAGCACTGTAGAGCAGCAGAGAAAGG- 2830
                           v i   i  --i    ---- i iv  ii ---v  iii i     i-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCAT---TCAATGGGGAAAGAA 392

  chr1_68272439_6   2831 --GTCATT-CAGTAAATAGTGCTCAGTCTATTGAGTAACTGTCTGGGGAG 2877
                         --   v  -  ii    i     vi v v i  ii  ? iiiv  v----
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC---- 438

  chr1_68272439_6   2878 AAAAAGA--GAAACTTGATCATTATGTCATACCACACATAAAAATCAATT 2925
                         -      --   ii v  i vi  iv   i    i i i      i  i 
  L1M4_orf2#LINE/    439 -AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_68272439_6   2926 CTCAGTGCATGGTAGCTCTAAATGTAAAGGGTAAAATAATAGAGCTTCTA 2975
                          vv i  v  vi?  vi          ii v     iv   i i  ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_68272439_6   2976 TTAGATAAAATAAGAAAATATCTTCATGATGTGAGGCTAGAGAAAAAAAT 3025
                         vv   v  v   i ?iv v      i   iv vi  i   iv  vii-- 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG--T 585

  chr1_68272439_6   3026 TTATTAAAT--GACACAAAGATCACTAACAATACAGGAAAATATGAATAA 3073
                           v   i  --     v  i v   v i   i v i     v  ii    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_68272439_6   3074 ATTGGA-TACATTACATTAAATTAAGAGCTTTTGTTCATCAAATGACATT 3122
                               - v   i ----       i i       v v     v    i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCA----AAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_68272439_6   3123 ATTAAAAGAGAGGGAAAGTAAGCCAAAGAGT---AGAAGATATTTGCAAC 3169
                           i  i i  v ii  iii  v   v   i ---    i          v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_68272439_6   3170 ACATGTAAATG-TGAGCAACTTATGTCCAAAACACATGAAAAACTTATAC 3218
                         v   i  vv  - i  vi    i i    i  i i  i  i    iv   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_68272439_6   3219 AA----ACA-TAAAAATACAGACAATTCAA------GATG--C------T 3249
                           ---- i -      v   i i  ii   ------i   -- ------ 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_68272439_6   3250 TCCTGTATAAA---------AAAGAGGATAC-CAAATAGCTAATATATCT 3289
                          --  v   i ---------     i    i-     i  i    viivi
  L1M4_orf2#LINE/    832 T--TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_68272439_6   3290 ATGAAAGG-TGCTCAACCTCATTAGTAAT 3317
                               i -        v   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (151 / 80)
Gap_init rate = 0.04 (37 / 906), avg. gap size = 3.49 (129 / 37)  


1285 27.98 2.07 0.52  chr1_68512387_68515060.rev      960  1345 (1329)    L1M4_orf2#LINE/L1        1   392 (516)  

  chr1_68512387_6    960 TGGAAAAACAGTCCATGCCCATGGATTGAAAGAATCAATATTGTTAAAAT 1009
                               i i vi     ii         i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68512387_6   1010 AGCTATACTGCTTAAAGCAATCTACAGATTCAATGCTATCCTTACGAAAC 1059
                         i  v     v ii   vii              i  v    i  iv   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68512387_6   1060 TACCAACATCTTTTTTTTCAGA--TTTAGAAAAAAAATTT-AAATTGATA 1106
                          v   i vv i      v    --  v v  ivvi vii -     v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_68512387_6   1107 TGGAATCAAAAAAGAGCACAAATAACCAAA-TAACTTTGAAGCAAAAAGA 1155
                              viiv  ii  v vvi    i     -i  ii     i-  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGAAGA 199

  chr1_68512387_6   1156 ACAAAGCCAGAGGTATCACATTACCTGACTTCAAA--CTACTATAAGGTT 1203
                               iii    vv     i v  ii i      --i     i  i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_68512387_6   1204 ACAGTAACCAAAATAGCATGGTACTGGTACAAGAGCAGATATATAGACCA 1253
                                i   i i  ii         i i   iii   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_68512387_6   1254 ATGGAACAGAATAGAGAGCCCAAAATTAAGCCT-CACATCTACAGCCATC 1302
                               i     v     i   i  v   i  i-i    i  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_68512387_6   1303 TGACCATCAACAAAGCTGACAAAAACCA-ACAATGAGAAAAGGA 1345
                            iiv  i    i v  v   i -   -v     i i    i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAA 392

Transitions / transversions = 2.27 (75 / 33)
Gap_init rate = 0.02 (8 / 392), avg. gap size = 1.25 (10 / 8)  

1836 27.39 0.19 0.19  chr1_68512387_68515060.rev     1662  2183 (491)    L1M4_orf2#LINE/L1      387   908 (0)  

  chr1_68512387_6   1662 AAAGGATTCCCTATTCAATAAATGGTGCTGGGTTAGCTGGCTAGCCATAT 1711
                             i  vvi  v     i             vi i    v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_68512387_6   1712 GCAGAAGGAGGAAACTGGACCCCTATCTTTTACCATATGCAAAAATTAAC 1761
                            i   i v   ii          i  ivi       i           
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_68512387_6   1762 TCAAGATGGATTAAAGATTTAAATGCAAGACCTCAAACTATAATAACCC- 1810
                             i      i ?   ii      i    v  v         -   i -
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCT 535

  chr1_68512387_6   1811 TGGAAGAAAGAATACGAGTTGCCCTTCTCGACATCGGCTTTGGCAAAAAA 1860
                          i       iv   v ?  vivi    vi   v i  v  v     viiv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_68512387_6   1861 TCTATGGCTAAGTCCTTAAAAGCAATTACAACAAAAACAAAAATTGACAA 1910
                          iiv i v  v v vii       vvvi        iv      v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_68512387_6   1911 GTAGGACCTAATTAAACTAAAGAGTTTCTGCATATCAAGAAAAACTATCA 1960
                         i v    i v  i   v v  i ii  i  iiiv    iii v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_68512387_6   1961 ACAGGGTAATTAGACAATATATAGAATGGGAGAAAATATTCATAACCCAT 2010
                          v ii  i vv      ivi i                  iii  vi   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_68512387_6   2011 GCATCTGACACAGTTTTAATATCCGGAATCTATAAGGAACATAAACAACT 2060
                         ii      i vi vvi vi     i    v     i    vivv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_68512387_6   2061 CAATAAGCAAAAAACGAATAAGCACATTGAAGAGTGGGCAAAGGACATGA 2110
                               vv    i  i     v vv   ?  i i           iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_68512387_6   2111 AGAGACACTTCTCAAAAGAAGACATAAAAGCAGCCAACAAACATATGAAA 2160
                          v     i     v        i   v  iii     i  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_68512387_6   2161 AAATGCTCAACATCACTAATCAT 2183
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (82 / 57)
Gap_init rate = 0.00 (2 / 522), avg. gap size = 1.00 (2 / 2)  


2467 25.57 3.75 1.20  chr1_68667897_68669626      497  1243 (487)    L1M4_orf2#LINE/L1      143   908 (0)  

  chr1_68667897_6    497 AACTCATATGGAACCAAAAAGAGCCCA-AATAGCCAAGGCTATCCTAAGA 545
                           i          viiv  i ii    -         ii v   i i i 
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_68667897_6    546 AAAAAGAACAAAGCTGGAGGCATCATGCTACCAGAATTCAAACTATACTA 595
                           i          i      vv   ii  v  vi v      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_68667897_6    596 CAGGCCTGTAGTAACCAAAACAAAATGGTACTGGTATAAAAACCAACACA 645
                           iiv  ii     i   i   ivi         i    ii ivi   i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_68667897_6    646 TAGACTAATGAAACAGAATACAGAGCCCAGAAATAAGGCCATGCACCTAC 695
                             ii    i  i     vv    i          iv    i  ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_68667897_6    696 AACCAACTGATCTTCAGCAAAGCTGACAAAAACAAGCAATGGGGGAAATG 745
                         iii   i    i   ii   i v  v   i v  vv        -   vi
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGA 391

  chr1_68667897_6    746 ATTTCCTATTTAACAAATAGTGCTGGGATAACTGGTAAGTTACATGCCGA 795
                           vvi  v  i       i         i      vv ?ii      vi 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_68667897_6    796 AGATTGAAATGGGACACCT-TCTTACACCATATACAAAAATTAACTCAAC 844
                            v    i v    v   -i  i                         v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_68667897_6    845 ATGGATTAAAGAGTTAAGTGTAAAACCCAAAACTATAAAAAACCTGGAAG 894
                               i ?   vi   i     i v i            vv i i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_68667897_6    895 AAAACCTAGGCA-ATATCATTCTGGACATTAGAATGGGCAAAGATTTCAT 943
                              v    ?i- v   -   vv   v  i iv i     v i    v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_68667897_6    944 -GATGAAGATGCTAAAAGCAGTTGCAACAAAAGCAAAAATTGACAAAT-G 991
                         -   - v  ii i       vvv          v      v  i    - 
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_68667897_6    992 GACTGTAGTTACATGAAGGA-------GCTACACAGCAAAAGAAAACTAT 1034
                             vi viv v  v  ii -------   v  ------   i v     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCA------AAGGACACTAT 683

  chr1_68667897_6   1035 CAATGGAGTCAACAGACAACCTATCGAATGGGAGAAAATTTTTGCAAACT 1084
                            vii   v  v        i iv              v        ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_68667897_6   1085 ATGAATCTGACAAAGGTCTAGTATCCAGCATTTACAAGGAACT--TA-AA 1131
                           iv      i  i  v  v        v  v  i  i     --  -  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_68667897_6   1132 TTTAA------------AAGCAACTCCATTAAAAAGGGGGCAAAGGACAT 1169
                         i i  ------------  ii   i v   ?    iv          iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_68667897_6   1170 GAACTGACACTTTTCAAAAGAAGACATATATGCAGCCAACAAGCATATGA 1219
                            iv    i  i  v        i   i viii     i     i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_68667897_6   1220 AAAAA-GTTCAATATTACTGATTGG 1243
                            i - i    i  i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (114 / 73)
Gap_init rate = 0.02 (14 / 766), avg. gap size = 2.64 (37 / 14)  


3087 25.62 2.24 0.67  chr1_68677950_68682123     2788  3681 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68677950_6   2788 TGGAAACACATCCCATGCTCATGGATAGGTAGAATCAATATTGTAAAAAT 2837
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68677950_6   2838 GACCATACTGCCAAAAGCAATCTACAAATTCAATGAAATTCCCATAAAAA 2887
                          i v     v  v   vii       i      i v   i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68677950_6   2888 TACCACCATTG--TTCTTCACAGAACTAGAAAAAAGAATCCTAACATTCA 2935
                          v   v --  --  i  ii     v v  v  ivvi       v     
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_68677950_6   2936 TATGGAAC--CAAAGAACATTCCACA-TAGCCAAAGCAA----------A 2972
                                v--   i i  ---   v -        i   ----------i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_68677950_6   2973 AAGAATAAATCTGAAGGCATCACATTACCTGATTTCAAACTATACTGTAG 3022
                              i   vi  i   vv     i v  ii        viv    ii i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_68677950_6   3023 AGCCATGGTCACCAAAACAGCATGGTACTGGTGTATAAATAGTCACAGAG 3072
                            i ii  v i   i    ii         ii  vii    v  i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_68677950_6   3073 ACCAATGGAGCAGAATAGAGAATGCAGAAATAAGCCCAAATACTTACAGC 3122
                          i       ii     v    i v         i    v i i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_68677950_6   3123 CAACTGATTTTTGACAAAGCAAAGAAAAACATAAAGTAGGGAAAGAACAC 3172
                            i       i     i vvivv  i v   vv i i         i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_68677950_6   3173 CCTATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAGAA 3222
                         i  v                    i  i   vv ?       i ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_68677950_6   3223 TGAAACTGAATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGG 3272
                             ii  i i  ii i   v    v           i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_68677950_6   3273 ATCAACGACTTAAATCTAAGACCTGAAACTATAAATATTTTAAAAGATAA 3322
                             ?v   i     v     v  i          vv i   i    v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_68677950_6   3323 CATTGGA--AAACCTTTCTATACATTAGCTTAGGCAAGGATTTCATGACC 3370
                            v  ?--   i   iv i-  v  i v        v i    v iivi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_68677950_6   3371 AAGAACCCAAAAGCAAATTCAATAAAAACAAAGATAAATAGCTGGCATTT 3420
                          v  vv         v vv   i    iv   i   i   iv v v i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_68677950_6   3421 AATTAAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAA 3470
                         v  i   v v  i i      ii vv    i iv  vi   iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_68677950_6   3471 ATAGACAACCCACAGAGTAGGAGAAAATCTTCACAATTTATACATGTGAC 3520
                          v              i i         v  ii   v i   i  v   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_68677950_6   3521 AAAGGACTAATATCCAGAATCTACAATGAACTCAAACAAATTGGCAAGGA 3570
                           i     vi          v  i  v      vv    v iiii  vi 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_68677950_6   3571 AAA-ATAAACAATCTCATCGAAAAATGGGCTAAGGACATGAATAATCAAT 3619
                            - i   i  i iv  i?          v     iv      iv  v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_68677950_6   3620 TCTCAAAACAAGATATACAAATGGCCAACAA--ACATGAAAAAATGCTCG 3667
                             v   v                   i  --         i      i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_68677950_6   3668 ACATCACTAATGAT 3681
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (129 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.60 (26 / 10)  


3024 26.55 1.33 0.88  chr1_68725610_68731340     4335  5238 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68725610_6   4335 TGGAGAAACATTCCGTGCTCATGGATAGAAAGAATCAATATCATGAAAAT 4384
                             i i i  i  i  i        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68725610_6   4385 GGCCATAATGCCCAAAGCAATCTATAGATTCAATGCCATTTCTATCAAAC 4434
                            v   v v      vii     i        i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68725610_6   4435 TGCCATCAATATTCTTCACAGAATTAGAAAAAAAAACACCTTAAAATTTA 4484
                          v   v viiv  i  ii     v v  v  ivvi i-- i       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT--CCTAAAATTCA 148

  chr1_68725610_6   4485 TATGCAACAAAAAAGAGCCCA-AATAGCCAAGGTAATCCTAAGCAAAAAG 4533
                             v  vviv  i ii    -         iii    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_68725610_6   4534 AACAAAGCTGAAGGCATCCCACTACCTGACTTCAAACTATACTATAGGGA 4583
                                i  i   vv  v    v  ii i      viv     i ii v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_68725610_6   4584 TACAGTAACCAAAACAGCATGGTACTGGTACAAGAACAGACACATAGACC 4633
                                 i   i    ii         i i   i i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_68725610_6   4634 AATGGAACAGAATAGAGAACCCAGAAATAAGGCCATACACCTATGACCAT 4683
                                i     v    ii          iv       ii    ii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_68725610_6   4684 CTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGCAAAAGAT--TCC 4731
                         i    i   i    ivv  v   i v  vv       v   ii  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_68725610_6   4732 TTATTTAATGAACGGTGATGGCAGAACTGGCTAGCCATATACAGAAAATT 4781
                           -- i  ii  i    v   v v      v  ?   i  i  i  i v 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_68725610_6   4782 GAAACTGGACTTCTTTCTTACACCATATACAAAAATCAACTGAAGATGTA 4831
                            ii     ii  vi  i                 i    v  i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_68725610_6   4832 TTAAAGGCTTAAATGTAAAACCCAAAACTATGAAAACCCTAGAAGAAAAC 4881
                          i ?  i i         i v i        i   vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_68725610_6   4882 CTAGGCA-ATACCATTCAGGGCATAGGCATGGGCAAAGATTTCAT-GATG 4929
                         v    ?i- v i -   iv i v v  vv i     v i    v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr1_68725610_6   4930 AAGATGCCAAAAGCAATTGCAACAAAAGCAAAAATTAACAAATGGGATCT 4979
                          v  ii         vvv          v      vi i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_68725610_6   4980 AATTAAACTTAAGAACTTCTGCCCAGCAAAAGAAACTGTCAACAGAGTAA 5029
                         v  i   v    i     i  iv vv    i  v   i    v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_68725610_6   5030 ACAGATAACCTACAGATTAGGA--AAACATTTGTCAAATCTATGTATCTG 5077
                          v   i    i     v i   --   i     -      -  i      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTG-CAAATC-ATATATCTG 742

  chr1_68725610_6   5078 ATAAAGGTCTAATATCCAGCATCTATAAGAAACTTAAACAAATTTACAAG 5127
                             i  v  vi       v  v     ii    ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_68725610_6   5128 AAAAAACC---CAACCACAGTAAAAAGTGGGCAAAAGACATGAACAGACA 5174
                              iv ---i    vv v ?    i        i  iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_68725610_6   5175 CTTCTTAAAAGAAGGTATGTATGTGGCCAACAA--ACATGAAAAAAAGCT 5222
                         i    iv       i   ii vi       i  --         i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_68725610_6   5223 CTACATCACCAGTCAT 5238
                          v      ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


2725 23.40 2.87 3.64  chr1_68755771_68758297     1129  2034 (493)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr1_68755771_6   1129 ATTCCATGCTCATGGATTGGAAGAATCAATCTTGTTAAAATGACCATACC 1178
                           i     i               v i   v       i   i v    i
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_68755771_6   1179 ACCAAAAGCAATCTACAGATTCAAAGCAATTCCTGTCAAATTACCAACAT 1228
                         v  v   vii              v     i   i     v v   i vv
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_68755771_6   1229 CATTTTTCATAGACTTAGAAAAAACAATTCTAAAACTCATATGGAAACAA 1278
                          v     iii   vv v  v  ivii  i      i           iiv
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_68755771_6   1279 AAGAGAGCCCAAATAGCCAAAGAAATCCCAAGCAAAAAGAACAAAGTGAG 1328
                            i  v  vi          iv    iii iv  i           vi 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_68755771_6   1329 AGGCAACACATTACCCCACTTCAAACTATAGTTGTAGTAACTATAGTTGA 1378
                            vvv    i v   v i      ---- v  ------    i i----
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAA----ACTT------ACTACAA---- 245

  chr1_68755771_6   1379 CAACTGTAGTTGACAAAGCAGCATGTTTGTGGTACAAAAATTGACATAAG 1428
                         - i  ii   viv   ii   ii  v vv   i i  ii  v      vi
  L1M4_orf2#LINE/    246 -AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_68755771_6   1429 GATCAATGGAACAGAATTGAAAG-CCAAAACATAAAGCCACACACTTACA 1477
                                    i        i  -   i  -     v   i   i   ii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAA-ATAAACCCATACATTTATG 343

  chr1_68755771_6   1478 ACCAACTGATCTTTGACAAAG---TCAAGAAAAACTAAAACTGGCACAGG 1524
                         ii   i    i  i     i ---i     vv vii  ---   viv i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA---TGGGGAAAG 390

  chr1_68755771_6   1525 GTCACCCTATTCAATAAATGGTGCTAGGAAAAAAGCCTGG----CCACTT 1570
                         ivi vi  v     i          i   v  ----    ----    v 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAA----CTGGATAKCCACAT 436

  chr1_68755771_6   1571 GCAGAAGAAAAACACTGGACCCCTACCCTCTCATCATATACAAAAATTAA 1620
                            i     vi vii            -  v  i                
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACC-TCACACCATATACAAAAATTAA 485

  chr1_68755771_6   1621 CTCAAGATGGATTAAAGACTTCAATGTAAGACCTAAAACTATAAAAATCC 1670
                              i      i ?    i v         v              v  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_68755771_6   1671 T-GAAGAAAACCTAGAAAAAACTCTTCTGGATACTGGCATAGACAAATAA 1719
                          -         v   i?iv  v     vv  ivi   vv   i   - ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGG 584

  chr1_68755771_6   1720 TTT-TTGACTAAGACCTCAAAAGCAATTGCAACAAAAGCAAACATTGACA 1768
                            -  iiv  v   vi        vvv          v   v  v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_68755771_6   1769 AATAGGGCTTAATTAAA-TGAAAGAGCTTCTGT-----AAAGAAAACAAA 1812
                            v  i   v  i   - v   i -   i   -----    i v  ---
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACAC--- 680

  chr1_68755771_6   1813 ATAATCAACAGGTT--AAATACAACCTTCAGAA--AGAGTAAATATTTGC 1858
                         -  -    v iiv --   v      iv     --i   v          
  L1M4_orf2#LINE/    681 -TA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_68755771_6   1859 AAACTATGTATCTGACAAAG-ACTAATATCTAGAATATATAA-GAA-TCT 1905
                            ii  i       i  i -   vi    i           -   -   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_68755771_6   1906 TAAACAAATCAACA-TGAAATAA--AACAACCCAATTAAAAAGTGTGCAA 1952
                           --   v    i - i   vi --  i         ?    i  v    
  L1M4_orf2#LINE/    779 TA--CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_68755771_6   1953 AGGACATGAACAGACACTTCTCAAAAGAAGACACAGAAACAACCAAAAAA 2002
                             iv    i     i     v        i i v   iii    v  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_68755771_6   2003 CATATGAAAAAATGCTCAACATCAATAATTCT 2034
                           i       i             ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (122 / 87)
Gap_init rate = 0.03 (26 / 899), avg. gap size = 2.27 (59 / 26)  


 679 29.91 8.39 6.50  chr1_68837328_68839165      500  1345 (493)    L1M4_orf2#LINE/L1       47   908 (0)  

  chr1_68837328_6    500 AGATGTCAGTTCCCTCGAAATTAATTTATAGATTTAAAGCAATCTCAATA 549
                              v  i v i i v     i  i  i     i  v      i v  v
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_68837328_6    550 AAAAT---AGCAAATTTTTATG---AAGTTAGGAAAATTGATACGAAAGC 593
                              ---   vivi    v  ---  i  - iv  ii    v v   ii
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAAT 145

  chr1_68837328_6    594 TACTATTGAAAAATAAATATTGCAAGAATAGCTGAAA-AACACTGAAAAA 642
                          vv   v    vii  iviviv  -       ii   -  ivi       
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAA 194

  chr1_68837328_6    643 GAAAAAC-----TACAAGAGCC---CTGCCAAATATTAAAATATGCTGTA 684
                            i   ----- iv i  vi ---  v  v   v i    iv i  ii 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_68837328_6    685 ACCCCCTTGT---TAAAACAATGTGAAACTGGTACCTAAATGAATAGACA 731
                          vv iviv  ---i  i   i    iv     i --   -- i       
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCA--TAA--GGATAGACA 290

  chr1_68837328_6    732 TGT----CAGGGAAATGGAATGGGAAGTACAGAAA--GACACAGAAGTCA 775
                          i ----  iv i   i    v ii   v      --i  v  v vi i-
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT- 339

  chr1_68837328_6    776 CATGGATATTTGGTTTATGATGAAGGTG---AGATC--TCAAATTACTTG 820
                         i    vi v   i   vi  ii i    ---   i --    ----- v 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-----TGG 384

  chr1_68837328_6    821 ACAAAGA-TGGACTTTTAAATAAATGCTTCTGGGACTATTGCATAGACAA 869
                         iv     - i v     v  i     v v       v i  v   ?v  -
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA- 433

  chr1_68837328_6    870 TAGACATTGAGAAAAAAACTAGTAAAATGAAAACTTTATATT-CAGTTTA 918
                         ----   --iv    i  ---- i  i vii v ii  iv i-  viv  
  L1M4_orf2#LINE/    434 ----CAT--GCAAAAGAA----TGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_68837328_6    919 CATAAGCATTAACTTATGCTTATGTGGATAAGGGATATGGATAAGGGATG 968
                         i i  iv       i -------------  -----      v ?i  iv
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCA-------------AA-----ATGGATCAWAGACC 505

  chr1_68837328_6    969 TAA-TGTAAAATAATAAAAGCATGTAAGTACTATAAGAAAA--TGGGAAT 1015
                            -     i -iv     vi  iv  v vi  v       -- i  ?i 
  L1M4_orf2#LINE/    506 TAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_68837328_6   1016 AAATTCCTGCATAACCTTGGTGTAGGCAAAGACTTTCTAACTATGCC-TC 1064
                             --  v i i       vv       v ii  ii  iv    v -i 
  L1M4_orf2#LINE/    555 AAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_68837328_6   1065 AAAATT-CAGATT-CAGGAAAAACAATGACTACATTTAACTATATACAAA 1112
                             vi-  iiiv-  ii i   v   iiv  v   vi   vi  vv   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_68837328_6   1113 TAAAAAAGGGTTGTAT-------GACAA-ATCAA---AGTTAAATGACAA 1151
                          v     vvv    ii-------    v-     ---   v   v     
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_68837328_6   1152 -------AATAAAATAATGTGTTAATAA--TATATATCTCAAGTATTATA 1192
                         -------   iii v  vi i  vii  --i        --- ----   
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT---G----ATA 745

  chr1_68837328_6   1193 AAAGAAAGTG-ATTCCTAATTTATAAAGGACCCTTAAAAACTGAGAACAA 1241
                          ii  v-v  -  i vv   v       i  i    v  viii v  i  
  L1M4_orf2#LINE/    746 AGGGAC-TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_68837328_6   1242 AAAGAC------CTTA--TAGAAACCTGGCAGAAGACATGAACAGACAAT 1283
                               ------ ii -- ?i   viv    i i  iv    i     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_68837328_6   1284 T----AATGAAGAATATATTAAAATGGTTCTTAAATATA-AAAAAGATAT 1328
                          ----  v     -    i--      iivv   ii i -i       ii
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGA-TATAC--AAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_68837328_6   1329 TTAATTTCACTTATGAT 1345
                          i  iv   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (144 / 105)
Gap_init rate = 0.05 (45 / 862), avg. gap size = 2.80 (126 / 45)  


2694 20.24 2.72 1.96  chr1_68843225_68844862.rev      486  1147 (491)    L1M4_orf2#LINE/L1      242   908 (0)  

  chr1_68843225_6    486 ACAAAGC----ATCATCTATACAATATAGTCTTGACATAGGGATAAACTT 531
                                ----i v   v v   i i i  vi  i    i     i  v 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_68843225_6    532 AAAAACCTATGAAGTAGAACTGAGAACC---AAATAACCCCCACCTCATA 578
                          v i i v   i i     i     ii ---      -----   -    
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA-----ACC-CATA 335

  chr1_68843225_6    579 CATTTATGGCCAACTCATTTTTAACAAGGGTGCCAACTCCATTTCATAGA 628
                                  i   i v     ii             vv     iv  i i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_68843225_6    629 AAAAGCATAGTATCTTCAACAAATTGTACTGGTACAATTGGAAAACAATG 678
                         i    v     v i          v  i    v    i    v ? v ii
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_68843225_6    679 TATAAAATAATGAATGAACCTAGGCTCCTACTTCATGCCATGTAAAAAAA 728
                          ii    ----       vi i i i     i   ii    i  v     
  L1M4_orf2#LINE/    436 TGCAAAA----GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_68843225_6    729 AATTAATTCAAAATAAATCACAGACCTAAAATTAAGAGTTAAAATTATAA 778
                         --    i       ii    ?         vv      i     i     
  L1M4_orf2#LINE/    482 --TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_68843225_6    779 ACCTATTACAAGAAAACATAAGGGCAAATCTTCACAAGTTTGGACTTGGC 828
                          v  v   v           i ? i        iii vi    ii v   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_68843225_6    829 AATAAATTCTGAGATTTGACACTAAAAGCACTAGCAACAAAAGAAAAAAT 878
                            iiv    v    v      i        v                  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_68843225_6    879 AAATG--TTA---TTCCTAAAAAT-AAAAACATGTGTA--TCAGAGGACA 920
                          i  i--  i---   v v     -      v v   i--   i      
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_68843225_6    921 TTATCCAGAAAGTGAAAAGACAATCTATAGAATTGGAGAAAATATTTGCA 970
                         i    v                 i i i     v                
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_68843225_6    971 AATCATATATCTGATAAGG--TTTACTATCTAGAATATAGAAAGCAAACT 1018
                                            --i  i-    i        v    v vv  
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCT 778

  chr1_68843225_6   1019 TA-AACTCATCAACAATAAAGCCAACATCCCGATCAAATAAAGGGCGAAT 1067
                           -      vi  i  v  ii v  i v   i  i?  v  v    i  v
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_68843225_6   1068 TACTTGAATAGACATATCTCTAAAGAAGATATATAAATGGCTAACAAGCA 1117
                         v i            v    i            i       i  i     
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_68843225_6   1118 TATGAAAAGATGTTCAACATCATTGGTCAT 1147
                         i           i         ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (81 / 49)
Gap_init rate = 0.02 (13 / 667), avg. gap size = 2.38 (31 / 13)  


3128 27.21 1.00 0.55  chr1_68859454_68865840.rev     4993  5896 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68859454_6   4993 TGGAAGAATAGTCCATGCTCATGGGTAAGAAGAATCAATATCGTGAAAAT 5042
                              ii   vi     i      i vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68859454_6   5043 GGCCATACTGCCCAAGT-AACTTATAGATTCAATGCCATCCCCATCAAGC 5091
                            v     v     i -i ii  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68859454_6   5092 TACAAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5139
                          v v iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_68859454_6   5140 TATGGAACCAAAAGAGAGCCCACATTGCCAAGTCAATCCTAAACCAAAAG 5189
                                viiv   i  v  viv  v     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_68859454_6   5190 AACGAAGCTGGAGGCATCACGCCACCTGACTTCAAACTATACTACAAGGC 5239
                            i   i      vv    i iv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_68859454_6   5240 TACAGTAACCAAAATGGCATGGTACTGGTACCAAAACAGAGATATAGACC 5289
                                 i   i ii ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_68859454_6   5290 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5337
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_68859454_6   5338 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5387
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_68859454_6   5388 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5437
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_68859454_6   5438 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5487
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_68859454_6   5488 TTAAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5537
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_68859454_6   5538 CTAGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCATGTCTA 5586
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_68859454_6   5587 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5636
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_68859454_6   5637 ATTAAACTAAAGAGCGTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAA 5686
                           i   v v  i i v i  ii vv    i  v    i ivv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_68859454_6   5687 CAGGCAACCTACAGAACGGGAGAAAATTTTTGCAATCTACTCATCTAACA 5736
                         v  i     i      i          v       vii ivi    i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_68859454_6   5737 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAGGAAA 5786
                          i  i  vi          v  i  v      vv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_68859454_6   5787 AAAGCAAACAACCCCA---AGAAGTTGGCAAAGGATATGAACAGACACTT 5833
                           ii    i     v --- i  i v          v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_68859454_6   5834 CTCAAAAGAAGACATTTATGCAGCCAAAAGGCACATGAAAAAATGCTCAT 5883
                            v        i  vi viii     v i           i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_68859454_6   5884 CATCACTGGCCAT 5896
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2608 27.87 1.44 1.08  chr1_68896404_68898228      497  1332 (493)    L1M4_orf2#LINE/L1       70   908 (0)  

  chr1_68896404_6    497 ATTTATAGATTCAGTGCTATTCCCATCAAAATACCATTGACATTCTTCAC 546
                           i  i       ii  v  i  i        v   vivi v  i  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chr1_68896404_6    547 AGAATTAGAAAAAAAACT-ACTTTAAATTTCATATAGAA-T-CAAAGAAA 593
                             v v  v  i---  - iii    v       i   - -   i i -
  L1M4_orf2#LINE/    120 AGAAATTGACAAG---CTGATCCTAAAATTCATATGGAAATGCAAGGGA- 165

  chr1_68896404_6    594 ACCCTTTATAGCCAAGACAATTCTAAGCAAAAAGAACAAGGCTGGAGGCA 643
                         -   vvv        i     ii i iv  i        i i      vv
  L1M4_orf2#LINE/    166 -CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_68896404_6    644 TCACACTATCTGATTTTAAACTATA-TATAAGGCTATAGTAAACAAAACA 692
                                vi ii    i   viv  -  i  i    i     v   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_68896404_6    693 GCATGGTACTGCTACCAAAACAGAGGCGTAGACTAATGGGACAGAACAGA 742
                          ii        vi iv ii i   viii    ii     i i    iv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_68896404_6    743 GAACTCGGAAATAACACCACACATCTATAACCATCTGATCTTTGACAAAC 792
                           iii i       vv   i    i   iii  vi    i  i     iv
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_68896404_6    793 CCGATAAAAACAAGCAATGAGGAAAGGATCTCCTGTTCATTAAACAGTGC 842
                         vi vi  i v  vv     i      i  vvi  v    vi   ii    
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_68896404_6    843 TGGGAAAACTGGCTAGCCATATGCAGAAGC-TGAAACTGGACCCTTTCTT 891
                              v      v  ?   i     i   v-    ii       i v i 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_68896404_6    892 TACACCTTATACAAAAGTTAACTCAAGATGGATTGAGGACCTAAATGTAA 941
                         i     v         i         i      ii?i             
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_68896404_6    942 AACGCCAAA-CCATAAAAACCCTAGAAGAAAACGTAGGCA-ATACCATTC 989
                         i -  i   - i      vi i           i    ?i- v i -   
  L1M4_orf2#LINE/    515 GA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC 562

  chr1_68896404_6    990 AGGACATAGGCATGGGGAAAGACTTCATGACTAAAACACCAAAA--ACAA 1037
                         iv   v v  vv i  v  v ii   v iiv  vi         --    
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_68896404_6   1038 TTGCAACAAAAGCCAAAATTGACAAATGTGATCTAATTAAACTAAAGAGC 1087
                         --          vv     v  i    vv  ii v  i   v v  i i 
  L1M4_orf2#LINE/    613 --GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_68896404_6   1088 TTCTGCACAGCAAAAGAAACTAGCATCAGAGTAAACAGGCAACTTATAGA 1137
                           i  ii vv    i  v    v  vv i   i  v  i    ii i   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_68896404_6   1138 ATGGGAGAAAATTTTCACAACCTACCCATCTGACAAATGTCTAATATCCA 1187
                                     v  ii   vii ivi      i  iv v  vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_68896404_6   1188 GAATTTACAAGGCACTTAAACAAATTCACAAGAAAAA-ACAAATCACCCC 1236
                             v  i  i v   ivv    v iv i  v     -      v    v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_68896404_6   1237 ATCAAAAAGTGGACAAAGGATATGAACAGGCACTTCTCAAAAGAAGGTAT 1286
                           i?    i   i        v    i  i  i     v       i   
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_68896404_6   1287 TTGCATGGCCAACAAACATATGAAAAA--GCTCAACATCACTGATCAT 1332
                         viiv        i  i  i       i--           ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (142 / 87)
Gap_init rate = 0.02 (15 / 839), avg. gap size = 1.40 (21 / 15)  


3258 26.77 0.88 0.44  chr1_68912065_68918340.rev     4882  5785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68912065_6   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68912065_6   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68912065_6   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_68912065_6   5030 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_68912065_6   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_68912065_6   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_68912065_6   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5227
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_68912065_6   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_68912065_6   5278 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_68912065_6   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_68912065_6   5378 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_68912065_6   5428 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_68912065_6   5478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5527
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_68912065_6   5528 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_68912065_6   5578 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5627
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_68912065_6   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_68912065_6   5678 AAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5723
                          i    ----   v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_68912065_6   5724 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5773
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_68912065_6   5774 ATCACTGGCCAT 5785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2563 28.10 1.09 2.18  chr1_68937606_68942710     3695  4612 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_68937606_6   3695 TAGAAACATATACCATTCTCATGGATAAGTAGAATCGACATTGTGAAAAT 3744
                          i    v    v    vi        vi v   v ii i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_68937606_6   3745 GGCCATACTGACAAAGGCAGTCTATAAATTCAATGAAATTCCCATAAAAA 3794
                            v     vv v  iviii    i i      i v   i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_68937606_6   3795 ATAATACCATCATCATTCTTCAC-GAACTAAAAAAA--AATCCTGAAATT 3841
                         ---- v   v vv v  i  ii -   v vi v  i--i     i     
  L1M4_orf2#LINE/    101 ----TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_68937606_6   3842 CATATGGAACCAAAAAAGAGCCCACATAGCCAAAGCAACACTAAGCAAAA 3891
                                  viiv  ii  v  viv         i   ivi i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_68937606_6   3892 AGAATAAATTTGGAGGTATTGCATTACCTGACTTCAAA-CTAACTACAAG 3940
                             i   v       vv ii  i v  ii i      -  v       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_68937606_6   3941 GCGTTAGTTACCAA-ACAGCATGATACTGGTATAAAAATAGGCACATAGG 3989
                           vvi   v i   -    ii  i      i    ii    i  i    i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_68937606_6   3990 TCAATGCAACCAAATAGAGAACCCAGAAAGAAAGCCAAATACCAGCAGCC 4039
                               v  ivi   v    ii       v   v   v i iiviii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_68937606_6   4040 AACTGATCTTCGACAAAGCAAGCCAAAAC-ATATAGTGAGGAAAGGACAC 4088
                           i    i        i -iv     i  -  vi i  i      i i v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_68937606_6   4089 CCTATTCAACAAATGATGCTGGGATAATTGGCAAGCCACATGTAGAAGAA 4138
                         i  v           i        i  i   vv ?       i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_68937606_6   4139 TGTAACTGGATCCTCATGTCTCATCATATACAAAAATCACCTCAGGATGG 4188
                           v ii    i  ii iv  v  i             i v    ii    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_68937606_6   4189 ATCAAAGACTTAAATCTAATATCTGAAACCATAAAAATTCTAGCAGATAA 4238
                             ?    i     v   v v  i    i      v ii   v   v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_68937606_6   4239 CATCAGAAAAGCTCTTCTAGACAGTGGCTTAGGCA--GAATTCATGACCA 4286
                            vi ?iv iv     vv   vv   v       -- iv   v iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_68937606_6   4287 AGTAC-CCGAAAGAAAATACAACAAAAGCAAAGATAAATAGATGGAACTT 4335
                         v -  -  i    v v vi         v   i   i   i  v i    
  L1M4_orf2#LINE/    596 TG-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_68937606_6   4336 AATTAAACTAAAATGTTTCTGCACAGCAAAAATAATAATAATAATCAGCA 4385
                         v  i   v v   vii  i  ii vv    ii----- i v  -   iv 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGG-----ACACTA-TCAAGA 688

  chr1_68937606_6   4386 AAGTAAACAGACAACCCATAGAGTGGGAGAAAATATTCACTAACTATTCA 4435
                             i  v          i   i              ii v  ii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_68937606_6   4436 TCCAATGAAGGACTAATATCCACAATCTACAAGGAACTCAAAACAAATCA 4485
                           ii  i i     vi      v   v  i  i      vv -   v   
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCA 787

  chr1_68937606_6   4486 GCAAGAACAACAACAACAAATAATAATCCCATAAAAAAGTGGACTAAGGA 4535
                         ii  v  v  ----i        i---  v  v?    i   i v     
  L1M4_orf2#LINE/    788 ATAATAAAAA----GACAAATAAC---CCAATTWAAAAATGGGCAAAGGA 830

  chr1_68937606_6   4536 GATGCACAGATATTTCTCAAAAGGAGATAGATAAATGGCCAACAAACACA 4585
                         vv  v i   i       v    i     v i          i  i    
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_68937606_6   4586 TAAAAAAA-GTTCAATGTCACTAATGAT 4612
                          i    i - i    ii   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (150 / 104)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


2897 26.91 1.44 1.00  chr1_69017393_69021682.rev     2897  3799 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_69017393_6   2897 GGAAACACATCTCATGCTCATGGATGGGATGATCAAATCAATATTGTAAA 2946
                              v i   i    i        v   v  i---- i        v  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGAC----TTAATATTGTTAA 47

  chr1_69017393_6   2947 AATGACTATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCA 2996
                         i   i v     v  v   vii       i      i     i  i    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_69017393_6   2997 AAATACCACCATCATTCTTTACAGAACTAGAAAAAA-AATCCTAAAATTC 3045
                             v   v vv v  i   i     v v  v  iv-i            
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_69017393_6   3046 ATATGGAACTAAAAAAGAGCTCACATAGCTAAAGCAACACTAAGCAAAAA 3095
                                 v iv  ii  v iviv     i   i   ivi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_69017393_6   3096 GAACAAATCTGGAGGCATCACATTACCGGATTTCAAACTATACTATAAGA 3145
                                vi      vv     i v  vi        viv     i  ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_69017393_6   3146 CCATAGTCACTAAAACAGCATGGTACTTGTATAAAAATAGGCACATAGAC 3195
                          i i   v ii  i    ii       v i    ii    i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_69017393_6   3196 CAATGAAACAGAA--GAGAACCCAGAAATAAAGCCAAATACTTACAGCCA 3243
                              i  i    --    ii           v   v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_69017393_6   3244 ACTGATCTTTGACAAAGCAAACAAAAACATAAAGTAGGGAAAGGGCACCC 3293
                          i    i  i     i vviv   i v   vv i i       iii vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_69017393_6   3294 TATTCAACAAATGGTGCTGAGATAACTGGTAAGCCACAAGTAAGAGATTA 3343
                          v                 i  i      vv ?     v i  i   v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_69017393_6   3344 AAACTGGATTCTCATCTCTCACCTTATACAAAAATCAACTCAGGATGTAT 3393
                           ii    ii ii i   v    v           i      ii   v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_69017393_6   3394 GAAAGACTTAAATCTAAGACCTGAAACTATAAACATTCT-AGAAGATAAC 3442
                         v ?    i     v     v  i          - i   -      v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chr1_69017393_6   3443 GTCAGAAAAACCCTTCCAGACATCGACTTTGGCAAAGATTTCATGACCAA 3492
                         i vi ?iv  vi    vv   v i iv  v     v i    v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_69017393_6   3493 GATCCAAAAAACAAATACAACAAAACAAAGA-TAAATTGATGGGACTTAA 3541
                           iv v    i  v vi        v   i -  i  vi  v      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_69017393_6   3542 TTAATCTGATGAGCTTCTGCACAGCAAAAGGAACAGTCAGCAGAGTAAAC 3591
                          i  vv v vi i   i  ii vv    i iv  vi   iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_69017393_6   3592 AGATAACCCAGAGA--GGAAGAAAATCTCCACAATCTATATATCCAACAA 3639
                            i      v   --  i       v iii   vii       ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_69017393_6   3640 AGTACTAATATTCAGAATCTATAAGGAACTC----AAATTAGCAAGAAAA 3685
                         i v   vi   i      v     i      ----  v i ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_69017393_6   3686 AAAACAAACAATTCCATCAAAAAATAGGCTAAG--TTCATGAATAGACAA 3733
                          i -    i  ii v  i?      i   v   --  --          v
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATT--TGAATAGACAT 843

  chr1_69017393_6   3734 TTCTCAAAAGAGGATATACAAATGGCCAACAAACACATGAAAAAAATGCT 3783
                              v     i                 i  i          i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr1_69017393_6   3784 CAACATCACTAATGAT 3799
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 1.83 (22 / 12)  


 496 28.84 1.40 3.26  chr1_69028731_69030396.rev        1   215 (1451)    L1M4_orf2#LINE/L1       11   221 (687)  

  chr1_69028731_6      1 TTCCATAATCACGAATTTGAAGAATCCATAT-G--AAAATGACCATGCTG 47
                          i    iv   i i   v     v iv    - --  i   i v  i  v
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chr1_69028731_6     48 TCCAAAGAAATCTACAGATTTCAATGCAATTCCTATCAAAATATCAACAT 97
                         i     vvi           -   i     i           vi  i vv
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATT-CAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_69028731_6     98 CATTTTTCACTGAGTTAGAAAAAAAAATCCTAACATTCATTTGTAACAGA 147
                          v     ii v  iv v  v  ivvi       v      v  ------i
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG------G 153

  chr1_69028731_6    148 AAAAAAAAAAAAACCTCAATAGCCAAAGCAATCCTAATCAAAAAGAACGA 197
                            viv  iii v  vv          i     i i vv  i      i 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_69028731_6    198 ATCTGGGCGAGGCACACT 215
                          vi   iv  vv      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACT 221

Transitions / transversions = 1.00 (31 / 31)
Gap_init rate = 0.02 (4 / 211), avg. gap size = 2.50 (10 / 4)  

1951 24.16 8.78 1.61  chr1_69028731_69030396.rev      493  1175 (491)    L1M4_orf2#LINE/L1      177   908 (0)  

  chr1_69028731_6    493 CAAAACAAA--TGAACAAACAATAAAACAAATCTGGAGGAGTCAAACATT 540
                                 v--    -   v  --i      vi       v   --  i 
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAA-AAAGAA--GAACAAAGTTGGAGGACTCA--CACT 221

  chr1_69028731_6    541 GGTTGACTTCAAATAATACTACAAGCCTATAGCAACCAAAATAGTATGGT 590
                         vviii i      vvv        iv   i  i  i   i i   i    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_69028731_6    591 AGTGGCATAAAAGTAGACACATAGGCCAATGTAACAGAATTGAGAACCCA 640
                          v        iii      i    ii     v  i          ii   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_69028731_6    641 GAAATAAAGCCAAATACTTATAATCAAGTTATCTTTGACAAAA------- 683
                                 v   v i i    ii    v v  i  i     ii-------
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_69028731_6    684 ---CAT---ATA---AAAACATA--------------------------A 698
                         ---   ---  i---   iv   -------------------------- 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_69028731_6    699 ATT-----------TGTAGAGGAATGAAACTGGATCTCTGTCTCTCACCA 737
                          i -----------  i i i       ii    i i  ii   v     
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_69028731_6    738 CATACAAATATCAACTCCAGATGGATTAGAGACTTAAATCTAAGACCTGA 787
                         i       v  i     v i      i ?    i     v     v  i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_69028731_6    788 AACTATAAAAATTCTGTAAAATAAAACCTAGAAAAAATTCTTCTGGACAT 837
                                   -i   -  i  v     v   i?iv  v     vv   v 
  L1M4_orf2#LINE/    522 AACTATAAAA-CTCT-TAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr1_69028731_6    838 TTGCCTAGGCAAAGAATTTATGACTATGACCACAAAAGCAAATACAACAA 887
                          v vi       v iv  iv iiv      vv        v vi      
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_69028731_6    888 AACAAAAAAATAAACCGATGGGACTTAAGTAAACTAAAAAGCTTCTGTAC 937
                           -i        i ivi  v      v vi   v v    i   i   i 
  L1M4_orf2#LINE/    620 AA-GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_69028731_6    938 AGCCAAAGAAAGAACCATCAG---AGTACACAGACAACCCACAGAAAGGG 984
                         -vi     i v--  i    i---   iv v               v   
  L1M4_orf2#LINE/    669 -TTCAAAGGAC--ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_69028731_6    985 AGGAAATATTTGAAAACTATGCAACTGACAAAGGACTAATATCCAGAATC 1034
                           i         v   ii  ii v    i  i     vi          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_69028731_6   1035 TATGAGGAACTCAAACAAATCAGCAAGAAAAA-ACAA-TAATCCCATTAA 1082
                            i i      vv    v   ii  v     -    -   i  v   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_69028731_6   1083 AAAGTGAACAAATGACATGAATAGACGTTTCTCAAAAGAAGATATGCAAA 1132
                            i  ii    v  iv         i      v           i    
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_69028731_6   1133 TGGCCAACAAACATGTGAAAAAAAGTTCTACACCACTAATCAT 1175
                                i  i  ii      i v i  v   i  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (98 / 64)
Gap_init rate = 0.02 (17 / 732), avg. gap size = 4.18 (71 / 17)  


3140 26.92 0.66 0.88  chr1_69047550_69049482      531  1440 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_69047550_6    531 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAACATTGTGAAAAT 580
                               i i  i     i        v      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_69047550_6    581 GGTCACACTGCCCAAAGTAAATTATAGATTCAATGCTATCCCCATCAAGC 630
                           iv i   v      v i vi  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_69047550_6    631 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAACTTCA 678
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_69047550_6    679 TATGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTGGGCAAGAAG 728
                                viiv  ii  v  v v        i      i  iiv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_69047550_6    729 AACAAAGCTGGAGGCATCACGCCACCTGACTTCAAACTATACTACAAGGC 778
                                i      vv    i iv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_69047550_6    779 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATAAATAGACC 828
                                 i   i    ii         i iv ii i   i v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_69047550_6    829 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 876
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_69047550_6    877 ATCTGATCTTTGACAAATCTGACACAAACAAGCAACGGGGAAAAGATTCC 926
                          vi    i  i     ivv  v  vi v  vv   i       ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_69047550_6    927 CTACTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 976
                           vi i  i        i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_69047550_6    977 GAAACTGGACCCCTTCCTTACATCTTATACAAAA-TCAACTCAAGATGGA 1025
                            ii         v   i   i v         - i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_69047550_6   1026 TTAAAGATGTAAATGTAAGGCCTAGGACCATAAAATTCCTAGAAGAAAAC 1075
                          i ?   iv          iv   ii  i      i  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_69047550_6   1076 CTGGGCA-ATACCATTAAGGACACAGGCATGGGCAAAGACTTCATGTCTA 1124
                         v i  ?i- v i -  viv   viv  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_69047550_6   1125 AGACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1174
                         v             vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_69047550_6   1175 ATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATTATCAGAGTGAA 1224
                           i   v v  i i   i  ii vv    iv v     i vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_69047550_6   1225 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACCCATCTGACA 1274
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_69047550_6   1275 AAGGGCTAATATCCTGAATCTACAAAGAACTTAAAGAAATTTACAAGAAA 1324
                          i  i  vi     v    v  i        ivv v  v ---   v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAAT 792

  chr1_69047550_6   1325 AAAAAAAAAAACAATCCCATCAAAAAGTGGGCAAAGGATATGAGCAGACT 1374
                              i v   i  i  v  i?    i            v   ii    v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_69047550_6   1375 ATTCTCAAAAGAAGACATTTATGCAGCCAACAGACGTATGTAAAAATGCT 1424
                         v     v        i  vi viii     i ii ii   v   i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_69047550_6   1425 CATCATCACTAGTTAT 1440
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3301 26.16 0.66 0.44  chr1_69053737_69060009.rev     4877  5782 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_69053737_6   4877 TGGAAGAACATTCCATGCTCATGGATAAGAAGAATCAATATCATGAAAAT 4926
                              ii i  i     i        vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_69053737_6   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_69053737_6   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_69053737_6   5025 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_69053737_6   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_69053737_6   5125 TACAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                 v   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_69053737_6   5175 AATGGAACAGAA--AAGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5222
                                i    --i    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_69053737_6   5223 ATCTGATCTT-GACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5271
                          vi    i  -     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_69053737_6   5272 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5321
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_69053737_6   5322 GAAACTGGATCC-TCCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5370
                            ii    i  - v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_69053737_6   5371 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5420
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_69053737_6   5421 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5470
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_69053737_6   5471 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5520
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_69053737_6   5521 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5570
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_69053737_6   5571 AGGCAACCTATAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5620
                           i     i i i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_69053737_6   5621 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5670
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_69053737_6   5671 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGAAATGAACAGACACTTC 5720
                          i     i     v  i?    i     i     vv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_69053737_6   5721 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5770
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_69053737_6   5771 ATCACTGGCCAT 5782
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3134 27.43 0.88 0.44  chr1_69100691_69106964     4878  5781 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_69100691_6   4878 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4927
                              ii i  i   i i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_69100691_6   4928 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_69100691_6   4978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAACGTTCA 5025
                          v   iivi i  i  ii     -   -- v  i  - iii   vi    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_69100691_6   5026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_69100691_6   5076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAATTATACTACAAGGC 5125
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_69100691_6   5126 TACAGTAACCAATACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5175
                                 i   v    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_69100691_6   5176 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5223
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_69100691_6   5224 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCG 5273
                          vi    i  i     ivv  vv  i v  vvv           i  vvv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_69100691_6   5274 CTATTTAATAAAAGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACT 5323
                           v  i  i   v          v      v  ?   i   i i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_69100691_6   5324 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5373
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_69100691_6   5374 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_69100691_6   5424 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGGCTTCATGTCCAA 5473
                         v    ?i v viv   iv   v v  vv i     v  i   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_69100691_6   5474 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAA 5523
                         i            vvi          vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_69100691_6   5524 TTAAACTAAAGAGCTTCTGCACAGCAAAACAAACTACCATCAGAGTGAAC 5573
                          i   v v  i i   i  ii vv    iv v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_69100691_6   5574 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5623
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_69100691_6   5624 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5673
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_69100691_6   5674 AAACAA----CCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5719
                          i    ----   v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_69100691_6   5720 TTAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5769
                          iv           vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_69100691_6   5770 ATCACTGGCCAT 5781
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3089 25.43 0.76 2.49  chr1_69164861_69169418     3142  4065 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_69164861_6   3142 TGGAAAAAAAACTTCCATGCGCATGGATAGGATGAATCAATATTGTGAAA 3191
                               i v -- i     iv       v   v  v i        v  i
  L1M4_orf2#LINE/      1 TGGAAAGATA--TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_69164861_6   3192 ATGGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAA 3241
                              v     v      v i  i  i        i  v     i     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_69164861_6   3242 GCTACCA-CTGACTTTCTTTGCAGAATTAGACAAAACT-ACTTTAAATTT 3289
                         iv v   -   v    -         v v     i-  - iii    v  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTT-TTTGCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chr1_69164861_6   3290 CATATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGAAAAA 3339
                                  viiv  ii  v  viv        i      i i -    i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAG 195

  chr1_69164861_6   3340 AAGAACAAAGCTGGAGACATCATGCTACCTGACTTCAAATTATACTACAA 3389
                                   i     ivv   ii  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_69164861_6   3390 GGCTACAGTAACCAAAACAGCATGGTGTTGGTACCAAAACAGATATATAG 3439
                         i          i   i    ii    ii   i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_69164861_6   3440 ACCAATGGAACAGAACAGAGACCTCAGAAATAACATCAGACACTTACAAC 3489
                          i        i    iv    vii         vvi  v   i   iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_69164861_6   3490 CACCTGATCTTCGACAAATATGAGAAAAACAAGCAATGGGGAAAGGAATC 3539
                           vi    i        ivi  vv  i v  vv            -   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATA 394

  chr1_69164861_6   3540 -CCTATTTAATAAATGGTGCTTGGAAAACTGGCTACCCATAGGCCGAAAA 3588
                         -i  v  i  i          v   v      v  ?   i v  vi  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_69164861_6   3589 CTGAAACCAGACCCCTTCCTTACACCTTACACAAAAATTAACTCAAAATG 3638
                         v    iiii       v   i     v  i                    
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_69164861_6   3639 TATTAAAGACTTAAATGTAAAACCTAAAACCATAAAAACCCCAGAAGAAA 3688
                         v  i ?    i         i v       i      vi ii        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_69164861_6   3689 ACCTAGGCAATAGCATTCAGGACATAGGCATGGGTAAAGACTTCATGACG 3738
                           v    ?ivv iiv   iv   v v  vv i  i  v ii   v iivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_69164861_6   3739 AAAATACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCT 3788
                          vi i          vvv          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_69164861_6   3789 AACTAAACTAAAGAGCTTCTTCACAGCAAAAAAAAAAAAAAAAAAAAAAA 3838
                         v ii   v v  i i   i vii vv    ii v ---------------
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA--------------- 679

  chr1_69164861_6   3839 AACTATCATTAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTG 3888
                         --      vv i      v  i     i                 v    
  L1M4_orf2#LINE/    680 --CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_69164861_6   3889 CAATCTATACATCTGACAAAGGTCTAATATCCAGAATCTACAAGGAACT- 3937
                            vii   i      i  i  v  vi          v  i  i     -
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_69164861_6   3938 -TA-AATTTA-CAAGACAAAAACAGACAACCCCATCAAAAAGTGGGTGAA 3984
                         -  -  i i -i  v v   i   i i     v  i?    i    ii  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_69164861_6   3985 GGATATGAACAGACACTTCTCAAAAGAAGACATTTATGTGGCCAATAAAC 4034
                             v    i     i     v        i  vi vi          i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_69164861_6   4035 ATAGGAAAAAAAGCTCATCATCACTGGTCAT 4065
                          i v     i v     v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (133 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.50 (30 / 12)  


1635 23.92 10.82 7.97  chr1_69186818_69190980.rev     2795  3672 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_69186818_6   2795 AAATATAC-ATGTTTGTAGATCAAAAGATTCAATAATGTTAAAATG---- 2839
                          i    v -     ii i   iii    i i    v      i   ----
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_69186818_6   2840 TAATTTTTAAATATTGATCCATTGATTCAATACAATCTCAATAAAATTCC 2889
                           v iiii    --     i iv       ii     i v  v   v   
  L1M4_orf2#LINE/     56 TACTCCCCAAAT--TGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_69186818_6   2890 CAGCAGACTT----ATAAAAATATAAAGCAGCAAGCTAAATCTAAAGTCT 2935
                             v v   ----ii i    - i -----      i vi     i ii
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAAT-TGA-----CAAGCTGATCCTAAAATTC 147

  chr1_69186818_6   2936 AATTGGAAATTCAAAGGGCTTAGAATAGC-AACACAATTTTTGAGAAAAG 2984
                          vv       v   i  i ii        -  v     i  ---     i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT---GAAAAA 194

  chr1_69186818_6   2985 AAAAAAGAGAATT--AAGACTTGTTCTATTTAATTTCAAGATATTTTGCA 3032
                         i  i  v i i  -- i    iiiv  viii        i iv vi i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_69186818_6   3033 AAGTCATAGTAATCTAGACAGTTTGATATTAGCAAAAAGATAAAAA-ATA 3081
                            ii i       v       v  i  i i   v  i    i v -   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_69186818_6   3082 GATCAATGAAACAGAATAGAGAGTCCAGAGATA----CACATTTTTGTGC 3127
                                 i  i     v           i   ----  i iv   i  -
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG- 343

  chr1_69186818_6   3128 AGTCAATTCATT----AAAAAAATAGTCAAAGCAATTTAATGTGGAAAGG 3173
                         -       v   ---- v  iii - i   ii v   i    v      i
  L1M4_orf2#LINE/    344 -GTCAATTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGA 391

  chr1_69186818_6   3174 AAAGTCTTT-CAGCATATTGTA--AAAACA---------CTAC-TG-AGA 3209
                          v       -  i  v  v  i--iii   --------- i  -  - i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_69186818_6   3210 AGATATAAA-TTAAACCTTTAT---------------------------- 3230
                            -  i  -  ii   ii  i----------------------------
  L1M4_orf2#LINE/    442 AGA-ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_69186818_6   3231 ----------AGATCTAAGTATAGACCCCAAAACTATAAATCGTTTAGGT 3270
                         ----------   i    i i  iivv i           v vi    iv
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_69186818_6   3271 GAAAATATAAGAATA--TTTTCATGACCTCGGGGTAAGTAAATAACTT-T 3317
                              i   i ?i  -- i   i      i   v  i i  - iii  - 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chr1_69186818_6   3318 TAGATAAAGCACAGAAAGCAATAGGCAT-------AAAAACCGATAACTT 3360
                               vii   vi      -i i   v-------     iv     v  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_69186818_6   3361 ACATTTACTTAAAAATTAAAA---TGTCTGCTCATCAAAAGGCAGTATCA 3407
                         iv i  - v v          --- v v    --     i i  v     
  L1M4_orf2#LINE/    639 GGACTT-CATCAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTATCA 685

  chr1_69186818_6   3408 AGAAAATGTGTAGGCAAATCATAGAGTGGCATACAACAATAAGTACATAT 3457
                              i  viv  i   vi  i   i   -----------i  v v    
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGG-----------GAGAAAATAT 724

  chr1_69186818_6   3458 TTGGGCATACACACACACACACACACATACACACATAGACATGTATGTAA 3507
                            ----------------------------  v  ---   i   v i 
  L1M4_orf2#LINE/    725 TTG----------------------------CAAAT---CATATATCTGA 743

  chr1_69186818_6   3508 ATACACATACTTGCATCCAGAGTATATAAAGAATCCCTACAAGTCACTAA 3557
                         -  - viv     i       i           ii i     v   v   
  L1M4_orf2#LINE/    744 -TA-AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_69186818_6   3558 --AAAATA-AAGTAACCCAATTTTTTAAAAAATGGTTTAA--ATCTG--T 3600
                         --    v -  i          ?----        viv  --  i  -- 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTW----AAAAATGGGCAAAGGATTTGAAT 837

  chr1_69186818_6   3601 AAAC-TTCCATCACAAAAAAGATATGTGAACGGCCAATAAGCATATGAAA 3649
                          i  -  i -  -    i       iii  i            i      
  L1M4_orf2#LINE/    838 AGACATTTC-TC-CAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_69186818_6   3650 AGGAATTCATCATTATTCACACA 3672
                           ivii   v   i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.20 (143 / 65)
Gap_init rate = 0.05 (43 / 903), avg. gap size = 3.84 (165 / 43)  


 477 27.85 2.53 2.53  chr1_69243641_69249685.rev     4329  4486 (1559)    L1M4_orf2#LINE/L1        1   158 (750)  

  chr1_69243641_6   4329 TGGAAAAATATTGCATGCTCATGGATAGGAAGAATCAATAT---AAAAAT 4375
                               i    iv    i        v      v i     ---v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_69243641_6   4376 GGCCATCCTGCCCAAAGTAATTTATAGATTCAGTGTTATTCCCATTGAAC 4425
                            v  v  v      v i  i  i       ii iv  i  i  ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_69243641_6   4426 TACCATTGACATTTTTCACAGAATTTTTTTTTTAAACT-ATTTTAAAATT 4474
                          v   vivi v     ii     v  ----vvi  i  -  ii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT----GACAAGCTGATCCTAAAATT 146

  chr1_69243641_6   4475 TACATGAAACTG 4486
                         i i   i  v  
  L1M4_orf2#LINE/    147 CATATGGAAATG 158

Transitions / transversions = 1.44 (26 / 18)
Gap_init rate = 0.02 (3 / 158), avg. gap size = 2.67 (8 / 3)  

2226 27.28 1.96 1.57  chr1_69243641_69249685.rev     4789  5554 (491)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr1_69243641_6   4789 TAAAATTTACATGAAAC--CAAAAAACCCATA-TAGCCAAGACAATCCTA 4835
                                i i   i  v--   iii     v -       i      i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_69243641_6   4836 AGCAAAAAGAATGCAGCTCAGCTGGAGGCATCACGCTATCCGACTTCAAA 4885
                          iv  i     --  i---  i      vv    i  vi  i i      
  L1M4_orf2#LINE/    190 AAAAAGAAGAA--CAA---AGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_69243641_6   4886 CTATACTACAATGCTACAGTATCCAAAACAGCATAGTACTGGTACCAAAA 4935
                         viv        v         vi   i    ii i       i iv ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_69243641_6   4936 TAGACAAATAAACCAATGGAACAGAATAGAGATCTCAGAAATAAGTCCAC 4985
                               v   i i        i     v    vii         ii   i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_69243641_6   4986 ACGTCAACAACCATCTGATGCTTGACAAACCTGACAGAAAAAAATCAATG 5035
                           i iv iiii  vi    vi i     ivv  v  - i vv v      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATG 383

  chr1_69243641_6   5036 GGGAAAGTATTCCCTATTTAATAAATGGTGCTGGGAAGACTGGCTAGCCA 5085
                                v  vvi  v  i  i              vi     v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_69243641_6   5086 TATGCAGAAAACTGAAACTGGACTCCTTCATTGGATTTTATACAAAAATT 5135
                         i     i  i v    ii     i   v v iiv iiv            
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_69243641_6   5136 ---TTAGGATGAATTAAAGACTTAAATGTACAACACAAAACCATAAAAAC 5182
                         --- i ii   i  i ?    i        vi vvi     i      vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_69243641_6   5183 CCTAGAAGAAAATCTAGGCAATACAAT--TCAAGACATAGGCATGGGCAA 5230
                          i          iv    ?i-  -   --  iv   v v  vv i     
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_69243641_6   5231 AGATTTTATG---ATGAAATTGCCAAAAGCAATTTCAACAAAAGCAAAAT 5277
                         v i   iv i---    v ---         vvvv         v    v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACA---CCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_69243641_6   5278 T-GATAAATGGGATCCAATTAAACTAAAGAGCTTCTGTACAGCAAAAAA- 5325
                          -       v   iiiv  i   v v  i i   i   i vv    ii -
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_69243641_6   5326 ACTATCATCGGTGTGAACCAGCAGCCTACAGAATGGGAGAGAATTTTTGC 5375
                                vviiv     vvii  i  i             i   v     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_69243641_6   5376 AATCTACCCATCTGACAAATGACTAATATCCAGAATTTACAGGAAACTTA 5425
                           vii ivi      i  iv    vi          v  i iii    iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_69243641_6   5426 AAAAAGTTTACAAGAAAAAAACAAAGAACTCCATCAAAAATTGGGCAAAG 5475
                         v v  v iv i  v     i     v   i v  i?    v         
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_69243641_6   5476 GACATGAACAGACCACTTCTCAAAAGAAGACATTTATGGGGCCAACAA-- 5523
                           iv    i    - i     v        i  vi viv      i  --
  L1M4_orf2#LINE/    829 GATTTGAATAGAC-ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_69243641_6   5524 ACATGAAAAAAAGCTCAACATCACTGATCAT 5554
                                  i v           ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (120 / 85)
Gap_init rate = 0.02 (15 / 769), avg. gap size = 1.80 (27 / 15)  


3133 26.90 0.66 0.55  chr1_69274481_69280872.rev     4995  5901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_69274481_6   4995 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5044
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_69274481_6   5045 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5094
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_69274481_6   5095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 5142
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_69274481_6   5143 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5192
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_69274481_6   5193 AACAAAGCTGGAGGCATAATGCTACCTGACTTCAAACTCTGCTACAAGGC 5242
                                i      vv v ii  v  ii i      vii i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_69274481_6   5243 TAGAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5292
                           v     i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_69274481_6   5293 AATGGAACAGAAC--AGAGTCCTCAGAAATAATACCACACATCTACAACC 5340
                                i    i--       --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_69274481_6   5341 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5390
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_69274481_6   5391 CTATTTAA-AAATGGTGCTGGGAAAATGGGCTAGCCATATGTAGAAAATG 5439
                           v  i  -              v  iv  v  ?   i   i i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_69274481_6   5440 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTAAACATGGA 5489
                            ii    i    v   i     v              i v  v     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_69274481_6   5490 TGAAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5539
                          v ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_69274481_6   5540 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5588
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_69274481_6   5589 AAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAGTGGGATCTA 5638
                         vi    v       vvi          vv     v  i  i v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_69274481_6   5639 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTCAA 5688
                           i   v v  i i   i  ii vv    i  v    i  vv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_69274481_6   5689 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5738
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_69274481_6   5739 AAGCGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5788
                          i vi  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_69274481_6   5789 AAAACCAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5838
                           i  v  i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_69274481_6   5839 CTCAAAAGAAGACATTTATGCAGCCTACAGACACATGAAAAAATGCTCAT 5888
                            v        i  vi viii   v i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_69274481_6   5889 CATCACTGGCCAT 5901
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (137 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3306 26.43 0.55 0.55  chr1_69292427_69298715.rev     4891  5798 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_69292427_6   4891 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4940
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_69292427_6   4941 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4990
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_69292427_6   4991 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5038
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_69292427_6   5039 TATGGAACCAAAAAAGACCCCGCATCGCCAAGTCAGTCCTAAGCCAAAAG 5088
                                viiv  ii     v v  v     iv  i  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_69292427_6   5089 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGC 5138
                                i      vv       v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_69292427_6   5139 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5188
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_69292427_6   5189 AATGGAACAGAAC--AGAGCCCTCAGAAATCATGCCGCATATCTACAACT 5236
                                i    i--    i  --      v vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_69292427_6   5237 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5286
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_69292427_6   5287 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5336
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_69292427_6   5337 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5386
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_69292427_6   5387 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5436
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_69292427_6   5437 CTAGGCATTA-TCATTCAGAACATAGGCATGGGCAAGGACTTCATGTCTA 5485
                         v    ?i v -  -   ivi  v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_69292427_6   5486 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5535
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_69292427_6   5536 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5585
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_69292427_6   5586 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5635
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_69292427_6   5636 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5685
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_69292427_6   5686 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGAGACTT 5735
                           i     i     v  i?    i     i     iv    i   v i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_69292427_6   5736 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5785
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_69292427_6   5786 CATCACTAGCCAT 5798
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2288 25.25 4.40 1.13  chr1_69329761_69334538.rev     3583  4287 (491)    L1M4_orf2#LINE/L1      181   908 (0)  

  chr1_69329761_6   3583 ATACTCATGAAACACAAAAATAAACATTGTTAAAAGGAC-CATACTTCCC 3631
                          i v  v     v v  i  i   ----   ii -    -  i       
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAA----GTTGGA-GGACTCACACTTCCC 225

  chr1_69329761_6   3632 AATCTACAGATTCAATG-AAATCC----TTATCAAAATACCAATGTCAT- 3675
                            i vv i i i v i-   v i---- v     i ---  i   vi -
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA---CAGTGTGGTA 272

  chr1_69329761_6   3676 TTTTCATA----------TGTAGATCAATGGAACATAATAGAGAGCTTAG 3715
                         i vv    ---------- i             i v   v     iii  
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_69329761_6   3716 AAACAAAGCTATATATTTAAAGCCAACTGGTCCTTGACAAAATCAACAAG 3765
                            i   v i   i     vi i   i  i ii i     iiviiv    
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_69329761_6   3766 AAAAGACATTGGGGAAAATATACTGTTTTCAATAAATGGTGCTGGGAAAA 3815
                          vv vv  v        iv   v v       i              v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_69329761_6   3816 CTGAATTGTCATATGCAGAATAATAAAACTAG---CCCATCTTAC--CAC 3860
                            i  v?i  i     i  v   i  ii i ---  i i  i  --  i
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_69329761_6   3861 ATACAAAATTCAAATCAAGATGGATTAAAAACTTGAATGTAAGTCTCAAA 3910
                                 v i  v    i      i ? i  i i        vvii   
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_69329761_6   3911 ATTATA---------GAAGAAAACCTAGGGAAAACTCTTCTGGACATTGG 3951
                          i    ---------         v    ?iv  v     vv   v    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_69329761_6   3952 TTCAGACAAAGAATTTATGACTAAGACCTCAAAAGCACAGGCATGAAAAA 4001
                         v i  i   v iv  iv iiv  v   vi          i   vv    i
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_69329761_6   4002 CAAAAATAGACAAATGAGACTTAATTAAACTACAAAACTTCTGCACAGCA 4051
                         v         i    vi     v  i   v vv       i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_69329761_6   4052 AAAGAAACAATCAACAGAGTAAAGAGACAACCAGAAGAATGGGAGAAAAT 4101
                           i  v  v     v i   i  i        viv               
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_69329761_6   4102 ATTTGCAAACTATGTATCTGACAGTGGACTAATATCCAGAATATATAAGG 4151
                                  ii  i       i iv     vi                i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_69329761_6   4152 AACTCAAACAATTCCACATTAAGAAAACAAATGATTTCATCAAAAAATGG 4201
                              vv    i  v i v   i  i      i iiiv  i?        
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_69329761_6   4202 GCAAAGGATATGAACAGACATTTCTCAAAAGAAGACATACAAATGGCCAA 4251
                                  v    i           v        i              
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_69329761_6   4252 CAGGTATGTAAAAATATGCTCAACATCACTAATCAC 4287
                         i i i ii i    v             ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (103 / 71)
Gap_init rate = 0.02 (11 / 728), avg. gap size = 3.55 (39 / 11)  


2854 27.81 1.10 0.88  chr1_69484379_69490226.rev     4452  5357 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_69484379_6   4452 TGAAAAAAGATTTCATCCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4501
                           i   i v  ii   vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_69484379_6   4502 GGTCATATTGCCCAGAGTAATTTATAGATTCAATGCTATTCCCTCCAAAC 4551
                           iv   i v    i v i  i  i        i  v  i  ivi    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_69484379_6   4552 TATCATTAACATTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTCAT 4600
                          vi  vivi v  i  ii     v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_69484379_6   4601 ATGGAA-T-CAAAGAAGACCCCATATAGCCAAAACAATCCTAGGCAAAAA 4648
                               - -   i --     viv               i iiiv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_69484379_6   4649 GAACAAAGCAGGAGGTATCATGCTACCTGTCTTCAAACTATACTACAAGG 4698
                                 iv     vv   ii  v  iivi      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_69484379_6   4699 CTACGGTAACCAAAATAGCATGGTACTGGTACCAAAACAGACATATAGAC 4748
                             i    i   i i  ii         i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_69484379_6   4749 CAGTGGAGCAGAACAGAGACCTCAGAAATAACACCACACATCTGCAACCA 4798
                           i    ii    iv    vii         vv   i    i iiiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_69484379_6   4799 TCTGATCTTCAGCAAATCTGCTAAAAACAAGCAATGGGGAAAGGATCTCC 4848
                         vi    i   ii   ivv   i  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_69484379_6   4849 TATTCAATAAATGATGCTGGGAAAACTGGCTAGCTATATGCAGAAAACAG 4898
                          v     i     i        v      v  ? i i     i  i vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_69484379_6   4899 AAACTGGACCCCTTCCTTACAACTTATACAAAAATTAACTCAAGATGGAT 4948
                           ii         v   i   v v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_69484379_6   4949 TAAAGACTTA--TGTAAAACTCAAAACCATAAAAACCCTAGAAGAAAAAA 4996
                         i ?    i  --     i vii     i      vi i          --
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-- 545

  chr1_69484379_6   4997 CCTAGGCA-ATACCATTCAAGACATAGGCATGGGCAAAAACTTCATGACA 5045
                          v    ?i- v i -   iv   v v  vv i     viii   v iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_69484379_6   5046 ACGCCACCAAAAGCAATTGCAACAAAAATCAAAAT-GACAAACAGGATTT 5094
                          i v           vvv         ivv     -  i   iv   i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_69484379_6   5095 AATTAAACTAAAGTGCTTCTGCACAGCAAAAGAAGCTATCATCAGAATGA 5144
                         v  i   v v  ivi   i  ii vv    i  vi      vv i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_69484379_6   5145 ATAGGCAACCTATACGATGGGAGAAAATTTTTGCAA-TCAATCCATCTGA 5193
                          v  i     i i vi            v       -   - vi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGA 743

  chr1_69484379_6   5194 CGAAGGTCTAATATCTAGAATCTACAAGGAACTTAAACAAATTTACAAGA 5243
                         ii i  v  vi    i     v  i  i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_69484379_6   5244 AGAAATCAAACAACCCTAT-AAAAAGTGGGCAAATAATATGAACAGACAC 5292
                          i  iv    i     v  -?    i        vi  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_69484379_6   5293 TTCTCAAAAGAAGACATTTATGTGGCCA-CAAACATACAAAAAAAAAGCT 5341
                              v        i  vi vi      -i  i  i ii    i v-   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCT 892

  chr1_69484379_6   5342 CAATATCACTGATCAT 5357
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.20 (18 / 15)  


2435 25.29 2.30 2.30  chr1_69521394_69523107.rev      495  1277 (437)    L1M4_orf2#LINE/L1      126   908 (0)  

  chr1_69521394_6    495 TGATGAGCT----TTTAATTTCATATAAAACCAAAAAAGAGCCCGTATAG 540
                            ii    ----i v  v       ii  viiv  ii  v  v v    
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr1_69521394_6    541 CCAAGACAATCCTAAGCAAAAAAAAAAAAACAAAACTGGAGGTATCACAT 590
                             i      i i -----    i  i      ii      vv     i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGA-----AAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr1_69521394_6    591 TACCTGACTTCAAACTATACTACAAGGCTGCAGTAACCAAAACAGCATGG 640
                          v  ii i      viv        i   i      i   i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr1_69521394_6    641 TACTAGTACCAAAACAGACATATAGACCAATGGAACAGAAC--AGAGCCC 688
                             i i iv ii i           i        i    i--    i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_69521394_6    689 TCAGAAATAACGCCACACATCTACAACCATCTAATCTTTGACAAACCTGA 738
                         --        vv   i    i  iiii  vi i  i  i     ivv  v
  L1M4_orf2#LINE/    321 --AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_69521394_6    739 CAAAAACAG-CAATGGGGAAAGGATTCCCTATTTAATAAATGGTGTTGGG 787
                            i v  v-            i  vvi  v  i  i        i    
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_69521394_6    788 AAAACTCACTAGCCACATGCAGAAAACTGGAAATGGACCCCTTCCTTACA 837
                          v    viv  ?         i  i v  i iv         v   i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_69521394_6    838 CCTTATACAACAATTAACTCAAGATGGATTAAAGACTTAAACCTAAGACC 887
                           v       v           i      i ?    i    iv     v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_69521394_6    888 TAAAACCATAAAAACCCTT-GAAGAAAACCTAGGCA-ATACCATTCAGGA 935
                               i      - i   -         v    ?i- v i -   iv  
  L1M4_orf2#LINE/    519 TAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGA 566

  chr1_69521394_6    936 CATAGGCATGGGCAAAGGCTTCATGACTAAAACACCAAAAGCAGTAGCAA 985
                          v v  vv i     v  i   v iiv  vi            vv     
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_69521394_6    986 CAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAGTGAGCTTTTGC 1035
                               vv     v  i    v   ii v  i   v vivi i      i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_69521394_6   1036 ACAGCAAAATAAATTATCATCAGAGTGAACAGGCAGCCTACAGAATGGGA 1085
                         i vv    iv v i     vv i      v  i  i  i           
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_69521394_6   1086 GAAATT-TTTGCAA-TC---TATCTGACAAAGGGTTAATATCCAGAATAC 1130
                             v -       -  ---       i  i  ii vi           i
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_69521394_6   1131 ATTAAAAACTTGAACAAATTTACAAGAAAAAAACAAACAACCCCATCAGA 1180
                           v  i    ivv    v iv i  v     i     i     v  i?i 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_69521394_6   1181 AAGTGGGCAAAGGATATGAACA---ATTTCTTCTTAAATATAAAA-ACAA 1226
                           i            v    i ---      i --   v vi v -    
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCC--AAAGAAGATATACAA 864

  chr1_69521394_6   1227 TTAAGCTATAATAAGTGACAAGATAAAATATAAATCTATGTCAGTCTGAT 1276
                         v i-  i --     i-   v  v  i  ii---  v ii   ???????
  L1M4_orf2#LINE/    865 ATG-GCCA--ATAAGC-ACATGAAAAGATGC---TCAACATCAZZZZZZZ 907

  chr1_69521394_6   1277 T 1277
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.46 (115 / 79)
Gap_init rate = 0.02 (19 / 783), avg. gap size = 1.89 (36 / 19)  


3133 27.07 1.68 0.11  chr1_69545926_69551325.rev     4022  4915 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_69545926_6   4022 TGAAAAAGCATTCCACGCTCATGGATAAAAAGAATCAATATTGTTAAAAT 4071
                           i   iii  i   i i        vii    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_69545926_6   4072 GGCAACACTGCTCAAAGTAATTTATAGATTCAATACTATTCCTATCAAAC 4121
                              i   v i    v i  i  i        ii v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_69545926_6   4122 TACCAAAGAAATTCTTCATAGAACCAGAAAAATCTATTTTGAAATTCATA 4171
                          v   ivvivv  i  iii    viv  v  iiiv  ii i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_69545926_6   4172 TGGAACTAAAAAGAGCCCAGA-TAGCCAAGGCAATCCTAAGCAAAAAGAA 4220
                              v iv  i ii      -       ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_69545926_6   4221 CAAAGCTGGAGGCATCACACTACCTAACTTCAAACTATACTATAGGGCTA 4270
                              i      vv       v  i  i      viv     i ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_69545926_6   4271 CAGTAACCAAAACAGCATGGTACTGGTACAA-AACAGACACATAGACCAA 4319
                               i   i    ii         i i  -i i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_69545926_6   4320 TGGAACAGAATAGAGAGCCCAGAAATAAGGCCACACACCTACAACCATCT 4369
                              i     v     i          iv   i   ii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_69545926_6   4370 GATCTTCGACACAGCTTACAAAAACAAGCAATGGGGAAAGGCAT-CCCTA 4418
                            i       vi v vv   i v  vv            i-  -vi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTT 399

  chr1_69545926_6   4419 TTCAACAAATGGTGCTGGGATAACTGGCTAGCACTATGTGGAACACTGAA 4468
                                             i      v  ? vvi   iii  v v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_69545926_6   4469 ACTGGACTACTTCCTTACATCATATACAAAAATCAACTCAAGATGGATTA 4518
                         ii     iv  v   i   i             i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_69545926_6   4519 AAGACTTAAATGTAAAACCCAAAACTGTAAAAACCCTGGAAGACAACCTA 4568
                         ?    i         i v i      i     vi i i     v   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_69545926_6   4569 GGCAATACTATTCTGGACAAAGGAACTGGCAAAGATTTTGTAACAAAGAT 4618
                           ?ivv v v   vv   vvv  iviv     v i   iv  ivv v  i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_69545926_6   4619 GCCAAAAGTGATTGC-ACAAAAGCAAAAATTGACAAATGGAAGCTAATTA 4667
                         i       iivvv  -       v      v  i    v i vi v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_69545926_6   4668 AACTAAAGAGCTTCTGCACAGCCAAAGAAACTATCAAGA--GTAAACAGA 4715
                           v v  i i   i  ii vv v  i  v          --  i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_69545926_6   4716 TAATCTACAGAATGGGA-AAAATATTTGCAAACTACACAACTGATAGAGG 4764
                         i  i i           -              ii i i v      ii  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_69545926_6   4765 TCTCATATCCAGCATCTATAAGTAACT----TAAGTTTACAAGAAAAAAA 4810
                         v  ii       v  v     iv    ----i  v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_69545926_6   4811 CAA----CCCCATTAAAAAGTGGGCAAAGGACATGAACAGACATTTTTCA 4856
                            ----   v   ?    i           iv    i        i  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_69545926_6   4857 AAAGAAGACATACAAGCAGCTAACAAGCATATGATGAAAACCTCAATATT 4906
                                 i      iii  i  i     i    vi i vv     i  i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_69545926_6   4907 ACTGATGAT 4915
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.62 (147 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


 805 29.26 11.28 4.43  chr1_69556944_69559315.rev     1142  1886 (486)    L1M4_orf2#LINE/L1      113   908 (0)  

  chr1_69556944_6   1142 TCTTTGTAAAATTTTACAAACTAGTTTTTAAAATT-ATTTGAGAGAATAA 1190
                          i    i i  v  v    i  - v ii       -  v  ii ivii  
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCT-GATCCTAAAATTCATATGGAAATGCAA 161

  chr1_69556944_6   1191 AGG----------GCCAAAACTAGTCCTGAA---GAAGAATA---TT--- 1221
                         i  ----------        - i  i    ---      i ---  ---
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAAC-AATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_69556944_6   1222 ----------TTCTTAACTATAATAAAAATTACTGTGAAGCTATAGTAAT 1261
                         ----------   ii  i - --i    v     iii      i      
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATT-T--CAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_69556944_6   1262 TTTAATAATACCACATTGGTTCAAGAATAGAATTCTAGACAAATGCAACA 1311
                         ivvi i i iivii i   ivi   i     vv v    iv    v  i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_69556944_6   1312 GAACAGACAGTTCAGAAATGATCACATGCATATATGAAAATTTAACTTAA 1361
                            iv  v   i       i v v   i   v    i---- i  -  i 
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGG----TCAA-TTGA 352

  chr1_69556944_6   1362 TTTTTGATA--GTTGGCAATGT-ATATCAATGGAGAGTAGTATGGT-TTT 1407
                             i  i -- v  v   vii-  -       i  i-  v  i  -   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAA-AGAATAGTCTTT 400

  chr1_69556944_6   1408 TCA-TAAATGGTTCTGGGATCATTGTTTA-CCACTTGAGAAAAAATG--- 1452
                            -i       v      iv i  vv  -    v  vi   i    ---
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_69556944_6   1453 TCAGAT---TAACTCTACATCATTTA-AAGAATCAACTGTAGATGAAT-A 1497
                          ii  i---  v   -   i   v  -  i   i    vv i   i  - 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTC-ACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_69556944_6   1498 AAAATGTAAGTG--GGAATGGAGACTTATATAATTATTACAGGACAA--- 1542
                         ? i iv   i  --i  iivi i   -   v  i v   v i  v  ---
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTTAGAAGAAAACAT 548

  chr1_69556944_6   1543 -----------TTTATGACCTCAGGGAAGGAGACAGTTTATTAAGCAAGA 1581
                         -----------  ii      ii  vv   vi ii    v   iii v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_69556944_6   1582 AACAGAAAATGCTTACGATAGAGTGTAATATATTTTACATAAAATATATT 1631
                         v  vi   iii vvi i i i iviv  v   v-----     v iv i 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAG-----ATAAATTGGACT 643

  chr1_69556944_6   1632 ATTGATTAAAATTATGAACTTTTGGTCATCAAAAGACATCAT--AGAGAC 1679
                         -- v  i       vi        vv v     i    ii  --   i v
  L1M4_orf2#LINE/    644 --TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_69556944_6   1680 TACAATGTACAAATTA-AGAACTGAGAAAAAAT-TTCACAA--CATATAT 1725
                          iv  v -    vii -    -  i  i     -  ii   --       
  L1M4_orf2#LINE/    692 TGAAAAG-ACAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_69556944_6   1726 AACCAACAAAGGATTAGTATCC------TACCAA----TC----AA-TCA 1760
                         -- ii i  i   i v      ------  iv  ----  ----  -   
  L1M4_orf2#LINE/    740 --CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_69556944_6   1761 ACAAGAAAAAAAGGAAACAACC-AATT-AAAATTGAACAACAACAACAAA 1808
                          i  v     i v-   i    -    -    v  ii   ------- ii
  L1M4_orf2#LINE/    788 ATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAA-------AGG 829

  chr1_69556944_6   1809 AAGCAAACAGGCATTTC-ATAGAGGAGGTAGATGAATGACCTTTGAATAC 1857
                          vvii  i  i      -vi i  i  i  v ii    i  vv i ii  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_69556944_6   1858 ATGAACAGACGCTTAAATTTATTAGCAAC 1886
                              v   i   i  vv i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.06 (44 / 796), avg. gap size = 2.66 (117 / 44)  


2942 28.22 0.66 0.55  chr1_69567403_69573794.rev     4995  5901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_69567403_6   4995 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5044
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_69567403_6   5045 GGCCATAGTGACCAAAGTAATTTATAGATTTAATGCCATCCCCATCAAGC 5094
                            v   v vv     v i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_69567403_6   5095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACCTTAAAGTTCA 5142
                          v   iivi i  i  ii     -   -- v     - i i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_69567403_6   5143 TATGGAATCAAAAAAAAGCCTGCATTGCCAAGAGAATCCTAAGCCAAAAG 5192
                                viiv  iii v  v v  v     i v    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_69567403_6   5193 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCTATACTACAGGGC 5242
                                i      vv    i  v  ii i     iviv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_69567403_6   5243 TACAGTAACCAAAACAGCATGGTA-TGGTACCAAAAAAGAGATATAGACC 5291
                                 i   i    ii     -   i iv ii v   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_69567403_6   5292 AGTGGAACATAAC--AGAGCCCTCAGAAATTATACCACACATCTACAACC 5339
                          i     i v  i--    i  --      v vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_69567403_6   5340 ATCTGATCCTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATCCC 5389
                          vi    ii i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_69567403_6   5390 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5439
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_69567403_6   5440 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAAGTCAAGATGGA 5489
                            ii    i    v   i     v              v    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_69567403_6   5490 TTAAAGAATTAAATGGTAGACCTAAAACCATAAAAAGTCTGGCAGAAAAC 5539
                          i ?   vi      vv   v       i      vvii i v       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_69567403_6   5540 CTAGGCA-ATACCATTCCAGACATAGGCATGGGCAAGAACTTCATGACTA 5588
                         v    ?i- v i -   vv   v v  vv i     viii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_69567403_6   5589 AAACACCAAAAGCAATGGCAACAAAAGCCAGAATAGACAAATGGGATCTA 5638
                         vi            vvi          vv i      i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_69567403_6   5639 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATAATCAGAGTGAA 5688
                           i   v v  i i   i  ii vv    i  v     v vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_69567403_6   5689 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATTTGACA 5738
                         v  i     i                 v       vii ivi  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_69567403_6   5739 AAGTGCTAATATCTAGAATCTACAAAGAACTTAAACAAATTTGCAAGAAA 5788
                          i vi  vi    i     v  i        ivv    v ivii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_69567403_6   5789 AAAGGAAACAACCTTATCAAAAAGTGGGCAAAGTATATGAACAAACACTT 5838
                           iiv   i    iv  i?    i         v  v    i i   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_69567403_6   5839 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAGAAAGCTCAT 5888
                            v        i  vi viii     v ii         ii v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_69567403_6   5889 CATCACCGGTCAT 5901
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (145 / 107)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1254 29.00 7.75 3.62  chr1_69633794_69635586.rev      503  1302 (491)    L1M4_orf2#LINE/L1       76   908 (0)  

  chr1_69633794_6    503 AGATTCAATACAATCCCAATTAAAAGCCCAAG-ACATTTTTTGAGGTGGG 551
                                 ii       v  i    v    iv-i v       -------
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG------- 118

  chr1_69633794_6    552 GTGTTAAAAACTGACAAGCCAATTTCAAAATGTTTATGGAAACCTAAAAG 601
                         ----i i   i        ii  iii     viv        ivi  ii 
  L1M4_orf2#LINE/    119 ----CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_69633794_6    602 CCCAAGAATAGTGAAGACAATATTTTAAA----GAACAAAGTTGAGCTAG 647
                         v  v       iv  i     v  vv   ----           i---  
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG---AG 211

  chr1_69633794_6    648 GATTTATACTATCAGGTATACAAACTTAGTACAGAGTTAGTACATTTAAA 697
                           i i i   vi vii v vv       v    i  i  vvii v i  i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_69633794_6    698 ACAGTATAGTACTGTGCA--AGGAGTGATAAATAGACTGATGAAACAGAA 745
                              i i      -   --    vv  i v     iii   i  i    
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTG-GCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_69633794_6    746 -----AGCTCAGAAACAAACCCACTTACAT--ATGGTCACTTTA----CA 784
                         -----  ii      i       --     --       v  v ---- i
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAATTGATTTTCG 358

  chr1_69633794_6    785 ACAAGT-TGACACTGCAATGCAGTGAAGAAAATATGATGGTGTTTTAAAT 833
                              v-  v  vvi v  v  i  ii    i---i  i  v    v  i
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAG---AATAGTCTTTTCAAC 405

  chr1_69633794_6    834 ACCTGATGCTAGATTGATTGGTATAATTAAAGGAGAAAAAA-GAACCTTA 882
                          vv  i    i ivii i   -   ?ii v v vi   i  -   vi vi
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGG-ATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_69633794_6    883 ACTTCTAATTCACA---TATATAAAGAT---------ATGATTTTTACAC 920
                           ii   vi     ---    i   i  ---------   iv iv? v  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_69633794_6    921 CCAACTGTGAAATTTAACACAGTAAATCTTCTAGAAGATACCACTAAAA- 969
                          i  v   i i vi   v  vi    v  ii       v v  -  ii?-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-TAGGNG 553

  chr1_69633794_6    970 -AAATGTT-GTGGCCTTGAGATAAGCAA--ATATTTTAAA---AACACGA 1012
                         -    v  -   i     i v  i    --i v i   i ---i    v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_69633794_6   1013 AAAAAA-ATTCATCACAAAGGAAAAGATAGA-AAATTGGACTTCATTAAC 1060
                            iv - vv  --     i     i     -              i  v
  L1M4_orf2#LINE/    604 AAAGCACAAGCA--ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_69633794_6   1061 ATTTTTAAAAA--TCTGTTCATCAAAAT-CTCCATTAGCAGAATGAACAC 1107
                            ---     -- i   v v     iv- v i  i iv i i    v v
  L1M4_orf2#LINE/    652 ATT---AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_69633794_6   1108 TCCAGCCACATAATAAATAGGAATATTTG-AAATACAGATACGTTATAAA 1156
                         v v v     v   iiiviii        -    -  v   iv v    i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAAT-CATATATCTGATAAG 747

  chr1_69633794_6   1157 GAACTAAAATCCATGGTATGCACAAAATTTGTATTG-TCA-TAA--AAAA 1202
                          i   viv     vii   ii v i  i iv  ivi-   -   --    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_69633794_6   1203 GACAG-TAGATACTATAGAAATATTAGTGAAATATTTAAACAAA-AT--- 1247
                             i-  - iv v  v?   v  vi ii  iv    i  i i -  ---
  L1M4_orf2#LINE/    798 GACAAATA-ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_69633794_6   1248 ------GAATATATCCTATTGACTA-TAAGCATATTGAAAGGTGTTCAAC 1290
                         ------   v    v v v  i i -      i  vi    i  i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_69633794_6   1291 CTCACTAATCAT 1302
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.04 (37 / 833), avg. gap size = 2.46 (91 / 37)  


2376 26.27 1.89 4.38  chr1_69667288_69669123      499  1343 (493)    L1M4_orf2#LINE/L1       85   908 (0)  

  chr1_69667288_6    499 GCAATTTCAAGCAAAATCTGAGCAAATTATTTTGAGGATATCAGCAAATT 548
                              ii v v       iv   vivi v     vi  v  iii   ii 
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr1_69667288_6    549 GATTCTAAAATTTTATTTAGGAAAGCCAACTACCCAGAATAATCAAA-TA 597
                            i        i-  v i i  v  v ivv          ii    -i 
  L1M4_orf2#LINE/    135 GATCCTAAAATTC-ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr1_69667288_6    598 ATACCGAAAGAGAAGAA----GTCACAGGATTGACACTACCTAACTTCAA 643
                           vii    i       ----  iiv    i v     v  i  i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_69667288_6    644 GATTTTACTATAAAACAATACTAGCCAAGACTGTATGGTATTGGTGAAAG 693
                         i i  -    i   i v i v  ii      v  i     i   iiv   
  L1M4_orf2#LINE/    234 AACTT-ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_69667288_6    694 AACAGACAAATAGATCTATGGAACAGAATAGAGAGCCCAGGAATAGACTC 743
                         i i     v       v      i     v     i    i    i  i 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_69667288_6    744 ACATAAATGTAGTCAACTGATCTTTGGCAAAGGAGCAAAGACAATGGCAA 793
                          i i vv i i     i    i  i i   i  v  v     v  -----
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT----- 377

  chr1_69667288_6    794 TACAATGGAGCAAAGATACTTACTCAACAAAGGGACCATTTCAACACATG 843
                          -      i v  ii   v --  --------------        v   
  L1M4_orf2#LINE/    378 T-CAATGGGGAAAGAATAGT--CT--------------TTTCAACAAATG 410

  chr1_69667288_6    844 GTATTAGAACAAAGAGACATCCACAGGCACACACAAAAAG---GGCCTCA 890
                           ii i i    vvi  i ?     v   v viv vi   --- i  i v
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_69667288_6    891 ACACAGATCTTTCATCCTTTGTAAACATTAACTTAACAATAGATCATAGA 940
                           ------  iv  i v v ii   v       i  -   i     ?   
  L1M4_orf2#LINE/    461 AC------CTCACACCATATACAAAAATTAACTCAA-AATGGATCAWAGA 503

  chr1_69667288_6    941 CCTAAAGGTAAATTATAAAACAATAAAACTTTTAGAAGGATAATGCAAGA 990
                               v    ivvv      v        i       i -  iii i ?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA-AACATAGGN 552

  chr1_69667288_6    991 ATAAATCTAGATGACCTTAGGTATGGTGATGATATTTTAGGTATAACATA 1040
                         i       vvi       i   vv  ii   i v i    i   i   iv
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_69667288_6   1041 AAAGGC-CATTCCATGAAATAACCAATTGATAAAATGGATTTTCTTAAAA 1089
                            i  -  vv v ii   v  vv   v      v    i  iv i    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_69667288_6   1090 CTAAAA-CTTCTACACTGTGAAAGACAACATC--GAAAGATTAGAAGACA 1136
                         i     -   i iii  vii  i    vi   --     - v i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG-TGAAAAGACA 701

  chr1_69667288_6   1137 AGCCACAGAATGGGAGAAAATATTTCCAAAG-ACATATCTAATAAAAGAC 1185
                          v                       v    v- i      i    ii   
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_69667288_6   1186 TGTTATCCAAAATACACAAAAAGTGCTTAAGAACTCAACAG---ACAAAC 1232
                          vv      i    i i   i iiv    v-       i i--- v i  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTAC-AACTCAATAATAAAAAGAC 800

  chr1_69667288_6   1233 CAACAACTTGTTTTTAAAAAAATGAGTAAAAGACTTGAACAGACACCTCA 1282
                         v  i   iiiv  ?---       i i   i  i     i     ii  v
  L1M4_orf2#LINE/    801 AAATAACCCAATTW---AAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_69667288_6   1283 CGAAAGTAGATATACAGATGGAAAGTATGCATATGAAAAAATGTTCAACA 1332
                          v    v         i    vv i  v   i       i   i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_69667288_6   1333 TCATATATCAT 1343
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.63 (135 / 83)
Gap_init rate = 0.02 (20 / 824), avg. gap size = 2.65 (53 / 20)  


1129 30.37 7.72 3.40  chr1_69801479_69803221.rev      489  1252 (491)    L1M4_orf2#LINE/L1      112   908 (0)  

  chr1_69801479_6    489 TTTTTTGAGGTCTTTGACGAATTGTTTCTAAAATGTATATGAAAATG--- 535
                                vi vvv     i ii  v i       vi     i     ---
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_69801479_6    536 GGGAT--GGTATAGCTTAGTTTTATGACAGTATTGAAGAATAAGGA--AA 581
                             i--i v     iv i-------   i v     i  v   i --  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAA-------ACAATCTTGAAAAAGAAGAACAAA 204

  chr1_69801479_6    582 G--AGAATATTCTCAC----AAATGGTATAAATTAATATAAGGTTACAGT 625
                          --i  iv i  v   ----v   vvi v  v   v  i  i i      
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_69801479_6    626 AATAAAGATA-TATGGTAATGGCTTAAGGACTGAGAAATAGATCAATGAA 674
                            v    i - i     v    v      iv  v v           i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_69801479_6    675 AAACAAC----AGTCCAGAAGGTGA--TTAGGCATATGTGGACT-TTGAT 717
                          v v  i----         i- i --ii vi   v i   v v-     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGTCAATTGAT 353

  chr1_69801479_6    718 TAGCAACAAATATGACACTGCTAAAC-ATTCA----GAAAAGGATGAGCT 762
                          vv i    ivi  v  ----- i  -     ---- i    i  iiv  
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCA-----AGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_69801479_6    763 TTTCAGTAAATGCAGCTAGGTGAATTGGATAGTCATATTGGACAAAATGA 812
                              ii     vv   i  vv  i      ?i  i  ---i     --i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT---GCAAAA--G 443

  chr1_69801479_6    813 AATAAAACTTGACATCCACATCATGACATATACAAAAGTAAAATTTAGAT 862
                            i  ii v   vi i  v   iiv           i v  v iv i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_69801479_6    863 GAGT-GTAGATTAAAATGTAAAAATCAAAG------AACTTTTGGAATTT 905
                          ii -i?   iiv        i iii   i------    i  i   vvv
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_69801479_6    906 AATGCAGGAAAATATTTTCATGCCTTTGGATATCTAAATA----TTTCTT 951
                           iii   ?iv v  i   i  v i    i ---  iii ----      
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGT---TAGGCAATGGTTTCTT 590

  chr1_69801479_6    952 AAGCAGGATACAAAAAGCCTACCCCACTGAAAAAAGATTA-ATAAATTTG 1000
                          iii v  i  v      vi vv v  vi  i   i v  -       v 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_69801479_6   1001 ATATTAAAAAAATTTAACCCTTCTGCTCGTTGAATGATA----------A 1040
                          iv i vv      v  vv   i  iv v ii  v  i ---------- 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_69801479_6   1041 GTGGAAAAAACAAATTATGGAGTGGGAGAAGATATTTGCAAATAAT---- 1086
                            -    i    vii ii  i        i            v  ----
  L1M4_orf2#LINE/    691 GTG-AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_69801479_6   1087 -CAATATAGAATATTTATGTGGAATA----AAGGATTTCTATTAATAAAT 1131
                         -ii   vi i iv v   vii     ----   i i ii  iv v v   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_69801479_6   1132 AAGACCAAAATGAATTGTC--ATATATACATATATATATGTGCATCTTTA 1179
                           v vv  i ii   vii --  v? v v  ivii v v ---  -  v 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG---AT-TTGA 835

  chr1_69801479_6   1180 ACAGGAACTTCTTAAATGAACATATACAAATGGCTAATAAACATATAAAA 1229
                          i  iv i    iv  v   v             i     i  i  i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_69801479_6   1230 AGGTGCTCAATATCATTAGTTAT 1252
                           i       i    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.04 (28 / 797), avg. gap size = 3.04 (85 / 28)  


3278 23.80 1.20 2.72  chr1_69841763_69846044.rev     2872  3791 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_69841763_6   2872 GAAAGATATTCCATGTTCATGAATTGGAAGAATCAACAATGAACAAAGAA 2921
                                  i           i         v i  i ------------
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA------------ 40

  chr1_69841763_6   2922 TCAATCAATGTAAAAATGTCCATACTACTCAAAGCAATCTACAAATTTAA 2971
                         ---- ---   v  i   v v     v i    vii       i   i  
  L1M4_orf2#LINE/     41 ----T---TGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAA 83

  chr1_69841763_6   2972 GGCAATCCTTATCAAAATACTAATGACATTCTTCACAGAAATAGAAAAAA 3021
                         v       i         v i iivi v  i  ii       v  v  iv
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC 133

  chr1_69841763_6   3022 CAATTTTAAAATTTATATGAAACCACAAGAGACTCAGAATAGCGAAAGCC 3071
                         ii  ii       i     i  vii    i   i         v   i v
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr1_69841763_6   3072 ATCCTGAGCAAAAGAAGGA---AACTGAAGGAATCACATTACCTGCCTTT 3118
                            i   --        i --- ii  i    v     i v  iivi  i
  L1M4_orf2#LINE/    184 ATCTTGA--AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_69841763_6   3119 AAATTACACTACAGAGCTATAGTAAACAAAATGGCATTTCACTGGCATAA 3168
                            vivi      i     i     v   i ii ii vvi          
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_69841763_6   3169 AAACAGACATATAGATCAGTGTAACAGAATGGAGAACCCAGAGATAAATC 3218
                         ii i              i  v  i     v    ii     i     i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_69841763_6   3219 CATATATCTACAGTGAACTCATTTTTGATGAAGGTGCCATGAACACACAT 3268
                             i  i  ii  v  i v     i  ii i       v  v  iv  v
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_69841763_6   3269 TGGGGAAAGGACAGTTTCTTCAATTAATGGTTGTAGAAAAACTGGATATC 3318
                                  i i   i i     iv      vv i i v         ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_69841763_6   3319 CACTGGCAAAAAAAATGAAATTCGACACCTATCTCTCACCATATACAAAG 3368
                            vv      i  -    i  v   v    i   v             i
  L1M4_orf2#LINE/    432 CACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_69841763_6   3369 ATCAAATCAAAATGGATTAAAGACTTAAATCTAAGACCTTGGACTATGAA 3418
                           i  v           i ?    i     v     v  vii     i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_69841763_6   3419 ACTGCTAAAAGTAAACATTGAAGAAATTCTCCAGGACATTGA-TCAGGGC 3467
                            vi  i   v      v i? v  v   i iv   v   i- i   - 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG-C 579

  chr1_69841763_6   3468 AAAAATTTTTTGAAGAGTACCCCAAAAGCACAGGCAACCAA-GCCCAAAC 3516
                           vii   i  ii v vv  v           i     v  - vvv   i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_69841763_6   3517 AGACAAATAGGATCACATCAAG-TTAAAAAGTTTCTGCACAGCAAAGGAT 3565
                            i    v   iiv      i-       v   -  ii vv       i
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGAC 678

  chr1_69841763_6   3566 ACAATCAACAAAGTGAAACAACAACCCACAGAATTGGAGAAGATATGTGC 3615
                           v     v         vi              v      i    v   
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_69841763_6   3616 AAACTACCCATCTGACAAGGGATTAATAACCAGATTATATAATGAACTCA 3665
                            ii ivi      i      i vi  v     v       v      v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_69841763_6   3666 AGCAAT---ATGATAGGAAAATCTAATAATCCGATT-AAAAATGGACAAA 3711
                         vi   i---  i   ii  i - v     i  i   -        i    
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_69841763_6   3712 ATATCTGAATAGACATTTCTCAAAAGAAGAGATACAAAAGGCAAATAATT 3761
                         iv  i                v        v       v   v     vi
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_69841763_6   3762 ATATGAAATG-TGGTCAACATCACTGAAAAT 3791
                          i      v -  v         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (129 / 87)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 2.57 (36 / 14)  


3284 26.87 0.44 0.44  chr1_70060569_70066847.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70060569_7   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70060569_7   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_70060569_7   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_70060569_7   5029 TATGGAACCAAAAAAGAGCCCACATCGCCAAGGCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  viv  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_70060569_7   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_70060569_7   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_70060569_7   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_70060569_7   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_70060569_7   5277 CTATTTAATACATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i v            v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_70060569_7   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_70060569_7   5377 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_70060569_7   5427 CTAGGCATTACCATTCCGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5476
                         v    ?i v viv   vv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_70060569_7   5477 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5526
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_70060569_7   5527 TTAAACTAAAGAGCTTTTGCACAGCAAAACAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i      ii vv    iv v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_70060569_7   5577 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5626
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_70060569_7   5627 AGAGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i ii  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_70060569_7   5677 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_70060569_7   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5776
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_70060569_7   5777 ATCATTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3130 27.39 0.44 0.55  chr1_70083213_70089552.rev     4941  5849 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70083213_7   4941 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAATATCGTGAATAT 4990
                              ii i  i     i    i i v      v i     i  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70083213_7   4991 GGCCATATTGCGCAAGGTAATTTATAGATTCAACGCCATCCCCACCAAAC 5040
                            v   i v v   iv i  i  i           v     i i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_70083213_7   5041 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 5088
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_70083213_7   5089 TATGGAACCAAAAAAGAGCCCTCATCGCCAAGTCAATCCTAAGCCAAAAG 5138
                                viiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_70083213_7   5139 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5188
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_70083213_7   5189 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5238
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_70083213_7   5239 AATGGAACAGAAC--AGAGCCCTCAGAAATCATGCCACATATCTACAACC 5286
                                i    i--    i  --      v vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_70083213_7   5287 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5336
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_70083213_7   5337 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTGGCCATATGTAGAAAGGT 5386
                           v  i  i              v      v i?   i   i i  iii 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_70083213_7   5387 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5436
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_70083213_7   5437 TTGAAGACTTACATGTTAGACGTAAAACCATAAAAACCCTAGAAGAAAAC 5486
                          ii?    i  v    v   vv      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_70083213_7   5487 CTAGGCAATACTATTCAGGACATAGGCAAGGGCAAGGACTTCATGTCTAA 5536
                         v    ?ivv v v   iv   v v  vvvi     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_70083213_7   5537 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5586
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_70083213_7   5587 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5636
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_70083213_7   5637 AGGCAACCCACAAAATGGGAGAAAAAATTTTGCAACCTACTCATCTGACA 5686
                           i         i            v    -    vii ivi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGATA 745

  chr1_70083213_7   5687 AAGCGCTAATATCCAGAATCTACAATGAACTCACACAAATTTACAAGAAA 5736
                          i vi  vi          v  i  v      vi    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_70083213_7   5737 AAAACAAACAACCCCATCAAAAAGTGGGTGAATGATATGAACAGACACTT 5786
                           i     i     v  i?    i    ii  v   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_70083213_7   5787 CTGAAAAGAAGACATTTATGCAGCCAAAAAACACATGAACAAATGCTCGC 5836
                           vv        i  vi viii     v  i        v i      iv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_70083213_7   5837 CATCACTGGCCAT 5849
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (139 / 106)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3159 26.99 0.88 0.44  chr1_70100763_70107156.rev     5002  5905 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70100763_7   5002 TGGAAGAACATTCTATGCTCATGGGTAGGAAGAATCAATATCGTAAAAAT 5051
                              ii i  i i   i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70100763_7   5052 GCCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5101
                          v v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_70100763_7   5102 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_70100763_7   5150 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_70100763_7   5200 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5249
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_70100763_7   5250 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5299
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_70100763_7   5300 AATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATCTACAACT 5347
                                i    i-- v  i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_70100763_7   5348 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5397
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_70100763_7   5398 CTATTTAATAAATGGTCCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5447
                           v  i  i       v      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_70100763_7   5448 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5497
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_70100763_7   5498 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5547
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_70100763_7   5548 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5597
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_70100763_7   5598 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATATAA 5647
                         i            vvi           v     v  i    v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_70100763_7   5648 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5697
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_70100763_7   5698 AGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5747
                           i         i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_70100763_7   5748 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5797
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_70100763_7   5798 AAACAAATAACACCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5847
                          i         v v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_70100763_7   5848 TGAAAAGAAGACATTTATGCAGCCAAAAAACACATGAACAAATGCTCA-- 5895
                          vv        i  vi viii     v  i        v i       --
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_70100763_7   5896 --CAGAAATGCA 5905
                         --  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3174 25.84 2.46 0.89  chr1_70121968_70124533.rev     1182  2075 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70121968_7   1182 TGGAAAGATATCCTATATTCATGGATGGGAAGAATTAATATTGGTATAAT 1231
                                      i  i         v      v         v  vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70121968_7   1232 GCCCATACTACCCAAAGTGATCTACATATTTAATGCAATCCCCATACAAA 1281
                          v v     v      v         v   i  i        i  vv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_70121968_7   1282 TTCTAAC---ATTTTCCACAGAATTATAAAAAATGATTCTAAAACAAGCA 1328
                          i i i ---v    iii     v vv v  iv    i      ivvii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_70121968_7   1329 TGAAATCACAAAAGTTCACAAATAGACAAAGCAATCTTGAGCAAAAAGAA 1378
                           i  vii   ii vi vvi     v    i         iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_70121968_7   1379 CAAAGCTAGAGGCATCATACTATCTGATCTCAAAATCTACTAAAAAGTTA 1428
                              i i    vv   i   vi ii  i      ii     v    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_70121968_7   1429 TGGTAATTGAAACAGCATGGTACAGGCACAGAGAACAGACACATAGACCA 1478
                         ii     ii i    ii      v    i -  i i     i     i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATA-AGGATAGACATATAGATCA 299

  chr1_70121968_7   1479 ATGAAATAAAACAGAGAGCCCAGAAATAAAACCA--CATTTATACTAATG 1526
                            i    i  iv     i           v   --       i---i v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG---GTC 346

  chr1_70121968_7   1527 AACTGATCTTCAATAAAGGTGTCAACAGCACCACAATGGGGAAAGGATAG 1576
                           i    i   i i  i    i   v v  ii-            i    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAG 395

  chr1_70121968_7   1577 TCTCT--GATAAATACTTTTGGGAAAGTTGGATA------TGCTGAAGTA 1618
                            i --i i    iv vi     v ii      ------   vi   v 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_70121968_7   1619 TGAAATTGGACCATTATTCCACCCCATATGCAAAAATCAACTCAAAATGG 1668
                             i       vi  iii   v      i       i            
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_70121968_7   1669 GTTGAAGACTTAAGTAATGTACGTCCCGAAACTGTAAAACTTCTAGAAGA 1718
                         i ii?    i   ---     v vv ii     i       ii       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAA---ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_70121968_7   1719 AAATACAGAAA-AAAGTTTCTTGGCGTTGTTCTTGGCAAAGACTCTTTGG 1767
                            i i  i?i-   vi   v  i v   vvi v     v ii ii  i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_70121968_7   1768 ATATAAC-CCAAAAGCAGAGACAAAAGAAGTAAAAATAGACAAGTGGGAT 1816
                             i  -         v ii   v i   v         i  i v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_70121968_7   1817 TACAGCAAACT--AAATCTTCTGCAAGTCAAAGGAAACAATCAACAGAGT 1864
                          v  v    v --   v   i  iivv        v  v     v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_70121968_7   1865 GAAGAGACAACATATGGAATGGGAGAAAGTATTTGCAAACTACATATCTG 1914
                            i       vi ii            i          ii i       
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_70121968_7   1915 ATAAGGGATCAATATCTAAAATATATGAGGAATTAAAAAGACTCAATAAT 1964
                                 iivi    i i       i i   i vvv vi          
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_70121968_7   1965 AGTAAAACAA----CCTGGTTAAAAAACAGA-AAGGAACCTTAAGAGTCA 2009
                          iv  i    ----  iii  ?     ii i-  i i ii v  v  v  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_70121968_7   2010 TTTCTTAAAAAAAGACATACAAATAACCCACAGGTATAAGAAAAAATGCT 2059
                              iv   i    i        ii  v i i i i v     i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_70121968_7   2060 CAACATCAGTAATAAT 2075
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (150 / 78)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.31 (30 / 13)  


3167 25.69 1.11 0.55  chr1_70145458_70150733     3881  4783 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70145458_7   3881 TGGAAACACATCCCATGTTCATGGATGGGTAGAATCAATATTGTGAAAAC 3930
                               v i                 v  v   v i        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70145458_7   3931 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAACTCCCATCAAAA 3980
                          i v     v  v   vii       i      i    ii  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_70145458_7   3981 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATCCTAAAATTCATA 4030
                          v   v vv v  i  ii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_70145458_7   4031 TGGAACCAAGAAAGAG-CCCACA-TAGCCAAAGCAAGACTAAGCAAAAAG 4078
                              -- v v   i -    v -        i   vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_70145458_7   4079 AATAAATCTGGAGCCATCACATTACCTGATTTCAAACTATACTATAAGGC 4128
                           i   vi     vvv     i v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_70145458_7   4129 CGTAGTCACCAAAACAGAATGGTACTGGCATAAAAATAAGACACATAGAC 4178
                         iii   v i   i    vi              ii   -    i     i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGAT 297

  chr1_70145458_7   4179 CAATGGAACAGAATAGCGAACTCAGAAATAAACCCTCATACTTACAGCCA 4228
                                 i     v v  iii             vi i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_70145458_7   4229 ACTGATCTTTGACAAAGCAAACAAAAAGGTAAAGTGGAGAAAGGACACCT 4278
                          i    i  i     i vviv   i vvi vv i   i     i i vii
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_70145458_7   4279 TATTCAACAAATAGCGCTGGGATAATTGGCAAGCCACATGTAGGAGAATG 4328
                          v          i i       i  i   vv ?       i ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_70145458_7   4329 AAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGAT 4378
                           ii    i  ii i   v    v           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_70145458_7   4379 GAAGGACTTAAATCTAAGACCGGAAACTACAAAAATTCTAGAAGACAGTG 4428
                         v ?i   i     v     v vi      i    v ii       v iii
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_70145458_7   4429 TTGGAAAAACCCTTCTAGATATTGGCTTAGGCAATGATTTCATAACCAAG 4478
                          v  ?iv  vi    vv  iv    v          i    v  ivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_70145458_7   4479 AACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAAT 4528
                          vv         v v    i    iv   i   i   iv v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_70145458_7   4529 TAAACTAAAGAGCTTTTGCA-TACAAAAGAAAC----AGCAGAGTAAACA 4573
                         i   v v  i i      ii- v    i  v  ---- iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_70145458_7   4574 GACAACCCACGGAGTGGGAGAAAATCTTCACAATCTATACATCTGAAAAA 4623
                                   i  i           v  ii   vii   i      v  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_70145458_7   4624 GGACTAATGTGCAGAATCTACAACAAACTC--A-AACTAATTAGCAAGAA 4670
                              vi i v      v  i  vi     -- -    v v  ii  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_70145458_7   4671 AACAAACAATCCCATCAAAAAAGTGGGCTAAGGACATGAATAGACAATTC 4720
                         i     i  i  v  i?     -     v     iv          v   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_70145458_7   4721 TAAAAAGAAGATATACAAATGGCAAACAAACATATGAAAGAAATGCTCAA 4770
                          vv                    v  i  i  i      - i        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATGCTCAA 895

  chr1_70145458_7   4771 CATCACTAGTGAT 4783
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2638 18.77 3.72 1.13  chr1_70262102_70263693.rev      484  1101 (491)    L1M4_orf2#LINE/L1      275   908 (0)  

  chr1_70262102_7    484 GGCATACGTCAAGAAACAACATAGATCAGTTTAATAGAATAGAGACTCCA 533
                               v --i v i   -i        i vv        v    v    
  L1M4_orf2#LINE/    275 GGCATAAG--GATAGACA-TATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_70262102_7    534 AAAATAAATCCTAACATTTATAGTCAGATGATTTT-GACAAAGGGTTCAA 582
                         i       i  vv        i    iv       -     i  vvi   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_70262102_7    583 GGTAATTCACTGGGAGAAAGAAGAGTCTTT-CAGTAAATGGTGCTGGGAC 631
                          iiv     v    -       v       -  ii               
  L1M4_orf2#LINE/    372 GACCATTCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_70262102_7    632 AA---GATACCCACATGCAGAAGAATAAATCTGTACTCATATCTCACACC 678
                           ---    ?         i      i  vi  v  i v  i        
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_70262102_7    679 ATACACAAAAGTTA-TGTAAAGTAGACCAGAGGCTGAAACATAAGAGCTA 727
                            i      i   -ivi   i i  i  ?  i iv   ii         
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_70262102_7    728 GA-TTATAAAACCCTTTGATGAAAATACAAAAGGAGTAAAG-TTCATCAC 775
                         i -i        i   v  v     i i ---  ?     v-   i v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATA---GGNGTAAATCTTCGTGAC 567

  chr1_70262102_7    776 CTTAGATTAGGCAATGATT-CTTAAATATGAAACCAAAG---------AT 815
                            i i          i  -    i      v      i--------- i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_70262102_7    816 GATATAAGAGATTGATATGTTGGACTTCATAAAAACTAAAAACTTTTGTG 865
                         i v v  i i  v    vi           v    i              
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_70262102_7    866 CTTCAAAGAAGACCATCAA-AAAGTGAAAAGAAAACCCACAGAATGAGAG 914
                                 i v  i     -            v             i   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_70262102_7    915 AAAATATTTGCAAATAATATATCTGATTAGGGTTGTATATCCAGAATATA 964
                                        v           v    viv i             
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_70262102_7    965 TAGATAACTTTTACAATCCAATAATAAAAAGACA--T--CCAAATTTAAA 1010
                           i v    i      ii                -- --  v    ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_70262102_7   1011 AATAGGCAAAATATTTTTAAAGATGTTTCTCCAAAGAAGATACATAAACA 1060
                            i      iv    vv v   ii                 i i   ii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_70262102_7   1061 TTCAAAAAGCATATGAAAATATACTCAATATCATTAGTCAT 1101
                         vi   v     i       v  i     i    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (68 / 44)
Gap_init rate = 0.02 (15 / 634), avg. gap size = 2.00 (30 / 15)  


3758 17.39 6.29 2.40  chr1_70346679_70349798     1754  2627 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70346679_7   1754 TGGAAAAACATTCCATGCTCATGAAT-GGAAGACTTAATATTGTTAGGAT 1802
                               i i  i     i     i  -                   i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70346679_7   1803 ---AATATTCCCCAAACTGATCTACAGA---AATGCATAAACTTTATC-- 1844
                         ---    i        i           ---  i   -- v ii    --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA--ATCCCTATCAA 98

  chr1_70346679_7   1845 ----------------TTTGTAGAAATTCACAAGTTAATTCTAAAATTCA 1878
                         ----------------    i       v     i i  i          
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_70346679_7   1879 TATGGAATTGCAAGAAATCCATAATAGCCAAAGCAATCCTGAGAAACAAG 1928
                                v      ii i   v          i     i   i   --- 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA---G 195

  chr1_70346679_7   1929 AGGAGCCCTCCTAAAGTAGGAGCCCTCAATCTTCCTGATTTGATTTCAAA 1978
                          i  i ------     v    vv    vv     ii    -----    
  L1M4_orf2#LINE/    196 AAGAAC------AAAGTTGGAGGACTCACACTTCCCAATTT-----CAAA 234

  chr1_70346679_7   1979 ACTTACTACAAAACAATGGTAATCAAGACAGTGTGGAACTGGCA-AAGGT 2027
                                     i v ii                  v       -    v
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_70346679_7   2028 CAGACATATAGATCAACAGAATAAAACTGATGGTAGAAAAATAAACCAAT 2077
                         i               ii     i  i   vi  vv i         v  
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_70346679_7   2078 ACATTTATAGTCAGTTGATTTTTTACAAGAATGCCAAGACCATTCAAAGT 2127
                                 i    i        iv     ii                v v
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_70346679_7   2128 AGAAAGAATACTCTTTTCAACAAATGGTGCTGAGA-AACTGAATATCCAT 2176
                         i         v                     i  -     i   ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_70346679_7   2177 GTACAAAACAATGAAATTGAACCCTTACCTCACACTGCATATAAAAGT-A 2225
                         i i     v      i   i    i          iii   i    i - 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_70346679_7   2226 ATTCAAAACTGATCAAAGACCTAAATTTTAAAACAATGGCGTTATAAAAT 2275
                          i      iv     ?          v v i i v vii --       i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC--TATAAAAC 532

  chr1_70346679_7   2276 GTTTAGAAG----TATAGGC-CAAATCTTTATAACCTAGGATTTTGTAAA 2320
                         vi       ----i     ?-i       ii i    v  i  vv i  v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_70346679_7   2321 GCTTTCTTAGATTTAA----AAAAA---AATGAACAAAA-AAAAAAT-GA 2361
                          v          v i ----    i---  vv       -       -  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_70346679_7   2362 AAAATTGGACTTGCTCAAAATTAAAA-CTTTTATACTTCAAAGAACAACA 2410
                         v           vv            -     i i        i   vi 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_70346679_7   2411 TCAAGAAAATGAAAAGACAACCCACAGAGAACTATAAAATATCTGCAAAT 2460
                                 i                   ivivv v       i       
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_70346679_7   2461 CATATATTTAACAAAGGATTTGTATCTAAAGTATGTAAAGAACACTTACA 2510
                                i i i  i   i       i i i   i        v      
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_70346679_7   2511 GCTCAATGATTTAAAAAAACAA---------TTAAAAAATAGACAAAGAA 2551
                         i      i  --     i    ---------  ?      i i     i 
  L1M4_orf2#LINE/    783 ACTCAATAAT--AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_70346679_7   2552 TCTGAATAGCCATTTCTCTAAAGA---TGCACAAATGACTAATAAAGCAC 2598
                          i       v        i     --- ii       i i     -    
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA-GCAC 879

  chr1_70346679_7   2599 AGGAAAAGATGCTCTACATTAATACTCAT 2627
                          v            v    i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (101 / 47)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.30 (76 / 23)  


 747 24.19 1.08 0.54  chr1_70370281_70373662     1892  2077 (1305)    L1M4_orf2#LINE/L1       26   212 (696)  

  chr1_70370281_7   1892 TTGGAAGACTCCATATTACAAAGATGTCGCTTCTCCCCAAGT-GACTTAT 1940
                                   iv     iiv      v iv v        i -  ii  i
  L1M4_orf2#LINE/     26 TTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chr1_70370281_7   1941 AGATTCAGCACAATCCTAATAAAAATCCCAGAAAGCTTTTCTGTAGAAAT 1990
                                i i      iv  v          vviv     i  i      
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr1_70370281_7   1991 TAACAAGCCAATTCTAAAATGTGTATTGAAATGCAAAAGAACTAAATTAG 2040
                          i      ii  i       vii   v         ii  v i i v   
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr1_70370281_7   2041 GTCAAAA-AATTTTGAAATAAAAGAACAAAACAGGAGG 2077
                         -i     -   i      v i         iiv     
  L1M4_orf2#LINE/    176 -CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

Transitions / transversions = 1.81 (29 / 16)
Gap_init rate = 0.02 (3 / 187), avg. gap size = 1.00 (3 / 3)  

2271 25.50 5.32 2.48  chr1_70370281_70373662     2082  2889 (493)    L1M4_orf2#LINE/L1       78   908 (0)  

  chr1_70370281_7   2082 ATTCAGCACAATCCTAATAAAAATCCCAGAAAGCTTTTCTGTAGAAATTA 2131
                              i i      iv  v          vviv     i  i       i
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chr1_70370281_7   2132 ACAAGCCAATTCTAAAATGTGTATTGAAATGCAAAAGAACTAAATTAGGT 2181
                               ii  i       vii   v         ii  v i i v   vi
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr1_70370281_7   2182 CAAACAATTTTGAAATAAAAGAACAAAACAGGAGGCTTTATAGTATTTGA 2231
                         v       i      v i         iiv     vi i i v viiii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_70370281_7   2232 TTCCAAGTCTGACCATGAAGCTACATTTGTCAAGATAGTGTAGTATTAGC 2281
                           i   iv  v  i ii        v vi      i     i   i i  
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_70370281_7   2282 ATAAGGATAAACACATAGGTCAATGGAA---AA---AGAGTTCAGAAAAA 2325
                                  i   i    i         ---  ---     i      v 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_70370281_7   2326 ATTCCATACAATAAAATATTGAAAATTGATTTTCAACAAAGGTGCCAATA 2375
                          vi       v ----   v vv           i    i        v 
  L1M4_orf2#LINE/    328 AACCCATACATT----TATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_70370281_7   2376 TAATTTAATAAAAAAGGAATCATGTTTTCAACAAATGGTACTGGAATAAC 2425
                         iv   i   iiii  i    vi v               i    i i   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_70370281_7   2426 TATAAAATAAACTATAAAA--ATGAACCTCAACCTTTACCTTGTGACACA 2473
                          iv v ?iv vv ii    --     vi vi   ii     iiiiv  i 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_70370281_7   2474 CTCAAAAATTAACTCCAAATGGACCACGGACTTATATGTAAATGATGAAA 2523
                         iv             v       i  ?i   i  v      iv v i   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_70370281_7   2524 CTAAAAAATTCT-AAAAGAAA-CAGAGGAAAAAATTTTCACAGCCTTCAG 2571
                            v    i   - i      -  v   ?iv    i   iiii    vi 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_70370281_7   2572 ATGGGCAAAAAATGTCTTGG----GACAGAAAAAGTTCA--TCATAAAAG 2615
                         v i     vii- v    i ----    vv     iv  --iv i     
  L1M4_orf2#LINE/    574 TTAGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_70370281_7   2616 AAAAACAATTGATAAACTAGATTTCATAAAAATTTATAACTTACATGTTT 2665
                              --  v      i i  i     v      v v     vii  i  
  L1M4_orf2#LINE/    623 AAAAA--ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_70370281_7   2666 CTAAAGCTACCATTAATAAAAT---AAGCTAA---AC----TGGGAGAAA 2705
                          v  i vi  i  i  v   i ---   vi  ---  ----         
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_70370281_7   2706 ATATTAGACAGATACTGATATAGATATCTGAGACGGAA-TTGTATCTCAA 2754
                              v -  i  -----i   --       v v  i -       ivi 
  L1M4_orf2#LINE/    721 ATATTTG-CAAAT-----CATA--TATCTGATAAGGGACTTGTATCCAGA 762

  chr1_70370281_7   2755 ATATATACAAAGTCGTTAC---CCAAGAATAAAAA---------CCCATT 2792
                                v i iiiv    ---i   v        ---------    v 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_70370281_7   2793 TAAAAAAAAAAAAAGACAAAAG-TTGGAACAAACA---CTTAACAGAAGA 2838
                          ?     vi----- i    i -  v   i i   ---  iv v      
  L1M4_orf2#LINE/    813 TWAAAAATG-----GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_70370281_7   2839 TATATAAATGGCTAAAAGGCAGTAGAAAAGATGCTAAACATCATTAGTTT 2888
                             i       i  v i   vvv           v       ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_70370281_7   2889 T 2889
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.52 (122 / 80)
Gap_init rate = 0.03 (22 / 831), avg. gap size = 2.86 (63 / 22)  


2754 27.73 2.93 0.56  chr1_70646039_70652400     4983  5869 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70646039_7   4983 TGGAAAAACATTTCATGCCCATGGATAGGAAGAAACAATATCATCAAAAT 5032
                               i i  ii    ii       v      vvi     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70646039_7   5033 TGCCATACTGCCCAAGC-AATTTATAGATTCAATGCTATTCCTATTAAAT 5081
                         v  v     v     ii-i  i  i        i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_70646039_7   5082 TACCAATGACATTCTTCACAGAA--TGAGAAAAAACTAATT-TAAAATTC 5128
                          v   iivi v  i  ii     --   v  i---  i  i-        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr1_70646039_7   5129 ATATGGAAACAAAAAAGAGCATAAATAACCAAGGCAATCCAACGCAAAAA 5178
                                  iiv  ii  v vvi    i    ii     iviviv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_70646039_7   5179 GAACAAAGCCAGAGGAATCATGCTACCTGCCTTTAAACTATACTAGAGTA 5228
                                 iii     v   ii  v  iivi  i   viv     v ivi
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_70646039_7   5229 CTACAGTAATCAAAAT-GCACGCTATTGGTAGAAAAACAGACACATAGAC 5277
                                      i i- iii v  i   i v  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_70646039_7   5278 CAATGGAACATAATAGAGGGCCTAAAAAGAAAGCCACACACCTACAACTA 5327
                                 i v   v   i i i i   v   v   i   ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_70646039_7   5328 TGTAATCATCAACAAAGCTGACAAAAATAAGCAATGGGAAAAGGACTCCC 5377
                         vv i  iv  i    i v  v   i vi vv       i    i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_70646039_7   5378 TATTCAATAAATGGTGCTTGGATAATTGGCTAGCCATATGCAGAAGATTG 5427
                          v     i          v   i  i   v  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_70646039_7   5428 AAACTGGACCCCTTCCTTATACCATATACAAAAATTAGC-----ATGGCT 5472
                           ii         v   i i                 i -----    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_70646039_7   5473 TAAAGACTTAAATGTAAAACTCAAAGATATAAAAATGTGGGAAGACAACC 5522
                         i ?    i         i vii   iv       v v vi     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_70646039_7   5523 TAGGCA-ATACCATTCTGGACATAGGAATGGGCAACAATCCCAT-GATGA 5570
                             ?i- v i -   vv   v v  iv i     iii ii v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr1_70646039_7   5571 AGACATCAAAAGCAATTGCAACAAAAGTGAACATTGAAAAAT-GGATCTA 5619
                         v    i        vvv          vi  v  v  v    -   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_70646039_7   5620 ATTAAACTAAAGTACTTCTGCACAGCAAAATAAACTATCAATAGAGTAAA 5669
                           i   v v  iv    i  ii vv    iv v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_70646039_7   5670 CAGACAAACTACAGAATGGGAGAAAATATTTGCAAACTATGCATCTGACA 5719
                         v      v i                          ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_70646039_7   5720 AAGGTCTAATATCCAGCATCTATAAGGAGCTTAAACAAATTTACAAGAAA 5769
                          i  v  vi       v  v     i  i  ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_70646039_7   5770 AAAA------AC---ATTAAAATGTGGGCAAAGGAC----ATAGACATTT 5806
                           i ------  ---   ?   vi           i----          
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_70646039_7   5807 TTCAAAAGAAGACATACATGTGGCCAAAAAGCATATGAAAAAAAGCTCAA 5856
                         i  v        i     vi       v     i       i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_70646039_7   5857 CATTACTGATCAT 5869
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.21 (31 / 14)  


3223 27.31 0.44 0.44  chr1_70773072_70779482.rev     5013  5920 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70773072_7   5013 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5062
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70773072_7   5063 GGCCATACTGCCTAAGGTAATTTACAGATTCAGTGCCATCCCCATCAAGC 5112
                            v     v  i  iv i  i          ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_70773072_7   5113 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5160
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_70773072_7   5161 TATGGAACCAAAAAAGAGCCCGCATCACCAAGGCAATCCTAAGCCAAAAG 5210
                                viiv  ii  v  v v  vi    ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_70773072_7   5211 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5260
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_70773072_7   5261 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5310
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_70773072_7   5311 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5358
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_70773072_7   5359 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCATTGGGGAAAGGATTCC 5408
                          vi    i  i     ivv  vv  i v  vv  v         i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_70773072_7   5409 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5458
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_70773072_7   5459 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5508
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_70773072_7   5509 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5558
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_70773072_7   5559 CTAAGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5608
                         v  i ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_70773072_7   5609 AACACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATCTAA 5658
                         i            vvi          vv   i v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_70773072_7   5659 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5708
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_70773072_7   5709 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5758
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_70773072_7   5759 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5808
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_70773072_7   5809 AAACAAAAAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5858
                          i     v     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_70773072_7   5859 TCAAAAGAAGACATTTATGCAGCCAAAAAACACACGAAAAAATCCTCACC 5908
                           v        i  vi viii     v  i    i     i  v    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_70773072_7   5909 ATCACTGGCCAT 5920
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1135 19.65 1.31 0.00  chr1_70798110_70800179.rev      502   730 (1340)    L1M4_orf2#LINE/L1      125   356 (552)  

  chr1_70798110_7    502 TTGACAAAATGATTCTAAAGTTTTTATGGAGAGGCAAAGGACCCAGAATT 551
                                iv    i     i  iv      i v    i           v
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr1_70798110_7    552 GCCAAATCAATATTGAA---GAAGAACAAAGGTGGAAGACTGATACCACC 598
                               v    v     ---           v    i    v i  iv  
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr1_70798110_7    599 CAACTTCAAGACTTACTATAAAGCTACAGTAATCGAGAAAGCATGTTATT 648
                            i     i        i               i   v  ii  v  i 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_70798110_7    649 GGCGAAAGAATAAACAAATAGATCAGTGGAACAGAATAGAGAGCCCAGAA 698
                            iv   i   i   v        i     i     v     i      
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_70798110_7    699 ATAAATCCATATAAATATAACCAACTGATCTT 730
                              i     i vv   iii   i    i  
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 1.81 (29 / 16)
Gap_init rate = 0.00 (1 / 232), avg. gap size = 3.00 (3 / 1)  

1701 25.97 4.24 0.55  chr1_70798110_70800179.rev     1037  1579 (491)    L1M4_orf2#LINE/L1      346   908 (0)  

  chr1_70798110_7   1037 CAACTGATCTTTAACAAAGAAGGAAAGGCAATACAATGGAGCAAAGATAG 1086
                            i    i  ii    i iv vv   i v  v      i v  ii    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_70798110_7   1087 TATTTTCAACAAATGGTACCAGAACAACTGGATATC-ACATGCAAAAAAG 1135
                          v               i ii i           ? -          i i
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_70798110_7   1136 AAAAGAAAAAAATCTAGAGCAGACCTTATACC----TT---TTA---TGG 1175
                         vi   vvii vvi   vvv  v   v     v----  --- i ---   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_70798110_7   1176 ATCACAGACCTGAATGTAAAATACAAAACTACAAAACTCCTAGAAGATAA 1225
                             ?      i       i vvi       i       i       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_70798110_7   1226 CA-AAATGTAGAT------GACCTTGAGTATGGCAATGATTCTTTAAATA 1268
                           - ii?   i  ------       i  vv       i  ii   i   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_70798110_7   1269 CAACATAAAAGACATA-TCCATGAAAGAAATAATTGATAAGCTG-ACCTC 1316
                         ii   iv   ii  i -v v ii       v   v     ii  -  i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_70798110_7   1317 ATTAGAATTTAAGATTTCTGCCTTATGAAAGATAATACCAAGAAAATGAG 1366
                           i i    v  i i  i  ivi vii  i  i v  i       i   i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_70798110_7   1367 AAGAGAAGACATAGACTGAGAGAAA-TACTTGCAAAAGACACATCTGATA 1415
                             v  vv  i   v  i      -  i       vv i i        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_70798110_7   1416 AAGGACCATTACAT--AAAATATACAAAGGCCTCTTATGACTCAAAAATA 1463
                          i    --  ii  -- i      i    iv      ii      v    
  L1M4_orf2#LINE/    746 AGGGAC--TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_70798110_7   1464 AAGAAATGAACAACCTGATTTAAAAAATGCGCAAAATACCTAAAAAGACA 1513
                           i i ii  i    ii   ?     -  v     iv ii i  v     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chr1_70798110_7   1514 TCTCACCAAAGAAGATATTCAGATAGCAGGTAAGCACATTAAAAGATGTT 1563
                          i  v             v  i  i  vii         v        i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_70798110_7   1564 CAATATCATACATCAT 1579
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (90 / 47)
Gap_init rate = 0.02 (12 / 563), avg. gap size = 2.17 (26 / 12)  


2347 24.52 5.41 0.32  chr1_70839507_70841510.rev      500  1127 (877)    L1M4_orf2#LINE/L1      164   823 (85)  

  chr1_70839507_7    500 GACC--AAACAGCCAAAACAATCTTGAGGGAAAAAAAACAAAACTAGAGG 547
                             --i  i                 ii-  i  i      ii i    
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAA-AAGAAGAACAAAGTTGGAGG 212

  chr1_70839507_7    548 CCTCAAAAGTTCTGATTTTAAAATATATTTCAAAGCGATAGTAATCCAAA 597
                         v    v vv i ii    i    iv  i v      v i       v i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_70839507_7    598 CAGTAAGGTACTGGTAGAAAGACAAACATATAGTCCTGTAGAATGGAAT- 646
                             iv        i v  i  i i        vi vi i    i    -
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_70839507_7    647 -AGAGCCCAAAAATAAGCCCTTTCATATATGGTCAAATAATCTTTGACAA 695
                         -    i   i      i   v v   v         v i  i  i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_70839507_7    696 ACATGCCCAGGCTATACAATGGAGAAAGACTAGTCTCTTCAATAAACAGT 745
                         ivi    v  i i  v      i      v      i     i   ii  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_70839507_7    746 ATTGGGAAAATTAGATATCCACATGACAAAAAATT--AGTTAAATTCTAA 793
                         ii     v  i i    ?       -     i v --    ii ii iv 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATG-CAAAAGAATGAAGTTGGACCCCTA 461

  chr1_70839507_7    794 TTTTAAACTATATACAAAAATTAATTCAAAATGGA-------CCTAGCCA 836
                         ii i v  i               i          -------    ivii
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_70839507_7    837 TAAGACCTGAAACTATAGAACTCCTAGAAGAAAACATAGGAAAAAAGCTT 886
                              v  i        i     i                ?iv   v   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_70839507_7    887 CATGACATTAGTCTTGGCAATAATTTTTTGGAAATGACACCAAAAGTACA 936
                          i    v  i vi v      ii   i  i  v             i   
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_70839507_7    937 GGTAACAGAAGCAGAAATAGACAAAT-GAACTACATCAAAATTTAAAG-- 983
                         i i    i   v i       i    - i   v          v   i--
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_70839507_7    984 --TGTGTGGCAAAGGAAATAAACAGTAGAGTAAAAAGGTAACTTACAAAA 1031
                         --    ivv       v iv v  iv i   i     ii   ii   i  
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_70839507_7   1032 TAAGAGAAAATCTTTGCAAACCATATATCT---AAGTGGTTAATAACCAG 1078
                          ii        v        i         ---   v ii vi  v    
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_70839507_7   1079 AATATA-------------CAACTCAACAACTGCTCAACAAATAACCTAA 1115
                               -------------        i  ivivvvi          i  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_70839507_7   1116 TTAAGAGATGAG 1127
                           ? i i   i 
  L1M4_orf2#LINE/    812 TTWAAAAATGGG 823

Transitions / transversions = 2.08 (102 / 49)
Gap_init rate = 0.02 (10 / 660), avg. gap size = 3.60 (36 / 10)  

 494  9.89 1.10 0.00  chr1_70839507_70841510.rev     1423  1513 (491)    L1M4_orf2#LINE/L1      817   908 (0)  

  chr1_70839507_7   1423 AAATGGACAAAGGACTTGAATAGACATTTATCCAAAGAAGATATACAAAT 1472
                               i       i              v                    
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_70839507_7   1473 GCCCATCAAGCAAATGAAA-GATACTAAACATCACTAATCAT 1513
                          v   vi     v      -   i  v       ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.80 (4 / 5)
Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1)  


2800 28.03 1.78 0.78  chr1_70900084_70905842.rev     4372  5270 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70900084_7   4372 TGGAAAAACATTCAATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4421
                               i i  i v   i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70900084_7   4422 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGTTATTCCCATTAAAC 4471
                            v     v      v i  i  i        i iv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_70900084_7   4472 TACCACTAACATTCTTCACAGAATTAGAAAAAAACT-ATTTTATACTTCA 4520
                          v   vivi v  i  ii     v v  v  i--  -  ii  v v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_70900084_7   4521 TATGGAACCAAAAAAGAGCTCAAATACCCAAGACAATTCTAAGCAAAAAG 4570
                                viiv  ii  v ivi    v    i     ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_70900084_7   4571 AAGAAAGTTGGAGACATCACACTACCCGACTTCAAACTATACTACAAGGA 4620
                           v          ivv       v   i i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_70900084_7   4621 TACAGCAGCCAAAACAGCATGTTACTGTTACAGAAACAGACACACAGACC 4670
                              i ii   i    ii  v     vi i iii i     i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_70900084_7   4671 GGTGGAACAGAATAGAGAACTCAGAAAAAAGACTGCACACCTACAACTAT 4720
                         ii     i     v    iii      v  iv iii   ii  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_70900084_7   4721 CTGATCTTCAGCAAACCTGATAAAAACAAGCAATTGGGAAAGGATTCCCT 4770
                         i    i   ii   ivv  vi  i v  vv    v       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_70900084_7   4771 ATTTAATAAATGCTGCTGGGAAAACTGGCTAGCCATATGCAGAAAATTGA 4820
                         v  i  i     v        v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_70900084_7   4821 AGCTAGACCCCTTCTTTACACTTTATACAAAAGTTAACACAAGATGGATT 4870
                           i i       v i i    iv         i     v   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_70900084_7   4871 AAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGAAAATCT 4920
                          ?    i         i v i            vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_70900084_7   4921 AGGCA-ATACCATTCAGGACATAGGGACAGGAAAGGATTTCGT-GATGAA 4968
                            ?i- v i -   iv   v v   vi   v  v i    v -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr1_70900084_7   4969 AACACCAAAAA-GCAATTGCGACAAGAGCAAAAATTGACAAATGGGATCT 5017
                         i         i-i   --  i    i  v      v  i    v   ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_70900084_7   5018 AATTAAACTAAAGAGCTACTGCACGGCAAAAGAAACT--CATGAGAGTGA 5065
                         v  i   v v  i i  vi  ii vv    i  v   --  v  i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_70900084_7   5066 ATACACAACCTACTGAATGGGAGAAATT-TTTGCAATCTATCCATCTGAC 5114
                          v v      i  v            v -       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_70900084_7   5115 AAAGGTCTAATATCCAGAGTCTACAAGGAACTTGAACAAATTTACAAGAA 5164
                           i  v  vi        i v  i  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_70900084_7   5165 AAAG-CAAAAAACCGCATCAAAAAAGTGGGCA-------TAAACAGACGC 5206
                             -    v    vv  i?     -      ------- i  i    ii
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACAT 843

  chr1_70900084_7   5207 TTCTCCAAGAAAGACATTTATGGGGCCAACAAACATATGAAAA-AGGCTC 5255
                                 ii    i  vi viv      i  i  i       - v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_70900084_7   5256 AACATTGCTGATCAT 5270
                              ii????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


2689 28.34 1.87 1.76  chr1_70917968_70922913.rev     3549  4455 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70917968_7   3549 TGAAAAAACATACTATGCTCATGGATTGGAAGAATCAATATCATTACAAT 3598
                           i   i i  v i   i               v i     ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70917968_7   3599 GGTCATACTGCCCAAAGCAGTCTACAGATTTAATGCTAGTTCTATCAAAC 3648
                           iv     v      viii          i  i  v vii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_70917968_7   3649 TACCAACATCTTGTTTTTACAGAA-TTGGAAAAAAACTC-TTCTAAAATT 3696
                          v   i vv i -     i     -   --- v  i  v- i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr1_70917968_7   3697 CACATGGAACCAAAAAAGATTCTGAATAGCCAAGACAGTACTAAACAAAA 3746
                           i      viiv  ii  ii v          i   i vi i  v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_70917968_7   3747 TGAACAAAGCAAGAAGCATCACATTACCTGACTTTAAACTATACTACAAG 3796
                         v        ivi  i vv     i v  ii i  i   viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_70917968_7   3797 GCTACAGTAACCAAAACAGTATGGTACTCACGCAAAAACAGACACATAGA 3846
                                   i   i     i       vi ii  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_70917968_7   3847 CCAATGGAATAGAATAGGTAACTCAGAAATAAAGCCACACAACTGCAACC 3896
                         i              v iv iii          v   i   vi iiiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_70917968_7   3897 ATCTTATCTTTGACAACGCCAACAAAAACAAGCAATGAGGAAAGGA--GT 3944
                          vi v  i  i     v viiv   i v  vv     i      i --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_70917968_7   3945 CCCTATTCAATAAATGGTGTTGGGATAACTGACTAACTCTATGCAGAAGA 3994
                          -- v     i        i     i     iv  ? ivi     i    
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_70917968_7   3995 TTGAAGCTGGACCCATACCTTTCAGCATATATAAAAATTAATTTGAGATA 4044
                         v     i       v     iv  v      i         i ii i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_70917968_7   4045 GATTAAAGATTTAAATATATGACCTCAAACTATAAAAATCCTATAAGAAA 4094
                            i ?   ii     i  v  v  v           v  i  v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_70917968_7   4095 ATCTAGA---AAATACCCTTCTCAACATCAACCCAAATATGTGAAAGAAT 4141
                          iv   i---    ---    vii  v iiivii iii ----- v iv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCA-----ATGGTT 586

  chr1_70917968_7   4142 TTATGGCTAAGTCCCCAAAAGCAATTACAACAAAGACAAAAATTGACAAG 4191
                          iv i v  v v v         vvvi       iiv      v  i  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_70917968_7   4192 TTGGACCTAATTAAACCTAAGAGGTTCTACACAGCAAGGGAAACTATCAA 4241
                               i v  i   vi   i iv  i iii vv   i   v        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_70917968_7   4242 CATAATAAACAAA--ACCTATAGAACAGGAGAAAATAGTCACAAACTATG 4289
                         v v i i  v i --   i i    ii          v ii    ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_70917968_7   4290 CACCTGACAAAGGCCTAATATCCATCATCTATAAGGAACTT----AAATC 4335
                         i i    i  i  v  vi      vv  v     i     i----  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_70917968_7   4336 AACAAGCAAAAAACAA----CCTCATTAAAAAGTGGGCAAAGGACATGAA 4381
                           i  vv    i    ----  iv   ?    i           iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_70917968_7   4382 CAAATACTTCTGAAAAGAATACATGTAAGCAGCCAACAAATATATGAAAA 4431
                         i i i i    vv      v i  ii  iii     i  ii i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_70917968_7   4432 AAAAAGCTCAACATCACTAATCAT 4455
                         i v--           ????????
  L1M4_orf2#LINE/    887 GAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (163 / 91)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.54 (33 / 13)  


2677 25.51 1.51 3.35  chr1_70945672_70950930.rev     3844  4768 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_70945672_7   3844 TGGAAATACAGCCCATGCTCATGGACAGGAAGAACCAATATTGTTAAAAT 3893
                               v i v      i       iv      vii           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_70945672_7   3894 GGCCATTCTGCCCAAAGAAATTTACAGATTCAATAAAAACAACCATTATG 3943
                            v  v  v      vvi  i           ii----   --------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACG----CAA-------- 88

  chr1_70945672_7   3944 AGTTATTCCTATCAAACTACCAA-TGACATTCTCACACAACTAGAAGAAA 3992
                         ----- i         v v   i-  v v  i ii  v  v v  v-  i
  L1M4_orf2#LINE/     89 -----TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAG 132

  chr1_70945672_7   3993 CT-ATTTTAAAATTCATATGAAACCAAAAAGTAGCCTAAATAGGCAAGGC 4041
                           -  ii             i  viiv  i v v  vi     v   ii 
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr1_70945672_7   4042 AACCCTAAGCAAAAAGAACAAAGCTGGAGGCATCACGTTTCCCAACTTCA 4091
                           i i i iv  i          i      vv    ii       i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_70945672_7   4092 AACTATGCTACAGGACTACAGTAGCTAAAACAGCCTGGTACTGGGACAAA 4141
                           viv i     iii        iii  i    iv         v i  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_70945672_7   4142 AATAGACA-------CAATGGAACAGAATAAAGAGCCCAGAAATAATGCC 4184
                         i       -------        i     vi    i          vv  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_70945672_7   4185 ACAGAGCTACAACCATCTGATTTTCAATAAGGTCAACAAAAAAAAAAAAG 4234
                          i v vi  iiii  vi        i i    viiv   i vv vvv  -
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA- 381

  chr1_70945672_7   4235 CGAGGAAAAAAGACTCCCTATTCAATAAATGGTGCTGGGATAACTGGCTA 4284
                         i i     i  v v  -- v     i              i      v  
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_70945672_7   4285 ACCACACGCAGAAGATTGAAGCTGGACACCTTCGTTACATCATATACAAA 4334
                         ?     i   i    v     i     v   v v i   i          
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_70945672_7   4335 AATCAGCTCAAGTTGGACTAAAGATTTAAATGTAAAACCCAAAACTATAA 4384
                            i i     iv    ii ?   ii         i v i          
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_70945672_7   4385 AAACCCTGGAAGACAACCTAGGCA-ATACCATCCTGGACATAGGAATAGA 4433
                           vi i i     v   v    ?i- v i v  v  -  v v  iv   i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGG 578

  chr1_70945672_7   4434 CAAAGATTTCATGACAAAGACATCAAAAGCAATCA--CAACAAAAGCAAA 4481
                            v i    v iivv v    i        --  --         v   
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCA--CAAGCAACAAAAGAAAA 626

  chr1_70945672_7   4482 AATTGAGAAGTGTCG-CCTAATTAAACTTAAGAGCTTCTACACAGTAAAA 4530
                            v  v  i - v - i v  i   v    i i   i iii vvi   i
  L1M4_orf2#LINE/    627 AATAGATAAAT-TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_70945672_7   4531 GAAACCATAAACAAAGTAAACATACAACCTACAGAATGGGAGAAAATATT 4580
                           v  i  v  v     i  v v      i                    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_70945672_7   4581 TGCAAACTATGCATCCAACAGAGGTCTAATATCCAGCATCTATAAGGAAC 4630
                               ii  ii   ii i ii  v  vi       v  v     i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_70945672_7   4631 TTAAACAAATTTACAAGAGAAAAACAAA-AAAAAAGTTAAAAAATGGGCA 4679
                          ivv    v iv i  v i   i     -  vvv i  ?           
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_70945672_7   4680 AAGGACATGAACAGACAGACACTTCTCAAAAGAAGATACACATGCAGCCC 4729
                              iv    i     ----i     v          i   viii   v
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACA----TTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_70945672_7   4730 AGAAGCATACAAAAAAAAAAGCTCAATATCACTGATCAC 4768
                          v     --  vi    i v      i    ????????
  L1M4_orf2#LINE/    872 ATAAGCA--CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (133 / 99)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.65 (45 / 17)  


1796 24.22 1.57 7.49  chr1_70970916_70973505      867  1440 (1150)    L1M4_orf2#LINE/L1        4   543 (365)  

  chr1_70970916_7    867 AAAAACATTCCATGCTCGTGGATTAGAAGAATTAATATTATTAAAATGGC 916
                            i i  i     i  i      i     v        i    i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_70970916_7    917 CATACTTACCAAAGCAATCTACAGATTCAACACTATTCCTATTAAGCTAC 966
                         v     iv     vii               i v  i     i  iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_70970916_7    967 CAA-TGTTATTGTTTACAGAGTAAAAAAAATTCCCA--CT-ATTCTAAAA 1012
                           i-  ii-  v   i    --------    vv  --  -  i      
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGA--------AATTGACAAGCTGATCCTAAAA 144

  chr1_70970916_7   1013 TTCATATAGAACTGAAAAAGAGACTGCATAACCAAAGCAATCTAAGCAAA 1062
                                i   v  v  ii  vv v v   i     i      ---ii  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT---TGAA 191

  chr1_70970916_7   1063 AACAAACAAACAAACAACAACAACAACAACAAAAACAAAGCTGTAAGCAT 1112
                           -------------------------- v  i       i  v i ---
  L1M4_orf2#LINE/    192 AA--------------------------AGAAGAACAAAGTTGGAGG--- 212

  chr1_70970916_7   1113 CACATTACATTCCTTGACTACAAACTATATTATAAGGCTA-AGTAGTCCA 1161
                         -  - i   i i iii i v    viv  i  i  i    -    i  v 
  L1M4_orf2#LINE/    213 -AC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr1_70970916_7   1162 AACAGCATGGTACTAGTATAAAAACAGACAAATAAACCAATGGAACAGAA 1211
                         i    ii       i i    ii i     v   i i        i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_70970916_7   1212 TAGAGAGCCTGGAAGTAAAGCTGCACACCTACAGCCATCTGATCTTTGAC 1261
                          v     i ii   i    v iii   ii  ii i  vi    i  i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr1_70970916_7   1262 AAAGTTGATGAAAATATGCAATGGGGAAAGGACTCCCTATTCAATAATTG 1311
                           i v  vii i vi  v            i ivvi  v     i  v  
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_70970916_7   1312 GTGCTGGGATTGCTGTCTAGACATATGCAAAAGAATGAAACTGGACCTCT 1361
                                  ivi   vv  ?v  i               ii      i  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_70970916_7   1362 --CTTAC--CATATATAAAAATTAACTCAAGACAGATTAAATATTTAAAT 1407
                         --  i  --      i              i ii   i ? v ii     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_70970916_7   1408 ATAAGACCTCAAACTGTAAGAATCCTAGAAGAA 1440
                         i     v  v     i   i v  i        
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

Transitions / transversions = 2.26 (95 / 42)
Gap_init rate = 0.02 (12 / 540), avg. gap size = 4.33 (52 / 12)  

 967 21.97 11.56 1.45  chr1_70970916_70973505     1752  2097 (493)    L1M4_orf2#LINE/L1      528   908 (0)  

  chr1_70970916_7   1752 AAAATTCT-AGAAGAAAACCTAGG---AAA----CAC--CCTTG---TGG 1788
                             i   -          v    ---   ---- ii--     --- i 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_70970916_7   1789 ACATTGGC--CTTAAA---------------ACAATTTCAACAAAAACAA 1821
                         i  v   i--    i ---------------    v--        iv  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAG--CAACAAAAGAAA 625

  chr1_70970916_7   1822 AAATTGACAAGTGGGATCTAAGTAAACCAAAGAGCTTCTGCACAGCAACA 1871
                             v  i  i v   ii v vi   viv  i i   i  ii vv   vi
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_70970916_7   1872 GAAACTAACAACAGAGTAAACAGACAACCTATAGAATGGGAGAAAATATT 1921
                           v    v   v i   i  v        i i                  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_70970916_7   1922 CACAAACTATGCATCTGACAAAGGTCTAATATCCAGAATCTATAAGGAAC 1971
                         ii    ii  ii      i  i  v  vi          v     i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_70970916_7   1972 TT----AAATCAACAAGCAAAAAACAA----CCCCATTAAAAAGTGGGCA 2013
                          i----  v    i  vv    i    ----   v   ?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_70970916_7   2014 AAAAGGAT--GAACAGACACTTCTCAAAACAAGGACATACAAGTGGCCAT 2061
                           --    --   i     i     v   v   - i      i      v
  L1M4_orf2#LINE/    826 AA--GGATTTGAATAGACATTTCTCCAAAGAAG-ATATACAAATGGCCAA 872

  chr1_70970916_7   2062 CAAACATATGAAAACGTGCTCAGCATCACTAATGGT 2097
                         i  i  i       vi      i     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (47 / 28)
Gap_init rate = 0.03 (13 / 381), avg. gap size = 3.46 (45 / 13)  


2802 21.35 2.76 0.77  chr1_71030935_71032577      500  1150 (493)    L1M4_orf2#LINE/L1      245   908 (0)  

  chr1_71030935_7    500 AAGTTACAGTAATCTAAACGGTGTGGTACTGACATAAGGACAGACATATG 549
                            i          v i  i           i        i        i
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_71030935_7    550 GATCAATAGAATAGAATAGAGGTCCCAGA--TAAACCCTTGTGCACGCAC 597
                                i         v   ivi     --       --i i  ivi i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC--ATACATTTAT 342

  chr1_71030935_7    598 --TCAATCAATCTTTGACAAGAGTGCCAAAACCATACAATGGGCTTAAAG 645
                         --     ii  i  i      i       i     v       v--    
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAAG 390

  chr1_71030935_7    646 GGTAGTCCTGTCAATAAATGGTGTTGAGAAAACTGGATATCCACATGCAA 695
                         ii     i v    i        i  i  v         ?          
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_71030935_7    696 AAGAATGAAGTCGGATCCTTACTTTACACAATATACAAAAATAAACTCAA 745
                                    i   i  i   i i    v            v       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_71030935_7    746 AATGAATTAAAGACCTAGGCATAAGACCTTAAAATATAAAACTATAAGAA 795
                             i  i ?       iiii     v  v   v         v v    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_71030935_7    796 GAA--CACAGGAGAAAAATTTTATAACAGTGGATTTGGCAATGTTTTCTT 843
                            --  i   ? v   vi  ii i  vv   i  v       v      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_71030935_7    844 GGAGATGACACCAAAACCACAGGCAATAAAAGCAAAAATAGACAAATGAG 893
                         i  v            v    i    i     v         i    vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_71030935_7    894 AGTACATCAAACTTAAAGCCTTTTGCACATGAAAGGAAGCAATCCTTAGA 943
                          v v       v     iv      ii v v      vi v   vvv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_71030935_7    944 GTGAAAAATTAACCTACGAGATGGGAGAAAATATTTCCAAATCATATATC 993
                                ivi    i  iii                v             
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_71030935_7    994 TGGTAAGG-AGTTAGATTCAGAATATATAAAGAATGCCTATAATTTAACA 1042
                           i     - v  iv  i                iv i  i  i i  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_71030935_7   1043 ACAAG----CAAATAGCCTAGTTAAAAAAATGGGTAAAATCCTCAAAGTG 1088
                          i  i----      i  i i  ?     -    i   ivvi ii  vv 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAG 839

  chr1_71030935_7   1089 GTATTTCTCC---GAAGAGTTATAAATGGCTAACAAG----TGACAAGAT 1131
                         ii        ---     vv  i       i  i   ----   v     
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_71030935_7   1132 ATTCAATGTCACTAACCAT 1150
                         ii    ii   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (87 / 48)
Gap_init rate = 0.02 (10 / 664), avg. gap size = 2.30 (23 / 10)  


2888 26.65 1.30 2.93  chr1_71053394_71059330.rev     4524  5446 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_71053394_7   4524 TGTAAAAACATTCCATGCTTGTGGATAGGGAGAATCAATATTGTTAAAAT 4573
                           v   i i  i     i ii     v  i   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_71053394_7   4574 GACCACACTTCCCAAAGCAATTTACAGTTTCAATGCAATTTCTATCAAAC 4623
                          i v i   i      vii  i     v     i     ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_71053394_7   4624 TACCAATGAAATTCTTCACAGAATTGGAAAAAATTGTTTCAAAATTCATA 4673
                          v   iivivv  i  ii     v v  v  iv vi iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_71053394_7   4674 TGGAGCCAAAAAAGAGCTTGAATGGCCAAGGCCATTCTAAGCAAAAAGTA 4723
                             iviiv  ii  v iv    i     ii v  ii i iv  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_71053394_7   4724 CAAAGCTGGAGGCATCACGTTACCCAACTTCAAACTATACTACAAGGCTA 4773
                              i      vv    ii v     i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_71053394_7   4774 CAGTAATCAAAAGGGCAGGGTGCTGATACAAAAACAGACACATAGACCAA 4823
                                   i vi iiv   i   ii i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_71053394_7   4824 TAGAACAGAATAGAAAGCCCGGAAGTAAAGCCACAGACCTACAGGCATCT 4873
                          i   i     v  i  i  i   i    v   i v ii  ii v  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_71053394_7   4874 TGTTTTTGACAAAGTTGACAAAAACAAGTAATGGGGAAAGGACTCCCTAT 4923
                         vi    i     i v  v   i v  vvi           i ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_71053394_7   4924 TCAATAAATGGTGCTGGGATAACTTGCTGGCCATACGCAGATGATTGAAT 4973
                             i              i    v v i?   i i   i v  v    v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_71053394_7   4974 GTGGACCCCTTCTTTATACCATATACAAAAATCAACTCAAGATGGATTAA 5023
                         v         v i i i               i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_71053394_7   5024 AGGCTTAAATGTAAAACCCACAAC-ATGAAAACCCTGGAAGATAACCTAG 5072
                           i i         i v i v   -  i   vi i i     v   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_71053394_7   5073 GAA-ACATCATTCTGGACATAGGCTCTGGCAGATAGTTTATGAA----GA 5117
                          ?i- v   -   vv   v v  v iv    -  i    v v i----  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAGATATGA 598

  chr1_71053394_7   5118 CACCAAAA--ACAATTGCAACAAAAACAAAACTGGACAAATATTTTCTCC 5165
                                 --    --         iv    v i  i    ---------
  L1M4_orf2#LINE/    599 CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAAT--------- 637

  chr1_71053394_7   5166 CATTCTCTAGTTTATCTGTTTATTCAATTGATAGTTTCT-CACAGCAAAA 5214
                         ----- vv v  i   vi-------    i v ii  i -ii vv    i
  L1M4_orf2#LINE/    638 -----TGGACTTCATCAA-------AATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_71053394_7   5215 GAAACTATCAATTGACTAAACAGACAACCTAGAGAATGGGAGAAAATGTT 5264
                           v        vvi v i  v        i v               i  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_71053394_7   5265 TGCAAACTACACATCTAACAAAGGTCTAATATCCAGAATCTACAGGGAAC 5314
                               ii i i    i i  i  v  vi          v  i ii    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_71053394_7   5315 TTAAACACATTAATAAGCAAAAAAAAAAAAAACCCA-TTAAAAAGTAGGC 5363
                          ivv   vv i     -i     i v   v      -  ?    i i   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_71053394_7   5364 AT-GGACATGAACAGAC-TGTGTCCAAAAGAAGACATACACATGGCCAAC 5411
                          v-   iv    i    - v v      -     i     v        i
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAA-GAAGATATACAAATGGCCAAT 873

  chr1_71053394_7   5412 AAGCATATTATAAAATGTTCAACATCACTAACCAG 5446
                              i  v v  i   i         ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.60 (39 / 15)  


2627 22.28 3.74 0.00  chr1_71312359_71313965      500  1114 (493)    L1M4_orf2#LINE/L1      271   908 (0)  

  chr1_71312359_7    500 TACTGGCATAAAAACAGACATATAAA--------ACAGAATAGAGATTCC 541
                                    ii i         i -------- i     v    v   
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_71312359_7    542 AGAAATAAATCCACACAT--ATGGCCAATTGATCTTTGACATAGGTGCCA 589
                                  i   i    --    i        i  i    vi       
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_71312359_7    590 AGAACATATAATGGGATGAGGACAATCTCTTCAATAAATAGTGTTAGGAA 639
                            v   vi      ivi  i i i   i     i    i   i i   v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_71312359_7    640 AACT--ATATCCACATGCAGAAGAGTCAAACTGGCCCCTTATTTTACACC 687
                             --   ?         i    i v  ii   v   i  ii i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_71312359_7    688 ATGTACAAAAGTCAACTCAAAATGGATTGAAGACTTAAATGTAATATCTG 737
                           i       i i              ii?    i         v v  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_71312359_7    738 AAACTATAAAACTACTAGAAGAAAACATAGAGAAAAAGCTTCTTGACGTT 787
                                      vi               i?iv   v    v    v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_71312359_7    788 GGACTTGGCAGTGATTTTT--GA----AC-CCAAAAGCACTGGCAACAAA 830
                           ii v    i  i   i --  ----  -          vi        
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_71312359_7    831 AGTAAAAATAGACAAGTGGGATTGTATCAAACTAAAAAGCTTCTGCACAC 880
                           v         i  i v   i vi      v v    i   i  ii vi
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_71312359_7    881 TAAAGGAAACTATCAGTAGAGTGAAGAGCCAACCCTGGGAATGAGAGAAA 930
                         i      v       iv i      i  v      vvi     i      
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_71312359_7    931 ATATTTGCCAACCATACATCTGATACAGGGTTAATCTCCAAAATATATAA 980
                                 v  i    i        vi  ii vi v    i         
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_71312359_7    981 GGAAATCAAACAACTCAATGGCAAGAA----AATGACCCAATTAAAAAAT 1026
                         i   v  vv          iii  i  ----   i        ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_71312359_7   1027 GTACAAGGAACATGACTAGACATTTCTCAAATGAAAACGTCCAAATAGCC 1076
                          vi   i i iv   v            v  v   i ii v     i   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_71312359_7   1077 AACAGGAATCTAAAGAAATGTTCAACATCACTAATCAT 1114
                           i i v iv i  i i   i         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (89 / 44)
Gap_init rate = 0.01 (7 / 638), avg. gap size = 3.29 (23 / 7)  


3264 23.01 6.01 1.04  chr1_71320886_71327406.rev     5166  6030 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_71320886_7   5166 TGGAAAGATATTCCATGTCAGTGGATTGGAAGAATCAATATTGTTAAAAT 5215
                                    i      ivi            v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_71320886_7   5216 GTCCATACTGCCCAAAGCAATCTACAGATTCAATGCAGTCTTTATCAAAA 5265
                          v v     v      vii              i   i  ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_71320886_7   5266 TGCCAATGATGTTACTCACAGAAATAGAGAAAACAATCCTAAAGTTTATA 5315
                          v   iiviiv  vi ii       v  v  ivii        i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_71320886_7   5316 TGGAATATGGAACCACAAAAGACCCAGAATAGACAAAGCTATTCTGAACA 5365
                              -   ------   ii            v    i v  ii    v 
  L1M4_orf2#LINE/    151 TGGAA-ATG------CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_71320886_7   5366 AAAAGAACAA-GCTGGAGGAATTACATTACTTGACTTCAAATTATACTTC 5414
                          i        - i       v i   i v iii i      viv    v 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_71320886_7   5415 AGTGCTATAGCAACCACAACAGCATAGTACTGGCATAAAAACAGACACAT 5464
                          iv    i  i  i  vi    ii i            ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_71320886_7   5465 AGACTGATGGAACAGAATAGAGAACCCAGAGATAAATCCATACATCTACA 5514
                            iii      i     v    ii     i     i        i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_71320886_7   5515 GT-----GACCT----CAAAAGTGCCAGGAACATATGTTGGGTAAAAGAC 5555
                           -----  ii ----   ii      i  v   viiv    v   ii i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_71320886_7   5556 AGTCTCTTTAATAAATGGTGCTGGAGAAACTGGATATTCATATGCAGAAG 5605
                              i  i  i            iiv         ?i  i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_71320886_7   5606 AATA------GACCTGTATCTCTTGCCATATACAAAGATGAAATCAAAAT 5649
                            i------    iv  i   vii           i  v  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_71320886_7   5650 GGATTAAAGAATTAAACCAAAGACCTCAAACTATGAAACTACTACAAGAA 5699
                             i ?   vi    ivv    v  v       i     vi  v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_71320886_7   5700 AACATTTAAGAAACTCTCCAGGACATTGGAGTGGGCAAAGATTTCTTGAG 5749
                              vvi? v  v   i iv   v    iv i     v i      iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_71320886_7   5750 TAATAC-CCAACAAGCACAGGCAACCAAAGCAAAAACAGACAAATGGGAT 5798
                           vv  -    -       i     v    v     i   i    v   i
  L1M4_orf2#LINE/    594 TATGACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_71320886_7   5799 CACATCAAG-TTAAAAAGCTTCTGCACAGCAAAGGAAGCAATCAACAAAG 5847
                         iv      i-       -   i  ii vv       vi v     v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_71320886_7   5848 TGAAGAGATAACCAACTGAATGGGAGAAAATATTTGC----CATATAT-- 5891
                             i   i    v  v                    ----       --
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_71320886_7   5892 ---AAGGAGCTC----------------AAG--------CAACTCTACAG 5914
                         ---    ii  i----------------   --------      v i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_71320886_7   5915 GAAAAAACCTAATAATCCAATTTTAAAATAGGCAAAAGATCTGAGT-GAC 5963
                         v     iv v     i      ?v     i      i   i   i -   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_71320886_7   5964 ATTCCTCAAAAGAAGAAATACAATTGGCAAATATGTACATGAAAAGGTGC 6013
                            i   v        v      v    v    v i          i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_71320886_7   6014 TCAACATCACTGATTAT 6030
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (124 / 71)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.07 (61 / 15)  


3038 27.29 1.10 0.77  chr1_71393124_71398782     4262  5166 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_71393124_7   4262 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4311
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_71393124_7   4312 GGCCATACTGTCCAAGT-AACTTATAGATTCAATGCCATCCCCATCAAGC 4360
                            v     vi    i -i ii  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_71393124_7   4361 TACCAATGACTTTCTTCACATAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4408
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_71393124_7   4409 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 4458
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_71393124_7   4459 AACGAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4508
                            i   i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_71393124_7   4509 TACAGTAACCAAAACAGCATGTTACTGGTACCAAAACAGAGTTATAGATC 4558
                                 i   i    ii  v      i iv ii i   vv        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_71393124_7   4559 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATC-ACAACT 4605
                                i    i--    i  --        vv   i i  i- iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_71393124_7   4606 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGG-AAAGGATTCC 4654
                          vi    i  i     ivv  vv  i v  vv       -    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_71393124_7   4655 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4704
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_71393124_7   4705 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4754
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_71393124_7   4755 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4804
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_71393124_7   4805 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGA---CTTAATGTC 4851
                         v    ?i v viv   iv   v v  vv i     v i---    i-i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-ATA 595

  chr1_71393124_7   4852 TAAACCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 4901
                          i --           vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    596 TGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_71393124_7   4902 TAATTAAACTAAAGAGCCTCTGCACAGCAAAAGAAACTACCATCAGAGTG 4951
                          v  i   v v  i i i i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_71393124_7   4952 AACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGA 5001
                           v  i     i   i             v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_71393124_7   5002 CAAAGGGCTAATATCCAGCATCTACAATGAACTCAAACAAATTTACAAGA 5051
                         i  i  i  vi       v  v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_71393124_7   5052 AAAAAACAAACAACGCCATCAAAAAGTGGGCGAAGGACATGAACAGACAC 5101
                             i     i   v v  i?    i     i     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_71393124_7   5102 TTCTCAAAAGAAGACATTTATGCAGCCAAAAACCACATGAAAAAATGCTC 5151
                              v        i  vi viii     v  v          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_71393124_7   5152 ACCATCACTGGCCAT 5166
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


3064 24.91 6.29 0.58  chr1_71494159_71496239      737  1595 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_71494159_7    737 TGGAGGGATTTTCCATGTTTGTGGACAGGAAGAATCAATAGTGTCAAGAT 786
                             ii   v i       ii    iv      v i    v   i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_71494159_7    787 GTAAGTTCTCCCCAGCTTGATCTATAGATTCAATGCAATCCCAATTAAAA 836
                          vv i v       iv        i        i        v  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_71494159_7    837 TATCAGC-AAGTTATCTGTGGATATCTACAAACTGATTTTAAAGTTTTTA 885
                          vi    -ivv  v i  ii  v  iv    i     ii    i  i-- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC--A 148

  chr1_71494159_7    886 TATGGGGAGTCAAAAGACCCAGACTAGTCTATGCAATATTAAATGAAAAG 935
                              ii vv   ii        v   i v vi    v  i  vi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_71494159_7    936 AGCAAAATAGGAGGACTGACACAACCCAACTTCATGACTTAGTATAAAAG 985
                          i    i v        v    vv     i    vi     v  i   iv
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_71494159_7    986 TGCAGAATTCAAGAAAGTGTGATATTGGTGAGAGAATAGACAAATAAATC 1035
                          i   v v      v      i  i   iivi  i       v   i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_71494159_7   1036 AATGGAAAAGAATAGAGAGGACAGAAATAGACC--TACATGAATACCATC 1083
                                v     v     vv        i   --     vv  i--i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG--GTC 346

  chr1_71494159_7   1084 AACCAATCTT-GACAAATGAGAAAAGGCAATACAATGGAGAAAAGACAGT 1132
                           iii  i  -     iv v vv   i v  v      i    ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_71494159_7   1133 CTCTTCAACAAACGCTGCTAGAACAACTGGACATCCACATGCAAAAAAAT 1182
                           i         i v    i i         i ?            i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_71494159_7   1183 GAATCTAGACACAGACTTTATACCTTTTACAAAAATTAACTCAAAATGAA 1232
                            vi i   v vv  i i i   v v                     i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_71494159_7   1233 TCATAGACCTAAATGTAAAAGGCAAAACTATAAAACTCCTAGGAGATGAC 1282
                            ?              i  vi               i   i   vi  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_71494159_7   1283 ATGAGAGAAAATCTTGAT-ACCTTGGGCATAGTGATGACTTTTTAGATAG 1331
                           ii ? v       vi -        ivvi ii   ii  i       v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_71494159_7   1332 AACACAAATGGCGT--------------------GATAAGCTAGATTTCA 1361
                         i    v  vi  ii--------------------     ii i  i    
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_71494159_7   1362 TTAAAATTAAGAACTTCTCTGT---AAAAGACAGTACCAAGAGACTTAGA 1408
                          i        i     i v  i---   i    v  i     i v v i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_71494159_7   1409 AGACCAGCCAAAGATTTGGAGAAAATATTTGCAAAAGACATATCTCATAA 1458
                             v v   v   v v                  vv i      v    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_71494159_7   1459 AGGTTTTTTAATCCAAAATATACAAAGAACTCTTAAAACTTAACAATAAG 1508
                         i  vi  v  -    i      i            v    i  i     i
  L1M4_orf2#LINE/    747 GGGACTTGTA-TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_71494159_7   1509 AAAGTGAGCCACCCAGTT-AAAAGTGAGCAAAAGACCTAAACAGTCATCT 1557
                           iiii iiv     i  -    i  i     i  ii i  i  v   i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_71494159_7   1558 C-------------------------ATAAGCATGTAAAAAGATGCTCCT 1582
                          -------------------------       ii i           vv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_71494159_7   1583 CATTATATGTCAT 1595
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (130 / 81)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 5.36 (59 / 11)  


2352 25.50 4.53 4.86  chr1_71533462_71535358.rev      501  1406 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_71533462_7    501 AAACATTACATTTCCATGGACTGGAAAAATCAGTATCATTAAAATGGCCA 550
                          i i  iv   v i      i     i v i i   ii    i     v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_71533462_7    551 TACTGCCCAAA------------------GCAATTCTTATCAAACTACCA 582
                             v      ------------------     i i       v v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_71533462_7    583 GCATCATCTTTCACAGATTTCGAAAAAATGATTCTAAAATTCATATGGGA 632
                           vv v i   ii    vv i  v  iv    i               i 
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_71533462_7    633 CCAAAGAGGAGCCCAAATATCCAAAGCAATCCTAAGCAAGAAGAACAAAC 682
                         viiv ii   v  vi    v     i     i i iv            v
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_71533462_7    683 CCAGAGGCATCACA-TTACTGACTTCAAA--CTGTTACTAAGCTGCAGCA 729
                         iii    vv     -  v ii i      --i ii   v     i   i 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_71533462_7    730 ACCAAAACAGTATGGTACCGGTACAAAAACA-ACACATATGCCAGTGAGA 778
                          i   i     i      i  i i  ii i -   i   vii  i  ii 
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_71533462_7    779 CAGAACAGAAAAGCCAGAAGTAAAGCCACATATCCACAACCATCTGATCT 828
                         i    iv  i iv      i    v   i i  ii iiii  vi    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_71533462_7    829 TTGACAAAATCAATAAAA--ATTAAAAATGGGGAAAGGAC--TCCATATT 874
                          i     iiviivi  i --   v  --         i i--  -- v  
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTC--TTTT 401

  chr1_71533462_7    875 TAATAAATGGTGCTGGGATAGCTGGCTAGCCATATGCCATAGTCATAAGC 924
                         i  i              i i    v  ?   i    -------------
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGC------------- 438

  chr1_71533462_7    925 AGAAGAATGAAACTGGATCCCGCCCTATCACTATATACAACAATTAACTG 974
                          i         ii    i   vv   vv   i        v        v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_71533462_7    975 AAGATGTATTAAGGACTTAAATGTAAGACCTCAAACTATAAAAATTCTAG 1024
                           i   v  i ?i   i           v  v           v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_71533462_7   1025 AAGAAAACCTGAGAAATACCTATCT-CAACATCT---GTCTGGCAAAGAA 1070
                                 v -  i?i  v--    - ivv i  ---  iv     v iv
  L1M4_orf2#LINE/    539 AAGAAAACAT-AGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_71533462_7   1071 TGTATGGGTG-GTCCTCAAAAGCAATTGCAATAAAAAAATTACTAAGTCA 1119
                          viv i i i- v vi        vvv    i    i  -----  ivi 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA-----AAAATA 630

  chr1_71533462_7   1120 GACCTAGA--GAGCTTCTGCACAGCAAGCTAAACTTAAACTAGAGGGCTT 1167
                           --  i -- ii    ----- v   ----  -     ------ii   
  L1M4_orf2#LINE/    631 GA--TAAATTGGACTTC-----ATCAA----AA-TTAAA------AACTT 662

  chr1_71533462_7   1168 CTGCACAGCAAAGAA-ACTA-CAACAGAGTAAATAGACAACCTG-AGAAT 1214
                         i  ii vv     i -    -   v i   i  v        ii-     
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_71533462_7   1215 GGGAGAAAATATCTGCAAACTATGTATCCAACAAAGGTCTAATATCCCGA 1264
                                     i      ii  i    ii i  i  v  vi     v  
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_71533462_7   1265 ATCTATAA-GAACCATAAACAATTCAACAAACAAAAAACAAATAACCCCA 1313
                           v     -    iv v -   i    i  vv    i           v 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTA-CAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_71533462_7   1314 TCAAAAAGTGGGCAAAGGACATGAACCAACACTTCCAAAAAGAAGATA-- 1361
                          i?    i           iv    ivi   i   ivv          --
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_71533462_7   1362 CAAATGGCCAGCAA--ACATGAAATAATGCTCATTATCACTAATCAT 1406
                                   ii  --        vi       vi    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (147 / 80)
Gap_init rate = 0.03 (28 / 903), avg. gap size = 3.04 (85 / 28)  


2949 26.49 2.82 0.45  chr1_71563856_71568766     3532  4418 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_71563856_7   3532 TGAAAAGATATTCCATGTTCATGTATTGGATAA-TTAATATTATTAAAAT 3580
                           i        i           v      vi -        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_71563856_7   3581 GTCCATACTATCCAAAACAATCTGCAGATTCAATGTAATCTCTATCAAAA 3630
                          v v     vi     vii    i         i i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_71563856_7   3631 TACCAATGAAATTCTCTACAGAAATAGAAAAAA-AATTGTAAAATTTATA 3679
                          v   iivivv  i i i       v  v  iv-i  iv       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_71563856_7   3680 TGTAACCACCAAAGACCCAGAATAACCAAAGAAATCCTAAGCAAAAGGAA 3729
                           v  vii v ii           i     iv    i i iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_71563856_7   3730 CAAAACTGGATGATTCACATTTCCTGACATTAAATTATATTACAGAGCTA 3779
                             ii    v  i     i    ii iv i   viv  i    i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_71563856_7   3780 TAGTAAACCAAACAGCATAATACTGCCACAAAAACATACACATAGGCCAA 3829
                         i     v v i    ii ii     v  i  ii i v   i    ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_71563856_7   3830 TGGAACAGAATAGAGAACCCATAGATAAATCCATGTGTCTATGGTGAACA 3879
                              i     v    ii   v i     i    iii i      v  iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_71563856_7   3880 CATTTTTGAGAGAGGTGCCAAGAACATAGATTGGAGAAAGAATAGTATT- 3928
                         v     i  v ii          v   vv v   i           v  -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_71563856_7   3929 -CAATATATGGTGCTAGAAAAACTGGATATCCATAAGCAAAAGAATAGAA 3977
                         -   i v        i i v         ?   i v          ii i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_71563856_7   3978 CTATGCCCCATAACTTGC--CTTATACAAAAATAAAATGAAAATGGATTA 4025
                         i ivi    -  v  ii -- v           v  v v         i 
  L1M4_orf2#LINE/    451 TTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_71563856_7   4026 AAGACTTAAATCTAAGACCTCAAACTATGAAACTACTACACAAAAACTTT 4075
                         ?    i     v     v  v       i     vi  v vi     v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_71563856_7   4076 GGGGGAACGCTCCAGAACATTGGACTGGGCAAAGATTTCTTGAATAATAC 4125
                           ? v  vv  i ivi  v    ii i     v i      ii   vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_71563856_7   4126 TCCACAAGCATGGTCAGTCAAAACAAA-----GACAAATGTGATCCCATC 4170
                         v   v     iiiv  i-     v   -----  i    vv  iii    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAA-CAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_71563856_7   4171 AAA-TTAAAAAGCTTCTGCACAGCAAACGAAAAAATCAACAAAGTGAGTA 4219
                            -       -   i  ii vv    v  v vv     v       iv 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_71563856_7   4220 GACAACCCACAGAATGGGAGAAAATATTTGCAAACTAACCACCTAATAA- 4268
                                                           ii vvi i  i    -
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_71563856_7   4269 -----TG------AAACATATAAGGATCACAAAAAACTCCATAGTGAAAA 4307
                         -----  ------i  i      i  v v vv v     v   i i    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_71563856_7   4308 -ATAGATTTATCTGATTTTTAAATTGGCCAAAGATCTCAATAAGTATTTC 4356
                         - i i  v- i ii   ?vv    v   v  i   i v    iii     
  L1M4_orf2#LINE/    798 GACAAATA-ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_71563856_7   4357 TTAAAAGAAGACATACAAATGGCAAACAGGTGTATGAAAAGGTGTTCAAC 4406
                          iv        i           v  i i iii        i  i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_71563856_7   4407 ATCATTAGTCAT 4418
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.23 (29 / 13)  


3302 26.87 0.44 0.44  chr1_71690903_71697194     4892  5799 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_71690903_7   4892 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4941
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_71690903_7   4942 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4991
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_71690903_7   4992 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5039
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_71690903_7   5040 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5089
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_71690903_7   5090 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5139
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_71690903_7   5140 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5189
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_71690903_7   5190 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5237
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_71690903_7   5238 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCCATGGGGAAAGGATTCC 5287
                          vi    i  i     ivv  vv  i v  vv v          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_71690903_7   5288 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5337
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_71690903_7   5338 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5387
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_71690903_7   5388 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5437
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_71690903_7   5438 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5487
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_71690903_7   5488 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5537
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_71690903_7   5538 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5587
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_71690903_7   5588 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5637
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_71690903_7   5638 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5687
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_71690903_7   5688 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5737
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_71690903_7   5738 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5787
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_71690903_7   5788 ATCACTGGCCGT 5799
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 688 29.54 10.29 5.81  chr1_71971392_71973176      500  1325 (460)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_71971392_7    500 AATATGTTAACTCTTCCCCCCTTAAATCTATAAATGTGATACAATTAC-A 548
                           v   vi  iv  i   vvv  i -    i i  vii ii    iv - 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGA-TCTACAGATTCAACGCAATCCCTA 94

  chr1_71971392_7    549 TTAAA-TTCCA----TTTTATTTACAGAA-TTAAAAAATTCATCCTATCA 592
                          i   - i   ----ii  v   i     -  i v  ii v      vv 
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_71971392_7    593 CTCATATTGAAGAGTAAAGGACCAAGAGTAGCCAAGAACAATCCTAACTA 642
                         i      v   iv i  i     v   i       -       i i vv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAA-AACAATCTTGAAAA 193

  chr1_71971392_7    643 AGAAAAATAAAAGAGAATAACTTATCCTTTCAAATTCTCAATGCTAATTA 692
                             i  i   ivv i vi   i iv   i v    -    vi  v i  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT-TCAAAACTTACTA 242

  chr1_71971392_7    693 TAAAATGCCGGGAAAAAATACAGC------CTAGAATAAAACTGGCACAC 736
                         i   iivv i v  vv  v    i------  i v    iiv i -   i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG-ACAT 291

  chr1_71971392_7    737 ACAAAACTCA------CAGCACTCA-----CAGAA-CAGACACACACA-- 772
                          i i --   ------i  v i v -----     -i i  v  i   --
  L1M4_orf2#LINE/    292 ATAGA--TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_71971392_7    773 ---GGTT--TTGAATAT-GATAGCGGAGTATTA---CAAATCAGTGTAGA 813
                         ---   i--    v v -  i i-- i  iii --- v v   i  vi  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAA--GGGTGCCAAGACCATTCAATGGGGA 387

  chr1_71971392_7    814 AAGA--------TTCAATCAATGGTGCTAGG-CAATTGTCTACCCTGTGG 854
                             --------     iv         i  -   i  vv  ?  -----
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC----- 432

  chr1_71971392_7    855 GGAAAAAAAAACAATACAAATGAATTTGGACC------TCATGCCATGTA 898
                         ------ v vi   - vi      v       ------   ii    i  
  L1M4_orf2#LINE/    433 ------ACATGCAA-AAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_71971392_7    899 CATAAAT-AAGTTATGCATAGATTAAAAGTCCAAATATTAAAATCAAAAT 947
                           v    -  v i -iv  i   i ? iii i    i v i iii    i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCA-AAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_71971392_7    948 TTTAAAATATTTTA----ATAATATAGAATTA---CTTTATAGCATTGAA 990
                          v     i- i   ---- v  i    i?v  ---   ii ii v   i-
  L1M4_orf2#LINE/    525 TATAAAAC-TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG- 572

  chr1_71971392_7    991 GTTGGAAAAAGAGTA---AGATGT-------AAAACACAAGC--CAGATG 1028
                            i iv  v iv v---    i -------   i       --  i v 
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_71971392_7   1029 AAAAAGATTGGTAAATGTGACTATCTTAAATGTAAACAGGTAAACTTTGG 1078
                              -  v i     vv    viv i   vv    ------      v 
  L1M4_orf2#LINE/    623 AAAAA-ATAGATAAATTGGACTTCATCAAAATTAAA------AACTTTTG 665

  chr1_71971392_7   1079 TATATGTGAG-ATACCAT----AAACTGATTTAAATA-AAGCCACA---T 1119
                          iiv vvi  - i  i  ----   v   ---   v -  v     --- 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGA---AAAGACAACCCACAGAAT 712

  chr1_71971392_7   1120 TGCAGGAAGCATTCCCAGAGAATTTAAACAAACAAACAAAAGATTAGTAT 1169
                         v v  i  ii   iv  i vv  v  v----- vi i  ii  i v    
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATAT-----CTGATAAGGGACTTGTAT 757

  chr1_71971392_7   1170 TCTGAATATATAAATAATTTCAACAAGTCAA-AATGTTAAAAAAGGTC-- 1216
                         i v           v  i iiv    v    -   ----      iiv--
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAAT----AAAAAGACAAA 803

  chr1_71971392_7   1217 TA--CTAATAGAAAAATGGATAAAGAATATGAATGCACAATTTTAAAAAG 1264
                           -- i   v?        ii    i  v     iv   v  i vv    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_71971392_7   1265 GGGAAACTTTAATGGCCAATTATTTGAATTACTTGACAAGAAGTGCACCT 1314
                         ii  v iviv          ------  vi  v   v    v iv  v v
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAAT------AAGCACATGAAAAGATGCTCAACA 897

  chr1_71971392_7   1315 TCACTTTTAGG 1325
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.29 (135 / 105)
Gap_init rate = 0.05 (45 / 863), avg. gap size = 2.96 (133 / 45)  


2578 26.22 1.17 4.78  chr1_71989853_71993872.rev     2588  3529 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_71989853_7   2588 TGGAAGAACATTCCATTCTCATGGATAGGAAGAATCAATATCATGAAAAT 2637
                              ii i  i    vi        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_71989853_7   2638 GGCCATAGTTTCCAAAAGAATTTATAGATTCAATGCTATTTCCATTAAAC 2687
                            v   v ii     vvi  i  i        i  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_71989853_7   2688 TACCATTGACATTCTTCACAGAATTAGAAAAAAGCT-ACTTTAAAATTCT 2736
                          v   vivi v  i  ii     v v  v  --   - iii        v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr1_71989853_7   2737 TATGGGACCAAAAAAGAGCCCATATAGGGAAGACAACCGTAAACAAAAAG 2786
                              i viiv  ii  v  viv    vv  i    i v i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_71989853_7   2787 AAAAAAGCTGGAGGCATCATGCTATTTGACTTCAAA--TTATCCTATAAG 2834
                           v    i      vv   ii  viiii i      --   --   i  i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAA 246

  chr1_71989853_7   2835 GCTACAGCAACCAAAACAGCGTGGTACTGGCACAAAAACAGACACATAGA 2884
                                i  i   i    i            i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_71989853_7   2885 CCAATGGAACAGAATAGAGTACTCAGAAAGAAGACTGCACATCTACGACC 2934
                         i        i     v   viii      v  iv iii    i  i ii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_71989853_7   2935 ATCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCT 2984
                          vi    i   i    ivv  v   i v  vv            i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_71989853_7   2985 CTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATATACAGAAAATT 3034
                           v  i  i  i           v      v  ?   i  i  i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_71989853_7   3035 GAAACTGGACTCCTTCCATACAACTTATAAAAAAATTGACTCAAGATGGA 3084
                            ii     i   v  vi   v v    v       i      i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_71989853_7   3085 TTAAAGACTTAAATATAAAATCCAAATTTGTAAAAATCCTAGAAGTAAAT 3134
                          i ?    i     i   i v i   vi i     v  i      v   i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_71989853_7   3135 CTAGGCAATACAAT--TCGGGACATAGGCATGGAGAA-AATTTCAT---T 3178
                         v    ?i-  -   --   v   v v  vv i iv  -ii    v --- 
  L1M4_orf2#LINE/    547 ATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_71989853_7   3179 ATGAAAACATCAAAAGCAATTGCGACAAAAGCAAAAATTGACGCATTGGA 3228
                             ---  i        vvv  i       v      ---------i  
  L1M4_orf2#LINE/    595 ATGA---CACCAAAAGCACAAGCAACAAAAGAAAAAAT---------AGA 632

  chr1_71989853_7   3229 TATAATTACACTAAAGAGCTCAGCAAGTGGGATCTAATTAAACTAAAGAG 3278
                           -    iv   -------   v   i----  -   --     vvv v 
  L1M4_orf2#LINE/    633 TA-AATTGGACT-------TCATCAAA----AT-TAA--AAACTTTTGTG 667

  chr1_71989853_7   3279 CCCAACAAAAGAAACTATCATCAGAGTGAACAGACAGTCTACAGAATGGG 3328
                          ii--    i  v       vv i      v     ii i          
  L1M4_orf2#LINE/    668 CTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_71989853_7   3329 AGAAAATTTTTGCAATCTCTTCATCTGAATAAGAT-CTAATATCTGGGAT 3377
                                v       viiv vi      -    iv-  vi    ii i  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGA-TAAGGGACTTGTATCCAGAAT 764

  chr1_71989853_7   3378 CTACAAGGACTTTAAACAAATTTACAAGAAAAAAACACAATAAAAACACA 3427
                         v  i  i  vi ivv    v iv i  v     i   -     -------
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACA-AATAA------- 806

  chr1_71989853_7   3428 ACTCCATTAAAAAGTGAGCAAAGGACTTGAATAGACACTTCTCAAAATAA 3477
                         - i v   ?    i  i        i           i     v   v  
  L1M4_orf2#LINE/    807 -CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_71989853_7   3478 GACATTGATGCAGCCCACAAACAT-TGAAAAGAAGTGCAACATCACAGAT 3526
                           i  vv viii   v i  i  i-        v iv        ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_71989853_7   3527 CAT 3529
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.55 (56 / 22)  


3302 26.76 0.44 0.44  chr1_72065408_72071687     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_72065408_7   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_72065408_7   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_72065408_7   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_72065408_7   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_72065408_7   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_72065408_7   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_72065408_7   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_72065408_7   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_72065408_7   5276 CTATTTAATAAATGGTGCTGCGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i           v  v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_72065408_7   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_72065408_7   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_72065408_7   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_72065408_7   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_72065408_7   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_72065408_7   5576 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_72065408_7   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_72065408_7   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_72065408_7   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5775
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_72065408_7   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1809 24.56 9.31 1.77  chr1_72356007_72358926      492  1114 (1806)  C L1M4_orf2#LINE/L1   (0)   908   239  

C chr1_72356007_7   1114 ACTGCAGAATCTCAATAACATTCAAAACAGCATGGTATTGGAACAAAACC 1065
                            i  i iiiv  i   ---    i    ii     i   v i  iivi
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAA---TCAAGACAGTGTGGTACTGGCATAAGGAT 285

C chr1_72356007_7   1064 AGACACATAAAGCAATGGAACAGG--TGAGAGAACCCAGAAATAAAGCTG 1017
                              i   i v        i  i--      --i           v ii
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAG--TCCAGAAATAAACCCA 333

C chr1_72356007_7   1016 CACACCTACAACCATCTGATTTTCAACAAAGGTGACAAAAAAAAGCAATG 967
                         i   ii  iiii  vi        i    i    v   i vv vv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

C chr1_72356007_7    966 GGGAAAGGACACCCTATTCAATAAATGCTGCTGGGATAACTGACTAAGCC 917
                                i i vi  v     i     v        i     iv  -?  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA-KCC 432

C chr1_72356007_7    916 ATATGCAG--GATTGAAAGGGAACTCCTACCTTTCACTGTATACAAAAAT 869
                          i     i--  v    ivv i  i       iv   ii           
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

C chr1_72356007_7    868 CAACTCAAGATGGATTAAAGATTTAAATGTAAAACCTCTCACTATAAATA 819
                         i       i      i ?   ii         i v  vvv        - 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-A 531

C chr1_72356007_7    818 C-CTTAGAAGAAAATCTAGG---AAATACCATTCTGGACATCAGCTCAGG 773
                          -            iv    ---    -- -   vv   v ii v i   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGG 578

C chr1_72356007_7    772 CAGAGACGTC------ATGATG---AAGACAAAAGCAATTAT-GAAAAAA 733
                           iv iiv  ------    ii---  ii  v      iv v-       
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

C chr1_72356007_7    732 -------------CCTC--TAAAATTGGGAA-----GTG----------- 714
                         ------------- i  --i      iii  -----   -----------
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

C chr1_72356007_7    713 ----TCAACAGAGAAAACAGACAACCTATAGAATGGGAGAAGATATTTAC 668
                         ----    v i  vi  v        i i            i      i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

C chr1_72356007_7    667 AAACTATGCATCTGACAAATGTCTAATATCCAGAATCTATAAGCAACTCA 618
                            ii  ii      i  iv v  vi          v     iv     v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

C chr1_72356007_7    617 AACAAAT---TAACAAGCAGA--ACCAACCCCATTAAAAAAATGAGCAAA 573
                         v    v ---   i  iv   -- vi     v   ?     -  i     
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAA 827

C chr1_72356007_7    572 GGGCATGAACAGACATTTCTCAAAAGAAGACATACACACAGCCAACAAGT 523
                           iiv    i           v        i     v ii     i   i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

C chr1_72356007_7    522 ATATGAAGAAAAGCTCAATATCAGTAAGTAT 492
                          i     i i v      i    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (99 / 51)
Gap_init rate = 0.03 (20 / 670), avg. gap size = 3.45 (69 / 20)  

2193 25.57 9.96 0.96  chr1_72356007_72358926     1595  2427 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_72356007_7   1595 TGGAAAGATATCCCTTGCCAATGTATCAAAAAA-TTAGTGTTGTTAAAAT 1643
                                       v  iiv   v  iii  i -   i i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_72356007_7   1644 GTCAATACTATGCAAAAT-ATCTGCAGATTCAATGGAATACCCATCAAAA 1692
                          v       viv    v -    i         i v   v  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_72356007_7   1693 TCCCAATGGCATTTATAACAGAAATAGAAAAA--AATCCTAAAATTTGCA 1740
                              iiv  v   v vi       v  v  i--i           iii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_72356007_7   1741 TAGAACCGTAAAAGACTCCAAGTAGCCAAAACAATTCCAAGAAGAAAGAA 1790
                          i   vi i  ii   i vi i             iiii i  ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_72356007_7   1791 -AAAGTTGGAGGCATCACACTTACTGATTT-AAAATTATATTACAAAGAC 1838
                         -           vv        v ii    -    i -  i       vi
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr1_72356007_7   1839 ATAGTATTCAAAACAGTATTTTACTGGCACAAA-ATAGA-A-ACAGTCCA 1885
                          i    v    i     i vv        i  i-     - - i  vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_72356007_7   1886 GTGGAAAAGAATGAAGAGTCAAGAAACAAATCTAAACCTAGATAGTTAAC 1935
                         i     v     vi      v     i   i i v  v vv  i  i  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_72356007_7   1936 TAATTATTGAGAAAGG---CA--------CAA-----AAAGGATA----- 1964
                          i   v i  v  i  ---  --------   -----    i   -----
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_72356007_7   1965 -----TAAA--GTG------------------------------AATGAA 1977
                         -----i   --   ------------------------------      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_72356007_7   1978 ACTGTACTCTTAT-----ATCATGCACAAATATCAATTCAAAACGGATAA 2022
                         ii  v  i i  i----- i   ii     v  i  i      i    v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_72356007_7   2023 AAGACCCAAACATAAAACCAAAAACTATAACATTCATAAAAGAGAATGCA 2072
                         ?     i   ii   i v v          v i  v  i    i  iii 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_72356007_7   2073 TGGGAAAAACTTCTGGGCATTGGCCATGGAAGTGATATTTAAAAAAAAAA 2122
                         v ? v   v    vv i v    vivv  v i  i v i v i v vi -
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA- 598

  chr1_72356007_7   2123 ATACCAAAATCTCAGGCCACAAAAGCAAAAATAAATAAATAGAATTACA- 2171
                         -i       v v  i  v       v       i      v i i v  -
  L1M4_orf2#LINE/    599 -CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_72356007_7   2172 -AAAACTAAAAATCTTCTGCATAGTAAAGGAAACAATCAACAAAATGAAA 2220
                         -    i      -   i  iiivvi      v  v     v   i     
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_72356007_7   2221 CAGAGG---TATGGATTGGGAAAAGCTATTTATAAACAATATATCTGATA 2267
                         -   vi---i ii  v     i  iv     ii   iv            
  L1M4_orf2#LINE/    697 -AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_72356007_7   2268 AGGGGTTAATATTCAAAATTTATGAAGAACTCATACAATTCAATAGTGAA 2317
                             ii vi   i  i   v   i        v     i      i i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_72356007_7   2318 AA---AAATCACCCAATTAAAAAATGAGCAAA---TTTCCCGAACAGACA 2361
                           ---    v        ?       i     ---   ---   i     
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT---GAATAGACA 842

  chr1_72356007_7   2362 TTTCTCCGAATAAGACGTAAATATGGCCAAAAGATATATGAAAAAGTGCT 2411
                                i  v    ii  v v        v iii i       ii    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_72356007_7   2412 CATCATTAATCATGAC 2427
                           v   i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (131 / 79)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.79 (91 / 24)  


2900 26.03 2.22 1.67  chr1_72392130_72393824      304  1202 (493)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr1_72392130_7    304 AAAACATTCCATGCTTATAG----GAAGAATCAATATCATGTAAATGGCC 349
                           i i  i     i i  i ----     v i     ii vv i     v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_72392130_7    350 ATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGCTACC 399
                              v      v i  i  i        i  v  i  i     iv v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_72392130_7    400 ATTGAATTTCTTCTCAGAATTAGCGAAAAAAAAAAAAATACTAATG-TAA 448
                          vivivi  i  iv     -- vi  v  i----------  i  v-   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAA--ATTGACAAG----------CTGATCCTAA 142

  chr1_72392130_7    449 ATTTCATATGGAACCAAAAAAGAGTCTGTATAGCCAATACAATCCTAAGC 498
                          v           viiv  ii  vi v v        v      i i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_72392130_7    499 AAAAAGAACAAAACTGGAGGCATCATGCTACCTGAATTCAAA-----CTA 543
                           i         ii      vv   ii  v  ii v      -----   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_72392130_7    544 CAATGTTACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGATACA 593
                            v i        i   i    ii       v i iv ii i   i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_72392130_7    594 GAGACCAATGAAACTGAACAGAGACCTCAGAAATAACACCACACATTTAC 643
                         v   i     i  iv   iv    vii         vv   i       i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_72392130_7    644 CACCAATTGATCTTCAACAAACCTGACAAAAACAAGTAATGGGGAAAGGA 693
                         vii        i   i    ivv  v   i v  vvi           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_72392130_7    694 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAA 743
                          vvi  v  i  i              v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_72392130_7    744 AATAGAAACTGGACCCCTTCCTTAGACCTCATACAAAAATTAACTCAAGA 793
                         i vv   ii         v   i v   vi                  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_72392130_7    794 TGGATTAGAGACTTAAATGTAAAACCCCAAACCATAAAAATCCTAGAAGA 843
                              i ?    i         i v iv    i      v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_72392130_7    844 AAACCTAGG---AAATACCATTCAGGACATAGGCACGGGCAAAGACTTCA 890
                             v    ---    -- -   iv   v v  vvii     v ii   v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_72392130_7    891 TAACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAAAAATGG 940
                           iv  vi            vvi          vv     v  v    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_72392130_7    941 TATCTAATTAAACTAAAGAGCTTCTGCACAGTAACAGAAATTATTATCAG 990
                         v ii v  i   v v  i i   i  ii vvi  vi  v i   i vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_72392130_7    991 AGTGGACAGGCAACCTACAGATTGGGAGAAAATTTTTGCAATCTAACCAT 1040
                             i v  i     i     v           v       vii vvi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_72392130_7   1041 CAGACAAAGGTCTAGTATCCAGAATCTACAAGGAATT--TA-AATTTAA- 1086
                          v  i  i  v  v           v  i  i   i --  -  i i  -
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_72392130_7   1087 AAGAAAAAAACAAACAACCCGATCAAAAAGTGGGCAAAGGATATGAATAG 1136
                           v     i     i     i  i?    i            v       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_72392130_7   1137 ACACTTCTCAAAAGAAGATATTTATGTGGCCAACAA--ATGTGAAAAAA- 1183
                            i     v           vi vi       i  -- ii      i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_72392130_7   1184 GCTCATCATCACTGGTCAT 1202
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (131 / 100)
Gap_init rate = 0.01 (13 / 904), avg. gap size = 2.69 (35 / 13)  


2189 25.28 5.64 4.51  chr1_72468406_72470972.rev     1191  2076 (491)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr1_72468406_7   1191 CCATGCTCATGGATTGAAAGTCTCAATAAATATTA---TCCCAATTATCC 1237
                              i          i   v  i    v- i   --- vv    vv   
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATAT-TGTTAAGATGGCAATACTCC 61

  chr1_72468406_7   1238 CAAAATTGATATATATTTTGAACAAAATTCCTATCAAAATCCTAGCAATA 1287
                          v        v  i vv  v   iv   i             i   viiv
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr1_72468406_7   1288 TTTT----AGACATACACAAACTTATTCTAACTGTATGTATATAGAGATA 1333
                             ----   v  vv    i  v  i    v---  vi    i  i  i
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAA---ATTCATATGGAAATG 158

  chr1_72468406_7   1334 CAAAGGAACTTGAAGATCTAAAATAATTTTGATTAA--AGAGTAAAGTGG 1381
                            i   v iv   v v i    i   i    vv  --   ii     v 
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_72468406_7   1382 GAGGAACTATACTGCCTCATTTGAAGACTTA-TATATAGTTAAAATAACC 1430
                              vii i   v  iv    v  i     -  i v  i  v i   i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_72468406_7   1431 AGGA----ATGGT---GG---AGGGATAGACACATAGATTAATTGAACAG 1470
                          i  ----i    ---  --- i         i      i   v   i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_72468406_7   1471 AATAGAGAACCTAGAAATAG-CCC-TACAT--------AACTAACTTTTG 1510
                            v    ii i       i-   -     --------  i i i   i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_72468406_7   1511 ACAAAGATGCAAAAGCAATTCAATGGAGGAAATATGGCCATTTCAAAAGA 1560
                             i i   v  ii v         i i  iv  i i v      ----
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA---- 404

  chr1_72468406_7   1561 AATGGTGCTAAAATGGTGTTGGAGCAATTGAATATCCATAGTCAAAATAA 1610
                         ------- --        i   ii   i  i   ?   i vv     ---
  L1M4_orf2#LINE/    405 -------C--AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA--- 442

  chr1_72468406_7   1611 ATAAATAAAAAGCAACTTTACCTGAACTTCATATCTTGTAAAAAATTTGA 1660
                         --i   i  ivvvi  i---   --  i   i i v i  v    v  i 
  L1M4_orf2#LINE/    443 --GAATGAAGTTGGACC---CCT--ACCTCACACCATATACAAAAATTAA 485

  chr1_72468406_7   1661 CTCAAAATGAATCATAGATTTAAAC---AGA----AAACTATAAAAACCT 1703
                                  i    ?   ii    i---   ----           - ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTC 534

  chr1_72468406_7   1704 TTAGAAAAAAAAATCATAGA---AAATCTTCAGAAACTAGTGCCTAGTGA 1750
                               i    ---     i---        ivi v  v v i-   vv 
  L1M4_orf2#LINE/    535 TTAGAAGAAAA---CATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCA 580

  chr1_72468406_7   1751 A--ACTTTTTAGATATGATACCAAAAGCATAATTCATAAAAGGAAAAAAA 1798
                          --ii  i          i          i  viv i     i     v 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_72468406_7   1799 AGTAAACTAGACTTCACTGAAATTTAAAACCTCTG--CTTTATGAAAGAT 1846
                         ii    i i       iii     v     i i  --   i --  i  i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGAC 678

  chr1_72468406_7   1847 ATTGTTAAGAAGATGAAAAGAAAAGTTACAGACTGGATGAATATATTTAC 1896
                          i i i     ii        v  vii     v   iv   v      i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_72468406_7   1897 AA-CCACATATCTGAAAGAGGACTCAGAGCTATAATATATATCAAAAAAA 1945
                           -i  i        v ii     iiv v i v        ----  i  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA----AAGAA 774

  chr1_72468406_7   1946 ATTTCAAAACTGAACAGTAAGAAAAAATAACAATCCAATTAGAAAATGG- 1994
                         v i i v    v  i i   i  i v -  i  i      ?i       -
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACA-AATAACCCAATTWAAAAATGGG 823

  chr1_72468406_7   1995 CAAAACA----AAGAGACACTTCACTGACAAGGATACATGGATTATAAAA 2040
                             iv ----  v     i   v ii vi i    i iii  viiv  v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_72468406_7   2041 AAGCACAGAAAAAAGATGTTCAACATTACTAGTCAT 2076
                                vi    -    i       i ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (143 / 78)
Gap_init rate = 0.04 (32 / 896), avg. gap size = 2.81 (90 / 32)  


1327 26.63 10.96 3.49  chr1_72532504_72535132.rev     1374  2203 (426)    L1M4_orf2#LINE/L1       17   908 (0)  

  chr1_72532504_7   1374 GCTTAAAGGTCAGAATATTGAATATTTTTAAGATGTCAATTTTCTTCAAA 1423
                          i i vi i ii   v i v      v        v    vi  ii    
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chr1_72532504_7   1424 TTGATCTATAGATTTAACGCAATTCCAATCTAAAATGCAGCAGGCATCAC 1473
                                 i     i        i  v   v   viv    v v v i--
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT-- 114

  chr1_72532504_7   1474 TTTGTAGAAAGTTA-AAACTATTCCTAAAATGCATATCAAAATACAAAG- 1521
                             i     v v -  i  iv         v     vi    i   i -
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_72532504_7   1522 --------TA-------TAATTTTGGAAAGG-----CAAAAT--GA---- 1545
                         --------  -------i   i   i   i -----    i --  ----
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_72532504_7   1546 --ATACTTCCTA-TTTCAGGTCTTCCTATGAAGATACTGTAAGCAAGAAT 1592
                         -- i      i -     iiv   v   ii   v   v    v     vv
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_72532504_7   1593 GTGTGGTGTCT--CATTGGG-TATGACAATTAAATCAAAAGAAGAATATG 1639
                                i-  --   vi  -  -    vv  i     vi   v iv  v
  L1M4_orf2#LINE/    265 GTGTGGTA-CTGGCATAAGGATA-GACATATAGATCAATGGAATAGAATT 312

  chr1_72532504_7   1640 AAGAGTTAAGAAATTGACCTAAACACATATAGACAGTTGATACTTGACAA 1689
                         i     iv      vi   i v   iv   i v  i     vi i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_72532504_7   1690 AGGTGCT--GGCAATTCAACAGAGAATTGATAGTCATTTCAACAA----- 1732
                         i     i-- i v      ii i   vvi      v         -----
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_72532504_7   1733 ----------TTGGATACTTACA--CAAAA------AGTAACATACATAC 1764
                         ----------i      ?ii   --     ------   viv iv v   
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_72532504_7   1765 C--ACATCATA--CAAAAAT--ATATGAAATAGAACACCAACTTTAGTAT 1808
                          --   i    --       -- ivii    i  v  ?vi  i v i i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_72532504_7   1809 AAAATTGAAAACTTGGAGAATTATT-GAATAAG-TATAGAAG--AACATT 1854
                           i viv      -iv i  i v  -   v  i-i    i? --  iv  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACT-ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_72532504_7   1855 TATGATTTCAAGTTATAGAG-GATTTTAAAAATATGACA----AATCATA 1899
                         ii   ii iii    viv i- i   ivv i        ----  v  i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_72532504_7   1900 ATCCATAAAATGCAAAAA-AAATAACTTTGACATCATCAAA-TTAAAAAC 1947
                          v v i    - v     - i    v  v   v        -        
  L1M4_orf2#LINE/    612 AGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_72532504_7   1948 TTCTGCTCTTTAAAA-ATAATGTTAGGAGAATGAAAAGAGCAGTCACAGA 1996
                           i  iv   i   i- i v i i i  i i        vv vi      
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_72532504_7   1997 CTGGGA--AAATATTTATAACTAAAATA-ATAATACATTACTTTTATCTA 2043
                         v     --        ii  v v v   -v i   vivv    v    i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_72532504_7   2044 GAATATATA--GTAC-CACAAAATCCAATAATAAAACAAACAAA---CCC 2087
                                  -- v  - vi v  ii           - i     ---   
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAA-AGACAAATAACCC 809

  chr1_72532504_7   2088 ATTTTTAAAAAGTGACTGCAA--GATGTAAACAGGTACCTCAACAACAAT 2135
                          v  ?--    i  i--    --   v i  i  ii ii  vv   ----
  L1M4_orf2#LINE/    810 AATTW--AAAAATGG--GCAAAGGATTTGAATAGACATTTCTCCAA---- 851

  chr1_72532504_7   2136 AAAAACAGAA-AGATACAAAGGTAGATAATAACTGAGCTCAGAAAGAGTC 2184
                         ------    - v       -- i vi     ----  v  vi  i  --
  L1M4_orf2#LINE/    852 ------AGAAGATATACAAA--TGGCCAATAA----GCACATGAAAAG-- 887

  chr1_72532504_7   2185 ATGC--AACTTGATTAGTTTG 2203
                             --   v v ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (123 / 94)
Gap_init rate = 0.05 (44 / 892), avg. gap size = 2.73 (120 / 44)  


 423 28.46 0.00 0.00  chr1_72560439_72562470      496   618 (1414)    L1M4_orf2#LINE/L1      173   295 (613)  

  chr1_72560439_7    496 TAGGCAAAGCAATCCTAAGCAAGAAGAATAAAGCCAGAGGCATCATACCA 545
                            v    i     i i iv        i    iii    vv   i  iv
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_72560439_7    546 CTGAACTTCAAACTATCCTACAAAGCCACAGTAACCCAGACAGCATAGTA 595
                          iv  i      viv v         i       i v      ii i   
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_72560439_7    596 CGGGCACAAAAGCAGACACATAG 618
                          v    i  iiii     i    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 2.18 (24 / 11)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.00 (0 / 0)  

1631 31.95 1.12 0.16  chr1_72560439_72562470      914  1539 (493)    L1M4_orf2#LINE/L1      277   908 (0)  

  chr1_72560439_7    914 CAAAAAAACAGATACATAGACTAATGGAACAAAATAGAGGACTCAGAAAT 963
                           v  ii i   i i     ii       i i   v   iiii       
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_72560439_7    964 AAAACTGCACACCCACAACCATCTCATCTTTGACAAAGCCAATCAAAACA 1013
                            v iii   iii iiii  vi v  i  i     i vii-i   i  v
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG-CCAAGACC 375

  chr1_72560439_7   1014 AG-CAATGGTAAATGGACTACCTATTCAATAAACGGTGCTGGAATGACTG 1062
                          v-      vi  v i ivii  v     i   i        i ii    
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_72560439_7   1063 GCTAGCCATATGCAGAAAATTGAAGCTGGAATCCTACCTTTCACCAAATA 1112
                          v  ?   i     i  i v     i    vi       iv     v   
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_72560439_7   1113 TCAAAATTAACTCAAAATATATGAAACATTTAAATATAAGACCGCAAGCT 1162
                         iv                iv  v ? v ii     i     v vv  i  
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_72560439_7   1163 ATAAAAATTCTGAAACACAACCTAGGAAATACTCCTTTTGACATCAGCTT 1212
                               v ii ii  v v   v    ?ivv v  i iv    v ii v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_72560439_7   1213 -GGCAAAGAATTTTTGGCTAAGTCCCTAAAAGCAATTGGAACAAAAGCAA 1261
                         -     v iv  i  i v  v v v i       vvv v        v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_72560439_7   1262 AAATAAAGAAGTGGGACCTAATTAAACTCAAAAGCTTCTATACAGCAAAA 1311
                              i v  i v    i v  i   v i    i   i i i vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_72560439_7   1312 TAAAATACTAACAAAGCAAGCAGACAGCCTATGGAATGGAAGAATATATT 1361
                         v v v  ii  v    ii iv     i  i ii      i    v     
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_72560439_7   1362 CATTAACTATGCATCCCACAAATGCCTAATATCCAGAATGAATGGGGAAC 1411
                         iiiv  ii  ii   iv i  iv v  vi          iv  iii    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_72560439_7   1412 TTAAACAAATCAGCAAGCAAAAAACAACTG---CA--TTAAAAATGGACA 1456
                          ivv    v   ii  vv    i    v i---  -- ?        i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_72560439_7   1457 TAGGACATGAACAGATACTTCTTAAAAGAAAACATACAAGCAGCCAACAA 1506
                         v    iv    i   i i    iv      i i      iii     i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_72560439_7   1507 ACATATGAAAAAGTGCTAATCATCACAAATCAC 1539
                         i  i       ii    v v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (122 / 74)
Gap_init rate = 0.01 (5 / 632), avg. gap size = 1.60 (8 / 5)  


1807 23.14 3.31 1.65  chr1_72597988_72600389      645  1128 (1274)    L1M4_orf2#LINE/L1        6   497 (411)  

  chr1_72597988_7    645 AGACATTCCATGTCCGTAGATCAGAAGACTTACTATTAACAAGGT--TAA 692
                            i  i      i i i   ii         v    ivi   i --i  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_72597988_7    693 TATTCCCCAGGTTGACGTGTAGATTCAATAAAATCC-TAT-AAAATCTCG 740
                           i      ii    iv ii        iiv     -   -      i i
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_72597988_7    741 TCTTGCTCTTTTGAAGAAATTCATAACATGATCATAAAATTTATACC-AA 789
                         v  vv  i     v       v i  vv     v       i   iv-  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_72597988_7    790 ATTCAAGTGATCCAGACTAGCCCAAATAAT-TTGGAAAAGAAG--TGATT 836
                           v    v  i     v     v   i   -   i        --ii vv
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_72597988_7    837 TTAGAGCACTCATGATTTCCAATTTCAAAACACACTACAAAGTTACAGTA 886
                           i   v     iiv  i             vi         i       
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_72597988_7    887 GTCAAAATAATTCAATACTGGCAAAAGAATAGACATACAGATTAATGGAA 936
                         i    i i i viii        v   i         i    i       
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_72597988_7    937 GAGAATTGAGAGTACAGAATAAAATAAAGTTTATGTATTTTTAGTAAATT 986
                         v            v     ----     -iii  ii    v i  v    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAA----ATAAA-CCCATACATTTATGGTCAATT 350

  chr1_72597988_7    987 GGTTTTCAACTAGGGAACCAAGACAATGCACTAGG-AAAGAATGCTCTTT 1035
                          i     i  v    vi       v  v  v i  -       iv     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_72597988_7   1036 TCAATAAATGATA---GGACAACTGCATGCCCATTTG-AAAACAGTGAAA 1081
                             i     i i---         v  i?   iv  -    v i    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_72597988_7   1082 TTGGACTTCTTATTTC-TAGCACATACAAAGAAAT--ATTCAAAAGAGAT 1128
                               ii  - ii  -i v  i       --   -- i      vi   
  L1M4_orf2#LINE/    451 TTGGACCCCT-ACCTCACACCATATACAAA--AATTAACTCAAAATGGAT 497

Transitions / transversions = 1.85 (72 / 39)
Gap_init rate = 0.03 (15 / 492), avg. gap size = 1.60 (24 / 15)  

1390 23.78 1.11 2.44  chr1_72597988_72600389     1460  1909 (493)    L1M4_orf2#LINE/L1      465   908 (0)  

  chr1_72597988_7   1460 CACACACACACACACACACACACACACGAGAGATAACTGACCTAAATGTA 1509
                              -  i i   v v ivv  v  vi vi   v ?v            
  L1M4_orf2#LINE/    465 CACAC-CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_72597988_7   1510 AGAGCTAGAAGTTGAAAAATTGTATATGTAGATACAGGAGTAAATACTAC 1559
                                i  v vv    v iv  v v v i i i   ?      -  v 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTC 562

  chr1_72597988_7   1560 ATATGTGACGTTGCATTAGACAAAGCCTTCTTAGATGTGACACCAAAAAA 1609
                         ----     v   vi    i   v vi         i           iv
  L1M4_orf2#LINE/    563 ----GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_72597988_7   1610 AGAGATGATAAAAGGAAAAATATGTAAATTGGGCTTCCTTAAAATTCAAA 1659
                          v iiii i     i       vi        i    v i      v   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_72597988_7   1660 -CTTTTGTGCTTCAAAATAAATGATCAAGAAAGTGAGAAGATATCCTATG 1708
                         -               iv v iv             i    i v  i ii
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_72597988_7   1709 AAACTTGGAGAAA-CATTAGTAACCTATATATCATATAAGGGAATTGTAT 1757
                         i  - v       -i   v i  vii       vv        v      
  L1M4_orf2#LINE/    709 GAA-TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_72597988_7   1758 TTGAAATATATACAATA-TCTTAAAACTCAATAATAAAAATAGAAATAGC 1806
                         iiii        v iv -     v                v v     i 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_72597988_7   1807 ACAATC-AAAAATGAGTAAAGAATCTAAATAAATGTTTTTTCAAAGTAGA 1855
                         v    i-       i i    i  i i    i ii   i i     v   
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_72597988_7   1856 TTTAAAAATAGCCAAAATCCACATTAAAAAAAAAAT-CTCAACATCATTA 1904
                          v  v    i     v vv     ----i    i  -          ???
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACAT----GAAAAGATGCTCAACATCAZZZ 903

  chr1_72597988_7   1905 GCTAT 1909
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.14 (56 / 49)
Gap_init rate = 0.02 (10 / 444), avg. gap size = 1.60 (16 / 10)  


2588 26.65 2.64 2.64  chr1_72629887_72634251     2965  3872 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_72629887_7   2965 TAGAAAGATATTTCTTGCTTATGGACTGAAATAATTAATATCATTAAAAT 3014
                          i         ii v  i i     i  i  v v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_72629887_7   3015 GACCATACAACCCAAAGCAATCTATAGATTCAATGCAA-CTCTATCAAAA 3063
                          i v    vv      vii     i        i    - i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_72629887_7   3064 TTTCAATGACATTCATCACAGAAATAAATAAATAACT-ATCCTGAAACTC 3112
                          ii  iivi v  iv ii       vi i  i---  -     i   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr1_72629887_7   3113 CTATGAACCCCCCAAAAAACCCAGG-TAGCCAAAGTAACACTCAGGAAAA 3161
                         v    i vviv -  iii      i-        ii  ivi v ii  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_72629887_7   3162 AGAACAAAGTTGGAGCA-TGACAAAACCAAACTTCAAAATGTACTATAAA 3210
                                        v - v   vvv  v  i       iv     i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_72629887_7   3211 GATATAGTAACCAAAACAGCATGGTATTGTAATAAAAACAAACACAAAAA 3260
                          v  i     i   i    ii     i  vv    ii i i   i v i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_72629887_7   3261 CTAGTGCAGTGTTCCACTGGTTTACAGATAACCCAGAAATAAATCCATGT 3310
                         ii i  v i i------- iv  ---  v ii           i    ii
  L1M4_orf2#LINE/    297 TCAATGGAATA-------GAATT---GAGAGTCCAGAAATAAACCCATAC 336

  chr1_72629887_7   3311 ATTTAAACCCAATTGATTTTCAACAAATGTGCATAGAGC-TTAAATTTGG 3359
                              vivi            i    iv    vv   v -  v   vv  
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_72629887_7   3360 AATAGGACACCCTGTTTAAGAAATAGTACTGGGAAACCTGGATATCCACA 3409
                           -  i i vi  v  i  v    i  i      v v       ?     
  L1M4_orf2#LINE/    387 AA-AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_72629887_7   3410 TGCAGAGGGATGAAAACAGTTCCCTACCTCTCACTGGATACAAAAATCAA 3459
                             i i i     ivii vi         v   iiv          i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_72629887_7   3460 CTAAAAATGGATTAAACACTGAAATGTAAAATCCAGAACTATAAAATTAC 3509
                           v         i ? v  iv        i v i i          i vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_72629887_7   3510 AAGACGATGTCATAGG-GTAAATACCTCAAAACATTAGGCTAGA----GA 3554
                         v   v  viv      -      - i  ivi  v  i  i   i---- i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_72629887_7   3555 TTTAT-GGCTAAGGCCTCAAAATCACAGGCAACAGAAACAGAAATAGACA 3603
                            v -i v  v i vi     v    i      i  iv i       i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_72629887_7   3604 AACGAGGCCATTTTAAAATGTATAAAAAGTTTCTTCACAGCAAAGGA--- 3650
                           ivi i iviv i     ---      v   iv -i vv       ---
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAAT---TAAAAACTTTTGT-GCTTCAAAGGACAC 680

  chr1_72629887_7   3651 ----AAGAACAGAGTCATGATAAAACTTGTAGGATGGGAGAAAACATTTA 3696
                         ----     ---   v vi v v   iiii  i           i    i
  L1M4_orf2#LINE/    681 TATCAAGAA---AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_72629887_7   3697 CAAACTATTCATCTGACAAGGGACTAAAGTTCAGAATATAGAAGGAAGTT 3746
                             ii  vi      i        vivi i         v  i   v i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_72629887_7   3747 AAACAACTCAACAA-AAACA---AAATAAT--AATTTTAAAGTGAGCAAA 3790
                         vv         i  -   v ---      i--    ?v   i  i     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_72629887_7   3791 TAATATGAGTAGACATTTCTCAAAAGAAGGCATACAAATGGCCAATAAGT 3840
                         vi  v   i            v       ii                  i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_72629887_7   3841 ATATGGAAAAAAAGTTCAATATCAGTAACAGG 3872
                          i   -    i v i    i    ????????
  L1M4_orf2#LINE/    878 ACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (149 / 90)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.18 (48 / 22)  


1988 28.00 6.36 1.96  chr1_72798194_72801482.rev     1973  2790 (499)    L1M4_orf2#LINE/L1        1   854 (54)  

  chr1_72798194_7   1973 TGGAGAAATATAGCTTGTTCATTGGTTGGGAGAACTCAATATGGTTAAGG 2022
                             i i    vv v       v i    i   -  i     v      i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA-CTTAATATTGTTAAGA 49

  chr1_72798194_7   2023 CGTCAAT---TCTCAAATTGATCCATAGCTTCAATGCCACCCTAATTAAT 2069
                         i v    ---i i          i i  v     i  v i  iv  i  v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_72798194_7   2070 GTTCTCACACACCTTTTTGTAGAAGTTGATAAGCTGATTCTAAAATTAAT 2119
                         i i ivi vvv i      i    i    i        i        v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_72798194_7   2120 ATAGTAGTATAA-------AGAATAGCCAAAACAA-CTTCAGAAAGAA-- 2159
                           i v i ii  -------                -   v i      --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_72798194_7   2160 -CAAAGTTGGAAGACCAAGAAAGTTTAATTTGAAGACTTATTTTAAAACC 2208
                         -          i   iv v vvviii     v  i     i vi   i i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_72798194_7   2209 ACAATTACCCAGA--ATATGAGATTGACATAAAAATCAACAAATAAATCA 2256
                            i v i v   --i i  iv i  i     ii  vi   v   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_72798194_7   2257 AGGGGACAAAATAGAGA-TCTAAAAATAAACCAACTCATACATTGA---- 2301
                          v  i i i   v    -  i i         ----        v ----
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACC----CATACATTTATGGT 345

  chr1_72798194_7   2302 CAACTGATTTTTGACAAAAGGGCAAAAGTAATTCAATGAAAAAATAAGAG 2351
                            i       i     ii v  v  iiiv        iii   v  v  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_72798194_7   2352 TTGTTTCA----------TTCAG-----TGGATATTAATATTTAAAAAAA 2386
                          iv     ----------i vi -----      ?iv i  vi    i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_72798194_7   2387 AATTAACTAACTTTGATACATTGCTCTTACCACCAAGAAAAAAAA--AAA 2434
                         --- i --- v  v  iv -i i -  i  -    viv v     --  v
  L1M4_orf2#LINE/    446 ---TGA---AGTTGGACCC-CTAC-CTCAC-ACCATATACAAAAATTAAC 486

  chr1_72798194_7   2435 TCAAAATAGGTCATGGACCTAAATGTAAAACCCCAAATTATAAAACTTCA 2484
                                i i   ?i             i v iv   i         iiv
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_72798194_7   2485 ATAAGCAAACAGAGGAA-AAGTTGTTTTGATTTTTATGTAGGCAAAAATT 2533
                          v   v     v   ?i-  i iv iv   ii  vivv       vii  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_72798194_7   2534 TCATGGCTACATCACCAAAA-TATGATATTTGAAAGAAATGTCTGAAAAA 2582
                           v i v  iiv        -i ii vvvvii       viviv  v   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_72798194_7   2583 TTGGACTATAT-AAAATTGTAACATTTTGATCTTCTGAAGACACTGTTTA 2631
                                vi  -      iv  vv     vv    vi i      i iv 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_72798194_7   2632 GAAAATGAAAA---AGCCCAAAGACTGATAAATAATGTTTGCAAATTACA 2678
                             i      --- i    v   v  iv i v   i         i i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_72798194_7   2679 TATCTGATAATGGACTTTTATCCAAAATATATAAAGAACTGTTAAAGTTT 2728
                                   v      v      i               v   v ii i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_72798194_7   2729 AATTATAAG----CAAA----CTGATTATAGGAATGGAAAAAAATATTTG 2770
                            v    i----    ---- ii   ?- ii     iv   ii-     
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGG-ATTTG 834

  chr1_72798194_7   2771 ACTGGAGACTTCATCAAAGA 2790
                          v i  v i   vi      
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGA 854

Transitions / transversions = 1.45 (133 / 92)
Gap_init rate = 0.03 (25 / 854), avg. gap size = 2.72 (68 / 25)  


2811 25.73 1.95 3.78  chr1_72890736_72893128.rev      978  1902 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_72890736_7    978 TGGAAAAACATCCCATGCTCATGGAT----AGAATCAATATGATTAAAAT 1023
                               i i        i        ----   v i     vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_72890736_7   1024 GGCCATATTGACTAAAGCAATTTACAGATTCAGTGTGA-CTCTATCAAAC 1072
                            v   i vv i   vii  i          ii ii - i        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_72890736_7   1073 TACCAATGGTATTCTTCACAGAACTAAATAAAATAATAAAAAATAAAATA 1122
                          v   iiv iv  i  ii     v vi i  iv i  -------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT------------- 137

  chr1_72890736_7   1123 AACTATTTTAAAATTCACATGGAACCAAAAAAGAGCCAGAATAACCAAAG 1172
                         ------ii         i      viiv  ii  v        i     i
  L1M4_orf2#LINE/    138 ------CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_72890736_7   1173 CATTCCTAATCAAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTC 1222
                           v  i i vv  i          i      vv   ii  v  ii i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_72890736_7   1223 ACGCTATACTACAGAGATACAGTAACCAATACAGCATAGTACTGGTACAA 1272
                          viviv       i  v        i   v    ii i       i i  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_72890736_7   1273 AAACAGACACCTAGATCAATGGAACAGAATAAAGAGTGCAGAAATAGGAC 1322
                         ii i     iv             i     vi     v        iiv 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_72890736_7   1323 CATGTATCTATGACCATCTGATCTTCGACGGAGCTGACAAAAACAAGCAA 1372
                            ii  i    ii  vi    i      iii v  v   i v  vv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_72890736_7   1373 TGGGGAGAAAAC--TCCCAATTCAATAAATGTTGTTGGGATAATTGGCTA 1420
                               i i  i--  ii--     i     v  i     i  i   v  
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTT--TTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_72890736_7   1421 GCCATATGCTGAAGATTGAAGCTGGACCTGTTCCTTACACCATATACAAA 1470
                         ?   i    vi    v     i      iv v   i              
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_72890736_7   1471 AATCAAGTCAAGATGGTGTAAAGACTCAAATGTAAAACCCAAAACTATAA 1520
                            i  v    i    vvi ?    ii        i v i          
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_72890736_7   1521 AA-TCCTGAAAGACAGCCAAGG--TAATACCTTCCTGGACATAGCAACGG 1567
                           -  i ii    v i vv   --   - i    v  -  v v vivii 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTG-ACCTTGGGTTAG 577

  chr1_72890736_7   1568 GCAAAGATTTTATGACAAAAAATACCAAAAGCAATCA--CAACAAAAGCA 1615
                             v i   i- v v v vi i          --  --         --
  L1M4_orf2#LINE/    578 GCAATGGTTTC-TTAGATATGACACCAAAAGCA--CAAGCAACAAAAG-- 622

  chr1_72890736_7   1616 AAAAAATTGACAAATGAGATCTAATTAAACTTCTAATTAGAG-CTTCTGC 1664
                                v  i    vi  ii v  i   ------    i i-   i  i
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAA------ATTAAAAACTTTTGT 666

  chr1_72890736_7   1665 ACAGCAAAAGGAATTATCAACAGAATAAACAGACAACCTACAGAATGGGA 1714
                         i vv    i iv i      v i i i  v        i           
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_72890736_7   1715 TAAAATTTTTGCAAAT-----ACCTAAAAAAGGTCTAATATTCAACATCT 1759
                         v     v         ----- i  i v  i  v  vi   i  iv  v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_72890736_7   1760 ATAAGGAACCAAAACAAATTTACAAGAGAAAAACAAACAACCCCATTAAA 1809
                             i    ivvv    v iv i  v i   i     i     v   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_72890736_7   1810 AAGTGGGCAAAGTACATGCACAGACACTTCTCAAAAGAAGACATACATGC 1859
                           i         v iv  v i     i     v        i     vii
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_72890736_7   1860 AGCCAACAAGCATATGGAAAAAAAGCTCAATATCACTGATGAT 1902
                         i     i     i   -    i v      i    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (147 / 88)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.12 (53 / 17)  


2269 23.02 2.01 10.85  chr1_72900382_72902972.rev     1108  2102 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_72900382_7   1108 GGAGAGCTATCCCATGTTCATGGTTTGGAAGAATTAATATTGTTAATAAG 1157
                            i  v                v        v             v v 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_72900382_7   1158 TTTCATACTACCCAAAGTGGGCTACAGATCGAATGCAATACCTATGAAAA 1207
                         vi-v     v      v  iv        iv  i     v     v    
  L1M4_orf2#LINE/     52 GC-AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_72900382_7   1208 TGCCAGTGACAAGCTTCACAGAAATAGAAAAGC-AATACTAAAATTTATA 1256
                          v    ivi vvvi  ii       v  v    -i  v        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_72900382_7   1257 TGAAGTCACAGAGTACCCTGAATAGCCTAGG-AATTTTCAGCAAAAATAA 1305
                           i ivii  ii v    v        v ii-   i  v iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_72900382_7   1306 CAAAACTAGAGGCATCACATTATCTGATTTCAAGGTATACTACAAA-CTA 1354
                             ii i    vv     i vi ii       iiiv         -   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_72900382_7   1355 TAGTAACCAAAGCAGCATGATACTTGCAAAAAAGCAGACACATAACCCAA 1404
                         i     i   ii   ii  i    v   v  iiii     i   ivi   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_72900382_7   1405 TTGAACTGAACAGAGAACACAGAAATAAATTCACACACTTACAACCAACT 1454
                          v   iv   iv    iiv          ii  i   i   iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_72900382_7   1455 AATATTTGACAACAGCGCCAAGAACATACACTGGGGAAAGAATAGCCTCT 1504
                         i  v  i     vi i       v   v  v              i  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_72900382_7   1505 TCAATAAATGGCGCTAAAAAAGCTGGATAACCACATGTAGAAGAATGAAA 1554
                             i      i   iii v i       ?       i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_72900382_7   1555 C--GACTCTTATCTCTTACCACATACAAAAATCACATCAAAACTTATGTA 1602
                         i--   i i  i   vi    i          i vv      ivv  vv?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_72900382_7   1603 AGCCTTAAATGTAAGACCTGGAATTATGAAAATAGTAGAATAAAACATTG 1652
                           v i           v  ii  i   i   v vv     v       v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_72900382_7   1653 GAAATGTAGAAGAAATATTGGAAATGGAATGGAATAATGGAAATATTGGA 1702
                          ?---   -----   v  v ----------------  --- iv    -
  L1M4_orf2#LINE/    551 GN---GTA-----AATCTTCG----------------TG---ACCTTGG- 572

  chr1_72900382_7   1703 AGTAGTATAAGAAAATTGGAAATGGTTCAGGACATTGAT-TTACACAAGG 1751
                         ----  -  --------  v       i---- v v   - v    v ii
  L1M4_orf2#LINE/    573 ----GT-TA--------GGCAATGGTTT----CTTAGATATGACACCAAA 605

  chr1_72900382_7   1752 ATATTTTGAGTA-AGGCAACAAAAATCAAACAACAGACAAATAGAATTTC 1800
                          -------- i - i         i--   v  i   i    v i i   
  L1M4_orf2#LINE/    606 A--------GCACAAGCAACAAAAG--AAAAAATAGATAAATTGGACTTC 645

  chr1_72900382_7   1801 ATCATGCCAAAATATTTCTGAACTTCATCAGAAACTTCTGAATTTCATCA 1850
                             -----    ---------------i i      i  vii    ---
  L1M4_orf2#LINE/    646 ATCA-----AAAT---------------TAAAAACTTTTGTGCTTCA--- 672

  chr1_72900382_7   1851 TGCCAAAAATATTCTGAATAACAAAGAAACAGTGAATGGAATAAAGATAC 1900
                         ----  ii i i ------- iv      --     -------    -- 
  L1M4_orf2#LINE/    673 ----AAGGACACT-------ATCAAGAAA--GTGAA-------AAGA--C 700

  chr1_72900382_7   1901 AGCCTACAGAATGAAAGAAAAGATTT-----------ATTTGACAATAGA 1939
                          i  i        ii      v    -----------  i   i  vi  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_72900382_7   1940 TTAATGACCAAAATGTATTTTAAAAAA-TCAAACAACTCAACAG-AAAAA 1987
                         i vi iv   i   i   ---   i  -  vv         i i-     
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATAT---AAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_72900382_7   1988 AACCCCACATAATCTGTTTTAAAAAATGGACAGAGTATCTGAATAGATAT 2037
                         i  --- v    i iiv  ?     -   i  i  v  i        i  
  L1M4_orf2#LINE/    798 GAC---AAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACAT 843

  chr1_72900382_7   2038 TTATCAAAAGAAGACATGCAAATGGCTAACAGGCACTTGAAAGAATTCTT 2087
                           v  v        i  i        i  i i    v     ii  v  i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_72900382_7   2088 AACATAATTAACCAT 2102
                              v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (140 / 85)
Gap_init rate = 0.03 (30 / 907), avg. gap size = 4.27 (128 / 30)  


2592 25.82 4.66 1.37  chr1_73008220_73013877     4287  5165 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73008220_7   4287 TGGAAAAACATCCCATGCTCATGGTTAGGAAGAATCAGTATTGTGAAAAT 4336
                               i i        i      v v      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73008220_7   4337 GGCTGTACTGCCCAAGT-AATTTATAGATTCAATCCTATTCCCATCAAAC 4385
                            vi    v     i -i  i  i        iv v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73008220_7   4386 TACCC--TTGACATTCTTCACAGAATTAGAAAAATCTACTTTAAATTTCA 4433
                          -   --i  v -  i  ii     v v  v  iiiv iii    v    
  L1M4_orf2#LINE/    101 T-CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_73008220_7   4434 TATGGAACCAAAAGTGAGCCTGTACAGCCAAGACAATCCTAAGCAAAAAG 4483
                                viiv   v  v  v v i      i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_73008220_7   4484 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATTACAAAGC 4533
                                i      vv   ii  v  ii i      viv  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_73008220_7   4534 TACAGTAACCACAACAGCATGGTACTTGTACTAAAACGGTTATATAGACT 4583
                                 i  vi    ii       v i iv ii ii vi       ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_73008220_7   4584 AATGAAACAAAA--AAGAGACAGCAGAAATAACACC---ACAT------- 4621
                             i  i i  --i    v --         -   ---    -------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC--CAGAAATAA-ACCCATACATTTATGGT 345

  chr1_73008220_7   4622 ------ATCCT-GACAAAAA---CAGG------TAATGAGAAAAGAATTC 4655
                         ------  ii -     iii---  i ------i    i i       vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_73008220_7   4656 CCTATTTAATAAATGGTGCTGGGAATACTGGCTAGTCATATGCAAAAAAC 4705
                         i  v  i  i              vv     v  ?i  i        i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_73008220_7   4706 TGAAACACAACCCCTTCCTTACACCCTATACAAAAATTAACTCAAGATAT 4755
                             iivvi      v   i     v                   i  iv
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_73008220_7   4756 ATTAAAGACTTAAAAGTAAAACCCAAAACCATAAAAACTCT-AGAGGAAA 4804
                           i ?    i    v    i v i     i      -    -   i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr1_73008220_7   4805 ACCTAGGC---AATGGCATTCAGGACATAGGCAT-GGCAAAGACTTCATT 4850
                           v    ?---   -- -   iv   v v  vv -     v ii   -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TT 590

  chr1_73008220_7   4851 AAAAA--ACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGG 4898
                          i v --            vvv          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_73008220_7   4899 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAACTAGAAACAG 4948
                          ii v  i   v v  i i   i  ii vv    i  v -   vv  v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGAA 689

  chr1_73008220_7   4949 AGTGAACAAGA-AACCTATAGGATGGGAGAAAAGTTTAGCAACCTACCCA 4997
                               -    -    i i  i           vv  v    vii ivi 
  L1M4_orf2#LINE/    690 AGTGAA-AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_73008220_7   4998 TCTGGCAATGGTCTAATATCCAGAATCAACAAGGAACTTAAACAAATTTA 5047
                             ii  v  v  vi          vv i  i     ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_73008220_7   5048 CAGGAAAAGGA--AACAAACCCATCAAAAAGTGGGCAAAGGATATGAACA 5095
                         i iv    i  --  i  v  v  i?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_73008220_7   5096 GACACTTCTCAAAAGAAGACATTTATGCAGCCAACGAACATATGAAAAAA 5145
                             i     v        i  vi viii     ii i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_73008220_7   5146 AGCTCAACATCACTGATCAT 5165
                         v           ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (131 / 92)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.21 (53 / 24)  


3292 25.91 0.66 0.55  chr1_73075973_73082545     5174  6080 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73075973_7   5174 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5223
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73075973_7   5224 GGCCGTACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAAC 5273
                            vi    v     iv i  i           i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73075973_7   5274 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTC 5320
                          v   i-       i  -i     -   -- v     - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_73075973_7   5321 ATATAGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGTCAAAA 5370
                             i   viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_73075973_7   5371 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5420
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_73075973_7   5421 CTACAGTAACCAATACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5470
                                  i   v    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_73075973_7   5471 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAGC 5518
                                 i    i--    i  --        vv  ii i  i  ii i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_73075973_7   5519 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5568
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_73075973_7   5569 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA-AG 5617
                         i  v  i  i              v      v  ?   i   i i  - i
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_73075973_7   5618 CGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5667
                         i   ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_73075973_7   5668 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5717
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_73075973_7   5718 CCTAGGCATTACCATTCAAGAAATAGGCATGGGCAAGGACTTCATGTCTA 5767
                          v    ?i v viv   iv  vv v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_73075973_7   5768 AAACACCAAAAGCAACAGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5817
                         vi            vv           vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_73075973_7   5818 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5867
                           i   v i  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_73075973_7   5868 CAGGCAACCCAGAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5917
                         v  i       v i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_73075973_7   5918 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5967
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_73075973_7   5968 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAAACACTT 6017
                           i     i     v  i?    i           iv    i i   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_73075973_7   6018 CTCAAAAGAAGACATTTGTGCAGCCAAAAAACCCATGAAAAAATGCTCAC 6067
                            v        i  viiviii     v  i v        i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_73075973_7   6068 CATCACTGGCCAT 6080
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (135 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2921 24.07 5.09 0.23  chr1_73110133_73112533     1045  1908 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_73110133_7   1045 GAAAAACAGGACATGTTCGTGGATC---AGAC---ATATT--TAAGATTT 1086
                             i i vvv       i     i---    ---     --      vv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_73110133_7   1087 TAAGACTATTAAGAGTGATCTACAAA----ATGAAATCATTATCAAAATT 1132
                         i  v   viiv i v         i ---- i v    vi         i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_73110133_7   1133 TCTACAATGTTTTATGTAGAAATAGAAAAATCAATTCTAAAATTTGTATG 1182
                         i vi viiv    v  i      v  v  iiii  i        ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_73110133_7   1183 GCATCTCAAAT-ATACAGAACATCCAAAACAATCTT--AAAAGAAGAACA 1229
                          v viv   iv- iv     i v             --            
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_73110133_7   1230 AAGTTGGATGTCTTATACTTTCTTATTTCACAAATTACTGTAAATCCACA 1279
                                 v v  i i    i iv      v  v     ii   v i   
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_73110133_7   1280 ATAAATAAAATAATTCAATAATGGGATAAAAACAGACAGGTAGACCAA-- 1327
                         i   vi  i i i viii  v   v    ii i     vi    i   --
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_73110133_7   1328 --ATAGAATAGAGAGATCATAAATAAACCCTCATATATATGGTCAAATGA 1375
                         --       v     vi  v          vi i  v         v   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_73110133_7   1376 TTTTTCACAAGGGTTCCCAGTCCATTCAGTGGAGTAAAAGCAGAATTTTA 1425
                             iv        v  v  v       i   i v  i ii  vv    v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_73110133_7   1426 AACAAATGGTGTTTGGAAAACTGGATGTCTGCATACAAATAAA-AAAGGT 1474
                                    i v   v        i? ii   i    vi  -i   v 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_73110133_7   1475 GTACCCTTACCATATACTATATATGAAAATTAACTTAAAAAATAGATCAA 1524
                          v    i    vi i  i     ii          i    -- i     ?
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA--TGGATCAW 500

  chr1_73110133_7   1525 AGTCCTAAACATAATAGATATAATTGTGAAACTCTTCAAAGAAAATACAA 1574
                           v      ii   v  v  v  i i i        vi       i i i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_73110133_7   1575 GAAAAAAATTTCATGGCATTACATTTGGCAATGATATCTTGAATATGACA 1624
                          ?iv   vi   i  i v  ivi  v       i v    ii        
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_73110133_7   1625 ACAAAATCACATGCAACAAAAGAAAAAA---ATACA-----CTT-ATCAA 1665
                         v     v    v                ---   v -----   -     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_73110133_7   1666 AATTTAAAA--TTTGTGTATCAAATGATATTATCAACAGAGTGAAAAGGC 1713
                             v    --      iv     v  i i      v i         i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_73110133_7   1714 AATCCACAGAATAAGATAAACTATTTGCAAATCATATATCAGATAAGAGG 1763
                           i         ii  v   v                   v      i i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_73110133_7   1764 TTAATATCCAGGATGTATAAAAAACTCATACAGCTCAAAAACCAAAAACC 1813
                         i vi       i  i      i     v    i     v  iv    iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_73110133_7   1814 AAATAGCCCCATTAGAAAATT--CAAAAG-CTTGAATAG-C-TTTCTCCA 1858
                              i   v   ?i     v--    i -i        - -        
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_73110133_7   1859 GAAAAGACATTCAAATTGTCAAGAATCA-------AG-TGTTCAACATCA 1900
                         i i    i  v     v i   v  v  -------  -  i         
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_73110133_7   1901 CTAATCAT 1908
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.34 (117 / 87)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 2.42 (46 / 19)  


2003 26.38 4.76 6.59  chr1_73129625_73132220.rev     1192  2116 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73129625_7   1192 TGGGGAGATATTCCATTCTCACAGATAGGAAATTTCGATATTTTCAAGAT 1241
                            ii      i    vi   ii   v    ivi ii     v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73129625_7   1242 GTTTATCCCTTCCAATATGACCTATATACTCAATATAACCATGATTAAA- 1290
                          viv  v iii    vv   i   i v i    iii  i viv  i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73129625_7   1291 -----------TTT-------AAAACAATAAAATGTTTCTAAAGTTTACA 1322
                         -----------   -------   vii i  iv  v i     i  i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_73129625_7   1323 TAGAGAGACAAAAGAGCTGAAATAGACAATCCAATATTGAAGGAGAAGAA 1372
                          i  i vi   ii  v iii     v   vv    v     ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_73129625_7   1373 CAAAGCTAGAGGACTGACACTCTCCA-CTTCAAGACTTACTATAAACATA 1421
                              i i       v     ii   -i     i        i   vv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_73129625_7   1422 CAGTAATAAACACTGTATGGTACTGGAGAAAATAGAGACAAATAGATCAA 1471
                                v  v  v  i         viv  iv v     v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_73129625_7   1472 TGGAACATAATAGAGATCCCAGACATAGACCAAAATAAATATAGTCAATT 1521
                              i v   v    vi     v   i   v v i vv   i       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_73129625_7   1522 GATCTTTGAAAAAAACAGTAAAGGCAATGCAATGAAGCAAAGATAGTCTT 1571
                            i  i  v  iiii- iv   i v  v     ii v  ii        
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_73129625_7   1572 ---AA-GAATGGTGCTGAAAAAATTAGACATTCAC--GCAAAGAAAATGA 1615
                         ---  -i          ii v  i i  i ?i   --     - i     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-AGAATGA 448

  chr1_73129625_7   1616 ATCTAGACAG--ACCTTATACCATTCA-AAAAGTTAAGTCAAAACAGATC 1662
                          vi i   vv--    i i     vi -    i    v      ii    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_73129625_7   1663 ATAGACTACTGTATGTAAATG-TAAAACTATCAAACTTCTAGAAGATGAC 1711
                          ?    --  iv      iv -         v     ii       vi  
  L1M4_orf2#LINE/    499 AWAGAC--CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_73129625_7   1712 ACAGGAGAAAAACTAAGTGAGC--------AGTACTGATTTGCTTTCCAA 1753
                          i   ? v   v  vv    v --------i i v  i   -   -----
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-CTT----- 590

  chr1_73129625_7   1754 CCAGAAATGAATGACAGTATCTGTTGCTTCACATCCTCAGAAGCACAATC 1803
                         --   v    -------------------   -----  i        --
  L1M4_orf2#LINE/    591 --AGATATGA-------------------CAC-----CAAAAGCACAA-- 612

  chr1_73129625_7   1804 CATGAAATGCACAATCCATGAAAAGAAGGCATA-ATCACCTAGAGCTCCT 1852
                         ----------i   i-----       iiv   -  v vi i  vi  v 
  L1M4_orf2#LINE/    613 ----------GCAAC-----AAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_73129625_7   1853 TAAAATTAAGAAAAATCTTCT-CTTCAAAAGACAATACCAAGAGAAAAAG 1901
                         i        --   v i  v -       i    v  i     i ivi i
  L1M4_orf2#LINE/    648 CAAAATTAA--AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_73129625_7   1902 AAGACAAGCAGCAGTCTAGGAGACATTATTTGCAAAAGGCATATCTGATA 1951
                                v vi   vv i     v v          vvii          
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_73129625_7   1952 AAGAAATCTTATTCAAAATACACAAAGAACTCCTAAAACTCAACAATAAG 2001
                          i i v iv   i  i    i i         i  v       i     i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_73129625_7   2002 ACCATTAACAAACTGATTAAAAAATGAGAAAAAGACCCAAGCAGACACAG 2051
                          vv iv  i  v ii   ?       i v   i  iiii ------ i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA------ATAG 839

  chr1_73129625_7   2052 ACACCTCACTAGGGACG---TACAAGTAGCAAGTAAGCA-GTGAAAAGAT 2097
                            ii  v i ii  v ---     i i  v i      -i         
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_73129625_7   2098 TTGGGGCATCATATGTTAT 2116
                         vivvii     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (147 / 93)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 4.20 (105 / 25)  


2162 26.67 5.62 1.70  chr1_73179569_73181325      500  1264 (493)    L1M4_orf2#LINE/L1      114   908 (0)  

  chr1_73179569_7    500 TTTTATAACAGCTGACAATCCGATTATTAAATTTATTTGGAAATGTGAAT 549
                             ii iv ii      v i   iv v     i  v        ii iv
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_73179569_7    550 AACCTAGAATAGCCAAAACAATTTTTGAAAAAGAGAAACAAAGTTAGGGG 599
                         i   i                 i  -        ii         i i  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGG 212

  chr1_73179569_7    600 ACTTA-ACATACCTGATTTCAGGACTTATTCTAAAACTACAGTAATCAAA 648
                            i -  v -  ii      ii     i vi   i             i
  L1M4_orf2#LINE/    213 ACTCACACTT-CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_73179569_7    649 AGAGAATGGTGTTGGCATAAGGATAGATAATACAAATCAACTGAGCAAAA 698
                          v  vi    ii               i -  i i     iv  ii i  
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACA-TATAGATCAATGGAATAGAA 310

  chr1_73179569_7    699 TATAAAGTTCAGAAACAGATCCACA--------GCCAACTGATTTTCATC 740
                          vv i   i      i i i   i -------- i   i        iv 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr1_73179569_7    741 AAGG-TGCCCAAGTAGTTTAATAA--AAGGGGTAATAATTATAACAACTG 787
                             -    v iiivi  i   ii--  i ii  i vv  vi     v  
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_73179569_7    788 TTGCTAAAGCCATTGAATTGTTATATGGAAAA-ACTGAATCCCAACTTTT 836
                         v    iiii v i  i  v?ii i   v    - v    viivi  iii 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_73179569_7    837 ATTTCATATCATAGGCAGAAATTATCTTGAAATAAAG-ATAGACCTAAAC 885
                          ii   i i    vi  i      v  ii    ii v- ?         i
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_73179569_7    886 ACAAGAACTAAATCTATAAAAGTTGTAGAAAAAA---TAGGAAAAAAATT 932
                         ii    i     v        v iv     i   ---    ?iv   vi 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_73179569_7    933 GTGTAACATTGGTTTAGGCAAAAATT-CTTAG----GACACAAAAAGTAC 977
                         vi  i  v    v        vii  -     ----     v     i  
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_73179569_7    978 GAATCTTTTACAAAA--AACAATCTATA--TTGACATTTGA-CAAAATTA 1022
                         i iiv----      --  v   vv   --   i- i  v -        
  L1M4_orf2#LINE/    611 AAGCA----ACAAAAGAAAAAATAGATAAATTGG-ACTTCATCAAAATTA 655

  chr1_73179569_7   1023 AAAG--TACATGCTCATCAGAAGACACTATAAAGAAAATAAAAACACAAG 1070
                            i-- vii    --   i i        v      i i    v    v
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCT--TCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_73179569_7   1071 CTATATAGACTGAAAGACAATATTTGCAAAATATATATCTAATAAAGAAC 1120
                          i i --  v  ii   v            vi        i    i i  
  L1M4_orf2#LINE/    704 CCACA--GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_73179569_7   1121 TTGCCTACAGTAT-TAAACATAATTTCCTATGATGCAATAATAAAA---C 1166
                            iv v   v  -  v v v  i - i  ii iv           --- 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACT-CTTACAACTCAATAATAAAAAGAC 800

  chr1_73179569_7   1167 AATCAACCATATTAAAAACTGCACAAAAGACCTGAAGAGCCATGTCGCCA 1216
                           vi    vv   ?    v  vi    i  ii    v  v   v  v   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_73179569_7   1217 AAGAAG----------GGCTAATAAATATATGAAAAGATGCTTAACATCA 1256
                               ----------   i     ii i             i       
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_73179569_7   1257 TTTGTTTT 1264
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.94 (132 / 68)
Gap_init rate = 0.03 (24 / 795), avg. gap size = 2.33 (56 / 24)  


2933 21.91 4.66 1.76  chr1_73204744_73206527      498  1291 (493)    L1M4_orf2#LINE/L1       92   908 (0)  

  chr1_73204744_7    498 CTATCAAAATCTAAGCTGCTCTTTTCCAAAAAAATTAACAAGTTTGTTTG 547
                                    iv      -     iiiv i     i     i vi iiv
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr1_73204744_7    548 AAAATTCATATTGATAACTAAAGGATCCAGAAAACTCAAAGGAATCTTGA 597
                                    v  v vvi  i   i      v vi    iv        
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_73204744_7    598 AAATGAAGAACAAACAGATCAGAGGTGGAAGACTCACACCAGGCCGTTAC 647
                            v          --------- v    i         ivvv vi  v 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAA---------GTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_73204744_7    648 AAAACTGACTATAAAGCTATAGTGATGAAGGCAGAG--GTATTGACATTA 695
                               v    i       i   i  v   i   v --   i  i   v 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_73204744_7    696 AGACAGATGAATAAATAGATCAATGGAAGAGGAATGAAAGTACAAAAATA 745
                         i  i   i--   --             v  i v   i   v  i     
  L1M4_orf2#LINE/    282 GGATAGAC--ATA--TAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_73204744_7    746 AATCCAGGTATTTATGGGCAATTGATTTTTGACAAGTGTGCCAAGATAAT 795
                           i   vii        v           i      v         iv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_73204744_7    796 TAAATGGGAAA----TAGTATTT-CAATATATGATACTGGGAAAAGTGTG 840
                          v      i  ----    v   -   i v   i i      v  v  vi
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_73204744_7    841 TATCCACATACAAAAAAATAAAATCGGATCTCTAACTCAAACCATGTACA 890
                           ?      i     i   i  i i   i i   v    v     i    
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_73204744_7    891 AAAATTCACTCAAAATGAACTAATCAGCTAAATTGAAAAGCTAAAACTA- 939
                               v          i ii ?vv v      vv  i           -
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_73204744_7    940 AAAA-TCTCAGAGGAAAACACAACAGTAAATTTTTCTTACCTTTGATTAG 988
                             -   i   i       i iv?      i  iv v     v i    
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_73204744_7    989 GTAATGATTTATTAGATATGACACCAAAAGCATAAATGACAAAA-----A 1033
                          i    i   v                     i  iii      ----- 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_73204744_7   1034 ATGGATAGGTTAGATTTCTT---AATTAAAATATTTTGTGTTTCAAATAA 1080
                           i    ii  i  i   v ---        vv       i      vi 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_73204744_7   1081 TACCATTAA-AAAGTGAAAAGATAATCCATATAATGGCAAAAAATATTTA 1129
                         i  i  i  -            i  i   i v     v i         i
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_73204744_7   1130 TAAATAATATATCTGATA-GTGCCTAGCATGCAAATTATGTA-----TTT 1173
                         i    v            - v v  v i  v  i v   i  -----i i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_73204744_7   1174 TTATAACTAAACAACACAAAGA------------TTTTAAAATATGCAAA 1211
                            i    v  i  i v     ------------  ?v     iv     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_73204744_7   1212 TGATTTGAATACAGATTTTTCTAAAGAAGGTGCACAAATAACAAATA-GT 1260
                         v          v v    i  i       i ii      ii v    - i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_73204744_7   1261 ACATGAGAAGATATTTAACATCATTATTCTT 1291
                               i     ii i       ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (102 / 68)
Gap_init rate = 0.02 (16 / 817), avg. gap size = 3.19 (51 / 16)  


2576 27.22 2.22 2.11  chr1_73223916_73228850     3543  4442 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_73223916_7   3543 ACATCCCATGCTCATGGATGGGAAGATCTTGTATTGTGAAAATGACCATA 3592
                          i        i        v      ii vi      v  i   i v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_73223916_7   3593 TTGCGTAAAGCAACCTACAGATTCAATGTAATTCC-ATCAATATACCATC 3641
                         i v vi   vii i            i i   i  -     v  v   v 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr1_73223916_7   3642 ATCATTTTTCACAGAACTATAAAAGC-AATTCTAAAATTCACATGAAACC 3690
                         vv v     ii     v vv v    -i  i          i   i  vi
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_73223916_7   3691 AACAAAGAGCCCACATAACAAAATACTGAGTGAAAAAGCAATACTGAATG 3740
                         i-   i ii    -------i    ---- iv    --    vi    vi
  L1M4_orf2#LINE/    158 G-CAAGGGACCCA-------GAATA----GCCAAAA--CAATCTTGAAAA 193

  chr1_73223916_7   3741 AAAATAATAAATCTGGGGGTATCACATAACTGGGCTTCAAATTATACTGC 3790
                          i  v  i   vi   i  vv     ivv iviii      viv    i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_73223916_7   3791 AAGGCTGTAGTTACCAAAAATGCATGGCACTGGTATAAAAGTAGGCACAT 3840
                           i   ii   v i   i vv ii   i     i    iii   i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_73223916_7   3841 AAACCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTAAG 3890
                          i i        i     v    ii           v   v i i   v 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_73223916_7   3891 TGCCAACTGATTTTCGACAGAGCAAACAAAATCAG--AGTGGGGAAAGGA 3938
                         - i   i            ii vviv   i i  v-- i         i 
  L1M4_orf2#LINE/    344 -GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_73223916_7   3939 CACCCTAGTCAACAAATGGTACTGGGAAAACTGGCAAGCCAAATGTAGAA 3988
                         i vi  vv            i      v      vv ?   v   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_73223916_7   3989 GAATGAAACTGGATCCTTATCTCTCACCTTACACAAAAATCAACTCAAGT 4038
                                ii    i  i  i   v    v  i        i       iv
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_73223916_7   4039 CGGATCAAGAACTTAAATCCAAGACCTGAAACCATAAGCATTCT--AAAA 4086
                         i      ?ii  i     vi    v  i    i    i- i   --i  i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAG 541

  chr1_73223916_7   4087 ATAACATTGAAAAAATTTTTCTGGAAATTGGCTTCAGCAAAGAATTTATG 4136
                          v     v i?iv  v i   vv  vv    v  vi    v iv  iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_73223916_7   4137 ACTAAGACTCCAAAAGTAAAAGCAACAAAACAACAAATAAATAAAATATA 4186
                         iv  v   v       i v           v  v     i     v iv 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_73223916_7   4187 CCTAATTAAA-CTAATAACCTTATGCACAGCAAAATAAATAATCAGCAGA 4235
                          i v  i   -i   v   i  -  ii vv    iv v iv    iv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_73223916_7   4236 GTAAACAGACAATCCACAGAGTGGGAGAAAATATTTGCA---------TC 4276
                           i  v      i       i                  ---------  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_73223916_7   4277 CAACAAACGACTAGTATCCAAAATCCACAAGAAACTCAAACAAATCAGGA 4326
                         ii i  iv    v       i   vi i  ii     vv    v   iv 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_73223916_7   4327 AGGAAAAAAAAAAT--CCCA--TAAAAAAAGTGGACAAAAGATATGAATA 4372
                          vi    i v    --    -- ?     --   i    i   v      
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATA 838

  chr1_73223916_7   4373 GATATTTCTCAGAAAAATATATACAAATAGCCAACAAACGTATTTAAAAA 4422
                           i       vi  i  v          i     i  i ii  vv   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_73223916_7   4423 AGCTCAACTTCACTAATCAT 4442
                         v       v   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.02 (16 / 901), avg. gap size = 2.44 (39 / 16)  


1163 26.85 2.46 2.22  chr1_73229307_73231233      500   905 (1022)    L1M4_orf2#LINE/L1      290   696 (212)  

  chr1_73229307_7    500 ACATAGACCAGTGATACAGATTAGAGAACTCAGAAATAAATCCAAACACA 549
                          i     i  i  iv i   v v    iii          i   v   iv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_73229307_7    550 TACAGTCAACTCAGTTTTGATAAGAGCACCAAGAGAACACAATGGGGAAA 599
                           ii     i v v   i  i   i ii      vv iv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_73229307_7    600 CAAAAATCTCTTCAATAAATGGTACTTGGAAAACTGGAGTTTTCACATGC 649
                         v  v i   i     i       i  v   v       - v?i       
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA-TAKCCACATGC 438

  chr1_73229307_7    650 AAATGAATGAAATTGCACCCTTATCTAATGATATACACAGAAATCTACTG 699
                            v       i   v    i  i  v iivi   i   i    iv   v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_73229307_7    700 AAAATGAATAAAAGACCTAAATATATGA-CAAGAAACAACACAACCCCTA 748
                               i  v ?          i  v  - v -    v i v   i i  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTA 537

  chr1_73229307_7    749 GAAGAGAACATAGAGGAGAAT------GAC--TGGACATTAGCCATCGCA 790
                              i       i? vi   ------   --   i--    -----   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAG-----GCA 580

  chr1_73229307_7    791 ACAATTTATTGAATATTACACCAAA-GCTCTGGCCACGAAAGCAAAAATT 839
                          iii   v  ii    v        -  v vi  v  i    v      v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_73229307_7    840 AATAAATGAGACTATGTCAATCTAAAAAGCTTCTGCATAGCAAAGGAAAC 889
                         i      vi    vii    vv v    i   i  iiivv       v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_73229307_7    890 AGTCAACGAAATAAAA 905
                         vi    vi  i i   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAA 696

Transitions / transversions = 1.41 (62 / 44)
Gap_init rate = 0.02 (8 / 407), avg. gap size = 2.38 (19 / 8)  

 720 25.00 2.73 0.91  chr1_73229307_73231233     1215  1434 (493)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_73229307_7   1215 AAGAAAG--AAATGACACCCTACAGGTTGGGAAAAGGATGTTTGTGAACC 1262
                                --   v    v  i    iv     i  i-  i    ii  i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA-ATATTTGCAAATC 733

  chr1_73229307_7   1263 -TACAT---ATGAGGAGTTAATATCCAAAATTTATAAATAACTCATACAA 1308
                         -  i  ---  i   iii vi      i   v      v     v     
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_73229307_7   1309 TTCAATGGTGGAAAAACAAACAAACTGATTTTTTAAATGGGCAAAAAAAC 1358
                         i     ii ii   i     i  v ii   ?vv-           ii vi
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATT 832

  chr1_73229307_7   1359 TGAATAGATATGTATCCAGAGAAGACATAAACATGCACAATAGGTATGTG 1408
                                 i  v v    i      i   v v   vv     i i ii  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_73229307_7   1409 ATAAGGTGCTCAGCATCATTAGTCAT 1434
                          v   i      i     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (36 / 18)
Gap_init rate = 0.02 (5 / 224), avg. gap size = 1.60 (8 / 5)  


 284 21.92 11.64 3.42  chr1_73253081_73255726       19   164 (2482)    L1M4_orf2#LINE/L1      751   908 (0)  

  chr1_73253081_7     19 CTAGTACCTAGA---TATAAAGCA---TTACAATTTAATAATATAGAGAC 62
                           v   i i   ---       v ---      i i       v i    
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_73253081_7     63 AAGCAACCTTGTTTAAAAAAAAAATTGTCCAAAGATTTGAACATA-GTTT 111
                           ii    ivi  ?     ----- v v v  i        i v -i   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAA-----TGGGCAAAGGATTTGAATAGACATTT 845

  chr1_73253081_7    112 CACCAAAAAAGATA----AATGGTT--T--GCAAATGATAA--TGACAGA 151
                          v     i      ----     ii-- --   v    v  --  vivi 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_73253081_7    152 CATTATTAATTAT 164
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (18 / 13)
Gap_init rate = 0.05 (8 / 158), avg. gap size = 2.75 (22 / 8)  

2026 27.47 4.94 4.37  chr1_73253081_73255726     1292  2161 (485)    L1M4_orf2#LINE/L1        1   875 (33)  

  chr1_73253081_7   1292 TGGGGAGGTAAACCATGCTTAAGGATCAAAATACTCAATATTGTTA---T 1338
                            ii  i  vv     i i v    iii  v   i          --- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73253081_7   1339 --CAACTTTTCCCAAATTGTTCTTTAGATTCAACACAATCCCAAACAAAT 1386
                         --   ivi i         v   vi         i       v v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73253081_7   1387 TCCCAGCATATTCTTTTGTAGGAATTCCCAGCATATTCTTTTGTAGGAAT 1436
                                ---------  ---------  ------- i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGC---------TG---------CC-------TTTTTTGCAGAAAT 125

  chr1_73253081_7   1437 TATCAGGTTAATTCTCAAATTTATATCAAAATGCAA---------AATAG 1477
                          iv  i i i  i  v     i    vi        ---------     
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr1_73253081_7   1478 CCAATTTTTTTTTGAAAAATTACAGTATTAGAGTTGTGAG--C-----CT 1520
                             vvivv i        --iv  v i- i     -   -- -----  
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAA--GAAGAAC-AAAGTTG-GAGGACTCACACT 221

  chr1_73253081_7   1521 ACCTGATT-CGTGAATTACTCTTAAGCTGAACTAATCAAAAGAGTAAGGC 1569
                         v  ii   - ivi v     viv     iv v       i v   iv  i
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_73253081_7   1570 ATTGGCATAAAGGTAGACATAGATAGA--AAT--AACAAAATAAAATATT 1615
                          i        i i        --    --   --  i i   vi ivi i
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATA--TAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_73253081_7   1616 TA-AAATAGACCAATACATATATGGCCAATTGAATTTCAAAATAGGTGTC 1664
                         i -     i   v      v     i       v    i v vi    i 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_73253081_7   1665 AAGGTAATTTAGTTGGGAAATGATAATTGTGTCAAAACGTGGTGCTGGTA 1714
                            iiv   i i v      vi   i iv v    v vi         v 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_73253081_7   1715 AAAC-AGACATTTCTATGCAATAGAGGGAACCTTGACAGATACTTCATCT 1763
                         v   -i  i ?iivi      v   iv   vi v   vvv   i   ivi
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_73253081_7   1764 CATACACAA----TAACCTGAGCTGCAGAATAGACTGAAATATAAATGCT 1809
                             i    ----    iii iv  v vv ?    iv    i   iv   
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_73253081_7   1810 AGAGATATAAAACCTCTAGAAAAAAATACCATAGA---AAATCTTAATGA 1856
                          i iv        iii     i    ---     i---       vi   
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAA---CATAGGNGTAAATCTTCGTGA 566

  chr1_73253081_7   1857 TCTTGGTTTAGTTAATGCTTTTTTTTAATAGGACACGAAAGACATAAGTT 1906
                         i     v    vi    v   i  v-i   v     v   ii  i   iv
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTA-GATATGACACCAAAAGCACAAGCA 615

  chr1_73253081_7   1907 ATAAAGGAAAATTTGG-TAACTTGAACTTT-TCCAAATTAAAAACATTTC 1954
                          i   i     vv i -   v   i    i-  v           v   v
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_73253081_7   1955 CTCTTCAACTAATGTGATTAAGAAAATCAAAAGATAACT-ATAGACTGAG 2003
                         iv      vvi iiiv  i      i v      i   i- i   v  i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_73253081_7   2004 AGATATTTGTTTGCCAAACATATGCCCTCTAAGGAATTAGTACCCAGCAT 2053
                            v v -i     v  v     ii ivv     i i v   i    v  
  L1M4_orf2#LINE/    716 AGAAAAT-ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_73253081_7   2054 ATATAA----CCATGACAATTTAATAATACAAAGACAAGCAACCTTGCTT 2099
                               ---- iv v    i i       v        ii    ivii ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_73253081_7   2100 AAAAAAATAGCCCAAAATTTTGAATAGA-GCTTCACCAAAAAAGATAAAT 2148
                              -- i v v  iiv          -ii   v     i      v i
  L1M4_orf2#LINE/    815 AAAAA--TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_73253081_7   2149 GAGTCGTGAATGA 2161
                         i i v iv   i 
  L1M4_orf2#LINE/    863 AAATGGCCAATAA 875

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.03 (28 / 875), avg. gap size = 2.89 (81 / 28)  


3043 25.67 2.91 1.12  chr1_73259592_73263938.rev     2965  3856 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73259592_7   2965 TGGAAGAACATTCCATGCTCATGGATAGGAAGAGTCAATATCGTGAAAAT 3014
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73259592_7   3015 GGCCATACTGCCCAAGGTAATTTATAGATTTAATGCTATCCCCATCAAGC 3064
                            v     v     iv i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73259592_7   3065 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTGAAGTT 3111
                          v   -   v    i  -i     -   --- v  i  - iii i  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr1_73259592_7   3112 CATATGGAACCAAAAGAGAGCCTGCATAGCCAAGAGAATCCTAAGCAAAA 3161
                                  viiv   i  v  v v        i v    i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_73259592_7   3162 AGAACAAAGCTGGAGGCATCATGCTACCTGAATTT--AAACTATACTGCA 3209
                                  i      vv   ii  v  i-     --     -    i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCC-AATTTCAAAACT-TACTACA 244

  chr1_73259592_7   3210 AGGCTACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATA 3259
                          i          i   i    ii    i    i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_73259592_7   3260 GACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAA 3309
                           i        i    iv   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_73259592_7   3310 CCATCTGATCTTTGATGAACCTGACAAAAACAAGTAATGGGGAAACGATT 3359
                         i  vi    i  i  ii ivv  v   i v  vvi          vi  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_73259592_7   3360 CCCTATTTAATAAATGGTGCTGGGAAAACTGGGTAGCCATATGTAGAAAG 3409
                         vi  v  i  i              v      i  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_73259592_7   3410 CTGAAACTGGATCCCTTCTTTATACTTTATACCAAAAATTAACTCAAGAT 3459
                         v    ii    i    v i i i  iv     -              i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAAAT 493

  chr1_73259592_7   3460 GGATTAAAGACTTTAATGTAAGACCTAACACCATAAAAACCATAGAAGAA 3509
                             i ?    i v         v    v  i      vi v        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_73259592_7   3510 AACCTAGGCA-ATACCATTCAGGACAT--AGTCATGGGCAAAGACTTCAT 3556
                            v    ?i- v i -   iv   v --i  i --     v ii   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTT 590

  chr1_73259592_7   3557 AACTAAAACACCAAAAACAATGGCAACAATAGCCAAAATAGACAAATGGG 3606
                          iv  vi         i  vvi       v  vv        i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_73259592_7   3607 ATCTAATTAAACTAAATAGCTTCTGCACAGCAAAAGAAACTATCA----- 3651
                          ii v  i   v v  v i   i  ii vv    i  v       -----
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_73259592_7   3652 -TCA---GACAACCTACAGAATGGGAGAAAATCTGCGCAATCTACCCATC 3697
                         - v ---       i                 v vi    vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_73259592_7   3698 TGACAAAGGGCTAATATCCAGAATCTACAGAGAACTTAAACAAATTCACA 3747
                            i  i  i  vi          v  i i      ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_73259592_7   3748 AGAAAAAAACAAACAGCCCCATCAAAAAGTGGGCAAAGTATATGAATAGA 3797
                          v     i     i i   v  i?    i         v  v        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_73259592_7   3798 CACCTCTC-----AATTTATGCA----GCAAACAGACATATGAAAAAATG 3838
                           ii    -----  vv   i  ----  v  i ii  i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_73259592_7   3839 CTCATCATCACTGGTCAT 3856
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (138 / 87)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


2913 26.81 1.09 1.75  chr1_73316447_73320877.rev     3028  3941 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73316447_7   3028 TGGAAACATATCCCATGCACATGGGTCGGTAGAATTAATATTGTGAAAAT 3077
                               v          iv     i i  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73316447_7   3078 GACCATATTGTCAAAAGCAATCTACAAATTCAATGCAATTCTCATCAAAA 3127
                          i v   i vi v   vii       i      i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73316447_7   3128 TACCA-CCGTAATTCTT-CAGAGACCTAGAAAAAACAATCTTAAAATTCA 3175
                          v   - i ivv  i  -    i -- v  v  ivii   i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA--TTGACAAGCTGATCCTAAAATTCA 148

  chr1_73316447_7   3176 TATAGAACCAAAAAAGAGTCCACATAGCCAAAGCAAGACTTAGCAAA-AA 3224
                            i   viiv  ii  vi viv         i   v-   iiv   -  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAA 197

  chr1_73316447_7   3225 GAACAAATCTGGAGGCATCATATTACTTGACTTCAAAGTGTACTATAAGG 3274
                                vi      vv   i i v iii i      iiv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_73316447_7   3275 CCATCCATGGTACTAGTATAAACAGCATGGTACTGGTATAAAAATAGGCA 3324
                          i --  --   v --i - i    ii         i    ii    i  
  L1M4_orf2#LINE/    248 CTA--CA--GTAAT--CA-AGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_73316447_7   3325 CATGGACCAATGGAACAGAATAGGGAA-CCAGAAATAAATCCAAATACTT 3373
                         i  i  i        i     v i  i-           i   v i i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_73316447_7   3374 ACAGACAATTGATCCTTGACAGAGCAAACAAAAACGTAAAGTGGGGAAAA 3423
                          ii v        ii i    ii vviv   i v i vv i        i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_73316447_7   3424 GACACCCTATTCAACAAATTATGCTGGGATAATTGACAAGCCACATGTAG 3473
                         i i vi  v          vi        i  i  ivv ?       i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_73316447_7   3474 AAGAATGAAACTGGATCCTCATCTCTCACCTCATACAAAAATCAACTCAA 3523
                                  ii    i  ii i   v    vi          i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_73316447_7   3524 GATGAATCAAAGAC--AACTCTAAGGCCTGGAACCATAAAAATTCTAGAA 3571
                         i   i    ?    --  v v    iv  ii   i      v ii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_73316447_7   3572 GATAACTTTGGAAAAACTCTTCAAGACATTGGCTTAAGTGAAGACTTCAT 3621
                           v   v v  ?iv  v     iv   v    v   i ii v ii   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_73316447_7   3622 GACCAAGACCAAGAACCCAAAAGCAAATACAATAAAAACAAAAATAAATA 3671
                         -----   i- v  vv         v vi   i    iv       i   
  L1M4_orf2#LINE/    591 -----AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_73316447_7   3672 GATGGGACTTAATTAAACTAAAAAACTTCTGCACAGTAGAAGAAACAATC 3721
                         i  v      v  i   v v        i  ii vvi i i  v  v   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_73316447_7   3722 AGCAGAGTAAACAGACAACCCATGCAGTGGAAGAAACTCTTTGCAATCTA 3771
                          iv i   i  v          iiv i   i     v v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_73316447_7   3772 AACATTTGACAAAGGACTAATGTTTAGAATCTATAAGGAACTCCAACAAA 3821
                         v i  i   i  i     vi i ii     v     i      iv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_73316447_7   3822 TCAGCAAAACAAAAACAA----TCCCATCAAAAATTGGGCTAAGGACATG 3867
                            ii  v v   i    ----i  v  i?    v     v     iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_73316447_7   3868 AATAAACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAA 3917
                             i   v     v                       i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_73316447_7   3918 AAAATGTTCAACATCGCTAATAAC 3941
                           i   i        i????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (150 / 91)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.86 (26 / 14)  


 309 26.83 1.22 10.98  chr1_73331445_73335815     2661  2824 (1547)    L1M4_orf2#LINE/L1      112   259 (649)  

  chr1_73331445_7   2661 TTTTTTGCAAGAATGAAAAAA--AATCCTAAAATTTGTATGGAACCTCAA 2708
                                  ii   vi v  i--i           ii       ------
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA------ 155

  chr1_73331445_7   2709 AAACAAAACAAAACAAAAAAACAAAAACCACGCCAAAGTAGTCTTGGGCA 2758
                         ---------- vi   iii v v i  i- -      ii i     iiv 
  L1M4_orf2#LINE/    156 ----------ATGCAAGGGACCCAGAAT-A-GCCAAAACAATCTTGAAAA 193

  chr1_73331445_7   2759 AAACAAACAAAGCCGGAGACATGACATTACCTGATTTCAAAATGTATTAC 2808
                          i vi       ii    ivv v   i v  ii         iv  i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_73331445_7   2809 AAAAGTATAGTTATCA 2824
                            iv  i   v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCA 259

Transitions / transversions = 2.14 (30 / 14)
Gap_init rate = 0.03 (4 / 148), avg. gap size = 5.00 (20 / 4)  

2144 26.64 2.80 0.93  chr1_73331445_73335815     3239  3880 (491)    L1M4_orf2#LINE/L1      255   908 (0)  

  chr1_73331445_7   3239 AAACAAAACCCAGCACAGTATTGGCATAGAAACAGACATATAGACTAAAT 3288
                           v   i  --  iiii   i       iii i           ii  vv
  L1M4_orf2#LINE/    255 AATCAAGAC--AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_73331445_7   3289 ATACAGAAGAGAGAGCCCAGAAATAAATTCAAACATTTACAGTCAACTG- 3337
                         iv i    vv     i           ii  v       ii     i  -
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_73331445_7   3338 --CTGAACAAATGTGCCAGAATACAT--AATATGGAAAGGACAGTCTTTT 3383
                         --i vi    iv      ii i-   --   iv      i i        
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_73331445_7   3384 AAATAAATAATGTTGGGAAAACTGGATATCCATAGGTAGAAAAATAAAAT 3433
                         v  i    ii  i     v         ?   i v i i  i   i  i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_73331445_7   3434 TAGAACCTCATCTCACATCATATGTAAAAATCAACTCAAAATAGATT--- 3480
                          i  v  ii i      i     ii      i          i   i---
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_73331445_7   3481 ----TAAATGTAAGGCCTGAAACTAGAAAACTACTAGAAGAAAACACAGA 3526
                         ----          iv  i      v      vi            i  i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_73331445_7   3527 GA-AAATCGCCTTGACATTGATCTGGGCAAAGTTTTTTCTGAATGTGACC 3575
                         ?i-     vi v    v   ivi i     v v   i - ii  i    v
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT-TAGATATGACA 600

  chr1_73331445_7   3576 CCAAAGGCACGGGTAATGAAATAAAAGG-AGACAAGTAAGATTACATCAA 3624
                              i    ii i  ii   v    ii-   i  i vi  i v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_73331445_7   3625 A-CAAAAAGCG---GCACAGCAAAGAAAACAATCAACAGGGTGATGAAAC 3670
                          -iv    i v--- ii vv     i v  v     v ii    vi i  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_73331445_7   3671 AACCTCCAGAATGTGATAAACTATTCTCAAACCATACATCTGACAGGAGG 3720
                             iv       v  v   v    iv    i    i      i i i i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_73331445_7   3721 TTAATGTCCAAAATATATAAGGAACTCAAATAAGTCAATACCAAGAAAAC 3770
                         i vi i    i         i      vv i  v      vi  i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_73331445_7   3771 AAGTAACCTGATTAAAAAATGGGCAAAGAACCTGAATAGACATTTCCCCA 3820
                           i     ii   ?              i ii              i   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_73331445_7   3821 AATATAAGACAAAAATGGCCAACAGGTATATGAAAAAAAATGTTTAACAT 3870
                           v vi v i v          i i i i       i --  i i     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAACAT 898

  chr1_73331445_7   3871 TTTTATATTT 3880
                         iv????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.36 (118 / 50)
Gap_init rate = 0.02 (11 / 654), avg. gap size = 2.18 (24 / 11)  


 634 28.57 1.43 5.36  chr1_73373082_73375351      832  1111 (1158)    L1M4_orf2#LINE/L1      177   445 (463)  

  chr1_73373082_7    832 CAAAAAAA----AAAAAAAAAAAAAAAAGACAAAGAACACTATCATTTTT 877
                              v  ----i     i  i  v    viii  i  ----   -----
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC----TCA----- 217

  chr1_73373082_7    878 CCACTAGCTGATTTCAGGATTTAGTACTCATCTGGAGTGGTCAAGATAAT 927
                         -    vv ii      ii i   v   vv v  iv   ii      i i 
  L1M4_orf2#LINE/    218 -CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr1_73373082_7    928 ATGATATAGGCAAATAGATAGTCATATACGTCAGTGAAAGAGATTAGAGA 977
                         i  i  iv    v vi     v      vi   i  i  v   v v    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr1_73373082_7    978 GTACAGAAATAAACTCACAACATAAGTGGCCAATTTTATTTCACCAAAGG 1027
                           v           i  i -   vvi   i     vvv    iv   i  
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATA-CATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_73373082_7   1028 AATCAAACTAACTTAATTGAGAAATGATTGTCTTTTTAACAAATAGTCCT 1077
                         vii   iviv i i   v i    vi  v       i       i  v  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_73373082_7   1078 GGAGTAACTGAATACACATATGTTGTCAAAATAA 1111
                           iii     i   ?v  i   ----     v  
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATG----CAAAAGAA 445

Transitions / transversions = 1.32 (45 / 34)
Gap_init rate = 0.02 (5 / 269), avg. gap size = 3.80 (19 / 5)  

 324 23.75 14.25 9.25  chr1_73373082_73375351     1416  1815 (454)    L1M4_orf2#LINE/L1      489   908 (0)  

  chr1_73373082_7   1416 AAAAAGCATTAAAGAAAAAAATGTAAAAACCCCAAATTACAAAATTCTCA 1465
                             v v  i ?   vvv        i i iv-   i  i    i   i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTA 537

  chr1_73373082_7   1466 GAAAAATAAAAAAACTCAAGGGAAAAAAATTGTGACCTTTGCATAGGCCA 1515
                            i  ------   vi i ? v   vvv i        v vv     --
  L1M4_orf2#LINE/    538 GAAGAA------AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC-- 579

  chr1_73373082_7   1516 ACTAAATGGGCCCATTTAGTCCCATTCCTAAATGGGACTCAAAAGGCACA 1565
                         ----     -----   --------- i  i  iv   v v   i     
  L1M4_orf2#LINE/    580 ----AATGG-----TTT---------CTTAGATATGACACCAAAAGCACA 611

  chr1_73373082_7   1566 AGTCATAAAA--------------ATT---TTTTA--AAAATTGTTTAAA 1596
                           iv i    --------------   ---i  i --      iv--   
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA--AAA 659

  chr1_73373082_7   1597 CTTC-G-ACTAATTAATAGACACTATTATGAAAATGAAAAAGACA----- 1639
                            i- -i  -- i  vi        i v    i      -    -----
  L1M4_orf2#LINE/    660 CTTTTGTGCT--TCAAAGGACACTATCAAGAAAGTGAAAA-GACAACCCA 706

  chr1_73373082_7   1640 TAAACTTGAAGAAAATAT-----------ATATCTGA-------CTTTTA 1671
                         i i v v i         -----------        -------   v  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_73373082_7   1672 TTAAGA-TG-ATAAAAGTCTCCAATATCTCAATGATAAGAAAATAGCAGA 1719
                          iv   - i-     iiv   iv i v      i    i  i i i- v 
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA-ATA 805

  chr1_73373082_7   1720 A---AACTACAAAGTGGGTAAAT-ATTTGGATAGGCAACTCATGAAAGAA 1765
                          ---  i ?v   i    i   v-     i    i  vi  viv      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_73373082_7   1766 GATA----AGTAATCAGATTTAA---CATGTCAAACATGCTCAATATTTT 1808
                             ---- i iii  i---   ---    -v   v        i  iv?
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAA---TAAGCACATG-AAAAGATGCTCAACATCAZ 901

  chr1_73373082_7   1809 TAGCTAT 1815
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.49 (55 / 37)
Gap_init rate = 0.06 (25 / 420), avg. gap size = 3.76 (94 / 25)  


2558 27.96 2.10 1.77  chr1_73383598_73388839     3845  4749 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73383598_7   3845 TGCAAAAACATTCCATGCTCATGGATTGGAGGAATAAATATTGTAGAAAT 3894
                           v   i i  i     i            i  v v        vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73383598_7   3895 GATCAAACTGCCAAAAGCAATTTACAAATTCAATGCTATTTCTATCAAAT 3944
                          iiv v   v  v   vii  i    i      i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73383598_7   3945 TATGAACATTGTCTTC---ACAGAA-TTAAAAAAAAACT-ATTCTAAAAT 3989
                          viv i --  i   i---i     -  i v  i---  -  i       
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAAT 145

  chr1_73383598_7   3990 TCTAATGGAAC--CAAAGAAGTGCTCA-AATAGTCAAAGCAATTCTAAGC 4036
                           vv      v--   i i --- i  -     i    i    ii i iv
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_73383598_7   4037 AAAAAGAATAAAGCTGGAGGCATCACATTACTTGACTTCCAATTATACTA 4086
                           i     i    i      vv     i v iii i   v  viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_73383598_7   4087 TAAAGCCATAGTAATCAAAACAGCTG-GATACTAGTACAAAAACAGACAT 4135
                         i     i i         i    -  - i    i i i  ii i      
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAG-TGTGGTACTGGCATAAGGATAGACAT 291

  chr1_73383598_7   4136 ATAGACCAATAAAACAGAATAGAAAATTCAGAAATAAAGCCACACACATA 4185
                              i    ii  i     v  i i i          v   i   iv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_73383598_7   4186 CAACTATCTGATCTTTGACAAAGCTGACAAAAACAAGCAGAGTGGAAG-- 4233
                         iiiii vi    i  i     i v  v   i v  vv  iv v    i--
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_73383598_7   4234 -TGGCTTCCTATTCAATAAATGATACTGGGATAACTGGCTAGCGACATGT 4282
                         - i --  i -     i     i i      i      v  ? v     i
  L1M4_orf2#LINE/    392 ATAG--TCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_73383598_7   4283 AGAAGAATGAAGCAGGATCCCTAACTTTCAACATATGCAAAATATTAATG 4332
                          i          iv   i     v  iv  v     i     -     iv
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTAACT 487

  chr1_73383598_7   4333 CATAAGGTATTAAAGATTTAAATGTGAGACCTCAAATTACAAAAATCCTA 4382
                           v  v v  i ?   ii       i   v  v   i  i    v  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_73383598_7   4383 GAAGAAATCCTAGGAAATAATCTTCTCGACATTGGCCTTGGAAAATTATT 4432
                                v v    ?ivv       vi   v    v-  i iv   vi  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTT 586

  chr1_73383598_7   4433 T-TTGGCTGAGTCCCCAAAAGCAATTTCAAGAAAAAATAAAATTGGCAAG 4481
                          -  i v iv v v         vvvv   v    i v     v ii  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_73383598_7   4482 TGAAACCTAATTAAACAAAAGAGCTTCTGCATAATAAAGAA-ACTATCAA 4530
                          vii  i v  i   vvv  i i   i  iiivvi    i -        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_73383598_7   4531 CTGAACAAACAGATACCCTACAGA-TGGGAGAAGATATTTACAAAGTATG 4579
                         vvi iii  v   i v  i     -        i      i    vi  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_73383598_7   4580 CATCCAACAAAGATCCAACATCCAATATCTATAAGGAGCTT----AAATC 4625
                         i   ii i  i iv ivii     iv  v     i  i  i----  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_73383598_7   4626 AACAAGCAAAAAAACAAATAAGCTCATTAAAAGATGGGCAAATGACATGA 4675
                           i  -i     i        v iv   ?   i         v  iv   
  L1M4_orf2#LINE/    787 AATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_73383598_7   4676 ACAGACACTTCTCAAAAGAAACCATACAAGTGACCAACAAACATATGAAA 4725
                          i     i     v      ivi      i  i    i  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_73383598_7   4726 AAAATGGTCATCATCACCAATAAT 4749
                          i -  v   v     ????????
  L1M4_orf2#LINE/    886 AGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (156 / 93)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.67 (35 / 21)  


2354 26.65 1.38 4.99  chr1_73418687_73423637     3517  4458 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73418687_7   3517 TGGAAAAGTATTCCATGCTCACTGGAACTGGAAGAATCAATATTGTTAAA 3566
                               ii   i     i   -    -i       v i           i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCA-TGGA-TTGGAAGACTTAATATTGTTAAG 48

  chr1_73418687_7   3567 ATGGCCACAATGTCCGAAGCAATTTATAGATTCAATGCTTTGCCTACAAA 3616
                              v i v vi  i  vii  i  i        i  vv v    iv  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_73418687_7   3617 AGTACCAACATTATTTTTCACAGAAATAGGAAAACCTATTCTAAAATTCA 3666
                          i v   i vviv     ii       v iv  i iv  i          
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_73418687_7   3667 TATGGAATAATAAAAGAG-CCCA-AATAGTCAAAGCAATCCTAAACAAAA 3714
                                --  iv   i -    -     i    i     i i  v  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_73418687_7   3715 AGAGCAAAGCCAGAGGCATCACATTACCAGACTTCAAACTGTACTATAAG 3764
                            i     iii    vv     i v  vi i      viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_73418687_7   3765 GCAGTTTGAACCTACCTTAAATAAACTAAAAAAAAAAAAAAAAAAAAATG 3814
                           ----------   ---- i   v -------------  i v ivi  
  L1M4_orf2#LINE/    247 GC----------TAC----AGTAATC-------------AAGACAGTGTG 269

  chr1_73418687_7   3815 ATACTGGTACAAACACAGACACATAGACCAATGGAACACAATAGAGAACC 3864
                         i      i i  iv i     i     i        i v   v    ii 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_73418687_7   3865 CAGAAACAAAGCCACACACCTGCAACCATCTGATCTTTAACAAAGTCGAT 3914
                               i   v   i   ii iiiii  vi    i  ii    i vi vi
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_73418687_7   3915 GAAAACAAGCAATGAGGAAAGAA-ATTCCTATTCAATAACTTGTGTTGGT 3963
                         i i v  vv     i        - v  i -     i  v v   i   v
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGG 418

  chr1_73418687_7   3964 ATAACTGGCTAGCCATATGCAGAAGAATGAAAC--AACTCCCACCTTTCA 4011
                          i      v  ?   i     i         ii--i  i  i    iv  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_73418687_7   4012 ACATATACAAAAATTAACTCAAGATAGATTA-AAACTTAAATGTAAGATA 4060
                         v                     i  i   i - i  i           vv
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_73418687_7   4061 TCAAGTTATAAAAATCCTTGGTGAAAATCCAGG---AAATACCCTTC-TC 4106
                          v  ii       v  i v iv     ivi   ---    ---    - v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTG 565

  chr1_73418687_7   4107 AACACGGGCCTTAGGAAAGAATTT-TCAGCTAAGTCCACAAAAGCAATTT 4155
                          v vi   --     v  vii   - i  v  v v vv        vvvv
  L1M4_orf2#LINE/    566 ACCTTGGG--TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_73418687_7   4156 CAACAAAAACCAAAAGTGACAAGTGAGACTGAATTAAACTAAAGAGATTC 4205
                                 ivv    vv  i  i vi    vv  i   v v  i iv  i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_73418687_7   4206 TGCATGGAAAAAAGAATTACCAACAGAGTATACAGACAGACTACAGAATG 4255
                           iiivvv   iiiv i  i   v i   iv v     iv i        
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_73418687_7   4256 GGAGAAAATATTCACAAACTGTACATCTAATAAAGGGCTAATATCCAGAA 4305
                                     ii    iii  i    i    i  i  vi         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_73418687_7   4306 TCTATAAGGAACTTCATCATCAAAAAGCAAAAAAAAAAAAAAAAAAAAAA 4355
                          v     i     i----- i v  vv   v  v     i v   v  vv
  L1M4_orf2#LINE/    764 TATATAAAGAACTC-----TTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_73418687_7   4356 AAAAAAAAATTAAAAATGGGCAAAAAACATGAACAGGCACTTCTCAAAAG 4405
                         v  v----- ?             ii iv    i  i  i     v    
  L1M4_orf2#LINE/    809 CAAT-----TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_73418687_7   4406 AAGACATACAAGTGACCAACAA--ACATGTTGAAATGGTCAACATCACTA 4453
                             i      i  i    i  --     vvi i   v         ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_73418687_7   4454 ATCAT 4458
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.00 (60 / 20)  


 954 23.78 11.57 13.95  chr1_73440530_73445647      491  1415 (3703)  C L1M4_orf2#LINE/L1   (0)   908     6  

C chr1_73440530_7   1415 AGATTTTACAGATTAACAAATCAGAAGATTCATTATTTTTAA-ATACCAA 1367
                             v iv  vi  v iii  ii     i i v    v    -  iv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

C chr1_73440530_7   1366 TTTAAATTTATCTCCAG--TGACATATAGATTCAATGAAATTCTAGTCAA 1319
                          ---- i --- i   i--   iv  i        i v   i ivi    
  L1M4_orf2#LINE/     56 T----ACT---CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

C chr1_73440530_7   1318 AGTCTCAGCAATTTGTTTT--AGAAATTGATAA-----TCATAAAATTTA 1276
                          i  i    viii v    --         i  -----  v       i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

C chr1_73440530_7   1275 TATGGAAATGAAAAAGAACTAGAATAGTCAA-----TTTTAAAAAA---- 1235
                                   v  ii  v i       i   ----- i  i     ----
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr1_73440530_7   1234 -------TTAGAG---CCACCACTAATTGATTT-AAAACTTTCTAGTAAG 1196
                         -------  i   ---i   -   vviii    -       v   vv   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTTACTACAAAG 247

C chr1_73440530_7   1195 ATACAGTAAT-AAAATAGTATGTTATAGTCCT-----TACATATATAG-- 1154
                         v         -  i i   i  v  iv v v -----  v i      --
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chr1_73440530_7   1153 ----GAAACAGAATAGGAAGTTCATTAATTGACCCATGCATATATGATCA 1108
                         ---- i  i     v ii   i  vv   vi      i   v    i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

C chr1_73440530_7   1107 ATAGACATTCATCAAAGATGTCAAGAAAATCCACTGAAAAAAAAAT---C 1061
                           v  iv   iv   i i  i     vv  i  v  iii   i   --- 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chr1_73440530_7   1060 CTTTCAACACATAGTCCTCAAAACTGGAGATTATATATATATATATATAT 1011
                         i        v  i  -------i    i----------------------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGT-------GCTGGG---------------------- 418

C chr1_73440530_7   1010 ATATATGTACATATGTGTGTACACGTGTGTATGCATATATATACACTTAT 961
                         --------   -----------  -------  v   ?------------
  L1M4_orf2#LINE/    419 --------ACA-----------AC-------TGGATAK------------ 430

C chr1_73440530_7    960 ACATATTTCACATGTATACACATATACATATTTCACATATATATGTGAAC 911
                         -------i      i ------------------------------i  -
  L1M4_orf2#LINE/    431 -------CCACATGCA------------------------------AAA- 442

C chr1_73440530_7    910 TAAATGAACAATCATACAATCTTAGTTTGAATCATGTATAAAAATTAACT 861
                         -i      --i iiv  --i i  vi iiv i   i  i           
  L1M4_orf2#LINE/    443 -GAATGAA--GTTGGAC--CCCTACCTCACACCATATACAAAAATTAACT 487

C chr1_73440530_7    860 AAAAATGAATCTTAAGACTCTAAATCTAAATATAAGAATTTAAACGTTAA 811
                         v      i   v? -   -------      i     ii v    vv   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWA-GAC-------CTAAATGTAAGAGCTAAAACTATAA 529

C chr1_73440530_7    810 CACTTCCAGAACAAAATATCAGAGAAAAATTTCGTGACCTTGTGTTAAAC 761
                         v   iii    v    i  vi ? v   vi            v    ii 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

C chr1_73440530_7    760 AGGGATTTTCAAAATAAGACACAAAAAACATGAG-----ATATAAAAAAT 716
                          iv i   iiv i   v     v    i  ii  ----- v v       
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

C chr1_73440530_7    715 AACGATTAATAAGACTCCATTAATATTAAAACTTTCTAATCTTTGCAAAA 666
                          --   v   vi    i   i  v       vi  i ivv   iiv ii 
  L1M4_orf2#LINE/    630 A--GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

C chr1_73440530_7    665 CATAGTTAAGAAA-----------------------------AATATTTA 645
                           ivi i      -----------------------------       i
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

C chr1_73440530_7    644 CAAAACGTGTCTTTAATAAAGAACTTTTTTT--GAGTCAAATAAAGAAAT 597
                             v i i v i i    i i    v v i--  i - v        v 
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAAT-ATATAAAGAACT 776

C chr1_73440530_7    596 TTCACA-TTCAATATTGAAAAGAGAAGCAATCCAAT--AAAAATGGGCAA 550
                         i i   -i      v i      v  ii  i     --            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

C chr1_73440530_7    549 A-----------------------AAGGTGATATATAAATGTTTGATACA 523
                          -----------------------   iv      i     viii   vi
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

C chr1_73440530_7    522 CACATTTAAAGATGCACAATATCCTTATACAA 491
                              vv        v   i   v????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (135 / 82)
Gap_init rate = 0.04 (34 / 903), avg. gap size = 6.94 (236 / 34)  

2719 24.46 5.41 3.04  chr1_73440530_73445647     3739  4625 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73440530_7   3739 TAAAAAGATATTTCATGTTTATGTATTGGAAGAAATAATACAGTTATTAT 3788
                          ii        ii      i   v         vv     ---  i   -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA---TTGTTA- 46

  chr1_73440530_7   3789 ATCAATGTATAATAAACAATGACAATATTACCCAAAGCAATTTTCAGATT 3838
                         ------------- i ---  i     i v      vii  i v      
  L1M4_orf2#LINE/     47 -------------AGA---TGGCAATACTCCCCAAATTGATCTACAGATT 80

  chr1_73440530_7   3839 CAATGCAATCCCTATCAACATACCAATGACTTTCTTTATAGAATTTT--- 3885
                            i              v  v   iivi i  i   ii    v  v---
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA 130

  chr1_73440530_7   3886 --TTAATCTTAATATTAATATGGAATCACAAAGGATCCTGAATAGCCAAA 3933
                         --i i   i   v   v        vii   i   i  v           
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr1_73440530_7   3934 GCAATCCTGAGCAAACAGAACAAAGCTGGAGGCATTATACCACCTTACTT 3983
                         i     i   iv  iv         i      vv i i  iv  iv i  
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_73440530_7   3984 CAAAA--TATTACAAAGTTATAGTAAGCAAATCAACATGGTAATGGCATA 4031
                              --  i       i  i     v   iv  iii     v       
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_73440530_7   4032 AA-ACAGATACATAGACCAATGATATGAAATGGAGAATCCAGAGAAAAAT 4080
                          i- i   i i     i     iv  ii   v    i      i v   i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_73440530_7   4081 CCATACATTTACAGTCAACTCTTTTTTGACAAGG-CACCAATAACACAGA 4129
                                    ii     i vv    i       -ii    v v  ivv 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_73440530_7   4130 ATGAGAAAA----ACCCTCTTCAATAAATTGTGCTGGGAAAAATGGATAA 4175
                            i i   ---- vi  i     i    v         v  v      ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_73440530_7   4176 CCATATGCAGAAGAAT----------------CTCTTGCCATATACAAAA 4209
                            i     i      ----------------   vii            
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_73440530_7   4210 ATCAAATCAATATGGATTACATACTGAATCCTAAGATGTGAAACTAAGAA 4259
                           i  v    v      i ? v  iv  viv     vv i      vi  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_73440530_7   4260 ATTACCAGAAAAATCTACTAG----AAATGCACCAAGATGCTGATCTAGA 4305
                          i vii    i  vvi -   ----    - vi iv  ivi  ivi   i
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACA-TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGG 578

  chr1_73440530_7   4306 CAAAGATTTTTTTCTGTGTGTAAGACCTCAAAGGCATATGCAAGAAAAGC 4355
                            v i   i  -----ivi  v   vi    i   i v    v     v
  L1M4_orf2#LINE/    579 CAATGGTTTCTT-----AGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_73440530_7   4356 AAAACTAGGCAAAATGGGTTACATTAAGCTAAAAAGCTTCTGTACAACAA 4405
                             v   ii   v   ii v   i  iv v    i   i   i vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_73440530_7   4406 AGAAAACAAT-AAAAAAGTGAAGAGATA-CACACAGAATGAGAAAACATA 4453
                           i v  v  -  i        i   i - v         i  i  v   
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_73440530_7   4454 TTT-CAAGTTATCCATCTGATAAGGAATTAATAACCAGAATGCATAAGGA 4502
                            -   i i  vi           i i vi  v       ii    i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_73440530_7   4503 GCTC----AA-------ATAAACAAACAAA-AAAATGATTTAAAAATGGG 4540
                         i   ----  -------     v i     -  vvii   ?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_73440530_7   4541 CAAAAGATCTCAATAGACATTTCTCAAAAGAAGACATACAAATAGCCAAC 4590
                             i   i v              v        i        i     i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_73440530_7   4591 AGGTATATGGAAAAATGCTCAACATCACGAATCAT 4625
                          i i i   i   i             ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (134 / 80)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.95 (75 / 19)  


2792 24.97 2.18 3.16  chr1_73499349_73503599.rev     2844  3760 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73499349_7   2844 TGGAAAAACATTCCAAGTTCATGCATTGGAAAAGTCAATATCATTAAAAT 2893
                               i i  i   v       v       i v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73499349_7   2894 GACCACATAACCCAAATAGATCTACAGATTCAACACAATTCCTGGCAAAT 2943
                          i v i ivv       v                i    i   iv    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73499349_7   2944 TACCAG-TATCATTTTT-CATAGATTAGAAAAAGCGATCCTAAAGTTCAT 2991
                          v    - ii v     -  v i   -  v  ivi         i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chr1_73499349_7   2992 ATGGAACCAAAAGAAAAAAAAAATAGGCCA-AATAGCCAAAGCACTTCTA 3040
                               viiv   ii v----------   -          i  v ii i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC----------CCAGAATAGCCAAAACAATCTTG 189

  chr1_73499349_7   3041 AGCAAAAAGAACAAATTCAGTGGCATCACATTGCCTGACTTCAAATTATA 3090
                          iv  i         v ii v  vv     i v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_73499349_7   3091 CTACAAATCTATAGTAACTAAAACAGCATGGTCCTGGTA-AAAAATAGAC 3139
                                v   i     ii  i    ii    v    i -  ii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_73499349_7   3140 ACATACATCAGTGGAACAGCATACAGAACCCAGAAATAAAGCCACAGACA 3189
                          i   v    i     i  v  vv   ii           v   i v iv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_73499349_7   3190 TACAACCAACCAATCTTTAATAAAGTCAACAAAA--A---AATGTGGAAA 3234
                           iiii   iii  i  ii i  i viiv   i -- ---    v     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_73499349_7   3235 GAACACCCTATTTAATAAACGGTGCTCAGAAAACTGGCTAACCATATGAA 3284
                            i vi  v  i  i   i      vi  v      v  ?   i   v 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_73499349_7   3285 GAAGAATGAAACTGGACCTCTGCCTGTCACCACATACAAAAATTAACTGA 3334
                         i         ii      i  i   vv     i               v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_73499349_7   3335 AGATGGATTAAAGGCCTAAACATAAGAGCTGACACTATCAACATCATAGG 3384
                          i      i ?  i      ii        i v     v  vv  v   i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_73499349_7   3385 AGAAAACCTAGGGA-AAATACTTCTGGACATTGACCTAGGCAAAGA---A 3430
                                v    ?i-    -    vv   v   ivi       v i---v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_73499349_7   3431 TTA---ATGACAAAGACCCAAAAAAGCAAATGCAACAAAACAAAAAATAG 3477
                            ---      -----      --   v v         v         
  L1M4_orf2#LINE/    589 TTAGATATGACA-----CCAAAA--GCACAAGCAACAAAAGAAAAAATAG 631

  chr1_73499349_7   3478 ATAAATGAGACTTAATTAAAGTAAAAAGCTTCTGCACAGCAAAAGAAATA 3527
                               vi     v  i   i v    i   i  ii vv    i  v iv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_73499349_7   3528 ACCAAAAGAATAAGCAGATAACCTATAGGATAGGAGAAAACATTTGCAAA 3577
                          i   i i i i iv   i    i i  i  i        i         
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_73499349_7   3578 TTATGCCTCTGACAATTGATGGATATTCAGAATCTAGAAGGAACTC--A- 3624
                          i  iiv     i  vv  ivvi   i      v  v  i      -- -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_73499349_7   3625 AACTAAA-AGGAAAAAAATGAGCAACCCCATTAAAAATTGGGCAAAGGAC 3673
                             v  - iv     i ii ii     v   ?    v           i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_73499349_7   3674 ATAATCAGATTTTTCTCAAAAAAAAAAAAAGAAGAAATACAAGTGGCCAA 3723
                         v i vi   iv      v   ---------     v      i       
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAA---------GAAGATATACAAATGGCCAA 872

  chr1_73499349_7   3724 GAAAAATGAAAAAAAAATGCTCAACATCACTGATCAT 3760
                         v  iv i- vi    i             ????????
  L1M4_orf2#LINE/    873 TAAGCAC-ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (136 / 89)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.58 (49 / 19)  


2950 27.77 1.33 0.88  chr1_73664256_73666858.rev     1209  2112 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73664256_7   1209 TAGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 1258
                          i   ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73664256_7   1259 AGCCATACTGCCCGAGGTAATTTATAGATTCAATGCCATCCCCTTCAAGC 1308
                         i  v     v   i iv i  i  i        i  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73664256_7   1309 TACCAATGACTTTCTTCACAGAA-TTGAAAAAAAAAAATTAAAGTTTATA 1357
                          v   iivi i  i  ii     -    v  ivvi vvi    i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_73664256_7   1358 TGGAACCAAAAAAGAGCCTGCATTGACAAGACAATCCTAACCAAAAAGAA 1407
                              viiv  ii  v  v v  v v   i      i i vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_73664256_7   1408 CAAAGCTTGAGGCTTCACACCACCTGATTTCAAACTATACTACAAGGCTA 1457
                              i v    vi      iv  ii        viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_73664256_7   1458 CAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGATATATAGACCAA 1507
                               i   i    ii       v i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_73664256_7   1508 TGGAACAGAA--AAGACTCCTCTGAAATAACAACACACACCTACAACCAT 1555
                              i    --i   v   v--       vvv  i   ii  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCA--GAAATAAACCCATACATTTATGGTCAA 348

  chr1_73664256_7   1556 CTGATCTTTGACAAACCTGATAAAAACAAGAAATGGGGAAAGGATTCCCT 1605
                         i    i  i     ivv  vi  i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_73664256_7   1606 ATTTCTTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1655
                         v  ivvi              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_73664256_7   1656 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGATT 1705
                          ii    i    v   i     v              i    ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_73664256_7   1706 AAAGACTTAGATTTTAGACCTAAAACCGTAAAAGCCCTAGAAGAAAACCT 1755
                          ?    i  i  v v   v       ii     vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_73664256_7   1756 AGGCA-ATACCATTCAGGACATAGGCATGGGCAACAACTTCATGACCAAA 1804
                            ?i- v i -   iv   v v  vv i     iiii   v iivi vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_73664256_7   1805 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1854
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_73664256_7   1855 TAAA-TTAAAGGGCTCCTGCATGGCAAAAAAAAAAAACTACCACCAAAGT 1903
                         i   -     ii-  ii  iiivv    ii v ----   i  vv     
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA----CTATCAAGAAAGT 692

  chr1_73664256_7   1904 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTG 1953
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_73664256_7   1954 ACAAAGGGCTAATATCCAAAATCTACAAATAACT--TA-AATTTA-CAAG 1999
                          i  i  i  vi      i   v  i   v    --  -  i i -i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_73664256_7   2000 AAAAA---AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAAGAGACA 2046
                              ---   i     v  i?    i            v    v     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_73664256_7   2047 CTTCTCAAAAGAAGACATTTATGCAGCCAATAGACACATGAAAAAATGCT 2096
                         i     v        i  vi viii       ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_73664256_7   2097 TGTCATCACTGGTCAT 2112
                         iiv     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (151 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


1148 20.68 2.33 21.04  chr1_73685763_73687905      536  1652 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73685763_7    536 TGGAGAAATATCTCATGCTCATGGATCAAAAGAATGAATATTCTTATGAT 585
                             i i     i    i        iii    v v      v   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73685763_7    586 GTCAGTTCTCCCCAAATTGGTCTATA-ATTCTTTGACATCTCTATAAAAC 634
                          v  i v            i    i -    vvi vv   i    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73685763_7    635 ACTCAGGAGGCCTTTATTTTAAATATTCACAAACTGTTTCTCATGGAATA 684
                         v i   v-v      v  vi i v   v    i   v i  v ---   v
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA---AATT 146

  chr1_73685763_7    685 CATACAGAAATGCAAAGGACTGAGAAGAGCCAAA-CAACTTTGCAAAAGA 733
                             ii         i    iv    v       -   ii   v      
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_73685763_7    734 AAAAAAAAAGTTATAGAATTTACACTTTCTGTCTTAAAGAACCCTC-ATA 782
                          i  v   -   iv  i i i      i iivi  v  -   iiv - i 
  L1M4_orf2#LINE/    197 AGAACAAA-GTTGGAGGACTCACACTTCCCAATTTCAA-AACTTACTACA 244

  chr1_73685763_7    783 AAGGTGCAGGAATCACCTGCAGTATCAATGTCAACTTACATCAGTGAAAC 832
                            v i   v     -----  - -  i   vi---   -----  i-- 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCA-----AG-A-CAGTGTGG---TAC-----TGG--C 277

  chr1_73685763_7    833 AAGTAAAGATTAAATAAGTATGTCCATACACATATATATGTTCAAAGGAT 882
                          --   i   ------  -----------       v  ---   v   v
  L1M4_orf2#LINE/    278 A--TAAGGAT------AG-----------ACATATAGAT---CAATGGAA 305

  chr1_73685763_7    883 TTTCAAAAAAGCTGCAAAGCCCGTTCCAGGAGTCAGCAAACCTTTTGTAA 932
                          ------ i ii  - i  -----     i i ----     i-------
  L1M4_orf2#LINE/    306 T------AGAATTG-AGAG-----TCCAGAAAT----AAACCC------- 332

  chr1_73685763_7    933 CAATCCAGGTAGTAAATATATTAGACTTTTCTATCTATATAGTCTTTGCC 982
                         ---------------   i   ---------------   i   ------
  L1M4_orf2#LINE/    333 ---------------ATACATT---------------TATGGTC------ 346

  chr1_73685763_7    983 ACAACTACTCAAATCTGCTGTTGCAGCACATGGGTGGCCATAAAAAATAC 1032
                         -----------   -  v v  ----------------------------
  L1M4_orf2#LINE/    347 -----------AAT-TGATTTT---------------------------- 356

  chr1_73685763_7   1033 CTATACGAATGAGAGGGACTATATTACAATAAAACTTTATTTATAAAAAC 1082
                         -----   ------------------   ---------------------
  L1M4_orf2#LINE/    357 -----CGA------------------CAA--------------------- 362

  chr1_73685763_7   1083 AGGTGCCAGAACGGATTAGACTGGCAGGAGACAGTTTGTCAACCCCTGAG 1132
                         i       --------------------    vi  ---   ----  i 
  L1M4_orf2#LINE/    363 GGGTGCCA--------------------AGACCATT---CAA----TGGG 385

  chr1_73685763_7   1133 ACAGTCGATAAAGAAGAGACAAGTTTTTCCATTAATAGTACTAGAAAAAA 1182
                         i--------      v  v ----     v iv   i  i  i i v  -
  L1M4_orf2#LINE/    386 G--------AAAGAATAGTC----TTTTCAACAAATGGTGCTGGGACAA- 422

  chr1_73685763_7   1183 ATTGTATATCCGTTTGCAAAAAACTAAAATATAATTCATACATCACATTA 1232
                         -i  v   ?  iiv       i v i  i vvi ii v   v     ii 
  L1M4_orf2#LINE/    423 -CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_73685763_7   1233 TATGCAAAAAGTATCTCAAAATGGATTAAAAAATTAGATGTAAAACTAAA 1282
                            i      v  v            i ? i vi  i      i viv  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_73685763_7   1283 AAGTATAAATTTCT-AAAAGAAAACATAAGGAAAAACATTTGTGATCTTG 1331
                           v      vi   - i           i ?iv   iv  i    i    
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_73685763_7   1332 TTTTAAGCAAATATCTCTGATAGGTAAGACACTAAAATTA-AATCCGTAA 1380
                         vv   i    vvi i   --   i  v     i    vi -  --- i  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCT--TAGATATGACACCAAAAGCACAA---GCAA 616

  chr1_73685763_7   1381 CACAA----AAATACA---ATTGTACTTCAAAAAATTTATGAACTTTTGT 1423
                           v  ----     v ---    v      vv   v   vi         
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_73685763_7   1424 CCTTCAAACAGC-CTCTTAAAAGAATGGAA-GTCAAAC-ACAGATTAGGA 1470
                         v       vii -  v i  i i i  i  - v   v -     v i   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_73685763_7   1471 AAAAATATTTGTGAATCACCTCTATGGCAGAATACT-GTATGCAGAATAT 1519
                         i          ii     iv v v  ii iiiv   -    v        
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_73685763_7   1520 GTGTAGAATGCTCAAATCTCAACAATAGTAT------TAACCCAATTTAA 1563
                         i iv    iv  i v v     i    iv v------          ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_73685763_7   1564 AAAATAATCAA--GATTTGAGTGTAGACTTCACCAGAGAAATCATGTAGT 1611
                            - iiv   --       i iv v i   v   i    ivi  ii iv
  L1M4_orf2#LINE/    817 AAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_73685763_7   1612 TGACAAGTAAGTAC-TGAAT-GATGCTCAACATGATTCGCTAT 1652
                           i v i    i  -    v-            v ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (128 / 99)
Gap_init rate = 0.05 (49 / 908), avg. gap size = 5.33 (261 / 49)  


2586 27.81 1.99 1.77  chr1_73709770_73712313.rev     1149  2054 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73709770_7   1149 TGGAAAAACATTTCAAACTCATGGATAGAAAGAATCAATCTTGTTAAAAT 1198
                               i i  ii  vii        v i    v i   v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73709770_7   1199 GGCCATATTGTCCATAGCAATTTATAGATATAATGCTATTCCTATCAAAC 1248
                            v   i vi   v vii  i  i    vi  i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73709770_7   1249 TACCAAAGATTTTTCATCACAGAA-TTAGGAGAAACT-ATTTTAATATTC 1296
                          v   ivviii   i- ii     -  --  v  i  -  ii   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATT--GACAAGCTGATCCTAAAATTC 147

  chr1_73709770_7   1297 ACATGGAACCAAGAAAGAG-CCCATA-TACTCAAGACAATCCTAAGCAAA 1344
                          i      -- v v   i -    v -  vi   i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_73709770_7   1345 AATAACAAACCTGCAGGTATCACTTTACTTAACTTCAAAATATACTGCAA 1394
                           v      vi  v   vv    vi v ii  i       iv    i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_73709770_7   1395 GACTACTGTAGCCAAAACACAGTGTAATACTGGTACAAAAACAGACACAT 1444
                         ii    v   ii   i   --    ii      i i  ii i     i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACA--GTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_73709770_7   1445 AGACCAATGGAACAGACTAAAGATCCCAGAAATAATTCCACACACCTATA 1494
                            i        i   v vi   vi          vi   i   ii   i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_73709770_7   1495 ACCA-TCAATCTTTGACAAAGTCTACAAAAACAAGCAATGAGGAAAGGAC 1543
                         ii  - ii  i  i     i vivv   i v  vv     i      i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_73709770_7   1544 TCCCTATTCAGTATGTTGTGCTGGAATTACTGGCTAGCCGTA-ACAGAAG 1592
                         vvi  v    ii vi v       i iv     v  ?  ii -i  i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_73709770_7   1593 ATTGAAACTGTTCCGCTTCCTTATAGCGTATACAAAAATCAACTCAAGAT 1642
                          v    ii  vv  v  v   i i v i           i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_73709770_7   1643 GGTTTTAAATACATAAATGTAAAACCCAAAACTCTCAAAACCCT-AGAAG 1691
                           v i- ? v  v         i v i      v -     i  -     
  L1M4_orf2#LINE/    494 GGATC-AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAG 541

  chr1_73709770_7   1692 ATAATCTAGGAAATACCATTTTGGACTGACACCCTGGG------AAAGAT 1735
                          v  iv    ?i-  v-  i  v --    -- i    ------  v i 
  L1M4_orf2#LINE/    542 AAAACATAGGNG-TAA-ATCTTCG--TGAC--CTTGGGTTAGGCAATGGT 585

  chr1_73709770_7   1736 TTTTT-GATGTAGATACCAACAGCAATTGTGA-AAAAGCAAAAATTGAAA 1783
                           i  -   i -  i     v    vvv ii -     v      v  v 
  L1M4_orf2#LINE/    586 TTCTTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_73709770_7   1784 AATGGGACCTAATTGTAATACAGAGCTTCTGCATAGCAAAAGAAAATATC 1833
                            v    i v  iiv   vv i i   i  iiivv    i  v v    
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_73709770_7   1834 AACATAGTGTA--TACAACCTACAGAATGGAAGAAAATATTTGGAAACTA 1881
                           v v    v --v      i         i            v   ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_73709770_7   1882 GGCATTCAACAAAAGTCTCATATCCAGAATCTGTAAGGAACTTAAACAAA 1931
                         vii  iii i  ii v  ii          v i   i     ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_73709770_7   1932 TGCACAAGTATAAAACAAACAACCCCATTAAAAAGTGGGCAAAGTATATG 1981
                          vv i  vv v  i     i     v   ?    i         v  v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_73709770_7   1982 AACAGACACTTTTTTAAAGAAGACATACACATGGCCAGTAAGCATATGAA 2031
                           i     i  i ii        i     v       i      i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_73709770_7   2032 AA-ATGTTCAACATCCCTAATCAT 2054
                           -   i        v????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.48 (34 / 23)  


2100 25.30 1.78 2.51  chr1_73738967_73740642      508  1183 (493)    L1M4_orf2#LINE/L1      238   908 (0)  

  chr1_73738967_7    508 TACTACAAAACTGTAATAACAAAAAACAGCACGGTAGTGGCATTTAAAGA 557
                                  i  ii i   iv  i -   iii    v      --  i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCAT--AAGGA 284

  chr1_73738967_7    558 -AGACACTTAGAACAACAGAAAAAAAGCAAGAACTTTGAAATAAATTCAT 606
                         -     iv    v   ii   v i  vii   iiiiv        ii   
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_73738967_7    607 GTATTTATACTCAACTCATTTTTGGTCAATGAC-CCAAGAACATATATTG 655
                         ii      iv    i v     i i-   v ii-      v   vi v  
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATG 383

  chr1_73738967_7    656 GGGAAAGGACAGTCTATTCAATAAATAAATGGTGGTTGGAAAACTGAACA 705
                                i i     v     i    ----    v v   v     i i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAAT----GGTGCTGGGACAACTGGATA 429

  chr1_73738967_7    706 CTCATATGAAGAAGAATGAAACTAGACCCCTATTTCTTACCATATAAAAA 755
                         ?i  i   v i         ii i        ii  vi        v   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_73738967_7    756 AATCCACTCAAAATAGATTAAAGACTTAAATGTAAGACATGAAAGTAACA 805
                            iv         i   i ?    i           vv i   v  -i 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA-TA 528

  chr1_73738967_7    806 AAATTACTAGAATAAATCGTTGGAA-AAATGCTC-CAACTTCTTAATCTG 853
                            i vi     v   v i v  ?i-    vi  -ii  --   iivi i
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC--CTTGGGTTA 576

  chr1_73738967_7    854 GGCAAAGATTTCTTGAGTAAGACCTCAAAAGCACAGGCAGCCTAAGCAAA 903
                              v i      iii  v   vi          i   i vv   v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_73738967_7    904 AATATACAAATAGAA--TCACCAAG-CTAAAAAAGGTTATGCATGACAAA 950
                             v i    v i --   i   i-i      vvv  i   v --    
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAA 674

  chr1_73738967_7    951 GGAAAC----AACAAAATGAAGAGATAACCTACAGAATGAGAGAAAATAT 996
                            v  ----  v   i    i   i    i        i          
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_73738967_7    997 TTGCAAACTATTCAATTGACAAGGAACTAGTAACCAGTACATGTAAGCAA 1046
                                ii  vi vi   i    i   v   v    v i  i   iv  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_73738967_7   1047 CTCAGAAATCTCTACAGCAAAAAACCTCACAAATAATC-AATTTAAAAGT 1095
                            vv v v   v i ii     i----        i -    ?    i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAG----ACAAATAACCCAATTWAAAAAT 820

  chr1_73738967_7   1096 GGGCAAAATATCTGAACAGATATTTCTCAAAAGAAGACATACAAATGAGC 1145
                                iv  i    i   i       v        i         iv 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_73738967_7   1146 AACAGGTATATGGAGAAATGTTCAACATCACTAATCAT 1183
                           i i i i   i i i   i         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (109 / 58)
Gap_init rate = 0.02 (16 / 671), avg. gap size = 1.81 (29 / 16)  

 943 27.49 0.00 0.00  chr1_73738967_73740642     1300  1590 (86)    L1M4_orf2#LINE/L1      618   908 (0)  

  chr1_73738967_7   1300 AAAAACCAAAATTCACAAATGGGACCTAATTAAACTAAAGAGCTTCTGCA 1349
                             ivv     vv i    v    i v  i   v v  i i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_73738967_7   1350 CAGCAAAAGAAACTATCATCAGAGTGAAAAGGCAACCTACAGAATGGGAG 1399
                          vv    i  v       vv i         i     i            
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_73738967_7   1400 TAAATTTTTGCAATCTATCCATCTGACAAAGGGATAATATCCAGAATCTA 1449
                         v    v       vii  vi      i  i  iv vi          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_73738967_7   1450 CAAAGAACTTAAAAAAAATTACAAGGAAAAGACAAACAATCCCATCAAAA 1499
                         i        ivv v  vviv i  vi          i  i  v  i?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_73738967_7   1500 AGTGGGCAAAGAATATGAACAGACACTTCTCTAAAAAAGACACTTATGTG 1549
                          i         i  v    i     i     i   i    i ivi vi  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_73738967_7   1550 GCCAGCAAACATACGAAAAAAAGCTCATTGTCACTGGTCAT 1590
                             ii  i  i i     i v     vii   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (46 / 33)
Gap_init rate = 0.00 (0 / 291), avg. gap size = 0.00 (0 / 0)  


 329 24.27 1.94 2.91  chr1_73744167_73746708     1107  1209 (1333)    L1M4_orf2#LINE/L1        2   103 (805)  

  chr1_73744167_7   1107 GGAGATACATGCAATGTTTCTGATTTGGAAAGCTCAATATTGATAATATA 1156
                            i v i  v v     iv  iv      ii  i       v   v  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_73744167_7   1157 CCAATTCTCCCTAACTTTGATCTATATATTCAATACAAATTCCC--CCCA 1204
                         v    v     i  v  -      i v      ii   --    --i v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATT-GATCTACAGATTCAACGCAA--TCCCTATCAA 98

  chr1_73744167_7   1205 AATCC 1209
                              
  L1M4_orf2#LINE/     99 AATCC 103

Transitions / transversions = 1.08 (13 / 12)
Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.67 (5 / 3)  

1871 27.15 8.87 0.68  chr1_73744167_73746708     1317  2049 (493)    L1M4_orf2#LINE/L1      116   908 (0)  

  chr1_73744167_7   1317 TTGCTAATATTGTTATAAGCTAATTTTAAAATGTATATGAAAAGATGAAA 1366
                             vi v    -- i     i  ii      vi     i   viii ii
  L1M4_orf2#LINE/    116 TTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_73744167_7   1367 GA---AGAATGGTCAAAACAATTTTAGCAAAGAA---CATATTTGGGACA 1410
                           ---     i i         i  iiv      ---  v v    iiv 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_73744167_7   1411 CTAATATTTTCCAATTTCCAGGCTCACTATAAAGCTACAGTAATCTTGAC 1460
                           v i i  i        v ii  i    i               vv   
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_73744167_7   1461 AGTATGGTCTTTGCGAATATACAGACACATAGATTAATGGAACAGAATAG 1510
                            i    vi v  iv viv i     i      i       i     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_73744167_7   1511 ATAGCCCAGAAATAGACTGACAAAACT-TAGACAATTGAATTTTGATTAA 1559
                          v  i         i  iv i v vi - i v       v   i  iv i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_73744167_7   1560 GATATTAAAACAGTTTGATGGAGAAA----AGTATTTTCAACAAGT--TG 1603
                          i iii  i  vi  ii    i    ----   v          i --  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_73744167_7   1604 C-AAACCAATAGAATGTTCATATGCAACCTAATAAACCTCAACACATGTC 1652
                          -iiiv   iv i  i?i  i      vvv   i  vi vi  v v ii 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_73744167_7   1653 TCACACTTTACAGCAATGTTATCTCAAA-TAAATCACAGCTCTCAATGTA 1701
                               iv  i vv  vi   v      - ii    ?  vi  v      
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_73744167_7   1702 AAATTTAAACCTATAACACTAGTAAAAGAAAATGTAGGACAAAATATGCA 1751
                          i vi    v      v   vv  i       ii    ?vv    v v i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_73744167_7   1752 TGACCTTGGATTTGGCAATTAGATTT--TAAATACGATGGCAAAATCACA 1799
                                  i  v      -- i   --  i   i  iiv     v    
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAAT--GGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_73744167_7   1800 ATTCATGAAAGAAG---CTGATAAACTAGACTTCATTAAA-TTAAAA-TT 1844
                          viv ii      i---iv      i i        i   -      -i 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_73744167_7   1845 TTTGCTCTGCAAAATAAGCTATTAAGAGAAT--------AGCTTACATAT 1886
                             iv  v    iv vi    i    i i -------- i ii   v v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_73744167_7   1887 TGGGAGCAAATATTTCCCAATAACATAT-----AGAAGATTCATAT---- 1927
                               v        v v   v i    ----- iii  i ii   ----
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_73744167_7   1928 AAAATATTAAGAACATTTATAACTCAACAATAA-----CA-------CAC 1965
                           v    v      vi   i       i     -----  -------  v
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_73744167_7   1966 TT-AAAAATAG-CA---GATCTGA-TAAATACTCCTTCAAA-AAGATATA 2008
                           -      i -  ---   i   -  i i i i  i    -        
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_73744167_7   2009 CA--T-----ATAAGGATATGAAAAACATGCTTAACATTAATAGTTGT 2049
                           -- -----     v i       i-     i     i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (123 / 73)
Gap_init rate = 0.03 (26 / 793), avg. gap size = 2.69 (70 / 26)  


2334 28.88 4.53 1.70  chr1_73755774_73759775     2630  3512 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73755774_7   2630 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATAT----AACAT 2675
                               i i  i     i               v i     ----  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73755774_7   2676 GGTCATACTGCCCAAAGCAATCTGCAGATTCAACACGATTCCTATCAAAC 2725
                           iv     v      vii    i          i i  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73755774_7   2726 TGCTAACTTCATTTTTCACAGAACTAGAAAAAAAACT-ATTATAAAATTC 2774
                          v i i  v v     ii     v v  v  i---  -  iv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr1_73755774_7   2775 ATATAGAACTGAAAAAGATCCCAAGTAGCTA------TCTTAAGCTAAAA 2818
                             i   v  v  ii  i  vi i    i ------    i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_73755774_7   2819 GAACAAAGCCAGAGTCATCACATTATCTGACTTCAAGCTATAGTATAATA 2868
                                 iii   vvv     i vi ii i     iviv  v  i  vi
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_73755774_7   2869 CTATAGTAACCAAAACAGCATGGTACTAGTACAAATACAGACACATAAAT 2918
                            i     i   i    ii       i i i  iv i     i   i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_73755774_7   2919 CA---GAATACA-----GAACCCAGAAATAAAGCTGCACACCTACAGCCA 2960
                           ---     v -----  ii           v iii   ii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_73755774_7   2961 TCTGATCTTTAAGAAAGTCGGCAAAAATAAGCAACAGTAAAGGACT--CC 3008
                         vi    i  ii v  i vi v   i vi vv   ii vi  i  v --i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_73755774_7   3009 TTATTCAATGAGCAGTACTGGGATAGCTGGTTAGTCATATGCAGAAGAGT 3058
                           -     ii iii  i      i i    v  ?i  i     i    i 
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_73755774_7   3059 AAAAATAAACCCCTACCTTTCACAATATACAAAAAACAAAAAACAGTACG 3108
                         i  iv ii          iv   v           vi  -------iv i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA-------CTCA 489

  chr1_73755774_7   3109 GGATGGATTA-AGATTTAAATGTAAGACCTCAAACTGTAAGAATCCTAGA 3157
                         ii      i -   ii           v  v     i   i v  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_73755774_7   3158 AGAAGGAAACACCATCCTGGA-CATTGT--CCTTGGG------AAAGAAT 3198
                             ---    iviv?v ii - v i  --       ------  v iv 
  L1M4_orf2#LINE/    540 AGAA---AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_73755774_7   3199 TTATAACTAGGCCCTCAAAAGCAATTGCAACAAAACCAAAATT-GACAAG 3247
                          iv  iv  v v vi        vvv         vv    v -  i  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_73755774_7   3248 TGGGACCTAATTAAAATAAAGAGCTTCTGCACCAGAAAAGAAACTATGAA 3297
                          v    i v  i     v  i i   i  ii ivv   i  v     v  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_73755774_7   3298 CAGAGTAAACAGACAGCCCACAGACTGGAATAAAATATTCAAAAACTATG 3347
                         v i   i  v     i        v   i v        iiv   ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_73755774_7   3348 CATCTGA-----GGTCTAAATCCAGAATCTATAAGGGACTTAAACAAATG 3392
                         i      ----- iii iv         v     i i   ivv    v v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_73755774_7   3393 TACAAGCAGAAAACAAGTCACCCCATTAAAAAATGAGTGAAAGGCATGAA 3442
                         v i  vv i  i    i v    v   ?       i ii  i iiv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_73755774_7   3443 CAGA-ATCTTCTCAAAAGAAGACATACAAGTGCCTAACAA--ACGTGAAG 3489
                         i   -  -     v        i      i  v i  i  --  i    i
  L1M4_orf2#LINE/    837 TAGACAT-TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_73755774_7   3490 GAAAGCTCAACAAAACTAACCAT 3512
                         ii v        vv ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (159 / 93)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.89 (55 / 19)  


3125 25.45 2.46 1.12  chr1_73791053_73794651.rev     2212  3107 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73791053_7   2212 TGGAAAGATATTCCATGTTTGTAGATTGGAAGAATCAATATTGTTAATGT 2261
                                    i       ii i          v i           vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73791053_7   2262 ATCCATACCACCTAAAGCAGTCTACAGATTTAGTGCAGTCCCTATCAAAA 2311
                         iv v    iv  i   viii          i ii   i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73791053_7   2312 TACCAATGATATTCTTCACAGAAATAGA-AA----------AAATTTATG 2350
                          v   iiviiv  i  ii       v  -  ----------     i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_73791053_7   2351 TGAAACCACAAAAGAGCCAGAATAGCCAAAGGTGTCTTAAGCAAAAAGCG 2400
                           i  vii   ii  v              ivvi    i iv  i   vi
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_73791053_7   2401 CAAAACTGGAGGAGTTGCATTACCTGACTTCAAATTATACTGAAGAGCTA 2450
                             ii       v ii  i v  ii i      viv    iv i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_73791053_7   2451 TAGTAACCAAAA-GGTCGTTTTACTATCATAAAAGCAGACCCATAGACCA 2499
                         i     i   i -i  -  vv    iv     iiii    vi     i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGT-GTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_73791053_7   2500 ATGGAACCGAACGGAGAACCCAGAAACAAATCCACACACCTCCTGTGAAC 2549
                               iv   iv    ii       i   i   i   ii viv  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_73791053_7   2550 TCATTTCCG-CGGAAGTGCCAAGAACATACACTGGGGAAAAGACAGTCTC 2598
                          v    i  - iiii         v   v  v        ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_73791053_7   2599 TTTCATAACTAGTGCTGGGAAAACTGTGTATCCATAGGCAGAAGAATGAA 2648
                           iv i  v i         v     vi  ?   i v   i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_73791053_7   2649 ACTAGACCCCCTATCTCCCACCATGTACAAAAATAAAATCAAAATGGATT 2698
                         ii i      -  i   v      i         v  v           i
  L1M4_orf2#LINE/    450 GTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_73791053_7   2699 AAATAATTAAGTATAAGACCTCAAAGTATGGAACCACTACAAAAAAAAAA 2748
                          ? v vi   i i     v  v   v   ii   i-  -i i  i    v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CT-TAGAAGAAAAC 546

  chr1_73791053_7   2749 ATAGCAA-AAATCTCCAGGATGTTGGTGGTCTGGGCAGT--TTTCTT-GA 2794
                             v?i-      i iv  iv    --  - i    i --      -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGG--GT-TAGGCAATGGTTTCTTAGA 593

  chr1_73791053_7   2795 CCAATGTC-CCACGAGCACCGGCAGCCAAAGCAAAAATGGACAAATGGGA 2843
                         i--   v -   vi     vi   i v    v      i  i    v   
  L1M4_orf2#LINE/    594 T--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_73791053_7   2844 TCACATCAAG-TTAAAAAGCTTGTGCACAGCAAAGGATACAATCAAAAAA 2892
                         iiv      i-       -   v  ii vv       i  v     i   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_73791053_7   2893 GTAAAGAGACAACACAGAGAATGGGAGAAAATATTTGCAAACTACTCCTC 2942
                           i  i       v  v                        ii iviv  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_73791053_7   2943 TGACAAGGAATCAATAACCAGAATATATAAAGAGCTCAAACAACTCTATC 2992
                            i    i iivi  v                i   vv       v  v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_73791053_7   2993 AGAAAAAAATTAATAATTTGAT-AAAAAATGGGCAAAATATTTGAATACA 3041
                          v     i iv     iiii  -?             iv         v 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_73791053_7   3042 AATTTCTC-AAAGAAAACATACAAACTGCAAACAGGCGTATGAAAAGGTG 3090
                         v       -      i i       iv  v  i i  ii        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_73791053_7   3091 C-CAACATCATTGATCAT 3107
                          -        ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (145 / 79)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.60 (32 / 20)  


2320 21.98 1.36 13.04  chr1_73836799_73839375     1057  2084 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_73836799_7   1057 TGGAAACACATTCCATGCTCATGAATGAGAAGAATCAATATTGTTAAAAT 1106
                               v i  i     i     i  vi     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_73836799_7   1107 GGCCATACTGGCCAAAGCAATTTACAGATTCAATGTTATTTATATCAAAC 1156
                            v     vv     vii  i           i iv  iiv       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_73836799_7   1157 TACCAATGACATTTTTCACAGAATTAGAAAAAGAAGATTCTAAAATTTAT 1206
                          v   iivi v     ii     v v  v  - vv   i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_73836799_7   1207 ATGAAACCAAAAAAGAGCCACAACAGTGAAATCAAACCTATGAAAAAAGA 1256
                            i  viiv  ii  v   v  i  iv   v   v i ivi   i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_73836799_7   1257 ACAAAGCAGGAGCCATCACACTACCCAACTTCAAACTATGCTACAAGGCT 1306
                               iv    vvv       v     i      viv i      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_73836799_7   1307 ACAGTAACCAAAACAGCATGGCACTGGTACAAA-ACAAACAAATAGACCA 1355
                                i   i    ii   i     i i  i- i i   v     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_73836799_7   1356 ATGGAACAGAATAGAGAACCCAGAAATAAAGTCATACACCTACAACCATC 1405
                               i     v    ii           vi      ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_73836799_7   1406 TGATTTTTGACAAAGTTAACCAAAACAAG-CAATGGGGAAAAGAATC-CC 1453
                                i     i v i-    i  v v-           -    v-i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAA-GAATAGTC 397

  chr1_73836799_7   1454 TATTCAATAAATGGTGCTGGGATAAGTGACTAGCCACATGCGTAAGATTG 1503
                          v     i              i  v  iv  ?        iv    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_73836799_7   1504 AAAATGGACCCCTTCTTTTCACCATATATAAAAATCAAATTAAGATGAAT 1553
                           iv         v i iv         i      i  v i  i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_73836799_7   1554 GAAAGACTTAAAGATAAAACCTTAAACTATAAAATTCATAGAAGATAACA 1603
                         v ?    i    vi   i v  v           i  v       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_73836799_7   1604 TTGGAAATGACATTTGATGAATAAAAGACTTAAAGATGAAACCTTAAACT 1653
                          v  ?i----------- i   ------   -----i vi     iiii 
  L1M4_orf2#LINE/    548 TAGGNG-----------TAAAT------CTT-----CGTGACCTTGGGTT 575

  chr1_73836799_7   1654 ATAAAACCATAGAAGATAACATTGGAAATGACATTTTGGACCTAGGTCCT 1703
                          ----------------------  v    i---   --- i   i ---
  L1M4_orf2#LINE/    576 A----------------------GGCAATGG---TTT---CTTAGAT--- 594

  chr1_73836799_7   1704 GGCAAAGGTTACATGATGATGATACCAAAAGCGATTGCAACACAAATAAA 1753
                         ------------------    i         ivvv      v  iv   
  L1M4_orf2#LINE/    595 ------------------ATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_73836799_7   1754 AATTGACAAATAGAAACTGATTGCAGAGCTCCTGGGAGGCAAAATAAAAC 1803
                            v  i    v i -------------  i -----------  -----
  L1M4_orf2#LINE/    627 AATAGATAAATTGGA-------------CTTC-----------AT----- 647

  chr1_73836799_7   1804 AAAACAAAAACAAAATAAAAAAAAACCCAAACCAACAACCAAGAACAACA 1853
                         ----------      v     --- iivvii--i vv v   i   ---
  L1M4_orf2#LINE/    648 ----------CAAAATTAAAAA---CTTTTGT--GCTTCAAAGGACA--- 679

  chr1_73836799_7   1854 CAACAAAACCCTATTAAGAGAGTAAATGGGCAACCTACAGAATTGGAGAA 1903
                         ----------    i    i   i  vi i     i       v      
  L1M4_orf2#LINE/    680 ----------CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_73836799_7   1904 AATATTTGCAAACTATGCATCCAACAAAGGCCTAATGTCTACAATCTAAA 1953
                                     ii  ii   ii i  i  v  vi i  i v   v  v 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_73836799_7   1954 AGGAACTT----AAATCAACAAGCAAAAAGCAAA---CCTCATT-AAAAA 1995
                          i     i----  v    i  vv    ii    ---  iv   -     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_73836799_7   1996 TGGGCAAATAATGTGAACAGACACTTCCAAAAAGGAGACATACA---GGC 2042
                                 vi  v    i     i   ivv    i   i     ---   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_73836799_7   2043 ATACAACAAGCACATGAAAAAATATTCAACATCACTAATCAT 2084
                         ---   i             i  ii         ????????
  L1M4_orf2#LINE/    870 ---CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (136 / 87)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 6.17 (148 / 24)  


3849 20.85 2.58 0.78  chr1_74025949_74027948.rev      620  1511 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_74025949_7    620 TGGAACTACCTCTCATGTTCATTAATTGGAAGGC--AATATTGTTAGGAT 667
                              vv iv  i         vi        i --          i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_74025949_7    668 ATCAGTATTACCCAAAGCAATCTATAGCTTCAATGCAATCCC-ATTAAAA 716
                         iv  i  i v      vii     i  v     i        -  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_74025949_7    717 CCCCAATAATATTTTTTGCAGAAATAGAAAACCCCACTCCAAAATTCATA 766
                         i    iiviiv              v  v  v iv ii i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_74025949_7    767 TGGACTCTCAGGAGATCCTAAATAGCCACAACAGCCTTGAAAAAGAA--- 813
                             vviv  i i  i  vi        v    ii            ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_74025949_7    814 TAAAGTTGGAGGACTCACACTTTCTGATTTCAAA-CTTACTACAATGCTA 862
                         i                     i ii        -          v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_74025949_7    863 AATTAGTCAA-ATAGTGTGGTATTGACATAATGACAGATGTATAGAACAA 911
                         v v  i    - i         i  i     v  i   ii      v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_74025949_7    912 TGGAATAGAATAGATAGCACAGAAATAAACCTTCACATACATGA--AAAT 959
                                    v  v  iv            ivi    vi   i--  v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_74025949_7    960 GATTTTTGACAGGGGTACCAAGACCACTCA-TTGGTAAAGAACAGTCTTA 1008
                               i    i    i         i   - v  v      i      v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_74025949_7   1009 TCAGCAAATGGTACTGGGAAAACTAGATATCTGTATGAAAAATAATGAAG 1058
                            i        i      v    i    ? iii   v    v       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_74025949_7   1059 TTAGATTATTA----AGACCATATATAAAAATTAACTTAA--TGGATCAA 1102
                           i  iivi  ---- v        i           i  --       ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_74025949_7   1103 AGGCCTAAATGTAAGACTTAAAGCTATAAAACTCTTAGAAGAAGACATAG 1152
                           i             vi    i                    i      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_74025949_7   1153 AACAAGAGCTTCAGAACACTGGATTTGGCATTAATTTCTTACATATGATA 1202
                         i?vv i v    ivi  vi   i  v    v ii       v      i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_74025949_7   1203 C--AAAGCATATGCAACCAAGTAAAAAAACAGAAAAATTTGACTTAATGG 1250
                          --      i v     v  i-i      i   v     v     v  vi
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_74025949_7   1251 AAATTTAAAAAAA----TATGCAGCAAGAGACACTATTAACACAGTTAAT 1296
                              ---     ---- i   vv   ii        i  v v   v  v
  L1M4_orf2#LINE/    650 AAATT---AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_74025949_7   1297 AGGGAACTCACAAAATGGGAGAAAAGATTTGCAAGTTATATTTTTGATGA 1346
                           iv   i    i            v        i i    v i    i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_74025949_7   1347 AGGACTAATATTCAGAATATATTACGAATTTCTAAAACTCAATGACAGGA 1396
                         i     vi   i          v v   i ii  v        i i -- 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA--A 794

  chr1_74025949_7   1397 AAACAACAAACAACTAAATTAAGAAATGGGCAAGGAACTTGAATAGACAT 1446
                            -i     i   iv    ? i          i i i            
  L1M4_orf2#LINE/    795 AAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_74025949_7   1447 TTCTCCGAAGAAAATATATGAATAGCGAATAAGCACCTGAAAGGATGCTC 1496
                               i     i     ii   i  v         v     i       
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_74025949_7   1497 AACATGACTAATCAA 1511
                              v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (112 / 70)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.00 (30 / 15)  


2712 24.50 8.60 1.65  chr1_74155310_74157163.rev      516  1364 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_74155310_7    516 TGAAATGACATCTCATGCTCATGGATTGGAAGAATTAATATTTTTAATGA 565
                           i  v  i   i    i               v        v    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA-GA 49

  chr1_74155310_7    566 CCATACATACTACACAAAGCAATCTATAGAGTCAATGCAGTCTCTATCCT 615
                         ivii -     v v    vii     i   v    i   i  i     vv
  L1M4_orf2#LINE/     50 TGGCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_74155310_7    616 AATACCAATAACATTCTTCAGAGAAATAAAAAAA---AT--TAAAATTTG 660
                            v   iivi v  i  iiv      vi v  i---  --       ii
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_74155310_7    661 TATGGAATCACAAAAGGTCCCAAATAGCCAAAACAATCCCGAGCAAAAAT 710
                                vii   ii ii  vi                ii  iv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_74155310_7    711 AACAGAACTATAGATATCACATTACCTAACATCGAAATATACTACAAAGC 760
                             i ii iv  ivv     i v  i  iv  i   iv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_74155310_7    761 TATAGTAACCAA---AGTA--------GCATAAAAACAGACATATAGAAA 799
                           i     i   ---   i--------      ii i           vv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_74155310_7    800 AAGGGAACAGAATAGAGAACCCAGAAATGAATCCATATATCTACAGTCAA 849
                           v    i     v    ii        i  i     i  i  ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_74155310_7    850 TTGATTTTTGACAAAGATGCCAAGAACACTCACTGGGGAAATTATAGTCT 899
                                 i     i i        v  i   v        vv       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_74155310_7    900 TTTCAATTAGGAGTGCTGGGAAAACTGGATATCCATCTGCAAAAGAATGA 949
                               iv ivi         v         ?   iv             
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_74155310_7    950 AATTAGACCCCATCCCCACCTCTCGCTCTTTATAAAAATCACCTCAAAAT 999
                          i  i      -----i     v i iv v  i      i v        
  L1M4_orf2#LINE/    449 AGTTGGACCCC-----TACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_74155310_7   1000 G-ATCAAAGGTCTAAATGTAAGGCCTGAAACTATAAAATGACTAGAAAAA 1048
                          -    ?  ii           iv  i           ivvi     i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_74155310_7   1049 AAAACATAGGAA-AAATGCTTCAGGACATTGTTCTGGATAAAGATTT-TT 1096
                           --      ?i-    -    iv   v   vvi i ii  v i   -  
  L1M4_orf2#LINE/    544 AA--CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_74155310_7   1097 GAATAGGATCTCAAAAGCAGAAACAACAAAAGCAAAAATAAATAAATGGG 1146
                         ii   v  ivi        v  i         v       i      v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_74155310_7   1147 ATCATATTAAATAGAAAAGCTTCTGCAAAGCT-CAGAGTAAAACAATCAA 1195
                          iivi  i   vvv    i   i  i---   -  i  -i v  v     
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGT---GCTTCAAAG-GACACTATCAA 686

  chr1_74155310_7   1196 CAGAGTGAAAAGGTGACCTACGTAATAGGAGAAAATATTTGTAAACTATT 1245
                         v i         iii   i  iv   i              i   ii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_74155310_7   1246 CATTTAACAGGGAATTCATATCCAGAA----------------------- 1272
                         i  i i i i  i i ii         -----------------------
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_74155310_7   1273 -----------------------------AAAATAGACAAATCATCTGAA 1293
                         -----------------------------     i i    vv  i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_74155310_7   1294 TGGACATTTCTCAAAAGAAAACAAAAAAATTGCCAACAAATAAATAAAAA 1343
                          i          v      i i v v    v     i  ii v  i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_74155310_7   1344 -ATACTCAACATCGCTAATCAC 1364
                         -  i         i????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (134 / 71)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 5.12 (87 / 17)  


 331 20.00 0.00 0.00  chr1_74234350_74236187       83   147 (1691)    L1M4_orf2#LINE/L1        1    65 (843)  

  chr1_74234350_7     83 TGGAAAACTATCCTGTGTTCATGGATTGTCAGAATTAGTATTGTTAAAAT 132
                               iv     ii             vv   v   i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_74234350_7    133 GTCCATACTACCCGA 147
                          v v     v   i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA 65

Transitions / transversions = 0.86 (6 / 7)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.00 (0 / 0)  

2581 23.09 5.54 4.95  chr1_74234350_74236187      497  1345 (493)    L1M4_orf2#LINE/L1       55   908 (0)  

  chr1_74234350_7    497 ATACTACCCAAAGTGGTCTACAGATTCATTGCTATTCCTATCAAAATACT 546
                              v      v  i            vi  v  i           v i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_74234350_7    547 AACGACATTCTTCACAGAAATAGAAAAA--AATTCCCCAAATT-ATAT-- 591
                          i vi v  i  ii       v  v  i--i  -  iv     -    --
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCATATGG 153

  chr1_74234350_7    592 ------AAG--ATCCTGAATATCCAAAGCAACTCTGAGCCAAAAGAATAC 633
                         ------   -- i  v     v     i   iii   ivv i     i -
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA- 202

  chr1_74234350_7    634 AAGTTACTATAGCTTTTTAGTATATTTTAATGTCAGGTAGTGGAAGCATA 683
                              i--------------------------------- v   vv  i 
  L1M4_orf2#LINE/    203 AAGTTG---------------------------------GAGGACTCACA 219

  chr1_74234350_7    684 GTACCTGACATTAAAATATACTAAAACGGTATAGTAACCAAAGCAGAATG 733
                         v v  ii iv i    iv     v  v v  i     i   ii   vi  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_74234350_7    734 GTACTGGCATAAATGGAGACACATAGATCAGTGGAACATAATAGAGAGCC 783
                                     iviv     i        i     i v   v     i 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_74234350_7    784 CATAAATAAATTCATACATTCACAGCCAACTGATTTTAGACATAGGTGGC 833
                           v       ii        i ii i   i       v    vi    v 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_74234350_7    834 AAGAATACTCATTCAAC-----AAGGACAGTCTTTTTAATAAATGGTGCT 878
                             ----i       i-----   i i        i  i          
  L1M4_orf2#LINE/    370 AAGA----CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_74234350_7    879 GCAAACACTAAATATTCACATGCAGAAGAATGAAACTAGACCCCTATCTC 928
                          vi vv   ii   ?i        i         ii i        i   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_74234350_7    929 TCACCATATA-AAAAATCTACTCAAAATGCATTAAAGACTTATATGTAAG 977
                         v         -      iv          v  i ?    i  v       
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_74234350_7    978 ACTTGAAACTTTGAAACTACTAGAA---AACAAAAGAG-AAATGCTGCAT 1023
                          vi i     v i     vi     ---    v i ? -    -  v i 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGT 564

  chr1_74234350_7   1024 GACATAGGACTGGGCAAGGACTTTTTGAAATA-GACTTCAAAGGCACAGG 1072
                            v v  ii i     v ii  i  - i   -   vi    i     i 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAAG 613

  chr1_74234350_7   1073 TAACAAAAGCAAAAATAGACAAATGGGATTACACCAAACTGAAAAGCTGC 1122
                         i        v         i    v   i v  i    v v    i  vi
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_74234350_7   1123 TGCACAGCAAAGGA-AC-------------------CAATCAGCAGAATT 1152
                           ii vv       -  -------------------   i vi      v
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_74234350_7   1153 GGAGAACATATTCACAAACTATACATGTGATAAGGGGTTAATATCAAAAA 1202
                               v     ii    ii   i  v         ii vi    v i  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_74234350_7   1203 TACATAGGGAACTC--A-AACTCAATAGCTAAAAAAACAAGCAACCCAAC 1249
                           i   ii      -- -         i-      i    ii       i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAAT 812

  chr1_74234350_7   1250 TAAAAAATAGTCAAAATCCCTGACTAGACATTTATCAAAAGAAGATATAA 1299
                          ?      i v    ivvii   v         v  v            v
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_74234350_7   1300 AACTTGCCAGCAGGTATATGACAAAATGCTTAATATCACCAATCAT 1345
                           v v    ii i i i    v  i     i  i    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (119 / 73)
Gap_init rate = 0.02 (20 / 854), avg. gap size = 4.45 (89 / 20)  


2606 19.71 2.61 0.81  chr1_74265674_74267279      500  1113 (493)    L1M4_orf2#LINE/L1      284   908 (0)  

  chr1_74265674_7    500 ACAGACATACGTATCAATAAAATAGAACTTAGAGTCCAGGAATAAATCC- 548
                          i       iiv      ii       i v         i      i  -
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_74265674_7    549 TTCA-ATATAGTCAATTGAATTCTGACAACAGTACCAAGATAATTCAATA 597
                          v  -v   i         v  ii     vi  i      iv       i
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_74265674_7    598 GAGATAAGAA-ATTTTTCTCAACAAATGGTAGTGGGACAAGTGGATATCT 646
                          i  -     - v i  i            iv        v      ? i
  L1M4_orf2#LINE/    384 GGGA-AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_74265674_7    647 ATATGTAAAATAATAAAGTCAAACCTTTACCTCACACCACAT--GAAAAT 694
                          i   i    v   i    iii   ii            i  --i     
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_74265674_7    695 TAGCTCATGATAGATTATAGGTCTAAATATAAGAGCTAATACTATAAA-C 743
                           i    vi  i   i ?  ii      i          v        - 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_74265674_7    744 GCTTAGAAGAAAACATAGAAAAAAAATCTTTGAGGCCTCAAGTGAAAGAA 793
                         v                 i?iv   -    i v i   iii  v iiv  
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_74265674_7    794 TGGTTTCTTAGATATGACACAAAAAATAAAGGCAACAAGA-AAAAAATA- 841
                                             v    ii v i       i -        -
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_74265674_7    842 -TAAATGTAAGTTTACCAAAATAAAAAGCATCTGGGATTTAAAGAATACC 890
                         -     vvi v  i i      v    i v i  v v  i    i i  i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_74265674_7    891 ATTGAGAAAGTGAAAAGACAACCCACATAATG--AGAAAATAACTCACAA 938
                           ii                       v    --        -i ii   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA-TTTGCAA 730

  chr1_74265674_7    939 ATTATATATGTGATAAAAGATTTGTATCAAGAATATGTAAAGAATTCTCA 988
                           i      v      ii  i       v       i       i   i 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_74265674_7    989 CAACTCAATAATAAAAAGA----TAATCT-ATTATAAAATGATCAAAGGA 1033
                                            ----   i i-   ?v      iv       
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_74265674_7   1034 TTTAAATAGACAGTTCTCCATAGAAGATATATAAAGGGACAATAAATACA 1083
                            i        v       v          i   v  v      ii   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_74265674_7   1084 CAAAAAGATGCTGGCATCATCAACTGCTAG 1113
                         ii          --  v     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCT--CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (80 / 37)
Gap_init rate = 0.02 (14 / 625), avg. gap size = 1.50 (21 / 14)  


2993 27.75 0.77 0.77  chr1_74274326_74279525     3800  4707 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_74274326_7   3800 TGGAAGAACGTTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 3849
                              ii ii i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_74274326_7   3850 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATAAAGC 3899
                            v   i v     iv i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_74274326_7   3900 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 3947
                          v i iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_74274326_7   3948 TATGGAACCAAAAAATAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 3997
                                viiv  iiv v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_74274326_7   3998 AACAAAGCCGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4047
                                ii     vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_74274326_7   4048 TACAGTAACCAAAAACAGCATGGTACTGGTACCAAAACAGAGTTATAAGC 4097
                                 i   i -   ii         i iv ii i   vv    iii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_74274326_7   4098 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACAACTACAAC 4145
                                 i    i--    i  --        vv   i   vi  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_74274326_7   4146 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 4195
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_74274326_7   4196 CCTATTTAATACATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 4245
                         i  v  i  i v   i        v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_74274326_7   4246 TGAAACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 4295
                             ii    iv   v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_74274326_7   4296 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4345
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_74274326_7   4346 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 4394
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_74274326_7   4395 AAAACACCAAAACCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 4444
                          vi         v  vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_74274326_7   4445 AATTGAA-CTAAAGAGCTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 4493
                         v  ii  -i    i vi i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_74274326_7   4494 ACAGGCAATCTACAGAACAGGAGAACATTTTTGCAATCTACTCATCTGAC 4543
                          v  i   i i      ii      v  v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_74274326_7   4544 AAAGGGCTAATAACCAGAATCTACAAAGCACTCAAACAAACTTA-CAAGA 4592
                           i  i  vi  v       v  i    v    vv    -  i -i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chr1_74274326_7   4593 AAAAAACAAACAACCCCATCAAAAAGTGGGCAATGGATATGAACAAACAC 4642
                             i     i     v  i?    i       v    v    i i   i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_74274326_7   4643 TTCTCGAAAGAAGACATTTATGCAGCCAATAGACACATGAAAAAATGCTC 4692
                              v        i  vi viii       ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_74274326_7   4693 ATCATCACTGGCCAT 4707
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3100 27.28 1.22 0.11  chr1_74301323_74303223.rev      515  1412 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_74301323_7    515 TGGAAATACAT---ATGTTCCTGGATTAGAATAATTAATATTTTTAAAAT 561
                               v i  ---      v      i   v v        v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_74301323_7    562 GTCCATACTACTCAAAGCAATCTATAGATTCAATGCAATCCCTACCAAAA 611
                          v v     v i    vii     i        i          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_74301323_7    612 TATCAATGACATTCTTCACAGAAATAGAGAAAACAATCCTAAAATTTTTA 661
                          vi  iivi v  i  ii       v  v  ivii           iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_74301323_7    662 TGGAACCACAAATGACCCAGAATAGCCAAAGTCAGCTTGACCAAGAAGAA 711
                              vii   iv                 iiv v     vv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_74301323_7    712 CAAAACAGGAGGAATCATATTACCTGACTTCAAATTATACTACAGAGATA 761
                             iiv      v   i i v  ii i      viv       i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_74301323_7    762 TAGTAACCAAAACAACATAGGACTGTTCTAAAAACAGACATATAGAACAA 811
                         i     i   i   iii i v    viv   ii i           v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_74301323_7    812 TGGAATAGAATAGAGAACTCAGAACCAAATCTATATATCTACAGTGAACT 861
                                    v    iii     vi   i i   i  i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_74301323_7    862 GATTTTTGATAAAGGTGCCAAGAACATGCATTGGAGAAAGA-CAGTCTCT 910
                               i  i  i          v   v  v   i      -i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_74301323_7    911 TCAGTAAGTGGTGTTGGGAAAATTGGGTATCTGCAGTCAGAGCAATGATA 960
                            ii  i     i     v  i   i  ? ii  vv  i iv     vi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_74301323_7    961 TTGGACCACCATCTCTGACCATATAGAAAAATCACATCAAAATGGATTTG 1010
                                v i i   vv        v      i vv           iv?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_74301323_7   1011 CAGCTTAACGCTAATACCTCAAACTATGAAACTACTATAAGAAAACGTTG 1060
                         vii i   vvv   v v  v       i     vi  v        i v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_74301323_7   1061 GGGAAATTCTCCAGGACATTGGACTGTGCAACAAGCTTTGAG-TAATACT 1109
                          ? v  v   i iv   v    ii iv    iiivi i v  -  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_74301323_7   1110 CCACAAGCACAGGCAACCAAACAAAAT-TAGACAAATGGGATCACAT-AA 1157
                            v       i     v   v    v-    i    v   iiv   -  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_74301323_7   1158 AGTTAAAGAGCTTCTGCACAGCAAAGGAAAC----AATAAAATGAAGAGA 1203
                          i     i -   i  ii vv       v  ----  v   i    i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_74301323_7   1204 CAACCTGCAGAAATTGATAATATATTTGCAAAATATCCATGTGACAATGA 1253
                              ii     vvv  v  v           vi  vi  v   i  v i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_74301323_7   1254 ATTAATAGCTACAATATATAAGGAGCTCAAACAACTCTATAGGAAAAAAT 1303
                          i vi  v i v         i  i   vv       v   iv     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_74301323_7   1304 CTAATAATTTGATTAGAAAATGGGCAAAAGTTCTGAATGAACACTTCTCA 1353
                          v     iiii   ?i            i v i     ii   i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_74301323_7   1354 AAAGAAGACATATACATGGAAAACATATATATGAAAATGTGCTCAATATA 1403
                                 i   i v    vv  i vii i       vi       i  v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_74301323_7   1404 ATTTATCAT 1412
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.27 (135 / 106)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  

 280 23.68 0.00 2.63  chr1_74301323_74303223.rev     1517  1592 (309)  C L1M4_orf2#LINE/L1   (611)   297   224  

C chr1_74301323_7   1592 CCAATGTCAAATTATACTACAGAGATATAGTAACCAAAACAACATAGTAC 1543
                              v     viv       i  v  i     i   i   iii i    
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

C chr1_74301323_7   1542 TGTCATAAAAACAGACATCTACAGAT 1517
                           v     ii i      -- i    
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACAT--ATAGAT 297

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.01 (1 / 74), avg. gap size = 2.00 (2 / 1)  


1659 27.75 4.34 3.61  chr1_74341198_74343463.rev      502  1193 (1073)    L1M4_orf2#LINE/L1       46   742 (166)  

  chr1_74341198_7    502 AAGATCTCAATTCTACCGAAATTTATATACAGCTTCAATGCAATTCTTAT 551
                              vv    v  v  v     v  v     v     i     i i   
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_74341198_7    552 CAAAATTCCATAAGA-----TTGTAGATGTAGTCAAGATTATACTGAATT 596
                               i   vvv v-----   i   vi v v    v v  v  i  v 
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_74341198_7    597 TTATATGGAAATATAAACAAACTAGAATTGTTAAAAGAACTTAGAAAAAC 646
                          i          ii  ivi v i     v ii    v  ii v      v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_74341198_7    647 AAGAAAAAAGTGGGATGCATCA-GTTACCTTATTTTTAGAC--AC-GTGT 692
                              v     v   v vv   -ii v  iv    iv i  --  -iiiv
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_74341198_7    693 AGCTATCGTAATCAAGACTGTGGTGGTATTG--ATAACACATGGGCACAT 740
                              iv           v   -     i  --    vi-  i i  i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTG-TGGTACTGGCATAAGG-ATAGACATAT 293

  chr1_74341198_7    741 AGATCAATAGAACAGAAAATAAAACCTAAAAATAGGTTCATGCAAT-ATG 789
                                 i   i    vvv i ii i i     iiii   i  v -   
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_74341198_7    790 TCCAAATGAATTTTGGCAAAGGTACAAATGTAATTTGATGAAGTAAAAA- 838
                         vi   v   v   i i   i   i v  viiv   ii   ii v  i  -
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_74341198_7    839 AGTCTTTTCAATAAATGGTCCTGGAGCAATTGGGTATCCATAGCCAAAAG 888
                                    i       v    ii   i   i  ?   i vv      
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_74341198_7    889 ACCAATAACATCAAAACTCCTCAGTCTAAGTTTCATACTTTATACAAAAA 938
                          ---  i vi iii - i   --------iii   i  iv          
  L1M4_orf2#LINE/    444 A---ATGAAGTTGGA-CCCCT--------ACCTCACACCATATACAAAAA 481

  chr1_74341198_7    939 TTAACTCAAAATAGGTCAAGCAGTTG--TGTAAGATGTAAAGTTACAGAA 986
                                     i i   ?iv vi i--       vv    ii  i i  
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_74341198_7    987 TT-TTAGAAAA----------GTAATACTTTTGGGCATCTAGGACTAGAC 1025
                         i -      i ----------    - ii  i v - i  v  ii   i 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTG-ACCTTGGGTTAGGC 579

  chr1_74341198_7   1026 A--GAATTCTTAGACCTGACATCAAAAGCATACTTTGTAAAAGGAATAAA 1073
                          -- iv        iv     i        i vvivii     i  -   
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA-AAA 628

  chr1_74341198_7   1074 T-GATAAAATGCATGTAATCAAATTTTTTTTCAAAAA-TTTTGCTCTATG 1121
                          -      v  v iv v      v  ------     -     iv  vii
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATT------AAAAACTTTTGTGCTTCA 672

  chr1_74341198_7   1122 AAAGACCCTGTTAGGAGAATGAAAAGATAAGCTACAGATTTGGGGCAAGT 1171
                           i   v  i i i  i i        i  v i     v v  i v  i 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_74341198_7   1172 ATTTGCAAACTCTATGTATTTG 1193
                                  -  -  i   i  
  L1M4_orf2#LINE/    723 ATTTGCAAA-TC-ATATATCTG 742

Transitions / transversions = 1.50 (114 / 76)
Gap_init rate = 0.03 (24 / 697), avg. gap size = 2.29 (55 / 24)  

 349 22.22 1.85 1.85  chr1_74341198_74343463.rev     1668  1775 (491)    L1M4_orf2#LINE/L1      801   908 (0)  

  chr1_74341198_7   1668 AAACAATCTAATTAAAAATTGAACAAA--ATCCAGAAGAGGAATTTCACC 1715
                            i  i i    ?    v  ii    --  ii-   v  iv     v  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTT-GAATAGACATTTCTCC 849

  chr1_74341198_7   1716 AAAGGGTATATACAGATGGCAAAGTAATCACGTGAAAAAATATTCAATAT 1765
                             iiv       i     v  -   v   i      i  ii    i  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGATGCTCAACAT 898

  chr1_74341198_7   1766 CATTAGCTGT 1775
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.03 (3 / 108), avg. gap size = 1.33 (4 / 3)  


3174 23.38 2.74 3.29  chr1_74347129_74351592.rev     3070  3980 (484)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_74347129_7   3070 GGAAGGTATCCTGGGTTCATGGACTAAAAAA-TTAGTATTGTTAAAATGT 3118
                          i   i     iiv         i ii  i -   i         i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_74347129_7   3119 CTATCCCACCCAAAGCAAT--GCAGATTTGAT-CAATTCCTATCAAAATA 3165
                          v  v iv      vii  --i      ii i-    i           -
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT- 101

  chr1_74347129_7   3166 CCTAAGTAC-TTTTTTACAGAAATGGAAAAA--AATCCTAAAATTAATAT 3212
                           i iv i -      i       v  v  i--i           v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_74347129_7   3213 GGCACCACAAAAGATCCTGAATAGCCAAAACAATCTTAAGCAAAACAAAC 3262
                           v vii   ii  i  v                   i --    v  i-
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG- 198

  chr1_74347129_7   3263 ACAAAAACCAAATAAAGCTGGAGGCATCACACTTACTGGTTTCAAAATAC 3312
                         ----------  i    i      vv        v iii        ivi
  L1M4_orf2#LINE/    199 ----------AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_74347129_7   3313 GTTACAAATCTATAGTAATTAAAACAGTGTAGTACTGGCATACAAGTAGA 3362
                         ii      v   i      i  i       i           viii    
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_74347129_7   3363 CATATAGAACAATAGAACGGAATACAGAACCTAGAAATAAACCCATGGAT 3412
                                 v    i   ii    vv   ii i              iv  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_74347129_7   3413 ATATGTTCAACTAATTTTCAGCAAGGGTGCCAAGAATACACAGCAGAGAA 3462
                         v    v    i i      ii              vi iv  iii i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_74347129_7   3463 AAGATATTCTCTTCAATAGATGATGTTGAGAAAACTGGATATCCATATCA 3512
                          ii   v   i     i i   i  i  i  v         ?   i  vv
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_74347129_7   3513 AAAAGAATGAAATTGGACCTTTGTCTTACACTATACTCAAAAAAGAATT- 3561
                                    i       ii ii  i    i   iv      vv  i -
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_74347129_7   3562 AAAAT----------CTTAAAGGTAAGATCTGAATCTATAAAACTTCTAG 3601
                              ---------- i    v      v  i  v          ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_74347129_7   3602 AAGGAAA-A-AGGGGAAAACCTTCTTGACATCGGTCTTGGCAATGGTTTC 3649
                            i   - -   ? v   i    v    v i  vi v            
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_74347129_7   3650 TCCAATATCCCACTAAAAACACAATCAACAAAAGCAAAAACAG-TCCATT 3698
                          ivi    vv   i    i     v         v     i  - vv   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_74347129_7   3699 AAGACTACATCAAACTAAAAAGCTGCTACACAGCAAGGGAAACAATCAAC 3748
                         i-    v       v v    i  vi iii vv   i   v  v     v
  L1M4_orf2#LINE/    639 G-GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_74347129_7   3749 AGAGTGAAATGGCAACTTATAGACTAGGAGAAAATATTGGCAAATCATTT 3798
                          i       v i    ii i   v i            v         v 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_74347129_7   3799 ATTTAATGAGGGGTAAATTTCTAAATTATATAAGGAACTCTTATACCTTA 3848
                           i i  i    iivvi v  i i v       i         i v  i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_74347129_7   3849 ATAGCAAAGACAAACAAACAAAAAATAACCCGAATAAGGAATGGTTAACA 3898
                            ------ i   v i     ---      i v ? ii     vi  vi
  L1M4_orf2#LINE/    788 ATA------ATAAAAAGACAAA---TAACCCAATTWAAAAATGGGCAAAG 828

  chr1_74347129_7   3899 GACTTGAATAGACATTTCTCCAAAGAATACATAAAAATGAATACATAAAA 3948
                           i                        v i   v     ivi -    i-
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA-ATAAG- 876

  chr1_74347129_7   3949 AAGATATATGAAAAGAT----AACACTACTAATCAT 3980
                         ----i i          ----    ii ????????
  L1M4_orf2#LINE/    877 ----CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (135 / 75)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 2.89 (55 / 19)  


3383 25.44 1.10 1.10  chr1_74403077_74407288     2812  3719 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_74403077_7   2812 TGAAAAAATTGTCCATGTTTGTGAATTGAAAAAATTAATATTGTTAAAAT 2861
                           i   i  vvi       ii  i    i  i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_74403077_7   2862 GTTCATACTACCCAAAGCAATCTACAGACTCAATGCAATCCCTATCAAAA 2911
                          viv     v      vii         i    i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_74403077_7   2912 TACCAATGACATTATTCAGTGAAATAGAAAAAAAAATT-TAAAATTTATA 2960
                          v   iivi v  v  iivv     v  v  ivvi  i-       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_74403077_7   2961 TGGAACCACAAAAGACCCAGAGTAGCCAAAGCTATCCTACGCAAAAAGAA 3010
                              vii   ii        i        i v   i iviv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_74403077_7   3011 CAAAACTGGAGGAATCACACTACTTGACTTTAAA--TTATTCTACAGAGC 3058
                             ii       v       v iii i  i   --   --     i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGC 248

  chr1_74403077_7   3059 TACAGCATCCAAAATGGCATGATACTGGCATAAAAACAGACACATAGATG 3108
                              i vi   i ii ii  i           ii i     i      v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_74403077_7   3109 AACGGAACAGAATAGACAACCCAGAGGTAAATTCATACATCTACAATGAA 3158
                           i    i     v  v ii     ii    ii       i  iii v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_74403077_7   3159 CTCATTTTTGACAAGGATGCCAAGCACATACATTGGGAAAAGGACAGTGT 3208
                         i v     i       i       vv   v  v    i    i i   v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_74403077_7   3209 CTTCAATAAATGGTGCTGGGAAAACTCGGTATCTATATGCAGAAGAAAGA 3258
                         i     i              v    v i  ? i i     i     v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_74403077_7   3259 AACTAGACCTCTATCTCTTGCCATATAGAAAAATTACATCCAAATGGATT 3308
                          ii i    i   i   vii       v        vv  v        i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_74403077_7   3309 AAAGACTTAACTACAAGACCTCAAAGTATGACACTACTAAAATAAAACAT 3358
                          ?    i   v ii    v  v   v   i v   vi  i  v       
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_74403077_7   3359 TGGGGAAACTCTCCAGGACATTGAACTGGGCAAAGATTTCTCAAGTAGTA 3408
                         v  ? v  v   i iv   v   iii i     v i     i ii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_74403077_7   3409 TCCCATGAGCACAGGCAACCAAAGCAGAAATGGACAGATGGGATCACATC 3458
                         iv   vi      i     v    v i    i  i i  v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_74403077_7   3459 AAG-TTAAAGAGTT----GCTGCATAGAAAAGAAACAATCAACAATGTGA 3503
                           i-     i v  ----   v  ----  i  v  v     v  v    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCA----AAGGACACTATCAAGAAAGTGA 694

  chr1_74403077_7   3504 A--GACAACACACGAAATGGGTGAAAATATTTGCAAACTACCCGTCTGAT 3551
                          --      v   ii      v               ii ivii      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_74403077_7   3552 AGGGATTCATTAATATCCAGAATTTTATAAAGAGCTCAGACAAGTTTACA 3601
                          i  i--- i vi          v -       i   vv    v iv i 
  L1M4_orf2#LINE/    745 AAGGG---ACTTGTATCCAGAATAT-ATAAAGAACTCTTACAACTCAATA 790

  chr1_74403077_7   3602 GGAAAAACATCAATAATCTTATTTAAAAATGTGCAAAATATTTGAAAAGA 3651
                         iv     v iv     i iv   ?       v     iv       v   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_74403077_7   3652 TATTTCTCAGAAGAAGACATACAAATGACAAACAGGCATATGAAAAGGTG 3701
                         i       vi       i         i v  i i   i        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_74403077_7   3702 CTCAACATCATTTATAAT 3719
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (140 / 87)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


3251 26.88 1.00 0.55  chr1_74524957_74530493.rev     4143  5046 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_74524957_7   4143 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATGTCGTGAAAAT 4192
                              ii    i     i      i v      v i   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_74524957_7   4193 GGCCATACTGCCCAAGGTAATTTATAGATTCAATAGTATCTCCATCAAGC 4242
                            v     v     iv i  i  i        iivv   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_74524957_7   4243 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCT 4290
                          v   iivi i  i  ii     -   -- v  i  - iii    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_74524957_7   4291 TATGGAACCAAGAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCAAAAAG 4340
                                viivi ii  v  v v  v     iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_74524957_7   4341 AACAAAGTTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4390
                                       vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_74524957_7   4391 TACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGAGATATAGACC 4440
                                 i   i    ii        vi iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_74524957_7   4441 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCTTATCTACAACT 4488
                                i    i--    i  --        vv iiivi  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_74524957_7   4489 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 4538
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_74524957_7   4539 CTATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCACATGTAGAAAGGT 4588
                           v  i  i              v      v  ?       i i  iii 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_74524957_7   4589 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4638
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_74524957_7   4639 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4688
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_74524957_7   4689 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4737
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_74524957_7   4738 AAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTA 4787
                         vi            vvii         vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_74524957_7   4788 ATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 4837
                           i   v v  i     i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_74524957_7   4838 CAGGCAACCTATAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 4887
                         v  i     i i               v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_74524957_7   4888 AAGGGCTAATATCCAGAATCTACAATGAACTCATACAAATTTACAAGAAA 4937
                          i  i  vi          v  i  v      v     v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_74524957_7   4938 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 4983
                           i    ----   v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_74524957_7   4984 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5033
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_74524957_7   5034 CATCACTGGCCAT 5046
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2128 25.49 8.19 3.81  chr1_74618961_74625726      480  1346 (5420)  C L1M4_orf2#LINE/L1   (0)   908     4  

C chr1_74618961_7   1346 AGAGATAAACCATGTTTATTGAGCAGAAGACT-AACACGGTTAAGATGTT 1298
                          i     vv       i  v  vii       -  i iv         vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

C chr1_74618961_7   1297 CATTCTTCCCAAATTGATCTAATAATTCAATACAATCGA-ATCAAA-TTC 1250
                         v  v  i              vvi      ii     vv-      - i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

C chr1_74618961_7   1249 CAACAAGCTTTTT-ATAGGAATATAGACAAGCTGATTCTAAAATTTATAT 1201
                           i viv      -ii  i   - -           i        i    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAAT-T-GACAAGCTGATCCTAAAATTCATAT 151

C chr1_74618961_7   1200 GGAAAAGCAAAAAAAATCTAGA-TGGCCAGAGCCTTTTTAACAAAGAAGA 1152
                              v    iii --i i   - i    i i vv i  i v        
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

C chr1_74618961_7   1151 ACAAAGTTGGAGGATTCACATTACTTAATTTCACGACTCACTATAA---T 1105
                                       i     i v ii       vi   i    i  --- 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

C chr1_74618961_7   1104 ATAGTAA----GATAGTGTGGTATTGATTTAAGGGTAGACACAT-GATCA 1060
                          i     ----  i         i  iiv     i      i  -     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

C chr1_74618961_7   1059 GTGAAACAGAAT--AGAGTT-GGAAATAAGTGCATACATATATGGTCAAC 1013
                         i  i  i     --     i-i       iiv       v         i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

C chr1_74618961_7   1012 TGATTTTTGAAAAATGTACCAAAATAATTTAATAAG-AAAGGATAGTAGT 964
                                i  v  iv  i    i iv   i   ii -    i     vv 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

C chr1_74618961_7    963 TTTGAAAAATTATGAGAAAAGAATTGGACATCTGTATTAAAAAAAACAAA 914
                           ii v    vi  vviii v  i    i ? iii  vv    i  ii  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chr1_74618961_7    913 GGAATAAACCAAAGAATACCAAATTCAACCCAAACTGGGTACTTTAAAAA 864
                          v-- ii   --------  v vi   vv   v -----   -----   
  L1M4_orf2#LINE/    450 GT--TGGACC--------CCTACCTCACACCATA-----TAC-----AAA 479

C chr1_74618961_7    863 AATAAGAACTCAAAATAGATCTTA----TAAATATAAAACCTAAACCTGT 818
                            --v          i    v? ----     i   i v     v  i 
  L1M4_orf2#LINE/    480 AAT--TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

C chr1_74618961_7    817 AAGACTTCTATAAAAAAA-ATAGGGGGAAGTTTTTATGGCTTTGAGTAAG 769
                           i   ii  v  i    -     ? v  i i  ii  i i   i  v  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

C chr1_74618961_7    768 GCAAAAATATTTTTAGATAGGATAC---AAAT--------TGATTTAAAA 730
                             vii -  i       v  i  ---  ii--------ii vvv    
  L1M4_orf2#LINE/    578 GCAATGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

C chr1_74618961_7    729 TTTTCATAAGATGGATTTCATTGACATTAAAAACATCTGCTCTTTGAAAG 680
                         vv vv    iv    i     ii v         v i  iv   ii  i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

C chr1_74618961_7    679 ACATTGCTGAGAATACAAAAAGGCAAGCCACAGATTACAGGAAAATCCTT 630
                            i iiii    viii     i   v       v ivii      vi  
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

C chr1_74618961_7    629 GCAAAACATGTAGCAGATAAAGTACTTCTCCCTATAATCCCTATAATCTA 580
                              v   i  v v     i v    v vi i v   v--     ----
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA--TATAA---- 770

C chr1_74618961_7    579 AGAACTCTTACAACTAAATGATGA---GAC---TA--------------- 551
                                        v   i  i ---   ---  ---------------
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

C chr1_74618961_7    550 ----------TTTAAACAAACATTTCAC---AGAAGAAATATGGATATCA 514
                         ----------   i  i i       v ---      v   iii  iv v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

C chr1_74618961_7    513 AACAAGCACAT--AAAG-TG-TCAATATTTCTAGTCAT 480
                           i        --    -  -    i  iv????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (138 / 80)
Gap_init rate = 0.04 (33 / 905), avg. gap size = 3.15 (104 / 33)  

1843 26.06 3.94 3.33  chr1_74618961_74625726     3290  3949 (2817)    L1M4_orf2#LINE/L1        1   664 (244)  

  chr1_74618961_7   3290 TGGAAAAACATTCCATACTCATGGAGAGAAAGAATCAACATCATGAAAAT 3339
                               i i  i    ii       vv i    v i  i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_74618961_7   3340 GGCCAGACTGCCCAAAGTAATTTATAGATCCAATGCTATTACCATTAAGT 3389
                            v v   v      v i  i  i    i   i  v  iv i  i  --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-- 98

  chr1_74618961_7   3390 AA--CTATTGACGTTCTTCACAGAATTAGAAAAAA-AATTT--AAATTCA 3434
                           -- i vivi v  i  ii     v v  v  iv-i  ii--       
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_74618961_7   3435 TATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAA 3484
                                viiv  ii  v  viv        i      i i iv  i  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_74618961_7   3485 AATAAAGCTGGAGGCATCATGGTACCCAACTTCAAACTGCACTACAAGAC 3534
                           i    i      vv   iiv v     i      vivi       ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_74618961_7   3535 TACA-TAACCAAAACATCATGGTACTGGGAAAAAAAAAAAAGACACATAG 3583
                             -   i   i   vii         v v  ii v ---    i    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA---GACATATAG 295

  chr1_74618961_7   3584 ACCAATGGAAGAGAACAAAGAACTCAGAAATAAGACCACACATTTACACA 3633
                          i        v    ivi   iii         iv   i       ----
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA---- 341

  chr1_74618961_7   3634 TCTATAACCATCTGATCTTTGACAAACCTAACAAAAACAAGCAATGGGGA 3683
                         ---- iii  vi    i  i     ivv iv   i v  vv         
  L1M4_orf2#LINE/    342 ----TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_74618961_7   3684 AC------CCTATTTAATAAATTGTGCTGGGAGAACTGGCTAGCCATATG 3727
                          v------i  v  i  i    v         v      v  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_74618961_7   3728 CAGAAAACTGAAGCTGGACCCCTTCCTTATATCTTATACAAAAATTAACT 3777
                           i  i v     i         v   i i i v                
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_74618961_7   3778 CCAGATGGATTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTA 3827
                          v i      i ?    i         i v i     i      vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_74618961_7   3828 GAAGAAAATCTAGGCA-AGACCATTCAGGACATAGGCATGGACAAAGATT 3876
                                 iv    ?i- i i -   iv   v v  vv i i   v i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_74618961_7   3877 T------TATGACA--AAAATGTCAGAAGCAATGTGGCAAAAGCAAAAAT 3918
                          ------       --    - -  v      -----      v      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAA-G-CACAAGCAA-----CAAAAGAAAAAAT 629

  chr1_74618961_7   3919 TGACAAA-----CGTGATCTAAACTAAAGAACTTCT 3949
                         v  i   ----- v v   v   i    -     i 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAA-AACTTTT 664

Transitions / transversions = 1.52 (102 / 67)
Gap_init rate = 0.03 (17 / 664), avg. gap size = 2.82 (48 / 17)  

3283 27.09 0.44 0.44  chr1_74618961_74625726     5027  5934 (832)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_74618961_7   5934 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5885
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_74618961_7   5884 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCCATTCCCATCAAGC 5835
                            v     v      v i  i           i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_74618961_7   5834 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5787
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chr1_74618961_7   5786 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5737
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr1_74618961_7   5736 AACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAAGGC 5687
                                i      vv     i v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr1_74618961_7   5686 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5637
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr1_74618961_7   5636 AATGGAACAGAAC--AGAGCCCTCAGAATTAACGCCGCATACCTACAACT 5589
                                i    i--    i  --    v   vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chr1_74618961_7   5588 ATCTGATCTTTGACAAATCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5539
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chr1_74618961_7   5538 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5489
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chr1_74618961_7   5488 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5439
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chr1_74618961_7   5438 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5389
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chr1_74618961_7   5388 CTTGGCATTACCATTCAGGACATAGGCATGGGCAAGGATTTCATGTCCAA 5339
                         v v  ?i v viv   iv   v v  vv i     v i    v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chr1_74618961_7   5338 AGCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5289
                         ii           vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chr1_74618961_7   5288 TTAAAATAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5239
                          i     v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chr1_74618961_7   5238 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5189
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chr1_74618961_7   5188 AGGGCTAATATCCAGAATCTACAATGAATTCAAACAAATTTACAAGAAAA 5139
                         i  i  vi          v  i  v   i  vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chr1_74618961_7   5138 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5089
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chr1_74618961_7   5088 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5039
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chr1_74618961_7   5038 ATCACTGGCCAT 5027
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

 569 22.37 0.00 0.00  chr1_74618961_74625726     6122  6273 (493)    L1M4_orf2#LINE/L1      757   908 (0)  

  chr1_74618961_7   6122 TCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAA 6171
                                 v  i  v      vv    v iv i  v     i     i  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_74618961_7   6172 CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAG 6221
                            v  i?    i     i     iv    i     i     v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_74618961_7   6222 ACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCACTGGCC 6271
                          i  vi viii     v  i        i i       v     ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_74618961_7   6272 AT 6273
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.36 (19 / 14)
Gap_init rate = 0.00 (0 / 152), avg. gap size = 0.00 (0 / 0)  


2241 27.05 0.93 0.31  chr1_74709891_74711528      499  1145 (493)    L1M4_orf2#LINE/L1      258   908 (0)  

  chr1_74709891_7    499 CAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACA 548
                            i    ii         i iv ii i   v                i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_74709891_7    549 GAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACTATCTGATCT 596
                            i--    i  --        vv iii i  i  iiiii vi    i 
  L1M4_orf2#LINE/    308 GAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_74709891_7    597 TTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAAT 646
                          i     ivv  vv  i v  vv            i  vvi  v  i  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_74709891_7    647 AAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGA 696
                                       v      v  ?   i   i i  iiv    ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_74709891_7    697 TCCCTTCCTCACACCTGATACAAAAATTAATTCAAGATGGATTAAAGACT 746
                         i    v         vv             i    i      i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_74709891_7    747 TAAACGCTAGACCTAAAACCATAAAAGCCCTAGAATAAAACCTAGGCATT 796
                             i iv   v       i      vi i     v     v    ?i v
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_74709891_7    797 ACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAACACCAAA 846
                          viv   iv   v v  vv i     v ii   v ivvi vi        
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_74709891_7    847 AGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAA 896
                             vvi          vv     v  i    v   ii v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_74709891_7    897 AGAGCTTCTGCACAGCAAAAGAAAGTACCGTCAGAGTGAACAGGCAACCT 946
                          i i   i  ii vv    i  v v  i ivv i      v  i     i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_74709891_7    947 ACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAAT 996
                            i             v  i    vii ivi      i  i  i  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_74709891_7    997 ATCCAGAATCTACAATGAACTC----AAATTTACAAGAAAAAAACAAACA 1042
                                  v  i  v      ----  v iv i  v     i     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_74709891_7   1043 TCCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAA 1092
                         v   v  i?    i           iv    i     i     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_74709891_7   1093 GACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGC 1142
                           i  vi viii     v  i          i       v     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_74709891_7   1143 CAT 1145
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.38 (99 / 72)
Gap_init rate = 0.00 (3 / 651), avg. gap size = 2.67 (8 / 3)  


3247 26.32 0.55 0.99  chr1_74731223_74736036     3410  4321 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_74731223_7   3410 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCGTGAAAAT 3459
                              ii i  i     i        v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_74731223_7   3460 AGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 3509
                         i  v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_74731223_7   3510 TACCAA-TGACTCTACACAGAGTTGGAAAAA--AAAAAACT-ACTTTAAA 3555
                          v   i-  v  i -------v   v i   --i v  i  - iii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-------TTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_74731223_7   3556 GTTCATATGGAACCAAAAAAGAGCCCGCATAGCCAAGACAATCCTGGGCA 3605
                         i           viiv  ii  v  v v        i      i  iiv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_74731223_7   3606 AGAAGAATAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTTTACTAC 3655
                                i    i      vv   ii  v  ii i      vi       
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_74731223_7   3656 AAGGCTACAGTAACCAAAACACCATGGTACTGGTACCAAAACAGATATAT 3705
                           i          i   i   vii         i iv ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_74731223_7   3706 AGACCAATGGAACAGAACGGAGGCCTCAGAAATAACACTACACATCTACC 3755
                            i        i    iv   ivii         vv i i    i  iv
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_74731223_7   3756 ACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT 3805
                         ii  vi    i  i     ivv  v   i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_74731223_7   3806 TCCCTATTTAATAAATGGTATTGGGAAAATTGGCTACCCATATGCAGAAA 3855
                         vvi  v  i  i       ii     v  i   v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_74731223_7   3856 ACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGAT 3905
                          v    ii         v   i     v           i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_74731223_7   3906 GGATCAAACACTTAAATGTAAGACCTAGGACCATAAAAATCCTAGAAGAA 3955
                               ? v  i           v   ii  i      v  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_74731223_7   3956 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGT 4004
                            v    ?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_74731223_7   4005 CTAAAACACCAAAAGCAATGGCAACAAAATCCAAAATTGACAAATGGGAT 4054
                         v  vi            vvi         vvv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_74731223_7   4055 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTCTCATCAGAGT 4104
                         i v  i   v v  i i   i  ii vv    i  v   v   vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_74731223_7   4105 GAACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATTAATCCATCTG 4154
                            v  i     i                vv       v v  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_74731223_7   4155 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAG 4204
                          i  i  i  vi          v  i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_74731223_7   4205 AAAAAAGCAAACAATCCCATCAAAAAATGGGCAAAGGGTATGAACAGACC 4254
                              ii    i  i  v  i?               i v    i    v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_74731223_7   4255 CTTCTCAAAAGAAGATATTTATGCAGCAAAGCAGACATATGAAACAATGC 4304
                         i     v           vi viii  v  -i ii  i      vi    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGATGC 891

  chr1_74731223_7   4305 TCATCATCACTGATCAT 4321
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  


3194 26.21 0.99 0.99  chr1_75054326_75060608     4883  5790 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75054326_7   4883 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATAACGTGAAAAT 4932
                              ii i  i     i      i v      v i    vi  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75054326_7   4933 AGCCATACTTTCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAG 4982
                         i  v     i-     iv i  i           i  v     i     i
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_75054326_7   4983 CTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5030
                         v v   iivi i  i  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_75054326_7   5031 ACATGGAACCAAAAAAGAGACC--GCATCGCCAAGTCAATCCTCAGCCAA 5078
                          i      -- viv   i    -- v  v     iv     i v ivv i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_75054326_7   5079 CAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAA 5128
                         v         i      vv       v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_75054326_7   5129 GGCTACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 5178
                         i     i    i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_75054326_7   5179 ATCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACA 5226
                                   i    i--    i  --        vv   i i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr1_75054326_7   5227 ACTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT 5276
                         iii vi    i  i     ivv  v   i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_75054326_7   5277 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5326
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_75054326_7   5327 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGT 5376
                         iv    ii    i    v   i     v              i    ii 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_75054326_7   5377 GGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5426
                             i ?    i    i  v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_75054326_7   5427 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5476
                            v    ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_75054326_7   5477 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAATTGGGATC 5526
                           vi            vvi          vv     v  i  v v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_75054326_7   5527 TAATTAAACTAAAGGGCGTCTGTACAGCAAAAGAAACTACCTCAG---AG 5573
                          v  i   v v  iii v i   i vv    i  v    --   i---  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA--TCAAGAAAG 691

  chr1_75054326_7   5574 TGAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCT 5623
                             v  i     i   i             v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_75054326_7   5624 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 5673
                           i  i  i  vi          v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_75054326_7   5674 GAAAAAAACAAACAACACCATCAAAAAGTGGGCGAAGGACATGAACAGAC 5723
                         v     i     i   v v  i?    i     i     iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_75054326_7   5724 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGC 5773
                          i     v        i  vi viii     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_75054326_7   5774 TCACCATCACTGGCCAT 5790
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


 601 31.01 1.16 0.78  chr1_75093648_75099224.rev        1   258 (5319)    L1M4_orf2#LINE/L1      441   699 (209)  

  chr1_75093648_7      1 AAAATTAAAACTAGATCCTTTCCTTACGCCATATACTAAA-TCAACTCAA 49
                           i v i  ii i  i  i v   i  i        v   - i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_75093648_7     50 CATGATTTTAATACTTAAATGTAAAACCCAAAACTGTAAAAATCCTCGAA 99
                         v   iv iv? v  i         i v i      i     v  i v   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_75093648_7    100 GAAAATCTAGGCAGTAACATTCAGGAATAAGAACT-GGCAAAGATTTCAT 148
                              iv    ?ivv  iv   iv  vivv iii -     v i    v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_75093648_7    149 -GATGAAGATGCCAAAAGCAATTGCAACAAAAGCAAACATTGATAAGTGA 197
                         -   - v  ii         vvv          v   v  v     i vi
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_75093648_7    198 GATCTAATTAAACTTAAGAGCTTCCGCACAGCAAAAGAAACTATAAAGAG 247
                           ii v  i   v    i i   ii ii vv    i  v     v    i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_75093648_7    248 AACAAACAAGA 258
                          iii  -    
  L1M4_orf2#LINE/    690 AGTGAA-AAGA 699

Transitions / transversions = 1.29 (44 / 34)
Gap_init rate = 0.02 (5 / 259), avg. gap size = 1.00 (5 / 5)  

3166 27.31 0.55 0.55  chr1_75093648_75099224.rev     4179  5086 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75093648_7   4179 TGGAAGAGTATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4228
                              iii   i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75093648_7   4229 GGCCATACTGCCTAAAGTAATTTATAGATTCAATGACATCCCCATCAAGC 4278
                            v     v  i   v i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75093648_7   4279 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACC-ACTTTAAAGTTC 4326
                          v   iivi i  i  ii     -   --- v  i i- iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_75093648_7   4327 ATATGGAACCAAAAAAGATCCTACATTGCCAAGACAATCCTAAGCCAAAA 4376
                                 viiv  ii  i  viv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_75093648_7   4377 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 4426
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_75093648_7   4427 CTACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGAC 4476
                                  i   i    ii       v i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_75093648_7   4477 CAATGGAACACAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 4526
                                 i v  iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_75093648_7   4527 TCGGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGAATTCTC 4576
                         viv   i  i     ivv  v   i v  vvv              vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_75093648_7   4577 TATTTAATAAACGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCTG 4626
                          v  i  i   i          v  i   v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_75093648_7   4627 AAACTGGATCCCT-TCTTACACATTATTAAAAAATTAATTCAAGATCAAT 4675
                           ii    i    -i  i    vv   vv         i    i  vi  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_75093648_7   4676 TAAAGATTTAAATGTTAGAACTAAAACCATAAAAACCCTAGAAGAAAACC 4725
                         i ?   ii       v   i       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_75093648_7   4726 TAGGCA-ATACCATTCTGGACATAGGCATGGGCAAAGACTTTATGACTAA 4774
                             ?i- v i -   vv   v v  vv i     v ii  iv iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_75093648_7   4775 AACACCCAAAGGCAATGGCAACAAAAGCCAAAATAGATAAATGGGTTCTA 4824
                         i     -   i   vvi          vv             v  vii v
  L1M4_orf2#LINE/    597 GACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_75093648_7   4825 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4874
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_75093648_7   4875 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 4924
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_75093648_7   4925 AAGGGCTAATATCCAGAATCTACAAAGAACTTACACAAATTTACAAGAAA 4974
                          i  i  vi          v  i        ivi    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_75093648_7   4975 AAAACAAACAACCCCATCAAAAAGTGGGCTAAGGATATGAACAGACACTT 5024
                           i     i     v  i?    i     v      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_75093648_7   5025 CTC-AAAAAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5073
                            -   i    i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_75093648_7   5074 CATCACTGGTCGT 5086
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


2558 28.28 2.81 0.90  chr1_75101750_75107517     4385  5275 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75101750_7   4385 TGGAAAAACATTCCATGCTGATGGATAAGAAGAATCAATATCGTGAAAGT 4434
                               i i  i     i v      vi     v i     i  v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75101750_7   4435 GGCCATACTGCCCAAAGAAATTTATAGATTCATTGCTATTTCCATTAAAC 4484
                            v     v      vvi  i  i       vi  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75101750_7   4485 TACTATTGACACTATTTAGAGAATTAGAAAAAACT-ATTTTAAAATTTAT 4533
                          v i vivi vi v   iv    v v  v  i-  -  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_75101750_7   4534 ATGGAATCAAAAAAGAGGCTGAAGAGCAAAGACAACCCTAAGCAAAAAGA 4583
                               viiv  ii  vv v   v   v  i    i i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_75101750_7   4584 ACAAAGCTGGAAGTATCATGCTACCTGACTTCAAACTATACTACAAGGAT 4633
                               i    i vv   ii  v  ii i      viv        i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_75101750_7   4634 ACAGTAACCAAAGCAGCACAGTACTGTTACAAGAACATACACATAGACCA 4683
                                i   ii   iiii      vi i   i i v   i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_75101750_7   4684 ATGGAACAGAATAGAGAACCCAGAAACAAGACTGCACACCTACAACCATC 4733
                               i     v    ii       i  iv iii   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_75101750_7   4734 TGATCTTTGACAAACCTGACAAAAACAAGCAATGTGGAAAGGAT--TCCT 4781
                             i  i     ivv  v   i v  vv     v      i  --  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_75101750_7   4782 TATTTAATAAATGGTGCTGGGAGAACTGGCTGGCCATATGAAGAAAATTG 4831
                          -- i  i              v      v i?   i   v i  i v  
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_75101750_7   4832 AAACTGGACACCTTCCTTACACCATATAAACAAAATCAACACAAGATGGA 4881
                           ii     v   v   i          v -     i   v   i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACA-AAAATTAACTCAAAATGGA 496

  chr1_75101750_7   4882 TTAAATACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAGT 4931
                          i ? v  i         i v i     i      vi i         ii
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_75101750_7   4932 CTAGGCA-ATACCACTCAGGACATAGGCATGGGCAAAGATTTCATGACGA 4980
                         v    ?i- v i -i  iv   v v  vv i     v i    v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_75101750_7   4981 AAACACCAAAAGCAATTGCAACAAAAGCAAACATTGACAAAT-GAAATCT 5029
                         vi            vvv          v   v  v  i    - i v ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_75101750_7   5030 ATTTAAACTAAAGAGCTTCTGGACAGCAAAAAAAATGATCAACAGAG--- 5076
                           iv   i    i -   i  vi vv    ii v iv     v i  ---
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_75101750_7   5077 ----ACAACCTACAGAATGGGAGAAA-TATTTGCAGTCTATACATCTGAC 5121
                         ----      i               -        ivii   i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_75101750_7   5122 AAAGGTCTAATATCCAGCATCTATGATGAACTTAAACAAATTTATTTATT 5171
                           i  v  vi       v  v   i v     ivv    v iv  -- v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT--AAT 792

  chr1_75101750_7   5172 TAAAAAA----------AATTGAAAAGTCGGCAAAGGACATCAACAGAAA 5211
                         v    i ----------    ?    i v         iv v  i   v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_75101750_7   5212 CTTTTCAAAAGAAGACATACATATGGCT--CAGGAACATGAAAAAAAACT 5259
                         i  i  v        i     v     i--i i v         i vi  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_75101750_7   5260 CAATATCAACAATCAT 5275
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.36 (33 / 14)  


2937 25.62 2.91 1.34  chr1_75107696_75110215     1134  2027 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75107696_7   1134 TGAAGAGATATTCCATGTTCATGGACAGAAAGACTCAACACTGTCAAGGC 1183
                           i i      i             iv i      i  i i   i   ii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75107696_7   1184 GTTCATTCTCCTTAAGTTGATTTATAAATTAAATCAAATTCCAATAAAAA 1233
                          viv  v    ii  i     i  i i   v  ivv   i  v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75107696_7   1234 TCCTAGTAAGTTATTTTGTGAATATTGCCAAAGTTATTCTAAAGTTTAGA 1283
                            i  ivivi v     iii v    v   iv v  i     i  i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_75107696_7   1284 TGGAGAGGCAAAAGACCCAGAAGAGCCAACCCAATATTGAA---GAAGAA 1330
                             i v    ii         v      vv    v     ---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_75107696_7   1331 CAAAGTCACAGG-CAGATACTACCCAACTTCAAGGCTTACTGTAAAGCTT 1379
                               iiv   - vv i   v     i     ii      ii      v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_75107696_7   1380 TCATAATCAAGATAGTGTGGTATTGGTGAAAGTATAGACAAATGGATCAT 1429
                         ivi         i         i   iiv   v       v  i     v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_75107696_7   1430 GAAAACAGAATAGAGAGTCCAGAT-TAGACCCACATAAATATGCACAACT 1478
                         vii  i     v           v-  i     i i vv    vv   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_75107696_7   1479 GATCTTTGATAAGGGAGCAAAGGCAATACAATGAAGCAAAGAGAGTTTCT 1528
                            i  i  i     v  v   i v  v     ii v  ii v   i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_75107696_7   1529 TCAGCAAATGTTGCTGGAAGAACTGGACATCCCTATCCAAAAAAAAAAAA 1578
                            i      v      i v       i ?  vi  v     i  vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_75107696_7   1579 AAAAATCTAGACACAGATAGACCTTACACCTTTCACAAAAACTAACTCA- 1627
                         ------i i   v v--  --   i     v vi       i       -
  L1M4_orf2#LINE/    451 ------TTGGACCCC--TA--CCTCACACCATATACAAAAATTAACTCAA 490

  chr1_75107696_7   1628 -------CA--GACCTAAATGTAAAATGC-AAAACTATAAAACTACTAGA 1667
                         -------  --             i -  -              vi    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGA 539

  chr1_75107696_7   1668 AGATAACCTAGGAGAGAACCTAGATGAGCTTGGGTTTGTTAAAAACTTTT 1717
                            v   v    ? vi  i  vvi   v        v vi  viii  i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_75107696_7   1718 AAAACACAATACCAAAGGTATAATCCATAAAAGAAATAGTTGATACACTA 1767
                         v i i ii i      i i i  v v i        v i v    v i i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_75107696_7   1768 AACATCATCAAA-TTAAAAACTTCCCCTCTGTGAAG-ACACCCT---GAA 1812
                         i  v        -          iiviv  vii   -    iv ---   
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_75107696_7   1813 --TGAGAATACAAGCAACAGACAGGAAGAAAATATATGGAAAACACATAT 1860
                         --   i  v    v v     vv  i         v  v   v  i    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_75107696_7   1861 CTGATAAAGGACAGGTATCCAAACTACACAAATAATTCATTA-AATTCAG 1909
                                i    vv       i v  i i   v  i  -   -  i   i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC-TTACAACTCAA 788

  chr1_75107696_7   1910 CAATAAGAAAACAAACAACTCAGTTTAAAAATGACTAAAG-ATCTGAACA 1958
                         i     i  i     i   i  i  ?       ivi    -  i    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_75107696_7   1959 GACACCTCACCAAAGAAGATGTAAAGATGGCAAATAAGTATATGAGA-GA 2007
                             ii  v           i  v i     v      i i    i -  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_75107696_7   2008 TGCTGAACATCACATGTCAT 2027
                             v       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.11 (38 / 18)  


3094 26.65 1.21 1.21  chr1_75164859_75170081     3823  4730 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75164859_7   3823 TGGAAGAGCATTCCATGCTCATGGGTTGGAAGAATCAATATCGTGAAAAT 3872
                              iiii  i     i      i        v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75164859_7   3873 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3922
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75164859_7   3923 TACCAATGACTTCCTTCACAGAA-TTGGAAAAAACTA--CTTTAAGTTCA 3969
                          v   iivi i ii  ii     -   -- v  i  i-- i v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_75164859_7   3970 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAGG 4019
                                viiv  ii  v  v v  v     iv     i i ivv i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_75164859_7   4020 AACAAAGCCAGAGGCATCATGCTACCTGAATTCAAACTATACTACAAGGC 4069
                                iii    vv   ii  v  ii v      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_75164859_7   4070 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4119
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_75164859_7   4120 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCAAATATCTACA 4167
                          ---      i    i--    i  --        vv   v i  i  ii
  L1M4_orf2#LINE/    299 A---ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr1_75164859_7   4168 ACTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAA 4217
                         iii vi    i  i     ivv  v   i v  vv            -  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AA 392

  chr1_75164859_7   4218 TC-CCTATTTAATATATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 4266
                          v-i  v  i  i v            v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_75164859_7   4267 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAGAAATGAATTCAAGA 4316
                         iiv    ii    i    v   i     v      i    v  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_75164859_7   4317 TGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAATA 4366
                              i ?    i       v   v       i      vi i     v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_75164859_7   4367 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 4415
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_75164859_7   4416 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 4465
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_75164859_7   4466 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCTCAG--- 4512
                         ii v  i   v v  i i   i  ii vv    i  v    --   i---
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA--TCAAGAA 689

  chr1_75164859_7   4513 AGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCAT 4562
                               v  i     i   i             v  i    vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_75164859_7   4563 CTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAC 4612
                             i  i  i  vi          v  i  v      vv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_75164859_7   4613 AAGAAAAAAACAGACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAG 4662
                           v     i   i i     v  i?    i    ii      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_75164859_7   4663 ACACTTCTCAAAAGAAGACATTTATGCAGCCAA-AAACACATGAAAAAAT 4711
                            i     v        i  vi viii     -  i          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_75164859_7   4712 GCTCATTATCACTGGCCAT 4730
                              vi    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


3399 20.35 7.09 1.63  chr1_75204847_75211802     3793  4652 (2304)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_75204847_7   3793 GGATGGCTATTCTATGTTTCTGGATCTATATAGTTAACGTTTTTTAAGAT 3842
                            vi v   i i     iv     iviv v v    ii  v  -     
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAGAT 50

  chr1_75204847_7   3843 GGTGATGCTAACTACAATGATCTACAGATCTAAAACAATTCCTATCAAAA 3892
                           ii  i  vv i v v            ii  vi    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75204847_7   3893 CCTCAGCTGC-TTTTTTGAAAAAATTAACAAACTTACCTTAAAGTTTATT 3941
                         i i       -       v i     i    i  v i i    i  i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_75204847_7   3942 CGAAAATGCAAGGGACCCAAAGTAAACAAAACAA-CTTGGAAAAAAA--A 3988
                         i i                i i  iv        -    i    i  -- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_75204847_7   3989 CCAAGTTGTAGAATGTATACATCTTAATTACAAAACATACCAAAAAGCTA 4038
                          v      v  i ivi i  v  ii    v      v   i v       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_75204847_7   4039 CAGAAATCAAGACAGAATGGCACTGGCATAAGAGTCGACA-ATAGATTAA 4087
                            v           vi   i           ii v    -      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_75204847_7   4088 TAGAATAGAATTTAGAGTCCAGAAATAAGTCCAAAC-TGTATTGTCAATT 4136
                          i          v               ii   v  - v   v       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_75204847_7   4137 AATTTTTAAC--------CA---------------GAAAGAATAGTCTT- 4162
                         i     ii  --------  ---------------              -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_75204847_7   4163 -CAATAAATAGTGCTGAGGCAACTGGTTATCCACATGCTAAAGAATGAAT 4211
                         -   i    i      i i       v  ?        v          v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_75204847_7   4212 TTGACATTCTAACACACATCGTATACAAAAATTAACTCAAGATGGATGAC 4261
                            ivvii   v v    i i                   i      -- 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT--C 498

  chr1_75204847_7   4262 AGAACTAAATGTAAGACCTAAATGTAAGAGCTAAAACTATAAAACTGTGA 4311
                          -----------?                                 v v 
  L1M4_orf2#LINE/    499 A-----------WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_75204847_7   4312 GAAGAAAACACAAAACTATATCCTCAGGACTTTGCATTAGGCATTAGTTT 4361
                                   i ii?v  v   i  iv   i   vi       v i    
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_75204847_7   4362 CCTAGA----------------CAAGAAATAATAGATAAATTAGATGAAT 4395
                          i    ----------------    v  i  v   v   v     i   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_75204847_7   4396 TGAAATTT-------TTAAA--CTTT----CTTGAAAGAACACTACCAAA 4432
                           i v  i-------     --    ----   v    i      i   i
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_75204847_7   4433 AAGATAAAAAGACAGTCGACAGACTGAGAGAAAATATTTGTGAATTGTAA 4482
                           ii i        ii v     v  i             ii   ii  v
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_75204847_7   4483 ATTAGGTCAAGGACTTGTATCAAGAATATACAAAGAACCCTTACAAATCA 4532
                           iv i v i           v        i       i       v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_75204847_7   4533 ACAACATAAAGACAAACAACCCAAGTAAAAAATAGACAAAGAATTTAAGT 4582
                          i  i v         i       v ?      i i     i    i i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_75204847_7   4583 ACACATTTCTCCAAAGAAGACAAAACAATAATCAA-AAGCACATGAAAAA 4631
                          v                  i v vv   iii   -             i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_75204847_7   4632 ATGTACAACACCATTAGTCAT 4652
                            iv     i  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (106 / 65)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 4.69 (75 / 16)  

3251 23.52 3.64 0.45  chr1_75204847_75211802     5584  6463 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75204847_7   5584 TGAAAAGATATTCCATGTTTATGAATTGTAAGAAATAATATTGTTAAAAT 5633
                           i        i       i   i    v    vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75204847_7   5634 GTCCATACCACCCAAAGCAATCTATAGACTCAGTGCAATTCCAATCAAAA 5683
                          v v    iv      vii     i   i   ii     i  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75204847_7   5684 ATCCACTGGCCTTTTTCACATAAATAGAAAAAAAAATCCTAAAATTTATT 5733
                         vi   viv        ii  v    v  v  ivvi           i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_75204847_7   5734 TT----TG------ACCCC-AATAGCTATAGCAATCTTGAGCAAAGTGAA 5772
                          v----  ------    v-      i v i         iv  iiv   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_75204847_7   5773 CAAAAGCTAGAGGGATCACTTTATCTGATTTCAAAATATACTACAAAGCT 5822
                             - i i    iv    vi vi ii         iv            
  L1M4_orf2#LINE/    201 CAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_75204847_7   5823 AAAGTAATCAAAACAGCATGGTACTGGCATAAAAACAGACATACAGACCA 5872
                          v         i    ii              ii i       i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_75204847_7   5873 ATG-AGCAAAAT--AGAATCCAGAAATAAATTCACATATTTATAATCAAT 5919
                            - ii i   --   i            ii  i i      ii     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_75204847_7   5920 TGATCTTTGGTAAAG---TCAAAAACACACAATAAGAAAAGGACAATCTC 5966
                             i  i ii  i ---i   i v  iv    ii i    i i i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_75204847_7   5967 TTCAATAAATGATGTTTGGAAAACAAGATATCCACATGCAGAAGAATAAC 6016
                              i     i  i v   v   vi    ?         i      i v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_75204847_7   6017 ATTGTACTCTTATCTCATACTACATATGAAAATAAATTCAAAATACATTA 6066
                         i   v  i i  i    i  i i   ii     v  i       iv  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_75204847_7   6067 --GAATTAAA-GTAAGACCTGGGACTGTAAAACTACTGGAAGAAAACATA 6113
                         --  vi    -      v  iii   i       vi i            
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_75204847_7   6114 GGAG-AAATGCTTCTTGACATCTGTCTGAGCAATGATTTTTTTTGATGTC 6162
                           ? -    -    v    v iv vi ii      i   i  v-   i v
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GATATG 597

  chr1_75204847_7   6163 ACCCCAAAAACACAGGCAACAAAAGCAAAAATAAACAAATGGTATTATAT 6212
                           v      i    i          v       i i    v v i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_75204847_7   6213 CAAACTAAAGAGGTTTTGCAAAGCAAAGAA-GCAAGCAGCAAAACAAAAA 6261
                             v v  i iv     iivvv     i -i v v  iv   iii    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_75204847_7   6262 GGCAACCTATAGAATGGGAGAAA-TACTTGCAAAGCATACATTTGATAA- 6309
                          i     i i             -  i       v    i  i      -
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_75204847_7   6310 -------TATCCAAAAGATATAAAGAACTCAAACAATAAAATAGAAAGAA 6352
                         -------      i  v             vv    ivv    iv  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_75204847_7   6353 AACAAATAACCCAATTAAATCATAGGCAAAGGAATTAAGTAAACATTTCT 6402
                         i               ?  vv  i         v  i i  i        
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_75204847_7   6403 CAAATGAATACATAGAAATGGCCAA-AAGTTACATGAAAAGATGCTCAAC 6451
                          v  v   v i   v          -   i-                   
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGC-ACATGAAAAGATGCTCAAC 896

  chr1_75204847_7   6452 ATCACTAATCAT 6463
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (131 / 73)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


 413 26.17 2.80 0.00  chr1_75236292_75238243      489   595 (1357)    L1M4_orf2#LINE/L1      228   337 (571)  

  chr1_75236292_7    489 TTTTAGAGCTCAC---AGATCTATAGTAAACAAAACAGCATGCTACTGGC 535
                            i i i  i  --- i v   i     v   i    ii  v       
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_75236292_7    536 ATAAAAACAGACACATAGACCAATGGAACAGAATAGGGAATGGAGAAATT 585
                             ii i     i     i        i     v i  i vv      v
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_75236292_7    586 AATTCACATA 595
                           ii  i i 
  L1M4_orf2#LINE/    328 AACCCATACA 337

Transitions / transversions = 3.00 (21 / 7)
Gap_init rate = 0.01 (1 / 110), avg. gap size = 3.00 (3 / 1)  

1900 25.39 2.78 0.52  chr1_75236292_75238243      885  1459 (493)    L1M4_orf2#LINE/L1      321   908 (0)  

  chr1_75236292_7    885 AAAAAAAAATCCACACACCAACTATGAACTCATTTTTGACAAAGGTGCCA 934
                          i   v   i   i   iiv ivi v  i v     i     i       
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_75236292_7    935 GAAACATACACTGAGGAAAAGACAGTCTCTTCAATAAATGCTGCTGGGAA 984
                         ii v   v  v  i     ii i     i     i     v        v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_75236292_7    985 AACTGGATATCCATATGCAGAAGAATAAAACAAGACCCCTATCTTTAGCC 1034
                                  ?   i     i      i  iivi        i  ivvi  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_75236292_7   1035 ATATAAAAAAATCAAATCAAAACG-ATTAAAGACTTAAACTG-AAGACCT 1082
                              v      i  v      i -  i ?    i    -  -    v  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA-TGTAAGAGCT 519

  chr1_75236292_7   1083 CAAACCGTGAAACTACTACAAGAAAACATTGGGGAAACTCTCCAGGATAT 1132
                         v    ii i     vi  v          v  ? v  v   i iv  iv 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr1_75236292_7   1133 TGATCTGGGCAAAAATTTCTTA--TGTAATATCCCACAAGCACAGGCAAC 1180
                           ivi i     vii       -- i i i --   v       i     
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACA--CCAAAAGCACAAGCAAC 617

  chr1_75236292_7   1181 CACAATAAAAATGGGCAAATGGGATTACATCAAG-TCAAAG--TTCTGGA 1227
                         v v iv      i ii    v   i v      i- i   i--  i  vi
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_75236292_7   1228 CACCTAAGGAAACAATCAAAACAGTGAATAGACAACCCAGAGAATCAGAG 1277
                          vi v     v  v     i v      v          v     vi   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_75236292_7   1278 AAAATAGTTGTCAACTACCCATCTGAGAAGGAATTAATAACCAGAATATA 1327
                               v   iv  ii ivi      v    i i vi  v          
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_75236292_7   1328 TAAGGAGCTC--A-AACTCTATAGAAAAAATATAA-TAATCTGATTAACA 1373
                            i  i   -- -     v   iv     v i  -   i ii   ? v 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_75236292_7   1374 AATGAGCAAAAG-TTGAAACAGACATCTCTCAAAAGAAGACATAG----G 1418
                             i     i -  vi  i      i    v        i   v---- 
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_75236292_7   1419 GCAAACATGTATATGAAAAGGTACTCAACATCATTGATCAT 1459
                           v  i v i i        i i          ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (86 / 56)
Gap_init rate = 0.02 (12 / 588), avg. gap size = 1.58 (19 / 12)  


3169 27.20 0.55 0.55  chr1_75284817_75291093.rev     4879  5786 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75284817_7   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGATTCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      i i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75284817_7   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75284817_7   4979 TACCAATGACTTCCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i ii  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_75284817_7   5027 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAAACCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv   v i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_75284817_7   5077 AACAAAGCCAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                iii    vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_75284817_7   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_75284817_7   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_75284817_7   5225 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_75284817_7   5275 CTATTTAATAAAGGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCC 5324
                           v  i  i   v          v      v  ?   i   i i  iivi
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_75284817_7   5325 AAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGGTGGT 5374
                         i  ii    i    v   i     v           i  i    ii   v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_75284817_7   5375 ATAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                         vi ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_75284817_7   5425 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5473
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_75284817_7   5474 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGTATCTA 5523
                         vi            vvi          vv     v  i    v v ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_75284817_7   5524 ATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAA 5573
                           i   v v  i i   i   i vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_75284817_7   5574 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5623
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_75284817_7   5624 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTAACAAGAAA 5673
                          i  i  vi          v  i  v      vv    v i  i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_75284817_7   5674 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5723
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_75284817_7   5724 CTCAAAAGAAGACATTTATGCAGCCAGAAAACACATGAAAAAATGCTCAC 5773
                            v        i  vi viii    iv  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_75284817_7   5774 CATCACTAGCCAT 5786
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 204 22.78 0.00 12.66  chr1_75335346_75337321.rev      343   421 (1555)    L1M4_orf2#LINE/L1      377   445 (463)  

  chr1_75335346_7    343 TTCGAAGGAGCAAGAAGGTCAATAGCTGACTTTACCAATAAATGGGGCCA 392
                            i v  i v     ------   i---    -i   i      v  ii
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAA------TAGT---CTTT-TCAACAAATGGTGCTG 416

  chr1_75335346_7    393 GGTTAATTAGCTATCCATATGCAAAACAA 421
                           vi  i i v  ?   i        v  
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAA 445

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.04 (3 / 69), avg. gap size = 3.33 (10 / 3)  

1344 27.33 10.12 4.53  chr1_75335346_75337321.rev      626  1485 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75335346_7    626 TGGAAAGACATGCTAAAGTTCATGGTATGGAAGAA--AATACTGTTAAGA 673
                                 i  v i v-        vv       v--    i        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_75335346_7    674 TGGCAAT-TTCCTAAAACTGATCAATATATTTGCTGTAATAGATTGTATC 722
                                -i   iv   i     v i v   iivi i   ---iiv    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT---CCCTATC 96

  chr1_75335346_7    723 AAAATCTTAATTGTTTTCCCTTTTGGGGTAGAAATAGACAAGTAGGT--- 769
                               ii ii  ii  ---     ---i      v      iv i ---
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTT---TTTTG---CAGAAATTGACAAGCTGATCCT 140

  chr1_75335346_7    770 -AAATTT-TATGAAAACATAAAGGGCCAAGAATGGGCAATACAAACTTGA 817
                         -     i-    i   iii  i  i  v     i v   v    v     
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_75335346_7    818 A---TAACAACAAAATAGAAA----CACATTATCATATATTAAAA---AT 857
                          ---v  v      i v i i----    i vi vv  v i    --- i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_75335346_7    858 TATAGACCTACCATGATTAGAATGATTAAGTAGCAACACAAAAATAAA-- 905
                           i i v    vi i  i ii iii vvi   viii  i  ii   i --
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_75335346_7    906 --TAGACCAATAAAATAGAACAGAAGGTACAGAAATTGACACA-ACAT-- 950
                         --    i    ii       iv  ii  v       vi  v  -    --
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_75335346_7    951 ACGGACATTTGATTTATGGCAAATATGTC--------TCTACAGAGAAGC 992
                          i  v  v       vi i   ivi  i --------  v ii i   i-
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA- 389

  chr1_75335346_7    993 TGGACA---TTTTC---------TATT-------TT---CATCAACATAA 1020
                         - i i ---     --------- ii -------i ---i ? v    i-
  L1M4_orf2#LINE/    390 -GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG- 437

  chr1_75335346_7   1021 CAAAA-----AAGCTTCACTTTCTACCTCACACCACACACAAAATTCAGT 1065
                              -----   i vv  ii-             i i      v i ii
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCC-CTACCTCACACCATATACAAAAATTAAC 486

  chr1_75335346_7   1066 TCCAAATGAATTGTAAATCTACACAGCAAAGGTAAAAC---AAAGTTTCT 1112
                           v     i  ii? i i   v iivv i  v      ---   ii ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_75335346_7   1113 AGATGATATCATAGAAGATATATCTTCATTATCTTTGAGTATAAACAAT- 1161
                            v  v v     i? -  v      i v i   - i  -  ii    -
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNG-TAAATCTTCGTGACCTT-GGGT-TAGGCAATG 583

  chr1_75335346_7   1162 --TTCTTGCACATGTCACCAAAAA---AAGCATGGCTCATGAAGGAAAAA 1206
                         --     iv i   v        i---     v----  -i   i     
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAA----CA-AAAGAAAAAA 628

  chr1_75335346_7   1207 T-GATGAAATAAACTACATTAAAATTAGGAACTT--GTGCT-CAATGAAA 1252
                          -   i  v ii   v   i       ii     --     -   v i -
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA- 677

  chr1_75335346_7   1253 CATTCCATTAAGAGAGTAGAAAAAGCCAAGCAACTAAGTAGGAGAAAATA 1302
                           i --  i    i   i--     v   v v  vi i i          
  L1M4_orf2#LINE/    678 CACT--ATCAAGAAAGTG--AAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_75335346_7   1303 TT--CTAAGCACATACAATTATCAAAAAGCTTTATATGCAGATTACATGA 1350
                           -- v  v  i   iv- v  --  ii vi  i   v    v  i  i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATC-TGAT--AAGGGACTTGTATCCAGAATATATAA 770

  chr1_75335346_7   1351 AGAAATTAAGCAAATCCATTTAAATAAATAATAAAGACAAGCCAGTAGGC 1400
                             v ivvi   v  v  ---      -  v v i i  v   i ---i
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAAT---AATAAA-AAGACAAATAACCCAAT---T 813

  chr1_75335346_7   1401 CAAAA---GACAAAAAGACTTGTACAG-CTCTTCACAAAAGAGAATATAC 1446
                         ?    --- i    i-  i   v i  - vi   v v     ii      
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAG-GATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_75335346_7   1447 AAATACCTGAT--------GAAAAAATGCTCAGTCATCAGGGAAAGG 1485
                             iv ii  --------     i       i-     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (150 / 81)
Gap_init rate = 0.05 (48 / 908), avg. gap size = 2.62 (126 / 48)  


1438 26.83 3.66 1.02  chr1_75353629_75360036.rev        2   493 (5915)    L1M4_orf2#LINE/L1      319   823 (85)  

  chr1_75353629_7      2 CTAGAAATAAAGCTAAATATTTACAGCCAACTGATCTTTGACAAAGCAAA 51
                          i         v i v i     ii i   i    i  i     i vviv
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_75353629_7     52 CAAAAACATAAAGTGGGGAAAGGACATCCTATTCAACAAATGGTGCTGGG 101
                            i v   vv i         i i vi  v                   
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_75353629_7    102 ATAATTGGCAAGCCACATATAGAAGAATGAAGCTGGATCCTCATCTCTCA 151
                          i  i   vv ?      ii i          i    i  ii i   v  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_75353629_7    152 CGTTACACAAAAATCAACTGATGATGGACCAAAGACTTAAATCTAAGACC 201
                          vv  i        i    v vi     i  ?    i     v     v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_75353629_7    202 TGACACCATAAAAATTCAAGAAGATAACATTTGAAAAACTTTTCTCAATG 251
                          i v  i      v iiv      v     vv ?iv  v i   vii iv
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_75353629_7    252 TTAGCTTAGGCAAAGAATTCATGACCAAGA-ACCCAAA-CACAAATGCAA 299
                           i v        v iv   v iivi v  -   v   -     --    
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GCAA 616

  chr1_75353629_7    300 CAAAAACAAAGATAAATGGATGGGACCTAATTAAACTAAAAAGCTTCTGT 349
                              iv   i   i  ii  v    i v  i   v v    i   i   
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_75353629_7    350 ACAGCAAAAGAAATAATCAGCAAAGTAAACAGGCAACACACAGAATGGGA 399
                         i vv    i  v iv    iv     i  v  i    v            
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_75353629_7    400 GAAAATTTTTTGTAACCTATGCACCCAACGAAGGACTAATATCCAGAATC 449
                               v   - i  vii  ii i ii ii i     vi          v
  L1M4_orf2#LINE/    717 GAAAATATTT-GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_75353629_7    450 TACAAGAAACTC----AA---AA-AATAAAGCAAGAAAAAAAAC------ 485
                           i  ii     ----  ---  -      --    v   v   ------
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAA--AAGACAAATAACCCAATT 813

  chr1_75353629_7    486 --AAAATGGG 493
                         --        
  L1M4_orf2#LINE/    814 WAAAAATGGG 823

Transitions / transversions = 1.39 (75 / 54)
Gap_init rate = 0.02 (9 / 505), avg. gap size = 2.56 (23 / 9)  

3199 26.73 0.66 0.77  chr1_75353629_75360036.rev     5009  5917 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75353629_7   5009 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5058
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75353629_7   5059 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75353629_7   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_75353629_7   5157 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5206
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_75353629_7   5207 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5256
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_75353629_7   5257 TATAGTGATCAAAAAAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5306
                           i   i     i v  ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_75353629_7   5307 AATGGAACAGAACAGAGCTCTCAGAAATAACACCACACATCTACAACCAT 5356
                                i    iv   vvii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_75353629_7   5357 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGGAAGGATCCCCT 5406
                         i    i  i     ivv  v   i v  vvv       i   i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_75353629_7   5407 ATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5456
                         v  i  i          i   v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_75353629_7   5457 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5506
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_75353629_7   5507 AAAGACTTACATTTTAGACCTAAAAACCATAAAAACCCTAGAAGAAAACC 5556
                          ?    i  v  v v   v      - i      vi i           v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACA 547

  chr1_75353629_7   5557 TAGGCA-ATACCATTCGGGACATAGGCATGGGCGAGGACTTCATGACTAA 5605
                             ?i- v i -    v   v v  vv i   i v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_75353629_7   5606 AACACCAAAAGCAATGGCAACAAAAGCCAAAGT---TTCAAATGGGATCT 5652
                         i            vvi          vv   i --- --    v   ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT--AAATTGGACTT 644

  chr1_75353629_7   5653 AATTAAACTAAAGAGCATCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5702
                         v  i   v v  i i v i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_75353629_7   5703 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCGTCTGAC 5752
                          v  i     i                 v       vii ivii     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_75353629_7   5753 AAAGGGCTAATATCCAGAATCTACAAAGAACTTACCCAAATTTACAAGAA 5802
                           i  i  vi          v  i        iviv   v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_75353629_7   5803 AAAAATCAAAGGACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5852
                            i -    vi    v  i?    i            v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_75353629_7   5853 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 5902
                              v        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_75353629_7   5903 ATCATCACTGGCCAT 5917
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


3340 17.35 5.54 0.15  chr1_75393912_75395585.rev      498  1183 (491)    L1M4_orf2#LINE/L1      186   908 (0)  

  chr1_75393912_7    498 CTTGAAAAGGAACAAAAAAGCTGGAAGACTCATACTTCCTGATTTCAAAA 547
                                 i   v  v    i    i      i      ii         
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_75393912_7    548 CTTATCATAAATCTACAGCAATCAAAAGAGTGTGGTACTAGCATAAGGAC 597
                             ii i   v      i      i v           i         i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_75393912_7    598 AGACATATAGA--GGTAAAATAAAACAGAAATCCCAGAAACTAACTCTCA 645
                                    --ii ii    i  iv  i vi       iv   i vi 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_75393912_7    646 CAT--AT---------------------------AAGACCATTCAATGGG 666
                            --  ---------------------------                
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_75393912_7    667 AAAAGATCAGTCTTTTCAACTAATGGTGCTGGGAAAATGGGATATCCACA 716
                         i     vi            v             v  iv     ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_75393912_7    717 TGCAAAAGAATGAAGTTCAACCT-TATCTTACATTAACATACAAAAATTA 765
                                          vi   i-  i  i   ii -i            
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA-TATACAAAAATTA 484

  chr1_75393912_7    766 ACTAAAAATGGATCAAAGACCTAAACAAAAGCACAAAAACTATAAAACTC 815
                            v           ?         iiv   vi v               
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_75393912_7    816 TTAGAAGAAAACATAAGATGAAAGCTTCATGACATTGGATTTGGTGATTA 865
                                        i ?vv   v    i    v    i  v  ii  vi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_75393912_7    866 TTTCTTAGATAGTACACCCAAAGCATAGGCAACAAAAGAAAAA-----TA 910
                                    vv     v      i i               -----  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_75393912_7    911 AATTGAACTTCATCAAATTTAAAAACATTTATTCAACAAAGAACACTACC 960
                              i           v        v   i v vv     i      i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_75393912_7    961 AAGAGAGTGAAAAGACAGCCCACATGATGGAAGAAAATATTTCCAAATCA 1010
                             i            i      vi    i           v       
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_75393912_7   1011 TATGCCAGATAAGGAATTCATATCCAGAACATA-AAAGAACTTCTACAAC 1059
                            ii v       i i ii         i   -        ii      
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_75393912_7   1060 TCAACAGCAAAATAATAAGCAACCCAGTTCAAAAATGGACAAAGAACTTG 1109
                             i ii    vi i  ii      i  ?        i     i i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_75393912_7   1110 AATAGATATTTCTCCAAAAATGATATACAAATGGCCAATGAGGACATGAA 1159
                               i           i v                  i  v       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_75393912_7   1160 AAGATGCTTAATATCACTAGTCAT 1183
                                 i  i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (78 / 37)
Gap_init rate = 0.01 (7 / 723), avg. gap size = 5.57 (39 / 7)  


2859 27.62 1.22 0.88  chr1_75437584_75441598     2618  3522 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75437584_7   2618 TGGAAAAATATTTCATGCTTATGGATAGGAAGAAACAATATTGTGAAAAT 2667
                               i    ii    i i      v      vvi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75437584_7   2668 GCCA-TATTTCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 2716
                          v  -  i i      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75437584_7   2717 TACCA-CTGACTTTCTTCATAGAA-TTGGAAAAAACTA--CTTAAAAGTT 2762
                          v   -   v    i  -ii    -   -- v  i  i-- i     -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAA-TT 146

  chr1_75437584_7   2763 CATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAA 2812
                                  viiv  ii  v  v v  v     i      i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_75437584_7   2813 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 2862
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_75437584_7   2863 GCTACAGTAATAAAAACAGCATGGTACTAGTACCAAAACAGATATATAGA 2912
                                    v  i    ii       i i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_75437584_7   2913 CCAATGGAACAGAACAAAGGCCTCAGAAATAACGTCACATATCTACAACC 2962
                         i        i    ivi  ivii         vvi  i i  i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_75437584_7   2963 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATCTGGAAAGAAT--T 3010
                          vi    i  i     ivv  v   i v  vv    vv         -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_75437584_7   3011 CCCAATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAG 3060
                          ii--  i  i        i     v      v  ?   i     i  ii
  L1M4_orf2#LINE/    397 CTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_75437584_7   3061 CTGAAACTGGATCCCTTCTTTAC--CTTATACAAAAAGTAACTCAATATG 3108
                         v    ii    i    v i i  -- v          v        v   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_75437584_7   3109 GATTAACGACTTAAAAATAAGACCTTAAACCATAAAAAACCCTAGACAAA 3158
                            i ?v   i    vi     v  v    i      v-i i    vi  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAA 543

  chr1_75437584_7   3159 AACTTAGGCA-ATACCATTTAGGACATAGGCATAGGCAAGGACTTCATGA 3207
                            v    ?i- v i -  iiv   v v  vv       v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_75437584_7   3208 CTAAAACAT-GAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGGT 3256
                         v  vi   i-i      vvi          vv     v  i    v  ii
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_75437584_7   3257 CTAATTAAACTAAAGAACTTTGGCACAGCAAAAGAAATTAACATCAGAGT 3306
                         i v  i   v v  i      v ii vv    i  v i  v  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_75437584_7   3307 GAACAAGCAACCGACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTG 3356
                            v ii     v                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_75437584_7   3357 ACAAATGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAG 3406
                          i  iv i  vi          v  i   v    ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_75437584_7   3407 ATAAAAACAAACAACACCATCAAAAAGTGGCTGAAGGATATGAACAGACA 3456
                          v   i     i   v v  i?    i   vii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_75437584_7   3457 CTTCTTAGAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCT 3506
                         i    ivi       i  vi viii     i  i  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_75437584_7   3507 CATCATCACTGGTCAT 3522
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (143 / 103)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.36 (19 / 14)  


2589 22.14 2.16 8.65  chr1_75449275_75452218.rev     1485  2455 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75449275_7   1485 TGGAAACCCATCCTATGCTCATGGATGGATAGAATTAATATTGTGAAAAT 1534
                               vvi    i   i        v iv   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75449275_7   1535 GACCATACTGCCAAAAGCAATCTACAAATTCAGTGCAATTCTCATCCA-- 1582
                          i v     v  v   vii       i     ii     i ii   v --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75449275_7   1583 --CCAG--GA-TTCCTCACAGAACTAGAAAAAAACAATCCTAAAATTCAT 1627
                         --    -- v-  ii ii     v v  v  iv-ii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_75449275_7   1628 ACGGAATAAAAAAAGAGCCCACA-TAGCCAAAGCAA----GACTAAGCAA 1672
                          i    - viv  i ii    v -        i   ----  vv   -  
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG-AA 197

  chr1_75449275_7   1673 GAACAAATCTGGAGACATCTCATTACCTGACTTCAAACTGTACTTTAAGG 1722
                                vi     ivv  v  i v  ii i      viv    vi  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_75449275_7   1723 CCATAGTCACCAAAACAGCATGGTACTGATATAAAAATAGGCACATAGAC 1772
                          i i   v i   i    ii        ii    ii    i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_75449275_7   1773 CAATGGAAAAGAATAGAGAACCCAGAAGTAAAGCCAAATACTTAACACCC 1822
                                 v     v    ii      i    v   v i i   -iivi 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTC 346

  chr1_75449275_7   1823 AACTGATCTTTGACAAAGCATAC-AAAACG--TAAATTGGGGAAAGGACA 1869
                           i    i  i     i -i i -  i  v-- v   -        i i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGG-GTGCCAAGACCATTCAAT-GGGGAAAGAATA 394

  chr1_75449275_7   1870 TCCTGTTCAATAAATGGTGCTAGGAAAACTGGCAAGCCACATGTAGAATA 1919
                         vi  v     i          i   v      vv ?       i i  v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_75449275_7   1920 ATGAAACTGGATCCTCATCTCTCACTTAATACAAAAATCAACTCAAGATG 1969
                              ii    i  ii i   v   ivv          i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_75449275_7   1970 GATCA--GACTTAAATCTAGGACCTGAAACCATAAAACTTCTAGAAAAAA 2017
                              --   i     v  i  v  i    i        ii     i   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_75449275_7   2018 ACATTGGAAAAACTCTTCTGGACATTGATTTAGGCAAAGAATTCATGACT 2067
                             v  ?iv  v     vv   v   iv        v iv   v iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_75449275_7   2068 AAGAT-CCAAAAGCA-AAGCAACAAAAACAAAAATAAAAAAAAAATAAAA 2115
                          v  i-         -           i-----------        i -
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAG-----------AAAAAATAGA- 632

  chr1_75449275_7   2116 GCAAACTGGTCATGATACAATATCTATCTTGTGAGAAATAAAATATTACA 2165
                         -i   i   -------  ---- ii   ----- i  v     vv  vii
  L1M4_orf2#LINE/    633 -TAAATTGG-------AC----TTCATC-----AAAATTAAAAACTTTTG 665

  chr1_75449275_7   2166 AGTCTAAAAAAAAAAAAAAGAAATGGGACCAAATTAAACTAAAAAGCTTC 2215
                         v ii v   ----------------    --------    ---------
  L1M4_orf2#LINE/    666 TGCTTCAAA----------------GGAC--------ACTA--------- 682

  chr1_75449275_7   2216 TGCTCAGCAAAATAAATAAGCAGAGTAAATAGACAACTCAAAGAGTGGGA 2265
                         ---   -- i  -----------   i  v       i  v   i     
  L1M4_orf2#LINE/    683 ---TCA--AGAA-----------AGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_75449275_7   2266 GAAAGTATTTGCAAACTATGCATCTGACAAAGGACTAGTGTCCATAATCT 2315
                             i          ii  ii      i  i     v  i    v   v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_75449275_7   2316 ACAAGTAACTCAAACAAATCAGCAAGAAAAATACAAACAATCCCATC-AA 2364
                          i  iv     vv    v   ii  v     v     i  i  v  i-  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_75449275_7   2365 AAGTGGGCTAAGGACATGAATAGACATTTCTCAACAGAAGATATACAAAT 2414
                           i     v     iv                v v               
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_75449275_7   2415 AGCCAACAAACATATGAAAAAATGCCCAACA-CACTAATCAT 2455
                         i     i  i  i       i    i     -  ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (131 / 82)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.75 (105 / 28)  


2831 26.10 1.76 1.76  chr1_75460455_75464714.rev     2862  3769 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75460455_7   2862 TGGAAACACATACCATGCCCATGGGTGGGTAGAATCAATATTGTGAAAAT 2911
                               v i  v     ii     i v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75460455_7   2912 GACCATACTGCTGAAAACAATGTACAGATT--AGGCCATTTCACATCAAA 2959
                          i v     v iv   vii  v        -- v  v  ii -i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC-TATCAAA 99

  chr1_75460455_7   2960 ATACCA-TTA--TTCTTCACAGAAGTCGAAAAAACAATCTTAAAATTCAT 3006
                           v   -i i--  i  ii     i i  v  ivii   i          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_75460455_7   3007 ATGGAATCAAAAAGGAGCCTGCATAACCAAAGCAAGAGTAAGCAAAAAGA 3056
                               viiv  i   v  v v   i     i   vvv i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_75460455_7   3057 ACAAATCTGAAGGGATCACAGATCACATCACCCAACTTCAAACTATACTA 3106
                              vi  i   ----  ---     iiv     i      viv     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG----AC---TCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_75460455_7   3107 TAAGGCCATAGTCACCAAAACAGCATTGTACTGCTATAAAAATAGGCACA 3156
                         i  i  i i   v i   i    ii v      vi    ii    i  i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_75460455_7   3157 TAGCCCAATGGGGCAGAATAGAAAACCCAGAAATAAAGCCAAATACTTAC 3206
                            vi      iii     v  i ii           v   v i i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_75460455_7   3207 AGCCAACTGATCTTCGACAAAGCAAACAAAAAAA---AAAGTAGGGAAAG 3253
                         i i   i    i        i vviv   i vv ---  -- i       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAG 390

  chr1_75460455_7   3254 GAAATCCTGCTCAACAAATGGTGCTGGGATAATTGGTAAGCCACATGTAG 3303
                         i v vi  vi                   i  i   vv ?       i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_75460455_7   3304 AAGAATAAAACTGGATCTTCATCTCTCACCTTATACAAAAATCAACTGAA 3353
                               i  ii    i iii i   v    v           i    v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_75460455_7   3354 GATGAATCAAAGATTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAA 3403
                         i   i    ?   ii     v     v  i    i      v ii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_75460455_7   3404 TATAACATCAGAAAAACTCTTCTGGACATTGGCTTAGACAAAAAGTTCAT 3453
                         v v     vi ?iv  v     vv   v    v    i   viiv   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_75460455_7   3454 GACCAAGAACCCACAAGCAAATGTGACAAAAAAACAAA--GATAAATTGA 3501
                         iivi v  vv   v     v v ii      i  v   --         -
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG- 639

  chr1_75460455_7   3502 TGGGACTT------AACTAAAAAGCTTCTGCACAGAAAAAGAAATAATCA 3545
                         ---     ------  i      -   i  ii vvv   i  v iv    
  L1M4_orf2#LINE/    640 ---GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_75460455_7   3546 GCAGAGTAAACAGACAACACACAGAGTTGGAGAAACTCTTCACAAAATAT 3595
                         iv i   i  v       v      i v       v v  ii    vi  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_75460455_7   3596 GTGTCTGACAAAGGACTAATATCCAGAATCCACAAAAAACTCAAACAAAT 3645
                         i i     i  i     vi          vi i   i     vv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_75460455_7   3646 CAGAAAGAAAAACACCAAAGAATCTGATCAAAAAGTGGGCAAAGGACATG 3695
                           iv  v     v  -   v  i ii  i?    i           iv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_75460455_7   3696 AATAGACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACACATGAA 3745
                                 v     v                       i  i        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_75460455_7   3746 AGAATGCTCAAGATCACTAATTAC 3769
                          ii        v    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.46 (32 / 13)  


2583 22.25 0.96 14.23  chr1_75537125_75541537.rev     2876  3922 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75537125_7   2876 TGGAAAGATATCTTGTGTTCATGGAATGGAAGAATTAATATTGTTAAAAT 2925
                                     iii          v       v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75537125_7   2926 GTTCATACTATGCAAAGTGCTCTACACATTCAGTGCAATCCCTATCAAAA 2975
                          viv     viv    v  v      v     ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75537125_7   2976 TTTCAATGGCATTTTTCACAAATAGAGATAAAC-AATTGTTAAATTT-TA 3023
                          ii  iiv  v     ii  i v vv  i  i -i  iv v     i-  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_75537125_7   3024 TGGAACCACA-TAAACCCTGAAGAGCCAAAACAGTCTTGAGCAAAAGGAA 3072
                              vii  -vii    v   v          i      iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_75537125_7   3073 CAAAGCCAAAGACATTGCACCCCCTGATTTCATAATATATTATAAAGTAG 3122
                              iiii  ivv ii   ii  ii      v  iv  i  i    ivi
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_75537125_7   3123 TTGTAATCAAAATAGCATGACACTGGCATTAAAAACAGACACGTTTAACA 3172
                         iv        i i  ii  ii        -  ii i     ii vv v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATCA 299

  chr1_75537125_7   3173 ATGGCACGGGACAGAGAACCTACAAATAAAACTCACACATTTACATTCAA 3222
                             v ii i iv    ii i v       - i  i       iiv    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTCAA 348

  chr1_75537125_7   3223 GTGATTTTCAACAAAGGTGCTAAGAACACTCAATGGGAAAAAAAGATAGT 3272
                         v        i    i     i    v  i        i   i  --    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA--TAGT 396

  chr1_75537125_7   3273 TTCTTTGATAAGTAGTGTTGGGAAAACTGGATATCCAAATGTAGAAGAAT 3322
                         i i  ii i  i i   i     v         ?   v   i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_75537125_7   3323 TAAATTGAATTATTATCTCACATCATATACAAAAAACAACTGGCCAGGTG 3372
                         v  i   i iivi  i      i            vi    ---------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT--------- 487

  chr1_75537125_7   3373 CAGTGGCTCACACCTCTAATCCCAGCACTTTGAGAGGCCAAGGTGGGAGG 3422
                         --------------------------------------------------
  L1M4_orf2#LINE/    488 -------------------------------------------------- 487

  chr1_75537125_7   3423 ATCACTTGAAGCCAGGAGTTCAAAACCAGCCTGGACAACAAAGTGAGACC 3472
                         --------------------     ------    i--  ?  ----   
  L1M4_orf2#LINE/    488 --------------------CAAAA------TGGAT--CAWAG----ACC 505

  chr1_75537125_7   3473 CCCGTCTATGAAATAAAATAAATATTCAGCTTAAAATGGACAAAAGAATT 3522
                         ------------------     i ------------------    ii 
  L1M4_orf2#LINE/    506 ------------------TAAATGT------------------AAGAGCT 519

  chr1_75537125_7   3523 AAATATATACCTGAAACTATAAAACTACTAGAACAAAACAGAAGA--AAA 3570
                            ------------           vi     v      v i ?--   
  L1M4_orf2#LINE/    520 AAA------------ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_75537125_7   3571 TTTCCATGACACTTG--TCTGGTCATGGATTTTTTTGATATGAACCCAAA 3618
                          i i i    -    -- iv  iv    -   i  v       vv     
  L1M4_orf2#LINE/    558 TCTTCGTGAC-CTTGGGTTAGGCAATGG-TTTCTTAGATATGACACCAAA 605

  chr1_75537125_7   3619 AATATAGCCAACAAAAGCAAAAATGGACAAATGAGATTGCATCAAA-TAA 3667
                          ii i iv         v      i  i    vi  i v       - v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_75537125_7   3668 AAAGCTTTTGAACAGTAAAGGAAGTAATTAACAAAGTGAAAAGGCAGACA 3717
                            i      vi vvi      viiv  i  v           ----   
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG----ACA 701

  chr1_75537125_7   3718 ATTTGC-GAGTGGGAAAACTTATTTTCAAACCATACATCTGATAAGAAAT 3766
                          iiii -  i     i  vv     v    i    i          ii i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_75537125_7   3767 TTATGTCCAAAATACATAAGAGGCTCAAACAACTCAGTAGCAAGGAAACA 3816
                           i i    i    i    iiii   vv        i  ii  ii i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_75537125_7   3817 AGTAACTCAATTAAAACATAGGGAAAGGACCTGAACAGACATTTCTCAAA 3866
                          i    i     ?   v  i  v      ii    i           v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_75537125_7   3867 AAAAGATATATAAATGACTGACAGG-ATGTGAATAAATGCTCAATATTAC 3915
                          i        i     i ii i i - ii    v i        i  i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_75537125_7   3916 TAATCAC 3922
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.32 (160 / 69)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 7.57 (159 / 21)  


3309 26.76 0.44 0.44  chr1_75560665_75565678     3614  4521 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75560665_7   3614 TGGAAGAACATTCCATGCTCATGGGTAGGAAAAGTCAATATCGTGAAAAT 3663
                              ii i  i     i      i v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75560665_7   3664 GGCCATACTGTCCAAGGTAATTTACAGATTCAATGCCATCCCTATCAAGC 3713
                            v     vi    iv i  i           i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75560665_7   3714 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3761
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_75560665_7   3762 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 3811
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_75560665_7   3812 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3861
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_75560665_7   3862 TACAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3911
                                 v   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_75560665_7   3912 AATGGAACAGAAC--AGAACCCTCAGAAATAACGCCGCATATCTACAACT 3959
                                i    i--   ii  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_75560665_7   3960 ATCTGATCTTTGACAAACCTGAAAAAAACAAGCAATGGGGAAAGGATTCC 4009
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_75560665_7   4010 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4059
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_75560665_7   4060 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4109
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_75560665_7   4110 TTAAAGACTTACAAGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAAC 4159
                          i ?    i  v v  v   v       i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_75560665_7   4160 CTAGGCATTACCATTCAGGACATAGGCTTGTGCAAGGACTTCATGTCTAA 4209
                         v    ?i v viv   iv   v v  v  iv    v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_75560665_7   4210 AATACCAAAAGCAACGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4259
                         i i          vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_75560665_7   4260 TTAAACTAAAGTGCTTCTGCGCAGCAAAAGAAACTACCATCAGAGTGAAC 4309
                          i   v v  ivi   i  i  vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_75560665_7   4310 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4359
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_75560665_7   4360 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4409
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_75560665_7   4410 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 4459
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_75560665_7   4460 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 4509
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_75560665_7   4510 ATCACTGGCCAT 4521
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2047 25.11 0.61 4.29  chr1_75566008_75570620     2915  3567 (1046)    L1M4_orf2#LINE/L1        1   629 (279)  

  chr1_75566008_7   2915 TGAAAAAATATTCCTTGCACATAGATTGGAAGAATCAATATTGTTTAAAT 2964
                           i   i    i  v  iv   i          v i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75566008_7   2965 GGCCATACTGCCCAAAGCAATATACAGATTCAACATTATGCCTATCAAAC 3014
                            v     v      vii  v            iiv  v         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75566008_7   3015 CACCAACACCATTTTTTGCAGAATTAGAAAAAACTAATC-TAAAATTTAT 3063
                         iv   i vv v            v v  v  i-  i   -       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_75566008_7   3064 ATAAAACCAAAAAAGAGCCCAAATAGCCAAAGCA-TCCTAAACAAAAAGA 3112
                           ii  viiv  ii  v  vi          i  -  i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_75566008_7   3113 ACAAAGTTGGCATCACATTACCCAACTTCAGACATCACATTACCTAATTT 3162
                                   ------------- i-----   -     i v  i     
  L1M4_orf2#LINE/    200 ACAAAGTTGG-------------AG-----GAC-TCACACTTCCCAATTT 230

  chr1_75566008_7   3163 CAAACTATACTATAAGGCTACAGTAATCAAAACAGCATGGTACTGACATA 3212
                             viv     i  i              i    ii        i    
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_75566008_7   3213 AAAACAGACGTATAGACCCATGGAATAGAATAGAGAACTCAGAAATAAAG 3262
                          ii i    i      i v            v    iii          v
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_75566008_7   3263 CTGCACTCCTACAACCAACTGACTTTCAACAAAGCCAACAATAATAAGCA 3312
                          iii  vii  iiii   i   i    i    i viiv   v vi vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_75566008_7   3313 ATAAGGAAAGGACTCCCTGTTTAATAAATGGTGTTGTGGTAGCTGGCTAT 3362
                           ii      i ivvi  v  i  i        i  v ii i    v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_75566008_7   3363 CCATATGCAAAAGAAAGAAACTAGACCTCCTACCTATCACCATATACAAA 3412
                            i           v   ii i    -       vv             
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACC-CCTACCTCACACCATATACAAA 479

  chr1_75566008_7   3413 ACTTAACTCGTGATGGATTGAATATTTAAATGTAAGACCTCAAACTATAA 3462
                          v       ivi      ii? v ii           v  v         
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_75566008_7   3463 GAATACTAGAACACCACCTAGGAAATAACCTTCTAGACATTGGTCTTGGC 3512
                         i v vi     v vv  v    ?ivv  i    vv   v    vi v   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_75566008_7   3513 AAAGAATT--TAGAACTAAGTCCACAAAAGCAATTTTAACAACAACGACA 3560
                           v iv  --    --  v v vv        ---iv i      -- vi
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGA--TATGACACCAAAAGCA---CAAGCAACAA--AAG 622

  chr1_75566008_7   3561 AAAAAAT 3567
                                
  L1M4_orf2#LINE/    623 AAAAAAT 629

Transitions / transversions = 1.30 (91 / 70)
Gap_init rate = 0.02 (11 / 629), avg. gap size = 2.91 (32 / 11)  

 715 24.45 8.03 1.46  chr1_75566008_75570620     3847  4120 (493)    L1M4_orf2#LINE/L1      617   908 (0)  

  chr1_75566008_7   3847 CAAAAAAAAAAATTGACAAGTGGGACCTAATTAAACTGAAGAGCTTCTGC 3896
                              i       v  i  i v    i v  i   v v  i i   i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_75566008_7   3897 ACAGCAAGAGAAACTATCAACAG-GTAAAGAGACAACTGACATAATGGGA 3945
                         i vv   ii  v        v i-  i  i       iv   v       
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_75566008_7   3946 TAAAATATTAATAGCAAACTATGCACCCAACAAAGGTCTAATATCCAGAA 3995
                         v        -- -     ii  ii i ii i  i  v  vi         
  L1M4_orf2#LINE/    717 GAAAATATT--T-GCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_75566008_7   3996 TCTATAAGGAACTT----AACCAAACAAGTAAAAAACAATT---CCA-TT 4037
                          v     i     i----   iv  i  vv    i    v ---   -  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_75566008_7   4038 AAAAGGTGGACAAGATACTTCAA-------------AAAGAAGATATACA 4074
                         ?   ii   i   iiv i  v  -------------              
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_75566008_7   4075 AGTGGCCAAGAAACAAACGAAAAAAATGCTTCACATCATGCATCAT 4120
                          i       v  i  v i     i -    iv      ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (42 / 24)
Gap_init rate = 0.03 (8 / 292), avg. gap size = 3.25 (26 / 8)  


3322 26.15 0.44 0.66  chr1_75579602_75586329     5327  6236 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75579602_7   5327 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5376
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75579602_7   5377 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5426
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75579602_7   5427 TACCATTGACTTTCTTCACAGAATTAGAAAAAAACTAACTC-AAATTTCA 5475
                          v   vivi i  i  ii     v v  v  i--  i ii -   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_75579602_7   5476 TATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAACAAAAAG 5525
                                viiv  ii  v  viv        i      i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_75579602_7   5526 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5575
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_75579602_7   5576 TACAGTAACCAAAACAGCATGGTACTGGTACCAGAACAGATATATGGACC 5625
                                 i   i    ii         i iv  i i   i    i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_75579602_7   5626 AATGGAACAGAACAGAG-GTCTCAGAAATAATGCCACACATCTACAACCA 5674
                                i    iv   -   -         vv   i    i  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chr1_75579602_7   5675 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5724
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_75579602_7   5725 TATTTAATAAATGATGTTGAGAAAACTGGCTAGCCATATGCAGAAAAGTG 5774
                          v  i  i     i  i  i  v      v  ?   i     i  i i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_75579602_7   5775 AAATTTGACCCCTTCTTTATACCTTATACGAAAATTAACTCAAGATGGAT 5824
                           i  v       v i i i   v     i             i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_75579602_7   5825 TAAAGTCTTAAATGTAATACCTAAGACCATAAAAATCCTAGAAGAAAACC 5874
                         i ?  v i         v v    i  i      v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_75579602_7   5875 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGGCTTCATGACTAA 5923
                             ?i- v i -   iv   v v  vv i     v  i   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_75579602_7   5924 AACACCAAAAGCA-ATGCCAACAAAAGCCAAAATTGACAAATGAGATCTA 5972
                         i            - v  -        vv     v  i    vi  ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_75579602_7   5973 ATCAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTATCATCAGCGTGAA 6022
                               v v  i ii  i  ii vv    i  v       vv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_75579602_7   6023 CACACAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACA 6072
                         v v      i                 v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_75579602_7   6073 AAGGGCTAATATCCAGAATCTACAAGAAACTTACACAAATTTAGAAGAAA 6122
                          i  i  vi          v  i  ii    ivi    v iv v  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_75579602_7   6123 AACAACAAATAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 6172
                           -i           v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    796 AA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_75579602_7   6173 TCTCAGAAAAAGACATTTATGTGGCCTACAAACATATGAAAAAAAGCTCA 6222
                             vi  i    i  vi vi     v i  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_75579602_7   6223 TTGTCGCTGGTCAT 6236
                         vii  i????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


2735 26.16 3.61 1.24  chr1_75629013_75633975     3584  4470 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75629013_7   3584 TGCAAAAACATTCCATGCTCATGGATTGAAAGAATAAATATCATTAAAAT 3633
                           v   i i  i     i          i    v v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75629013_7   3634 GAACATACTGCCCAAAGCAATCTACAGATTCAATGCTATTCCTATCA--- 3680
                          ivv     v      vii              i  v  i       ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75629013_7   3681 ---CA-CTATCATCTTCACAGAAATAGAAAAAAACT-ATTCTAAAATTCA 3725
                         ---  -  ii v i  ii       v  v  i--  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_75629013_7   3726 TATGGAACACAAAAAGAGCCCA-AATAGCCCAGACAATTCTAAGCAAAAA 3774
                                - iiv  i ii    -       v i     ii i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_75629013_7   3775 GAACAAAGTCAGAAGCATCACATTACCAAACTTCAAACTATATTATAAGG 3824
                                  ii  i vv     i v  v  i      viv  i  i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_75629013_7   3825 TTGTAGTAACCAAAACAGCATGGTAC------AAAAACAGACACATGGAT 3868
                         i ii     i   i    ii      ------  ii i     i  i   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_75629013_7   3869 CAATAGAACAGAATAGAGAACTCAGAAATAAAGCCACATACCTAAAGCCA 3918
                             i   i     v    iii          v   i i ii  vi i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_75629013_7   3919 TATGATCTTCAGCAAGT-CAACAAAAATAAACAATGCGGAAAGGACTCTC 3967
                         vv    i   ii    v-iiv   i vi vv     v      i ivv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_75629013_7   3968 TATTCAATATATGGTGCTGGGATAGCTGGCTAGCCATGTGCAGAAGAGTG 4017
                          v     i v            i i    v  ?   ii    i    i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_75629013_7   4018 AAACTGGACTCCTACATATCACCATAGACAAAATTTAACTCAAAATGGAT 4067
                           ii     i     v vv       v      v                
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_75629013_7   4068 TAAATATTTAAATATAATACCTCAAACTATAAGAATCCTAGAAGAAAATT 4117
                         i ? v ii     i   v v  v         i v  i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_75629013_7   4118 CAGAC--AAAACAATTCTGGACATTGGCCTTGAGATAA-AATTTATGACT 4164
                         i  i?--   v --   vv   v    vi --  ii  -ii   v --- 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC--TTCGTGACCTTGGGTT--AGGCAATGGTTTCT---T 590

  chr1_75629013_7   4165 AAAT----CCTCAATAGCAATTGCAACAAAAGCAAAAATTAACAAGTGAG 4210
                          i  ---- vi   v    vvv          v      vi i  i vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_75629013_7   4211 AACTAATTAAACTAAAGCACTTCTTCACACCAAAAGATACTATCAACAAG 4260
                          vi v  i   v v  iv    i vii vi    i  i        v  i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_75629013_7   4261 GTAAACAGGACAGCCTACAGAATCAGAGAAAATATTTGCAAACTACACAT 4310
                           i  - i    i  i       vi                 ii i i  
  L1M4_orf2#LINE/    691 GTGAA-AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_75629013_7   4311 CCAACAAAATTCTAATATTCAGAATC----AATAACT-----AACTTAAC 4351
                          ii i  iivv  vi   i      v----  v    -----    i  i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_75629013_7   4352 AAGCAAAAAACAAATAACCCCATTGAAAAGTAGGCAAAAGACATGAACAA 4401
                           vv    i           v   ?    i i      i  iv    i i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_75629013_7   4402 ACACTTCTCAAAATAAGACATACAAGAGGCCAACAAATATATGAAAAGAT 4451
                            i     v   v    i      iv      i  ii i          
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_75629013_7   4452 TGTCAACATCACTAAGCAT 4470
                         vv         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (144 / 84)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.53 (43 / 17)  


3222 26.34 1.67 0.33  chr1_75641748_75646287     3152  4047 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75641748_7   3152 TAGATAAATATTCCAGGTTCATATACTGAAAGAATCAATGTTGTTAAAAT 3201
                          i  v i    i   v      iv i  i    v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75641748_7   3202 GTCCATACTACCCAAAGCAAGCTACAGATTCAATTCAATCACTATCAAAA 3251
                          v v     v      vii v            iv     v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75641748_7   3252 TACCAATGATATTCTCCACAGAAATAGAAAAAACAATCCTAAAATTTATA 3301
                          v   iiviiv  i iii       v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_75641748_7   3302 TGGAACCACAGAGGACCCAGAATAACCAAAGCTATCCCAAGCAAAAAGAA 3351
                              vii  ii            i     i v   iii iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_75641748_7   3352 CAAAATTGAAGAAATCAAATTACCTAATTGCAAATTATACTATGGAGCTA 3401
                             i   i  i v   v i v  i    v    viv     iii     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_75641748_7   3402 TAGAAACCAAAAACAGCTTGATAGTGACATAGAAACAGACACATAGACCA 3451
                         i  v  i   i -   iv  i  v  i    iii i     i     i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_75641748_7   3452 ATGGAACAGAATAGAGAACACAGAAATAAATCTACACACCTACAGTGAAC 3501
                               i     v    iiv          i i i   ii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_75641748_7   3502 TCATTTTCAATAAAGGTGCCAAGAACATACACTGAGGAAAAGACAGTCTC 3551
                          v      i i  i          v   v  v  i     ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_75641748_7   3552 TTCGATAAATGATGCTGGGAAAACAGGTTATCTATATGCAGAAGAACGAA 3601
                            i i     i        v   v  v  ? i i     i     i   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_75641748_7   3602 AGTAGATGCCTATCTCTCGCCATATACAAAAACTAAATCAAAATGGATTG 3651
                         iv i  iv    i   v i             i   v           ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_75641748_7   3652 AAGGTGTAAATCTAAGACTTCAATCTATGAAATTACTAAAAGAAAACTTC 3701
                         ?  iiv     v     vi v  v    i   i vi  i        v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_75641748_7   3702 AGGGAAACTCTCCAGGACATTGTTCTGGGCAAGAATTTCTTGAGTAATAC 3751
                         i ? v  v   i iv   v   vvi i     vii      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_75641748_7   3752 CCCACAAGTGCAGGCAATCAAAGCAAAAATGGACAAATGAGATAACATTA 3801
                         v   v   ii  i    iv    v      i  i    vi  ivv   i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_75641748_7   3802 A-GTTAAAAAGTTCTGCACAACAAAGAA-ACAATCAACAAAGTGAAGAGA 3849
                          -i       v  i  ii vv     i -  v     v        i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_75641748_7   3850 CAACTCACAAAATGGGAGAAAATATTTGCAAA-CAACCATACGACAAGAG 3898
                             i    i                      -  vvi  vi  i   i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_75641748_7   3899 ATTCATAACCAGAATACATAAGGAACTC----AACTCTATAGGAAAAAAA 3944
                          i ii  v        i    i      ----     v   iv     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_75641748_7   3945 TCTAATAATCCAATCAAAAGATGAACAAAAGATTTGAATAGACATTTCTC 3994
                         - v     i     i?   i   ii    i                    
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_75641748_7   3995 AAAAAAAAGGCATACAAA--------AGGCATATAACAAGGTTTTCAACA 4036
                         v   i  - ii       -------- i   i  i v   i vi      
  L1M4_orf2#LINE/    849 CAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_75641748_7   4037 CCATTGATTAT 4047
                         i  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.83 (150 / 82)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.25 (18 / 8)  


3211 27.86 0.44 0.44  chr1_75653468_75659872     5005  5912 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75653468_7   5005 TGGAAGAACATTCCATGCTCATTGGTAGAAAGAATCAACATTGTGAAAAT 5054
                              ii i  i     i    v i v i    v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75653468_7   5055 GGTCATACTGCCCAAGGTAATATATAGATTCAATGCCATCCCCATCAAGC 5104
                           iv     v     iv i  v  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75653468_7   5105 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5152
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_75653468_7   5153 TATGGAACCAAAAAAGAGCCCTCATCGTCAAGTCAATCCTAAGCGAAAAG 5202
                                viiv  ii  v  vvv  v i   iv     i i ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_75653468_7   5203 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5252
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_75653468_7   5253 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5302
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_75653468_7   5303 AATGGAACAGAAC--AGAGCCCTCAGAAGTAACGCCACATATCTACAACT 5350
                                i    i--    i  --    i   vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_75653468_7   5351 ATCTGATCTTTGGCAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5400
                          vi    i  i i   ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_75653468_7   5401 CTGTTTAATAAATGTTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5450
                           v  i  i     v        v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_75653468_7   5451 GAAACTGGATCCCTTCCTTATGCCTTATACAAAAATTAATTCAAGATGGA 5500
                            ii    i    v   i ii  v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_75653468_7   5501 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAACCCCTAGAAGAAAAC 5550
                          i ?    i       v   v       i       i i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_75653468_7   5551 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATATCTAA 5600
                         v    ?i v viv   iv   v v  vv i     v ii   v  vv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_75653468_7   5601 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAG 5650
                         i            vvi          vv     v  i    v   ii vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_75653468_7   5651 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGAAC 5700
                          i   v i  i i   i  ii vv    i  v    i  vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_75653468_7   5701 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5750
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_75653468_7   5751 AGGGCTAATATCCAGAATCTACAATGAGCTCAAACAAATTTACAAGAAAA 5800
                         i  i  vi          v  i  v  i   vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_75653468_7   5801 AAACAAACGACCCCATCAAAAGGTGGGCGAAGGACATGAACAGACACTTC 5850
                          i     ii    v  i?   ii     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_75653468_7   5851 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCACC 5900
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_75653468_7   5901 ATCACTGGCCAT 5912
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (153 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3008 21.92 1.90 4.27  chr1_75673264_75675099      500  1343 (493)    L1M4_orf2#LINE/L1       85   908 (0)  

  chr1_75673264_7    500 GTAATCCCTATCAAATTTTTAAAAGCAATTTTCACAGAAAT-GA------ 542
                          i             v iii ivv  vv    ii       -  ------
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr1_75673264_7    543 AATCCTAAAATTTGTACAGAACCACAAACAACCCCAAATAGCCCAAACAA 592
                         i           ii  ii   vii   ivi    vi       v      
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_75673264_7    593 TCTTGAGAAAGAAGAACAAAGTTG-ACAACATCACACTTTCTGATTTCAA 641
                               i                 - vi  -        i ii       
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAA 233

  chr1_75673264_7    642 ATTATACTACAAAGCTATCCTAATCAAAACAAGATGATACTAGTATAAAA 691
                          viv             ivv       i   ivi  i    i i    ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_75673264_7    692 TCAGACACACAGACCAGTGGAACAGAATAAGAGAGCCCAGAAAGAAACCC 741
                         vi     i i   i  i     i     v-     i       v      
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATT-GAGAGTCCAGAAATAAACCC 332

  chr1_75673264_7    742 ACAAATAAATTGTCAAATAATAATTGACAAGGGTACCAAGAACAGACAAT 791
                          i v  vv  v     v i  vv i         i      v  vv    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_75673264_7    792 GGGGAAAAGACAGTCTCTTCAATAAATGGTGTTGGAAAAACTGGATATCC 841
                                ii i     i     i        i   i v         ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_75673264_7    842 ATATGCAAAGAAAAGAAAAATGGAATTGGACCCTTATCTTACAATATACA 891
                          i       ------- i    i i        i  i  i   vi   i 
  L1M4_orf2#LINE/    433 ACATGCAAA-------AGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_75673264_7    892 CAAAAATCAACTCAAAATGGATTAAAGACTTAAACCTGAGACTTGAAACT 941
                                i              i ?    i    iv i   vi i     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_75673264_7    942 GTAAAACTTCTAAGAGAAAACATAGGGAACAAGCTCTATGATGTTGGTCT 991
                         i       ii  ii            ?ivv  v  iii   iv    vi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_75673264_7    992 TGATGAAGATTTTTTTTTGCATATGACATCACAAGCACACAAGGAAACAG 1041
                         v iii v i   i  ---iv        i  v       -----------
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTT---AGATATGACACCAAAAGCACA----------- 611

  chr1_75673264_7   1042 ACAACAACAACAAAAAAAAAAACA-ATAAAAGTGGGACTACATCATGCTA 1090
                         ----- i        i      i -     -- v     v     ---- 
  L1M4_orf2#LINE/    612 -----AGCAACAAAAGAAAAAATAGATAAA--TTGGACTTCATCA----A 650

  chr1_75673264_7   1091 AA--AACAAACTTCTGCAAAGCAAAGGAAACGAT-AAGA---TGAAAAGG 1134
                           --  -      i  iivvv       v  v  -    ---       i
  L1M4_orf2#LINE/    651 AATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_75673264_7   1135 CAACCTACAAAATGAAAGAAAATATTC-CAAACCATATATCTAATAAAGA 1183
                              i   i    ii          i-    i         i    i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_75673264_7   1184 GTTAATATCCAAAATATATAAGAAACTCATAGAACTTAATAGCAAAAATA 1233
                         ii vi      i         ii     v  v    i    ii     v 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_75673264_7   1234 CAAATAGCCCAATTAAAAATATGGGCAAAGGACTTAAATAAAAATTTTTC 1283
                               i       ?    -            i  i    i v    i  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_75673264_7   1284 CAAGGAAGACATAGAGTTTGCCACTAAGTATGTAAAAAGATGGTTAATAT 1333
                            i     i   v iv v    v    i ii i        v i  i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_75673264_7   1334 CACTAATCAT 1343
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.12 (123 / 58)
Gap_init rate = 0.02 (17 / 824), avg. gap size = 3.06 (52 / 17)  


2658 27.64 2.22 1.44  chr1_75682818_75685102.rev      901  1801 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75682818_7    901 TGGAAATACATTCCATGCTCGTCAATTGGAAAAATTAATATAATTAAAAT 950
                               v i  i     i  i vi       i v       vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75682818_7    951 AGCAATACTACCCAAAGCAATCTATAGATTCAAGCCTGTTCTTATCAA-- 998
                         i        v      vii     i        vv vi i i      --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75682818_7    999 --TCAACATCATTTTTCATAGAATTAGAAACAAACT-ATTCTAAAGTTCA 1045
                         --i  i vv v     iii    v v  --   i  -  i     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCA 148

  chr1_75682818_7   1046 CATAGAACCAAAAAGGAACCTGAATAGCCAAAGTAATCCTAAGCAAAAAG 1095
                         i  i   viiv  i   v  v           ii    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_75682818_7   1096 AACAAAGCTTGAGGCATCACATGATCCAACTTCAAATGATATTATAAATC 1145
                                i v    vv     ivvi    i      vvv  i  i   v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_75682818_7   1146 TACAGTAACCAAAACAACATCGTACTGGTACAAAAACAGACATACAGACC 1195
                                 i   i   iii v       i i  ii i       i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_75682818_7   1196 AATGGAACAGAAGAGAGAACCCAGAAATAAACCCACACACCTACAACTGT 1245
                                i    vv    ii               i   ii  iiiiiiv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_75682818_7   1246 CTGGTCTTCAACAAAATCAACAAAAATAAGCAATGGGGAAAGGACTTCCT 1295
                         i  i i   i    iiviiv   i vi vv            i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_75682818_7   1296 ATTCAATAAATGGTACTGGGATAGTTTGCTGGCCATATGCAGAAGAATGA 1345
                         v     i       i      i ii v v i?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_75682818_7   1346 AACTAGACCCCTACCTTGAACCATATACAAAAATTAATGTGAGATGGATT 1395
                          ii i           iiv                  ivii i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_75682818_7   1396 AAATATTTAGATGTAA-ACCTCAAACTATAAAAAACCTAGAAAAAATTCT 1444
                          ? v ii  i      - v  v           vv i     i   viv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_75682818_7   1445 AGG---AAATGCCATTTTG-GACACTAGTCTTGGCAAATAGTTTATGACT 1490
                            ---    ----i  i -   vi i vi v     - i    v --- 
  L1M4_orf2#LINE/    549 AGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT---T 590

  chr1_75682818_7   1491 AAGTCTTTCCTCAAAAGTAATTTCAATAAAACAAAAAACAAGTGA----G 1536
                          ii v vv vi      i vvvv   i    v      i ii i ---- 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_75682818_7   1537 ACCT-AGCTAAACTAAATAGATTTTGCACAACAAAAGAAACTATCAACAA 1585
                           i - v v   i    - iv     ii vv    i  v        v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_75682818_7   1586 ATTAAACA-ACAACACACAGAATAGGAGAAAATATTTGCAACT-ATGCAT 1633
                          v i  v -     v        i                 v -  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_75682818_7   1634 CCAACAAAGGTCCAATATCTGAAATCCA-AAAGTA-TCTTATAGAACTCA 1681
                          ii i  i  v ivi    iii   vi -    v -     i --     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA--ACTCA 787

  chr1_75682818_7   1682 ACAAGCAAAACCCAGATAACCCCATTAAAAAGTGGGCAAAGGACATGAGC 1731
                          i  vv    vv  i       v   ?    i           iv   ii
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_75682818_7   1732 AGACACTTCTGAAAAGAAGACATTCAAACAGCGAA-AAAAGTATGAATAA 1780
                              i    vv        i  v    ii  v  -  ivii     v i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_75682818_7   1781 ATGCTCCATACCGTTAATCAT 1801
                               v i i i????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (154 / 92)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.83 (33 / 18)  


3045 23.30 1.81 5.21  chr1_75781004_75783296.rev      929  1868 (425)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75781004_7    929 TGGAAAAACATTCCATGATCATGGATTGGAAGAAT-AATA------AAAT 971
                               i i  i     v               v -    ------ i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75781004_7    972 GGTCAAACTCCCCAAAGCAATCTACAGATTCAATGCTATTTCTATGAAGC 1021
                           iv v          vii              i  v  ii    v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75781004_7   1022 TACCAATGGCATTTTTCACAGAATCAGAAAAAACT-ATTCTAAAATTCAT 1070
                          v   iiv  v     ii     viv  v  i-  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_75781004_7   1071 ATGGAAGTAATAAAGTAATAAAGAGCCCA-AATAGGCAAAGTAATCCCAA 1119
                               i i---------i  i ii    -     v    ii    iii 
  L1M4_orf2#LINE/    150 ATGGAAATG---------CAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_75781004_7   1120 GAAAAAAGAACAAAGCCAGAAGCATCACATTACCTGGCTTCAAACTATAT 1169
                         i   i          iii  i vv     i v  iiii      viv  i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_75781004_7   1170 TGTAAGGCTACAGTAAGCAAAACAGCATGGTACTGGTACAAAAACAGACA 1219
                          ii  i          v   i    ii         i i  ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_75781004_7   1220 CATAGACCAATGGAACAGAAGAAAGAACCCAGAAATAAAGC--TGCATTC 1267
                         i     i        i    vvi   ii           v -- i    -
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT- 339

  chr1_75781004_7   1268 CTATAGCCAGCTGACCTTCAACAAAGTAAACCAAAATCAG-CAATGGGGA 1316
                         -   i i  ii   ii   i    i -ivi    i i  v-         
  L1M4_orf2#LINE/    340 -TATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGA 387

  chr1_75781004_7   1317 AAGGACTCTCTACTCAATAAATGGTGCTGGGATAACTGGCTATCCATATG 1366
                            i ivv   vi    i              i      v  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_75781004_7   1367 CAGAAGAATGAAACTGGACCCCTACCTTGTTTGATATGGAAAAATTAACT 1416
                           i         ii             iiiviv    iv           
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_75781004_7   1417 CAAGATGGATCAGAGAATTAAATGTAAGACTTCAAACTATAAGAATCTTA 1466
                            i        ?   vi           vi v         i v     
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_75781004_7   1467 GAAGAAAACATAGGAA-ACACCATTCTGGACATTGACTTTGGGAAAAATT 1515
                                       ?i- v i -   vv   v   iv  v  v  vii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_75781004_7   1516 TAT--GACTAAGTCCTCAAAAGCAATGACAACAAAAGCAAAAATTG-CAA 1562
                          v --  -  v v vi        vvii         v      v -i  
  L1M4_orf2#LINE/    587 TCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_75781004_7   1563 GTGAGACCTAATTAAACTGAGTAGCTTTTGCACAACAAAAGAAACTATCA 1612
                         i vi   i v  i   v v iv i      ii vv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_75781004_7   1613 ACAGAGTAAACAGACAACCTACAGAGTGGGAGAAAATATTCACAAACTGT 1662
                          v i   i  v        i     i              ii    iii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_75781004_7   1663 GCATCTGACAGAGGTCTAATATCTAGAATCTATAAGGAACTTAAACAATT 1712
                         ii      i ii  v  vi    i     v     i     ivv    i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_75781004_7   1713 GAACAAGTAAAACACCAATAACCCCATT-AAAAATAGGCAAAAGAAAGAC 1761
                         v  i  vv    v  v        v   -      i      i  ----i
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA----T 831

  chr1_75781004_7   1762 ATGAATGGACAGTTCTCAAAAGAAGACATACAATTAAAAAAAAGAAGACA 1811
                         v     i    v     v        i      v i---------- v  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATG----------GCCA 871

  chr1_75781004_7   1812 TACAAGCAGCAAAAAAAAAAAAAAAAACATGAAAAAATGCTCCACATCAC 1861
                         - i     -------------------        i      v      ?
  L1M4_orf2#LINE/    872 -ATAAGCA-------------------CATGAAAAGATGCTCAACATCAZ 901

  chr1_75781004_7   1862 TAATTAC 1868
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.70 (136 / 80)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.30 (66 / 20)  


3064 22.87 2.13 5.53  chr1_75834042_75839963     4490  5429 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75834042_7   4490 TGGAAAAATATCTCATGCTCATGGATTGGAAGAATTATTATGGTTAAAAT 4539
                               i     i    i               v   -------------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTA------------- 37

  chr1_75834042_7   4540 GACCATATTGTTGTTAAAATGTCCATACTTTGTAGACCCAAAGAAATCTG 4589
                         ----        ---  i   v v     i------      vvi    i
  L1M4_orf2#LINE/     38 ----ATATTGTT---AAGATGGCAATACTC------CCCAAATTGATCTA 74

  chr1_75834042_7   4590 CAGATTTAATGCTATCCTTATCAAAATACCAATGACATTCTCCACAGAAA 4639
                               i  i  v    i         v   iivi v  i iii      
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr1_75834042_7   4640 TAGAAAAAC-AATCCTAAAATCTGTATGGAATCACAAAAGATCCTGAATA 4688
                          v  v  i -i          iii       vii   ii  i  v     
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr1_75834042_7   4689 GCCAAAGCAATTCTGAGCACAAAGAACAAAGCTGGAGGTACT-ATATTAC 4737
                               i    ii   iv vi          i      -   - i i v 
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-ACTCACACTTC 223

  chr1_75834042_7   4738 CTGACTTCAAAATATACTACAAAAGCGTAGTAACCAAAACAGCTTAGTAC 4787
                          ii i       iv         iviii     i   i    iv i    
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_75834042_7   4788 TTGCATACAAACAGACACACAGACTAATGGAACAGAATTGAAAACACAGA 4837
                          v     vii i     i i   ii       i        i iiv    
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_75834042_7   4838 AATAAATCCACACATTTATAGCTAACTTATTTTTGACAAAGGCACCAAAA 4887
                               i   i        i ii  i v     i     i  ii    i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_75834042_7   4888 ATATACACTGGGAAAATGAGAGTCTCTTCAATAAATGGTGCTGAGA-AAT 4936
                         vi  v  v    i   vi v     i     i           i  -  i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_75834042_7   4937 TGGATATCCATATGTA---GAATGAAACTAGAACTCTATTTCTCAT-ATA 4982
                               ?   i   i ---       ii i  v i   ii  v  i-   
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_75834042_7   4983 TACAAAAATTAAATCAAAATGGATTAAAGACTGAAATGTATGACCTAAAA 5032
                                     v           i ?    iv       v  v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_75834042_7   5033 CTATGAAACTACTGCAAGTAAAAAAAAAAAAAAAAAAAAAAAAAAAACAC 5082
                             i     -  -----  i  i    v v ii?---------------
  L1M4_orf2#LINE/    524 CTATAAAACT-CT-----TAGAAGAAAACATAGGN--------------- 552

  chr1_75834042_7   5083 CATGGAAATGCTTTAGCACATTTGTCCAGGCAAAGATTTTTGGGGTAAGA 5132
                         --- v    -   iivv  v  v vii      v i   i vi i  v  
  L1M4_orf2#LINE/    553 ---GTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_75834042_7   5133 CTTCAAAAGCACAGGCAACAAAAGCAAAAATTGACAAATGGGATCACATC 5182
                          vi          i          v      v  i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_75834042_7   5183 TACCTAAAAAGCTTCAGTACAGCAAAGGAAAAAATCAGCACAGTCAACAG 5232
                         v vv v    i   iv  i vv       v vv    iv v   v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_75834042_7   5233 ACAACCTACAGAATGGGAGAAAATGTTTGCAAACTATCTATCTGACAAGA 5282
                               i                 i        ii  v       i   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_75834042_7   5283 AATTAATA-AAAGACTATATAAGGAACTCAAACAACTCAAC--CAAAAA- 5328
                         i i vi  -vv   v       i      vv         i--i     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_75834042_7   5329 ------AATCCAATTAAAAAA---ACAAAACATTTGAATAGCCATTTCTC 5369
                         ------  i      ?     ---i    iv          v        
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_75834042_7   5370 AAAAGGAGACATACAAATGTTCAACAGGTATATTTTAAAATGCTAAACAT 5419
                         v    i   i         vi   i i i i  vvv  i     v     
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_75834042_7   5420 CACTAATAGT 5429
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.67 (132 / 79)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.24 (72 / 17)  


2648 27.04 2.18 3.16  chr1_75840717_75844084     1960  2876 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75840717_7   1960 TGGAAAAACATTATACGTTTATAGATGGGAAGAATCAATATTATTAAAAT 2009
                               i i  ivi i   i  i   v      v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75840717_7   2010 GGCCATACTGCCCAAAGCAATCAACAGATTCAATGCTATTTCGATCAAGC 2059
                            v     v      vii   v          i  v  ii v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75840717_7   2060 TACCAACATCATTTTTCACAGATCTAGAAAGAACT-ATTTTAAAATTCAT 2108
                          v   i vv v     ii    vv v  v - i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr1_75840717_7   2109 AAGGAAACAAACAAAAAAAAGAACTCA-AATAGTCAAAGCAATCTTAAGA 2157
                          v     ii--   i----- i  i  -     i    i       i i 
  L1M4_orf2#LINE/    150 ATGGAAATG--CAAG-----GGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_75840717_7   2158 AAAAAGAACAAAGTCAGAAG---CAC------CATCTTCAAACTGTACTA 2198
                           i           ii  i ---   ------  vi      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_75840717_7   2199 TAAGGCTACAATAACCAAAATAGCACGTTACTGGTACAAAAACAGACACA 2248
                         i  i      i   i   i i  iii v      i i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_75840717_7   2249 TAGGCCAATTGAACAGACTGGAG-GACCAGAAATAAAGCCACACACCTAT 2297
                            ii    v   i   v v   - v           v   i   ii   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_75840717_7   2298 AGTCACTTGATCTTAAACAAAGTCAACAAAAATAAGCAGTAGGGAAAGAA 2347
                         i    v     i  vi    i viiv   i vi vv  i i         
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_75840717_7   2348 CTCTCTATTCAATAAATGATGCTACGTTAACTGTCCAGCCATATGCAGAA 2397
                         ivv   v     i     i    iv vi     vvi ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_75840717_7   2398 GAAAGAAACTGGACTCTTACATTTCATCATATGCAAAGATTAACTCAAGA 2447
                            v   ii     i i   v iv  i     i    i          i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_75840717_7   2448 TGGATGAAATATTTAAATGTAAGATCTCAAACTATAAAAATCCTAGAAGA 2497
                              v ? v ii           v  v           v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_75840717_7   2498 AAACTTAGGGAACACTATTCTGGACATCAGCCTGGGGAAAGAATTTATAA 2547
                             v    ?ivv v v   vv   v ii vi i  v  v iv  iv  i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_75840717_7   2548 CTAAGTTTTCAGAAGCAATTGCAACAAAAATAAAAGTTGAAAAGCAGAGC 2597
                         v  v vivi  i     vvv         iv    i v  v  iiv ii 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_75840717_7   2598 CTAATTAAAA----GACCTTCTGCACAGCAAAAGAAACTAACAG---AGT 2640
                         i v  i    ----i v   i  ii vv    i  v    v  i---   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_75840717_7   2641 AAATGGAAAACCTATAGAATGGGATAAAATATTCGCAAACTATACATCCC 2690
                         i  vi  v    i i         v        i     ii   i   iv
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_75840717_7   2691 ACAAACTACTCATCCTAGAACTATGCATTCTAATATCTGGAACCTATAAA 2740
                          i  i------------ i   -  --------    ii   iv      
  L1M4_orf2#LINE/    743 ATAAG------------GGACT-TG--------TATCCAGAATATATAAA 771

  chr1_75840717_7   2741 GAACTAAAACAATTCAACAAGCAAAA-ATAAATAACCCCATTTAGAAATG 2789
                              vvv    i    i  vv    - i         v   ? i     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_75840717_7   2790 GGGAAAAGACATGAACAGACATTTCTGAAAAGAGGATATATGAGCAGTCA 2839
                           v   i  iv    i          vv     i      ii iii i  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_75840717_7   2840 ACAAATACACTAAAAAATGCTCAACATCGCTAATGAT 2876
                          i  ii   iv    i            i????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.50 (49 / 14)  


3237 26.21 0.66 0.66  chr1_75854957_75861223     4867  5774 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75854957_7   4867 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4916
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75854957_7   4917 GGCCATACTGCCCAAGGTAATTTACGGATTCAATGCCATCTCCATCAAGC 4966
                            v     v     iv i  i   i       i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75854957_7   4967 TACGAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5013
                          v v i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_75854957_7   5014 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTCAGCCAAAA 5063
                                 viiv  ii  v  v v  v     iv     i v ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_75854957_7   5064 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5113
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_75854957_7   5114 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5163
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_75854957_7   5164 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5211
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_75854957_7   5212 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5261
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_75854957_7   5262 CCTATTTAATAAATGGTGCTGAGAAATCTGGCTAGACATATGTAGAAAGC 5311
                         i  v  i  i           i  v v    v  ?v  i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_75854957_7   5312 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5361
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_75854957_7   5362 ATTAGAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5411
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_75854957_7   5412 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5460
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_75854957_7   5461 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5510
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_75854957_7   5511 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGA 5560
                         v  i   v v  i i   i  ii vv    i  v    i  vv i v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_75854957_7   5561 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGTC 5610
                          v  i     i   i             v  i    vii ivi     vi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_75854957_7   5611 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTAACAAGAA 5660
                           i  i  vi          v  i  v      vv    v i  i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_75854957_7   5661 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAATAGACACT 5710
                            i     i     v  i?    i     i     iv          i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_75854957_7   5711 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5760
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_75854957_7   5761 CCATCACTGGCCAT 5774
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3235 26.84 0.55 0.66  chr1_75874846_75881127     4881  5789 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75874846_7   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4930
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75874846_7   4931 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCAACAAGC 4980
                            v     v     iv i  i  i        i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75874846_7   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5028
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_75874846_7   5029 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTCAGCCAAAA 5078
                                 viiv  ii  v  v v  v     iv     i v ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_75874846_7   5079 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5128
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_75874846_7   5129 CTACAATAACGAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGAT 5178
                              i   iv  i    ii         i  v ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_75874846_7   5179 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5226
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_75874846_7   5227 CATCTGATCTTTGACAAACCTGATAAAAACAAGAAATGGGGAAAGGATTC 5276
                           vi    i  i     ivv  vi  i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_75874846_7   5277 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5326
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_75874846_7   5327 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5376
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_75874846_7   5377 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5426
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_75874846_7   5427 CCCAGGCA-ATACCATTCAGGACATAGGCATGGGCGAGGACTTCATGTCT 5475
                          vi   ?i- v i -   iv   v v  vv i   i v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_75874846_7   5476 AAAACACCAGAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5525
                          vi      i     vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_75874846_7   5526 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGA 5575
                         v  i   v v  i i   i  ii vv    i  v    i  vv i v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_75874846_7   5576 ACAGGCCACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5625
                          v  i v   i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_75874846_7   5626 AAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACGAGAA 5675
                           i  i  vi          v  i  v      iv    v iv ii v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_75874846_7   5676 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACC 5725
                            i     i     v  i?    i            v    i     ii
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_75874846_7   5726 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCGCA 5775
                             v        i  vi viii     v ii          i    v  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_75874846_7   5776 TCATCACTGGCCAT 5789
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


2785 26.98 1.30 2.93  chr1_75892179_75894278      685  1607 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75892179_7    685 TAGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTTAGAAT 734
                          i    i i  i     i        v      v i          ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75892179_7    735 GACTATACTTCCCAAAGCAATTTACAGATTCAATGCTATTCCTGTCAAAC 784
                          i v     i      vii  i           i  v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75892179_7    785 TACCAATGGCATTCTTCACAGAGTTTAAAAAAACAATATTTTAAAATGTA 834
                          v   iiv  v  i  ii    iv  i v  ivii  --ii      vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT--CCTAAAATTCA 148

  chr1_75892179_7    835 TGTGAACCAAA---AAGGAGCCCA-AATAGCCAGGGCAACCCTAAGCAAA 880
                          i  i ---  ---    ii    -        iii   i i i iv  i
  L1M4_orf2#LINE/    149 TATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_75892179_7    881 AAGAACAAAGCTAGAGACATCATGCTACCCAAATTCAAACTATACTACAA 930
                                   i i   ivv   ii  v     v      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_75892179_7    931 GGCTACAGTAACCAAAACGGCATAGTACTGGTACAAAAACAGACGTAAAG 980
                         i          i   i  i ii i       i i  ii i    i  v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_75892179_7    981 ACCAATGGAATAGAATAGAGAGCCCAGAAGTAAAGCTGCACACCTACAAC 1030
                          i              v     i      i    v iii   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_75892179_7   1031 CATCTGATCTTCAACAAAGTCAACAAAAACAAGCGATGCGGATAAGACTC 1080
                           vi    i   i    i viiv   i v  vv i   v   -    v v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATA 394

  chr1_75892179_7   1081 -CCTATTCAATAAATGGTGTTGAGGTAACTGGCTACCCATATGCAGAAAA 1129
                         -i  v     i        i  i ii      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_75892179_7   1130 TTAAAACTGGATGCCTTCTTTATATCATATACAAAAATTAACTTAAGGTG 1179
                         v i  ii    iv   v i i i i                  i  ii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_75892179_7   1180 GAGTAAAGCCATAAATGTAAAAGCTAAAACTATAAAAACTCT-GGAACAT 1228
                           vi ?  v v         i                -    -i   v v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chr1_75892179_7   1229 AACCTAGG---AAATACCATTCTGGACACAAGCCCTGGCAAAGATTTCAT 1275
                            v    ---    -- -   vv   vivi viiv     v i    v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_75892179_7   1276 GACAAAGACGACAAAA--ACAATTGCAACAAAAATGAAAATTGACAAATA 1323
                         iivv v   iv     --    --         ivi     v  i    v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATT 638

  chr1_75892179_7   1324 GGACCCAATTAAAGTAACGAGCTTCTGAACAGCAAAATAAACCATCAACA 1373
                             iiv  i   i v vi i   i  vi vv    iv v  i     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_75892179_7   1374 AAGTAAGCAGACAAACTACAGAATGGTAGAAAGTATTTGCAAA-CAAAGA 1422
                             i iv      v i         v     i          -  v v 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_75892179_7   1423 TCTAATATAAAATATTTGCAATGAAGGTCAATATCTAGAATCTATAAGGA 1472
                            i   -- iiv i   -------------    i     v     i  
  L1M4_orf2#LINE/    739 TCTGATA--AGGGACTTG-------------TATCCAGAATATATAAAGA 773

  chr1_75892179_7   1473 ATTTAAATAAATTAACAAGCAAAAAGCAAACAATTCCGTTAAAAAGTAAG 1522
                          i ivv i  v i  i  vv    ii    i  ii vi  ?    i ii 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_75892179_7   1523 CAAAAGACATGAACAGATACTTTTGAAAAGAAGAGAGACACGTGGCCAAC 1572
                             i  iv    i   i i  i vv        v v   vi       i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_75892179_7   1573 AAGCATATGAAAAAATGTTCATCATCAGTAATCAA 1607
                              i       i   i   v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (159 / 87)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.44 (39 / 16)  


2979 28.19 1.44 0.67  chr1_75933033_75935673     1248  2148 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75933033_7   1248 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1297
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75933033_7   1298 GGCCATATTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCTTCAAGC 1347
                            v   i v     iv i  i  i       ii  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75933033_7   1348 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1395
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_75933033_7   1396 TATGGAAC--CAAAAAAGCCCACATTGCCCAGACAATCCTAAGCCAAAAC 1443
                                v--   iii v  viv  v   v i      i i ivv i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_75933033_7   1444 AACAAAGATGGATGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1493
                                v    v vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_75933033_7   1494 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACA 1543
                                 i   i    ii         i iv ii i   i       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_75933033_7   1544 AATGGAACAGAAT--AGAGCCCTTGGAAATAATACCACATGTCTACAACC 1591
                                i     --    i  --i       vv   i ii i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_75933033_7   1592 ATCTGATCTTTGACAAACCTGACAAACACAAGAAATGGGGGAAGGATTCC 1641
                          vi    i  i     ivv  v   ivv  vvv       i   i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_75933033_7   1642 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1691
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_75933033_7   1692 GAAACTGGATCCCTTCCTTAC--CTTATATAAAAATTAATTCAAGATGGA 1739
                            ii    i    v   i  -- v    i         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_75933033_7   1740 TTAAAGACTTAAATGTTAGACCTAAAACCATAAGAACCCTAGAAGAAAAC 1789
                          i ?    i       v   v       i    i vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_75933033_7   1790 CTAGGCAGTA--CCATTCAGGACATAGACATGGGCAAGGACTTCATGTCT 1837
                         v    ?-   --i -   iv   v v ivv i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_75933033_7   1838 AAAACACCAGAAGCAATGGAAACAAAAGCCAAAATTGACAATTGGGATCT 1887
                          vi      i     vvi v        vv     v  i  v v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_75933033_7   1888 AATTAAACTCAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 1937
                         v  i   v i  i ii  i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_75933033_7   1938 ACAGGCAACCTACAGAATGGGAGAAAATTTTTATAATCTACCCATCTGAC 1987
                          v  i     i                 v   ii  vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_75933033_7   1988 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 2037
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_75933033_7   2038 AAAAAT---CAACCCTATCAAAAAGTGGGTGAAGGATATGAACAGACACT 2084
                            i i---i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_75933033_7   2085 TCTCAAAAGAAGACATTTATGCATCCAACAGACACATGAAAAAATGCTCA 2134
                             v        i  vi viiiv    i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_75933033_7   2135 TCATCACTGGCCAT 2148
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (153 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


3095 26.00 0.76 2.80  chr1_75954803_75961203     4982  5908 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_75954803_7   4982 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5031
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_75954803_7   5032 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5081
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_75954803_7   5082 TACTAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5130
                          v i iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_75954803_7   5131 ATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCTTGAGCCAAAAGA 5180
                               viiv  ii  v  viv  v     iv         ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_75954803_7   5181 ACAAAGCTGCAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5230
                               i  v   vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_75954803_7   5231 ACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGACCA 5280
                           i    i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_75954803_7   5281 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTA 5328
                               i    i--    i  --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_75954803_7   5329 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5378
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_75954803_7   5379 TATTTAATAAATGGTGCTAGGAAAACTGGCTAGATATATGTAGAAAGCTG 5428
                          v  i  i          i   v      v  ?vi i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_75954803_7   5429 AAAGTGGATCCCTTCCTTACACCTTATACAAAAATGAATTCAAGATGGAT 5478
                           iv    i    v   i     v           v  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_75954803_7   5479 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5528
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_75954803_7   5529 TAGGTAATACTATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5578
                             ?ivv v v   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_75954803_7   5579 ACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTAAT 5628
                                     vvi   i      vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_75954803_7   5629 TAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGTGAACA 5678
                         i   v i  i i   i  ii vv    i  v    i  vv v      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_75954803_7   5679 GGCAACCTACAGAATGGGACAAAATTTTTGCAACCTACTCGACAAAATGT 5728
                          i     i           v     v       -------------  --
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAA-------------AT-- 732

  chr1_75954803_7   5729 TTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAA 5778
                         ---  ---  i--      i  i  i  vi          v  i  v   
  L1M4_orf2#LINE/    733 ---CA---TAT--ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_75954803_7   5779 CTCAAACAAATTTACAAGAAAAAAACAA----CCCCATCAAAAAGTGGGC 5824
                            vv    v iv i  v     i    ----   v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_75954803_7   5825 AAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 5874
                                v    i     i     v        i  vi viii     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_75954803_7   5875 AACACATGAAAAAATGCTCATCATCACTGGCCAT 5908
                          i          i       v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (137 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.67 (33 / 9)  


2729 28.63 1.55 0.78  chr1_76006032_76012397     4973  5873 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_76006032_7   4973 TGGAAGCACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5022
                              iv i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_76006032_7   5023 TGCCATACTGCCCAAGGTATTTTATATATTCAGTGCCATCCCCTTCAAGC 5072
                         v  v     v     iv iv i  i v     ii  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_76006032_7   5073 TACGAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5120
                          v v iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_76006032_7   5121 CATGGAACCAAAAAAGAGCTCGCATTAACTGGA-CAATCCTAAACCAAAA 5169
                         i      viiv  ii  - i iv v  i iii -     i i  vv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_76006032_7   5170 GAACAAAGATGGAGGCATCACGCTACATGACTTCAAACTACACTACAAGC 5219
                                 v      vv    i  v vii i      vivi       iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_76006032_7   5220 CTACAGTAACCAAAACAGCATGGCACTGGTACCAAAACA--TATATAGAC 5267
                                  i   i    ii   i     i iv ii i --i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_76006032_7   5268 CAATGGAACAGAGT--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5315
                                 i   i --    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_76006032_7   5316 CATCTAATCTTTGACAAACCTGACAAAAACAAGAAATGAGGAAAGGATTC 5365
                           vi i  i  i     ivv  v   i v  vvv    i      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_76006032_7   5366 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAACC 5415
                         i  v  i  i              v      v  ?   i i i i  ivv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_76006032_7   5416 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAACATGG 5465
                             ii    i    v   i     v              i    v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_76006032_7   5466 ATTAAAGACGCAAATGTTAGACCTAAAACCTTAAGAACCCTAGAAGAAAA 5515
                           i ?    vi      v   v       iv   i vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_76006032_7   5516 CCTAAGCA-ATACCATTCA-GGTCATAGGCATGGGCAAGGACTTCATGAC 5563
                          v  i ?i- v i -   i- ii v i  i- i     v ii   v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGA 593

  chr1_76006032_7   5564 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATAGGATC 5613
                           vi            vvi          vv    iv  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_76006032_7   5614 TAATTAAACTAAAGAGATTCTGCACAGCAAAAGAAACTATCATCAGAGTG 5663
                          v  i   v v  i iv  i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_76006032_7   5664 AACAGGCAACCTACAGAATGGGAGAAAAT-TTTACAATCTACCCATCTGA 5712
                           v  i     i                 -   i   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_76006032_7   5713 CAAAGCGCTAATATCCAGAATCTACAAAGAACTTAAACAAATGTACAAGA 5762
                         i  i vi  vi          v  i        ivv    v vv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_76006032_7   5763 AAAAATCAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5808
                             iv   ----   v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_76006032_7   5809 TTCGCAAAAGAAGACATTTATGCATCCAACAGACACATGAAAAAGTACTC 5858
                            v v        i  vi viiiv    i ii          ii i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_76006032_7   5859 CTTATCACTGGCCAT 5873
                         vvi    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (153 / 101)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


2999 26.44 3.05 0.45  chr1_76034246_76040622.rev     5003  5887 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_76034246_7   5003 TGGAAAAATATTCCATGCTCATGGATAAGAAGAATCAATATCGTGAAAAA 5052
                               i    i     i        vi     v i     i  v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_76034246_7   5053 AGCCATACTGCCCAAAGTAATTTATAGATTCAAGGCCATCCCCATCAAGC 5102
                         i  v     v      v i  i  i        v  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_76034246_7   5103 TACCA-CTGACTTTCTTCACAGAATTGGAAAAATT-ATTTTAAAGTTCAT 5150
                          v   -   v    i  -i     v v  v  ii -  ii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_76034246_7   5151 ATGGAACCAAAAAAGGGCCCGCATAGCCAAGA-----TTAAA-------- 5187
                               viiv  ii iv  v v        i -----  i  --------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_76034246_7   5188 -CAAAGC---A----TCACGGTACCTGACTTCAAGCTGTACTACAAGGCT 5229
                         -     i--- ----    iv v  ii i     iviv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_76034246_7   5230 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5279
                                i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_76034246_7   5280 ACGGAACAGAACGGAGGCCTCAGAAATAACACCACACATGTACGACCATC 5329
                          i    i    iv   ivii         vv   i    v  i ii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_76034246_7   5330 TGATCTTTGACAAACCTG---AGACATACAAGCAATGGGGAAAAGATTCC 5376
                             i  i     ivv  ---    ---  vv           ii  vvi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAAAGAATAGT 396

  chr1_76034246_7   5377 CTATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCATATGCAGAAAACT 5426
                           v  i  i              v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_76034246_7   5427 GAAACTAGACCCCTTCGTTACACCTTATACAAAAATAAACTCAAGATGGA 5476
                            ii i       v v i     v           v       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_76034246_7   5477 TCAAATACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5526
                            ? v  i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_76034246_7   5527 CTGGGCA-ATACCATCAGGACATAGGCATGGGCAAAGACTTCATGTCTAA 5575
                         v i  ?i- v i v  iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_76034246_7   5576 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAGTGGGACCTAA 5625
                         i            vvi          vv     v  i  i v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_76034246_7   5626 TTAAACTAAAGAGCTTCTGCACAGTGAAAGAAACTATCATCAGAGTGAAT 5675
                          i   v v  i i   i  ii vvii  i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_76034246_7   5676 AGGCAACTTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCCGACAA 5725
                           i    ii                 v       vii  vi   i  i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_76034246_7   5726 AAGGCTAACATCCAGAATCTAGAAATAACTTAAAGAAATTTACAAGAAAA 5775
                         ii i  vii         v  v   v    ivv v  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_76034246_7   5776 AAGCAAACAACCCCATCAAAAAATGGGCAAAGGATATGAACAGACAATTC 5825
                          ii    i     v  i?                 v    i     v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_76034246_7   5826 TCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTTATC 5875
                           v        i  vi viii     i ii  i       i     i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_76034246_7   5876 ATCCCTGGTCAT 5887
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (132 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.10 (31 / 10)  


2569 24.92 3.54 4.65  chr1_76080003_76084564.rev     3202  4104 (458)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr1_76080003_7   3202 TGTTCATTGATTGGAAGAATAAATACTGCTAAAATGTCAATACTATTCAA 3251
                                v          v v    i  i   i   v       vii   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_76080003_7   3252 TGTAATCTATAGATTCAATACAATCCCTATCAAAATAACAG--ACATTCT 3299
                         vv i     i        ii                vv   --i v  i 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_76080003_7   3300 TCACAGAAGTGGAAAAA--AATCCTAAAATTTATATGGAACCACAAAATA 3347
                          ii     i v  v  i--i           i        vii   iiv 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_76080003_7   3348 CTTCAAATAGTCAAAGCAACCCTGAACAAAAAGAACAAACCTAGAAACAT 3397
                          iivi     i    i   i i    v  i         vi i  iivv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_76080003_7   3398 CATGCTATCTGACTTTAAAATATACTACAAAGCCATAGTAACCAAAACAA 3447
                           ii  vi ii i  i    iv           i i     i   i   i
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_76080003_7   3448 CAGAGTCCTGGCATAAATACAGACACATCAAAAAATTGAACAGAACAGAG 3497
                         iivi  v         iv i     i  vi vv   v   i    iv   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_76080003_7   3498 AACCCAGAAATAAGTCCAAGCATTTACAGCCAACTCATTTTCAACAAGA- 3546
                          ii          ii   vi      ii i   i v      i     i-
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_76080003_7   3547 TACCAAGA---------------AGA-CAGTCTCTTCAATAAATAGTGCT 3580
                          i      ---------------   -i     i     i    i     
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_76080003_7   3581 GGGAAAAATAGATAACTATATATAGAAGAATGAAGCCAGACTCATATTTC 3630
                             v  v i    ? i i  ii i          iii   i v  ii  
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_76080003_7   3631 TTACCATATATAAAAATCTAA-TCAAAATGAATTAAAGACTTAAATGTAA 3679
                         vi        i      -   -        i  i ?    i         
  L1M4_orf2#LINE/    466 ACACCATATACAAAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_76080003_7   3680 GACCTGAAACTATGAAACTACTT-GAAGAAAACATTGGG--AAATGCTTT 3726
                           v  i       i     -   -           v  ?--    -   i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNGTAAAT-CTTC 562

  chr1_76080003_7   3727 AGGATATTAATGTGGGCAAAGACTTTTTGGGTAAAACCTCAAATGTGCAG 3776
                         iv  iv  iivv i     v ii  i  i i  vi  vi    v ii  i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_76080003_7   3777 GCAATAAAAGCAAAAATACACTTATAT--AATTACATTATG-TTAAAAAG 3823
                             i     v       v --  v  --i i v   i vi-       -
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGA--TAAATTGGACTTCATCAAAATTAAAAA- 659

  chr1_76080003_7   3824 CTTCTGCATAGCAAAAAAAAAAATTAACAAAGTGAAGAGACAGCCTACAG 3873
                            i  iiivv    ii v vv  i  v        i     i  i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_76080003_7   3874 AAGGGGAGGAAATATTTTCAAGCTCTCCTTCTGACAACCAAATTAAGCAA 3923
                           v     i        v   --------------- i  v  -- v --
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAA---------------ATCATAT--ATC-- 740

  chr1_76080003_7   3924 AATAATAACAAAGAAATAATAACCAAAACATCTAAGTAACTC----AACT 3969
                         ----- i i  i i v vi  v   i  i  v   iv     ----    
  L1M4_orf2#LINE/    741 -----TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_76080003_7   3970 CAATAGCAAAAAAATCCCACCAAATAAACCCAATTAAAACATTGGCAAAA 4019
                              ii     i ------       -       ?   v  v      i
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA------CAAATAA-CCCAATTWAAAAATGGGCAAAG 828

  chr1_76080003_7   4020 CATCTGAATAGATGTTTCTCAAAAGAAGACATACAAATAGCCAACAGGTG 4069
                         v  i        ii      v        i        i     i i ii
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_76080003_7   4070 GTGGGAATGTAAATTAGTTCAACCTTACGGAGATT 4104
                         vvv i  --- i  -- i     v i ????????
  L1M4_orf2#LINE/    879 CATGAAA---AGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (148 / 73)
Gap_init rate = 0.03 (23 / 893), avg. gap size = 3.22 (74 / 23)  


3236 26.87 0.55 0.55  chr1_76119178_76121402.rev      827  1734 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_76119178_7    827 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 876
                              ii i  i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_76119178_7    877 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCTTCAAGC 926
                            v i   v     iv i  i  i        i  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_76119178_7    927 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 974
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_76119178_7    975 TATGGAACCAAAAAAGGGCCTGCATTTCCAAGTCAATCCTAAGCCAAAAG 1024
                                viiv  ii iv  v v  vv    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_76119178_7   1025 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1074
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_76119178_7   1075 TATAGTAACCAAAGCAGCATGGTACTGGTAGCAAAACAGAGATATAGACA 1124
                           i     i   ii   ii         i vv ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_76119178_7   1125 AATGGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 1174
                                i     v   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_76119178_7   1175 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 1224
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_76119178_7   1225 ATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1274
                         v  i  i   i          v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_76119178_7   1275 AACTGGATCCCTTCCTTACGCCTTATACAAAAATTAATTCAAGATGTATT 1324
                          ii    i    v   i  i  v              i    i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_76119178_7   1325 ATAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1374
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_76119178_7   1375 AGGC---AATGCCATTCAGGACATATGCATGGGCAAGGACTTCATGTCTA 1421
                            ?---   -- -   iv   v vv vv i     v ii   v ivv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_76119178_7   1422 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 1471
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_76119178_7   1472 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGTGAA 1521
                           i   v v  i i   i  ii vv    i  v    i  vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_76119178_7   1522 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 1571
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_76119178_7   1572 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 1621
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_76119178_7   1622 ATAACAAACAACCCCAGCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1671
                          vi     i     v vi?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_76119178_7   1672 CTCAAAAGAAGACATTTATACAGCCAACAGACACATGAAAAAATGCTCAT 1721
                            v        i  vi v ii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_76119178_7   1722 CATCACTGGCCAT 1734
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


1480 17.56 1.38 27.91  chr1_76123676_76125941      538  1773 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_76123676_7    538 TGGAAAGACATCCCATGCTCATGGGTCAAAAGAACTAATATT---AAAAG 584
                                 i        i      i iii    vi       ---  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_76123676_7    585 GACCATACTACTCAAAGCAATCTAAAAATTCAATGCAATCCCTATCAAAA 634
                          i v     v i    vii     v i      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_76123676_7    635 CACCAATTTCATTTTTCACAGAA-TTAAAAAAACACTCCTAAAATTTGTA 683
                         iv   ii v v     ii     -  i v  iviiv          ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_76123676_7    684 TGAAACAACAACAAAAAAGCCCAGA-TAGCCAAAGCAATCCTGAACCAAA 732
                           i  -- ii-   iii -      -        i     i    vv i 
  L1M4_orf2#LINE/    151 TGGAA--ATG-CAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_76123676_7    733 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAAATATATTACAAG 782
                                  i      vv       v  ii i       iv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_76123676_7    783 GGTATGGTAACCAAAACAGCATGGTATTGGTATAAAAACAGACACATAGA 832
                          v  ii    i   i    ii     i   i    ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_76123676_7    833 TGAATGGAACAGAATAGATAATCTAGAAATATATCCATATATTTATAGCC 882
                          v       i     v  v i  i       v i     i      i i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_76123676_7    883 AGCTGATTTATCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 932
                          ii      -----------------------------------------
  L1M4_orf2#LINE/    347 AATTGATTT----------------------------------------- 355

  chr1_76123676_7    933 CCTTCCTTCCTTCTTCCACAGGGTCTCACTCTGTCACCTAGGCTGGAGTG 982
                         --------------  v   i  ------------------------   
  L1M4_orf2#LINE/    356 --------------TCGACAAGG------------------------GTG 367

  chr1_76123676_7    983 CAGTGGTGTGATCTTGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGTG 1032
                          -------------------------------------------------
  L1M4_orf2#LINE/    368 C------------------------------------------------- 368

  chr1_76123676_7   1033 ATTCTCCCAGCTTAGCCTCCCAAGTAGCTGGAATTACAGGTGTGAGCCAC 1082
                         --------------------    ------------------------  
  L1M4_orf2#LINE/    369 --------------------CAAG------------------------AC 374

  chr1_76123676_7   1083 CATGCCTGGCTAATGTTTTAGTATTTTTAGTAGAGATGGGGTTTTGCCAT 1132
                            ----------------------- i ------      ---------
  L1M4_orf2#LINE/    375 CAT-----------------------TCA------ATGGGG--------- 386

  chr1_76123676_7   1133 GTTGCCCAGGCTGGTCTTGAACTTCTGGCCTCAAGTGATCCACCTGTCTT 1182
                         --------------------------------------------------
  L1M4_orf2#LINE/    387 -------------------------------------------------- 386

  chr1_76123676_7   1183 GGCTTCCCAATCAACTGATTTTAAATTAAAGCTATAAGAACATACATCAG 1232
                         ---------------------------    -------------------
  L1M4_orf2#LINE/    387 ---------------------------AAAG------------------- 390

  chr1_76123676_7   1233 GAAAAGGACTCCTTCTTCAATAAATGATGCTGGGGAAATTGGATATCCAT 1282
                         -  v  ---  i  --    i     i       iv  i      ?   i
  L1M4_orf2#LINE/    391 -AATAG---TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_76123676_7   1283 ATGCAGAAAAATGAAACCAGACTCCTATCTTTTGCTGTATACAAAAATAA 1332
                              i  i      iiii   i    i  ivii ii           v 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_76123676_7   1333 ACTCAAGACAGATGAAAGACTTAAATATAAGACCTGAAACTACAAAACTA 1382
                               i ii   v ?    i     i     v  i      i      v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_76123676_7   1383 CTAGAAGAAAACATAG-CGTAATCACTTCAGGACATTAGTATAGGCAAAG 1431
                         i               -?    vi-    iv   v  i vv       v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_76123676_7   1432 ATCTCATGGCTAAAAGATCAAAAGTGCAGACAAAAAAACAAACAAAAAAA 1481
                         i i  v i v  vi v i      i------------    i   v    
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGC------------ACAAGCAACAAAA 621

  chr1_76123676_7   1482 AAACCAAAACAAGAAAAACTGATAGAACTATATTAAGATATTAAGCTAAA 1531
                         i  --    i -  v   i  i----   vi  i  i  -------    
  L1M4_orf2#LINE/    622 GAA--AAAATA-GATAAATTGG----ACTTCATCAAAAT-------TAAA 657

  chr1_76123676_7   1532 AATCTTCTGCACAGCAAAG-ACAGTA--AACAGAGTAAAGGGACAACCTG 1578
                           -   i  ii vv     -   v  --  v i   i  ii       ii
  L1M4_orf2#LINE/    658 AA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_76123676_7   1579 TTGATTGGGAGAAAATATTTTTAAACTATTGATTTGACAAGGAAGTTAAT 1628
                         iv  v               vi   ii  vv  i   i    i v  i- 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG-T 755

  chr1_76123676_7   1629 ATCT-GAATATACAAGAAACTC--AAAAC--AACAATTAAAAAATGAAT- 1672
                            i-       i  ii     -- v   --  i   v    i ii   -
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_76123676_7   1673 --TCAATTAAAAAGTGGGAAAAGGATGCAAATGGACATTTCCCAAAAGAA 1720
                         --i     ?    i    v       vii   i        i v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_76123676_7   1721 GATATAAAAATGGCCAACAGCTGTGTGTGGAAATTTTTAACATCACTAAC 1770
                               v          i iviiii  vii i  vi i       ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_76123676_7   1771 CAT 1773
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.38 (150 / 63)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 11.68 (362 / 31)  


 399 24.96 9.77 10.68  chr1_76163311_76164939.rev      502  1166 (463)    L1M4_orf2#LINE/L1      250   908 (0)  

  chr1_76163311_7    502 ACAGTA-TTAAGACAGTGTGAGATTTGC-CAGAGACAGACAAA-AGACCA 548
                               - i           iv i v  -i ii  i     v -   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_76163311_7    549 ATGGAACA--ATGGGGATCCCAGAAACTGACTCATGCATATCTAG--AAT 594
                               i --  v i  vi       ivi  i   i   v v i --   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_76163311_7    595 CCTAATATAAGACATATGCAGCAT-CAAAGGTTATT----GGGTAAAGGA 639
                         -- i  v vv    -----  vi - v   iii   ----   v    i 
  L1M4_orf2#LINE/    350 --TGATTTTCGACA-----AGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_76163311_7    640 TAAAGTATTCAAAAAATCATGCTAATTCCATCACAACTTGGTGAAATGAA 689
                           ivv v     v    vi    iiv------      -  ---------
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGG------ACAACT-GG--------- 426

  chr1_76163311_7    690 AAAAAACATACTAAAATAATCAATTTTTTCAATGTGGAAAAAATAAAAGT 739
                         ---------------   ?i  -------  -  ii-   i   i  iv 
  L1M4_orf2#LINE/    427 ---------------ATAKCCA-------CA-TGCA-AAAGAATGAAGTT 452

  chr1_76163311_7    740 ATACTCCTACTGCACACTACAAACAAAA-TAAATCCCAGGTG-ATTAAAA 787
                         iv  i     iv     i i v      - v  ii v ii  -  i ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_76163311_7    788 ACCTAAATGTAAAAAC-----CCA---AGCTTTTAAAA------ATTAGA 823
                                     i i ----- i --- i  i   i  ------  vi ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_76163311_7    824 ATATAT-----TGACCACAGGTT--TTTGTGATT-CTCACACAAAACACG 865
                         i  v  -----     vii    --vivi  i  -  i v i vi    v
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_76163311_7    866 AAAATCAAAAAC--CATGAGGAAAAATAT-TAA--TAAACT----CAAGG 906
                             v  v  i --  vi  i       v-   -- ii   ----   i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA- 651

  chr1_76163311_7    907 TATTAAAA---TTTGCACTTTCAGTTCATTACA-TATCATAAAAATGAAA 952
                         -       ---    ii   iv ---- vv   -     vi   i     
  L1M4_orf2#LINE/    652 -ATTAAAAACTTTTGTGCTTCAA----AGGACACTATCAAGAAAGTGAAA 696

  chr1_76163311_7    953 AGATAA--------ATTAGACAAATGTTTTGCTCA-CATATATCT-ACAA 992
                            i  --------  vi  v   vvv     vv -         - i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_76163311_7    993 A--ACTGTTGTTCCCATAATATCATAACATTAAAAGTCTCGAACAAATTG 1040
                         i--   --   vi   v     -    ---- i  v   i--    v ii
  L1M4_orf2#LINE/    747 GGGACT--TGTATCCAGAATAT-ATAA----AGAACTCTT--ACAACTCA 787

  chr1_76163311_7   1041 ATAAAGAAAAAGATAAACAACTCAAATGGAAACTAAGCAAACAATACTAA 1090
                             -v       i   i   i   v ?i   v ii     vi  viv  
  L1M4_orf2#LINE/    788 ATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_76163311_7   1091 CAGACAATACT--AGAAAAGA-ACACCCAATGACTAATAACACTCGCTCA 1137
                         i     v v  -- i i    - i  v-    i i     -----  -- 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACA-AATGGCCAATAA-----GC--A 878

  chr1_76163311_7   1138 CAT-AATAGATATTGAGCAACTGGACCGTG 1166
                            -  v    ii v i  v v????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (96 / 66)
Gap_init rate = 0.07 (46 / 659), avg. gap size = 2.96 (136 / 46)  


1269 30.08 6.26 4.69  chr1_76275731_76277543.rev      492  1322 (491)    L1M4_orf2#LINE/L1       65   908 (0)  

  chr1_76275731_7    492 AATT--TTTAAGGATTCAATGCAGTCTTAAATAAAAACTCAGTAAATAAG 539
                             -- i  vi       i   i  iiv vi    v i   --------
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG-------- 106

  chr1_76275731_7    540 ATCCACAATTTTTGTGGAATTTTATGAGCTAATTCTAAAACTCAAA-GGA 588
                         -- ii vv      ii   v  v ii    i  i      i   v -   
  L1M4_orf2#LINE/    107 --CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_76275731_7    589 AGTATAAAGG----------GCCAGGATCACCTTAAAGAGAAACAGCAAG 628
                          i ii  i  ----------    ii iv i   i  i ii  v i   i
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_76275731_7    629 GTGGGAGGTTTGGCTCTATCAGAAATAAAGACTTATCATAAAACTTATCA 678
                           v     vi vi v  vi vi vv v  i     ii i   i  - ivi
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT-ACAG 253

  chr1_76275731_7    679 TAAAAAACTACAGTGTGACATTGGTATTAAAATGAACAAATAGATCAATG 728
                            vv  v-        ii i   i  v ii  ii   v           
  L1M4_orf2#LINE/    254 TAATCAAG-ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_76275731_7    729 GATCACTAGAATTTAGCAACATATCCAGAAAAAGACTCAAACAT--ATGA 776
                           -- -       v  - i----        v i  i  v    --   i
  L1M4_orf2#LINE/    303 GA--A-TAGAATTGAG-AG----TCCAGAAATAAACCCATACATTTATGG 344

  chr1_76275731_7    777 ACA------TTTCGGTGTCTCTGCCAAG------CAGTAGCGAAAGCACA 814
                         v  ------     iiivvvv       ------  i i v     v i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_76275731_7    815 GTCTTTTCAATGAAAGATGCCAGGAAAATTGGATA-CCATATTGGGGTAA 863
                                   ii  v i   ii   v  i      -   i  ---- i  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT----GCAA 440

  chr1_76275731_7    864 AA-AATGA---TG---CCCTATTTTACATCATACAGAAAAATAAAATCGA 906
                           -     ---  ---     ii i   i    i v      v  v  i 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_76275731_7    907 AATAGATTTTAAATCTAAATTTGAAAGGCAAAATAATGTAGTTTCTAGAC 956
                            i   iv? i i      v i i  vi    iv  iv ii ii    v
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_76275731_7    957 ATTAATAT-GCTAAAATATTTTCAAGAAATCAAACTAGTGAAAGACTTCT 1005
                         ivv  i  - v?iv  -  i   iv  vv iiiii   vv  v ii    
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_76275731_7   1006 TAAGGAGGGATTTTAACAATTATTAATTGTAAAATAAAAAATTAAGAAAA 1055
                           iiv v - ivii  -  vi iv iivii    v       vi v   v
  L1M4_orf2#LINE/    590 TAGATATG-ACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_76275731_7   1056 TAGGCTGTAGTATAATTG-----TTTTGTTCAT-AAAAGACACCAGTAAA 1099
                          i i  vi vi v    i-----      v v -   i     i vi  i
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_76275731_7   1100 GGAATGAAAAGACAAGCTAAAATGTGGAAGAAGATATTTGCAA--CACAT 1147
                         ii i           v i v ivi   i    i          --  i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_76275731_7   1148 AT--GATTGGAAAATATATATTAATGCATAAAATATATATAAAACACTCC 1195
                           --   vi ii v - i   i------i i        -  i -    i
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACT-TGTATC------CAGAATATATA-AAGA-ACTCT 778

  chr1_76275731_7   1196 TACCCCCC-----TAAAAGGTAAAAGAGAACCCATTTTTTTAAATGGGGA 1240
                            vv i -----     i -- v i v      v  ?vv-       v 
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAG--ACAAATAACCCAATTWAA-AAATGGGCA 825

  chr1_76275731_7   1241 AAAGACTAATACAGGCAGTTCACACAAGAAGATATTCAAATAGCCAATAA 1290
                           i  i viv i  i  v   v vv          v     i        
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_76275731_7   1291 ATATCT-AAAAGGTGTTCAACCTCATTCTTAAT 1322
                         ii iv -     i  i     v   ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (152 / 95)
Gap_init rate = 0.04 (34 / 844), avg. gap size = 2.68 (91 / 34)  


2822 26.43 3.15 1.01  chr1_76342975_76348224.rev     3871  4759 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_76342975_7   3871 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCGATATTGTTAAAAT 3920
                               i i  i     i        v      v ii          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_76342975_7   3921 GGCCATGCTGCCCAAAGTATTTTATAGATTCAATGCTATTCCTGTTAAA- 3969
                            v  i  v      v iv i  i        i  v  i   i i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_76342975_7   3970 --CTAGCATTGACATTCTTCACAGAACTAGAGAAAACAATTTTAAAATTC 4017
                         -- i   --  v -  i  ii     v v  v  ivii  ii        
  L1M4_orf2#LINE/    101 TCCCAGC--TGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_76342975_7   4018 ATATGGAA--GCAAAAAATGAGCCCA-AATAGTCAAGGCAATCTTAAGCA 4064
                                 --    iii ----    -     i   ii       i iv 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_76342975_7   4065 AAATGAACAAAGCTGGACACATCATGCTACTGGACTTCAAACTGTACTAC 4114
                          i v        i    vivv   ii  v ivi i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_76342975_7   4115 ACAGCTACAGTAACCAA-ACAGCATAGTACTGGTACAAAAAGAGAAA-AC 4162
                          v           i   -    ii i       i i  ii v   v - i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_76342975_7   4163 AGACCAATCAAAAAGACTGGAGAACCCAGAAATAAGGCCATACACCTACA 4212
                            i    vi  v   v v    ii          iv       ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_76342975_7   4213 ACTATCTGATATTCAACA----TGACAAAAACAAGCAATGGGGAAAGGAT 4258
                         iii vi    v   i   ----  v   i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_76342975_7   4259 TCCCTATTCAGTAAGTTGTTCTGGGATAATTGGCTAGCCACAAGCAGAAT 4308
                         vvi  v    ii  i v  v      i  i   v  ?     v   i  v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_76342975_7   4309 ACTTAAACTGGACCCCTTCCTTCCGCCATATACAAAAATTAACTCAAGAT 4358
                          v v  ii         v   iv i                      i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_76342975_7   4359 GAATTAAGGACTTAAATGTAAAACCCAAAACTAGAAAAACTCC------- 4401
                          i  i ?i   i         i v i       v    -   i-------
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGA 542

  chr1_76342975_7   4402 -AACTTAGGCA-ACACCATTCTGGCCATAGAAACAGGGAAAGATTTCATG 4449
                         -   v    ?i- v i v iv  i  v i iv-i   v  v i    v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTA 591

  chr1_76342975_7   4450 ACGAAGACACCAAAAGCAATTACAAGAAAAGCAAAAGTTTACAAACAGGA 4499
                         ivv v             vvvi   v     v    i vv i   iv   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_76342975_7   4500 TCTAATTAAACTAAAGATCTTCTGCACAGCAAAAGAAACTCTCAACAAAG 4549
                         ii v  i   v v  i v   i  ii vv    i  v   v    v    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_76342975_7   4550 TGAACAGACAACCTACAGAATGGGAGGAAATTTGTGCAAACTATGCATCT 4599
                             v        i            i    v v      ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_76342975_7   4600 GACAAAGGTCTAATATCTAGCATTTATAAGAAA----TACAAACAAATG- 4644
                           i  i  v  vi    i  v  v     ii  ----     viv   i-
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_76342975_7   4645 TACAA-GAAAAAAAACCCA-TTAGAAAGTGGACAAAGGACATGAACAGAC 4692
                           v  -  v   v      -  ?i   i   i       iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_76342975_7   4693 ACTTTTCAAAAGAAGATGTACATGCAGCCAATAATCATATGAAAAAAAAC 4742
                          i  i  v         i    viii        v  i       i vi 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_76342975_7   4743 TCAGCATCACTGATTAT 4759
                            i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.18 (37 / 17)  


2997 27.00 1.33 0.44  chr1_76420411_76424796.rev     2996  3895 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_76420411_7   2996 TGAAAAAAAAATCCATGTTCATGGATAGGAAGAATCAATATTGTGAAAAT 3045
                           i   i v vi              v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_76420411_7   3046 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3095
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_76420411_7   3096 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 3144
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_76420411_7   3145 ATGGAA-CAAAAAGGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGA 3193
                               -iiv  i   v  v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_76420411_7   3194 GCAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTATAAGGCT 3243
                         i     i      vv   ii  v  ii i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_76420411_7   3244 ACAGTAACCAAAACAGCATGGTACTGGTACCAA-ATCGA---ATAGACCA 3289
                                i   i    ii         i iv i-  v  ---     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_76420411_7   3290 AAGGAATAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCATC 3339
                          v         iv    vii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_76420411_7   3340 TGATCTTCAACAAACTTGACACAAACAAGCAATGGGGAAAGGATTTCCTA 3389
                             i   i    ivv  v  vi v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_76420411_7   3390 TTTAATAAATG-TACTGGGAAAACTAGCTAGCCATAGGCAGAAAACAGAA 3438
                           i  i     - i      v    i v  ?   i v   i  i vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_76420411_7   3439 ACTTGACCACTTCCTTATGCCTTATACAAAAATTAACTCAAGATGAATTA 3488
                         ii v    v  v   i ii  v                   i   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_76420411_7   3489 AAGACTTAAATGTAAAACCCCAAACCATAAAAAACCTAGAAGAAAACCTA 3538
                         ?    i         i v iv    i      vv i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_76420411_7   3539 GGCAGTA--CCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 3586
                           ?-   --i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    550 GGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_76420411_7   3587 TCATCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATCTAAT 3636
                         v  i        vvi          vv   i v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_76420411_7   3637 TAAACTAAAGAGCTTCTGCCTGGCAAAACAAACTATGTCAGA--GTGAAC 3684
                         i   v v  i i   i  ivivv    iv v     -iv   --     v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT-CAAGAAAGTGAAA 696

  chr1_76420411_7   3685 AGGCAACATACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 3734
                           i    vi                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_76420411_7   3735 AGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 3784
                         i  i  vi          v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_76420411_7   3785 AAACAGACAACCCCATCAAAAAGTGGGCGAAGGATATGAAAAGACACTTC 3834
                          i   i i     v  i?    i     i      v    v     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_76420411_7   3835 TCAAAAGAAGACATGTATGTGGTCAA-AAACATATGAAAAAAAGCTCATT 3883
                           v        i  ii vi   i   -  i  i       i v     vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_76420411_7   3884 ATCATGGTCATT 3895
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (136 / 103)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


 924 27.23 21.73 2.88  chr1_76576184_76578562.rev     1128  1891 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_76576184_7   1128 TGGAGAGACATAACATATACATGGAATAGAAAATTCAATGGTGTAAAGA- 1176
                             i   i  vv   i v      v i   i i i   iv   v    -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_76576184_7   1177 GGTAAATTA-TCCTCAAATGAATCTATAGGTTCAAGATAATCTCAATCAA 1225
                           i  --  -   i     vi     i  i     vii    i v     
  L1M4_orf2#LINE/     51 GGCAA--TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_76576184_7   1226 AATCCCCAAATACCACAAGATTTCTTCCATGGAACTCTACAAACTGATCC 1275
                               - iv i  ------   i  v  --   v iv    i       
  L1M4_orf2#LINE/     99 AATCCC-AGCTGCC------TTTTTTGCA--GAAATTGACAAGCTGATCC 139

  chr1_76576184_7   1276 TAACATTTTTATAGAGATGCAAAGGGCCAAGAA-AGCTAATGC--CCTTG 1322
                            v   iv   i  i      i  i  v    -   i  vi --i    
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_76576184_7   1323 ATGAAGAGGAACAA------------------------------------ 1336
                          vi    i      ------------------------------------
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_76576184_7   1337 ---------------------GATGGTGTGG-----ACACAAGGGCAGAC 1360
                         ---------------------  ii      -----i  i    ii    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_76576184_7   1361 ACATTGACCCATGCAACATAAT--AAAG-----------ACCC------- 1390
                          i  v  i v   v  i v   -- i  -----------    -------
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_76576184_7   1391 ------CAAGTG-TTTGTGATGAAAGTGCCAA-ACAGAGTACTGGGCAGA 1432
                         ------   v  -   vi  ii ii       -  vivvi v    v i 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_76576184_7   1433 GGAAATGAGACATTTTTAA-AAAC------------ACTGAATAACCTCA 1469
                          --   -  v -    i  -   i------------    i   ?  v  
  L1M4_orf2#LINE/    390 G--AAT-AGTC-TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_76576184_7   1470 TGGAAAAAGGTGAATCTAGACCCTTACTT------ATACACAAATTTCAG 1513
                           v    iii    vi i     i   i ------   i     vv i i
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_76576184_7   1514 TTCTAGGTGAATTGAAAACCTG--TATCAGAAATACAA-TAGAGTAATGC 1560
                         i  v ii  i  ii? i    i-- i v   iv  v  -  ---   vi 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA---TAAAAC 532

  chr1_76576184_7   1561 TTTAAGATGAAAGTGCAGGAGAAAATTTTCAT-ACCATCAGGTAGGAAAC 1609
                          i v   v    iiii   ? v    i   i -   v vi v    v  i
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_76576184_7   1610 ATTTTTATTAAACAAAATAG-AAAAGCACTCACAGTAGAAGAAAAGACTG 1658
                         iv   i-   i i vi i v-        vvi  ii i       i iv 
  L1M4_orf2#LINE/    583 GGTTTC-TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_76576184_7   1659 ATAAAATG-----------AATTATA-----CTATCCCTCAAAAGACATT 1692
                              v  -----------     v -----i i v i     i    i 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_76576184_7   1693 A-----AAAGTGAAAGG-CAGGCTATGGAGAGGGAGAACACA-------A 1729
                          -----         i -  iv i ii  iv       v i ------- 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_76576184_7   1730 TCATA-----GG-AAGGG-TTAATATACAAAATACATAACAAATTCCTAT 1772
                              ----- i-     -i vi   v  i    i    vi  i  i  i
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_76576184_7   1773 ATATAGATAATAAAATCAGCCAAA--AC--AAT-AAAAAATTGGCATAAG 1817
                          vv vi         --  v    --  --   -?      v    v i 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAA--AGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_76576184_7   1818 ATGCAATTA-----TTGATTAAAGAGGAAATCCAA-TGGCAAATACACAC 1861
                           vii v  -----  vvii     i  v  v   -    v    vi   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_76576184_7   1862 AAGAAAAGGTCCTTATCATTCATAATCCAG 1891
                          v      i v  i v   -  ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACAT-CAZZZZZZZZ 908

Transitions / transversions = 1.58 (125 / 79)
Gap_init rate = 0.05 (42 / 908), avg. gap size = 4.48 (188 / 42)  


2451 28.26 3.49 0.58  chr1_76627542_76632984.rev     4105  4964 (479)    L1M4_orf2#LINE/L1       24   908 (0)  

  chr1_76627542_7   4105 GATGGGTAGAATCAATATTGTGAAAATGACCATACCGCTAAAAGCAATCT 4154
                            v  v   v i        v  i   i v    iv iv   vii    
  L1M4_orf2#LINE/     24 GATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCT 73

  chr1_76627542_7   4155 GCAAATTCAATGCAATTCCCA--AAAAATACAACCATCGTTCTTCACAGA 4202
                         i  i      i     i  i --    viv  i iii -  i  ii    
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGA 122

  chr1_76627542_7   4203 ACTAGAAAAAACAATCCTAAAATTCATGTGGAACCCAAAAGGAGCCTTTC 4252
                          v v  v  ivii              i     vivv  i   -  ivvv
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA-CCCAGA 171

  chr1_76627542_7   4253 ATAGCCAAAGCAAGACTAAGCAAAAAGAACAAATCTGAAGACATCACATT 4302
                                  i   vvi i iv  i         vi  i  ivv     i 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_76627542_7   4303 ACCTGACTTCAAACTATACTATAAGGCCATAGTCACCAAAACAGCATGTT 4352
                         v  ii i      viv     i  i  i i   v i   i    ii  v 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_76627542_7   4353 ACTGGTATAAAGATAGGCATATAGACCAATGGA-CAGAATGTAGAACCCA 4401
                              i    i     i        i       -i     vv   ii   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_76627542_7   4402 GAAATAAAGCCAAATACTTACATCCAACTGATCTTTGACAAAGCAAACAA 4451
                                 v   v i i   iivi   i    i  i     i vviv   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_76627542_7   4452 AA--ATGAAGTGGGAAAAGGACCCCCTATTCAACAAATGGTGCTGGGATA 4499
                         i --  vv i    i    i ivvi  v                    i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_76627542_7   4500 ATTGGCAAACCACATGTAGAAGAATGAAACTGGATCCTCATCTCTTAC-- 4547
                          i   vv ?       i i         ii    i  ii i   vi  --
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_76627542_7   4548 TTTACAAAAATCGACTCAAGATGGCTCAAGCATTTATATCTAAGACCTGA 4597
                          v         ii      i    v   ?iv ii  v  v     v  i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_76627542_7   4598 AACCATAAAAATTCTAGAAGATAACATTGGAATAACCCTTCTAGACATTG 4647
                            i      v ii       v     v  ?i   vi    vv   v   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_76627542_7   4648 GCTTAGGCA--GACTTCATGACCAAGA-ACCCAAAGTAAATGCAACAAAA 4694
                          v       -- ii   v iivi v  -   v    i v v         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_76627542_7   4695 CAAAGA-TAAATAGATGCAACTTAATTGAA-CTAAAAG-----GCACAGA 4737
                         v   i -  i   i  vvi    v  ii  -i     i----- ii vvv
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_76627542_7   4738 AAAAGTAACAATCA-----GTAAACAGACAACCTGTAGAGTGGGAGAAAA 4782
                            i vv  v    -----  i  v        iii   i          
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_76627542_7   4783 TCTTCACAATCTATACATCTGACAAAGGAATAATATCCAGAATCTACGAG 4832
                          v  ii   vii   i      i  i   v vi          v  ii i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_76627542_7   4833 GAACTC----AAGTCAGCAAGAAAAAAGCAA----TCTCATCAAAAAGTG 4874
                               ----  v   ii  v     ii   ----i iv  i?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_76627542_7   4875 GGCTAAGGACAAGAATAGACAATTCTCAAAAGAAGATATGCAAATGGACA 4924
                            v     ivv         v     v           i       v  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_76627542_7   4925 TCAAACATATTTTAAAAAATCACTAATGATCAGAGAAATA 4964
                         vi  i  i  v--    i  -i  v vv    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATG--AAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.02 (16 / 885), avg. gap size = 2.19 (35 / 16)  


3279 26.55 1.11 0.66  chr1_76660682_76666244.rev     4169  5072 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_76660682_7   4169 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4218
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_76660682_7   4219 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 4268
                            v     v     iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_76660682_7   4269 TACAAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4316
                          v v iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_76660682_7   4317 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 4366
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_76660682_7   4367 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTCTGCTACAAGGC 4416
                                i      vv   ii  v  ii i      vii i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_76660682_7   4417 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACT 4466
                                 i   i    ii         i iv ii i           ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_76660682_7   4467 AATGGAACAGAA--GAGAGCCCTCAGAAATAATACCACACATTTACAACC 4514
                                i    --     i  --        vv   i       iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_76660682_7   4515 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4564
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_76660682_7   4565 CTATTTAATAAATGGTGCTGGGAAAGCTGGCTAGCCGTATGTAGAAAGCT 4614
                           v  i  i              v i    v  ?  ii   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_76660682_7   4615 GAAACTGGATGCCTTCCTTGCACCGTATACAAAAATTAATTCAAGATGGA 4664
                            ii    iv   v   ii    i              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_76660682_7   4665 TTGAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTGGAAGAAAAC 4714
                          ii?    i       v   v       i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_76660682_7   4715 TTAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGTCT 4762
                         v    ?i- v i -   i- i  v i  i- i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr1_76660682_7   4763 AAAACACAAAGAGCAATGGCAACAAAAGCCAAAACTGACAAATAGGATCT 4812
                          vi    v  i    vvi          vv    iv  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_76660682_7   4813 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 4862
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_76660682_7   4863 ACAGGCAACCTACAGAATGGAAGAAAATTTTTGCAATCTACTTATCTGAA 4912
                          v  i     i         i       v       vii iv       v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_76660682_7   4913 AAAGGGCTAATATCCAGAATCTACAAAGAACTC----AAATTTACAAGAA 4958
                           i  i  vi          v  i         ----  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_76660682_7   4959 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5008
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_76660682_7   5009 TCTCAAAAGAAGACACTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5058
                             v        i ivi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_76660682_7   5059 TCATCACTGGCCAT 5072
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (150 / 86)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3008 24.67 3.29 3.73  chr1_76690109_76694306.rev     2796  3707 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_76690109_7   2796 TGGAAAGATATCACATATTTATAGATTAGAAGAATTGATATTGTTAAAAT 2845
                                     v   i  i  i    i     v  i          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_76690109_7   2846 GTCCATACTACCCAAAGTTATCCACAGATGTAATGCAATTCTTATCAAAA 2895
                          v v     v      v v   i      vi  i     i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_76690109_7   2896 CACCAAATACCAAAATACCAAAATACCAAATTCTTATCAAAATAAAGAAA 2945
                         iv   iv i  -------------------  i  ------- iv     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-------------------TTTTT-------TGCAGAAA 124

  chr1_76690109_7   2946 TAGAAAAAGAAAATCCTAACATTTATATGGAACCACAAAAGGCCCGACAT 2995
                          v  v  - vvi       v   i        vii   ii i   iiv  
  L1M4_orf2#LINE/    125 TTGACAA-GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chr1_76690109_7   2996 AGCTAAAGCAATCCTGAACAAAAAGAACAAAGCTGGAGGCATCACACTAC 3045
                            i   i     i    v  i          i      vv       v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr1_76690109_7   3046 CTGACTTTAAAATAGATTACAAAGCTGTAAGTACCAAGACATTATGGTAC 3095
                          ii i  i    ivv i         ii ivv i       v i      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_76690109_7   3096 TAACATATAAGCAGACACACAGATCAATGGAACACAATAGAGAGCCCAGA 3145
                          ii    viiii     i i            i v   v     i     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_76690109_7   3146 AATAAATTCACCTAGCTACATTCAACTTATTTTCAACAGAGGTGCCAAGA 3195
                               ii  ivi vi  iiv    i v      i   ii          
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_76690109_7   3196 ATACACATTATAGAAAAGACAGTGTTTTAAATAAACAGTGCTGGAAAAAT 3245
                         vi iv  v ivi    ii i   v    v  i   ii       i v  i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_76690109_7   3246 AGGATATCCACGAGCAGAAGAATGAGTCTAGACCCTTACTTCTCACCACA 3295
                         v     ?    iv   i        ivi i     i   i  v     i 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_76690109_7   3296 TGCAAAATCCAACT--AAATGGATTAAAGGC-TAATTGTAAAGTCTATAA 3342
                          i     vii    --        i ?  i -   v     iiv   v  
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_76690109_7   3343 CTATGAAACTACTAGAAGAAAACATAGGGGGAATGCTTTACAACATTGGG 3392
                             i     vi                ? v  vv   iiii  v     
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_76690109_7   3393 CATGGCAGGGATTTTAAAAATAAGACCTCAAAAGCATAGGACACAAAAGC 3442
                         ivv    iv i   ivv i   v   vi        i i vv       v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_76690109_7   3443 AAAAATAGACAAATAGAATTATGTCAAACTTAAAAGGTTTTGCACAGCAA 3492
                                  i    v i i vii     v      iv     ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_76690109_7   3493 GAAAAACAATTAACAAAGAGAAGAGACAACCTATAGAATGGGAGAAAATA 3542
                         iii v  v  i  v    v   i        i i                
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_76690109_7   3543 TTTGTAAACTATACATTCGACAAGGAGTTAATATCCAGAATATATTAGGG 3592
                             i   ii   i  ii  i    iii vi              v i i
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_76690109_7   3593 ACT--TA-AAC---------AAAAGAAAAAAAACCCAAT------AT--- 3621
                            --  -   ---------      v   v        ------  ---
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_76690109_7   3622 ------ACCTAAATAGATATTTTTCAAAAGAAAAAGTGAGACACACAAAT 3665
                         ------ ii i      i    i  v      -------  i i      
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAA-------GATATACAAAT 866

  chr1_76690109_7   3666 GGCCAATAGGCACATGAAAAAATGCTTGACAGCATTAATAAT 3707
                                 i           i     ii   v  ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (142 / 80)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 5.82 (64 / 11)  


3600 19.24 1.66 1.66  chr1_76733832_76735596.rev      490  1274 (491)    L1M4_orf2#LINE/L1      124   908 (0)  

  chr1_76733832_7    490 ATTGATGAGTTAATCCTAAAATTCACACGGAAATTCAAGGGACCCAGCAT 539
                              ii  i i             i i      v            v  
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chr1_76733832_7    540 AGCCAGAAGCAATCCTATGAAAGGATAAAAAAGTTGGAGGATTCACACTT 589
                              i  -     i ivi    i v  v            i        
  L1M4_orf2#LINE/    174 AGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_76733832_7    590 TCTGATTTCAAAATTTGCCACAAAGTTATGGTAATCAAAACTGCAC-GCA 638
                         i ii         i  i i      i  ii        i  v iii- i 
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_76733832_7    639 GTGGAAGAAGGAAATACATGAAGATCAATGGAATAAACTTAAGAGTCCCA 688
                         v   v v     v v    iv              i v  i       vi
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_76733832_7    689 AAATAAGAATATATATCTATGATCAATT--TTTT--ATGAGAGTGCTAAG 734
                               ivvi   i  i    i      --    -- ii  i    i   
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_76733832_7    735 ACAATCCAATGGTGAGGGTCGGGGAGGGGGTAATTTTTTCAACATCTGGT 784
                           v  i      ----------   ii ii  i i         vv    
  L1M4_orf2#LINE/    373 ACCATTCAATGG----------GGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_76733832_7    785 TCGGTGATAACTGTATATTCACATGCAAAAAAAGTGAAGTTAGACACCTT 834
                         v v v  i     v   ?i           i  -       i   v   v
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCTA 461

  chr1_76733832_7    835 CCTCACACCATTCACAAAATTAAACTCAAAATAGATAATAGACCTAAGCA 884
                                    vi      v v          i   v ?        iii
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_76733832_7    885 TAAGAGCTAAAATTCTACTACTCTCAAAAGAAAATGTAGGAGTAAATACT 934
                                     i v  vv     i i       ii    ?      vi 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_76733832_7    935 CCTTACTTTGGATTAGGCAA-GCCTTTTTAAATACGACACTAAAAGCATA 983
                          v v  i    i        - vi  i   i   i     i       i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_76733832_7    984 AGTGACAAAAGAAAAAAACAGATAAATTGGATTT-ATCAAAATTAAAAAC 1032
                           ii             -i            i  -               
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_76733832_7   1033 ATTTGTG-TTCAAAGCACACTGGCAAGAAAGTGAAAAGATAGCCCACAAG 1081
                         v      -       v     iv                i i      ii
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_76733832_7   1082 GTGAGAGAAAATATTTGCACATCATACATATAATTAAGGATGTGCATGTA 1131
                         i  i               v      i  v i  v i   iv  i  vi 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_76733832_7   1132 GAATATATAAAGAATTTTTAAAGCTCAATAAGAAAAAGATAAATAGCCCA 1181
                                       i i   v i        v       i     i    
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_76733832_7   1182 ATT-AAAAATGGTCAAACGATTTGAAGAAACATTTATCCAAAGAAGATAT 1230
                            -        v    v        v i      v              
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_76733832_7   1231 ATA----GTCAGTAAGTACAGGAAAAGATGCTCAACATTATTAGCCAA 1274
                          i ---- i  i    i   v                 i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (97 / 51)
Gap_init rate = 0.02 (12 / 785), avg. gap size = 2.17 (26 / 12)  


 408 19.10 0.00 1.12  chr1_76737201_76738799        1    89 (1510)    L1M4_orf2#LINE/L1      614   701 (207)  

  chr1_76737201_7      1 CAACAATAAAGAACAATAGATACGTTAAACTTTGTCAAAATTAAAAACCT 50
                               -  ii  v        vi  ii    ii              i 
  L1M4_orf2#LINE/    614 CAACAA-AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_76737201_7     51 TTGTCCTTCAAAGGGTACCATCAAGAAAATGAAAAATCA 89
                             v         ii  i         i      iv  
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)  

2354 23.08 1.60 1.92  chr1_76737201_76738799      484  1107 (492)    L1M4_orf2#LINE/L1      287   908 (0)  

  chr1_76737201_7    484 GACATA-----CAATGGAGCTCCAATAAAGCATAGAGAACCCAGAAACAA 528
                               -----       ------   i --  v    ii       i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGA------ATAGA--ATTGAGAGTCCAGAAATAA 328

  chr1_76737201_7    529 ATCCATGCACCTAAAGTGAACTCATTTTTGACAGAGGAGAACCAAGATCA 578
                          i    i  ii  vi  v  i v     i    ii  v --      i  
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG--CCAAGACCA 376

  chr1_76737201_7    579 TGCACTGGGGAAAAGACCATCTCTTCAATAAATGATGCTGGGAAAACTAG 628
                          v  v        ii ivi   i     i     i        v    i 
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_76737201_7    629 ATATCCATATGCAGAAGAATAAAACTAGACCCCCTATCTCTCACCATATA 678
                            ?   i     i      i  ii i      -  i   v         
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCC-TACCTCACACCATATA 475

  chr1_76737201_7    679 CAAAAATCAAATCAAAATGGATTTAAGACTTAAGTCTGAGACCTCAAACT 728
                                i  v           iv?    i   i v i   v  v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_76737201_7    729 ATAAAACCACTACAGGAAA-CATTGGAGAAACTCTTCAGGACGTTGATTT 777
                                ivi  v i    -   v  ? v  v     iv   v   iv  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_76737201_7    778 GGGCGAAATTTTATTGAGATA---CCCCAAAAGTAGAGGCCACCAAAGCA 824
                         i   i viv   v  -     --- v       i v i  v  v    v 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_76737201_7    825 AAAATGGACAAATGGGATCACCTCAAG-TTAAAAAGCTCTGCACAGCAAA 873
                              i  i    v   iiv v    i-       vi i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_76737201_7    874 AGAAATAATTAATGAAGTGAAGCGACAACCCACAGAATGGGAGAAAATAC 923
                         i  v iv  i  vi       iv                          i
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_76737201_7    924 TTGCAAACTACCCATCTGACAAGAGATTAACAACCAGAATATATAAGGAG 973
                                ii ivi      i   i  i vii v             i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_76737201_7    974 CTGAAACAACTCCATAGGAAAAAATCTAATAATCCAATTAAAAAATGAGC 1023
                           vvv       v   iv     iv v     i      ?       i  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_76737201_7   1024 AAAATATTTGAATAGATATTTCTCAAAGGAAGACATACAAATGGCAAACA 1073
                            iv           i       v  i     i           v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_76737201_7   1074 GGCATATGAAGTAGTGCTCAACATCGCTGATCAT 1107
                         i   i     ivii           i????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (85 / 55)
Gap_init rate = 0.01 (9 / 622), avg. gap size = 2.44 (22 / 9)  


3266 26.65 1.90 0.22  chr1_76837933_76839907      591  1483 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_76837933_7    591 TGGAGAAATTATTCCATGTTCACAGATAGGATGACCCAATAGTGTCAAGA 640
                             i i  -  i         ii   v   v   ii    v   i    
  L1M4_orf2#LINE/      1 TGGAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_76837933_7    641 TGTCTGTTCTTGTCAACTTGATATATAGATTCAATGAAATCTC------- 683
                           v vi v  ivi   v     v  i        i v    i -------
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_76837933_7    684 --CCCAATTGA-TATTTTGTGGATATCAACAAAATAATTCCAAAGTTTAT 730
                         --    ii  v- v     ii  v  ii    iv i  i i   i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_76837933_7    731 ATGGAA--GCAAAAGACCTAGAATAGTCACCGTGATATTGAGTTAAAGGA 778
                               --    ii    i       i  vviii  v    ivv i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_76837933_7    779 ATAAATTTGAAGCACTGACATTACCCAACTTCGATACTTACTATAAGACT 828
                          i   v   i  v   v   i v     i   i v        i  ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_76837933_7    829 ACAGTAATCAAGATTGTGTAGTATTGG--TAAAAATAAACAAAGAGAAGA 876
                                      iv    i   i   --   ii   i   v v   vv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_76837933_7    877 ATGGAATAGAATAGAGAGTCCAGAAATAGGCCCACATGAATATATTCAAC 926
                                     v               ii    i iivv   iv    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_76837933_7    927 TGATCTTTGACAAAGGAACAAAGGCAACACAAAGAAGGAAAGAA-AGTCC 975
                             i  i     i  vi v   i v iv   v i-        -    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCT 398

  chr1_76837933_7    976 TTTCAACAAATGGTGCTGGAACAACTGGACATTTACATGCAAAAAAATCA 1025
                                            i         i ?ii          i   v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_76837933_7   1026 ATCTAGACACAAGCCTTACACCCTTCACATAAAATAACTCAGAATGAATC 1075
                          vi i   v vvi   i     v vi   v   v       i    i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_76837933_7   1076 ACAAACCTGAATGTGGAATGAAAAACTATAAAACTCCTAGAACATGAGAT 1125
                          ? i    i     iii vvv               i     v vi v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_76837933_7   1126 AGGGGAGAATCTAGATGACCTTGGATTTGGCAATGACCTTTTTGATATAA 1175
                            ? vi     vvi         i  v       iii i  v     i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_76837933_7   1176 CACCAAAGGCACACTTCATGAAAGGAAGAATGAATAAGATGGACTTTATT 1225
                                i     vviv ii    i  i   ii    iv       i  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_76837933_7   1226 AGAGTTAAAA-TTTCTGCTCTGTGAAAGGCACTGTCAAAAGAATAAAAAG 1274
                          i i      -i  i  iv  vii  i i    i    i i i i     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_76837933_7   1275 ACAAGGCACTGATTAGGAGAAAATATTTGTAAAAGACACATCTTCTAAGG 1324
                             vv   v  v i              i   vv i i    vv     
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_76837933_7   1325 GATTGTTATCTAAAATACACAAAGAACTTTTAGAAGTCCACAATAAGGAA 1374
                           i vv    i i    i i        i   v  v  v i     ii i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_76837933_7   1375 ACAAA-AAACAGATGAAAAAATGAACCAAAGCCCTTAATGGACACCTTGC 1423
                              -  v vi  v?       ii v  i vii v   i    ii iv 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_76837933_7   1424 CAAAGAAGATATGCAGATGGTAAATAAGCATATGAAAATATGTTCCACAT 1473
                                     i  i    iv        i       v   i  v    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_76837933_7   1474 CTTATGTCGT 1483
                          v????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.66 (146 / 88)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


 313 20.31 0.00 0.00  chr1_76909854_76912929.rev      964  1027 (2049)    L1M4_orf2#LINE/L1        1    64 (844)  

  chr1_76909854_7    964 TGGAAAGACAACCCAATCTGATGGATTGGAAGATTTAATATTGTTAAAAT 1013
                                 i v    vvi v             i             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_76909854_7   1014 GTTCATACTACCTA 1027
                          viv     v  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCA 64

Transitions / transversions = 0.86 (6 / 7)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.00 (0 / 0)  

2811 23.73 3.23 4.84  chr1_76909854_76912929.rev     1718  2585 (491)    L1M4_orf2#LINE/L1       55   908 (0)  

  chr1_76909854_7   1718 ACACTGCCCAAAGCAATTTACAGATTCAACAGAATTCTTATTAAA-TCTG 1766
                          i   v      vii  i            iv   i i   i   -  iv
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_76909854_7   1767 AA--GTTTTTTT---AGGAATAGATATAAAAAACCAATACTTAAATTTAC 1811
                          i-- ii     ---  i   v  i ----- i ii  v  v     i i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACA-----AGCTGATCCTAAAATTCAT 149

  chr1_76909854_7   1812 CTAGAACCACCAAAGAAACTCACAAGTAGCCAAATCAGTCTTAAGAAGGA 1861
                         v i   vii --   ii  i  v  -        v  i    i i  i  
  L1M4_orf2#LINE/    150 ATGGAAATGC--AAGGGACCCAGAA-TAGCCAAAACAATCTTGAAAAAGA 196

  chr1_76909854_7   1862 AGAAAAAAGCTAGAGGCATCAAATTTCCTGATTTCAAAATAAGTTACAAA 1911
                             v    i i    vv   v i    ii         ivvii      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_76909854_7   1912 TCTA--GTGGTCAAACC--TGTGATACTGACATAAAGACAGGTACG-AGG 1956
                         v   --  ii    iv --    i     i     i  i  ii ii-  i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_76909854_7   1957 CCAATGGAACAGAATAGAGAGCCAAGAAATAAATCTGTGCATATATAGTT 2006
                         i        i     v     i v         i ii i   v   i  i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_76909854_7   2007 AACTGACGTTTGACAGAGGTACCAAGAATATACAGTGAGGAAAGGATAGG 2056
                           i   iv  i    ii   i      vi  v  i  i      i    v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_76909854_7   2057 CTTATCAACAAATGGTGTTGGAACAACTGGACATCCACATGCAAAATAAT 2106
                            v             i   i         i ?            v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_76909854_7   2107 GAAATTGGACTCTTA----A-ACCATTCACAAAAATCAACTCAAACTGGA 2151
                            i      i i  ---- -     vi        i        v    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_76909854_7   2152 TTAAAGACCTAACCCTAAGACCTGAAACCACAAAACTCCTAGGAGAAAAC 2201
                          i ?        viv     v  i    i i       i   i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_76909854_7   2202 AGAGGGGAAAATCTTCATGACATTATTCTTGTCAATAATTTAATGGATAT 2251
                          v   ? v        i    v  ivvi v v    ii   vv i     
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_76909854_7   2252 AACACTGAAATCACAGGTAGCAAAAACAAAAAATAAAACAAGTGGGACTG 2301
                         i    ii   v    i i i     i-        i -i  i v     v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGA-TAAATTGGACTT 644

  chr1_76909854_7   2302 CATCAGA-TTACAAAGTTTC-TCCATAGCAAAGGAGAC----AACAAAGT 2345
                              i -   v   v   i- v v --       v  ----  v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGT 692

  chr1_76909854_7   2346 GAAAGG-TAGCCTATAGAATGAGGGGAAAATATTTGCAAAC----TATCA 2390
                             i -i i  i i      -  i               i----    v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATG-GGAGAAAATATTTGCAAATCATATATCT 741

  chr1_76909854_7   2391 GGAGAGGGATTAATTTCTAAGATATCTGAGGAACTTCTGTAACTCAGTAG 2440
                          ivi     i vi v  i ii    v i i     ii ii      i  i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_76909854_7   2441 TACTACCCCCCCCACGAAAAAAAAACCTAACAGTAGTAAAAAGACCCTCT 2490
                           -----------------    i  ------------   vi    vv 
  L1M4_orf2#LINE/    792 TA-----------------AAAAGAC------------AAATAACCCAAT 812

  chr1_76909854_7   2491 T-AAAAATGGACTAAGAACTTGAATACACATTTCTCCAAAGGAGACATAC 2539
                          -        i v   i i       v              i   i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_76909854_7   2540 AAGGGGTCAACAGACATATGAAAAAATGCCCGGTATCATTAATCAT 2585
                           iv  i   i ii  i       i    i iii    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.27 (141 / 62)
Gap_init rate = 0.03 (23 / 854), avg. gap size = 3.04 (70 / 23)  


3264 21.63 2.83 4.13  chr1_77023911_77027661.rev     2342  3261 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_77023911_7   2342 TGGAAAGACATCCAA-GTTCATGGATTAAGAAAGA----ATATTGTTAAA 2386
                                 i    v -           -- i    ----          i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT--GGAAGACTTAATATTGTTAAG 48

  chr1_77023911_7   2387 ATGTTCATACTACCCAAAGTGATCTACAGATTCTATATAATTCCTATCAA 2436
                            viv     v      v              v iii   i        
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_77023911_7   2437 AATCCCAATGGCTATCTTTAAATACATAGA--AGAAAATTCTAAAATTCA 2484
                                iiv  iv i   iv v v  v  --  vvi  i          
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_77023911_7   2485 TATAGA--TCCCAAAATGACCATGAATAGACAAAGTAATATTGAACAAGA 2532
                            i  -- v --  iv    vv      v    ii   v     v    
  L1M4_orf2#LINE/    149 TATGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_77023911_7   2533 AGAATAAAGCTGAAAGCATCACTCTCCCTGATTTTAAAACATATTACAAA 2582
                             i    i  i i vv    v  i  ii    i     v  i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_77023911_7   2583 GCTACATTAATCAAAATGGCATGATACTGGCATTATAAAAAAAGACATAT 2632
                               v       i ii ii  i         ---  ii v        
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCAT---AAGGATAGACATAT 293

  chr1_77023911_7   2633 GAACTAAATGGAACAGAAT-ACGGATCCCAAAATAAATCTATGCCTTTAA 2681
                         ii - v       i     -iv ii   vi       i i  i v    v
  L1M4_orf2#LINE/    294 AGA-TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_77023911_7   2682 AGTCACTTGATCTTT-ACAGAAGTGCCAAGAACACACACTAGGGAAGGGA 2730
                         i    v     i  i-   iii         v  iv  v i     i i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_77023911_7   2731 AGAGCACACACTAGTCTCTTCGATAAATGATATTGGGAAAACTGGATATC 2780
                         -----------      i   i i     i ii     v         ? 
  L1M4_orf2#LINE/    393 -----------TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_77023911_7   2781 CACATGCA---GAATGAAATTGGACCCTTA--TCATACCATATACAAAAA 2825
                                 ---       i        i  --   i              
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_77023911_7   2826 AGAACTCAAAATGGATTAAAGGCTCAAACATAAGGCCTGAAACTATAAAC 2875
                         vv              i ?  i ii   ii    iv  i          -
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA- 530

  chr1_77023911_7   2876 GACT---AGAAGAAAACATAGGGAAAAAGCTTCTTGACAATGGACTGGGC 2922
                         -   ---               ?iv   v    v    vv   ii i   
  L1M4_orf2#LINE/    531 -ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_77023911_7   2923 AATGATTTTTTTGGATATGACAGCAAAAGTACAGGCAACAAAAGCAAATA 2972
                             i   i  -i         v      i   i          v   v 
  L1M4_orf2#LINE/    580 AATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_77023911_7   2973 TAGACAAATGAGATTACACCAAACTAAAAAGCTTATTATGGTCAGCAAAG 3022
                             i    vi  i v  i    v v    i   -  i  v i--     
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTT-TTGTGCTT--CAAAG 675

  chr1_77023911_7   3023 AAAACTATCAGCAGAATGAAAAGGCAAT--ATGGGAAGGGCAGAAAATAT 3070
                         i v       iv i i       i   i-- ii i v   -         
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG-AGAAAATAT 724

  chr1_77023911_7   3071 TTATAAACCATACACCTGATAAGGGGTTAAAATCCAAAGTATATAAGGAA 3120
                           ii   i    i i          ii viv     i i       i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_77023911_7   3121 TTAA-AAAACTCAATAGCAAAAAAACACAAAACAAAACAAAAAACAGATT 3169
                         i vv- v         ii     i   ---  i  vv   --------  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACA---AATAACCCAA--------TT 813

  chr1_77023911_7   3170 ACAAAATGGGCTAAGGACCTGAATAGATAATTTCTC----AAAGGCATGT 3215
                         ?v         v     ii        i -      ----i   ii  ii
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACA-TTTCTCCAAAGAAGATATAC 862

  chr1_77023911_7   3216 AAATGGCCAACAGGTATATGAAAAAGTACTCAACATCTCTGATCAT 3261
                                   i i i i       ii i         v????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (129 / 66)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.56 (64 / 25)  


4101 17.88 2.28 3.90  chr1_77079324_77081502      764  1686 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_77079324_7    764 TAGAAAAACAGCCCATGTTCATGGACAAGAAGATTTTAATCTTGTTAAGA 813
                          i    i i v              ivi     i  -   v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTT-AATATTGTTAAGA 49

  chr1_77079324_7    814 TAATAGTGCTCCTCAAATAGATCTAAAGATTCAGTACAATCTCTGTTGCA 863
                          iii i i    i     v      v       iii     i  i --  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT--CA 97

  chr1_77079324_7    864 ACTGGGATTCTCTAGGCCAGTTGACTTCTTTGTACAAATTGATGAGCTGA 913
                          ----- v  ------    i  v   i    i v       ii      
  L1M4_orf2#LINE/     98 A-----AATC------CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr1_77079324_7    914 TCCCAAAATTCATATGGAATTGCAGGGGACTCAGAATAGCCAAAACAATC 963
                            i               v    i     i                   
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_77079324_7    964 TTTAAAAAGAAGAATAA-GTTGAAGGCCTTTCAAATTTCATAACTTCCCA 1012
                           v           i  -    i   v  ---------  i -       
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACT---------CACA-CTTCCCA 226

  chr1_77079324_7   1013 ATTTCAAAACTTACAATAAAGTGACGATAATCAA-ACA-TATGTTACTAA 1060
                                       v i    iv  ii       -   - i  v    ii
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr1_77079324_7   1061 CATAGGGATAAACATATAGATTAGTGGGATAGAATTGAGAGTCTACAAAT 1110
                             i     i          i i   i               i v    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_77079324_7   1111 AAATCTATATGTCTTTGGTCACCCGAATTT-AACAAGGGCACCATGGTTA 1159
                            i i   ii i v      vii  v   -i       ii   v iii 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_77079324_7   1160 TTCAAT----AAAGAATA-TTTTTTAAACAAATGGTGCTAGGATGATTGT 1204
                               ----        - i    v             i   ii i  v
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_77079324_7   1205 ATATCCACATGTAAAACAATGAAATTGGGCCCTTACCTCACACAATATAG 1254
                            ?       i    v      i    i   i          v     v
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_77079324_7   1255 AAAAATTAACTCAAAGCAGATCAAAGATGTAAATCTAAGATGTATGTACA 1304
                                        iii     ?   iv     v     -------i -
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-------GC- 518

  chr1_77079324_7   1305 TATAAATCTATTAAACTCCTAGAAGAAAACTCAGGGATAAATCTGCAGGA 1354
                         --    v    v      i           vi   ?i       v iv  
  L1M4_orf2#LINE/    519 --TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_77079324_7   1355 CCTCAGATTTGCCAACGAATTCTTAGGTGTAATTCCCAAAACATGAGCAA 1404
                            ii i  v v   i iv       i i i iv  v   i  ii     
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_77079324_7   1405 CAACAACAACAAA-----AAATTGGTTTTCACCAAAATTAAAATTTTCTG 1449
                            -  v  v   -----       vi    i           vi  i  
  L1M4_orf2#LINE/    617 CAA-AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_77079324_7   1450 TGCTTCAAAGGATGCTATCAAGAA-GTAAAAAAACAACCCATGGAATAAG 1498
                                     ii          -  i    i        ii    ii 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_77079324_7   1499 AGAAAATATTTTCAAATTATATATCCCCTTTGGAACTTGTATCCAGAATA 1548
                                    v     i       ivv vv  i                
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_77079324_7   1549 TGTAAAGA-CCCATACAACTCAATAATAAAA---CAAATTAACCCAATTT 1594
                          i      - i v                  ---     -         ?
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT-AACCCAATTW 814

  chr1_77079324_7   1595 TAAAATGGGCAAAGAATCTCAATAGACGTATCTCCATAGAAGGCATACAA 1644
                         v             i  i v       i v      v     ii      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_77079324_7   1645 ATAGACAA--AGCACACGGAAAGATTCTCAACATCATTAGCCAT 1686
                           i v   --      i i      v          ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (109 / 52)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.71 (57 / 21)  


3127 27.20 1.67 0.45  chr1_77142569_77147251.rev     3295  4191 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_77142569_7   3295 TGGAAGAACCTTCCATGCTCATGAATAGGAAGAATCAATATGGTGAAAAT 3344
                              ii iv i     i     i  v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_77142569_7   3345 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 3394
                            v   i v     iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_77142569_7   3395 TACCAATGACATTTTTCATAGAA-TTGGAAACAA-------CTAAAGTTC 3436
                          v   iivi v     iii    -   ---    -------     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_77142569_7   3437 ATATGGATCCAAAAAGGAGCCCACATTGCCAAGACAATCCTAAGCAAAAA 3486
                                vviiv  i   v  viv  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_77142569_7   3487 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTCTACTACAAGG 3536
                                 i      vv    i  v  ii i      vii        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_77142569_7   3537 CTACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGATATATAGAC 3586
                                  i   i    ii   i     i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_77142569_7   3587 CAATGGAGCAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 3636
                                ii    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_77142569_7   3637 TCTGATCTTTGACAAACCTGACAAAAGCAAGAAATGGG-AAAGGATTCTC 3685
                         vi    i  i     ivv  v   i v  vvv      -    i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_77142569_7   3686 TATTTAATAAATGGTGCTGGGAAAACTAGCTAGCCATATGTAGAAAGCTG 3735
                          v  i  i              v    i v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_77142569_7   3736 AAATTGGATCCCTTCGTTACACCTTATACAAAAATTAATTCAAGATGGAT 3785
                           i     i    v v i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_77142569_7   3786 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAACC 3835
                         i ?    i       v   v       i      v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_77142569_7   3836 TAGGCAATACCTTTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 3885
                             ?ivv vii   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_77142569_7   3886 ACATCAAAAGCAATGGCAACAAAAGCCAAACTGGATAAATGGGATCTAAT 3935
                            i        vvi          vv   v i       v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_77142569_7   3936 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTGTCAGAGTGAATG 3985
                         i   v v  i i   i  ii vv    i  v    iiivv i      vi
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_77142569_7   3986 GGAAATATAGAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGATAAA 4035
                          iv  ivi v               v       vii ivi         i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_77142569_7   4036 GGGCTAATATCTAGAATCTACAAAGAACTTAAACAAATT--TAG-AAGAA 4082
                           i  vi    i     v  i        ivv    v i--  i-  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_77142569_7   4083 GA-AAACAACCCCATCAAAAAGAGGGCAAAGGATATGAACAGACACTTCT 4131
                           -   i     v  i?    iv           v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_77142569_7   4132 CAAAAGAAGACATTTA--TGCACCCGCAGACACATGAAAAAATGCTCATC 4179
                          v        i  vi --  -i  vii ii          i       v 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATG-GCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_77142569_7   4180 ATCACTGGTCAT 4191
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


1853 18.05 1.00 1.25  chr1_77158230_77164631       86   484 (5918)    L1M4_orf2#LINE/L1      377   774 (134)  

  chr1_77158230_7     86 TTAAATGGGGGAAAGAATAGGTTTTTCAACAAATGCTACCTGGACAACTG 135
                           v       -         vi             v i iv         
  L1M4_orf2#LINE/    377 TTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_77158230_7    136 CATATCCATATG-AAAAGAAGGGAATGGAACCACCTTTC-CACTCCATAC 183
                         v   ?   i   -       v i i v i   -   vi -   v     i
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACC-CCTACCTCACACCATAT 474

  chr1_77158230_7    184 ACAAAAATTAACTCATAATGAATCAAAGAGCTAAATGTAAGAAATAGCAC 233
                                        v    i    ?   v            iv  iv  
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_77158230_7    234 TATGAAATTCTCAAAAGAAAATGTAGGTATAAATCTTTATGACCTTGA-T 282
                            i   i   i i       ii    ?i        ii        i- 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_77158230_7    283 TAGGTA-TGGATTCTTAGATGTGATACCAAAAACACAAGCAACATAAGAA 331
                             i -   v         i   i       i           v     
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_77158230_7    332 AAAATAGAGAAAGTGGAAATAATCAAAATTAAAAACGTTTTTCCTTCAAA 381
                                 v   v    vv v               v   v v       
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_77158230_7    382 GGATACCATCAAGAAAATAAAAAAATAACCCAAGGATTTGGAGAAAATTT 431
                            i  i         i i    i i      vi  v v         v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_77158230_7    432 TAACAAGTCATATATGTGATAAGGGACTTGTATTTAAAATAATATGTAAT 481
                          vi   i        v                 ii i    --- i   v
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA---TATAAA 771

  chr1_77158230_7    482 GAA 484
                            
  L1M4_orf2#LINE/    772 GAA 774

Transitions / transversions = 1.30 (39 / 30)
Gap_init rate = 0.02 (7 / 398), avg. gap size = 1.29 (9 / 7)  

3274 26.92 0.55 0.77  chr1_77158230_77164631     5000  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_77158230_7   5000 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5049
                              ii    i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_77158230_7   5050 GGCCACACTGCCCAGGGTAATTTATAGATTCAAGGCCATCCCC-TTAAGC 5098
                            v i   v    iiv i  i  i        v  v     i- i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_77158230_7   5099 TACCAATGACCTTCTTTGCAGAA-TTGGAAAACT-ACTTTAAAGTTCATA 5146
                          v   iivi    i         -   iv  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_77158230_7   5147 TG-AAGCAAAAAAGAGCCCGCATTGCCAAGTAAATCCTAAGCAAAAAGAA 5195
                           -  iiiv  ii  v  v v  v     ivv    i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_77158230_7   5196 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5245
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_77158230_7   5246 CAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATATAGACCAA 5295
                               i   i    ii  i      i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_77158230_7   5296 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAATCATCT 5345
                              i    iv   ivii         vv   i    i  iii   vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_77158230_7   5346 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGAATTCCCTAT 5395
                            i  i     ivv  v   i v  vvv              vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_77158230_7   5396 TTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5445
                          i  i        i     v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_77158230_7   5446 TTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGATTAA 5495
                              i    v   i i   v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_77158230_7   5496 AGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5545
                             i       v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_77158230_7   5546 GCGATACCTTTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAAACA 5595
                          ? vv vii   iv   v v  vv i     v ii   v iiv  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_77158230_7   5596 CCAAAAGTGATGGTAACAAAAGCCAAAAGCCAAAATAGACAAATGGGATC 5645
                                iivvi i        --    -----      i    v   ii
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAG--AAAA-----AATAGATAAATTGGACT 643

  chr1_77158230_7   5646 TAATTAAACTAAAGAGCTTCCGCACAGCAAAAGAAACTATCATCAGAGTG 5695
                          v  i   v v  i i   ii ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_77158230_7   5696 AGCAGACAACCTAAAGAGTGGGAGAAAATTTTTGCAATCTACACATTTGA 5745
                          iv        i v   i           v       vii i i  i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_77158230_7   5746 CAAAGGGCTAATTTCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 5795
                         i  i  i  vi v        v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_77158230_7   5796 AGAAAACAAACAACCCCATCAAAAAGTGTGCAAAG-ATATGAACAGACAC 5844
                          i  i     i     v  i?    i  v      -  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_77158230_7   5845 TTCTCAAAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAATGCTC 5894
                              v        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_77158230_7   5895 ATCATCACTGGTTAT 5909
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


3231 27.64 0.22 0.22  chr1_77177448_77183721.rev     4876  5783 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_77177448_7   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAACAT 4925
                              ii i  i     i      i v      v i     i  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_77177448_7   4926 GACCATACTGGCCAAGGTAACGTACAGATTCAATGCCATCCCCATCAAGC 4975
                          i v     vv    iv i iv           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_77177448_7   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_77177448_7   5024 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_77177448_7   5074 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATATTACAAGGC 5123
                                i      vv    i  v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_77177448_7   5124 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5173
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_77177448_7   5174 AATGGAACAAAACGGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5223
                                i i  iv   vvii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_77177448_7   5224 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5273
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_77177448_7   5274 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTACAAAGCTGA 5323
                         v  i  i              v      v  ?   i   i v  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_77177448_7   5324 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5373
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_77177448_7   5374 AAGGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5423
                          ?i   i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_77177448_7   5424 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAA 5473
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_77177448_7   5474 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5523
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_77177448_7   5524 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5573
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_77177448_7   5574 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5623
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_77177448_7   5624 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5673
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_77177448_7   5674 ATAAACAACCCCATCGAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 5723
                          i   i     v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_77177448_7   5724 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 5773
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_77177448_7   5774 CACTGGCCAT 5783
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (147 / 100)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


 858 28.61 9.40 4.35  chr1_77246987_77248687.rev      502  1214 (487)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr1_77246987_7    502 AAAAAAACCAGAATAAGCAAGACATTCCCCGAAG-GCAGAATAAGGT--G 548
                           iii v        iv   i   v  iivi  i- v    i  i  -- 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_77246987_7    549 AGGAAGAAATTTTACCACAAGATATCAAGATTTATTATAAAGTTATAGTA 598
                             vvv vvi  v   ----  v    i i   i  i    i  i    
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCA----ATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_77246987_7    599 ATTAAGACCATGATTTTTATTG-TAAAGAGATAGTCAATTTGATCAGAAT 647
                           i     vi  -- vv  i  -i v ii     v  vv v     --  
  L1M4_orf2#LINE/    256 ATCAAGACAGTG--TGGTACTGGCATAAGGATAGACATATAGATCA--AT 301

  chr1_77246987_7    648 TGAACAGATTACAGAGAG--CAGAAATAAATTCCCACATATATGAAAATT 695
                         v   i   -- iv     --          ii vi    v    ivv v 
  L1M4_orf2#LINE/    302 GGAATAGA--ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_77246987_7    696 TGATT------------GCAAA------TCACTAGGGAAA-AACAAATTC 726
                              ------------  v  ------   v i      -  i ivi i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_77246987_7    727 TTCAGTAAATTGTGCTGGCTGGGACAGTTGG-TATCTATATA-AAAACAA 774
                             ii    v       ----    ii   -  ? i i  i-    v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGG----GACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_77246987_7    775 --AAGT--GAGTTCTACCTCACATCATACA--------AGC---AAATAA 809
                         --    --  vii          i    i -------- i ---    ii
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_77246987_7    810 ATC-----CCTAACTGCCATGTGAAAGACAAAACCTTTGAAATTTCTAGA 854
                            -----     -----    i i  vi     - v i   i ii    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAA-----ATGTAAGAGCTAAAAC-TATAAAACTCTTAGA 539

  chr1_77246987_7    855 ATAAGATATAGGA--AAATAGTTAATGA--TTAAG---AACAGTGGAAGA 897
                          v  i i     ?--    v-  vi   --  ii ---ii  i   ----
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG---- 584

  chr1_77246987_7    898 GTTATTAAATAAGGAATAAGAAGCTGTAATGATGTAAGATAGAAAACATG 947
                         v  v   i   v iv iv i    vvv iii iiv    v i  v v  -
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT- 633

  chr1_77246987_7    948 AAATTG-ACATAAACAGTACAATGTAAAACTTTTGTTCCTTGAAACGCAC 996
                               -  v ---  vi v   vv           v i ii  ivi   
  L1M4_orf2#LINE/    634 AAATTGGACTT---CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_77246987_7    997 CACAGAGAAAAAGAAAAGACAAGCCACAAATTGGAAGGAGATGTTTATAA 1046
                         i ivi     iv          v     i v   i  i i  i   ii  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_77246987_7   1047 CACATAGAATCAACAAAAG--TAGTATCAAGAATATACTAAGAATTCTT- 1093
                         vv    v viii i  ii -- v     v        iv     i    -
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_77246987_7   1094 TAAATCAA------AAAGTAAAGTAACCCAGGAGAAGAGTGAACAAAGA- 1136
                         i  v    ------    vv  i       ivv?  i i  ii     i-
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_77246987_7   1137 --TGAATAGCCATTTTCACAGATGAAGTAACACTCATAGAGAATTAACAA 1184
                         --       v     iiv  i -    vv i  vv  i vv   v i  -
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCA- 878

  chr1_77246987_7   1185 TAGGAAAAAATGCTAAACTACATAAAAAAT 1214
                         i v     i     v   vv  ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (115 / 86)
Gap_init rate = 0.05 (35 / 749), avg. gap size = 2.80 (98 / 35)  


2995 23.32 2.24 5.54  chr1_77326424_77330990     3136  4074 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_77326424_7   3136 TGGAAAGACATCCCATGCTCATGGATTGCACGAAATAACATTGCTAAAAT 3185
                                 i        i          v v  vv   i    i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_77326424_7   3186 GTCCATACTACCAGAAGAAGTATATTTATTGATCTATACATATGCAAT-- 3233
                          v v     v  vi  ------------        --  v  v   i--
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA------------TTGATCTA--CAGATTCAACGC 86

  chr1_77326424_7   3234 AATCTCTATCAAAATTCCAATGGCACTTTTCATATAAATAGAAAAATCAA 3283
                             i          i   iiv  vi    iii v    v  v  iiii 
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr1_77326424_7   3284 CCCTAAAATTTCTATGGAACCACAAAAGACCCAGAATAGCTAAAGCAACC 3333
                         i         iv       vii   ii             i   i   i 
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_77326424_7   3334 CTGAGCAAGAAGAACAAAGCTGGACGCATCATACTATTTGATTTCAAATT 3383
                         i   iv             i    v vv   i   viiii        vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_77326424_7   3384 ATACTACATAGCTACAGTAATCAAAACAGCATGGTATAGGGATAAAAACA 3433
                         v       v               i    ii     iv  v    ii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_77326424_7   3434 GACACACAGACCAATGGAACA-AATAGAAAACTCAGAAATAAATCCAAGC 3482
                             i i   i        i -   v  i iii          i   vi 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_77326424_7   3483 ACTTACAGCCAACTCATTTCCAACAAAGGTGCCAAGAATATACA-TTGGG 3531
                          i   ii i   i v    i i    i          vi  v  - v   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_77326424_7   3532 AAAGGACACTCTGTTTAATAA-TCGTGCTGGGAAAACTGGATATCCATAT 3580
                             i i v   v  i  i  - v         v         ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_77326424_7   3581 GCAGAAGAATGAAACTAGATCCCCAACTTTCACCATATCCCAAAATCAAA 3630
                            i         ii i  i   i v  iv        v v     i  v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_77326424_7   3631 TCAAAATGGATTAAAGACTTAAATCTAAGACCTGAAACTGTGACACTACT 3680
                                    i ?    i     v     v  i     i i v   vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_77326424_7   3681 AAAAGGAAACACTGGGG-AAATGTTCCAGGACATTATTCTGGGCAGAAAT 3729
                          i   i     iv  ? -    v   -iv   v  ivvi i    ivii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGT 585

  chr1_77326424_7   3730 TTTTTAGGTAAAACCTCAAAAATCATAGGCAACAAAAGCAAAAACAGAAA 3779
                           i    i  vi  vi     i-  i i          v     i   v 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_77326424_7   3780 AATGAAATTACATCAAGCTAAAAAGATTCTGCATAGCAAAGGAAACAATG 3829
                            vii i v      iv v    iv  i  iiivv       v  v  -
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT- 683

  chr1_77326424_7   3830 TTTAAG---GTGAAGAGACAACGTACAGAATGAGAGAAAATATTTGCAAT 3876
                         --i   ---     i       vi        i                v
  L1M4_orf2#LINE/    684 --CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_77326424_7   3877 TCATCCACCTGACAAGCAATTAATAACCAGAAAATATAAGGAATTTGAAA 3926
                             vi i    i   vi i vi  v      v      i   i ivv -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA- 780

  chr1_77326424_7   3927 CAACTCAATGGCAAAAAACAAAACAAAACAAAACAAAAAAACAAAAAAAC 3976
                                  ------------------------------  i     i  
  L1M4_orf2#LINE/    781 CAACTCAAT------------------------------AATAAAAAGAC 800

  chr1_77326424_7   3977 AAAAAAAATCTAATTATAAAATGGGCAAATCATCTGAATAGACATTTCAC 4026
                            v  --i i    ?v            vv  i              v 
  L1M4_orf2#LINE/    801 AAATAA--CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_77326424_7   4027 AGAAGAAGA------------CAACAGGTATATGAAAAAATGCTCAAAAT 4064
                         vi       ------------   i i i i       i        v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_77326424_7   4065 CACTAATCAT 4074
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.62 (133 / 82)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.87 (73 / 15)  


3125 24.92 2.11 1.11  chr1_77426845_77431133     2904  3802 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_77426845_7   2904 TGGAATGATATCCCATGTTCATGGATTGGAATAATCAATATTGCTAAAAT 2953
                              v                         v v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_77426845_7   2954 GTCCATACTACCCAAAACAATCTACAAAGTCAATGCAATCCCTATCAAAA 3003
                          v v     v      vii       i v    i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_77426845_7   3004 CACCAATGATATTATTCACAGAAGAAGAAAAAAACAATTTTAAAATTTGT 3053
                         iv   iiviiv  v  ii     - vvi v  ivii  ii       ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_77426845_7   3054 TTGGAACCACTAAAGACCCCAAATAACCAAAGCAAACCTGAGAAA-AAGA 3102
                         v     vii v ii     vi    i     i   v i   i   -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_77426845_7   3103 ACAAAGCTGGAGGTATTACACT----GATTTCAGAATATACTGCAAGGCT 3148
                               i      vv i     ----i      i  iv    i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_77426845_7   3149 ATAGTAATAAAAACAGCGT---ACTGGCATAAAAACAGACACTTAGGCCC 3195
                          i      v  i    i  ---          ii i     iv   ii -
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC- 298

  chr1_77426845_7   3196 AATGGAACAGAATAGAGAACACAGAAATAAATCCACATGTTTATAACCAA 3245
                                i     v    iiv          i   i ii     iii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_77426845_7   3246 ATCATTTTTGACAAAGGTGCCAAGAACATACTTTGGGGAAAGAACAATCT 3295
                         v v     i     i          v   v vv           i i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_77426845_7   3296 CTTCAATACATGG------GAAAGCTAGATATCCATATGCAGAAAAATAA 3339
                         i     i v    ------  v i  i    ?   i     i  i   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_77426845_7   3340 AATTAGATTTCTATCCTTCACAATATTCCAATACCAAATATAAAGGGATA 3389
                          i  i  iii   i iiv   v    v v  v ii  v vv   v    v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_77426845_7   3390 AAAGATTTAAAAATAAGACCTGAAACTATGAAATTACTAAAAGAAAACAG 3439
                          ?   ii    vi     v  i       i   i vi  i         v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_77426845_7   3440 CGAGG--AATCACTTCAGGACATTGGTGTGGGCAAAGATGTATGGGGTAA 3487
                         v i? --    --   iv   v    vv i     v i v v vi i  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_77426845_7   3488 GACCTCAAAAGCACACACAATAAAACCTGGATA--TAGACAAGTTGGATT 3535
                            vi          vi   i    --- i v --    i  i     i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAA---GAAAAAATAGATAAATTGGACT 643

  chr1_77426845_7   3536 ACATCAAG-CTAAAAATGTTTTACATAGCAAAGAAAACAATCTATAAAGT 3584
                         v      i-i      i-    iiiivv     i v  v   v v     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_77426845_7   3585 TAAGAGACAACCTACAGAATGGAAGAAAATATTTGCAAAGCATCTATCTG 3634
                         v  i        i         i                v   v      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_77426845_7   3635 AAAAGTGATTACTAAACAGAATATATAAGGAACTCAAACAACTCAATAAG 3684
                          v   v  i vv  vv            i      vv            v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_77426845_7   3685 AAAAAAACAAATAATTCAATTTTTAAAATGGGCAAATGATCTAAATAGAC 3734
                              i        ii     ?v-            v   i i       
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_77426845_7   3735 ATTTCGCCAAAGCAGACATACAAATGGCAAAGAGGAATATAAGACAAGTG 3784
                              v      v   i           v  v i v i  i i - ii  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATG 890

  chr1_77426845_7   3785 TTCAGTACTGCTCATCAT 3802
                         i   ii iii????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (131 / 89)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.07 (29 / 14)  


 240 32.30 13.66 0.00  chr1_77486941_77489208.rev      660   820 (1448)    L1M4_orf2#LINE/L1       15   197 (711)  

  chr1_77486941_7    660 ATGTTCATGGATGGGAATATGTGA----GTT------------CTCTTAA 693
                                     v    v iv i ----   ------------   iiv 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_77486941_7    694 AATTAATCTATATACATAATATAATCTATATTGAAATTCAAATCAAAATC 743
                             i     i v ivi  iii    iv   ii    i v iiiivvv i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr1_77486941_7    744 TCAGCAGAATCTGACAAACTGATACTAAAATTTATAAAGAAG---AATAA 790
                          iv      vi      i     v        i   vi   i---  vii
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_77486941_7    791 AT---GTATAGGCATACCTAACTTAAAAAAGAA 820
                          i--- v    v  v v v v   i        
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

Transitions / transversions = 1.36 (30 / 22)
Gap_init rate = 0.02 (4 / 183), avg. gap size = 5.50 (22 / 4)  

 462 26.27 13.31 5.78  chr1_77486941_77489208.rev     1199  1769 (499)    L1M4_orf2#LINE/L1      268   881 (27)  

  chr1_77486941_7   1199 TGATATTGGT----GCAGAAATATATAAA-CAGAAGAA-AGAACTGAATA 1242
                           i  i   i---- v v i i     i -  ivi   -    i   i- 
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG-A 316

  chr1_77486941_7   1243 G---AGAAA-----CCATA----TACAGACCAGTG--TCTATACAGGAAT 1278
                          ---     -----     ----  ii v v v  -- i vv   i ii 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_77486941_7   1279 ---AAGTCATTTCAATGAAGGAAAAGATGCGCAAGTCAACAAACGTTCTT 1325
                         ---   v vv       i-     ii  ivv vvv        i v vi 
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_77486941_7   1326 TGGACCACTGAATACATTTTTCATTTCCATTCAAAACATGCAATAAAGTT 1375
                         v    v    i   -----?i  ----   v     --- -   i     
  L1M4_orf2#LINE/    416 GGGACAACTGGATA-----KCCA----CATGCAAAA---G-AATGAAGTT 452

  chr1_77486941_7   1376 ATATTGCTACCTCACACTATACAAAAGAATTAGTGCACA-TAGAATAAAT 1424
                         iv iiv           i   i v  i     iiv  v - i  vi ? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_77486941_7   1425 ACCTGGACCTTTAAAA--CAAAACTAAAAATAACT------AGAAAACTA 1466
                             ii -- v   i --i       v   --   ------       - 
  L1M4_orf2#LINE/    503 ACCTAAA--TGTAAGAGCTAAAACTATAAA--ACTCTTAGAAGAAAAC-A 547

  chr1_77486941_7   1467 TAGAAG---ATTTTTATGA-----GATTATGGGGAACACTTTCTTAAGAT 1508
                            i? ---  i  ii   ----- i   --  v  iiv       -   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTA--GGCAATGGTTTCTTA-GAT 594

  chr1_77486941_7   1509 ------CCAAATGCAAAAGC--CAAAGGGAAAA-TA-ATGAA---AAATA 1545
                         ------     v   v    --    i i    -  -  i  ---i v v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_77486941_7   1546 CACCAATTCCAATTTAAAATTTCTGCAGGACAAA--ACA-TATCTCGAAC 1592
                           i   ----    v    i  i  iivvv    --   -    vv   v
  L1M4_orf2#LINE/    645 CATCAA----AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_77486941_7   1593 ATGACTGAGAAAAAATATA-AATGAAAGAAAATATT-----ATAAGATAT 1636
                         i   v-i   v  vvi i -    ii          -----  v v    
  L1M4_orf2#LINE/    691 GTGAA-AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_77486941_7   1637 GTAGCAAAGGATTAGTATCTAGAACATCCAAA-------------TCGAT 1673
                         v iii  i   i v     i    i  vi   -------------  i  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_77486941_7   1674 TTTAAAAACTCAAACAATCTAACAAGAAAAGAGTGGGGGCAGGGTTATGT 1723
                         vv      vv    i  i i  iv?i    ---    viv   i  -  v
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAA---TGGGCAAAGGATT-TGA 835

  chr1_77486941_7   1724 TTTAGAAATT-CTCAAAAAATGAAATACAAGTGGCCAAAAAACACAT 1769
                         v -   v   -   v   i v  v      i       v  i     
  L1M4_orf2#LINE/    836 AT-AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 1.21 (80 / 66)
Gap_init rate = 0.07 (40 / 614), avg. gap size = 2.73 (109 / 40)  


2659 23.56 1.09 0.31  chr1_77622586_77624901.rev      635  1275 (1040)    L1M4_orf2#LINE/L1       16   661 (247)  

  chr1_77622586_7    635 TGCTCATGGATCAGAGTAATTAATATTGTGAAAATGGCCATACAACCTAA 684
                           i        ii  iv v          v  i     v    vv  i  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_77622586_7    685 AGCAATATATATATTCAATACAATCCCTATAAAAATCCCAAAGATATTTT 734
                          vii  v  i v      ii          v         ivviiv    
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_77622586_7    735 TCTCAGAAATAGAAAAAGCAATTCTAAAATTTGTATTTATCCACAAAAGA 784
                          iv       v  v  ivii  i        ii   vv vvii   ii  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_77622586_7    785 TCCTGAATACCCAAAGCAATTCTGAGA-GGAAAAACAAAGTTGGTGGCAT 833
                         i  v     v     i    ii   i -i   i           v  vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_77622586_7    834 CACACTTCCTGATTTGAAATTATATTACAAAGCTATAGTAATCAAAACAG 883
                                  ii    v   viv  i          i         i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_77622586_7    884 TAGGATACTGGCATAAAAACAGAAATATAGACCAGTGGAACAGAAT--AG 931
                          iv i           ii i   v       i  i     i     --  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_77622586_7    932 AGTCCAGAAATAATTGCAAACATATATGGTCAACCAATTTTCAGCAAGGG 981
                                      viv  v    v         iii      ii      
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_77622586_7    982 CACCAAAAAGACACAATGGGGAAAGGATAGTCTCTGCAATAAATGGTGCT 1031
                         ii    i vv iv            i       i v   i          
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_77622586_7   1032 AGGGAAGCTAGATTTCCACTTGCAAAAGAGTGAAATTGGACTCTTATTTT 1081
                         i  iv i  i   v?    v         i    i      i i  ii i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_77622586_7   1082 ATACCAGATACAAAACTCAACTCAAAATGGATAAGAGACCCAAAAGTAAG 1131
                          i    v        v i              v ?     i   v     
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_77622586_7   1132 A-CTGAAATAATAAAACTCCTAAAAGAAAACACAGGAGAAAAGATCTT-- 1178
                          -  i   iv         i  i         i   ? v   --    --
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA--TCTTCG 563

  chr1_77622586_7   1179 -GACATTGGCCTTGGCAATGATTTATTGTGTATTACACCAAAAGCTCAGG 1227
                         -   v    vi v       i   v  ivi   v           v  i 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_77622586_7   1228 CTACAAAAGCAAAAATAAATACATGGAACTACATCAAACTAAAAAGCT 1275
                          v       v       i   v  v i   v       v v    i  
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

Transitions / transversions = 1.39 (86 / 62)
Gap_init rate = 0.01 (5 / 646), avg. gap size = 1.80 (9 / 5)  

 943 21.85 2.94 0.84  chr1_77622586_77624901.rev     1588  1825 (490)    L1M4_orf2#LINE/L1      666   908 (0)  

  chr1_77622586_7   1588 TGTCTCAAAAAA----ATAAAGTA--TGAAAGGTTAACCTACAGATTAGG 1631
                           ii     ii ----  v   v --     i vi    i     v i  
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_77622586_7   1632 AAAAAGTATTTGCAAACCATATGTCAGATAAGTGGTTAATATTCAAGATT 1681
                          i   i          i     i  v      v ii vi   i  ii  v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_77622586_7   1682 TGTAAAGAACTCATACA-CTCTGGTAGCAGGAAAATATATAAGCTGATTA 1730
                          i          v    -   -ii  ii ii  i i v    v ii   ?
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTC-AATAATAAAAAGACAAATAACCCAATTW 814

  chr1_77622586_7   1731 CAAAATGGGCAAAGGACTTGGATAGACATTTCTCCAAAGATGATATTAAA 1780
                         v               i   i                   v     - v 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT-ACA 863

  chr1_77622586_7   1781 AATGGCCAACAGGTACATGAAAAGGTACTCAACATCCCTAATAAT 1825
                                  i i i          i i         v????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (36 / 15)
Gap_init rate = 0.02 (5 / 243), avg. gap size = 1.80 (9 / 5)  


2936 23.22 6.99 1.78  chr1_77786230_77790407     2842  3685 (493)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr1_77786230_7   2842 ATACATGGGAAGAATTAATACTATTAAAATGTCCATACTACTCGAAGCAA 2891
                           iv  v      v      i i    i   v v     v i i  vii 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr1_77786230_7   2892 CCTACAGATTTAATGCAATCCCTATCAAAATTCCAA-TGTCATTTTTCAT 2940
                         i         i  i                 i   i-  i -     iii
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGC 119

  chr1_77786230_7   2941 AGATATAGAAAAAACAATCCTAAAATTTGTATGGAACCACAAAAGACTCC 2990
                            v  v  v  ivii           ii       vii   ii   i v
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_77786230_7   2991 AAATAGCCAAAGCAATCTTGAGCAAAAAACAAAAACAAAACCCAAAGCCG 3040
                         i          i         ----    v  i      ------- ii 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGA----AAAAGAAGAACAAA-------GTTG 208

  chr1_77786230_7   3041 GAAGCATCACACTCAATGATTTCAAAATATACTACACAAAGCTATTACAA 3090
                           i vv       ivvii         iv       --      ivii  
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACA--AAGCTACAGTAA 256

  chr1_77786230_7   3091 TCAAAATAGGATGGTACTGACATAAAAA-------ACAGA-AAATGAAGT 3132
                             i i  vi        i     ii ------- i   -v    i i 
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_77786230_7   3133 AAAAC----AGTGCAGAAATAAACCCACGTGTTTGCAGTCAATTGGTCTT 3178
                          i  i----   v              iiii   iii        i i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_77786230_7   3179 TGACAAAGGTGGCGAAAACACACAAT----AAGGGACAGTCAGTTCAATA 3224
                         i     i    v i i v  iv    ----  i i i    vv     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_77786230_7   3225 AACGATGCTGGGGAAACTGGATATCCACAAGCATAAGGACAAAATTAGAC 3274
                           i i       iv         ?     v   v   i ii  i  i   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_77786230_7   3275 CTTTATCCCATACCATATACAAAAATCAAATGAAAACGAGTGAAAGACCT 3324
                          ii  i i  i               i  v v    i ii v ?      
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_77786230_7   3325 AAATATAAGACCCAAAACCATAAA----CTAGAAGAGAACATAGGAGGAA 3370
                             i     v i     i     ----i       i        ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_77786230_7   3371 AGTTCCTCAACATTGGTGTT-GGCAATGATTTTTTGGGTAATACACAAAA 3419
                          vi i vii  v    -   -       i   i  i i  vv    v   
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_77786230_7   3420 AGCTTA-GCTACAAAGGTAAAAATAAATGA----GACTAGCTCAAACTAA 3464
                            vi -  v     i v       i  i ----    vvv     v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_77786230_7   3465 AAAGCTTCAGCGTGGCAAAGGAAACAAACAACAAAATAAAAAGGCAACCT 3514
                            i   iv i ivv       v  v v   v   i i     i     i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_77786230_7   3515 ACAAAGAAGGA-AAAATGTTTGCAAATCAAATATCTGATAAGGGATTAGT 3563
                            i ivi   -     i           v               i v  
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_77786230_7   3564 ATCTAAAAT-------------TTA---------------AAGACAAATA 3585
                            i i   -------------   ---------------          
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_77786230_7   3586 ATCCAATTTAAAAATGAGCAAAGGAGTTGAACAGATATTTCTCCAAAGA- 3634
                          i      ?       i        v     i   i             -
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_77786230_7   3635 --CATAAAAATGGTCAATGGGTATATGAAAAGGTACTCAACATCACTAAT 3682
                         --i   v      i    ii i i        i i          ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_77786230_7   3683 CAT 3685
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.10 (130 / 62)
Gap_init rate = 0.02 (18 / 888), avg. gap size = 4.11 (74 / 18)  


2666 18.62 14.45 0.00  chr1_77964513_77967394.rev      636  1258 (1624)    L1M4_orf2#LINE/L1        3   715 (193)  

  chr1_77964513_7    636 GAAACACATCCCATGTTCATAGATTAGAAGACTTAACATTGTTAAGATGT 685
                             v i             i    i          i            v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_77964513_7    686 CAATACTACCCAAAGCAATCTACAGATTCAATGCAGTCTCTATCAAAATC 735
                                v      vii              i   i  i           
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_77964513_7    736 CCAA-TGATTTTTTGGCAGAAATAGAAAAACCCATCCTAAATGTCATACG 784
                            i-  vi     v        v  v  i iv        vv     i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_77964513_7    785 GAATCTCAAGGGACTTAGAATAGCCAAAATAAACTTGAAAAAGAAGAACA 834
                            viv        ii             i  v                 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_77964513_7    835 AAGCTGGAGGACTCACATTTCCTAATTTCAAAACTCACTATAAAGCGACA 884
                            i             i    i            i    i     v   
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_77964513_7    885 GTAATCAAAACAGTAAGGTACTGGCAT------------------CAAGG 916
                                 i     iv           ------------------   v 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_77964513_7    917 GCA--------------CAGAAATAAAACCTCACATATATCATCAAATGA 952
                          v --------------          v  vi    v   vi    v   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_77964513_7    953 TTTTCCACAGGGGTGC-AAGACCATTCAGTCGGAAATGGAGAGTTTTTTC 1001
                              v   i      -           i v  i  v i v   i     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_77964513_7   1002 AACAAATGGTATAGGGAAAACTGGA------------------------- 1026
                                   iiv    v       -------------------------
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_77964513_7   1027 ---CCCTTACCTAATAATACATACAAAAATTAACTCAAAATGGATCAAAG 1073
                         ---   i     v i vi i                           ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_77964513_7   1074 ACCTAAATATAAGTCCTAAAACCCTAA--------GAAG----------- 1104
                                 i    vv       iv   --------    -----------
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_77964513_7   1105 ------CTTCACAACATCGGATTTGGCAATGACTTCTTAAATATGACAAT 1148
                         ------    iii  v i  i  v       ii      i        vi
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_77964513_7   1149 GAAGACACAGGCAACAAAA-AAAAGATA--CAAACAAGACTTGATGAAAA 1195
                         i  ii    i         -    i   --i   ivi     v  v    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_77964513_7   1196 TTTTAAAATTTTGTGCATCAAAAGACACCATCAACAGAATAAAAAAGTAA 1245
                           vv   v        v     i     i     v i i i    iii  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_77964513_7   1246 TTCACAGGGTTGG 1258
                         ii     ii v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGG 715

Transitions / transversions = 1.50 (69 / 46)
Gap_init rate = 0.01 (9 / 713), avg. gap size = 10.00 (90 / 9)  

 402 19.08 10.69 0.00  chr1_77964513_77967394.rev     1870  2000 (882)    L1M4_orf2#LINE/L1      685   829 (79)  

  chr1_77964513_7   1870 AAGAAAA-GAAAAG-TAATTCACAGAATTGGAGAAA-TATATGGAAATCA 1916
                               i-      -i  ii        v       -   v  v      
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_77964513_7   1917 TATAACTAACAAGGAATTAATATCCAGACTATACAGAGAACT---AAAAC 1963
                             v  i i    i i vi        v    i i      --- v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_77964513_7   1964 TCCACGAGAACAAAACAA-T-------TTCAAAAATGGGCAAAGG 2000
                           v ii v  v  i    - -------  ?               
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.40 (14 / 10)
Gap_init rate = 0.04 (6 / 145), avg. gap size = 2.33 (14 / 6)  

 522 12.77 0.00 0.00  chr1_77964513_77967394.rev     2298  2391 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_77964513_7   2298 AAAAAAGGGCAAAGGACTAAAATATACATTTCTTCAAAGGATACATATAA 2347
                              v          i vi    v        i     i v i   i  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_77964513_7   2348 ATGGTCAATAAGCACATGAGAAGATGCTCAACATCATCAGGGAA 2391
                             i              i                ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3087 27.43 1.00 0.55  chr1_78073984_78077125     1746  2649 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78073984_7   1746 TGGAAGAACATTCCATGCTCATGCATAGGAAGAATCAATATCATGAAAAT 1795
                              ii i  i     i     v  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78073984_7   1796 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1845
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78073984_7   1846 TACCAATGACTTTCTTCACGGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1893
                          v   iivi i  i  ii i   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_78073984_7   1894 TATGGAACCAAAAAAGAACCCGCATCACCAAGCCAATCCTAAGCCAAAAG 1943
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_78073984_7   1944 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1993
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_78073984_7   1994 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGATC 2043
                                 i   i    iii        i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_78073984_7   2044 AATGGAACAGGAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 2091
                                i  i i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_78073984_7   2092 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2141
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_78073984_7   2142 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2191
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_78073984_7   2192 GAAACTGGATCCCTTCCTTATACCTTGTAGAAAAATTAATTCAAGATGGA 2241
                            ii    i    v   i i   v i  v         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_78073984_7   2242 TTAAATACTTAAATGTTAGACCTAAAAGCATAAAAACCCTAGAAGAAAAC 2291
                          i ? v  i       v   v      vi      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_78073984_7   2292 CTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTA 2340
                         v    ?i- v i -   iv   viv  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_78073984_7   2341 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTA 2390
                         vi            vvi          vv     v  i    v i ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_78073984_7   2391 ATTAAACTAAAGAGCTTCTGCACAGAAAAAGAAACTACCATCAGAGTGAA 2440
                           i   v v  i i   i  ii vvv   i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_78073984_7   2441 TAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 2490
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_78073984_7   2491 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 2540
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_78073984_7   2541 AAAACAA----CCCCATCAAAAAGTGGGCAAAGGTTATGAACAGACACTT 2586
                           i    ----   v  i?    i          v v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_78073984_7   2587 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 2636
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_78073984_7   2637 CATCACTGGCCAT 2649
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3571 23.51 0.97 0.12  chr1_78086928_78091708     3091  3911 (870)    L1M4_orf2#LINE/L1        2   829 (79)  

  chr1_78086928_7   3091 GGGGGGACATACTGTGTTCATGGATCAGAAGACTTAACATTATTAAGATA 3140
                           iii  i  v ii           ii          i   i       i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_78086928_7   3141 TTAATTCTCCCTAGATCCATCTACAGATTCAATGCAATCCCAATCAAAAT 3190
                         vi   v     i i  iv              i        v        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_78086928_7   3191 CCCAGCATATTATTTTGTGGATATTGACAAACTGATTCTAAAGTTTATAT 3240
                               vvvi v     ii  v        i     i     i  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_78086928_7   3241 GAAAAGGGAAAAGACTTGGAATAGCCAACACAGTGTTGAAGGAGAAGAAC 3290
                          i   v v  ii   iii          v   i v     ii        
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_78086928_7   3291 AAAGCTGGAGGACTAACACTACTCAACTTTAAGACATACTATAAACCTAC 3340
                             i         v     v i   i  i  i  v     i   v    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_78086928_7   3341 AGTAATTGATACAGTGCAGTGTTGGTGAAATAATAAACAAAAAGATCAAT 3390
                               ii v      ii  ii   iiv  vi   i   v v        
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_78086928_7   3391 GAAACCGAATAGAGAGCCCAGAAATAGATCCACGTAAATATAATCAACTG 3440
                          i  iv    v     i         i i   iii vv   ii    i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_78086928_7   3441 ATCTTTGACAAAGGAGCAAAGGCAATAAAATAGAGAAAAGAT--TATTTT 3488
                           i  i     i  v  v   i v  vv   i i    ii  -- v    
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_78086928_7   3489 CAACAAATGGTGCTGGAACAACTGGACATCCACTTGCAAAAAACTGAATC 3538
                                         i         i ?    v       i v    vi
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_78086928_7   3539 TAGAAATAGACCTTACATTCTTCACAAAAATTAACTCAAAATGAATCACA 3588
                          i  vvivv    i   iiv vi                    i    ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_78086928_7   3589 GACTTACA-GCA-----TAGAACTATAAAACTCCTAGAAGAAAACATAGA 3632
                            i  v - i -----  i             i               i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_78086928_7   3633 CAGAAATCTAGATGACCTCAGATTTGGAGTTCACTTTTTAGCTATGATAC 3682
                         ?iv      vvi      ii i  v  viv vii  i    v     i  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_78086928_7   3683 CAAAGTCACAATTCATGAAAGAAAGAATTGATAAGCTGGACTTCATTAAA 3732
                             iv     viv ii       i   v     ii          i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_78086928_7   3733 ATTAAAAAATTCTGTTCTGCAAAAGACACTGTGAAAAGAATTAAAAAATA 3782
                                 v  i   v  v    i      i v  i i i v    i i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_78086928_7   3783 AGCCATAGACTTGGAGAAAATATTTGCAAGTGACATATCAGATAAAGGAC 3832
                          v   i   v v                 i v i     v     i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_78086928_7   3833 TGTTATCCAAAATACACAAAGAACTCTTACAACTCTGTAATAAGAATACA 3882
                          vv      i    i i                  vi      i  v   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_78086928_7   3883 AACAACCCAATTAAAAAATGGACCAAAGG 3911
                           i         ?        i -     
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGC-AAAGG 829

Transitions / transversions = 1.74 (120 / 69)
Gap_init rate = 0.00 (4 / 828), avg. gap size = 2.25 (9 / 4)  

 288 17.71 3.12 5.21  chr1_78086928_78091708     4201  4296 (485)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_78086928_7   4201 AAAAATGGACCAAACAAAGATCTTAGGAGACATCTCACTGAAGAAGATA- 4249
                                 i -   ---i   i v iv      i  v ii         -
  L1M4_orf2#LINE/    815 AAAAATGGGC-AAA---GGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_78086928_7   4250 -CAGATGGCAAATAAACATATGAAAAGGTGCTTTAATAT-ATTATTTAA 4296
                         -  i     v     i  i        i    i-  i  - ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTC-AACATCAZZZZZZZZ 908

Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.05 (5 / 94), avg. gap size = 1.60 (8 / 5)  


2951 24.24 3.06 3.93  chr1_78264275_78266203      535  1450 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78264275_7    535 TGGAAAAATATCCCATGCTTGTGGATAGGAAGGGTCAATATCATTAAAAT 584
                               i          i ii     v     iv i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78264275_7    585 GGCTATACTACCTAAATCAATTTGCAGATTCAATGCTATTCCTATCAAAT 634
                            v     v  i    ii  i i         i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78264275_7    635 TACCAATGACATTCTTCACAGAACTATAAAAAATT-ATTTTAAAATTCAT 683
                          v   iivi v  i  ii     v - i v  ii -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_78264275_7    684 ATGGAACAACAGTGACAAAAAAGCCTGAATAGCCAAGATAATCCTAAGCA 733
                               -----i  -   iii v  v          i i    i i iv 
  L1M4_orf2#LINE/    150 ATGGAA-----ATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_78264275_7    734 AAAAGAACAAAGCTGGAGGCATCATATTACCCGACTTCAAACTGTACTAC 783
                          i          i      vv   i i v   i i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_78264275_7    784 AGGGCTACAGTAACCAA-ACAGCATGGTACTTGTACAAAAACAGGCACAT 832
                          ii          i   -    ii       v i i  ii i  i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_78264275_7    833 AGACCAATGGAACAGAATAGAGAGCCCAGAAATAAGGCTGCACAGCTACA 882
                            i        i     v     i          iv iii   vi  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_78264275_7    883 ACCACCTGATATTTAACAAAGCTGACAAAAATAAGCAATGGGGAA-GACT 931
                         ii  vi    v  ii    i v  v   i vi vv          -  v 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_78264275_7    932 C-CCTATTTAATAAATGATGCTGGGATAGCCATATGCAGCTAAGAAATGA 980
                         v-i  v  i  i     i        i i --------------------
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAAC-------------------- 423

  chr1_78264275_7    981 TGCTGGCTAGCCATATGCAGAAGACTGAAGCTGGACCCCT-CCTTACACC 1029
                         ---   v  ?   i     i    v     i         -   i     
  L1M4_orf2#LINE/    424 ---TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_78264275_7   1030 ATATACAATAATTAA-----GATGAATTAAAGACTTAAATGTAAAATTCA 1074
                                 v      -----i   i  i ?    i         i vii 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_78264275_7   1075 AAACTATAAAAACTCT-GGAAGACAATGTAGGCA-ATATCATTCTGAACA 1122
                                    -    -i     v  ii    ?i- v   -   vvi  v
  L1M4_orf2#LINE/    521 AAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACC 568

  chr1_78264275_7   1123 TTGGAATGGGCAAAGATTTCATGACAAAGACACCAAA-GCAATCAG-AAT 1170
                             iv i     v i    v iivv v         -   -iv  -  i
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA-CAAGCAAC 617

  chr1_78264275_7   1171 AGAAGCAAATATTGACAAGTGGGATCTAATTAAACTTAGGAGCTTCTGCA 1220
                          i   v   v  v  i  i v   ii v  i   v   ii i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_78264275_7   1221 CAGCAAGAGAAACTATCAACAGAGTAAACAGACAACCTACAGAATAGGAG 1270
                          vv   ii  v        v i   i  v        i       i    
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_78264275_7   1271 AAAAATATTTGCAAACTATGTATCTGATAAAGGTCTAATATCCAGCATCT 1320
                             -          ii  i          i  v  vi       v  v 
  L1M4_orf2#LINE/    718 AAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_78264275_7   1321 TTAAGGAAAG-TTAC----CAGAAA-AAAAAGACAA----CTCCATTAAA 1360
                         v   i   vv-    ----  iv  -          ---- i v   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_78264275_7   1361 AAGTGGACAAAGGACATGAA----CACTTTTCAAAAGCAGACACACATGT 1406
                           i   i       iv    ----  i  i  v    v   i i   vi 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_78264275_7   1407 GGCCAACAATAATATTAAAAAAAAAGCTGAACCTCACTGATCAT 1450
                               i  vv i  --i    i v   v   v   ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACAT--GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (140 / 78)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.67 (64 / 24)  


1689 22.06 3.26 15.16  chr1_78363918_78370812.rev      666  1463 (5432)    L1M4_orf2#LINE/L1        1   703 (205)  

  chr1_78363918_7    666 TGGAAAAACATTCCACACTCATGGATAGGAAGAATGAATATCGTGGAAAT 715
                               i i  i   iii        v      v v     i  vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78363918_7    716 GGCCAAACAGCCCAAAGTAACTTATAGATTCAATGCTATTCCCATCAAAC 765
                            v v  vv      v i ii  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78363918_7    766 TATCA-CTGACATTCTTTACAGAATTAGAAGAAACT-ATTTTAAAATTCA 813
                          vi  -   v -  i   i     v v  v-  i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCA 148

  chr1_78363918_7    814 TGTGGAACTGAATAAGAGTTTGCATAGCCAAGACAATCCTAAGCAAAAAG 863
                          i     v  v vii  viiv v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_78363918_7    864 AACAAAGCTGGAGGCATCACGCTACCCAACTTCAAACTATCCTTCAAGGC 913
                                i      vv    i  v     i      viv v  v   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_78363918_7    914 TACTGTAACCAAAATAGCATGGTACTGGTACTAAAACAGACACATAAACC 963
                            v    i   i i  ii         i iv ii i     i   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_78363918_7    964 AATGGAACAGAATAGAGAACCCAGAAATAAGACCACACACCTACAACCAT 1013
                                i     v    ii          iv   i   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_78363918_7   1014 TTGATCCTTGACAAAGGTTATTTCACACCGTGTTTATCCATTCACCTGTG 1063
                              ii i     i   --------------------------------
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGT-------------------------------- 366

  chr1_78363918_7   1064 GATGAACATTTGAGTTATTTCAGATTTTGGCCATTAACAAATAAAGGTAC 1113
                         -----------------------------    -----------  ----
  L1M4_orf2#LINE/    367 -----------------------------GCCA-----------AG---- 372

  chr1_78363918_7   1114 TATAAATGCTTGTGTACAACTATTTATGTATCAGGATAAAAACAAGCAGT 1163
                         ------------------  i   ----------------------  i 
  L1M4_orf2#LINE/    373 ------------------ACCATT----------------------CAAT 382

  chr1_78363918_7   1164 GGGGAAAGGAT--TCTTTATTCTCCCAATG---CTGGGAGAACTGGCTAG 1208
                                 i  --     --  vv v    ---      v      v  ?
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_78363918_7   1209 TCATATGCAGAAAATTTAA-CTGGACGCCTTCCTTAAACCATATACAGAA 1257
                         i  i     i  i v v  -i     v   v   i v          i  
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_78363918_7   1258 ATCAATTCAAAATGGATTGAAGACTTAAATGTAAAACCCAAAACTAGAAA 1307
                           i  i           ii?    i         i v i       v   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_78363918_7   1308 AACCCTAGAAGAAAACCTAGGC---AACCATTCAGGACATAGGCACAGGC 1354
                          vi i           v    ?---  i -   iv   v v  vvi    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGC 579

  chr1_78363918_7   1355 AAAGATTTCATA---ATGA------------AGACAACAAGAGCCAAAAT 1389
                           v i    v  ---    ------------ ii      i  vv     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_78363918_7   1390 TGACAAATAGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAATAAA 1439
                         v  i    v   ii v  i   v v  i i   i  ii vv    iv v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_78363918_7   1440 CTATCATCAGAGTAAACAGACAAC 1463
                               vv i   i  v       
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAAC 703

Transitions / transversions = 1.47 (103 / 70)
Gap_init rate = 0.02 (16 / 703), avg. gap size = 9.19 (147 / 16)  

 827 21.56 2.75 0.00  chr1_78363918_78370812.rev     1757  1974 (4921)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_78363918_7   1757 AAAAGAGTAAAGAGACAACCTACAGAATGGGAGAACATTTTTGCAATCTA 1806
                           i i   i  i        i              v  v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_78363918_7   1807 TCCATCTGACAAAGGTCTAATATCCAGCAACTACAAGGAACTTAAACAAA 1856
                          vi      i  i  v  vi       v vv  i  i     ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_78363918_7   1857 TTTACAAGAAAAAAACAA----CCCCATTAAAAAGTGGGCAAAGGACATG 1902
                          iv i  v     i    ----   v   ?    i           iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_78363918_7   1903 AACAGACACTTCTCAGAAGAAGACATACATGTGCCCAACAA--ACATGAA 1950
                           i     i     vi       i     vi  v    i  --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_78363918_7   1951 AAAAAGCTCAACATCACTGATCAG 1974
                           i v           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (26 / 20)
Gap_init rate = 0.01 (2 / 224), avg. gap size = 3.00 (6 / 2)  

3210 27.31 0.44 0.44  chr1_78363918_78370812.rev     5497  6404 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78363918_7   5497 TGGAAGAACATTCCATGCTCACAGGTAGGAAGAATCAATATCGTGAAAAT 5546
                              ii i  i     i   ii i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78363918_7   5547 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5596
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78363918_7   5597 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5644
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_78363918_7   5645 TATGGAAGCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5694
                                iiiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_78363918_7   5695 AACAAAGCCAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5744
                                iii    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_78363918_7   5745 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGATC 5794
                                 i   i    ii         i iv ii i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_78363918_7   5795 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 5842
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_78363918_7   5843 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGCATTCC 5892
                          vi    i  i     ivv  vv  i v  vv            v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_78363918_7   5893 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAAGTAGAAAGCT 5942
                           v  i  i              v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_78363918_7   5943 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5992
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_78363918_7   5993 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 6042
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_78363918_7   6043 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 6092
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_78363918_7   6093 AACACCAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGGATCTAA 6142
                         i            vvi          v      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_78363918_7   6143 TTAAACTAAAGAGCTTCTGCACAGAAAAAGAAACTACCATCAGACTGAAC 6192
                          i   v v  i i   i  ii vvv   i  v    i  vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_78363918_7   6193 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 6242
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_78363918_7   6243 AAGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 6292
                         ii i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_78363918_7   6293 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATAGACACTTC 6342
                          i     i     v  i?    i            v          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_78363918_7   6343 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 6392
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_78363918_7   6393 ATCACTGGCCAT 6404
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3150 27.10 0.77 0.33  chr1_78380318_78387034     5321  6224 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78380318_7   5321 TGGAAAAACATCCCATCCTCATGGGTAGAAATAATCAATATTGTGAATAT 5370
                               i i       vi      i v i  v v i        v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78380318_7   5371 GGCCATACTGCCTAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5420
                            v     v  i   v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78380318_7   5421 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 5469
                          v   vivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_78380318_7   5470 ATGGAACCCAAAAAGAGCCCGCATAGCCAAGACACTCCTAAGCAAAAAGA 5519
                               vivv  ii  v  v v        i   v  i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_78380318_7   5520 ACAAAGCTGGTGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5569
                               i   v  vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_78380318_7   5570 ACAGTAACCAA-ACAGCATGCTACTGGTACCAAAACAGATATATAGACCA 5618
                                i   -    ii  v      i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_78380318_7   5619 ATGGAACCGAACAGAGGCCTCAGAAATAACTCCACACATCTACAACCATC 5668
                               iv   iv   ivii         vi   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_78380318_7   5669 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 5718
                             i  i     ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_78380318_7   5719 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATACGCAGAAAACTGAA 5768
                           i  i        i     v      v  ?   i i   i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_78380318_7   5769 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 5818
                         ii    i    v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_78380318_7   5819 AAGACTTAAACATAAGACCTAAAACTGTAAAAACCCTGGAAGAAAATCTA 5868
                         ?    i    ii     v        i     vi i i        iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_78380318_7   5869 GGC--AATTCCATTAAGGACATAGGCATGGGGAAAGACTTCATGACTAAG 5916
                           ?--  v  --  viv   v v  vv i  v  v ii   v iiv  v 
  L1M4_orf2#LINE/    550 GGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_78380318_7   5917 TCAT-GAAAGCAATGGCAACAAAAGCCAACATTGACAAATTGGATCTAAT 5965
                         v  i-i      vvi          vv  v  v  i        ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_78380318_7   5966 TTAACTAAAGAGCTTCTACACAGCAAAAGAAACTGTCATCAGAGTGAACA 6015
                         iv  v v  i i   i iii vv    i  v   i   vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_78380318_7   6016 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATACATCTGACAAA 6065
                          i     i                 v       vii   i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_78380318_7   6066 GGTCTAATATCCAGAATCTACAAAGAATTTAAACAAATTTACAAGAAAAA 6115
                           v  vi          v  i      i ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_78380318_7   6116 AACAAACAACTCCATCAAAAAGTGGGAAAAGGATATGAATAAACACTTCT 6165
                         i     i   i v  i?    i    v       v      i   i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_78380318_7   6166 CAAAAGAAGACATTTATGCAACCAATAA--ACATGAAAAAAAGCTCATCA 6213
                          v        i  vi viiii       --         i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_78380318_7   6214 TCACTGGTCAT 6224
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.34 (138 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2478 26.21 1.14 7.43  chr1_78437584_78440779     1735  2703 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78437584_7   1735 TGGAAAATCATTCCATGCCTATGGATAGGAAGAATCAATATTATGAAAAT 1784
                               ivi  i     iii      v      v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78437584_7   1785 GGCCATACTACCCAAAGTAATTTATAGATTCAATGCTATTCCCATTAAAC 1834
                            v     v      v i  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78437584_7   1835 TACCA-CTGACATTCTTCACAGAATTAAAAAAGCCTACTTTAAAATTCAT 1883
                          v   -   v -  i  ii     v vi v    iv iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_78437584_7   1884 ATAGAA---CCAGAAATATTCTGTATAGCCAAGACAATCCTAAGTAAACA 1930
                           i   --- v  ii i--i v v        i      i i iv  iv 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_78437584_7   1931 GATCAAAGCTGGAGGCATCATGCTACCTGACTTCATACTATACTACAAGG 1980
                           v     i      vv   ii  v  ii i    v viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_78437584_7   1981 CTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACATGTGGAT 2030
                                  i   i    ii         i i  ii i      i i   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_78437584_7   2031 CAATGGAGCAGAATAGAGAACTCAGAAATAAGACCACACATCTACAACCA 2080
                                ii     v    iii         iv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_78437584_7   2081 TCTGATCTTTGATAAACCTGA-AAAAGCAAGCAATGGGGAAAGCATTCCC 2129
                         vi    i  i  i  ivv  v-  i v  vv            v  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_78437584_7   2130 TATTTAATAAATGGTACTGGGAGAACTGGCTAGCTATATGCAGAAAATCG 2179
                          v  i  i       i      v      v  ? i i     i  i vi 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_78437584_7   2180 AAACTGGATCCCTTCCATATACCTTATACAAAGGTTAACTCAAGATAGAA 2229
                           ii    i    v  vi i   v        ii         i  i  v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_78437584_7   2230 TAAAAACTTAAAGGTAAAACCCCAAATTGTAGAAACCCTGGAAGAAAATC 2279
                         i ? i  i    v    i v iv   i i  i  vi i i        iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_78437584_7   2280 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGATTTCAT-GATGA 2327
                             ?i- v i -   iv   v v  vv i     v i    v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr1_78437584_7   2328 AAACGTGAAAAGCAATGGCCACAAAAGCAAAAATTGAAACATGGAATCTA 2377
                         vi  iiv       vvi  v       v      v  v v  v i ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_78437584_7   2378 ATTAAACTACAGAGCCTCTGCACAGCAAAAAAAAAAAAATATATGTATAT 2427
                           i   v vv i i i i  ii vv    ii ------------------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGA------------------ 677

  chr1_78437584_7   2428 GTATACATATATACATATATATACACACATATATATGTATATATATATAA 2477
                         -------------------------   -----------------   v 
  L1M4_orf2#LINE/    678 -------------------------CAC-----------------TATCA 685

  chr1_78437584_7   2478 ACTCATAAGAGTGAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAA 2527
                          -----i i      v        i                 v       
  L1M4_orf2#LINE/    686 A-----GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_78437584_7   2528 TCTGTCCATCTGACAAAGGTCCAATATACAGAATCTAAAAGGAACTTAAA 2577
                         viii vi      i  i  v ivi   v      v  v  i     ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_78437584_7   2578 CAAACTTA-CAAGAAAAAAACCAAACAACCCCATTAAAAAGTGGGCAAAG 2626
                            -  i -i  v     i  -   i     v   ?    i         
  L1M4_orf2#LINE/    781 CAA-CTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_78437584_7   2627 GACATGAACAG-CACTTCTCAAAAGAAGACACTTATGTGCCCAA--AATA 2673
                           iv    i  -  i     v        i ivi vi  v    -- ii 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_78437584_7   2674 CATGAAAAAAAAACTAACATCACTGATAAT 2703
                                 i vivii       ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (153 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.88 (83 / 17)  


3103 26.19 0.76 2.49  chr1_78487261_78493635     4959  5882 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78487261_7   4959 TGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATTGTGAAAAT 5008
                              ii i  i     i     i  v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78487261_7   5009 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5058
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78487261_7   5059 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5106
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_78487261_7   5107 TATGGAAGCAAAAAAGAGCCCACATTGCCAAGATAATCCTAAGCCAAAAG 5156
                                iiiv  ii  v  viv  v     i i    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_78487261_7   5157 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTCTACTACAAGGC 5206
                                i      vv    i  v  ii i      vii        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_78487261_7   5207 TACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGAGC 5256
                                 i   i    ii        ii iv ii i   v       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_78487261_7   5257 AATGGAACAGAAT--ACAGCTCTTGGAAATAATACCACACATCTACAACC 5304
                                i     -- v  ii --i       vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_78487261_7   5305 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGAAGAAAGATTC-C 5353
                          vi    i  i     ivv  v   i v  vvv    ii      v v-i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_78487261_7   5354 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5403
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_78487261_7   5404 GAAACTGGATCCCTTCCTTACACCTTATTCAATTAATTCAATTGAATTAC 5453
                            ii    i    v   i     v   v   ------------  ----
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAA------------AA---- 480

  chr1_78487261_7   5454 AATTAATTCAAGATGGATTAAAGACTTAAATGTTAGATCTAAAACCATAA 5503
                         -     i    i      i ?    i       v   v       i    
  L1M4_orf2#LINE/    481 -ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_78487261_7   5504 AAACCCTAGAAGAAAACCTAGGC--AATTCCATTCAGGACATAGGCATGG 5551
                           vi i           v    ?--  v  --   iv   v v  vv i 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAG 577

  chr1_78487261_7   5552 GCAAGCACTTCATGACTAAAACACCAAAAGTAATGGCAACAGAAGCCAAA 5601
                             vvii   v iiv  vi          i vvi      i   vv   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_78487261_7   5602 ATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGA 5651
                           v  i    v   ii v  i   v v  i i   i  ii vv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_78487261_7   5652 AACTACCATCAGAGTGAACAGACAACCTACAGAATTGGAGAAAATTTTTA 5701
                         v    i  vv i      v        i       v         v   i
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_78487261_7   5702 CAATCTACCCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTC 5751
                            vii ivi      i  i  i  vi          v  i  v      
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_78487261_7   5752 AAACAAATTTACAAGAAAAAATCAAACAACCCCATCAACAAGTGGGCAAA 5801
                         vv    v iv i  v     iv    i     v  i? v  i        
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_78487261_7   5802 GGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGAC 5851
                             v    i     i     v        i  vi viii     i ii 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_78487261_7   5852 ACATGAAAAAATGCTCATCATCACTTGCCAT 5882
                                  i       v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.00 (30 / 10)  


2999 19.22 4.02 3.77  chr1_78558568_78560246.rev      398  1193 (486)    L1M4_orf2#LINE/L1      111   908 (0)  

  chr1_78558568_7    398 CTTCTCCACAGCTATTGGCAATTTTGTGGTCCCACCACATACAATATAAG 447
                            i iii   vv    i   vi --- i   i -- v  v  -   iii
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCT---GATCCTA--AAATTCA-TATGGA 154

  chr1_78558568_7    448 AAAGAAAAAAAAGTAGCATCTGAACCGAGACTAATTTACTCAATGAAAGA 497
                           v v  iii vvi  v  --- i  i i  -   i -- v  --     
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAAT---AGCCAAAAC-AATCT--TGAA--AAAGA 196

  chr1_78558568_7    498 A-AGTAAAAACAAAGGACAGTATCATCTCCTGATTTCAAAACTTGCTACA 546
                          - ii   iviii     -- vv  ii   ii            i     
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGAC--TCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_78558568_7    547 AAGCTACAGTAGTCAA-ATAGC-TAGCATGCTGGCATAAGGACAGACATA 594
                                    i    - i  i- i i --            i       
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTA--CTGGCATAAGGATAGACATA 292

  chr1_78558568_7    595 TAGATCTATGAAGTATAATTGAGAATTCAAAAATAAACCCTCACATTTAT 644
                               v   i i  v        i i  i          vi        
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_78558568_7    645 G-TCAATTTATAGTTGACATGGTTGTCAAGATCATCTAATGAGAAGAGAA 693
                          -      v  vv i    v  v  i     i   ii    i i i    
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_78558568_7    694 TAATCTT--CAAAAACTAATGCTGGGACAACTAGAT--------GCAAAA 733
                           i    --   v  v ii             i   --------      
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_78558568_7    734 GAATGAAGTTGGACCCC-----------ATACACAAAAATTAACCCCAAA 772
                                          -----------   i            i v   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_78558568_7    773 CTGATTAAAGACCTCAATTTAAGCACTAAAACTTTATTTAAACATAAATA 822
                         iv   i ?      v   v    vi        v  ---    -------
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA---AAAC------- 532

  chr1_78558568_7    823 TCTTAAAAGAAAACATAGAAATAAATCTTAATTACTTTGGATTTGGCAAA 872
                              i            i?i        vi v  i    i  v     -
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA- 581

  chr1_78558568_7    873 TGGTTTCTCAGCTATGACATCAAAAGCACAAGCAAGGAAAGAAAAA-TAG 921
                                 i  v       i               vi         -   
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_78558568_7    922 GTAAATTGGATTTCGTCAAAATTTAAAACTTCTGTTCATTAAAGAACATT 971
                         i         i   i        v       i   v v i    i   i 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_78558568_7    972 ATCAAGAGAGTGAAAATACAATCC-CAGAATGGAA-AAAATATGTGCACA 1019
                                i        v    i  -        i -       v    v 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_78558568_7   1020 TTATATGTGTAATGAGAGTTTGGTATCCAGAATATATAAAGAACTCTTAC 1069
                          i    i v i  i  i vi v                            
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_78558568_7   1070 AAATCAACAAAAAATAGACA--CAACCCAGTTTTTAAAATTGGTAAAGTG 1117
                           v    i  v   v     --i      i  ?v-     v  i    vi
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGA 830

  chr1_78558568_7   1118 CTTGGATAGACAGTTCTCCAAA-AATATA-AAAAATAGCCAACAAGCACA 1165
                         i   i       v         -  v   - v    i     i       
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_78558568_7   1166 TGAAAAGATGCTAAATGCCATTAGACAT 1193
                                     v  iii  ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (96 / 54)
Gap_init rate = 0.03 (26 / 798), avg. gap size = 2.38 (62 / 26)  


2846 27.03 2.93 0.68  chr1_78637448_78641650.rev     2825  3712 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78637448_7   2825 TGGAAAAACATTCTATGTTAATAGACAGGGAGAATCAATATTGTTACAAT 2874
                               i i  i i     v  i  iv  i   v i          vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78637448_7   2875 AGCCATACTACCCAAAGCAATTTACAGATTCAATGCGATTTCTATCAAAC 2924
                         i  v     v      vii  i           i  i  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78637448_7   2925 TACCAATGACATTCTTCACAGAATTAGGAAAA--AATTACTAAAACTCCT 2972
                          v   iivi v  i  ii     v v iv  i--i  i-      i  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-CTAAAATTCAT 149

  chr1_78637448_7   2973 ATGGAGCCAAAAAAGTGCCTGAATAGCCAAG-CAACCCTAACCAAAAAGA 3021
                              iviiv  ii vv  v          i-   i i i vv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_78637448_7   3022 ACAAAGCTGGAGACATCACATTACACAATTTCAAACTATATCACAAAGCT 3071
                               i     ivv     i v v          viv  ii        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_78637448_7   3072 ACAGTA------------TGGTACTGGTACAAAAACAGACACATAGACTG 3109
                               ------------         i i  ii i     i     iii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_78637448_7   3110 ATGGAACAGGTTAGAGAACCCAGAAATAAAGCCATACACCTACAACCATC 3159
                               i  iv v    ii           v       ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_78637448_7   3160 TGATCTTTGACAAAGCTGGTAATAACAAGCAATGGGGAAAGGACCCTCTA 3209
                             i  i     i v  vi  v v  vv            i ivv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_78637448_7   3210 TTCAATAAATCATGCTGCAATAACTAGCCAGCCATATGCAGAAGATTGAA 3259
                              i    vi     vi i    i vi ?   i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_78637448_7   3260 GCTGGACCTGTTCCTTTCACCATATGCAAAAAATCAACTCAACATCTATT 3309
                          i      iv v   iv        i      - i       v  vv  i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATC 498

  chr1_78637448_7   3310 AAATATTCAAATGTAAACA-TAAAACTATAAAAATCCTAGAAGAAAAC-T 3357
                          ? v iii        ivi-             v  i           - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_78637448_7   3358 AAG---AAATACCATTCTGGATATTGGTCCTAGCAAAGACTTTATGACAA 3404
                          i ---    -- -   vv  iv    viivi    v ii  iv iivv 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_78637448_7   3405 AGACTCCAAAAGCAATTGCCACAAAAACAAAAATTGAAGTGTGGGACCTA 3454
                         v   v         vvv  v      iv      v  vivi v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_78637448_7   3455 ATTAAA--CAAACAACTTTTGCATACTGAAAGAAACTATCAGCAGAATAA 3502
                           i   --i   -        iiiviii  i  v       iv i i i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_78637448_7   3503 ACAGACAACATACAGAATGGGAGAAAATGTTTGAAAACAATGCATCTGAC 3552
                          v       vi                 i    v   iv  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_78637448_7   3553 AAAGGTCTAATATCCAGAATCTATAAGGAACTTAAGCAAATCAACAAGCA 3602
                           i  v  vi          v     i     ivvi   v    i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_78637448_7   3603 TAAAACAA----CCCCATTTAAAAATGGACAAAGGACATGAACAGATAGT 3648
                         v  i    ----   v   ?        i       iv    i   i v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_78637448_7   3649 TCTCAAAAGAAAACATACACATAGCCAATAAGCATATGAAAAAATGTTCA 3698
                             v      i i     v  i           i       i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_78637448_7   3699 ATATCATTGATCGT 3712
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.46 (32 / 13)  


2375 27.91 2.44 2.21  chr1_78725622_78727894      878  1780 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_78725622_7    878 AAAAACATTCCATGCTCATGGATTGGGCAAATCAATATCATTAAAATGGC 927
                            i i  i     i           ivi v i     ii    i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_78725622_7    928 CCTAACTGACCAAAGCAATGTATAGATTCAACACTACCCCTATAAAACTA 977
                         vv  -  vv     vii  v  i         i v i      v   v v
  L1M4_orf2#LINE/     54 AATA-CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_78725622_7    978 CCAAA-GTCTTTCTTCATAGAAATAGAAAATAACT-ATTCTAAAATACAC 1025
                            iv- i    i  -ii      v  v  --i  -  i       v  i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT-GCAGAAATTGACAA--GCTGATCCTAAAATTCAT 149

  chr1_78725622_7   1026 ATGGAACCAGACAAGA-ACCCA-AATAGCCAAG-CAATCCTAAGCAAAAA 1072
                               -- vi    i-     -         i-     i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_78725622_7   1073 GAAGAAAGCCATAGGCATCACAGTACCTGACTTCGAATTATATTGTAAGG 1122
                            v    iiiv   vv     v v  ii i   i  viv  i ii  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_78725622_7   1123 CTACAGAAGTAAAAACAAGATTGTGCTGGTTAAAAAAAAAAAGAGAGACA 1172
                               v i v  i   ivi v  i    i------- v  i  v     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGC-------ATAAGGATAGACA 290

  chr1_78725622_7   1173 CATAGACAAATGGAA-AAAATAGAAACTCAAGAAAAAAATAAAGCTGCAT 1221
                         i     iv       - i   v  i v  v     ----    v iii i
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAA----TAAACCCATAC 336

  chr1_78725622_7   1222 ACCTATAGCCATCTGATGTTTAACAAAATCAACAAATATAAGCAATGGGA 1271
                          ii   i i  vi    v  ii    iiviiv   ivvi vv       i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_78725622_7   1272 AAAGGACACCCTATTCAATAAATTGTGTTGGGTTAGCCGGCTAGCCAAAA 1321
                             i i vi  v     i    v   i    vi i i  v  ?   v v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_78725622_7   1322 GCAGAAGATTGAACCTGCATCCTTATCTTCCACCATATGCAAAAATTAAC 1371
                            i    v    vi  v i  i  i  iv        i           
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_78725622_7   1372 TCAACATGGATTAAAGAGTTAAATATAAGACCTCAAACTATAAGAATCCT 1421
                             v      i ?   vi     i     v  v         i v  i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_78725622_7   1422 AAAA-AAAACCTAGGAA-ACGCCATTCTGGACATCGGCCTTGGGAAAGAA 1469
                          i  -     v    ?i- vii -   vv   v i  vi v  v  v iv
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_78725622_7   1470 TTTATGACTAAGTCCTCTAA--CACAATTACAACACAAACAAAAATTGAC 1517
                           iv iiv  v v vi v  --     --i     v  iv      v  i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGAT 633

  chr1_78725622_7   1518 AAGTAGAAGCT------AATTAAAGAGCTCTGCAAAGCAAAAGAAACTAT 1561
                           i v i vi ------       i vi i  iivvv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_78725622_7   1562 CAGCAGAGTAAACAGACAACCTACAGAATGAGAGAAAATATTTGCAAACT 1611
                           iv i   i  v        i        i                 ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_78725622_7   1612 ATGCATCCAGCAAAGGTCTCATATCCAGAATCTATAAAGAACTT----AA 1657
                           ii   iiii  i  v  ii          v           i----  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_78725622_7   1658 ATCAACAAACAAGAACCAAATAAACCCATTAAAAAATGAGCAAAGAACAC 1707
                         v    i  vv  i iv       v  v   ?       i      i ivi
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_78725622_7   1708 GAACAGACATTTCTCAAAAGAAAACATACAAGCAGCCAACAA--ACATGA 1755
                            i           v      i i      iii     i  --      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_78725622_7   1756 AAAAATGTTCTATATCACTAATCAT 1780
                            i   i  v i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.02 (20 / 905), avg. gap size = 2.10 (42 / 20)  


2685 25.64 1.61 4.18  chr1_78731808_78736909     3678  4609 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78731808_7   3678 TGGAAAAGCATTCCATGCTCATGGGTTAGAAGAATCAATATGGTTAAAAT 3727
                               iii  i     i      i  i     v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78731808_7   3728 GGCCATACTCTTCAAAGCAATGTACAAATTCAATGCTATTCCTATCAAAT 3777
                            v      ii    vii  v    i      i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78731808_7   3778 TACCAAAGTGATTTTTTCCCAGAA-TT-AGAAACAAATGGTAAAATTCAC 3825
                          v   iv-  vi     iv     -  - v  i vi  vv         i
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_78731808_7   3826 ATGGAACCAAAAAGAGCCCA-AATATCCAAG-CAATCCTAATAAA-AAGG 3872
                               viiv  i ii    -    v    i-     i i v   -   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_78731808_7   3873 ACAAAGCTGGAAGCATCACATTACCTGATTTCAAACTATACTACAAGATC 3922
                               i    i vv     i v  ii        viv        iiii
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_78731808_7   3923 ACAGTAACTAAAACAGCAGGATACTGGTACGAAAATAGACACA--GACCA 3970
                                ii  i    iiv i      i ii ii       i --  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_78731808_7   3971 ATGGAACAGAAT--GGAGCTCACTGAAATAAAGCCACATACTTACAACCA 4018
                               i     --i   ii  --        v   i i i   iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCA--GAAATAAACCCATACATTTATGGTCA 347

  chr1_78731808_7   4019 GCTGATCTCTGACAAAGCTGACAAAAAATAAACAATAAGGAAAGGATA-C 4067
                         ii    i ii     i v  v   i v-i vv    ii      i   -i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGT 396

  chr1_78731808_7   4068 CCTTTCAATAAATGGTGATGAGAAAACTGGCTAACATAATAAGCAGAAGA 4117
                          i      i        v  i  v      v  ? v-- i v   i    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC--ACATGCAAAAGA 444

  chr1_78731808_7   4118 ATAAAACTGGACCCTCTATGTATCACTAAATA-AAAAATTAACTTGAGAT 4166
                           i  ii       -   iv vv   i v   -           ii i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_78731808_7   4167 GGATTACAAACTTAAATGTTAGACTGTTACATTCTAGATTTTATTCATCT 4216
                             i ? i  i       v   -- i  ------ i i ----------
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGA--GCTA------AAACT---------- 525

  chr1_78731808_7   4217 GGAATGGAAATTATAGAAGAAAACTTAGGAAATACTCTGCTAAACACTGG 4266
                         ---  ii  v iv           v    ?ivv v   v vvi  vi   
  L1M4_orf2#LINE/    526 ---ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_78731808_7   4267 CATAGGCAAATAATTTAT--GATGAAAGCCCCAAAAGTAAATGCAACAAA 4314
                         vv       - ii   v --   ivi - v       i v v        
  L1M4_orf2#LINE/    573 GTTAGGCAA-TGGTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAAA 620

  chr1_78731808_7   4315 AACAAACATTGACAAGTGGGACTTAAGTAAACTAAAGAGCCTCTGCACAG 4364
                          iv   v  v  i  i v      v vi   v v  i i i i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_78731808_7   4365 CAAAAAAAAAAAAAAAAATTATCAACAGAGTAAACAGACAACCTACAGAA 4414
                             ii v ---------i      v i   i  v        i      
  L1M4_orf2#LINE/    671 CAAAGGACA---------CTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_78731808_7   4415 TGGGAGAAAATATTCACAAACTATGCATTTGACAAAGGTCTAATATCCAG 4464
                                       ii    ii  ii  i   i  i  v  vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_78731808_7   4465 CATCTATAAGGAGCTTAAATAAATCAACAAGAAAAAACCAAACAACCCCA 4514
                         v  v     i  i  ivv i  v    i  v     iv    i     v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_78731808_7   4515 TTAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCGAAAGAAAACATA 4564
                           ?    i           iv    i     i     v      i i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_78731808_7   4565 CAAACAGCCAACAA--ACATGAAAAAGTGCTCTACATCACTAATCAT 4609
                             ii     i  --         ii     v      ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (151 / 84)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.45 (54 / 22)  


2219 23.89 8.72 3.70  chr1_78751835_78753659.rev      502  1338 (487)    L1M4_orf2#LINE/L1       30   908 (0)  

  chr1_78751835_7    502 AAGATTTAGCAGTGTTAATATGTCCATTCTTCC-ATATTGATCT-TAGAC 549
                             i   ii v      v   v v  v  i  - v        -i   i
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGAT 79

  chr1_78751835_7    550 TCCACACAATCACTATCAAA-TTATAGCAGGATTTTTTTTTG-AGAAACT 597
                           v  i     v        - ivi   v ---ii       -     i 
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTG---CCTTTTTTGCAGAAATT 126

  chr1_78751835_7    598 GATAAGCCAATTCTAAAATTTATATTAAAATGTAAAAGATCTAAACT-GC 646
                           i    ii  i        i    vi     i  ii  i i i v -  
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr1_78751835_7    647 TAAAAAAAAAAAAAAAAAAAAAAAACT---AAAAGAAGAAAAATGTTGAA 693
                         i    v  v----------------  ---          v  v    i 
  L1M4_orf2#LINE/    177 CAAAACAAT----------------CTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_78751835_7    694 GGACTTACACTACCTGATTCCAAA-CTTGTTGTAAAGCTACTGTAATACA 742
                              i     v  ii   i    -   ii ii        v     -  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT-CA 259

  chr1_78751835_7    743 AAA-AGTGTGATATTGACATA-GGATGGA----TACATCAATGGAAAAAA 786
                          i -      i  i  i    -    i  ----  v          v i 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_78751835_7    787 ATAATAGAGTCTAGGGATAAGTGCACACGTATGCATTCAGTTGATTTTCC 836
                           vi-      i  ii    iiv  i  i v iiiv   i         v
  L1M4_orf2#LINE/    310 ATTG-AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_78751835_7    837 ATCAAGATACCAGTAGA--ATTCATTAGGGTAAGAAAAGTGTTTTTAACA 884
                          iv i i i   --   --     v i   v     v   v    i    
  L1M4_orf2#LINE/    359 ACAAGGGTGCCA--AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_78751835_7    885 AAAGGCATTTAAACAACTAGATAGTCATATGAAAGTAAACAAACCTTGGT 934
                           v  iii vii      i    ?i  i   v  ivi  ii  vi v ii
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_78751835_7    935 CCTTAGCT-ACTACATATTAAAAAAATTAAT--AAAGT---TCATAGAC- 977
                           i  v  -  vv     - v         i--   i ---   ?    -
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_78751835_7    978 TGAACATAAAACCTAGAACCA-AAAGCTCTTA-----AAGCATAAAG--- 1018
                          i  ii   i v   i   i -   i      -----  i    ii?---
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_78751835_7   1019 AATATCCTTCCCTTTTAGT-AGACAAACACTTCTTGGATATGACA----- 1062
                            v i v vv i  vi  -  i   vvii     i         -----
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_78751835_7   1063 ------------AAAAGAAAACA------------ACTTCATCAAAATTT 1088
                         ------------         v ------------              v
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_78751835_7   1089 GAAAGTTTTACTCATCCAAAGACACCATGAAAAAAATTAAAAGGCAAGTC 1138
                         i   v    iiv v  v  i     i  v  i   i v     i   vi 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_78751835_7   1139 ACAGATTGAGAAAAAA-------AAATCAGTATGTATATCTGACAAAGGA 1181
                              v  i  i    -------      -----         i  i   
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCA-----TATATCTGATAAGGGA 750

  chr1_78751835_7   1182 TTTATATACAGATTATATGAAGAACTC--ATAAATCA-CAATAAAAAGTC 1228
                         i  i   v    v     i        -- i  v   -i         v 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_78751835_7   1229 AAACAACCCATTTAAAAAATGGACAAAAGACTTGAACAGATACTTCACAA 1278
                            i      v  ?        i    i  i     i   i i   v v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_78751835_7   1279 AAGAAGACACATGAATAGTCAACAAGCAGAAGAGAAGATACGTAACATTT 1328
                                i i ii   i i   i     v v  i     i vi     --
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT-- 898

  chr1_78751835_7   1329 CACATCCACT 1338
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.88 (128 / 68)
Gap_init rate = 0.04 (32 / 879), avg. gap size = 3.25 (104 / 32)  


3130 26.17 0.76 1.74  chr1_78784906_78791187     4873  5789 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78784906_7   4873 TGGAAGAACATTCCATGCTCATGGATAAGAAGAATCAATATCATGAAAAT 4922
                              ii i  i     i        vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78784906_7   4923 TGTCATACTGCCCAAGGTAATTTATAGATTCAGTGCTATCGCCATCAAGC 4972
                         v iv     v     iv i  i  i       ii  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78784906_7   4973 TACCA-CTGACTTTCTTCACA-AAATTGGAAAAAAAAACT-ACTTTAAAG 5019
                          v   -   v    i  -i  -      ----- v  i  - iii    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG-----ACAAGCTGATCCTAAAA 144

  chr1_78784906_7   5020 TTCTTATGGAACCTGCATAGCCAAGAGCCTGCATAGCCAAGACAATCCTA 5069
                            v       v-    -  ---i  v  v v        i      i i
  L1M4_orf2#LINE/    145 TTCATATGGAAA-TGCA-AG---GGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_78784906_7   5070 AGCAAAAAGAACAAAGCTGGAGGTATCATGCTACCTGACTTCAAACTATA 5119
                          iv  i          i      vv   ii  v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_78784906_7   5120 CTACAAGGCTACAGTAACCAAAATTGCATGGTACTGGTACCAAAACAGAT 5169
                               i          i   i iv ii         i iv ii i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_78784906_7   5170 ATAATAGGCCAGTGGAACAGAACAGTGGCCTCAGAAATAACACCACACAT 5219
                            -   ii  i     i    iv v ivii         vv   i    
  L1M4_orf2#LINE/    290 ATA-TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_78784906_7   5220 CTACAATCATCTGATCTTTGACAAACCTGACAAAAGCAAGCAATGGGGAA 5269
                         i  iii   vi    i  i     ivv  v   i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_78784906_7   5270 AGGATTCCCTATTTAATAAATGGTGCTAGGAAAACGGGCTGGCCATATGT 5319
                           i  vvi  v  i  i          i   v   v  v i?   i   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_78784906_7   5320 AGAAAGCTGAAACTGGAACCCTTCCTTACACTGTATACAAAAATTAACCC 5369
                          i  iiv    ii    v    v   i    ii               i 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_78784906_7   5370 AAGATGGATTAAAGACTTAAATGTAAGACCTAACACCGTAAAACACTT-G 5418
                           i      i ?    i           v    v  ii      v   - 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_78784906_7   5419 AAGAAAACCTAGG--TAATACCATTCAGGACATAGGCATGGGCAAAGACT 5466
                                 v    --   - i -   iv   v v  vv i     v ii 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_78784906_7   5467 TCATGAGTAAAACACCAAA-GCAATGGCAACAAAAGCCAGAATAGACAAA 5515
                           v iii  vi        -   vvi          vv i      i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_78784906_7   5516 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAT 5565
                          v   ii v  i   v v  i i   i  ii vv    i  v       v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_78784906_7   5566 CTGAGTGAACAGGCAACCTACAGAATGGGAGACAATCTTTGCAATCTACC 5615
                         vvi      v  i     i             v   v       vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_78784906_7   5616 CATCTGACAAAGGGCTAATATTCCAGAATCTACAAAGAACTTAAACAGAT 5665
                         i      i  i  i  vi   -       v  i        ivv   iv 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTAT-CCAGAATATATAAAGAACTCTTACAACT 785

  chr1_78784906_7   5666 TTACAAGAAAACAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATG 5715
                         iv i  v    - i     i     v  i?    i    ii      v  
  L1M4_orf2#LINE/    786 CAATAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_78784906_7   5716 AACAGACACTTCTCAAAAGAAGACATTTATGTGGTCAACAGACATATGAA 5765
                           i     i     v        i  vi vi   i   i ii  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_78784906_7   5766 AAAGTGCTCATCATCACCGGTCAT 5789
                           ii      v     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (146 / 91)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.44 (23 / 16)  


2705 25.57 4.93 0.80  chr1_78792999_78794968      606  1477 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78792999_7    606 TGGAAAAACATCTAATACTCATGAATAGGAAAAATAAATATCATTAAAAT 655
                               i i   iv  ii     i  v    i v v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78792999_7    656 GACCATACTTCCCAAATCAGTTTACAGATTCAA-----TTACTGT----- 695
                          i v     i       iii i           ----- iv  i -----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78792999_7    696 ----AGT--CATTTTTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 739
                         ----  i-- v     ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_78792999_7    740 TGGAACCAAAAATGAACCCAAAA--GTCAAAACAGTCTGAGCAAAAACGG 787
                              viiv  i- i     i  -- i       i   viiv   i v i
  L1M4_orf2#LINE/    151 TGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_78792999_7    788 ACAAAGCCAGAGGCATTACATTACCTGACTTTA-----TACTATGTGGCT 832
                               iii    vv i   i v  ii i  i -----     iivi   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_78792999_7    833 GTAGTAACCAAAACAGCATGGTACTGGTACAAAAATAGATACATAGTTCA 882
                         ii     i   i    ii         i i  ii     i i    v   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_78792999_7    883 ATGGGACAGAATAGAGAACTCAGAAATAAAGCCCCATAC--CTACAACAA 930
                             i i     v    iii          --       --i  iiiiv 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACATTTATGGTCA 347

  chr1_78792999_7    931 ACTGATATTTTACAAAACTGACAAAAATAAACAATGAGGAAGGGATACGC 980
                          i    v  iv    iiv  v   i vi vv     i    i i   vv 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_78792999_7    981 TATTCAGTAAATGGTACTGGGAAAACTGACTTGCCA--TGCAGAAGAATG 1028
                          v    ii       i      v     iv v?   --    i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_78792999_7   1029 AAACTGGACCCCATATATCAC--CATATACAAAAATTAACTAAAGGTGGA 1076
                           ii        -  iv    --                  v  ii    
  L1M4_orf2#LINE/    448 AAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_78792999_7   1077 TGAAAACATTAAGTGTAAAGCCTGAGAGTATAAAAATCATAGAAGAAAAC 1126
                          v ? ivvi   i     iiv  i i v       v  v           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_78792999_7   1127 GTAGGAAAAAATTCTTCTGGACATTGGCCTAATCAAATAATTTAT--GAC 1174
                         i    ?iv    -    vv   v    vi  iv   - ii   v --  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA- 593

  chr1_78792999_7   1175 TAAGACCTAAAAAGCAAATGCAACAAAAACAAAAATAGAGAAATGGGACT 1224
                           v   viv       v v         iv         v    v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_78792999_7   1225 CAATTAAACTAAAGAGCTTTTGCACAGAAAAAGA----AGCAACAGAGTT 1270
                         iv  i   v v  i i      ii vvv   i  ---- v   v i   v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_78792999_7   1271 AACAGACAACCTACGAAATGAGAGAAAATATTTGCAAACTATGCATCTGA 1320
                           v        i  ii    i                 ii  ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_78792999_7   1321 CAAAGAACTAATGTCCAGAATCTATAAGGAA----TACAAA-CAA--ATC 1363
                         i  i i   vi i        v     i   ----     v-   --  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_78792999_7   1364 AACAGAAAAATAACCCCTTTAAAAAGTGGGCAAAGGACATGAACAGACAT 1413
                           v   v         vv  ?    i           iv    i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_78792999_7   1414 TACTCAAAAGAAGACAGAAAAGAGGCCAACAAACATATGAAAA-ATGTTC 1462
                          v   v        i v v  iv      i  i  i       -   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_78792999_7   1463 AACATCACTAATTGT 1477
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (135 / 84)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.50 (50 / 20)  


2738 25.33 3.41 3.41  chr1_78884689_78888026     1939  2846 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78884689_7   1939 TGGAAAGATATT-----TTCATGG-TTGGAAATAATTAATGTTGTTAAAA 1982
                                    i-----       -      i- v     i       i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGA 49

  chr1_78884689_7   1983 TGTGCATT-CTACTCAAAGCAGTATACAGAATTAATGCATTTAATTTGTT 2031
                           -   v -  v i    viii v      v i  i   -----------
  L1M4_orf2#LINE/     50 TG-GCAATACTCCCCAAATTGATCTACAGATTCAACGCA----------- 87

  chr1_78884689_7   2032 GATCACTTTGGATATTATGGACATTTAATTCCAATGGCGTACTTCACAGA 2081
                         -   v  ------  i ----- ---   i   iiv  v vi  ii    
  L1M4_orf2#LINE/     88 -ATCCCT------ATCA-----A---AATCCCAGCTGCCTTTTTTGCAGA 122

  chr1_78884689_7   2082 AATATAAAAAC-AATTCTAAA-TTTATACAGAACCATTAAAAAACCAAAA 2129
                            vv v  i -i  i     -  i   ii   viiiv iii v   i  
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr1_78884689_7   2130 TAGTGAAAGCAATACTGACAA-GAAAAACAAAGTTGGAGGAAACACGTTT 2178
                            iv   i    vi   v  -   i               vv   ii  
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_78884689_7   2179 CTAATATATCAGAA---AATGCAAAGCTATAGTAATCAAAACAATATTGT 2225
                          iv -  v   i  --- v i        i         i   i i v  
  L1M4_orf2#LINE/    223 CCCA-ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_78884689_7   2226 CCTGGTATACAAACAGAAATATAGAGTAATGAAATATATTAGAAAGCCCA 2275
                         v    i   vii i   v       vi    i    v v v  i  i   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_78884689_7   2276 GAAATGAATTCCAACATATATGCTCTACTACTTTTCAGCAGGGTCACCAA 2325
                              i  ii vv    v    v  v i iv     ii  i  vii    
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_78884689_7   2326 GAGGACACAATGCAGAAAGTATAGTCTCTTCAATAATTTATGTTGGTAAA 2375
                           vv iv     vi     v       i     i  v vi  i   v v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_78884689_7   2376 ACTGGATTTCCATATGGAAAAAAATGAAATTGGCCACTTATCTTACACCC 2425
                                v?   i   v    i      i    v v i  i  i     v
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_78884689_7   2426 TAGACAAAAGTCAACTCAAAAGGGATAGAAGACCTAAATGTATGACCTGA 2475
                           v      i i         v    vi?             v  v  i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_78884689_7   2476 AATCATAAAACTCCTAGAAAAGACCACAGGAGAAAAGCTCCTTGACATTG 2525
                           ii         i     i i v  i   ? v   v  i v    v   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_78884689_7   2526 GCCTTGGCAACAATTTTTCGAATATCACACTAAAC-CTCAGACTACAAAG 2574
                          vi v     iii   i iii    v    i   v- v  ii v     i
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_78884689_7   2575 --ACAAATAAATAAATGGGACTACATCAAACTCAAAAGC----------- 2611
                         -- v     i      v     v       v i    i -----------
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_78884689_7   2612 AAGGGAAACAATTAACAAAATGAAAAGGCAACCCACAGACTGGGAAAAGG 2661
                           i   v  v  i  v   i       i           v     i  ii
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_78884689_7   2662 TTATTTTCAAATCACATACTTAAGAATGTGTTAATATTCAAAATTTGTAA 2711
                          -    v       i   ii i v  v vii vi   i  i   v i   
  L1M4_orf2#LINE/    722 T-ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_78884689_7   2712 GGAACTCCTAACAGCTCAATGA----AAGACAAATGACCCAATTTAAAAG 2757
                         i      i  -  i      i ----         i        ?    i
  L1M4_orf2#LINE/    771 AGAACTCTTA-CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_78884689_7   2758 TGGGCAAACAGCTTGAACAAATATTTCTCTAAATAAAACATAAAAATGGC 2807
                                 viii     i i i       i   v  i i   v       
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_78884689_7   2808 CAACAGATGTATGAAAAGGTGATCAACATCCTAATTATA 2846
                            i iiiii        i  v        v????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (138 / 88)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.10 (62 / 20)  


1941 25.62 18.99 0.91  chr1_78968507_78971107     1340  2108 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_78968507_7   1340 TGGAAAAACAATCACTGTTTGTGGATTGGAAGGATCAATATTGCTAAAAT 1389
                               i i vi vv    ii           iv i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_78968507_7   1390 GACCATAGTGCCCAAAGCAATCTACATAT-CAATGGTATTCCTATAAAAT 1438
                          i v   v v      vii       v  -   i vv  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_78968507_7   1439 TACCA--TAA-TCTTTCACAGAA-TTAGGATAGAG--AATTCTATAATTC 1482
                          v   -- iv- i   ii     -  --  i -  --i  i   v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACA-AGCTGATCCTAAAATTC 147

  chr1_78968507_7   1483 ATATAGAACCAAAAAAGGGCCTGAATAAT-GAAGCAATCCTAAGCAGAAA 1531
                             i   viiv  ii iv  v     ii-i  i     i i iv ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_78968507_7   1532 GAACAAAGCCAGAGGCAC-CGCACTATCTAACTT-GAGACTATACTACAA 1579
                                 iii    -  - i    vi i  i  -i i   -        
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chr1_78968507_7   1580 AGATATAGCAACCAAAACATCATGATATTGGTGCAAAAACAGACACATAG 1629
                           v  i  i  i   i   vii  i  i   iii  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_78968507_7   1630 ATCAATGGAACAGAATAGAGAACTCAGAAATAAACTGACACACGTACCAC 1679
                                   i     v    iii           iv i   iv  ivii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_78968507_7   1680 TAAGTGACTTTCAAAAAAAGCTGACAAAAATAAGCACTAGGGAAAAGATA 1729
                         i  v   i    i v  ii -  v   i vi vv  v i      ii   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_78968507_7   1730 CCCTATTTGATAAATGGTGCTGGGAAAGCTAGCTAGCCATATGCAGG-GA 1778
                         vi  v  ii i              v i  i v  ?   i     ii-  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_78968507_7   1779 ATGACACTGGACTCTTACTTCTCGCCATATGCAAAAATTAACTCAAGATG 1828
                             vii     i i   i  v i      i               i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_78968507_7   1829 GATTAAAGACTTAAATGTAAAACCTTAAACTATTAAAACCCT-AGAAGAA 1877
                            i ?    i         i v  v       -     i  -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAA 543

  chr1_78968507_7   1878 AACCTAGGAAAAATTCTTC------------TAGACA------------- 1902
                            v    ?iv  v     ------------   i  -------------
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_78968507_7   1903 -------------------------------------------------- 1902
                         --------------------------------------------------
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_78968507_7   1903 -------------------TTGCCCT------------------------ 1909
                         -------------------   iv  ------------------------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_78968507_7   1910 ---------CCCA-AGCATGGGAGAAAATATTTGCAATCTATGCCTCCAA 1949
                         ---------    -  v                    vii  iiv  ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_78968507_7   1950 CAAAGGACTAAGATCCAGAATCTATAGAGAACTT----AAATAAACAAGA 1995
                         i  i     viv         v    i      i----  v v  i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_78968507_7   1996 AAAA-ACAAATAACCCCATTAAAAAGTGGGCAAAGGGGATGAACAGACAC 2044
                             -           v   ?    i          ivv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_78968507_7   2045 TTTTA-AAAGAAAACACACAAGAGGCCCACAAACACATGAAACAGTGCTC 2093
                           i v-      i i i    iv    v i  i         vii     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_78968507_7   2094 GACATCACTCATCAC 2108
                         i      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (130 / 63)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 6.65 (153 / 23)  


3236 27.42 0.44 0.44  chr1_79023401_79029680.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_79023401_7   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4931
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_79023401_7   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_79023401_7   4982 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_79023401_7   5030 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_79023401_7   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAGACTATACTACAAGGC 5129
                                i      vv       v  ii i    i viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_79023401_7   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_79023401_7   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5227
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_79023401_7   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_79023401_7   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_79023401_7   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_79023401_7   5378 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_79023401_7   5428 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_79023401_7   5478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGGCAAATGGGATCTAA 5527
                         i            vvi          vv     v ii    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_79023401_7   5528 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_79023401_7   5578 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5627
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_79023401_7   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAGATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vv   iv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_79023401_7   5678 AAGCAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5727
                          ii    i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_79023401_7   5728 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5777
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_79023401_7   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (150 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2648 25.91 4.20 1.02  chr1_79108239_79113021     3411  4290 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_79108239_7   3411 TGGAAAAATTGTCCGTGTTCACAGATAGGAAGAATCAATATCGTGAAAAT 3460
                               i  vvi  i      ii   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_79108239_7   3461 GGCCATACTGCCCAAAGTAATCTATAGATTCA-TGCTAT-----TCAAAC 3504
                            v     v      v i     i       -i  v  -----     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_79108239_7   3505 TACCA-TTGACTATTTCACAGAATTAGAAAAAA-AATACTTTAAATTTCA 3552
                          v   -i  v  v   ii     v v  v  iv-i  v  --   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chr1_79108239_7   3553 TATGGAA-T-CAAAGAAGACCCCATATAGCCCAGACAATCCTAAGCAAAA 3600
                                - -   i --     viv      v i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_79108239_7   3601 AGAACAAAGTTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 3650
                                         vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_79108239_7   3651 GCTACAGTAACCAAAACAGCATGGTACTAGTAC----------------- 3683
                                   i   i    ii       i i i-----------------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_79108239_7   3684 -CAA---AA-AGAACAGAGACCTCAGAAATAACACCACACATCTACAACC 3728
                         -   ---  -    iv    vii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_79108239_7   3729 ATCTGATCTTCAACAAACCTGACAAAAACAAGCAAAGGGGAAAGGATC-T 3777
                          vi    i   i    ivv  v   i v  vv   v        i  v- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_79108239_7   3778 CTTATTCAATAAATGGTGCTGGTAAAACTGGCTAGCCATATGCAGAAAAC 3827
                            -     i            v v      v  ?   i     i  i v
  L1M4_orf2#LINE/    397 CTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_79108239_7   3828 TGAAATGGGACCCCTTCCTTACACCACAGACAAAAATTAACTCAAGATGG 3877
                             i v        v   i      i v                i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_79108239_7   3878 ATTAAAGACTTAAATGTAAAACCCAAAACCATAAAACTCCTAGAAGAAAA 3927
                           i ?    i         i v i     i         i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_79108239_7   3928 TGTAGG--TAATACCATTTAGGACATAGGCATGGACAAAAACTTCATGAC 3975
                         ii    --   - i -  iiv   v v  vv i i   viii   v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_79108239_7   3976 AAAAACACCAAAAACAGTTGCTACAAAAGCCAAAATTGAAAAATGAGATC 4025
                         v vi         i  vvv  v       vv     v  v    vi  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_79108239_7   4026 TAATTAAACTAAAGAGCTTCTGCACAGCCAAAGAAGTTATCATCAAAGTG 4075
                          v  i   v v  i i   i  ii vv v  i  vii     vv      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_79108239_7   4076 AACTGGAAACCTAAAGAATGGGAGAAAATTTTCACAATCTATCCATCTGA 4125
                           vv iv    i v               v  ii   vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_79108239_7   4126 CAAAGGTCTAATACCCAGCATCTACTAGGAACTTCAACAAATTTACAAGA 4175
                         i  i  v  vi  i    v  v  iv i     iiv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_79108239_7   4176 AAAAAATCAAGCAACTCCATCAAAAAGTGGGCAAAGGATATGGACAGACA 4225
                             i -   ii   i v  i?    i            v  i i     
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_79108239_7   4226 CTTCTCAAAAGAAGACATTTATGCAGGCAACAA--ACATGAAAAAAAAGC 4273
                         i     v        i  vi viii v   i  --         i v-  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GC 891

  chr1_79108239_7   4274 TCGACATTACTGATCAC 4290
                           i    i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (125 / 100)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.42 (46 / 19)  


2778 27.48 2.70 0.45  chr1_79235929_79239466     2160  3047 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_79235929_7   2160 TAGAAAATTATCCCATATTCATGGATTGGAAGAAGTAATATTCTTAAAAT 2209
                          i    iv        i                vv       v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_79235929_7   2210 GAGTTTAGAGCCCAAAACAATGTACAGATACAATGCAATTCCTATCAAAT 2259
                          ivvv  vvv      vii  v       v   i     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_79235929_7   2260 TACCAA-TGTCATTTTCACACAATTATAAAAAC-AATTCTAAAATTCATA 2307
                          v   i-  i v    ii  v  v vv v  i -i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_79235929_7   2308 TGAAACCAAAGGAAAGCCTGAGTAGC-AAAGCAATCCTGAGCAAAAAGAA 2356
                           i  viiv i ii v  v  i    -   i     i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_79235929_7   2357 CAAAGCCAGAGGCAACACATTACTTGACTTCAAACTATATGACAAGGCTA 2406
                              iii    vvv    i v iii i      viv  iv    i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_79235929_7   2407 TAGTAACAAAAACAGCATGGTATTGGTACAAAAGAAGACACATAGATCAA 2456
                         i     iv  i    ii     i   i i  iiiv     i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_79235929_7   2457 TGGAACAGAATAGAGAACTCAGACATAAAGCCACACACCTACAACCAACC 2506
                              i     v    iii    v     v   i   ii  iiii   ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_79235929_7   2507 GACTGTTGGCAAAGTTTACAAAAGTAAACAATGGGAAATGGGTACCCTAT 2556
                           i v i i   i v vv   i vi vv       i  v ii  vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_79235929_7   2557 TCAATAAATGACATTGGGAAAGCTGGCCAGCCATATG---AAG--TCAAA 2601
                             i     iiii     v i    vi ?   i   ---   -- v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_79235929_7   2602 CTGGACCCCTACCTCTCACCATATACAAATATTAACTCAAGATAGACTGA 2651
                         i              v             v          i  i  iii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_79235929_7   2652 AGATGTAAATATAAGACCTGAAACTATGCAATCGCTAGAAGAAAATCTAA 2701
                            iv     i     v  i       iv  iivi          iv  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_79235929_7   2702 GAAGAACTCTTCTAGATATTGGCCTAGGCAAAGAATT------TATGACT 2745
                          ?iv  v     vv  iv    vi       v iv  ------      -
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC- 599

  chr1_79235929_7   2746 AAGGCTAAAGGCAAATGCAACAATA---AAAATGGACAAATGAGATCTAA 2792
                         ---i i   i   v v       v ---     i  i    vi  ii v 
  L1M4_orf2#LINE/    600 ---ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_79235929_7   2793 TTAAACT---AAACTTTTGCACATAAAAAAATA--GTCAACAGAATAAAC 2837
                          i   v ---         ii v v   ii i --i    v i i i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_79235929_7   2838 AGACAACCAACAGAATGGGAGAAAAAAAT-GCAAACTGTGCATCTGACAA 2886
                                 v                v v -     iii ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_79235929_7   2887 AG-ACTAATATCCAGAATCTATGAGGGACTTAAACAAATCAACAAAAACC 2935
                         i -   vi          v   i i i   ivv    v    i  v  vv
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_79235929_7   2936 AAACAAATAATCCAATTAAGAAGTGGGCAAAGGACATGAACAGACACTTC 2985
                          i        i      ? i  i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_79235929_7   2986 TCAAAACAAGACATACAAGAGGACAACAAACATATTAAAAAGTGCTCAAC 3035
                           v   v    i      iv  v   i  i  i  v    ii        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_79235929_7   3036 ATAACTAATCAT 3047
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.33 (28 / 12)  


3278 26.21 0.66 0.66  chr1_79345908_79348530     1223  2130 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_79345908_7   1223 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATAAATATTGTGAAAAT 1272
                              ii i  i     i i    i v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_79345908_7   1273 GGCCATACTACCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1322
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_79345908_7   1323 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1370
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_79345908_7   1371 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1420
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_79345908_7   1421 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGTC 1470
                                i      vv       v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_79345908_7   1471 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1520
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_79345908_7   1521 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTCCAACT 1568
                                i    i--    i  --        vv iii i  i viiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_79345908_7   1569 ATCTGATCTTTGACAAACCTGACAAAAACAATCAATGGGGAAAGGATTCC 1618
                          vi    i  i     ivv  v   i v  v             i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_79345908_7   1619 CTATTTAATAAATGGTGCTGGGAAAACAGGCTAGCCATATGTAGAAAGCT 1668
                           v  i  i              v   v  v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_79345908_7   1669 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1718
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_79345908_7   1719 TTAAAGACTTAAATGTTAGACCTAAAACCATAAACACCCT-ACAAGAAAA 1767
                          i ?    i       v   v       i     -  i  - v       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chr1_79345908_7   1768 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 1816
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_79345908_7   1817 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 1866
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_79345908_7   1867 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGA 1916
                         v  i   v v  i i   i  ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_79345908_7   1917 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 1966
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_79345908_7   1967 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 2016
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_79345908_7   2017 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 2066
                            i     i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_79345908_7   2067 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 2116
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_79345908_7   2117 TCATCACTGGCCAC 2130
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1225 26.76 7.69 3.01  chr1_79425410_79426987.rev      490  1087 (491)    L1M4_orf2#LINE/L1      283   908 (0)  

  chr1_79425410_7    490 GACAGAGCA-ACGGATCAATGGGGAAAAA---AGAATCCAAAAATAGAAC 535
                           i   -  - ii         iiv i  ---   i    i     i v 
  L1M4_orf2#LINE/    283 GATAGA-CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_79425410_7    536 CATACTTACATGTTTGATTGATATTTTGACAAAAGGTCTAAGATAATTCA 585
                              v vi   v ii      -   i     ii vv i    iv     
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGAT-TTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_79425410_7    586 ACGGGAAATGGAAAATCTTCCTCTCAAATTGTGTTGAAACAAGGAGATAA 635
                          i   i  v i v i    iiivv     v   i  ii    vvi    ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_79425410_7    636 --ACATAAGAAAAAATAAAGCATGATCCTTTTCTCAAACCACACATGAAA 683
                         --    ivi   i   i   ivv  i  i vi    v    i i ii   
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_79425410_7    684 ATTAATTTGAGATTGAC-----ACTTAAATGTAAAGGAGAAAATGTTAAA 728
                              i ii i  v  i-----  i         ii vv    ivv    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_79425410_7    729 GTTTATAGTAGGAAAGATAGG-GCAATATCTCCAGG---TT---TTACAA 771
                         ii iv   v  i   v     - i  -    i iv ---  ---   viv
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGC 579

  chr1_79425410_7    772 AAATGTTTTTTAGCATAT-ACAATGGACAAAACATAAG--ACAAAT--AA 816
                           vv    i    -    -   vii---   i  i   --     v--  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAG-ATATGACACCA---AAAGCACAAGCAACAAAAGAAA 625

  chr1_79425410_7    817 TAATGTATAAATTGGGCTCTATTAAA--TAGA--CTTCT---CCCTAAAA 859
                         v   iv         i  ii  i   --  i --   i --- iii   i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_79425410_7    860 GGTAGCATTAAGAATACGAAAGG-CAAGCCATAGACTGTGAGAAAATATT 908
                          ii vi  i     vii    i -   v   i   v  v           
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_79425410_7    909 TGTAATGCATATATACCTGACCAAGAATGTGTCTACAGAATATATTTAAA 958
                           i  vv       --    iv i i iv   v v          ---  
  L1M4_orf2#LINE/    726 TGCAAATCATATAT--CTGATAAGGGACTTGTATCCAGAATATAT---AA 770

  chr1_79425410_7    959 AAGATTCCTACATGACT--ATAATAAAGTGACAAATAA----ATT----A 998
                          ii i  i    --   --        iv         ----   ---- 
  L1M4_orf2#LINE/    771 AGAACTCTTACA--ACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_79425410_7    999 CTGG----AAGCCTTGAACAGACACTG-TACAAAAAAGCCTAATAAACAA 1043
                         v   ---- i vi     i     i v- v    i   ----   v    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG----ATATACAA 864

  chr1_79425410_7   1044 ATGGCTAAAAAGAATATGAAAAATTGTTCAATCTCATCTGTCAT 1087
                              i  v   v i       iv  i    iv   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (101 / 58)
Gap_init rate = 0.04 (28 / 626), avg. gap size = 2.29 (64 / 28)  


3762 21.91 3.41 0.34  chr1_79566308_79568605.rev      929  1809 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_79566308_7    929 TAGAAACATAGCTTATGCTTATGGATAAGAAGAAGGCTTAATATTGTTAA 978
                          i    v   v ii   i i      vi     ---              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA---CTTAATATTGTTAA 47

  chr1_79566308_7    979 GATAGCAGTAATACCCAAAGCCATATACAATGGCAATGCAATCTCCCTCC 1028
                            i   i  v v      viv  v    ivvv   i      i iv  v
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_79566308_7   1029 AAATTCTAGCAGGTTTTTCTGCATAAATGGAAAAATTGATCTTCAAATTC 1078
                             i i   v vi    i    v    v  v  ii     i v      
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_79566308_7   1079 ACAGAGAATGGCAAGGGGCTCCAAATAGCTAAAACAATCTTGAAAAAGAA 1128
                          i vi   vv       i i vi      i                    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_79566308_7   1129 AAACTAAATTGGAGGACCTATGCTTCTTGATTTCAAACCTTACTACAAAG 1178
                         i   v  i         ii ii    iii        v            
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_79566308_7   1179 GTATGGTAATTAAAATAGGGAAGTACTGCTATAATGATAGACATATGAAC 1228
                         v  ii     i  i i  v vi      vi    v           ii i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_79566308_7   1229 CAA---AA-AAAATTGAGAGTCCA-AAATAAACCTATATATCTATAGACA 1273
                            ---  - i             -         i   i  i   i v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_79566308_7   1274 ATGGATTTT--------GTTTT----TCACTCAATGGGGAAAAAATAATC 1311
                           v      --------  vii----i  i            i    i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_79566308_7   1312 TCTTCAACAGCTGGTG-TGAGATGACTGGATTTCCATACACAAAAGAATG 1360
                          i       iv     -  i  ii       v?   i ii          
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_79566308_7   1361 AAGT-GGAACCTTATCTTGGGCTCTATA-AAACATTAATTCAAA-TAGGT 1407
                             -   v  i  i  iivi iv    -   v     i     - i i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_79566308_7   1408 CAGTGACCTAAACCTAAGAATTAAG-CCATAAAACTCTTAGAAGAAAACG 1456
                           ?v        iv     ii   i- i                     i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_79566308_7   1457 TTGGAGTAA-TCTTCATGACCTTGAATTTGGCAATGAATTCTTCAATATG 1505
                          v  ?    -     i        ii  v       iv     vi     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_79566308_7   1506 ACAACAAAGACATGAGCAACAAAAGGAAAAA---ATAGACTGAACTTCAT 1552
                            v    ii  ii           i     ---   i i  i       
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_79566308_7   1553 CAAAATTAAAAACATTGGCATATGAAAGAACATTATCAAAAAGGTGAGAA 1602
                                      v  v iiiv v    i   i      i  i    i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_79566308_7   1603 AACAATCCACAGAATAGAA-AAAATATTTTAAAATTGTACATCAGATAAG 1651
                         i    i         i i -         vv    ii  i   v      
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_79566308_7   1652 GG-TTTACATTTAGAATATATAAAGAATTCTCACAACTCAACAACAAAAA 1700
                           -i  ii  ii               i   i         i  i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_79566308_7   1701 GGCAAACAATTCAACTTAAAATTGGGCAAAAGCGCTGAATAGACATTTCT 1750
                          i    i  ii   i ?    v        i vvi               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_79566308_7   1751 CCAGAGAAG-CATAAAAATGGCCAATAAGAATATTAAAA-ATACTCAGTA 1798
                            i     -i   v              v i  v    -  i    ii 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_79566308_7   1799 TGATTGTCATT 1809
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.15 (129 / 60)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.94 (33 / 17)  


2426 23.76 3.02 3.85  chr1_79571291_79573010      500  1227 (493)    L1M4_orf2#LINE/L1      187   908 (0)  

  chr1_79571291_7    500 TTGAAGATGAAGAACAAAGTTGGATGACTGATATTACCTGACTTTAAGAC 549
                              i v                v    v i i v  ii i  i  i  
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_79571291_7    550 TGACTGACTATAAAGCTACCATAATCAAGACAGTGTGCTATTGGTGAAAG 599
                          --- -    i        vi                v  i   iiv   
  L1M4_orf2#LINE/    237 T---T-ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_79571291_7    600 AATAAACACA--GATTAATGTAACAGGACAGAGAGCCCAGAAGTAGAACC 647
                         i   i   i --   i    v  i  i iv     i      i  i v  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_79571291_7    648 ACATCAATT-TTGTTAACATATTTTTGACAAGAGAGCAAAATGTCCAGTT 696
                          i -  v  - v  i  ivv     i      i -------  i v  --
  L1M4_orf2#LINE/    333 ATA-CATTTATGGTCAATTGATTTTCGACAAGGG-------TGCCAAG-- 372

  chr1_79571291_7    697 GATCCAGCACCATTTATT-----AAAAATATGGGTCTTTTTAATAAATGG 741
                         --------      i v -----  i    ---       i  i      
  L1M4_orf2#LINE/    373 --------ACCATTCAATGGGGAAAGAATA---GTCTTTTCAACAAATGG 411

  chr1_79571291_7    742 TGCTGGAAGAGCTGTACATTCATAAGTAAAAAAAATGAATCCAAACATAG 791
                               i v i   v i ?i  i v i    i  -    viiii  vivv
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCT 460

  chr1_79571291_7    792 ACCTTACACCTTTCACGCAAATTAACTCAAAATGAGTCACAGATCTGAAG 841
                             i     v vi  iv                ii   ?   i  i  v
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_79571291_7    842 GTAAAACACAATACTATATAAAACTTCCAAAAGATAATGTAGAGGAAAAT 891
                             i vvi  v      --     iii i    v  ii   i? v    
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATA--AAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_79571291_7    892 CCT---------GGGTTTGGCAATGACTTTTCAGATACAACACCAAAGGC 932
                          i ---------     v       ii  i i     ii        i  
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_79571291_7    933 ACAAACCATGAAAGAAATAATTGATAAACTGGATTTTATTAGAATTAAAA 982
                             i v ii       v   v      i    i  i  i i        
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_79571291_7    983 TTGTTTGCTCTGTGAAAGACACTGTAAAGAAAGAGAAAAGACTAGGCACG 1032
                         viv    iv  vii  i      i v       v        v vv   i
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_79571291_7   1033 GACTGGTAGGAAATATTTGCAACGGATGTATCTGATAAAGGACTGTTAAC 1082
                           v   v  i            vvv  i          i     vv  v 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_79571291_7   1083 CAAAATATAAAAAGAACACTTAAAACTCAACAATACAAATATGAACAATT 1132
                           i      v       v    v       i    v   v ii  i  ii
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_79571291_7   1133 CAATTGAAAAATGGGCAAAAGATCTG----GACATCTTATCACAGAAGAT 1178
                              ?             i   i  ----     i ivi  v       
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_79571291_7   1179 ATACAGATG-TAAATAAGTATATAAAAAGATGTTACATATCATATGCTTT 1227
                              i   -iv      i i  i        i vv i    ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (106 / 63)
Gap_init rate = 0.02 (14 / 722), avg. gap size = 3.57 (50 / 14)  


3112 28.38 0.33 0.44  chr1_79591389_79597754     4965  5873 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_79591389_7   4965 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTATGAAAAT 5014
                              ii i  i     i        v      v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_79591389_7   5015 GGCCATACTGTCTGAGGTAATTTATAGATTCAATGCTATCCTCAACAAGC 5064
                            v     vi ii iv i  i  i        i  v    ii v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_79591389_7   5065 TACCAATGACTTTCTTCACAGAATTGGAGAAAACGACTTTAAAGTTCATA 5114
                          v   iivi i  i  ii     v v  v  ivi  iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_79591389_7   5115 TGAAACCAAAAGAGAGCCTGCATTACCAAGACAATCCTAAGCCAAAAGTA 5164
                           i  viiv   i  v  v v  vi    i      i i ivv i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_79591389_7   5165 GAAAGCTAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5214
                         v    i i    vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_79591389_7   5215 CAGTAACCAAAACACCATGGTACTGGTACCAAAACAGAGAGATAGGCCAA 5264
                               i   i   vii         i iv ii i   v v    ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_79591389_7   5265 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACAAATCTACAACCAG 5312
                              i    i--    i  --        vv   i v  i  iiii  i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_79591389_7   5313 GTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5362
                         v    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_79591389_7   5363 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5412
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_79591389_7   5413 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5462
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_79591389_7   5463 AAAGACTTCAATGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5512
                          ?    i v     v i v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_79591389_7   5513 AGGCA-ATACCATTCAGGACATAGGCTTGGGCAAGGACTTCGTGACTAAA 5561
                            ?i- v i -   iv   v v  v  i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_79591389_7   5562 ACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5611
                                     vvii         vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_79591389_7   5612 TAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGAACA 5661
                         i   v v  i i   i  ii vv v  i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_79591389_7   5662 GACAACCTACAGAATGGGAGAAAATTTTTACAGTTTACCCATCTGACAAA 5711
                                i                 v   i  iv i ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_79591389_7   5712 GGGCCAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 5761
                           i ivi          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_79591389_7   5762 AATCAAACAACCCCATCAAAAGGTGGGTGAAGGATATGAACAGATACTTC 5811
                         i -    i     v  i?   ii    ii      v    i   i i   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_79591389_7   5812 TCAAAAGAAGACATTTATGCAGCCAACAGATAAATGAAAAAATGCTCATC 5861
                           v        i  vi viii     i iii v       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_79591389_7   5862 ATCACTGGCCAT 5873
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (154 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


3241 26.08 0.88 0.55  chr1_79689216_79695486.rev     4876  5780 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_79689216_7   4876 TGGAAGAGCATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                              iiii  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_79689216_7   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_79689216_7   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_79689216_7   5024 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_79689216_7   5074 AACAAAGATGGAGGCATCACACTACCTGACTTCAAA--CTA-TACAAGGC 5120
                                v      vv       v  ii i      --i  -     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_79689216_7   5121 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 5170
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_79689216_7   5171 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACGACT 5218
                                i    i--    i  --        vv   i i  i  i iii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_79689216_7   5219 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5268
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_79689216_7   5269 CTATTTAATAAATGGTTCTGGGAAAACAGGCTAGCCATATGTAGAAAGCA 5318
                           v  i  i       v      v   v  v  ?   i   i -    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAA 445

  chr1_79689216_7   5319 -GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5367
                         -   ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_79689216_7   5368 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5417
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_79689216_7   5418 CCTAGGCATTACCATTCAGGACATAGACTTGGGCAAGGACTTCATGTCTA 5467
                          v    ?i v viv   iv   v v iv  i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_79689216_7   5468 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5517
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_79689216_7   5518 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5567
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_79689216_7   5568 CAGGCAACCCACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5617
                         v  i         i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_79689216_7   5618 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5667
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_79689216_7   5668 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5717
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_79689216_7   5718 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5767
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_79689216_7   5768 CATCACTGGCCAT 5780
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (136 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2416 25.56 0.51 7.87  chr1_79713842_79715996.rev      687  1664 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_79713842_7    687 GAAAAAAATCCCACGCTTATTGATCCAGACAAAC--AATATTGCTAAAAT 734
                             i v      i i i  v   i-i  - i  --       i   i  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATT-GGA-AGACTTAATATTGTTAAGAT 50

  chr1_79713842_7    735 TACCATACTACCCAAAACAATCTACAGATTCAATTCGGTTCCTATCAAAA 784
                         vi v     v      vii              iv ii i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_79713842_7    785 TACCAACTACATTTTTCACA-AAATTAGTAAAAATAATGCTAAACTTCAA 833
                          v   i  i v     ii  -     iii  iv- i  v     v    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_79713842_7    834 ATGGAAGGAAAAAAGAGCCTAAGTAACCAAAAGAAATCCTAAATAAAAAG 883
                               iviv  ii  v  vi i  i      v  -  i i  v  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAG 198

  chr1_79713842_7    884 AACAAAGCTGGAGACATTACATTACCTGACTTGGAGACATTACATTACCT 933
                                i     --------------    i---------   i v  i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAG--------------GACTC---------ACACTTCCC 225

  chr1_79713842_7    934 GACTTTAAATTATACTAAAAGGCTTGTGTAATCAAAAAAGCATGCCACTG 983
                         i i  i   viv     v  i   vvv        i v  ii  vi    
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_79713842_7    984 GTATAAAAATATACACACAGATCAATGAAACAGAATAGAGAACCAAGAAA 1033
                          i    ii   v   i i         i  i     v    ii v     
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_79713842_7   1034 TAAAGCCACACACCTACAGCCACTTGATCTTTAACAAAGTTGGCAAAAAC 1083
                             v   i   ii  ii i  v     i  ii    i v  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_79713842_7   1084 ATGCACTGGGGAAAGGACATCCTATTCAATAAATGGTGCTGACACAATTG 1133
                           v  v         i i vi  v     i           iv    i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_79713842_7   1134 GATTGCCATGTGCAGAAGAATGAAACTGAACCCCTACATCTCACCATATG 1183
                            v?   ii    i         ii  i        v  v        i
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_79713842_7   1184 CAGAATTAACTCAAGGTGCTCTCAATGAAGAGGTTGAAAATGTTGGGGAA 1233
                           ------------------------------------------------
  L1M4_orf2#LINE/    476 CA------------------------------------------------ 477

  chr1_79713842_7   1234 AAAATTAACTCACAATGGATTACAGATTTAAATATAAGACCTGAAACTAT 1283
                                     v       i ?   ii     i     v  i       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_79713842_7   1284 AAAAACAATGGCAGAAAACCTAGTAAAAACTCTTCTGGACATTTTTCTAG 1333
                             vivv i v       v   v?iv  v     vv   v  vvvi   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_79713842_7   1334 GCAAATAATTCACAACTAAGAGCTCCAAAGCAAATGCAACAAAAACAAAA 1383
                             vviv   vi iv  v  vvi v      v v         iv    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_79713842_7   1384 AGAGGCAAATGGCAAATAATTAAACTAAAAAGCCTCCGCACAGCAAAATA 1433
                          v  ii    v v vv v  i   v v    i i ii ii vv    iv 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_79713842_7   1434 AACAATACATCAAGTGAACAGACAACCTGCAGAATGAGAGAAAGTAGC-G 1482
                         v  v  vv vv       v        ii       i      i  vi- 
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_79713842_7   1483 CTAACTATGCATCTGACAAAAGATTAATATACAGAATCTACAAAGAACTC 1532
                          v  ii  ii      i  ii  i vi   v      v  i         
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_79713842_7   1533 AAAGAACTTAACAATAAACAAATCAAAATAATCCCTCTAAAAAGTAAA-A 1581
                         vv v    i  i      v i i--      i  vvi ?    i iii- 
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGAC--AAATAACCCAATTWAAAAATGGGCA 825

  chr1_79713842_7   1582 AAGGACATGAACAGACGTTTTTCAAAAGAAGACATACAAATGGCTAACAG 1631
                              iv    i    i   i  v        i           i  i i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_79713842_7   1632 GCATAATAAAAAATGCTCAACATTAATTTTCAT 1664
                            i vv    i           i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (141 / 105)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 6.83 (82 / 12)  


2772 27.32 2.77 2.32  chr1_79758013_79763276.rev     3870  4773 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_79758013_7   3870 TGGAAAAATATCCAGTGTTCATGGATTGGAAGAATTAATGTTGCAAACCT 3919
                               i      vi                  v     i   iv  vv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_79758013_7   3920 GTCCTTACTACCCCAAAT-AATCTGCAGATTCCTTGTAATCATTATCAAA 3968
                          v vv    -        -i    i       vvi i    vi       
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_79758013_7   3969 ATTCCAA-TGTTATTTTTCATAGAAATAGAATAAAATAATCCTAAAATTT 4017
                           i   i-  ii-     iii      v  -i  iv i           i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTC 147

  chr1_79758013_7   4018 GCAGAAAATCATAAAAAAAATC--AAATAGACAAGGCAATCATGAGCAAA 4065
                         ii vii  --  iv  iii i --i     v   ii     v   iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_79758013_7   4066 AAGACCAAATCTGGAGGTATTACACTACCTGATTTCAAACTATATTGCTA 4115
                             v    vi      vv i     v  ii        viv  i i v 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_79758013_7   4116 AGCGATAGTAATTAAAACAGCATTGTACTGACATAAACCTACACTCATCT 4165
                            v i      i  i    ii v      i     ivv  v  vi  vv
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_79758013_7   4166 TTCAACGGAACAGGATGGAGAGCCCAGTAATGAGCCCACACATGTATAGT 4215
                         v    i    i  i  v     i    v   i i    i    v   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_79758013_7   4216 CAATTGACTTTTGACAAAAGTGACAAG--TATACATTGGCAATTGGACAG 4263
                                i   i     ii   v    --i  v  v   vi vv i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_79758013_7   4264 TTTATTTAATAAATAGTGTTTAGAAAACTAGATATCCATATGTAGAAGAA 4313
                          i v  i  i    i   i vi  v    i    ?   i   i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_79758013_7   4314 TGAAATTGGACCCTTATCTCACACCGTATACAAAAATCAACTAAAAATGG 4363
                             i        i  i        i           i    v       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_79758013_7   4364 A--------CTAAACATAACACCTGGAATTGTAAAATACCAAAAAGAAAC 4405
                          --------     ii   v v  ii  i i     iv iv i      v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_79758013_7   4406 CATAGGGGAAAAACTACACAGTATTAGTCTGGGCAGTAATTTTTTTGATT 4455
                               ? v   v  v iiiiiv  i vi i    i ii   i  v   v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_79758013_7   4456 TG---------TTGCAGACAACAAAAGCAAAAATAGATGAATGTGATTAC 4496
                           ---------vii  ii         v          i   vv  i v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_79758013_7   4497 ATTAAA-TAAAAAGCTTCCCCACAACAGACAAAACAATTAATAGAATTTA 4545
                           i   - v    i   iivii vv  i vi v  v  i  v i i vv 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_79758013_7   4546 GATATAACCTAAGGATTAGAAGAAAATTTTGGCAAGCCATGCATCTGATA 4595
                         i v i    i vi  v i i       v  v    ii   ii        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_79758013_7   4596 TGGGATTAACATCCAAAATATATAAAACACTCA-ACAATTCTATTTTCTC 4644
                         v    i vii     i          iv    v-    i  v  v-----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA----- 790

  chr1_79758013_7   4645 TCTTTTCTATAGAAAGAAAACAAATAATCCAATTATGAAATAGGCAAGAG 4694
                         --------   i     ---       i      ?vi    i     ii 
  L1M4_orf2#LINE/    791 --------ATAAAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_79758013_7   4695 GCCTGAATAGACTTTTCTCAAAAGAAGAGATACAAATAGCCAACTGATAT 4744
                         iii         v      v        v        i     iviii i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_79758013_7   4745 ATTAAAAAATGCTCAGTATCACTAATCAT 4773
                           v    i       ii    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (152 / 92)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.29 (46 / 14)  


3033 26.78 0.55 0.88  chr1_79852077_79856675.rev     3198  4108 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_79852077_7   3198 TGGAAACACATCCTTTTGTCATGGATTGGTGGAATCAATATTGTGAAAAT 3247
                               v i    iv vv           vi  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_79852077_7   3248 GACCATAATGCCAAAAGCAATCTACAAATTCAGTGCAATTCCCATCAAAA 3297
                          i v   v v  v   vii       i     ii     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_79852077_7   3298 TACCACCATCATTCTTCACAGAA-CAGAAAAAACAATCCTAAAATTCAGA 3346
                          v   v vv v  i  ii     -iv  v  ivii             v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_79852077_7   3347 TGGAACCAAAAAAGAGCCTGCATATCCAAAGCAAGACTAAGCAAAAAGAA 3396
                              viiv  ii  v  v v   v     i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_79852077_7   3397 CAAATCTGGAGGCATTACATTACCTGACTTCAAACTATACTACAAGGCCA 3446
                             vi      vv i   i v  ii i      viv        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_79852077_7   3447 TAGTCACCAAAACAGCATGGTACTAGCATAAAAATAGGGGTATAGACCAA 3496
                         i   v i   i    ii       i      ii    ivi      i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_79852077_7   3497 TGGAACAGTATAGAGAACCCAGAAATAAAGCCAAATACTTACAGCCAACT 3546
                              i  v  v    ii           v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_79852077_7   3547 GATCTTTGACAAAG---CAAACAACATAAAATGGGGAAAGA-CACTCTAT 3592
                            i  i     i --- v  v v   vv            -i v   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_79852077_7   3593 TCAACAAATGGTGCTGGGATAACTGGCAAGCCACATGTATGTAGAAGAAT 3642
                                            i      vv ?       i ----i      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA----AAAGAAT 446

  chr1_79852077_7   3643 TAAACTGGATTGTCATCTCTCACATTATATGAAAATCAACTCAAGATGAA 3692
                         v  ii    iivii i   v   vv    ii     i       i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_79852077_7   3693 TCAAAAGCTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAAC 3742
                            ? ii i     v     v  i    i      v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_79852077_7   3743 GTTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCATGACCAA 3792
                         i v  ?iv  vi    vv   v    v        v ii   v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_79852077_7   3793 AAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGAGATGGGGCTT 3842
                         i vv         v v         iv   i   i   i -- v  i   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA--TTGGACTT 644

  chr1_79852077_7   3843 AATTCAACTGTAAAGCTCCTACACAGCAAACAAGAAATAATCAACAGAGT 3892
                         v  iv  v vv   i  ii iii vv    --i  v iv     v i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAA--GGACACTATCAAGAAAGT 692

  chr1_79852077_7   3893 TAACAGACAACCCACAGAGTGAGAGAAAATCTTCACAATCTATACATCTG 3942
                         v  v              i  i        v  ii   vii   i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_79852077_7   3943 ACAAAGAACCAATATCCAGAATCTACAAAGAATTCAAACAAATTAGCAAG 3992
                          i  i i  ivi          v  i      i  vv    v i ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_79852077_7   3993 AAAAAAACAAACAATCCCATCAAAAAGTGGGCTAAGGATATTAATAGACA 4042
                              i     i  i  v  i?    i     v      v v        
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_79852077_7   4043 ATTCTCAAAAGAAGATATACAAATGGCCAACAAGCATATGGAAAAATAAT 4092
                         v     v                       i     i   i   i  iv 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_79852077_7   4093 CAGCATCAATAATGAT 4108
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (136 / 104)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.17 (13 / 6)  


1740 27.76 4.42 2.49  chr1_79900497_79902208      500  1223 (489)    L1M4_orf2#LINE/L1      171   908 (0)  

  chr1_79900497_7    500 AATAGTTAAAATAATTTTGAAAACAAAGAATAAAGTGGGAGGAACCAATC 549
                              ii    i   i       vi     i     v      vi  vv 
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr1_79900497_7    550 TACCTGAAACCAAGAC--ATTATATAGCTACAATAATCAAGAGTGTATAG 597
                          v  ii vvi   i  -- i  i v       i         vv  i i 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr1_79900497_7    598 TTTTGGACGAGGGATAAACTCAATGATCAATGGAACAGAATAGAAAACCA 647
                          vi   vvv i     i  vi vv           i     v  i ii v
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_79900497_7    648 AGAAGTAGACCCACAGAAGTAGACCCAACGGATTCTTGAGAAAGGTGC-A 696
                             i  i     i v vv  vivi   iv    i i  v  i     - 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_79900497_7    697 ATAGTAGTTTACTAGTGAAAAGATAACATTTTCAGCAA-TAATGCTGAAA 745
                          v vi -  i v i v    ii   iiv      i   - ii     ii 
  L1M4_orf2#LINE/    371 AGACCA-TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_79900497_7    746 TAATGGAATATTCACAGGCAGGCAAGCAATAAATAAATGAGCTTCAACCT 795
                         i  iv i   ?i    v   ----------   -i     iv  vi   i
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCA----------AAA-GAATGAAGTTGGACCC 458

  chr1_79900497_7    796 AATTATCTCAAGT--TATACAAAAATTGATGTAAAAATGGACCATGAAAT 843
                         --i  i    vii--            i i- v        i  ?ii vi
  L1M4_orf2#LINE/    459 --CTACCTCACACCATATACAAAAATTAAC-TCAAAATGGATCAWAGACC 505

  chr1_79900497_7    844 TAAATGTAATACATAAAATTATAAAATATTTAGTGAAACACGTAAGAG-A 892
                                  v vv     i       ivi    vii  v  i  i ? - 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_79900497_7    893 AATCTTTGAGATCTAGAATTAGGTGAAGTGTTCTTAGACTTGATTCTGAA 942
                               i v  i  v ii     ii v vv        iv   iv ii  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_79900497_7    943 AGTAAAATCAATAAAAAGAAAGATTGATAAGCTAGATAAAATCAAAATTA 992
                           i v  v   i    ii   i  v     ii i  ivvv          
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_79900497_7    993 AAAACTTTTTATG----AAAAG-CATTGTTAAGATAATGAAAG------C 1031
                                  -i  ----   i -  i i i    v i     i------ 
  L1M4_orf2#LINE/    656 AAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_79900497_7   1032 TACAGACAGTGAGAAAATATTTGCAAGCAACATATCTTACAAAAGACTAC 1081
                         i     vv v                iiv i      v i  ii    vv
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_79900497_7   1082 TATT-AGAATATATACAAAGAACTTTCAAAGGTCA-TCATAAAA---C-- 1124
                            i-          --       i i v iv   - v      --- --
  L1M4_orf2#LINE/    755 TATCCAGAATATATA--AAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_79900497_7   1125 -T--TTCTATTAGAAAATGGGCAAAAGACATGTAGAAGCATTTTATTGAA 1171
                         - --ii v   ?i            i  iv  v v ii     iviii  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_79900497_7   1172 GAGGATAT-CAGATGACAAATAAGCACATGAAAAGATTCTC--C-TCACC 1217
                           i     -  i   i v                   v   -- -   ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_79900497_7   1218 CCTAGC 1223
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.59 (121 / 76)
Gap_init rate = 0.03 (23 / 738), avg. gap size = 2.17 (50 / 23)  


2512 24.37 3.82 1.98  chr1_79971498_79973259.rev      513  1271 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_79971498_7    513 ATACTGAAATGTATGTGGAACCATACAAGA-ACCCA-AATAGCCATAGCA 560
                           v  i    vi  i     --  i    i-     -        v i  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr1_79971498_7    561 ATCTTGAACAAAAAGAATAAAGTAGGGGGCATTGTACTATATTATTTTAA 610
                                 v  i     i     v  i  vv iii   viviv    i  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_79971498_7    611 AATACACTACAGAGCTATAGTACTCAAAACAACATGGTACTGGCATAAAA 660
                           ivi      i     i    v    i   iii              ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_79971498_7    661 ACAGATATATCAACCAATAAAACAGGATAGAAAGTCCAAAAACAAACCCA 710
                          i   i    vi i    ii  i  i  v  i      i   i       
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_79971498_7    711 CTCATTTACGGTCTATTGAATTTCAAGGAAGATGCCAAGAATACATGATG 760
                         iv      i    v     v    i vi i i        vi ivii   
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_79971498_7    761 GGGAAAGGAGAGTCTCCTCAATGAATGGTGTTGGGAAAACTAGATGTCAA 810
                                i v     ii    ii       i     v    i   i? v 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_79971498_7    811 CATGCTGAAGAATAAAATTCGACTTTTATCTGACACTATATACAAAAACT 860
                              vi      i  i  v   iii  i  v    i           i 
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_79971498_7    861 ACTTTAAAAATTATCAAAGACTTAAGAGTAAGACCTGAACATATAAAACT 910
                          vi i    vvv    ?    i   iv      v  i  vv         
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_79971498_7    911 ATGAGAAAAAAATTT-TTTTTAAA-CTTCTTGACATTGCTGTGG--AAAA 956
                         v v    i    iv -vv?v    -    v    v   ----  -- iiv
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG----GGTTAGGC 579

  chr1_79971498_7    957 AATGATTTTTCAGATATAACCCCAAAAACACAGGTAA---------AAAT 997
                             i   i i      i  v      i    i i  ---------    
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_79971498_7    998 TGACAAAAAAGATTGCATCAAAATTAAAAGCATCTGCACAGCAAAGGAAA 1047
                         v  i   vvi  i v              i v i  ii vv       v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_79971498_7   1048 CAATCAACTGAGTGAAGAGACAATCTACGTAATTTAAGAAAATATCTGCA 1097
                          v     vvi      i      i i  iv   vvi         i    
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_79971498_7   1098 AACCATGCATCTGACTAGGG-CTACTATCAAAAATATGCAAGGAACTCAA 1146
                           i   ii      iv    -  vv    v i     ii  i      vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_79971498_7   1147 ACAACTCAACAGTGAGAAAAATAAATAAC--AATGCAAAAA-GGGCAAAG 1193
                                  i i i -   i i       --   v?     -        
  L1M4_orf2#LINE/    780 ACAACTCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_79971498_7   1194 GACCTGAATAGACAATTCTCTACAACAACAAAAAAGACACAAAAATGGCC 1243
                           ii          v     --------    i    i i v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTC--------CAAAGAAGATATACAAATGGCC 870

  chr1_79971498_7   1244 AACA-------GAAAGG---TTCAACATCACTAATCAT 1271
                           i -------    i ---i         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (114 / 67)
Gap_init rate = 0.02 (15 / 773), avg. gap size = 2.93 (44 / 15)  


2489 27.28 2.75 2.86  chr1_79984791_79987068.rev      879  1787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_79984791_7    879 TGGAAAAACATTCCATGTGCATGGATTGGAAGAATCAATATTATTTAAAT 928
                               i i  i      v              v i      i  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_79984791_7    929 GGCCATACTGCCCAAAGCAATGTACAGAATCAATGCTATTCCTATGAGAC 978
                            v     v      vii  v      v    i  v  i     v i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_79984791_7    979 TACCAATCTCATTTTTCACAGAATTAGAAAAAAACT-ATACTAAAATTAA 1027
                          v   iiiv v     ii     v v  v  i--  -  v        v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_79984791_7   1028 TATGGAACCTAAAAGGAGTCCA-AATAGCCAAAGCAATCCTAAGAAAAAA 1076
                                v- iv    iii   -          i     i i i   i  
  L1M4_orf2#LINE/    149 TATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_79984791_7   1077 CAAACAAACAAAAACACACAACTGGAAGCATCACATTACCTGAATTCAAA 1126
                         -----i      i--------i    i vv     i v  ii v      
  L1M4_orf2#LINE/    198 -----GAACAAAG--------TTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_79984791_7   1127 --CTACTATAATTCTACAGTAACCAAAACAGTGTGATACTGGTAGAAAAA 1174
                         --i     i  vv         i   i        i      i v  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_79984791_7   1175 GAGAAAACAGATACATACACCAGTGGAACAGAATAGACACCCCAGAAATA 1224
                         -------i   i i   v i  i     i     v  v vi         
  L1M4_orf2#LINE/    285 -------TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_79984791_7   1225 AAGCCACAGACCCACAGCCATCTGACTTTCAACAAAGTTGACAAAAATAA 1274
                           v   i v iii ii i  vi   i    i    i v  v   i vi v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_79984791_7   1275 GCAATGGCAAAAGGACTCCCTATTTAATCCATGA-GCTGAGACAGCTGGC 1323
                         v      vi    i ivvi  v  i  ivv   i-    i    i    v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_79984791_7   1324 TAGCCATATGCAGAAGAGTGAAACC--ACTTTTATCCCACAC-------- 1363
                           ?   i     i    i    iii--  iii  i i     --------
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_79984791_7   1364 AAAATTTACTCAAGATGGATTAAAGATTTAAATATAAGACTTCAAGCTAT 1413
                               v      i      i ?   ii     i     vi v  i    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_79984791_7   1414 AAGAATCCTAGCAGAAAATCTAGGAAACACTATTCTGGACGTCAGCCTTT 1463
                           i v  i   v      iv    ?ivv v v   vv   v ii v-  v
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTA 576

  chr1_79984791_7   1464 GGAAAGAATTTAT--GACTAGGTCCTCAAAAGCAATTGCAACAAAAACAA 1511
                           v  vii   v --  -  v v vi        vvv         iv  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_79984791_7   1512 AAATTGACAAGCGGGATCTAATTAAACT---AAACTTTTGCACAGCATAA 1558
                             v  i  iiv   ii v  i   v ---         ii vv  v i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_79984791_7   1559 TAAACTATCAACAGAGTAAGCAGACAACTTACAGAATGAAAGAAAATATT 1608
                         v v        v i   i iv       ii        ii          
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_79984791_7   1609 CACAAATTATACATCCAACAAAGGTCTTATACTCAATAATCTACAAGAAA 1658
                         ii     i   i   ii i  i  v   i  ii  i-   v  i  ii  
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAG-AATATATAAAGAA 774

  chr1_79984791_7   1659 CGTAAACAAATCTACAAGCAAAAAACAA----CCCCATTAAAAAGTGGGC 1704
                          vivv    v  v i  vv    i    ----   v   ?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_79984791_7   1705 AAAAGACATGAACAGACACTACTCAAAAGAAGACATACAAGCAGCCAACA 1754
                            i  iv    i     i v   v        i      iii     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_79984791_7   1755 AACATACAAAAA-ATGCTCCAAATCACTAATTAT 1787
                          i  i ii    -      v v    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.83 (51 / 18)  


2921 25.42 3.00 2.22  chr1_80054339_80059754     4029  4929 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80054339_8   4029 TGGAAAAACATTCCATATTCATGGATAGGAAGAGTCAATATTGTTAAAAT 4078
                               i i  i    i         v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80054339_8   4079 GGCCATACTGGCTAAAGCAATTTACAGATTCAATGC------TAT----- 4117
                            v     vv i   vii  i           i  ------   -----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80054339_8   4118 TCCCA----CATTCTTTCCAGAATTAGAAAAAAAAAAAACT-ATTTTAAA 4162
                              ---- v  i   v     v v  v  i-------  -  ii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-------CTGATCCTAAA 143

  chr1_80054339_8   4163 ATTCATATGGAACCAAAAAGGAGTCTGAATAGACAAGGAAATACTAAGCA 4212
                                     viiv  i   vi v      v   iiv   vi i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_80054339_8   4213 AAGAGTACAAAGCTGGAGACATCACGTTACCCAACTTCAAACTATACTAC 4262
                          ii  v      i     ivv    ii v     i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_80054339_8   4263 AGAGTTACAATAACCCAAATAGCATAGTACTGCTACAAAAACAGAAATGT 4312
                          i  i    i   i v i i  ii i      vi i  ii i   v  i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_80054339_8   4313 AGACCAGTGGAACAGAATAGAGAGCCCAGAAGTAGTGCTGCACACCTACA 4362
                            i  i     i     v     i      i  ivv iii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_80054339_8   4363 ACCATCTGATCTTTGACAAAGCTGGCAAAATCAAGCAATGGGGAAAGGA- 4411
                         ii  vi    i  i     i v  v   i i  vv            i -
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_80054339_8   4412 ---CTTTATAGTCAATAAATTATGCTGGGTTAACTAGCTAGCCATATGCA 4458
                         ---    ----    i    vi       vi    i v  ?   i     
  L1M4_orf2#LINE/    394 AGTCTTT----TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_80054339_8   4459 GAAGATTGAAACTGGACCCCTTCCTTACACCATATAAAAAAATCAACTCA 4508
                         i    v    ii         v   i          v      i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_80054339_8   4509 AGATGGAATAAAGTCTTAAATGTAAAACCTAAAATGGTTAAAATCCTGGA 4558
                          i     vi ?  v i         i v      ivi v   v  i i  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_80054339_8   4559 AGATAACCTAGGA-TATACCATCCTGGACATATGAGCT-GGCAAAGATTT 4606
                            v   v    ?-  v i v  v  -  v -  i i -     v i   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTG-ACCT-TGGGTTAGGCAATGGTTT 587

  chr1_80054339_8   4607 CAT---TATGAAGGTGCCAAAAGCAATTGCAACAAAAACAAAAATTGACA 4653
                          v ---     ---ii         vvv         iv      v  i 
  L1M4_orf2#LINE/    588 CTTAGATATGA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_80054339_8   4654 AATGGGACCTAATTAAACTAAAGAACTTCTTCATAGCAAAAGAAACTATG 4703
                            v    i v  i   v v  i     i viiivv    i  v     v
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_80054339_8   4704 AAAAGAGTAAATAGGCAACCTACAGAATGGGAGAAAGTATTTGCAAACTA 4753
                           i i   i  v  i     i               i          ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_80054339_8   4754 TGCATCCAAAAAAGGTCTAATATCCAGAATCTATAAGAAACTCAAACAAA 4803
                          ii   ii v  i  v  vi          v     ii     vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_80054339_8   4804 CCA-CAAGCAAAAACCAAACAACCCCCCTATTACAAAGTGGGCAAAGGAC 4852
                         i  -i  vv    iv    i     v---   ?v   i           i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCA---ATTWAAAAATGGGCAAAGGAT 831

  chr1_80054339_8   4853 ATAAACAGACACTTTTCAAAAGAAGACATATATTTGGCCAACAA-CATAT 4901
                         v i  i     i  i  v        i   i vv       i  -  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_80054339_8   4902 GAAAAAATTGTTCAAAATTGCTAATCAT 4929
                              i  - i    v  ii????????
  L1M4_orf2#LINE/    882 GAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (137 / 88)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.76 (47 / 17)  


3229 26.87 0.66 0.66  chr1_80066517_80072944.rev     5031  5938 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80066517_8   5031 TGAAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5080
                           i  ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80066517_8   5081 GGCCATAGTGCCTAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 5130
                            v   v v  i  iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80066517_8   5131 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5178
                          v    ivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_80066517_8   5179 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCCAAGCCAAAAG 5228
                                viiv  ii  v  v v  v     i      iii ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_80066517_8   5229 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5278
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_80066517_8   5279 TACAGTAACCAAAGCAGCATGGTACTGGTAACGAAACAGATATATAGACA 5328
                                 i   ii   ii         i vviii i   i       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_80066517_8   5329 AATGGAACAGAACACAGGCCTCAGAAATAACACCTCACATCTACAACCAT 5378
                                i    ivv  ivii         vv  vi    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_80066517_8   5379 CTGATCTTTGACAAACCTGGGAAAAACAAGAAATGGAGAAAGGATTCCCT 5428
                         i    i  i     ivv  vv  i v  vvv     i     i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_80066517_8   5429 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGAAAGCTGA 5478
                         v  i  i              v      v  ?  ii   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_80066517_8   5479 AACTGGATCCCTTCCTTATACCTTATAGAAAAATTAATTCAAGATGGATT 5528
                          ii    i    v   i i   v    v         i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_80066517_8   5529 AAAGACTTAAATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAATCT 5578
                          ?    i       v   v       i      vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_80066517_8   5579 AGGC---AATGCCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5625
                            ?---   -- -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_80066517_8   5626 AAAGACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5675
                         vi v          vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_80066517_8   5676 ATCAAACTAAAGAGCTTCTGTGCAGCAAAATAAACTATCATCAGAGTGAA 5725
                               v v  i i   i     vv    iv v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_80066517_8   5726 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5775
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_80066517_8   5776 AAGGGCTAATATCCAGAATCTACAAAAAACTCAAACAAACTTA-CAAGAA 5824
                          i  i  vi          v  i   i     vv    -  i -i  v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAA 794

  chr1_80066517_8   5825 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACATT 5874
                            i     i     v  i?    i     i      v    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_80066517_8   5875 TCTCAAAAGAAGACATATATGCAGCCAACAGACACATGAAAAAATGCTCA 5924
                             v        i   i viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_80066517_8   5925 TCATCGCTGGCCAT 5938
                         v    i????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3419 25.52 0.55 0.66  chr1_80116345_80121403.rev     3660  4568 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80116345_8   3660 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3709
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80116345_8   3710 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3759
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80116345_8   3760 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 3806
                          v   i-       i  -i     -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr1_80116345_8   3807 CATATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAA 3856
                                  viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_80116345_8   3857 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 3906
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_80116345_8   3907 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 3956
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_80116345_8   3957 TCAATGGAACAGAAC--AGAGCCCTTAGAAATAATGCCACCTATCTACAA 4004
                                  i    i--    i  --        vv   ivi  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_80116345_8   4005 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 4054
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_80116345_8   4055 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 4104
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_80116345_8   4105 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 4154
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_80116345_8   4155 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 4204
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_80116345_8   4205 ACCTAGGCATTACCATTCAGGACATAGGCTTGGGCAAGGACTTCATGTCT 4254
                           v    ?i v viv   iv   v v  v  i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_80116345_8   4255 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4304
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_80116345_8   4305 AATTAAACTAAAGAGCTTCTGTGCAGAAAAAGAAACTACCATCAGAGTGA 4354
                         v  i   v v  i i   i     vvv   i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_80116345_8   4355 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACTTACTCATCTGAC 4404
                          v  i     i   i             v       v i ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_80116345_8   4405 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAGATTTACAAGAA 4454
                           i  i  vi          v  i  v      vv   iv iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_80116345_8   4455 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACT 4504
                            i     i     v  i?    i    ii     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_80116345_8   4505 TCTCAAAAGAAGACATTTAGGCAGCCAAAAACCACATGAAAAAATGCTCA 4554
                             v        i  vi iiii     v  v          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_80116345_8   4555 TCATCACTGGCCAT 4568
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3709 21.58 4.00 0.34  chr1_80212091_80214134.rev      678  1553 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80212091_8    678 TGGGAAAACATCCTACATTCATGTATTGGAAGACTTAATACTGCTAAAAT 727
                            i  i i    i ii      v                i  i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80212091_8    728 GTCAGTACTACCCAAAGTGATCTAAAAATTCAGTGCAATCCCTATAGAAC 777
                          v  i    v      v       v i     ii           vi  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80212091_8    778 TTCCAAGGATGC--TTTTTGCAGAAATAGAGAAACTTATTTAAAAATTCA 825
                          i   -- v   --             v  v  i  v  iiv        
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_80212091_8    826 TATGGGATTTTAAGTTACCTTGAATGGCTAAA-CAATATTGAAAAACAA- 873
                              i v vi   vv   iv    i  i   -    v        v  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_80212091_8    874 --CAAAGCCAGAACACTTACATTTTCTGATTTCAAAACTTACTTCCATGC 921
                         --     iii  iv   i   i  i ii               v v v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_80212091_8    922 TGTGGTAATCAAAACAGTGTGCTACTGGCATAAAGACATACATACAGACC 971
                          iii        i        v           i  i v     i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_80212091_8    972 AATGGAATAAAAT----AGTCCAGAAATAAGCCCTTTAAAATATGGTCAA 1017
                                  i   ----             i   v vv vv         
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_80212091_8   1018 ATGATTTTTGAACAAGGATGACAAGAGCATTCAATGGAGCAAAGACAGTC 1067
                         v       i  -     i  v     v          i v  ii i    
  L1M4_orf2#LINE/    349 TTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_80212091_8   1068 TTTTCAGTAAGTGGTGCTGTGAAAACTGTATACTCACATGTAAAAGAATG 1117
                               ii  i        v  v     v   ?i      i         
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_80212091_8   1118 AAATTGGGTTCCCACCTTATATCATGTACAAAAATTAACTCAAG-TGGAT 1166
                           i    iii  i    i i i   i                 i-     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_80212091_8   1167 CAAAGAACTGAATGTAAGACCTGAAACTGTAAAACTCTTAAAAGAAAATG 1216
                           ?   v  i         v  i     i           i       ii
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_80212091_8   1217 CAAGACAAAAAGTTCACAACATTGCATTTAACC-TGATTTCTTGACTATG 1265
                         i i ?vv   vv   iii  v   vi  vii v-  i      iiv    
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_80212091_8   1266 ACACCAAAGACACAA--------AGAAAAAAAAGATGAATTGAACTTCAT 1307
                                 ii     --------        v    i     i       
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_80212091_8   1308 GAAGATTAAAAAATGTGTTGCATCAAAAGACAGTATCAACAGAGTAAAGA 1357
                         v  i        v v vv   v     i    v      v i   i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_80212091_8   1358 TGTGATGTACAGAATAAGAGAAGATACTTGCAAACTGTATATCTGATAAT 1407
                         viii ivi       ii     i   i       iii            v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_80212091_8   1408 GGATTAATATGCAAAATATATAGAGAACTCCTAAAACTCAACAACAAAAA 1457
                            i vi   v  i        i       i  v       i  i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_80212091_8   1458 AAAAAA-AAC---------AAAGAGGCAAACAATTTGAATAGATATTTAT 1497
                         i v   -   ---------   vi      vi           i    v 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_80212091_8   1498 CCAAAGAAGGTATATAA-----TAATAAGCATATGAAAAGATGACCAGCA 1542
                                  i    i  -----i        i           vi  i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_80212091_8   1543 TCACTAATAAT 1553
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.74 (118 / 68)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.17 (38 / 12)  


2659 27.40 3.16 0.90  chr1_80266477_80268369.rev      517  1403 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_80266477_8    517 GGAAAGATATTTAATATTCATAGATTGGAAGAA-TAATAATTATTAAAAT 565
                                   iiv  i     i          v-     -  i    i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA-TTGTTAAGAT 50

  chr1_80266477_8    566 GTCCATACTACCCAAAGTAATCTGTAGATTCAATGCAATCTCTCTCAGAA 615
                          v v     v      v i    ii        i      i  v   i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80266477_8    616 TACCAATGACATCCTTCAGAGAAATAGAAAACATAATTCTAAAATTTATA 665
                          v   iivi v ii  iiv      v  v  vv i  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_80266477_8    666 TGAAACCACAAAAGAGCCAGAATA-CCGAAAGACATGCTGAGCATAAACA 714
                           i  vii   ii  v        -  i   v -  vi   iv vi  v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACA-ATCTTGAAAAAGAAGA 199

  chr1_80266477_8    715 ACAAAACTGGAGAA-TCACATT-----ACTTCAAATAATACTATGAAGCT 758
                              ii     i -     i ----- i      vvv     ii     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_80266477_8    759 ATAGTAACCAAAACAGTATGGTGCTGGCATAA----AAACACACAGACTA 804
                          i     i   i     i    i         ---- i   i i   ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_80266477_8    805 AAAGAACAGAATAAAGCACCCAGAAATAAATCCATGCATTTACAGTCAAC 854
                          vi   i     vi  vii           i    i      ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_80266477_8    855 TCATCTTTGACAAAGAGACCAAGAACAAACATTGAGGAAAGGACAGTCTC 904
                          v  i  i     i ivi      v  vv  v  i      i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_80266477_8    905 TTCAATAAATGTTACTAGGAAAACTGGATATCCATATGCAGAAGGATAAA 954
                              i     v i  i   v         ?   i     i   i  i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_80266477_8    955 ATTAGAACCCAATCCCTCACCATTTACATAA-TCAAATAGAAATGTCTTT 1003
                         i  i  v   v i i v      v    v  - i  v vi     vv iv
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_80266477_8   1004 AAAACTTAA-TCTAATATCTGAAGCTATGAAGCTACTAGAAGAAAACACT 1052
                         ? i  i   - v   v v  i  i    i  i  vi            iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_80266477_8   1053 GATAAAACACACTAGGACATTGTTCTAGGCAAAGATTTTTGGAATA-AAT 1101
                          i?iv  vv viiiv   v   vvi       v i   i vii   -i i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_80266477_8   1102 CCTCAAAACTCTGGCAGCCAATGCAAAAATGGACATATGAGATCACAT-A 1150
                         v iv   i v vi   i v  v v      i  i v  vi  iiv   - 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_80266477_8   1151 AAGCTAAAAATCTTCTGTCCGGTAAAGGAAACAATAAACAAAATGAAAAG 1200
                           ii      -   i   v vvi      v  v  v  v   i       
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_80266477_8   1201 CTAACTCACAGAATTGGAGAAAATATTTGCAAACTACCCA-CTAACAAAG 1249
                         vi   i        v                  ii ivi -  i i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_80266477_8   1250 GATTAATGACCTGAATATATAAGGACTTCAAACGACTCTACAGTAAAAAA 1299
                           i vi iv  v          i  vi  vv  i    v i i      i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_80266477_8   1300 AAAAAACAAATAATATAATT-AAAAATAGGCAAA-AATTTGAATAGACAT 1347
                          -----       ivi    -      i      -i              
  L1M4_orf2#LINE/    799 A-----CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_80266477_8   1348 TTCCTAAAAGAAG---------TGGCCAACAGTTATACAAAATAATGTTC 1388
                            iiv       ---------       i ivi i ii   vi   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_80266477_8   1389 AACATCCCTAATCAT 1403
                               v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (147 / 93)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 2.12 (36 / 17)  


3020 27.48 0.88 0.66  chr1_80310504_80316783.rev     4884  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80310504_8   4884 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4933
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80310504_8   4934 GGCCATGCTGCCCAAGGTAATTTAGAGATTCAATGCCATCCCCATCAAGC 4983
                            v  i  v     iv i  i  v        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80310504_8   4984 TGCAAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5031
                          v v iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_80310504_8   5032 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5081
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_80310504_8   5082 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGCC 5131
                                i      vv   ii  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_80310504_8   5132 TACAGAAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5181
                              v  i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_80310504_8   5182 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5229
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_80310504_8   5230 ATCTGATCTTT-ACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5278
                          vi    i  i-    ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_80310504_8   5279 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5328
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_80310504_8   5329 GAAACGGGATCCCTTCCTTACACCTTCTACAAAAATCAATCCAAGATGGA 5378
                            iiv   i    v   i     v v         i  ii   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_80310504_8   5379 TTAAAGACTTAAACGTTCGACCTAAAACCATAAAAAACCTAGATGAAAAC 5428
                          i ?    i    i  vv  v       i      vv i    v      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_80310504_8   5429 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5478
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_80310504_8   5479 AACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAA 5528
                         i            vvi     v    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_80310504_8   5529 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAAC 5578
                          i   v v  i i   i  ii vv    i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_80310504_8   5579 AGGCAACCTACAAAATGGGA-AAAATTTTTGCAACCTACTCATCTGACAA 5627
                           i     i   i       -     v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_80310504_8   5628 AGGACTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5677
                         i     vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_80310504_8   5678 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_80310504_8   5728 TCAAAAGAAGAGATTTATGAA--GCCAAAAAACACATGAAAAAATGTTCA 5775
                           v        v  -- ii  --     v  i          i   i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_80310504_8   5776 TCATCACTGGCCAT 5789
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3003 24.62 0.97 3.33  chr1_80326354_80330707.rev     2934  3863 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80326354_8   2934 TGGAAACACACTCCATGCTCATGGAGGGGTAGAATCAATATTGTGAAAAT 2983
                               v i ii     i       vv  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80326354_8   2984 GACCATACTTCCAAAAGCAATCTACAAATTCAATGCAATTTCCATCAAAA 3033
                          i v     i  v   vii       i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80326354_8   3034 TATCA-CCATCATTCTTCAAGAACTAGAAAAAAACAG-TTCTAAAATTCA 3081
                          vi  - iii v  i  vv    v v  v  i-- v - i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_80326354_8   3082 TACGGAACCTAAAAGGAGCCCACA-TAGCCAAAGCAA----GACAGCAAA 3126
                           i    v- iv    ii    v -        i   ----  v --  i
  L1M4_orf2#LINE/    149 TATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA--AAG 195

  chr1_80326354_8   3127 AAGAACAAATCTGGAGGCATTACGTTACCCTATTTCAAACTATATTTTAA 3176
                                  vi      vv i  ii v   v        viv  i vi  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_80326354_8   3177 GGCCGTAGTCACCAAAACAGCATGGAACTGGAATAAAAGCAGGCATATAG 3226
                         i  iii   v i   i    ii   v     v    iiii  i       
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_80326354_8   3227 ACCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAGT 3276
                          i        i     v    ii           v   v i i   ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_80326354_8   3277 CATCTGATCTTTAACAAGGCTAACAAAAACATAAAGTGGGGAAAGGACAT 3326
                           vi    i  ii      v iv   i v   vv i         i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_80326354_8   3327 GATATTCAACAAATGGTGCTGCAATAACTATCAAGCCACATGCAGATGAA 3376
                         vv v                 vi i    ivvv ?         i v   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_80326354_8   3377 TGAAACTGGATCCTTATCTCTCACCTTATACAAAAATCAACTCAAAATGG 3426
                             ii    i  i  i   v    v           i            
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_80326354_8   3427 AGCAAAGACTTAATTATAAGACTTGAAACCATAAAAATTCTGGAAGATAA 3476
                          v  ?    i   v i     vi i    i      v ii i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_80326354_8   3477 CATTGGAACAACCCTTCTAGACATTGGCTTAGGCAAAGACTCTATGACTA 3526
                            v  ?ii  vi    vv   v    v        v ii iiv iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_80326354_8   3527 AGAACCCAAAAGCAAATGTAACAAAAACAAAGATGAATAGATGGGACTTA 3576
                         v  vv         v v i       iv   i  ii   i  v      v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_80326354_8   3577 A-CTAAATTAAAAAGCTTCAGCACAGTAAAAAAACAAAACAAAACAAAAC 3625
                          - v          -   iv ii -v v   ii   vv i----------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGC-TTCAAAGGACACTAT---------- 683

  chr1_80326354_8   3626 AAAACAAAAAACAGCAGCAGAGTAAACAGACAACCCACAGAGTGGGAGAA 3675
                         ----   i   ----------  i  v              i        
  L1M4_orf2#LINE/    684 ----CAAGAAA----------GTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_80326354_8   3676 AATATTCACAATCTATACATCTGACAAAAGACTAATATCCAGAGTCTACA 3725
                               ii   vii   i      i  ii    vi        i v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_80326354_8   3726 AGGAACTCACACAAATCAGCAAGAAAAAAACAAACAAACCCATCAAAAAA 3775
                          i      vi    v   ii  v     i     i  v  v  i?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_80326354_8   3776 TAGGCTAAGGATATGAATAGACAATTCTCAAAAGAAGATATACAAATGGC 3825
                          i   v      v          v     v                    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_80326354_8   3826 TAACAAACATATAAAAA-ATGCTCCACATCACCAGTTAT 3863
                         i  i  i  i  i    -      v      ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (131 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.08 (40 / 13)  


3402 18.63 3.79 5.42  chr1_80360954_80362893      525  1447 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80360954_8    525 TGGAGAGGCTTCCCATCTTCATAAATTAAAAGGCTTAATATTGCTTAAAT 574
                             i  iiv      v     ii   ii   i          i v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80360954_8    575 AA-AATATTATCCAAGTTGACATATAAATTCAACTAAATCTCTTTCAACA 623
                         ii-    i vi    i    iv  i i       vv    i  v    v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80360954_8    624 TCCCAGTTGGCTTTTTGTTTTTCAGGAATTGCCAAGCTGATCCAAAAATT 673
                               i  v      ---- v   i     v           v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT----TGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_80360954_8    674 TGTATGAGAATTCAAGGGACACAGAAGAGCCAAA-CAATCTTGAAAAAGA 722
                         ii    ii   v        v     v       -               
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_80360954_8    723 A---CAAAGACAGAGAATTGTCACTTCTCAATTTAGAAACGTGAGAAAAA 769
                          ---     vii   i i vv      i      vi    v ivv v   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_80360954_8    770 TCTACAGTAATCAAGACACTGTAATACTGTGGTACTGGCACAAGTATAGA 819
                         v                 --  ------            i   v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACA--GT------GTGGTACTGGCATAAGGATAGA 288

  chr1_80360954_8    820 CAGCTAA--CAATGGAGTAGAATGTTAAAGTCAGGAAATAAATCTTTACA 867
                           vv  i--       i      - v i    vi        i iv    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACA 337

  chr1_80360954_8    868 TTTATAGTTAATTGATTTTGAACAATGGTACCAAGAAAATAAAATGGGGC 917
                              i  i          vi    v   i      vv  vv       v
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_80360954_8    918 A-TAATAAT--TTTCAACAAACAATGCTGGGACAACTGGATACCCAAAAG 964
                          -v    i --          iii                  ?   v v 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_80360954_8    965 AAAAAAGAAAGCAAGAGAGAGCGAGACTTAG-CCATTTCTTCATACCATA 1013
                         v    -   v -   ------------  i -  vi v i   i      
  L1M4_orf2#LINE/    438 CAAAA-GAATG-AAG------------TTGGACCCCTACCTCACACCATA 473

  chr1_80360954_8   1014 CATCAAAATTATCTTAAAATTAATCAGAGAGCTAAATATAAGAGC-AAAA 1062
                         i iv       v  i     vi    ?   v      i       -    
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_80360954_8   1063 -------ACTCT------AAAACATAGGAGTAAATCTTTATAAATTTGAA 1099
                         -------     ------          ?         ii i vi   ii
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_80360954_8   1100 TTAGGTGATAATTTCTTAGATACAGCACCAAAAGTGCAAGCAACAAAAGA 1149
                              ii  ii           iii         ii              
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_80360954_8   1150 AAAAA-AAATTCAACAAAAAACAACAAAAGAAAA--AAATTTCTTTCAAT 1196
                              - i  ---------------------   --ii i   v -   v
  L1M4_orf2#LINE/    624 AAAAATAGAT---------------------AAATTGGACTTCAT-CAAA 651

  chr1_80360954_8   1197 ATTGAAAACTTT-ATTCTGTAAATGATATCATCAAGAAAGGGAAAAGACA 1245
                            i        -i v  vi   v  i ii          v         
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_80360954_8   1246 ACCCCCTGCAGGAAAGAAAATGTTTACAAATCATATTATCTGATAAGAGA 1295
                             v v v v ii       i   i          -          i  
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGGGA 750

  chr1_80360954_8   1296 CTTTTATCCAGAATGTACAAAGAATCCTCCCAACTCAAAAATATAAAAAC 1345
                            v          i  i      ii  iv        v    v   i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_80360954_8   1346 A-----CCAAATTTAAAAATGGAAGAAGTATTTGAATAGATATTTTTCCA 1390
                          -----  v    ?        ivi   v           i    i    
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_80360954_8   1391 AACAATGTATACAAATGGCCAATAA-TACATGAAAAGATTCTCAACATCA 1439
                           v  vi                  -i            v          
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_80360954_8   1440 TTAATCAT 1447
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.40 (98 / 70)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.40 (85 / 25)  


2320 27.19 4.66 3.88  chr1_80441309_80443209      529  1429 (472)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80441309_8    529 TAGAAAAATATTTTATGTTCATGGATAGAAAGAATCAATGTTGAAAAAAA 578
                          i    i    iii            v i    v i   i   vv  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr1_80441309_8    579 ATGGCCATACTGCCCAAAGCAATCCATAGATTCAATGCTATTTCCTTCAA 628
                         -    v     v      vii   i i        i  v  ii iv    
  L1M4_orf2#LINE/     50 -TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_80441309_8    629 ACTACCAA-TGTTATTTTTCACA-AAATTAGAAAAAAGCT-ATTTTAAAG 675
                          v v   i-  ii-     ii  -     i--- v     -  ii    i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAA 144

  chr1_80441309_8    676 TGTATATGGAACCAAAAAAATAGCCTGAAGAGCCATGGAAATCCTGAGCA 725
                          vi        viiv  iii- v  v   v     viiv    i   iv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_80441309_8    726 AAAAGAACAAAGCCAGAGGCATCACATTACCTGACTTCAAACTATACTAT 775
                          i          iii    vv     i v  ii i      viv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_80441309_8    776 AAAGTTACAGAAACCAAAATAGCATGATACTGGTAAAAAATAAAAAAAAA 825
                             i     v  i   i i  ii  i      i ---------------
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA--------------- 278

  chr1_80441309_8    826 TTTAAAAACTGAACACATAGACCAATGAAACTAAATGCAGAGCCTAGGAA 875
                         --   ii - ii   i     i     i  ivi   vv    i i  i  
  L1M4_orf2#LINE/    279 --TAAGGA-TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_80441309_8    876 TAAAGCCACACACCTACAGCCATCTGACCTTCAACAAAGTTGACGAAAAT 925
                             v   i   ii  ii i  vi   ii   i    i v  v i i vi
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_80441309_8    926 AAGCAATGGGAAAAGGACTCCCTATTCAATAAATGGTGCTGGGATAGTTG 975
                          vv       i    i ivvi  v     i              i ii  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_80441309_8    976 GCTAGCCATATGCAGAAGAATGAAAATAGACCCCTATATGTTACCATATA 1025
                          v  ?   i     i         iv i        iv vvi        
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_80441309_8   1026 CAAAAATTAACAAAAGATAGATTAAAGATTTAAATGTAAGACTTCAAACG 1075
                                    vv  i  i   i ?   ii           vi v    v
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_80441309_8   1076 GTAAGAATTGTAGAAGAAAACCTAAGAAACACCATCCTGTACGTCAGTCT 1125
                         i   i v iv           v  i ?ivv --   i ---   v -i  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAA--ATCTT---CGTGA-CCT 569

  chr1_80441309_8   1126 TGGGA-AAGAAATTATTACTAAGTTCT-----TAAAAGCAATTGCCACAA 1169
                             v- i v   vi  v  v  v v -----i       vvv  v    
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_80441309_8   1170 TA-AAAAAATTGACAAATGGGACCTAATTAAACTAAAGAGTTTCTGCACA 1218
                         v -       v  i    v    i v  i   v v  i ii  i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_80441309_8   1219 GCAAAATA-ACTGTTAATACAATGAA----CAGCCTACAGAATAGGAGAA 1263
                         v    iv -   i i  v v i    ----  i  i       i      
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_80441309_8   1264 AATATTCGCAAACAACACCTCTGACAAAGGTCTCATATCCAGAATCTGTA 1313
                               i     iv i iv     i  i  v  ii          v i  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_80441309_8   1314 AGGAACTT----AACCCAATAA-------GCA----------TTAAAAAA 1342
                          i     i----   i      -------i  ----------  ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_80441309_8   1343 TGGGCAAAAGACATGAACATATGCTTCTC-AAAGTA---ACACAAACAGC 1388
                                 i  iv    i v iii     -    v --- i     ii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_80441309_8   1389 CAACAAATATATATTTTAAAA--CGTTCCACATCACTAATTGT 1429
                            i  ii i  i----    --i i  v      ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATG----AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (155 / 86)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.21 (77 / 24)  


2786 28.59 0.99 0.77  chr1_80511026_80515619     3196  4101 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80511026_8   3196 TGGAAAACCACTCCATGCTCATGGCTAGGAAAAATCAATATTGTGAAAAT 3245
                               ivi ii     i      v v    i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80511026_8   3246 GGCTACACTGCCCAAAGTAATT----GATTCAATGCTATCCCTGTCAAGT 3291
                            v i   v      v i  i----       i  v      i    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80511026_8   3292 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAC 3340
                          v   iivi i  i  ii     v v  v  i-  - iii    v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_80511026_8   3341 ATCAAACCAAAAAAGAGCCCGTATAGCCAAGGCAATCCTAAGCAAAAAGA 3390
                           vi  viiv  ii  v  v v        ii     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_80511026_8   3391 ATAAAGCTGGAAGCATCAGGCTACCTGACTTCAAACTATACTACAAGCCT 3440
                          i    i    i vv   vi  v  ii i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_80511026_8   3441 ACAGTAACCAAAACAGCATGGTAATGGTAACAAAACAGATATATAGACCA 3490
                                i   i    ii     v   i vv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_80511026_8   3491 ATGGAACAGAGCGGAGGCCTCAGAAATAACTCCACACATCTACAACCATC 3540
                               i   iiv   ivii         vi   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_80511026_8   3541 TGATCTTTGACAAACCTGAAAAAAAAAACGAGAAATGGGGAAAGGATTCC 3590
                             i  i     ivv  vv  i v--- ivvv           i  vvi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAAAGAATAGT 396

  chr1_80511026_8   3591 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATACCGAAAACA 3640
                           v  i  i        i     v      v  ?   i  i vi  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_80511026_8   3641 GAAACTGGACCCCTTCTTTACACCTTACACAAAAATTAACTCAAGATGGA 3690
                            ii         v i i     v  i                i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_80511026_8   3691 TTAAAGTCTTAAACATAAGACCTAAAATCATAAAAACCCTAGAAGAAAAC 3740
                          i ?  v i    ii     v      ii      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_80511026_8   3741 CTAG---TCAATACCATTCAGTACATAGGCATGGGCAAAGCCTTCATGAC 3787
                         v   --- v   -- -   ivv  v v  vv i     v vi   v iiv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_80511026_8   3788 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACATATTGGATC 3837
                           vi            vvi          vv     v  i v      ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_80511026_8   3838 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 3887
                          v  i   v v  i i   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_80511026_8   3888 CCAGG-CAACCTACAAAATGGGAGAAAATGTCTGCAATCTACCCATCTGA 3936
                         vv i -     i   i             i i     vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_80511026_8   3937 CAAAAGGCTAATAGCCAGAATCTACAAAGAACATAAACAAATTTACAAGA 3986
                         i  ii i  vi  v       v  i       vivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_80511026_8   3987 ATAAAACAAACAAGCCCATCAAAAAGTGGGCAAAATATATGAACAGACAC 4036
                          v  i     i  v  v  i?    i        iv  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_80511026_8   4037 TTCTCAAAAGAAGACATTTATAAGGCCAACAAACATATGAAAAAAAGCTC 4086
                              v        i  vi v v      i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_80511026_8   4087 ATCATCACTGGTCAT 4101
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (147 / 109)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


1955 27.42 1.11 0.16  chr1_80521009_80522631.rev      502  1132 (491)    L1M4_orf2#LINE/L1      272   908 (0)  

  chr1_80521009_8    502 ACTGGTACCAAAACAGACATATAGACCAATGGAACAGAAAAGAGACCTTA 551
                              i iv ii i           i        i    vv    viii 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_80521009_8    552 AAAATAACACCACACATCTA----CATCTGATCTTCAACAAATCTGACAA 597
                         i      vv   i    i  ----  vi    i   i    ivv  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_80521009_8    598 AAACAAGCAATGGGGAAAGGATCTCCTATTCAATCAATGGTGCTGGGAAA 647
                         i v  vv            i  vvi  v     iv             v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_80521009_8    648 ACTGGCTAGCCATATGCAGAAAACAGAAACTGGACCCCTTCCTTATACCA 697
                              v  ?   i     i  i vv   ii         v   i i    
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_80521009_8    698 CAGACAAAAATTAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCAA 747
                         i v                i      i ?    i         i v i  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_80521009_8    748 AACCATAAAAACCTTAGAAGAAAACCTAGGCAATACTATTCAAGATACAA 797
                            i      vi             v    ?ivv v v   iv  ivivi
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_80521009_8    798 GCATAGGCAAAGTCTTCAT-GATGAAAACGCCAAAAGCAATTGCAAGAAA 846
                          vv       v vi   v -   - vi  i         vvv    v   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAA 620

  chr1_80521009_8    847 AGCCAAAATTGACAAATGGAATCTAATTAAACTAAAGAGCTTCTACACAG 896
                           vv     v  i    v i ii v  i   v v  i i   i iii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_80521009_8    897 TAAAATAAACTATCATCAGAGTAAACAGATAAGCTACAGAATGGAAGAAA 946
                         i   iv v       vv i   i  v   i  v i         i     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_80521009_8    947 ATTTTCGCAATCTACCCATCTGATAAAGGCCTAATATCCAGAATCTACAA 996
                           v  i    vii ivi         i  v  vi          v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_80521009_8    997 AGAACGTAAACAAATTTACAAGAAAAAAA-AAATGACCCCATCCAAAAGT 1045
                              vivv    v iv i  v     i -    i    v  i?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_80521009_8   1046 GGGCAAAGGATATGAGCTGACACTTCTCAAAAGAAAACATTTACGCAGCC 1095
                                    v   iiv    i     v      i i  vi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_80521009_8   1096 AACCAACATACGAAAAAA-GCTCACCATCACTGATCAT 1132
                           iv i  i i     i -     v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (91 / 78)
Gap_init rate = 0.01 (5 / 637), avg. gap size = 1.60 (8 / 5)  


3224 23.13 1.48 5.60  chr1_80566197_80568336      703  1649 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80566197_8    703 TGAAAAGACCTCCCATATTTATGGACTGGAGGAATTAATATTGTCAAAAT 752
                           i     iv      i  i     i    i  v          i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80566197_8    753 GATTATACTACTAAAACAGTTGTACAGATTCAGTGCTATCCCTACTGAAA 802
                          iiv     v iv   iv v v          ii  v       iii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80566197_8    803 TACCAAC---ATTTTCCACAGAAATAGAGAAACTTATACTAAAATTTCTA 849
                          v   i ---v    iii       v  v  i  v  v        iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_80566197_8    850 TGGAACTAAAATTTATATGGAACCAAAAAAGACCCAGAGTAGCCAAAATA 899
                              -----------   ----   ii--        i         i 
  L1M4_orf2#LINE/    151 TGGAA-----------ATG----CAAGG--GACCCAGAATAGCCAAAACA 183

  chr1_80566197_8    900 ATCCTGAGCAAAAAGAGCAAAGCTGGAGACATCACACTAGTTGTCTTCCA 949
                            i   iv  i    i     i     ivv       vviiivi   v 
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_80566197_8    950 AATACACTACAAAGCTATAGTAAACAAAACAGCATGGTACTGGCATAAAA 999
                           ivi            i     v   i    ii              ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_80566197_8   1000 ACAGACACATAGACCAATGGAGCAGAATAGAGAACCCAGAAACAAATCCA 1049
                          i     i     i       ii     v    ii       i   i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_80566197_8   1050 CATATTTACAGTCAACTAATTTTCATCAAAGAAGCCAAGAACATACATTG 1099
                         i i     ii     i i      iv   i iv       v   v  v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_80566197_8   1100 AGAAAACAATAGTCTCTTCAATAAATAGTGTTGGAAAAACTCAATATCTG 1149
                         i i   v        i     i    i   i   i v    vi   ? ii
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_80566197_8   1150 TATGCAGA----TGAAACTAGACCCCTATCTCTCACCAAAATCACCCCCT 1195
                         i     i ----    ii i        i   v     ------------
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA------------ 471

  chr1_80566197_8   1196 CTCCCTTACACCCCTATCTCTCATACAAAAATAAACTCAAGATGAATTAA 1245
                         ---------------------i          v       i   i  i ?
  L1M4_orf2#LINE/    472 ---------------------TATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_80566197_8   1246 AGACTTGAATGTGAGACCTGAAACCGTGAAAGTATTGGAAGAAAACATAA 1295
                             i i     i   v  i    ii i   v v  i            i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_80566197_8   1296 GGG-AAATGTTTCAGGATATTGGTCT-GACAAAAGATTTATGGATAAAAT 1343
                          ? -    -i   iv  iv    vi - i   vi v  iv i    vi i
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_80566197_8   1344 CTCAAAAGCACAGACAACAAAAGCAAATATAGACAAATGAGATTCTATCA 1393
                         vi          ii         v   v     i    vi  i ii    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_80566197_8   1394 AGCTAAACAGCTTCTGCACAGCAAAGAA-ATTCATCAAAATAGTGAAGAG 1442
                          iv v  v i   i  ii vv     i - i -     i v      i  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGAAAGTGAAAAG 698

  chr1_80566197_8   1443 ACAATTTGCAGAATGGGAGAAAATGTATGTAAATTATTTATCTGATAAGG 1492
                             iiii                i v  i    i  v            
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_80566197_8   1493 GAAAAAATTCTAGAATATATAAGGAACTCCAACAAATCAAGTGCGAAAAA 1542
                           vvvivv  i           i      iv    v    - ivv     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA-TAATAAAAA 797

  chr1_80566197_8   1543 AACAAATAATCTGATTAGCAAGTGGGCAAATGATCT-AACAGACATTTCT 1591
                         i        i ii   ?iv  i        v   i -  i          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_80566197_8   1592 CAAAAGAAGATATACAAAAGGCCAA---GCATATGAAGAAATGCTCAAAA 1638
                          v                v      ---   i     i i        v 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_80566197_8   1639 TAATTAATTAT 1649
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.95 (142 / 73)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.79 (67 / 14)  


3186 27.20 0.55 0.55  chr1_80572307_80575948.rev     2244  3151 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80572307_8   2244 TGGAAGAACATTCCATGCTCATGGTTAGGAAGAATCAATATTGTGAAAAT 2293
                              ii i  i     i      v v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80572307_8   2294 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2343
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80572307_8   2344 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 2392
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_80572307_8   2393 ATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAGA 2442
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_80572307_8   2443 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 2492
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_80572307_8   2493 ACAGAAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 2542
                             v  i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_80572307_8   2543 ATAGAACGGAAC--AGAGCCCTCAGAAATAACGCCACCTATCTACAACTA 2590
                           i   ii   i--    i  --        vv   ivi  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_80572307_8   2591 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 2640
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_80572307_8   2641 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 2690
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_80572307_8   2691 AAACTGGATCCCTTCCTTACACCTTCTACAAAAATCAATTCAAGATGGAT 2740
                           ii    i    v   i     v v         i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_80572307_8   2741 TAAAGACTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAACC 2790
                         i ?    i    i  v i v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_80572307_8   2791 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 2840
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_80572307_8   2841 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 2890
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_80572307_8   2891 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 2940
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_80572307_8   2941 GGCAACTCACAAAATGGGAGAAAATTTTCACAAACTATTCATCTGACAAA 2990
                          i    i    i             v  ii    ii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_80572307_8   2991 GGGCTAATATCAAGAATCTACAATGAACTCAAACAAATTTACGAGAAAAA 3040
                           i  vi    v     v  i  v      vv    v iv ii v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_80572307_8   3041 AATAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCT 3090
                         i i   i     v  i?    i     i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_80572307_8   3091 CAAAAGAAGACATTTATGAA--GCCAAAAAACACATGAAAAAATGCTCAC 3138
                          v        i  -- ii  --     v  i          i       v
  L1M4_orf2#LINE/    848 CCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_80572307_8   3139 CATCACTGGCCAT 3151
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3663 19.08 2.24 5.44  chr1_80727524_80730314     1367  2304 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80727524_8   1367 TGAAAAGACATTTTTGAGTTCATGAATTGGAAGACTTGTTATTATGATGA 1416
                           i     i  iii-iv       i            iv    i v v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_80727524_8   1417 TGCCAATATTCCCCAAATTTATCTACAGATTTAATGCAATCTCTATAAAT 1466
                           v     i          v           i  i      i    v  v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_80727524_8   1467 ATCCCAACTGCCATTTT-GCAGACATTGACAACCTGATTCCAACATTCAT 1515
                               i     v    -     v        v     i i  v      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_80727524_8   1516 ATGAAAAGGCAAGAGATCCAGAATAGTCAAAACTGTCTTGGAGAAAAAAA 1565
                            i   v     i  i         i      vi     ---     i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG---AAAAAGA 196

  chr1_80727524_8   1566 AATAAATAAATAAAACAAAACAAAGTTGCAGGATTCACACTTTCGAAATT 1615
                          i----------------          v    i        i v  v  
  L1M4_orf2#LINE/    197 AG----------------AACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_80727524_8   1616 AAATTTGTAATAACTCTTGAATTCACATTTCAAAATT----TAATGAAGA 1661
                         v  ----------------  i i  -- v    ii ----    v    
  L1M4_orf2#LINE/    231 CAA----------------AACTTAC--TACAAAGCTACAGTAATCAAGA 262

  chr1_80727524_8   1662 CATTGTGGTACTGGCATAAGAAGAGGCATATATAACAATGAAGTAGAACT 1711
                           v                 i v  i      v v     i i     i 
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_80727524_8   1712 GAACATTCAGAAATAAATCTTTACATTTATGGTGAAAGAATTTTCAATAA 1761
                           ivi i          i iv            v  vvi      i i  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_80727524_8   1762 GGGTGCCA---TAATTCAATAAGAAAAAAAATAGTCTTTCCAATAAATGA 1808
                                 ---iv       ii i   i  -        i   i     i
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTTTTCAACAAATGG 411

  chr1_80727524_8   1809 -GTTGGAGACAACCGAATATTCACATACAAAAGAATGAAATAGGAACCTT 1857
                         - i   -      i i   ?i     i            i v   v  i 
  L1M4_orf2#LINE/    412 TGCTGG-GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_80727524_8   1858 ACCTCACACTATATATAAAGATTTACTCAAAATATACCAACTACCTAAAT 1907
                                  i     i   i   v         iv i  ?vv        
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_80727524_8   1908 GAAAGAGGCAAAACTGTAAAACTTTTATTAGAAAACACAGTCATAAATCT 1957
                          v     vi      i       i   vv        i  v?i       
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_80727524_8   1958 CAGTGACTTTAGATTAAGCAACGGTTTCTCAGATATGACACCAAAAGCAC 2007
                         iv     i  i i   i    i       i                    
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_80727524_8   2008 ATACAACAAAAAGAAAAATAAGGAATAAATTGAACGTGGTCAAAATTAAA 2057
                          vi        ii       i---        i  v vi           
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAG---ATAAATTGGACTTCATCAAAATTAAA 657

  chr1_80727524_8   2058 G-CTGTTGT-----AGAGAATACTATCAAGAAAAAGATATGGAAAGACAT 2101
                         i-  v    ----- i  i i            i-----  i       v
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAG-----TGAAAAGACAA 702

  chr1_80727524_8   2102 CTCACAGAATGGAATAAAATATTTGTAAATATTAT-TCTGATAAGGTTGT 2150
                          i          i v          i    vv   -          vvv 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_80727524_8   2151 AGTATTGAGATTGTATATGAAGAACTGTTACAATTCAACAACAAAAAAGA 2200
                         v    iv   --i     i       v      i    i  i     -  
  L1M4_orf2#LINE/    753 TGTATCCAGA--ATATATAAAGAACTCTTACAACTCAATAATAAAAA-GA 799

  chr1_80727524_8   2201 CAAGTAATCAAATTTAAAA-TGGGTGAGAAATTTAAACAGACATTTTTCC 2249
                            i   i v    ?    -    ii iii    i  i        i   
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_80727524_8   2250 AAATAAGATA--CAAAGAGCCAA--AGACCCCGGAACGATGTTCACTATA 2295
                            v      --    vi     --  vv vi i  v    i   vi  v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_80727524_8   2296 AATCATCTT 2304
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.69 (110 / 65)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.43 (72 / 21)  


 973 29.10 8.80 2.54  chr1_80768742_80770308.rev      499  1089 (478)    L1M4_orf2#LINE/L1      281   908 (0)  

  chr1_80768742_8    499 AAAATAGAAAAATAGATCACTAGAACA-AATGGAGAATCCAAAAACAGAT 547
                          ii     v v        v i   i -   v    i    i   i i i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_80768742_8    548 ---TATATGTA--GTCACCTAATTTGAGAGAAA------AAGACTATTCC 586
                         ---  i  v  --    vi i    vv  v  i------     i    -
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC- 379

  chr1_80768742_8    587 ACTGAAGTAGGGAAAATAATGATCTTCTCAAGGAATTGTACATGATA-AA 635
                         ----- i i      i-   ii    i    vi   v  i -  iv -  
  L1M4_orf2#LINE/    380 -----AATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGC-TGGGACAA 422

  chr1_80768742_8    636 TTAGATATCCATATG-----GAATC--TTTTTACCCCTACCTCATACCAT 678
                         i i    ?   i   -----    v--v  vv            i     
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_80768742_8    679 ACACAAAAATCAATTCCAGATATATTTCAGATGCAAATATGCAAAGTAAA 728
                          i        i  i  v i  iv  iv?   ivi    i ivi iv    
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_80768742_8    729 AC----AAAGTTGTAGAAGGAAACACTGAAAAACATCTTTGTGA---TAG 771
                           ----   v iv      i     iv i?iv v     i    --- i 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_80768742_8    772 GAAAAGCAAATATTTTTTAATCATGACATGAGATTGATAA---ATATGAC 818
                          vv i    vvi   i   ivi      iv i vvv i  --- i vi v
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_80768742_8    819 TAAAAATTGGTAAATGAGACTGCTTTAAAATTGGAAACCTCTGTTTATTA 868
                         v      v i     vi    v v i      ii    i i   viv i 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_80768742_8    869 AAGCACATCCTTGCAAGAA--TGAAAAGGCAATTCACTGAATATGAGAAA 916
                            v   --  vv      --       i   ii   v    iv      
  L1M4_orf2#LINE/    673 AAGGACA--CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_80768742_8    917 ACATTATCAATGCACATGTACAACAAAAGAC--AAAT----AATGTACTA 960
                          i   vv   vv  i  i vii i  ii   --iv  ----   i  iv 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_80768742_8    961 A-AACTACTATGAATCAATAAGCTAAAATCATCCAACACAATCT--TTTA 1007
                          -    vi  ii v       --     -- vv   - i  i i--  ? 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAA--TAAAA--AGACAA-ATAACCCAATTWA 815

  chr1_80768742_8   1008 A----GTGTAAAATATTTGAATATACACTTCACAAAAGAGGTTAT----- 1048
                          ---- v i   iv         v   i   v v     i v   -----
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_80768742_8   1049 --GCCAATAAATATCTGAAAAGCGACCTCACATTAATCATCTT 1089
                         --        ii iv       vvi iiv    i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (97 / 71)
Gap_init rate = 0.04 (24 / 628), avg. gap size = 2.79 (67 / 24)  


2900 27.20 1.56 0.33  chr1_80772335_80780263     3904  4800 (3129)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80772335_8   3904 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3953
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80772335_8   3954 GAACATACTTCCAAAAGCAATCTACAAATTCAATGCAATTATCATCAAAA 4003
                          ivv     i  v   vii       i      i     ivii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80772335_8   4004 TACCA----CCATTTTTCACAGAATTAGAAAAAATTATCCTACAATTCAT 4049
                          v   ----  -     ii     v v  v  iv v      v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_80772335_8   4050 ATGGAACCAAAAGAGAACCCACATAGCCAAAGCAACACTAAGCAAAAAGA 4099
                               viiv   i  v  viv         i   ivi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_80772335_8   4100 GCAAATCTGGAAGCATCACATTACCTGACTTCAAACTATACTATAAGGCC 4149
                         i    vi    i vv     i v  ii i      viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_80772335_8   4150 ATAATCACCCAAATAGCATAGTACTGATATAAAAATAGGCACATAGACCA 4199
                          i i v i v i i  ii i      ii    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_80772335_8   4200 ATGGAACAGAAC----ACTT---AAATAAAGCCAAATATTTACTGCCAAC 4242
                               i    i---- v i---       v   v i     iv i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_80772335_8   4243 TGAACTTCAACAAAGCAAACAAAAGCATAAAGTGGGGAAAGGACACCCTA 4292
                            vi   i    i vviv   i v   vv i         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_80772335_8   4293 TTCAACAAATGGTACTGGGATAATTGGCAAGCCACATGTTGAAAAATAAA 4342
                                      i      i  i   vv ?       ivi  i   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_80772335_8   4343 ACTGGATGTTCATCTCTCACCTTATATAAAAATCAACTCAAGATTGATAA 4392
                         ii    iviii i   v    v    i      i       i  v   v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_80772335_8   4393 AAGACTTAAGTCTAAGACCTAAAACCATAAAAATTCTATAAGATAATATC 4442
                         ?    i   i v     v       i      v ii  v    v  i  v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_80772335_8   4443 GGAAAACACTTTTGTAGTCATTGGCTTAGGTAAAGACTTCATGACCAAGA 4492
                           ?iv v ii  i  iii -    v     i  v ii   v iivi v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_80772335_8   4493 ACCTAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGACTTAACT 4542
                         vv i       v v         iv   i   i   i  v      v ii
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_80772335_8   4543 AAACTAAAAAGCTTCTGCACAGCAAAAGAAAC-A-CAGCAGAGTAAACAG 4590
                            v v    i   i  ii vv    i  v  - -  iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_80772335_8   4591 ACAACCCACAGAATGGGAGAAAATCTTCACAATCTATACATCCAACAAAG 4640
                                                 v  ii   vii   i   ii i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_80772335_8   4641 GACAAATATCCAGAATCTACAACAAACTCAAACAAATCAGCAAGAAAAAA 4690
                            vvi          v  i  vi     vv    v   ii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_80772335_8   4691 TACAAACAATCCCATAAAAAAGTGGGCTAAGGACATGAATAGACAATTCT 4740
                         -     i  i  v  v?    i     v     iv          v    
  L1M4_orf2#LINE/    799 -ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_80772335_8   4741 C-AAAGAAGATATACAAACAGCCAACAAACACATGGAAAAACGCTCAACA 4789
                          -                ii     i  i      i   i i        
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_80772335_8   4790 TCACTAATAAT 4800
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  

2810 23.67 2.39 1.20  chr1_80772335_80780263     6326  7077 (852)    L1M4_orf2#LINE/L1      111   871 (37)  

  chr1_80772335_8   6326 CTGTTTTATAGAAATATTAAAAAGTT----CTAAACTTTACATAGAA-CA 6370
                           v    ii      -- i v   i ----     v  i i  i   -ii
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr1_80772335_8   6371 CAAAGGACTCTGAATAGACAAAACGATCTTGAGAAAGAAAAAAAAAGCTG 6420
                            i    i v      v      i       i      i  v    i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_80772335_8   6421 AATTATTCACACTTCCTGATTTCCAAATATGTCAGAAAGCTACAGTAATC 6470
                         i vv i          ii     v   iv iii v               
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_80772335_8   6471 AAAACAGTATGGTACTGGCATAAAGGCAAGCATATAGACCAATGGAGCAG 6520
                           i     i              i ii ii        i       ii  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_80772335_8   6521 AA--GAAAGTCCAAAAATAAACCCATGCATAAATGGTCAATTGATCTTCA 6568
                           --  i      i            i   vv             i   i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_80772335_8   6569 ACAGGTTTGCCAAAAATACACAGTAGGAAAAGGATTGTCTCTTCAAAAAA 6618
                            i vv      i vi iv  i i  i    i  v    i     v   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_80772335_8   6619 TTGTGTTGAAA-AACTGGATGTACAAATGCAAAGAAATTAAATAGAATTA 6667
                          v   i  ii -        i?v  v       ii   v  i v i iiv
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_80772335_8   6668 TTATCTTACACTATAT-TAAAAATTAACTCAAAATGAATTAAATACTCAA 6716
                         i  i  i    i    -i                  i  i ? v  ii  
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_80772335_8   6717 ACCTAATACCTGAAACTGTAGAACT---AAAAGAAAATATATGGGAAAAG 6763
                          iv   v v  i     i  i    --- i       i   v ? v   v
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_80772335_8   6764 TTTCATTTAA--TTGTTCTTGGCAATGATTTCCTGAATGTGACACCAAAA 6811
                         i   i --i --   vvi v       i    i ii  i           
  L1M4_orf2#LINE/    559 CTTCGT--GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_80772335_8   6812 GTAAAGGCAACACAATTAAATATAAACAAGTGCAACTATATTTAA-CTAA 6860
                          i v i      v  vv   v   i i  i vvi   vi  iv  -i   
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_80772335_8   6861 AAATCTTCTTTATGTACAGCAAGGAAAACAATCATGAGAGTTAAAAGGCA 6910
                            ----    -   i vv   i i v  v    v  i   v     i  
  L1M4_orf2#LINE/    657 AAA----CTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_80772335_8   6911 ACCTACAGAATGGGA-AAAATATTTGCAGACCACATATCTGATAAAGGAT 6959
                            i           -            i i  i           i   i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_80772335_8   6960 TAATATCCAAAATATATAAGAAACTCTTACAACTCAATAGCAAAAA--CA 7007
                          vi      i         ii                  ii     --  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_80772335_8   7008 AATAATCAAATTAACAAATGAACATAGAACTTCAAAAGAGTTTTCTTCAA 7057
                              i v    ? v     ii  v  i i  v  v   vv     i   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_80772335_8   7058 AGACAACATACAAATGGCCA 7077
                            vi i             
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.95 (115 / 59)
Gap_init rate = 0.02 (14 / 761), avg. gap size = 1.93 (27 / 14)  


2437 27.02 4.04 2.24  chr1_80793422_80796188     1383  2274 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80793422_8   1383 TGGAAAAACAACCCATGTTCATGGACTGGAAGAATCAATATCATTATAAT 1432
                               i i v              i       v i     ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80793422_8   1433 GACCACACTAACCAAAGCAATCTACAAATTCAACAGAATTTCTATCAGTG 1482
                          i v i   vv     vii       i       iv   ii      ivi
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80793422_8   1483 TGCCAGCATCATTCTTCACA-AAATT----AGTTTATATAGATCTAAAGG 1527
                          v     vv v  i  ii  -     ----  i v  -----i     iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-----CCTAAAAT 145

  chr1_80793422_8   1528 TCTTAAGGAATAATAATAATAAAAAAGAGCCTGAATAGTGAAAGAAAACC 1577
                           v  v    --------  iv  ii  v  v      iv   iv  v i
  L1M4_orf2#LINE/    146 TCATATGGAA--------ATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_80793422_8   1578 TAAGCAAAAAGAGTAAAACTGGAGACATCATCTTACCTGACTTCAAATTA 1627
                          i iv  i    ii   ii     ivv   ivi v  ii i      viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_80793422_8   1628 CACTACAAA-TTATAGCAA------------GGTACTGGTACAAATATAT 1664
                         i        -i  i  i  ------------        i i  iv   v
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_80793422_8   1665 ATACATAGATCAATGGAACAGAATGAAGAACCAATAAATAAAGCCATATA 1714
                          i i              i     vi   ii v v       v     i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_80793422_8   1715 CCTAAAATCAACTGATCTTTCATAAAGTCAGTAAAATTAAACAATGGGGA 1764
                         ii  vii    i    i  iv i  i viivi  i ii vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_80793422_8   1765 AAGGACACTTTATACAATAAATGATGTTTGGAAAATTGGCTAGCCATACG 1814
                            i i v i v v   i     i  i v   v  i   v  ?   i i 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_80793422_8   1815 TAGAAGACTAAAACTGGATTTCTATTTTTCATTATATACAAAAATTAGCC 1864
                         i i    v i  ii    iii   ii iv  ii              i i
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_80793422_8   1865 CAAGATGGATTAGAGTCCCAAATGTAATACCTGAAATCATAAAAATATTA 1914
                            i      i ?  v  i        v v  i   ii      v v   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_80793422_8   1915 GAAGAAAACCTAGGAAAACCTCTTC-TGGTTATTGGCCTAGGCAAAGAGT 1963
                                  v    ?iv vv     -  iii-    vi       v iv 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTT 586

  chr1_80793422_8   1964 TTATAGCTAAGACACAAAAAGCAAATGCAACAAAACCAAATATAGACAAA 2013
                          iv   v  v     v       v v         vv   v     i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_80793422_8   2014 G-GGACTTAATTAACCTAAAAAGTTTTTGAA----GAAGAAAACAAATAA 2058
                         v-      v  i  vv v    ii     vi----i   i v  ---  -
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC---TA- 682

  chr1_80793422_8   2059 TCAATAAAGTAAA----TAACCTACAAAATGGGAGAAAAGATTTTCAATT 2104
                             v     i  ----i    i   i            v    v   v 
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_80793422_8   2105 TATGTCTCTGACAAAGGACTAATATTTAGAATCTACAATGAACTCAAATA 2154
                         i  i v     i  i     vi   ii     v  i  v      vv i 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_80793422_8   2155 ACT-AACAAGAAAAAAACATACATCCTG-TTAAAAAGTGGGAAAAGGACA 2202
                            -  i  v     i   v i v  ii-  ?    i    v      iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_80793422_8   2203 T--ATA-ACATAATTCTCAAAAGAAGTTACACAAGTGGACAA-AA--ACA 2246
                          --   -    --     v       v  i    i   v   -  --   
  L1M4_orf2#LINE/    833 TGAATAGACAT--TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_80793422_8   2247 TGAAAAAATGCCCAATATCACTAATCAT 2274
                               i    i   i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.80 (56 / 20)  


2346 25.62 5.51 3.48  chr1_80803451_80806313.rev     1483  2372 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80803451_8   1483 TGGCAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTTAAAAT 1532
                            v  i i  i     i        v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80803451_8   1533 GGCCATACTTACCAGAGCAACTTACAGATTCAATGCTATTTCTATCAAAC 1582
                            v     iv   i vii ii           i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80803451_8   1583 TACCAA-TGTTATTTTT-CACAGATTTAGAAAAAACT-ACTCTAAAATTT 1629
                          v   i-  iiv     -  v i   ---i v  i  - ii        i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chr1_80803451_8   1630 ATAGAGAACCAAAAAAGAGTCCAAATA---AAGA-AATCTTAAGCAAAAA 1675
                            vi   viiv  ii  vi vi    ---  i -      i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_80803451_8   1676 GAACAAAGCTGGAGGCATCACACTACCCAATTTTAAACTATACTGTAAGA 1725
                                 i      vv       v        i   viv    ii  ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_80803451_8   1726 CTGCAATAACCGAAACAGTATAGTACTGGTACAAATATAGACACAGAGAC 1775
                           i  i   i i i     i i       i i  iv       i v   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_80803451_8   1776 AAATTAAACAGGATAGAAGATCCAGAGAAAAAAGCTTCACACTTAAAACC 1825
                         v   vi  i  i  v  iii      -  v   v ivi   i   viii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGA-AATAAACCCATACATTTATGGTC 346

  chr1_80803451_8   1826 ATCTGATTAAAGTCAACAA---TAACAAG------CAATGGAGAAAGGAC 1866
                          vi     ---v  i    --- iv    ------      i     i i
  L1M4_orf2#LINE/    347 AATTGATT---TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_80803451_8   1867 --TCCTTATTCAATAAATGGTGCTAAGATAA------------GTGCAGA 1902
                         --  i  --    i          ii  i  ------------i    i 
  L1M4_orf2#LINE/    394 AGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_80803451_8   1903 AGATTGAAACCTGGCTCCTACCTTTCACTGTATACAAAAATTAACTCAAG 1952
                            v    iiiv i i       iv   ii                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_80803451_8   1953 ATAGAT-AAAGACTTAAATG-AAGACCTACAACTATAAAAATCCTAGAAG 2000
                           i   - ?    i      -    v   v          v  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_80803451_8   2001 AAAATGTAGA---AAATACCATTCTGGACATCAGCCTTGACAAAAAAAAA 2047
                             ii   i---    -- -   vv   v ii vi v i   -------
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAA------- 581

  chr1_80803451_8   2048 AAAAATAA------AGGTATGACTAAGTCCCCAAAAGCAATTGCAACTGA 2091
                         ----- ii------  i      -- ----         vvv     vi 
  L1M4_orf2#LINE/    582 -----TGGTTTCTTAGATATGAC--A----CCAAAAGCACAAGCAACAAA 620

  chr1_80803451_8   2092 AACAAAAATTGACAAGTGGGATCTGATTAAACTAAAGCACTTCTGCACAG 2141
                          iv      v  i  i v   ii v  i   v v  iv    i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_80803451_8   2142 CAAAAGGAACTATCAACAGAGT-AACAGACAAACTATGGAATGAGTGAAG 2190
                             i iv        v i   -  v      v i ii     i v   i
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_80803451_8   2191 ATATTTTCAAACTATGCATCTAATAAA--ATTTAATATTCAGAATCTGTA 2238
                               v    ii  ii    i    i-- i  i-   i      v i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTG-TATCCAGAATATATA 769

  chr1_80803451_8   2239 AGAAAATTAAACAAGTCAAGAA---AAATGCAAATAAACCTATT-AAAAA 2284
                          ii  v ivv    v    v  ---   vi       v  v   -     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_80803451_8   2285 TGTGCAAAGGACGTGAACAGTCACTTCTC-AAAGAATACAAACTTATGGT 2333
                           v        iv    i  v  i     -      v i v  vv    i
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_80803451_8   2334 CAACAAAAATATAAAATAATGCTCAACATCAGTAGTAAT 2372
                            i  iv i  i   vi             ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (144 / 83)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.86 (80 / 28)  


 209 26.23 0.00 0.00  chr1_80886453_80889880     1628  1688 (1740)  C L1M4_orf2#LINE/L1   (103)   805   745  

C chr1_80886453_8   1688 AAAGAACTCATTTCTAGAATGTATAAAGAACCCTCAATACTCAACAATAT 1639
                           i i   ii v  i     i          i  i vv      i    v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

C chr1_80886453_8   1638 GAAAACAAACA 1628
                         i  i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATA 805

Transitions / transversions = 3.00 (12 / 4)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.00 (0 / 0)  

2322 24.30 5.71 4.82  chr1_80886453_80889880     2047  2939 (489)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_80886453_8   2047 ATATACTGTTTTTATGGGTTAAAAAGACTCTTTATTGTTAAGATGTTAAT 2096
                             v ii v  i    i  ii  -    ivv             vi   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAA-GACTTAATATTGTTAAGATGGCAAT 56

  chr1_80886453_8   2097 -TTCCCC----TAATTTA---ATTATGTGTGATACCAGTGAAAAACCCAG 2138
                         -i     ---- i  i  ---   vvii ii  v  vi v    v     
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_80886453_8   2139 CAGGTTGTTCTTTTTGTTGTTGTTGTTGTTGTTTATGTCAAACTTGACAT 2188
                          ----  iii      iv --------------------   -      -
  L1M4_orf2#LINE/    107 C----TGCCTTTTTTGCAG--------------------AAA-TTGACA- 130

  chr1_80886453_8   2189 CATCTCATGCTAAAGTTTATATGGGAATTCAAATGAACGAGAAAAATCCA 2238
                         - v  v  v     i  i      i   v   iv  v v    v ii v 
  L1M4_orf2#LINE/    131 -AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr1_80886453_8   2239 AACAACTTTGAAAGAGGAATGAACAAAATAGGGGAACTAATACACTCTGA 2288
                              ii      i  i --       i v  i i   v i  vii ii 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAA--GAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_80886453_8   2289 TTTTAAGGCTCATTATAAAGCTAAAATAA--------GTGTAGTACTGGC 2330
                            i  ii  i i  i       v i   --------    i        
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_80886453_8   2331 TTTAG-ACAGATAAATAGAACAATGGTGTAAAAC--AGTGTCCAGAAATA 2377
                         v v  - i   i v     v      vi  i  i--  v           
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_80886453_8   2378 GACCCACATGTATATGG-AAATCCTTTTTGGACACAAGTGCAAAAGAAAT 2426
                         i     i ii v     -v   ivv    v    vii    v  iivv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_80886453_8   2427 TCAGTAGAGAAAGGATAATCATTTCAAAACATATTTCTGCAAATATTGGA 2476
                            i i i     i   i  v      v v  iv v   vi vv i    
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_80886453_8   2477 CATCTATATGTAAAAAGAAGAAAATTGAACTTTGATCACTGCTTTGTAAT 2526
                         i ? i i   i    -   vi  i   i  ------ v  i i i--- i
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAA-GAATGAAGTTGGAC------CCCTACCTC---AC 467

  chr1_80886453_8   2527 ATCATATACAAAACTCAATTCAAAATGGATCATAGATCTAAATGTAAAAC 2576
                          i           v i  i             ?   i          i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_80886453_8   2577 CTAAAACCCTAACACTTTCAGAAAAAAA-AGAGAAAAAAATTT-----AC 2620
                                iv   v   i i    i    - v  i?iv    i -----  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_80886453_8   2621 TTTGAATTATGCACATA-TTTCTTAGATATGTTATCAAAAGTACATTC-- 2667
                         i   ii   v   -  i-             vi i      i   vv --
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCA-ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_80886453_8   2668 CA---GAAAAAA-AGATAAATTAGTGTTCAT-AAAA--AAAAATCACTAT 2710
                           ---       -         i vv     -    --     iivi i 
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_80886453_8   2711 --TTCAAAAGTCACTAGTAAAGAGAATGAAAAGACAAGCCATGGACTGAA 2758
                         --      i v     - v    i i           v   ii  v  ii
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_80886453_8   2759 AGAAAACATTTGCAAATTATGTATCTGATAAAGAACTCATTTCTAGAATA 2808
                               i          i  i          i i   ii v  i      
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_80886453_8   2809 TACTCAAAACTCTCTATG-TTCAACAAGAAAA---CAAACAACGCAAT-- 2852
                           ivv i      -  ii-i    i  v    ---    i   v    --
  L1M4_orf2#LINE/    766 TATAAAGAACTCT-TACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_80886453_8   2853 ATAAATGATTAAAATGTTTGAATAGACCCTTCACCAAAGA---TATACAG 2899
                          v     ivi   ivi           vi   v       ---      i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_80886453_8   2900 ATG---AA-AAGCCCATGAGATGATGCTCAACCTTGTTAATCAT 2939
                            ---  -    v     i v          v ii????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (134 / 80)
Gap_init rate = 0.04 (34 / 901), avg. gap size = 2.76 (94 / 34)  


1713 17.73 0.25 23.49  chr1_80914685_80918576     2221  3399 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_80914685_8   2221 AAAGGTATTCCATGTTCATGGATTGGGCAAATTAATATTGTTAAAATGGC 2270
                             i   i                 ivi v             i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_80914685_8   2271 CATACTACCCAAAGCAATCTTCAGGTCCAATGTAATCCCCTTCAAAACAC 2320
                         v     v      vii    v   i i   i i      iv      iv 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_80914685_8   2321 CAATGACATTCTTCACTGAAATGGAAAAAGAGAATCCTAAAATTTATATG 2370
                           iivi v  i  ii v     v  v  - vvi           i     
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATG 152

  chr1_80914685_8   2371 GAATCACAAAAACCCCAGAATACTCAAAGCCATCCTGAACAAAAAGAACA 2420
                            vii   iiiv         vi    i v   i    v  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_80914685_8   2421 AAACTGAAGGAATAACATTACCTAACTTTAGGTACTATACTATACCTATA 2470
                           ii  i    v v   i v  i  i  i ------ v   -   -  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCA------AAACT-TAC-TACA 244

  chr1_80914685_8   2471 GAGCTATAGTAATCAAAACAGCAAGGTACTGGCATAAAATCATACATATG 2520
                         i     i         i    iiv             iivi v      i
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_80914685_8   2521 GAACAATGGAATAGATTGAAGTATCTTGAAATAATTTCATACATCTACAG 2570
                           v            v vi  vi  iv       vii       i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_80914685_8   2571 TATATTAGTCTGTTCTCATACTGCTAATAAAGACATATCTGAGACTGACT 2620
                          vv   ii i ----  i-------- i  i iii--- ii    i----
  L1M4_orf2#LINE/    345 TCAATTGATTT----TCG--------ACAAGGGTG---CCAAGACC---- 375

  chr1_80914685_8   2621 AATTTATAAGGGAAAGAGGTTTAATGGACTTATAGTTCCACATGGCTGGG 2670
                         -   i vvi        ------  i v   ----   v   --------
  L1M4_orf2#LINE/    376 -ATTCAATGGGGAAAGA------ATAGTCTT----TTCAACA-------- 406

  chr1_80914685_8   2671 AGGCCTCACAATCATGGCCGAAGGTGAAGGAAGAACAAGGAAAGTCTTAC 2720
                         ---------   ----------    vv  i v   v-   v ?i --  
  L1M4_orf2#LINE/    407 ---------AAT----------GGTGCTGGGACAACT-GGATAKCC--AC 434

  chr1_80914685_8   2721 ATAGCATCAGGCAAGAGAGTGTATGCAGGGGAACTCCCCTTTATAAAACC 2770
                           --------    i   ----   v  vv i  --    -------   
  L1M4_orf2#LINE/    435 AT--------GCAAAAGA----ATGAAGTTGGAC--CCCT-------ACC 463

  chr1_80914685_8   2771 ATCAGAACTTGTGAGACTTATTCACTATCATGAGAACAACATGGGAAAAA 2820
                         -   ------------------   i  -  ----    --------   
  L1M4_orf2#LINE/    464 -TCA------------------CACCAT-AT----ACAA--------AAA 481

  chr1_80914685_8   2821 CTCGCCCCCACAATTCAATTACCTCCCACTGGGTCCCTCTCATGACACAT 2870
                         i ---------  i    --------- v   i  ----------- ? -
  L1M4_orf2#LINE/    482 TT---------AACTCAA---------AATGGATC-----------AWA- 501

  chr1_80914685_8   2871 GGGAATTATGGGAGCTACAATTCAAGATGAGATTTGGGTGGGAACACAGC 2920
                         -----------  v   -   vi    ---------------------  
  L1M4_orf2#LINE/    502 -----------GACCTA-AATGTAAGA---------------------GC 518

  chr1_80914685_8   2921 CAAACCATATCATACAATGATCTCATTTTCAACAAAGGTGTCAAGAATAT 2970
                         i   ---- ii   v  ----   ---  ------  -----     v i
  L1M4_orf2#LINE/    519 TAAA----ACTATAAAA----CTC---TT------AG-----AAGAAAAC 546

  chr1_80914685_8   2971 ATATTGGAGGAAAAAACACTCTCTTCAATAAATTGTACTGAGAAAACTAG 3020
                            --  ? v   --------     i-----------------------
  L1M4_orf2#LINE/    547 ATA--GGNGTAAA--------TCTTCG----------------------- 563

  chr1_80914685_8   3021 ATATTCATATGCAGAAGAAAGAGACTATAACATTGGTTTTCGCAAATATT 3070
                         --------------------------- i  v    v  vv    vvi  
  L1M4_orf2#LINE/    564 ---------------------------TGACCTTGGGTTAGGCAATGGTT 586

  chr1_80914685_8   3071 TCTTGAGTAATACCCCAAAAGCATAGGCAACCAAAACAAAAAAAAAAATG 3120
                             iii  vv  v         i i     ------    i       i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAAC------AAAAGAAAAAATA 630

  chr1_80914685_8   3121 GACAAATAGGAATCACATCGAAAT-AAAAACTTCTGCACAGCAAAGGAAA 3169
                           i    v   v i-    i    -        i  ii vv       v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTT-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_80914685_8   3170 TAAT-AACAAAGTGAAAAGAAAACTCACAGAATGGGAGAAAAATATTTGC 3218
                         iv  -  v            v   i                 -       
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGC 728

  chr1_80914685_8   3219 AAATTATTCATCTGACAAGGGATTTATAACCAGTATATATTTAAGGAGCT 3268
                             i  vi      i      i  i  v    v      --  i  i  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT--AAAGAACT 776

  chr1_80914685_8   3269 CAAACCACTCAATAGGAAAAAG-CTAGTAACCCAATTTAAAAATGGGCAA 3317
                          vv  v        iv      - v i          ?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_80914685_8   3318 AACATCTGGATAGACATTTCTCAAAAGAAGACATACAAATGGCAAATAGG 3367
                          iv  i  i             v        i           v    i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_80914685_8   3368 TTTGTGAAAATGTATTTAACATCACTCATCAT 3399
                         ivii      vi ii i       ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (122 / 83)
Gap_init rate = 0.05 (44 / 905), avg. gap size = 6.36 (280 / 44)  


1632 25.90 6.19 5.52  chr1_80923550_80925892      963  1850 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr1_80923550_8    963 ATGTCCATGGTTTGGAA-ATTCAAAATTATAAAGATGTCAATTCCTCCTA 1011
                             i     v      - i i  v   i v      v    v ii  i 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_80923550_8   1012 AATTGATTTATAGATTAAGTGCATTTTCAATTAAAATACCAGCAAAGGAG 1061
                                i  i     v ii   v ii v  i     v     -------
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC------- 107

  chr1_80923550_8   1062 TGTGTGTGCATGTGTGTGTGTTTGTA--AATGGACA----GATCCTAACA 1105
                         ------   v v -------    i --   v    ----        v 
  L1M4_orf2#LINE/    108 ------TGCCTTT-------TTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_80923550_8   1106 TCCATATGAAAACAAAAGGTGATA-AAAATACTCAAAGCAATCCTGAAGA 1154
                          i      i   iiv    -  iv- i    vi    i     i    i 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_80923550_8   1155 AAGCAAACAAAGTTAAA---CTCAC--TTCACA-TATCAATATCTAAAAT 1198
                          iivi         ii ---     --   v  - v    v ii  vv i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_80923550_8   1199 AAAGTTGTAGTAATTTGATCAGTGGGATACTGACACAACAATAGAC---T 1245
                             i ii      iviiv     v i     i  i  vi      --- 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_80923550_8   1246 AGTTTACCATGAGAATAGAATAAAAAGTTAAGAAATAGACCCACTTATAA 1295
                           v i --   -         vi i   iv       i     ivi  vv
  L1M4_orf2#LINE/    294 AGATCA--ATG-GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_80923550_8   1296 ATGTTCACCTGATTTATGACAAAGGTGACACTGTGGTTCTCTGAAGAATG 1345
                            v   vi      vi     i    v  vviivi   vv  ii   v 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_80923550_8   1346 AATAATCTTTTCAATAAATGGTGCTGAGTCCATT--ATA-----AGGCAA 1388
                             i         i           i v v i --   ----- v    
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_80923550_8   1389 AACAA-AACGTATATGGATTCCTACCTCGTACATTATG-AAAAATCAATT 1436
                           v  -i v  ---    ii        ii  vv   i-      i  i 
  L1M4_orf2#LINE/    441 AAGAATGAAGT---TGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_80923550_8   1437 AAAGATTGATAGCAGATCAAAATGTGAAAGGTAAATCAATAAAGCTTTTA 1486
                         v  i  v   vi?   i v      i i  v    v v     i  i   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_80923550_8   1487 GAGAGATGA-ATAGAAGAAAATTTT-ATAAGGT-GAATT-GGAAAAAAAT 1532
                           -   vi -    i? v    i  -i i vv - ii  -  v  viiv 
  L1M4_orf2#LINE/    538 GA-AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_80923550_8   1533 TCTCAAATTGGACACAAAACGTCTCAATCA-TAAAAGAAAAAATAAATTA 1581
                            i i  vv     v   v - v   v  -i             i  - 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGAT-A 634

  chr1_80923550_8   1582 AAT--GATGTTA----AATTAAGAACTGCTTATCTGAAGCCATCTTTCTT 1625
                            --  iv i ----      i    -i  i -----  --------- 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACT-TTTGT-----GC---------T 669

  chr1_80923550_8   1626 TTTGAAGTCATCTTTAACAAC----AAAGA-ATTTCATAGATTGAAAGAA 1670
                          ivi i v  iiv i  v  v----     - vii  i   v  ii    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_80923550_8   1671 GATATTCACTAA--ATATAACTGACTAAGGACAAATTTCT-GAATACCGC 1717
                         i     ii v  --     v    iv i    vvi v  i-     ivvv
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_80923550_8   1718 AA--ATTCTT-CAATACGTCAATAAGAAAAACATAG-TA-TCCAAT--AG 1760
                           -- i    -   i---       v     v i i-  -i     -- i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAAC---TCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_80923550_8   1761 ATATGGGGAAA---TTTGGACAAACATTTCAGAAAAAAAAGATATACAAA 1807
                          v     v   ---    i i i       -vvv   i            
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTC-TCCAAAGAAGATATACAAA 865

  chr1_80923550_8   1808 TTACCAATAAATACACGGAAATATGTTTACCTTCATTATCTAT 1850
                          vi       ii   i i   v   i i v v   ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (131 / 97)
Gap_init rate = 0.05 (43 / 894), avg. gap size = 2.42 (104 / 43)  


2354 26.94 6.71 1.73  chr1_80931532_80935247     2359  3223 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80931532_8   2359 TGGAGGGATTTACTATATTTATGGATTAGAAGACTTGATATATTTAATAT 2408
                             ii   v v i  i  i       i        i    vv    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80931532_8   2409 GTGAGTTATT----AAACTGTTCTATAGATTTGGCACAATTCCAATCCAA 2454
                          vv i - i ----   i  v    i     iii i    i  v   v  
  L1M4_orf2#LINE/     51 GGCAAT-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_80931532_8   2455 ATTTGAACAGG-TTTTTTGCATAGAAATTGATAAGCTG-TTCTGAATTAT 2502
                           iiv i v v-         --        i      - i  i  v vi
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCA--GAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_80931532_8   2503 ATACGAAAACACAGAGGACCTAGAA------AAACAA------AACATAA 2540
                            i i   ii  ii     i    ------      ------  v v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_80931532_8   2541 GAACAAAGTTGGAGGACTCATACTACTAAAAATTT--GGACCTGTTATAA 2588
                                             i   v iv  --   --ii  i ii  i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAA--TTTCAAAACTTACTACAA 245

  chr1_80931532_8   2589 GGTTACAGAAATCAGGACAGTATTTTATTGGAGAAAGGATAAACCCATAG 2638
                         i i     v     i      i vv  i   viv       i  vi    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_80931532_8   2639 ATCAATGGAACAGAATTGAGAGCCTAAAAATGAAGCCACACATGTATGGT 2688
                                   i           i i i    i  v   i    v      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_80931532_8   2689 CAATT---TTTTGACAAAGTTACAACAGCAATTCAATGGAGAAAGGGTAG 2735
                              ---   i     i v i v vii v         i     ii   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_80931532_8   2736 TCTT--CAGTGAAAAATGATAAAA-AAGTATGCGTTCATATACAACAAAG 2782
                             --  iii  vii  v iii -  v iviii?i  i  i   v i i
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_80931532_8   2783 TACTCATTG--TTCCTACCTCACGTCATATACAAAACTTAACTCAAAGTC 2830
                          iv-vi   --ii          ii           v          i v
  L1M4_orf2#LINE/    446 TGA-AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_80931532_8   2831 TATCACTGACCTAAACACAATACATAAAACTGTAAAACATCTAGAAGAAG 2880
                         v    ?v        iii  v vv       i      vii        i
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_80931532_8   2881 ACAAAGAAGAATACATTTATGAGCCCAGTTAAGGTGA-GATCTTCTTGGA 2929
                            v  i? v v iv  ii   v iii v v   ii - i -     i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGA 593

  chr1_80931532_8   2930 TACACCACCAAAATAATGAAT--CAAAACAAAAAATATGAATAAGTTGGA 2977
                           iiv        vv ii ii--     v        --i    i     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGA 641

  chr1_80931532_8   2978 CTTTGTAAAAATTAAGAACATTTGCTCTTTGAAAGACAATATTGAAAGAA 3027
                            ii v        i   v    iv   ii  i    v   ii i i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_80931532_8   3028 TTAAAAG-----TGACAGACTAGGAGAAAATAAGTTCAAAGCACATATAA 3072
                          v     -----iv     v i          vv v    v  i    vv
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_80931532_8   3073 AACAAATCAC--ATATCTAGAATATATAAGCGTCTTCTAAAATTTAATAA 3120
                         i i  ivv  --i    i           iviv  ii  v  i i     
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_80931532_8   3121 --GAAAGCTAA------CAACTAAAAAATAAATAAG-----TAAATAAAA 3157
                         --i    vi  ------   i ?      iiii  i----- i    i v
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_80931532_8   3158 ATTTGAACTCACCCACAAAAGA-------ATGGCAAATCAGGACATGAAA 3200
                             ---   ---  v i    -------     v   v  v        
  L1M4_orf2#LINE/    842 ATTT---CTC---CAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_80931532_8   3201 AGATGCTCAACACCATTAGCCAT 3223
                                     i  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (148 / 81)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.81 (73 / 26)  


3008 26.42 1.33 0.55  chr1_80961006_80967119     4721  5621 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_80961006_8   4721 TGGAAAAACATTCCATGCTCCTGGATAGGAAGAATGAATATTGTGAAAAT 4770
                               i i  i     i  v     v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_80961006_8   4771 GGCCATACTGCCCAAAGTAATTTATAGAGTCAATGCTACCCCCATCAAGC 4820
                            v     v      v i  i  i   v    i  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_80961006_8   4821 TACCA-CTGACTTTCTTCACAGAATTAGAAAACACT-ACTTTAAATGTCA 4868
                          v   -   v    i  -i     v v  v  -i  - iii    vv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr1_80961006_8   4869 TATGAAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAAAAG 4918
                             i  viiv  ii  v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_80961006_8   4919 AACAAAACTGGAGACATCACACTACCTGATTTCAAACTATACTATAAGGC 4968
                               ii     ivv       v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_80961006_8   4969 TAAAGTAACCAAAACAGCATGGTACTGGTACCAACACAGATATATACACC 5018
                           v     i   i    ii         i iv iv i   i     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_80961006_8   5019 AATGGAACAGAACAGAGGCCTCAGAAACAATGCCATACATCTACAACCAT 5068
                                i    iv   ivii      i  vv        i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_80961006_8   5069 CTGGTCTTTGACAAACCTGACAAAAACAACCAATGGGGAAGGATTC-CCT 5117
                         i  i i  i     ivv  v   i v  vi          i  v v-i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_80961006_8   5118 ATTTAATAAATGATTTTGTGAATACTGGCTAGCCATATGCAGAAAACTGA 5167
                         v  i  i     i vi  v  vv     v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_80961006_8   5168 AACTAGACCCCTTCCTTACACCTTATACAAAAATTAACTCAACGTGGATT 5217
                          ii i       v   i     v                   vi     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_80961006_8   5218 AAAGACTTAAATGTAAGACCTAAAACCACAAAAACCCTAGAAGAAAACCT 5267
                          ?    i           v       i i    vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_80961006_8   5268 AGGCA-ATACCATTCAGGAAATAGGCATGGGCAAAGACTTTATGACTAAA 5316
                            ?i- v i -   iv  vv v  vv i     v ii  iv iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_80961006_8   5317 ACACCAAAAGCAATGGCAACAAAAGCCAAACTAAACAAATGTGATCTAAT 5366
                                     vvi          vv   v  i i    vv  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_80961006_8   5367 TAAA-CTAAAGATCTTGGCACAGCAAAAGACACTATAATCAGAGTGAACA 5415
                         i   -i    i ii  v ii vv    i        v vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_80961006_8   5416 GGCAACCTACAGA-TGGGAGAAAA-ATTT-CACAATCTATCTATCTGACA 5462
                          i     i     -          -    -  -    -  v       i 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGATA 745

  chr1_80961006_8   5463 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5512
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_80961006_8   5513 AAAGCAA----CCCCATCAAAAAGTGGGGAAAGGATATGAACGGACACTT 5558
                           ii   ----   v  i?    i    v       v    ii    i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_80961006_8   5559 CTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCAT 5608
                            v        i  vi viii     i  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_80961006_8   5609 CATCACTGGTCAT 5621
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (134 / 100)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.21 (17 / 14)  


3310 26.87 0.44 0.44  chr1_81117192_81121403.rev     2814  3721 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_81117192_8   2814 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2863
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_81117192_8   2864 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2913
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_81117192_8   2914 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2961
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_81117192_8   2962 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3011
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_81117192_8   3012 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3061
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_81117192_8   3062 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3111
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_81117192_8   3112 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3159
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_81117192_8   3160 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3209
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_81117192_8   3210 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3259
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_81117192_8   3260 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 3309
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_81117192_8   3310 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3359
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_81117192_8   3360 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 3409
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_81117192_8   3410 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3459
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_81117192_8   3460 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3509
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_81117192_8   3510 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3559
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_81117192_8   3560 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3609
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_81117192_8   3610 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 3659
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_81117192_8   3660 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 3709
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_81117192_8   3710 ATCACTGGCCAT 3721
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3243 26.68 0.55 0.44  chr1_81123354_81129005     4253  5159 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_81123354_8   4253 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4302
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_81123354_8   4303 GGCCATACTGTCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4352
                            v     vi    iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_81123354_8   4353 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4400
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_81123354_8   4401 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 4450
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_81123354_8   4451 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4500
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_81123354_8   4501 CACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGTTATAGATC 4550
                         i       i   i    ii         i iv ii i   vv        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_81123354_8   4551 AATGGAACAGAAC--AGACCCCTCAGAAATAACACCGCATATCTACAACT 4598
                                i    i--   vi  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_81123354_8   4599 ATGTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4648
                          vv    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_81123354_8   4649 CTATTTAATAAATGGTGCTGGGA-AACTGGCTAGCCATATGTAGAAAGCT 4697
                           v  i  i              -      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_81123354_8   4698 GAAACTGGATCCCTTCCTCACACCTTACACAAAAATCAATTCAAGCTGGA 4747
                            ii    i    v         v  i        i  i    iv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_81123354_8   4748 TTAAAGACTTCAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4797
                          i ?    i v  i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_81123354_8   4798 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4847
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_81123354_8   4848 AACACCAAAAGCAATTGCAACAAAAGACAAAATTGACAAATGGGATCTAA 4897
                         i            vvv           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_81123354_8   4898 TTAAACTAAGGAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4947
                          i   v v ii     i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_81123354_8   4948 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 4997
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_81123354_8   4998 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5047
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_81123354_8   5048 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACAGGAACAGACACTTC 5097
                          i     i     v  i?    i           ivv   i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_81123354_8   5098 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5147
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_81123354_8   5148 ATCACTGGCCAT 5159
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3066 22.18 8.30 1.19  chr1_81131530_81133513      652  1494 (490)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_81131530_8    652 AGACATTTTATGTTCATGGATTGGAAGAC-----ATTATAAAGATA-CAA 695
                            i  iii                    -----   i v     i-   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_81131530_8    696 TTTTTCCCAAATTGATCTGTAGATTCAGTATAATTTCTATCCAAATCCCA 745
                          vi i             ii       iiii   ii     v        
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_81131530_8    746 GTAGATTTTCCTTTGCAGAAATTTTCAGGTTGACCCTAAAATTTATGTGG 795
                          iv vi   --            vv  i i   i         i  i   
  L1M4_orf2#LINE/    106 GCTGCCTTT--TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_81131530_8    796 AAATGCAAAGGTTCCAGAATAGCCAAATTGATTTTGAGGAAAAA-----A 840
                                 i  vi              vii  i    ii  i  ----- 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_81131530_8    841 TGTTAGAGGGTATGAACTTTCTAATTTCAATACTTGCTATCAAGCTACAA 890
                         v   i    iiviiv    i i        v    i   iv        i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_81131530_8    891 TAATCAAAACAG-ATGATGCTGGCATAGAGATAAACATATGGATCAATGG 939
                                i    -i  i i        ii    i      i         
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_81131530_8    940 AACAGAAT-------------------------ATTTATGGTCAATTGAT 964
                           i     -------------------------                 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_81131530_8    965 CTTATGCAAAATGTACCAAGGCAATTTAATGGGGGAAAGGATAGTCTTTT 1014
                         i  vvi   ii-  i     i v   i       -    i          
  L1M4_orf2#LINE/    354 TTTCGACAAGG-GTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTT 401

  chr1_81131530_8   1015 CAACAAATACCGTTTG--CCATTGTGATATCCATA------ACTATAAAT 1056
                                 ivi i v -- v i  -    ?   i ------ vv  i  v
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTG-GATAKCCACATGCAAAAGAATGAAG 450

  chr1_81131530_8   1057 TAAGAGCCTTATTTCATGTTATATA----AATTAACTCCAAGTAAAAAGT 1102
                          vi  v  i  ii   iiii     ----         v  i ii vvi?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_81131530_8   1103 AAACCGAAATGTAGGAGCAAAAACCATACATCTTGTACAAGAAAACATAA 1152
                          i   v       i    v     i   v v  iv  v           i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_81131530_8   1153 AAGAATATCTTCATGATCTTGGGTCA--TA--GAGTTCTGAAGTAGTATA 1198
                         i? v v      i   i       i --i -- iv    v ii  vv i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_81131530_8   1199 CCAAAAGCTTAATCCATAAAAGAAAAACTCAGA--------ACT-CATCA 1239
                                 vi  v v i          v -   --------   -     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAATTGGACTTCATCA 649

  chr1_81131530_8   1240 AAAT-AATAACTTTT-TATTTCAAAATACACCATTAAGGAAAATGAGAAG 1287
                             -  v       - ii      iv    i  i   -   i   i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAAAG 698

  chr1_81131530_8   1288 ATAAGCCACAGAATGAATGAAAATAGTTGCAAATCATTATATGTGACAGA 1337
                          i  v          iiv       v           -    v   i ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-ATATCTGATAAG 747

  chr1_81131530_8   1338 GGACTTCTATCCAAAATATATAAAGAACATGTATAACTCAATG-TGAACA 1386
                               v      i              viv  i        i- i  v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_81131530_8   1387 --CAAA--ACTTCCAATTTAGAAATGGGTAAAAGATCT-AATATGCATCT 1431
                         --    --  --      ? i       i   i   i -    vi   i 
  L1M4_orf2#LINE/    798 GACAAATAAC--CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_81131530_8   1432 CACTAAAGAAGATAATCAAATGGCTAAAATGCACATGAAAAGATACTTAG 1481
                          v i          vv        i  v v              i  i i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_81131530_8   1482 CAATATTTGCCAT 1494
                           vi ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (122 / 61)
Gap_init rate = 0.03 (26 / 903), avg. gap size = 3.08 (80 / 26)  


2025 24.13 4.77 2.46  chr1_81269260_81270943      500  1191 (493)    L1M4_orf2#LINE/L1      201   908 (0)  

  chr1_81269260_8    500 CAAAGTTGGAGGACAGGCAGTATCTGATTTTGAGATCTTTTAAAACTCTA 549
                                       vvi  v vi ii    ii i ii vi  v  vv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_81269260_8    550 CAGTAATCAAGACATTTTAGTATTGGCATAAAACTAGATAAATAAGTCAA 599
                                       v v i   i        iiv    i v   ii    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_81269260_8    600 TA-AACAGAAAAGACAGTCCAGAAATAGACCCACACGTATATATGCAATT 648
                          i-  i    vv  v            i     i  i v   ivv     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_81269260_8    649 GATTTTTGACAAAAATGTCAAGGCAATTCAATGGAAAAAGA-TAATCTTT 697
                               i     iii  i    i v         ii     -  i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_81269260_8    698 TCAAGAAATGATGC-AGGAAAATTTGA--GTTACA--AAAAACAAAAAAC 742
                             v     i   -i   v  i v  --?ii   --v    v  vi  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_81269260_8    743 ATTGACCCTGGCCTCCTACCATATACAAAATATTAACTTGGAACAG-TCA 791
                         v v     ivi    vi             -       iii  ii -   
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATGGATCA 499

  chr1_81269260_8    792 TAGACA-GGATGTAAGAGCTGTAACTATAAAACTTCTAGAAGGAAACGTA 840
                         ?    v-ii           iv            ii      i    i  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_81269260_8    841 GGAGCAAATCTTATTGACCTCAGATTTCGCAAAGATTTCCTAAATAT--- 887
                           ? i       vv      ii i  vv    v i    i  i    ---
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_81269260_8    888 ATCAAAA-TACTTACTATAAAAGAAAAAACTTGATAAATAGGACTGTATC 936
                          i     -i  vvi v i           - v       v     vi   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATC 648

  chr1_81269260_8    937 AAAATGAAACACTTTTGCCACTCAAAAGACACTGTTAAGATATTGTTATG 986
                              v   v       ivvi     i      i i    v -----i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA-----GTG 693

  chr1_81269260_8    987 AAAAGGAATAAAGCCAAAGA-TA----AAAATATTTGCAAAACATCACAT 1031
                              -- i  v-   v   - i----              ---   -- 
  L1M4_orf2#LINE/    694 AAAAG--ACAAC-CCACAGAATGGGAGAAAATATTTGCAAA---TCA--T 735

  chr1_81269260_8   1032 ATATCCAACATAAGATATGCAGCTAGAATATA-AAAGAACACATAT--TT 1078
                              ii i vii  iv  i v i        -       v v  i--i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_81269260_8   1079 CAGTTACAA---GACAG----CACAATGAAAAAATGAGCAAA--ATTACT 1119
                           i v i  ---    i---- v    v?       i     --   -- 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT--T 833

  chr1_81269260_8   1120 GAGCAGCAACTTCACCAAAAAC--TGTGTAAATG-TCAGTGAGCACATGA 1166
                           ii  vv i   v     i v-- i ii     -i  i i         
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_81269260_8   1167 AAATATGTTCAATACCATTGTCATC 1191
                            v   i    i i  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (100 / 63)
Gap_init rate = 0.04 (26 / 708), avg. gap size = 1.92 (50 / 26)  


2720 28.49 1.22 0.55  chr1_81282354_81286269.rev     2524  3425 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_81282354_8   2524 TGGAAAAACATTTCATTCTCACGAACTGGAATAATCAATATCATTAAAAT 2573
                               i i  ii   vi   i i i     v v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_81282354_8   2574 GGCCATACTGCCCAAAACAATTTACAGATTTAGTGTTATTTCCTTCAAAC 2623
                            v     v      vii  i        i ii iv  ii iv     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_81282354_8   2624 TACCAACATTATTTTTCACAGAATTAGAAAAAAACT-ATTGTAAAATTCA 2672
                          v   i vviv     ii     v v  v  i--  -  iv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_81282354_8   2673 CATTTAACCAAAAAAGAGTCTGAATAGCCAAAG--ATTTTAAACAAAAAG 2720
                         i  vv  viiv  ii  vi v           i--  i  i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_81282354_8   2721 TACAAAGCAGGAGGCATCATACTACCTGACTTCAAACTACACTACAGGGC 2770
                         v      iv     vv   i   v  ii i      vivi      ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_81282354_8   2771 TACATTAACCAAAACAGCATGGTACTCATACAAAAACAGGCACATAGACC 2820
                             v   i   i    ii       vii i  ii i  i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_81282354_8   2821 AATGAAACAGAATAGAGAGCTCAGAAATAAAGCTGCACACCTACAACCAT 2870
                             i  i     v     ii          v iii   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_81282354_8   2871 CTGATCTTCAACAAAGTTGACAAAAACAAGCAACAGGTAAAGGACTTTCT 2920
                         i    i   i    i v  v   i v  vv   ii  v    i ivv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_81282354_8   2921 ATTCAATAAATGGTACCTGGATAACAGCCTGGCCATATGCAGAAGATTGA 2970
                         v     i       i iv   i   v vv i?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_81282354_8   2971 AACTGGAACCCTTCCTTACACCATATACAAAAAACAACTAAAGAAGCATT 3020
                          ii    v    v   i                vi    v  i v v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_81282354_8   3021 AAACACTTAAATGTAAAACCTAAAACTATAAAAATCCTTGAAGAAAACCT 3070
                          ? v  i         i v              v  i v         v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_81282354_8   3071 AGGCAATACGATTCTGT-ACATAGGACCTGGCAAAGATTTTAT-GATGAA 3118
                            ?i-  vivi ii  -  v v  iiiv     v i   iv -   - v
  L1M4_orf2#LINE/    549 AGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr1_81282354_8   3119 GACATCAAAAACAACTGCAACAAGACAAAAATT-GACAAATGCGACCTAA 3167
                             i     i  vvv       i v     v -  i    vv   i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_81282354_8   3168 TTAAACTAAAGAGCTTCTGCACAGAAAAAGAAACCATCAACAGAGTAAAC 3217
                          i   v v  i i   i  ii vvv   i  v  i     v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_81282354_8   3218 AGACATCCTACATAATGAGAGAAGATATTTGCAAAGTATGCAACTGACAA 3267
                              v  i   v    i     i           vi  ii v    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_81282354_8   3268 AGGTATAATATCCAAAATTTATAAGGAACTT----AAATTAACAAGCAAA 3313
                         i  vv vi      i   v     i     i----  v i  i  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_81282354_8   3314 A-ACAAGACAACTCCATTTAAAAGTGGGCAAAGTATATGAATAGACATTT 3362
                          -    - i   i v   ?    i         v  v             
  L1M4_orf2#LINE/    797 AGACAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_81282354_8   3363 TTCAAAAGAAGACATACATGCCACCAACAAGCATATAAGAAAATGCTTAA 3412
                         i  v        i     viivi    i     i  i i  i     i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_81282354_8   3413 CATCACTAATCAT 3425
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (151 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3468 24.03 1.44 0.89  chr1_81339747_81343903     2764  3666 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_81339747_8   2764 TGAAAAGATATTCCATGTTCATTCATTGAATGAGTCAATATTGTTAAAAT 2813
                           i        i          vv    i v  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_81339747_8   2814 GTTCATACTACCCAGAGCAACCTACAGATTCAGGGCAATCCCTATCAAAA 2863
                          viv     v    i vii i           iv                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_81339747_8   2864 CGTCAGGGACATTCTTCACGGAAACAGGGAAAACAATCCTAAAATGTATA 2913
                         ivi   vvi v  i  ii i    iv iv  ivii          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_81339747_8   2914 TGGAACCACAAAAGACACAGACTAGATAAAGCTATCCTGAGCAAAAAAGA 2963
                              vii   ii   v    v   vi   i v   i   i-   i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chr1_81339747_8   2964 ACAAAACTGGAGGAATCGCATTACCTGACTTCAAATTATACTACAGCACT 3013
                              ii       v  i  i v  ii i      viv       ivi  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_81339747_8   3014 ATAGTAACCAAAACAGTATGGTACTGGCATAAAAACAGACTCACAGACCA 3063
                          i     i   i     i              ii i    vi i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_81339747_8   3064 ATGGAACAGAC-----AACCCAGAAACAAATGCATACATCTACAGTGAAC 3108
                               i   v----- ii       i   iv       i  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_81339747_8   3109 TTATTTTCAACACAAGTGCCAAGAACATACACTGGGGAAAAGACAGTCTC 3158
                          v      i   vii         v   v  v        ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_81339747_8   3159 TTCAATAAATGGTGCTGAGAAAACTGGATATTCATATGCAGAAGAACAAA 3208
                              i           i  v         ?i  i     i     ii  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_81339747_8   3209 AGTAGACCCC-A--TCAATTGCCATATACAAAA-TCAAATCAAAATAGAT 3254
                         iv i      - --   --ii            - i  v       i   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCA--CACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_81339747_8   3255 TAAAGACTTAAACCTAAGACCTCTAACTATGAAACTACTACAAGAAAACA 3304
                         i ?    i    iv     v  vv      i     vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_81339747_8   3305 TGTGTG-AAATCCTCCAGGACATTATTCTGGGCAAAAAAATTTTTTAAGA 3353
                          iv ? -     i  -iv   v  ivvi i     vii--   i   iiv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGG--TTTCTTAGAT 594

  chr1_81339747_8   3354 AT-ACCCCAAGAGCACAAGCAACCAAAGTAAAAATGGACAAATGGAATCA 3402
                           -  v    i            v    v      i  i    v i iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_81339747_8   3403 CATCAAG-TTAGAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTG 3451
                               i-   i   -   i  ii vv       v  v     v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_81339747_8   3452 ATGAGACAACCCACAGAGTGGGAGAAAATACTTGCAAATTACCCATCTGA 3501
                          vi              i            i        i ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_81339747_8   3502 CAAGGGATTTGTAATCAGAATATATAAGGAGTTCCTAACAATTATATAGG 3551
                         i      i     vi            i  ii  i  -   i vv   iv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAAT 792

  chr1_81339747_8   3552 AAAAAATCTAATAATCCAATT-AAAAATAGGCAAAAGATCTGAATAGACA 3600
                              iv v     i      -      i      i   i          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_81339747_8   3601 TTGCTCAAAAGAATACGTACAAACAGCAAACAGGCATATGAATAAGTGCT 3650
                           v   v      v ii      ii  v  i i   i     v ii    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_81339747_8   3651 CAACATAATTGATCAT 3666
                               v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (138 / 76)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


2871 23.98 5.91 2.73  chr1_81572489_81575880.rev     2022  2901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_81572489_8   2022 TGGAAAGACTTCCCATGCTCATGGATTAGAA---TTAACATTGTAAAAAT 2068
                                 iv       i         i   ---    i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_81572489_8   2069 GACCATACAACCAAAAGTGATCTATAGATTCAATGCAATGC-------AA 2111
                          i v    vv  v   v       i        i     v -------  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_81572489_8   2112 TGACA----------TTGCATAG---GAAAAA--AATCCTAAAATTAATA 2146
                          vv  ----------     v i---  v  i--i           v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_81572489_8   2147 TGGAACCTCAAGAGACTGTGAATAACCAAAGCAATCCTGAGCAGAAAGGA 2196
                              viv    i   ivv     i     i     i   iv ii   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_81572489_8   2197 -----TTGCCAGAACCATCACACTATCTGACTTCAAAATATACTGCAAAG 2241
                         -----   v-  i  --       vi ii i       iv    i     
  L1M4_orf2#LINE/    201 CAAAGTTGG-AGGAC--TCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_81572489_8   2242 CTA-AATAA-CA--------TGGTACTAGCATAAAAACAGACACACAGAC 2281
                            - i   -  --------       i      ii i     i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_81572489_8   2282 GAATAGAACAAGCTAGAGAACCTAGAAATAAATTCACATATTTACGGCTA 2331
                         v   i   i iiv v    ii i         ii  i i     i  ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_81572489_8   2332 ACTGATTTTTGACAAAGTTGCTAAGAACATTTATTAGACAAAAGTCAGTC 2381
                          i       i     i v   i    v    i v i iv   iivi    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_81572489_8   2382 TCTTCAATAAATAGTTCTGGGA-AACTGGATATTCATATGCAGAAGAATG 2430
                          i     i    i  v      -         ?i  i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_81572489_8   2431 AAACTAGACCCCCATCCTTCACTGTATACAAAAGCTGACTCAAAATGGGT 2480
                           ii i      i i iiv   ii         ii i           i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_81572489_8   2481 TAAATATTTAAATGTAAACACTGAAACTATAAAACTACTAGAGGAAAACA 2530
                         i ? v ii         ivi  i             vi    i       
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_81572489_8   2531 TAAGGG-AAACCACTTCAGGACATTGGCCTGGACAAAGATTTTATGGAAA 2579
                           i ? -   i --   iv   v    vi i i   v i   iv i  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_81572489_8   2580 AGACCTCAAAAACACA-GCAA---------GAATAGACAAACGGGGTTAT 2619
                         v   vi     i    -    ---------i      i   iv  ii - 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT-T 644

  chr1_81572489_8   2620 ATATCAAACTGAAATGCTACTGCCCAGCAAAGAAAGGAAACAATCCACCA 2669
                         -i      v v   vi  vi  iv vv     ----  v  v   v vv 
  L1M4_orf2#LINE/    645 -CATCAAAATTAAAAACTTTTGTGCTTCAAAG----GACACTATCAAGAA 689

  chr1_81572489_8   2670 AGTGAAGAGACAACTAGCAGAATGGGAGAAAATATTTACAAAGTATTCAT 2719
                               i       ivi                    i    vi  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_81572489_8   2720 CTGACAAACTATTACTAACCAGAATATGCAAGGATCTCGAACAACTAAAT 2769
                             i  ivv i vv  v         ii  i  v   vv      v   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_81572489_8   2770 AGCAAAAACCTGACAAACCCCCAAATAATCTCATTTGAAAATAGGTAAAT 2819
                          ii     ---      --------   i iv   ?i     i  i   v
  L1M4_orf2#LINE/    790 AATAAAAA---GACAAA--------TAACCCAATTWAAAAATGGGCAAAG 828

  chr1_81572489_8   2820 GAGTTGAATAAGCATCTCTCTCAAAAAAAGACATACAAGTGGCCAAGAAG 2869
                           v       ii   i    i--   i    i      i       v   
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCC--AAAGAAGATATACAAATGGCCAATAAG 876

  chr1_81572489_8   2870 TATATGAAAAAATGCTCAACATCACTAATCCT 2901
                         i i       i             ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (136 / 71)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.45 (76 / 22)  


3215 23.23 5.03 1.14  chr1_81818367_81822834     3102  3975 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_81818367_8   3102 TGGAGAGAGATTCCATATTCATGGATAAGAAGACTCAATATTGCCAAGAT 3151
                             i   v  i    i         vi       i       ii     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_81818367_8   3152 GTCAGTTCTTCCCAACTAAATCTATAGATTTAAAGCAATCTCAATTTGTC 3201
                          v  i v  i     v vi     i     i  v      i ---- i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC----TATC 96

  chr1_81818367_8   3202 AAAATAATTCTGGCAAATTATTTTGTGGATATCAACAAACTGATTCTAAA 3251
                              ---i ii  vivi v     ii  v  ii    i     i     
  L1M4_orf2#LINE/     97 AAAAT---CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_81818367_8   3252 GT----------------------------AACCAACATAATATTGAAGG 3273
                         i ---------------------------- i    v i   v     ii
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_81818367_8   3274 AAGAGAACAAAGTTGAAGGACTGATTCTACCCAACCTCAAGACATACCAT 3323
                          ii            i      v iv  v     ii    i  v   i i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_81818367_8   3324 AAATTTACATTAATCAAGACACTGTGGTATTTGTGGAAGAAGAGACAAAT 3373
                            vi    v           v       i v iiv   i v     v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_81818367_8   3374 AGATCAAAGAAACAGAAT--AGAGCCCAGAAATAGACCCACAGAAATATA 3421
                                v i  i     --    i         i     i v vv   i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_81818367_8   3422 GTCAACTGATCTTTC--CAAGAGGAACAAAGGCAATATATTGG---AAGA 3466
                              i    -    --    -  vi v   i v  vi v   ---    
  L1M4_orf2#LINE/    344 GTCAATTGAT-TTTCGACAAG-GGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_81818367_8   3467 A-AGTCTTCTCAACAAATGGCGCTGA-ACAACTG-ACATCTACATGTAAA 3513
                          -      i           i    i-       - i ? i     i   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_81818367_8   3514 A-AATAAATGTAAACCCAGAGCATACACCCTTTACAAAAATTAACTCAAA 3562
                          -   i  vv ii    vv v vi     v v                  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_81818367_8   3563 ATGGATCATCAATCTAAATGTAAACCACAAAAGTATAAAACTCCTAGAAG 3612
                                 ?vi i          ivvvi    v          i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_81818367_8   3613 ATAACGTAGGAGGAAAT-TTGATGGCATTGGGTTTGGAAACAGCTTTTTA 3661
                          v   i    ? v    -  vi  i v       v  v  ii i  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_81818367_8   3662 GAAGGAAAAACAAAGGCATAATCTATGAAAGAAAAAAATTGATAAAGTGG 3711
                           vivi v v    i   i  v v ii          - v      v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGG 640

  chr1_81818367_8   3712 ACTTCATTAAGATTTAAAATTTCTGCTTTGCAAAAGACACTGGCTAGAGA 3761
                                i  i   v    i  i  ivi v    i      iv v   i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_81818367_8   3762 ATGAAAAGAGAAGTCACAGACTGGGAGAAAATATTTGTGAAAGATGTATC 3811
                         i        v  vi      v                ii  vv  i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_81818367_8   3812 AGATAAAGAACTGTTACCTAAAATATACAAAGAACTCCTAAAATTCAACA 3861
                         v     i i   vv  i i i      i         i  v  i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_81818367_8   3862 ATAAGAACACAAA---CCCGATTTAAAAATGGGCCAAAGACCTTAACAGG 3908
                             i  v     ---   i   ?          v  i  ii v  i  i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_81818367_8   3909 CACCTCCCCAAAGAAGATATACAGATGGCAAATAAGCATATGAAA-GATG 3957
                           ii  i                i     v        i      -    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_81818367_8   3958 TTCCATGTCATATGTCAT 3975
                         i  v ii   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (120 / 79)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.38 (54 / 16)  


3088 27.42 0.44 0.44  chr1_81861591_81865881.rev     2893  3800 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_81861591_8   2893 TGGAAACACATCCTATGCTCATAGATTGGTAGAATCAATATTGTGAAAAT 2942
                               v i    i   i    i      v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_81861591_8   2943 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATGAGAA 2992
                          i v     v  v   vii       i      i        i  v i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_81861591_8   2993 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 3042
                          v   v vv v  i  ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_81861591_8   3043 TGGAACCAAAAAAGAGCTCGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 3092
                              viiv  ii  v iv v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_81861591_8   3093 CAAATCAGGAGGCATCACACAACCTGATTTCAAACTATCCTATAAGGCCA 3142
                             viv     vv      vv  ii        viv v   i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_81861591_8   3143 TAGTTACCCAAACAGCATGGTACAGGTATAAAAATAGGCACATAGACCAA 3192
                         i   v i v i    ii      v  i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_81861591_8   3193 TGGAACAAAATAGAAACTC-AGAAATAAACCCAAATACTTACAGCCAACT 3241
                              i i   v  i v  -             v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_81861591_8   3242 GATCTTCAACAAAGCAAACAAAAACATAAAATGGGAGAAAGGACACCCTT 3291
                            i   i    i vviv   i v   vv      -     i i vi   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTT 399

  chr1_81861591_8   3292 TTCAACAAATGGTGCTGGGATTATAATTGGCTAGCCACATGTAGGAGAAT 3341
                                             i---  i   v  ?       i ii     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGAC---AACTGGATAKCCACATGCAAAAGAAT 446

  chr1_81861591_8   3342 GAAACTGGATCCTCATCTCTTACCTTATACAAATATCAACTCAAGATGGA 3391
                            ii    i  ii i   vi   v        v  i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_81861591_8   3392 TTGAAGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGGTAAC 3441
                          ii?    i    iv     v  i           v ii      iv   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_81861591_8   3442 ATTGGGAAAACCCTTCTAGACATTAGCTTAGGCAAGGATTTAATGACCAA 3491
                           v  ?iv  vi    vv   v  i v        v i   vv iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_81861591_8   3492 GAACTCAAAAGCAAATGCAATAAAG--AAAGCTAAATAGCTGGGACCTAA 3539
                           vvi        v v    i   i--   iv  i   iv v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_81861591_8   3540 TTCAACGAAAGAGCTTTTGCATGGCAAAAGGAACAGTTGACAGAGTAAAC 3589
                          iv  vvv  i i      iiivv    i iv  vi ii v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_81861591_8   3590 AGACAACCCACAGAGTGGGAGAAAATCTTCACGATCTATATGTCTGACAA 3639
                                       i           v  ii i vii    i     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_81861591_8   3640 ATGACTAATATCCAGAATCTACAATGAACTCAAACAAGTCAGTAAGAGAA 3689
                         iv    vi          v  i  v      vv    v   i   v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_81861591_8   3690 AAACAAACCATCCCATCAAAAAGCAGGCTAAGGACATGAATAGACAATTC 3739
                          i     iv i  v  i?    iii   v     iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_81861591_8   3740 TCAAAAGAAGATATACAAACGGTGAACAAACATA-GAAAAAACGCTCAAC 3788
                           v                i  iv  i  i  i -     i i       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_81861591_8   3789 ATCACTAATAAT 3800
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3357 26.32 0.44 0.44  chr1_82308867_82315095.rev     4831  5738 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_82308867_8   4831 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4880
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_82308867_8   4881 GGCCATACTGCCCAAGCTAATTTACAGATTCAATGCCATCCCCAACAAGC 4930
                            v     v     ii i  i           i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_82308867_8   4931 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4978
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_82308867_8   4979 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5028
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_82308867_8   5029 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5078
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_82308867_8   5079 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5128
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_82308867_8   5129 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACTGCATATCTACAACT 5176
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_82308867_8   5177 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5226
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_82308867_8   5227 CTATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCATATGTAGAAAGCT 5276
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_82308867_8   5277 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5326
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_82308867_8   5327 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5376
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_82308867_8   5377 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5426
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_82308867_8   5427 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5476
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_82308867_8   5477 TTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAAC 5526
                          i   v v  i i   i   i vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_82308867_8   5527 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5576
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_82308867_8   5577 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5626
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_82308867_8   5627 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5676
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_82308867_8   5677 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5726
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_82308867_8   5727 ATCACTGGCCAT 5738
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2828 25.23 1.88 0.94  chr1_82350963_82352698      499  1243 (493)    L1M4_orf2#LINE/L1      157   908 (0)  

  chr1_82350963_8    499 TACAAAAGACCTCAAATAGCCAGAGAAATCATGAGCAAAAGTAACAAAGC 548
                          i   ii    ivi        i iv    v   iv  i iv       i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_82350963_8    549 TGGAGGCATCACACTAGTTTGGCTTCAAAATATGCTATGAAGTGATCGTA 598
                               vv       -viiiiii       iv i   ii   iv iv   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACT-TCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_82350963_8    599 ATCAAAA-AGCATGGTAGTGGCATAAAAACAGACACATAGACCAAGGAAG 647
                              i -  ii     v        ii i     i     i   v i i
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_82350963_8    648 CAGAATGAGGAGACCAGAAATAAGTCCATGAATTTGCAGCCATTTGATTT 697
                         i     vii   v          ii    iv    iii i  v       
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_82350963_8    698 TTGACAAAGATGTCAAGAACACACAATGAGGAAAGAACAGTCTCTTTAAT 747
                          i     i i  i     v  iv     i        i     i  i  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_82350963_8    748 AAATGGTGTTGGGACAACTGGATATCCACACACAGAAGAAGGAAACTAGA 797
                                 i               ?     ii  i     v   ii i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_82350963_8    798 CTCCTATTTCTCACCATATAAGAAAATAAACTCAAAATAGATTAAAGACT 847
                          i    ii  v         vi     v          i   i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_82350963_8    848 TAAATATAAGATCCAA--CTGTAAAACTACCAGAAGAAAACATGAGGAAA 895
                              i     v i  --  i       vii            ii ?iv 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_82350963_8    896 AATCTCTGCGATCTTGGCCTGGGCAGTGGATTTTTAGGTACAGGCAACAA 945
                              ii i  i     vi i    i   v  i    i  i- i  v   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-GACACCAA 604

  chr1_82350963_8    946 A-GCACAGGCAACAAATGCAAAAATAGACAAAT-GAATTACATCAAA-CT 992
                          -     i        v v         i    - i i v       -i 
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_82350963_8    993 AAAAAGCTCTACACAATT--GAGGAAATAATCAACAGAGTCAAGAGACAA 1040
                              vi i iii --  --i    v iv     v i   v  i      
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGC--TTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_82350963_8   1041 CTTACTGAGTGGGAGAATATATTTGCAGACCACATATCTGATGAGAGGTT 1090
                          ii  v  i        v         i i  i         i  i ii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_82350963_8   1091 AATATCCGAAGCATATAAGGAGCTCAAATAACTCAACAGTTAAAAAAACA 1140
                         vi     ii ii      i  i   vv i       i i -     i   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAAAAGACA 801

  chr1_82350963_8   1141 AACTGCTTAA---AAAAATGGGCAGAGGATCTGAACAGATACTTATCAAA 1187
                           ivi ii  ---           i     i    i   i i  v  v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_82350963_8   1188 AGAAGACATATAAATATGGCCAA---GTATATATAAAAAGGGTCAGCATC 1234
                               i   i    --      --- i i  iv   i v v   i    
  L1M4_orf2#LINE/    852 AGAAGATATACAAAT--GGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_82350963_8   1235 AATAATTAT 1243
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.85 (137 / 48)
Gap_init rate = 0.02 (13 / 752), avg. gap size = 1.62 (21 / 13)  


1903 29.64 0.18 0.00  chr1_82411762_82417821.rev     4354  4903 (1157)    L1M4_orf2#LINE/L1        1   551 (357)  

  chr1_82411762_8   4354 TGGAAAATCATTCCATGCTCATGGATAGGAAGAATCATTACCCTGAAAAT 4403
                               ivi  i     i        v      v i v  iiv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_82411762_8   4404 GGCCATACTGCCCAAACTAATTTATAGATTCAATACTATTCCCATTAAAC 4453
                            v     v      i i  i  i        ii v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_82411762_8   4454 TACCATTGACATTCTTCAAAGAATTAGAAGAAACAATTTAAAAATTCATA 4503
                          v   vivi v  i  iiv    v v  vi ivii  iiv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_82411762_8   4504 TGGAACCAAAAAGGAGCTCATATAGCCAAAACAATTCCAAGCAAAAAGAA 4553
                              viiv  i   v iviv              iiii iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_82411762_8   4554 CAAAGCTGGAAGCATCATGCTATCCTTCTTCAAACTATACTACAAGGCTA 4603
                              i    i vv   ii  vi  vvi      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_82411762_8   4604 TAGTAACCAAAACGGCATGGTACAGGTCTAAAAGTAGACACATAGACCAA 4653
                         i     i   i  i ii      v  iv   iii      i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_82411762_8   4654 TGGAACAGAATTGATAACTCAGAAATAAGGCTACACATCTACGACCATCT 4703
                              i        v iii         iv i i    i  i ii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_82411762_8   4704 TATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATTCCCTAT 4753
                         v  i  i     ivv  v   i v  vvv          vi  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_82411762_8   4754 TTAATAAATGATGCTGGGGGAACTGGCTAGCCATATGCAGAAAATTGAAA 4803
                          i  i     i       iv      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_82411762_8   4804 CTGGATCATT-CTTTACACCTTATACATAAATTAACTCAAGATGGATTAA 4852
                         i    i vi - i i     v      v            i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_82411762_8   4853 ATAAGTAAATGTAAAACTCAAAACTATAAAAACCCTATAAGAAAATCTAG 4902
                          v vv         i vii            vi i  v       iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_82411762_8   4903 G 4903
                          
  L1M4_orf2#LINE/    551 G 551

Transitions / transversions = 1.56 (98 / 63)
Gap_init rate = 0.00 (1 / 551), avg. gap size = 1.00 (1 / 1)  

 905 30.00 2.78 0.00  chr1_82411762_82417821.rev     5210  5569 (491)    L1M4_orf2#LINE/L1      539   908 (0)  

  chr1_82411762_8   5210 AAGAAAATCTAGACAATACTATTTAGGACATAGGCACAGGCAAAGGTTTT 5259
                                iv   i?ivv v v  iiv   v v  vvi      v     i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_82411762_8   5260 ATGACTAAATCGCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATG 5309
                         v iiv  viv i         vvv          v      v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_82411762_8   5310 GTATCAAATTAAGATAAAGAGCTTCTGCACAGCAAAATAAACTATCATCA 5359
                          v iivv  i  i  v  i i   i  ii vv    iv v       vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_82411762_8   5360 GAGCAAACAGGCAACCTACAGAGTGGGAGAAAAGTTTTGCAATCTGTCCG 5409
                         i  ii  v  i     i     i          vv       viii vii
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_82411762_8   5410 TCTGACAAATGTCTAATATCCAGAATCTATGAGGAATTTAAACAAATT-- 5457
                              i  iv v  vi          v   i i   i ivv    v i--
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_82411762_8   5458 ---TACAGGGAAAACTA---CA--TTAAAAATGGGCAAAGGATATGAACA 5499
                         ---  v ii  v  v  ---  -- ?                 v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_82411762_8   5500 GACACTTCTCAAAAGGTGTCATTCATGTGGCCAATAAACATATCAAAAAA 5549
                             i     v    iv vi  v  vi          i  i  v    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_82411762_8   5550 AGCCCAACATCATTACATCA 5569
                         v  i        ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.96 (52 / 54)
Gap_init rate = 0.01 (3 / 370), avg. gap size = 3.33 (10 / 3)  


3250 26.76 0.66 0.66  chr1_82427250_82433527     4878  5785 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_82427250_8   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_82427250_8   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-- 98

  chr1_82427250_8   4978 AA--CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 5023
                           --   iivi i  i  ii     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chr1_82427250_8   5024 CATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAA 5073
                                  viiv  ii  v  v v  vi    iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_82427250_8   5074 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5123
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_82427250_8   5124 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5173
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_82427250_8   5174 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATACCTACAA 5221
                                  i    i--    i  --        vv  ii i ii  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_82427250_8   5222 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5271
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_82427250_8   5272 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5321
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_82427250_8   5322 CTGAAACTGGATCCCTTCCTTACACCTTATATAAAAATCAATTCAAGATG 5371
                         v    ii    i    v   i     v    i      i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_82427250_8   5372 GATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5421
                            i ?   ii    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_82427250_8   5422 ACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCC 5471
                           v    ?i v viv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_82427250_8   5472 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5521
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_82427250_8   5522 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5571
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_82427250_8   5572 ACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5621
                          v  i     i   iv            v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_82427250_8   5622 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5671
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_82427250_8   5672 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5721
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_82427250_8   5722 TCTCAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTCA 5771
                             v        i  vi viii     v  ii         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_82427250_8   5772 TCATCACTGGCCAT 5785
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2734 26.39 2.90 1.78  chr1_82707083_82712311.rev     3841  4738 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_82707083_8   3841 TGGAACAACATTCCATGCTCATTTATAGGATAAATCAGTATCGTGAAAAT 3890
                              vi i  i     i    vv  v   vi v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_82707083_8   3891 AGCCATACTACCAAAAGTAATTTGTAGACTCAATGATATTTCCATTAAAC 3940
                         i  v     v  v   v i  i ii   i    i vv  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_82707083_8   3941 TATCATTGACATTCTTCACAGA---TGGAAAAAACT-ATTTTAAAATTTA 3986
                          vi  vivi v  i  ii    ---  -- v  i  -  ii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_82707083_8   3987 AATGGAACCAAGTAAGAG-CTCA-AATAGCCAAGTCAATCCTAAACAAAA 4034
                         v      -- v i   i - i  -         iv     i i  v  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_82707083_8   4035 AGAACAAAGCTGGAGGCATCACGCTATCTGACTTCAAACTATATTACAAG 4084
                                  i      vv    i  vi ii i      viv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_82707083_8   4085 ACTACAGTAATCAAAACAGCATGGTACTGGTACAAAAACAAACATACTGA 4134
                         i             i    ii         i i  ii i i     iv  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_82707083_8   4135 CCAATGTAACAGAATAGAGAATTCAAAAATAAGACCGCACACCTACAACC 4184
                         i     v  i     v    i i  i      iv  ii   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_82707083_8   4185 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGCAAAAGAT--T 4232
                          vi    i  i     ivv  v   i v  vv       v   ii  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_82707083_8   4233 CCGTTTCATAAATGGTGCTGGAAAAACTGGCTAGCCATACACAGAAAATT 4282
                          iv  iv i            i v      v  ?   i ii  i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_82707083_8   4283 GAAACTGGACCCCTTACTTACACCATATACAAAAAATTAACTCAAGATTA 4332
                            ii         vv  i                -         i  vi
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGG 495

  chr1_82707083_8   4333 ATTAAAGACTTAAATGTAAAATGC-AAAACTATAAAAACCCTAGAGGAAA 4381
                           i ?    i         i -  -            vi i    i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_82707083_8   4382 ATCTAGGC--AATTCCATTCA-GAACATAGGCAAGGGCAAAGATTTC--- 4425
                          iv    ?--  v  --   i-  v v i  iv   -   v i    ---
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGG-CAATGGTTTCTTA 591

  chr1_82707083_8   4426 ---ATGACAAAAATGCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAA 4472
                         ---      ------         vvv          v      v  i  
  L1M4_orf2#LINE/    592 GATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_82707083_8   4473 ATGGGATTTAATTACA-TTAAAGAGCTTTGCAGAGCAAAAGAAACTGTCA 4521
                           v   i  v  i v -     i vi    iivvv    i  v   i   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_82707083_8   4522 TCAGAGTGAATAGACAACCTACAGAATGGGAGAAAATTTTTGCAACCTAT 4571
                         vv i      v        i                 v       vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_82707083_8   4572 CCATCTGAGAAAGGTCTAATATCTAGAGTCTACAAAAAACCTAAACAAAT 4621
                         vi      v  i  v  vi    i   i v  i   i   iivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_82707083_8   4622 TTAGATGTAAAAA-ACAA-----CCTTTTAAAAAGTGGGCAGAGGGCACA 4665
                         iv v -i      -    -----  vv  ?    i      i   iivii
  L1M4_orf2#LINE/    786 CAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_82707083_8   4666 AACAGATACTTCTTAAAAGAAGACACTCATGTGGCCAAAAAACATATGAA 4715
                           i   i i    iv        i iv  vi       v  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_82707083_8   4716 AAAA-GCTCAACATCACTGATCAT 4738
                           i -           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.00 (42 / 21)  


2639 25.63 1.78 6.90  chr1_82718987_82723285     2851  3806 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_82718987_8   2851 GGGAAGATACCCCATGTTCATGGATTGGAATAATTAATATTATTGGAAAA 2900
                           i      i                    v v        i  ---  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT---AAG 48

  chr1_82718987_8   2901 ATTAATAATATCAATCTTTCATACTATCCAAATCCATACTGCCAAATTCA 2950
                           -iii    i---------------------   ------       --
  L1M4_orf2#LINE/     49 AT-GGCAATAC---------------------TCC------CCAAATT-- 68

  chr1_82718987_8   2951 TAGTAATCCATACTACTCAAAGCAATCCACAAACTCAATGCAATCTCTAT 3000
                         -----------------------i   i   i i    i      i    
  L1M4_orf2#LINE/     69 -----------------------GATCTACAGATTCAACGCAATCCCTAT 95

  chr1_82718987_8   3001 CAAAATATCAG-TGCTATCCAATGTCATAGAAATAGAAAAAATAATACTG 3049
                               vi   -   iv ---- v iii      v  v  iv i  v  i
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTT----TTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr1_82718987_8   3050 AAATTCACATGAAACCACAAAAAAATCCTAAATAGCTGAGGCAATTATGA 3099
                                i   i  vii   iii -i  vi      ii ii    iv   
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGA 190

  chr1_82718987_8   3100 AGAAACAGAACAAAGCTGGAGGTATCAAACTATCTGATTTTAAAGTATAT 3149
                          i  iv         i      vv   v   vi ii    i   iiv  i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_82718987_8   3150 TACAAAGCAATAATAACTAAAATAGTGTGGTATTAGCCAAATAAAAA--G 3197
                                 v i i   ii  i i         i i  ---    ii -- 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC---ATAAGGATAG 287

  chr1_82718987_8   3198 ACACATTGACCAATGAAACAGAATAGAAGGCCAAGAAGTCAACTTACATA 3247
                            i  v  i     i  i     v  ii i v    i v   ii i i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_82718987_8   3248 TATATAGTTAGCTGATTTTTGACAAATGTGCTAAGAATACACAATGGAAA 3297
                          v   i  i ii       i     iv    i    vi iv      ii 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_82718987_8   3298 AAGGACAGTCTCCTCAATAAATTGTGTTGGGAAAAGCAGACTTCCAAGCG 3347
                            i i     ii    i    v   i     v  vii  iv?   vii 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_82718987_8   3348 CAGTAAAATGAAATTGGATTGCTGTTGCATGCCATATA--GAAATCAACT 3395
                           iv i      i     iiv  iiiv  ii       --i    i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_82718987_8   3396 CAAAATGGATTAAAGAATTGAACATAAAACCAGATACTCTGAGACTAAAA 3445
                                   i ?   vi i  ii   i v vi v   v i i   vvv 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_82718987_8   3446 GAAGAAAACCTAGAAAAAAA-CTGTATAACATTGATCTGGACAATTATTT 3494
                                  v   i?iv   -  vii i  v   ivi i i    vi   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_82718987_8   3495 CTTTTATTTGACCACAAAAATACAGGCAATGAAAGTTAAAATAGACAAAT 3544
                            vv  v    vv     ii   i    ii    vv        i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_82718987_8   3545 GTGATTTCATCAAA-TTAAAAAGTTTCTGCACAGCAAAAGAAACAATTAA 3593
                         vv  i         -       v   -  ii vv    i  v  v  i  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAA 686

  chr1_82718987_8   3594 CATTGTGCAGCAACAACCTACAACGTGAGAGAAAATATTTGCAAGTCACA 3643
                         v vv   v ivi      i   ivi  i                i   i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_82718987_8   3644 CATCCGATAAGGAGTTAATATCTAAAATATGTAAGGAGCT--TA------ 3685
                         i   i       iii vi    i i     i   i  i  --  ------
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_82718987_8   3686 AACAATGGCAAGA-AAACAACCCAATT-AAAAATGGGAAAGGGGCCTGAA 3733
                           i   iiv    -   i         -         v  i  iii    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_82718987_8   3734 CAGACATTTCTCAAAAGAAGACATACAAATGTCAAATAGATATATGGAAA 3783
                         i           v        i         v v    iii i   -   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAA 885

  chr1_82718987_8   3784 AAATGTTCAACATCACTAATCAT 3806
                          i   i         ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.23 (167 / 75)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 4.37 (83 / 19)  


3966 19.75 2.71 0.23  chr1_82825245_82829551     2929  3814 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_82825245_8   2929 TAGAAAGATATCCCATGCTCATGAATCAGAAGACTTAA-ATTATGAAGAT 2977
                          i               i     i  ii          -   i v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_82825245_8   2978 GACAAGATTCCCCAAATTGATCTACAGATTCAATGAATTTCCTAACAAAT 3027
                          i   v i                         i v v i    v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_82825245_8   3028 TCCCAGCTGGCTTTTT--CAAAACTTGATAATCTGATCATACAACTGATA 3075
                                  v      --  i  v    i  v      v  v  i v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_82825245_8   3076 TTAAAAATGCAAGAGACACAGAATGGC-AGAACAATCTTGAAAAAGAAAA 3124
                          -ii         i   v      i  - i                  i 
  L1M4_orf2#LINE/    151 T-GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_82825245_8   3125 ACAA-GTGTCAGGACTCACGTTTCTCGATTTCAACACTT----TAAAGCT 3169
                             -  vvv         ii   i i       v    ----i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_82825245_8   3170 ACAATAATCAAAACCATGTGGTACTAACACAAAGATGAACAAACAGA-CT 3218
                            i       i  vi         ii  i  i   ii   v i   - v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_82825245_8   3219 ATAAAATAGA-TTGAGAATAGAGAAATAAACATTTACATGTATGGTCAAT 3267
                           ii      -      i vv          viv     v          
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_82825245_8   3268 TGATTTTTGACAATGCTGCCAA--CAATTCAATGGAGAAAGAATCGTTTT 3315
                                i     v v      -- v         i        v  i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_82825245_8   3316 TT-AAGAAATGGTACCCGGACAACTGGATATCCACATGCCAAAAGATGAA 3364
                           -  v       i iv             ?        v   ii     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_82825245_8   3365 GATGGATGCCTTCCTCATATCATACATAAAAATTAACTCAGAATGAATCT 3414
                          v    iv   v     i i    i i             i    i   v
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_82825245_8   3415 TAGACCTTAATGTGACAGCTACAACTATAAA-TTCCTAGAATAAAATTTA 3463
                         ?      v     i v     v         -i  i     v    iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_82825245_8   3464 AGAGAAAATTCTTATAGTATTTTATTAAGTAATGGTTTCT-AGGTACAAT 3512
                         i ? v    ii ii iiiv  vvi   i i          -  i  ii i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_82825245_8   3513 ACCAAAACCACAAACTGTAAAAGAAAAA-TAGATGCATTGGACTTCATCA 3561
                                v     i vii          -     iv              
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_82825245_8   3562 AA-TTAAACAACTTT-ATGCTTCCTATGACACAATCAAGAAAGTGACAAG 3609
                           -     -      -i      vv v     v             v   
  L1M4_orf2#LINE/    650 AAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_82825245_8   3610 AAAATCCATAGAATGGGAGAAAATAGTTTTAAATGATGTATTTGATGAGG 3659
                          v  i   i                v  vi    v  i   i    i   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_82825245_8   3660 AGTTAATACCCAG----CATAAAGAATTCTTAGTATTCAACAATAAAAAC 3705
                         iii vi  i    ----i        i     vv i    i        v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_82825245_8   3706 ACAA-CAAGGCAATTAAAAAATGGGAAAAATCTTTAAGTAGACATGTACC 3754
                             -i  vv     ?         v   ivv   i i       v vi 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_82825245_8   3755 CAAAGAAAATGTGCAAATGGCCAATAAGCATATTAAAAGATCCTCAATAT 3804
                                i  i i                 i  v       v     i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_82825245_8   3805 CATTAGTCAT 3814
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (101 / 70)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.44 (26 / 18)  


3247 24.73 0.24 0.37  chr1_82897779_82899591.rev      502  1322 (491)    L1M4_orf2#LINE/L1       89   908 (0)  

  chr1_82897779_8    502 TCCCTGTCAGAATACCAATGACATTCTTCACAGAAATAGAAAAACCAATC 551
                              i   i   v   iivi v  i  ii       v  v  i ii   
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chr1_82897779_8    552 CTAAAATTCATATGGAACCACGAAAGACCCAATATAGCCAAAGCTATCCT 601
                                          vii i ii      iv         i v   i 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_82897779_8    602 AAGAAA-AAGAACACAACTGGAGGAATCACATTAGCTGACTTCAAATTAT 650
                         i i   -       v ii       v     i vv ii i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_82897779_8    651 ACTACAGAACTATAGTTAACAAAACAGCATGGTGCAGGCCTAAAGGCAGA 700
                               i i   i   v v   i    ii    i v   v   i ii   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_82897779_8    701 GGCATAGACAAATGGAACAGAATAGAGAACCAAGAAACAAATCCATGCAC 750
                         vii     iv       i     v    ii v     i   i    i  i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_82897779_8    751 CTGTAGTAAACTCATTTTTGACAAAGGTGACAAGAACATACACTGGAGAA 800
                         i i i  v  i v     i     i    v     v   v  v   i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_82897779_8    801 AACAAAGTCTCCTCAATAAATGGTGCTGGGCAAACTGTATATCCATATGC 850
                          iv v     ii    i             vv     v   ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_82897779_8    851 AAAAGAATGAAACTAGACTCCTATATCTTGCCATATACAAAATTCAAATA 900
                                    ii i   i    iv  vii            v i  v v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_82897779_8    901 AAAATGGATTAAAGACTTAAATCTAAGATCTCAAACTATGAAACTGCTAC 950
                                  i ?    i     v     v  v       i     vi  v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_82897779_8    951 AAGAAAACATTGGGGAAAATCTCCAAGACATTGGTCTGGGCAAAGATTTC 1000
                                   v  ? v      i iv   v    vi i     v i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_82897779_8   1001 TTGAGCAATACCTCATAAGCACAGGCAACCAAAGCAAACATGGACAAATG 1050
                           iiii vv  vi  v       i     v    v   v  i  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_82897779_8   1051 GGATCACATCAAG-TTATAAAGTTTCTGCACAGCAAAAGATACAGTCAAC 1099
                            iiv      i-   -   ii  i  ii vv    i  i  vi    v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_82897779_8   1100 AAAGTGAAGAGACAATCCACAGAATGGGAGGAAATATTTGCAAACTACCC 1149
                                 i      i              i             ii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_82897779_8   1150 TTCTGACAAGGGTTTAATAACTAGAATATATAAGGAGCTCAAACAACTCA 1199
                         v     i     vi vi  v i           i  i   vv        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_82897779_8   1200 ATGGAGAAAAAATCTAATAATCTGATATTTAAAATGGGCAAAATATTTGA 1249
                           i- v     iv v     i ii  - ?v            iv      
  L1M4_orf2#LINE/    788 ATA-ATAAAAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGA 835

  chr1_82897779_8   1250 ATAGACATATCTCAAAAGAAAACACACAAATGGCAAACAGGCATATGAAA 1299
                                 v    v      i i i         v  i i   i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_82897779_8   1300 AGGTGCTCAACATCACTGATAAT 1322
                           i            ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (122 / 77)
Gap_init rate = 0.01 (5 / 820), avg. gap size = 1.00 (5 / 5)  


2540 25.47 4.03 1.66  chr1_83305630_83307462      500  1343 (490)    L1M4_orf2#LINE/L1       45   908 (0)  

  chr1_83305630_8    500 TAAGATGTATACATTCCCCCAACTAATCTATAAATGCAACAAAATTCCAA 549
                                vvv i i     v  i i     i i  v    iv   i  v 
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr1_83305630_8    550 TAAAAAAACCCATGC-GCATATTTT-TAGGAATTAAACAAGCTAATACAT 597
                          v    v-    -  -  v v    -i  i    i -      i  v --
  L1M4_orf2#LINE/     95 TCAAAAT-CCCA-GCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCC-- 139

  chr1_83305630_8    598 TAAAAT--ATCTGTGA---CAAAGGAACTAAAATAACCAAAACAATTTTG 642
                               --  v  vi ---   i   v i i    i          i   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_83305630_8    643 AACTAGAAGAATGAACTTGAAGGATTCATGCTACCTGATTTCAGAATTTC 692
                           vv       ii  v   i    i   ii  v  ii      i  i  v
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_83305630_8    693 CTATAAAACTACAGTAATCAAGACAGTGTGGTGCTG--AAAAGGATATAG 740
                            i   i                        i   -- v       v v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_83305630_8    741 GTACAGATACACAGAAGACAACAATGAATACA---ATAGACTCAGACAT- 786
                         i  i    vv ii   v v  iviv  i v  ---   i  i  v    -
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_83305630_8    787 -ATAGTCTGTTGGTTTTCAACAAAGGTATAGAGGTAGTTCAATGGAGAAT 835
                         -  i   vi   i     i    i   iivi  iivi        i   v
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_83305630_8    836 GAAAAAGCCTTCTCAGCAAA-GTTGCTCTAAAAGTTCAGATATCTA--TG 882
                            v - i   i   i    - v    vvi v ii -i    ? i --  
  L1M4_orf2#LINE/    390 GAATA-GTCTTTTCAACAAATGGTGCTGGGACAACT-GGATAKCCACATG 437

  chr1_83305630_8    883 CACAA-AATAAACTTTAATCTGTACCTCACTCCCTTCATAAA------CT 925
                           v  -   i  v  vi i iv        v  v vi i   ------  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_83305630_8    926 CAAAATGACTTGTACACCTAAATCTGAAACTTAAAACTACAAAAATTCTA 975
                                iv ii? v        v i i vi        i    v ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_83305630_8    976 GAAGGTAACATGGGACAAAACCTATGTGACCTGGAGTTAAACAAAATTGT 1025
                             iv     i  ?vv   i  vi       v i    ii   -- v  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA--TGGT 585

  chr1_83305630_8   1026 TTTT--GAT----CACACAAAATCATAATTCATAAAGAAAAAAAGAGATA 1069
                           i --   ----   -     v  i  viv i   ii      v     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACAC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_83305630_8   1070 AATTG-ACTTTCCCAAAATTAATAATTTTTGTTCTTTAAAATACTCTGCT 1118
                              -    ivi         v  i      v   i   iv  v  iii
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_83305630_8   1119 AAAAGACTGAAAAGACAAGCCACAGATTGGGAGAAAATATTTGCATATCA 1168
                           i i v           v       v                  v    
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_83305630_8   1169 CATTTATGATAAAAGACTTGCATCCAGATTCTAATAAGTATTCT-AAAAT 1217
                         i  v v      ii      i       v v  vv   v i   - v  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_83305630_8   1218 CTAAGGA--AGGAAACAAATAATTCGATTAAAAAATGGACAAACGGCTTG 1265
                         ii  vi -- ii i        ii i   ?        i    v ii   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_83305630_8   1266 AACAGAGACTTCACCAAAGATGATTGGTATACAGATGGCAAATAAACACC 1315
                           i   v i   v       v   ----     i     v     i   v
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGAT----ATACAAATGGCCAATAAGCACA 880

  chr1_83305630_8   1316 TAAAAAGATACTCAATAGGAAATAGAGA 1343
                          i       i     i vv ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (123 / 88)
Gap_init rate = 0.03 (25 / 864), avg. gap size = 1.92 (48 / 25)  


2800 25.80 2.76 2.65  chr1_83313317_83318285.rev     3572  4478 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83313317_8   3572 TGTAAAAACATTCCATGCTCATGAATAGGAAGAATCAAAATTGTTAAAAT 3621
                           v   i i  i     i     i  v      v i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83313317_8   3622 GGCCATACTACCCACAGCAATTTA--GATTGAATGCTATTCCTCTTAAAC 3669
                            v     v    v vii  i  --    v  i  v  i   v i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83313317_8   3670 CACCAATTACATTCTTCACAGAATTATAAAAAACTGTTTC-AAAATTCAT 3718
                         iv   ii i v  i  ii     v - i v  i   v i -         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_83313317_8   3719 ATGGAAACATAAAAGAGCTCAAATAGCCAAGGTGATCCTAAGCAAAAATT 3768
                                iii  ii  v ivi         iiii   i i iv  i  vv
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_83313317_8   3769 AAAAAGCTGGAGGCATCACATTACCTGACTTCAAACCATACCACAAGGCC 3818
                          v    i      vv     i v  ii i      v v   i    i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_83313317_8   3819 ACAGTAATCAAAACAGCATGGTACTGGTACAAAAACAGACACATACACCA 3868
                                    i    ii         i i  ii i     i   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_83313317_8   3869 ACTGAACAGAATAGAGAGCCCAGAAATAATGCCAGACAGCTACAACCACC 3918
                          iv   i     v     i          vv   v   vi  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_83313317_8   3919 CAATTTTTGACAAAGTTAACAAAAAACAAGCAATAGGACAAGGACTCCCT 3968
                         ii     i     i v iv   i v-  vv    i  iv   i ivvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCT 398

  chr1_83313317_8   3969 ATTCCATAAATGGTGCTGGGATAACCTGCTAGATATATGCAGAAGACTGA 4018
                         v   v i              i   iv v  ?vi i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_83313317_8   4019 AACTAAACCCCTCCCTGACACCATATACAAAAATCAATTCAAGATAGATT 4068
                          ii ii      v   v                 i  i    i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_83313317_8   4069 AAAGACCTAAATGTAAAACCTAAAACTA-AAGAC-CTTAGAAGGTAACCT 4116
                          ?              i v         -  i  -        iv   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_83313317_8   4117 ACAAATTACCATTC-TGGACATAGGTCCTGGGAAA-ATTTTCTTCCCAAA 4164
                          vi?i v viv   -  iv v i   -- i  v  -iv      --- i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT--TAGGCAATGGTTTCTT---AGA 593

  chr1_83313317_8   4165 GATG---CCAACAGCAATGGCAACAAAAACAAAAATTGACAAACGGGACC 4211
                         v   ---    v    vvi         iv      v  i   iv    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_83313317_8   4212 C------AATTAAAGAGCTTCCGCACAGCAAAAGAAACTATCAACAGAGT 4255
                         i------       i -   ii ii vv    i  v        v i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_83313317_8   4256 AAACAGACAACTTCCACAAGGGGAGAAAATATTTGCAAATTATG-ATTTG 4304
                         i  v       iiv  v  v                    i  i-  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_83313317_8   4305 ATGAAGATAGGTTCTTCATAGATTCTAATATCCAGAATCTATAAGGAACT 4354
                           i i --------------  --  vi          v     i     
  L1M4_orf2#LINE/    743 ATAAGG--------------GA--CTTGTATCCAGAATATATAAAGAACT 776

  chr1_83313317_8   4355 T----AAATTAACAAGCAAAAAACAA----CCCCATTGAAAAGTGGGCTA 4396
                         i----  v i  i  vv    i    ----   v   ?    i     v 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_83313317_8   4397 AAAACCTGAACAGACACTTTTCAAAAGAAGACATACATGTGGCCAATAAG 4446
                          ii ii    i     i  i  v        i     vi           
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_83313317_8   4447 CATATGGAAACAAGCTCAACATCACTAATAAT 4478
                           i   i   v v           ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (141 / 89)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.72 (49 / 18)  


3087 27.75 0.55 0.55  chr1_83346679_83351038     2960  3867 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83346679_8   2960 TGGAAGAAAATTCCATGCTCATGGGTAGGAGGAATTAATATCGTGAAAAT 3009
                              ii v  i     i      i v   i  v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83346679_8   3010 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3059
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83346679_8   3060 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3107
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_83346679_8   3108 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 3157
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_83346679_8   3158 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3207
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_83346679_8   3208 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATTGATC 3257
                                 i   i    ii         i  v ii i   v    v    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_83346679_8   3258 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 3305
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_83346679_8   3306 ATCTGATCTTTGAAAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 3355
                          vi    i  i  v  ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_83346679_8   3356 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCACATGTAGAAAGCT 3405
                           v  i  i              v      v  ?i      i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_83346679_8   3406 GAAACTGGATCCTTTCCTAACACCTTATACAAAAATCAGTTGAAGATGGA 3455
                            ii    i  i v   v     v           i ii v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_83346679_8   3456 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGGTAAC 3505
                          i ?    i  v    v   v       i      vi i      iv   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_83346679_8   3506 TTAGGCA-ATACCATTCAGGACATAAGCATGGGCAAGGACTTCATGTCTA 3554
                         v    ?i- v i -   iv   v vi vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_83346679_8   3555 AAAGACCAAAAGCAATGGTAACAAAAGCCAAAATCAACAAATGGGATCTA 3604
                         vi v          vvi i        vv     vi i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_83346679_8   3605 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3654
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_83346679_8   3655 CAGGCAACCTATAAACTGGGAGAAAATTTTTGCAACCTACTCATCTGACA 3704
                         v  i     i i i v           v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_83346679_8   3705 AAGGTCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 3754
                          i  v  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_83346679_8   3755 AAGACAAACCACCCCATCAAACAGTGGGAGAAGGACATGAACAGACACTT 3804
                                 iv    v  i?  v i    vi     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_83346679_8   3805 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 3854
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_83346679_8   3855 CATCACTGGCCAT 3867
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (143 / 105)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3322 26.21 0.55 0.55  chr1_83359379_83365654     4876  5783 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83359379_8   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83359379_8   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83359379_8   4976 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5022
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_83359379_8   5023 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTGAGCCAAAA 5072
                                 viiv  ii  v  v v  v     ii     i   ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_83359379_8   5073 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACATGG 5122
                                 i      vv       v  ii i      viv       vi 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_83359379_8   5123 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5172
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_83359379_8   5173 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5220
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_83359379_8   5221 TATCTGATCTTTGAAAAACCTGAGAAAAACAAGCAATGGAGAAAGGATTC 5270
                         i vi    i  i  v  ivv  vv  i v  vv      i     i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_83359379_8   5271 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5320
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_83359379_8   5321 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5370
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_83359379_8   5371 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5420
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_83359379_8   5421 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5470
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_83359379_8   5471 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5520
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_83359379_8   5521 ATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAA 5570
                           i   v v  i i   i   i vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_83359379_8   5571 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5620
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_83359379_8   5621 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAGAAGAGA 5670
                          i  i  vi          v  i  v      vv    v iv v  v i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_83359379_8   5671 AAAACAAACAACCCCATCAAAAAGCAGGTGAAGGACATGAACAGACACTT 5720
                           i     i     v  i?    iii  ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_83359379_8   5721 CTCAAAAGAAGACATTTATGTAGCCAAAAAACACATGAAAAAATGCTCAT 5770
                            v        i  vi vi i     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_83359379_8   5771 CATCACTGGCCAT 5783
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 216 30.99 1.41 0.00  chr1_83426871_83432318.rev     3845  3915 (1533)    L1M4_orf2#LINE/L1       64   135 (773)  

  chr1_83426871_8   3845 AAATTAGTATATAGATGCTATACAATCCCAGTAAAAAT-TCAGTCATGCT 3893
                              ii v  i    v v ii       vi v     -i   iiiivi 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr1_83426871_8   3894 TTTTAAAACAATTGACAAGCTG 3915
                             iv iv             
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTG 135

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1)  

1829 26.90 9.86 1.55  chr1_83426871_83432318.rev     4240  4949 (499)    L1M4_orf2#LINE/L1      126   894 (14)  

  chr1_83426871_8   4240 TGACAAACTGTTTCTAAAATTTTTATGAAAATGCAAAC-ACCTAAAATAG 4288
                               i   v i        iv    i        iv-   i i     
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr1_83426871_8   4289 CTGAAGCCATTTTCAGAAGGAAG-------TTG---------TATTGCCT 4322
                          ii  i v  i  v i  i    -------   ---------i i v  i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr1_83426871_8   4323 TATTTTAATACTTATTTAAAAAGCTACAGTAATCAAAACAGTGTAGCATT 4372
                         v    i  v     i - v                 i       i i i 
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACT-ACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_83426871_8   4373 GTTGTAAGGATT--CAGGTAGATCAATGCAACAGAATTAAGAGTTTAGAA 4420
                          vii       v--  vi          v  i      i     ii    
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_83426871_8   4421 ATAGAC----ACTTTCATAGTAAATAGATTTTTTTAAAAAGATATTGCAT 4466
                            i  ----  v  i  i  v   v      iv- v  i i iiiiviv
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCG-ACAAGGGTGCCAAGA 373

  chr1_83426871_8   4467 TTATTCAATGGGGAAA-AATA-TCTTTTTAACAAAT--TCCT-------- 4504
                         ii              -    -      i       -- v  --------
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_83426871_8   4505 -----ATCCCTGTGGAAAA-AATGAACCATAACCCATACCTCATGCCATA 4548
                         ----- ?  vii  v    -      vivvi    v       ii     
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_83426871_8   4549 CACAGAAATAAACTAAAAA----------ACTTTAG----AAAGCT---- 4580
                         i   i    v    v    ----------  i v i---- i    ----
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_83426871_8   4581 ---TACAATTTCCAGAAGAAAACATAGGACAAAATTGTTGCAATCTTTTA 4627
                         ---  v  i iii               ?vv    iv i ii i   vvi
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_83426871_8   4628 TTAGGTAAATGTTACTTAGATGAGATGC-AAAA----AAACTGTAAATAA 4672
                              i  vv   v       iv  ii -    ----  i vii   - i
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA-AG 622

  chr1_83426871_8   4673 AAAGAACTGATAAGCTTGATTTCATCAAAATTAATACAGCACTTCTCTTC 4722
                            i  iv     ii v  i              v ----    i v v 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAA----ACTTTTGTGC 668

  chr1_83426871_8   4723 TTTGAAGACTACCATCAAGAAGATAAAAAGGCAACCTAAAGATGAGGTGG 4772
                           ii   ivi  i        ii i     i     i v   vvi  v i
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_83426871_8   4773 ACATATTTGCATTGCATATATCTGACAAAGGACTTATATTCAAAATATAA 4822
                          v         vvv           i  i      i   i  i      v
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_83426871_8   4823 AAATCATTCTTACAATTCAGTAAGAAAA---CTAGCAACCAGATTTTTTT 4869
                            vv i        i   i   v    --- v ii    vi   ?vvv-
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA- 817

  chr1_83426871_8   4870 TTTAATGGGCGAAATAGTTGACTAAATATTTTACCAAAAAAGATACATTC 4919
                         ---       i  iv v    v  i i    iv     i      i ivv
  L1M4_orf2#LINE/    818 ---AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_83426871_8   4920 ATGACTAACAAACACAAAACAAGAGGTTCA 4949
                            i i  i  i    vi v    v i   
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.58 (115 / 73)
Gap_init rate = 0.03 (21 / 769), avg. gap size = 3.86 (81 / 21)  


3300 26.76 0.44 0.44  chr1_83440812_83447083     4872  5779 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83440812_8   4872 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4921
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83440812_8   4922 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAAC 4971
                            v     v     iv i  i           i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83440812_8   4972 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTGAAAGTTCA 5019
                          v   iivi i  i  ii     -   -- v  i  - iiiv   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_83440812_8   5020 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGGCAATCCTAAGCCAAAAG 5069
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_83440812_8   5070 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACACGGC 5119
                                i      vv       v  ii i      viv       vi  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_83440812_8   5120 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5169
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_83440812_8   5170 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5217
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_83440812_8   5218 ATCTGCTCTTTGACAAACCTGAGAAAAACAAGTAATGGGGAAAGGATTGC 5267
                          vi  v i  i     ivv  vv  i v  vvi           i  v i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_83440812_8   5268 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5317
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_83440812_8   5318 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5367
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_83440812_8   5368 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5417
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_83440812_8   5418 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5467
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_83440812_8   5468 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5517
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_83440812_8   5518 TTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAAC 5567
                          i   v v  i i   i   i vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_83440812_8   5568 AGGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5617
                           i     i   iv            v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_83440812_8   5618 AGGGCTAATATCAAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5667
                         i  i  vi    v     v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_83440812_8   5668 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTT 5717
                          i     i     v  i?    i           iv    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_83440812_8   5718 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5767
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_83440812_8   5768 ATCACTGGCCAT 5779
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3070 26.03 2.68 1.23  chr1_83477180_83482478     3912  4806 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83477180_8   3912 TGGAAACGCATGCCATGCCCATGAATGGGTAGAATCAATATTGTGAAAAT 3961
                               vii  v     ii    i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83477180_8   3962 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAGA 4011
                          i v     v  v   vii       i      i        i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83477180_8   4012 TACCACCATCATTCTTCACAGAGTTAGAAAAATCAATTCAAAAATTCATA 4061
                          v   v vv v  i  ii    iv v  v  iiii  i v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_83477180_8   4062 TGGAACCAAAAAAAAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCA 4111
                              ------- viv  ii  v  v v         i   vvi i iv 
  L1M4_orf2#LINE/    151 TGGAA-------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_83477180_8   4112 AAAAGAACAAATCTAGAGGCATCACACTGCCTGATTTCAAACTATACTAT 4161
                          i         vi i    vv       v  ii        viv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_83477180_8   4162 AAAGCCATAGTCACCAAAACAGTGTGGTACTGATATAAAAATGGGCACAT 4211
                              i i   v i   i              ii    ii  i i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_83477180_8   4212 AGACCAATGTAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTAGA 4261
                            i     v  i     v    ii               v i i   vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_83477180_8   4262 GCCAACTGATCTTCAACAAAGCAAACAAAAA-ATAAAGTGGGGAAAGGAC 4310
                          i   i    i   i    i vviv   i v-  vv i         i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_83477180_8   4311 ATCCTTTTCAATAAATGGTGCTGGGATAGTTGGCTAGCCGCGTGTGGGAG 4360
                          vi        i              i ii   v  ?  i i  iiii  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_83477180_8   4361 AACGAAACTGGATCCTCATCTCTCACCTTATACAAATATCAACTCAAGAT 4410
                           i   ii    i  ii i   v    v        v  i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_83477180_8   4411 GGATTGAAGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGAT 4460
                             ii?    i    iv     v  i           v ii       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_83477180_8   4461 AACATTAGAAAAACCCTTCTAGACATTGTTTTAGGCAAGGATTTCGTGAC 4510
                              vi ?iv  vi    vv   v   vv        v i    v iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_83477180_8   4511 CAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAACAGCTGGGAC- 4559
                         i v  vv         v v    i    iv   i   i i iv v    -
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_83477180_8   4560 -----AAAACTAAAAGAGTTTTTGCATGGCAAAAAGGA-ACAGTTAGCAG 4603
                         -----    i     ivv   v   v --    --   -  vi i iv i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTT--CAAA--GGACACTATCAAGAA 689

  chr1_83477180_8   4604 AGTAAACAGACAACCCACAAAGTGGGAGAAAATCTTCACAATCTATACAC 4653
                            i  v            i i           v  ii   vii   i i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_83477180_8   4654 CTGACAAAGGACTAATATCCAGAATCTACAACAAACTC------------ 4691
                             i  i     vi          v  i  vi     ------------
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_83477180_8   4692 ----AAAAAACAAACAATCCCATCAAAAAGTGGGCTAAGAACATGAATAG 4737
                         ----    i     i  i  v  i?    i     v   i iv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_83477180_8   4738 AAAATTCTCAAAAAAAGACATGCAAATGGCCAACAAACATATGAAAAAAT 4787
                          v v     v   i    i  i           i  i  i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_83477180_8   4788 GCTCAACATCACTAATGAT 4806
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (139 / 90)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 5.00 (35 / 7)  


3173 25.91 0.43 2.80  chr1_83528365_83530493.rev      709  1638 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83528365_8    709 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 758
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83528365_8    759 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 808
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83528365_8    809 TACCAATGACTTTCTTCACAGAT-TTGGAAAAAACT-ACTTTAAATTTCA 856
                          v   iivi i  i  ii    v-   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_83528365_8    857 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 906
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_83528365_8    907 AACAAAGCCGGAGGCATCACACTACCTGACTTCAAACTATACTACACGGC 956
                                ii     vv       v  ii i      viv       vi  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_83528365_8    957 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGCATGGTACTGG 1006
                                 i   i    ii         i --------------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA-------------------- 278

  chr1_83528365_8   1007 TACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAA 1054
                           -- ii i   v                i    i--    i  --    
  L1M4_orf2#LINE/    279 TA--AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAA 324

  chr1_83528365_8   1055 ATAACGCCGCATGTCTACAACTATCTGATCTTTGACAAACCTGAGAAAAA 1104
                             vv  ii ii i  iiiii vi    i  i     ivv  vv  i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_83528365_8   1105 CAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACT 1154
                           vv            i  vvi  v  i  i              v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_83528365_8   1155 GGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTAT 1204
                           v  ?   i   i i  iiv    ii    i    v   i     v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_83528365_8   1205 ACAAAAATCAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAAC 1254
                                 i  i    i      i ?    i    i  v   v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_83528365_8   1255 CATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCA 1304
                         i      vi i           v    ?i v viv   iv   v v  vv
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_83528365_8   1305 TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGAC 1354
                          i     v ii   v ivv  vi            vvi           v
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_83528365_8   1355 AAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 1404
                              v  i    v   ii v  i   v v  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_83528365_8   1405 AGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTT 1454
                         i  v    i  vv i      v  i     i   i             v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_83528365_8   1455 TCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAA 1504
                          i    vii ivi      i  i  i  vi          v  i  v   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_83528365_8   1505 CTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGC 1554
                            vv    v iv i  v     i     i     v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_83528365_8   1555 AAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 1604
                               iv    i     i     v        i  vi viii     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_83528365_8   1605 AACACATGAAAAAATGCTCATCATCACTGGCCAT 1638
                          i          i       v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 4.29 (30 / 7)  


2854 27.91 1.55 1.00  chr1_83534171_83539146.rev     3583  4485 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83534171_8   3583 TGGAAAAACTTTCCATGCTCGTGGCTAGGAAGAATCGATATGGTTAAAAT 3632
                               i iv i     i  i   v v      v ii    v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83534171_8   3633 GGCCATACTGCCCAAAGCAAATTACAGATTCAATGCTATTCTTATCAAAA 3682
                            v     v      vii vi           i  v  i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83534171_8   3683 TACCAATGACATTCTTCACAGAATTAGAAAAGAACT-ATTTTAAAATTCA 3731
                          v   iivi v  i  ii     v v  v   --  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_83534171_8   3732 CTTGGAAGCAAAAAAGAGCCCAAGTAGCCAAGGTAATCCTAAGCAAAAAG 3781
                         iv     iiiv  ii  v  vi i       iii    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_83534171_8   3782 AGCAAAGCTGGAGACATCAAGTTACCCATCTTCAAATCATACTACACAGC 3831
                          i     i     ivv   vii v    vi      v v       v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_83534171_8   3832 TACAGTAACCAAAACCACATGGTACTGTTACAACAACAGGCATATAGACT 3881
                                 i   i  viii        vi i  vi i  i        ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_83534171_8   3882 AATAGAACAGAATAGAGTACCCAGAAATAATGCCACACACCTACAACCAT 3931
                            i   i     v   vii          vv   i   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_83534171_8   3932 CTGATTTTCCTCAAAGGTGACAAAAGCAAGCAATGGGCAAAGGACTTTCT 3981
                         i        vv   i    v   i v  vv       v    i ivv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_83534171_8   3982 CGTTAATAAATGGTGCTGTCGTAACTGGCTAGCAATATGCAGAAGATTAA 4031
                         iv i  i           vvii      v  ? v i     i    v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_83534171_8   4032 AACGGAATCCCTTCCTTATACCATATACAAAAGTCAACTCATCATAGATT 4081
                          iiv i i    v   i i             i i      vv  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_83534171_8   4082 AAAGACTTAAATGTAAAACTTAAAACTATAAAAACTCT-GGAAGATAACC 4130
                          ?    i         i vi             -    -i     v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr1_83534171_8   4131 TAGG---AAGTGCCATTCTGGACATAGGCCCTGGCAAAGACTTCAT-GAT 4176
                             ---  i -- -   vv   v v  viiv     v ii   v -   
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_83534171_8   4177 GAAGACACCAAAAGCAATGGTAACAAAAACAAAAGTTGACACATAGGACC 4226
                         - v             vvi i       iv    i v  i v  v    i
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_83534171_8   4227 TAATTTAACTAACCAGTTTCTGCACAGCAAAAGAAACTATCAAGAGAGTA 4276
                          v  iv  v v vv ii  i  ii vv    i  v          i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_83534171_8   4277 AACAGATAACCTACAGAACAGAAGAAGATATTTTGCAAACTGTGCTTCTG 4326
                           v   i    i      ii i    i      -     iii iiv    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTG 742

  chr1_83534171_8   4327 ACAAAGATCTAATATCCAGAATCTATAAGGAACTTAAACAAATTAACAAG 4376
                          i  i iv  vi          v     i     ivv    v i  i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_83534171_8   4377 CAA----TAAATAACCCCATGAAAAAGTTGGCTAAGGACACGAACAGCCT 4422
                         v  ----i         v  v?    i v   v     ivi   i  v v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_83534171_8   4423 CTTTTTAAAAGACGTATCTGCA----GCCAACAAGCATATGAAAAAATGT 4468
                         i  i iv     v -  v i  ----     i     i       i   i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAG-ATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_83534171_8   4469 TCAGCATCAGTAATCAT 4485
                            i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (146 / 103)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


3252 27.14 1.22 0.22  chr1_83561965_83565439     2084  2982 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83561965_8   2084 TGGAGAGA-ATTCCATGTTCATGGGTTGTACAATACAATGTTGTCAAGAT 2132
                             i   -  i            i   v vi ivi   i    i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83561965_8   2133 GTCCGTTCTCCCCAGCTTGATCCATAGATTCAATGCAATTCCATTAAAAA 2182
                          v vi v       iv      i i        i     i  vv v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83561965_8   2183 TCCTAGCAAGTTATGTTGGGGATATCAAGAAATGAATTCTAAAGTTTATA 2232
                            i   vivi v v   vi  v  ii v  iivi  i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_83561965_8   2233 TGGAGAGGCAAAAGATCCAGA-TAGCCAATATAATATTGAAGGAGAAGAA 2281
                             i v    ii  i     -       v i   v     ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_83561965_8   2282 CAAAGTTGGAGGACTAACACTACTTGACTTCAACACTTACTTTAAAGCTA 2331
                                        v     v iii i     v       vi       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_83561965_8   2332 CAGTAATCAAAACAGTATGATACTGGCAAAAGAATAGACAAATAGATCAA 2381
                                   i     i  i        v   i       v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_83561965_8   2382 TGAAACAAAATAGAAAGCTCAGGAATAAGCCCACAAAAATATTGTCAGCT 2431
                           i  i i   v  i  ii   i     i    i v vv   v    ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_83561965_8   2432 GATCCTGAGAAAGGAGAAAAAGGCAATACAATACAGAAAGA---GTCTTT 2478
                            ii viiv    ivivv   i v  v    ivi      ---      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_83561965_8   2479 TCAACAAGGAGTGCTGAAAAAACTGGACATCCACATGCAAAACCATGAAT 2528
                                ivi      ii v       i ?            vv     v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_83561965_8   2529 CTAGACAGAGATTTTGCATTCTTCATAAAAACTAGCTCAAAATGAATGAC 2578
                         i i   vvvv ii ii  iiv vi i     i  i         i  v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_83561965_8   2579 AGACCTGAATGTAAAACTCAAAACTACAAAACTCCTTGAAGATAACATAG 2628
                               i       i vii       i       i v     v       
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_83561965_8   2629 G-GTAAAAAATAGATGGCTGTGGGTTTGGCTATGATCTTTTAGATACAAC 2677
                          -     vvv v -  i iv      v   v   i i i       ii  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_83561965_8   2678 ACCAAAGCTATGGTCCATAAAAGAAATAATTGATAAGCTGGACTTCATTA 2727
                               ivi iiiv v i        v   v     ii          i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_83561965_8   2728 AAATTAAAAGCCTCTGCTCTCTAAACAGAAAGTGTCAAGAGAATTTGAAC 2777
                                  i i i  iv  ii   -i  v v i      i i vvi  v
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAAAG 698

  chr1_83561965_8   2778 ACAAGCCACAGAGGAAGAGAAAGTGTTTGTAGAACAAACATCTGACAAAG 2827
                             v       ivii      i i    i i v  v i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_83561965_8   2828 GATTT-TATCCAAACTATTCAAAGAATTCTTAAATCACAACAATAAGGAA 2876
                           i  -      i v   vi      i     v v v   i     ii i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_83561965_8   2877 ACA----GCCTGATTTAAAAATTGGCAAAAGACCTTAACAGATGCCTCAC 2922
                            ----i  ii   ?      v      i  ii v  i   iiii  v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_83561965_8   2923 CAAAGAAAATATACAGATGGTAAGTAAGCCTACCAAAACAGGTTTCACAT 2972
                                i       i    iv i     vi iv    v v i iv    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_83561965_8   2973 CATATGTCAC 2982
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.65 (150 / 91)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3376 24.22 2.80 1.01  chr1_83712397_83715664     1884  2775 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83712397_8   1884 TGGAAAAAAGTT--ATATTTATGGATAGGAAGACTAAATACTGTCAAGAT 1931
                               i vi i--  i  i      v        v    i   i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83712397_8   1932 GTCAGTTCTTTTCAATTTGATCTATAAATTCAATGCAATGCCAATTAAAG 1981
                          v  i v  iii   v        i i      i     v  v  i   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83712397_8   1982 TCTCAGCAAGTTTTTTGGGGGGTATCAACAAACTGATCCTAAATTGTATA 2031
                           i    vivi     v vi iv  ii    i           v vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_83712397_8   2032 TAGAGAGGCAAAAGACCCAAAATAGCCAACATAACATTGAA---GAGGAA 2078
                          i  i v    ii      i         v i  iv     ---  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_83712397_8   2079 TAAAGTTGGAGGATTGACCCTACTTGACTTCAAGACTTAATATATAGCTA 2128
                         i            i v  v  v iii i     i     v  i v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_83712397_8   2129 CAATAATCGAGACAGTGTGGTATTGGCAAAAGAATAAACAAATAGATCAA 2178
                           i     i             i     v   i   i   v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_83712397_8   2179 TGGAATGGAATAGAGATCCCAGAAATAGACCAACAAAACTATAGTCAATT 2228
                               i    v    vi         i   v i v vi   i       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_83712397_8   2229 GATCACTGACAAAGGAACAAAGGCAATAAAAAGAAGAAAAGATAGTCTTT 2278
                            ivii     i  vi v   i v  vv  v ii    ii         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_83712397_8   2279 T-AACAAATGATGCTAGAACAACTGAACATATATACACAAAA-AATAAAA 2326
                          -        i    i i       i i ?vi i ii     -   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_83712397_8   2327 --AGA-----ATCTAGACACTGCCCTTCACAAAAACTAACTCAGAATGGA 2369
                         --i  ----- i  ---   -i  v vi       i       i      
  L1M4_orf2#LINE/    451 TTGGACCCCTACCT---CAC-ACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_83712397_8   2370 TCACAAACCTAAGTGTAAAACGTGGGACTACAAAACTCCTAGAAGATAAG 2419
                            ? i      i     i vv iii    i       i       v  v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_83712397_8   2420 ATAGAAAAAAAATCTAGATGACCTTAGGTTTGGTGATGACTTTTTAGAGA 2469
                             i?iv   -   vvi       i    v  ii   ii  i     v 
  L1M4_orf2#LINE/    547 ATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_83712397_8   2470 CAGCACCAAAGGCATGATCCATGAAAGAAAGAATTGTTAAGCTGGACCTC 2519
                         iii       i   ii v v ii       i   v v   ii     i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_83712397_8   2520 ATTAAAATTAAAAATTTCTGCTCTTTGAAAGACACTATCAAGAGAATGAA 2569
                           i           i  i  iv   ii  i             i i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_83712397_8   2570 AA-----CCCATAGTCTGGGAGAAAATATTTGTAAAGGACATATCTGATT 2614
                           -----    i  vv                i   vv i         v
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_83712397_8   2615 AAGGACTGTTACACAAAATACACAAAGAACTCTTAAAATTCAACAATAAA 2664
                          i     vv  iv  i    i i            v  i    i      
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_83712397_8   2665 AA---AAAT---CCAATTTTTAAAATAGGCCTTAACAGACCTTAACAGAC 2708
                           ---    ---      ?v-     i   ---  vi  ii v  i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWA-AAAATGGGC---AAAGGATTTGAATAGAC 841

  chr1_83712397_8   2709 ACCTCACCAAAGAAGACATGCAGATGACAAATAAGCATATGAAAACTCAC 2758
                          ii  v          i  i  i   i v        i       vvii 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_83712397_8   2759 TCCACATCATATGGCAC 2775
                           v      ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.99 (141 / 71)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.43 (34 / 14)  


2541 22.22 5.98 5.37  chr1_83753818_83756027.rev      531  1349 (861)    L1M4_orf2#LINE/L1        1   824 (84)  

  chr1_83753818_8    531 TAGAGATACATGCCTTATTCATGTGTTGGAAGACTCAATATTTCTAACAT 580
                          i  i v i  v  v i      vi          i      vi   v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83753818_8    581 GTCAGT--TGTCCAAAT--------------AATGGAATTCAAATAAAAA 614
                          v  i -- vi      --------------  i v   i vv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83753818_8    615 TTTCAGTAGGTTATTTTGTAAAAATTGGCAACCAGACTTTAAAATTCATA 664
                          ii   iv vi v     i i      i   v v  iii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_83753818_8    665 TGGAAATGTAAGGGACCTAGATTAGCCAAAACAAAACCAAAGTTGAAAAC 714
                                 i        i   v            --i ----       v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAA--TC----TTGAAAAA 194

  chr1_83753818_8    715 -AAGAATGAAGATGGTGAACTAACACTACTTGATTTCAAA--TTATTATA 761
                         -     ii   v   v i   v     v iii        --   i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_83753818_8    762 AAGCTATAGTAATCACGGCAGTATTATATTG-CATAAATATAGAGAAACA 810
                               i        v i    i vi  i  -     iv     v v i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_83753818_8    811 GATCA---GAATAGG-----GAGCTCAGAAATAGACTCACAAATATATGA 852
                              ---      i-----   ii        i  i  i v  v    i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_83753818_8    853 ACAAGTGATTTTTGATGAAGGCAC-AAGAGCAATTCAGTGGAGAAA---- 897
                         v   v       i  ii i  ii -    v  -    i   i    ----
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAAT 393

  chr1_83753818_8    898 AGTCTTTTCAAGAAATAATGTGTAGAAAAATTGGCTAGCCATATGCCAAC 947
                                    v    ii  i- i i v  i   v  ?   i    ----
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGC-TGGGACAACTGGATAKCCACATGC---- 438

  chr1_83753818_8    948 AAAAAAGAAGAATGAAAAAGAAAAAAAAATGACTTTGATTCATACCTTGC 997
                         ----- i         i----------------  v  ii v     -- 
  L1M4_orf2#LINE/    439 -----AAAAGAATGAAG----------------TTGGACCCCTACCT--C 465

  chr1_83753818_8    998 ATACTTTGCACCATATACAGATATTAACTCAAAATAGATTCTGGACCTAA 1047
                          -------           i v             i   iv?i       
  L1M4_orf2#LINE/    466 A-------CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_83753818_8   1048 ATGTAA-------AACTTCAAA---CTTAGGAGAAAATCTCTG---AAGT 1084
                               -------    vi   ---     i      iv vv ---  i 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_83753818_8   1085 CTCTGTGACCTTGGGTTAGGTA--GAGTTCTTAGATATAGCACCAAAAGC 1132
                           ii                i -- iv           ii          
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_83753818_8   1133 TTGATTTATGAAACAACAAATTGATAAGTTGAACTTCATTAACATTAAAA 1182
                         vii viv ii   v  v    v     i   i       i  v       
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_83753818_8   1183 AGTTCTGCTCTT-AAAAAACAATATAAAGAAAAGAAGAAAGCAAGCCACG 1231
                          v  i  iv   -   ii   v   v      ivi i  ii   v    i
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_83753818_8   1232 TACTGGAAGAAAGTATTTCTAACTCACATATCTGATGAAAGACTTGTATC 1281
                         v v   i     i     vi  v   i         i ii          
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_83753818_8   1282 CCTAATATATATAAACAGTCTCAAAACTCAATAATAAAAAACTCAAACAA 1331
                          vv        -  iv v   i v                iv-    i  
  L1M4_orf2#LINE/    759 CAGAATATATA-AAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAA 806

  chr1_83753818_8   1332 CAAAATTAAAATATGGGC 1349
                          vv    ?   v      
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGC 824

Transitions / transversions = 1.52 (108 / 71)
Gap_init rate = 0.03 (24 / 824), avg. gap size = 3.88 (93 / 24)  

 383 17.58 3.30 0.00  chr1_83753818_83756027.rev     1629  1719 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_83753818_8   1629 AAAAGTGCACAAAAGATTTGAACAAACAT---CCCACAAAGGATATAAAA 1675
                             i  vi    i        i i    ---i   v i i      v  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_83753818_8   1676 ATGACAAATAAGCATAGGAAAAGATGCTCAACACCATTGTTAAT 1719
                            i v        i v                i  ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.20 (11 / 5)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 3.00 (3 / 1)  


3514 24.16 1.68 0.45  chr1_83765606_83769861.rev     2872  3765 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_83765606_8   2872 AAAGACATTCCACGTTTGAGGGTTTGAAAAATCAGTATTGTTGAAATGTC 2921
                              i  i   i   iiv  i  v   i v i i       i i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_83765606_8   2922 CATACTATGCAAAGCAATCTATAGATTCAATGCAATCCCTATCAAAATAT 2971
                         v     viv    vii     i        i                 vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_83765606_8   2972 CAATGACATTCTTCATAGAAATAGAAAAATTAATCCTAAAATTTATATGG 3021
                           iivi v  i  iii      v  v  ii i           i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_83765606_8   3022 AACCACAAAAGAACATAAGTAGTCAAAACCATCCTTAACAAAAAAGAACA 3071
                           vii   ii  v vvi i   i      v   -  i v   i       
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAAGAAGAACA 202

  chr1_83765606_8   3072 AAATTGGAGGAATCACATTGCCTGACTTTAAATTATACTACAGAGCTA-- 3119
                           i        v     i v  ii i  i   viv       i     --
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_83765606_8   3120 -TAATCAAAACAGCATGACACTGGCATAAAAACGGACATATAGACCAATG 3168
                         -       i    ii  ii          ii ii          i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_83765606_8   3169 GAACAGACTAGAGAACCAAGAAATATATCCATACACCTACAATTAACTCA 3218
                            i   v v    ii v       v i       ii  iii i  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_83765606_8   3219 TTTTTGGCAAAAGTGCCAAGAACATAC--TT---AAAGGACAGTATCTTC 3263
                             i i   ii         v   v -- v---    i i   v i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_83765606_8   3264 AATAAAGGGTTC-GGGAAAACTGGATATTCACATACAGAAGAATGAAACT 3312
                           i   v   v -    v         ?i     i  i         ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_83765606_8   3313 AGACTCCTATCTCTCACTATGTACAAAAATCAAATCAAAGTGGGTTAAAG 3362
                         i   i    i   v   i  i         i  v     i   i i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_83765606_8   3363 AGTTAAATCTAAGATTTCAAACTATGAAACTATTGGAATAAAACATTAGG 3412
                          vi     v     vi v       i     v  i   v       vi ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_83765606_8   3413 G-AAA-CTTCAGGATATTGGTCTGGGTGAAGATTTCTTGAGTA--ATACC 3458
                          -   -    iv  iv    vi i  ii v i      iii  -- i   
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_83765606_8   3459 ATAAAAGCTCCGTCAACCAAAGCAAAAATAGACAAATGGGATCACATCAA 3508
                          --     v viv    v    v         i    v   iiv      
  L1M4_orf2#LINE/    603 A--AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_83765606_8   3509 G-TTAAAGCATGTCTGTACAGCAAAGAAAACAATAAAAAAAATGAAGAGA 3557
                         i-     i- iv i   i vv     i v  v  v  i   i    i   
  L1M4_orf2#LINE/    651 AATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_83765606_8   3558 CAACCCACAGAATGGGGGAAA-TATTTGCAAACTATCTATTTGTCAAGGG 3606
                                         i    -          ii  v   i  vi     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_83765606_8   3607 ATTAAAAACCAGAATATATAAAGAGCTCAAACAACTCAATAGGAAAAAGT 3656
                          i viv v                i   vv           iv      v
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_83765606_8   3657 CAAATAATCCAATTTAAAAATGGGCAAAAGATCTGAATAGACATTTTTCA 3706
                                i      ?             i   i             i  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_83765606_8   3707 AAAGAAGACAAACACATGGCAAACAGGTATGTGAAAAGGAGCTCAACATC 3756
                                 i v   v     v  i i i ii       iv          
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_83765606_8   3757 ATTGGTCAT 3765
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.83 (137 / 75)
Gap_init rate = 0.01 (12 / 905), avg. gap size = 1.58 (19 / 12)  


3291 23.70 3.97 1.02  chr1_83777528_83781647     2746  3627 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83777528_8   2746 TAAAAAGATAGTCCATGTTCATGCATCAGAAGGATTAATATTGTTAAAAT 2795
                          ii       vi           v  ii    iv             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83777528_8   2796 GTCCATACTGCCTAAACCAATATATATGTTCAATGTAATCCTTATCAAAA 2845
                          v v     v  i   iii  v  i vi     i i     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83777528_8   2846 TCCCAATGGCATTTTTCACAGAAATAGAAAAAAACAATCCTGAAATTTAT 2895
                              iiv  v     ii       v  v  iv-ii     i     i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_83777528_8   2896 GTGAAACTACAAGTGATCCCGAATAGTCAAAGCAATTCTGGGGAAAAA-- 2943
                         i  i  v i    v  i  v      i    i    ii  iii  i  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_83777528_8   2944 ---AAGTTTGGGGCATCAAACTTCCTGATTT-AAAATTATATTACAAAAC 2989
                         ---     v i  vv   v      ii    -    i -  i      i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr1_83777528_8   2990 TATAGTAATAAAAACAGTATGGTATGGGAGGAAAAACAGACGCATAGAGA 3039
                           i      v  i     i     iv  viv  ii i    ii     vv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_83777528_8   3040 AGTGGAACAGTATAGAGGGACTAGAAACACATCCAAACATATATGGCCAA 3089
                          i     i  v  v   i v i     i v i   v    v     i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_83777528_8   3090 TGAATTTTTGACAAGAATACCAGAAAGAC-AT--GATGAAAAAAGAATAG 3136
                          vi     i      ii i   ---    -  --i   iii         
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCA---AGACCATTCAATGGGGAAAGAATAG 395

  chr1_83777528_8   3137 TCTCTTCAATAAATGGTGCTGGGA---------------------AAGAA 3165
                            i     i              ---------------------     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_83777528_8   3166 TGAAACTGGACTCTTATCTTAACAACATATACAAAAATTAACTCAAAATG 3215
                             ii     i i  i  i -  v                         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATG 494

  chr1_83777528_8   3216 GATAAAATACCTAAATATAAGACCTGAAACCATGCAATTCCTGGAAGGAA 3265
                            v ? v        i     v  i    i  iv  i  i i    i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_83777528_8   3266 ACATAGGGGGAAAATTCTT--TTACATGGGCCTTGGCAATAATTTCTTGG 3313
                                ? v   --    -- v  v v  vi v      ii      i 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_83777528_8   3314 ATGTCATACCAAAACCTCAGGCTACACAAGCAAAAATAAATAAATGGGAC 3363
                           i v i       v v  i  v   v   v       i      v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_83777528_8   3364 TATATCAAGCTAAAAAGTTTTCGCACAGCAAAGGAAATAGTAAACAAAAT 3413
                          vi     iv v    ii   i ii vv       v ivi v  v   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_83777528_8   3414 GAAATGGCATCCTACAGGCTGGGAAAAAAATATTTGCAAATGATCTATGA 3463
                             v i  v  i    iv     i    -           v  v   vv
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCT 741

  chr1_83777528_8   3464 GATAAAGGGTTAATATCCAAGATTTATAAAGAACTTATATAAGTCAATAG 3513
                              i  ii vi      ii  v           iv  i  v      i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_83777528_8   3514 CAAGAAAACCTATAACCTTATT-AAAAATGAGCAAAGGACCTGAATAGTA 3562
                         i  i  i  vv      iv   -       i        ii       vv
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_83777528_8   3563 ATTTCTCCAAAGATGACATA-AAATGGTCAA-AGGTATAAGAAAAAATGC 3610
                                      v  i   -      i   - i i i v     i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_83777528_8   3611 TCAACATCACTAGTCAT 3627
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (129 / 78)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.93 (44 / 15)  


2701 23.10 0.78 1.09  chr1_83857063_83858698.rev      501  1145 (491)    L1M4_orf2#LINE/L1      266   908 (0)  

  chr1_83857063_8    501 TATGGTACTGACATAAAAATGGGCATATAGACCAGTGGAACAGAATAGAG 550
                          i        i     ii  i i        i  i     i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_83857063_8    551 ACTCTGGAAATAAATCCAAACATATATGGTCAACTAATTTTTGACAAGAA 600
                          v  ii        i   v    v         i i     i      ii
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_83857063_8    601 CACCAAAAAAGACA--CAATGGGGAAAAGGATGATCTATTTAATAAATGG 648
                         ii    i v---  --           - i  ii   v  i  i      
  L1M4_orf2#LINE/    366 TGCCAAGAC---CATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGG 411

  chr1_83857063_8    649 TGAAGGTAAAATTAGATATCCACATGCAAAAGAATGAAATTGGACCCTTA 698
                           vv  v v  i i    ?                   i        i  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_83857063_8    699 TCTTACCCCACACACAAAAATCAACTCAAAATGGGCAAAAGGCCTAAATA 748
                         i  i  v   i i        i            iiv ?  i       i
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_83857063_8    749 TAACACTTGAAACCATGAAACTCCTAGAAGAAAACATAGGGGAAGA-CTC 797
                            v vi i    i  i      i                ? v i -  i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_83857063_8    798 CTTGACATTGGCTTTGGCAATGATTTTTTTGGATGTCACACCAAAAACTC 847
                          v    v    v  v       i   i  -i   i v         i v 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCAC 610

  chr1_83857063_8    848 AGGCTACAAAAGCAGAAATAAATAAGTGGGATTATATTGAACTAAAAAGC 897
                          i  v       v i     i    i v   i vi  ii  v v    i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_83857063_8    898 TTTTGCACAGCAA-GTAAATAATCAACAAAATGAAAAAGGCAGTCTACAG 946
                              ii vv   - v v iv     v   i      - i  ii i    
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GACAACCCACAG 709

  chr1_83857063_8    947 AATGGGAGAAATTATTTGCAAATCATGTATCTGATTAGAGATTACTGTCC 996
                                    v              i        v  i  i vv i   
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_83857063_8    997 AAAACGTATCAGGGACTCATACAGCTTGGTAGAAAAAAATCAAATAATCA 1046
                          i  ii   v i i    v    i  iii  iv     iv       i v
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_83857063_8   1047 GATT-ACAAATAGGCAAAGGACCTGAATAGATATTTTTTCTGAAGAAGGC 1095
                         i   - v    i         ii        i    i i -i      ii
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC-AAAGAAGAT 858

  chr1_83857063_8   1096 ATACAAATGGTCAACAGGTACGTGCAAATGTGCTCAACGTTACTAATTAT 1145
                                   i   i i i  i  v   vi        i i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (101 / 45)
Gap_init rate = 0.01 (9 / 643), avg. gap size = 1.33 (12 / 9)  


3065 27.89 0.66 0.55  chr1_83862470_83867763.rev     3897  4803 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_83862470_8   3897 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAA 3946
                              ii i  i     i      i v      v i     ii v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83862470_8   3947 GGCCCTACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGA 3996
                            vv    v     iv i  i  i       ii  v     i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83862470_8   3997 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4044
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_83862470_8   4045 TATGGAACCAAAAAAGAGCCCGAATCGCCAAGTCAATCCTAAGCCAAAAG 4094
                                viiv  ii  v  v    v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_83862470_8   4095 AACAAGGCTGGAGGCATCACTCTACCTGACTTCAAATTATACTACAAGGC 4144
                              i i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_83862470_8   4145 TACAGTAACCCAAACAGCAAGGTACTGGTACCAAAACCGAGATATAGACC 4194
                                 i v i    iiv        i iv ii iv  v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_83862470_8   4195 AATGGAAGAGAAC--AGAGTCCTCAGAAATAATGCCGCATGTCTACAACT 4242
                                v    i--       --        vv  ii ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_83862470_8   4243 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4292
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_83862470_8   4293 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4342
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_83862470_8   4343 GAAACTGGATCTCTTCCTTACACCTTATGCAAAAATTAATTCAAGATGAA 4392
                            ii    i i  v   i     v   i          i    i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_83862470_8   4393 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTGGAAGAAAAC 4442
                          i ?    i       v   v       i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_83862470_8   4443 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4491
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_83862470_8   4492 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4541
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_83862470_8   4542 ATTAAACTGAAGAGCTTCTGCACAGCAAAAGGAACTACCATCAGAGCGAA 4591
                           i   v v  i i   i  ii vv    i iv    i  vv i  i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_83862470_8   4592 CAGGCAACCTACAGAATGGGAGAAAATTTTAGCAACT-ACTCATCTGACA 4640
                         v  i     i                 v  v    v - ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_83862470_8   4641 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACATGAAA 4690
                          i  i  vi          v  i  v      vv    v iv i vv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_83862470_8   4691 AAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTT 4740
                           i     i     v  i? v  i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_83862470_8   4741 CTCAAAAGAAGACATTTATGCAGTCAAAAGACACAAGAAAAAATGCTCGT 4790
                            v        i  vi viii i   v ii    v     i      iv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_83862470_8   4791 CATCACTGGCCAT 4803
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1144 25.90 10.30 6.71  chr1_83898081_83899689.rev      491  1131 (478)    L1M4_orf2#LINE/L1      245   908 (0)  

  chr1_83898081_8    491 AAGTTACACTAACAGGTATCAAGACTTTGAGCGTGGTGTTATCCATGCAA 540
                            i    v   ------       ----  i     ii iv -  --  
  L1M4_orf2#LINE/    245 AAGCTACAGTAA------TCAAGAC----AGTGTGGTACTGGC-AT--AA 281

  chr1_83898081_8    541 GGGTGGACAAATAGGCCAATGAAATTGAATAAAGAATCCAGAAACATACC 590
                           i i    v    ii     i   v    vi   i        i v   
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_83898081_8    591 TGTACATATATGGCCACCTGATCTACAACAAAAGCACCACTGCAATTCAG 640
                         ii     v     i  vi    i v i    ii ii   vvi v     i
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_83898081_8    641 CGGGGGCAAAGGTGTGTCTTCTGTAAATGGT------ACAATTGGATATC 684
                         i    iv i ivv  v i   vii       ------    i      ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_83898081_8    685 AACATGGAAACGTAATAGATTTG--------------------------- 707
                         v     v   v -   ii v   ---------------------------
  L1M4_orf2#LINE/    432 CACATGCAAAAG-AATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_83898081_8    708 ---------AGATGGAT---AGACCTAAACTTGAAAGGTAAAGCAGTAAA 745
                         --------- i      ---         iv i i  v    i vi    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_83898081_8    746 CTTTCTAGAAGAAAATACAGGAG--AATCT-CACAACCTTGAGATAGGCA 792
                         vi ii          i i   ? --     - iii      i v      
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_83898081_8    793 ATGGTTTCTTAAAGAAGACATGAAACGCACTAATCATAAAAACAAAAGAT 842
                                    i v v    iv   v    v iiv i    i-    i  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAAT 629

  chr1_83898081_8    843 TAATAAATTGCACTTTGATAAAATGGAAAACT-----GCTAATAAAAACA 887
                         vi        v    iivi     vi      -----   vvv  ii   
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_83898081_8    888 CCATAAAGGGAGTGAAAGTGTGGGTCACAAA----GAGAAGAAATTGACA 933
                          i  v   ii       iviiiivi    i ----     i v   vi  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_83898081_8    934 ATGCATATG-CTAAACTA--GGACTTGTATCCATGGTATA-----AACTC 975
                          vv     i-  i --  --             vii    -----     
  L1M4_orf2#LINE/    730 AATCATATATCTGA--TAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_83898081_8    976 CTACAAATACAAAAAAATAAAATAAAATAAAGAAAACACAAAAAAGGAAA 1025
                         i     v -   -----   --     ---   -----    --------
  L1M4_orf2#LINE/    778 TTACAACT-CAA-----TAA--TAAAA---AGA-----CAAA-------- 803

  chr1_83898081_8   1026 GACAATCTGATGAAGAGATGGGCAAGATACTCAAATAGGCACTTCACAAA 1075
                         --i  i ii  v? i i        iiv i ii     i  i   v v  
  L1M4_orf2#LINE/    804 --TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_83898081_8   1076 AGAGAATTTCAAAAAGGCCAACAGGACTATAAAAATGTGGACA-CATCTG 1124
                            ii  v vv   v      i i vvi  i    vi  vv  -    v?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_83898081_8   1125 AAAAATG 1131
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.63 (101 / 62)
Gap_init rate = 0.04 (24 / 664), avg. gap size = 4.54 (109 / 24)  


1714 25.38 4.83 5.74  chr1_83960733_83964788     2386  3047 (1009)    L1M4_orf2#LINE/L1        1   656 (252)  

  chr1_83960733_8   2386 TGGAAAGACATGCCACATATATGAATCATAAAACTCAGTAGTATTATAAT 2435
                                 i  v   ii vi   i  iiv  i   i i  v i   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_83960733_8   2436 GCCCCTTCTTTCCAAATTTGTCTATATCTTCAACACAATCTCTATCAAAA 2485
                          v vv v  ii       vi    i vv      i     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_83960733_8   2486 TTTCAGCAAGGATTTTTTA-AACAATTGA-AAGTTAATTCTAAACCTTAT 2533
                          ii    v- vv      i- iv      -   i i  i     vi i  
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_83960733_8   2534 ATA-AAATGCAACAGACAAAGAATAGCCTAAACAAT-TTGAAAAAGAATA 2581
                           i-        vi   vv         v       -           v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_83960733_8   2582 A----GTCGAAGGACTTACACTACTTGATTTTAAGACTTATTGTAAA-CC 2626
                          ----  i i      i     v iii    i  i     i ii   - i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_83960733_8   2627 AAAATAATCAAGACAATATGGTACTGGCATA-GGAT-GTCA----AATCA 2670
                          v i           i i             -    - v  ----i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_83960733_8   2671 ATGAAA-AAAAT---GAGTCAATAAATAGACCCTGATATATAAGGAAAAT 2716
                            i  - i   ---     v v     i    vv i  v  v  ---- 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG----T 345

  chr1_83960733_8   2717 GGATTGTTTTTTAAAACCACAGCACTGAG-----TTAATGGAAAAAAGGC 2761
                         vi    v    ii -- v vi ii ii  ----- i     ii   iii-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGA--CAAGGGTGCCAAGACCATTCAATGGGGAAAGAA- 392

  chr1_83960733_8   2762 TTTTTTTGTTGTTTGTTTGTTTAACAAACAGCGCTGCAACAACTAAATAT 2811
                         ------------ v  i v  i      ii i    vi      ii   ?
  L1M4_orf2#LINE/    393 ------------TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_83960733_8   2812 CTGCATGGAAAAATAATAA---TAAACCTTAATGCTGTTTCACTCCATAT 2858
                          ii    v    i-   i --- ii   i-----  iii    v      
  L1M4_orf2#LINE/    431 CCACATGCAAAAG-AATGAAGTTGGACCC-----CTACCTCACACCATAT 474

  chr1_83960733_8   2859 ACAAA---TAATTCTAAATGTACCATATACTTAAATA-AAAAACTCAGAA 2904
                              ---   i  v     v i  ? v  i     i-  i i  - i  
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAA 523

  chr1_83960733_8   2905 CTATGAAGTTTCTAAAAGGAAATATGGCACACAAGAAACTGTCTTTGCGA 2954
                             i  ii ii  i   i   i  i -----i? v  --i    i i  
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAG-----GNGTAA--ATCTTCGTGA 566

  chr1_83960733_8   2955 GCTTGGGGTAGGCAAAAATTCTTTGGACAGGACAGAAAAAGCTTAA-CAA 3003
                         v      v       vii  ii  i  i v    vv      vi  -   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_83960733_8   3004 TGATAAAAAGAAAAAACTGATGAATTGGGCTTCATCAAAAATAA 3047
                         i----           iv   i      i           v   
  L1M4_orf2#LINE/    617 C----AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

Transitions / transversions = 2.11 (112 / 53)
Gap_init rate = 0.04 (26 / 656), avg. gap size = 2.69 (70 / 26)  

 436 24.00 8.00 3.20  chr1_83960733_83964788     3330  3579 (477)    L1M4_orf2#LINE/L1      647   908 (0)  

  chr1_83960733_8   3330 TCAAAA--AAAAAATATTCTGTTTATCAAAAGACACCATTATGAAACCGA 3377
                               --     v v  v  i  --    i     i  i v    vi  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGA 694

  chr1_83960733_8   3378 ATAGGCAAACCCCAGACTGGGA-AAAAT-TTTGGAACACGTATATTTTAA 3425
                          v  i   v  v    v     -     -    v  vv i     i v v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_83960733_8   3426 AAAGG-CATATAACTGGAATACATTTTTTAAA---TTCCTACAATTTGAG 3471
                           i  - v i  v ii     i  -----   ---i  i     i ii v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATAT-----AAAGAACTCTTACAACTCAAT 789

  chr1_83960733_8   3472 ACTAAAAATACAAACAACCAAAT--AAA---GAGCAAAGA---CG--TAA 3511
                          v      v     i    v   --   --- i      i---i --  i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_83960733_8   3512 CCACTTCAAAAAAAAAAGATAAACAAATGACTAGTAAGGACATGTCAG-- 3559
                         v  i   vvv   i  -    v       i i i    v     vv i--
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_83960733_8   3560 TGCTCACGGTCAAACCCATA 3579
                               vvi   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (30 / 30)
Gap_init rate = 0.05 (13 / 262), avg. gap size = 2.15 (28 / 13)  


1625 27.00 6.78 5.89  chr1_84052920_84055642.rev     1338  2237 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84052920_8   1338 TGGAAAAGTATGTCTTATTCATC-ATTGCA---CTCAATATTATTGATAT 1383
                               ii   vi v i     v-    v ---  i      i  i v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84052920_8   1384 GTCAGTTCTTCTCAAATAATTTCCTACATCTGTAAATTCAATGTAATTCT 1433
                          v  i v  i i     ------- i-    ii i      i i   i -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-------TG-ATCTACAGATTCAACGCAATCC- 91

  chr1_84052920_8   1434 ACTAT--AAATCTCAACAAATGTTTATTTTTTATTTTTGGCGGGGAGAAG 1481
                         -    --     i  i ---  ii --------      - -------  
  L1M4_orf2#LINE/     92 -CTATCAAAATCCCAGC---TGCCT--------TTTTTG-C-------AG 121

  chr1_84052920_8   1482 AATTTGACCAAAGTTTGTTCTATCACT-ATACACAAAAGCAAAGGACCAA 1530
                           v     --   i vi i   vv i -   iiv   v    i     v 
  L1M4_orf2#LINE/    122 AAATTGAC--AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_84052920_8   1531 GAATAAGTAAGACAATCTTGAAATAGAGCAATATAACATCATAGGATTTA 1580
                              ivi  i            v   -- iv i  vi iiv    i i 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGA--AGAACAAAGTTGGAGGACTCA 217

  chr1_84052920_8   1581 GTAACTACAGTGTCTCAAGACTTACAATAAAGCTAAAGTAATTTAAGATA 1630
                         v--   v vvvi i    i      v i       v      i-    i 
  L1M4_orf2#LINE/    218 C--ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC-AAGACA 264

  chr1_84052920_8   1631 GTATAATATTGGCAAAAAGGATAGACAAATAGACCATTGGAACC--ATTC 1678
                           i ii  i     v  -         v     i  v     iv--   -
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAA-GGATAGACATATAGATCAATGGAATAGAATT- 312

  chr1_84052920_8   1679 AGAAAAACCATAAACCAACCCAGGCCTACCTGGAGACTTGATTTATGACA 1728
                         -  i iv   v   iv      vi v viv   vv v       vi    
  L1M4_orf2#LINE/    313 -GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_84052920_8   1729 AAAGTGGTGTACACCTGATTTATGACAAATAGGAAAAGGA-AGTTTGTTT 1777
                          ii   vii- v   --   i ------  i  i    i -   i v  i
  L1M4_orf2#LINE/    362 AGGGTGCCA-AGACC--ATTCA------ATGGGGAAAGAATAGTCTTTTC 402

  chr1_84052920_8   1778 AAACAATGGTTCTAGGACAATTGTATTTCCAAATAATAAAAAAGAAACTT 1827
                           vv      v  i      i  v  v?   v  ivv   i  vi  v  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_84052920_8   1828 AA--CTTTACCT-ACACCATAAATGAAAACCATTTCCAGATGAAAT-TAG 1873
                         ii-- ii     -        v ii    ii vi  v i   i vi-?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_84052920_8   1874 TATGTAGATGTGAAAGGTAAAACTGCATAAAGATTTCAGAAGATAATACA 1923
                         - iv  i    i i  v       --     iv i i      v  i i 
  L1M4_orf2#LINE/    503 -ACCTAAATGTAAGAGCTAAAACT--ATAAAACTCTTAGAAGAAAACATA 549

  chr1_84052920_8   1924 GGGGAATATTTTCATGACCTTGAGGTATGCAAAGATT-----AATAGAAC 1968
                           ? v v  i   i        i v  v    v i  -----i   vi  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_84052920_8   1969 -CAAAAAATTTTAATAACAAGTGAAAA-------------GATTATATTA 2004
                         - v    iiviv ii     iv     -------------  i vi  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_84052920_8   2005 AAATTAAAAACATATGTTCATCAGAAGACCCCATTAAGAG-GTGGAAAAG 2053
                                    v v   v v   i i   v i  i    i-   i   ii
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_84052920_8   2054 CAAGCCACAGGATGGAAGGAAGTGTTTGCAACCCATATAATCTG-TAAAA 2102
                            v      i    i  i  i i       vi      -    -   ii
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA-TCTGATAAGG 748

  chr1_84052920_8   2103 AATTCTTA-CAAGATTATATAA-TAACTCCTACCAATTTCA-AAGAAAAA 2149
                         i i iv  - v   v       -v     i   -  i iv -  v     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTAC-AACTCAATAATAAAAA 797

  chr1_84052920_8   2150 AGCAGACCACACAATAGAAAAATGGGGAAGATAATTGAA-AAAC------ 2192
                         ii  i iv  v    v?         v  iiv v     - i  ------
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_84052920_8   2193 -----GAGGA-----------CCAATAAACATTTGAAAAAGTGTTTAAGC 2226
                         -----  i  -----------       i  iv      ii  i i  vv
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_84052920_8   2227 TAATAATCAGG 2237
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.04 (40 / 908), avg. gap size = 2.85 (114 / 40)  


3623 23.61 1.56 0.45  chr1_84150030_84151991.rev      575  1472 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84150030_8    575 TGGAGATATATTCCAAGTTCAGTTATAGGAAGGCTCAACATTGTCAAGAT 624
                             i v    i   v     vvv  v     i  i  i     i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84150030_8    625 CTCCATTATTCTCAACTTGATCTATAGATTCATTGCATTCCC----AAAA 670
                         vv v  vv i i   v        i       vi   v    ----    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84150030_8    671 TTTCAGCAATTTGTTTTGTGGATATTGACAAACTGATTCTAAAATTTTTA 720
                          ii    viii v     ii  v        i     i        iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_84150030_8    721 TGGAAAGGCAAGAGACCCAGAAGAGCCAACACAATATCGAAGGAGAAGAA 770
                               v     i         v      v     v i   ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_84150030_8    771 CAAAGTTGGAGGACAGACACTACCCAACTTTAAGACTTACTATAAAACTA 820
                                       vv     v     i  i  i        i   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_84150030_8    821 CAACAATTGAAACAGTATGGTATTGGCAAAAGAATAGACAAATAGATCAA 870
                           ii   ii i     i     i     v   i       v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_84150030_8    871 TAGGACAAAATAGAGAGCTTGGAAATAGAACCACATAAATATAATGAGCT 920
                          i i i i   v     iiii      i v   i i vv   ii v ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_84150030_8    921 GATCTTTGACAATGATGCAAAGGCAATACAATGGAGCAAACATA-TCTTT 969
                            i  i     v i   v   i v  v      i v  iv   -     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_84150030_8    970 TCAACAAATCATGCTGGAACAACTAGACATC-ACATGCAAAAAGATGAAT 1018
                                  vi      i      i  i ? -          ii     v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_84150030_8   1019 TTATACACAGGCTTTACACTCTTCACAAAAATTAACTCAAAGCAGACCAA 1068
                           iv  v vvi i i    iv vi                 iii  i  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_84150030_8   1069 ATAGCTAAATGTACAATGC-AAAAGTATAAAACTCCTAGAAAATAATGTA 1117
                          v v         vi -  -    v          i     i v  ii  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_84150030_8   1118 GGAGAAAA-CTTAGATGATCTTGGGTATGGCAATGACATTTTAACTATAA 1166
                           ? v   -   v -   i       vv       iiv i   iv   i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_84150030_8   1167 CACCAAAGGCATGATCCATGAAAGAAATTATTGATAAGCTGGACTTCATT 1216
                                i   ii v v ii       vv  v     ii          i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_84150030_8   1217 AAAATTAAAAACTTACATTCTGTGAAAAACAGAGTCAAGAGAATGAGAAG 1266
                                       vii v  vii  ii   vvi      i i   i   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_84150030_8   1267 ACAGGTCATATACTGGGAGAAAATATTTGCAAAAGACACATCTGACAAAG 1316
                            ivi  i v v                    vv i i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_84150030_8   1317 GACTATTATCCAGAATATACAAAGAACTCTTAAAACTCAACAATAAGAAA 1366
                             vv             i            v       i     i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_84150030_8   1367 ACAAACAACTCAA----ACAATGGGCCAAAGACCTTAACAGATATCTCAC 1412
                              i   i   ---- v       v  i  ii v  i   i  i  v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_84150030_8   1413 TAAAGAAGATATATAGAGATGGC-AATAAGCATATAAAAAGA-GCTCCGC 1460
                         i            i i --    -        i  i      -    vi 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAA--TGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_84150030_8   1461 ATCTATGTCATT 1472
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (128 / 81)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


1121 29.95 1.56 1.04  chr1_84159686_84162383      683  1066 (1632)    L1M4_orf2#LINE/L1        1   386 (522)  

  chr1_84159686_8    683 TGGAAAAATATTCCATGCCCTTGGATTGAAAGAATCAGAATCATTTAAAT 732
                               i    i     ii v       i    v i iv  ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84159686_8    733 GGCCACACTGCCCAAAGTAACTTGTAGATTCAATGCTATTCCTATCAAAA 782
                            v i   v      v i ii ii        i  v  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84159686_8    783 TACCAA-TGTTATTTTTCACAGAAGTAGAAAAAAACT-ATTTGAAAATTC 830
                          v   i-  ii-     ii     i v  v  i--  -  iiv       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr1_84159686_8    831 ATATAGAACCAAAAAAGAGCCCTGA-TAGCCCAAACAATCCTAAGCAAAA 879
                             i   viiv  ii  -   v  -     v        i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_84159686_8    880 AGGACAAAGCTGGAGGCATCACATTACCAGACTTCAAA-CTG--TACAAG 926
                           i      i      vv     i v  vi i      -  v--     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_84159686_8    927 GCTGCAGTAAACAAAATAGCATGGTAATGGTAGAAAAACAAATACAAAGA 976
                            i      v   i i  ii     v   i v  ii i i i i v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_84159686_8    977 CCAATGGAACAGAACAGAGAACACAGAAATAAAGCCGCATAGCGACACCT 1026
                         i        i    iv    iiv          v  ii i viv iivii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_84159686_8   1027 CTCTGATCTTTGACAAAGTCGACAAAAATAAGCAATAAGG 1066
                         vvi    i  i     i vi v   i vi vv    ii  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

Transitions / transversions = 1.95 (76 / 39)
Gap_init rate = 0.02 (8 / 386), avg. gap size = 1.25 (10 / 8)  

1581 24.78 0.66 1.75  chr1_84159686_84162383     1373  1828 (870)    L1M4_orf2#LINE/L1      379   829 (79)  

  chr1_84159686_8   1373 CAATAAGAAAAAGACTGTCTATTCAATAAATGACACTGGAATAACTGGCT 1422
                             ii i   ii iv    v     i     iii    i i      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_84159686_8   1423 AGCCACATGCAGAAGCAAGAAACTGGACAAACTACCTCTCACCACAAGCA 1472
                          ?         i   v v   ii     vv-       v     i vi  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCC-CTACCTCACACCATATACA 477

  chr1_84159686_8   1473 AAAATTAACTCAAGATGGATTAAAGATTTAAATGTAACCCCTCAAACTAT 1522
                                      i      i ?   ii         vvv  v       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_84159686_8   1523 AAAAATCCTAGAAGAAAACCTAGG---AAATACCCTTCCTAGCAAACACT 1569
                             v  i           v    ---    ---    v i----  vi 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTG----ACCTT 570

  chr1_84159686_8   1570 GGCTTTGACAAAGAGTTTATGGCTAAGTGCCCAAATGCAACTGCAACAAT 1619
                           v  v i   v iv  iv i v  v vvv     v   vvv       v
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_84159686_8   1620 AACAAAAATTGACAAGTGGGATCTCATCAAACTAAAGAGCTTTTGTACAG 1669
                          iv      v  i  i v   ii        v v  i i       i vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_84159686_8   1670 CAAAAGAAACTATCAACAGAGTAAACAGACAACCTACAGAATGGGAGAAA 1719
                             i  v        v i   i  v        i               
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_84159686_8   1720 ATATTTGCAAACCATGTATCTGACAAAGCTATAATATCCAGAATCTGAAA 1769
                                    i   i       i  i vvv vi          v iv  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_84159686_8   1770 GGAACTTAAATAGCTGAAAAATCAAAAAACAAATAATTTTGTTAAAAAAT 1819
                         i     ivv i i  v  v   v    i        iiivi  ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_84159686_8   1820 GGGCAAAAG 1828
                                i 
  L1M4_orf2#LINE/    821 GGGCAAAGG 829

Transitions / transversions = 1.04 (56 / 54)
Gap_init rate = 0.01 (4 / 451), avg. gap size = 2.75 (11 / 4)  

 471 11.96 2.17 0.00  chr1_84159686_84162383     2114  2205 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_84159686_8   2114 AAAAATGGGCAAAAGACATGAACAGACACTTCTCAAAAGAAGATGGACAA 2163
                                      i  iv    i     i     v         iv    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_84159686_8   2164 GTGGCCAACAA--ACATGAAAAAATGCTCAACATCACTAATCAT 2205
                         i       i  --         i             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 2.00 (2 / 1)  


 449 14.43 10.31 0.00  chr1_84165841_84168733.rev      409   505 (2388)  C L1M4_orf2#LINE/L1   (0)   908   802  

C chr1_84165841_8    505 AATAACCCTATTTAAAAATGGGCTAATGCCTTGAATAGA----------A 466
                                 v   ?          v  v vi         ---------- 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

C chr1_84165841_8    465 AGAGGATATACAAATGACCAATAAGCAAATGAAAAGATGTCCAATGTTAC 416
                            i            i          v           ii   ii i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

C chr1_84165841_8    415 TAATCAT 409
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.01 (1 / 107), avg. gap size = 10.00 (10 / 1)  

2276 26.04 4.91 3.44  chr1_84165841_84168733.rev     1211  2024 (869)    L1M4_orf2#LINE/L1        4   829 (79)  

  chr1_84165841_8   1211 AAAAACATTCCATGCTCATGGATTGGATTAATCAATATTGTTAAAATGGC 1260
                            i i  i     i            vv v i           i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_84165841_8   1261 CATACTGCCCAAAGCAGTCTACAGATTCAGTGCTATACTTATCAAGCTAC 1310
                         v     v      viii            ii  v  v i      iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_84165841_8   1311 CAAAGTCATTTTTCACAGAACTAAAAAAACAAAACAAAACAAAAACTATT 1360
                           ivvv v     ii     v vi v  i vi v ----------   --
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC----------CTA-- 141

  chr1_84165841_8   1361 TGAAAATTCATAGGGAACCAAAAAAGACCCTGCATAGCTAAAGCAATCCT 1410
                         ---         v    viiv  ii     v v     i   i     i 
  L1M4_orf2#LINE/    142 ---AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_84165841_8   1411 AAGCAAAAAGAACAAAGCTGGAGGCATCACAATACCTGACTTCAAACTAT 1460
                         i iv  i          i      vv     v v  ii i      -- i
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--AC 236

  chr1_84165841_8   1461 ATACTGTAAGGCTGTAGTAAACAAAATAGCCATAGTACTGGTACAAAAAC 1510
                         v    ii  i   ii     v   i i  i-i i       i i  ii i
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGT-GTGGTACTGGCATAAGGAT 285

  chr1_84165841_8   1511 AGACACATAGACCAGGGAAATAGAATAGAGAATCCAGAAATAAAGCCACA 1560
                              i     i  iv i        v    i            v   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_84165841_8   1561 ------TGGTTAA-----------CAAAGTTGACAAAACTAAT--ATGGA 1591
                         ------    i  -----------   i v  v   i  i v --    i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_84165841_8   1592 -AAAGACTTCCTGTTTCCCTGTTCAATAAAAGATACTGGGATAACTGGCT 1640
                         -     v v---  ----  v     i   v i i      i      v 
  L1M4_orf2#LINE/    386 GAAAGAATA---GT----CTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_84165841_8   1641 AGCCATATGCAGAAAAATGAAACTGGACACCTACCCCTCACCGTGTAGAA 1690
                          ?   i     i  i      ii     v      i v    i i  v  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_84165841_8   1691 AAACTAGCT------GTTTTAAAGATTTAAATATAAGTCCTCAAACTATA 1734
                            i  i  ------ vv i ?   ii     i    vv  v        
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_84165841_8   1735 AAAATCCTATAAGAAAACCTAGG---AAATACCCTTCCCAACATTGCCTT 1781
                            v  i  v        v    ---    ---    vii  v   vv  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTT 575

  chr1_84165841_8   1782 -GATGAAGGATTTATGGCTAAGTCCCCAAAAGCAATTGCAGCAAAA---- 1826
                         - iii v  v  iv i v  v v v         vvv   i     ----
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_84165841_8   1827 AAATTTATAGGTGGGACCTAGCCAAAGTAAAGAGCTTCTGTACGGCAAAA 1876
                             vv   ii v    i vii    i v  i i   i   i vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_84165841_8   1877 TAAACTAACAGCAGAGTAGACAGACAACCTACAGAATGGGAGAAAATGCC 1926
                         v v    v  iv i   ii v        i                 iii
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_84165841_8   1927 TGCAAACTATGTATGTGACAAAGGTCTAATATCCAGAATCTA--AAGAAC 1974
                               ii  i   v   i  i  v  vi          v  --      
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_84165841_8   1975 TTAAACAGTTGAACAAACAAAAAACAAC--ACC--ATTAAAAGGTGGGCA 2020
                          ivv   ii v  i  vv    i    v--   --   ?   ii      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_84165841_8   2021 AAAG 2024
                           i 
  L1M4_orf2#LINE/    826 AAGG 829

Transitions / transversions = 1.35 (120 / 89)
Gap_init rate = 0.02 (18 / 826), avg. gap size = 3.78 (68 / 18)  

 330 19.35 2.15 1.08  chr1_84165841_84168733.rev     2310  2402 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_84165841_8   2310 AAAAAGGTGGCCAAAGACACGAACAGACACTTCTCAAAAGAAGATGGACA 2359
                              v -   v  i  ivi   i     i     v         iv   
  L1M4_orf2#LINE/    815 AAAAATG-GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_84165841_8   2360 ACTGGCTAACAA--ATATGACAAAGTGCTCAACATCACTAATCAC 2402
                          v    i  i  -- i    v  ii            ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (11 / 7)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.50 (3 / 2)  


3321 26.76 0.44 0.44  chr1_84230333_84236610.rev     4880  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84230333_8   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84230333_8   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84230333_8   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_84230333_8   5028 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_84230333_8   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_84230333_8   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_84230333_8   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_84230333_8   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_84230333_8   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_84230333_8   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_84230333_8   5376 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_84230333_8   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_84230333_8   5476 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5525
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_84230333_8   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_84230333_8   5576 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_84230333_8   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_84230333_8   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_84230333_8   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_84230333_8   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 976 25.82 9.01 11.43  chr1_84270032_84272535.rev     1107  2016 (488)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr1_84270032_8   1107 ATGGACTTAAAAATTCAATATCATAAAGATGAAAATTCTTCTCAAACTA- 1155
                              i vi  i i i     ii v      iv   v  i i    i i-
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr1_84270032_8   1156 -CTATATATTCAATGCAATC----TCAAGATTCCTATAAGGTTCGTGTAT 1200
                         -   i v      i      ----    i  i  ----  v v v v --
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCC----AGCTGCCTTT-- 114

  chr1_84270032_8   1201 ATAATTATGTATGTGAAAATTGACAAGCTGATTTAAAAAT--------AA 1242
                         ----  -----  iii                iiv     --------  
  L1M4_orf2#LINE/    115 ----TT-----TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_84270032_8   1243 A-------------GAATATTCAAAAT--TTTTGTAAAATATGAA----G 1273
                          -------------     vi     i-- i   v    v v   ---- 
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_84270032_8   1274 TTTTAGGATTTATACTACTGATTATGATGACTTCTATTATAAAGTTATAT 1323
                           vv    i i i   v iv v v v vi    -- i  i    i  i v
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTT--ACTACAAAGCTACAG 253

  chr1_84270032_8   1324 GAATTCATGCAGTTTTGTACTGACACTAAAATAGACA---AAACCAATGG 1370
                         v   iv vi    v v      i  iv ii       --- i i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_84270032_8   1371 AACAGAA---A------AGAAGGAAACCAGATATATTCA--GCCT-TTGA 1408
                           i    --- ------    iv     v-   i   i -- i v-    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCC-ATACATTTATGGTCAATTGA 352

  chr1_84270032_8   1409 T----AACAAAGATGTCATTACAGTGCTTTGGGGAAGGGACAATTTCTTT 1454
                          ----i    i i  i  vv  vi v vv       i i i i i i  i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_84270032_8   1455 TTCCTTTTAAATGGTGATGTGTCAAATAAATACTGATAT-TAACA-AATG 1502
                         vv -----        v  v v   v ii   ?iv i  -i  v -    
  L1M4_orf2#LINE/    403 AAC-----AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_84270032_8   1503 A-------CTCCTACCTCACCACACACACACAGAAGCGCATACACAGAGA 1545
                          ------- i          ---------  -------    i   i i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCAC---------AC-------CATATACAAAAA 481

  chr1_84270032_8   1546 GAGAGAGAGAGAGAGAGATGCACACACTTGATTCCAGACAGACTGTAGTT 1595
                         ---------------------------  i i  v i ii  iii?  vi
  L1M4_orf2#LINE/    482 ---------------------------TTAACTCAAAATGGATCAWAGAC 504

  chr1_84270032_8   1596 CTAAATATGAAAGGCAAAAG---AAAGCTTCTA-AACCTAACATAGGA-- 1639
                               i i i  vi    v---   i  ii  -  vvv        ?--
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_84270032_8   1640 AAATATCTATGACCCTAGGGTAG-TGAGAACTTCTTAAAGAAGACCGAGG 1688
                             v iii     i i  v   -ii viii      i v v   -----
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC----- 599

  chr1_84270032_8   1689 AAGGCCAAACAAAACACAAATCATAAAGGAAATGATTTGTAAATTA---T 1735
                         ---i     --- i     iiv i   i    vi  vvi      i--- 
  L1M4_orf2#LINE/    600 ---ACCAAA---AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_84270032_8   1736 TTGT-ACGTTTGAAAATTATTAAACAGTATGAAGGAGACATCGTTAAGAA 1784
                          ii - viv  i    i v  ivi -- vii     --  iii i     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGC--TTCAAAGGA--CACTATCAAGAA 689

  chr1_84270032_8   1785 AGTGAAAAGGCAAGCTATGAAACGGAAGAAGACATTTGTAGTACATACGT 1834
                                  i   v i iii  i  i    i i     i ivv    ii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_84270032_8   1835 CTGG--GGGGAAAATCCTGTACCCA---TGT-TAAATAACTCT-ACAAAT 1877
                            i--i    ---- i    i   --- i -    v      -    v 
  L1M4_orf2#LINE/    740 CTGATAAGGGA----CTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_84270032_8   1878 CAATTTTTTTGAAAAATACAACAGAATACCACAA--AAAAAGGGATGGGG 1925
                             vv ----     v    ----   v v   --?    ---     v
  L1M4_orf2#LINE/    786 CAATAAT----AAAAAGACAA----ATAACCCAATTWAAAA---ATGGGC 824

  chr1_84270032_8   1926 AAAT-ACCTGAAAAAAAAAAAAACATTTTATAAAAAGAGGATATCCAAAT 1974
                            v- ii    v i -------     i- vv     i     v     
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGA-------CATTTC-TCCAAAGAAGATATACAAAT 866

  chr1_84270032_8   1975 GACCAATACCAACATGAAAAAGTGATCAACACTATCAGTCAT 2016
                          i      vvv         ii  v      ii ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (144 / 87)
Gap_init rate = 0.05 (46 / 888), avg. gap size = 4.04 (186 / 46)  


1774 19.32 2.90 23.18  chr1_84283430_84285946      892  2030 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84283430_8    892 TGGAAGAGCACTCCATGCTCTTAGATAGGAAGAATCAATATGGTTAAAAT 941
                              iiii ii     i  v i   v      v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84283430_8    942 GGCCATACTGCCTAAAGCAATTTACAGATTCAATGCTATTTCTATCAAAC 991
                            v     v  i   vii  i           i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84283430_8    992 TACCAATTACATTCTTCACAGAACTAGAAAATACT-ATTCTACCATTCAT 1040
                          v   ii i v  i  ii     v v  v  -i  -  i   vv      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_84283430_8   1041 ATGAAACCAAAAAAGAGCCCAAATAGCCAAGGCAATCCTAAGCAAAAAGA 1090
                            i  viiv  ii  v  vi         ii     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_84283430_8   1091 ACAAAGCTGGAAGAATCACATTGCCTGACTTCAAACTGTACTATAAGGCT 1140
                               i    i  v     i v  ii i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_84283430_8   1141 ACAGTAACCAAAACAGCATAGTACTGGTATAAAAACAGACACATGGACCA 1190
                                i   i    ii i       i    ii i     i  i  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_84283430_8   1191 ATGGAACAGAATAGAGAGCCCAGAAATGAAGCCACACACCCAGGAGGAGG 1240
                               i     v     i        -----------------------
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAAT----------------------- 326

  chr1_84283430_8   1241 GAGAGGTTCAGAAGAGAAAGATAAAAAGGAAAACAAATGAACAAACAAAA 1290
                         --------------------------------------------------
  L1M4_orf2#LINE/    327 -------------------------------------------------- 326

  chr1_84283430_8   1291 AAACCAAACCTGTTGAGTAGTATGCTTAGTACCTGGGTGACAAAATAATC 1340
                         --------------------------------------------------
  L1M4_orf2#LINE/    327 -------------------------------------------------- 326

  chr1_84283430_8   1341 TGTACACCACACCCCCAAGTCACAAGTTTACCTATATAACAAACCTACAG 1390
                         ----------------------------------------     i ---
  L1M4_orf2#LINE/    327 ----------------------------------------AAACCCA--- 333

  chr1_84283430_8   1391 ATATGCCCCCGAACCTAAAATAAAAGTTAAAATATATTTTAAAACATATA 1440
                         --------------------------------  i    -----------
  L1M4_orf2#LINE/    334 --------------------------------TACATTT----------- 340

  chr1_84283430_8   1441 TAAAATGGATATATGTGTCAGTTTTAACCAACTGATGTTTGACAAGGCTG 1490
                         ----    -------------------i   i    v  i       v  
  L1M4_orf2#LINE/    341 ----ATGG-------------------TCAATTGATTTTCGACAAGGGTG 367

  chr1_84283430_8   1491 ATTAAACAAG-CAATGGAGAAAGGACTCCCTGTTCAATAAATGGTTCTGG 1539
                         viv i  v v-      i     i ivvi  v     i       v    
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_84283430_8   1540 GATAATTGGCTAGCTGTATGCAGAAGACTGAAACTGGACCCCTTCCTTAT 1589
                           i  i   v  ? iii     i    v    ii         v   i i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_84283430_8   1590 ACCATATGCAAAAATCAACCCAAAATGAATTAAAGACCTAAATGGAGAAC 1639
                                i       i   i       i  i ?           v ii v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_84283430_8   1640 CTAAAACTGTAAAGCCCATGGAAGATAACCTAGG---AAATACCATTTTG 1686
                                 i    i i v i     v   v    ---    ----i  i 
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT----CTTCG 563

  chr1_84283430_8   1687 -GACATAAGAACGGGCAAAAATTTC----ATA----ACGAAAATGGCACA 1727
                         -   v vi ivii     vii    ----   ----  v    --     
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA--GCACA 611

  chr1_84283430_8   1728 AGCAATTTCAACAATAGCAAAAGTTGACAGATGGGACCTGTTTAAAG--- 1774
                              ------   v  v    i v  i i  v    i vv i   i---
  L1M4_orf2#LINE/    612 AGCAA------CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_84283430_8   1775 --AGCTTTTGCATAGCAAAAGAAACTATCAACAGAATAAACAAACAACCT 1822
                         -- i      iiivv    i  v        v i i i  v i      i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_84283430_8   1823 ACA---------AAAATATTTTCAAACTATGCATCTGACTAATGTATAGT 1863
                            ---------         v    ii  ii      -   --------
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA-TAA-------- 746

  chr1_84283430_8   1864 TAGTCTGGGTCTAATATCCAGAATCTACAGGGAACTTAAACAAATGTACA 1913
                         ------   v  vi          v  i ii     ivv    v ---  
  L1M4_orf2#LINE/    747 ------GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CA 787

  chr1_84283430_8   1914 A--ACAAAAAG-CAAACAGCCCTATTAAAATGTGCACAATGGACATGAGC 1960
                          -- i      -    i i   v   ?   vi  vi   v   iv   ii
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_84283430_8   1961 AGACACTTTTCAAAAGAAGACATACATGCGGCCAACAA--ACATGAAAAA 2008
                              i  i  v        i     vii      i  --         i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_84283430_8   2009 AATGCTCAATATGACTAATCAT 2030
                          -       i  v ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (142 / 75)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 12.91 (297 / 23)  


2064 26.00 2.97 0.35  chr1_84292491_84296142.rev     1953  2525 (1127)    L1M4_orf2#LINE/L1        3   590 (318)  

  chr1_84292491_8   1953 GAAAAA-AGTCCATGCTCATGAATTAGAA---TTAGTACTGTTAAAAATG 1998
                             i - vi     i     i   i   ---   i  i      i -  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-TG 51

  chr1_84292491_8   1999 ACCATACTTCCCAAAGCAATCTACAGACTCAACATAATCA-TATCAAAAT 2047
                         i v     i      vii         i     ii    v-         
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_84292491_8   2048 ACTAACATCATTCTTCACAGAATTAGAAAAAATAATTCTAAAATTCATGT 2097
                         v i i vv v  i  ii     v v  v  iv i  i           i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_84292491_8   2098 GCAACCTAAAAGGAGCCCA-AATAGCCAAAGCAACTCTGAGCAAAAAGAA 2146
                          v  v- iv    ii    -          i   iii   iv  i     
  L1M4_orf2#LINE/    152 GGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_84292491_8   2147 CGAAGCTGGAGGCATCACATTACCTGATTTCAAAGTATATTAGAAGGCTA 2196
                          i   i      vv     i v  ii        iiv  i  v  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_84292491_8   2197 TAATAACCCAAACAGCACAGTATTGGTATAAAAAAAGACACATA-----A 2241
                         i i   i v i    iiii   i   i    ii v     i   ----- 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_84292491_8   2242 TGGAACTAAATAGAGAACCTAGAAATAAAGCCACATATTTACAGCCAATT 2291
                              ivi   v    ii i         v   i i     ii i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_84292491_8   2292 GATCTTTGACAAACCTGACAAGAGCTTCCACTGGGGAAAAGACACTCTCT 2341
                            i  i     ivv  v     v v i  v        ii i v   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_84292491_8   2342 TCAATAAATGGTCCTGGGAAAACTGAATAGCCACATGCA---GAATGAAA 2388
                             i       v      v     i   ?         ---       i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_84292491_8   2389 CTAGAACCCTATTTCTCCCCACATAGAAACATCAACTCAAAATGGATTAC 2438
                         i i  v     ii  v v   i   v   v  i              i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_84292491_8   2439 AGACT---ATGTAAGACCACAAATTATAAAAATACTAGAAGAAAACCTAG 2485
                             i---        v vv   i       v vi           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_84292491_8   2486 GAAAAACTCTCCTGGACATTGCTCTAGGCAAAGAATTTTT 2525
                          ?iv  v   i vv   v   vvi       v iv  i  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.65 (91 / 55)
Gap_init rate = 0.02 (9 / 588), avg. gap size = 2.11 (19 / 9)  

 856 29.66 4.24 0.28  chr1_84292491_84296142.rev     2808  3161 (491)    L1M4_orf2#LINE/L1      541   908 (0)  

  chr1_84292491_8   2808 GAGATTATAGGCGTGAGCCACCGC-ACCT-GGCCTAGGCAAAGAATTTAC 2855
                           i vi     ?  i ii vi  i-    -  vi       v iv  ivi
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_84292491_8   2856 AACTAAGACCTCAAAAATACAGGCAACAAAAACACCAATAGACAAATGAA 2905
                          iv  v   vi     ii   i         iv vv      i    vii
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_84292491_8   2906 ACTTAATTAAACTAAAAAGCTTCTGCACAGAAAAAAAAAATAATCAACAG 2955
                             v  i   v v    i   i  ii vvv   ii v v  -    v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAA 689

  chr1_84292491_8   2956 GGTGAAGAGACAACCTTTTCAATAGGAGAAAATACCTGCATGCTACTCAT 3005
                         i     i        ivivv   i          ii    viii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_84292491_8   3006 GCAACAGGGGACTAATATCCAGCATATACAAGAAACTCAAAAAACTTAAT 3055
                         vii i i      vi       v     i  ii     vv v    i   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_84292491_8   3056 AGGAAAAA--CA--TAATCCCATTAAAAAGCAGGTAAATGACATGAGTAG 3101
                          iv     --  --   i  v   ?    iii  i   v  iv   i   
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_84292491_8   3102 ACATTTTGCAAAAGAAGACA--------GCCAACAGGTTTATGAAAA-AT 3142
                               iv v        i --------     i i ivi       -  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_84292491_8   3143 GCTCAACATCACTAATCAT 3161
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (63 / 40)
Gap_init rate = 0.02 (7 / 368), avg. gap size = 2.29 (16 / 7)  


3264 22.74 4.91 1.14  chr1_84335626_84338957.rev     1967  2841 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84335626_8   1967 TGGAGAGACATTTCATGTTCATGGATTCCAAGACTCAAAATTGTTAAAAT 2016
                             i   i  ii              vv      i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84335626_8   2017 AACAATTCTCTACAAGTTAATCTATGAACTCAATATATAATCTCTATGAA 2066
                         ii    v   iv   i  i     iii i    iii --   i    v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA--ATCCCTATCAA 98

  chr1_84335626_8   2067 AATCTAATAAAGCTTTTCTTTAGAAACTGACAAATTGATCCAGAAATTTA 2116
                             iv vvviv     i vi     i      ii      vi     i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_84335626_8   2117 TATGAAAATGCAAAGGACCCCAAAATAGACAAAACAATTTTGATAAAAGA 2166
                             i        i      - i     v         i    -      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCC-AGAATAGCCAAAACAATCTTGA-AAAAGA 196

  chr1_84335626_8   2167 AGAACAAAGTTGGAGGACTTACACTATGTGATTTCAAAACTTACCTTAAA 2216
                                            i     vivii              ivi   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_84335626_8   2217 GTTTTAGTAATCAAGACAGTGTAGTATAGGAATGAGGACAGACATGTAGT 2266
                          i vi                 i   iv  v  i    i      i   v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_84335626_8   2267 TCACTGGGACAGAATTGAGAATTCAGAAGTGAACCCTTTCATTTATGGTC 2316
                            v   i i          i i     i i     v v           
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_84335626_8   2317 AACTGATTTTTGAGAAAGATGCCAAGATAATTAAATAGAGAAAGGAAATT 2366
                           i       i  v  i i        iv   v   i i     i v v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_84335626_8   2367 CTTTTTAACAAGTAGTGCAGTAAAAAATGGAT--CTACATGTTGAAAAAA 2414
                              i     i i    v vi v  v     -- i     ivi  i  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_84335626_8   2415 GAACTTCAATTCATACTTCACAACATATATAAAAATTAACTCAAAA---- 2460
                            v  vi ii v   i     v      i                ----
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_84335626_8   2461 -----------AAT------------------AGACTTTTAGAAGGAAGT 2481
                         -----------   ------------------ i   i       i  ii
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_84335626_8   2482 ACAGATTGAAAATCTTCATTACCTTGCGTTAGATACAAATTTCTTAAGAT 2531
                          i  i?- v        i v      v     ii vvii       -   
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GAT 594

  chr1_84335626_8   2532 CTGGTACCAAAAGTACAATCCAAAAAGGAAAAAAC-GATAAATTGGACTT 2580
                         v  ii        i    v v v   i       i-              
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_84335626_8   2581 CACTAAAATTACAAA-TTTTGCTCTTCAAAT-ACATCATTTTTAAAAA-- 2626
                           ii       v   -     iv       v-   ii  i---  i  --
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC---AAGAAAG 691

  chr1_84335626_8   2627 TGACAACATAAG--ACAGACTAGAAGGAAATATTTGATATTTATATTTTT 2674
                            v  v i  v--     v i i  i         vv v i    v i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_84335626_8   2675 GGAAAAGAACTTA-GTTCAGAATATACAAAGAATTATTGAGAATTGATAA 2723
                          iv  i i    i-i i         i      i v  ivi v ii    
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_84335626_8   2724 TAAGAAGAAAAACGACTCAATTTTGAAAGTGGGCAAAAGATTTGAAAATA 2773
                            i    v   ii  i     ?-i   i        i        v v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_84335626_8   2774 CATTTCTCCAAAGTACATACACAAATGGGTTATAAAAACTTGAAAATATG 2823
                                      v v   i        viv    iv  v      v   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_84335626_8   2824 CTCAACATCATAAAGTTA 2841
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (124 / 73)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.31 (53 / 16)  


2120 26.36 1.02 1.19  chr1_84396096_84400645.rev     2841  3428 (1122)    L1M4_orf2#LINE/L1        1   587 (321)  

  chr1_84396096_8   2841 TGGAAAGACATCCCATGGTCATGGTCATGAATCAGAAAAATAAATAT-AT 2889
                                 i        v      ------  ii   i v v     -i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGG------ATTGGAAGACTTAATATTGT 44

  chr1_84396096_8   2890 TAAAATGATCA-ACTATGCAAATAAATTTACAGATTCAATGCAATTCCTA 2938
                            i   iiv -   viv     vi  i           i     i    
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr1_84396096_8   2939 TCAAAATACCAATGATAGTCTTCACAGAAATAGAAAAAAAAATCCTAAAA 2988
                                v   iiviivv i  ii       v  v  ivvi         
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_84396096_8   2989 TTTGTATGGAACCACAAAAGAGCCTGAATAGCCAAAGGAATCCAGAGCAA 3038
                           ii       vii   ii  v  v           iv    iv  iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_84396096_8   3039 AAAGAGCAATGCTGGAGGCATCACACTACCTGACTTCAAAATATACTATA 3088
                         i    i   v i      vv       v  ii i       iv     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_84396096_8   3089 AAGCTATAGTAACTAAAACAGCATGGTAGTGGTATAAAAACAGACACAGA 3138
                               i     ii  i    ii     v   i    ii i     i v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_84396096_8   3139 GACCCATGGAACAGAATAGAGAACCCATAAATAAATCCACATATT-ACAC 3187
                           i v      i     v    ii   v       i   i i   - iiv
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_84396096_8   3188 CTAAGTGATTTTTGACAAAGGCATCAAGAACATACAGTGGGGAAAGGACA 3237
                         ii  v       i     i  iii     v   v  i         i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_84396096_8   3238 CTCTCTTCAATACATGGTGC-GGAAAAACTGGATATCCATATGCAGAAGA 3286
                         v   i     i v       -  i v         ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_84396096_8   3287 CTGAAACTAGATCCCTCTCTCTCACCATATCCCCAAATCA-CTCAAAATG 3335
                         v    ii i  i    vi   v        v vv    i -         
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_84396096_8   3336 AATTAAGTACTTAAAAATAAGGCCCCAAACCATAACAATACTAGAAGAAA 3385
                         i  i ?iv  i    vi    iv iv    i    v v vi         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_84396096_8   3386 ACATACGGG-AAATGCTCTAGAACATTGGTCTAGTCAAAGATTT 3428
                              v ? -    -  iiivi  v    vi   v   v i   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTT 587

Transitions / transversions = 1.67 (95 / 57)
Gap_init rate = 0.01 (8 / 587), avg. gap size = 1.62 (13 / 8)  

1196 21.38 1.64 0.99  chr1_84396096_84400645.rev     3756  4059 (491)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr1_84396096_8   3756 AAAAGTACAAGCAACAAAAACAAAAATAGGCACATTGGGCTATATTAAA- 3804
                              i             iv        ii v     i  vi  i   -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_84396096_8   3805 TTAAAAGCTTTTGCAGAGCAAAGGAGACATTCAAAAGAGTAAAGAGACAA 3854
                               i      iivvv       v  vv    i i   i  i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_84396096_8   3855 CCTGTTGAATGGGAGAAAAAAATATTTGCAAACTATTCATCCAAGAAGGG 3904
                           iiiv             ---          ii  vi   ii v     
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAA---TATTTGCAAATCATATATCTGATAAGGG 749

  chr1_84396096_8   3905 ACTAATATGCAGAATATACAAGGAACTCCAATAATTCAGTAGCCAAAA-A 3953
                            vi   v         i  i      iv i  i   i  iiv    - 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_84396096_8   3954 TAAACAATCTAATT--AAAATGGGTAAAGGATATGTGTACACATTTCTCA 4001
                         i   i  i i    --        i       v  vi  v         v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_84396096_8   4002 AAACCAGATTTACAA-TGGCCAACAGGTACATGAAAAAATGCTCAACACC 4050
                            vv    v     -       i i i         i          i 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_84396096_8   4051 ATTAATCAT 4059
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.83 (42 / 23)
Gap_init rate = 0.02 (5 / 306), avg. gap size = 1.60 (8 / 5)  


3291 27.23 0.33 0.22  chr1_84406887_84413144.rev     4861  5767 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84406887_8   4861 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCATGAAAAT 4910
                              ii i  i     i      i v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84406887_8   4911 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4960
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84406887_8   4961 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5009
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_84406887_8   5010 TGGAACCAAAAAAGAGCCCGCATCGCCAAATCAATCCTAAGCCAAAAGAA 5059
                              viiv  ii  v  v v  v      v     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_84406887_8   5060 CAAAGCTGGAGGCATCTCACTACCTGACTTCAAACTATACTACATGGCTA 5109
                              i      vv  v    v  ii i      viv       vi    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_84406887_8   5110 CAGTAACCAACACAGCATGTTACTGGTACCAAAACAGAGATATAGATCAA 5159
                               i   v    ii  v      i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_84406887_8   5160 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTAT 5207
                              i    i--    i  --        vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_84406887_8   5208 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5257
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_84406887_8   5258 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAGCTGA 5307
                         v  i  i              v      v  ?   i   iii  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_84406887_8   5308 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGGTT 5357
                          ii    i    v   i     v           i  i    i    i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_84406887_8   5358 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5407
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_84406887_8   5408 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5457
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_84406887_8   5458 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5507
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_84406887_8   5508 AAACTAAAGAGCTTCTGCACATCAAAAGAAACTACCATCAGAGTGAACAG 5557
                            v v  i i   i  ii v     i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_84406887_8   5558 GCAACCTACAAAATGGGAGAAAATTCTTGCAACCTACTCATCTGACAAAG 5607
                         i     i   i             vi      vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_84406887_8   5608 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5657
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_84406887_8   5658 ATAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 5707
                          i   i     v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_84406887_8   5708 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5757
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_84406887_8   5758 CACTGGCCAT 5767
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.67 (5 / 3)  


1832 28.55 0.88 0.53  chr1_84418513_84420447.rev      475  1045 (890)    L1M4_orf2#LINE/L1      237   809 (99)  

  chr1_84418513_8    475 TTATTAAGAAGTTTATAA-AACCAGTACCAACATGGTAGTGGTATAAAAA 523
                            i  vi   -i  i i-  i  iv -  iii     v   i    ii 
  L1M4_orf2#LINE/    237 TTACTACAAAG-CTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGA 284

  chr1_84418513_8    524 TAAGCACATAGACCAAGGGAAGAGAATAGAGAACGCAGAAATAAAGCCAA 573
                           ii  i     i   v    v     v    iiv          v   v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_84418513_8    574 GCATTTACACCCAACTGATCTTCGACAAAGCAAAACAAAAACATAAAGTG 623
                         i      iivi   i    i        i -iviv   i v   vv i  
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATG 383

  chr1_84418513_8    624 AGAGAAAGACACCCTATTTAACAAATGGTGCTGGGATAATTGACAAGCCA 673
                         i ii  ii i vi  v  i                 i  i  ivv ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_84418513_8    674 CATGTAGAAGAATGAAACTGGATCCTCATCTCTCACCTTATACAAAAATC 723
                             i i         ii    i  ii i   v    v           i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_84418513_8    724 AATTCAAGATGGATCAAAGACTTAAATCTAAGACTTGAAACCATAAAGAT 773
                           i    i        ?    i     v     vi i    i     iv 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_84418513_8    774 TCCAGAAGATAACATCGGTAAAACTCTTCTAGACACTGGCGTAGGCAAAG 823
                         iii      v     v  ?iv  v     vv   vi   vv       v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_84418513_8    824 ACTTCATGACCAAGAACCCAAAAGCAAATGTAACAAAAACAAAGATAAGT 873
                         ii   v iivi v  vv         v v i       iv   i   ii 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_84418513_8    874 AGATGGGACTTAATTAAACTAAAAAGCTTCTGCACAGCAAAGGAAATAAT 923
                          i  v      v  i   v v    i   i  ii vv       v iv  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_84418513_8    924 CAGCAGAGTTAACAGGCAGCCCACAGAGTGGGAGAAAATCTTCATAATCT 973
                           iv i   v  v  i  i        i           v  iii  vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_84418513_8    974 ATACATCCGACAAAGGACTAATATCCAGAATCTACAAAGAACTC----AA 1019
                            i   i  i  i     vi          v  i         ----  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_84418513_8   1020 ATCAGCAAGTAAAAAACAAACAATCC 1045
                         v   ii  vv    i     i  i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCC 809

Transitions / transversions = 1.67 (100 / 60)
Gap_init rate = 0.01 (5 / 573), avg. gap size = 1.60 (8 / 5)  

 311 20.17 11.76 0.00  chr1_84418513_84420447.rev     1326  1444 (491)    L1M4_orf2#LINE/L1      776   908 (0)  

  chr1_84418513_8   1326 TCTCAAAACAAAACAA-AACAAAACAAA--ATCCCACCAAAAAGTAGCCT 1372
                            i v   vv  i  -  v  i     -- i  v ii?    i i v v
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_84418513_8   1373 AAGGAC--------ACATT---CAAAAGAATATGTACAAATGGCCAACAA 1411
                              i--------     --- v      v  i             i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_84418513_8   1412 GCATATGGAAAAATGCTCAACATCATTAATTAT 1444
                            i   i   i             ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.03 (4 / 133), avg. gap size = 3.50 (14 / 4)  


3305 23.02 2.17 3.58  chr1_84450863_84452920.rev      647  1567 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84450863_8    647 TGGAAAAATACTACGTGTTCGTGGATGGGAAGATTCAATGTTGTCAAGAT 696
                               i   iiv i     i     v      i i   i    i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84450863_8    697 GTCAGCTGTTGCCAACTTGATCTATAGATTCAGTGTAATCAAAATTAAAA 746
                          v  iivv iv    v        i       ii i    vvv  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84450863_8    747 TCCCAGCGAGCCATTTTGTGGAGATTAACAGGTTGATTCTAAAGTTCATC 796
                                viv iv     ii  i   i   i i    i     i     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_84450863_8    797 TGCAGAGACAAAAGACCCAGAAGTGCCAACACAACATTGAA---GAAGAA 843
                           v i vi   ii         vv     v    iv     ---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_84450863_8    844 TAAAGTTGGAGGACTGACACTATCTGACTTCAATAGTTAATATAAAGCTA 893
                         i              v     vi ii i     v v   v  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_84450863_8    894 TAGTCATCTAGACAGTGTGGTATTGGTAAAAGAATAGACAAATAGATCAG 943
                         i   v   v             i   i v   i       v        i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_84450863_8    944 TGGAACAGAATAGAGAGCTCAGAGATAAACCC-TGCAG--ATAGTGTAT- 989
                              i     v     ii    i        - i  v--  i  vv  -
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_84450863_8    990 -------GTCAAAGGAGCAAAGGCAATACAATGG--AACAAAGAGTCTT- 1029
                         ------- v   i  v  v   i v  v      --  vi  v      -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_84450863_8   1030 -CAACAAATGATCCCAGAACAACTGGACATC-ACATACACACAAAAAATG 1077
                         -         i v ii i         i ? -    i  ---   i    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA---AAAGAATG 447

  chr1_84450863_8   1078 A-GTAAGACACGACCCTTACTTTCTTCACAGAAATTAACTCAAAATGGAT 1126
                          -  vi   v vvv   i  viiv vi   i                   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_84450863_8   1127 CGCAGACCTAAATGTAAAATGTAAAACTGTAACACTCCTAGAATGTAATG 1176
                          i?              i vv       i   v    i     - v  --
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA-GAAA-- 544

  chr1_84450863_8   1177 AGACAGGAGAAAATCTAGATGAGTATGGGTATAGTGATGACTCTTTAGAT 1226
                          v i   ? v      vvi   viv     vvi ii   ii ii      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_84450863_8   1227 ACAACACCAAAGACATAATCCATGAAAGAAATAATTGATAAACCAGACTT 1276
                          ii        ii  i  v v ii       v   v      iii     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_84450863_8   1277 CACTAAAATTAAAAAACTTCTGCTTTACAAAAGACAATGTCAAGATAATG 1326
                           ii           -   i  ivi v    i    v i      v i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_84450863_8   1327 AGAAGATAATCCAAAGACTGGGAGAAAATATTTGCAAAAGACACTTCTGA 1376
                          i    i  i   v   v                    vv i iv     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_84450863_8   1377 TAATGGACTGTTTTCCAAAATACAAAAAAAACAAAAAACAAAAAACAAAA 1426
                            v     vv v    i    i v   i   ------------------
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAAC------------------ 775

  chr1_84450863_8   1427 GAAAACCTCTTAAAACTCAGCAATAAGAAAACAAACAACCCAATTAAAAA 1476
                         -------     v      ii     i  i     i         ?    
  L1M4_orf2#LINE/    776 -------TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_84450863_8   1477 AATGGGCCAAAGATCTTAACAGACACCTTACTAAAGAAGATATGCACATG 1526
                          -     v  i   i v  i     ii iv i           i  v   
  L1M4_orf2#LINE/    819 A-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_84450863_8   1527 GCAAATAAGCATATGAAGAGATGTTCCATATCATATGTCAT 1567
                           v        i     i     i  v i    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (122 / 86)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.79 (53 / 14)  


2829 22.60 6.51 2.85  chr1_84482463_84484720.rev      892  1767 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84482463_8    892 TGGAGAAAAATACTGTGTTCATTTGTTGGAAGACACAATATTGTTAAAAT 941
                             i i v  v ii       vvi         vi           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84482463_8    942 ACCAACTCTCTTCAAATTGATATATA-ATTCAATGCAATGCCAGTCAAAA 990
                         iv   iv   ii         v  i -      i     v  vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84482463_8    991 TGTCAACAGATTTTCAAAAAAAAATTTGGTGGAAACTGACAAGCTAATTC 1040
                          vi  i v vi   ----------    -ii    i         i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT----------TTTG-CAGAAATTGACAAGCTGATCC 139

  chr1_84482463_8   1041 TAAAATTCATATGGAAATGTA-------CAGA---GGCAAAACAACCTTG 1080
                                            i -------    --- v        i    
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_84482463_8   1081 AAAAA----AACAAAGTTGGATTGCTAACACTACCTGATTTCAA------ 1120
                              ----            vvi  v     v  ii       ------
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_84482463_8   1121 -------GTTATATTTATCAAAACAGTGTTATATTGGCATAAATATATGC 1163
                         ------- i  i v v     i       vi  i        iv   vi 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_84482463_8   1164 AAAAAGATCAATGGAATACAATAGAGAGCCCAGAAATAAGCCTGCACATA 1213
                          v v              v   v     i          i  iii    v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_84482463_8   1214 TGTGATCAATTATTTTTCAGCAAAGTTGCAGAAGTGTTTGAACAGAGGTG 1263
                          i  i      iv     ii   i v   vi iiivv  v  ii ---- 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG----G 385

  chr1_84482463_8   1264 GAAAGATTGG-ATATCCA-----TAGCACCACTACCACCA-----CCACA 1302
                               v i -v v i  ----- i ii iivv  v  ii-----     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_84482463_8   1303 --CAAAGCACTTCAACCCTTCAAACCCTTATCTCACACTACAAACAAAAA 1350
                         --    iv v vv i---- iii    i  i       i i v       
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAG----TTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_84482463_8   1351 TTAACTCAAAA---ACCATAGTCCTAAACCCTGAAACCTAAAATTGTGAA 1397
                                    --- i  ?  v      iv- i i v      i i i  
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATG-TAAGAGCTAAAACTATAAA 530

  chr1_84482463_8   1398 ACTTCTAAAAGAAAACAGAGGAGACAATAATTGTAACCTTGCATTAGGCC 1447
                            ii  i         v   ? vv   vv i  i      vi      v
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_84482463_8   1448 AAGATTTCTTAAATATGACACCAAAAGCACTATCCATAAAAGAAAAAAAT 1497
                          v i       i                  v v v i           - 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-T 629

  chr1_84482463_8   1498 TGATAAACTAGACTTCATTAAAATTTAAAAACTTTGATACTTTGAAAGAT 1547
                         v      i i        i      -         vi i   ii  i  i
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_84482463_8   1548 GCTATGGAGAGAATGAAATGATAGGTCACACACTTAAAGAAAATATTTTC 1597
                         i    vi   i i     v  i ivi    v v vii           v 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_84482463_8   1598 AAATAATATATATGATAAAGGAC--ATATTCATAATATATAAA-AACTCT 1644
                             v      v      i    --i   i  v          -      
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_84482463_8   1645 CTATACAA-TAAATA-TGAAAA-------AACCCGATACAAATATGGGCA 1685
                         ---     - v    - i    -------     i  v?   v       
  L1M4_orf2#LINE/    779 ---TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_84482463_8   1686 AAAGATTTGAACA-ATACTTCATCTAGGAAGATACATGAATGGCAAATAA 1734
                           i        i - i i   vi v i       i ii      v     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_84482463_8   1735 GCACAGGAAAAGATGCTCAACATCATTAGTCAT 1767
                              v                   ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (117 / 78)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.42 (82 / 24)  


3689 22.35 1.33 0.88  chr1_84493170_84496383.rev     1820  2723 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84493170_8   1820 TGCAAAGACATCTCAAGTTCATGGA-TGGAAGATTTAATATTGTTATAAT 1868
                           v     i   i  v         -       i            vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84493170_8   1869 TTCCATATGACCCAAAGCAATCCACAGATTCAATGCAATCCCCATCAAAA 1918
                         vv v   ivv      vii   i          i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84493170_8   1919 TCCTAA-TGATATTTTTATAGAAATAGAAAAAA-AATTCTAATATTCATA 1966
                            i i-  viv     ii      v  v  iv-i  i    v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_84493170_8   1967 TTGAACCAGAAAAGATCTTGAATAGCCAAAACAAT-TTGAAAAAGAA--- 2012
                          v   viiv  ii  i iv                -           ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_84493170_8   2013 CAGTGTTGGAGGCAACACACTTCCTGATTTCAAAATATATTACAAAGTAA 2062
                           iv        vvv         ii         iv  i       iv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_84493170_8   2063 CAGTAATTTAAACAGTATGGCAATGGCATAAAGACTGACATATAGATCAA 2112
                                iv i     i   i v        i  iv              
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_84493170_8   2113 TGGAACAGAAGAGAGAGCCCAGAAATACATCCATGGATATGTGGTCAAAT 2162
                              i    vv     i         v i    iv  v i       v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_84493170_8   2163 GATCTTTGACTGGAATGCCAAGAACACAAAATGGAGAAAGATGAGTCTCT 2212
                            i  i   vi ii        v  ivv     i      vv     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_84493170_8   2213 TCAACTAATGGTGTTGGGAAAACTGGATATCCACATGCAAAAGAATAAAA 2262
                              v       i     v         ?                i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_84493170_8   2263 CTGGA---TTATCTTTTACCATACACAAAATATCAACTCAAGATGGATTA 2309
                         i    ---i  i  ivi      i      -  i       i      i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATGGATCA 499

  chr1_84493170_8   2310 AAGACTTAAACATAAGACTTGAAACTGTAAAATTTCTAGAAGAAATCACA 2359
                         ?    i    ii     vi i     i     i ii         v  i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_84493170_8   2360 GAGGGAAAGCTTCAAGACATTAGTTTTGGCAATAGTTTCATGGATATGAC 2409
                          i? v   v    iv   v  i v  v      i     v i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_84493170_8   2410 ACCAAAAAGCATAGGCAACAAAAGCAAAAATAAACAAGCAGGGCTAAAT- 2458
                                -   i i          v       i i  iiv  i  vv  -
  L1M4_orf2#LINE/    600 ACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_84493170_8   2459 AAAACTAAAAAGCTTCTATACAGCCAGGGAAATATTCAATAGAGTAAAAA 2508
                             i      -   i i i vv v i   v ivv    v i   i    
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_84493170_8   2509 GGAAACCTATGGAATGAGAGAAAATACTTGCAAACTATATATCTGATAAG 2558
                          iv    i ii     i         i       ii              
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_84493170_8   2559 AGGTTACTTTCTAAAATATATAAGGAATGCTTACAATTCTATAGCAAAAA 2608
                         i ii vv v  i i         i   iv       i  v   ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_84493170_8   2609 AACTAATAACTCAATTGAAAAAATGGTCGAAGGACAT-AATAGATATCTC 2657
                         i  v      i     -?        v i     iv -      i  i  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_84493170_8   2658 TGAAAAGAAGACACACAAATAGCCAATATGTATATATATGAAAAGAGGTT 2707
                          vv        i i      i       v i i  ----       v i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACAT----GAAAAGATGCT 892

  chr1_84493170_8   2708 CAAAATCACCAATCAT 2723
                            v    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (121 / 77)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


3125 26.21 0.88 0.88  chr1_84619982_84626682     5301  6208 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84619982_8   5301 TGGAAAAACATTCCATGCTCATGGATAGGAAGAAGCAATAATGTGAAAAT 5350
                               i i  i     i        v      vvi    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84619982_8   5351 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCTCATCAAGC 5400
                            v     v      v i  i  i       ii  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84619982_8   5401 TACCATTAACTTTCTTCACAGAATTAGAAAAAAAAACT-ACTTTAAATTT 5449
                          v   vivi i  i  ii     v v  v  i----  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chr1_84619982_8   5450 CATATGGAGCCAAAAGAGAGCCCGTATAGCCAAGACAATCCTAAGCGAAA 5499
                                 iviiv   i  v  v v        i      i i ivi i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_84619982_8   5500 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTCTACTA-ATT 5548
                                  i      vv       v  ii i      vii     - vv
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_84619982_8   5549 GTCTACAGTAACCAGAACAGCATGGTACTGGTACCAAAACAGATATATAG 5598
                          -         i  ii    ii         i iv ii i   i      
  L1M4_orf2#LINE/    247 G-CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_84619982_8   5599 ACCAATGGAACAGAA--GAGAGGCCTCAGATATAATACCACACATCTACA 5646
                          i        i    --     v  --   v    vv   i    i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr1_84619982_8   5647 ACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAACGGGGAAAGGAT 5696
                         ii  vi    i  i     ivv  v   i v  vv   i        i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_84619982_8   5697 TCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATTCAAAAA 5746
                         vvi  v  i  i        i     v      v  ?   i  v     i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_84619982_8   5747 ACTGAAACTAGACCCCTTCCTTACACCTTAAAGAAAAATTAACTCAAGAT 5796
                          v    ii i       v   i     v  v v              i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_84619982_8   5797 GGATTAAAGACTTAAATGTAAGATCTAAAACCATAAAAACCCTAGAAGAA 5846
                             i ?    i           v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_84619982_8   5847 AACCTAGCCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGG 5895
                            v   v?i- v i -   iv   v v  vv i     v ii   v i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_84619982_8   5896 CTAAAACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGAAT 5945
                         v  vi            vvi          vv     v  i    v i i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_84619982_8   5946 CTAATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACAATCATCAGAGT 5995
                         i v  i   viv  i i   i  ii vv    i  v  v    vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_84619982_8   5996 AAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTG 6045
                         i  v  i     i                 v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_84619982_8   6046 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAG 6095
                          i  i  i  vi          v  i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_84619982_8   6096 AAAAAAA--AATAACACCATCAAAAAGTGGGCAAAGAGTATCAACAGACA 6143
                              i --      v v  i?    i         ii v v  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_84619982_8   6144 CTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAA-GCT 6192
                         i     v        i  vi viii     i  i  i       i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_84619982_8   6193 CATCATCACTGGTCAT 6208
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (134 / 100)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


1411 28.22 10.99 2.17  chr1_84756164_84757885      498  1234 (488)    L1M4_orf2#LINE/L1      107   908 (0)  

  chr1_84756164_8    498 CTGTTTAGTTTTGGTGGAATTTGATAAGCTGATTCTAAAATATATAAGAA 547
                            ii --    v ii   v    i        i       vi   v i 
  L1M4_orf2#LINE/    107 CTGCCT--TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_84756164_8    548 AATATAAA--------AATAGTTGTGACATTGCTC-------AAGAACAA 582
                            ii  i--------     iiivi   v -  i-------        
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAACAA 203

  chr1_84756164_8    583 GGTGGGAAGTCTT---CTACATATTCTCAAGACTTA--AAAAGATTA-AG 626
                         i  v   i v  i---  v vi v i    i     -- v  iii  -  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_84756164_8    627 TAATAAATTCCACTCACTATTGGTGCAAGCATAAACAAATGAACCAATGG 676
                             v  vv viiviiv  i   iii   v   i   v  ii i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_84756164_8    677 CACAGAGTTGAGAACTCACAAA-AGATCCATGTGTATA----CACTTGAT 721
                         v i   i      iii  v   - i i    iii v  ----  v     
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_84756164_8    722 TAATGACAAAGG------AATCACTGCA--GAGCAGCAGAA--------- 754
                          vvi     i  ------i i  i -  -- i v i-    ---------
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAA-AGAATAGTCTTTT 401

  chr1_84756164_8    755 -AAAAGATAATGTTGTGACAACTGGATATTAATATGGAAAAAACCTGAAA 803
                         -  v i  ii  i  v            ?iv i   v    i v-    i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAG 450

  chr1_84756164_8    804 CTTGACCTCTACCTCACACCATATACAAA---CAACTCTAGGTGATTTCT 850
                         i v    i                     ---i     v ii  iv iv?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_84756164_8    851 AGACTTAAATGTAAAAGGCAAAACAACAAAGTTATCAGAAAATAATATAG 900
                             i         i  vi     v i   ii v i    i v  i    
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_84756164_8    901 AGAATA---TTTCATGATCTC----TAGAGAATAAACCCTTA--CATGAA 941
                         - ?i  ---i   i   i  i----   iv   iivii    --i    v
  L1M4_orf2#LINE/    551 -GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_84756164_8    942 GCCCGAAAAGTATTAACTACAAAGGGAAAAAATCAATACATTTGGCTAC- 990
                         i  --     i iv i v     i -       vi   v   v i  v -
  L1M4_orf2#LINE/    600 ACC--AAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCA 646

  chr1_84756164_8    991 TCAATATTTAAGAACTGTTTAT----CAAAAAACAC----AAGAGAGTAA 1032
                             v   -  i    -   i ----    ii    ----    i   i 
  L1M4_orf2#LINE/    647 TCAAAATT-AAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_84756164_8   1033 AAAG-----CCACAGTATGGAACAAGGTATTATTTGTAAAATATATAACC 1077
                             -----      v    i v  --- v      i   vi     v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAA---AATATTTGCAAATCATATATCT 741

  chr1_84756164_8   1078 AACAATGGACTGGTGTGAAGAATATATAAAGAACTCATATAAATTCAAAG 1127
                         i i  v     v  i vv                  v  i  -i    vi
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATA 790

  chr1_84756164_8   1128 A-AAAAAG-----TAATCTAGA-GGAAAATGGCTAGGAAATCAGAA---- 1166
                          -      -----   i i iv-?i       vi iiii  iv   ----
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_84756164_8   1167 CACTTTACAAAAGAGGATATCTGTATGTTCAATAAACATATGAAAAGATG 1216
                           i  iv v     i     viiv   vi      i  i           
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_84756164_8   1217 CTTAATCTTGGTAACCAG 1234
                           i  iv ii????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (134 / 70)
Gap_init rate = 0.04 (34 / 802), avg. gap size = 2.85 (97 / 34)  


2881 25.14 3.00 2.00  chr1_84766726_84772950     4834  5732 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84766726_8   4834 TGGAAAAACATACCATGCTCATGGATAGGAAAAATCAATATTGTGAAAAT 4883
                               i i  v     i        v    i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84766726_8   4884 GCCCATATACTGCCCAAAGCAATTTATATATTCAATGC----TTTAATAA 4929
                          v - -     v      vii  i  i v      i  ----ii  vi  
  L1M4_orf2#LINE/     51 GGC-A-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_84766726_8   4930 AACTACCATTGACATTCTTCACAGAATTAGAAACAACT-ATTTAAAAATT 4978
                           - v   vivi v  i  ii     v v  v - i  -  iiv      
  L1M4_orf2#LINE/     99 AA-TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATT 146

  chr1_84766726_8   4979 TATATGGAACCAAAAAAAAGCCCGAATAGCCAAGACAATCCTAAGCAAAA 5028
                         i        viiv  iii v  v          i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_84766726_8   5029 AGAACACAGCTGGAGGCATCATAGTACCCAACTTCAAACTATACTACCAA 5078
                               v  i      vv   i v v     i      viv      -  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC-AA 245

  chr1_84766726_8   5079 GGCTACAGTAGCCAAAACAACATGGCACTGGTACAAGAACAGACATATAG 5128
                         i         ii   i   iii   i     i i   i i          
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_84766726_8   5129 ACCAGTGGAACAGAATAAAGAATCCAGAAATAAGGTTACACACCTATAGC 5178
                          i  i     i     vi   i           ivii i   ii   i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_84766726_8   5179 CATCTAATTTTCAACAAACTTGACAAAAACAAGCAATGGGGAAAGGATTC 5228
                           vi i      i    ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_84766726_8   5229 CCTATTTAATAAATGGTGCTGGAAGAACGGGGTAGCCATATGCAGAAAAT 5278
                         i  v  i  i            i v   v  i  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_84766726_8   5279 TGAAACTGGACCTCTTCTTTACACCATACACAAAAATCAACTCAAGATGG 5328
                             ii      i  v i i        i        i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_84766726_8   5329 ATTAAAGACTTAAATGTAAAACTCCAAACTATAAAAACCTTAGAACAACC 5378
                           i ?    i         i viiv           vi       v  --
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA-- 543

  chr1_84766726_8   5379 CTAGAACAAAATCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAG 5427
                         ----    -----    ?i- v i -   iv   v v  vv i     v 
  L1M4_orf2#LINE/    544 ----AACA-----TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chr1_84766726_8   5428 ATTTCATCATGAAGACTCCACAAGCAATTGCAACAAAAGCAAAAATCAAC 5477
                         i    v vivv v   v   v     vvv          v      vi i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_84766726_8   5478 AAACGAGA-TCCAGTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA 5526
                            ivi  - i  viv   i    i -   i  ii vv    i  v    
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA 682

  chr1_84766726_8   5527 TCATCAGAGTGAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAATT 5576
                            vv i      v        i                 v       v 
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_84766726_8   5577 TATCCATCTGACAAAGG--------------TATACAAGGAACTTAAATA 5612
                         i  vi      i  i  --------------    i  i     ivv i 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_84766726_8   5613 AATTAACAACAACAA--CAAA-AA---AATTAAAAAGTGGGCAAAGGACA 5656
                          v i  i  i  v  --    -  ---    ?    i           iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_84766726_8   5657 TGAACAGATGCTTCTCAAAAGAAGACATATATGTGCCCAACAAACATATG 5706
                             i   iii     v        i   i vi  v    i  i  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_84766726_8   5707 AAAAGAAGCTCAACATCACTGATCAT 5732
                               v           ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (133 / 89)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.65 (45 / 17)  


3071 26.01 2.47 0.67  chr1_84905565_84910789.rev     3843  4734 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84905565_8   3843 TGAAAAAACATTCCATGCTCCTGAATAAGAA----TAACATTGTTAAAAT 3888
                           i   i i  i     i  v  i  vi   ----   i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84905565_8   3889 GGCAATACTGCCCAAAGCAACTTATAGATTCAATGCTATTCCTATCAAAA 3938
                                  v      vii ii  i        i  v  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84905565_8   3939 TACCAATGACATTCTTCACATAATTAGAAAGAAACT-ATCCTAAACTCCA 3987
                          v   iivi v  i  ii  v  v v  v -- i  -        v i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA--AGCTGATCCTAAAATTCA 148

  chr1_84905565_8   3988 TGTGGAACCAAAAGAAGAGCCTGAATAGACAGGGCAATCCTAAGCAAAAA 4037
                          i     viiv   i-  v  v      v  iii     i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_84905565_8   4038 GAACAGAGCTGGAGGCATCACATTACCTGACTT-AAAACTATACTACAAG 4086
                              i  i      vv     i v  ii i  -      -        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr1_84905565_8   4087 GCTA--GTAACCAAAACAGTGTGGTACTGGTACAAAAATAGATGCATAGG 4134
                             --    i   i               i i  ii     iii    i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_84905565_8   4135 CCAATTGAACA----TGAGAGCACAGAAATAACGCTGCACACCTCCAACC 4180
                         i    v   i ----      iv         vv iii   ii viiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_84905565_8   4181 ATCTAATCTTCAGCAAAGCTGATAAAAACAAACAATAAGGAAAGGACTTC 4230
                          vi i  i   ii   i v  vi  i v  vv    ii      i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_84905565_8   4231 CTGTTCAATAAATGGTTCTGGGATAACTGGCTAGCCATATGCAAAAGATT 4280
                           v     i       v      i      v  ?   i          v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_84905565_8   4281 GAAACTGGACCCCTTCCTTACACAATATACAAAAATTAACTCAAGATGGA 4330
                            ii         v   i    v                    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_84905565_8   4331 GTAAAGACTTAAATATAAAACCCCAAACTGTAAAAACCCTGGAAAGCAAC 4380
                         vi ?    i     i   i v iv     i     vi i i   iiv   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_84905565_8   4381 CCAGGCA-ATATCATTCTGGTCATAGGAACAGGCAAAGATTTCATGACAA 4429
                         vi   ?i- v   v iv  ii v i  v-i      v i    v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr1_84905565_8   4430 AGATGCCAAAAGCAAATGCAACAAAAGCAAAAATTGACAAATGGGATCTA 4479
                         v  ii         v v          v      v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_84905565_8   4480 ATTAAACATAAGAGCTTCTGCGCGGTAAAAGAAACTATCAACAAAGTAAA 4529
                           i   vv   i i   i  i  vvi   i  v        v     i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_84905565_8   4530 CAAACAACCTACAGAATGGGAGAAAATGTTTACAAACTATCTATCTGACA 4579
                         v i      i                 i   i    ii  v       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_84905565_8   4580 AAGGTCTAATATCCAGCATCTATAAGGAATT--TA-AATTTA-CAAGAAA 4625
                          i  v  vi       v  v     i   i --  -  i i -i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_84905565_8   4626 AA--CAAG--ACCCCATT-AAAAGTGGGCAAAGGACATGAACAAACACTT 4670
                           --   i--    v   -    i           iv    i i   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_84905565_8   4671 TTCAAAAGAAAACATACATGCAGCCAGCAAGCATATGAAAAAAATGCTCA 4720
                         i  v      i i     viii    ii     i       i -      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCA 894

  chr1_84905565_8   4721 CCATCACTAATCAT 4734
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (148 / 81)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.65 (28 / 17)  


1391 27.15 4.30 9.12  chr1_84967575_84970637     1632  2585 (478)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_84967575_8   1632 TGGAGAGATATAC--TGTTCCTAGGTAGAGAGATCCAATTTCATAAATAT 1679
                             i      v --     v i i v ii   iii   v ii v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_84967575_8   1680 GCCAATTCTCCCTAAAT------ACA------ATGCAATTCCAGTCAATA 1717
                          v    v     i    ------   ------ i     i  vi    v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_84967575_8   1718 TCTCAATTG--TTTATCAT-GAAACTTATTATCTGATTTCAAAACTTACA 1764
                           i  ii  --   v iii-    i v iv v     iii    i i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_84967575_8   1765 TGGAAGAGTAAAAG-CCTACAAATAGTCAAGATACTTTTGAGGAATAACA 1813
                              iv i  ii -  i -i     i   i i v i    ii  v  v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_84967575_8   1814 ACAAAGTGTGTGTGTGTGTGTGTGTGAGATGGGGTAGAGGTAGGGGTTGC 1863
                                ----------------------   ---------   iv ii 
  L1M4_orf2#LINE/    200 ACAAAGT----------------------TGG---------AGGACTCAC 218

  chr1_84967575_8   1864 CCTGC--AATTTGTGGTAAATCTATGTAAATCATGTAAGTCATGATAAAT 1911
                         v  v --     ----i   v  -----------------i iv i   v
  L1M4_orf2#LINE/    219 ACTTCCCAATTT----CAAAACT-----------------TACTACAAAG 247

  chr1_84967575_8   1912 CTAT-GTAAATAAGATAATGTGGTATTGGAAGACAGATAAACAAATAGAC 1960
                            i-    vi    i i       i   v v vi    i   v     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_84967575_8   1961 CAGAGGAA-AGAATAGTGAGCCCCAAAATGAATCCATGAATATATGAAGA 2009
                           iv    -     v v   i  vi    i  i    iv  v    i---
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG--- 344

  chr1_84967575_8   2010 CTTACCTACAGGCATTGCATAGTGGCTGAGGTGT-GGGGCCGGGGTAGAA 2058
                         - i ---------    vv vvi i vii    i-ii i  i--- vv  
  L1M4_orf2#LINE/    345 -TCA---------ATTGATTTTCGACAAGGGTGCCAAGACCA---TTCAA 381

  chr1_84967575_8   2059 GGCATGGTAGAGAATGAACTGCTCAATAAATAGTGGGGGAACAAGAGTTT 2108
                         v ---  v i     iiv  vi    i    i   vv  i    vv vv 
  L1M4_orf2#LINE/    382 TG---GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_84967575_8   2109 ATCCATATTGGAAAAAAATGATATTGGATCCCTCCCTTATACCGTTTATA 2158
                          ?   i  - v    i     vi     i    v   i i   i v  i 
  L1M4_orf2#LINE/    429 AKCCACAT-GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_84967575_8   2159 AAA-TAAAGTCCAGGTAAAATAAAGACTTAAATGTAAAAGGAAAAACTTT 2207
                            - v  v  v ii ii vi ?    i         i  vv      v 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_84967575_8   2208 AACATGTTTAAAAGTCAATATAGAACAATAGTTATGTGACTTTGGCTAAG 2257
                           v ivi   i   vv  i    i?vv v vi vi     i    v v  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_84967575_8   2258 AGAGTACTTTCT-AAACA--ACACTCAGAGAATACAAGCCATAAAATAAA 2304
                         iv i iv     - i i --    -  i - ii      v i    v   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACAC-CAAA-AGCACAAGCAACAAAAGAAA 625

  chr1_84967575_8   2305 ATATTGATAAATTAAAGAAATTCA----AATAAAAAATTTCTAATTTTTA 2350
                          v  v        --- i v    ----   v     i  i ivvi  i 
  L1M4_orf2#LINE/    626 AAATAGATAAATT---GGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_84967575_8   2351 CCTAAAGACACCAT----AAAGTGAAAAGACTAGCCA-AAAATCTAGAGG 2395
                         ---  i     i  ----             v v   - i   v-i   i
  L1M4_orf2#LINE/    673 ---AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG-GGAGA 718

  chr1_84967575_8   2396 GCATATTTTCCATGCATATAATTAATAAAAGATTAGTATTGAGAATCCAT 2445
                         iv      v v vv      vi i    ii  i v    iv     vi  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_84967575_8   2446 AAAGAAGTCCTAAAAATCAGTGAGAGAAAATACAAACAACCCAAT-AGAA 2494
                               v  i  v  v   i i v -    v     i        -?i  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATA-AAAAGACAAATAACCCAATTWAAA 817

  chr1_84967575_8   2495 AATGGCCAATAGGAAT-GAAAAGATTTTTCACAGCAAAGAAAACATA--A 2541
                              v   -    v -   v   iv    v --       i i   -- 
  L1M4_orf2#LINE/    818 AATGGGCAA-AGGATTTGAATAGACATTTCTC--CAAAGAAGATATACAA 864

  chr1_84967575_8   2542 ATGGCAAATCAATATACAAAATGTAT-CTTAATTTCATAAGTACC 2585
                              v   v ii i ii   v -  -  i  iv   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (145 / 110)
Gap_init rate = 0.04 (39 / 908), avg. gap size = 3.28 (128 / 39)  


 506 24.39 1.63 0.00  chr1_85078693_85084347     3886  4008 (1647)    L1M4_orf2#LINE/L1       43   167 (741)  

  chr1_85078693_8   3886 GTTAAGATTTTAATTCTCCCCAATTCAATCTGTAGAATCAACGCTATCTA 3935
                                 vvi   v        v ii    ii   v       v   iv
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chr1_85078693_8   3936 -ATCAGAACTCCACCAGGCCTTTTTGCAGAAATTGACAAACCGATTCTAA 3984
                         -    i  ii   v v v i                   i i   i    
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr1_85078693_8   3985 -TTTTATATAAGAAAGCAAAGGACC 4008
                         -v  i    iii  v    i     
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACC 167

Transitions / transversions = 1.50 (18 / 12)
Gap_init rate = 0.02 (2 / 125), avg. gap size = 1.00 (2 / 2)  

2340 24.38 5.92 1.65  chr1_85078693_85084347     4446  5171 (484)    L1M4_orf2#LINE/L1      152   908 (0)  

  chr1_85078693_8   4446 GGAA--GGAAAGGACCTAAAATGACCAAAAAAATTTTGAAAAAGAA-ATC 4492
                             -- v  i     i i   ii      v   i           - v 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_85078693_8   4493 AAAGTTGGAGGATTTATACTACTTGATTTCAAGGCC----ATAAAATTAC 4538
                                     i i i   v iii       ii i---- i   ii   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_85078693_8   4539 AGTAATCAAGACAGTGTGATATTGAGGCAGGGTTAGTTAAGTAGATCGCT 4588
                                           i  i  ivii i  v   vi vi      iv 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_85078693_8   4589 GGGACAGAAT--AGAGTCCAAGAATAGTCTTCCACATATATAGTCAATTG 4636
                           i i     --        ii    iv iivi    v   i        
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_85078693_8   4637 ATTTTCAACAAAGGAGCCAAGGTAATTCAATAGCGAAAGCATAGTCTTT- 4685
                               i    i  v      iiv       i v     v         -
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_85078693_8   4686 CAACAAATGGTACCAAAACAACTAGGTATCTATGTGGAAAA--ATTA-GA 4732
                                    i iiii      i i  ? i ii  v    --  v - v
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_85078693_8   4733 TGAACCTCCACCTCAATTTCATAC-CAAAAATTAATTAGAGATAAATCAT 4781
                           i   i i      -ivi    i-          i vi i  ii    ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_85078693_8   4782 AGACCTATGCATAAAATGTAAAATTATAAAATTTCTAGAAGAAAGGTTAT 4831
                                viii   i vv     i       i ii         i--i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA--CAT 548

  chr1_85078693_8   4832 AGG---ACACTATAATGA----GAG--AGGCAAAAATTT-------ATGA 4865
                            --- v iiv vi   ---- i --      vii   -------    
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_85078693_8   4866 GACAAGAA--ACAA-CACTAAAAGAAAAAAATTAATAAATCAGACTTCA- 4911
                         v  v i  --    -  vi           - vi      ii       -
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCAT 647

  chr1_85078693_8   4912 --AAATTATAAACGTCTGGTCTTCAAAAGATACCATCAAAAAAATGAAAA 4959
                         --      v    v i  vv       i  i  i     i   i      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_85078693_8   4960 TGCAATCCATAGACTGGGAAAAAATATTTCTTCTA--CACGTGTTTGATA 5007
                         vi   i   i   v     i         v-- v --  ii i i     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTG--CAAATCATATATCTGATA 745

  chr1_85078693_8   5008 AAGGATTTGTATCTGGAATACACAGAGATCTCCTAAAAATTAATAATAAA 5057
                          i   i       ii     i i i   v   i  v  v i         
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_85078693_8   5058 AAGA----TAACCCAATTTAAAAGTGAGCAAAATACTTGAACTGGCACTT 5103
                             ----          ?    i  i     iv i     iv i  i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_85078693_8   5104 -TGCAAAAAGAATGTAAATGAATGGCTAATAGACCCACAGAAAGATTATC 5152
                         - v    i ii  i  v --      i    ii v  iii      vv  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACA--AATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_85078693_8   5153 AAAAGGCACCAGGGAAATA 5171
                           ----  i  ????????
  L1M4_orf2#LINE/    894 AA----CATCAZZZZZZZZ 908

Transitions / transversions = 2.48 (124 / 50)
Gap_init rate = 0.03 (24 / 757), avg. gap size = 2.29 (55 / 24)  


3057 23.87 4.05 2.36  chr1_85154574_85159269     3316  4203 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_85154574_8   3316 AGAAATTTCATGTTCATAAATTGGAAGAATCAATAGTGTTAAAACGTCCA 3365
                            v  ii         ii         v i    v      i i v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_85154574_8   3366 CACTCC--AAAGGAATCTACAGACTCAATGCAATCCCTATCAAAATATCC 3413
                         i     --   vvi         i    i                 vi v
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_85154574_8   3414 ACGACATTCTTCATAGAAATAGAAAAA--AACCCTAAAATTGATATGGAA 3461
                         i vi v  i  iii      v  v  i--i i         v        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_85154574_8   3462 CCACAAAGAACCCAGAATAGTCAAAGCTATCCTCAGCAAAAAGAACACAA 3511
                         vii   i i           i    i v   i v iv  i       v i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_85154574_8   3512 CTGGAGGAATCACATTATCTGACTTCAAAATATACCACATAGCTTTACTA 3561
                         i       v     i vi ii i       iv   i   v    vi v  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_85154574_8   3562 ACCAAAACAGCATGGTATTACACAGATACAAAACACAAAAACAGATACAC 3611
                          i   i    ii     i i------------i  i  ii i   i i i
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTG------------GCATAAGGATAGACATAT 293

  chr1_85154574_8   3612 AGACCAATGGAATGGAATAGAGAACCCAGAAACAAATCCACACACCTACA 3661
                            i         i    v    ii       i   i   i   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_85154574_8   3662 GTGAACTCATTTTTGACAAAGGTGACAAGAACATAAACTGGGGAAAAGGC 3711
                           v  i v     i     i    v     v   vv v        iiii
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_85154574_8   3712 AGTCTCTTAAATAAATGGTGTTGGGGAAACTGGATATCCATATGCAAAAG 3761
                              i  v  i        i    iv         ?   i         
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_85154574_8   3762 AATGAAACTAAACCCCTATCTATCACCATATACAAAAATCAAATCAAAAT 3811
                               ii ii       i  vv                i  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_85154574_8   3812 GGATTAAAGACTT-----TAAGACCTCAAACTATGAAACTACTACAAGAA 3856
                             i ?    i -----     v  v       i     vi  v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_85154574_8   3857 AACACTGGGGAAAATCTCCAGGAC------------AAAAATTTACTGAG 3894
                             iv  ? v      i iv   ------------  vii   -  v  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-CTTAG 592

  chr1_85154574_8   3895 CAAT-ACCCCACAAGCACAGAT--CCAAAGCAAACATGAACGAATGGGAC 3941
                         vv  -  v   v       iii-- v    v   v  ii ii   v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_85154574_8   3942 CAAATCAAGTTTAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGT 3991
                         ivv     iv      i   i  ii vv       v  v     v     
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_85154574_8   3992 GAAAAGACAACCCATAGAAAGGGAGAAGATATTTGCAAA--------CTG 4033
                                       i    v       i           --------   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_85154574_8   4034 ----GAGATTAACAGCCAGAACATATAAGGAGTTCAAACAATTCTATAAA 4079
                         ---- i  i vii v      i      i  ii  vv    i  v    v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_85154574_8   4080 AAATAACCTAATAATCTGGTTATGGCAAAATGGGCAAAAGACTTGAATAG 4129
                            v iv v     i iii  ?---v            i  i        
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTW---AAAAATGGGCAAAGGATTTGAATAG 839

  chr1_85154574_8   4130 ACTCGTTATGTCTCAAAAGAAGACATACAAATCACAAACAGGGATATGAA 4179
                           -----  v    v        i        vi v  i i v i     
  L1M4_orf2#LINE/    840 AC-----ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_85154574_8   4180 AAGGTGCTCAACATCACTGATCAC 4203
                            i            ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (129 / 79)
Gap_init rate = 0.01 (12 / 903), avg. gap size = 4.75 (57 / 12)  


2800 22.67 6.22 1.42  chr1_85289879_85292771.rev     1234  2005 (888)    L1M4_orf2#LINE/L1        2   810 (98)  

  chr1_85289879_8   1234 GAACAGATATACTGTGTTTATGGGTTAGAAGACTCATT-TTGTTA-GACG 1281
                          i v      v ii    i    i  i       i v -      -  i 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_85289879_8   1282 CTAATTCTCATAATACTGACCTACAGATTCAATACAATCTCAGTCAAAAT 1331
                         vi   v   viv v i   i            ii     i vi       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_85289879_8   1332 CACAGCTAGCTTTTTATGCA-----TAACAAGCTGTTCCTAAAATTCACA 1376
                          v     iv      -    ----- i        v            i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_85289879_8   1377 TGGAAAAGCAAAAAACTTACAACAGTCAAAAACTACTTTGAAAAAAAA-- 1424
                               v    iii  ii v  i  i     - v ii        i  --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGA 199

  chr1_85289879_8   1425 --AAGGTTGGAAAACTAACACTATCTAATTTCAAGACTAATTATAAAGCT 1472
                         --  i      ii   v     vi i        i   v i  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_85289879_8   1473 AGCATAATCAAAACAGTGTCGTATTGCTCTAAAGATAGG--------TCA 1514
                          vvi       i       v   i  viv   i     i--------   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_85289879_8   1515 ATGGAACAGAAT--AGAGTTTAGAAATAGACTCACATATATATGGACAAG 1562
                               i     --     ii       i  i  i i  v     v   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_85289879_8   1563 TGTTTTTTGACAAAGGTGCAAAG-CAGTTCAGTAGAAAGAGGATGGTGTA 1611
                           v    i     i     v   - vi    i i ii i  i  i  v v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_85289879_8   1612 TTCAACAAATGGTG-TGGGA-------ATA-CCATACACAAAAAAATGAA 1652
                                       -     -------   -   i ii     i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_85289879_8   1653 CTTTGATCCATAACATATACCAATTACAAAAATTAACTCAAAAGAAATCA 1702
                         v  v  i  v  v vi i    vv                   vii    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_85289879_8   1703 TAGCCCTAAATGTAAAACCATAAAACTAGAAAAAT--TAGGAAAAAACAT 1750
                         ?  v           i v -        v    v --   i i       
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_85289879_8   1751 TGGCA------------ACTGTGGGCTAGGCAAACATTTCTTAAATTCAA 1788
                         v  ?i------------  iv    i       vvi       i  vii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_85289879_8   1789 CACCAAAACCATGATCCACAAAAGAATAAATTGATAAGCTGGACTTCCTC 1838
                                 v  ii v v         v    v     ii        v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_85289879_8   1839 AAAATTAAAAACTTCTGATTTTCAAAAGAC--TGCTAAGAGA-TGAGACA 1885
                                       i  vvi      i   -- iii    i -   i vi
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_85289879_8   1886 ACAAATCACAGACTAGGAGAAAATATTTAAAAATCACATATCACTAGTCC 1935
                             vi      v i             iv      i     --------
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC-------- 740

  chr1_85289879_8   1936 TGAGAAAGAACTAGTATATAAGATATATTAAGAACTCTCAGAATTCAATA 1985
                            v  i i   v    vi ii      v         i v  i      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_85289879_8   1986 ATAAGAAAACAAACAGGCCA 2005
                             i  i     i iv   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCA 810

Transitions / transversions = 1.62 (107 / 66)
Gap_init rate = 0.02 (18 / 809), avg. gap size = 3.28 (59 / 18)  

 454 19.38 0.78 3.88  chr1_85289879_85292771.rev     2279  2407 (486)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_85289879_8   2279 CTCAAAAATAAAAATAAAACAAACAACCCAACTGATAAATGGGCAAAAGA 2328
                              v        ---i     i       i ? v           i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAA---GACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_85289879_8   2329 TTTGAACAGACACTTAACCAGGGAAGATATACAGGTGGCAAA-AAACATG 2377
                               i     i  vv   ii           ii    v  -  i  ii
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_85289879_8   2378 CGAAAATTTGCTTGACAACTTAAGTCATTA 2407
                         i     vv    ii   -- i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACA--TCAZZZZZZZZ 908

Transitions / transversions = 2.43 (17 / 7)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 2.00 (6 / 3)  


2155 24.48 9.60 2.23  chr1_85324561_85326258.rev      502  1220 (478)    L1M4_orf2#LINE/L1      137   908 (0)  

  chr1_85324561_8    502 TTTTAAAATATACATACACATACGAAGGAC------TAACCAAAACAACT 545
                          ii      vi i  iv v  i i i    ------  i         ii
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_85324561_8    546 TTGAAAAAGAA---CAGAGTTGGAGGACCAACATTATCTGATTTTAAGG- 591
                                    ---  i           iv   i vi ii    i  ii-
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_85324561_8    592 TGACTTATAAAGTGACAGTAATCAAGATGGTATAGTAATGGCATCAAAAT 641
                          v   - i    iv             ii  i i   v      v ii  
  L1M4_orf2#LINE/    237 TTACT-ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_85324561_8    642 AGACA----AATCAATAGAATAAAA------GTTCAGAAATAGATTCATA 681
                              ----i      i     i  ------  i        i ii    
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_85324561_8    682 CATATACGGACAACTGATTTTTGA------TG---AGACAATTCAGTGAA 722
                            v  i  v   i       i  ------  ---    v     i  ii
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_85324561_8    723 GAAAGAATAGTCTTTTCAACAAATGGTGCTGCAACAATAAAATATTTGCA 772
                                                        vi    ivii   ?iii  
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_85324561_8    773 TG-AAAAAAATGC--TTTGATCCACATCTCATACCATATGTAAAAGTGAA 819
                           -    i    v--  v  i  vi i    i       ii    i v  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_85324561_8    820 CTCAAAATACATAATAGACCTAAATGTAAAGCCTAAAAGTATAAAACTTC 869
                                 iv  v ?              iiv      v         ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_85324561_8    870 TAGAAGAAAAC---------------------CTTGGATTATGCACAGAT 898
                                    ---------------------     i   v   vv i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_85324561_8    899 TTCTCAGATTGGTCACCAAAAACATGAT--ACATAA-----AATTTTTTT 941
                             i    vv v        i  ii v--   v  -----   v-----
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA----- 630

  chr1_85324561_8    942 TTTTTAATAAACTGAACTTCATCAAATTTACAAACTTCTGCACTTTGAAA 991
                         -----i     i  i           v   v      i  ii   ii  i
  L1M4_orf2#LINE/    631 -----GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_85324561_8    992 GACCCTGTTGAGAGAATAAGAAGATGAACCACAT--TGGGAGTATATATT 1039
                            v  i ii   i i i i    ii v     v--      v v     
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_85324561_8   1040 TGCA-----TATATCTGATAATGG-CTGGCATCTGGGATGTATAAAAAAT 1083
                             -----            v  -  v i   ii i  i      i  i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_85324561_8   1084 TCCAAAACCTCAATAATAATTAAAAAAACACTCCCCTTGCTCCCTGCAAT 1133
                           iv v v           vv i v   i vi  vv  ?v-----iv   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-----AAAAT 820

  chr1_85324561_8   1134 GAGCAAAATACATGAACAAACACTTCATGAAAGAGTATATATGAATGGCA 1183
                          i     iv iv    i i   i   viv     iv     ii      v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_85324561_8   1184 AATGAAGACATGAAAAT-TAACCACTATCATTAGTCAT 1220
                            i iv         v- ivi  vi    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (112 / 61)
Gap_init rate = 0.02 (19 / 772), avg. gap size = 4.47 (85 / 19)  

 565 23.49 3.01 0.00  chr1_85324561_85326258.rev     1528  1693 (5)    L1M4_orf2#LINE/L1      738   908 (0)  

  chr1_85324561_8   1528 ATCTGACAAAGGTCTAATATCCAGAATCCACAAGGAATTTAAACAATTTT 1577
                               i  i  v  vi          vi i  i   i ivv    i iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_85324561_8   1578 ACAAGAAAAA---AAACAACCCCATCGAAAAGTGGGCAAAGGATATGAAC 1624
                          i  v     ---   i     v  i?    i            v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_85324561_8   1625 AGACACTCCTCAAAAGAAGACATCTATGCAGCCAACAA--ACATGAAAAA 1672
                              i i   v        i  vi viii     i  --         i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_85324561_8   1673 AAGCTCATCATCATCACTGGT 1693
                          v     v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (24 / 14)
Gap_init rate = 0.01 (2 / 171), avg. gap size = 2.50 (5 / 2)  


3839 12.38 3.43 16.95  chr1_85487396_85490059.rev     1124  2173 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_85487396_8   1124 TGGAAAAACTGCTTATGTTCATGTATTAGAAGACTTAATATTGTTAGGAT 1173
                               i ivv ii         v   i                  i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_85487396_8   1174 GACAACACTCCTCAAGTTGATAAACCGATTAAATGCAAGCCCAATTAGAA 1223
                          i   i     i   i     vv  v    v  i    v   v  i i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_85487396_8   1224 TCCCAGCTGGCTGCTTTGTAGAAACTGACAGGCTGATTCTAAATTTCACA 1273
                                  v  vi    i     i     i      i     v    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_85487396_8   1274 TGGAATTACAAGGGGCCTCAAATAGCCAAAACAATATTGAAAA-GAAGAA 1322
                              v i      i  ivi               v       -      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_85487396_8   1323 TAAGCTTGGGGGACTCGCACT-CCCAATTTCAAAACTT--TA-AAAGCAA 1368
                         i  iv    i      i    -                --  -     v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_85487396_8   1369 CAGTAATCAAGACCATGCAGTACTGGCGTAAAGATAAACATATAGATGAA 1418
                                      vi  ii        i   i    i          v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_85487396_8   1419 TGGAATAGAATTGAAAGTCCAGAAATAAGTCCATGTCTCTATGGTCAACT 1468
                                       i             ii    iiv i         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_85487396_8   1469 GATTTTCAACAAGGGTACCACGACTATTCAGAGGGGAAAGGACAGTCTTC 1518
                                i        i   v   i     iv        i i      i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_85487396_8   1519 TCAAC---TGCTGCTGGGACAACTGGATACCCACATATCCAGCAAAAGAA 1565
                              ---  v                  ?      -----         
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-----GCAAAAGAA 445

  chr1_85487396_8   1566 TGAATGAAGTTGGATCCTTTCTTCACACCATATACAAAAAGTAACTCAAA 1615
                             ----      i  i v i                  v         
  L1M4_orf2#LINE/    446 TGAA----GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_85487396_8   1616 ATGAATCAAAGACCTAAATATAAGAGCTAAAA-TATAAAACTC--AGAAG 1662
                            i    ?          i            -          --     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_85487396_8   1663 AAAACTTAGTGATAAATTTTCATAACCTCAG-------AATTGCCACTTA 1705
                              v   v?i     i   i i    ii -------   v iiv    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_85487396_8   1706 CATATGACACCAAAAGCACAAGCAACAAAAGAAAAACTA----AATTGAA 1751
                         v                                   v  ----     i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_85487396_8   1752 CAACATCAAAATTTAAAACTT--GTGCTTCAAAAGACACTGTCAAGAAAA 1799
                          vv          v       --          i      i        i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_85487396_8   1800 GGAAAGACAGGCACGGTAGTGCACACCTATAGTCTCAGCTTCTCGGGAGG 1849
                         --------------------------------------------------
  L1M4_orf2#LINE/    692 -------------------------------------------------- 691

  chr1_85487396_8   1850 GTGAGGCAGGAGGATCCCTTGAGCCCAGGAGTTCGAGGCTGCAGTAAGCT 1899
                         --------------------------------------------------
  L1M4_orf2#LINE/    692 -------------------------------------------------- 691

  chr1_85487396_8   1900 ATGATCTCACCATTGCACTCCAGCCTGGGTGACAAAGTGAGATCCCATCT 1949
                         --------------------------------------------------
  L1M4_orf2#LINE/    692 -------------------------------------------------- 691

  chr1_85487396_8   1950 CTTAAAAAACAAACAACTGAAAAGATAACCCACTGAACCAGAGAAAACAT 1999
                         -----------------        i       v   ivi       i  
  L1M4_orf2#LINE/    692 -----------------TGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_85487396_8   2000 TTGCAAATTATATATCTGATAAGGGACTTCTATCTAAAATACATAATGAA 2049
                                 i                    v    i i    i    v   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_85487396_8   2050 CTCTTACAGCTTGATAATAGAAAAGACAG---------TTTGAAAACAGG 2090
                                 i  ii      -        i---------  ?i    ii  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATA-AAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_85487396_8   2091 CAAAGGATCAGA---GACATTTTTCCAAAGAAGATATACAAATGGCCAAC 2137
                                 iv  ---       i                          i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_85487396_8   2138 AGCCACATGAGAAAGATGTTTGACATCATCAGTCAT 2173
                          iv       -       i ii      ????????
  L1M4_orf2#LINE/    874 AAGCACATGA-AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (86 / 40)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 12.59 (214 / 17)  


1361 25.33 2.40 2.13  chr1_85599366_85602543.rev     1422  1796 (1382)    L1M4_orf2#LINE/L1        3   378 (530)  

  chr1_85599366_8   1422 GAAAGAAATCCAGTTCCTTGTTAATGAATTGGAAGACTCAA-ATTGTTAA 1470
                               v    ----- v    v   i           i  -        
  L1M4_orf2#LINE/      3 GAAAGATATCC-----CATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chr1_85599366_8   1471 GATGTTAATTATTCTCTTCTTCACCTATAGATTTGATTTATTCCCAATTA 1520
                             vi   vv i i vvv  v i   i     ii ivi v    v  i 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_85599366_8   1521 AAATTCTAGCAAAAGCTTTCCTGTAGATAATGGCAAACTGATTCTAAAGC 1570
                             i i   viv--    ii  i   v v  i   i     i     ii
  L1M4_orf2#LINE/     98 AAATCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_85599366_8   1571 ATATATGGAAAGGTGAGAAACCTAGAATAGCTAACATAATACTGAA---G 1617
                         vi         v ii  ii   i        i  v i   vi    --- 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_85599366_8   1618 AAGAATGAG--TGGAAGACTCACACTACCTGATCTCCAGATTTCCTATAA 1665
                              ii i--    i          v  ii  i  v i i  v   i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_85599366_8   1666 AGTCACGGTAATCAGTACAGTGTA-TATTGGTGATAAA-ATAGGCACATA 1713
                           ii  i       iv       i-  i   i-    i-    i  i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGACATATA 294

  chr1_85599366_8   1714 GATCAATGAAACAGAATAGAGAGCCCAGAAATAGACCCACACAAGTATAG 1763
                                 i  i     v     i         i     i   vv   i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_85599366_8   1764 GCAATTTATCTTTGACAAGGAT-TAAAAGCCATT 1796
                         v     v  i  i       i -iv  ii     
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

Transitions / transversions = 2.06 (64 / 31)
Gap_init rate = 0.02 (9 / 376), avg. gap size = 1.89 (17 / 9)  

1823 24.42 3.27 0.19  chr1_85599366_85602543.rev     2170  2689 (489)    L1M4_orf2#LINE/L1      373   908 (0)  

  chr1_85599366_8   2170 ACCACTCAGTGGCAAAAGGAT---CTTTTCAACAATTGTTGCTGGAACAA 2216
                             i   i   vi    i  ---           v  v      i    
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_85599366_8   2217 TAGGATGTCCATAAG-AAAAAAGTGAATCTAGGCACAGACCTTATACCTT 2265
                         iv    i?   i v -    i i    vi i i v vv    i i   v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_85599366_8   2266 TCATAAGTATTAATGCAAAATGGATCATACACCAAAACGTAAAATGC-AA 2314
                         vi i  iv     iv            ? v   v   i    i -  -  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAA 521

  chr1_85599366_8   2315 AACTA-AAATTTCTT-GAAGAAAACA--GGATAAAATATAGGTGGCCTTG 2360
                              -   vi    -          --  ?vv    v vv   i     
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_85599366_8   2361 GGTTTGGCAATAAATTTTTATATACAACACCAAAAGTATGATTTATGACA 2410
                             v      iiv  i   v   ii          i ii viv ii v 
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_85599366_8   2411 GAAAAATTTTATAATCTACACTTTATTAAAATTAAAAACTTCTGCTCTAT 2460
                               v vv    vi iv    i  i              i  iv  vi
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_85599366_8   2461 GAAAGAAACTGTTAAATTAAT-AAAAGACAAGCCACAGGATGGGAGAAAA 2509
                         i  i  v   i i  ivv i -         v      i           
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_85599366_8   2510 TACTTGCAAAACACATATCTGATAGAGGAGTTGTATCCAAAATATACGAA 2559
                           i       v  i          ii   v         i      ii  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_85599366_8   2560 GAACTCTTAAAACACAGCAATAAGAAAACAGG----CTAATTAAAAAGTA 2605
                                  v   v  ii     i  i   ii---- i    ?    i i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_85599366_8   2606 GGAAAAAGGCCTGAACAGACTCTTCACCAAAGAAGATATGCAGATGG--A 2653
                           v   i iii    i    vi   v             i  i    -- 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_85599366_8   2654 A-AAAAATTTGAAAAGATGCTTAACATAATTTGTTGT 2689
                          -  iv iv            i     v ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (75 / 48)
Gap_init rate = 0.02 (11 / 536), avg. gap size = 1.64 (18 / 11)  


3178 26.19 1.33 0.99  chr1_85619984_85622706.rev     1328  2232 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_85619984_8   1328 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 1377
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_85619984_8   1378 GACTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1427
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_85619984_8   1428 TACCAA-TGACTTTCTT-CAGAGAATTGGAAAAAACT-ACTTTAAAGTTC 1474
                          v   i-  v    i  -    -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_85619984_8   1475 ATATGGAACCAACAAAGAGCCCCCATT-GCCAAGACAATCCTAAGCCAAA 1523
                                 vii-   i ii   vv v -     i      i i ivv i 
  L1M4_orf2#LINE/    148 ATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_85619984_8   1524 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 1573
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_85619984_8   1574 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 1623
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_85619984_8   1624 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAA 1671
                         i        i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_85619984_8   1672 CCATCTGATCTTTGACAAACCTAACAAA--CATAAGAAATGGGGAAAGGG 1719
                         i  vi    i  i     ivv iv   i--   --vv           ii
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAA 392

  chr1_85619984_8   1720 TTACCTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAA 1769
                          vii  v  i  i              v     iv  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_85619984_8   1770 AGCTGAAACTGGATCCCTTCCTTACACCTCATACAAAAATTAATTCAAGA 1819
                         iiv    ii    i    v   i     vi             i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_85619984_8   1820 TGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAGAA 1869
                              i ?    i       v   v       i      v  i    ii 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_85619984_8   1870 AAACCCAGACA-ATACCATTCAGGACATAGGCATAGGCAAGGACTTCATG 1918
                             vi  i?i- v i -   iv   v v  vv       v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_85619984_8   1919 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 1968
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_85619984_8   1969 TCTAATTAAACTAAAGAGCTTCTGCATGACAAAAGAAACTACCATCACAG 2018
                         ii v  i   v v  i i   i  iiivv    i  v    i  vv v  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_85619984_8   2019 TGAACAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCT 2068
                             v  i  i  i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_85619984_8   2069 GACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAA 2118
                           i  i  i  vi          v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_85619984_8   2119 GAAAAAAAT---CAACCCCATCAAAAAGTGGGCAAAGGATATGAGCAGAT 2165
                         v     i i---i     v  i?    i            v   ii   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_85619984_8   2166 TCTTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGC 2215
                         vi     v        i  vi viii     i ii  i       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_85619984_8   2216 TCATCATCACTGGCCAT 2232
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (146 / 87)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


3281 26.95 0.33 0.44  chr1_85685555_85691968     5013  5921 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_85685555_8   5013 TGGAAGAGTATTCCATGATCATGGATAGGAAGAATCAATATTGTGAAAAT 5062
                              iii   i     v        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_85685555_8   5063 GGCCATACAGCCTAAGGTAATTTACAGATTCAATGCCATCCCCATCGAGC 5112
                            v    vv  i  iv i  i           i  v     i   i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_85685555_8   5113 TACCAATGACTTTCTTCACAGAATTGGAAAAATCTAATT-TAAAGTTCAT 5161
                          v   iivi i  i  ii     v v  v  i-  i  i-    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_85685555_8   5162 ATGGAACCAACAAAGAGCCTGCACT-GCCAAGACAATCCTAAGCAGAAAG 5210
                               vii-   i ii  iiv v -     i      i i iv ii   
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_85685555_8   5211 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5260
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_85685555_8   5261 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATATAGACC 5310
                                 i   i    ii  i      i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_85685555_8   5311 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACGTCTACAACCAT 5360
                                i    iv   ivii         vv   i  i i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_85685555_8   5361 CTGATATTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCCCT 5410
                         i    v  i     ivv  v   i vv vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_85685555_8   5411 ATTTAATAAATGGTGCTGGGGAAACTGGCTAGCCATATGTAGAAAACTGA 5460
                         v  i  i             iv      v  ?   i   i i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_85685555_8   5461 AACTGGATCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGGATT 5510
                          ii    i    v   i i   v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_85685555_8   5511 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5560
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_85685555_8   5561 AGGCA-ATACCATTCAGGACACAGGCATGGGCAAAGACTTCATGACTAAA 5609
                            ?i- v i -   iv   viv  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_85685555_8   5610 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5659
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_85685555_8   5660 TAAACTAAAGAGCTTCTGCACGACAAAAGAAACTACCGTCAGAGTGAACA 5709
                         i   v v  i i   i  ii vv    i  v    i ivv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_85685555_8   5710 GGCAACCTACAGAGTGGGAGAAAAAGTTTGCAATCTAGTCATCTGACAAA 5759
                          i     i     i          vi       vii vvi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_85685555_8   5760 GGGCTAATATCCAGAATCTGTGATGAACTCAAACAAATTTACAAGAAAAA 5809
                           i  vi          v i i v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_85685555_8   5810 AAACAAACAACCCTATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5859
                         i -    i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_85685555_8   5860 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5909
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_85685555_8   5910 ATCACTGGTCAT 5921
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.00 (7 / 7)  


3158 27.64 0.44 0.44  chr1_85819071_85825476     5006  5913 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_85819071_8   5006 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAATATCGTGAAAAT 5055
                              ii i  i     i    i i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_85819071_8   5056 GGCCATAATGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5105
                            v   v v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_85819071_8   5106 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTAAAGTTCA 5153
                          v   iivi i  i  ii     -   -- v  i  - i i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_85819071_8   5154 TATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 5203
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_85819071_8   5204 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5253
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_85819071_8   5254 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5303
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_85819071_8   5304 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5351
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_85819071_8   5352 ATCCGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5401
                          vii   i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_85819071_8   5402 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5451
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_85819071_8   5452 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAGGCA 5501
                            ii    i    v   i     v              i    i v v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_85819071_8   5502 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGATGAAAAC 5551
                          i ?    i    i  v   v       i      vi i    v      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_85819071_8   5552 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5601
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_85819071_8   5602 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5651
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_85819071_8   5652 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5701
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_85819071_8   5702 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5751
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_85819071_8   5752 AGGGCTAATATCCAGAATCTACAGTGAACTCAAACAAATTTACAAGAAAA 5801
                         i  i  vi          v  i iv      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_85819071_8   5802 AAACAAACAACCCCATCAAAAAGTGGACGAAGGACACGAACAGATACTTC 5851
                          i     i     v  i?    i   i i     ivi   i   i i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_85819071_8   5852 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGACAAAATGCTCATC 5901
                           v        i  vi viii     v  i       v  i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_85819071_8   5902 ATCACTGGTCAT 5913
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (147 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1386 27.40 7.20 2.82  chr1_85880556_85882240      485  1192 (493)    L1M4_orf2#LINE/L1      170   908 (0)  

  chr1_85880556_8    485 GAATAGCCA---TACTCTAGAAAAA--------AAGTGGGAGGACTTAAT 523
                                  ---i v   v      --------    v        i --
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA-- 217

  chr1_85880556_8    524 CAGATAACAAGTTTCAG-------TAAAAAACCACAATAATTCAGAGAGC 566
                           vv vv   -     i-------  v   i i   i    iv   v  i
  L1M4_orf2#LINE/    218 CACTTCCCAA-TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr1_85880556_8    567 ATAGTATTGGTGCA-GGATATACCAGTAGGCCAACAGAATGGAAAAGACA 615
                         i i   i   iii -     v  vvi   ii   ii    i   vv  -i
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA-G 315

  chr1_85880556_8    616 AGGCCACAAAATGACCCAAGCATATAGGG---ATGCTGATATATGACAAA 662
                           v   v   vvi     vi   v  v  ---  --    v vi     i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAAT--TGATTTTCGACAAG 363

  chr1_85880556_8    663 GGTGGTCCTACAGAGCA----ATAGGGAAAGGATGAACTTTCCAATAAAT 708
                             --- i -   v  ----  i       i  iiv    i   i    
  L1M4_orf2#LINE/    364 GGTG---CCA-AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_85880556_8    709 GGTGCTGGGAAAAGTGGATTATCTATATG---AAAAATTAAATGGGAACT 755
                                   v  v     - ? i i   ---  i   v  i v   - i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGAT-AKCCACATGCAAAAGAATGAAGTTGGA-CC 457

  chr1_85880556_8    756 CCT-CTGTATATGATAC-CAAAAATCAATTCCAG-----TTAAAGACATA 798
                            - ivi i iv   i-       i  i  v i----- i ?    v  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_85880556_8    799 AGTGTAAAACACAACAGTATAAAGCTTTTAGGCAATAACTATAAAAGAAT 848
                          i     i vvi  v v      i  i    ivi v   -   ii? v v
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC-ATAGGNGTAA 556

  chr1_85880556_8    849 AACTTCCTAACTTCAAGGTAGA-GATGGATTTCTT---TATAAACATATA 894
                          v    v i  i iii v   i-i    -      ---   i -  i-i 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGA-CAC-CA 603

  chr1_85880556_8    895 AACCTACTAACTATAAAGGAAACAAAT-GATAAATTTGACTACATTAAAA 943
                           vvi  v i v i   i    -    -        v    v   i    
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAAA 652

  chr1_85880556_8    944 CTAAGAACATCCATTCACCACAAGACACTAT----AAAATGAAAAGACAA 989
                         i   i   v iii v vi  v i        ----   i           
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_85880556_8    990 GACAAAGACTAGAAGAAGGTATTTATAA--CATACAACCAACTT---GCA 1034
                         vv  v   v i i    ii     ii  --    i v ii -- --- v 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA--TAAGGGA 750

  chr1_85880556_8   1035 CTAGCATCCAAGAAATACCAAGAATTCTCACAAACCAGTAAGAAAAATAA 1084
                           v i     ii v   iv     i   i    vi  i   v     v v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_85880556_8   1085 AGCTGACC-AATGAAAAGATGAGCAAAAGACTTGAACAGGCACTGCATAA 1133
                          iv i   -   v?   i   i     i  i     i  i  i v viv 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_85880556_8   1134 AAGAGGAAATCCAAATGGCCAATAAAGTATTTGAAAGGTGGTTCAATCTC 1183
                             i  v  v              - i iv     i vv i    iv  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAA-GCACATGAAAAGATGCTCAACATC 899

  chr1_85880556_8   1184 ATCAGGAAT 1192
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.41 (111 / 79)
Gap_init rate = 0.04 (32 / 739), avg. gap size = 2.22 (71 / 32)  


3281 26.98 0.44 0.44  chr1_85925724_85932002     4879  5786 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_85925724_8   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_85925724_8   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_85925724_8   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_85925724_8   5027 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_85925724_8   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_85925724_8   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_85925724_8   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCTTACCTACAACT 5224
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_85925724_8   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_85925724_8   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_85925724_8   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_85925724_8   5375 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_85925724_8   5425 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_85925724_8   5475 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5524
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_85925724_8   5525 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5574
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_85925724_8   5575 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5624
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_85925724_8   5625 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_85925724_8   5675 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_85925724_8   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5774
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_85925724_8   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2941 17.70 1.65 6.45  chr1_85932613_85934675      500  1228 (835)    L1M4_orf2#LINE/L1      164   857 (51)  

  chr1_85932613_8    500 GACCCCAAGTAGCCAAAATAATTTTGAAAAA--AGAA-GTTGTTAGAGGC 546
                              vi i         i   i        --    -ivv   i    v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_85932613_8    547 ATCATGTTTCCTGATTTCAAAACTTACTATAAAGCTGCTGTAATCAAAAC 596
                         v   iii    ii                i      i v        i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_85932613_8    597 AGT-TGGTACTGTCATAAAGACAGACATAAAGA---ATGAAATATAATAG 642
                            -        v     i  i       v   ---   i    v   v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_85932613_8    643 AGAGTCCAGAAATAAACCTTCTCATTTATGATCAAATTATTTTCAACAAG 692
                                           iviv        i    v v      i     
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_85932613_8    693 AGTGCTAAGACCATTCAATGAAGAAAGGATGGTCTTTTCAACAAACAGTG 742
                         i    i              ii     i  i              ii   
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_85932613_8    743 CTGGAAAAATGGAATATCCACATGGGATAGAATGAAGTTAGACCCTTAAC 792
                             i v  iv i   ?       vi v           i     i  v 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_85932613_8    793 TTACATCAAGTACAAAAAAACTTACATCATGAGTTATACCATGAACTCAA 842
                          i   i  vi        ---------------   --------      
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAA---------------TTA--------ACTCAA 490

  chr1_85932613_8    843 AATGAATCAAAGACTTGAACATAAGAGGTAAAACTATAAAATTATTAGAA 892
                             i    ?    i i  ii      v             i v      
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_85932613_8    893 GCAAA--TAGGA--AAAGCTTGATAACATTTGATTTTGCAATGATTTCTT 938
                          v   --    ?--   v   vi i  v  v i  vv      i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_85932613_8    939 GGA-ATGATACCAAGAGCACAGTCAACAAGAGAACAAAGTAGATAAATTA 987
                         i  -    i     i      iv      i    -   i          i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAA-AAAATAGATAAATTG 639

  chr1_85932613_8    988 GACTATATCAGAAAAAAAAAAAAACTTCTGTGCATCAAGGGACACTATAA 1037
                             vi    ----   vv        i     v    i         v 
  L1M4_orf2#LINE/    640 GACTTCATCA----AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_85932613_8   1038 AGAGAGTGAAAAGGCAACCCAACGGATGGAAAAAAATAACTGCAAATTGT 1087
                            i         i       vv i    i i      vi       ii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_85932613_8   1088 CTTTCTGGTAAAGGATTAATATCTAGAATATTTAAAGAGCTTCTACAACT 1137
                         v v    i   i   i vi    i       v      i  ii       
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_85932613_8   1138 TACTAACAACCAAAAAAAAAAAAAAAAAAAAAAAGGCAACCCAATTCAAA 1187
                         ----------   v  v     i v   --------i         -?  
  L1M4_orf2#LINE/    786 ----------CAATAATAAAAAGACAAA--------TAACCCAATT-WAA 816

  chr1_85932613_8   1188 AAATGGGCAAATAACTTGAATAGACATTTCTCTAAAGAAGA 1228
                                    vi i                 i        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

Transitions / transversions = 1.72 (79 / 46)
Gap_init rate = 0.02 (14 / 694), avg. gap size = 4.21 (59 / 14)  

 250 13.56 0.00 0.00  chr1_85932613_85934675     1512  1570 (493)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_85932613_8   1512 AAAAAAAAAATACAAATGTCTAATAAACACATGAAAATATGCTCAACACC 1561
                            i  i v         v i     i          v          i 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_85932613_8   1562 ACAAATCGT 1570
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


3288 26.76 0.44 0.44  chr1_86002879_86009148.rev     4872  5779 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86002879_8   4872 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4921
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86002879_8   4922 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4971
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86002879_8   4972 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5019
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_86002879_8   5020 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5069
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_86002879_8   5070 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5119
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_86002879_8   5120 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATC 5169
                                 i   i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_86002879_8   5170 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5217
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_86002879_8   5218 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5267
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_86002879_8   5268 CTATTTCATAAATGGTGCTAGGAAAACTGGCTAGCCATATATAGAAAGCT 5317
                           v  iv i          i   v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_86002879_8   5318 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5367
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_86002879_8   5368 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5417
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_86002879_8   5418 CTAGGCATTACCGTTCAGGACATAGGCATGGGCAAGGACTTCACGTCTAA 5467
                         v    ?i v viv   iv   v v  vv i     v ii   viivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_86002879_8   5468 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5517
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_86002879_8   5518 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5567
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_86002879_8   5568 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5617
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_86002879_8   5618 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5667
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_86002879_8   5668 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5717
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_86002879_8   5718 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5767
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_86002879_8   5768 ATCACTGGCCAT 5779
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 459 29.28 9.63 6.95  chr1_86023192_86024842      417  1164 (487)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_86023192_8    417 AAAGTTCACATGAAAG---AGGAAATCATAGCAAGAGTCAAA-CTTTTTT 462
                            i    i   i  i--- i ii i -i  -  v  i    - vv i  
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACC-CAG-AATAGCCAAAACAATCTT 188

  chr1_86023192_8    463 GTAAAAT--GAATTA---TGAAGTATTTGC----CCTAA---CAGAAGGT 500
                          v    v--   iv ---  i  v i ii ----  i  ---  i  vv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_86023192_8    501 ATCACAATAGTATAGTAAGTAAAATAGTGTGGTATTGACCCAGAAATAGA 550
                          ii    viv  i     vi  i i         i  i vi iii     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_86023192_8    551 C-TACTAGATTCAGAGAATAAAGTAGA-AG---AAAAACAGACTAATGAA 595
                          -  -     iv vi     i i v  -  --- i   i i  iv  -- 
  L1M4_orf2#LINE/    289 CATA-TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT--A 335

  chr1_86023192_8    596 TATTTGAG---AATTCAGTTTATGGTAAGGG----AAG--CATTTCAGAA 636
                         i    iv ---    v v   -i ii     ----   --    -  - v
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTT-CGACAAGGGTGCCAAGACCATT-CA-AT 382

  chr1_86023192_8    637 AAGCAGAAAACAGACTGACCACTCAATAAATAGAATTGGAACAACTG--- 683
                         ii v i i  i  v  v----i    i    i vii   i       ---
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTT----TTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_86023192_8    684 -TCTATAAGTTTGGAAAAAATAAACTTAGTCTTCTAC---ACCTTATATA 729
                         -? i i v i---i   i   i  v  i v ii    ---  vii     
  L1M4_orf2#LINE/    429 AKCCACATGC---AAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_86023192_8    730 AAAAAAT--ACCCACAAAAAAACCAAAAACCTCCATACATCTTAAAGAGT 777
                         v      --  i  -   vii i  ? i    ---- v  v --     i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCA-AAATGGATCAWAGACCT----AAATGT--AAGAGC 518

  chr1_86023192_8    778 TAAGGTAAAAATAAAGTTATAAAAGTATTAGAAGAA--TATGGAAGAATA 825
                            ----------- ii       v v         --i  i i? v v 
  L1M4_orf2#LINE/    519 TAA-----------AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_86023192_8    826 TTCTTATATACTTTAGGT-AGGGGAGGCATTTCT--AATAAAATA---AA 869
                          ii ii i-  i  i   -   vi v -i     --i   vi i ---  
  L1M4_orf2#LINE/    558 TCTTCGTG-ACCTTGGGTTAGGCAATG-GTTTCTTAGATATGACACCAAA 605

  chr1_86023192_8    870 CACAGAAACTGAAAGGGAAAAGACTGACAAGTTTGACTATATAAAAATTA 919
                         vi  v  i viv  ii     i iv  i  i  v    vi  v       
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_86023192_8    920 AAATGATCTATACAGCAAAAGATAT-----ACAAAATTAAAAGATAAATT 964
                            vvv i i i vv    i  i i----- v   i v      i  vii
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_86023192_8    965 GCAGAA----AGAAAAGCATTTGTAATATATTTTGTAACATATTTAACAA 1010
                         i     ----      -i     i  ---  i----- i    i i i  
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAA-TATTTGCAA---ATC-----ATATATCTGATAA 746

  chr1_86023192_8   1011 AAATATATTAATATTTTAAGCATATAAGGAGTGATTGCAAATCAATAAGA 1060
                         iii--- i vi   iivi ii      i  iivv  i   v       v 
  L1M4_orf2#LINE/    747 GGG---ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_86023192_8   1061 AAAAGGCAA------CAATCTAA---TGTGCAGTATATATGAACAGGCAA 1101
                              i   ------    i?  ---  v   iviv  v    i  i  v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_86023192_8   1102 CT-TCCATAAGAAAAAAGTGCAATTGGGAAAGTGTAAATA---GAAAAAA 1147
                         i -    -     i v - i   v   vv  ---   ii ---     i 
  L1M4_orf2#LINE/    844 TTCTCCA-AAGAAGATA-TACAAATGGCCAA---TAAGCACATGAAAAGA 888

  chr1_86023192_8   1148 TGC--AATA-CACATTCTCA 1164
                            --  i -  ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (144 / 71)
Gap_init rate = 0.06 (49 / 768), avg. gap size = 2.53 (124 / 49)  


 924 25.94 6.57 11.52  chr1_86028907_86031018.rev      693  1621 (491)    L1M4_orf2#LINE/L1        1   883 (25)  

  chr1_86028907_8    693 TGGACAGTTATTTTATATTCATG-ATAGGAAAACTCAATATTATAAAATT 741
                             v  v   iii  i      -  v    i   i      i v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86028907_8    742 ATCAATCTTCTCCTATATTAATGAATACACTTAATACAATTTCAACCAAA 791
                         iv    vi  i  v -   i  vv i v i i  ii    ii v i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA-ATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_86028907_8    792 ATCCCAATGGGATTTTTAATAAAACTTGATTGATAAAAAGTGATTTAAAA 841
                               iiv vv     vii i  ----     i  iv--    iiv   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAA----ATTGACAAGC--TGATCCTAAA 143

  chr1_86028907_8    842 ATTTGTGTGGAAAACCAAAGGGCC---AATA-TTAAGACAACTTTAAAGA 887
                            ii i      vv   i  i  ---    -ii  i    ii  i  i 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_86028907_8    888 ATAAGTTGTGCAGAGGTGGGATGGTTGTGGAGGAGGTGGAAGAGAGAATC 937
                          v   v---i  i  ---------   --     --------------- 
  L1M4_orf2#LINE/    194 AGAAGA---ACAAAG---------TTG--GAGGA---------------C 214

  chr1_86028907_8    938 TGAC-CTATCTGATAT---AACTTATTATTGAAGCTAGAGTAATTAAGTT 983
                          v  -  vi ii  v ---      i  i-i      v      i   vi
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTAC-AAAGCTACAGTAATCAAGAC 263

  chr1_86028907_8    984 AGTTAGTGCCATACT--CATTCACAAATAAACAAACAGACCAATGGAAAT 1031
                            --   --i    --   -- vii   i   v i   i        - 
  L1M4_orf2#LINE/    264 AGT--GTG--GTACTGGCAT--AAGGATAGACATATAGATCAATGGAA-T 306

  chr1_86028907_8   1032 TGAA--GATAATGTAGAATCAGATATAAGTATATTT-TGA--AACTTGAT 1076
                         v   --  v i vi    vi i ivi --  i    -  i--  -     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAA-TTGAT 353

  chr1_86028907_8   1077 TTTTGATAAATTGATTATGCACTACAGATCTATAAGGAAATGAACAATTT 1126
                            i  i  --- iv ii-  vv  viv  v  ii     -   i i i 
  L1M4_orf2#LINE/    354 TTTCGACAA---GGGTGC-CAAGACCATTCAATGGGGAAA-GAATAGTCT 398

  chr1_86028907_8   1127 ----AATAAATGATACCAGTACAATTGGTTATCCAAATG-AAAAAAA--A 1169
                         ----  i     i i ii v    i   v  ?   v   -    i  -- 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_86028907_8   1170 AAT---ACTC-TCCCTCACACAAATGCGCACGTGCGCGCACACACACAAA 1215
                          i ---  i - v        -------------------  i i     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACAC-------------------CATATACAAA 479

  chr1_86028907_8   1216 CACACACCCCGCAAAATTACATTCCAA-TTGATTAAAGGCTTAACTGTTA 1264
                         --------------     - i  v  - v   i ?  i i   v   v 
  L1M4_orf2#LINE/    480 --------------AATTA-ACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_86028907_8   1265 AAATCAAAATCTTAAAACTCTTGGGAGAACATTTAAGA-TAATATTTTAT 1313
                         i iii    iiv          i i    v iv  i ?-   vvi  ii 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_86028907_8   1314 GACCTTATAAGGAAAGGGGAAGCAGTAAAGATTTCTTAAA----ACA--- 1356
                               ---------   vv  -- i  v i       i ----   ---
  L1M4_orf2#LINE/    565 GACCTT---------GGGTTAG--GCAATGGTTTCTTAGATATGACACCA 603

  chr1_86028907_8   1357 -AAGCACTAAAAGAAACAGAAAGAAAATATTAATGACTTTGACTGCATTA 1405
                         -      ---   v    -        v  vi  i v  v    v   i 
  L1M4_orf2#LINE/    604 AAAGCAC---AAGCAACA-AAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_86028907_8   1406 AAATTGCAAACTT--GTGTTAGTCCAAAGTCGTAATAAACAAGGTGAGAA 1453
                              iv      --   i --  v  i v iiv  v  v  i    i  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCT--TCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_86028907_8   1454 AATAAGATACAAGCTGGGAGAAGAGATTTG----TGATATATGGAATGAA 1499
                         i i  vvi   iiv        i v     ---- v      vvi  i i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_86028907_8   1500 CAAAATATA---AGTATGTATAAAAACATATACATGTAACTAAATAA--- 1543
                         vi vv i  ---  v  i      i --- iv v ii    v     ---
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGA---ACTCTTACAACTCAATAATAA 794

  chr1_86028907_8   1544 ---GACAG----CCCAGTAGAATAACGGGCACAAGATAGGAACCAGAAAT 1586
                         ---    i----    i v?  v  i     v i   vv   i-   v  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT-AGACAT 843

  chr1_86028907_8   1587 T----CACATA-GAGATATAGATGTCCGATAACTTTATGA 1621
                          ----  v v -  v   i i   v  i    vivi    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.06 (52 / 883), avg. gap size = 3.23 (168 / 52)  


2934 27.87 1.78 0.56  chr1_86046522_86051300     3390  4286 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86046522_8   3390 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTCAAAAT 3439
                              ii i  i     i        v      v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86046522_8   3440 GGCCATATTGCCCAAGGTAGTTTATAGATTCAATACCATCCCCATCAAGC 3489
                            v   i v     iv ii i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86046522_8   3490 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3537
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_86046522_8   3538 TATGGAAACAAAAAAGAGCCTGCATTACCAAGACAATCCTAAGCCAAAAG 3587
                                 iiv  ii  v  v v  vi    i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_86046522_8   3588 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACCAGAAGGC 3637
                                i      vv       v  ii i      viv   i v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_86046522_8   3638 TACTGTAACCAAAACAG-------CTGGTACCAAAACAGAGATATATACC 3680
                            v    i   i    -------    i iv ii i   v     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_86046522_8   3681 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATCTCTACAACC 3728
                                i    i--    i  --        vv   i iv i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_86046522_8   3729 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATAGGGAAAGGATTCC 3778
                          vi    i  i     ivv  v   i v  vvv   i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_86046522_8   3779 CTATTTAGTAAATGGTGTTAAGAAAACTGGCTAGCCATATGTAGAAAGCT 3828
                           v  i ii        i ii  v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_86046522_8   3829 GAAAACGGATCCCTTTCTTACACCTTATACAAAAATTAATTCAAGATGGA 3878
                            ivi   i    vi  i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_86046522_8   3879 TTAAAGACTTAAATGTTACACTTAAAACCATAAAAACCCTAGAAGAAAAC 3928
                          i ?    i       v v vi      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_86046522_8   3929 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 3978
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_86046522_8   3979 AACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4028
                         i    v       vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_86046522_8   4029 TTAAACTAAAGAGCTTCTGCACAGAAAAAGAAACTACCATCAGAGTGAAC 4078
                          i   v v  i i   i  ii vvv   i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_86046522_8   4079 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTTTCAA 4128
                           i     i                 v       vii ivi    vvi  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_86046522_8   4129 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAACTTA-CAAGAAA 4177
                         i  i  vi          v  i         vv    -  i -i  v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAA 795

  chr1_86046522_8   4178 AAAACAAG---CCCA-TCAACAAGTGGGTGAAGGATATGAACAGACACTT 4223
                           i    i---    - i? v  i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_86046522_8   4224 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 4273
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_86046522_8   4274 CATCACTGGCCAT 4286
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


1228 22.10 5.07 0.00  chr1_86056039_86061285.rev     3414  3689 (1558)    L1M4_orf2#LINE/L1        1   290 (618)  

  chr1_86056039_8   3414 TGGAAGGATATTTCATGGTTATGGGTAGAAAGACTCAATATTGTTGAGAT 3463
                              i     ii    v i    i v i      i         i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86056039_8   3464 ATTAGTTCTTCACAAATGGATCTATCAAGTCAATTCAATTCTAATCAAAA 3513
                         ivi i v  i v     v      ivi v    iv    i iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86056039_8   3514 TCCAAGCAAGTTACATTGTAGATATTAACA----GATTCTGAAGTTCCTA 3559
                            v   vivi viv   i   v   i   ----   i  i  i   v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_86056039_8   3560 TGGAAAGGCAAAAGACCCAGAATAGCCAATACAATATTGAA------GAA 3603
                               v    ii                v     v     ------   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_86056039_8   3604 CAAACTTGGAGAACTGACACT----GACTTCAAGATTTACTGTAAAACTA 3649
                             v      i   v     ----i i     i i     ii   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_86056039_8   3650 CAGTAATCAAGACAGTGTGATATTGGCAAAAGAATAGACA 3689
                                            i  i     v   i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

Transitions / transversions = 1.65 (38 / 23)
Gap_init rate = 0.01 (3 / 290), avg. gap size = 4.67 (14 / 3)  

1898 19.23 3.70 10.50  chr1_86056039_86061285.rev     4081  4756 (491)    L1M4_orf2#LINE/L1      279   908 (0)  

  chr1_86056039_8   4081 TAAGTGTCGAC-TGTAGATCATTGGAACAGAGTGGTAAGCCCAGAAATAG 4129
                             vi v   - i       v     i   i v vi  i         -
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA- 327

  chr1_86056039_8   4130 AACAGTTATACTCTTTGTTCTACACAATATACACAACATATAGTCACAAA 4179
                            ---------------- i i   v ----------   i    ----
  L1M4_orf2#LINE/    328 AAC----------------CCATACATT----------TATGGTCA---- 347

  chr1_86056039_8   4180 TAAAATCAAGTGATCTGTGACAAAGGAGCAAAGGCAATACAATGG----- 4224
                         ----  ----    i vi     i  v  v   i v  v      -----
  L1M4_orf2#LINE/    348 ----AT----TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_86056039_8   4225 --ATAGTCTTTTCAACAAATTATGCTGGAACAAATAGATATCCACATGCA 4272
                         --                  vi      i    v i    ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_86056039_8   4273 AAACGTGAATCTAGATGCAGATCTTACACCTTACACACACACACACACAC 4322
                            ---    vv  v  --  i ii-i    i    -----------  i
  L1M4_orf2#LINE/    440 AAA---GAATGAAGTTG--GACCCC-TACCTCACAC-----------CAT 472

  chr1_86056039_8   4323 ACACACACACACACCCTCAAAATGAATCATAGACTTAAATGTAAAAAACA 4372
                          i   v v ivv  --        i    ?    i         i ivi 
  L1M4_orf2#LINE/    473 ATACAAAAATTAAC--TCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_86056039_8   4373 AAGCCATAAAACTCCTAAAATATAAACATAGAGA-AAATCTATGTGACCT 4421
                           i i         i  i  v -        i?i-      vi       
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGA-AAACATAGGNGTAAATCTTCGTGACCT 569

  chr1_86056039_8   4422 GAGGTTTGTTGATGAGTTTTTAGCTATATCACCAAAAGCACAACCCATGA 4471
                         vi    v vii   iv  i    v   iv              v v ii 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_86056039_8   4472 AAGAAAAAACTGGTAAGTTGGACTTCATTAACATCTTTTTAAA----TCT 4517
                                  iv i   i           i  v  -----    ---- i 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAAT-----TAAAAACTTTT 664

  chr1_86056039_8   4518 GC-CTTGAAAAAACACTGTTAAGAGAATGAAGAGACAGTCCACAGACTGG 4566
                          i-   v   ii     i i    i i    i     ii       v   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_86056039_8   4567 GAGAAAATATTTTCAAAACATATATCTGATAAAAGACTTGTATCCAAAAT 4616
                                     v    v              ii            i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_86056039_8   4617 ATAGAAAAAAAAATTAAAACTCAACAATTTTCTTTAAAAA---------- 4656
                            v   i  vvv   v       i   -------     ----------
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAAT-------AAAAAGACAAATAAC 807

  chr1_86056039_8   4657 CCAGTTAAAATGTTGGCAAAA-ATCTGAACAGACACCACACCAAAGAAGA 4705
                            i  ?   vi v      i-  i    i     iiv v          
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_86056039_8   4706 TATAGAAATGGCATAGAAGAATGTAAAAATATGCTCAACATCATATGTCA 4755
                             v       vv v   v ii i    v             ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_86056039_8   4756 T 4756
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.42 (74 / 52)
Gap_init rate = 0.03 (20 / 630), avg. gap size = 4.80 (96 / 20)  


3225 26.84 0.55 0.66  chr1_86098193_86110552     4697  5605 (6755)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86098193_8   4697 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATCAATATCATGGTAAT 4746
                              ii i  i     i       iv      v i     ii vivi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86098193_8   4747 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATGAAGC 4796
                            v     v     iv i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86098193_8   4797 TACCAATGACTTTCTTCACGGAA-TTGGAAAAAACT-ATTGTAAAGTTCA 4844
                          v   iivi i  i  ii i   -   -- v  i  -  iv    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_86098193_8   4845 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4894
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_86098193_8   4895 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4944
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_86098193_8   4945 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGCTATAGATC 4994
                                 i   i    ii        vi iv ii i   vv        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_86098193_8   4995 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5042
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_86098193_8   5043 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5092
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_86098193_8   5093 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5142
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_86098193_8   5143 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5192
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_86098193_8   5193 TTAAAGACCTAAATGTTAGACTTAAAACCATAAAAACCCTAGAAGAAAAC 5242
                          i ?            v   vi      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_86098193_8   5243 CTAAGCATTA-CCATCCAGGCCATAGGCATGGGCAAGGACTTCATGACTA 5291
                         v  i ?i v -i v  vv i  v i  i- i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr1_86098193_8   5292 AAACACCAAAAGCAAAGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 5341
                         vi            v i          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_86098193_8   5342 GTTAAACTAAAGAGCTTCTGCACAGAAAAAGAAACTACCATCAGAGTGAA 5391
                         i i   v v  i i   i  ii vvv   i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_86098193_8   5392 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5441
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_86098193_8   5442 AAGGGCTAATATCCAGAAACTACAAAGAACTTAAACAAATTTACAAGAAA 5491
                          i  i  vi         vv  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_86098193_8   5492 AAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTT 5541
                           i     i     v  i? v  i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_86098193_8   5542 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAAATGCTCA 5591
                            v        i  vi viii     i ii          i -      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCA 894

  chr1_86098193_8   5592 TCATCACTGGCCAT 5605
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  

3250 27.20 0.44 0.44  chr1_86098193_86110552    10960 11867 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86098193_8  10960 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 11009
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86098193_8  11010 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 11059
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86098193_8  11060 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 11107
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_86098193_8  11108 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 11157
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_86098193_8  11158 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACCACAAGGC 11207
                                i      vv       v  ii i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_86098193_8  11208 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 11257
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_86098193_8  11258 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 11305
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_86098193_8  11306 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 11355
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_86098193_8  11356 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 11405
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_86098193_8  11406 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 11455
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_86098193_8  11456 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 11505
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_86098193_8  11506 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 11555
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_86098193_8  11556 AACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAA 11605
                         i            vvi     v    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_86098193_8  11606 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 11655
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_86098193_8  11656 AGGCAACCTACAACATGGGAGAAAATTTTCGCAAGCTACTCATCTGACAA 11705
                           i     i   iv            v  i    iii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_86098193_8  11706 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 11755
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_86098193_8  11756 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 11805
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_86098193_8  11806 TCAAAAGAAGACATTTATGCAACCAAAAAACACGTGAAGAAATGCTCATC 11855
                           v        i  vi viiii    v  i   i    i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_86098193_8  11856 ATCACTGGCCAT 11867
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3014 22.85 5.20 0.85  chr1_86182859_86185095      918  1744 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_86182859_8    918 AAGAAGTAAATTCTTCCCAATGTGATCTATAGATTCAATGCAATACCAAA 967
                             v vv   v  i     vv       i        i     v  v v
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_86182859_8    968 CAAAATCCCA--TAAGTTATTTGTGGATACTGACAAACAGATTCTAAACT 1015
                                   -- ivv  v    ii  v i      i v   i     v 
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_86182859_8   1016 TTATACAGAGAGGCAAAAGACCCAAAACAGCCAACCCAA-CTTGAAAGAG 1064
                          i   ii  i v    ii      i  i      vv   -       i  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_86182859_8   1065 GA---CAGAGTTGGAGGACTGATACTACTGGACCTCAAGACTTACTATAA 1111
                         i ---  i            v i   v ivi ii    i        i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_86182859_8   1112 AGCTACAATATTCGAGACAGTGTGGTAATGAAGAAAAAAACAGATAAGTA 1161
                                i  v  i             v  iv- v  ii i   i vi  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGACATATA 294

  chr1_86182859_8   1162 GATGAGCGGAACAGAATAGAGAACCCAGAAATAGACCCACATAAATACAG 1211
                            v ii    i     v    ii         i     i i vv  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_86182859_8   1212 TCACCTGATCTTTGACAAAGGAGCGAAGGCAGTACAATGGAGCAAAGATA 1261
                            vi    i  i     i  v  v   i vi v      i v  ii   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_86182859_8   1262 GTCTTTTCAACAAACGGTGCTGAAATAACTGGACATCTACATGCAAAAAA 1311
                                       i       ii i       i ? i          i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_86182859_8   1312 GAAATGAATTTAGACACAGACCTTACACC-TGTCACAAAAATTAACTCAA 1360
                         ---     v  i   v vv    i     - i -                
  L1M4_orf2#LINE/    445 ---ATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAA 490

  chr1_86182859_8   1361 AATAGATCACAGACCTAA-TGTAAAATGC-AATATTATAAAA-TCCTAGC 1407
                            i     ?        -     i -  -  v i       -  i   v
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGA 539

  chr1_86182859_8   1408 AGATAATACAGGAGAAAATCTAGATGACCTTGGGT------ATGTTGTTT 1451
                            v  i i   ? v      vvi           ------   v -  i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTC 588

  chr1_86182859_8   1452 TTAGAAACAACACAAAAGACACAATCCATA------------------CT 1483
                              v ii    v   ii     v v i ------------------i 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_86182859_8   1484 GAACTTCATTAAAATTTAAAACTTCTGCCCTGCAGAAAACAATGTCAAGA 1533
                          i       i      v       i  iv  v  i ii   v i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_86182859_8   1534 GAATAAGAAGACAAACCACAGACGGGAAGAAAATATTTGCAAAAGGCACA 1583
                         i i i i       v       vv  i                vvii i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_86182859_8   1584 TCTGATAAAGAACTGTTACCCCAAATATACAAAGAACTCTGAAAACTCAA 1633
                                 i i   vv  i  vi      i          v v       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_86182859_8   1634 CAATTAAAAAA-----AAC---ATTAAAAAAAGGCCAAAGACCTT-AACA 1674
                         i   v    i -----   ---   ?     v  v     ivi  -  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_86182859_8   1675 AACACCTCACCAAGGAAGATATACAGATGGTAAATAAGCATATGAACAGA 1724
                         i   ii  v    i           i    iv        i     v   
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_86182859_8   1725 TGCTCCACATTATATGTCAT 1744
                              v    i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (112 / 73)
Gap_init rate = 0.02 (17 / 863), avg. gap size = 2.94 (50 / 17)  


 370 34.06 6.19 3.72  chr1_86185733_86188677      954  1276 (1669)    L1M4_orf2#LINE/L1        3   333 (575)  

  chr1_86185733_8    954 GAAAGACAACCGTTGTTGTTGAA----AAGACTGAGTCAACATCATAAAT 999
                               i v  vv    vv  i ----      ----i  i  ii v  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACT----TAATATTGTTAAG 48

  chr1_86185733_8   1000 ATCCCAGGGCTCTC----TTAATTTATAAGTGTAAGTTGAAGCCAAGAAA 1045
                           vv  ivi   i ----  i  i  i ii vi  vvii vv  v vv  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_86185733_8   1046 AATACTAACAATATTTTTTAATGAAGCTAGATAGATTGATGTTAAGGTTT 1095
                            v i i viiv      ivv   ii -  i iii    vi   ii  i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTC 147

  chr1_86185733_8   1096 ATATGGAAAAACAAGA-ATGCAAATGTAGCCAGGAAAACACTGAAAAA-- 1142
                                  vi    i- iv  i -i      ii v  ivi       --
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGA-ATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_86185733_8   1143 --AGC----TCAGAGGACTTAAAACCTTTCCAGACATCTCAACAC--ACC 1184
                         -- i ---- ii       i v --   i   ---  i    v  --  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACA--CTTCCCA---ATTTCAAAACTTACT 241

  chr1_86185733_8   1185 ATAAAGTTTCTATCATTAGAACAAGGTAGGACTTGTGCATGAACAGACA- 1233
                          i    i v vi v  i ii   iv  i v   v iii v i i     -
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_86185733_8   1234 ACCACTCAGATGGAATAGAAAATAAAGTACAGACATAGATCCA 1276
                          iviv   -           vvv i   v    v   i i   
  L1M4_orf2#LINE/    292 ATAGATCA-ATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

Transitions / transversions = 1.50 (66 / 44)
Gap_init rate = 0.04 (13 / 331), avg. gap size = 2.46 (32 / 13)  

 855 28.30 4.40 3.63  chr1_86185733_86188677     1930  2452 (493)    L1M4_orf2#LINE/L1      382   908 (0)  

  chr1_86185733_8   1930 TGAAGCAAAGACAGATTGTTTAACGAATGATTCTGAGAAAACTGATTAGC 1979
                           ii v  ii i  vi v  i   i    i v   i  v     iv  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_86185733_8   1980 CATTTAGAAAAATGTGAAATGAAATACATAAATCACAACATTCACACACA 2029
                           iv iv    ivi    i vii iv v  vv     v   ------ i 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT------ATA 475

  chr1_86185733_8   2030 CAAAAAA-AACTTTTAATGTATCAGAGACCTAAATATAAAAAAGGAAACT 2078
                               v-    ivv    v    ?          i   i ivvi     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_86185733_8   2079 AGTCAAGAATC--AGAAGAAAACATAGGTG-ATTTCTTTAAAATCT-GGA 2124
                          --i  i v  --               ? - vv    iivi i  -  i
  L1M4_orf2#LINE/    526 A--TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_86185733_8   2125 TATAGGAAAAGGTTCTCTAATGATGAC-TCAAAATC-CAAATTCCCTAAA 2172
                          -    v  v    iii  ivv     -i     v -   i-- vvi   
  L1M4_orf2#LINE/    574 T-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG--CAACAAA 620

  chr1_86185733_8   2173 AGA-----CTGACAAATTTGGCTATGT-AAAATTGTAAAGCTGCTTTCTG 2216
                            -----iv  i     v i  vii -      i-   i  --   v  
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTA-AAAACT--TTTGTG 667

  chr1_86185733_8   2217 --TCAAAAAACACTACAAACAAAGTCAAAAGACAAGTGACAAATTGGGAA 2264
                         --     ii      iv  v     v         viv   i v     i
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_86185733_8   2265 AAAATACTTGTAA--TAGTTATCAAAGGTAAAGGGCTAATTTCCCTAATA 2312
                               i   i  --i vv    vi --   i  i  vi v   vv    
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGA--TAAGGGACTTGTATCCAGAATA 765

  chr1_86185733_8   2313 CCCAAATAATTCTTA-AACATTTAGAGTAAAATGACCAAATA-CCTAGTA 2360
                         ivi   v  i     -   - iv v i     v   -     -  i i v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAAC-TCAATAATAAAAAGAC-AAATAACCCAATT 813

  chr1_86185733_8   2361 GAAAAATGGGCAAAAAACATAAACAGAC--TTTTGCAAGAAAGATTATA- 2407
                         ?             ii iv i  i    --  i v   ii     -   -
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT-ATAC 862

  chr1_86185733_8   2408 AAACAGTCCTCAAACAAA-AAAAAGATGTTCAGTGTCACTTATAGT 2452
                            ii i vvi  i  v -i        i   iii   ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (84 / 60)
Gap_init rate = 0.05 (25 / 527), avg. gap size = 1.68 (42 / 25)  


2609 27.57 6.39 0.59  chr1_86249472_86255453     4636  5480 (502)    L1M4_orf2#LINE/L1        1   894 (14)  

  chr1_86249472_8   4636 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATATCATGAAAAT 4685
                               i i  i     i               v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86249472_8   4686 GGCCATACTGTCCCAAGTAATTTATAGATTCAATGCTATCCCCATTCAAG 4735
                            v     vi  v  v i  i  i        i  v     i  -   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-CAAA 99

  chr1_86249472_8   4736 CTATCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 4784
                         v vi  vivi i  i  ii     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_86249472_8   4785 TATGGAAACAAAAAAGAGCCCT--ATGGCCTAGACAACCCTAAGCCAAAA 4832
                                 iiv  ii  -   v--  i   v i    i i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_86249472_8   4833 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTATAAGG 4882
                                 i      vv    i  v  ii i      viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_86249472_8   4883 CTACAGTAACCAAAACAG--------------------AGGCCT------ 4906
                                  i   i    --------------------  i v ------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_86249472_8   4907 ----------------------CAGAAGTAACACCATACATCTACAACCA 4934
                         ----------------------     i   vv        i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_86249472_8   4935 GCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAAGATTCCC 4984
                         ii    i  i     ivv  v   i v  vv           ii  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_86249472_8   4985 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAATCTG 5034
                          v  i  i        i     v      v  ?   i     i  ivv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_86249472_8   5035 AAACCAGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 5084
                           iiii       v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_86249472_8   5085 TACAGACTTAAATGTTAGACCTGAAACCATAAAAGTCCTAGAAGAAAGCC 5134
                         i ?    i       v   v  i    i      v  i         i v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_86249472_8   5135 TAGGCA-ATACCATTCTGGACATAGGCATGGGCAAAGACTTCATGACTAA 5183
                             ?i- v i -   vv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_86249472_8   5184 AACACCAAAAGCA-ATGCCAACAAAAGCCAAAATTGACAAATGGGATCTA 5232
                         i            - v  -        vv     v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_86249472_8   5233 ATTAAA-CTAAAGAGCTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5281
                           i   -i    i vi i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_86249472_8   5282 CAGGCAACCTACAGGACAGGAGAAAATTTTTGCAATCTATCCATCTGACA 5331
                         v  i     i    i ii         v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_86249472_8   5332 AAGGGCTAATATCCAGAATCTACAAGAAACTTAAACAAATTCACAAGAAG 5381
                          i  i  vi          v  i  ii    ivv    v iv i  v  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_86249472_8   5382 AAAACAGACAACTCCATCAAAATGTGGGCAAAGGCTATGAACAGAGACTT 5431
                           i   i i   i v  i?   vi          v v    i   v i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_86249472_8   5432 CTCAAAGGAAGACATTTATGCAGCCAACACACATATGAAAAAAAGCTCA 5480
                            v  i     i  vi viii     i vi  i       i v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.01 (12 / 894), avg. gap size = 4.92 (59 / 12)  


3492 24.72 1.90 0.34  chr1_86255769_86257907      753  1646 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86255769_8    753 TGGAAAGGTATTCCATGTTCATGAATTGGAAGAATCAATATTTTTAAGAT 802
                                i   i           i         v i      v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86255769_8    803 GTCCGTACTGCCCAAAGTAATCTACAGATTCAATACAATCTGTATCAAAA 852
                          v vi    v      v i              ii     iv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86255769_8    853 TACCAGTAATATTCTTCATAGAAATAGAAAAAAGC-AATCCTAAAATTTA 901
                          v    iviiv  i  iii      v  v  --  -i           i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr1_86255769_8    902 TGTGGAACCACAAAA-ACCCAGAATAGCCAAAGCTATCCTAAGCAAAGAG 950
                          i     vii   ii-                i v   i i iv  ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_86255769_8    951 AACAAAACTAGAGGAATCACATTACCTGATTTCAAATTATACTGCAGAGC 1000
                               ii i     v     i v  ii        viv    i  i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_86255769_8   1001 TACAGTAACCAAAACAGCATGGTACCAGCATAAAAACAGACACACAGACA 1050
                                 i   i    ii      ii      ii i     i i   iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_86255769_8   1051 AAAGTAACAGAATAGAGAACCCAGAAATAAATCCACACACCTACAGTGAA 1100
                           v v  i     v    ii           i   i   ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_86255769_8   1101 CTCATTTTCGACAAAGTTGCCAAGAACAGACATTGAGGAAAAGACA--CT 1148
                         i v           i v        v  vv  v  i     ii i --  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_86255769_8   1149 CTTCAATAAATTGTGCTGGGGAAACTGGATATCCATATGTAGAATAATGA 1198
                         i     i    v        iv         ?   i   i i  v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_86255769_8   1199 AACTTGATCCCTATCTCTTGCCTTGTACAAAAATCAATTCAAAATAGATT 1248
                          ii v  i     i   vii  v i         i  i       i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_86255769_8   1249 AAAGACTTAAATCTAAAACCTCAAACTATGAAACTACTACAAGAAAATAT 1298
                          ?    i     v   i v  v       i     vi  v       i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_86255769_8   1299 TGGGGAACCTCTCCAGGACATTGGTCTGGGCAAAGATTTCTTCAGTAATA 1348
                         v  ? v vv   i iv   v    vi i     v i      vii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_86255769_8   1349 CCTCACAAGCACAGCCAGCCAAAGCAAAAATGAACAAATGGGATTGCATC 1398
                          vi  v       iv  i v    v      ii i    v   i v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_86255769_8   1399 AAG-TTAAAAAGTTTCTACACAGCAAAGGAAACAATCAATAAAGTGAAGA 1447
                           i-       v   - iii vv       v  v     v        i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_86255769_8   1448 AACAACCCAGAAAATAGGAGAAAATATTTGCAAACTACCTATCTCATGAG 1497
                         i        v i   i                  ii iv     v  i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_86255769_8   1498 AGATGAATAACTAGAATGTAGAAGGTGCTCAAACAACT-AAT-------- 1538
                         i  ivvi  v i     i  v  i vi   vv      -   --------
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_86255769_8   1539 --CAAGTAATCCAATT-AAAAATGGGCGAAAGATTTGAACAGATATTTTT 1585
                         --   i   i      -          i  i        i   i    i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_86255769_8   1586 CAAAATGAGACAAGGAAATGGTAAACAGGCATATAAAAAAGTGCTCAACA 1635
                          v   vi   i viv      iv  i i   i  i    ii         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_86255769_8   1636 TTATTGATCAT 1646
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.73 (138 / 80)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


3150 27.17 0.44 0.55  chr1_86309320_86313642.rev     2924  3832 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86309320_8   2924 TGGAAGAACATTCCGTGCTCATAGGTAGGAAGAATCAATATCGTGAAAAA 2973
                              ii i  i  i  i    i i v      v i     i  v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr1_86309320_8   2974 GGGCCATACTGCCCAAGGTAATTTACAGATTCAATTCCATCCCCATCAAG 3023
                         v   v     v     iv i  i           iv v     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_86309320_8   3024 CTACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCA 3072
                         v v   iivi i  i  ii     v v  v  i-  - iii    i    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_86309320_8   3073 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCCATCCTAAGCCAAAAG 3122
                                viiv  ii  v  v v  v     iv v   i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_86309320_8   3123 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACCACAAAGC 3172
                                i      vv       v  ii i      viv   i       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_86309320_8   3173 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3222
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_86309320_8   3223 AATGGAACAGAAC--AGAGCCCTCAGACATAATGCCACATATCTACAACT 3270
                                i    i--    i  --   v    vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_86309320_8   3271 GTCTGATCTTTAACAAATCTGACAAAAACAAGAAATGGGGAAAGGATTCC 3320
                         ivi    i  ii    ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_86309320_8   3321 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 3370
                           v  i                 v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_86309320_8   3371 GAAAATGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3420
                            iv    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_86309320_8   3421 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3470
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_86309320_8   3471 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3519
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_86309320_8   3520 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3569
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_86309320_8   3570 ACTACACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCACAGTGAA 3619
                          ii v v v  i i   i  ii vv    i  v    ii vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_86309320_8   3620 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 3669
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_86309320_8   3670 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTCACAAGAAA 3719
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_86309320_8   3720 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAGCAGACACTT 3769
                           i     i     v  i?    i            v   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_86309320_8   3770 CTCAAAATAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 3819
                            v   v    i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_86309320_8   3820 CATCACTGGCCAT 3832
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3134 26.79 0.88 0.77  chr1_86340305_86346693.rev     4992  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86340305_8   4992 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5041
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86340305_8   5042 GGCCATACTGCCCAAGGTAGTTTATAGATTCAATGCCATCTC-ATCAAGC 5090
                            v     v     iv ii i  i        i  v   i -     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86340305_8   5091 TACCAATGACTTTCTTCACCGAA--TGGGAAAAAACT-ACTTTAAAGTTC 5137
                          v   iivi i  i  ii v   --  --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_86340305_8   5138 ATATGGAACCAAAAAAGAGCCCACATGGCCAAGTCAGTCCTAAGCCAAAA 5187
                                 viiv  ii  v  viv  i     iv  i  i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_86340305_8   5188 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACCACAAGG 5237
                                 i      vv    i  v  ii i      viv   i    i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_86340305_8   5238 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACACAGATACAGAC 5287
                                  i   i    ii         i iv ii i v v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_86340305_8   5288 CAATGAAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5335
                              i  i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_86340305_8   5336 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5385
                         i vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_86340305_8   5386 CCTACTTAACAAATGGTGCTGGGAAAACTGGCCAGCCATATGTAGAAAAC 5435
                         i  vi i                 v      vi ?   i   i i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_86340305_8   5436 TGAAACCGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5485
                             iii   i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_86340305_8   5486 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAA 5535
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_86340305_8   5536 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5584
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_86340305_8   5585 AAAACAACAAAAGCA-ATGTCGACAAAAGCCAAAATTGACAAATGGGATC 5633
                          vi   v        - v - i       vv     v  i    v   ii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_86340305_8   5634 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5683
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_86340305_8   5684 AATAGGCAACCTGCAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5733
                           v  i     ii                v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_86340305_8   5734 CAAAGGGCTAATATCCAGAATTTACAAAGAACACAAACAAATTTACAAGA 5783
                         i  i  i  vi          v  i       v vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_86340305_8   5784 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5833
                             i     i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_86340305_8   5834 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 5883
                              v        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_86340305_8   5884 ATCATCACTGGCCAT 5898
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3239 20.30 3.61 7.44  chr1_86427124_86430680     2124  3064 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_86427124_8   2124 AGAGACATCCCATGTTCATCAACTTAAA-ACTCCATATTGTCAAGATAAC 2172
                          i   i             vi i vi  -   iv       i     ii 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_86427124_8   2173 AATCCTCTCCAAATTGACCCATGGATTCAAAGTAATCCTTATCAAAATCC 2222
                            v   i         i i ii       v i     i           
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_86427124_8   2223 CATTTGACATTTTAATAGAAATTAACTAGTTCATCTTAAAACGTATACAA 2272
                           vi  v v    vii       i  v  i v   i     ivi   iii
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_86427124_8   2273 AAATGCAAAGCATCTACATTTACCAAAACAACTTTGAAAAAAAATGAACA 2322
                                 i v i i v v vi         ii        i  -     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GAACA 202

  chr1_86427124_8   2323 AAGTTAAAGGACTTATGCTTCCTTATTACCGAATCTCAAAATTTA----- 2367
                              ii      i ii     i--------   i      i   -----
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCC--------AATTTCAAAACTTACTACA 244

  chr1_86427124_8   2368 AGTCCACAGCAATCAAGACAGTGTGGTATTGATGTAAGTGGGTACTCCCT 2417
                          iv i    i                  i  iii    ------------
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG------------ 282

  chr1_86427124_8   2418 GCACACAATCAAGACCCTTGCAAATATAATAGGCATATGAATCAATGGAA 2467
                         ---------------------------i    i     ii          
  L1M4_orf2#LINE/    283 ---------------------------GATAGACATATAGATCAATGGAA 305

  chr1_86427124_8   2468 CAGGATTGAAAGCCTAGAAATAAACCCTTACATGTATGGTTATTTGATTT 2517
                         i  i     i  i i            v     v      i v       
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_86427124_8   2518 TGGGCAAAGGTACCATTATAATTCAATGGGGGAAAGGGTAAACTTTTCAA 2567
                          v i   i   i   vv iv           -    ii  iv        
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAA 404

  chr1_86427124_8   2568 TAAATAATGTAGGGATAACTGGATATCTACATGCAAAAATATGATCTTAG 2617
                         i    ii  iv    i         ? i          iv    vv  i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_86427124_8   2618 ATTCTTATCTCAAACCAGACACACAAATTAACTCAAAATGGATTATAAAA 2667
                          ii i  i    v    v i   v                   i ? i v
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_86427124_8   2668 CTAAATTTAAGACCTAGACCTATAAAACT---GGAAGAAA---TAGGAGA 2711
                               v     v   i v          ---i       ---    ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_86427124_8   2712 AAGTCTTTGTGGCCTCGGGTGAGGCAAAGGGTTTTTAATTATGAAAGGAA 2761
                           i    i   i   i    v      v  v  i   iv     v vv  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_86427124_8   2762 AAGCACAATCCATTAAATCCATTAAAATTTATAAAATTAGACAAATTTTA 2811
                                 v v i-   ------ i  -----     -   i     --i
  L1M4_orf2#LINE/    605 AAGCACAAGCAAC-AAA------AGAA-----AAAAT-AGATAAATT--G 639

  chr1_86427124_8   2812 AATTTCTATTTCAAAATTTAGAACTTTATTTTCTT-AATGGTGTCTTTTT 2860
                         i i   -  --       v i      - v v   -  v  vvv  v iv
  L1M4_orf2#LINE/    640 GACTTC-AT--CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCA 685

  chr1_86427124_8   2861 A---AGTGCAAA--CAGCT-ACGGACTGTGAGAAAATATTTGCAAATCAC 2904
                          ---    v   --  i i-  i  v  v                    i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_86427124_8   2905 ATCTCTGATAAAGAATGTGCACCTCTAGCATATATAAAGAATTCTTACAA 2954
                           v        i i iv  i --  i  v            i        
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTA--TCCAGAATATATAAAGAACTCTTACAA 783

  chr1_86427124_8   2955 CTTGATAATACAAAGACAAA---CCCAAGTAAGAAATGAGCAA------- 2994
                           ii      v         ---     v ? i     i    -------
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_86427124_8   2995 -----GATATTTCACCAGGAAAGATATATGGACTGCTAATAAGTACATGA 3039
                         -----  i     v   iii        iii iv  i      i      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_86427124_8   3040 AAAGATGCTCTACATCATTAGTCAT 3064
                                   v      ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (121 / 66)
Gap_init rate = 0.03 (23 / 905), avg. gap size = 4.52 (104 / 23)  


2193 23.77 11.88 3.60  chr1_86468057_86470967.rev     1239  1987 (924)    L1M4_orf2#LINE/L1       56   866 (42)  

  chr1_86468057_8   1239 TGCCCCCTCCATTAATGTATAGATTTAATGAAATTCCGATCATAATCCTG 1288
                          i i   ivv   i  v  i     i  i v   i  v    v     ii
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_86468057_8   1289 AAAGTCTCTTTTGTAGGTATTGATAAAAACAATTATAAAATTTACTTTGA 1338
                         ivv i  i     i  iv     i  iv-ii  iv       i iv v  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATGGA 154

  chr1_86468057_8   1339 AATGCAAAG-ACCTAGAATAGCCAAAACAATGTTGAAAAAGAA---CAAA 1384
                                i -   i                 v           ---    
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_86468057_8   1385 GTTAGAGGACTAACACTACCTGATTTTAAGGTTTATTATAATGCTAAAGT 1434
                            i       v     v  ii    i  iii   i  i  v    v   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_86468057_8   1435 AAGCAAGACTA-GTGGTACTAGTGCAAAGATAAAGAAATGAATCAGTAGA 1483
                           v      vi-        i iii  i    i v v  ii    i i  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_86468057_8   1484 AAAAAATGGAGCGCCCAGAAGTACACCCAC-----------CAATT---T 1519
                          v i   v   v i      i  v     i-----------     --- 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_86468057_8   1520 TTGAACAA-----CTAAT----TTCAA-------------GTCTTTTTAG 1547
                           vi    ----- i  v----     -------------       i i
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_86468057_8   1548 CAAAAGTTG-------------------------AAGAAAAGGAACCTCA 1572
                             v v  -------------------------  i i  v   vi vi
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_86468057_8   1573 ATCCATTCCTTAACACCATTTACACAAATTCACCAAAAATGGATCATAGA 1622
                          i  v v   i -      v    v     v  iv           ?   
  L1M4_orf2#LINE/    455 ACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_86468057_8   1623 CCTAAACCTGAAACCTAAAACTATAGAACTTCTAGAAGGAAACATAGAAA 1672
                               iv i i v           i    ii      i        i?-
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN- 552

  chr1_86468057_8   1673 GAAAATCTTTGCTGCTTTGGATTAGGCCAAGATTTCTTAGACACAGCACT 1722
                          v       i ivi i    i      v v i         i iii   i
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_86468057_8   1723 GAAAGCATGATCTATAGAGGAAA---TATGATATATTGAAATTCATCAAA 1769
                         i      ii v v i i i    ---  -    v    i v         
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTCATCAAA 651

  chr1_86468057_8   1770 GTTAAAAACTTCTATTTCTTGAAAGA-------AAGAAAATG------CA 1806
                         i          i i vii ii  i  -------      i  ------  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_86468057_8   1807 AGCTACAGA------GAAAATACTTGCAAATCATATATCTGATATATCAT 1850
                          v i     ------       i                     ------
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA------ 745

  chr1_86468057_8   1851 CTATATGATATATTTGAATAAACTTGTATCCAAAATATATAAATAACTCT 1900
                         ----------------- vii           i          v      
  L1M4_orf2#LINE/    746 -----------------AGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_86468057_8   1901 CAAGATTTAATG-TAAGAAGGCAAATGAACTAATTAAAAAATGGGCAAAA 1949
                         i vi i i   i-   i   i     i v i    ?             i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_86468057_8   1950 GATTTGATCAGATTCCTCACCAAAGATTATATATAAGT 1987
                                vi   ivii  v       vv     i  i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

Transitions / transversions = 1.92 (115 / 60)
Gap_init rate = 0.02 (19 / 811), avg. gap size = 6.11 (116 / 19)  


3140 26.57 0.77 0.66  chr1_86507450_86512430     3582  4488 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86507450_8   3582 TGGAAGAACATTCTATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 3631
                              ii i  i i   i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86507450_8   3632 GGCCATACTGCCCAAGGTAATTTGCAGATTCAATGCCATCCCCATCAAGC 3681
                            v     v     iv i  i i         i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86507450_8   3682 TACCAATGACTTTCTTCACAGAATTGAAAAAACT-ACTTTAAAGTTCATA 3730
                          v   iivi i  i  ii     v vi v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_86507450_8   3731 TGGAA-T-CAAAGAAGAGCCTGCATTGCCACGACAATCCTAAACCAAAAG 3778
                              - -   i --  v  v v  v    vi      i i  vv i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_86507450_8   3779 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTGCAAGGC 3828
                                i      vv   vi  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_86507450_8   3829 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3878
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_86507450_8   3879 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACTTCTACAACC 3926
                                i    i--    i  --        vv   i  v i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_86507450_8   3927 ATCTGGTCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 3976
                          vi  i i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_86507450_8   3977 CTATCTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 4026
                           v ii  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_86507450_8   4027 GAAAATAGATCCCTTCCTTACACCTTATACAAAAATAAATTCAAGATGGA 4076
                            iv i  i    v   i     v           v  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_86507450_8   4077 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAATGCTAGAAGAAAAG 4126
                          i ?    i       v   v       i      v vi          v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_86507450_8   4127 CTAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 4174
                         v    ?-   --i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_86507450_8   4175 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCT 4224
                          vi            vvi          vv    iv  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_86507450_8   4225 AATTAAACTAAAGAGCTGCTGCACAGCAAAAGAAACTACCATCAGAGTGA 4274
                         v  i   v v  i i  vi  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_86507450_8   4275 ACAGGAAACCTACAGAATGGGAAAAAAATTTTGCAATCTACTCATCTGAC 4324
                          v  iv    i           i    vv       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_86507450_8   4325 AAAGGGCTAACATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 4374
                           i  i  vii         v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_86507450_8   4375 AAAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACT 4424
                            i     i     v  i? v  i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_86507450_8   4425 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 4474
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_86507450_8   4475 TCATCACTGGCCAT 4488
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (136 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


1532 23.79 12.46 1.62  chr1_86578760_86580372.rev      505  1122 (491)    L1M4_orf2#LINE/L1      224   908 (0)  

  chr1_86578760_8    505 CCAATTTTAAGACTTA-TATAAAACTACAGTAATCAAGAGAATGTCATGT 553
                                i  i     -  i   i               v i   vi ii
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_86578760_8    554 AGGCAAATGTTTTGAT-TATAAATTATTAGAATAGAATGGATTGTCCAGA 602
                         v    v v vv v  i-    i  i v i         v  vv       
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_86578760_8    603 AATAAACACACACACACATGGTCTAATCATTTTCAACAAAAGCACTAAAT 652
                                v  i   ivi      v v v      i    ii ii i  iv
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_86578760_8    653 TGATTCAATGGGGAAGAGAA-AGTCTTTTAAATAAATGGTG---GTACCA 698
                         iv             -    -        v  i        --- v  --
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAA-AGAATAGTCTTTTCAACAAATGGTGCTGGGAC-- 420

  chr1_86578760_8    699 AATTGGGTATCTGTATAAAACAAAGTGAATCTTGACCCCTTACATCATTC 748
                           i   i  ? iii  iv  v i i    vi v       -  v   iv 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT-ACCTCACAC 469

  chr1_86578760_8    749 C---TAAAAAACTTAATTCAAGATAGGTCATATACTTACTTATAAAAGCT 795
                          ---  v    v    i    i  i i   ? v  i  vv i   i    
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_86578760_8    796 TCAAATAATAAAACTTCTAGAAGAAAACATAGCGA-----CTTCACAAAT 840
                         -v   iv        ii               v?i-----    iii vi
  L1M4_orf2#LINE/    520 -AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_86578760_8    841 GTGGAGTT--GC---GGT------------ACATTAAA--------CTAT 865
                         v   -   --  ---   ------------   ii   -------- v i
  L1M4_orf2#LINE/    569 TTGG-GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_86578760_8    866 AAAAGAAAAATGCTGGTAAGTTAGATGTT-TCAAA--TAAAAATTTTCTG 912
                                   -iiv i   i  i  iv i-     --      i   -  
  L1M4_orf2#LINE/    618 AAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TG 665

  chr1_86578760_8    913 CTCTTCAAAAGATACCATTAAGAAAATATATGAGA----------AATAG 952
                         iv       i  i  i  i      i iv -i   ----------   i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAA-AAGACAACCCACAGAATGG 714

  chr1_86578760_8    953 GAGGAAAGTATTAGTTA--CATATATCTGACAAATCGTTT---TTCAGAA 997
                            i   -    v iv --           i  ivvii  --- i     
  L1M4_orf2#LINE/    715 GAGAAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_86578760_8    998 TATGTAAACAACTCCTGAAAATCAACAATAAAACAACAA----TCCAA-- 1041
                            i    v     i iv  v    i       vi    ----i    --
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_86578760_8   1042 -AAAAATGGGTAAAAGACTTGAACA-ACA---CTTCATAAATGATGTAC- 1085
                         -         i   i  i     i -   ---  i  v i v   i   -
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_86578760_8   1086 ---GGTCAATAA-C---TGAAAGG-TGCTAAACATCATTCATTAC 1122
                         ---  i      - ---     i -    v       ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (91 / 53)
Gap_init rate = 0.05 (32 / 685), avg. gap size = 2.72 (87 / 32)  


1788 25.27 13.36 4.09  chr1_86640218_86643168     1628  2458 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86640218_8   1628 TGAAGAGCCATACCATCTCCATGGTTTGAAATACACAATATAATAAAGAC 1677
                           i i  vi  v    v i     v   i  v  vi     vi v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86640218_8   1678 GTCAATTTTTCCAAAATTGATCTGTAAACTTAATGCA-CCCCTAT-AAAA 1725
                          v    vi i  v          ii i i i  i   -i      -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86640218_8   1726 -CCCAGATA-----TTTGTATGTGAAATTGACAAGCTGCTTTTAAATTTT 1769
                         -     v i-----    i ---               v ii    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA---GAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_86640218_8   1770 ATATTGAAATGCA-----CCTAATGTAGCCAAAATAGTCTTGAA---TAA 1811
                             v        -----  i ivi         i i       ---v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_86640218_8   1812 AAACAAATCTGGACTGTTTACACTACC---------------------AG 1840
                         i      vi    vvii i     v  ---------------------  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_86640218_8   1841 -----ATAATCAAGG----------------TAAGGATAGTCACACAGAC 1869
                         -----i        i----------------         v  i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_86640218_8   1870 CAATGGAACAAGGAACAGAACAGAGAGTTCAGAAGCAGACCTGCACATCT 1919
                                 i -------   iv      i     ii i   iii    i 
  L1M4_orf2#LINE/    298 CAATGGAATA-------GAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_86640218_8   1920 GTAGTCACCTCATGCACAACAAAAGCACAACTGTAATTCAGTAGGGGAAA 1969
                         i i    vi v  viv i    ii ii v vviiv     i -       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAA 389

  chr1_86640218_8   1970 TTATGGTCTTTTCAATAAATACT-CTCAACTTACTGGCTATCACAGAGGA 2018
                         vv  i          i    iv -  viiviv     v  ? -  v v -
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC-CACATG- 437

  chr1_86640218_8   2019 AAACAAAACAAAACAAAAACCTTGAACCTTT-CCTCACACCATACACAAA 2067
                         ---     --i  ii  i---   i   ii -            i     
  L1M4_orf2#LINE/    438 ---CAAAA--GAATGAAG---TTGGACCCCTACCTCACACCATATACAAA 479

  chr1_86640218_8   2068 AAT-ATTTTGAGATCAATCAGTATACCTAAATGTTAAAGGTCAAGCAGCA 2116
                            - vi ii i  vi    -? v          v i  v v  i vii 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCA-WAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_86640218_8   2117 AGGCTTCTAGAATCATATAT-TGTATAATATCTTCATGAATTTGGG---- 2161
                          ii  ii     vv v i  -v ?i   -      i   vi     ----
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAG 577

  chr1_86640218_8   2162 --AAAGCTGTCTTAAATATGACAC-AAAAACATTATACATAAAAGA---- 2204
                         --  v v v     i         -    i  iv vvv i      ----
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_86640218_8   2205 -T---TAAATTGGACTGTACTAAAATTAAAAATCTCTATTCATCTAATGA 2250
                         - ---           vi ii           ii i i v v  v  v  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_86640218_8   2251 TACTATTAAGG-----------CAAGCTACAAACTAGGAGAAAATATTTT 2289
                         i     i   i-----------   v i   i v i             v
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_86640218_8   2290 CAA----TATATCTTTCAATACAAAAGACTCAGTATCCAGAACATATAAA 2335
                            ----       ---i   -- ii    i-          i       
  L1M4_orf2#LINE/    728 CAAATCATATATCT---GATA--AGGGACTT-GTATCCAGAATATATAAA 771

  chr1_86640218_8   2336 GAACTCCCATAAATCAATAA-GAAAAGACAA----TTTAATTAAAAATTG 2380
                               ii i  v       -i         ----iii    ?    v  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_86640218_8   2381 TGCAAAAAAAAAAACTTGAAGAGATACTTC--------------ACAAAA 2416
                         v     ii -----i     v   i i   --------------     v
  L1M4_orf2#LINE/    822 GGCAAAGGA-----TTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_86640218_8   2417 GACCAATATGTATATAAAAAGGTCTTTAACAACATTAGCCAT 2458
                          i      v i i  i     i vi i    v  ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (131 / 75)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 4.14 (145 / 35)  


3220 23.86 2.79 1.56  chr1_86710050_86712283.rev      847  1743 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86710050_8    847 TGGGAAGATATTTCATGTTCATGGATAAGAAGATTCAATATTGTCAAGAT 896
                            i       ii             vi     i i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86710050_8    897 GTCAGTTCTTCCCAACTTGATGTATAGATTCAATGCAACCCCAATCTAAA 946
                          v  i v  i     v     v  i        i    i   v   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86710050_8    947 TCCAAGCAAGTTAGTCTGTGGATATCAGCAAACTCATTTTAATGTTTATA 996
                            v   vivi vv i  ii  v  iii   i  v  ii   vi  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_86710050_8    997 GGGAGAGCCAAT--ACCCTGAATAGTCAATATAATATTGAAGGAGAAGAA 1044
                         v   i vv   v--    v      i   v i   v     ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_86710050_8   1045 CAAAATTGGATTATTGACACTACCTGACTTCAGGACTTACTACAAAGCTA 1094
                             i     vv i v     v  ii i    ii                
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_86710050_8   1095 TAGTAATTCAGACAGTGTGATACTGGCAAAAGAATAGGTAAATAGATCAA 1144
                         i      iv          i        v   i    ii v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_86710050_8   1145 -GGACACGAATAGATAGCCCAGAAATAGACCAAGAAAT--ATGCTTAACT 1191
                         -   vvv    v  v  i         i   v v v  --   v i  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_86710050_8   1192 GATCATAACTGATGACAAGGGAGCAAAGGAAATACAATTAAGTAAAGATA 1241
                            iv ------i        v  v   ivv  v    vii v  ii   
  L1M4_orf2#LINE/    351 GATTTT------CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_86710050_8   1242 GTTT-----------GGTGCTAGAACAACTGGACACCCACATGCAAAACA 1280
                           i -----------      i i         i ?            v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_86710050_8   1281 AAAGAGAATTTAGTCGCAAACCTGACACCCTTCACAAAAAAGTTAACCCA 1330
                          v---   v  i v v vv    v     v vi       --     i  
  L1M4_orf2#LINE/    445 AT---GAAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCA 489

  chr1_86710050_8   1331 AAATGGATCACAGACCTAAATGTGAAATGC-AAAACTATAAAACTCCTTG 1379
                                   ?            i i -  -               i v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAG 538

  chr1_86710050_8   1380 AAGATAACATAGGAGAAAACTTAAATGACCT---GTATATGGTGATGACT 1426
                             v        ? v   ii vvi      ---  -  -  ii   ii 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TA-GGCAATGGTT 586

  chr1_86710050_8   1427 TATTAAATACAGTAC-AAAGGCACAATTCATGAAATAAATCATTGATAGG 1475
                          v   i   iiii  -   i      viv ii   v   vv  v    ii
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_86710050_8   1476 CTGTATTTCATCAGCATTTAAAACTTCTGCTCTGCAAAAGACAATGTCTA 1525
                         i  v i       iv   v       i  iv  v    i    v i  v 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_86710050_8   1526 GTGAATAAGAAGATAAGCCAGAGATTGGGAGAAAATATTTGCAAAAGACA 1575
                          vi i i i    i  v   v   v                    vv i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_86710050_8   1576 CATCTGAGAAAGGACAGTTATTCAAAATGTATGAAGGATTCTGA-AATTC 1624
                         i      v  i    vvv   i  i   i   i   i i   v -  i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_86710050_8   1625 AACAATAAGAAAAC---CAACCTAATTAAAAAATGGGCTAAGGACCTTAA 1671
                           i     i  i  ---i    i    ?          v     ii v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_86710050_8   1672 CAGACAACTCACCAAAGAAGATATGCAGACGGAAAATAAGCATATGAAAA 1721
                         i     vi  v             i  i i  vv        i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_86710050_8   1722 GATGCTCCACATCATAGGTCAT 1743
                                v      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (117 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.60 (39 / 15)  


2858 27.68 2.12 0.78  chr1_86732163_86737367.rev     3819  4714 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86732163_8   3819 TGGAAA-ACATCCCATGCTCATCGATAGGAAGAATCAATATCACTAAAAT 3867
                               - i        i    v   v      v i     iii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86732163_8   3868 GGTTATATTGCCCAAAGCAATTTATAGATTCATTGCTATTCCTATCAAAC 3917
                           iv   i v      vii  i  i       vi  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86732163_8   3918 TAGCAACAACATTTTTCACACCACTAGAAAAAAACT-ATTTTAAAATTCA 3966
                          vv  i vi v     ii  vv v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_86732163_8   3967 TATGGAA-TAAAAAAGAGCCTGAACAGCCAAGGCAATCTTAAGCAAAAAG 4015
                                - iv  ii  v  v   i      ii       i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_86732163_8   4016 AACAAAACTGGAGGCATCATGTTACCTGATTTCAAACTACACTACAGGGA 4065
                               ii      vv   iii v  ii        vivi      ii v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_86732163_8   4066 TGCAGTAACCCAAAGAGCATGGTACTGGTATAAAAACAGGCCTA--GACC 4113
                          i      i v i v  ii         i    ii i  i v  --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_86732163_8   4114 AACAGAACACAACAGAGAGCCCAGAAATAAGGCTGCACATCCACCACCAT 4163
                           ii   i v  iv     i          iv iii    ii ivii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_86732163_8   4164 CTAATCTTCAACAAAGCTGACAAAAACAAGCAATGGGGAAAAGATTCCCT 4213
                         i i  i   i    i v  v   i v  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_86732163_8   4214 ATTAAATCAATGGTGCTGGGATAACTGGCTAACCATATGCA---GATTGA 4260
                         v  v  iv             i      v  ?   i     ---  v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_86732163_8   4261 AGCTGGATCCCTTCCTTACACCATGTATAAAAATCAACTCAAGATTAAGA 4310
                           i    i    v   i       i  i      i       i  --i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT--GGA 496

  chr1_86732163_8   4311 TTAAAGACTTAAATGTAAAACTGAAAACTATAAAAACCCTAGAAGACAGC 4360
                          i ?    i         i viv            vi i       v i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_86732163_8   4361 CTAGGC---AATAC-----ATCCTGGACATAGGCAAAGATTTTATAACAA 4402
                         v    ?---   vi----- i i   ii-       v i   iv  ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr1_86732163_8   4403 AGATGCCTAAA--ACAATTGCAACAAAAGCAAAAATTGACAAGTGGAATC 4450
                         v  ii  v   --    --          v      v  i  i v i ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_86732163_8   4451 TAATTAAACTTAAGAGCTTGTGCACAGCAAAAGGAACTATCAACAGAGTA 4500
                          v  i   v    i i   v  ii vv    i iv        v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_86732163_8   4501 AACAGACAACCTACAGAATAGAAGAAAATATTTGCAAATTATGCGTCCAA 4550
                           v        i       i i                 i  iii  ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_86732163_8   4551 CACCGGTCTAATATCCAGCATTTAAAAGGAATGTAAACAAATTTACAAGA 4600
                         i vv  v  vi       v  v  v  i   ivivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_86732163_8   4601 GAAAAACAAACAATGCA-TTAAAAAGTGGGCAAAGGACATGAACAGATGC 4649
                         i   i     i  iv  -  ?    i           iv    i   iii
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_86732163_8   4650 ATTTCAAAAGAAGATAGACATGTGGCCAACAAGCAAGTGAAAAAAAGCTC 4699
                         v i  v          v   vi       i     vi      i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_86732163_8   4700 AGTATCACTGATCAT 4714
                          ii    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (151 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.00 (26 / 13)  


1893 25.30 3.23 5.52  chr1_86775388_86777987      957  1699 (901)    L1M4_orf2#LINE/L1       31   756 (152)  

  chr1_86775388_8    957 AGAATCAATAATGTAAAGATAGTAATTGTGCCAAAATTGATCCGTAAATT 1006
                            v i    v   v     i i   vv v  v         iii i   
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chr1_86775388_8   1007 TGACAAAATCCCAATCAAAACTCCAGCAGGTTTTTTGATAGAATGTGAGA 1056
                         ii  iv      v       ii     v vi     vii    vv   v 
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA 130

  chr1_86775388_8   1057 GGACT-ATTATGAACTT-ACG-GGAAATTCAAAAGACCTAGAATGACAAC 1103
                         i -  -  iv i  v  - ii-      v   ii    i     ii ---
  L1M4_orf2#LINE/    131 AG-CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC--- 176

  chr1_86775388_8   1104 AACAACAACAAATCTGAAAAAGAAGAACAGAGTTGAAGGACTTACACTAG 1153
                         --   -     vii               i     i      i     vv
  L1M4_orf2#LINE/    177 --CAA-AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr1_86775388_8   1154 CTGACTTCAAGGCTTCCTGTAAAACTACGGTAGTCAAGATAATATGGTAT 1203
                          ii i     ii   v  ii   i    i   i      i i i     i
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_86775388_8   1204 TTGCAAGAGAATAGACACATAGATCAGTGAAACAGAAT--AGAGCCTAGA 1251
                          v   vi  i       i        i  i  i     --    i i   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_86775388_8   1252 AATAGACCCACAGAAATAGGGTTAACTGATTTTTGATGAAAGTTCAAAGG 1301
                             i     i v vv  v   i  i       i  ii ii  v v   i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_86775388_8   1302 GAATTCAA--AGGAAAAAGTA-TCACTTCATTGAACAGTGCTGGAAAAAT 1348
                         vv      --i     i i  -  vi    vii  ii       i v  i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_86775388_8   1349 TGGACATCCTTATCCAAAAAAAGAAATAATAACATTGTTGACACATATAT 1398
                             i ?  vi  v     i  vi  -------i   --   v v  iv 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAA-------GTTG--GACCCCTACCT 464

  chr1_86775388_8   1399 AACACCTCATACAAAAATTAACTCAAAATAAGGA---AAGACCTAAATAC 1445
                         v     vi                     --   ---?          ii
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAAT--GGATCAWAGACCTAAATGT 512

  chr1_86775388_8   1446 AAAATATAGATCTAAATACAAAATATTAAACTATGTTTCTAGGAGAAAAA 1495
                           ------  v     -  ----   v     v -----   i      v
  L1M4_orf2#LINE/    513 AA------GAGCTAAA-AC----TATAAAACTCT-----TAGAAGAAAAC 546

  chr1_86775388_8   1496 AGTATAAGAAAATCTCTATATGTTTTCCATTTA---AATGAGTTTTGAGA 1542
                          -  vi? v      iii -- vii iviv   ---    iv  i v   
  L1M4_orf2#LINE/    547 A-TAGGNGTAAATCTTCGT--GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_86775388_8   1543 AATGACAACAAAAACATAATCCGTAAAAGAAAAATCTGA--AACTTAACT 1590
                         v      v     i  i  v vii          viv  --  i vi   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_86775388_8   1591 TTATCAAAAATTTAAAACTTT-GTTCTGTGAAAGATTTTGTTAAAAAAAA 1639
                          i       -  v        -  v  vii  i  ivi i i  i   i-
  L1M4_orf2#LINE/    644 TCATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG- 691

  chr1_86775388_8   1640 CATGAAAAGACAAGCTTCAAA---GGAAAA----TTTGCAAATCATATAT 1682
                         --           v iv  i ---   i  ----                
  L1M4_orf2#LINE/    692 --TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_86775388_8   1683 CCAATTAAAAACTTGTA 1699
                          ii  v iii       
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTA 756

Transitions / transversions = 1.72 (117 / 68)
Gap_init rate = 0.04 (26 / 726), avg. gap size = 2.50 (65 / 26)  

 277 23.94 4.23 5.63  chr1_86775388_86777987     1979  2120 (480)    L1M4_orf2#LINE/L1      769   908 (0)  

  chr1_86775388_8   1979 AAAAAAGACTTGTAACTC--TAATAAAAATATAAACAACCCAGTGAAAAA 2026
                            i  vv   ii     --         v i   i      i v?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_86775388_8   2027 AAAATAAACAAAAAGTCCGAACAGA----TCTTCAGCAAAGATACACAGT 2072
                          --- iii    iii ii   i   ----   i  ivi      i   iv
  L1M4_orf2#LINE/    819 A---TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_86775388_8   2073 TAACAAAAATAAGCATATGAAAAGATGGGCTTCACCTGCAACAATTAT 2120
                          ii v  --      i           --  iv  v -  ????????
  L1M4_orf2#LINE/    866 TGGCCAA--TAAGCACATGAAAAGATG--CTCAACAT-CAZZZZZZZZ 908

Transitions / transversions = 2.67 (24 / 9)
Gap_init rate = 0.04 (6 / 140), avg. gap size = 2.33 (14 / 6)  


 557 17.82 0.00 0.00  chr1_86779863_86784637.rev     2935  3035 (1740)    L1M4_orf2#LINE/L1        1   101 (807)  

  chr1_86779863_8   2935 TGGAAAGATATTCCATGTTTATGAATTGGAAGAATCAACATTGCTAAAAT 2984
                                    i       i   i         v i  i    i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86779863_8   2985 GTCCATACTAATCAAAGCAATCTACAAATTCAATGCAATCCCTATCAAAA 3034
                          v v     vvi    vii       i      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86779863_8   3035 T 3035
                          
  L1M4_orf2#LINE/    101 T 101

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.00 (0 / 101), avg. gap size = 0.00 (0 / 0)  

2926 22.96 1.36 3.46  chr1_86779863_86784637.rev     3475  4284 (491)    L1M4_orf2#LINE/L1      116   908 (0)  

  chr1_86779863_8   3475 TCGCAGAAGTAGAAAAAGCAATCCTAAAATTTATATGGAACCACAAAAGA 3524
                          i      i v  v  ivii           i        vii   ii  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_86779863_8   3525 CCCAGAATAGCCAAAGCTATCCTAAGCAAAAAGCACAGAACAGGAGGAGT 3574
                                        i v   i i iv  i   v   i iiv      v 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_86779863_8   3575 CACATTACATGACTTCAGATTATACTAAAGAGCTATAATAACCAAAACAG 3624
                             i v vii i    i viv     v i     i i   i   i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_86779863_8   3625 CATTGTACTGACATAAAAACAGACACCTAGACCAATAGGATAAAATAGAG 3674
                         ii v      i     ii i     iv    i    i i   i   v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_86779863_8   3675 AACTCAGAAACAAATCCATACACTTACAGTTAGTGAGATGAGTTCACTAA 3724
                          iii      i   i       i   ii  i i ----   ---------
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAAT----TGA--------- 352

  chr1_86779863_8   3725 CTCATTTTTGACAAAGGTGCCAAGAACATACACTTGGAAAAAGACAGTCT 3774
                         ----    i     i          v   v  v v  i   ii i     
  L1M4_orf2#LINE/    353 ----TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_86779863_8   3775 CTTCAATGAATGGTACTGTGGA-AACTGGATATCTGTATGCAGAATAATG 3823
                         i     ii      i   -   -         ? iii     i  v    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_86779863_8   3824 AAACCAGACCCCTATCTATTGCCATATACAAAAATCAAATCAAGACGAAT 3873
                           iiii        i  vvii              i  v    i i i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_86779863_8   3874 TAAAGACTTACATCTAAGACCTCAAACTATGAAACTGCTACAAAAAAACT 3923
                         i ?    i  v  v     v  v       i     vi  v  i     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_86779863_8   3924 T-GGTGAAATTCTCCAGGACATTGGTCTGGGCAAAAATTTATTGAGTA-- 3970
                          -  ? v  v   i iv   v    vi i     vii   v  iii  --
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_86779863_8   3971 ATACCACATGAGCACAGGCAACCAAAGTAAAAATAAACAAATAGG--TTT 4018
                          i    v --      i     v    v       i i    v  --  i
  L1M4_orf2#LINE/    598 ACACCAAA--AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_86779863_8   4019 ACTCACATTAAAAAGC---GACTGCCTAACAAAGGAAACAGTCAACAAAG 4065
                          iiv v        vi--- --   i --       v  vi    v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTG--TGCTT--CAAAGGACACTATCAAGAAAG 691

  chr1_86779863_8   4066 TGAAGAGACAACCCACAAAATGGAAGAAAATATTTGCTAACTACCCATTT 4115
                             i            i     i             v  ii ivi  i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_86779863_8   4116 GACAAGGGA--TGACTAACCAGAATGTATAAGGAGCTCAAACAAGTCTAC 4163
                           i      --  --  v       i     i  i   vv    v  v i
  L1M4_orf2#LINE/    742 GATAAGGGACTTG--TATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_86779863_8   4164 AGAAAAAAAAATCTAATAACCCAATCAAAAAATGGGCAAAAGATTTAAAT 4213
                          iv     i -- v           i?             i     i   
  L1M4_orf2#LINE/    790 AATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_86779863_8   4214 AGACATTTCTCAAAAGAAGACATACAAATGGCAAACAGGCACATGAATAG 4263
                                    v        i           v  i i         v  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_86779863_8   4264 GTGCTCAACATCATTGATCAT 4284
                         i            ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (121 / 61)
Gap_init rate = 0.02 (14 / 793), avg. gap size = 2.79 (39 / 14)  


3209 25.89 1.22 0.33  chr1_86801224_86803633     1018  1917 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86801224_8   1018 TGGAAACACATCTTATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 1067
                               v i   ii   i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86801224_8   1068 AACTATACTGCCAAAAGCAATCTACAAATTCAATGCAATTTCCATCAAAA 1117
                         ii v     v  v   vii       i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86801224_8   1118 TACCACCATCATTTTTCACAGGACTAGAAAAAACAATTCTGAAATCCACA 1167
                          v   v vv v     ii   i v v  v  ivii  i  i    i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_86801224_8   1168 TGTAACAAAAAAGAGTCCACA-TAGCCAAAGCAAGACTAAGCAAAAAGGA 1216
                           v  vviv  i iii   v -        i   vvi i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_86801224_8   1217 CAAATCTGAAGGCATCACATTACCCAATTTCAAGCTATACTGTAAGACTA 1266
                             vi  i   vv     i v           iviv    ii  ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_86801224_8   1267 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACAAAGACCAA 1316
                         i   v i   i    ii         i    ii    i  i v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_86801224_8   1317 TGGAACAGAATAAAGAACCCAGAAATAAACCCAAATACTTACAGCCAACT 1366
                              i     vi   ii               v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_86801224_8   1367 GATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGATACCCTTT 1416
                            i   i    i vviv   i v   vv i         i   vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_86801224_8   1417 TCAACAAATGGTGCTGGGATAACTGGCAAGCCAAATGTAGGAGAATGATA 1466
                                            i      vv ?   v   i ii       vi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_86801224_8   1467 TTGCATCCTCACCCCTCACCTTATATAAATATCAACTCAAGATGGATCAA 1516
                            v i  ii   i v    v    i   v  i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_86801224_8   1517 GGACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATGG 1566
                         i   i     v     v  i           v ii       v     i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_86801224_8   1567 GAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCAT-GACA-AACA 1614
                          ?iv  vi    vv   v    v        v i    v -  i -i   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_86801224_8   1615 ACCCCAAACCACATGCAGTAAAAACAAAGATAAATAGCTGGGACTTAAT- 1663
                         --  v   v    v   ii    iv   i   i   iv v      v  -
  L1M4_orf2#LINE/    601 --CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_86801224_8   1664 AAAACTAAAGAACTTTTGCACGGCAAAAGGAACAGTCAGCAGAGTAAACA 1713
                             i    -        ii vv    i iv  vi   iv i   i  v 
  L1M4_orf2#LINE/    649 AAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_86801224_8   1714 GACAACCCATAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAA 1763
                                  i   i           v  ii   vii   i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_86801224_8   1764 GGACTACTATCCAGAATCTACAATAAACTCAAACAAATTAGCAAGAAAAA 1813
                              vv          v  i  vi     vv    v i ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_86801224_8   1814 -----ACAATCCCATCAAAAAGTGTGCTAAGGACATGAACAAACAATTCT 1858
                         ----- i  i  v  i?    i  v  v     iv    i i   v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_86801224_8   1859 CAAAAGAAGATATATAAATGGCCAACAA--ACATGAAAAACTGCTCAACA 1906
                          v            i          i  --         iv         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_86801224_8   1907 TCACTAATGAT 1917
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  

1348 27.18 1.06 1.32  chr1_86801224_86803633     2032  2410 (0)  C L1M4_orf2#LINE/L1   (475)   433    56  

C chr1_86801224_8   2410 TACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCA 2361
                             v     iv i  i  i        i  v     i     iv v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

C chr1_86801224_8   2360 AGGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTCATATG 2313
                         ivvi i  i  ii     -   --- v  i  - iii    i        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCATATG 152

C chr1_86801224_8   2312 GAACCAAAAAAGAGCCCGAATCGCCAAGTCAATCCTAAGCCAAAAGAACA 2263
                            viiv  ii  v  v    v     iv     i i ivv i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

C chr1_86801224_8   2262 AAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACA 2213
                            i      vv       v  ii i      viv        i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

C chr1_86801224_8   2212 GTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGATCAATG 2163
                             i   i    ii         i iv ii ii  v             
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

C chr1_86801224_8   2162 GAACAGAAC--AGAGCCCTCAGAAATAATGCCACGTATCTACAACTATCT 2115
                            i    i--    i  --        vv   iii  i  iiiii vi 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATT 350

C chr1_86801224_8   2114 GATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTAT 2065
                            i  i     ivv  vv  i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

C chr1_86801224_8   2064 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCA 2032
                          i  i              v      v  ?   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

Transitions / transversions = 1.68 (64 / 38)
Gap_init rate = 0.01 (5 / 378), avg. gap size = 1.80 (9 / 5)  


3159 26.82 1.10 0.88  chr1_86834653_86841065     5015  5920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86834653_8   5015 TGGAAGAACATTCCATGCTCATGGATGGGAAGAATCAATATCGTGAAAAT 5064
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86834653_8   5065 GGCCATACTGCCCCAGGTAATTTATAGATTCAATGCCATCCTCATCAAGC 5114
                            v     v   v iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86834653_8   5115 TACCAATGACTTTCTTCACAGAATTGGAAAAAAGTACTTTAAAATTCATA 5164
                          v   iivi i  i  ii     v v  v  ivvv iii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_86834653_8   5165 TGGAACCAAAAAAGAACCTGCACTGCCAAGACAATCCTAAGCCAAAAGAA 5214
                              viiv  ii  v  v v iv     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_86834653_8   5215 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5264
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_86834653_8   5265 CAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGACCAA 5314
                               i   i    ii        ii iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_86834653_8   5315 TGGAACAGAACAGAGGCCTCAGAAATAATACTACACATCTACAACCATCT 5364
                              i    iv   ivii         vv i i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_86834653_8   5365 GATCTTTGACAAACCTGACAAAAACAAGCAATGGGGGAAGGAATC-CCTA 5413
                            i  i     ivv  v   i v  vv        i   -   v-i  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTT 399

  chr1_86834653_8   5414 TTTAATAAATGCTGCTGGGA-AATTGGCTAGCCATATGTAGAAAGCTAAA 5462
                           i  i     v        -  i   v  ?   i   i i  iiv i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_86834653_8   5463 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA 5512
                         ii    i    v   i     v              i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_86834653_8   5513 AAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5562
                         ?    i       v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_86834653_8   5563 GGCA-ATACCACTGAGGATACAGGCATGGGCAAGAACTTCATGACTAAAA 5611
                           ?i- v i vii v ivivii  i- i     viii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGA 598

  chr1_86834653_8   5612 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACGAATGGGATCTAATT 5661
                                    vvi          vv     v  ii   v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_86834653_8   5662 AAACTCAAGAGCTTCTGCACAGCAAAAGAAACACCATCAG---AGTGAAC 5708
                            v i  i i   i  ii vv    i  --   i    i---      v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGA--CACTATCAAGAAAGTGAAA 696

  chr1_86834653_8   5709 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAA--TATACCCATCTGAC 5756
                           i     i                 v       --i   i--      i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGAT 744

  chr1_86834653_8   5757 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGTA 5806
                           i  i  vi          v  i        ivv    v iv i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_86834653_8   5807 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5856
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_86834653_8   5857 TCTCAAAAGAAGACATTTATGAA--GCCAACCGACACATGAAAAAATGCT 5904
                             v        i  -- ii  --     ivii          i     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_86834653_8   5905 CTTCATCACTGGTCAT 5920
                          vv     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (150 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


3276 24.33 2.23 0.89  chr1_86846679_86849677     1611  2506 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86846679_8   1611 TGGAAAGATATTCCATGTTCAAGAATTGGAAGAATCAATATTCTTAAACT 1660
                                    i         v i         v i      v    iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86846679_8   1661 GTCCATACTACCAAAAGCAATCTACAGATTCAGTGCAATCACTATCAAAA 1710
                          v v     v  v   vii             ii      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86846679_8   1711 TATCAACAACATTCTTCACAGAAATAGAAAAAA-AATCCTAAAATTTATA 1759
                          vi  i vi v  i  ii       v  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_86846679_8   1760 TGAAACCACAAAAGACCCAGAATACTCACGGTAATCCTGAGCAAAAAGTA 1809
                           i  vii   ii           vi  viii    i   iv  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_86846679_8   1810 CAAAATTGGAAGAATCACATTACCTGACTTCAAA-TGTACTACAGAGCTA 1858
                             i     i  v     i v  ii i      -iv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_86846679_8   1859 CAGTACCCAAAATAACATGGTACTGGCATAACAACAGACATGTAGACCAA 1908
                              vi   i i iii              vi i      i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_86846679_8   1909 CAAAATGGAACAGTGAATCCACAAATAAATCCATACATCTACAGTGAACT 1958
                         iii   i   iv v  i    v       i        i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_86846679_8   1959 ATTTTTTGACAAAAATACCAAGAACATACATTTAGGAAAGGGCAGTCTT- 2007
                         iv    i     iii i      v   v  v vi      iii      -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_86846679_8   2008 -CAATAAATGGTGCTGGGAAAACTGGATATCTATAC-------AATGAAA 2049
                         -   i              v         ? i i i-------      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_86846679_8   2050 CTAGACCCCTAACTCTTACCATAGACGAAA-CCAAATAAAAATGTATTAA 2098
                         i i        v   vi      v  i   -ii  v v      v  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_86846679_8   2099 AGACTTATATCTAATACCCCAAACTATGAAACTACTGAAAGAAAACAT-T 2147
                             i  v  v   v v iv       i     vi ii          -v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_86846679_8   2148 GTGCAAATTCTCCAGGACATTAGACTGAGCAAAGATTTCTTGAGTAATAC 2197
                          ? i    -  i iv   v  i ii ii    v i      iii  vv  
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_86846679_8   2198 CCCACAAGCTCAGGCAACCAAAGCAAACATGGACAAAT-GG----TATCA 2242
                         v   v    v  i     v    v   v  i  i    -  ----i    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_86846679_8   2243 AACCAAGTTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGA 2292
                           ----i       -   i  ii vv       v  v     v       
  L1M4_orf2#LINE/    650 AA----ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_86846679_8   2293 AG-GACAACCCACTGAATAGGAAAAAATATTTGCAAATTATCCATCTAAC 2341
                          i-          v    i   i               i  vi    i i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_86846679_8   2342 AAGAAATTAATAACCAGAATGCATAAGGAGCCCAAACAACTCAACAGGAA 2391
                            ii i vi  v       ii    i  i i vv         i iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_86846679_8   2392 AAA-ATATAATAATCCAACCTAAAAACTGTGCAAAAGATCTCAATAGACA 2440
                            - i -     i    ii?     -  v     i   i v        
  L1M4_orf2#LINE/    795 AAAGACA-AATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chr1_86846679_8   2441 TTTCTCAAAAGAAGACATACAAATGGCAAGCAGGTATATGAAAAGGTACT 2490
                               v        i           v ii i i i        i i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_86846679_8   2491 CAACATCACTGATCAT 2506
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (138 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.87 (28 / 15)  


3305 26.87 0.44 0.44  chr1_86857037_86863315.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_86857037_8   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_86857037_8   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_86857037_8   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_86857037_8   5029 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_86857037_8   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_86857037_8   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_86857037_8   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5226
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_86857037_8   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_86857037_8   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_86857037_8   5327 GAAACTGGATCTCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i i  v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_86857037_8   5377 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_86857037_8   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_86857037_8   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_86857037_8   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_86857037_8   5577 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_86857037_8   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_86857037_8   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_86857037_8   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_86857037_8   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2209 25.35 2.83 3.54  chr1_86943481_86945181.rev      505  1210 (491)    L1M4_orf2#LINE/L1      208   908 (0)  

  chr1_86943481_8    505 GGAGGCATCAGACTACCCAAGTTCAAACTGTACTCTAAAGCTACAATAAA 554
                              vv   v   v     v      viv    vi         i   v
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_86943481_8    555 CAAAACAGCATTCTACTGGTACAAGAACAGACACATAGACCAATGGAACA 604
                            i    ii vv      i i   i i     i     i        i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_86943481_8    605 GAATAGGGAACCCAGAAATAAAGCTGCACATCTACCACTATCTGATCTTC 654
                             v i  ii           v iii    i  iviii vi    i   
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_86943481_8    655 AACAAAGTTGACAAAAATAAGCAATGGGGAAAGAACTCCCTATTCAATAA 704
                         i    i v  v   i vi vv              ivvi  v     i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_86943481_8    705 ATGGTGCTGGGGATAGCTGGCTAGTTA--TGCAGAAGAATGAAACTGGAC 752
                                    - i i    v  ?ii --    i         ii     
  L1M4_orf2#LINE/    408 ATGGTGCTGGG-ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_86943481_8    753 CCTTTCCTTTCACCATATACAAACATTAACTCAAGATGGATTAAAGATTT 802
                           i v   iv             v          i      i ?   ii 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_86943481_8    803 AAATATAAGACCTCAATCTATATTTTATAGATTCTATATTCTAGAATTCT 852
                             i     v  v  v     ------ i i   -------------- 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATA------AAACTCT--------------T 536

  chr1_86943481_8    853 AGAAGGAAACCTAGGAA-ACACCATTCTGGACATCAGCCTTGGGAAAGAA 901
                              i    v    ?i- v i -   vv   v ii v-  i  v  vii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGG 584

  chr1_86943481_8    902 TTTCTGAG-TAAGGTCTCAAAA--ATAATTGCAACAAAACAAAAAATTGA 948
                              v  -  v iivi     -- i  --         v       v  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGA 632

  chr1_86943481_8    949 CAAGTGGGACCTAGTTAAACAAAAGAGGTTTTGAACAACAAAATAAATTA 998
                         i  i v    i vi i   vvv  i iv     vi vv    iv v i  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_86943481_8    999 TCAATAGAGTAAATAGATAACTTATAGAATGGGAGAAAATATTCATAAAC 1048
                             v i   i  v   i   ii i                  iii   i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_86943481_8   1049 TGTGCAGCCAACAAAGGTCC-ATATCCAGAATCTATAAGGAATTTACACA 1097
                         ii ii v ii i  i  v i-i          v     i   i ivi   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_86943481_8   1098 ATTCAACAGGCAAAAAACAAATAACCCCATTAAAAAGTGGACAAAAGACA 1147
                          i    i ivv    i           v   ?    i   i    i  iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_86943481_8   1148 TGAACAAACACTTCTGTAAAGAAGACATACAAAT-------------ATG 1184
                             i i   i    vi        i        -------------   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_86943481_8   1185 AAAAAATGGTCAACATCACTAGTCAT 1210
                             i   v         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (109 / 66)
Gap_init rate = 0.02 (12 / 701), avg. gap size = 3.75 (45 / 12)  


2444 25.23 5.97 4.28  chr1_87135848_87138883     1667  2554 (482)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_87135848_8   1667 AGATATTCCATGTTCATGCTTAGGCAGACTCAATATTGTTAAGATGTCAA 1716
                               i           vv v  v     i               v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_87135848_8   1717 GTTCTTCCCAACGTGATCTATAGATTCAGTGTAATT--TAATTCAGAATC 1764
                         - v  i     vv       i       ii i   i--  --   i    
  L1M4_orf2#LINE/     56 -TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA--TCAAAATC 102

  chr1_87135848_8   1765 GCAGCAGGTTATTTTGTGGCTATCAGCAAAGTTATTCTAAAGTTTATATT 1814
                         v    v vi v     ii vv  iii   iv v  i     i  i    v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_87135848_8   1815 G----GTCAGAGACCTAGACTAGGCAACACAATATT---ATAGGAGAACA 1857
                          ---- iv  i    i   v   v   v     v  --- v  i      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_87135848_8   1858 AAGTCAGA---CTGACACTATTGTACTTAAAGACTTAT---GAAGCCACA 1901
                             ii  ---  v     viivv i  v  i     i---i    i   
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_87135848_8   1902 GTAATCAAGACATTGTGGTATTGTTGAAAGAATAAA----TAGATCATTG 1947
                                     v       i  viiv   i   i ----       v  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_87135848_8   1948 AAGCAAAAT----AGCGCATAGGTAGACC---ACGAATATAGTAAATTGA 1990
                         i ii i   ----  iv  v ii  i   ---  ivv   i  v      
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_87135848_8   1991 TCCTTGACAAAGGAGCAGAGAC-----AA-GGAAAAACGGTAATTTTTTC 2034
                          ii i     i  v  vi    -----  -  ii   vii  i i     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_87135848_8   2035 CACAAGTGGCACTGGAATAACAGGATATCTCATTCCCCTCCACGCCACCA 2084
                         v    i   ii    i i   v     ? -  --------  i  -----
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKC-CA--------CATGC----- 438

  chr1_87135848_8   2085 AAAAAAAAAAAAAAAAGAATCTTGACACAGACTTTATACTTTTCACAAAA 2134
                         --------    i  v   vi v   v vv  i i i  iv vi      
  L1M4_orf2#LINE/    439 --------AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_87135848_8   2135 ACTACCTCAGAGTGAATTGTAGCCTTTAATGTTAAGCAC-AAAAATGTAA 2183
                          i  v    i i  i  ii?  v i v     -   vi -    v i   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAA 529

  chr1_87135848_8   2184 AACTCCTAGAAGATAATAAAGGAGAAAATCTG-GTGACCTTAGGTTTGGT 2232
                              i       v  i v   ? v      v-        i    v  i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_87135848_8   2233 GATAACTTTTTAGACAAAACACCAAAAGCATACTCCATGAAAGAAAGACG 2282
                         i  iii  i     i vi            i vv v ii       i -i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-A 628

  chr1_87135848_8   2283 TTGTTAAGTTGGACTTCGTTAAAAT-AAAATATGTACGTTTTGTG----- 2326
                          v v   i         i i     -    -----  -       -----
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAA-----AC-TTTTGTGCTTCA 672

  chr1_87135848_8   2327 AAAGTTACTGTTTAGGGACTAAAGAGATAAGTCACAGACTGGGAGAAAAT 2376
                           i vi   i iv  ii v i  i   i  vi      v           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_87135848_8   2377 CTTTGGAAAATACATACCTGAAAAAGAACTGGCATCCAAAAATATTCAGA 2426
                         v    v   vi i   i    v  i i   v i     i  -   vi i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA-TATATAAA 771

  chr1_87135848_8   2427 GAACCCTTATAACTCAATAATAAA----TGAACAACACAATT---AAATG 2469
                             i    i              ----ii  i   v     ---     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_87135848_8   2470 GACAAAAAAATCTGAAC------CTCCTTGGAGAAGATATACAGATGGCA 2513
                          i    ii - i    i------i  iiiii            i     v
  L1M4_orf2#LINE/    822 GGCAAAGGA-TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_87135848_8   2514 AGCAAGCATTTCAAAAGATGTTTCCACATATCATTAGAGAA 2554
                          ii     iv v        i --  - i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCT--CA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (140 / 81)
Gap_init rate = 0.03 (30 / 903), avg. gap size = 3.03 (91 / 30)  


2424 22.50 8.52 5.91  chr1_87224419_87228427.rev     2653  3532 (477)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_87224419_8   2653 AGATATGCCACATTCATG-ATTGAAAGACT----ACTGTTAAGATGTCAA 2697
                               v   ii      -    i      ---- i          v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_87224419_8   2698 TTCTCCAAAAATTTATATACAGATGCCATGCAATCCCAATCAAAATCCCA 2747
                          v    vv     v  v       v v i        v            
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_87224419_8   2748 GGACACTTTTTGGTATGAATTGACCAACTAAT------------ATGGAA 2785
                          vvvv      v i vi       v i  i  ------------      
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_87224419_8   2786 ATGTAAATAATTTGGAATAGGCAAAACAA-ATTGAAAAATAAGAA---AA 2831
                            i  ivi iiii      v        -v        v     --- i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_87224419_8   2832 TTGAAGGATTTACACCACTTTATCTCAAGACTTGTTATCAAGTTACAGTA 2881
                            i    i i    iv iiv  i    i    ii  iv   i       
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_87224419_8   2882 ATCCAGACAGTATAGTACTGGCATGAAGACAGACATCCAGATCAATGGAA 2931
                            v       i i          i i  i      vi            
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_87224419_8   2932 CAGAATAGTGAATCCAGAAATATAACTATACAAATATGATCAATTGATTT 2981
                         i     v v  i          v v i     vv    i           
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_87224419_8   2982 TAGAAAAACTTGGATACAAATATGATCAATTGATTTTAGAAAAACTTGGT 3031
                          v  v  ----  i i v  ---  i  ----------------------
  L1M4_orf2#LINE/    356 TCGACAA----GGGTGCCAA---GACCA---------------------- 376

  chr1_87224419_8   3032 AGGATAGTTCAATGAAGAAAATGATCACCTCTTCAACAAATAGTATGGGA 3081
                         -------       ii    i-i  vii  i          i  iiv  i
  L1M4_orf2#LINE/    377 -------TTCAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_87224419_8   3082 ACAACTGGATAGCCATTTTTTTAAGG--GAATCTTCATTCTTTCTTCATT 3129
                                    ?   iv vivv   i--   vi vv ii i ----- --
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT-----A-- 461

  chr1_87224419_8   3130 CTTCACATCATATACAAAAATGAATTTAAAATGAATCACAGACCTAAATA 3179
                          i     i             v  i i      i    ?          i
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_87224419_8   3180 TAAGAGCTAAAATTATAAAACTTATAGAAGAAA-CA---------ATCCT 3219
                                     i         iv         -  ---------   i 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_87224419_8   3220 AGTAATTTTAGGTTTGGCAAAGATTTCTTAAATATGACACAGTAAACAAG 3269
                         v  i ii  i    v     v i       i         viv  i  vi
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_87224419_8   3270 AACTACAAAAACAAACATCAATATAGTGGACTTCACTGAAATTAAAA--- 3316
                          i v      iv   v  vi   v v         iii         ---
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_87224419_8   3317 --------------GATAC-----AGAAA-TGAAAAGGAAAGCCACATAA 3346
                         --------------  i  -----     -       iv  v     v  
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_87224419_8   3347 -AGGAAAAAA-ATTTGTGAAATGTATAGCCAACAAAAGATTTGTATC--- 3391
                         -i   i    -     ii  vii    v ii i  ii  i       ---
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_87224419_8   3392 -ATATCAACAAAAAATGTGTATCTTACAACC---TAATGAGAAAATAGCC 3437
                         -    -- i   i  i-----         i---    i i  i i ivi
  L1M4_orf2#LINE/    762 AATAT--ATAAAGAAC-----TCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_87224419_8   3438 AGTCCATTTTTTTAAATGAACTAAGGATTTG----GACACTTCCCCAAAA 3483
                          ii   v  ?vv-     ii v         ----    i   i     i
  L1M4_orf2#LINE/    805 AACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_87224419_8   3484 AAGAGATAT-----GCAGATAAGAAGATGAAA-GACGTTTGTCATTAGAG 3527
                             v   i-----  vi     v v      -  i i iiv   i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_87224419_8   3528 AAAAT 3532
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.67 (122 / 73)
Gap_init rate = 0.03 (27 / 903), avg. gap size = 4.70 (127 / 27)  


2719 17.40 7.02 4.24  chr1_87436483_87438090.rev      434  1117 (491)    L1M4_orf2#LINE/L1      206   908 (0)  

  chr1_87436483_8    434 TTGAAGAACATGCTCAAACTTCCTGAGCCTTTAAA--TTACTAGATACTA 481
                            i  i  ----   v      ii --i  i   --      v ---- 
  L1M4_orf2#LINE/    206 TTGGAGGAC----TCACACTTCCCAA--TTTCAAAACTTACTACA----A 245

  chr1_87436483_8    482 ACCTTCCTCACATAGTTCCTATAAAGAC--TAAGGCACTGGCATT-GGAT 528
                          v  ------- i   v---  v     -- iv  i        v-    
  L1M4_orf2#LINE/    246 AGCT-------ACAGTA---ATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_87436483_8    529 AGACATACAGGTCAAAGGACTAGAATTGAGAGTCCAGAAATAAAACCTTG 578
                                i  i    v   v                        v  v i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_87436483_8    579 CCTTTTTTATGGTCAATTGGTTTTCTATAAGGATGCTGAGAC-----AAT 623
                          v   ---           i     v i    i   ii    -----   
  L1M4_orf2#LINE/    336 CATTT---ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_87436483_8    624 ------------------TCAACAAAGCATGCTGAGTTAACTAAATATCA 655
                         ------------------        vvi     i vi    ii   ? v
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_87436483_8    656 ACCTGCTTTGAAAAGAAATAACTTAGACCCGTACTTCACATTATATACAA 705
                           v   ----       vv  v  i     v   i     ii        
  L1M4_orf2#LINE/    433 ACATGC----AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_87436483_8    706 AAATTAACTCAAAGTGAGTCGTAGGCCTAAATATAAGAGCTAAA-CTATA 754
                                      i  ii  i?  i       i           -     
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_87436483_8    755 AAACTTTTAAAAGAAGACATAGGAGTAAACAGTGACAACCTTGGATTGGA 804
                              i   i     i       ?     ivv viii       i  i i
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_87436483_8    805 CAATGATTTCTTAGACATGACATAAAAAGCACTAGTGACAAAATAAGAAA 854
                              i         i      iv        v  ii      v  i   
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_87436483_8    855 TAGTTAAATTGGATTTCATCAAAATTAAAGAATTTTGTGCTTCAAAAGAC 904
                            v         i               i v              i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_87436483_8    905 ACCACCAAG---GTGAAAA--------ACAAAATGTAAGAAAATATTTGC 943
                           i i    ---       --------   i    vi             
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_87436483_8    944 AAAGTATTCATCTAATAAGGGATTTGTATCCAGCATATACAAAGAACACT 993
                            vi  vi    i        i          v     i       v  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_87436483_8    994 TACAATT------TAAAAATTTAAA-AAACCAATTACGAAATAGGCAAAG 1036
                              i ------      vvi   -  v      ?vi    i       
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_87436483_8   1037 GCTTAGAATAGACAATTGTCCAAAAAGAAAACCCACAGATGGCCAATA-G 1085
                          v  v         v  v      --   i ivi   i          - 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAA--GAAGATATACAAATGGCCAATAAG 876

  chr1_87436483_8   1086 CACATGAAAGGATGTTCAACATTATTGGTATT 1117
                                  i    i       i ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (71 / 44)
Gap_init rate = 0.03 (19 / 703), avg. gap size = 4.05 (77 / 19)  

 955 23.11 0.00 0.00  chr1_87436483_87438090.rev     1205  1442 (166)    L1M4_orf2#LINE/L1      671   908 (0)  

  chr1_87436483_8   1205 CAAAAGAAATAATCAGCAGAGTAAACAGAAAACCCACAGAGTGGGAGAAA 1254
                             i  v iv    iv i   i  v   v          i         
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_87436483_8   1255 ATATTCATAAACTATGCATCTGACAAAGGACTAATATCCAAAATCTACAA 1304
                              iii   ii  ii      i  i     vi      i   v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_87436483_8   1305 GGAATTCAAACAAATCAGCAAGAAAAAAACAAATAGTTCTATCAAAAAGT 1354
                         i   i  vv    v   ii  v     i       iii v  i?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_87436483_8   1355 GGGCAAAGGACATGAATAAATAATTCTCAAAAGAAGATACACAAATGGCC 1404
                                   iv      i i v     v          i          
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_87436483_8   1405 AATGAACATACGCAAAAATGTTCAACATCACTAATTAT 1442
                            i i  i i v   i   i         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (38 / 16)
Gap_init rate = 0.00 (0 / 238), avg. gap size = 0.00 (0 / 0)  


3089 26.62 1.10 1.21  chr1_87542549_87545307.rev     1360  2268 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_87542549_8   1360 TGGAAAAACATTCCATGCTCATGGATAGGAAGAACGAGTATCGTGAAAAT 1409
                               i i  i     i        v      viv i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_87542549_8   1410 GGCCATACTGCCCAAAGTAATTTATAGAATCAATGCTATCCCCATCA--- 1456
                            v     v      v i  i  i   v    i  v     i    ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_87542549_8   1457 TCTACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTC 1505
                           --   vivi i  i  ii     v v  v  i-  - iii    v   
  L1M4_orf2#LINE/    101 TC--CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr1_87542549_8   1506 ATATGGAACCAAAAAAGAGTCCATATAGCCAAGACAATCCTAAGCCAAAA 1555
                                 viiv  ii  vi viv        i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_87542549_8   1556 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 1605
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_87542549_8   1606 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAAGAGATATATAGAC 1655
                                  i   i    ii         i iv ii v   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_87542549_8   1656 CAATGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACAACCA 1705
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_87542549_8   1706 TCTGATCTTTGACAAACCTGACAAAAACAAGCAACGGGGAAAGGAT--TC 1753
                         vi    i  i     ivv  v   i v  vv   i        i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_87542549_8   1754 CTTATTTAATAAATGGTGTTGAGAAAACTGGTTAGCCATATGCAGAAAAC 1803
                         i  -- i  i        i  i  v      v  ?   i     i  i v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_87542549_8   1804 TGAAACTGGACCCCTTCCTTAGGCCTTATAAGAAAATTAATTTAAGACGC 1853
                             ii         v   i vi  v    vi        i i  i i v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_87542549_8   1854 ATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1903
                           i ?    i           v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_87542549_8   1904 CCTAGCCAATAAA-ATGCAGGACATAGGCATGGGAAAGGACTTCATGACT 1952
                          v   v?i-    -v v iv   v v  vv i  v  v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_87542549_8   1953 AAAACACCAAAAGCAATGGCAACAAAAGCCGAAATTGACAAATGGGATCT 2002
                          vi            vvi          vvi    v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_87542549_8   2003 AATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCAG---AGTGA 2049
                         v  i   v v  i i   i  ii vv    i  v       i---     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_87542549_8   2050 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTATCCATCTGAC 2099
                          v  i     i                 v   i   vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_87542549_8   2100 AAAGGGCTAATATCCAGAATCCACAAGGAACTTAAAAAAATTTACAAGAA 2149
                           i  i  vi          vi i  i     ivv v  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_87542549_8   2150 AAAAACAAACAACTCAACCCCGTCAAAAAGTGAGCAAATGATATTAGCAG 2199
                            i     i   i   ----- i?    i  i     v   v v ii  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAA-----TTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_87542549_8   2200 ACACTTCTCAAAAGAAGACATTTATGTGGCCAATAAACATATGAAAAGAA 2249
                            i     v        i  vi vi          i  i         v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_87542549_8   2250 GCTCATCATCACTGGTCAT 2268
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


3297 26.51 0.66 0.77  chr1_87552658_87557498.rev     3442  4350 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_87552658_8   3442 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTATTAAAAT 3491
                               i i  i     i        v      v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_87552658_8   3492 GGCCATACTACCCAAACCAATTTAGAAATTCAATGCTATTCCTATCAAAC 3541
                            v     v      iii  i  v i      i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_87552658_8   3542 TACCAATGACATTTTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 3590
                          v   iivi v     ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_87552658_8   3591 ATGGAACCAAAAAAGAGTGTGAATAGCCAAGGCAATCCTAAGCAGAAAGA 3640
                               viiv  ii  vivv          ii     i i iv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_87552658_8   3641 ACAAAACTGGAGGCATCATGTTACCTGACTTCAAACTATACTACAAGGAT 3690
                              ii      vv   iii v  ii i      viv        i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_87552658_8   3691 ACAGTAATTAAAACAGCTTGGTACTGGTACAAAAACAGATACATAGCCCA 3740
                                 i  i    iv         i i  ii i   i i    vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_87552658_8   3741 ATGGAACATAAAAGAGGTCCCAGAAATAAGGCCACATACCTACAACCATC 3790
                               i v  vv   ivi          iv   i i ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_87552658_8   3791 TAATCTTTGGCAAAGCTGACAAAAAACAAGCAATGGGGAAAGAACTCCCT 3840
                          i  i  i i   i v  v   i v-  vv              ivvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCT 398

  chr1_87552658_8   3841 ATTCAATAAATGGTGCTGGGGTAACTGACTAGTCATATGCAAAAGATTGA 3890
                         v     i             ii     iv  ?i  i          v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_87552658_8   3891 AATTGGACCCCTTCCTTACACCATGTACAAAAATCAACTCAAGATGGATT 3940
                          i          v   i       i         i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_87552658_8   3941 AAAGACTTAAAGGTAAAACCCAAAATCATAAAAACCCTGGAAGACAACCT 3990
                          ?    i    v    i v i    ii      vi i i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_87552658_8   3991 AAGC---AATGCCATTCTGGACACAGGAATGGGCAAAGATTTCATGACGA 4037
                          i ?---   -- -   vv   viv  iv i     v i    v iivv 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_87552658_8   4038 AGATGCCAAAAGCAATCA--TAACAAAAGCAAAAATTTACAAATGGGATC 4085
                         v  ii         --  --i        v      vv i    v   ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_87552658_8   4086 TGATTAAACTTAAGAGCTTCTGCATTGTAAAAGAAACTATCAACAGAGTT 4135
                          v  i   v    i i   i  iii vi   i  v        v i   v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_87552658_8   4136 AATAGAAAACCTACAAAATGGGAGGAAATATTTGCAAACTATGCATCTGG 4185
                           v   v    i   i        i             ii  ii     i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_87552658_8   4186 CAAAGGTCTAATATCCAGCATTTATAAGGAACTTAAACAAATGTACAAGA 4235
                         i  i  v  vi       v  v     i     ivv    v vv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_87552658_8   4236 AAAAAACAAACAGCCCCATTAAAAGGTGGGCAAAGAACATGAACAGACAC 4285
                             i     i i   v   ?   ii         i iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_87552658_8   4286 TTTTCAAAAGAAGACATACATGCGGCCAACAAGCATATGTAAAAAAGCTC 4335
                           i  v        i     vii      i     i   v   i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_87552658_8   4336 AATATCATTGATAAT 4350
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (150 / 87)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3392 25.44 1.10 1.10  chr1_87718503_87722751.rev     2850  3757 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_87718503_8   2850 TGGAAAGATATTTCATGTTCATGGATTGAAAGACTCAATATCATTAAAAT 2899
                                    ii               i      i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_87718503_8   2900 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCATTCCCTATCAAAA 2949
                          v v     v      vii              i   v            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_87718503_8   2950 TACCAATGACATTCTTCACA-AAACTACAAAAAAAAAAAAAATCCTAAGA 2998
                          v   iivi v  i  ii  -   i i------ v  ivvi       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG------ACAAGCTGATCCTAAAA 144

  chr1_87718503_8   2999 CTTATACAGAACCACAAAAGATCCAGAATACTCAAAACTATCCTGAACAG 3048
                         i i   ii   vii   ii  i        vi      v   i    v i
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_87718503_8   3049 AGAGAACAAAACTGGAGAAATCACATTACTTGACTTCAGG-TATACTACA 3097
                         ii        ii     i v     i v iii i    ii-iv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_87718503_8   3098 GAGCTATAGTAACTGAAACAGCATGGTCCTGACATAAAAACAGACACAAA 3147
                         i     i     iii i    ii    v   i     ii i     i v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_87718503_8   3148 GACCAATGGAACAGGATAGAGAACCCAGAAACAAATCCATACATCTACAG 3197
                           i        i  i  v    ii       i   i        i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_87718503_8   3198 TGAACTCATTTTTGACAAAGGTGTCAAGAACATACATTGGGGAAAGGACA 3247
                          v  i v     i     i    i     v   v  v         i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_87718503_8   3248 GTTTCTTCAATAAATGGTACTGGAAAAAACTGGATAACCATATGCAAAGG 3297
                           i i     i       i    i v  -       ?   i       i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAG 443

  chr1_87718503_8   3298 AATGAAACTAGGTCCCTATCTCTCACTACATACAAAAATGAAAACAAA-T 3346
                               ii i ii     i   v   i i          v  vv    - 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_87718503_8   3347 GGATTAAAAACTTAAGTCTAACACCTGAAGCTATGAAACTACTAAAAGAA 3396
                             i ? i  i   i v   v v  i  i    i     vi  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_87718503_8   3397 AACTTTAAGAA-AACTCTCCAGGACATTGGTCTGGGCAGAAATCTCTCAG 3445
                            v - i ?i-  v   i iv   v    vi i    ivii i   i  
  L1M4_orf2#LINE/    544 AACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_87718503_8   3446 GTAATACCCTACAAGCACAAATAACCAAAGCAAAAATTGACAAACAGGGC 3495
                         i  vv  v i v        ii   v    v      v  i   iv  i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_87718503_8   3496 CACATCAAG-TTAAATAGCTTCTGCACAGCAACAGAAACAATCAACAAAA 3544
                         iv      i-     - i   i  ii vv   vi  v  v     v   i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_87718503_8   3545 TGAAGAGACAACCCATAGATTAGGAGAAAATATTTGTAAACTACCCATCT 3594
                             i          i   v i              i   ii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_87718503_8   3595 GACAGGGGATTAATAATCAGAATATATAAGTAGCT---GAAAC--AATAG 3639
                           i i    i vi  vi            iv i  ---iv   --    i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_87718503_8   3640 GAAAAAAATCTACTCATCTGATTAAAAACTGAGCAAAGGATCTGAATAGA 3689
                         v     i - v v v i ii   ?    v  i         i        
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_87718503_8   3690 TATTTCTTAAAAGAAGGTATACAAGTGGCAAACAAGTATATGAAAAAGTG 3739
                         i      iv       i       i    v  i   i i       ii  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_87718503_8   3740 CTAAACATCAGTGATAAT 3757
                           v       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (157 / 70)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


1928 24.77 2.02 4.52  chr1_87758671_87760863.rev      502  1143 (1050)    L1M4_orf2#LINE/L1       35   660 (248)  

  chr1_87758671_8    502 TTAATATTATTCAGATATTAATTCTCCCTCAAACTGATCTAGAGATTCAA 551
                                 i  v    ivi   v     -    i       v        
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCC-CAAATTGATCTACAGATTCAA 83

  chr1_87758671_8    552 TAAAATCACAGTCAAATATGCCTTCATTGGCAAGAAAAAGCCTTTTTTTT 601
                         iiv    v vi     -  v  ------i  v-------         v-
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAA-ATCCC------AGCT-------GCCTTTTTTG- 118

  chr1_87758671_8    602 TCAGAAGTTGACATGTTGATTCTAAAATGTATATGATAATA----GAACC 647
                         -     i      v i    i       vi     iv   i---- i   
  L1M4_orf2#LINE/    119 -CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr1_87758671_8    648 TAAAAGAGACAAAACAATCTTGAAAAAGAA-AATAAAGGATTTG----AC 692
                         i i  v  v                     -  i    ---   ----  
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG---TTGGAGGAC 214

  chr1_87758671_8    693 TTGT--CTGCTGATTTGAAGATTTACTCTAAAGCTACAGTAATCAAGACT 740
                          iii--i v ii    v  i i     vi                    v
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_87758671_8    741 GTGTGATAATGATGAAAGGACAGACAAATAGGTCAATGCAACAGAATGAA 790
                              i  v  iiiv     i     v    i      v  i     vi 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_87758671_8    791 GAGTTCCAAAAAGAGACCCACACAAACCCGCTCAATTGTTTTTTAGCAAA 840
                             -   i   v i     i   vvivi v       v    iii   i
  L1M4_orf2#LINE/    315 GAGT-CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_87758671_8    841 GATGCCAAGGCAAGTCAATGGGAAAAGGAAAGTCTTTTCAAAAACTGGTG 890
                          i       i v v        i    i v           v  v     
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_87758671_8    891 TTGAAACACCTAAATATCTGTATGAAAAAGTAAAATGAACATTGATCACA 940
                         i  ii   v  ii   ? iii   v     ---      vv v  i v v
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAG---AATGAAGTTGGACCCCT 460

  chr1_87758671_8    941 ACCTTACACAATGCACAAATAATAGTCATTTGAGATGGATCATAAACATA 990
                             i    v  ii     -   -- v i ii i        ? i  v  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAA-AAT--TAACTCAAAATGGATCAWAGACCTA 507

  chr1_87758671_8    991 ACCATGAAAGCTGAAACTATAAATTTTCTAAATTAAAATGTGGAAGAATA 1040
                          vii i i    i          vi ii  i vv    ii i i? v v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_87758671_8   1041 TCTTCATGACTTTCATGTCCAGAAAATAATATTTTAGGGAGGATACAAAA 1090
                              i    i  vi-  i-  iv   ii v i    iv v  i  v   
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGG-GTT-AGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_87758671_8   1091 AGCACTAATCATAAAAGAAAAA-T-GATACATTCAACTTTATAAAAAGTA 1138
                              v iiv i          - -    v   vi    i  v    v  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_87758671_8   1139 AAAAC 1143
                              
  L1M4_orf2#LINE/    656 AAAAC 660

Transitions / transversions = 1.48 (93 / 63)
Gap_init rate = 0.03 (18 / 626), avg. gap size = 2.33 (42 / 18)  

 518 21.43 13.10 1.19  chr1_87758671_87760863.rev     1535  1702 (491)    L1M4_orf2#LINE/L1      721   908 (0)  

  chr1_87758671_8   1535 ATGTGTGCATGTGCGTGCATCTGGAAAAAGACTTGTATCCAGCATATATA 1584
                           i v    vi - i ii     iv  ii             v       
  L1M4_orf2#LINE/    721 ATATTTGCAAAT-CATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_87758671_8   1585 AAATAGTCTTACAATTTAATAATAA---GACAAATCATGCA--TTAAAAA 1629
                           iv v        i i        ---       v iv  -- ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_87758671_8   1630 TAG-CAGAAAGATTTGAACAGACACT----------------ACAAAAGT 1662
                          i -  -  i        i     i ----------------     v v
  L1M4_orf2#LINE/    820 TGGGCA-AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_87758671_8   1663 TCAGTGAGTACCAGAAAAGGTGTTTAACATCACTAGTCAT 1702
                         i  i i  i  vv      i  i i       ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (23 / 12)
Gap_init rate = 0.03 (6 / 188), avg. gap size = 4.00 (24 / 6)  


3735 22.81 1.33 0.78  chr1_87782444_87784706.rev      893  1795 (468)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_87782444_8    893 TGGAAGAATAGCCCTGTGTTCAAGGATCAGAAGAATTAATATTGTTAAAA 942
                              ii   v   -i      v    ii     v             i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_87782444_8    943 TGTCCATATTACCCAAAGTGATCTATAGATTTAAGTCAATCCCTA-CAAA 991
                           v v   i v      v       i     i  vv         -    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_87782444_8    992 ATTTCCAAATTTGTTTTTCACAGAACTAGAAAAAACAGTTGTAAAATTCA 1041
                           i-   iv viv     ii     v v  v  iviii iv         
  L1M4_orf2#LINE/    100 ATC-CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_87782444_8   1042 TGTGGAATCATAAAAGACTCCAAATAGCCAAAGCAATCCTGAGCAAAAAG 1091
                          i     viii  ii   i vi          i     i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_87782444_8   1092 AACAAAGCAGGAGGCATCACACTACCTGATTTTAAAATCTACTGCAAGGC 1141
                                iv     vv       v  ii    i    ii    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_87782444_8   1142 CATAGTAATCAAAACAGCATGGCATTGTCATAAAAATAGACAGCTAGACC 1191
                         i i         i    ii   i i  v     ii       vv    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_87782444_8   1192 AATGGAACAAAATAGAAAGTCCATAAATAAATTCACAC-----TGGTCAA 1236
                                i i   v  i      v       ii  i  -----       
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_87782444_8   1237 TGGATTTTTGACAATGTGACCAAGAACATACAATGGTGAAAGGACAGTCT 1286
                          v      i     v vvi      v   v      v     i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_87782444_8   1287 CTTCAATAA-TGGTGTTGGGAAAACTGGATATCCACATGCAGAAGAATAA 1335
                         i     i  -     i     v         ?         i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_87782444_8   1336 AATCAAATCATTATCTCACACTATATAGAAAAATAAACTCAAAATGGATT 1385
                          i iii i vi  i       i     v      v              i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_87782444_8   1386 AAAGGCTTAAATATAAGATCTGAAACTGTAAAACTACTCAAAGAAAACAT 1435
                          ?  i i     i     v  i     i       vi vi          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_87782444_8   1436 GGGAGAAAAGCTCCATGCTGTTGGTCTGGGCAATACTTTCT-GGCTATGA 1484
                         i  ? v   v  i i  viv    vi i      iv     -i v     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_87782444_8   1485 CCCCAAAAGCACGGGCAACAAAAGCAAAAATAGAGAAATGGGATTATGTC 1534
                          v          ii          v         v    v   i vii  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_87782444_8   1535 AAA-CTAAAAATATTTTCACAGCAAAGGGAACAATCAACAGAGTGAAAAG 1583
                            -i      iv   vii vv      iv  v     v i         
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_87782444_8   1584 ACAGCATACAGAATAGGAGAAAACATTTGTAAACCATACATCAGAGAAGG 1633
                            i vi       i        i     i   i    i   v  v    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_87782444_8   1634 AGTTAATATCCAAAGCATATAAGGAACTCAAACAACTCAATAGCAAGAAA 1683
                         iii vi      i ii      i      vv           ii  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_87782444_8   1684 ACAAATAATCCAATTTAAAAATGGGGAAAGGACCTGAAAAGACACTTCTC 1733
                                 i      ?         v      ii    v     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_87782444_8   1734 AAAAGAAGACATACA--TGGCCAATAGCTATATTTTTAAATGCTATACTG 1781
                         v        i     --         ivi i  v---   v --  i  v
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATG---AAAAG--ATGCTC 893

  chr1_87782444_8   1782 AA-ATCATTAGGGTA 1795
                           -    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (127 / 75)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


4388 15.82 3.43 2.99  chr1_88088575_88091697.rev     1729  2632 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_88088575_8   1729 TGGAAAGACATCTCATGTTCACTGATCGGAAGACTTAATATTGTTAAGAT 1778
                                 i   i        iv   i                       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_88088575_8   1779 GACAAACAATTTCCAAATTGAGTTGCAGGTTCAATGCATTCCTCATTAAA 1828
                          i   -i v ii         vi i   i     i   v   ii  i   
  L1M4_orf2#LINE/     51 GGCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_88088575_8   1829 -TCCCTATTGCCTT---------ACTTGACAAGCTGATCCTAAAATTCAT 1868
                         -    vii      --------- v                         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_88088575_8   1869 AAAGAAATGCAAGAAACCCAGAATAGGTAAAAGAACCTTTAGAAAGGAAG 1918
                          vi          ii           vi    v  i   v i    -   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG-AAG 198

  chr1_88088575_8   1919 AAAACAAAGTTGGAGGACTCACACTTCC-AATTTCAAAACTTACTACAAA 1967
                           --                        -                     
  L1M4_orf2#LINE/    199 AA--CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_88088575_8   1968 GCTACAATAATCAAGACAGCATGATACTAGCAGATGAATGAGGCACATGG 2017
                               i            ii  i    i   v v i  -  i  i  i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAG 295

  chr1_88088575_8   2018 TTCAGTGGAACAGAATTGAAATTCCAGAAGGCAACCT-TACATTTATGGC 2066
                         v   i     i        i v       ivv    i-           i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_88088575_8   2067 CAATTGATTTTCAACAAGAGTGCCAAGATAGTTCAGTGGGGGAAAAAGAA 2116
                                     i     i         ivi    i     ---      
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG---AAAGAA 392

  chr1_88088575_8   2117 CAGTCTTTACAACGAATGATCCTGCCACAACTGAATATTCACATGCAAAA 2166
                         i       v    i    i v   vv       i   ?i           
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_88088575_8   2167 GTTTGGAGATGGACCATTAGCTAACACTGCACACAAAAATTAACCCAAAA 2216
                          vv  i  v      vi  v  v    iii i            i     
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_88088575_8   2217 GGGATCATAGACCTAAATACAAGAGCAAAAACTATAAAATTCTTTGAAGA 2266
                         v      ?          ii      v            i    v     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_88088575_8   2267 AAACA--GGTATAAATCTTTCTGAAGTTGGAGTAGACCATGATCTCTTAA 2314
                              --  ?i        iv   vv    iv   i v   i i     i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_88088575_8   2315 ATGTGACACCAAAACCACAAGTGTCAAAAGTAAAAAATATTTATTAGGCT 2364
                           i           v      iiv      -        -----------
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATA----------- 630

  chr1_88088575_8   2365 TCAAAATTAATTGAAATTTAAAGTCAAAATTAAAAACATTTGTGTTTCAA 2414
                         ----i  v     i v  i ---              v      i     
  L1M4_orf2#LINE/    631 ----GATAAATTGGACTTCA---TCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_88088575_8   2415 ACAACGCTATCGAGAAAATGAAAA---AGCCCACAGAATGGAAGAAAATA 2461
                          vi  i     i     i      --- i            i        
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_88088575_8   2462 TTTGCAAA--------------AAGGATTTTTATCCAGAATATATAGAGA 2497
                                 -------------- i   i  v               i   
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_88088575_8   2498 AATCTTATAAGTCAAGAATAAAAAGACAAACTACCCACTTGAAAAATGGG 2547
                          v     i  v    v              iv     v  ?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_88088575_8   2548 CAAAGGACTTATATAGACATTTCTCCAAAGAAGAGATACAAATTGCCAAT 2597
                                i  iv                      v        v      
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_88088575_8   2598 AATCATGTGAAAAGATGCTCAAAATCACTAATCAT 2632
                           v  ii               v    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (87 / 52)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.87 (58 / 15)  


2119 28.26 1.41 0.47  chr1_88197891_88207167.rev     5429  6065 (3212)    L1M4_orf2#LINE/L1        1   643 (265)  

  chr1_88197891_8   5429 TGGAAAAACATTCCATAGTCATGGATAGGAAGAATCAATATCATTAAAAT 5478
                               i i  i    iv        v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_88197891_8   5479 GGCCACACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 5528
                            v i   v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_88197891_8   5529 TACCAACTTCATTTTTCACAGAATTAGAAAAAGACT-ATTATAAATCTCA 5577
                          v   i  v v     ii     v v  v  i--  -  iv    vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_88197891_8   5578 TATGGAACCAAAAAAGATCCTGAATAGTCAAAGCAGTCCTAAGCCAAAAG 5627
                                viiv  ii  i  v      i    i  i  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_88197891_8   5628 AACAAAGCCATAGGTATCACGCTACCCAACTTCAATCTATACTACAAGTG 5677
                                iiiv   vv    i  v     i     vviv        ivv
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_88197891_8   5678 TAAAGTAACAAAAATAGCAGGGTACTCGTACAAAAATAGACACATAGACC 5727
                           v     iv  i i  iiv      v i i  ii       i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_88197891_8   5728 AATGGAACAGAATAGAGGGCCCA-AAATAAAGCCACACATCTGCAACCAT 5776
                                i     v   i i   -       v   i    i iiiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_88197891_8   5777 CTGATCTTTGACAAAGTTGACAATAAGAATCGATGTGGAAAGGCTTCCCT 5826
                         i    i  i     i v  v   v vv v  i   v      iv vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_88197891_8   5827 GTTGAATAAATGGTGCCAGGATAACTGGCTGGCCATATGCAGAAGATTCA 5876
                         v  v  i         ii   i      v i?   i     i    v v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_88197891_8   5877 AACTGGATCCCTTCCATTTACCATGTACAAAAATCAACTGAAGGTGGATT 5926
                          ii    i    v  vivi     i         i    v  ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_88197891_8   5927 AAGGATTTAAAGGTAAAAACCTAAAACTATAAAAACCCTAGAAGAAAACC 5976
                          ?i  ii    v    i i -             vi i           v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_88197891_8   5977 TAGGA--AAACCATTCTG-----GAATCTGGAAATGACTTCATGAATAAG 6019
                             ?--   i v iv  ----- ii iv  v    ii   v ii   v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_88197891_8   6020 ACTCCAAAAGAAATTGCAACAAAAACAAAAATTGACAAGTGAGACT 6065
                           v       v vvv         iv      v  i  i vi    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

Transitions / transversions = 1.42 (104 / 73)
Gap_init rate = 0.01 (6 / 643), avg. gap size = 2.00 (12 / 6)  

 945 23.79 0.74 0.37  chr1_88197891_88207167.rev     8518  8786 (491)    L1M4_orf2#LINE/L1      639   908 (0)  

  chr1_88197891_8   8518 GGATCTTATTAAACCAAAGAGCTTCTGCGCAGCAAAAGAAAATATCAACA 8567
                            ii i  i   viv  i i   i  i  vv    i  v v      v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_88197891_8   8568 GAGTAAATAGACAACCGGCAGAAAGGGAGAAAATATCTGCAAACTATCCA 8617
                         i   i  v        vi     v            i      ii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_88197891_8   8618 TCCAAAAAAGGTCTAATATCCAGAATCTATAAGGAACTTAAACAAAATTA 8667
                           ii v  i  v  vi          v     i     ivv    -v i 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCA 787

  chr1_88197891_8   8668 ATAATCATAAAACAAACAACTCCATT-AAAATTCGGCAAAGGATATGAAC 8716
                              v v  i     i   i v   -    v v          v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_88197891_8   8717 AGACACTTCTCAAAAGAAGACGTATGTACAGCCAATACGCATATAAAAA- 8765
                              i     v        ii  iiv ii       v   i  i    -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_88197891_8   8766 ATGCTCAACATCACTAATCAT 8786
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (37 / 27)
Gap_init rate = 0.01 (3 / 270), avg. gap size = 1.00 (3 / 3)  


4319 18.69 0.87 1.86  chr1_88209649_88211829      776  1690 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_88209649_8    776 GAAAACCATCTTATGATCATGAATTGGAAGAC--AATAATATTAATATAG 823
                             ivi   ii   v     i          --    v i    v  i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_88209649_8    824 CCATATTCCCTAAATTAATCTATAAATTCAATGCAACTATTATTAAAATT 873
                          v   i    i     i     i i      i    iivi   i     i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_88209649_8    874 CCTACTGCTTCATTTTTTGCAACAATTAACAAGCTTACCCTGAAATTTAC 923
                           vi    i ---        iv    i       v i   i     i i
  L1M4_orf2#LINE/    103 CCAGCTGCCT---TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_88209649_8    924 TTGGACATGCAAGGGACCCAGAATAACTTAAATGATATTGAAATA-AAGA 972
                         v    v                   i iv   ii  v      v -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_88209649_8    973 ACAAGGTTGGAGGACTTACACTTCTCAGTTTCAAAACTTACCAGAAATCT 1022
                             i           i       i  i             i v   v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_88209649_8   1023 ATAGTAATCAAGACAGCGTGGTATTGGCCTAAG--TAGACATAGATAAAA 1070
                          i              i      i    v    --        --  i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA--TAGAT 297

  chr1_88209649_8   1071 CAACAGAATAGAACTGGAAGTTCAGAAGTAAACTCTTATATTTATGGTAA 1120
                            ii        i  ii   i     i     i v  i         v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_88209649_8   1121 ATTGATTTTTCACAAGGGTTTCAAGTCAATTCAATAGGGGAAAAGAAATC 1170
                                  iv        vi    v v       i   i  i iv i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_88209649_8   1171 TTTTCAAAAATTGGCACTGAGACTACTGGATATTTTCATGTAAAATAAAA 1220
                                v  v   ii   i   v        ?iiv    i    --i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA--GAA 445

  chr1_88209649_8   1221 TGGAAATGAACCCCTATCTCACATTCCATTCAGAAATTAATTCGAAATGG 1270
                           i iv  i       i      iivi  v  i       i  i      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_88209649_8   1271 ATCATAG-TCTACAATATAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 1319
                             ?  -i   -   i                                 
  L1M4_orf2#LINE/    496 ATCAWAGACCTA-AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_88209649_8   1320 ACAATAATGATAATTATTCATTGACCTTGGATTAGGTAATGGCTTCTTAA 1369
                            -  iv?i   v v   i -        i     i     i      i
  L1M4_orf2#LINE/    545 ACA-TAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_88209649_8   1370 ATATGACACCAAAAGTACAACTATGAAAAGAAAAAAAAATAGATAAATTG 1419
                                        i    vi vv           ---           
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA---TAGATAAATTG 639

  chr1_88209649_8   1420 GACATCATTAAAATGTAAAAACTTGCAT-TTTCAAAAGACACCATTAATA 1468
                            v    i     -         vii -i      i     i  i  v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_88209649_8   1469 AAGTGAAAAGACAGCCCATGGAATGGGGGAAAATATTTGCAAATCATTTA 1518
                                      i    ii       i                   v  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_88209649_8   1519 TCTCCTAAG-AACTTCTGTTCAAGACATACAAAGCACTCTTATAACTCAA 1567
                            vv    -i    v i i  ii i   i    v       i       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_88209649_8   1568 CAATAAAAATAAAAAATACTCCAATTTTTTAAAATGGGCAAAAGATTAGA 1617
                         i        -i v     vi      --?v            i    v  
  L1M4_orf2#LINE/    789 TAATAAAAA-GACAAATAACCCAATT--WAAAAATGGGCAAAGGATTTGA 835

  chr1_88209649_8   1618 ATAGACATTTCTCCAAAGAAAATACATTAATGGTCAACAAGCACATAAAA 1667
                                             i   i iv     i   i        i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_88209649_8   1668 AGATGGTTAACATTTCTAGTCAA 1690
                              v i     iv????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (114 / 53)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 1.56 (25 / 16)  


3246 26.95 0.44 0.55  chr1_88519047_88525324     4877  5785 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_88519047_8   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_88519047_8   4927 GGCCATACTGCCCAAGGTAGTTTACAGATTGAATGCCATCCCCATCAAGC 4976
                            v     v     iv ii i        v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_88519047_8   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_88519047_8   5025 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_88519047_8   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATCCTACAAGGC 5124
                                i      vv       v  ii i      viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_88519047_8   5125 TACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                     i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_88519047_8   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATACCTACAACT 5222
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_88519047_8   5223 ATCTGATCTTTGAAAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i  v  ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_88519047_8   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_88519047_8   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_88519047_8   5373 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_88519047_8   5423 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5472
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_88519047_8   5473 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5522
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_88519047_8   5523 TTAAAATAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5572
                          i     v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_88519047_8   5573 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5622
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_88519047_8   5623 AGGGCTAATATCCAGAATCTACAGTGAACTCAAACAAATTTACAAGAAAA 5672
                         i  i  vi          v  i iv      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_88519047_8   5673 AAATCAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5722
                          i -    i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_88519047_8   5723 CTCAAAAGAAGACATTTATGCAGCCAAAAACCACATGAAAAAATGGTCAT 5772
                            v        i  vi viii     v  v          i   v   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_88519047_8   5773 CATCACTGGCCAT 5785
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3641 19.88 1.89 0.71  chr1_88598502_88600324      500  1344 (479)    L1M4_orf2#LINE/L1       54   908 (0)  

  chr1_88598502_8    500 AATACTAACCAAAGTAATCTACAGATTCAATGCAATACCCATCAAAATCT 549
                               vv     v i              i     v  i         i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_88598502_8    550 CAA-TGA-TGTTTTGCACAAATAGAAAAAA-AATTCTAAAATTCATTTGG 596
                           i-  v- v       v    v  v  iv-i  i           v   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_88598502_8    597 AATCTAAAGGGATGCAGATTCGCAAAAACAATCTTGAAAAAGAAGAATAA 646
                           vivv      iv    v v  v                       i  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_88598502_8    647 AGCTGGAGAACTCACACTTCATGATTT-AAAACTTACTACAAAACTACAG 695
                           i     i           vii    -               i      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_88598502_8    696 TAATCAAAAGAGTGTAATGCCTTCATAAAGAAAGATTTATAGACCAGTGG 745
                                i v     ii i ivv     i  v   iv      i  i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_88598502_8    746 AATAGAAGGGAGAA-CAAAAAAAAAACCC-TGCATATATAGTCAGTC-AT 792
                                vv    i- v i   v      - i   v   i    i i-  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_88598502_8    793 TTTTGACAATGATGCCAAAAACCACTCAATGTGGAAAGAACAGTCTTTTC 842
                            i     v i      i -   i      v        i         
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_88598502_8    843 AGCAAATGGTACTAAGAAAACTCAATATTCACATGCAAA-TAATAAAATT 891
                          i        i  ii  v    vi   ?i          -v   i  i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_88598502_8    892 AGACCCCTACCCAACACCATATGCAAAAATTAACTCAAAATGTGTTAAAG 941
                         i          iv         i                   vi i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_88598502_8    942 ACCTAAGTGTAAAACCTAAAACTGTGAAACTTTTAGAAGAAAAGATAGGG 991
                               i     i v        i i     i           v     ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_88598502_8    992 CAAAAGTTTTATGCCATTGGATTTAGCAATGACTT--TGAATATGA---- 1035
                         vv   vi  ii  v v    i  vi      ii  -- ii      ----
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_88598502_8   1036 -AAGGCATAGACCACAAAAACAAAAATTGATAAATTGGACTCCATGAAAA 1084
                         -  i   i ii v      iv      v             i   v    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_88598502_8   1085 GTAAAACGTTTTGTGCATCAGAAAATACTATCAACGATGTAAAAAGGCAA 1134
                         v     vv        v   i ii i        vi v  i     i   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_88598502_8   1135 CACACAGAATGAGAGAAAATATTTGCAAATCATATATTTGATAAGGGATT 1184
                          v         i                         i          i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_88598502_8   1185 AATACCCAAAACATAGAGAGAACTTCTAAAACTCAGTAATAACAAAAACA 1234
                         vi  i   i  i   v i      ii  v      i      -   i   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AAAGACA 801

  chr1_88598502_8   1235 AACA-CCTAGATTCAAAAATGGGCAAAGGACTTCAATAGGCACCTCTCCA 1283
                           i -  i -   ?                i  v     i  ii      
  L1M4_orf2#LINE/    802 AATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_88598502_8   1284 AAGAACATATACAAATGGCTAAAAATGACATGAGAAAATATGACTAATCA 1333
                              v             i  v  vv      i  i  i---  v v  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG---CTCAACA 897

  chr1_88598502_8   1334 TTAAGTAAAGC 1344
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.52 (99 / 65)
Gap_init rate = 0.02 (15 / 855), avg. gap size = 1.47 (22 / 15)  


2839 25.77 2.94 1.23  chr1_88604742_88607233      808  1622 (870)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr1_88604742_8    808 TAGAAAGACATTCCATGCTTATGGATTGGAATAATTAATATT---AAAAT 854
                          i      i  i     i i           v v        ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_88604742_8    855 AACTATATTGCCCAAAGCAATCTATAGATTCAATGTGATCCCTATGAAAA 904
                         ii v   i v      vii     i        i ii        v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_88604742_8    905 TACCAACATCATTGTTTACAGAAATAGAAAAAAAGAAATCCCAAAATCTT 954
                          v   i vv v  v   i       v  v  ivv  --   i     iiv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chr1_88604742_8    955 TATGGAACCAAAAAAGAGCCAAAATAGCCAAAGCAGTCCTGAGCAAAAAG 1004
                                viiv  ii  v   i          i  i  i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_88604742_8   1005 AACAAAGCTAGAGGCATCACAATTCCTTACTCTA-----TATTACAAGGT 1049
                                i i    vv     v    iv i ii -----  i     i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_88604742_8   1050 TATAGTAACTAAAACAGCACAGTATTGGTATAAAAACAGACACATGGACC 1099
                           i     ii  i    iiii   i   i    ii i     i  i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_88604742_8   1100 AATGGAACAGAATAGAGAATACAGAAATAAGTTCACATATTTACTGTCAA 1149
                                i     v    i v         iii  i i     iv     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_88604742_8   1150 CTGGTTTTTCTAAAAAAATGCCAAGAACATACC-TGGGAAAAAGACAACT 1198
                         i  i    - v v  iii        v   v v-    i   ii i iii
  L1M4_orf2#LINE/    349 TTGATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_88604742_8   1199 TTTTCAATAAATAGTGCTGGGAAAATTAGATATCCATATCCAAAAGAATG 1248
                                i    i         v  i i    ?   i  v          
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_88604742_8   1249 AAACTGGACCCTTATCTCTCATCATATACAAAAATCAACCCAAGATGGAT 1298
                           ii       i  i   v  i             i   i   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_88604742_8   1299 TAAAAACTTAAACATAAAACCCAAAACTATTAAAATACTAGAAGAAAACC 1348
                         i ? i  i    ii   i v i        v   v vi           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_88604742_8   1349 TAGGGAAAACACTTCAGGACATTGGTTTAGGC--------------TAAG 1384
                             ?iv  vv    iv   v    v      --------------  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_88604742_8   1385 ACTTCAAAAGCACAGACAGCAAAAACAAAAATAGACAAACAGGACTATAT 1434
                           vi          ii  i     iv         i   iv     vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_88604742_8   1435 ATATTAAACTAAAAAGTTTCTGCACAGCAAAGGAAACAATCAACATAGAG 1484
                         -i --   i      v   -  ii vv       v  v     v v  v 
  L1M4_orf2#LINE/    648 -CA--AAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_88604742_8   1485 AAGAGACAGTCTGTTGAATGGAAGAAAATATTTGTAAACTTATTTCTCTG 1534
                           i     ii iiiv      i            i   - i  v v    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTG 742

  chr1_88604742_8   1535 ACAAGGAGCTAATATTCAAAATATACAAGGAACTAAAAGAATTCAACAGT 1584
                          i    ii  vi   i  i      i  i     vvv v  i    i i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_88604742_8   1585 AAATA-ATAATGATAATCCTGTTAAAAAGTGGGTAAAAG 1622
                            v - i  --    i  vi  ?    i    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAA--ATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.99 (137 / 69)
Gap_init rate = 0.01 (12 / 829), avg. gap size = 2.83 (34 / 12)  

 441 18.00 2.00 0.00  chr1_88604742_88607233     1900  1999 (493)    L1M4_orf2#LINE/L1      807   908 (0)  

  chr1_88604742_8   1900 CTCAA--AAAAAGTGGAGAAAAGACATAAATAGACATTTCTCAAAAGAAG 1947
                          i   --?    i   iv   i  iv i              v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_88604742_8   1948 ACACACAAATGGCCAACAGACACATGAAAAATTGTTCAACATCACTAATC 1997
                          i i            i ii          iv  i         ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_88604742_8   1998 AT 1999
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.01 (1 / 102), avg. gap size = 2.00 (2 / 1)  


3176 24.72 2.93 0.45  chr1_88612755_88616912     2780  3665 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_88612755_8   2780 TGGAAAAATATTCCATGTTCATAGATTAGAATAATCTATATTTTTAAAAT 2829
                               i    i          i    i   v v iv     v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_88612755_8   2830 GTCCATACTACCCAAAGCAATCTACAGATTCAGTGTAATCCCTATCAAAA 2879
                          v v     v      vii             ii i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_88612755_8   2880 TACCAATGATATTCTTCAAAGTAGTAGAAAAAA-AATCCTGAAATTTATA 2928
                          v   iiviiv  i  iiv  v i v  v  iv-i     i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_88612755_8   2929 TGGAACTGCAAAAGATCCAGAATAGCCAAAGCTATCCTTAAGCAAAAAGA 2978
                              v     ii  i              i v   -  i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAAGAAGA 199

  chr1_88612755_8   2979 ACAAAACTGGAAAAATCACATTACCTGACTTCAAATTATACTACAGAGCT 3028
                              ii    ii v     i v  ii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_88612755_8   3029 ATAGTAACAAAAACAGCATGGCACTGGC-TAAAGAAAGACATATTGACCA 3077
                          i     iv  i    ii   i      -   i  v        v  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_88612755_8   3078 ATTGAATAGACTAGAGAACTCAAAAACAAATCCTTACATTTAACAGTAAA 3127
                           v       v v    iii  i   i   i  v        -ii  v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAA 348

  chr1_88612755_8   3128 CTCATTTTAG-CAAAGGTGTTAAGAACATAAACTGCAGAAAAGACAGTCT 3176
                         i v     v -   i    ii    v   vv v  vi    ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_88612755_8   3177 TTTCAATAAATGGTGATGGGAAAACTAGATATCCATATGCAGAAGA---- 3222
                               i        v     v    i    ?   i     i    ----
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_88612755_8   3223 -------CCCCTATCTCCTGCCATATACAAAAATCAAATCAAAGTGGATT 3265
                         -------      i   vii              i  v     i     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_88612755_8   3266 AAAGACTTAAACCTAAGACCTCAAACTATGAAACTACTACAAGAAAATAT 3315
                          ?    i    iv     v  v       i     vi  v       i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_88612755_8   3316 CGGGA-ACCTCTTTAGGACATTGGTTTGGACAAAAATTCTTTGAGCAATA 3364
                         v  ?i- vv    iiv   v    v  i i   vii  ii  iiii vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_88612755_8   3365 C-CCAACAAGCACAGGTAACCAAAGCAAAAATGGACAAATGGAATCACAT 3413
                          -    -       i i   v    v      i  i    v i iiv   
  L1M4_orf2#LINE/    599 CACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_88612755_8   3414 CAGG-TTAAAAAGCTTCTGCACAGCTAAGGAAAC----AACAAAATTACA 3458
                           ii-       -   i  ii vv v     v  ----  v   i v v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_88612755_8   3459 AGACTTCCCACAGGATGG-AGAAAATATTCACAAACTACCCATCTGACAA 3507
                             vv       i    -          ii    ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_88612755_8   3508 GAGATTAATAACCAGAATATATAAGGAGCTCAAACAACACTATAGGAAAA 3557
                          i  i vi  v             i  i   vv     v v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_88612755_8   3558 AATCTAATAATCCAATC----AAGGGTCAAAAGATTTGAATAGACATTTC 3603
                          iv v     i     i----  v  v    i                  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_88612755_8   3604 ACAAAGGAAGACATACAAATGGAAAACAGGCACATGAAAAGACACTGAAT 3653
                         v v  i     i          vv  i i             ii  v  i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_88612755_8   3654 ATCATTAATCAT 3665
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (130 / 86)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


2860 27.44 2.13 0.45  chr1_88762066_88771358     2774  3666 (5627)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_88762066_8   2774 TGGAAAAATATTCCATCCTCATTGATAGAAAGAATCAATATCATGAAAAT 2823
                               i    i    vi    v   v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_88762066_8   2824 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 2873
                            v     v      v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_88762066_8   2874 TACCATTGACATTATTCACAGAACTAGAAAAAGGTACTTTAAATTTCATA 2923
                          v   vivi v  v  ii     v v  v  ivvv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_88762066_8   2924 TGGAAACAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAGAAAGAA 2973
                               iiv  ii  v  v v        i      i i iv ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_88762066_8   2974 CAAAGCTGGAGGCATCATGCTATCTGACTTCAAACTATACTACAAGGCCA 3023
                              i      vv   ii  vi ii i      viv        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_88762066_8   3024 CAGTAACCAAAACAGCATGGTTCTGGTACCAAAAGAGACATATAGACCAA 3073
                               i   i    ii    v    i iv ii v           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_88762066_8   3074 TGGAACAGAA---------CAGATAC---CTCACATATCTATAACCATCT 3111
                              i    ---------    v i--- i  i i  i   iii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_88762066_8   3112 GATCTTTGACAAACCTGACAAAAACAAGCAACAGGCAAATGATTCCCTAT 3161
                            i  i     ivv  v   i v  vv   ii  v   vi  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_88762066_8   3162 TTAATAAATGGTGTGGGGAAAA-TGGCTAGCCATATGCAGAAAACTGAAA 3210
                          i  i        iv    v  -   v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_88762066_8   3211 CTGGACCCTT-CCTTACATCTTATACAAAAATTAACTCAAGATGGATTAA 3259
                         i       i -   i   i v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_88762066_8   3260 AAACTTAAATGTAAAACCCAAAACCATAAAAGCCCTAGAAGAAAACCTAG 3309
                          i  i         i v i     i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_88762066_8   3310 GCA-ATACCATTCAGGACATAGGCATAAGCAAAGACTTCAT-GATGAAAA 3357
                          ?i- v i -   iv   v v  vv  i    v ii   v -   - vi 
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGA 598

  chr1_88762066_8   3358 CACCAAAAGCAATTACAACAAAAGCCAAAATTGACAAATGAGATCTAATT 3407
                                    vvvi         vv     v  i    vi  ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_88762066_8   3408 AAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGAATAA 3457
                            v v  i i   i  ii vv    iv v       vv i      v i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_88762066_8   3458 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA-- 3505
                         i     i                 v       vii ivi      i  --
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_88762066_8   3506 -ACTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAGGAAAA 3554
                         -   i--i          v  i  i     ivv    v iv i iv    
  L1M4_orf2#LINE/    749 GACTT--GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_88762066_8   3555 ATACAAACAACCACATCAAAAAGTGGGCAAAGCATATGAACACACACTTC 3604
                          v     i    vv  i?    i         v  v    i v   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_88762066_8   3605 TTGAAAGAAGACATTTATGTAGCCAACAAACATATGAAAAAAAGCTCATC 3654
                          iv        i  vi vi i     i  i  i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_88762066_8   3655 ATCACTGATCAT 3666
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.30 (23 / 10)  

 307 14.00 0.00 0.00  chr1_88762066_88771358     7046  7095 (2198)  C L1M4_orf2#LINE/L1   (858)    50     1  

C chr1_88762066_8   7095 TGGAACAATATTCCATGTTCATGGATTGGGAGAATCAATATTGTTAAAAT 7046
                              vi    i                 i   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.00 (0 / 0)  

1953 27.04 0.58 0.19  chr1_88762066_88771358     7607  8120 (1173)    L1M4_orf2#LINE/L1       38   553 (355)  

  chr1_88762066_8   7607 ATATTGTTAAAATATCCATGCTACCTAAAGCAATCTACAGATTCAGTGCA 7656
                                   i  iv v  i  v  i   vii             ii   
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chr1_88762066_8   7657 ACCCCTATCAAAATATCAATGACATTCTTTAACAAAATAGAAAAAGCAAT 7706
                          i            vi  iivi v  i   ivvi    v  v  ivii  
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chr1_88762066_8   7707 CCTAAAATTTATGTGGAACCACAGAAGACCCAGAATAGCCAAAGCTATCC 7756
                                  i  i     vii  iii                 i v   i
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_88762066_8   7757 TAAGCAAAAAGAAAAAAAACTGG--GAATCACGTTACCTGACTTCAAATT 7804
                          i iv  i     v   i-i   --  v    ii v  ii i      vi
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_88762066_8   7805 ACACTACAGAGCTATGGTAACTAAAACAGCATGGTACTGGCATAAAAAGT 7854
                         vi      i     ii    ii  i    ii              ii vv
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_88762066_8   7855 GACACATAGAGCAAGAGAACAGAATAAAGAA-CCAAAAGTAAATCCACAC 7903
                             i     v   vi   i     vi   i-   i  i    i   i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_88762066_8   7904 ATCTACAGTGAACTCATTTTTGAAAAAGTTTCCAGGAACGTACACTAGGG 7953
                           i  ii  v  i v     i  v  i v v   i  v i v  v i   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_88762066_8   7954 ATAGGATATTCTCTTCAATAAATACTGCTGGGAAAACTGAATATCCATAT 8003
                          v  i   v   i     i    iv        v     i   ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_88762066_8   8004 GCAGAAGAATGAAACTTGACCTCTATCTCTCATCATATATAAAAATCAAA 8053
                            i         ii v    i   i   v  i      i      i  v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_88762066_8   8054 TCTAAATTGATTAAAGACATAAATCTGAGACCTCAAACTATGAAACTACT 8103
                           v    v   i ?    v     v i   v  v       i     vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_88762066_8   8104 ACAAGAAAACACTGGGG 8120
                          v         iv  ? 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNG 553

Transitions / transversions = 1.78 (87 / 49)
Gap_init rate = 0.01 (3 / 516), avg. gap size = 1.33 (4 / 3)  

1315 24.25 1.91 0.54  chr1_88762066_88771358     8434  8800 (493)    L1M4_orf2#LINE/L1      537   908 (0)  

  chr1_88762066_8   8434 AAAAGAAAATGTTAGAGAAACTCTCTAGGACATTACAGTGGGCAAAGATT 8483
                          i       ii vi ? v  v   iiiv   v  iviv i     v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_88762066_8   8484 TCTT-----T-ACCCCACAAGCACAGGCAACCAAAGCAAAAATGAACAAA 8527
                             ----- -  v   v       i     v    v      ii i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_88762066_8   8528 TGGGATCACACCAA-GTTAGAATGCTTCTGCACAACAAAGGCAACAATCA 8576
                          v   iiv  i   -i   i  -i   i  ii vv      vv  v    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_88762066_8   8577 GCAAAGTGAAAAGACAACCCACAGAATGGGAAAAAATATTTGCAAACTAC 8626
                         iv                             i              ii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_88762066_8   8627 TCATCTGACAAGGGATTAATAACCAGAGTATGTAAGGAGCTCATACAACT 8676
                         vi      i      i vi  v     i   i   i  i   v       
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_88762066_8   8677 CTATAAGAAAAAAATTTCATAATTCAATTAAAAAATTGGCACAGGATATG 8726
                          v    v     i -ivv    ii     ?      v    v     v  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_88762066_8   8727 AATAGGCATTTCTCAAAAGAAGACATAAAAATGGCAAACAGGTTTGTGAA 8776
                              i        v        i   v       v  i i ivii    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_88762066_8   8777 AAGGTGATCAATGTCATTGATCAT 8800
                            i  v    ii   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (51 / 36)
Gap_init rate = 0.01 (5 / 372), avg. gap size = 1.80 (9 / 5)  


2491 26.50 4.48 3.18  chr1_88797125_88802782     3970  4818 (840)    L1M4_orf2#LINE/L1        2   861 (47)  

  chr1_88797125_8   3970 GGAAAAACATTCCATGTTCATGAATAGAAAGAATTGATATCATTAAAATG 4019
                              i i  i           i  v i    v  i    ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_88797125_8   4020 GCCATACTACCCAAAGCAATTTACAGATTCAGTGCTATTCCTATCAAACT 4069
                           v     v      vii  i          ii  v  i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_88797125_8   4070 ACCAATGACATTGTTCACAGAACTAAAAAAAAAAAAAAAAAAAAAAAAAA 4119
                         v   iivi v  v  ii     v vi v  i-------------------
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG------------------- 132

  chr1_88797125_8   4120 AAAACT-ATTTTAAAATTTACATGGAATAACAAAAGAGCACAAATAGCCA 4168
                         ----  -  ii       i i      vvi   ii  v vvi        
  L1M4_orf2#LINE/    133 ----CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr1_88797125_8   4169 AGGCAATCCTAAGCAAAAAGAATAAAAGTGAAGACATCACATTACCCAAT 4218
                          ii     i i iv  i     i   iv  i  ivv     i v      
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_88797125_8   4219 CTCAAATTATACTACAGGGCTACGGTAACAAAAACAGCATGGTTCTGGTA 4268
                         i     viv       ii     i    iv  i    ii    v    i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_88797125_8   4269 CAAAAACAGGCACATAGACCAACGGAACAGAATAGAGAGCTCAGAAATAA 4318
                         i  ii i  i  i     i   i    i     v     ii         
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_88797125_8   4319 TGCTGCAAACCTACAACCATCTGATCTTCTTCAAAGTTGACTAAAACAAG 4368
                         vv iii v ii  iiii  vi    i   vv   i v  v v i v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_88797125_8   4369 CAATGGGAAAAGTGCTCCCTATTCAATAAATGGTGTTGGGATAACTGGCT 4418
                                i    viivvi  v     i        i     i      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_88797125_8   4419 ACCCATATTTGGAAGATTGAAACTGGATCCCT----TGCACCATATACAA 4464
                          ?   i  viii    v    ii    i    ----ii            
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_88797125_8   4465 AAATCAACTCAAGATGGATTAAAGACTTAAATATAAAACCCAAAACTGTA 4514
                             i       i      i ?    i     i   i v i      i  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_88797125_8   4515 AAAACCGTGGAAGACAACCTAGGCA-ATACCATTCTGGACATAGGAAT-G 4562
                            vi v i     v   v    ?i- v i -   vv   v v  iv - 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG 577

  chr1_88797125_8   4563 GCAA-GATTTCAT-GATGAAGACACCAAAGTTAATCA--CAACAAAAGCA 4608
                             - i    v -   - v         ivi --  --         v 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGAT-ATGACACCAAAAGCA--CAAGCAACAAAAGAA 624

  chr1_88797125_8   4609 AAAATTGACAAATGGGATCTAACTAAACTTAAGAGCTTCTGTGCAGCAAA 4658
                              v  i    v   ii v ii   v    i i   i     vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_88797125_8   4659 TGA-ACTATCAACAGAGTAAATAGACATCTTACAGAATGAGAGAAAATAT 4707
                         v  -        v i   i  v     v ii        i          
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_88797125_8   4708 TTGCAAA----------------AGCCTAATATCGAGCATCTGTAAGGAA 4741
                                ----------------i v  vi    v  v  v i   i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_88797125_8   4742 CTTAAACAAATTA-CAAGAAAAAAA-----AATTCCATTAAAAAGTGGGC 4785
                           ivv    v i -i  v     i -----  ii v   ?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_88797125_8   4786 AAAGGGTGTGAA----CACTTTCCAAAAGAAGACATA 4818
                              i v    ----  i  ii v        i   
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

Transitions / transversions = 1.60 (136 / 85)
Gap_init rate = 0.02 (16 / 860), avg. gap size = 4.06 (65 / 16)  

 252 14.04 3.51 0.00  chr1_88797125_88802782     5109  5165 (493)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_88797125_8   5109 AAAAAAGACATATATGTGGCCAACAA--ACATGAAAAGAAGCTCAATATC 5156
                            i    i   i vi       i  --           v      i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_88797125_8   5157 ACTGATCAT 5165
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 2.00 (2 / 1)  


1189 22.41 2.36 9.43  chr1_88882128_88884948.rev     1107  1530 (1291)    L1M4_orf2#LINE/L1        1   394 (514)  

  chr1_88882128_8   1107 TGGAAAGACATACTTTGTTTATCATAGAACAGACAACTTAATATTGTTTG 1156
                                 i  v iv    ---   i  vii  vi             vi
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTT---CATGGATTGGAAGACTTAATATTGTTAA 47

  chr1_88882128_8   1157 GAAGTCAGTTCTCCTC---TTAATCTA-AGATTCAGTGCAACCCCATTCA 1202
                           v v  i v    i ---  i     -       ii    i   vv   
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_88882128_8   1203 AAAATCCGTATAGACTTTTTC-TAGAAATTGGCAAGCCGGTTTTAAAAAT 1251
                            -   vviiv v      i-i        i     i i ii     v 
  L1M4_orf2#LINE/     98 AAA-TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_88882128_8   1252 TATATGGAAATATAAAGAACCTAGA-TAGTCAAAACAAATTTGAAAAAGG 1300
                         i          ii  i i   i   -   i        vi         i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_88882128_8   1301 AGAGTAAATTTGGAAGACTAATACTCCCAGATTCCGAGACTTATAAAAAA 1350
                            ii   v     i    v i   i  vi   i i i     iv v   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_88882128_8   1351 GCACCAATAATCAAAACAGCATGGGACTGGCAAAAAATTAATAAATACAG 1400
                           vv  i       i    ii   v       v  ii---   i -----
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG---ATAGA----- 288

  chr1_88882128_8   1401 CATGGGACTGGCAAAAAAAAATAATAATAAATATAGCAATGGATCAGGA- 1449
                            -----------------------   i  ----       vi  i -
  L1M4_orf2#LINE/    289 CAT-----------------------ATAGAT----CAATGGAATAGAAT 311

  chr1_88882128_8   1450 -GAGAG--CAGAAATTGTCGCACACATATATGAACAACTGATTTTCTGAC 1496
                         -     --       viv v  i    v    iv   i        -   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC-GAC 360

  chr1_88882128_8   1497 AAAGATATAAAGGCAATTCAGTGGAGAAAGAATA 1530
                           i i iiv   i v     i   i         
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

Transitions / transversions = 1.88 (62 / 33)
Gap_init rate = 0.03 (13 / 394), avg. gap size = 3.85 (50 / 13)  

1533 18.71 8.85 4.02  chr1_88882128_88884948.rev     1834  2330 (491)    L1M4_orf2#LINE/L1      388   908 (0)  

  chr1_88882128_8   1834 AAGAATATATTTTTTAAATAAATGTTGCTGAAACAAAT--ATGTCCATAT 1881
                                -i i    v  i     v     ii    v --  i?   i  
  L1M4_orf2#LINE/    388 AAGAATA-GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_88882128_8   1882 G-AAAAATATGAACTTTGATCAACACCTGGCACCATAAACAAAAATTACC 1930
                          -    iv     v  v  i vvi    vi       v          v 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_88882128_8   1931 TCACAATGGATCATAAAACTAAATGTAAAACCTAAAACTA--AAATTCT- 1977
                            v         ? i v          i v         --   i   -
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_88882128_8   1978 AGAAGAAAACA--GGAG--AAT-------AGCTT----TA---------- 2002
                                    --  ? --   ------- v   ----  ----------
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_88882128_8   2003 TCTTGGATACCAAACCAAAAACACAGTGTGCAAAAGAAAAATGTTGATAA 2052
                             i    iv v       i    ivvvi           -i v     
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAA 635

  chr1_88882128_8   2053 ACTGGA-TCCATCAGAATTAAGAACTTCTGCTCCTGGAAAGATACTGTTT 2101
                          i    - i     i      i     i  iv i vi  i  i   i i-
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC- 684

  chr1_88882128_8   2102 AAAAAAAAAAAGAAAAGAAAA-GAAAAGATAAGCTACAGAATTG---AAA 2147
                         --------------      i-       i  v i       v ---   
  L1M4_orf2#LINE/    685 --------------AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_88882128_8   2148 ATATTTGCAACTCACACATCTGATAAAGGTATTAAATTCAGAATATATAA 2197
                                   v   i i         i  vv  iv  i            
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_88882128_8   2198 AGA-CTCTCAACATTCAATAA------GA-AAATAACTCAATTTTTAAAA 2239
                            -    i vv i       ------  -       i     ?--    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW--AAAA 818

  chr1_88882128_8   2240 ATAGACAAAAGATTTGAATAGATACTTCACCAAAGAGGATATACAGATAG 2289
                           i i    i            i i   v       i        i  i 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_88882128_8   2290 CAGATACGATCATGAAAAGATGGTTCAACATCATTCAATAA 2330
                          vi   v vv            -i         ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATG-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (53 / 36)
Gap_init rate = 0.04 (20 / 521), avg. gap size = 3.20 (64 / 20)  


3117 26.54 0.66 1.10  chr1_88890732_88893128.rev      995  1906 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_88890732_8    995 TGGAAGAACGTTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 1044
                              ii ii i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_88890732_8   1045 GGCCACACTGCCCATGGTAATTTATAGATTCAATGCCATCCACATCAAAC 1094
                            v i   v    viv i  i  i        i  v    vi      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_88890732_8   1095 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 1141
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_88890732_8   1142 ATACGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAA 1191
                            i    viiv  ii  v  v v  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_88890732_8   1192 GAACAAAGCTGGAGGCATCATGCTACCTGAATTT--AAACTATACTACAA 1239
                                 i      vv   ii  v  i-     --     -        
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCC-AATTTCAAAACT-TACTACAA 245

  chr1_88890732_8   1240 GGCTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAG 1289
                         i          i   i    iii        i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_88890732_8   1290 ACAAATGGAACAGAACAGAGGCCTCAGAAATAATACCACCCATCTACAAC 1339
                          iv       i    iv   ivii         vv   iv   i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_88890732_8   1340 CATCTGATCTTTGACAAACCAGACAGAAACAAGAAATGGAGAAAGGATTC 1389
                           vi    i  i     ivvv v  ii v  vvv     i     i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_88890732_8   1390 CCTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1439
                         i  v  i  i  i           v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_88890732_8   1440 TGAAACTGGATCCCTTCCTTACACCTTGTACAAATATTAATTCAAGATGG 1489
                             ii    i    v   i     v i      v     i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_88890732_8   1490 ATTAAAGACTTAAATGTTAGACGACCTACAACCATAAAAACCCTAGAAGA 1539
                           i ?    i       v   - --   v   i      vi i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA-G--CTAAAACTATAAAACTCTTAGAAGA 542

  chr1_88890732_8   1540 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 1588
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_88890732_8   1589 ACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGA 1638
                         iv  vi            vvi          vv        i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_88890732_8   1639 TCTAATTAAACTGAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAG 1688
                         ii v  i   v v  i i   i  iiivv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_88890732_8   1689 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCATCC 1738
                             v  i     i                 v       vii  vi   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_88890732_8   1739 GACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAA 1788
                           i  i  i  vi          v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_88890732_8   1789 GAAAAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACGGA 1838
                         v     i -    i     v  i?    i            v    ii  
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_88890732_8   1839 CACTTCTCAAAAGAAGACATTTATGCAGGCAACGGACACATGAAAAAAAG 1888
                           i     v        i  vi viii v   iiii          i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_88890732_8   1889 CTCATCATCACTGGCCAG 1906
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.23 (16 / 13)  


1745 24.81 4.55 2.84  chr1_88910640_88912921.rev      514  1041 (1241)    L1M4_orf2#LINE/L1      138   674 (234)  

  chr1_88910640_8    514 CCTAA---CCATAAAGAAAGACAACAAGAGAACATAAATAGCCAAAGTAA 560
                              ---i    vi    vi   --- i  v vvi          ii  
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAA---GGGACCCAGAATAGCCAAAACAA 184

  chr1_88910640_8    561 TCTAAAGCAAAAAGAACAAAGCTGGAGGCATCATACTACTTGACTTCAAA 610
                            vi iv  i          i      vv   i   v iii i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_88910640_8    611 ACACATTACATAGCTATAGTAATCAAAATAGCATGCTACTGGTATAAAAA 660
                           vi i    v     i         i i  ii  v      i    ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_88910640_8    661 -AGACACACAAATCAATGGAACAGAA--GACAGTCCAGAAATAAATC-AT 706
                         -     i i i          i    --  v              i -  
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_88910640_8    707 CTATCTACAGTTTATTAATTCTTGACAAAGGGGCCAAGTACACTCAATGG 756
                         vi  i  ii  iv   i   i i     i  v      vv  i       
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_88910640_8    757 GAAAAGGG---------CAACAAGTGGTGTTGGGAAAACTGGATATCCAC 797
                          i    ii---------      i     i     v         ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_88910640_8    798 ATG--AGAGAATGAAATTAGATTCTTATCTCTCACCACAGACAAAACTCA 845
                            -- i        i  i  ii i  i   v     i v      v i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_88910640_8    846 ACTCAAAATGGATTAAAGACTTAAATGTAAGACCCCAAACTACAAAATCA 895
                                      i ?    i           v iv      i    iiv
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_88910640_8    896 CAAGAAGAAAATATGGAGGAAATATAGGGGAAAGCTCCATGTCACTGGTC 945
                         iv         i  i ---------- ? v   v  i i  v vi   vi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAG----------GNGTAAATCTTCGTGACCTTGGGT 574

  chr1_88910640_8    946 TAGGCAAGAATATTTTGGACAAAACCTGAAAAGCATGGGCAACAAAAGCA 995
                                vii v i  i  i vi  viv       iii          v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_88910640_8    996 AAAACAG-T---TTGAGCAT--TCTAAATCCAAAACTCTAAAACGCTCCA 1039
                             i  - ---   ii v --  v    iv      i vi--i   i  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG--TGCTTCA 672

  chr1_88910640_8   1040 AA 1041
                           
  L1M4_orf2#LINE/    673 AA 674

Transitions / transversions = 2.05 (86 / 42)
Gap_init rate = 0.02 (12 / 537), avg. gap size = 3.25 (39 / 12)  

 844 26.91 2.91 0.73  chr1_88910640_88912921.rev     1517  1791 (491)    L1M4_orf2#LINE/L1      628   908 (0)  

  chr1_88910640_8   1517 ATAGACAAATGGAATTGTATCAAACTAAAAATCTTCTGCATAGTAAAGGT 1566
                              i    v i i vi      v v    v   i  iiivvi     v
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_88910640_8   1567 AACAATCAACAGAGCAAGGATGCCAGTCATAGACTGGGAGAACACATTTA 1616
                         v  v     v i  ii ii vi v vi  i   v        v i    i
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_88910640_8   1617 CAAACTACACAACTGATAAAGGGTTAATACCCAAA---TATAAAGAACTC 1663
                             ii i i v       i  ii vi  i   i ---            
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_88910640_8   1664 AAAC-ACTCAATAACAAA----CAAATAACCTGATCAAAAAATGGGCAAA 1708
                         vv  -         i   ----         ii  i?             
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_88910640_8   1709 AGGCCTACATAGACATTTCTCCAAAAAAAGAACATACAAACAACCCACAG 1758
                         i iii iv                 i  --i i       iii  v i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAA--GATATACAAATGGCCAATAA 875

  chr1_88910640_8   1759 GTGTATGAAAAAATGTTCAACATCACTAATCAT 1791
                          iii       i   i         ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.32 (51 / 22)
Gap_init rate = 0.01 (4 / 281), avg. gap size = 2.50 (10 / 4)  


3152 20.32 4.32 6.16  chr1_88922214_88924722     1093  2017 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_88922214_8   1093 TGGAAAAATCTCCTGTGTTCATGAATTGGAAGACTTAATATTGTTAAAAT 1142
                               i  v   ii        i                       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_88922214_8   1143 GTCCATACTACCCAATGTGATCTACAGATTCAAGGTAATTCGTATCAAAA 1192
                          v v     v     vv                v i   i v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_88922214_8   1193 TCCCAACATCATTCTTCACAGAAATAGAAAAAGAAATCCTAAAATTTATA 1242
                              i vv v  i  ii       v  v  ivvi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_88922214_8   1243 TGGAATCAGAAAAGACCC----TA--CA---CCATCTTGAGCAAAAAGAA 1283
                              viiv  ii     ----  --  --- v       iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_88922214_8   1284 CAAAACTAGAAGCATCACACTACCAAATTCCAAAA--TATTACAAAGCTA 1331
                             ii i  i vv       v  v    i     --  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_88922214_8   1332 TAGTAATCTAAACAGCATCATAATGACATAAAAATAGACTCATTAACCAA 1381
                         i       v i    ii vi  v  i     ii      vi  vi i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_88922214_8   1382 TGGAATAGAAAAGAGAGCCCAGAAATAAACCCACGCAATTCAAATCAATT 1431
                                   vv     i               ii  v  vvii      
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_88922214_8   1432 GATTTTTGACAAAGCTGCCAAGAACACACGGTGGGGACTGGACAGTCTT- 1480
                               i     i v        v  iv ii      vv i i      -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_88922214_8   1481 -CAATAAATGGTGTTGGGAAAACTGGATATCGACATGCAGAAGAAGGAAG 1529
                         -   i        i     v         ? v       i     v    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_88922214_8   1530 ATGAACCTTTATCTTACCCTTATACGTAATACCTTTATACCTTATACCTT 1579
                         v  i   ii  i  i  ---------------------   v     ---
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCAC---------------------ACCATATAC--- 476

  chr1_88922214_8   1580 TAAACCTTATACCTTTATACCTTATACCTTTATCTTACCTTATACGTTTA 1629
                         -   vv   ---------  - i v ---------------  i- v i 
  L1M4_orf2#LINE/    477 -AAAAATTA---------AC-TCAAA---------------ATG-GATCA 499

  chr1_88922214_8   1630 TAAGACTTAAATGTCAGTCCTGAAACTATAAAACTGCTAGAAGAAAATAT 1679
                         ? -   i       v  vv  i             vi          i  
  L1M4_orf2#LINE/    500 WA-GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_88922214_8   1680 AGAGGGAAAGCTCTATGACATTGGTCTAGGCAGTGATTTCTTGGATA--- 1726
                           i? v   v  iii    v    vi      i  i      i    ---
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_88922214_8   1727 -----AAAGCAGAGGCAA---AAGCAAAAATAGATAGATGGGTTTGCATC 1768
                         -----      v i    ---   v           i  v  vi v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_88922214_8   1769 AAA-TTGGAAACTTCTGCACAGCAAAGGAAACAATTAGCAGAGTGAAGAG 1817
                            -  ii      i  ii vv       v  v  i iv i      i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_88922214_8   1818 ACAACCCAAAGAATGGGAGAAAATATTTATAAATTATATATTGGATAAGG 1867
                                 v                   ii    i      iv       
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_88922214_8   1868 G----GT---CAG------TAAGGAACTCAAACTACTGAATTCAAGGAAA 1904
                          ----  ---   ------   i      vv  v   v   --  vi   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT--AATAAAA 796

  chr1_88922214_8   1905 AGA--AATAATCTTATTTAAAAAATGGGCAAAGGACCTGAGTAGACATTT 1952
                            --     i iv   ?     -           ii   i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTT 845

  chr1_88922214_8   1953 ATCAAAAGAAGGCATATAAATGGCCGACAGATAATATGAAAAAAATGATC 2002
                         v  v       ii   i        i i iii -i       i -  v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCA-CATGAAAAGA-TGCTC 893

  chr1_88922214_8   2003 AGTATCTCTAGCCAT 2017
                          ii   v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (107 / 77)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 4.22 (97 / 23)  


2748 21.71 10.37 2.93  chr1_89192986_89195912     1615  2434 (493)    L1M4_orf2#LINE/L1       28   908 (0)  

  chr1_89192986_8   1615 GGAAGAGTTAA-ATAATTAGAAAGACA----TCCTGTAAAAGTGACATAC 1659
                               v    -  vi   ii v i  ----   iv--   v   iv   
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAATACTCCCC--AAATTGATCTAC 75

  chr1_89192986_8   1660 AGATTCAATGCAATCCCTATCAAAATTCCAA-TGATTTTTTTATAAATAA 1708
                                 i                 i   i-  vi      ii i ---
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA--- 122

  chr1_89192986_8   1709 AAACATCAAAAATATCCACACTAACTTTCATATGAAATTTCAAGAGATCC 1758
                           viiv   ivvv    ----   vv        i  v v    i  -  
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCC----TAAAATTCATATGGAAATGCAAGGGA-CC 167

  chr1_89192986_8   1759 CCAAATTGTCAAAATAATCTCAAAAAGGAAGAAGAAAGTCAGAGG-CTCA 1807
                          vi   v i     i     ii    i      v     ii    -    
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr1_89192986_8   1808 CAGTTTCTGAGTTCTGAAACTTACTACAAAATCAGGATAATCAACACAGT 1857
                           v  i ii v   -i              iii vii       v     
  L1M4_orf2#LINE/    218 CACTTCCCAATTTC-AAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr1_89192986_8   1858 TTGGTATTGGCTTAAACACTGT--TATCAACTAATGGAGTAAAGTAGAGA 1905
                         v     i    v   iv iv v--   vi ii      i  i i v    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr1_89192986_8   1906 GCCTAGAAATGAACTCTCACATCTATAGTCAAAAAATTTTCAACATGGAT 1955
                          i i      i   i vi    i   i     vvi      i   v  i 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_89192986_8   1956 GCTAAAATCATTCAACGCAGAAAGAGGAGTCTCTACAACAAATGACATTG 2005
                           i  i i       i vi      iv     i v         iiii  
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_89192986_8   2006 GGAAAACTGGATATTCACATGCTCACATGCCAAAAAAAAAAAAAAAGTTG 2055
                            v         ?i       -------------    i  vi      
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGC-------------AAAAGAATGAAGTTG 453

  chr1_89192986_8   2056 GACTGTTAGCTTACAC-A-ATCCAAAACGTAACTCAAAATGGATCAAAGA 2103
                            ivi  v  i    - -  v     vv                 ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_89192986_8   2104 ACTAACCATTAGAGCTAAAACTATAAAACTCATGGGAGAAAACAAAGGGG 2153
                         v    vii v                     v i i        v   ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_89192986_8   2154 -------------------------------------------------A 2154
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_89192986_8   2155 AAA--ACAGACAGTAAAAGGAAAAACAGATAACTTTGACTTCATCAAAAT 2202
                            --   ii  ii     i     i      v  v              
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_89192986_8   2203 GAAAAACTTTTGTGCATCAAATGACACTATCAACAGAATAAAAAGGCAAC 2252
                         v              v     v           v i i i     i    
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_89192986_8   2253 ACATGGAATGGAAGAAAACATTTGCTAAACGTGTATCTGATAAGGAATTG 2302
                         v  ii      i      i      v  v i i            i i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_89192986_8   2303 ATGTCTAGCAAATATAAAGAATTCCTACAATGCAACA---------CAAA 2343
                         i i  i  v v          i  i     iv   i ---------    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_89192986_8   2344 CAG----ATTAAAAAGTAAAGAAAGAACTTGAATAGACATTTCTCTAAAG 2389
                         i i----   ?    i iiiv    i i                 i    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_89192986_8   2390 AA----------TGGCCAATAAGCACCTGAAAAGATGCTCAACATTACTA 2429
                           ----------              v                  i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_89192986_8   2430 GTCAT 2434
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.72 (110 / 64)
Gap_init rate = 0.02 (18 / 881), avg. gap size = 6.06 (109 / 18)  


2803 28.01 0.87 2.28  chr1_89206474_89212313.rev     4429  5349 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89206474_8   4429 TGGAAGAACATTTCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4478
                              ii i  ii    i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89206474_8   4479 GGCCATACTGCCCAAGGTAATTTATAGATTCCATGCCATCCCCATCAAGC 4528
                            v     v     iv i  i  i      v i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89206474_8   4529 TACCAATGATTTTCTTCACAGAA-TTGGAAAAAACTA--CTTTAAATTAC 4575
                          v   iiviii  i  ii     -   -- v  i  i-- i v     - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT-C 147

  chr1_89206474_8   4576 ACATGGAACCAAAAAAGAGCCCACATTGCCAAGGCAATCCTAAGCAAAAA 4625
                          i      viiv  ii  v  viv  v     ii     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_89206474_8   4626 GAACAAAGCTGGAGGCATCATGCCACCTGAATTCAAACTATACTACAAGC 4675
                                 i      vv   ii iv  ii v      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_89206474_8   4676 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGAC 4725
                                  i   i    ii         i iv ii i   v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_89206474_8   4726 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTAGAACTA 4775
                                 i    iv   ivii         vv   i    i  viiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_89206474_8   4776 TCTGATCTTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCCC 4825
                         vi    i  i     ivv  v   i vv vvv           i  ----
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT---- 393

  chr1_89206474_8   4826 TATTTATTCCCTATTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTG 4875
                         ----- v  ii - i  i              v      v  ?   ii  
  L1M4_orf2#LINE/    394 -----AGTCTTT-TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_89206474_8   4876 TACAAAGCTGAAGCTGGATCCCTTCCTTACATCTTATACAAAAATTAATT 4925
                         i v  iiv     i    i    v   i   i v              i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_89206474_8   4926 CAAGATGGATTAAAGACTTAAATGTTAGACCTAAAATCATAAACGCCCTA 4975
                            i      i ?    i       v   v      ii     vvi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_89206474_8   4976 GAAGAAAACCTGGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACT 5024
                                  v i  ?i- v i -   iv   v v  vv i i   v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_89206474_8   5025 TCATGACTAAAACACCAAAAGCAACGGCAACAAAAGCCAAAATTGACAAA 5074
                           v iiv  vi            vvi          vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_89206474_8   5075 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAGAAGAAACTTCCAT 5124
                          v   ii v  i   v v  i i   i  ii vv  i i  v   vi  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_89206474_8   5125 CAGAGTGAACAGGCAACCTACAGAATGGGAGACCATTTTTGCAATCTACC 5174
                         v i      v  i     i             vv  v       vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_89206474_8   5175 CATCTGACAAATGGCTAATACCCAGAATCTACAAAGAACTTAAACAAATT 5224
                         i      i  iv i  vi  i       v  i        ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_89206474_8   5225 TACAAGAAAAAAACAAACAACCACATCAAAAAGTGGGCAAAGGATATGTC 5274
                         v i  v     i     i    vv  i?    i            v  --
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG-- 834

  chr1_89206474_8   5275 TTATTTTGAGAGAAGTCTCAAAAGAAGACATTTTTGCAGCCGA----CAC 5320
                         -- v ---   v vv    v        i  vivviii   i ----   
  L1M4_orf2#LINE/    835 --AAT---AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_89206474_8   5321 ATGAAAAAATGCTCATCATCACTAGTCAT 5349
                                i       v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (148 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.64 (29 / 11)  


3318 23.62 4.59 0.46  chr1_89237700_89240119     1056  1927 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89237700_8   1056 TAGAAAGACATCCTGTGTTTATGGATTGGAAGACTTAATATTCTTAAGAT 1105
                          i      i    ii    i                      v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89237700_8   1106 GTCACTACTACCCAAAGTGATGTACAGGTTTGATATAATCCCTACCAACA 1155
                          v  v    v      v    v     i  ii iii        i   v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89237700_8   1156 TTCCAATTAC----TTTGTATAAATAGAAAAATCCACCATAAATTTCATA 1201
                          i   ii i ----    i v    v  v  iiiv i v    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_89237700_8   1202 TGAAATTTCCAGAGATCCCCTAATTATAAAAATAA------AAAGGAAGA 1245
                           i  v v v  i  -   vv   viiv    i  ------   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_89237700_8   1246 GCAAAGTTGGAGT-CTCACAGTTTCTGAGTTGTGAAACGTATTACAAAAC 1294
                         i           v-      v  i ii v  -ii    v  i      i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTT-CAAAACTTACTACAAAGC 248

  chr1_89237700_8   1295 CAT-------------GTGTGGTACTGGTATAAAGACTGACATATAAACC 1331
                         i i-------------            i    i  iv        i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_89237700_8   1332 AATAGAATAGAAAAGACAGCCCATGAATAAACTCTGATATATATGGTCAA 1381
                            i        vv  v  i   vi       i vv i  v         
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_89237700_8   1382 ATGATTTCCAGTATGGGTGTCAAGATCATTTAATGAAGAAAGGAGAGTCT 1431
                         v      i iii v     i     i    i    ii     i v     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_89237700_8   1432 CTTTAACAAATGATGTTGAGGAAATGATATATCTCCTT--AAAA------ 1473
                         i  i        i  i  i iv  iviv   ? iv v --    ------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_89237700_8   1474 AGTTGGGCTATTACCTTATA--ACTTACAAATATGAACTCAAAATGGATC 1521
                               i ivi     i i -- iv      v  v               
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_89237700_8   1522 AAAGAACCAAACATTAGAGTTGAAACTATAAAAGTTGTAGAAGAAAATAA 1571
                          ?   v i   ii v    i i           v iv          i v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_89237700_8   1572 AGGGTAAAAGTTTTATAATATTGGATTTGGAAATTATTTTTTGAATAAGA 1621
                            ?vv   vi  ii i iv    i  v  v   vi   i  ii   v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_89237700_8   1622 AACCAAAACTATAGACAATAAAAGAAAAAATAGATTAGTGGGACTTCAGC 1671
                         v       vi i ii   i                v i v        v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_89237700_8   1672 AAAATTTAAAACTTTTGTGTATTAACGGACACTATCAACAGAGTTAAAAA 1721
                               v            iv i  v            v i   --i   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT--GAAA 696

  chr1_89237700_8   1722 AGGCAACACACGGAATGTAAGAAAATGGTTTCTAAACATGTATATGATAA 1771
                           i    v   i     vi       iv  v v  v   i   v      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_89237700_8   1772 GGGATTGATATCTAGAAAATATAAAAAAAT-TTACAA---AGCAACAGAA 1817
                             i vi    i    v       i  v -      --- ii  i i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_89237700_8   1818 A--TAAACAACCAGATTAATAAATGAACAATGGACTTGAATAGACATTCT 1865
                          --i   i    vi   ? v     ii   v   i             ii
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_89237700_8   1866 CCCAAAGAAGATATACAAGTGGCCAATAAGCACGTGAAAAGATGCTCAAC 1915
                         i                 i              i                
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_89237700_8   1916 ATCACTAGTCAT 1927
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (123 / 79)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.38 (44 / 13)  


1629 26.80 8.76 0.35  chr1_89248228_89255444      500  1070 (6147)    L1M4_orf2#LINE/L1      280   898 (10)  

  chr1_89248228_8    500 AAAAACAGACACGTAGACCAATGGAACAGAATAGAGAATTCAGAAATAAA 549
                           ii i     ii    i        i     v    i i          
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_89248228_8    550 TTTACATATTTAAAGTCACCTTATTTTTGACACAAAGGCCAGCAATATAC 599
                         iii i i     vi    vi v     i    viiiv    iv vi  v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_89248228_8    600 ATTGGGGAATGTATG-----TTCA-TAATTGATGCTGGGAAATGTGGATA 643
                          v       v v  i-----    -i  v  i        v vv      
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_89248228_8    644 TT------------AATG----TG---------------CTGTATG-AAA 661
                         ?i------------    ----  --------------- ii   i-   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_89248228_8    662 AATCAATTCAAAATGGATTAAATATTTAAATGTAAGACCCCCAGCTTTAA 711
                            i  i           i ? v ii           v ivv i  v   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_89248228_8    712 AACTATCACAGAAAAACATAGGGA-AAACACTTGTGGACATCAGTCCAGG 760
                             v i v ii          ?i-   ivi i   -  v ii vii   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGG 578

  chr1_89248228_8    761 CAACAATTTGATGGGTAAAACTTCAATAGCACACTCAACAAAAGCAAAAA 810
                            iii   vv i i  vi  vi   v      vv         v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_89248228_8    811 TAGACAAATGAGACT--GTTAAACTAAAAGGTTTTTGTGCAGCAAAGGAA 858
                             i    vi    --i i   v v   iii        vv       v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_89248228_8    859 AAAACCAACAGAATGGAGAGTCATCTTATGTAATGGGATAATGTATTTGC 908
                          vv i   v i i  i i  v  v ii iiv       v  vi       
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_89248228_8    909 AAGCTATTCAACTGACAAAGGACTAATATTCAGAATATACAA-GAG-TCT 956
                           iii  vi v    i  i     vi   i         i  -  i-   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_89248228_8    957 --CAACTCAA----AAACAAACAAACAATCTTATTTAAAAAATGGGCAAA 1000
                         --        ----   v i     i  i iv   ?     -        
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAA 827

  chr1_89248228_8   1001 ATATATGAATAGACGTTTCTCAAAAGAAGACATACAAATGGCTAACAAGT 1050
                         iv  v         i      v        i           i  i   i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_89248228_8   1051 ATATAAAAA-ATGCTCAACAT 1070
                          i  i    -           
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACAT 898

Transitions / transversions = 1.66 (93 / 56)
Gap_init rate = 0.02 (15 / 619), avg. gap size = 3.47 (52 / 15)  

2907 28.32 0.55 0.88  chr1_89248228_89255444     5814  6724 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89248228_8   5814 TGGAAAAACATTCCATACATACTTATGGATAGGAAGAATCAATATCGTGA 5863
                               i i  i    ii---- i      v      v i     i  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGT----TCATGGATTGGAAGACTTAATATTGTTA 46

  chr1_89248228_8   5864 AAATGACCATACTGCCCAAAGTAATTTTCAGATTCAATGCTATTCCCATG 5913
                          i   i v     v      v i  i v         i  v  i  i  v
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_89248228_8   5914 AAGCTACCATTGACTTTCTTCACAGAACTAGAAAAAACT-ACTTTAAATT 5962
                           iv v   vivi i  i  ii     v v  v  i-  - iii    v 
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAAT 145

  chr1_89248228_8   5963 TCACATGGAACCAAAAAAGAGCCTGTATATCCAAGACAATACCAAGCAAA 6012
                            i      viiv  ii  v  v v   v    i     viii iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_89248228_8   6013 AAGAACAAAGCTGGAGGCATCGTGCTATCTGACTTCAAAGTATACTACAA 6062
                                   i      vv  iii  vi ii i      iiv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_89248228_8   6063 GGCTATAGTAACTAAAACAGCATGCTA-TGGTACCAAAACATGTATATAG 6111
                         i    i     ii  i    ii  v  -   i iv ii i vii      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_89248228_8   6112 ACCAATGGAAGAGAACAGAGGCCTCAGAAACAACACCCA--CAACTACAA 6159
                          i        v    iv   ivii      i  -     --  vi  iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGG 344

  chr1_89248228_8   6160 CCATCTGATCTTCGACAAACCTGACAAAAGCAAGCAATAGGAAAAGGATT 6209
                         i  vi    i        ivv  v   i v  vv    i  i    i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_89248228_8   6210 CCCTATTTAATAAATGGTGCTGGGAATACTGGCTAGCCATATGAGGAAAA 6259
                         vi  v  i  i              vv     v  ?   i   vii  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_89248228_8   6260 CTGAAACTGGACCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATG 6309
                         v    ii         v   i     v  i           i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_89248228_8   6310 GATTAATGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAG 6359
                            i ?v   i         i v i     i      vi i        i
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_89248228_8   6360 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAC 6408
                           v    ?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_89248228_8   6409 TAAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATC 6458
                           vi            vvv          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_89248228_8   6459 TAATTAAACTAAAGAGCTTCTGCACAGCAAAACAAACTATCATCAGAGTG 6508
                          v  i   v v  i i   i  ii vv    iv v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_89248228_8   6509 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTATCCATCTGA 6558
                           v  i     i                 v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_89248228_8   6559 CAAAGATCTGGTTTCCAGGATCTACAACAAACTTGAACAAATTTACAAGA 6608
                         i  i iv  v  v     i  v  i  vi    ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_89248228_8   6609 AAAAAAACAAAAAACCCCATCAAAAAATGGGCAGAGGATATGAACAGACA 6658
                             i -    v     v  i?           i     v    i     
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_89248228_8   6659 CATCTCAAAAGAAGACATTTATGTGGCTAACAAACATATGAGAAAAGGCT 6708
                         iv    v        i  vi vi    i  i  i  i    i  i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_89248228_8   6709 CATCATCACTGGTCAT 6724
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (148 / 106)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2682 25.78 1.73 3.78  chr1_89311916_89317286     3958  4884 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89311916_8   3958 TGGAAAATTATTTCATGCATATGGATAGGAAGAATCAATGTTGTTAAAAT 4007
                               iv   ii    ivi      v      v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89311916_8   4008 AGCCATACTGCCCAAATTGATTTACATATTCAATGCTATTCCTATCAAAT 4057
                         i  v     v           i    v      i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89311916_8   4058 TATC-GATGACTTTTT---AAAAATAGAATTAGTAAAAACT-ATTCTAAC 4102
                          vi - v  v      --- i    v  v-------  i  -  i    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-------AAGCTGATCCTAAA 143

  chr1_89311916_8   4103 ATCCACATGGAACAACAACAACAAAAAAACCCCGAGTAGCCAAGGCACTC 4152
                           i  i      vvi   -------iii    v  i       ii  v  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAA-------GGGACCCAGAATAGCCAAAACAATC 186

  chr1_89311916_8   4153 CTAAGCAAAAAGAACAAAGCCAGAGACATCACATGACTTGAGTTTAAACT 4202
                         i i iv  i          iii   ivv     ivv iii v  i   vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_89311916_8   4203 ATATTACAAGACTACAATAACCAAAATAGCATGGTGCTGGTCAAAAAACA 4252
                         v  i     ii     i   i   i i  ii    i    -  v  ii--
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG-CATAAGG-- 283

  chr1_89311916_8   4253 AAACAAAACAAAACAGACACATGAACAAATGGAAAAGTTTAAAGAAAGCA 4302
                         ------------ i     i  ii iv       v  vv vi   ivv  
  L1M4_orf2#LINE/    284 ------------ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_89311916_8   4303 GAAATAATACCACACACCTACAACTATCTGATCTTTGGTAAAGCTAACAA 4352
                                vv   i   ii  iiiii vi    i  i ii  i v iv   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_89311916_8   4353 AAAAAG-CAATGGAGAAAGAAT-GCATTATTCAATAAATGGTGCTGGGTT 4400
                         i vv v-      i        - iv  -     i             vi
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGGAC 420

  chr1_89311916_8   4401 AACTGGCTAGCTATATGCAGAAGATTGAAACTGGACCCCTTCTTCTCACT 4450
                               v  ? i i     i    v    ii         v i  v   i
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_89311916_8   4451 ATATACAAAAATCAACTCAAGATGAGTTAAAGATGTAAATGTAAAATTTA 4500
                                     i       i   ii i ?   iv         i vi  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_89311916_8   4501 AAACTATAAAACCACCAAAAGAAAACCTAGG---AAATACCATTCTGGAC 4547
                                     ivii i        v    ---    -- -   vv   
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGAC 567

  chr1_89311916_8   4548 ATAGGCACTGGCAAAGATTTCCT-GATGAAAACTTCAAAAGC-CACTGCA 4595
                         v v  vviv     v i    i -   - vi  vi       -  v-   
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAA-GCA 615

  chr1_89311916_8   4596 ACCGAACAAAAAGTTAACAAGAGGGACCTAATTCAACTAAAGAGTTCATG 4645
                           vi  v     i vi i  ivv    i v  iv  v v  i ii iv  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_89311916_8   4646 CACAACAAAGGAAACTATAAACAGAGTAAACAGACAACCTACAGAATGGG 4695
                         ii vv       v     v  v i   i  v        i          
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_89311916_8   4696 AGAAAATATCTGCAAACTATGCATCTGAAAAAAGTCTAATATCCAGAATC 4745
                                  i      ii  ii      v  ii v  vi          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_89311916_8   4746 TATAAGGAAGTTAAAGAAATTAAGAACAAAG---CAAACAACCCCATTAA 4792
                              i   v ivv v  v i  v  i   i---    i     v   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_89311916_8   4793 AAAATGGGCAATGGACATTAACAGACATTTATCCAA-GAAGACATACACA 4841
                                    v   iv v  i        v     -     i     v 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_89311916_8   4842 TGGCCAGCAAGCATATGAAAAAATGCTCAACACCAAAACAGAG 4884
                               ii     i       i          i  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.68 (51 / 19)  

1799 25.87 0.62 0.62  chr1_89311916_89317286     4885  5371 (0)    L1M4_orf2#LINE/L1      290   776 (132)  

  chr1_89311916_8   4885 ATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATA 4932
                                         i    i--    i  --        vv   i i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACA 337

  chr1_89311916_8   4933 TCTACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGA 4982
                          i  iiii  vi    i  i     ivv  v   i v  vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_89311916_8   4983 AAGGATTCCCTATTTCATAAATGGTGCTGGGAAAACTGGCTGGCCATATG 5032
                            i  vvi  v  iv i              v      v i?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_89311916_8   5033 TAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATGAATT 5082
                         i i  iiv    ii    i    v   i     v           v  i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_89311916_8   5083 CAAGATGGATTAAAGACTTAGATGTTAGACCTAAAACCATAAAAACCCTA 5132
                            i      i ?    i  i    v   v       i      vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_89311916_8   5133 GAAGAAAACCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACT 5181
                                  v    ?i- v   -   iv   v v  vv i     v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_89311916_8   5182 TCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAA 5231
                           v ivv  vi            vvi          vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_89311916_8   5232 TGGGATTTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAT 5281
                          v   i  v  i   v v  i i   i  ii vv    i  v    i  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_89311916_8   5282 CAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACT 5331
                         v i      v  i     i   i             v       vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_89311916_8   5332 CATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACT 5371
                         i      i  i  i  vi          v  i  v     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.24 (68 / 55)
Gap_init rate = 0.01 (4 / 487), avg. gap size = 1.50 (6 / 4)  


2510 24.52 7.30 3.76  chr1_89322797_89324906      741  1617 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89322797_8    741 TGGAGAGATATTCCATGTACATTGACTGGAAAAATTAATATTGTTAAAAT 790
                             i      i      v   v  i     i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89322797_8    791 GTTCATACTATCTAAAAAAAATCTACAGGTTTA-CACAATTTCTATCAAA 839
                          viv     vi i   vvi -       i  i - i    ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGA-TCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_89322797_8    840 ATTCCAATGGTGTTTTTTCACAGCAGTAA--GA-AAACCAATTATAAAAT 886
                           i   iiv iv      ----    v  --  -  i ii  iv      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT----GCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_89322797_8    887 TCATATGGAACCATAAAAGACCCCAAATAGCCAAAACAA----------G 926
                                   viii  ii     vi              ---------- 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_89322797_8    927 AAAAACAGAGCCAAAGGCATCATACTATCTGACTTCAAAATCTACTACAA 976
                           i    i  iiii   vv   i   vi ii i       ii        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_89322797_8    977 AG-----GTA-TCAAG-TAGTGTAATGCTGGCATAAAGA--GACATCTAA 1017
                           -----   -     -i     ii i         i  --     v  i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_89322797_8   1018 CTGCATGGAACAGAATAGAGAGCCAGGAAACAAACCCACACATTTACAGT 1067
                         v vv      i     v     i vi    i       i       ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_89322797_8   1068 CAAAGACTTTTCAAAAAAATGTGTCAAGAGTACACCATGAGAAAAAGATA 1117
                            vviv     i v  ii-   i     vi iv v   i i   ii   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_89322797_8   1118 GTATCTTTAATAAATGGTG---GAATGG-TGG---------TG----GGA 1150
                           v i  i  i        --- i iii-   ---------  ----i  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_89322797_8   1151 A---AACTGGACCCTTGT-----ACTACACACAAATGTCAACTAAAAATT 1192
                          --- ii       i ii-----  i i i     vi i    v     v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_89322797_8   1193 GGTTAAAGATTTGAACATAAGACCAGAGACTGTAAAACTCCTAAGAGAAA 1242
                          i i ?   ii i  ii     v vi i   i        i  ii     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_89322797_8   1243 ACCCAGG---AAATACTCCTTGACACTGGTCTTGGCAATGATATTTTTGA 1289
                           vi   ---    -  i v    vi   vi v       i -  i  ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAG 592

  chr1_89322797_8   1290 ATTTCACACCAAGAGCACAGGAAACAAGTGCTAAAAGAAACTAGTGGGAC 1339
                           v v       i      i v     iv vv    v i iv i v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_89322797_8   1340 TACATCAAA-CTAAG----TTACCACTCAATGAAAAAACA-----AAGAA 1379
                          v       -i   i----  vvii  --- v   ii   -----     
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCT---TCAAAGGACACTATCAAGAA 689

  chr1_89322797_8   1380 AGGAAAAAAGAAAAGGCAACATACAGAAT---AGAACATATTTGCAAACC 1426
                           v------      i    vi       ---    v           i 
  L1M4_orf2#LINE/    690 AGT------GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_89322797_8   1427 ATATATCTGATAAGTGCTTAATATCCAAAATATATAATGAGCTCATATAA 1476
                                       v vi vi      i         v  i   v  i  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_89322797_8   1477 CTCAATAGCAACACAACAAAACAAAATACAACAAAACTGATTTTTAAAAA 1526
                                ----- i  v  i     ---i   ---- ii   ?----   
  L1M4_orf2#LINE/    784 CTCAATA-----ATAAAAAGACAAA---TAAC----CCAATTW----AAA 817

  chr1_89322797_8   1527 AATGAGCAAAAGACCTGAACAGACATCCCTCAAAAGAAGACATTTAAATG 1576
                             i     i  ii    i      ii   v        i  vi     
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_89322797_8   1577 GCCATCAAGTATGTGAAAGCATGTTCCGCATCACTAATCTT 1617
                             vi   i ii     iv   i  vi     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (145 / 68)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 3.23 (97 / 30)  


3201 26.21 0.88 0.88  chr1_89332022_89337827     4406  5313 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89332022_8   4406 TGGAAGAGCATTCCATGTTCATGGATAGGAAGAATCAATATCGTGAAAAT 4455
                              iiii  i              v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89332022_8   4456 GGCCCTACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4505
                            vv    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89332022_8   4506 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAACT-ACTTTAAAGTT 4553
                          v   iivi i  i  ii     -   ---- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr1_89332022_8   4554 CATATGGAACCAAAAAGAGCCC-GCATTGCCAAGAGAATCCTAAGCCAAA 4602
                                  viiv  i ii   - v  v     i v    i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_89332022_8   4603 AGAACAAAGCTGGAGGCATCACACTACCCGATTTCAAACTATACTACAAG 4652
                                  i      vv       v   i        viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_89332022_8   4653 GCTACAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 4702
                                   v   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_89332022_8   4703 CCAATGGAACAAAAC--AGAGCCCTCGGAAATAATACCACACATCTACAA 4750
                         i        i i  i--    i  --i       vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_89332022_8   4751 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 4800
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_89332022_8   4801 CCCTATTTGATAAATGGTGCTGGGAAAACTGGCTAGCCCTATGTAGAAAG 4850
                         vi  v  ii i              v      v  ?  vi   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_89332022_8   4851 CTGAAACTGGATCCCTTCCTTACACCTTATAAAAAAATTAATT-GAAATG 4899
                         v    ii    i    v   i     v    v         i -i     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_89332022_8   4900 GATTAAAGTCTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 4949
                            i ?  v i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_89332022_8   4950 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAC 4998
                           v    ?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_89332022_8   4999 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATT 5048
                           vi            vvi          vv        i    v   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_89332022_8   5049 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAGTACCATCAGAGTG 5098
                          v  i   v v  i i   i  ii vv    i  v v  i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_89332022_8   5099 AACAGGCAACCTACAGAAGGGGAGAAAATGTTTACAATTTACCCATCTGA 5148
                           v  i     i      v          i   i   v i ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_89332022_8   5149 CAAAGGGCTAATGTCCAGTATATACAAAGAACTTAAACAAAGTTACAAGA 5198
                         i  i  i  vi i     v     i        ivv    vviv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_89332022_8   5199 AAAAAATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACA 5248
                             i -    i     v  i?    i     i      v    i     
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_89332022_8   5249 CTTCTC-AAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAATGAT 5297
                         i     -        i  vi viii     i ii          i   v 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_89332022_8   5298 CATCATCACTGGCCAT 5313
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


2486 26.89 2.41 2.74  chr1_89338728_89341809.rev     1681  2591 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89338728_8   1681 TGGAAAAACATTCCTTCCTCATGGAGAGACAGAATCAATATTGTTAAAAT 1730
                               i i  i  v vi       vv iv   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89338728_8   1731 TACCTTACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCTATTAAAC 1780
                         vi vv    v      vii  i  i        i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89338728_8   1781 TACCATTGAGATTCTTCACAGAATTAGAAAAAAACTGTTTTTAAAAAATT 1830
                          v   vivivv  i  ii     v v  v  i--   v ii     --  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAA--TT 146

  chr1_89338728_8   1831 CATATGGGACAGAAAAAGAGCTCAGGCAAAAAATAGCCAACGCAATTCTA 1880
                                i vv v  ii  - i   ------         vi    ii i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA-CCCAG------AATAGCCAAAACAATCTTG 189

  chr1_89338728_8   1881 AGCAAAAAGAACAAAGCTGGATG-------CTACTCGACATCAAACTATA 1923
                          iv  i          i    v -------  v i i iv     viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_89338728_8   1924 CTACAGGGCTACAGTAACCAAAATA-CATGGAACTGGTACAAAAACAGAC 1972
                              ii          i   i i -ii   v     i i  ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_89338728_8   1973 ACATAGACCAATGGAACAGAACAGATAACCCAGAATTTAAGACTGCACAA 2022
                          i     i        i    iv  v ii      v -  iv iii   v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT-AAACCCATACAT 338

  chr1_89338728_8   2023 CTACAACTATCTGATCTTTGACAAACCTGAAAAAAAAAAAAAGCAATGGG 2072
                         i  iiiii vi    i  i     ivv  vv  i vv v---v       
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT---TCAATGGG 385

  chr1_89338728_8   2073 GAAAAGATTCCCTATTCAATAAATGGTGCTGGGATAACAGGCTAGCCATA 2122
                             ii  vvi  v     i              i   v  v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_89338728_8   2123 TGCAGAAGATTGAAATTGGACCCTTTACTTAGACCATATACAAAAGTTAA 2172
                             i    v    i        i vv  i v             i    
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_89338728_8   2173 CTCAAGATGGATTAAAGACTTAAATATACAACCCAAAACTATAAAAACCC 2222
                              i      i ?    i     i  vi v i            vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_89338728_8   2223 TGGAAAACCACCCTGGC-CATATCATTCAGGACATAGGCATGGGCAAAGA 2271
                          i   i vv  viv  ?-i v   -   iv   v v  vv i     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_89338728_8   2272 TGTCAC-GATGAAGACACCAAAAAAGCTATAGTAACAAAAGCAAAAATTG 2320
                          v  vi-   - v          ivi - -  i        v      v 
  L1M4_orf2#LINE/    585 TTTCTTAGAT-ATGACACCAAAAGCAC-A-AGCAACAAAAGAAAAAATAG 631

  chr1_89338728_8   2321 ACAAATGGGAACT------AACTAAAGAGCTTCTGCACAGCAAAAGAAAC 2364
                          i    v   vi ------  i    i -   i  ii vv    i  v  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACAC 680

  chr1_89338728_8   2365 CATCAACAGAGTAAACAAACAACCTAAAGAATGGGAGAAAATATTTGCAA 2414
                         i     v i   i  v i      i v                       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_89338728_8   2415 ACTCTGCAGCTGACAAAGGACTAATATCCAGCATCTATAAGGAACGTAAA 2464
                          iiv ii v    i  i     vi       v  v     i    vivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_89338728_8   2465 CAAATTCACACACACAAAAA--AATA---CA-TTAAAAAGTGGGCAAAAG 2508
                            v iv i - i v   i --    ---  -  ?    i        i 
  L1M4_orf2#LINE/    781 CAACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_89338728_8   2509 ACATGAACAGACACTTTTCAAAAGAAGACATACATGCAGCCAACAATCAT 2558
                          iv    i     i  i  v        i     viii     i  v  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_89338728_8   2559 ATGGAAAAAAAAAAGCTTAACATCACTGACCAT 2591
                            ----    i v   i       ????????
  L1M4_orf2#LINE/    880 ATG----AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.24 (47 / 21)  


3047 27.49 0.68 0.45  chr1_89403167_89405270.rev      721  1604 (500)    L1M4_orf2#LINE/L1        1   886 (22)  

  chr1_89403167_8    721 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATACCATGAAAAT 770
                              ii i  i     i        v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89403167_8    771 GGCCTTACTGCCCAAGGTAAT--ATAGATTCAATGCCATCCCCATCAAGT 818
                            vv    v     iv i  -- i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89403167_8    819 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTGA 866
                          v   iivi i  i  ii     -   -- v  i  - iii    i  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_89403167_8    867 TATGGAACCAAAAAATAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAG 916
                                viiv  iiv v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_89403167_8    917 AACAAAGGTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 966
                                v      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_89403167_8    967 TAAAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGATATATAGACA 1016
                           v     i   i     i         i iv ii i   i       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_89403167_8   1017 AATGGGACAAAACAGAGGCCTCAGAAATAACCCCACACATCTATAACCAT 1066
                              i i i  iv   ivii         v    i    i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_89403167_8   1067 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 1116
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_89403167_8   1117 ATTTAATAAATTGTGCTGGGAAAACTGGCTGGCCATATGTAGAAAGCTGA 1166
                         v  i  i    v         v      v i?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_89403167_8   1167 AACTGGATCCCTTCCTTACAACTTATACTAAAATTAATTCAGGATGGATT 1216
                          ii    i    v   i   v v     v        i   ii      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_89403167_8   1217 AAAGACTTAAATGTTAGACCTAAAACCATAAACACCCT-AGAAGAAAACC 1265
                          ?    i       v   v       i     -  i  -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chr1_89403167_8   1266 TAGGCACTACCATTCAGGACATAGGCATGGGCAAGGATTTCATGACTAAA 1315
                             ?iiv viv   iv   v v  vv i     v i    v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_89403167_8   1316 ACACCAAAAGCAAAGGCAACAAAAGCCAAAATAGACAAATGGGATCTAAT 1365
                                     v i          vv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_89403167_8   1366 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1415
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_89403167_8   1416 GGCAACCTACAGAATGGGAGAAAATTTTTG-AAATCTATCCATCTGAAAA 1464
                          i     i                 v    -     -  vi      v  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAA 746

  chr1_89403167_8   1465 AGGGCTAATGTCCAGAGTCTACAAAGAACTTAAACAAATTTACAAGAAAA 1514
                         i  i  vi i      i v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_89403167_8   1515 AAGCAAACAACCCCATCAAAAAGTTACCAAAGGATACGAACAGACACTTC 1564
                          ii    i     v  i?    i viv        vi   i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_89403167_8   1565 TCAAAAGAAGACATCTATGCAGCCAACAGACACATGAAAA 1604
                           v        i  vi viii     i ii          
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (8 / 886), avg. gap size = 1.25 (10 / 8)  


2790 28.46 1.22 0.66  chr1_89408261_89413964.rev     4311  5213 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89408261_8   4311 TGGGAAAACATTCTGTGCTCACAGATAGGAAGAAGAAATATCATGAAAAT 4360
                            i  i i  i ii  i   ii   v      vvv     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89408261_8   4361 GGCCATACAGCCCAAAGTAATTTATAGATTCAATGCTGTTCCCATTAAAC 4410
                            v    vv      v i  i  i        i  vi i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89408261_8   4411 TACCATTAACATTCTTCACAGAAATAGAAAAAACT-ACTATAAAATTCAT 4459
                          v   vivi v  i  ii       v  v  i-  - iiv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_89408261_8   4460 CTAGAACCAAAAAAGTGCCTGTATAGCCAAGATAATCCTAAGCAAAAAGA 4509
                         v i   viiv  ii vv  v v        i i    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_89408261_8   4510 ACAAAGCTGGAGACATCACACTACCCAACTTCAAACTATACTACAAGGCT 4559
                               i     ivv       v     i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_89408261_8   4560 ACAGTAACCAAAACATCATGGTACTGGTACCAAAACAGACACATAGACCA 4609
                                i   i   vii         i iv ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_89408261_8   4610 ATGAAACAGGCTAGATATATAAGAAATCAGACCACACATCTACAACCATC 4659
                            i  i  iv v  v vviv      v iv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_89408261_8   4660 TGATTTTCAACAAACCTGACAAAAACAAGCCATGGGGAAAGGATTCTCTA 4709
                                 i    ivv  v   i v  vv v          i  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_89408261_8   4710 TTTAATAAATGGTGCTGGGAAAACTCACTGACCATATGTACAAAACTGAA 4759
                           i  i              v    viv i?   i   i v  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_89408261_8   4760 ATTGGACCCTTTCCTTACACTTTATACAAAACTTAACTTAAGATGGATTA 4809
                         i        i v   i    iv         v      i  i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_89408261_8   4810 AAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAAAAGAAAATCTA 4859
                         ?    i         i v i     i      vi i  i       iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_89408261_8   4860 GGCA-ATACCATTCAGGACATAGGCATGGGCAAATATTTTATGATTAAAT 4908
                           ?i- v i -   iv   v v  vv i     vvi   i----   i  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC----TTAGAT 594

  chr1_89408261_8   4909 -TG---CCAAAAGCAATTGCAACAAAAGCCAAAATTGACAGATTGTATCT 4954
                         -  ---         vvv          vv     v  i i    v ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_89408261_8   4955 -ATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGA 5003
                         -  i   v v  i i   i  ii vv    iv v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_89408261_8   5004 ACAGACAACCTACAGAATGGGAGAAAATCTTTGCAATCTACCCATCTTAC 5053
                          v        i                 v       vii ivi    v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_89408261_8   5054 AAAGGTTTAATATCCAGAATCTACAAGGAATTTAAACAAATTCACAAGAA 5103
                           i  vi vi          v  i  i   i ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_89408261_8   5104 AAAAACAA----CCTCATCAAAAAGTGGTCAAAGGACATGAACAGAGACT 5149
                            i    ----  iv  i?    i   v       iv    i   v i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_89408261_8   5150 TCTCAAAAGAAGACTTTTATGTGGCCAACAAATGTATGAAATAAAGCTCA 5199
                             v        iv vi vi       i  iiii      vi v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_89408261_8   5200 ATATCACTGATAAT 5213
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (144 / 109)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


1242 22.64 2.03 2.36  chr1_89428408_89432953     2819  3114 (1432)    L1M4_orf2#LINE/L1        1   295 (613)  

  chr1_89428408_8   2819 TGGAAAGATATTCCATCTTCATGGATTGGAAGAATCAATATTGTTAAAAT 2868
                                    i    v                v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89428408_8   2869 GTTCATACTGCCCAGAGCAATCTACAGATTCAATGCAATCTCCATCAAAA 2918
                          viv     v    i vii              i      i i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89428408_8   2919 TACTAATGACATTCTTCACAGAAATAGAAAAAAATAAAGCT-ATCCCAAA 2967
                          v i iivi v  i  ii       v  v  -------   -    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-------GCTGATCCTAAA 143

  chr1_89428408_8   2968 ATTTATTTGAAACCACGAAAGACCCAGAATAGCCACAGCTATCCTGAGCA 3017
                            i  v  i  vii i ii               v i v   i   iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_89428408_8   3018 AAAAGAACAAAACTGGAGGAATCACATTACCTAACTTCAAA-----TTAC 3062
                          i         ii       v     i v  i  i      -----i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_89428408_8   3063 AGATCAATAGCAACCAAAACAGCATGGTAGTGGCATAAAAACAGACACAT 3112
                          i v v i  i  i   i    ii     v        ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_89428408_8   3113 AG 3114
                           
  L1M4_orf2#LINE/    294 AG 295

Transitions / transversions = 2.19 (46 / 21)
Gap_init rate = 0.01 (3 / 295), avg. gap size = 4.33 (13 / 3)  

2246 26.07 0.64 0.32  chr1_89428408_89432953     3425  4053 (493)    L1M4_orf2#LINE/L1      278   908 (0)  

  chr1_89428408_8   3425 ACAAAAATAGACACATAGACCAGTGGAACAGAATAGAGAACCCAGAAAGA 3474
                          i  ii       i     i  i     i     v    ii       v 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_89428408_8   3475 AATCCACACACCTTTAGTAAACTCATATTCAACAAAGATGTCAAGGACAT 3524
                           i   i   ii v i  v  i v  v   i    i i  i    iv   
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_89428408_8   3525 ACACCAAAGAAAAGACAATCTCTTCAATAATTTATGCTGGGAAAACTGGA 3574
                         v  viiii    ii i i   i     i  v vi        v       
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_89428408_8   3575 TATCCATATGCAAAAGAATGAAACTAGGCCCCTATCTCTTGACATATACA 3624
                           ?   i               ii i i      i   viiv        
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_89428408_8   3625 AAAATCAAATCGAAGTGGATTAAATACTTACATCTAAGACTTCAAACTAT 3674
                              i  v  i  i     i ? v  i  v  v     vi v       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_89428408_8   3675 AAAACTACTACAAG-AAACATTGGGGAAACTCTCCAGGACATTGGTCTGG 3723
                               vi  v   -      v  ? v  v   i iv   v    vi i 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_89428408_8   3724 GCAAAAATTGTTTGGGTAATACCCCTCAAGCACAGGGAACAAAAGCAAAA 3773
                             vii  vi  i i  vv  v  vv       i v        v    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_89428408_8   3774 ATGGGTAAATGGGA--TCATGTCAAGTTAAAAAGGTTCTGCACAGCAAAG 3821
                           i i     v   --    -iv  i       -v  i  ii vv     
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCAT-CAAAATTAAAAA-CTTTTGTGCTTCAAAG 675

  chr1_89428408_8   3822 GAATCCATAAACGAAGTGAAGACACAACATAGAGAATGCAAGAAGATACT 3871
                           vv i  v  vi       i v     vi v      vi    i   i 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_89428408_8   3872 TGCAAACTACCCATCTGACAAAGGATTAATAACTAGAAAATATAAGAAGC 3921
                               ii ivi      i  i   i vi  v i    v      ii i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_89428408_8   3922 TTAAACAACTCTATAGGAAAAAATCTAATTATCCAATCAAAAAATGGGCA 3971
                          ivv       v   iv     iv v   v i     i?           
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_89428408_8   3972 AAAGATTTGAATAGACATTTCTC-AAAAAAGACATATGAATGGAAAACAG 4020
                           i                    -   i    i   ii     vv  i i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_89428408_8   4021 TCATATGAAAAGGTGCTCAACATCATGGATCAT 4053
                         v  i        i            ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (96 / 64)
Gap_init rate = 0.01 (5 / 631), avg. gap size = 1.20 (6 / 5)  


2258 27.62 2.49 1.80  chr1_89480591_89482969.rev      487  1210 (1169)    L1M4_orf2#LINE/L1       42   770 (138)  

  chr1_89480591_8    487 TGTGTGAGATAATATCACACTACCCTAAGGGCTCTACAGATTCAATGCAA 536
                            - i    iii -- i   v   v  vv v             i    
  L1M4_orf2#LINE/     42 TGT-TAAGATGGCA--ATACTCCCCAAATTGATCTACAGATTCAACGCAA 88

  chr1_89480591_8    537 TTCTTATCAAAATACCAATGATATTCTTCACAGAAATAGAAAACAAAATT 586
                          i i         v   iiviiv  i  ii       v  v  vvvi  i
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chr1_89480591_8    587 CAAAAATGTATATGGAACCACAAAATAACATGAATAGTCAAAGTAATCTT 636
                          v     vi        vii   iiv v vv      i    ii      
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_89480591_8    637 GAGCAAGAA---CAAAGCTGGAGGCATCACACTACCAGAGTTCAGTATAT 683
                           iv     ---     i      vv       v  vi v    iv iv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_89480591_8    684 ACTATTTATTCAAAGCCCTAGTAGCCAAAGCACCTTGGTACTAGTATAAA 733
                             ------      ivi    ii   ii  viv       i i    i
  L1M4_orf2#LINE/    239 ACTA------CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_89480591_8    734 -ACAGAAACACAGACTA------CACAATTGAAAATCCAATAATAAATTC 776
                         - i   v i i   ii ------i v      i i    iv      ii 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_89480591_8    777 ACACATTTACAGTTAACTTATTTTTGACAGCAATTCCAATAAAACAT--A 824
                          i       ii  i  i v     i    ivii v    --i v   -- 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA--GACCATTCA 380

  chr1_89480591_8    825 TTGGGGAAAAAGACAGTTTCTTCAATAAATGGTTCTGGGG-AACTGAATG 873
                         v        i - i   i i     i       v     i-     i  i
  L1M4_orf2#LINE/    381 ATGGGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_89480591_8    874 TCCATATGCACAA---TGGAACTAGACCCCTGTATTTCACCATATACAAA 920
                         ?   i     v  ---  i ii i       iiv iv             
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_89480591_8    921 AATCAACTCAAAATATATTAAAGACTTAAATATAAGACTCAAAACTATAA 970
                            i          iv  i ?    i     i     vii          
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_89480591_8    971 AACTACTAGGAGAAGACATAGGGG-AAATACTTCATGACAC-GGTCTGGG 1018
                             vi   i    i       ? -    -    i    vi-  vi i  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGG 578

  chr1_89480591_8   1019 CAAGGAATTTTTGGATAGGACCTCAAAAGCATGTGCAACAAAAGCAAAAA 1068
                            v iv  i  i    v   vi        iiv          v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_89480591_8   1069 TAAACAAATGGGATTACATCAAATGAAAAAACTTCTGCGCAGCAAAGGCA 1118
                           i i    v   i v       vvv        i  i  vv      vv
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_89480591_8   1119 ACAGTTAACAGGGCAAAGAGGCAACCTACAGAATGGGAAAAAACATTAGC 1168
                           vi i  v ii ii  i  i     i           i    i   v  
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_89480591_8   1169 AAACTATGCACTCAACAAAATGTTACTATCCAAAATATACAA 1210
                            ii  ii iiii i  iivii vv      i      i  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

Transitions / transversions = 1.86 (128 / 69)
Gap_init rate = 0.02 (14 / 729), avg. gap size = 2.21 (31 / 14)  

 320 22.60 4.11 4.79  chr1_89480591_89482969.rev     1754  1899 (480)    L1M4_orf2#LINE/L1      764   908 (0)  

  chr1_89480591_8   1754 TATATACAAAACTCAAACAACTCAATAA-AACAA---AAATA-TCTGATT 1798
                               v i     vv            -  v  ---     -i ii   
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_89480591_8   1799 TAAAAA-AGGAAAAATATCCAATTAGACACTTCTCAAAAGAAAACACACA 1847
                         ?     -i  v   iv  iii v      i     v      i i i   
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_89480591_8   1848 AATGGCCAGCAGGTATAGAACAAAATATTCAACTTGGCTAATCATAAGGG 1897
                                 ii i i i vi v  i  ii     -------    ??????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAAC-------ATCAZZZZZZ 906

  chr1_89480591_8   1898 AA 1899
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.20 (22 / 10)
Gap_init rate = 0.03 (5 / 145), avg. gap size = 2.60 (13 / 5)  


1307 29.45 7.89 2.38  chr1_89484429_89486757.rev     1046  1843 (486)    L1M4_orf2#LINE/L1       67   908 (0)  

  chr1_89484429_8   1046 TTTATCTATAGATTTGAGGTAATTCCAAGCAAAAGCCAAGTTGGGTATAT 1095
                           v     i     ii v i   i  v v     v  v  i  --iv v 
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG--CCTTT 114

  chr1_89484429_8   1096 TAATAATTTTAGGAAATGGCTAACTTATTCTAAAATTTATACGGAAAAGC 1145
                          -----  vi  i  v  i v i  v  i        i   i     v  
  L1M4_orf2#LINE/    115 T-----TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_89484429_8   1146 AAAAAACTGAGAACAACCAAGGCAATTCTGAAGAAGAAAACCAAA--TGA 1193
                           iii  iv    i i    ii    ii    i     i v    --  i
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_89484429_8   1194 AAAA---ACA------GATGTCAAAACTTATTATAAAGCTAGTGTAATTG 1234
                          ii ---   ------i  v          i  i       vv     ii
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_89484429_8   1235 AGATAGCATGGTATTGGTGCATGCATGAAG-TA-ATATATAGAT----GC 1278
                            i  ii     i   ------   i i -  - i        ---- v
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGG------CATAAGGATAGACATATAGATCAATGG 303

  chr1_89484429_8   1279 AATAAACTAGAGGGCTCAGAAAGAGACTGACATATGTATGGGGAGTTGAT 1328
                             i v v   i ii      v i  iv i i  v     vv i     
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_89484429_8   1329 T-----CATGG----TAA-------CTATAGGGAAACAATAGTCTTTTCA 1362
                          -----  v  ----i  ------- v  i      v             
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_89484429_8   1363 ATAAATGGCACTAGGCCAATGTTATAGGCATAAGAAAAAACAAAAACTTG 1412
                          i      ii  i  v   ivvv   ?v  i v v    iv vi  v   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_89484429_8   1413 T-TTCTTGCATCCTGTCATCCACAAAAGTCAATTCCACATGGATTGTAGA 1461
                         v-ii i i v  viii   vi      i i  i  v v      ii?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_89484429_8   1462 TTCAAATGTAAAAGACAAAACAATAAACATTTTT----TAAAATGTCAGA 1507
                         iii        i  vi     v     - i i  ----v    ii vi ?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGN 552

  chr1_89484429_8   1508 GATGATTTTCAT--CTTT---TT---CAA--GTTTGG-AAACAGGACAC- 1545
                          vvi  i   i -- i  ---  ---   --    vv- i i v     -
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_89484429_8   1546 AAAAGCACTAAGTGT--AAACAACACATGGAAAAATTTCACTAC-TTAAA 1592
                                 -   iiv--   v  v v  i  v     vv   v - i   
  L1M4_orf2#LINE/    603 AAAAGCAC-AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_89484429_8   1593 ATGAAGAATTCTTGTTCCTCCAAACACACCATGAAATAA-TGAAAAGGCA 1641
                           v  i  i i    v i  v  iv    i  v  iv  -       i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_89484429_8   1642 AACTAAAGT-TACCAGTATATACATAGACATGCATAGAACT-ACACACAA 1689
                          v i v  v- ivv  v v   iv iv v  -    v v  - i - vii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAAT-CATATATCTGATA-AGGG 749

  chr1_89484429_8   1690 ACTCAACCTCAGAATATATTTGGCAGTCAT-CAAGTCATGAAAAAAAGAG 1738
                            iivvii          vvi v v  v -   v   vv  v    -  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA-AG 798

  chr1_89484429_8   1739 ACAGACAAGCCATTAGGAAAATATTCAA-GAATCTTGAATAGGCAAGTG- 1786
                            i i  v   v v?i     ivv   - i  -        i  vv v-
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGACATTTCT 847

  chr1_89484429_8   1787 --AAAAAGAATATTCAAATAAGCAA-AAG-ATATGAAAAGATGCCCAATT 1832
                         --   i ii    v     iiv   -   - i            i   iv
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_89484429_8   1833 TCCCTGTTTAT 1843
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.22 (127 / 104)
Gap_init rate = 0.04 (36 / 842), avg. gap size = 2.28 (82 / 36)  


2897 27.80 1.33 0.78  chr1_89502373_89509047     5280  6182 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89502373_8   5280 TGGAAGCACATTCCATGCTCATGG-TAGGAAGAATCAATATCGTGAAAAT 5328
                              iv i  i     i      - v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89502373_8   5329 GGCCATACTGCCCAAGGTAATTTATACATTCAGTGCCATCCCCATCAAGC 5378
                            v     v     iv i  i  i v     ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89502373_8   5379 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5426
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_89502373_8   5427 ATATGGAACCAAAAAAGTGCCCACATT-GCAAAGTCAACCCTAAGCAAAA 5475
                                 viiv  ii -i    v v -  v  iv   i i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_89502373_8   5476 AGAACAAAGCCAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 5525
                                  iii    vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_89502373_8   5526 GCTACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGA 5575
                                   i   i i  ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_89502373_8   5576 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAA 5623
                         i        i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_89502373_8   5624 CCATCTGATCTTTGACAAACCTGATAAAAACAAGAAATGGGGAAAGGACT 5673
                         i  vi    i  i     ivv  vi  i v  vvv           i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_89502373_8   5674 CCCTATTTAATAAATGCTGCTGGAAAAACTGGCTAGCCATATGTAGAAAG 5723
                         vi  v  i  i     v      i v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_89502373_8   5724 CTGAAACTGCATCCCTTGCTTACACCTTGTACAAAAATTAATTCAAGATG 5773
                         v    ii  v i    vv  i     v i            i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_89502373_8   5774 GATTAAAGGCTTAAATGTGAGACCTAAAACCATAGAAACCCTAGAAGAAA 5823
                            i ?  i i       i   v       i   i  vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_89502373_8   5824 ACCTAGGCA-ATACCATTCAGGACATAACCATGGGCAAAGACTTCATGTT 5872
                           v    ?i- v i -   iv   v vivvv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_89502373_8   5873 TAAAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGAATC 5922
                           vi            vvii         vv     v  i    v i ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_89502373_8   5923 TAATTACACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTG 5972
                          v  i v v v  i i   i  ii vv    i  v   ii  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_89502373_8   5973 AAAAGGCAACCTACAGAATGGGAGAAACTCTTTGCAATCTACTCATCTGA 6022
                              i     i               v v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_89502373_8   6023 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 6072
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_89502373_8   6073 AAAAAACAA-T--CCCA--TCAAAAGTGGGCAAAGTATATGAACAGACAC 6117
                             i    - --    -- ?    i         v  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_89502373_8   6118 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 6167
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_89502373_8   6168 ATCATCACTGGCCAT 6182
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


1697 25.91 8.98 0.86  chr1_89577020_89584623.rev      502  1080 (6524)    L1M4_orf2#LINE/L1      273   898 (10)  

  chr1_89577020_8    502 CTGACAGTAAAAACAGACACATAGACCAATGGAACAGAATAGAGAATTCA 551
                            i  -   ii i     i     i        i     v    i i  
  L1M4_orf2#LINE/    273 CTGGCA-TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_89577020_8    552 GAAATAAATTCACATATTTTAAGTTGCCTCATTTTTGACACAGAGACCAG 601
                                 ii  i i    vvi  iivi v     i    vi ivi   i
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_89577020_8    602 TAATATACATTGGGGAATGTAT-GTTT-----ACAATTGGTGCTGGGA-A 644
                         v vi  v  v       v v  -  i -----    v           - 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_89577020_8    645 ACGTGGATATTAATATGC-------------------------------C 663
                           -      ?iv i    ------------------------------- 
  L1M4_orf2#LINE/    422 AC-TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_89577020_8    664 ATATA------TCAATTCAGAATGGATTAAGTATTTAAATGTAAGACCCC 707
                              ------ i  i   i       i ?iv ii           v iv
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_89577020_8    708 AAACAATAAAACTACTGGAGGAAAACATAGGGA-AAACACTTGCAGACAT 756
                             v        vi i  i           ?i-   ivi i i-   v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACCT 569

  chr1_89577020_8    757 CTGTCCAGGCAACAATTTGATGGGTAAAACTTCAATAGCACACTCAACAA 806
                         iv vii      iii   vv i i  vi  vi   v      vv      
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_89577020_8    807 AAGCAAAAATAGACAAATGAGACT--GTTAAA-TTAAAAGGCTTTTGTGC 853
                            v         i    vi    --i i   -      i-         
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGC 668

  chr1_89577020_8    854 AGCAAAGGAAAAAAACCAACAGAATGGAGAGTCATCCTGCGTAATGGGAT 903
                         vv       v vv -i   v i i  i i  v  v  ii iv       v
  L1M4_orf2#LINE/    669 TTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_89577020_8    904 AATGTATTTGCAAGCTATTCAACTTACAAAGGACTAATGTTCAGAATATA 953
                           vi         iii  vi v  v i  i     vi i i         
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_89577020_8    954 CAA-GAG-TCT--CAACTCAAAAACAAACAAACAAATACTCTTATTAAAA 999
                         i  -  i-   --        v  i   v i       vi iv   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_89577020_8   1000 AATGGGCAAAATATCTGAATAGACATTTCTCAAAAGAAGAGATACAACTG 1049
                                   iv  i                v        v      v  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_89577020_8   1050 GCTAACAAGTATATAAAAAAATGCTTAACAT 1080
                           i  i   i i  i    i     i     
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACAT 898

Transitions / transversions = 1.61 (90 / 56)
Gap_init rate = 0.03 (16 / 626), avg. gap size = 3.56 (57 / 16)  

2951 26.47 1.78 0.78  chr1_89577020_89584623.rev     6215  7113 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89577020_8   6215 TGGAAAAACATTTCACGCTCATGGATAAGAAGAAGTAATATTGTGAAAAT 6264
                               i i  ii  i i        vi     vv         v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89577020_8   6265 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCAACCAAAC 6314
                            v     v     iv i  i  i        i  v     v i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89577020_8   6315 TACCA-TTGACTTTCTT-CACGGAATTGGAAAAAACT-ACTTTAAAGTTC 6361
                          v   -i  v    i  -  - i     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_89577020_8   6362 ATATGGAACCAAAAAAGAACCCGCATAGCCAAGAAAATCCTAAGCCAAAA 6411
                                 viiv  ii  v  v v        i v    i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_89577020_8   6412 GAGCAAAGCTGGAGGCATCACGCTACCTGACTTCAAACCATACTACAAGG 6461
                           i     i      vv    i  v  ii i      v v        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_89577020_8   6462 CTACAGTAACCAAAATAGCATGGTACTGGTGCCAAAACAGATATATAGAC 6511
                                  i   i i  ii         iiiv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_89577020_8   6512 CAATGGAACAGGACAGA-AGCCTCAGAAATAACACCACACATCTACAACC 6560
                                 i  i iv  -  i -         vv   i    i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTC 346

  chr1_89577020_8   6561 ATCTGATCTTTGACAAAGTTGACAAAAACAAGCAATGGGGAAGGATTC-C 6609
                          vi    i  i     i v  v   i v  vv          i  v v-i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_89577020_8   6610 CTATTAAATAAATGGTGTTG-----ACTGGCTAGTCATATGTAGTAAACT 6654
                           v  v  i        i  -----     v  ?i  i   i iv i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_89577020_8   6655 GAAACTGGACCCCTTCCTTACACCTTGTACAAAAATTAACTCAAGATGGA 6704
                            ii         v   i     v i                 i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_89577020_8   6705 TTAAAGACTTAA-TGTAAGACCTAAAACCATAAAAATCCTTGAAGAAAAC 6753
                          i ?    i   -       v       i      v  i v         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_89577020_8   6754 CTAGGCAATACTATTCAGAACATAGGCATGGGCAAAGACATCATGTCTA- 6802
                         v    ?ivv v v   ivi  v v  vv i     v iiv  v ivv  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_89577020_8   6803 AACACCAAAA---CAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 6849
                         i         ---   --          vv     v  i    v   ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_89577020_8   6850 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCATCATCAGACTGA 6899
                         v  i   v v  i i   i  ii vv    i  v  i    vv i v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_89577020_8   6900 ACAGGAAACCTACAAAATGGGAGAAAATTTTTG-AAATCTATCCATTTGA 6948
                          v  iv    i   i             v    -     -  vi  i   
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGA 743

  chr1_89577020_8   6949 CAGAGGGCTAATATCCAGAACCTACAAAAAACTTAAACAAATTTACAAGA 6998
                         i ii  i  vi         iv  i   i    ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_89577020_8   6999 AAAAAACAAACAACCCCATCAAAAAGTTGGTGAAGGATATGAACAGACAC 7048
                             i     i     v  i?    i v  ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_89577020_8   7049 TTCTCAAAAGAAGACATTTTTGCAGCCAACAAACATATGAAAAAAAGCTA 7098
                              v        i  vivviii     i  i  i       i v   v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_89577020_8   7099 ATCATCACTAGTCAT 7113
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.53 (23 / 15)  


1791 23.26 3.38 0.99  chr1_89590412_89596695.rev        2   504 (5780)    L1M4_orf2#LINE/L1      316   830 (78)  

  chr1_89590412_8      2 AGCCCATGAATATACTCTGACATATATGGTCAGT-GATTTCCAGGATGGG 50
                           i   vi    v  i vv    v        i -     i iiv v   
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_89590412_8     51 TGTCAAGATCATTTAATTAAGAAAGAAGAGTCTCTTTAACAAATGATGTT 100
                           i     i    i   vii       v     i  i        i  i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_89590412_8    101 GAGGAAATGAGATATCTCCTT--AAAAAAA----GTTGGGCTCTTACCTT 144
                          i iv  ivi    ? iv v --    i  ----     i i i     i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_89590412_8    145 ATA--ACTTACAAATATGAACTCAAAATGGATCAAAGAACCAAACATTAG 192
                          i -- iv      v  v                ?   v i   ii v  
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_89590412_8    193 AGTTAAAACTATAAAATTTGTAGAAGAAAACA-AGG-GTAAAAGTTATAT 240
                           i             i iv            -   -     vv  -ii 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT-CGT 564

  chr1_89590412_8    241 AATATTGGATTTGGCAATGATTTTTTTTAATAAGAAACCAAAAGTATAGA 290
                         i iv    i  v       i   i  v-i   v  v        i i ii
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTA-GATATGACACCAAAAGCACAAG 613

  chr1_89590412_8    291 CAATAAAAGAAAAAATAGATTAGTTG-ACTTCATCAACATTTAAAACTTT 339
                            i                v i   -          v   v        
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_89590412_8    340 TGTGTATTAACAGACACTATCAACAGAGTTAAAAAAAAGCAACACACAGA 389
                             iv i  vi           v i   v    i ---    v      
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA---CAACCCACAGA 710

  chr1_89590412_8    390 ATGTAAGAAAATATTTGTTAAACATGTATATGATAAGGGATTTATATCTA 439
                            vi            iv  v   i   v          i  i    i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_89590412_8    440 GAAAATATAAAAAAAATTTACAAAGCAACAC-----AGATAAACAACCAG 484
                            v       i  vvi      vv   i v-----   i   i    vi
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_89590412_8    485 ATTAATAAATGAATAAAGGA 504
                            ? v     iii      
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.48 (68 / 46)
Gap_init rate = 0.02 (11 / 515), avg. gap size = 2.00 (22 / 11)  

3298 26.21 0.88 0.88  chr1_89590412_89596695.rev     4886  5793 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89590412_8   4886 TGGAAGAACATTCCATGCTCATGAGTAGGAAGACTCAATATCGTGAAAAT 4935
                              ii i  i     i     ii v        i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89590412_8   4936 GGCCGTACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4985
                            vi    v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89590412_8   4986 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5033
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_89590412_8   5034 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5083
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_89590412_8   5084 AACAAAGCTGGAGGCATCACACTACCTAACTTCAAACTATACTACAAGGC 5133
                                i      vv       v  i  i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_89590412_8   5134 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5183
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_89590412_8   5184 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5231
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_89590412_8   5232 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAGAGGATTCC 5281
                          vi    i  i     ivv  vv  i v  vv         i  i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_89590412_8   5282 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGATAGCT 5331
                           v  i  i              v      v  ?   i   i i viiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_89590412_8   5332 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGA 5381
                            ii    i    v   i     v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_89590412_8   5382 TTAAAGACTTAAAAGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5431
                          i ?    i    v  v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_89590412_8   5432 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGATTTCATGTCTAA 5481
                         v    ?i v viv   iv   v v  vv i     v i    v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_89590412_8   5482 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5531
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_89590412_8   5532 TTGAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5581
                          ii  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_89590412_8   5582 AGGCAACCTATAAAATGGGAGAAAATTTTTGCAACCTATTCATCTGAAAA 5631
                           i     i i i             v       vii  vi      v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_89590412_8   5632 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5681
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_89590412_8   5682 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5731
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_89590412_8   5732 TCAAAAGAAGACCTTTATGCA----GCCAAAAAACACTTGAAAAAATGCT 5777
                           v        ----   i  ----     v  i   v      i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_89590412_8   5778 CATCATCACTGGCCAT 5793
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


2758 26.77 3.04 0.90  chr1_89650936_89656762     4446  5334 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89650936_8   4446 TGGAAAAATATTCTGTGCTCATGGATAGGAAGAATCAAGATTATTAAAAT 4495
                               i    i ii  i        v      v i  v   i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89650936_8   4496 GGCCATACTGCCCAGAGCAATTTACAAATGCAGTACTATTCTCATTAAAC 4545
                            v     v    i vii  i    i  v  iii v  i ii  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89650936_8   4546 TACCATTGACATTTTTCACAAAATAAAAAAAAACT-ATTTTAAAATTCAT 4594
                          v   vivi v     ii  i  - vvi v  i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_89650936_8   4595 ATGGAACTAAAATAGAGCCTGAATAGCCAAGACAATCCTAAGCAAAAAGA 4644
                               v iv  vi  v  v          i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_89650936_8   4645 ATCTACAG--GGAGGCATCACGCTACCGGACTTCAAACTATTCTATAAGG 4692
                          i-- v  --     vv    i  v  vi i      viv v   i  i 
  L1M4_orf2#LINE/    200 AC--AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_89650936_8   4693 CTACAGTAATTAAAACAGCATGATAATGGTACAACAACAGACACATAGAC 4742
                                   i  i    ii  i  v   i i  vi i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_89650936_8   4743 CAATAGCACAGAATAGAGAACCCAGAAATAAGACCACACATTAAACACCA 4792
                             i v i     v    ii          iv   i     v vvii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_89650936_8   4793 CTTGATCTTCAACAAACCTGACAAAAACAAGCAATAGGGAAAGGA--GTC 4840
                         v     i   i    ivv  v   i v  vv    i       i --   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_89650936_8   4841 CCTATTTAATAAATAGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAAT 4890
                         -- v  i  i    i         v      v  ?   i     i  i v
  L1M4_orf2#LINE/    398 --TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_89650936_8   4891 TGAAACTGGACCCCTTCTTTACACCATATACAAAAATCAGCTCAAGATGG 4940
                             ii         v i i                 i i     i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_89650936_8   4941 ATTAAAGATATAAATGTAAAATCAAAAACTATAAAAACCCTACGAAAAAA 4990
                           i ?   iv         i v v            vi i  vi i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_89650936_8   4991 TCTAGGCA-ATACCATTCAGGACATAAGCACTGGCAAAGATTTCTT-GAT 5038
                         iv    ?i- v i -   iv   v vi vviv     v i      -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_89650936_8   5039 A---------AAG---ATGCGA--AAAGCAAAGATTGACAAATGCAATCT 5074
                          ---------   --- v  i --    v   i  v  i    vvi ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_89650936_8   5075 AATTAAACAAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5124
                         v  i   vvv  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_89650936_8   5125 ACAGACAACCCACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAA 5174
                          v                          v       vii  vi      v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_89650936_8   5175 AAAGGCCTAATATCCAGCACCTACTAGGAACTTAAACAAAT---TTACGA 5221
                           i  v  vi       v iv  iv i     ivv    v --- v ii 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_89650936_8   5222 GAAAACAAACAACCCCATTAAGAAGTGGGTAAAGGACATAAACAGACACT 5271
                         i  i     i     v   ? i  i    i      iv i  i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_89650936_8   5272 TCTCAAAAGAAGAC---CACATGCAGCCAAAAAGCATATGAAAAAAAATT 5318
                             v        i---  v   --     v     i       i vii 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCT 892

  chr1_89650936_8   5319 CAGCATCACTAATCAT 5334
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.33 (35 / 15)  


3228 27.20 0.55 0.55  chr1_89668069_89674464     4996  5903 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89668069_8   4996 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAGTCAATATCGTGAAAAT 5045
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89668069_8   5046 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89668069_8   5096 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_89668069_8   5144 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5193
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_89668069_8   5194 AACAAAGCTAGAAGCATCACCCTACCTGACTTCAAACTATATTACAAGGC 5243
                                i i  i vv    v  v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_89668069_8   5244 TACAGTAACCAAAACAGCATGGTACTGGTGCCAAAACAGAGATATAGATC 5293
                                 i   i    ii         iiiv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_89668069_8   5294 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 5341
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_89668069_8   5342 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5391
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_89668069_8   5392 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5441
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_89668069_8   5442 AAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5491
                         i  ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_89668069_8   5492 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 5540
                          i ?    i       v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_89668069_8   5541 CCTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTA 5590
                          v    ?i v viv   iv   viv  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_89668069_8   5591 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5640
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_89668069_8   5641 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTGTA 5690
                           i   v v  i i   i  ii vv    i  v   ii  vv i    v 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_89668069_8   5691 CAGGAAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5740
                         v  iv    i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_89668069_8   5741 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5790
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_89668069_8   5791 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5840
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_89668069_8   5841 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5890
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_89668069_8   5891 CATCACTGGCCGT 5903
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2688 20.47 0.54 0.00  chr1_89686667_89689875.rev     1387  1938 (1271)    L1M4_orf2#LINE/L1        1   555 (353)  

  chr1_89686667_8   1387 TGGAAACATATCTGATGTTCATGGATTGGAAGACATAATATTGTTAACAT 1436
                               v     iv                    v            v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89686667_8   1437 GTCAATACTATCGAAAGAAATCAACAGATTCAATTCAATCTCTATCTAAA 1486
                          v       vi v   vvi   v          iv     i     v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89686667_8   1487 TCCCAAAGATTTTTTTTGCAGTAATAGAAAAAATCATCCTCAAATTTATA 1536
                              ivviii          v   v  v  iv v     v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_89686667_8   1537 TGAAATAGCAAGGGAACCCAAATAGCATAAATAATCTTGCAAAGGAAGAA 1586
                           i  vv        v  vi      vv   i       v   i      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_89686667_8   1587 CAAAGCTGAAGAACTCATGTTTTCTGATTTTGTACCTTACTATAAATCTA 1636
                              i  i  i     iii  i ii    iiv v       i   v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_89686667_8   1637 TAATAATCAAAACAGTGTGGCACTGGCATAAAGACAGACAGACAGACTAA 1686
                         i i       i         i          i  i     v i   ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_89686667_8   1687 TGGAATAGAATAAAGGGTTCAGAAATAAACTCTCACACATACAATCAAAG 1736
                                    vi  i  i           i vi   iv  iii    vv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_89686667_8   1737 GATTTTCGACAAGGATGTTAAGACCATTCAGTGTGGAATGGACAGTCTTT 1786
                                       i  ii           i  v    v i i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_89686667_8   1787 TCAACAAATGGTGCTGATAAAATGGGATAACCACATACAAAAGAATGAAG 1836
                                         iv v  iv     ?      i             
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_89686667_8   1837 TTGGACCCTTACCTAGCACCGTATACAAAAATTAACTCAAAATGAATCAA 1886
                                 i     vi    i                       i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_89686667_8   1887 AGAAGTAAATGTAAGACCTAAAATAATGCCACCATTA--AGAAGACATAG 1934
                            vv           v      iv  ivv  iv   --    i      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_89686667_8   1935 G-GTA 1938
                          -   
  L1M4_orf2#LINE/    551 GNGTA 555

Transitions / transversions = 1.27 (62 / 49)
Gap_init rate = 0.00 (2 / 555), avg. gap size = 1.50 (3 / 2)  

1506 20.45 2.99 1.75  chr1_89686667_89689875.rev     2318  2718 (491)    L1M4_orf2#LINE/L1      503   908 (0)  

  chr1_89686667_8   2318 ACTTAAAGTATAATAATAAAAAAT-TAAAA------AAAGAAGACATAGG 2360
                           i    - i   v iiv    v -     ------i     i       
  L1M4_orf2#LINE/    503 ACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_89686667_8   2361 GTAAAAACTTCAAGACTGTGTATTTGGCAATGGTTTCTTAGATATGACAC 2410
                         ?vv   v    iv   iv  vi  v                         
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_89686667_8   2411 CAATGGCACAGGCAACAAAAGAATAAGTAGACAAATGGAACAGTATGAAA 2460
                            vi     i            v  i    i    v i  vvi  v   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_89686667_8   2461 AGTAAATAGTTTTGTGCACCAAAAAGACACTATCAATAGAGTTTAAAAAG 2510
                          v    v v        vi    i-           v i   v-    ii
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTG-AAAAGA 699

  chr1_89686667_8   2511 CACCTCACAGAATGAGAGAAACTATTTGCAAACCATATATCTGTTAAGGG 2560
                           v i         i      v          i          v      
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_89686667_8   2561 ATTAATACCCAG--TATGTAGAGAACTCCTGTATCTTAAAAACAGAAAAA 2608
                          i vi  i    --   i  i       i ii v  i  v  i i   i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_89686667_8   2609 CAAA---CTGATTTTAAAAAAGGGGAAAGGACTCAAATAGACATTGCTCC 2655
                             --- iv v  ?     v   v      i ii          v    
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_89686667_8   2656 AAATAATTTATACAAATGACTAGTAAACAAATACATAAAAAGATGCTCAA 2705
                            v  vv          i i i   i  ----   i             
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCA----CATGAAAAGATGCTCAA 895

  chr1_89686667_8   2706 CATCACCCAACCA 2718
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (44 / 36)
Gap_init rate = 0.02 (8 / 406), avg. gap size = 2.38 (19 / 8)  


3276 27.09 0.44 0.44  chr1_89924859_89931133.rev     4877  5784 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_89924859_8   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_89924859_8   4927 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_89924859_8   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_89924859_8   5025 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_89924859_8   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_89924859_8   5125 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_89924859_8   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5222
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_89924859_8   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_89924859_8   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_89924859_8   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_89924859_8   5373 TTAAATATTTAAGCGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ? v ii   ii  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_89924859_8   5423 CTAGGCATTACCATTCGGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5472
                         v    ?i v viv    v   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_89924859_8   5473 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5522
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_89924859_8   5523 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACGATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv    i  v    iv vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_89924859_8   5573 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5622
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_89924859_8   5623 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5672
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_89924859_8   5673 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5722
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_89924859_8   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5772
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_89924859_8   5773 ATCACTGGTCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 596 28.17 6.41 8.49  chr1_90026696_90028356.rev      500  1170 (491)    L1M4_orf2#LINE/L1      252   908 (0)  

  chr1_90026696_9    500 AATAAATAAAACAGTGTATCAAAGGCCCAAGAACATACAATTAAGTCAAC 549
                          i   vi  i       ivi vv   vi   i i v   vv  ii    -
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA- 300

  chr1_90026696_9    550 TGGAACCAAATAGAGATCTCAGAAAGATACATCTACATATATG--CA-CT 596
                              ivi   v    vii      v v  viv     v    --  -i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_90026696_9    597 GACATCC--TAGGGGTAGCACCAAAAC---TCTGTGGAGAAAGAAT-GTA 640
                           iv i --i i    i---    i  ---  vi   i        -  -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG---CCAAGACCATTCAATGGGGAAAGAATAGT- 396

  chr1_90026696_9    641 CTAGTTGGCAAATAGTGCTGGGAAAACTGGCTCACAATATGACCAGATTT 690
                           vv iii     i         v      v v? v i   --  i ---
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG--CAAA--- 441

  chr1_90026696_9    691 TTAAAAATAAAAATTGGGTTAATACTTCGTATCTCA------AATTA--- 731
                         --- i   i  i-    iiivv   i  ii i vi ------     ---
  L1M4_orf2#LINE/    442 ---AGAATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_90026696_9    732 CAAAG-AGTTTAAAAACCCAAATAATAAGAGT--AACCTTTGAAGTTAAT 778
                             i-i v i ? i   i    i-      i--  v  v i  ii vv 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATG-TAAGAGCTAAAACTATAAAACTCTT 536

  chr1_90026696_9    779 AAAAGAAAATG-AGGAGAGACAACATTGTGAGCCCAGAATAGGGGAGGAT 827
                          i       ii-   ? vi - v v i    v iii iv    vi v i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_90026696_9    828 TTCTTAAAT--GACTCAAAATGCACAGACCATAATA-ATAATATAAAGTG 874
                               i  --   v v   v     ii v i  v - v  v   i vvi
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_90026696_9    875 ATGAGACAAGTACATTAAAACTAAAGATTTTATTGTTGCTATTACTGAAA 924
                           vi   --- v   i    i    i i   --   -   - i ---  i
  L1M4_orf2#LINE/    636 ATTGGAC---TTCATCAAAATTAAAAACTTT--TGT-GCT-TCA---AAG 675

  chr1_90026696_9    925 GGCACCATAGACAAAGTTATTAGGAAAGTGACACACTAGAAGAAAGT--- 971
                          i   i  vi v     v vv  iv  viv   v v i i     i ---
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_90026696_9    972 TACAA------TGTCTAAAGACAAAGAGGAATTAATTTCTAGAATACACA 1015
                          i   ------ i   ---  i  ---  i i vi v  i      i i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCT---GATAA---GGGACTTGTATCCAGAATATATA 769

  chr1_90026696_9   1016 AGAAAC-ATTACAAAAATTCTCTCAAGAAGTTCTTGCAAGAAAAAGGCAA 1064
                          ii   -v      -------     ----------i  v      i   
  L1M4_orf2#LINE/    770 AAGAACTCTTACAA-------CTCAA----------TAATAAAAAGACAA 802

  chr1_90026696_9   1065 GAGACCCAAC-AGAAAATAAAGGGCAGGCTAAAGACATAAAAAGACAATT 1113
                         ivi      i-?i     ---     ----  i  iv i  v     v  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAAT---GGGCA----AAGGATTTGAATAGACATTT 845

  chr1_90026696_9   1114 CATGGAAAAGGGAAAT-TAAAT------TAAGTAAATGAAGACATGTTCA 1156
                          - vv   iii  v  -i    ------    i v     i v   i   
  L1M4_orf2#LINE/    846 C-TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_90026696_9   1157 GCCTCACTAGCAAT 1170
                         i v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (111 / 74)
Gap_init rate = 0.06 (38 / 657), avg. gap size = 2.63 (100 / 38)  


3313 25.88 0.66 0.66  chr1_90235117_90241391.rev     4877  5784 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_90235117_9   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90235117_9   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCATTGCCAGCCCCATCAAGC 4976
                            v     v     iv i  i          vi  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_90235117_9   4977 TACCAA-TGATTTTCTT-CAGAGAATTGGAAAAAACT-ACTTTAAAGTTC 5023
                          v   i-  vi   i  -    -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_90235117_9   5024 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5073
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_90235117_9   5074 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACGAGG 5123
                                 i      vv       v  ii i      viv      i i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_90235117_9   5124 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5173
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_90235117_9   5174 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5221
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_90235117_9   5222 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5271
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_90235117_9   5272 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5321
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_90235117_9   5322 TGAAACTGGATCCCTTCCTTACACCTTGTACAAAAATCAATTCAAGATGG 5371
                             ii    i    v   i     v i         i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_90235117_9   5372 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5421
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_90235117_9   5422 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5470
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_90235117_9   5471 AAAACACCAAAAGCAATGGCAACAAAGGACAAAATTGACAAATGGGATCT 5520
                          vi            vvi        i  v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_90235117_9   5521 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5570
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_90235117_9   5571 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5620
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_90235117_9   5621 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAGAAGAA 5670
                           i  i  vi          v  i  v      vv    v iv v  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_90235117_9   5671 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5720
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_90235117_9   5721 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5770
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_90235117_9   5771 CCATCACTGGCCAT 5784
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3185 26.57 0.77 0.66  chr1_90346679_90350319     2242  3148 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_90346679_9   2242 TGGAAGAACATTTCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 2291
                              ii i  ii    i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90346679_9   2292 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCTGCCCCATCAAGC 2341
                            v     v     iv i  i           i  vvv   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_90346679_9   2342 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGCTC 2388
                          v   i-       i  -i     -   -- v  i  - iii    ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_90346679_9   2389 ATATGGGAGCAAAAAAGAGCCTGCATCGCCAAGACAATCCTAAGCCAAAA 2438
                               i iiiv  ii  v  v v  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_90346679_9   2439 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 2488
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_90346679_9   2489 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 2538
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_90346679_9   2539 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAAC 2586
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_90346679_9   2587 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 2636
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_90346679_9   2637 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2686
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_90346679_9   2687 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATGAATTCAAGATGG 2736
                             ii    i    v   i     v           v  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_90346679_9   2737 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2786
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_90346679_9   2787 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCT 2835
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_90346679_9   2836 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACATATGGGATCT 2885
                          vi            vvi          vv     v  i v  v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_90346679_9   2886 AATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 2935
                         v  i   v v  i ii  i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_90346679_9   2936 ACAGGAAACATACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 2985
                          v  iv   vi                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_90346679_9   2986 AAAGGGCTAACATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 3035
                           i  i  vii         v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_90346679_9   3036 AAAAA-ACCCCACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACT 3084
                            i - vviv    v  i? v  i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_90346679_9   3085 TCTCAAAAGAAGACATTTACGCAGCCGACAGACACATGAAAAAATGCTCA 3134
                             v        i  vi viii   i i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_90346679_9   3135 TCATCACTGGTCAT 3148
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3306 26.13 0.66 0.55  chr1_90392554_90396851.rev     2900  3806 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_90392554_9   2900 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2949
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90392554_9   2950 GGCCATACTTCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2999
                            v     i     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_90392554_9   3000 TACCAAG-GCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 3046
                          v   iv-      i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_90392554_9   3047 ATATGAAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 3096
                              i  viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_90392554_9   3097 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 3146
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_90392554_9   3147 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 3196
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_90392554_9   3197 CAATGGAACAGAAC--AGAGTCCTCAGAAATTATGCCGCATATCTACAAC 3244
                                 i    i--       --      v vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_90392554_9   3245 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 3294
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_90392554_9   3295 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3344
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_90392554_9   3345 TGAAACTGGATCCTT-CCTTACACCTTATACAAAAATCAATTCAATATGG 3393
                             ii    i  i -   i     v           i  i    v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_90392554_9   3394 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3443
                           i ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_90392554_9   3444 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3493
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_90392554_9   3494 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 3543
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_90392554_9   3544 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3593
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_90392554_9   3594 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 3643
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_90392554_9   3644 AAGGGCTAATATCCAGAATCCACAAAGAACTCAAACAAATTTACAAGAAA 3693
                          i  i  vi          vi i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_90392554_9   3694 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 3743
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_90392554_9   3744 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACACGAAAAAATGCTCAC 3793
                            v        i  vi viii     v  i    i     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_90392554_9   3794 CATCACTGGCCAT 3806
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3464 22.83 1.20 2.61  chr1_90404350_90411783.rev     3199  4118 (3316)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_90404350_9   3199 GGAAAAATAT-----GTTCATGGATTATAAGCATCAATATTGTTAAAATT 3243
                              i    -----           iv   vv i           i  v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_90404350_9   3244 CCA-TGCTACCCAAAGCAATGTACATATTCAGTGCAATCTCTATCAAAAT 3292
                         v  - i  v      vii  v    v     ii      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_90404350_9   3293 ACCAATGATATTCTTCACAGAAATAGAAAAACCAATTCTAAAATGTATAT 3342
                         v   iiviiv  i  ii       v  v  i ii  i       vi    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_90404350_9   3343 GGAATCACAAAAGACTCAGAATAGCCAAAGCTATCCTGAGCAAAAAGAAC 3392
                             vii   ii   i             i v   i   iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_90404350_9   3393 AA--CTGCAGGAATCACATTTCCTGACTTCACATTATACTACCAAGCTAT 3440
                           --i  v    v     i    ii i    v viv      v      i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_90404350_9   3441 AGAAAGCTCTGTAGCTCTATAGTAAAACTGCATGCAGTACTGGCATAAAA 3490
                           v  ----------  ------  i  v ii  --            ii
  L1M4_orf2#LINE/    252 AGTAA----------TC------AAGACAGTGTG--GTACTGGCATAAGG 283

  chr1_90404350_9   3491 ACAGACACATAGACCAATGGAACAGAGTAGAGATCCCAGAAACAAATCCA 3540
                          i     i     i        i   i v    vi       i   i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_90404350_9   3541 CACATCTACAGTGAACTTATTTTTTACAAAGGTGCCAAGAATATACATTG 3590
                         i    i  ii  v  i v     iv    i          vi  v  v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_90404350_9   3591 GGGAAAAGACAGTCTTT-CAATAAATGGTGCTGGGAAAACTAGATATCCA 3639
                               ii i       -   i              v    i    ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_90404350_9   3640 TATGCAGAAGCATGGAATTAGACCC-TATCTCTCACTATATACAAAAAAA 3688
                         i     i   v   i i  i     -  i   v   i           vv
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_90404350_9   3689 AAAAAAAAAAAAAACGGATTAAAGACTTAAATGTAAGACCTCAAACTATG 3738
                           vvv    -----i    i ?    i           v  v       i
  L1M4_orf2#LINE/    484 AACTCAAAA-----TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_90404350_9   3739 AAACTACTAAAGGAAGGCATTGGGGAAACTCCCCAGGACATTGGCCTGGG 3788
                              vi  i i   ii   v  ? v  v  ii iv   v    vi i  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_90404350_9   3789 CAAAATTTTTTTGGGTAATACCTCACAAGCACAGGCAACCAAAGCAAAAA 3838
                            viv   i  i i  vv  vi  v       i     v    v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_90404350_9   3839 TGGAAAAATGGGATCACATCAAC-TTAAAAAGCTTCTGAACAGCAAATGA 3887
                          i  v    v   iiv      v-       -   i  vi vv    v  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

  chr1_90404350_9   3888 AACAATCAACAAAGTGGAGAGACAACCCACAGAAAGGGAGAAAATATTTG 3937
                         v  v     v      i i               v               
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_90404350_9   3938 CAAACTACCCATCTGACAAGGGATTAATAACCAGAATGTATAAGGAGCTC 3987
                             ii ivi      i      i vi  v       i     i  i   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_90404350_9   3988 AAACAACTCTATACGAAAATCTCTAACAATCCAATTTTAAAATGGGCAAA 4037
                         vv       v   vv    vvv v  i  i      ?v            
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_90404350_9   4038 ACATATGAATAGACATTTCTCAAAAGAAGATATACAAATGGCAAACAGGC 4087
                         iv  v                v                    v  i i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_90404350_9   4088 ATACAAAAAGGTGCTCAGCATCACTGATCAT 4118
                          i ii     i      i     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (118 / 88)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 3.18 (35 / 11)  

 258 27.05 9.84 4.10  chr1_90404350_90411783.rev     5672  5793 (1641)    L1M4_orf2#LINE/L1        1   129 (779)  

  chr1_90404350_9   5672 TAGAAAGATACACCATATTCAAAGATGAAAAGATTTAATATTGTTGAGAT 5721
                          i        iv    i    vi   vii    i           i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90404350_9   5722 GTTGTTATGGGCTGAATTGTGTCCTCTA-AGATTCA----------TGTT 5760
                          viiv  ivvv ii     ----v    -       ---------- i i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG----ATCTACAGATTCAACGCAATCCCTATC 96

  chr1_90404350_9   5761 AAGCTCCTAATTCCCATTATTTG-AGAATGTGAC 5793
                           iv   i ii v  v  -    -    vv    
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTT-TTTGCAGAAATTGAC 129

Transitions / transversions = 1.36 (19 / 14)
Gap_init rate = 0.04 (5 / 129), avg. gap size = 3.40 (17 / 5)  

1894 27.02 6.39 2.41  chr1_90404350_90411783.rev     6115  6943 (491)    L1M4_orf2#LINE/L1       47   908 (0)  

  chr1_90404350_9   6115 AGATTTTAAT-CTCCCCAAGTTGATCAATAGATGCTATGCTATTGTAATC 6163
                             vvi   -        i      v i    v v i  v  iviv   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_90404350_9   6164 AAAGTCCAAACAGGCATTTTTGTAAAAATTGATAAATGGATCCTAAAATG 6213
                            i   v i v v v      i i       i  iiv           v
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_90404350_9   6214 TATATG-AAATA-AAGGAAACAAGTAAGTTATGTAAAAAACAAAATAATC 6261
                         i     -    i-    i v v  ----------  v iv     i    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAG----------AATAGCCAAAACAATC 186

  chr1_90404350_9   6262 TTGAAAGATAATA-------CGGAAGATTTATACTACCTGATTTAAAGAC 6304
                               i v  v -------i   i  i i i   v  ii    v  i  
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_90404350_9   6305 ATA--ATAAAACTACTGTAATCTAGGCAGTAAGGAAT-------AGGAGA 6345
                         v  -- i   i    v      v  i    iv  v i-------    v 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_90404350_9   6346 AGCAAACAGATCAAATGAACAGAATAAAGAATACATAAATAGACCCACAT 6395
                         ii  v i       vv   i     vi   i v  v     i     i i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_90404350_9   6396 ATATATCATCAATTG-TTT---ACAGAGGCAATAAGGA-ATTCAGAGGGG 6440
                           v   vi       -   ---   ii  iivi   iv-     iv    
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_90404350_9   6441 AAAGGAAA--CTTTCTAACAAATAATTCTAGAAGAACTGGATAACTATAT 6488
                             i v --    ii       ii v  i i v         ? i i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_90404350_9   6489 GACAAAAAAAT-AATTTCAACTCCTACCTCACACCATGAACAAAAATTAA 6537
                          -     i   -  v  vi  i               iv           
  L1M4_orf2#LINE/    437 G-CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_90404350_9   6538 TTTTGGATGGCTCATAGATCCAATTACAAAAGTTGAAACTACAAAGCTTC 6587
                         i ivii    v   ?   i i  v ii  i  i i      i   i  ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_90404350_9   6588 TAGAAGAAAACATAAGAGAATATTTTCATGAACTTGAATAAGAAAA-ATT 6636
                                       i ? v v  i   i   v    ii v  iv  -iv 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_90404350_9   6637 TTCTTAGGCAAGTCTTAAAGAGCATTA-----AAAAGAAAATTTTGA-AA 6680
                                ii v v viv  i    iv -----         vv v  -  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_90404350_9   6681 AT--GACTGGTGGACAAAATGTAAAGCTTCTGCTTGTCAAA--ACAAAA- 6725
                           --    -- viv      vv   i   i  iviv     --   vv -
  L1M4_orf2#LINE/    636 ATTGGACT--TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_90404350_9   6726 AAAGAAAATGAATAGGCAA---AAAAAGTGAGAAAAAATATTCATAACAC 6772
                         v      i    v  i   --- v i i  i  i        iii  vv 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_90404350_9   6773 ATCCCTCCAGCAAAGAACTTATGATCAGAATGTATAAAGAGCTC---CGA 6819
                           viv  iiii  i i    i ivi      i        i   --- i 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_90404350_9   6820 CT-AATAGCAAAAAGACAG----TGCA-TTGATAATATCAGCAACAGATT 6863
                           -    ii         i----iv  -  ? v  -  vi    vi    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGGATT 832

  chr1_90404350_9   6864 TGAACAGCC-TCTCATAAAACAAGATATATGAATATATATGGCCAG-AAC 6911
                             i  v - i  viv   v        ii   ------     i-  v
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAAT------GGCCAATAAG 876

  chr1_90404350_9   6912 CCAATGAAAAGGTATTCAACATCATTAGTTGC 6943
                          vv        i ii         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (131 / 89)
Gap_init rate = 0.03 (29 / 862), avg. gap size = 2.52 (73 / 29)  


2924 28.44 1.11 0.22  chr1_90424664_90430471     4416  5315 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_90424664_9   4416 TGGAAAAACATTCCATGCTCATGGGTAGGA-GAATCAATATCGTGAAAAA 4464
                               i i  i     i      i v   -  v i     i  v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90424664_9   4465 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCCATCCCTATCAAAC 4514
                            v     v      v i  i  i       ii  v            v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_90424664_9   4515 TACCATTGACTTTCTTCACAGAATTAGAAAGAACT-ACTTTAAATTTCAT 4563
                          v   vivi i  i  ii     v v  v - i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr1_90424664_9   4564 ATGGAACCAAAAAAGAGCATGTATAGCCAATACAATCCTAAGCAAAAAGA 4613
                               viiv  ii  v vv v        v      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_90424664_9   4614 ACAAAGCTGGAGACATCATGCTACCTGACTGCAAACTATACTGCAAGTCC 4663
                               i     ivv   ii  v  ii i v    viv    i   iv i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_90424664_9   4664 ACAGTAACTAAAACAGCATGGTACTTGTACCAAAACAGATACATAGACCA 4713
                                ii  i    ii       v i iv ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_90424664_9   4714 ACGGAACAGAACAGAGGCCTCAGAAATAACAACACACATCTACAACCATC 4763
                          i    i    iv   ivii         vvv  i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_90424664_9   4764 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 4813
                             i  i     ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_90424664_9   4814 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 4863
                           i  i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_90424664_9   4864 ACTGGAACCCTTCCTTACACC-TACACAAAAATTAATTCAAGATGGATTA 4912
                         ii    v    v   i     -  i           i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_90424664_9   4913 AAGACTTAAATGTTAGACCTAAAACTGTAAAAACCCTAGGATAAAACCTA 4962
                         ?    i       v   v        i     vi i   i v     v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_90424664_9   4963 GGCA-ATACCATTCAGGACACAGGCATGGGCAGTGACTTCATGACTAAAA 5011
                           ?i- v i -   iv   viv  vv i    i  ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_90424664_9   5012 CACCAAAAGCAATGGCAACAAAAGCCAAAATGGACAAATGAGATCTAATT 5061
                                    vvi          vv     i  i    vi  ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_90424664_9   5062 AAACTAAAGAGCTTCTGCACAGAAAAAGAAACTACCATCAGAGTGAACAG 5111
                            v v  i i   i  ii vvv   i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_90424664_9   5112 GCAACCTAAAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAG 5161
                         i     i v               v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_90424664_9   5162 GGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTGCAAGAAAAAA 5211
                          i  vi          v  i  i     ivv    v ivii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_90424664_9   5212 ACAA----CCCCATCAAAAAGTGG-TGAAGGATATGAACAGACACTTCTC 5256
                             ----   v  i?    i   -ii      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_90424664_9   5257 AAAAGAAGGCATTTATGTGGCCAAAAAACGTATGAAAAAA-GCTAATCAT 5305
                         v       ii  vi vi       v  i ii       i -   v v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_90424664_9   5306 CACTGGTCAT 5315
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (150 / 102)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2362 27.73 2.40 3.82  chr1_90495075_90498097.rev     1617  2532 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_90495075_9   1617 AGATATGCTTTTCTTCATGAGTTAAAAGACTCAACATGGTAAAGATATCA 1666
                               - iiv v      ii  ii      i  i  v  v     iv  
  L1M4_orf2#LINE/      6 AGATAT-CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_90495075_9   1667 ATTTTCCCCAAAATGATATACAAGTTTAACTGAATTTTTATAAAAATACC 1716
                           vi        v    v    ii  i   vv   iii   v     v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_90495075_9   1717 AGCAAGAGTTTTTCTAGTCACAGACAAGATTATTCTAAAATTTATGTTTA 1766
                            vivvv     vi  vv iv      v v  i        i  i vv 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_90495075_9   1767 AAGGCAAAAAAAAAAAAACCTTGAATACGCAAAACTATTTTTTAAAAAAA 1816
                           v    iii -------  iv     vv      v  i  vv    i  
  L1M4_orf2#LINE/    155 AATGCAAGGGA-------CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_90495075_9   1817 ---TAAAGTGGGAGCAATCATCCATACTCGATTCCAAGACTCATTGTAGA 1863
                         ---i     v    v v   iv v - i i   i   i   i i ii i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAA 246

  chr1_90495075_9   1864 GCTACAGTAATCAGTTT--TATGGTTCTGGCAGAGAGACAGACACA--GA 1909
                                      ivvi-- i    v      v ii  i     i --  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_90495075_9   1910 CTCATGAGACAGAACAGA-AGACTTAAAGTAGACTCATCCACAAAAATAT 1958
                         iiv   ii i    iv  -  v ivi  i  i  i   v  iv----   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT----TAT 342

  chr1_90495075_9   1959 G-TCCACTGATATTTGAGAACTATGCAAAAAGAATTCAATAGAGAAAGAA 2007
                          -  v i    v  i  v  vvi   v  i vv       i i       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_90495075_9   2008 GATTGTCTTTTCAAAAAATGGTACTGGATCAATTAGACGTCCATAAGCAA 2057
                         v --          v       i    iv   i i  ii?   i v    
  L1M4_orf2#LINE/    393 TA--GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_90495075_9   2058 AAAAAAAAAA--AAACGCCTCAAACTGAGTCTCGGACTTTACACAAAAAT 2105
                           i  vi  i--ii  v   ---  -----   iv  iv  i        
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCT---AC-----CTCACACCATATACAAAAAT 482

  chr1_90495075_9   2106 CAACT-AACATGGATTATTGACTTAAATGTAAAATTTTAAACTATAAAAC 2154
                         i    -  v      i ?v   i         i vi v            
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_90495075_9   2155 TCTTAGAAAAAA---TAGA---ATATTTTCAGAAACTAGGGCTAGGCAAA 2198
                                 i   ---   i--- v  i   ivi v  v   i       v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_90495075_9   2199 GAGTTCTTAGACTTAATACCAAAAGTGTGATTCTTAAAAGGAAA--T-GA 2245
                          iv        iv i i        iiii vivvi     i   -- -  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_90495075_9   2246 TAAATTTAACTTCATTGATATTAAAAATGTTTGCTCGGTGGAAGATCCTG 2295
                               vi       ii v        iv    iv vviii i  iv  i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_90495075_9   2296 TTAAGTGGATGAAAAGACAAGCTATACATTGGAAGAAGATATTTGCAAAC 2345
                          i   viii           v i i v v   i    i           i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_90495075_9   2346 CACATATCCAACAAAGGACTAGTACCTAGCATATACTGTAGAAGGCACTC 2395
                           i     ii i  i     v   i i  v     i-----  i v    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATAT-----AAAGAACTC 777

  chr1_90495075_9   2396 TGGAAA-TCAAAAGTAAAAATAAATAAATAAATAAATTCAAATAGAAAAT 2444
                          viv  -    v i      ------i i      -ii   v ?i     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAA------GACAAATAA-CCCAATTWAAAAAT 820

  chr1_90495075_9   2445 GGACAAAAGACATGCACAGATATTTCACTGAAGCTGATATATATATGGCA 2494
                           i    i  iv  v i   i     v ii   vv      i v     v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_90495075_9   2495 AATAAGCACGTGAAATGATGTTAAATATCATTAGCCAG 2532
                                  i     v    i v  i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (148 / 103)
Gap_init rate = 0.02 (22 / 903), avg. gap size = 2.59 (57 / 22)  


3156 25.40 3.63 0.68  chr1_90507363_90510176     1440  2321 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_90507363_9   1440 TGGAAAGATATTCCATGTTTACAGATTAGAAGACTCAATATTGTTAAAAT 1489
                                    i       i ii    i       i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90507363_9   1490 GATCTTACTACTTCAAGCAATGTACAGATTCAATGCAATCTCTATCAAAA 1539
                          iivv    v iiv  vii  v           i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_90507363_9   1540 TACCAATGACATTCTTCACAGAAATAAAAAAA--GATTCTGAAATTTATA 1587
                          v   iivi v  i  ii       vi v  i--   i  i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_90507363_9   1588 TAGA-----------CCCA-------CAAAGCTGTCCTGAGCAAAAAGAA 1619
                          i  -----------    -------    i vi  i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_90507363_9   1620 CAAAACTGGAGGCATAAGACTACCTGGCTTCAAATTATACTACA--GCTA 1667
                             ii      vv v v   v  iiii      viv       --    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_90507363_9   1668 TAGTAACCAAAACAGCATGGTACTGGCATAACAACAGATACATAGACCAA 1717
                         i     i   i    ii              vi i   i i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_90507363_9   1718 TGGCACAGAATAGAGAACCCAGAAGCAAATCCGTAAATCTACAGTGAACT 1767
                            v i     v    ii      ii   i  i  v  i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_90507363_9   1768 CATTTTCAACAAAGGTGC-AAGAACGTACACTGGGGAAAGCACAGTGTCT 1816
                         v      i    i     -    v i v  v         v i   v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_90507363_9   1817 TCAATAAATGATGCTGGGAAAACTGGATATCCATATGCAGACAAATAAAA 1866
                             i     i        v         ?   i     i vi   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_90507363_9   1867 CTAGACCCCGTATCTTGT--TATATACAAAAATCAAAGCAAAATGGATTA 1914
                         i i      -  i  iii--i            i  vv          i 
  L1M4_orf2#LINE/    451 TTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_90507363_9   1915 AAGACTTAAGTCTAAGACCTCAAACTCTGAAGCCCCTAAAAGAAAACATT 1964
                         ?    i   i v     v  v     v i  i i i  i          -
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT- 548

  chr1_90507363_9   1965 CAGGA--AACTCTCCAGGACATTGGAGTGGGCAAAGATTTCTTGAGTAAT 2012
                         -   ?--  v   i iv   v    iv i     v i      iii  vv
  L1M4_orf2#LINE/    549 -AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_90507363_9   2013 ACCCCACAAGCAGAGGCAACCAAAGCAAAAATGGACAAATGGGATCACAT 2062
                           v   v     v i     v    v      i  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_90507363_9   2063 CAAG-TTAAACATCTTCTGCACAGCAAAGGAAGCAATCAACAAAGTAAAG 2111
                            i-     v -   i  ii vv       vi v     v     i  i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_90507363_9   2112 AGACAACACACAGAATGGGAGAAAATATTTGCAAACTACCCATCCAATAA 2161
                                v                           ii ivi   ii    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_90507363_9   2162 GGGATTAATAACCAGCACATAGAAGTAGCTC--A-AACACGATGGGGGAA 2208
                             i vi  v    v i   v  iv i   -- -   v i  iivii  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_90507363_9   2209 AATCTAG-AACTCTGATTTTTAAAGTGGGAAAAAGAACTGAATAGACATT 2257
                          iv v i-   i -- v  ?v   i    v   i  vi            
  L1M4_orf2#LINE/    797 AGACAAATAACCC--AATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_90507363_9   2258 TCTCAAAAGAAAACTTGCAAATGGAAAACAGATGTATGAAAAGATGTTTA 2307
                             v      i iv i       vv  i iiiii           i i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_90507363_9   2308 ATATCATGGATTAG 2321
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (142 / 78)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.53 (38 / 15)  


3343 23.93 3.84 1.35  chr1_90600704_90604933     2852  3737 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_90600704_9   2852 TGGAAAGATATTTCATGCTCATGAATTGGAAGAATCAATATTGTCAAAAT 2901
                                    ii    i     i         v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90600704_9   2902 GTCCATACTACCCAAAGCGATATACATATTTAATGCAATCTCTATCAAAA 2951
                          v v     v      vi   v    v   i  i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_90600704_9   2952 TACCAATGACATTCTTCACAGAAATAGGAAAAA-AATCCTAAAATTTATA 3000
                          v   iivi v  i  ii       v iv  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_90600704_9   3001 TGGAACCACAAAATACCCAGAATAGCCAAAACTATCCTAAGCAAAAAACA 3050
                              vii   iiv                  v   i i --    i - 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGA-A 197

  chr1_90600704_9   3051 AAACAAAACAAAAAAACTGGAGGAATCATGTTTCCTGGCTTCAA------ 3094
                         i      ii--------       v   iii    iiii     ------
  L1M4_orf2#LINE/    198 GAACAAAGT--------TGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_90600704_9   3095 -------GTTATAA-----AAAACAGCATGGTACTGGCATAACAACAGAC 3132
                         ------- i  i i-----  i    ii              vi i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_90600704_9   3133 ACATAGACCAATGGAACAGAATAGAGAA-CCAGAAACGAATCCACACACC 3181
                          i     i        i     v    i-       ii  i   i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_90600704_9   3182 TACAGTGAACTCATTTTCAACAAAGGTGCTAAGAACACACACTGGGGAAA 3231
                           ii  v  i v      i    i     i    v  iv  v        
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_90600704_9   3232 AGACAGTCTCTTTAATAAATGGTGCTGGGAAAATTGGGTATCTATATACA 3281
                         ii i     i  i  i              v  i   i  ? i i  i  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_90600704_9   3282 GATGAATGAAACTAGGCCCCTATCTCTCACCATGCACAAAAAT-AAATCA 3330
                         i v       ii i i      i   v      ii        -  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_90600704_9   3331 AAATGAATTAAAGACTTAAA-----GACCTCAAACTATGAAACTACTACA 3375
                              i  i ?    i    -----  v  v       i     vi  v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_90600704_9   3376 AGAAAACATTGGAGAAAATCTCCAGGACGATTGGTCTGGGCAAAGATCTC 3425
                                  v  ? v      i iv   v-    vi i     v i i  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTC 588

  chr1_90600704_9   3426 TTGCATAATACCCCACAGGCACAGGCAACCAAAGCAAAAATTGACAAGTG 3475
                           iv   vv  v   v i     i     v    v      v  i  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_90600704_9   3476 AGATCGTATCAAGTGTAAAATCTTCTGCAAAGCAAAGAAAACAATCAACA 3525
                         i  iivi     ivv     v   i  iivvv     i v  v     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_90600704_9   3526 AAGTGAAGAGATAACCCACAGAATGAGAGAAAATATTTCTAAACTGCCCA 3575
                                i   i             i            vi   iiiivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_90600704_9   3576 TCTGACAAGGGATTGATAACCAGAATATATATGAAACTCAAACAACTCTA 3625
                              i      i vi  v            vii     vv       v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_90600704_9   3626 CAGGAAAAAATCTAATAATCCAATT-AAAAATGGGCAAAAGATTTGAATA 3674
                         i iv     iv v     i      -             i          
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_90600704_9   3675 AGCATTTCTTTTAAAAAGACATAAAAACAG-------ACATATGAAAAGG 3717
                         ii       iiv  i    i   v   ii -------i  i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_90600704_9   3718 TACTTAACATCACTGATCTT 3737
                          i  i       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.99 (139 / 70)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.83 (46 / 12)  


2936 21.45 3.20 8.00  chr1_90607240_90609168.rev      502  1438 (491)    L1M4_orf2#LINE/L1       17   908 (0)  

  chr1_90607240_9    502 GTTTATAGATTAGAAAATGTAATATTGTTAAGATGTCAATTCTTCCCAAA 551
                            i  i    i   i iv                v    v  i      
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chr1_90607240_9    552 TTGATCCACAGACATAACACAATTCCAGTCAAAATTCCAGTAGGCTTTTT 601
                               i     ivi   i    i  vi       i    iv v      
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTT 116

  chr1_90607240_9    602 TATAGAAATGGATAAGTTGATTCTAAAATGTGTATGGAAATATGAAGGAC 651
                          ii      v  i   i    i       vii         iii i    
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr1_90607240_9    652 CTAGAA-AAACAAAACAATTTTTCTAAAGAA---CGAAGATGGAGGACTT 697
                          i    - iv         i  vvv      --- i   v         i
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr1_90607240_9    698 AT-CTTCCTGATTTAAAGACTTATTATAAAGCTTCATTAACCAAGGTAGA 746
                          i-     ii    v  i     i  i      v  v   i    ii  v
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr1_90607240_9    747 TTAATATTGGCA-AAAAATATACATATAGATCATTGGAACAGAGTAGAGA 795
                         v ii  i     -  ii   v            v     i   i v    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr1_90607240_9    796 ATTCAGAAATAGATCAACATGTATATGGTAAATTGTTTTTTGTAAATAAA 845
                         i i        i i v i ii v      v     ---------------
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTG--------------- 351

  chr1_90607240_9    846 ATTTTTTACTTTTATTTTTTGTGAGTATATCATAGGTATATACATTTGGT 895
                         --------------------------------------------------
  L1M4_orf2#LINE/    352 -------------------------------------------------- 351

  chr1_90607240_9    896 AAATTCATTTTTAACAAGAGTGTCAAAGCAATTTAATGGGGGAAAGAAAA 945
                         ------     ii     i   i   ii v   i       -      v 
  L1M4_orf2#LINE/    352 ------ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chr1_90607240_9    946 GTCTTTTCAACAAATGGTGTTGGATCAAATGAATATCCATACAGAAAAAA 995
                                            i   iv   v  i   ?   i iiv    i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_90607240_9    996 ATTAGCATTAACTCTTACCTCACATTATACACAAAAAATTATCTCAAAAT 1045
                           v ivv vi  i i         ii   i       -   v        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAAT 493

  chr1_90607240_9   1046 GGATGATAGACCTAAATGTAATACTTAAAACAATAAAACTTCTGGAAGAA 1095
                             v ?              v vi      v        ii i      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_90607240_9   1096 AATATAGGAGAAAATTTTACAGCATC---AGTGATGGCAAAGTTTTCGTA 1142
                           i     ? v    i  - ivv i ---i  v -     v v    v  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTT-CGTGACCTTGGGTTA-GGCAATGGTTTCTTA 591

  chr1_90607240_9   1143 TACATGA-----AAAGCTTAAATGATATAAAAAAAAAT-TATAAATTGAA 1186
                         v i    -----     vi  iii i v  i       -v        i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_90607240_9   1187 CTTCATCAGAATCTAAAACCTCTGCTTTTCAGATGACACCATTAAGAAAA 1236
                                 i   iv     i i  ivi    i v     i  i      i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_90607240_9   1237 CAAAAAAGTAAGCCACAGAGTG--AGGAAATATTTGTAGCATATATATCA 1284
                         ii    iii  v       i  --  i         i ivvi       v
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_90607240_9   1285 GATAA----CTTGTATCCAAAGAATATAAAAAACTCTTACAACTGAATAA 1330
                              ----          i iv       i             v     
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_90607240_9   1331 CAA---GATAAGCACCTCAATT-ATAAATGGTCAACATATT-AAACAGAT 1375
                         i  ---  i  ii v i     - v      v   viv   -i  i   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_90607240_9   1376 ATTTT---ATATAAGATATAAACATGGCCAGTAAGCACATCAAAA-ATAT 1421
                             i--- v v        v v       i         v    -  ii
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_90607240_9   1422 TCCACATTATTAGTCAC 1438
                           v    i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (128 / 70)
Gap_init rate = 0.02 (19 / 892), avg. gap size = 5.53 (105 / 19)  


1704 25.90 4.72 2.61  chr1_90629581_90632218      971  1584 (1054)    L1M4_orf2#LINE/L1        1   627 (281)  

  chr1_90629581_9    971 TGGAGAGGTATATTGTATTTGTGTATTGAAAGATTTAGCATTTTTAAGCT 1020
                             i  i   viii i  ii  v    i    i   ii   v     v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90629581_9   1021 ATTAGCTCTCCCCAGATTTTTCTGTCGATTCAATG-AATCCCAATCATGA 1069
                         ivi iiv       i   vv   iiv       i -      v    vi 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_90629581_9   1070 TGGCCAAA--ACCTTCTTTTGTAGAAA----CAAGCTT-TTATGGAAAAT 1112
                          --  v i--i    -     i     ----      v- iv --     
  L1M4_orf2#LINE/    101 T--CCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCT--AAAAT 145

  chr1_90629581_9   1113 TTATATAAAAATGCAAAGAAACTAAAATAGCCTA-----TTTTTAAAAAT 1157
                          i    ii        i i v i i       v ----- i  v     v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_90629581_9   1158 AAAAACAGAAGTAAATAATATGTTACCTCAATCCATATCATTACTTATGA 1207
                           i    i iv ii vi i- vvi  i  --i v  v   vv     iv 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGAC-TCACACTTC--CCAATTTCAAAACTTACTA 242

  chr1_90629581_9   1208 TAATGCTACAGGAGTTAAGACACTGTGGTATTGGCATA-GGACAGACA-- 1254
                         i  v       v i i      v       i       -   i     --
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_90629581_9   1255 -AGATCAAGGGAGCAGAATAGAATGTC-AGAAGTAAAACTTCACATTTAT 1302
                         -       v   ii     v  iv   -    i    v ivi        
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_90629581_9   1303 GGTAATTTCATTTTCCAACAAAGGCACCAAGATAATTTCATGGGGGAAAA 1352
                            v v  v      -i    i  ii      iv   iv      i  i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_90629581_9   1353 GATAGTCTTT-AAACAAATTGTGATGGAA-ATCTGGATATCTATATAGAA 1400
                         -         -v       v   v   i - v       ? i i  iv  
  L1M4_orf2#LINE/    392 -ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_90629581_9   1401 AAAAATA---T---ACCTCCACTTTTACACCATACACAAATATTGACATA 1444
                           i   i--- ---   i i  i i-        i     v   i  vi 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTC-ACACCATATACAAAAATTAACTCA 489

  chr1_90629581_9   1445 AAATGAATCATAGTCCTAAACATAAAAGCTAAAACTATAAAATTTCTGGA 1494
                              i    ?  v      ii   i                i ii i  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_90629581_9   1495 A--AAATATCACTGGAAAGGTCTTCATGACCTTGTGATACGTAAAGATTT 1542
                          --   i  viv? v   --     i        v v  v i  v i   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_90629581_9   1543 CCTAAGTCATAAACATACACAAATTAAAACA-TAAAAGAAAAA 1584
                          i  ii -  i -  i-  v  iivv  i  -i          
  L1M4_orf2#LINE/    588 CTTAGAT-ATGA-CAC-CAAAAGCACAAGCAACAAAAGAAAAA 627

Transitions / transversions = 1.69 (98 / 58)
Gap_init rate = 0.04 (26 / 627), avg. gap size = 1.73 (45 / 26)  

 567 28.67 3.67 1.00  chr1_90629581_90632218     1846  2145 (493)    L1M4_orf2#LINE/L1      601   908 (0)  

  chr1_90629581_9   1846 CCAAAA--AAAAGAAAAAAAAGAAAAATTAAATAAACCCAACATCATAAA 1893
                               -- v   v  v          v  i     iivi  v    v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_90629581_9   1894 AATGTAAAACTTTTGCTCTTCAAAAGATACTGTTAAGAAAATTGTAAGCT 1943
                            vv          iv       i  i   i i      i viv   vi
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_90629581_9   1944 AGGCCATCGACTAAGTCAAAGTATTTATAATATGTTTATCTTACAAAGGA 1993
                          iv   iv  v ii vv   i     ii  vvii v     v i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_90629581_9   1994 TTTCTATTTAAAATATTGTAAAATAATATTGTA---CAATTTTAAAATAA 2040
                         i  v   ii i     -i    iv v v  ii ---    vv     vi 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATAT-ATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_90629581_9   2041 CCAAAAAT--GAT--AGAAAGGGGCAAAATATTTGAACAGAAACTTTACA 2086
                          v  v  i--i  -- i   v       iv       i   v i  iv v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_90629581_9   2087 AAATAAGATGTATAAATGTCCAACTAATATATTTTAAAGGAT--TCAACA 2134
                            v     i  i     v    iv ii i  v--   i   --      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATG--AAAAGATGCTCAACA 897

  chr1_90629581_9   2135 TCATTTAGGGA 2145
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.15 (46 / 40)
Gap_init rate = 0.02 (7 / 308), avg. gap size = 2.00 (14 / 7)  


3007 26.16 2.93 0.56  chr1_90666869_90671094.rev     2859  3745 (481)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_90666869_9   2859 TGGAAACACATCTCGTGCTCGTGGATAGGTAGAATCAATATTGTGAAAAT 2908
                               v i   i i  i  i     v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90666869_9   2909 GACCATACTGCCAAAAGTAATCTACAAATTTAACACAATCCCTATCAAAA 2958
                          i v     v  v   v i       i   i   i               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_90666869_9   2959 T----ACTGCCATCATTCTTCACAGAAATAGAAAAAACAATTCTAAAATT 3004
                          ----i     ----  i  ii       v  v  ivii  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_90666869_9   3005 CACATGGAACCAAAAAAGAACCCTCATAGACAAAGCAAGGCTAAGCAAAA 3054
                           i      viiv  ii  v  vvv    v    i   vvi i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_90666869_9   3055 AGAA---ATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAG 3101
                             --- vi      vv       v  ii        viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_90666869_9   3102 GCCATAGTCACCAAAGCAGCACGGTACTGGTATAAAAATAGGCATATAGA 3151
                           i i   v i   ii   iii        i    ii    i        
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_90666869_9   3152 ACAATGGAACAGAACAGTGAAACCAGAAAGAAGCCCAAA----TACAGCC 3197
                         v        i    iv v  iv       v  i    v ----  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_90666869_9   3198 AAATGATCTTCGACAAAGCAAACAAAAACATAAAGTGGGGAAGGGACACC 3247
                           v    i        i vviv   i v   vv i       i i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_90666869_9   3248 CTTTTTAACAAATGGTGCTAGGATAATTGGTTAGCCACATATAGGGGAAT 3297
                              i             i   i  i   v  ?      ii iii    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_90666869_9   3298 GAAAGTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGA 3347
                            iv    i  ii i   v    v           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_90666869_9   3348 CTAAGGACTTAAATCTAAGACCTGAAACTACAAAAATTCTAGAAGATAAC 3397
                         ii ?i   i     v     v  i      i    v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_90666869_9   3398 ATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAA 3447
                           v  ?iv  vi    vv   v    v        v i    v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_90666869_9   3448 GAACCCAAAAGCAAATGCAATAAAAACAAAGATAAA-AAGCTGGGCCTTA 3496
                           vv         v v    i    iv   i   i -  ii   i i i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_90666869_9   3497 T-----TTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAA 3541
                          -----     i -      iiivv    i iv  vi   iv i   i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_90666869_9   3542 TAGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACA 3591
                         v              i           v  ii   vii   i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_90666869_9   3592 AAGGACTAATATCCAGAATCTACAATGAACTG----AAATCACTAAGAAA 3637
                          i     vi          v  i  v     v----  v   v   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_90666869_9   3638 AA--CAAACAATTCCATCAAAAAGTGGGCTAGGTACATGAAT-GACAATT 3684
                           --    i  ii v  i?    i     v i v iv     -    v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_90666869_9   3685 CTCAAAACAACATACACAAATGGCCAACAAACATAT-AAAAGAAGTTTA- 3732
                            v   v  v   i            i  i  i  -      v i i -
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_90666869_9   3733 CGTCACTAATGAT 3745
                          i   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (137 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


3196 19.78 5.22 6.52  chr1_90696414_90701634     1878  2797 (2424)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_90696414_9   1878 TGAAGAGATATATCATTTTCATAGATCGGAAAA-TCAATATTGCTAAGAT 1926
                           i i      vi   v     i   i    i - i       i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90696414_9   1927 GGCAATTCTCCCCAAATTAATCTATAAAT-CAATGTAATCCCTATCAAAA 1975
                               v           i     i i  -   i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_90696414_9   1976 TCCCCACAGGAACCCTT---GTAGAAATTAAC----T-ATCTTAA--TTT 2015
                             vi v ---  i  --- i       i  ---- -   i   --  i
  L1M4_orf2#LINE/    101 TCCCAGCTG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_90696414_9   2016 AGGTAGAAATATAGAGAACCAAGATTAGACACAACAACTTTGAACAAGCA 2065
                          vi i     ii ii i   v   v   v  v     ii     v   v 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_90696414_9   2066 GAACAAAGCTGGGGGACTTAAACTGCCTGGTTTCAAAACTTAT---AAAG 2112
                                 i   i     i v   v  iii            i---    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_90696414_9   2113 TTATGGTAATCACATCAATGTGGTATTGGCAAAATGATGCTAATACCATA 2162
                         i  ii       viv  i       i     v  v   i-----------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA----------- 286

  chr1_90696414_9   2163 TTGACAAATGGATCAGTAGAAAAGAAT--AGAGTCTTGATATAAAACCTT 2210
                         --    v  i     i i   v     --      iv  v     v  v 
  L1M4_orf2#LINE/    287 --GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_90696414_9   2211 CACATTTATGGT---------------AAG-----TAAGACAATTCAATA 2240
                         -           ---------------   -----i     v       i
  L1M4_orf2#LINE/    335 -ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_90696414_9   2241 AAGAAAGGATAGTCTTTTCAACAAATGGTGCTGA-ACAATTGGCTATCCA 2289
                         ii     i                         i-    i   v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_90696414_9   2290 TATGTAAAAAAGGAACTTTTATCTCTTGGAAGAAAAGGAGGAGGAGGAGA 2339
                         i   i    ---------------------------------------  
  L1M4_orf2#LINE/    434 CATGCAAAA---------------------------------------GA 444

  chr1_90696414_9   2340 AAGAACTTACACCTTTACCTAGCACCATACACAAAAATTAATTTAAAATG 2389
                          v   v  iv   ii     vi       i           i i      
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_90696414_9   2390 AATTTCAGTCCTGAATGTAATAACTAAAACTA--AAAC-CTTATAAAGAA 2436
                         i  iv?  v   i       v i         --    -    -i     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA-GAAGAA 543

  chr1_90696414_9   2437 AATATAGGGGCAAATTTTTGTGACCTTAAGGCAGATAAAGCTTTCATAAA 2486
                           i     ? i    i  i        ii vi  ii  v v    v  i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_90696414_9   2487 TATAATACCAAAGGCAAAACCCATTCAAAA----AAATTGACAAATCTGA 2532
                            i i      i   v  v v --     ----    v  i    iv  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAA--CAAAAGAAAAAATAGATAAATTGGA 641

  chr1_90696414_9   2533 CCTCATCAAAACTGAAAACTTTTGTTCTCCAAAAGACATCATTAATGAAA 2582
                          i         i i           v  i    i    ii  i  vi  i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_90696414_9   2583 TGAAAAGCCAAGCCACA-AATAGGCAGATAATATTCGCAAATGCTATAGC 2631
                                v   v     -   i  -   v      i      vv    v 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGG-AGAAAATATTTGCAAATCATATATC 740

  chr1_90696414_9   2632 TGATAAAGGACTTTCACCTGGAATATATAAAGAACTTTAGCAACTCAATA 2681
                               i      vi i ii                i vi          
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_90696414_9   2682 ACAAGAAGACAGACAAACCAATTTTAAAAGAGGGGAAAAAACTGAACAGA 2731
                          i  i      i i  v      ?v    vi  vi  ii vi    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_90696414_9   2732 CATTTTATTAAAGA-GAAATATAAATGGCTAATAAATACATGAAAA-ATG 2779
                              ivii     -  v   i       i     ii         -   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_90696414_9   2780 TTCAACATCATTAGTTAC 2797
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (119 / 59)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 4.50 (108 / 24)  

3397 22.60 4.11 0.80  chr1_90696414_90701634     3853  4728 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_90696414_9   3853 AAAGACAGCCTATGCTCATGGATTGGAAGAATCATTATTGTTAAAATGAC 3902
                              i v  i   i               v i v         i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_90696414_9   3903 CATACTACCCAAAGCAATCTATAGATTAAATGCAATCCCTATCAAAATGC 3952
                         v     v      vii     i     v  i                 v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_90696414_9   3953 CAATGACATTTTTAACAGAAATAGGAAAAATAATCCTAAAATTTATATGG 4002
                           iivi v     vi       v iv  iv i           i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_90696414_9   4003 ATCCAAAAAGAGCCCAGA-TAGCCAAAGCAATTCTGAGCAAAAAGAACAA 4051
                          vviiv  i ii      -        i    ii   iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_90696414_9   4052 AAGTGGAGGTATCACACTACCTGACTTCAAAATATATTTCCAGGCTATAG 4101
                          iv      vv       v  ii i       iv  i v v i    i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_90696414_9   4102 TAACCAA-ACAATATGATATTGGTATAAAAACAGACACATAGCCCAATGG 4150
                            i   -   i i  i  i   i    ii i     i    vi      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_90696414_9   4151 GACAAAATAGAGAACCCAGAAATAAACACATGGATTTATGGCTAACTAAT 4200
                         i i i   v    ii            v   iv        ii  i i  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_90696414_9   4201 TTTCGACAAAGGCACCAAGAACCTATATTAGGGATAGGACACAGTCTT-- 4248
                                  i  ii      v v vi v i    - i  - i      --
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGA-ATAGTCTTTT 401

  chr1_90696414_9   4249 CAATAAAGAGTGCTTGGAAAACTGAATATCCATATGCAGAAGAATGAAAC 4298
                            i   vi     v   v     i   ?   i     i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_90696414_9   4299 TAGAGCCCTATCTCTCACCATATACAAAAATCAACTCAAAATAGATTAAA 4348
                          i  v     i   v                i          i   i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_90696414_9   4349 GACTTAAATGTAGAAACCAAAACTATAAAACTACTAGAAGAAAACA---G 4395
                            i        ii i i              vi            --- 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_90696414_9   4396 AAAAACTCTTCAGGATGCTGGTCT-GGCCATGGCT--------AAGACCC 4436
                         ?iv  v     iv  ivi   vi -   v    i -------- v   v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_90696414_9   4437 CAAAAGCACAAGGAACAAAAAACAAAATAGACAAATGGGACT--AT---- 4480
                                     v       i v        i    v     --  ----
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_90696414_9   4481 ATTAAA--CT----------AAAGGAAATAATCAACAGGGCGAAGAGGCA 4518
                               --  ----------      v iv     v ii i   i  i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_90696414_9   4519 ACCTGATGAATGGGAGAAAATATCTGCAA--CATATTCATCTGAGAAGGG 4566
                            iivv                i     --     --      v     
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGATAAGGG 749

  chr1_90696414_9   4567 ACTAATTTCTAGAATACACAGGGAACTCAAGCAACTCAACAGCAAAAAAA 4616
                            vi v  i      i i ii      vvi        i ii     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_90696414_9   4617 ACAAAAAAAATTCTGCTAAAAAGTAGGCAAAGAATCTCAATAAACATTTC 4666
                         -    v  --ii vii ?    i i       i  i v    i       
  L1M4_orf2#LINE/    800 -CAAATAA--CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_90696414_9   4667 TTACAAGAAGACATACAAATGGTAAACCGGCATATGAAAAAATGCTCAGC 4716
                          ivv       i          iv  ivi   i       i       i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_90696414_9   4717 ATCACTAATCAT 4728
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (127 / 67)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 2.69 (43 / 16)  

 268 22.64 0.00 0.00  chr1_90696414_90701634     5168  5220 (1)    L1M4_orf2#LINE/L1        1    53 (855)  

  chr1_90696414_9   5168 TGGAAGAATATTCCATGCTCCTGAATAGGAAGAATCAATATCATTAAAAT 5217
                              ii    i     i  v  i  v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90696414_9   5218 GGC 5220
                            
  L1M4_orf2#LINE/     51 GGC 53

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.00 (0 / 0)  


3268 21.98 7.17 0.36  chr1_90806820_90809247     1099  1935 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr1_90806820_9   1099 ATATTTATTGGGTCAGAGGGATTAATATGGTTAAAAGGTCCATGCTATCC 1148
                           i  i  -  i ii  i iv       v     i v v v  i  vi  
  L1M4_orf2#LINE/     15 ATGTTCAT-GGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr1_90806820_9   1149 AAAGTGATTGACAGATCCAATGCAAATCCTATCAAAAAACCAATAGCATT 1198
                            v    iv      i   i    vi          vv   iiv  v  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr1_90806820_9   1199 TTTTACAGAAATT------TTAA----AAAGTACA----------CAAAA 1228
                             i        ------i i ----   i v  ----------   ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_90806820_9   1229 GACTCTAAATAGCCAAAGGAATTTTCAGCAAGAAGAACCAAATCGGAGG- 1277
                            i vi          iv   i  v iv         v  i i     -
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_90806820_9   1278 --TATATTTTCTGATTTCAAAACATATTACAAATCTACAGTAATCAAAAC 1325
                         --i i i  i ii          v  i      v             i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_90806820_9   1326 AGTGTGGTACTGGCATAAAAAC-GACATATAGATCAATGGAACAGAATAG 1374
                                           ii i-                   i     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_90806820_9   1375 AGAGCCCAGAGATACACCTACACATATATGATCAAATGGTATTTGACACG 1424
                             i     i   v   i i    v    i    v  i v  i    v 
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_90806820_9   1425 GGTGCCAAGAATATACA----GGAAAAAATAGTCTCTTCAATAA-TGCTA 1469
                                   vi  v  ----     i        i     i  -  v i
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_90806820_9   1470 CTGGAAGAACTGGATATCCACATGCAAAAGAATAAAATTGGGCACTTAGC 1519
                             i v         ?                i  i    i v i  v 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_90806820_9   1520 TTATACCATGCACAAAAAT-----------GGATTAAAGAC--AAATCTA 1556
                          i i     ii        -----------    i ?    --    v  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_90806820_9   1557 AGATCTGAAATCATAAAACTCCTAGAAGAAAACATAGGAAACAAGCTTCT 1606
                            v  i   ii         i                ?ivv  v    v
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_90806820_9   1607 TGACAATGATCTGGGCAATGGCTTCTTGGATATGACACCAAAAGCA---- 1652
                             vv  ivi i        i     i                  ----
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_90806820_9   1653 -----------ATAATAAACAAGTGGTATTGCATCAAACTAAAAAGCTTC 1691
                         ----------- v    i i  i v v i v       v v    i   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_90806820_9   1692 TGCACAGCAAAGGAAACAATCAATGAAATGAAAAGGTAACCTACAATATG 1741
                           ii vv       v  v     vi  i       ii    i   iv   
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_90806820_9   1742 GCAAAAAAAAAGTTTGAAAACCATTTAAATGATAAATGACTAATATCTAG 1791
                          v i    v --    v   i   v  vv      iv    vi    i  
  L1M4_orf2#LINE/    714 GGAGAAAATA--TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_90806820_9   1792 AATATATAAGGAACTTCTACAACTCAATAGGAAAATAATAA-TAACCCAA 1840
                                  i     ii            iv    vi i  -        
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_90806820_9   1841 TT-AAAAATGAATAAAGGACCTCAATAGATATTTCTCCAAAGAAGACCTA 1889
                           -       iii      ii v      i                iv  
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_90806820_9   1890 TAAATGGCCAATGGATATATAAAAAAA-GTTCAATATCACAAATCAT 1935
                         i           iiii i  i    i - i    i    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (115 / 66)
Gap_init rate = 0.02 (15 / 894), avg. gap size = 4.20 (63 / 15)  


2821 25.53 3.14 1.46  chr1_90853630_90858168     3166  4058 (481)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_90853630_9   3166 TAGAAAGGCACTCCATTTCCATAGATTAGAATATTCAACATAAATAAGAT 3215
                          i     ii ii    v i   i    i   v i i  i  viv      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_90853630_9   3216 GTCAATTTTCCCCAAAGTAATCTA--GATTTAACACAATAGCAATTAAAA 3263
                          v    vi        v i     --    i   i    vv v  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_90853630_9   3264 TCCCAGAGAGATATTTTGCAGATATAGATAAGCCTGTTCTAAAATTTGTA 3313
                               vvivv v         v  v  i    ivi i        ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_90853630_9   3314 TGGAAAAGTAAAGGAACTACAACAGTTAAAACAATTTTGAAAAAGAATGA 3363
                               v i  i   v i v  i  ii        i           -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GA 199

  chr1_90853630_9   3364 ACCAAGCTGGATAACTCAACATTACCCAACAGTAAAATGTATGATAAAAC 3413
                           v   i    vi     -  i v     ivvi    iv  iv i   i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_90853630_9   3414 TATATCAATCAAGAC----TGGTAAAAG-ATGAAAGGACAGACACATAGA 3458
                           i vi         ----     vvi -  --     i     i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGA 296

  chr1_90853630_9   3459 TCAATGCAACATTACAAAAAGTTCACAAATACATCCACATAATTATGGTT 3508
                               v  i vv ivi i   i  v     v i   i i v       i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_90853630_9   3509 GGTTGATTTTTAATAAAGGTGCAAAGGAAATTCAATGGAGAAAGGGTGAT 3558
                         ii        ii i  i     v   ivv         i     ii ii 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_90853630_9   3559 CTTTTCAACAAACGATACTTAGAACAACTGCATATC-ATATGCAAAAAAT 3607
                                     i i i  -i i       v   ? - i        i v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_90853630_9   3608 TGAACTTCAGCCTTAACCTAATACCACACACAAATGTTAGCTCAAAATGT 3657
                             v  vii  iiv    v i    i i     vi   i         v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_90853630_9   3658 GTCAGAGACTTAAGTGTAAAATAGAAAAATATGAAACTC--AGAAAAGAA 3705
                         i   ?    i   i     i vvv    v   i      --    i -  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA-AA 544

  chr1_90853630_9   3706 ATGTAGATAAACATCTTCATGACCTTGGGTTAATCAAAGAGTCTTTTGAT 3755
                          ii   i?iv v      i             iv   v iv ii  v   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_90853630_9   3756 AAGACACCAAGTGATCAATCCGTTATAAAAGAATAATTA-ATAAATTGGA 3804
                          v        iv vv   --- iv i       v  v  -          
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA---GCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_90853630_9   3805 CTTCATCAAAATGAAAATATATTGTTCTATGAAGAAAATCATAAAGAGAA 3854
                                     v    vv v    v  vii   i v ii  v    i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_90853630_9   3855 TGAGAAGACAAATCATAGATTGGAGAAAAAATATTTGTAAATCTCATACC 3904
                            i       vi  i   v   -  i          i     vi   i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGG-GAGAAAATATTTGCAAATCATATATC 740

  chr1_90853630_9   3905 TGATAAAGGATTTGTTTCCAGAATACACTTTAAAAACTCACAAAACTCAG 3954
                               i   i    v         i -- v  i     vi v      i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATA--TAAAGAACTCTTACAACTCAA 788

  chr1_90853630_9   3955 CAATAAGAAAACAATCAACTTCATTTTTAAAATGGGAAAAAGATATGAA- 4003
                         i     i  i    vi   i-  v  ?v        v   i   v    -
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_90853630_9   4004 -GACA-----------AAAATG----AATGTCTAATAAACACATGAAAAG 4037
                         -    -----------  i  i----    v i     i           
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_90853630_9   4038 AAATATGATATCATTAGGCAT 4058
                          viivii i    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (135 / 89)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.28 (41 / 18)  


3309 12.12 4.96 18.32  chr1_91052640_91057322.rev     3145  4192 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91052640_9   3145 TGGAAAGACATCCTGTGT-CTTGGATTGGAA-----AATATTGTTTAGAT 3188
                                 i    ii   - v          -----         v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91052640_9   3189 GAAAGAACTCCCCAAATAGATCTACAAATTCAATGCAATTCTCTATGAAA 3238
                          iv iv           v        i      i     i -    v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC-CTATCAAA 99

  chr1_91052640_9   3239 ATTCCAATGGCTTTCTTTTGAAGAAATGGAAAAGCTGGTTCTAAAACGTA 3288
                           i   iiv  i  -     v      v  v      i i      ivi 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_91052640_9   3289 TATGGAAATGCAAGGAACCCTGAATAGCCTAA-CAGTTTTTTTTAA--AG 3335
                                        i    v        v  -  i i  vvvv  --  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_91052640_9   3336 AACATAATTGGAG-ACACACAGTTCCCAATTTCAAAACTTACTGCA---- 3380
                             v i      -  v    v                     i  ----
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_91052640_9   3381 ----GCAATCAACACAGAGTGGTACTGGCATAAGGATAGACATA--AATC 3424
                         ---- i      v    v                          --i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_91052640_9   3425 CGTGGAATAGAATTGAGACTTCACAAAGAAACCCATACAT--A------- 3465
                         vi                v i  v   v            -- -------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_91052640_9   3466 --GATGTTCAGTAAGGGTGCCAAGACCATTCAATGGACAAAGAACAGTCT 3513
                         --   v   iii                        iv      i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_91052640_9   3514 TTTCAACAAATGGCGTAGGAATAACTAGCTATCCTAGTACAAAATGCAAA 3563
                                      i iv  i i    i v  ?  ----   ---      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCC----ACA---TGCAAA 441

  chr1_91052640_9   3564 AGAATGAATTTGGACCACTATCTTACACCATATAGAAAAATTAACTCAAA 3613
                                 v       v   i  i          v               
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_91052640_9   3614 ATAAATCAACAATCTAAATTTTGTCAGAGCTAAAACTTTAAAAACTCTTT 3663
                           ii    ?vi i      ---  v            v     -     -
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAAT---GTAAGAGCTAAAACTATAAAA-CTCTT- 536

  chr1_91052640_9   3664 TTTTTTTTTTTTCTCAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTG 3713
                         ---------------   v i ----------------------------
  L1M4_orf2#LINE/    537 ---------------AGAAGAA---------------------------- 543

  chr1_91052640_9   3714 CAGTGGTGCGATCTCCGCTCACTGCAAGCTCTGCCTCCCGGGTTCACACC 3763
                         -------------------------  ---------------------- 
  L1M4_orf2#LINE/    544 -------------------------AA----------------------C 546

  chr1_91052640_9   3764 ATTCTCCTGCCTCAGCCTGCCGAGTAGCTGGGACTACAGGCACCCGCCAC 3813
                           -----------  ------ ?   ------------------------
  L1M4_orf2#LINE/    547 AT-----------AG------GNGTA------------------------ 555

  chr1_91052640_9   3814 CACGCCTGGCTAATTTTTAAAACCTCTTAAAGGGAAACAAATGTAAAGTT 3863
                         -----------   i  iivi    i------------------------
  L1M4_orf2#LINE/    556 -----------AATCTTCGTGACCTT------------------------ 570

  chr1_91052640_9   3864 TTTCGGGTTTAAGACTTAGGCAACAGTTTCTTACGTATGACAGCAAAA-C 3912
                         ----     --------      ii        vi       v     - 
  L1M4_orf2#LINE/    571 ----GGGTT--------AGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_91052640_9   3913 ATAAACAACAAAAGAA----TAGGTAA-TTGGACTTCATCGAAATTAAAA 3957
                          i  i           ----   i   -            i         
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_91052640_9   3958 GTTTT---GCATCCAAAGACACTATCAAGAATGTGAAAAAACAATCTACA 4004
                         ii   ---  v  v  i              v       i    i i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_91052640_9   4005 GAATGGAAGAAAATGTTTGCAAATGATATATCTGATAAGGATCTAGTGTC 4054
                               i       i         v               iv  v  i  
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_91052640_9   4055 CAGAACATATAAAGAACTCTTACACTTCAA------------AAATAACC 4092
                              i                  vi    ------------        
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_91052640_9   4093 CAATTTTAAAACAGGCAAGGAGTTTGAATAGACATTTCTCGAAAAAAGAT 4142
                              ?v    ii     i ii                  v   i     
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_91052640_9   4143 ATACAAATGGCCAATAAGCACATTAAAAGATGTTCAACATCATGTCAGTA 4192
                                                v        i         ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (73 / 50)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 8.71 (244 / 28)  


3425 18.30 10.41 1.79  chr1_91133946_91137245     1973  2808 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91133946_9   1973 TGGAAACACATCT-ATGTTCATGGATTTCAAGACTTAGTATTGTTAAGAT 2021
                               v i   i-             vv        i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91133946_9   2022 GGCAAAATTCCCCCAAAGTGATCC-CAGATTCAACTCTATCCCTATCAAA 2070
                              v i     -   v     i-          v v            
  L1M4_orf2#LINE/     51 GGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_91133946_9   2071 ATTCTAAAGGCCTTTTT-GCAGGA-TTGTAAAAGCTTATCCTCAAACTCA 2118
                           i i ivv        -    i -   - v     v     v   i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCA 148

  chr1_91133946_9   2119 TATGGAACTGAACGAGTCCCTGAACAACAAAAACAGTACCGAGAAAGAAA 2168
                                v  v v i v   v   i i v      i vii  i      i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_91133946_9   2169 AAGAA----GGAGTACTCACACTCCCTGATTTCAGAACACTGATTACAAA 2214
                           v  ----    v         i  ii      i   -- v i      
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC--TTACTACAAA 246

  chr1_91133946_9   2215 ACTATAGTAATCAA-----TGTGGCAGTAGAAGCAGGGTAGACATACAGA 2259
                         i   i         -----     i v i v vv   i        i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_91133946_9   2260 TCAATGGAATAGATTTAAGAGTCCAGAAATAAGCCCAATCGTCTATGGCC 2309
                                      v  i               i    vv i i     i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_91133946_9   2310 AATTCATTTCCAACAAAG-TGCCAAGACCATTCAATGGGGAAAAGAACAG 2358
                             v    i i    i -                        -   i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAG 395

  chr1_91133946_9   2359 TCTTCTCAACAAATGGTACTGGGACAACTGGATAACCACGTGCAAAAGAA 2408
                             i            i                ?    i          
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_91133946_9   2409 TGAAGTTGGAAGCCTGTCTCACACCAGGTACAGAAACTAAATCAAAATGG 2458
                                   vv   ii         vi    i   i   v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_91133946_9   2459 ACCAACAATCTGAATATAAAAGCTAAATTTGTAAAGCTCTCAGAAGG--- 2505
                          i  ?vi i  i   i   i       vi i    i    i     i---
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_91133946_9   2506 CATGGGT-TGGATCCTCATGACTCTTGATTTGGCAATGGATTCTT----- 2549
                            i  ?- ii   i  i    ii v i  v        v     -----
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_91133946_9   2550 TGACATCAAAAGCACGAACAGCAAAAAACAAAACAAACAAAAAACAGAAA 2599
                              i         i i  i     i v    i i i   ---------
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA--------- 636

  chr1_91133946_9   2600 TTGAACTTTATCAAAATAAAAATCCTTTGTTTATCAACAGGTATTATT-- 2647
                            i    i        v    v i     viv    vi ii i   i--
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_91133946_9   2648 ----------------------GAAT--------ATATTTG-AAAT-ATA 2665
                         ----------------------    --------       -    -   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_91133946_9   2666 T------TAA--------TATCCAGAACACATAAAAAACTC--------- 2692
                          ------   --------         i i     i     ---------
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_91133946_9   2693 AACAACAAAAAGACAA----CCTAATTTTTTAAATGAGCAAAGGACGTGA 2738
                           i  i          ----  i    ?vv-     i        iv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGA 835

  chr1_91133946_9   2739 ACAGATATTTCTCAAAAAAAGATATATAAATGACCAA---GCCCATAAAA 2785
                          i   i       v   i        i     i    ---  v   i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_91133946_9   2786 AGACGTTCAACATCGTGGTCATT 2808
                            i i        i????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (99 / 50)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 4.08 (102 / 25)  


3622 20.69 4.34 0.57  chr1_91164961_91167344     1023  1897 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91164961_9   1023 TGGAAACACA--CTGTACCCACAGATTGGAAGATTTA---TTGTTAAAAT 1067
                               v i -- ii iii  ii          i   ---       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91164961_9   1068 GTCCATACTACCCACAGCAATCTACAGATTCAATGCAATCCCTGTCAAAG 1117
                          v v     v    v vii              i         i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91164961_9   1118 TCCCAA-TGGCATTTTTGCAGAAACAGGAAAACCTATCCTTAAATTCATA 1166
                              i-  v v            iv iv  i iv     v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_91164961_9   1167 TGGAATCTCAAAGGACCCCATAGAGCCAAAACAAACTTGAAAAAGAACAA 1216
                              viv   i      viv v           v            v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_91164961_9   1217 CAAAGTTGGAGGCCTTACATGTCCTGATTTCAAAACATACTAAATACAAA 1266
                                     v  i   iv   ii          v     v v vvv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_91164961_9   1267 TAGTAATCAAGACAACAATGGTGCCAGCATAAAAA--GACATATAAACCA 1314
                         i             iii-    i ii      ii --        i i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTG-TGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_91164961_9   1315 ATGAAACAAAATATAGATAGCCCAATAATAAACCCATGCATTTCTAGTCA 1364
                            i  i i   - -  v  i   iv           i     v i    
  L1M4_orf2#LINE/    300 ATGGAATAGAAT-T-GAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_91164961_9   1365 AATGGTGTTTGACAAGGGGGCCAATACTATACAGAGAGGAAAGGACAGTC 1414
                          v  i v  i        v     v  i  v  iv i      i i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_91164961_9   1415 TTTTCAACAAATGGTACTGGGA-AATCCAATATCCACGTGAAAAAGAATG 1463
                                        i      -  iivi   ?    i  v         
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_91164961_9   1464 AAGTCGGACCCTTACTT-ACACCACATACAAAAATTAATTCAAAATGGAT 1512
                             i      i   i -      i             i           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_91164961_9   1513 -AAAGACCAAAGCATAAGAACTAAAACAATAAAACTATTA-AAGAAAACA 1560
                         - ?     v  iii     i       v        v   -         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_91164961_9   1561 TAGGGG-AAGGCTTCGGGACACTGGATTTAGCTATGAATTCTTGAACATG 1609
                             ? -  iv     v   vi   i  vi  v   iv     ii i   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_91164961_9   1610 ACACCAAAAGCACAGGGAACAAAA-----AATGGA---ATTA-----CAT 1646
                                       i v       -----   i  ---   i-----   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_91164961_9   1647 TAAAAGTTAAAAACTTCTGTACATCAAAAGAAGTAATCAATGGAGTGAAA 1696
                         i    -          i   i v     i  viiv     vii       
  L1M4_orf2#LINE/    648 CAAAA-TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_91164961_9   1697 AGACAACCTACAGACTGGGAGAAAATATTTGCAAATCATGTATCTGATAA 1746
                                 i     v                        i          
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_91164961_9   1747 GAGGTTAAAATCCAAAATATGTAATATAATG-----AACTTGACAACAAA 1791
                          i ii viv     i     i   - v  iv-----    ii i  i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAA-AGAACTCTTACAACTCAATAATAAA 795

  chr1_91164961_9   1792 AAAAGAAATGACTGAATTTAAAAATGGGCCAAGTACTTCAATGGACAATC 1841
                           i v    i  iv    ?          v   v i  v   i    v i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_91164961_9   1842 CTCCAAAGACAGCATATAAA------ACAAGCACACAAAAAGATGCTCAG 1885
                                  viii   i   ------ i       ii            i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_91164961_9   1886 C-CCAGTGTAGTG 1897
                          -i  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (113 / 64)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.15 (43 / 20)  


3101 27.28 0.44 0.55  chr1_91174649_91181020     4971  5879 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91174649_9   4971 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCGGGAAAAT 5020
                              ii i  i     i        v      v i i   i vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91174649_9   5021 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCAACAAGC 5070
                            v     v     iv i  i  i        i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91174649_9   5071 TACCAATGAATTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5119
                          v   iivivi  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_91174649_9   5120 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAACAGA 5169
                               viiv  ii  v  v v  v     iv     i i ivv iv   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_91174649_9   5170 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCC 5219
                               i      vv    i  v  ii i      viv        i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_91174649_9   5220 ACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5269
                                    i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_91174649_9   5270 ATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACAGCTACAACCA 5317
                               i    i--    i  --        vv   i   vi  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_91174649_9   5318 TCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCC 5367
                         vi    i  i     ivv  vv  i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_91174649_9   5368 TATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTC 5417
                          v  i                 v      v  ?   i   i i  iiv v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_91174649_9   5418 AAACTGGATCCCTTCCTTACACCTTATATGAAAATTAATTCAAGATGGAT 5467
                           ii    i    v   i     v    ii        i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_91174649_9   5468 TAAACACTTACATGTTAGACCTAAAACCACAAAAACCCTAGAAGAAAACC 5517
                         i ? v  i  v    v   v       i i    vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_91174649_9   5518 TAGGCA-ATACCATTCAGGACACAGGCATGGGTAAAGACTTCATGTCTAA 5566
                             ?i- v i -   iv   viv  vv i  i  v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_91174649_9   5567 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5616
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_91174649_9   5617 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5666
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_91174649_9   5667 AGGCAACCTACAGAACGGGAGAAAATTTTTGCAATTTACTCATCTGACAA 5716
                           i     i      i          v       v i ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_91174649_9   5717 AGGGCTAATATCCAGAATCTATAATGAACTCAAACAAAGTTACCAGAAAA 5766
                         i  i  vi          v     v      vv    v- i vi iv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAATAATAAA 795

  chr1_91174649_9   5767 AAAACAAACAACCCCATTAACAAGTGGGCAAAGGATATGAACAGACACTT 5816
                           i     i     v   ? v  i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_91174649_9   5817 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5866
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_91174649_9   5867 CATCACTGGCCAT 5879
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (139 / 105)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


2372 19.68 7.04 1.60  chr1_91208748_91210357      500  1124 (486)    L1M4_orf2#LINE/L1      250   908 (0)  

  chr1_91208748_9    500 ATAGTAATCAAGATAGTGTGGTATTAACATTAAGATAGGCAAATAGATCA 549
                          i           i         i ii   v i     i  v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_91208748_9    550 ATAAAAGAAAATAGAGGGTCCAGAAATAGACCCACA-ATTACATGGTCAA 598
                           ii  v i   v   i           i     i -   -i        
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGGTCAA 348

  chr1_91208748_9    599 TTAAATTTCAGCAAAGGTGCAAAGGCAATTCAATAGAGAAGGA-TAGTCT 647
                           i v    ii   i     v   i v       i i   i  -      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_91208748_9    648 TTTCAACAAATGATACTGGAAAAATTAAATATCCATATGTAAGAAATTGA 697
                                     i i    i v  i ii   ?   i   i  i i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_91208748_9    698 AATTTGATTC------------ATATACTAAAATTAACTCAAAATGAATT 735
                          i  v  ii ------------      v                 i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_91208748_9    736 ATAGACCTAA-TCTAAAACCTAGACC---AAAA----------AAAATTT 771
                          ?        - v   i v   i v ---    ----------    iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_91208748_9    772 AGGAGAAAATCTTTGTGAGCTTGGGCTAGGCAAAAATTTTTGAGAAATGA 821
                            ? v       i    v      i       vii   i v   v    
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_91208748_9    822 CACCAAAAGCACAATTCATGAAAGAAAAAGTTGTTAAAATCAACTTCATT 871
                                       viv ii         i v v    v vi       i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_91208748_9    872 GAAATTTAGAATTTTTGCTCCTTAAAAGAC-TTA----GAGAATGAAAGG 916
                         i     v i  i     iv i i   i   -i  ----  i i     i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_91208748_9    917 ACAACCC-CAGACTACGAAAAAATATTTGCAAATTACACAACTGATAAGG 965
                                -    v iv  i               i i i v         
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_91208748_9    966 GACTTGTATCCATAATATATAAAGAATTCTCAAAACACAATAAGTAAA-- 1013
                                     v             i   i v   v      -    --
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAA 797

  chr1_91208748_9   1014 --TAAATAACCTAAT-AAAAAATGGACAAACGAAT-GAACAGGCACTTCA 1059
                         --i        i   -?        i    v  v -   i  i  i   v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_91208748_9   1060 CCAAAAAAGATATA---ATGGTGTAAAAAAAAAAAGCACATGAAAA-ATA 1105
                              i        ---    iv-------  v             -  i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCC-------AATAAGCACATGAAAAGATG 890

  chr1_91208748_9   1106 CTCATTAGTCATTAGAGAA 1124
                             vi -   ????????
  L1M4_orf2#LINE/    891 CTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.98 (79 / 40)
Gap_init rate = 0.03 (18 / 659), avg. gap size = 3.00 (54 / 18)  


2358 19.93 2.45 6.29  chr1_91273360_91276275.rev      935  1506 (1410)    L1M4_orf2#LINE/L1        1   550 (358)  

  chr1_91273360_9    935 TGAAAAGACATTCCATGTTCAT--ATTCAAAGACTCAATAT-GTCGAGAT 981
                           i     i  i          --   vi      i     -  ii    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91273360_9    982 GGCAATCTTTCCCAAATTGATTTATAAATTTAATGCA-TCCCTATCAAAA 1030
                               vi i           i  i i   i  i   -            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91273360_9   1031 TCATAGCAGCTTTTTTTTTGTTAATTCACAAATGAATTTTAAAATTTATA 1080
                           vi   v  i      viivv    v    iivi  ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_91273360_9   1081 TGAAAATGTAAAAGACCTAGAAAAGTCAAAATAATTTTTTAAAAAGAGAA 1130
                           i     i  ii    i    v  i     i   i  vv    ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_91273360_9   1131 CAGAGGTGGGGGATTTATACTGCTAAATATTAAAATTTACTGTAAGGCCA 1180
                           i  v   i   i i i   v iv   v i    i     ii  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_91273360_9   1181 CAGTAGTCAAGACAGTGTAGTATTAACGCAAGGACAGGCATATAGATCAA 1230
                              i            i   i ii ii     i  i            
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_91273360_9   1231 TGAAACAGAATTGACAGTCCAGAAATAAACCT-TACATTTATGGGGAATT 1279
                           i  i        v                i-           vv    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_91273360_9   1280 GATTTTTAACAAAGGTGTCAAAACAATTCAATGAGGAAATTGTAGCCTTT 1329
                               ii    i    i   i  v        i     vvi   i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_91273360_9   1330 CCAACAA-TGGTGCTGGGACAATTATTAATAGATACCCATATACAGAAAA 1378
                         i      -              i i------    ?   i  i  i  i 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTG------GATAKCCACATGCAAAAGA 444

  chr1_91273360_9   1379 GTGAA--------CTTCCGTCATAAAATACACAAAGATTATCTCATAGAC 1420
                         i    -------- i v v   i vv   i     i    v    -----
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA----- 489

  chr1_91273360_9   1421 TTAAATGTAGGATCATAGACTTAAATGTAGGATCATAGACTTAAATGTAA 1470
                         ----------------------     ---     ?    i         
  L1M4_orf2#LINE/    490 ----------------------AAATG---GATCAWAGACCTAAATGTAA 514

  chr1_91273360_9   1471 CAGCTAAAATGATAAACCTCCTAGAAGAAAATATAG 1506
                         v        iv     v   i          i    
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

Transitions / transversions = 2.73 (82 / 30)
Gap_init rate = 0.02 (9 / 550), avg. gap size = 5.56 (50 / 9)  

 776 20.20 22.80 1.63  chr1_91273360_91276275.rev     2119  2425 (491)    L1M4_orf2#LINE/L1      537   908 (0)  

  chr1_91273360_9   2119 AAAAGAAAATATAGCAGAAAATATTTGTGACTTCGTATTAGGCAAAGGTT 2168
                          i       i    v? v    v  i     i i vi        v    
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_91273360_9   2169 TCTTAGATTT---ATCAAAAGTA-----AACCTATTTTTTGAAAACAT-G 2209
                                 v --- i      i -----   vv v-----     v  - 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAA-----GAAAAAATAG 631

  chr1_91273360_9   2210 ATGAATTGCATTTTATCAAAATTTAAAACATTGGTACTTCCAAAAATAC- 2258
                           i     v i  i         v     v  v  i    v  ii i  -
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_91273360_9   2259 -----------------------CAC--------------TA-------- 2263
                         -----------------------   --------------  --------
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_91273360_9   2264 ------ATCGGTTAAGGCACTTGTATCTAGAATATA-AAAGAATTCTTAT 2306
                         ------   v v     v         i        -      i     i
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_91273360_9   2307 AACTTAACAATTAAAA----AATAATG-AATTAGAAAATAGGCAAATGAT 2351
                             i  i   v    ----     iv-    ?i     i      v   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_91273360_9   2352 TCAAATGAACTTTTTCCCAAAGA---TATACAACTGGTGAATATGCACAC 2398
                          ii   ii  v   ii       ---       v   iv    v     i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_91273360_9   2399 AAAAATGTACTCAACATCATTTAGTTA 2425
                         i    vi i          ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (34 / 26)
Gap_init rate = 0.03 (11 / 372), avg. gap size = 6.82 (75 / 11)  


2920 26.18 1.65 1.76  chr1_91360518_91367152.rev     5236  6144 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91360518_9   5236 TGGAAAAACATTCCATGCTCATAAATAAGAAGAATCAGTGTCATGAAAAT 5285
                               i i  i     i    ii  vi     v i i i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91360518_9   5286 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5335
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91360518_9   5336 TACCA-TTGACTTGCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 5383
                          v   -i  v   -i  ii     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_91360518_9   5384 TATGGAACCAAAAAAGATCCTATATAGCTAAGACAATCCTAAGCAAAAAG 5433
                                viiv  ii  i  viv     i  i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_91360518_9   5434 AACAAAACTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5483
                               ii      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_91360518_9   5484 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATGGACC 5533
                                 i   i    ii         i iv ii i   i    i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_91360518_9   5534 AATGGAACATAACAGAGGCCTCAGAAATAATGCCACACATCTACAGCCAT 5583
                                i v  iv   ivii         vv   i    i  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_91360518_9   5584 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAAAAGGAT--TCC 5631
                         i    i  i     ivv  v   i v  vv       i    i  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_91360518_9   5632 TTATTTAATAAATGGTGTTGGGAAAACTGGCTAACCATATGCAGAAAACT 5681
                           -- i  i        i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_91360518_9   5682 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 5731
                            ii         v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_91360518_9   5732 TTAAAGACTTAAAAGTAACACCTAAAAACCATAAAAACCCTAGAAGAAAA 5781
                          i ?    i    v    v v      - i      vi i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAA 545

  chr1_91360518_9   5782 ACTA--CGCAATACCATTCATGACATAGGCATGGGCAAAGACTTCATGAC 5829
                         vv  --? i  - i -   i    v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_91360518_9   5830 TAAAACACCAAAAGCAATGGTATCAAAAGCCAAAATTGACACAGGTGAAC 5879
                           vi            vvi i v      vv     v  i - iv  i  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA-AATTGGAC 642

  chr1_91360518_9   5880 T-AATTAAACTAAAGAGTTTCTGCACAGCAAATAAC-CTACCATCAGAGT 5927
                          -v  i   v v  i ii  i  ii vv    vi  -   i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_91360518_9   5928 GAACAGGCAACCTACATACAGAATGGGAGAAAATTTTTGCAATCTATCCA 5977
                            v  i     i   ----              v       vii  vi 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACA----GAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_91360518_9   5978 TCTGACAAATGGCTAATATCCAGAATCTACAATGAACT--TA-AACACAT 6024
                              i  iv i  vi          v  i  v     --  -   v  v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_91360518_9   6025 TTACAAGAAAAAAAACAACCCCATTAAAAAGTGAGTGAAGGATATGAACA 6074
                          v i  i  i v   i     v   ?    i  i ii      v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_91360518_9   6075 GACACTTCTCAAAAGAGGACAATTATGCA----GCCAACAAAAATATGAG 6120
                             i     v     i  ----   i  ----     i  iv i    i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAA 884

  chr1_91360518_9   6121 AAAAGGCTCATAATCACTGGTCAT 6144
                           i v     vv    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (144 / 90)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.72 (31 / 18)  


3292 26.87 0.44 0.44  chr1_91392129_91394273      745  1652 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91392129_9    745 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 794
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91392129_9    795 GGCCATACTGCCCAAGATAATTTACAGATTCAATGCCATCCCCATCAAGC 844
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91392129_9    845 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 892
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_91392129_9    893 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 942
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_91392129_9    943 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 992
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_91392129_9    993 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1042
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_91392129_9   1043 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 1090
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_91392129_9   1091 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1140
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_91392129_9   1141 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1190
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_91392129_9   1191 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1240
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_91392129_9   1241 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1290
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_91392129_9   1291 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 1340
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_91392129_9   1341 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1390
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_91392129_9   1391 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1440
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_91392129_9   1441 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 1490
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_91392129_9   1491 AGGGCTAATATCCAGAATCTACAATGAACTCAAGCAAATTTACAAGAAAA 1540
                         i  i  vi          v  i  v      vvi   v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_91392129_9   1541 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 1590
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_91392129_9   1591 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 1640
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_91392129_9   1641 ATCACTGGCCAT 1652
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3095 26.70 1.67 0.67  chr1_91424413_91428730.rev     2929  3827 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91424413_9   2929 TGGAAGAAAGTTCCATGCTCATGGATAGGAAGAACCAATATCGTGAAAAT 2978
                              ii vi i     i        v      vii     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91424413_9   2979 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCGACAAGC 3028
                            v     v     iv i  i  i       ii  v     iiv   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91424413_9   3029 TACCAATGAGTTTCTTCACAGAACTGGAAAAA---A--CTAAAGTTCATA 3073
                          v   iivivi  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_91424413_9   3074 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 3123
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_91424413_9   3124 CAAAGCTGGAGGGATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 3173
                              i      iv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_91424413_9   3174 CAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGACCAA 3223
                               i   i    ii  i      i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_91424413_9   3224 TGGAACAGAAC--AGAGCCCTTAGAAATAATACCACACATCTACAACCAT 3271
                              i    i--    i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_91424413_9   3272 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 3321
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_91424413_9   3322 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAATGCTGA 3371
                         v  i  i              v      v  ?   i   i i  viv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_91424413_9   3372 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3421
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_91424413_9   3422 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAATCCT 3471
                          ?    i  v    v   v       i      vi i         v v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_91424413_9   3472 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 3520
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_91424413_9   3521 ACACCAAAAGCAACAGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 3570
                                     vv           vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_91424413_9   3571 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTGAACA 3620
                         i   v v  i i   i  ii vv    i  v    ii vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_91424413_9   3621 GGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 3670
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_91424413_9   3671 GGGCTAATATCCAGAATCTACAAAGAATGCAAACAAACTTACAAGAATAA 3720
                           i  vi          v  i      iv vv    -  --   v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CT--CAATAATAA 794

  chr1_91424413_9   3721 AA-------CAACCCCATCAAAAAGTGAGTGAAGGATATGAACAGACACT 3763
                           -------i     v  i?    i  i ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_91424413_9   3764 TCTCAAAAGAAGACATTTATGCAACCAAAAGACACATGAAAAAATGCTCA 3813
                             v        i  vi viiii    v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_91424413_9   3814 TCATCACTGGCCAT 3827
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.33 (21 / 9)  


2495 26.01 4.95 2.70  chr1_91431972_91437859     4532  5419 (469)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91431972_9   4532 TGGAAAAACATTCCATCCTCATGGATAAGAATAATCAACATCATTAAAAT 4581
                               i i  i    vi        vi   v v i  i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91431972_9   4582 GGCCATACTGCCCAAAGT-------AGCATCCAATGCTACTCCTATCAAA 4624
                            v     v      v -------  -  i   i  v ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAG-ATTCAACGCAATCCCTATCAAA 99

  chr1_91431972_9   4625 CTACAAATGACATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCA 4673
                         v v v iivi v  i  ii     v v  v  i-  -  ii         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_91431972_9   4674 TATGGAACCCAAAAAAGAG-CCCA-AATAGCCAAGGCAATCCTAAGCAAA 4721
                                --- viv   i -    -         ii     i i iv  i
  L1M4_orf2#LINE/    149 TATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_91431972_9   4722 AAGAGCAAAGCTGCAAGTATCACGTTACCCAACTTCAAACTGTACTA-AG 4770
                             i     i  v i vv    ii v     i      viv     - i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_91431972_9   4771 GGCAACAATAACCAAAACATCATGGTATTGGTACAAAAACAGACACATAG 4820
                         i  v   i   i   i   vii     i   i i  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_91431972_9   4821 ACCAATGTC-TATGAATAGAGAGCCCAGAATTAAGGCTGCACACCTACAA 4869
                          i     vv-  -    v     i      v   iv iii   ii  iii
  L1M4_orf2#LINE/    296 ATCAATGGAATA-GAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_91431972_9   4870 CCATCTGATCTTTGACAAAGCTGTCAAAAACAAACAATGGGGAAAGGACT 4919
                         i  vi    i  i     i v  i   i v  vv            i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_91431972_9   4920 CCCTCCCTATTCAATAAATCGTGCTAGGATAACTGGCAAGCTGTATGCAG 4969
                         vi  i----     i    v     i   i      vv ? iii     i
  L1M4_orf2#LINE/    395 GTCTT----TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_91431972_9   4970 AAGACTGAA-CTGGACCCTTCTCTTACACCATATACAAAAACCAATTCAA 5018
                             v    -i       i vi  i                ii  i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_91431972_9   5019 GATGGATTAAAGACTTAACTGTAAAATGC-AAAAATATAAAA-------- 5059
                         i      i ?    i   v     i -  -    v       --------
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGA 539

  chr1_91431972_9   5060 --AAACCAT------------TTGGGACATAGGAATGGGCAAAGGTTTCA 5095
                         --   v   ------------ i v   v v  iv i     v      v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_91431972_9   5096 TGACAATGATGCCAAAAGCA-ATGTCAACAAAAGGAAAAACTGACAAATG 5144
                          iivv    ii         - v -         i     iv  i    v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATT 638

  chr1_91431972_9   5145 GGATCTAATTAAACTTAAGAACTTCTGCACAGCAAAAGAAATTATCAGCA 5194
                            ii v  i   v    i     i  ii vv    i  v i     iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_91431972_9   5195 GAGTAAAGAAACAACCTACAGAAAGGGAAAAAAT---TGCAAACTATGCA 5241
                         i   i  i i      i      v    i     ---      ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_91431972_9   5242 TCTGTACAAAGATCTAATATCCAGAATCT-TAAGGAACTTAGATTTACAA 5290
                             - i  i iv  vi          v -   i     i----      
  L1M4_orf2#LINE/    739 TCTG-ATAAGGGACTTGTATCCAGAATATATAAAGAACTC----TTACAA 783

  chr1_91431972_9   5291 ---GGAAAAAAAAAAACCAAAACAATCTCATTAAAATGTGGGCAAAGAAC 5337
                         ---iiv  v     i  --   i  i iv   ?   vi         i i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_91431972_9   5338 ATGAACAAACATGTTTCAAAAGGAGACATACATGAGGCCAACAAGCATAT 5387
                         v    i i    v i  v    i   i     viv      i     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_91431972_9   5388 ATATATATAAAAAGCCCAATATCACTGATCAT 5419
                         iv -----  i v  i   i    ????????
  L1M4_orf2#LINE/    882 GAA-----AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (149 / 79)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.72 (68 / 25)  


3263 26.91 0.78 0.22  chr1_91466972_91471538     3172  4074 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91466972_9   3172 TGGAAGAACATTCCATGCTCACGGGTAGGAAGAATCAATATCATGAAAAT 3221
                              ii i  i     i   i  i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91466972_9   3222 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3271
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91466972_9   3272 TACCAATGACTTTCTTCACAGAAATGGAAAAAACTACTTTAAAGTTCATA 3321
                          v   iivi i  i  ii       v  v  iviv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_91466972_9   3322 TGGAACAAAAAAAGAGCTCGTATCACCAAGTCAATCCTAAGCCAAAAGAA 3371
                              vviv  ii  v iv v  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_91466972_9   3372 GAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 3421
                         v    i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_91466972_9   3422 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 3471
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_91466972_9   3472 TGGAACAGAAT--AGAGCCCTCAGAAATAACGCCACATATCTACAACTAT 3519
                              i     --    i  --        vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_91466972_9   3520 CTGATCTTTGACAAACCCGACAAAAACAGGAAATGGGGAAAGGATTCCCT 3569
                         i    i  i     ivvi v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_91466972_9   3570 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3619
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_91466972_9   3620 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3669
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_91466972_9   3670 AAAGACTTGAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3719
                          ?    i i  i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_91466972_9   3720 AGGCATTACCATTCAGGACGTAGGCATGGGCAAGGGCTTCATGTCTAAAA 3769
                            ?i v viv   iv   v v  vv i     v  i   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_91466972_9   3770 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 3819
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_91466972_9   3820 AAACTAAAGAGCTTCTGCACAGC-AAGAAAACTACCATCAGAGTGAACAG 3868
                            v v  i i   i  ii vv -   i v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_91466972_9   3869 GCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 3918
                         i     i                 v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_91466972_9   3919 GGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTATAAGAAAAAA 3968
                          i  vi          v  i         vv    v iv    v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_91466972_9   3969 ACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 4014
                             ----   v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_91466972_9   4015 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAAGGCTCACCAT 4064
                         v        i  vi viii     v  i          i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_91466972_9   4065 CACTGGCCAT 4074
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.25 (9 / 4)  


 201 20.73 16.46 6.10  chr1_91472212_91480270      477   640 (7419)  C L1M4_orf2#LINE/L1   (0)   908   728  

C chr1_91472212_9    640 CAAATTA-ATACACTGG-AAAGAACGATTTTA--CATAATATATAAAGAA 595
                              i -   i-   i-  i i  --  v  --  v             
  L1M4_orf2#LINE/    728 CAAATCATATAT-CTGATAAGGGAC--TTGTATCCAGAATATATAAAGAA 774

C chr1_91472212_9    594 CTCCTATATGT--ATAAGTAAA-------------CATTTTAAAAATGGG 560
                            i  i vv --    -    -------------  v  ?         
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGG 823

C chr1_91472212_9    559 TACTCAA----TTAAACAGACA---CTTCAAAATAGAGGATATCCAAAAA 517
                         i ---  ----  i  i     ---  i    ---  i     v    vi
  L1M4_orf2#LINE/    824 CA---AAGGATTTGAATAGACATTTCTCCAAA---GAAGATATACAAATG 867

C chr1_91472212_9    516 GTCAGGAACC-TATGAAAGAGTATTTAAGTTCATTAGACAA 477
                          i  iv  v -i      iii ii i  vv   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (22 / 11)
Gap_init rate = 0.07 (13 / 181), avg. gap size = 2.85 (37 / 13)  

 677 22.67 6.67 5.67  chr1_91472212_91480270     1005  1304 (6755)  C L1M4_orf2#LINE/L1   (166)   742   440  

C chr1_91472212_9   1304 AAAGAA-AAAATTGTATGTCAACTCTGACCTCACACTGTACACAAAACTT 1256
                               -i  i   ------i  i iv         ii  i      v  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTG------GACCCCTACCTCACACCATATACAAAAATT 483

C chr1_91472212_9   1255 ATTTGCAAATAGATGACTGATTTAAATGTGAAAGA-AAAACAATAAAACT 1207
                          vi vv    i   v ?v  ii       i i  v-     v        
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

C chr1_91472212_9   1206 TTTAGAGGAGAAAAAATAGG------TCTTCGAGACCTTGGGATAGGT-- 1165
                         i     --      v     ------      v         v    i--
  L1M4_orf2#LINE/    534 CTTAGA--AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

C chr1_91472212_9   1164 TGACTTTTTTAAA---AAAAC--AGGGCACAAAACTTTCTAACCATA-AA 1121
                           i-   i   i ---i v  -- ii      i------i   v v -  
  L1M4_orf2#LINE/    582 TGG-TTTCTTAGATATGACACCAAAAGCACAAG------CAACAAAAGAA 624

C chr1_91472212_9   1120 AACATA-ATGAATTTGACTATGTTAAAATTAAGAACTCT-GTTCATCAAA 1073
                           v   -  i    v    vii i        i    i -  v v     
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

C chr1_91472212_9   1072 AAGATACCATTAAGA--GTGAAGGGTGCAACTCACAGAATGTGAGGAAAA 1025
                         i-  i  i  i    --     ii -i    i         v   i   v
  L1M4_orf2#LINE/    675 G-GACACTATCAAGAAAGTGAAAAG-ACAACCCACAGAATGGGAGAAAAT 722

C chr1_91472212_9   1024 AAATGGAATACATATACCTG 1005
                          vv  v  vv      i   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTG 742

Transitions / transversions = 1.48 (40 / 27)
Gap_init rate = 0.05 (16 / 303), avg. gap size = 2.31 (37 / 16)  

1290 24.66 4.52 4.30  chr1_91472212_91480270     1592  2033 (6026)  C L1M4_orf2#LINE/L1   (461)   447     5  

C chr1_91472212_9   2033 AAGATA--CCGT-TTCAAGAACTGAAAAGTTTAATATTATAAAGATGTCA 1987
                               --  i -    v i i  i  iii        i v      v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

C chr1_91472212_9   1986 GTTCTCCCCAAATTAATCTTTATATTCAGTGTCATCCCAATTTCAGCAGG 1937
                         i v           i    vi v     ii iv     v  -----  ii
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-----CAAA 99

C chr1_91472212_9   1936 GTTTTGTTGTTGTTGTCATTTTTTTTTCTGAAAT-AACCAGCTAATTATA 1888
                         i iiii----- i  i ---      v v     -i  v    i  iv  
  L1M4_orf2#LINE/    100 ATCCCA-----GCTGCC---TTTTTTGCAGAAATTGACAAGCTGATCCTA 141

C chr1_91472212_9   1887 AAATTCATATGAAAATTCAAAAGGAC--AGGGTAGTCAGGGCAAACTTGA 1840
                                    i    v   i-    --  ii   i  iii   v     
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGA 190

C chr1_91472212_9   1839 A---GAAAAACATA-TTGGGCAACCTAC-TTTACTAGATATCAAGACCTG 1795
                          ---   i    v -    ivi  ii  -i  v i -  v    i  i i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTA 239

C chr1_91472212_9   1794 TTATTAAACAGTAGATAAT-AAGA--ATGTGATGTAGGCATAAGGATAGA 1748
                         i  iv  i vii  -    -    --i    i iiv              
  L1M4_orf2#LINE/    240 CTACAAAGCTACAG-TAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

C chr1_91472212_9   1747 CACATTAACCAGTGGAATGGACT--AGAGTCCAGAAATACACCTACAAAT 1700
                           i  vi i  i      i  v --              v   i i v  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

C chr1_91472212_9   1699 AATACAGTCA-TTGATTTCTGACAAAGGTG--AAGTGCCATGCAGTTGGA 1653
                         v-  ii    -       ii     i    --   -i    v  i v  i
  L1M4_orf2#LINE/    339 T-TATGGTCAATTGATTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGG 386

C chr1_91472212_9   1652 AAACGGACAGTCTTT-CAATAAATGCTGCTAGATCAACTGGATGTCCATA 1604
                            - i i       -   i     v    i iv         i?   i 
  L1M4_orf2#LINE/    387 AAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

C chr1_91472212_9   1603 TGGAAAAAATTG 1592
                           v    i v  
  L1M4_orf2#LINE/    436 TGCAAAAGAATG 447

Transitions / transversions = 2.38 (76 / 32)
Gap_init rate = 0.05 (22 / 443), avg. gap size = 1.77 (39 / 22)  

3058 27.15 1.21 0.99  chr1_91472212_91480270     6663  7568 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91472212_9   6663 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 6712
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91472212_9   6713 GGCCATACTGCCCAAGGTAATTTATAGATACAATGCCATCCCCATCAAGC 6762
                            v     v     iv i  i  i    v   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91472212_9   6763 TACAAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6810
                          v v iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_91472212_9   6811 CATGGAACCGAAAAAGAGCCCGCATTGCCAAGTCAATTCTATGCCAAAAG 6860
                         i      vi v  ii  v  v v  v     iv    ii ivivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_91472212_9   6861 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6910
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_91472212_9   6911 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGACC 6960
                                 i   i    ii  i      i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_91472212_9   6961 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 7008
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_91472212_9   7009 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 7058
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_91472212_9   7059 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGCT 7108
                           v  i  i              v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_91472212_9   7109 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGCA 7158
                            ii    i    v   i     v              i    i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_91472212_9   7159 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 7208
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_91472212_9   7209 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 7257
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_91472212_9   7258 AAACATTAAAAGCAATGGCAACAAAAGCCAAACTTGACAAATGGGATCT- 7306
                         vi   ii       vvi          vv   v v  i    v   ii -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_91472212_9   7307 -----AATTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGA 7351
                         -----       i -   i   i vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_91472212_9   7352 ATAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 7401
                          v  i  i  i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_91472212_9   7402 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 7451
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_91472212_9   7452 AATATCAAACAACCCCATCAAAAAGTGGTTCGTGAAGGATATGAACAGAC 7501
                           viv    i     v  i?    i   --- ii      v    i    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGG---GCAAAGGATTTGAATAGAC 841

  chr1_91472212_9   7502 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAGAAAATGC 7551
                          i     v        i  vi viii     v ii       i  i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_91472212_9   7552 TCATCATGATTGGCCAT 7568
                            v   v ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2820 17.88 0.74 1.68  chr1_91480842_91483523.rev      633  1169 (1513)    L1M4_orf2#LINE/L1        3   534 (374)  

  chr1_91480842_9    633 GAAAAATATTTTATGTTCGTGGATTGAAAG--TCAATATTGTTAAGATGG 680
                             i    iii      i       i   -- i                
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_91480842_9    681 CAGCACTTCTCATATTAATTCATAAATTCAACAAAGTCTGTATCAAAATC 730
                           ii   i i  v   i  ii i i       iv i  iv          
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_91480842_9    731 CTAGCTGTAGTTTTTGCAGAAATTCACAGGCTGATCCTAAAATTCACGTG 780
                          i     ivv              v   i                 ii  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_91480842_9    781 GAAATACAAGGGACCCAGAATAGCTAAGCCAACCTTGAAAAGAAAAAGAA 830
                              i                  i  iv   i        -- i     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA--AGAAGAA 200

  chr1_91480842_9    831 GGAAGGTAGAGGACTCACAATTCTTGGTTTCAAAACTTGTTACAAAGCTG 880
                         vi   v i           v   iiii           ii         i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_91480842_9    881 CAGTGATTAAGACAAGGTGGTGCTGTCATAATAATAGACATAAAGATCAA 930
                             i  i      iv     i   v     vi         v       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_91480842_9    931 TGGAATACAACTGAGAGTGTAGAAATAAACCTTTACCTCTCTG-CCAGTT 979
                                v  i       vi           iv   v i v  -i  i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_91480842_9    980 TATTTTTGACAAGGATGCCAAAACAATTTGATGGTAAAAGAATTTGAAAA 1029
                         v     i       i      i  v   ii    vi       ----- i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT-----AG 395

  chr1_91480842_9   1030 TAATTTTTCAAGTAATAGGGCTGGG-CAACTGCATAGACACATGCAAAAG 1078
                          --i       vv   i v      -      v   ?v            
  L1M4_orf2#LINE/    396 T--CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_91480842_9   1079 GATGAATTTGGACTCCTACCTCATACCATATACAAAAATTAACTCAAAAT 1128
                         i     v      i         i                          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_91480842_9   1129 GAATCAAAGACCTAAAGGTAAAACTTAAAACTATAAAACTC 1169
                          i    ?         v    i vi                
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

Transitions / transversions = 2.13 (64 / 30)
Gap_init rate = 0.01 (6 / 532), avg. gap size = 2.17 (13 / 6)  

1589 15.36 2.41 2.11  chr1_91480842_91483523.rev     1462  1793 (889)    L1M4_orf2#LINE/L1      497   829 (79)  

  chr1_91480842_9   1462 TCAAAAAC--AAACAAACAAACAAAAACCTATAAAACTCTTAAAAGAAAA 1509
                            ? i  --   iiv vi i v     -             i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAAC-TATAAAACTCTTAGAAGAAAA 545

  chr1_91480842_9   1510 CATAGGTGTATATCTTCATTCATTACCTTGTACAAGGCAACAGTTTCTTA 1559
                               ?   v      i v----      viiv      ii        
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTG----ACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_91480842_9   1560 GGTATGACATATAAAGCTCAAGTAACCAAAGAAAAAATAGATGAATTGGA 1609
                          i       ivv     v    i   v               i       
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_91480842_9   1610 CTT----AAGAT-GAAAACTTTTGTGCTTCAGAGGACACTATTCAGAAAG 1654
                            ----  i  -i                 i          iv      
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_91480842_9   1655 TGAAAAGACAACCCACGGAATGGGAGAAAATACTTGCAAATCATATATAT 1704
                                         i               i               --
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT-- 739

  chr1_91480842_9   1705 CTGATAACTAACTTGTATTGAGTATATATAAAGAAATCTTACACTTCAAC 1754
                                vvi        iv  v            v       vi    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_91480842_9   1755 AGTAAAAAGACAAATAGCCCAATT-AAAACTAGTCAAGGG 1793
                          i              i       -    v i v   i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.45 (29 / 20)
Gap_init rate = 0.02 (7 / 333), avg. gap size = 2.14 (15 / 7)  

 426 15.93 10.62 0.00  chr1_91480842_91483523.rev     2081  2193 (489)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_91480842_9   2081 CTCAAAAATAAAA---TAAA------AAT--AAAACTAGTCAAGGGATCT 2119
                              v       ---i   ------   --    v i v   i    i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_91480842_9   2120 GCATAGACATTT-TCCAAAGAAGTGATACAAATGGTCAACACACATATGA 2168
                          v          -          vv          i   i vi  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_91480842_9   2169 AAAGATGCTCTACATTGTTAGTCAA 2193
                                   v    ii????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (10 / 8)
Gap_init rate = 0.03 (4 / 125), avg. gap size = 3.00 (12 / 4)  


1552 23.96 3.69 0.69  chr1_91535834_91541522       45   478 (5211)    L1M4_orf2#LINE/L1      137   583 (325)  

  chr1_91535834_9     45 TCATAAAATTAGTATGGAACCACAATAAACCCTGGATAGTGACAGCAAAA 94
                           v       vi       vii   vii    v i    iv v i   vv
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_91535834_9     95 CTGAGAAGGAA-AAGAAAGTTGGAG--CTACACACTTTCTGATTT-AAAA 140
                         i   i  i   -  v          --  -       i ii    -    
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACT-CACACTTCCCAATTTCAAAA 235

  chr1_91535834_9    141 TTATACTACAAAGCTGGACTAACCAAAACAATATAGTACTTGCATAAAAA 190
                         i -            iv v   i   i   i i i     v      ii 
  L1M4_orf2#LINE/    236 CT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_91535834_9    191 CAGAAACACAGACCAATGGAACAGAACAGAGAGCCCAGAAATAAGTCCAA 240
                         i   v i i   i        i    iv     i          ii   v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_91535834_9    241 ACATACACAGTCAACTAATTTTCCATTAGGGCACCAAAAA-A---AATGG 286
                             vi ii     i i      v iv    ii    i v- ---     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_91535834_9    287 GGAAACAATAGTTTCTTCTATAAATGAGGCTGGAAAAAC--AATTTCCAT 334
                              v      i i   v i     iv     i v   --i  v?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_91535834_9    335 ATCCAAAAGAATAAAATTGCACCCTTAT-----ACCATACACAAAAATCA 379
                           v         i  i   v    i  i-----      i        i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_91535834_9    380 ACTCAAAAATTGACAAAAGATCTAAATGTAAGACCTGAAATCATAAAACT 429
                                 - v  iv ?   i            v  i   ii        
  L1M4_orf2#LINE/    485 ACTCAAAA-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_91535834_9    430 CCCAGAAGAGAACATAGG-GCAAAGCACCTTGATATTGGCCTTGGCAATG 478
                          ii      i        - i   v vi v   iv    vi v       
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

Transitions / transversions = 1.83 (66 / 36)
Gap_init rate = 0.02 (11 / 447), avg. gap size = 1.73 (19 / 11)  

2943 25.56 2.90 1.56  chr1_91535834_91541522     4301  5196 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91535834_9   4301 TAGAGAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4350
                          i  i i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91535834_9   4351 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTGTTCCCACTAAAC 4400
                            v     v      v i  i  i        i  vi i  i ii   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91535834_9   4401 TACCATTGACATTATTCACAGAATCAGAAAAAAACT-ATTGTAAAATTTA 4449
                          v   vivi v  v  ii     -- vvi v  i  -  iv       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr1_91535834_9   4450 TATGGAA-----------CCA-AATAGCTGAGATGATCCTAAGCAA-AAG 4486
                                -----------   -      ii i ii   i i iv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_91535834_9   4487 AACAAAGCTGGAGGTATCATTCTACCCATCTTCAAACTATACTAT----- 4531
                                i      vv   iv  v    vi      viv     i-----
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_91535834_9   4532 TATAGTAACCAAAACAGCATGGGGCTGGTACAAGAACAGACACATAGACC 4581
                           i     i   i    ii   vi    i i   i i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_91535834_9   4582 AAAGGAAAAGAATAGAGAACCCAGAAATAAGACGACACACCTACAAACAT 4631
                           v    v     v    ii          iv v i   ii  iiiv  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_91535834_9   4632 CTGATCTTCAACAAATGTGACAAAAGCAAGCAATGGGGAAAGGACACCCT 4681
                         i    i   i    iv   v   i v  vv            i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_91535834_9   4682 ATTTAATAAATGGTGCTGGGAGAGCTGGCTAGCCATATGCAGAAAATTGA 4731
                         v  i  i              v i    v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_91535834_9   4732 AACTGGACCCCTTCCTTACACCCTACACAAGAATTAACTCAAGATGGATT 4781
                          ii         v   i     v  i    i           i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_91535834_9   4782 ACAGACTTAAATGTAAAACCGAAAACTATAAAAACCCCAGAAGAAAATCT 4831
                          ?    i         i v v            vi ii         iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_91535834_9   4832 AGGCAATACCCTTCAAGTCATAGGCACGGGCAAAGATTTCATGAAGAAAA 4881
                            ?ivv vi    iv v v v  vvii     v i    v ii v vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_91535834_9   4882 CACCAAAAGCAATTACAACAAAAGCAAAAATTGACAAAT--GGCATCAAA 4929
                                    vvvi         v      v  i    -- i v   --
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA-- 646

  chr1_91535834_9   4930 TTAAAATCAAAATAAGGAGCTTCCATTCAGCAAAAGAAA-TATCATGAGA 4978
                          i     i    ------i   iii v vv    i  v -     v  i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAA------ACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_91535834_9   4979 GTAAATAGACAACCCACAGAATAGGAGAAAATTTCTGCAATCTATCTATC 5028
                           i  v                i         v i     vii  v    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_91535834_9   5029 TGACAAAGGTCTCATATCCAGAGTCTACAAGGAACTTGAACAAAATTACA 5078
                            i  i  v  ii        i v  i  i     ivv    --i -  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CT-CA 787

  chr1_91535834_9   5079 AGAA--AAAAAACAAACAACCCCATTAAAAAGCGGGCAATGGACATGAAC 5126
                          v  --    i     i     v   ?    ii      v   iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_91535834_9   5127 AGACACTTTTCAAAAGATGACACACG--TGGCCAACCAATATTATGAAAA 5174
                              i  i  v     v  i i  i--       iv ii i-       
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC-ATGAAAA 886

  chr1_91535834_9   5175 AAAGCTCAACATCACTGATCAT 5196
                         i v           ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (136 / 89)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  


3140 26.91 1.22 0.66  chr1_91543716_91550077     4967  5869 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91543716_9   4967 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCCTGAAAAT 5016
                              ii i  i     i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91543716_9   5017 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5066
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91543716_9   5067 TACAAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5114
                          v v iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_91543716_9   5115 CATGGAACCGAAAAAGAGCCCGCATTGCCAAGTCAATTCTATGCCAAAAG 5164
                         i      vi v  ii  v  v v  v     iv    ii ivivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_91543716_9   5165 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5214
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_91543716_9   5215 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGACC 5264
                                 i   i    ii  i      i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_91543716_9   5265 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 5312
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_91543716_9   5313 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5362
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_91543716_9   5363 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGCT 5412
                           v  i  i              v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_91543716_9   5413 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGCA 5462
                            ii    i    v   i     v              i    i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_91543716_9   5463 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5512
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_91543716_9   5513 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5561
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_91543716_9   5562 AAACATTAAAAGCAATGGCAACAAAAGCCAAACTTGACAAATGGGATCT- 5610
                         vi   ii       vvi          vv   v v  i    v   ii -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_91543716_9   5611 -----AATTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGA 5655
                         -----       i -   i   i vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_91543716_9   5656 ATAGGCAGCCTACAGAATGGGAGAAAATTTTTGCCATCTACTCATCTGAC 5705
                          v  i  i  i                 v     v vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_91543716_9   5706 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5755
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_91543716_9   5756 AAAAACAAACAACCCCAACAAAAAGTGGGTGAAGGATATGAACAGACACT 5805
                            i     i     v vi?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_91543716_9   5806 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5855
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_91543716_9   5856 TCATCACTGGCCAT 5869
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


3172 25.97 1.10 0.77  chr1_91600205_91606103.rev     4504  5408 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91600205_9   4504 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4553
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91600205_9   4554 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTCTTCCAATCAAGC 4603
                            v     v      v i  i  i        i  vv i  v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91600205_9   4604 TACCATTGGCTTTCTTCACAGAATCAAAAAAACT-ACTTTAAATTTCATA 4652
                          v   viv  i  i  ii     vivi v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_91600205_9   4653 TGGAGCCAAAAAAGAGCCTGTATAGCCAAGACAATCCTGAGCAAAAAGAA 4702
                             iviiv  ii  v  v v        i      i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_91600205_9   4703 CAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAGGCTA 4752
                              i      vv   vi  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_91600205_9   4753 CAGTGACCAAAATAGCATGGTACTGTTACCAAAAGAGATATATGGACCAA 4802
                             i i   i i  ii        vi iv ii v   i    i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_91600205_9   4803 TAGAACAGAACAGAG-GCCACAGAAATAACACCACACATCTAAAACCATG 4851
                          i   i    iv   - i -         vv   i    i  viii  vv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_91600205_9   4852 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAATGGATTCCCTA 4901
                             i  i     ivv  v   i v  vv          v i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_91600205_9   4902 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAGACTGAA 4951
                           i  i              v      v  ?   i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_91600205_9   4952 ACTGGACTCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 5001
                         ii     i   v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_91600205_9   5002 AAGACTTACATGTAAAACCTAAAGCCATAAAAACCCTAGAAGAAAACCTA 5051
                         ?    i  v      i v     i i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_91600205_9   5052 GG--TAATACCATTCAGAACATAAACATGGGCAAAGACTTCGTGACTAAA 5099
                           --   - i -   ivi  v viivv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    550 GGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_91600205_9   5100 ACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCTAAT 5149
                                     vvi          vv i   v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_91600205_9   5150 TAAACTAAAGAGTTTCTGCACGGCAAAAGAAACTATCACCAGAGTGAACA 5199
                         i   v v  i ii  i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_91600205_9   5200 GGCAACCTAAGGAATGGGAGAAAATTTTTGCAATCTACCCATCTGATAAA 5249
                          i     i vi              v       vii ivi         i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_91600205_9   5250 GGGCTAATATCCAGGATCTACAAAGAACTTAAACAAATTTATGAGAAAAA 5299
                           i  vi       i  v  i        ivv    v iv  i v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_91600205_9   5300 AACAAACAACCCCATCAAAAAGTGGGCAAAGAATATGAAGAGAAACTTCT 5349
                         i     i     v  i?    i         i  v    v   v i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_91600205_9   5350 CAAAAGAAGACATTTATGCAAA---CCA-CAA--ACATGAAAAAAAGCTC 5393
                          v        ----   i    ---   -i  --         i v    
  L1M4_orf2#LINE/    848 CCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_91600205_9   5394 ATCATCACTGATCAC 5408
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (133 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


3216 26.36 1.11 0.55  chr1_91619404_91625335     4538  5440 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91619404_9   4538 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCAGGAAAAT 4587
                              ii i  i     i        v      v i     iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91619404_9   4588 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCAACCCCATCAAGC 4637
                            v     v     iv i  i  i        i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91619404_9   4638 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4685
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_91619404_9   4686 TACGGAACTAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAG 4735
                           i    v iv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_91619404_9   4736 AACAGAGCTGGAGGCATCACCCTACCTGACTTCAAACTGTACTACAACGC 4785
                             i  i      vv    v  v  ii i      viv        v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_91619404_9   4786 TACAGTAACCAAAACAGCATGGTAATGGTACCAAAACAGAGATATAGATC 4835
                                 i   i    ii     v   i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_91619404_9   4836 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 4885
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_91619404_9   4886 CTGATTTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 4935
                         i       i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_91619404_9   4936 ATTTACTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 4985
                         v  i vi              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_91619404_9   4986 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5035
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_91619404_9   5036 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5085
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_91619404_9   5086 AGG--TAATGCCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5133
                            --   vv --   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_91619404_9   5134 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 5183
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_91619404_9   5184 TTAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5233
                          i   v v  i i  ii  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_91619404_9   5234 AGGCAACTTACAGAATGGAAGAAAATTTTTGCAATCTACCCATCTGACAA 5283
                           i    ii         i       v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_91619404_9   5284 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTATAAGAAAA 5333
                         i  i  vi          v  i        ivv    v iv    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_91619404_9   5334 A-ACAA-----CCACATCAAAAAGTGGGCAAAGGATATGAGCAGACACTT 5377
                          -    -----   -  i?    i            v   ii     i  
  L1M4_orf2#LINE/    797 AGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_91619404_9   5378 CGCAAAAGAAGACATTTATGCAACCAACAGACACATGAAAAAATGCTCAT 5427
                          v v        i  vi viiii    i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_91619404_9   5428 CATCCGGCCAGGC 5440
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


3471 18.51 10.10 0.96  chr1_91721041_91723252.rev      890  1721 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_91721041_9    890 TGGAAAGACACACAATGTTCATGGATCGGAAGATTCAATATTGTTAAGAT 939
                                 i iv v            i      i i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_91721041_9    940 AGTAATTGTCCCCAAATTAAACTATAGTTTCAGCTCAACCCATATCAAAA 989
                         i i   vv          i v   i  v    i v   i  v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_91721041_9    990 TA--GGTTG--TTTTTTGTAGGACTTGACAAGCTGATACTAAAATTTATA 1035
                          v--i i  --       i  i v             v        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_91721041_9   1036 TGAAAATGCAAAGGATCTAGAGAAATCAAAACAACTTTGAAAAAGAA--- 1082
                           i        i   i i   iv ii        ii           ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_91721041_9   1083 CAAAGTTGGAGGATTTA--------------AAAA------ATAAAGCTA 1112
                                      i i --------------    ------ i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_91721041_9   1113 CAGTGATCAAAACAGTGTGGTATTGACTTAAAGATAGGCATACA--TCCA 1160
                             i     i           i  i v   i     i    i --  v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_91721041_9   1161 TAGAACAGAGT--ATATTCCAGAAATAAACTCTTACATTTATGGTCTATT 1208
                          i   i   i -- v v             i v             v   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_91721041_9   1209 GATTTTTGACAAGGGTGTCAAGGTAATTCAAT-----------AGTCAT- 1246
                               i          i    iiv       -----------    v -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_91721041_9   1247 -CCATAAATGATGCTGGAGCAA-TGGATATTCCTGTGCAAAAAAAAAAAA 1294
                         - v i     i      ii   -      ?i vii       i  vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_91721041_9   1295 ACTTACATTCTTACCTCACAACAACCATATGCAAAAATTAACTAAAAATG 1344
                         --  iv ii i         ----      i            v      
  L1M4_orf2#LINE/    451 --TTGGACCCCTACCTCACA----CCATATACAAAAATTAACTCAAAATG 494

  chr1_91721041_9   1345 AATCACAG-CCTAAATGTAAGAGTTAAA-CTATAAAATTCCTAGAAGAAA 1392
                         i    ?  -              i    -        i  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_91721041_9   1393 TCATAGGAG-AAA----------CATGGATTAGGGCAAAGGCTTCTTAGA 1431
                         v      ? -   ---------- v   i     -   v  i        
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTAGA 593

  chr1_91721041_9   1432 TGTGATACCAAAAACGTGATCCTTAAAA----AAATTAATAAACTCAACT 1477
                          i   i       i iii v vvi    ----    vi     i vi   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_91721041_9   1478 TTATCAAAATTTAAAACTTTTGTTTTTCAGAAGATACCATTGAGAAAATG 1527
                          i         v           vi    i i  i  i  ii     i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_91721041_9   1528 GAAAGGCAAGCCACAGACTTGAATAAAATATTTGCAAATCATATACCTGA 1577
                         i    i   v       v v i v                     i    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_91721041_9   1578 TAAGGTATTTATATTCAGAA-ATATAAAGAATTC---------AATAA-- 1615
                              v i  i   i     -          i  ---------     --
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_91721041_9   1616 ----GACAAACTGATTTTTTT----AATGAGCAA--GATTTGAATATATA 1655
                         ----      - i iiivv  ----    i    --          v i 
  L1M4_orf2#LINE/    794 AAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_91721041_9   1656 TTGCACCAAAGCAGACATATGAATGGTGAATAAGCATATAAAAAGATGTT 1705
                           v v      v   i   ii     iv        i  i        i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_91721041_9   1706 CAACATCATTACTCAT 1721
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (104 / 47)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.83 (92 / 24)  


 851 28.45 8.72 5.26  chr1_92250031_92251638      500  1107 (501)    L1M4_orf2#LINE/L1      241   869 (39)  

  chr1_92250031_9    500 TATAAAGCCTCTATAATTAAAAC--TGTGATATTGGCACATGAATAGATG 547
                           i     iv vi    i  i  --    i  i     i v i     ii
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_92250031_9    548 GCCTGAACAATGTGATAGACTAGAAAGTCCAGAAATAGAACTA------- 590
                         vviv  v     vi     v v  i            i v i -------
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_92250031_9    591 AGGGACAAAACAATTTAGCATACGATAAAAGTGGCATCTAAAATGA---G 637
                          v  v   ------  iiiv v   i  ii   ---- i  i iv ---i
  L1M4_orf2#LINE/    341 ATGGTCAA------TTGATTTTCGACAAGGGTG----CCAAGACCATTCA 380

  chr1_92250031_9    638 AAGGGGAAAAGCT-GACTTTT-AATAAACGGTATTGGGATAACTAGATAG 685
                          v       iiv - v     -  i   i   ii     i    i    ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_92250031_9    686 CCACTTGGAAAAAAAGGAAATATACAATTGGATCTTTTCTTCATACCATG 735
                             v  v    i  v   i -------    i ii v i   i     i
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGT-------TGGACCCCTACCTCACACCATA 473

  chr1_92250031_9    736 TAACAAGATAAATTCCAAATGAATTAAATAGCTAAGTATAAAAAGTGAAA 785
                           vv  i  v  i  v     i  i ? v v    i i   i iv i   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_92250031_9    786 TCACACA-TTATTAGGGGAAAGCGTATGAAT---TCTTTTACAATCTGGA 831
                         ii i v -i v    ii    i i  v ?i ---    i-iii i  v i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGG 572

  chr1_92250031_9    832 AGTCAGG--ATAATCTTTCCACCTATGACTC--AAAGTCCAGAAAAAATG 877
                         -  i   --  ii i i i- vv      v --    --  v  iv  ii
  L1M4_orf2#LINE/    573 -GTTAGGCAATGGTTTCTT-AGATATGACACCAAAAG--CACAAGCAACA 618

  chr1_92250031_9    878 AACAAAAAGAAAGAATAAATTTGACTACATTAAAAC-AAAAACACCAGGG 926
                           vi    i v   -      v    v   i    i-      viiv v 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGA-TAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_92250031_9    927 GAAAAAAAAAACCCACCAAAAGCCAAGCCAAGTCAGAAGACAAATGACA- 975
                         vvvv   ii vv i i   i --------    v i       viv   -
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGA--------AAGTGAAAAGACAACCCACAG 709

  chr1_92250031_9    976 AATGGGAAAAATATATTTGCAAATTATATCACAGACAAC--ACTAATATC 1023
                                i   -            i    vv v  i  v--   vi    
  L1M4_orf2#LINE/    710 AATGGGAGAAA-ATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_92250031_9   1024 TCCAACATCTAAA---------------AATAGAGAAAAGACCAAAAGC- 1057
                         ivv  i  v    ---------------    ivi       v  v i -
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_92250031_9   1058 -------AAAATGGACAAAGGATATGAATAATCATT----CAAAGAAGAA 1096
                         -------       i        v      iv    ----         v
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_92250031_9   1097 ATTAAAATGGC 1107
                           vv       
  L1M4_orf2#LINE/    859 ATACAAATGGC 869

Transitions / transversions = 1.39 (99 / 71)
Gap_init rate = 0.04 (25 / 629), avg. gap size = 3.40 (85 / 25)  


4047 16.42 6.31 2.07  chr1_92275762_92278678.rev     1556  2426 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92275762_9   1556 TGGAAACACATCTCGTGTTCACGGATTAGATGACTTAATATTGTTAAGAT 1605
                               v i   i i      i     i  v                   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92275762_9   1606 AGTAGTACTTTCTGAATTGATCTACAGATTAAATGCAATCTCTATTAAAA 1655
                         i i i    ii ii                v  i      i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_92275762_9   1656 TTCCAGCTGACTTTTTTTTTTTTTTTGCAGAAATTGACAAGCCAATCCTC 1705
                          i       v       ---------                ii     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT---------GCAGAAATTGACAAGCTGATCCTA 141

  chr1_92275762_9   1706 AAATTCAAATGGAAATACAAGGGGCCCAGAACAGCCAAAACAATCTTGCA 1755
                                v        i      i       i                v 
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_92275762_9   1756 AA----TAACAAAGTTGGTGGATTCACACTTCTCAATTTTCTAAGCTTCC 1801
                           ----v           v   i         i      - v  i   v 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT-CAAAACTTAC 240

  chr1_92275762_9   1802 TACAAAGCTACAGTAATCAAGACTGTGTAGTACTGACATAAGAATGGTGG 1851
                                                v    i      i      i  i ---
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG--- 287

  chr1_92275762_9   1852 ACATGTAGATCAGTGGAATAGAACTGAG--TCTAGAA-------CATACA 1892
                             i       i          i    --  i    -------      
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_92275762_9   1893 TTTATGGGCAACTAATTTTTGACAAGGGTGTCCAGACAATAACACAATGG 1942
                                v   i i     i          i v    v  v---      
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGG 384

  chr1_92275762_9   1943 GGAAAGAACAGTCTCCCCCATAAATGGTGCTGAGACAAGTGAACATCCAA 1992
                                 i     iii v i           i     v  i i ?   v
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_92275762_9   1993 ATGCAAAAGAATGAAGTTAGACGCTAACCTCATACCATATACAAAAATTC 2042
                                           i   v iv      i                v
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_92275762_9   2043 AC-CAGAATAGATCAAAGACCTAAATGGAAAAGCTAAAAGTACAAAACTG 2091
                           -  i   i     ?           v  i        v  i      v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_92275762_9   2092 TTTTAAGTAAACATAGGCATAAATCTTCATGACCTTGG---------TG- 2131
                           vv   v         ?i         i         ---------  -
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_92275762_9   2132 --TCTTAGATATGATTCCAAAAGCACA-GCGACAAAAGAAAA----GATA 2174
                         --            iv           -  i           ----    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_92275762_9   2175 AAGTGGAAATCA-CACAAATTAAAGATGTTTGATTTCCAGAATACCCTA- 2222
                           v    vv   -  -        i iv    vvi i  i iv  v   -
  L1M4_orf2#LINE/    635 AATTGGACTTCATCA-AAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_92275762_9   2223 -----------AAAGAGAACCCAGAGAATGAGAGAAAACTTCTGCAAATC 2261
                         -----------     v      v      i       iv i        
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_92275762_9   2262 ATGT--CTGATAAGAGTCTAGTATTCCAGTATATACAGAAATCTCTAAAA 2309
                           i --        i v  v    -    v     i i i v    v v 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTAT-CCAGAATATATAAAGAACTCTTACA 782

  chr1_92275762_9   2310 GCATAATAGTTTAAAGAGAA----CCCAATTTTAAAATGGGCAAAGGACG 2355
                         i vi    i vv     v  ----       ?v               iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_92275762_9   2356 TGATTAG----TTTTCCAAAGAATATGTAAAAATAACTGATAAGCATACA 2401
                            v   ----  i         v  i  v    ii ii       i ii
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_92275762_9   2402 AAAAT-TGCTCAAGATCATTACCTAT 2426
                             v-       v    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (82 / 57)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.65 (73 / 20)  


3473 23.11 3.89 0.23  chr1_92331614_92336345.rev     3368  4241 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_92331614_9   3368 GAAAGACATGCAGTACTCATGGATTGGAAGACTTAATGTTGCTAAAAAGT 3417
                               i  v vi ii                     i   i   i v v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_92331614_9   3418 CCATACTACACAAAGTGATCTATGGATACAATGCAATCTCTATCAAAATC 3467
                          v     v v    v       ii   v   i      i           
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_92331614_9   3468 TTGATTGCATTTTTTATAGAAATAGAAAACACAATTCTAAAATTCATACG 3517
                         iiiii   v      ii      v  v  vvii  i            i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_92331614_9   3518 GAACCACAAAATACCCTGAATAGCCAAATTAATCTT----AAGAAGGAAA 3563
                            vii   iiv    v           vi      ----      i v 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_92331614_9   3564 AAGTTGGAGTGACTTTGATTTTCTGATTTCAAAATATATAACAAAGCTGT 3613
                                  -    ivv i  i ii         iv  iv        ii
  L1M4_orf2#LINE/    203 AAGTTGGAG-GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_92331614_9   3614 AGTAACTAAAACAGTGTGGTACTGGCCTAAAGACAGACATAGAGATCAAT 3663
                              ii  i                v   i  i       v        
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_92331614_9   3664 GGAACAGAACAGAGAGCCCAGAAATACATCCA--CATACATAA--AACTG 3709
                             i    iv     i         v i   --   vi  ii--  i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_92331614_9   3710 CTCTTTAGTAAAGGTGCCAAGAATACACAATGGGTCAGGAA-AGTCTCTT 3758
                         v i  iiii  i          vi iv       vv i   -     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_92331614_9   3759 CAACAAACAGTGCTGGGAAAACTGGATATCCATAAGCAAAAGAATACAAT 3808
                                ii         v         ?   i v          iv i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_92331614_9   3809 TTCACCCTTATCGTACAACATACCCAAATATCAACTCAAAATGGATTTAA 3858
                          vv    i  i vi   v    iv    v  i              iv? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_92331614_9   3859 GACTTCTACCTAAGACCTGAAACTCTAAAACTCCTAGAAGAAAGC----- 3903
                            i vv iv     v  i     v        i         i -----
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_92331614_9   3904 --------TTCATGACATTGGTCTTGGTAATGATTTCACAGATATGATAC 3945
                         --------   i    v    vi v  i    i    vi        i  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_92331614_9   3946 CAAAAGGACAAGCAATAAAAGCAAACATAAACGAGTGAAACTACATCAAA 3995
                               v        i     v   v   i ii i vii   v       
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_92331614_9   3996 -TTAAAAAGCCTCCATACAGCAAAGAAAAC----AAGACATTGAAAA--- 4037
                         -       - i iii i vv     i v  ----    v v      ---
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_92331614_9   4038 AATCTACAGAATGGGGAAAAATACT-GCAAACCATACATGTCATAAGGGG 4086
                           i i          ii      i -     i    i  v v       i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_92331614_9   4087 CTAAT-TCCAAAATATATAAGAAACTCCTACAATTTAATAGCAAAAAT-C 4134
                           vi -    i         ii     i     i i    ii     v- 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_92331614_9   4135 TGATAACACTGTT-AAAAATTGGCTGAAGACTTGAATACACATTTCACCA 4183
                         vi     v vi  -      v   vi i  i       v       v   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_92331614_9   4184 AAGATGACATACAAATGGCCAACAGGTATATGAAAAGATGTTCTATGTCA 4233
                             v  i              i i i i           i  v ii   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_92331614_9   4234 TTAATCAT 4241
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.67 (125 / 75)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 2.57 (36 / 14)  


3531 24.20 3.54 0.11  chr1_92383056_92387076.rev     2655  3530 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_92383056_9   2655 GAAAGATATTCTGTGTTTATAAACTGGAATAATTAATATTGTTAAAATGT 2704
                                  i ii    i  ii i     v v             i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_92383056_9   2705 CCATACCACTCAAAGCAATCAACAGATTCAATGTAATCCCTACCAAAATT 2754
                          v    iv i    vii   v          i i        i      i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_92383056_9   2755 CCAATGATATTTTTCACAGAAATAGAAAAAAAG-TTCTAAAATTTGTGTG 2803
                            iiviiv     ii       v  v  ivv - i        ii i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_92383056_9   2804 GAACCCCAAAAGACCCTGAATAGCCAAAGCAATCTTGAGAAAAAGGAACA 2853
                            viv   ii     v           i         i   i i     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_92383056_9   2854 A-GCTAGAGGCATCATGCTACCTGATCTCAAAAATATACTACAAAGCTAT 2902
                          - i i    vv   ii  v  ii  i      v -             i
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTAC 251

  chr1_92383056_9   2903 GGTAACCAAAACAGCATGGTATTGACACAAAAATGGACATAAAGACCAAT 2952
                         i    i   i    ii     i  i  i  ii  i      v   i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_92383056_9   2953 GGAACAAAAT----GGCACAGAA---------TACATTTATGGTCAACTG 2989
                             i i   ----i iv     ---------               i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_92383056_9   2990 GTCTTTGACAAGG-TGCCAAGAACACACAATGGGGAAAAGGCAGCCTCTT 3038
                         i i  i       -        v  iv           iiii  i  i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_92383056_9   3039 CAATGAATGGAACCAGGAAAAT--GATATCCACATGCAGAAGAATGAAAT 3086
                            ii     vi ii   v  i--    ?         i         i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_92383056_9   3087 TAGACCCTTATCTCA-A----GTACAAAAATCAACTCAAAATGGATTAAA 3131
                          i     i  i    - ----i         i              i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_92383056_9   3132 GACTATACCATAAGA-CTGAAACTGTAAAACTCCTAGAAGAAAATATAGG 3180
                            ivv vii     -  i     i        i          i     
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_92383056_9   3181 GAAAAAGCTTCTTGACATTGACCTGGGTGATGATTT-TTGGCCTTAGCCC 3229
                         ?iv   v    v    v   ivi i  ii   i   -  i viv ii v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_92383056_9   3230 CACAAACACAGGCAACAAAAGCATAAATAGACAAATGGGATTTTATCAAA 3279
                           v  i    i          v v       i    v   i  i      
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_92383056_9   3280 GTAAAAAGCTTCTGCACAGCAAGAGAAACAGTCAACACAGCGAAGAGACA 3329
                         i v    i   i  ii vv   ii  v  vi    v v  i   i     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_92383056_9   3330 -CCTATGGAATTGGCGAAGATATTTGTAAACCATACATCTGATAAGGGGT 3378
                         -  i ii    v  v   i       i   i    i            ii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_92383056_9   3379 TAATAGTCAAGATCTATAAGGAGC----ACAACTCAACAACAAGAAAACA 3424
                          vi  vi  ii  v     i  i ----         i  i  i  i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_92383056_9   3425 AATAATTTGATCGAAAAATGG-CAAAGATCCTGAATAGACATTTCTGAAA 3473
                              iiii  i?        -     ivii               vv  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_92383056_9   3474 AGAAGACATACAAATGGTTAACAGGTATAAGAAAAGGTGCTCAACATCAC 3523
                               i          ii  i i i i v      i            ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_92383056_9   3524 AAATTAC 3530
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.65 (151 / 57)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 2.29 (32 / 14)  


3136 27.86 0.44 0.44  chr1_92409938_92415740.rev     4405  5312 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92409938_9   4405 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGGGAAAAT 4454
                              ii i  i     i      i v      v i     i vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92409938_9   4455 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4504
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_92409938_9   4505 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4552
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_92409938_9   4553 CATGGAACCAAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCCAAAAG 4602
                         i      viiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_92409938_9   4603 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4652
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_92409938_9   4653 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4702
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_92409938_9   4703 AACGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATCTACAACT 4750
                           i    i    i-- v  i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_92409938_9   4751 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4800
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_92409938_9   4801 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4850
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_92409938_9   4851 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4900
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_92409938_9   4901 TTAAAGACTTAAACGTTAGACCTAAAATCATAAAAACCCTAGAAGAAAAC 4950
                          i ?    i    i  v   v      ii      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_92409938_9   4951 CTAGGTATTACCACCCAAGACATAGGCATGGGCAAGGACTTCACGTCTAC 5000
                         v    ?i v vivii iv   v v  vv i     v ii   viivv  i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_92409938_9   5001 AATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5050
                         i i          vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_92409938_9   5051 TTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTACCATCAGAGTGAAC 5100
                          i   v v  i i   i  ii vvi   i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_92409938_9   5101 AGGCAACCCACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5150
                           i         i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_92409938_9   5151 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATCTACAAGAAAA 5200
                         i  i  vi          v  i  v      vv    v  v i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_92409938_9   5201 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5250
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_92409938_9   5251 CCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5300
                         i v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_92409938_9   5301 ATCACTGGCCAT 5312
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (152 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3116 25.11 1.75 2.19  chr1_92430416_92436242     4423  5334 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92430416_9   4423 TGGAAAAACATTCCATGCTCATCGGTAGGAAGAATCAATATTGTGAAAAT 4472
                               i i  i     i    v i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92430416_9   4473 GGCCATACCGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4522
                            v    iv      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_92430416_9   4523 TACCA-CTGACTTTCTTCACA-AAATTAGAAAAAACT-ACTTTAAATTTC 4569
                          v   -   v    i  -i  -     i-- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_92430416_9   4570 ATATAGAACCAAAAAGTGTCCGGA-TAGCCAGGACAATCCTAAGCAAAAA 4618
                             i   viiv  i vii  i  -      ii      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_92430416_9   4619 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAGGG 4668
                                 i      vv   ii  v  ii i      viv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_92430416_9   4669 CTAAAGTAACCAAGACAGCATGGTACTGGTACCAAAACAGATACATAGAT 4718
                            v     i        ii         i iv ii i   i i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_92430416_9   4719 CAATGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACAACCA 4768
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_92430416_9   4769 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 4818
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_92430416_9   4819 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 4868
                          v  i  i              v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_92430416_9   4869 AAATTGGACTCCTTCCTTACCCCCTATACAAAAATTAACTTGACATGGAT 4918
                           i      i   v   i  v  v                ii v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_92430416_9   4919 TAAAGACTTAAACATAAAATCTAAAACCATAAAAACCCAAAACCATAAAA 4968
                         i ?    i    ii   i v       i      - i ------------
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTC------------ 534

  chr1_92430416_9   4969 ACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGACATGGGCA 5017
                         ---i           v    ?i- v i -   iv   v v ivv i    
  L1M4_orf2#LINE/    535 ---TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chr1_92430416_9   5018 AAGACTTCATGACTAAAACACCAAAAGAAATGGCAACAAAAGCCAAAATG 5067
                          v ii   v iiv  vi          v vvi          vv     i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_92430416_9   5068 GACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAACAAAAGAAAC 5117
                           i    v   ii v  i   v v  i i   i  ii vv    i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_92430416_9   5118 TATCATCAGAGTAAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAA 5167
                              vv i   i  v  i     i                 v       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_92430416_9   5168 TCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAA 5217
                         vii  vi      i  i  i  vi          v  i  i     ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_92430416_9   5218 CAAATTTATAAGAAAAAAA-----AACCCA-TCAAAAAGTGGGCAAAGGA 5261
                            v iv    v     i -----      - i?    i           
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_92430416_9   5262 TATGAACAGACACTTCTCAAAAGAAGATATTTATGCAGCCAACAA--ACA 5309
                          v    i     i     v           vi viii     i  --   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_92430416_9   5310 TGAAAAAAAGCTCA---TCACTGGTCAT 5334
                               i v     ---   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (137 / 88)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.57 (36 / 14)  


3138 25.72 1.33 0.67  chr1_92456566_92462955     4996  5897 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92456566_9   4996 TGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATCATGAAAGT 5045
                              ii i  i     i     i  v      v i     ii v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92456566_9   5046 GGTCATACTGCCCAAAGTAATTTACAGATTCAATGCTATCCCCATCAAGC 5095
                           iv     v      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_92456566_9   5096 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAAAGTTG 5142
                          v   -   v    i  -i     -   -- v  i  -  ii    i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_92456566_9   5143 ATATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCCAAAA 5192
                                 viiv  ii  v  v v        i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_92456566_9   5193 GAACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAGG 5242
                                 i      vv   vi  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_92456566_9   5243 ACACAGTAACCAAAACAGATTGGTACTGGTACCGAAACAGATATACAGAC 5292
                         vi       i   i    vv         i iviii i   i   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_92456566_9   5293 CAATGGAACAGAACAGAGGCCTCAGAAATAACACTACACATCTACAACCA 5342
                                 i    iv   ivii         vv i i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_92456566_9   5343 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5392
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_92456566_9   5393 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5442
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_92456566_9   5443 AAACTGGATCCCTTCCTTACACCTTATGCAAAAATTAACTCAAGATGGAT 5492
                           ii    i    v   i     v   i               i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_92456566_9   5493 TAAAGACTTAAATGTAAGACTTAACACCATAAAAACCCTAAAAGAAAACC 5542
                         i ?    i           vi   v  i      vi i  i        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_92456566_9   5543 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGATTAA 5591
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_92456566_9   5592 AACACCAAAAGGA-ATGTCAACAAAAGCCAAAATAGACAAATGGGA-TTA 5639
                         i          v - v -         vv        i    v   -  v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_92456566_9   5640 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAGTATCATCAGAGTGAA 5689
                           i   v v  i i   i  ii vv    i  v v     vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_92456566_9   5690 CAGGCAACCTACAGAATGGGAGAAAAATCTTTGCAATCTACCCATCTCAC 5739
                         v  i     i                - v       vii ivi    v i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGAT 744

  chr1_92456566_9   5740 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5789
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_92456566_9   5790 AAAAA-AAAT--CCCA-TCAAAAAGTAGGCAAAGGATATGAACAGACACT 5835
                            i -    --    - i?    i i          v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_92456566_9   5836 TCTCAAAAGAAGACATTTATACAGCCAACAG--ACATGAAAAAATGCTCA 5883
                             v        i  vi v ii     i i--         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_92456566_9   5884 TCATCACTGGTCAT 5897
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.20 (18 / 15)  


3250 25.47 1.33 0.78  chr1_92565481_92573926     4941  5843 (2603)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92565481_9   4941 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGACAAT 4990
                               i i  i     i        v      v i     ii v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92565481_9   4991 GGCCTTGTTGCCCAAACTGATTTATAGATTCAATGCTATCCCCATCAAGC 5040
                            vv ii v      i    i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_92565481_9   5041 TACCA-CTAACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAGATTC 5087
                          v   -  iv    i  -i     -   -- v  i  - iii   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_92565481_9   5088 ATATGGAACCAAAAAAGAGCCCACCTAGCCAAGACAATCCTGGGCAAGAA 5137
                                 viiv  ii  v  vivv       i      i  iiv     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_92565481_9   5138 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTTTACTACAAGC 5187
                                 i      vv       v  ii i      vi         iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_92565481_9   5188 CTACAGTAACCAAAACAGCATGGCACTGGTACAAAAACAGATATGCAGAC 5237
                                  i   i    ii   i     i i  ii i   i  ii   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_92565481_9   5238 GAATGGAACAGAATGGAGGCCTCAGAAATAACACCACACGTCTACCACCA 5287
                         v       i     v   ivii         vv   i  i i  ivii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_92565481_9   5288 TCTGATCTTTGACAAACCTGACACACACAAGCAATGGGGAAAAGATTCCC 5337
                         vi    i  i     ivv  v  vivv  vv           ii  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_92565481_9   5338 TATTTAATAAATGGTGTTGGGAAAACGGGCTAGCCATATGCAGAAAACTG 5387
                          v  i  i        i     v   v  v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_92565481_9   5388 TAACTGGACCCTTTCCTTACACCTTATACAAAAATCAACTCAAGATGGAA 5437
                         v ii       i v   i     v           i       i     v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_92565481_9   5438 CAAAGACTTAAACGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAACC 5487
                           ?    i    i      v   ii  i      v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_92565481_9   5488 TGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAA 5536
                          i  ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_92565481_9   5537 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG--TTC- 5583
                         i            vvi          vv     v  i    v  --   -
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_92565481_9   5584 T---AATTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGAA 5630
                          ---       i -   i  ii vv    iv v       vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_92565481_9   5631 CAGGCAACCTACAGAATGGGAGAACATTTTTGCAA--TATATCCATCTGA 5678
                         v  i     i              v  v       --i    --      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chr1_92565481_9   5679 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 5728
                         i  i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_92565481_9   5729 AAAAAGCAAACAACCCCATCAAAAAATGGGCAAAGGATATGAACAGATAC 5778
                             ii    i     v  i?                 v    i   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_92565481_9   5779 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTC 5828
                              v        i  vi viii     i ii  i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_92565481_9   5829 ATCATCACTAGTCAT 5843
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  

2927 17.71 7.52 0.47  chr1_92565481_92573926     6811  7448 (998)    L1M4_orf2#LINE/L1       13   695 (213)  

  chr1_92565481_9   6811 CCATGTTCATGAATTGGAAGATCAAATGTTGTTAAGATAGCAGTTCTCCC 6860
                                    i         iiv   i          i   i v     
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_92565481_9   6861 CAAATTAATCTACA------ATGCAATCCCTATCAAAATCACAGCAGGCT 6904
                               i       ------ i                  v    v v  
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_92565481_9   6905 TTTTTG-AAAAATTGACAAGCCAATCTTAAAATCTGTATGAAAACATAAA 6953
                               - i            ii   i      iii    i   iii  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr1_92565481_9   6954 GGATTCAGAATAGCCAAAATAATTCTGAAAATGAAGAA------------ 6991
                            ii              i   ii      v      ------------
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr1_92565481_9   6992 ----ATAATTCTGA--TCCAGAACTTACTACAAAGCTACATTAATCAAGA 7035
                         ---- i v   iv -- i  i                   v         
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_92565481_9   7036 CAGTGTGGTACTGATATAAAGATAGGCATACAGATCAGTGGAACAGA--- 7082
                                      ii    i     i    i      i     i   ---
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_92565481_9   7083 ----GTCCAGGAATAAACCTTCACATTTATGATCAATTAAGTTTTGACAA 7128
                         ----      i        ivi         i      i v   i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_92565481_9   7129 AAATCCCAATGAA-ATT--ATGGAGAAAAGATGGTCTTTTCAACAAATAG 7175
                         iii v    -  v-   --    i    ii  i               i 
  L1M4_orf2#LINE/    363 GGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_92565481_9   7176 TGCTAGGATATTTGGATATCAA-ATGCAGAAGAAATTAATTTAGATTCTT 7224
                             i   i vi      ? v -     i     - v  v  i  ii i 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCT 460

  chr1_92565481_9   7225 ACCTCCTACCATATGCAAAAATAAACTCAAAATTGATCACACACCTACAT 7274
                              vi       i       v          v     ? v     v  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_92565481_9   7275 GTAAGAGCTAAAACTATAAAACATGTAGAAGAAAACATGGGAGAAAACCT 7324
                                               viv             i  ? v   i  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_92565481_9   7325 AGATGACCTTGGTTTAGG-AA-GAATTCTTAA----GACACTAATAGCAC 7368
                         vvi         v     -  - iv      i----     i  v     
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_92565481_9   7369 AATTCATAAAAGAAAATATTAATAAATTGGACTTCATTAAAATATAAAA- 7417
                           viv i         v  vi                i     -     -
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAA 659

  chr1_92565481_9   7418 -TTTTGT--TTCAAAAAAC--TATTAAGAAAATTAA 7448
                         -      --      ii  --   i      i v  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

Transitions / transversions = 2.14 (75 / 35)
Gap_init rate = 0.02 (17 / 683), avg. gap size = 3.00 (51 / 17)  

 806 18.14 6.51 2.33  chr1_92565481_92573926     7749  7963 (483)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_92565481_9   7749 AAAAAAATTAATTGAAAAATCACAGACTGGGAGAAAATATTTTCAAACCA 7798
                           i   i v  vv  v  vi      v               v    i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_92565481_9   7799 TAATAAGTATCTGATAGAGGACTTGTATCTAGACTATGTAAAGAATTCTT 7848
                           -----         ii           i   v   i       i    
  L1M4_orf2#LINE/    735 TA-----TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_92565481_9   7849 AAAACTCAAAAATAA---GGCAGACAAC-----TTAAAAATGGACAAAAT 7890
                          v       v     --- i  i i   ----- ?        i    iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_92565481_9   7891 GTTTGAATAGATATTTCAGCAAAGA---TATACAAATTGC---TTAGCAT 7934
                         i          i     vv      ---         v  --- v    i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_92565481_9   7935 ATGAAGAGATGTGTACTATCACTAGTCAT 7963
                              i     ivi vi    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (21 / 17)
Gap_init rate = 0.02 (5 / 224), avg. gap size = 3.80 (19 / 5)  


3171 25.80 1.44 0.89  chr1_92608594_92614966.rev     4980  5882 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92608594_9   4980 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5029
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92608594_9   5030 GGCCATACCGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5079
                            v    iv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_92608594_9   5080 TAGCA-CTGACTTTCTT-CAAAGAATTGGAAAAAACT-ACTTTAAAGTTT 5126
                          vv  -   v    i  -  i -     -- v  i  - iii    i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_92608594_9   5127 ATATGGAATCAAAAAAAAGCCTGTATAGCCAAGACAATCCTAAGCCAAAA 5176
                                 viiv  iii v  v v        i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_92608594_9   5177 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATGCTACAAGG 5226
                                 i      vv       v  ii i      viv i      i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_92608594_9   5227 CTACAGTACCCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGAC 5276
                                 vi   i     i         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_92608594_9   5277 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5324
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_92608594_9   5325 CATCTGATCTTTGACAAACTTGACAAAAACAAGGAATGGGGAAGGATTC- 5373
                           vi    i  i     ivv  v   i v  vvv         i  v v-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_92608594_9   5374 CCTATTTAATCAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5423
                         i  v  i  iv             v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_92608594_9   5424 TGAAACTGGATCCCTTCCTTTCACCTTATACAAAAATTAATTCAAGATGG 5473
                             ii    i    v   iv    v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_92608594_9   5474 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5523
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_92608594_9   5524 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5572
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_92608594_9   5573 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5622
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_92608594_9   5623 ------AATTAAAGAGCTTCTGCACAGCAATAGAAACTACCATCAGAGTG 5666
                         ------       i -   i  ii vv   vi  v    i  vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_92608594_9   5667 TACAGGCAACCTACAGAATGGGAGAAAAATTTTTACAATCTACCCATCTG 5716
                         v v  i     i                - v   i   vii ivi     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTG 742

  chr1_92608594_9   5717 ACAAAGAACTAATATCCAGAATCTACAAAGAACTTAAAGAAATTTACAAG 5766
                          i  i i   vi          v  i        ivv v  v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_92608594_9   5767 AAAAAACCAAACAACCCCATCAAAAAGTGGGCAAAGGATGTAAACAGACA 5816
                              iv    i     v  i?    i            v i  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_92608594_9   5817 CTTCCCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCT 5866
                         i   i v        i  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_92608594_9   5867 TATCATCACTGGCCAT 5882
                         i v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


1737 25.59 1.07 1.49  chr1_92629647_92632469.rev      502   970 (1853)    L1M4_orf2#LINE/L1       29   495 (413)  

  chr1_92629647_9    502 GACGACTCAGTGTCATTAAAATATAAGTTCTCCCCAAATTGATTTATAGA 551
                           v    i i i ii    i  ivv i v              i  i   
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chr1_92629647_9    552 TTCAATTATGTCCCAATCAAAATCCCAACAGGCTTTTTTGGTATAAATTA 601
                              ivvvi    v            i v v        -i v     i
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG-CAGAAATTG 127

  chr1_92629647_9    602 ACCTACTTATTCTGTAGTTTACATAGAAATGGAGTTTATATAGACCTAGA 651
                           vvi  v  i  iv i  i i  i      v ------ vi    i   
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCA------AGGGACCCAGA 171

  chr1_92629647_9    652 ATAACTAAAGCAACATTAAAAAAACCCCACAAAATTGGAGTACTTACACT 701
                            i i   i   iv  i     ivvvv     i      v   i     
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_92629647_9    702 GCCAGATTTCAGAACTTATTATAAAACTACAATAATTAAGACAGCATAGT 751
                         v  vi      i      i  i   i     i    i       ii i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_92629647_9    752 CTTGGTGTAAAGATAGACAAATCAATCAGTATAAAAGAACAGAAAGTCAA 801
                         vi   ii   i        v  vi    i iv  v    iv  i    v 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_92629647_9    802 GAAATAGACCCAGGCATATCTGGTCAGTTGCTTTTCAACAAAC-TACCAA 850
                               i     vi   v v      i   v     i    iv- i    
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_92629647_9    851 GATAATTCAATGGGGGAA-AATAATCTTTTCAACAAATAGTGTTGGAATA 899
                           iv           i  -    i              i   i   i i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_92629647_9    900 ATTG-ATAGCCACATGGAAAGATATCAACTTTGATGC-TACATCCTACCA 947
                          i  -   ?       v   iiv  v  v  v  iv -   v  vi    
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_92629647_9    948 TATTTACAAATTAACTCAGA-TGG 970
                            vi v           i -   
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGG 495

Transitions / transversions = 1.48 (71 / 48)
Gap_init rate = 0.01 (7 / 467), avg. gap size = 1.71 (12 / 7)  

 519 26.53 6.63 1.53  chr1_92629647_92632469.rev     1261  1456 (1367)    L1M4_orf2#LINE/L1      475   680 (228)  

  chr1_92629647_9   1261 ATAAAAATGAACTCAACAC---TCA----CCTAAACATATAGAATCAAAA 1303
                          i      v       v i---   ----      ii  -   iii    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA-AGAGCTAAAA 523

  chr1_92629647_9   1304 CTAGGAAATTTCTGGATGCAAATGTACAAGAAAATCTT----ACCTTGAA 1349
                            vi   i ii i  v v   ii  vi? v       ----      ii
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_92629647_9   1350 TTTGTCAAAGATTTTTAATAG-TGTGACACAAAAATCATGA-CTATAATA 1397
                           v v   v i   i --   - i      v    v  ii - v i  v 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCT--TAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_92629647_9   1398 GGAAACATAAATAAACTGGACTTCATCAAGATTTAAAAGTTTTGCTTTTC 1447
                          i   v   i     i             i   v    v     ivi   
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_92629647_9   1448 GCTGGGCAC 1456
                         ivv  i   
  L1M4_orf2#LINE/    672 AAAGGACAC 680

Transitions / transversions = 1.55 (31 / 20)
Gap_init rate = 0.03 (7 / 206), avg. gap size = 2.29 (16 / 7)  

 588 11.79 8.13 17.07  chr1_92629647_92632469.rev     2087  2332 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_92629647_9   2087 AAAAAAGGGAAAA------CTACTGAATGGGAGAAAATATTAGCAAAATA 2130
                           i    v     ------ i  v                 v     vi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_92629647_9   2131 TATATCTAAATTCTTATATCTTGGGTGAGTAGGGAAGGTGGGGTGAAAAA 2180
                                i -------  ------------     ---------------
  L1M4_orf2#LINE/    735 TATATCTGA-------TA------------AGGGA--------------- 750

  chr1_92629647_9   2181 AATAAATTCGTACATCTAGAATATATAA----TTATTACAACT---TAAT 2223
                         ------i i   --  i           ----i v        ---    
  L1M4_orf2#LINE/    751 ------CTTGTA--TCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_92629647_9   2224 GAGAAGACAA----TCTAATTTAAAAATAGTCAAAACATTTGAACAGACA 2269
                         i i       ----i i    ?      i v    iv       i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_92629647_9   2270 TT-CACCAAAGAAGATATG--ATTGGCAAATAATCACATGAAAACATGCT 2316
                           - v             i-- v    v     v          v     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_92629647_9   2317 CAACATCATTAGTCAT 2332
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (16 / 12)
Gap_init rate = 0.04 (10 / 224), avg. gap size = 6.20 (62 / 10)  


2953 24.80 3.48 1.57  chr1_92710314_92713254     1558  2448 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92710314_9   1558 TGGAAAAACATTCCATGCTTATGGATAGGAAGAATCAATATTGTGACAAT 1607
                               i i  i     i i      v      v i        v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92710314_9   1608 GGCCATACTGCCCAAAGTAATTTCTAGATTCAATGCTATCCCCATCAAGC 1657
                            v     v      v i  i vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_92710314_9   1658 TACCA-TTGACTTTCTT-CAAATAATTGGAAAAAACT-ACTTTAAATTTC 1704
                          v   -i  v    i  -  i -     -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_92710314_9   1705 ATATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAAAAA 1754
                                 viiv  ii  v  v v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_92710314_9   1755 GAACAAAGCTGAAGGTATCACGCTACCTGACTTCAAACTATACTACAAGG 1804
                                 i  i   vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_92710314_9   1805 CTACAGTAACCAAAACAGCATGGTACTGGTGCCAAAACAGATATATAGAC 1854
                                  i   i    ii         iiiv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_92710314_9   1855 CAATGGAACAGAATAGAGGCCTCAGAAATAACGCCACACATGTACAACCA 1904
                                 i     v   ivii         vv   i    v  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_92710314_9   1905 TGTGATCTTTGACAAACCTGACAAAAACCAG-AAATGGGAAAAGATTC-C 1952
                         vv    i  i     ivv  v   i -   v-v      i     v v-i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAGT 396

  chr1_92710314_9   1953 CTATTTAATAAATGG-------AAAACTGGCTAGCCATATCCAGAAAGCT 1995
                           v  i  i      ------- v      v  ?   i  v  i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_92710314_9   1996 GAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAACTCACGATGGA 2045
                            ii    i    v   i    iv                  vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_92710314_9   2046 TTAAAGACTTAAACGTAAGACCTGAAACCATAAAAACCCTAGAAGAAAAC 2095
                          i ?    i    i      v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_92710314_9   2096 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGATTA 2144
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_92710314_9   2145 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 2194
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_92710314_9   2195 ACTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGGGTGAA 2244
                          ii   v v  i i   i  ii vv    i  v       vv ii     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_92710314_9   2245 AAGGCAACATACAGAATGGGAGAAAATTTTTGCAATTTATATTTTGCATC 2294
                            i    vi                 v       v i    -----   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-----ATC 740

  chr1_92710314_9   2295 TGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACA 2344
                            i  i  i  vi          v  i        ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_92710314_9   2345 AGAAAAAAA-----AACCCA-TCAAAAAGTGGACGAAGGATATGAAC--- 2385
                          v     i -----      - i?    i   i i      v    i---
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_92710314_9   2386 ---TTCTCAAAAGAAGAAGTTTATGCAC----CCAAGA--CATATGAAAA 2426
                         ---     v        ----   i  v----    v --  i       
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_92710314_9   2427 AAAGCTAATCATCACTGGTCAT 2448
                         i v   v v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (126 / 91)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.50 (45 / 18)  


3122 27.24 1.00 0.44  chr1_92766208_92772906     5304  6206 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92766208_9   5304 TGGAAAAACATTCCATGCTTATGGGTAGGAAGAATCAATATCGTGAAAAT 5353
                               i i  i     i i    i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92766208_9   5354 GGTCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5403
                           iv     vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_92766208_9   5404 TACCAATGACTTTCTTCACAGAACTGGAAAAA---A--CTAAAGTTCATA 5448
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_92766208_9   5449 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5498
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_92766208_9   5499 AAAAGCTGGAGGCAC-CATCCCACCTGACTTCAAATTATACTACAAGCCT 5547
                         v    i      -  -  iv iv  ii i      viv        iv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_92766208_9   5548 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATTA 5597
                                i   i    ii         i iv ii i   v        i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_92766208_9   5598 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTATGACTA 5645
                               i    i--    i  --        vv   i i  i    iii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_92766208_9   5646 TCTGATCTTTGACAAACCTAACAAAAACAAGAAATGAGGAAAGGATTCCC 5695
                         vi    i  i     ivv iv   i v  vvv    i      i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_92766208_9   5696 TGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5745
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_92766208_9   5746 AAACTGGATCCCCTCATTACACCTTATACAAAAATTAATTCAAGATGGAT 5795
                           ii    i   iv v i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_92766208_9   5796 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5845
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_92766208_9   5846 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5894
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_92766208_9   5895 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5944
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_92766208_9   5945 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5994
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_92766208_9   5995 AGGCAGCCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 6044
                           i  i  i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_92766208_9   6045 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAAGTTACAAGAAAA 6094
                         i  i  vi          v  i  v      vv    vviv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_92766208_9   6095 AAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTTC 6144
                          i     i     v  i? v  i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_92766208_9   6145 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 6194
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_92766208_9   6195 ATCACTGGCCAT 6206
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3344 25.68 0.44 1.63  chr1_92807497_92813875.rev     4970  5888 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92807497_9   4970 TGGAATAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5019
                              vi i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92807497_9   5020 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5069
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_92807497_9   5070 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5117
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_92807497_9   5118 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5167
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_92807497_9   5168 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5217
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_92807497_9   5218 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5267
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_92807497_9   5268 AATGGAACAGAACAGACCAATGGAACAGCCCTCAGAAATAATCCCACATA 5317
                                i    -------- v  i-  i  --        v    i i 
  L1M4_orf2#LINE/    299 AATGGAATAGAA--------TTGAG-AGTCC--AGAAATAAACCCATACA 337

  chr1_92807497_9   5318 TCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGA 5367
                          i  iiiii vi    i  i     ivv  vv  i v  vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_92807497_9   5368 AAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATA 5417
                            i  vvi  v  i  i              v      v  ?   i  i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_92807497_9   5418 TAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATT 5467
                         i i  iiv    ii    i    v   i     v              i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_92807497_9   5468 CAAGATGGATTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTA 5517
                            i      i ?   ii       v   v       i      vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_92807497_9   5518 GAAGAAAACCTAGGCAGTA--TCATTTAGGACATAGGCGTGGGCAAGGAC 5565
                                  v    ?-   --  -  iiv   v v  vv i     v ii
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_92807497_9   5566 TTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAA 5615
                            v ivv  vi            vvi          vv     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_92807497_9   5616 ATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCA 5665
                           v   ii v  i   v v  i i   i  ii vv    i  v    i  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_92807497_9   5666 TCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTAC 5715
                         vv i      v  i     i                 v       vii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_92807497_9   5716 TTATCTGACGAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAAT 5765
                         v       ii i  i  vi          v  i  v      vv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_92807497_9   5766 TTACAAGAAAAAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGA 5815
                         iv i  v     i     i     v  i? v  i    ii      v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_92807497_9   5816 ACAGACACTTCTCAAAAGAAGACACTTATGCAGCCAAAAGACACATGAAA 5865
                          i     i     v        i ivi viii     v ii         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_92807497_9   5866 AAATGCTCATCATCACTGGCCAT 5888
                          i       v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


2933 11.43 2.57 27.34  chr1_92826204_92828582.rev      682  1888 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92826204_9    682 TGAAAATCTATCTCGTATTTGTATATTGGAAGTCTTAAT---GTTAAGAT 728
                           i   vv    i i i  ii iv        v      ---        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92826204_9    729 GTCAGTACTACCCAAAATCACCTACAGATTCAATCCTATCAAACCTATCA 778
                          v  i    v      v v i            iv v   ---       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC---CCTATCA 97

  chr1_92826204_9    779 AAATTCCCATGGACTTTT--GCAGAAATGCAAAAGCTGATCTTAAAATTC 826
                             i  viiv v     --        vv v         i        
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_92826204_9    827 ACATGGAATTGCAAGTGGCCTTGAATAGCCAAA-CAATCTTGAAAAAAAA 875
                          i      v      v i  iv           -             i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_92826204_9    876 GAACAAAGTTGGAGGACTCACACTTTCTGATTTGTAAACTTAATACAAAG 925
                                                  i ii    vv       v       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_92826204_9    926 CTAGAGTAGTCAAA-----GTAGTACTGGCATAAGGATAGACACATAGAT 970
                            v    i    i-----  i                     i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_92826204_9    971 TAATGGAATAGAAATGAGAGTCCAGAAATAAACCCATACATCTATGGCCA 1020
                         i            v                           i     i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_92826204_9   1021 GTTGGTTTTCCACAAGGATGCTAAGAACATTCAATGAGGAACGAATAGTC 1070
                         i   i     v      i   i    v         i    v        
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_92826204_9   1071 TCTTCAACAAATGATGCTGGGAAAACTGGATATTCTCCTGCTAAAGAATG 1120
                          i           i        v         ?i v v   v        
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_92826204_9   1121 AAATTAGATGCCTAAC--ATACTGTATACAAAAATTAACTAAAAATATTC 1168
                           i  i  iv    v -- i  ii                v     ----
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT---- 493

  chr1_92826204_9   1169 CATAGATTTTACAGTTTTGTTTTGTTTTAGGCAGGGTCTTTCTCTGTCGC 1218
                         --------------------------------------------------
  L1M4_orf2#LINE/    494 -------------------------------------------------- 493

  chr1_92826204_9   1219 CAGGCTCGAGTGTAAGGGCACAATCAGCTCACTGCAGCCTTAACCTCCAG 1268
                         --------------------------------------------------
  L1M4_orf2#LINE/    494 -------------------------------------------------- 493

  chr1_92826204_9   1269 GGCTCAAATGATCCTCTCACCTCAGCCTCCCGAGTAGCTGAGACTACAGG 1318
                           v   ? ---------------------------------   ------
  L1M4_orf2#LINE/    494 GGATCAWA---------------------------------GAC------ 504

  chr1_92826204_9   1319 CACATGCCACCATGCCCAGCTAATTTCCATATTTTTTAATAGAGATGAGG 1368
                         -------------------    ---------------------------
  L1M4_orf2#LINE/    505 -------------------CTAA--------------------------- 508

  chr1_92826204_9   1369 TTTTGCCATGTTGCCCAGGCTGGCCTCAAGCTGAACTCAAGCGATCTGCC 1418
                         -------    ---------------------------------------
  L1M4_orf2#LINE/    509 -------ATGT--------------------------------------- 512

  chr1_92826204_9   1419 TGCCTCAGCCTCCCAAAGTGCTGAGATTACAAGCATAAGCCACTGTGCTC 1468
                         ------------------------------------   -----------
  L1M4_orf2#LINE/    513 ------------------------------------AAG----------- 515

  chr1_92826204_9   1469 AGCCAACTTTATGATTTAAAAATAACATGTTTATGTTTTTAAAGCCATAA 1518
                            ------------------------------------    i i    
  L1M4_orf2#LINE/    516 AGC------------------------------------TAAAACTATAA 529

  chr1_92826204_9   1519 AACCCTGAGAAGAATACATAGAGATAAATCTTCATGACCTTGGATTTGTC 1568
                            i  v       v      i?i         i         i  v v 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_92826204_9   1569 AGTGGTTT--TAGATATTGGTTCTTAGGCACCAAAGGCATGAGCAACAAA 1616
                          i      --       --------- i       i   ii         
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATAT---------GACACCAAAAGCACAAGCAACAAA 620

  chr1_92826204_9   1617 AGA---------TAAACTGGACTTCATCTAAATGAAAACTTTTTGTGCAT 1657
                            ---------    i           v    v    vi        v 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_92826204_9   1658 CAAAGGAGATTA---AGAAAGTGAAAAGGCAACCTGTAGAATGGTAGAAA 1704
                                v i  ---             i     iii       v     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_92826204_9   1705 ATAGTTGCAAGTTTTGTAGCTGATCAGGATCTACCATCCAGAATATATCA 1754
                            v      i iv i  v     v   iv  vvi             v 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_92826204_9   1755 TGAACTCTTACAACTCAACAACAAAAAGACAA----CCCAGTTATAAAGT 1800
                         v                 i  i          ----    i  ?v   i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_92826204_9   1801 GGGCAAAAGACTTGAGTGGACTTTTCTCCAAAGAAGATATGCAGATGGCC 1850
                                i  i    i i   v                  i  i      
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_92826204_9   1851 AAAAAGCAAATGAAAAGATGCTCAACATCATTTTTCAT 1888
                           v     v                     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (76 / 58)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 20.06 (361 / 18)  


3190 27.46 0.78 0.33  chr1_92860300_92865876     4182  5084 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_92860300_9   4182 GGAAGAACATTCCATGCTCATGGATTGGAAGAATCAATATCATGAAAATG 4231
                             ii i  i     i               v i     ii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_92860300_9   4232 GCCATACTGCCCAAGGTAATTTATAGATTAAATGCCATCCCCATCAAGCT 4281
                           v     v     iv i  i  i     v  i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_92860300_9   4282 ACCACTGGTTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCATA 4330
                         v   viv ii  i  ii     v v  v  i-  - iii    i      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr1_92860300_9   4331 TGGAACCAAAAAAGAGCCCACATTGCCGAAACAATCCTAAGCAAAAAGAA 4380
                              viiv  ii  v  viv  v   i        i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_92860300_9   4381 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 4430
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_92860300_9   4431 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 4480
                               i   i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_92860300_9   4481 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 4530
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_92860300_9   4531 GCTCTTTGACAAACCTGACAAAAACAAAAAATGGGAAAAAGATTCCCTAT 4580
                          v i  i     ivv  v   i v  vvv      i   ii  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_92860300_9   4581 TTAATAAATGATGCTGGGAAAACTGGCTAGCTATATGTAGAAAGCTGAAA 4630
                          i  i     i        v      v  ? i i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_92860300_9   4631 CTGGATCCCTTCCTCACACCTTATACAAAAATTAATTCAAGATGGATTAA 4680
                         i    i    v         v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_92860300_9   4681 AGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 4730
                             i       v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_92860300_9   4731 GCAGTA--CCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 4778
                          ?-   --i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    551 GN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_92860300_9   4779 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 4828
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_92860300_9   4829 AAACTAAAGAGCTTCTGCACAGCAGAAGAAACTATCACCAGAGTGAACAG 4878
                            v v  i i   i  ii vv  i i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_92860300_9   4879 GCAACCTAAAGAATGGGAGAAAATCTTTGCAATCTACCCATCTGACAAAG 4928
                         i     i v               v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_92860300_9   4929 GGCTAATATCCAGCATCTACAAAGAACTTAAACAAATTTACAAGAAAAAG 4978
                          i  vi       v  v  i        ivv    v iv i  v      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_92860300_9   4979 ACAA----CTCCATCAAAAAGTGGGCCAAGGATATGAACAAATACTTCTC 5024
                             ---- i v  i?    i     v      v    i i i i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_92860300_9   5025 AAAAGAAGACATTTATGCAGCCAACAGACATGTGATAAAATGCTCATCAC 5074
                         v        i  vi viii     i ii  ii   v  i       v  i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_92860300_9   5075 CACTGGTCAT 5084
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (6 / 907), avg. gap size = 1.67 (10 / 6)  


3028 27.57 1.00 0.44  chr1_92892571_92899011     5046  5948 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_92892571_9   5046 TGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATACTGTGAAAAT 5095
                              ii i  i     i     i  v      v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_92892571_9   5096 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCAT-GAAG 5144
                            v     v      v i  i  i        i  v     i  -i  i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_92892571_9   5145 CTACAATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5192
                         iiv  ii  v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_92892571_9   5193 ATATGGAACCAAAAAAGAGCCCACATTGCCGAAACAATCCTAAGCAAAAA 5242
                                 viiv  ii  v  viv  v   i        i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_92892571_9   5243 GAACAAAGCTGGAAGCATCATGCCACCTGACTTCAAACTACACTACAAGG 5292
                                 i    i vv   ii iv  ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_92892571_9   5293 CTACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGAC 5342
                                  i   i    ii         i  v ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_92892571_9   5343 CAATAGAACAGAACAGAGGCCTCAGAAATAACACCGCACATCTACAACCA 5392
                             i   i    iv   ivii         vv  ii    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_92892571_9   5393 TCTGCTCTTTGACAAACCTGACAAAAACAAAAAATGGGGAAAGGATTCCC 5442
                         vi  v i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_92892571_9   5443 TATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5492
                          v  i  i     i        v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_92892571_9   5493 AAACTGGATCCCTTCCTTACACCTTATACAAAAAGTAATTCAAGATGGAT 5542
                           ii    i    v   i     v          v   i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_92892571_9   5543 TAAAGACTTAAATGTTAGACCTGAA-CCATAAAAACCCTAGAAGAAAACC 5591
                         i ?    i       v   v  i  - i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_92892571_9   5592 TAAGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGACTAA 5640
                           i ?i- v i -   iv   viv  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_92892571_9   5641 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTAACAAATGGGATCTAA 5690
                         i            vvi          vv     vi i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_92892571_9   5691 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5740
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_92892571_9   5741 AGGCAACCTACAGAATGGGAAAAAATCTTTGCAATCTACCCAACTGACAA 5790
                           i     i           i     v       vii ivi v    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_92892571_9   5791 AGGGCTAATATCTAAAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5840
                         i  i  vi    i i   v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_92892571_9   5841 AAACAAACAACCCCATCAAAAAATGGGCAAAGGTTATAAACAGACACTTC 5890
                          i     i     v  i?               v v i  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_92892571_9   5891 TCAAAAGAAGACATTTATGCAGC--ATA--CAAATGAAAAAATGCTCATC 5936
                           v        i  vi viii  --   --  v       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_92892571_9   5937 ATCACTGGTCAT 5948
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


 557 26.69 5.26 8.27  chr1_92957543_92960601      500   765 (2293)    L1M4_orf2#LINE/L1      201   458 (450)  

  chr1_92957543_9    500 CAAAGTTGGAGAGCTTATATTACCACATATCAAAGCTTATTATAAAGTTA 549
                                    ii  i i i v  vv  v     i    i  i    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_92957543_9    550 CATTAAT----ACAGTG--ATATTAGTGCAAGGAT-GACAAATATACAAA 592
                           v    ----      --i  i i iii      -    v   v iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_92957543_9    593 TAGAACAAAGT-----ATCCAGAAACAGACCCACACTAATTTCATAAATT 637
                          i   i i i -----i        i i     i  --    --------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC--ATTT-------- 340

  chr1_92957543_9    638 AGCTGACCATACTGTTATCTAATTTATGAAAAAAAGTGCCAC-ACAGTGC 686
                         --------  i--  i vi i    vi  v  ii-      v-  vi v 
  L1M4_orf2#LINE/    341 --------ATG--GTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTC 379

  chr1_92957543_9    687 AGATGGACAAGGA-TGGTATTTGCAATAAATGGTGCTGGATCAAACAGAC 735
                          -    iv  i  - i  v   v   i            iv   vii  i
  L1M4_orf2#LINE/    380 A-ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_92957543_9    736 GTCTATATAGAAAAAAGTGAATCTTGGCCC 765
                         i? i i  iv    i i    vi v i   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCC 458

Transitions / transversions = 2.18 (48 / 22)
Gap_init rate = 0.04 (11 / 258), avg. gap size = 3.27 (36 / 11)  

 446 27.89 2.04 0.00  chr1_92957543_92960601     1550  1696 (1362)    L1M4_orf2#LINE/L1      510   659 (249)  

  chr1_92957543_9   1550 TGCAAAAAGTAAAA---TAAAATTGCTATAAGACAACACAGAAAAATATG 1596
                           i  i iv     ---     i vi  v    v    i  i?iv v  v
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_92957543_9   1597 TTCATATTCTCAGGTTAGGCATTGATTTCTTAAATAGGACACAAAAAGCA 1646
                            i ivi  ii         v  i       i   v     v       
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_92957543_9   1647 GTAACCATAAAGGACAAGATTGATAAAGTATACTTCATTAAAATTAAGAA 1696
                         vv i v i   i  v  i  v      v iv       i        i  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

Transitions / transversions = 1.22 (22 / 18)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)  

 381 25.31 10.37 2.90  chr1_92957543_92960601     2326  2566 (492)    L1M4_orf2#LINE/L1      650   908 (0)  

  chr1_92957543_9   2326 AAATTAAGAATCTCCAGGCATGAAAAAAAACACCATTAAAAGACTGAAAA 2375
                                i  ii iiiv  v v   ii --   i  i  i i v      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGA--CACTATCAAGAAAGTGAAAA 697

  chr1_92957543_9   2376 GGCAAAATACAGACTGAAAAAAATAAAAATGCAATACAT-ATATATCCTA 2424
                          i   vvi     v  ii i   - v vv     ---  -       iv 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAA-ATATTTGCAA---ATCATATATCTGA 743

  chr1_92957543_9   2425 GAAAGGACTCATATCCAGAATA----AAGCA---TTATAA----ATGAGA 2463
                         v  i     ii           ----   v ---   i  ----  i v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_92957543_9   2464 GAAAAATAAGCATATCAAC-GAAAACTGGGCAAAAAGACTT-AACAGGCA 2511
                         i   i i  ii vvi   i-?    v        i-  i  -  i  i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAG-GATTTGAATAGACA 842

  chr1_92957543_9   2512 CTTCAC--AAGAGGAAATATAAATGGTCAACAA---------AAGATACT 2550
                         i   v --    i  v   i      i   i  ---------     i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_92957543_9   2551 CAACCTCAGTACCAGG 2566
                             v   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (40 / 20)
Gap_init rate = 0.05 (12 / 259), avg. gap size = 2.67 (32 / 12)  


1646 21.85 1.66 3.56  chr1_92989330_92991271      502   922 (1020)    L1M4_orf2#LINE/L1      268   680 (228)  

  chr1_92989330_9    502 TGGTACTGGCATAA----AAACAAATAGACCAATGGAGCAAAACAGAAAG 547
                                       ---- i   v     i       ii i  iv  i  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_92989330_9    548 TCCAGAAATAAACTCATGCATCTACAGTCAACTGATTTTCAACAAAGGTG 597
                                      i   i   i  ii     i        i    i    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_92989330_9    598 CCCAGTACC---CAAACTGGAGAAAGAGCAGCCTCTTCAATAAAAGATGC 644
                           v  -   ---   --   i      ii  i  i     i   v i   
  L1M4_orf2#LINE/    368 CCAAG-ACCATTCAA--TGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_92989330_9    645 TGGGAAACCTGGCTATCCAGATGCAGAAGAATGAAACTAGACCCTTATCT 694
                              v v    v  ?   v     i         ii i     i  i  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_92989330_9    695 CTCACCATATGCAAAAATTAACTCAAAATGGATTACAGACTTACATGTAA 744
                          v        i                      i ?    i  v      
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_92989330_9    745 GACCCAAAATGACAAAACTACTAGAAGAAAACACAGAAGGGGAAGCTCTG 794
                           v i    iv i      vi            i  i? vi-  v  ii 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA-AATCTTCG 563

  chr1_92989330_9    795 TGATATGTGGCCTAGGCAAGGATTTTTGTGTGTGTGTGTGTGTAAAACTC 844
                            iv -   vi       v i   i --------- ivi i i v  - 
  L1M4_orf2#LINE/    564 TGACCT-TGGGTTAGGCAATGGTTTCT---------TAGATATGACAC-C 602

  chr1_92989330_9    845 AAAAACACAAACAACAAAAGCTAATGTAGACAAATAGGATTACATCAAAC 894
                             i     i         vv  vi    i    v   i v       v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_92989330_9    895 TCAGAAGCTTCTGCACAGCAAAAGAAAC 922
                          i i  i   i  ii vv    i  v  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACAC 680

Transitions / transversions = 2.07 (60 / 29)
Gap_init rate = 0.02 (8 / 413), avg. gap size = 2.75 (22 / 8)  

 782 22.95 1.23 2.46  chr1_92989330_92991271     1206  1449 (493)    L1M4_orf2#LINE/L1      668   908 (0)  

  chr1_92989330_9   1206 CTTAAAAAAAAAAAATCAACAGAGAAAAGAGATAACCTACTGAACAGGAG 1255
                            v   ii v vv     v i  vi  i   i    i  v   ii    
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_92989330_9   1256 ACTACATTAGCAAACTATACATCTCATAAGGTG-TAATAACCCAAATATG 1304
                          vv i   v     ii   i    v      vi- vi  v  vi     i
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_92989330_9   1305 TAAGGAACTCAAACGACTCAGCAACCATAACAACAA-ACAAATCATCTGA 1353
                            i      vv  i     ------    i  v  -      v i ii 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCA------ATAATAAAAAGACAAATAACCCAA 811

  chr1_92989330_9   1354 TTTTAAAATGGGCAAAAAACCTGAATAGACATTTCTCAAAAGAAGATATA 1403
                           ?v            ii ii                v            
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_92989330_9   1404 CAAATGGCCAGCATATATGTGAAAA-ATGCTCAACATCACTAATCAT 1449
                                   ii vii ii      -             ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (33 / 22)
Gap_init rate = 0.02 (4 / 241), avg. gap size = 2.25 (9 / 4)  


3044 25.51 4.69 0.92  chr1_93065857_93074994      492  1365 (7773)  C L1M4_orf2#LINE/L1   (0)   908     2  

C chr1_93065857_9   1365 GGAAAGATATCTCATGTTAATGGATTGGAAGAATGAATATTGTTAACTTG 1316
                                    i      v             v v           vv  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

C chr1_93065857_9   1315 ACCATACTACCAAAAGCAATCTACAGATTCTGTGCAATCCCTATCAAAAT 1266
                         i v     v  v   vii            vii                 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

C chr1_93065857_9   1265 ACCAATGACATTATTCACTGAAATATAAAAAAGCAATCCTAAAACTAATA 1216
                         v   iivi v  v  ii v     - i v  ivii         i v   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATA 150

C chr1_93065857_9   1215 TAGAACTATAAGAGACCCTGAATAGCCAAAGTAATCCTGAGAAAAAAGAA 1166
                          i   v ii   i     v           ii    i   i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chr1_93065857_9   1165 CAAAGCTTTAGGCATCACACTACCAGATTTCGAAATATACTACAAAGCTA 1116
                              i vv   vv       v  vi     i   iv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chr1_93065857_9   1115 TAATAACAAAAACAGCATGGTACTAGCCATAAAAACAGACCAATAAACCA 1066
                         i i   iv  i    ii       i  -    ii i    vv   i i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGACATATAGATCA 299

C chr1_93065857_9   1065 GTGGTACAGAACCCAGAACCCAGAAATAAAC------------AGCTATC 1028
                         i   v i    iiv   ii            ------------i ii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

C chr1_93065857_9   1027 TGATATTTGATGAAGGTGCCAGGAACATTTATTGGGAAACGGACTATCTC 978
                             v  i  ii i       i  v    i v    i  v i ivi   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

C chr1_93065857_9    977 TTCAGTAAGTAGTGTTGGAAAAACTGGATAGCCATATGGAGAAATGTGAA 928
                             ii  i i   i   i v         ?   i   v i  ivi    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chr1_93065857_9    927 AACAGACCTCTATCTTTCACCATAT-TAAAAGTCAACTCAAAATGGATTA 879
                         ivii    i   i  iv        -i    i i              i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chr1_93065857_9    878 AAGACTTGAATAGAAG-GCATGAAATTATGAAACTATTAGTAAAAAGCCT 830
                         ?    i i   iv   -  - i   i   i     v    v i   i v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACAT 548

C chr1_93065857_9    829 AGGGGAAACACTTTATGACAGTAGTTTGGGCAAAGATCTTATGGAGAAGA 780
                            ? v  vv   ii    vv i v  i     v i i iv i  v v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

C chr1_93065857_9    779 CCTCAAAAGCACAGGCAA----------AATAGACAAATGGGATTATATC 740
                          vi          i    ----------      i    v   i vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

C chr1_93065857_9    739 AAACAAAAAAGCTTCTGCACAGCAAAGGAAAAAAATCAACAGAGTGAAGA 690
                            vvv    i   i  ii vv       -v vv     v i      i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGA-CACTATCAAGAAAGTGAAAA 697

C chr1_93065857_9    689 GACAACGTGCAGAATGAGAGAAAATATTTGCAAACTATTCATCTAACAAG 640
                               vii       i                 ii  vi    i i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

C chr1_93065857_9    639 GAATTAATATCCAGAATATACAAAGAGCTCAACAGCAAACCAACAACAAT 590
                          i i vi             i     i   --ivi   vi   i  i  v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCAATAATAAA 795

C chr1_93065857_9    589 AACACA--TAATTCTATTTAAAACTGGGCAAATGAGCTGAATGGACACAT 542
                           v   --   ii v   ?    v        v  vi     i    -- 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA--T 843

C chr1_93065857_9    541 CTTTCAAAAGAAGACA---------------GGTACATGAAAAAATGCTT 507
                         i i  v        i ---------------i i         i     i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

C chr1_93065857_9    506 AACATCACTAATCAT 492
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (138 / 81)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 4.08 (49 / 12)  

3294 26.46 0.66 0.55  chr1_93065857_93074994     7739  8645 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_93065857_9   7739 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTAAAAAT 7788
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_93065857_9   7789 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 7838
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_93065857_9   7839 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 7886
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_93065857_9   7887 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 7936
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_93065857_9   7937 AACAAAGCTGGAGGCATCTCACTACCTGACTTCAAACTATACTACAAGGC 7986
                                i      vv  v    v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_93065857_9   7987 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATGTAGACC 8036
                                 i   i i  ii         i iv ii i   v  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_93065857_9   8037 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 8084
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_93065857_9   8085 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 8134
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_93065857_9   8135 CTATTTAATAAATGGTGCTGGAAAAACTGGCTAGCCATATATAGAAAGCT 8184
                           v  i  i            i v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_93065857_9   8185 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 8234
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_93065857_9   8235 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 8284
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_93065857_9   8285 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCGTGTCTA 8333
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_93065857_9   8334 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 8383
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_93065857_9   8384 ATTAAACTAAAGAGCTTCTGCACAGCAAAGAA-ACTACCATCAGAGTGAA 8432
                           i   v v  i i   i  ii vv     i -    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_93065857_9   8433 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACC 8482
                         v  i     i                 v       vii ivi      iv
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_93065857_9   8483 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 8532
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_93065857_9   8533 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 8582
                           i     i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_93065857_9   8583 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 8632
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_93065857_9   8633 CATCACTGGCCAT 8645
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1074 23.57 1.91 1.59  chr1_93162494_93166858.rev     2005  2318 (2047)    L1M4_orf2#LINE/L1        1   315 (593)  

  chr1_93162494_9   2005 TGGAGAGTCATACTTTGTTC-TGATCCAGAAAACTAAATATTGTTATGAT 2053
                             i  vi  v iv     -  iviii   i   v          v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_93162494_9   2054 GTCAATTATTTCCAATTTGTTCTACATATTCAAAGCAATTCAAATCAAAA 2103
                          v    vv ii    v   v      v      v     i vv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_93162494_9   2104 TCCCAGCAGACTTTTTT-TGGAATTTG-CAAATTGATTATAAAATTTATG 2151
                                v v       -ii   v   -   ii    iv       i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_93162494_9   2152 TGGAAATGTAAAGTACT-GCAATAACCAAAACAATTTTGGAAAAAAAAAG 2200
                                 i  i v  i-iv    i          i   --     i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG--AAAAAGAAG 198

  chr1_93162494_9   2201 AACAAATTTGGAAGGCAAATACTACCTGATTTAAAGACTTA-TA-AAGAC 2248
                               v     i i vv i   v  ii    v  i     -  -  ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_93162494_9   2249 TTATACAGTATTCAAGACTGTGTATTATTGGTGTGAAGATAGAAAAATAG 2298
                          ---      v       v    iv  i   ii i i      v v    
  L1M4_orf2#LINE/    249 T---ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_93162494_9   2299 AACAAAACAATAGAATTGAG 2318
                          v   viv            
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAG 315

Transitions / transversions = 1.18 (40 / 34)
Gap_init rate = 0.03 (8 / 315), avg. gap size = 1.38 (11 / 8)  

1132 21.40 6.02 1.00  chr1_93162494_93166858.rev     2699  2997 (1368)    L1M4_orf2#LINE/L1      313   626 (282)  

  chr1_93162494_9   2699 GAGAGTCTGAGAAAAACACCCACATATT-ATGGACA-CTGATTTTTAACA 2746
                                i-     v v     i i   -    v  -i       ii   
  L1M4_orf2#LINE/    313 GAGAGTCC-AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_93162494_9   2747 AATGTATGAAGAAAATTCAGTGGGTCAAGGATAGTCTTTTCAATAAATGG 2796
                          iv  iiv    vv     i    vv   i             i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_93162494_9   2797 TGCTGGAACAATTGCATATCCAGATGGAAAACAATGAACTCCCATCCATA 2846
                               i    i  v   ?   v   v    v      v ivv i  v  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_93162494_9   2847 CCTCATATCATATGCAGAAATTAACTCAAAATGGATCATAG-CCGAAACA 2895
                              i i     i  i                     ?  -  v   ii
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_93162494_9   2896 TAAAACCTAAAGCTATAACATTTCTTATAA------ATAGAA-TAAAGTC 2938
                            i v     i      v i -    v  ------    i?-    -  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNGTAAA-TC 559

  chr1_93162494_9   2939 T--GTGATACTAGGTCAGGTAAAGATTTCCTAGGTATAGCACCAAAATC- 2985
                          --    ivi i   i   i  v i    i   i   ii        v -
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_93162494_9   2986 CA-----TAAAAGAAAA 2997
                           -----i         
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAA 626

Transitions / transversions = 1.54 (37 / 24)
Gap_init rate = 0.04 (11 / 314), avg. gap size = 1.91 (21 / 11)  

1089 22.03 2.03 0.00  chr1_93162494_93166858.rev     3580  3874 (491)    L1M4_orf2#LINE/L1      608   908 (0)  

  chr1_93162494_9   3580 CAAAAAAAAGAAAGAAAGAAAGAAAGAAATTCAACTTCAGAAAAATTAAA 3629
                           v  iv  v   ii  i   v i v     vi      vv         
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_93162494_9   3630 AACTTCTGCTCTTCAAAATATACTGTTAAGATAATGAAAAGACAAGTCAT 3679
                              i  iv       iv i   i i    v i           vi  i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_93162494_9   3680 CAACCAGGAAAGAACATTT-CAAAGGATACATCTCATAAAGAACTTGTAC 3728
                         vi vii   i i  i    -    vv   i    v    i i       i
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_93162494_9   3729 TCAGAATATATAAAGAACTCTTACAACT--ACA-TAAGAAAACAAACC-T 3774
                         i                           -- i -   i  i     iv-i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_93162494_9   3775 CCAAT-AAAAAATGGGCAAACTATTTGAGCTGTTGCTTCACCAAAGAAGC 3823
                              -?             vv      iiv viii   v         v
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_93162494_9   3824 TATACAGATGACAAATAAGCATATGAAAAGATGCTCAACATCATTAGACA 3873
                               i   i v        i                     ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_93162494_9   3874 T 3874
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.56 (39 / 25)
Gap_init rate = 0.02 (5 / 301), avg. gap size = 1.20 (6 / 5)  


3590 16.79 12.50 1.23  chr1_93260905_93262798.rev      590  1405 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_93260905_9    590 TGGAAAGGCATCCCATGTTCATAGAT-G------TTAATAATATTAAAAT 632
                                ii             i   - ------      v i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_93260905_9    633 GGCAAGTCTTCCCAAATCAATCTATAGATTCAATACAATACCTACCAAAA 682
                              vv  i       ii     i        ii    v    i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_93260905_9    683 TCCCAGCTGCGTTTTTTTGCACAGACTCACAGATTGATCCTAAAATTTAC 732
                                   -i         v i i v   iii             i i
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_93260905_9    733 ATGGAAAAGTGAAAGGAACCCAGAATAGCCAAATTGTTTTTTAAAAAGAA 782
                                --  v    i                viiv i  v        
  L1M4_orf2#LINE/    150 ATGGAAA--TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_93260905_9    783 AAA--AACTTG-AGGACTCACAACGTCCCAATTTCAAAACTTACTATGAA 829
                         i  --  v   -          - v                     ii  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACA-CTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_93260905_9    830 GTAATGGTAATTAAAATATTATGGTACAGTCCTAAGTACAGACACATAAA 879
                          iv ii     i  i i v i      v v v    v i     i   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_93260905_9    880 TCAATGGAATAAAACTGGGA-TCCAAGAACAAACTTTTACATGTATGGTT 928
                                    i  i  i  -    ii  i    iiv     v      i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_93260905_9    929 AATTTATTTTTGACAAGATTGTCAAACACAAGTCAATGAGGAAAGAATTA 978
                             v     i      iv  i   i-  v v      i         - 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAAT-A 394

  chr1_93260905_9    979 GTTTTTTTTAACAAATGGTACTAGAA-AACTGG-TATCCACATGCAAAAC 1026
                           i    i-          i  i i -      -  ?            v
  L1M4_orf2#LINE/    395 GTCTTTTC-AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_93260905_9   1027 ACTGAAGTTGGACCCCTACCTCACACCATATATAAAAAATTGACTCAAAA 1076
                          v                              i     -  i        
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAA 492

  chr1_93260905_9   1077 TAGATGACGGACCTAAATGTAAAAGCTAAAACTATAAAGCTCTT------ 1120
                          i   v ?i             i               i     ------
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_93260905_9   1121 -----------------------------------------------TAG 1123
                         -----------------------------------------------   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_93260905_9   1124 ATACGGCATCAAAAGCATAAGCAA----AAAAAAAAGGAATAAATTGAAC 1169
                            i i  i        i      ---- i      vii        i  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_93260905_9   1170 TTTATCAAAATTAAGAATATTTGTGCTTAAAAGGACACCATCAGGAAAGT 1219
                           i           i  iv         v         i    i      
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_93260905_9   1220 GAAAAGATAATGCACAGGATGGGGGAAGAAAAGTCTGCAAATCATAT--C 1267
                                i  iv     i     i   i v -- i            -- 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATA--TTTGCAAATCATATATC 740

  chr1_93260905_9   1268 TGATAACAGGCTTGTATCCA----------AGAA---------------- 1291
                               vi i          ----------    ----------------
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_93260905_9   1292 -TAAAAAGACAG-T--CCCATTTTTTAAATGAGCAAAAGACTTAAATAGA 1337
                         -          i- --    v  ?vv     i     i  i  i      
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_93260905_9   1338 CAGTTCTCCAAAGAAGGTATACAAATGGCCAACAAGTATGTGGAAAGATC 1387
                           v             i               i   i ii  i      v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_93260905_9   1388 CTCAATATAATTAGCCAT 1405
                              i  v ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.44 (95 / 39)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 5.09 (112 / 22)  


3358 26.32 1.79 0.11  chr1_93467278_93472100     3438  4330 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_93467278_9   3438 TGGAAAGATATTCCATGTTAATGGATTGGAAGAATCAATATT---AAAAT 3484
                                    i       v             v i      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_93467278_9   3485 GTCCATACAACCCAAAGCAATCTACAGACTCAGTGCAGTCCTTATAAAAA 3534
                          v v    vv      vii         i   ii   i   i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_93467278_9   3535 TACCAATGACATTCTTCCCAGAAATAGAAAAAACAATCCTACAATGTATA 3584
                          v   iivi v  i  iv       v  v  ivii      v   vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_93467278_9   3585 TGGAACCACAAAAGACC----------AAAGTTATCCTAAGCAAACAGAA 3624
                              vii   ii    ----------   iiv   i i iv  iv    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_93467278_9   3625 CAAAACTGGAAGAATCACATTACCTGAGCT-AAAATTATACTACAGAGCT 3673
                             ii    i  v     i v  ii vi -    i -       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr1_93467278_9   3674 ATAGTAACCAA-ACGGCATGGTACTTGCATAAAAAGACACACATAGACCA 3722
                          i     i   -  i ii       v      ii v v   i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_93467278_9   3723 ATGGAACAGAATAGAGAATGCAGAAACAAATTCACACCCCTACAGTGAAC 3772
                               i     v    i v      i   ii  i  vii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_93467278_9   3773 TCATTTCTGACAAAGGTCCCAAGAACATACACTGGGGAAAAGACAGTCTC 3822
                          v    ii     i   v      v   v  v        ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_93467278_9   3823 TTCAATAAATGGTACTGGGAAAACTGAATATTAATATGCAGAAGGATGAA 3872
                              i       i      v     i   ?iv i     i   i     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_93467278_9   3873 ACTAGACCCCTGTCTCTCACTGTATACAAAAATCAAATTAAAATGGATTA 3922
                         ii i       ii   v   ii           i  v i         i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_93467278_9   3923 AAGACTTAAATCTAAGACTTCAATCTATGAAACTCCTAAAAGAAAACACT 3972
                         ?    i     v     vi v  v    i      i  i         iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_93467278_9   3973 GGGGAAACTCCTCAGGACATGAGACTGGGCAAAGATTTCTTGAATAATAT 4022
                           ? v  v  i  iv   v vi ii i     v i      ii   vv i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_93467278_9   4023 CCCACAAGCACAGGCAACTGAAGCAAAAATAGACAAATGGGATCACATCA 4072
                         v   v       i     vi   v         i    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_93467278_9   4073 AGTTGAAAAGCTTCTGCACAGCAAGAGAAATAATCAACAAAGTGAAGAGC 4122
                          iv v    i   i  ii vv   ii  v iv     v        i  v
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_93467278_9   4123 TAATCCATAGAATGGGAGAAAATATTTTCAAACTATCCATCTGACAAGAG 4172
                         i  i   i                   v    ii  vi      i   i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_93467278_9   4173 ATTAACAACCAGAATATATAAGGAGCTCAAACAACTCAACAGGAAAAAAT 4222
                          i vii v             i  i   vv         i iv     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_93467278_9   4223 CTAATAATCTGATTTTAAAGCAGGCAAAAGATCTACATAGACATTTCTCA 4272
                          v     i ii   ?v   iii      i   i iv             v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_93467278_9   4273 AAAGAATGCATGCAAATGG-AAGCAGGTATATGAAAAAGCATTCAACATC 4321
                               vii  i       -v ii i i i       iiiii        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_93467278_9   4322 ATTGATTAT 4330
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.85 (150 / 81)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.83 (17 / 6)  


3189 26.83 1.22 0.55  chr1_93579787_93586176.rev     4998  5899 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_93579787_9   4998 TGGAAGAACATTCCATGCTCATCAGTAGGAAGAATCAACATTGTGAAAAT 5047
                              ii i  i     i    vii v      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_93579787_9   5048 GGCCACACTGCCCCAGGTAATTTATAGGTTCAATGCCATCCCCATCAAGC 5097
                            v i   v   v iv i  i  i  i     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_93579787_9   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_93579787_9   5146 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5195
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_93579787_9   5196 AACAAAGTTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5245
                                       vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_93579787_9   5246 TACAGTAACCAAAAT-GCATGGTACTGGTACCAAAACAGAGATATAGACC 5294
                                 i   i i- ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_93579787_9   5295 AATGGAGCAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5342
                               ii    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_93579787_9   5343 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5392
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_93579787_9   5393 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5442
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_93579787_9   5443 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5492
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_93579787_9   5493 TTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCT-AGAAGAAAGC 5541
                          i ?    i     i v   v       i      vi  -        i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_93579787_9   5542 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5590
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_93579787_9   5591 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 5640
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_93579787_9   5641 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5690
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_93579787_9   5691 CAGGCAACCTACAGAATAGGAGAAGATTTTTGCAATCTACTCATCTGACA 5740
                         v  i     i       i      i  v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_93579787_9   5741 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAGTTTACAAGAAA 5790
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_93579787_9   5791 AAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5836
                           i    ----   v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_93579787_9   5837 GTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5886
                         v  v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_93579787_9   5887 CATCACTGGCCAT 5899
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


1949 23.94 4.38 4.53  chr1_93593777_93595451      498  1182 (492)    L1M4_orf2#LINE/L1      225   908 (0)  

  chr1_93593777_9    498 CAACTTCAAACTATACTACAAGGCTGTAGTTACCAAAACAGCATGGTACT 547
                            i      viv        i   ii   v i   i    ii       
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_93593777_9    548 GATATTAAAATATAAA-GTAGACCAATGGAAAAGAATAGAGAAGCCAGAA 596
                          ii  v ii   v v -i    i        v     v    iv      
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_93593777_9    597 ATGAAGCCAAATACTTACAGCCAACTGAATTTGGACAAAACATAC-AAAA 645
                           i  v   v i i   ii i   i   v   v     ii-i i -  i 
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGA 373

  chr1_93593777_9    646 --ATACAAATTAAGGAAAGAACACTCTATTCAATAAATGATGCTGGAAAA 693
                         --  v   -- ii        i v   v     i     i      i v 
  L1M4_orf2#LINE/    374 CCATTCAA--TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_93593777_9    694 ACTGGCAAGCCACATGTAGAAGAATGAAACTGGAACCCCATCTCACACCT 743
                              vv ?       i i         ii    v   i i        v
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_93593777_9    744 TATACAAAAATCAATTCAAGATGGATTAAACACTTAAGTCTAAGACCTGA 793
                                    i  i    i      i ? v  i   i v     v  i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_93593777_9    794 AACCATAAAAATTCTATAAGATAACATTGTCTGAGCAAA----------- 832
                            i      v ii  v    v     v --- ? i   -----------
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAG---GNGTAAATCTTCGTGACC 568

  chr1_93593777_9    833 --GAATTA----ATGA---CTAAGTC----CCCCCAAAGCAAATGCAATA 869
                         -- ii   ----   i---  v  vi---- v  v      v v    i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_93593777_9    870 ACCACCAAAAAGTAAATAAATGAGACCTAATTAAACAAAAAAGCTCCTGC 919
                          -- vv     i  i      vi   i v  i   vvv    i  ii  i
  L1M4_orf2#LINE/    619 A--AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_93593777_9    920 ACAGCAAAAGAAATAATCAGCAGAGTAAACAGTCACCCCATAGAGTGGGA 969
                         i vv    i  v iv    iv i   i  v  v  v    i   i     
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_93593777_9    970 GAAAATTTTTGCAAACTATACATCTGACAAAAGACCAGTATCCAGAATCT 1019
                               v        ii   i      i  ii   iv           v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_93593777_9   1020 ATAAGGAACTCAAACAAATTAGTAATTAAAAAATAAATAATCCCATCAAA 1069
                             i      vv    v i i    v    i i      i  v  i?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_93593777_9   1070 AAGTTGGCAAAGTACATGAATAAAAGTGGCCAAAAGTGGGCGAAGAACAT 1119
                           i v       v iv      i -----------------------   
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGA-----------------------CAT 843

  chr1_93593777_9   1120 TTCCCAAAAGAAAATATACAAACAGCCAACAA--ACATGAAAAAGTGTTC 1167
                            i v      i         ii     i  --         ii  i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_93593777_9   1168 AATATCATTAGTTAT 1182
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (99 / 61)
Gap_init rate = 0.02 (13 / 684), avg. gap size = 4.69 (61 / 13)  


1702 20.67 4.37 13.25  chr1_93605515_93611419     3721  4407 (1498)    L1M4_orf2#LINE/L1        3   628 (280)  

  chr1_93605515_9   3721 GAGAGATATGGCAGGTTCATGAATCAGAAGACTCAATATTGGTCAGATAT 3770
                           i      vv  v       i  ii       i       v v    iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_93605515_9   3771 TAGTTCTCCCC--------CTGGAGATTCAAAGCAATCCCAAT-AAAAGG 3811
                         i i v      --------  iv        v        v  -    vv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_93605515_9   3812 CCAGC-GCAATTTTTTAATAGAAATTGACAAGCTGATTCTACAATGTGTT 3860
                              -  --i     vii                  i   v   vii v
  L1M4_orf2#LINE/    103 CCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_93605515_9   3861 TGAAAATGAAAAGAATCTAAAACAGCCAAAACAACTTTAAAAAATAA--- 3907
                           i     v  i i i i i  i           ii  i     v  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_93605515_9   3908 TAAAGCTAT-TTATTTACACTATTTGATTTTAAGAC---CTATAAAGCTA 3953
                         i    i iv-vv i i     viiii    i  i  ---   i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_93605515_9   3954 CAGTAATCAAGACGGTATGGTATTGGTGTA--GATAGAAA-ATAGAACAG 4000
                                      i  i     i   ii  --      v -     v  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_93605515_9   4001 AGCAGATACTCTGGAATTAGAGGTAAGGCTACAGTAATCAATGTGATATG 4050
                         -----------      -   iv i  iv v   v   ------------
  L1M4_orf2#LINE/    301 -----------TGGAAT-AGAATTGAGAGTCCAGAAAT------------ 326

  chr1_93605515_9   4051 GTAGTGTAAAGACAGACAATAGAATAGAATAGAGAGTTTGGAATTAGAAA 4100
                         -------   vv  v   ------------------   ivii i ----
  L1M4_orf2#LINE/    327 -------AAACCCATACA------------------TTTATGGTCA---- 347

  chr1_93605515_9   4101 TATAATTGATTTTTCACAAAGG-GTCAATGCAATTCAATAGTGAAAGGAT 4149
                         ----         iv    i  - i   vi v       i v     i  
  L1M4_orf2#LINE/    348 ----ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_93605515_9   4150 AATTTTTTTAAACAAATGACACTGAAGCAATTGAATTGCTATATGTGACA 4199
                          i i    i  -      iii   iii   i  i  v? i i   ii v 
  L1M4_orf2#LINE/    394 AGTCTTTTCAA-CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_93605515_9   4200 AAATGAATCTCATGCTATACACAGATTATATACACTTACCTCACACTATA 4249
                         i      ------ i iv  ------------ - i          i   
  L1M4_orf2#LINE/    443 GAATGAA------GTTGGAC------------C-CCTACCTCACACCATA 473

  chr1_93605515_9   4250 TGCATACTGTCCACAAAAAATTAACTCAAAATGGCTCTTAGACTTAATTG 4299
                          i  ------------                  v  v?    i   v  
  L1M4_orf2#LINE/    474 TACA------------AAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_93605515_9   4300 TAAGGGTTAATACTATAAAATTTCTAGAAGAAA-CA-AGGAGAAAATATT 4347
                             i i   v         i ii         -  -   ? v    v  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_93605515_9   4348 CATGACCTTGGATTTGGCAAAGATTTCTTAAACAGGATACAAAAAGCATA 4397
                          i         i  v     v i       i i v  i  v       i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_93605515_9   4398 A-------AAGAAAAAA 4407
                          -------         
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAA 628

Transitions / transversions = 1.84 (90 / 49)
Gap_init rate = 0.04 (23 / 626), avg. gap size = 5.26 (121 / 23)  

 429 21.94 21.29 1.29  chr1_93605515_93611419     4988  5142 (763)    L1M4_orf2#LINE/L1      636   821 (87)  

  chr1_93605515_9   4988 ATTGAACTTTACAAAAATTAAAATCTTTTGCTCTTCTGAAGACATTGTCA 5037
                             i    i iv          v      iv    vi i    i i   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_93605515_9   5038 ---------------------TAGACTGGGAAAAAACATT---------- 5056
                         ---------------------i   v     i    i   ----------
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_93605515_9   5057 --ATCCAATAAAAGAACTGTTATCTAAAATATATAAAGAATTCACACAGT 5104
                         --   ii    ii  vi   -   i i             i  vi   ii
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_93605515_9   5105 TCAATAATAAAAAGACAAACAATTCCATTTTCAAAATG 5142
                                            i  i-   v  ?v      
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAAC-CCAATTWAAAAATG 821

Transitions / transversions = 2.67 (24 / 9)
Gap_init rate = 0.02 (4 / 186), avg. gap size = 8.75 (35 / 4)  

 435 18.37 1.02 0.00  chr1_93605515_93611419     5315  5412 (493)    L1M4_orf2#LINE/L1      810   908 (0)  

  chr1_93605515_9   5315 AATAAAAAACTGGGCAAAAGATTTAAATAGATACTTC-ATAAAAAATATA 5363
                            v?    v        i     i      i i   -vi   i  v   
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_93605515_9   5364 TGTGGATGGCAAATAAGTACATGACAAGATGCTCAACATCATTATTTGT 5412
                          iiii     v      i      v                ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.01 (1 / 99), avg. gap size = 1.00 (1 / 1)  


3132 27.65 0.88 0.44  chr1_93686679_93693254     5180  6083 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_93686679_9   5180 TGGAAGAACATTCCATGCTCGTGGGTAGGAAGAATCAATATCGTGAAAAT 5229
                              ii i  i     i  i   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_93686679_9   5230 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5279
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_93686679_9   5280 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5327
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_93686679_9   5328 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5377
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_93686679_9   5378 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5427
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_93686679_9   5428 TACAGTAACCAAAACAGCATGGTACTGGTACCAACACAGAGATGTAGATC 5477
                                 i   i    ii         i iv iv i   v  i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_93686679_9   5478 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATGTCTACAGCT 5525
                                i    i--    i  --        vv  ii ii i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_93686679_9   5526 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCATTGGGGAAAGGATTCC 5575
                          vi    i  i     ivv  vv  i v  vv  v         i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_93686679_9   5576 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5625
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_93686679_9   5626 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5675
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_93686679_9   5676 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5725
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_93686679_9   5726 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5775
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_93686679_9   5776 AACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCGAA 5825
                         i            vvi          vv i   v  i    v   iivv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_93686679_9   5826 TTAAAATAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5875
                          i     v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_93686679_9   5876 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAG 5925
                           i     i   i             v  i    vii ivi      i i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_93686679_9   5926 AGGGCTAATATGCAGAATCTACAACGAACTCAAACAAATTTACAAGAAAA 5975
                         i  i  vi   v      v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_93686679_9   5976 AAACAA----CCCCATCAAAAAGTGGGTGAAGGACATTAACAGACACTGC 6021
                          i    ----   v  i?    i    ii     iv v  i     i v 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_93686679_9   6022 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCGCC 6071
                           v        i  vi viii     v  i          i      iv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_93686679_9   6072 ATCACTGGCCAT 6083
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2686 25.74 4.44 1.03  chr1_93735165_93737371.rev      846  1723 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_93735165_9    846 TGGAAAATCAATCAGTGTTCATGGGTTGGAAGAATCAATATCATTAAAAT 895
                               ivi vi vi         i        v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_93735165_9    896 GTCTATATTGCCCAAAGCAATATATAGATTCAACACTATTCCTATGAAAT 945
                          v v   i v      vii  v  i         i v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_93735165_9    946 TACCAA-TGTCACTTTTCACA-AAATTAGAAAAAACT-ATTCTAAAATTC 992
                          v   i-  i -i    ii  -     i-- v  i  -  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_93735165_9    993 ATATGGAACGAAAAAAGAGTTGGAATAGCTAAGGCAATCCTAAGCAAAAA 1042
                                 vviv  ii  viii       i  ii     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_93735165_9   1043 GAATAAAGTGGAAGGTATCACATTACCTGACTTCAAACTATACTACAAGG 1092
                            i     v i   vv     i v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_93735165_9   1093 CTACAGTAACCAAACCAGCATGGTACTGGTACAAAAATAGACACAATAGA 1142
                                  i   iv   ii         i i  ii       i -    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGA 296

  chr1_93735165_9   1143 CCAATGGAACAGAGTAGGGACCCCTGAAATAAAGCTGCTGCACACCTA-- 1190
                         i        i   i v i  vi  v        - -- iii   ii  --
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAA-C--CCATACATTTATG 343

  chr1_93735165_9   1191 --CAACTTATCTTCAACAAAGTCAACAAAATAAAT-AATAGGGAAAGGAT 1237
                         --   i v  i   i    i viiv   i iv v -   i       i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_93735165_9   1238 ACCCTATTCAATAAATGGTGCTGGGAAAACT----AACCATATGCAGAAG 1283
                          vi  v     i              v    ---- ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_93735165_9   1284 AATGAAGCTGGACCCCTACTTATCACAATATACAAAAATTAA-----GAT 1328
                                i           i vv   v               -----i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_93735165_9   1329 GAACTAAAGACTTAACTGAAAGACCTCAAACTATAAAAAGCCTAGAAGAA 1378
                          i ii ?    i   v  v    v  v           vv i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_93735165_9   1379 AACCTAGAAAATACTCTTCTAGATATTGGCCTAAGCAAAGAATTTATGAC 1428
                            v   i?ivv v     vv  iv    vi  i    v iv  iv iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_93735165_9   1429 TAAGTCCTCTAAAGCAAATGCAACAAGAACAAAAGTTGACAACTAAGACC 1478
                           v v vi v      v v       i iv    i v  i  v vi   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_93735165_9   1479 -CAACTAAACCAAAGAGTTTC-TGCATAGCAAAAGAAACTATCAACAGAT 1526
                         -  v v   ii   i v   i-   v --    i  v        v i v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAG 691

  chr1_93735165_9   1527 TAAACGGACAATCTACAGAATGGGAGCAAATATTTGCACACTACACATCT 1576
                          i  vi     i i            v           v ii i i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_93735165_9   1577 GACCAAGGACTAATATCCAGAATCTATAAGGAACTT----AAATCAGCAA 1622
                           iv i     vi          v     i     i----  v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_93735165_9   1623 ------GA-AAATAACTACATTAAAAAGTGGGCAACGGACAAGAACAGAC 1665
                         ------  -       ivv   ?    i       v   ivv   i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_93735165_9   1666 ACTTCTC---AGAAGACATACTAGCAGCCAACAA--ACATGAAAAAAT-- 1708
                          i     ---      i    v iii     i  --         i  --
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_93735165_9   1709 T--ATATCATTAGTCAT 1723
                          -- i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (134 / 88)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.18 (48 / 22)  


 430 27.05 14.49 4.83  chr1_93859409_93861329      500   706 (1215)    L1M4_orf2#LINE/L1      210   436 (472)  

  chr1_93859409_9    500 AAGACTTAACACTATCTTATATCAAGATCCATTATAAAGTCATAG----- 544
                          i    i -    vi iv  v    i iii i  i    ii i  -----
  L1M4_orf2#LINE/    210 AGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_93859409_9    545 -AAATAGT-----------AGAAGGATAGACAAACTGACCAATGGAATAA 582
                         - i i   ----------- v           v iv  i          i
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_93859409_9    583 A-------GTCCAAAAACAGATTTACA-ATATGTGGTCACTTGATTTATG 624
                          -------     i   i i iii i -  v i      v       vi 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_93859409_9    625 TCA--GGTGCTG---CTGTGCTGTATTGGGGGTCAGATTAGCTCTCTCTT 669
                         v  --     ii--- ii v --- v     i-v   v   -----    
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTC---AATGGGGA-AAGAATAG-----TCTT 399

  chr1_93859409_9    670 TCCAGTAAATGATGCTGGATCAACTGAATCCCCCCAT 706
                          i  ii     i      iv      i  v?  v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

Transitions / transversions = 2.24 (38 / 17)
Gap_init rate = 0.04 (10 / 227), avg. gap size = 4.00 (40 / 10)  

 750 25.72 6.73 5.05  chr1_93859409_93861329     1020  1435 (486)    L1M4_orf2#LINE/L1      486   908 (0)  

  chr1_93859409_9   1020 CTCCAGATGGATT------TTAAAGGTAAAAAGTAAACCAATAACACGAT 1063
                            v i      i------i    v    i iv    v v    v  vv 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_93859409_9   1064 CCAAAGAAAATGTCCAAAAAAATCTTCATTACCTTGGGGTAGACAAAGAC 1113
                         ivi       ii vvi?iv        i v        v   i   ---i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA---T 582

  chr1_93859409_9   1114 GATGTCTTAAA-----CACATGTAGTAC---TAATATAAAGAAAAAA-AA 1154
                          i v     i -----   vviv  i  ---i  i -          - i
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACA-AAAGAAAAAATAG 631

  chr1_93859409_9   1155 CTCATCATTGGACAAGATTAAAATTAAGAGCTTCTGTTCATGAAAAGACA 1204
                         v v --       vvv  i        i i   i   v v v   i    
  L1M4_orf2#LINE/    632 ATAA--ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_93859409_9   1205 C---CACGA--GTGAAAAGGCAAACCGCAGAGTGAGAAAACATAATTGCA 1249
                          ---  v  --        i   v  i    i  i  i  v   v     
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_93859409_9   1250 ACACATACATCCAAAAAAGG-TTTGTTTACAGA-TATATAAAGAACACCT 1297
                          vv    i   ii v  i  -i    v v    -            v i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_93859409_9   1298 ACGGATCAGCCAGAATAAGGCAGAAAATCCAATT-AAAAACAGGCAGAAT 1346
                           iiv   iiv v  v   i  i v  i      -     ii    i iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_93859409_9   1347 ATTTCAACTG----TCCTCAAGAGAGGACAAACAGGCATTTCTCAAAAAA 1392
                             v  iv ---- i   v i   i  i v   ------------  vi
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACA------------AATG 867

  chr1_93859409_9   1393 GCCAATAAACATATGGAAAATAT-CTCAATTTATTAACCATCCC 1435
                                 i  i   -    v  -     i--  i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATG-AAAAGATGCTCAAC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (58 / 48)
Gap_init rate = 0.04 (17 / 423), avg. gap size = 2.88 (49 / 17)  


3339 26.54 0.44 0.44  chr1_93968480_93974758.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_93968480_9   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_93968480_9   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_93968480_9   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_93968480_9   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_93968480_9   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_93968480_9   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_93968480_9   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATCCCACATATCTACAACT 5226
                                i    i--    i  --        v    i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_93968480_9   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_93968480_9   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_93968480_9   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_93968480_9   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_93968480_9   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_93968480_9   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_93968480_9   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_93968480_9   5577 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_93968480_9   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_93968480_9   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_93968480_9   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5776
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_93968480_9   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3131 26.66 1.33 0.88  chr1_94032810_94039197     4992  5895 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_94032810_9   4992 TGGAAGAACACTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 5041
                              ii i ii     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_94032810_9   5042 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5091
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_94032810_9   5092 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAACT-ACTTTAAAGTT 5139
                          v   iivi i  i  ii     -   ---- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr1_94032810_9   5140 CATGTGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAA 5189
                            i     viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_94032810_9   5190 AGAACAAAGCTGGAGACATCACGCAACCTGACTTCAAACTATTCTACAAG 5239
                                  i     ivv    i vv  ii i      viv v      i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_94032810_9   5240 CCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5289
                         v         i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_94032810_9   5290 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 5337
                         i        i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_94032810_9   5338 CTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5387
                         ii vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_94032810_9   5388 CCCTATTTAA----TGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5433
                         vi  v  i  ----           v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_94032810_9   5434 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5483
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_94032810_9   5484 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTGGAAGAAA 5533
                            i ?    i       v   v       i      vi i i       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_94032810_9   5534 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5582
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_94032810_9   5583 TAAAACACCAAAAGCAAGGGCAACAAAAGCCAAAATTGATAAATGGGATC 5632
                           vi            vii          vv     v       v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_94032810_9   5633 TAATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5682
                          v  v   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_94032810_9   5683 CA--GGCAACCCACAGAATGGGAGAAAATTTTTTCAA-TCTTCTCATTTG 5729
                         v -- i                       v   v   -  v v -  i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTG 742

  chr1_94032810_9   5730 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTATTAG 5779
                          i  i  i  vi          v  i  v      vv    v iv  v v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_94032810_9   5780 AAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGGTATGAACAGACA 5829
                              i     i     v  i?    i    ii    i v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_94032810_9   5830 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCT 5879
                         i     v        i  vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_94032810_9   5880 CATCATCACTGGCCAT 5895
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


3265 26.80 0.78 0.22  chr1_94105726_94110707     3587  4489 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_94105726_9   3587 TGGAAACACATCCCATGCTTGTAAATGAATAGACTCAATATTGTAAAAAT 3636
                               v i        i ii ii  viiv     i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_94105726_9   3637 GACCATACTCCCAAAAGCAATCTACAAATTCAATGTAATCCCCATCAAAA 3686
                          i v        v   vii       i      i i      i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_94105726_9   3687 TACCACCATCATTCTTCACAGAATTAGAAAAAC-AATTCTAAAATTCATA 3735
                          v   v vv v  i  ii     v v  v  i -i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_94105726_9   3736 TGGAACCAAAAAAGAGCTTGCATAACCAAAGCAAGATTAAGCAAAAAGAA 3785
                              viiv  ii  v iv v   i     i   vv  i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_94105726_9   3786 CAAATCTGGAGGCATCATACTACCTGATTTCAAACTATACTATAAGGCCA 3835
                             vi      vv   i   v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_94105726_9   3836 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCAA 3885
                         i   v i   i    ii         i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_94105726_9   3886 TGGAACAGAATAGAGAATCTGGAAATACACCCAAATACTTACAGCCAACT 3935
                              i     v    i  ii      v     v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_94105726_9   3936 AATCTTTGACAAAGCAAACAAAAACATAAGGTGGGGAAAGGACTCTCTTT 3985
                         i  i  i     i vviv   i v   vvii         i ivv     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_94105726_9   3986 TCAACAAATAGTGCTGGGATAATTGGCTAGTCACATGTAGGAGAATGAAA 4035
                                  i         i  i   v  ?i      i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_94105726_9   4036 CTGGATCCTCATCCCTCACCTTATACAAAAATCAACTCAAGATGGATTAA 4085
                         i    i  ii i i v    v           i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_94105726_9   4086 GGACTTAAATCTAAGACCTGAAACTGTAAAAAATATAGAGGATAACCTTG 4135
                         i   i     v     v  i     i     vviv    i  v   v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_94105726_9   4136 GAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAAC 4185
                          ?iv  vi    vv   v    v        v i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_94105726_9   4186 CCAAAAGCAAATGCAATAAAAAGAAATATAAATAGCTGGGACTTAATTAA 4235
                                  v v    i    ii   v   i   iv v      v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_94105726_9   4236 ACTGAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAATAAACAGAC 4285
                          v v  i i      iiivv    i iv  vi   iv i i i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_94105726_9   4286 AACCCACGGAATGGGAGAAAA-ATCTTCACTGTCTACGCATCTGACAAAG 4334
                                i             -  i v  v-i  - iii      i  i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAA-ATC-ATATATCTGATAAGG 748

  chr1_94105726_9   4335 GACTAATATCCAGAATCTACAACAAAGTCAAACAAATTGGCAAGAAAAA- 4383
                             vi          v  i  vi  v  vv    v iiii  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_94105726_9   4384 ---AATATCCCA-TCAAAAAGTGGGCTAAGGACACGAATAGGCAATCTTC 4429
                         ---    v    - i?    i     v     ivi      i  v ii  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_94105726_9   4430 AAAAGAAGATATGCAAATGGCCAACAAACATATGAAAAGATGCTCAACAT 4479
                         v           i           i  i  i                   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_94105726_9   4480 CACCAGTGAT 4489
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3041 27.71 0.66 1.20  chr1_94311197_94317589     4988  5900 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_94311197_9   4988 TGGAAGAACATTCCACGCTCATGGGCAGGAAGAATCAATATCATGAAAAC 5037
                              ii i  i   i i      iiv      v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_94311197_9   5038 GGCCATACTGCCCGAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5087
                            v     v   i iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_94311197_9   5088 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5135
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_94311197_9   5136 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5185
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_94311197_9   5186 AACAAAGCTGGAGGCATCATGCCAGCTGACTTCAAACTATACTACAAGGC 5235
                                i      vv   ii ivv ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_94311197_9   5236 TACAGTAACCAAAACAGCATGATACTGTTTTGGTACCAAAGCAGAGATAT 5285
                                 i   i    ii  i     ----- i iv iiii   v    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTG-----GCATAAGGATAGACATAT 293

  chr1_94311197_9   5286 AGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTA 5333
                            i        i    i--    i  --        vv   i    i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chr1_94311197_9   5334 CAACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGG 5383
                         iiiii vi    i  i     ivv  v   i v  vvv           i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_94311197_9   5384 ATTCCCTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGA 5433
                           vvi  v  i                 v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_94311197_9   5434 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAGG 5483
                          iiv    ii    i    v   i     v                  ii
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_94311197_9   5484 ATGGATTAAAGACTTAAATGTAGTACCTAAAACCATAAAAACCCTAGAAG 5533
                               i ?    i        iv v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_94311197_9   5534 GAAACCTAGGCA-ATATCATTCA-GGCCATAGGCATGGGCAAGGACTTCA 5581
                         i    v    ?i- v   -   i- i  v i  i- i     v ii   v
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCT 589

  chr1_94311197_9   5582 TGTCTAAAACACCAAAAGCAATGACAACAAAAGCCAAAATAGACAAAGAG 5631
                          ivv  vi            vvii         vv        i   vv 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_94311197_9   5632 GATCTAATTAAACTAAAGAGTTTCTGCACAGCCAAAGAAACTACCATCAG 5681
                           ii v  i   v v  i ii  i  ii vv v  i  v    i  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_94311197_9   5682 AGCGAACATGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCTT 5731
                           i   v vi     i                 v       vii iviv 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_94311197_9   5732 CTGACAAAGGGCTAATATACAGAATCTACAATGAATTCAAACAAATTTAC 5781
                             i  i  i  vi   v      v  i  v   i  vv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_94311197_9   5782 AAGAAAAAAACAAACAACCCCATCAAAAAGTAGGCGAAGGGTGTGAACAG 5831
                           v     i     i     v  i?    i i   i    i v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_94311197_9   5832 ACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAGAT 5881
                            i     v        i  vi viii     v ii             
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_94311197_9   5882 GCTCATCATCACTGGTCAT 5900
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (155 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


3298 25.58 1.56 0.56  chr1_94465325_94471690.rev     4977  5875 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_94465325_9   4977 TGGAAGAACATTCCATACTCATGGATAGGAAGAATCAGTATTGTGAAAAT 5026
                              ii i  i    ii        v      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_94465325_9   5027 GGCCATACTGCC-AAGTTAATTTATAGATTCAATACTATCCCCATCAACC 5075
                            v     v  -  i  i  i  i        ii v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_94465325_9   5076 TGCCA-CTGTCTTTCTTCACATAATTGGAAAAACTA--CTTAAAATTTCA 5122
                          v   -   i    i  -i  v  v v  v  i  i-- i       -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATT-CA 148

  chr1_94465325_9   5123 TATGGAAACAAAAAAGAGCCCACATAGCCAAGTCAATCCTAAGCAAAAAG 5172
                                 iiv  ii  v  viv        iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_94465325_9   5173 AAAAAAGCTGGAGGCATCACGCTACCTGACTTCA-------CTACAAGGC 5215
                           v    i      vv    i  v  ii i    -------      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_94465325_9   5216 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5265
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_94465325_9   5266 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACT 5313
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_94465325_9   5314 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5363
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_94465325_9   5364 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5413
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_94465325_9   5414 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 5463
                            ii    i    v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_94465325_9   5464 TTAAAGACTTAAATGTAGTACCTAAAACCATAAAAACCCTAGAAGGAAAC 5513
                          i ?    i        iv v       i      vi i      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_94465325_9   5514 CTGGGCA-ATATCATTCAGGACATAAGCATGGGCAAAGACTTCATGACTA 5562
                         v i  ?i- v   -   iv   v vi vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_94465325_9   5563 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5612
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_94465325_9   5613 ATTAAACTAAAGAGCTTCTGCACTGCAAAAGAAACTATCATCAGAGTGGA 5662
                           i   v v  i i   i  ii  v    i  v       vv i    i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_94465325_9   5663 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5712
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_94465325_9   5713 AAGGGCTAATATCCAGAATCTACAAAGAACTTAGACAAATTTACAAGAAA 5762
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_94465325_9   5763 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATACGAACAGACACTT 5812
                           i     i     v  i?    i            vi   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_94465325_9   5813 CTCAAAAAAACACATTTATGCAGCCAACATACATATGAAAAAATGCTCAT 5862
                            v   i  v i  vi viii     i vi  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_94465325_9   5863 CATCACTGGTCAT 5875
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (137 / 89)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


3240 26.65 0.66 0.66  chr1_94540105_94548485.rev     4990  5897 (2484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_94540105_9   4990 TGGAAGAACATTCCATGCTCATGGTTAGGAAGAATCAATATCATGAAAAT 5039
                              ii i  i     i      v v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_94540105_9   5040 GGCCACACAGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5089
                            v i  vv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_94540105_9   5090 GATCAATGACTTTCTTCACAGAATTGGAAATAACT-ACCTTAAAGTTCAT 5138
                         vvi  iivi i  i  ii     v v  v - i  - i i    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr1_94540105_9   5139 ATGGAACCAAAAAAGAACCCACATTGCCAAGACAATCCTAAGCAAAAAGA 5188
                               viiv  ii  v  viv  v     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_94540105_9   5189 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5238
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_94540105_9   5239 ACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5288
                                    i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_94540105_9   5289 ATGGAACAGAAC--AGAGCCCTCAGAAATAATATCACACATCTACAACCA 5336
                               i    i--    i  --        vvi  i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_94540105_9   5337 TCTGATCTTTGACAAACTTGACAAAAACAAGAAATGGGGAAAGGATTCTC 5386
                         vi    i  i     ivv  v   i v  vvv           i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_94540105_9   5387 TATTTAATAAAAGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCTG 5436
                          v  i  i   v          v  i   v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_94540105_9   5437 AATGTGGATCCCCTCCTTACACTTTATACAAAAATTAATTCAAGGTGGGT 5486
                           vv    i   iv   i    iv              i    ii   i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_94540105_9   5487 TAAAGACTTAAATGTAATACCTAAACCCATAAAAACCTTAGAAGAAAACC 5536
                         i ?    i         v v     v i      vi             v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_94540105_9   5537 TAGACA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5585
                            i?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_94540105_9   5586 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 5635
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_94540105_9   5636 TTAAACTAAAGAGCTTCTGCACAGCAAAAGACATGACCATCAGAGTGAAC 5685
                          i   v v  i i   i  ii vv    i    iv i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_94540105_9   5686 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 5735
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_94540105_9   5736 AGGGCTAATGTCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5785
                         i  i  vi i        v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_94540105_9   5786 AAACAAACAACCCCATCAAAAAGTGGGTAAAGGATATGAACAGACACTTC 5835
                          i     i     v  i?    i    i       v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_94540105_9   5836 TCAAAAGAAGACATTTATGAA--GCCAACAGACACATGAAAAAATGCTCA 5883
                           v        i  -- ii  --     i ii          i       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_94540105_9   5884 TCATCACTGGTCAT 5897
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  

 583 27.88 5.29 1.92  chr1_94540105_94548485.rev     6655  6862 (1519)    L1M4_orf2#LINE/L1        1   215 (693)  

  chr1_94540105_9   6655 TGGCAAAACATAGTGTGTTCATGGATTGGAAGACAACTTAATA-----AA 6699
                            v  i i  vvii                   ---      -----  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC---TTAATATTGTTAA 47

  chr1_94540105_9   6700 GATATTGATTTTCCCTAAATTAATATACAAGTGTAATGTAATTCCTATCA 6749
                            ivii  vi    i     i  v    ii vi  i i   i       
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_94540105_9   6750 CGGTA--AGATGTTTTTGTTGATAGA----GACAAGATTATCCTAAGATA 6793
                         vii v--  v  ii   v   -i   ----      v v       i  v
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_94540105_9   6794 TATATGGAAAGGTAAAGAAAGTAACATAGCTAAAATTACTTTGAAAAAGA 6843
                         i         v i  i i vvi iv     i    iv ii          
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_94540105_9   6844 AAAATAAATTGAAAGGGCT 6862
                          i  i   v vii   i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACT 215

Transitions / transversions = 1.76 (37 / 21)
Gap_init rate = 0.02 (5 / 215), avg. gap size = 3.00 (15 / 5)  

1961 23.47 3.73 6.27  chr1_94540105_94548485.rev     7141  7890 (491)    L1M4_orf2#LINE/L1      178   908 (0)  

  chr1_94540105_9   7141 AAAACTAACTAAATAAATAAATAAATAAAGTGAAAAGATTCAGTTTACCT 7190
                              v v  vi v   v  i--  i     vii i  i   vvi v  i
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAG--AACAAAGTTGGAGGACTCACACTTCCC 225

  chr1_94540105_9   7191 GATTTCAAGACTTAATATACAGCTACAGTAATCAAAACTGTATTGTTTTG 7240
                         i       i     v  i v               i  v  i v  vi  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_94540105_9   7241 GTAGAGAGACAGACACATAGATTAAGGAAACAGGATAGAGAACTCAGAAA 7290
                          i v ii  i     i      i  v i  i  i  v    iii      
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_94540105_9   7291 TACACCCACAAAATAA-GCCCAACTGGTTTTTGACAAATGTACAAAAGCA 7339
                           v     i v v v - vi   i  i    i     iv  i v  ii v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_94540105_9   7340 ATTCAATGGAGGAAAGATAGCCTTT-CAATAAATGGGGCTGGAGCAATTG 7388
                                  i i  ii    i    -   i      v     ii   i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_94540105_9   7389 GACAGACATACATAGGCAAGAAAAACACACACACACACACACACACACAC 7438
                           i ?v  --   --    i i  vv -----------------------
  L1M4_orf2#LINE/    426 GATAKCCA--CAT--GCAAAAGAATGA----------------------- 448

  chr1_94540105_9   7439 ACACACACACACACACCTTGTCCTATATACCACATTGTATACAAAAATTA 7488
                         -------------- vi v v  iv  ivi    iii             
  L1M4_orf2#LINE/    449 --------------AGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_94540105_9   7489 ACTCAAAATGGATCATTAACTTACCATGTA-----TAAAATTATACAACT 7533
                                        ?vi  i  v-     -----     i    v    
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAA-ATGTAAGAGCTAAAACTATAAAACT 533

  chr1_94540105_9   7534 TATAGAAAAAAA-GTAAGAGGAAAATTGTG-GAGTTTAGAGCCAGGCAAA 7581
                         iv     i    -i  i ? v   vi vi -  vi  i - ii      v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAAT 582

  chr1_94540105_9   7582 GAGTTCTTAGATTTGACACTAAAAACACAATCA-TAAAGGAAAAAACTGA 7630
                          iv         v      i    i     v  -i   i       iv  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_94540105_9   7631 TACATTGGACTTTATCAAAATTATAAACTTTTGATCTGCAAAAAATCAC- 7679
                           v         i          v         vv  v    ii -   -
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-CACT 681

  chr1_94540105_9   7680 ATTAATAA-GAGGAAAGACAAGCTACATAGTG----AAAGTATATGCAAA 7724
                           i  v  - v i        v i   v i  ----   i   v      
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_94540105_9   7725 TCACATATCTGAAAAAGCACTAATATCTAGAATATGTAAAGAA------- 7767
                            i        v  i v   vi    i       i       -------
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_94540105_9   7768 AA---AACAGTGAAAAAA-AAACAATTCAATTAGAAAATGGGAAAAATAC 7813
                           ---  i i i    i -   i  ii     ?i        v   iv i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_94540105_9   7814 ATGAAGAGACATTTCACCAAAGAAGATACACAGATGGA-AATAAAACACA 7862
                         v    v         v            i   i    v-     i-    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACA 880

  chr1_94540105_9   7863 TGAAAATATTTTCAATGTTATTAGCCAT 7890
                               v  vi    ii i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (104 / 68)
Gap_init rate = 0.03 (21 / 731), avg. gap size = 3.57 (75 / 21)  


1355 27.84 5.75 3.18  chr1_94582761_94584412.rev      502  1162 (490)    L1M4_orf2#LINE/L1      231   908 (0)  

  chr1_94582761_9    502 CAAAA--TACTATAAAGACTCTA-TCATTAAAACAGTGTGGTACTAGTAC 548
                              --     i    -  vi - v  i  i             i i i
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAG-CTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_94582761_9    549 ATGAATAGACA----GATCGACAGAATGGAA-----AGTCCAGAAATGGA 589
                          v i       ----    i ii    i   -----           ii 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_94582761_9    590 GACAAGTGCAT--ATAAAAATTTAGTGTATGATAAAGGTAATATCCCTTC 637
                         vv  -- i   --  iivv v  ii v vi  i  i   ivi vvv ivi
  L1M4_orf2#LINE/    330 CCCA--TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_94582761_9    638 TCACTCAGGCAAATATAGTTGTTTTTTTTTTTAATAAATGGTGTTGAGAT 687
                            v vi  v  iv     i-------    i  i        i  i  i
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTC-------TTTTCAACAAATGGTGCTGGGAC 420

  chr1_94582761_9    688 CGCTGGATAACCATTTGAAAAA-----AAGTTAAATTCCTTCCTCAGACC 732
                         vi       ?   iv  v    -----     ii ii   v     v   
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_94582761_9    733 ATACACAGGAATAAACTCCACATGGATCACAGATATAAATGTGGAAAATA 782
                            i   ii   v     v v        ?   iv       iii iv  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_94582761_9    783 AAATTACACAAGTACAACAAGAAAACAT--GGGTAAATACCTCTGTAATC 830
                            i  i v  v viv v          -- ?      --  ii  i i 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTGACC 568

  chr1_94582761_9    831 TAGATATCAGAAAA-GGTTT------TCTGTTACTAAAAATTCAAATGCA 873
                          v i-i i  iv  -     ------ v  vi  i    iiv   --   
  L1M4_orf2#LINE/    569 TTGG-GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GCA 615

  chr1_94582761_9    874 CTAAAAGAAAAAATTGATAAATATAATTT--TTAAAAATTTCTAAACTTT 921
                         vi            v       vvi i  -- i    --  vv       
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA--TTAAAAACTTT 663

  chr1_94582761_9    922 GGCATGCCAAAA---ACCAT-AAGCAAAGTCAAAAGGCAAACAACAAACT 967
                         v iiivi    i---  i  -   -     v     i   v v   i v 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAG-AAAGTGAAAAGACAACCCACAGAAT 712

  chr1_94582761_9    968 AGAAGAAAACATTTGCAGCCTACATTGCAAATAAAAAATCAGTATCCCTA 1017
                         i i      i       ivii i  vv vi    iii iiv      vv 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_94582761_9   1018 ACTGATAAAGAACTTATAAAACTTAAGGA--AAAAGACCAAAAATCCTAC 1065
                          ivv          iv  v    i  vi --       v  v  i  v i
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_94582761_9   1066 AGAAAAATAGGCAAATGACAAGAACAGACAATT-TACAAA-AAGAGATAC 1113
                         v?      i      v  ivv   i     v  - v    -    v    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_94582761_9   1114 AAAAGCTGGTCTTTAAACACGTTGGAAGATGTTCAACATCGCTCCTAAT 1162
                            ---   i vv   i   i vii      i        i????????
  L1M4_orf2#LINE/    863 AAA---TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (104 / 76)
Gap_init rate = 0.04 (24 / 678), avg. gap size = 2.46 (59 / 24)  


3217 27.20 0.44 0.44  chr1_94684819_94690300.rev     4084  4991 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_94684819_9   4084 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4133
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_94684819_9   4134 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4183
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_94684819_9   4184 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4231
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_94684819_9   4232 TATGGAACCAAAAAAGAGCACGCATCGCCAAGTCAATCCTAAGCCAAAAG 4281
                                viiv  ii  v vv v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_94684819_9   4282 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACCATACTACAAGGC 4331
                                i      vv       v  ii i      v v        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_94684819_9   4332 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATC 4381
                                 i   i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_94684819_9   4382 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 4429
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_94684819_9   4430 ATCTAATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGCATTCC 4479
                          vi i  i  i     ivv  vv  i v  vv            v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_94684819_9   4480 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4529
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_94684819_9   4530 AAAACTGGATCCCTTCCTTACATCTTATACAAAAATCAATTCAAGATGGA 4579
                         i  ii    i    v   i   i v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_94684819_9   4580 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAAC 4629
                          i ?    i    i  v   v       i      vi i   i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_94684819_9   4630 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4679
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_94684819_9   4680 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4729
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_94684819_9   4730 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4779
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_94684819_9   4780 AGGCAGCCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4829
                           i  i  i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_94684819_9   4830 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4879
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_94684819_9   4880 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 4929
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_94684819_9   4930 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAACAATGCTCACC 4979
                           v        i  vi viii     v  i         vi       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_94684819_9   4980 ATCACTGGCCAT 4991
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2542 27.85 3.02 1.45  chr1_94751320_94757719.rev     5023  5916 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_94751320_9   5023 TGGAAAAACATTCCATGCCCATGGATAGGAAGAATCAATATCGTGAAAAT 5072
                               i i  i     ii       v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_94751320_9   5073 GACAATACTGCCCAAAGCAATTTATAAATTCAGTGCTATTCCCATTAAAC 5122
                          i       v      vii  i  i i     ii  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_94751320_9   5123 TACCATTTCACATTCCTCACAGAATTAGAAAAAACT-ATTTAAAAATTTA 5171
                          v   vi -i v  ii ii     v v  v  i-  -  iiv      i 
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_94751320_9   5172 TATGGA---GCCAAAAAAGGGCCCA-AATAGCCAAGGCAATCCTAAGCAA 5217
                               ---  ----  i  i    -         ii     i i iv  
  L1M4_orf2#LINE/    149 TATGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_94751320_9   5218 -AAGAACAAAG----------CCTGTTACCTGACTTCAAACTATACTACA 5256
                         -          ---------- viii v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_94751320_9   5257 AGGCTACAGTAACCAAAACAGCA-GATACCAGTATTAAAAACAGACACAT 5305
                          i          i   i    ii- i   ii i  -  ii i     i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATAT 293

  chr1_94751320_9   5306 AGACCAATGGAACAGAACAGAGAACCCAGAAATAAGACTGCACACCTACA 5355
                            i        i    iv    ii          iv iii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_94751320_9   5356 ACCATCCGATCTTTGACAAACCTGAAAAAAACAAGCAATGGAGAAAGGAC 5405
                         ii  vii   i  i     ivv  vv  i v  vv      i     i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_94751320_9   5406 TCCCTATTTAATAAATGGTGCTGGGAGAACTACTTGACTATATGCAGAAA 5455
                         vvi  v  i  i              v    ivv i? i i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_94751320_9   5456 ATTGAAACTGGATACCTCTCTTACACCATATACAAAAATCAACTCAGAAT 5505
                          v    ii    iv   vi  i                 i      i   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_94751320_9   5506 GGACTAAAGACTTAAATACAAAACCCAAAACTATAAAAACCCTAGAAGAA 5555
                            ii ?    i     ii  i v i            vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_94751320_9   5556 AACCTAGGCA-ATACCATTCAGGACATGGGCACTGACAAAGATTTCATGA 5604
                            v    ?i- v i -   iv   v v  vviv i   v i    v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_94751320_9   5605 CAAAGACACCAAAAGCAATTGCAACAAAAGCAATAATTGACAAAT-GGAA 5653
                         vv v             vvv          v  v   v  i    -   v
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_94751320_9   5654 TCTGTTTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCAACAGAA 5703
                          iii iv   i    -     i  ii vv    i  v        v i i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_94751320_9   5704 TAAACAGATAACATACAGAGTGGGAGAAAAATTTTACAATCTGTCTACCT 5753
                          i  v   i   vi     i          vv   i   viii v  i  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_94751320_9   5754 GGCAAAGGTCAAATATTCACCATCTATAAAGAATTTAAACAAATTTATAA 5803
                          ii  i  v vvi   i  vv  v         i ivv    v iv    
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_94751320_9   5804 GACAAAAACAA----CCCCATTAAAAAGTGGGCAAAGGACATGAA----C 5845
                         v v   i    ----   v   ?    i           iv    ---- 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_94751320_9   5846 ACTTTTCAAAAGAAGGCACACATGCAGCCAACAAACATATGAAAAAAAGC 5895
                          i  i  v       ii i   viii     i  i  i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_94751320_9   5896 TCATCACTGATCATTAGAGAA 5916
                            --  --    ????????
  L1M4_orf2#LINE/    892 TCA--AC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (157 / 88)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.22 (40 / 18)  


5083 14.06 1.22 0.66  chr1_94808900_94810982.rev      690  1592 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_94808900_9    690 TGAAAAGACATCTGATGTTTGTGGACCAGATAACTTAATATT---AAGAT 736
                           i     i   iv     ii    iii  vi          ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_94808900_9    737 GGATACACTCCCCAAATTGATATACAAGACT-AACAAAATCCCTGTCAAA 785
                           vv i               v    -  i -   iv       i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA-GATTCAACGCAATCCCTATCAAA 99

  chr1_94808900_9    786 ATCCTAGCTGGATTTGTTTCAGAAATTGACAAGCTGATACTAAAATTCAT 835
                             i     vv   v  v                   v           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_94808900_9    836 ATGGAAATCCAAGGGACCCAGAATGGCCAAAACAGTCTTGAAA-TGAAGA 884
                                 v               i         i        -v     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_94808900_9    885 ACAAAG----AGAACTCACACTTCCCAATTTCAAAACTTACTGCAAAGCT 930
                               ----  i                             i       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_94808900_9    931 ACTGTAATCAAGACACTGTGGTACTGCTATATGGATAGACATATATAGAT 980
                           v            v          vi   v             --   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA--GAT 297

  chr1_94808900_9    981 GAATGAAATCAAATGGAGAATATAGAAATAAACCTTTGCATTTATGGTCA 1030
                         v    i   vi   v    i vi           iv i            
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_94808900_9   1031 ATTAATTTT-GACAAGGGTGCCATGATAATTTACTAGGAGAAAGAATACT 1079
                            i     -             v  iv   i v i  -         v 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGT 396

  chr1_94808900_9   1080 CTTTTTAACAAAATGTTTTGGGATAAGTGTATATCCACATGGAAAAGAAT 1129
                              i      vv  vi     i  v  v   ?       v        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_94808900_9   1130 GAAGTTGGATTCCTACCTTACACCATGTACAAAAATTAACTTGAAAAGGA 1179
                                  ii       i       i              ii   v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_94808900_9   1180 TCAAAGACCTAAATGTAAGAGCTAACACTAAAAAACTCTTAGAAGAAATT 1229
                            ?                     v    v                 vi
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_94808900_9   1230 TTAGATGTAAATCTTTATGACCTTGGATTTGGCAATGGTTTCCTAGAAGT 1279
                         v   i?         ii         i  v            i    vi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_94808900_9   1280 GACACCAAAAGCAAAAGCAACCAAAGACAAAAATAGATAAGCTGGATTTC 1329
                                      v       v     -            ii    i   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTC 645

  chr1_94808900_9   1330 ATCAAAATGGAAAACTCTTGTGCTTCAACAGGCACTGTGAAAAAAGTGAA 1379
                                 vi      i           vi i    i v  i        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_94808900_9   1380 AAAACAAC-TACAGAGTGGGAGAAAATATTTGCAGATCGTATGTCTGATA 1428
                           i     -i     i                  i   i   i       
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_94808900_9   1429 AGGGTCTAGTATCTAGAATATATAAAGAACTCTTACAACTCAACAATAAA 1478
                             v  v     i                             i      
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_94808900_9   1479 AAACACATGTAACACAATTTTAAAATGGGCAGAGGATCTGAATAGACATT 1528
                           i-   vi    v     ?v          i     i            
  L1M4_orf2#LINE/    796 AAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_94808900_9   1529 TCTCCAAAGAAGATACCCAAATGTTCAATAAGTACATGAAATTATGCTCA 1578
                                        iv      vi       i        vv       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_94808900_9   1579 ACACCATTAGCTAT 1592
                            i  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (70 / 53)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


3478 23.26 1.41 2.72  chr1_94872075_94874465      979  1898 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_94872075_9    979 TGAAAAGATACTCTGTGTTCATGGATTGGAAGAATTAATATTGTTAAAAT 1028
                           i       ii ii                  v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_94872075_9   1029 GGCCATACTGCCGAAAGCAATCTGTCAATCTGTGGACCTATTAAAACTAT 1078
                            v     v  v   -------- ii    iii  iii -------- i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--------TTGATCTACAGATTCA--------AC 84

  chr1_94872075_9   1079 GGAATCCCTATGAAAATACCA--TGACATTCTTCACAGAAATAGAAAAAA 1126
                          v         v     v   --  v -  i  ii       v  v  iv
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC 133

  chr1_94872075_9   1127 -AATCCTAAAATTCATATGGAACCACAGAAGATCCCCTAATAGCCAAAGC 1175
                         -i                    vii  iii  -   vv          i 
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAAC 182

  chr1_94872075_9   1176 AATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCACACTACTTGACTTCA 1225
                             i i iv  i          i      vv       v iii i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_94872075_9   1226 AAATATATTACAATGCAGTAGTAACCATAATAGCGTGGTACTGGCACAAA 1275
                            iv  i     v  vii     i  vi i  i            i  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_94872075_9   1276 AACAG-CACATAGAGAAATGGCACAGAAT-AAGAGCTCAGAAATAAATTC 1323
                         i i  -  i     vv     v i     -i    ii          ii 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_94872075_9   1324 ATGCTCCCACAGCCAACTGATTTTCTACCAAGTTGTTAAGAACACACATT 1373
                           i viii ii i   i        v  v i v  ii    v  iv  v 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_94872075_9   1374 AGGGAAAAGACAGTCTTTTCAATAAATGGTG----GAAAATTAGATATCC 1419
                         i      ii i           i        ----  v  i i    ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_94872075_9   1420 ACATGTAGAAGAATGAGACTAGATCCCTATCTTTCGCCATATAAAAAAAT 1469
                              i i        iii i  i     i  iv i       v      
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_94872075_9   1470 CAACTCAAAATGGATTAAAGACTTAAATGTAAAACTTAAGA-TATGAAAC 1518
                         i              i ?    i         i vi   i -   i    
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_94872075_9   1519 TACTAGAAGAAAACATGGGGATACA-CTTCACAACATTGCACTGGGCAAA 1567
                          vi             i  ?i  v -    iii  v   vii i     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_94872075_9   1568 AATTTGTTTAAATAAGACCTTAAAAGCACAAGCAGCAATAGCAAAAATAG 1617
                         ii   -i   i   v   vii             i   v  v        
  L1M4_orf2#LINE/    583 GGTTT-CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_94872075_9   1618 ACAAACAGGATTATATCAAA-CTAAAAATCCTTTTGCACAGCAAAGGAAA 1666
                          i   iv   i vi      -i      --      ii vv       v 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACA 679

  chr1_94872075_9   1667 CTATTAGCAGAATGAAGAGATAACCTACAGAATGTGAAAAAATATTTGCA 1716
                             i iv i i    i   i    i        v  i            
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_94872075_9   1717 AACTATACATCTGACAAGGGGTTAATTTCCAGAATACATAAAGAACTTAA 1766
                           ii   i      i     ii vi v         i          ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_94872075_9   1767 ACAACTCAACAGAAAACAAAAACAAATAACCAGACTTAAAAAAATGGGCA 1816
                                  i iv   --  i          vi i ?     --      
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAA--AAGACAAATAACCCAATTWAAAAA--TGGGCA 825

  chr1_94872075_9   1817 AAATACCCTAATAGACATTTTTCAAAAGAAGAC-TACAAATGGCCAGCAG 1865
                           iv iiiv           i  v        i-            ii i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_94872075_9   1866 GTATATAAAAAAATACTCAACATCACTAATCAT 1898
                          i i  i    i  i          ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.44 (149 / 61)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  


3079 26.95 1.67 0.56  chr1_94937584_94941947     2974  3871 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_94937584_9   2974 TGGAAGAACATTCCATACTCATGGATAGGAAGAATCAATATCGTGAAAAT 3023
                              ii i  i    ii        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_94937584_9   3024 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3073
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_94937584_9   3074 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3121
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_94937584_9   3122 TATGGAACCAAAAAAGAGCCCACATTGTCAAGACAATCCTAAGCAAAAAG 3171
                                viiv  ii  v  viv  v i   i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_94937584_9   3172 AACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTATACCACAAGTC 3221
                                i     ivv    i  v  ii i      viv   i    iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_94937584_9   3222 TACAGTAACCAAAACAGGATGGTACTGTCACCAAAAGAAAGATATAGACC 3271
                                 i   i    vi        v  iv ii v i v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_94937584_9   3272 AATGGAACAGAACAGAGGCCTTAGAAATAACACCACACATTTACAACCAT 3321
                                i    iv   iviii        vv   i       iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_94937584_9   3322 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCTCT 3371
                         i    i  i     ivv  v   i v  vvv           i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_94937584_9   3372 GTTTAATAAATG---CTGGGAAAACTGACTAGCCATATGTAGAGAGCTGA 3418
                         v  i  i     ---      v     iv  ?   i   i i iiiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_94937584_9   3419 AACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGATT 3468
                          ii    i    v   i   i v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_94937584_9   3469 AAAGACTTAAATGTTAGA-CTAAAACCATAAAAACCCTAGAAGAAAACCT 3517
                          ?    i       v   -       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_94937584_9   3518 AAGCA-ATACCATTCAGGACATAGGCATGAACAAGGACTTCATGACTAAA 3566
                          i ?i- v i -   iv   v v  vv iii   v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_94937584_9   3567 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 3616
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_94937584_9   3617 CAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTAAATA 3666
                             v v  i i   i  ii vv    i  v    i ivv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_94937584_9   3667 GGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGATAAA 3716
                          i     i i               v       vii  vi         i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_94937584_9   3717 GGGCTAATATCCAGAATCTACAAAGAACTTAAATAAATTTACAAGAAAAA 3766
                           i  vi          v  i        ivv i  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_94937584_9   3767 ACCAA----CCCCATC-AAAATTGGGCAAAGGATATGAACAGACACTTCT 3811
                         iv   ----   v  i-    v            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_94937584_9   3812 CAAAAGAAGACATGTATATGCAGCCAACAGACACATGAAGAAATGCTCA- 3860
                          v        i  ii v   --     i ii        i i       -
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_94937584_9   3861 --TCAGAGAAATG 3871
                         --   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


1330 23.20 8.51 0.26  chr1_94965062_94968427        1   388 (2978)    L1M4_orf2#LINE/L1      346   765 (143)  

  chr1_94965062_9      1 CAACTGATTTTTTACAAAGGTGCAAAGGCAATAAACTGGAAAAAAGATGA 50
                            i       iv    i     v   i v  vv v   ii   ii  ii
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_94965062_9     51 TCTTTTCAATGA-TAGTGCTGGAATAAATGGACATCCATGTGCCAAATA- 98
                                  ii - i       i i  v    i ?   ii   v   v -
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_94965062_9     99 TAAAA----------ATCTAA------ACACAAAAATTAACTCAAAACAG 132
                          i  i---------- i  v ------ i                  ii 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_94965062_9    133 CTCATAAACCTGAATTTAA-AGCATGAAACTATAAAACTCCTAGAAAATA 181
                         v   ? i    i   v   -   - i              i     i v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_94965062_9    182 ACATAGGAGAAAATCTAGATAATCTTGGGTTTGGCAATTACTTTTTAGAT 231
                                ? v      vvi i i        v      vii  i      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_94965062_9    232 ATGACAGCAAAGTCATAACCCATGAAA---AAAATTAATAGGCTGGACTT 278
                               v    iv  i  v v ii   ---     vi   iii       
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_94965062_9    279 CATCAAAATTAAAAACT---------CAAAAGACCCT-TTAGGAGAATTA 318
                                          ---------    i   v  - i i  i i v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_94965062_9    319 AAACACAAGCCACAGACTTGGAGAAAATATTTGAAACAGATGTATCTGAT 368
                            v    v       v v              v  vvv  i        
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_94965062_9    369 AAAAGACTATTACCCA-AATA 388
                           ii    vv  i   -    
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATA 765

Transitions / transversions = 1.49 (52 / 35)
Gap_init rate = 0.02 (10 / 420), avg. gap size = 3.40 (34 / 10)  

2475 21.81 6.23 2.69  chr1_94965062_94968427      459  1164 (2202)    L1M4_orf2#LINE/L1       75   805 (103)  

  chr1_94965062_9    459 CAAACTAAACATACTCT-TACCATATGATCC-AGAGACCCTGCTTTTGTA 506
                           i i v   ii v  i-  i  v --    -  vvi  i --     i 
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAA--ATCCCAGCTGCCTT--TTTTGCA 120

  chr1_94965062_9    507 GAAATTAACAAACTGATTGTAAAATTTATGTGAAAATTCAAAGGACTGCG 556
                               i    i     iv       i  i  i    v   i    ivv 
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr1_94965062_9    557 AACAACCAAAAAAAAAAAAACTGAACAAAAAGAACAAAGTTGGAGGACTT 606
                           i i      v  vv----i    v  i                    i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATC----TTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr1_94965062_9    607 A--------AA---CAAAATTTACTATAAATCTATAGTAATCAAGACAGT 645
                          --------  ---     i      i   v   i               
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr1_94965062_9    646 ATGCTATTTGTGTATGGACAGACATAATTGATCAAACAGACAGAAT--AG 693
                         i  v  i v ii  v   i       - v      vvii i     --  
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATA-TAGATCAATGGAATAGAATTGAG 315

  chr1_94965062_9    694 AGTCCAGAAATAAATCTTCATACTTACAGTCAATTGATTTT-GACAAAGG 742
                                       i ivi i i   ii             -     i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_94965062_9    743 TGACAAAGCAATTCAATGAGGGAAAAGAGAGTCTTTTCAATAAATGGTGC 792
                           v   ii v        -      ii v           i         
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_94965062_9    793 TGGAACAATTATATATTCATATACAAAAAAAACAAAAAAAATCTTAGACC 842
                            i    i iv   ?i  i  i     i  -ii  i------  i    
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAG------TTGGACC 457

  chr1_94965062_9    843 CTCATCTCTTACCATGTA-------TAACTCAAAATAGGTCATAGGTTAA 885
                          ii i   vi     i  -------           i i   ?  iiiv 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_94965062_9    886 AATGTAAGTCCTAAGTCTATAAAACTTCTAGAAAAAAAAAACAGAG--AA 933
                                 vv    iv          ii     i    v vvi ? --  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_94965062_9    934 TCTTTGTGACTTTGGGTTAAGCAAACACTTGTTAGATGTGACAC--AAAG 981
                             i     i        i    vvii  v      i      --    
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_94965062_9    982 CAAGATCCATAAAAGAAAAAA-AATTACACTGGAATTTATCAAAATTAAG 1030
                           vi v v i           - iv  v i    v  i           i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_94965062_9   1031 --TGTTTACTTTTCAAAAGACATCACTAAGAAAATTAAAACAGAAGCCAC 1078
                         --iv   iivi      i    ii ii      i v    v v  v    
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_94965062_9   1079 C--ATCAGGGAGAAAATATTTGCAAATCACATTTCTGATAAAAGACTTGT 1126
                         v--  --                      i  v        ii       
  L1M4_orf2#LINE/    708 AGAAT--GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_94965062_9   1127 ATGCAGAA-----------CTCTTACAACTTAATAATATAA-GACAAACA 1164
                           v     -----------           i       v  -      i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

Transitions / transversions = 1.90 (99 / 52)
Gap_init rate = 0.03 (22 / 731), avg. gap size = 2.86 (63 / 22)  

1576 22.32 4.16 1.75  chr1_94965062_94968427     1167  1623 (1743)    L1M4_orf2#LINE/L1      441   908 (0)  

  chr1_94965062_9   1167 AAGAATGAAATTAGACTCCTATCTCTC-CTATATACAAAAATAAAGTCAA 1215
                                  i  i   i    i   v - i            v  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_94965062_9   1216 AAGGGATTAAAGATTTAAATCTAAGACGTGAAACTACAAAACTACTAGAA 1265
                           v    i ?   ii     v     vv i      i      vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_94965062_9   1266 GAAAACATTAGGG-AAATGCTTCAGGATATTGGTCTGGGCA--GATTATT 1312
                                 vi ? -    -    iv  iv    vi i    -- i  - i
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTT-TC 588

  chr1_94965062_9   1313 TTGTGTAAGACCTGAAAAGCACAGGCAATAAAAGCAAAAATAGACAAATG 1362
                           ivi  v   viv         i    i     v         i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_94965062_9   1363 GGATGACATCAAG-CTAAAAACCTTTTTGCACAGCAAAAGAAACAATCAA 1411
                            ivv      i-i       --     ii vv    i  v  v     
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAAC--TTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_94965062_9   1412 CAAAGTGAAGAGACAACCCAC-GAATAGGAGAAAATACTTGCGAACTATC 1460
                         v        i           -    i          i    i  ii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_94965062_9   1461 CGTCTGATAAAGGGTGAATAACTAGAATACATAAGGAA----TGCAATGC 1506
                         ii        i  iivvi  v i      i    i   ---- i   iv 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_94965062_9   1507 AATTGTTTTTAAAAAATCAAAT-------TTTGAAA-CAAGCAAAAGATC 1548
                            vi ----     iv     -------  ?i   -iii     i   i
  L1M4_orf2#LINE/    787 AATAAT----AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_94965062_9   1549 T-AATAGACATTTCTCAAAAGATGGCATACAAGTGGCAAACAGGTATATG 1597
                          -              v     v ii      i    v  i i i i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_94965062_9   1598 AAAAAATGCTCACCATCACTAATTAT 1623
                             i       v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (63 / 36)
Gap_init rate = 0.03 (13 / 468), avg. gap size = 2.08 (27 / 13)  

 340 24.17 0.83 1.67  chr1_94965062_94968427     2754  2873 (493)    L1M4_orf2#LINE/L1      790   908 (0)  

  chr1_94965062_9   2754 AAAAAAAAAAAAGACAACTCAGTTTTTAAAATGGGCAA-TAATGTAAATA 2802
                           v     i v i i   i  i  ?v-           -vi  v i    
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATA 838

  chr1_94965062_9   2803 GACATTTTATCAAAAAAGGAAACACATATGACTAATAAGCATACGAAAGG 2852
                                ivi    i   - v i   v   i i        i i    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_94965062_9   2853 ATTTCCAACATTAGTAGTCAT 2873
                           vii      i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (19 / 9)
Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.00 (3 / 3)  


2190 19.93 5.50 3.95  chr1_95055746_95058013      500  1081 (1187)    L1M4_orf2#LINE/L1      240   830 (78)  

  chr1_95055746_9    500 CTACAAAGCCACAGTAATGAAAATGGTGTGGTACTGGCATAAACATAGAT 549
                                  i        v  i ii                 iv     i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_95055746_9    550 ACACTGTGCTACATAGATCTATAGACCATGTGAACAGAATAGGAAGCACA 599
                          i ----------      v  i  -------- i     v ii  iv  
  L1M4_orf2#LINE/    290 ATA----------TAGATCAATGGA--------ATAGAATTGAGAGTCCA 321

  chr1_95055746_9    600 GAAATAATGCCTTGCATATGTGGCCAAATGATTTTTGGCAAAGATACCAA 649
                                vv  v i   v i   i   v       i i   i i i    
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_95055746_9    650 GACCACACAATGGGGAAAGGACAGTCTCTTCAACAAATGATCTTGGGAAA 699
                              iv            i i     i           i vi     v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_95055746_9    700 ACCAGATATCCACAAGCAAAAGAATGAAGTGGGACCCTTACCTTATAC-- 747
                           ii    ?     v               v      i     i i  --
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_95055746_9    748 ---AGGAAAATTAA-----AATGAACTAAAGACCTAAA----AGACCTAA 785
                         --- vi        -----    i ii ?         ----   v    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_95055746_9    786 AACTATAAAACTCTTAGAATAAAATACAGGAGAAAAGTGTCAGAACATTG 835
                                            v    i i   ? v   viv  ivi  v   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_95055746_9    836 GATTTGGCAGTGATTGCTTGGATATGACACCAACAGCACAGGCAACACAA 885
                          i  v    i  i  v   i             v      i      v  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_95055746_9    886 TAAAAG-TAGACAAATGGGACCACATCAAACTTAAAAACTTCTACACATC 934
                         v    i-    i    v    iv       v          i iii v  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_95055746_9    935 CAAGAA-------AATAGAGTGAAAAT-CATCCTATAGAATGGGAGAAAA 976
                         v   i -------  v i        v-  v  i i              
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_95055746_9    977 TA------AATTATATATGCTTAGAAGTTACT---GTCCAAAATACATAA 1017
                           ------   i      -  v v   vv   ---i    i    i    
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATAT-CTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_95055746_9   1018 GGAACTTCTACAATTTAACAACAACTACAAAAAAAAAAAACCCGATTTTA 1067
                         i     ii     i i  i  i  ----   i v   v     i   ?v 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAA----AAAGACAAATAACCCAATTWAA 816

  chr1_95055746_9   1068 AAATGGGCAAAGGA 1081
                                       
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGA 830

Transitions / transversions = 1.60 (69 / 43)
Gap_init rate = 0.02 (12 / 591), avg. gap size = 4.58 (55 / 12)  

 335 14.68 14.68 0.00  chr1_95055746_95058013     1667  1775 (493)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_95055746_9   1667 CTCAA-AA-AAAAAAAAAAAGAA--------AAAAAAAGGAAAAGGACTT 1706
                              -  -     i v   v  --------     vi  v      i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_95055746_9   1707 GAAGAGACATTTCTTTAGAGAAGCTATACAAATGGCCAATA--CA----A 1750
                            v          ii i     v                 --  ---- 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_95055746_9   1751 AAAGACACTCGATATCACTAATCAT 1775
                              ii   i i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.04 (5 / 125), avg. gap size = 3.20 (16 / 5)  


 467 31.00 16.00 1.75  chr1_95285129_95288129.rev     1506  1905 (1096)    L1M4_orf2#LINE/L1       60   516 (392)  

  chr1_95285129_9   1506 CCCCTAATT--TTTA--AATGTATTACAATATCAATGAAAACACTAATTG 1551
                             v    -- i  --i  vi vii    vi v  v    iv i ii  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_95285129_9   1552 GCAATTTTCTG--GAATAGGACAAAATGATTCCAAAGTCCACATGGGAAA 1599
                         v --    i  --   vvv     iv    i i   i i  i    i  v
  L1M4_orf2#LINE/    110 CC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_95285129_9   1600 ATAAACAAACAAGTTTA-CCAGAAGAACAATTTTTAAAA----GATCAGT 1644
                         ii  ivi v v  vv  -   i  ---    i  v    ----  v  iv
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAA---CAATCTTGAAAAAGAAGAACAAA 204

  chr1_95285129_9   1645 GAGGAAGGAATAAC-CTTCTGTATATTAAAAAATACTATAGAATCTCAAT 1693
                          vv i    v v  -    ivv  v i    vv     i i iiiv  i 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_95285129_9   1694 AATTAATAC--TTTGGGATTTCCAATGGAATAGA----TAGGCTAATGGA 1737
                            i  v  -- v   v i vv  vvi i     ----   iii      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_95285129_9   1738 ATTAAATAGAAAGCCCAGAAATAGACCCAAATA-----AG---------- 1772
                           vi   v  i  i         i     v i -----i ----------
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_95285129_9   1773 --CAGCA----TCTCAAG-----TCAGTGGGGTAAGA-TGG--------A 1802
                         -- ii  ---- vi    -----   i     v    - i -------- 
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_95285129_9   1803 CA-------CTTGAATAAATGGATAGC-ACCTGGAAAA-AATAAAGTTAA 1843
                           -------  v i i  v      ? -  v  v    -   i     ii
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_95285129_9   1844 ATCTATGTCTCATTCTGTATGCTAGTAAAT--ATTCCAAATGGGCCAAAG 1891
                          i iv ii    iv ii   i v --    -- i  v      ii  ?  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAA--AAATTAACTCAAAATGGATCAWAG 502

  chr1_95285129_9   1892 ACTTAAATGCAAAA 1905
                           i      i  i 
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGA 516

Transitions / transversions = 1.39 (71 / 51)
Gap_init rate = 0.05 (21 / 457), avg. gap size = 3.38 (71 / 21)  


3080 27.40 0.99 0.66  chr1_95336336_95342711.rev     4981  5885 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_95336336_9   4981 TGGAAGAGCATTCCATGCTCATGTGTAGGAAGAATCAATATCGTGAAAAT 5030
                              iiii  i     i     vi v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_95336336_9   5031 GGCCATGCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5080
                            v  i  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_95336336_9   5081 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5128
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_95336336_9   5129 TATGGAATGAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5178
                                vviv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_95336336_9   5179 AACAATGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5228
                              v i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_95336336_9   5229 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTTGACC 5278
                                 i   i    ii         i iv ii i   v  i v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_95336336_9   5279 AATGGAACAGAGCAGGGGCCTCAGTAATAATACCACACATCTACAACCAT 5328
                                i   iiv i ivii   v     vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_95336336_9   5329 CTGATCTTTGAGAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5378
                         i    i  i  v  ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_95336336_9   5379 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCTGA 5428
                         v  i  i              v      v  ?       i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_95336336_9   5429 AACTGCATCCCTTCCTTACACCTTAAACAAAAATTAATTCAAGATGGATT 5478
                          ii  v i    v   i     v  v           i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_95336336_9   5479 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAACC 5527
                          ?    i       v   v       i      -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr1_95336336_9   5528 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5576
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_95336336_9   5577 AACACCAAAAGCAATGGCAACAAAAGCCAAAAGTGACAAATGCGATCTAA 5626
                         i            vvi          vv    vv  i    vv  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_95336336_9   5627 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTCCATCA-----GTGA 5671
                          i   v v  i i   i  ii vv    i  v   --    -----    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT--ATCAAGAAAGTGA 694

  chr1_95336336_9   5672 ACATGCAACCTACAGAATGAGAGAAAATTTTTGCAATCTACCCATCTGAC 5721
                          v vi     i        i        v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_95336336_9   5722 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5771
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_95336336_9   5772 AAAATCAAACAACCCAATCAAAAAGTGGCCAAAGGATATGAACAGATACT 5821
                            iv    i        i?    i   v        v    i   i i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_95336336_9   5822 TCTCAAAAGAAGACATCTATGCAGCCAACAGACACGTGAAAAAATGCTCA 5871
                             v        i  vi viii     i ii   i      i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_95336336_9   5872 TCATCACTGGCCAT 5885
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2478 24.93 3.87 0.80  chr1_95367816_95369551.rev      501  1250 (485)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_95367816_9    501 ATTTTAAAATTCAGTGAAGGAGGAGCAAAGGGCCTAGAATAGCATACGCA 550
                           ii         - - v   iiv    i  i  i        vv vi  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCA-T-ATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr1_95367816_9    551 ATGCTGAAAAAGAA---CAAAGTTGGAGGACTCACACTACCCATTTCCAA 597
                           vi          ---                     v    v  i   
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_95367816_9    598 GACTTAACTATAAAGCGACAGTAATCAAGTCAGCATGGTGTTAGTG-AAA 646
                         i     -   i     v            v   ii    ii i ii-  i
  L1M4_orf2#LINE/    234 AACTTA-CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_95367816_9    647 GAT---CA-ATAAACCAATGGAAGAGAAAAGAGAGCTCAGAAATAGACCC 692
                            ---  -   i i        v    vv     ii        i    
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_95367816_9    693 ACACAAATATACTCAACTGATTTGTGACAAAAGCATAAAGGTAATTCAGT 742
                          i   vv   iv    i      vi     ii iiiv   iiv     i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_95367816_9    743 GGAGAAAAAA-AGTCTTTTCAACAA--GGTG-TGCAA-AATTGTATATCA 787
                           i    i  -              --    -  vi -  i  v   ? v
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_95367816_9    788 ACATCGAGAAAAATGAAGTTAAGCAGAGATCTCACACCTTACACAAAAAT 837
                             vv i  i         iii vvvv i        v  i        
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_95367816_9    838 TAACTCAAAATGGATCATAGACCTAAATGTAAAATGC-AAAACTATAAAA 886
                                          ?              i -  -            
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAA 531

  chr1_95367816_9    887 CTTCCATAAGAAAAAA-GGAAAAAAACCTGTATGATCTTGCATCTGGTGG 935
                           iii v       v -i i?iv   i  vii   i    vi iv  iii
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_95367816_9    936 TGCTATTTTAGATACAACACCAAAAGTGTCATCCATGGAAGAAAAAGTTA 985
                           v v i       ii          iiiv v v iii        i - 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT-A 630

  chr1_95367816_9    986 GTTAAGTTGGACTTCGTTAAAATTAAAA---CTTGCTCTGCGAAAGACAC 1032
                          v   i         i i          ---i   iv  v i  i     
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_95367816_9   1033 TGTTAAA-----GAAAAGACAACC-ACACACTAGGAAAAAATATTTA-AA 1075
                          i i  i-----            -   v v i   i         i-  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_95367816_9   1076 ATATACATGTATGGTAAAGTACATGTATACAAAGTACACAAAGAATTCTT 1125
                           -i i  i v  i   i v  v     v  i i  i i      i    
  L1M4_orf2#LINE/    731 AT-CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_95367816_9   1126 AAAAGTCAACAATAAGAAAACAA----CCCAATTAAAACACTGGTAAAAG 1171
                          v  v    i     i  i    ----       ?   v iv  i   i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_95367816_9   1172 AGCATAACAAAAACCTCATCAGAAAATATATATAGATGAAAACTAAGCAT 1221
                          vivv  i i v ii  vi  i i  v     i i   ivv v      i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_95367816_9   1222 ATAAAAAGATGTTCACTATTGTCATTAGG 1250
                           i        i   vi  ii????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (120 / 63)
Gap_init rate = 0.03 (21 / 773), avg. gap size = 1.67 (35 / 21)  


3219 26.51 0.44 0.55  chr1_95388512_95393127.rev     3217  4125 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_95388512_9   3217 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 3266
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_95388512_9   3267 GCCA-TACTACCCAAAGTAGTTTATAGATTCAAAGCTATCCCCATCAAGC 3315
                          v  -    v      v ii i  i        v  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_95388512_9   3316 TACCA-CTGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTTA 3363
                          v   -   v    i  -i     v v  v  i-  - iii    i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_95388512_9   3364 TATGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAACCAAAAG 3413
                                viiv  ii  v  v v        i      i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_95388512_9   3414 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGTC 3463
                                i      vv       v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_95388512_9   3464 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGGCC 3513
                                 i   i    ii         i iv ii i   v      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_95388512_9   3514 AATGGAACAGAACAAAGGCCTCAGAAATAACACCACACATCTAAAATCAT 3563
                                i    ivi  ivii         vv   i    i  vii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_95388512_9   3564 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 3613
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_95388512_9   3614 ATTTTATAAACAGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCTGA 3663
                         v  iv i   ii         v      v  ?       i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_95388512_9   3664 AAGTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGTATT 3713
                          iv    i    v   i     v              i    i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_95388512_9   3714 AAAGACTTAAATATAAGACCCAAAATCATAAAAACCCTAGAAGAAAACCT 3763
                          ?    i     i     v i    ii      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_95388512_9   3764 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 3812
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_95388512_9   3813 ACACTAAAAGCAATGGCAACAAAAGCCAAAAGAGACAAATGGGATCTAAT 3862
                             i       vvi          vv    v   i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_95388512_9   3863 TAAACTAAAGAGCTTTTGCACAGCAAAAAAAAAACTATCAGCAGAGTGAA 3912
                         i   v v  i i      ii vv    ii v --      iv i      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACA--CTATCAAGAAAGTGAA 695

  chr1_95388512_9   3913 CAGACAACCTACAGAATGGGATAAAATTTTTGCAATCTACCCATCTGACA 3962
                         v        i           v     v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_95388512_9   3963 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 4012
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_95388512_9   4013 AGATCAAACAACCCCATCAAAAAGTGGGCAAAAGATAGGAACAGACACTT 4062
                          iiv    i     v  i?    i        i   vv   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_95388512_9   4063 CTCAAAAGAAGACATTTGTGCAGCCAACAGACATATGAAAAAATGCTCAT 4112
                            v        i  viiviii     i ii  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_95388512_9   4113 CATCACTGGTCAT 4125
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


3381 25.08 0.22 1.85  chr1_95448368_95452726     2946  3866 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_95448368_9   2946 GGAAGACATCCTATAATCACGTATCAGAAGAATTAAAAATATTGTTAAAA 2995
                          i    i    i  iv   i v  ii     v    ---         i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAA---TATTGTTAAGA 49

  chr1_95448368_9   2996 AGACCATACCAATCAAAGCAATCTGCAGATTCAATGCAATCCCTATCAAA 3045
                         v i v    ivvi    vii    i         i               
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_95448368_9   3046 ATACCAATGACATTCTTCACAGACATAGAAAAATAAAACCTAAAATGTGT 3095
                           v   iivi v  i  ii    v  v  v  iivi v        vii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_95448368_9   3096 GCAGAACCACACACACAAAAAAAATCCCA-AAGAGCCAAAACAATCCTAA 3144
                         iii   ------ ii   iii ---    -  v             i i 
  L1M4_orf2#LINE/    150 ATGGAA------ATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGA 190

  chr1_95448368_9   3145 GCAAAAAAAACGAAGCTAAAGACATCACATTACCAGGCTTTGAAATATAA 3194
                         iv  i  i   i   i ii  ivv     i v  viii  ii   iv  v
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_95448368_9   3195 TACAATGCTGTAGTAACAAAAACAGCATGGTACTGGCACAATAACAGACA 3244
                              v   ii     iv  i    ii           i  vi i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_95448368_9   3245 CATAGACCAATGGAACAAAATAGAGAACCCATAAACTAATCCACGTATTT 3294
                         i     i        i i   v    ii   v   iv  i   iii    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_95448368_9   3295 ACAGTCAACTGATTTTTGACAAAGATGCCAAGAACACTTATTGTGGAAAG 3344
                          ii     i       i     i i        v  i i v  v      
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_95448368_9   3345 AGCAATCTCCTTAATAAATGATGCTAGGGAAACTGGATATCCATATACAG 3394
                          ii i   ii i  i     i    i  iv         ?   i  i  i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_95448368_9   3395 AAGAAGGAAACTAGACCCCTGCCTCTCATTCTATACAAAAATCAACTGTA 3444
                              v   ii i       i    v  iiv           i    vv 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_95448368_9   3445 AAAGGGGCAAAGATCTAAATGTAAGACCCAAAACTATAAAATTACTAGAA 3494
                           v  iv  ?   i            v i            i vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_95448368_9   3495 GAAAACATAGGGGAAACACTTCAGGACATTGGCTTGGGAACAGACTTATT 3544
                                    ? v  vv    iv   v    v  i  v vv ii  v  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_95448368_9   3545 ATGA-ATGAGACCTCAAAAGCACAGAGAGCAAAAGCAAAAATAAGCAAAT 3593
                          -  -    v   --         iiv i      v       iii    
  L1M4_orf2#LINE/    591 A-GATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_95448368_9   3594 GGGATTATGTCAAATCAAAAAACTTTTGCACAGCAAAGGAAACAACCAAT 3643
                         v   i vii     viv           ii vv       v  v i   v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_95448368_9   3644 AGAGTGAAAAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTGTTC 3693
                          i               i                          iii vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_95448368_9   3694 ATCTGACAGGAGATTTATATCCAGAATATACAAGGAACTCAAACATCTCA 3743
                               i i i  i  i             i  i      vv   v    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_95448368_9   3744 ATAGCAAAAAGGCAAAAAAAATCTGATTAAAAAGTGGGCAAAGGATCTGA 3793
                            ii      i    v  --i ii   ?    i            i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAA--CCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_95448368_9   3794 ACAGACATTTCTCAAAAGAAGAAATACGAACAGACAACAAAGGTATAAAA 3843
                          i           v        v    i  ii v   i  ivii  i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_95448368_9   3844 GGATGCTCAACATCACTAATAAT 3866
                         i              ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (152 / 75)
Gap_init rate = 0.01 (8 / 906), avg. gap size = 2.38 (19 / 8)  


3255 26.25 1.22 0.66  chr1_95470067_95476335.rev     4876  5778 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_95470067_9   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4925
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_95470067_9   4926 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_95470067_9   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTGAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iiiv   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_95470067_9   5024 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_95470067_9   5074 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5123
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_95470067_9   5124 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5173
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_95470067_9   5174 AATGGAACAGAAC--AGAGCCCTTAGAAATAATGCCACGTATCTACAACT 5221
                                i    i--    i  --        vv   iii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_95470067_9   5222 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5271
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_95470067_9   5272 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5321
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_95470067_9   5322 GAAACTGGATCCCTTCTTTACACCTTATACAAAAATCAATTCAAGATGGA 5371
                            ii    i    v i i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_95470067_9   5372 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5421
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_95470067_9   5422 CTAGGCA-ATACCATTCAGGGCATAGGCATGGGCAAGGACTTCATGTCTA 5470
                         v    ?i- v i -   iv i v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_95470067_9   5471 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT- 5519
                         vi            vvi           v     v  i    v   ii -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_95470067_9   5520 -----AATTAAAGAGCTTCTGTACAGCAAAAGAAACTACCGTCAGAGTGA 5564
                         -----       i -   i   i vv    i  v    i ivv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_95470067_9   5565 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5614
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_95470067_9   5615 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5664
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_95470067_9   5665 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5714
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_95470067_9   5715 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5764
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_95470067_9   5765 TCATCACTGGCCAT 5778
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


2678 24.62 6.91 0.63  chr1_95621624_95623411.rev      502  1297 (491)    L1M4_orf2#LINE/L1       63   908 (0)  

  chr1_95621624_9    502 CAAAGCTATCTACAAATTCAATGCAATCTCTATCAAAATACAAATGACTT 551
                             viv       i      i      i          v v iivi i 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_95621624_9    552 TCTTCACA-AAATGGAAAAAAAAACCTTGAAATTCCTGTGAAGCCAAAAA 600
                          i  ii  -    v  v  ivvi i i i      v i  i iviiv  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr1_95621624_9    601 AGATCCAAAATAGCCAAAGCAATCCTGAGCAAAAAGAACAAAGCTTGGGG 650
                         i  i   i          i     i   iv  i          i v i  
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr1_95621624_9    651 CATCACACTACCTAA-------------------GTTATAGCAACCAAAA 681
                         vv       v  i  ------------------- i  i  i  i   i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_95621624_9    682 CAGTATAGTACTAACATAA----AAACACATAGACCAATGAAACTAAATA 727
                             i i     ii     ---- i   i     i     i  ivi   v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_95621624_9    728 GAAAATCCAGAAATAAGTCCACACATTTATAGCCAATTCATTT-CAACAA 776
                           i i           ii   i        i i     v    - i    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_95621624_9    777 AGGTGCCAAGAACATACACTGGGGAAAAGACAGTCTCTTC---------- 816
                         i          v   v  v        ii i     i   ----------
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_95621624_9    817 -TTGGAA-ACCTAGATATCCATATGCAGACAAAAGAAACTAGACCCTTAT 864
                         -i   i - v  i    ?   i     i vi  v   ii i     i  i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_95621624_9    865 CTCTCACCATATAAAAAAATCAAATCAAAATGAATTAAAGATTTAAATGT 914
                            v         v      i  v        i  i ?   ii       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_95621624_9    915 AAGACCTGAAACTG--AAACTTCTAGAATAAAGCACAAGAGGAAATGCTT 962
                             v  i     i--     ii     v   i  i i ? v    -   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTT 561

  chr1_95621624_9    963 CAGGACGTTGGTCTGGGCAAAGATTTCTTGAATAAGATCTCAAAAGCATA 1012
                          iv   v    vi i     v i      ii   v  ivi        i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_95621624_9   1013 GGTAATCAAAACAAAAATTGACAAATGGGATTACATCAAGCTAAAAAGCT 1062
                         i i  iv   iv      v  i    v   i v      iv v    i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_95621624_9   1063 TCTGCATAGCAAAGAA-ACAATCAGCAAAGGGAA--GAAAAT-----GAA 1104
                          i  iiivv     i -  v    iv    v   --  v  i-----   
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_95621624_9   1105 -GAAAGAAAATATTTGCAAACTATCCATCCAATAAGGGATTAAGAATCAG 1153
                         - ii                ii  vi   ii        i viv vi   
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_95621624_9   1154 AATATATAAAGAACTGAAACAACTCAACAGCCAAAAC-CAAATAATCTGA 1202
                                        vvv         i iiv    v-       i ii 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_95621624_9   1203 TTAAAAAATGGGCAAAAGATCTGAATAAACATTTCTCAAAAGAAGACATA 1252
                           ?             i   i      i         v        i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_95621624_9   1253 CAAATTGGGT------GCATCATGAGAAAAGTGCTCCACATCACTCACCA 1296
                              --  i------   -     i  i -     v      ???????
  L1M4_orf2#LINE/    862 CAAAT--GGCCAATAAGCA-CATGAAAAGA-TGCTCAACATCAZZZZZZZ 907

  chr1_95621624_9   1297 T 1297
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.10 (130 / 62)
Gap_init rate = 0.02 (17 / 846), avg. gap size = 3.53 (60 / 17)  


3690 24.56 0.33 0.33  chr1_95642222_95646679.rev     3060  3967 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_95642222_9   3060 TGGAAAGATATTCCATGTTCATGGATTGGAAGAATGAATATTGTTAAAAT 3109
                                    i                     v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_95642222_9   3110 ATCCACACTACCCAAAGCAATCTACAGATTCAACATGATTCCTATCAAAA 3159
                         iv v i   v      vii               iii  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_95642222_9   3160 TACCAATGACATTTTTCACAGGAATAGAAAACACAATCCTAAAATTTATA 3209
                          v   iivi v     ii   i   v  v  vvii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_95642222_9   3210 TGGAACCACAAAAGACCAAGAAGAGCCAAAGCTATCCTGAGCAAAAAGAA 3259
                              vii   ii    v    v       i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_95642222_9   3260 CAAAACTGAAGAAACTACATTACCTAACTTCAAATTATACTTCAGAGCTA 3309
                             ii  i  i vii   i v  i  i      viv    v  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_95642222_9   3310 TGGTAACCAAAACAGCATGGTACTGGAGTAAAAACAAATGCACAGACCAA 3359
                         ii    i   i    ii         vi   ii i i iii i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_95642222_9   3360 TGGAATGCAATAGAGAACCCAGAAGCAAATGCACATACCTAGAGAGAACT 3409
                               iv   v    ii      ii   iv  i i ii  vi vv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_95642222_9   3410 CATTTTCGACAATGATGCCAAGAACATATATTGGGGAA--GACAGTCTCT 3457
                         v           v i        v   vi v       --i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_95642222_9   3458 TCAATAAATGGTGCTGGGAAAACTGGATATCCATATTCTGAAGAATGAAA 3507
                             i              v         ?   i  v vi         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_95642222_9   3508 CCAGACCCCTATCTCTCACCATGTACAAAAATCAAATCAAAATAGATTAA 3557
                         iii        i   v      i         i  v       i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_95642222_9   3558 AGATGTAAATCTAAGACCTTAAACTATGAAATGTCTATAAGAAAACATTG 3607
                            iv     v     v  v       i   ivii  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_95642222_9   3608 GGGAAACTCTCCAGGACATTGGTCTGGGCAAAGATTTCTTGAGTAATATC 3657
                          ? v  v   i iv   v    vi i     v i      iii  vv iv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_95642222_9   3658 TCACAAGCCCAGGCAATCAAGGCAAAAATGTACAAATGGAATCACATCAA 3707
                         i  v    v  i    iv  i v      iv i    v i iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_95642222_9   3708 -GTTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAAGAAAGTGAAGAGA 3756
                         -i       -   i  ii vv       v  v              i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_95642222_9   3757 CAACTCACATAAAGGCAGAAAATATTTGCAAACTATCCCTCTGACAAGGG 3806
                             i    v  v  v                ii  viv     i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_95642222_9   3807 ATTAATAACTAGAATATATAAGGAGCTCAAATAACTCCATAGGAAAAAAA 3856
                          i vi  v i           i  i   vv i     v   iv     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_95642222_9   3857 TCTAATAATCCAATTTTTTAAATGAACAAAAGATCTGAATAGACATTTCT 3906
                         - v     i      -?vv     ii    i   i               
  L1M4_orf2#LINE/    800 -CAAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_95642222_9   3907 CAAAAGAAGACATACAAATGGCAAGCAGGCATATAAAAAGGTGCTCAACA 3956
                          v        i           v ii i   i  i     i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_95642222_9   3957 TCACTGATCAT 3967
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.64 (136 / 83)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


2759 28.54 1.78 0.56  chr1_95660877_95666549     4284  5180 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_95660877_9   4284 TGGAGAAACAGTCCATACTCATGGATAGCAAGAATCAATATCATGAAAAT 4333
                             i i i vi    ii        v v    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_95660877_9   4334 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCTCATCAAAC 4383
                            v     v      v i  i  i        i  v  i ii      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_95660877_9   4384 TATCATTGACATTATTCACAGAATCAGAAAAAACT-ACTTTAAATTTCAT 4432
                          vi  vivi v  v  ii     viv  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_95660877_9   4433 ATGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATTCTAAGCAAAAAGA 4482
                               viiv  ii  v  v v        i     ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_95660877_9   4483 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC- 4531
                               i      vv    i  v  ii i      viv        i  -
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_95660877_9   4532 GCAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGACATATAGACCA 4581
                         i      i   i    ii       i i iv ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_95660877_9   4582 ATGGAACAGAACAGAGACCTCAGAAATAACAATACACATCTACAATCTTC 4631
                               i    iv    vii         vvvi i    i  iii  vvi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_95660877_9   4632 TGATCTTTGACAAACAGGCCCAAATCAAGCAAAGGGGAAAGAATCCCTAT 4681
                             i  i     iviv   v i i  vv   v           vviiv 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_95660877_9   4682 TTCA-TAAATGATACTGGAGAAACTGGCTAGCCATATGCAGAAAACTGAA 4730
                             -i     i i    iiv      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_95660877_9   4731 ACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAACATCAACTA 4780
                         ii         v   i     v                   v  vi ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_95660877_9   4781 AAGACTTGAATGTACATCAG--AAAATCATA----CCCTAAAAGAAAACC 4824
                         ?    i i      vi--  --    ii   ----i i  i        v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAG--AGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_95660877_9   4825 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCAT-GATGA 4872
                             ?i- v i -   iv   v v  vv i     v ii   v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr1_95660877_9   4873 AAATGCCAAGATCAATTGCAGCAAAAGCCAAAACTGACAAATGTGATTTA 4922
                         vi ii    i v  vvv   i      vv    iv  i    vv  i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_95660877_9   4923 ATTGAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 4972
                           ii  v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_95660877_9   4973 CAGGCAACCTACAGAATTGGAGAAAATTTTTGCAATCTACCCATCTGACA 5022
                         v  i     i       v         v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_95660877_9   5023 AAGGTCTGATATCAAAAATCTACAAGGAACTTAAACAAATTTACAAGAAA 5072
                          i  v  vi    v i   v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_95660877_9   5073 AA-----ACAACCCCATCAAAAAGTGGGCAAAGGCTGTGAACAGACACTT 5117
                           ----- i     v  i?    i          v v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_95660877_9   5118 CTCAAAAGAAGACATTTGTGTGGCCCACAAACATATGAAAAAAAGCTCAA 5167
                            v        i  viivi     v i  i  i       i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_95660877_9   5168 CATCACTGATTAT 5180
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (148 / 104)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


2146 26.20 2.71 1.96  chr1_95741520_95744669.rev     1463  2126 (1024)    L1M4_orf2#LINE/L1        7   675 (233)  

  chr1_95741520_9   1463 GATA-CTCATGCTCATGAGTCAAACAACTCAATATT---AAGATGTAAAT 1508
                             - i    i     ii iii vi   i      ---      vv   
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_95741520_9   1509 TCTTCCCAAATTGATCTATAGATTCAACACAATCTCAATCAAAATTCCAG 1558
                         v  i              i         i     i v        i    
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_95741520_9   1559 TAGGCTTTTT-GTGGAAATTAACAAGCTCTTCCTAAAACTTACAAGGAAA 1607
                         iv v      - ii      i       vv        i i i v     
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_95741520_9   1608 ATCAAAGAATCTAAAATTGCCAAAATAATTTTGAAAA-GAAGAACAAATT 1656
                         vv   i i i i i   v       i   i       -          v 
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_95741520_9   1657 TGCAGGATTCACATTATTTGACTTCAAGACATCATT-TGAAACTATAATA 1705
                           v    i     i viiii i     i  - i i -ii  i   i i  
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAAC-TTACTACAAAGCTACAGTA 255

  chr1_95741520_9   1706 ATCAAGACAGTTCAGTAGTGT--TAGAGATAGACACACAGAGCAAAGAAA 1753
                                    vii   v  v--  ii        i i   v   v i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_95741520_9   1754 TCAAATAGAGTGTCCAGAAATAGACTTACATATATATGGTCAATTAATTT 1803
                          vi   v   v           i  ii i i  v           i    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_95741520_9   1804 TTGACAAAGGTGACAGTA--ATTCACTAGGGGAAGGACTGTCTTTTTAAC 1851
                          i     i    v  iv --     v i   i   i iv       i   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_95741520_9   1852 AAATGATGTTAAAACTATTAGATATTCATGTGCAAGAAGAAACAAATACA 1901
                              i  i iii  v i i    ?i  ii     -     vv  i ---
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAA-AAGAATGAAGT--- 451

  chr1_95741520_9   1902 CCTTGACCCATATTGTATATCACACCA-A-AGAAAAGCAAACTGAAAATG 1949
                         -- v     v  ii-----        - - v    iiv    v      
  L1M4_orf2#LINE/    452 --TGGACCCCTACC-----TCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_95741520_9   1950 GGTAACAGACCTAAATGTAGGAGCTAAAACTATAATATTTCTAGAAAACA 1999
                          i v ?             i               v i ii     i v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_95741520_9   2000 ATTTAAAAGAAAAATATTTGTGACC--AAGTTTAGAAAAAAATTCTTGCA 2047
                          iv  ii? v   - v  i      --ii   vi v  viiv     iv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_95741520_9   2048 TAGGATACAAAAAAGATAAACAGTT---TTTAAAACTGCTAAAATAGACT 2094
                           v  i  v    iv i  i  iiv---vvv    iv v    v i    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_95741520_9   2095 TCACCAAAATGGAAAACATTCACTCTTCAAGG 2126
                            i      vi     v  iiiv      i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

Transitions / transversions = 1.80 (110 / 61)
Gap_init rate = 0.02 (16 / 669), avg. gap size = 1.94 (31 / 16)  

 909 21.72 3.00 2.62  chr1_95741520_95744669.rev     2397  2663 (487)    L1M4_orf2#LINE/L1      641   908 (0)  

  chr1_95741520_9   2397 ACTCCATCTCAAAAAAAAAAAAA---TTGCTCTTCAAAAGATACCATTAA 2443
                            i    ----    vv     ---   iv       i  i  i  i  
  L1M4_orf2#LINE/    641 ACTTCATC----AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_95741520_9   2444 GAAAGTGAAAATTTATGCCATACACTGGGGGAATATATTTTCAAAATAGA 2493
                                    vvi vv   i v v    i   v      v    vi v 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_95741520_9   2494 TATCTGATAAAGAACTTTTATCCAGGATA----AAGAACTGCTACAACTC 2539
                                   i i    v       i   ----       vi        
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_95741520_9   2540 AATAACAAGAAGACACACAACCTGACTTTTTTTTATTGAGCAAAAGAATT 2589
                              i  i      v i    ii ---  ?vvv v  i     i  v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAA---TTWAAAAATGGGCAAAGGATTT 833

  chr1_95741520_9   2590 GAAAGGACATTTCCACAAAGCAGATGTTCAA-TGGTAAATAAGCGCATTA 2638
                            vi        iv     v    i v   -   iv       i   v 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_95741520_9   2639 AAAAATGCTCAACCCCGTTAGCAGG 2663
                            i         vi i????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.04 (29 / 28)
Gap_init rate = 0.02 (5 / 268), avg. gap size = 3.00 (15 / 5)  


 847 26.91 10.55 0.36  chr1_95844397_95846309      494   768 (1145)    L1M4_orf2#LINE/L1      290   592 (316)  

  chr1_95844397_9    494 ATTTAG-TCAATGGAACAAAATGGAGATTTCAGAAATAGAC--------T 534
                           v   -         i i   v    v i        i  -------- 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_95844397_9    535 TATAGTTGGTTGTTTCTAAACAGAGGTGCCAAAGTGATTCAGTGGGAAAA 584
                            i  iii   v  i vi   ii        iiiv     i    i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_95844397_9    585 GA----TCCTTAAAACAAGTGGCTCTCAAACAACTGGAAATCCAGGTGTA 630
                           ----  i  vv     i   iv  vii         v ?   vi  i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_95844397_9    631 TAACCATGTACCTAAACCC-TGTCTCATGCCGTACACAAAAATTAGTTCA 679
                         v  vv   v vi ii    - ii    ii  i  i          ii   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_95844397_9    680 ATATGAACCTTAGACTTTAATATAAAAATCTAAAACTGTTAAGCTTTTAG 729
                          v   i i v?    i v   i   i i-        i v  i  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAG-CTAAAACTATAAAACTCTTAG 538

  chr1_95844397_9    730 AAGATAATATAGG-GCA-------GTAACTTAGGGC-AGGCA------TC 764
                             v  i     - i -------  i  i v   i-     ------  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_95844397_9    765 TTAG 768
                             
  L1M4_orf2#LINE/    589 TTAG 592

Transitions / transversions = 2.13 (49 / 23)
Gap_init rate = 0.03 (9 / 303), avg. gap size = 3.33 (30 / 9)  

 524 24.67 12.83 2.96  chr1_95844397_95846309     1117  1420 (493)    L1M4_orf2#LINE/L1      575   908 (0)  

  chr1_95844397_9   1117 TAAGCAAAGATTTCTTAAATAGGATA--AACAGCAATAGTAATTTTTAAG 1164
                           i    v i       i   v  i --  v    vv  i  ivv--   
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA--AAG 622

  chr1_95844397_9   1165 AAA-----GAGAAATTATACTTTCTCAAAATTAAAAAACTTTTACTTATT 1209
                            -----  v     iv    iv             -     iiviv i
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTC 671

  chr1_95844397_9   1210 AAAAGACAACAGTAAGAAAATAATTAGGCAAGCTACAGGTTGTGATAAAA 1259
                            i    vi vi      i i vv  i   v i    iv  v  v    
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_95844397_9   1260 TATCATACAG-T--TATATTAAATAAAACCCTTAAATTCAGAACATATAG 1306
                            i- i  i- --     ivi    iivv   iv  i     i     i
  L1M4_orf2#LINE/    722 TATT-TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_95844397_9   1307 AAAATTCTTCCA-CTTAGTAATAAAAA-------------ATT------T 1336
                          i  i    v  -  i i         -------------   ------ 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_95844397_9   1337 GGG-AAAAGATTTGAATAGTTTAGACACTGC-ACAAAGAA-----ACA-- 1377
                            -   i           -----   i v -v       -----   --
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAG-----ACATTTCTCCAAAGAAGATATACAAA 865

  chr1_95844397_9   1378 TGGTTAATAAACACATATAAAACTCATTGACATCATTAGTCGT 1420
                            ii     i     iv   iv vv ii      ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (44 / 31)
Gap_init rate = 0.04 (15 / 334), avg. gap size = 3.20 (48 / 15)  


3196 23.43 1.17 4.47  chr1_95882251_95884242.rev      565  1503 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_95882251_9    565 TGTAAAGGTATTTTGTGTTCATTGATTTGATGAACTAATAGTTTTAAAAT 614
                           v    i   iiii       v    v  v  vi     v v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_95882251_9    615 GTTTGTACTAAACAAAGTGATCTACAGATTCAATGCAATCCTTATCAAAA 664
                          vivi    vvv    v                i       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_95882251_9    665 TTCCAA-TGACATTTTTACATAAGTAGAAAAA--AATCCTAAAATTTGTG 711
                          i   i-  v v     i  v  i v  v  i--i           ii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_95882251_9    712 TAGAACCACAAAAGACCCTGAACAACCAAGGCAATCTTGATTTTTTTTAA 761
                          i   vii   ii     v   i i    ii         v-------  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-------AA 193

  chr1_95882251_9    762 AAAAGAGCAAAACTGGAAGCATTATACTATCTGACATAAAAAAATATACT 811
                          i    i    ii    i vv i i   vi ii iv v    --iv    
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA--CTTACT 241

  chr1_95882251_9    812 GCAAAGCCATAGTAAATAAAATAACATGGTA--AACAGAAAAACAGATAT 859
                         i      i i     vi  i i iii     --ii  v  ii i   i  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_95882251_9    860 ATCGACCAATAGAATAGAAGAGAGAGCCCAGAAATAAATCTATACATTTA 909
                           v  i    i        vv     i           i i         
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_95882251_9    910 CAGTCAATTGATTTTCAACAAAGGTGCCAAGAACACACAATGGGGAAAGG 959
                         ii              i    i          v  iv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_95882251_9    960 ATAGTCTCTTCAATAAACTTTCTTGGAAAAACAGGAGATTCCCCTGCAGA 1009
                                i     i   ivv vi   i v   v   v ?i v v    i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_95882251_9   1010 AGAATAAAATTTGACCCTTTTCTCATACCATATGCAAAAATTAACTTAAA 1059
                              i  i  v     i vi    i       i            i   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_95882251_9   1060 AAAAGTGAATTAAAGATGTAAACATAAGACCTAAAACTGTAAAACTATTA 1109
                          ----  i  i ?   iv    ii     v        i       v   
  L1M4_orf2#LINE/    492 A----TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_95882251_9   1110 GAAGAAAACATAGGAG-AAATGCCCCAAAACATTGTTCTGGGCAAAAATT 1158
                                       ? -    - ii ivi  v   vvi i     vii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_95882251_9   1159 TTCTTA-ATATAACCTCAAAAGCACAGTCAACAAATGTAAAAAATAAACA 1207
                          -    -    i  vi          iv       v -        i i 
  L1M4_orf2#LINE/    587 T-CTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATA 634

  chr1_95882251_9   1208 ---TGGAATTGCATCAAACTAAAAGGCTTCTGCACAGCAAAAAA-ACAAA 1253
                         ---    v  -       v v   ii   i  ii vv    ii -  v v
  L1M4_orf2#LINE/    635 AATTGGACTT-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_95882251_9   1254 CAAAAACAAAACAAAATAAAAAACTATTAGAGTGAAGAGACAATCCATGT 1303
                            i  ------------------------      i      i   iiv
  L1M4_orf2#LINE/    684 CAAGAA------------------------AGTGAAAAGACAACCCACAG 709

  chr1_95882251_9   1304 ATTGAAAGAAAATATTTGCAAACTATATATCTGATAAGTGGTTAATATCC 1353
                          v  ii                ii              v ii vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_95882251_9   1354 AAAATATTTAAGAGACTCAAACAACTCAATAACAAATAAAACAAATAATC 1403
                          i     v   iii    vv            i   -  i        i 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAAATAACC 808

  chr1_95882251_9   1404 CAATGAAATAATGGGCAGAGAACCTAAATAGATATTTCTCAAAAGAAGAC 1453
                             v?  v        i  i ii i      i       v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_95882251_9   1454 ATACAAATGGTCAACAGATATATGAAAAAGTGCTCATCATTGCTAAGCAT 1503
                                   i   i iii i       ii      v   ii????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (143 / 73)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.31 (53 / 16)  


3174 25.78 1.11 0.22  chr1_95915019_95919882.rev     3474  4373 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_95915019_9   3474 TGGAAACACATCCCATGCTCATGGATGGGTAAGA-TCAATATTGTGAAAA 3522
                               v i        i        v  -    - i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGG-AAGACTTAATATTGTTAAGA 49

  chr1_95915019_9   3523 TGACCATACTGCCAAAAGCAATCCACAAATTCACTGCAATTCTCATCAAA 3572
                           i v     v  v   vii   i   i     vi     i ii      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_95915019_9   3573 ATACCATC-ATTATTTTCACAGAACTAGAAAAAA-AATCCTAAAATTCAT 3620
                           v   v -iiiv    ii     v v  v  iv-i              
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_95915019_9   3621 ATGGAACCAAAAAGGAGCCTGCATAGCCAAAGCAAGACTAAGAAAAAAGA 3670
                               viiv  i   v  v v         i   vvi i i   i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_95915019_9   3671 ACAAATCTGGAGGCATCTGATTACCTGACTTCAAACTATATTATAAGGCC 3720
                              vi      vv  vv i v  ii i      viv  i  i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_95915019_9   3721 ATAGTCACCAAAACAGCATGACACTGCCATAAAAATAGGCTTATAGACCA 3770
                          i   v i   i    ii  ii    v     ii    i v      i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_95915019_9   3771 ATGAAACAGAATAGGGAACACAGGAGTAAACCCAAATACTTACAGCCAAC 3820
                            i  i     v i  iiv   i i        v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_95915019_9   3821 TGATATTCTATAAAGCAAACAAGAACATAAATTGGGGAAAGGACATACTA 3870
                             v   v i  i vviv     v   vv v         i i vv  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_95915019_9   3871 TTCAACAAATGGTGCTGGGATAATTGGTAAGCCACATGTAGAAGAATGAA 3920
                                             i  i   vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_95915019_9   3921 ACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGAATCA 3970
                         ii    i  ii i   v    v           i       i   i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_95915019_9   3971 AGGACTTAAATATAAGACCTGAAAGGATAAAAATTGTAGAATATAACATT 4020
                         ?i   i     i     v  i   vv      v iv     v v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_95915019_9   4021 GGAAAAACTTTTCTAGACATTGGCTTAGGCAAAGACTTCATGACCAAGAA 4070
                           ?iv  v i   vv   v    v        v ii   v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_95915019_9   4071 CCCAAAAGCAAATGCAACAAAAAGAAAGATAAATAGATTGGACTTAATTA 4120
                         v         v v         ii   i   i   i         v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_95915019_9   4121 AACTAAAAAGCTTCTGCATGGCAAAGGAAATAATC-GCAGAGTTAACAGA 4169
                           v v    i   i  iiivv       v iv   -iv i   v  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_95915019_9   4170 CAACCCACAGAGTGGGAGAAAATCTTTA-AAATCTATACATTCGACAAAG 4218
                                    i           v   i-     -   i  ii  i  i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGG 748

  chr1_95915019_9   4219 GACTAATATCCAGAATCCACAAAGAACTCAAACAAATCAGCAAGAAAAAA 4268
                             vi          vi i         vv    v   ii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_95915019_9   4269 A-----AATCCCATAAAAAAGTGGGCTAAGGACATGAAGAGACAATTCTC 4313
                          -----  i  v  v?    i     v     iv    v     v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_95915019_9   4314 AAAAGAAGATATACAAATGCCCAACAGGTATATGGAAAAATGATCAACAT 4363
                         v                  v    i i i i   i   i   v       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_95915019_9   4364 CACTAACTAA 4373
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.28 (128 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


2432 26.52 1.62 2.17  chr1_95937585_95941804      526  1264 (2956)    L1M4_orf2#LINE/L1        1   735 (173)  

  chr1_95937585_9    526 TGGAAAGATATTCCATGTTCATCAATTGGAAAAGTCAATATTATTAAAAT 575
                                    i          vi       i v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_95937585_9    576 GTCCATACTACCAAAAGAAATCTAGAGATTCAATGTAATTCCTATGAAAA 625
                          v v     v  v   vvi     v        i i   i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_95937585_9    626 TACCAATAACATTCTTCACAGAAATATAATAAAC-AATCCTAAAATTTAT 674
                          v   iivi v  i  ii       - i i  i -i           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_95937585_9    675 ATCAAACCACAAAAGACCCAGAATAGCCAAGCTAGTGTGTGCAAAAT--T 722
                           vi  vii   ii                ivi i v -  v    v--v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT-TGAAAAAGAAG 198

  chr1_95937585_9    723 AACAAAACTGAAGGAATCATATTACCTGACTTCAAACTATACTACAGACC 772
                               ii  i    v   i i v  ii i      viv       i v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_95937585_9    773 TATAGTCACCAAAACAGCATGATACTGGCATAAAAACATACACATAGACC 822
                           i   v i   i    ii  i           ii i v   i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_95937585_9    823 GATGAAACAAGATAGAGAACCCAGAAACAAATTCATATGCCTACAG--AA 870
                         i   i  i ii  v    ii       i   ii    iiii  ii --  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_95937585_9    871 CTCATTTTTGACAAAGGTGCCAAGAACATACACTGGGGAAAAAGATAGTC 920
                         i v     i     i          v   v  v        i -      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTC 397

  chr1_95937585_9    921 TC--CAATAAATGGTGCTGGAAATACTGGATATCCATATACAGAAGAATT 968
                          i--   i            i vv        ?   i  i  i      v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_95937585_9    969 AAAGTAGACCCTTATGTCTTGCTATATACAAAAACCAAACGAAAATGAAT 1018
                           iv i     i  iv  vii i           ii  viv      i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_95937585_9   1019 TAAAGACTTAAACCTAATACTTCAGTCTATGAAGCTACTGAAAGAAAACA 1068
                         i ?    i    iv   v vi v iv    i  i  vi ii         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_95937585_9   1069 TTGGGAAAACTCTCCAGGATATTGAACTGGGAAAATATCTCCAGGATATT 1118
                          v  ?iv  v   i iv  iv   iii i  v  vvi i  ivi     -
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT- 596

  chr1_95937585_9   1119 GAACTCCTTGAGTAATACCCACAAGCCCAGAAAAAAAAAAAAAAAGGAAA 1168
                         -i  v  vvi  -------       ---i v    i      v  iv  
  L1M4_orf2#LINE/    597 -GACACCAAAAG-------CACAAGC---AACAAAAGAAAAAATAGATAA 635

  chr1_95937585_9   1169 ATGGGATCACATCAAG-TTACAAAGCTTCTGCATAGCAAAGGGAACAATC 1217
                           v   iiv      i-   -   i   i  iiivv      iv  v   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_95937585_9   1218 AAG----TGAAGAGACAACCCACAGAATGGAAGAAAATATTTGCAAACCA 1263
                            ----    i                  i                i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_95937585_9   1264 T 1264
                          
  L1M4_orf2#LINE/    735 T 735

Transitions / transversions = 1.88 (126 / 67)
Gap_init rate = 0.02 (13 / 735), avg. gap size = 2.15 (28 / 13)  

 628 14.35 0.96 14.35  chr1_95937585_95941804     3519  3727 (493)    L1M4_orf2#LINE/L1      728   908 (0)  

  chr1_95937585_9   3519 CAAACCATATCACTACCAATCTGATAATGGATTAATAACCAGAATATAGA 3568
                             i     --------         v   i vi  v          v 
  L1M4_orf2#LINE/    728 CAAATCATAT--------ATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_95937585_9   3569 AGGAGCTCAAACAACTCTATAGGAATGCTCTAGGAATTTGTTACTATAAA 3618
                          i  i   vv       v   iv  ----------------------   
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAA----------------------AAA 797

  chr1_95937585_9   3619 TTCCAATAATCCAATT-AAAAATGGACAAAATATTTGAATAGACAATTCT 3667
                         vv v     i      -        i    iv             v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_95937585_9   3668 CAAAAGAAGACATACAAGTGGC-AATAGGCATATGAAAAGGTGCTCAGCA 3716
                          v        i      i    -    i   i        i      i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_95937585_9   3717 GCACTGATAAT 3727
                         v  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.00 (15 / 15)
Gap_init rate = 0.02 (4 / 181), avg. gap size = 8.00 (32 / 4)  


2777 28.19 1.04 0.46  chr1_95973984_95980618     5282  6143 (492)    L1M4_orf2#LINE/L1        1   867 (41)  

  chr1_95973984_9   5282 TGGAAAAACATTCCATGCTCATGGATAGAAAGAATCAATATAATGAAAAC 5331
                               i i  i     i        v i    v i     vi v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_95973984_9   5332 GGCCATACTGCCCAAAGTAATTTATACATTCAATGCTATCCCCATCAAGC 5381
                            v     v      v i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_95973984_9   5382 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5430
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_95973984_9   5431 ATGGAACCAGAAAAGAGCCCTTATAACCAAGACAATCCTAAGCAA-ATGA 5479
                               viiv  ii  v  vvv   i    i      i i iv  - v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_95973984_9   5480 ACAAAGCTGGCA---TCACGCTACCTGACTTCAAACTGTGCTTCAAGGCT 5526
                               i   vi---    i  v  ii i      viv i  v   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_95973984_9   5527 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5576
                                i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_95973984_9   5577 GTGGAACAGAA--GAGTGGCCTCAGAAATAATACCACACATCTACAACCA 5624
                         i     i    --   v v  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_95973984_9   5625 TCTGATCTTTGACAAAC-TGACAAAAACAAGCAACAGGGAAAGAATTCCC 5673
                         vi    i  i     iv-  v   i v  vv   ii          vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_95973984_9   5674 TATTTAATAAATGGTGGTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5723
                          v  i  i        v     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_95973984_9   5724 AAATTGGATCCCTTCCTTACACCTTATAGAAAAATTAACTCAAGATGGAT 5773
                           i     i    v   i     v    v              i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_95973984_9   5774 TAAAGACTTAAATGTAAAACCTGAAACCATAAAAACCCTAGAAGAAAACC 5823
                         i ?    i         i v  i    i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_95973984_9   5824 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5872
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_95973984_9   5873 AACACCAAAAGCAATGGCAACACAAGCTCAAGTTGAGAAATGGGATCTCA 5922
                         i            vvi      v   vvv  i v  v    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_95973984_9   5923 GTAAAGTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAGAGTGAAC 5972
                         vi   i v  i i   i  ii vv    i  v    v  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_95973984_9   5973 AGGCAACCTACAGAATTGGAGAAAATTTTTGCAATCTACCCATCAGACAA 6022
                           i     i       v         v       vii ivi   v  i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_95973984_9   6023 AGAGCTAATACACAGAATCTATGAAGAACTTAAACAAATTTACAAGAAAA 6072
                         i ii  vi  iv      v   i       ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_95973984_9   6073 AAATTAACAACCCCATCAAAAAGTAGGGAAAGGGCATGAACAGACACCTC 6122
                          i iv  i     v  i?    i i  v     iiv    i     ii  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_95973984_9   6123 TCAAAAGAAGACCAACACATG 6143
                           v        ivv   v   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATG 867

Transitions / transversions = 1.32 (136 / 103)
Gap_init rate = 0.01 (9 / 867), avg. gap size = 1.44 (13 / 9)  


2868 27.54 1.78 0.56  chr1_96146801_96153456.rev     5269  6165 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96146801_9   5269 TGGAAAAACATTCCATCCTCATGGTTAGGAAGAATCAATATTGTGAAAAT 5318
                               i i  i    vi      v v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96146801_9   5319 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAA- 5367
                            v     v      v i  i  i        i  v  i  i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96146801_9   5368 --CTATTGACATTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTCA 5414
                         -- i vivi v  i  ii     v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_96146801_9   5415 CATGGAACCAAAAAAGAGTCTGTATTGCCAAGATAATCCTAAGCAAAAAG 5464
                         i      viiv  ii  vi v v  v     i i    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_96146801_9   5465 AATAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGTC 5514
                           i    i      vv   ii  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_96146801_9   5515 TACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGGAATATAGACC 5564
                             i   i   i    ii         i iv ii i  iv       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_96146801_9   5565 AATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAT 5614
                                i    iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_96146801_9   5615 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGAG-AAAGGATTCCCT 5663
                         i    i  i     ivv  v   i v  vv     i -    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_96146801_9   5664 ATTCAATTAGTGGTTCTGGGAAAACTGGCTAGCCATATCCAGAAAACTGA 5713
                         v     iv i    v      v      v  ?   i  v  i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_96146801_9   5714 AACTGTACTCCTTCCTTACACCTTATACCAAAATTAACTCAAGATGGATT 5763
                          ii  v  i   v   i     v     v             i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_96146801_9   5764 AAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAACCT 5813
                          ?    i         i v i     i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_96146801_9   5814 AGGCA-ATACCATTCAGAACATAGACATTGGCAAAGATTTCATGACGATA 5862
                            ?i- v i -   ivi  v v ivv v     v i    v iivv  i
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_96146801_9   5863 ATGCCAAAAGCAATTGCAGCAAAAGGCAAAATTAACAAAAGGGATCTAAT 5912
                          ii         vvv   i      iv     vi i   vv   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_96146801_9   5913 TAAACTAAAGGGCTTCTGCACAACTAAAGGA-ACTAGCATCAGAGTGAAC 5961
                         i   v v  iii   i  ii vv -      -    v  vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTC-AAAGGACACTATCAAGAAAGTGAAA 696

  chr1_96146801_9   5962 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 6011
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_96146801_9   6012 AGGTGTAATATCCAGAATCTATAAGAGA---CTTA-AATTTA-CAAGAAA 6056
                         i  vv vi          v     -   ---    -  i i -i  v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAA-AGAACTCTTACAACTCAATAATAAA 795

  chr1_96146801_9   6057 AAAACAA----CCCCATCAAAAAGTGAGTGAAGGATATAAAGAGACACTT 6102
                           i    ----   v  i?    i  i ii      v i  v     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_96146801_9   6103 CTCAAAAGAAGACATTTACATGACCAACAAACATATGAAAAAAAGCTCAC 6152
                            v        i  vi v   i    i  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_96146801_9   6153 CATCACTAATCAT 6165
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


2655 24.16 3.34 5.39  chr1_96177074_96179400      908  1834 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96177074_9    908 TGGAGATACATTCTATATTCATGACTTGAAAGAATCAATATTGTGAGGAC 957
                             i v i  i i  i      iv   i    v i        v i  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96177074_9    958 GTCAGTTTTTTCCAGCTTGATGTACAGGCTCAATGCAATCACAATAAAAA 1007
                          v  i vi ii   iv     v     ii    i      v v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96177074_9   1008 TAACAGCAAGTTATTTTGTGGATATCAACAAAATGATTCTGAAGTTTATA 1057
                          vv    vivi v     ii  v  ii    iv    i  i  i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_96177074_9   1058 AGGAGAAACAAAAGACCTAGAATAGC-GACACTATATTGAA------GAA 1100
                         v   i vi   ii    i        -i v  v  v     ------   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_96177074_9   1101 TAAAGTCAGAGGACTGACACT-ACCAACTTCAAGACATACCATAAAACTA 1149
                         i     ii       v     -v    i     i  v   i i   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_96177074_9   1150 CA-CAATCAAGACAGTGTGGTGTTGGCAAATAAACAGGCAAATAGATCAA 1198
                           -i                 ii     v vii i  i  v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_96177074_9   1199 TGGAAAAGAATAAAGAGCCCAGAAAAAAACCCACATAAATATAGTTAACT 1248
                              v     vi    i       v       i i vv   i  i  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_96177074_9   1249 AATCTTTTATAAAA-----ACGAATAT--AATGGACAAAAGATAATCTCT 1291
                         i  i  iv i  ii----- v  vi  --     iv   ii   i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_96177074_9   1292 TTAACAAATGGTGCTGGGACAATTGGACAACCACACATAAAAAAAAAAAA 1341
                          i                    i    i ?     iii    i  vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_96177074_9   1342 --GGAATCTAGAGACAGGGTTACAACCATA-GCAAACATTAACTCAAAAT 1388
                         --   vi i---v  v--- i   -     -i    v             
  L1M4_orf2#LINE/    451 TTGGACCCC---TACC---TCACA-CCATATACAAAAATTAACTCAAAAT 493

  chr1_96177074_9   1389 --ACCATAAACCTAGATAAATAAATAAATAACTAAATAAGTAATAAGCCT 1436
                         -- i  ? i     i  i------------------    -----   - 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATG------------------TAAG-----AGC-T 519

  chr1_96177074_9   1437 AAATGTAATATTATATATATACATATAAAACTCCTAAAAGAAAACACAAG 1486
                            -----------------  -          i  i         i i 
  L1M4_orf2#LINE/    520 AAA-----------------AC-TATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_96177074_9   1487 AGAACATCTAGATGACCGAGGGCACAGTAATGACTTTTTAGATGTATCAC 1536
                         ? v v    vvi     vv   ivvi i    ii  i      i iv   
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_96177074_9   1537 CAAAAATA-AAGCCCATAAAAGACATAATTGATGAGCTGGATTTCACTA- 1584
                              ii -    v- i      v v   v   i ii    i    ii -
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCA-ACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_96177074_9   1585 --TTAAAAACTTCCGCTCTATGAAAGACACTGTCAAGAATAGGAAAAGAC 1632
                         --          ii iv  vii  i      i       viv        
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_96177074_9   1633 AAACCACAGACTGGGAGTGAATATTTGTAGAAGATATATCTGATAGAAAA 1682
                           v       v      vi        i i vv            iiii 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_96177074_9   1683 CTGATATTCCGAATATACAAAGAACTCTT-CAGATTAA-AATGTAA-GA- 1728
                           vi   i v       i           -  iv i  -   iv  -  -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_96177074_9   1729 AAACAACTTGATTTAAAAATATGCAAAAGACATGAATGGACACATCACCA 1778
                            i   iii   ?      iv     i  iv     i    iv  v   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_96177074_9   1779 GAGAAGATATAATGATGAC-AA-AAGTATATGAAAAGATGCCCAAAATCA 1826
                         i          vvi   i -  -   i i            i   v    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_96177074_9   1827 TTTTTCAT 1834
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.89 (144 / 76)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.12 (81 / 26)  


3336 26.43 0.44 0.44  chr1_96229405_96235810.rev     5008  5915 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96229405_9   5008 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5057
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96229405_9   5058 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5107
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96229405_9   5108 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 5155
                          v   iivi i  i  ii     -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_96229405_9   5156 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5205
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_96229405_9   5206 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5255
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_96229405_9   5256 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAGC 5305
                                 i   i    ii         i iv ii i   v       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_96229405_9   5306 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCTTATCTACAACT 5353
                                i    i--    i  --        vv  iivi  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_96229405_9   5354 ATCTGATTTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAAGGATTCC 5403
                          vi       i     ivv  vv  i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_96229405_9   5404 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5453
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_96229405_9   5454 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5503
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_96229405_9   5504 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5553
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_96229405_9   5554 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5603
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_96229405_9   5604 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5653
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_96229405_9   5654 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5703
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_96229405_9   5704 AGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5753
                           i         i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_96229405_9   5754 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5803
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_96229405_9   5804 AAACAAACAACCCCATCAAAAAGTGGGCAAAGAACATGAACAGATACTTC 5853
                          i     i     v  i?    i         i iv    i   i i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_96229405_9   5854 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5903
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_96229405_9   5904 ATCACTGTCCAT 5915
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2804 23.77 5.60 1.94  chr1_96243792_96248853.rev     3701  4575 (487)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_96243792_9   3701 GGGAAAACATCTCATGTTCATAGATCAAAAGAATAAATATCATTAAAATG 3750
                           i  i i   i         i   iii    v v     ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_96243792_9   3751 ACCATACTGACCAAACTAATCTAGAG--TCAATGCAATCCCTATCACAAT 3798
                         i v     vv     i i     v  --    i             v   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_96243792_9   3799 GCCAA-TGTCATTTTTCACAGAATTAGAACAAA---ATCCTAAAATTCAT 3844
                         v   i-  i -     ii     v v  -   i---              
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr1_96243792_9   3845 ATGGAACCAAAAAAGAGCTCATATAGCCATAGCAATCCTGAGCAAAAAGA 3894
                               viiv  ii  v iviv       v i     i   ---      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGA 196

  chr1_96243792_9   3895 AAAAAAAAGTGAAAAGCATCACATTATCTGATTTTA-----TATTATAAG 3939
                          i  v     vii i vv     i vi ii    i -----  i  i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_96243792_9   3940 GCTATAGTAACCAAAACAGCATGGCACTGGTGTAAA-ACAGACACATAGC 3988
                             i     i   i    ii   i     ii   i- i     i    v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_96243792_9   3989 TTAATGGAACAGAATAAGGAACTCAGAAATA----------TTTACAGCC 4028
                          i       i     vii  iii        ----------    ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_96243792_9   4029 AACTGATCTTTGACAAAGCCAACAAGAACATACACTGGGAAAAGAAGACT 4078
                           i    i  i     i viiv     v   v  v    i      v v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_96243792_9   4079 GTCTTCAATAAATTGTACTGGGAAAATTGGATAGTCACATGCAGAAGAAT 4128
                         v i     i    v  i      v  i      ?i        i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_96243792_9   4129 GAAAT-GAACTC-----TCTCACCATACA-AAAAATCAACTCAAGATGGA 4171
                            i - i  i -----  v       i -      i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_96243792_9   4172 TTAAAGACTTAAATGTAAGACCCCAAACTATAAAAATAGTAGAAGAAAAC 4221
                          i ?    i           v iv           v vv           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_96243792_9   4222 ATAATGAAAATTCTTCTGGACATTGGTGTATGCAAAAAAATTATTAT-TA 4270
                            iv?iv  v     vv   v    vv  v    viiv-  v   v-  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATA 595

  chr1_96243792_9   4271 AGATGTCAAAAGCACAGGCAACAAAAAGAGAAGTAGACAAATGGGACTTA 4320
                         v  iii          i         ii i  i    i    v      v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_96243792_9   4321 AACAAAA----AAGCT-----GCTACACAGCAAAATA--AATAGAGTGAA 4359
                          v     ----  i  -----   v  v  v v v  --  v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_96243792_9   4360 GACACAACCTGT----TAGGAAAAAAAATT-GCAAAATATTCATTTGACA 4404
                         i v      iii---- i   i    v   -     vi  vi  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_96243792_9   4405 GGGTACTAATATCCAGGATATACAAGGAACTCAAATAACAAC--AACAAC 4452
                         i  v   vi       i     i  i      --- v     --  i  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTC---TTACAACTCAATAAT 792

  chr1_96243792_9   4453 AAAAATCCAAAATTTATAAAACCTCCATTAAAATGTGGGCAAATGTCTTG 4502
                              vv    -----   --- i v   ?   vi        v vi   
  L1M4_orf2#LINE/    793 AAAAAGACAAA-----TAA---CCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_96243792_9   4503 AATAGACATTTTTCAAAAGAAGACATACAAATGGCTAACAGGTATATGAA 4552
                                    i  v        i           i  i i i i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_96243792_9   4553 GAAATGCTCAA-ATTACTAATCAT 4575
                         i i        -  i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (128 / 76)
Gap_init rate = 0.03 (24 / 907), avg. gap size = 2.75 (66 / 24)  


 610 29.78 3.56 0.00  chr1_96377866_96380873     1388  1612 (1396)    L1M4_orf2#LINE/L1        4   236 (672)  

  chr1_96377866_9   1388 AAAGATAAAGCATATTCATGAAATGGATAACT----GTT-TTA-GA-GAC 1430
                                vvv   i      i v    vi   ----i  -   -  - i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_96377866_9   1431 AAGAGTTCTCTATTTAGTCAGTAGATTCATGACAAACCCAACCAAAATTT 1480
                           v v i i v v  ii  vii       vvi   v   v i      ii
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_96377866_9   1481 CAAAAGGTTGGTTTGTGAAAGTTGACAAGATGATTCTAATATTTATATGG 1530
                           ivv vi vv    iii  i        v    i    v   i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_96377866_9   1531 ACATACAAAGGTCTAAGAATAGCCAAGATA-TCTTGAAGAAGAGAAATGA 1579
                          v  i   i  v iv           i i -       i    ii  ii 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_96377866_9   1580 AGGTGGAGAAGTTACACTGTAAGATATCAAAAC 1612
                           v     i v i     vivvi  v       
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

Transitions / transversions = 1.23 (37 / 30)
Gap_init rate = 0.02 (5 / 233), avg. gap size = 1.60 (8 / 5)  

 751 27.65 9.90 5.80  chr1_96377866_96380873     1922  2507 (501)    L1M4_orf2#LINE/L1      256   865 (43)  

  chr1_96377866_9   1922 ATCAAAACCATGAAGTTTTGGCATAAAAACAAACAAAAAAAGCAGACAAA 1971
                              i  vi  vi  vi        ii i i   v v i v  - iii 
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA-ATGGA 304

  chr1_96377866_9   1972 AATAACGGAATACAAATTCCAAAAAGAGATTTACAC-TGAATAGT-AATA 2019
                          -  ---    vv i v    i   v i iii i  - vv  i  -   v
  L1M4_orf2#LINE/    305 A-TA---GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_96377866_9   2020 AAAGTGAAATAAAAATGATGTTA----CATTGCAGTGGGGATAGACATTG 2065
                         i vv vvi i  i--- i  ii ----    -  i      v   -----
  L1M4_orf2#LINE/    351 GATTTTCGACAAG---GGTGCCAAGACCATT-CAATGGGGAAAGA----- 391

  chr1_96377866_9   2066 ATAATTTT----ATAAATGATG---GGCCAACTGGATATTCATTTGC--- 2105
                            i i  ---- i     i  ---  v          ?i  iv   ---
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_96377866_9   2106 ------------GGCCCCTTCCTCACACCATACATAAAACCAAATCCAGT 2143
                         ------------ i     v            i i    viv  ii  iv
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_96377866_9   2144 ATG-ATTATAGATATAAGTAGGACAGGTAAAAATAAATTTAAAATAAATA 2192
                            -  i ?   iv   i ivi v  v     v  ----     ------
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA----TAAAA------ 531

  chr1_96377866_9   2193 AATAAGCTTTGAGAAGAAAATATAAGAGAACATCATAATGAG-TTGGGTT 2241
                         ------  i v         i   i ? v v   v vi   v-       
  L1M4_orf2#LINE/    532 ------CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_96377866_9   2242 AG-CAAAATTTTCTTATATAGGATAC-AAAA--ATAGG------AAGTCA 2281
                           -   viv       v   v  i  -    -- i i ------   vv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_96377866_9   2282 AAGTGGACAA---------CGTTAGAATTGAGAACTTTAAATGAT-CAAA 2321
                           i i  i  --------- i i i    i i      vi-  v -    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAA 674

  chr1_96377866_9   2322 AAATACTCCTAAGGAAGATAAAACAACAACCCACAAGATGGTAATAGTTA 2371
                         ii i   vii   i   - i   vi          ii    v iv iv  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAG-TGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_96377866_9   2372 TTTTCAATACATATACCCAACAAGGGAGTCCTATTCAGAACATATAAAGA 2421
                            v   vv      i ii i      v iv   i     i         
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_96377866_9   2422 TCTTCTACAAATCAATAA--AATAGA--AATAATC--ATTTTGTTAAATG 2465
                         v  ii     v       --  v   --     i --   ?vi--     
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA--AAATG 821

  chr1_96377866_9   2466 TAGAAAA-ACTTAAACATGCATGTCCCAAAATAAAATG-ACAAA 2507
                         viv   i- i  i  i vi   v  i v   v  i  i-     
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

Transitions / transversions = 1.51 (95 / 63)
Gap_init rate = 0.05 (30 / 610), avg. gap size = 3.07 (92 / 30)  


3331 25.80 0.77 0.66  chr1_96418601_96425193.rev     5196  6102 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96418601_9   5196 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5245
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96418601_9   5246 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5295
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96418601_9   5296 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 5342
                          v   i-       i  -i     -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr1_96418601_9   5343 CATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAA 5392
                                  viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_96418601_9   5393 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5442
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_96418601_9   5443 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5492
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_96418601_9   5493 TCAATGGAACAGAAC--AGAACCCTCAGAAATAATGCCACTTATCTACAA 5540
                                  i    i--   ii  --        vv   ivi  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_96418601_9   5541 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5590
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_96418601_9   5591 CCCTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAG 5640
                         vi  v  i  i              v  i   v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_96418601_9   5641 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5690
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_96418601_9   5691 GATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5740
                            i ?    i    ii v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_96418601_9   5741 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5790
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_96418601_9   5791 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5840
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_96418601_9   5841 CATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5890
                            i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_96418601_9   5891 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5940
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_96418601_9   5941 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5990
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_96418601_9   5991 AAA--CAAACAACCCCATCAAAAAGCGGGCAAAGGACATGAACAGACACT 6038
                            --    i     v  i?    ii          iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_96418601_9   6039 TCTCAAAAGAAGACATTTATGCAGCCAAAATACACATGAAAAAATGCTCA 6088
                             v        i  vi viii     v vi          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_96418601_9   6089 TCATCACTGGCCAT 6102
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (136 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


1579 23.81 7.94 3.33  chr1_96441388_96443338      883  1512 (439)    L1M4_orf2#LINE/L1      250   908 (0)  

  chr1_96441388_9    883 ACAGCTAAACAATATCAATGTGGTATCAATGTCATGAGAGACAAACAGAT 932
                             -   v   v -  i       iiiiii v v  v     v i    
  L1M4_orf2#LINE/    250 ACAG-TAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_96441388_9    933 AAAATGGGAAAGAAT--ACAGGCCACAAATAGACCCACACATATATGGAC 980
                         v  -   i v     -- v  v   v     i     i    v     v 
  L1M4_orf2#LINE/    298 CAA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_96441388_9    981 TGCTTATTTTTGACAAAGGTGCAAAAAAAATTCAGTGGGGAAAGAATAG- 1029
                         vii v     i     i     v  i vv     i              -
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_96441388_9   1030 CTTT--AAAAAATGCTGTTATAAAAACCTGTTATCCATATGCCAACATAA 1077
                             --  v     v  i ivi v   iv v  ?   i    v  - v  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-AGAA 445

  chr1_96441388_9   1078 ATAAAT---ACCAATGCATACACAATCTAATTTATATAAAAATTAATCCC 1124
                         vv  i ---   vv i v -    -- i ---    i         ii v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCT-CACA--CCA---TATACAAAAATTAACTCA 489

  chr1_96441388_9   1125 AAATGGATCATAGACATAAATATAAAACCTAAAACTGTAAAACTTGTATA 1174
                                   ?    v     i   i v        i       iv  v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_96441388_9   1175 AGAAAACAAACGAGAAAGCCTTTATGACCTTGGGTTAGGCAA-------- 1216
                                 v v ? v  ii   ii                  --------
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_96441388_9   1217 -AGA---------AAAA-------------AATTAAAAATTGATAAATTA 1243
                         -   ---------    -------------  vv      v        i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_96441388_9   1244 GACTTTATCTAAATTTAAAACCTCTGTTCTT--AAAGACATTGCTAATTG 1291
                              i   v     v     i i   v   --  i    i iii  vvi
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_96441388_9   1292 GATGAAAACATAATTTTCTAC----TGGAACAAAATATTTGCAAGT-ATA 1336
                         ii      v i  i--- i  ----   i v             i -   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAAC---CCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_96441388_9   1337 TGTCTGATAATAGGCTTGCACCCAGCACATACAAAGAAATCTCAAAACTC 1386
                          i        vi i    i i    v i   i      v   i v     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_96441388_9   1387 AAAAGTAAGAAATCAA----CCCAATAAACAACTGAGCAAAAGATTTAAA 1432
                           v i   i  iv   ----      v? v  v  i     i     i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_96441388_9   1433 CAGACACTTGTCCAAAGAGTGCATGAAGAAAAATAATTTTAAGTAAGGCA 1482
                         i     i  v        ivii  ---- v    iiii--- i    -  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATAT----ACAAATGGCC---AATAAG-CA 878

  chr1_96441388_9   1483 CATAAAAATATATATAGCATTATATATATT 1512
                            i    v  iivi i   i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (83 / 63)
Gap_init rate = 0.03 (22 / 659), avg. gap size = 3.23 (71 / 22)  


3103 23.09 2.84 5.58  chr1_96450093_96454951.rev     3074  3987 (871)    L1M4_orf2#LINE/L1        1   889 (19)  

  chr1_96450093_9   3074 TGGAAAGATATCT-GTGTTCATGGATTGTAAGTATTAATATTGTTCAAAT 3122
                                     i-i             v   vv           v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96450093_9   3123 GTTCATATTACCCAGAGCAATGTATAGAGATTCAATGCAATCCATACCAA 3172
                          viv   i v    i vii  v  i   --     i       v  i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGA--TTCAACGCAATCCCTATCAA 98

  chr1_96450093_9   3173 AATTCCAA-TGTCATTTTTTCACAAAAATAGAAAAAGCAATGCTAAAATT 3221
                            i   i-  i --     ii  i    v  v  ivii  v        
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_96450093_9   3222 AATATAGAACCACAAAAGACCCTGAGTAGCCAAAGCAATCTTGAGCAAAA 3271
                         v    i   vii   ii     v  i        i         iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_96450093_9   3272 GGAACAAAGCAAGATGTATCATAATACTTACAGTATTTGTTCTGTACTGT 3321
                         i        ivi  v ---------   i   v ------  i-------
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG---------ACTCACACT------TCC------- 224

  chr1_96450093_9   3322 AGTATAGTATAACATTGTATTGCAATTTCAAATTATACTACAAAACTAAA 3371
                         ----------------------          viv         i   v 
  L1M4_orf2#LINE/    225 ----------------------CAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_96450093_9   3372 GTAATCAAAACAGCATGGTACTGACATAAAAATGGGCATATAGA-CAATG 3420
                                 i    ii        i     ii  i i        -     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_96450093_9   3421 AAACAGAATAGAGCAGCTCAGAAATGAATTCATGCATTTATGGCCAATTG 3470
                         i  i     v   -  ii       i  ii   i         i      
  L1M4_orf2#LINE/    303 GAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_96450093_9   3471 ATCTTTGACAGAGATGTCAAGAGTATACAATGGAGAAAAGATGGTCTCTT 3520
                           i  i    ii i  i     vi  v      i    ii  i    i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_96450093_9   3521 TAATAAACAATG---GGAAAATTTGTTTTCTACCCACAGAAGAATGAATT 3567
                         i  i   iii  ---   v  i v v v? i  vii  i         v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_96450093_9   3568 TGGACCCTTATCTCACACCATAAACAAAAAATCCACTCAAAATGGATTAA 3617
                                i  i           v       - iv             i ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAW 500

  chr1_96450093_9   3618 AATCTTAAACATAAAAACTGAAACTCTATAATTACTAGGAAAAAA-ATTG 3666
                          iv i    ii   i i  i     v  v  i vi   i i    -  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_96450093_9   3667 AGGGAAAACTACATAACATTGGTCTGGGCAGTGATGTTTTGAATATGATC 3716
                         i? v   v  v i i  v    vi i    i  i v i  ii      iv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_96450093_9   3717 CTAAAAGCA---------------AAAATAGATAAATCTGA--TCATTTC 3749
                          i       ---------------             iv  --    i-v
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC-A 649

  chr1_96450093_9   3750 AAACTAAAAACCTCTGTGCAGCAAAGGAAATAATCAACAGAATGAAGAGA 3799
                            i       i i     vv       v iv     v i i    i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_96450093_9   3800 AAATCTACAGAATAGGA-AAAATATTTGTAAGCCATACATCTTATAAGGG 3848
                         v  i i       i   -          i  ii    i    v       
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_96450093_9   3849 GATAATATTTAAAATACATAAGCAACTAA-ACAACTCAATAGTGAAAAAA 3897
                         iv vi   ii i    i    iv    vv-           i i    i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_96450093_9   3898 CAAATAACCTGATTAAAAAGTGGATGAAGGATCTGAGTAGACATTTCTCA 3947
                                  ii   ?    i   iii      i   i            v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_96450093_9   3948 AAAGAATACATACCAATGGCCAATAGGTGTATGATATGAT 3987
                               v i    v           i iii    v v   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

Transitions / transversions = 2.14 (141 / 66)
Gap_init rate = 0.02 (17 / 889), avg. gap size = 4.53 (77 / 17)  


2290 23.71 2.99 9.38  chr1_96461097_96466589.rev     4033  5002 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96461097_9   4033 TGCAAAAAC-TTCCATGCTTATGGATAGGAAGAATCACTATTGTTAATAT 4081
                           v   i i- i     i i      v      v i v         v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96461097_9   4082 GGCTACAGCACCCAAATCAATGTATAAATTCAATGCTATTCCCATTAAAC 4131
                            v i viv       ii  v  i i      i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96461097_9   4132 TACCATTGAAATTCTTCATGGAACTAAAACCAACCAAACAAACAAAAAGC 4181
                          v   -----------------i  i------------------------
  L1M4_orf2#LINE/    101 TCCCA-----------------GCTG------------------------ 109

  chr1_96461097_9   4182 AAAAAAAAAAAAAAACCCTATTTTAAAATAGTAAAATAGTTAAAAAACT- 4230
                         ----------------   v    ------ i i  --i  i v  i  -
  L1M4_orf2#LINE/    110 ----------------CCTTTTTT------GCAGAA--ATTGACAAGCTG 135

  chr1_96461097_9   4231 ATTTCAAAATTCATGTGAAACGAAAAAAGAGCCTGAATACCCAAGGCAAT 4280
                           iii         i  i  vviv  ii  v  v     v    ii    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_96461097_9   4281 CCTAAGCAAAAAGAACAAAGCTGGAGGCATTACACTAACCGACTTCAAAT 4330
                          i i iv  i          i      vv i     vv  i i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_96461097_9   4331 TATATTACAGGGCTACAGCA------------TGGTACTGGCACAAAAAC 4368
                         iv  i    ii       i ------------           i  ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_96461097_9   4369 AGACACATAATAGAG-AATTGAACAGAATAGAGAACCCAGAAATAAGGAC 4417
                              i   ---  v-   v   i     v    ii          --  
  L1M4_orf2#LINE/    286 AGACATATA---GATCAATGGAATAGAATTGAGAGTCCAGAAATAA--AC 330

  chr1_96461097_9   4418 ACATGC--TTAGAACTATCTGATCTTTGACATACCTGACAAAAAACAAGC 4465
                         v   i --   viiii vi    i  i    vivv  v   i v-  vv 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTC 379

  chr1_96461097_9   4466 AATGGGGAAAGAATC-CCTATTCAATAAATGGAGCTGGGATAAAAGACTA 4514
                                       v-i  v     i      v       i  vv iv  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_96461097_9   4515 GCCATAGGCAAATGATTGAAACTGGACCACTTTCTTACACCATATACGAA 4564
                         ?   i v     v  v    ii      v  vi  i           i  
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_96461097_9   4565 AATTAACTCAAGATGGATCAAAGACTTAAATGTAAAACCCAAAACTAAAA 4614
                                    i        ?    i         i v i       v  
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_96461097_9   4615 AACAAACAAACAAACAAAAACCCTGGAAGACAACCTAAGCAATACTATTT 4664
                            -----------------i i i     v   v  i ?ivv v v  i
  L1M4_orf2#LINE/    530 AAC-----------------TCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_96461097_9   4665 AGGATATAGGCACAGGCAAGCATTTCAT-GATGAAGACACCAAAAGCAAT 4713
                         iv  iv v  vvi      vvi    v -   - v             vv
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACA 611

  chr1_96461097_9   4714 TGCAACAAAAGCAAAAATTGATGAAT-GAATCTAATTGAACTAAACAGCT 4762
                         v          v      v   i   - i ii v  ii  v v  v i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_96461097_9   4763 TCTGCACAGCAAAAGAAACTAT--AAACAATAAAAAGGCAACCTACAGAA 4810
                          i  ii vv    i  v     -- i v i i     i     i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_96461097_9   4811 TGGGAAAAAATTTTTGCAAACTATGCATCTGGAACAAAAGTGTAATATCA 4860
                              i     v        ii  ii     -- i  ii vv vi    v
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTG--ATAAGGGACTTGTATCC 759

  chr1_96461097_9   4861 AGCATCTATAAGGAACTG----AAATCTACAAGAGAAAAACAAGTGACCC 4906
                           v  v     i     v----  v  v i  v i   i    i i    
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_96461097_9   4907 CATTAAAAAATGGGCAAAAGACATGAACAGACACTTTTCAAAAGAAGACA 4956
                         v   ?             i  iv    i     i  i  v        i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_96461097_9   4957 TACATGTGGCCAAGAATCA--TGAAAAAA-GCTCAATATCATTGATCAC 5002
                             vi       v  v  --      i -      i    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (128 / 98)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 5.45 (120 / 22)  


 395 17.14 10.48 0.95  chr1_96498111_96502772     3026  3130 (1532)    L1M4_orf2#LINE/L1      794   908 (0)  

  chr1_96498111_9   3026 AAAAAATAAA------AAT--AAAAATAGGCAAAGAACCTGAGTAGACAT 3067
                             i i   ------   --      i       i ii   i       
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_96498111_9   3068 TTCTCAGAGGAAGACATACAAATGGCCAA---GTATATGAAAAAAATGTT 3114
                              vi i     i              --- i i       i -  i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr1_96498111_9   3115 CAATATTGCTAACCAT 3130
                            i  ii????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 17.00 (17 / 1)
Gap_init rate = 0.03 (4 / 115), avg. gap size = 3.00 (12 / 4)  

3318 23.31 2.07 3.38  chr1_96498111_96502772     3252  4169 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_96498111_9   3252 GAAAAATGTCCTGTGTTAATGGACTGGAATAATTAACATTGTTTGTATAT 3301
                             i  i   ii    v     i     v v    i      viv  iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_96498111_9   3302 CCATAGTACCCAAAGTGATCTACAGATTCAATGCTATCCCTA---AAGTT 3348
                          v   v v      v                i  v       ---  i i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_96498111_9   3349 CCAATGGTATTTTTTAAAGAAATAGAAAAA-TAATCATAAAATTTTTATG 3397
                            iiv iv      iv      v  v  i- i   v       iv    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_96498111_9   3398 GAACCACAAACGACTTTGAATAGCCAAAGGAACCTTAGGGGAAAAAAAAA 3447
                            vii   iv   iiv           iv  i   --- i    i  i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT---GAAAAAGAAGA 199

  chr1_96498111_9   3448 ACACCAAAAAATCAAAACAAAACTAAGCTGGAGGCATCACACTACCAAAT 3497
                            ---------------------   i      vv       v  v   
  L1M4_orf2#LINE/    200 ACA---------------------AAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_96498111_9   3498 TTCAAAATATGCTACAAAACCATAGTAATAAAAATAGCATGGTATGGGCA 3547
                                iv i       i i i      v  i i  ii     iv    
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_96498111_9   3548 TAAAAACAGACACATCAACCAATGGAACAGGATTGATAGCCCAGATATAA 3597
                            ii i     i  vi i        i  i     v  i     v    
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_96498111_9   3598 ATCCATGCATTTATGGTCAATTGATCTTCAGCAAAGTTGCCAAGAACACA 3647
                          i    i                  i   ii   i v        v  iv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_96498111_9   3648 AAATGAGAAAAGGATGGTCTCTTCCATAGATGATGGTGGGAAAACTGTAT 3697
                         v    i i    i  i    i   v i i   i  v     v     v  
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_96498111_9   3698 ATCCACATGCAGAAGAATGAAATTGAATGCTTATTTCACACCATATACAA 3747
                          ?         i         i   i iv i  ii               
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_96498111_9   3748 AAATCAACTAAAAATGAATTAAAGATTTAAACATAAGGCCTGAAGGTATA 3797
                             i    v      i  i ?   ii    ii    iv  i  iv    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_96498111_9   3798 AAAATACTAGAAAAAAATCATAGGGTGAAAGTTCCATGACATTGGTCTAG 3847
                            v vi     i    -      ?vv   vi i i    v    vi   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAA-CATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_96498111_9   3848 GCAATGATTCCTTGGATATGAACCCAAAAACACA-GTAACCAAAAAAAAA 3896
                               i  i   i       vv      i    - i   v   i     
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_96498111_9   3897 AAAAA-AAA-----------CAAATTCTAAAAAGTTTCTGCACAGCAAAG 3934
                          v i -   -----------    v -      v   -  ii vv     
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTT-TGTGCTTCAAAG 675

  chr1_96498111_9   3935 GAAACAGTCAACA--GTGAAGACACTACCCATGGTTTGAGAAAAAAATGT 3982
                           v  vi    v --     i v  v     ii vv  i  i    - i 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TAT 724

  chr1_96498111_9   3983 TTTCAAACCATACACCTAAGTTATGGGGTTAAGTATCCAAAATATAGAAG 4032
                           v    i    i i  i --  v   ii v-       i      v  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGA--TAAGGGACTT-GTATCCAGAATATATAAA 771

  chr1_96498111_9   4033 GAATGCAAATGACTCAATAGCGAGAAAACAAATAATCTGATTTTAAAATA 4082
                            iv vv ii        iii i  i        i ii   ?v     i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_96498111_9   4083 GGTAAAGAATCTGAGTAGACATTTCTCAGAGGAAGACATACAAATGGCCA 4132
                           i    i  i   i            vi i     i             
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_96498111_9   4133 ACAAGTATATGAAAAAATGTTCAACACCACTAACCAT 4169
                          i   i i       i   i      i  ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (135 / 75)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 3.57 (50 / 14)  


2576 25.48 2.43 0.90  chr1_96520959_96522696.rev      467  1247 (491)    L1M4_orf2#LINE/L1      116   908 (0)  

  chr1_96520959_9    467 TTG-AGGAATTGCCACACTG-TCTTCCA---CA-ATGGT--TGAAAGAG- 507
                            -  i     v  vi   -  i vv ---  -    v--  v   i -
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_96520959_9    508 CCC-GTATAGCCAAGGCAATCCTAAGCAAAAGGAACAAAGCTAGATGCAC 556
                            - v        ii     i i iv  i i        i i  v -  
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-AC 214

  chr1_96520959_9    557 -CATGCTACCTGACTTTAAACTATACTATAAGGCTACAGTAACCAAAACA 605
                         -  ii  v  ii i  i   viv     i  i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_96520959_9    606 GCATGGTACTGGTACCAAAACAGACATATAGACCAATGGAACAGAACAGA 655
                          ii         i iv ii i           i        i    iv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_96520959_9    656 GACCTCAGAAATAACACCACACATCTACAACCATCTGATCTTCAACAAAG 705
                           vii         vv   i    i  iiii  vi    i   i    i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_96520959_9    706 CTGATAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGC 755
                         v  vi  i v  vv            i  vvi  v  i  i         
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_96520959_9    756 TGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAACTAGACTCCTCCTT 805
                              v      v  ?   i     i  i v    ii i   i   v i 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_96520959_9    806 CCTTACCCCATATACAAAAATGAACTCAAGATGGATTAAAGACTTAAATG 855
                          ---  v              v       i      i ?    i      
  L1M4_orf2#LINE/    465 C---ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_96520959_9    856 TAAAACCCAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCAT 904
                            i v i     i      vi i           v    ?i- v i - 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-T 560

  chr1_96520959_9    905 TCAGGACATAGGCATGGGCAAAGACTTCAT-GATGGAAACACCAAAAGCA 953
                           iv   v v  vv i     v ii   v -   ivi -           
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-CACCAAAAGCA 609

  chr1_96520959_9    954 ATTGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAG 1003
                         vvv          vv     v  i    v   ii v  i   v v  i i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_96520959_9   1004 CTTTCTGCACAGCAAAAGAAACTATCATAATAATTAACAGGCAACCTACA 1053
                             -  ii vv    i  v       vi v i v  v  i     i   
  L1M4_orf2#LINE/    660 CTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_96520959_9   1054 GTATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAGGTCTAATATC 1103
                          v            v       vii ivi      i  i  v  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_96520959_9   1104 CAGAATCTACAAGGAAATTAAACAA----AT--TTACAAGAAAAGCAGCC 1147
                               v  i  i   v ivv    ----  -- v v    v  ii i  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_96520959_9   1148 CCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGAC 1197
                          v  i?    i            v    i     i     v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_96520959_9   1198 ATTTATGCAGCCAACAAACATATGAAAAAAAGCTCAACATCACTGATCAT 1247
                           vi viii     i  i  i       i v           ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (115 / 80)
Gap_init rate = 0.02 (17 / 793), avg. gap size = 1.53 (26 / 17)  


2122 23.35 5.16 3.72  chr1_96549284_96550973      500  1197 (493)    L1M4_orf2#LINE/L1      201   908 (0)  

  chr1_96549284_9    500 CAAAGT--GAGAAGGGACATTGC--AATATCAAGACTTACTATAAAAATG 545
                               --   i vvv   i v --   v    i        i   iv i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_96549284_9    546 TAGTAATCAAGACAGCATGATATTGACACAAAGGT---TA-ATCGAACAA 591
                         i              ii  i  i  i  i  i i ---i -  v  v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_96549284_9    592 TGGAAAAGAATGGAGGGTCAAGAAATAGATCGATACAT----GAGGAATT 637
                              v     v   i   v       i i v      ---- ivv    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_96549284_9    638 GATTTTTAATCAAGGTGT-AAAACAATTTTCATTGG----AGAATAGTCT 682
                               ii iv i    i-  i  v   --  v   ----          
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATT--CAATGGGGAAAGAATAGTCT 398

  chr1_96549284_9    683 TTTCAAAAAATGGTGCCAGAACAATTGGATATCCATATACCAAG---T-A 728
                               v         ii i    i      ?   i  i v  i--- - 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_96549284_9    729 AGT---ACTCCTATC-CACA--ATATTGAAAAAGTAACTCAAAATGAATA 772
                            ---  i    i -    --    vv     v            i  v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_96549284_9    773 ATATACCTAAATGTTAAACCGAAAGCTATAGAACTTCAAGAAGAAAAGAT 822
                          ? v          v i v v   i     i    iiv         v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_96549284_9    823 AAAAGAAAATCTCTGTGATGGTATTTTAGAAAAAGAATTCCTAAATACAA 872
                          ii? v      ii    ivv ivv    iv  v iv   i  i   ii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_96549284_9    873 TACCAAAGTCACAATCCAAAAAACAAAAAGTGG-TACATTGGATTTTATG 921
                         i      iv     v v v    v     i i -  v      i  i  v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_96549284_9    922 AAAATTAAAAACTTCCCCTCTTCGAAAAACACTATTAAGAAAGTAAAAAA 971
                                       iiviv    i  ii       i        i    -
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA- 697

  chr1_96549284_9    972 GACAAGCCACAGACCAAAAGATAATGTTTGTAAATCACAAACAAAGTGAC 1021
                              v       viiii   v   i    i      i -----------
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA----------- 736

  chr1_96549284_9   1022 TTGCAAATTACTTATCTGATAAAGGATGTGTATCTACAATATGTAAATAA 1071
                         ------------          i   iv      i v     i    v  
  L1M4_orf2#LINE/    737 ------------TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_96549284_9   1072 CTCTCAAGACGTAATT-TGAAAA---AAAT----CATTTAAAAAATGGAC 1113
                             i vi  vi   v- i    ---    ----  v  ?        i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_96549284_9   1114 AAAAGATTTAAGTAGACACTTCATCAGCAAACATGTGTGGATAGCAAATA 1163
                            i     i i      i   vi  ivi  v  i iiii  i  v    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_96549284_9   1164 AGCACATAAAAAGATATTCAACATCATTTGTCAC 1197
                                i       ii         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (99 / 60)
Gap_init rate = 0.03 (19 / 708), avg. gap size = 3.26 (62 / 19)  


3252 27.20 0.44 0.44  chr1_96554582_96563866     3608  4515 (4770)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96554582_9   3608 TGGAAGAACATTCAATGCTCATGGATAGGAAGAACCAATATTGTGAAAAT 3657
                              ii i  i v   i        v      vii        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96554582_9   3658 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3707
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96554582_9   3708 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3755
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_96554582_9   3756 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCGAAGCCAAAAG 3805
                                viiv  ii  v  v v  vi    iv     ivi ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_96554582_9   3806 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3855
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_96554582_9   3856 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3905
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_96554582_9   3906 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGAATATCTACAGCT 3953
                                i    i--    i  --        vv iiv i  i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_96554582_9   3954 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4003
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_96554582_9   4004 CTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCT 4053
                           v  i  i              v  i   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_96554582_9   4054 GAAACTGGATCCCTTCCTTACACCTTATACAGAAATTAATTCAAGATGGA 4103
                            ii    i    v   i     v      i       i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_96554582_9   4104 TTAAAGACTTAAACGTTAGAACTAAAACCATAAAAACCCTAGAAGAAAAC 4153
                          i ?    i    i  v   i       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_96554582_9   4154 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4203
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_96554582_9   4204 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4253
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_96554582_9   4254 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4303
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_96554582_9   4304 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 4353
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_96554582_9   4354 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAGA 4403
                         i  i  vi          v  i  v      vv    v iv i  v  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_96554582_9   4404 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 4453
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_96554582_9   4454 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 4503
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_96554582_9   4504 ATCACTGGCCAT 4515
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

2891 27.69 0.99 1.21  chr1_96554582_96563866     6546  7455 (1830)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96554582_9   6546 TGGAAACTCATCCCATGCTCATGGTTGGGTAGAATCAATATTGTGAAAAT 6595
                               vvi        i      v v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96554582_9   6596 GGCCATACTGCCAAAAGCAATCTACAAATTCAG-GCAATTCTCATCAAAA 6644
                            v     v  v   vii       i     i-     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96554582_9   6645 TAACACCATCATTCATCATGGAACTAGAAAAAACAATCCTAAAATGTATA 6694
                          vv  v vv v  iv iiii   v v  v  ivii          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_96554582_9   6695 TGGAACCAAAAAAGAGCCCTCATAGCGAAAGCGAGACTAAGCAAAAAGAA 6744
                              viiv  ii  v  vvv     v   i i vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_96554582_9   6745 CAAATCTGGAGGCATCACAGTGCCTGATTTCAGACTATACTATAAGGCCA 6794
                             vi      vv     v v  ii      i viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_96554582_9   6795 TAGCCACTATAACAGCATGGTACTGGTATAAAAAGAGGCCCATAGACCAA 6844
                         i  iv ii vi    ii         i    ii v  i vi     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_96554582_9   6845 TGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAGCCAACT 6894
                              i     v    ii           v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_96554582_9   6895 GATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGAACACCCTAT 6944
                            i  i     i vviv   i v   vv i           i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_96554582_9   6945 TCAACCAATGGTGCTAGTATAATTGGCAAGCCACGTGTAGGAGAATGAAA 6994
                              v         i v i  i   vv ?    i  i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_96554582_9   6995 CTGGATCCTCATCTCTCACCTTATATAAAAATCAACTTGAGATGGATTAA 7044
                         i    i  ii i   v    v    i      i    ii i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_96554582_9   7045 GGACTTAAATCTAAGATGTGAAACTATAACAATTCT-AGAAGATGACATT 7093
                         i   i     v     vv i         -  i   -      vi    v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACATA 549

  chr1_96554582_9   7094 GGAAAAACCCTTCTAGAGCCTGGCTTAGGCAAGGATTTTATGACCAAGAA 7143
                           ?iv  vi    vv  v i   v        v i   iv iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_96554582_9   7144 CCCATAAGCAAATGCAATAAAAACAAGGATAAATAGATGGGACTAGCTGG 7193
                         v   v     v v    i    iv  ii   i   i  ---------   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT---------TGG 640

  chr1_96554582_9   7194 GACTTAATTTAACTGAAGAGCTTTTGCACGGCAAAAGGAACAGTCAGCTG 7243
                         -    v  iv  v v  i i      ii vv    i iv  vi   ivvi
  L1M4_orf2#LINE/    641 -ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_96554582_9   7244 AGTAAACAGACAACCCACAGAGTCGAAGAAA-TCTTCACAATCTATACAT 7292
                            i  v              i v i     - v  ii   vii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_96554582_9   7293 CCAACAAAGGACTAATATCCAGAATCTACAAGGAACTCTAACAAATCAGC 7342
                          ii i  i     vi          v  i  i       v    v   ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_96554582_9   7343 AAGAAAAAAACAA-T--CCC--TCAAAAAGGGGGCTAAGGACATGAGTAG 7387
                           v     i    - --   -- i?    iv    v     iv   i   
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_96554582_9   7388 ACAATTCTCAAAAGAAGATATACAAATGACCAACAAGCACATAAAAA-AT 7436
                            v     v                  i    i        i    -  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_96554582_9   7437 GCTCAATATCACTAATGAT 7455
                               i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (142 / 106)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  

2609 22.30 2.10 2.10  chr1_96554582_96563866     8081  8793 (492)    L1M4_orf2#LINE/L1      196   908 (0)  

  chr1_96554582_9   8081 AAGAACAAATTGGGAAGACTGACACTACCCAACCTCAAAGCTTACTATGA 8130
                                  v v   i    v     v     ii     i       ii 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_96554582_9   8131 AGCTAAAGTAATCAAGACAGTTTAGTACTGGC-TAAAGACTAGACAAATA 8179
                              v               v i        -   i  -      v   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATA 294

  chr1_96554582_9   8180 AATCAATGGGAAAGAAT--AGAGTCCAGAAATAGGCCCATATAAATATAG 8227
                         i        i v     --              ii      i vv   i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_96554582_9   8228 TCAACTGATTTT-GACAAAGGAGTAAAGGCAATACAATGGAGCAAAGAGT 8276
                             i       -     i  v iv   i v  v      i -     i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAAT 393

  chr1_96554582_9   8277 AAT--TTTCAACAAATGGTGCTGAAACAATTGGACATCCACATGCAGAAA 8324
                          i --                  ii    i    i ?         ----
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA---- 439

  chr1_96554582_9   8325 GAAAAAAAAATGAATCTAGACACAGACCTTACACCCTTTACAAAAATTAA 8374
                         ----   i      vi i   v vv    i     v v            
  L1M4_orf2#LINE/    440 ----AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_96554582_9   8375 CTCTAAATGCATCATAGACCTAAATGTAAAGTATAAAATTATAAAGCTCT 8424
                            v     v    ?              iivv     i      i    
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_96554582_9   8425 CAGAAGACAATGTAGGAG---ACTTTGATGACGTCAGGTATGGCAATAAC 8471
                         i      v  ii    ? --- ii  vi    v ii   vv      iii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_96554582_9   8472 TTTTTATATATTGTACCGAAGGCACAATTCATGAAAGAAATGATTAATAA 8521
                           i   v    vii   i  i      viv ii       vi  vi    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_96554582_9   8522 GCTAGACCTCACTAAAATTAAAAACTTCTGCTCCGCAAAAGACAATGTTA 8571
                         ii i   i   ii              i  iv iv    i    v i i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_96554582_9   8572 AGAGACTAAGAAGACAAGCCACAGACTGGAAGGAA-TATCTGCAAAAGAC 8620
                            i v i i       v       v   i  i  -   i      vv i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_96554582_9   8621 ACATCTGGTAAG--ACTGTTAACCAAAAAACACAAAAGACTCATTA-AAT 8667
                          i     i    --   vv  v   i  v i i   ii    -   -  i
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC-TTACAAC 784

  chr1_96554582_9   8668 TCAACAATAAGAAAGAAAAGAAACAACACAATT-AAAAATGGGCCAAAGA 8716
                             i     -     v  --- i   v     -          v  i  
  L1M4_orf2#LINE/    785 TCAATAATAA-AAAGACAA---ATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_96554582_9   8717 CCTTAAGAGACACCTCATTAAAGAAAATATACAGATGCTAAATA-GCATC 8765
                         ii v  v     ii  vii      i       i   viv    -   iv
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_96554582_9   8766 TCAAAAGATGATTTACACCCCATGTCAC 8793
                          v        v iv   i v????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (96 / 60)
Gap_init rate = 0.02 (16 / 713), avg. gap size = 1.88 (30 / 16)  


1800 24.96 3.28 4.52  chr1_96576714_96578355.rev      503  1143 (499)    L1M4_orf2#LINE/L1      262   894 (14)  

  chr1_96576714_9    503 ACAGCATGGTACTTGTACACAAACAGACACATAGACCAATGAAACCCATT 552
                             ii       v i i vii i     i     i     i  ivv v 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_96576714_9    553 AGAAAGCTCAGAAATAAAGC--TACACCTATAATCATCTGATCTTCAACA 600
                         v  i  ii          v --    ii   ii   vi    i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_96576714_9    601 AGGCTG--AAAAACAT--AAGCAACAAAGGACTCCCTATTCAACAAATGG 646
                            v  --  i v   --  vviiv    i ivvi  v            
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_96576714_9    647 TGCTGGGATAACTGGAAAGCCATGTGCAGAAGAATGAAACTAGACCCTTA 696
                                 i       v ?   ii    i         ii i     i  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_96576714_9    697 GCTTTCACCACATACTCAAGATGAATTAAAGATTTAATTCAAGATTAACT 746
                         v  iv     i    ------------   i   ------------    
  L1M4_orf2#LINE/    462 CCTCACACCATATAC------------AAAAATT------------AACT 487

  chr1_96576714_9    747 CAAGATGAATTAAAGATTTAAATGTAAGA-CTCAAACTATAAAAGTTTTA 795
                            i   i  i ?   ii           -  v           v i   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_96576714_9    796 AAGGAAAACCTAGG---AAATACCCTTCCCAACATCGGCCTTGGCAAAGA 842
                         i i      v    ---    ---    vii  v i  vi v     v i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_96576714_9    843 ATTTATGACCAAGTCCCAAAAAGCAATTGCAACAAAGCCAAAAATTAATA 892
                         v  iv iivi v v v v       vvv        ivv      vi   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_96576714_9    893 AGTGGGACCTAATTAAACTAAAGAGCTTATGCACAGCAAAATAAACCATC 942
                          i v    i v  i   v v  i i   v  ii vv    iv v  i   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_96576714_9    943 AATAGAGTAAATAGACAACCTACAGAATGGGAGAAAATATTCACAAACTA 992
                           v i   i  v        i                    ii    ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_96576714_9    993 TCCATCTGAGAAGA-ACTTAATATCCAAAATATATAAGGAACTT----AA 1037
                          vi      v   i-    i-      i         i     i----  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_96576714_9   1038 ATGAGCAAGCAAAAAACAAATAACCCCAGTAAGAAGTGGGCAAAGGC--- 1084
                         v v ii  vv    i           v v ? i  i          v---
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_96576714_9   1085 --ATAGAGACTTCTA-AAAGAAGACATACAAGCAGCCAACAAAAATGTGA 1131
                         --     v i    v-        i      iii     i  iv ii   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_96576714_9   1132 AAAAAATGCTCA 1143
                            i -      
  L1M4_orf2#LINE/    884 AAAGA-TGCTCA 894

Transitions / transversions = 1.49 (94 / 63)
Gap_init rate = 0.02 (14 / 633), avg. gap size = 3.57 (50 / 14)  


2989 28.04 0.33 0.11  chr1_96606495_96610774.rev     2884  3789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96606495_9   2884 TAGAAACACATCTTGTGTTCATGGGTGGGTAGAATCAATATTGTGAAAAT 2933
                          i    v i   iii         i v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96606495_9   2934 GGCCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 2983
                            v     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96606495_9   2984 TACCAGCATCATTTGTCACAGAGCTATAAAAAAC-AATCCTAAAATTCAT 3032
                          v     vv v   v ii    iv - i v  i -i              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_96606495_9   3033 TTGGAACCAAAAGAGAGCCCTAATAGCCAAAGCAAGACTAAGCAAAAGGA 3082
                         v     viiv   i  v  vv          i   vvi i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_96606495_9   3083 ACAAATCTGGAGGCATCACATTACCCGACTTCAAACTATGCTATAAAGTT 3132
                              vi      vv     i v   i i      viv i   i    i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_96606495_9   3133 TTAGTCACCATAACAGCATGTAACTGATATAA-AATATGCACATAGACCA 3181
                         vi   v i  vi    ii  vv    ii    -i   vi  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_96606495_9   3182 ATGTAACAGAATACAGAATCCTGAAATAAAGCCAAATATTTACAGCCAAC 3231
                            v  i     vv   i   v        v   v i     ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_96606495_9   3232 TGATCTTTGACAAAGCAAACAAAAACATAAAGTGGAGAAAGCACACCCTA 3281
                             i  i     i vviv   i v   vv i   i     v i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_96606495_9   3282 TTCAACCAGTGATGCTGGTATAATTGGCAAGCCACATGTAGAGGAATGAA 3331
                               v i  i      v i  i   vv ?       i i i       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_96606495_9   3332 ACTGGGTTCTCATCTCTCACCTTATACAAAAATCAAATCAAGATGGATCA 3381
                         ii   iii ii i   v    v           i  v    i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_96606495_9   3382 AAGGCTTAAATCTAAGACCTGAAACCATAAAGATTCTAGAAGATAACACA 3431
                         ?  i i     v     v  i    i     iv ii       v    i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_96606495_9   3432 GGAAAAACACTTTTAGACATTGGCTTAGGCAAAGACTTCATGACCAAGAA 3481
                           ?iv  vv   ivv   v    v        v ii   v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_96606495_9   3482 CCCAAAAGCAAATGCAACAAAAACCAAGATAAATAGATGGGACTTAATTA 3531
                         v         v v         ivv  i   i   i  v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_96606495_9   3532 AACTAAAGAGCTTCTGCACAGCAAAATAAATAATTAGTAGAATTAACAGC 3581
                           v v  i i   i  ii vv    iv v iv  i iv i i v  v  v
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_96606495_9   3582 CAACCCACAGAGTGAAAGAAAATCTTCACAATCTATACATCCGACAAAGA 3631
                                    i  ii       v  ii   vii   i   i  i  i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_96606495_9   3632 ACTAATATCTAGAATCAACAAAGAACTCAAACAAATCAGCAAGAAAAA-A 3680
                            vi    i     vv i         vv    v   ii  v     - 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_96606495_9   3681 TAAACAATCCCATGAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCA 3730
                         i   i  i  v  v?    i     v     iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_96606495_9   3731 AAATAAGATAAACAAATGGCTAACAAGCATATGGAAAAATGCTGAACATC 3780
                            v      v         i  i     i   i   i     v      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_96606495_9   3781 ACTAATTAT 3789
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.25 (139 / 111)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.00 (4 / 4)  


3349 26.07 0.55 0.66  chr1_96611267_96617677.rev     5012  5920 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96611267_9   5012 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5061
                              ii    i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96611267_9   5062 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCTCCACCAAGC 5111
                            v     v     iv i  i ii        i  v   i i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96611267_9   5112 TACCAATAACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5159
                          v   iivi    i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_96611267_9   5160 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAG 5209
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_96611267_9   5210 AACAAAGCTGGAGGCATCATGTTACCTGACTT-GAAACTATACTACAAAG 5258
                                i      vv   iii v  ii i  -i     -          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_96611267_9   5259 CTACCGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5308
                             v    v   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_96611267_9   5309 CAAGGGAACAGAAT--AGAGCCCTCAGAAATAATATCATACATCTACAAC 5356
                            v    i     --    i  --        vvi       i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_96611267_9   5357 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5406
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_96611267_9   5407 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5456
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_96611267_9   5457 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5506
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_96611267_9   5507 ATTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5556
                           i ?   ii       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_96611267_9   5557 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5606
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_96611267_9   5607 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5656
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_96611267_9   5657 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5706
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_96611267_9   5707 CATGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5756
                         v vi     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_96611267_9   5757 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5806
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_96611267_9   5807 AAAACCAAACAACCCAATCAAAAAGTGGCCAAAGGGTATGAACAGACACT 5856
                           i  -   i        i?    i   v      i v    i     i 
  L1M4_orf2#LINE/    796 AAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_96611267_9   5857 TCTCGAAAGAAGACATTTATGCAGCCAACAGACACGTGAAAAAATGCTCA 5906
                             v        i  vi viii     i ii   i      i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_96611267_9   5907 TCCTCACTGGCCAT 5920
                         v v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


 459 26.49 4.86 5.95  chr1_96625701_96629186     1540  1724 (1762)    L1M4_orf2#LINE/L1        7   189 (719)  

  chr1_96625701_9   1540 GATATACCATGGTCATTGATTAGAAGTTTCAGTGTCGTAGAGATGTTAGT 1589
                              v     v    v    i    vi i i i i  vi     vi i 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_96625701_9   1590 CCTTCCTAGATTGAT--------TCAGTTCAATCCTAATCAAATTTTCAG 1631
                         v  i  i i      --------   iiv      iv      v ii   
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_96625701_9   1632 CATGTTTTTGTGTTAGAATGTAGGAAAATTCAACATATTAATTCTTAAAT 1681
                          -  ii   ---  ----  i  --     -i   vii i  i  v    
  L1M4_orf2#LINE/    107 C-TGCCTTT---TT----TGCAG--AAATT-GACAAGCTGATCCTAAAAT 145

  chr1_96625701_9   1682 ATATATGAAACTTCAAAGGACTAAGAA-AATCAAGACAATTTTG 1724
                         vi     i  v v   i    iv    - ii   i     i   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

Transitions / transversions = 2.06 (33 / 16)
Gap_init rate = 0.04 (7 / 183), avg. gap size = 2.86 (20 / 7)  

 230 37.50 4.76 2.38  chr1_96625701_96629186     2037  2204 (1282)    L1M4_orf2#LINE/L1      232   403 (505)  

  chr1_96625701_9   2037 AAGATTTATTATAATGTTACAACAATTAAGATAATATGAT----GTATAA 2082
                           i i   i  i  v i    ii   i    i i i  i ---- i    
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_96625701_9   2083 ACACGATAATCA-ATTAATCCAGTGAAACAGTACTGAG--TCCCAAAAGG 2129
                         i---    iv  -  vi   - i  i  i  v i    --   vi   vi
  L1M4_orf2#LINE/    282 G---GATAGACATATAGATC-AATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_96625701_9   2130 AATC-ACATGTTTGCAGTTCACTGAAAGCTGGCAAAGCTGATACTACAAC 2178
                           i - i ii   iii  iv i   vvvii i   i v  vi vv  v i
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_96625701_9   2179 CCAGTAAATAAGGAACACTCTTCCCA 2204
                         i  i iiiv  i   i v    ii  
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCA 403

Transitions / transversions = 2.71 (46 / 17)
Gap_init rate = 0.03 (6 / 172), avg. gap size = 2.00 (12 / 6)  

 823 30.06 6.12 3.71  chr1_96625701_96629186     2459  2997 (489)    L1M4_orf2#LINE/L1      357   908 (0)  

  chr1_96625701_9   2459 CGACA-GAGTG---AGACTCCACCTCAAAAAAAAAAAAAAAAACTCTTTA 2504
                              - i   ---    --  i-    viiii   i  v i--     v
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGAC--CAT-TCAATGGGGAAAGAATAG--TCTTTT 401

  chr1_96625701_9   2505 TAATAAGTTGTGGTAGGTCATATGAGATTGGGTATTTATATA-AAAATAT 2553
                         i  i  i v   v i  v  ------ i   i  ?ii i  i-    v v
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACA------ACTGGATAKCCACATGCAAAAGAA 445

  chr1_96625701_9   2554 TTATCTATCTTAACCCCATGCTTATACTAC-CACAAAAGTCAATAGCAGA 2602
                          v --- vi vi     vvv  i i  i i-i      i i  ivvv i 
  L1M4_orf2#LINE/    446 TGA---AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_96625701_9   2603 TG-ATCGCAGACACAAATGGAAG-GCTAAAA-TACAAACACTTCTGGAAA 2649
                           -   i?    vi     v   -       -  i   -   ii i   i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAG 541

  chr1_96625701_9   2650 ATAATATAAGA-TAATATTTTATGATGTTGAGGTAGGCAAAGATTTCTTA 2698
                          v  i   i ?-   vvi  ii   iv   i v       v i       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_96625701_9   2699 AACAGAACATAAAAAGTGCTACTCAAAAAGGAAAAGACTGATACATTACA 2748
                         i i vi   iv     ii v viv v   i     i iv    v   iv 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_96625701_9   2749 TTT-----AAGTTTAGAACATCCATTTATTAAATG-CACTAG-AAGAGAA 2791
                         i  -----  i  v i   v iii viv i   v -     v-    i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_96625701_9   2792 GAAAAATTCAAGTCATAGAATGAGAGAAGGTATTTCCAAAACATATATCC 2841
                         vi    vv   vi  i      i     ii     v    v        i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_96625701_9   2842 AACAAATAACTCATACCTGGAATATATTTTTTGAAAACTGCTACTTGTCA 2891
                         i i  ivi   ii  i ii        v----i i    vi   vvv   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATA----AAGAACTCTTACAACTCA 787

  chr1_96625701_9   2892 ATAAAGCAAATACAGACAAACCAATATAAAAATAAGCAAA---------- 2931
                             viv   v   i i  v     v?      ii     ----------
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_96625701_9   2932 --ACATTTC---AAAAAATGATATGCAAATAGC-AGTAAGTATATGACAA 2975
                         --       ---   i  -     i     i  - i    i i    v  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_96625701_9   2976 GATACTCCACTTTGACAGTTAT 2997
                            i   v  v ii????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (98 / 60)
Gap_init rate = 0.04 (22 / 552), avg. gap size = 2.41 (53 / 22)  


2343 26.16 0.80 0.32  chr1_96632295_96636278.rev     2263  2889 (1095)    L1M4_orf2#LINE/L1        1   630 (278)  

  chr1_96632295_9   2263 TAGAGAGATATTCTATGTTCATGGAAAGGAAGAATCAATATAGTCAAGAT 2312
                          i  i      i i           vv      v i     v  i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96632295_9   2313 GTCAGTTCTTCCCAAAATGACCTATAAATTTAATGCAATTCCAAACAAA- 2361
                          v  i v  i      v   i   i i   i  i     i  v v    -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96632295_9   2362 TTCCAGCAAATTGTTTTGTAGATACTGACAAATTTAAACTAAAGTTTATC 2411
                          i     vivi v     i   v i      ii v vv     i  i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_96632295_9   2412 TGAAGAGGCAAAAGACTCAGACTAGCCATCACAATATTTAAGGAGAAGAA 2461
                           i i v    ii   i    v      vv     v  v  ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_96632295_9   2462 CAAAGTTGGAAGACTGACACTATCCTTTATCAAGACTTAATATAAAGCTA 2511
                                   i    v     vi  vv v    i     v  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_96632295_9   2512 CAATAATCAAGATTGTGTAATATTGGTGAGAGAATAAACGAATAGATCAA 2561
                           i         iv    ii  i   iivi  i   i  iv         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_96632295_9   2562 TAAAACAGAATGGAGAACCCAGAAATAGATCCACATAAATATAGTCAACT 2611
                          ii  i     v    ii         i i   i i vv   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_96632295_9   2612 AATCTTTGAAAAAGGAGAAAAGGCAATT-AATGGAACAAAGATAGTTGTT 2660
                         i  i  i  v  i  v vv   i v   -     iiv  ii     iv  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_96632295_9   2661 TCAACAAATGGTGCTGGAACAATGGAAAATTCACATG-AAAAAAACAAA- 2708
                                          i    iv i v ?i      -    i  ii  -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_96632295_9   2709 CCAGACACAGACCTGGCACCCTTCACAAAAATTAACTCTAAATGGATCAT 2758
                         iii   v vv    vi    v vi              v          ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_96632295_9   2759 AGACCTAAATGTAAAATGC-AAGATCATAAAACTCCTAAGAGATAACACA 2807
                                       i -  -  i ii         i  ii   v    i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_96632295_9   2808 AGAGAAAATATACATAATGTTGGGCTTGGCAATGACTTTTTAAATATAAG 2857
                         i ? v    v v i i iv     i v       ii  i   i    i v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_96632295_9   2858 ACTGAAGGCAGAAACCACAAAAGAAATGAATA 2889
                           ii  i   v  i v          -i    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAA-AAATA 630

Transitions / transversions = 1.68 (101 / 60)
Gap_init rate = 0.01 (7 / 630), avg. gap size = 1.00 (7 / 7)  

 851 22.79 2.72 3.74  chr1_96632295_96636278.rev     3200  3493 (491)    L1M4_orf2#LINE/L1      618   908 (0)  

  chr1_96632295_9   3200 AAAAGAAATGAATA-ATAAGCTGAACTTTATTAAATTTAGGA---CTCAT 3245
                                 -i    -    ii  i    i  i   v   ii ---i ii 
  L1M4_orf2#LINE/    618 AAAAGAAA-AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_96632295_9   3246 GCTATGCAAAAATAAAAGACCCCCTGCCAAAAGAACAAAGAGACAAGCCA 3295
                            - -------i   i   v -- ii   i i iii  i      v   
  L1M4_orf2#LINE/    667 GCT-T-------CAAAGGACAC--TATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_96632295_9   3296 CTGATTGATAGAAA-TATTTAAAAA--GTATATCTTATAAAAGACTGTTA 3342
                          v  v  iv     -     iv   --i       v    ii    vv  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_96632295_9   3343 TTTAAAATATACAAAGAACTCTTAAAACTCCACAATAAGATAATGAAAAA 3392
                          ii i      i            v     v i     i vi ii  v  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_96632295_9   3393 CCCAATT-AAAAATGGGCTAAAGTCTTTAATAGACAACTCACCGAAGAAA 3441
                                -          v  i vi  v        vi  v  i     i
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_96632295_9   3442 ATATACAGATGCTAAATGAACATATGAAAAGATGCTCCACATCATATATC 3491
                                i   viv   i i  i              v      ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_96632295_9   3492 AT 3493
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.05 (45 / 22)
Gap_init rate = 0.03 (9 / 291), avg. gap size = 2.11 (19 / 9)  


3204 27.06 0.44 0.55  chr1_96781464_96787724     4860  5768 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96781464_9   4860 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4909
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96781464_9   4910 GGCCATACTGCCCAAGGTAATTTACAGTTTCAATGCCATCCCCATCAAGC 4959
                            v     v     iv i  i     v     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96781464_9   4960 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5007
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_96781464_9   5008 TATGGAACTAAAAAAAGAGCCCGCATCACCAAAGCAATCCTAAGCCAAAA 5057
                                v iv  ii-  v  v v  vi     i     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_96781464_9   5058 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5107
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_96781464_9   5108 CTACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGAT 5157
                                  i   i    ii       v i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_96781464_9   5158 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5205
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_96781464_9   5206 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGACTC 5255
                         i vi    i  i     ivv  vv  i v  vv            i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_96781464_9   5256 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5305
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_96781464_9   5306 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAGTTCAAGATGG 5355
                             ii    i    v   i     v           i ii    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_96781464_9   5356 ATGAAAGACTTAAACATTAGACCTAAAACCGTAAAAACCCTAGAAGAAAA 5405
                           v ?    i    ii v   v       ii     vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_96781464_9   5406 CCTAGGCATCACCATTCAGGACATACGCATGGGCAAGGACTTCATGTCCA 5455
                          v    ?i v viv   iv   v vv vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_96781464_9   5456 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5505
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_96781464_9   5506 ATTAAACTAAAGAGCTTCTGCGCAGCAAAAGAAACTACCATCAGAGTGAA 5555
                           i   v v  i i   i  i  vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_96781464_9   5556 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5605
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_96781464_9   5606 AAGGGCTAATCTCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5655
                          i  i  vi v        v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_96781464_9   5656 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5705
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_96781464_9   5706 CTCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5755
                            v           vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_96781464_9   5756 CATCACTGGCCAT 5768
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3241 24.97 1.32 1.43  chr1_96789559_96796065.rev     5108  6016 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96789559_9   5108 TGGAAGAATATCCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5157
                              ii          i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96789559_9   5158 GGACATACTGCCCAAGGGAATTTATAGATTCAATGCCATCCCCATCAAGC 5207
                           vv     v     ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96789559_9   5208 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5255
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_96789559_9   5256 TATGGAAC--CAAAAAACAGCCTGCATTGCCAAGACAATCCTAAGCATAG 5303
                                v--   iii  --  v v  v     i      i i iv -  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAA-AG 195

  chr1_96789559_9   5304 AA-AACAAAGTTGGAGGCATCACACTACCTGACTTCAAACTATGCTACAA 5352
                           -              vv       v  ii i      viv i      
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_96789559_9   5353 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 5402
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_96789559_9   5403 GCCAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACA 5450
                         ii        i    i--    i  --        vv   i    i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr1_96789559_9   5451 ACCATCTGATCTTTGACAAACCTGACAAAAAAGAAGA---AATGGGGAAA 5497
                         ii  vi    i  i     ivv  v   ----  vv ---          
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAA----GACCATTCAATGGGGAAA 389

  chr1_96789559_9   5498 GGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTA 5547
                          i  vvi  v  i  i              v      v  ?   i   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_96789559_9   5548 GAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCA 5597
                         i  iiv    ii    i    v   i     v           i  i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_96789559_9   5598 AGATGGATGAAAGACTTAAATGTTAGACCTAAAGCCATAAAAACCCTAGA 5647
                          i      v ?    i       v   v     i i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_96789559_9   5648 AGAAAACCTAGGCA-ATACCATTTAAGACACAGGCATGGGTAAGGACTTC 5696
                                v    ?i- v i -  iiv   viv  vv i  i  v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_96789559_9   5697 ATAACTAAAACACCAAAAGCAATGGCAACAAAAGTCAACATAGACAAATG 5746
                         v  iv  vi            vvi          vv  v     i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_96789559_9   5747 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCA 5796
                            ii v  i   v v  i i   i  ii vv    i  v    i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_96789559_9   5797 GAGTGAACAGGCAACCTACAGAATGGGAGAACATTTTTGCAA-TCTTCCC 5845
                         i      v  i     i              v  v       -  v vi-
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT- 737

  chr1_96789559_9   5846 ATGTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTT 5895
                           v   i  i  i  vi          v  i        ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_96789559_9   5896 ACAAGAAAAAATCAAACAATCCAATCAAAAAGTGGGCAAAGGATATGAAC 5945
                          i  v     iv    i  i     i?    i            v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_96789559_9   5946 AGACACTTTTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAA 5995
                              i  i  v        i  vi viii     i ii          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_96789559_9   5996 ATGCTCATCATCACTGGTCAT 6016
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (134 / 89)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


 967 27.49 6.40 2.61  chr1_96806072_96808157      500   921 (1165)    L1M4_orf2#LINE/L1      124   561 (347)  

  chr1_96806072_9    500 ATTGATAAGCTGATTCTAAAATTTAATTTGAAATGCACATGGAC----AA 545
                              i        i        i vv v        - v    ----  
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA-AGGGACCCAGAA 172

  chr1_96806072_9    546 AAGCAATAATAATTTTTAAAAAGAA---CAAAGTTAATGGTCTTACACTA 592
                         v   v v  i   i  v        ---       iiv  v  i     v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_96806072_9    593 TCAGATATGAAGATTTATTATGAAGTTACAATAATTTAAACAGTAAAAT- 641
                         i vi  v v  i i   i  ii   i    i    iv i     ivii -
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_96806072_9    642 -TGGTACAAGAATAGA------GA--GATGGATTAGAATATAGAATTAAG 682
                         -   i i   i     ------  --i     v      vv   i iv  
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_96806072_9    683 AAAAAGACTCATCTCTACACAGCCAGTTTTTATTTACTAATAACAAAGGT 732
                            v i  i   viv vi ii i  i  v--    v ----i    i   
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTG--ATTTTC----GACAAGGGT 366

  chr1_96806072_9    733 ACCACTGCAATGCACTGAAGAAAGAGTGATCATTTCAATACATGGTGCTA 782
                         i   vvi v  v  v  ii      i ii  v      i v        i
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_96806072_9    783 GGTTAATTT-ACATTCATATAGGTATAAG--TGAACGTTG-ACCT----- 823
                           vi  i v- i ?i  i  -- i v   --    -    -   i-----
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACAT--GCAAAAGAATGAA-GTTGGACCCCTACC 463

  chr1_96806072_9    824 TCATATCATACAGAAAAATTAGTTTCATATGGGTCCTACACTTAAATGTG 873
                            i i    i v        ii iv v    i  v? v  i       -
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT- 512

  chr1_96806072_9    874 AAGAA-TAAAACAATAAAGCTTATAGAAGTAAATATAGAAGAATATCTT 921
                             i-      v     i  iv      v   i    i? v v     
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

Transitions / transversions = 1.46 (67 / 46)
Gap_init rate = 0.04 (16 / 438), avg. gap size = 2.38 (38 / 16)  

1082 26.33 2.24 1.12  chr1_96806072_96808157     1238  1594 (492)    L1M4_orf2#LINE/L1      548   908 (0)  

  chr1_96806072_9   1238 TAGAAGAATATTTTTATGTCCTCAGAGAAGACAATGCTTTTTTAAACAAA 1287
                            i? v v  i  ii  v   ii ivv  i     v   i   i i vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_96806072_9   1288 ACACAAAAAGCACTAATCATAAAA-AAGAAATGGGCAAATAGGACTTCAT 1336
                             v        v iiv i    -  i    i ii    v         
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_96806072_9   1337 TGACATTGAGAACTTCTGCTTTTTGA--GTCACCATTAAGAGATTAGAAA 1384
                         ii v   i i     i  ivi  ii -- v   i  i    i v ii   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_96806072_9   1385 TTCAAGACACGG--TGAGAGAAAATATTTGTAATACATACATCTGATGAA 1432
                         vv   vv   i --  i             i  vv    i       i i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_96806072_9   1433 A-ACTCATATCCAGAATATATAATGAATTCCTACAAATCAAATAATAAAA 1481
                         i-   ii                v   i  i     v    -        
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA-TAATAAAA 796

  chr1_96806072_9   1482 -GATAGAAAACTCAATTTTAAAACATGGGCAACATACTTGAACTAG-CAC 1529
                         -  i i v   i     ?-    -        viv i     -   -  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTW-AAAA-ATGGGCAAAGGATTTGAA-TAGACAT 843

  chr1_96806072_9   1530 TTTATAAAACAGGATATACAAAGAGCCAATAAATGTATGAAAATGTGCTC 1579
                           iviv   v i          vi        iiii       vi     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_96806072_9   1580 AATATCGTTAGTCAT 1594
                           i   i????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (61 / 31)
Gap_init rate = 0.03 (10 / 361), avg. gap size = 1.20 (12 / 10)  


2007 24.81 3.88 1.40  chr1_96815584_96817220      500  1144 (493)    L1M4_orf2#LINE/L1      248   908 (0)  

  chr1_96815584_9    500 CTGCATTAATCAAGACAGTATAGTATTAG---AAGTGAGTTAAACGCATA 546
                           i  v             i i   i i ---   -  --  i  ii   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GA--TAGACATATA 294

  chr1_96815584_9    547 GATCAATGGAACAGTACAGAGAAACAAGAAATAAAACCATACAAGTGTGC 596
                                    i  v iv    iv v         v       vv i  v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_96815584_9    597 ACAACTGATTTTTTTAGAAAGGT-CCAAAAGTAATTCAATGAAGAAAAGA 645
                         v   i       iv- v  i   -    i vi -       ii    ii 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCG-ACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAA 392

  chr1_96815584_9    646 CATTCTTTCCAATAAATATTGTCATAACAAATGGACATAAATAGGCAAAA 695
                         i v     i   i    iv  iiivi    v    i ?vv i v      
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_96815584_9    696 ACAAGAACCTTGACTGAAACCTCAC-CTTTTTA-AAAACTATTAACTCAA 743
                         iv v   vi v   ivvv       - iv v  -    --          
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAA--ATTAACTCAA 490

  chr1_96815584_9    744 AATAGATGATAAATCTAAGTGTAAAATGAAATACTATAAAACTTTTAGAA 793
                            i   v ? i i    i     i vvv  v           i      
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_96815584_9    794 GAAAACAGAGAGGAAAATATTTGTGACCTAGTATTAGACAAACAGTTCTG 843
                                v  i? v    v  i       v vi    i   vviv    v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_96815584_9    844 AGATATGACACTAAAAGCA--------AAGGAAAAAAATCAATAAACTAG 885
                                    i       --------  iii       vi     i i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_96815584_9    886 ACTTCATAAAAATTTCAGACTTTTGCTCTGTGAATGACCCTGTTAAGAAG 935
                                v      vv i       iv  vii  v   v  i i     i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_96815584_9    936 ATAGGAAGACAAACCACTGACTAGAAAAAAATATTTGCAAATCACATATC 985
                         i iii       v    v  v i i i                 i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_96815584_9    986 TGAAAAAGGACTTATATGACCA--ATATGTAAAGAACTCTCTCAACTGAA 1033
                            v  i      i   --   --    i           iv     v  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTAT--CCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_96815584_9   1034 CAATAAAAGAACAAGCAGTCCAATTAAGAAACGGGCAAAAGATTCTAA-- 1081
                         i       ii    ii ii      ? i   i       i    iv  --
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_96815584_9   1082 GACAATTTACCAAAGAGGG----CAGAAGAAAAACAAGAACATGA---GA 1124
                             v  iv       i i----  i v ivv  i   v      ---  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_96815584_9   1125 TGTTCAATATTATCAGCCCT 1144
                           i    i  i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (92 / 64)
Gap_init rate = 0.02 (15 / 661), avg. gap size = 2.27 (34 / 15)  


2947 25.87 2.91 1.23  chr1_96828343_96834740     5013  5905 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_96828343_9   5013 TGGAAGAACATCCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5062
                              ii i        i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_96828343_9   5063 GGCCATACTGCCCAAGGTAATTTGTAGATTCAGTGCCATCCCCATCAAGC 5112
                            v     v     iv i  i ii       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_96828343_9   5113 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5160
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_96828343_9   5161 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAACCAAAAG 5210
                                viiv  ii  v  v v  v     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_96828343_9   5211 AACAAAGCTGGAGACTTCACGCTCC----------AACTATACTACAAGG 5250
                                i     ivi    i  i ----------    -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_96828343_9   5251 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGAC 5300
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_96828343_9   5301 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATCCGGCATATCTACAAC 5348
                                 i    i--    i  --        v  vii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_96828343_9   5349 TATCTGATCTTTCACAAACCTGACAAAAACAAGAAATAGGGAAAGGATTC 5398
                         i vi    i  iv    ivv  v   i v  vvv   i       i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_96828343_9   5399 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5448
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_96828343_9   5449 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5498
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_96828343_9   5499 ATGAAAGACTTAAATGTTAGACCTAAAACCACAAAAACCCTAGAAGAAAA 5548
                           v ?    i       v   v       i i    vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_96828343_9   5549 CCTA--TGCAATACCATTTAGGACATAGGCATGGGCAAGGACTTCATGTC 5596
                          v  --? i  - i -  iiv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_96828343_9   5597 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAAAGGGATC 5646
                           vi            vvi          vv        i   vv   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_96828343_9   5647 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG---G 5693
                          v  i   v v  i i   i  ii vv    i  v    i  --  --- 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--AGAAAG 691

  chr1_96828343_9   5694 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAA-TCTTCCCATC 5742
                             v  i     i                 v       -  v vi-   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATC 740

  chr1_96828343_9   5743 TGACAAAGGGCTAGTATCCAGAATCTACAATGAACACAAACAAATTTACA 5792
                            i  i  i  v           v  i  v    v vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_96828343_9   5793 AGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAAGGTATG--T--- 5837
                          v     i     i     v  i?    i        i i v  -- ---
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_96828343_9   5838 CTTCTTTTCAAAAGAAGACATTTATGCAGCCAA-AGACACATGAAAAAAT 5886
                          v -  i  v        i  vi viii     - ii          i  
  L1M4_orf2#LINE/    841 CAT-TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_96828343_9   5887 CTTCATCATCACTGGACAT 5905
                         vi   v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (137 / 90)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.06 (37 / 18)  


2678 26.88 2.88 0.25  chr1_96839465_96842418.rev      998  1797 (1157)    L1M4_orf2#LINE/L1        4   824 (84)  

  chr1_96839465_9    998 AGAGATATTCTGTGTTCATGGGTAGGAAGAC-CAATATTATCAAGATGTC 1046
                          i      i ii         i v       -i      i i      v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_96839465_9   1047 AGTTCTTTCCAATTTAATCTGCAGATTCAA-----TCCCAGTCAAAATCA 1091
                          i v  ii    v  i    i         -----    vi        v
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_96839465_9   1092 CACCAAATTATTCTATGGCTTTTGATAAATTGATTCTAAAGATTAC-TGA 1140
                           v vivi v  i iii vvv    i  ii    i     iv i i-  i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_96839465_9   1141 AAAGGTAAAAGACATAGAAGAGCCA-TACAATTTTGAAGGAAAAGAATAA 1189
                            v i  ii   vi    v     -v     i     ii i     i  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_96839465_9   1190 AGTTGGAGGACTGATATTACCTGTCATCAAGACATACCATAAAGAATCCA 1239
                                     v i i v  iiviv    i  v   i i    -v v  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG-CTACA 252

  chr1_96839465_9   1240 GTAATCCAGACAGTATGGTATTGTTGAAAGAACAGACAAATAGAACAATG 1289
                               v       i     i  viiv   i i     v     v     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_96839465_9   1290 GAACAGTATAGGGAACCCAGAAATAGGCACATAAAT--ATAGTTAATTGA 1337
                            i  v  v i  ii         ii v    v  --  i  i      
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_96839465_9   1338 CCTTTGACAAAGAAACAAAGGCAATGCAATGGACCAAAGATAGTTTTTTA 1387
                         ii  i     i ivi v   i v  v      ivv  ii     i    v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_96839465_9   1388 AACAAATGATGTTGGAACGACTGAACAATCACATGCAAAA-AATAAATCT 1436
                                 i  i   i  i    i i ?i           -   i  vi 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_96839465_9   1437 AGACACAAACCTTACACCCTTCACAAAATTTAATTCTAAAGGGGTCATAG 1486
                         i   v vv    i     v vi      v    i  v   v  i   ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_96839465_9   1487 ACCTAAACATAAAATGC-AAAATTGTAAAACTCCTGGATGATAATGTAAT 1535
                                ii   i -  -    i i        i i  v  v  ii  iv
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_96839465_9   1536 AGAAAACCTAGGTAACCCTAGGATTAACAATGAGTGTTTAGATATGACAT 1585
                         ? v   i  vv  i   i i  v vii     iv vi            i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_96839465_9   1586 CAAAGACAGAATCAATTAAA---AAAATTGATAAGCTGGAATCCATTAAA 1632
                             ii  v  v   iv   ---     v     ii    v i   i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_96839465_9   1633 AT------CTTCTATCTGACAAAGG-CAATGTCAAGAGAATCCGAAGACA 1675
                           ------   i i vivv      -  v i      i i vvi      
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_96839465_9   1676 AGCCACAGACTTGGAGAAAATATTTGCACAAAAAAGATCTGATAGAGGAC 1725
                          v       v v                v vv v v        ii    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_96839465_9   1726 TGCTATTTAAAATATACAAATAACTCTTAAAACTCAACAATAACAA-ACA 1774
                          vv   ii i      i   v        v       i     v  -   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_96839465_9   1775 AAAAATGCAATTAAAAAATGGGC 1797
                           v  iv     ?          
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGC 824

Transitions / transversions = 1.45 (125 / 86)
Gap_init rate = 0.02 (13 / 821), avg. gap size = 1.92 (25 / 13)  

 213 19.35 1.61 3.23  chr1_96839465_96842418.rev     2403  2464 (490)    L1M4_orf2#LINE/L1      848   908 (0)  

  chr1_96839465_9   2403 CCAGAGACCATATATACAGGTGTCAAATAAGCATGTGAAAAAGTGTTCCA 2452
                            i   -- v       ii  v v        ii      ii  i  v 
  L1M4_orf2#LINE/    848 CCAAAGA--AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_96839465_9   2453 CAT-ATGCCATCA 2464
                            - ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.50 (3 / 2)  


1456 23.52 7.16 2.66  chr1_96904722_96907569.rev     1220  1708 (1140)    L1M4_orf2#LINE/L1       43   553 (355)  

  chr1_96904722_9   1220 GTCATGATGCCAATTTTCCCCAAATTTGCTCTACAGATTCAAGTCAAATC 1269
                           i v    v    vi          - v             vv   vi 
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATT-GATCTACAGATTCAACGCAATCC 91

  chr1_96904722_9   1270 C-AGTAAAATCCAAGCAG---TTTTTCTAAGAACTGAC------------ 1303
                          - vi       v   v ---     vi ii  i    ------------
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr1_96904722_9   1304 ----TCATATGAAAATACAAAGGACTCAGAAGAGTTAAAAACAACTTTGA 1349
                         ----       i    i   i    i     v  ii    -   ii    
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGA 190

  chr1_96904722_9   1350 AAAAGAA---CAGAGTTGGAGGGCCAAGACTAAGTAAGTGGTTTCAAGAC 1396
                                ---  i         i iv v   vvvi  ----      i  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA----TTTCAAAAC 236

  chr1_96904722_9   1397 TCAATATAAAGCTACAATGATTAAGACAGTATGTTTCCAGCATCTAGATA 1446
                          i v  i         i i  i        i  v v ii    vvi    
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_96904722_9   1447 AAGGAAAATGGGTCAAT---ACAAAA--AAGAGTACAGACATAAAATCAC 1491
                         i v-- v  i i     --- i i  --i     v    v     vi  i
  L1M4_orf2#LINE/    287 GAC--ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_96904722_9   1492 ACAT--ACAGACATAAGTGATTTTTCATGAAGCTGCAAAGCCAAGTGAAT 1539
                             -- ii v  -- v       iv ii i v   v   v v v v   
  L1M4_orf2#LINE/    335 ACATTTATGGTCA--ATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_96904722_9   1540 GGAGAAAGGATAGTCTTTTCAACAAATGATGCTGTAAACACTGGATATCC 1589
                           i     i                   i     vi vv        ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_96904722_9   1590 CCATGCAAAACCAAAT-ACTTCTGACCCACACTTTGTACCATATTCAAAA 1638
                         v         --i   - vv iv     vi  i iii       v     
  L1M4_orf2#LINE/    433 ACATGCAAAA--GAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_96904722_9   1639 TATTAAGTCAAAATGAA--AGAGACCCAAATGTTAAACC--AAAGTATAA 1684
                         -     v        i -- ?     i      v i v --   v     
  L1M4_orf2#LINE/    481 -ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_96904722_9   1685 AACTTCTATTAGAAAACAAAGGTG 1708
                             ii  vv        v   ? 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNG 553

Transitions / transversions = 1.15 (60 / 52)
Gap_init rate = 0.03 (17 / 511), avg. gap size = 2.82 (48 / 17)  

1088 22.42 7.27 0.00  chr1_96904722_96907569.rev     2028  2357 (491)    L1M4_orf2#LINE/L1      555   908 (0)  

  chr1_96904722_9   2028 AAATCTTCATGGCTTACAGTCAGGCAAAAATGGCTCAGACAAGACCCCAA 2077
                                 i  i i vvi  i      vii vv  i   i v   v    
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_96904722_9   2078 AACTACAATCCATAAAAGAAAAAATTGGTAAACTGGAGTCCATCAGATTT 2127
                           vi    v v i            v i    i    v i     i v  
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_96904722_9   2128 AATAACTGTTGCTCTTCAAAAGACAATG-CGAGAA--TAAGAAGAT---- 2170
                           v    v   iv       i    v i- i    -- i i    i----
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_96904722_9   2171 ----GAGTGGCAGAAAATATTTGCAGGCCTTATGGCTGATAAAGGACTTG 2216
                         ----  i   v              iii v   iv       i       
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_96904722_9   2217 TAACCACAATG----AAGACCTCTCAAAACTCAATT-TAAAA---TAAAT 2258
                           v   v   i----    v    i v        v-     ---i    
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_96904722_9   2259 AACCAAATAAAAAATTGGGCTAAAGATATAAACAGACACTTCACCAAAGA 2308
                             v   v?    v     v  i   v i  i     i   v       
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_96904722_9   2309 ---TA-ACAGCTGACAAA-AAGCACACGAAAAGATGTCCAACATCATAGA 2353
                         ---  -   iv  i v  -       i         ii        ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_96904722_9   2354 TATT 2357
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.21 (40 / 33)
Gap_init rate = 0.03 (9 / 354), avg. gap size = 2.67 (24 / 9)  


2290 24.37 5.46 2.53  chr1_96931646_96933333      445  1195 (493)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_96931646_9    445 ATTCTAAGTGTAATCTCATTTAAAAAGATAAAAAGA---AGTATAACGAA 491
                           i    ----   -    v ii   vii  ii-  ---  v   i v  
  L1M4_orf2#LINE/    136 ATCCTAA----AAT-TCATATGGAAATGCAAGG-GACCCAGAATAGCCAA 179

  chr1_96931646_9    492 AAGCCAAT--------AGAGGAA--AAATTGGAGCATTGAC---TACCAG 528
                           --    --------   i   --  i      v i v  --- v   i
  L1M4_orf2#LINE/    180 AA--CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_96931646_9    529 TTTTCAAGAATTACTGCAAAGCTACGGTAATTAAAAATAGCATCATAATA 578
                            -   i v     i         i     i  i -i  ii vi  v i
  L1M4_orf2#LINE/    228 TTT-CAAAACTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTG 275

  chr1_96931646_9    579 ACATAAAGATAAA----TAGGTCAGTGAGACAGAGCAGAGAGTTCAGAAG 624
                         i     i    i ----   i   i  ii i   iiv      i     i
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_96931646_9    625 TTAACTCACACAATTATGGATAACTGATTTTTGACAAAGGTGCAAAGTCA 674
                          v   i  i   v      vi  i       i     i     v   v v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_96931646_9    675 ATTCAGTGGAGAAAAAGTAGACTTC-CAACAAAGGGTGCTACAGCAGTTG 723
                              i   i    i i   v   i-       v      ivii  ii  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_96931646_9    724 GAGCTATCCGTATGCAAAAAAATGATCTTGGATCTGTATCTCACACTGCA 773
                           --  ?  ii        i     vv     i iv  i       iii 
  L1M4_orf2#LINE/    426 GA--TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_96931646_9    774 TATGAAAATTAACTCCAAATGGATCATGG-CCTAA-TGTAAAACCAAAAA 821
                           ii           v          ?i -     -     i v v    
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_96931646_9    822 TTATAAAATCTCTAGAAAAAAATACAGA---AAATCTTCGTGACTTTGGA 868
                         i       iiii     i    i i  i---             i    i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_96931646_9    869 TTAAGCAGGAATGTATTTGATATGACCCTAAAAGCACAATCTAT----TA 914
                            i   ivii v v  v        v i          v v i----v 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_96931646_9    915 AAAAATGGA---ATTTGAC---ATCAGAATTAAAATCTTCTGCCATTCAA 958
                               i  ---   v   ---    i        v   i  ivv     
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_96931646_9    959 AAGAAACTGCTAGGGAA-TGAAAAGACAAGCCATAAACTGGAAGAACATC 1007
                          i  v   iii i i  -           v   i i v   i    v  v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_96931646_9   1008 ATAACAAAGCATATAGCTGATAAAGGACTTCTATCCAGAATAT-TAAAAG 1056
                         v vi    v      v       i      v            -    ii
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_96931646_9   1057 ATTCAGTATATGTAAAATCAGCAGTCAAGCAACAAACTACTCAAT---GA 1103
                          i  -- -  i---  v   ii i v  ivi     iv  i    ---i 
  L1M4_orf2#LINE/    774 ACTC--T-TAC---AACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_96931646_9   1104 ATTGGCCAAAATATTTGAACAGGTAGTACAGCACAAAAGATACACAGATG 1153
                          v   v    iv       i  ii v v vv  v i      i   i   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_96931646_9   1154 GTAAGTAAGCACGTGAAAAAGCTGGTCAGCATCATTAGTTAT 1195
                          iv i       i      - v  v   i     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (118 / 63)
Gap_init rate = 0.03 (26 / 773), avg. gap size = 2.31 (60 / 26)  


1263 25.65 19.35 2.10  chr1_96935243_96938353     1493  2112 (999)    L1M4_orf2#LINE/L1       13   739 (169)  

  chr1_96935243_9   1493 CCATGTTCATGAATTAGAAGGCTCAATAT-GTTAACATGCCAGTTCTCCC 1541
                                    i   i    i  i     -     v   v  i v     
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_96935243_9   1542 TAAATTGG------GATGGCATTG-AATC--TATAAAGA----------C 1572
                         i      i------   v-  vi -    --   v  i ---------- 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATT-CAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr1_96935243_9   1573 TT------ATAAATTGA-GAGTACATTCTAAAATTTATGTGGAAATAAAA 1615
                           ------ v       -i  ivv  i        i  i       iv  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_96935243_9   1616 AGGAGCTAGGACAATTAAAACCATTTTGAAAAAG-----TAAATTTTG-- 1658
                         i   v i  i i iii     v  i         -----i   v  v --
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_96935243_9   1659 ---CCACAGTTC------TCAAGACTCACTACAAACCTGTAGTTAATCCA 1699
                         ---i    v   ------    i   i        v  ii   -    - 
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT-AATC-A 259

  chr1_96935243_9   1700 AAACAGTTTACTACTAGCATAG---------------TTAGTGACACAGA 1734
                          i     v iv    i     i--------------- i i  iv i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_96935243_9   1735 AT--AGCGTTCAGGGAATAA-CTCATGCATT------------------- 1762
                           --  v  i   i-     - i   i    -------------------
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGA-AATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_96935243_9   1763 --AAAGTTGCCTTGATCACTCAGTGAAGAAAGAGAAGGCCTTTCAACAGA 1810
                         --  i v    vv  i  i   i  ii      iv  v i        i 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_96935243_9   1811 TG-TGCTAGAACAGCTGAATAT--ACATACAAAAAAGCAAAAGAAACTTA 1857
                           -    i i   i   i   ?--    i     i ---- v   ii vi
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA----ATGAAGTTGG 454

  chr1_96935243_9   1858 AACCCTACATCATTCTGTATAAAACAAT------GAGATTAATTA----- 1896
                          v      v   iv ii    v  v   ------i i  vi  i -----
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_96935243_9   1897 -----TATAAAAACTAATA-TATAGAGTTTTTAGGAAAAAGCATAGG--- 1937
                         ----- i   i i    v -    i ii i    i i   i      ---
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_96935243_9   1938 ATATACTTGCAACTTTGGGATAAATGAAGATTTCTTAAA----ATAGAAA 1983
                          v  vi i ii  i     v  iiii v i       i ---- i vv  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_96935243_9   1984 AATCTTAA-----------AGGAATATATAAACTTGACTCCATCAAAATG 2022
                           v vi  ----------- ii    v     i v    i         v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_96935243_9   2023 GGAAATTTCTGCTTCATCAAAAGACATTGTTAAGACATTGAAAAGACAAG 2072
                         ii   i  i  - v v     i    i i i    v v           v
  L1M4_orf2#LINE/    655 AAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_96935243_9   2073 GCACAGACTTGGAGAATATAATATTTGTGTATCAATACAT 2112
                         v      v v      ---        iiv    -  i  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAA---AATATTTGCAAATCA-TATAT 739

Transitions / transversions = 1.93 (104 / 54)
Gap_init rate = 0.04 (30 / 727), avg. gap size = 4.43 (133 / 30)  

 256 20.71 15.38 8.28  chr1_96935243_96938353     2464  2632 (479)    L1M4_orf2#LINE/L1      728   908 (0)  

  chr1_96935243_9   2464 CAAACCATATCAATGACAAAGGACTTGTATCCCAAAGGACTTGTAAAAAA 2513
                             i     vvv   i  i            vi  -------  v v  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAA-------TATATAA 770

  chr1_96935243_9   2514 AAAACTCCTCCAA-TCAATAA-----ATATGAGCAGCCCAATTTTTTTTT 2557
                          i     i v   -       ----- v ii ii i       ?vv----
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA---- 816

  chr1_96935243_9   2558 AAGTGG-CAAAAGA----AGT-GACATT--------------ATAAGGAT 2587
                           i   -    i  ---- i -      --------------   vii  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_96935243_9   2588 GGGTAACAAGCACATGAAAAGATAATGTTAGTCATCAGGTGATCA 2632
                           vi  i                --- i viv     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGAT---GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (20 / 14)
Gap_init rate = 0.05 (9 / 181), avg. gap size = 4.44 (40 / 9)  


3078 26.75 0.87 1.75  chr1_97031027_97037439.rev     5007  5922 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_97031027_9   5007 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5056
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97031027_9   5057 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAACC 5106
                            v     v     iv i  i  i        i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_97031027_9   5107 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTGAAAGTTCA 5154
                          v   iivi i  i  ii     -   -- v  i  - iiiv   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_97031027_9   5155 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5204
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_97031027_9   5205 AACAAAGCTGGAGGCATCACGCTACCTGACTACCTGACTTCAAACTATAC 5254
                                i      vv    --------   v  ii i      viv   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCAC--------ACTTCCCAATTTCAAAACTTAC 240

  chr1_97031027_9   5255 TACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGA 5304
                              i          i   i    ii         i iv ii i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_97031027_9   5305 TATAGATCAATGGAACAGAGC--AGAGCCCTCAGAAATAACGCTGCATAT 5352
                                        i   ii--    i  --        vv iii i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACAT 338

  chr1_97031027_9   5353 CTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAA 5402
                         i  iiiii vi    i  i     ivv  vv  i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_97031027_9   5403 AGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGT 5452
                           i  vvi  v  i  i              v      v  ?   i   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_97031027_9   5453 AGAAAGCTGAAACTGGATCCCTTCCTTACACATTATACAAAAATCAATTC 5502
                          i  iiv    ii    i    v   i    vv           i  i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_97031027_9   5503 AAGATGGATTAAAGACTTAAACATTAGACCTAAAACCGTAAAAACCCTAG 5552
                           i      i ?    i    ii v   v       ii     vi i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_97031027_9   5553 AAGAAAACCTAGGC----ATTTCCATTCAGAACATAGGCACGGGCAAGGA 5598
                                 v    ?----  i i i ---  v v i  i-ii     v i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGT---GACCTTGGGT-TAGGCAATGG 584

  chr1_97031027_9   5599 CTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCGAAATTGACA 5648
                         i   v ivv  vi            vvi          vvi    v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_97031027_9   5649 AATGGGATCTAATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACC 5698
                            v   ii v  v   v v  i i   i  ii vv    i  v    i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_97031027_9   5699 ATCAGAGTGAACAGGCAACCCACAAAATGGGAGAAAATTTTCACAACCTA 5748
                          vv i      v  i         i             v  ii   vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_97031027_9   5749 CTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACACAAACAAA 5798
                         ivi      i  i  i  vi          v  i  v    v vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_97031027_9   5799 TTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATG 5848
                          iv i  v     i     i     v  i?    i           iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_97031027_9   5849 AACAGACACTTCTCAAAAGAAGACACTTATGCAGCCAAAAAACACATGAA 5898
                           i     i     v        i ivi viii     v  i        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_97031027_9   5899 AAAATGCTCACCATCACTGGCCAT 5922
                           i       v     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  


2907 28.16 0.55 0.66  chr1_97073895_97075948.rev      655  1563 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_97073895_9    655 TGGGAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 704
                            i  i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97073895_9    705 GGCCATAATGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 754
                            v   v v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_97073895_9    755 TACCATTGACTTTCTTCACAGAATTAGAAAAAAAAAACAACTAAATTTCA 804
                          v   vivi i  i  ii     v v  v  ivvi v --     v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC--CTAAAATTCA 148

  chr1_97073895_9    805 TATGGAACCAAAACAGAGCCTGTATATCCAAGACAATCTTAAGCAAAAAG 854
                                viiv  vi  v  v v   v    i        i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_97073895_9    855 AACAAAGCTGGAGGTATCACACAACCTGACTTCAAACTATACTACAAGGC 904
                                i      vv      vv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_97073895_9    905 TACAATAACCAAAACAGCATTATACTGGTACCAAAACAGATATATAGACC 954
                             i   i   i    ii vi      i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_97073895_9    955 AATGGAACAGAACAGAGGCCTCAGAAACAACACCACAAATCTACAACCAT 1004
                                i    iv   ivii      i  vv   i v  i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_97073895_9   1005 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 1054
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_97073895_9   1055 GTTTAATAAATGATGTTGAGAAAACTGGCTAGCCATATACATAAAACTGA 1104
                         v  i  i     i  i  i  v      v  ?   i  i  v  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_97073895_9   1105 AATTGGACCCCTTCCCTTCACCTTATAAAAAAATTAACTCAAGATGGATT 1154
                          i          v  iiv    v    v              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_97073895_9   1155 AAAGACTTAAACATAAGACCTAAAAGCATAAAAACCCTAAGAGAAAACCT 1204
                          ?    i    ii     v      vi      vi i  ii       v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_97073895_9   1205 AAGCAAGACCCTTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 1254
                          i ?ivi vi    iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_97073895_9   1255 CACAAAAAGCAATGGCAACAAAAGCCAAATTAG-CAAATGGGACCTAATT 1303
                            v       vvi          vv   v   -i    v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_97073895_9   1304 AAACTAAAGAGCTTCTGCACAGCAAAAGAAATTATCATCAGAGTGAACAG 1353
                            v v  i i   i  ii vv    i  v i     vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_97073895_9   1354 GCAACCTACAGAATGGGAGAAAAATTTTGTAGTCTATCCATCTGACAAAG 1403
                         i     i                vv    i ivii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_97073895_9   1404 GGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA- 1452
                          i  vi          v  i        ivv    v iv i  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_97073895_9   1453 --AAACAACCCCATGAAAAAATGGATGAAAGATATGAACAGACACTTCTC 1500
                         --   i     v  v?        iii  i   v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_97073895_9   1501 AAAAGAGGACATTTATGCAGCCAACAAATATATATATATAAAAAT-CTCA 1549
                         v     i  i  vi viii     i  ii i  i--- -   i  -    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATG---A-AAAGATGCTCA 894

  chr1_97073895_9   1550 TCATCACTGGTCAT 1563
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (145 / 107)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


2641 27.83 1.52 0.64  chr1_97196249_97198027      500  1286 (493)    L1M4_orf2#LINE/L1      115   908 (0)  

  chr1_97196249_9    500 TTCACAAAAATGGAAAAAACAATCCTAAAATTCAAGTGGAACCACAAAA- 548
                           ii  i    v  v  ivii             vi     vii   ii-
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_97196249_9    549 ATACTGAATAGCCAAAGCAAACCTGAGCAAAAAGCAAAAAGCTTGAGACA 598
                          iv v           i   v i   iv  i   v v    i v   ivv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_97196249_9    599 TCCTACAACCTGAGTTCAAAATATGCTATGAAGATATAGTAGCTAAAACA 648
                           vi  vv  ii v       iv i   ii   v  i    iii  i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_97196249_9    649 ACATGGTCCTGGCATAAAAACAAACATGTAACTCAATGGAATAGAATAAA 698
                         iii    v         ii i i    i  iv               vi 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_97196249_9    699 GGGCCCGTAAATAAATGCATGTACCTACAGCCAACTGATTTTCAACAAAG 748
                          i i  iv       iv   ii ii  ii i   i        i    i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_97196249_9    749 GTGCCAAGAACA--CAAATTGAGGGAAAGACAGTCCCTAAAACAAATGGT 796
                                  v  --   --  i  i  ii i    ii vv          
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAA--TGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_97196249_9    797 GCTGAGAAAGTTAAATATCCACGTGCAGAAGAATGAGACTAGACCTCTAC 846
                             i  v ii ii   ?    i    i        iii i    i    
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_97196249_9    847 CTCTTGCCAAATGCAAACATCAACTCAAAATGGATTGAAGACTTAAATGT 896
                            vii   v  i    v  i              ii?    i       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_97196249_9    897 AAAACCCCCAATTATTAAACTACCAGAAGAAAACATAGGG--AAACACTT 944
                           i v ivv  i   v     vii               ?--   i-   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTT 561

  chr1_97196249_9    945 TATGAC-TTGGATTGGGCAGGGATTTTTTGAATAAGAT-CTAAAGAGCAC 992
                         ii    -    i  i    iv i   i  ii   v  i- i   -     
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA-AGCAC 610

  chr1_97196249_9    993 CGGCAACAAACATAAAAATAGACAAATGGGATTAAATCAAACTGAAACAC 1042
                         vi        viv         i    v   i vv      v v   v  
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_97196249_9   1043 TTTTGCACAGCAAAGGAAACCAT----ACAGTGATGATGCAGCCTACAGA 1088
                              ii vv       v  i  ---- v     vi vi  i  i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_97196249_9   1089 ATGGGAGAAAATACTTGCAAACTACATACCTGACAAGGGGTTAATACCCA 1138
                                      i       ii i   i    i     ii vi  i   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_97196249_9   1139 GACT-TCCAAAGTATTTAGGAGACTTAACTGTAGAAAAATAAACAACTAA 1187
                           v - vi    v i ivvivi   i  ivi  i   i i   i   iv 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_97196249_9   1188 ATTTAAAAAATGGCTAAAATACCCCAATAGATATTTATCAAAAGAAGACA 1237
                            ?     -   vi   iv iiiv      i    v  v        i 
  L1M4_orf2#LINE/    811 ATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_97196249_9   1238 TTCAAATGGCCAACAGGTACATGGAAAAATGCTTGTCATCACTAATCAT 1286
                          v           i i i     i   i     iiv     ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (145 / 70)
Gap_init rate = 0.01 (11 / 794), avg. gap size = 1.55 (17 / 11)  


2906 24.97 2.45 1.34  chr1_97215772_97221205.rev     4047  4943 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_97215772_9   4047 GAAAAAATATCCCCTACTCATGGATAGGAAGAATCAATGTTGTTAGAATG 4096
                          i   i       v ii        v      v i   i      ii   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_97215772_9   4097 GCCATTTTGTCCAAAGCAATTTATATATTCAATGCTATTCCTGTCAAACT 4146
                           v  vi vi     vii  i  i v      i  v  i   i     v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_97215772_9   4147 ATGAATGGCATTTTTTCACAGAATTAGAAGAGAAAATTCTAAAATTCATT 4196
                         viv iiv  v      -i     v v  vi  vvi  i           v
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_97215772_9   4197 TGGAAAGAAAAAAAGAGTCCA-AATAGCCAAAGCAACCCTAAGCAAAAAG 4245
                               viv  i-- iii   -          i   i i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_97215772_9   4246 AACAGAGCAGGAGGCATCACATTACCCAATTCCAAACTATATCACAAAGC 4295
                             i  iv     vv     i v       i    viv  ii       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_97215772_9   4296 TGCAGTAATAAAAACAGTAAGGTACTGGTACAAAAACAGACATATACACC 4345
                          i       v  i     iv        i i  ii i         v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_97215772_9   4346 AATAGAAAAGGTTAGAGAACCCAGAAATAAAGACAGACACTTAGTATGTC 4395
                            i   v  iv v    ii           vv  v   i   - i-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TG-GTC 346

  chr1_97215772_9   4396 TCTGTGATTTTCAACAAAGCAGACAATAACAAACAATAGAGAAAGGAC-T 4444
                         vv -        i    i vv v   v v  vv    i i     i i-v
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_97215772_9   4445 TCTTATTCAA-AAATGGTGCTGCAATAACTGGCTAACCATATGCAGAAGA 4493
                             -     -           vi i      v  ?   i     i    
  L1M4_orf2#LINE/    396 TCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_97215772_9   4494 TTGAAACTGGACCCCTCCCTTTCATCATATACAAAAATCAACTCAAAATA 4543
                         v    ii         v   iv  i             i          i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_97215772_9   4544 GATTAAAGCCTTAAACGTAAAACCTGTAACTATAAAAACTCT-AGAAGAA 4592
                            i ?  v i    i    i v  iv          -    -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chr1_97215772_9   4593 AACCTAG---TA----TTCTGGACATTGGCCCTGGCAGAGACTTCAT-GA 4634
                            v   ---  ----   vv   v    viiv    iv ii   v -  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_97215772_9   4635 TGAAGACTCCAAAAGCAACTGCAACAAAAACAAAAATTGACAAGTAGGAT 4684
                          - v   v         vvv         iv      v  i  i v   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_97215772_9   4685 CT------AATTAAAGAGTTTCTGCACACCAAAAGAAACTATCAACAAAG 4728
                         i ------       i v   -  ii vi    i  v        v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_97215772_9   4729 TAAACAGAAAACCTACAGAAAGGGAGAGAACAGTTGCAAACTATGCATCC 4778
                          i  v   v    i      v      i  i v       ii  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_97215772_9   4779 AACAAAGGTCTAATATCCAGAATCTATAGGGAAATT----AAATCAACAA 4824
                         i i  i  v  vi          v    ii   v i----  v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_97215772_9   4825 GCAAAAAACTAACAACCCCATTAAAAAAGTGGGCAAAGGACATGAACAGA 4874
                         vv    i  v  i     v   ?     -           iv    i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGA 840

  chr1_97215772_9   4875 TAATTCTCAAAAGAACATGTACACGTGACTATTGAGCATTTGAAAAAAAT 4924
                         i v     v      v  i    vi  i i v i    iv      i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-T 889

  chr1_97215772_9   4925 GCTTAGTATCACCAACGAA 4943
                            i ii    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (125 / 96)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 1.70 (34 / 20)  


3016 27.89 0.47 0.58  chr1_97339395_97341427      676  1532 (501)    L1M4_orf2#LINE/L1        1   856 (52)  

  chr1_97339395_9    676 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATTAGTATCATGAAAAT 725
                              ii i  i     i      i v      v   i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97339395_9    726 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 775
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_97339395_9    776 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 823
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_97339395_9    824 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 873
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_97339395_9    874 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATAGTACAAGGC 923
                                i      vv   ii  v  ii i      viv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_97339395_9    924 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 973
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_97339395_9    974 AATGGAACAGAAC--AGAACCCTCAGAAATAACGCCACATATCTACAACT 1021
                                i    i--   ii  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_97339395_9   1022 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1071
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_97339395_9   1072 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1121
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_97339395_9   1122 GAAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1171
                            ii    i i  v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_97339395_9   1172 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1221
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_97339395_9   1222 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1271
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_97339395_9   1272 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1321
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_97339395_9   1322 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAAC 1371
                          i   v v  i i   i  ii vv    i  v    i  vv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_97339395_9   1372 AGGCGACCTACAAAATGGGAGAAAATTTTCGCAACCTACTTATCTGACAA 1421
                           i i   i   i             v  i    vii iv       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_97339395_9   1422 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 1471
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_97339395_9   1472 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTT 1521
                          i     i     v  i?    i    ii     iv    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_97339395_9   1522 TCAACATGAAG 1532
                           v v -    
  L1M4_orf2#LINE/    847 TCCAAA-GAAG 856

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.01 (6 / 856), avg. gap size = 1.50 (9 / 6)  


1752 26.94 8.32 5.43  chr1_97425880_97427913      677  1541 (493)    L1M4_orf2#LINE/L1       19   908 (0)  

  chr1_97425880_9    677 TCATAGACTTGTTGACTCAATACTGTTAAGATGTTAA-ACTTCACCAAAT 725
                             i  i v vv    i    i          vi  -   i -      
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC-CCAAAT 67

  chr1_97425880_9    726 TGATCTGTAGATTCAACACAACTCAAAACAAAAATCCAAAAAGGTTTCTT 775
                               ii         i   ii vv v     -   v ivv vi  i  
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCCAGCTGCCTTTTT 116

  chr1_97425880_9    776 TGAAGAAACTGATAAGCTGATTCTTAACATTATTTAAAAATACAAAGGAT 825
                           v     i   i        i  v  vv i  v ii    i   i   i
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr1_97425880_9    826 GTAGATTAGCAAAAACAATCAGGAAAGAAAATAAC-----TCAAGGAC-- 868
                         vi   v    v         vv    i i  v   ----- vi     --
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr1_97425880_9    869 ACGATTTC--ATTTTAGGACTTGCTTTAAATTTATAGTAATAAAGACAAT 916
                           iv  i --    i ii    i  vi   vi  i      v      i 
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr1_97425880_9    917 G--------GCATTAGAATATACG-ACAAATAAGTGAAAGAGAAC--GGA 955
                          --------    v  i   v  i- i i  v i  i  v    i--i  
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr1_97425880_9    956 GTCCTGATATAGTCCCA--CAGGTAAGGCCAATTAATTTTTGACCAAGGC 1003
                             v  v   iv    --  vv  v  i     i     i   v i  i
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_97425880_9   1004 AGGAAGTCAGTTCAATGAGGGGAAAAAAGCCATTCTAACAAATGGTGTGA 1053
                         ivv   v vi       i  ii i  v  i v  ii           ivi
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_97425880_9   1054 GAAAAGCAGGATATTTTTAAGAGGAAGGGGGGAGAAAAGAAAAGAAAAGA 1103
                          i v i v     ?iivi v v----------------------------
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGC---------------------------- 438

  chr1_97425880_9   1104 AAGGAAAAAAATGAAACCATGG-CCTCTACCTCACTTCATATACAGTTTT 1152
                         ----    i      ii--   -  i         vi        i----
  L1M4_orf2#LINE/    439 ----AAAAGAATGAAGT--TGGACCCCTACCTCACACCATATACAA---- 478

  chr1_97425880_9   1153 TTTAAA--GATTCAAGATGAATTGTAAATCTAAATGTAAAACTTGAAACC 1200
                         ---   --i i    i   i  ii? i i          i vi i    i
  L1M4_orf2#LINE/    479 ---AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_97425880_9   1201 ATAAAGTTCCTAGGGAGAAGAAA-AGGAGAATATTTCTGTAACCCTGAAT 1249
                              ii  i   i-    i v -   ? v v  i ii  i   i  ii 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGA-AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_97425880_9   1250 TAGGCAAAAATTTCATGGAAAGGATGTTAAAAGCAACGACTAATTTAAAA 1299
                                vii    v i  v v  iiii       - i vi  iv-   i
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCA-CAAGCAACA-AAAG 622

  chr1_97425880_9   1300 AAAAAATTGATAAACTGGAC--------ACTTGAA-------------CA 1328
                                v      i     -------- v  i  -------------  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_97425880_9   1329 AAATACATCATTAAGAAAAT--AAAGA--AGCCAAAGTCTAGAAAAAAAT 1374
                           iv   ii  i      i --     -- v   v  vv i i i     
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_97425880_9   1375 ATATTCACACACATATATTTTAAAACGAACTCATATGTAAAATACATGAA 1424
                           v v  v i-       i v v  v i   ii   vi i    i  i  
  L1M4_orf2#LINE/    723 ATTTGCAAAT-CATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_97425880_9   1425 GAACT---AGAAACCAACAGTTAAAAGA----TTAC----------AATA 1457
                              --- v  vi   i i v      ---- v  ----------   i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_97425880_9   1458 GACAAAATACTTGAACA-ATACTTTTT--AAAAAGACATACAAATGATCA 1504
                          i    iv i     i - i i  i i--  i    i         ii  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_97425880_9   1505 ATAAATACATAAAAAAGTGTTCCACATCAGGGAACTC 1541
                             ii    i    ii  i  v      ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (149 / 81)
Gap_init rate = 0.03 (29 / 890), avg. gap size = 4.10 (119 / 29)  


3107 27.97 0.44 0.44  chr1_97464953_97469175     2823  3730 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_97464953_9   2823 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2872
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97464953_9   2873 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2922
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_97464953_9   2923 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2970
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_97464953_9   2971 TATGGAACCAAAAGAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAC 3020
                                viiv   i  v  viv  v     iv     i i ivv i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_97464953_9   3021 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3070
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_97464953_9   3071 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3120
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_97464953_9   3121 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 3168
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_97464953_9   3169 ATCTGATCTTTGAGAAACCTGACAAAAACAAGAAATAGGGAAAGGATTCC 3218
                          vi    i  i  v  ivv  v   i v  vvv   i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_97464953_9   3219 CTATTTAATAAATGGTTCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3268
                           v  i  i       v      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_97464953_9   3269 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATAGA 3318
                            ii    i    v   i     v              i    i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_97464953_9   3319 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAACAAAAC 3368
                          i ?    i    i  v   v       i      vi i     v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_97464953_9   3369 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 3418
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_97464953_9   3419 AACACCAAAAGCAATGGCAACAAAAGCCAGAGTTAACAAATGGGATCTAA 3468
                         i            vvi          vv i i vi i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_97464953_9   3469 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3518
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_97464953_9   3519 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 3568
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_97464953_9   3569 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3618
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_97464953_9   3619 AACCAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 3668
                          iv    i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_97464953_9   3669 TCAAAAGAAGACATTTATGCAGCCATCAGACAAATGAAAAAATGCTCATC 3718
                           v        i  vi viii    vi ii  v       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_97464953_9   3719 ATCACTGGCCAT 3730
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (149 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3231 27.12 0.55 0.44  chr1_97495022_97499572     3152  4058 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_97495022_9   3152 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAGTCAATATCGTGAAAAT 3201
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97495022_9   3202 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3251
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_97495022_9   3252 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3299
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_97495022_9   3300 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 3349
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_97495022_9   3350 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3399
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_97495022_9   3400 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3449
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_97495022_9   3450 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3497
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_97495022_9   3498 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3547
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_97495022_9   3548 CTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCT 3597
                           v  i  i              v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_97495022_9   3598 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 3647
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_97495022_9   3648 TTACAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3697
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_97495022_9   3698 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 3747
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_97495022_9   3748 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3797
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_97495022_9   3798 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3847
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_97495022_9   3848 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3897
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_97495022_9   3898 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3947
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_97495022_9   3948 AAA-AAACAGCCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 3996
                          i -   i i   v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_97495022_9   3997 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 4046
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_97495022_9   4047 ATCACTGGCCAT 4058
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2506 24.07 1.41 10.27  chr1_97533259_97541290      491  1483 (6549)  C L1M4_orf2#LINE/L1   (0)   908     4  

C chr1_97533259_9   1483 AAATATATCTTGTGTTCATGGATTAGAAGAATTGGT-TTGTTAAAATGTT 1435
                            v     iii            i     v  ii -       i   vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

C chr1_97533259_9   1434 CATATTATCTCCCAAAGCAATCTACACAATCAGTGTAATACCTATGAAAA 1385
                         v   i ---i      vii       v v   ii i   v     v    
  L1M4_orf2#LINE/     54 AATACT---CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_97533259_9   1384 TTTAATATAG-TTTTTCATAGACATAGAAAATATAATTCTAAAATGTGTA 1336
                          iiv vv iv-     iii   v  v  v  vv i  i       vii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr1_97533259_9   1335 TGGAACTGCAAAAAAACCCTGAATAGCCAAGTCAGTCC-GAGCAAAAAGA 1287
                              v     iii -   v          iv  i  i-  iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

C chr1_97533259_9   1286 ACAAAGCTGT-GGACATCATACTAACTGATTCTGAACTCTACCACCAAGT 1238
                               i  v-    -   i   vv ii   iii  vii   i  v   i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr1_97533259_9   1237 GATGTTAGTTAA-ACAGCATGATGTTGGCATAAAAATAGACTAATTGACC 1189
                         v iiv  i i  -    ii  i ii        ii      vv  v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr1_97533259_9   1188 AGTGGAGCAGAATGGAAAACTCAGCAGTGAACCTATTCATATATAGTCAA 1139
                          i    ii     v  i iii   v i i    i  v   v   i     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

C chr1_97533259_9   1138 TTGATGTTAAGCAAGGGTGCCAAGTATAACCATT----GGAAAAAGGACA 1093
                              v  vii             ----      ----  ii    i i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAG----ACCATTCAATGGGGAAAGAATA 394

C chr1_97533259_9   1092 -TCTTTTCATTAAAGGGTGTTGTGAAAAATGTATATCCATGTGCAGAAGA 1044
                         -        vi   v    i  v  v  v  v   ?   ii    i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chr1_97533259_9   1043 ATGAAATTAGATCATTATCTCACAGCATTAACAGAAATATTA--TCAAG- 997
                              i  i  i vi  i      v   vv   i    --  --    i-
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT--TAACTCAAAA 492

C chr1_97533259_9    996 TGGATTAAAGAGGTAAATGTAAGACCTTAAACTGTAAAACTACTAGAAGA 947
                              i ?   vv           v  v     i       vi       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

C chr1_97533259_9    946 AAATATAGGAGAAAAAGTGCACAATATTGGTCTAGATAATGATTTTTTAA 897
                            i     ? v   vv v iii iv    vi   ii    i   i   i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

C chr1_97533259_9    896 TTTTTTAATTGCTGGAGCTCCACTCCAGACCCTGTTTGCCTGGGTGTCAC 847
                         --------------------------------------------------
  L1M4_orf2#LINE/    593 -------------------------------------------------- 592

C chr1_97533259_9    846 CAGCGGAGGCTGCAGAACAGCAAATATTGCAGAACAGCAAATATTGCTAC 797
                         -----------------------    -----i   v    ---------
  L1M4_orf2#LINE/    593 -----------------------ATAT-----GACACCAAA--------- 605

C chr1_97533259_9    796 CTGATCACAGGCAACAAGTGCAAAAATAGACAAATTGGATTACATCAAAA 747
                         --- v    i       iv v         i        i v        
  L1M4_orf2#LINE/    606 ---AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

C chr1_97533259_9    746 TAAAAAGCTTCTGCACAGCAAAGGAAACAATTAACAGAGTGAAGAAGCAA 697
                          v    i   i  ii vv       v  v  i  v i      i ii   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

C chr1_97533259_9    696 CCCATGGATTTGAAGAAAATATTTTTGGGCCATAAATCTGATAAGGGGTT 647
                             ii  v v i           viiiii    v            ii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

C chr1_97533259_9    646 AATATCAAATATATATAAGGAGACTAA-ACAACTCTTTGGAAAGAAAAGA 598
                         vi    v iv        i  -   vv-       vv iiv  i  i v 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGA-ACTCTTACAACTCAATAATAAAAAGACA 801

C chr1_97533259_9    597 AATAGTTTGAATAAAAAATGAGCAAGGGAGCTGAATAGACATTTCTTAAA 548
                             iiiii v ?       i    i   vi               iv  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

C chr1_97533259_9    547 AGAAATAACACAAATGACCAATAGGCATATGAAAAAATGCTCAACATCGG 498
                             ivv i       i      i   i       i            i?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

C chr1_97533259_9    497 TGATCAC 491
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.64 (146 / 89)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 6.11 (116 / 19)  

2977 27.37 1.32 1.10  chr1_97533259_97541290     6634  7539 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_97533259_9   6634 TGGAAGAACATTCCATGCTCAGGGATAGGAAGAATCAATATCGTGAAAAT 6683
                              ii i  i     i   v    v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97533259_9   6684 GGCCATACTGCCCAAGGTAATTCATAGAATCAATGCCATCCCCATCAAGC 6733
                            v     v     iv i  ii i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_97533259_9   6734 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6781
                          vi  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_97533259_9   6782 TATGGAA-T-CAAAAAATAGCCCACA-TAGGTAAGACAATCCTAAGCAAA 6828
                                - -   iii ---    v -   vi  i      i i iv  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_97533259_9   6829 AAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTCTATTACAA 6878
                                   i      vv       v  ii i      vii  i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_97533259_9   6879 GGCTACAGTAACCAAGACAGCATGATACTGGTACCAAAAGAGCTATATAG 6928
                         i          i        ii  i      i iv ii v  vi      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_97533259_9   6929 ACCAACGGAACAGAACAGAGGCCTCAGAAATAACATCACACATCTACAAC 6978
                          i   i    i    iv   ivii         vvi  i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_97533259_9   6979 CATCTGATCTTTGACAAACCTGACGAAAACAAGAAATGGGGAAAGGAT-- 7026
                           vi    i  i     ivv  v i i v  vvv           i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_97533259_9   7027 TCCTTATTTAATAAATGGTTCTGGGAAAACTGGCTAGCCATATGTAGGAA 7076
                           i  -- i  i       v      v      v  ?   i   i ii i
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_97533259_9   7077 GCTGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGAT 7126
                         iv    ii    i    v   i     v  i           i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_97533259_9   7127 GGATTAAAGACTCACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 7176
                             i ?    ii v    v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_97533259_9   7177 AACCTAGGCAATACCAATC---AGGACACAGGCATGGGAAAGGACTTCAT 7223
                            v    ?i-  --    ---iv   viv  vv i  v  v ii   v 
  L1M4_orf2#LINE/    544 AACATAGGNG-TA--AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_97533259_9   7224 GTCTAAAACACCAAAAGCAATGGCAACAGAAGGCAAAATTGACAAATGGG 7273
                         ivv  vi            vvi      i   iv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_97533259_9   7274 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAATAAATTACCATCAGA 7323
                          ii v  i   v v  i i   i  ii vv    iv v i  i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_97533259_9   7324 GTGAACGGACAACCTACAGAATAGGAGAAAATTTCTGCAATCTACCCATC 7373
                              vi       i       i         v i     vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_97533259_9   7374 TGACAAAGGGCTAATAACCAGAATCTACAA-GAACTTAAACAAATTTACA 7422
                            i  i  i  vi  v       v  i  -     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_97533259_9   7423 AGAAAAAAACATACAACCCCATCAAAAGGTGGGCAAAGGATATGAACAGA 7472
                          v     i   v i     v  i?   ii            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_97533259_9   7473 CATTTCTCAAAAGAAGACACTTATGCAGCCA-CAGACACATGAAAAAATG 7521
                                 v        i ivi viii    -i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_97533259_9   7522 CTCATCATCACTGGTCAT 7539
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (154 / 90)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.57 (22 / 14)  


2362 24.09 2.74 1.68  chr1_97578141_97581214.rev     1370  2025 (1049)    L1M4_orf2#LINE/L1        1   663 (245)  

  chr1_97578141_9   1370 TGGAGAGATATTCCATGTTCATGTATAGGAAGAC--AGTACTGTCAAGAT 1417
                             i      i           v  v       -- i  i   i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97578141_9   1418 GTGAGTTCTTCCCAGCTTGATCTATAGATGCAATGTAATCACAGTAGAAA 1467
                          vv i v  i    iv        i    v   i i    v vi vi   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_97578141_9   1468 TCCCCGCAAGTTGTGTTGTGGGCATTAACAAACTGATTCTAAAGTTTAAA 1517
                             v  vivi v v   ii iv   i    i     i     i  i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_97578141_9   1518 --GGCATGCTAGAAGACCCAGAATAGCTAACACAATATTGAAGGAGAAGA 1565
                         -- iv    v  i-             i  v     v     ii      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_97578141_9   1566 ACAAAGTTAGAGGACTGACACTACCTAACCTCAAGACTTACTATAAAGCT 1615
                                 i       v     v  i  ii    i        i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_97578141_9   1616 ACAGTAATCT-GACAGTGTAATATTGGTTAAAGAATAGACAAATAGATCA 1664
                                  v-        ii  i   ivv   i       v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_97578141_9   1665 ATTGAACAAAAAAGACATCCCAGAAATAGACCCACATAATTA-AATCAAC 1713
                           v   i i  vv  v vi         i     i i v   -ii    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_97578141_9   1714 TGATTTTTGACAAAGCAGT-AAGACACTTCAGTGGAGAATACATAGTAAT 1762
                                i     i vv i-     vv    i   i   viv     vv 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_97578141_9   1763 TT-ACCAAATGGTGCTGGAACAACTGCATGTTCACATGCAACAAAAAATT 1811
                           - v             i       v  i?i         --  i   v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA--AAGAATG 447

  chr1_97578141_9   1812 AATCTAGAC---------ACACCCTTCACCAAAATTAACTCTAAATGGAT 1852
                           vi i   ---------     v vi  v           v        
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_97578141_9   1853 CATACATCTAAATGTAA-AGCACAAAAATATAAAATTCCTACAAGATAAC 1901
                           ? v i          -   -i    v       i  i  v    v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_97578141_9   1902 ACAGAAGAAAACCTAGATGATCTTGAATATGTTGATGACACATGTGTTTT 1951
                          i  i? v   i  vvi   i    i----   i-- i  -   vv  i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGG----GTTA--GGCA-ATGGTTTCT 589

  chr1_97578141_9   1952 TAAATACAACTCCAAAGGCAATATTCATGAAAGAAATTATTGATACGCTG 2001
                           i   ii  v     i   vv viv ii       vv  v    vii  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_97578141_9   2002 GGTTTCATTAAAATAAAAAACTCT 2025
                          ii     i     v       i 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTT 663

Transitions / transversions = 1.28 (87 / 68)
Gap_init rate = 0.02 (14 / 663), avg. gap size = 2.07 (29 / 14)  

 892 24.52 0.77 0.77  chr1_97578141_97581214.rev     2323  2583 (491)    L1M4_orf2#LINE/L1      648   908 (0)  

  chr1_97578141_9   2323 CAAAA--AAAAACTTCCGCTCAGTGAAAGATAATGTCAAGAGAATGAGAA 2370
                              --        ii iv vvii  i  i v i      i i   i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_97578141_9   2371 GACAAGCCACCGACTGGGAGAAAATATTTGTAAAAGATGCATTGGAGAAA 2420
                              v    v  v                i   vv  ii  iv  v  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_97578141_9   2421 GTACGGTTATCCAAAATACACAAAGAACACTTAAAACTCAACAATAAGAA 2470
                          v  vvv      i    i i       v    v       i     i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_97578141_9   2471 AACAACGAACCAGATTTTAAAAAATGAGCTAAAGACTTTAACGGACACCT 2520
                         i    vv    vi   ?--       i  v  i  i  v  ii    ii 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_97578141_9   2521 CATCAAAGAAGATAAACAGATAGCAGATAAGCATATGAAAAGGTACTCTA 2570
                          vi           v   i  i  vi       i        i i   v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_97578141_9   2571 CATCATGTCAGGA 2583
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (37 / 26)
Gap_init rate = 0.01 (2 / 261), avg. gap size = 2.00 (4 / 2)  


2952 25.97 1.89 1.11  chr1_97698351_97700367      653  1553 (464)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_97698351_9    653 TGGAAAAACATTTC-----CACGGATAGGAAGAATCAATATCATGAAAAT 697
                               i i  ii -----  i    v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97698351_9    698 GGCCATACTGCCTAAAGTAATTTACAGATTCAATGCTATCCCAATCAAGC 747
                            v     v  i   v i  i           i  v     v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_97698351_9    748 TACCAG-TGACTTTCTT-CAGAGAATTAGAAAAAAGTACTTTAAATTTCA 795
                          v    -  v    i  -    -    -  v  ivvv iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATT-GACAAGCTGATCCTAAAATTCA 148

  chr1_97698351_9    796 TATGGAACCAAAAAAGAGCCTGTATAACCAACACAATCCTAAGCAAAAAG 845
                                viiv  ii  v  v v   i    v      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_97698351_9    846 AACAAAGCTGGAGGCATCACTCTATCTAACTTCAAACTATACTACAAGGC 895
                                i      vv    v  vi i  i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_97698351_9    896 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGACC 945
                                 i   i    ii         i iv ii i   v i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_97698351_9    946 AATGGAACAGAAC--AGAACCCTCAGAAATAATATCACACATCTACAAAT 993
                                i    i--   ii  --        vvi  i    i  iiivi
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_97698351_9    994 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 1043
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_97698351_9   1044 CTATTTAATAAATGGTGTTGGTAAAACTGGCTAGCCATATGCCGAAAACT 1093
                           v  i  i        i   v v      v  ?   i    vi  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_97698351_9   1094 GAAACTGGACCCCTTCCTTACACCTTATACAAAAAATAACTCAAGATGGA 1143
                            ii         v   i     v          v        i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_97698351_9   1144 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1193
                          i ?    i           v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_97698351_9   1194 CTAGTC--AAATACCTCAGGACATAGGCATGGGCA--GACTTCATGACTA 1239
                         v   v?--    - i  iv   v v  vv i    -- ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_97698351_9   1240 AAACACCAAGAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1289
                         vi       i    vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_97698351_9   1290 ACTAAACTAAAGAGCTTCTGCACATCAAAAGAAACTATCATCAGAGTGAA 1339
                          ii   v v  i i   i  ii v     i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_97698351_9   1340 CAGGCAACCTACAGAACAGGAGAAGATTTCTGTAGTCTATCCATCTGACA 1389
                         v  i     i      ii      i  v i  i ivii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_97698351_9   1390 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAACTTA-CAAGAA 1438
                          i  i  vi          v  i        ivv    -  i -i  v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAA 794

  chr1_97698351_9   1439 AACAAACAAACAACCCCATCAAAAAGTAGATGAAGGGTATGAACAGACAC 1488
                           - i     i     v  i?    i i iii    i v    i     i
  L1M4_orf2#LINE/    795 AA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_97698351_9   1489 TTCTCAAAAGAAGATATTTATGTGGCTATTC--CACAGTTTAAAATATGC 1536
                              v           vi vi    i v v--    -- v    v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA--TGAAAAGATGC 891

  chr1_97698351_9   1537 TGCTAC-TCAGCTGTCAT 1553
                          - v  -   ????????
  L1M4_orf2#LINE/    892 T-CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (133 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.59 (27 / 17)  


2804 25.38 2.18 3.27  chr1_97707947_97711189.rev     1842  2759 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_97707947_9   1842 TGGAAAGACATCTTATATTCTTGGATTGGAAAAACTAAT---GTTAAAAT 1888
                                 i   ii  i   v          i vi    ---     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97707947_9   1889 ATCCAT-TTCACCTAAAGCAATGTACAGATTCAATGAAATCCTTATCAAA 1937
                         iv v  -i  -  i   vii  v           i v     i       
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_97707947_9   1938 ATTCCAAATACATTTTT-ACAGAAATAGAAAATGTAATCCTAAAATATGT 1986
                           i   iv i v     -i       v  v  vv i          vii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_97707947_9   1987 ATGAATCCACAAAATACCCA-AATAACAAAAACAATTTT---AAATAAGA 2032
                            i vvii   iiv     -    i v        i  ---   v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_97707947_9   2033 ATAAAGCTAGAAACATTATACTTCCTGATTTCAAAA-TAATTACAAAGC- 2080
                          i    i i  iivv i i      ii         - v i        -
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_97707947_9   2081 --AATAATCAGAGTAGTATGCTACTGGCATAAAAACAAACATGTAGAGCA 2128
                         -- i      iiii   i  v           ii i i    i    v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_97707947_9   2129 TTGGAACA--ATAGAGAGCTTATATCCTACAGCCATGTCATGTACAGTCA 2176
                         v     i --  v     iii v -vv  v v    i-   v  ii    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGA-AATAAACCCATA-CATTTATGGTCA 347

  chr1_97707947_9   2177 ACTATACAACATATACAATGACTTTCAATACGAAAGTCAAGAATGCATAG 2226
                          i ----------------  i    i i v iiv i     viiivi i
  L1M4_orf2#LINE/    348 ATT----------------GATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_97707947_9   2227 CGGGGAAAGGATTGTCTCTTCAATAAATGTTACATTGGGAAAAGTGGCTA 2276
                         i        i  v    i     i     v i --     v  v   v  
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGC--TGGGACAACTGGATA 429

  chr1_97707947_9   2277 TGTACATGCAAAATAATTAAATTGGAATGTTTTCTTTCACCACAGACAAA 2326
                         ?vi          v   v  i     vivi vi  iv     i v     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_97707947_9   2327 AATTAACTCACAATTAATTAAAGACTAAAATGTAAGACCTGCAACTCTAA 2376
                                   v   vi  i ?    iv          v  iv    v   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_97707947_9   2377 AACTCCTTAGAAGGAAGCATATGGGAAAAGCTTCATGACATTGGTTTTGG 2426
                              -       i  i    v ? v   v    i    v    v  v  
  L1M4_orf2#LINE/    530 AACTC-TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_97707947_9   2427 CAATAATTTCATGGATATGACACCAAAAGTGCAGTCAACAAAAGCAAAAG 2476
                             ii    v i                ii  iv         v    i
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_97707947_9   2477 GAGATTAAGTGAGATTACAACAAACTAAAAGAACTTCTGCATAGCTAAGG 2526
                         v    v  v  -  i v  v    v v   -     i  iiivv v    
  L1M4_orf2#LINE/    629 TAGATAAATTG-GACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGG 676

  chr1_97707947_9   2527 AAACAATCAACAGAGTAATAAAGCAGCCTTTAGAATGGGAAGAAATATTT 2576
                          v  v     v i   i v  ii  i  ivi         ii        
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_97707947_9   2577 AC----CAT-TAATTAACCAGCAGTTAATTTCCAAAAAATATAAGAAACT 2621
                         i ----   -  vi i iv  viii vi v    i  v      ii    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_97707947_9   2622 TTTAAAATTCAATAGCAAAATATTTAAATAGTCCAATTTTAAAAATTAGC 2671
                         i   v  i      ii    - vvi     ii      ?-      vi  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAA-AGACAAATAACCCAATTW-AAAAATGGGC 824

  chr1_97707947_9   2672 AAGGGACTTGAATAGATATTTTTTCAAACAAGCCATACAAATGGCCAACA 2721
                           i   i         i    i i    v   vi              i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_97707947_9   2722 GGTACATGAAAAAATGCTTATCACTGATCATCAGGAAA 2759
                         i i         i     i --  --    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCA--AC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.27 (50 / 22)  


2940 25.91 1.94 0.68  chr1_97800606_97802460      487  1362 (493)    L1M4_orf2#LINE/L1       22   908 (0)  

  chr1_97800606_9    487 TGGATCA-AAGTCATAATATAATGAAAATAAC--TACTGACAAAAGGAAT 533
                              ii-   v v      vi v  i  ii --    vv v   vvi  
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGAT 71

  chr1_97800606_9    534 CTACAGGTTCAGTGCAATCCCCATGAAAATTCCAACTTTAATTTTCATAG 583
                               i    ii        i  v     i   i  vivv    iii  
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAG 121

  chr1_97800606_9    584 AAATAGAGAAAACATTACCAAAACACATATGGAACCAT-TGAAAAACCCT 632
                             v  v  iviiv v i    iv         --  -ii iii    v
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAA--ATGCAAGGGACCCA 169

  chr1_97800606_9    633 GAATAGCCAATGCAATCATGAGCAAAAAGAACAAAACTGGAGGTATCACA 682
                                   vi     v   iv  i         ii      vv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_97800606_9    683 TTACCTGATTTCAAACTATACAACAAAGCTAGAGTAATTAAAACAGAAAG 732
                         i v  ii        viv   v         v      i  i    viv 
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_97800606_9    733 GTATTCGCCAAAAAAAAATAGACACATCAACCAAGGGAACAGAGTAGAGC 782
                            i v  --- v  ii       i  vi i   v    i   i v   v
  L1M4_orf2#LINE/    270 GTACTGGC---ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr1_97800606_9    783 ATCCAGAAATAAACCCATGCATATATGATCAACTGATTTTTGACAAAGGT 832
                         i                 i   v    i    i       i     i   
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_97800606_9    833 GCCAAGAATAAGCAATGGGTAAAGGATAGTCTCATTGAAAAGTACTATTG 882
                                vi vv       v    i       iv ii v  i iv ii  
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_97800606_9    883 GGAAAACTGGATTTCCACATGTAGAAGAACAAAATTTGACC------TTG 926
                            v        v?       i i     ii  i  v    ------ ii
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_97800606_9    927 CACCATATA-AAAAACCAACTCAAAATGTACTAAATACTGAAACATAAAA 975
                                  -     ii           v ii ? v  iv   ii   i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_97800606_9    976 CCAGAAACTCTAAAATTGCCAGAAGAAAGGATAGGAGAAAAGCTACATGA 1025
                         v vi     v     i vii        iv     ? v   v  v i   
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_97800606_9   1026 CATTGGTCTGGGAAATGATGTTTTGGATTTGATCCCAAAAGCACAGGCAA 1075
                          v    vi i  v    i v i  i   v   iv           i    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_97800606_9   1076 CAAAAGCAAAAATAGAGAAATGGGATTTGATCAAACTAAAAGACTTCTGC 1125
                               v         v    v   i  v      v v   i    i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_97800606_9   1126 ATTACCAAGGAAGCAATTAACAGTGTGTAGAGACAACTTACAGATCAAGA 1175
                         ii v v     vi v  i  v iv   v i       ii     viii  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_97800606_9   1176 GAAAATATTTGAAAGCTGTACCTCAGATAAGGAGTTAATATCCAAAATAC 1225
                                    v  iiii  iv  v       iii vi      i    i
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_97800606_9   1226 TTAAGAAACT---A-AACTCAACAGCAGTAAAACAAAAATCCCAATT-AA 1270
                         v   ii    --- -       i ii iv  i     v v       -  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_97800606_9   1271 AAATGGGCAAGGGATCTAAATAGACATTTCTCAAAAGATGACATACAAAT 1320
                                   i    i i              v     v  i        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_97800606_9   1321 GGCCTAGAA-TATATGAAAATTATCCTCAATATCACTAATCAC 1362
                             v v  -i i       v-  v     i    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (130 / 94)
Gap_init rate = 0.01 (12 / 887), avg. gap size = 1.92 (23 / 12)  


1785 27.90 1.18 0.20  chr1_97861566_97865465     1859  2367 (1533)    L1M4_orf2#LINE/L1        2   515 (393)  

  chr1_97861566_9   1859 GGAAAAATACTCCATGCTCATGAATAAGAATAATTAATAT-GACAATA-G 1906
                              i   ii     i     i  vi   v v       - vi  v - 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_97861566_9   1907 GCA-TCCTGCCCGAAGCAATTTATACATTCAATGCTATTCCCATTAAACT 1955
                            - v  v   i  vii  i  i v      i  v  i  i  i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_97861566_9   1956 ACCATTGACATTCCTCACAGAGTTAGAAAAAACT-ACTTTAAAATTCATA 2004
                         v   vivi v  ii ii    iv v  v  i-  - iii           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr1_97861566_9   2005 TGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCCAAAAGAA 2054
                              viiv  ii  v  viv        i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_97861566_9   2055 CAAAACTGGAGGCATCATGCTACCCGACTTCAAACTATACTATAAGGCTG 2104
                             ii      vv   ii  v   i i      viv     i  i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_97861566_9   2105 CAGTAACCAAAACAGCATGGTACTGGAA-AAAAATAAACACATAGACCAA 2153
                               i   i    ii         v -  ii   i   i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_97861566_9   2154 TGGAACAGAACAGAGATCTCAGAAATAAGACCACACAAT-ACAACCATCT 2202
                              i    iv    vii         iv   i   v - iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_97861566_9   2203 GGTCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 2252
                          i i  i     ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_97861566_9   2253 TTAATAAATGGTGCTGGGAAAGCTGGCTAGCCATATGCAGAAAATTGAAA 2302
                          i  i              v i    v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_97861566_9   2303 CTAGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAA 2352
                         i i       v   i     v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_97861566_9   2353 AGACTTACATATAGG 2367
                             i  v  i  i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAG 515

Transitions / transversions = 1.75 (89 / 51)
Gap_init rate = 0.01 (7 / 514), avg. gap size = 1.00 (7 / 7)  

 957 24.77 3.36 1.83  chr1_97861566_97865465     2673  2999 (901)    L1M4_orf2#LINE/L1      499   830 (78)  

  chr1_97861566_9   2673 AAAGACTTACATATAAAACCCAAAACTATAAAACTCT-AGAAGAAAATCT 2721
                          ?    i  v  i   i v i                -         iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_97861566_9   2722 AGG---AAATACCATTCAGGACATAGGCACGGGCAAAGATTTCAT---CA 2765
                            ---    -- -   iv   v v  vvii     v i    v ---i 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_97861566_9   2766 TGAAAACATCAAAAGCACCTGCA-CAAAAGCAAAAATTGACAGATGAGAT 2814
                            ---  i         vv   -      v      v  i i  vi  i
  L1M4_orf2#LINE/    596 TGA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_97861566_9   2815 TTAATTAAACAAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 2864
                           v  i   vvv  i i   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_97861566_9   2865 GAAGAGGCAACCTACAGAATGGGAGAAAATTTTTGGAATCTATCCATCTG 2914
                            i  i     i                 v    v  vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_97861566_9   2915 ACAAAGGTCTAATGTCCAGAATCTACAAGGAACTTAAACAAATTTACAAG 2964
                          i  i  v  vi i        v  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_97861566_9   2965 AAAAAAAC---CAACCCCATTAAAAAGTGGACAAAGGA 2999
                              i  ---i     v   ?    i   i       
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.14 (42 / 37)
Gap_init rate = 0.02 (8 / 332), avg. gap size = 2.12 (17 / 8)  

 308 23.08 3.85 1.54  chr1_97861566_97865465     3278  3407 (493)    L1M4_orf2#LINE/L1      776   908 (0)  

  chr1_97861566_9   3278 TCCTCCATCTCAA--ACAAACAAACAAACAAACAAA---AAACTTACGTA 3322
                           i v  v     -- i   v i     i  v v  ---   vv iv i 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_97861566_9   3323 AAGGACATGAACAGACATTTCTCAAAATGAGACATTTATGTGGCCAACAA 3372
                              iv    i           v   vi   i  vi vi       i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_97861566_9   3373 ACAAACATGAAAAAAAGCTCAAAATCATTCAATCA 3407
                         i  --        i v      v    ????????
  L1M4_orf2#LINE/    876 GCA--CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (15 / 15)
Gap_init rate = 0.02 (3 / 133), avg. gap size = 2.33 (7 / 3)  


2401 21.79 2.02 14.88  chr1_97884842_97887210.rev      850  1891 (478)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_97884842_9    850 TAGAGACATATTCCGGGTTTCCAAAT-AGAAGACTTAGTATTTTCAAGAT 898
                          i  i v    i  iv   iviii  -i         i    v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97884842_9    899 GTCAGGTCTTCCCAATTAGATCTATAGATTCAGTACAATCCCAAATCAAA 948
                          v  ivv  i     v v      i       iii       v -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAAA 99

  chr1_97884842_9    949 ATCTCAGGAAACTATTTTATAGATATTGACAAACTGATTCTAAAGTTTAT 998
                            i   vviv  v    ii   v        i     i     i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_97884842_9    999 ATAGAGAGGCAAAAGAT------TAACCAACATAATAT------AGAACA 1036
                           i  i v    ii  i------  i    v i   v ------    v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_97884842_9   1037 ACAAAGTTGGAGGACTCGGACTACCTGATTTTAAGACTTACTGTAAAGCT 1086
                                          iv   v  ii    i  i       ii      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_97884842_9   1087 GCAGTAATCAAGACAGTGTGATATTGTTAAAATAATAGACA-ATAGATCA 1135
                         i                   i  i  vi v  vi       -        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_97884842_9   1136 CTGGAACAGAATAGAGAGCCCAGAAATAGACACACGTAAATATAGCCAAC 1185
                         v     i     v     i         i  v  iii vv   i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_97884842_9   1186 TTATCTTTGACAAAAGAGCAAAGGCAATATAATGGAGAAGGGATAGTCCT 1235
                          v  i  i     ii v  v   i v  vi     i   i i      i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_97884842_9   1236 TTCAACGAATGATATTTATACCACCCTACTTCCATATGTAAAAAAGTGAA 1285
                               i    i ii viv  v  ivv iv?   i   i    i i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_97884842_9   1286 TCTAGAAACAAACCTTACACC-CAT-TAAAAATTAATTAAAGATGGATCA 1333
                         vi i  vv vv    i     -i  -i         i v  i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_97884842_9   1334 TAAACCTCAATGTAAAATACAAAACTACAGAACTCTTTGAAGATAACATG 1383
                         ? i    v       i vvi       i i       v     v     i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_97884842_9   1384 GGAGACCATGTAGATGACCTTCGGTTAGACAATGACTTTTTAGGTACAAA 1433
                           ? vvv  v vvi       v      i     ii  i    i  ii v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_97884842_9   1434 ATCAAAGGCAAGATTTATAAAATAAATTATTGATAAGATAGACTTCATCA 1483
                          i    i   vi viv i    v   vv  v     iv i          
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_97884842_9   1484 AATATAAAAAATTCTGAGCTGGGTGTGGTGGCATGTACCTGTAGTCCTGG 1533
                           vv      v  i  ----------------------------------
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTG---------------------------------- 665

  chr1_97884842_9   1534 CTACTCAGAAGGCTGAGGGAGGTTTGCTTGAATGCAGGAGTTTGAGACCA 1583
                         ------------------------     ---------------------
  L1M4_orf2#LINE/    666 ------------------------TGCTT--------------------- 670

  chr1_97884842_9   1584 GCCTGGGGAGCATAGTGAGACTCTCATCTCAAAACAAACACAGAAACAAA 1633
                         ----------------------------------------------    
  L1M4_orf2#LINE/    671 ----------------------------------------------CAAA 674

  chr1_97884842_9   1634 ATTAAAACTTCTACTCTGCAGGAAACTGTCTTGAAAGAAAATGAAAAGAC 1683
                         --------------------   v   i  ----      i         
  L1M4_orf2#LINE/    675 --------------------GGACACTATC----AAGAAAGTGAAAAGAC 700

  chr1_97884842_9   1684 AAGCCACAGGCTGGGAGAAAATATTTGCAAAAGACATACTTCATAAAGAA 1733
                           v      iv                    vv i   ii v    i i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_97884842_9   1734 CTGTTATGCAAAATGTCCAAAAGTCTCTTACAACCCAACAATATGAAAAC 1783
                           vv   v  i   i vi   iiv          i   i    vi  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_97884842_9   1784 AA----CCCATTTAAAAAATGATACAAAGACCTT-AGCAGATATCTCACC 1828
                           ----    v  ?       i-i     ivi  - ii   i  i  v  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGG-GCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_97884842_9   1829 AAGAAAGATATACAGATGGAAAATAAGCATCTGAATAGATGCCTCATATG 1878
                           ii          i    vv        iv    v      -   ---i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC-TCA---A 895

  chr1_97884842_9   1879 TATCATCAGGGAA 1891
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (134 / 89)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 11.00 (176 / 16)  


2129 23.82 3.82 3.82  chr1_97970262_97972540      542  1221 (1058)    L1M4_orf2#LINE/L1        1   680 (228)  

  chr1_97970262_9    542 TGGAAAGTTATACTATGTTCATGGGTCAGAAGACTCAATTTTGTTAAGAT 591
                                v   v i          i ii       i   v          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97970262_9    592 GGTGATTCACCTCAAATTGATATATCAAGTCAACACAGCCCCAATCAAAA 641
                           ii  v v  i         v  ivi v     i  ii   v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_97970262_9    642 TCCTAGCAGATGC--TTTTAGTAAAAATAGACAAACTTATTCTAAAATTC 689
                            i   ---   --    v i i    v     i  v  i         
  L1M4_orf2#LINE/    101 TCCCAGC---TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_97970262_9    690 ATATGGAATTTCAGGTGACCTAGAATAGCCAAA-CAA-CTTATAAAAAGG 737
                                 v v  i v    i            -   -   i-      i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-AAAAAGA 196

  chr1_97970262_9    738 AAAACTAACTTTGAGAACTATAACTAACTGATTTCAAGACTAACT----- 782
                          i   v  v  v   i   vvv   vv ii       i   v   -----
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_97970262_9    783 ------GTGA---AGACAATATGATACCAGTGTTAATATAGAAAAAAAGA 823
                         ------  i ---     i i  i   ii ii v iv     v v v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_97970262_9    824 TCAATGCCACAGAATACAAAGTCCAGAAAGAGACCCACAAATATACTGAC 873
                               vv i     vv i          v i     i v  v  iv v 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_97970262_9    874 AACTGGTTTTC-ATAAAAGTGCAAAGTCAATTCCGTGGAGAAATGA--GT 920
                           i  i     - i  ii    v   v v    vi   i    vi --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_97970262_9    921 CTTTTCCACAA-TGGTGTTAAAACAATTGGATGCCCATATGAAAAAAACA 969
                               v    -     i iii    i     i?   i   -------  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-------CA 439

  chr1_97970262_9    970 AAAACAAAACAAAACGAAAAAAAACTTTGACCA-TAACTCATACCATATA 1018
                            i--------  i   i------  v    v-  v    i        
  L1M4_orf2#LINE/    440 AAAG--------AATGAAG------TTGGACCCCTACCTCACACCATATA 475

  chr1_97970262_9   1019 TAAAATTTAACGTGAAATGTAACCTAGAGCCAAATGTAAAACACAAAACT 1068
                         i    v     vii     v v v?   v i        i vvi      
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_97970262_9   1069 ACACAACTTCTAGAGGAAAACATGGCAGAAAATATTTGCAACCCTAGGGT 1118
                          i v    ii    i        i v? v    v  i ii   i i  v 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_97970262_9   1119 AGACAAAGATTTTTTTAGATATGACACCAAAA-TACACATCATAGCACAA 1167
                           i   v i   i  -                -i   viiv i iv v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_97970262_9   1168 GAAATTGATAAATTTAACTTCATCAAAAATAACAATTTCTGTTCTTTAAA 1217
                         i    v        vi            v   v  i  i   v   i   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_97970262_9   1218 --ACAC 1221
                         --    
  L1M4_orf2#LINE/    675 GGACAC 680

Transitions / transversions = 1.27 (89 / 70)
Gap_init rate = 0.03 (17 / 680), avg. gap size = 3.06 (52 / 17)  

 732 21.28 3.40 2.13  chr1_97970262_97972540     1552  1786 (493)    L1M4_orf2#LINE/L1      671   908 (0)  

  chr1_97970262_9   1552 CAAAAGACATTCTTAAGAGAATGAAAAGACAACCCACATACTAGGAGGAA 1601
                             i    i v i    i i                 v v i    i  
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_97970262_9   1602 ATATTTTCAAGGCACATATCTGATAAGA-ACTTGAATCCATAATATTGTT 1650
                               v   iv  i            i-     v     v     v---
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA--- 767

  chr1_97970262_9   1651 TAAA---CTCTCAAAAATAAATAATAACAGAAACAAGCCGACCAA--AAA 1695
                             ---    i v  v v        - i i    iiviv    --?  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAA-AAAGACAAATAACCCAATTWAA 816

  chr1_97970262_9   1696 AAATAAACAAATGTCCTAAACAGACACATTACCAAATAAGACATACAGAT 1745
                             iii    v vii i  i     iv iv     v    i     i  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_97970262_9   1746 GGC--ATAAAACACATGAAAAGATATTCAGCATCATTCACCAT 1786
                            --    i-             ii   i     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAG-CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (31 / 18)
Gap_init rate = 0.03 (7 / 238), avg. gap size = 1.86 (13 / 7)  


2383 28.41 5.73 1.72  chr1_97984480_97986784.rev      948  1820 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_97984480_9    948 TGGAAACATCTTTTGTGTTTCTGGACAGGAATACTCACAATTCTCAAGAT 997
                               v  v iiii    iv    iv    v   i vv   v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_97984480_9    998 GTTGGTTCTTTCCAAATTGTTCCACAGATTCAGTGTAATTACAATCAAAA 1047
                          viii v  ii        v  i         ii i   iv v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_97984480_9   1048 TATCAGGAGGTTATATCTTGCTT------ATGGACAAAATGATTCCAAAC 1091
                          vi   v------ ii   vi  ------  v     iv    i i   v
  L1M4_orf2#LINE/    101 TCCCAGC------TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_97984480_9   1092 CTTATATAGAAAAGCAGAAGACTCAGAATAACTAACATA-TATTGAA--- 1137
                         i i    i    v   iii   i       i i  v i - v     ---
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_97984480_9   1138 GGAGAACAAAGTCTGAGAATTGACAGTACCCAAATTTAAGACTTACTGTA 1187
                          i          iv   i i v   v v     v  i  i       ii 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_97984480_9   1188 AAGCTGCAGTAGTCAAGGCAATGTGGTGTTATTGAAAGGATAGACAC--- 1234
                              i     i     i  i      ii iviiv           i---
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_97984480_9   1235 GATCAATGAGCTGGAATACAGAGCCCAGAAATAGGCC--TACAT----AA 1278
                                 iiv i    vv    i         ii  --     ----ii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_97984480_9   1279 TCAACTTGTCTTTGACAAAGGTGCAAAGGCATTTCAAT------------ 1316
                             i vi i  i     i     v   i vv      ------------
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_97984480_9   1317 -------CGATAAATGATACTGGAACCACTGGACATACACATGCTAAAAA 1359
                         ------- i i     i i    i  v      i ?v       ---   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC---AAA 441

  chr1_97984480_9   1360 AAAATCTAGACACACTGGACACAGATCTAACACCTTTCACAAACATTAAC 1409
                          i   vv  -----i     v vv i  v     v vi     v      
  L1M4_orf2#LINE/    442 AGAATGAAG-----TTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_97984480_9   1410 TCAAAATGAAGTGTAGAACTAAATAGAAAACACATGCCTACTATATTCTG 1459
                                 i vii?   v      iv  i vvi viv   iv v i   v
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_97984480_9   1460 AGAAGATAACATAGA---AAATATAGATGTTATTGGATTTGGTGATAACA 1506
                               v       i---    v vvi  viv    i  v  ii  iiiv
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_97984480_9   1507 TTTTAGATACAAATCCAAAGGCATGATCCATGAAATAAACAATTGATAAG 1556
                          i       ii vv     i   ii v v ii   v   v   v     i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_97984480_9   1557 TTAGACTTTATTACAATTAAATACTTCTGCTCTGCAAAAGACACTGTCAA 1606
                           i     i  i v       v    i  iv  v    i      i    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_97984480_9   1607 GGAAATGAAAAGATAAGCTACAGACTGGTTAAAAATTTTATGAAAGAAAC 1656
                          i  i        i  v i     v   vvi     v  -  v  ivv i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT-TGCAAATCAT 735

  chr1_97984480_9   1657 ATAACAGATAAATAAATGACATA-AAAATATAAAAAGAAGCACTAAAATC 1705
                            v v     ivi v vii  v- i      v      vivi  v  ii
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_97984480_9   1706 CAACAATAAGAA----AATAACCTGATTTTAAAATGGGCAAGAGATCTGA 1751
                            i     i  ----       ii   ?v           ii   i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_97984480_9   1752 ACATACACCTCATCAAGAAAGATATACAGATGGCAAATAACCATGTGAAA 1801
                          i v   ii  vi   ii          i     v     v  ii     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_97984480_9   1802 ATATGT----CATTAGGGAATTG 1820
                          v   i----   i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.33 (65 / 15)  


1430 25.48 7.52 7.07  chr1_98135672_98138442     1415  2305 (466)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr1_98135672_9   1415 CATGCTCAAGAGTTGTAAGAAATAACAGTGTATAAGATGGTCATTCTCCA 1464
                             i   v ii   v    vv   i v   -        iv  v    v
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGT-TAAGATGGCAATACTCCC 62

  chr1_98135672_9   1465 CAGAATGATCTATAGATTCAATGCACTCCCAATCAAAATCCCAGACAAGT 1514
                           i v       i        i   v    v             -----i
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG-----C 107

  chr1_98135672_9   1515 TTTCATTCTGGTGGAAATTGATCATCCGATTCTAAAATTTGTATAGAAAT 1564
                          vi v  i v ii        iv v i   i        ii   i     
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_98135672_9   1565 GCCAAGACCTAAGACTAGCCAAAGCAGTCTTGTA---GGAGAAAAAAGCA 1611
                           v i iv iv   v        i  i     v --- i    v    iv
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_98135672_9   1612 GAAGGACTTTCA-TTACCAGTTATCATGTCTTATTGTCAGACTGCAGTAA 1660
                          i      iv  -  v   i  -   viv    i iiv ii  i      
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATT-TCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_98135672_9   1661 ATATGACAGTGTGATATTGGCAAAAAAAAAAGAAAAAAGACAAATAGA-C 1709
                         vi v         i  i     v  ii v --------    v     - 
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATA--------GACATATAGATC 298

  chr1_98135672_9   1710 AA---AATAAACAAATGAAGGTCCAAAAAGAGACCCA--CATTCATTTGG 1754
                           ---    i -- v   ii     i   v i     --    i  --  
  L1M4_orf2#LINE/    299 AATGGAATAGA--ATTGAGAGTCCAGAAATAAACCCATACATTTAT--GG 344

  chr1_98135672_9   1755 CCACAT--------GACAAAGATGACATTGCAGGGCCA------GGGG-- 1788
                         i  -  --------     i i  - ----  i i   ------    --
  L1M4_orf2#LINE/    345 TCA-ATTGATTTTCGACAAGGGTG-C----CAAGACCATTCAATGGGGAA 388

  chr1_98135672_9   1789 -GAATA------------AATGTTACTGATTCCATTTAATATTCATA--C 1823
                         -     ------------    v i   ivv v i vi   ?i  i -- 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_98135672_9   1824 AGAAAAATTGCAATTTTTGACAACTACCTCATGCCATACAGAGAAGTAAA 1873
                          i  i   - v i  v--   vv        ii     i v i  i v  
  L1M4_orf2#LINE/    439 AAAAGAAT-GAAGTTG--GACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_98135672_9   1874 TCTCAGAA-GAATTGTAGGCCAAAATATTAAAATGAAAACAAAGAGATT- 1921
                         -    i  - i  ii?  i  v    i v i iiv     v vi i i -
  L1M4_orf2#LINE/    486 -CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_98135672_9   1922 ----AAGAATATA-AATAATGGATTTTT-TG---TTGGAAGAATCAATGA 1962
                         ----     v i - iv?i ii  i  i-  ---    ivv iv     i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_98135672_9   1963 TTTATTAATCAGGACACAGACCACACTAGTTTTACATAAAGGAAAAAAT- 2011
                            v   ivi v     vi vvi   v  i--- - i   i        -
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGC---A-ACAAAAGAAAAAATA 630

  chr1_98135672_9   2012 GATAAAATTGA--TAAT-AGAGTTAAGTGTATAAGTTTTATTACAGTAGG 2058
                               v v  -- v  - i i    i-----  v    i -------- 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAA-----AACTTTTGT--------G 667

  chr1_98135672_9   2059 CTT--AAGGATGTTCAATATTTAAAAACATAGAATCAAAACCAAGACACA 2106
                            --     ----  v   i-  i  vi ii  vv v    ----    
  L1M4_orf2#LINE/    668 CTTCAAAGGA----CACTATC-AAGAAAGTGAAAAGACAACC----CACA 708

  chr1_98135672_9   2107 G--TGGTAAAAAATATTTACACACATAGACACACGTAAAACAAAAGACTT 2154
                          --   v i         i  v i-----  i ii vvi i  ii     
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAAT-----CATATATCTGATAAGGGACTT 753

  chr1_98135672_9   2155 ATAT--AGAATAAACTAAGAACATCTT-CAAATCAATTTTTTAAGTATA- 2200
                         i   --      v iv      -    -   v     vv vv  iv i -
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAAC-TCTTACAACTCAATAATAAAAAGACAA 802

  chr1_98135672_9   2201 -TAATCCAATGGAAAGATTGGCAAAGGACTTGAATAGACAAATCACAAAA 2249
                         -   i     v?   i  v         i           vv  v v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_98135672_9   2250 TATTATATCCAAATGACCAATG-GC-TGTGATACAAGAAGCTCAATTCCA 2297
                         v vv    v      i     i-  -ii   - -    v      ivi  
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGA-A-AAGATGCTCAACATCA 900

  chr1_98135672_9   2298 GTGATCAT 2305
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.32 (127 / 96)
Gap_init rate = 0.05 (48 / 895), avg. gap size = 2.71 (130 / 48)  


3259 26.79 0.55 0.44  chr1_98389880_98393102.rev     1826  2732 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_98389880_9   1826 TGGAAGAACATTCCATGCTCATGGTTAGGAAGAATCAATATCGTGAAAAT 1875
                              ii i  i     i      v v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_98389880_9   1876 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1925
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_98389880_9   1926 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1973
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_98389880_9   1974 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 2023
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_98389880_9   2024 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 2073
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_98389880_9   2074 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2123
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_98389880_9   2124 AATGGAACAGAAC--AGAGCCCTAAGAAATAATGCCGCATACCTACAACT 2171
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_98389880_9   2172 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 2221
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_98389880_9   2222 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 2271
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_98389880_9   2272 GAAACTGGATCCCTTCCTTCTACCTTATACAAAAATTCATTCAAGATGGA 2321
                            ii    i    v   ivi   v            v i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_98389880_9   2322 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 2371
                          i ?    i    i  v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_98389880_9   2372 CTAGGCATTACCATTCAGGACATAAGCATGGGCAAGGACTTCATGTCTAA 2421
                         v    ?i v viv   iv   v vi vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_98389880_9   2422 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 2471
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_98389880_9   2472 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2521
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_98389880_9   2522 AGGCAACCCACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 2571
                           i         i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_98389880_9   2572 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2621
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_98389880_9   2622 A-ACAAACAACCCCATCAAAAAGTGGGTAAAGGATATGAACAGACACTTC 2670
                          -     i     v  i?    i    i       v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_98389880_9   2671 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 2720
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_98389880_9   2721 ATCACTGGCCAT 2732
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2587 28.52 2.13 0.89  chr1_98410665_98416359     4309  5202 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_98410665_9   4309 AAAAACACTTCATGCTCATGGATAGGAAGAATCCAAATTGCGAAAATGGC 4358
                            i i iii    i        v      v iv v    iv  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_98410665_9   4359 CATACTGCCCAAAGTAATTTATAGATTAAATGCTATTCCCATTAAATTAC 4408
                         v     v      v i  i  i     v  i  v  i  i  i   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_98410665_9   4409 AATTTACATTCTTCACAGAAATAGAAAACACT-ACTTTAAAATTCACATG 4457
                         v vi i v  i  ii       v  v  -i  - iii         i   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATG 152

  chr1_98410665_9   4458 GAACCAAAAAGGAGCCCATATAGCCAAGACAATCCTAAGCAAATAGAACA 4507
                            viiv  i   v  viv        i      i i iv  iv      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_98410665_9   4508 AAGCTGGAGACATCACACTACCTGACTTCAAACTATACTACAATGCTGCA 4557
                            i     ivv       v  ii i      viv        v   i  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_98410665_9   4558 GTAACCAAAACAGCATGGTACTGGTACAAAAATAGACACATAGACCAATG 4607
                             i   i    ii         i i  ii       i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_98410665_9   4608 CAATGGAATAGAGAACTCTTCTAAGACTGCACACAGGCA------ACCAT 4651
                         v   i    v    i----  i ii v iv  v  vi  ------ii  v
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAG----TCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_98410665_9   4652 CTGATCTCTGAAAAATCCAACAAAAACAAGCAATGAGGAAATGACTCCCT 4701
                         i    i ii  v  ivviiv   i v  vv     i     vi ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_98410665_9   4702 ATTTAATAAATGGTGCTGGGAGTTCTGGCTAGCCATATGCAGAAAATTGA 4751
                         v  i  i              vvv    v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_98410665_9   4752 AAGTGGACCCTT-TCTTATACCATATACAAAAATTATCTCAAGATGGATT 4800
                          iv       i -i  i i                 v     i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_98410665_9   4801 AAATACTTAAATGCAAAACCCCAAACTATAAAAACCCTAGAAGGAAATCT 4850
                          ? v  i      i  i v iv           vi i      i   iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_98410665_9   4851 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTCCAT-GATGAA 4898
                            ?i- v i -   iv   v v  vv i     v i  i v -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr1_98410665_9   4899 AATGCCAAAAGCAATTACAACAAAAGCCAAAATTGACAAATGGGATCTAA 4948
                         i ii         vvvi         vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_98410665_9   4949 TTAAACTAAAAAGCCCCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 4998
                          i   v v    i iii  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_98410665_9   4999 ATACAACCTACAGAATGGGAGAAAACTTTTTCAATCTATCCACCTGACAA 5048
                          v      i                iv   v   vii  vi i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_98410665_9   5049 GGGTCTAATATACAGAGTCTTCAAGGAACTTAAACACATTTACAAGAAAA 5098
                            v  vi   v    i v vi  i     ivv   vv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_98410665_9   5099 AGACAA-----CCACTTTAAAAAGTGGGCAAAGGATATGAA-AGACCCTT 5142
                               -----   v  ?     -            v    -    vi  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTT 845

  chr1_98410665_9   5143 CGC---AAAAGACATACATGCAGCCAAGAAATGTACAATAAAAAGCTCAA 5189
                          v --- i    i     viii     v  iiii ii v  i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_98410665_9   5190 CATCACTAATCAA 5202
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (142 / 109)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 2.08 (27 / 13)  


2118 24.97 11.25 4.81  chr1_98422272_98424199.rev      585  1437 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_98422272_9    585 TGAAGAGA-ATATCATGTTCGTGAGTCAGAAAA--TACTACTCTTAAGAT 631
                           i i   -  vi       i  ii ii   i --  v  i v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_98422272_9    632 TTCAGTTCTCTCTGATTTGGTCTATAGATTTAGTGCAATCCAAATCAAAA 681
                         vv  i v   i ii v   i    i     i ii       vv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_98422272_9    682 TCTCAAACAGGCCTTTTTTTTGTTTTGGTTTGGTTTGGGGTTTTTTGTAA 731
                           i  -----  --------  ii  ----------------     i i
  L1M4_orf2#LINE/    101 TCCCA-----GC--------TGCCTT----------------TTTTGCAG 121

  chr1_98422272_9    732 AAATCAGTAAGCCGATTCTAAAATTTAGGTGCAAAGAGCGAAGAACCTAG 781
                             iiii    i   i        i vi  v   v-  i i i   i  
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAAT-GCAAGGGACCCAG 170

  chr1_98422272_9    782 AATAATGGAGGCAAT-TTAAGACAAAATTAAGGAATAAAGATGAAGAACC 830
                             iivi ii    -  i ---    --i i   i    v  i  i  i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGA---AAAA--GAAGAACAAAGTTGGAGGACT 215

  chr1_98422272_9    831 CTCACTACTCCATTTCCAGATTGACTGTAAAGC----------------- 863
                          v    v i v     v i i v   ii     -----------------
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_98422272_9    864 ------ATTGGTATA------------TAGAACAATTGAACAAAAT--GG 893
                         ------ i   i   ------------    v    v   i i   --i 
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_98422272_9    894 AGTCCAGAAATAGACCCAAACATATATGATAGATTGATTACTTAGTAAAG 943
                                     i     v    v    i vi       -i iiii  i 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT-TTCGACAAGG 364

  chr1_98422272_9    944 TTGCCGGGGCAATTCAGTGTATAAAGAATGACCTTTCCA-CAAATGATGC 992
                         v    ii i v     i  viv       iii    i  -      i   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_98422272_9    993 TAGAACAATTGGGCATACATTTTTTAAAAGTAT----TTAAA----TAC- 1033
                          i i    i   ii ?v  iv vi-     v  ----  ii ----   -
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGC-AAAAGAATGAAGTTGGACCCCTACC 463

  chr1_98422272_9   1034 TCATATCATATTTATAAAAG--AACTCAAAATGAACTATAAACCTTGATG 1081
                            i i     -- i    i--           i ii ? i    vi   
  L1M4_orf2#LINE/    464 TCACACCATAT--ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_98422272_9   1082 TAAAACCCAAAACT-TAGGAC----------------AGGAG--AATCTC 1112
                            i v i      -  ii  ----------------   ? --     i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_98422272_9   1113 TGTGATCTTAAATTAGGCAA-AATATTTTAGAGAGGACAGAAAAATCACA 1161
                         i    i   iii        -ii v i     v v    vv    v    
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_98422272_9   1162 ATTCAT----TAAAAAATTGGTAAATTGGAAC-CATAAAAACTAAAA--- 1203
                          viv i----v       v i         vi-   v    i     ---
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_98422272_9   1204 -CTGCTCTTCAAAAGACACTATTAAGAAAATGAAAAGGCAAAACACAGAT 1252
                         -i  iv       i        i      i       i   vv      v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_98422272_9   1253 TAGGAGAAAATATTTGCAAA-CACGTGTTTGAAAAAGAACTTGTAGTCAT 1301
                          i                  -  ii i i   v  i i       vi  v
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_98422272_9   1302 AATACATAAAAAAGGCTCATGAAGTGAGAATAGGAAAACAAACTGCCCAA 1351
                             i     i  vv  i ii vvii v    ii  i     ivi     
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_98422272_9   1352 TTTAAAAATGTTGGCAAAAGAATTGAACAGACA---CTTCACAAAAGAGC 1398
                           ?       --      i  v     i     ---  i  v i    vv
  L1M4_orf2#LINE/    812 TTWAAAAATG--GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_98422272_9   1399 TATTGATGGC----------ATGAAAAGATGCTCAACATCATTCGTCAT 1437
                           ivi     ----------                     ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.27 (145 / 64)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 4.42 (137 / 31)  


3089 26.99 1.44 1.00  chr1_98462583_98464843      865  1768 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_98462583_9    865 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGGGAAAAC 914
                              ii i  i     i        v      v i       vv  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_98462583_9    915 GGCCATACTGCCCAACGTAATTTACAGATTCAGTGCTATCCCCATCAAGC 964
                            v     v     vv i  i          ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_98462583_9    965 TACCA-CTGACTTTCTTCACAGAA-TTGAAAAAAAAAAAAACTGCTT-TA 1011
                          v   -   v    i  -i     -    v  i--------   v i-  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--------CTGATCCTA 141

  chr1_98462583_9   1012 AAGTTCATGTGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAG 1061
                           i     i     viiv  ii  v  v v        i      i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_98462583_9   1062 CAAAAAGAACAAAACTGGAGGCATCACGCTACCTGACTTCAAACTATACT 1111
                         v  i         ii      vv    i  v  ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_98462583_9   1112 ACAAGGCTACAGTAACCAAAAC-GCATGATACTGGTAGAAAAACAGATAT 1160
                             i          i   i  - ii  i      i v  ii i   i  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_98462583_9   1161 ATAGACCAATGGGACAGAACAGAGGCCTCAGAAATAACAGCACACATCTG 1210
                              i      i i    iv   ivii         vvv  i    i i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_98462583_9   1211 CAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGG 1260
                         iiii  vi    i  i     ivv  v   i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_98462583_9   1261 ATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGA 1310
                           vvi  v  i  i              v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_98462583_9   1311 AAGCTGAAACTGGATCCCTTCCTTACCCCGTATATAAAAATTAACTCAAG 1360
                          iiv    ii    i    v   i  v  i    i              i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_98462583_9   1361 CTGGATTAAAGATTTAAATGTAAGACCTAACAGCATAAAAACCCTAGAAG 1410
                         v     i ?   ii           v    v vi      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_98462583_9   1411 AAAACCTAGGCAATACCCTTCAGGACATAGGCATGGGCAAAGACTTCATG 1460
                              v    ?ivv vi    iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_98462583_9   1461 ACTCAAACACCAAAAGCAATGGCAACAAAAACCAAAATAGACAAACGGGA 1510
                         iv vvi            vvi         ivv        i   iv   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_98462583_9   1511 TCGAAGTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCGTCAGAG 1560
                         iivv vi   v v  i i   i  ii vv    i  v      ivv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_98462583_9   1561 TGAACAGGCAACCTGCAGAATGGGAGAAAATCTTTGCAATCTACCCATCT 1610
                             v  i     ii                v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_98462583_9   1611 GACAAAGGGCTAATATCCAGAATCTACAAAGAATTTCAACAAATTTACAA 1660
                           i  i  i  vi          v  i      i iiv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_98462583_9   1661 GAAAAAAA------ACCCA-TCAAAAAGTGGGCAAAGGATATGAACAGAC 1703
                         v     i ------     - i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_98462583_9   1704 ACTTCTTAAAAGAAGACATTTATGCATCCAACAG--ACATGAAAAAATGG 1751
                          i    iv        i  vi viiiv    i i--         i   v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_98462583_9   1752 TCATCATCACTGGTCGT 1768
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.44 (22 / 9)  


2595 26.13 9.55 1.19  chr1_98684626_98688807     2853  3690 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_98684626_9   2853 TGGAAAGATATTCTGTGCCCATGGATTGGAAGAATTATTATTGTTAAAAT 2902
                                    i ii  ii              v   v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_98684626_9   2903 GACAATACAACTCAAAGCAACTTGAAGATTCAATGCAATCCCTATCCAAA 2952
                          i      vv i    vii ii iv        i            v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_98684626_9   2953 TACTGATGACATTATACACAGAAATAGGAAAAAAAAAATCCTAAAATTTA 3002
                          v iiiivi v  v vii       v -- v  ivvi           i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_98684626_9   3003 TGTGGAATTCCAACAGACTAAG--CAGCCCAAGTA-TCCTGAGCAAAAAG 3049
                          i     v v   vi   iv  --i    v  ii -  i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_98684626_9   3050 AACAAAGCTGGAGGCATCACATTACCTGACTTCAAAATGTATTACAAAGC 3099
                                i      vv     i v  ii i       iv  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_98684626_9   3100 TGTAGTAACCAAATCAGTATGGTACTGGCATAAAAACAGACACATAGGCC 3149
                          ii     i   iv    i              ii i     i    ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_98684626_9   3150 AACAGAATAGAATGGAGGACTCAAATATAAATTTACATATTTACAGCCAA 3199
                           ii         v   iiii  i v     iii i i     ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_98684626_9   3200 CTCATCTTCAACAAGG-TGCCAAGAACATACAATGGGTAAAGGACAGTCT 3248
                         i v  i   i      -        v   v       v    i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_98684626_9   3249 TTTCAATAAGCGGTGCTGTGAAAACTGGACAACTATATGCAGAAGAATAA 3298
                               i  ii       v  v       i ? i i     i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_98684626_9   3299 AACGAGAACTTTATCTCTCACCACACTA-AAAAATCAAATCAAAATGAAG 3347
                          iivi  v ii  i   v     i -  -      i  v        i -
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATA-TACAAAAATTAACTCAAAATGGA- 496

  chr1_98684626_9   3348 TTTAAGACTTAAATCTAAAACTTGAAATTATGAAAGTACTAAAGGAAAAC 3397
                          iv?    i     v   i vi i   i   i   v vi  i i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_98684626_9   3398 ATTGGGG-AAATGCTCCAGGACACTGGTGTGGGGAAAAATGT-TTGTGTA 3445
                           v  ? -    -  i iv   vi   vv i  v  vii v -  ivi  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_98684626_9   3446 AGATCCCAAAAGTACAGGCAATCAAAGCAAAACTAGACCAATGAGATTTC 3495
                         v  iv       i   i    iv    v    v    iv   vi  i   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_98684626_9   3496 ATTAAGCTAAAAAGCTTCTGCACAGCAAAGGAAACAACGAACAAAGTGGA 3545
                           i  iv v    i   i  ii vv       v  v iv  v      i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_98684626_9   3546 --GACAACCCACAAAA---------------------------------- 3559
                         --           i  ----------------------------------
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_98684626_9   3560 -----------------------------------CAATTTAATAGCAAA 3574
                         -----------------------------------   i i    ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_98684626_9   3575 AAT-CAAATAATCTAATTTAGAAATGGCTACAAGATATGAATGGACATTT 3623
                           v-       i i    ? i      vi v i   v     i       
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_98684626_9   3624 TTTTTTTCAAAAGAAGACATACAAA-GGCCAACAGGTATATAAAGAAATG 3672
                         i ----- v        i       -      i i i i  i  i i   
  L1M4_orf2#LINE/    846 CT-----CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_98684626_9   3673 CTCAACATCGCTAATCAT 3690
                                  i????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (142 / 73)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 6.00 (90 / 15)  


3071 26.71 1.21 1.32  chr1_98695902_98700545     3246  4151 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_98695902_9   3246 AGAGATATTTCATATTCATGGATTTAAAGAATCAAAATTGTTAGAAAGTC 3295
                          i      ii   i          vi    v i  v       ii v v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_98695902_9   3296 CATACTATCCAAAGTAATTTACAGATTTAATGCAAACCCTATCAAAATAC 3345
                         v     vi     v i  i        i  i    v            v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_98695902_9   3346 CAA-TGACTAG---ACAAAAATTT-TAAA--AATCCTAAAATTTATATGG 3388
                           i-  v  vv---i  i     v-i  i--i           i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_98695902_9   3389 AAGCACTAAAGACCCAGGATAGCCAAAGCTATCCCAAGCAAAAAAAAAGA 3438
                           iii v ii       i         i v   iii ----    i    
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA----AAAAGAAGA 199

  chr1_98695902_9   3439 ACAAAACTGGGAGAATAACATTACCTGACTTTAAATTGCACTGCAGAGTT 3488
                              ii   ii  v v   i v  ii i  i   vivi   i  i  i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_98695902_9   3489 ATGGTAACCAAAAAGGCATGGTACTGGCATCAGAACAGACACAACAATCA 3538
                          ii    i   i vi ii            v  i i     i vvi    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_98695902_9   3539 GTGGAACAAAAATAGAAAACCCAGAGATAAATTCATACATCTACGGTGAG 3588
                         i     i i  v -  i ii     i     ii       i  i   v i
  L1M4_orf2#LINE/    300 ATGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_98695902_9   3589 CTCATTTTTGACAAGGATGCCAAGAACATATACTAGGGGAAAGATAGTTT 3638
                         i v     i       i        v   vi v i   i  ii     i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_98695902_9   3639 CTTCAATAAATGATGTTAAGTAAACTGGATATCTGCATGCAAAAGAATGA 3688
                         i     i     i  i ii vv         ? ii               
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_98695902_9   3689 AAT-AGACCTCTATCTCTCACCATATAAGAAAGTCAAATCAAAATAGATT 3737
                          i -i    i   i   v         vi   i i  v       i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_98695902_9   3738 GGAGCCTTAAATCTCAGACCTCACACTGTGAAACAACTACAAGAAAACAT 3787
                         i?  v i     v v   v  v v   i i    vvi  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_98695902_9   3788 TGGGGAAACTCTCCAGAAAATTGGACTGGACAAAGATTTCTTGAGGAATG 3837
                         v  ? v  v   i ivi vv    ii i i   v i      -  iv   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chr1_98695902_9   3838 CC-CCAAAAGCGCAGGCAACCAAAGCAAAAATGGACAAATGGGATCACAT 3886
                         v -        i  i     v    v      i  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_98695902_9   3887 CAAG-TTAAACAACTTCTACATAGAAAAGGAAAGGATCCATAAAGTGAAA 3935
                            i-     -     i iiiivvv      v vv   v v         
  L1M4_orf2#LINE/    648 CAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_98695902_9   3936 GGACAACTCACAGCATGGGAGAAAATGTTTGTAAACTACCCCTCTGACAA 3985
                         i      i     v            i    i   ii iviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_98695902_9   3986 GGAATTAATAATCAGGATATATAAGGAATGTGAACAGCTCTACAGGAAAA 4035
                           i i vi  vi   i        i   ivivv   i   v i -- v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA--ATAA 794

  chr1_98695902_9   4036 AAAAATACAATAATCCAATTTTTAAAAA-GGACAAAAGATCTGACTAGAT 4084
                            i i -     i      ?--     -  i    i   i   v    i
  L1M4_orf2#LINE/    795 AAAGACA-AATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_98695902_9   4085 ATTTATCAAAAGAAGACATACTAATAGCAAACAGGTATTTGAAAAAGTGC 4134
                             v  v        i    v   i  v  i i i iv      ii   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_98695902_9   4135 TAAATATCATTGCTTAT 4151
                          v  i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (155 / 83)
Gap_init rate = 0.02 (15 / 905), avg. gap size = 1.53 (23 / 15)  


2849 25.51 3.85 0.91  chr1_98797081_98802849.rev     4397  5278 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_98797081_9   4397 TGGAAAAACAGTCCATGCTTATGGATAGAAAGAATCAATATCACGAAAAT 4446
                               i i vi     i i      v i    v i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_98797081_9   4447 GGCCGTACTGCCCAAAGTAATTTATAGATTAAATGCTATCCCCATCAAAC 4496
                            vi    v      v i  i  i     v  i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_98797081_9   4497 TACCA-CTGACTTTCTT-CACATAATTGGAAAAAAGACT-ACTTTAAATT 4543
                          v   -   v    i  -  v -     --- v   -  - iii    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAG-CTGATCCTAAAAT 145

  chr1_98797081_9   4544 TCATAAGGAATCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGTAAA 4593
                              v    viiv  ii  v  v v        i      i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_98797081_9   4594 AAGAACAAAGCTGGAGGCATCACACTACCTTACTTCAAACTATACTACAA 4643
                                   i      vv       v  iv i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_98797081_9   4644 GGCCACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATCTAG 4693
                         i  i       i   i    ii         i iv ii i   i  v   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_98797081_9   4694 ACCAATGGAACAGAACAGA-AGCCTCAGAAATAATGCCACATATCTACAA 4742
                          i        i    iv  -  i -         vv   i i  i  iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGG 344

  chr1_98797081_9   4743 CCATTTTATGTTTGACAAACCTGATAAAAACAAGCAATAGGGAAAGGATT 4792
                         i  v  v  v  i     ivv  vi  i v  vv    i       i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_98797081_9   4793 CCCTATTTAATAA-TGGTGTTGGGAAAACGGGTTAGCCATATGCAGAAAG 4841
                         vi  v  i  i  -     i     v   v  v  ?   i     i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_98797081_9   4842 CTGAAACTGGATTCCTTCCTTACCCCATATACAAAAATTAACTCAAGATG 4891
                         v    ii    ii   v   i  v                      i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_98797081_9   4892 GCTTAAAGACCTAAA-------------ATCATAAAAACCCTAGAAGAAA 4928
                          v i ?         ------------- ii      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_98797081_9   4929 ACCTAGGCA-ATACCATTTAGGACATGGGCATGGGCAAAGACTTCATGAC 4977
                           v    ?i- v i -  iiv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_98797081_9   4978 TAAAACACCAAAAGCAATGGCAACAAGAGCCAAAATTGACGAATGGGATC 5027
                           vi            vvi       i  vv     v  ii   v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_98797081_9   5028 TGATCAAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTG 5077
                          v      v v  i i   i iii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_98797081_9   5078 AACAGGCAACCTACAGAATGGGAGAAAATTTTTG--AATC---TATCCAC 5122
                           v  i     i                 v    --    ---    iiv
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_98797081_9   5123 CTAAGGG-CTAATATCCAGAATCTACAGAGAA-----ACAAATTTACAAG 5166
                         -      -  vi          v  i i    -----    v iv i  v
  L1M4_orf2#LINE/    744 -TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_98797081_9   5167 AAAAAAACAAACAACCCCGTT-AAAAGTGGGTAAAGGATATGAACAGACA 5215
                              i     i     vi  -    i    i       v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_98797081_9   5216 CTTCTCAAAAGAAGACATTTATGTAGCCAACAA--ACATGAAAAAA-GAT 5262
                         i     v        i  vi vi i     i  --         i - v 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_98797081_9   5263 CATCATCACTGGTCAT 5278
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (129 / 93)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.10 (42 / 20)  


2741 28.44 1.33 0.44  chr1_98961648_98967539     4501  5400 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_98961648_9   4501 TGGAAAAATATTTCATCCTCATGGATAAGAAGAATCAATATCATGAAAAT 4550
                               i    ii   vi        vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_98961648_9   4551 GGCCATACTGACCAAAGTAACTTATGGATTCAATGCTATTCCCATCAAGC 4600
                            v     vv     v i ii  ii       i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_98961648_9   4601 TACCAATGACTTTCTTCACAGAATTAGA-AATCT-ACTTTAAATTTCATA 4648
                          v   iivi i  i  ii     v v  -  v  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_98961648_9   4649 -GGGAATGAAAGAAAACCTCGTATAGCCAAGAAAATCCTAAGCAAAAAGA 4697
                         -  i    v   ii -  iv v        i v    i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_98961648_9   4698 -CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTA--AGTCT 4744
                         -     i      vv       v  ii i      viv     -- iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_98961648_9   4745 ACAGTAACCCAAACAGCTTACTACTGGTACCAAAACAGACATACAGACCA 4794
                                i v i    iv iv      i iv ii i       i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_98961648_9   4795 AGGGAACAGAATAGAGACCTCAGAAATAACACCACACATCTACTACCATC 4844
                          v    i     v    vii         vv   i    i  ivii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_98961648_9   4845 TGATCCTCGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTTCCTA 4894
                             ii       ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_98961648_9   4895 TTCAGTAAATGGTGCTGGGAAAACTCGCTAGCCATATGCAGAAAACTGCA 4944
                             ii              v    v v  ?   i     i  i v  v 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_98961648_9   4945 ACTGGACCTCTTCTTTATGCCTTATACAAAAATTAACTCAAGATGAATTA 4994
                         ii      i  v i i ii  v                   i   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_98961648_9   4995 AAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAATCTA 5044
                         ?    i         i v i     i      vi i          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_98961648_9   5045 GGCA-ATACCATTCAGGACATAGGCATGGACAA-AATTTCATGACGAAAA 5092
                           ?i- v i -   iv   v v  vv i i   -ii    v iivv vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_98961648_9   5093 CGCCAAAAGCAATTGCGACAAAAGCTGAAATTGACAAATGAGATCTAATT 5142
                          i         vvv  i       vvi    v  i    vi  ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_98961648_9   5143 AAACTAAAAAGCTTCTGTATAGCAAAAGAAAATATTATCATAGTGAACAG 5192
                            v v    i   i   iivv    i  v v   i vv v      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_98961648_9   5193 GCAACCTACATAATGGAAGAAAATTTTTGCAATCTACCCATCTGACAAAT 5242
                         i     i   v     i       v       vii ivi      i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_98961648_9   5243 G--TTGAATATCCAGTACTTACAAGGAACTTAAACAAATTTACAAAAAAA 5290
                          --   --       v iv  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    749 GACTTG--TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_98961648_9   5291 AAAAAAAAAACC--ATGAAAAAGTGGACAAAGGATACAAACAGACACTTC 5338
                          i v   v    --  v?    i   i        vii  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_98961648_9   5339 TCAAAATAAGACATTTATGTGGCCAAGAAACATATGAAAAAAAACTCAAC 5388
                           v   v    i  vi vi       v  i  i       i vi      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_98961648_9   5389 ATCTCTGATTAT 5400
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (144 / 108)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


2497 26.89 3.06 3.83  chr1_98977170_98979128.rev      554  1468 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_98977170_9    554 TGGAAAAACATTCCATGCTTATGAATTGAAAGAATCAATATTATTAAAGT 603
                               i i  i     i i   i    i    v i      i    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_98977170_9    604 GGCCATACTGCCCAAAGCAATCTACAGATTCAATATACTTCCCATCAAAC 653
                            v     v      vii              iii v i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_98977170_9    654 TACCAA-TGTCATTTTTCACAGAACTAGAAAAAACTT-TTCAAAAATTCA 701
                          v   i-  i -     ii     v v  v  i-  v- i v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_98977170_9    702 TGTGGAACCACAAAAGAGCCTGAATAGCTGAAGCAATGCTAAGAAAACAA 751
                          i     vii   ii  v  v       ii  i    vi --     vi 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--GAAAAAGA 196

  chr1_98977170_9    752 ACAAACAAACAAACAAAAAAAACAAGAGGCATCACATTACCCAACTTCAA 801
                          ---------i      i----ivi    vv     i v     i     
  L1M4_orf2#LINE/    197 A---------GAACAAAG----TTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_98977170_9    802 ACTATACTACAAGGCTACAGTAACCAAAATAGCATGGTACTGGTACAAAA 851
                          viv        i          i   i i  ii         i i  ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_98977170_9    852 GCAGACCCATAGACCAGCAGAACAGAATAGAGAACCCAGAGATAAAGCTG 901
                         ii    vi     i  iii   i     v    ii     i     v ii
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_98977170_9    902 AACACCTAAAGCCATCTGATCTT-GATAAAGTTGACAAAAACAAGTAATG 950
                         v   ii  vi i  vi    i  -  i  i v  v   i v  vvi    
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_98977170_9    951 GGGAAAGGACA--CTATTGAATAAATGGC------ATAGCTGACTGTCCA 992
                                i i --  v  v  i      i------ i i   iv i?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_98977170_9    993 TATGCAGAAGAATGAAACTGAACCCTTGCCTTTAACCACATACAAAAATT 1042
                         i     i         ii  i    i i   ivv    i           
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_98977170_9   1043 AACTCAAGATGGATTAAAAATTTAAATGTAAGCCATCAAACTGTAAGAAT 1092
                                i      i ? i ii          vvv v     i   i v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_98977170_9   1093 CCTAGAAAGAAACCTAGGAA-ACACCATTCTGGACACCAACTTTGAGA-A 1140
                          i     ii    v    ?i- v i v iv  -------  i   i v- 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTG-------ACCTTGGGTTA 576

  chr1_98977170_9   1141 AGAAAT------TAAGACCAAGTCCTCAAAA--ACAATTACAATATAAAC 1182
                         i v   ------ v   i- v v vi     --    --i   i v  iv
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAA--GCAACAAAAGA 623

  chr1_98977170_9   1183 AAAAACTGACAAGTCAGACCTAATGAAACTAAAGAGCTTCTGCACAGCAA 1232
                              iv  i  i ii   i v  v   v v  i i   i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_98977170_9   1233 AAGAAACTCTCAACAGAGT-AAAAGACAATCTAGAGAATGGTAGAAGATA 1281
                          i  v   v    v i   -         i i v       v    i   
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_98977170_9   1282 TTCACAGGCTGCACATCTGGCAAAGGTCTAGTACCCAGAATCTATACGGA 1331
                           ii  iiiiii i     ii  i  v  v   i       v    vi  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_98977170_9   1332 ATTT----AATTGAATAAGTAGAAAACAAATAACCCCATTAAAAAAATGA 1377
                          i i----  i v     vv i  i           v   ?     -  i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGG 822

  chr1_98977170_9   1378 GCAAAATACTTG--TGGAACCATGTATTTTGTCGAAACAAGACATACAAG 1425
                              iv i   -- i  --   -----  v  v   v    i      i
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGA--CAT-----TTCTCCAAAGAAGATATACAAA 865

  chr1_98977170_9   1426 CAGCCAGCAAACTTATGAAAATGTGCTCAACATCACTAATCAT 1468
                         ii    ii  i vi       vi            ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (160 / 82)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.74 (63 / 23)  


 772 30.28 1.59 0.80  chr1_99024238_99028942.rev     2984  3234 (1471)    L1M4_orf2#LINE/L1        1   253 (655)  

  chr1_99024238_9   2984 TGGAAAAACATTCCATGCTCATGGATAGGAAAA-TCAGTATCATTAAAAT 3032
                               i i  i     i        v    i - i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_99024238_9   3033 GGCCATACTGCCCAAAGCAGCTTATAGATTCAATGCCATTACTATCAGAC 3082
                            v     v      viiiii  i        i  v  iv      i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_99024238_9   3083 CACCAATGACATTCTTCACAGAACTAGAAAAAAACTG---TAAAAATTTA 3129
                         iv   iivi v  i  ii     v v  v  i--   ---iv      i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_99024238_9   3130 AATGGAACCAAAAAAGAGCCTGAATAGCCACGGCTATCCTAAGCAAAAAG 3179
                         v      viiv  ii  v  v         vii v   i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_99024238_9   3180 AAAAAAGCTGAAGGCATCACATTACCCAGCTTCAAACTGTATTATAAGGC 3229
                           v    i  i   vv     i v    ii      viv  i  i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_99024238_9   3230 TACAG 3234
                              
  L1M4_orf2#LINE/    249 TACAG 253

Transitions / transversions = 1.71 (48 / 28)
Gap_init rate = 0.01 (3 / 253), avg. gap size = 2.00 (6 / 3)  

1930 26.22 1.77 3.83  chr1_99024238_99028942.rev     3536  4214 (491)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr1_99024238_9   3536 AAGGCTACAGTAACCAATACAGCATGGTACTGCTACAAAAGCAGACACAT 3585
                           i          i   v    ii        vi i  iiii     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_99024238_9   3586 AGACCAATGGAACAGAATAGCAAGCCCAGAAATAATGCTGCACACCTACA 3635
                            i        i     v vi  i          vv iii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_99024238_9   3636 AGCATCTAATCTTCAATAAAGTCAACAAAAACAAGCAATGGGCCGGGGCG 3685
                         iv  vi i  i   i i  i viiv   i v  vv       ------- 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-------G 386

  chr1_99024238_9   3686 GGGGGACAGGACTCCCTATTCAATAAATGGTGCTGGATTAAATATCTAGT 3735
                         iii i i  -----i  v     i            ivi  v ivv  ?i
  L1M4_orf2#LINE/    387 AAAGAATAG-----TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_99024238_9   3736 CATATGCAGAAGATTGAAACTGGAACCCTTCCTTGCACCATATACAAAAA 3785
                           i     i    v    ii    v    v   ii               
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_99024238_9   3786 ATCAACTCAAGATATATTAAATATTTAAATGTAAAACCTAAAACTAAAGA 3835
                         - i       i  iv  i ? v ii         i v         v i 
  L1M4_orf2#LINE/    482 -TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_99024238_9   3836 AACCCTGGAAGATAAAC-TAGG---AAATACCTTTCTGAACACAGGCCCT 3881
                          vi i i     -    -    ---    --   iv   v vii  iiv-
  L1M4_orf2#LINE/    531 ACTCTTAGAAGA-AAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTA- 576

  chr1_99024238_9   3882 GGCAAGGATTTC------ATGACA--AAAACTCCAAAAGCAATTGCAAAA 3923
                              v i    ------      --    v--  v      ---     
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAG--CACAAGCAA---CAAAA 621

  chr1_99024238_9   3924 AAACCCCAAAATTAACAAGAGGGACCTAATTAAACTAAAGAGCTTCTACA 3973
                         i  ----     vi i  ivv    i v  i   v v  i i   i iii
  L1M4_orf2#LINE/    622 GAA----AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_99024238_9   3974 CACCAAAAGAAACTATTAACAAAGTAAACAGACAACCTTCAGGATGGGCA 4023
                          vi    i  v     i  v     i  v        iv   i     vi
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_99024238_9   4024 AAAATACTTGCAAACTATGTATCTGACAGAGTCCTACTATCCAGAATCTA 4073
                               i       ii  i       i ii vv  vv          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_99024238_9   4074 TAAGGAGCTTAAACAAATTAACAAGCAAAAAATCAACAACTCCATTAAAA 4123
                            i  i  ivv    v i  i  vv    i iv  i   i v   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_99024238_9   4124 AGTGGGCAAAGGACATGAACAGACACTTATTAAAAGAAGACATACACATG 4173
                          i           iv    i     i  v iv        i     v   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_99024238_9   4174 ACCAACAAGTATATGAAAAAATGACCAACATCACTGATCAT 4214
                         i    i   i i       i   vi        ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (113 / 62)
Gap_init rate = 0.02 (13 / 665), avg. gap size = 2.92 (38 / 13)  


2999 28.16 1.22 0.55  chr1_99053431_99059805.rev     4983  5884 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_99053431_9   4983 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCACGAAAAT 5032
                              ii i  i     i        v      v i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_99053431_9   5033 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATTAAGC 5082
                            v     v     iv i  i  i       ii  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_99053431_9   5083 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5130
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_99053431_9   5131 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5180
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_99053431_9   5181 AACAAAGCTGGAGGCATCAACACTACCTGACTTCAGACTATACTACAAGG 5230
                                i      vv   -    v  ii i    i viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_99053431_9   5231 CTACAGTAACCAAAACAGCATACTACTGTTACCAAAACAGAGATACAGAC 5280
                                  i   i    ii iv     vi iv ii i   v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_99053431_9   5281 CAATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATCTACAACCA 5330
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_99053431_9   5331 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5380
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_99053431_9   5381 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5430
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_99053431_9   5431 AAACAGGATCCCTTCATTATACCTTATACAAAAATTAATTCAAGATGGAT 5480
                           iiv   i    v v i i   v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_99053431_9   5481 TAAAGATTTAAATGTTAGACCTAAAATCATAAAAACCCTAGAAGAAAACC 5530
                         i ?   ii       v   v      ii      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_99053431_9   5531 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTTATGACTAA 5579
                             ?i- v i -   iv   v v  vv i     v ii  iv iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_99053431_9   5580 AACACCAAAAGCAATGGCAACAAATGTCAAAAGAGACAAACGGGATCTAA 5629
                         i            vvi        v vv    v   i   iv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_99053431_9   5630 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGGGAAG 5679
                          i   v v  i i   i  ii vv    i  v    i  vv i  v   i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_99053431_9   5680 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAA--------TCTGACAA 5721
                           i     i                 v       --------     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_99053431_9   5722 AGGGCTAATATCTAGAATCTGCAAAGAACTTAAACAAATTTACAAGAAAA 5771
                         i  i  vi    i     v ii        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_99053431_9   5772 AAATCAAACAACCCCATCAGAAAGTGGACAAAGGATATGAACAGACACTT 5821
                          i -    i     v  i?i   i   i        v    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_99053431_9   5822 TTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGATCAT 5871
                         i  v        i  vi viii     i ii          i   v   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_99053431_9   5872 CATCACTGGCCAT 5884
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (154 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


2075 26.73 0.91 0.36  chr1_99217147_99223419     4584  5133 (1140)    L1M4_orf2#LINE/L1        1   553 (355)  

  chr1_99217147_9   4584 TAGAAAAACATTCCATGCTCATGGAT-AGAAGAATAAATATTGTGAAAAT 4632
                          i    i i  i     i        -i     v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_99217147_9   4633 GGCCATACTGCTCCAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 4682
                            v     v i v  v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_99217147_9   4683 TACCATTGACTTTCTTCGCAGAACTAGAAAAAGCT-ACTTTAAGTTTCAT 4731
                          v   vivi i  i  i      v v  v  -   - iii   iv     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_99217147_9   4732 ATGGATCCAAAAAAGACCCTGTATAGCCAAGACAATCCTAAGCAAAAAGA 4781
                              vviiv  ii     v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_99217147_9   4782 ACAAAGCTGGAGGCATCATGCTACCTGACTTTAAACTATACTACAAGGTT 4831
                               i      vv   ii  v  ii i  i   viv        i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_99217147_9   4832 ACAGTAACCAAAACAGCACGGTATTGGTACCAAAACAGATATATAGACCA 4881
                                i   i    iii    i   i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_99217147_9   4882 ATGGAACAGAAC--AAAGCCTCAGAAATAACACCAGGCATCTACAACCAT 4929
                               i    i-- i  i -         vv   vi   i  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_99217147_9   4930 CTGATTTTCGACAAACCTGATAAAAACAAGCAATGGGGTAAGGATTCCCT 4979
                         i             ivv  vi  i v  vv        v   i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_99217147_9   4980 ATTTAATAAATGGTGATGGGAAAACAGGCTAGCCATATGCAGAAAACAGA 5029
                         v  i  i        v     v   v  v  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_99217147_9   5030 AACTATATCCCTCCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 5079
                          ii iv i    v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_99217147_9   5080 AAAGACTTAA-CATAAAACCTAAAACTATAAAAACCCTAGAAGAAAACCT 5128
                          ?    i   -ii   i v              vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_99217147_9   5129 AGGCG 5133
                            ? 
  L1M4_orf2#LINE/    549 AGGNG 553

Transitions / transversions = 1.67 (90 / 54)
Gap_init rate = 0.01 (6 / 553), avg. gap size = 1.17 (7 / 6)  

 882 28.93 2.20 0.28  chr1_99217147_99223419     5418  5780 (493)    L1M4_orf2#LINE/L1      539   908 (0)  

  chr1_99217147_9   5418 AAGAAAACCTAGGCA-ATACCATTCAAGACATAGGCATGGGCAAAGACTG 5466
                                 v    ?i- v i -   iv   v v  vv i     v ii v
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_99217147_9   5467 CATGGCTAAAATACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAAT 5516
                          v i v  vi i       i  vvi          vv     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_99217147_9   5517 AGGATCCAATTAAACTAAAGAACTTCTGCTCAACAAAAGAAACAAGCGCC 5566
                         v   iiiv  i   v v  i     i  iv vv    i  v  v v ivv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_99217147_9   5567 AGAGTGAAAAGGCAACCTACTTAATTGGAGAATATTTTTGCAATCTATAC 5616
                          i         i     i  vv   v      v  v       vii   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_99217147_9   5617 ATATGACAAAGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTT 5666
                           v   i  i  v  vi          v  i  i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_99217147_9   5667 ATAAGGAAAAAACAA----CCCCATCAAAAAGCAGGTGAAGGATATAAAC 5712
                             vi    i    ----   v  i?    iii  ii      v i  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_99217147_9   5713 AGACATTTCTCAAAAGAAGACATTTATGCATCCAACAAACAGA--AAAAG 5760
                                    v        i  vi viiiv    i  i  v --     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_99217147_9   5761 A-GCTCATCATCACTGGTCAT 5780
                          -     v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.98 (51 / 52)
Gap_init rate = 0.01 (5 / 370), avg. gap size = 1.80 (9 / 5)  


2890 27.73 1.33 0.99  chr1_99302936_99308463.rev     4141  5045 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_99302936_9   4141 TGAAAGAACATTTCATGCTTATGGATAGGAAGAATCAATAACATTAAAAT 4190
                           i  ii i  ii    i i      v      v i    vii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_99302936_9   4191 GGCCATACTGCCAAAAGCAATTTATTGATTCAATGCTATTCCCATTAAAC 4240
                            v     v  v   vii  i  iv       i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_99302936_9   4241 TACCA-CTGACATTCTTCATAGAACTAGAAAAATCTATTTTTAAAATTCA 4289
                          v   -   v -  i  iii    v v  v  i-  iv ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_99302936_9   4290 TATAAAACCAAAAAAAGAGCCCCAAAA--GCCAAGGCAATCCTAAGCAAA 4337
                            ii  --- viv   i v    i  --     ii     i i --   
  L1M4_orf2#LINE/    149 TATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAA 193

  chr1_99302936_9   4338 AAAGAAAAAAAGCTGGAGGCATTACACTATTTAACTTTAAAATATACCAC 4387
                          i ii  v    i      vv i     viii  i  i    iv   i  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_99302936_9   4388 AGGGCTACAGTAACCAAAACAGCATGGTACCGGTATGAAAGCAAGCAGAT 4437
                          ii          i   i    ii      i  i  i iiii ii  v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_99302936_9   4438 AGACCAATAGAACAGAATAGGAAACCCGGAAATAAAACTGCACACCTACA 4487
                            i    i   i     v ii ii  i        v iii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_99302936_9   4488 A-CGATCTGATTTTTGATAAACCTTACAGAAATAATCAATGGGGAAAGAA 4536
                         i- i  -       i  i  ivv vv  ii vi v               
  L1M4_orf2#LINE/    344 GTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_99302936_9   4537 CTCTCTATTCAATAAATGTTGCTGGAGTAACTGGCTAGCCATATGCAGAA 4586
                         ivv   v     i     v      iii      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_99302936_9   4587 AATTGAAACTACACCCCTTCCTTATACCACGTACAAAAATTAACTCAAGA 4636
                         i v    ii iv      v   i i    ii                 i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_99302936_9   4637 TGGATTAAAGACTTAAATATAAAATCCAAAACTATAAAAACCATTGGAGA 4686
                              i ?    i     i   i v i            vi v v i   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_99302936_9   4687 AAATCTAGGCA-ATACCATTCAGGACATAGACACAGGCAAAGATTTTAT- 4734
                            iv    ?i- v i -   iv   v v ivvi      v i   iv -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_99302936_9   4735 GACAAAACATCAAAAGCAATTGCAACAAAAGCAAAATT-GATAAATGGGT 4783
                           i vi   i        vvv          v    v -       v  v
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_99302936_9   4784 TTTAATTAAACTAAGGGGCTTCTGCACAGCAAAAGAGACTATCAACAGAG 4833
                         i  v  i   v v iiii   i  ii vv    i  v        v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_99302936_9   4834 TAAACAGACAACCTACAGAATTGGAGAAAATTTTTGCAAACTATGCATCT 4883
                          i  v        i       v         v        ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_99302936_9   4884 GACAAAGGTCTAATATCCAGCATCTACAAGGAAATTAAACAACTTA-CAA 4932
                           i  i  v  vi       v  v  i  i   v ivv      i -i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_99302936_9   4933 GATAAAAACAA----CCCCATTAAAAAGTGGGCAAAGGACATGAACAGAC 4978
                         v v   i    ----   v   ?    i           iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_99302936_9   4979 ACTTCTTAAAAGAAGACATATATGTGGCCAAGAAGCATATGAAAAAAAGC 5028
                          i    iv        i   i vi       v     i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_99302936_9   5029 TAAAGAACACTGATCAT 5045
                          v  v v  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (157 / 90)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


3042 27.28 0.88 0.99  chr1_99333982_99340766.rev     5386  6294 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_99333982_9   5386 TAGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5435
                          i    i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_99333982_9   5436 GACCATAGTGCCCAAAGTAATTTATAGATTCAATGCTATCCCTATCAAGC 5485
                          i v   v v      v i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_99333982_9   5486 TACCA-TTGACTTGCTTCACAGAATTAGAAAAAAAACT-ACTTTAAACTT 5533
                          v   -i  v   -i  ii     v v  v  i---  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chr1_99333982_9   5534 CATATGGAACCAAAAAAGAGCCCACATTGCCAAGATAATCCTATGCAAAA 5583
                                  viiv  ii  v  viv  v     i i    i iviv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_99333982_9   5584 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5633
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_99333982_9   5634 GCTACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGATATATAGA 5683
                                   i   i    ii     i   i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_99333982_9   5684 CAAATGGAACAGAACAGGGGCCTCAGAAATAACACCACACATCTACAACC 5733
                         iv       i    iv i ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_99333982_9   5734 ATCTGATCTTTGACAAACCTGACAAAAACAG-CAATGGGGAAAAGATTCC 5782
                          vi    i  i     ivv  v   i v  v-           ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_99333982_9   5783 CTATTTAGTAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5832
                           v  i ii        i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_99333982_9   5833 GAAACTGGACCCCTTCCTTACACCTGATACAAAAATCAACTCAAGATTGA 5882
                            ii         v   i     vv          i       i  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_99333982_9   5883 TTAAAGACTTTAATGTAAGACCTAAAACTGTAAAAATTCTAGAAGAAAAC 5932
                          i ?    i v         v        i     v ii           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_99333982_9   5933 CTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATGTCATGTCTA 5981
                         v i  ?i- v i -   iv   v v  vv i     v i v  v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_99333982_9   5982 AAACACCAAAAGCAATGGCAACAAATGCCAAAATTGACAATTGGGATCTA 6031
                         vi            vvi        v vv     v  i  v v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_99333982_9   6032 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTCTTATCAGAGTGAA 6081
                           i   v v  i i   i  ii vv    i  v   v i vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_99333982_9   6082 CAGGCAACCTACAGAAAGGGAGAAAAATTTTGCAATCTATCAATCTGACA 6131
                         v  i     i      v         vv       vii  vv      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_99333982_9   6132 AAGGGCTAATATCCAGAATCTACAAAGAACTT----AAATGAATTTTCAA 6177
                          i  i  vi          v  i        i----  v v   ----  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT----AA 791

  chr1_99333982_9   6178 GAAAAAAGCAGACAACTCCATCATAAAGTGGGAGAAGAATATGAACAGAG 6227
                         v     ii  i i   i v  i?v   i    vi   i  v    i   v
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_99333982_9   6228 ACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATGTGAAAAAATGC 6277
                          i     v        i  vi viii     i  i  ii      i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_99333982_9   6278 TCGTCATCACTGGTCAT 6294
                           iv     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (140 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


3358 22.39 4.55 0.37  chr1_99396876_99398683.rev      505  1317 (491)    L1M4_orf2#LINE/L1       62   908 (0)  

  chr1_99396876_9    505 CCAAAGTAATCTGTAGACTTAAATGCAATCTTTGTCAAAACCTCAATTGA 554
                              v i    ii   -  v  i      ii i      i i  ii  v
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGA-TTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr1_99396876_9    555 AATTTTTTTTAGAAGTAGATAAAACAAACGTAAAATTGATACAAAACTAC 604
                         v-      vi    i v  i  ivii v v       v   iii  v i 
  L1M4_orf2#LINE/    111 C-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_99396876_9    605 AAAGG--CCATGAATAGCCAGAACAACTTTGAGAAAGAAGAACAAAGTTG 652
                           i  --   -         i     ii    i                 
  L1M4_orf2#LINE/    160 AAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_99396876_9    653 GAGGCTTCACACTTCCTGATTTCAAAACATATTACAAAGCTACAGGAATC 702
                             vi          ii          v  i             v    
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_99396876_9    703 AAAACAGTCTGGTACTGGCATAAAGACAGACATACAGAAAAATGGAACAG 752
                           i     v              i  i       i   vv       i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_99396876_9    753 AATAGAGAG-------------CCATACCTTTA--GTCACCTGACGTTTG 787
                            v     -------------      v    --    vi   iv  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_99396876_9    788 ACAATGATGCCAAGACTACACAAGGGGGAAAGAACAGTTTCTTTAACAAT 837
                             v i         i iv   v          i   i i  i     v
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_99396876_9    838 TGGTGTTGGGGAAACTGAATGTTTACATGCAAAA---------TGAACCC 878
                              i    iv     i  i?ii          ---------  i    
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_99396876_9    879 TTATCTTACACCACACATAAAAATCAACTCAAAGGAGATTAAAAACTTAA 928
                         i  i  i      i i i      i        ivi   i ? i  i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_99396876_9    929 ATGTAAGATCTAAG-CTATAAACCCCCTGGAAGAAAACATAGGGGGAAAG 977
                                 v    i-       v i i i              ? v   v
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_99396876_9    978 CCTTATAACTTTGGTCTTAGTAATGATTTCTTGGATACGACACAAAAAGT 1027
                          i ii i  i    vi vi i    i      i    i     v     i
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_99396876_9   1028 ACAGGTAACAATAGCAAAAATAGGTAAATGGGACTACACCAAACTAAAAA 1077
                            i i     v  v        i     v     v  i    v v    
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_99396876_9   1078 GTTTCTGTGTAGCAAAGGAAGGAATCAACAGAATAAAAAGGCAATCAACA 1127
                         ii  i    ivv       vivv     v i i i     i   i v   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_99396876_9   1128 GAATGGGGGAAGATATTAACAAATCACACATATAATAATGGGTTAATATC 1177
                                i   i     vi       i i  v i    v  ii vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_99396876_9   1178 CAAAATACATGAGGAGCTTTTAAAACTAAATAG-AAAAAAAAAAAT---- 1222
                           i    i  i i  i  i   v    v    i-     i v    ----
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_99396876_9   1223 CAATTAGAAAATAGGCAAAGGACTTGAATAGACATT-CTTCAAAGAAGAC 1271
                              ?i     i         i             -  i         i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_99396876_9   1272 ATACAAGTAGTAAATATGCA----AAAAGATGTTCAATTTCACGAATAAT 1317
                               i i iv    v   ----        i    iv   ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (121 / 57)
Gap_init rate = 0.01 (12 / 847), avg. gap size = 3.33 (40 / 12)  


 795 25.65 3.04 0.87  chr1_99497842_99499782        2   231 (1710)  C L1M4_orf2#LINE/L1   (673)   235     1  

C chr1_99497842_9    231 TAGAAAGATATCCCATTCTCATAGATTGGAA----TAATTTAGTTAAAAT 186
                          i              vi    i        ----    v v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_99497842_9    185 GTCCAATACTACCCAAAGTTATTTACATATTCAATGCAATACTCATTAAA 136
                          -v       v      v v  i    v      i     v ii  i   
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

C chr1_99497842_9    135 ATTTCAA-TGTTATTTTTCACAGAAATAGAAAAAC-AATCCTAGAATTTG 88
                           ii  i-  ii-     ii       v  v  i -i      i    ii
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

C chr1_99497842_9     87 TATGGAACCACCATAGACCC-CAATAGATAAAGCAGTCTAGAGAAAAATG 39
                                vii v vi     -v     vi   i  i   v  i   i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr1_99497842_9     38 AACAAAGCTGGAGGCACCACATGATCTGATTTTGAAA 2
                                i      vvi    ivvi ii    ii   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

Transitions / transversions = 1.68 (37 / 22)
Gap_init rate = 0.03 (6 / 235), avg. gap size = 1.50 (9 / 6)  

2041 23.43 2.40 1.85  chr1_99497842_99499782      500  1041 (900)    L1M4_orf2#LINE/L1      284   828 (80)  

  chr1_99497842_9    500 ACAAACACATTAGCCAATGGAATAGGATGAAAAGCCCAGATATAAACCCA 549
                          i i   i  viii           i  vi i  i     v         
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_99497842_9    550 CACACTTATGGACAATTAATTTTCCACAAAGGTGTCACAAATATACAATG 599
                         i   i      v     i      v    i    i  vi vi  v     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_99497842_9    600 GTGAAAGA-CAGTCTTTTCAAAACACATGGTGTTGGAAAAACTGGACATT 648
                          v      -i           --  v      i   i v       i ?i
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAA--CAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_99497842_9    649 CACATATAAAA-AGTGAAGTTAGATCCTCATCTTGTACCATATACAAATA 697
                              ii    - i       i  i  ii i  iii            v 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_99497842_9    698 TCTACTTGAAATAGATTAAAGACTTAAACATAAGACCTTAAATTGTAAAA 747
                          iv   ii    i   i ?    i    ii     v  v   i i     
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_99497842_9    748 CTATTAGGATAAAAC---GGGAAAATTCTTCATGACATTTATCTGGGAAG 794
                           v    i v     ---  ?iv  v     i    v  vivi i  v i
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_99497842_9    795 TGATTTCTTGGCTATAACCTCAAAAGCAAAGGCAAAAAAAAAGCAAAAAT 844
                           i      i v   i  vi        v i    v    i --      
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA--AAAAAT 629

  chr1_99497842_9    845 AGACAAATGGAATTTCATT----TCAAAAATATTTTACATAGCAAAGAAC 890
                            i    v i i     i---- i     i-    iiiivv     i  
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGAC 678

  chr1_99497842_9    891 ATAATTAACAGAGTGAAGAGACAACCCACGGAATAGAAAAGTAAATATTT 940
                          iv  i  v i      i           i    i i i --        
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA--AAATATTT 726

  chr1_99497842_9    941 GCAAATCATATATCTTGTAAGGGGCAAATATCCAAAAATATATAAGGAAG 990
                                        vi      i vvi      i  -       i   v
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAA-TATATAAAGAAC 775

  chr1_99497842_9    991 TC----AACTCAATAGCAAGAAAAAAAAAATAACCTGATTAAAAAATGGA 1036
                           ----         ii  --   i v        ii   ?        i
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAA--AAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_99497842_9   1037 CAAAG 1041
                              
  L1M4_orf2#LINE/    824 CAAAG 828

Transitions / transversions = 2.32 (86 / 37)
Gap_init rate = 0.02 (11 / 545), avg. gap size = 2.09 (23 / 11)  

 238 24.03 3.10 6.20  chr1_99497842_99499782     1321  1449 (492)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_99497842_9   1321 CTCAA-AGCAAAAAAAAAAAAAA---AAAAAAAAAAAAGACAAAGGACAC 1366
                              - ii     i v   v  ---  vv?     vi i       iv-
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT- 832

  chr1_99497842_9   1367 GAACACATAAACAGACAGTTCTCAAAAGTAGACATATGAATGGCCAACTG 1416
                         ------- i  i     v     v    v   i   ii         ivi
  L1M4_orf2#LINE/    833 -------TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_99497842_9   1417 ATATATGAAAAAATGCTCAATGTCGCTATCATC 1449
                         ii i       i        ii  i????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 4.00 (12 / 3)  


3195 27.42 0.44 0.44  chr1_99577651_99584050.rev     5002  5909 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_99577651_9   5002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAC 5051
                              ii i  i     i      i v      v i     i  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_99577651_9   5052 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATGAAGC 5101
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_99577651_9   5102 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTCA 5149
                          v   iivi i  i  ii     -   -- v  i  - iii i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_99577651_9   5150 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_99577651_9   5200 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5249
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_99577651_9   5250 TACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAAATAGATC 5299
                              i  i   i    ii         i iv ii i   v v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_99577651_9   5300 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5347
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_99577651_9   5348 ATCTGATCTTTGACAAACCTGAGGAAAACAAGCAATGGGGAAATGATTCC 5397
                          vi    i  i     ivv  vvi i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_99577651_9   5398 CTATTTAATAAATGGTGCTGGGAAAACTGGCTCGCCATATATAGAAAGCT 5447
                           v  i  i              v      v v?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_99577651_9   5448 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATTGA 5497
                            ii    i    v   i     v              i    i  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_99577651_9   5498 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5547
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_99577651_9   5548 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5597
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_99577651_9   5598 GACACCAAAAGCAATGGCAACAAAAGCCTAAATTGACAAATAGGATCTAA 5647
                                      vvi          vvv    v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_99577651_9   5648 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5697
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_99577651_9   5698 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5747
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_99577651_9   5748 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5797
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_99577651_9   5798 AAACAAACTACCCCATCAAAAAGTGGGCGAAGGACGTGAACAGACACTTC 5847
                          i     iv    v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_99577651_9   5848 TCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5897
                           v           vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_99577651_9   5898 ATCACTGGCCAT 5909
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2888 25.23 3.86 0.68  chr1_99596111_99601057     3575  4454 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_99596111_9   3575 TGGAAACACACCTCATATTCATAGATGGGTAGAATCAATATTGTGAAAAT 3624
                               v i i i   i     i   v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_99596111_9   3625 GAACATACTGCCAAAAGTAATCTACAAATTCAATGCAATTCCCATTAAAA 3674
                          ivv     v  v   v i       i      i     i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_99596111_9   3675 T----ACTGCCATCATTCTTCACAGAACCAGAAAAAA-AATCCTAAAATT 3719
                          ----i     ----  i  ii     viv  v  iv-i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_99596111_9   3720 CATATGGAACCAAAAAAGAATCCACATAGCCAAAGCAAGACTAAGCAAGA 3769
                                  viiv  ii  vi viv         i   vvi i iv    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_99596111_9   3770 AGAACAAATCTGGAGGCATCACATTACCCAACTTCAAACTATACTATAAG 3819
                                 vi      vv     i v     i      viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_99596111_9   3820 GCCATAGTCACCAAAACAGCATGGTACTGGTATAAAAACAGGCACATAGA 3869
                           i i   v i   i    ii         i    ii i  i  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_99596111_9   3870 CCAATGGAACAGAATAGAAGACCCTGAAATAAAGCCAAA----TAGAGCC 3915
                         i        i     v  iiii  v        v   v ----  vi i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_99596111_9   3916 AACTGATCTTCAACAAAGCAAACAAGAACATACAGTGGGGAAAA------ 3959
                           i    i   i    i vviv     v   v  i        i------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_99596111_9   3960 -----CAACAAATGGTGCAGAGATAATTGGCAAGCCACACAC----GTAG 4000
                         -----             v i  i  i   vv ?     ii ---- v v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_99596111_9   4001 GAAACTGGATCATCATCTCTCACCTTATACAAAAATCAATTCAAGATGGA 4050
                            ii    i vii i   v    v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_99596111_9   4051 TCAAATACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGACAAC 4100
                            ? v  i     v     v  i    i      v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_99596111_9   4101 ATCAGA--AAACCCTTCTAGAATTGGCTTAGGCAAAGACTTCATGACCAC 4148
                           vi ?--   i i iv iivv    v        v ii   v iivi i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_99596111_9   4149 -ACACCCAAAAGCAAATGCAACAAAAACCAAGATAAACACATGGGACTTA 4197
                         -     -       v v         ivv  i   i i v  v      v
  L1M4_orf2#LINE/    597 GACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_99596111_9   4198 ATTAAA-CTAAAAACCATCTGCACAGCAAAAGAAATAATCAGCAGAATTA 4246
                           i   -i       i- i  ii vv    i  v iv    iv i i v 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_99596111_9   4247 ACAGACAACCCACAGAGTGGGAGAAAATCATCACAATCTATATATCTGAC 4296
                          v              i           vv ii   vii          i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_99596111_9   4297 AAAGGACTAATATCCAGAATCTACAAAGAACTC----AAATCAGCAAGAA 4342
                           i     vi          v  i         ----  v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_99596111_9   4343 AAA-ACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAAT 4391
                            -     i  i  v  i?    i     v     iv          v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_99596111_9   4392 TGTC-AAAAAAGATATACAAATGGTCAACAAGCATATGGAAAAATGCTCA 4440
                          v  -   i               i   i     i   i   i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_99596111_9   4441 ACATCACTAACCGA 4454
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (132 / 86)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.86 (40 / 14)  


2466 26.15 4.69 3.24  chr1_99654417_99656667      864  1758 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_99654417_9    864 TGGAAAAGCATTCCATGCTCAT-------------CAATGTCATTAAAAT 900
                               iii  i     i    -------------i   i ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_99654417_9    901 GGTAATACTGCACAAAACAACACTGGAGAGAGATTTAGTGATTTAACACT 950
                           i      v v    ------i  -------  i  vv    i   i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA------TTG-------ATCTACAGATTCAACGCA 87

  chr1_99654417_9    951 ATTCTTATCAAATTACCAA-TGTCATTCCTGATAGAATTAGAAAAAACT- 998
                           i i       v v   i-  i v  ii  -i    v v  v  i-  -
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAG-CTG 135

  chr1_99654417_9    999 ATTCTAAAATCTATATGGAACCAAAAAAAAAAGCCCCA--ATAGCCAAAG 1046
                           i       ii        ---- viv  ii v    --         i
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAA----ATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_99654417_9   1047 CAATCCTAAGCAAAATGTACAAAGCCAGAGACATCACACTACTTGACTTC 1096
                              i i iv  i v v      iii   ivv       v iii i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_99654417_9   1097 AAACTACACTATAATGATATAATAACCAGAATAGCATGGTATTGGTACAA 1146
                            vivi    i  v v  i i   i  ii i  ii     i   i i  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_99654417_9   1147 AAACAGACACATAAACCAGTGGAACACAATAGAAAACTTAGAAATAAAGC 1196
                         ii i     i   i i  i     i v   v  i iiii         v 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_99654417_9   1197 CATACACTTACAACCATCTGATCTTTAATAAGGCAAACAAAAACAAGCAA 1246
                               i   iiii  vi    i  ii i    vviv   i v  vv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_99654417_9   1247 TGGGAAAAG-----TCCTCATTATTCAATAGTGATGAAATAACTGGCTAG 1291
                             i    -----  i i- i viv   i   v  ii i      v  ?
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTT-TCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_99654417_9   1292 TCATATGTAGAAGAATGAAACTGGACATTTAACTTTTACTATATACAAAA 1341
                         i  i   i i         ii     vii  v  ivi  i          
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_99654417_9   1342 ATTAACTACAGATGG-TTAAAGTTTTAAGTGTAAGACACCAAACTATAAA 1390
                                vv i    - i ?  vii   i       vviv          
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_99654417_9   1391 AATCCTAGAAGAAAACCTAGG---AAATACCCTTC-TGAACATCAGTCTT 1436
                          v  i           v    ---    ---    -   v v vi  - v
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGT-TA 576

  chr1_99654417_9   1437 GGCAAATAATTT-TTGGCTAAGTTACCAAAAGCAATAGCAATAAAAACAA 1485
                              - ii   -  i v  v vi          vv     i    iv  
  L1M4_orf2#LINE/    577 GGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_99654417_9   1486 AAATTGACAAGT-GGAATCCAATTAAACTTAAGAGATTCTGAACAGCAAA 1534
                             v  i  i -   v i  - i   v    i iv  i  vi vv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCA-TCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_99654417_9   1535 ATAAACTATCAATAGAGTAAACAGACAACCTACAGAATGGGAGAAAATAT 1584
                         iv v        v i   i  v        i                   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_99654417_9   1585 TTGCAAACTATGCATCTAACAACAGTCTAAGATCCAGAATCTATAG-GAA 1633
                                ii  ii    i i  vi v  viv         v    i-   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_99654417_9   1634 CT--TA-AAC---------AAAAAACAAATAACCCCATTTTTCAAAAATG 1671
                           --  -   ---------    i           v   ?---       
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW---AAAAATG 821

  chr1_99654417_9   1672 AGTGAAGGACATGAACAGACACTACTCAAAAGAAGATATACAAGTGGCCA 1721
                         i ii     iv    i     i v   v               i      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_99654417_9   1722 ACAAACGTATGAAAAAATGCTCATTCTCACTAATCGC 1758
                          i  i ii       i       viv   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (150 / 81)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.84 (71 / 25)  


3179 26.04 0.55 1.20  chr1_99730869_99733157      883  1796 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_99730869_9    883 TGAAAATGCATCCCATGCTCATAGATTGGCAGAATCAATAAATGTCATGA 932
                           i   vii        i    i      v   v i    ---- ii v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA----TTGTTA 46

  chr1_99730869_9    933 AAATGACCACACTGCCCAAAGCTATTTACAGATTCAATGTAATTCCTATC 982
                          i   i v i   v      viv  i           i i   i      
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_99730869_9    983 AAAATACCAACATCATTGTTCACAGAATTAGACAAAAAG-TCCTAAAATT 1031
                              v   i vv v  v  ii     v v     ivv -          
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_99730869_9   1032 TGTATAAAACCAAAAAGGAGCCCAAATAGCCAAAGTAATTCTAAACAAAA 1081
                         ii   ii  viiv  i   v  vi          ii   ii i  v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_99730869_9   1082 AGAACAAATCTGGAGGCATCACATTACCTGACTTCAAATTATACTGCAAG 1131
                                 vi      vv     i v  ii i      viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_99730869_9   1132 GCTATGGTTACCAAAATAGCATGGTACTAGTACCAAAGTAAATACACAGA 1181
                             ii  v i   i i  ii       i i iv iii  i i i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_99730869_9   1182 CCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTATAACC 1231
                         i        i     v    ii           v   v i i    iii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_99730869_9   1232 AACTGATCTTTGACAAAG-CACACAAAAACATAAACTGGGGAAAGA-TAC 1279
                           i    i  i     i -ii -   i v   vv v          -  v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_99730869_9   1280 CCTATTCAATAAATGGTGCTGGGAAAACTGGATAGCCACATGTAGAAGAA 1329
                         i  v     i              v         ?       i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_99730869_9   1330 TGAAACTGGATCCTTATCTCTCACCATATACAAAAAACAACTCAAGATAG 1379
                             ii    i  i  i   v               vi       i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_99730869_9   1380 ATTAAAGGCTTACATCTAAGACCTGAAATCATAGAAATTGTAGAAGAGAA 1429
                           i ?  i i  v  v     v  i   ii   i  v iv       i  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_99730869_9   1430 CCCGAGGAAAAACTCTGCTGGACATTGGCCTAGTCAAAGAATTTATGACT 1479
                          vi-   ?iv  v   v vv   v    vi   v   v iv  iv iiv 
  L1M4_orf2#LINE/    546 CAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_99730869_9   1480 AAGACCCCAAAAGCAAATGCAACAAAAACAAGAATAAATAAATAGGACCT 1529
                          v   v         v v         iv  i    i      v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_99730869_9   1530 AATTAAA-CAAAAAGCTTCTGCACGGCAAAAGAAATAATCATCAGAGTAA 1578
                         v  i   -iv    i   i  ii vv    i  v iv    vv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_99730869_9   1579 ACAGACAACCCACAGAATGATAGAAAATATTTGCCAACTATGCATCTGAC 1628
                          v                 iv             v  ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_99730869_9   1629 AAAAG-CTAATATCCAGAATCTACAAGGAACTCAAACAACTCAGAGAGAA 1677
                           ii -  vi          v  i  i      vv        --- v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA---ATAA 791

  chr1_99730869_9   1678 AAAAAACAACAAATAATTCCATCAAAGAGTAGGCAAGTGACATGAATAGG 1727
                         v     -i        ii v  i?  i i i     iv  iv       i
  L1M4_orf2#LINE/    792 TAAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_99730869_9   1728 CATTTATCTAAAGAAGATATATAAATAGCTAACAAACATATGAAAAAAAT 1777
                              v  i            i    i  i  i  i  i       i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-T 889

  chr1_99730869_9   1778 GCTCGACATCACTAATCAT 1796
                             i      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (147 / 87)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3152 24.20 5.05 0.92  chr1_99785278_99787511.rev      872  1743 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_99785278_9    872 TGGAAAAACATTCTATGCTCATGGATTGAAAGGATCAATATTGTTAAAAT 921
                               i i  i i   i          i   iv i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_99785278_9    922 GGCCATACTGCCCAAAGCAGTTTACAGATTTAACACTATTCCTATCAAAT 971
                            v     v      viii i        i   i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_99785278_9    972 TACCAATGACATTCTTAACATAATTAGAGAAAACT-ATTCTAAAATTCAT 1020
                          v   iivi v  i  vi  v  v v  v  i-  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_99785278_9   1021 ATGGAAATAAAAGAGATCCTGGATAGCCAAGGCAATCCTAAGCAAAAAGA 1070
                                 iv   i  i  v i        ii     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_99785278_9   1071 GCAAAACTAGAGCCATCACACTACCCAACCTCAAACTATACTACAAAGCT 1120
                         i    ii i   vvv       v     ii     viv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_99785278_9   1121 AGAGTAATGAAAACAGCATAGTACTGGTACAAAAACAGACATATAGATCA 1170
                          v      v  i    ii i       i i  ii i              
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_99785278_9   1171 ATGGAA------------------------------CACCTATGACCATC 1190
                               ------------------------------  ii    ii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_99785278_9   1191 TGATCTTTGGCAAGGCTGACAAAAACAAGCG--GGGGAAAGGAC--TCCT 1236
                             i  i i     v  v   i v  vv i--        i i--  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_99785278_9   1237 TAGTCGATAATTGGTGCTGGGATAACTGGCTAGCCATACACAGAAGAATG 1286
                          --  i i  v           i      v  ?   i ii  i       
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_99785278_9   1287 AAACTAGTCCCTTACCTTTCACCATATACAAAAATTAACTCAAGAT---- 1332
                           ii i v   i     iv                        i  ----
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_99785278_9   1333 -AAAGATTTAAATGTCAGACCTCAAATGATAAGAATCCTAGAAGAAAACC 1381
                         - ?   ii       v   v  v   iv    i v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_99785278_9   1382 TAGG---AAATACCCTTCTTGACATCAGTCTTGGCAAAGAATTTTTAGCT 1428
                             ---    ---    v    v ii vi v     v iv  i    v 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_99785278_9   1429 AAGTCACCAAAAGCAATTGCAACAAAAGCAAAAATCGACAAGTGGGACCT 1478
                          v v           vvv          v      v  i  i v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_99785278_9   1479 AACTAAACTAAAGAGCTTTTACACAGCAAAAGAAAGTATCAACAGCATAA 1528
                         v ii   v v  i i     iii vv    i  v v      v ivi i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_99785278_9   1529 ACAGACAACCTACAGAATGGGAGAACATATCTGAAAACTATGCATTTGAC 1578
                          v        i              v    i  v   ii  ii  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_99785278_9   1579 AGAAGTCTAATATCCAGAATCTATAAGGAACTTAAACCAATCAACAATCA 1628
                          iii v  vi          v     i     ivv  v v    i   v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_99785278_9   1629 AAA-ACAAATAACCCTATTAAAAAATGGGCAAAGAACACGAACAGACACT 1677
                            -           v   ?              i ivi   i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_99785278_9   1678 TCTCAAAAGAAGAGATTCATGTCGTCAACAAGCACATGAAAAAAAATACT 1727
                             v        v  v  vi v i   i             i -- i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGCT 892

  chr1_99785278_9   1728 CATCATCATTAATCAT 1743
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (124 / 84)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 4.73 (52 / 11)  


3050 20.54 2.27 0.45  chr1_99877893_99879542.rev      500  1161 (489)    L1M4_orf2#LINE/L1      235   908 (0)  

  chr1_99877893_9    500 ACATATTACAAAGCTACAATAATCAAAATAGTGTGGTACTGGCATAAAAA 549
                           v  i            i       i i                  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_99877893_9    550 CAGACATATAGATCAGC-GAATGGAACAGACAGCCCTGAAATAAGCCCTC 598
                         i              ii-    i   iv  v  i  v       i   vi
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_99877893_9    599 TTGTCTATGGTCAAATGATCTTTGATGAGGGTGCCAGGATCACTCAGTGG 648
                         vii i         v    i  i  ii         i  i  i   i   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_99877893_9    649 GGAATGGGCAGTCTCTTCAACAAATGGTGTTGGAAAAACTGAATATCCGT 698
                             v iii     i              i   i v     i   ?  ii
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_99877893_9    699 ATACAAAAGAATGAAGTGAGCCCTTTATGTTACATTATATACAAAAATTA 748
                           i              vi v  ii  iv i   ii              
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_99877893_9    749 ATTCAAA-TTGATGAAAGGCCTAAGCTGAAGACCTAAAACTGTA---CTC 794
                          i     - v   v ?  i     iivv    v        i  ---   
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_99877893_9    795 CTAGAAGAAAACATGGGGAAAAAGCT-CATGACATTGGATTTAGTCATAC 843
                         i             i  ?iv   v  - i    v    i  -  v  - i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT-AGGCA-AT 582

  chr1_99877893_9    844 AACTTCTTGGATATGACAACAAAAGGCATAGGCAACAAA-GCAAAAATAG 892
                         iii     i         v      -  i i        - v        
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAG-CACAAGCAACAAAAGAAAAAATAG 631

  chr1_99877893_9    893 ACAAATGGGACTACATCAAACCTCAAAACTCCTATATATCAAAAGA---- 938
                          i    v     v       vi v      ii i iiv     i  ----
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_99877893_9    939 ---AATAGAGTGAAAAG-CAACCCACAGAATGGGAGAAAATAATTGCAAA 984
                         ---  v i         -                        v       
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_99877893_9    985 TCTTATATCTGATAAGGTGTTAATATGCAGAATATATAAGGAATTCCTGC 1034
                           v              vii vi   v            i   i  i i 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_99877893_9   1035 AACCCAACAATAAAAAACCAAGTAACAAAATTTAAAAATGGGCAAAGGAC 1084
                            i   i        iv   i    vv    ?                i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_99877893_9   1085 TTGAATAGATATTTCTCCAAAGAAGATACACATATGGCTGACGAACGTAT 1134
                                  i                  i   v     ii ii i ii  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_99877893_9   1135 GAAAAGATGTTTAAAATTGTTAATAAT 1161
                                  i i  v  ii????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (93 / 39)
Gap_init rate = 0.01 (10 / 674), avg. gap size = 1.80 (18 / 10)  


3011 24.95 2.75 2.97  chr1_99972427_99979120.rev     5294  6203 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_99972427_9   5294 TGGAAAAACATTTCATGCTCGTGGATAGGAAGAATCAATATAGTGAAAAT 5343
                               i i  ii    i  i     v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_99972427_9   5344 GTCCATACTGCCCAAAATAATTTATAGATTCAGTGCTATCCCCATCAAGC 5393
                          v v     v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_99972427_9   5394 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTC 5440
                          v   -   v    i  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_99972427_9   5441 ATATGGAAA-----------CAAAA-----AAGACAATCCTGGGCAAGAA 5474
                                  -----------  i  -----  i      i  iiv     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_99972427_9   5475 GAACAAAGCTGGAGGTATCACACTACCTAACTTCAAACTTTGCTACAAGG 5524
                                 i      vv       v  i  i      vi  i      i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_99972427_9   5525 CTACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGATATATATAT 5574
                                  i   i    ii         i -   ii-------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGG------------- 283

  chr1_99972427_9   5575 ATATATATATATATATATATATATGAATAGAACAGAATGGAGGCCTCAGA 5624
                         ----------   v i     v  v   i   i     v   ivii    
  L1M4_orf2#LINE/    284 ----------ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_99972427_9   5625 AATAACACCACACATCTACCACCATCTGATATTTGACAAACCTGACACAC 5674
                              vv   i    i  ivii  vi    v  i     ivv  v  viv
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_99972427_9   5675 ACAAGCAATGGGGAAATGATTCCCTATTTAATAAATGGCGTTGAGAAAAC 5724
                         v  vv           vi  vvi  v  i  i      i i  i  v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_99972427_9   5725 TGGCTAGCCATATGCAAAAAATTGAAACTGGACCCCTTCCTTATACCTTG 5774
                            v  ?   i        i v    ii         v   i i   v i
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_99972427_9   5775 TATGAAAATCAACTCAAGATGGATCAAAAACTTAAACATAAGACCTAGGA 5824
                           ii     i       i        ? i  i    ii     v   ii 
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_99972427_9   5825 CCATAAAAATCCTAGAAGAAAACCTGGGCACCACCATTCAGGACATAGGC 5874
                          i      v  i           v i  ?iiv viv   iv   v v  v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_99972427_9   5875 ATGGGCAAAGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGC 5924
                         v i     v ii   v ivv  vi            vvi          v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_99972427_9   5925 TAAAATTGACAAGTGGGATCTAATTAAACTAAAGAGCTTCTGCACAACAA 5974
                         v     v  i  i v   ii v  i   v v  i i   i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_99972427_9   5975 AAGAAACTCTCATCAGAGTGAACAAGCAACCTACAGAATGGGAGAAAATT 6024
                          i  v   v   vv i      v ii     i                 v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_99972427_9   6025 TTTGCAATCTATCCTTCTGACAAAGGGCTAATATCCAGAATCTACAAAGA 6074
                                vii  viv     i  i  i  vi          v  i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_99972427_9   6075 ACT--TA-AATTTA-CAAGAAAAAAGCAAACAGCCCCATCAAAAAATGGG 6120
                            --  -  i i -i  v     ii    i i   v  i?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_99972427_9   6121 CAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAC 6170
                                 v    i     i     v        i  vi viii     i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_99972427_9   6171 AG--ACATGAAAAAATGCTCATCATCACTGGTCAT 6203
                          i--         i       v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (132 / 91)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.00 (52 / 13)  


2845 25.20 4.45 0.91  chr1_100008284_100010856     1204  2080 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100008284_   1204 TGGAAACATATCCCATGCTTATG------------------TATCAGGAC 1235
                               v          i i   ------------------ i i i  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100008284_   1236 GACCATACTGCCAAAAGCAATCTACAGATTTAATGCAATTCCCATCAAAA 1285
                          i v     v  v   vii           i  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100008284_   1286 TACCA-TTACCATTCTTCACAGAACTAGAAAAAACAATCCTAAA-TTCAT 1333
                          v   -i i  -  i  ii     v v  v  ivii        -     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_100008284_   1334 ATGGAA-TGAAAAAAGAGCCCACA-TAGCCATAGCAAGACTAAGCAAAAA 1381
                               -  v  i-- ii    v -      v i   vvi i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_100008284_   1382 GGACAAATCTGGAAGCATCACATTACCTGACTTCAAACTATACTACAAGG 1431
                          i     vi    i vv     i v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_100008284_   1432 CTATAATCACCAAAACAGCATGGTATTG-TATAAAAATTGGCACACAGAC 1480
                            i i v i   i    ii     i  -i    ii  v i  i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_100008284_   1481 CAATGGAACAGAATAGAGAACCCAGAAATAAAGTCAAATACTTACAGCCA 1530
                                 i     v    ii           vi  v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_100008284_   1531 ACTGATCTTAGACAAAG----CAAGCATAATATAAAGTGGGGAAAGGATA 1576
                          i    i  v     i ----    - iv  vi  --         i   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAG-ACCATTCAA--TGGGGAAAGAATA 394

  chr1_100008284_   1577 TCCTTTTCAACAACTGGTGCTGGGATAATTGGCAAGCCACATGTA---GA 1623
                         vi           v           i  i   vv ?       i ---  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_100008284_   1624 ATGAAACTGGGTCTTCATTTCTCACCTTATACAAAAATCAACTCAAGGTG 1673
                              ii   ii iii ii  v    v           i       ii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_100008284_   1674 GATCA-AGGCTTAAATCTAAGACCTGAAACCATAACATTCT-AGAAGATA 1721
                              -  i i     v     v  i    i    v i   -      v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_100008284_   1722 ATACTGGA--AAACCCTTTTAGACGTTGGCTTAGGCAAAGACTTCATGAG 1769
                          i iv  ?--   i i iv -   v    v        v ii   - v  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTC-TTAG 592

  chr1_100008284_   1770 AAAGAAC-CTAAAAGCAAATGCAGCAAAAACAAAGATAAACAGATGAAAC 1818
                          v vi  - i       v v   i     iv   i   i i i  vii  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_100008284_   1819 TTAATTAAA-CTAAAAAGCTCTACACAGCAAAAGAAACAATCAGCAGAGT 1867
                           v  i   -i      vi i iii vv    i  v  v    iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_100008284_   1868 AAACATACAACCCACAGAGTGGGAGAAAATATTCACAAACTATGCATCCA 1917
                         i  v v            i              ii    ii  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_100008284_   1918 ACAAAGTACTAATATCCAGAATCTATAAGGAACTCAAACA-TTAAGCAAG 1966
                          i  i v   vi          v     i      vv   -i v ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_100008284_   1967 ACAAAG-CAAATAATCCCATCAAAAAGTGGGCAAAGAACGAGAATAGAAA 2015
                          v    -       i  v  i?    i         i ivv       v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_100008284_   2016 ATTCTCAAAAGAAGATATACAAATGGCAAAAAAAAATATAAAAA-ATGCT 2064
                         v     v                    v  v  iv i  i    -     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_100008284_   2065 CAACATCACTAATTAT 2080
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (140 / 78)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.14 (47 / 22)  


4291 16.17 5.77 0.92  chr1_100015684_100018139     1098  1963 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100015684_   1098 TGGAAAACCATCCCATGGTTCATGGATTAGAAGA-TTAATATTGTCAAAA 1146
                               ivi        -          i     -          i  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATG-TTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_100015684_   1147 TGTCAGTACTACCCAAAGTGATCTACAGATTGA-------CTTT------ 1183
                           v  i    v      v             v ------- ii ------
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_100015684_   1184 ------------TTTTTTACAGAAATAGAAAAATTAGTTTTAATATTCAT 1221
                         ------------      i       v  v  ii ii ii   v      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_100015684_   1222 GTGGAATCTTAAGGGACCCTGAACAGCTAAAACAATCTTGAAAAAGAAGA 1271
                         i     vivi         v   i   i                      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_100015684_   1272 ACAACATTGGAGGACTCACATTTCCTGATTTTAAAACTTACTACAAAACT 1321
                             vi              i    ii    i               i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_100015684_   1322 TTGGTAATTGAAACAGTGTGGTACTGGCATAAAGACAGATATATAGATAG 1371
                         vii     ii i                    i  i   i        --
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT-- 297

  chr1_100015684_   1372 ACAAATGAAATAGAATAGAGAGCCCAGAAATAAACCCCAGTATATATAGT 1421
                         -   -  i        v     i              vvii  v   i  
  L1M4_orf2#LINE/    298 -CAA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_100015684_   1422 CAAATGTTTTCCAACAACAGTACTAAGACCATTCAGTGGGGAAAGGACAG 1471
                            v  v   i i    vi  i i           i         i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_100015684_   1472 TCTTTTCAACAAATAGTGCTGGGAAAACTGAATAGCCACATGCAAAATAA 1521
                                       i         v     i   ?            v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_100015684_   1522 TGAAAATGGACTGTTAACCTAACCCCATATACAAAAATTAATTCAAAATG 1571
                             iv     ivi  -   v  v                 i        
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_100015684_   1572 AATCATAGACCTAA-CAAAAGAGCTAAAACTATATAATTCTTAGAAGAAA 1620
                         i    ?        -iiv                v  i            
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_100015684_   1621 ATATAGG-GCAAAACTTCATGATATTGAATTTGGCAATGA--------AT 1661
                          i     - i   v    i   iv   ii  v       i--------  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_100015684_   1662 ATGACACCAAAGACACAGGCAA--AAAGCAAA--TAGATTAATTGGATTT 1707
                                    ii    i    --    v   --     v       i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_100015684_   1708 CATTAAAATGTAAAACTTTTGTGCTTCAAAGGACACTATCAATAGCATGA 1757
                            i     vv                               v ivi   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_100015684_   1758 AAAGACAGCCTACAGAATGGGGGAAAATATTTTAAAATCATACATCTGAT 1807
                                i  i          i          vv        i       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_100015684_   1808 AAGGGATTAATATCTAGAATATGTAATGAACTAATCTAAAACTCAACAAC 1857
                               i vi    i       i   v     --ii  v       i  i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACT--CTTACAACTCAATAAT 792

  chr1_100015684_   1858 AACAA--CAAA------AATTCAAAAGTAGGCAGAGGACTTAAATAGACA 1899
                           v  --    ------    ?    i i    i    i  i        
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_100015684_   1900 TGTCTCCAAA--AGATTTACAAATGGCCAGTAAGCACATAAAAAAATGTT 1947
                          v        --    v            i         i    i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_100015684_   1948 CAACATCACTACCCAT 1963
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (92 / 45)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.62 (58 / 16)  


3490 18.92 3.86 1.67  chr1_100084853_100086622.rev      503  1279 (491)    L1M4_orf2#LINE/L1      115   908 (0)  

  chr1_100084853_    503 TTTGTAGAAATAGAAAATTCCATCTTAAAATAAATATGGAATCTCCAGGG 552
                             i      v  v  viiv   i      vv        viv v    
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_100084853_    553 ACCTTGAATAGCCAAAACAATCTAGAAAAAGAA---CAAAGTTAGAAGAC 599
                            iv                  v         ---       i  i   
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_100084853_    600 TCATGCTTCCTCATTTCAAAACTTACTACAAAGCTACACTAACCAAAACA 649
                            ii     iv                          v   i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_100084853_    650 GTGTGGTTCTGTCATAAAGACAGACACAGAGGCCTATGGAACAGA----- 694
                                v   v     i  i     i v  ii v      i   -----
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_100084853_    695 GAACCCAGAAATAAACCC-TGTATATGCAGTCAAATTTTTTTTGACAAGG 743
                           ii              - ii  v iii     v vv    i       
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_100084853_    744 GTGCCAAGACCATTCATTGGGGAAGGGACAGTTTATATTTTTTTTGGCAA 793
                                         v       i i i   i -------   iii   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT-------TTTCAACAA 407

  chr1_100084853_    794 ATGGAGCTGAGTAAACTGGATATTCACATGCAAAAAAAAAAAAT-GGACT 842
                             v    i vv         ?i           i  vi  i -    i
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_100084853_    843 TGGACTTAATATCATATGCAAAAATTAACTCAATATGGATCAAAGACCTA 892
                         ivv  i v i i     i               v        ?       
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_100084853_    893 AACACAAGAGTTAAAACTATAAAATTCTTAGACAAAAATGTATGGCAAAA 942
                           iii     i             i       vi    ii  v ?vv   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_100084853_    943 GCTTCATGACATTGAATTTGATGAGGCTTTTTTGCATATGATACAATAGG 992
                         v    i    v   ii  v iii v v   i  iv      i  v v i 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_100084853_    993 CACAGGTAACAAAAG------TAGATAAATTGGACTTAATCAAAATCAGA 1036
                             i i        ------                v        i i 
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_100084853_   1037 AACTTTTGTTTATCAAAGGATACTTTTAAGATAGTGAATAGACAACCCAC 1086
                                  viv        i   v i    v      v           
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_100084853_   1087 AATATGGGAGAAAATATTTGCAAACCATAT--CTAATAAGTGTTTCGTAT 1134
                          iv                     i     --  i     v vi i    
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_100084853_   1135 CCAGAATATACAAAGCACCCT-GCACCTCAATAACAAAAG-------AAC 1176
                                   i    v  i  -i  v        i    i-------   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_100084853_   1177 TCAATTCATTCCCTAAATT---CAAAGGATGTGAATAGACATTTCTCCAA 1223
                         i     ? ------   v ---        v                   
  L1M4_orf2#LINE/    808 CCAATTWA------AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_100084853_   1224 AGAAGATATATGTATG-CCTGCAAGCACATGAAGAGATGCTCAACATCAC 1272
                                   iiv   -  vii           i               ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_100084853_   1273 TAAGAAA 1279
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.51 (86 / 57)
Gap_init rate = 0.02 (12 / 794), avg. gap size = 3.58 (43 / 12)  


3044 25.79 2.70 0.45  chr1_100161913_100164149.rev      859  1746 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100161913_    859 TAGAAATACATCCCACACTCACGGATGCGTAGAATCAATATTGTGAAAAT 908
                          i    v i      iii   i    vv v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100161913_    909 GACCATACTGCCAAAAGCAATCTATAAATGCAGTGCAATTCCCATCAAAA 958
                          i v     v  v   vii     i i  v  ii     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100161913_    959 TGCCAGCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCATA 1008
                          v     vv v  i  ii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_100161913_   1009 TGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 1058
                              viiv  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_100161913_   1059 CAAATCTGGAGGTATCACATTACCTGACTTCAAACTATACTATAAGGCCA 1108
                             vi      vv     i v  ii i      viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_100161913_   1109 TAGTCACTAAAACAGCATGGTACTGTTATAAAAATAGGCACATAGACCAA 1158
                         i   v ii  i    ii        vi    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_100161913_   1159 TGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAGCCAACT 1208
                              i     v    ii           v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_100161913_   1209 GATCTTCAACAAAGCAAACAAAAACATAGAGTGGGGAAAGGACACCCTAT 1258
                            i   i    i vviv   i v   vv i         i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_100161913_   1259 TCAACAAACGATGCTTGGATAATTGG----CCACGTTCAGAAGAATGAAA 1304
                                 i i    v   i  i   ----    i v  i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_100161913_   1305 CTGGATCCTCCTCTCTCACCTTACACAAAAATCAACTCAAGGTGGATCAA 1354
                         i    i  iivi   v    v  i        i       ii       ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_100161913_   1355 GGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAATATTA 1404
                         i   i     v     v  i    i      v ii       v  i  vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_100161913_   1405 GAAAAACCCTACTAGACATTGGCTTAGGCAAAGA---CTTAATGATCAAA 1451
                          ?iv  vi  v vv   v    v        v i---    --   -- v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA--GAT--AT 596

  chr1_100161913_   1452 AAC-CCAAAAGCAAATGCAACAAAAACAAATATAGAT------GACT--- 1491
                         i  -         v v         iv   v      ------    ---
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_100161913_   1492 --AAAAT-----GTTTCTTCACAGCAAAAGAAATAATCAGCAGAGTAAAC 1534
                         --     -----ii  i vii vv    i  v iv    iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_100161913_   1535 AGACAACCCACAGAGTGGGAGAAAATATTTGCAATCTATACATCCAACAA 1584
                                       i                   vii   i   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_100161913_   1585 ACAACTAATATCCAGAATCTACAAGGAACTCAAGCAAATCAGCAAGAAAA 1634
                         ivi   vi          v  i  i      vvi   v   ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_100161913_   1635 AAACAAAGAATCCCATCCAAAATTGGGCTAAGGACATGAACAGACAATTC 1684
                          i     v  i  v  i?    v     v     iv    i     v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_100161913_   1685 TCAAAAGAAGATATACAAATGGCCAATAAACATATGAAAAAATGCCCAAT 1734
                           v                          i  i       i    i   i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_100161913_   1735 ATCACTAATTAT 1746
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (135 / 91)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.50 (28 / 8)  


2453 20.58 2.71 14.98  chr1_100177408_100181207.rev     2275  3309 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100177408_   2275 TGGGAAGATATACCATGCTTGTGGATTAAAAGAATTAATATTGTTAAAAT 2324
                            i       v     i ii      ii    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100177408_   2325 CACCATATTACCAAAAGCGATCTTCGGATTCAGGACAATCCCCATCAAAA 2374
                         vi v   i v  v   vi     v i      ivi       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100177408_   2375 TACCAATGACACTCTTCACAGAAACAGAAAAAACAATCCTAAAATTCATA 2424
                          v   iivi vi i  ii      iv  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_100177408_   2425 TGGAACCACAAAG-ACCCTGAATAATAGCCAAAGCAACCCTGAGCAAAAA 2473
                              vii   i -    v     ---      i   i i   iv  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATA---GCCAAAACAATCTTGAAAAAGAA 197

  chr1_100177408_   2474 GAACAAAGCTAGAGGCATCACACT--ATGACTTCCAAATATACTACAAGG 2521
                                 i i    vv       --vii i   v   iv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_100177408_   2522 CTATAGTAACCAAAATAGCATGGAATTTGTTTAATAACAGGCACAAAGAC 2571
                            i     i   i i  ii   v i v iv   vi i  i  i v   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_100177408_   2572 CAATGGAACAAAATAGAGAACCCCAAAATACATTTACATGTTTACAGCCA 2621
                                 i i   v    ii  vi     v iii i ii    ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_100177408_   2622 ACTGATTTTTGACGAAGGTGCCAGGAGCATGCATTAGAAAAAGGACATCC 2671
                          i       i   i i       i  v   v  v i ii    i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_100177408_   2672 TCTTCGATAAATGACGCTGAGAAAATTGGATATGAATATGAAGAAAAATG 2721
                          i   i i     ii    i  v  i      ?vv i   v i  i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_100177408_   2722 ACACTAGATCCC-ATCTCTCACCATATAAAAAAAA-AACCCAAAATGGAT 2769
                          vii i  i   - i   v         v     v-   i          
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_100177408_   2770 TAAAGATGTAAACATAAGACTCAAAACTATAAAACTACTACTAGAAGAAA 2819
                         i ?   iv    ii     vii              -  --         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CT--TAGAAGAAA 544

  chr1_100177408_   2820 ATAGAGGAG-AAATGTTTCAGGACATTGGTCAGGGCAGATTTTATGGCTG 2868
                          i v   ? -    -i   iv   v    -------------------- 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTGG--------------------G 573

  chr1_100177408_   2869 TTATTTCAAAAGCACAGGCAGTGCTTGCTTCAGCAGCAAACATACTAAAA 2918
                            -------------    i  v  v   --------------------
  L1M4_orf2#LINE/    574 TTA-------------GGCAATGGTTTCTT-------------------- 590

  chr1_100177408_   2919 TTGGAATTACACAGAGAAGATTAGCATGGCCCCTGCATAAGGATGACAAA 2968
                         -----------------    ---------------------      --
  L1M4_orf2#LINE/    591 -----------------AGAT---------------------ATGACA-- 600

  chr1_100177408_   2969 CAAATTCATGAAGTGTTCCATATTTTAAAAGATATACAAATAAATACATA 3018
                         -----------------   ------------------------------
  L1M4_orf2#LINE/    601 -----------------CCA------------------------------ 603

  chr1_100177408_   3019 AGAAAAAAAGCACAGGCAATGAAAACAAAAATAGAATAATGGAACTATAT 3068
                         ------        i    ii   iv         vv   v i   vi  
  L1M4_orf2#LINE/    604 ------AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_100177408_   3069 TAAACTAAAAAGCTTCTG-----CAAAG--CA--AAGAAAAAAATACAGA 3109
                         i   v v    i   i  -----     --  -- vv  i   i iv i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_100177408_   3110 CACAATCTGTAGAATGGGAGAAAATATTTGCACTAATCATGT----GACA 3155
                         v    i iii                      --      i ----  i 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCA--AATCATATATCTGATA 745

  chr1_100177408_   3156 AGAAACTAATATCCATAATATATAAAGAACTCC-AGAGC------GTAAG 3198
                           ii   vi      v                i- v i ------i   i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_100177408_   3199 AA--CAAATAATCCCATTAAAAAGTGGGCAAAGGACCTCAATAAACATTT 3246
                           --       i  v   ?    i           ii v    i      
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_100177408_   3247 CTCAAAAGAAGACATACAAATAGCCAACAGGTATATGAAAAAATGCTCAA 3296
                            v        i        i     i i i i       i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_100177408_   3297 CATCACTAGTCAT 3309
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (142 / 67)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 7.96 (183 / 23)  


3350 21.20 5.10 2.15  chr1_100270867_100274871     2631  3512 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100270867_   2631 TGGAAAGAC-TCTTAATATTCATGGATTGGAAGACACAATACTGCCAAAA 2679
                                 i-  ii - i                 vi    i  ii  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCA-TGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_100270867_   2680 CAGCATTTCTTTGAAAACTGACCTATAAATTC--CTTATATACCTATCAA 2727
                         ii   v v  iivv   i   i   i i    -- vi -  v        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA-ATCCCTATCAA 98

  chr1_100270867_   2728 AATCCAAACAAACCATTTTGTAGAAATTGAGAAGGTGACC-----ATTTT 2772
                              v i viv iv     i         v   v   i -----   iv
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_100270867_   2773 CATGAAACTGTAAAAGATCTA---------AAACAATTTTGAAAAGGAAG 2813
                         i   i  v  i  ii  i i ---------       i       i    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_100270867_   2814 AATAGAGTCTGTAGATTTATACTACTGACTTTCAAAACTTTTAATATAAA 2863
                           i i   iv vi  i i i   v iv v           -- v  i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT--ACTACAAA 246

  chr1_100270867_   2864 GTCATAGTGATTAAGATGCTGTGACACTGGCACA-GGATAGGCATAAAAA 2912
                          ii i   i  i    iiv    ii       i -      i    v i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_100270867_   2913 TCAATGAAACAGAATTGAGAATCCTGAAATAAATCCTTACAT----GGTC 2958
                               i  i          i   v        i  v     ----    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_100270867_   2959 AACTGATTTTCAACAAAGGTGCTTAGACAATTCAACAGAGAAAAA---GA 3005
                           i        i    i     iv    v      ii i    i --- v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_100270867_   3006 CTTTTCA-TAAATGGTACTAAGA--ACTGGATATTCAGA-GCAGGGGGGA 3051
                                -i       i  ii  --        ?i  v -   i----- 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA-----A 441

  chr1_100270867_   3052 AAAATGAACTTAGATCCTTACTTCAAGCCATGCACACAAATTATTTCAAA 3101
                          i      v  i  i  i   i   vi    ii   v      vi     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_100270867_   3102 ATGGATCACAGATCTAAATGTAACAACTAAAACTATAAAAGTTGTAGAAG 3151
                                 ?   i          v i              v iv      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_100270867_   3152 AAAACAAAGGAGAAAATGTTTTCAACCTGTGGTTGGACA--GAGTTCTTA 3199
                               v   ? v    v  ivii    vv    i i  -- iv      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_100270867_   3200 TATACAACTCCAAAAGCAAGATCCACAAAAGAAAAAAGTTTGATAAATTG 3249
                         v   ii  v         vi v v             -- v         
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAAATTG 639

  chr1_100270867_   3250 CACTCCATCAAATATTAAAAACTTTTGTATTTCAAAAGACAC-ATTGAGA 3298
                         v   i       -               ii      i     -  ii   
  L1M4_orf2#LINE/    640 GACTTCATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_100270867_   3299 AAATGAAAAGGGAAGCCAC----TGGGAGAAAATATTTGCTAATCATATA 3344
                           i       iv  v    ----                 v         
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_100270867_   3345 CTTGATAAAGGACTTGTATCCAGAATATACAAAGAACT--TATAATTCAA 3392
                         ii      i                    i        --  i  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_100270867_   3393 TAA---AAAGACAA----CCTTGTTTAGCAATGGTCAAAAGATTCAAATA 3435
                            ---        ----  ivi  ? iv     v    i    ii    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_100270867_   3436 GAAATATCACCAAAGTGGTATTTTAATATTGATGTTAAATAAGCACATGA 3485
                           v  v  v      vi -  ----   ivi   viv             
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAG-AT----ATACAAATGGCCAATAAGCACATGA 883

  chr1_100270867_   3486 ATAGAGATACTCAACCTCATTAGGTTT 3512
                          --i    i      v   ????????
  L1M4_orf2#LINE/    884 A--AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (119 / 64)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.56 (64 / 25)  


1211 21.17 6.93 0.36  chr1_100359549_100363230.rev     1542  1815 (1867)    L1M4_orf2#LINE/L1        1   292 (616)  

  chr1_100359549_   1542 TGAAAAGATATCCCATGTTCATAGATTGGAAGAATTAATATTGTTAAAGT 1591
                           i                   i          v             ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100359549_   1592 GTCCATACTACCCAAAGTGATCTACAGATTCAATGAAATCTCTATCAAAA 1641
                          v v     v      v                i v    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100359549_   1642 TCCTAATGACTGTTTTCACAGAAATAGAATAAAC-AATCCTAAAGTTC-- 1688
                            i iivi iv    ii       v  -i  i -i        i   --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr1_100359549_   1689 -------CACAAAAGACTTCAAATAGCCAAAGCAATCTTGAGCAAAAAGA 1731
                         -------ii   ii   iivi          i         iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_100359549_   1732 ACAAAGCTGGGGTGTTGACACTACCTGACTTCAAAATATACCACACCGCT 1781
                               i   i vii v     v  ii i       iv   i   vv   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_100359549_   1782 ACAGTAATCAA-ACAGCATG--------ATAAGGCTGGACACA 1815
                                    -    ii  --------      v i    i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

Transitions / transversions = 2.22 (40 / 18)
Gap_init rate = 0.02 (5 / 292), avg. gap size = 4.00 (20 / 5)  

 558 20.69 1.72 0.86  chr1_100359549_100363230.rev     2227  2342 (1340)    L1M4_orf2#LINE/L1      240   356 (552)  

  chr1_100359549_   2227 CTCTAAAAATACAAATAAGTAAAACAGTATGGTACTGGCATAAAAACAGA 2276
                           vi   iv    i-   vi  i     i              ii i   
  L1M4_orf2#LINE/    240 CTACAAAGCTACAG-TAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_100359549_   2277 CGCA--GACCGATAGAACAGAATAGAGAGCCCAGAAATAAATTCACACAT 2324
                          ii --  i i  i   i     v     i           ii  i    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_100359549_   2325 TTATGGTCAATTGGTTTT 2342
                                      i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTT 356

Transitions / transversions = 5.00 (20 / 4)
Gap_init rate = 0.02 (2 / 117), avg. gap size = 1.50 (3 / 2)  

1885 24.38 5.16 1.07  chr1_100359549_100363230.rev     2630  3191 (491)    L1M4_orf2#LINE/L1      324   908 (0)  

  chr1_100359549_   2630 AATATGCCCAGCCA---ACAGTCAACTGATTTTTGACAAAGGTGCCAAGA 2676
                             vi    vv  --- ii     i       i     i          
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_100359549_   2677 ACACACAATCAGCAAACAACACTCTCTTCACTCAATGGTGTTGGGACAAC 2726
                         v  iv    vi v   v  i v   i    viv       i         
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_100359549_   2727 TGGATATCCATATACAGAGGAATAAAACTAA-----TACTTCATGCTACA 2771
                               ?   i  i  i i    i  ii ii-----   i   ii i i 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_100359549_   2772 TTAAAAAATAAACTACAAATGAATTAAAGACTTAAATATAAGACCTAAAA 2821
                          vv      v    vv     i  i ?    i     i     v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_100359549_   2822 CTATAAAACTACTAGAAGAAACCATAGAAGAAAAGCTCCATGACATTCAT 2871
                                   vi         v     i? v   v  i i    v  viv
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_100359549_   2872 CTGGGCAATAATTTTTTGGATACAAATCCAAAAACACAGGCAACAAAAAC 2921
                         i i      ii   i  i    ii vv      i    i         iv
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_100359549_   2922 AAACATTGACAAATGGGATTACACCAAACTAAAAATCTCTTGCACGGCCA 2971
                            v  v  i    v   i v  i    v v    v  i   ii vv v 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_100359549_   2972 AGAACACAAACAACAAAGTGAAGAGACAACC-----------------TG 3004
                           i    v v   v        i        ----------------- i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_100359549_   3005 TCTGCAAATCATACATCCGATAAGGGGTTAATAAAAAAAAAAAAAAAAAA 3054
                          i           i   i        ii vi  vvv i  v v v   i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_100359549_   3055 AAAGAAACTC----AACTCAGCAATGAGAAAACAAAGAACTCAATTTAAA 3100
                          ------   ----      ii   i i  i     v   i     ?   
  L1M4_orf2#LINE/    774 A------CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_100359549_   3101 AATTGGCAAAGGATCTGAGTAGACATTTCTCCAAAGAAGACATAAAAATA 3150
                            v          i   i                     i   v    i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_100359549_   3151 TCCAACAGGTATATGAAAAAGTGCCCCAAATCAAAAATCAC 3191
                         v    i i i i       ii   i v v    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (80 / 53)
Gap_init rate = 0.01 (5 / 585), avg. gap size = 7.00 (35 / 5)  


3131 26.76 0.55 0.55  chr1_100376679_100383443     5365  6272 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100376679_   5365 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5414
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100376679_   5415 GGCCAAACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 5464
                            v v   v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100376679_   5465 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTTAT 5513
                          v   vivi i  i  ii     v v  v  i-  - iii    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_100376679_   5514 ATGGAACCAAAAAAAAAGCCCACA-TAGCCAAGATAATCCTAAACAAAAA 5562
                               viiv  iii --    v -       i i    i i  v  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_100376679_   5563 GAAGGAAGCTGGAGGCATCATGCTACCTGACCTCAAACTATACTACAAGG 5612
                            vi   i      vv   ii  v  ii ii     viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_100376679_   5613 CTACAGTAACCAAAACAGCATGGTAATGGTACCAAAACAGAGAGATAGAC 5662
                                  i   i    ii     v   i iv ii i   v v     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_100376679_   5663 CAATGGAACCGCACAGGGGCCTCAGAAATAACACCACACATCTACAACCC 5712
                                 iv v iv i ivii         vv   i    i  iiii v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_100376679_   5713 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGCGGAAAGGATTCC 5762
                           -    i  i     ivv  v   i v  vv     v      i  vvi
  L1M4_orf2#LINE/    348 AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_100376679_   5763 CTATTTAATAAATGGTGTTGGGACAACTGGCTAGCCATATGCAGAAAACT 5812
                           v  i  i        i            v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_100376679_   5813 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 5862
                            ii         v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_100376679_   5863 TTAAAGACTGAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5912
                          i ?    iv          v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_100376679_   5913 CTAGGCA-ATACCATTTAGGACATAGGCATAGGCAAAGACTTCATGACTA 5961
                         v    ?i- v i -  iiv   v v  vv       v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_100376679_   5962 AATCACCAAAAGCAATTGCAACAAA-GCCAAAATTGACAAATCAGATGTA 6010
                         viv           vvv        - vv     v  i    ii  iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_100376679_   6011 ATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGAGAA 6060
                           v   v v  i i   i  ii vv    i  v       vv i  v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_100376679_   6061 CAGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTATCTATCTGACA 6110
                         v  i     i              v  v       vii  v       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_100376679_   6111 AAGGGCTAATATCCAGAATCTACATGGAACTTAAACAAATTTACAAGAAA 6160
                          i  i  vi          v  i vi     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_100376679_   6161 AAAACAAACAACCCA-TCATAAAGTGGGCGAAGGATATGAACAGACACTT 6209
                           i     i      - i?v   i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_100376679_   6210 TTCAAAAGAAGACATTTATATGGCCAACAAACATATGAAAAAAAGCCCAT 6259
                         i  v        i  vi v        i  i  i       i v  i  v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_100376679_   6260 GATCACTGGTCAT 6272
                         v    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (135 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


1915 25.14 2.23 1.30  chr1_100546564_100549787.rev     1255  1791 (1433)    L1M4_orf2#LINE/L1        1   542 (366)  

  chr1_100546564_   1255 TGAAAAAACATTACATGCTCATGGATTGGAAGAAACAATATGGATAAAAT 1304
                           i   i i  iv    i               vvi     v v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100546564_   1305 CACTATATTGCCCAAAGCAATCTACAGTTTCAACACTATTCCTATTACAC 1354
                         vi v   i v      vii        v      i v  i     i v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100546564_   1355 TACCAGTATCATTTTTCACAGAATTAGAAAAAAAACT-ATTCTAAAATTC 1403
                          v    ivv v     ii     v v  v  i---  -  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr1_100546564_   1404 ATATGGAACCAAAATAAGG---CCA-AATAGTCAAAGCAAT---AAGCAA 1446
                                 --- vii    ---   -     i    i    ---i iv  
  L1M4_orf2#LINE/    148 ATATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_100546564_   1447 AAAGAACAAAGCCAGAGGCATCACATTACCCAAATT-AAAACTCTACTCT 1495
                         i          iii    vv     i v     v  -      -    vi
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTAC 243

  chr1_100546564_   1496 AAGGCTATAATAACCAAAACAGCATGGTACTGGTACAAAAACAGACACAT 1545
                           i    i i   i   i    ii         i i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_100546564_   1546 AGAACAATGGAACATTATAGAGAACCCCGAAATAAACCTGTACACCTACA 1595
                            v        i vv  v    ii  v          ii    ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_100546564_   1596 GCCATCTGATCTTCAACAAAATCAACAGAAATAG-CACTAGGGAAAGGAC 1644
                          i  vi    i   i    iiviiv  ii vi v-  v i       i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_100546564_   1645 TTCCTATTCAATAAATGGTGCTGGGATAGCTGGCTAGCCAAATGCAAAAG 1694
                         vvi  v     i              i i    v  ?   v         
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_100546564_   1695 AATGAAACTGGTCTCCTATCTATCACCGTATACAAAAATTAACTCAAGAT 1744
                               ii   v i    i  vv    i                   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_100546564_   1745 AGATTAAAGATTTAAATGTAAGATCTCAAACTA--AATGTCCCAGAAGA 1791
                         i   i ?   ii           v  v      --  vv  ii      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

Transitions / transversions = 1.66 (83 / 50)
Gap_init rate = 0.02 (10 / 542), avg. gap size = 1.90 (19 / 10)  

 850 25.63 7.89 0.56  chr1_100546564_100549787.rev     2379  2733 (491)    L1M4_orf2#LINE/L1      528   908 (0)  

  chr1_100546564_   2379 AAAATTTTTAGAAGAAAACCTAGGAA-ACACCATTCTAAATATCGGCCTC 2427
                             i i            v    ?i- v i -   vvi iv i  vi -
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTT- 575

  chr1_100546564_   2428 AGGAAAGAATTT-------ATGAC--TAAGTCCTCAA------AAAGCAA 2462
                            v  vii   -------     --i  ivv v   ------    v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_100546564_   2463 ACATTGACAAGTGGGACCTAATTAAACTAAAGAGCTTCTGAACAGCAAAA 2512
                          v  v  i  i v    i v  i   v v  i i   i  vi vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_100546564_   2513 TAAACTATCAACAGAGTAAACAGACAACATACAGAAGGGGA-AAAATATT 2561
                         v v        v i   i  v       vi      v    -        
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_100546564_   2562 CGCAAACTATGTATCTGACAAAGGTCTAATATCTAGAATCCATAG-GAAT 2610
                         i     ii  i       i  i  v  vi    i     vi   i-   i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_100546564_   2611 T-TAACAGTTGAACAA----GAGAAAAATAACCCCATTAAAAAATGAGCA 2655
                          - v   ii v  i  ----i   v         v   ?       i   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_100546564_   2656 AAAGACATGAACAGACACTTCTCAAAAGAAGAAACACAAGCACCTAA--- 2702
                           i  iv    i     i     v        v i    iiiv i  ---
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_100546564_   2703 -CATATGAAAA-ATGATCAACATCACTAATCAT 2733
                         -  i       -   v         ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (50 / 39)
Gap_init rate = 0.03 (12 / 381), avg. gap size = 2.50 (30 / 12)  


1518 26.78 8.40 3.13  chr1_100648628_100650287      479  1180 (480)    L1M4_orf2#LINE/L1      170   908 (0)  

  chr1_100648628_    479 GAAAAGATAAAGATTATCTTGAA---TAAGATCAAAGCTGGAGGATTTAC 525
                            v  vi   - iv        ---v    v     i       i i  
  L1M4_orf2#LINE/    170 GAATAGCCAAA-ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_100648628_    526 ACTCCCAGATAT--GGATTCATTTTAAAACTGCAGCAATTATGATATTGA 573
                            i  vi  v --ii i i i vi   i  i   i   i v  i v  v
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_100648628_    574 GATATTGGTGTCAAGACAGACAAATTAACCAATAGAATAGAATATAAAGT 623
                          i  i   ii v i  i     v  vi i    i         vv i   
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_100648628_    624 GCAGAAACAAATTCAAAAATATACAGACACTTGATTTATGATAAAGGTGA 673
                         v      i   ii  v v  v  ii v  v       vi  i  i    v
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_100648628_    674 CATGTTAGAGCA----ACAGGAAAAG----GTCTTTTTAGTAAATTCTGC 715
                           ----   v  ---- ii  i    ----       i ii    vv   
  L1M4_orf2#LINE/    369 CA----AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_100648628_    716 TGGGTCAACTGGATATCTATATGGGGAAAAAGAA-GAACCTTGGCTCCTA 764
                             v          ? i i   v---       -   vi v i i    
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGC---AAAAGAATGAAGTTGGACCCCTA 461

  chr1_100648628_    765 TCTCACAACCTATTTTTTAAAGG--AATTCCTGATGAGTTGTTGATTCAA 812
                         i      v v   vi---   ii--  i  vvi   ii ii?v  iii  
  L1M4_orf2#LINE/    462 CCTCACACCATATAC---AAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_100648628_    813 ATGTGACAGAAAAATCAGTGAAGCTTCTGGAAGATAACATAAAA-TAATG 861
                             i v  vv   v vi i  i  ii i     v      ii?-   -i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-A 557

  chr1_100648628_    862 TATTCAT-ACTTTGAAGTTAA-CAAAGATATCTTAAGTGGTACATGGAAA 909
                          v   i -  i   i-    i-   v i v     ii ivv   ivi   
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_100648628_    910 GCATTACCTATAACTGAG----TTGA--AATTG--------TAAAATT-- 943
                            iv v v i  vv  i---- v  --     --------i      --
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_100648628_    944 ---CTCTT---CATCAAAG-ACACTATTAAGAGAGTGAAAATGAAAACC- 985
                         ---  i  --- v      -       i    i        -  v    -
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GACAACCC 705

  chr1_100648628_    986 ACAAGAGTAGGAGAA--TATTTACA--TCACATA----ATAATGGGCACT 1027
                            -  i i      --     i  --   i   ----    -   ----
  L1M4_orf2#LINE/    706 ACA-GAATGGGAGAAAATATTTGCAAATCATATATCTGATAA-GGG---- 749

  chr1_100648628_   1028 GTACTTGTACCCAGAATACTTACA---CTCCTACACATTAACAATAAAAA 1074
                         --       i        iv  v ---   i    vv i  i        
  L1M4_orf2#LINE/    750 --ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_100648628_   1075 GACAA----TCTGAT-AAAAAATGTGTAAGAAACATGAAAAGACATTTCA 1119
                              ----i ii  -?       v i  iii iv    v         v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_100648628_   1120 TAGAAGAGAATGTACAAATGGCCAATAAACATACGAAAAGCGATTCACCC 1169
                         ivi    ii  i                i  i i      vvii   v v
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_100648628_   1170 TCATTAGCTAT 1180
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.63 (114 / 70)
Gap_init rate = 0.04 (32 / 739), avg. gap size = 2.53 (81 / 32)  

 707 23.21 10.00 1.43  chr1_100648628_100650287     1380  1659 (1)  C L1M4_orf2#LINE/L1   (104)   804   501  

C chr1_100648628_   1659 AGACTTAAATGTGAATG-TAAAACTATAAACTTTTTAGAAAAAAAAATAT 1611
                             i       i iv -            vi i      i    v   v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

C chr1_100648628_   1610 GAG-AAATCATTGAG-TCTAGGGCTAAACTAAGAGTCTC--AGACA--AT 1567
                          ? -     v i v -i  v   i  ii -  vi  i  --   i -- i
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTAGATATGAC 599

C chr1_100648628_   1566 ATCAAAA--------------AGAAAAAAGTGATAAAAGGGATTTCATCA 1531
                          i     --------------        vv      vv   i       
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

C chr1_100648628_   1530 AAATTTAAAACTTTTATTCTGTAAAAGACCCTATTAAGAGGATGAAAAGA 1481
                              v         i v  vi   i   v    i    iii        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

C chr1_100648628_   1480 CAAGTTATAGACTGAAAAAAACC--TTGAAAAACATTTACCAGACAAAGG 1433
                            vii i   v  ii i   vi--   v   v   v  i v  i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

C chr1_100648628_   1432 ACTAGTATCTAGAATATACAAAGATTGAC-CTTAG---TCATCAAGAAAA 1387
                            v     i        i     ---  -    v---   vi  v    
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGA---ACTCTTACAACTCAATAATAAAA 796

C chr1_100648628_   1386 AG-CAAAT 1380
                           -     
  L1M4_orf2#LINE/    797 AGACAAAT 804

Transitions / transversions = 1.37 (37 / 27)
Gap_init rate = 0.04 (12 / 304), avg. gap size = 2.67 (32 / 12)  


3205 27.04 0.66 0.44  chr1_100776067_100782458.rev     4996  5901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100776067_   4996 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5045
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100776067_   5046 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100776067_   5096 TACCAATGACTTTCTTCCCAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   iivi i  i  iv     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_100776067_   5144 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTATGCCAAAAG 5193
                                viiv  ii  v  v v  v     i      i ivivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_100776067_   5194 AACAAAACTGGAGACATCACACT-ACTGACTTCAAATTATACTACAAGGC 5242
                               ii     ivv       -v ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_100776067_   5243 TACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGATATATAGACC 5292
                                 i   i   iii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_100776067_   5293 AGTGGAACAGAACAGAGGCCTCAGAA-TAATATCACACATCTACAACCAT 5341
                          i     i    iv   ivii     -   vvi  i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_100776067_   5342 CTCATTTTTGACAAACCCAACAAAAACAAGAAATGGGGAAAAGATTCCCT 5391
                         i v     i     ivviiv   i v  vvv          ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_100776067_   5392 ATTTAATAAATGGTGCTGGGAAAACTGACTAGTCATATGGAGAAAGCTGA 5441
                         v  i  i              v     iv  ?i  i   v i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_100776067_   5442 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5491
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_100776067_   5492 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCTTAGAAGAAAACCT 5541
                          ?    i  v    v   v       i      vi             v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_100776067_   5542 A--CGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5589
                          --? i  - i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_100776067_   5590 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 5639
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_100776067_   5640 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5689
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_100776067_   5690 AGGCAACCTACAGAATGGGAGAAAATGTTTACAATCTATCCATCTGACAA 5739
                           i     i                 i   i   vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_100776067_   5740 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5789
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_100776067_   5790 AATCAGACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACATTTC 5839
                          iv  i i     v  i?    i            v    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_100776067_   5840 TCAAAAGAAGACATTTATTCAGCCAACAGACACATGAAAAAATGCTCATC 5889
                           v        i  vi vvii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_100776067_   5890 ATCACTGGCCAT 5901
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


3218 26.91 1.00 0.44  chr1_100810071_100816467.rev     5004  5906 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100810071_   5004 TGGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5053
                              ii i  ii    i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100810071_   5054 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5103
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100810071_   5104 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5151
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_100810071_   5152 TATGGACCCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5201
                               vviiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_100810071_   5202 AACAAAGCTGGAGGGATCACACTACCTGACTTCAAACTATGCTACAAGGC 5251
                                i      iv       v  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_100810071_   5252 TACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGAGATATAGATC 5301
                                 i   i   iii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_100810071_   5302 AGTGGAATAGAAT--AGAGCCCTCAGAAATAACACCGCGTATCTACAACC 5349
                          i           --    i  --        vv  iiii  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_100810071_   5350 ATCTGATCTTTTACACACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5399
                          vi    i  iv   vivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_100810071_   5400 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5449
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_100810071_   5450 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5499
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_100810071_   5500 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5549
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_100810071_   5550 CTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGACTAA 5599
                         v    ?i v viv   iv   viv  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_100810071_   5600 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5649
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_100810071_   5650 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5699
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_100810071_   5700 AGGCAACCTACAAAATGGGAGAAAATTTTTGCTACTCAT----CTGACAA 5745
                           i     i   i             v     v v    ----    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_100810071_   5746 AGGGTTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAC 5795
                         i  ii vi          v  i  v      vv    v iv i  v   v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_100810071_   5796 AAACAAG-AACCCCATCAAAAAGTGGGCAAAGGATATGAATAGACACTTC 5844
                          i    i-     v  i?    i            v          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_100810071_   5845 TCAGAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCACC 5894
                           vi       i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_100810071_   5895 ATCACTGGCCAT 5906
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3095 27.99 0.88 0.44  chr1_100840808_100847197.rev     4996  5899 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100840808_   4996 TGGAAGAACATTTCATGCTCATGGTTAGGAAGAATCAATATCAAGAAAAT 5045
                              ii i  ii    i      v v      v i     iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100840808_   5046 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100840808_   5096 TACCAATGACTTTTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   iivi i     ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_100840808_   5144 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5193
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_100840808_   5194 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGGC 5243
                                i      vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_100840808_   5244 TACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGACC 5293
                                 i   i    ii    i    i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_100840808_   5294 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5341
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_100840808_   5342 ATCTGATCTTTGATAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5391
                          vi    i  i  i  ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_100840808_   5392 CTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCT 5441
                           v  i  i              v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_100840808_   5442 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5491
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_100840808_   5492 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5541
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_100840808_   5542 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5591
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_100840808_   5592 AACACCAAAAGCAATGGCAAAGAAGGCCAAAATTGACAAATGGGATCTAA 5641
                         i            vvi    vi  i vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_100840808_   5642 TTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTACCATCAGAGTGAAC 5691
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_100840808_   5692 AGGCAACCTACAGAATGGGAAAAAATTTTCGCAATCTACTCATCTGACAA 5741
                           i     i           i     v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_100840808_   5742 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAGTTTACAAGAAAA 5791
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_100840808_   5792 AAACAA----CCCCATCAGCAAGTGAGTGAAAGATATGAACAGACATTTC 5837
                          i    ----   v  i?iv  i  i ii  i   v    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_100840808_   5838 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5887
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_100840808_   5888 ATCACTGGCCAT 5899
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3225 27.09 0.55 0.55  chr1_100854753_100860567.rev     4417  5324 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100854753_   4417 TGGAAGAACATTCCATGCTCATGGTTAGGAAGAATCAATATCGTGAAAAT 4466
                              ii i  i     i      v v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100854753_   4467 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4516
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100854753_   4517 TACCAATGACTTTTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4564
                          v   iivi i     ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_100854753_   4565 TATGGAACCAAAAAAGAGCCCATATCGCCAAGTCAATCCTAAACCAAAAG 4614
                                viiv  ii  v  viv  v     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_100854753_   4615 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGGC 4664
                                i      vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_100854753_   4665 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGACC 4714
                                 i   i    ii       v i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_100854753_   4715 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGTCGCATATCTACAACT 4762
                                i    i--    i  --        vvi ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_100854753_   4763 GTCTGATCTTTGACAAACCTGACAGAAACAAGAAATGGGGAAAGGATTCC 4812
                         ivi    i  i     ivv  v  ii v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_100854753_   4813 CTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCT 4862
                           v  i  i              v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_100854753_   4863 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGAA 4912
                            ii    i    v   i     v              i    i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_100854753_   4913 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4962
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_100854753_   4963 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5011
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_100854753_   5012 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCGA 5061
                         vi            vvi          vv     v  i    v   iivv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_100854753_   5062 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5111
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_100854753_   5112 CAGGCAACCTACAGAATGGGAGAAAATGTTTACAATCTATCCATCTGACA 5161
                         v  i     i                 i   i   vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_100854753_   5162 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAGATTTACAAGAAA 5211
                          i  i  vi          v  i  v      vv   iv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_100854753_   5212 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5261
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_100854753_   5262 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5311
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_100854753_   5312 CATCACTGGCTGT 5324
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3113 26.56 0.89 0.33  chr1_100864741_100867621.rev     1495  2390 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_100864741_   1495 ACATCCCATGCTGACAGATGGATAGAATAAATATTGTGAA-----CA-TA 1538
                          i        i v ii   v iv   v v        v  -----  -  
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_100864741_   1539 CTGCCAAAAGCAATCTACGAATTCAATGCAATCACCATCAAAATATCATC 1588
                           v  v   vii      ii      i      v i        vi  v 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr1_100864741_   1589 ATCATTCTTTACGGAATTAGAAAAAACAATTCTAAAATTTATATGGAACC 1638
                         vv v  i   i i   v v  v  ivii  i        i        vi
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_100864741_   1639 AAAAAGGAGCCTGCATAGCCAAAGCAAGACTAAACAAAAAGAACAAATCT 1688
                         iv  i   v  v v         i   vvi i  v  i         vi 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_100864741_   1689 GGAGGCTTCACACTACCTGATTTCAAACTATACTATAAGGCCATAGTCAC 1738
                              vi       v  ii        viv     i  i  i i   v i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_100864741_   1739 AAAAACAGCATGGTACTCGTATAAAAATAGACACATAGACCAATGGAACA 1788
                         v  i    ii       v i    ii       i     i        i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_100864741_   1789 GAATAGAGAACCCAGAAATAAACCCAAATACTTAAAGCCAACTGATCTTT 1838
                             v    ii               v i i   vi i   i    i  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_100864741_   1839 GACAAAGCAAACAAAAACATAAAGTGGGAAAAGGATGCCCTTTTCAACAA 1888
                              i vviv   i v   vv i    i    i  ivi           
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_100864741_   1889 ATGGTGCTGAAATATTTGGCTAGCCACATGTAGGACAATGAAACTGGATT 1938
                                  ii i vi   v  ?       i ii v      ii    ii
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_100864741_   1939 CTCATCTTTCACCTTATACAAGAATCAACTCAAGATGAATTAAGGATTTA 1988
                          ii i  iv    v       i   i       i   i  i ?i  ii  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_100864741_   1989 AATTGAAGACCTGAGACTATAAACATTCTT-GAAGATAACATTAGAAAAA 2037
                            vv    v  i i        - i    -     v     vi ?iv  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_100864741_   2038 CCCTTCTAGACATTGGCTTGGGCAAGGATTTCAT-GATCAAGAACCCAAA 2086
                         vi    vv   v    v  i     v i    v -   - v  vv     
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAA 605

  chr1_100864741_   2087 AGCAAATGCAGTAAAAACAAAGATAAATAGTTGGGACTTAATTAAACTAA 2136
                             v v   ii    iv   i   i   iv v      v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_100864741_   2137 AGAACTTTTGCACAGCAAAAGGAACAGTCTGCATAGTAAAAAGACAATGC 2186
                          i        ii vv    i iv  vi  viv v   i         iv 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_100864741_   2187 ACAGAGTGGGAGAAAATCTTCTCAATCTATACATTTGACAAAGCACTACT 2236
                              i           v  iv   vii   i  i   i  i v   vv 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_100864741_   2237 ATCCAGAATCTACAACTAACCCAAACAAGCCAGTAAGAAAAAAAACAAAT 2286
                                  v  i  vv   i vv    vi  i   v     i -     
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAAT 804

  chr1_100864741_   2287 AATCCCATCAAAAAGTGGTCTAAGGACATGAATAGGCAATTCTCAAAAGA 2336
                           i  v  i?    i   v v     iv       i  v     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_100864741_   2337 AGATTTACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCACTAA 2386
                             v             i  i  i       i             ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_100864741_   2387 CAGT 2390
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.29 (132 / 102)
Gap_init rate = 0.01 (7 / 901), avg. gap size = 1.57 (11 / 7)  


3394 24.81 0.99 0.88  chr1_100872804_100875295.rev     1095  2001 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_100872804_   1095 TGGAAAGATATTCCATGTTCAGGAATTGGAAGAATAAATATTGTTAAAAT 1144
                                    i         v i         v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100872804_   1145 GTTCATACTACCTAAAGCAATCTACAGATTCAATTCAATCCCTATCAAAA 1194
                          viv     v  i   vii              iv               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100872804_   1195 TACCAAAGACATTCTTCACAGAAGTAGAAAAAA-AATCCTAAGATTTATA 1243
                          v   ivvi v  i  ii     i v  v  iv-i       i   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_100872804_   1244 TGGAAGCAAAAAAGGCACACAATAGCCAAATCTGTCCTAACCACAATTAA 1293
                              iiiv  ii i v  v          v vi  i i vv vi vv  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_100872804_   1294 CAAAACTGGAGGCATCACATTACCTGACTTCAAATTATACTACAAAGCTA 1343
                             ii      vv     i v  ii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_100872804_   1344 TAGCAACCAAAATAGCATGGTAGTGGCATAAAAACAGACAAATACACCAA 1393
                         i  i  i   i i  ii     v        ii i     v   v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_100872804_   1394 TGGAACAGAATAGACAACCCAGAAAAAAATCTACACATCCACAGTGAACT 1443
                              i     v  v ii       v   i i i    ii ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_100872804_   1444 CATTTTTGACAAAGGTGCCGAAAACATATTTTGGGGAAAGGACAGTGTCT 1493
                         v     i     i      i i v   vivv         i i   v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_100872804_   1494 TCAATAAATGGTGCTGGGAAAACTGTATGTATATTCGTAAGCAGAAGAAT 1543
                             i              v     --- -   ?i ii v   i      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTG---G-ATAKCCACATGCAAAAGAAT 446

  chr1_100872804_   1544 GAAATTACACCCTTATCTTTCACCATATATAAAAATCAAATAAAAACAGA 1593
                            i  iv    i  i  iv         i      i  v v    ii  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_100872804_   1594 ----AGTCTTAAATCTAAGACCTCAAACTATGAAACTGCTAAAAGAAAAC 1639
                         ----  v i     v     v  v       i     vi  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_100872804_   1640 ACTAGGGA-AACTCTTTAGGACATTGGAT-GTGCAAAGATTTCTTGAGTA 1687
                          -    ?i-  v    iiv   v    i -iv    v i      iii  
  L1M4_orf2#LINE/    547 A-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_100872804_   1688 ATACCCCACAAGCACAGACAATGAAAGGAAAAATGGACAAATGGAATCAC 1737
                         vv  v   v       ii   ii    i      i  i    v i iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_100872804_   1738 ATCAAG-TTAAAAATCTTCTGTATAGGAAAGGAATCAATTAACAAAGTGA 1786
                              i-       -   i   iivvv      vv v  i  v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_100872804_   1787 AGAAACAACCCACAGAATAGGAGAAAACATTTGCAAACTACCCATCTGAC 1836
                          i i              i        i         ii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_100872804_   1837 AAGGGACTAATAACCACAATATATAAGGAGCTCAAACAACTCTATAGGGA 1886
                                 vi  v   v         i  i   vv       v   ivi 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_100872804_   1887 AAGAAATCTAATAATCTGATTTAAAAATAGATAAAA-ATCTGAATAGATG 1935
                           ii -- v     i ii   ?      i ii   i-  i        ii
  L1M4_orf2#LINE/    795 AAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_100872804_   1936 TTTCTCAAAAGAAGACATACAAATGGCAAACAAGCATATGAAAAGGTGCT 1985
                               v        i           v  i     i        i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_100872804_   1986 CAATGTCATTGATAAT 2001
                            ii   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (139 / 83)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


 380 27.27 0.00 0.00  chr1_100947695_100949907.rev      502   600 (1613)    L1M4_orf2#LINE/L1       20   118 (790)  

  chr1_100947695_    502 CATGGATTGGAAAACTAAATATTGTTAAGACATCAGTCTTCCCTAAATTG 551
                                     i   v             iiv  i vi    i      
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chr1_100947695_    552 ATGTATAGACCTGAGGCAATATCATTTAAATTCCAAGCAAGCTATTTTG 600
                           v  i   iiii v     vi vv i   v   v   viv  v     
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG 118

Transitions / transversions = 1.08 (14 / 13)
Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.00 (0 / 0)  

1577 28.68 4.91 2.71  chr1_100947695_100949907.rev      949  1722 (491)    L1M4_orf2#LINE/L1      118   908 (0)  

  chr1_100947695_    949 GTAGAAACTGATA-GCTAAACCTAAACTTTATATGAAAATGCAAAGGACC 997
                          i     i   i -   i v      v  i     i        i     
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr1_100947695_    998 TGGAATA-------TAACCTTAAAAAATAAGAATAAAATTGTAGTAGTTA 1040
                         ii     -------i  i   i     v     i   i   v  v v i 
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr1_100947695_   1041 CACTGACTCCATAACTTATTAACTCATTAAAAAGCTATA-TAATCATAAT 1089
                             ---   -i  i  vvv    i i  v       i -      vi i
  L1M4_orf2#LINE/    218 CACT---TCC-CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_100947695_   1090 AGTAAGATGTTAATA-AAATATAGATCAGTAGGTCAATAAAACTGGATAG 1138
                            iv i ii iii -  iv     ivvi   i     ii  iv i  v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_100947695_   1139 ACAGACCAAAAATAAACATATACACTTTTAAAAGTCAATT-ACTTTTGAC 1187
                          v  v   i        vi     i  v i---       - i   i   
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATG---GTCAATTGATTTTCGAC 360

  chr1_100947695_   1188 AAGG-TACCGAGACAATTCAATAGAGAAGGGGAAGTCTTT-AAACAAATG 1235
                             - i  i    v       i i   i iiv       -v        
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_100947695_   1236 TTGCTGTAACAACAGGATTTTTGTAAGGAAAAAATATGAATCTTAACTGC 1285
                         v     vi     v    v?iiii v v    i -     vi vi  iv 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGA-ATGAAGTTGGACCCC 459

  chr1_100947695_   1286 TATGTTATGTAATACATAAATATTAATGTGAAATGAATGACAGGACTAAA 1335
                           iv i iiiv   i i   v     ivii     i  v ?  iv     
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_100947695_   1336 C-TAAAA----AAACTGTAAAGCTTCTAGGAAAAATAACAGGAAAACATA 1380
                         i-   i ----     i    i  ii   i i   vv i   ?iv v  v
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_100947695_   1381 TTTAAGACTTTCTGATATGCAGAGATTTCTTAGA----ATTCTAAAAGCA 1426
                           iiv   i  vv v  v   iv i         ---- iv i       
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_100947695_   1427 TTAAGCAT--AAAGAAAAATT-GATACAGTGTAATTTATAAATATTAAGA 1473
                         i-     v--         v -    v v  v v  i  v  v     i 
  L1M4_orf2#LINE/    610 C-AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_100947695_   1474 ACTTCT----CTCAATGAAACACTGATAATAAAACAATGATGTGAGCTAA 1519
                             i ----i    v i -    ivi  v   iii vi viii v i v
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGA-CACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_100947695_   1520 AGACTGTGG--AAACATTTGCTACATGTATATCTGATGAAGGACTTGTTT 1567
                            v  v i--   i      v vvii          i i        v 
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_100947695_   1568 CTAAGTTATATAGACAATTATGGTATTAAGTAACAATAATTTTAAAAATC 1617
                          i iiv      i v  i v --  iv vvi  i     ----   i iv
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCT--TACAACTCAATAATAA----AAAGACA 801

  chr1_100947695_   1618 AACAACCCAGTTTTTAAAATTTGGGCAGAAAATTTTGA--GACAATT--- 1662
                           i      i  ?--    v -     i ii    vi --    v  ---
  L1M4_orf2#LINE/    802 AATAACCCAATTW--AAAAAT-GGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_100947695_   1663 -AAAAACAGAATATATGAATGGTCAATAAACACAGAAAAAGCT-CCCAAC 1710
                         -   i -   -    ii     i      i    vi     v - i    
  L1M4_orf2#LINE/    849 CAAAGA-AGA-TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_100947695_   1711 AGCACTCGTCTT 1722
                          v  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (133 / 85)
Gap_init rate = 0.04 (29 / 791), avg. gap size = 2.03 (59 / 29)  


 200 11.90 2.38 0.00  chr1_100979505_100981513      462   503 (1506)  C L1M4_orf2#LINE/L1   (0)   908   866  

C chr1_100979505_    503 TGGCAAA-AGACACATGAAAAAATGCTCATCATCACTGGCCAT 462
                             v  - ii          i       v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (3 / 2)
Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1)  

3012 27.36 0.80 0.57  chr1_100979505_100981513      642  1511 (498)    L1M4_orf2#LINE/L1        1   872 (36)  

  chr1_100979505_    642 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 691
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_100979505_    692 GGCCATGCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 741
                            v  i  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_100979505_    742 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 789
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_100979505_    790 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 839
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_100979505_    840 AACAAAGCTGGAGGCATCATGCTAACTGACTTCAAACTACACTACAACGC 889
                                i      vv   ii  vv ii i      vivi       v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_100979505_    890 TACAGTAACCACGACAGGATGGTACTAGTACCAAAACAGAGATACAGACC 939
                                 i  v     vi       i i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_100979505_    940 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCATATATCTACAACT 987
                                i    i--    i  --        vv     i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_100979505_    988 CTCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 1037
                         vvi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_100979505_   1038 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1087
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_100979505_   1088 GAAACTGGATCCCTTCCTTACACCTCATACAAAAATTAATTCAAGTTGGA 1137
                            ii    i    v   i     vi             i    iv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_100979505_   1138 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1187
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_100979505_   1188 CTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1236
                         v    ?i- v   -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_100979505_   1237 AAACACCAAAAGCAGTGGCAAAAAAAGCCAAAATTGACAAATGGGA-TTA 1285
                         vi            vvi    v     vv     v  i    v   -  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_100979505_   1286 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1335
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_100979505_   1336 CAGGCAACCTACAGGATGGGAGAAAACTTTTGCAATCTACTCATCTGACA 1385
                         v  i     i    i           iv       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_100979505_   1386 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1435
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_100979505_   1436 AA-ACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTT 1484
                           -     i     v  i? v  i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_100979505_   1485 CTCAAAAGAAGACATTTATGTAGCCAA 1511
                            v        i  vi vi i     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAA 872

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.01 (9 / 872), avg. gap size = 1.33 (12 / 9)  


3133 25.40 2.93 0.56  chr1_100990698_100995488     3413  4298 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_100990698_   3413 GGAAACACATCTCATGTTCATGAATGGGTAGAATCAGTATTGTGAAAATG 3462
                              v i   i          i  v  v   v i i      v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_100990698_   3463 ACCATATTGCCAAAAGCACTATACAAATTCAATGCAATTCCCATCAAAAT 3512
                         i v   i v  v   viiv v    i      i     i  i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_100990698_   3513 ACCACCATCATCCTTCACAGAATTAGAATAAAAACAATTTTAAAATTCAT 3562
                         v   v vv v ii  ii     v v  v--  ivii  ii          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCAT 149

  chr1_100990698_   3563 ATGGAACCAAAACAAAGCCTGCATAGCCAAAGCAAGACTAAGAAAAAAGA 3612
                               viiv  vii v  v v         i   vvi i i   i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_100990698_   3613 ACAAATCTGGAGGCAGCACATTACCTGATTTCAAACTATGCTATTAGGTC 3662
                              vi      vvv    i v  ii        viv i   iv i ii
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_100990698_   3663 ATAGTCACCAAAACTGCATGGTATTGGTATAAAAATAGACACATAGACCA 3712
                          i   v i   i  v ii     i   i    ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_100990698_   3713 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAAC 3762
                               i     v    ii               v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_100990698_   3763 TGATCTTTGACAAAG----CAAA--CATAAAGTGAGGAAAAGACACCCTT 3806
                             i  i     i ----   i--   vv i  i     ii i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_100990698_   3807 TTCAACAAATGGTGCTGGGATAATTGGCTAGCCACACATAGAAGAATGAA 3856
                                             i  i   v  ?     iii i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_100990698_   3857 ACTGAATCCTCATCTCTCACCTTATACAAAAAT---------------CA 3891
                         ii  i i  ii i   v    v           ---------------  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_100990698_   3892 AGGACTTAAATCTAAGATCTGAAACTCTACAAATTCT-AGAAGATAACAT 3940
                         ?i   i     v     v  i     v  -   i   -      v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACAT 548

  chr1_100990698_   3941 TGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCAT-GACCAAT 3989
                         v  ?iv  vi    vv   v    v        v i    v -  i--  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--AT 596

  chr1_100990698_   3990 AAC-CCAAAAGCAAATGCAATAGAAACAAAGATAGATAGTTGGGACTTAA 4038
                         i  -         v v    i i  iv   i       iv v      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_100990698_   4039 TTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAAC 4088
                          i   v v  i i      iiivv    i iv  vi   iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_100990698_   4089 AGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAA 4138
                                       i           v  ii   vii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_100990698_   4139 AGGACTAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAAGAAAA 4188
                         i     vi          v  i  i      vv    v   ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_100990698_   4189 AAACAAACAATCCCACCAAAAA--GGGATAAGGACATAAATAGACAATTC 4236
                          i     i  i  v ii?    --   vv     iv i        v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_100990698_   4237 TCAAAAGAAGATATACAAATGGCCAAAAAACACATGAAAAAATGCTCAAC 4286
                           v                       v  i          i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_100990698_   4287 ATCACTAATGAT 4298
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 3.10 (31 / 10)  


3012 26.13 1.21 1.10  chr1_101017454_101024168.rev     5318  6224 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_101017454_   5318 TGGAACAACATTCCATGCTCATGGATAGTAAGAATCAATATCATGAAAAT 5367
                              vi i  i     i        v v    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_101017454_   5368 GGCCATACTACCCAAAGTAATTTACAGATTCAATGCTATTCCCATCAAGC 5417
                            v     v      v i  i           i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_101017454_   5418 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 5465
                          v   -   v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_101017454_   5466 TATGGAACCAAAAAAGAGCTCATATAGCCAAGACAATCCTAAGTAAAAAG 5515
                                viiv  ii  v iviv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_101017454_   5516 AACAAAGCTGGAAGCATTACATTACCTGACTTCAAACTATACCTCAAGGC 5565
                                i    i vv i   i v  ii i      viv   iv   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_101017454_   5566 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATGTAGACC 5615
                                 i   i    ii         i iv ii i   i  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_101017454_   5616 AATGGAACAAAAC--AGAGTCCTCAGAAATAACACCACATATCCACAACC 5663
                                i i  i--       --        vv   i i  ii iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_101017454_   5664 ATCTGATCATTGACAAACCTGATGAAAACAAGCAATGGGGAAAGGAAAGG 5713
                          vi    iv i     ivv  vii i v  vv            i v  -
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG- 395

  chr1_101017454_   5714 ATTCCTTATTAATAAATGGTGTGGAGAAAACTGGCTAGCCATATGCAGAA 5763
                         --  i  - i  i        iv i  v      v  ?   i     i  
  L1M4_orf2#LINE/    396 --TCTTT-TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_101017454_   5764 AACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGA 5813
                         i v    ii         v   i     v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_101017454_   5814 TGGATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGA 5863
                              i ?    i    ii     v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_101017454_   5864 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTT-TAA 5911
                             v    ?i- v i -   iv   v v  vv i     v ii  - v 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_101017454_   5912 GACTAAAACACCAAAAGCAATTGTAACAAAACCCAAAATTGACAAATGGG 5961
                           -  vi            vvv i       vvv     v  i    v  
  L1M4_orf2#LINE/    592 GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_101017454_   5962 ATCTAATTAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTATCATCAGA 6011
                          ii v  i   v v  i i   i  ii vv    i  v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_101017454_   6012 GTAAACAGGCAACCTACAGAATCGGAAAAAAT-TTTGCAA-TC-TAT-CC 6057
                           i  v  i     i       v   i     -       -  -   -i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_101017454_   6058 TGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACA 6107
                            i  i  i  vi          v  i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_101017454_   6108 AGAAAAAACCAAACAACCCCATCAAAAAGTGGGCAAAAGTTGTGAACAGA 6157
                          v     iv    i     v  i?    i        i v v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_101017454_   6158 CACTTCTCAAAAGAAGACATTTATGTGGTGAACAAACATATAAAAA-ACA 6206
                           i     v        i  vi vi   iv  i  i  i  i    - ii
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_101017454_   6207 CTCATCATCATGGGTCAT 6224
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.24 (21 / 17)  


3236 16.46 13.42 0.28  chr1_101114648_101116362.rev      502  1224 (491)    L1M4_orf2#LINE/L1       91   908 (0)  

  chr1_101114648_    502 CCTATCAAAATCCCAGTGACATTTTTTTCTAGAAATAGAAAAATCTATCT 551
                                         ivi v      v -      v  v  iiiv   i
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGC-AGAAATTGACAAGCTGATCC 139

  chr1_101114648_    552 TAAAATTCCTATGGGATCTCAAGAAACCCATAATAGTCAAAACAATCTTG 601
                                 v     i viv    ii     v     i             
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_101114648_    602 AAAAAGAA---CAAGGTTGCAGGTCTCACACTTCCTAATTTCAAG--TTA 646
                                 ---   i    v   v           i        i--   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_101114648_    647 CTACAAAGC------AATAAAAACAGTGTGGCACTGACATAAAAACAGAC 690
                                  ------   v  i         i    i     ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_101114648_    691 ATATAGACCACTGGGATAGAACAGACAGCCCAGAAATAAACTCTGACATA 740
                                i  v   i      iv  v  i            i vv    v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_101114648_    741 CATGGTTAAATGGTTTTCAACATAGATGCCAAGGCAATTCAATGGGGAAA 790
                         i     i  v  i     i   vi i       i v              
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_101114648_    791 GGACAGACTTCTCAATAACTGGTGATGGGAAAACTGGATTTTTACATGCA 840
                          i i  v   i    i  v     v     v        v?ii       
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_101114648_    841 AAAGAAGGAAGCTGGACCCTTACCTCACACCATATATAAAAATTAACTCA 890
                               v    i       i                i             
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_101114648_    891 GAATA------------AAATGTAAGACCTAAAACTATAAAACTCTTAGA 928
                         i   i------------          v                      
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_101114648_    929 AGAAAACATAGGAG-AAAGCTTCATGACATTGGTTT-GGT--TGATTTCT 974
                                     ? -   v    i    v    v  -  i--  i     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_101114648_    975 CAGATATGACACCAAAAGCTTAGGAAACAAAAGAAAAAA----------- 1013
                         i                  vi i v              -----------
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_101114648_   1014 -----CATGAAAATTAA--------------------------------- 1025
                         -----   v        ---------------------------------
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_101114648_   1026 --------GGCAAATCATGGAAAAAGAGAAAATATCTGCATATTATACAT 1067
                         -------- i   vi  ii   vii          i    v  i   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_101114648_   1068 CTGATAAAGAGTTAATATCCAGAATATATAAAGAACACCCACAATTCAAC 1117
                                i iii vi                     v ii    i    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_101114648_   1118 AACAA-----CAAA-----CAATTTAAAAATGGACAAAGTATTTGAATAG 1157
                           i  -----    -----     ?        i     v          
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_101114648_   1158 ACATTTTCCCAAAGA---TATACAAAATGGCCAATAAGTACAAGAAAAAA 1204
                               ii       ---        -           i   v     i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACATGAAAAGA 888

  chr1_101114648_   1205 TGTTCAACATCAGTAATCAT 1224
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (74 / 42)
Gap_init rate = 0.02 (14 / 818), avg. gap size = 7.07 (99 / 14)  


3118 27.96 0.66 0.33  chr1_101122117_101128192.rev     4681  5585 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_101122117_   4681 TAGAAGAACATTTCATGCTTGTGGATAGGAAGAATCAATATCATGAAAAT 4730
                          i   ii i  ii    i ii     v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_101122117_   4731 GGCCATACTGCCCAAGGTAATTTATAGATTCAATACCATTCCCATCAAGC 4780
                            v     v     iv i  i  i        ii v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_101122117_   4781 TACCAAGGACTGTCTTCACAGAA-TTGGAAAAAACT-ACTTGAAAGTCCA 4828
                          v   ivvi iv i  ii     -   -- v  i  - iiiv   i i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_101122117_   4829 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAG 4878
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_101122117_   4879 AACAAAGCTGGAGGCATCACGTTACCTGACTTCAAACTATACTATGAGGC 4928
                                i      vv    ii v  ii i      viv     ii i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_101122117_   4929 TACAGTAACCAAAATAGCATGCTACTGGTACCAAAACAGAGATATAGACC 4978
                                 i   i i  ii  v      i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_101122117_   4979 AATGGAACAGAACAGAGGCCCCAGAAATAATACCACACATCTACAACCAT 5028
                                i    iv   ivi          vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_101122117_   5029 CTGATCTTTGACAAACCTGAAAAAAACAAGAAATGGGGAAAGGATTCCCT 5078
                         i    i  i     ivv  vv  i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_101122117_   5079 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5128
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_101122117_   5129 AACTGGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5178
                          ii    i  i v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_101122117_   5179 AAAGACTTAAATGTTAGACCTAAAACCATAAAACCCCTAGAAGAAAACCT 5228
                          ?    i       v   v       i       i i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_101122117_   5229 AGGCA-ATACCATTCAGGACATAAGCATGGGCAAGGACTTCATGACTAAA 5277
                            ?i- v i -   iv   v vi vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_101122117_   5278 ACACCAAAAGCAATGGCAACAAAAGCCAAAAGAGACAAATGAGATCTAAT 5327
                                     vvi          vv    v   i    vi  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_101122117_   5328 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAACA 5377
                         i   v v  i i   i  ii vv    i  v    i ivv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_101122117_   5378 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5427
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_101122117_   5428 GGGCTAATATCCAGAATCTACAAAGAACT--TAAAACAAATTTACAAGAA 5475
                           i  vi          v  i        --  v   vv v v i  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_101122117_   5476 AA-AAACAACCCCATCAAAAAGTGGGAGAAGGATATGAACAGACATTTCT 5524
                         i -   i     v  i?    i    vi      v    i          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_101122117_   5525 CAAAAGAAGACATTTATGCAGCCAACGGACACATGAAAAAATGCTCATCA 5574
                          v        i  vi viii     iiii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_101122117_   5575 TCACTGGCCAT 5585
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.62 (154 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


1944 23.80 15.78 1.47  chr1_101162417_101164156      500  1247 (493)    L1M4_orf2#LINE/L1       54   908 (0)  

  chr1_101162417_    500 AATAAACCCCAAAAT-ATCCACACCATCTCAA-ACAATTCCAATCCAAAT 547
                             vv       v -   i   v-  -    -i    i  v   v    
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAG-AT-TCAACGCAATCCCTATCAAAAT 101

  chr1_101162417_    548 CTCA-CAACCTCTTTTGTATATGTCAACAAGCTCATTCTAACGTTTATAT 596
                          i  - vi   i     i v vi ii       v  i    vi  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_101162417_    597 GGAAAGGCAAAGGAACTAGAATAGCTAAAACAACTTTGAAAAA--AGAAT 644
                              v    i   v i        i       ii        --    i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_101162417_    645 ---GTTAAAGGAACCACACCACCTGTTTTTAAGACTTACCATAAAGCTAA 691
                         ---   ii    vi     iv  iiv   i  i      i i       v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_101162417_    692 AGTAATTAAGACAGCATAGTAT---CATAGAAGGGAGAGATGCACAGATC 738
                               i       ii i   i---    i---   v   iii i     
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAA---GGATAGACATATAGATC 298

  chr1_101162417_    739 AATAGAACAGCA---AGAGTTCAGAAAGAAACCTACATAAATAGGGCTTA 785
                            i   i  v ---     i      v     i i i vv  v  - i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG-TCA 347

  chr1_101162417_    786 AT-GATTTTT-ACAATGGTGCAGAAACAATTCAATGG---AAGAACAGTC 830
                           -      i-    v     vi i  v         ---     i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_101162417_    831 TTCTTATCAA--GATGTTG---TAACTAAACATTTACATGAAAAAAAAAA 875
                           i i v   -- i  i  ---i    ii i ?ii     v    i  vi
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_101162417_    876 ATGAGTGTGGATCTAAAACTCACTTCATA--CAAATATT----------- 912
                          --   -    i ivv v     vi    --    v   -----------
  L1M4_orf2#LINE/    448 A--AGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_101162417_    913 --------------------GAGT-------------CTGTT-GAA---- 924
                         --------------------   i-------------  v  -   ----
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_101162417_    925 ---------------TTTGTGA---TGGG-------AT-----CTTAGAC 944
                         ---------------  i    ---    -------  -----      i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_101162417_    945 ATGGCAACAGAAGCATAATCTATGTAAGAAAACATA----AACTGGATTT 990
                            i  v  i     i  v v iiv       v   ----  i    i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_101162417_    991 AATCAAAATTTAAAACGTTTGCTTTATCAAAA---ATGGTTAAGGGAATG 1037
                         v         v     v    ivi -     i--- ivi i   ii i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAAGTG 693

  chr1_101162417_   1038 AAAGGACAAGCTACA-AATGGGAAGAAAATATTTGCAGGTCATATATCTT 1086
                            i     v i   -       -             ii          v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGA-GAAAATATTTGCAAATCATATATCTG 742

  chr1_101162417_   1087 ACAAAAGGTTT-TATCCAGAATATGTAATAAACACTCAAAATTTCACCAT 1135
                          i  ii ii  -            i   vi   v  i v  i iv iv  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_101162417_   1136 ATGGAAACAA----TCCAATTTAAAAGTAGGCAAAAGACATGAACTGATG 1181
                          vii i    ----i      ?    i i      i  iv    iv  ii
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_101162417_   1182 CTTCATCAAATAGGATATAAGAATGGTGAATAAGCACATGAAAAGATGAT 1231
                         i   vi    v i      vi     iv                    v 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_101162417_   1232 CCACATCATTAGGTAT 1247
                          v      ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (115 / 61)
Gap_init rate = 0.04 (33 / 855), avg. gap size = 3.91 (129 / 33)  


2387 27.64 0.71 0.43  chr1_101390871_101392564      500  1201 (493)    L1M4_orf2#LINE/L1      205   908 (0)  

  chr1_101390871_    500 GTTAGAGGATTGACACTACCAAACTTCAAGACTTACTATAAAGTAACAGT 549
                            i     i v     v  v  i     i        i    iv     
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_101390871_    550 AATTGGGATAGT--AATATTGGTGAAAGAATAGAAAAATAAATCAATGGA 597
                            iii  i   --ii  i   iiv   i     v v   i         
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_101390871_    598 ACTGGACAGAGAGCCCAGAAATAGACCCACATAAACATAGTCAACTGATC 647
                          iv i iv     i         i     i i vvi  i     i    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_101390871_    648 TTTGACAAAGGAGCAAAGGAAATACAATGGGGCAAAGATATTCCTTTCAC 697
                           i     i  v  v   ivv  v        v  ii   v  i     v
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_101390871_    698 CAAATGGTGCTGTAACATCTGCACATCCACATGCAAAAGTATGAATCTAG 747
                                     vi   v   v i ?             v     vi i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_101390871_    748 ACACAAAACTTATATCATTCAGAAAAGTTAATTCAAAGTGAATTATAGGC 797
                           v vv v  i i i   vi v    i    i     i  i  i ?  i 
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_101390871_    798 TGAAATATAAAACATAGAACTCTAAAATTCCTAGAAGATAACAGAGGACA 847
                         iv    i   i vv  i    v     i  i       v    v   ?vv
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_101390871_    848 AAATCTAGGTGACCTTGG-TTATGACAATGACTTTTCAGATGCAACATCA 896
                               vv          -   - i     ii  i i    iii   i  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATATGACACCA 603

  chr1_101390871_    897 AAGGTACAATTTATGAAAGAAATACTTGATAAACTGGACTTT-TAAAAAT 945
                           i i    viv ii       v v v      i       i- v     
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_101390871_    946 TAAAAGCCTCTACTATGGAAAAGACAATGTCAATAGAATGAGAAGACAGG 995
                              i i i iivv vv   i    v i    v i i   i      iv
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_101390871_    996 ACATAGACTGGGAGAAAGTATTTTTGGAAGACACGTCCGATAAAGAACTA 1045
                         v  i   v         i     viii vv i ii  i     i i   v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_101390871_   1046 TTCTCTGAAATACACATAGACCTCTTAAAACTCAACATTAAGAAAACAAA 1095
                         v v  iii    i i v   v      v       i v   i  i     
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_101390871_   1096 CAAGGTAATTTTAAAATGGGTTAAAGGAGCTTCACAGACGCCTCACCAAA 1145
                         i  vvi    ?v        -i      vi vv i    iii  v     
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGG-CAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_101390871_   1146 GCAGATATACAGAATG-CAAGTGAGCATATGGAAAGGTATCCAACATCAT 1194
                          v         -    - v i i    i   i    i iii        ?
  L1M4_orf2#LINE/    853 GAAGATATACA-AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_101390871_   1195 CTGTCAT 1201
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.57 (116 / 74)
Gap_init rate = 0.01 (7 / 704), avg. gap size = 1.14 (8 / 7)  


2827 24.57 3.04 4.35  chr1_101549508_101551426.rev      509  1428 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_101549508_    509 TGAAAACATGTCCCATGCTCATGGATGGGTAGAATCAGTATTATGAAAAT 558
                           i   v  i       i        v  v   v i i    i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_101549508_    559 GACCATACTGCCAAAAGCAATCTACACATTCAATGCAATTTCCATCAAAA 608
                          i v     v  v   vii       v      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_101549508_    609 TACCATCATCATTCTCCACAGAACTAGAAAAACTAATCCTAAAATTCATG 658
                          v   v vv v  i iii     v v  v  i  i              i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_101549508_    659 TGGAA--GCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCA 706
                              --    iii v-------------------------------   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC-------------------------------CCA 169

  chr1_101549508_    707 ACCCTAATAGCCAAAAAAAGACTAAGCAAATAAAAAAACAAATCTGGAAG 756
                         i----           v  vvi i --   - i  i      vi    i 
  L1M4_orf2#LINE/    170 G----AATAGCCAAAACAATCTTGA--AAA-AGAAGAACAAAGTTGGAGG 212

  chr1_101549508_    757 CATCACATTACCTGACTTCAAACTATACTACAAGGCTATAGTTACCAAAA 806
                         vv     i v  ii i      viv        i    i   v i   i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_101549508_    807 CAGTATGGTACTGGTATAAAAATAGGCATGTAGACTAATGGAACAGGATA 856
                             i         i    ii    i   i    ii       i  i  v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_101549508_    857 GAGAATCCAGAAATAAAGCCAAATACTTAACAGCTAACTGATCTTCAACA 906
                             i            v   v i i   -ii ii  i    i   i   
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAATTGATTTTCGACA 361

  chr1_101549508_    907 AAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTATCCAACAAATGG 956
                          i vviv   i v   vv i         i i vi  v i          
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_101549508_    957 TGCTGGGATAATTGGTAAGCTACATGTAGAAGAATGAAGCTGGATCTTCA 1006
                                 i  i   vv ? i     i i          i    i iii 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_101549508_   1007 TCTCTCACCTTATACAAAAATAAACACAACATAGATCAGAAACTTAAGTC 1056
                         i   v    v           v   v   v  i     ? i  i   i v
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_101549508_   1057 TAAGATCCAAAACTGTAAAAATTCTAGAAGATAACATCCAAAAAACTCTC 1106
                              v i      i     v ii       v     vvi?iv  v   i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_101549508_   1107 CTAGATATTGGCTTAGGCAACGAGTTCATGACTAAGAACCCAAAAGCA-A 1155
                          vv  iv    v        i iv   v iiv  v  vv         - 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_101549508_   1156 TGCAACAAAAACAAAGATAAATAGATGGGACCTAATTAAA-TTAAAAAGC 1204
                         v         iv   i   i   i  v    i v  i   -       - 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-C 660

  chr1_101549508_   1205 TTCTG-----CACAG--------CAA-------AAGAAATAATCAGCAGA 1234
                           i  -----  v  --------   -------  i i i  i vi    
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_101549508_   1235 GTGGGAGAAAATATTCACAAACTATGCATCTTACAAAGCACTAATATTCA 1284
                         i              ii    ii  ii    v i  i v   vi   i  
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_101549508_   1285 GAAGCTACAAGAAACTC----AAAGCAGCAAGAAAAGAGCAAGTAATCCC 1330
                            vv  i  ii     ----  vv  ii  v    iii   i   i  v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_101549508_   1331 ACCAACAAGTGGACAAAGAACATGAATAGACAATTCTCAAAAGAAGATAT 1380
                          ii? v  i   i     i iv          v     v           
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_101549508_   1381 ACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCACTAATGAT 1428
                                     i  i  i       i             ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (138 / 84)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 5.23 (68 / 13)  


2846 25.41 1.96 2.94  chr1_101589130_101594068     3530  4446 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_101589130_   3530 TGGAAACACATCCTACACTCATGGATGGGCAGAATCGATATCATAAAAAT 3579
                               v i    i iii        v  v   v ii    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_101589130_   3580 GACCGTACTGCCAGAAGAAATCTATACATTCAATGCAATTTCCATCAAAA 3629
                          i vi    v  vi  vvi     i v      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_101589130_   3630 TACCA--T-CATTCTTCACAGAACCAGAAAAAA-AATTCTAAAATTCATA 3675
                          v   -- - v  i  ii     viv  v  iv-i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_101589130_   3676 TGGAACCAAAAAAGGG-CTCACG-TAGCCATAGCAAGGCTAATCAAAAGG 3723
                              -- viv     - i  vi-      v i   vvi i vv  i i 
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_101589130_   3724 AACAAATCTGGAGGCATTACATTGCCTGATTTCAAAGTATACTATAAGGC 3773
                               vi      vv i   i v  ii        iiv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_101589130_   3774 CATAGTCACCAAAACAGCATGGTATTGGTATAAAAATAGGCACATAGACC 3823
                         i i   v i   i    ii     i   i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_101589130_   3824 AATGGAACATAATAGAGAACCCAGAAACAAAACCAGATACTTACAGACAA 3873
                                i v   v    ii       i   v   v i i   ii v   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_101589130_   3874 TTGATCTTCGACAAAGCAAACCAAAAC--TTAAAGTGGGGAAAGAACACT 3921
                              i        i -ivi    i  --  v  -           i v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAA-TGGGGAAAGAATAGT 396

  chr1_101589130_   3922 GTCTTCAACAAATGGTGCTGGGATAGTTGGCAACCCACATGTAGAAGAAG 3971
                         v i                    i ii   vv ?       i i     v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_101589130_   3972 GAAACTGGATCCTTATCTCTTACCTTATACAAGAATCAACGCAAGATGGA 4021
                            ii    i  i  i   vi   v       i   i   v   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_101589130_   4022 TCAAGGACTTAAATCTAAGACCTGAAACCATTAAAATTCT-AGAAGATAA 4070
                            ?i   i     v     v  i    i  -    i   -      v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chr1_101589130_   4071 CATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCATGAGCA 4120
                            v  ?iv  vi    vv   v    v        v ii   v iiii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_101589130_   4121 AGAACCCAAAAGCAAATGCAGCAAGACAAAGA-TAAATAGATGGTACTTA 4169
                         v  vv         v v   i   i v   i -  i   i  v v    v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_101589130_   4170 ATTAAACT--AAAAGGTCTGCACATCACAAGAAACAACCAGCAGAGTAAA 4217
                           i   v --    vv i  ii v   v i  v  v i  iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_101589130_   4218 CAGACAACCCATAGAGTGGGAGAAAATATTCCCAATCTATACATCTGACA 4267
                         v          i   i              iv   vii   i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_101589130_   4268 AAGGACTAATATCCAGAATTTACAAGAAACTGAAACAAATTCTCAAGAA- 4316
                          i     vi          v  i  ii    vvv    ---     v  -
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA---CTCAATAAT 792

  chr1_101589130_   4317 -AAAAAACAA----TCCCATCAAAAAGTGGACTGAGAACATGAATAAACA 4361
                         -    i    ----i  v  i?    i   i vi  i iv      i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_101589130_   4362 ATTCTCAAGAGAAGATATACAAAGATATGATATACAAAGATATGGCCAAA 4411
                         v     v i              -------------------       v
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAA-------------------TGGCCAAT 873

  chr1_101589130_   4412 AAACATATGAAAAAATCCTGAACATCACTAATTAT 4446
                           i  i       i  v  v       ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (137 / 92)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.65 (45 / 17)  


2586 26.95 4.30 1.47  chr1_101666694_101670957.rev     2891  3773 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_101666694_   2891 TGGAAAAACATTCCATGCTCATGGATTGAAAGAATGAACATCTTTAAAAT 2940
                               i i  i     i          i    v v  i  iv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_101666694_   2941 GGCAGTGCTGCCAAAAGCAATCTATAGATTTAACAC------TATCAATC 2984
                             i i  v  v   vii     i     i   i ------      vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_101666694_   2985 TACCAACATCATTTCTCATAGAAATAGAAAAACCTATTCTAAAATTCATA 3034
                          v   i vv v   i iii      v  v  i iv  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_101666694_   3035 TGAAATCAAAAAAGAACCCCAG--TAGTCCAGGAAATGCTAAGCAAAAAG 3082
                           i  viiv  ii  --     --   i v iiv   vi i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_101666694_   3083 AGCAAAGCCGGAG-----ACATCTC---ATTACCAAACTATACTATAAGT 3124
                          i     ii    -----   ii  ---   v v     -     i  iv
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_101666694_   3125 CTACAGTAACCAAAACAGCATGGCACAGGTACAAAAACAGACATATAGAC 3174
                                  i   i    ii   i  v  i i  ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_101666694_   3175 CAATG-AATAAAAGAAAGAACCCGGAATTAAAGCTGCACATGTACAGACA 3223
                              -    i  vvi   ii  i   v    v iii    v  ii v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_101666694_   3224 TTTGATCTTTGACAAAA---TCAAAGAAATAAGCAATAGGGAAAAGACTC 3270
                         v     i  i     ii---i   i-- vi vv    i      ii ivv
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAG--ACCATTCAATGGGGAAAGAATAG 395

  chr1_101666694_   3271 CCTGTTCAATAAATGCTG-TGGTATAGCTGGCTAGTGATACACAGAAGAG 3319
                         i  v     i     v  -   v i i    v  ?iv i ii  i    i
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_101666694_   3320 TGAAACTTGACCCCTATCTTTCACTATATACAATAATTAATTCAAGATGG 3369
                             ii v        i  iv   i        v      i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_101666694_   3370 ATTAAAGAC-TCAATGTAAGGCCTTAAATTATAAGATTCCTAGAAGAAAA 3418
                           i ?    - v        iv  v   i     i i  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_101666694_   3419 CCTAGAAA-ACACCATTTTG-GACATCAGCCTTGGAAAAA-------AAG 3459
                          v   i?i- v i --  i -   v ii vi v  v  vi------- ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_101666694_   3460 TATGCCCACATCCTCAAAATCAATTGCAACAAAAACAAAAATTGACAAGT 3509
                             ---   i ---    v  vvv         iv      v  i  i 
  L1M4_orf2#LINE/    594 TATG---ACACC---AAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_101666694_   3510 AGGACCTAAGTGAACTAAAGAGCTTCTGAACAGCAGAAGAAACTATCAAC 3559
                         v    i v vii  v v  i i   i  vi vv  i i  v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_101666694_   3560 AGAGTAAACAGACAACTTACAAAATGGGAGAAAATATTTGAAAACTATGC 3609
                          i   i  v       ii   i                  v   ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_101666694_   3610 ATCTGATAAAAGTCTAATATCTAGAATGTATAAGGAACTTAAACAGTTGA 3659
                                  ii v  vi    i     i     i     ivv   ii v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_101666694_   3660 ACAAGCAAAAAACAA----CCCCATT-AAAAATGAGCAAAAGACATGAAC 3704
                          i  vv    i    ----   v   -       i     i  iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_101666694_   3705 AGACACTTCTCAAAAGAAGATGCACAAGCAGCCAAAAA--ACATGAAAAA 3752
                              i     v         ii    iii     v  --         i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_101666694_   3753 ATGCTCAACATCACTAATCAT 3773
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (151 / 84)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.55 (51 / 20)  


 209 26.79 5.36 4.46  chr1_101789159_101791450      384   495 (1797)  C L1M4_orf2#LINE/L1   (667)   241   129  

C chr1_101789159_    495 CAAATTGACTTTAATATTTATGTGGAAGAT-CAAAGAATA-AGAATAGCC 448
                            ii   iii   v   i  i     -  -   i i iv-         
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCC 177

C chr1_101789159_    447 AAGATACTCCTAAAGTACAAGAACAC-TTTGTGAAGATATGTAACAT--- 402
                           i i v  i i  iv v       v-v   -  i  i--- v   i---
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTG-GAGGAC---TCACACTTC 223

C chr1_101789159_    401 CAAATTTCAAAATTGATT 384
                          v          i v i 
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACT 241

Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.06 (7 / 113), avg. gap size = 1.57 (11 / 7)  

2195 27.10 8.26 1.46  chr1_101789159_101791450      977  1799 (493)    L1M4_orf2#LINE/L1       30   908 (0)  

  chr1_101789159_    977 AAGACTGGATGTCATAAAGCTGTCAATTCTTCCAAAACTGAATTGCAGTT 1026
                               vi  i ii v   v  v    v  i  v   i   vi i   v 
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGAT 79

  chr1_101789159_   1027 TTAATGGCATTCCTACCACAATCCCAGCAAGGCATTTTTATAGAGATAGA 1076
                          i  i vv  i    i  v         v- v v     ii   i  v  
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCT-GCCTTTTTTGCAGAAATTGA 128

  chr1_101789159_   1077 CAGGCTTATTTTAGAATTTATATGAAATAATGCA--GGTCTTGGAATACC 1124
                           i   v  ii  i    i     i  --     --  v iii     v 
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGC 176

  chr1_101789159_   1125 TAGAGTAATCTTGAAATGAAAGAATAAAATAGGAGAAATCATTCTACCTG 1174
                         i i ii          vii     i   i v    i v   iv  v  ii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr1_101789159_   1175 ATTTTA---TTTTTTTTAAA-------------------TGTGGAGACT- 1201
                             i ---i  vi vi   -------------------     -v   -
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG-TACTG 275

  chr1_101789159_   1202 ---------TAGTCACGTGGATCAGTGGAATGCTGTAGAGAACCCAGAAA 1242
                         ---------   v  ii i     i      ivvi v    ii       
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_101789159_   1243 TAAACTCATACAAATATAACCAACTAATTTTAGACAAAGAAGCAAAAGCA 1292
                              i      vv   iii   i i     v     i iv  v  ii v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_101789159_   1293 ATTCAATGGAAGAAGGATAGCCTTTACAACAAGTCATTCTGGAACAACTG 1342
                                  iii   i    i    v      i vi v    i       
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_101789159_   1343 GACATCCATAGGAAAAAAAATGAACATTGACCTAAACCTTTATAAAAAGT 1392
                           i ?   i v v    i      vv v    ivv    i----- v vi
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC-----ACACC 470

  chr1_101789159_   1393 GTATACAAAAACCAACTCAAAATAGATCATAGACTTAAATGTAAAAAATA 1442
                         i          ii          i     ?    i         i iv  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_101789159_   1443 AAACTATAAAGCTTTTAGAA-AAAATACAAAAA-AAGTCTTTG------- 1483
                                   i  i      -    i i ii?i-  i    i -------
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_101789159_   1484 --GCTAGGCA--GAGTTCTTAGAATTGATAACAAAGAAATGATCCAAAAA 1529
                         -- i      -- iv        vv   i v    iiv ii v v v   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_101789159_   1530 AGGGAAAATTGATAAACTGTATCTCATCAAATTTAACAAGTTT---GCCT 1576
                           ii     v      i  v ii        v    v  v   ---  i 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_101789159_   1577 GCAAAAGACACTCCTAAGTAGATAAAATGATAAACTATATATAGAGAAAA 1626
                         -    i      vii   v ii i   v  i  v i i v vv i  i  
  L1M4_orf2#LINE/    671 -CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_101789159_   1627 ATTGGTAGTATATCATGTATCTAAAACAGTACTAGTATCT------TGTA 1670
                          v iv v i v     i     i v vi v   v     i------ i  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_101789159_   1671 AA-----------ACTCAACAGTAAAAATCCCAAATAATCCAAGCAGAAA 1709
                           -----------      i i      vv -      i    vi?-   
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTW-AAA 817

  chr1_101789159_   1710 AATGGGCAAAAGACATGAACAGACATTTCAACAAAGAGGATATACACATG 1759
                                   i  iv    i         vv      i        v   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_101789159_   1760 AAAAATAAGCATATGGAAC-ATTTTCAACATCATTAGTCAT 1799
                         ivv        i   i  v-  vi         ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (131 / 88)
Gap_init rate = 0.02 (19 / 879), avg. gap size = 4.21 (80 / 19)  


3225 23.37 4.35 0.34  chr1_101837053_101839098.rev      684  1556 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_101837053_    684 TGGAAAGATTTCTCATGTTTATGGATTGGAATAATTAACATTGT-AAAAT 732
                                  v  i      i           v v    i     -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_101837053_    733 GGCAATTCTACTCAAAGTAAGCTACAGAGTCT-TGCAATCCCTATAAAAA 781
                               v  v i    v i v       v  v-i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_101837053_    782 TAC-AATGACATTTTTAATAAAAATAGAAAAA--AATCCTAAAATTCATA 828
                          v - iivi v     vii i    v  v  i--i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_101837053_    829 CGGAACTACAAGAGAATTCAAATAGCCAAAGCAATCTTGAACAAAAGGAA 878
                         i    v i    i  viivi          i          v  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_101837053_    879 CCAAGCTGGAGGCATCGAACTATCTGATTTCAAAATGTACTACGAAGCTA 928
                          v   i      vv  iv   vi ii         iv      i      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_101837053_    929 TACCAACCAAAACAGAATAGTTCAGGCATAAAAAGAGACATATACATCAA 978
                         i vi  i   i    vi i  v v       ii v         v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_101837053_    979 TGGAACAGAATAGGAGAGCTCAGAATTAAATCCA--CATTCATGGCCAAT 1026
                              i     -v     ii     v    i   --    i    i    
  L1M4_orf2#LINE/    301 TGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_101837053_   1027 TTACCTTCAATAAATATGCCAAGAACACAAAATAAGGAAAG-----TCTC 1071
                          v ii   i i  ivi        v  ivv   ii      -----   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_101837053_   1072 CTCAATATACTGTGCTGGGAAAACTGGATATCCACAGTCAAAAGAATGAA 1121
                         i    i v iv         v         ?     vv            
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_101837053_   1122 ATTGGA-----ATCTTATACCATATGCAAATATAAACTCAAAATGAATTT 1166
                         i     ----- i  i i       i    v  v           i  iv
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_101837053_   1167 AAGACTTAA---------------CTGTAAAATTGCTAGAATAAAATATA 1201
                         ?    i   ---------------  i     i vi     v    i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_101837053_   1202 GGGGAAAA-CTTATTTACATTAGGATAGGCAATAACTTTTTTGATATGAC 1250
                           ? v   -   vv v  v  i  v        iii  i  v        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_101837053_   1251 ACCAAG-GCACAGGCAGCAAAAGCAAAATAGTAGACAAATGGGAATGCAT 1299
                              i-     i   i      -    - i    i    v   v v   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAG-AAAA-AATAGATAAATTGGACTTCAT 647

  chr1_101837053_   1300 CAAACTAAGAAGCTTCTGTACAACAAAGAAAATGATTGAAGGAGTAAAGA 1349
                             v v i  i   i   i vv     i v iv  ii iii   i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_101837053_   1350 CACAACCTAAGAAATGGGAGAAAAT-TTTGCAAGCCATATATCTGATAAT 1398
                         v      i vii             -       ii              v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_101837053_   1399 GTGTTAATAGCCAAAA-ATATAGA-AACTCAAATAACTCAATAGCAAGAT 1446
                          vii vi  v   i  -     i -     vv i         ii  i v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_101837053_   1447 AACAAATAACTCTATTAAAAAGTGTGCAAATGACCTGAACACACTTTTCT 1496
                         i         i v   ?    i  v     v  ii    i v  v     
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_101837053_   1497 CAGAGGAAGACATACAAATAGCCAATAAGTATATGAAAAGATACTCAACA 1546
                          vi i     i        i         i i          i       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_101837053_   1547 T-ACCTAATCA 1556
                          - ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.50 (120 / 80)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.41 (41 / 17)  


2465 26.90 0.99 0.14  chr1_101869227_101870923      495  1204 (493)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr1_101869227_    495 AAAAGGAACAAAGCTGGAGGTATCATGCTACCTGATTTCAAACTATACTG 544
                           i i        i      vv   ii  v  ii        viv    i
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_101869227_    545 AAAGGCTACAGTAACCCATACAGCATAGTACTGGTATCAAAACAGACAAA 594
                         v  i          i v v    ii i       i  v ii i     v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_101869227_    595 TAGACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTAC 644
                             i        i    iv   ivii         vv   i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_101869227_    645 AACCATCTGATTTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGA 694
                         iii  vi       i     ivv  v   i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_101869227_    695 TTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAA 744
                          vvi  v  i  i        i     v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_101869227_    745 AACTGAAACTGGATCCCTTCCTTATACCTTATAAAAAAGTTAACTCAAGA 794
                         i v    ii    i    v   i i   v    v    i         i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_101869227_    795 TGAATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGA 844
                           i  i ?    i           v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_101869227_    845 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAACGACTTCATG 893
                             v    ?i- v i -   iv   v v  vv i     i ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_101869227_    894 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAGTGGGA 943
                         vv  vi            vvi          vv   i v  i  i v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_101869227_    944 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAG 993
                         ii v  i   v v  i i   i  ii vv    iv v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_101869227_    994 TGAACAGGCAACCT---GAATGGAAGAAAATTTTTGCAATCTATCCAACA 1040
                             v  i     i---      i       v       vii  vi v v
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_101869227_   1041 GACAAAGGGCTAATATCCAGCATCTACAAAGAACTTAAACAAATTTACAA 1090
                           i  i  i  vi       v  v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_101869227_   1091 GAAGAA-ACAAA--GCCCTATCAAAAAGTGGGCAAAGGATATGAACAGAC 1137
                         v  i  -     --i   v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_101869227_   1138 ACTTTTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGC 1187
                          i  i  v        i  vi viii     i  i  i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_101869227_   1188 TCATCATCACTGGTCAT 1204
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (108 / 79)
Gap_init rate = 0.01 (5 / 716), avg. gap size = 1.60 (8 / 5)  


1615 24.62 2.60 8.07  chr1_101923558_101925221      455  1185 (479)    L1M4_orf2#LINE/L1      218   908 (0)  

  chr1_101923558_    455 CATTTTCAGATTT-AAGACTT----CAT-GCTGAAGAAAATAAGCTACAA 498
                           i  i vi    -  i    ----  v-   iv  v  vi   --   i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG--ACAG 265

  chr1_101923558_    499 T----TACTGGTACGGAAACAGACACACAGACCAATGGAACAGAATAGAG 544
                          ----      i iiiii i     i i   i        i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_101923558_    545 GATCCAGAAATAAAGCAGCACACCTTCA--ATCATCTTATCTTTGTCAAA 592
                         ii            v --  i  v  i --i   vi v  i  i v   i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACC--CATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_101923558_    593 ACCATTAGAAAAAAACAAAAAACAAACAAACAAAAAAACAAGTGATGGGG 642
                         i--i ---------i v  i v  vv   ----------------     
  L1M4_orf2#LINE/    364 G--GT---------GCCAAGACCATTCAA----------------TGGGG 386

  chr1_101923558_    643 AAAGGACTCCCTACTCAATAAACGATGCTGAGACAACTGGCTAGTCATAT 692
                             i ivvi  vi    i   i i     i         --------  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG--------AT 428

  chr1_101923558_    693 AGTCATATGCGGAAGAATGAATTTGGACCC-TACTTTTCACCACATACAA 741
                          ?i  i    ii         v        -   i iv     i      
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_101923558_    742 AAATTAACTCAAGATGGATTAAAGATTTAAATGAAAGACTTCAAACATTA 791
                                     i      i ?   ii      v    vi v    vv  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_101923558_    792 AAAATCCTAGAAGAGAACCTAGA---AAATGACCTCA--ACATCAGCTTT 836
                            v  i       i   v   i---    -- i  i--  v ii v  v
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTA 576

  chr1_101923558_    837 GGCAAACAATTTATGGCTAAGTCCTCAAAAGCAATTACAATAGAAACAAA 886
                              vviv  iv i v  v v vi        vvvi   i i  iv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_101923558_    887 AATTGAGAAGTGTAACCTAATTAAA-TGAAAGAACTTCAGCACAGCAAAA 935
                            v  v  i vvi  i v  i   - v   -     iv ii vv    i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAG 675

  chr1_101923558_    936 GAAAGTATCAACAGAGTGAACAGACAATCTACAGAATGGGAGAAAATATT 985
                           v v      v i      v      i i                    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_101923558_    986 CACAAACTATGCATCCAAAAAGTGTCTAATATCCACAATGTATAAGGAAC 1035
                         ii    ii  ii   ii v   v v  vi      v   i     i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_101923558_   1036 GTAAACAACTCAAAAAGCCAAAAAAGAAAATACAAAAAAAAAAAAACCCT 1085
                         vivv         v  --------------  -    i v   v     v
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAA--------------TA-AAAAGACAAATAACCCA 810

  chr1_101923558_   1086 ATTAAAAAGTGAGCAGAGGACATGAAGAGATACTTCTCAAAAGAAGACAT 1135
                            ?    i  i   i    iv    v   i i     v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_101923558_   1136 GCAAGTGACCAATAAACATATGAAAAAAAATGATCCACCTTACTAATCAC 1185
                         i   i  i       i  i       i --  v  v  v i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (104 / 73)
Gap_init rate = 0.03 (20 / 691), avg. gap size = 3.90 (78 / 20)  


2046 27.28 8.20 1.87  chr1_102301087_102302938      506  1359 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_102301087_    506 TGGAGAAATGTTCTCTATTCATGTGTGTGCAGACTCAATAATGTTAAGGT 555
                             i i  i i iv i      vi vv v     i    v       i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_102301087_    556 ACCAATA-TCTTCAACTTGATATCTGGATTCCAAGTAATCACGATTATAA 604
                         iv     -  ii   v     v vii     v v i    v v  i -  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA-AA 99

  chr1_102301087_    605 GTCACAA-TGCAGGGTTTTTTTTAAGAAATTAATA---TAATTTGTATAT 650
                         i  v  i-   ----i      vv       i i --- i  ii---  v
  L1M4_orf2#LINE/    100 ATCCCAGCTGC----CTTTTTTGCAGAAATTGACAAGCTGATCC---TAA 142

  chr1_102301087_    651 AAGT-ATAATGAAATG-AGAAGAGCCACAATAACAAATAATAAAAAGATG 698
                           v -   vv      - iii  v   v    i v  ----  v  vv v
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA----AACAATCTT 188

  chr1_102301087_    699 AAAAAAGATGAACAAAGTTGAAGGACTTACA-------AGCTCAAGACTT 741
                         i       v           i      i   ------- vi    i    
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_102301087_    742 CTTATAAAGCCATATTAAAAAAGACAGTGTGGTATTGGTGTA--GACAGA 789
                         vi  i     i i v   vv              i   ii  --  i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_102301087_    790 CAAATGG-TCAA-GGAA--GAA--GAGA------------ACCCACACAT 821
                           v  i -    -    --   --    ------------     i    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_102301087_    822 GTATAGACAACTAACTAGCAACGAATTTGCAAATGCAATTCAGCAGAGAA 871
                         v   i v   i i i vv i  i ivv   v  vi v     iii i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_102301087_    872 ATGA--GTCTCTTTAACAAATTGTGCTGGAAAAGTTGGATAT----ATGC 915
                          vi --    i  i       v       i v ii      ?----    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_102301087_    916 AATAATGTGAATTTTGATCTATGTTTTGTATCATATA--AAAAT-AATTA 962
                           v ivi    v  v  i iv iii iii i      --     -  i v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_102301087_    963 AAAATGGATCCTAGACATAA-CGTAAAACCAAAAACTATAAAACATCTAG 1011
                                   v?    v   -i    i v v             vii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_102301087_   1012 AAG------------TAAACCTTAGTGACCTTGGGTTAGGTAAAGATTTT 1049
                            ------------    i   v                i  v i   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_102301087_   1050 TTATGTATCACAACAAAGTCACAGTCTACAAAAGAACAGATTGATACTAT 1099
                            vi   v   v    iv    iv v         v i  v    vvv 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_102301087_   1100 GAACTTCATCAAAAT-GAAAATTTCTGTCTTTTAATAGATATTGTTAAAA 1148
                          i             -i    i  i   vi  i  vi  i i i i  i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_102301087_   1149 GAGTTGACAATTAAGTCATGGATTGCGAGAATGTCATCTATGTGATATCA 1198
                         i   vi v ivi  vi  ii  v  v     ---v  v v  ii -    
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAA---AATATTTGCAA-ATCA 734

  chr1_102301087_   1199 TCTATGTGATAAAGGATTTGTTCCTAGAATATATAAGTAACTCTCGGAAC 1248
                          v   v      i   i    vi i           iv      iiv   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_102301087_   1249 TCAATAACATGAA----AATAACCCAAGAAAAAACCTGGCAAAATACTGT 1294
                                i vi  ----          vv?    viv      iv i vv
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_102301087_   1295 TATA---------CCAAGGAAGATATATGGAGAGTACATAACCATGTGAA 1335
                         v   ---------    i         iii vi ivv    v  ii    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_102301087_   1336 CAGAAGCTTAATATCATTCATCAT 1359
                         v   v   i  i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (128 / 102)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.19 (86 / 27)  


1778 26.25 3.49 1.33  chr1_102312035_102313627      499  1100 (493)    L1M4_orf2#LINE/L1      294   908 (0)  

  chr1_102312035_    499 AGACCATTGGAACCGAAAAGAGAACTCAGAAATAAGACCTCATATCTACA 548
                            i  v     iv   vv    iii         iv  vi i  i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_102312035_    549 ACCACCTGA-------CAAAGA---CAAG------CAATGAAGAAAGGAT 582
                         ii  vi   -------   i i---    ------     ii     i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_102312035_    583 TTCCTATTTAACAAATGGAGCTGGGAGAACTGGCTAGCCATATGCAGGAA 632
                         vvi  v  i         v       v      v  ?   i     ii i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_102312035_    633 CTTGAAACTGGACCCCTTCCTTATATTATATACAAAAATTAACTCAAGAT 682
                         vv    ii         v   i i ii                    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_102312035_    683 GGAATAAAGACTTAAATATAAAACCTAAAACTATAAAAACCCTAGATGAA 732
                            vi ?    i     i   i v              vi i    v   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_102312035_    733 AATCTAGGCAATACCCTTCAGGACATAGGGATGGACAAAGATTTCAT-GA 781
                           iv    ?ivv vi    iv   v v   v i i   v i    v -  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_102312035_    782 TGAAAATTTCAAAAGC-CAATTGCAACAAAAGCCAAAATTGACAAATGGG 830
                          - vi ivi       -   --          vv     v  i    v  
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_102312035_    831 ATCTAAGTAAACTAAACAGCATCTGCACAGCAAAAGAAACTATCATCAGA 880
                          ii v vi   v v  v i v i  ii vv    i  v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_102312035_    881 GTGAACAGACAAGCTATAGAATGGGAGAAACTTTTTGCAATCTATCCATC 930
                              v      v i i             v v       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_102312035_    931 TGACAAAGGTCTAATATCCAGAATTTACAAGGAACTTAAACAAATTTACA 980
                            i  i  v  vi          v  i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_102312035_    981 AGATAAAAACAAACAACCCCGTT-AAAAGTGGGCAAAGGACATGAAATGA 1029
                          v v   i     i     vi  -    i           i- ----   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-T----TGA 835

  chr1_102312035_   1030 ACAAACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAA--ACCTGAAA 1077
                          i i   i     v        i  vi viii     v  --  v     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_102312035_   1078 AAAAGCTCAACACCACTGATCAT 1100
                          i v        i  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (86 / 69)
Gap_init rate = 0.02 (11 / 615), avg. gap size = 2.64 (29 / 11)  


2475 25.53 4.57 3.34  chr1_102322368_102324708.rev      963  1859 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_102322368_    963 TGGAAA-ACATCCTATGCTTATGCATTTGAATAATAAATATTGTCAAAAT 1011
                               - i    i   i i   v   v   v v v        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_102322368_   1012 GGCCATACTGCCCAAAGCAATCTACAGATTCAATGCTATTCCTATCAAAC 1061
                            v     v      vii              i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_102322368_   1062 TATCAATATCATTTTTCACAGAACTAGAAAAA--AATTATTAATTGTATA 1109
                          vi  iivv v     ii     v v  v  i--i  iv v  v vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_102322368_   1110 TGGAACTAAAAAAGAGCCCAGA-TAGCCAAAGAAATCCTAAGCAAAAAGA 1158
                              v iv  ii  -      -        iv    i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_102322368_   1159 ACAAAGCTGGAGGCATCACATTGTCCAACTTCAGACTATACTACAGGGCT 1208
                               i      vv     i vi    i    i viv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_102322368_   1209 ACAGGAAGCAGAATAGCATGGTACTGGTACAAAAAAAAAAAAAGGACACA 1258
                             v  v  ii i  ii         i i  ii v -------    i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-------GACATA 292

  chr1_102322368_   1259 TAGACCAGTGGAACAGAATGGAGAACCTAGAAATAAAGCTGCACACCTAC 1308
                             i  i     i     v    ii i         v iii   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_102322368_   1309 AGCTATCTGATATTCAACAAAGTTGACAAAAGCGAGCAATGGAAAGGGGC 1358
                         i ii vi    v   i    i v  v   i v ivv      ii ii iv
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_102322368_   1359 TC-CCTATTCAATAAACAATGCTAGGATAGCTGGCTAGCTGTATGCAGAA 1407
                          v-i  v     i   iii    i   i i    v  ? iii     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_102322368_   1408 GAATGAAACTAGGCCACTACCTATCACCATATACAAACATTAACTCAAGA 1457
                                ii i i  v      vv             v          i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_102322368_   1458 TGGATTGAAGATTTAAATGAAAGACCTAAAACTATAAGAATCCTAGAAGA 1507
                              ii?   ii      v    v            i v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_102322368_   1508 AAATCTCAGAA-ACACCATTCTGGACAACAGCCTTGGG--AAAAAATG-- 1552
                            iv vi ?i- v i -   vv   ------      -- iiv    --
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGAC------CTTGGGTTAGGCAATGGT 585

  chr1_102322368_   1553 --------TATGAC--CAA--GTCCTCAAAAGCAATCACAAAACAAAAAT 1590
                         --------      --   -- ----  v      -  v  i -      
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAG----CACAAGCAA-CAAAAGA-AAAAAT 629

  chr1_102322368_   1591 TGACAAGAGGGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAA 1640
                         v  i  ivv    i v  i   v v  i i   i  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_102322368_   1641 CTATAAACAGAGTAAACAGATGACCTAAAGAATGGGAGAAAATATTTGAA 1690
                             v  v i   i  v   ii   i v                    v 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_102322368_   1691 AACAATGCATTTGA--AAATACTTTAATATCTAGAACTTATAAGTAACT- 1737
                           iv  ii  i   -- iiv    --i    i    iv     iv    -
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTT--GTATCCAGAATATATAAAGAACTC 777

  chr1_102322368_   1738 -TAT--TTCAA----AAAGCAGA-AAACAATCCCATTAAAAAAAAATGGG 1779
                         -  i--i    ----   i-   -   i  i  v   ?     ---    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAA-AGACAAATAACCCAATTWAAAAA---TGGG 823

  chr1_102322368_   1780 TAAAAGAC------AGACACTTCTCAAAAGAAGACACATAAGTGACCAAT 1823
                         i   i  i------     i     v        i i i  i  i     
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_102322368_   1824 AAACAT-TAAACAAAAATGCCTCAA-ATGACTAATCAG 1859
                           i  i- i  --  i    -    -  v ????????
  L1M4_orf2#LINE/    874 AAGCACATGAA--AAGATGC-TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (143 / 82)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.45 (71 / 29)  


2881 26.45 2.34 1.00  chr1_102383158_102387545.rev     3002  3897 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_102383158_   3002 TGGAATCATATCCCATGCTCATAGATGGGTAGATTCAATATTCTGAAAAT 3051
                              vv          i    i   v  v   i i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_102383158_   3052 GACCATACTGCCAAAACCAATCTTCAAATTCAATGCAATTCTCATCGAAA 3101
                          i v     v  v   iii    v  i      i     i ii   i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_102383158_   3102 TATCATCATCATTCTGCACAGAACTAGAAAAAAAAAAATCCTAAAATTCA 3151
                          vi  v vv v  i vii     v v  v  ivvi --            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chr1_102383158_   3152 TATGGAACCAAAAGAGAACCTGCATAGCCAAAGCAAGACTAAGAGAAAAG 3201
                                viiv   i  v  v v         i   vvi i i i i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_102383158_   3202 AACAAATCTGGAGGCATCACATGATCTGATTTCAAATTATACTCTAAGGC 3251
                               vi      vv     ivvi ii        viv    vi  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_102383158_   3252 CATAGTCACGCCAAAATAGCATGGTACTGGCATAAAAATAGGCATGTAGA 3301
                         i i   v i--   i i  ii              ii    i   i    
  L1M4_orf2#LINE/    249 TACAGTAAT--CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_102383158_   3302 CCAATGGAACAGAATAGAGAACCCAGAAATAGAGCCAAATATGTACAGCC 3351
                         i        i     v    ii         i v   v i  v  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_102383158_   3352 AACTGATCTTCGACAAGGCAAACAAAAACATAAAGTGGGGAAGGGACAGC 3401
                           i    i          vviv   i v   vv i       i i i  i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_102383158_   3402 CTATACAACCCATGGTGCTGGGGTAATTAGCAAGCCACCTGTAGAAGAAT 3451
                           v v    vv           ii  i i vv ?    v  i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_102383158_   3452 GAAACTGGATCCTTATCTCTCACCTTACACAAAAATCAACTCAAGATGGA 3501
                            ii    i  i  i   v    v  i        i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_102383158_   3502 TCAAAAACTTAAATCTAAGACTCAAAACCATAAAGATTCT--GAAAAATA 3549
                            ? i  i     v     vii     i     - i   --   i  - 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAA-A 544

  chr1_102383158_   3550 ACATCAGGA--AAACCTCTA-GACTTTGGCTAAGGCAAAAAGTTCATGAC 3596
                             -   ?--   i  iii-   i    v v      viiv   v iiv
  L1M4_orf2#LINE/    545 ACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_102383158_   3597 CAC-ACACCCAAAAGCAAATGCAACAAAAACCAAGATAAATAGATT---- 3641
                         i i-     -       v v         ivv  i   i   i   ----
  L1M4_orf2#LINE/    594 TATGACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_102383158_   3642 -------AAACTAAGAAGCTTCTGCACAGCCAAAGAAATAATCAGCAGAG 3684
                         -------   i   i  -   i  ii vv v  i  v iv    iv i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_102383158_   3685 TTAACAGACAACCCACAGAGTGGGAGAGAATCTTCACAATCTATACATCC 3734
                          v  v              i       i   v  ii   vii   i   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_102383158_   3735 AACAAAGAACTAATATCCAGAAACTACAAAGAACTC----AAATCAGTAA 3780
                         i i  i i   vi         vv  i         ----  v   i   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_102383158_   3781 GAAAAAATAAAACAATCTCATCCAAAACTGGGCTAAGGACACAAACAGAC 3830
                         v     ivv   i  i iv  i?    v     v     ivii  i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_102383158_   3831 AATTCTCAAAAGAAGATATACAAATGGCCAACAAGCATATGGAAAAATTC 3880
                          v     v                       i     i   i   i  v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_102383158_   3881 TCAACCTCACTAATCAT 3897
                              v   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.31 (30 / 13)  


2271 25.11 5.07 3.60  chr1_102392251_102396523     2893  3780 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_102392251_   2893 ATATTCAATGATTATGGAT---AAGTCTCAATGTTGTCAAAATGTCAATT 2939
                             i v   v i      ---   v  i   i    i  i   v    v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_102392251_   2940 CTTCCCAACTTAACATACAGATTTAATGCAATCCCAACCAAAATCCCAGC 2989
                           i     v  i iv        i  i        v i            
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr1_102392251_   2990 AAGTTATTTTGTGGGTATTTACAAACTGATTCTAAAGTTTATGTAGTGAT 3039
                         vivi v     ii iv   v    i     i     i  i  i i vi  
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_102392251_   3040 ATCAACAACATATAATAGT--AAGCTGAATATT---AAAGAAGAACAATG 3084
                         iiv ivi  vi v     i--  i --   v  ---            v 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAAC--AATCTTGAAAAAGAAGAACAAAG 205

  chr1_102392251_   3085 TCGAAAGACTGA----TTCTAACTTAAAGACTTAGTATAAATATACAGTA 3130
                          i i i    v ---- i i  i  v  i     v  i   vv       
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_102392251_   3131 ATCAAAAAAGGATGGTG-------AAGGA-AAAAATATA--TCAGTGAAA 3170
                              i v  vi    i-------     - i v     --   i  i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_102392251_   3171 TAGAAGAGAGAGCTCAGAAATAGATCCACAAAAATATAGTCAGTATATAG 3220
                              vv     ii        i i   i v vv   i    ----  v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA----ATTG 351

  chr1_102392251_   3221 GTAATATAGACAATGCAATATGGGCATCATAGGCAATGCAATAGAGA--- 3267
                         i -- v v     --------   iii  -  i v  v    i i  ---
  L1M4_orf2#LINE/    352 AT--TTTCGACAA--------GGGTGCCA-AGACCATTCAATGGGGAAAG 390

  chr1_102392251_   3268 --TAGTCTTTTAAATAAATGGTTCTGTAAAAACTAGATATCCACATGCCA 3315
                         --         v  i       v   vi v    i    ?        - 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-A 439

  chr1_102392251_   3316 AAACAATGAATCTAGATATAGACTT-ACACTCTTCACAAAA-TTAACTCA 3363
                            v      vi i  ivivv  i -    iv vi      -        
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_102392251_   3364 AAATGGAACATAGA--TAAGACGCAAAA--TAAGGAACTCTAAAACTCCC 3409
                                v  ?   --   - i i  i --   --    v        ii
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAA-ATGTAAGAGCTAA--AACTATAAAACTCTT 536

  chr1_102392251_   3410 TAAAGATAACATAGAAGAAAATCTAGATAACTTGGGGCTTAGCAATAACT 3459
                         vi    v       i? v      vvi i  i v   i vi     iii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_102392251_   3460 TTTTTGATAGGACACCAAATACATAATGAATAAAA-----AATTGGTAAA 3504
                          i  v    v         vi  i  vv  i    -----   v i    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_102392251_   3505 CTGGACTTCTTTAAAATTGAAAACATCCACTTTGTG-----AAGGAGACT 3549
                         i        v i      i     -----i      -----     v   
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAAC-----TTTTGTGCTTCAAAGGACACT 681

  chr1_102392251_   3550 ATCAACAAAATGGAAAAAAAAACCGAAGCACAGACTAAGAGAAAATATTT 3599
                              v   i  -    i v    ----      v ii            
  L1M4_orf2#LINE/    682 ATCAAGAAAGTG-AAAAGACAACC----CACAGAATGGGAGAAAATATTT 726

  chr1_102392251_   3600 GCAAAAGACATATATTATAAAGAACTGTTATAACAAATATACAAAGAACT 3649
                              vv i    v v    i i   vv   vvvi      i        
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_102392251_   3650 CTTAAAACTAAGCCATAAGAAAATAAACCTATTCAATTAAAAAATTGGTC 3699
                             v    v iiv    i  i i   iv- ii     ?      v  iv
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATA-ACCCAATTWAAAAATGGGCA 825

  chr1_102392251_   3700 AAAGACCTTAACAGAG--CTCATCAAAGTAGAGACGTAGATGCTAAATAA 3747
                           i  ii v  i   v--i  vi     v   v iii i   viv     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_102392251_   3748 CCACGTTAAAATTTACTCCACATCATATGTCAT 3780
                         v   i v    vv i   v      ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (123 / 96)
Gap_init rate = 0.03 (27 / 901), avg. gap size = 2.85 (77 / 27)  


 651 25.85 5.51 12.29  chr1_102414691_102416361      500  1207 (464)    L1M4_orf2#LINE/L1      249   908 (0)  

  chr1_102414691_    500 TAAAGAAATTAAGAAACTGTGATACTACTCCAAGGATAGATATATTTATC 549
                           v  v   i    v v    i    ivivi         i    vv   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_102414691_    550 AATG--ACAGAGTAGAGAGTACAGAAAAAGATCCATACATGTATGATCGT 597
                             -- i   i v      v      v i i        v    i  iv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_102414691_    598 TTGATTTATAAAAAGGGTAACGACACAACACAATTGATAAA-AATTGTCT 646
                                vii v      iv i v  v iv    v iv   -   v    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_102414691_    647 CTTTACCAAACG-TACTAAGTCAATTGGATATTAAAATATAGAATATATG 695
                         i  i v    i - i  ii v   i      ?iv v  ii i  v -   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-ATG 447

  chr1_102414691_    696 TACACACACACACACACACACACACACACACACACACACACAGT--GACC 743
                         --------------------------------------- -   --    
  L1M4_orf2#LINE/    448 ---------------------------------------A-AGTTGGACC 457

  chr1_102414691_    744 TGAACTTCAAACCTTACACAAAAGTCAATTCCA---GTATTTCAGGCGTA 790
                         ivv  i   v   v  i      i i  i  v --- v  iv?  i v  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_102414691_    791 AACGTAAAAGGTAAACCAATAAAGCTTTTAGAAGAAAAAACAAGAC--AA 838
                           i    i  v    v v     i  i           v i i ?v--  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_102414691_    839 CTTTCTTAAG-TTGCAGTAGGCAAAAATTCCTAAATTTCTCTTACCTCGC 887
                         ii   v i v-   viv       vii  ----------     vv ---
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTT----------TCTTAGAT--- 594

  chr1_102414691_    888 CCCCCACAACCCCCGGCTATACGATGTAAAATCACAAGTAATTATAAAGA 937
                         ----- ii  v  --------------    v      i  i- -     
  L1M4_orf2#LINE/    595 -----ATGACACC--------------AAAAGCACAAGCAAC-A-AAAGA 623

  chr1_102414691_    938 AAAAA-----AAAT-GGAGTATATCAGAATTAATAA----TGTGTTTCCA 977
                              -----    -   v vi    i      v  ----    i   --
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC-- 671

  chr1_102414691_    978 TGAAAAGAT-CTAATTAGATCAGTGAAAAGGCTAAATACATAGTGTGGAT 1026
                         --   i  i-   viv   -v         i v vvi   v i  -   v
  L1M4_orf2#LINE/    672 --AAAGGACACTATCAAGA-AAGTGAAAAGACAACCCACAGAATG-GGAG 717

  chr1_102414691_   1027 GAGGTATTTGCAGTACACACTCCTAACAAAATCTTTGAATATAGAATATA 1076
                         i ii        ivv  i ivi  i i  iivvi   v  vi        
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_102414691_   1077 TG------TCATAAAAATTAATAAACATTTAATTGATAAATAG------- 1113
                          i------  v  v  v i     ---- v  vv  i     i-------
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAA----TAAAAAGACAAATAACCCAATT 813

  chr1_102414691_   1114 AAAAAGCAGGCAAAAGATT-AAGCAGGCACTTA-ACAAAGTAATATAT-C 1160
                         ?    iii      i    -i ii  i  i  v-v     -  v    - 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG-AAGATATAC 862

  chr1_102414691_   1161 AAGATGCCCATTATATCTTTGAAAATGTACTGCACTTTATTAATTAG 1207
                           -   v   v  viiviv      vi i  vv  v i ????????
  L1M4_orf2#LINE/    863 AA-ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (94 / 85)
Gap_init rate = 0.05 (30 / 660), avg. gap size = 4.20 (126 / 30)  


2401 23.85 3.96 4.84  chr1_102431584_102435702     2726  3635 (484)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr1_102431584_   2726 GATATTC-ATGTTCATGGACAGAAAGACTCAATATTGTCAAGATCCCAGT 2774
                              i -           iv i      i        i     vv  i 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_102431584_   2775 TATTCTCAACCAGGCCTATA-ATTTAATACAATCCCAATCAAAATTTCAG 2823
                         vv i i   viv ii   i -   i  ii       v        ii   
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_102431584_   2824 CAACAGATTGTTTG--GATATTGCCAAACTGATTCTAAAATTTATATGGA 2871
                          vi v--  v    --  v    v   i     i        i       
  L1M4_orf2#LINE/    107 CTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_102431584_   2872 GGAGGAAAACATCCAGAATAGCCAACACAATAATGAAAAAGAAG------ 2915
                         iiv v  iiv i             v     vv           ------
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_102431584_   2916 -TTGAAGCACTAACACTACTTAAATTCAGA-CTTATAGTAAAGCT-CAAT 2962
                         -   i  v   v     v ii  v    i -    ivii      -  i 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_102431584_   2963 AA--AAGACAGTATAGTGTTAATA-AAAAATTGACACATATATTAATGTA 3009
                           --        i i  ii iii -  ii  v    i   v  i    v 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_102431584_   3010 ACAGAGTGGAGAGCCCC-ATTTAGATCCACACAAATAGAATGAACAGATC 3058
                          i   i v     i  v- vv  i i   i   vv  vii v  iv   i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_102431584_   3059 TTTGACAAAGGAGC-AATATATATATATATATATATATATATATATATAT 3107
                           i     i  v  -  v i------------------------------
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGAC------------------------------ 374

  chr1_102431584_   3108 ATATATATGAATGGAGAAGAGAGTA---TTTTAAACAA-TAGTGCTTGTA 3153
                         ---i  - v     i   -   i  ---    v     - i     v v 
  L1M4_orf2#LINE/    375 ---CAT-TCAATGGGGAA-AGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_102431584_   3154 AAATAGGACATCCACATGCAAAATAATGAATCTAAACACAGACCTTAAAC 3203
                         v  iv   i ?            v      vi ii  v vv    i v  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_102431584_   3204 T-TGTCACAAAAATGAACACTAAATGGACCATC-ACCTGTAATACAAAAT 3251
                         i- i -        v   v v       i  ?v-    i-   ii  i -
  L1M4_orf2#LINE/    470 CATAT-ACAAAAATTAACTCAAAATGGATCAWAGACCTA-AATGTAAGA- 516

  chr1_102431584_   3252 GC-AAAACTATACAACTCTTTGAAGAAAACATAGTAGAAAACCTAAATGA 3300
                           -         v       v             v? v   i  vvi   
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_102431584_   3301 GCTTGGTGTAGG-GATGATTTTTTTACAT-TAACACCAAAGACACATACC 3348
                         v     vv    -i   i   i  - v  - i        ii    vi v
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAAGCA 615

  chr1_102431584_   3349 ATAAAAGAAAACATTTATAAGCTGGACTTCATTAAAATTCAAAACTTCTA 3398
                          i         v  vv    ii          i      v       i i
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_102431584_   3399 --CT--AAAGGG-GCTCCCAAGGAAATGAAAACACATGGCACAGTATGGG 3443
                         --  --     i-i  vi    i  i      v   vvv     v     
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_102431584_   3444 AGGAAATATTTGCAGAAAGCATATCTGATAAAGGTATATTATCCAAAATA 3493
                           i           i vvii           i  vv vv      i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_102431584_   3494 TAGAAAGAATTATTAAAACTCAACAATAAACAG-CAAACAATCCACTTTT 3542
                           v      i v   v       i      v  -    i  i   v  ?-
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW- 814

  chr1_102431584_   3543 TAAAACATTGGCCAAAGACCTTAAAAAGCACCTCACCAAAGA---TATAT 3589
                         -    -  v   v  i  ii v  v ii  ii  v       ---    i
  L1M4_orf2#LINE/    815 -AAAA-ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_102431584_   3590 AGATAGCAAATAAGCACATGAAAAGATGCGTCACTTTACATGTTAT 3635
                          i  i  v                     viv  v i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (117 / 96)
Gap_init rate = 0.04 (32 / 902), avg. gap size = 2.50 (80 / 32)  


3621 20.11 5.29 0.92  chr1_102447416_102452288.rev     3522  4391 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_102447416_   3522 TGAAAAGAAACCTCATGTTCATGGATCAAAAGACTCA------------T 3559
                           i     v i i             iii      i ------------ 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_102447416_   3560 GGCAACATTTCAC-----------CAG-TTCAACACAATCGCTATCAGAA 3597
                              i i i v -----------   -      i     v      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_102447416_   3598 TTCCAGCTATGTTTTTTACAGAAATTGACAAGCTAATAC-AAAATTCATT 3646
                          i      iiv      i                i  v -         v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_102447416_   3647 TGGAAATACAAAGGACTCCAAGTAGTCAAAACAATCTTGAAAACGAAAAA 3696
                                i   i    i vi i   i                 v   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_102447416_   3697 TAAAGTTAGA--ATTTACACACTTACTGATTTCAAAACCTGCTACAAATC 3744
                         i      i  -- i --       v ii          i i       v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACT--CACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_102447416_   3745 TACCTTATTCAAGGCAGTATAGCAGTTGTATGAGGATAAACATATATATC 3794
                            vv  v     i    i i i v v i  i      i       v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_102447416_   3795 AATGGAATAAAAGTTATAGTGCAGAATTATGTCCTCACA-----AATTAG 3839
                                  i  v v v   v     v  vii  vi   -----ii i i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_102447416_   3840 TTGAATATTAACAAGGGTTTCAAGGCAATGTTATGTGGAAAAAAATAGTC 3889
                             v v ii        vi    i v  viv   -  i   i       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTC 397

  chr1_102447416_   3890 TTTTCAGCAAGTGGTGCTGAGACAACTTGATATCCACATGCAAAATTATG 3939
                               i   i        i       v    ?            vv   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_102447416_   3940 AAACTGGATTTCTACTGCATATTATATA--AAAATTATCTCAAAACAGAT 3987
                           ii    iii    iv  i ii     --       v       ii   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_102447416_   3988 CAAAAACCTAAATATTAGAGCTAAAACTTTAAAACTCTTTTTAAGAAAAC 4037
                           ? i        i v            v          vv-        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG-AAGAAAAC 546

  chr1_102447416_   4038 ATAGGCCTAAATCTTTGTAACCTTATAGTGAGA-AATGGTTTCTTGGATA 4086
                              ?v        i  i     i-i  v  i-           i    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGATA 595

  chr1_102447416_   4087 TGCCACCAAAAGCACAAATGACAAAAGAAAAATATAGATAAATTTTACCT 4136
                           v              iii            -           vv  i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTT 644

  chr1_102447416_   4137 CATCAGAAT-AGAAACTTCT---TTTGAAAGGTTACATTCAAAAAAATGA 4182
                              i   - i      i ---i  v     vi  vv    i   i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_102447416_   4183 AAAGACAACTCAGAGAAGTGGCAAAAGCATTTGTAAGTCATATAACTGTT 4232
                                  i  v    vv  vi   ii     i  i       v   v 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_102447416_   4233 AAAAGACTATTATCCATAATATATAAAGAACTCTCACGACTCAACAAATT 4282
                           ii    vv      v                 i  i      i  -- 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA--T 792

  chr1_102447416_   4283 AAAAAGACAAA-AA---AAT-AGAAAATGGAAAACAAATTTGAATAGATA 4327
                                    -  ---   -?i       iv  vii           i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_102447416_   4328 TTTCTCCAGAGAA-ATACACAAATGACTGATGAGAACATGAAAATATGTA 4376
                                 i    -   i       i ii  i  v         v   iv
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_102447416_   4377 CA-TATCATTAGTTAG 4391
                           -i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (110 / 61)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.57 (54 / 21)  


2173 25.98 2.87 1.66  chr1_102466841_102469099.rev      508  1169 (1090)    L1M4_orf2#LINE/L1      110   779 (129)  

  chr1_102466841_    508 CTTTCTTCACAGAAATAGAAAAAAAACT-ACTTTAAATTTCATATGGAAC 556
                          i  i  ii       v  v  i---  - iii    v           v
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCATATGGAAA 156

  chr1_102466841_    557 CAACAAAGAGCCC-GTTTGGCCAAAACAATCCTAAGCAAAAAGAATAAAG 605
                         ii-   i ii   - vv i            i i iv  i     i    
  L1M4_orf2#LINE/    157 TG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_102466841_    606 CTGGAGGCATCATGCTACCTGACTTCAAACTGTACTACAAGGCTACAGTA 655
                         i      vv   ii  v  ii i      viv        i         
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_102466841_    656 AT-AAAACAGCATGGTGCTGCCACCAAAGCAGATATATAGACCAATGGAA 704
                           -  i    ii    i   v  iv iiii   i       i        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_102466841_    705 CAGAACAGAGGCCTCAGAAATAACACCACACTTCTACAACCATCTGATCT 754
                         i    iv   ivii         vv   i  v i  iiii  vi    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_102466841_    755 TTGAGAAACCTGACAAAAACAAGCAACGGGG---GAATGGTTCCCTATTT 801
                          i  v  ivv  v   i v  vv   i    ---    i  ---  v  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT---CTTTTC 402

  chr1_102466841_    802 AATAAATGGTATTGGAAAAATTGGCTAGCCATATGCAGAAAACTGAAACT 851
                           i       ii   i v  i   v  ?   i     i  i v    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_102466841_    852 GGACCCCTTCCTTACACCTTTTACAAAAATTAACTCAAGATGTATTAAAG 901
                                 v   i     v v                 i   v  i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_102466841_    902 CCTTCA---TAAGACCTAAAACCATAAAACCCT-AGAAGAAAACCTAGG- 946
                         v i v ---     v       i       i  -          v    -
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_102466841_    947 -TAATACCATTCA-GATCATAAGTATGGGCAAAGACTTCATGACTAAAAC 994
                         -   - i -   i-  i v ii  - i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    553 GTAA-ATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGAC 599

  chr1_102466841_    995 ACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGTATCT----- 1039
                                   vvi          vv     v  i    v v ii -----
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_102466841_   1040 -AATTAAAGAGCTTCTGCACAGCAAAAGAGACTATCATCAGAGTGAACAG 1088
                         -       i -   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_102466841_   1089 GCAACCTACAGAATGGGAGAAAAATTTTGCAATCTATCCGTCTGACAAAG 1138
                         i     i                vv       vii  vii     i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_102466841_   1139 TGCTAATATCCAGAGTCTACAAAGAACTCTT 1169
                         vi  vi        i v  i           
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTT 779

Transitions / transversions = 1.66 (106 / 64)
Gap_init rate = 0.02 (16 / 670), avg. gap size = 1.88 (30 / 16)  

 406 25.00 0.00 0.86  chr1_102466841_102469099.rev     1653  1768 (491)    L1M4_orf2#LINE/L1      794   908 (0)  

  chr1_102466841_   1653 AAAAAACAAACAGCCTCATCAAAAAGTGGGCGAAGGATGTAATCAGACAC 1702
                             i     i i  iv  i?    i     i      v i vi     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_102466841_   1703 TTCTCAAAAGAAGACATATATGTGCCCAACAAATATATGAAAAAAAAGTG 1752
                              v        i   i vi  v    i  ii i       i -v iv
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr1_102466841_   1753 CATCATCACTGGTCAT 1768
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (19 / 9)
Gap_init rate = 0.01 (1 / 115), avg. gap size = 1.00 (1 / 1)  


2425 29.12 0.87 0.99  chr1_102532848_102537435     2876  3682 (906)    L1M4_orf2#LINE/L1        1   806 (102)  

  chr1_102532848_   2876 TGGAAAAACATTCCATGTTCATGAATAGGAAGAATCAATATCATGAAAAT 2925
                               i i  i           i  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_102532848_   2926 GGCCATAATGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 2975
                            v   v v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_102532848_   2976 TACCATTGAATTTCTTCGCAGAATTAGAAAAACT-ACTTTAAATTTCATA 3024
                          v   vivivi  i  i      v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_102532848_   3025 TGGAACCCAAAAAGGCCTCTA-TAGTCAAGACAAGCCTAAGCAAAAGGAA 3073
                              vivv  ii i  ivv -   i   i    v i i iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_102532848_   3074 CAAAGCTGGTGAAATCATGCTACCTGACTTTAAACTATACTACAAGGCTA 3123
                              i   v i v   ii  v  ii i  i   viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_102532848_   3124 CAGTAACCAAAACAGCATGGTACTGGGCCCAAAACAGATATATAGACCAA 3173
                               i   i    ii         vviv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_102532848_   3174 TGGAACAGAACAGAGGCCTCAGAAGTGACACCACACTTGTACAACCATCT 3223
                              i    iv   ivii     i i vv   i  v v  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_102532848_   3224 GATCTTTGACAAACCTGATAAAAATAAGCAATGAGGAAATGATTCCCTAT 3273
                            i  i     ivv  vi  i vi vv     i     vi  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_102532848_   3274 TGAATAAATGGTGCTGGGAAAACTGGCTATCCATATGCAGAAAACTGAAA 3323
                          v  i              v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_102532848_   3324 CTGGACCCCTTCATTACACCTTATACAAAAATTAAGTCAGGATGGATTAA 3373
                         i         v v i     v              v   ii      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_102532848_   3374 AGACTTCAATGTAAAACTCAAAACCACAAAAACACTAGGATAAAAGCTAG 3423
                             i v       i vii     i i    vivi   i v    vv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_102532848_   3424 GCA-ATACCATTCAGGACAT--AGTCATAGGCAAAGACTTCATGACTAAA 3470
                          ?i- v i -   iv   v --i  --       v ii   v iiv  vi
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGT--TAGGCAATGGTTTCTTAGATATG 597

  chr1_102532848_   3471 ACACCAAAA--ACAATTGCAACAAAAACCAAAATTGACAAATGGGATCTA 3518
                                  --    --         ivv     v  i    v   ii v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_102532848_   3519 ATTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTATCATCAGTGTGAA 3568
                           i   v v  i i      ii vv    i  v       vv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_102532848_   3569 GAGGCAACCTAAAGAATGGGAGAATATTTTTGCTATCTATCCATCGGACA 3618
                         i  i     i v            v  v     v vii  vi   v  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_102532848_   3619 AAGGTCTAATATCCAGGATCTGTAAGGAACTTAAACAAATTTGCAAGAAA 3668
                          i  v  vi       i  v i   i     ivv    v ---   v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAAT 792

  chr1_102532848_   3669 AAAAAAAAAAAAAA 3682
                              i v   v  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAA 806

Transitions / transversions = 1.30 (131 / 101)
Gap_init rate = 0.01 (9 / 806), avg. gap size = 1.67 (15 / 9)  

 284 22.54 3.52 3.52  chr1_102532848_102537435     3963  4104 (484)    L1M4_orf2#LINE/L1      767   908 (0)  

  chr1_102532848_   3963 ATAAAAAACA---ACAAC--AACAACAACAACAAAAACCAACCCCATCAA 4007
                              i   v---     --  i  i  v  v v   i-     v  i? 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT-AACCCAATTWA 815

  chr1_102532848_   4008 AAAGTGGTTGAAGGATATAAACAGATATTTCTCAAAAGAAGACATTTATG 4057
                            i   vii      v i  i   i       v        i  vi vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_102532848_   4058 TGGCCAACAAAAAATATGAAAAAAAGCTCACACTGGTCATTAGAGAA 4104
                                i  iv -i       i v     -  --i   ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCA-CATGAAAAGATGCTCA-AC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (19 / 12)
Gap_init rate = 0.04 (6 / 142), avg. gap size = 1.67 (10 / 6)  


3170 27.31 0.55 0.55  chr1_102619404_102625555     4752  5659 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_102619404_   4752 TGGAAGAACATTCCATGCTCAAGGGTAGTAAGAATCAATATCATGAAAAT 4801
                              ii i  i     i   v  i v v    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_102619404_   4802 GGCCATACTGCACAAGGTAATTTATAGATTCAATGCCATTCTCATCAAGC 4851
                            v     v v   iv i  i  i        i  v  i ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_102619404_   4852 TACCAATGACTTTCTTCACATAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4899
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_102619404_   4900 TATGGAACCAAAAAAGAGGCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 4949
                                viiv  ii  vv v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_102619404_   4950 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4999
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_102619404_   5000 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5049
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_102619404_   5050 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCGCTTATCTATAATC 5097
                                i    i--    i  --    i   vv  iivi  i   ii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_102619404_   5098 ATCTGATCTTTGACAAACCTGACAGAAACAAGCAATGGGGAAAGCATTCC 5147
                          vi    i  i     ivv  v  ii v  vv            v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_102619404_   5148 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5197
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_102619404_   5198 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGCA 5247
                            ii    i    v   i     v              i    ii  v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_102619404_   5248 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5297
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_102619404_   5298 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5346
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_102619404_   5347 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5396
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_102619404_   5397 ATTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5446
                           i   v v  v i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_102619404_   5447 CAAGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTTATCTGACA 5496
                         v ii     i                 v       vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_102619404_   5497 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5546
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_102619404_   5547 AAAACAAACCACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5596
                           i     iv    v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_102619404_   5597 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAACTGCTCAT 5646
                            v        i  vi viii     v ii          iv      v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_102619404_   5647 CATCACTGGCCAT 5659
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1727 26.00 2.79 2.27  chr1_102689690_102692829        2   574 (2566)    L1M4_orf2#LINE/L1      130   705 (203)  

  chr1_102689690_      2 AAACT-ACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCGCATTGCCAA 50
                           i  - iii    i           viiv  ii  v  v v  v     
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr1_102689690_     51 GTCAATCCTAAGCCAAAAGAACAAAGCTGGACGCATCACACTACCTGACT 100
                         iv     i i ivv i          i    v vv       v  ii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_102689690_    101 TCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTAC 150
                              viv        i          i   i    ii         i i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_102689690_    151 CAAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAA-A 197
                         v ii i   v                i    i--    i  --     - 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATA 327

  chr1_102689690_    198 AACGCCACATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACA 247
                            -   i i  i  iiiii vi    i  i     ivv  vv  i v  
  L1M4_orf2#LINE/    328 AAC-CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_102689690_    248 AGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGG 297
                         vv            i  vvi  v  i  i              v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_102689690_    298 CTAGCCCTATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATAC 347
                         v  ?  vi   i i  iiv    ii    i    v   i     v     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_102689690_    348 AAAAATCAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCA 397
                               i  i    i      i ?    i    i  v   v       i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_102689690_    398 TAAACACCCT-AGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCAT 446
                             -  i  -          v    ?i v viv   iv   v v  vv 
  L1M4_orf2#LINE/    527 TAAA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_102689690_    447 GGGCAAGGACTTCATTTCTAAAACACCAAAAGCAATGGCAACAAAAGACA 496
                         i     v ii   v vvv  vi            vvi           v 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_102689690_    497 AAATCTACCAATC--ATTTAAAGAATAACTAACACAAATTCTTTTG---- 540
                             vv iv   i-- i  v vv  -  i   ---   i i  v  ----
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAA-AATTAA---AAACTTTTGTGCTTC 671

  chr1_102689690_    541 AAA-----CTATTCCAGAAAGTCAAAGAAAAAATAATTC 574
                            -----    - v       ----     i i  ii 
  L1M4_orf2#LINE/    672 AAAGGACACTAT-CAAGAAAGT----GAAAAGACAACCC 705

Transitions / transversions = 1.35 (84 / 62)
Gap_init rate = 0.02 (14 / 576), avg. gap size = 2.07 (29 / 14)  

2656 25.57 5.09 2.38  chr1_102689690_102692829     1766  2649 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_102689690_   1766 TGGAAAGATATTTTATTTTTGTGGATTGGAGGAAATAATATTGTTAAAAT 1815
                                    iii  v  ii         i  vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_102689690_   1816 ATCCATACTAGCCAAA------------------GCAATCCA-GTCAAAG 1846
                         iv v     vv     ------------------       v-i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_102689690_   1847 --------ACATTCTTCACAGACATTTAAAAA---ATCCTGAAATTTATA 1885
                         --------i v  i  ii    v   v v  i---     i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_102689690_   1886 TGTAACCACAAAATATCC-TAATATCCAAAGCAATCATAAGACAAAATAA 1934
                           v  vii   iiv i  -v    v     i     v i ----------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---------- 190

  chr1_102689690_   1935 AAAAAAAAAAAGAAAGGCTGGAGGCCTCACACTAACTCACTTTGAAATAT 1984
                         -    i  i  v    -i      v        vv iv i  ii   iv 
  L1M4_orf2#LINE/    191 -AAAAGAAGAACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_102689690_   1985 ACTACAAAGATATAATAACCAAAAATAGCTCGGTACTGGCATGAAAACAA 2034
                                  v  i i   i   i -i  ivi           i ii i i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAG 287

  chr1_102689690_   2035 ACACATAGACAAATAAAAGAAAATAGAGAGTGCAGAAATAAATCTACACA 2084
                            i     iv   ii  v i   v      v          i i i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_102689690_   2085 TCTATAGTATACTGATTTTTGACAAAGATGCCAGAAACACATATTGGGGA 2134
                          i   i  vv i       i     i i     ii v  ivi v      
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_102689690_   2135 AAGGGCAGTCTCTTTAATAAATGATGCTAGAAAAATTGAATATTCACATG 2184
                            iii     i  i  i     i    i i v  i  i   ?i      
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_102689690_   2185 TAGAAGAAGAAAGCTAGGCCCCTATTACTCATCATATACAAAAGTAAAGT 2234
                         i i     vi   i i i      iiv v  i           i v  v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_102689690_   2235 CAAAATAGATTAAAGAAAGTAAATTAAAGTAAGA-CTAGAAACTATGAAA 2283
                               i   i ?   vv-     ----      -   -       i   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACC-TAAAT----GTAAGAGCTA-AAACTATAAAA 531

  chr1_102689690_   2284 CTACTAGAAGAAAACATAGTGG-AAATGCTTCATGACATTGGACTGGGGA 2332
                           vi               v? -    -    i    v    ii i  v 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCA 580

  chr1_102689690_   2333 A---------AAACA-GACGTTGAAAGCACAGGCAATGTAAGCAAAAATA 2372
                          --------- i i -   iiii        i    iiv   v       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_102689690_   2373 GATAAATGTGATGACATCAAACTAAAAAGCTTCTGCA-TAGAAAGGGCAA 2421
                                vv  ivv       v v    i   i  ii- vv     i  v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_102689690_   2422 CAGTCAACACAGTGAAGAGATAACGTACAGGATGGGAGAAAATATTTGCA 2471
                         i -    v v      i   i   vi    i                   
  L1M4_orf2#LINE/    681 TA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_102689690_   2472 AACTATATGTTTAACAAGTAGTTAACATCTAGAATATATAAGAAATGTAA 2521
                           ii    i i i i   viii vii   i           ii  ivivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_102689690_   2522 ACAACTCAATAACAAATA-ACAAATTGTACCATTAAAAATTGAGCAAAAG 2570
                                     i   v -      viiv v   ?    v  i     i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_102689690_   2571 ACCTGAATAGACATTTATCAAAAGAAGACATATAAAAGGACAACAGTTAT 2620
                          ii             v  v        i   i   v  v   i ivi i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_102689690_   2621 ATGGAAAAATGCTCAATATTTCTAATCAT 2649
                            i   i        i  iv????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (145 / 77)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.47 (66 / 19)  


2609 29.69 0.66 0.77  chr1_102795469_102801152.rev     4304  5209 (475)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_102795469_   4304 AAAGAAATTTCATACTCGTGGACAGGAGAAATCAATATTGTGAAAATGGC 4353
                              v  ii   ii  i    iv   ii v i        v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_102795469_   4354 CATACTGCCCAAAGCAATTTACAGATTCAATCCTATTCCCATTAAACTAC 4403
                         v     v      vii  i           iv v  i  i  i   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_102795469_   4404 CA-CTGACATTCTTCACAGAACTAGAAAAACT-ATTTTGAAATTCATATG 4451
                           -   v -  i  ii     v v  v  i  -  ii i           
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_102795469_   4452 GAATCAAAAGAGAACCTGAATAGCCTAGGCAATCCTAAGCAAAAAGAACA 4501
                            viiv   i  v  v        v ii     i i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_102795469_   4502 AATTTGGAGGCATCATGCTACCTAACTTCAAACTATGCTACAGGTCTGCA 4551
                           v       vv   ii  v  i  i      viv i     iiv  i  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_102795469_   4552 GTAACCAAAACAGCATGATCACTGGTAGAAGAACTGACACATAAACCAAT 4601
                             i   i    ii  i -     i v   i iv    i   i i    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGT-ACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_102795469_   4602 GAACCAGAATGGAGAA-CCTGAAATAAGAACACACACCTACAA-CTATCG 4649
                          i vi     v    i-  v       ivv  i   ii  iii- v  i 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_102795469_   4650 AATCTCCAACAAATCTGACAAAAATAAGCAATAGGGAAAGGATTCTCCAC 4699
                          - i i i    ivv  v   i vi vv    i       i  vv  ivi
  L1M4_orf2#LINE/    352 A-TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_102795469_   4700 TCAATAAATTGTGCTGGGATAACAGGCTAACCATAATCAGAAAATTGAAA 4749
                             i    v         i   v  v  ?   i vv  i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_102795469_   4750 CTGGAACCCTTCCTTACATTACATACAAAAATCTACTCAAGATGAAATTA 4799
                         i    v    v   i   ii i          iv      i   i - i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA-TCA 499

  chr1_102795469_   4800 AAGACTTAAATATAAAACCCAAAACTTTAAAAATGCTAGAAGAAAATCTA 4849
                         ?    i     i   i v i      v     v vi          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_102795469_   4850 GGCA-ATACCATTCAGGACATAGGCAAGGGCAAAGATTTCATGACAAAGA 4898
                           ?i- v i -   iv   v v  vvvi     v i    v iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_102795469_   4899 TGTCAGAAGCAATTGCAATGAAAGTAAAAATTGATGAATCAGATGTAATT 4948
                         iii  i     vvv    ii    v      v   i   ii  iv v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_102795469_   4949 AAACTAAACAGCTTCTGCACAGCAAAATAAACTATCAACTGAGTAAACAC 4998
                            v v  v i   i  ii vv    iv v        vvi   i  v v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_102795469_   4999 ACAACCTACAGAATGGGAGAAAAATTTTGCAAACTGTGCATCTGACAAAG 5048
                               i                vv        iii ii      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_102795469_   5049 GTCTAATGTCCAGCATCTATATGGGATTTAAACAAATTTACAAGAACAAG 5098
                          v  vi i     v  v    vi i i ivv    v iv i  v  v   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_102795469_   5099 AAAAACAACTCCATTAAAAAGTGGGCAAAGGACACGAACAGACACTTTTT 5148
                          v   i   i v   ?    i           ivi   i     i  i i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_102795469_   5149 -AAAGAGGACATACATGTGGCTAGGAATCATATAAAAATAAACTCTCAAT 5197
                         -     i  i     vi    i iv  v  i  i    --i iv     i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA--GATGCTCAAC 896

  chr1_102795469_   5198 ATTACTGTTAAA 5209
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (156 / 109)
Gap_init rate = 0.01 (12 / 905), avg. gap size = 1.08 (13 / 12)  


1297 27.39 14.92 0.00  chr1_102818232_102820323.rev      439   887 (1205)    L1M4_orf2#LINE/L1        1   516 (392)  

  chr1_102818232_    439 TGGAAAAATATCCTATGTTCAACGATTTAAAGAATTAATACTTTTAAAAT 488
                               i      i       vv    vi    v      i v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_102818232_    489 GTTTATACTCCCCAAAGCTACCTCCAGATT-------------------- 518
                          viv            viv i  v      --------------------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_102818232_    519 -------TG-----TTTAAAGAA---------------CCA-----CATA 536
                         -------  -----   iv    --------------- i -----    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_102818232_    537 ------------AGATCTCACACAGCTAAAGTAATCCTGAGCAAAAAGAA 574
                         ------------i  i iviv i   i   ii    i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_102818232_    575 CAAAGCTGGAGGTATCACACCATCTGATTTGAAATTACACTACAAAGCTG 624
                              i      vv      ivi ii    v   vivi           i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_102818232_    625 TAGTAGTTAAAATCACATGGTACTGGAATAAGAAAAAAAA-ATAAACTAA 673
                         i    i i  i iviii         v     i v i v -   i ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_102818232_    674 TGAAATAGAATAGAGAACCCAGAAATATATCTATGCTCTTACAGTAAACT 723
                           i        v    ii         v i i  i vi   ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_102818232_    724 CATTTTTGACAAAGGTGCCAACAACATACCTTGGAGAAAGGACAGCATCT 773
                         v     i     i        v v   v vv   i     i i  iv i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_102818232_    774 TTAATAAATGGTGATAGGACAACTGGATACTCCTATGGAAAAGAATGAAA 823
                          i  i        v i             ?i vi   v           i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_102818232_    824 CTAGATCCATATTTTTCACTGTAT-TAAAAATCAACT-AAAATCAATTAA 871
                         i i  i  v  ii iv   ii   -i      i    -     vi  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_102818232_    872 AGATTTTAATGTAAGA 887
                            ii v         
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA 516

Transitions / transversions = 1.88 (79 / 42)
Gap_init rate = 0.02 (8 / 516), avg. gap size = 8.38 (67 / 8)  

1185 26.82 0.52 0.26  chr1_102818232_102820323.rev     1218  1601 (491)    L1M4_orf2#LINE/L1      524   908 (0)  

  chr1_102818232_   1218 CTAGAAAACTACTAGAAGTAAACATTGAGAAAACACTACAGGACATTGAT 1267
                            v      vi      v      v i?iv  vv  v iv   v   iv
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_102818232_   1268 CTGGGCAAAGATTTTTGGGGTAAGTTCTCAAAAGCACAAACGAAAAAAGC 1317
                         i i     v i   i vi i  v vivi           i i v     v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_102818232_   1318 AAAAATAGACAAACAGGGTTTCATCAAGTTGAAAAGCTTCTGAACA-AAA 1366
                                  i   iv  ii        iv v    i   i  vi v-v  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_102818232_   1367 ATGAAACAATTAGCAAAGTGAAGAGACAACCTAGAGGATAGGAGAAAATA 1416
                          v  v  v  i iv        i        i v  i  i          
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_102818232_   1417 TTAG-AAACTACCTATTTGAAAAGAGATTAATAAACAGAATATAAAAGGA 1465
                           v -   ii iv   i   v   i  i vi  vv         v  i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_102818232_   1466 ACTCAGGCAACTCAATAGCAAAACAACCAAATAACCCAGTTAAAAAACAG 1515
                             vvi          ii    vi  -          i  ?     ii 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGG 822

  chr1_102818232_   1516 GCAAGGGACATAAACAGACATTTCTCAAATGAATGCATACGAATAGCCAA 1565
                             i   iv i  i           v  v   vii    i   i     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_102818232_   1566 CAAGTAAATGGAAAAATGCTCAACATTATTTATCAT 1601
                         i   i v   i   i           i ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (57 / 44)
Gap_init rate = 0.01 (3 / 385), avg. gap size = 1.00 (3 / 3)  


3129 28.41 0.22 0.22  chr1_102827846_102830091.rev      848  1755 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_102827846_    848 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATAAAAAT 897
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_102827846_    898 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATGCTCATCAAGC 947
                            v     v      v i  i  i        i  v  v ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_102827846_    948 TGCCATTGAGTTTCTTCACAGAATTAGACAAAACT-ACTTTAAATTTCAT 996
                          v   vivivi  i  ii     v v     i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_102827846_    997 ATGGAACCAAAAAAGAGCCCACATAGCCAAGAGAATCCTAAACAAAAAGA 1046
                               viiv  ii  v  viv        i v    i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_102827846_   1047 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 1096
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_102827846_   1097 ACAGTAACCAAAACCACTTGGTACTAGTATCAAAATGGATATACAGGCCA 1146
                                i   i  viiv       i i  v ii  i  i   i  ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_102827846_   1147 ATGGAACAGAACGGAGGCCTCATAAATAACACCACACATCTACAACCATC 1196
                               i    iv   ivii  v      vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_102827846_   1197 TGATCTTTGACATACCTGACAAAAGCAAGCAATGAGGAAAGGACTCCCTA 1246
                             i  i    vivv  v   i v  vv     i      i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_102827846_   1247 TTTAATAAACGGTGTTGGGAAAAGTGGCTAGCCTTATACAGAAAACTGAA 1296
                           i  i   i    i     v  v   v  ?  vi  i  i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_102827846_   1297 ACTATACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 1346
                         ii iv      v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_102827846_   1347 AAAACTTAAATGTAAGACCTAAAACCATAAAATCTCTAGAAGAAAACCTA 1396
                         ? i  i           v       i      iiii           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_102827846_   1397 GGCA-ATACCATTCAGGATGTAGGTAAAGGCAAAGACTTCATGACTAAAA 1445
                           ?i- v i -   iv  iv v  vvv      v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_102827846_   1446 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 1495
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_102827846_   1496 AAACTAAAGAGCTTCTGCACGGCAAAAGAAACTATCATCAGAGTGAACAG 1545
                            v v  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_102827846_   1546 GCAACCTACAGAATGGGAGAAAAATTTTGCCGTCTATCCATTTGACAAAG 1595
                         i     i                vv     vivii  vi  i   i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_102827846_   1596 GGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAGAGAAAA 1645
                          i  vi          v  i   v    ivv    v iv i  v i   i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_102827846_   1646 ACAAACCACCCCATCAAGAAGTGGGCAAAGGATGTGAACAGACACTTCTC 1695
                              iv    v  i? i  i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_102827846_   1696 AAAAGAAGACATTTATGCAGTCAACAAACATACGAAAAAATGCTCATCAT 1745
                         v        i  vi viii i   i  i  i i     i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_102827846_   1746 CACTGGTCAT 1755
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (151 / 103)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.00 (4 / 4)  


 282 26.45 5.79 3.31  chr1_102931373_102932898      141   261 (1265)    L1M4_orf2#LINE/L1        3   126 (782)  

  chr1_102931373_    141 GAGAGATACACAATATTAATGAATTGAAGTGA-TTGGTATT-TTAAA--G 186
                           i     iv v  i  v   i    i i-  -  ii    -    i-- 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAA-GACTTAATATTGTTAAGATG 51

  chr1_102931373_    187 ACAACACTCTCTAAATTGACCAATAGATTTGTTTCACTACAGCTCAAAAT 236
                         i   i    i i       i v i     iiviv  v v vvv       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_102931373_    237 TCCAACT---TTTTTTTCAGGGAAAATT 261
                         i   i  ---      v   ---     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAG---AAATT 126

Transitions / transversions = 1.67 (20 / 12)
Gap_init rate = 0.05 (6 / 124), avg. gap size = 1.83 (11 / 6)  


 376 31.85 2.22 0.00  chr1_102979642_102981850.rev      480   614 (1595)    L1M4_orf2#LINE/L1      266   403 (505)  

  chr1_102979642_    480 TGTGGTGCT-GTACAAGGGCAGGCAAATACATTAATAGAATAGCGTACAG 528
                               i  - i i    ii  i  v   v  i   i      vi vv  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_102979642_    529 AGTACAGGAACAGATTCACACATATACAATTACTTGAGTTATGA-AAGAA 577
                            v   i  i i ii  i    v  iii i v    v  vi  -   ii
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_102979642_    578 -GTCACTACACTTCAGGGGAAAAAGTATAGTCTTTTTA 614
                         - i  vv  vv    iv  ii    v          i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

Transitions / transversions = 1.69 (27 / 16)
Gap_init rate = 0.02 (3 / 138), avg. gap size = 1.00 (3 / 3)  

 531 28.36 6.72 2.24  chr1_102979642_102981850.rev     1049  1316 (893)    L1M4_orf2#LINE/L1      532   811 (97)  

  chr1_102979642_   1049 CTCTTACAATATAACATTAGAGAATATCTCCATAGGCTTGGAGCAAGCAA 1098
                               v  v v     vi ? v v    i i iiv     ivi i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_102979642_   1099 AAATTTCTTAAACATGGTA--AAAGGCTCAAAC--CATTAGCAAAAATAT 1144
                         vii       i i   ii --   i  v   i --  vv  v       -
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA- 630

  chr1_102979642_   1145 TGATAAATTGGACTTTGTTAAGAAATAGGAAAGTTT---GCCTAATAAAG 1191
                         -              ii i  --   vii   v   ---  i v -  i 
  L1M4_orf2#LINE/    631 -GATAAATTGGACTTCATCAA--AATTAAAAACTTTTGTGCTTCA-AAGG 676

  chr1_102979642_   1192 ATATTATTAAGAAATT-AAAAGGCACATCTCAGAGTGGG-GAGAAGACGT 1239
                          i i   i      v -     i  vvi v    i    -  i  v iv 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_102979642_   1240 GCAA------TATCTGACACACTACTC--ATTCAGAAGATATACATGTCT 1281
                             ------       i vivv   i--  i     v     v viv  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_102979642_   1282 CTTCTAAACTAATAAGGAAAAAAACAGA-AGCTCAA 1316
                            vi  vii     v-     i   i - i i   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAAT-AAAAAGACAAATAACCCAA 811

Transitions / transversions = 1.34 (43 / 32)
Gap_init rate = 0.04 (12 / 280), avg. gap size = 2.00 (24 / 12)  


3069 27.36 1.56 0.56  chr1_102982215_102985038.rev     1435  2333 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_102982215_   1435 TGGAAGAACATTCTATGCTCATGGGTAGGAAGAATTAATATCATGAAAAT 1484
                              ii i  i i   i      i v      v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_102982215_   1485 GGCCATACTGCACAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1534
                            v     v v   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_102982215_   1535 TACCAATGACTTTTTTCACAGAA-TTGGAAAAAACT-ATTTTAAAGTTCA 1582
                          v   iivi i     ii     -   -- v  i  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_102982215_   1583 TATGGAACCAAAAAAAGGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 1632
                                viiv  iiiiv  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_102982215_   1633 AACAAACCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGAC 1682
                               vi      vv       v  ii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_102982215_   1683 TACCGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1732
                            v    i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_102982215_   1733 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCGTATCTACAACT 1780
                                i    i--    i  --        vv  iiii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_102982215_   1781 ATCTGATCTTTGACAAACCTGACAAAAAACAAGCAACGGGGAAAGGATTC 1830
                          vi    i  i     ivv  v   i v-  vv   i        i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAG 395

  chr1_102982215_   1831 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1880
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_102982215_   1881 TGAAACTGGATCCCTTCATTACGCCTTATACAAAAATTAATTCAAGATGG 1930
                             ii    i    v v i  i  v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_102982215_   1931 ATTAAAGACCTAAATGTTAGACCTAAAACCATAAAAACCACAGAAGAAAA 1980
                           i ?            v   v       i      vi vi         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_102982215_   1981 CCTAGGCAATACTATTCAGGACATAGGCATGGGCAAGGACTTCATATCTA 2030
                          v    ?ivv v v   iv   v v  vv i     v ii   v  vv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_102982215_   2031 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2080
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_102982215_   2081 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 2130
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_102982215_   2131 CAAGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 2180
                         v ii     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_102982215_   2181 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAA-------ATGTA 2223
                          i  i  vi          v  i  v      vv    -------  iv 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_102982215_   2224 CAAGCAAA---CCCCATCAAAAAGTGAGTGAAGGATATGAACAGACACTT 2270
                         v ii    ---   v  i?    i  i ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_102982215_   2271 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAC 2320
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_102982215_   2321 CATCACTGGCCAT 2333
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  


2961 27.94 0.55 0.66  chr1_103003573_103009986     5013  5921 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_103003573_   5013 TGGAGGAACATTCCATACTCATGAATACGAAGAATCAATATCATGAAAAT 5062
                             iii i  i    ii     i  vv     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_103003573_   5063 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCAACAAGT 5112
                           iv     v     iv i  i  i        i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_103003573_   5113 TACCAAGGGCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5160
                          v   ivv  i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_103003573_   5161 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCTTAAGACAAAAG 5210
                                viiv  ii  v  v v  v     iv       i i v i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_103003573_   5211 AACAAAGCTGGAGGCATCACGCTACCTGACATCAAACTACACTACAAGGC 5260
                                i      vv    i  v  ii iv     vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_103003573_   5261 TACAGTAACCAAAACAGCATGGTACTGATACTAAAACACAGATATAGACC 5310
                                 i   i    ii        ii iv ii i v v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_103003573_   5311 AATGGCACAGAAC--AGAGCCCTCAGAATTAATACCACACATCTACAACT 5358
                              v i    i--    i  --    v   vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_103003573_   5359 ATCTGATCTTTGAGAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5408
                          vi    i  i  v  ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_103003573_   5409 CTATTCAACAAATGTTGCTGGGAAAACAGACTAGCCATATGTGAAAAGCT 5458
                           v           v        v   v iv  ?   i   ii   iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_103003573_   5459 GAAACTGGATGCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 5508
                            ii    iv   v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_103003573_   5509 TTAAAGAGTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5558
                          i ?   vi     i v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_103003573_   5559 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGATTTCATATCTA 5607
                         v    ?i- v i -   iv   v v  vv i     v i    v  vv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_103003573_   5608 AAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTA 5657
                         vi            vvii         vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_103003573_   5658 ATTAAACTCAAGAGATTCTGCACAGCAAAACAAACTACTATCAGAGTGAA 5707
                           i   v i  i iv  i  ii vv    iv v    ii vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_103003573_   5708 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5757
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_103003573_   5758 AAGGGCTAATATTTAGAATCTACAAAGAACTCAAACAAATTTACAAAGAA 5807
                          i  i  vi   ii     v  i         vv    -i i vv  v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAA 794

  chr1_103003573_   5808 AAAAACAAACATCCCCATCAAAAAGTGAGTGAAGGATATGAACAGACAGT 5857
                            i     i v   v  i?    i  i ii      v    i     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_103003573_   5858 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5907
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_103003573_   5908 CCATCACTGGCCAT 5921
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (144 / 106)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2891 27.62 1.66 1.33  chr1_103022861_103026754     2497  3401 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_103022861_   2497 TAAAAAGATATTCCATGTTTATAGATTTCAAGAATCAATATTATTAAAAT 2546
                          ii        i       i  i    vv    v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_103022861_   2547 GTTCATGCTATCCAAAGCATTCTACAGATTCAGTGCAGTGCCTATCAAAA 2596
                          viv  i  vi     viiv            ii   i v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_103022861_   2597 TGCCAGTGATATTCTTCACAGAAACAGAAAAAAAAATTCTAAAATTTATA 2646
                          v    iviiv  i  ii      iv  v  ivvi  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_103022861_   2647 TGGAAACACTAAAGACCCAAAATAGACAAAA--GTCTTCTAAGCACACAG 2694
                               ii v ii      i     v     --i    vv  i-----  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA-----AG 195

  chr1_103022861_   2695 AAAAAGAAAACTATAGGAATCACGTTACCTGACTTCAAATTATACTACAG 2744
                           i  v   ii iv    v    ii v  ii i      viv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_103022861_   2745 AGCTATAGTAACCAAAACAGTATGGTACTAGCATAAAAACAGACACATAA 2794
                              i     i   i     i       i      ii i     i   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_103022861_   2795 ACCAAAAGAATAGA-----GAATCCAGAAACAAATCCACACGCCTACAGT 2839
                          i   vi       -----  i        i   i   i  iii  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_103022861_   2840 TAACTCATCTTCAACAAAGTTTCCAACAATGTACATACAATGGAAAAAAT 2889
                         i  i v  i   i    i v v    -i i---   v      ii   iv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAA-GAC---CATTCAATGGGGAAAGA 391

  chr1_103022861_   2890 ACAGTCTCTTTAATAAATGGTACTGGGAAAACTGAATATTTCTATGTAGA 2939
                          i     i  i  i       i      v     i   ?iivi   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_103022861_   2940 AGAATGAAACTAGAACTCTACCTCTTTCTGTATGCAAAAATCAAATTAAA 2989
                                 ii i  v i       viv ii   i       i  v i   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_103022861_   2990 ATGGATAAAAGGCTTATATCTAAGAACCCAAACTGTATAACTACTATCAG 3039
                               v ?  i i  v  v     i iv     i  v    vi  vv  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_103022861_   3040 AATACATGGGGGAAACTCTCCAGGACATTGTCCTGGGCAAACATTTCTTG 3089
                           v    i  ? v  v   i iv   v   vvi i     vvi      i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_103022861_   3090 CCCAGTACCTCACAAGCACAGGTAACCAAAGCAAAAATGGACAAATGGGA 3139
                         vvi vv  vi  v       i i   v    v      i  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_103022861_   3140 TCACATCAAG-TTAAAGAAGACTCTGTACAGCAAGGAGAAACAGTCAACA 3188
                         iiv      i-     i v--i i   i vv   i -  v  vi    v 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAAC--TTTTGTGCTTCAAAG-GACACTATCAAGA 688

  chr1_103022861_   3189 AAGTGATGAGACAACCCACGGAAGGAGATAAAATATTTGCAAACTACCCA 3238
                               vi           i   v i  v              ii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_103022861_   3239 TCTCACAAGGGATTAATAAACCAAATATATAAGGAGCTC--A-AACTCCA 3285
                            v i      i vi  vv vi         i  i   -- -     v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_103022861_   3286 TA-CAGAAAATTCAATAG---ATTTTAAAAATCAGTAAAATATTTAAATA 3331
                           -i i   iviv    i--- v  ?      vi i   iv    i    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_103022861_   3332 TGTATTTCTCAAAAGAAGACATACAAATGACAAACAAGCATATGAAAAGA 3381
                         vii       v        i         i v  i     i         
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_103022861_   3382 CATACAACATCACTGATCAT 3401
                         iiiv        ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (156 / 90)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.25 (27 / 12)  


3138 26.88 1.00 0.55  chr1_103105923_103112190.rev     4874  5777 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_103105923_   4874 TGGAAGAACATTCCATGCAAATGGGTAGGAAGAATCAATATCATGAAAAT 4923
                              ii i  i     ivv    i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_103105923_   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4973
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_103105923_   4974 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5020
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_103105923_   5021 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5070
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_103105923_   5071 AAACAAAGCTGGAGGCATTACACTACCTGACTTCAAACTATACTACAAGG 5120
                         i       i      vv i     v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_103105923_   5121 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5170
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_103105923_   5171 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5218
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_103105923_   5219 TATCTGTTCTTTGACAAACCTGAGAAAAACAAACAATGGGGAAAGGATTC 5268
                         i vi  v i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_103105923_   5269 CCTATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGTAGAAAGC 5318
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_103105923_   5319 TGAAAATGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5368
                             iv    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_103105923_   5369 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAA 5418
                           i ?    i    i  v   v       i      vi i   i      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_103105923_   5419 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5468
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_103105923_   5469 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5518
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_103105923_   5519 ATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTACCGTCAGAGTGAA 5568
                           i   v v  i i   i  ii vv    iv v    i ivv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_103105923_   5569 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5618
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_103105923_   5619 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5668
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_103105923_   5669 AAAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5714
                           i    ----   v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_103105923_   5715 CTCAAAAGAAGACATCTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5764
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_103105923_   5765 CATCACTGGCCAT 5777
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3167 27.72 0.33 0.44  chr1_103223433_103229827.rev     4996  5904 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_103223433_   4996 TGGAAGAACATTCCATGCTCATGGGTAGGAAAAATCAATATCGTGAAATT 5045
                              ii i  i     i      i v    i v i     i  v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_103223433_   5046 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCGTCCCCATTGGGC 5095
                            v     v     iv i  i           i  vi    i  iiiiv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_103223433_   5096 TACCAATGACTTTCTACACAGAATTGGAAGAAAACT-ACTTTAAAGTTCA 5144
                          v   iivi i  i vii     v v  v--  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chr1_103223433_   5145 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCCAAGCCAAAAT 5194
                                viiv  ii  v  v v  vi    iv     iii ivv i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_103223433_   5195 AACAAAGCTGGAGGCATCCCACTACCTGACTTCAAACTATACTACAAGGC 5244
                                i      vv  v    v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_103223433_   5245 TACAGTAACCAAAACAACATGGTACTTGTACCAAAATAGAGATATAGACC 5294
                                 i   i   iii       v i iv ii     v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_103223433_   5295 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAGCT 5342
                                i    i--    i  --        vv  ii i  i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_103223433_   5343 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5392
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_103223433_   5393 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5442
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_103223433_   5443 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5492
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_103223433_   5493 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5542
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_103223433_   5543 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAA 5592
                         v    ?i v viv   iv   v v  vvii     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_103223433_   5593 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5642
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_103223433_   5643 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5692
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_103223433_   5693 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTATTCATCTGACAA 5742
                           i     i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_103223433_   5743 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5792
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_103223433_   5793 AAACTAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5842
                          i  v  i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_103223433_   5843 TCAAAACAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGTTCATA 5892
                           v   v    i  vi viii     v  i          i   i   vv
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_103223433_   5893 ATCACTGGCCAT 5904
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.75 (7 / 4)  


2664 27.72 2.58 1.01  chr1_103237962_103242041     2697  3587 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_103237962_   2697 AAAAATATTCTATGTTCATGGATAGAATGACTCAATACTGTCAAGATGTC 2746
                            i    i i            v i v    i    i   i      v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_103237962_   2747 AGTTCTCCTCAACTTGATCTATAGATTCAATACACTCACAATTAATTTCC 2796
                          i v    i   v        i        ii  v  v v  i  vv   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_103237962_   2797 CAGCATGT-TATTTTGTGGATCTTTCCAAACATATTCCAAA-TTCATAAG 2844
                             -  i- v     ii  vv  vv   i vv  i i   -      v 
  L1M4_orf2#LINE/    104 CAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_103237962_   2845 AAGA---AAAACATCCAGAATAGTCAATTAACTCAATATTAAAGGTAAAG 2891
                         i i ---  iiv i         i   --   --   v  i  iivi   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAA--AAC--AATCTTGAAAAAGAAG 198

  chr1_103237962_   2892 AACAAAGACAGAGAACTGACATTATCTGACTTTAAGACTTAATATAATAT 2941
                                vii   i   v   i vi ii i  i  i     v  i  vii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_103237962_   2942 TACAATAATGAATACAACGTAGTATTGGTGGAAGAACTGATAAGTAGATC 2991
                             i    v  v   ii  i   i   iiv   i iv  i vi      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_103237962_   2992 AATGGAATAGAATAAAGATCCTAGAAAAAGATCCATATAAATATACTAAA 3041
                                      vi   vi i     v i i     i vv   iv v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_103237962_   3042 CTGATCTTTGACAAAAGGAGCAAATGAA-ATACAATGGAGCAATGATAAT 3090
                         i    i  i     i-  v  v  -  v-  v      i v  vi   i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAG-GGTGCCAA-GACCATTCAATGGGGAAAGAATAGT 396

  chr1_103237962_   3091 CTTTTCAACTAATAGTGCTGGAACAACTGGACAGCCACATGCAAAAAAAT 3140
                                  v   i       i         i ?            i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_103237962_   3141 --ATCTAAATACAAACCTTAAATTGTTCAGAAAAATTAAGTCATAATGGT 3188
                         -- vi ii iv vv    i v iii vi v         v   v     v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_103237962_   3189 TCA------TAAATGTAAAACACAAAACCATGAAACTCCTAGAAGACAAT 3232
                            ------         i vvi     i  i      i       v  i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_103237962_   3233 ATAGGAGAAAACCTAAATAACCTTGGGTATGGTGATGACTCTTCAGACAC 3282
                              ? v   i  vvi i         vv  ii   ii ii i   i i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_103237962_   3283 AACACCAAAGATATATTCCATGAAAGAATTTATTGATAATCTAGGCTTTA 3332
                         i        iii i vv v ii      vvv  v     vi i i   i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_103237962_   3333 TTAAAATTTAAAACTTCTATTCTG-AAAAGACAATATCAAGAGAATCAGA 3381
                          i      v       i i v  v-   i    v        i i --  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT--GA 694

  chr1_103237962_   3382 AAATACA--CCACACAGCAGGTGCATGTGTTTGCAAAAGACATACCTGAT 3429
                            v   --     v iii  v v vi i        vv i   i     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_103237962_   3430 AAAGGACTGTTATCCAAAACATACAAAAAGTTC--AATATTCAACAATAA 3477
                           i     vv      i  i   i   i ii  -- vv i    i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_103237962_   3478 AAAAGCTAACAATCTGACTTAAAAATGCACAAATATGTTGAA----CACC 3523
                            ii v  i  i ii i ?       vi    vivv     ----  ii
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_103237962_   3524 TCAACAAGGAAGATATACAGATGGAAAGTAAGCCTATGAAAATATGTTCA 3573
                           vv   i           i    vv i     vi       v   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_103237962_   3574 ACATCATATGTCAT 3587
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 2.00 (32 / 16)  


2112 27.12 4.52 2.49  chr1_103243719_103247891     2796  3680 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_103243719_   2796 AGTTATATTATGTACAGGAAATAGAAAACTCCATGATTTTTAAAAATTTC 2845
                           v   vii    v  v i v i   i   iv  -   v    i - vv 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAAT-ATTGTTAAGA-TGGC 53

  chr1_103243719_   2846 AATTGTCTTCATTATGATCTGTAGGTTAAATGAAATCCCCATTAAAACCA 2895
                            vv  ii  vvv      ii  i  v  i v      i  i    i v
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_103243719_   2896 CAACT-----TCTTGTAGAAGTTAATAAGCTTATTCTAACATGTGTGTAG 2940
                           i  ----- i   i    i  i i     v  i    v  vii i i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_103243719_   2941 AAATGAAAATGACCCAAAATTGCTACAACAATGTTTTACAAAGAATAA-A 2989
                              v  iv      i   v  i v      -i  v v      v  - 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAACA 202

  chr1_103243719_   2990 AAGTAGGAGTATTTAC-CCACATGATTTTAAAATGTTTTCTAAAACTACA 3038
                             v    v i i  - iv vii    i    iv vi vi   i     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_103243719_   3039 GTAATCAAGATATTATGGTAGTAGTAAAAAAA-------ATGAATAAAT- 3080
                                   i v i     v i i v  ii -------  ii  v   -
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_103243719_   3081 -AATAAGGTAGAGAGTTCAGTAATAGGTGCACTA-ATTGGTAGTCAATTA 3128
                         -    iii v      i   v    iiiv  -  -   vi i       i
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTATGGTCAATTG 351

  chr1_103243719_   3129 ATTTCTGATTTAAAGA--CCAAGGCAATATAAATCATGAAAAGAA-AGTC 3175
                             ii  i--  i i--     i v  - v   vi- i      -    
  L1M4_orf2#LINE/    352 ATTTTCGAC--AAGGGTGCCAAGACCAT-TCAATGG-GGAAAGAATAGTC 397

  chr1_103243719_   3176 GTTTCAGAAAAATG-TGCTGAATGAACTGGATATGATTATGTAGAAAACA 3224
                         v     - v     -     iivv         ?--ii ii iv    v 
  L1M4_orf2#LINE/    398 TTTTCA-ACAAATGGTGCTGGGACAACTGGATAK--CCACATGCAAAAGA 444

  chr1_103243719_   3225 GTGAACATTGACCTTTACCTTACATCATACACAAATATTAACTCAAAATG 3274
                         i    vv v    ii     i   i    i     v              
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_103243719_   3275 GGTCAT-GACCCATGTGCAAATCCTGAAACAACAACGTTCTGATACTAAA 3323
                          i   ?-    i vi  i  ivv  i    v i  vii   v v vv   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_103243719_   3324 A-ATAGAAGAAAATCTTTGTGATCTTGGA----GTAAAAGTTTCTTAGA- 3367
                          -    i? v       i    i     i---- i  vi          -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_103243719_   3368 ---ACACAAAGAGTGTCA--AACATAACAACAAAATTGATAAATTAAACT 3412
                         ---    v  i  iiiv --    v  v  -     v        ii   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAA-AAAATAGATAAATTGGACT 643

  chr1_103243719_   3413 TTATCAAAATTAAAAGCATTTACACTTGGAAAGACACCAATAAGAAAACA 3462
                          i             i v   iii   vi  i     i vi      iii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_103243719_   3463 AAAAAAAGGCAAGTCACATACTGGAA-AAAATATTTGCAAA-CATATATC 3510
                             i ---   vi    v v   i -              -        
  L1M4_orf2#LINE/    694 AAAAGA---CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_103243719_   3511 AGACAAAAAATCTTTATGCAGGATAAAGTTTTATATA---CTCTTAAAAC 3557
                         v  i  iii ii v   v   i   ------    v ---      v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATA------TATAAAGAACTCTTACAAC 784

  chr1_103243719_   3558 TCCTTAA-ACTAAAACAAACAGCTCAATTTTTTAAATGGGCAAAAAATTT 3606
                           vv   - vv  i     i i i     ?vv-           ii    
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTT 833

  chr1_103243719_   3607 GAAAAGACACCTCACAAAACAATATGCATAAATGGCCCACAAGAACCTGG 3656
                            v     ii  v v   v  v  ii i        v i   v  v  i
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_103243719_   3657 CAAAATGC-AGACATCATCAGTCAA 3680
                         v  i    -vi      ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.04 (32 / 903), avg. gap size = 1.94 (62 / 32)  


3024 19.76 5.06 6.14  chr1_103298879_103300700      500  1329 (493)    L1M4_orf2#LINE/L1       88   908 (0)  

  chr1_103298879_    500 ATCCCTGTCCAAATTCCAATGGCCTCTTTTGCAGAAATGGAAAGGTTGGT 549
                               i  v    i   iiv    i            v  v i i  i 
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chr1_103298879_    550 ACTCGGATTTCATACAGAACTGCAAGGGGTTTTAAATAGCCAAAACAATA 599
                         v  vii   -    ii   v        iiiivi               v
  L1M4_orf2#LINE/    138 CCTAAAATT-CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_103298879_    600 TGGAAAAAG-----CAGTGTTGGAGGGCTCAAAATCTTCCCAACTTCAGA 644
                          v       -----  iv        i    v --        i    i 
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACA--CTTCCCAATTTCAAA 234

  chr1_103298879_    645 ACTTGCTA-------------ATCAAAACAGTGTGATATT---------- 671
                             i   -------------     i        i  i ----------
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_103298879_    672 -AGACATATTGATCAATGGAATAAAATTGATCATCAAGAAACTGATCCAT 720
                         -        v             i      vvi  v     ivi i    
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_103298879_    721 ATATTTTATAAACAGTTAATTTT-GACAAGGATGACAAGATCATTCATTA 769
                          i    -  iiv  i  i     -       i  v     i      v i
  L1M4_orf2#LINE/    335 ACATTT-ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_103298879_    770 GGGAAAAAGTACTATCTTCAACAAATGGTGCTGAAATGATTGGATATCCA 819
                               i i  v v i                 ii ii i      ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_103298879_    820 TGTGCAAAAGAATGAAATTGGATTCTTACCTCACATCATATGCTAACATT 869
                         ii              i     ii i         i     i v  v   
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_103298879_    870 AACTTGAAATGGATCA-AG---TAAATATAACAGCTAAAATAATAAAAAT 915
                             ii          -  ---     i   v        iv      -i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-C 532

  chr1_103298879_    916 TCTTAGAAGAAAACATAAGGGTAGG-CTTCAGGATCTTGAATTTGCCAAG 964
                                          i ?   ii-    iv  i    ii  v v   v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_103298879_    965 GCATTCTTAGGTATGGCACCAAAACCAGGAACAGCAAAACAAAAAATAAA 1014
                          vv       i    i        v  vi i  i     v        i 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_103298879_   1015 TAAATATGACTTTGTCAAAAT-AAAAAATTTTGTTTATCAAAAGATACAT 1063
                              vv     ii       -     v      viv     i  i  --
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC-- 680

  chr1_103298879_   1064 TATCAAGAAAGTGAAAAGACGACCTACAAAATAAGCAAAAATATCTGCAA 1113
                                             i   i   i   ii vi       i     
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_103298879_   1114 ATCATGTATCTGATTGTCATCTAATAT--AGAATATATAAAGAGCTCTTA 1161
                              i        vivviv  vi   --              i      
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_103298879_   1162 CA-TTCAACAACAAA--GATAAACAACCCAGTTTTCACCCATTTTGAATG 1208
                           -i    i  i   --  i   i      --------------------
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCA-------------------- 810

  chr1_103298879_   1209 GGCAACCCATTTTAAAACAACCAATTTTAAAATGGACAAATAACCTGAGT 1258
                         -----------------------   ?v       i    vi ii   i 
  L1M4_orf2#LINE/    811 -----------------------ATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_103298879_   1259 ATACGTTTCTCTTAAGAATAGGTACAAATGGCCAAGAAGAACA-AATAAG 1307
                          v  i      iv     v vi             v   v   -i v   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_103298879_   1308 TATGTCCAACATTATTGACATT 1329
                         -   ii      i ????????
  L1M4_orf2#LINE/    888 -ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (106 / 55)
Gap_init rate = 0.02 (19 / 821), avg. gap size = 4.89 (93 / 19)  


 276 20.59 0.00 0.00  chr1_103310308_103312753      445   512 (1934)  C L1M4_orf2#LINE/L1   (0)   908   841  

C chr1_103310308_    512 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATG 463
                           i     v        i  vi viii     v ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

C chr1_103310308_    462 CTCATCATCACTAGCCAT 445
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.00 (0 / 0)  

2791 28.95 0.58 0.58  chr1_103310308_103312753     1081  1940 (506)    L1M4_orf2#LINE/L1        1   860 (48)  

  chr1_103310308_   1081 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1130
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_103310308_   1131 GGCCATACTGCCCAAGGTAATTCATAGATTCAATGCCATCACCACCAAGC 1180
                            v     v     iv i  ii i        i  v   v i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_103310308_   1181 TACCAATGACTTTCTTCACAGAA--TGGGAAAAAAATACTTTAAAGTTCA 1228
                          v   iivi i  i  ii     --  iv  ivvi  v  --   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chr1_103310308_   1229 TATGGAACCAAAAAAAGGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1278
                                viiv  iiiiv  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_103310308_   1279 AACAAAACTGGAGGCATCACGCTACCTGAATTCAAACTATACTACAAGGC 1328
                               ii      vv    i  v  ii v      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_103310308_   1329 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGACC 1378
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_103310308_   1379 AATTGAACAGAAC--AGAACCCTCAGAAATAATGCCGCATATCTACAACT 1426
                            v   i    i--   ii  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_103310308_   1427 ATCTGATCTTTGACAAATCTGACAAAAACAGGAAATGGGGAAAGGATTCT 1476
                          vi    i  i     ivv  v   i v  vvv           i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_103310308_   1477 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAAGCT 1526
                           v  i  i              v      v  ?   i i i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_103310308_   1527 GAAACTGGATGCCTTCCTTACACCTAATACAAAAATCAATTCAAGATGGA 1576
                            ii    iv   v   i     vv          i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_103310308_   1577 TTAAAGACTTAAATGTTGGACCTAAAACCATAAAAACCACAGAAGAAAAC 1626
                          i ?    i       vi  v       i      vi vi          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_103310308_   1627 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1675
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_103310308_   1676 AAACAGCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCTGATTTA 1725
                         vi   v        vvi          vv     v  i    iv  i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_103310308_   1726 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1775
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_103310308_   1776 CAGGCAACCTACAAAATGGGAGAGAATTTTTGCAATCTACTCATCTGACA 1825
                         v  i     i   i         i   v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_103310308_   1826 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAGTTTACAAGAAA 1875
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_103310308_   1876 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGATACCT 1925
                           i     i     v  i?    i    ii      v    i   i ii 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_103310308_   1926 GTCAAAAGAAGACAT 1940
                         v  v        i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATAT 860

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (6 / 860), avg. gap size = 1.67 (10 / 6)  

1189 28.13 0.95 0.47  chr1_103310308_103312753     2022  2444 (2)  C L1M4_orf2#LINE/L1   (0)   908   484  

C chr1_103310308_   2444 AACTCAAGTTGGATTAAGGACTTAAATCTAAGACATGAAATAGATAAAAT 2395
                                iv     i ?i   i     v     vv i   i-v      i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC-TATAAAAC 532

C chr1_103310308_   2394 TCT-AGAAGATAACATTTGAAAAACCCTTTTAGACATTGGCTTAGGCAAG 2346
                            -      v     vv ?iv  vi   ivv   v    v        v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

C chr1_103310308_   2345 GATTTCATGACCAAGAACA-CAAAAGCAAATGCAATAAAAACAAAGATAA 2297
                          i    v iivi v -   -        v v    i    iv   i   i
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATG-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

C chr1_103310308_   2296 ACAGGTGGGACTTAATTAAACTACAGAGATTTTCCACAGCAAAAGGAACA 2247
                          i ii v      v  i   v vv i iv    vii vv    i iv  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

C chr1_103310308_   2246 GTTGGCAGAGTAAACAGACAACCCACGGAGTGGGAGAAAATCTTCACAAT 2197
                         i iiiv i   i  v           i  i           v  ii   v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

C chr1_103310308_   2196 CTATACACTTGACAAATAACTAATTTCCAGAATCTACAATGAACTCAAAC 2147
                         ii   i ii   i  ivi   vi v        v  i  v      vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

C chr1_103310308_   2146 AAATCAGTAAGAAGAAAACAATCAATTCCATCAAAAAGTGGGCTATGAAA 2097
                           v   i   v  i  i    vi  ii v  i?    i     v v i v
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

C chr1_103310308_   2096 ATGAATAGACAATTCTCAAAAGAA--TATACAAATGGCCAACAAACTTAG 2049
                         v          v     v      --               i  i vi v
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

C chr1_103310308_   2048 GAAAAAATGCTCAACATCACTAATGAT 2022
                              i             ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (61 / 55)
Gap_init rate = 0.01 (5 / 425), avg. gap size = 1.20 (6 / 5)  


2769 26.41 1.63 2.93  chr1_103315909_103319190     1870  2789 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_103315909_   1870 TGAAAGAAGATTTCATGCTCATGGATAGGAAGAATTAATATCCTTAAAAT 1919
                           i  ii v  ii    i        v      v       iv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_103315909_   1920 GTCCATACTGCCTAAAGTAATCTATAGATTCAAAGCTCTTCCTATCAAAC 1969
                          v v     v  i   v i     i        v  vv i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_103315909_   1970 TACCAATGACACTCTTCACAGAACT--ACAAAAAAAAAAAAAACT-ATTC 2016
                          v   iivi vi i  ii     v --    i-----------  -  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----------CTGATCC 139

  chr1_103315909_   2017 TAAAATTCATATGGAACCAAAAAAAGAAAGAG-CACA-AATAGCCAAGTC 2064
                                         ------- v v   i - v  -         iv 
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAA-------ATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr1_103315909_   2065 AGTCCTAAGAAATGGTGTCACAGCTGTAGGAATCACATTGCCTGACTTCA 2114
                          i  i i i   viiviv  v  i  v    v     i v  ii i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_103315909_   2115 AACTGAACTACAAGGCAACAGTAACCAAAACAGCATGGTACTGGTACAAA 2164
                           vivv       i  v       i   i    ii         i i  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_103315909_   2165 AACAGACACATAGACCAATGGAACAGAATGGAGAACCTTAAAATTAATCC 2214
                         i i     i     i        i     v    ii ivi    v  i  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_103315909_   2215 ACACACCTACAACCATCTGATCTTTGACAAAACTGATAAAAATAAGCAAC 2264
                          i   ii  iiii  vi    i  i     iiv  vi  i vi vv   i
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_103315909_   2265 AGGGAAAGAA--GTTCCTATTCAATAAATGCTGTTGGGATAACTGGCTAG 2312
                         i         --  --  v     i     v  i     i      v  ?
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGT--CTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_103315909_   2313 CTATATGCAGGAGATTGAACCTGGTCCCTTCCTTTAAAACTTATGCAAAA 2362
                          i i     ii   v    vi   v   i v i i v v v   i     
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_103315909_   2363 ATCAACTCAATATGGATCAACGGCTTAATTATAAAATCTAATCCTATAAA 2412
                           i       v        ?v i i   v i   i v    vv       
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_103315909_   2413 AACCTTGGAAGATAACCTAGG---AAATACCATTTTG-GACATAGGAACT 2458
                          vi   i     v   v    ---    ----i  i -   v v  iviv
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAAT----CTTCGTGACCTTGGGTTA 576

  chr1_103315909_   2459 GGCAAAGATTTCAT-GATGAAAATGCCAAAAGCAATTGCAACACAAGCAA 2507
                              v i    v -   - vi ii         vvv      v   v  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_103315909_   2508 AAATGGGCAAATGCAACTGAATTAAACTAAAGAGCTTCTGCACAGCAAAA 2557
                             i ii    vvi   vv  i   v v  i i   i  ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_103315909_   2558 GAAACTATCAGCAGAGTAAAATAGGCAACTTGAAGAATGGGAGAAAATAT 2607
                           v       iv i   i   -  i    iiiv                 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAA-AGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_103315909_   2608 TTGCAAATTATATATCTGACCAAGGTGTAATATCCAGAATCTACAAGGAA 2657
                                 i          iv i  vv vi          v  i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_103315909_   2658 CTTAAACAAA-CATACAAGCAATAAATAAACAACCCA-TTCAAAAGTAGA 2705
                           ivv    v-  - i  vv  v i i   i      -  ?    i i i
  L1M4_orf2#LINE/    775 CTCTTACAACTCA-ATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_103315909_   2706 CAAAGAGCATGAACAGAAACTTTTCCAAAGAAGACATACATGTGGTAAAG 2755
                              iiiv    i   v i  i           i     vi   iv  v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_103315909_   2756 AAACATATGAAAA-ATGCTCAATATCACGAATCAT 2789
                           i  i       -        i    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.33 (42 / 18)  


2256 27.18 1.57 1.72  chr1_103330389_103332863      601  1299 (1176)    L1M4_orf2#LINE/L1        1   698 (210)  

  chr1_103330389_    601 TAGAATGATTGCTTGTGTTCATTATTAACATTGTAATATAATTAATATTA 650
                          i   v   vv iii       vi-----    v  v i--        i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGG-----ATTGGAAGAC--TTAATATTG 43

  chr1_103330389_    651 TAAAAATGGCCATTCCACTCAAAAAGAACTATAGACTCCGTGCAATCCTT 700
                          v  i     v  v iv i    vv  v   i   i  vii       i 
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr1_103330389_    701 ATCAAAATCCCAATGGCATTCTTCAGAGAAAT-AAGAAAAAAATTCCAAA 749
                                     iiv  v  i  iiv      -i v  ivvi  i i   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_103330389_    750 ATTTGTATTGAATCAGGAAAGATTCAAGGTAGCCAAAGCAATCTTGAGAA 799
                            ii   v   viivi ii  ii  iii        i         i  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_103330389_    800 AGAAGAACAAATCTGGAGTAATCACACTTTCTAATTTCAAAGTGCATTAC 849
                                    vi     v v        i i         iivi i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_103330389_    850 AATGCTACAGTAATCAAACTAGTGTGGTACTTGCATAAAAACAGACACAT 899
                           v              ivi           v      ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_103330389_    900 AGACCATTGCAATAGAATGAACAACTCAGAAATAAACTCAGGCGTATATG 949
                            i  v  v        vi v iii           i  vi i v    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_103330389_    950 GTCAACTAATATTTGACAAGAGTGTCAA--CAATACAGAAAATGGGGACA 997
                              i i  v  i      i   i   -- v  v  ----       v 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA----ATGGGGAAA 389

  chr1_103330389_    998 TGATAATCTCTTCAATAAATGGTGTTGGGA-AATTGGCTATCTTCATTAA 1046
                         vi   i   i     i        i     -  i   v  ? iv   vv 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_103330389_   1047 AATAAATAAAATTAGATGGCTATTGTACATCACTCATAAAAATTAACTTG 1096
                           vi   i  i  i  ivv   iivi   i  ivi i           ii
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_103330389_   1097 AAATAGATTA--AACTTAAATGCAAGCTCTGAAACTATAAAAG-CAGGGA 1143
                             i   i --i  i      i   vv  i           v- vvi  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_103330389_   1144 AAAAGAACATAAGGTAAAAGCTTT-TGACAATGCTCTTTGCAATGACTTT 1192
                          i  -      i ?vv   v   i-    vv  vvi vv      ii  i
  L1M4_orf2#LINE/    540 AGAA-AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_103330389_   1193 TTGGATACAACACCAAAAGCACAAGAAACAAAAGCAAAAATAAGTAAGTG 1242
                           i    ii                v        v       ii   i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_103330389_   1243 GGACTATATCAAG-TTAAAG-TTTCTGTGAGGCAAAGAA-ACAATCAGCT 1289
                              vi     i-     i-i  i    vvv     i -  v    ivv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_103330389_   1290 AAATGAAAAG 1299
                           i       
  L1M4_orf2#LINE/    689 AAGTGAAAAG 698

Transitions / transversions = 1.54 (114 / 74)
Gap_init rate = 0.02 (13 / 698), avg. gap size = 1.77 (23 / 13)  

 657 17.84 0.00 12.68  chr1_103330389_103332863     1776  1988 (487)    L1M4_orf2#LINE/L1      723   908 (0)  

  chr1_103330389_   1776 ATCTGCAAGCCATATGTCCAATAAGGTTTTAATATCCAGAATATGTAAGA 1825
                           i     ii     i  ii      vvi vi            i   ii
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_103330389_   1826 AACTCATACAACTCAATAGCAAAAATTAGTCAAACAAACAAATATCAAAA 1875
                              v            ii     ------------------------i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAA------------------------G 798

  chr1_103330389_   1876 ACAAATAATTCAACTAAAAACGGGAGAAAGCGCTTGAATAGACATTTATC 1925
                                 ii   i ?    vv  iv    vii              v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_103330389_   1926 CAAAGTAAGTATACAAACGACCAACATGTACATGAAAAAGATGCTCAACT 1975
                              v ii        i i    i v i         -          -
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAAC- 896

  chr1_103330389_   1976 AATCACCAGGAAA 1988
                         -    ????????
  L1M4_orf2#LINE/    897 -ATCAZZZZZZZZ 908

Transitions / transversions = 2.36 (26 / 11)
Gap_init rate = 0.02 (3 / 186), avg. gap size = 9.00 (27 / 3)  


2842 27.97 1.44 0.67  chr1_103506294_103512210.rev     4526  5426 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_103506294_   4526 TGGAAA-ACACTCTCTACACTTAAGAATAGAGAGAATCAGTATCATTTAA 4574
                               - i -  i - iii i v i  v ii   v i i   ii  v i
  L1M4_orf2#LINE/      1 TGGAAAGATA-TCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_103506294_   4575 GTGGCCATATTGCCCAAAGCAATTTATAAACTCAATGTTGTTCCCATTAA 4624
                         i    v   i v      vii  i  i i i    i ivi i  i  i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_103506294_   4625 ACTACTA-CTGACATTTGTGCAGAACTAGGAAAATCTATT-TAAAATTTA 4672
                          v v i -   v v   v       v v iv  iiiv  i-       i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_103506294_   4673 TATAGAACCTAAAAAATGCCCA-AATAGCCAAGGCAATCCTAAGCAAATA 4721
                            i   v- iv  iivi    -         ii     i i iv  iv 
  L1M4_orf2#LINE/    149 TATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_103506294_   4722 GAACAAAGTTGGAGGAATCATGCTACCTGACTTCAAACTATACTACATGG 4771
                                         v   ii  v  ii i      viv       vi 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_103506294_   4772 CTACAGTAACCAAAACAGCATGATACTGGTACAAGAACAGGTACATAGAC 4821
                                  i   i    ii  i      i i   i i  ii i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_103506294_   4822 AAATGGAACAGAATAGAGAACACAGAAATAAGACCATACACCTACAACTA 4871
                         v       i     v    iiv         iv       ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_103506294_   4872 TCTGATCTTTGAAAAACCTGACAAAAACAAGCAATAGGGAAACAATTCCC 4921
                         vi    i  i  v  ivv  v   i v  vv    i      v   vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_103506294_   4922 TATTTAATAAATGGTGCTAGGAGAACTGGCTAGCCATATGCAGAAAACTG 4971
                          v  i  i          i   v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_103506294_   4972 AAACTGGAATTCTTCCTTACACCATATACATAAATTAACTCTAGATGGAT 5021
                           ii    vii  v   i            v          v i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_103506294_   5022 TAAAGACTTAAATTTAAAACTCCAAACTATGAAAACCCTGGAAGACAATC 5071
                         i ?    i     v   i viiv       i   vi i i     v  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_103506294_   5072 TAGGCA-ATATCATTCAGGACATAGGCACAGGCAAAGATTTTATG---AT 5117
                             ?i- v   -   iv   v v  vvi      v i   iv i---  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_103506294_   5118 GACACCCAAAGCAATCGCAGAAAAAGCAAAAAATTGACAAATGGGATCTA 5167
                               v      vvv   iv     -       v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTC 645

  chr1_103506294_   5168 ATTAAACTAAATAGCTTCTGCATAGCAAAAGAAACTATCAACAGAGTAAA 5217
                           i   v v  v i   i  iiivv    i  v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_103506294_   5218 CAGACAACCTACTGAATGGGAGAAAATTTTTGCACACTATGCATCTGACA 5267
                         v        i  v              v      v ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_103506294_   5268 AAAGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAA 5317
                          ii v  vi       v  v     i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_103506294_   5318 AAAACAA----CCCCATTAAAAAGTGGGCAAAAGACT-GAACAGACACTT 5362
                           i    ----   v   ?    i        i  i -   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_103506294_   5363 CTCAAAAGAAGACATACATGCAGCCAACAAGCATATGAAAAAAAATCTCA 5412
                            v        i     viii     i     i       i vi-    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG-CTCA 894

  chr1_103506294_   5413 ACATCACTCATCAT 5426
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (152 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.36 (19 / 14)  


3096 27.18 0.77 0.66  chr1_103631360_103637735     4979  5883 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_103631360_   4979 GAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAATGC 5028
                            ii i  i     i      i v      v i     ii v  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_103631360_   5029 CCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 5078
                          v     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_103631360_   5079 CCACAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 5126
                            vvvi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr1_103631360_   5127 TGGAACAAAAAAGGGGCC--GCATTGCCAAGTCAATCCTAAGCCAAAAGA 5174
                              - viv     i  -- v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_103631360_   5175 ACAACGCCAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5224
                             v iii    vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_103631360_   5225 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAATAGAGATATAGACCA 5274
                                i   i    ii         i iv ii     v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_103631360_   5275 ATGGAACAGAGC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACTA 5322
                               i   ii--    i  --        vv iii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_103631360_   5323 CCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAACGATTCCC 5372
                         vi    i  i     ivv  v   i v  vv           vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_103631360_   5373 TATTTAATAAATGGTGCTGGGAAAACTGGCTACCCATACGTAGAAAGCTG 5422
                          v  i  i              v      v  ?   i i i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_103631360_   5423 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAA 5472
                           ii    i    v   i     v              i    i     v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_103631360_   5473 TAAAGACTTACGTGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5522
                         i ?    i  vi   v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_103631360_   5523 TAGGCGTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5572
                             ?  v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_103631360_   5573 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT-AT 5621
                                     vvi          vv     v  i    v   ii -  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_103631360_   5622 TTACACTAAAAAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5671
                         iv v i      -   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_103631360_   5672 AGGCAACCTACACAATTGGAGAAAATTTTTACAACCTATGCATCTGACAA 5721
                           i     i   v   v         v   i   vii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_103631360_   5722 AGGGCTAATATTCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAG 5771
                         i  i  vi   i      v  i  v      vv    v iv i  v   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_103631360_   5772 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 5821
                          i     i     v  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_103631360_   5822 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAGAATGCTCACC 5871
                           v        i  vi viii     v  i         ii       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_103631360_   5872 ATCACTGGCCAT 5883
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 1.44 (13 / 9)  


2842 27.97 1.44 0.67  chr1_103646027_103651942.rev     4525  5425 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_103646027_   4525 TGGAAA-ACACTCTCTACACTTAAGAATAGAGAGAATCAGTATCATTTAA 4573
                               - i -  i - iii i v i  v ii   v i i   ii  v i
  L1M4_orf2#LINE/      1 TGGAAAGATA-TCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_103646027_   4574 GTGGCCATATTGCCCAAAGCAATTTATAAACTCAATGTTGTTCCCATTAA 4623
                         i    v   i v      vii  i  i i i    i ivi i  i  i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_103646027_   4624 ACTACTA-CTGACATTTGTGCAGAACTAGGAAAATCTATT-TAAAATTTA 4671
                          v v i -   v v   v       v v iv  iiiv  i-       i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_103646027_   4672 TATAGAACCTAAAAAATGCCCA-AATAGCCAAGGCAATCCTAAGCAAATA 4720
                            i   v- iv  iivi    -         ii     i i iv  iv 
  L1M4_orf2#LINE/    149 TATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_103646027_   4721 GAACAAAGTTGGAGGAATCATGCTACCTGACTTCAAACTATACTACATGG 4770
                                         v   ii  v  ii i      viv       vi 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_103646027_   4771 CTACAGTAACCAAAACAGCATGATACTGGTACAAGAACAGGTACATAGAC 4820
                                  i   i    ii  i      i i   i i  ii i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_103646027_   4821 AAATGGAACAGAATAGAGAACACAGAAATAAGACCATACACCTACAACTA 4870
                         v       i     v    iiv         iv       ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_103646027_   4871 TCTGATCTTTGAAAAACCTGACAAAAACAAGCAATAGGGAAACAATTCCC 4920
                         vi    i  i  v  ivv  v   i v  vv    i      v   vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_103646027_   4921 TATTTAATAAATGGTGCTAGGAGAACTGGCTAGCCATATGCAGAAAACTG 4970
                          v  i  i          i   v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_103646027_   4971 AAACTGGAATTCTTCCTTACACCATATACATAAATTAACTCTAGATGGAT 5020
                           ii    vii  v   i            v          v i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_103646027_   5021 TAAAGACTTAAATTTAAAACTCCAAACTATGAAAACCCTGGAAGACAATC 5070
                         i ?    i     v   i viiv       i   vi i i     v  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_103646027_   5071 TAGGCA-ATATCATTCAGGACATAGGCACAGGCAAAGATTTTATG---AT 5116
                             ?i- v   -   iv   v v  vvi      v i   iv i---  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_103646027_   5117 GACACCCAAAGCAATCGCAGAAAAAGCAAAAAATTGACAAATGGGATCTA 5166
                               v      vvv   iv     -       v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTC 645

  chr1_103646027_   5167 ATTAAACTAAATAGCTTCTGCATAGCAAAAGAAACTATCAACAGAGTAAA 5216
                           i   v v  v i   i  iiivv    i  v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_103646027_   5217 CAGACAACCTACTGAATGGGAGAAAATTTTTGCACACTATGCATCTGACA 5266
                         v        i  v              v      v ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_103646027_   5267 AAAGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAA 5316
                          ii v  vi       v  v     i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_103646027_   5317 AAAACAA----CCCCATTAAAAAGTGGGCAAAAGACT-GAACAGACACTT 5361
                           i    ----   v   ?    i        i  i -   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_103646027_   5362 CTCAAAAGAAGACATACATGCAGCCAACAAGCATATGAAAAAAAATCTCA 5411
                            v        i     viii     i     i       i vi-    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG-CTCA 894

  chr1_103646027_   5412 ACATCACTCATCAT 5425
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (152 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.36 (19 / 14)  


3049 27.23 0.88 0.77  chr1_103737513_103741860     2949  3855 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_103737513_   2949 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2998
                               i i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_103737513_   2999 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3048
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_103737513_   3049 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3096
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_103737513_   3097 TATGGAACCAAAAAAGAGACC--GCATCACCACGTCAAACCTAAGCCAAA 3144
                                -- viv   i    -- v  vi   viv   v i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_103737513_   3145 AGAACAAAACTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 3194
                                 ii      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_103737513_   3195 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAA-AGAGATATAGA 3243
                                   i   i    ii         i iv ii -   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_103737513_   3244 CCAATGGAACAGAAC--AGAGCCCTCAGAAATTATGCCGCATATCTACAA 3291
                         i        i    i--    i  --      v vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_103737513_   3292 CTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 3341
                         ii vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_103737513_   3342 CCCTATTTAATAAATGGTTCTGGGAAACCTGGCTAGCCATATGTAGAAAG 3391
                         vi  v  i  i       v      v v    v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_103737513_   3392 CTGAAACTGGATCCCTTCCTTACACCTTATAGAAAAATTAATTCAAGATG 3441
                         v    ii    i    v   i     v    v         i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_103737513_   3442 GATTAGAGACTTAAATGTTAGACCTAAAACCTTAAAAACCCTAGAAGAAA 3491
                            i ?    i       v   v       iv     vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_103737513_   3492 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 3540
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_103737513_   3541 TAAAACACCAAAAGCAATGACAATAAAAGCCAAAATTGACAAATGGGATC 3590
                           vi            vvii   i     vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_103737513_   3591 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGCAACTACCATCAGTGTG 3640
                          v  i   v v  i i   i  ii vv    i vv    i  vv iv   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_103737513_   3641 AACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAATCTGCTCATCTGA 3690
                           v  iv    i                 v       viiiivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_103737513_   3691 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 3740
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_103737513_   3741 AAAAAACTAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 3790
                             i  v  i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_103737513_   3791 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 3840
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_103737513_   3841 ATCATCACTGGCCAT 3855
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2304 28.26 4.77 1.93  chr1_103859258_103861135      505  1385 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_103859258_    505 GAAAGACATTCTGTGTTCATCAATGTGAGAAATTAATATTGTCAAAATG- 553
                               i  i ii       vi  vv  ii v          i  i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_103859258_    554 C--TATTACACAAAGCAATCTACAGATTCAATGTAATCCCTATCAAAAGT 601
                          --  i v v    vii              i i              vi
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_103859258_    602 CCAA-TGGCATTTTTCCAGAAACAGA--AATAAATCCTAAAATTTGTATG 648
                            i-  v v     v      iv  -- iivi           ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_103859258_    649 AAATTACAAAAGACTATAATTACCCAAACTGATCTTGAGCAAGACGAACA 698
                         i  v i   ii   ivvi v  v     vii       iv    v     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_103859258_    699 AAGTAGGAGGTAC-CACACTTCTCACTTTCAAGTTATATTACTAAACTAC 747
                             v     -  -        i  v      iviv  i   v  i    
  L1M4_orf2#LINE/    203 AAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_103859258_    748 AGTAATATATATATATATATATGATACTGGTATGAAAACAGTCACATAGA 797
                               vv v i -----i i  i      i  i ii i  v  i     
  L1M4_orf2#LINE/    252 AGTAATCAAGACA-----GTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_103859258_    798 AGAATGGAGCAGAATAGAAAGCC------TACACCAATA------TCGTC 835
                         vv      ii     v  i  i ------  v   v   ------ v   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_103859258_    836 AAAGAATCTTCAATAACA-TGCCCAAAACACCTAATGGAGACAGGATAGT 884
                           vvi  i   i i  vi-    v i v  iii     i  v  i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_103859258_    885 CTCTTCAATAAATAGCGTTGGAATTATTGGAGGCCCACATGCAAAAGAAT 934
                           i     i    i i i   i iv i    vi?                
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_103859258_    935 GAAATTGGA-----GTGTTATGCTATGCACAGGAATAAATTGAAAATTGA 979
                            i     -----iiv i ii i  ii   ii   v  i v     v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_103859258_    980 --AAAGGAATTTAAACATAACATCTGAAACCAAAGAATCCCTAGAAGAAA 1027
                         -- ?  -- ii    ii   v v  i    i v i  ii i         
  L1M4_orf2#LINE/    497 TCAWAG--ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_103859258_   1028 ACA--GGGG-AAATCCTCCATAACATTGACCTTGGCA-TGATATTTTGGC 1073
                            --  ? -     i  -i i  v   ivi v    -  i v i  i v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_103859258_   1074 TATGAATCCCAATGTATAGACAAGATAAACAAAAATAAACACATACAACT 1123
                              vv  v  v i i ii   v v  iv       i i v  vvi   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_103859258_   1124 ACATCAAACTAAAAGATTGTGGCACAGTAAATAAATAAATAAATAAATAA 1173
                         v       v v   i i v v ii vvi   -----ii i --iv vi  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAA-----GGACA--CTATCAA 686

  chr1_103859258_   1174 ATAAATAAAAAGTCA-CCCATGGAATGGTAGAATGTACTTGAAAACAATA 1222
                         iv  i i     v  -    ii      v    vi  i   v   iv   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_103859258_   1223 TATCTGATAATGCATTAATATCTAAAACATATAAGAAACTC--------- 1263
                                   v v i vi    i i  i      ii     ---------
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_103859258_   1264 -ATAATCAGAAAAAAAGTAACCTGATTAAAACATGAGCAAGAGACCTGAA 1312
                         -     v i  i v  i     ii   ?   v   i    ii  ii    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_103859258_   1313 TAGACATTTTTTCAAAGGAAGATTTACACACGGCCAACACATGAATGAAG 1362
                                  i i     -     v    v i      i viiiv     i
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_103859258_   1363 AGGTGCACAAAATCACTAAACAT 1385
                           i   v   v    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (152 / 93)
Gap_init rate = 0.02 (22 / 906), avg. gap size = 2.68 (59 / 22)  


1957 29.93 4.37 2.80  chr1_103891558_103893474      533  1424 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_103891558_    533 GAAAGACTTTCTGTGTTCATCAATGGGAGAAATCAATACTGTCAAAATG- 581
                               iv i ii       vi  v   ii v i    i   i  i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_103891558_    582 C--TATTGGACAAAACAATCTACAGAT-AAATGTAATCCCTATCAAATGT 628
                          --  i vvv    vii          -v  i i             vvi
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_103891558_    629 CCAGCGGCATTTTTCACAGAAACAGA--AATAAATACTAAAATTTGTATG 676
                              v  v     ii      iv  -- iivi  v        ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_103891558_    677 AAATTACAAAAGACTATAAGTACCTAAAGTGATCTTGTGCAAGAAGAACA 726
                         i  v i   ii   ivvi i  v i   iii      viv          
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_103891558_    727 AA-CAGGAGGTAC-CACACTTCTCACTTTCAAGTTATATTACAAAACTAC 774
                           -iv     -  -        i  v      iviv  i      i    
  L1M4_orf2#LINE/    203 AAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_103891558_    775 AGCAAATTTTATATA------TACTGACATGAAAACAGTGACATAGAAGA 818
                           i  -- iv v i ------     i   i ii i  vv i     vv 
  L1M4_orf2#LINE/    252 AGTAA--TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_103891558_    819 ATGGAACAGAATAGAAAGCCTAGAAATAAACCTACACCAAGACGGTCAAA 868
                               i     v  i  i i           i i  vvvv i      v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_103891558_    869 AAATCTTCAATAACA-TGCCCAAAATACCTAATGGAGACAGGATAGTCTC 917
                         vi  i   i i  vi-    v i vi iii     i  v  i       i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_103891558_    918 TTCAATAAATAGCGTTTAGAAAAACTGCAGGCCCACATGCAAAATAATGA 967
                              i    i i i -i i v     v vi?            v     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_103891558_    968 AATTTGAC----AGTT-ATAATATGCACAGGAATAAATTGAACATTGA-- 1010
                          i  v   ---- vi - i vi  ii   ii   v  i v  v  v  --
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_103891558_   1011 AAAGGAATTTAAACTTAACATCTGAAACCAAAGAATCCCTAGAAGAAACC 1060
                          ?  -- ii    iv   v v  i    i v i  ii i         v 
  L1M4_orf2#LINE/    499 AWAG--ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_103891558_   1061 A--GGGG-AAATCCTCCTTAAGATTGACCTTGGCA-TGATTTTTTGGCTA 1106
                          --  ? -     i  v -i vv   ivi v    -  i   i  i v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_103891558_   1107 TGAATCTCAAAATATAGACAAGACAAACAAAAATAAACACATGGAACTAC 1156
                            vv iv   ii i ii   v v  iv       i i v  v i   v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_103891558_   1157 ACCAAAGTAAGAGGTTGCTGCACAGTAAAAAAAAAAATAATAATTAATTA 1206
                          i    i v i iii vi  ii vvi   ii v ----------------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA---------------- 679

  chr1_103891558_   1207 ATTAATTAATTAATTAAAAAGGTCACCCATGGAATGGTAGAAAATACTTG 1256
                         -i  - i  vv  v i     iiv     ii      v        i   
  L1M4_orf2#LINE/    680 -CTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_103891558_   1257 AAAACAATATATCTGATAATGGATTAATATCTGAAACAGATAAGAAACT- 1305
                         v   iv             v   i vi    iii  i v    ii    -
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_103891558_   1306 ---------AATAATCAGAAAA-AAAT--CCTGATTAGAACATGAGCAAG 1343
                         ---------      v i  i -    --  ii   ?i  v   i    i
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_103891558_   1344 AGACCTGAACAGACTTTTTTCCAAGGTAGACTTGCACATGGCCAACACAT 1393
                         i  ii    i    v   i     i v   iv i  v        i vii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_103891558_   1394 GAATGAAGAGGTGCACAAAATCACTAAACAA 1424
                         iv     i  i   v   v    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (164 / 99)
Gap_init rate = 0.03 (24 / 906), avg. gap size = 2.67 (64 / 24)  


2304 28.26 4.77 1.93  chr1_103927634_103929511.rev      507  1387 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_103927634_    507 GAAAGACATTCTGTGTTCATCAATGTGAGAAATTAATATTGTCAAAATG- 555
                               i  i ii       vi  vv  ii v          i  i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_103927634_    556 C--TATTACACAAAGCAATCTACAGATTCAATGTAATCCCTATCAAAAGT 603
                          --  i v v    vii              i i              vi
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_103927634_    604 CCAA-TGGCATTTTTCCAGAAACAGA--AATAAATCCTAAAATTTGTATG 650
                            i-  v v     v      iv  -- iivi           ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_103927634_    651 AAATTACAAAAGACTATAATTACCCAAACTGATCTTGAGCAAGACGAACA 700
                         i  v i   ii   ivvi v  v     vii       iv    v     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_103927634_    701 AAGTAGGAGGTAC-CACACTTCTCACTTTCAAGTTATATTACTAAACTAC 749
                             v     -  -        i  v      iviv  i   v  i    
  L1M4_orf2#LINE/    203 AAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_103927634_    750 AGTAATATATATATATATATATGATACTGGTATGAAAACAGTCACATAGA 799
                               vv v i -----i i  i      i  i ii i  v  i     
  L1M4_orf2#LINE/    252 AGTAATCAAGACA-----GTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_103927634_    800 AGAATGGAGCAGAATAGAAAGCC------TACACCAATA------TCGTC 837
                         vv      ii     v  i  i ------  v   v   ------ v   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_103927634_    838 AAAGAATCTTCAATAACA-TGCCCAAAACACCTAATGGAGACAGGATAGT 886
                           vvi  i   i i  vi-    v i v  iii     i  v  i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_103927634_    887 CTCTTCAATAAATAGCGTTGGAATTATTGGAGGCCCACATGCAAAAGAAT 936
                           i     i    i i i   i iv i    vi?                
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_103927634_    937 GAAATTGGA-----GTGTTATGCTATGCACAGGAATAAATTGAAAATTGA 981
                            i     -----iiv i ii i  ii   ii   v  i v     v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_103927634_    982 --AAAGGAATTTAAACATAACATCTGAAACCAAAGAATCCCTAGAAGAAA 1029
                         -- ?  -- ii    ii   v v  i    i v i  ii i         
  L1M4_orf2#LINE/    497 TCAWAG--ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_103927634_   1030 ACA--GGGG-AAATCCTCCATAACATTGACCTTGGCA-TGATATTTTGGC 1075
                            --  ? -     i  -i i  v   ivi v    -  i v i  i v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_103927634_   1076 TATGAATCCCAATGTATAGACAAGATAAACAAAAATAAACACATACAACT 1125
                              vv  v  v i i ii   v v  iv       i i v  vvi   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_103927634_   1126 ACATCAAACTAAAAGATTGTGGCACAGTAAATAAATAAATAAATAAATAA 1175
                         v       v v   i i v v ii vvi   -----ii i --iv vi  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAA-----GGACA--CTATCAA 686

  chr1_103927634_   1176 ATAAATAAAAAGTCA-CCCATGGAATGGTAGAATGTACTTGAAAACAATA 1224
                         iv  i i     v  -    ii      v    vi  i   v   iv   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_103927634_   1225 TATCTGATAATGCATTAATATCTAAAACATATAAGAAACTC--------- 1265
                                   v v i vi    i i  i      ii     ---------
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_103927634_   1266 -ATAATCAGAAAAAAAGTAACCTGATTAAAACATGAGCAAGAGACCTGAA 1314
                         -     v i  i v  i     ii   ?   v   i    ii  ii    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_103927634_   1315 TAGACATTTTTTCAAAGGAAGATTTACACACGGCCAACACATGAATGAAG 1364
                                  i i     -     v    v i      i viiiv     i
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_103927634_   1365 AGGTGCACAAAATCACTAAACAT 1387
                           i   v   v    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (152 / 93)
Gap_init rate = 0.02 (22 / 906), avg. gap size = 2.68 (59 / 22)  


1957 29.93 4.37 2.80  chr1_103985700_103987616      533  1424 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_103985700_    533 GAAAGACTTTCTGTGTTCATCAATGGGAGAAATCAATACTGTCAAAATG- 581
                               iv i ii       vi  v   ii v i    i   i  i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_103985700_    582 C--TATTGGACAAAACAATCTACAGAT-AAATGTAATCCCTATCAAATGT 628
                          --  i vvv    vii          -v  i i             vvi
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_103985700_    629 CCAGCGGCATTTTTCACAGAAACAGA--AATAAATACTAAAATTTGTATG 676
                              v  v     ii      iv  -- iivi  v        ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_103985700_    677 AAATTACAAAAGACTATAAGTACCTAAAGTGATCTTGTGCAAGAAGAACA 726
                         i  v i   ii   ivvi i  v i   iii      viv          
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_103985700_    727 AA-CAGGAGGTAC-CACACTTCTCACTTTCAAGTTATATTACAAAACTAC 774
                           -iv     -  -        i  v      iviv  i      i    
  L1M4_orf2#LINE/    203 AAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_103985700_    775 AGCAAATTTTATATA------TACTGACATGAAAACAGTGACATAGAAGA 818
                           i  -- iv v i ------     i   i ii i  vv i     vv 
  L1M4_orf2#LINE/    252 AGTAA--TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_103985700_    819 ATGGAACAGAATAGAAAGCCTAGAAATAAACCTACACCAAGACGGTCAAA 868
                               i     v  i  i i           i i  vvvv i      v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_103985700_    869 AAATCTTCAATAACA-TGCCCAAAATACCTAATGGAGACAGGATAGTCTC 917
                         vi  i   i i  vi-    v i vi iii     i  v  i       i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_103985700_    918 TTCAATAAATAGCGTTTAGAAAAACTGCAGGCCCACATGCAAAATAATGA 967
                              i    i i i -i i v     v vi?            v     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_103985700_    968 AATTTGAC----AGTT-ATAATATGCACAGGAATAAATTGAACATTGA-- 1010
                          i  v   ---- vi - i vi  ii   ii   v  i v  v  v  --
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_103985700_   1011 AAAGGAATTTAAACTTAACATCTGAAACCAAAGAATCCCTAGAAGAAACC 1060
                          ?  -- ii    iv   v v  i    i v i  ii i         v 
  L1M4_orf2#LINE/    499 AWAG--ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_103985700_   1061 A--GGGG-AAATCCTCCTTAAGATTGACCTTGGCA-TGATTTTTTGGCTA 1106
                          --  ? -     i  v -i vv   ivi v    -  i   i  i v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_103985700_   1107 TGAATCTCAAAATATAGACAAGACAAACAAAAATAAACACATGGAACTAC 1156
                            vv iv   ii i ii   v v  iv       i i v  v i   v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_103985700_   1157 ACCAAAGTAAGAGGTTGCTGCACAGTAAAAAAAAAAATAATAATTAATTA 1206
                          i    i v i iii vi  ii vvi   ii v ----------------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA---------------- 679

  chr1_103985700_   1207 ATTAATTAATTAATTAAAAAGGTCACCCATGGAATGGTAGAAAATACTTG 1256
                         -i  - i  vv  v i     iiv     ii      v        i   
  L1M4_orf2#LINE/    680 -CTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_103985700_   1257 AAAACAATATATCTGATAATGGATTAATATCTGAAACAGATAAGAAACT- 1305
                         v   iv             v   i vi    iii  i v    ii    -
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_103985700_   1306 ---------AATAATCAGAAAA-AAAT--CCTGATTAGAACATGAGCAAG 1343
                         ---------      v i  i -    --  ii   ?i  v   i    i
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_103985700_   1344 AGACCTGAACAGACTTTTTTCCAAGGTAGACTTGCACATGGCCAACACAT 1393
                         i  ii    i    v   i     i v   iv i  v        i vii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_103985700_   1394 GAATGAAGAGGTGCACAAAATCACTAAACAA 1424
                         iv     i  i   v   v    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (164 / 99)
Gap_init rate = 0.03 (24 / 906), avg. gap size = 2.67 (64 / 24)  


1569 26.94 22.25 0.80  chr1_104024868_104026608      505  1250 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_104024868_    505 GAAAGATATTCTGTGTTCATCAATGGGAGAAATCAATATTGTCAAAATG- 553
                                  i ii       vi  v   ii v i        i  i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_104024868_    554 C--TATTACACAAAGCAATCTACAGATTCAATGTAATCCCTATCAAAAGC 601
                          --  i v v    vii              i i              v 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_104024868_    602 CCAACAGCATTTTTCACAGAAACAGA--AATAAATTCTAAAATTTGTGTG 649
                            i v  v     ii      iv  -- iivi  i        ii i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_104024868_    650 AAATTACAAAAGACCTTAATTACCTAAAGTTAACTTGAGCAAGAAAAACA 699
                         i  v i   ii    ivi v  v i   iiv v     iv     i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_104024868_    700 AAGCAGGAGGTAC-CACACTTC-------------TTAC----------- 724
                            iv     -  -        -------------    -----------
  L1M4_orf2#LINE/    203 AAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_104024868_    725 ------------------------------------------------AT 726
                         ------------------------------------------------  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_104024868_    727 G---------------CCCA-----AAAC--------------------- 735
                          ---------------i   -----    ---------------------
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_104024868_    736 ---------------------ACC---TAATGGAGACAGGATAGTCTCTT 761
                         ---------------------   ---i     i  v  i       i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_104024868_    762 CAATAAATAGCATTGGAAAAACTGGAGGTGCACATGCAAAATAATGAAAT 811
                            i    i iii   i v       vi?v           v      i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_104024868_    812 TGAACTGTTAT-----GCTATGCACAGGAATAAACTGAAAATTGATAAGG 856
                           i  ivi  i-----i i  ii   ii   v    v     v   v ?i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_104024868_    857 AATTTAAACATAGCATCTGAAACCAAAGAATCCCTAGAAGAAAACA--GG 904
                         i ii    ii  iv v  i    i v i  ii i            --  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_104024868_    905 GG-AAATCCTACATGACATTGACCTTGGCG-TGATATGATTGGATATGAT 952
                         ? -     i - i    v   ivi v   i-  i - vv  i       i
  L1M4_orf2#LINE/    552 NGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATATGAC 599

  chr1_104024868_    953 TGCCAACA-TATAGGCAATACAAACAAAAATAAACACATGGGACTACATC 1001
                         -i    v -i i i    i v  iv       i i v  v     v    
  L1M4_orf2#LINE/    600 -ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_104024868_   1002 AAACTAAAAGGTTGCTGCGCAGTAAAA-ATAA-ATAAATAAAAATAAAAA 1049
                            v v   iii vi  i  vvi   i- i v-  v  -i   i i    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA-GAAAGTGAAAA 697

  chr1_104024868_   1050 GGTTACC-ATGGAATGGTAGAAAATACTTGCAAACGATGTATCTGATAAT 1098
                          iiv   - ii      v        i       iv  i          v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_104024868_   1099 GGGTTAATATCTAAAATATATAAGAAACTC----------ATAATCAGAA 1138
                           ii vi    i i         ii     ----------     v i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_104024868_   1139 AACAAATAACCTGATTAAAACATGAGCAAGAGACCTGAATAGACATTTTT 1188
                         i          ii   ?   v   i    ii  ii             i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_104024868_   1189 TCTTAGGAAGACTTACACATGGCCAACACATGTATAAAGAGATGCACAAC 1238
                         i v- i     iv    v        i viiii  i  i      v    
  L1M4_orf2#LINE/    848 CCA-AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_104024868_   1239 ATGAGGGAAATA 1250
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (134 / 63)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 6.88 (172 / 25)  


1103 25.42 7.13 12.60  chr1_104061636_104063930      490  1386 (909)    L1M4_orf2#LINE/L1       22   869 (39)  

  chr1_104061636_    490 TGAGTTATACGACTCAA-ATAGTAAATATGCAAAT-TTCTGCAAATTAAT 537
                           ii  iv v    i  -  v  v  v   vv   -i  iv      i  
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGAT 71

  chr1_104061636_    538 GAATAGGTGTAATACAATTTCTATCAAAACTCCAGCCGTACATTTTGTAG 587
                         vv i  i vi  ii    ii         ii     i iviv     i  
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAG 121

  chr1_104061636_    588 ATATAAATGAGACT-ATTCTAAAATTTATATGGAAAAGCAAAGAAACTAG 636
                          v  vi ii  -  -  i        i         v    i i v i  
  L1M4_orf2#LINE/    122 AAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr1_104061636_    637 CTAAAGTCTCTCTGGATAAAGAAGAATATTTAACAAACCTGCACGTTGTG 686
                         ---  ------- i vi   ------------    v i  ---------
  L1M4_orf2#LINE/    171 ---AA-------TAGCCAAA------------ACAATCTTG--------- 189

  chr1_104061636_    687 CACATGTACCCTAGAACTTAAAGTATAATTAAAAAAAAAAAAAACAAGAA 736
                         ---------------------------------     i  i     ---
  L1M4_orf2#LINE/    190 ---------------------------------AAAAAGAAGAACAA--- 203

  chr1_104061636_    737 GAAAGTGGGACAAATCAT-CTACCTGAATTCAAGACTT-TTAATGTGGTA 784
                         ---   v   vi v   i-  v  ii v     i    -i  vviv v  
  L1M4_orf2#LINE/    204 ---AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_104061636_    785 TATTAATCAAGAC--TCTCATATTGGTGGAAGGACGGACACATTTTGTGT 832
                         i v          -- v vi  i   iiv     ii    i  -------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT------- 293

  chr1_104061636_    833 CAATTAAATAAAACAGAATGTGTAATTATGAATCCATAGAATAAGATACA 882
                         - iv v   ii  i     --- i ----  i    --   ----   v 
  L1M4_orf2#LINE/    294 -AGATCAATGGAATAGAAT---TGA----GAGTCCA--GAA----ATAAA 329

  chr1_104061636_    883 CCTATACCCAGCAGATATAGGTGGGTA-TTGGT----GAAAAGGCAGAGG 927
                           i    -------  v  --   vi -   i ----  v    ----- 
  L1M4_orf2#LINE/    330 CCCATAC-------ATTTA--TGGTCAATTGATTTTCGACAAGG-----G 365

  chr1_104061636_    928 TGAAAACGCAATTGAATAGAGGAAAGAGTA---TTTTCAATGTATAATAG 974
                           vv  vi v   v   i -       i  ---       iiv  ii iv
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_104061636_    975 TGAAGCGATTAGACATCCAC------------------GG--------CT 998
                           iii i i i  i ?    ------------------  --------  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_104061636_    999 TAAA------ACACAAGTAAACTAAAAATGGACCTATGGCGTAAATGTAA 1042
                         i v ------   v  i v    v        i v?v i v         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_104061636_   1043 AACGTAAATCTGTAAAACTTTTAGA-GAAACGTTAGGAGAAAATCTTCAG 1091
                         i vv    v  i       i     -    vvv    ? v        iv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_104061636_   1092 AACCTAGGGCCAGGCATGTAGTTCCT-AGATGTAACAGCTGAAGTACAAT 1140
                         i    v   ii     -i i   i  -    i i   v vi   i    v
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCA-ATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_104061636_   1141 CCATGAACACAAAAATTGATAAATTGGGCTTTATTGAAATTGAAAACTTT 1190
                          v ii  viv      v          i   i  ii     i        
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_104061636_   1191 TGCTTTGCAGAAGATCATGTTAAGACAGTGAAAAGATGAGCTACACAGTG 1240
                           ivi v  i i  ivv i i    v          ii v i   v i  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_104061636_   1241 GGA-AAAATATTTATAAACCACATGTTGAAAAAAGGATT---ATCATTAA 1286
                            -         ii   i  i  i ivi v  i   i ---   --i i
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC--CAG 761

  chr1_104061636_   1287 AATAAATCAAGAATACTCAAAACTCAAGGTT--TAAAAAG--------TC 1326
                             v  v     iv  i v       --- --       --------i 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAA---TAATAAAAAGACAAATAACC 808

  chr1_104061636_   1327 CAAGAAGAAAGTAG-CAAAAGACATATAGAAAAATTTCACCATAAAGGAT 1375
                            vv?i   i i -    i  iv iv v i v     v   v i i   
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_104061636_   1376 GTACAGATGAC 1386
                         i    i   i 
  L1M4_orf2#LINE/    859 ATACAAATGGC 869

Transitions / transversions = 1.52 (135 / 89)
Gap_init rate = 0.04 (37 / 848), avg. gap size = 4.78 (177 / 37)  

 214 12.77 6.38 0.00  chr1_104061636_104063930     1757  1803 (492)    L1M4_orf2#LINE/L1      859   908 (0)  

  chr1_104061636_   1757 ATACAAA---CAAGTAGGCACAGGAAAAGATGTTCAACATCGTTGGCCAT 1803
                                --- v i  i     v         i        i????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (4 / 2)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 3.00 (3 / 1)  


2610 25.28 4.85 2.37  chr1_104078288_104081030     1365  2250 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104078288_   1365 TGAAAAGA-----CATGCTCACGTATCGGAATAATTATTATTA--AAAAG 1407
                           i     -----    i   i v  i    v v   v    i--  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104078288_   1408 GACCATATTATGCAAAGCAAACTATAGATTAAATGCAATCCCTATCAAAA 1457
                          i v   i viv    vii v   i     v  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104078288_   1458 AACCAA-TGTCATTTTTCACAGAAATACAGCAAAC-AATTCTAACATTTG 1505
                         vv   i-  i -     ii       -iii   i -i  i    v   ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chr1_104078288_   1506 TATGGTCAAAAAATTAAAATATAAAGGAACCC----CAGTCAAAGTAATC 1551
                              -----------    ii  i   -   ----i  i    ii    
  L1M4_orf2#LINE/    149 TATGG-----------AAATGCAAGGGA-CCCAGAATAGCCAAAACAATC 186

  chr1_104078288_   1552 CTGAGCAAAAA-ATCAAAACTGAAGGCATCACATTAGCTGACTTCAAAAT 1600
                         i   iv  i  - v    ii  i   vv     i vv ii i       i
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_104078288_   1601 GTATTAAAAGGCTATAGTAAGCAAAATAGCGTGGTGCTGATATAAAAGTA 1650
                         v  i  v  i    i     v   i i  i     i   ii    iii  
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_104078288_   1651 AACACATAGGACAATCAAACAGAATAGAGAACCCAGAAATAAATCCACAT 1700
                         i   i    iv    vi  i     v    ii           i   i i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_104078288_   1701 GTTTACAGCCAACAGATTTG-AACAAGGTTGCCAATAACTTATAGTGGG- 1748
                         i    ii i   iv     v-i      v      v v v vi i    -
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_104078288_   1749 AAAGGACACCCTTTTCAATAAATATTTC-AGAAAAATTGGATATCTATAT 1797
                             i i vi        i    iv v -i i v  i      ? i i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_104078288_   1798 GCGGAAGAATGAAACAGGACCTCTATATCTCACCATATACAAAAGATTAA 1847
                           ii         iiv     i   iv  v              -     
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTAA 485

  chr1_104078288_   1848 CAGAAGATGGAATAAAGCCTTAAAACTATATAAAATCTTAAACTCTAAAC 1897
                          vv  i     vi ?  v i    ---- i   i v  v     v    v
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAA----TGTAAGAGCTAAAACTATAAAA 531

  chr1_104078288_   1898 CACT-ACAAAAAAACATAGGGAAAACACTTCAGGGCTTTGGTCTAGGTAA 1946
                          v  - v  i          ?iv  vv    iv i i    vi    i  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_104078288_   1947 AGATTTTACAGCTAAGATCTCAAAAGGACAGATAACTGAAGCAAAAATAG 1996
                         v i   ivi  v  v  ivi      v   iii   vi   v        
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_104078288_   1997 ACTACTTGGACT-----AAAATGAAAA--TATTCTGCTTGGCAAAGGA-- 2037
                          iv v       -----     v    -- v  v     --       --
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACA 679

  chr1_104078288_   2038 --ATCAACAGAGAGAAGAGACAACCTGTTAAATTAAAGAAAAGATTTGCA 2085
                         --     v i  v   i        iiivi   vii      v       
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_104078288_   2086 AATTATTCATCTGACATTGGACTAATATTCAGAATATATAAGGTACTC-- 2133
                            i  vi      i vv     vi   i            i v    --
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_104078288_   2134 --AACTCAACAATAAAAA-----ATA---CATTTAAAAAGTGAGCAAAGA 2173
                         --       i        -----   ---  v  ?    i  i      i
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_104078288_   2174 ACATGAATAGTCATTTTTCCAAA-ATGACATACAAATGGCCAACATGTAT 2222
                          iv       v     i      - v  i              i v i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_104078288_   2223 AAGAAAA-ATGCTTAACATCACTAATCAT 2250
                          v     -     i       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (136 / 84)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.56 (64 / 25)  


3194 27.35 0.89 0.33  chr1_104105918_104108389.rev     1079  1981 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104105918_   1079 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAGAAT 1128
                              ii    i     i      i v      v i        v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104105918_   1129 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 1178
                            v     v     iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104105918_   1179 TACCAATGACTTTCTTCACACAATTGGAAAAAATTACTTTAAAGTTCATA 1228
                          v   iivi i  i  ii  v  v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_104105918_   1229 CAGAAACAAAAAAGAGCCCGCATAGCCAAGGCAATCCTAAGCCAAAAGAA 1278
                         ii    iiv  ii  v  v v        ii     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_104105918_   1279 CAGAGCTGGATGCATCACGCTACCTGATTTCAAACTATGCTACAAGGATA 1328
                           i  i    v vv    i  v  ii        viv i      i v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_104105918_   1329 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 1378
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_104105918_   1379 TGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACCAT 1426
                              i    i--    i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_104105918_   1427 CTGATCTTTGACAAACCTGAAAAAAACAAGCAATGGGGAAAGGATTCCCT 1476
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_104105918_   1477 ATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1526
                         v  i  i     i        v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_104105918_   1527 AACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAACATGGTTT 1576
                          ii    iv   v   i     v              i    v    v i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_104105918_   1577 AAAGACTTAAATGTTAGCCCTAAAACCATAAAAACCCTAGAAGAAAACCG 1626
                          ?    i       v  vv       i      vi i           vv
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_104105918_   1627 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 1675
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_104105918_   1676 ACACCAAAAGCAGTGGCAACAAAAGCCAAAGCAGACAAATGGGATCTAAT 1725
                                     vvi          vv   ii   i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_104105918_   1726 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 1775
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_104105918_   1776 GGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGATAAA 1825
                          i     i                 v   i   vii ivi         i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_104105918_   1826 GGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAGAAAAA 1875
                           i  vi          v  i   v    ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_104105918_   1876 AA-----AACCCCATCAAAAAATGGGCAAAGGATATGAACAGGCACTTCT 1920
                         i -----     v  i?                 v    i  i  i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_104105918_   1921 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCTTCA 1970
                          v        i  vi viii     i ii          i      vv  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_104105918_   1971 TCAGTGGCCAT 1981
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.20 (11 / 5)  


2720 25.36 3.77 3.21  chr1_104110428_104112376      556  1458 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104110428_    556 TAGTAAGATATTTCATGTTCATAAATTGGAAGAATTAGCACTGTTAA--- 602
                          i v       ii         ii         v   ii i      ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104110428_    603 ---AATATTCATGCCAAAAGCAGTCTACAGATTCAATGCAATTCTTATCA 649
                         ---    i  ---  v   viii             i     i i     
  L1M4_orf2#LINE/     51 GGCAATACTC---CCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_104110428_    650 AAATACAAA-TGTCATTCTTCCTCAGAGAAATAGAAAAAACAATTCTAAA 698
                             v v i-  i v  i  v ----      v  v  ivii  i     
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGC----AGAAATTGACAAGCTGATCCTAAA 143

  chr1_104110428_    699 ATTTATATGGAGCCACAAAAGACCCAATATAGCCAAAGCTATTCTGTGAA 748
                            i       ivii   ii      iv         i v  -  -    
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT-TGAA 191

  chr1_104110428_    749 AAAAAAACAAAAAACAAAAAAAACAGAACTGGAGGAATCTTGTTACCTCA 798
                            i  i--------------    i ii       v  viii v  iv 
  L1M4_orf2#LINE/    192 AAAGAAG--------------AACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_104110428_    799 CTTTAAGTTATACTACAGAGCTATAGTAACAAAAACAACATGGTATTGGC 848
                         i  i  iviv       i     i     iv  i   iii     i    
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_104110428_    849 ATAAAAACAGACACACAGACCAATAGAACAGAGTAGATAACCCAGAAACA 898
                             ii i     i i   i    i   i   i v  v ii       i 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_104110428_    899 AATCCATACATCTACAATGAGCTCGTTTTCAACAAAGTTGCCAAGAACAC 948
                           i        i  iii v ii vi     i    i v        v  i
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_104110428_    949 GCACCAGGGAAAAGATAATTTCTTCAATAAACGTTGTTGGGAAAACTGGG 998
                         v  vii      ii   i i i     i   i v  i     v      i
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_104110428_    999 TATCCATATGCAGAAGAATAAAACTATGTCCATATCTCTTGCAACATATG 1048
                           ?   i     i      i  ii ivii  v  i   vii v i   ii
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_104110428_   1049 AAAATCAAACTCTA---------------TAATTCTAATACCTTAAACTA 1083
                              i  -   v ---------------   v v   v v  v      
  L1M4_orf2#LINE/    478 AAAATTAA-CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_104110428_   1084 TGAAAATATTAGAAGAACCACATTTGGGAAACTCTCCAGGACATTAGTCT 1133
                          i   v v         v-    vv ? v  v   i iv   v  i vi 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAA-ACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_104110428_   1134 GGGCAAAAATTTATTG-------C-CCAACAAGCACAGGCAAGCAAAGCA 1175
                         i     vii   v  i------- -    -       i    vv    v 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAA-AAGCACAAGCAACAAAAGAA 624

  chr1_104110428_   1176 GAAATGCACAAAT-GGAGTAACATCAAGCTAAAAAGTTTCTGCACAGCAA 1224
                         i    iv i    -   v v-      iv v    ii  i  ii vv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTT-CATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_104110428_   1225 AGAAGACATTCAACAAAGTGAAAAGAGAAACCATAGAATGGGAGAAAATA 1274
                           i v  vv    v            v  v   i                
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_104110428_   1275 TT-GCAACCTCTCCATCTGACAAGGGATTAATAACCATATTATATAAGGA 1323
                           -    viiv vi      i      i vi  v   v v       i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_104110428_   1324 GCTCAAACAACTCTATAGGAAAAAAAAACAAATAATCTAAT--ATAAATG 1371
                         i   vv       v   -- v     i        i i   -- v     
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATA--ATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_104110428_   1372 GGCAAAAGATATAAATAGACATTTCTCAAAATAAGATGTACAAATGGCAA 1421
                               i   v i              v   v     i          v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_104110428_   1422 ACATGCATATGAAAAGGTATTCAACATAATTGATTAT 1458
                          i v   i        i ii       v ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (140 / 87)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.50 (63 / 18)  


1446 17.78 1.44 29.03  chr1_104131578_104134306      983  2236 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104131578_    983 TGGAAAGACATCTTGTGTTCATGGATTGGAAGACTTAATATTGTTAAAAT 1032
                                 i   iii                                i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104131578_   1033 GTTTGTGCCATCCACAGTGATCTTTAGAGTCAACAAAAT---TATGGCAA 1079
                          vivi i ivi   v v      vi   v     iv   ---   --   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT--CAA 98

  chr1_104131578_   1080 AATCTCAATGGCATTTTCTACAGGAAAAGAAAAATGACAATACCCAAATT 1129
                             i  iiv  v    i i   i  vv  v  -- vii  v iv     
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATT 146

  chr1_104131578_   1130 CATACGGAACCACAAAAGATCCTGAAGAGCCAAATC---CTTGAGAAAAA 1176
                             i    vii   ii  i  v   v       v ---     i   i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_104131578_   1177 ATAACAAAACTAAATACATTATACTTTCTGATTTAAAGGTATATTACAAA 1226
                          v      ii ii vivv i i    i ii    v  iiiv  i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_104131578_   1227 ATTATCGTAATTAAAACAATATAGGACTAGCATAAAAACAGATGTATAAA 1276
                         ii  iv     i  i   i i i v   i      ii i   ii    i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_104131578_   1277 CTGATGGAACAGAGTAGAGATCTCAGAAATCAATCCATACACATGTGGTC 1326
                         iii      i   i v    vii       v  i       iv i     
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_104131578_   1327 AACTGATCTTGGACAAGTGTGTGAAATTATATCCAGTGGGGAAAGAATAG 1376
                           i    i  v      v   iv  ivi-i  i  i              
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAG 395

  chr1_104131578_   1377 CCTCT-CAATAA-TGGTGCTGGGAAAACTGGATATCC-TATGCAAAAAAG 1423
                         i  i -   i  -           v         ?  -i        i -
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA- 444

  chr1_104131578_   1424 GAAATTTTGTTTGTTTGTTTGTTTTGTTTTGTTTTGTTTTGGGTTTTGTT 1473
                         --------------------------------------------------
  L1M4_orf2#LINE/    445 -------------------------------------------------- 444

  chr1_104131578_   1474 TTGTTTTGAGACAGAGTCTCACCGTGTAGTTCAGGCTGGAGTGCAGTGGT 1523
                         --------------------------------------------------
  L1M4_orf2#LINE/    445 -------------------------------------------------- 444

  chr1_104131578_   1524 GCAATCTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGTGATTCTCC 1573
                         --------------------------------------------------
  L1M4_orf2#LINE/    445 -------------------------------------------------- 444

  chr1_104131578_   1574 CACCTCAGCTGGGATTATAGATGTGCACCACTGCACCCAGGTAATTTTTG 1623
                         --------------------   -------------------  ------
  L1M4_orf2#LINE/    445 --------------------ATG-------------------AA------ 449

  chr1_104131578_   1624 TATTTTTTGGTAGAGACAGGGTTTTGCCATGTTGGTAAGGCTGGTCTCAA 1673
                         ------------------------------     ---------------
  L1M4_orf2#LINE/    450 ------------------------------GTTGG--------------- 454

  chr1_104131578_   1674 ACTCCTGACCTCAAGTGATCTGCCCACCTCAGCCTCCCAAAGTGCTGAGA 1723
                           i   -------------------      -------------------
  L1M4_orf2#LINE/    455 ACCCCT-------------------ACCTCA------------------- 466

  chr1_104131578_   1724 TTACAGGCGTGAGCCACCACACCGGACCATAGATTTTTATACTATACACT 1773
                         --------------     -----------------------      --
  L1M4_orf2#LINE/    467 --------------CACCA-----------------------TATACA-- 477

  chr1_104131578_   1774 AAAATCAACTCAAAATTGATTAAAATCTTAAATGTAGGACCAAAAATTGT 1823
                              i          v   i ? iv i        i  v v    i i 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_104131578_   1824 AAGACTCCTGGAAGAAAATTTAGGGAAAAA-CTTCACAGTATTGGTCTCA 1872
                           i    i i        iv    ?iv   -    iiiiiv    vi vi
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_104131578_   1873 GCAATGACTTCATGGGTATGACACCAAAAGCACAGGCCATAAAAGCAAAT 1922
                               ii   v i i                  i  v i     v   v
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_104131578_   1923 ATAAACAA-T---ACTATATCATACT--AAAATGTTTCTGCATAACAACA 1966
                            i i  - ---   vi    v v --    iv   v   v --   --
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAA-- 673

  chr1_104131578_   1967 AGGAAACAATCAACAGAGTAAAAAGGCAACCTGTGTGATGGAAGATAATA 2016
                             v  v     v i   i     i     iiiivi    i   v    
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_104131578_   2017 TTTGCAAACCATATACCTAATAAGAAATTAATTTCTGAAATATATAATAA 2066
                                 i      i  i     ii i vi v  iii         vi 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_104131578_   2067 ATGTCTACAACTCAATAGCAAACATATGCATACATACACAATACATTCCC 2116
                          ivii            ii   -----------------  v   -----
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAA-----------------AAGACA----- 801

  chr1_104131578_   2117 CCACACCCAAACACTAATAACCTAATT--AAAATAGGCTAAATAATTGAA 2164
                         ---------------       i    --     i   v  iv v     
  L1M4_orf2#LINE/    802 ---------------AATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_104131578_   2165 TAGATACTTTTCCAAAGAAGATACACAAATGACTGACAGACATAAGAAAA 2214
                             i i  i             i       i ii i ii  i v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_104131578_   2215 GATGCTCAACATCACTAATTAT 2236
                                       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (150 / 70)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 15.28 (382 / 25)  


1407 30.13 2.45 1.88  chr1_104136551_104144652        3   533 (7569)    L1M4_orf2#LINE/L1       14   547 (361)  

  chr1_104136551_      3 CATGCTCATGAATAGGAAGAATCAATGTCTTTAAAATGGCTGTACTGCCC 52
                             i     i  v      v i   i iv    i     vi    v   
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr1_104136551_     53 AAAGCAATCCACAGATTTGATACTATTCCTATCAAACTACAAAG-GTCAT 101
                            vii   i       ii ii v  i         v v v iv- i v 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr1_104136551_    102 TTGT-CAACAAAATTAGAATAAACT-ATTCTAAAATTCATATGAAACTAC 149
                           v -  i--     i-- i  i  -  i              i  v i 
  L1M4_orf2#LINE/    114 TTTTGCAG--AAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_104136551_    150 CAAAAACCTCTAATAGGCAAGGAAATCTTAATCAAAAAGAATAAAGCCAG 199
                         v iii   ivv     v   iiv      i vv  i     i    iii 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_104136551_    200 AGGCATGACATTACCAGACTTCAAACTATACTTTAAGACTACATTAACCC 249
                            vv v   i v  vi i      viv    vi  ii     v   i v
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_104136551_    250 AAACAGAATGGTACTGGTACAAAAACACACATATAGACCAATGAAACAGT 299
                          i    vi         i i  ii i v         i     i  i  v
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_104136551_    300 A--GAGAGCCCAGAAATAAAGCCACACACCTACAGCCATCTAATCTTTGA 347
                          --     i           v   i   ii  ii i  vi i  i  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_104136551_    348 CAAAGTTAACAAAAATAAGCAACAAGAAAAAGACTCACTATTCAATAAAT 397
                            i v iv   i vi vv   iii i   ii ivvv  v     i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_104136551_    398 GGTGCTATTTATTAATAA-TAAATAGCCATATTTAGAAAAATAAAACTGG 446
                               iv-----i i  - ii   ?   i  vi i  i   i  ii   
  L1M4_orf2#LINE/    410 GGTGCTGG-----GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_104136551_    447 ACCCCCACATTTCATCATACACAAAAATTAACTCAAGATGGTTTAAAGAT 496
                              i  v iv  i    i                i    v i ?   i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_104136551_    497 TTAAG----AGAACTC---TTACAAGATTCTACACAAGACAATA 533
                         i   i----   i  v---i  i  i i   -i v    v  i 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAACA 547

Transitions / transversions = 1.98 (105 / 53)
Gap_init rate = 0.02 (11 / 534), avg. gap size = 2.09 (23 / 11)  

3065 28.13 0.33 0.55  chr1_104136551_104144652     1758  2667 (5435)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_104136551_   2667 TGGAGGAACATTCCATGCTCATGGGTAGGAAAAATCAATATCCTGAAAAT 2618
                             iii i  i     i      i v    i v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_104136551_   2617 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2568
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_104136551_   2567 TACCAATGATTTTCTTCACAGTA-TTGGAAAAAACT-ATTTTAAAGTTCA 2520
                          v   iiviii  i  ii   v -   -- v  i  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chr1_104136551_   2519 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAGGCCAAAAG 2470
                                viiv  ii  v  v v  v     iv     i iiivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr1_104136551_   2469 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 2420
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr1_104136551_   2419 GACAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGTCC 2370
                         v       v   i    ii         i iv ii i   v      vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr1_104136551_   2369 AATGGAACAGCATAGAGAGCTCAGAAATAATGGCCGCATATCTACAACTA 2320
                                i  v  v     ii         -iv  ii i  i  iiiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCA 347

C chr1_104136551_   2319 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 2270
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chr1_104136551_   2269 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 2220
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chr1_104136551_   2219 AAACTGGATCCCTTCCTTGCACCTTATACAAAAAATAATTCAAGATGGAT 2170
                           ii    i    v   ii    v          v   i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

C chr1_104136551_   2169 TAAAGAGTTACATGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAACC 2120
                         i ?   vi  v    v   v       i      vi i   i       v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

C chr1_104136551_   2119 GAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2071
                         v   ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chr1_104136551_   2070 AACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAGTGGGATGTAA 2021
                         i            vvi     i    vv     v  i  i v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chr1_104136551_   2020 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAG 1971
                          i   v v  i i   i  ii vv    i  v  i i  vv i      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chr1_104136551_   1970 AGGCAAACTACAGAATGGGAGAAAATTTTTGGCAACCTACTCATCTGACA 1921
                           i   v i                 v    -   vii ivi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTG-CAAATCATATATCTGATA 745

C chr1_104136551_   1920 AATGGCTAATATCCAGAATCTACAATGAACTCAGACAAATTTACAAGAAA 1871
                          iv i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chr1_104136551_   1870 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1821
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chr1_104136551_   1820 CTCAAATGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1771
                            v  v     i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chr1_104136551_   1770 CATCACTGGCCAT 1758
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (146 / 106)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  

2434 27.77 2.74 3.07  chr1_104136551_104144652     6699  7609 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104136551_   6699 TGGAAAAACATCCCATGCTCTTGGATAAGAAAAATCAATATCATTAAAGT 6748
                               i i        i  v     vi   i v i     ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104136551_   6749 GTCCATACCGTCCTTAG--CAATTTACACTTTCAATTCTATTCCTATCAA 6796
                          v v    --   ii i--ii  i    vv     iv v  i        
  L1M4_orf2#LINE/     51 GGCAATAC--TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_104136551_   6797 CCTACCAATGACATTCTTCACACAACTAGAAAAAAAAAAACT-ATTTTAA 6845
                         vv v   iivi v  i  ii  ------    vvi v  i  -  ii   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCA------GAAATTGACAAGCTGATCCTAA 142

  chr1_104136551_   6846 AATATATATAGTACCAAAAAAAAAAAAGCCTGAATAGCTAAGGCAATCCT 6895
                            vi    i ----   viv  iii v  v       i  ii     i 
  L1M4_orf2#LINE/    143 AATTCATATGG----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_104136551_   6896 AAGCAAAAAGAACAAAGCTGGAGGCATCATGATACCTGACTTCAAACTAT 6945
                         i iv  i          i      vv   iiv v  ii i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_104136551_   6946 ACTACGTGGCTACAGTAACCAAAATAGCATGGTACTCATACAAAAACAGG 6995
                              ivi          i   i i  ii       vii i  ii i  i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_104136551_   6996 CACATAGACAAATGGAACAGAATAGAGAACTCAGAAATTAGGCTACACAC 7045
                           i     iv       i     v    iii       v iv i i   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_104136551_   7046 CTACAACAAGCACCATCTTTAGTTTGTCTTTGACAAAGCTGACAAGAATA 7095
                         i  iii------------ i i  vi i  i     i v  v     vi 
  L1M4_orf2#LINE/    339 TTATGG------------TCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_104136551_   7096 AGCAATAGGGAAA----ACTCTTTAATCAATAAATGGTCCTGAGATAACT 7141
                         vv    i      ---- v     --    i       v   i  i    
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACT 424

  chr1_104136551_   7142 GGCTAGTTA--TGCAGAAGATTGAAGCTGGATTCCTTCATTACATCATCT 7189
                           v  ?ii --    i    v     i    ii   v v i   i   v 
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_104136551_   7190 ACAAAAATCAACTCAAGATGGATTAAAGACTTAAATTTAAAA-CCAAAAC 7238
                                 i       i      i ?    i     v   i - i     
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_104136551_   7239 TATAAAAACCCTGCAAGAAAACCTGGACA-ATACCATCATGAACACATGA 7287
                                vi i iv        v i i?i- v i v  i   - - v  i
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA-C-CTTGG 572

  chr1_104136551_   7288 AC-AGGCAAAGATTTCATAAAAAAGACACGAAAAGCAATTGCAACCAAAG 7336
                         ii-      v i    v  i v v     v       vvv     v    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_104136551_   7337 CAAAAATTGACAAATGGGATATGATTAAGCTTAAGAGCTTCTACACAGCA 7386
                         v      v  i    v   iv v  i  iv    i i   i iii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_104136551_   7387 AAAGAAACTATCAACAGAGTAAACAGACAACTTACAGAATAAGAGAAAAT 7436
                           i  v        v i   i  v       ii       ii        
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_104136551_   7437 ATTTGCAAGATATGCATCTGACAAAGGTCTAATATTCAGCATCTATAAGG 7486
                                 ivi  ii      i  i  v  vi   i   v  v     i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_104136551_   7487 A--TCTTA-AATTTA-CAAGAAAAAGA-AAA---CCCA-TTGGAAAGTTG 7527
                          --     -  i i -i  v       -   ---    -  ?i   i v 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_104136551_   7528 GCATGGGACATGAACATAC--TTTTCAAGTGAAGACATACATGCAACCAA 7575
                            vi   iv    i v  --  i  v iv     i     viiii    
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_104136551_   7576 CAA--ACATAAAAAAAAGCTAAATATCACTGATTAT 7609
                         i  --    i    i v   v  i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (159 / 90)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.41 (53 / 22)  


2475 28.09 2.92 0.90  chr1_104174245_104177096.rev     1474  2363 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104174245_   1474 TGGAAAAATATTACATGCTCATGGATAGGAAAAATCAATATTATTATAAT 1523
                               i    iv    i        v    i v i      i   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104174245_   1524 GGTCATACTGCCCAAAGCAATCTATAGATTTAATGTTATTCCTATCAAAT 1573
                           iv     v      vii     i     i  i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104174245_   1574 TACCAAAGTCATTTTTCACAGACATAGAATAAACTGCTC-TAAAATTCAT 1622
                          v   ivvv v     ii    v  v  -i  i   v  -          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr1_104174245_   1623 ATGGAACTA-AAAAGAGCCTGAATAGTCAAAGTACTCCGAAGCAAAAAGA 1671
                               v i-  ii  v  v      i    ii v  ivi iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_104174245_   1672 ACAAAGCGAGATGCATCACATTATCAGACTTCAAACTATATTCTAAGGTT 1721
                               ivi  v vv     i vi vi i      viv  i vi  i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_104174245_   1722 ACTGTAACCTCAACAGCATGATATTGGTACAAAAACAGTCACACAGATTA 1771
                           v    i vvi    ii  i  i   i i  ii i  v  i i    i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_104174245_   1772 AGAG---------GAAA---CAGAAATAAAGCCTTTCACCTGCAAACATC 1809
                          vi ---------  i ---          v  v v  ii iiiiv  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_104174245_   1810 TGATATTTGACAAAGCCAGCAAAAATAAGCAATGAGGAAAGGACATATTA 1859
                             v  i     i viiv   i vi vv     i      i i vvi v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_104174245_   1860 TTCAATAAATGGAGCTGGGATAACTTTTAAGCCATATGCAGAAGATTGAA 1909
                              i      v       i    vvvv ?   i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_104174245_   1910 ACTGGACTCCTACTTTTCACCATATAAAAACATCAATTCAGTATGGATTA 1959
                         ii     i     i iv         v   v  i  i   iv      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_104174245_   1960 AAGATTTAAATATGATAGCTAAAACCATAAAAATCCTAGAAGAAAACTTA 2009
                         ?   ii     i i v         i      v  i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_104174245_   2010 GA---AAATGCCCTTCTTGACACTGGCCTTAGCCCAAAAGTTTAT-GGCT 2055
                          i---    ---    v    vi   v-    v -  vi    v -i v 
  L1M4_orf2#LINE/    550 GGNGTAAAT---CTTCGTGACCTTGGG-TTAGGC-AATGGTTTCTTAGAT 594

  chr1_104174245_   2056 AGGTCCTCAAAAGTAATTGCAAAAAAACAAAAATTTG-CAAGTGGAATCT 2104
                          v v vi      i vvv    v    v     v v -i  i v i ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_104174245_   2105 AATTAAAATAAAGAGATTCTGAACATTAAAAGAAATTATTAAGA--GTAT 2152
                         v  i     v  i iv  i  vi v i   i  v i   i    --  iv
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_104174245_   2153 ACAGACAACCTATAGAATGAGAGAAAATATTCTCAAACTATGCACAAGAT 2202
                          v        i i      i           iv    ii  ii ivv   
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_104174245_   2203 AAAGGTCTAGT-TCCAGAATTTATATGGAACTGAAACAATTCAACAAGCA 2251
                           i  v  v  -        v    vi     vvv    i    i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_104174245_   2252 AAA-ACAAATAACACCCTTTAAAAGTGGGCAAAA-ACATACACAGACATT 2299
                            -         v vv  ?    i        i- iv iv i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_104174245_   2300 TCTCAAAAGAAGACAAACATTAGTGGCCAAAAA--ACATGAAAAAATTCT 2347
                             v        i v   -- i       v  --         i  v  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACA--AATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_104174245_   2348 CAACATAACTAATCCT 2363
                               v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (135 / 112)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


2840 24.12 4.89 1.71  chr1_104208451_104212515.rev     2696  3574 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_104208451_   2696 GAAGAGCTATTCCTTGTTCATGGATAAGAAAATGAAATATTGTCCAGATG 2745
                          i i  v   i  v           vi   i ivv        iv     
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_104208451_   2746 ----TATTTCCCAACTCAATCTCTAGATTCAATGCAATCTCAATCAAAAT 2791
                         ----  i i     v ii    vi        i      i v        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_104208451_   2792 CCCAGC-AAGTTATTTACTGGATATTGATAAACTGATTCTAAAGTTTATA 2840
                               -ivv  v   i v i -     i  i     i     i  i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_104208451_   2841 TAGA-------GAGAC--AGTATAGTCACCACAATCTT--AAAAGA-GAA 2878
                          i  ------- i   --  v    i  vv        --      -   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_104208451_   2879 CAAAGTTAGAGGACTGACATTACTCGACTTCAATACTTAATATGAAATGA 2928
                                i       v   i v i i i     v     v  ii  iiv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_104208451_   2929 TAGTAATCAAGATGGTGTGGTATTGGTGAAAAAAATAAACACATAGAACA 2978
                         i           ii        i   i- v  ii   i   i     v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGACATATAGATCA 299

  chr1_104208451_   2979 ATGGAAACGAACAAAGAGCCCAAAACTGGACCAAAATAATCATAGACAAC 3028
                               vv   ivi    i   i  v ii   v v i v i  i v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_104208451_   3029 TGATCTTTGACAAAGAAGCAAAGGTAATACCATGGAGGAAAGATTA-TCT 3077
                             i  i     i iv  v   iiv  v v    -       v  -   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCT 398

  chr1_104208451_   3078 TTTAAACAAATGGTTCTGAGACAAGTGGACATCCA-ATGCCAAAAAAT-A 3125
                            v          v   i     v    i ?   -    v   i   - 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_104208451_   3126 ACTTG-ACTCAGACCTTATATGCTCTGCAGAAATTAACTCAAAATGGCTC 3174
                          v   -  i vv    i i ivv v i  i                 v  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_104208451_   3175 CCAGAGCTAAATGCAAAATACAAAACAATGAAACTCCTAGAAAATAACAT 3224
                         v?   v       i  i vvi     v  i      i     i v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_104208451_   3225 AGGAGAAACTCCAGATGATCTTGGGTTTGGCTATTACTTTTTACACACAA 3274
                            ? v  v  ivvi   i        v   v  vii  i   v i ii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_104208451_   3275 CATTGTTTAGATAGCATA-GCAATCCATGAAAATAAGAACAGATAGACTA 3323
                           ii---- i -    i -    --  --   iv  i  i     i i i
  L1M4_orf2#LINE/    599 CACC----AAA-AGCACAAGCAA--CA--AAAGAAAAAATAGATAAATTG 639

  chr1_104208451_   3324 GACTTCATTAAAATTT----CTGCTTTGTG-----AAAGACAC----AAG 3360
                                 i      v----  --      -----  i     ----   
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACT--TTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_104208451_   3361 AGAATAAAAAGACAATCCACATACTGGAAGAAAATATTTGCAAAAGACAT 3410
                          i i i         i     v v   i                vv i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_104208451_   3411 ATCTGACAAAAGACTGTTATCCAAAATGCACAAAGAACTCCTAAAAC--- 3457
                               i  ii    vv      i   ii i         i  v   ---
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_104208451_   3458 --AGTAAGAAAACATACAACCTA-TTAGAAAGTGCATCAAA--ATTTTAA 3502
                         -- i   i  i   v i    i -  ?i   i  vi-    --    v  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGG-CAAAGGATTTGAA 836

  chr1_104208451_   3503 CAGAAATATAATCAAAGAAGATATACTAATGGCAAATAGACATACATAAA 3552
                         i   v  v vvi              v      v    ii  i iiv   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_104208451_   3553 GATGCTCCACGTTATTTGTCAT 3574
                                v  i i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (126 / 82)
Gap_init rate = 0.03 (26 / 907), avg. gap size = 2.23 (58 / 26)  


3280 22.61 2.61 3.91  chr1_104221914_104226369.rev     3046  3965 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104221914_   3046 TGGAATAACATGCCAAGTTTATGGATTGAAAGACTCAATATTGTCTGGAT 3095
                              vi i  v   v   i        i      i        ivi   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104221914_   3096 ATCAATAATATCCAAAGCAATCTACAGATATAATTCAATATCTGTCAAAA 3145
                         iv     v vi     vii          vi  iv    vi  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104221914_   3146 TCCCAAAGACATTTTCTGCA-AGATTCATAAAAAAATCTGAAAATTCACA 3194
                              ivvi v    i    - i   v i  ivvi   iv        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_104221914_   3195 TG-AAATACAAAGGACCCTGAGTAGCAAAAACAGTCCTAAAAGAGAAGAA 3243
                           -    i   i      v  i    v      i  i i   i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_104221914_   3244 CAAAGTTGGAGGTCTCCTTCTTTCTGACTTCAAAATTTAACACAAAGTTA 3293
                                     v   viv   i ii i       i   vi      i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_104221914_   3294 CAGTAATCACAACAGTGTAGTACTGGCATAAAGGCAGATATAAAGAC--- 3340
                                  vi       i            i ii   i   v   i---
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_104221914_   3341 ----ATAAA-----GAGCCCAGAAATAAACCCTGACAGATATGGCCAAAG 3381
                         ----   i -----   i              vv   vv     i   vv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_104221914_   3382 GTTTTTCAACGACAGTAGCAGGACCACTCGATGGGGGAAAAAAAGACAGT 3431
                          v     i  i vi  iv  i     i  i      i  i  ----i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA----TAGT 396

  chr1_104221914_   3432 TTTTTCAATAAAT--T-CTGAGAAAACTGCATATCCATATGAAAAAGAAT 3478
                         i       i    -- -   i  v     v   ?   i   v        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_104221914_   3479 AAAGTTCAACCCTTACCTAAAACCATATGCAAAAACTGACT-AAAATGAA 3527
                         i     vi    i     v v       i      i i   -      i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_104221914_   3528 TTCATGTCCTAAATGTAAGACCTAAAACTACAACACTCTTAGAAGATAAC 3577
                          iv?v v             v         i  v            v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_104221914_   3578 ATAGGAAAAAAAATACCTTTGCAATATCAAACCTTGCAGTGTTTTCTTAG 3627
                              ?iv   ----i   i ii iv iiiiiivv   i  v        
  L1M4_orf2#LINE/    547 ATAGGNGTAAA----TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_104221914_   3628 ATATAAAACCAAAGATGCAGGCAAAGAAAGAAAAAATACACAAGTTGCAC 3677
                             i v      iiii  i    vi            v i  i   v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_104221914_   3678 TTCATACAAATTCTAA--TTTTC--CAACAAAAGGCACTATCAACAGAGC 3723
                              vv     vv  --    v-- vv    i i         v i  i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_104221914_   3724 AAAAAATACATCCAACAAAATTGGATAAAATGTTTATAAA--ACATATCT 3771
                         i    i-   v  v   i   v   v     i   ii   -- i      
  L1M4_orf2#LINE/    693 GAAAAG-ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_104221914_   3772 GGTAAAAGATTAATATCCAGAATATATGGGAAAGTTCTACAATTTAACAA 3821
                          i   ii  i vi              iiii  v ii     i i  i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_104221914_   3822 CAACAACAAGAAACAAAACAAACAAACAAAAAAAACAAAGAACACAACTC 3871
                         i  ---------------------------   i     v   v   i ?
  L1M4_orf2#LINE/    792 TAA---------------------------AAAGACAAATAACCCAATTW 814

  chr1_104221914_   3872 AAAAATGGACCAAGGACTCAAATAGACATTTTTCCAAAGAGGACATACAA 3921
                                 i v     i ii           i        i  i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_104221914_   3922 ATGGTCAATAAGCAGATGAAAAGATGCTCAACATCACTAATCTT 3965
                             i         v                     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (130 / 74)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.29 (60 / 14)  


1911 25.65 7.45 0.00  chr1_104249584_104251152.rev      502  1078 (491)    L1M4_orf2#LINE/L1      289   908 (0)  

  chr1_104249584_    502 CACATAGACCAATG-AACAAAATATAGGCCCTGAAAATATATCCATACAT 550
                           i     i     -  i i   vv  ivi iii     v i        
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_104249584_    551 TTACAGCCAACTGATTTTTAACAAAGGTGTCAAGAATACACACTGGGGAA 600
                            ii i   i       ii    i    i     vi iv  v       
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_104249584_    601 AGGAGAATCTCTTTAATAAATGGTTCTGGGAAAACTGGATATTCACATGC 650
                           i v i   i  i  i       v      v         ?i       
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_104249584_    651 AGAA-AATGACACTAGACCCCTCTCTCTCACCGTGTATAAAAATCAACTC 699
                          i  -     vii i       vi   v    i i  i      i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_104249584_    700 TAAATGGATTAAAGAAATAAGTGCAAGACTCAAAACTGTAAAGCTACTAG 749
                         v        i ?   vv   i  i    vii      i    i  vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_104249584_    750 AAGTAAACATAGGAA-AAAGCTT---GATATTTGTCTGGGCAAGAATTTT 795
                            v         ?i-   v   ---  iv  v vi i     vii   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_104249584_    796 TTTAGTAAGATCTCAAAAGCACAGACAACAAAACAGAG--TAGACAAACG 843
                           vii  v  ivi          ii        v i i--    i   iv
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_104249584_    844 GTATTACATCAAACTAAAAAGCCCCTG-----CACAACACACAATTAATA 888
                          v i v       v v    i iii  -----  v iv    v  i  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_104249584_    889 AGGTGAA-------------------GAGAAATTAGTTGCACACTATGTA 919
                          i     -------------------      v  v     v ii  i  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_104249584_    920 TCTGAGGAGGGATTAATATCCAGAGTATATAAGGAACTCAAACAACTAAA 969
                              vi     i vi        i       i      vv      v  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_104249584_    970 TACCAAAAG----AATAATTTGATT-AAAAATGAGCAAAAAACCTGAATA 1014
                           vi    i----     iiii   -       i     ii ii      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_104249584_   1015 GACACT----CACAGAAGACATACAAATGGCCAACAGATCAATAAAAAA- 1059
                             i ----  v      i              i iiivv  i    i-
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_104249584_   1060 -GTTCAACATCACTAATCAT 1078
                         - i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (96 / 49)
Gap_init rate = 0.02 (11 / 620), avg. gap size = 3.91 (43 / 11)  


3015 27.57 0.89 0.33  chr1_104261044_104263792.rev     1356  2258 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104261044_   1356 TGGAAAAACATTCCATACTCATGGATAGGAAGAATCAATATCATGAAAAT 1405
                               i i  i    ii        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104261044_   1406 GGCCATACTGCCCAAAGTAATTTATAGATTCATTGCTATTCCCATCAAGT 1455
                            v     v      v i  i  i       vi  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104261044_   1456 TACCA-CTGATCTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 1503
                          v   -   -i   i  ii     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTG-CCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_104261044_   1504 TATGGAACTGAAAAAGAGCCTGTATGACCAAGATAATCCTAAACAAAAAG 1553
                                v  v  ii  v  v v  ii    i i    i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_104261044_   1554 AACAAAGCTGGAGACATCACACCACCTGATTC--AAACTATACTACAAGG 1601
                                i     ivv      iv  ii   i--     -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_104261044_   1602 CTACAGTAACCAAAAGAGCATAGTACTGGTGCCAAAACAGATATATAGAC 1651
                                  i   i v  ii i       iiiv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_104261044_   1652 CAATGGAACAGAACAGAGGCCTCAGAAATAACACTGTACATCTACAACCA 1701
                                 i    iv   ivii         vv ii     i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_104261044_   1702 ACTGATATTTGACAAACTTGACAAAAACAAGCAGTGGG-AAAGGATTGCC 1750
                          i    v  i     ivv  v   i v  vv  i    -    i  v i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_104261044_   1751 TATTTAATAAATGGTGTTGAAAAAACTGGCTAGCCACATGCAGAAAACAG 1800
                          v  i  i        i  ii v      v  ?         i  i vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_104261044_   1801 AAACTGGACCCCTTCCTTACACCTTACACAAAAATTAAACCAAAATATAT 1850
                           ii         v   i     v  i           vi      iv  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_104261044_   1851 TAAAGACTTAAACGTAAGAGCTAAAACCATAAAAACCCTAGAAGAAAACT 1900
                         i ?    i    i              i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_104261044_   1901 TAGGCATTACGATTCAGGACATAGGCATGAGCAAGGACTTCATGACTAAA 1950
                             ?i v vvv   iv   v v  vv ii    v ii   v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_104261044_   1951 ACACCAAAAGCAACGACAACAAAAGCCAAAACTGACAAATGATATGTAAT 2000
                                     vvii         vv    iv  i    viv iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_104261044_   2001 TAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 2050
                         i   v v  i i  ii  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_104261044_   2051 GGCAACCTACAGAATGGTAGAAAATATTTGTAATCTATCCATCTGACAAA 2100
                          i     i         v            i  vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_104261044_   2101 GGTCAAATATCCAGAATCTACAAGCAGCTTATACAAATTTACAAGAAAAA 2150
                           v vvi          v  i  iv i  iv     v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_104261044_   2151 AACAAACATCCTCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 2200
                         i     i v  iv  i?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_104261044_   2201 CAAAAGAAAACAT-TATGCAGCCAACAA--ACATGAAAAAAAGATCATCA 2247
                          v      i i  -i viii     i  --         i v v   v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_104261044_   2248 TCACTTGTCAT 2258
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.22 (11 / 9)  


2754 27.11 4.33 0.91  chr1_104267518_104272107.rev     3222  4099 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104267518_   3222 TAGAAAAATATTTCATGTTCATAAATTAGAAAAATCAATATTATCAATAT 3271
                          i    i    ii         ii   i   i v i      i i  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104267518_   3272 GTCCATACTACCCACAGCAATCTACAGATTCAATGCAATTCCTATTAAAA 3321
                          v v     v    v vii              i     i     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104267518_   3322 TACCAATGACATTCTTCACAAAAAAAAAAATAAAATGAT---AAAAATTA 3368
                          v   iivi v  i  ii  i   vvi --i  iv    ---    v i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCA 148

  chr1_104267518_   3369 TGTGGAATCACAAAAAACCCAGAA----CAAAAC---------------- 3398
                          i     vii   iii        ----      ----------------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_104267518_   3399 --------TGGAGAAATCACGTTACCTGACTTCTAATTATACTACAGAGA 3440
                         --------     i v    ii v  ii i   v  viv       i  v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_104267518_   3441 TATAGTAACAAAAACAATATATTAATAATACTTGTATAAAAACAGACACA 3490
                           i     iv  i   i i i------i    v i    ii i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTG------GTACTGGCATAAGGATAGACATA 292

  chr1_104267518_   3491 TAGACCAATGAGCAAGAATAGAGAACTCAGAAACAAATCCATACACCTAC 3540
                             i     iivv     v    iii      i   i       ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_104267518_   3541 GGTGAACTATTTTTTGACAAAGGAGCCCACAACATAAACTGGGAAAAGA- 3589
                            v  i iv    i     i  v   v v v   vv v    i     -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_104267518_   3590 CAGTCTCTTCAATAAATAGTGTTGAGAAAACTGAATACACATATGCAGAA 3639
                         i     i     i    i   i  i  v     i   ?v  i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_104267518_   3640 GAATGAAGGTAAACACCTATTTCTCACCATGTATGAAAGCCAAATAAAAA 3689
                                 v ii  v    ii  v      i  ii   iii  v v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_104267518_   3690 TGCATTGAAGGCTCAAATATAAGACCTCAAACTATGAAACTACTAATAGA 3739
                           v  ii?  i ii    i     v  v       i     vi  iv   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_104267518_   3740 AAACATTGGAGAATCTCTCCAGAACACTGGTTTGGGCAA-AACTTCTTAA 3788
                               v  ? v vv   i ivi  vi   v  i     -iii      i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_104267518_   3789 GTAATATCCCACAAGCATAGGCACCCAAAGCAAAAGTAAACAAATGGAAT 3838
                         i  vv iv   v     i i   v v    v    i  i i    v i i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_104267518_   3839 CACAACAAA-TTATAACCTTCTGCACAACAAAGAAAACAATCAACAAAAT 3887
                         iv  v    -   v  v   i  ii vv     i v  v     v   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_104267518_   3888 GAGGAGACAACACACGAAATTGGAGAAAATATTTTCTATTCAT----CTG 3933
                           ii       v   ii   v             v v v    ----   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_104267518_   3934 ACAAGGGGTTAATAACCAGAATATATAAGGAGCTTAAACAACCCTATAGA 3983
                          i     ii vi  v             i  i  ivv     i v   iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_104267518_   3984 AAAAAATCTACTAATCTGATTTAAAAATGGGCAAAATATTTGAATAGACA 4033
                              iv v v   i ii   ?             iv             
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_104267518_   4034 TTTCTCAAATGAAGACATATAAATGACCAACATGAATATGAAAAGATGCT 4083
                               v  v     i   i     i    i v v i             
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_104267518_   4084 CAACATCATTGTTCAT 4099
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (144 / 90)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 5.11 (46 / 9)  


2430 26.39 0.30 0.30  chr1_104289459_104291117.rev      502  1168 (491)    L1M4_orf2#LINE/L1      242   908 (0)  

  chr1_104289459_    502 ACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAT 551
                             i          i   i    ii         i iv ii i   v  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_104289459_    552 ATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATC 599
                                       i    i--    i  --        vv  ii i  i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATT 339

  chr1_104289459_    600 TACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAACAATGGGGAAA 649
                           iiiii vi    i  i     ivv  vv  i v  vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_104289459_    650 GGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTA 699
                          i  vvi  v  i  i              v      v  ?   i   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_104289459_    700 GAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCA 749
                         i  iiv    ii    i    v   i     v           i  i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_104289459_    750 AGATGGATTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGA 799
                          i      i ?   ii       v   v       i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_104289459_    800 AGAAAACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCA 849
                                v    ?i v viv   iv   v v  vv i     v ii   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_104289459_    850 TGTCCAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGG 899
                          ivvi vi            vvi          vv     v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_104289459_    900 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG 949
                           ii v  i   v v  i i   i  ii vv    i  v    i  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_104289459_    950 AGTGAACAGACAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCAT 999
                               v        i   iv            v  i    vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_104289459_   1000 CTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAC 1049
                             i  i  i  vi          v  i  v      vv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_104289459_   1050 AAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAG 1099
                           v     i     i     v  i?    i     i     iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_104289459_   1100 ACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAAT 1149
                            i     v        i  vi viii     v  i        i i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_104289459_   1150 GCTCATCATCACTGGCCAT 1168
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (101 / 71)
Gap_init rate = 0.00 (2 / 667), avg. gap size = 2.00 (4 / 2)  


 538 29.58 0.47 2.82  chr1_104296117_104299662.rev     1776  1988 (1558)    L1M4_orf2#LINE/L1        1   208 (700)  

  chr1_104296117_   1776 TGGAAAAACATTCCATGTCCATGGAGAGGAAGAATCAGTACTGTAAAAAT 1825
                               i i  i      i      vv      v i i  i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104296117_   1826 GGCCAGACTGCCCAGAGAAATTTACAGATTCAATGCTATTCCTATCAGAC 1875
                            v v   v    i vvi  i           i  v  i       i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104296117_   1876 TAACAATGACATTCTTCAGAGAACTAGAAAAAAAATCATTCTTAAATTCA 1925
                          vv  iivi v  i  iiv    v v  v  iv-- v  i  v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chr1_104296117_   1926 TACG-AAATGAAAAATATACCAAATAACCAAAGCAATTCCAAGCAAAAAA 1974
                           i -     v  iiv iv vi    i     i    iiii ----    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA----AAAA 194

  chr1_104296117_   1975 AAAAAAAAAAGCTG 1988
                         i  i  v    i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTG 208

Transitions / transversions = 1.33 (36 / 27)
Gap_init rate = 0.01 (3 / 208), avg. gap size = 2.33 (7 / 3)  

1835 26.72 1.75 2.19  chr1_104296117_104299662.rev     2371  3055 (491)    L1M4_orf2#LINE/L1      227   908 (0)  

  chr1_104296117_   2371 ATTTAAAAACATATACTACAAGGCTACAATAATCAAAATGGCATGGCACT 2420
                             v     - -        i      i       i ii ii   i   
  L1M4_orf2#LINE/    227 ATTTCAAAAC-T-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_104296117_   2421 TGCACAAAAACAGACACATCAACAAATAGAACAGAATAGAAAGTA-AGAA 2469
                         v   i  ii i     i  vi iv   i   i     v  i   v-    
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_104296117_   2470 ATAAGCTGCATGCCTACAACCATCTTC---TGATCTTCAATAAAGTAGAC 2516
                             i i-   ----   vii  vv  ---    i   i i  i vv v 
  L1M4_orf2#LINE/    325 ATAAACC-CAT----ACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_104296117_   2517 AAAAACAAGCAATGAGGAAAGAACTTTCTATTCAATAAGTGATTCTGGGA 2566
                           i v  vv     i        ivv   v     i  i  i v      
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_104296117_   2567 TAACTGGCTAGCTATATGCAGAAGATTAAAGCTGGAACCCTTTCTTACAC 2616
                         i      v  ? i i     i    v i   i    v    vi  i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_104296117_   2617 AATATACAAAAATCAGCTTGAGATAGATTAATGACTCAAAT--AAAATCT 2664
                         v            i i  ii i  i   i ?v   ii    --  i v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_104296117_   2665 AAAACAATAAAAACCATAGACAAAAACCAAGAAAATAACATTCTGGACAT 2714
                              v      vi v    vi     vv  i?ivv  iv   vv   v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr1_104296117_   2715 AGGTCCTGACAAAGATTTCTT-GATGAAGATGCCAAAATCAATTATGACA 2763
                         v  viiv i   v i      -   - v  ii      v  vvviii   
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACA 618

  chr1_104296117_   2764 AAAACAAAAATTGACACATGGGACCTAATTAAACTAAAGAGCTTCTGCAC 2813
                            iv      v  i v  v    i v  i   v v  i i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_104296117_   2814 AGCAACAGAAACTATGAATAGAGTAAATAGATACCCCACAAAACGAAAGA 2863
                         vv   vi  v     v  v i   i  v   i v      i  i ii   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_104296117_   2864 AAATATTTGCAAACTATGCATCCGACAAAGGTCTAATATCTAGAATCTAT 2913
                                      ii  ii   i  i  i  v  vi    i     v   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_104296117_   2914 AAGGAACT--TAAAAA--AAGAAGTACAAGCAAAAACCAAACAACCCTAT 2959
                           i     --  v  v--  v  -  -----    iv    i     v  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAA-TA-----AAAAGACAAATAACCCAAT 812

  chr1_104296117_   2960 TAAAAAAATGGGCAAAAGACATAAAAATGCACTT-TCCAAAGAAGACATA 3008
                          ?     -        i  iv i  v vi  i  -           i   
  L1M4_orf2#LINE/    813 TWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_104296117_   3009 CACATAGCCAATAAGCATATGAAAAAGTGTTCAACAACACTAATCAC 3055
                           v  i           i       ii  i      v  ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (104 / 75)
Gap_init rate = 0.02 (15 / 682), avg. gap size = 1.80 (27 / 15)  


1676 29.03 3.97 5.19  chr1_104303811_104305764      565  1470 (484)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr1_104303811_    565 CATGTTCACTGTTTGAAAGACCATCATA--GTAAATATATAAATTATTTG 612
                                 iv v   i     i- v   --  v  v  ivv   vv iiv
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACT-TAATATTGTTAAGATGGCAATACTCCC 62

  chr1_104303811_    613 CATAGTGATATACAGATTTAACTCAATTCCTATTAAAATTTAGGTCTCAT 662
                           v v    v        i   v    i     i     iivi iiv v 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_104303811_    663 TTTTTGTAGGTATGTAAAAGATTATTCTAAAATGTATGTGGACAGGGAAA 712
                               i  iv  vv v   v v  i       vi  i    v v v  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr1_104303811_    713 GATACTATAATAAATAACACTAATTTGGAAAAGAAGAATAAAGTGGGCAG 762
                          ivv i v    ivi  v  v vi   i          i     v  vi 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr1_104303811_    763 AATCAG----TCTA---TCAGATTGTATTATATAGATGCAGATATCAAGA 805
                          v   v----i i ---   i viv  i  i v  v i   vv       
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_104303811_    806 T--TGTGATATTGA-AGGTGGATTGGCCCACAGACTGATAAAACAAAATA 852
                         i--    i  i  i- viv    v i vi i   iii  ii  i i   v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_104303811_    853 AAAAAAAACCCACACAAAGTAGACACATTCAAATATCCTCAAATTACTTT 902
                         i i i---i   ---i  i  i  v   v  vv   vv    v v i   
  L1M4_orf2#LINE/    313 GAGAG---TCCA---GAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_104303811_    903 TTACAAGTAT-TCAAAATAATTCAATAGAAAATAGATAGCCTTATATAGA 951
                         iv     vi -i   i iv       i ii  vii    i   v vv v 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_104303811_    952 GGAATGATGTTGGAGCAATTGTGTATATATAGGCCAAAAAATACACAAAG 1001
                         --    i  i   ii   i  vi  ?vi i v  v   i   i-------
  L1M4_orf2#LINE/    407 --AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG------- 447

  chr1_104303811_   1002 ACACAAAACAAAACAAATCCTTGATGTAATCATCACATCTTCTAAAAATA 1051
                         ---------  iviii i  i ------ i -     i v v  v   v 
  L1M4_orf2#LINE/    448 ---------AAGTTGGACCCCT------ACC-TCACACCATATACAAAAA 481

  chr1_104303811_   1052 TTAGCTCCAGATGGATTAAAGAGTTAAATATA-----TAA---TATGAAA 1093
                            i   v i      i ?   vi     i  -----   ---   i   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_104303811_   1094 CTTTTAGAAAAGTGAATAGAAAGAAATAGTCATGACCTTGGGT-AGGCAA 1142
                           i      i iviv    i?iv    vv  i           -      
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_104303811_   1143 AAATTTCTTAGACATGACAGCAAAAACACA-GTACATAAAAGAAAAATT- 1190
                         vii         i      v     i    - i - i          v -
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCA-ACAAAAGAAAAAATA 630

  chr1_104303811_   1191 TATAAATTGGGCTTAATCCAAACCAAAAAACGGTTTTCT-CTGT----GA 1235
                         v         i   v   v   ii     - --    v -  vi----  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAA-C--TTTTGTGCTTCAAAGGA 677

  chr1_104303811_   1236 CTCCTTTAAGAGGATGAAAATACAAATTACTGAGTGGGAGAAAATATTTA 1285
                          v iv i    iii      v    vii  v  i               i
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_104303811_   1286 CATATCACATACAAAACAAGAG--TAGTACCTAGAATACATGAAGAATGT 1333
                           v    i   ivvi i   i -- v   i i      i  i     ivi
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_104303811_   1334 TCAAAACTCAACAGTGAGTAAACAAATAATTTGATTAGAAAATTGACAAA 1383
                          i v       i i i iv i        iiii   ?i     v i    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_104303811_   1384 AAACATGAAGAAACATTTCACCTATTTTACCAGAGAGAATGTACAAATGG 1433
                         ii iv    v i       -------- -   i   ii  i         
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTC--------T-CCAAAGAAGATATACAAATGG 868

  chr1_104303811_   1434 CAGATAAGCAAATAAGAAGA-----AACATTTCACACATTTT 1470
                          vi       v  i i    -----     --  ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACAT--CAZZZZZZZZ 908

Transitions / transversions = 1.44 (153 / 106)
Gap_init rate = 0.03 (28 / 895), avg. gap size = 2.96 (83 / 28)  

 264 16.67 1.67 0.00  chr1_104303811_104305764     1472  1531 (423)    L1M4_orf2#LINE/L1      848   908 (0)  

  chr1_104303811_   1472 CCAGAGAGAATGTACAAATGGCAAATAAGCAGATTAAAAAGT-TTCAACA 1520
                            i   ii  i          v        v  v    ii -i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_104303811_   1521 TCATTATCCAT 1531
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1)  


2528 26.75 2.74 3.18  chr1_104363396_104366228.rev     1431  2342 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104363396_   1431 TGGGGAGCTCTTTCATGTTCATTGATAGGAAAACTCAATTTTATTCCTGA 1480
                            ii  v v ii         v   v    i   i   v  i  ---- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT----A 46

  chr1_104363396_   1481 AAACTAATAGGTGTCAGT-TTTCATAAATTAGTCTATAGATTTAATACAA 1529
                          i --------  v  i -i i vi     ii    i     i  ii   
  L1M4_orf2#LINE/     47 AGA--------TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAA 88

  chr1_104363396_   1530 TCTCAAACAAAATCCAAAAGATA----TTTTGTCAATATCAACAAATTCA 1575
                           i v v        v -- v i----     ivi v  ii    ii v 
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr1_104363396_   1576 TTCTAAAGTTTATATTGAAAAGCAAA--ACCGAGAATAGCCAAAACAATA 1623
                          i     i  i    v    v    i--   v                 v
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_104363396_   1624 TTGACGGAGAA-AACAAAGTTGAAGAAATGATACCATCCAACTTCAAAAC 1672
                             vii    -          i  i v v i  ivi    i        
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_104363396_   1673 CTACTATAAAGCTATAGTAATCAA--CAGTGGTGGTGTTGGCAAAACAAC 1720
                         i     i       i         --     -    ii     v  vi i
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTG-TGGTACTGGCATAAGGAT 285

  chr1_104363396_   1721 AGATGAATAGATTAATGGAACAGCATAGAGAGACCAGAAGTAGACCCACA 1770
                            iiv      i       i  v  v     v      i  i     i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_104363396_   1771 TAAAAGTAGTCAACTGACCTTTGACAAAAAAAAAAAAAGTAAAGGCAATA 1820
                         i vvvi i     i   ii  i     iiiv------- iv   i v  v
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGT-------GCCAAGACCATT 378

  chr1_104363396_   1821 AAATGGAGAAAATATTGTCTTTTCAACAAATATTGCTGGAACATCTAGAC 1870
                         v     i    iv  v               iv      i   v  i  i
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_104363396_   1871 ATCCA-ATTCAAAAAAAC-AATTTTAACACAGTTTTTAAACCCTTCTCAG 1918
                          ?   -  v     i  i-  v  vi  v vvvii i v   v viv  i
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_104363396_   1919 ACATTAACTCACAATGAA--ACAGACTTATATGTAAAATGTGAAATTATA 1966
                          v         v    i -- ?    i  v      i vv i   i    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_104363396_   1967 AAACT---AAAAGATAATATAGGAGAAAGTC--AATGACCCTGATTTTGT 2011
                              --- i    v  i     ? v  i  --vi     i  iv  v v
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_104363396_   2012 CAGTAACTCTTTA---ATTACCACAAAGTTGTCATTCATGAAAGGAATAA 2058
                           i iii ii   ---  v  vv    iviiiv viv ii    i  v  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_104363396_   2059 TTAGTAATTTGTACTTTGTTAAAATTAAAAATGTATGTTCTGCAAAAGAA 2108
                          vii   v   v    ii i           iv v   v  v    i  -
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA- 677

  chr1_104363396_   2109 TGATATTTCACCAAGATAATGAAAAGAGAGTCCACAGA-TTAAAGAAAAT 2157
                         ---i i -- i     v i        v ii       - vii       
  L1M4_orf2#LINE/    678 ---CACT--ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_104363396_   2158 ATTTGCAAA--ACATGCCTTATAAAGTACTGGTAACAAAAATATACAAAG 2205
                                  -- i  ii  v    i v   v   v v i      i    
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_104363396_   2206 AACTTTTAAAACTCAGCAATAAGAAAATAGATATCCCAGCCTAAAACACA 2255
                             i   v      ii     i  i i i   v    iii?    - ii
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA-ATG 821

  chr1_104363396_   2256 GGCAATGTATCTGAACAGATATCTTACCAAAAAAGTTGTAGAGATGGCAA 2305
                              v v  i    i   i  i iv     i   v i  v i     v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_104363396_   2306 ATAAACATATGAAAAGATGCTCACCATCATATGACAG 2342
                             i  i               v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.57 (54 / 21)  


2303 26.88 0.43 3.56  chr1_104470262_104478355.rev     5002  5704 (2390)    L1M4_orf2#LINE/L1        1   681 (227)  

  chr1_104470262_   5002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5051
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104470262_   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104470262_   5102 TACCAATGACTTTTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i     ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_104470262_   5150 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_104470262_   5200 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5249
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_104470262_   5250 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGCATGGTACTGG 5299
                                 i   i    ii         i --------------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA-------------------- 278

  chr1_104470262_   5300 TACCAAAACAGAGATATAGACCAATGGGACAGAACAGAGGCCTCAGAAAT 5349
                           -- ii i   v       i      i i    iv   ivii       
  L1M4_orf2#LINE/    279 TA--AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_104470262_   5350 AATACCACACATCTACAACTATCTGATCTTTGACAAACCTGACAAAAACA 5399
                           vv   i    i  iiiii vi    i  i     ivv  v   i v  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_104470262_   5400 AGAAATGGGGAAAAGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGG 5449
                         vvv          ii  vvi  v  i  i              v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_104470262_   5450 CTAGCCATATGTAGAAAGCTGAATCTGGATCCCTTCCTTACACCTTATAC 5499
                         v  ?   i   i i  iiv    vi    i    v   i     v     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_104470262_   5500 AAAAATTAATTCAAGATAGATTAAAGACTTACATGTTAGACCTAAAACCA 5549
                                  i    i  i   i ?    i  v    v   v       i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_104470262_   5550 TAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCAT 5598
                              vi i           v    ?i- v i -   iv   v v  vv 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTT 575

  chr1_104470262_   5599 GGGCAAGGACTTCATGTCTAAAACATCAAAAGCAATGGCAACAAAAGCCA 5648
                         i     v ii   v ivv  vi   i        vvi          vv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_104470262_   5649 AAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGTAAAA 5698
                             v  i    v   ii v  i   v v  i i   i  ii vvi   i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_104470262_   5699 GAAACT 5704
                           v   
  L1M4_orf2#LINE/    676 GACACT 681

Transitions / transversions = 1.48 (111 / 75)
Gap_init rate = 0.01 (7 / 681), avg. gap size = 4.00 (28 / 7)  

 860 24.43 0.00 0.00  chr1_104470262_104478355.rev     7383  7603 (491)    L1M4_orf2#LINE/L1      688   908 (0)  

  chr1_104470262_   7383 AGAGTGAAAAGGGAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTC 7432
                          i         iv    i                 v       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_104470262_   7433 ATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTT 7482
                               i  i  i  vi          v  i  v      iv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_104470262_   7483 ACAAGAAAAAATCAAACAACCCCATCAACAAGTGGGTGAAGGATAGGAAC 7532
                          i  v     iv    i     v  i? v  i    ii      vv   i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_104470262_   7533 AGATACTTCTCAAAAGAAGACATTCATGCAGCCAAAAGACACGTGAAAAA 7582
                            i i     v        i  v  viii     v ii   i      i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_104470262_   7583 ATGCTCATCATCACTGGCCAT 7603
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (32 / 21)
Gap_init rate = 0.00 (0 / 221), avg. gap size = 0.00 (0 / 0)  


2364 27.78 6.25 1.16  chr1_104574450_104576378.rev      576  1439 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104574450_    576 TGGAAACACATCTTACACTCAAGGATGGGTAGAATCAATATTGTGAAAAT 625
                               v i   ii iii   v    v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104574450_    626 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 675
                          i v     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104574450_    676 TGCCACCATCATTCTTCACATAACTAAAAAAAAAAAAAACCCTAAAACTC 725
                          v   v vv v  i  ii  v  v vi v  ivvi ---i       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA---TCCTAAAATTC 147

  chr1_104574450_    726 ATATGAAACCAAAAAGGAACCCACACAGCCAAAGCAAGACTAAGCAAAAG 775
                              i  viiv  i   v  viv i       i   vvi i iv  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_104574450_    776 GAACAAATCTGGAGGCATCACATTACCCAACTTCAAACTATACTATAAGG 825
                                vi      vv     i v     i      viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_104574450_    826 CCATAGTCACTGAAACAGTGTGGTACTGGTATAAAAATAGGTACATAGAC 875
                          i i   v iii i               i    ii    ii i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_104574450_    876 CAATGGAACAGAATAGAGAA--CAGAAATAAATCCAAATGCTTAAAGTGA 923
                                 i     v    i--          i   v iii   vi  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_104574450_    924 ACTGAGCATTTACAAACCAAA----CCAAAAC-ATAAAGTGGGGGGAAAA 968
                          i   ---   v i --   i----    i  -  vv i     ii i  
  L1M4_orf2#LINE/    348 ATTGA---TTTTCGA--CAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_104574450_    969 -AGCCCTATTCAACAAATGGTGCTAGGGTAACTGGCAAGCCACATATAAA 1017
                         -  i i -                i  ii      vv ?      ii   
  L1M4_orf2#LINE/    393 TAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_104574450_   1018 AAAATGAAACTGAATCCTCAACTTTCCCCTTAAATGAAAATCAACTTAAG 1067
                          i      ii  i i  ii v  iv v  v  v ii     i    i  i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_104574450_   1068 ATGTATCAAAGTCTTAAATCTAAGAACTGAAACCATAAAAACTTTAGA-- 1115
                            v    ?  v i     v     i  i    i      vii     --
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_104574450_   1116 ----CAT---------------------TGGATTAGACAAAGATTTTGTG 1140
                         ----   ---------------------   i    i   v i   iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_104574450_   1141 ACCAAGAACCCAAAAGCAAATGCAACTAAAACAAAGATAAATAAGTGGGA 1190
                         ivi v  vv         v v     v   iv   i   i    i v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_104574450_   1191 CTTAATTAAGCTAAAAAGCTTCTGCATGGCGATAGATACAATCAGCAGAG 1240
                            v  i  iv v    i   i  iiivv i vi  i  v    iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_104574450_   1241 TAAACAAACAAACCACAGAAGTGGAGAAAATCTTCAC-----------CT 1279
                          i  v i    v        vv         v  ii -----------  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_104574450_   1280 GACAAATGGCTAATATCCAGAATCTGCAAGGAACTCAAGCATATCAAGAA 1329
                           i  iv i  vi          v ii  i      vvi  vv    v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_104574450_   1330 AAAAAA-------AATCTCATCAAAAAGTGGGCTAAGGACATGACTAGAC 1372
                         v     -------  i iv  i?    i     v     iv   v     
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_104574450_   1373 AATTCTC-AAAAAAGATATACAAACAACCAACAAACATAGGAAAAAAATG 1421
                          v     -   i            iii    i  i  i v     i -  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chr1_104574450_   1422 CTCAACATCTCTAATGAT 1439
                                  v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.57 (64 / 14)  


2965 27.00 0.99 1.32  chr1_104586896_104593642.rev     5346  6256 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104586896_   5346 TGGAAGAACATTCTATGCTCATGGATAGGAAGAATTAATATTGTGAAAAT 5395
                              ii i  i i   i        v      v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104586896_   5396 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCTTCAAGC 5445
                            v     v     iv i  i  i       ii  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104586896_   5446 TAC-GGATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 5492
                          v -i v  v    i  -i     -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr1_104586896_   5493 CATATGGAACCAAAAAAGAGCCTGCATTGCCGAGACAATCCTAAGCAAAA 5542
                                  viiv  ii  v  v v  v   i i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_104586896_   5543 AGAACAAAGCTGGAGGCATCACACTACCTTACTTCAAACTATACTACAAG 5592
                                  i      vv       v  iv i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_104586896_   5593 GCTAAAGTAACCAAAACATCATGGTACTGGTACCAAAACAGAGATACAGA 5642
                             v     i   i   vii         i iv ii i   v   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_104586896_   5643 CCAGTGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCAACAA 5690
                         i  i     i    i--    i  --        vv   i    iv iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_104586896_   5691 CCATCTGATCTTTGGCAAACGTGACAAAAACAAGAAATGGGGAAAGATTC 5740
                         i  vi    i  i i   iv   v   i v  vvv            v v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_104586896_   5741 -CCTATTTACTAAATGGTGCTGGGAAAACTGGCTAGCTATATGTAGAAAG 5789
                         -i  v  i vi              v      v  ? i i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_104586896_   5790 CTGAAACTGGATCCCTTCCTTACACCTAATACAAAAATTAATTCAAGATG 5839
                         v    ii    i    v   i     vv             i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_104586896_   5840 AATTAAAGTCTTAAATGTTTGACCTAAAACTCTAAAAAACCCTGGAAGAA 5889
                         i  i ?  v i       vv  v        v     v-i i i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAA 543

  chr1_104586896_   5890 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGAC 5939
                            v    ?i v viv   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_104586896_   5940 TAAAACACCAAAAGTAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5989
                           vi          i vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_104586896_   5990 TAATTAACCTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAACAGAGTG 6039
                          v  i  vv v  i i   i  ii vv    i  v    i   v i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_104586896_   6040 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 6089
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_104586896_   6090 CAAAGGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACTAGA 6139
                         i  i  i  vi          v  i   v    ivv    -i i v  iv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAAT 792

  chr1_104586896_   6140 AAAAAATTTAAAAAAAAATCAA---AAAAGTGGGCGAAGGATATGAACCG 6186
                              i--- v   v  vi   ---    i     i      v    iv 
  L1M4_orf2#LINE/    793 AAAAAG---ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_104586896_   6187 ACACTTCTCAAAAGAAGACATTTATGCAGTCAACAGACACATGAAAAAAA 6236
                            i     v        i  vi viii i   i ii          i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA- 888

  chr1_104586896_   6237 TGCTCATCATCACTAGCCAT 6256
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


2097 24.78 6.58 5.25  chr1_104616011_104620314     2916  3811 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104616011_   2916 TGAAAAGACACAGTGTGTTCATGGATTAGAAGAC--AATATTGTTAA--- 2960
                           i     i ivvii            i      --           ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104616011_   2961 ---AATATTACC-AAGTTGATCTACAGATTCAATGCTATCTCCAT-AAAA 3005
                         ---    i v  -  i                 i  v   i i  -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104616011_   3006 TGCCATCTCCATAAAATGTCTATGAGATTTTTTAACAGAAACTAAAACAA 3055
                          v   v  --------- i  -------     i-      i i --   
  L1M4_orf2#LINE/    101 TCCCAGCT---------GCCT-------TTTTTG-CAGAAATTGA--CAA 131

  chr1_104616011_   3056 AACT-ATTTTTAAATTTATGTGGA--------------------GCCA-- 3082
                         i-  -  ii v     i  i    --------------------    --
  L1M4_orf2#LINE/    132 G-CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr1_104616011_   3083 -CAA-----AGAAAGAAGAACAAAGCAGAAGGCATCACACTTTCTGATTT 3126
                         -   ----- i              iv i   vv        i ii    
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_104616011_   3127 CAAAATATATTACCAAGTTACAG-AA--AATACTCAGTATGGTACCAGCT 3173
                              iv  i   v   i     -  --  v  --   i      ii  v
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGAC--AGTGTGGTACTGGCA 278

  chr1_104616011_   3174 CAAAGA-AGATGGGTACACCAATGCAACATAAT-AAAAGCCCCGGAAATA 3221
                         i  i  -   iivi  v i     v  i v   -i i  i  -i      
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC-AGAAATA 327

  chr1_104616011_   3222 AAACCATGTATATAAAGTCACCCAATTTCCAACAAAGCTGACAAGAATAC 3271
                           v    ii  v  vi    viii    i i    i v  v     vi i
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_104616011_   3272 AGAATATAAAATGGATATGGTCTT--CAACAAATAGTTTTTGGAAAACTC 3319
                         vv   ivii  v i   --     --        i  vi v   v    v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATA--GTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_104616011_   3320 TATATCAGCATGCAAAAACATAAAACTGTACCTCCATATTAAACCATACA 3369
                         v   ? vi         iv  i  ii  v   i i iv i v      i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_104616011_   3370 CAATA-TTAACTAAAAATAGATTAAAGACTTAAATGTAAGAACTTAAACG 3418
                            v -      v     i   i ?    i           i  v    v
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_104616011_   3419 GTAAAATTCCTAGCAGAAGGATAAAAACCCCTTGTTGAAAACA-AGGAAA 3467
                         i     i  i   ---   ------------------      -   ?iv
  L1M4_orf2#LINE/    526 ATAAAACTCTTAG---AAG------------------AAAACATAGGNGT 554

  chr1_104616011_   3468 CAACCTAT-TGACATTAGTTGAAGCAATGAATT-TTGGATATGACCTCAG 3515
                         v  i  vi-    v  i v v i      iv  -  i        vi  i
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_104616011_   3516 AAGCA--GTTAACAGAAGCAAAAATGTACAAGTGTAACTACGTCAAACTA 3563
                              --ivi    i   v      iv i  i vvi   v i     v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_104616011_   3564 CAAAGCTTCTCAGCAGCAAAATAAACAATAAACAGAATGAAAAGGAAACC 3613
                         v   i   i vv  vv    iv v  v  v  v i i       iv    
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_104616011_   3614 TTTGGAATGGGAGAAAATATTCGCAAACCATATATCTCATAAGCAGTTAA 3663
                         ivii                 i     i         v     viii vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_104616011_   3664 TTTCCAAAACATAAAAGAAACTCTTACAACTCAACAACAC---GACACCC 3710
                          v    i  i   v  ii                i  i v---    vvi
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_104616011_   3711 CCCCACAAA-AAAAAATTGGCAAAAGACTTGAACAGCTATATC---AAAG 3756
                         vv  -   v-?      v      i  i     i  vi  v  ---    
  L1M4_orf2#LINE/    805 AACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_104616011_   3757 AAGACATACAAATAGCTACCAGATATATGAAGTGATACTCAATATCATTA 3806
                             i        i  i vi iii i     iv   i     i    ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_104616011_   3807 ATTAT 3811
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.51 (131 / 87)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 3.31 (106 / 32)  


3242 27.09 0.55 0.55  chr1_104626599_104632836     3086  3993 (2245)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104626599_   3086 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAATATTGTGAAAAT 3135
                              ii i  i     i    i i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104626599_   3136 GGCCATACTCCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3185
                            v           iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104626599_   3186 TAGCAATGATTTTCTTCACAGAA-TTGGAAAAAGCT-ATTTTAAAGTTCA 3233
                          vv  iiviii  i  ii     -   -- v     -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_104626599_   3234 TGTTCAACCAAAAAAGAGCCCACTTTGCCAAGTCAATACTAAGCCAAAAG 3283
                          i vv  viiv  ii  v  vivv v     iv    vi i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_104626599_   3284 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGGC 3333
                                i      vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_104626599_   3334 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3383
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_104626599_   3384 AATGGAACAGAAC--AGAGTCCTCAGAAATAATGCCACATATCTACAACT 3431
                                i    i--       --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_104626599_   3432 ATCTGGTCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 3481
                          vi  i i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_104626599_   3482 CTATTTAATAAATGGGGCTGGCAAAACTGGCTAGCCATATGTAGAAAGCT 3531
                           v  i  i      v     v v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_104626599_   3532 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 3581
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_104626599_   3582 TTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3631
                          i ?    i     i v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_104626599_   3632 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3680
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_104626599_   3681 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATGAATGGGATCTA 3730
                         vi            vvi          vv     v   i   v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_104626599_   3731 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGTGAA 3780
                           i   v v  i i   i  ii vv    i  v    i  vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_104626599_   3781 AAGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTACCCATCTAACA 3830
                            i     i                 i       vii ivi    i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_104626599_   3831 AAGGGCTAATATCCAGAATCTACAATGAACTTCCACAAATTTACAAGAAA 3880
                          i  i  vi          v  i  v     iii    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_104626599_   3881 AAAACAAGCAACCCCATCAAAAAGTGGGCAAAGGATATGAGCAGACACTT 3930
                           i    ii     v  i?    i            v   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_104626599_   3931 CTCAAAAGAAGACATTTATGTAGCCAAAAAACACATGAAAAAATGCTCAT 3980
                            v        i  vi vi i     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_104626599_   3981 CATCACTGGCCAT 3993
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

2374 28.08 2.64 2.64  chr1_104626599_104632836     4840  5747 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104626599_   4840 TGGAAACACATCCCATGCTCATGGATATGTAGAATCAGTATTGTGAAAAT 4889
                               v i        i        vv v   v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104626599_   4890 GACCATACAGCCTAAAGCAATCTACAGATTCAATGTAATTCCCATGAAAA 4939
                          i v    vv  i   vii              i i   i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104626599_   4940 TGTCATC-ATCATTCTTG-AGAGAACTAGAAAAATAAATTTCAATTTTAT 4987
                          vi  v -ii v  i   -   -  i iiv  iv i vii v  v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_104626599_   4988 ATGGAACCAAAAAAGAGCCCACATGGACAAAGCAAGACTAAGCAATATGA 5037
                               viiv  ii  v  viv  i v    i   vvi i iv  v v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_104626599_   5038 ACAAATCTGGAGGCATCGCATTACCTGACTTCA----TTACTATGAGGTA 5083
                              vi      vv  i  i v  ii i    ----      ii i iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_104626599_   5084 ATAGTTACCAAAAAAACATGATACTAGTATAAAAATAGGCATGTAGATCA 5133
                          i   v i   i v iii  i    i i    ii    i   i       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_104626599_   5134 ATGGAACAGATTAGATAACCCAGATATAAAGCCAAATACATACAGCAAAC 5183
                               i   v v  v ii     v     v   v i iv  ii iv  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_104626599_   5184 TGATCTTCTACAAAACATACAAAAAC-ATAAAGTGGTGAAAGTACACTTT 5232
                             i   v    ii-i i v  i  -  vv i   v     v i v i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_104626599_   5233 ATTCAATAAATCATGCTGAGAAAACTGGCAAGCCACATGTA---GAATTA 5279
                         v     i    vi     i  v      vv ?       i ---    v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_104626599_   5280 AACCTAATCCTCATCTCTCACCTTATGCAAAAATGAACTCAAGGTGGATC 5329
                          iiivi i  ii i   v    v   i       v       ii      
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_104626599_   5330 AAAGACTTGAATCTAAGA-TTGAAACCACAAAATTTCTAGAAGATAACAT 5378
                          ?    i i   v     -i i    i i    i ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_104626599_   5379 TAAAAAAACTTTTCTAGACATTGGCCGAGGCAAAAA------AAAAAAAA 5422
                         vii?iv  v i   vv   v    viv      vii------ i -----
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA----- 593

  chr1_104626599_   5423 AAAGAACTATGAC--TAAGAACA-AAGAAACAAATGGAATAAACACAAAA 5469
                         -------      --i  i i  -   v      v i  -   i ----i
  L1M4_orf2#LINE/    594 -------TATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATA----G 631

  chr1_104626599_   5470 ATAAATGGGACTTAAT-GAAACTAATAAGCTTCTACACAGCAAAAGAAAT 5518
                               v      v  -i   i   -  i   i iii vv    i  v i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACAC 680

  chr1_104626599_   5519 AATTAGCAGAGTAAACAGACAATGCACAGAGTGGGAGAAAATGTTTGCAA 5568
                         v  i iv i   i  v      iv      i           i       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_104626599_   5569 ACCATGCATCTGACAAAGGACCAATATCCAGAATCTACAAAGAATTCAGA 5618
                          i   ii      i  i    ivi          v  i      i  vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_104626599_   5619 TAAATCAGAAAAAGCAAAGAAACAAACAATCTCATCAAAAAGTGGGCAAA 5668
                         i  v   iv  ---i   i i     i  i iv  i?    i        
  L1M4_orf2#LINE/    781 CAACTCAATAA---TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_104626599_   5669 ATACGTGAATAGACAATTCTC-AAAGGAAATATACAAATGGTCAACAA-- 5715
                         iv iv          v     -    i i            i   i  --
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_104626599_   5716 ACATGAAAAAAATGCTCAACATAACTAATTGT 5747
                                  i -          v ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (156 / 95)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.40 (48 / 20)  


1798 26.64 5.65 5.88  chr1_104642783_104644820      671  1537 (501)    L1M4_orf2#LINE/L1        4   868 (40)  

  chr1_104642783_    671 AAATATATTCCAAGTTGATGAATTGGAAGAATTAATATTTTTAAAAAGTT 720
                            v    i   v   v   i         v        v    i v vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_104642783_    721 TATACTGCC-AAAGCAGTCTGCAGATTCAACGCAATCACTATAAAAATAC 769
                         v     v  -   viii   i                v    v     v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_104642783_    770 CAATGGCTCTCTTCACAGAAACAGAAAAAAAACT-ATCCTAAAATCC-CA 817
                           iiv  ii i  ii      iv  v  i---  -          i -i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCATA 150

  chr1_104642783_    818 TGAAAGCACAAATGACTATGAATTATGAAAGTAATTATGGAAGCAAAAAA 867
                           i  iii   iv   ivv    viiv   ii   iv  i  --  i  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA--AAGAAG 198

  chr1_104642783_    868 AATGAAGCTAAATGCATCACACTACCTAAGATTTGGTGTTAGTCACAGAC 917
                           ii   i ii v vv       v  i  --   ----------------
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAA--TTT---------------- 230

  chr1_104642783_    918 TAAGACAAAGATTTGTATGACAGGCAAAGCTATAGTCATGCCAACAGCAT 967
                         -----    iv  vv  -------        i   v  vvvi    ii 
  L1M4_orf2#LINE/    231 -----CAAAACTTACTA-------CAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_104642783_    968 AGTATTGTTATAAAAAGAGACACACAGACCAATGTAATAGAATAAATGCT 1017
                         i   i  vi    ii v     i i   i     v        vi viv 
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_104642783_   1018 TCAAAAA-AA-----TGCATCTACAGCCAACTAAGTTTTTCCAAAGTTGT 1061
                         i  i   -  ----- i   i  ii i   i i v   ivv   i v  i
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_104642783_   1062 CAAAAACTCACATTGGAGAACGAATAGTCTCTTCAATAAATAGTA-TGAT 1110
                            i v viv  v   i   v         i     i    i  i-  --
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG-- 416

  chr1_104642783_   1111 GGA-AATTTGATATCAACATGCAAGAATAATGAAACTAGAC----ACCT- 1154
                            -  i v    ? v        -  v      ii i   ----    -
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAA-AAGAATGAAGTTGGACCCCTACCTC 465

  chr1_104642783_   1155 ---------------ATTGACTCAAA-----TTAAAAACTAAAATGTGAG 1184
                         ---------------   i       ----- i ? i  iv      i  
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_104642783_   1185 AATGAAAAGTATGAAACTACTAGAAGACAACGTAGGGAACACACTTCGTG 1234
                          iiv    v   i     vi       v   i    ?ivv vv       
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_104642783_   1235 ACATTG--CTCGGCATAAAGACTTTTTAGATAAAAATCTCAAACATAAAA 1282
                           v   --i v    -- v ii  i       vi -ivi    vii v  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCA--ATGGTTTCTTAGATATGA-CACCAAAAGCACAA 612

  chr1_104642783_   1283 GCAGCAAAAGCAAAAATAGACAAA--GGATTTCATCAAA-TTAAAAAGCT 1329
                            i      v         i   --   i         -       -  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CT 661

  chr1_104642783_   1330 TCTGCACAAAAAAAGAAAACAATCAACAGGGTGAAGTAA-AGCCTACATA 1378
                          i  ii vvv   i  v - v     v ii     ivi - i  i   v 
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACA-CTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_104642783_   1379 ATGAAACAAAATATTAACAAACTATACATCTGATTATCTGATAGGAGTTT 1428
                            ii v        vi    ii   --------         i i vi 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATA--------TATCTGATAAGGGACT 752

  chr1_104642783_   1429 AATATCCAAAATATGTATGAAACTCAAATAATTCAGCAGTTATTATAC-- 1476
                         vi      i     i  vii     vv i  i   ii i v vv v  --
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_104642783_   1477 ----TTCAAT-AAAAAGTAGGCAAAAAACCTGTATAGACATTTCTTAAAA 1521
                         ----ii    -?    i i      ii ii  v            iv   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_104642783_   1522 GAAGATATACAAATAG 1537
                                       i 
  L1M4_orf2#LINE/    853 GAAGATATACAAATGG 868

Transitions / transversions = 1.55 (138 / 89)
Gap_init rate = 0.03 (28 / 865), avg. gap size = 3.57 (100 / 28)  


2197 27.48 0.46 0.61  chr1_104682717_104684371.rev      502  1156 (499)    L1M4_orf2#LINE/L1      201   854 (54)  

  chr1_104682717_    502 CAAAGCTGTAGGCATCATGCTACCTGACTT-GAAACTATACTACAAGACT 550
                              i  v   vv   ii  v  ii i  -i     -        ii  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr1_104682717_    551 ACAGTAACCAAAACACTGTGGTACTGGTACCAAAACAGAGATATAGACCA 600
                                i   i   v           i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_104682717_    601 ATGGAGCAGAACAGCGACCTCAGAAATAACACCACACATCTACAACCATC 650
                              ii    iv v  vii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_104682717_    651 TAATCTTCAACAAACCTGATTAAAAATAAGCAATGGGGAAAGGATTTCCT 700
                          i  i   i    ivv  -ii  i vi vv            i  vvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_104682717_    701 ATTCAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAAGTGA 750
                         v    ii              v      v  ?   i     i  i i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_104682717_    751 AACTAGACCCCTTCCTTACACCTTATATAAAAATTAACTCAAGATGGATT 800
                          ii i       v   i     v    i              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_104682717_    801 AAAGACTTAAATGTAAAATCCAAAACCATAAAAACCCTAGAAGAAAACCT 850
                          ?    i         i v i     i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_104682717_    851 AGGAA-ATACCATTCAGGACATATGCACGGGCAAAGACTTCATGACAAAA 899
                            ?i- v i -   iv   v vv vvii     v ii   v iivv vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_104682717_    900 ACACCAAAAGTAATTGCAACAAAAGTCAAAATTGACAAATGGGATCTAAT 949
                                   i vvv          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_104682717_    950 TAAACTAAAGAGCTTCTGCACAGCAAAAGAGACTACCATCAGAGTGAACA 999
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_104682717_   1000 GACAACCTACAGTATGGGAGAAAGTTTTTTGCAATCTACACATCTGACAA 1049
                                i    v          i v   -    vii i i      i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGATAA 746

  chr1_104682717_   1050 AGGTCTAACATCTAGAATTTACAAGGAAATTAAACATATTTACAAGAAAA 1099
                         i  v  vii   i     v  i  i   v ivv   vv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_104682717_   1100 GAACAAACAACCTA-TCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 1148
                         ii     i    i - i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_104682717_   1149 TCAAAAGA 1156
                           v     
  L1M4_orf2#LINE/    847 TCCAAAGA 854

Transitions / transversions = 1.48 (105 / 71)
Gap_init rate = 0.01 (7 / 654), avg. gap size = 1.00 (7 / 7)  


 481 26.97 1.97 0.00  chr1_104704646_104708918.rev      672   823 (3450)    L1M4_orf2#LINE/L1        1   155 (753)  

  chr1_104704646_    672 TGGGAAAACATCCCATGCTCATGGAAAGAAAGATTCAATATT-TTAAAAT 720
                            i  i i        i       vv i    i i      -    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104704646_    721 AGCCATACAGCCAAAAGCAAT-TACAGATTGAATACTATATCTATCAAAC 769
                         i  v    vv  v   vii  -        v  ii v  vi        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104704646_    770 TACCAATGATATTTTTTACAGAACTAGAAAATCTAA-CTTAAAATTTATA 818
                          v   iiviiv      i     v v  v  v  i - i       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_104704646_    819 TGAAA 823
                           i  
  L1M4_orf2#LINE/    151 TGGAA 155

Transitions / transversions = 1.28 (23 / 18)
Gap_init rate = 0.02 (3 / 155), avg. gap size = 1.00 (3 / 3)  

2012 27.19 2.69 2.83  chr1_104704646_104708918.rev     3047  3789 (484)    L1M4_orf2#LINE/L1      167   908 (0)  

  chr1_104704646_   3047 CCTGAATAGCCAAGGTAATCCTAAGCAA-AAGAACAAAGCTAGAGGCATC 3095
                           v          iii    i i iv  -          i i    vv  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr1_104704646_   3096 ACATTATCTTAATTC--AAACTATACTATAGGGCTACAGTACCCCACACA 3143
                            i -  ii    i--     -     i ii         vi v v   
  L1M4_orf2#LINE/    217 ACACT-TCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACA 264

  chr1_104704646_   3144 GTATGGTACTGGTACAAAAACAAGCACATAGTTCAGTGGAACAGAATAGA 3193
                           i         i i  ii i ii  i    v   i     i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_104704646_   3194 GAGCCCAGAAATAAGGCCACACACCTAC-------TGATTTTTGACAAAG 3236
                            i          iv   i   ii  i-------       i     i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_104704646_   3237 CTTGCAAAAACAAGCAGTGGGGAAAAGACTCCCTATTCAATAAATACTTC 3286
                         v vv   i v  vv  i        ii ivvi  v     i    iv v 
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_104704646_   3287 TGGAAAAACCAGTT-GCCATATGCAGAAGATAGAAGCCAGATACCTTCCT 3335
                            i v   ii v -?   i     i    vv    iii  iv   v   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_104704646_   3336 TACACCATATACAAAAATCAAGTCAAGATGGACTAAAGAGTTAAATATAG 3385
                         i                 i  v    i     ii ?   vi     i  i
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_104704646_   3386 AACCCCAAAGAATAAAAACCCTGGAAGACAACCTAGG--TAATACTACAG 3433
                         i v iv   vv      vi i i     v   v    --   vv  v iv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_104704646_   3434 GACATAGAACCAGGCAAAAATTTCAGGACAAAGATTTCACTACAAAAAGA 3483
                            v v iiii      vii    vv-----    v v  --------- 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTT-----AGATATGAC---------A 600

  chr1_104704646_   3484 CCAAAAGCAATCA--CAACAAAAGCAAAAATTGACAAGTGAGAACTGATT 3531
                                  --  --         v      v  i  i vi  vi v  i
  L1M4_orf2#LINE/    601 CCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_104704646_   3532 AAACCTAACAGATTCTGCACAGCAAAAGAAACTATCAATGGAGTAAACAG 3581
                            vi   v iv  i  ii vv    i  v        vii   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_104704646_   3582 ACAACCTACATAATGGAAAAATTTTTTTGCAAACTATGCATTTGACAAAG 3631
                               i   v     i i  vv v        ii  ii  i   i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_104704646_   3632 GTCTAATATCCAGAATCTATAAAGAAGTTAAGAAATTTACTAG-AAATAA 3680
                          v  vi          v         v ivviv  i i v  i-   v i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_104704646_   3681 ATGAACAACCTCATTAAAAAGCGGGCAAAGTAAATGAGTAGACACTTTTT 3730
                          ii  i    iv   ?    ii        v vv   i      i  i i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_104704646_   3731 AAAAGAAAA---ACAAATACACGCCAACAAGCATATGAGAAAAAGCTGAA 3777
                         v      i ---      i---     i     i    i  i v   v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATG---GCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_104704646_   3778 -ATCACTGATCAT 3789
                         -    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (119 / 80)
Gap_init rate = 0.02 (15 / 742), avg. gap size = 2.73 (41 / 15)  


2918 26.84 2.94 0.45  chr1_104745959_104750774     3443  4325 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_104745959_   3443 AAATATATTCCATGTGCATGGATTAAAAGAATCAATATTGTTAAAACGTC 3492
                            v    i      v        ii    v i           i i v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_104745959_   3493 CATAGAACCCAAAGCAATCTACAGATACAATATAATCCCTATCAAAATAC 3542
                         v   vvv      vii          v   iii               v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_104745959_   3543 CAATGGCATTCTTTAGAGAAA--GAAAAAAAG-TCTGAAAAGTTACATAG 3589
                           iiv  v  i   iv     --  v  ivv -  iv    v i i  i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_104745959_   3590 AACCACAAATGGGCCAGAATAGCCAAAGCTATCCTGAACAAAAGGAA-AA 3638
                           vii   iv iv              i v   i    v  i i   -  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_104745959_   3639 AACTGGAGGAATCACAGTGTCTTACTTCAAA--TTAAACTATAGAGCTAT 3686
                          ii       v     v vi iv i      --   --   i i     i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGCTAC 251

  chr1_104745959_   3687 AATAACCAAAAGGGCACAGTACCAGC----GCACAGAC--------CAAT 3724
                          i   i   i vi iiii    ii  ---- v i    --------    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_104745959_   3725 GGAATAGAATAGATATCCCAGAAATAAACTCAGAAATCTACAGTGAACTT 3774
                                   v  v vi            i  v v  i  ii  v  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_104745959_   3775 GTTTCTGACAAAGGTGCAAAGAATATACTTTGGGGAAAGGACAGTCTTTT 3824
                         i   ii     i     v    vi  v vv         i i        
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_104745959_   3825 CCATAAATGATGCTGGGAAAACTAGGTATTCACATGCAGAAGAATAAAAC 3874
                          v i     i        v    i i  ?i        i      i  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_104745959_   3875 TAAACTTCTATCCCTCTCCAAGTA--AAAATCAGATCATAATGAATTAAA 3922
                          ii  ii   i i v v   vi  --     i iv   v    i  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_104745959_   3923 GACTTAAATATAAGACCTTAAACTATGAAACTACTAAAAGACAATAT-TG 3971
                            i     i     v  v       i     vi  i    v  i  -v 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_104745959_   3972 AGAAACTCTCCAGGACATTGAACTGGGCAAAGAGTTCTTGACTAATACCC 4021
                         ? v  v   i iv   v   iii i     v iv     iiv  vv  v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_104745959_   4022 CAAAAGCATAGGCAACCAAAGCAAAAATGGATAAATGGGATTGCATCAAG 4071
                                 i i     v    v      i       v   i v      i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_104745959_   4072 -TTAAAAAGCTTCTGCACAGCAAAGGATATGATCAACGAAATTAAGAGAC 4120
                         -       -   i  ii vv       i iv     vi  i v  i    
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_104745959_   4121 AACATGCAGAATGGGAGAGAATGTTGGAAAACTTATCTATTTAACAAG-- 4168
                            vii            i   i  v v   - i  v   i i i   --
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATAAGGG 749

  chr1_104745959_   4169 ATTAATAACCAGAATATATAAGAAGCTCAAATAATTCTATTGGAAAAAAT 4218
                          i vi  v             ii i   vv i  i  v  viv     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_104745959_   4219 CTTATAATCCAATT-AAAAATGAGCAAAAAATCTGAATAGACATTCTTCA 4267
                          vv    i      -       i     ii  i            ii  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_104745959_   4268 AAAGAAAACATACAAGTGATAAGTAGGTATATGAAAGG-TGCTCATCATT 4316
                               i i      i  iiv i  i i i      i -      v   i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_104745959_   4317 GATTATCAG 4325
                         i????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.60 (144 / 90)
Gap_init rate = 0.02 (15 / 905), avg. gap size = 2.00 (30 / 15)  


2841 25.42 2.79 1.56  chr1_104771128_104773891     1375  2271 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104771128_   1375 TAGAAAGCTATTCCATGCACATGGAGTGAAAGAGTCAATATTATTAAAAT 1424
                          i     v   i     iv      v  i    v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104771128_   1425 ATCAATACTGCCCAAAGCAATCTATAGATTCAATGCAATCCCTATCAAA- 1473
                         iv       v      vii     i        i               -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104771128_   1474 TACCAA-TGCCTTTATTCACAGAAATGGAACAAAAACT-ATCCTAAAATA 1521
                          v   i-       -  ii       v  -   i--  -          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGA-CAAG--CTGATCCTAAAATT 146

  chr1_104771128_   1522 TATATGGAACTACAAAAGACCCTAAAAAGCAGAAGTAACCC----GAAGA 1567
                         i        v i   ii     vi  v   vi  ii  i i----i    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_104771128_   1568 AAAATAAATCTGACAGCGTTACACTATGTGATTTCAAAATATACTTCAAA 1617
                          i  i   vi  ivi vv i     vivii         iv    v    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_104771128_   1618 GCTTTAATAACCAAAACAGCATAACAATGGCCTTAAAATAGACACATAGC 1667
                            vi i   i   i    ii iii v    v v ii       i    v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_104771128_   1668 CCAATAGAACAGAATAGAGAGCCCAGAAAGGAATCCGCATATCTACAATC 1717
                         i    i   i     v     i       vi  i  ii i  i  iii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_104771128_   1718 AACTCATTTCC-ACAAAGGTCCCAAGAACATGTACTGAGGA-----CGGT 1761
                           i v    i -    i   v      v   vi v  i   -----ii  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_104771128_   1762 TTTTTAAATAAATGGTG-TGGGAAAACATGAAT-CCCATATGCAGACAAT 1809
                         i    v  i        -     v   -  i  -?   i     i vi v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAAC-TGGATAKCCACATGCAAAAGAA 445

  chr1_104771128_   1810 TAAAACTAGGCTCCTATCTCTCATCATCTACCAAAATGAAATCAGAATGG 1859
                          i  ii i i i    i   v  i   v   v     v  v   i     
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_104771128_   1860 ATAAAAGAGTTTTGCATCTAAGAACTGAAAGTCTGAAACTACTATAAGAA 1909
                           v ?   --ii iv  v     i  i   v v i     vi  v     
  L1M4_orf2#LINE/    496 ATCAWAGA--CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_104771128_   1910 AACATAACAAAAAAT-TTCAGGACATTTGTCTTAG-CAAAGATTTATTGA 1957
                               iv?iv    -   iv   -i   vv    -   v i   v  ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_104771128_   1958 TTACAACCTCAAA-GCAGAGGCAACAAAAGCAATAATAGACAAATGGGAT 2006
                         v  ii  vi    -   v i          v  v      i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_104771128_   2007 TACAT-AAAGCTAAAAGGTTTC-TGCATAGCGAAGGAAAAAATCAACAAA 2054
                          v   -   ii     iv   i-   v -- i     v vv     v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAA 690

  chr1_104771128_   2055 GTGAAAAGACAACTCGCAGAATGGGAAATAATATTTGCCAACTATCCATC 2104
                                      i i          i v         v  ii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_104771128_   2105 CAAGAAGGGATTAGTAGCCAGAATATATAACAAATTC----AACTCAATA 2150
                         ii v      i v   v             vi  i  ----         
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_104771128_   2151 GCAAAAACAAAAAAAAAAGTCTGATTAAAAACTGGGCAAAATACTTAAAT 2200
                         ii     v v   v  ---i ii   ?    v        iv i  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAA---CCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_104771128_   2201 AGACATT-CTCAAAAGAAGACATAAAAAGAGCTAACAGATATGTGCAAAA 2249
                                -   v        i   v   vi  i  i iii ii  -    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAA 886

  chr1_104771128_   2250 AATGCTCAACACCACTAATCAT 2271
                         i          i  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.62 (39 / 24)  


2263 25.42 2.75 6.57  chr1_104861010_104863072      627  1570 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104861010_    627 TGAGAATATTCCCCATGTTCATGGATTGGAGAAATGAATATTATCAAATT 676
                           ii  v  vi                   ii v v      i i  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104861010_    677 GTCTACATTACTTAAAATAAT--A-AGATTCAATGAAATGCCTATCAAAA 723
                          v v i i v ii   v i  -- -        i v   v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104861010_    724 TCTCCATGATAC--TGTTCACAGAAATTGAAAACGC-AATTCTATAAT-- 768
                           -   - v i -- v  ii          v  -  -i  i   v   --
  L1M4_orf2#LINE/    101 TC-CCA-GCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTC 147

  chr1_104861010_    769 ----AGAAACTACCAAAAATCGAGAATAGCTAAAGTAATCTTGATCAAGA 814
                         ----i    - i v iii i v        i   ii        vv    
  L1M4_orf2#LINE/    148 ATATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_104861010_    815 GTAGCAAAGTTGGAAACATCACAGTGCTTGATTTTTAAATTATATTATAA 864
                         iv i          iivv     v v iii    iv   i -  i  i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chr1_104861010_    865 AGCTACAGTAATCAAAGCAGTATGTTATGGGTGTATAAACAGACACATAG 914
                                        ii    i  v  iv  ii  vii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_104861010_    915 ACCAATG-AACAGAAGAGAAAGCACAGAAATAAACTGACACATATATAGA 963
                          i     -  i    vv  i  iv           iv i    v   i -
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG- 344

  chr1_104861010_    964 GTTAAGTAACCTTTGACAAAGCAATGTAGAGTGCA--CCATGGGGAAAAG 1011
                         - i  v i ii  i     i --i  ivi  vv  -- v         ii
  L1M4_orf2#LINE/    345 -TCAATTGATTTTCGACAAGG--GTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_104861010_   1012 TTAGTCTCTTTAATAATTACTGTTAAAAAAAAAAAACTAGATATCCACAT 1061
                         v      i  i  i  v iv  i iii v  -----  i    ?      
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAA-----CTGGATAKCCACAT 436

  chr1_104861010_   1062 AGGTAAAAAAGAAACCAAAACAAAAAAATTTGTATTTGTATCTTACACCA 1111
                         i--------------     v  vi  i  v - iiiv  i  i      
  L1M4_orf2#LINE/    437 G--------------CAAAAGAATGAAGTTGG-ACCCCTACCTCACACCA 471

  chr1_104861010_   1112 TAAACAAAAACCATCTCAAAATGTGTTAAAGACTGAAACATAGAATATGA 1161
                           v       ii v         vi i ?    iv   ii  ii vv i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_104861010_   1162 AACCATAAAACCTTTAAAAGTAAACATAGGGGAAAAGATCCATGACATTT 1211
                            i       ii   i   v         ? v   vv i i    --i 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC--CT 569

  chr1_104861010_   1212 TTCATT--GCAATAATTT-TTGGATATGACACTAAAATCACAGACAACAA 1258
                          vvi  --     ii   -  i          i    v    ii      
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_104861010_   1259 AAGCAAAAACAAGCAAGTAAGACTAAATCAAA-TTGAAAACTA--GCACA 1305
                            v     i iii  i vi    vv      -  i      v-- ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_104861010_   1306 ACAAAGGAAATAATAAACAGAGTGAAGAGAAAATGCACAGGATTGGAGGA 1355
                         v       v iv  v  v i      i   v  iv     i  v    i 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_104861010_   1356 AATATTCATAAGCTGTATGTCTGATAAGGGGATAATATCCAAAAT-TATA 1404
                               iii  iiii   i           iv vi      i   -    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_104861010_   1405 AAAAACA--TACAACTCAATGGTGGTTGTGGTGGTGGTGATGATGATGAT 1452
                           i   v--           ii ---------------- vi v  ii -
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAAT----------------AAAAAGACAA- 802

  chr1_104861010_   1453 AATAACAGCAACATGATTAAAACATAGGCAAATG-CCTGAA-AGGCTTTT 1500
                         -     -- --  --   ?   v  i      v -ii    -  i ----
  L1M4_orf2#LINE/    803 -ATAAC--C--CA--ATTWAAAAATGGGCAAAGGATTTGAATAGAC---- 841

  chr1_104861010_   1501 TATTTTTTTTCTAAGAAGACATATAGATAGCCAACACATACATGAAAAGG 1550
                         -    i i-- v       i   i i  i     i vii          i
  L1M4_orf2#LINE/    842 -ATTTCTC--CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_104861010_   1551 TGCTCAACATCACTAATCAT 1570
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (154 / 82)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 2.67 (88 / 33)  


3234 26.54 0.55 0.55  chr1_104913749_104920015.rev     4869  5776 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104913749_   4869 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4918
                              ii i  i   i i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104913749_   4919 GGCTATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4968
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104913749_   4969 TACCAA-TGCCTTTCTTCACAGAATTGGAAAAAAGTACTTGAAAGTTCAT 5017
                          v   i-       i  -i     v v  v  ivvv iiiv   i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_104913749_   5018 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5067
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_104913749_   5068 ACAAAGCTGGAGGCATCACACTACCAGACTTCAAACTATACTACAAGGCT 5117
                               i      vv       v  vi i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_104913749_   5118 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5167
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_104913749_   5168 ATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATAC--CTACAAC 5213
                               i    i--    i  --        -   -     --i  iiii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAA-ACC-CATACATTTATGGT 345

  chr1_104913749_   5214 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5263
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_104913749_   5264 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5313
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_104913749_   5314 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAGTTCAAGGTGG 5363
                             ii    i    v   i     v           i ii    ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_104913749_   5364 ATTAAAGACTTGAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5413
                           i ?    i i  ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_104913749_   5414 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5463
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_104913749_   5464 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5513
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_104913749_   5514 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5563
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_104913749_   5564 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTTGTCTGACA 5613
                         v  i     i   i             v  ii   vii iv i     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_104913749_   5614 AAGGGCTAATATCCAGAATCTACAATGATCTCAAACAAATTTACAAGAAA 5663
                          i  i  vi          v  i  v  v   vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_104913749_   5664 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5713
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_104913749_   5714 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5763
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_104913749_   5764 CATCACTGGCCAT 5776
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2238 28.46 1.68 1.81  chr1_104933847_104935611      500  1272 (493)    L1M4_orf2#LINE/L1      137   908 (0)  

  chr1_104933847_    500 TTCTAAAATTTTGATG-AAATCAGAAATAAAACCCTAAAGAATTAAG-CA 547
                          i        ivv   -    -- v  -iii    vi  v iii  i-  
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAAT--GCAA-GGGACCCAGAATAGCCAAAACA 183

  chr1_104933847_    548 AGCATGAGCAAAATAAACAAAGGCAGAGGCATTATATTACTTGACCTAGA 597
                          v v   iv  i vi       vii    vv i i i v iii ii vi 
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_104933847_    598 AATCTACCACAAAGTTATGGTAATCTAAACAGCATGATACTGGCATAAAA 647
                           ii   i      i  ii      v i    ii  i           ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_104933847_    648 ACACAACATTCACACATAAACCAATAGAACAGAATCAAGAGCCCATAAAT 697
                          i -i    ------   i i    i   i     ii    i   v    
  L1M4_orf2#LINE/    284 ATA-GACAT------ATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_104933847_    698 AAATCTTCACATTTACTATCAATTGTTTTTCAACAAAGAAGCCAAAATTA 747
                            i ivi       ivi       v     i    i iv     i ii 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_104933847_    748 CACTGTGAGGAAAG--CAGTTTCTTCAATAAATGGTGGTAGGAAAACTGG 795
                         iv vi  i      --i   i i     i        v i   v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_104933847_    796 ATATCCACATGCAAAAGAATACAATTATGCCCTCATCTCACATAATATAT 845
                            ?                iv i  ivi   ii i      iv     i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_104933847_    846 AAAAATCAACTAAAAATGGATCA-AGTCTCAAATGGAAGACCCAAATTTG 894
                               i    v           -  v ii     v    v i   vi i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_104933847_    895 TAGAAAGACAAGATAAAAACATAGGGGGAAAGCTCTATGATATTGGTCTT 944
                           i  vvviv   vi          ? v   v  iii   iv    vi v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_104933847_    945 GGCGAATAATTT--TAAATATGGTCCCAAAAGCACATTCAGCAAAAGCAG 992
                            -   ii   --  i     iiv           vv  i      v i
  L1M4_orf2#LINE/    577 GGC-AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_104933847_    993 ---TAGACAAGCGGGATTACATCAAA--CAAAAACCCTTCTGCACAGCAA 1037
                         ---    i  iiv   i v       --i      --  i  ii vv   
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAAC--TTTTGTGCTTCAA 673

  chr1_104933847_   1038 AGAAAACAATCAACAGAGTGAAAATGCAATCTATAGAATTCGAGAAAATA 1087
                           i v  v     v i        vi   i i i     vv         
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_104933847_   1088 TCTGCAAATTATACATTTGATAAGAGGTTAATTTTCAAAATATATAAGAA 1137
                          i       i   i  i       i ii vi v i  i         ii 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_104933847_   1138 AATTATACAACTCAATAGTAAGAAAATGAATTACCTGATTTTAAAAGGAA 1187
                          v iv            i   i  i ii   v   ii   ?v    v i-
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG- 822

  chr1_104933847_   1188 GAAAAGGACC-AAGCAGACATTTCTAAAAAGGAGTAATACAAGTAAATAA 1236
                          v      ii-i ii          vv    i  vv      i iivi  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_104933847_   1237 CAGGTATCTGAAAGTATGATCAAGATCACTAAGTAT 1272
                         i i i iv     iv   v    v    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (144 / 73)
Gap_init rate = 0.02 (15 / 772), avg. gap size = 1.80 (27 / 15)  


2806 28.09 0.43 1.95  chr1_104947599_104953680     4668  5589 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_104947599_   4668 TGGAAAAAGATTCCATGCTCATGGATGGGAAGAATCAATATCGTGAAAAT 4717
                               i v  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_104947599_   4718 AGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4767
                         i  v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_104947599_   4768 TACCAATGACTTTCTTCACAGAA-TTGAAAAAAAAAACAAAACACTTTAA 4816
                          v   iivi i  i  ii     -    v  i----- vi v ---i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATC---CTAA 142

  chr1_104947599_   4817 AGTTCACATGGAACAACAACAACAACAAAAAGCCCACATT-GCCAAGATA 4865
                          i    i      -------- ii-   iiii    v v -     i i 
  L1M4_orf2#LINE/    143 AATTCATATGGAA--------ATG-CAAGGGACCCAGAATAGCCAAAACA 183

  chr1_104947599_   4866 ATCCTAAGCCAAAAGAACAAATCTGCAGTCATCATGCTACCTGACTTCAA 4915
                            i i ivv i         vi  v  vvv   ii  v  ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_104947599_   4916 ACTATACTACAAGGCTACAGTAACCAAAACAACACCGTCCTTGTACCAAA 4965
                          viv        i          i   i   iiiiv  v  v i iv ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_104947599_   4966 ACAGATATATAGACCAATGGAACAGAACAGAGACCTCAGAAATAACACCA 5015
                          i   i       i        i    iv    vii         vv   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_104947599_   5016 CACATCTACAATCATCTGATCTTTGACAAACCTGACAAAAACAA-AAATG 5064
                         i    i  iii   vi    i  i     ivv  v   i v  v-v    
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_104947599_   5065 GGAAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTCACCA 5114
                           i    i  vvi  v  i  i              v      v v?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_104947599_   5115 TATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTCTACAAAAATT 5164
                         i   i i  iiv    ii    i    v   i     v v          
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_104947599_   5165 AATTCAAGTTGGATTAAAGACTTAAATCATAGACCTAAAACCATAAAAAC 5214
                           i    iv     i ?    i     vvv   v       i      vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_104947599_   5215 CCTAGAAGAAAACCAAGGCA-ATACCATTCAGGACCTAGGCATGGGCAAG 5263
                          i           vv   ?i- v i -   iv     v  vv i     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chr1_104947599_   5264 GACGCCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGA 5313
                          iivi v iiv  vi            vvi          vv        
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_104947599_   5314 CAAATGAGATCTAATTAAACTAAAGAGCTTCTGCATGGCAAAATAAACTA 5363
                         i    vi  ii v  i   v v  i i   i  iiivv    iv v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_104947599_   5364 CCATCAGAGTAAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATC 5413
                         i  vv i   i  v  i     i                 v       vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_104947599_   5414 TACCCATCTGACAAAGGGCTAATATCCAGAATGTACAAATAACTTAAACA 5463
                         i ivi      i  i  i  vi          i  i   v    ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_104947599_   5464 AATTTACAAGAAAAAAACAAACTACCCCATCAAAAAGTGGGCAAAGGATA 5513
                          v iv i  v     i     iv    v  i?    i            v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_104947599_   5514 TGAACAGACACTCCTCAAAAGAAGACATCTATGCAGCCAAAAGACACATG 5563
                             i     i i   v        i  vi viii     v ii      
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_104947599_   5564 AAAAAATGGTCATAATCACTGGTCAT 5589
                             i   v   vv    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (151 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.44 (22 / 9)  


3152 24.97 3.16 0.68  chr1_104956329_104959640     1935  2819 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_104956329_   1935 GGAAAGATATTTCATGTTCATGAATTGGAAAAATCAATATTGTTAAAATG 1984
                                   ii          i       i v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_104956329_   1985 TCCATAGAACTCAAAGCAATCTACAGATTTAATGCAATCACTATCAAAAT 2034
                         v v   vvv i    vii           i  i      v          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_104956329_   2035 ACCAATGATATTCTTCACAGAAACAGAATAAACAGG-ACTAAAATTTACA 2083
                         v   iiviiv  i  ii      iv  -i  i v i-v        i i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATA 150

  chr1_104956329_   2084 TGGAACCACAAAAGACCCAGAATAGCCAAAGCTATCTTAAGCATATAAAA 2133
                              vii   ii                 i v     i iv viv i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_104956329_   2134 CAAAACTGGAGGAATCACATTACTTGATTT--AAATTATACTGCAGAGCT 2181
                             ii       v     i v iii    --   i -    i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr1_104956329_   2182 ATCATAATCAAAATAGCATAATGCTGGCATGAAAACAGACAC------CA 2225
                          ivi       i i  ii ii i       i ii i     i------  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_104956329_   2226 GTGGAATTGAATAAAGAACTCATATATAAATCCATACATCTACAGTAAAA 2275
                         i      v    vi   iii  v v     i        i  ii  v  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_104956329_   2276 TCATTTTTGATGAGGTT-CCAAGAACATTCACTGAAGGAAAAGACAGTCT 2324
                          v     i  ii   v -      v      v  i-     ii i     
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCT 398

  chr1_104956329_   2325 CTTCAACAAATGGTGCTGGGAAAACTAGATATTTATATGCAAAAGAATAA 2374
                         i                    v    i    ?ii i            i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_104956329_   2375 AGCTAGAACCCTATCTTTCACCCTATACAAAAATCAAATCAAAATGGATT 2424
                           i i  v     i  iv    v           i  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_104956329_   2425 AAAGAC--AAGTATAAGA-CTGCAAACCATAAAACTACTAATAAAAATAA 2471
                          ?    --  i i     -  i-    i        vi  iv i   vv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_104956329_   2472 TTGGGGAAACTCTTCAGGACATTGGAGTGGGCAAAGACTTTTTGAGCAAT 2521
                          v  ? v  v     iv   v    iv i     v ii  i  iiii vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_104956329_   2522 ACTCCACAGGCACAGGCAACCGAAGCAAAAGTGGACCAGTGAGATTACAT 2571
                           v   v i     i     vi   v    i i  iv i vi  i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_104956329_   2572 CAGG-TTAAAAACCTTCTGCAAAGCAAAGGGAACAATGAACAAAGTGAAG 2620
                           ii-        i  -  iivvv      iv  v  v  v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_104956329_   2621 AGACAACCCACAGATTGGGAGAAA----TTGC----C---TGTCTGACAA 2659
                                       v         ----    ---- --- i     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_104956329_   2660 GGGATTAATAATCAGAATATATGGTG--CTCATACAACTCCATAAGAAAT 2707
                             i vi  vi          iiv --   v        v    v   v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_104956329_   2708 AT-CTAATAATCCAATTTTTTAAATGAACAAAAGATCAGAATAGACATTT 2756
                          v- v     i      ?vv-     ii    i   iv            
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_104956329_   2757 CTCAAAAGAAAACATACAGATGGAAAACAAGTATATTAAAAGATGCTTAA 2806
                            v      i i     i    vv  i   i i  v          i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_104956329_   2807 CATCATCGATTGT 2819
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (136 / 81)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 1.89 (34 / 18)  


2407 24.39 6.39 2.30  chr1_104962544_104964276.rev      461  1243 (490)    L1M4_orf2#LINE/L1       94   908 (0)  

  chr1_104962544_    461 ATTAAAATTCCACTGAATATGCCACATTTCATTTATATATTAAGAAAC-A 509
                           i     i   --------  ii v   iv vi v v   i v  i -i
  L1M4_orf2#LINE/     94 ATCAAAATCCCA--------GCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chr1_104962544_    510 ATTCTAAAATTTGTATGGAACCACAAAAGACT--GAATAATCTAAACAAC 557
                           i        ii       vii   ii   i--     ii v      i
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_104962544_    558 CTTGAAAAGGAAGAATAGAG--------------CTTCCTGATTTCAGAA 593
                                 i      i i  --------------     ii      i  
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_104962544_    594 CATATTACAGCACTACAA-AATTAAAACAGTAAGGTGCTGGCATAAAAAT 642
                          v  i    ivi     i-   i  i     iv   i         ii  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_104962544_    643 AGACATTTCTAGCAATTCAACAGAATAGAGAGCCAAGAAGTAAACTCATA 692
                               v vv v    vv  i     v     i v    i     i    
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_104962544_    693 CATATTCAGTCAATTTATCTTTTACACGGATGCCAAA--CATACATAATG 740
                            v vii       v  i  iv   v  i      i--   v  --   
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA--ATG 383

  chr1_104962544_    741 GGAAAAGGATA-TATCTTCAACAAATGGTATTTGATAAACCAC-GTATA- 787
                           i    i   - v i             ii v i---  v  - v   -
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG---ACAACTGGATAK 430

  chr1_104962544_    788 --ACATGCAAA-GAATGAAATTGAACCTTTATCCTATACTATACACAAAA 834
                         --         -       i   i   ii  i ii i  i   i      
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_104962544_    835 ATCAACTCAAAATAGACTAAAGACTTAAACACAAGATCTGAAACTGTAAA 884
                           i          i  ii ?    i    iii    v  i     i    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_104962544_    885 CCTCCTACAAGAAA---CAGGGAGGAAGCTTCCTGACATTG--TTATTGG 929
                         v   i  v      ---i   ?ivi  v    v    v   --   --  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA--GG 578

  chr1_104962544_    930 CAATCATTCCTTGGATAT-ACACCAACAGCGCAAGTAATGAAAACAAAAA 978
                             vi  i   i     -       v   i    i  ii   iv     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_104962544_    979 TA----AAGTGAAGCTATAT-AAAAGGAAAAGCTCTT-CACAGCAAAGAC 1022
                           ----  v  i -  vi  -    vv    i  i  -ii vv     i-
  L1M4_orf2#LINE/    629 TAGATAAATTGGA-CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG- 676

  chr1_104962544_   1023 AAAAAAATCAAAATGGTGAAAAGGCAATCTAGGTAATGGGAGGAAATATT 1072
                         - v vv     i vi        i   i i viv        i       
  L1M4_orf2#LINE/    677 -ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_104962544_   1073 TGCAAACCACACATCTGATAAGAGGCTAATAGTAAAAATATATAAGAAAC 1122
                               i  i i          i i  vi  viv i         ii   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_104962544_   1123 TCACACAACT--------GAAAGA--AATAATCCAATTAAAAAATCAGCA 1162
                           vi      --------i     --     i      ?      vi   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_104962544_   1163 AAAGTCTTTAGTAAATATTTCTTCTAAGAAGACAGGCAAATAATCAACA- 1211
                           i vi  v i  i i      i v       i vi     iii   i -
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_104962544_   1212 -CATATGAAGAGATACTCAACATCGCTAATCCT 1243
                         -  i     i    i         i????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (128 / 60)
Gap_init rate = 0.03 (24 / 815), avg. gap size = 2.83 (68 / 24)  


2648 22.42 7.07 1.09  chr1_104972434_104975847     1757  2492 (922)    L1M4_orf2#LINE/L1        1   780 (128)  

  chr1_104972434_   1757 TGCAAAGACATCCCACAAACGACAAATTGGAAGACTTAATATTGCAAAGA 1806
                           v     i      iivv - iii                   iv    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTC-ATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_104972434_   1807 TAGAAATACTCCCCAAATTGATGTATAGATTCAAAGCAATCCCTGT-ATA 1855
                          i v                  v  i        v         i - v 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_104972434_   1856 ACTCCAGTTGG-TATTTTGCAGAAATTGGTAAACAGATTCAAAAATTTGT 1904
                          ii    i  v- v              ii  i v   i v      ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_104972434_   1905 ATGGAAGTTTAAGGGACCTAGAAGAACTAAAATAATTTTGAACAAAAAAG 1954
                               i vi        i    v i i    i   i     -   i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAG 198

  chr1_104972434_   1955 AACACAATTAGTGGACTCACTCTTTCTGATT--GA----TACTACAAAGC 1998
                             v i  i v        v   i ii   --i ----           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_104972434_   1999 TGTTGTGACCAAGACAGTCTTGGATAGACATAAAGATAGACATGTAGATC 2048
                          iiv  i i         v v v iv i     i         i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_104972434_   2049 A-TGGAGTAGAGTTAGGAGTTAAGAAATACATTCTTACACTTATGATGAA 2097
                          -    i    i  ii    iv       v ii v    i     i v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_104972434_   2098 TTCATTTTTAACATGAATGCCCAGAAAACTTAGTGGATAATG--T-TTTT 2144
                           v     ii   v ii    v   vv i i i   iv  v -- -v i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_104972434_   2145 TTTCAATAAATGGTGCTGGA-----TGACTAGTCACATGCAAAATAATGA 2189
                               i            i-----  iv  ?i           v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_104972434_   2190 CTTT------CTAC-TGATATTATGT-CTAAAATGAACTCAAAATGAATC 2231
                         vv  ------    - v i ii  i - v     v           i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_104972434_   2232 A------TAAATGTAAGAGTTAAACTCACAAAATTC---------AACAA 2266
                          ------            i    vii i    i  ---------    -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA- 547

  chr1_104972434_   2267 TAGGAGTAAATATCTGTGATTTCGAGTTTGATAATAGTTTCTTATATATG 2316
                             ?      v ii    ii i i   v ii   i        v     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_104972434_   2317 TCACCAACTGAAAAAATGACAAATGAAGAAA---ATAAATCGGACTTAAT 2363
                         v      vv v v  iii     v   i   ---      i      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_104972434_   2364 CAAAAATTAAAA---TTTGCAGCTTCGAAAGACACTGTTTAAAAAAGGAG 2410
                              -      ---    i-     i  i      i i-  i    vii
  L1M4_orf2#LINE/    648 CAAAA-TTAAAAACTTTTGT-GCTTCAAAGGACACTATC-AAGAAAGTGA 694

  chr1_104972434_   2411 AAAAACA---CA---AATGGTAGGAAATATTTCCAAGTTATATACCTGAA 2454
                            i   ---  ---     v  i        v   i i     i    v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_104972434_   2455 AAGGGACTTATAATTCTAGACTATAAAAACAATACTTA 2492
                                  i  --  i   v    v   v  iv    
  L1M4_orf2#LINE/    745 AAGGGACTTGTA--TCCAGAATATATAAAGAACTCTTA 780

Transitions / transversions = 1.72 (103 / 60)
Gap_init rate = 0.03 (24 / 780), avg. gap size = 2.50 (60 / 24)  

 554 10.85 6.20 3.88  chr1_104972434_104975847     2785  2913 (501)    L1M4_orf2#LINE/L1      763   894 (14)  

  chr1_104972434_   2785 ATATATAATAATAATAATACTTACCACTCAATAATAAAAAGACAAATTAT 2834
                                 ----- v  iv     v                      v i
  L1M4_orf2#LINE/    763 ATATATAA-----AGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_104972434_   2835 CCAATT-AAAAATGG-------ATTTGAATAAACATTTCTCCAAGCAAGA 2876
                               -        -------         i            iv    
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_104972434_   2877 TATATAAATGACCAATAAACACATGAAAATATCCTCA 2913
                             i     i       i          v  v    
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.00 (7 / 7)
Gap_init rate = 0.02 (3 / 132), avg. gap size = 4.33 (13 / 3)  


2020 20.23 3.46 17.09  chr1_104977087_104981464     2934  3887 (491)    L1M4_orf2#LINE/L1       85   908 (0)  

  chr1_104977087_   2934 GTAACCTCTATCAAAATTCCAA-TGACTTTTT-ACATAAAT-AAAAAATT 2980
                          i  i i          i   i-  v      -i  v    -i v  ii 
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr1_104977087_   2981 CGTTCTAAAATTTGTATGGAACCACAAAAGAC--AGGCAACTAGCAAAAG 3028
                         vi i        ii       vii   ii   --  --  -    v   i
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAG--AA-TAGCCAAAA 181

  chr1_104977087_   3029 CAATCTTGAGAAAAAAGAACAAAGCCAGAGGTATCACACTACCT------ 3072
                                  i   i          iii    vv       v  i------
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_104977087_   3073 -----------CAAAGCTATAGTCATCAAAACAGCATGGCACTAGTATAA 3111
                         -----------        i   v     i    ii   i   i i    
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_104977087_   3112 AAACA--CACACAGACCAATGGAACAGAATAAAGAGCCCAGAAAGATAGT 3159
                         ii i --  i i   i        i     vi    i       v v vi
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_104977087_   3160 TTCACATTTACTGTCAACTGATTTTTAACAAAAATGGCAGGAACACACAA 3209
                         ivi       iv     i       ii    iii  v  i  v  iv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_104977087_   3210 ---GGAAAGGAGAGGGCCTTCAATAAATGGTGCTGGACAAACTGGATATC 3256
                         ---      i v  vvii     i            ivv         ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_104977087_   3257 CATATGCAGAAGAAGGAAATTAAACTCTCATTTGATATCATATTAAAAAA 3306
                           i     i     v   i  ii  i i----------------------
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCC---------------------- 459

  chr1_104977087_   3307 TAACTGAAAATGGGCCAGGCACACTGGCTCATGCCTTTAATACCAGAACT 3356
                         ----------------------------------------    ------
  L1M4_orf2#LINE/    460 ----------------------------------------TACC------ 463

  chr1_104977087_   3357 TTCACAGGCCTAGGCAGGAGGATTGCTTGTGCCCAGGAGCTAGAGACCAG 3406
                         -     ----------------------------------------   -
  L1M4_orf2#LINE/    464 -TCACA----------------------------------------CCA- 471

  chr1_104977087_   3407 CCTGGGCAACATAGGAAAACCCGATCTCGACTTAAAAATATAGAAATAAA 3456
                         --------------------------------------    --------
  L1M4_orf2#LINE/    472 --------------------------------------TATA-------- 475

  chr1_104977087_   3457 TCTAAAAATTAACTGGAAATGGATTAAAGTCTTAAATATAAGATACAAAA 3506
                         --i           vi        i ?  v i     i     vvi    
  L1M4_orf2#LINE/    476 --CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_104977087_   3507 CTGTAAAACTACTGGAAGAAATCTTAAAGGAGAAGCTTCATGTCATTGGT 3556
                           i       vi i       v v  ii? vi  v    i  v v    v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_104977087_   3557 CTTGGCAGAGGTATTTCGGATATGATCCAAAAAGCACATTCAACAAAAGC 3606
                         i v    iv   v i ii       iv v         vv         v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_104977087_   3607 AAAAATAGACAAATAGGATTACATCAAACTTTAAAGCTTATTCATAGCAA 3656
                                  i    v   i v       v  v   i   v viiivv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_104977087_   3657 AGAAAACAATCAATAGAGTGGAAAGGCAACCTACAGAATAGGAGAAAATA 3706
                           i v  v     v i    i    i     i       i          
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_104977087_   3707 TCTGCAAACCATACATCTGATAAGGGATTAATATCCAAGCTATGTAAGGA 3756
                          i      i    i             i vi      iiv   i   i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_104977087_   3757 ACTCATACAACTCAATAGTGAGAA-AC---TGACACAATTATAAAATGGA 3802
                             v            i i i  -  --- i  v     ?v       i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_104977087_   3803 CAAAGGTCCTAAATAGACAT--ATCAAAAGTAGACATACAAATAGCCAAT 3850
                               vii i         --v  v    v   i        i      
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_104977087_   3851 TGATATATGGAAAAAATGTTTATACATTCTTCAGGGA 3887
                         viii i   -    i   i i -    iv????????
  L1M4_orf2#LINE/    874 AAGCACATG-AAAAGATGCTCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (122 / 67)
Gap_init rate = 0.02 (19 / 824), avg. gap size = 10.32 (196 / 19)  


2039 29.05 2.30 3.56  chr1_104983871_104985734.rev      503  1373 (491)    L1M4_orf2#LINE/L1       49   908 (0)  

  chr1_104983871_    503 ATGACCATATTGCCAAAAGCAATTTACAGATTTCATGAAATCTCTATCAA 552
                            i v   i v  v   vii  i        iv i v    i       
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_104983871_    553 AACACCAA-TGCCATTTTATGTAGAACTTGGGAAAACAAACGCTGACATT 601
                           iv   i-    v    -  i    v   iv  ivii v -  i v   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATC-CTAAAATT 146

  chr1_104983871_    602 TATATGAAACCAAAAAGAAGCCCAAATAACCAACCCAATTCTAAGCAGAA 651
                         i     i  viiv  i i v  vi    i    vv    ii i iv ii 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_104983871_    652 AGAACAAAGCTTGAAGCATCATGTTACCTGAAATAAAAATATATAACTAG 701
                                  i v  i vv   iii v  ii vv v    iv  iv  v i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_104983871_    702 CCTATAGTAACCAAAACAGTTGAGTATTGGTATAAAAATACACATATAAA 751
                         v   i     i   i     vvi   i   i    ii   v       i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_104983871_    752 CCAATGGAA-----------ATACACATATAAACCAATGGCCACAGACTT 790
                         i        -----------i v  v v       ------  i v i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACC------CATACATTT 340

  chr1_104983871_    791 GTGGCCAACTGATCTTTGACAAAGCTGGTAAGA--ACTCACATTGGGAAT 838
                         i   i   i    i  i     i v  vi    -- i   -  v     -
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAA- 388

  chr1_104983871_    839 AGAATATTCTGTTCGATATATGATTCCAGGAAAATGAGATACTCACACAC 888
                               v   v   i i v   i v ii   v  ivi    ?i    ii 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_104983871_    889 AAAAGAATGAAACTGGATTTGTATCTCTTATCATATATAAAAATCAACTC 938
                                    ii    iiiv  i   vi i      i      i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_104983871_    939 AAAATGGACTAAGGACTTAAATTGGAGACCTGAAATTGTAAAAAGCTAAA 988
                                 ii ?i   i     vvi   v  i   i i     --  ---
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA--CT--- 533

  chr1_104983871_    989 CCTAAACAACAACAACAACAAACAAACAGGGGAATCTCTTCTGGATTTTG 1038
                          i  i vi ----------     --i   ? v vv     vv  ii   
  L1M4_orf2#LINE/    534 CTTAGAAGA----------AAACA--TAGGNGTAAATCTTCGTGACCTTG 571

  chr1_104983871_   1039 GTCTGGGCAA--ACAACTTATGACTAAAACTACAAAAAACACAGGCAACA 1086
                          vi i     --iivv    -  -  vi  -  v    i    i      
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTA-GA-TATGAC-ACCAAAAGCACAAGCAACA 618

  chr1_104983871_   1087 AAA---ATAATAGACAAATGAGACATAATTAAACTAGAAAGCTTAATTAC 1133
                            --- v      i    vi   v v  i   v vi   i   vvv i 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_104983871_   1134 AGCAAATGAAATAATCAACGGAATGAAAAGACAGTCTTCAGAATGGCAGA 1183
                         vv    v  v iv     vii i          ii iv        v   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_104983871_   1184 AAATATTTGCAAACTATTCAGCTGAACAGGGGATTAATATACAGACTCTA 1233
                                      ii  vi v    -i i    i vi   v    v v  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGA-TAAGGGACTTGTATCCAGAATATA 767

  chr1_104983871_   1234 CAAGTAACTCAAAGAACTCAACAGGGAGAAAGCAAATAATCTCATTACAA 1283
                         i  iv     vv v       i ivi i  ii       i iv   ?v  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_104983871_   1284 AGTGGACCAAGGGCATAAATAAACATTTCTAAAAAGGAGACATACACATG 1333
                          i   i v    iiv i    i        vv    i   i     v   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_104983871_   1334 AACAACATATATATATAAA-ATACCCAACATCACCAATCAT 1373
                         iv   i vii i  iv   -  i i        ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.02 (19 / 860), avg. gap size = 2.68 (51 / 19)  


3310 26.87 0.44 0.44  chr1_105025142_105031421.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105025142_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105025142_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105025142_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_105025142_   5030 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_105025142_   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_105025142_   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_105025142_   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5227
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_105025142_   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_105025142_   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_105025142_   5328 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v  i        i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_105025142_   5378 TTAAAGATTTAAACGTTAGACCTCAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii    i  v   v  v    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_105025142_   5428 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_105025142_   5478 AACACCAAAAGCAATGGCAGCAAAAGACAAAATTGACAAATGGGATCTAA 5527
                         i            vvi   i       v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_105025142_   5528 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_105025142_   5578 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5627
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_105025142_   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_105025142_   5678 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_105025142_   5728 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5777
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_105025142_   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2561 26.74 6.40 0.81  chr1_105063416_105066465.rev     1700  2559 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105063416_   1700 TGGAAATGCATCTCATGCTCATGGATGGGTAAAATCAGTGTTGTGTAAAT 1749
                               vii   i    i        v  v i v i i i    vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105063416_   1750 GACCATTAC-ACCCAAAGAAATCTACAGATTCAATGCAGCTCCCATCAAA 1798
                          i v  -  -v      vvi              i   iii  i      
  L1M4_orf2#LINE/     51 GGCAAT-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_105063416_   1799 TAACATAA-----TTTTTCACA-AAATTAGAAAAAAAATCCTAAAATT-A 1841
                         - v vi i-----     ii  -     iiv  ivvi           - 
  L1M4_orf2#LINE/    100 -ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_105063416_   1842 TCTGGAACCAAAAAAGAGCTTGCATAGCCAAAGCAATTCTAAGCAAAAAG 1891
                          v     viiv  ii  v iv v         i    ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_105063416_   1892 AACAAATCTGGAAGCATCACATTACTGGACTTCAAATGATACTATAAGGT 1941
                               vi    i vv     i v ivi i      vvv     i  i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_105063416_   1942 TATAGTTACCAAAATAGCCTTGTACTGGTATAAAAATAGGCACGTGCACA 1991
                           i   v i   i i  iv v       i    ii    i  ii iv iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_105063416_   1992 AGTGGAACAGAATAGAGAGCCCAGAAATAAAGCCAAATATGTATAGCCAA 2041
                          i     i     v     i           v   v i  v   i i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_105063416_   2042 CTAATCTTTGACAAAGCATACAAAAAC-ATAAATTGGGGAATGGACACCC 2090
                         i i  i  i     i -i i v  i  -  vv v       v i i vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_105063416_   2091 TATTTAATAAATGGTGCTGGGAAAACTGGCAAGCCACATGTAGAAGAATG 2140
                          v  i  i              v      vv ?       i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_105063416_   2141 AAACTGGATCCTTATTTCTCATCTTATACAAAG-TCAACTCAAGATGGAT 2189
                           ii    i  i  ii  v  i v        i- i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_105063416_   2190 CAAAGACTTTTATATAAGTCCTAAAACTTTAAAAATTCTAGAAGACAGTG 2239
                           ?    i vv  i    vv        v     v ii       v iii
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_105063416_   2240 TTGGAG--AACCT-------CTT---TTAGACATTGG---CTTAG----- 2269
                          v  ? --  i  -------   ---    i  v   ---     -----
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_105063416_   2270 ---------------GCAA-------AGAATTTAATAGATGGGACCTAAT 2297
                         ---------------    ------- i  v vi   i  v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_105063416_   2298 TAAACATAAAAGCTT--GTGCATGGGAAAAGAAATAATCAGCAGAATAAA 2345
                         i   vv     i   --    v v--   i  v iv    iv i i i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTC--AAAGGACACTATCAAGAAAGTGAA 695

  chr1_105063416_   2346 CAGATAATTTTCAGAATGGG-GAAAGTATTTGCCACCTATACATCTGACA 2394
                         v   i  iiiv         -    i       v vii   i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_105063416_   2395 AAAGACTAGTATCCAGAATCTACAAGGAACTCAAACAAACCAGCAAGAAA 2444
                          ii    v           v  i  i      vv    vi  ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_105063416_   2445 AAGCCCAAATAATCCCATTAAAAATTTGTCAAAGAACACAAATAGACATT 2494
                            v -      i  v   ?    v v v     i ivii          
  L1M4_orf2#LINE/    796 AAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_105063416_   2495 TCTTAAGAGAAGATATACAAATGGCCAACAAATACAGGAAAAAAATGCTC 2544
                            iv i                     i  ii   v     i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chr1_105063416_   2545 AGCATCATTAATCAT 2559
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (137 / 89)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.10 (62 / 20)  


2186 22.84 8.38 3.11  chr1_105076718_105078445.rev      503  1242 (486)    L1M4_orf2#LINE/L1      130   908 (0)  

  chr1_105076718_    503 AAACCTATCCTAAAATTCCTA-GGAAA----------CTA--ATAGTCAA 539
                           i iv            v  -     ---------- i --    i   
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr1_105076718_    540 AACAAAATTGACAAAGATGATCAAA----------TC----TTTCTGATT 575
                              vv    v     v  v    ----------  ----  i ii   
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_105076718_    576 TCAAAACATATTCCAAAGCTACAATAATTATAACTCTCTAGAATTAGCAT 625
                                v  i v          i    i vi  vv v i v i i    
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_105076718_    626 ATTAATAGACA-ATAAGATTATTAGAACAGAATAGAGAACACAGAAATAA 674
                          vvi       -   -   i v i   i     v    iiv         
  L1M4_orf2#LINE/    280 AAGGATAGACATATA-GATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_105076718_    675 ACCCATACATGTACGATTAAATAATCTTTGACAAGGAGGCCAAGAATATA 724
                                   v  i i i  v i  i  i       iv       vi  v
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_105076718_    725 CAATGGGGAAATGATAGTCTCTGCAACAAATGGTATTAGGAAAATTGGGT 774
                                    vi       i v           ii i   v  i   i 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_105076718_    775 AGCCACATGTAAAATAATGGAATTTGACTCATAT-----ATCATATACAA 819
                          ?       i    v    i i  v   i v  i----- i         
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_105076718_    820 AAATTA--TCAACAAGAAAACATTGAAGACTGAAATGTAAGACCTGAAAC 867
                               --    v v i ---- ii?    iv          v  i    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGA----TCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_105076718_    868 TATAAAAATCCTGAAAGAAAACAAACAAACAAACAAACAAACAAAAACCT 917
                                v  i ii         --------------i ii?iv   i  
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACA--------------TAGGNGTAAATCT 560

  chr1_105076718_    918 TAATGGGATTGATCT-GGCAATAATTTTTTGGATATAATACCAAAAGCAT 966
                          vi  ivv   ivi -      ii   i  i     i i          i
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_105076718_    967 AGGCGTCAAAAGCAAAAATAGACAAGTAGGACTACATTAAA-TTAAAAAC 1015
                          i  iv      v         i  i v     v   i   -        
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_105076718_   1016 CTCTGCATAGCAAAAAAC-TTATCAA--AATTAAAA------CTGTATGC 1056
                         i i  iiivv    ii  -i      --  v i   ------ i-i iiv
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC-CACAG 709

  chr1_105076718_   1057 AATGGGAGAATATACTTGCAAATTATATATCTAATAAGA-ATTAACATCC 1105
                                   v   i        i        i     i- i vii    
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_105076718_   1106 AAAATATA----GAAGTCCTACAACTGAATACTAAAA----------CCT 1141
                          i      ----   v  i       v    v     ----------  i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_105076718_   1142 GATTTTTTTAAATGAACAAAGGATTTAAATACATATTTCTTTAAAGAAGA 1191
                         i   ?vv--     ii          i    v i      ii        
  L1M4_orf2#LINE/    810 AATTWAA--AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_105076718_   1192 AGATACAACTTGCCAAAATGTATATGAAAAGATGCTCAGT-TCACTAATT 1240
                         -v      v v     v v i i               ii-   ??????
  L1M4_orf2#LINE/    858 -TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_105076718_   1241 AT 1242
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.70 (104 / 61)
Gap_init rate = 0.03 (23 / 779), avg. gap size = 3.70 (85 / 23)  


3170 27.68 0.33 0.98  chr1_105086948_105091997     3644  4557 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105086948_   3644 TGGAAGAATATTCCATGCTCATGCATAGAAAGAATCGATATCATGAAAAT 3693
                              ii    i     i     v  v i    v ii    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105086948_   3694 GGCCATACTGCCTAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGT 3743
                            v     v  i   v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105086948_   3744 TACCAATGACTTTTTTCACA-AAATTGGGGGAAAAAAAAACT-ACTTTAA 3791
                          v   iivi i     ii  -      -------- v  i  - iii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--------ACAAGCTGATCCTAA 142

  chr1_105086948_   3792 CGTTCATAGGGAACCAAAAAAGAGCCCACATTGCCAAGACACTCTTAAGC 3841
                         vi      v    viiv  ii  v  viv  v     i   v    i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_105086948_   3842 AAAAATAATGAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTA 3891
                           i  v  ii   i      vv    i  v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_105086948_   3892 CAAGGCTACTGTAACCAAAACAGCATGGTACTGGTACTAAAACAGATATG 3941
                            i     v    i   i    ii         i iv ii i   i  i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_105086948_   3942 TGGACCAATGGAACAGAACAGAGGCCTCAGGAATAATGCCACACATCTAC 3991
                          i  i        i    iv   ivii   i     vv   i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_105086948_   3992 AACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGAGAAAGGA 4041
                         iii  vi    i  i     ivv  v   i v  vvv     i     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_105086948_   4042 TTCCCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 4091
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_105086948_   4092 AGCTGAAACTGGATCCCTTCCTTACATCTTATACATAAATTAATTCAAGA 4141
                         iiv    ii    i    v   i   i v      v       i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_105086948_   4142 TGGGTTAAAGACTTAAATGTTAGACCTAAAACCATAAAAATTCCAGAAGA 4191
                            i i ?    i       v   v       i      v iii      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_105086948_   4192 AAACCTAGGCA-ACACCATTCAGGACATAAGCATGGGCAAGGCCTTCATG 4240
                             v    ?i- v i -   iv   v vi vv i     v vi   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_105086948_   4241 ACTAAAACACCAAAAACAATGGCAACAAAAGCCAAAATAGACAAATGGGA 4290
                         iv  vi         i  vvi          vv        i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_105086948_   4291 TCTAATTAAACTAAACAGCTTCTGCACGGCAAAAGAAACTACCATCAGAG 4340
                         ii v  i   v v  v i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_105086948_   4341 TGAACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 4390
                             v  iv    i                 v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_105086948_   4391 GACAAAAGGCTAATATCTAGAATCTATAAAGAACTCAAACAAATTTATAA 4440
                           i  ii i  vi    i     v            vv    v iv    
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_105086948_   4441 GAAAAAAACAAAAAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 4490
                         v     i     v     v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_105086948_   4491 ACTTCTCAAAAGAAGACATCTATGCAGTGAACACACACATGAAAAAATGC 4540
                          i     v        i  vi viii iv  i vi          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_105086948_   4541 TCATCATCACTGGTCGT 4557
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.40 (12 / 5)  


3313 26.76 0.44 0.44  chr1_105098729_105105007.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105098729_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105098729_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105098729_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_105098729_   5029 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_105098729_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_105098729_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_105098729_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5226
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_105098729_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_105098729_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_105098729_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_105098729_   5377 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_105098729_   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_105098729_   5477 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5526
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_105098729_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_105098729_   5577 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_105098729_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_105098729_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_105098729_   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_105098729_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3022 28.06 1.67 0.56  chr1_105152127_105154378.rev      864  1761 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105152127_    864 TGGAATGGCATCCCATGCTCATGGATCAGAAGAGTTAATATCATTAAAAA 913
                              v ii        i        ii     v       ii    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105152127_    914 GATAATATTACACAAAGTAATATATAGATTCAATGCAATCCCTATCAAAA 963
                          ii    i v v    v i  v  i        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105152127_    964 TATCAGTGACATTATTCACAGAAGTAGAAAAA--AATACTTAAAATTTTT 1011
                          vi   ivi v  v  ii     i v  v  i--i  - i       iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chr1_105152127_   1012 ATAGAACCACCAAAGACTCTAAACAGCCAAATAAATCTTGACCAAAAGGA 1061
                           i   vii v ii   i vi  i       vv        vv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_105152127_   1062 ATAAAGCTGGAAGCATCACACTATCAGATTTCAAACTATACTACTAAGCC 1111
                          i    i    i vv       vi vi        viv      v    i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_105152127_   1112 ATGCTAACCAATACAGCATGGTACTCACATAGAAATAGA----TCAACTA 1157
                          iiv   i   v    ii       vi    iii     ---- vi ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_105152127_   1158 AAGGAACTGGATAGAGAGCCCAGAAATTAATCTATGTATCTATAGCTAAC 1207
                          v    iv i  v     i        v  i i  ii  i   i ii  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_105152127_   1208 TGATTCCTGACAAAGTCGCCAAGAACATCCACTGGGGAAAGGATTGTCTC 1257
                              iii     i vi       v   i  v         i  v    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_105152127_   1258 TCTAACAAAGGGTGTTGGGAAAACTAGATATCTATATGCAGAAGAATTAA 1307
                          ii      v    i     v    i    ? i i     i      v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_105152127_   1308 ACTAGACCTGCATCTCTCATCTTATGCAAAAATCAACTTAAAATGGATCA 1357
                         ii i    ivi i   v  i v   i       i    i           
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_105152127_   1358 AAGACCTACATATAAGACCTAAAACAATATAATTCTTATTAGAAAACACA 1407
                         ?       v  i     v       v   v  i     vv        i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_105152127_   1408 GGGAAAACATTTCAGAACATTGGTCTTGGCAAATATTTTGGGGGTAAGAC 1457
                           ?iv  vvi   ivi  v    vi v     vvi   ivvi i  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_105152127_   1458 CTCACAATTATAGGCAATAAAAACAAAAACAAACGAACGTGATTTTATCA 1507
                         vi  v  vi i i    i    iv     i i ii  ivv  i  i    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_105152127_   1508 AACTAAAAAGCTCTT-CACGGCAAAGAAAAC----AATGGAGTGAAAAAA 1552
                           v v    i  i  -ii vv     i v  ----  vii        i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_105152127_   1553 AAAAACCCTACAGAATAGGAGAAAATATTTGCCAGCTATTCATTTGACAG 1602
                         v  ---  i       i               v iii  vi  i   i i
  L1M4_orf2#LINE/    700 CAA---CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_105152127_   1603 GGGATTAATGTCCAGAATATACAAGGGACCAAAACATTGCAATAGCCAAA 1652
                             i vi i           i  i i  ivvv   viv     iiv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_105152127_   1653 AAAGGAATAATCTGATTAAAAAATGG-CAAATAATCTGAATAGACATTTC 1701
                          i vi     i ii   ?        -    vi  i              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_105152127_   1702 TC---AAAAGAGATACAAATGATCATCAAATATATGAAAAAAATGTTCAA 1748
                           --- i    v         ii  vi  ii i       i -  i    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

  chr1_105152127_   1749 CATCACTAATCAT 1761
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (158 / 90)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


2833 26.41 1.58 2.48  chr1_105173344_105175741     1012  1897 (501)    L1M4_orf2#LINE/L1        1   878 (30)  

  chr1_105173344_   1012 TGGAAAAACATTCCATGCTCATGGATAGAAAGAATCATTATCGTGAAAAT 1061
                               i i  i     i        v i    v i v   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105173344_   1062 GACCATACTGCCCAAAGTAATTTATAGTTTCAATGCTATCCCCATCAAGC 1111
                          i v     v      v i  i  i  v     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105173344_   1112 TACCATTGACTTTCTTCATAGAATTAGAAAAAACT-ACTTTAAATTTCAT 1160
                          v   vivi i  i  iii    v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_105173344_   1161 ATGGAAA--CAAAAAGCCC-GTATAGCCAAA-CAATCCTAAACAAAAAGA 1206
                                --   iiii   - v         -     i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_105173344_   1207 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATGCTACAAGGCT 1256
                               i      vv   ii  v  ii i      viv i      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_105173344_   1257 ACAGTAACCAAAACA-TCAGGTACTGGTACCAAAACAGATATATAGACCA 1305
                                i   i   - vv        i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_105173344_   1306 ATGCAACAGAACAGAGACCTCAGATGTAATGCCACACATCTACAACCAAC 1355
                            v  i    iv    vii    vi   vv   i    i  iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_105173344_   1356 TGATCTTTGACAAACCTGACAAAAACAAGCAACGGGAAAAGGATTCCCTA 1405
                             i  i     ivv  v   i v  vv   i   i    i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_105173344_   1406 TTTAATAAATGGTGTTTGGAAAACTGGATAGCCATATGCAGAAAACTGAA 1455
                           i  i        i v   v         ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_105173344_   1456 ACTGGATCCCTTCCTTACGCCTTATACAAAAATTAACACAAGATGGCGTA 1505
                         ii    i    v   i  i  v               v   i    vvi 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_105173344_   1506 CATACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 1555
                         ? v  i           v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_105173344_   1556 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAAAA 1604
                           ?i- v i -   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_105173344_   1605 CACCAAAAGTAATGGCAACAAAAGCCAAATT-GACAAATGGGATCTAATT 1653
                                  i vvi          vv   v -  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_105173344_   1654 AAA-CTAAATTTTAGAGTTAATTGTTGTGCTTTCTGCACAGCAAAAGAAA 1702
                            -i    ----------  i v        ---------    i  v 
  L1M4_orf2#LINE/    649 AAAATTAAA----------AACTTTTGTGCTT---------CAAAGGACA 679

  chr1_105173344_   1703 TTACCATTGGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCC 1752
                         i  i  vvii      v  i     i                 v     v
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_105173344_   1753 ATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAAATTAA 1802
                          vii  vi      i  i  i  vi          v  i  i   v ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_105173344_   1803 ACAAACTTA-CAAGAAAAAAACAA----CCCCATCAAAAAGTGGGTGAAG 1847
                             -  i -i  v     i    ----   v  i?    i    ii   
  L1M4_orf2#LINE/    780 ACAA-CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_105173344_   1848 TATATGAACAGACACTTCCCAAAAGAAGACATTTATGCAGCCAATAAACA 1897
                         v  v    i     i   i v        i  vi viii        i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

Transitions / transversions = 1.47 (137 / 93)
Gap_init rate = 0.02 (15 / 878), avg. gap size = 2.40 (36 / 15)  


3150 27.56 0.77 0.66  chr1_105190038_105196323.rev     4889  5795 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105190038_   4889 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4938
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105190038_   4939 GGCCATACTGCCCAAGGTAATTCATAGGTTCAATGCCATCCCCATCAAGC 4988
                            v     v     iv i  ii i  i     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105190038_   4989 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTACTTTTAAAGTTCA 5037
                          v   iivi i  i  ii     -   -- v  i  iv ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_105190038_   5038 TATGGAGCCAAAAAAGAGCCCGCATCACCAAGTCAATCCTGAGCCAAAAG 5087
                               iviiv  ii  v  v v  vi    iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_105190038_   5088 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5137
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_105190038_   5138 TACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGATC 5187
                                 i   i     i         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_105190038_   5188 AGTGGAACAGAAC--AGAGCCCTCAGAAACAACGCCGCATATCTACAACT 5235
                          i     i    i--    i  --     i  vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_105190038_   5236 ATCTGATCTTTGAAAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT--T 5283
                          vi    i  i  v  ivv  vv  i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_105190038_   5284 CCATATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5333
                          -- v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_105190038_   5334 CTGAAACTGGATCCTTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5383
                         v    ii    i  i v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_105190038_   5384 GATTAAAGACTTAAACTTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5433
                            i ?    i    iv v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_105190038_   5434 ACCTAGGCATTACCATTCAGGACATAGGCCTGGGCAAGGACTTCATGTCT 5483
                           v    ?i v viv   iv   v v  vi i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_105190038_   5484 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5533
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_105190038_   5534 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5583
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_105190038_   5584 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5633
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_105190038_   5634 AAAGCGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACCAGAA 5683
                           i vi  vi          v  i  v      vv    v iv iv v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_105190038_   5684 AAAAACAAACAACCCCATCAACAAGTGGGTGAAGGACATGAACAGACACT 5733
                            i     i     v  i? v  i    ii     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_105190038_   5734 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACAC--GAAAAAATGCTCA 5781
                             v        i  vi viii     v  i   --     i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_105190038_   5782 CCATCACTGGCCAT 5795
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2679 27.49 6.03 0.70  chr1_105213278_105215185      554  1415 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105213278_    554 TAAAAATATATTTTACACTCATGAGCTAGAAAATTTAATATTGTTCAAAT 603
                          ii   v    iii iii     iii i   i i           v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105213278_    604 ATTTATGCTAC-----TTAATCTACAGATTCAGTGAAATCCCTATCAAAA 648
                         iviv  i  v -----  i             ii v              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105213278_    649 ATGTGGTGGCATTTTTTAC-GAAATTAGAAAGAATAATTTTGAAATTCAT 697
                         vivii iv  v      i -      iiv   v- i  ii i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_105213278_    698 ATGAAAGTACAAAAGACC-------AC--AAATATTC---------AAGC 729
                            i  i i   ii    -------i --   i v  ---------   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_105213278_    730 ATA-----------C---CACTTTCTCATTTCAAAATACATTACAAAGCT 765
                          i ----------- ---     i iv         ivi i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_105213278_    766 ACAGTAATTAAAACAATATGACACTAGCATGAAAACAGACATACTGACCA 815
                                 i  i   i i  ii   i    i ii i       iv  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_105213278_    816 ATGATATAGAATATAGAGCTGATAAATAAACTCATGCATATACAGTTAAC 865
                            iv       vv    iiv v        i   i   v  ii  i  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_105213278_    866 TAATTTTTGATC-GTATGGCAAGAACACATAATAAAGAAAAGATAGTGTC 914
                          i     i  iv- vi  v     v  ivi   iii    ii     v i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_105213278_    915 CTCAACAAATGGTGTTGGGTAAACTGTATATCAATGTGCAAATGAATAAA 964
                         i             i    vv     v   ? v ii      v    i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_105213278_    965 TTTGTATTCTTATCTCACATAATACACAAAAATTATCCCAAAAATAGATT 1014
                         v   v ii i  i      iv   i          v i     - i   i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGATC 498

  chr1_105213278_   1015 AAAGGCTTAAACATAAAAGCTGAAACTGTTAAGTTTCCAGAAGAAAAGAA 1064
                          ?  i i    ii   i    i     i v  ii iii         v v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_105213278_   1065 GAGAATAA-TCTTCATGACATTGGTCTTTGCAATGATGTCTTAGATATGA 1113
                         ii ?i   -     i    v    vi vv      i v            
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_105213278_   1114 CACCAAAAACATAGAAAACAATAGCAAAA-CAGACAAATGGGACTACATC 1162
                                 i  i iiv     v  v    -i   i    v     v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_105213278_   1163 AAA-CTAAAATGTCTTTCACAGCAAAGGTAATAATCAACAGAGTAATAAG 1211
                            -i     vv i  vii vv      vv iv     v i   i v   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_105213278_   1212 ACAACCTACAGAGTCAGAAAGAAAAACATTTAGAAGCCATATATCTGATA 1261
                               i     i -- ii      -i    iv  ii             
  L1M4_orf2#LINE/    699 ACAACCCACAGAAT--GGGAGAAAA-TATTTGCAAATCATATATCTGATA 745

  chr1_105213278_   1262 AAGGGTTAATATCCAAGATATATAAGACATTTCTACAACTCAATAGCAAA 1311
                          i  ii vi      ii        iiv i ii            ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_105213278_   1312 AAAA-AAGGGG------TAGGGAA---GCAAAGGGCTTCAATAGACATTT 1351
                           i -  ivii------ ?iii  ---       ii  v           
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_105213278_   1352 TTCCAAAGAAGACATACGAATTGATAATGGGTATATAAACAGGATGCTTA 1401
                         i           i    i   v vi   ii i i  i  - i      i 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGATGCTCA 894

  chr1_105213278_   1402 ACATCATTAATTAG 1415
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.43 (165 / 68)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.05 (58 / 19)  


 317 16.67 0.00 3.03  chr1_105238577_105240998.rev      697   762 (1660)    L1M4_orf2#LINE/L1        1    64 (844)  

  chr1_105238577_    697 TGGAAAGTTATCCCATGCTCATGGATTTGAAAAATTAATGTTATTAAATA 746
                                v         i         v   i v     i  i    --i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA--G 48

  chr1_105238577_    747 ATGTCAATACTGGCCA 762
                            v       vv   
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCA 64

Transitions / transversions = 0.83 (5 / 6)
Gap_init rate = 0.02 (1 / 64), avg. gap size = 2.00 (2 / 1)  

2255 26.55 2.91 2.15  chr1_105238577_105240998.rev     1141  1931 (491)    L1M4_orf2#LINE/L1      112   908 (0)  

  chr1_105238577_   1141 TTCTTCACAGAAATAAAAAAGCC------AAATTTCACATGAAACCACAA 1184
                           i  ii       vi v    i------   v    i   i  vii   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_105238577_   1185 AAGACCCCAAATAGACATAGCAATCATATGCAAAAAAAAAAAAAAAAGCT 1234
                         ii     vi     v  v i     v i----     i  i  v    i 
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTG----AAAAAGAAGAACAAAGTT 207

  chr1_105238577_   1235 AGAGGCATCACACTACCTGACTTCAAAATATACTAAAAAGCTATGGTAAA 1284
                         i    vv       v  ii i       iv     v       ii    v
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_105238577_   1285 CAAAACAGCATGGCATTGACATTAAAAGAGATACACAGAGAAGCAGAACA 1334
                            i    ii   i i  i   v ii v   i i i   vv iii   i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_105238577_   1335 TAATGGAGAACCTAGAAATAAACCTACATATTCACAGCCAGCTCATTTTC 1384
                         v   v    ii i           i i i   i ii i  ii v      
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_105238577_   1385 AACAAAGACACCAAAAACATACATAAGCAAAAGAGTAGTATTTTCAATAA 1434
                         i    i iii    i v   v  vvi vi     i    v       i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_105238577_   1435 ATGATGCTAAAAAAAACTGGATAACCATATGCCAAAAAAAAAATGAAGCA 1484
                            i    iii v  -       ?   i    ----    i       iv
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAA-CTGGATAKCCACATGC----AAAAGAATGAAGTT 452

  chr1_105238577_   1485 AGACACCTATCTCTCATCATACACAAAAATTAACTTAAAATGGATGAAAC 1534
                         i   v    i   v  i    i             i         v ? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_105238577_   1535 ACTTAAATATAGGACTTGAAACTATGAAAGTACTAGAAGAAAACATTGGT 1584
                           i     i  i  vi i       i   v vi             v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_105238577_   1585 AAAACATTTTAG-GATATTG---TAAGTGAAGAATTTGTA--TAAGACCT 1628
                         iv  -  i  v -  iv   ---  i ii v iv  iv  --  v   vi
  L1M4_orf2#LINE/    553 GTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_105238577_   1629 CAAAAGGACAGACAA-------AAAAATAGACAAAT--GACGTTACTTCG 1669
                               v   ii   -------         i    --   v i - ivi
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA-TCAA 650

  chr1_105238577_   1670 AGCTAAAATGTTCAGGACAGCAAAGGAAACAATCAATAATGTTAAGAAAC 1719
                          ii     vv  iv vi vv       v  v     v  v  v  i i  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_105238577_   1720 AACATCACAGAATGGGAGAAAATGTTTGCAAGTTACCCATCTGA-AGGGG 1768
                            -i                  i       i i ivi      - i   
  L1M4_orf2#LINE/    701 AAC-CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_105238577_   1769 CATTAATAACTAGAATATATAAGGAATTCAACCAACTCACTAGGAAGTAA 1818
                         - i vi  v i           i   i  vvv       v  iv  --  
  L1M4_orf2#LINE/    750 -ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA--AA 796

  chr1_105238577_   1819 TAATAATAATAATTTCATTTTAAAATGGGTAAAGTGTATGAATAGACATT 1868
                         vi i  --    iiiv   ?v        i    vi v            
  L1M4_orf2#LINE/    797 AGACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_105238577_   1869 TCTTAAAAGAAAACATACAAATAGTCAACAGGTATATGAAAAC-TGTTCA 1917
                            iv      i i        i i   i i i i       v-  i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_105238577_   1918 ACATCACTCATCAT 1931
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (131 / 75)
Gap_init rate = 0.02 (17 / 797), avg. gap size = 2.35 (40 / 17)  


2495 27.54 3.03 1.98  chr1_105273005_105274981.rev      625  1481 (496)    L1M4_orf2#LINE/L1        1   866 (42)  

  chr1_105273005_    625 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 674
                               i    i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105273005_    675 GCCCATACTACCCAAAGGAATTTATAGATACAATTCTATTCCCATTAAAC 724
                          v v     v      vvi  i  i    v   iv v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105273005_    725 TACCATTGACAGTCTTTGCAGAACTAGAAAAAAAAAACT-ATTTTAAAAT 773
                          v   vivi vv i         v v  v  i-----  -  ii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAAT 145

  chr1_105273005_    774 TCGTATGGAACCAAAAAAGAGGCTCA--ATAACCAAGGAAATCCTAACAA 821
                           i       -- viv   i i i  --   i    iiv    i i v  
  L1M4_orf2#LINE/    146 TCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_105273005_    822 A-AAGAACAAAGCTAGAAGCATCATGCTACCCAACTTCAAACTCTACTGT 870
                          -          i i  i vv   ii  v     i      vii    ii
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_105273005_    871 AAGGCTATAGTAACCAAAACACCTTGATACTGGTACAAGAACAGACACAT 920
                           i    i     i   i   viv  i      i i   i i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_105273005_    921 AGGCCAATGGAACCGAATAGAAAACCCAGGAATAAGACCGCACACCTGCA 970
                           ii        iv    v  i ii    i     iv  ii   ii iii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_105273005_    971 ATCATCTTATCTTTGACAAACCTGACAAAAACAAGCAATAGGGAAAGAAC 1020
                         i   vi v  i  i     ivv  v   i v  vv    i         i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_105273005_   1021 TCCCTATATAATAAATGGTTCTGGAAAAATTGGCTAGCCATATGCAGAAA 1070
                         vvi  v vi  i       v    i v  i   v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_105273005_   1071 AGTGAAACTGGGCCCCTTCCTTACGTCATACACAAAAATCAACTCAACAT 1120
                          i    ii   i     v   i  ii    i        i       v  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_105273005_   1121 GGGTTAAAGACTGAAATGTAAAACCTAAAACTATAAAAACCCTGGAAAAA 1170
                           i i ?    iv        i v              vi i i   i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_105273005_   1171 ATCCTAGGCA-ATACCATTCAGTACATAGGCATGGGCAA--ATATTTTAT 1217
                          v v    ?i- v i -   ivv  v v  vv i     --i v i   -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA- 591

  chr1_105273005_   1218 GATGAAGATGCCAAAAGCAATTGCAACAAAAGCAAAATTTGACAAATGGG 1267
                            - v  ii         vvv          v    v v  i    v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_105273005_   1268 ATCT------AATTAAGAGCTTCTG--CATAGAAAAATAAGCTATCAACA 1309
                          ii ------      i i   i  -- v vi  ii i --       v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA--CTATCAAGA 688

  chr1_105273005_   1310 GAGTAAACAGACAACCTGCACAATGGGGGGAAATTTTTGCAAACTATGCA 1359
                         i   i  v        ii  v      i i    v        ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_105273005_   1360 TTTGACA---------TATCCAGGATCTATAAGCAACTAAAACAAATTTA 1400
                          i   i ---------       i  v     iv    vvv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_105273005_   1401 CAAGAACAAAACAAACAACCCTAGTAAAAAGTG--CAATAAGGACATGAA 1448
                         i  v  v  i     i     v v ?    i  --   --    iv    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA--AGGATTTGAA 836

  chr1_105273005_   1449 CAGGCACTTCTCAAAAAAAAGACATATGCAAAT 1481
                         i  i  i     v   i  i---    i     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAG---ATATACAAAT 866

Transitions / transversions = 1.58 (142 / 90)
Gap_init rate = 0.02 (17 / 866), avg. gap size = 2.53 (43 / 17)  


2856 24.07 6.16 0.93  chr1_105320389_105324605.rev     2867  3726 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_105320389_   2867 AAAGATATTCCATGTTCATTAATTAGAAGAATAAATATTGTTAAAATGGC 2916
                                 i          vi   i     v v           i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_105320389_   2917 CCTA-TGGCCAAATGCAATATGCAGATTTGATGTAATCTCTATCAAAATA 2965
                         vv  - vv      -ii  v i      ii i i    i          v
  L1M4_orf2#LINE/     54 AATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_105320389_   2966 TCAATGACAGTCTTCATAAAAATAGAAAAA--AATCATAACATTCATATG 3013
                         i  iivi vv i  iii i    v  v  i--i   v   v         
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_105320389_   3014 AAA-----------CCA---CAG--AAAAC-------------------- 3027
                         i  -----------   ---i  --     --------------------
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_105320389_   3028 ----TGGAGGAATTACATTACCTGACTTCAAATTATACTACAGAGCTATA 3073
                         ----       v i   i v  ii i      viv       i     i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_105320389_   3074 CTAACCAAAACCACATGGTATTGGCATAAAAATAGACACATAGACCGAGG 3123
                         v   i   i  viii     i        ii       i     i i v 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_105320389_   3124 GAACAGAATTGAGAACCCAGACACACATCCATACACTTAGAGTAAACTTA 3173
                            i          ii     v i v i       i   vi  v  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_105320389_   3174 TTTTGAACAAAGGTGCCAAGAACATACACTGGAGAAAAGACAGTCTCTTA 3223
                             vi    i          v   v  v   i    ii i     i  v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_105320389_   3224 AATAAATGGTGCTGGGGAAACTAGATATCCATATGCAGCAGAAAGGAACT 3273
                           i             iv    i    ?   i     iv    v i ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_105320389_   3274 AGACCCCTATCTCTCGCCATATACAAAAATCAAGTCAAAATGAATTAAAG 3323
                         i        i   v i              i  v        i  i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_105320389_   3324 AGTTAAACCATAGATGTTAAA-CTATAAAACTACTAAAATGAAACATTGG 3372
                          vi    i-i  iiv i    -          vi  i  vi      v  
  L1M4_orf2#LINE/    503 ACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_105320389_   3373 TAAAACTCTACAGAACAC--GGTTATGGGCAAAAATTTATT-GAGAAAAC 3419
                         ?iv  v   v ivi  vi--     --     vii   v  -  v vi  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATATGAC 599

  chr1_105320389_   3420 -CTATAAGAATAGGCAACCAAAACAAAAACGGACAAATAGGATTACATCA 3468
                         - i v   v i i     v   iv     ii  i    v   i v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_105320389_   3469 CA-TTAAAAAGCTTTTGAACAACAAAGAA-ACAATCAACAAAGAGAAGAA 3516
                         v -       -      vi vv     i -  v     v    v   i i
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_105320389_   3517 ACAACCCAAAGAATGGGAGAAAATATTTGCCAACTACCTCTCTGTCGAGG 3566
                                 v                     v  ii iv v    vii   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_105320389_   3567 GATTAATAACCAGAATATATAAGGAGCT--TAATCAACTCTACAGGAAAA 3614
                           i vi  v             i  i  --  --      v i iv    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAAA 796

  chr1_105320389_   3615 AAATATGATATTCCAATTTAAAAATGGGCAAAATATTTGAATAGACATTT 3664
                          i i -i   vi      ?             iv                
  L1M4_orf2#LINE/    797 AGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_105320389_   3665 -TACAAAGAAAACATACAAATGGCAAACAAGCATATGTAAAGACGCTCAA 3713
                         - v       i i           v  i     i   v     i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_105320389_   3714 TATTATGGCCATC 3726
                         i  i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (124 / 79)
Gap_init rate = 0.02 (20 / 905), avg. gap size = 3.05 (61 / 20)  


1919 27.41 2.26 1.36  chr1_105372114_105373769      500  1163 (493)    L1M4_orf2#LINE/L1      239   908 (0)  

  chr1_105372114_    500 ACAATAAAGTTATAGTCACCGAAACAGTATGGTATTGCTATAAAAATAGG 549
                           v i    i  i   v i i i     i     i  vi    ii    i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_105372114_    550 CACATA--CCAATGGCGGAGAATAGAGAACCCAGGAATACAGCCAAATAC 597
                           i   --i      viv     v    ii    i    v v   v i i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_105372114_    598 TTATAGATAAATAAT----AATAATAATAATAATAATAAATAAGTGGGGA 643
                             i vi  v i  ----i i  vii ivi  -i iv v v i      
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGA 387

  chr1_105372114_    644 AAGGACACCCTATTCAACAAATGGTGC-GAGATAATTGGCAAGCCACTTG 692
                            i i vi  v               - i  i  i   vv ?    v  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_105372114_    693 TAGAAGAATCAAACCAGATCCTCATCTATCACCTAATACAAAAATCAACT 742
                         i i      v  iiii  i  ii i  vv    vv          i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_105372114_    743 CAAGATGGATCAAAGACTTAAATCTAAGACCTGAAGCCATAAAAATTCTA 792
                            i        ?    i     v     v  i  i i      v ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_105372114_    793 GATGGCAACATCAGGA--AAACCCTTTTAGACACTGGCTTAGGCAAAGAC 840
                           v iv     -   ?--   i i iv -   vi   v        v ii
  L1M4_orf2#LINE/    538 GAAGAAAACAT-AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGT 585

  chr1_105372114_    841 TTCATGACCAAGAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAG 890
                            v iivi v  vv         v v         iv   i   i   i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_105372114_    891 ATGAAACTTTA--AAACTATAAACACTTCTGCACAACGAAATAAATAATC 938
                           vii    i --   v -    v    i  ii vv i  iv v iv   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_105372114_    939 AGCAGAGTTAGCAGACAACCCACAGAGTGGGAGAAAAATCTTTACTATCT 988
                          iv i   v iv              i          - v   i v vii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATC 733

  chr1_105372114_    989 ATACATCCAACAAAGGACTAACATCCAGAATCTACAAACAACTCAAATTA 1038
                            i   ii i  i     vii         v  i   v     ---   
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC---TTA 780

  chr1_105372114_   1039 ----TCAGCAAGAGAAAAAGCAAGTAATTCCATCAAAAAGTCGGCTAAGG 1084
                         ----   ii  v i   i -   i   ii v  i?    i v   v    
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_105372114_   1085 ACATGAATACACAATTCTCAATAGAAGATATACAAATGGCCAACAAACAT 1134
                          iv      v   v     v v                     i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_105372114_   1135 ATGAAAAAATGTTCAACATCACTAATTAT 1163
                                i   i         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (109 / 69)
Gap_init rate = 0.02 (13 / 670), avg. gap size = 1.85 (24 / 13)  


2523 27.30 4.55 1.25  chr1_105408165_105410754.rev     1225  2103 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105408165_   1225 TGGAAAGATATTCTGTGTT-ATCAATAGGAATAGTTAGAATT-TTA---- 1268
                                    i ii    -  vi  v    v v   iv   -   ----
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105408165_   1269 ----------CCCAAAAAGATGTCCAGAGTCAATGAAATTCCTGCCAGAA 1308
                         ----------      vv   v v    v    i v   i   ii  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105408165_   1309 TTCCAATGACATATTTCACAGAAAGAGAAAAAGAAACTCTGTAATTAGTA 1358
                          i   iivi v v   ii      vv  v  ivvi ii  iv    vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_105408165_   1359 TGTAACCACAAAAGATGT-TAACAACCAAATAAATCCTTAGCAAAAATAG 1407
                           v  vii   ii  ivi-v  i i     vv    i v iv  i  v i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_105408165_   1408 CAAAGCTAGAGGTGTGACACTATCTGATTTCAAAATCTACTACAAAGATA 1457
                              i i    vv v     vi ii         ii          v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_105408165_   1458 AAATAATTTAAACAGTATGGTACTGGCACAAATATAAACACATAGACCAA 1507
                         v i    iv i     i           i  iv   i   i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_105408165_   1508 TGAAACAAAAT--AGAGCCCAGAAATAATTCCATGCATTAACACTCAATA 1555
                           i  i i   --    i          vi    i    v iiv     v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_105408165_   1556 GAATTTTGACAAAAATGTCAAGAACACACAATAGGGCAAGCATAGTGTCT 1605
                           v   i     iii  i     v  iv    i   v   v     ----
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT---- 396

  chr1_105408165_   1606 TCTCCTCAATACATGGTGCTGGGAAAACTGCATAACCACATGCAGAGAAA 1655
                         -  ii    i v            v     v   ?         i ii  
  L1M4_orf2#LINE/    397 -CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_105408165_   1656 TAAAAATAGAACCTAATCTTACATTATGTATGAAAATCAACTAAAAAT-- 1703
                          i  iv i  v  iv i  i   ii  i  ii     i    v     --
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_105408165_   1704 ---AAAGACTTAAATGTAAGGCCCGAAACTGTAAAACTGCTAGAAGAAAA 1750
                         --- ?    i          iv ii     i       vi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_105408165_   1751 CATTGGGAAAATTTTTCTTATAGTTGGTCTAGGCAATGATTTTTT---TT 1797
                            v  ?iv  v i   v ivvv    vi         i   i  --- v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_105408165_   1798 TGGTACCATCCACAAACCACAGGCTACAGAGGCAAAAATAGATAAATGAG 1847
                           ii    -----   v    i  v   i i v              vi 
  L1M4_orf2#LINE/    596 TGACACCA-----AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_105408165_   1848 ATTACATCCAACTAAAAAGCTTCTGCACAGCTAAGTAAACAAT--AGCA- 1894
                          i v    v  v v    i   i  ii vv v   v v  v  --  v -
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_105408165_   1895 -TGAAGTAACAACTTATAGAATGGAAGAAAATAACTGCAAACTATATATC 1943
                         -    ivi     ii i       i        vi      ii       
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_105408165_   1944 TGTTA-GGTAATTATCATTCAAAATATGTAAGGAACTC----AAGTCAAT 1988
                           v  -  v v  i -  i  i     i   i      ----  v     
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_105408165_   1989 AGCAAGAAAACAAATAACTCAATTTAAAAATTGTCAAAGGACCTGAA--- 2035
                          ii  i  i         i     ?      v v       ii    ---
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_105408165_   2036 -CAATTAAAAAAAAAAGATATAAAAATGGTCAACAGTTATATCTAAAGGC 2084
                         -  v  vvvv   i        v      i   i ivi i  vv    ii
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_105408165_   2085 ACTTAACTTTATGGAAATG 2103
                         i  i   v i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.40 (51 / 15)  


2056 28.28 2.28 1.88  chr1_105420851_105422598      521  1266 (482)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr1_105420851_    521 AAAGAGCCCACACACATAGCTAAAGCAAACACTAAGCAAAAGGAACAAAT 570
                           i ii    v ---     i   i   v -i i iv  i i       v
  L1M4_orf2#LINE/    160 AAGGGACCCAGA---ATAGCCAAAACAATC-TTGAAAAAGAAGAACAAAG 205

  chr1_105420851_    571 CTGGTGGCATCCCATTACCTGACTTCAAACTATACCATTAGGCTATAGTC 620
                         i   v  vv  v  i v  ii i      viv   i iv i    i   v
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_105420851_    621 ACCAAAACAGTATGGTACTGGTATAAAAAAAGGAACATAGAACAATGGAA 670
                          i   i     i         i    ii v  iv i     v        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_105420851_    671 CAGAATAGAGAACTAAGAAATAAAGCCAAATACTTATACCCAACTGATCT 720
                         i     v    iiiv         v   v i i    ivi   i    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_105420851_    721 TTGACAAACCAAACAAAAACATAAAGTGGGAAAAGAACACTCTAGTTAAC 770
                          i     ivvviv   i v   vv i    i      i v   vv i   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_105420851_    771 AAACAGTACTTGGATAATTGGCAAGCCACATGTAGAAGAATGAAACTGGA 820
                            ii  i  v   i  i   vv ?       i i         ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_105420851_    821 TCTTCCTCTCTCACCTTATACAAAAATTGACTCAAGATGAATCAAAAACT 870
                         i iiivi   v    v            i      i   i    ? i  i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_105420851_    871 TAAATCTAAGACCTGAAACCATACATATTCT--------AACATTGGTAA 912
                              v     v  i    i   v - i   --------     v  ?iv
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGT 554

  chr1_105420851_    913 AACCCTTCCAGACATGGGCTTAAGCAAAGACTTC------ATGAC--CAA 954
                           vi    vv   v v  v   i    v ii   ------     --   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_105420851_    955 AACCTCAAAATAAAATTCAACAAAAACAAAAATAAATAGATGGGACTTAA 1004
                           v v   i--------        iv       i   i  v      v 
  L1M4_orf2#LINE/    605 AAGCACAAG--------CAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_105420851_   1005 TTGTACTAGAGAAGCTTTTGTACAACAAAATAAATAATCCATAGATTTAA 1054
                          iiv v -v i  i       i vv    iv v iv   v v i v v  
  L1M4_orf2#LINE/    647 TCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_105420851_   1055 CAGAAAACCCACAAAGTGGGAGAAAATCTTCACAAACTATGCATTCGACA 1104
                         v   v        i i           v  ii    ii  ii  ii  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_105420851_   1105 AAGGACTAATATTCAGAATCTACAACAAACGCAAACAAATCAGTAGGAAA 1154
                          i     vi   i      v  i  vi   v vv    v   i  iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_105420851_   1155 TAAACAAACAATCCCCTCAAAAATTTGATTAATGACATGAATAGACAATT 1204
                         v i     i  i  vv i?    v v iiv  v  iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_105420851_   1205 CTTAAAAGAAGATATACAAATGGCTAACAAACATATGAAAAAA-GTCCAA 1253
                           iv                    i  i  i  i       i - ii   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_105420851_   1254 TATTACTAATTAT 1266
                         i  i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (120 / 87)
Gap_init rate = 0.01 (9 / 749), avg. gap size = 3.44 (31 / 9)  

 700 27.65 0.00 0.00  chr1_105420851_105422598     1392  1608 (140)    L1M4_orf2#LINE/L1      692   908 (0)  

  chr1_105420851_   1392 TGAACAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 1441
                             v  i     i i               v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_105420851_   1442 GACAAAAGGCTAATATACACAATCTACAAAGAACTTAAACAAATTTACAA 1491
                           i  ii i  vi   v  v   v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_105420851_   1492 AAACGAAACAAACAACCCCATCAAAAAGTGGGTGAAGCATATGAACATTT 1541
                         v  vi i     i     v  i?    i    ii   v  v    i vvi
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_105420851_   1542 ACTTCTCAAAAGAAGACATCTATGCAGCCAAAAAACATATGAATAAATGC 1591
                          i     v        i  vi viii     v  i  i     v i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_105420851_   1592 TGATCATCACTGGTCAT 1608
                          v v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (33 / 26)
Gap_init rate = 0.00 (0 / 217), avg. gap size = 0.00 (0 / 0)  


2465 28.94 2.12 0.67  chr1_105461715_105467293     4192  5086 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105461715_   4192 TGGAAATACACTCCATGCTCACAGATTGGAAGAATCAATATTTTGAAAGT 4241
                               v i ii     i   ii          v i      v v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105461715_   4242 GACCATGCTGCCCAAAGCAATCTATAGATTCAATGTAATTTCCATCAAAA 4291
                          i v  i  v      vii     i        i i   ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105461715_   4292 TACCAACATCATTTTTCAGAGAATTAGAAAAACAG-TCCTAAAATTCACA 4340
                          v   i vv v     iiv    v v  v  i v -            i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_105461715_   4341 TGGAACCACAAAAGAATCCAAATAACCAAAGCAATCCTAAGCAAAATGTA 4390
                              vii   ii  vi vi    i     i     i i iv  i v v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_105461715_   4391 CAAATCTGGATACATTAGATTACCAGACTTCAAATTATATTACAA--CAA 4438
                             vi    vivv i v i v  vi i      viv  i     -- v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_105461715_   4439 TGGTTACCAAAACAACATGATAGTGATATAAAACTAGGCACATAGACCAA 4488
                         ii  v i   i   iii  i  v  ii    iiv   i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_105461715_   4489 TGGAACAGAATGGAGAACACAGAAATTAGGGCAAATAAGTACAACCAACT 4538
                              i     v    iiv       v ivv  v i vv  iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_105461715_   4539 GATCTTTGGCAAAGCTTACAAGAGCATATATTGAGAAGTGGGAACTCTAC 4588
                            i  i i   i v vv     v   vi v  i i iv iiv v   vi
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_105461715_   4589 TTAATAAATAATGCTGGGA-AACTGGCAAACCACATGTCAAAGAGTGAAA 4637
                          i  i    ii        -      vv ?       iv     i    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_105461715_   4638 CTGGATCCCTATCTCTTATCACATACAAAAATCAATGCAAGATGGAGCAA 4687
                         i    i     i   vi i  i          i  iv   i     v  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_105461715_   4688 AG--TGAAATCTAATATGTGAAACCACAAACATTCT-AGATGACAACATT 4734
                           --iv    v   v vv i    i i   - i   -   v  v     v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATA 549

  chr1_105461715_   4735 GAAAAAACTCTTCTAGAAATTGGCCTAGTCAAATAATTCATAACTAAGAT 4784
                          i?iv  v     vv  vv    vi   v   vviv   v  iv  v  i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_105461715_   4785 GCCCAAAGTAAATGCAACAAAAACAAAAATAAATAAATGAGACTAGTAAT 4834
                         i  v    i v v         iv       i      vi    -- v  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT--TCAT 647

  chr1_105461715_   4835 TAAACTAAAAAGTTTCTGCACAGCAAAAGAAATAGTCAACCGAGTAAACA 4884
                         i   v v    ii  i  ii vv    i  v ivi    vvi   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_105461715_   4885 GACAAGCCACAGAATGGGAGAAAGTATTTGCAAACTACACATCCGACAAG 4934
                              v                 i          ii i i   i  i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_105461715_   4935 GGACTAGTATTGAGAATCTATAAAAAAACTC----AAATCACCAAGAAAA 4980
                              v    iv     v      i  -   ----  v   vi  v    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATAATAAAA 796

  chr1_105461715_   4981 A-ACAAATAATTCCAAT--AAAAA-GTGCAAAAATACTGGAAAAGGTATT 5026
                          -        -i     --     - v     ii- i v   v  ii   
  L1M4_orf2#LINE/    797 AGACAAATAA-CCCAATTWAAAAATGGGCAAAGG-ATTTGAATAGACATT 844

  chr1_105461715_   5027 TCTCAAAAAAAGGTA----AATGGTCAACAAACATATGAAAAACTGTTCA 5072
                             v   i   i  ----     i   i  i  i       iv  i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_105461715_   5073 ACTTCACTAATCAT 5086
                           v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (147 / 109)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


2501 28.31 2.43 1.70  chr1_105503416_105507940.rev     2819  3641 (884)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr1_105503416_   2819 TGGAAAGGTATTCCATATTCATGTTTTGGAAGAATCAATATTATTAAAAT 2868
                                i   i    i      vv        v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105503416_   2869 CTCCTTACTACCTTAAGTACTCAAGAGATTCAATGTAATCCCTATCCAAA 2918
                         vv vv    v  iv  v iv  v v        i i          v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105503416_   2919 TACCAATGATATTCTTCACAGAAATAGAAGAAACATTTCTTAAATGTATG 2968
                          v   iiviiv  i  ii       v  vi iviiv i  v    vi  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_105503416_   2969 TGGAACCACAAAAGACTCAGAGTAGCCAAAGCTATACTAAGCAAAAATAA 3018
                              vii   ii   i    i        i v  vi i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_105503416_   3019 GAAAACTGGAGGAATCATGTTACCTGACTTCAAA--TTATCCTACAGAAC 3066
                         v   ii       v   iii v  ii i      --   --     i i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGC 248

  chr1_105503416_   3067 TTTAGCAATAAAAATAGGATACTATATTATAGTACTGACATAAAAACAGA 3116
                          vi  i   v  i i  ---------- i i      i     ii i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAG----------TGTGGTACTGGCATAAGGATAGA 288

  chr1_105503416_   3117 AACATAGACCAATGAAAGAGAATAGATAACCTAGAAATAAATTCATACAT 3166
                         v i     i     i  v     v  v ii i         ii       
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_105503416_   3167 CTACAGTAAACTCATTTTTGACAAAGTTTCCAAGAATATACACTGGGGAA 3216
                         i  ii  v  i v     i     i v v      vi  v  v       
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_105503416_   3217 AGGACAGTCTTTTCAATAAGTGGTGCTGGGAAAACTGAATGTTCATATGC 3266
                           i i           i  i           v     i  i?i  i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_105503416_   3267 AAAAGAATGAAACTAGACTCC-ATCTCTTGCCATATATAAAAATAAACTC 3315
                                    ii i   i  - i   vii       i      v     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_105503416_   3316 AAAATGGATTAAATAC-----TGAAAGGCCTGAAA--ATA------CTAA 3352
                                  i ? v  -----  v   iv  i   --   ------i  i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_105503416_   3353 GAGAAGACATTGGGGAAGCTCTCCAGGGCAATAAACTGGACAA-AACTTC 3401
                         i    i    v  ? v iv   i iv i vv iiii i i   -iii   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_105503416_   3402 TTTAACAATACCCCACAGGCACAGGTAACCAAAGCAAAAATGGACAAATG 3451
                           vi i vv  v   v i     i i   v    v      i  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_105503416_   3452 GAATTATATCAAGTTTAAAACCT---GTACAGCAAAGAAAATAATCAACA 3498
                          i i vi     iv      v  ---  i vv     i v iv     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_105503416_   3499 AAGTGAAGACACAATCCAGAGAATGGGAGAAAATGTTGTCAAACTACCCA 3548
                                i v    i   v               i  vv    ii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_105503416_   3549 ACTGACAAGAGATTAATAAACAGACTATATAAGGATATCAAACAATTCCG 3598
                         v    i   i  i vi  vv    v       i  vv  vv    i  vi
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_105503416_   3599 TGGGAAAAAATCTAATAATCCAGTTAAAAAAATGGGCCAAAGG 3641
                          iiv     iv v     i   i  ?     -     -     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGC-AAAGG 829

Transitions / transversions = 1.54 (139 / 90)
Gap_init rate = 0.01 (11 / 829), avg. gap size = 3.09 (34 / 11)  

 342 20.65 2.17 0.00  chr1_105503416_105507940.rev     3943  4034 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_105503416_   3943 AGAAAAGG--AAAAGATTAGCATAGACATTTCTCAAAATAAAGCATACAA 3990
                          i   v  --   i    v v             v   v  iii      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_105503416_   3991 ACGGGAAACAGGTAAATGACAAGGTGCTCAACATCATTGGTCTT 4034
                          i  vv  i i i v    v   i            ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 2.00 (2 / 1)  


2326 26.43 2.12 5.73  chr1_105521096_105523462      933  1874 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105521096_    933 TGGAAAAATATTTTATGTTCATGGATTGGGAAAAGCAATATAGTTAAAAT 982
                               i    iii               i i vvi     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105521096_    983 AGCCATACTGTCCAAAGCAATTTAAAGATTCAACACTATCACTATCAAAA 1032
                         i  v     vi     vii  i  v         i v   v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105521096_   1033 TACCAACCTCATTTTTCACAGAATTAGAAAAAAGAAAAAAACT-ATTCTA 1081
                          v   i iv v     ii     v v  v  i---------  -  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---------CTGATCCTA 141

  chr1_105521096_   1082 AATTGTATTTAGAAGAAAAAAAGTGCCGGAATAGCCAAAGCAATCCTCAG 1131
                           v vi  v i   iviv  ii vv  i           i     i v i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_105521096_   1132 CAATAAAAGTAAGGCTAGAGGCATTACATTACCCGACTTCAAAATACACT 1181
                         v  v  i ii  i i i    vv i   i v   i i       ivi   
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_105521096_   1182 AAAATGCTACAGTA-CCAAAAGAGCATGATACTGGAGCAAAAACTGACAC 1230
                          v  v         -i   i v  ii  i      vii  ii iv    i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_105521096_   1231 ATAGACAAGTGGAACA-AATAGAGAACTCAGAAATAAACCTACAAGTCTA 1279
                              iv i     i -   v    iii            i i vi i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_105521096_   1280 CAGCCACCTGATGATTGAAAAAATTAACAAAAATAAGCAATGGGGAAAGG 1329
                         ii i  vi    vv i  v  iiv iv   i vi vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_105521096_   1330 ATTCCTTTTTCAGTAAATGGTGCTGGGATAACTGTCTAGCTCTGTGTAGA 1379
                           vvii      ii              i     vv  ? ivii  i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_105521096_   1380 TTAAAA-GAAACTGAACTG-TACCTCTCACCTTATACAAAA-----CTTA 1422
                         -- i  -   ii  i  iv-      v    v         -----  i 
  L1M4_orf2#LINE/    442 --AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_105521096_   1423 AGATGGATTAAAGATGTAAACATAAGAGAGAAAGCTGTAAGAATTTTAGA 1472
                          i      i ?   iv    ii      vv   i  i   i v i     
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_105521096_   1473 AGAAAATCTAGG---AAATACCCTTCA--ACATAGTCTTTGGCAAGGAAT 1517
                               iv    ---    ---    i--  v v vv  v     v iv 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_105521096_   1518 TTATGGCTA-AATACCCAAAAGCAATTGCCACAAAAACAAAAACTGATAA 1566
                          iv i v  -i i   -       vvv  v      iv     iv     
  L1M4_orf2#LINE/    587 TCTTAGATATGACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_105521096_   1567 ATGGGTTCTGATTAAA-TTAAAGAGCTTCTCCACAGTAAAAACAAAATAA 1615
                           v  vii v  i   -     i -   i -----  -------------
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTT-----GT------------- 666

  chr1_105521096_   1616 CAGCAACAACAACAAAAACAACAATTACTAACACAGTAAACAGAAAGCCT 1665
                         --  vv   ----- ii   ----i  ii  v v   i  v   v i  i
  L1M4_orf2#LINE/    667 --GCTTCAA-----AGGACA----CTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_105521096_   1666 ACAGAATGAAAGAAAATATTCACGAACTATGCATCTGACAAAGGTCTAAT 1715
                                 ii          ii i  ii  ii      i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_105521096_   1716 ATCCAGTATCTACAAGGAACTTAAACAAATCAACAAGCGAAAAAACAGAA 1765
                               v  v  i  i     ivv    v    i  -ii    i   ---
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAGACA--- 801

  chr1_105521096_   1766 CAAAAACAAATCAAGT-AAAAACGGGCAAAGGACATGAACAGACACTTCT 1814
                         ----  i  vi   v -     i          iv    i     i    
  L1M4_orf2#LINE/    802 ----AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_105521096_   1815 TACAAGAAGACATACAAGTGGCCAACAA--ACATGAAAAAAATGTTCAAC 1862
                         ivv       i      i       i  --         i -  i     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAAC 896

  chr1_105521096_   1863 ATCACTAATCAC 1874
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (152 / 95)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.08 (74 / 24)  


1038 27.99 0.68 0.68  chr1_105572696_105577244.rev     2891  3183 (1366)    L1M4_orf2#LINE/L1        4   296 (612)  

  chr1_105572696_   2891 AAAAAAATTCTATGTTCTTGGATTAGAGAAATTGGTATTATTAAAATGTC 2940
                            i v  i i      v      i  ii v  ii    i    i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_105572696_   2941 CATACTACCCAAAGCAATGCAAAGATTCAATTTACTCCCTATCAAAATAC 2990
                         v     v      vii  vi v        ivi v             v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_105572696_   2991 CAATGGCTTTCTTCACAGAAAT--ATAAAAAAAACCCACTAAATTTATAT 3038
                           iiv  i  i  ii       -- i  ivvi v  i --     i    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA--AAATTCATAT 151

  chr1_105572696_   3039 AGAACTACAAAAGATCCAAAATAGCTAAAGTTATCCTAAGCAAAAAGAGA 3088
                         i   v i   ii  i   i      i   iiv   i i iv  i    iv
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_105572696_   3089 AAAACTGGAGGAATCACATTACCAGATTTCAAATTATAGTACAGAGCTAT 3138
                            ii       v     i v  vi        viv  v    i     i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_105572696_   3139 AGTAACCAAAACAGTATGGCACTGGCATAAAAACAGACACACAGA 3183
                              i   i     i   i          ii i     i i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

Transitions / transversions = 2.15 (56 / 26)
Gap_init rate = 0.01 (2 / 293), avg. gap size = 2.00 (4 / 2)  

1565 27.68 1.96 0.89  chr1_105572696_105577244.rev     3499  4058 (491)    L1M4_orf2#LINE/L1      343   908 (0)  

  chr1_105572696_   3499 GGTGAACTCATTTTTAACAAAGGTACCACAAGCATACATTGGTGAAAATG 3548
                            v  i v     ii    i   i   vi v   v  v   v    ivi
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_105572696_   3549 TAATCTTTTCAATAAATGATACTGGGAAAACTAGATATTCACATGCAGAA 3598
                           i         i     i i      v    i    ?i        i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_105572696_   3599 CACTGAAAC-AGACCTGTATCTCTTACCATATACCAAAGTCAAATAAAAA 3647
                         v v    ii-i    iv  i   vi         v   i i  v v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_105572696_   3648 TGGATTAGAGGCTTAAAACTAAGTTCTCAAAGTCTGAAAGTACCACAAGA 3697
                              i ?  i i    vv    vv  v   v v i   v vii v    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_105572696_   3698 AAAT---GGGAAAAATCTCTAGGACATTGGTCTGGAAAAAAAGAATTATT 3744
                            i---  ?iv      iiiv   v    vi -- iiv  v iv  v  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTT--AGGCAATGGTTTCTT 590

  chr1_105572696_   3745 GTGAAGTAAC-CCACAAGCACAGGCAAACACAGCAAAAATGGACAAATGA 3793
                         i-  vi i  -   v       i    vv v  v      i  i    vi
  L1M4_orf2#LINE/    591 A-GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_105572696_   3794 GATCACATCAAA-TTAAAAA--TCTGCACAGCAAAGAAAACTGTCAACAA 3840
                           iiv       -       -- i  ii vv     i v   i    v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_105572696_   3841 TGTGAACAGACAGTCCCCAAAACGGGAGAAAATATTGGCAAACTACCCAA 3890
                         v     v     ii  v  i  i             v     ii ivi v
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_105572696_   3891 CAGACAAGGGATTAATCACCAGAATATGTAAAGAGTTCAAACAACTTTAT 3940
                          v  i      i vi vv         i      ii  vv      iv  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_105572696_   3941 AGGGAAAAAATCTGAAAAATTGATT-ACAAATGTGCAAAAGACTTTAATA 3989
                          ivi    i - vi v  viii   - v     v     i  i  v    
  L1M4_orf2#LINE/    790 AATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_105572696_   3990 GACATCG-TCCAAAGGAAGACATACAA-TGGCAAACAGGTATATGAAAAG 4037
                              iv-       -    i      -    v  i i i i        
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_105572696_   4038 GTGCTCACCATCATTAATCAT 4058
                         i      v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (83 / 69)
Gap_init rate = 0.02 (12 / 566), avg. gap size = 1.33 (16 / 12)  


1115 28.30 1.57 0.63  chr1_105601802_105605277     1658  1975 (1501)    L1M4_orf2#LINE/L1        1   321 (587)  

  chr1_105601802_   1658 TGGAAAAACACTCCATGCTCATGGATAGGAAGAATCAATATTATTAAAAT 1707
                               i i ii     i        v      v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105601802_   1708 GGCCATACTACCTGCAGCAATTTATAGATTCAATGTTATTACTATCAAAC 1757
                            v     v  iiv vii  i  i        i iv  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105601802_   1758 TACCAATGACATTCTTCACAGAACTAGAAAATCT-ATTTTGAAATTCATA 1806
                          v   iivi v  i  ii     v v  v  v  -  ii i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_105601802_   1807 TGGAACCAAAAAAGGAGCCC-TAACAGCCAAAGTAATCCTAAGCAAAATG 1855
                              -- viv    ii   -v  i       ii    i i iv  i v 
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_105601802_   1856 AACAATGCTGGAGGCATCATGTTACCTGACTTCAAACTAAACTACAATGC 1905
                              v i      vv   iii v  ii i      vivv       v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_105601802_   1906 TACAGTAACCAAAGCAGCATGGTACTGGTACAAAAACAGGCACACAGGCC 1955
                                 i   ii   ii         i i  ii i  i  i i  ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_105601802_   1956 AATGGAATTGTATT---AGTCCA 1975
                                 v v   ---      
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCA 321

Transitions / transversions = 1.90 (59 / 31)
Gap_init rate = 0.01 (4 / 321), avg. gap size = 1.75 (7 / 4)  

1675 26.09 4.38 2.19  chr1_105601802_105605277     2390  2983 (493)    L1M4_orf2#LINE/L1      302   908 (0)  

  chr1_105601802_   2390 GGAACACAGTAGAGAGACCAGAAATAAGGACACACATCTACGATCACCTG 2439
                             i v i v     v          ivv  i    i  i i   vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_105601802_   2440 ATCTTTAACATAGCTGACAAAAACGGGCAATGAGGAAAAGACTCCCTATT 2489
                           i  ii   vi v  v   i v ivv     i     ii ivvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_105601802_   2490 CAATAAATGGTGCCAGCATTTACTGGGATAACTGGTTAGCCATATGCAGA 2539
                            i         ----------     i      v  ?   i     i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGC----------TGGGACAACTGGATAKCCACATGCAAA 441

  chr1_105601802_   2540 AGATTGAATCTGGACACCTTCCTTACACCATATAAAAAAATCAACACAAG 2589
                            v    vi     v   v   i          v      i   v   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_105601802_   2590 ATGGATTAAAGACTTAAATGAAAAACCCAAAACTACAAAAACGCTGGGAG 2639
                               i ?    i      v  i v i       i    vivi i i  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_105601802_   2640 GCAATATC-------ATCCTGGAAACA--GGAATGAACAAAGATTTCATG 2680
                         iv  i  v-------   i v vi  v--  iv iii   v i    v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_105601802_   2681 ACTAAGACACCAAAAGCAATCA--CAACAAAAGCACAAATTGACAAGTGG 2728
                         iv  v             --  --         v v    v  i  i v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_105601802_   2729 AATGTAATTAAACTTAAGAGATTCTGCATGGTCAAATAA-ACTATTAATA 2777
                         i iv v  i   v    i iv  i  iiiv-     vi -     i  v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGA 688

  chr1_105601802_   2778 GAGTAAA----CAACCTACAAAATGGGA-AAAATATTTGCAAACTATGCA 2822
                         i   i  ----     i   i       -              ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_105601802_   2823 TCTGAGAAATGTCTAATATCCAACATCTATAAGGAACT--TA-AATTTAC 2869
                              v  iv v  vi      iv  v     i     --  -  i i v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_105601802_   2870 -----AAGAGAAAAACAACCCA-TTAAAAAGTGGGCAAATAACATGAATA 2913
                         -----  i   v   i      -  ?    i        vi iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_105601802_   2914 GACACTGCTCAAAAGAAGACACAAATGTGGCCAACATGCATGTGAAGAAA 2963
                             i v   v        i i v vi       i v   ii    i i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_105601802_   2964 AGCTCAATATCAGTGATCAT 2983
                         v      i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (89 / 63)
Gap_init rate = 0.02 (13 / 607), avg. gap size = 3.00 (39 / 13)  


1484 24.95 10.25 3.09  chr1_105629001_105631544      934  1450 (1094)    L1M4_orf2#LINE/L1        1   554 (354)  

  chr1_105629001_    934 TAGAAAGATAGTCTGTCTTCTGGGGTTTGAAAATTTGATATTTTTGAGAT 983
                          i        vi ii v   vv  i  v   i i  i     v  i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105629001_    984 GTCAGTACTACCCAAA------------------GCA--TTCTAT----- 1008
                          v  i    v      ------------------   --ii    -----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105629001_   1009 ---------------TTGCAGAAATAGAAAAATCTATTCTAAAATTAATG 1043
                         ---------------          v  v  iiiv  i        v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_105629001_   1044 TAGAA-TACTAAAGGACACCAAACAGCCTAAATATTCTTGTAAAATAAAT 1092
                          i   - i -  i    v vi  i    v   i v     v    -----
  L1M4_orf2#LINE/    151 TGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA----- 194

  chr1_105629001_   1093 ATTATAAATGAAAAACAAAGTCAGATGTCTCAAATTTTCTGATTTCAAAA 1142
                         ---------   i        ii  v v    v i  i ii         
  L1M4_orf2#LINE/    195 ---------GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_105629001_   1143 TATACTACAAAGCTAAAATACTCAAAACAGTGTGTTACTGGTATAC---C 1189
                         iv             v i  v    i        v      i   v---i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_105629001_   1190 ACACAGTGAGGTACAATAGAATAGGATAGAGAGCCCAGAAATAAACTGTC 1239
                          v   vvv  i -    i      i  v     i            ivvi
  L1M4_orf2#LINE/    286 AGACATATAGAT-CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_105629001_   1240 TCATGTATGACCAAATTACTTTTGATAATCACGCTAAAACCACTGAA--A 1287
                         v   v    ii   v v i   i  i  vvii  i  i    i v  --i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_105629001_   1288 GAAAAGAGGA--CTTTACAAGAAATAGTGTTGGGAAAACTAGATATACAC 1335
                          i     iv --    v   v    i   i     v    i    ?v   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_105629001_   1336 ATGCAAAAATATGAAGTTGGATCTTTAC-----AGCATAGACAAAAATTA 1380
                                 iv           i ii   ----- v    v          
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_105629001_   1381 ACTGAAAATTGATAAAAAGTCTAAACATAGGAGCTAAAACTACAAAATTG 1430
                            v     v   v ? iii     ii  i            i    i v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_105629001_   1431 TTAAGAATAAACATGGAGGT 1450
                            ii iv      i i?  
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGT 554

Transitions / transversions = 1.42 (74 / 52)
Gap_init rate = 0.02 (11 / 554), avg. gap size = 6.27 (69 / 11)  

1126 19.00 9.00 0.67  chr1_105629001_105631544     1744  2043 (501)    L1M4_orf2#LINE/L1      537   861 (47)  

  chr1_105629001_   1744 AAAAGAATAAACATGGGAG-AAAT--TCATGATAT-------GGCAATAA 1783
                          i     --     i  ? -    --  i   iv -------      ii
  L1M4_orf2#LINE/    537 AGAAGAA--AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_105629001_   1784 TTTCTTAGATATAACAACAATAGCACAGGGAACAAAAGAAA---TG--TA 1828
                                     i   v   v      i v           --- i--  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_105629001_   1829 AACTGGACTACATCAAAATTAGAAACTTTTGTGCAGGTAAGGGTACTATC 1878
                           i      v           i            vvvv    ii      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_105629001_   1879 GACAGAGTGAAAAGGCAACCCAGAGAAAAGGAGAAAATTTTTCTAAATCA 1928
                         i v i         i       v    vi         v   vi      
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_105629001_   1929 TGTATTTGATAAGAAATTAGTATTAGGAAAATATAAA-AACTTCTACACC 1977
                          i   i       ii i v    ivi   v       -    ii    v 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_105629001_   1978 ACAATAACAAAAAAA----------AATTTAAAAATAGGCGAAGTATT-G 2016
                         v      i     i ----------    ?      i   i   v   - 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_105629001_   2017 AATAGGTATTTCTCCAAAGATGACATA 2043
                              ii             v  i   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATA 861

Transitions / transversions = 1.62 (34 / 21)
Gap_init rate = 0.03 (9 / 325), avg. gap size = 3.22 (29 / 9)  

 264  5.08 0.00 15.25  chr1_105629001_105631544     2093  2151 (393)    L1M4_orf2#LINE/L1      859   908 (0)  

  chr1_105629001_   2093 ACACAAGTGGCCAATAAGCACATGAAAAGATTGAAATGAAGCTCAATATC 2142
                          i    i                        ---------      i   
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGAT---------GCTCAACATC 899

  chr1_105629001_   2143 AATATTCAT 2151
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.00 (3 / 0)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 9.00 (9 / 1)  


 855 25.00 0.43 0.86  chr1_105645233_105649875.rev     2742  2973 (1670)    L1M4_orf2#LINE/L1        2   232 (676)  

  chr1_105645233_   2742 GGAAAGATATTCCATTTTCATGTGTTGGAATAACCTA-TATTGTTAAAAT 2790
                                   i    v      vi      -i  i  -         i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAA-GACTTAATATTGTTAAGAT 50

  chr1_105645233_   2791 GTCCATACTACCCAAATCAATCTAAAGATTCAATGCAGTTCCTAGCAAAA 2840
                          v v     v       ii     v        i   i i    v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105645233_   2841 TACCAATGACATTATTTGCAGAAATAGAAAAAAAAAATTCTAAAATTTAT 2890
                          v   iivi v  v           v  v  -ivvi  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_105645233_   2891 ATAAAATAACAAAAGGCTTAGAATAGCCAAAGATATCATGAGCAAAAATA 2940
                           ii  vvi   ii i ii            ivv   v   iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_105645233_   2941 ACAAAACTGGAGGAATCACATTACCTGATGTCA 2973
                              ii       v     i v  ii  v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

Transitions / transversions = 1.32 (33 / 25)
Gap_init rate = 0.01 (3 / 231), avg. gap size = 1.00 (3 / 3)  

2089 26.64 1.89 1.89  chr1_105645233_105649875.rev     3466  4152 (491)    L1M4_orf2#LINE/L1      222   908 (0)  

  chr1_105645233_   3466 TTCCTGTTCCAA----TACTACAGGGCTATAGTAACCAAAACAGTATGGT 3511
                          i  vi  i   ----       ii    i     i   i     i    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_105645233_   3512 ACTGCCGTAAAAACAGACACAGAGACCAATGGAACAGAATAGAGACCGTA 3561
                             v i   ii i     i v   i        i     v    vivi 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_105645233_   3562 GAATCACATTCATACACCTACAGTAAATTTATTTCCCACAGAGGTGTCAA 3611
                            vi v ii      ii  ii  v    v    i v   ii    i   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_105645233_   3612 GAACATACATTGGGGAAAAGACAGTGTCATCAACAAATGATGCGAGGAAA 3661
                           v   v  v        ii i   v iv          i   vi   v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_105645233_   3662 ACTAGATATCCATATGGTAAAAGAATGAAACT--ATTCCTATCTCTCACC 3709
                            i    ?   i   -i           ii -- ii    i   v    
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATG-CAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_105645233_   3710 TAATACACAAATAAAATCAAAATTGACTAAATAGTTAAGTCTTAAGACCT 3759
                         vv     v    v  v       v  ii ? v vi   i v -    v  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCT 519

  chr1_105645233_   3760 CAAACTATGAAACCACTACAAGAAAACATTGGGA-AAATTTTCCAGGACA 3808
                         v       i    ivi  v          v  ?i-    i   -iv   v
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACC 568

  chr1_105645233_   3809 TTGATCTGAGCAAAAAATTTCTT-GACA-AATACCCTGCAAGTATAGGCA 3856
                            ivi ii    vii-      -  i -i i   --iv   i i i   
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGG-TTTCTTAGATATGACACC--AAAAGCACAAGCA 615

  chr1_105645233_   3857 ACCAAAACAAAAATGGACAAATGAGATCACATCAGG-TTAGAAAGCTTCT 3905
                           v   iv      i  i    vi  iiv     ii-   i   -   i 
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTT 664

  chr1_105645233_   3906 GCAGAGCAAAGAATACAATCAACAAAGTGAAGAGACAACCTACAGGATGG 3955
                          iivvv     i i  v     v        i        i    i    
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_105645233_   3956 GAAAAAAAAAAAAATTTGCAAACTACCCATCTGATGAGGGATTAATAACT 4005
                           i    v -----        ii ivi       i     i vi  v i
  L1M4_orf2#LINE/    715 GAGAAAATA-----TTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_105645233_   4006 GGAATATATAAGAAGCTCAAACAATT--ATAGAAAAAAATCTAATAATCC 4053
                         i          ii i   vv    i --   iv     iv v     i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_105645233_   4054 AACTAAAAAAATGGCTAAAATCCTT-AACAAACATTTCTCAAAAGAAGAC 4102
                           i ?     -   vi   ivvi  -  i i         v        i
  L1M4_orf2#LINE/    810 AATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_105645233_   4103 ATATGAATGGCAAACAGGCATATAAAAACTTGCTGAATGTCATGGATAAT 4152
                            ii      v  i i   i  i    vv    v  ii   ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (115 / 64)
Gap_init rate = 0.02 (16 / 687), avg. gap size = 1.62 (26 / 16)  


2459 25.85 3.08 3.64  chr1_105674939_105676808      500  1377 (493)    L1M4_orf2#LINE/L1       36   908 (0)  

  chr1_105674939_    500 TAATAGTGTTAACATGTCCATACTACCCAATGTGATATACTGATTTAATA 549
                              v      v   v v     v     vv    v   v    i  ii
  L1M4_orf2#LINE/     36 TAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACG 85

  chr1_105674939_    550 CAATTTCTATCAAAATCCCAATGGTATTTTTCACAGAAATAGAAAA---- 595
                             ii              iiv iv     ii       v  v  ----
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chr1_105674939_    596 AACCTAAAATGTATATGTAACAACAAAATGTCTTTAATTGCCAATA-AAT 644
                          v        vi     v  vvi   iivii ivv   v     v -   
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_105674939_    645 CATAAGAAAGAAAGACAAAGTTGGAGACATCACACTTCCTGAGTTTAATC 694
                          v i i      ii            ivv          ii v  i  vv
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_105674939_    695 TATATTACAATGCTCTCACAATCACAAAAGTGTAGTACAGGCACAAAACC 744
                         iv  i     v   vivii     vi v     i    v    i  iivi
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_105674939_    745 AGACACAAAGACCAATGGAACACAACAGAGATATCAGAGAAAATAAACCC 794
                              i v   i        i v  iv    vvi    ---         
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA---AATAAACCC 332

  chr1_105674939_    795 AAGCATACGAAGTCAATTAAGTTTTAACAGGGGAACCAAGAATACATAAT 844
                          vi   viivi       i v   ii   i   vi      vi ivi   
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_105674939_    845 TGGGAAAAAATGTTTTTTTTCCAATAAAGGGAATTGATAAAA-TGAATAT 893
                         v      i   iv i    --   i   v  vii  iv v  -  i   ?
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTT--CAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_105674939_    894 CTATATGCAAAAGAATGAAATTGGGCCCTTATCTTACAGTAT-TGTAAAA 942
                          i i               i    i   i  i  i   vi  - ii    
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_105674939_    943 --CAACC--AAATAGATTAAAGATCTAAACACAAGATGC-AAAATTATAA 987
                         --i   i--    i   i ?   i     iii    -  -    i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAA 529

  chr1_105674939_    988 ATCTCTTAGAAGGAAA----------ACTTTTTGGAA--TTGACCTCGAC 1025
                          v          i   ---------- v i  i vi --   ivi v i 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_105674939_   1026 AATGATTTTTATATATATATATATATATATCTCACACTAAAGCCTCAAGC 1075
                             i   i -----------  v    i----    i   iv v     
  L1M4_orf2#LINE/    580 AATGGTTTCT-----------TAGATATG----ACACCAAAAGCACAAGC 614

  chr1_105674939_   1076 AACAACAACAACAAATAAGCAATTGGGACTGTATCATACTGAATTGCTTC 1125
                              -  v  v     iii  v v     vi    v v v  vvi   i
  L1M4_orf2#LINE/    615 AACAA-AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_105674939_   1126 TGTACAGCAAAAGCAACAATCAACAAAACATAAAGGCAAGCTACATGTTA 1175
                            i vv    i vv  v     v   iiiv    i   v i   viv i
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_105674939_   1176 AGAAAAAATATTTGCAAAGCATATATCTGATAAGGGATTAATATTCAAAA 1225
                         i  i              v                  i vi   i  i  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_105674939_   1226 TATGTAAGGAAGTC--ACAAATCTCAATACTAAGCAAATAAATAAATAGA 1273
                            i   i   v  --    --       --------     v i i i 
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAA--CTCAATA--------ATAAAAAGACAAA 803

  chr1_105674939_   1274 CAACCCAATT-AAAAATGAGGAAAGGTTCTAAACAGACCTTATTTCAAAG 1322
                         i         -       i v     v i i  i    v  vi i     
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_105674939_   1323 AAGATGTAAAACTGGCCAACAAGTAAGTGAAAAGGTGCTCAACATCACTA 1372
                              i  v  v       i   i vi       i            ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_105674939_   1373 ATCAT 1377
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.37 (130 / 95)
Gap_init rate = 0.02 (19 / 873), avg. gap size = 3.11 (59 / 19)  


 734 26.11 7.39 6.40  chr1_105703719_105705991      500   905 (1368)    L1M4_orf2#LINE/L1      127   536 (372)  

  chr1_105703719_    500 GAAAAGGTAATTTTAAATTTCATATGAAAA-ATGAACAATCTAGAACAAC 548
                           v   v i  ii    v        i   -iii ivi i i    i i 
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr1_105703719_    549 AAAACCAATGT-GAAAAAAATTCCTTAA-AAAGTTAGAGAATTTATAACC 596
                         v   v    v -      i vv----  -      i   i i i i - i
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAG----AACAAAGTTGGAGGACTCACA-CT 221

  chr1_105703719_    597 ACCTTATTTCAA----CAATATAAATCTA---TGCTC--TGTATTGTGTT 637
                         v  iv       ----i v  i   v   --- iv  --vii v    v 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_105703719_    638 ATTAACATGGAGACAGATATATC-ACGAGTGAAATAAAATAAAGAATCTA 686
                          i ii   iii  i   i    v- iv i  i    i   vi   i  i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_105703719_    687 GAAATAGTTCCAAATAT--ATAGTCAATTGATTTTTGACAAATATGTCAA 734
                               ivi   v i  --  i             i     ivi  i   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_105703719_    735 -----TTTAACAGGAAAAGAATAATCTTTTCAA-ATATAGCAATGAAAAA 778
                         -----  i  ii  i        i         - v  i iiv  ii v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_105703719_    779 ATTGGATACAAATATTCCAAAATACACACATTCACAAACACAACAAAAAA 828
                          i      -------?   ---------   --i    --- iv vi  i
  L1M4_orf2#LINE/    422 ACTGGATA-------KCCA---------CAT--GCAAA---AGAATGAAG 450

  chr1_105703719_    829 TTGGACC--TACTTCACAACAAATACAAAA-TTAATTCAAAATTAGTCA- 874
                                --   i     v  v        -    i       vii   -
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_105703719_    875 -----TAAGTATAAGAGCTAACATTACAAAACTCCT 905
                         -----   i i          v i  i       i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

Transitions / transversions = 2.28 (73 / 32)
Gap_init rate = 0.05 (19 / 410), avg. gap size = 2.95 (56 / 19)  

 346 26.43 10.36 6.07  chr1_105703719_105705991     1125  1404 (869)    L1M4_orf2#LINE/L1      537   828 (80)  

  chr1_105703719_   1125 AGAAGAAAGCATAAACAAAAATCTGAATGACCTCAGTATAAGAAAAGATT 1174
                                 i    ii?iv      vvi      ii vv  i v  v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_105703719_   1175 TCTTAAATAT-ACACAAAAAATGCAATCTATAAAACA-----TCAATAAG 1218
                              i    -    v    iii   v v i    v ----- vi    i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_105703719_   1219 TTAAATTTTTT-----TTAA----TTTTGTATTTTCAAAGGACAGTTTTA 1259
                           ii i  iv -----    ----      ii  -         ---i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTT-CAAAGGACA---CTA 682

  chr1_105703719_   1260 TTTCTTATATTTGTATAAAAAT-AAAACTCAAGCTATGTACTGGGATAAA 1308
                          i------------ vi   i -    vv   v i iiv v     v   
  L1M4_orf2#LINE/    683 TC------------AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_105703719_   1309 ATATATACAGCACATATGTCTT-TACATGTACTTATACCTAGAATATATA 1357
                             v i  ivv     i   v-  - v v    i  i i          
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATA-AGGGACTTGTATCCAGAATATATA 769

  chr1_105703719_   1358 A----CTTCTATAATT---TAATAAGTAGACAAA--AT---GTTTTAAAA 1395
                          ----  ii  i  i ---      iv       -- i---i  ?v    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_105703719_   1396 TTGGCCAAG 1404
                          v   v   
  L1M4_orf2#LINE/    820 TGGGCAAAG 828

Transitions / transversions = 1.40 (42 / 30)
Gap_init rate = 0.05 (14 / 292), avg. gap size = 3.29 (46 / 14)  


2824 26.55 1.85 3.05  chr1_105758682_105761195     1103  2021 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105758682_   1103 TGGAAAGATATCCCATATTCATGAATTGGAAGAACCAATCTTGTTGAAAT 1152
                                         i      i         vii   v     i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105758682_   1153 ATCTATACTCCCTAAAGCAATCTGCAGATTCAACACAATCCCCATCAAAA 1202
                         iv v        i   vii    i          i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105758682_   1203 TTTCAATGATATTATTAATAGAAATAGAAAAA--AATTCTAAACATTTTT 1250
                          ii  iiviiv  v  vii      v  v  i--i  i     -   iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA-ATTCAT 149

  chr1_105758682_   1251 -TGAAAACACAGAAGACCCTGAGCAGCCAAAACATTCTTGAACAAAATAA 1299
                         -  i   ii  iii     v  ii          v       v  i vi 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_105758682_   1300 ACAAAACTGGAGACATCATATTACCTGATTTAAAAATCTACCTCAAAGCT 1349
                              ii     ivv   i i v  ii    v    ii   iv       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_105758682_   1350 ATAGTAATTCAGACAGTATGATGCTGGCATAAGAACAGATACATAGTTCA 1399
                          i      iv       i  i i          i i   i i    v   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_105758682_   1400 GTGGAATAGA---GAAAAACCAAAAAATAAATCTAAGCATACGCATTTAA 1446
                         i         ---  i iv   i   -    i i vi   viiiiv i  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGTCAA 348

  chr1_105758682_   1447 TTTATTTTTGACAAGTGCCTCAATAATGCACAGTGGGAAAAGGATAGTCT 1496
                           v     i      v ivi   v viiiv  i    i    i       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_105758682_   1497 CTTCAATAAATGGTGTATGGAAAACAGAATATCCACATGCAAAATAATGA 1546
                         i     i        ivv   v   v i   ?            v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_105758682_   1547 AATTAGGCTGTTACATTACACTATATTCAAAAACAAACT---AATGTGTT 1593
                          i  i i ivi   v i    i    v      iv    ---    vi i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_105758682_   1594 AAAGACCTAAATGTAAAATCTGAAATCATAAAACTCC-AAAAGAAAATAT 1642
                          ?              i v  i   ii         i- i       i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_105758682_   1643 AGAGGAAAA-CTCCTTGACATTCAACTTGGCAATGATTTTTTTTGATAGA 1691
                           i? v   -  i v    v  viii v       i   i  v-    vi
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GATATG 597

  chr1_105758682_   1692 ACACCACAATGATAAACCACAAACACAAAAATAAACAAGTGGGAATACAT 1741
                               v  vv i  i v     viv       i i  i v   v v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_105758682_   1742 -AAAATTAAAATGCTCAGCACAGCACAGGA-ACCAACCAGCAAAACTAGA 1789
                         -          vvi iv ii vv  v    -  i v v  -   iiv i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAA 696

  chr1_105758682_   1790 AGGCAGACTGTGGATTGGAAAAAAAAGTATTTGTGAACCACATATAAGAT 1839
                           i  iv iiii  v   i i    --      ii  i  i    vv   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAA--TATTTGCAAATCATATATCTGAT 744

  chr1_105758682_   1840 AAGGGATTAATATTCAAAGTCTATAAGGAACTCCCACAATTTGATAGTCA 1889
                               i vi   i  i i v     i      ii    i ii   i - 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-A 793

  chr1_105758682_   1890 AATTTTTTTTAAATGACCCTTTTTTAAATGACCCAGTGAAAAAATAGGCT 1939
                           ---------  -   --------    i     i v?      i   v
  L1M4_orf2#LINE/    794 AA---------AA-GAC--------AAATAACCCAATTWAAAAATGGGCA 825

  chr1_105758682_   1940 GAGGACTCAAAGAGACATAGGACCTCCCAA----ATATGTAAATAGCCCA 1985
                         i    i ii  v      v---i    v  ----    ii    i   v 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATT---TCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_105758682_   1986 CAGGTATATGAACAGATGCTCACCATCACTAATCAT 2021
                         i i i i     v         v     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (157 / 83)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.37 (45 / 19)  


2679 23.42 6.45 2.63  chr1_105784533_105787190.rev     1326  2162 (496)    L1M4_orf2#LINE/L1        1   869 (39)  

  chr1_105784533_   1326 TGGAAAGACATCTCATTTTTAGAGATTAAAAGACTTAATATTACTAAAAT 1375
                                 i   i   v  i vi    ii             ii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105784533_   1376 GTCAATATACC------TAACCTACAGATTTAATGTAAACCTTATCAAAA 1419
                          v     iv  ------ i i         i  i i  v  i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105784533_   1420 TTCCA-----TTTTTTTGCAGAAATAATAAAACTTTTCTTAAAATTTATA 1464
                          i   -----i              vivv  i  vv  i       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_105784533_   1465 TGGCATCTG-AATAAACCCCAAATAATTCAAACAATCTTGAAAAATAA-- 1511
                            v -v  -  vii    vi    iiiv                v  --
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_105784533_   1512 -CAAAGTCGGAAGACTCACACTTTCTGATTTCAAAATTTACTACAAAGCT 1560
                         -      i   i           i ii         i             
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_105784533_   1561 ACAGTAATCAATACAATGCAGTAGTAACACGAGGACAGACGTACAGCTCA 1610
                                    v   i  ii   v ii  ii    i    i  i  v   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_105784533_   1611 ATAGAATAAA---GAAACAGCTCAGAAATAAACCCTTACATACATGGTCA 1657
                           i     i ---  i -- ii             v     vi       
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGA--GTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_105784533_   1658 AATAAATATCAACAAGAAAGCCAAGGCCTTTTCATGGAGAGCAAATAGTC 1707
                          v i v v  i     iiv      i  v  iv    i  ivi       
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_105784533_   1708 TTTTCAACAGATGATGTTGGGAAAACTAATTATCGGCATACAAAAG---- 1753
                                  i   i  i     v    iiv  ? vi   i      ----
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_105784533_   1754 ---TTAGAACCTAACCAAATGTTACGTCCAGAAACAAACTCAAAATAAAT 1800
                         ---  i  v  iv   vv iiii ii v  i   iv          ii  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_105784533_   1801 TAAATATGTCCACTTAAGAGCTAAAAGTATATAAGTTATAGAAAAAA--- 1847
                         i ? v iv vv iv            v    v  v iv     i   ---
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_105784533_   1848 TAA-TGCAAAGCTCCTTGACATTGGATTTAGCAATGATATCTAAGATATG 1896
                           i-? i   v  i v    v    i  vi      i v   v       
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_105784533_   1897 AAACCTAAGTCACAGGCAATAAAAGAAAAAA-AAACAAACTAATGGGACT 1945
                          v   v  iv    i    i           - i i   i ----     
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT----GGACT 643

  chr1_105784533_   1946 T-A--AAAACTAAAAATTTTTGTGTGATT----GGATA------------ 1976
                          - --    i      i       i--  ----   i ------------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGC--TTCAAAGGACACTATCAAGAAAG 691

  chr1_105784533_   1977 --AAAAGGCAACATGTGGAATGGGAGAAAATACTTGTATATCATGGATTT 2024
                         --     i    viiii               i   i v     --  --
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT--AT-- 737

  chr1_105784533_   2025 TGATATGATTTTTGCCAAGGGATTAATATTTAGTATATATAGAGAAAACC 2074
                         --  v    -------      i vi   ii  v       i    vv i
  L1M4_orf2#LINE/    738 --ATCTGAT-------AAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_105784533_   2075 TGAAACCCAACAATCAAAAG-CACTTAGCCCAAATAAAAAATAGTCAAAG 2123
                          iv   i   i   v     -  vv  i     v ?      i v     
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_105784533_   2124 TAATTGAATAGACATGACTCCAAAGAGCATGTA-AAA-GGC 2162
                         v v            vv         iv  i  -   -   
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

Transitions / transversions = 1.63 (119 / 73)
Gap_init rate = 0.03 (23 / 869), avg. gap size = 3.30 (76 / 23)  


2233 29.13 1.01 3.37  chr1_105787395_105789275.rev      502  1390 (491)    L1M4_orf2#LINE/L1       41   908 (0)  

  chr1_105787395_    502 TTGTAAAAATAACCACACTGCCAAAAGCAATCTACAGATTTAATGCAATT 551
                             v  i  ii v i   v  v   vii           i  i     i
  L1M4_orf2#LINE/     41 TTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chr1_105787395_    552 TCCGTTGAAATACCATCATCATTCTTCACCGAACTAGCAAAAAAAAGACA 601
                         i ii ii    v   v vv v  i  ii v   v v ----- v   vii
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG-----ACAAGCTG 135

  chr1_105787395_    602 GTTGTAAAATTTATATAGAACCAAAAAAGAGCCTGAATGGCCAAGGCAAG 651
                         i iv       i    i   viiv  ii  v  v    i     ii   v
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_105787395_    652 ACTAAGCAAAAAGATCCAATCTGGAGGCATCGCATTACCTGACTTCAAAC 701
                         vi i iv  i    v v  vi      vv  i  i v  ii i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_105787395_    702 GATACTACAAGTCTATAGTCAACAAAACAACATAGTACTGGTATAA--AT 749
                         vv        iv   i   v v   i   iii i       i    --  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_105787395_    750 AGGCATATAGACCAATGAAACAGACTAGAGGACCCAGAGAAAAAGCCAAA 799
                           i        i     i  i   v v   iii     i v   v   v 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_105787395_    800 TACTTACAGCCAACTGATCTTTCACAAATCAAACAAAAACATATAGTGGG 849
                         i i   ii i   i    i  iv    ivvviv   i v   vi i    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_105787395_    850 GAAGGA-CATCCTATTCAATAAATGGTCCTGAGATAATTGGCAAGCCACA 898
                            i  -i vi  v     i       v   i  i  i   vv ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_105787395_    899 TATAGGAGAATAAAACTGGGTCCTCATCTCTCACCTTGTACAAAAAACAA 948
                          ii ii     i  ii   ii  ii i   v    v i        vi  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_105787395_    949 CTCAAGGCGAATCAAAGACTTAAATGTAAGACATGAATCCATGAAAATTC 998
                              iii i    ?    i           vv i  v i  i   v ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_105787395_    999 TAGAAGGTAACTTCAGAAAAACTTTTCCAGACATTGGCTTACACAAAAAG 1048
                               iv   v vi ?iv  v i   vv   v    v   vi   viiv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_105787395_   1049 TTCATGACCAAGAACTCAAAAGCAAACACAAAAATAAAACAAAATAAAAT 1098
                            v iivi v  vvi        ----   iv ----      v    -
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCA----CAAGCA----ACAAAAGAAAA- 626

  chr1_105787395_   1099 AAAATAACATAAAATAACAGATGGGACCTCATTAAACTTAAAAGCTTCCA 1148
                         --    i-     -------- v    i    i   v      i   iii
  L1M4_orf2#LINE/    627 --AATAG-ATAAA--------TTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_105787395_   1149 GACCTCATAAAAAA--AATAAGCAGAGTAAACAGACAAACCACAGAGTGG 1196
                         vi i   v ii v -- vi   - i   i  v      v       i   
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAG-AAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_105787395_   1197 AAGAAAATACTTGCAAACCATGCATTTGACAAAGGACTAATATCCAGAAT 1246
                         i        i       i   ii  i   i  i     vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_105787395_   1247 CTACAAGTAACTTAAACTAATCAGCAAACAAACAAAAAACAAATAATCTC 1296
                         v  i  iv    ivv  v v   ---- i  vv    i        i iv
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCA----ATAATAAAAAGACAAATAACCCA 810

  chr1_105787395_   1297 ATCAAAAAGTGGGCAAACAATATGAATAGACAGTTCTC----AAAAATAT 1342
                           i?    i        vi  v          v     ----i  i    
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_105787395_   1343 ACAAGTGACAAACAAACATATTAAAAAATGCTCAACATCAGTAATTAT 1390
                             i  i v  i  i  i  v    i             ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (154 / 101)
Gap_init rate = 0.01 (12 / 868), avg. gap size = 3.25 (39 / 12)  


 407 20.22 0.00 1.12  chr1_105829087_105833836      402   490 (4260)    L1M4_orf2#LINE/L1      455   542 (366)  

  chr1_105829087_    402 ACCCAAGCTTCATGTCTTACACAAAAATTAACTCAAAATGGTTCATGGGC 451
                             vvi i   iii v  i                     v   ?i i 
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_105829087_    452 TTAAATGTAAGACATAAAACTATAAAACCTTTAAGAAGA 490
                         i           vv              ii   -     
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTA-GAAGA 542

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)  

3174 27.04 0.44 1.42  chr1_105829087_105833836     3341  4257 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105829087_   3341 TGGAGGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCATGAAAAT 3390
                             iii i  i     i      i v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105829087_   3391 GGCCATACTGCCCATGGTAATTTATAGATTCAATGCCATTCCCATCAAAC 3440
                            v     v    viv i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105829087_   3441 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTAA 3488
                          v   iivi i  i  ii     -   -- v  i   v i-    i  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_105829087_   3489 TATGGCACCAAAAAAGAGCCCGCATCGCCAAGTCAATCTTAAGCCAAAAG 3538
                              v viiv  ii  v  v v  v     iv       i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_105829087_   3539 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3588
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_105829087_   3589 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3638
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_105829087_   3639 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCGCATATCTACAACT 3686
                                i    i--    i  --    i   vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_105829087_   3687 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3736
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_105829087_   3737 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3786
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_105829087_   3787 GAAACTGGATCCCTTCCTTGCACCTTATACAAAAATTAATTCAAGATGGA 3836
                            ii    i    v   ii    v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_105829087_   3837 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3886
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_105829087_   3887 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 3936
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_105829087_   3937 AACACCAAAAGCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAT 3986
                         i             ---      ------      vv     v  i    
  L1M4_orf2#LINE/    597 GACACCAAAAGCAC---AAGCAA------CAAAAGAAAAAATAGATAAAT 637

  chr1_105829087_   3987 GGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATC 4036
                         v   ii v  i   v v  i i   i  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_105829087_   4037 AGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTC 4086
                          i      v  i     i   i             v  i    vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_105829087_   4087 ATCCGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTT 4136
                            i  i  i  i  vi          v  i  v      vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_105829087_   4137 ACAAGAAAAAAACAAACAACCCTATCAAAAAGTGGGTGAAGGACATGAAC 4186
                          i  v     i     i     v  i?    i    ii     iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_105829087_   4187 AGATGCTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAA 4236
                            iii     v        i  vi viii     v  i          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_105829087_   4237 ATGCTCACCATCACTGGCCAT 4257
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.43 (17 / 7)  


2103 28.96 5.13 1.60  chr1_105836418_105838506.rev      723  1599 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105836418_    723 TGGAAAAATATTTCATGCTCATGGATTGGAAGAATCAATAATGTTAAAAT 772
                               i    ii    i               v i    v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105836418_    773 GGCCATATATCCCAAAGCAATCTGTAGAATCAACACTATTTTTATCA--- 819
                            v   ivi      vii    ii   v     i v  iii     ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_105836418_    820 -----------CTTTCCACAGAATTAGAAAAAACT-ATAGTAAAATTCAT 857
                         -----------i   iii     v v  v  i-  -  vv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_105836418_    858 AT-------CAAAG--TCCAAAATAGCCAGAATAG-CTACAAAAAAAA-- 895
                           -------   i --i   i        i  i i-  vv     i  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_105836418_    896 ------TTGAAGCA-TCACATTACACAACTTCAAACTCTACTATAAGGCT 938
                         ------   i  v -     i v v   i      vii     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_105836418_    939 ACAGTAGCAAAAAACACCATGGTACTTGTGGTACGAGAACAGATACATAG 988
                               iiv  i -  vii       ---  i ii  i i   i i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGA-CAGTGTGGTACT---GGCATAAGGATAGACATATAG 295

  chr1_105836418_    989 ACCAATGGAACAGAATAGAGAACCCATAAATAAAGCTACACACCTATAGC 1038
                          i        i     v    ii   v       v i i   ii   i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_105836418_   1039 CATCTGATCTTTGACCAAGTCAACAAAAGTAGGGAATGGAGAAATGACTA 1088
                           vi    i  i   v i viiv   i vi vvv     i    -  v  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATA 394

  chr1_105836418_   1089 -CCTATTCAATAATTGAGGCTGAGATAGC-AGCTAGCCACATG---GAGA 1133
                         -i  v     i  v  iv    i  i i -i v  ?       ---i   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_105836418_   1134 ATAAAAATAGACCCCCACTTTTCATTACATACAAAAATCAACTCAAGATG 1183
                           i  iv i      i  i iv  ii i          i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_105836418_   1184 GATTAAAGATTTAAATGTAAGACTCCAAACTATAAAAATCCTAGAAGAAA 1233
                            i ?   ii           viiv           v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_105836418_   1234 ACCTAGGAA-ACATCATTATATACATTGGCCATGGGAAAGCATATAT--G 1280
                           v    ?i- v   v ii i-  v    vi- i  v  vvi v v -- 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTG-ACCTTGGGT-TAGGCAATGGTTTCTTAG 592

  chr1_105836418_   1281 ACTAAGGCCTCAAAAGCA-ATTCGAAGGAAAACAAAAATTGACAAGTAGG 1329
                          -  v i vi        - vv -  vi   iv      v  i  i v  
  L1M4_orf2#LINE/    593 A-TATGACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGG 640

  chr1_105836418_   1330 ACCTAGTTAAACCAAAAATCTTCGGCACAGCAACGCAAACTATCAAAAGA 1379
                           i vi i   viv    v   iv ii vv   v v v        i i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_105836418_   1380 GAAAACATACAGCCTACAGTATAGG-GAAACTATTTGCAAACTAGGCCT- 1427
                          vi  v v   i  i    v  i  -    v          ii viiv -
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_105836418_   1428 TCAGGAAAGATTTAATATTCAGAATCGATGAGGAAATTAAACAATTGAAC 1477
                          v vi ii  i  i-   i      vv  i i   v ivv    i v  i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_105836418_   1478 AGGTAAAAAAAACCAAATAACTCCATTAAATAATGGGAAAGAGACATGAA 1527
                          i-      i --        i v   ?  v      v  ii  iv    
  L1M4_orf2#LINE/    790 AA-TAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_105836418_   1528 CAAACACTTCTTAAAAGAATGCATACGCGCTGCCAACAAATCTATCAATA 1577
                         i i   i    iv      vii    iviiv     i  iivi  v  v 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_105836418_   1578 AGTGCTCCACATCTCTATTCAT 1599
                         ii     v     v????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (153 / 97)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.27 (59 / 26)  


3230 24.31 2.33 1.55  chr1_105898158_105902207     2657  3557 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_105898158_   2657 TGAAAAATTATTTCACGTTCATGGATTGGAAGAATCAATATTCTTAAAAT 2706
                           i   iv   ii  i                 v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_105898158_   2707 GTCCATACTACCCCAAAC-ACTTTACAGATTTAATGCCATCCCTATCAAA 2755
                          v v     -       i-iv i        i  i  v            
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_105898158_   2756 ATGCTCATGATG--TTCCTCACAAAAATATTTTTGA------AATCCTAA 2797
                           - i  - v  --  ii ii  i    -----   ------i       
  L1M4_orf2#LINE/    100 AT-CCCA-GCTGCCTTTTTTGCAGAAAT-----TGACAAGCTGATCCTAA 142

  chr1_105898158_   2798 AATTTATATGGAACCACAAAAGACTCAGAATACCCAAAACTATCCTAAAC 2847
                             i        vii   ii   i       v       v   i i  v
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_105898158_   2848 AAAATGAACAAAACTGGAGGAATCATTTTACCTGACTGCAAATTATACTA 2897
                           i v       ii       v   ivi v  ii i v    viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_105898158_   2898 CAGAGCTATAGTAACCCAAACATCATGATACTGGCATGAAAACAGACCCA 2947
                           i     i     i v i   vii  i         i ii i    vi 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_105898158_   2948 CAGACTAATGGAACAGAATAGAGTACCCAGAAACAAATCTACACACCTAC 2997
                         i   ii       i     v   vii       i   i i i   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_105898158_   2998 AGTAATATTGGTTTT-GACAAAGCTAACAAGAATATACAGTGGGGAAAAA 3046
                         i  v -    i    -     i v iv     vi  v  i        i 
  L1M4_orf2#LINE/    343 GGTCA-ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_105898158_   3047 AGACAGCCTCTTTAATAAATAGTGCTGGGAAAACTGGATATCCATATGCA 3096
                          --i  i  i  i  i    i         v         ?   i     
  L1M4_orf2#LINE/    392 A--TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_105898158_   3097 GAAGAATGAAACTAGACCCCTGTCTCTCGCTATATACAAAAATCAAATCA 3146
                         i         ii i       ii   v i i            i  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_105898158_   3147 AAATGAATTAAAGACTTGAA-----GACCTCAAGCTATGAAACTACTGCA 3191
                              i  i ?    i i  -----  v  v  i    i     vi iv 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_105898158_   3192 AGAAACCAT--TTGGAAGTCTCCAGAACATTTGTTTGGGCAAAATTTTCT 3239
                              v   --v? v  i   i ivi  v  v v  i     viv     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_105898158_   3240 TTAGCAATTTTGCCACAAGCACAAGCAACCAAAGCAAAAATGGACATATG 3289
                          -  vv  vvii   v             v    v      i  i v  v
  L1M4_orf2#LINE/    590 T-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_105898158_   3290 GGATCACAT-GAAGTAAACAACTTCTGCATATCACAGGACACAATCAACA 3338
                            iiv   -i  i v  v     i  iiiv   v       v     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_105898158_   3339 ACATGAAGAGAAAACCCAGAGAATGGGTTCAAAATTTTTGCAAACTATCT 3388
                          vi    i   v      v        vv-     v        ii  v 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAG-AAAATATTTGCAAATCATAT 737

  chr1_105898158_   3389 ATCTGACAAGTAATTAGTAACCAGAATAT-TCAAGGGCTCAAACAACTTT 3437
                               i   vi i v   v         - v   ii   vv      iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_105898158_   3438 ATAGAAAAAAAATCTAATAATCTGAT--AAAAAAGGGTGAAATATTTGAA 3485
                            iv     i - v     i ii  --     v   ii  iv       
  L1M4_orf2#LINE/    788 ATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_105898158_   3486 TAGACATTCCTCAAAAGAAGATCTACAAATGGCAAGCACGCATATGAAAA 3535
                                 i   v         v          v ii v   i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_105898158_   3536 GGTGCTCAACATCATTGAGATC 3557
                          i            ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (133 / 83)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.94 (35 / 18)  


1829 26.53 4.59 1.36  chr1_105928681_105931098.rev      502  1089 (1329)    L1M4_orf2#LINE/L1      142   748 (160)  

  chr1_105928681_    502 AAATTCATATGGAACAAAAAAAGAGCCCACA-TAGCCAAAGCAATCCTAA 550
                                       - viv  i ii    v -        i     i i 
  L1M4_orf2#LINE/    142 AAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_105928681_    551 GAAAAAAGAACAAAGCCAAAGGCATAATACTAGCTGATTTTAAACTATAC 600
                         i   i          iiii   vv v i   vv ii    i   viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_105928681_    601 TATAAGGCCACAGTAACCAAAACAGTATGACACTGGTA-AAATACAGATA 649
                           i  i  i       i   i     i  ii     i -  iv i   i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_105928681_    650 CATAGATAAATCAAACAGAATAGAGAACC----GATAAAGTGATACACCT 695
                         i      v   vi  i     v    ii ----i     viv     ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_105928681_    696 GCAACCAGTTGATCTTTGATAAACCTGATGGTAACAAG------CAATGG 739
                         iiiii  i     i  i  i  i------   iv    ------      
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAG------GGTGCCAAGACCATTCAATGG 384

  chr1_105928681_    740 GTAAAGGATTCCCTATTCAACAAATTGAGCTGGGATAACTAGTTAGCCAT 789
                          v    i  vvi  v          v v       i    i v  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_105928681_    790 ATGCAGAAGAATAAAACTGGACCCCTTCCTTTCACCATAAACAAAAAGTA 839
                              i      i  ii         v   iv       v       v  
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_105928681_    840 ACTCAGAATGGATT-------TAAATGTAAGACCTCACATTACAAAAATA 882
                              i       i-------           v  v v i  i    v v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_105928681_    883 CTAGAAGAAAACCTAGGAG-ATATACTTCTTGATATCAGCTCTGGCAAAG 931
                         i           v    ? - v  -    v   iv ii v iv     v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_105928681_    932 AGTTTTTGGCTACTCC-TCAAAAGTAATTGCAACAAAAACAAAAATTGAC 980
                         iv  i  i v  ivv -i      i vvv         iv      v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_105928681_    981 AAATTG-ACTG-ATTAGACTGAAGAGCTCCTGCACAGCAAAAGAAACTAC 1028
                               -   v-  i i v v  i i  ii  ii vv    i  v    i
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_105928681_   1029 CAACAGAGTAAA----CAATCTACAGAATGAGAGAAAATATTTGTAAGTC 1074
                            v i   i  ----   i i        i             i  i  
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_105928681_   1075 ATGCATCTTATATGG 1089
                           ii    v   v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGG 748

Transitions / transversions = 1.66 (96 / 58)
Gap_init rate = 0.02 (13 / 607), avg. gap size = 2.69 (35 / 13)  

 278 18.29 10.98 0.00  chr1_105928681_105931098.rev     1533  1614 (804)    L1M4_orf2#LINE/L1      780   870 (38)  

  chr1_105928681_   1533 ACAATTCAATAAGCAAAATACAATT---CCAAT--GAAAATCAGCAAAGG 1577
                             i       vv    v    v ---     --i     vi       
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_105928681_   1578 ACATGAACAGACACTTTTCAAAAGAAGACATA----TGGCC 1614
                          iv    i     i  i  v        i   ----     
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

Transitions / transversions = 1.14 (8 / 7)
Gap_init rate = 0.03 (3 / 91), avg. gap size = 3.00 (9 / 3)  


2967 16.94 4.39 13.37  chr1_105967618_105970401.rev     1305  2284 (499)    L1M4_orf2#LINE/L1        2   893 (15)  

  chr1_105967618_   1305 GAAAAAACATCTCATGTCAATGGAATA-AAGGCTTAACATTTTTAAGAAG 1353
                          i   i i   i     iv     v i-   i     i   v      v 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_105967618_   1354 GCAATATTCCCAAAACTGATCTGCAGATTCAATGTCATTCCTATATAGAA 1403
                               i    v   i      i         i iv  i     -i i  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-CAAAA 100

  chr1_105967618_   1404 TTTTAAATGATCTCTTTT-TAGAAACTGATAAGCTGATTCTAAAGTT--- 1449
                          iii iv  -i  i    -i     i   i        i     i  ---
  L1M4_orf2#LINE/    101 TCCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_105967618_   1450 --GAAAATA-AATTGA---AGAAAAAACAAAATAATCTTGAAAAAAA--- 1490
                         -- i    i-  vv  ---    v iv     i            i ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_105967618_   1491 ------------------CACTTTCCAATTTCAAAACTTGCTACAGAGAA 1522
                         ------------------     i               i     i  vv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_105967618_   1523 ACAGTAATCAAATCAGTGTAGGCATGTAGATGGAACAAGATTTTGGCTAT 1572
                                    iv      i -----------------------------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGG----------------------------- 270

  chr1_105967618_   1573 CATAAATGAATTATCAGTAGAATAGAAGGATTGCTATCATGTTTTCTTGT 1622
                         --------------------------------------------------
  L1M4_orf2#LINE/    271 -------------------------------------------------- 270

  chr1_105967618_   1623 TGACACTGGCAGTGCCTACTGGAGCTTATAATCAAGGATAGGCATGTAGA 1672
                         ---i       ---------------------i        i   i    
  L1M4_orf2#LINE/    271 ---TACTGGCA---------------------TAAGGATAGACATATAGA 296

  chr1_105967618_   1673 TCAATGAAATAGAAACAAAAGTGCAGAAATAAACCAATACATATATGGTT 1722
                               i       vii i   v            v      v      i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_105967618_   1723 AAGTGAATTTTGACAAGAGTGCCAAGACAATTCAATGGGAAAAAGAATAG 1772
                           v   v   i      i          v          i   -      
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAG 395

  chr1_105967618_   1773 GCTTTG-AACAAACGGTTGAGTTGCTCCAGTTGGGACAACTGGAAACTGT 1821
                         v    v-      i   ------------ i             ------
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGT------------GCTGGGACAACTGGA------ 427

  chr1_105967618_   1822 GTAGTCAAATGCAAAA---TAAAGTTGGATCC-TAAGTCACTCCATATAA 1867
                         -  ?i  v        --- i        i  -  vv    v       v
  L1M4_orf2#LINE/    428 -TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_105967618_   1868 AAAAAATTAACTCAAAATAAATCAACAACCTAAACGTAATAACTAAAAGT 1917
                              -            ii    ?vi       i    v i      v 
  L1M4_orf2#LINE/    477 AAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_105967618_   1918 CTAAGAGTCGTAGAAGAAAAGATATG-GTA--TTTTCATAACCATGGACC 1964
                         v   i v  v          v   v -   -- i   i i   v   iii
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_105967618_   1965 TGGCAAAGAATTCTTAAATATGGAAACAAAAACATGAGCTTCAAAAGAAA 2014
                         v     v iv      i     iv v     i  ii   vv         
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_105967618_   2015 GAACAATATAGGTAAATTGGATTTCATCAAAATTAAAAATTTTTGTAATT 2064
                         i  -----   i         i                 i      iv  
  L1M4_orf2#LINE/    626 AAA-----TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_105967618_   2065 CAAAGGACACCATCAAGAAAGTGAAAAACCAAACCACAAAATGGTAGAAA 2114
                                   i                iv   v     i     v     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_105967618_   2115 ATATTTGCCAATCATATATCTGACAGACAAATTGTATTTCAAATGTATGA 2164
                                 v              i iivi v      iivi   i   i 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_105967618_   2165 CAAACACTTAGAACTCTGTAATAAAAAGACAATTT-CCTAACTAAAAAAT 2213
                         vi   v    v     vi              v v-  i  i ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_105967618_   2214 GGGCAAAGATTCTGAATAGACATTTCTCTAAGGAAAATATGCAAATA--T 2261
                                 iv i                i  i   i    i     i--i
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_105967618_   2262 AATAATCTCATGAAAATATGCTC 2284
                              v v        v      
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.63 (101 / 62)
Gap_init rate = 0.02 (22 / 892), avg. gap size = 7.91 (174 / 22)  


 585 27.36 1.49 1.00  chr1_106065387_106068730     1787  1987 (1357)    L1M4_orf2#LINE/L1        1   202 (706)  

  chr1_106065387_   1787 TGGAAA-ATATTCCATGTTCATTGATTAAAAGAATCAATAAT-TTAAAAC 1834
                               -    i          v    ii    v i    v -    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106065387_   1835 ATCCTTATTGCATAAAGCAATCTAT-GATTCAATGCAAACCTTATCAAAA 1883
                         iv vv  i v vi   vii     i-       i    v  i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106065387_   1884 TACCAAGGACATTCTTCACAGAAATAGAAAAAACAATCCTACAATTTATA 1933
                          v   ivvi v  i  ii       v  v  ivii      v    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_106065387_   1934 TGGAACCACAAAAGACCCAGATTACGCAAAGCTATTTTAACCAAGGCAAG 1983
                              vii   ii        v  vv    i v  i  i vv   --   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG--AAG 198

  chr1_106065387_   1984 AACA 1987
                             
  L1M4_orf2#LINE/    199 AACA 202

Transitions / transversions = 1.20 (30 / 25)
Gap_init rate = 0.02 (4 / 202), avg. gap size = 1.25 (5 / 4)  

2368 25.61 2.56 2.02  chr1_106065387_106068730     2110  2851 (493)    L1M4_orf2#LINE/L1      163   908 (0)  

  chr1_106065387_   2110 GAACTTAAAATAAAAGTTAAAAAAG----AAAAAAAAAGAACAAAACTAC 2155
                          i  ii i    --- ii    v i----i     i         ii iv
  L1M4_orf2#LINE/    163 GGACCCAGAATA---GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_106065387_   2156 AGGAATCACAATACCTGACTTCAAATTATACTACACAGCTGTAGTAACCA 2205
                             v     v v  ii i      viv       v    ii     i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_106065387_   2206 AAACAGCAAGGTACTGGCATAAAAACAGACACATAGACCAAGCAATGGAA 2255
                          i    iiv             ii i     i     i   ----     
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA----TGGAA 305

  chr1_106065387_   2256 TAG----GGGAACCCAGAAACAAATCCACAGATATACAGTGAACTTATTT 2301
                            ---- i  ii       i   i   i v  v  ii  v  i v    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_106065387_   2302 CTGATATAGTTACTAAGAACATATAGTGGAGAATAGACAGGCTCCTCAAT 2351
                         ii  i vi v i i    v   vi i   i   vii i  v  ii    i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_106065387_   2352 AAATGG-GTTTGT-TAACTAGATATCCATATGCAGAAGAATGAAACTAGA 2399
                               - i v v-i    i    ?   i     i         ii i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_106065387_   2400 CCACTATCTCTTGCCATATACAAAAATCAAATTAAAATAGATTAAAGACT 2449
                           v   i   vii              i  v i     i   i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_106065387_   2450 TAAATCTAAGACCTCAAACTATGAAACTACTATAAGAAAATTTTGGGG-A 2498
                              v     v  v       i     vi  v       iv v  ? - 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_106065387_   2499 GATGCTCCTGGACATTGGTGTGGGCAAAGAGTTCTTGAGCAATACACCAC 2548
                         i  -  i vv   v    vv i     v iv     iiii vv      v
  L1M4_orf2#LINE/    556 AAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_106065387_   2549 CTGCACAGTCAATCAAAGCAAAACTTGACAAAT-GGA----ATCAAATTG 2593
                         vv     iv   iv    v    v v  i    -   ----      ---
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA--- 651

  chr1_106065387_   2594 GGTTACAAACCTTC-TGCATAGCAAAGGATACAGTCAATAAAGTGTAGAG 2642
                         -i   v    i  i-   v --       i  vi    v      v i  
  L1M4_orf2#LINE/    652 -ATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_106065387_   2643 ACAACCCACAGAATGATAGAAAATGTTTGCAAACTACTCATCTGACAATG 2692
                                        iv       i        ii ivi      i  v 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_106065387_   2693 GATTAATATACAGAATATATAAGAAGCTCAAACAACTCTATAAGAAAAAA 2742
                           i vi   v            ii i   vv       v    v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_106065387_   2743 TCTAATAATCTGGTCAAAGAAATGGGCAAAAGATTTGAACAGACATTCCT 2792
                         v v     i iii i?  -           i        i       i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_106065387_   2793 CAAAGAAAGACAAACAAATGGAAAACAG--ACATAAAAAAGTGCTTAATA 2840
                          v  ii    i v        vv  i i--    i    ii    i  i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_106065387_   2841 TCAATGATGAT 2851
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.74 (118 / 68)
Gap_init rate = 0.02 (15 / 746), avg. gap size = 2.27 (34 / 15)  


2624 25.93 2.64 2.86  chr1_106191758_106194199.rev     1042  1951 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106191758_   1042 TGGAAAGGCATCCTGCATCCTGTATTCATGGATTAGAAGACTAAATACTA 1091
                                --  -----    ii i          i       v    i i
  L1M4_orf2#LINE/      1 TGGAAAG--AT-----ATCCCATGTTCATGGATTGGAAGACTTAATATTG 43

  chr1_106191758_   1092 TCAA-ATATCATCATACTATCCAAAATTATCTAAAGATTCAATGCAATTT 1140
                          i  -  iv  --     vi     v v     v        i     ii
  L1M4_orf2#LINE/     44 TTAAGATGGCA--ATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chr1_106191758_   1141 TTATCAAAGTCCCAATTAGAGTTTTTACAGAAATTGAAAATAAAAATCCC 1190
                         i       i     ii ivvv     i          v  -ivvi    i
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCT 140

  chr1_106191758_   1191 CCAATTTATAGAAAACTGCAAAAAAAGCCCCAAACAGGCAAAA-AATGT- 1238
                         vv    i   vii  v     iii --   vi  i  v     -   v -
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTT 188

  chr1_106191758_   1239 GAGTAAGAAGAATAAAGCTGGAGGCATCACATTTCCTGAATTCAAAATAT 1288
                           iv        i    i      vv     i    ii v       iv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_106191758_   1289 ATTACAAAACCACATTAATTAAAACCGTTTGGTACTGGCATAGAGGCAAA 1338
                          i      i i   v    i  i  v  v             ii ii i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_106191758_   1339 CCTATAGACCAATGGAACACATTAGAGAACCCTGAGATAAATCTATACAT 1388
                          v      i        i v v v    ii  v  i     i i      
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_106191758_   1389 AAATGTAGTAAACCAATATTTAATAGGTGTGTCAGGAATACACAGTGGGT 1438
                         vv   --  v  iii  v  ii i i v   i  i  vi iv  i    v
  L1M4_orf2#LINE/    339 TTATG--GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_106191758_   1439 AAATGATAGTTTTTTTTTTCAATAAATGATGTTGGGAAAACTGGCTATCA 1488
                            vi     i    ----   i     i  i     v      v  ? -
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTT----CAACAAATGGTGCTGGGACAACTGGATAKC- 431

  chr1_106191758_   1489 CACACACACACA---GAAATTGGATCCTTATTCCATACACAAA-AAAAAA 1534
                             ii  v vi---   i     i  i  iii  i  -  v - v    
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC-CATATACAAAA 480

  chr1_106191758_   1535 A--AACTCAAAATGGTTTACAACATTAAATATAACACCCAAAACTGTAAA 1582
                          --            v i ? ivvi     i   v v i      i    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_106191758_   1583 ATTTCTTCAAGAAAATAAAGGA--AAATACTTT---ACATTGATGTT--G 1625
                          i ii vv       i v   ?--    -   i---  v   i-   -- 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGG-GTTAGG 578

  chr1_106191758_   1626 CAGTAATTTCATGGCTATGACATCAAGAGCACAGGCAACAAAAGCAAAAA 1675
                           i ii    v i v       i   i      i          v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_106191758_   1676 TAGGCAG-TGGAACTACATCAAACTGTAAAGTCTCTGCACAGCAAAGGAA 1724
                            ii i- v i   v       v vv   iii i  ii vv       v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_106191758_   1725 AC----AATAAAC--AAAAGGCTACCTATGGAATGAGAGAACATATTTGA 1768
                           ----  v   v--     i v   i ii     i     v       v
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_106191758_   1769 AAACCATATATCTTATAAAGGATTAATATCTAAAACACATAAAAAAACTC 1818
                            i         v    i   i vi    i i  i i     i  -   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTC 777

  chr1_106191758_   1819 GTACAACCCAACAGCAATAAAAAACCAAATAACTAAATTTAAAAAGGGAC 1868
                         v      i   i ---       iv        iv    ?     v  i 
  L1M4_orf2#LINE/    778 TTACAACTCAATA---ATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_106191758_   1869 ATATGTCTTAAATAGCTATGTCTTTAAGAAAGAAAAGCAAATG-CCAAAA 1917
                          v v vi  i     vi  v   ii  ii    v vi      -    v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_106191758_   1918 GGTATTTAAAAATATATTCGATATCACTAGTTAT 1951
                         i i iv i    v  ii  i i    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (144 / 88)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 1.92 (50 / 26)  


3093 26.40 0.99 1.10  chr1_106194437_106202543.rev     2921  3829 (4278)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106194437_   2921 TGGAAGAACATTTCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 2970
                              ii i  ii    i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106194437_   2971 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3020
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106194437_   3021 TACCAA-TGACTTTCTT-CAGAAAATTGGAAAAAAACT-ACTTTAAAGTT 3067
                          v   i-  v    i  -      -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA-TTG---ACAAGCTGATCCTAAAATT 146

  chr1_106194437_   3068 CATATGGAACCAAAAAAGAGCCCGCATCACCAAATCAATCCTAATCCAAA 3117
                                  viiv  ii  v  v v  vi     v     i i ---   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAA 193

  chr1_106194437_   3118 AGAAGAA---ACCTGGAGGCATCACACTACCTGACTTCAAACTATGCTAC 3164
                                --- vi      vv       v  ii i      viv i    
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_106194437_   3165 AAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATAC 3214
                           i          i   i    ii         i iv ii i   v   i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_106194437_   3215 AGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTA 3262
                            i        i    i--    i  --        vv   i    i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chr1_106194437_   3263 CAGCCATCTGATCTTTGACAAATCTGACAAAAACAAGAAATGAGGAAAGG 3312
                         ii i  vi    i  i     ivv  v   i v  vvv    i      i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_106194437_   3313 ATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGA 3362
                           vvi  v  i  i              v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_106194437_   3363 AAGCTGAAACTGGATCCCTTTCTTACACTTTATTCAAAAATTAATTCAAG 3412
                          iiv    ii    i    vi  i    iv   v          i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_106194437_   3413 ATGGATAAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAG 3462
                               v ?    i       v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_106194437_   3463 AAAACCTAGGCA-ATACCATTCAGGACATAGGCAGGGGCAAGGACTTCAT 3511
                              v    ?i- v i -   iv   v v  vvvi     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_106194437_   3512 TACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 3561
                         viv  vi            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_106194437_   3562 ATCTAATTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGA 3611
                          ii v  i   v v  i i   i  iiivv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_106194437_   3612 CTGAACAGGCAACCTACAGAGTAGGAGAAAATTTTTACAATCTACCCATC 3661
                         v    v  i     i     i i         v   i   vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_106194437_   3662 TGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACA 3711
                            i  i  i  vi          v  i        ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_106194437_   3712 AGAAAAAATAAAAAAACCCGACCAGAAAGTGGGCAAAGGATACGAACAGA 3761
                          v     ivv   v     i ii?i   i            vi   i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_106194437_   3762 CACTTCTCAAAAGAAGATATTTATGCAGCCAAGAGACACATGAAACAATG 3811
                           i     v           vi viii     v ii         vi   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_106194437_   3812 CCCATCATCACTGGCCAT 3829
                          i  v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  

2689 29.00 1.32 1.21  chr1_106194437_106202543.rev     6710  7616 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106194437_   6710 TAGAAACACATCCTATGCTCATTGATGAGTAGAATCAATATTGTGAAAAT 6759
                          i    v i    i   i    v   vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106194437_   6760 GACCATACTGCCAAAAGCAATCTATGAATTCAATGCAATTCCCATCAAAA 6809
                          i v     v  v   vii     iii      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106194437_   6810 TTCCACCATCATTCTTCACAGAATTAGAAATGACAATCTTAAAATTTAAA 6859
                          i   v vv v  i  ii     v v  v v vii   i       i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_106194437_   6860 TGGAACTAAAAAAGAGCCTGCATAGCCAAAGCAAAGCTAAGCAAAAAGAA 6909
                              v iv  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_106194437_   6910 CAAATCTGGACACAGTACATTATCTGACTTCAAACTATGCTATAAGGCCG 6959
                             vi    vivvvi   i vi ii i      viv i   i  i  ii
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_106194437_   6960 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCAAATAAACCAC 7009
                         i   v i   i    ii         i    ii    i  v   i i  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_106194437_   7010 TGGAACAGAATAGAGAACTCAGAAATAGGGTCA-A-ATCCA--GCCAACT 7055
                              i     v    iii        iivi  - -  ii -- i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_106194437_   7056 GATCCTCAACAAAACAAGCAAAAACATTAAGTGGGGAAAGGACACCCTAT 7105
                            ii  i    iivviv   i v    v i         i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_106194437_   7106 TCAACACATGGTGCTGGGATAACTGGCAAGCCACATGTAAAAGAATAAAA 7155
                               v            i      vv ?       i        i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_106194437_   7156 CTGGATCGTCATCTCTCACCTTATACAAAATTCAACCCCAGATGGCTCAA 7205
                         i    i vii i   v    v         v i   i v i    v   ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_106194437_   7206 GGACTTAAATCTAAGACCTGAAACCATACAAATTCT-AGAAGATAAATTC 7254
                         i   i     v     v  i    i   -   i   -      -   ivi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGA-AAACAT 548

  chr1_106194437_   7255 TGGAA-AAACCTTTATGATATTAGCTTAGACACAGACTTCATGACCAAGA 7303
                         v  ?i-   i   ii   iv  i v    i  vv ii   v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_106194437_   7304 ACCCAAAAACAAATGCAGCAAAAACAATGATAAATAGGTGGGACTTAATT 7353
                         vv      i  v v   i     iv  vi   i   ii v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_106194437_   7354 AAACTAAAAAGTTTCTGCATAGCAAAAGAAACAATCAGCACAGTAAACAG 7403
                            v v    ii  i  iiivv    i  v  v    iv v   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_106194437_   7404 ACAATGCACAGTGTGGGAGAAAATCTTCACAATCTGTACATCTGACAAAG 7453
                             iv     vi           v  ii   viii  i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_106194437_   7454 GACTAATATCCAGAATCTACAAGGAACTC----AGATTAGCAA--AAAAG 7497
                             vi          v  i  i      ---- iv i ii  --     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_106194437_   7498 CCTAAACAGTCTCATCAAAAAATGGTCTAAGGACATGAATAGACAATTTT 7547
                         v -   i ii iv  i?        v v     iv          v  i 
  L1M4_orf2#LINE/    799 AC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_106194437_   7548 CAAAAGAAGATCTATAAATTGCCATGAAACATATAAAAATGTATAAAAAT 7597
                          v         v  i    v    vv  i  i  i    --------i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA--------GAT 889

  chr1_106194437_   7598 GCTCAACATCACTAATCAT 7616
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (156 / 103)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


3271 26.43 0.55 0.55  chr1_106202817_106204883      670  1577 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106202817_    670 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 719
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106202817_    720 GGCCATATTGCCCAAAGTAATTTACAGATTCAATGCCATCCCCATCAAGC 769
                            v   i v      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106202817_    770 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 816
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_106202817_    817 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 866
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_106202817_    867 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 916
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_106202817_    917 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 966
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_106202817_    967 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTAGAAC 1014
                                 i    i--    i  --        vv   i i  i  viii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_106202817_   1015 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAGGGATTC 1064
                         i vi    i  i     ivv  vv  i v  vv          i i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_106202817_   1065 CCTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGC 1114
                         i  v  i  i              v  i   v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_106202817_   1115 TGAAACCGGATCCCTTCCTTACACTTTATACAAAAATCAATTCAAGATGG 1164
                             iii   i    v   i    iv           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_106202817_   1165 ATTAAAGACTTGAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1214
                           i ?    i i  i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_106202817_   1215 CCTAGGCATTACTATTCAGGACATAGGCAGGGGCAAGGACTTCATGTCTA 1264
                          v    ?i v v v   iv   v v  vvvi     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_106202817_   1265 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 1314
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_106202817_   1315 ATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTACCATCAGACTGAA 1364
                           i   v v  i     i  ii vv    i  v    i  vv i v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_106202817_   1365 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 1414
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_106202817_   1415 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1464
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_106202817_   1465 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 1514
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_106202817_   1515 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1564
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_106202817_   1565 CAATATTCTTAAA 1577
                           vi ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 577 23.20 0.00 0.00  chr1_106211486_106216413.rev     2587  2711 (2217)    L1M4_orf2#LINE/L1        1   125 (783)  

  chr1_106211486_   2587 TGAAAAGATATCCCATATTTATGAACTGGAAAAATTAATATTGTTAAAAT 2636
                           i             i  i   i i     i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106211486_   2637 AGCCATACACCCCAAAGCTATCTACAGATTCAATACAATCCCTGTCACAA 2686
                         i  v    v       viv              ii        i   v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106211486_   2687 TACCAATGACATTCTACACAGAAGT 2711
                          v   iivi v  i vii     i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT 125

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.00 (0 / 125), avg. gap size = 0.00 (0 / 0)  

 269 29.70 9.90 0.00  chr1_106211486_106216413.rev     3034  3134 (1794)    L1M4_orf2#LINE/L1      140   250 (658)  

  chr1_106211486_   3034 TAAAATTTGTATGGGACTACAAAAGTCTATAAACAGCCAAAGCAA----- 3078
                                ii     i v i   ii v ivvi  i       i   -----
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_106211486_   3079 -----AAAGACCAAACCTGGAGGCATCACACTACCTGATTTTAAAATATC 3123
                         -----i    v    vi      vv       v  ii    i    iv v
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_106211486_   3124 CTGAAATGCTA 3134
                           iv  v    
  L1M4_orf2#LINE/    240 CTACAAAGCTA 250

Transitions / transversions = 1.31 (17 / 13)
Gap_init rate = 0.01 (1 / 111), avg. gap size = 10.00 (10 / 1)  

2008 25.84 3.04 2.58  chr1_106211486_106216413.rev     3788  4445 (483)    L1M4_orf2#LINE/L1      248   908 (0)  

  chr1_106211486_   3788 CTATAGTAACCAAAACAACATGAAATTGGCATGAAACTAGACATAAGGAC 3837
                            i     i   i   iii  iv i      i iiv        vi  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_106211486_   3838 CTATGAAATAGAATAGAGAATTCAAAAATAAATCTACACATCTACAGTCT 3887
                          v   i        v    i i  i       i i i    i  ii   v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_106211486_   3888 AGTGATTATTCG-CAAAGGTGCCTTTTCAAAAAGGTGCCGT--ATTGTGA 3934
                          v     -    -   i      ------  i ----  i -- v  v i
  L1M4_orf2#LINE/    348 ATTGATT-TTCGACAAGGGTGCC------AAGA----CCATTCAATGGGG 386

  chr1_106211486_   3935 TATAAACAGTCTCCTCAATAACTGGTACCCAAAACATTGGATATGCACAT 3984
                         v vi  i     ii    i  v    i ivii vv i      ?v     
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_106211486_   3985 GTAGAAAAATAAAACTGGACCTCTATCTTTCACCACGTACAAAAATCAGC 4034
                          i i  i   i  ii      i   i  iv     ii         i i 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_106211486_   4035 TCAAAGTGAATTACAAACTTAAATATAAGACTTGCAAATATGAAACTACT 4084
                              i  i  i ? i  i     i     vi iv  v   i     vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_106211486_   4085 AAAATAAAACATAGGGG-AAATGTTTCACGACTTTGGACTACACAAGAAT 4133
                          i  v          ? -    -i   ii   i    ii  vi   vii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_106211486_   4134 TTTT--GGTATGAGATCTCAAAAGCATAAGCAACAAAAGCAAAAGTAGAC 4181
                           i -- i     v i --       i            v    i    i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_106211486_   4182 AAGAAT--GATTTTATCTAA-TTAAAAAGCTTCTGCACAGCAATGGAAAC 4228
                           --  --  i  i   v  -       -   i  ii vv   v   v  
  L1M4_orf2#LINE/    634 AA--ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACAC 680

  chr1_106211486_   4229 AACCACCAAAATGAAG---CAACCTGCAGAATGGGACAA--TATTTGCAA 4273
                         v i  vv   i    i---     ii          v  --         
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_106211486_   4274 ACTATATATTTGAGAAGGGGTAAATATCCAGAATATATAAGAAACCCAAA 4323
                          ii      i   v     iivvi                ii   i vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_106211486_   4324 CAGCTCAATAGCAAAAGCACA--TAATT-ATTTTAAAAATGGGCAAATGT 4370
                           i       ii    iv   --   ii- v  ?             v v
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_106211486_   4371 CCT---TAGATATTTGTCAAAAGAAGACATAAAAATTTCCAGTACTTATA 4417
                         ii ---    i    v  v        i   v    vv   i  vvi i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_106211486_   4418 TGAAAAAATGTTAATTAATAATTATCAG 4445
                               i   i v vi vi ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (112 / 54)
Gap_init rate = 0.03 (18 / 661), avg. gap size = 2.06 (37 / 18)  


1751 28.57 2.44 5.13  chr1_106238628_106240449      511  1329 (493)    L1M4_orf2#LINE/L1      112   908 (0)  

  chr1_106238628_    511 TTTTTCACAGAATTGGAAAAACCTTTTATAAAATACATATGAAATCAAAA 560
                              ii     v v  v  i ivv iv      v      i  viiv  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_106238628_    561 TAGAGCCTGAAAATCCAAAGTGATCCCAACCAAAAAGAA---AGCTGAAG 607
                         vi  v  v   v v     iii   iii vv  i     ---  i  i  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_106238628_    608 GCCTCACATCACCTAATTT-AAAACTATACTACAAGGCTACAATAAGTAA 656
                          v      iiv  i     -      -        i      i   vi  
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAA 260

  chr1_106238628_    657 AACAGCAAGGTATTGGTTTTGGTTAAACACACACACACATACAACACCCC 706
                         i    iiv    i   ---------------------    ---------
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGG---------------------CATA--------- 280

  chr1_106238628_    707 AGAAAACCACACACATTGACAAGTGGGACAGAATAGAAAACTCAGAAATA 756
                           i ---i v   i  v  iv i   i i     v  i iii        
  L1M4_orf2#LINE/    281 AGGA---TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_106238628_    757 AAGCTGCACACCTACAACCACCTGATTTTCGTCAATTTTGACAAAGACAA 806
                           v iii   ii  iiii  vi         v   vvv  v   iiv  v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_106238628_    807 GCAATAGAAAAAGAACTCTCTGTTCAATAAATGATGCTGGAATAACTACA 856
                         v    i ii      ivv   v     i     i      i i    iv 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_106238628_    857 TAGCTACATGCTGAAGAATGAAACTAGAC----ATTTTAC--CATATAAA 900
                           ? i      vi         ii i   ---- ii i  --      v 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_106238628_    901 AAAACTAACTCAAAATGGAGGAAAGCTTTAAATACAAAACCTCAAACTAT 950
                             i              vv ?  vii     ii  i v  v       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_106238628_    951 AAAAATTGTAGAAGAAAACTTAGG---AAATGCCCTTAACAACATCAACC 997
                             v iv           v    ---    ---   viii  v iiivi
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGT 574

  chr1_106238628_    998 TTGGCAAATAATTTATGGCCAAATTT----TCAAAAGCAATTGTAACAAA 1043
                          v     - ii   v ---i i  v ----i        vvv i      
  L1M4_orf2#LINE/    575 TAGGCAA-TGGTTTCT---TAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_106238628_   1044 AACAAAAATTGGCAAGTGGGACCTGATTAAA-TTAAAGAGCTTCTGCATG 1092
                          iv      v ii  i v    i v  i   -     i -   i  iiiv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCT 669

  chr1_106238628_   1093 GCAAATGAAACTATCAACAGGGTAAATAGACAACCTTCAGAAATGAAGAA 1142
                         v    v  v        v ii  i  v        iv     vv i    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_106238628_   1143 AATATTCACAATCTATGCAACTGACAAAATCCTAATACTCAGAATCTATA 1192
                               ii   vii  ii v    i  iivv  vi  ii      v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_106238628_   1193 AGGTACTTAAACTAATCAGTTAGCAAAAACCACATAGCCCCAT-AAAGAA 1241
                          i v   ivv  v v   i v vv    iv  v   i   v  -?  i  
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_106238628_   1242 TGG-TAAAAGACATCAACAGACACTCCTTATAAGAGGATATAAAAGCAGC 1290
                            -i   i  iv v  i     i i  ivv    i      v  iii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_106238628_   1291 CAACAAACATATGAAAAAATGTTCATCATCAGAGAAATG 1329
                            i  i  i       i   i   v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.02 (17 / 797), avg. gap size = 3.65 (62 / 17)  


1132 25.29 2.30 0.00  chr1_106319566_106321643      507   767 (1311)    L1M4_orf2#LINE/L1      160   426 (482)  

  chr1_106319566_    507 AAAAGATACTGAATAGCCAAAGCAATCTCGAGGAAAAAAAATGAAGCTAA 556
                           ii  iv v           i      i  ii  i  i  ii   i ii
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_106319566_    557 AGGCTTCATACTACCTGACTTCAAAGTATACCACAAAGCTATAGTAACCA 606
                            vi   i   v  ii i      iiv   i         i     i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_106319566_    607 AAACAGCATGGTACTAGCATAAAAACAGACATATAAACCAATGTAACATA 656
                          i    ii       i      ii i         i i     v  i v 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_106319566_    657 AT----AGCCCAGAAATAAATCCATGCATTTACAGTCAATTCATTTTCAA 702
                           ----  i           i    i      ii       v      i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_106319566_    703 CAAAGTTGTCAAAAGCACACAATGAGGAAGGGAGAATACCTTCAATAAAT 752
                            i v  i   i v  iv     i    i i v i vii     i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_106319566_    753 GGTACTGGGA--GCTGG 767
                            i      --i    
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGG 426

Transitions / transversions = 4.08 (53 / 13)
Gap_init rate = 0.01 (2 / 267), avg. gap size = 3.00 (6 / 2)  

1859 22.70 1.44 4.14  chr1_106319566_106321643     1032  1586 (492)    L1M4_orf2#LINE/L1      369   908 (0)  

  chr1_106319566_   1032 CAAGACTCCATCTCAATAAATGAATAAATAAATTAATTAATTAATAAATG 1081
                               --   -     iii-   vi    ivi --  -- i  i     
  L1M4_orf2#LINE/    369 CAAGAC--CAT-TCAATGGG-GAAAGAATAGTCT--TT--TCAACAAATG 410

  chr1_106319566_   1082 GTACTGGGAAAACTGAATAACCATGTGGAGAAGAATGAAATTAGATTTCT 1131
                           i      v     i   ?   ii  v i         i  i  iii  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_106319566_   1132 ACTGTAGGCAATATAAAGAAATCAACTTAAAATGGATTAAAGACTTAAAT 1181
                           ivi vi v     v i    i    i         i ?    i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_106319566_   1182 GTACTACCTGAAACTGTGAACCACT-AGAAGAAAACA--GGGAAAAAGCT 1228
                            vv v  i     i i  v v  -           --  ?iv   v  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_106319566_   1229 TCATGACTTTGGTTTGGACAACTGTCTTTTGGATATGACCCCTCAAAACA 1278
                           i    i    v  i i   iv  i i  i        v  -v   i  
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC-AAAAGCA 609

  chr1_106319566_   1279 CAGATAGCGGAAGCAAAAAAAAACAAAAAAAATACATGAATGGAATTACA 1328
                           ---------     v    i ----       v  i   v i i v  
  L1M4_orf2#LINE/    610 CA---------AGCAACAAAAGA----AAAAATAGATAAATTGGACTTCA 646

  chr1_106319566_   1329 TTAAACTGAAAAGCTTCTGTATAATAATAAAAACAATTGACAAAGTGAAA 1378
                          i   v v    i   i   iivvi  vii v  v  ii v         
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_106319566_   1379 AGACAATCTAGAGAATGAGAGAAAAATATTTGCAAATTGTGTGTCTGGTA 1428
                               i i v      i       -           ii i i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATA 745

  chr1_106319566_   1429 AGGGGTAAATATCCAAAATATCTGAAGAACTCAAACAACTGAACAGCAAG 1478
                             iivvi      i     v i        vv      v  i ii  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_106319566_   1479 AAAACAAATAGCCCAATT-AAAAATGGGCAAAAGACCTGAAGAAACATTT 1527
                           i       i       -             i  ii    v i      
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_106319566_   1528 CT---GAAAAGCCATATAAATTGCCAATAAGTACATGAAAA-ATGCTCAA 1573
                           ---i i   vi   i    v         i         -        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_106319566_   1574 CATCGCTAATCGT 1586
                             i????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (82 / 41)
Gap_init rate = 0.03 (14 / 540), avg. gap size = 2.21 (31 / 14)  


3224 26.54 0.88 0.88  chr1_106419451_106423824     2974  3881 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106419451_   2974 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3023
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106419451_   3024 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3073
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106419451_   3074 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3121
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_106419451_   3122 TATGGAAC--CAAGGAAGAGCCCACATT-GCCAAGTCAATCCTAAGCCAA 3168
                                v--     i ---    v v -     iv     i i ivv i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_106419451_   3169 AAGAACAAAGCTGGAGGCATCACGCTACCTAACTTCAAACTACACTACAA 3218
                                   i      vv    i  v  i  i      vivi       
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_106419451_   3219 GGCTATAGTAACCAAAACAGCATGGTATTGGTATCAAAACAGAGATATAG 3268
                         i    i     i   i    ii     i   i  v ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_106419451_   3269 ACCAATGAAACAGAAC--AGAGCCCTCAGAAACAATGCCACATATCTATA 3316
                          i     i  i    i--    i  --     i  vv   i i  i   i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr1_106419451_   3317 ACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT 3366
                         iii vi    i  i     ivv  v   i v  vvv           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_106419451_   3367 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 3416
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_106419451_   3417 GCTGAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGAT 3466
                         iv    ii    i    v   i i   v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_106419451_   3467 GGATTAAAGATTCAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 3516
                             i ?   iii      v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_106419451_   3517 AACCTAGGCA-ATACCATTCAGGACATTGGCATGGGCAAGGACTTCATGT 3565
                            v    ?i- v i -   iv   v    vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_106419451_   3566 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 3615
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_106419451_   3616 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACAACCATCAGAGT 3665
                         i v  i   v v  i i   i  ii vv    i  v  v i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_106419451_   3666 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTG 3715
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_106419451_   3716 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 3765
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_106419451_   3766 AAAAAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACA 3815
                              i     i     v  i? v  i     i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_106419451_   3816 CTTTTCAAAAAGAGACATTTATGCAGACAAAAGACACATGAAAAAATGCT 3865
                         i  i  v   ii   i  vi viii v   v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_106419451_   3866 TATCATCACTGGCCAT 3881
                         i v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (145 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2559 29.04 0.70 1.51  chr1_106427710_106429582.rev      514  1374 (499)    L1M4_orf2#LINE/L1        1   854 (54)  

  chr1_106427710_    514 TGGTAAAACATTCCACGCTGATGGATGGGAAGAATCAATATCATGAAAAT 563
                            v  i i  i   i i v      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106427710_    564 GGCCATACTACCCAAAGTATTTTACAGATTCAATGCTATTCCCATTAAAC 613
                            v     v      v iv i           i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106427710_    614 TACCATTGACATTCTTCACA-AAATTAAAGAAAAAAATATTTTAAATTTC 662
                          v   vivi v  i  ii  -     ---  v  ivvv  ii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chr1_106427710_    663 ATATGAAACCAAAAAAAAGCCCGTATAGTGAAGAAAATCCTAAGCAAAAA 712
                              i  viiv  iii v  v v    iv  i v    i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_106427710_    713 GAACAAAACTGGAGGCATCACGCTACATGACTTCAAACTATACTATAAGG 762
                                ii      vv    i  v vii i      viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_106427710_    763 CTGCAGTAACCAAAAGAGCATGTTACTGGTACAAAAACAGACACATAAAC 812
                           i      i   i v  ii  v      i i  ii i     i   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_106427710_    813 CAATGGAACAGAATAGACATTTCAGAAATAAGGCTACATATCTACAACTA 862
                                 i     v  v v i         iv i i i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_106427710_    863 TCTGATCCTCAACAAACCTGACAAAAATAAGCAATGGGGAAAGGATTCCC 912
                         vi    ii  i    ivv  v   i vi vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_106427710_    913 TTATTTCATAAATGATGCTGGGAGAACTGGCTAGCCATATGCAGAACATT 962
                           -  iv i     i        v      v  ?   i     i  v v 
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_106427710_    963 GAAATTGGACCCCTTCTTTATACCTTATACAAATATTAACTCAAGAAGAA 1012
                            i          v i i i   v        v          i v i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_106427710_   1013 TTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGAAAAT 1062
                          i ?    i         i v i            vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_106427710_   1063 CTA--CCCAATACCACTCAAGACGTAGGGATAGACAGGGGCAAAAAATTC 1110
                         v  --?vi  - i -i  iv   v v   v   i  iv  i------   
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGT------TTC 588

  chr1_106427710_   1111 AT-GATGAAGACGTCAAAAGCAGCTGCAACAGAAGCAAAAATTTACAAAT 1159
                         v -   - v   ii        vvv      i   v      vv i    
  L1M4_orf2#LINE/    589 TTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_106427710_   1160 AGGATCTAATTAAACTAAAGAGCTTCTGCACAGTGAAGGAAGCTATCATC 1209
                         v   ii v  i   v v  i i   i  ii vvii     vi      vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_106427710_   1210 AGAATGAACAGACAACCTAGAGAATGAAAGAAAATTTTTGCAATCTTTCC 1259
                          i i    v        i v      ii       v       viiv vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_106427710_   1260 ATCAGACAAAGGTCTAATATCCAGAATCCATGAGGAACTTAAAAAATTTA 1309
                            v  i  i  v  vi          vi  i i     ivv v  i i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_106427710_   1310 TGAGTAAAAAGA--AACAATCCCATTAAAAAGTGGGCAAAAGACATGAAA 1357
                         vv i        --  i  i  v   ?    i        i  iv    v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_106427710_   1358 AGACACTTCTCAAAGGA 1374
                              i     v  i  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGA 854

Transitions / transversions = 1.39 (143 / 103)
Gap_init rate = 0.01 (10 / 854), avg. gap size = 1.90 (19 / 10)  


2105 25.15 9.61 2.02  chr1_106465621_106467769.rev      818  1660 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_106465621_    818 GGAAATATA---CA-GTCCATGAATTAAAAGTCTCAATATC-TTAAAATT 862
                              v   ---  -  i    i   ii   v  i     i-    i  v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_106465621_    863 CTGATTATTTCAAAGTTGATCTATAGATTGAGTGCAATTAAAACTAAAAT 912
                         vii  vv ii v  i        i     v ii     ivvv ii     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_106465621_    913 CACATTAGTCTTTTTT-CAAAAAATGACA--CTGATTCTAAAACTTTTAT 959
                          v  viv i       -  i   v     --     i      i iv   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_106465621_    960 AGAAGCTTTAAAAAGCTAGAATACCCAAAGCAACTTTGAAAAAGAACAAC 1009
                         i   iiviv iii v i      v     i   ii           v   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_106465621_   1010 ---GT--GAGGACT----------AATTTCAATAGGCATCATCGAGGCAA 1044
                         ---  --       ----------        v vvi ii - i i  --
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA-CAAAGC-- 248

  chr1_106465621_   1045 TATAGTATTT---------TAGTATTTGTTTAAAAATGGACACATAGATC 1085
                           i    v i--------- i   i v iv   ii  i    i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_106465621_   1086 CATGAAACATAATACAGAATCCAAAAATAGGCACACACATATTA-GATCA 1134
                         v   i  i v   vv   i    i     ii v  i    -   - i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-TTATGGTCA 347

  chr1_106465621_   1135 ATAGATTTTTGACAAAGATGC-AAAACCAATTCAGTTGAGAAAGA-TAGC 1182
                           v      i     i i   -  i    -    i v i      -   i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGT 396

  chr1_106465621_   1183 CTTTTCAATAAATGGTGCTAAAGCAATTGAATATCCATATGCCAAAACCA 1232
                                 i          iiii   i  i   ?   i    -    ---
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-AAAA--- 442

  chr1_106465621_   1233 ACAGAAATAAAAATCAATCTATTTCTTGCACCATAGGTAAAAAT------ 1276
                         ----i   i  iv vi i iv vi  ii       vii      ------
  L1M4_orf2#LINE/    443 ----GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_106465621_   1277 -AAATTGCTC-------CAAATGT-----TT-----TATAAATCT-TTAG 1307
                         -    v v  -------i      -----i -----      v  -    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_106465621_   1308 TTAGAAACATAGATGGAAATATTGGTGACCTCAGGTTAGATCAAGATTTA 1357
                         vvii        i? v    v  v       ii      iiv v i   v
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_106465621_   1358 TTTGATATAACAACAAAATGAGGATCCATAAAAGAAAAAAAAAAGCTAAA 1407
                           v     i   v     vv vi v v i           v i --    
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA--TAAA 636

  chr1_106465621_   1408 TTATACTTCA---AATTTATGGACTTCTGGCTTTCAAAACATTTTGTTAA 1454
                           iv      ---  v   vii    i  vvi      iv ivi i i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_106465621_   1455 AAGAATGAAAAGACAAGCCAC-GTGTGGGAAGAAAATAATTTTAAATCAA 1503
                         i i i           v    - vi     -       v  vi      v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGA-GAAAATATTTGCAAATCAT 735

  chr1_106465621_   1504 ATATCTGATAAGGGACCCATATCTAGAATATATAAAGAACTCTTG-AG-- 1550
                                         iii    i                    i- i--
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_106465621_   1551 -AATA-TAAAACAACACAATAA-------AAAAGATTGTCAGAAGAGTTG 1591
                         -    -     vi   -     -------?   i  v v  i i  v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_106465621_   1592 CATAGACATTTCACTAA-GAAGATACAGAGAAGAC----AACCACATGAA 1636
                         v           v i  -       i v i v i ----  v        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_106465621_   1637 GAGATTCTCAATATAATTAGTCTT 1660
                         i    v     i  v ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (128 / 81)
Gap_init rate = 0.04 (34 / 907), avg. gap size = 2.88 (98 / 34)  


2262 26.77 7.31 1.65  chr1_106470929_106473013      745  1592 (493)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr1_106470929_    745 CCATGG-CACAGCTTGCAAGCACCCAATAAT---AAGATACTAATTTTCC 790
                              v-  ii v   v   -  ii    v ---     ivi   vi   
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGATGGCAATACTCC 61

  chr1_106470929_    791 CCACATTTATCAATAGATTCAGAACAATTCCAATCAAAACCTCATCAGAA 840
                            v   v   v i       ivi    i  v       i i  v v v-
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC- 110

  chr1_106470929_    841 TTTTTTTATAGAAATTAAT--GCTTCCATTCTAAAATTCATATGGAAATG 888
                         i      ii       i i--   v--  i                    
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCATATGGAAATG 158

  chr1_106470929_    889 TTAAGTATCTTGAATAATTGAAATA-TCTTGGGGAAAAGTAACCAAATTG 937
                         iv i v i iv     iiii   i -     iii  i iv   v  i   
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_106470929_    938 TAGG-CTAGCAGTACCTAATTTCAGGAC---CCAGAAAGCAATACTCAGT 983
                         v   -  vi  v v  i       ii  --- i v     v i v v vi
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_106470929_    984 AAGAGGATATAGTTTTGACTTAAACATAGACGAGTAGGTCAAAGGAATAG 1033
                             vii i i  vi  i v   iv      ivi   i    v       
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_106470929_   1034 AATAGAGAATCCATAAATAGGCCCGTATATATATGGACAACTTATTTTTG 1083
                            v    i    v     ii   i  i  v     v   i v     i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_106470929_   1084 AAAATGTTGTAAGGGCAATTCAGTAGGAAAAGG-TAATTATTCTCCACAA 1132
                          v  v v  iv i i v     i i  i    i-  i i-  i  v    
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-TTTTCAACAA 407

  chr1_106470929_   1133 ATGGTGCTGGAACAACTAAAAGTCTGTATATATAAAAAGAACTGAAATTT 1182
                                   i      ii vi? iii  ii ---      -    i  v
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCA---AAAGAA-TGAAGTTG 453

  chr1_106470929_   1183 G-----TACCTTCCACTATATATAAAAATTAACTCTAAATGCATCATAGT 1227
                          -----     iv   i     i            v     v    ?  v
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_106470929_   1228 TGTAAATGCCAAAGCTAAAACTATAAAACTTGTGAGATAAAATTGTAAAA 1277
                         iv      iv i                  iv iii v    i---- v 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC----ATA 549

  chr1_106470929_   1278 GGAGCATATTTT----ACCTTGATTTATGCAAAGATTCCTTACATATAGC 1323
                           ? i v  i  ----      iv   v    v i  i    v    ii 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_106470929_   1324 AGCAAAAGCATAGTTCATTATAGAAAACATTGATGAAATGAACTTTCTCA 1373
                          v        i iviv iv v      v  v   i  v  i    iv   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_106470929_   1374 ACAT-AAAAACTTCT-TCTTTTA-----CA-----AAGTAAACAAAAAGA 1411
                          v  -        i - vi  i -----  -----   v  iii      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_106470929_   1412 TGAGCCAGAGACTGGAAGGAAATACTTGCTAAGCATAT-TTT-------- 1452
                         ii v   v   v   i  i     i    v  v     - i --------
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_106470929_   1453 --CTGTATCCAGAATATATAGGCAAACTCTCAAAACTCAC---------- 1490
                         --i                 ii-i      i v      v----------
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAA-GAACTCTTACAACTCAATAATAAAAAG 798

  chr1_106470929_   1491 -CAAAAAATTT--TTTGAAAATGGCCATTGAATTTGAAAAGACA---CTT 1534
                         -    v  iii--  ?i       v  vv i       v     ---  i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_106470929_   1535 TAAAAAAGAT-TAATAATAGCAAA-AAGCACATGAAAAGATATTCGGTAT 1582
                         i   i     -  vv   i  v  -                ii  iii  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_106470929_   1583 CATTAGTCAT 1592
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.51 (134 / 89)
Gap_init rate = 0.03 (28 / 896), avg. gap size = 2.71 (76 / 28)  


1796 28.47 9.61 1.90  chr1_106513660_106517827.rev     2835  3677 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106513660_   2835 TGGAAAAACATCCCAGAATCATGAATCAGAAGA---------------AT 2869
                               i i      viv     i  ii     ---------------  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106513660_   2870 CATAAT-CTGCACAAAGCAATCTATAGGTTCAATGCAATTCCTATTAAAT 2918
                         vii   -  v v    vii     i  i     i     i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106513660_   2919 TACCAATATAATTGCTCACAGAA-TT-ATAAAACAATTTTAAAATTCATA 2966
                          v   iivvvv  vi ii     -  - i  ivii  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_106513660_   2967 TGGAAACAAAATAGAGTTTGAATAGCCAAAGATATCCTAAGCAAAAATAA 3016
                               iiv  vi  viiv           ivv   i i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_106513660_   3017 CAAAGCTGGAAGCATCACATTACCTGACTTCCAATTATACTACAAGGTTC 3066
                              i    i vv     i v  ii i   v  viv        i i v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_106513660_   3067 TAGTAAACAAAACAGCATGGTACTGGTATAAAAATAGACACTTAGGTCAA 3116
                         i     v   i    ii         i    ii       iv   i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_106513660_   3117 CAGAACAGAAT-----------AAATAAAGA-ATAC--CTACCACCAACT 3152
                         ii   i     -----------       vv-    --i  ivii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_106513660_   3153 TATCTTCAACAAAGTTGAAAATACACACACTAGGAAAACATACACTGGAT 3202
                         v  i   i    i v  ------------ i -- i v   v  v   iv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG------------CCA--AGACCATTCAATGGGG 386

  chr1_106513660_   3203 AAAGGATACCCTATCCCATAAATGATACTGGGAAAATTGCATAGTTATAT 3252
                             i   vi  v i v i     i i      v  i  v   ?ii i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_106513660_   3253 GCAGAAGAAAGAAACTAGACC--------------------AAAAT-AAA 3281
                            i     v   ii i    --------------------     -  v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_106513660_   3282 GCAAAATAGATCAAAGCCTTAAATATAAAACCTGAAACTATAAATATTCT 3331
                         v      i     ?  v i     i   i v  i          - i   
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCT 535

  chr1_106513660_   3332 -AGAAGAACACCTAGGAA-AAGTATTCTAAACATTGGCCT-GGCAAACAA 3378
                         -       v  v    ?i-  i v   vvi  v    vi -     vviv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_106513660_   3379 TTTATAACTAATTCCTCAAAAGCAAACACAGCAAAAAGAAAGATAGAGAT 3428
                           iv  iv  vvv vi        v vi  i     ii   i     v v
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_106513660_   3429 ACGGGACTTAATTAAA-CTAAAAAGCTTCATAACAGCAAAAGATATAATC 3477
                          iv      v  i   -i      vi  ii i- vv    i  i iv   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTG-CTTCAAAGGACACTATC 684

  chr1_106513660_   3478 AACAGAGTAAATAGATAACCTGCAGAATAGGAGAACACATTTAAAAACTG 3527
                           v i   i  v   i    ii      i      v i    iv   iii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_106513660_   3528 TGCATCCAACAAAGGGCTAATATCCA-------CAAGGAAGTCAACCAAG 3570
                          ii   ii i  i  i  vi      -------i  i   v  vvv   v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_106513660_   3571 TAAATAAGAAAAA----AATAACCCTATTAAAAAGTGAGCAAAGGCCATG 3616
                          v     v     ----        v   ?    i  i       viv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_106513660_   3617 AACAGACATTTTACAAAAGAGGACAGAGAAA-------------CATAAA 3653
                           i        iv v     i  i v v   -------------   i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_106513660_   3654 AAAATGCTCAACATCAGTAACTGT 3677
                           i             ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.85 (97 / 20)  


2795 25.98 1.63 2.93  chr1_106523988_106526135.rev      739  1658 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106523988_    739 TGAAAAAACATCCCATGCTCATGGATCGGTAGAATTAATATCATTGAAAT 788
                           i   i i        i        i  v   v       ii  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106523988_    789 GACCATACTGCCCAAAGCAACCTCCAGATGCAATACAATACCTATCAAAA 838
                          i v     v      vii i  v     v   ii    v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106523988_    839 TATCAATAGCAGTTTTCATAGAA-TTAAAAAAAAAGAGATCATAAGATTT 887
                          vi  iiv  vv    iii    -  i v  ivv---    v   i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT---GATCCTAAAATTC 147

  chr1_106523988_    888 ATATAAAACCAAAAAAGATTTCACATAGCCAAAGCAA----GACAAAAGA 933
                             ii  viiv  ii  iiiviv         i   ----  -      
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGA 196

  chr1_106523988_    934 AGAA---ATCTAAAGGCATCTAACTAACCAACTTCAAAATATATTACAAG 980
                             --- vi ii   vv  vv   vv    i       iv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_106523988_    981 GCTATAGTAACCAAAACAGTATGGTATTGGCATAAAAACAGACACATAGA 1030
                             i     i   i     i     i        ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_106523988_   1031 CCAATGGAAGAAAATAGAGAATCCAGAAATAAATCCATGTAATGGTAGAC 1080
                         i        v i   v    i            i    ii v vi i v 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_106523988_   1081 AAATGATGTTTGACAAAGGTGCCAAGAACATACTTTGGGTAAACGATACC 1130
                           v    v  i     i          v   v vv    v   vi   vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_106523988_   1131 CTCTTTAATATGTCAGGCTGGGCACA-CTGGATACTCATATGCAGAAGAA 1179
                           i  i  i vi viv      -   -       ?i  i     i     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGG-ACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_106523988_   1180 TAAAACTTGACCCCTATCTCCCATGGCATACAAAAATCAACTCAAGGTGG 1229
                          i  ii v        i   v  ivii          i       ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_106523988_   1230 ATTAAAAACTTAAAAATAAGTCATGGAACTATAAGACTAACAGAAAAAAA 1279
                           i ? i  i    vi    vvv ii        i   vvi    i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_106523988_   1280 -ACAACTGAGGAAAACACTTCAGGGCAGTGGTTTAGGCAAAGATTTTATG 1328
                         - i --- i? v   i-    iv i vv   v        v i   iv i
  L1M4_orf2#LINE/    546 CATA---GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_106523988_   1329 GCTAAGACTTCAAATACACAGATAACGAGAGTAAAAATAGACAAATGGGG 1378
                          v  v   vi    vi    iii   i i  v         i    v  i
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_106523988_   1379 CCATATTAAA-TGAAAAAGCTTCTGCACAACAAAAGCAAACCATCAGCAA 1427
                          ivi  i   - v     -   i  ii vv    i - v  i    iv  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGG-ACACTATCAAGAA 689

  chr1_106523988_   1428 AATGGAGTGACTATCTGTTGAATGGATGAAAATATTTGCAAACTATTCAT 1477
                          i  i iv   v i iiiv      iv               ii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_106523988_   1478 CTGACAAGGAAGTAATATTTAGAAAA-A-AAAGAACACAAACAATTCAAT 1525
                             i    i v vi   ii    v - -       v vv    i     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_106523988_   1526 AATAAAAACA-AAATAAAACAAATTTTTTTTGTTTTCATTTAAAAGTGAG 1574
                                 v -      vv   ----------------  ?    i  i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAA----------------TTWAAAAATGGG 823

  chr1_106523988_   1575 CAAAGGACATGAATAAATATTTCTCTAAAGAAGATATACAAATGGC-AAC 1623
                                iv      i i       i                    -  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_106523988_   1624 AGGTATATGTAAAAATGCTCAACATCGCTAATCCT 1658
                          i i i   v   i            i????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (146 / 89)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.33 (42 / 18)  


1957 26.93 4.13 5.33  chr1_106569153_106570881      492  1241 (488)    L1M4_orf2#LINE/L1      168   908 (0)  

  chr1_106569153_    492 CAGAAAGTTAGTCGAAGCAGTTCTCCACAAAAAGAGCAAAGCTGGAGGCA 541
                              ---   i i  i  i ii vv v  i    i     i      vv
  L1M4_orf2#LINE/    168 CAGAA---TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_106569153_    542 TCACACTACTTGACTTCAAAATATATTACAAAGCTACAGTAACCAAAACA 591
                                v iii i       iv  i                i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_106569153_    592 GTGTAGTACCGGTATAAAAACAAACACAATGATCAGCAGAACCCAATAGA 641
                             i    i  i    ii i i   i vv     iii   ivv   v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_106569153_    642 GATCCCAGAAATAAATCCATGTATTTGCAGCCCACTTGTTTTTAATAAAG 691
                           vi           i    ii    iii i v i vi    ii i  i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_106569153_    692 ATGTTACGACTATACATTTGGAAAAAGACATGTTCTTCAATATATGATGC 741
                         i  ii v   i  v  v v  i   ii i vvi i     i v   i   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_106569153_    742 TGGAAAAACTGTATATCCATATATTAATGAATGAAACTAGACCCCTATTT 791
                            i v     v   ?   i  iiv  v       ii i        ii 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_106569153_    792 CTCATCATA--------------------------AAGACTTAAATGTAA 815
                          v  i    --------------------------?    i         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_106569153_    816 TAGTTGAAATTATAAAAGTACTAGAAGAAAACACAGAGGAACAGCTTCAG 865
                         v  i i   i       v vi            i  i? v v v    iv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_106569153_    866 GACATTGTCCTGTTTTGTCAAGTGATCTTGTTGGAAATTTTATAGCTAAG 915
                            v   ---- v  v v   -  i -  v  i  -----   ii -- -
  L1M4_orf2#LINE/    565 GACCTTG----GGTTAGGCAA-TGGT-TTCTTAGA-----TATGAC--A- 600

  chr1_106569153_    916 TGTTCAAAAGCACAGGCACCAAAAATAAGAATAGAAATATGGGACCATAT 965
                         ---i          i   v     iv  i      v v  v    ivi  
  L1M4_orf2#LINE/    601 ---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_106569153_    966 TAAAGTAAATAGTTTCTCCATAGCAGAGGAAACAATCAATCAACAGAGTG 1015
                         i   i v  v ii  i viiivv  i    v  -- --     v i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACAC--T--ATCAAGAAAGTG 693

  chr1_106569153_   1016 AGAAGACAACCTGTAAAATGGAAGAAAAATGTTTGTAAACTATTCATTTG 1065
                          i         iii i     i      - i    i   ii  vi  i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTG 742

  chr1_106569153_   1066 ATAAAAGACCAATATTCAGGATATTCAAGAAACCCAAACAATTCAACAGT 1115
                             ii   ivi   i   i    vi  ii   i vv    i    i i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_106569153_   1116 AAA----CAAATAAGCCCATGAAAAAGTAGGCACACTTTTTCTATTTACC 1161
                            ----       v  v  v?    i i    v vv------    i--
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG------ATTTG-- 834

  chr1_106569153_   1162 TCCATAAATAGACAATTGTC-AAAGAGAGACTTACAAATGGCCAACACGA 1210
                         ------        v  v  -     -   iv             i v v
  L1M4_orf2#LINE/    835 ------AATAGACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGC 877

  chr1_106569153_   1211 ATATGAAAAAATACTCAATGTTCCCAATCAT 1241
                          i       i  i     ii iv????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (129 / 69)
Gap_init rate = 0.02 (16 / 741), avg. gap size = 4.44 (71 / 16)  


2814 28.33 1.44 0.56  chr1_106583589_106589948     4968  5867 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106583589_   4968 TGGAAGAACATTCCATGCTCAGGGATAGGAAGAATCAATATTGTGAAAAT 5017
                              ii i  i     i   v    v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106583589_   5018 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGGCATCCCCATCAAGC 5067
                            v     v     iv i  i  i       ii vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106583589_   5068 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAGCTTTCA 5115
                          v   iivi i  i  ii     -   -- v  i  - iii  ivv    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_106583589_   5116 TATGGAACTAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5165
                                v iv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_106583589_   5166 AGCAAAGCTGGAGGCATCACGCTACCTGACTTCACACTATACTACAAGGC 5215
                          i     i      vv    i  v  ii i    v viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_106583589_   5216 TACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGTTAGAGACC 5265
                              i  i   i    ii         i iv ii i   vv  v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_106583589_   5266 AATGGAACAGAATAGAGCACTCAGAAATAATACCACATATCAACAACTAT 5315
                                i     v   viii         vv   i i  iv iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_106583589_   5316 CTGATCTTTGACAAATCTGAAAAAAACAAGAAATGGGGAAAGGATTCCCT 5365
                         i    i  i     ivv  vv  i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_106583589_   5366 ATTTAACAAAGGGTGATGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5415
                         v  i      v    v     v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_106583589_   5416 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5465
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_106583589_   5466 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACC--------AAACCT 5507
                          ?    i       v   v       i      vi --------    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_106583589_   5508 AGGCAATACAAT--TCGGTACATAGGCATGGGCAAGGACTCCATGTCTAA 5555
                            ?i-  -   --   vv  v v  vv i     v ii i v ivv  v
  L1M4_orf2#LINE/    549 AGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_106583589_   5556 AACACCAAAAACAATGGCAACAAAAGCTAAAATTGAAAAATGAGATCCAA 5605
                         i         i  vvi          vv     v  v    vi  iiiv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_106583589_   5606 TTAAGCTACAGAACTTCTGCACAGCAAAAGAAAGTACCATCAGAGTAAAC 5655
                          i  iv vv i     i  ii vv    i  v v  i  vv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_106583589_   5656 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACTA 5705
                           i     i                 v       vii ivi      -  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA-TA 745

  chr1_106583589_   5706 ACGG-CTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5754
                          v  -  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_106583589_   5755 AAAATAAACAACCCCATCAAAAAGTGGGCAAAGTATATGAACAGACACTT 5804
                           i i   i     v  i?    i         v  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_106583589_   5805 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGGATAT 5854
                            v        i  vi viii     v ii          i   vvi v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_106583589_   5855 CATCACTGGCCAT 5867
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (139 / 112)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


2765 25.06 9.52 0.12  chr1_106592240_106594235.rev      676  1505 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106592240_    676 TGGAAAGATATTCCATGTTCATGGATTGAAAGAATCAGTATCGTTAAAAT 725
                                    i                i    v i i   i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106592240_    726 GTCCATACTACTCAAAGCAATCTATAAATTCAGGGCAATCCATATCAAAA 775
                          v v     v i    vii     i i     iv       v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106592240_    776 TACCAATGACATTCTTCACAGAAATAGAAAAAATAATCCTAGAATTTATA 825
                          v   iivi v  i  ii       v  v  iv i      i    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_106592240_    826 TAGAAACACAAAAGACCCAGAACAGCCAAAGCCATTCTGAGCAAAAAGAA 875
                          i    ii   ii         i       i v  ii   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_106592240_    876 CAAAGCTGAAATAATTACATTACTTGACTTCAAATTATACTACAAAGCTA 925
                              i  i iv v i   i v iii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_106592240_    926 TAGTAACCAAAACAGCATGGTACTGGCATCAAAACAGACA--------GA 967
                         i     i   i    ii            v ii i     --------i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_106592240_    968 TG----------------CCAAGAATA------TACACT---GG------ 986
                           ----------------   ii    ------    i ---  ------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_106592240_    987 --------ACAAAGGTA--------------------------AGTCCTT 1002
                         --------    i   i--------------------------    i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_106592240_   1003 TCACTAAATGGTACTAGGAAAACTAGGTATCCATAAG-AAAAGAATGAAA 1051
                            vi       i  i   v    i i  ?   i v -           i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_106592240_   1052 CTAGGCCCCTATCTTTTGCCATATTCAAAACTCAAATCAAAATCGATTAA 1101
                         i i i      i  ivii      v     v i  v       v   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_106592240_   1102 AGACTGAAATCCAAGGCCCGAAATTATGAAGCTACTAGAAAAAAA-ATAG 1150
                             iv    vi   iv ii   i   i  i  vi     i    -    
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_106592240_   1151 GGAAAACCCTCCCAGATGTTGGTTT-GGCAAAGATTTATTGAATAAGACC 1199
                          ?iv  vi  i vv  iv    v  -     v i   v  ii   v   v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_106592240_   1200 TCAAAAGAACAGGCAACCAAAGCAAAAATAGATAAATAGAATCACATTAT 1249
                         i      v   i     v    v              v i iiv   i v
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_106592240_   1250 GCTAAAAAGCTTCTGCACAGCAAAGGAAACAATTAACAATGTGGAGTGAC 1299
                         iv v    i   i  ii vv       v  v  i  v  v   i iv   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_106592240_   1300 AACCCACAGAATGGCAGAAAATGTCTGCAAACTATTCATCTGACAAGGGA 1349
                                       v       i i      ii  vi      i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_106592240_   1350 TTGACAAACAGCATATATAAA-AGCTCAAAAAACTCAATAG-AAAAAAAT 1397
                         i vii vv   v         - i   vv v         i-     i i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_106592240_   1398 AA-TAATCTGATTAAGAAATGGGCAAAAGTTCTAAATAGACATTTCTCAA 1446
                           -   i ii   ? i           i v i i              v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_106592240_   1447 AAGGATACATAAAAATGGCCAACAGGTATATGAGAAAAATTCTCAACATC 1496
                            i v i   v          i i i i    -   i  v         
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTCAACATC 899

  chr1_106592240_   1497 ACTAATCAT 1505
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.83 (132 / 72)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 6.15 (80 / 13)  


3232 24.27 2.35 0.78  chr1_106676610_106679824     1831  2724 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106676610_   1831 TGAAAAGATATTCCATGTTCATGAATTGGAAGAACAAATATTGTTAAAAT 1880
                           i        i           i         viv           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106676610_   1881 GTTCATACTATCCTAAACAATCTACAAGTTGAAAGAAATGCCTATTAAA- 1929
                          viv     vi  v  vii       ii  v  v v   v     i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106676610_   1930 TGCCAACGACATTCTTCACAGAAATAGAAAAAAAATAGTCCTAACATGAA 1979
                          v   i vi v  i  ii       v  v  iv-- ii      v  vv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chr1_106676610_   1980 TATAGAACCACAAAAGACCCAGAATATCCAAAACTACCCTAAGCAAAAAG 2029
                            i   vii   ii           v       v i i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_106676610_   2030 AA-------GGA----TCACATTACCTACCTTCAAATTATACTACAGAGC 2068
                           -------   ----     i v  i vi      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_106676610_   2069 TATAGTAACCAAAACACCATGGTACTGGCATAG----AGACAAATAAACC 2114
                           i     i   i   vii             i----     v   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_106676610_   2115 AATGGAATAGAATAGAGAATCCAAAAACAAATTCAAACACCTACAGTAAA 2164
                                      v    i    i   i   ii  v   ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_106676610_   2165 CTCATTTTTGACACAGGTATCAAGAATACACATTGGGGAAAGAATGGTAT 2214
                         i v     i    vi   ii     vi iv  v            i  v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_106676610_   2215 CTTCAATAAATGGTGCTGGGAGAACTGGATATCCACATGCTGATGAATGA 2264
                         i     i              v         ?        vi v      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_106676610_   2265 AACAAGACCCCTGTCTGTCACCATATGCAGTAGTCAAATAAAAATGGATT 2314
                          iivi       ii  vv        i  iv i i  v v         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_106676610_   2315 GAAGACTTAAATCTAGG-GCTGAAAACTATGAAACTGCTACAAGAAAACT 2363
                         i?    i     v  i -   -        i     vi  v        v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_106676610_   2364 T-GGGGTAAGTCTCCAGGACATTGGACTGGGCAAAGATTTCTTTAATA-- 2410
                          -  ?    i   i iv   v    ii i     v i      vi   --
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_106676610_   2411 ATACCACACAAGGACACGCAACTAAAGCAAAACCGGACAAATAGAATAAC 2460
                          i    - -   v   v     v    v    vii  i    v i ivv 
  L1M4_orf2#LINE/    598 ACACCA-A-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_106676610_   2461 ATCAAG-TGAAAAAGCTTCTGCAAAGCAAAGGACACAATCAAGAAAGTGA 2509
                              i- v     -   i  iivvv          v             
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_106676610_   2510 AGAAACAACCCACAGAATGGGAGAAAATATTTGAAAATTACCCATCTGAC 2559
                          i i                             v    i ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_106676610_   2560 AAGGGACAAAAAACCAGAATATATAAGGAGCTCAAACAACTCTATGGGAA 2609
                                vviv v             i  i   vv       v  iiv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_106676610_   2610 AAATATCTAATAATCTGATTTAAAACTGGACAGAACATCTTAACCGGTAT 2659
                            v - v     i ii   ?    v   i  i iv  i v  iv ii  
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_106676610_   2660 TTCTCAGAAGAAGAGATACAAATGGCAAACAGACATATGAAAAGGTGCTT 2709
                              vi       v           v  i ii  i        i    i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_106676610_   2710 AACATAATTGACCAT 2724
                              v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (124 / 89)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  


3399 17.96 5.88 5.21  chr1_106702929_106705621.rev     1301  2202 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106702929_   1301 TGAAAACACATCCCATGTTTATGGGCTGGAAGACTAAATGTTGTTAAGAT 1350
                           i   v i          i    ii         v   i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106702929_   1351 GTTTATACTACCTAAAGTGATATAAAGAGTCAATGCAAGTCCCACCCAAA 1400
                          viv     v  i   v    v  v   v    i    vi  i i v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106702929_   1401 TTCCAATGACTTTTCTTTTTCTGCAGAAATAGTAAAAACTGATTATAAAA 1450
                          i   ii----- v i    i         v - v  i     iv     
  L1M4_orf2#LINE/    101 TCCCAGC-----TGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAA 144

  chr1_106702929_   1451 TTCATA-GAAAACCTAAAGGGACCACCCCAGA-T-GTCAAAATAAT-TTG 1496
                               - i   ivi  -      ----    - - i     i   -   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAA-GGGACC----CAGAATAGCCAAAACAATCTTG 189

  chr1_106702929_   1497 AAAAAGAA---CAAAGTTGGAAGACTCATACTTCCTGATTTCAAAAGGTA 1543
                                 ---          i      i      ii         vv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_106702929_   1544 GTAGAAATCTAGAGTAATCAAAACAATGTGGTGCTGGCATAAAGACAGGA 1593
                         v  v   v   v         i   i      i         i  i  iv
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_106702929_   1594 ATATAGATCAATGGAATAGAATAGAGAGCCCAGTAATATAACATCATGTA 1643
                                               v     i    v    -   -i   ii 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA-AAC-CCATACA 337

  chr1_106702929_   1644 T--ATAGCCAAATAATTTTTGACAGTGATTCCAAGACCATTAAGTAGGAA 1691
                          --  i i   v i     i    iv i v           v i i  i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_106702929_   1692 ACAAA-AATCTTTTCAACAAATGGTGTTGGGA------------------ 1722
                          vi  - i                  i     ------------------
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_106702929_   1723 -----------AGTTGGGTCCTTACTTTACATCATATT--AAAATTAACT 1759
                         -----------      ii  i   i i   i     v--          
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_106702929_   1760 AAAAATGGAATTAT-GAGCTAAATGTAAGAACTAAAAACATAAGACTCTT 1808
                         v        - i ?-  v            i      vi    i      
  L1M4_orf2#LINE/    488 CAAAATGGA-TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_106702929_   1809 AGAAAAAAAGCATAGAGGAATAGCTTCTTCACACTGGATTTGGCAATTAT 1858
                             i    -     i? v v v    v v  vi   i  v      vi 
  L1M4_orf2#LINE/    537 AGAAGAAAA-CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_106702929_   1859 TTCTTAAATATGACACTAAAGACATAAATAACAAAAGAAAAAATAGATAA 1908
                               i         i   ii  i  ii                     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_106702929_   1909 ATGGGATTATATCAAAATTTAAAACTTTTTTGCAGCAAAAGACATTATTA 1958
                           v   i vi         v         v   vv    i    i   i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_106702929_   1959 AGAGTATAAAAAGTCAACCTGTGGAATAGAGAAACATATTTGCAAATTTT 2008
                            ivi i     v     iiii    i iii  v            iv 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_106702929_   2009 ATATCTGGTTAGAGATTATATAAAGAGATTATATATCTGGTTATATCTGG 2058
                                i -------------   i  i ----------- i    i--
  L1M4_orf2#LINE/    736 ATATCTGAT-------------AAGGGACT-----------TGTATCC-- 759

  chr1_106702929_   2059 TTAGAGAACATATAAA-AACCC---CAACTCGACAATAAGAA-ACAAA-- 2101
                         ----    i       -   i ---      i i     i  -     --
  L1M4_orf2#LINE/    760 ----AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_106702929_   2102 --CCAATTTTAAAAAATTGACAAAGGCATTGAATAGACATGTCTTCAAAG 2149
                         --      ?--      v i      vv            v   i     
  L1M4_orf2#LINE/    806 ACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_106702929_   2150 AATATA-ACAAATGGTCAATAAGCACA-GAAAAGATGCTCAACATCAGTC 2197
                           v   -        i           -                   ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_106702929_   2198 TTCAA 2202
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.79 (102 / 57)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.57 (100 / 28)  


2324 28.95 3.47 2.27  chr1_106722999_106726804     2478  3313 (493)    L1M4_orf2#LINE/L1       63   908 (0)  

  chr1_106722999_   2478 CAAAGCAATCTACAAATTCAGCGCAATCTTAATCTAAATATCAA-TGTCA 2526
                             vii       i     i       iiv   v    vi  i-  i -
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC- 111

  chr1_106722999_   2527 TTTTTCACAGAAACTGTTTAAA--AATTCTAAACTTTGTATGGAGCCAAA 2574
                              ii      i  vi-  i--i  i     v  ii      iviiv 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr1_106722999_   2575 AAAGAGCCCCAATGGCCAAAGACAAAGAAATCCTGAGGGGGGAAAATAAA 2624
                          ii  v  vv   i      -    -----  i   iiii i i  i   
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAA-ACAA-----TCTTGAAAAAGAAGAACAAA 204

  chr1_106722999_   2625 GGCTGGAGATATCACACCACCTGACTTTAAAATATATTACAAAGTTATAG 2674
                          -i     ivv      iv  ii i  i    iv  i       i  i  
  L1M4_orf2#LINE/    205 G-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_106722999_   2675 TGAGCAAAACAGCATGGTATTAGTATAAAAATACACAC-----TTAATAG 2719
                          i v   i    ii     i i i    ii   v   i----- i   i 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_106722999_   2720 A----------GAACCCAGACATATAATTACATATTGACAACCAGCTGAT 2759
                          ----------  ii     v   v vii i i   v iiii  ii    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_106722999_   2760 TTTTAACAAAGACCCCAAGAACATATGTTGGGGAAATGACACCCTCTTCA 2809
                            ii    i iiv      v   viiv        vi i vi  i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_106722999_   2810 ATAAGTGGTGCTGGGAAAACTGATTATCCATATATAGAAGAATAAAACTT 2859
                          i  i           v     iv  ?   i  ii i      i  ii v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_106722999_   2860 GAGCCCTTTCATACACTATATA-AATAATCAACTCAAAGTGAACTAAAAA 2908
                           v    vi vi    i     -  v   i        i  i ii ? i 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_106722999_   2909 CTTAAATGTAAGATCTGAAACTA--AAAGTACTAGAAGAAAACCTAGAAG 2956
                          i           v  i      --   v vi           v   i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_106722999_   2957 AAACACTTCAGTATAATGGTCTAGGCAATGATTCTATATCTATGACCTTA 3006
                         v  vv    ivv ivv   vi         i  iiv  vv      vii 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_106722999_   3007 AAAGCCCAGGCAACAAAAACAAAAGTAGACACAT--GATTTTATATAAAA 3054
                              v  i         iv    i    i v  --  i  i  -i    
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT-CAAAA 652

  chr1_106722999_   3055 CTAAAACACTCT-GCACAACAAAGGAAACAATCAACAGAGTGAAGAGACA 3103
                         i     -   i - ii vv       v  v     v i      i     
  L1M4_orf2#LINE/    653 TTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_106722999_   3104 ACTTATTGAATGAAAGCAGATA----CAAACTATTCATCCAACAGGAGAC 3149
                           ii iv     ii  v i   ----    ii  vi   ii i i i   
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_106722999_   3150 CAATATTGAGAATATACAAAGGACTTAAATGACTCAACAACAACAAAATA 3199
                         ivi   iv        i    i   ivv ii      i  i  v  i i 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_106722999_   3200 AATAATTTTATTAAAAAGCGGTTGAAGACCTT-AGTAGATATCTCTCAGA 3248
                              iiiv   ?    ii  vii   ivi  - i    i  i    vi 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_106722999_   3249 AGAAGATAGAAGACATACAAATGGCCCACAGTTACATGAAAAAAATGCTC 3298
                                 -------           v i ivi         i -     
  L1M4_orf2#LINE/    852 AGAAGATA-------TACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chr1_106722999_   3299 AGCATCATTAATCAT 3313
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (166 / 72)
Gap_init rate = 0.02 (19 / 846), avg. gap size = 2.53 (48 / 19)  


2680 26.23 2.34 1.00  chr1_106729517_106737166     6262  7157 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106729517_   6262 TAAAAACATTTCCCATGCTCATTAATGAGAAGAACCGATATTATGAAAAT 6311
                          ii   v  v       i    vi  vi     viii     i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106729517_   6312 AATGATATTGCCCAAAGCAATCTACAGATTCAATGCAATTCCTATGAAAA 6361
                         iiii   i v      vii              i     i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106729517_   6362 TATCATCATTATTTTTCACAGAAATAGAAAAAAAAATCTTAAAATTCATA 6411
                          vi  v vviv     ii       v  v  ivvi   i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_106729517_   6412 TGGAAC--CAAAGAAAGCCCA-AATAGCTAAAGCAACACTAACCAAAAAG 6458
                              v--   i i --    -      i   i   ivi i vv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_106729517_   6459 AACAAATCTGGAGGCATAACATTACCAGACTTCAAATTATACTACAAGGC 6508
                               vi      vv v   i v  vi i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_106729517_   6509 TATATTTACCAAAACAGCATGGTACTGGTATAAAAACAGGCACATAGATC 6558
                           i v v i   i    ii         i    ii i  i  i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_106729517_   6559 AATGGGAAAGAATAGAGAACACAGAAATAAAGCCAAGTACTTACTGCCAA 6608
                              i v     v    iiv          v   vii i   iv i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_106729517_   6609 TGGATCTTTGACAAAGCATACAAAAAT-ATAAATTGGAGAAAGATC--CC 6655
                          v   i  i     i -i i v  i i-  vv v   i      vi--i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_106729517_   6656 TATTTGATAAATCATGCTAGGAAATATGGCAAGCTA-ATGTAGAAGAATA 6704
                          v  ii i    vi    i   v vv   vv ? i -   i i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_106729517_   6705 AAAAAGTATCCCCAACTCTTGCCTTATACAAAAATCAACTCATGATGGAT 6754
                           ivv v i   i v   vii  v           i      vi      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_106729517_   6755 CAAAGACTTAAATCTAAGACCTGAAACCATAAACATTCT-AGAAGATAAC 6803
                           ?    i     v     v  i    i     - i   -      v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chr1_106729517_   6804 ATTGGA--AAATCTCTCCTGGACATTGGCTTAGGCAAATAATTCATTAC- 6850
                           v  ?--      -  v  -  v    v        - ii  iv   v-
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCT-TCGTG-ACCTTGGGTTAGGCAA-TGGTTTCTTAGA 593

  chr1_106729517_   6851 TAGGACCCTAAAAG-ATAATGCAACCAAAGAAAAAATAAATAAATGGGAC 6899
                           v   v i     - i  -     v            i      v    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_106729517_   6900 CTAATTAAACTAACAAGCTTCTGCACAGGAAAAGAAAGAATCAGCAGAGT 6949
                         i v  i   v v v  i   i  ii vvv   i  v vv    iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_106729517_   6950 AAACAGACAACCTACAGAGTGGGTGAAAATATTAGCGAACTATGCACTCA 6999
                         i  v        i     i    v         v  i  ii  ii iiii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_106729517_   7000 ATAAAGGACTAGTATCCAGAATCTACAAGGAACTC----AAATCAGCAAG 7045
                             i     v           v  i  i      ----  v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_106729517_   7046 AAAAA-ATAA-TATCTCA-TCAAAAAGTGGGCAACGAACACAAAAAGACA 7092
                              - i  -  v i  - i?    i       v i ivii  v     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_106729517_   7093 TTTCTCAAAAGAAGATACACCAACAGCCAGCAA--ACATGAAAAAAGTGC 7140
                               v          i  v  ii    ii  --         i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chr1_106729517_   7141 TCAATATCACCAATCAT 7157
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.36 (30 / 22)  


1269 29.38 12.35 1.85  chr1_106772079_106775163     1783  2592 (493)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr1_106772079_   1783 CATGTGTATAAATTGGGAGAACCAATATTTTTAAGATACCAATTTTTTGA 1832
                              vi  ii     i   vii      v       iv    vi iivv
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr1_106772079_   1833 GAATT-ATTTATAGCTTTT-TGAAATCTTAATAAAAATCTCAACAAACAT 1880
                         i    -  i  i  v  iv-i v    iiv  v      i  i viv v 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr1_106772079_   1881 ATTGG--AAAATGGAGAAACAATTTCTGAAATTTATTCAAAACTGCAAAT 1928
                         v  v --i    v  v  i viv i  i     i  viii  v     iv
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_106772079_   1929 GACTTAGAATGTACAAAGTAACCATGAAGAGGTAGCATATAGTAGAAGAA 1978
                            ii     ivv    ii  i v    i i v  v i v   v i  i 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_106772079_   1979 TTTACACAACCTGATTTCAAGATTTACTATAAAGCTACAAAAATAAAGAT 2028
                         i i    vv  ii       i i      i         iv   v    i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_106772079_   2029 AGTGTGGTAATGGAAAAAATACCAGATACGTAGATCAACTTTACCAACAA 2078
                                  v   v v  iv i-   i ii        --- iv-  i i
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGAT-AGACATATAGATCAA---TGG-AATAG 308

  chr1_106772079_   2079 AATT------TCA-AAATGA--CCAATGTATATTT----TCACTTGGTGT 2115
                             ------i  -    i --   ---  i    ----   v   i v 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCA---TACATTTATGGTCAATTGATTT 355

  chr1_106772079_   2116 TTGACAAAGTTGTCAAAGTAGCTTAGTGGAGAAAG--------------- 2150
                          i     i v  i   iiivii i i   i     ---------------
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_106772079_   2151 -----GTATT------------------CATATAGGAGA--GAACTTAGA 2175
                         -----  ii ------------------   ii ii   --   v  i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_106772079_   2176 CTTTTACCTCAC--CATTCACAAAAAATAATTTTAAAACTATCATACAGC 2223
                          iii        --   vi       v   i iv   vvv    ? v v 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_106772079_   2224 TAAACATATAAGC---------AAAAGATTTAGTGGAAA-CGTAAGA-TA 2262
                             ii  vi   ---------    vvi    vi    - i  i ?-  
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_106772079_   2263 ATATGTTTGCAACATGAGGGTAAACA-TGGTTTTTCTTA-ATAGGGCACA 2310
                          -  v  i ii  v vi  v  ii  -      --    -   v i   v
  L1M4_orf2#LINE/    556 A-ATCTTCGTGACCTTGGGTTAGGCAATGGTTT--CTTAGATATGACACC 602

  chr1_106772079_   2311 TAAAGCAATAGTCACAAAAGGAAAACATTAATAACATAATCTTCATCAAA 2360
                         v      vv  iv       i    -  vi    vv iiv          
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAA 651

  chr1_106772079_   2361 A---AAGACA-----GCATTCGACAAAC-TTAT----AAAGCAAAA---- 2393
                          ---  i  v-----  -   i vii  -i   ----    ii   ----
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_106772079_   2394 ------TAGGCTCGTGGAAAATAATCATAACACTTATATCTGACAATGCA 2437
                         ------i  iv v vi       v iii  vv v         i  v v 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_106772079_   2438 --TATATC-AAAATAGGTAAATAATTCCTATAAGTCAATCATAAAATGAC 2484
                         -- i    - i    vi    v  i  i  i  v     v      v   
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_106772079_   2485 AAAACATCTCAATTAATAATAAGACAAATGACT--AAGAGACACTTCACA 2532
                            -i v i     ? v  vvi i    v  i --  v     i   v v
  L1M4_orf2#LINE/    801 AAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_106772079_   2533 AAAGAAGATTCACAAATAATCAATAAGCATGGGGAAAAAATGCTCAACAT 2582
                                  vi      iii         iiv -    i           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTCAACAT 898

  chr1_106772079_   2583 CAGTAGTCAT 2592
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.04 (34 / 895), avg. gap size = 3.38 (115 / 34)  


2935 28.65 1.00 0.55  chr1_106877702_106883493.rev     4398  5301 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_106877702_   4398 TGGAAAAGCATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4447
                               iii  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106877702_   4448 GGCCATATTTCCCAAAGTAATTTGTAAATTCAATGCTATCCCC-TCAAGC 4496
                            v   i i      v i  i ii i      i  v     i-    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106877702_   4497 TACCATTGACTTTCTCCACAGAATTAGAAAAAAACT-ACTTTAATTTTTA 4545
                          v   vivi i  i iii     v v  v  i--  - iii   vv  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_106877702_   4546 TATGGAACCAAAAAAGAGCTCATATAGCCAAGACAATCCTAAGCAAAAAG 4595
                                viiv  ii  v iviv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_106877702_   4596 AACAAAGCTGGAGGCATCACACGACCTGACTTCAAATTATACTACAAGGC 4645
                                i      vv      vv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_106877702_   4646 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATACAGACC 4695
                                 i   i    ii         i iv ii i   i   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_106877702_   4696 AATGAAACAGAACAGA-AGCCTCAGAAATAATGCTACACATTTACAACCA 4744
                             i  i    iv  -  i -         vv i i       iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chr1_106877702_   4745 TCTGATCTTTGACAAACCTGAAAAAAACAAGCAATGGGGAAAGGATTCCC 4794
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_106877702_   4795 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCTATATGCTGAAAACTG 4844
                          v  i  i        i     v      v  ? i i    vi  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_106877702_   4845 AAGCTGGAGCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGAT 4894
                            i    v    v   i i   v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_106877702_   4895 TAAAGACTCAAACCTAAGACCTGAAACCATAAAAACCCTT-GAAGGAAAC 4943
                         i ?    ii   iv     v  i    i      - i   -    i    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr1_106877702_   4944 CTAGGCA-ATACCACTCAGGACATAGGCATGGATGAAGACTTCATGACTA 4992
                         v    ?i- v i -i  iv   v v  vv i iii v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_106877702_   4993 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGGATCTA 5042
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_106877702_   5043 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTATCAGAGTGAA 5092
                           i   v v  i i   i  ii vv    i  v     i vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_106877702_   5093 CAGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTATCCATCTGACA 5142
                         v  i     i              v  v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_106877702_   5143 AAGGGCTAATATCCAGACTGCACAAGGAACTTAAACAAATTTACGAGAAA 5192
                          i  i  vi        v ii i  i     ivv    v iv ii v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_106877702_   5193 AAACCAA----CCCCATCAAGAAGTAAGCAAAGTATATGAACAAACACCT 5238
                           iv   ----   v  i? i  i ii      v  v    i i   ii 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_106877702_   5239 CTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAGAAAGCTCAT 5288
                            v        i  vi vi       i  i  i      ii v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_106877702_   5289 CATCACTAGTCAT 5301
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (158 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


 774 26.01 2.24 0.90  chr1_106918577_106923741     3397  3619 (1546)    L1M4_orf2#LINE/L1        1   226 (682)  

  chr1_106918577_   3397 TGGAAAGATATTTTATGTTTATGGACTGAATGAATCAATATTGTTAAAAT 3446
                                    iii     i     i  i v  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_106918577_   3447 GTCCATACTAACAAAAGCATTTTACAGATTCAATGCAATCCATATTAATA 3496
                          v v     vv v   viiv i           i       v   i  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_106918577_   3497 TACCAATGACATTCTTCACAGAGAA-GAAAAG-TAATCCTAAAATGTATG 3544
                          v   iivi v  i  ii    i v-  v   - i          vi  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_106918577_   3545 TGGAA---CACAGAATTCCCAGAATATCCAAAGCTATCCTAAGCAAAACG 3591
                              ---  vi i --         v     i v   i i iv  i v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_106918577_   3592 AACTAAACTGGAGGAATCACATTACCCA 3619
                            v  ii       v     i v    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCA 226

Transitions / transversions = 1.32 (33 / 25)
Gap_init rate = 0.02 (4 / 226), avg. gap size = 1.75 (7 / 4)  

2617 26.40 0.14 0.72  chr1_106918577_106923741     3976  4672 (493)    L1M4_orf2#LINE/L1      216   908 (0)  

  chr1_106918577_   3976 CATATCACCTACCTTTAAATTATACTACAGAACTATAGCAACCAAAGCAG 4025
                           i iiv  i vi  i   viv       i i   i  i  i   ii   
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_106918577_   4026 CATGGTACTGGCATAGAAAGATACACATGGACCAAGAGAATAGAGCAGAG 4075
                         ii             iii v v   i  i  i   vi       iiv   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_106918577_   4076 AACCCAGAAATAAATTCACACATCTGCGGTGAACCCATTTTTGACAAAGG 4125
                          ii           ii  i    i ii   v  iiv     i     i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_106918577_   4126 TGCCAAGAATATACCTTGGGGAAAGAACAGTCTCTTCAAAAAATGATGCT 4175
                                 vi  v vv           i     i     v     i    
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_106918577_   4176 GAGAAAACTAGATATCTACATGCAGAGGAAAGAAACTAGACCCCTGTTTC 4225
                          i  v    i    ? i       i i   v   ii i       iii  
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_106918577_   4226 TTGCCACATACAAAAATCAAATCAAAATGGATTAAAGACTTAAATATTAT 4275
                         vii   i          i  v           i ?    i     i v v
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_106918577_   4276 GCTTCAAACTATGAAACTACTACAAGAAAACGTTGAAGAAAATCTCCGGG 4325
                         ivi v       i     vi  v        i v i? v      i  v 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_106918577_   4326 ACATTGGTCTGGGCAAAAATTTCTTTAGCAATACCCCCACAAGCACAGGT 4375
                           v    vi i     vii      -  vv  iv v   v       i i
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAAGC 614

  chr1_106918577_   4376 AAGCAAAGCAAAAATGGACAAATGGGATCATATCAA-GTTAAAAAGCTTC 4424
                           vv    v      i  i    v   iivi     -i       -   i
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTT 663

  chr1_106918577_   4425 TGCACAGCAAAGGATGCAATCAACAAAGTGAAGAGACAACCCACAGAACG 4474
                           ii vv       ii v     v        i               i 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_106918577_   4475 GGAGAAAAGATTTGTAAACTTCCCATTTGTCAAGGGATTAATAACCAGAA 4524
                                 v     i   iivivi  i  vi      i vi  v      
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_106918577_   4525 CATATAAGGATATCAAACAATTCTATAGGAAAAACTCTAATAATCTGATT 4574
                         i      i  vv  vv    i  v   iv     vv v     i ii   
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_106918577_   4575 GAAAAAAACTGGGCAACAAATTTGAATAGATATTTCTCAGAAGAAGACAC 4624
                         ?     ---       vii           i       vi       i i
  L1M4_orf2#LINE/    814 WAAAAA---TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_106918577_   4625 ACAATTGGCAAAGAGACATATAAAAAGGTACTCAGCATCATTTATCAT 4672
                             v    v  v ii  i  i     i i    i     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (115 / 65)
Gap_init rate = 0.01 (4 / 693), avg. gap size = 1.50 (6 / 4)  


2995 24.26 4.33 0.91  chr1_107081262_107085170     2539  3416 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_107081262_   2539 TGAAAATATATCTTCTTTTCATGGATTGGAAGAAT-AATTTTGTAAAAAT 2587
                           i   v     iiv v                v -   v    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_107081262_   2588 GTATATATTACCCAAAGTGATCTACAGATTCAATGCAATCTCTATAAAAA 2637
                          vvv   i v      v                i      i    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_107081262_   2638 TTCCAATGACATTTTTCATAGAAATAGAAAAAA-AAT--TAAAATTTATA 2684
                          i   iivi v     iii      v  v  iv-i  --       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_107081262_   2685 TGGAACCACGAAAGACCCTGAATAGCCAAAGCAAACATGAGCAAGAA--- 2731
                              vii i ii     v           i   v v   iv     ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_107081262_   2732 CAAAGCTGAAGGCATCACACTCCCTGATTTCAA--CTATATTACAAAGCT 2779
                              i  i   vv       i  ii       --  -  i         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr1_107081262_   2780 GTAGTAATCAAAACAACATGGTACTGACATAAAAACAGATACATAGACCA 2829
                         ii         i   iii        i     ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_107081262_   2830 ATGGAGTAGAGCAAAGAATCCAGACATATACCCATACATACATGTTCAAC 2879
                              i    iivi   i      v   v          vi   v    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_107081262_   2880 TAATCTTTGACATGAGTGCCAAGATTACT--ATGGG--AAGA-TAGTCTC 2924
                          i  i  i    v i         ii i --     --    -      i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_107081262_   2925 TTTAATAAATGTTGTTGGGAAAACTGGGTATTAACATGAAAAAGAATGAA 2974
                           i  i     v  i     v      i  ?iv     v           
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_107081262_   2975 ATTGGAGCCTTGTCTTACACCATATACAAAAATTAGCTCCAAATGGATTA 3024
                         i     v  i ii  i                   i   v        i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_107081262_   3025 AAGACTTAAATGTAAGATTCAAAA-TATAAAACTTCTTGAAGAAAACAGA 3073
                         ?    i           vii    -         ii v          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_107081262_   3074 AATAGAAAACTCCTTGAATTT---TTAATGCATTGATTTTTTTATATATG 3120
                         ii?iv   v  i v   vi  ---   i-   v  i   i  - v     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAG-GCAATGGTTTCTT-AGATATG 597

  chr1_107081262_   3121 ACAACAAAAGCA---------------AAAATAAACAAATGGAAATATAT 3155
                            v        ---------------      i i    v i v vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_107081262_   3156 CAAACTAAAATGCGCCTGTATAGCAAAGAATAAAATTCAAAAAAATGAAA 3205
                             v v   vi vii   iivv     i i vv  -   i   i     
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT-CAAGAAAGTGAAA 696

  chr1_107081262_   3206 AGACAACCTATGAAATGAACTAAAATATTTCAAAATTGTATATTTGATAA 3255
                                 i iii    iivv         vv    ii     i      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_107081262_   3256 GGG--TTAAATGAGGAAT---TGACACAATTGCCAAAAACAAACAAACAA 3300
                            --  iv  vvi    --- i - v  i vii v  viv  i  -i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAA-AGAACTCTTACAACTCAATAA-TAA 794

  chr1_107081262_   3301 ACAAACAAAAAACCTATTCTTAAAAATAGGCAAAGAACCTGAACAAACTT 3350
                          v i     v    i v - ?      i       i ii    i i  v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_107081262_   3351 TTTTTTCAAAGAAGACATAAAAATGTTGAGCATGTACATGAAAAGGTGCT 3400
                           i i-         i   v     viv ii v i          i    
  L1M4_orf2#LINE/    844 TTCTC-CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_107081262_   3401 CAGTATCAACTGACCA 3416
                           ii    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (132 / 77)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.19 (46 / 21)  


 711 29.65 10.35 4.00  chr1_107105739_107113790      703  1552 (6500)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr1_107105739_    703 AAGATCTATACTATATTCTTAGATGGGAAAACTTAGTATCATTAAAATG- 751
                              --  v i  i   v i   v    i     i   ii    i   -
  L1M4_orf2#LINE/      5 AAGAT--ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_107105739_    752 TAAGTTTCCCCAAAAATTAATATATATTTTT----TAGTTCC----AACA 793
                         i  vvi        --  i  v  i vv  i----i i i  ----  v 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_107105739_    794 CCACAGAT----TTTTTAAAGGGATATGGATAAAGT-ATCTTAAAGTTAG 838
                         i v   v ----     iv  -- v  v  i  iv -   i    i  --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG--AAATTGACAAGCTGATCCTAAAATT-- 146

  chr1_107105739_    839 TATATCAGAATTATA-GGAACTCATAA-AG---AAACAG----GTAATGG 879
                         i    -i   v ii -  i  i  v  -  ---     i---- v  vi 
  L1M4_orf2#LINE/    147 CATAT-GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_107105739_    880 AAGAATA-----------TTCATTCCACCTGATATTAAAAATTATTATAT 918
                              i -----------i   iv iv  ii  v i    v   i  i v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_107105739_    919 ATTTTCTGCAATTCAA-------TTGTATTGTCATAGGAAGAAAAA-ATA 960
                          vi v v i   -   ------- v   i  v    i i v i v -   
  L1M4_orf2#LINE/    246 AGCTACAGTAAT-CAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_107105739_    961 GATCAATGGAACAAAACTAGTAGTTTAGAAATATAACACA-GCATAAGTG 1009
                                    i i  i iiv   ii       -   v  -i   vvi  
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATA-AACCCATACATTTATG 343

  chr1_107105739_   1010 GAGATCCACT-ATTT--GACAAAGGTGGTTTTAA------TTAATCAGCA 1050
                          ---  v i -    --     i    ---ii  ------ i   vi v 
  L1M4_orf2#LINE/    344 G---TCAATTGATTTTCGACAAGGGTG---CCAAGACCATTCAATGGGGA 387

  chr1_107105739_   1051 AATATATAATTTATTTAATAAAGAATGTTGGAACAACTGGCCATCCATCT 1100
                           v -   i i v  i  i   vii  i   i        vi ?   iv 
  L1M4_orf2#LINE/    388 AAGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_107105739_   1101 GGCAATACATAAAGCTGAACTGGTACCTCATAC-ATGAAGAGATACAAAA 1149
                          vv  viv  i   i  i  ivv       i  -  ------        
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT------ATACAAAA 480

  chr1_107105739_   1150 AT-AAATCCAAATGTGTTAAGAAACTAAATGTAAAA--TGAAA-TACATA 1195
                           -  v  v     vi i ?ii v          i -- i   -  i v 
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_107105739_   1196 A-----AGAAAGATAGATA--TGCAAAT----ATAACTTTGGAT-AGGGA 1233
                          -----    ii v v   --? i    ----i i  i    i -   v 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_107105739_   1234 A-AACTTCTTAAACA--AAATGAAAAATCCAGAAGTTTTAAAAGATAAGA 1280
                          -iii      i i -- v iv    i--  v   ivvi      v  i 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAG--CACAAGCAACAAAAGAAAAAA 628

  chr1_107105739_   1281 TAGCTATATTTAACTATGTAGAAATTAAACATTTTTTGTATGGAAAATAA 1330
                            v  v   vi   vii vi        v i    -  iivvv   vi 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTT-GTGCTTCAAAGGA 677

  chr1_107105739_   1331 TACCA-CAAAACAGTAAAAA--------ATAGATT---AAAAAATATTTT 1368
                         i  i -   i v   i    -------- i   v --- i         v
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_107105739_   1369 CAA--CATATTTAACAGAAAAAAAAATTGCTAACCATAGTACAAAAAGAA 1416
                            --     v -- v  v  iii v   -  v   v i  i v      
  L1M4_orf2#LINE/    728 CAAATCATATAT--CTGATAAGGGACTTG-TATCCAGAATATATAAAGAA 774

  chr1_107105739_   1417 CTTTTTCCAAATTCA-TAAGAAAAAGTCAAACCACTTAATAGAGAAATAA 1465
                           i  v --  i   -   v      v    iv  ii   v? i    ii
  L1M4_orf2#LINE/    775 CTCTTAC--AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_107105739_   1466 TCAAATAATACGAACACATAAATAACTGGAGAACAAATCCAAATGTAATT 1515
                         v    vi  vi   i v i vv vv iii    v v  v      --iii
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG--GCC 870

  chr1_107105739_   1516 AATATACA-GTCAGTAGACATATAACCTCATCAGTAGG 1552
                             vi  -i v iv   iiivi   v   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (144 / 104)
Gap_init rate = 0.05 (49 / 904), avg. gap size = 2.49 (122 / 49)  

3102 27.56 0.77 0.66  chr1_107105739_107113790     6653  7559 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_107105739_   6653 TGGAAAAATATTCCATGGTCATGGATAGGAGGAATCAATATCATGAAAAT 6702
                               i    i     v        v   i  v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_107105739_   6703 TGCCATACTGTCCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 6752
                         v  v     vi     v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_107105739_   6753 TACCATTGACTTTCTTCACAGAATTAGAAAAAATTGCTTTAAATTTCATA 6802
                          v   vivi i  i  ii     v v  v  iv viiii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_107105739_   6803 TGGAACCAAAAAGGAGCCTGTATAGCCAAGACAATCCTGGGCAAAAAGAA 6852
                              viiv  i   v  v v        i      i  iiv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_107105739_   6853 CAAAGCTGGAGGTGTCACGCTACCTGACTTCAAACTAAACTACAAGGCTG 6902
                              i      vv    i  v  ii i      vivv       i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_107105739_   6903 CAGTAACAAAAACAGCATGGTACTGGTACCAAAATAGATATGTGGGCCAA 6952
                               iv  i    ii         i iv ii     i  i i ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_107105739_   6953 TGAGAAAGAA--GAGAGGCCTCAGAAATAATCTCACACATCTACAACCAT 7000
                           ii v    --     v  --        v i  i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_107105739_   7001 CTGATCTTTGACAAACCAGACAAAAACAAGCAATGGGGAAAGTATTCCCT 7050
                         i    i  i     ivvv v   i v  vv            v  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_107105739_   7051 ATTTAATAAATGGGGTTGAGAAAACTGGCTAGCCATACGCAGAAAACTGA 7100
                         v  i  i      v i  i  v      v  ?   i i   i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_107105739_   7101 AACTAGACCCCTTCCTTATACCTTATACAAACCTTAACTTGAGATGGATT 7150
                          ii i       v   i i   v        vv      ii i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_107105739_   7151 AAAGACTTAAACATAAGATCTAAAACCATAAAAACCCTAGAAGAAAACCT 7200
                          ?    i    ii     v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_107105739_   7201 AGGCA-ATACCATTCAGGACGT--AATTATGGACAAAGAATTCATGGCTA 7247
                            ?i- v i -   iv   v --ii   -- i   v iv   v i v  
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATA 595

  chr1_107105739_   7248 AGACACCAAAAGCAATGGCAACAAAAAACAAAATTGACAAATGGAATCTA 7297
                         v             vvi         i v     v  i    v i ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_107105739_   7298 ATTAAACTAAAGAGCTTCTGCAGAGCAAAAAGAAACTATCATCAGAGTGA 7347
                           i   v v  i i   i  iivvv    i-  v       vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGA 694

  chr1_107105739_   7348 ACAGGCAACCTATGGAATGGGAGAACATTTTTGCAATCTATCCATCTGAT 7397
                          v  i     i ii           v  v       vii  vi       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_107105739_   7398 AAAGGGCTAATATCCAGAATCTACAAGAAACTTAAACAAATTTACAAGAA 7447
                           i  i  vi          v  i  ii    ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_107105739_   7448 AAAAA--AACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACT 7495
                            i --  i     v   ?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_107105739_   7496 TCTCAAAAGGAGACATTTATGCAGCCAATAAACATATGAAAAAAAGCTCA 7545
                             v    i   i  vi viii        i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_107105739_   7546 TCATCACTGGTCAT 7559
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2670 27.45 1.20 2.51  chr1_107124425_107126389.rev      557  1474 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_107124425_    557 GAATAAGATTTCGTGCTCATGGATAAGAAGAATCGATATCATTAAAATAG 606
                            vi v  ii i  i        vi     v ii    ii    i  i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_107124425_    607 CCATACTTCCCAAAGTAACTCGTAGATTCAATGCTATTCCCATTAAACTA 656
                          v     i      v i iiiii        i  v  i  i  i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_107124425_    657 CCATAGATATTCTTCACAGAGCTAGAAAAAAAAAACT-ATTTTAAAATTC 705
                            vvviiv  i  ii    iv v  v  i-----  -  ii        
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAATTC 147

  chr1_107124425_    706 ATATGGAACCAAAAAAGAGCCCAAATATCCAGG-CAATCCTAAGAAAAAC 754
                                 viiv  ii  v  vi    v   ii-     i i i   i -
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA- 196

  chr1_107124425_    755 AGAA-AAAGCTAGAGGCATCATGCTACTCAACTTCAAACTATACTAAAGG 803
                             -    i i    vv   ii  v i   i      viv     v ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_107124425_    804 GTTACAGTAA-CAAAACAGTATGGTACTGGTATAAGAACTGACACATAGA 852
                          i        -   i     i         i     i iv    i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_107124425_    853 CCAATGAAACAAAATAGATAGTCCATAAATAAGAAGAAATGCCTAAAACT 902
                         i     i  i i   v  v      v      ivvv v iiii  viiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_107124425_    903 ATCTGATCTTTGACAAACTTGGCCAAAACAAG-CAATGGGGAAAGTATTC 951
                          vi    i  i     ivv  -    i  v v-            v  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_107124425_    952 TCTATTCAATAAAAGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGAT 1001
                            v     i   v          i      v  ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_107124425_   1002 TGAAACTGGATCCCTTCCGTACACCATATACAAAAATTAACTCCAAATGG 1051
                             ii    i    v  vi                       v      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_107124425_   1052 ATTAAGGACTTAAATGTAAAACCCAAAAGTATAAAAAACCTTGGAAGACA 1101
                           i ?i   i         i v i    v       v-i   i     v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAA 544

  chr1_107124425_   1102 ACCTAGGCA-ATATCATTCAGGACATGGGCATGGGCATGGGCAAAGATTT 1150
                           v    ?i- v   -   iv   v -----    i- i     v i   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCT-----TGGGT-TAGGCAATGGTTT 587

  chr1_107124425_   1151 CATGAGGAAAATGCCTAAAGCA---ATTACAAAAAAACCCCAAAATTGAC 1197
                          v iiiv vi ii  v      ---iiv      i  ----     v  i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA----AAAATAGAT 633

  chr1_107124425_   1198 AAATGAGATCTAAT-GAAACTAAAGACTTTC-TGCAGAGAAAAAAAAAAT 1245
                             vi  ii v  -i   i    i     i-   vvvi  ii v vv  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_107124425_   1246 CAACAGAGTAAACAGACAGCCTACAGTAGGAGAGAACATTTTTGCAATCT 1295
                            v i   i  v     i  i    v v i     v  v       vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_107124425_   1296 ATCCATTCAACAAAGGTCTAATATCCAGCATCTACAAGGAACTTAAACAA 1345
                           vi  iii i  i  v  vi       v  v  i  i     ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_107124425_   1346 ATTTACAAGAAAAAAACAAACAACCCCATTAAAAAGTGGGCGAAGGACAT 1395
                         v iv i  v     i     i     v   ?    i     i     iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_107124425_   1396 GAACAGACATGTCCTTCTCAAAAGAAGACATACATGTGGCCAACAATAAT 1445
                            i      ----     v        i     vi       i  vv i
  L1M4_orf2#LINE/    834 GAATAGACAT----TTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_107124425_   1446 ATGAAATAAAGCCCAACATTACTGATCAT 1474
                               vi v  i      i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 1.89 (34 / 18)  


3076 26.64 3.05 0.56  chr1_107184937_107189285.rev     2973  3858 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_107184937_   2973 TGGAAGTACATTCCATACTCATGGATAGGAAGAATCAATGTTGTGAAAAT 3022
                              iv i  i    ii        v      v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_107184937_   3023 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3072
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_107184937_   3073 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3120
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_107184937_   3121 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3170
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_107184937_   3171 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTGTACTACAAGGC 3220
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_107184937_   3221 TACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGACC 3270
                                 i   i    ii        ii iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_107184937_   3271 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAATT 3318
                                i    i--    i  --        vv   i    i  iii i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_107184937_   3319 ATCTGATCTTTGACAAACCTGACAAAGACAAGAAATGGGGAAAGGATTCC 3368
                          vi    i  i     ivv  v   iiv  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_107184937_   3369 CTATTTAACAAATGGTGCTGGGAAAACTGGCTCGCCATATATAGAAAGCT 3418
                           v  i                 v      v v?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_107184937_   3419 GAAACTGGATCCCTTCCTTATACCTTATTCAGAAATTAGTTCAAGATGGA 3468
                            ii    i    v   i i   v   v  i      ii    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_107184937_   3469 TTGAAGACTTAAATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAAC 3518
                          ii?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_107184937_   3519 CTAGGCA-ATACCGTTCAGGACATAGGCTTGGGCAAGGACTTCATGTCTA 3567
                         v    ?i- v i -   iv   v v  v  i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_107184937_   3568 AAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTA 3617
                         vi            vvi      i   vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_107184937_   3618 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3667
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_107184937_   3668 CAGGCAACCCACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACC 3717
                         v  i         i             v       vii ivi      iv
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_107184937_   3718 AAGGGCTAATATCCAGAAT---CAAAAAA-------AA---------AAA 3748
                          i  i  vi          ---i   i  -------  ---------   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_107184937_   3749 AAAAC---CAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 3795
                           i  ---i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_107184937_   3796 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAACGCTCAC 3845
                            v        i  vi viii     v  i          i i     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_107184937_   3846 CATCACTGGCCGT 3858
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (143 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.91 (32 / 11)  


2483 26.81 6.64 0.82  chr1_107242012_107244732     1371  2228 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_107242012_   1371 TGGAGATACATTTTGTGTTCATAGGTTG-AAGATACAATATT---AAGAT 1416
                             i v i  iiii       i i   -    ivi      ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_107242012_   1417 AACAATTATTCTTAACTTGATATATAGAATCAATGCAATTCCAATCAAAA 1466
                         ii    vv i ii  v     v  i   v    i     i  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_107242012_   1467 TCCCAGCAAACATTTTTTATA----TTGACAATCTGAATCTAAAGTTTAT 1512
                                viv -      ii ----       v    vi     i  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_107242012_   1513 ACAGAAAGGCAAAAACCCCAAAATAACCAATACA-TCATTGAA------G 1555
                          ii    v    iiiv    i    i    v   -  -     ------ 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAAGAAG 198

  chr1_107242012_   1556 AACACATTAGAAGCACCGATATTATCCAAGATTAAGACTTGTTTTAA-GA 1604
                             v v v i  v  iv i i vi    vv i  i    ii vi  - v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_107242012_   1605 TACAGTGAACAAGACAGAGTGGTATTGGAGAAAGGGCTGACACCTTTATC 1654
                               i v        v      i   viv    iiv    iv vv   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_107242012_   1655 AATGGAATAGAAAAGAAAGCCCAGAAGCTGACCCCT-CAAATATACTCAA 1703
                                     vv  i  i      iivi    v -  vv   iv    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_107242012_   1704 CTGATCACTGACAAAGGAGC-AAGGCAATTCAATGGAAAATGGATAGTCT 1752
                         i    ivii     i  v  -   i v         ii  v i       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_107242012_   1753 TTTTAACAAATGATGCTGGAACAGTTGGTTGTCAATATACAAAAAAAAGT 1802
                            i        i      i   ii   v i? v i  i     i  -- 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--T 446

  chr1_107242012_   1803 AAATCTAGGAATAGTGCTT-ATACCTTCTGCAAAACCTAA-------TGG 1844
                         i  vi -   vivv i i - i   v v i     vi   -------   
  L1M4_orf2#LINE/    447 GAAGTT-GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_107242012_   1845 GTCATTTGCATAAATATAAAAAGCAAAACTATAAAATATTTGGAAGCCAA 1894
                         i   ?vvi v     i   i ivi            ivi  i    --  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG--AA 543

  chr1_107242012_   1895 ATTATGAAAAAAAATCTAGGAAAC---GAGTTTGA-AATGAGTTTTTAGA 1940
                          vi  iii?iv      vv vi  --- i   v i-    iv  i     
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_107242012_   1941 TACAACACCAACAGTACAATCCATA----------TATATATGCTGTATT 1980
                           ii       v  i    v v i ----------  v   vii  v i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_107242012_   1981 TT-TTAAAGCTAAAATCTTCTGTTCTATGAAAGACACTGTTAGGAGAATG 2029
                          i- i   ii     v   i   v  vii  i      i i i  i i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_107242012_   2030 AAAAGACAAGACACAGATGGGGAGAAAATATTTTCAAACGATATATCTGA 2079
                                  vv      vv              v    iv          
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_107242012_   2080 TTAAGGACTTTCATCCA-AATATACAAAGAACTTTTAAAATTTAAGAATG 2128
                          v i      vi     -      i        i   v  i i  v   i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_107242012_   2129 AAG---------------TTTTAAAATGAGCAAAGGATATGAACAGACAC 2163
                           i---------------  ?v      i         v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_107242012_   2164 ATCACCAAAGAAGATATACAGATGTCAAATATGCTTAATAAAAGATGCTC 2213
                         v  v                i   v v    v  vi vv           
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_107242012_   2214 AACATCATTTGTCAT 2228
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (132 / 94)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.05 (64 / 21)  


2483 27.88 1.04 1.96  chr1_107303653_107306160.rev      790  1657 (851)    L1M4_orf2#LINE/L1        1   860 (48)  

  chr1_107303653_    790 TGGAAAAACATTCCATTTTCATGGATAGGAAGAATCACTATTGTGAAAAT 839
                               i i  i    v         v      v i v      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_107303653_    840 GACCATACTGCGCCAAAGTAATTTG-AGATTCAATGCTATTCCCATTAAA 888
                          i v     v -     v i  i i-        i  v  i  i  i   
  L1M4_orf2#LINE/     51 GGCAATACTCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_107303653_    889 CTACCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAAAATCA 937
                         v v   vivi v  i  ii     v v  v  i-  - iii     v   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_107303653_    938 TACAGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAA- 986
                           ii   viiv  ii  v  viv        i      i i iv  i  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_107303653_    987 -ACAAAGCTGGAGGCATCATGCTACTCAACTTCAAACTATACTTACTACA 1035
                         -      i      vv   ii  v i   i      ----          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACTTACTACA 244

  chr1_107303653_   1036 AGGCTACAGTAAACAAAAAAAGCATGGTACTGGTATAAAAACAGACACAT 1085
                          i          v   i v - ii         i    ii i     i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACA-GTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_107303653_   1086 AGACCAATAGAACAGAATAGAGATCTTACAAATAAGGCCACACATCTGCA 1135
                            i    i   i     v    viii v      iv   i    i iii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_107303653_   1136 ACCATCTGACATTCAACAAACCTGATGAAAAGA--AG-CAATGGGAAAAG 1182
                         ii  vi   iv   i    i--- i  vv    -- v-       i    
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAG---GGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_107303653_   1183 GATTCCCTATTTAATGAATTGTGCTGGCAAAATTGACTAGTCATATTGAA 1232
                         i  vvi  v  i  ii   v       v v  i  iv  ?i  i  - v 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-GCA 439

  chr1_107303653_   1233 AAAGTGAAAATTGAAACTGGATCCCTTACTTATACCTTCTACAAATATTA 1282
                             ----   -   ii    i    vv  i i   v v      v    
  L1M4_orf2#LINE/    440 AAAG----AAT-GAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_107303653_   1283 ACTCAAGATGGATTAAAGACTTAAATGTCAAACCCAAAACTATAAAAACC 1332
                               i      i ?    i       v i v i            vi 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_107303653_   1333 CTAGAAGAAAATGTAGGCA-ATACCATTCAGGACATAGGCACAGGCAAAG 1381
                         i          ii    ?i- v i -   iv   v v  vvi      v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chr1_107303653_   1382 ACTTCATGACAAAAACATCAAAAGCAATTGCAACAAAAGCAAAAATTGAC 1431
                         ii   v iivv vi   i        vvv          v      v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_107303653_   1432 AAATGAGATCTAATTAAACTAAAGAGCTTCTGCAAAGCAAAAGAAACTAT 1481
                             vi  ii v  i   v v  i i   i  iivvv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_107303653_   1482 CATCAGAGTGAACAGGCACCCTACAGAATAGGAGAAAAATTTTGCAATCT 1531
                           vv i      v  i  v  i       i        vv       vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_107303653_   1532 ATCCATCTGACAAAGGTCTAATATTTGGCTTCTACCAAGAACTTAAACAA 1581
                           vi      i  i  v  vi   iii vv v  iv       ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_107303653_   1582 ATTTACAAGAATAA-ATAAACAACCCCATTAAAAAGTGGGCAAAGGACAT 1630
                         v iv i  v  v  - i   i     v   ?    i           iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_107303653_   1631 GAACACACACTTCTCAAAAGAAGACAT 1657
                            i v   i     v        i  
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.02 (16 / 860), avg. gap size = 1.62 (26 / 16)  


3801 20.00 2.10 1.77  chr1_107337011_107340735.rev     2332  3236 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_107337011_   2332 TGGAAGGATATCCCATGTTTATAGATTGAAAAACTTAATATTTTTAAGAT 2381
                              i             i  i     i  i          v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_107337011_   2382 GTCAGTACTACCAAAAGAGAATTACAAAT-----GCAATTTCCATCAAAA 2426
                          v  i    v  v   vv  vi    i  -----     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_107337011_   2427 CCTCAAGGACACTTTTTTGTAGAACTAGA-AAACCCACCCTAAAATTTAT 2475
                         i i  ivvi -        i    v v  -  i iv i         i  
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_107337011_   2476 GTGGAG-TGTTATGGGACCCTGATTAACTAAAATAATTTTGAAAGAGAAG 2524
                         i    i-  iv -       v  v  i i    i   i      i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_107337011_   2525 AACAAGACTGGAGTACTAATATTTCCTGATGTCAAAACTTACCACAAAGC 2574
                              iii     v   v i i    ii  v           i       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_107337011_   2575 CACAGTAATCAAAACAATGTGATAGTGGCATAAAAAAACAACAACCCAGT 2624
                         i           i   i    i  v        ii ----------i  -
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA----------TAG- 287

  chr1_107337011_   2625 AACATATAGACCAATCTAAAAGAACAGAGAGCCCAGAAATATACCATTGC 2674
                         -         i    vv  v    iv     i         v   vv i 
  L1M4_orf2#LINE/    288 -ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_107337011_   2675 CTATATAGTCACATAATTTCTGGCAAGGGTGCCGAGAACATTCAATGGGG 2724
                         v v   i    vv i    ii i          i   v            
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_107337011_   2725 GAAAGAACAGTCTTTTCAACAAATGGTGCTGGGAAAACTGGACAACT-CT 2773
                         -      i                          v       i ? i- v
  L1M4_orf2#LINE/    387 -AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_107337011_   2774 TACAAAAGAATGATATCAGACACTTACCTAAAATGATATA-AAAAATTAG 2822
                          i           vi ii   v i     v v iv     -        i
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_107337011_   2823 CTCAAAATATATAAGATATTTACATGTAAGAACTCAAACT-TAAAA-TCT 2870
                                 iv  v ? v ii  v        i  v     -     -   
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_107337011_   2871 TAGGAGAAAACTTACCA--AAAGCTCCAC-ATATTAGATTTGACAATAAT 2917
                            i       v  vv?--   v  i ii- iv  i i  v i    ii 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_107337011_   2918 TTCTTAGATATTGCACCAAAGGCACAGACAACAAAAGAAAACATAGGCAA 2967
                                    vi       i     ii             v    ii  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_107337011_   2968 ATTGGACTTCATAGAAATTAAAACATTTTGTGCATCAAATGATAATATCC 3017
                                     vi         vv        v     v  i v    -
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC- 684

  chr1_107337011_   3018 AACAAAGT-AAAAGGCCACCCACAGAATGGGAAAAAATATTTGCAAAGTA 3066
                           v     -     i v               i              vi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_107337011_   3067 TATACCTGATAAGGGACTAGTATCCAGA-T-CATAGAGAACTCCTAATAC 3114
                             i             v         - -i   i       i  vv  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_107337011_   3115 TCAACAACTAAAAACCAAATAACCTGATTCACA--TGCACAAAAGACTGG 3162
                             i  iv    iv         ii   ? v --  vi    i  i v 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_107337011_   3163 AGTAGACATTTCTCCAAAGAAGATGTACAATTTACCAATAAACACATGAA 3212
                          i                      i     v vi       i        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_107337011_   3213 AAGATGCTCCACATTGCAAATCAT 3236
                                  v    ii????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (106 / 71)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.84 (35 / 19)  


2687 27.60 0.88 1.42  chr1_107469047_107473652.rev     3203  4115 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_107469047_   3203 TAGAAACATATTCCATGCTTATCGATGGGTACAATCAATATTGTGAAAAT 3252
                          i    v    i     i i  v   v  v v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_107469047_   3253 GACCACACTGCCAAAAGCAATCCTA-AAATTCCTTGCAATTCTCATCAAA 3301
                          i v i   v  v   vii   -  - i    vvi     i ii      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATC-TACAGATTCAACGCAATCCCTATCAAA 99

  chr1_107469047_   3302 ATATCACCATCATTCTTCACAGAACTAGA-AAACAAATCTCAAAATTCAT 3350
                           vi  v vv v  i  ii     v v  -  i vi   ii         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_107469047_   3351 ATGGAACAACAACAACAACAAAAGCCTGCATGGCCAAAGCGAGACTAAGC 3400
                               vvi   -------iii v  v v  i      i i vvi i iv
  L1M4_orf2#LINE/    150 ATGGAAATGCAA-------GGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_107469047_   3401 AAAAAAAACAAATCTGGAGGCATTACATTACCTGACTTCAAACTATGCTA 3450
                           i  i      vi      vv i   i v  ii i      viv i   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_107469047_   3451 TAAGGCCATAGTCATCAAAACAGCATGGTACTGGTATAAAAACAGGCACA 3500
                         i  i  i i   v     i    ii         i    ii i  i  i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_107469047_   3501 TAGACCAATGTAACAGAATAGAGAACCCAAAAATAAAGACAAACACTTAC 3550
                             i     v  i     v    ii   i       vv  v   i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_107469047_   3551 AGTCAACTGATCTTTGACAAGACAAACAAAAACA--AAGTGGGGGAAGGA 3598
                         i     i    i  i      ivviv   i v  --v i     i   i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_107469047_   3599 CACCCTATTCAACAAAAGGTGCTGGGATAATTGGCAAGCCACATGTAGAA 3648
                         i vi  v         v          i  i   vv ?       i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_107469047_   3649 AAATGAAACTGGATCCTCATCTCTCACCTTATATAAAAATCAACTCAAGA 3698
                         i      ii    i  ii i   v    v    i      i       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_107469047_   3699 TGGATCAAATACTTAAATAAATCTAAGACCTGAAACCATACAAATTCT-A 3747
                                ? v  i     i----     v  i    i   -   i   - 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATG----TAAGAGCTAAAACTATA-AAACTCTTA 537

  chr1_107469047_   3748 GAAGATAACTTTGGAAAAACACTTCTCGACATTGGCTCAGGCAATGACTT 3797
                              v   v v  ?iv  vv    vi   v    v i        ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_107469047_   3798 CATGACCAAGAATCTAAAAGCTAATGCACCAAAATAAAGA-TATATAGAT 3846
                          v iivi v  vv i      vv v   v     v   i -  v   i  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_107469047_   3847 GATAATTAGTTAAACTAAAAAGCTTCTGCACAGCAAAATAAATAATCATC 3896
                         viv v  vi i   v v    i   i  ii vv    iv v iv    vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_107469047_   3897 AGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCACAATTTATAC 3946
                          i   i  v              i           v  ii   v i   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_107469047_   3947 ATCAGACAAAGGACTAATATCCAGAATCTACAAGGAACTCAAACAAA-AA 3995
                            v  i  i     vi          v  i  i      vv    v-v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_107469047_   3996 ATCAAGAAAAAACAAACAATCCCATCAAAAAGTGGGCTAAGGACA-AAAT 4044
                           v vi    i     i  i  v  i?    i     v     iv-i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_107469047_   4045 AGACAATTATCAAAAAAATATATACAAATGGCCAAAAAAAATATGAAACA 4094
                              v  v  v   i  v                v  iv i      vi
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_107469047_   4095 ATGCTCAACATCACTAATGAT 4115
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (138 / 110)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.91 (21 / 11)  


4460 16.42 1.17 4.98  chr1_107589890_107592046      721  1664 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_107589890_    721 TGGGAAGACATCCTATGTTCATGGATTGGAAG--TCAATGTTGCTAAGAT 768
                            i    i    i                  -- i   i   i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_107589890_    769 GTTAATACTACCCAAAGCTATGTACAGATTTAATAGAATCTCTATCAAAA 818
                          vi      v      viv  v        i  iiv    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_107589890_    819 TCCCA-TTGACGATATTTTCC-GAAATAGAAAACTTCATGCTAAAATTCA 866
                              -i  v -- v    v -     v  v  vi v  v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_107589890_    867 TATAGAATTTTAAGGGACCTGGAAATAGCCAAAATAACATTGAAAAAGAA 916
                            i   v vi        ii   -         i  iv           
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAA-TAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_107589890_    917 GAATAAAGTTAGTGGCGTCACTGGGGTTTTTATGTTGTTGTTCTTTTTTT 966
                            i      i v  vv    ---------- i-----------------
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCAC----------AC----------------- 220

  chr1_107589890_    967 TTTTTTAATTTCAAAACTTACTACAAAGTCACAGTAGTCAAAACTGTGTG 1016
                         -  iii                      ii      i    i  v     
  L1M4_orf2#LINE/    221 -TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_107589890_   1017 GTACTGACATAAAGATAGACATACGAACCAAAGAAATAGAATAGACAGTC 1066
                               i     i          iii i   v i        v  v    
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_107589890_   1067 CCAAAATAAACCCTCACATGTATGGTCAAATAATTTTCAACAACGTTGCC 1116
                          vi          vi    v         v i      i    v v    
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_107589890_   1117 AAGACCATCGAGTGAGGAAAAGACAGTCTTTTCAACAAATGATGTTGGGA 1166
                                 iv i  i     ii i                 i  i     
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_107589890_   1167 AAACTGAACAGTCACATGCAAGAAAAACAAACCAAAAAAGGAAGTTGGAC 1216
                         v     i i ?i         -------------  i  v          
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAA-------------AAGAATGAAGTTGGAC 456

  chr1_107589890_   1217 CCTTACCTTACACCATATACAAAAACTAATTCAAAATGCATTAAAGACCT 1266
                           i     i                i   i        v  i ?      
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_107589890_   1267 AAATGTAAGAGCTAAAACTATGAAATGTTTAGAAAAAAACAAAGGAAGAA 1316
                                              i   ivi      i      v   ?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_107589890_   1317 AACTTCATGACATTAAATCTGGCAATAATTTCTTGGATATAACATCAAAA 1366
                          v    i    v  iii iv      ii      i     i   i     
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_107589890_   1367 GCACAGTCAACAAAAGCAAAAATGGGTAAGTTGAACGTCATCAAAATTAA 1416
                              iv         v      i i   i   i  v             
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_107589890_   1417 CAACTTTTGTGCATCAAAGGACACTGTCAACAAAGTGAAAAAGCAACCCA 1466
                         v           v            i    v          ii       
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_107589890_   1467 CAGAATGGGTGGGAATATTTGTAAATCATATATTTGATAAGGGACTTTTA 1516
                                  v ii        i           i             v  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_107589890_   1517 TCCAGAATGTATAAATTACTCTTACAATTCAACAACAAAA-------TAA 1559
                                 i      vv          i    i  i    -------   
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_107589890_   1560 TCCTAATTAAAAAATGAGCAAAGGACTTAAATAAACATTTCTCCAAAGAA 1609
                         i  -    ?       i        i  i    i                
  L1M4_orf2#LINE/    807 CCC-AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_107589890_   1610 GATATATAAAAATGGTCAATAAACATAGGCAAAGATGCTCAAGATCATTA 1659
                               i   --   i      i  i v v            v    ???
  L1M4_orf2#LINE/    856 GATATACAAA--TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_107589890_   1660 GTCAT 1664
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.85 (98 / 53)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 5.27 (58 / 11)  


 212 26.53 0.00 0.00  chr1_107623669_107626179.rev      774   822 (1689)    L1M4_orf2#LINE/L1        1    49 (859)  

  chr1_107623669_    774 TGAAGAAATATACCTTGTCCATGGGCCAGAAGACTCAATATTGTAAAAA 822
                           i i i    v  v   i     iiii       i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.00 (0 / 0)  

2861 22.64 6.13 4.36  chr1_107623669_107626179.rev     1177  2024 (487)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_107623669_   1177 AAAATGACAATTCTCCCTAAACTTATCAATGGATTCAACGCACTCTCAAG 1226
                           i   i    v     i   i v   v ii           v  -----
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC----- 90

  chr1_107623669_   1227 TAATCCTCTCCTTTGGAGAAAAGCTCAGCAGCTTTTTTTTTTTTTTTTTT 1276
                         ----   v  --------    v i    v  i      vi---------
  L1M4_orf2#LINE/     91 ----CCTATC--------AAAATCCCAGCTGCCTTTTTTGC--------- 119

  chr1_107623669_   1277 AAGAAATTGACAAGCTCATTCTAAAATTTACATGGAAATGTAAAGGGCTT 1326
                         -               v  i        i i         i  i  i ii
  L1M4_orf2#LINE/    120 -AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr1_107623669_   1327 AGAATAGCCAGAACAATTTTTACAAAGAA---CAAAGCTGAAAGATTAAC 1373
                                   i      i  v v      ---     i  i i  i v  
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_107623669_   1374 ACTACCTGATTTCAAGACTTAT---AAAGCTACAGTAATTAAAACAGTGT 1420
                            v  ii       i     i---              i  i       
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_107623669_   1421 GATACTGGTATAAAGATAGAT---TGGA------GAACGGAATATAGCAT 1461
                          i      i    i      i--- i  ------   ii    vv  vi 
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_107623669_   1462 CCAGAAATAGGCC-ACGCATATATACACAACTGATTTTTGACAAAAATGC 1510
                                  ii  - ii   v   ivv   i       i     iii   
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_107623669_   1511 AAAGACACTTCAGTGGAAAAATGATAGTCTTTTCCATAAATGCTGTTAAA 1560
                         v     vv    i   ii   vi           v i     v  i iii
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_107623669_   1561 ACAATTAGATATTCATAT---AATAACTGAACT---ATTCATACCTT-CA 1603
                             i i    ?i  i  ---  vi v    v --- ii v     i-  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_107623669_   1604 TCGCTTACAAAAATTAATTCAAAACTGATCATAGGCTTAAATATGAAACC 1653
                         i iiv            i      iv     ?  i i     i i i v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_107623669_   1654 TAAAACTGTACA-TTTTTACAAGAAAACATAGCAGAAAGTCTTGGTGACC 1702
                                i  v -i i   v            v? v  i    v      
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_107623669_   1703 TTAGATTAGGAAAAGGTTTCTTAGATGTGGCACCAACAGGATGATCCATA 1752
                           i i     v  v            i  i      v  v ii v v i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_107623669_   1753 AA-GAACA------------------CACCTAGATCAA---CTTCTACTC 1780
                           -   v ------------------  i v i  i  ---   i iiv 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_107623669_   1781 TTCAAAAGACAATGTTAAGAGAAGGAAAAGATAAATTGGGAGATCCACAT 1830
                               i    v i i    i iv       i  ---------i     v
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAA---------CCCACAG 709

  chr1_107623669_   1831 ATTGAAATAAAATATTTGCAAAGCATACATGTGACAAAGAATATGCATCC 1880
                          v  ii v              v    i  v   i  i i iv  i    
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_107623669_   1881 AGAATACATAAAGACCTTTCTGAACTCAATAATAGGAAAATAATCAGCCC 1930
                               i       v  i ivv            ii  i i  vi i   
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_107623669_   1931 AATTTTTAAAATGAGCAAAAGTTTTGAACTGACACTTCACCAAGAAAGAT 1980
                             ?v-      i     i v      iv    i   v    ii     
  L1M4_orf2#LINE/    810 AATTWA-AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_107623669_   1981 ATA----TGGCAAATAAGCAAATGAAA-GATGTTCAATG-CAATTAGTTA 2024
                            ----    v        v      -    i    ii-  ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (124 / 64)
Gap_init rate = 0.02 (20 / 863), avg. gap size = 4.45 (89 / 20)  


2824 25.72 2.54 2.32  chr1_107680096_107682371.rev      880  1785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_107680096_    880 TGAAAAAATTTCCCATGTTCATGGGTTGAAAGAATTAATATTGTTAAAAT 929
                           i   i  v              i   i    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_107680096_    930 CACC-CATTACTCAAAGCAATCTA-AAATTCAGTGCAATTCCTATCAAAT 977
                         vi v-i i v i    vii     - i     ii     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_107680096_    978 TTCCAA-TGTCATTTTTCACAGAATCAGAAAAACCAATCCTGAAGTTCAT 1026
                          i   i-  i -     ii     viv  v  i ii     i  i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_107680096_   1027 ATGGAACCCCACCCCCCAAAAAAAGCCCAAATAGCCAAAGCCAAAGCATT 1076
                               ---- iv -----  iiii    i ----- v       i  v 
  L1M4_orf2#LINE/    150 ATGGAA----ATGC-----AAGGGACCCAGA-----ATAGCCAAAACAAT 185

  chr1_107680096_   1077 TCTAAGCAAAAGGAACCAATCCAGAGGCATCACATTTCCTGACTTCAAAT 1126
                         ii i iv  i i    v  viii    vv     i    ii i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_107680096_   1127 TATACTACAAGGCTATAGTAACTGAAACAGCATGGTACTGGTACAAAAAT 1176
                         iv        i    i     iii i    ii         i i  ii  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_107680096_   1177 AGACACATAGATCAATGGAAGAGAATAGAGAATCCAACAATAAAGCCACA 1226
                              i              v     v    i    iv      v   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_107680096_   1227 TACCCTACAACCT-CTGACCTTCCATAAAGTGGACAAAACTAAGCAATGG 1275
                         i ii-  iiii v-i   ii   v i  i vv v   i  i vv      
  L1M4_orf2#LINE/    336 CATT-TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_107680096_   1276 GGAAA-AGCACCCTATTCAATAAACAGTGCTGAGAAAACTGGCTCGCAAT 1324
                              - ii vi  v     i   ii      i  v      v v? v i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_107680096_   1325 ATGCAGAAAAATGAAACTGAACCTCTATCTCAC-CC-TATACAAATATTA 1372
                              i  i      ii  i   i   i     -  -        v    
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_107680096_   1373 ACTCAAGATGGATTAAGGACCTACATATAAGACCTGAAACCATAGAAATC 1422
                               i      i ?i      v  i     v  i    i   i  v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_107680096_   1423 CTGGAAGAAAACCTGGGAGAAACTCTTT-TGCACATCAGCCTAGGCAAAG 1471
                         i i         v i  ? v  v    i-  -  v ii vi       v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATG 583

  chr1_107680096_   1472 AATTTATA---ATGAAGACCGAAAAAACAAATACAACAAAAACAAAAATA 1518
                         iv  iv  ---    v-   i   iv    i--        iv       
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGAC-ACCAAAAGCACAAG--CAACAAAAGAAAAAATA 630

  chr1_107680096_   1519 ATAAAATGGGACTT-----AAACTAAAAAGCTTCTGCATAGCAAAATAAA 1563
                         ivv    v      -----   i      -   i  iiivv    iv v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA 679

  chr1_107680096_   1564 TAATCAACAGAATAAACAGACAACCTACAGAATGGGAGAAG-TATTTAGA 1612
                         iv     v i i i  v        i              i-     iv 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_107680096_   1613 AATTATGCCTCTAA----AGACCAATGTTTAAAATCTACAAGGAACTCAG 1658
                            i  iiv   i ----i   ivi i ii i   v  i  i      vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_107680096_   1659 ATAACTCAACAAGAATAAAACAAACAACCCCATTAAAAACTGGG-ACAGG 1707
                          i       i  v  v  i     i     v   ?    v    - v   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_107680096_   1708 -CATGAACAGACATTTCTCAAAAGAAGACATACAAGTAGCCAACAAACAC 1756
                         -iv    i           v        i      i i     i  i   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_107680096_   1757 ATGAAAAAATTCTCAGTATCACTAATCAA 1785
                                i  v    ii    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (153 / 76)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.91 (44 / 23)  


1835 27.09 1.64 1.31  chr1_107758193_107759794      501  1109 (493)    L1M4_orf2#LINE/L1      298   908 (0)  

  chr1_107758193_    501 CAGTGAAACAGAATAGAAAACTCAGAAATGAGACCACACATCTACAACTG 550
                           i  i  i     v  i iii       i iv   i    i  iiiiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_107758193_    551 TCTGATCTTCAATAAACCTGAAAAAAAAAAACAAGCAATGGGGAAAGGAT 600
                         vi    i   i i  ivv  vv  i v----  vv            i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGAC----CATTCAATGGGGAAAGAAT 393

  chr1_107758193_    601 TCCCTGCTTAATAAATTGTGCTGGGAGAACTGGCTAGCCATATGCAGAAA 650
                         vvi  vi i  i    v         v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_107758193_    651 ATTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGAT 700
                          v    ii         v   i     v                   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_107758193_    701 GGATTAAGAACTTAAACATAAAACTCAAGACTATAAAAACCTTAGAAGAA 750
                             i ?ii  i    ii   i vii  i         vi          
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_107758193_    751 AATGTATGCG-ATACCATTCAAGACATGGGCATGGGCAAAGATTTCATA- 798
                           ii  v ? - v i -   iv   v v  vv i     v i    v  -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_107758193_    799 ACAAAATCACCAAAAGCAATTGCAACAAAAGCAAACATTGACAAATGGGA 848
                          i vi -           vvv          v   v  v  i    v   
  L1M4_orf2#LINE/    593 ATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_107758193_    849 TCTAATTAAACTAAGGAGGTTCTGCACAGCAAAAGAAACTATCATCAGAG 898
                         ii v  i   v v ii iv  i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_107758193_    899 TGAACAGGAATCCTACAGAGTAGAAGAAAATTTTTGCAATCTGTCCATCT 948
                             v  iv v  i     i i i       v       viii vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_107758193_    949 GGCAAAGGCCTAAT-TCCAGCGTCTACAAGGAACT--TAAATTTC--CAA 993
                          ii  i  v  vi -     vi v  i  i     --  v vi  --i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_107758193_    994 GAAAAAAACAAA-AACCCCATTAAAAAGTAGGCAAAGGACATGAACAGAC 1042
                         v     i     -     v   ?    i i         iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_107758193_   1043 ACTTCTCGAAAGAAGACATTCA--TGTGCCAACAAACATATTAAGAAAAA 1090
                          i     v        i  v  --  -     i  i  i  v  -  i v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATG-GCCAATAAGCACATGAA-AAGAT 889

  chr1_107758193_   1091 GCTCAACATCATTGATCAT 1109
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (95 / 66)
Gap_init rate = 0.02 (12 / 611), avg. gap size = 1.50 (18 / 12)  


2197 20.79 2.79 16.75  chr1_107890496_107894749     2723  3761 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr1_107890496_   2723 ATGTTCAGTGATTAGAAGACTCAGTCTTGTTAGGATGTCAAT-TTTCCTA 2771
                                vv    i       i i v      i    v    -i i  i 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_107890496_   2772 TATTGATCTACA-ATTCAATGAGATTCCAATCAAAATCTCAACAAGCTTT 2820
                         v           -      i vi  i  v         i  i v-  i  
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT-GCCTT 113

  chr1_107890496_   2821 TTTATTGGTGAAGTTGACAAGGTGATCGCAAAATTCAT-TTGACATGCAA 2869
                            --  vv   i        v     vi         - v  v      
  L1M4_orf2#LINE/    114 TTT--TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_107890496_   2870 AGGACCAAGGAAACCCAAAACACCTATGAAAAAAGGAAAAGAACAAATTT 2919
                         i     v  i v v        viiv       i----         v  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAG----AAGAACAAAGTT 207

  chr1_107890496_   2920 GGA---CTAACATTGTCTGACTTCAGGACGTCTTATTA----GCTACAGT 2962
                            ---  v   i vi ii i    ii  ---   i  ----        
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAAC---TTACTACAAAGCTACAGT 254

  chr1_107890496_   2963 AATCAAGACAGCATCACATTGGTACAAAGATGGACAAAGAAATCAATGTA 3012
                                    ii vii i   i i  i   i    v v i       v 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_107890496_   3013 ACAAAAT-AACAGTCCAGAAACAGACCTACATATACATATATATGAAGAT 3061
                          i i   -i v          i i   -----------------------
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACC----------------------- 331

  chr1_107890496_   3062 ATATATACACACACATATAGATACACACACATATAAAGATACACACACAC 3111
                         --------------------------------------------------
  L1M4_orf2#LINE/    332 -------------------------------------------------- 331

  chr1_107890496_   3112 GGCATATATACACATAAAGATATATATATACACACACATATATAGTACAT 3161
                         --------------------------------------------------
  L1M4_orf2#LINE/    332 -------------------------------------------------- 331

  chr1_107890496_   3162 ATAAATATATGTGCACATACACATAAAGATATATATACACACATATGTAT 3211
                         ---------------      ------------------------ v   
  L1M4_orf2#LINE/    332 ---------------CATACA------------------------TTTAT 342

  chr1_107890496_   3212 GGACAACACATTATCTACAAACTTACAAAGGCAATCCAGTGGAGAAATAA 3261
                           v   ivv   v  v    ivv i v   i v  i  i   i    v  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_107890496_   3262 TTGCGTTTTCAACAAATGCTGCTGGAGCACCTAGATATCCACATGTAAAA 3311
                          v iv             v      ii  v  i    ?       i    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_107890496_   3312 AAA-----------CCTTA----GTACCATATACAAAAAAAAACCTCAAA 3346
                         i  -----------  i  ----ii              vv   -     
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC-TCAAA 491

  chr1_107890496_   3347 ATGAATCATAAATCTAAATGTAAAACCTAAAACTATAAGCCTTCTAGAAG 3396
                            i    ? i i          i v            iv  ii      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_107890496_   3397 ATAACAAAGGAGAATGTCTTTGTAACTTTGGGGTAGGCAAAGATTTGTTA 3446
                          v    v   ? v vi    i  i  i     v       v i   v   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_107890496_   3447 GATGTAATACCTTTAGCATGATCCATATAAAGAACAAATTAACAAACTGG 3496
                            i i i   vvv    ii v v i -      v    vi i   i   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAATTGG 640

  chr1_107890496_   3497 ACTACATCAAAGGTAAAAACTTCTGTTCTATGTATAACATTATCAAGAGA 3546
                            v       iv         i   v  viiv vi   i        i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_107890496_   3547 ATAAAAAAA-AAGCCACAGATTAGGAGAAG-CATATGGAAATAAAATATT 3594
                         i i    i -  v       v i      i-i  v  v    v v    i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_107890496_   3595 TTATGAAGGACTTTTACCCAAAATATCTAGGGAGCTCTCAAAGCCAAATA 3644
                          v  i i      v  i   i     v  ii  i    i v i iv    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_107890496_   3645 ATAAAAAAATGCATGGCTCA-TTAAAAAGCTGACAAAATATTTGAACAAG 3693
                                i iiv  ii i  -  ?    iiv i    iv       i ii
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_107890496_   3694 CACTTCACCAGCAAAGTTATATAGATGGTAAACAAGCACACAAAAAGATG 3743
                           i   v   ivi   v    i i    iv  i       ii        
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_107890496_   3744 TTCAACATTATTAATGAA 3761
                         i       i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (128 / 84)
Gap_init rate = 0.02 (19 / 894), avg. gap size = 10.68 (203 / 19)  


3232 27.12 0.33 0.22  chr1_107989068_107992780     2314  3220 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_107989068_   2314 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTAAAAAT 2363
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_107989068_   2364 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCCAGC 2413
                            v     v     iv i  i  i        i  v     i   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_107989068_   2414 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 2462
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_107989068_   2463 ATGGAAACAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAACAAAAAGA 2512
                                iiv  ii  v  v v  v     i      i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_107989068_   2513 ACAAAGCTGGAGGCATCACGCTAGCTGACTTCAAGCTATCCTACAAGGCT 2562
                               i      vv    i  vv ii i     iviv v      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_107989068_   2563 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 2612
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_107989068_   2613 ATGGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACAAACATC 2662
                               i     v   ivii         vv   i    i  iiiv  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_107989068_   2663 TGATCTTTGACAATCCTGACAAAAAGAAGAAATGGTGGAAGGATTCCCTA 2712
                             i  i     vvv  v   i vv vvv     v i   i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_107989068_   2713 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 2762
                           i  i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_107989068_   2763 ACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTTAAGATGGATTA 2812
                         ii    i    v   i     v           i  i i  i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_107989068_   2813 AAAGCATAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 2862
                         ? ii v       v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_107989068_   2863 GGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 2911
                           ?i- v i -   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_107989068_   2912 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCCAATT 2961
                                    vvi          vv     v  i    v   iiiv  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_107989068_   2962 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTGAACAG 3011
                            v v  i i   i  ii vv    i  v   ii  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_107989068_   3012 GCAACCTACAGAATGGAAGAAAATTTTTGCAATCTACCCATCTGACAAAG 3061
                         i     i         i       v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_107989068_   3062 GACTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAA 3111
                             vi          v  i         vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_107989068_   3112 TCAAACAACCCA-TCAAAAAGTAGGCAAAGGATATGAACAGACACTTCTC 3160
                         v    i      - i?    i i          v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_107989068_   3161 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 3210
                         v        i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_107989068_   3211 CACTGGCCGT 3220
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


3233 20.10 6.96 1.55  chr1_108006111_108007875      497  1272 (493)    L1M4_orf2#LINE/L1       91   908 (0)  

  chr1_108006111_    497 CTTATCAAAATCCCAGTGATGTTTTCTGCACAAATAGAAAATTCCATTCT 546
                          i              iviiv    i    v    v  v  viiv  i  
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr1_108006111_    547 AAAATTCTTATGGAATCTCAAGGGATTCTGAATAGTCAAAACAATCTTGA 596
                                v       viv       ii v      i              
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_108006111_    597 AAAGGAA---CAAAGCTGGAAGTCTCATACTTACTGACTTGTTTCCAAAA 643
                            i   ---     i    i v    i    v ii i  -----     
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT-----CAAAA 235

  chr1_108006111_    644 CTTATTGCAAAGCCACAATAATCAAAATCATGCGGCACTGGCATACAAAC 693
                             i i      i   i       i ivi  i  i         vii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_108006111_    694 AGGTATATAGACCAACAGAATAGTA--GAGAGCCCAGAAATAAGTCCTCA 741
                           ii       i   ii      v --     i          ii  vi 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_108006111_    742 CATATATGGTCAAATGATTTCCAACAAGG---TTAACACCATTAAATAGG 788
                            v         v      i i      ---ii  v      v   i  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_108006111_    789 GAAAGAATAGCCTTTTCAACAAATGGTGCTGGGAAAACTGGATATCCACA 838
                                   i                       v         ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_108006111_    839 TGTAAAAGAATAAAGGTAGACCCTTCATTACCTTACACCATAAATAAAGA 888
                           i        i   v i     i ----    i        v i   i 
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCT----ACCTCACACCATATACAAAAA 481

  chr1_108006111_    889 ATAACTAAAAATGTTTCAAATACCCAAACATAACAGTTAAAACTATAAAA 938
                         v     v      vv   ? v   i   ii   v  i             
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_108006111_    939 CTTTTACAAGAAAAT---GGGGAAAAACTTTATGACAATAGATTCAGCAA 985
                           i   v       i---  ? v   v   ii    vv i i  vi    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_108006111_    986 TTATTTCTT-------------------CGAG--------------ATTG 1002
                          vi      ------------------- i  --------------  v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_108006111_   1003 ATAAATGGGACTTTGTCAAAATTAAAAACTTTTGTGCCTCACAG-ACAAT 1051
                               v      ii                      i   v  -   v 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_108006111_   1052 ATCAACAGAGTGAAAAGCCAACAGACACAA---GA-AAAGTATTTGCAAA 1097
                              v i         v    vv   v  ---  -   i          
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_108006111_   1098 CCATATGTCTTATAAGGGATTGATATCTGGGATACAAATAAAGAGCTTCT 1147
                         i     i   v        i vi    ii i   i --      i  ii 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATA--TAAAGAACTCTT 779

  chr1_108006111_   1148 ACAACACAAAGACAAAAA-----ACAACTTGATTCAAAAATGGGCAAAGC 1192
                              v   vi i     ----- i   iii   ?              v
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_108006111_   1193 ATTTGAATAGGCATTTTTCCAAAGAGAATATACAAATGGCCAGCAAACAC 1242
                                   i     i        ii               ii  i   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_108006111_   1243 ACAAAGACAATATTCAACATCATTAGTCAT 1272
                          ii  i -i  ii         ????????
  L1M4_orf2#LINE/    880 ATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (101 / 51)
Gap_init rate = 0.02 (14 / 818), avg. gap size = 4.71 (66 / 14)  


3053 26.35 1.43 1.32  chr1_108098192_108105148     5558  6464 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108098192_   5558 TGGAAGAACATCCCATGCTCATGGATAGAAAGAATCAATATCGTGAAAAT 5607
                              ii i        i        v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108098192_   5608 GGCCATACCGCCCAAAGTAATTTGTAGATTCAATGCTACCCCTATTAAGC 5657
                            v    iv      v i  i ii        i  v i      i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_108098192_   5658 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5706
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_108098192_   5707 ATGCAACCAAAAAAAAAAAAAAGTCTGCATAGCCAAGACAATCCTAGGCA 5756
                            ------i   viv  iii vi v v        i      i iiiv 
  L1M4_orf2#LINE/    150 ATG------GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_108098192_   5757 AAAAGAACAAAGCTGGAAGCATCACACTACCTGACTTCAAACTATACTAC 5806
                          i          i    i vv       v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_108098192_   5807 AAGGCTACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGATATAT 5856
                           i          i   i    ii        ii iv ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_108098192_   5857 TGACCAATGGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACA 5906
                         v  i        i     v   ivii         vv   i    i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_108098192_   5907 GCCATCTGATCTTTGACAAACCTAACAAAAAAAAACAATGGGGAAAGGAT 5956
                          i  vi    i  i     ivv iv   i vv vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_108098192_   5957 TCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAACCATATGCAGAAC 6006
                         vvi  v  i  i        i     v      v  ?   i     i  v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_108098192_   6007 ACTGAAACTGGACCCCTTCCTTATACCTTATACAAAAATTAA-----GAT 6051
                          v    ii         v   i i   v              -----i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_108098192_   6052 GGATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGTAGAA 6101
                             i ?    i    ii     v       i      vi i   v    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_108098192_   6102 AACCTAGGCA-ATACCACTCAGGACACAGGCAGAGGCAAAGACTTCATGA 6150
                            v    ?i- v i -i  iv   viv  vvv      v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_108098192_   6151 CTATAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACACATGGGAT 6200
                         v   i            vvi           v     v  i v  v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_108098192_   6201 CT------AATTAAAGATCTTCTACACAGCAAAAGAAACTATCAACAGAG 6244
                         i ------       i -   i iii vv    i  v        v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_108098192_   6245 TGAACAGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTATCCATCT 6294
                             v  i     i       i         v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_108098192_   6295 GACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACACATTTACAA 6344
                           i  i  i  vi          v  i  i     ivv   - i --   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACT--CAA 788

  chr1_108098192_   6345 GAAAAAACAAACAAACAACCCCATCAAAAAGTGTGCAAAGGATATGAACA 6394
                         v  v   v i     i     v  i?    i  v         v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_108098192_   6395 GACACTTCTCAAAAGAAGACATTTATGTGGCCAACACACATATGAAGAAA 6444
                             i     v        i  vi vi       i vi  i     i i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_108098192_   6445 AGCTGATCATCACTGGTCAT 6464
                         v   v v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.50 (25 / 10)  


 212 30.43 8.70 6.52  chr1_108348242_108349842      393   484 (1117)    L1M4_orf2#LINE/L1       13   106 (802)  

  chr1_108348242_    393 CCACACTCCTGGGTAGAGAGATCTGATAC-------ATAACAATATTAAC 435
                            iii  v   i v ii   ii i   i-------  ii     i ---
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT--- 59

  chr1_108348242_    436 TGTCCTCAAATTCATCTGTAAACTGAATGTAGTTCC-ATCAAAACTCCAG 484
                         ---  i      v    ii i i v  i i i i  -       ii    
  L1M4_orf2#LINE/     60 ---CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

Transitions / transversions = 6.00 (24 / 4)
Gap_init rate = 0.03 (3 / 94), avg. gap size = 4.67 (14 / 3)  


1108 25.18 12.29 6.27  chr1_108416709_108424587.rev      502  1331 (6548)    L1M4_orf2#LINE/L1       29   908 (0)  

  chr1_108416709_    502 GAAGACTCAGTATAGAAAAGATGTACCTTCTCTCCAAATTGGTGATAGAG 551
                                i i   v vv      vvvv v   i        i v-  v  
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATC-TACAG 77

  chr1_108416709_    552 ATTCAATGCCAT---TAAAAAAA-CCCACCTGGTTTTTTTGAGGAATTTG 597
                               i  v  ---  vv    -    v   vi       vi   v   
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chr1_108416709_    598 TCAAGCTGAGTCTCAAATTTATATCAAAGAGCAAAGGCCTAAGAATATCC 647
                         v        vi  v     i    vi  iv    i  v iv      v  
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr1_108416709_    648 AGGACATTCCTGAAGAACTGTAAGGA----GCCAGGGGCCT-GCCCTATC 692
                          ii   v  i    i  -- -   i ---- iii i  v  -i v  vi 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAA--G-AAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr1_108416709_    693 AGATACCAAGGGTTGTTATTAAGCCA---TAACCAAGTCAGTGCTGTTTC 739
                         vi  vi   iiv  ii  iv    i ---   i    v     -  v v 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG-TGGTAC 273

  chr1_108416709_    740 T---ACAGAAACAGACAAGTTAACAAGTGAAACATAATAGAGAGCCCAGA 786
                          --- i iii i     vi vi iv i  i  i v   v     i     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_108416709_    787 AACAGACCCATCCATATTTTGG--ATTTGTCACGTGAAAGAAGTAGCTTT 834
                           i i      v   -  v   -- v   vivivi  v iii  -  ---
  L1M4_orf2#LINE/    324 AATAAACCCATACAT-TTATGGTCAATTGATTTTCGACAAGGGT-GC--- 368

  chr1_108416709_    835 GCAAAAC--TT---TGGGAAAAGGAGAGTGTGTGCAATAGATGATGCTCG 879
                         -   i  --  ---    i    i v   v v v   i i   i    v 
  L1M4_orf2#LINE/    369 -CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_108416709_    880 ------TG------CTCATGCAGACAAAAAGGAAATTGGGATACCTGCCT 917
                         ------  ------ v      i -- i  v   i    - iv   i   
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAA--AGAATGAAGTTGG-ACCCCTACCT 464

  chr1_108416709_    918 CTTACCGTACACAAA------------------CACCAACCTAAACGTGA 949
                          vi   i  i     ------------------  ?vi       i  i 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_108416709_    950 AAGTTAAA-CTATAACAGCTTGAGGTGG-----TGGGGAAGAAATATCTT 993
                         i  i    -      v vii v  iv i----- i  ?-- v  -     
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN--GTAA-ATCTT 561

  chr1_108416709_    994 TAT---CTCAGTGTAGGGAAGAATTTATTTTAAAAAGAAGACACAAAAGG 1040
                         ii ---  ii vv    v  vii   v  ---- i v v     v   i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTT----AGATATGACACCAAAAG 607

  chr1_108416709_   1041 CCATACATAGGAATGAAAAGATTGAATTCAGCTGCATTAAAAAGATTAAA 1090
                          ---   -  v  i-      ---  ------------   v    -   
  L1M4_orf2#LINE/    608 C---ACA-AGCAAC-AAAAGA---AA------------AAATAGAT-AAA 636

  chr1_108416709_   1091 TTCAGCTGCGTTAAAATCAAGAGCATCTGTACTT----GGACAGCAT--- 1133
                           vii  v i i     i  i i v i   i   ----     vi  ---
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_108416709_   1134 -AGAGTGGAAAGACAA-----------AGAGAAGGTATTTGCCAG-CTTA 1170
                         - i    i        -----------i     ii       v i- v  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_108416709_   1171 TAACT--TGAAGGATTAGAAT---GAATGATATAAAGAACTATGTA---- 1211
                           v  -- i i   i v v  ---    -            v -  ----
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAAT-ATATAAAGAACTCT-TACAAC 784

  chr1_108416709_   1212 --AATAAGAAAAAGACATACAACC-GGTTAGAAAAACGGGCAAAG-ACAT 1257
                         --     v         v i    -ii  ?-     i        - iv 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTT 833

  chr1_108416709_   1258 GAACAGCATATTTCACGTGAAAGAA-----ACAGCAGTAGCAAATGA--A 1300
                            i  - i     v v--      -----   -- i i  v   i -- 
  L1M4_orf2#LINE/    834 GAATAG-ACATTTCTCC--AAAGAAGATATACA--AATGGCCAATAAGCA 878

  chr1_108416709_   1301 CATGGTAAGAGATGCTCAACA-CGTTTAGTAA 1331
                             --  i            - i????????
  L1M4_orf2#LINE/    879 CATG--AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (117 / 89)
Gap_init rate = 0.06 (52 / 880), avg. gap size = 2.96 (154 / 52)  

3277 27.20 0.44 0.44  chr1_108416709_108424587.rev     6481  7388 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108416709_   6481 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 6530
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108416709_   6531 GGCCATACTGCCCAAGGCAATTTACAGATTCAATGCCATCCCCATCAAGC 6580
                            v     v     ivii  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_108416709_   6581 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6628
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_108416709_   6629 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 6678
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_108416709_   6679 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 6728
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_108416709_   6729 TACAGTAACCAAACCAGCATGGTACTGGTACCAAAACAGAGATATAGACC 6778
                                 i   iv   ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_108416709_   6779 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 6826
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_108416709_   6827 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 6876
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_108416709_   6877 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6926
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_108416709_   6927 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 6976
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_108416709_   6977 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAACCCCTAGAAGAAAAC 7026
                          i ?    i    i  v   v       i       i i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_108416709_   7027 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 7076
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_108416709_   7077 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 7126
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_108416709_   7127 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTGAAC 7176
                          i   v v  i i   i  ii vv    i  v    ii vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_108416709_   7177 AGGCAACCTCCAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 7226
                           i     iv  i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_108416709_   7227 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 7276
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_108416709_   7277 AAACAAACAACCCTATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 7326
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_108416709_   7327 TCGAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 7376
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_108416709_   7377 ATCACTGGCCAT 7388
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3114 26.65 0.66 0.66  chr1_108458335_108465060.rev     5328  6235 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108458335_   5328 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5377
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108458335_   5378 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTAATCCC-ATCAAG 5426
                            v     v      v i  i  i        i  -      -     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAAA 99

  chr1_108458335_   5427 CTACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTGA 5475
                         v v   vivi i  i  ii     v v  v  i-  -  ii    v  v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_108458335_   5476 TATGGAACCAAAAAAGAGCCCGTATAGCCAAGAAAATCTTAAGTAAAAAG 5525
                                viiv  ii  v  v v        i v      i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_108458335_   5526 AGAAAAGCTGGAGGCATCACTTTACCTGACTTTTAACTACACTACAAGGC 5575
                          iv    i      vv    vi v  ii i  iv  vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_108458335_   5576 TACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGATATAGACC 5625
                                 i   i    ii   i     i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_108458335_   5626 AATGGAACAGAAC--AGAGTCCACAGAAATAATGCCACACATCTACAACC 5673
                                i    i--        --       vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCA--GAAATAAACCCATACATTTATGGTC 346

  chr1_108458335_   5674 ATCTGAGCTTTGACAAGCCTGATAAAAACAAGCAATGGGGAAAGGATTCC 5723
                          vi   vi  i      vv  vi  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_108458335_   5724 CCATTTAATAGATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5773
                          iv  i  i i      i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_108458335_   5774 GAAACAGGACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5823
                            iiv        v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_108458335_   5824 TTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5873
                          i ?    i    ii     v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_108458335_   5874 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGGCTTCATGACTA 5922
                         v    ?i- v i -   iv   v v  vv i     v  i   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_108458335_   5923 AAACACCAAAAGCAATTGTGACACAAGCCAAAATTGACAAATGGGATCTA 5972
                         vi            vvv ii   v   vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_108458335_   5973 ATTAAACTAAAGAGCTTCTGCACAGAAAAAGAAACTATCATCAGAGTGAC 6022
                           i   v v  i i   i  ii vvv   i  v       vv i     v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_108458335_   6023 CAGGCAACATACAGAATGGGAGAAAATTTTTACAATCTATCCATCTGACA 6072
                         v  i    vi                 v   i   vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_108458335_   6073 AAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATCTACAAGAAA 6122
                          i  i  vi          v  i  i     ivv    v  v i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_108458335_   6123 AAAACAAACAACCCCATCAAAAACTGGGCAAAGGATATGAATAGATACTT 6172
                           i     i     v  i?    v            v        i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_108458335_   6173 CTCAAAAGAAGACATTTATGCAACCAAGAAACATACGAAGAAAAT-CTCA 6221
                            v        i  vi viiii    v  i  i i   -  i  -    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGATGCTCA 894

  chr1_108458335_   6222 TCATCACTGTTCAT 6235
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.20 (12 / 10)  


2503 22.20 1.89 0.52  chr1_108507990_108512354.rev     2671  3251 (1114)    L1M4_orf2#LINE/L1        1   589 (319)  

  chr1_108507990_   2671 TGGAAAGGAATCCCATGTTTATGGTATGGAAGAATAAATATTGTTAAAAT 2720
                                iv          i    vv       v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108507990_   2721 GTTCATACTGCCCTAAAGTGATCTACAAATTCAAGGCAATCCCTATCAAA 2770
                          viv     -   i   v         i      v               
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_108507990_   2771 ATTCCAATAGCATTTTTCACAGAAATAGAAAAAA-AACTCT-AAATTTGT 2818
                           i   iiv  v     ii       v  v  iv-i ii  -     ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_108507990_   2819 ATGGATCTGCCAAAAAACCAGAATAGACACAGCAGTCCTGAGGAAGAAAA 2868
                              vv   v iii v         v  v i  i  i   ii     i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_108507990_   2869 GCAGAGTTGAAGGGATCATACTAGCTAGTTTCAAATTATATTACAAAGTT 2918
                         i  i     i   iv   i   vv i i       viv  i       i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_108507990_   2919 ATAGTAATCAAAACTGTATGGGACTGGCATTAAAATAGACACATAGACCA 2968
                          i         i  v  i   v        v ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_108507990_   2969 --GGAACAGAATAGATAGCCCAGAAATAAACCCAAGTACAT--ACAGTCA 3014
                         --    i     v  v  i               --     -- ii    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCA 347

  chr1_108507990_   3015 ACTACTTTTTGACCATGCCCCCAATAACATACAATGAGGAAAGGATAGTC 3064
                          i iv    i   v v viv    v v   v     i      i      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_108507990_   3065 TCTTCAATAAATGGTGTTGGGAAAACTGGATATCCACATGCAAAAGAATG 3114
                          i     i        i     v         ?                 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_108507990_   3115 AAATTGGACTCATA---TACAAAATACACAAAAATCAACTCAAAATGGAT 3161
                           i      i v  ---i   vv   i        i              
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_108507990_   3162 TAAATACTTATGTGTAAGA--CAAAATCATAAAACTCCAAGAAGAAAACA 3209
                         i ? v  i  vi       --i    ii         iv           
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_108507990_   3210 AAGGGGAAAGGCTCCTTGACATTGGTCTTGGCAATGACTTTT 3251
                         v   ? v  iv  i v    v    vi v       ii  i 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

Transitions / transversions = 1.42 (74 / 52)
Gap_init rate = 0.01 (8 / 589), avg. gap size = 1.75 (14 / 8)  

 949 22.41 5.69 1.34  chr1_108507990_108512354.rev     3576  3874 (491)    L1M4_orf2#LINE/L1      597   908 (0)  

  chr1_108507990_   3576 GGCAACAAGAGCAAAACTCCGCCAAAAAAAAAAAAAAAAA-AAA--GGAC 3622
                          i  v   i    v  ----  v v    i      v i -   --    
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA----GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_108507990_   3623 CACATCAAACCAAATAGCTTCTGCACAGCAAAGGCAACAATCAACAACAT 3672
                         iv       viv  v i   i  ii vv      vv  v     v  vi 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_108507990_   3673 GAAAAGGCAGCCTATGGATTTGGAGAAAATATTTGCAAGCCATATATCTG 3722
                               i  i  i ii  v v                 ii          
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_108507990_   3723 TTAAGGAGTTTCTATCCAAAATATA--AGGAACTCATAGAACTCAATCAC 3770
                         v     iii  v      i      -- i      v  v        v i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_108507990_   3771 -------CAAATAA----AT-AAAAAATAGACAAAGGACCTGAATAGATA 3808
                         -------       ----  -?      i i       ii        i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_108507990_   3809 TTTCTCCAAAGAGAGCAAACAGATGGCCAGCACATATATGAAAAGTTGCT 3858
                                     iiii v   i       ii vii i        v    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_108507990_   3859 CAATATCACTAATCAT 3874
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (40 / 26)
Gap_init rate = 0.02 (7 / 312), avg. gap size = 3.00 (21 / 7)  


3966 19.50 3.99 0.46  chr1_108528547_108532791.rev     2878  3754 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108528547_   2878 TGGAAAGATGTCCCACGTTCATGGGCTGGAAGACTTAATATTGTTAAGAT 2927
                                  i     i        ii                        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108528547_   2928 GTCTATACTACCCAAAACAATTTACAGATTCAGTGCAATCCCTACCAAAA 2977
                          v v     v      vii  i          ii          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_108528547_   2978 TCCCAA-TGATGAATTTGCAGAAGTAGAAAAACCCATACTAAAATTCACA 3026
                              i-  vivvv         i v  v  i iv  v          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_108528547_   3027 TGGAATCTCAAGGGACCCCAAATAGCCAAAACAATTCTGAAAAAGAAGAA 3076
                              viv          vi               ii             
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_108528547_   3077 CAAAGCAGGAGGACTCAC--TTCTTGATTTCAAAACTTACTGCAAAACAA 3124
                              iv           --   iii               i    i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_108528547_   3125 GAGTGATTAAAACAGTGTGCTACTAACATAAAGACAGAAATATACACCAG 3174
                         v   i  i  i        v    ii     i  i   v     v i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_108528547_   3175 TGGAATAGAATAGAGAGCCAAGAAATAAACACTTAGGCATATGTGCTCAA 3224
                                    v     i v          v v  --   v i  v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATA--CATTTATGGTCAA 348

  chr1_108528547_   3225 ATAATTTTTGACAACAGTGCAAAGACCATTCAATAGGGAAAAGACAGTTT 3274
                         v i     i     vi    v             i      ii i   i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_108528547_   3275 TTTCAACAAATGAAGCTGGGAAAACTGAATATCTGCATGCAAAAGAATGA 3324
                                     iv       v     i   ? ii               
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_108528547_   3325 CATTGGACCCTTAATTAACACCCTAT-TAAAAATTAATTCAAAAAGGATC 3373
                         vi        i  vi v     v   -i         i      v     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_108528547_   3374 TATGACCTACATGTAACTCTTAAAATTATGAAACTTTAGAGAAGACGACA 3423
                         v?v      v      vvvi     i   i     i -v      vi   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAACA 547

  chr1_108528547_   3424 CAGGGCAAAATCTTCTCGACAATGGATTTGGCATTGATTTCTTAGACATG 3473
                         i   ?vv        vi   vv   i  v    v  i         i   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_108528547_   3474 ACATCAAAGGTACAGGCAACCAAA------ACACGACAAATTGGACTTCA 3517
                            i    i i   i     v   ------ i -  i             
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTCA 646

  chr1_108528547_   3518 TGAAAATTTAAAACTTT-GTGC-------------ATCAA--AAGTAAAA 3551
                          v      v        -    -------------     --    i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_108528547_   3552 AGGAGACTCATAAAACCGAAGTAAACATTTGCAAATCATATATATAATAA 3601
                           ivi  i  i i  iv i  v   i                 v i    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_108528547_   3602 GGGGTTCATATACAAACTATACAGAAAACTCCTAAAAATCAACAACAAAA 3651
                            ii ii   v  i v    i i i     i  v  v    i  i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_108528547_   3652 AAA-----AACCTAATTTGAAAATGAACAAAGAACTTG----GACATTTC 3692
                          i -----    i    ?i      ii     i i   ----        
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_108528547_   3693 TCCAAAGAAGTTATACAAATGGCTACTAAGCACATGTAAAGATGCCCAGC 3742
                                   v            i v          v        i  i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_108528547_   3743 ATCACTAAAGAG 3754
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (101 / 66)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.25 (39 / 12)  


 968 32.10 5.28 3.14  chr1_108539920_108541611.rev      504  1204 (488)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr1_108539920_    504 AAGGGGGACAAAGAGGAAGTATTTAC-TTTACCAGGT-CAGTATTATACT 551
                            ii i      vv i  v i i  -i  v   iv -  iv i -    
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACT 241

  chr1_108539920_    552 ACACAACCATAGTCATAAAGACAGTTCAATATTGGCATTAAAAAAGA--- 598
                            v i i i   v  v        viii  i      v ii v   ---
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_108539920_    599 --AAA-CAATGGAACAGAAAAGGAAGCTCAAGAAAATATCCAAGTATTTA 645
                         -- i -        i    vv ii  ii  ii  v v i   vii     
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_108539920_    646 TGG--AAGCTTGATGTGTGAGAAAGGTGGCATCACAAATGAATGTGAAAA 693
                            --  --     v vi  v  i    v  vv  v v v    v i   
  L1M4_orf2#LINE/    342 TGGTCAA--TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_108539920_    694 GAAT--TCAATGTTTAGTAGGGTATACTGGGAAAATTCCCT--CTACATA 739
                             --  -- v  i ii iivvi i      v  i vvv -- i    i
  L1M4_orf2#LINE/    390 GAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_108539920_    740 TAAAAATAATAAAATCAGAGCCCTGCTTTTAATCATGTAGAAATGTGAAC 789
                         i    i-   i  i ii  v    i i ivv i   i  v   vi v   
  L1M4_orf2#LINE/    438 CAAAAG-AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_108539920_    790 TAACAGATGCATTAAAGGCCTAAATGTAAAAGCAGAAACCATAGAACTAA 839
                          v - i   v  i ?  i           i   vi    i   i    vv
  L1M4_orf2#LINE/    487 TCA-AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_108539920_    840 TAGAAGA---TACAGA---ACGTCTTTGTGACCAAGAGGTAGGAAAGTAC 883
                                ---i i  i--- vi    i      vv i v    v  vvii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_108539920_    884 TTCTTA-ATAAGATACCAAAATTGTAAACCAT-----------TACATAT 921
                               -   v  i       viii  i v i-----------  v   v
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_108539920_    922 TTTGTGGATTTACTCACCAAAAATCAAATATTTCTGTTCAACCAGGAATA 971
                         v   --  i  ---  i     - i   v i  i   v vv v i i i 
  L1M4_orf2#LINE/    636 ATTG--GACTT---CATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_108539920_    972 TCATGGACAAAACAAAGAAACAACAGACA-AATGGCATACTAGAAAAAAT 1020
                         ii  vi v   iii  i i     vv   -     -------  i     
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGG-------GAGAAAAT 722

  chr1_108539920_   1021 ATGTGCACGTCAAA-GTACAACAAAG-ATTACTATCTAAGATAAATATGT 1068
                           v    vi   v -i vii i  i - i vv    i ii   v   viv
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_108539920_   1069 AACTCTTATGAAACATTAGGGACATGATAGAAAATCCA--TAAAAAACTA 1116
                                 ii vv  v  ivi v v  i i v  i   -- ?     - i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TG 821

  chr1_108539920_   1117 GATAAAGCATATAAACAGACAATTCATAGAAAAGAACATGTGAATGTCTA 1166
                          ii    v  v i  i     v   vivi  i ii i  iii    v i 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_108539920_   1167 ATATTCCTATGAAGAGATGTTCAAAATGTACTAGGAAT 1204
                            vv vi     i     i    v  -i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACAT-CAZZZZZZZZ 908

Transitions / transversions = 1.40 (130 / 93)
Gap_init rate = 0.04 (26 / 716), avg. gap size = 2.27 (59 / 26)  


2885 26.14 1.41 2.93  chr1_108553172_108558930.rev     4347  5268 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108553172_   4347 TAGAAAAACATTC-ATTCTCATGGATAGGAAGCATCAGTCTTGTTAAAAT 4395
                          i    i i  i -  vi        v     vv i i v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108553172_   4396 GGCTATACTGCCCAAAGCAATTTATAGATTCAATGCTGTTCA-GTCAAAC 4444
                            v     v      vii  i  i        i  vi i v-i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_108553172_   4445 TACCAATGACATTCTTCCAATGTCAAACTACCAATGACAGAACTAGAGAA 4494
                          v   iivi v  i  ----  ivi  v -----     - i  i-----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT----TGCAGAAAT-----TGACA-AGCTG----- 135

  chr1_108553172_   4495 AAACTATTTTAAAATTCATATGGAACCAAAAAAGAGCCTACATAGCCAAG 4544
                         -----  ii                viiv  ii  v  viv        i
  L1M4_orf2#LINE/    136 -----ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr1_108553172_   4545 ACAATCCTAAGCAAAAAGTACAAAGCTAGAGGCATCACATTACCCAACTT 4594
                               i i iv  i   v      i i    vv     i v     i  
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_108553172_   4595 CAAACTATGCTACTGGGCTCTTGTAACCAA-ACAGCAAGACACTGGTACA 4643
                             viv i    vii   viv    i   -    iiv ii     i i 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_108553172_   4644 AAAACAGACATACAGACCAAGGGAACAGAATAGAGAGCCCAGAAATAAGG 4693
                          ii i       i   i   v    i     v     i          iv
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_108553172_   4694 ATACACACCTACAA-CTATCCTGATCTTTGAAAAAGTTGACAAAAACAAG 4742
                         vi i   ii  iii- v  --    i  i  v  i v  v   i v  vv
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAAT--TGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_108553172_   4743 CAATGAGGAAAGGACTCCCTATTCAATAGATGGTGCTGGGATAACTGGCT 4792
                              i      i ivvi  v     i i            i      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_108553172_   4793 AGCCATGTGCAGAAGATTGAAACTGGATCCCTTCTTTGCACCGTATACAA 4842
                          ?   ii    i    v    ii    i    v i ii    i       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_108553172_   4843 AAATCAACTTGAGATGAATTAAAGATTTTAAATGTAAAACATAAAACTAT 4892
                             i    ii i   i  i ?   ii -        i vv         
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCT-AAATGTAAGAGCTAAAACTAT 527

  chr1_108553172_   4893 AAAAATCCTGGAAGATAGCCTAAG---AAATACCATTCTGGATATAGGAA 4939
                             v  i i     v i v  i ---    -- -   vv  iv v  iv
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGT 574

  chr1_108553172_   4940 AGGGCAAAGATTTCAT-GATGAAGACACCAAAAGCAATCGCAACAAAAGC 4988
                         vi     v i    v -   - v             vvv          v
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_108553172_   4989 AAAAATTGACAAATGGGATCTAACTAAACTAAAGAGCTTCAGCACAGCAA 5038
                               v  i    v   ii v ii   v v  i i   iv ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_108553172_   5039 AAGAAACTATCAACAGAGTAAACAGACAACCTACAGAATGGGAAAAAGTA 5088
                          i  v        v i   i  v        i           i   i  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_108553172_   5089 TTTGCAAACTATACATCTGACAAAGGTCTAATATCTATCATCTATGAGGA 5138
                                 ii   i      i  i  v  vi    i vv  v   i i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_108553172_   5139 ACT--TA-AATTTA-CAAGAAAAAAA-ATATAACTTCATTAAAAAGTGGA 5183
                            --  -  i i -i  v     i - v     iiv   ?    i   i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_108553172_   5184 CAAAGGACATGAACAGGCACTTTTCAAAAGAAGACATACACATGGCCAAC 5233
                                iv    i  i  i  i  v        i     v        i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_108553172_   5234 AAGCATATGAAAAAATGTTCAATATCAATAATATG 5268
                              i       i   i    i    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (149 / 89)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.11 (40 / 19)  


3460 23.88 2.46 1.12  chr1_108574518_108580017.rev     4114  5009 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108574518_   4114 TAGAAAGACATCC-ATGTCCAATGATTGAAAGAATTAACATTGTTCAAAT 4162
                          i      i    -    i  vv     i    v    i      v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108574518_   4163 GTCTATACTACCCAAAGCTATCTACAAATTCAATGCAATCCCCA--AAAA 4210
                          v v     v      viv       i      i        i --    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_108574518_   4211 TTCCAATGTTATTCCTTCTATAGAAATTTTTTAAA--AATCCTAAAATTC 4258
                          i   -- i iiiii  i ii       vvi-  i--i            
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTC 147

  chr1_108574518_   4259 ATCTGAAACCACAAAAGACCCTGAATAGACAAATCAGTCTTGCGCAAGAG 4308
                           v  i  vii   ii     v      v    v  i     viv    i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_108574518_   4309 GAACAAAGCTGG-GAACATAACCACTTTCCAATTTCAAAACATACTAATT 4357
                                 i   - i  vi --     i             v     ---
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCA--CACTTCCCAATTTCAAAACTTACTA--- 242

  chr1_108574518_   4358 ATAAAGCTATAATAACCAAAGGAGGATGGTA-----GTAAAGACAGACAA 4402
                         -i       i i   i   iiv  vi     -----i   i  i     v
  L1M4_orf2#LINE/    243 -CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_108574518_   4403 CTAGACCAATGGAACAGAAGAGAAAGCCTAGAAATAAACCCATTTATCTA 4452
                         v    i        i    vv  i  i i              vi  i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_108574518_   4453 CAGTCAACTGACCTTTGATAAGA-TGCCAAACACATGGAATGGGGAAAAG 4501
                         ii     i   ii  i  i   i-      ivv   vv          ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_108574518_   4502 ATAGTCTCTTCAACAAACAGTGTTGGAAAAATTGGATATTCACATGTAGA 4551
                                i         ii   i   i v  i      ?i      i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_108574518_   4552 AGAAAGA-----GACCCTTATGTCACACCATATACAAAAACCAACTAAAA 4596
                             v  -----     i  iv                  ii    v   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_108574518_   4597 ATGGATTAAAAACTTAAACATCAGGCCTAAAACAATACCACTACTAGAAG 4646
                               i ? i  i    ii v  iv       v   vv   vi      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_108574518_   4647 GAAACATAGGGGAAAAGCTTCTTGACATTCATCTGGGCGATGATTTTTCA 4696
                         i         ? v   v    v    v  vivi i   i   i   i i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_108574518_   4697 GATATGATACCAAA-GCATAGGTAGCAAAAGCAAAAATAAACAAGAGCAA 4745
                                i      -   i i i i      v       i i  ivvvi 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_108574518_   4746 TTACATCAAACTAAATATCTTCTGCATAGCAAAGGAAATAACTGGCAGAG 4795
                         i v       v v  v v   i  iiivv       v iv iiiiv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_108574518_   4796 TGAAAAGGCATCCTACAGAATGGGAGAAAATATTTGCAAATCATATTTCT 4845
                                i  v  i                                v   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_108574518_   4846 GATAAGAGTTTAGTATGCAAAATAGGTAAGGAACTCACGCAACTCAATAG 4895
                               i vi v    v  i    vi   i      vii          i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_108574518_   4896 CAAAAGAAACAAA----CTGATTGTAAAATAAACAAAGAACTTGAGTAGA 4941
                         i    - i     ---- ii   ?v     iii     i i    i    
  L1M4_orf2#LINE/    792 TAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_108574518_   4942 CGTTTCTTCAAAGAAGACATACAAATGGCCAACAGGTATATGAAAAGCTC 4991
                          i     i         i              i i i i        v v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_108574518_   4992 CTTAACATCACTAATAAT 5009
                           i       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (139 / 71)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.29 (32 / 14)  


3229 26.04 0.55 1.20  chr1_108613226_108619581.rev     4952  5865 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108613226_   4952 TGGAAGAACATTCCATGCTCATGGATAGGACAAATCAATATTGTGAAAAT 5001
                              ii i  i     i        v   vi v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108613226_   5002 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5051
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_108613226_   5052 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAAACTACTTC-AAAGTTC 5099
                          v    ivi i  i  ii     -   --- v  i  iv i -   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_108613226_   5100 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5149
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_108613226_   5150 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5199
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_108613226_   5200 CTACAGTAACCAAACCAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5249
                                  i   iv   ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_108613226_   5250 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5297
                                 i    i--    i  --        vv   i    i  iii-
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG- 344

  chr1_108613226_   5298 TATCTATCTGATCTTTGACAAACCTGACAAAAATAAGAAATGGGGAAAGG 5347
                         --  v  -    i  i     ivv  v   i vi vvv           i
  L1M4_orf2#LINE/    345 --TCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_108613226_   5348 ATTCCCTATTTAAAAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGA 5397
                           vvi  v  i  v              v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_108613226_   5398 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAG 5447
                          iiv    ii    i    v   i     v              i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_108613226_   5448 ATGGATTAAAGACTTAAATGTTAGACCTAAAACCATGAAAACCCTAGAAG 5497
                               i ?    i       v   v       i  i   vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_108613226_   5498 AAAACCTAGGCA-ATACCATTCAGTACATAGGCATGGGCAAGGACTTCAT 5546
                              v    ?i- v i -   ivv  v v  vv i     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_108613226_   5547 ATCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 5596
                          vv  vi            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_108613226_   5597 ATCTAATTGAACTAAAGAGCTTCTGCACAGGAAAAGAAACTACCATCAGA 5646
                          ii v  ii  v v  i i   i  ii vvv   i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_108613226_   5647 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATC 5696
                              v  i     i                 v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_108613226_   5697 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACA 5746
                            i  i  i  vi          v  i  v      iv    -i i vv
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAAT 789

  chr1_108613226_   5747 AAAAAAAAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAAGAG 5796
                           v     i     i     v  i? v  i     i      v    v  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_108613226_   5797 ACACTTCTCAAAAGAAGACATTTATGCAGCTAACAGACACATGAAAAAAT 5846
                            i     v        i  vi viii  i  i ii          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_108613226_   5847 GCTCATCATCACTGGCCAT 5865
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (135 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2885 26.14 1.41 2.93  chr1_108644971_108650535     4151  5072 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108644971_   4151 TAGAAAAACATTC-ATTCTCATGGATAGGAAGCATCAGTCTTGTTAAAAT 4199
                          i    i i  i -  vi        v     vv i i v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108644971_   4200 GGCTATACTGCCCAAAGCAATTTATAGATTCAATGCTGTTCA-GTCAAAC 4248
                            v     v      vii  i  i        i  vi i v-i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_108644971_   4249 TACCAATGACATTCTTCCAATGTCAAACTACCAATGACAGAACTAGAGAA 4298
                          v   iivi v  i  ----  ivi  v -----     - i  i-----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT----TGCAGAAAT-----TGACA-AGCTG----- 135

  chr1_108644971_   4299 AAACTATTTTAAAATTCATATGGAACCAAAAAAGAGCCTACATAGCCAAG 4348
                         -----  ii                viiv  ii  v  viv        i
  L1M4_orf2#LINE/    136 -----ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr1_108644971_   4349 ACAATCCTAAGCAAAAAGTACAAAGCTAGAGGCATCACATTACCCAACTT 4398
                               i i iv  i   v      i i    vv     i v     i  
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_108644971_   4399 CAAACTATGCTACTGGGCTCTTGTAACCAA-ACAGCAAGACACTGGTACA 4447
                             viv i    vii   viv    i   -    iiv ii     i i 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_108644971_   4448 AAAACAGACATACAGACCAAGGGAACAGAATAGAGAGCCCAGAAATAAGG 4497
                          ii i       i   i   v    i     v     i          iv
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_108644971_   4498 ATACACACCTACAA-CTATCCTGATCTTTGAAAAAGTTGACAAAAACAAG 4546
                         vi i   ii  iii- v  --    i  i  v  i v  v   i v  vv
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAAT--TGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_108644971_   4547 CAATGAGGAAAGGACTCCCTATTCAATAGATGGTGCTGGGATAACTGGCT 4596
                              i      i ivvi  v     i i            i      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_108644971_   4597 AGCCATGTGCAGAAGATTGAAACTGGATCCCTTCTTTGCACCGTATACAA 4646
                          ?   ii    i    v    ii    i    v i ii    i       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_108644971_   4647 AAATCAACTTGAGATGAATTAAAGATTTTAAATGTAAAACATAAAACTAT 4696
                             i    ii i   i  i ?   ii -        i vv         
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCT-AAATGTAAGAGCTAAAACTAT 527

  chr1_108644971_   4697 AAAAATCCTGGAAGATAGCCTAAG---AAATACCATTCTGGATATAGGAA 4743
                             v  i i     v i v  i ---    -- -   vv  iv v  iv
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGT 574

  chr1_108644971_   4744 AGGGCAAAGATTTCAT-GATGAAGACACCAAAAGCAATCGCAACAAAAGC 4792
                         vi     v i    v -   - v             vvv          v
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_108644971_   4793 AAAAATTGACAAATGGGATCTAACTAAACTAAAGAGCTTCAGCACAGCAA 4842
                               v  i    v   ii v ii   v v  i i   iv ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_108644971_   4843 AAGAAACTATCAACAGAGTAAACAGACAACCTACAGAATGGGAAAAAGTA 4892
                          i  v        v i   i  v        i           i   i  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_108644971_   4893 TTTGCAAACTATACATCTGACAAAGGTCTAATATCTATCATCTATGAGGA 4942
                                 ii   i      i  i  v  vi    i vv  v   i i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_108644971_   4943 ACT--TA-AATTTA-CAAGAAAAAAA-ATATAACTTCATTAAAAAGTGGA 4987
                            --  -  i i -i  v     i - v     iiv   ?    i   i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_108644971_   4988 CAAAGGACATGAACAGGCACTTTTCAAAAGAAGACATACACATGGCCAAC 5037
                                iv    i  i  i  i  v        i     v        i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_108644971_   5038 AAGCATATGAAAAAATGTTCAATATCAATAATATG 5072
                              i       i   i    i    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (149 / 89)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.11 (40 / 19)  


 968 32.10 5.28 3.14  chr1_108662096_108663787      502  1202 (490)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr1_108662096_    502 AAGGGGGACAAAGAGGAAGTATTTAC-TTTACCAGGT-CAGTATTATACT 549
                            ii i      vv i  v i i  -i  v   iv -  iv i -    
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACT 241

  chr1_108662096_    550 ACACAACCATAGTCATAAAGACAGTTCAATATTGGCATTAAAAAAGA--- 596
                            v i i i   v  v        viii  i      v ii v   ---
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_108662096_    597 --AAA-CAATGGAACAGAAAAGGAAGCTCAAGAAAATATCCAAGTATTTA 643
                         -- i -        i    vv ii  ii  ii  v v i   vii     
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_108662096_    644 TGG--AAGCTTGATGTGTGAGAAAGGTGGCATCACAAATGAATGTGAAAA 691
                            --  --     v vi  v  i    v  vv  v v v    v i   
  L1M4_orf2#LINE/    342 TGGTCAA--TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_108662096_    692 GAAT--TCAATGTTTAGTAGGGTATACTGGGAAAATTCCCT--CTACATA 737
                             --  -- v  i ii iivvi i      v  i vvv -- i    i
  L1M4_orf2#LINE/    390 GAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_108662096_    738 TAAAAATAATAAAATCAGAGCCCTGCTTTTAATCATGTAGAAATGTGAAC 787
                         i    i-   i  i ii  v    i i ivv i   i  v   vi v   
  L1M4_orf2#LINE/    438 CAAAAG-AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_108662096_    788 TAACAGATGCATTAAAGGCCTAAATGTAAAAGCAGAAACCATAGAACTAA 837
                          v - i   v  i ?  i           i   vi    i   i    vv
  L1M4_orf2#LINE/    487 TCA-AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_108662096_    838 TAGAAGA---TACAGA---ACGTCTTTGTGACCAAGAGGTAGGAAAGTAC 881
                                ---i i  i--- vi    i      vv i v    v  vvii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_108662096_    882 TTCTTA-ATAAGATACCAAAATTGTAAACCAT-----------TACATAT 919
                               -   v  i       viii  i v i-----------  v   v
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_108662096_    920 TTTGTGGATTTACTCACCAAAAATCAAATATTTCTGTTCAACCAGGAATA 969
                         v   --  i  ---  i     - i   v i  i   v vv v i i i 
  L1M4_orf2#LINE/    636 ATTG--GACTT---CATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_108662096_    970 TCATGGACAAAACAAAGAAACAACAGACA-AATGGCATACTAGAAAAAAT 1018
                         ii  vi v   iii  i i     vv   -     -------  i     
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGG-------GAGAAAAT 722

  chr1_108662096_   1019 ATGTGCACGTCAAA-GTACAACAAAG-ATTACTATCTAAGATAAATATGT 1066
                           v    vi   v -i vii i  i - i vv    i ii   v   viv
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_108662096_   1067 AACTCTTATGAAACATTAGGGACATGATAGAAAATCCA--TAAAAAACTA 1114
                                 ii vv  v  ivi v v  i i v  i   -- ?     - i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TG 821

  chr1_108662096_   1115 GATAAAGCATATAAACAGACAATTCATAGAAAAGAACATGTGAATGTCTA 1164
                          ii    v  v i  i     v   vivi  i ii i  iii    v i 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_108662096_   1165 ATATTCCTATGAAGAGATGTTCAAAATGTACTAGGAAT 1202
                            vv vi     i     i    v  -i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACAT-CAZZZZZZZZ 908

Transitions / transversions = 1.40 (130 / 93)
Gap_init rate = 0.04 (26 / 716), avg. gap size = 2.27 (59 / 26)  


3991 19.38 3.99 0.46  chr1_108670918_108675161     2875  3751 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108670918_   2875 TGGAAAGATGTCCCACGTTCATGGGCTGGAAGACTTAATATTGTTAAGAT 2924
                                  i     i        ii                        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108670918_   2925 GTCTATACTACCCAAAACAATTTACAGATTCAGTGCAATCCCTACCAAAA 2974
                          v v     v      vii  i          ii          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_108670918_   2975 TCCCAA-TGATGAATTTGCAGAAGTAGAAAAACCCATACTAAAATTCACA 3023
                              i-  vivvv         i v  v  i iv  v          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_108670918_   3024 TGGAATCTCAAGGGACCCCAAATAGCCAAAACAATTCTGAAAAAGAAGAA 3073
                              viv          vi               ii             
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_108670918_   3074 CAAAGCAGGAGGACTCAC--TTCTTGATTTCAAAACTTACTGCAAAACAA 3121
                              iv           --   iii               i    i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_108670918_   3122 GAGTGATTAAAACAGTGTGCTACTAACATAAAGACAGAAATATACACCAG 3171
                         v   i  i  i        v    ii     i  i   v     v i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_108670918_   3172 TGGAATAGAATAGAGAGCCAAGAAATAAACACTTAGGCATATGTGCTCAA 3221
                                    v     i v          v v  --   v i  v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATA--CATTTATGGTCAA 348

  chr1_108670918_   3222 ATAATTTTTGACAACAGTGCAAAGACCATTCAATAGGGAAAAGACAGTTT 3271
                         v i     i     vi    v             i      ii i   i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_108670918_   3272 TTTCAACAAATGAAGCTGGGAAAACTGAATATCTGCATGCAAAAGAATGA 3321
                                     iv       v     i   ? ii               
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_108670918_   3322 CATTGGACCCTTAATTAACACCCTAT-TAAAAATTAATTCAAAAAGGATC 3370
                         vi        i  vi v     v   -i         i      v     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_108670918_   3371 TATGACCTACATGTAACTCTTAAAATTATGAAACTTTAGAGAAGACGACA 3420
                         v?v      v      vvvi     i   i     i -v      vi   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAACA 547

  chr1_108670918_   3421 CAGGGCAAAATCTTCTCGACAATGGATTTGGCATTGATTTCTTAGACATG 3470
                         i   ?vv        vi   vv   i  v    v  i         i   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_108670918_   3471 ACATCAAAGGTACAGGCAACCAAA------ACACGACAAATTGGACTTCA 3514
                            i    i i   i     v   ------ i -  i             
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTCA 646

  chr1_108670918_   3515 TGAAAATTTAAAACTTT-GTGC-------------ATCAA--AAGTAAAA 3548
                          v      v        -    -------------     --    i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_108670918_   3549 AGGAGACTCATAAAACGGAAGTAAACATTTGCAAATCATATATATAATAA 3598
                           ivi  i  i i  i  i  v   i                 v i    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_108670918_   3599 GGGGTTCATATACAAACTATACAGAAAACTCCTAAAAATCAACAACAAAA 3648
                            ii ii   v  i v    i i i     i  v  v    i  i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_108670918_   3649 AAA-----AACCTAATTTGAAAATGAACAAAGAACTTG----GACATTTC 3689
                          i -----    i    ?i      ii     i i   ----        
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_108670918_   3690 TCCAAAGAAGTTATACAAATGGCTACTAAGCACATGTAAAGATGCCCAGC 3739
                                   v            i v          v        i  i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_108670918_   3740 ATCACTAAAGAG 3751
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (101 / 65)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.25 (39 / 12)  


2503 22.20 1.89 0.52  chr1_108691350_108695708     2664  3244 (1115)    L1M4_orf2#LINE/L1        1   589 (319)  

  chr1_108691350_   2664 TGGAAAGGAATCCCATGTTTATGGTATGGAAGAATAAATATTGTTAAAAT 2713
                                iv          i    vv       v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108691350_   2714 GTTCATACTGCCCTAAAGTGATCTACAAATTCAAGGCAATCCCTATCAAA 2763
                          viv     -   i   v         i      v               
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_108691350_   2764 ATTCCAATAGCATTTTTCACAGAAATAGAAAAAA-AACTCT-AAATTTGT 2811
                           i   iiv  v     ii       v  v  iv-i ii  -     ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_108691350_   2812 ATGGATCTGCCAAAAAACCAGAATAGACACAGCAGTCCTGAGGAAGAAAA 2861
                              vv   v iii v         v  v i  i  i   ii     i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_108691350_   2862 GCAGAGTTGAAGGGATCATACTAGCTAGTTTCAAATTATATTACAAAGTT 2911
                         i  i     i   iv   i   vv i i       viv  i       i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_108691350_   2912 ATAGTAATCAAAACTGTATGGGACTGGCATTAAAATAGACACATAGACCA 2961
                          i         i  v  i   v        v ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_108691350_   2962 --GGAACAGAATAGATAGCCCAGAAATAAACCCAAGTACAT--ACAGTCA 3007
                         --    i     v  v  i               --     -- ii    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCA 347

  chr1_108691350_   3008 ACTACTTTTTGACCATGCCCCCAATAACATACAATGAGGAAAGGATAGTC 3057
                          i iv    i   v v viv    v v   v     i      i      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_108691350_   3058 TCTTCAATAAATGGTGTTGGGAAAACTGGATATCCACATGCAAAAGAATG 3107
                          i     i        i     v         ?                 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_108691350_   3108 AAATTGGACTCATA---TACAAAATACACAAAAATCAACTCAAAATGGAT 3154
                           i      i v  ---i   vv   i        i              
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_108691350_   3155 TAAATACTTATGTGTAAGA--CAAAATCATAAAACTCCAAGAAGAAAACA 3202
                         i ? v  i  vi       --i    ii         iv           
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_108691350_   3203 AAGGGGAAAGGCTCCTTGACATTGGTCTTGGCAATGACTTTT 3244
                         v   ? v  iv  i v    v    vi v       ii  i 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

Transitions / transversions = 1.42 (74 / 52)
Gap_init rate = 0.01 (8 / 589), avg. gap size = 1.75 (14 / 8)  

 961 22.15 6.04 1.34  chr1_108691350_108695708     3569  3866 (493)    L1M4_orf2#LINE/L1      597   908 (0)  

  chr1_108691350_   3569 GGCAACAAGAGCAAAACTCCGC--CAAAAAAAAAAAAAAAAAAA--GGAC 3614
                          i  v   i    v  ----  --     i      v i v   --    
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA----GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_108691350_   3615 CACATCAAACCAAATAGCTTCTGCACAGCAAAGGCAACAATCAACAACAT 3664
                         iv       viv  v i   i  ii vv      vv  v     v  vi 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_108691350_   3665 GAAAAGGCAGCCTATGGATTTGGAGAAAATATTTGCAAGCCATATATCTG 3714
                               i  i  i ii  v v                 ii          
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_108691350_   3715 TTAAGGAGTTTCTATCCAAAATATA--AGGAACTCATAGAACTCAATCAC 3762
                         v     iii  v      i      -- i      v  v        v i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_108691350_   3763 -------CAAATAA----AT-AAAAAATAGACAAAGGACCTGAATAGATA 3800
                         -------       ----  -?      i i       ii        i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_108691350_   3801 TTTCTCCAAAGAGAGCAAACAGATGGCCAGCACATATATGAAAAGTTGCT 3850
                                     iiii v   i       ii vii i        v    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_108691350_   3851 CAATATCACTAATCAT 3866
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (40 / 25)
Gap_init rate = 0.02 (7 / 312), avg. gap size = 3.14 (22 / 7)  


3261 26.76 0.55 0.55  chr1_108745035_108749605     3171  4078 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108745035_   3171 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATGGTGAAAAT 3220
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108745035_   3221 GGCCATATTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 3270
                            v   i v     iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_108745035_   3271 TACCAATGACTTTCTTCACTGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 3318
                          v   iivi i  i  ii v   -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_108745035_   3319 TATGGAAACAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 3368
                                 iiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_108745035_   3369 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTATAAGGC 3418
                                i      vv       v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_108745035_   3419 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3468
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_108745035_   3469 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 3516
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_108745035_   3517 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3566
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_108745035_   3567 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3616
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_108745035_   3617 GAAACTGGATCCCTTCCTTACGCCTTATACAAAAATTAATTCAAGATGGA 3666
                            ii    i    v   i  i  v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_108745035_   3667 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3716
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_108745035_   3717 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3765
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_108745035_   3766 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3815
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_108745035_   3816 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3865
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_108745035_   3866 CAGGCAACCTCCAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 3915
                         v  i     iv  i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_108745035_   3916 AAGGGCTAATATCCAGAATCTACAATGAACACCAACAAATTTACAAGAAA 3965
                          i  i  vi          v  i  v    v iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_108745035_   3966 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 4015
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_108745035_   4016 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 4065
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_108745035_   4066 CATCACTGGCCAT 4078
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1340 27.84 6.84 5.34  chr1_108760180_108762082      541  1402 (501)    L1M4_orf2#LINE/L1       15   889 (19)  

  chr1_108760180_    541 ATGTTCAAGAAATAGAGGATGAAACATCATAAATACATCAATTCTCCCCA 590
                                v i v i  i  ivv  i  ii v  v iiv    v       
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_108760180_    591 ATATTAAGCTATTAATTCAATA-AATTGCAATCAAAATTCCAAAAATGAT 639
                          -   i v   ivi      ii-   iv v        i   iv------
  L1M4_orf2#LINE/     65 A-ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC------ 107

  chr1_108760180_    640 ATATATATATATGTGCATGTGTATGCACATGTATATAACAAAACAATCTG 689
                         -------------   v v v -    v vi --- i    i-----   
  L1M4_orf2#LINE/    108 -------------TGCCTTTTT-TGCAGAAAT---TGACAAG-----CTG 135

  chr1_108760180_    690 ATTCTAAAATTCATATAGAAGAGGAAAGGGTCAAAAATAGCATTGACACT 739
                           i             i   iv v  i  ii v i      vvvi   v 
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_108760180_    740 ATTGGAGATGAA---------TGTAAG---------TCCAGATGTCGAGA 771
                         v   i i v   ---------  v i ---------   vi  v  i i 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_108760180_    772 TGTATTATACAGTGATAGTAATTAAGACA-TGCGGTATTGATACACAG-T 819
                         iv  i  i v  iv i      i      -  i    i  ii i vi - 
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_108760180_    820 AGACA-ACA-ACTAATATAACAGGAAAAGGAAACCAGAAACACACCCATA 867
                              - i - ii   iv  i  i vvii  iv       i v       
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_108760180_    868 CACAGATGGAAATTTAATATATGACTAGAGGT---AAG--CATTTCAAAT 912
                           ivv    vv v  i  v vi   v  -   ---   --    -   --
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAG-GGTGCCAAGACCATT-CAA-- 381

  chr1_108760180_    913 CTGTAGGAAAAGGATGGGACTAACCAATAAATGGTGATAGGACAATTGAC 962
                         --- i  i    i  i v-  vvi   i        v i      i  iv
  L1M4_orf2#LINE/    382 ---TGGGGAAAGAATAGT-CTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_108760180_    963 TAT--ACA-GAAAAAAAAAGAAATTGAATCCCTATTTCACACCATACACA 1009
                           ?--   - v    i  v   i   i i     ii          i   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_108760180_   1010 AACATCAATTACAGGTGAATTAAAGAACTAAATATGAAATATCTAAA--T 1057
                           v  i  i vv ii  i  i ?   v      i --  v v     -- 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGT--AAGAGCTAAAACT 525

  chr1_108760180_   1058 AT-------TTA-AATAAGATATTGATGAATATCTTCATGCCCCAGGGTA 1099
                           -------   -  v  i i  v i? v v      i  v  iv    v
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_108760180_   1100 AGG-AAGAATTTCTCA-ATATG---TCAAAAGCACAACCA-TAAAAGAAA 1143
                            -  vii     i -     ---i           v  -i        
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_108760180_   1144 AAG-AGACAAATATAACTGCATTAAAATTTAAAATGTCTGCACAACAAAA 1192
                           i-   i    vvi   v   i      v    iv i  ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_108760180_   1193 AA-AC-ACCAAAAATTTGTTTTAAA---TAAGCAACAAGCTGGGAAAAGA 1237
                         i -  - i   i  vv  ----   ---i  v v   iiv     i  i 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTG----AAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_108760180_   1238 TATT--CATATTGCATA-ATGCCAACATAGGATTAATATCCAGAATTTAG 1284
                             --  v  --    -  - ii i vi   i vi          v  v
  L1M4_orf2#LINE/    722 TATTTGCAAAT--CATATAT-CTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_108760180_   1285 AAAGAACACCTACAAGCCATTAAGAAAAAGACAACCAATCTCGCTGAAAA 1334
                                v i     vi  v   v          vi  i ivii ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_108760180_   1335 ATTGACAAAAGGAATAAACAGGTAATTCACAAAAAAA---ATCCAAATGA 1381
                           v i    i ivv i  i  ii v   v v   i  ---  v      i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_108760180_   1382 CCAGCAAATATATGAAGAGAT 1402
                            ii  ii i     i    
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGAT 889

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.04 (38 / 875), avg. gap size = 2.76 (105 / 38)  


2694 25.82 3.08 3.30  chr1_108768696_108776357.rev     6263  7172 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108768696_   6263 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATAGTGAAAAT 6312
                               i i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108768696_   6313 GGCCATACTTCCCAAGGTAATATATAGATTCAATGCTGTTCCTATCAAGC 6362
                            v     i     iv i  v  i        i  vi i        --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-- 98

  chr1_108768696_   6363 TAGATTCAATGCTGTTCCCATCAAGCTATCATTGACTTTCTTCACAGAAT 6412
                         -------   ------    ----   ii -------  i  ii     v
  L1M4_orf2#LINE/     99 -------AAT------CCCA----GCTGCC-------TTTTTTGCAGAAA 124

  chr1_108768696_   6413 TAGAAAAAACTACTTC-GAATTTCACATGGAACCAAAAAGGAGCCCATAT 6461
                          v  v  i-  iv i -i  v    i      viiv  i   v  viv  
  L1M4_orf2#LINE/    125 TTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chr1_108768696_   6462 AGCCAAGAGAAACCTAAGTCAGAAAAACAAAGCTGGAAGCATCATAGTAT 6511
                               i v  v i i ivv    i       i    i vv   i v vi
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr1_108768696_   6512 CTGACTTCAAA-----CTAT---GCCACA-T--TC----TACTG-GGTAC 6545
                          ii i      -----   i---  i   - --  ----i v  -     
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_108768696_   6546 C------AAAACAGATGTATAGACCAATGGAACAGAACAGAGGCCTCAGA 6589
                         i------ ii i   ii      i        i    iv   ivii    
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_108768696_   6590 AATAACACCATACATTTGCAACCATTTGATCTTTGACAAAACTGACAAAA 6639
                              vv          iiiii  v     i  i     iiv  v   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_108768696_   6640 ACAAGCAATGGACAAAGGATTCCCTATTTAATAAATGGTGTTGGGAAAAC 6689
                         v  vv      iv    i  vvi  v  i  i        i     v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_108768696_   6690 TGGCTAGCCATATGAAGAAAACTGAAACTGGACCCCTTCCTTACACCTTA 6739
                            v  ?   i   v i  i v    ii         v   i     v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_108768696_   6740 TACAAAAATTAACTCGAGATGGATTA-AGACTTAAACATAAGGCCTAAAA 6788
                                        i i      i -    i    ii    iv      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_108768696_   6789 CCATGAAAACTCT-AGAAGAAAACCTAGGCA-ATACCATTCAGTATATAG 6836
                          i  -        -          v    ?i- v i -   ivv iv v 
  L1M4_orf2#LINE/    524 CTAT-AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chr1_108768696_   6837 GCACTGGCAAAGACTTCATGACTAAAACACCAAAGGCAATTGCAACAAAA 6886
                          vviv     v ii   v iiv  vi        i   vvv         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_108768696_   6887 GCCAAAATTGACAAATGGGA-TTAGTTAAACTAAAGAGCTTCTGCACAGC 6935
                          vv     v  i    v   -  vi i   v v  i i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_108768696_   6936 AAAAGAAATTATCATCAAAGTGAACAGGCAACCTACAGAATGGGAGAAAA 6985
                            i  v i     vv        v  i     i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_108768696_   6986 TTTTTGCAATCTACCCATCTGACAAAGGGCTAATATCCAGAATCTACAAA 7035
                          v       vii ivi      i  i  i  vi          v  i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_108768696_   7036 GAACTTTAACATATTTGCAAGAAAAAGACAAACTATCCCATCAAAAAGTG 7085
                              i v   vv ivii  v           iv i  v  i?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_108768696_   7086 GGTGAAGAATACGAACAGACACTTCTCAAAAGAAGACATTCATGTGGCCA 7135
                           ii   i  vi   i     i     v        i  v  vi      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_108768696_   7136 ACAAATATATGAAAAAAATG-TCATCATCCCTGGTCAT 7172
                          i  ii i       i -  -   v    v????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.76 (58 / 21)  


1626 25.04 3.05 4.57  chr1_108778674_108780822.rev      507  1097 (1052)    L1M4_orf2#LINE/L1      136   717 (191)  

  chr1_108778674_    507 ATTCTAAAATTCATATGGAACCAAAAAAGAGCCCACATAGCAAAAACA-T 555
                           i                 viiv  ii  v  viv     v      - 
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_108778674_    556 CCTAAGCAAAAAGAACAAAGCCAGAGACATCACATTACCTGACTTCAAAC 605
                          i i iv  i          iii   ivv     i v  ii i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_108778674_    606 TATACTACTAGGCTATAGTAACCAAAACAACATGATACTGGTGCAAATAT 655
                         iv      v i    i     i   i   iii  i      iii  iv  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_108778674_    656 AGACATA--GATGAATGGAACAGAATAGATAACCCAGAAATAAAGCCATA 703
                                --   v       i     v  v ii           v     
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_108778674_    704 TAGCTACAACCATCTGATCTTGAACAAAGTTGACAGAAATAAACAATGGA 753
                         i vi  iiii  vi    i  vi    i v  v  ii vi vv      i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_108778674_    754 GAAAGAACTCCCTATTCAATAAATGGTGCTGGGAAAACTGACTAACCACA 803
                                ivvi  v     i              v     iv  ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_108778674_    804 TGAAGAAGAATCAAACTGTACCCTTATCTCTCACTATATACAAAATTGTA 853
                           v i      v  ii  v    i  i   v   i          ---- 
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA----A 481

  chr1_108778674_    854 TATATCTCTTACTATATACAAAAAAAGATGGATTAAAGGCTTAAAAGTAA 903
                          -  v   ----------------  i      i ?  i i    v    
  L1M4_orf2#LINE/    482 T-TAACTC----------------AAAATGGATCAWAGACCTAAATGTAA 514

  chr1_108778674_    904 GACCTGAAACTACAAAAATCCTAGCAGAAAACTTAGGAAAAACTCTTCTG 953
                           v  i      i    v  i   v       v    ?iv  v     vv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_108778674_    954 GATATTGGCCTAGGCAAATAATTTAT--GATTAAGA-ACTGAAAAGCAAA 1000
                           iv    vi       - ii   v --   - v  -  i-       v 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAA-TGGTTTCTTAGAT-ATGACACC-AAAAGCACA 611

  chr1_108778674_   1001 TACAATGAAAACAAAAATAGACAAAT--AATT------AAATGAATGAGC 1042
                         vi   ii   iv         i    --i i ------    v  -i i 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA-AAAC 660

  chr1_108778674_   1043 TTCTGCACAGCAAAAGAAAC----AACAGAATAAACTAAGACAACCTACA 1088
                           i  ii vv    i  v  ----  v i i i  --         i   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA--AAGACAACCCACA 708

  chr1_108778674_   1089 GAATGGGAG 1097
                                  
  L1M4_orf2#LINE/    709 GAATGGGAG 717

Transitions / transversions = 1.54 (88 / 57)
Gap_init rate = 0.03 (15 / 582), avg. gap size = 3.00 (45 / 15)  

 571 20.00 7.57 1.62  chr1_108778674_108780822.rev     1474  1658 (491)    L1M4_orf2#LINE/L1      713   908 (0)  

  chr1_108778674_   1474 GGGAGAAAATGTTTACTTACTATGCATTCAACAAAAGGACTGATATCCAG 1523
                                   i   i vv ii  ii  iii i  i-     vi       
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAG-GGACTTGTATCCAG 761

  chr1_108778674_   1524 AATCTATAAGGAACTCAAATGAATCAACAAGAAAAAAACAAC---CCC-- 1568
                            v     i      vv ii v    i  v     i    v---   --
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_108778674_   1569 TTAAAAAAGTGGGCAAAGGACAAGAACAGACATTTCTT-AAA------AT 1611
                           ?     -           ivv   i          i-   ------  
  L1M4_orf2#LINE/    812 TTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_108778674_   1612 ACAAGTAACCAACAA--ACATGAAAAAAATGCTCAACATCATTAATCAT 1658
                             i ii    i  --         i -            ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.27 (25 / 11)
Gap_init rate = 0.04 (8 / 196), avg. gap size = 2.12 (17 / 8)  


2499 25.64 6.38 1.15  chr1_108792452_108794222.rev      500  1283 (488)    L1M4_orf2#LINE/L1       84   908 (0)  

  chr1_108792452_    500 CACTATTCCTATCAAACTACTAACTTCATTTTTCACAGAAATAGAAAAGA 549
                          i v  i         v v i i  v v     ii       v  v   -
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG- 132

  chr1_108792452_    550 CT-ATTCTAAAATTTGTATGGAAC--CAAAAAAGCTCACATAGCCAAAGC 596
                           -  i        ii       v--   iii v iviv         i 
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr1_108792452_    597 A-TCCTAAGCAAAAAGAACAAAGTCAGAGACATCACATTACCTGACTTCA 645
                          -  i i iv  i           ii   ivv     i v  ii i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_108792452_    646 AACTGTACTGCAAGGCTATGGTAACCAAAAAAAGCATGATGCTGGTACAA 695
                           viv    i   i    ii    i   i v - ii  i i    i i  
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACA-GTGTGGTACTGGCATAA 281

  chr1_108792452_    696 AAATAGAAA-ATC-ACCAATGGAAGGAACAGAATAGAGAACCCAAAAATA 743
                         ii     v -  v- i        ----i     v    ii   i     
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAA----TAGAATTGAGAGTCCAGAAATA 327

  chr1_108792452_    744 AAGCCACACATCTACCGCTAGT-----------AAG-------------- 768
                           v   i    i  iv ii i -----------   --------------
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_108792452_    769 -CAGTGGGAAAAGGAC--TCTATTCAATAAATGGTGTCTGGATAACTGGC 815
                         -  i    i    i i--   v     i        iiv   i      v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_108792452_    816 TGTCCATATGCAGAAGAGTGAATCTGGACCCCTATCTCTTACCATATACA 865
                          i?   i     i    i    vi          i   vi          
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_108792452_    866 AAGATTAACTCAAGATGGATTAAAGACTTAAATGTAAGACCTGAAACTAT 915
                           i          i      i ?    i           v  i       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_108792452_    916 AA------CAGAAGAAAGCCTAGG---AAATATCCTTCTCAACATCAGCC 956
                           ------i        i v    ---    ---    vii  v ii vi
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGT 574

  chr1_108792452_    957 TTGGCAAAGAATTTATGACTAAGTCCTCAAAAGCAATTGCAATAAAAGCT 1006
                          v     v iv  iv iiv  v v vi        vvv    i     vv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_108792452_   1007 AAAATTGACAAGTGGGACCTAATTAAACTGAGGAGCTTCTGAATAGCAAG 1056
                              v  i  i v    i v  i   v v ii i   i  viivv   i
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_108792452_   1057 AGAAACTATCAATGGAGTAAATAGATGACCTAGAGAATGGCAGGAAATAT 1106
                         i  v        vii   i  v   ii   i v       v  i      
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_108792452_   1107 TTGCAAGCTATGTATCTGACAAAAGTCTAATATGCAGAATCTATAAGGAA 1156
                               iii  i       i  ii v  vi   v      v     i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_108792452_   1157 CTT----AAATCAACAAGCAAAAAACAAATAACCCTATT-AAAAATGGGC 1201
                           i----  v    i  vv    i           v   -          
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_108792452_   1202 AAAGGACATGAAAAGACACTTCTTAAAAAAAGATATACAAGCAGCCAACG 1251
                               iv    v     i    iv   i           iii     ii
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_108792452_   1252 A--ACATGAAAAAATGCTCATCACTAATCATCAG 1283
                          --         i       v  ii ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (128 / 71)
Gap_init rate = 0.02 (17 / 825), avg. gap size = 3.47 (59 / 17)  


3210 27.42 0.33 0.33  chr1_108796508_108802438     4531  5438 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_108796508_   4531 TGGAAGAACATTCCATGCTACTGGATAGGAAGAATCAATATTGTGAAAAT 4580
                              ii i  i     i vv     v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_108796508_   4581 GGCCATACTGCTCAAGGTAATTTATAGATTCAACGCCATCCCCATCAAGC 4630
                            v     v i   iv i  i  i           v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_108796508_   4631 TACCAACGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4678
                          v   i vi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_108796508_   4679 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAGTCCTAAGCAAAAAG 4728
                                viiv  ii  v  v v  v     i   i  i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_108796508_   4729 AACAAAGCTGGAGCCATCACATTACCTGACTTCAAACTACACTACAAGGC 4778
                                i     vvv     i v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_108796508_   4779 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4828
                           i     i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_108796508_   4829 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCCACAACCAT 4878
                                i    iv   ivii         vv   i    ii iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_108796508_   4879 CTGATCTTTGACAAACCTGACAAAAATAAGAAATGGGGAAATGATTCCCT 4928
                         i    i  i     ivv  v   i vi vvv          vi  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_108796508_   4929 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATTTAGAAAGCTGA 4978
                         v  i  i        i     v      v  ?   i  vi i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_108796508_   4979 AACTGGATCCCTTCCATACCCCTTATACAAAAATTAATTCAAGATGGATT 5028
                          ii    i    v  vi  v  v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_108796508_   5029 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACTT 5078
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_108796508_   5079 AGGCA-ATACCATTCAGGGCATAGGCATGGGCAAGGACTTCATGACTAAA 5127
                            ?i- v i -   iv i v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_108796508_   5128 ACACCAAATGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCCAAT 5177
                                 v   vvi          vv        i    v   iiiv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_108796508_   5178 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5227
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_108796508_   5228 GGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACAAA 5277
                          i     i                 v   i   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_108796508_   5278 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5327
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_108796508_   5328 AACAAACAACCCCATCAAAAATTGGGCAAAGGATATGAACAGACACTTCT 5377
                         i     i     v  i?    v            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_108796508_   5378 CGAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATACTCATCA 5427
                          v        i  vi viii     i ii          i  i    v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_108796508_   5428 TCACTGGTCAT 5438
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


2477 22.62 7.09 0.45  chr1_108907842_108909496.rev      502  1164 (491)    L1M4_orf2#LINE/L1      202   908 (0)  

  chr1_108907842_    502 AAAGTTGGAGGCCTCACACTACTTGACTTGAAAATGTACTACAAAGCAGT 551
                                    v        v iii i  v    iv           vii
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_108907842_    552 AGTAATAAAAACATCGTGGTTCTGGTATAAAAACAGAGACATAGACCAAT 601
                               v  i   vi     v    i    ii i   v i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_108907842_    602 GGAACAGAATAGAGAGAACCCAGAAATAAATCCATGCATTTACAGCCAAC 651
                             i     v     --i           i    i      ii i   i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAG--TCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_108907842_    652 TGATTT-CAACAAAGACACCAAGAACATACATTGGCAAAAGGACACCCTC 700
                               - i    i iii      v   v  v   vi    i i vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_108907842_    701 CTCAATAAATGGTACTGGGAAAACTGCATATCCATATGCA---GAATGAA 747
                         i    i       i      v     v   ?   i     ---       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_108907842_    748 ATTAGACTCCTATCTCTCACTGTATACAAGCATCAACTCAAGATGGATTA 797
                         i  i   i    i   v   ii       iv  i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_108907842_    798 ACGAGTTAATTGCA-GACCTAAAACTATGAAAGTACTGGAAGAAAACA-- 844
                         ?v  vi   v  i -  v          i   v vi i          --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_108907842_    845 GG---AAATGCTTCAGGACATTGGTCTAGGCAAAGATTT--TGAGTAAGA 889
                           ---    -    iv   v    vi       v i   -- iii  v  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_108907842_    890 CTACAAAAGCACAGGCTACAAAC--AGAAATACACAAATGGGAATATATG 937
                          vv          i  v     v-- i     v i    v   v vi  v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_108907842_    938 AAACTGAAAGGTTTCTGCACAGCAAAGAATA---------GAGTGAACAG 978
                            v v   iii  i  ii vv     i i ---------i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_108907842_    979 A--ACCTATAGAATGGGAGAAAATACTTGCAAAGTATTCATC----AAGG 1022
                          --   i i                i       vi  vi   ----    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_108907842_   1023 GATTAATATCTAGAATATACAA-GAAT--------CTCAACAGCAAAAAA 1063
                           i vi    i        i  -   i--------     i ii     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_108907842_   1064 AC------CCCAAATAAAAAGTGGGCAAAGGACCTGAACAGATATTTCTC 1107
                           ------     v ?    i           ii    i   i       
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_108907842_   1108 ---AAAAGACATACAGATGGTTAACAAGTAGATGAAAAAATGCTCAACAT 1154
                         --- i    i     i    ii  i   i v       i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_108907842_   1155 CACTAGTCAT 1164
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.00 (98 / 49)
Gap_init rate = 0.02 (16 / 707), avg. gap size = 3.12 (50 / 16)  


1757 23.81 5.31 3.30  chr1_108942345_108944387      500  1045 (998)    L1M4_orf2#LINE/L1      150   706 (202)  

  chr1_108942345_    500 ATGGAAATATAAAGGACCTAGAGTAACCAAAGAGACTTTTAAAAGGAAGA 549
                                 ii  i     i   i  i     ivi ii  v    i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_108942345_    550 ATCAAGTTGGAATACTTACTCTACCTGATTCCAAAACTTACTGTAA-GTG 598
                          iv        iv   i  v  v  ii   i           ii  - iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_108942345_    599 ATAGTAGTTAAGATAGTTTTGTATCAGTGAAAAGATAAACACAAAGATCG 648
                          i    i i    i   v v   iii iiv  i    i   i v     i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_108942345_    649 ATAGAACACAG--------CCAGAAGTAGACCCACACATGGTAGGGTTGA 690
                           i   i v i--------      i  i     i    v-  v   ii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGGTCAA 348

  chr1_108942345_    691 TTGATTTTTGACAAAG-TGTTAAAGCAATTCCAAACGGAAAGGAAGGTCT 739
                                 i     i -  ii  ii v    v viv      i vi    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_108942345_    740 TTTCAACAAATTGTGCTGGATCAACTCAGGA---CC-TGTGGGGGGAAAA 785
                                    v       iv     --   ---  -ii  vi---   i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACT--GGATAKCCACATGCA---AAAG 443

  chr1_108942345_    786 AATGAACATCAACCC-TACCTCACACCATAAGCAAAAATTAATTCAAACT 834
                               vv vi    -              vi          i     v 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_108942345_    835 GGATCTGAGACCTAGATGTAAAAATCCAAACTATAC--CTTTTT--AGAA 880
                              v?       i      i iiiv        v--  i  v--    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_108942345_    881 AACATAGGAG--AATATTACACTCTCCTGTGTGGTTGAG-ATTGGTAGTT 927
                                 ? --   v  - iivvi i  ---    ii - v    --  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTT-CGTGACCTTG---GGTTAGGCAATGGT--TT 587

  chr1_108942345_    928 CTCAGA----ACACAAAAAGCAGGAATCACATAAACAAAACAAAAAATGG 973
                           i   ----    v       vi ii------       v       i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGC------AACAAAAGAAAAAATAG 631

  chr1_108942345_    974 ATAAATTGAACCTGATTAAAAAAAAAAACT---GCTCTTTGAAGGACATC 1020
                                 i  i v  i    vv       --- iv   ii       ii
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_108942345_   1021 ATTAAGAAAATGAAAAGGCAACCCA 1045
                           i      i       i       
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCA 706

Transitions / transversions = 2.05 (86 / 42)
Gap_init rate = 0.03 (19 / 557), avg. gap size = 2.47 (47 / 19)  

 531 24.30 5.14 0.47  chr1_108942345_108944387     1337  1550 (493)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_108942345_   1337 AAGATAATTCAATAG-CAAGCCAAAGACTGTGTAAAAATACTTGAAACAC 1385
                             -  v v  v  -   v   v   v  v vi      i   v  vv 
  L1M4_orf2#LINE/    685 AAGA-AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_108942345_   1386 ATATATAC-ACAAAAGACTTACATACAGATCATGTAACCAGTCCTTGCCA 1434
                               vi- i  ii     ii  v    vi  i   vv iii   i v 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_108942345_   1435 CTCAACAATAA---GACAAACAA---AATAACAAAATTGGCAAATTATTT 1478
                              i     ---      i  ---   v?v     v      vv    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_108942345_   1479 GAA--GTTACTTCACAGCAGAAAATATATAAATGAC-AATAAGCACCTGA 1525
                            -- vi i   v viv    i     i     i -         v   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_108942345_   1526 AAAAATGTTCAACATCATTAGTGGT 1550
                            i   i         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.89 (24 / 27)
Gap_init rate = 0.03 (7 / 224), avg. gap size = 1.71 (12 / 7)  


2504 23.71 6.00 1.00  chr1_108965473_108967117.rev      455  1154 (491)    L1M4_orf2#LINE/L1      174   908 (0)  

  chr1_108965473_    455 AACCAAGATAGGATTACAAAAAAGGGAAAAGAACTGCA---TTTACCGTC 501
                          i    i i ivv  i-     iii   v i ii  v ---i i  vv i
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTG-AAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_108965473_    502 CCTGACTTTAAGATTTACCATAAAGCTAAAATAAAATAGAGACCGGGTGG 551
                           ii i  i  i i    i i       v i   -- vi    v v    
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAA--TCAAGACAGTGTGG 270

  chr1_108965473_    552 TATTGGCATGAAGATAGATAAATAGATCAATGGGACAGA-----GAGTCC 596
                           i      i i      i v            i i   -----      
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_108965473_    597 AAAAATAAACCCACGCATATATAGATAATTGATTTTCAACAAAGATAC-A 645
                          i           ii   v   i vi           i    i i i - 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_108965473_    646 AGGCAATCCAAAGGAGAAAGAATAGACTTTTCAACAGATGGTGCTGGAAC 695
                           i v  i   v  i          v          i          i  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_108965473_    696 AACTGGATAACCATATGCAGAAAACATAAACTTTGGTTCATACCTCACAC 745
                                  ?   i     i  i -  i  v  v iii v          
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGA-ATGAAGTTGGACCCCTACCTCACAC 469

  chr1_108965473_    746 CACATTAAAAAATGAACTCAAAATGGATCATAGATCTAAATGTAGCACCT 795
                           i  vv      v                ?   i         iv v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_108965473_    796 GAAACTATAAAATGTCCAGAAAAAAAAACACAAGAGAATATCTTTGTGAC 845
                         i           iviii    i    --  i i ? v v     i     
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATCTTCGTGAC 567

  chr1_108965473_    846 TTTGGGTTAGGCAAAGATTTCTTATATACAACACTAAAAGTATAATC--C 893
                         i             v i       v   ii    i     i i  v -- 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_108965473_    894 ATTTTTAAAATTTGATAAATTTGACTTCATTAAAATGAAGAATATCTG-- 941
                          vvvvv    v v        v        i     v  i  iv i  --
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_108965473_    942 ----------CACTATTAAGGGAATGAAAAGATAAGCCACAGACTGCGGG 981
                         ----------      i   ii i        i  v       v  v i 
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_108965473_    982 AAAATAT-----------ATATCTTATAAAGGACTTGTATTCTGTGTGTG 1020
                                -----------      v    i          i v vi i i
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_108965473_   1021 T---GTATTCTCAAAACCCAGTAATAGGAAAACAA----CTCAAT-ACAA 1062
                          --- v i   i v   i  i     ii  i    ---- i    -?v  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_108965473_   1063 AATGGGCAAAAGATATGAACAAACACTTTACAAAAGAAGACATACTCGTG 1112
                                   i   v    i i   i  iv v        i    vvi  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_108965473_   1113 GAAAATAAAGGCATGGAAAAAATCCTCAGCATCACTAGTCAT 1154
                          vv     ivi    -    i  v    i     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (104 / 58)
Gap_init rate = 0.02 (14 / 735), avg. gap size = 3.50 (49 / 14)  


2491 18.41 3.04 1.71  chr1_109180531_109183432     1291  1817 (1085)    L1M4_orf2#LINE/L1        1   534 (374)  

  chr1_109180531_   1291 TGGAACAATATCCCATGTTCATGGATTAGAAGACTTAATAATGTTAACAT 1340
                              vi                    i            v      v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_109180531_   1341 TTCGATACTATCCAAAGTGACCTACAAATTCAGTGCAATCCCTGTAAAAA 1390
                         vv i     vi     v   i     i     ii         i v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_109180531_   1391 TCCAAA-TGACTTTTTCCTCCTACAGAAATAGAAAATAT-AGCCTAAAAT 1438
                            v i-  v      ----- i       v  v  vv - v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-----TGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_109180531_   1439 TCATATAGAACCTCAAGGGATCCCCAAATATCCGAAATAGTCTTGA---- 1484
                               i   viv       -   vi    v  i   i i      ----
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_109180531_   1485 ---GAATAAAGCTTTAGGGCTCACATTTTTTTATTTCAGG--TTATTACA 1529
                         ---   i    i vv   i      i  iiiv      ii--   i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_109180531_   1530 AAGCTACATTAATCAAAGCAGTGCAGTACTGGCATAAAAGACAGACATAT 1579
                                 v       ii     ii            i-  i        
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATAT 293

  chr1_109180531_   1580 AGACCAATGGAATAGAATACAGATCCCAGAAATAAACCCTTGCATGTGTG 1629
                            i              vv   vi              v i   v i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_109180531_   1630 GTCAAATAATATGCAACAGGGGTGCCAAGACCATTCAGTGGGGGAAAAGA 1679
                              v i  v v i   i                  i     i  i - 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-A 392

  chr1_109180531_   1680 CAGTTTTATCAACAAATGGTTCTGGGTAAACTAGAGAGCCACATACAAAA 1729
                         i   i  v            v     vv    i  v ?      i     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_109180531_   1730 AGAATGAAGTTGGACCCTTACCTAATACCATATGCAAAA-----CTCAAA 1774
                         -                i     v i       i     -----      
  L1M4_orf2#LINE/    443 -GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_109180531_   1775 GTGGGCCAAAGACCTAAGCATCAGAACTAAAACTATAAAACTC 1817
                         i   ii  ?        iii v   i                 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

Transitions / transversions = 1.50 (57 / 38)
Gap_init rate = 0.02 (10 / 534), avg. gap size = 2.50 (25 / 10)  

1104 19.24 9.15 1.89  chr1_109180531_109183432     2093  2409 (493)    L1M4_orf2#LINE/L1      532   871 (37)  

  chr1_109180531_   2093 CTCTAAAGGGAAAAAAAAGG---AAAGCCTCATGGCATTGGGTTTGGCAG 2139
                             v iii     v v   ---   v i  i  i v       v    i
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_109180531_   2140 TGATTTCTTGGTTATAAAACCAAAAGAGTGAGCAGGGAACAACAACAACA 2189
                           i      i v   i v        viii    ----    v iv  v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCA----ACAAAAGAAAAA 627

  chr1_109180531_   2190 ACGTAGACAAATTGGACTTCAT---AATTAAAAACTT--GTGCATCAAAG 2234
                          --    i              ---            --    v      
  L1M4_orf2#LINE/    628 A--TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_109180531_   2235 GACATTATCAACA--GTAAAAAGGCAACCCA--ACAT-----AAAATACT 2275
                             i      v --  i     i       --iv  -----      i 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_109180531_   2276 TGGAAATCACATATCTGATAAAGGATTAATACCCAGAATATATAGAAAAC 2325
                           v      i           i   i vi  i            i i   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_109180531_   2326 TCCTAAAACTCAACAA-----AAAC---CAACCTGATTCAAAAATGGGCA 2367
                           i  v       i  ----- i  ---i    ii   ?           
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_109180531_   2368 AAGAACTGGAAGAGGCATTTCT--ATAGA-GATA-ACAAGAGGCTA 2409
                            i i v   v  i       -- v   -    -    iv   i 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.73 (38 / 22)
Gap_init rate = 0.04 (13 / 340), avg. gap size = 2.69 (35 / 13)  


 564 18.58 2.65 0.00  chr1_109583342_109588824     3374  3486 (1997)    L1M4_orf2#LINE/L1        2   117 (791)  

  chr1_109583342_   3374 GGAAATATATCCTATGTTCCTGGATTGGAATAATTAATATTGTTAAAATG 3423
                              v      i      v          v v             i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_109583342_   3424 TCCATACTACCCAAAGTGATCTACAGATTAAATGTAATGCCTATTA---T 3470
                         v v     v      v             v  i i   v     i --- 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_109583342_   3471 TTTGACTGTCTTTTTT 3486
                         iiiii   i       
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT 117

Transitions / transversions = 1.10 (11 / 10)
Gap_init rate = 0.01 (1 / 116), avg. gap size = 3.00 (3 / 1)  

1765 16.19 2.29 28.00  chr1_109583342_109588824     3898  4990 (493)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr1_109583342_   3898 AAAATTCCAATGGTATTTTTCACAGAAATAGAAAAA---ATCCTAAAATT 3944
                              i   iiv iv     ii       v  v  i---           
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_109583342_   3945 TATATGGAACCACAAAAGACCCTGAATAACCAAAGTAATTGCAAGCAAAA 3994
                         i        vii   ii     v     i     ii   ivii iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_109583342_   3995 AGAACAAAGCTGGGGGTATCATGCTACCTAATTTCAAAATATATTATTGA 4044
                                  i   i  vv   ii  v  i          iv  i  ivi 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_109583342_   4045 GCTATAGTAATCAAAACAGCATGGTACTGGCGTTAAAA---ACAAATAGA 4091
                             i         i    ii          i v ii ---   v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_109583342_   4092 CCAATGGAACAGAATAGAGAGCACAGAAATAAATCTATGCATTTATTGTC 4141
                         i        i     v     iv          i i  i       v   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_109583342_   4142 AACTTAACTTT-GACAAGGGTGTCAAGAACACACAATGTGAAAAAGACAG 4190
                           -  i i   -          i     v  iv     v i   ii i  
  L1M4_orf2#LINE/    347 AA-TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_109583342_   4191 CCTCTTAAATAAACGGTGCTGGGAAAACTGAATATCTATATGCAGAAGAA 4240
                         i  i  v  i   i          v     i   ? i i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_109583342_   4241 TAAATTTCAACCCTTCTTTCTTTTTTTTGAGATGGAGTCTTGCTCTGTCG 4290
                          i  ----------------------------------------------
  L1M4_orf2#LINE/    446 TGAA---------------------------------------------- 449

  chr1_109583342_   4291 CCAGGCTGGAGTGCAATGGTGCGGTCTCGGCTCACTGCAACCTCCGCCTC 4340
                         ---- i    ----------------------------------------
  L1M4_orf2#LINE/    450 ----GTTGGA---------------------------------------- 455

  chr1_109583342_   4341 CCAGGTTCAAGCAATTCTCCTGCCTCAGTCTCCCAAGTAGCTGGGACTAC 4390
                         ---------------- i   i     -----------------------
  L1M4_orf2#LINE/    456 ----------------CCCCTACCTCA----------------------- 466

  chr1_109583342_   4391 AGGTGCACATCACCATACCCAGCTAATTTTTGTATTTTTGGTAGAGACGG 4440
                         ----------       ---------------------------------
  L1M4_orf2#LINE/    467 ----------CACCATA--------------------------------- 473

  chr1_109583342_   4441 GATTTCACCATGTTGGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCC 4490
                         --------------------------------------------------
  L1M4_orf2#LINE/    474 -------------------------------------------------- 473

  chr1_109583342_   4491 ACCCTCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACA 4540
                         --------------------------------------------------
  L1M4_orf2#LINE/    474 -------------------------------------------------- 473

  chr1_109583342_   4541 CCTGGCCTCAATCCTTATTTCATGTCATGTACAAAAATCAACTCAAAATG 4590
                         -----------------------------         i           
  L1M4_orf2#LINE/    474 -----------------------------TACAAAAATTAACTCAAAATG 494

  chr1_109583342_   4591 GATTAGAGACATAAATGTAAGACTTGAAACTGTAAAACTACTAGAAGGAA 4640
                            i ?    v           vi i     i       vi      i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_109583342_   4641 ATATAGGGAAAAAAGCTTCTTGACATTCATCTGGGCAATGGCTTTTTGGA 4690
                          i     ?iv   -v    v    v  vivi i        i  i  i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_109583342_   4691 TACGACCCTAAAAGCACAGGCAACAAAAAACAAAAACAGACAAATCAGAT 4740
                           i   v i         i         i -     i   i    ii  i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGAC 642

  chr1_109583342_   4741 TGTATCAAACTAAAAAGCTTCTGCAAAATAAAGGAAACCACCAAAAGAGA 4790
                          vi      v v    i   i  iivvvi      v  i i   i i  v
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_109583342_   4791 GAAGACAAACAATACACAGAATGGGAGAAAATACTTGCAAACCATACATC 4840
                            i --i    iv                   i       i    i   
  L1M4_orf2#LINE/    693 GAAAA--GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_109583342_   4841 TTATAAGGGGTTAATATCCAAA------------------CAAATCAGTA 4872
                          v       ii vi      i ------------------   v   i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_109583342_   4873 GCAAGAAAACAAATAATCCAACTAAAAAATGGGCAAAGGACCTGAACAGC 4922
                         ii  i  i        i    i ?                ii    i  v
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_109583342_   4923 CATTTATCAAAAGAAGACATATAAATGGCCAACAGGTATACGAAAAAATG 4972
                              v  v        i   i          i i i i i     i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_109583342_   4973 CCCAACATCACTAATCAT 4990
                          i        ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.60 (125 / 48)
Gap_init rate = 0.01 (12 / 812), avg. gap size = 27.58 (331 / 12)  


3215 26.76 0.55 0.55  chr1_109997691_110004105.rev     5017  5924 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_109997691_   5017 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5066
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_109997691_   5067 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5116
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_109997691_   5117 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5164
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_109997691_   5165 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5214
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_109997691_   5215 AACAACGCCAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5264
                              v iii    vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_109997691_   5265 TACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5314
                                 i   ii   ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_109997691_   5315 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATGTACAACC 5362
                                i    i--    i  --        vv   i i  v  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_109997691_   5363 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5412
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_109997691_   5413 CTATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5462
                           v  i  i       i      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_109997691_   5463 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5512
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_109997691_   5513 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5562
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_109997691_   5563 CTAGGCA-ATACCATTCTGGACATAGGCATGGGCAAAGACTTCATGTCTA 5611
                         v    ?i- v i -   vv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_109997691_   5612 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5661
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_109997691_   5662 ATTAAACTAAAGAGCTTCTCCACAGCAAAAGAAACTACCATCAGAGTGAA 5711
                           i   v v  i i   i vii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_109997691_   5712 CACGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5761
                         v vi     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_109997691_   5762 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5811
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_109997691_   5812 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5861
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_109997691_   5862 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5911
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_109997691_   5912 CATCACTGGCCAT 5924
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2047 23.09 2.68 0.82  chr1_110219082_110225684     3844  4328 (2275)    L1M4_orf2#LINE/L1        1   494 (414)  

  chr1_110219082_   3844 TGGAGAGATATTCCAAGTTCATAGATAGAAAGAGACAATATTGTCAAGTT 3893
                             i      i   v      i   v i    vvi        i   --
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-- 48

  chr1_110219082_   3894 ATGTTA----TTCCCAACTCAATCTGTAGATTCAACACAATCCCAATCAA 3939
                            vi ---- i     v ii    ii         i       v     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_110219082_   3940 AATTCCAACGAATTATTTTGTGAATATTGATAAACGGATTCTAAAGTTGA 3989
                            i   i vivi v     iii v     i  i v   i     i  v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_110219082_   3990 TATAGAAAGGCAAAAGACCCAGCATAGCCAATCCAATGTTGAAGGAGAAA 4039
                            i    v    ii       v        vv    v     ii    i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_110219082_   4040 AACAAAGTTGGAGGACCAACATTACCTGATATCAAGATTTACTATAAAGC 4089
                                         iv   i v  ii  v    i i      i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_110219082_   4090 TACAGTAGTCAAGACAATGTGCTACTGGTGAAGGAATAAACAAATCAATT 4139
                                i        i    v      iiv i i   i   v  vi  i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_110219082_   4140 AATGGAACAGAAT--AGTGTCCAGAAATAGGCTGCCACAAAT--ATAGTC 4185
                                i     --  v           ii --   i v  --  i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAAC--CCATACATTTATGGTC 346

  chr1_110219082_   4186 AACTGATTTTTGACAAAGGAGCAAAGGCAATTCAAT----AAAGA-CAGT 4230
                           i       i     i  v  v   i v       ----     -i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_110219082_   4231 CTTTTCAACAAATAGTTCTAGAACAACCGGATTTCCACACGTGAACGTAT 4280
                                      i  v  i i     i    v?     i ii  v v  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_110219082_   4281 GAATCTAGACACAGACTTTATACCTCTTATGAAAATTAACTCAAAATG 4328
                            vi i   v vv  i i i   viv  ii                 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

Transitions / transversions = 1.77 (71 / 40)
Gap_init rate = 0.01 (7 / 494), avg. gap size = 2.43 (17 / 7)  

 521 22.08 6.93 9.52  chr1_110219082_110225684     4644  4874 (1729)    L1M4_orf2#LINE/L1      477   701 (207)  

  chr1_110219082_   4644 AAAAA--AACTTGAAATGGATTACAGCCTTAAATGATGTAAAACTACACT 4691
                              --    ii        i ?  v i      ---   i ----i  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATG---TAAGA----GCT 519

  chr1_110219082_   4692 AAACTATATAAACACAAAACTATAAAACTCCTAGATGATAGCATAGGAGA 4741
                            ---------------            i    v  v i      ? v
  L1M4_orf2#LINE/    520 AAA---------------ACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_110219082_   4742 AAATACAGATAACTTTGGGAATGGCAATGACTTTATAGATACAACATTGA 4791
                             vivvi i  i     vvv       ii  iv      ii   iii 
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_110219082_   4792 AAGCA-----------AGAAATATTA-ATAAGCTACACTTCATTAAAATT 4829
                              -----------     v v  -    ii iv       i      
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_110219082_   4830 GAAAACTTCTGCTCTGTGAAAGAAACT--CAAGAAAATGAGAAGACA 4874
                         i       i  iv  vii  i  v   --       i   i      
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

Transitions / transversions = 1.88 (32 / 17)
Gap_init rate = 0.03 (7 / 225), avg. gap size = 5.43 (38 / 7)  

 791 20.77 9.18 0.00  chr1_110219082_110225684     5904  6110 (493)    L1M4_orf2#LINE/L1      683   908 (0)  

  chr1_110219082_   5904 TTAAAAGAATGGGAAGATAAGCCACATACTGGG-GAAAATATTTGCAAA- 5951
                          i  i i i  ii    i  v     v v    -               -
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_110219082_   5952 ---------------AGAC--ATATTCAAAATAAACAAAGAACTCTTAAA 5984
                         ---------------i   --i   i  i    v i            v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_110219082_   5985 ACTGAACAATAAGAAAACAAACAACCCGATTAAAAAATAGGCAAAAGACC 6034
                            v  i     i  i     i     i   ?      i      i  ii
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_110219082_   6035 TGTACAGTCACTTTACCAAAGAAGGTATACAGATGGCAAGTAAGCATGTA 6084
                           v i  v  i  iv         i      i     v i      ii i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_110219082_   6085 CAAAGATGCTCAACATTACATGTAAC 6110
                         v               i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.82 (31 / 11)
Gap_init rate = 0.01 (3 / 226), avg. gap size = 6.33 (19 / 3)  


1253 25.23 1.22 0.61  chr1_110226451_110228975.rev      873  1201 (1324)    L1M4_orf2#LINE/L1        1   331 (577)  

  chr1_110226451_    873 TGGAGAGATAAACCATGTTCAGGGATTGGAAAGCTCAATCGAGTAT--AC 920
                             i     vv         v         ii  i   -- v i -- v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT--ATTGTTAAG 48

  chr1_110226451_    921 ATT-CAATTCTCTGCAAATTGATAAATAAATTTAACTCAATTCTAATCAA 969
                           v-    v   iv         vv i i   i   v    i iv     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_110226451_    970 AACCCTGGCAGA-TTTTTGGTAGGCATAGACAAGCTGATTCCAAAGTTTA 1018
                           i  ii  v v-     v i  iv  v           i i   i  i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_110226451_   1019 TACAGAAACAAAAAGGAGCTAGAATAGCTAGAAAAATTTTGAAAAAGAAT 1068
                           ii    iiv  i   v i        i i  v   i           v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_110226451_   1069 AATAAAAGTGGATGAATCACACTACCTGATTTTAAGACTTACCACAAAGC 1118
                           i   iv    v  v       v  ii    i  i      i       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_110226451_   1119 TACAGTAATTGAAACATTGTGGTATTGGAAACAGAAGAGATACAAAGATT 1168
                                  ii i   v       i   v vv  i v   i i v    i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_110226451_   1169 AATGAAACAGAATAAAGAATCTAGAAATAGGCC 1201
                             i  i     vi   i  i       ii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

Transitions / transversions = 1.59 (51 / 32)
Gap_init rate = 0.01 (4 / 331), avg. gap size = 1.50 (6 / 4)  

1559 22.72 10.91 1.43  chr1_110226451_110228975.rev     1477  2035 (490)    L1M4_orf2#LINE/L1      297   908 (0)  

  chr1_110226451_   1477 TCAAAAAAAAAAAA---AAAATCTAGAAATAGACACAAACAAATGTTGCC 1523
                             vii  v i  --- i i  i       i  v  v   vv i v i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_110226451_   1524 AATTGATGTTTTACAAAGGTGCAAAGGCAATTCACCGGAGAAAGGATAAT 1573
                                v  iv    i     v   i v     vi  i     i   i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_110226451_   1574 CTTTACAACAAATTGTGTTGGAACAGATGGATATCTGTATGCAGAAAAAC 1623
                             v        v   i   i   iv      ? iii     i  i  i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_110226451_   1624 ----CTCAACCTAAACCTCACAC--TATACAAAAATCAATTCAGAATGGA 1667
                         ----i vi   ivv         --           i  i   i      
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_110226451_   1668 TCACAGATTTAAA----ACA--TAAAACTATAAAACTTTCAGGAGAAAAT 1711
                            ?   ii    ---- v --               i i  i      i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_110226451_   1712 GT-----TAA-------TGACCAGGAATTAGGCATAAAGAC--CTAAGAC 1747
                         i -----   -------     vv ii       -- v ii--  v   i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA--ATGGTTTCTTAGAT 594

  chr1_110226451_   1748 ATGACAA-AAAAGCATGATCCATAAAATAAAAATATGGGTATATTGGACT 1796
                               v-       ii v v i    v     -  i i  v        
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACT 643

  chr1_110226451_   1797 TCATCAAAGTTAAAAAAAAACT-----GCTGTAAAATACATAATAAAGGG 1841
                                 i       ----  -----   vi   iv   iv  v   ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA----CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_110226451_   1842 GGATGAAAA-ACAAGCTACAGACTATGAGAAAATATTTGCAAAACAGATT 1890
                         i -      -    v i     v iv                 v  v  v
  L1M4_orf2#LINE/    690 AG-TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_110226451_   1891 TTTAA--AAGGACTTGAATACAGAATATATAAAGAATTCTCAAAACTTCG 1938
                          i i -- i       v  v                i   i v    ivi
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_110226451_   1939 CA-CAAGAAATCAAACAACCCAATAAAAAAATGAGTAAA----------A 1977
                         i -i  i  iv    i        v?       i i   ---------- 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_110226451_   1978 GACGCTTTACCAAAGATGATATATAAA--GCAAATAAG----------GA 2015
                            ii  iv       v      i   --  v      ----------  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_110226451_   2016 TGTTCAACATCCTTAGCTAT 2035
                           i        v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (76 / 48)
Gap_init rate = 0.03 (20 / 612), avg. gap size = 3.45 (69 / 20)  


 794 30.83 9.74 2.56  chr1_110879402_110881010      500  1125 (484)    L1M4_orf2#LINE/L1      238   908 (0)  

  chr1_110879402_    500 TACTGTAAAACCTCAATAATCAGAAGAGTGTGGTGGTCCCAGCACA---- 545
                             ii   i iv  i      ii v        i--- ii   i ----
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTA---CTGGCATAAGGA 284

  chr1_110879402_    546 TAAATATACAGACCAATGGAATTGAATGGGAAGTTCAGACATAGCCTGAG 595
                           i i   i   i         v    v ii   i    v   iv iv v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_110879402_    596 GACATATATA---AATTTGTATAC-ATAAAGGTGACA-TCTCATATAACA 640
                         -    v   i---    vi v v - i  i    v  -vvi   - --  
  L1M4_orf2#LINE/    335 -ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT-T--CA 380

  chr1_110879402_    641 ATGAGAGTAGGGATGG-CTTTTTAATAAATGGTATAATGACTACTGAGTA 689
                            i - v i i  i -     i  i       iiviv   v    ii  
  L1M4_orf2#LINE/    381 ATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_110879402_    690 GCCACAC----------------------------CACACCCTCTGCCAG 711
                         ?     i----------------------------      v v i v i
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_110879402_    712 TATAAACTCCAAATAGACTGAATATTCAAATGTAAAAAGTAAAATTCTAT 761
                         v  v     v    i  iii? v iii        i iv     i v  v
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_110879402_    762 TACT---AGGAGAAATCTCAGGG--AAATATTTTATAATCATAA---AG- 802
                         v   ---  i     v vi   ?--    -i  ii i i v ii---  -
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGG 578

  chr1_110879402_    803 -AATA-TCTGTCAATATATGACTCATAAAACTAAAGCCATAAAACAAAAA 850
                         -   i- i v i i-       v vv   i vv    v i    v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAG-ATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_110879402_    851 ATTGATAAATTCAATTACAACAACAAC--AAAACTTTTGCACAGTAAAAA 898
                           v        vi i v  v   -  i--          ii vvi   ii
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAA-AATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_110879402_    899 ATATGGT-AAGACAATTCAAAGAAAAATGATAAAGTGGGA-AAAATATCT 946
                          i ivi -    v i vv     v  viv i i i     -       i 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_110879402_    947 GTAACTCAT-TATCCAGACAAATGGCTAATCTTCA---TATATAAAGAGC 992
                          i  v    -    i-  i  iv i  vi v i  ---          i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCT-GATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_110879402_    993 TGAAAGAAGTCAATAAGGTAAAAGGTAAGCAATACAATAAAAGAGTGGGA 1042
                          vvv v  v       vi-     ii  ii  iv    v?  i i    v
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATA-AAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_110879402_   1043 AATGGCAATGAACAATCAGTCCACAGACAAAGAAG---TGCATGTGCTCC 1089
                           v  vvv    i iv  v i v ---        --- i  vi  vi v
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTC---CAAAGAAGATATACAAATGGCCA 871

  chr1_110879402_   1090 TTAA-TATGTGAAAAGATACACTCCTTCATTCATAAT 1125
                         v   -i ii         i v vv v   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (107 / 82)
Gap_init rate = 0.04 (29 / 671), avg. gap size = 2.66 (77 / 29)  


2927 25.25 2.94 1.13  chr1_110932212_110934087.rev      503  1385 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr1_110932212_    503 ATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAATGGCCATACT 552
                           i     i        v      v i     i  v  i     v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_110932212_    553 GCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGCTACCC--CT 600
                         v      v i  i  i        i  v     i     iv -   --  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT-CCCAGCT 108

  chr1_110932212_    601 GACTTTCTTCACAGAATTATAAAAAACT-ACTTTAAATTTCATATGGAAC 649
                          v    i  -i     v - i v  i  - iii    v           v
  L1M4_orf2#LINE/    109 GCCTTTTTT-GCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_110932212_    650 CAAAAAAGAGCCCATATAGCCAAGACAATACTAAGCAA-AAGAACAAAGC 698
                         iiv  ii  v  viv        i     vi i iv  -          i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_110932212_    699 TGGAGGCATCACACTACCTGACCTCAAACTATACTACAAGGCTACAGTAA 748
                               vv       v  ii ii     viv        i          
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_110932212_    749 CCAAAAGAGCATGGTACTGGTACCAAAACAGATATATAGACCAATGGAAC 798
                         i   i v  ii         i iv ii i   i       i        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_110932212_    799 AGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCTG 848
                             iv  ---   v  --        vv   i    i  iiii  vi  
  L1M4_orf2#LINE/    307 AGAATTGA---GAGTCC--AGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_110932212_    849 ATCTTTGACAAACCTTACAAAAACAAGCAATAAGGAAAGACTCCCCTATT 898
                           i  i     ivv vv   i v  vv    ii       v vvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_110932212_    899 TAATAAATGG------GAAAACTGGCTAGCCATATGCAGAAAACTGAAAC 942
                         i  i      ------  v      v  ?   i     i  i v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_110932212_    943 TGGACCCCTTCCTTATACAGTATACAAAAATTAACTCAAGATGGATTAAA 992
                                  v   i i  vi                   i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_110932212_    993 GACTTAAACGTAAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGG 1042
                            i    i    i v       i      vi i           v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_110932212_   1043 CA-ATACCATTTAGGACATAGGCATGGGCAAAGACTGC------ATGAG- 1084
                         ?i- v i -  iiv   v v  vv i     v ii v ------    v-
  L1M4_orf2#LINE/    552 NGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_110932212_   1085 -TAAAAGCA-ATGCGAACAAAAGCCAAAATTGACAAATGGGGCCTAATTA 1132
                         -i       - v  -        vv     v  i    v  i i v  i 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_110932212_   1133 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAGA 1182
                           v v  i i   i  ii vv    i  v       vv i      v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_110932212_   1183 CAACCTACAGAATGGGAGAAAATTTTTGCCATCTATCCATCTGACAAAGG 1232
                              i                 v     v vii  vi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_110932212_   1233 GTTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAA 1282
                         ii vi          v  i  i     ivv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_110932212_   1283 CAA----TCCCATCAAAAAGCGGGTGAAGGATATGAACAGACACTTCTCA 1328
                            ----i  v  i?    ii   ii      v    i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_110932212_   1329 AAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAAGCTCACCATC 1376
                                 i  vi viii     i  --         i v     v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_110932212_   1377 ACTGGTCAT 1385
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.41 (128 / 91)
Gap_init rate = 0.02 (17 / 899), avg. gap size = 2.12 (36 / 17)  


2986 23.60 4.56 0.65  chr1_110952918_110954677      501  1267 (493)    L1M4_orf2#LINE/L1      112   908 (0)  

  chr1_110952918_    501 TTTTTTACAAAAATAGAAAAAC-AATCTTATAATTCATATGAAACCACAA 549
                               i  i    v  v  i -i   i  v          i  vii   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_110952918_    550 AAGACCCCAAATAGCCAAAGCAAACTTGAGCAAGAA---CAAAGCTGGAG 596
                         ii     vi          i   v     iv     ---     i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_110952918_    597 GCCTCACATTTTCTGATTTCAAAATATATTACCAAGCTACAGTAATCAAA 646
                          v      i  i ii         iv  i   v                i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_110952918_    647 ACAGTACAGTACTGGCATAAAAGCAGACATATAGACCAATGGAACAGACT 696
                              iii            iiii           i        i   v 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_110952918_    697 ATAGAG-CCTGAAATAAAACCATGCATTCATGGCCAACTGATCTTCAACA 745
                         vv    -  v        v    i    i    i   i    i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_110952918_    746 ATAGTGCCAAGAACATAAAATGGGGGAA-AATAGTCTCTTTAATAAATGA 794
                          vi         v   vv       i  -        i  i  i     i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_110952918_    795 TGTTAGGAAAACTGGATATTCATACCCAGAAGAACAACATGGAACCTTAA 844
                           i i   v         ?i  i iv  i     ii vi v i   iiv 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_110952918_    845 ACTCACACCTTATACAAAAGTCAACTCAAAATGGATTAAAGACTTAAATA 894
                         v        v         i i              i ?    i     i
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_110952918_    895 TAAGA-------CTAC--------TAGAAGAAATTTCACTGGGAAAAATC 929
                              -------   i--------         v--  iv  ?iv     
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATC 559

  chr1_110952918_    930 TTTATA---TTGGTCTGGGCAATGATTTTTTGGATTTGACACTAAAATCA 976
                           ii i---    vi i       i   i  i   v      i    v  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_110952918_    977 CAGACAACAAAAGCAAAAATGGACAAATGGGATTTGCACTGAACTAAGAG 1026
                           ii         v      i  i    v   i  -  iii  v v i i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATCAAAATTAAAA 658

  chr1_110952918_   1027 TCTTCAGCAAAGCAAAGGAAACAATCAACAGGGTGAAAA----------A 1066
                         v   iv iivvv       v  v     v ii       ---------- 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_110952918_   1067 GAGTAGGAGAAAATATTTACAAACCATAGATTAGAGAAGGGGTTAATATT 1116
                           i i             i    i    v  iv  v     ii vi   i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_110952918_   1117 CAAAATACATGAGGAGTTTGTGCAACTCAGTAGCAAAACTCCCCAAA-AA 1165
                           i    i  i i  ii iv i       i  ii    vvv --   -  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC--AAATAA 806

  chr1_110952918_   1166 CCTGATGGAAAAATGGGCAAAAGACCTGAATCAACATTTCTCCAAACAAG 1215
                           ii  v?             i  ii     vi             v   
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_110952918_   1216 ACATACAGATGCTCAACAGATATATGAAAAGATGCTCAGCATCACTAGTC 1265
                          i     i   vi   i iii i               i     ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_110952918_   1266 AT 1267
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.16 (121 / 56)
Gap_init rate = 0.02 (12 / 797), avg. gap size = 3.33 (40 / 12)  


2287 22.84 9.21 4.90  chr1_111008985_111011021.rev      689  1546 (491)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr1_111008985_    689 CATGTCCGTGAATTACAAGACTCAATATTGTTAAGATAGCCAGTCTTTC- 737
                              i i  i   iv      i              i  v vv  ii -
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr1_111008985_    738 ATATTAACCTATGGATTCAAT----TTTTTAAAAAACAGTCAAAATGCCA 783
                          v   i i   ii       i---- iii  --------       v   
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTA--------TCAAAATCCCA 105

  chr1_111008985_    784 -CAGGCTTTTGAAAAGAAATATGACAAGCTAATTCTATGATTTTTATGGA 832
                         - v v     vviv      -         i  i   vi   iv      
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_111008985_    833 AATGTAAAGGGTTTAGAATAGCTAAA-----CTTTAAAAAGATGAG-GGA 876
                             i  i  iiii        i   -----   v       v  i-ii 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_111008985_    877 GTTGGAAGGCTTACACTACTTGATTTCAAGAATTTCATTA-AAA--TACA 923
                               i i  i     v iii       -  i  - i  -   --    
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAA-AACTT-ACTACAAAGCTACA 252

  chr1_111008985_    924 GTTATTAA-ACTGTGTGGCACTGGAATAAGGATAGACAGATCAATCCAAT 972
                           v  i  -  v      i     v             v  vi   -   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC-AAT 301

  chr1_111008985_    973 GGAACAGAACACATAGTCCAAAAATAGTTCCCCATACA---A-AGTTAAC 1018
                             i    ivv v      i     i--v        --- -i  i  i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAA--ACCCATACATTTATGGTCAAT 349

  chr1_111008985_   1019 TGGCTTTTA--------GCCAAAGCC---CAA------------AGTGTT 1045
                           ii   ii--------     ii  ---   ------------   v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_111008985_   1046 TTATTCCATACAAAT--TTCTG-----------------TATGGAATAAA 1076
                           ----  -      -- v   -----------------i   v  v i 
  L1M4_orf2#LINE/    400 TT----CA-ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_111008985_   1077 ACAAACCTCAACCTCTGTTTTACACTTTACACAAAAACTAATTTGGGATG 1126
                          ii  vi vi   i  iii i    iv  i       i   i iiii   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_111008985_   1127 GATCACAGACCAAAATGTAAAAGCTAGAACCACAAAATTTCAAAAAGAAA 1176
                              ?     v        i     i   i i    i iiv i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_111008985_   1177 GCATAGAAGAATATCTCTGAAACCTTGAGGAAGGCAA-GATTTCTGTG-- 1223
                         i     i? v v    ii vi      i vv      - i     vv --
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_111008985_   1224 --GACACAAAAAGCACTGACTA-ATAAGAAAAAAT-GATACATTGTACTT 1269
                         --     v        vii v - v          -    v    v    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_111008985_   1270 CATAAATATTAAAAAATCATTGTACTTCATAA-ATATTAAAATTTTTCTG 1318
                            v  v        v i-    i     v i- i i  -----------
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTT-TTGTGCTTCAAAGGACACTA----------- 682

  chr1_111008985_   1319 CTAATCAAAAATCAAGAAAATGAATAGGGAACCCGAAGTCTGGG-GAAAA 1367
                         -----------        i    v  iv     iv  vv    -     
  L1M4_orf2#LINE/    683 -----------TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_111008985_   1368 AATTTGCAATGCATACATCTGACAAGG-ATGTATATCTAAAATGTGTAAA 1416
                         v        vv    i      i    - iv i    i i   i i    
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_111008985_   1417 CAATTCCTACAAATCAACAATAAAAGG-----TAACATT-TTTAAAAAGA 1460
                         v  i  i     v    i       i -----    viv-  ?     vi
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_111008985_   1461 GGCCATAGATTTGCACAGACATTTCACAAAAAGAGATATATAAATGGACA 1510
                            v vi      v i         v v   ii       i      v  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_111008985_   1511 ATATACACATGAAAAGG-GCTCAACATTATGAGTCAT 1546
                            vi           i-         i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (121 / 72)
Gap_init rate = 0.04 (35 / 895), avg. gap size = 3.46 (121 / 35)  


2707 26.61 2.66 2.00  chr1_111046014_111050536     3137  4038 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111046014_   3137 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATATTATTAAAAT 3186
                               i i  i     i               v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111046014_   3187 GACCCTGCTGCTTAAAGCATTCTACAGAGTCAATGCTATCCCTATCAAAC 3236
                          i vv i  v ii   viiv        v    i  v            v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111046014_   3237 TACTGGCATTTTACTGTCATTTTTACTATCAATTAGAAAAA--AATTCTA 3284
                          v ii  -------  i v     i - vv    -  v  i--i  i   
  L1M4_orf2#LINE/    101 TCCCAGC-------TGCCTTTTTTGC-AGAAATT-GACAAGCTGATCCTA 141

  chr1_111046014_   3285 AAAGTCATCTGGAACCAAACAAGAG-CCCA-AATAGCCAAAACAATCCTA 3332
                            v    v     -- vi    i -    -                i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_111046014_   3333 AGCTAAATGAACAAAGCAGTAGGCATCACATTACCCAACTGTGAATTATA 3382
                          ivv i v        iv v   vv     i v     i vii  viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_111046014_   3383 CTATAAAGCTAAGGTAACCAAAACAGCATAACACTGGTACAAATGCAGAC 3432
                            i       vi    i   i    ii iii     i i  ivii    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_111046014_   3433 ACATAGACTAATGGAACAGAAGAATCAAGAACCCAGAAATAAAGCTGCAC 3482
                          i     ii       i    --- ii   ii           v iii  
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAA---TTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_111046014_   3483 ACCTACAGCCATCTAATCTTCAACAAGTTGACAAAAATCAG-CAATGGGG 3531
                          ii  ii i  vi i  i   i     vvvi v  i i  v-        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_111046014_   3532 AAAGGATTCCCTATTCAATAAATGGTGCTGGGATAGCTAGCTAGCCATAT 3581
                             i  vvi  v     i              i i  i v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_111046014_   3582 GCAGAAGAATGAAACTAGACACCTACATTTCACCATATATAAAAATTAAC 3631
                            i         ii i   v     v iv         i          
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_111046014_   3632 TCAAGATAGATTAAAGATTTAAGTGTAAGACCTCAAACTATAAGAATCCT 3681
                             i  i   i ?   ii   i       v  v         i v  i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_111046014_   3682 AGAAAATATCAT---------TCT--G-GACATCAGCCTTAAGAAAAAAT 3719
                             i v v   ---------   -- -   v ii v-   i v  vii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGT 585

  chr1_111046014_   3720 TT----GAGTAAGTCTTCAAAAGCAATTGCAACAAAAACAAAAATTGCCA 3765
                           ----  -  v v vi        vvv         iv      v vi 
  L1M4_orf2#LINE/    586 TTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_111046014_   3766 AGTGGAACCTAATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTGTC 3815
                          i v i  i v  i   v v  i i   i  ii vv    i  v   i  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_111046014_   3816 AGCATATTAAACAG-CAGCCTACAGAATGGAAGAAAATATTCACAAACTG 3864
                          iv v v i  v  -  i  i         i          ii    iii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_111046014_   3865 TGCGATTCACAAAGGTTTAATATACAGAATCTATAAGAAACCTAAACAAT 3914
                          iiivi v i  i  vi vi   v      v     ii   iivv    i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_111046014_   3915 TCAATGAATCAAAA-ACAAATAGACCCA-TTAAAAAGTGGACAAAAGACA 3962
                              -   v    -       -     -  ?    i   i    i  iv
  L1M4_orf2#LINE/    785 TCAAT-AATAAAAAGACAAATA-ACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_111046014_   3963 TGAACAGACATTGCTCAAAAGAAGACATACACACAGACAACAAACATATG 4012
                             i       v   v        i     v ii v   i  i  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_111046014_   4013 AAAAAATGCTAAATACTAATCATTAG 4038
                             i     v  i ii ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (149 / 88)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.10 (42 / 20)  


2589 21.30 1.91 15.38  chr1_111064114_111066293      643  1689 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_111064114_    643 GAAAGATACCTTATGCTCTGAGATAAAAAGAATTAATATTATTAAAATGT 692
                                 i ii   i  vvi   vii    v        i    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_111064114_    693 ACATACTACCCAAAGTG---TACACATTCAATGTAATCTCTGTCAAAATC 739
                         vv     v      v  ---    v      i i    i  i        
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_111064114_    740 CCAATTACATTCTTCACAGAAATAGAAAAAACAATCCAAAAGTTTATATG 789
                            ii i v  i  ii       v  v  ivii    v   i  i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_111064114_    790 AAACCATAAAAGTTTCTGAATAGCCAAAGCAATTCTGAGAAAAAAGAATA 839
                         i  viii  ii vii v           i    ii   i   i     i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_111064114_    840 AAGTTGGAAACATCACACTTCCTGATTTTAAATTATGTTACAAAATGATA 889
                                 iivv          ii    i   viv ii      iiv i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_111064114_    890 GTAATCGAAACAGTTTGGTACTGGTAGAAAAACAGACACATAGACCAGTG 939
                               i i     v         i v  ii i     i     i  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_111064114_    940 GAACAGAATAGAGAGTGAAGACGTAAATTTAAACTTACATAGTTAACTAA 989
                            i     v      vv   vi    iii v  v vi  i  i  i i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_111064114_    990 CTTTTGACAGGGGCACTACAATGACACAATGGGAAAA-AACAGTTTCTTC 1038
                         i   i    i   ii i vi iv iv       i   -  i   i i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_111064114_   1039 AATAAATGGTGCTGGAAAAACTGGATTTCTGCATGCAAA-GAATGGAACT 1087
                           i            i v        v? ii        -     i ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_111064114_   1088 GGACCTTTATCTTACACCATACACACAAAATCAACTCAAAATGGATAAGA 1137
                              ii  i  i        i   -     i              v ? 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACA-AAAATTAACTCAAAATGGATCAWA 501

  chr1_111064114_   1138 AATCTGAATGTAAGACCTAAGACCATAAAACTCCTAGAAAAGAACACAGT 1187
                         i i  i         v    i  i         i     i i    i  v
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_111064114_   1188 GAAAAAGCTCCTTGACATTGGCCTTGTCAGTGACTTATTTCAACATCACA 1237
                         ?iv   v  i v    v    vi v v  i  ii  -i  vi i  v   
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-CTTAGATATGACA 600

  chr1_111064114_   1238 CCAGAA----AGGCTACAAAAGCAAAGATAAATACATGATACTATTTAAA 1283
                            i  ---- i  v       v   i   i   ----------------
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA---------------- 634

  chr1_111064114_   1284 AATGAAAAGCTAACTGGGCACAGTGGCATGCATCTGTAATTCCAGCTACT 1333
                         -----------  i   ------------------------------   
  L1M4_orf2#LINE/    635 -----------AATTGG------------------------------ACT 643

  chr1_111064114_   1334 TGTGTGGCTGAGGTGGGAGGATCCCTTGAGCCTAGGAGTCTGAGACCAGC 1383
                          -------------------------------------------------
  L1M4_orf2#LINE/    644 T------------------------------------------------- 644

  chr1_111064114_   1384 CTGGGCTATATAGCAAGACTCCCATCTCAGTAAATAAATAAATACGTAAA 1433
                         ----------------------    ---------------------   
  L1M4_orf2#LINE/    645 ----------------------CATC---------------------AAA 651

  chr1_111064114_   1434 ATAAAAAGCTTCTGCACAGCAAAGGAAACTATCAACAGAGTGAAGAGACA 1483
                           v    i   i  ii vv       v        v i      i     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_111064114_   1484 ACCTATGGAATGGAAGAAAATATTTTCAAGTCATATATCTGATAAGGG-T 1532
                            i ii      i           v   i                  -i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_111064114_   1533 TAATATCTAAAATGTATTTGTTTTGAATTATTTGCTTTCTACT--ATTGT 1580
                          vi    i i   i   -------i  vv i --   v v   --  vi 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATAT-------AAAGAACT--CTTACAACTCAATAAT 792

  chr1_111064114_   1581 G------TGTGTT-TTCAATT-AAAAGTGGGCAAAGGATCTGAATAGACA 1622
                         i------iivi v-ii     -    i            i          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_111064114_   1623 TTTTTGCCAGAGAAGACATAAAAATGGCCAATAGGTATAGAAAAAGATGC 1672
                            i -   i      i   v            i i i vi         
  L1M4_orf2#LINE/    843 TTTCT-CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_111064114_   1673 TTAACATAATTAATCAT 1689
                          i     v ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (152 / 68)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 10.06 (181 / 18)  


1146 24.12 0.00 0.00  chr1_111072361_111078731.rev     2024  2334 (4037)    L1M4_orf2#LINE/L1      598   908 (0)  

  chr1_111072361_   2024 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 2073
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_111072361_   2074 TAAACTAAAGAGCTTCTGTATAGCAAAAGAAACTACCATCAGAATGAACA 2123
                         i   v v  i i   i   iivv    i  v    i  vv i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_111072361_   2124 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 2173
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_111072361_   2174 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 2223
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_111072361_   2224 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 2273
                         i     i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_111072361_   2274 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 2323
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_111072361_   2324 TCACTGGCCAT 2334
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.31 (42 / 32)
Gap_init rate = 0.00 (0 / 311), avg. gap size = 0.00 (0 / 0)  

2826 25.42 3.60 1.46  chr1_111072361_111078731.rev     4992  5880 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111072361_   4992 TGGAAAAACATTTCATGGTCATGGATTAGAAGAATCAATATTATTAAAAT 5041
                               i i  ii    v         i     v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111072361_   5042 GGCTGTACTACATACAGTAATTTACA------ATGTTATTCATATCAAAT 5085
                            vi    v vi v v i  i    ------ i iv  i v       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111072361_   5086 TACCAATATCATTTTTCACAGATTAAAAAAAAAAAAACT-ATTCTAAAAT 5134
                          v   iivv v     ii    -----  vvi v  i  -  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-----AATTGACAAGCTGATCCTAAAAT 145

  chr1_111072361_   5135 TCACAAGGAACCCCAAAATAGCCCCAATAGCCAAAGCAATCCTAAGCAAA 5184
                            i v    viv   iiv v  vv          i     i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_111072361_   5185 AAGAACAAA-CTGGATGAATCACATTCCCCAACTTCAAACCATACCACAA 5233
                                  -i    v  v     i i     i      v v   i    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_111072361_   5234 GGCTATAGTAACCAAAACAGTGTGGTACTGGTACAAAAACAGACACAGAG 5283
                         i    i     i   i               i i  ii i     i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_111072361_   5284 ACCAATGGAACAGAATAGAAAGCCTAGAAATAAAGCCACACACCTACAAC 5333
                          i        i     v  i  i i         v   i   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_111072361_   5334 CACCTGATCTTTGACAAAGTCAACAATAACAAGCAATGGGGAAAGGACTC 5383
                           vi    i  i     i viiv   v v  vv            i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_111072361_   5384 CCTATTCAATAAAAGGTGCTGGGCTACCTAGCTAACCATGTGCAGAAGAT 5433
                         i  v     i   v         vi v  i v  ?   ii    i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_111072361_   5434 TGAACCTAGACCCCTTCCTTATACCATATACAAAAATTAAATCAAGATAA 5483
                             vi i       v   i i                  v    i  ii
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_111072361_   5484 ATTAAAGACTTAAATTTAAGACCTAAAGCTATAAAAATCTCTTTAAAAAA 5533
                           i ?    i     v     v     i        --     vi  i  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA--CTCTTAGAAGAA 543

  chr1_111072361_   5534 AACCTAGGGA-ATACCATTTAGGATATAGGCCTTGGCAAAGATTTCAT-G 5581
                            v    ?i- v i -  iiv  iv v  vi v     v i    v - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_111072361_   5582 ATG-GAGTCTCCAAAAGAAATTGCAACAAAACAAAAA-TAGACAAGTGGA 5629
                           i-  -- v       v vvv         v     -    i  i v i
  L1M4_orf2#LINE/    593 ATATGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_111072361_   5630 ACCTAATTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTATCAA---- 5675
                           i v  i   v v  v i   i  ii vv    i  v        ----
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_111072361_   5676 ------------CCTACAGAATTGGAGTAAATATTCATAAACTATGCATC 5713
                         ------------  i       v    v       iii   ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_111072361_   5714 TGACAAAG---TTATAACATCCAGAATCTATAAGCAATTTAAACAAATTA 5760
                            i  i ---  i  ---        v     iv  i ivv    v i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTA---TCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_111072361_   5761 ACAAACACAACACAAACGACCCCATT-AAAAATGGGCAAATGACATGAAT 5809
                          i  vv v  v     ii    v   -             v  iv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_111072361_   5810 AGACATTTCTCAAAAGAAGACATACATGTAGCCAATAAGCATGTTAAAAA 5859
                                    v        i     vi i           ii v    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_111072361_   5860 ATATTCAACATCACTAATCAT 5880
                           ii         ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (130 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.00 (45 / 15)  


3524 19.52 8.10 0.36  chr1_111092840_111095408     1237  2076 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_111092840_   1237 AAAGATATTC-ATGTTCATGGATTAGAGGACTTCATATT---AAGAAGAC 1282
                                 i -             i  i     v     ---    v i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_111092840_   1283 AATACTCCCCAAAGAGATATACAGATACATAAAAATAATTATCAATATCT 1332
                                      vv   v       v  vviv   vvi      v   i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_111092840_   1333 TAA-TGTCATTTTTTGCACAAATGGAAAATCTGATCTTAACATTCATATA 1381
                         i i-  i -         v    v  v  v      i   v        i
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_111092840_   1382 GAATTACAATAGATTC----TAGTCAAA-CAATTTTGAAAAAGAATAA-- 1424
                            v i   vi  ii ----   i    -    i           v  --
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_111092840_   1425 --GTTGAAGAATTTACATTTTCTGATATTAATATATATTTCAAAGCCACA 1472
                         --    i  i i i   i  i ii  v i  v iv  i v      i   
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_111092840_   1473 GAAACCAAACGTAGTATGGTACTGGCATAAGGATAGACACACAGGCTGAT 1522
                          v  i   i-ii   i                       i i  iiii  
  L1M4_orf2#LINE/    253 GTAATCAAG-ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_111092840_   1523 AGAACAGAATTCAGAGTGCAATTATAAACTCTCACATTCACAGACAATTC 1572
                         i   i      v     v  ivv      i vi     i ii v     v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_111092840_   1573 ATTTGTGACAAAGATACCAAGACAATTCAATGTGGAAAAAAATCATCTTT 1622
                             vi     i i i       v        -  i   i   vi     
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTT 400

  chr1_111092840_   1623 TCAATAAATTATGCTGGGACAACTTGATGTTGACATGTAAAAGAATGTAG 1672
                             i    vi             v   i?iv     i         v  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_111092840_   1673 --G---------CTCACATCATATACAGAATATAACTCAGAAT------- 1704
                         -- ---------      i        i  vv       i   -------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_111092840_   1705 -----------------------CTTTCAAA------GAAGAAAGCGTAG 1725
                         -----------------------  v v   ------       i i   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_111092840_   1726 TGATACATCTTCATGATCTTGGATTTTGCTATGGATTCTTAGATTTGACA 1775
                         v?i  v      i   i     i  vv  v    v         v     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_111092840_   1776 CCAAAAGCCCAAGACACAAAAGAGAAAAT-GATAAGTTGAAATTAATGAA 1824
                                 v    vv        i     -     i   i v  v  v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_111092840_   1825 AATTTAAAACTTTCCTGCATCAAGGCATATCATCAAGAAAGTGAAAAGAC 1874
                             v        iv   v    i v i ii                   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_111092840_   1875 AACTCACAAAATAGGAGAAAATATTTGCAG-CCATATATCTGATAAGGT- 1922
                            i    i   i                i-i                v-
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_111092840_   1923 CTGGTAATCAGAATATGTAAAGAACTCTTACAAGTCAACAACAAAAAGAC 1972
                           v   vi        i                v    i  i        
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_111092840_   1973 AA----CCTAATTTAAAGCTGGGCAAAGGACTTGAATAGACATTTCTCCA 2018
                           ----  i    ?   iv           i                   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_111092840_   2019 AAGAAGATATATAAAAGGCCAATAAGCACATGAAAATATATTCAATATCA 2068
                                    i   v                    v  ii    i    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_111092840_   2069 CCAGTCAC 2076
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.40 (94 / 67)
Gap_init rate = 0.02 (17 / 905), avg. gap size = 4.18 (71 / 17)  


2808 24.19 5.39 1.92  chr1_111097017_111098843.rev      502  1336 (491)    L1M4_orf2#LINE/L1       45   908 (0)  

  chr1_111097017_    502 TAAAAAGTCCATACTACCCAAAGTGATCTACAGATTCAATTCAATCCCTA 551
                            i v v v     v      v                iv         
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr1_111097017_    552 TCAAAATATCAATGACATTTTTTACAGAAATAGAAAAAAAGC-AATCCTA 600
                                vi  iivi v      i       v  v  ---  -i      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA---GCTGATCCTA 141

  chr1_111097017_    601 AAACGCATATTAAACCACAAAATACCCTAAATAGCTAAAGCTATCTTGAG 650
                            iv     vi  vii   iiv    vi      i   i v       i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_111097017_    651 AAAAGAGAACAAAAGCAGAGGCATCACACTACCTGACTTTAAGGTATGCT 700
                            ii        ivii    vv       v  ii i  i  iiiv i  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_111097017_    701 ACAAAGCAATAGTAACCAA-ACAGCATGCTGCTGGTATAAAAACAGACAT 749
                                v i     i   -    ii  v i    i    ii i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_111097017_    750 A--GACAAATGGAACAGAATAGAGTGCTCAGAA-TAAATTAACACATTTA 796
                          --  iv       i     v   v ii     -    iiv i       
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_111097017_    797 CAGCCAACTCATTTTTGACAAAGGTACCAAGAGCACACCTTGGAGAAAGG 846
                         ii i   i v     i     i   i      v  iv vv   i     i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_111097017_    847 ACCCTCTCTCCAATAAATGGTGCTGGGAAAACTGGATATCCATGTGCAGA 896
                          ivv   i i   i              v         ?   ii    i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_111097017_    897 AGGATGAAACTAGACCCCTCTCTCTCACCACTTACAAAAATCAACTTGAA 946
                           i     ii i       vi   v     iv         i    ii  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_111097017_    947 ACTGAAT-AAAGACTTAAATGTAAGACCCAAAGCTATGAAACTACTGGAA 995
                          -  i  - ?    i           v i   i    i     vi i   
  L1M4_orf2#LINE/    492 A-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_111097017_    996 GAAAACAT----------------GACATTGGTTTGGGCAAGAATATTTT 1029
                                 ----------------   v    v  i     vii v i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_111097017_   1030 TAATAAGACCTCAGAAACA-GAG----AAGAACAAAAATAGACAAAT-GG 1073
                         vi   v   vi  i  i  -i  ----  i iv         i    -  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_111097017_   1074 AGTGACATCAAACTGAAAAGCT---GCACAGCAAAGGAAACAATCAGCAG 1120
                          v v-       v v    i  --- ii vv       v  v    iv i
  L1M4_orf2#LINE/    641 ACTT-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_111097017_   1121 GGTGAAGAGACAGCCTGTGAAATGGGAGAAAATATTCTCAAACTATGCAT 1170
                         i     i     i  iiiii                iv    ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_111097017_   1171 CTTACAAGCTGTTAATATCCAGAGTATATAAACAATTCAAATAACTCA-T 1219
                           v i   vvii vi        i        v  i  vv i      - 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_111097017_   1220 AGCAAAAGAACAAATAAT----TTTTAAAATGAGCAAAAGATCTGAATAG 1265
                          ii    ii        i----  ?v      i     i   i       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_111097017_   1266 ACATTTC--------AGATATTTGACCCAAGACAAACAGCCAACA-TTAC 1306
                                --------      ----------     ii     i -vi  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATAT----------ACAAATGGCCAATAAGCAC 879

  chr1_111097017_   1307 ATGAAGAAAATGCTCGACATCACTAATCAC 1336
                              -  i      i      ????????
  L1M4_orf2#LINE/    880 ATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (131 / 68)
Gap_init rate = 0.02 (19 / 864), avg. gap size = 3.21 (61 / 19)  


2776 28.67 1.78 0.89  chr1_111118751_111124138     3997  4896 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111118751_   3997 TGGGAA-ACATTCCATGCTCATAAATTGGAAGAGTCAATATTGTTAAAAT 4045
                            i  - i  i     i    ii         v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111118751_   4046 GCCCATACTGCCCAAAGCAATTTGCAGATACTATGCTAATCCTATCAAAC 4095
                          v v     v      vii  i i     v v i  v vi         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111118751_   4096 TACCAACACTATTCTTCACAGGACTAGAAAAAAACT-ATTTTAAAATTCA 4144
                          v   i vviv  i  ii   i v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_111118751_   4145 TATGGA---GCTAAAAAC---AAATAGCCAAGATAATCCTAAGCAAAAAG 4188
                               ---  v iii  ---i         i i    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_111118751_   4189 AACAAAGCTGGAAGCATCATGTTACCTGACTTTGAACTATACTACAAGGC 4238
                                i    i vv   iii v  ii i  ii  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_111118751_   4239 TATCATAACCAAAACAGCATGGTACTGATACAGAAACAGATGCATAGACC 4288
                           ivi   i   i    ii        ii i iii i   iii     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_111118751_   4289 AATGGAACAGAATAGAGAGCCCAGAAATAATGCTGCACACCTACAACCAT 4338
                                i     v     i          vv iii   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_111118751_   4339 CTGATCTTCAACAAAGCTGACAAAAACAAGCAATATGGAAAGGAC--TCC 4386
                         i    i   i    i v  v   i v  vv    iv      i i--  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_111118751_   4387 ATACTCAATAAATGGTACTGGGCTAACTGGCTATCCATATGCAGAAGATT 4436
                         v --    i       i     vi      v  ?   i     i    v 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_111118751_   4437 GAAACTGGACCCCTTCCTTATACCATATACCAAAATCAACTCAAGATGGA 4486
                            ii         v   i i         v     i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_111118751_   4487 TTAAAT-TTTAAATCTGAAACCTAAAACTTTAAAAACCCTGGGAAATAAC 4535
                          i ? v-ii     v i i v        v     vi i i i i v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_111118751_   4536 CTAGG---AAATACCATTCTGGACAAAGGCCCTGGTAAAGACTTGAT-GA 4581
                         v    ---    -- -   vv   vvv  viiv  i  v ii  vv -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_111118751_   4582 TGAAGATGCCAAAAGCAATTGTGACAAAAACAAGAATTGATAAATAAGGC 4631
                          - v  ii         vvv ii      iv  i   v       vi i 
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_111118751_   4632 CTAATTAAACCAAAGAGCTTCTGAACAGAAAGGGAAACTATCAACAGAGT 4681
                         i v  i   viv  i i   i  vi vvv  i   v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_111118751_   4682 AAATAGACAGCCTGGAGCATGGGAGGAAATATCTGCAAACTATGTATCTG 4731
                         i  v     i  iiv  v       i      i      ii  i      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_111118751_   4732 ACAAAGGTCTAATATCCA-AATCTATAAGAAGGTTAAACTAATTAACAAG 4780
                          i  i  v  vi      -   v     ii iv ivv  v v i  i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_111118751_   4781 CAAAAACCAAACAACTCCATTAAAAAGTGAGCAAAGGACATGAATAGACA 4830
                         v    iv    i   i v   ?    i  i        iv          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_111118751_   4831 TTTGTCAAAGGAAGTCACACATGTAGCCAACAGGCATATGAAAAAATACT 4880
                            v  v  i    vi i   vi i     i i   i       i  i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_111118751_   4881 CAGCATCGCTAATTAT 4896
                           i    i????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (161 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.71 (24 / 14)  


2882 23.43 6.99 1.17  chr1_111136027_111140132.rev     2758  3615 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111136027_   2758 TGGAGAGATATACCACGTCCATCTACCAGGA-ATTCAATATTTTTAAGAT 2806
                             i      v   i  i   vv iii i - i i      v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111136027_   2807 GTCAATTCTTCC-AAATTTATCTATAGATT----GTAATCCCCATCAATA 2851
                          v    v  i  -     v     i     ---- i      i     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111136027_   2852 TTACAGCAGAATTTTTTGTAGGCTTCAAGAAATTAATTCTAAAATTCATT 2901
                          iv    v vv       i  ivv ii v  ii i  i           v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_111136027_   2902 TGGGAATGCAAAAGACTTAGAATAGTAAAAATGAGTTTGATAAAGAA--- 2948
                            i       ii   ii       iv    ii vi    v      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_111136027_   2949 CAAAATTGGAGTACAAACACTACCTAATTATATTGCTTTCTATAAAACTA 2998
                             i      v  vv     v  i    vi vvi   v   i   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_111136027_   2999 CAACAATAAAGACAGGATAGCACTGGTGT-----TAAATAAATATATCAA 3043
                           ii   v       vi i i     ii -----  i i v   v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_111136027_   3044 GAGAACAGAAT--AGAGTCCA----------TATGCAT--ATGGACAACT 3079
                         vi   i     --        ----------i  i   --    v   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_111136027_   3080 GATTTTCAAAAAAAATACAAAATTAATATATTACAGAATGAAGAATACTT 3129
                                i v  iii i v  iviv  vi v ivi   ---      v i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA---AGAATAGTC 397

  chr1_111136027_   3130 TTTTCAACAAATGGTGCTGGAACAATTGTCTATTAATATGCAAAA--ATG 3177
                                             i    i  vv  ?iv i        --   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_111136027_   3178 AACTTGCATTTATACCTCTCTCCATACG---AAATCGTAACTAGTGATGA 3224
                           v   v iiiv      v v     ii---    --     vivi   i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAAT--TAACTCAAAATGG 495

  chr1_111136027_   3225 ATCATAGATCTAAAGGTAAAATCCAAAACTATAATTCTCC-AGAAGGAAA 3273
                             ?   i     v    i v i          vv   i-     i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_111136027_   3274 TAT------------TTGCAACCTTGG-TTATGCAAAGAGTTCTCAGATA 3310
                         i  ------------ i ii       -   v    v iv    i     
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_111136027_   3311 AGACACCAAAAGCACAAT------------AAGTTGATAAATTGGACTTC 3348
                         v                v------------  i v               
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_111136027_   3349 TTCAAAATTAAAAACTTCTGCTCTTCAAAAGACACTGTTAAGAGAATGAA 3398
                         v                i  iv       i      i i    i i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_111136027_   3399 AAGACAAGGCACAGAA-GGGACAAAATATTTCCAAATCACACAGGAGATA 3447
                                vv       -    v         v       i i vvv    
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_111136027_   3448 AAAGGCATGTATCCAGAGTATAAAAACAACTCTTGAAGCTCAATGGTAAG 3497
                          ii i v          i    v   v       iv i      ii   i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_111136027_   3498 AAAATAAACAATCCAATTTTTAAAATGGGCAAAAGATCAGAACAGACAAT 3547
                           i i   i  i      ?v-            i   iv   i     v 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_111136027_   3548 TCACCAAAGAAGATACTATATGGATGGCAAATAAGGACATGAAAAAAATT 3597
                           v            ---  iii     v      v         i - v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATA---TACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chr1_111136027_   3598 CTCTACTTCATTACTCAT 3615
                            v  v   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (115 / 83)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.50 (70 / 20)  


2886 23.42 5.17 1.26  chr1_111162854_111168723     4507  5377 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_111162854_   4507 AAAAACATTCCATGCTCATAGATAGGAACAATCAATATTGTTAAAATGGC 4556
                            i i  i     i    i   v    v v i           i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_111162854_   4557 CATACTGCCCAAAGCAATTTGTAGATT-AGTGCTATTTCTATCAAACTAC 4605
                         v     v      vii  i ii     - ii  v  ii        v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_111162854_   4606 CAA-TGTCATTTTTTACAGAATTAGAAAATACT-ATTCTAAAATTCACAT 4653
                           i-  i -      i     v v  v  -i  -  i          i  
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATAT 151

  chr1_111162854_   4654 GGGTCTAGAAAAGAGCCCAAATAGTCAAAGCAATCATAAGCAAAAAGAAC 4703
                           ivv iv  ii  v  vi     i    i     v i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_111162854_   4704 AAAGCTGGAGGCAC-CACACAATCTGACTT-AAAACTATACTGCAACACT 4751
                             i      -  -     vvi ii i  -      -    i   vi  
  L1M4_orf2#LINE/    202 AAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr1_111162854_   4752 ATAGTAATCAAAACAGTATGGTACTGGTACAAACACAGACACACAGACTA 4801
                          i         i     i         i i  iv i     i i   ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_111162854_   4802 ATGGAACAGAATAGAGAATCCAGAAATAAAGCAACACATCTACAACCATC 4851
                               i     v    i            v v i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_111162854_   4852 TGATGTTTGACAA---TAACAAG------CAATGGGGAAAGGACTCCCTA 4892
                             v  i     --- iv    ------            i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_111162854_   4893 TTAAACAAATGGTGCTGGAATAACTGGCTAGCCATATACACAAGACTGAA 4942
                           v               i i      v  ?   i  i  v    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_111162854_   4943 ACTGGACCTCTTTCTTTCACCATATACAATAATCAAATCAAGATAAATTA 4992
                         ii      i  vi  iv            v   i  v    i  ii  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_111162854_   4993 AAGACTTAAATGTGAGACGTAAAACTATAATTAAAACCCTAGAAGAAAAT 5042
                         ?    i       i   vv           ---  vi i          i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAA---AACTCTTAGAAGAAAAC 546

  chr1_111162854_   5043 CT-GGGACATACCATTCTAGACATAGGTCTTGGCAAAGATTTCAT-GATA 5090
                         v -  ?ii v i -   vv   v v  vi v     v i    v -    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_111162854_   5091 AAGTGCCCAGAAGCAACTGAAACAAAACCAAAAATAGACAATTGGGACCT 5140
                         viiii  - i     vvv v       vv         i  v v    i 
  L1M4_orf2#LINE/    596 TGACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_111162854_   5141 AATTAAA-CTAAA-------GTACCT----GTGCAC-AGCAAGA----GA 5173
                         v  i   -i    -------  i i ---- vi   - v     ----  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_111162854_   5174 AACGATCAATCTACAGAATGAGAGAAAACATTTGCAAACTATACATCTGA 5223
                           v  -   i i        i       i         ii   i      
  L1M4_orf2#LINE/    695 AAAGA-CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_111162854_   5224 CAAA--ATTTATTATTCAGAATTTATAAGGAACT--TA-AATT----AAC 5264
                         i  i-- i  i -  i      v     i     --  -  i ----  i
  L1M4_orf2#LINE/    744 TAAGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_111162854_   5265 AAGGAGA-AAACAACCCCATT-AAAAATGGACAAAGTATATGGTCAGACA 5312
                           ii   -   i     v   -        i     v  v  ivi     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_111162854_   5313 CTTCTCAAAAGAAGGCATACATGTGGCCAACAACCATATGAAAA-ATGCT 5361
                         i     v       ii     vi       i  v  i       -     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_111162854_   5362 CAACATCACTTATCAT 5377
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (127 / 74)
Gap_init rate = 0.03 (30 / 905), avg. gap size = 1.87 (56 / 30)  


3136 25.68 1.53 0.71  chr1_111190895_111195406     3171  4019 (493)    L1M4_orf2#LINE/L1       53   908 (0)  

  chr1_111190895_   3171 CAA-ACTACCTAAAGCAATCTATAGATTCAATGCAATCCCTATCAAAGTA 3219
                            -   v  i   vii     i        i               i v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_111190895_   3220 CCAATGACATTCATCACAGAAATAGAAAAAAAAACT-ATCCAAAAACTTA 3268
                            iivi v  iv ii       v  v  i----  -    v    i i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATTCA 148

  chr1_111190895_   3269 TATGGAACCACAAAAGACCAAGAAGAGCCAAAGCTATCTTAAGCAAAAAG 3318
                                vii   ii    v    v       i v     i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_111190895_   3319 AACAAAACTGGAGGAATCATATTACCTGACTTTAAATTATGCCACAGAAC 3368
                               ii       v   i i v  ii i  i   viv i i   i i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_111190895_   3369 TATAATAACCAAAACAGCATGGCATTGGCATAAAACCAGACA----GACC 3414
                           i i   i   i    ii   i i        iivi     ----  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_111190895_   3415 CATGGAACAGAACAGAGAACCTGGAAACGAATCCACACATTTACAGTGAA 3464
                         v      i    iv    ii ii    ii  i   i       ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_111190895_   3465 CTCATTTTTGACAAAGGTGCCAAGAAAATATACTGGGGAAAAGACATTCT 3514
                         i v     i     i          vv  vi v        ii i v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_111190895_   3515 CTTCAGTAAATAGTTCTGGGA-AACTAGATATCCACATGCAGAAGAATGA 3563
                         i    ii    i  v      -    i    ?         i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_111190895_   3564 AACTAGACTCCTATTTCTCGCCATATACAAAAGTCATATACAAAGTAGAC 3613
                          ii i   i    ii  v i            i i - iv    i i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTA-ACTCAAAATGGAT 497

  chr1_111190895_   3614 TAAAGGATTAAATCTAAGACCTCAAACTATGAAACTACTATAAGAAAACA 3663
                         i ?  ivi     v     v  v       i     vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_111190895_   3664 TTGATGAAAATCTCCAGGACATTTGTCTGAGCAAAAATTTCTTGAGTAGT 3713
                          v i? v      i iv   v  v vi ii    vii      iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_111190895_   3714 ACCCCACAAACACAGACAACCAAAGCAAAAACGGACAAATGGGATCACAT 3763
                           v   v  i    ii    v    v     ii  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_111190895_   3764 CAAG-TTAAGAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAAG 3812
                            i-    i  -   i  ii vv       v  v     v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_111190895_   3813 AGACAACCTCCAGAATGGGACAAAATATTTGCAAACTACCCATCTGACAA 3862
                                 iv          v              ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_111190895_   3863 GGGATTAAAAACCAGAATACGTAAGGAGCTCTAACAACTCAACAGGAAAA 3912
                             i viv v        ii   i  i    v         i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_111190895_   3913 AAA-----AATCTGATCAAAAAATGAGCAAAAGATTTGAATACACATTTC 3957
                          i -----  i ii  i?       i     i          v       
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_111190895_   3958 TCAAAAGAAGACATACAAATAGCAAGCAGGCATATGAAAATGTGTTCAAC 4007
                           v        i        i  v ii i   i       vi  i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_111190895_   4008 ATCACTGATCAT 4019
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (145 / 69)
Gap_init rate = 0.01 (9 / 856), avg. gap size = 2.11 (19 / 9)  


2981 22.44 2.37 7.12  chr1_111242757_111244675      500  1426 (493)    L1M4_orf2#LINE/L1       26   908 (0)  

  chr1_111242757_    500 TTGGAAGAATGAATATTGTTAAAATGTCCACACTACCCGAAGTGATCTAC 549
                                 v v           i   v v i   v   i  v        
  L1M4_orf2#LINE/     26 TTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chr1_111242757_    550 AAATTCAATGCAATCTCTATCAAAATTCCAATGACATTTCTGACAGAAAT 599
                          i      i      i          i   iivi v   i vi       
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr1_111242757_    600 GGAAACAAA---ATTCTAAAATTCATATGGAGCAATATAAG--ACCATAA 644
                         v  --   i---  i                --   ii   --   vvi 
  L1M4_orf2#LINE/    126 TGA--CAAGCTGATCCTAAAATTCATATGGA--AATGCAAGGGACCCAGA 171

  chr1_111242757_    645 ATAGCTGACGCATTCCTGAGCAAAAATAACAAAGTTGGAGGCATCACACT 694
                              ii vi  v  i   iv  i  v              vv       
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_111242757_    695 ACCTTATCTCAAAATCTACTAGAAAGCTGTAGTAATCATAGCAGTATGGT 744
                         v  iv  i      ii     v      ii        vii    i    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_111242757_    745 GCTAACATGAAAGCAGACAGATAGACAAATGGAACAGAATAGAGA--CTA 792
                         i  ii   i iiii     v     iv       i     v    -- i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_111242757_    793 GAAATAAACACAAGCTTATGTGGTCAACT-ATTTTCAACAAGGACACCAA 841
                                  v  vi v v i       i -      i      iii    
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_111242757_    842 GAAGACATC--ACGGAGAAAAGACAGTCTCTTCCATAAACAGTGTTGGGA 889
                           v--   i-- i  i    ii i     i   v i   ii   i     
  L1M4_orf2#LINE/    372 GAC--CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_111242757_    890 AAACTGGCGTTGGGGATACATGCAAAAGAATAAAATCGAATCCCTA--TC 937
                         v      -i ---i?vi              i  i i i i     --  
  L1M4_orf2#LINE/    420 CAACTGG-AT---AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_111242757_    938 ACACCATATGCAAAAAATCAACTAAAAAATACACCAAAGATCTGAGTGTA 987
                                  i      - i    v    - iv i  ?   i  i i    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAA-TTAACTCAAAA-TGGATCAWAGACCTAAATGTA 513

  chr1_111242757_    988 AGACTTAAAATCACAAAACTCCTAGAATAAAACATGATGGGAAAGTTTCT 1037
                            vi     ii i       i     v       iiv? v   vi   v
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_111242757_   1038 TGACATTGGTCTTATCAGTGATTT-TTGGACAATATACCAAAAGCACAAG 1086
                             v    vi viv  i  i   -  i  i vv i              
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_111242757_   1087 CAACAAAAGCAGAAATAAATAAGTGGGACTGCATCAAACTTAAAAGCTCC 1136
                                  v i     i    i v     v       v      i  ii
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_111242757_   1137 TGCACAGCAAAGGATACAATCAAGAAAGGGAAAAG-CAACCTATGGACTG 1185
                           ii vv       i  v          v      -     i ii  v  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_111242757_   1186 ACA---AATGTTTGCAAACCAGTTAACTCTTAAGGGATTAAAATCTAAAG 1232
                         iv ---   i        i  vv  v  vv       i viv   i i i
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_111242757_   1233 TATATAAGAAACTGATGTAATTCAATAGCGAAACAATGAATAACCCAATT 1282
                                ii    vv ii  i      iii   vi ii            
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_111242757_   1283 TAAAAATGAGCAAAGGGAAGTTCCACCAAGTAATGGTGAGCATTCTGGGC 1332
                         ?       i       ----------------------------------
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGG---------------------------------- 829

  chr1_111242757_   1333 TCTGAAAAAATGAGCAAAGGATCTGAATAAACATTTCTTAAAAAAAGACA 1382
                         --------------------  i      i        iv   i    i 
  L1M4_orf2#LINE/    830 --------------------ATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_111242757_   1383 TATAA-----CAACAGATATATAAAAGGATGCTCAACATCACTAATCAG 1426
                           i  -----   i iii i  i   i              ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (136 / 68)
Gap_init rate = 0.02 (18 / 883), avg. gap size = 4.89 (88 / 18)  

 556 26.43 7.05 3.08  chr1_111242757_111244675     1578  1804 (115)  C L1M4_orf2#LINE/L1   (26)   882   647  

C chr1_111242757_   1804 TCAAACTAAAAGGCTCCTGCACAGCAAAAGATACAATCAAGAAAGTGAAA 1755
                              v v   ii  ii  ii vv    i  i  v               
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chr1_111242757_   1754 AAGCAACCTATAGACTGATA---AATGTTTGCAAACCATTTAACTCTGA- 1709
                          ii     i i   v  iv ---   i        i   v  --     -
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA--TCTGAT 744

C chr1_111242757_   1708 -AGGGATTAATATCTAAATTATATGAGAAACTGACCTA--ACACAGTAGC 1662
                         -     i vi    i i v     i ii    -- i  --  v  i  ii
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACT--CTTACAACTCAATAAT 792

C chr1_111242757_   1661 AAAACAATGATTAGCCCAGTTGAAAAATGAGCAAAGAGCAGTGAGTAAA- 1613
                             vi ii v  i    i  ?       i      iii-v   i  i -
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGAC 841

C chr1_111242757_   1612 --TCTTCC---GGAGATACTTACCAGAAGCCAA---GCAGATG 1578
                         -- ii   --- i     --   v ivi     ---   v   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATA--TACAAATGGCCAATAAGCACATG 882

Transitions / transversions = 2.47 (42 / 17)
Gap_init rate = 0.04 (10 / 236), avg. gap size = 2.30 (23 / 10)  


2693 26.04 8.32 0.36  chr1_111245806_111247654.rev      518  1358 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111245806_    518 TGAAAACACATCCCATGCTCATGGATGGATAAAATCAATATTGTGAAAAT 567
                           i   v i        i        v iv i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111245806_    568 GACCATACTGCCAAAAGCAATTTACAAATTCAATGCAATCCCCATCAAAA 617
                          i v     v  v   vii  i    i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111245806_    618 TACCACCATCATTCTTCACAGAGTTAGAAAAAACAATTCTAAAATTCATA 667
                          v   v vv v  i  ii    iv v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_111245806_    668 TGGAACCAAAAAGGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAATGAA 717
                              viiv  i   v  v v         i   vvi i iv  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_111245806_    718 --AACTCTGGGAACATCACACTACCTGATTTCAAACTATATTATAAGGCC 765
                         --  v iv i i  -       v  ii        viv  i  i  i  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_111245806_    766 ATAGTTACCAAAACAGCATGGTACTGGTATAAAAATATGCACATAGACCA 815
                          i   v i   i    ii         i    ii   vi  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_111245806_    816 ATGGAACAGAATAGAGAACCCAGAAATAAACCCGAATATTTACAACCAAC 865
                               i     v    ii              iv i     iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_111245806_    866 TGATCTTCAACAAAG----------------------------------- 880
                             i   i    i -----------------------------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_111245806_    881 -------------------------------CCACATGTAGGAGAATGAA 899
                         -------------------------------       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_111245806_    900 ACTGGATCCTCGTCTCTCACCTTATACAAAAATCAACTCAAGATGGATTA 949
                         ii    i  iiii   v    v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_111245806_    950 AGGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGACAATAACACT 999
                         ?i   i    iv     v  i           v ii    vi v    iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_111245806_   1000 GGAAAAACCCTTCTCGACATTGGCTTAGGCAAGGATTTCATGACCAAGAA 1049
                           ?iv  vi    vi   v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_111245806_   1050 GCCAAA-GCAAATGCAATAAAAACAAAGATAAATAGCTAGGACCTAATTA 1098
                         i     -   v v    i    iv   i   i   iv v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_111245806_   1099 AACTAAAGAGTGTTTGCACGGCAAAAGGAACAGTCAGCAGAGTAAATAGA 1148
                           v v  i iiv    ii vv    i iv  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_111245806_   1149 CAACCCACAGAGTGGGAGAAAA-ATCTTCACAATCTATACATCTGACCAA 1197
                                    i          -  i v  -    -   i      iv i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGATAAG 747

  chr1_111245806_   1198 GGACTAATATCCAGAATCTACAACGAACTCAAACAAATCAGTAAGAAAGA 1247
                              vi          v  i  v      vv    v   i   v   i 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_111245806_   1248 AACAAACAATCCCATCAAAAAGTTGGCTAAGGACATGAATAGAGAGTTCT 1297
                         i     i  i  v  i?    i v   v     iv        v v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_111245806_   1298 CAAAAGAAGATATACAAATGGCCAACAAACATTTGAAAAAATGCTCAACA 1347
                          v                       i  i  iv      i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_111245806_   1348 TCACTAATGAT 1358
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (130 / 86)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 10.43 (73 / 7)  


2650 24.75 3.88 3.11  chr1_111262739_111268559     4428  5328 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111262739_   4428 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAATATCATTAAAAT 4477
                               i i  i    vi        v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111262739_   4478 GGCCATACTGCCCAAAGTAATTTGTAGATTCAATGCTATTGAATTGAATG 4527
                            v     v      v i  i ii        i  ----------   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC----------AATC 90

  chr1_111262739_   4528 C--ATCAAACTACCATTGATATTCTTCACAGACTTAGAAAAAAACT-ACT 4574
                          --      v v   viviiv  i  ii    vv v  v  i--  - ii
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATC 138

  chr1_111262739_   4575 TTAAATTTCATATGGAA-TCAAAGAAACCCCCATATAGCCAAGACAATCC 4623
                         i    v           - vv   ii    vv -        i      i
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGA-ATAGCCAAAACAATCT 187

  chr1_111262739_   4624 TAAGCAAAAAGAACAAAGCTGGAGGTATCACACT-ACTGACTTCAAACTA 4672
                          i iv  i          i      vv       -v ii i      viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_111262739_   4673 TACTAGAAGGCTACAATAACCAAAACAGCAAGGTACTTGTATCAAAACTG 4722
                              v  i      i   i   i    iiv      v i  v ii iv 
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_111262739_   4723 ACATATAGACCAACGGAACAAAACAGAGACCTCAGAAGTAACACCACACA 4772
                                  i   i    i i  iv    vii     i   vv   i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_111262739_   4773 TCTAAAACCATCTGATCTTTGACAAATCTGACAAAAAAGAAGCAACAGGG 4822
                          i  viii  vi    i  i     ivv  v   i vv- vv   ii   
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC-ATTCAATGGGG 386

  chr1_111262739_   4823 AAAGGATC-TCTTATTCAATAAATGGTGTAAATAGTGCTGGAAAAACTGG 4871
                             i  v-    -     i        ---------    i v      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTT-TTCAACAAATGGTG---------CTGGGACAACTGG 426

  chr1_111262739_   4872 CTAGGCATATG-----GA--GAAACTGGACCCCTTCTTTACACCTTATAC 4914
                         v  ?v  i   -----  --   ii         v i i     v     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_111262739_   4915 AAAAATTAACTCGAGATGGATGAAAGACTTAAATGTAAAACCCAAAACCA 4964
                                     i i      v ?    i         i v i     i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_111262739_   4965 TAAAAACCCTAGAAGAAAACCTAGGC-CATACCATTCAGGACATAGGCAT 5013
                              vi i           v    ?-i v i -   iv   v v  vv 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTT 575

  chr1_111262739_   5014 GGGCAA-GACTTCATGAATAAAACACCAAAA--ACAATTGCAACAAAAGC 5060
                         i     - ii   v ii   vi         --    --          v
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGA 623

  chr1_111262739_   5061 AAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCCA 5110
                               v  i    v   ii v  i   v v  i i   i  ii vv v 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_111262739_   5111 AAGAAACTA----------------ACATACCTGCAGAATGGGAGAAAAT 5144
                          i  v    ----------------   -   ii                
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACA-ACCCACAGAATGGGAGAAAAT 722

  chr1_111262739_   5145 TTTTGCACTCTACCCATCTGACAAAGGTCTAATATCCAGAATTTACAAGG 5194
                         v      vvii ivi      i  i  v  vi          v  i  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_111262739_   5195 AACTTAAACAAATTTACAAGAAAAAAATAAACAATCCTATCAAAAAGTGG 5244
                             ivv    v iv i  v     i i   i  i  v  i?    i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_111262739_   5245 GCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGTGACCAA 5294
                                  v    i     i     v        i  vi vi  i    
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_111262739_   5295 AAA--ACAGGAAAAGAAGCTCAACATCACTGATCAC 5328
                         v  --   v       v           ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (126 / 93)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.00 (63 / 21)  


2875 27.44 1.10 2.41  chr1_111270953_111273678.rev     1326  2236 (490)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr1_111270953_   1326 ATTCCATGCTCATGGACCAAAGTAATTAATCCTGTTAAAATGACCATGCT 1375
                           i     i       iiii iv v     vi      i   i v  i  
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_111270953_   1376 ACCCAAAGCAATCTATAGATTCAATGCAATCCATATTAAAATACTAATGA 1425
                         v      vii     i        i       v   i     v i iivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_111270953_   1426 CATTCTTCACATAATTAGAAAATTTAA----AAAAATTGTATGGAATCAC 1471
                          v  i  ii  v  v v  v  vi i ----    v ii       vii 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_111270953_   1472 AAAAGACCTCAAACAGCTAAAGGAATACTGAGCAAAAAGAACAAAGCTGT 1521
                           ii    ivi  i   i   iv   vi   iv  i          i  v
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_111270953_   1522 AGGTGCCACACTACCAGACTTCAAAATGTACTACAAAGCTGTAGTAA-CA 1570
                            vvi      v  vi i       iv            ii     -  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_111270953_   1571 AGAACAACAAAAAGGAGCATGGTATCAGCATATAAACAGACACATAGACT 1620
                            ----  ------- ii     iii     vii i     i     ii
  L1M4_orf2#LINE/    260 AGA----CA-------GTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_111270953_   1621 AATGGAAGAGAATGGAGAATTCAGAAAGTAATCCATGTATCTCCAGCCAA 1670
                                v     v    i i      vv  i    ii  i vii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_111270953_   1671 TTGATTTTTGAATTTTGAATTAAAGGCACCAAGAACACTCATTGGAGAAA 1720
                                 i  ---------i  i  ii      v  i   v   i    
  L1M4_orf2#LINE/    349 TTGATTTTCGA---------CAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_111270953_   1721 GGATAGTCTCTTTAATATATGGTGCTGGGAAAACTGGATACCTATGTGCA 1770
                          i       i  i  i v            v         ? i ii    
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_111270953_   1771 GAAGAATGAAACTAAACTCCCACCTCTCACCCTATTCAACAATAAGCTCC 1820
                         i         ii ii  i  i     v    v   v   v   v i   v
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_111270953_   1821 AAATGGGACAAATAACCAAATCTAAGACCTCAAACTGTAAGACCACTAGA 1870
                               iv  ? v v i    v     v  v     i   i  ivi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_111270953_   1871 AAAAACAATAGTAGAAACACTTCAGGACATTGGTCTGGGAAAAGATTTTA 1920
                          i   vv    v? v  vv    iv   v    vi i  v  v i   iv
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_111270953_   1921 TGAATAAGACTTCAAACACACAGGTAACAAAAGCAAAAACA----AATGG 1966
                          ii   v   vi    vi    i i        v     i ----   v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_111270953_   1967 GGCTATATAAAACTAAAAAAGCTCTATATAACAAAGAAAATAATCAACAT 2016
                          i  vi  v   v v     vi i i iivv     i v iv     v v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_111270953_   2017 AAAGAAAAGACAGCCTACAAAATGGGAGAAAATATTTTCAAACTATTCAC 2066
                          iv         i  i   i                 v    ii  vi i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_111270953_   2067 CCAATAGGGGATTAATATCCAGAATACACAAGAAACTCAAATATCTCAAC 2116
                          ii   i    i vi           i i  ii     vv i v     i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_111270953_   2117 AGCAAAAGAACAAACAATTCAAT-AAAAAGGGGGCAAATAATATGAACGG 2165
                          ii    ii     i  ii    -?    iv       vi  v    ii 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_111270953_   2166 ACATTTCTCAAAAGAAGACATACAAATGGCTAATAAATCAATATACAAAA 2215
                                  v        i           i     ii-- i  iv   i
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC--ACATGAAAAG 887

  chr1_111270953_   2216 ACACTCAACATCGCTACGCAT 2236
                          ii         i????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (156 / 90)
Gap_init rate = 0.01 (8 / 899), avg. gap size = 4.00 (32 / 8)  


2295 26.84 6.68 2.07  chr1_111274287_111279833     4187  5054 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111274287_   4187 TGGAATAACATTTCATGCTCATAGATTGGAAGAATCAATATCATTAAAAT 4236
                              vi i  ii    i    i          v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111274287_   4237 GGTCATTCTGCCCAA-----TTTACAGATTCAATGATATTCTTAACAAAC 4281
                           iv  v  v     ----- i           i vv  i i  v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111274287_   4282 TACCAA-TATTATTCTTGACAAAATTAGAAAAACT-ATTCTAAAATTTAT 4329
                          v   i- iiiv  i   vvi     -  v  i  -  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chr1_111274287_   4330 ATGGATCCACAAGAG-CCTA-AATAGATAGAGCAATCCTAAGCAAAAAGA 4377
                              vvii    i -  i -     vi i i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_111274287_   4378 GTAAAGCCAGAGACATAACATTACCTGACTTTA-----TACTATAAAGCC 4422
                         ii    iii   ivv v   i v  ii i  i -----     i     i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_111274287_   4423 ACAGTTACCAAAACTGCTTGGTAGTAGTACAAACACAGACATA------- 4465
                              v i   i  v iv     v i i i  iv i       -------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_111274287_   4466 ATGGGACAAAATAGAAAATG-AGAAATAATGCTGCACACCTACAGCTATC 4514
                             i i i   v  i i v-        vv iii   ii  ii ii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_111274287_   4515 TGATCTTCAACAAGGCCAACAAAAACAAGCAAAGGGGAAGGGA----CTC 4560
                             i   i      viiv   i v  vv   v      i i ----  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_111274287_   4561 CAAGTCAATAAATGGTGCTTGGATAACTGGCTA-------GCAGAAGATT 4603
                         i---    i          v   i      v  -------   i    v 
  L1M4_orf2#LINE/    400 T---TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_111274287_   4604 GAAAATGGATCCATATCTTTTCCCTTTCACCAGATACAAAAATTAATTAA 4653
                            iv    i  v  -------   iv     v             i v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTA-------CCTCACACCATATACAAAAATTAACTCA 489

  chr1_111274287_   4654 AAATAGATTAAGAATGTAAATGCAAGACTTCAAACCATAAATATCCTAGA 4703
                             i   i ?ii iv      i    vi v    i     vv  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_111274287_   4704 AGAAAATCTAGGAAATACTCTTTTCAACATTAGCCTTGGGAAAGAATTTC 4753
                               iv    ?ivv v    ivii  v  i v-  i  v  vii    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTC 588

  chr1_111274287_   4754 T-GGCTAAGTCCCCAAAAGCTACT-GCAACAAAATAAAGCAAAAAAGACA 4801
                          -i v  v v v        -  v-         v   ---   v   i 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGC-ACAAGCAACAAAAGAAA---AAATAGATA 634

  chr1_111274287_   4802 AGTGGGACCTAATTAAACTAAAGAGCCTTTTCACATCGAAAGAAACTATA 4851
                          i v    i v  i   v v  i i i   vii v  i  i  v     v
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_111274287_   4852 AACAGAGTAAAAAGACAATCTGCAGAATGAGAGAAAATATTTGCAAGCTA 4901
                           v i   i         i ii       i                iii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_111274287_   4902 TGCATCCAAATAAGG--TTTAATGTGTAGAATCTATAAGGAACT-TAACA 4948
                          ii   ii -     --i  i- i vi     v     i     - v   
  L1M4_orf2#LINE/    735 TATATCTGA-TAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACA 782

  chr1_111274287_   4949 ACTGATTAA-AAAAAAAT---TAACCCCATTAGAAAGTGGGCAAAGGACA 4994
                            v v   -     i i---      v   ?i   i           iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_111274287_   4995 TTAACAGACAC--CTCAAAAG------------TGGCCAAGAA--ACATG 5028
                          v  i     i--   v    ------------       v  --     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_111274287_   5029 AAAAAATGCTCAGCATCACTAGTCAC 5054
                             i       i     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (144 / 86)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.81 (76 / 27)  


2798 26.39 1.74 2.73  chr1_111302573_111307693.rev     3714  4630 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111302573_   3714 TGGAGAAATATCCCATGCTCATGAATGGAAAGAATACATTTTGTTAAAAT 3763
                             i i          i     i  v i    v vv  v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111302573_   3764 GGCAACACTGTCCAAAGCAATTTATAGGTTACATGCTATTCCTATCAAAC 3813
                              i   vi     vii  i  i  i  vv i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111302573_   3814 TACCAAC---ATTTTTCACAGAATTAGAATGAACT-ATTCTAAAATTCAT 3859
                          v   i ---v     ii     v v  -ii i  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr1_111302573_   3860 TTGGAACAACAACAACAACAACAACAAAAGCCCTAACAGCCAAAGTAATC 3909
                         v     vvi   -------------iii v  vv  i       ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAA-------------GGGACCCAGAATAGCCAAAACAATC 186

  chr1_111302573_   3910 GTAAGCAAAAAGAAAAAAGCTGGTGGCATCACATTACTCAACTTTAAACT 3959
                         v i iv  i     v    i   v  vv     i v i   i  i   vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_111302573_   3960 ATATTACAAGGCTACAGTAATGAATATAGCATGGTACTAGTACAAAAACA 4009
                         v  i     i           v  v i  ii       i i i  ii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_111302573_   4010 GACACCTAGACCAATGCAACAGAATAGAGAGCCCAGAGATCATGCTACAC 4059
                             iv    i     v  i     v     i     i  v vv i i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_111302573_   4060 ACCTATAACCATCTGATCTTCAACAAAATCAACAAAAACAAACAAGGAGG 4109
                          ii   iii  vi    i   i    iiviiv   i v  vv   v i  
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_111302573_   4110 AAAG----GTCTCCCTATTCAATAATTAATGCTGAGTTAACTGGCTAGTC 4155
                             ----    i----     i  v ii     i vi      v  ?i 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTT----TTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_111302573_   4156 ATATGTAAAAGATTGAAACTGGACCCCTTCCTTACACCATATACAAAAAT 4205
                          i   i      v    ii         v   i                 
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_111302573_   4206 CAACTTAAAGGTGGATTAAATACCTAAATGTAAAACCTAAAAATATAAAA 4255
                         i    i   i-     i ? v            i v      v       
  L1M4_orf2#LINE/    483 TAACTCAAAA-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_111302573_   4256 ACTCT-AGAAGAAAAGCTAGG---AAATGCCATTCTGGATACAGGTCCTA 4301
                         -    -         vv    ---    -- v iv  ivivii   --  
  L1M4_orf2#LINE/    532 -CTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGT--TA 576

  chr1_111302573_   4302 GCAAATA-TTTCAT-GATGAGGATGCCGAAAGCAAATGCAATAAAAACAA 4349
                          vv   i-    v -   - v  ii  i      v v    i    iv  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_111302573_   4350 AAATTAATTAATGGGACCTTATTAAAGTAAAGAGCTTTTGCACAGCAAAA 4399
                             vi  v   v    i i  i   i v  i i      ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_111302573_   4400 TAAACTGCCAACAGAGTAAACAGAGAATTCACAGAACGGGAGAAAATATT 4449
                         v v   ii   v i   i  v   v  ii       i             
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_111302573_   4450 TGCAAACTGTGCATCTGACAAAGGTCTAATATCCACAATGTATAAGGAGC 4499
                               iii ii      i  i  v  vi      v   i     i  i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_111302573_   4500 TTAAAAAAATTAACAACTGGAAAACAAACAACCCTATAAAAAAGTGGGCA 4549
                          ivv v  v i  i  ivii  i     i     v  v?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_111302573_   4550 AATAGTATGAACAGACACTTCTCAAAAGAAGACAAACATGTGGTCAAAAA 4599
                           vii v    i     i     v        i v   vi   i   v  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_111302573_   4600 GCATATAAAAA--TCCTCACCATCAGCAATACA 4630
                            i  i    -- v    v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.56 (41 / 16)  

 996 24.01 3.95 2.43  chr1_111302573_111307693.rev     4647  4975 (146)    L1M4_orf2#LINE/L1      575   908 (0)  

  chr1_111302573_   4647 TGGGCAAAGACTTAATGACTAAAACACCAAAAGCAATGGCAACAAAAGCA 4696
                          i     v ii  vv iiv  vi            vvi          v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_111302573_   4697 AAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTG-----CAGA 4741
                              v  i    v   ii v  i   v v  i i   i  -----  i 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_111302573_   4742 G--CAC-ATGAAAATATGTTCAGTGTGAATAGGCAACCTACAGAATGGGA 4788
                          --   -  v  i v --------     v  i     i           
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAA--------GTGAAAAGACAACCCACAGAATGGGA 716

  chr1_111302573_   4789 GAAAATTGTTGCAACCTATCCATCTGACAAAGGGCTAATATCCAGAATCT 4838
                               vv      vii  vi      i  i  i  vi          v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_111302573_   4839 ACAAAGAACTTAAACAAATTTACAAGAAAAAAACAA----CCCCATCAAA 4884
                          i        ivv    v iv i  v     i    ----   v  i?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_111302573_   4885 AAGTGGGTGAAGGATATGAGCAGACACTTCTCAAAAGAAGACATTTAAGC 4934
                           i    ii      v   ii     i     v        i  vi  ii
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_111302573_   4935 AGCCAACAAACATATGAAAAAA-GCTCATCATCACTAGTCAT 4975
                         i     i  i  i       i -     v     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (46 / 32)
Gap_init rate = 0.02 (6 / 334), avg. gap size = 3.50 (21 / 6)  


2815 28.11 0.88 0.88  chr1_111308666_111312768.rev     2706  3612 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_111308666_   2706 GGAAATACATCCCATCCTCATGGATGGGTAGAATCAATATTGTGAAAATG 2755
                              v i       vi        v  v   v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_111308666_   2756 ACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCTCATCAAAAT 2805
                         i v     v  v   vii       i      i     i ii        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_111308666_   2806 ATCATCATCATTCTTCACAGAACTAAAAAAAAAAAAATCCTAAAATTTAT 2855
                         vi  v vv v  i  ii     v vi v  ivvi --          i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCAT 149

  chr1_111308666_   2856 ATGGTACCACAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGA 2905
                             v vii   ii  v  v v         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_111308666_   2906 ATAAATCTGGAGACATCACATTACCCGAATTCAAACTATACTATAAGTCT 2955
                          i   vi     ivv     i v   i v      viv     i  iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_111308666_   2956 TTAGTCACTAAAACAGCATGGTATTGGTATAAAAATAGGCACATAGACCA 3005
                         vi   v ii  i    ii     i   i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_111308666_   3006 GTGCAACAGAATAGAGAATGCAGAAGTAAGCCCAAATACTTACAGCCAAC 3055
                         i  v  i     v    i v     i   i    v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_111308666_   3056 TGATCTTCAACAAAGCAAACAAAAACATAAAGTAGGGAAAGGACACCCTA 3105
                             i   i    i vviv   i v   vv i i       i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_111308666_   3106 TTCAACAGATGGTGCTGGGATGGTTGGCAAGCCACATGTAGAAGAATGAA 3155
                                i            iiii   vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_111308666_   3156 ACTGGATCCTCATCTCTCAACAAAATCAACTCAAAAATCAACTCAAGATG 3205
                         ii    i  ii i   v  v  v --i ---       i       i   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATA--TA---CAAAAATTAACTCAAAATG 494

  chr1_111308666_   3206 AACCAAAGACTTAAATCTAACACCTGAAGCCATTAAAATCCTGGAAGATA 3255
                         i i  ?    i     v   v v  i  i i  v   v  i i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_111308666_   3256 ACATCAGAA-AAACCCTTGTAGACATTGGCTTAGGCAAGGATTTCATGAC 3304
                             vi ?i-   i i i  -   v    v        v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_111308666_   3305 GAAGAACCCAAAAGCAAATGCAACGGAAACAAAGATGAATAGATGGGACT 3354
                         v v  vv         v v     ii  iv   i  ii   i  v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_111308666_   3355 CAATTAAGCTAAAAAATTTCTGCACAGCAAAGTAAA-TATCAGCAGAGCA 3403
                         iv  i  iv v     i  i  ii vv     v v -     iv i  ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_111308666_   3404 AACAGACAACCCATTAACTGGGAGAAAATTTTCATAAACTATGCATTCTA 3453
                           v          ivi v           v  iii   ii  ii  iiv 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_111308666_   3454 CAGAGAACTAATATTCAGAATCTACAAGTAACTCAAATAAATCAGCAAGA 3503
                         i ii i   vi   i      v  i  iv     vv i  v   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_111308666_   3504 AAAAAA-AAAT--CCCA-TCAAAAAGTGGGCTAAGAACATGAATAGACAA 3549
                             i -    --    - i?    i     v   i iv          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_111308666_   3550 TACTCAAAAGAAGATATACACATGGCCAACAA--ACATGAAAAAATGCTC 3597
                          v   v              v        i  --         i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_111308666_   3598 AACATCACTAATTAT 3612
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (150 / 101)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 1.60 (16 / 10)  


2594 27.26 3.96 1.24  chr1_111323741_111327043.rev     1935  2818 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111323741_   1935 TGGAGAAACATTCCATGCTCATGTATAGGAAAAATCAATATTGTTAAAAT 1984
                             i i i  i     i     v  v    i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111323741_   1985 GGCCATATGGCCCAGAGCAATTCATAGGTTCAATGCTATTTGTATCAAAG 2034
                            v   ivv    i vii  ii i  i     i  v  iiv       i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111323741_   2035 TACCAAC---ATTTTTCACAAAAGTATAAAAAAACT-ATTTAAAAATTCA 2080
                          v   i ---v     ii  i  --  vi v  i  -  iiv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr1_111323741_   2081 TATGGAACCAAAAAAGAGCCTGAATAGCCAAGAGAATCCTAACCAAAAAG 2130
                                viiv  ii  v  v          i v    i i vv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_111323741_   2131 AACAAAGCTGCAGGCATCACATT-----ATT---AGACTATACTACAAAG 2172
                                i  v   vv     i -----   --- i   -          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_111323741_   2173 CTACAATACACAAAACAGCACAGTACTGGTACAAA-ACAGACACATAGAT 2221
                              i  vv   i    iiii       i i  i- i     i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_111323741_   2222 CAAAGGAACAGAATAAAGAGCCCAGAAATAATGCCACACAC----AACCA 2267
                            v    i     vi    i          vv   i   i----iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_111323741_   2268 TCTGATATTTCATAAAATTTACCAAAAACAAGCAATGTGGAAAAGACTCC 2317
                         vi    -    ivv  ivv i    i v  vv     v     ii ivvi
  L1M4_orf2#LINE/    348 ATTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_111323741_   2318 CTATTCCATAAATGGTGCTGTGATAACTGGCTAGCCATATGCAGGAGATT 2367
                           v   v i           v  i      v  ?   i     ii   v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_111323741_   2368 GAACCTGGACCCTTTCCTTACATCATATACAAAAAATAACTCATGATGGA 2417
                            vi       i v   i   i            v       vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_111323741_   2418 GTAAAGGCTTAAAT-CAAAAATCAAAATCTATAAAAATGCTGGAAGATAA 2466
                         vi ?  i i     -i  i iii    -        v vi i     v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAA 545

  chr1_111323741_   2467 CCTAGGAAATAGAT-TTC-TGGCTGTAGGACCTGGTAAAGACTTTAT-GA 2513
                          v    ?i-  i  -   -  i iv i  -iiv  i  v ii  iv -  
  L1M4_orf2#LINE/    546 CATAGGNG-TAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGA 593

  chr1_111323741_   2514 TGAAGATGCCAAAAGCAATTGCAGCAAAAACAACAATTAACAAATGGGAT 2563
                          - v  ii         vvv   i     iv  v   vi i    v   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_111323741_   2564 CTAATTAAACTAAAGAGCTTGTGCACAGCAAAAGAAACTATCAATAGAGT 2613
                         i v  i   v v  i i   v  ii vv    i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_111323741_   2614 AAA----CAACCTACATCATGGGAGAAAATATTTGGAAAGTATGCATTCA 2659
                         i  ----     i   vv                 v   vi  ii  iii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_111323741_   2660 ACAGAGG---TGTAAAATCCAGACTATAGGAAA----CTTA-AATT--AC 2699
                          i ii  ---    ---      v    vi  i----    -  i -- i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTA---TCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_111323741_   2700 AAGCAGAAAACAAACAACCCCATTAGAAAGTGGGCAAAGGACATGAGCAG 2749
                           vv i  i     i     v   ?i   i           iv   ii  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_111323741_   2750 ACATTTTTCCAAGGAAGACATTCATGCAACGAACAAGTACATGACAAAAT 2799
                               i     i     i  v  viiii v  i   i      v  i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_111323741_   2800 GCTCAATGTCATTAATTAT 2818
                               ii   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (148 / 89)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.00 (46 / 23)  


 234 31.82 1.52 0.00  chr1_111328443_111334819.rev        8    73 (6304)    L1M4_orf2#LINE/L1      301   367 (541)  

  chr1_111328443_      8 TGAAACAGGA-TAAAAGCTCAGAAATAAACCCACGTGTTTAAAGCCAATC 56
                           i  i  i - i i  ii              iiii    vi i    i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_111328443_     57 AACTTTTTACAAGAATG 73
                         i i   iv     ii  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG 367

Transitions / transversions = 9.50 (19 / 2)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1)  

3216 25.77 1.22 0.77  chr1_111328443_111334819.rev     4983  5886 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111328443_   4983 TGGAAGAACACACCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5032
                              ii i iv     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111328443_   5033 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5082
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111328443_   5083 TACCAATGACATTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5130
                          v   iivi v  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_111328443_   5131 TATGGAACCAAAAAAGGG-CTCACATT-GCCAAGACAATCCTAAGCCAAA 5178
                                -- viv     - i  v v -     i      i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_111328443_   5179 AGAACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTACAAG 5228
                                  i     ivv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_111328443_   5229 GCTATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5278
                             i     i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_111328443_   5279 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAA 5326
                         i        i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_111328443_   5327 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 5376
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_111328443_   5377 CCCTATTCAATAAATGGTACTGGAAAAACTGGCTAGCCATATGTAGAAAG 5426
                         vi  v     i       i    i v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_111328443_   5427 CTGAAACTGGATCCCTTCCTTACACCTTATACAAACATTAATTCAAGATG 5476
                         v    ii    i    v   i     v        v     i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_111328443_   5477 GATTAAAGCCTTAAATGTTAGATGTAAAACCATAAAAACCCTAGAAGAAA 5526
                            i ?  v i       v   vv      i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_111328443_   5527 ACCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5575
                           v    ?i- v   -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_111328443_   5576 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATC 5625
                           vi            vvi          vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_111328443_   5626 TAATTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGATTG 5675
                          v  i   v v  i i   i iii vv    i  v    i  vv i v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_111328443_   5676 AACAGGCAACCTATAGAATGGGAGAAAATCTTTGCAATCTACTTATCTGA 5725
                           v  i     i i               v       vii iv       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_111328443_   5726 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCGAACAAATTTACAAGA 5775
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_111328443_   5776 AAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5821
                             i    ----   v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_111328443_   5822 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5871
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_111328443_   5872 ACCATCACTGGCTAT 5886
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


2589 26.84 3.12 2.00  chr1_111335882_111339077.rev     1808  2705 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111335882_   1808 TAGAAAAACATTCCATGCTCATGAACAGGAAGAATCTGTATTGCTAAAAT 1857
                          i    i i  i     i     i iv      v ivi     i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111335882_   1858 GGCCATACTGCCCAAAGCAATTTATAGATTCATTGTTATTCCTACCAAAT 1907
                            v     v      vii  i  i       vi iv  i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111335882_   1908 TACCAACAATGTTTTTCACAGAATTAGAAAAAACT-ATT-TGAAATTTTT 1955
                          v   i viiv     ii     v v  v  i-  -  i- i     iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_111335882_   1956 ATGGAAACA-AAAAAAGCCTGAATAGCCAAATCAATCC----AAAGGAAA 2000
                                ii-  iii v  v           v     i----    i i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_111335882_   2001 ATAAAGACAGGTGGAGGAATCACATTACTCGACTTTAAAAGTATACTGGT 2050
                          i    ----v       v     i v i i i  i    v -    ivv
  L1M4_orf2#LINE/    200 ACAAAG----TTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACA 244

  chr1_111335882_   2051 AGCCTACAGTAATAAAAATAACATGTCACTAGTACAAAGACAGACAGATA 2100
                          iv          v  i i iii  vi   i i i  i  i     v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_111335882_   2101 GACCCATGGAACAGGTCAAAGAACCTACAAATAAAGCCAGACACCTACAA 2150
                           i v      i  ivivi   ii i v       v   v   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_111335882_   2151 TCATCAGATCTTCAACAAAACTGACAATTACAAGCAGTGGTGAACAGACT 2200
                            viv   i   i    iiv  v   vvv  vv  i   v   -   v 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAAT 393

  chr1_111335882_   2201 --TCCTATTCAATAAATGGTGCTAGGATAATGGGCTAGCCATAAGCA--- 2245
                         --  i -     i          i   i  iv  v  ?   i v   ---
  L1M4_orf2#LINE/    394 AGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_111335882_   2246 GAGTA---TTGGATCTCTCCCCTACCTTTCTCCATATACAAAAATAAACT 2292
                           i i---     -----         iv v              v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGA-----CCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_111335882_   2293 CAGGATGGATTAAAGACATAAATGTAAACCCTAAAACTATAGAAACCCTA 2342
                           ii      i ?    v         ivv           i  vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_111335882_   2343 GAAGAAAAACTAGG---AAATACCATTCTGGAAATAGGCCCTAGCAAAGA 2389
                                 vv    ---    -- -   vv  vv v  viivi    v i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_111335882_   2390 CTTCAT-GATAAAGAGCCCAAAAGCAATTACAACAAAAACAAAATTTGAT 2438
                         i   v -    v-  vv         vvvi        iv    v v   
  L1M4_orf2#LINE/    585 TTTCTTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_111335882_   2439 AAAGGGGACCTAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTAT 2488
                            vv    i v  i   v v  i i   i  iiivv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_111335882_   2489 TAACAGAGTAAACAGACAACTTGCAGAATGGGAAAAAATATTTGCAAACT 2538
                         i  v i   i  v       iii          i              ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_111335882_   2539 ATGCATCTGACAAAGGTCTAATATCCAGAATGTATAAGGAACTT------ 2582
                           ii      i  i  v  vi          i     i     i------
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_111335882_   2583 ---AAGAAGCCAAAAACAAACAACTTCATTTAAAAAGTGAGAAAAGGACA 2629
                         ---  v  vvv   i     i   iiv   ?     -  i v      iv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATT 832

  chr1_111335882_   2630 TGGACAGACACTTCTTACAAGAAGATATACACGTGGCCAATAAGCATATT 2679
                           i i     i    ivv             vi             i  v
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_111335882_   2680 TTAAAATGCTCAATATCATGAATCAT 2705
                         vv  i        i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (137 / 101)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.30 (46 / 20)  


1658 23.00 21.06 4.01  chr1_111359917_111362333.rev     1153  1926 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_111359917_   1153 GAACGATATCACATGTTCATGCATTAGAAGAATTAATATTGTTAAAATGT 1202
                            v      v          v   i     v             i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_111359917_   1203 TTATACTAACCAAAGTGATCAACAGATTTAATG-----------AAA--- 1238
                         iv     vv     v     v       i  i -----------   ---
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_111359917_   1239 CCAG-TGTCATTCTTTATAG----TGGGAAAACAATCCTTAAATTTGTAT 1283
                             -  i -  i   ii  ----  iv  ivii     v     ii   
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_111359917_   1284 GGACTCACAGAAGACCT-GAATAGCCAAAGCAATTGTGAACAAAAGTCAC 1332
                            vvii  iii    i-           i    iv    ----------
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA---------- 191

  chr1_111359917_   1333 AAAAGTCAGATGTAACAAAGTAACAAAGTCAGATGTATCACATTATGTTA 1382
                         -    ------------   -        ii  v vv     i viviv 
  L1M4_orf2#LINE/    192 -AAAG------------AAG-AACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_111359917_   1383 CCTCAAAATATACTACAAGGCTATAGTAAACAAAATAGCATAGTACTGGA 1432
                         ii      iv        i    i     v   i i  ii i       v
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_111359917_   1433 GCAAAAACAGACACATAAACCAGTAGAATAGAATAGAGAGTCCAGAAATA 1482
                         ii  ii i     i   i i  i i         v               
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_111359917_   1483 AATTCATACATTTACAGTCAGCT--CTTTTGACAAACAAGCCAAGACCAT 1530
                           ii          ii    ii --i   i     iviv           
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_111359917_   1531 ACATTAGGGAAAGGAT----------------GGTGCT------------ 1552
                         v  v i       i  ----------------      ------------
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_111359917_   1553 -------------------------------------------------- 1552
                         --------------------------------------------------
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_111359917_   1553 ----------------------------TAAACATAAGA--------TAC 1566
                         ----------------------------    ii     --------  i
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_111359917_   1567 GAAACTACTAGAAGAAAAC-TGGGC--AAATGTTTCAGAACATTTGTCTG 1613
                         i     vi           - i  ?--    -i   ivi  v  v vi i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTA 576

  chr1_111359917_   1614 GGCAAAGATTTCTTGAGTAAGAC-CTGA-----CAGGCAACCAAAGCCAA 1657
                              v i      iii  v   - ii -----  i     v    vv  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_111359917_   1658 AATTTAAAAATGGGATAACATCAAGCTAAAAAACT-----GCACAGAAAG 1702
                            vv v    v   ivv      iv v       -----  vivi  i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_111359917_   1703 AAAC-------AACGTGAATAGACAACCTACAGAATGGAAGGAAATATTT 1745
                          v  -------  v     v        i         i  i        
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_111359917_   1746 GAAAACTAGTCATCCAAAAAGGGATTAATAACCAGAATATATAAGGA--T 1793
                          v   ii vvi   ii v      i vi  v             i  -- 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_111359917_   1794 TTTAAATAACTCAATAGCAATAAAAA-ACAAATATTTCTATATAAAA-TA 1841
                         i   --i         ---       -       vii v  v?    - i
  L1M4_orf2#LINE/    777 CTTA--CAACTCAATA---ATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_111359917_   1842 GGCAAAAGATTTCAATAGACATTTGTAAAAAGAAAACA--CAAATTGTCA 1889
                               i     v           v vv      i i --     v i  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_111359917_   1890 ACAGATACATGAAGAAATGCTCAACATCACTTATAAT 1926
                          i iii       i i             ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (109 / 67)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 7.46 (194 / 26)  


3032 22.99 4.24 2.90  chr1_111515684_111520253.rev     3186  4081 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111515684_   3186 TGGAAAGATATTTCATGTTCCTGGATTTGGAAGAATCAATGTTGTTCAAA 3235
                                    ii       v      -      v i   i     -  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT-GGAAGACTTAATATTGTT-AAG 48

  chr1_111515684_   3236 ATGTCCATACTACCCCAAGCAATTTATAGATTAAATGCAATCCCTATCAA 3285
                            v v     v   v  vii  i  i     v  i              
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_111515684_   3286 AATACCAAA-GACATATTCACAGAAATAGAAAAAA-AATGCTAAAATTTA 3333
                            v   iv- v v v  ii       v  v  iv-i  v        i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_111515684_   3334 TGTGTAAGCACGAAAGACTGAGAATAGCCAAAGCTATCCTGAGCAAAAAT 3383
                          i  v  iii i ii   iv            i v   i   iv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_111515684_   3384 AACAAAACTGGAGGAATCACATTATCTGATTTCAAATTATACTACAGAGC 3433
                               ii       v     i vi ii        viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_111515684_   3434 TATAGTAACCAAAACAGCATGATACTGGCAT---GCT-GACACATAGACC 3479
                           i     i   i    ii  i         --- v -    i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_111515684_   3480 AATGGAATACAATATCTAACCCAGAAACATATCCGTACATCTACAGTGAG 3529
                                  v   vvvv ii       i v i  i     i  ii  v i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_111515684_   3530 TTCCTTTTTGACAAAGACACCAAGAACATACACTGGGGAAAGAACAGTCA 3579
                           vv    i     i iii      v   v  v           i    v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_111515684_   3580 CTTCAATAAATTGTGCTGGGAAAACTGGGTATCTATATGCAGAAGAATGA 3629
                         i     i    v         v      i  ? i i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_111515684_   3630 AACTAGACCCCTA--TCAGTCACCATATACAAAAATCAAAT-AAAATGGA 3676
                          ii i        --   --                i  v -        
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCA--CACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_111515684_   3677 TTAAAGACTTAAATCTAAGAACTCAAACTATGAAACTACTAAAATAAAAC 3726
                          i ?    i     v     i  v       i     vi  i  v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_111515684_   3727 ATTTAGA---AACTCTGTAGGACATTGGACTGAGCAAAGATTTCTTGAGT 3773
                           --  i---  v   viiv   v    ii ii    v i      iii 
  L1M4_orf2#LINE/    547 AT--AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_111515684_   3774 AATACCCCAAAAGCACAGGCAACCAAAGCAAAAATGGACAAATGGGATCA 3823
                          vv  v           i     v    v      i  i    v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_111515684_   3824 TATCCAGGTAAAAAGTTTTCGCATAGCAAAAAAAAAAAAACAAAAACACT 3873
                         i   v ii v    ii   i iiivv    ii -------------    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-------------CACT 681

  chr1_111515684_   3874 --TAACAAAGTGAAGAGACAACTCACAGAATGGGAGAAAATATTTGCAAA 3921
                         --i  v        i       i                           
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_111515684_   3922 CTATCCATCTGGCA-------TATAT-----ATATAGAAGAAGCTCAAAC 3959
                         ii  vi     ii ------- i   -----     v  ii i   vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_111515684_   3960 AACTCTATAGGAAATAAGTCTTTTACTAATAATTCAATT--AAAATGAGC 4007
                              v   iv   -   ------  v     ii     --      i  
  L1M4_orf2#LINE/    782 AACTCAATAATAAA-AAG------ACAAATAACCCAATTWAAAAATGGGC 824

  chr1_111515684_   4008 AAAAGAC------AGAAATT---CAAAAGAAGACATAAAAATGGCAAACT 4048
                            i  i------   v   --- v        i   v       v  iv
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_111515684_   4049 CGTGTATGAAAGG-TGCTCAACATAATCAATCAT 4081
                         v iii      i -          v ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (126 / 78)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.05 (64 / 21)  


3157 28.04 0.55 0.33  chr1_111549693_111556156     5066  5971 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111549693_   5066 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATTAATATCGTGAAAAT 5115
                              ii i  i     i        v      v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111549693_   5116 GGCCATACTACCCAAGGTAATTTATAGATTCAATGCCATCCCCATCCAGC 5165
                            v     v     iv i  i  i        i  v     i   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111549693_   5166 TACCAATGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5213
                          v   iivi i  i   i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_111549693_   5214 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGGAAAAAG 5263
                                viiv  ii  v  viv  v     iv     i i ii  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_111549693_   5264 AAGAAAGCTGGAGGCATCATGCTACTTGACTTCAAACTATACTACAAGGC 5313
                           v    i      vv   ii  v iii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_111549693_   5314 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGATATATAGACC 5363
                                 i   i    ii        vi iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_111549693_   5364 AATGGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5413
                                i     v   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_111549693_   5414 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGTGAAAGGATTCCCT 5463
                         i    i  i     ivv  v   i v  vvv     v     i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_111549693_   5464 ATTTAAAAAATGGTGCTGGGATAACTGGCTAGCCATATGTAGGAAGCTGA 5513
                         v  i  v              i      v  ?   i   i ii iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_111549693_   5514 ACCTGGATCTCTTCCTTACACCTTACACAAAAATTTATTCAAGACAGATT 5563
                          vi    i i  v   i     v  i         v i    i ii   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_111549693_   5564 AAAGACGTAAATATTAGACTTAAAACCATAAAAACCCTAGAGGAAAACCT 5613
                          ?    v     i v   vi      i      vi i    i      v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_111549693_   5614 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 5662
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_111549693_   5663 ACACCAAAGGAATGC-CAACAAAAGCCAAAATAGACCAATGGGATCTAAT 5711
                                 i v iiv-         vv        iv   v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_111549693_   5712 TAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTACTATCAGAGTGAAAG 5761
                         i   v v  i i   i  ii vv    i  v    ii vv i       i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_111549693_   5762 GGCAACCTACAGAATGGGAGGAAATTTTTGCAATCTACCCATCTGACAAA 5811
                          i     i            i    v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_111549693_   5812 GGGCTAATA-CCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 5860
                           i  vi  -       v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_111549693_   5861 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5910
                         i     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_111549693_   5911 CAAAAGAAGACATTTATGCAGCCAACAGACATGTGAAAAAATGCTCATCA 5960
                          v        i  vi viii     i ii  ii      i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_111549693_   5961 TCACTAGTCAT 5971
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.63 (155 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


3168 27.42 0.44 0.44  chr1_111589376_111595782     5007  5914 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111589376_   5007 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5056
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111589376_   5057 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5106
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111589376_   5107 TACCAATGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5154
                          v   iivi i  i   i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_111589376_   5155 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5204
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_111589376_   5205 AACAAAGCTGGAGGCATCACAGTACCTGACTTCAAACTATACTACAAGGC 5254
                                i      vv     v v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_111589376_   5255 TCCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGATC 5304
                          v      i   i    ii         i iv ii i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_111589376_   5305 AATGGAACAGAAC--AGAGCCCTCAGGAATAACGTCGCATATCTACAACT 5352
                                i    i--    i  --  i     vvi ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_111589376_   5353 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5402
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_111589376_   5403 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTGTATGTAAAAAGCT 5452
                           v  i  i              v      v  ? iii   i    iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_111589376_   5453 GAAACTGGATACCTTCCTTACAACTTATACAAAAATCAATTCAAGATGGA 5502
                            ii    iv   v   i   v v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_111589376_   5503 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5552
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_111589376_   5553 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5602
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_111589376_   5603 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5652
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_111589376_   5653 TTAAACTAAAGAGCATCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5702
                          i   v v  i i v i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_111589376_   5703 AGGCAACCCACAAAATTGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5752
                           i         i   v         v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_111589376_   5753 AGGGCTAATATCCAGAATCTACAATGAACGCAAACAAATTTACAAGAAAA 5802
                         i  i  vi          v  i  v    v vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_111589376_   5803 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5852
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_111589376_   5853 TCAAAAGAAGACATTTATGCAGCCAAAAATCACATGAAAAAATGCTCACC 5902
                           v        i  vi viii     v  v          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_111589376_   5903 ATCACTGGCCAT 5914
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2952 23.92 7.27 0.82  chr1_111629208_111632599     2047  2899 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111629208_   2047 TAGAAAGATATTCCATGTCATCCATGAATTGGAAGAATCAATATTGTTAA 2096
                          i         i      i---    i         v i           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTT---CATGGATTGGAAGACTTAATATTGTTAA 47

  chr1_111629208_   2097 AATGTCCATAGTTCTCAAAC-AATCTATAGATTCAATGCAATCTCTATCA 2145
                         i   v v   v i i    i-i     i        i      i      
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_111629208_   2146 AATTACCAACGACATGCTTCACAGAAATTTTGTAAA--AATTTCAAAATG 2193
                           v v   i vi v vi  ii        v-ii  i--i  iii     v
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATT 146

  chr1_111629208_   2194 TATATAGAACCACAAAAGACCCAAAATAGCCAAAGCTATCCTAAGGAAAA 2243
                         i    i   vii   ii      i          i v   i i ii  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_111629208_   2244 AGAACAAAAATGGAAAAACCACATTACCTGTCTTCAAATTATACAACAGA 2293
                                 iv    ii vi    i v  iivi      viv   v   i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_111629208_   2294 GCTATTGTAACCAAAACAGCATGGTACTGGCGTAAAAACAGACACATAGA 2343
                             iv    i   i    ii          i   ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_111629208_   2344 ACAGTGGAACAGAATAGAGAACCCAGAAATAAATC-ATACATCTACAGTG 2392
                         v  i     i     v    ii           i -      i  ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_111629208_   2393 AACTCATTTTTGACAAAGATGC---------------------------- 2414
                           i v     i     i i   ----------------------------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_111629208_   2415 ------------------TGGGAAAACTAGATTGCCTATATGCAGAAGAA 2446
                         ------------------     v    i   v?  - i     i     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC-ACATGCAAAAGAA 445

  chr1_111629208_   2447 TGAAACAAGATACCTATCTCTCACCGTATACAAAAATCAAATCAAAATAG 2496
                             iivi  iv    i   v    i           i  v       i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_111629208_   2497 ATTAAAGACTTAAATCCAAAACCTCAAACTATGAAACTACTAAAAGAAAA 2546
                           i ?    i     vi  i v  v       i     vi  i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_111629208_   2547 CATTGGGGAAACTCTACTGGACATTGGACTGGGCAGAGACTTCTTGAGCA 2596
                            v  ? v  v   v vv   v    ii i    iv ii     -  vv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGAT 594

  chr1_111629208_   2597 ATAAC-CCACAAGCACAGGCAACCAAAGCAAAAATGAACAAATGGGATTA 2645
                           i  -   v       i     v    v      ii i    v   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_111629208_   2646 CATCAAG-TTAAAAAGCTTCTGCACAGCAAAGGAAAC----AACAAAGTG 2690
                               i-       -   i  ii vv       v  ----  v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_111629208_   2691 AAGACACTACCCACAAAATGGGAGAAA-TATTTGCAAACCACCCATCTGA 2739
                           i v  v       i           -          i  ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_111629208_   2740 CAAGGAATTAATAACCAGAATATATAAGGAGGTCAAACAATTCTATAGGA 2789
                         i    i i vi  v             i  iv  vv    i  v   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_111629208_   2790 AAAAC-CTAATAATCTGATT-AAAAATGGGCAAAAGATCTGAACAGACAT 2837
                             v- v     i ii   -             i   i    i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_111629208_   2838 CTCTCAAAAGAAGACACACAACTAGCAAATAGGTA--TGGAAAGGTGTTC 2885
                         i    v        i i    v i  v    i i --  i    i  i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_111629208_   2886 A-CATCATTAATCAT 2899
                          -     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (132 / 69)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.06 (69 / 17)  


3145 26.04 0.99 1.21  chr1_111647932_111654315     4982  5891 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111647932_   4982 TGGAAGAACATTCCATGCTCATGCATAGGAAGAATCAATATTGTGAAAAT 5031
                              ii i  i     i     v  v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111647932_   5032 GGCCATACTGCCAAAGGTAATGTATAGTTTCAATGCCATCCCCATCAAAC 5081
                            v     v  v  iv i  v  i  v     i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111647932_   5082 TACCAA-TGATTTCTTTACAGAA-TTGGAAAAAAAAC--ACTTTAAAGTT 5127
                          v   i-  vi  i   i     -   ---- v  i -- iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr1_111647932_   5128 CATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATTTGCTAAGCAA 5177
                                  viiv  ii  v  v v  v     i     i -- i iv  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT--TGAAAAA 194

  chr1_111647932_   5178 AAGGAACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTACA 5227
                         i i        i     ivv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_111647932_   5228 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 5277
                          i          i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_111647932_   5278 GACCAATGGAACAGAAC--AGAGCCCTCAGACATAATACCACACATGTAC 5325
                           i        i    i--    i  --   v    vv   i    v  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chr1_111647932_   5326 AACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGA 5375
                         iii  vi    i  i     ivv  v   i v  vvv           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_111647932_   5376 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAACCATATGTAGAA 5425
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_111647932_   5426 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAACTAATTCAAGA 5475
                         iiv    ii    i    v   i     v          i   i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_111647932_   5476 TGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGA 5525
                              i ?    i       v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_111647932_   5526 AAACCTAGGC---AATGCCATTCAGGACATAGGCATGGGCAAGAACTTCA 5572
                             v    ?---   -- -   iv   v v  vv i     viii   v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_111647932_   5573 TGACCAAAACACCAAAAGCAATGGCAACAAAAGCCAAAACAGACAAGTGG 5622
                          iivi vi            vvi          vv    i   i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_111647932_   5623 GATCTAATTAAACTAAAGAGCTTCTGCACAGAAAAAGAAACTACCATCAG 5672
                           ii v  i   v v  i i   i  ii vvv   i  v    i  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_111647932_   5673 AGTGAACAGGCAACCTACAGAATGGGAGAACATTTTTGCCATCTACCCAT 5722
                               v  i     i              v  v     v vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_111647932_   5723 CTGATAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTAC 5772
                                i  i  vi          v  i         vv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_111647932_   5773 AAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAACAGATATGAACAG 5822
                           v     i     i     v  i?    i       vi   v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_111647932_   5823 ACACTTCTCATAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAAT 5872
                            i     vv       i  vi viii     i ii          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_111647932_   5873 GCTCATCATCACCCGTCAT 5891
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


3161 24.47 2.79 1.34  chr1_111663418_111665689      885  1779 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111663418_    885 TGGAATAATATCCCATGCTCGTGGATAGGAAGAATCAATATCATTAAAAT 934
                              vi          i  i     v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111663418_    935 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 984
                            v     v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111663418_    985 TACGAACAACATTCTTCGTAGAACTAGAAAAAACT-ATTTTAAAATTCAT 1033
                          v v i vi v  i  i i    v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_111663418_   1034 ATGGAACCAAAACAGAGCCCGAATAGCCAAGGCAAACCTCAGCAGAAAGA 1083
                               viiv  vi  v  v          ii   v i v iv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_111663418_   1084 ACAAAGCTAGAG-----ACATCACCCAACTTTAAACTATACTACAGGACT 1128
                               i i   -----   iiv     i  i   viv       iii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_111663418_   1129 ACAGTAACCAA-ACAGCATTGTACTGGTACAGAAACAGGTACATAGACCA 1177
                                i   -    ii v       i i iii i  ii i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_111663418_   1178 ATGGAACAGAGTAGAGAGCCCAGAAATAAGAATGCACACCTATGACCAGT 1227
                               i   i v     i          ivviii   ii    ii  i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_111663418_   1228 TGATCTTCAACAAAGCTGATAAAAACA---AAGGAGAAATGACTCCCCTA 1274
                             i   i    i v  vi  i v  ---  v i i  v  v vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_111663418_   1275 TTCAATAAAAGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAGATTGAA 1324
                              i   v          v      v  ?   i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_111663418_   1325 ACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAAATGGATTA 1374
                         ii         v   i                 i              i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_111663418_   1375 AAGACTTAAATGTAAAACCAAAAACTATAAAAACTCT-GGAAGACACC-T 1422
                         ?    i         i v v            -    -i     v v - 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr1_111663418_   1423 AGGCA-ATATCATCCTGGACATAGGAACGGGCAAAGATTTC------ATG 1465
                            ?i- v   v  v  -  v v  ivii     v i    ------   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_111663418_   1466 ACAAAGTTGCCAAAAACAATCA--CAACAAAAGGAAAAGTTGACAAGTGG 1513
                            ------      i  --  --         i    i v  i  i v 
  L1M4_orf2#LINE/    598 ACA------CCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_111663418_   1514 GATCTAATTAAACTTAAGAGCTTCTGCACAGCAAAGGAAACTATCAACAG 1563
                           ii v  i   v    i i   i  ii vv       v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_111663418_   1564 AGTAAACAGACAACTTACAGAATGGGAGAAAATATTTACAAACTATGCAT 1613
                            i  v       ii                     i    ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_111663418_   1614 CTGACAAAGATCTAAGAGCCAGCATCTATAAGGAACTTAAACAAATTTAC 1663
                             i  i iv  viv v    v  v     i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_111663418_   1664 AAGAGAAAAACGA----CCCCATCAAAAAGCGGGCAAAGGACATGAACAG 1709
                           v i   i  i ----   v  i?    ii          iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_111663418_   1710 ACACTTTTCAAAAGAACACATACATGTGGCCGATAAGCATATGAAAAAAA 1759
                            i  i  v      v i     vi     i       i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_111663418_   1760 AACTCAACATCACTGGTTAT 1779
                         i-          ????????
  L1M4_orf2#LINE/    890 G-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (134 / 81)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.31 (37 / 16)  


 908 29.38 9.70 4.31  chr1_111733201_111734963      529  1270 (493)    L1M4_orf2#LINE/L1      127   908 (0)  

  chr1_111733201_    529 GGCAGGCTTACTCTAAATTTCCTATGTAAACCATAAACAAGACAGCAAAT 578
                          i  i   v ii     v   v    v   i-ii  ivi vv   v v v
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAAT-GCAAGGGACCCAGAATAG 175

  chr1_111733201_    579 CCAGAAAAATGTATAAAAATAAATAATTAAAGTTATATGGGAAGGCTAGC 628
                            i  v   v - i    vi  v  i-      -----   i i  vi 
  L1M4_orf2#LINE/    176 CCAAAACAATCT-TGAAAAAGAAGAAC-AAAGTT-----GGAGGACTCAC 218

  chr1_111733201_    629 CCTAGTAGCTAACT--AAAAGTACTTGTTTTATTAAGCATCACTAATTAA 676
                         v  -- v- i  i --    ---   ii vi --    vv  v    i  
  L1M4_orf2#LINE/    219 ACT--TC-CCAATTTCAAAA---CTTACTACA--AAGCTACAGTAATCAA 260

  chr1_111733201_    677 AGCAATATGTTAATGGTACCTGAATAAA----TAAATCAATTGAATAGAA 722
                         ii  i i  v  v   i ivv i   i ----  i      v        
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_111733201_    723 TTTAAAGACCAGAAATACATCAAAATATATAAGG-AAATTTAGAGTAT-G 770
                           v i  v         v i v v i  v  v  -v    --  v v - 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT--GATTTTCG 358

  chr1_111733201_    771 ATGAAGATGGCATATGAAATCATTT----GGGAGAAATTGGTTTATTCAA 816
                          ii i i  v  ---- i i    i----    i i v i  i v     
  L1M4_orf2#LINE/    359 ACAAGGGTGCCA----AGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_111733201_    817 TAAGTGGTAGCAAGATAACTAGATAACCA--TGTAAATGAAAATAAAGTA 864
                         i  i    iviii  i    i    ?   --  i   -- i   i    v
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA--AGAATGAAGTT 452

  chr1_111733201_    865 GGATCCATATTTCACTTCTTATATGAAAATAAATCCCAGATG--TGAAAA 912
                            i  v  ii    vi v    ii     v  ii v i   -- v ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_111733201_    913 ATTTAACAGTAAAA---AAAATCATAAAAGCACTAGAAGAAAATATGGGA 959
                          ii   vv    i ---    ii      vivi          i  i  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_111733201_    960 G--AATTTTTAAAAATATTTTTG---TAGAGCATGCCTTTGAATGTATGT 1004
                          --   i  iivi ----ii   ---   ivv   vi  ivv vi    v
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGA----CCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_111733201_   1005 CAC--AAATCCCA-GAAACCA--GAAAAGAT---TAACTTG-ACTTCTAA 1045
                            --   v v  - v   v --     i  ---   v   -     ---
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC--- 645

  chr1_111733201_   1046 AGTACAATTAAAAG---------TCCAAAG--TACCATTAA-AAAGTCAA 1083
                          vi v        i--------- i     --i  i  i  -     v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_111733201_   1084 AAGGCAAATGACAAGCTT--AGAAAACACTTGCAAAGCAT---------- 1121
                            i   viv   iiv v--      i i       v   ----------
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_111733201_   1122 -----CTTATA-----GATATATAAAGATCATTTGTAAATCAACAGGGGA 1161
                         -----   i  -----i           v vi  ii  v    i ivi- 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA-A 794

  chr1_111733201_   1162 AAAAATGAACAACTCAAT--AGAAA-GGACAAGGGATAGGGGTGGGCAAT 1208
                            i ii  i   i    -- i   -  i   i    vv ii i i  v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_111733201_   1209 TTGTAGGAAAGAATATATAAATGGCT--CAAATATATGAAAAGATACTCG 1256
                          ivivii i ii     i       i--i  ii i          i   i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_111733201_   1257 ACTTCACTCATAAT 1270
                           v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (133 / 82)
Gap_init rate = 0.05 (38 / 782), avg. gap size = 2.74 (104 / 38)  


2595 26.10 8.70 0.72  chr1_111748376_111750538      832  1670 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_111748376_    832 GAAGAACATTCCATGCTCATAGATAGGAAGAATCAATATCATTAAAATGG 881
                            ii i  i     i    i   v      v i     ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_111748376_    882 CCATATTGACCAAAGCAATTTACAGATTCAATGTGATTCCTATCAAACTA 931
                          v   i vv     vii  i           i ii  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_111748376_    932 CCAAT-------------GAAATTGA--------------------TATG 948
                            ii-------------        --------------------    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_111748376_    949 GAATCAAAAAAGAGCCCAAATAGCTAAGGCAATCCTAAGCAAAAAGAACC 998
                            viiv  ii  v  vi      i  ii     i i iv  i      v
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_111748376_    999 AAGCTGGAGGATATGACATTACTCAACTTCAAACTATGCTACAGGACTAT 1048
                            i       i- v   i v i   i      viv i     iii   i
  L1M4_orf2#LINE/    203 AAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_111748376_   1049 AGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCAAT 1098
                              i   i    ii         i i  ii i     i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_111748376_   1099 GGAATAGAATGGAGAACCCACAAGTAAAGCTACACACCTACAACCATCTG 1148
                                   v    ii   v  i    v i i   ii  iiii  vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_111748376_   1149 ATCCTTGACAAAACTGACAAAACAAG-CAGTGGGGAAAAGACTCCCTATT 1197
                           ii i     iiv  v   i  v v-  i        ii ivvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_111748376_   1198 CAATAAATGGTGCTAGGATAACTGGCTAGCCATATGCAGAAGATTGAAAC 1247
                            i          i   i      v  ?   i     i    v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_111748376_   1248 TGGACCCCTTCCTTATACCATATACAAAAATCAACTCAGA-TGGATTAAA 1296
                                  v   i i               i      i -     i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_111748376_   1297 GATTTAAATGTAAAACTCAAAACTATAAAAACCCTGGAAGGCAAAC-TAG 1345
                           ii         i vii            vi i i    i-    -   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA-AAACATAG 550

  chr1_111748376_   1346 CCA-ATACCATTCTGGACATAGGAACTGGCAAAGATTTCATGATGAAATG 1394
                         v?i- v i -   vv   v v  iviv     v i    v i--  v   
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA--GATATG 597

  chr1_111748376_   1395 GC--CAAAAGCCACCA-CAACAAAAGCAAAAATTGACAAATGGGATCCAA 1441
                         i --       -  v -         v      v  i    v   iiiv 
  L1M4_orf2#LINE/    598 ACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_111748376_   1442 TTAAACTGAAGAGCTTCTCTGC--------ACA-----------GC-AAA 1471
                          i   v v  i i   i v   --------   ----------- i-   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_111748376_   1472 AGATATT-------ATGGGA-AAAGTATTTGCGAACTATTCATCTGACAA 1513
                            i vi-------      -   i       i  ii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_111748376_   1514 AGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAA 1563
                         i  v  vi       v  v     i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_111748376_   1564 AAACAAACAGCCCA-TTAAAAGGTAGACAAAGGACATGAA----CACTTT 1608
                          i     i i    -  ?   ii i i       iv    ----  i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_111748376_   1609 TCAAAAGAAGACATACATGTGGCCAAACAGCATGTGAAGAAAAGCTCAAT 1658
                           v        i     vi       vv    ii    i i v      i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_111748376_   1659 ATCACTGATCAT 1670
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (145 / 70)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 3.95 (79 / 20)  


3613 22.14 2.67 1.67  chr1_111775688_111781171.rev     4095  4993 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111775688_   4095 TGGAGAGATATGATGTGTGTGTTCGTAGATTGTAAGATTATGTGTTGTTG 4144
                             i      ----ivii     i i     v    i vvi i     i
  L1M4_orf2#LINE/      1 TGGAAAGATAT----CCCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chr1_111775688_   4145 AATTGGCAATTCTCTCCTAAACTGATTTGTCAATTTAACACAATCCA-AT 4193
                          iv       v   i  -   i    i iivi   i   i      v-  
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_111775688_   4194 CAAATTCCTAGAAGACTTTTTTGAAGAAATTGAAAAGCTGATTTTAAAAT 4243
                             v   i  vv v        v         v        ii      
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_111775688_   4244 GTATGTATGTGAACATTCAAAAGACCTAGAATAGCCAAAACAACTTTGAA 4293
                         vi  --   -   -  v   ii    i                ii     
  L1M4_orf2#LINE/    146 TCAT--ATG-GAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_111775688_   4294 AAAGAA---CCAAGTTGGAGTACCAATAATACCTGATTTCAAGACTTTCT 4340
                               --- v         v  iv i v v  ii       i    v  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_111775688_   4341 GTAAAATGACAACAATCAAGATGATGTGGTATTGGTATAAAGATAGACAA 4390
                         ii   iiv   ii        iii       i   i    i        v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_111775688_   4391 ATAGATTGATGTAACACAATACAGAG--CAAAAATGGAAATAAACCCATA 4438
                               ii   v  i v   vv    --  ------              
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCA------GAAATAAACCCATA 335

  chr1_111775688_   4439 CGTATATGGTCAATTGATTTTCAAGAAAGGTGCCAAAACAACTGAATGGG 4488
                          i v                  i v  i        i  v i v      
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_111775688_   4489 TAAAGGACAATCTTTTCAACAAATGGTGCTGAAGCAATTAAATAGCCATA 4538
                         v    i i i                     iii   i ii   ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_111775688_   4539 TGCAATAAAATGAACCTCAACCCTTACCTCATACCATATACAAAAATTAA 4588
                              v i      vi vi    i       i                  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_111775688_   4589 CTTGAAATGTAATATTGACTTGAATATAAGA-CTAAAACTATAAAATTTC 4637
                           ii     v vi ?v   i i   i     -              i ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_111775688_   4638 TAGGAGAAAACACAGGAGAAGGTCCTAGTGGCCTTGGGTTTGGCAAAGAT 4687
                            i        i   ? v ii  i v   i         v     v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_111775688_   4688 TTCTTAAATATAACAC-AAAAGCACAAAATATACGAGCAAAAAT---TAA 4733
                               i    i    -          ivv i vi  v      ---   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_111775688_   4734 ---------CAGTAAAGATGAAATCTTTTGTCCTTCATAAGGCACTCTTA 4774
                         ---------  vi   iv i   v       v     v i i    v i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_111775688_   4775 AGAATGTAAAAAGTTGGCC-ACAAACCAGGAGAAAAGATTTGCAAATCTT 4823
                             v  i     viii  -   i vii        v           v 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_111775688_   4824 ATATCTGACGAAAGACTTATAACTAAAATATACAAAGAATTCTAACAACT 4873
                                 ii ii     i  v i i      i      i   v      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_111775688_   4874 TCAT--TAAGAATATGAATAACCCAATAGAAAAATGGGCACAAAATTT-A 4920
                         iv  --   i  v ii           v?           v ii    - 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_111775688_   4921 ATAGTTACTTCACCAAGGATGATATACAAATGTCAAAAAAGCACATAAGA 4970
                             vi i   v    i  v            v v  v        i i 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_111775688_   4971 AGATGCTCAGTCTCAATGGTTAG 4993
                                  iiv   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (124 / 71)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.44 (39 / 16)  


3276 23.57 1.30 3.14  chr1_111781918_111784241.rev      912  1836 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111781918_    912 TAAAGAGATATTCCATTATCATGGATAGTAAGACTCAATATTATCAAGAT 961
                          ii i      i    vv        v v      i      i i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111781918_    962 GTCAGTTCTTCCCAACTATATCTATAGTTCTGAAACTATATCTATAGTTC 1011
                          v  i v  i     v vv     i  v iii vi v  vi    ---- 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT----C 96

  chr1_111781918_   1012 TGAAAATTCCACCAAGTTATTTTGTGGATATTAACAAACTGATTCCAAAA 1061
                         --     i   v vivi v     ii  v   i    i     i i    
  L1M4_orf2#LINE/     97 --AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_111781918_   1062 TTTATACGGAGAGACAAAAAACCCAGAATAGCCAACACGATATT---AAA 1108
                           i   i   i vi   iii               v  i  v  ---   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_111781918_   1109 GGAGAACAAAGTCAGAGGACTGATACTACCTGACTTCAAGACTCACTATA 1158
                          i          ii       v i   v  ii i     i   i    i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_111781918_   1159 AAGCTATAATAATCAAGACAGTGTAGTATTGGCAAATGAACAGACAAGTA 1208
                               i i               i   i     v v i i     vi  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_111781918_   1209 GATCAGTGGAACAGAATAGAAAGGCCAGAAGTAGACACATATAAATATGG 1258
                              i     i     v  i  v      i  i  v    i vv     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_111781918_   1259 TCAATTGATTTTTGACAAGTGAGCAAAGGCAATACAATGTCTCCATTGTA 1308
                                     i      v v  v   i v  v     ----------i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG----------G 384

  chr1_111781918_   1309 AGAAAGA-TAGTATTTTCAACCAGTGATGATGAG-CAAATG-ACATCCAC 1355
                         i      -    v        v i  i  v  i -   v  - i ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_111781918_   1356 ATGCAATAAAATAAAATAAAATCTGGACACAGACCTTACATCTCTCACAA 1405
                               v i   i  i ------     v vv    i   i vivi    
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGT------TGGACCCCTACCTCACACCATATACAA 478

  chr1_111781918_   1406 AAATTAACTCAAAACGGATTATAAACTTAAACATAAAATGC-AAAACTAT 1454
                                       i    i ? i  i    ii   i -  -        
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTAT 527

  chr1_111781918_   1455 AAGACTCCTAGAAGGTAATGCAGGAGAAAATCTAGATGACTTTTGGATAT 1504
                           i    i      iv  iii   ? v      vvi    i  v  v  -
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA- 576

  chr1_111781918_   1505 GATGATGCGTTTTTATATACAACTCCAAAAGCGTGATCCATGAAAAAAAA 1554
                          iii   vv  i   v   ii  v        iii v v ii   i    
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_111781918_   1555 AATTGACAAGCTAGACTTCATTACAA--AAAAACTACT---TTTCAAAAA 1599
                            v  i  ii i        i v  --       vi ---i      ii
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_111781918_   1600 AACAATGTTAAGAGAGAATGAGGTGATAAGCCACAGACTGAAAGATAATT 1649
                          -  v i i    i  --   iiv  i  v       v  ii   v   v
  L1M4_orf2#LINE/    677 A-CACTATCAAGAAAG--TGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_111781918_   1650 TTTGCAAAAGACATATCTGATACAGGAGACTGTTATCCAAAATATACAAA 1699
                                 vv i          -   -    vv      i      i   
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATA-AGG-GACTTGTATCCAGAATATATAAA 771

  chr1_111781918_   1700 GAACCCTTAAACCTCAACAATAAAAAAATTAACAACCCAATTAAAAGATG 1749
                             i    v v     i        i iv  i         ?   i   
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_111781918_   1750 GGCAAAAGACCTGAACAGACAGCTCACCAAAGATGATATAAGGATGGCAA 1799
                               i  ii    i     vi  v       v      vii     v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_111781918_   1800 ATAAGCATATGAAAAGATGATCCATCTCATATGTCAC 1836
                                i           v  v iv   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (132 / 82)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.41 (41 / 17)  


4567 17.21 0.93 0.81  chr1_111799538_111801389.rev      502  1361 (491)    L1M4_orf2#LINE/L1       48   908 (0)  

  chr1_111799538_    502 GATGGCAGTACTTTCTAAATTGCTCTGCAGTTTTAATGTAAAACTTATAA 551
                                i    ii i      v   i   v  i  i i  vv i   v 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_111799538_    552 AAATTCAAACTGCCTCCTTGGTTTTTGCAGAAATGGACAAGCAGATCCTA 601
                             i v i      ------             v       v       
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCT------TTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr1_111799538_    602 AAATCCATGTGGAAATGCAAGAGACCTTGAATAACCAAAATAGTTTTGAA 651
                             i   i            i    iv     i      i i i     
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_111799538_    652 AAAGAA----AAAATTGAAGGACTCACAATTCTGGATTTTAAAACTTAAC 697
                               ----   i   i          v   ivi    i        - 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-C 240

  chr1_111799538_    698 TACAAAGCTACAGTATTCTAAAGGGTATGGTACTCGCATAAGGCTAGACA 747
                                        v  v i vi  i       v        v      
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_111799538_    748 TATAGACTAACTGAATTAAACCGAAAGTTCAGAAATAAATCCATCCACCT 797
                               ii  iv    vi  ii  i   i          i    v  ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_111799538_    798 GTGGACAATTGATTTTCAACA-GGTTTCCAAGACTGTTCCGGGGAGAAAG 846
                         i   v            i   -  v v       ii   viv  i     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_111799538_    847 GACAGTCTTTTCAACAAATGGTGCTGGGACAACTGAATATCTACATATCA 896
                         i i                                i   ? i    iiv 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_111799538_    897 AAGAATGAAGTTGGACTCCCAGCTTACACTGTATACAAAAATTAAGTAAA 946
                                         i  i v  i    ii              v v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_111799538_    947 AATCGATCAAATAACTAACTATAAGAGCTAAAATAACAAAGCTTTTCAAA 996
                            v     ? v v    v i            iv i   i  i  vi  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_111799538_    997 GGAAACA--GGTGTAAATCTCTGTGACCTTAGATTAGGTAATGGTTTCTT 1044
                          i     --  ?        ii        i i     i           
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_111799538_   1045 AAATATGACACAAAAAGCACAAGCAATAAAAGACAAA-TAGAGAAGTTGG 1093
                          i         v              i      v   -    v  i    
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_111799538_   1094 ACTTCATCAAAATTAAAAACTTTAGTGCACCAAAGGGCACTAGCAAGAAA 1143
                                                v    vi      i     v       
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_111799538_   1144 GTAAAAGTACAAACCAGAGAACGGGGGAAAATATTTGTAAATCATATATC 1193
                           i   iv    v   v    i   i           i            
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_111799538_   1194 TGATAATAGTCTAGTAGCCAGAATACATAAAGAACCCTTAAAATTCAACA 1243
                               vi v  v   v        i         i    v  i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_111799538_   1244 ATAAAAGGACAAATAATCCAATTTAAAAATGAGCAAAGGACTCGAACAGA 1293
                               i         i      ?       i        i i   i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_111799538_   1294 TATTTCTGCAAAGAAAATATACAAATGATCAATAAGCATGTGAAAAGATG 1343
                         i      v       i           ii         ii          
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_111799538_   1344 CTTAACATCATTAGTCAT 1361
                           i       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (95 / 49)
Gap_init rate = 0.01 (6 / 861), avg. gap size = 2.50 (15 / 6)  


2829 27.95 2.12 1.00  chr1_111934759_111940699     4551  5448 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_111934759_   4551 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4600
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_111934759_   4601 GGTCATACTGCCCAAGGTAATTTATAGATTCAGTGC--TCCCCATAAAGC 4648
                           iv     v     iv i  i  i       ii  --    i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_111934759_   4649 TACCATTGAGTTTCTTCACAGAATTAGAAAAAAAGCTACTTC-AAATTTC 4697
                          v   vivivi  i  ii     v v  v  ---   iv i -   v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA---GCTGATCCTAAAATTC 147

  chr1_111934759_   4698 ATATGGAAC--CAAAAAACAGCCCATATAGCCAAGATGGTGCTAAGCAAA 4745
                                 v--   iii  --  viv        i iii vi i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_111934759_   4746 AAGAACAAAGCTGGAGGTATCACACTACCGGACTTCAAACTATACTATAA 4795
                                   i      vv       v  vi i      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_111934759_   4796 GGCTGCAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGATACATAG 4845
                         i   i   i  i   i    ii         i iv ii i   i i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_111934759_   4846 ACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACATATCTACAAC 4895
                          i        i    iv   ivii         vv   i i  i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_111934759_   4896 CATCTGATCTTTGATGAACCTAACAAAAACAAGCAATGGGGAAAGGAT-- 4943
                           vi    i  i  ii ivv iv   i v  vv            i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_111934759_   4944 TCCTTATTTAATAAATGGTGTTGGGAAAACTGG---------TTCAGAAA 4984
                           i  -- i  i        i     v      --------- v  i  i
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_111934759_   4985 ACTGAAACTGGACTCATTCCTTACACCTCATATAAAAATTAAGTCAAGAT 5034
                          v    ii     i v v   i     vi   i         v    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_111934759_   5035 GGATTAAAGACTTAAACATAAGCCCTAAAACCATAAAAACCCGAGAAGAT 5084
                             i ?    i    ii    vv       i      vi iv      v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_111934759_   5085 AACCTAGGCG-ATACCATTCAGGACATAGGCATGGGCAAAGTCTTCATGG 5133
                            v    ? - v i -   iv   v v  vv i     v vi   v i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_111934759_   5134 CTAAAACACCAAAAGCAATGGCAACGAAAGCCAAAATGCCACAAATGGGA 5183
                         v  vi            vvi     i    vv     iv- i    v   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG-ATAAATTGGA 641

  chr1_111934759_   5184 TCTAATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTATCAGCAGAG 5233
                         ii v  i   viv  i i   i  ii vv    i  v       iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_111934759_   5234 CGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 5283
                         i   v  i     i                 v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_111934759_   5284 GACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAA 5333
                           i  i  i  vi          v  i  i     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_111934759_   5334 AAAAAAGA--AACAACCTCATCAAAAAATAGGCGAAAGACATGAACAGAC 5381
                         v       --  i    iv  i?      i   i  i  iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_111934759_   5382 ACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGC 5431
                          i     v        i  vi viii     i  i  i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_111934759_   5432 TGATCATCACTGGTCGT 5448
                          v v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (152 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.33 (28 / 12)  


3176 26.54 0.66 0.66  chr1_112409711_112415974.rev     4866  5773 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_112409711_   4866 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4915
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_112409711_   4916 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATAAAGC 4965
                            v     v     iv i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_112409711_   4966 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5012
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_112409711_   5013 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAAACCTAAGTCAAAA 5062
                                 viiv  ii  v  v v  v     iv   v i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_112409711_   5063 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5112
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_112409711_   5113 CTACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAAATATAGAT 5162
                                  i   i    ii   i     i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_112409711_   5163 CAATGGAATAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5210
                                      i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_112409711_   5211 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5260
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_112409711_   5261 TCTATTTAACAAATGGTGCTGGGAAAACAGGCTAGCCATATGTAGAAAGC 5310
                            v  i                 v   v  v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_112409711_   5311 TGAAACTGGATCTCTTCCTTACATCTTATACAAAAATCAATTCAAGATGG 5360
                             ii    i i  v   i   i v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_112409711_   5361 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCCAGAAGAAAA 5410
                           i ?    i    i  v   v       i      vi ii         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_112409711_   5411 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5459
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_112409711_   5460 AAAACACCAGAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5509
                          vi      i     vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_112409711_   5510 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5559
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_112409711_   5560 ACAGGCAACCTACAAAATTGGAGAAAATTTTCACAACCTACTCATCTGAC 5609
                          v  i     i   i   v         v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_112409711_   5610 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5659
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_112409711_   5660 AAAAAAAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5709
                            i v   i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_112409711_   5710 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5759
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_112409711_   5760 CCATCACTGGCCAT 5773
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3111 26.29 1.21 1.32  chr1_112454059_112460467.rev     5010  5918 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_112454059_   5010 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCATGAAAAT 5059
                              ii i  i     i      i v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_112454059_   5060 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5109
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_112454059_   5110 TACCAATGACTTTCTTCACAGAA-TTGGAATAAACT-ACTTTCAAGTTCA 5157
                          v   iivi i  i  ii     -   -- i  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_112454059_   5158 TATGGA--TCCAAAAGAGAGTCCCCA---TCGCCAAGTCAATCCTAAACC 5202
                               -- v   ii  -----    --- v     iv     i i  vv
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-----CCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_112454059_   5203 AAAAGAACAAAGCTGGAGGCATCAGGCTGCCTGACTTCAAACTATACTAC 5252
                          i          i      vv   vi  v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_112454059_   5253 AATGCTACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATAT 5302
                           v          i   i    ii        vi iv ii i   v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_112454059_   5303 AGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTA 5350
                                     i    i--    i  --        vv iii i  i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chr1_112454059_   5351 CAACTATCTGATCTTTGACAAACTTGAGAAAAACAAGCAATGGGGAAAGG 5400
                         iiiii vi    i  i     ivv  vv  i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_112454059_   5401 ATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGA 5450
                           vvi  v  i  i              v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_112454059_   5451 AAGCTGAAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAG 5500
                          iiv    ii    i i  v   i     v              i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_112454059_   5501 ATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAG 5550
                               i ?    i    i  v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_112454059_   5551 AAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 5600
                              v    ?i v viv   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_112454059_   5601 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5650
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_112454059_   5651 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5700
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_112454059_   5701 TGAACAGGCAACCTACAAAATGGCAGAAAA-ATTTCACAACCTACTCATC 5749
                             v  i     i   i     v      -    -i   vii ivi   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATC 740

  chr1_112454059_   5750 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACTAATTCA-C 5798
                            i  i  i  vi          v  i  v      vv  -  i   -i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC-AACTCAAT 789

  chr1_112454059_   5799 AAGAAAAAAACAAACAACCCCATTGAAAAGTGGGCAAAGGACAAGTACAG 5848
                           v     i     i     v   ?    i           ivv v i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_112454059_   5849 ACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAAAA 5898
                            i     v        i  vi viii     v  i-          i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGA 888

  chr1_112454059_   5899 TGCTCACCATCACTGGCCAT 5918
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


3117 27.89 0.44 0.33  chr1_112465825_112472219     4996  5902 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_112465825_   4996 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGCAAAT 5045
                              ii i  i     i        v      v i        vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_112465825_   5046 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATAAAGC 5095
                            v     v     iv i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_112465825_   5096 TACCAATGACTTTCTTCACAGAACTGGAAAAAGCT-ACTTTCAAGTTCAT 5144
                          v   iivi i  i  ii     v v  v  -   - iii v  i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_112465825_   5145 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5194
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_112465825_   5195 ACAAAGCTGGAGGCATCAGGCTGCCTGACCTCAAACTATACTACAAGGCT 5244
                               i      vv   vi  v  ii ii     viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_112465825_   5245 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5294
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_112465825_   5295 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACTA 5342
                               i    i--    i  --        vv iii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_112465825_   5343 TCTGATCTTTGACAAACTTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5392
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_112465825_   5393 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5442
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_112465825_   5443 AAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5492
                           ii    i i  v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_112465825_   5493 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5542
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_112465825_   5543 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5592
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_112465825_   5593 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGACCTAAT 5642
                                     vvi          vv     v  i    v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_112465825_   5643 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAATGAACA 5692
                         i   v v  i i   i  ii vv    i  v  i i  vv i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_112465825_   5693 GGCAACCTACAGAATGGGGGAAAATTTTTACAATCTACCCATCTGACAAA 5742
                          i     i          i      v   i   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_112465825_   5743 GGGCAAATATCGAGAATCTACAAAGAAATTAAACAAATTTACAAGAAAAA 5792
                           i vvi    v     v  i      v ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_112465825_   5793 T-CAAACAACCCCATCAAAAAGTGGACAAAGGATATGAACAGACACTTCT 5841
                         v-    i     v  i?    i   i        v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_112465825_   5842 CAAAAGAAGAAATTTATGCAGCCAACAGACACAAGAAAAAATGCTTATCA 5891
                          v        v  vi viii     i ii    v     i     i v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_112465825_   5892 TCACTGACCAT 5902
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.37 (144 / 105)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


1766 24.00 0.20 6.00  chr1_112475583_112481851        1   500 (5768)    L1M4_orf2#LINE/L1       32   502 (406)  

  chr1_112475583_      1 GAATTAATATTGCTAAAATGACAAATATTACAATTTACAAATTATAAAGC 50
                           v         i   i   i   ----   -- iiv      i------
  L1M4_orf2#LINE/     32 GACTTAATATTGTTAAGATGGCAA----TAC--TCCCCAAATTG------ 69

  chr1_112475583_     51 AATTTGTAAAGCAATTTACAAATTTGATGCAATCTCTATCAAAATACCAA 100
                         -------------  i    i   ii i      i          v   i
  L1M4_orf2#LINE/     70 -------------ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_112475583_    101 TGACATTCTTTGCAGAAACAGAAAAAAC-ACTCTAAAATTTATATGGGAC 149
                         ivi v  i          iv  v  ivi- ii        i      i v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_112475583_    150 CACAAAATACCTTGAATAGCCAAAGCAATCCTGAGCAAAAAGAAGAAAGC 199
                         ii   iiv   iv           i     i   iv  i     v    i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_112475583_    200 TGGAGGCATCACACTACCTGACTCCAAAATTTATGACAAAGCTACAGTAA 249
                               vv       v  ii i i     i   iv               
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_112475583_    250 TCAAAACATCATATAATGGTACTGGCCTGAAAACAGACACAGAGACCAAT 299
                             i   --i i ---         v i ii i     i v   i    
  L1M4_orf2#LINE/    257 TCAAGACA--GTGT---GGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_112475583_    300 GGAACAGAATAGAGAACACAGATATAAATCCATGCACCTACAACCTACCC 349
                             i     v    iiv    v     i    i  ii  iiii v iiv
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_112475583_    350 ATCTTCAACAGAAGTGCCAAGAACATACAATGAGAAAAGGACAGTCTTTT 399
                           i   i   iii         v   v     i i    i i        
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_112475583_    400 CAAAAAATGGTGTCAGAAAAACTGGATATCCATATGCAGAAGAATAAAAC 449
                            v        iii i v         ?   i     i      i  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_112475583_    450 TAGAACCCTATCTCTCACCACACACAAAAATCAAATCAAAGTGAATTAAA 499
                          i  v     i   v     i i        i  v     i  i  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_112475583_    500 G 500
                          
  L1M4_orf2#LINE/    502 G 502

Transitions / transversions = 2.81 (87 / 31)
Gap_init rate = 0.01 (6 / 471), avg. gap size = 5.17 (31 / 6)  

3277 26.21 0.66 0.66  chr1_112475583_112481851     4869  5776 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_112475583_   4869 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATAGCGTGAAAAT 4918
                              ii    i     i      i v      v i    vi  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_112475583_   4919 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 4968
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_112475583_   4969 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5016
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_112475583_   5017 TATGGAACCAAAAAAGAGCCTGCATCACCAAGGCAATCCTAAACCAAAAG 5066
                                viiv  ii  v  v v  vi    ii     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_112475583_   5067 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5116
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_112475583_   5117 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5166
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_112475583_   5167 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5214
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_112475583_   5215 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5264
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_112475583_   5265 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5314
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_112475583_   5315 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATCAATTCAAGATGGA 5364
                            ii    i    v   i   i v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_112475583_   5365 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5414
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_112475583_   5415 CTAGGCATTA-TCATTCAGAACATAGGCGTGGGCAAGGACTTCATCTCCA 5463
                         v    ?i v -  -   ivi  v v  vv i     v ii   v vvvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_112475583_   5464 AAACACCAAAAGC-CATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5512
                         vi           -  -i          vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_112475583_   5513 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5562
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_112475583_   5563 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5612
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_112475583_   5613 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5662
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_112475583_   5663 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5712
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_112475583_   5713 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5762
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_112475583_   5763 TCATCACTGGCCAT 5776
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2745 17.14 1.46 21.06  chr1_112734553_112739070     2921  4017 (501)    L1M4_orf2#LINE/L1        4   885 (23)  

  chr1_112734553_   2921 AAAGATATCGCATGTCCATAGATTGAAAAA----ATATTGGTAAAATGTT 2966
                                  v     i   i     i  i ----      v   i   vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_112734553_   2967 CATACTACCCAAAGTGATCTACAGATTTAACGCCATCCCTATCAAAATCC 3016
                         v     v      v             i     v                
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_112734553_   3017 CAATGGTATTCTTTACAGAAATAGACAATAGAATCCTAAAATTCACATGG 3066
                           iiv iv  i   i       v     vvvi             i    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_112734553_   3067 GATGACAAAAGACCTAGAATGTCCAAAGCAATCTTGAGCAAGAA---CAA 3113
                         i vvi   ii    i     iv     i         iv     ---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_112734553_   3114 AGCTGGATTAATCACACTTCCCAATTTTGAAATGTATTATAGCCAGATAC 3163
                           i    vv v                ii   iv  i  i i--------
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA-------- 245

  chr1_112734553_   3164 AGGGTAGTCCCAGCTACCTGGGAGTGGAGTCTGAGGCAGGAGGATGCTTC 3213
                         -----------      ---------------------------------
  L1M4_orf2#LINE/    246 -----------AGCTAC--------------------------------- 251

  chr1_112734553_   3214 AGCCTAGGAGTTTGAGGCTGCAGTGTGCTATGATTGCACCTGTGAATAGC 3263
                         --------------------------------------------------
  L1M4_orf2#LINE/    252 -------------------------------------------------- 251

  chr1_112734553_   3264 CACTGCACTCTAGCCTGGGCAACATAGATACACACACACACACACACACA 3313
                         --------------------------------------------------
  L1M4_orf2#LINE/    252 -------------------------------------------------- 251

  chr1_112734553_   3314 CACACACACACACACACACATATACACACACACACACATTATAGTAATGA 3363
                         ------------------------------------------      v 
  L1M4_orf2#LINE/    252 ------------------------------------------AGTAATCA 259

  chr1_112734553_   3364 AAACAGTATGGTACTTGCATAAAAACA-ATATATAGAGCAAAGGGACAGA 3412
                          i     i       v      ii i - i       v   v  i i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_112734553_   3413 ATAGAGCTCCCAGAAACAAATCCATGCATCTATAGTCAACTGATCTTCAA 3462
                           v   vvi       i   i    i   i   i     i    i   i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_112734553_   3463 CAAGGATGCCAATAACACACAATTGGAAAAGGATCATCTCCTTGATA--- 3509
                              i      v v  iv    v  i    i  vi   ii ii i ---
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_112734553_   3510 -GTGTTGGAAAAACTGGATATACAAATGCAGAAGGATGAAATTGGATCCA 3558
                         -   i   i v         ?v  v     i   i     i     i  v
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_112734553_   3559 TGTCTCACACTATATACAAAAATCAACTCAAAAAGGATTACAGATCTAAG 3608
                          ii       i            i         v    i ?   i    i
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_112734553_   3609 CTTAAAAGCTAAAACCATAAAACTCCTAGAAGAAAACATAGGGGAACATT 3658
                         iv   i         i         i                ? v v  i
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_112734553_   3659 TTCTTGATATTGGCCTGGGAAATGATTTTTTTTTTGATGTGACACAAAAA 3708
                            v   iv    vi i  v    i   i  v---   i      v    
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA---GATATGACACCAAAA 606

  chr1_112734553_   3709 GCACAAGCAACAGAAGCAAAAATAGACAAATGAGACTGCATCAAACTAAA 3758
                                     i   v         i    vi    v       v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_112734553_   3759 AAGCTTCTGCACAGCAAAGGAAAC----AACAGAGAAAAAAGGCAGTCTA 3804
                           i   i  ii vv       v  ----  v i  vi     i  ii i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_112734553_   3805 AGGAATGGGAGAAAATATTTTCAAACTATGTATCTGATAAGAGGTTAACA 3854
                         vi                  v    ii  i           i ii vii 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_112734553_   3855 TTTAAAATATATAAGGAACTCATACAACTGAATAACAAAAAAAAAAAAAG 3904
                          ii i         i      v       v     i     i -------
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA------- 799

  chr1_112734553_   3905 AAAGAGAGAATAAATTTAAAAAATAAATAAATAACCCTACTTTAAAATGA 3954
                         ---------------------------i         v i ?v      i
  L1M4_orf2#LINE/    800 ---------------------------CAAATAACCCAATTWAAAAATGG 822

  chr1_112734553_   3955 GCAAAGGACCTGAATAGACATTTCCCAAAAGAAGGCATACAGATGGCCAA 4004
                                 ii              i v       ii     i        
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_112734553_   4005 TAAGTATATGAAA 4017
                             i i      
  L1M4_orf2#LINE/    873 TAAGCACATGAAA 885

Transitions / transversions = 1.83 (119 / 65)
Gap_init rate = 0.01 (9 / 882), avg. gap size = 27.44 (247 / 9)  


 395 28.57 4.76 0.00  chr1_113216833_113219302.rev      782   907 (1563)    L1M4_orf2#LINE/L1        1   132 (776)  

  chr1_113216833_    782 TGGAAAGACGTTTCATGTTCATGG-----GAGAATTAGTATTGTTAAAAC 826
                                 ii ii           -----i   v   i         i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_113216833_    827 ACTCATACTACCCAAAGTGATCTACAAACTAAATATAATCTCTATCAAA- 875
                         iviv     v      v         i i v  iii    i        -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_113216833_    876 TACCTATAATATATTTCACAGAAATAAAAAAG 907
                          v  viiviiv v   ii       vi v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG 132

Transitions / transversions = 1.77 (23 / 13)
Gap_init rate = 0.02 (2 / 132), avg. gap size = 3.00 (6 / 2)  

3064 22.24 2.21 0.91  chr1_113216833_113219302.rev     1212  1980 (490)    L1M4_orf2#LINE/L1      130   908 (0)  

  chr1_113216833_   1212 AAGACAATCATTAAATTCACATGGAGCCACAAAAGACTCA-AATAGGCAA 1260
                            vii   v v       i     ivii   ii   i  -     v   
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr1_113216833_   1261 ATCAATCCTGAGCAAAAATAACAAAGCTG-AGGCATCACAGTACTTGATT 1309
                          v     i   iv  i  v       i  -   vv     v v iii   
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_113216833_   1310 GCAAAATGTACTACAAGGCTATAGTAACCAAAACAGCATGGTATTGGCAT 1359
                         v     iv        i    i     i   i    ii     i      
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_113216833_   1360 AAACACAAACACAGAGACCAATGAAAGAGAATAAAGAACCCAGAAATAAA 1409
                           iv i i   i v   i     i  v     vi   ii           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_113216833_   1410 TTCATGCATCTATGGCCAACTGTTTTTCAACAAAGGTGCCAAGAACATGC 1459
                         ii   i   i     i   i  v     i    i          v   v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_113216833_   1460 ACTGGGAAAAAGACAGTTTCTTCAATAAATGGTGCTGGGAAAATTGGAAA 1509
                          v    i   ii i   i i     i              v  i    v 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_113216833_   1510 GTCACATGCAGAAGACTAAGACTAGACCC-TGTCTC-CACTATATACACA 1557
                         ?i        i    v i iii i     - ii   -   i       v 
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_113216833_   1558 AATCAACTCAAAATGGATTAAAGACTTATATATAAAACTTGAAACTATGA 1607
                            i              i ?    i  v  i   i vi i       i 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_113216833_   1608 AATTACTAAAAGAAAACATAAGGG-AAATGCTTTGCAACACCGGGTTGGG 1656
                           i vi  i           i ? -    -   i ii  vii     i  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGG 578

  chr1_113216833_   1657 CAAGGGTTT-TTAAAAA-GAGATCTCAAAGCACAGACAACAAAAGCAAAA 1704
                            v     -   i v -  v i -v        ii         -    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACC-AAAAGCACAAGCAACAAAAG-AAAA 626

  chr1_113216833_   1705 AATAGACCAATGGGATTACATCAAACTGAAAAGCTTTTGTACTTAAAAAG 1754
                               iv   v   i v       v v    i       i   v   - 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA-G 675

  chr1_113216833_   1755 GAAAC----AACAAAATGAAGAGAAAATCTACAGAATGGAAGAAAATATA 1800
                           v  ----  v   i    i   v  i i         i         v
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_113216833_   1801 AGCAAACTATACATCTCACAAGGAGTTAATATCTGAAGAATATATAA-TA 1849
                         v     ii   i    v i    iii vi    i--           -v 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCC--AGAATATATAAAGA 773

  chr1_113216833_   1850 ACTT----AATTCAACAATGAAAA-ACAAATTATCTTAATTTAAAAGTGG 1894
                            i----  i    i   i    -      v i i-    ?    i   
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCC-AATTWAAAAATGG 822

  chr1_113216833_   1895 GCAAAAGACCTTAATAGGCATTTCTCAAAAGAAGACATACAAATGGCCAA 1944
                              i  ii v     i        v        i              
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_113216833_   1945 CAGGTACATGAAAAAATGCTCAACATCCCTAATCAT 1980
                         i i i         i            v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (115 / 52)
Gap_init rate = 0.02 (17 / 779), avg. gap size = 1.41 (24 / 17)  


3128 25.25 1.66 1.44  chr1_113433543_113439054     4117  5019 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_113433543_   4117 AAAAACATTTCATGCTCATGGATCGGAAGAATCAAGATCATTAAAATGGT 4166
                            i i  ii    i        i      v i  v  ii    i    i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_113433543_   4167 CATACTGCCCAAAGCAATTTATAGATTCAACACTATTCCTATCAAACTAC 4216
                         v     v      vii  i  i         i v  i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_113433543_   4217 CAACATCATTTTTCACAGAATTAGA-AAACCGTATTCTAACGTTCATATG 4265
                           i vv v     ii     v v  -  i i -  i    vi        
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCATATG 152

  chr1_113433543_   4266 GAACCAAAAAAAGAGCCTGAATAGCCAAAGCAATCCAAAGCAAAAGGAAC 4315
                            viiv  ii-  v  v           i     ivi iv  i i    
  L1M4_orf2#LINE/    153 GAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_113433543_   4316 AAAGCCAGAGGCATCATATTACCTGACTTCAAGGTAATATACTACAAGGC 4365
                             iii    vv   i i v  ii i     ---  iv        i  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAA---AACTTACTACAAAGC 248

  chr1_113433543_   4366 TACAGTAACCAAAACAGCATGGTACTGGTACGAAAACAGACACATAGACC 4415
                                 i   i    ii         i ii ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_113433543_   4416 AATGGAACAGAATAGAGAACCCAGAAATAAAGCTGCACACCTACAGCCAT 4465
                                i     v    ii           v iii   ii  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_113433543_   4466 CAGCTCTTCAACAAAGTCAACAAAAACAAGCAATGGTGAAAGGACTCCCT 4515
                         iv v i   i    i viiv   i v  vv      v     i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_113433543_   4516 ATTCAATAAATGGTTTTGGGATAACTGGCTATCCATATGCAAA-GAATGA 4564
                         v     i       vi     i      v  ?   i       -      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_113433543_   4565 AACTGGACCTCTACC-CATCACCATATACAAAAATTAACTTATGATGGAT 4613
                          ii      i     -  -                     i vi      
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_113433543_   4614 TAAAGACTTAAATGTGAGACCTCAAACTATAAAAATCCTAGAAGGAAACC 4663
                         i ?    i       i   v  v           v  i      i    v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_113433543_   4664 TAGG---AAATATCCTTCTCAACACTGGTCTTGGCAAATAATGTAT-GGC 4709
                             ---    ---    vii  vi   vi v     - ii v v -i v
  L1M4_orf2#LINE/    548 TAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA 593

  chr1_113433543_   4710 TAAGTCCTCAAAAGCAATCA--CAACAAAAACAAAAATTGATAAGTGGGA 4757
                           v v vi        --  --        iv      v     i v   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_113433543_   4758 CCT------AGTTAAAGAGCATCTGCACAGCAAAAGAAACTTTCAACAGA 4801
                          i ------ i     i - v i  ii vv    i  v   v    v i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_113433543_   4802 GTAAACAGACAACCTACAAAATAGGAGAAATTATTTGCAAACTATGCATC 4851
                           i  v        i   i   i       v          ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_113433543_   4852 CAACAAAAATCTAATATCCAGAATCTAATGGGAACTTAAACAAATCAACA 4901
                         ii i  iiiv  vi          v  vvii     ivv    v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_113433543_   4902 AGCAAAAAGCAAATAACCCCACTGAAAAGTGGGCAAAGGACATGAACAGG 4951
                          vv    ii          v i ?    i           iv    i  i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_113433543_   4952 CACTTCTTAAAAGAAGACATACACATGGCCAACAGACATATTAAAAAATG 5001
                           i    iv        i     v        i ii  i  v    i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_113433543_   5002 CTCATCATCACTAATCAT 5019
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (143 / 82)
Gap_init rate = 0.02 (15 / 905), avg. gap size = 1.87 (28 / 15)  


3239 24.63 4.18 1.69  chr1_113439099_113441003      528  1412 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_113439099_    528 GGTAAGACATCCCATGTGCATGGATTGGAAGAATTAATATCACTAAAATG 577
                           v    i         v              v       iii   i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_113439099_    578 ACTATACTTCTCAAGTAAATCTACAGATTCACTGCAATTCTTGTCAAAAT 627
                         i v     i i   i vi             vi     i i i       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_113439099_    628 ACCAAC-ATCAATTTTCCAGAATTAGAATGAAC-AATCCTAAAATTCATA 675
                         v   i -ii vv    v     v v  -ii i -i               
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATA 150

  chr1_113439099_    676 TGGAACCAAAAAAAAAAAAAAAAAAGCCTGAATAGCCAAAGCAATCCTGA 725
                              ---------- viv  iii v  v           i     i   
  L1M4_orf2#LINE/    151 TGGAA----------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_113439099_    726 GCAAAAAGAACAAAACTGGAGGCATCACAGTATCTGACTTCAAAATATAT 775
                         iv  i         ii      vv     v vi ii i       iv  i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_113439099_    776 TACAAGGCTATAACAACCAGAACAGCATGGTATTAGTATAAAAAGAGACA 825
                              i    i ii  i  ii    ii     i i i    ii v     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_113439099_    826 CATAGA-CAATGGAACAGA-----GAATCCAGAAATACATTCAAGTATTT 869
                         i     -        i   -----  i          v ii  vii    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_113439099_    870 ACAGCCAACTGATTTTTGACAAAAGTGCCAGTAATATACACTGAGGAAAG 919
                          ii i   i       i     ii      iv vi  v  v  i      
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_113439099_    920 GACACCCTCTTCAATAAATGATGCTGAGAAAATTGGATATTTATATGCAG 969
                         i i vi  i     i     i     i  v  i      ?ii i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_113439099_    970 AAGAATGAAATTTCACTCCTAACTCTCACCATATACAAAAATTAA----- 1014
                                  i  vv  i    v   v                   -----
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_113439099_   1015 ----------AGACTTCAATGTAAGACTTCAAATTATAAAACTATCAGAA 1054
                         ----------    i v         vi v   i         v i    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_113439099_   1055 GAAAATACAGGGAAAACACTTCAGGATGTTGGTCTAG-CAAAGATTTTAT 1103
                              i i   ?iv  vv    iv  iv    vi   -   v i   iv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_113439099_   1104 GGCCAAGACCTCAAAAACACA----------GACAAAATATACAAATGGG 1143
                         i vi v   vi     i    ----------  v      v i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_113439099_   1144 ACTACGTTAAACCAAAGAGATTCTGCACAGCAAAGGAAACCATCAACAGA 1193
                            v i i   viv  i iv  i  ii vv       v  i     v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_113439099_   1194 GTGAAGAGACCACCTGTTGAATGGGAGAACGTATTTGCAAGCTATTCATC 1243
                              i    v   iiiv           vi         iii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_113439099_   1244 CAACAAGAGACTAATATCCAGAATACACAAGGAACTCAAACAACTCAACA 1293
                         ii i   i    vi           i i  i      vv         i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_113439099_   1294 GTAAAAACAAAAACAAATAATCTCATTAAAAGGTAGGCAAAGGACATGAA 1343
                         i      ----i        i iv   ?   ii i         iv    
  L1M4_orf2#LINE/    791 ATAAAAA----GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_113439099_   1344 TAGACATTTCTC---AAAAGATGTACAAGGGGCCAACAGGTATATGAAAA 1390
                                     --- i     i     iv      i i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_113439099_   1391 AATGCTCAACATTACTAATCAT 1412
                         i           i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (144 / 71)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 4.73 (52 / 11)  


3667 23.01 1.33 0.88  chr1_113458409_113460333.rev      531  1434 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_113458409_    531 TGGAAAAATATTCCACGTTCATGGATTGGAAGACTAAATCTTGTTAAAAT 580
                               i    i   i                   v   v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_113458409_    581 GTCCATACTACCCCAAAA-AATCTACAGATTCAATGCAATTCCTACAAAA 629
                          v v     -       v-i              i     i    iv   
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_113458409_    630 ATACCAATGGCATTCTTTACAGAAATAGAAGAAACAATCCTAAA---TAT 676
                           v   iiv  v  i   i       v  vi ivii        ---i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_113458409_    677 ATTGAACCACAAAATACCCAGAATAGCCAAAGCTATCCTAAGCAAAAAGA 726
                           v   vii   iiv                i v   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_113458409_    727 ATAAAACTGAAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCT 776
                          i   ii  i    v     i v  ii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_113458409_    777 ATAGTAACCAAAACAGCAAGGTACTGGCATAAAAACAGACACATAGACCA 826
                          i     i   i    iiv             ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_113458409_    827 ATGGAACAGAATAGAGAACCCAGAAACAAATCCACACACCTACAGTGAAC 876
                               i     v    ii       i   i   i   ii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_113458409_    877 TCATTTTTGACAAGA-TGCCAAGAACATATACTGGGGAAAAGACAGGCTT 925
                          v     i      i-        v   vi v        ii i  v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_113458409_    926 TTCCATAAATGATACTGCGAAAACTAGATATCCATATGCAGAGGAATGAA 975
                            v i     i i   v  v    i    ?   i     i i       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_113458409_    976 ACTAGACCCCTATCTCTCACCATATCCACAAATCAAATCAAAATGGATTA 1025
                         ii i        i   v        v  v    i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_113458409_   1026 AAGATTTAAATTTAAGACCTCAAACTATGAAACTACTATAGGAAAACATT 1075
                         ?   ii     v     v  v       i     vi  v i        v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_113458409_   1076 GGGGAAAATCTCCAGGGTATTGGTCTGCGGAAAAATTCCTTGAGCAATAT 1125
                           ? v      i iv iiv    vi iv v  vii  i   iiii vv i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_113458409_   1126 CCCACAAACACAGGCAACCAAAGCAAAAATGGACAAATAGGACCACATCA 1175
                         v   v  i    i     v    v      i  i    v    iv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_113458409_   1176 AG-TTAAAAAGCTTCTG-----CAGAGAAAATACAGTCAGCAAAGTGAAG 1219
                          i-       -   i  -----  i  i --i  vi   iv        i
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGA--CACTATCAAGAAAGTGAAA 696

  chr1_113458409_   1220 AGACAACCCACAGAATGGGAGAAAATATTTGCAAACTACCCATCCCACAA 1269
                                                            ii ivi   iv i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_113458409_   1270 GGGATTAATAACCAGAATACATAAGGAGCTCAAACAACTCTATAGGGGAA 1319
                             i vi  v        i    i  i   vv       v   ---- v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA----AT 792

  chr1_113458409_   1320 AAAAAATTTAATAATCCAAT-AAAAAATGAGCAAAAGATCTCAATAGACA 1368
                              iviv     i     -?       i     i   i v        
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_113458409_   1369 TTTCTCAAAAGAAGACATACAAATGGCAAACAGGTATATGAAAAGGTGCT 1418
                               v        i           v  i i i i        i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_113458409_   1419 CAGCATCACTGAGTAT 1434
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (132 / 72)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


3206 27.53 0.44 0.44  chr1_113595772_113600200     3029  3936 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_113595772_   3029 TGGAAGAACATTCCACGCTTACGGGTAGGAAGAATCAATATCGTGAAAAT 3078
                              ii i  i   i i i i  i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_113595772_   3079 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATGAAGC 3128
                            v     v     iv i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_113595772_   3129 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3176
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_113595772_   3177 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 3226
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_113595772_   3227 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3276
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_113595772_   3277 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3326
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_113595772_   3327 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 3374
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_113595772_   3375 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3424
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_113595772_   3425 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3474
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_113595772_   3475 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 3524
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_113595772_   3525 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 3574
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_113595772_   3575 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 3624
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_113595772_   3625 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3674
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_113595772_   3675 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3724
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_113595772_   3725 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTTATCTGACAA 3774
                           i     i   iv            v  i    vii iv       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_113595772_   3775 AGGACTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3824
                         i     vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_113595772_   3825 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 3874
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_113595772_   3875 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 3924
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_113595772_   3925 ATCACTGGCCAT 3936
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3147 26.40 0.66 0.99  chr1_113718920_113723398.rev     3087  3995 (484)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_113718920_   3087 GAAAGATATTCCATGTTTATTGATTAGAAGAATTAATATTGTTACTATGT 3136
                                  i       i  v    i     v            vv   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_113718920_   3137 CCATACTACCCTAAGCAATCTATAGATTCAATGCTATTTCTAACAAAATA 3186
                          v     v   v  vii     i        i  v  ii   v      v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_113718920_   3187 CCAGTAACACTCTTCACAAAAATAGAAAAAAAAA-CTTAACATTTATATG 3235
                             ivi vi i  ii  i    v  v  ivvi - i   v   i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_113718920_   3236 GAATCACAAAAGACCCCAAATAGCCAAAGGAATGCTGGGCAAAAAGAATG 3285
                            vii   ii     vi          iv   vi  iiv  i     ii
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_113718920_   3286 AAGCTGGAAGGGTCACACTACATGACTTCAAACTTTACTACAAAGCTATA 3335
                            i    i iv       v vii i      vi              i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_113718920_   3336 GTAACCAAATCAGCATGGTACTGGTATAAAAACAGACACATAGACCAATG 3385
                             i   iv   ii         i    ii i     i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_113718920_   3386 GAACAGAATAAAGAACACAGATATAAATACAAGCATTTACAGCCAACTCA 3435
                            i     vi   iiv    v     iv  vi      ii i   i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_113718920_   3436 TCTTCGACAAAGGTACCAAGAACATACAATGGGGAAAAGACAGTATTTTC 3485
                          i        i   i      v   v           ii i   v     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_113718920_   3486 AGTAGATGCTGCTGGGGAAACTGGATTAACCATATGCAGAAGAATGAAAC 3535
                          ii i   v       iv        - ?   i     i         ii
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCAAAAGAATGAAGT 451

  chr1_113718920_   3536 TATACCACTATCTCTCACCAAACACAAAAATCAAAGCAAAATGGATAAAA 3585
                          iv   v   i   v     v i        i  vv          v ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_113718920_   3586 TACTTAAATCTAAGACCTCGAACAACTGAAGAAAAACTACTAGAAGAAAA 3635
                         v  i     v     v  vi   v i------      vi          
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTAT------AAAACTCTTAGAAGAAAA 545

  chr1_113718920_   3636 CACTGGGG-AGATGCTCCAGGACACTGACCTGGGCCAAGATTTTCTGTGT 3684
                           iv  ? - i  -  i iv   vi  ivi i   v v i   ii ivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_113718920_   3685 AGGATGTCGAAAGCACAAGGCCACACA-GCAAAAATAGACAAATGGGATT 3733
                          v  iii i          - v   v - v         i    v   i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_113718920_   3734 ATATCAAG-CTAAAAGCTCTGG-ACAGCAAAGGAAACAACCAC-AAAGCA 3780
                         vi     i-i     i  i v -i vv       v  v i  v-    ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_113718920_   3781 AAGAGACAACCCACAGAATGAGAGAAAATCTTTGCAAATTATCCATATGA 3830
                           i                 i        v         i  vi  v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_113718920_   3831 CAAGGGATTAATAATCAGAATATTTATGGAGCGCAAACAACACAACAGCA 3880
                         i      i vi  vi        v  vi  i v vv     v   i ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_113718920_   3881 AAAAGCCAAAGAATCTGATTTAAAAACGGGCAAAAGATCTAAACAGACAT 3930
                              v    v  i ii   ?     i       i   i i  i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_113718920_   3931 TCCCGAAAATAAAACATACAAATGGCCAACAGGTAAGTGAGCAAATGCTC 3980
                          i ivv   v  i i              i i i vi   iv i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_113718920_   3981 CTTGTTAGTAATCAT 3995
                         vvii i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.50 (15 / 10)  


2914 26.62 3.98 0.68  chr1_113728182_113734556.rev     5006  5884 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_113728182_   5006 TGGAAGAATATTCCATGCTCATAGATAGGAAGAATCCATATTGTGAAAAT 5055
                              ii    i     i    i   v      v iv       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_113728182_   5056 GGCCATATTGCCCAAAT-AATTTATAGATTCAATGCCATCCCCATCAAGC 5104
                            v   i v       -i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_113728182_   5105 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5152
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_113728182_   5153 TATGGAACCAAAAAAGAGCCCACAGTA-CCAAGACAATCCTAAGCAAAAA 5201
                                viiv  ii  -    v i  -    i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_113728182_   5202 GAACAAAGCTGGAGGCATCACGCTACCTGACTT----------------- 5234
                                 i      vv    i  v  ii i  -----------------
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_113728182_   5235 -------AACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5277
                         -------  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_113728182_   5278 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCCGCAAC 5325
                                 i    i--    i  --        vv   i    iiiiiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_113728182_   5326 CATCGGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGATAGGATTC 5375
                           viv   i  i     ivv  v   i v  vvv        v  i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_113728182_   5376 CCTATGTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATACAGAAAGC 5425
                         i  v vi  i              v      v  ?   i  i  i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_113728182_   5426 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5475
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_113728182_   5476 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5525
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_113728182_   5526 CCTAGGCA-ATACCATTCATAACATAAGCATGGGTAAGGACTTCATGACT 5574
                          v    ?i- v i -   i i  v vi vv i  i  v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_113728182_   5575 AAAACATCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 5624
                          vi   i        vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_113728182_   5625 AATTAAACTAAAGAGCTTCTGCGTGGCAAAAGAAACTACCATCAGAGTGA 5674
                         v  i   v v  i i   i  i ivv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_113728182_   5675 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCGATCTACCCATCTGAC 5724
                          v  i     i                 v     i vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_113728182_   5725 AAATGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5774
                           iv i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_113728182_   5775 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATAAGAACAGACACG 5820
                            i    ----   v  i?    i            vv   i     iv
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_113728182_   5821 TCTCAAAAGAAGACATCTATGCACCCAACAGACACATGAAAAAATGCTCA 5870
                             v        i  vi viiiv    i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_113728182_   5871 TCATCACTGGTCAT 5884
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (141 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.42 (41 / 12)  


2729 26.12 0.63 5.75  chr1_113739574_113741676.rev      656  1612 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_113739574_    656 TGGAAACACATCCCATGCTCATGGATGAGTAGAATCAATATTGTGAAAAT 705
                               v i        i        vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_113739574_    706 GACCATACGGCCAAAAGAAAAGCAATCTACAAATTCAATGCAATTCCCAA 755
                          i v    vv  v   -----vii       i      i     i  ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-----TTGATCTACAGATTCAACGCAATCCC--- 92

  chr1_113739574_    756 TATCAAACTGGAATTGCAATTCTCAATATCAATGCAGTATCAAAATACCA 805
                         -------------------------------------         v   
  L1M4_orf2#LINE/     93 -------------------------------------TATCAAAATCCCA 105

  chr1_113739574_    806 CCATCATTCTTCACAGAACCATAAAAAAC-AATCCTAAAATTCATATGGA 854
                         v vv v  i  ii     vi- i v  i -i                   
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_113739574_    855 ACCAAAAAAGAGCCCGCATAGCCAAAGCAAGACTAAGCAAAAAGAACAAA 904
                          viiv  ii  v  v v         i   vvi i iv  i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_113739574_    905 TCTGGAGGCATCACATTACCTGACTTCAAACTACACTATAAGGCCATAGT 954
                         vi      vv     i v  ii i      vivi    i  i  i i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_113739574_    955 CATTAAAACAGCATGGTACTGGTATAAAAATAGGCACAAAGACCAATGGA 1004
                         v  i  i    ii         i    ii    i  i v   i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_113739574_   1005 ACAGAATAGAGAACCCAGAAATAAAGCCAAATATTTAAAGCCAACTGATC 1054
                          i     v    ii           v   v i     vi i   i    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_113739574_   1055 TTTGACAAAGCAAACAAAAACACACAGTAGGGAAAAGACACCCTATTCAA 1104
                           i     i vviv   i v  iv  i i      ii i vi  v     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_113739574_   1105 CAAATAGTGCCAGGGTAATTGGCAAGTCAGATGTAGAAAAATGAAACTGA 1154
                              i    ii  ii  i   vv ?i  v   i i  i      ii  i
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_113739574_   1155 ATACTCATCTCTCACCTTATACAGAAATCAACTCAAGATGGATCAAACAC 1204
                          iv ii i   v    v      i    i       i        ? v  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_113739574_   1205 TTAAATCTAAAACCTGAAATCATAAAGATTCTAGAAGATAACATTGGAAA 1254
                         i     v   i v  i   ii     iv ii       v     v  ?iv
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_113739574_   1255 AACCCTTCTAGACATTGGCTTAAGCAAAGACTTCATGACTAAGAACCCGA 1304
                           vi    vv   v    v   i    v ii   v iiv  v  vv  i 
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_113739574_   1305 AAGCAAATGCGACAAAAACAAATATAAGTAGATGAAACTTAATCAAACTA 1354
                              v v  i      iv   v   ii  i  vii    v      v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_113739574_   1355 TAAAGCTTCTGCGAAGCAAAAGAAATAATCAGCAGAGTTAATTGACAACC 1404
                         v   i   i  i vvv    i  v iv    iv i   v  vv       
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_113739574_   1405 CACAGAGTGAGAGAAAGTCTTCACAGTCTATACATCTGGTAAAGGACTAA 1454
                               i  i      i v  ii  ivii   i     i   i     vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_113739574_   1455 TATCCAGAATCTACAAATAA-----ACAAATTAGCAAGAAAAAAAACCAA 1499
                                   v  i   v  -----    v i ii  v     i -----
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA----- 799

  chr1_113739574_   1500 GCAAACAATTCCATCAAAAAAAAGTGGGCTAAGGACATGAATAGATAACT 1549
                         -    i  ii v  i?     ---     v     iv        i vi 
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAA---TGGGCAAAGGATTTGAATAGACATTT 845

  chr1_113739574_   1550 CTCAGAAGAAGATATACAAACGGCCAACAAGCATATGGAAAAATGTTCAA 1599
                            vi               i      i     i   i   i   i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_113739574_   1600 CATCACTAAGCAT 1612
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 8.71 (61 / 7)  


2693 28.30 3.64 0.45  chr1_113743545_113748943     4027  4906 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_113743545_   4027 TGGAAAAACATTTTATGCTCATGGATAGGAAGA----ATATTGCTAAAAT 4072
                               i i  iii   i        v      ----      i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_113743545_   4073 GGCCATACTGCCCAAAGCATTGTATAGATTCAATGCTATTCCTGTTATAC 4122
                            v     v      viiv v  i        i  v  i   i i v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_113743545_   4123 TACCATTTACATTTTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 4171
                          v   vi i v     ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_113743545_   4172 ATGGAACCAAAAAAGAGCCCAAATAGCCAAGGTGATCCTAATCAAAAAGA 4221
                               viiv  ii  v  vi         iiii   i i vv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_113743545_   4222 ACAAAGCTGGAGGCATTATGCTACCTGACTTAAAACCGTACTACAGGGCT 4271
                               i      vv i ii  v  ii i  v   v v       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_113743545_   4272 ACAGTAACCAAAACAGCATGATACTGCTACAAAAGCAGACAGATAGACCA 4321
                                i   i    ii  i     vi i  iiii     v     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_113743545_   4322 ATGGAATGGATTAGAGAACCCAGAAATAAGGCCATACACCTACAACTATC 4371
                                i  v v    ii          iv       ii  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_113743545_   4372 TGATCTTCAACAAACCTGACACAAACAAGCAATGGGGAAAAGATTCCCTA 4421
                             i   i    ivv  v  vi v  vv           ii  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_113743545_   4422 GTTAATAAATGGTGCTAG-ATAACTGACTAGAGATATGCGGAAAATTGAA 4470
                         v i  i          i - i     iv  ?vv i    ii  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_113743545_   4471 ACTGGATGCCTTCCTTACACCACATA-AAAAATTAAGC-----TGGATTA 4514
                         ii    iv   v   i      i   -         vi-----     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_113743545_   4515 AAGACTT-----TAAAATCCCAAACTATAAAAACGTTGGAAGACAACGTA 4559
                         ?    i -----   i v iv           viv  i     v   i  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_113743545_   4560 GGCA-ATACCATTCTGGGCATAGGAGTGGGCAA-ATTTTCATGACAAAGA 4607
                           ?i- v i -   vv i v v  iv i     -iv    v iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_113743545_   4608 TGCCAAAAGCAGCTGCAATAAAGGTAAAAATTGACAAATGGGATCTAATT 4657
                         ii         vvv    i   i v      v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_113743545_   4658 AAACGAAAGAGCTTCTGCATAGTGGAGGAAACTATCAACAGAGTGAACAG 4707
                            vvv  i i   i  iiivviii    v        v i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_113743545_   4708 ACAACCTACAGAGTGGCAGAAAATATTTGCAAATGATACATCTGTCAAAG 4757
                               i     i   v                 v   i     vi  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_113743545_   4758 GTCAAATATCTAGCATCTGTAATGAACTT---CGATTTA-CAAGAAAAAG 4803
                          v vvi    i  v  v i   v     i--- i i i -i  v      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_113743545_   4804 -----CAACCCCATTAAAAAGTGGGCAAAGAGCATGAACAGACAGTTTTC 4848
                         -----i     v   ?    i         iiiv    i     v  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_113743545_   4849 AAAAGCAGACATACA--TG--CAATCAACAATCATGAAAAAAGACTCAAC 4894
                         v    v   i     --  --    v i  --        i vi      
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCA--CATGAAAAGATGCTCAAC 896

  chr1_113743545_   4895 ATCACTAATTAC 4906
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.25 (36 / 16)  


3297 26.87 0.44 0.44  chr1_113751385_113757643     4859  5766 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_113751385_   4859 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4908
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_113751385_   4909 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4958
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_113751385_   4959 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5006
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_113751385_   5007 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5056
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_113751385_   5057 AACAAAGCTGGAGGCATCACACTACCTTACTTCAAACTATACTACAAGGC 5106
                                i      vv       v  iv i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_113751385_   5107 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5156
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_113751385_   5157 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5204
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_113751385_   5205 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5254
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_113751385_   5255 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5304
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_113751385_   5305 GAAACTGGATCTCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5354
                            ii    i i  v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_113751385_   5355 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5404
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_113751385_   5405 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5454
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_113751385_   5455 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5504
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_113751385_   5505 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5554
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_113751385_   5555 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5604
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_113751385_   5605 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5654
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_113751385_   5655 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5704
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_113751385_   5705 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5754
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_113751385_   5755 ATCACTGGCCAT 5766
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3118 27.89 0.33 0.22  chr1_113824807_113831252.rev     5049  5955 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_113824807_   5049 TGGAAAAACATTCCATGCTCATGAATAGGAAAAACCGATATTGTGAAAAT 5098
                               i i  i     i     i  v    i viii       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_113824807_   5099 GGCCACACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5148
                            v i   v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_113824807_   5149 TACCATTAACTTTCTTCACATAACTAGAAAAAACT-ACTTTAAATTTCAT 5197
                          v   vivi i  i  ii  v  v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_113824807_   5198 ATGGAAACA-AAAAGACCTCATATAGCCAAGACAATCCTAAGCAAAAGGA 5246
                                ii-  ii    iviv        i      i i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_113824807_   5247 ACAAAGCTGGAGGCGTCACACCACCTGTCTTCAAACTATACTACAAGGGT 5296
                               i      vv      iv  iivi      viv        i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_113824807_   5297 AAAGTAACCAAAACAATATGGTATTGGTACCAAAACCGATACATAGAACA 5346
                          v     i   i   i i     i   i iv ii iv  i i     v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_113824807_   5347 ATGGAATGGAACAGAGGCCTCAGACATGACACCACATATCTATAACCATC 5396
                                i   iv   ivii    v  i vv   i i  i   iii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_113824807_   5397 TAATCTTCAACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 5446
                          i  i   i    ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_113824807_   5447 TTTAATAAATGGTGTTGTGAAAACTGGCTAGCCATATGCAGAAAACTGAA 5496
                           i  i        i  v  v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_113824807_   5497 ACTGGACTCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGATTA 5546
                         ii     i   v   i     v  i           i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_113824807_   5547 AAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5596
                         ?    i    i      v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_113824807_   5597 GGCA-ATACCATTCAGGACGTAGGCATGGGCAAAGACTTCATGACTAAAA 5645
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_113824807_   5646 CACCAAAAACAATAGCAACAAAAGCCAAAATTGACAAATGGTATCTAATT 5695
                                 i  vv           vv     v  i    v v ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_113824807_   5696 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 5745
                            v v  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_113824807_   5746 GCAACCTATAGAATGGGAGAAAATTTTTGCATTCTATCCATCTGACAAAG 5795
                         i     i i               v      vvii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_113824807_   5796 GTATGATATCCAGAATCTACAAGGAACTTAAACAAATTTACATGAAAAAA 5845
                          vv vi          v  i  i     ivv    v iv i vv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_113824807_   5846 ACAAACTACCCCATCAAAAATTGGGCGAAGGATATGAACAGACACTTCTC 5895
                              iv    v  i?    v     i      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_113824807_   5896 AAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTCATCAT 5945
                         v        i  vi vi       i  i  i       i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_113824807_   5946 CACTGGTCAT 5955
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.39 (145 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


1769 25.42 13.87 0.46  chr1_113850252_113851892      500  1148 (493)    L1M4_orf2#LINE/L1      173   908 (0)  

  chr1_113850252_    500 TAGCCAAAG-AACCTTAAAAAAAAAAAGACAAAGTTGGAAGACATAGGGT 548
                                 i-  i   i     i  i -           i   vi viv 
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGA-ACAAAGTTGGAGGACTCACACT 221

  chr1_113850252_    549 ACCAGATCTGAAGACTTATTTTAGAGCTACAGTGATAAAGACAGTTTGGT 598
                         v  vi  i v  i     i vi i         i  v        v    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_113850252_    599 ATTGGCATAAGGATAGATAAATAGATCAGTGGAACAAAATAGAGAGTCTA 648
                          i               i v        i     i i   v       i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_113850252_    649 GAAATCAATACACATGTATGTAGTCACTTTATTTTCAACCAAAGTGCCAA 698
                              v  iv  i ii v i i    v  v      i  v ii       
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_113850252_    699 ------CTGATATGGAAAAA---------TGAAC--------CT----CA 721
                         ------iii  iv     i --------- v   --------  ----  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_113850252_    722 ATT----------ATGC------------------------CTCACTTCA 737
                          i ----------    ------------------------     vi  
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_113850252_    738 TACA-AACAGTTAATTTCAGATGAATCAAAGACCTAAGCATAAAAGCTAG 786
                           i -  v i    i iv i   i    ?        iii   i     i
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_113850252_    787 AACCACAAAGCTTTTGGAAGAAAATATAGGAGAGTGTCTTCATGAGTCAG 836
                            i i   i  i  i        i     ? vivi     i   viiv 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_113850252_    837 AATT-GGCAAAGATTTCTTAAACAGGCCACAAAAAATATGAACCATAGAA 885
                         ii  -     v i       i i v v   v    ii ii i v i i  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_113850252_    886 GAAAAAGTTAATATTTTGCATGTAATAGAAATTTTAAAATTCTCTTCATC 935
                               i vi   vv   v iv v  vi     vv   v  i v v v  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_113850252_    936 AGAAGACACCATTGAAAAA-TGAATAGACAAAGTCACAGACT-------- 976
                          i i     i  ii i   -    v      v-i      v --------
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAAC-CCACAGAATGGGAGAAA 720

  chr1_113850252_    977 ----TTGCAA--TATATATTTGCCAAAGGAATTAAATTCAGAATCTATAA 1020
                         ----      --i      i  vi  i   v  iv  i      v     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_113850252_   1021 -GAACTGTTTACAACTCAATAATA----------TTGCCAAATTTTAAAA 1059
                         -     -i                ---------- vi  v    ?v    
  L1M4_orf2#LINE/    771 AGAACT-CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_113850252_   1060 TGGGCAAAATATGTTAATAAACATTTCACCAAAGAAAATATACAAACAGC 1109
                                 iv  v v    i       v        i         ii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_113850252_   1110 CCATAAAAACATGAAAAGATATTTAAAATTATTAATCAT 1148
                          v    iv            ii i  v  i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (101 / 61)
Gap_init rate = 0.02 (17 / 736), avg. gap size = 5.47 (93 / 17)  


3258 23.30 3.46 2.23  chr1_113878629_113883206.rev     3196  4092 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_113878629_   3196 TGAAAAGATATTTCATGTTCATAG-TTGGAAGAATCAATATTCTT----T 3240
                           i        ii         i -        v i      v  ---- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_113878629_   3241 T-CAATACTACCCAAACCAATCTATAGATTCAATGCAATCTCTATCAAAT 3289
                         v-       v      iii     i        i      i        -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr1_113878629_   3290 CTCTATCAAAATACCAATGACATTCTTCACAGAAATAGAAAAAACAATTC 3339
                         ----   ------   iivi v  i  ii       v  v  ivii  i 
  L1M4_orf2#LINE/    100 ----ATC------CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr1_113878629_   3340 TGAAATTTATATGGAACCACAAAAGACCCAGAATAGCCAAAGCTAGCCTG 3389
                          i     i        vii   ii                 i v v i  
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_113878629_   3390 AGGAAAAAGAACACAACTGGAGGAATCACATTACCTGACTTCAAATTATA 3439
                          ii  i       v ii       v     i v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_113878629_   3440 CTACAGAGCTATAGTAACTAAAGGAAGATGGTATTGGCATAAAAACAGAC 3489
                              i     i     ii  iiv ivi     i        ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_113878629_   3490 ACATAGACCAGTGGAACAGAAT---------AGAAA--AATCCATACACC 3528
                          i     i  i     i     ---------     --  i       ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_113878629_   3529 TACAATGAACTCATTTTCAAGAAAGGTGCCAAGAACATACATTGGAGAAG 3578
                           iii v  i v      i v  i          v   v  v   i   i
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_113878629_   3579 --ATAGTCTCTTCAA----TGGTTCTAGGAAAATTGGATATCCACATGTA 3622
                         --       i     ----    v  i   v  i      ?       i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_113878629_   3623 GAAGAATGAAACTTGACTTCTATCTCTCGCTGTATACAAAAATCAAATCA 3672
                         i         ii v   ii   i   v i ii           i  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_113878629_   3673 AGGTGAATTAAAGACTTAAATCTAAGACTTCAAACTGTAAAACTAAAAAA 3722
                          ii  i  i ?    i     v     vi v     i       vvv i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_113878629_   3723 AGAAAACATTGGGGAAACTCTCCAGGACATTGGTCTGGGCAAAAATTTCT 3772
                                  v  ? v  v   i iv   v    vi i     vii     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_113878629_   3773 TCAG---TGATACTCCACAAGCCTAGGCAACTAAAGCAAAAATGGACAAA 3819
                          -  ---   i  --  v    vi i     v    v      i  i   
  L1M4_orf2#LINE/    590 T-AGATATGACAC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_113878629_   3820 TGGGATCACATTAAG-TTAAAAAGCTTCTGCATAGCAAAGGAAACAATCA 3868
                          v   iiv   i  i-       -   i  iiivv       v  v    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_113878629_   3869 GTCAAGTGAAGAGACAGCCCACAGAATGGGAGAAAATCTTTGCAAACTAT 3918
                         ivv       i     i                    v        ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_113878629_   3919 CCATCTCACAAGAGATTAATAACCAGAATATATAAGGAGCTCAAACAACT 3968
                         vi    v i   i  i vi  v             i  i   vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_113878629_   3969 CTATAGGAAAAAT-CTAATAATCTGATTAAAAAATGGGCAAAACATTGGA 4017
                          v   iv     v- v     i ii   ?             iv   v  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_113878629_   4018 ATAGACATTTCTCATGAAGAAGACATAGAAGACATAG--AAACAGCAATA 4065
                                      -ii       i   v  ---  i --  vv    -i 
  L1M4_orf2#LINE/    836 ATAGACATTTCTC-CAAAGAAGATATACAA---ATGGCCAATAAGCA-CA 880

  chr1_113878629_   4066 TGAATAAGTGCTCAG-GTCATTGATCAT 4092
                             v ii      i-i   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (133 / 72)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.55 (51 / 20)  


3224 26.88 0.88 0.44  chr1_113888151_113894544.rev     5000  5903 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_113888151_   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5049
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_113888151_   5050 GGCCATATTGACCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5099
                            v   i vv    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_113888151_   5100 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5147
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_113888151_   5148 TATGGAACCAAAAAAAAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5197
                                viiv  iii v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_113888151_   5198 AACAAAGCTGGAGGCATTACACTACCTGACTTCAA--CCTACTACAAGGC 5245
                                i      vv i     v  ii i     -- i        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_113888151_   5246 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5295
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_113888151_   5296 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCACATCTACAACT 5343
                                i    i--    i  --        vv  ii    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_113888151_   5344 ATCTGATCTTCGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5393
                          vi    i        ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_113888151_   5394 CTATGTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5443
                           v vi  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_113888151_   5444 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5493
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_113888151_   5494 TTA--GACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5541
                          i --   i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_113888151_   5542 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5591
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_113888151_   5592 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5641
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_113888151_   5642 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5691
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_113888151_   5692 AGGCAGCCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACGA 5741
                           i  i  i   i             v       vii ivi      ii 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_113888151_   5742 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGACAA 5791
                         i  i  vi          v  i  v      vv    v iv i  v v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_113888151_   5792 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5841
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_113888151_   5842 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5891
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_113888151_   5892 ATCACTGGCCAT 5903
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


 590 24.38 0.00 1.25  chr1_113975302_113979190     1834  1993 (1896)    L1M4_orf2#LINE/L1        1   158 (750)  

  chr1_113975302_   1834 TGGAAAGATATTCCATAGTTTATGAACTGGAAGAATGACTATTGTTAAAA 1883
                                    i    -   i   i i       v v v         i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_113975302_   1884 ATATCCATATTAACCAAAGCAATCTACAGATTCAATGCAATCCCTATAAA 1933
                         - iv v   i vv     vii              i           v  
  L1M4_orf2#LINE/     50 -TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_113975302_   1934 AATAACAATGACATTCTTCACAAAAATAGAAAAAACAATCCTAAAATTTA 1983
                            vv  iivi v  i  ii  i    v  v  ivii           i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_113975302_   1984 CATGGAATTG 1993
                         i      v  
  L1M4_orf2#LINE/    149 TATGGAAATG 158

Transitions / transversions = 1.29 (22 / 17)
Gap_init rate = 0.01 (2 / 158), avg. gap size = 1.00 (2 / 2)  

 843 26.29 1.88 0.00  chr1_113975302_113979190     2331  2543 (1346)    L1M4_orf2#LINE/L1      140   356 (552)  

  chr1_113975302_   2331 TAAAAATTATATGGAATCACAAAAGACCCAAAATAACCAAAGCTATCGTA 2380
                              v i        vii   ii      i    i     i v   v i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_113975302_   2381 AGTAAAAACAACAAAACTGAAGGAATCACATTACCTGACTTCAAATTGTA 2430
                          iv  i  v      ii  i    v     i v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_113975302_   2431 CTACAGCACTATAGTAACCAAAGGAGCATGGTAGTGGCATAA----AAAC 2476
                              ivi   i     i   iiv  ii     v        ---- i  
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_113975302_   2477 ACATCGGCCAATGGAACAGAATTGAGAATCCGGAAATAGATCCATACATC 2526
                          i  v ii        i          i   i      i i        i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_113975302_   2527 TACAGTGAACTCATTTT 2543
                           ii  v  i v     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTT 356

Transitions / transversions = 2.50 (40 / 16)
Gap_init rate = 0.00 (1 / 217), avg. gap size = 4.00 (4 / 1)  

2133 24.37 1.43 0.18  chr1_113975302_113979190     2844  3401 (488)    L1M4_orf2#LINE/L1      344   908 (0)  

  chr1_113975302_   2844 GTGAACTCAGTTTTGACAAAGATGCCAAGAACATACATTAGAGAAAGGAC 2893
                           v  i v v   i     i i        v   v  v i i     i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_113975302_   2894 AGTCTCTTCAATAAATGATGCTGGAAAAACTGAATATTCACATGCAGAAG 2943
                              i     i     i      i v     i   ?i        i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_113975302_   2944 AATGAAACTAGACCCTTATCTCTCACCATATGCAAAAATCAAATAAAAGT 2993
                               ii i     i  i   v        i       i  v v   i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_113975302_   2994 TAATTAAAGAACTAAACCTAGGACCCCAAACTATGAAATGACTAAAAGAA 3043
                         vi  i ?   v     iv  i  v iv       i   ivvi  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_113975302_   3044 AACATTAGGGAAACTCTCCA-GATGTTGGTCTGGGCAAAGATTTCTTAAG 3092
                              vi ? v  v   i i-  iv    vi i     v i       ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_113975302_   3093 TAATACTCCACAAGCACAGGCAACCAAAGCAAAA-TGGACAAATGAGATC 3141
                           vv  v   v       i     v    v    - i  i    vi  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_113975302_   3142 ACATCAA-GTTAAAAAGCATCTATATAGCAAAGGAAACAATCAACCAAGT 3190
                         v      -i       - v i i iivv       v  v     vv    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_113975302_   3191 GAAAATACAACTCACAGAATGAGAGAAAGTCTT---AAATTATCCATCTG 3237
                              v     i         i      i v  ---    i  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_113975302_   3238 ACAAGGGATTAATAACCAGAATATATAAGGAGTTCAAACAACTCTATAG- 3286
                          i      i vi  v             i  ii  vv       v   i-
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_113975302_   3287 AAAAAATCTAATAATCTGATTTTAAAATGGGCAAAAGATCTGAATAGACA 3336
                              iv v     i ii   ?v            i   i          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_113975302_   3337 TTTCTCAAAAGAAGACATATAAATGGTAAACAGGTATGTGAAAAGGTACT 3386
                               v        i   i      iv  i i i ii       i i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_113975302_   3387 CA-TATCATTGATCAC 3401
                           -i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (81 / 51)
Gap_init rate = 0.01 (7 / 565), avg. gap size = 1.29 (9 / 7)  


1615 12.07 2.80 31.37  chr1_114094722_114097469      500  1535 (1213)    L1M4_orf2#LINE/L1       63   802 (106)  

  chr1_114094722_    500 CAAAGTGATCTACAAGTGCAATGCAATTCTTATCAAAAACCCAA-TGGCA 548
                             v         ii v   i     i i        v    i-  v v
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_114094722_    549 TTTTTACATAATTTGTTTAAAAAACAGA--CTAAAATTCAT--GGAATTT 594
                              i  v  v   ---- v  i v  --           --    v v
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr1_114094722_    595 CAAGGGGCACTGAACAGTCAAAACAATCTTGAAAAAGAAGAGCAAAGTTG 644
                               i v v   i  i                       i        
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_114094722_    645 AATGAC--ACACTACCTGATTTCAAAAATTGCAACAGAGCTACAGTAATT 692
                         i v   --     v  ii         v  i v   i            i
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_114094722_    693 AAAACAGTGTGGTACTGACATA-GTATAGAC-TAAAGACCAATGGAATAG 740
                           i              i    - v      -  v   i           
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_114094722_    741 AA----GAGCTTTGAAAAAAACATTTACAT--ATGGTGGGCAATTGATTT 784
                           ----   iiiv    v    viv     --     ---          
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGT---CAATTGATTT 355

  chr1_114094722_    785 TTGACAAAAGTGCCAAGAAAATTCAATGGAGAAAGGAGAGTGTTTTCAAT 834
                          i     ii         vv         i     i v   v       i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_114094722_    835 AAATGATTCTGGGAAAAACTGAATATACACATGCAAAAGAATGAAGTTGA 884
                              i v      v  -   i   ?v                      -
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGAAGTTG- 453

  chr1_114094722_    885 GGCTGGGTGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGA 934
                         --------------------------------------------------
  L1M4_orf2#LINE/    454 -------------------------------------------------- 453

  chr1_114094722_    935 GGCGGGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGACCAACAT 984
                         -----------------------------------------    -----
  L1M4_orf2#LINE/    454 -----------------------------------------GACC----- 457

  chr1_114094722_    985 GGAGAAACCCCGTCTCTACTAAAAATACAAAATTAGCCAGGCATGGTGGC 1034
                         --------------------------------------------------
  L1M4_orf2#LINE/    458 -------------------------------------------------- 457

  chr1_114094722_   1035 GCATGCCTGTAATCCCAGCTACTCAAGAGGCTGAGGCCGGAGAATCACTT 1084
                         -----   ------------------------------------------
  L1M4_orf2#LINE/    458 -----CCT------------------------------------------ 460

  chr1_114094722_   1085 GAACCAGGGAGGTGGAGGTTCCAGTGAGCCAAGATCACGCCATTGCACTC 1134
                         --   -----------------------------    i    -------
  L1M4_orf2#LINE/    461 --ACC-----------------------------TCACACCAT------- 472

  chr1_114094722_   1135 CACCCTGGGCAGCAAGAACGAAACTCCATCTCAAAGGAAAAAAAAAAAGA 1184
                         --------------------------------------------------
  L1M4_orf2#LINE/    473 -------------------------------------------------- 472

  chr1_114094722_   1185 GAGAGAATGAAGTTGGACCCTTATCTTATGATACAGAAATTAACTCAAAA 1234
                         ------------------------------     i              
  L1M4_orf2#LINE/    473 ------------------------------ATACAAAAATTAACTCAAAA 492

  chr1_114094722_   1235 ATTGATCAAATACCTAAACATAAGAAGTAAAA-TGTAAAACTCTTATAAG 1283
                         - v     ? v       ii     iv     - i           v   
  L1M4_orf2#LINE/    493 -TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_114094722_   1284 AAAA--TGGGC---AAGCTTCATGACATTGGATTTGGCAACGATTTCTTG 1328
                             -- i  ?---  v    i    v    i  v     i i      i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_114094722_   1329 GATAGGACACCAAAGGCACAAACAACAAAAGAATAA-TAGGAAAATTGGA 1377
                             v         i      i           v  -   iv        
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_114094722_   1378 CTTCATTGAGATTAAGA-CTTTTACACACCAAAGGACAC------AAAGG 1420
                               ii i     i -     iii vi          ------i  i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_114094722_   1421 CAAAAAGGCAACCCATTGACTGAATGGAAGACGGTATTTGCAAATCACAT 1470
                         ii     i       ---- v      i   vii             i  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCA----CAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_114094722_   1471 ATCTGATAAGGGATCAATATCCAGAATACATAGAGAACTCCTAAAACTCA 1520
                                      iivi           i   i       i  v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_114094722_   1521 ACAACATGTAAACAA 1535
                          i  i viv i    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAA 802

Transitions / transversions = 1.60 (75 / 47)
Gap_init rate = 0.03 (24 / 740), avg. gap size = 14.75 (354 / 24)  

 438 15.91 0.00 1.14  chr1_114094722_114097469     2179  2266 (482)    L1M4_orf2#LINE/L1      822   908 (0)  

  chr1_114094722_   2179 GGCAAAGGACTTGAAGAGACATTTTTCCAAAGAGGATATACAAATGGCCA 2228
                                  i     v        i        i                
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_114094722_   2229 ATAAGACCACAGAAAGGTGTCTAATCATTAGGAAAATA 2266
                              vv  iii    i  iii  -   i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1)  


3222 17.87 9.55 2.94  chr1_114198995_114201131.rev      502  1318 (819)    L1M4_orf2#LINE/L1       21   891 (17)  

  chr1_114198995_    502 ATGGACTG----ACTTACTATT---AAGCTGTCAATACTACCCAAAGTCA 544
                              i  ----     v    ---   v  v       v      v v 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr1_114198995_    545 TCTACAGATTCATCGCTATCCTTAATAAAA-AGCAATTATGGTTTTTGTA 593
                                     v   v    i  vi    -vv  ii iivv      i 
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr1_114198995_    594 TAAAATAGAAAAACCCATCCTAAAATTTATATGGACCCTCAAAGACCCCA 643
                         -i    v  v  i iv           i       vviv   i iv    
  L1M4_orf2#LINE/    121 -GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_114198995_    644 -AATAGCCAAAACAATCTTGAAAAAGAA---CAAAGTTGGAGGTCTCACA 689
                         -                           ---            v      
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_114198995_    690 CTTCCTGATTTCAAA-CTTACTACAAAGCTACAATAATCAAAACAATGTG 738
                              ii        -                 i       i   i    
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_114198995_    739 GTACTGGCATAAAGACA--TATATAGATTAATGGAATAGAGAGCCCAACA 786
                                     i  i --i        i           --------- 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA---------A 310

  chr1_114198995_    787 TTGAAAATGGGAAAGCAATAGAAGATAAGAATTATTTGTATATATGTTCA 836
                             i i ------- --i    -    - vii  --ii  v    v   
  L1M4_orf2#LINE/    311 TTGAGAGT-------C--CAGAA-ATAA-ACCCAT--ACATTTATGGTCA 347

  chr1_114198995_    837 AATGATTC-CAACAAGGGTGCCCAAACCACCCAATGCAGAAAGGACAATC 885
                          v     i- i           v i    ii     vi     i i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_114198995_    886 TTCTTAGCAAATGGTGTTTGAAGAACTGAATAGTCACATGCCAAAGAATT 935
                           i i i         i v i v     i   ?i       v       v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_114198995_    936 ACACTGGATTTGTACCTTGGACCATAGACAAAAATCAAC--AAA--GAAT 981
                          vii    iiiv     iiv      v        i   --   -- i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_114198995_    982 CAAAGACCAAAATATAAGAGCTAAAACTATAAAACTCTTAGCAGAAAACA 1031
                           ?     v    i                           v        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_114198995_   1032 TAGGGGAAAATCTGTATGATTTCGACTTAA-CAGTGACTTCTTGGATATG 1080
                             ? v      vii   ii i iv   i-  i  ii     i      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_114198995_   1081 TCACCAAAAGCACAAGCAACCAAAGAAAAAGTAGACAAACTGCACTTCAC 1130
                         v                   v         i    i   i  v      i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_114198995_   1131 CAAAGTTAAAAACTTTTCTGTGTCAAA---CACTATCAACAG-GTAAAAA 1176
                             i            v  iv     ---         v i-  i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_114198995_   1177 GGCAACCCAAGGAATAGATGAAAAT---------------------TAAG 1205
                          i       vi    i iv      ---------------------    
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_114198995_   1206 ----------------TATATAGAGTA----TACAACTCAACAACAAAAA 1235
                         ----------------      i  v ----          i  i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_114198995_   1236 G--------CCCAATTCAAGAAATGAGGAAAGGACTTAAATAGACATTTC 1277
                          --------       ?  -     i v      i  i            
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_114198995_   1278 TCCAAAGAAGATATACAGATGTC----GGGCACATAAAAAAATGC 1318
                                          i   v ----ii      i    i    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

Transitions / transversions = 1.78 (91 / 51)
Gap_init rate = 0.03 (26 / 871), avg. gap size = 3.92 (102 / 26)  


4235 18.27 1.78 0.47  chr1_114338999_114340838      505  1347 (493)    L1M4_orf2#LINE/L1       55   908 (0)  

  chr1_114338999_    505 ATGTTACCCAAAGTAACCCACAGATTCAAGACAATTTCTATTAAAATCCC 554
                           ii v      v i i i          vi    ii    i        
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_114338999_    555 AATGATGTTTTTTAAAGAAATTGAAAAATTCATTCCAAAATTCATATGGA 604
                          iiviiv      iv         v  ii v  i i              
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_114338999_    605 ATCTCAGGGAACCCTACATAGCCAAAACAATTTTGAAAAAGAA---CAAA 651
                          viv  i  i    viv              i           ---    
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_114338999_    652 GTTGAAGGACTCATTCTTCCTGATTTCAAAGCTTACTTCGAAGCTACAGT 701
                             i        iv     ii        i      v i          
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_114338999_    702 AATCAAAACAGTATGGAACTGGCATGAAGACAAACATATAGACCAAATAA 751
                               i     i   v        i i  i i         i   vvi 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_114338999_    752 TTAGAACAGAGAGTTTAGTAATAAACCCTTGCATATATGGTCAAATGATT 801
                         v     iv      ii  v         v i   v         v     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_114338999_    802 TTTGACAAGAGTATCAGGACCATTCAATGGGAGAAAGGACAGTCTTTTCA 851
                           i      i  ii  i              -     i i          
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTTTTCA 403

  chr1_114338999_    852 ACAAATGATGATGGGAAAACTGGATACCCACAAGCAAAAGAATAAAGTAG 901
                                i  v     v         ?     v          i    v 
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_114338999_    902 GACCCTTACCTTAGAGTATATGGAAAAACTAACTCAAAATGGATCAAAGG 951
                              i     i v vi    iv     i                 ?  i
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_114338999_    952 CCTAAATGTAAAGAGCTAAACCTATACAACTCTTAGAAGAAAACAGAGG- 1000
                                    -        v     v                  v   -
  L1M4_orf2#LINE/    504 CCTAAATGTAA-GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_114338999_   1001 --AAATCTTCATGACATTGAATTTGGTGATGATTTACTGGATA------C 1042
                         --        i    v   ii  v  ii   i   vi i    ------ 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_114338999_   1043 AAAGGCACAAGCAACAGAAGAAAAAA--GACAAATTGGACTTCATCAGAA 1090
                            i            i         --  i                i  
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_114338999_   1091 TTAAAAGCTTTTGTGCCTCAAACAACATGGTCAACAGTGTTAAAATGCAG 1140
                               i         i     vi   ivi    v iv  v    vi  i
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_114338999_   1141 CCCACAGAATAGGAGATAATGTTTTCAAATCACATATCTGATAAAAGATT 1190
                                   i     v   i   v       i           ii  i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_114338999_   1191 AATGTCCAGAATATTTAGAGAAACTCCTACAACTCAACAATAACAACAGA 1240
                         vi i          v  i    -   i          i     v  v v 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATAATAAAAAGACA 801

  chr1_114338999_   1241 AACAACCCAGTTCGAAA-TGGGCAAAGGGCTTAAGTCAACATTTTTTCCA 1289
                           i      i  ?i   -          ii  i i vi      i -   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT-CCA 850

  chr1_114338999_   1290 AAGAAGACACACAAGTGGCCACTAAGCACATGAAAAGATGGTCAACATCA 1339
                                i i    i      v                  v         
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_114338999_   1340 CTAACCAT 1347
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.90 (99 / 52)
Gap_init rate = 0.01 (9 / 854), avg. gap size = 2.11 (19 / 9)  


3230 26.29 0.55 0.66  chr1_114437542_114443319.rev     4379  5287 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_114437542_   4379 TGGAAGAACATTCCATGCTCATGGATAGGAAGACTCAATATCATGAAAAT 4428
                              ii i  i     i        v        i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_114437542_   4429 GGCCAGACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4478
                            v v   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_114437542_   4479 TACCAACGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 4526
                          v   i vi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_114437542_   4527 TATGGAACCAAAAAAGAGCCCCCATTGCCAAGTCAATCCTAAGCCAAAAG 4576
                                viiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_114437542_   4577 AACAAAGCCAGAGGCATCACACTACCTGACTTCAAACTGTACTACAAGGC 4626
                                iii    vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_114437542_   4627 TACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4676
                               v i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_114437542_   4677 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAGCT 4724
                                i    i--    i  --        vv   i    i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_114437542_   4725 ATCTGACCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4774
                          vi   ii  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_114437542_   4775 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAAAAAGCT 4824
                           v  i                 v      v  ?   i   i    iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_114437542_   4825 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4874
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_114437542_   4875 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACGCTAGAAGAAAAC 4924
                          i ?    i       v   v       i      vivi           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_114437542_   4925 CTAGGCA-ATACCGTTCAGGACATAGGCATGGGCACGGACTTCATGTCTA 4973
                         v    ?i- v i -   iv   v v  vv i    vv ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_114437542_   4974 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTA 5023
                         vi            vvi          vv     v  i    v i ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_114437542_   5024 ATTAAACTAAAGAGGTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5073
                           i   v v  i iv  i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_114437542_   5074 CAGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTACTCATCTGACA 5123
                         v  i     i              v  v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_114437542_   5124 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5173
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_114437542_   5174 AAAATCAAACAACCCCATCAACAAGTGGGCAAAGGATATGAGCAGACACT 5223
                           i -    i     v  i? v  i            v   ii     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_114437542_   5224 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5273
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_114437542_   5274 TCATCACTGGCCAT 5287
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (135 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3178 26.59 1.11 0.33  chr1_114497907_114502367     3070  3968 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_114497907_   3070 GAAGAACTTTCCATGCTCATGGATAAAAAGAATCAATATCATGAAAATGG 3119
                            ii iv i     i        vii    v i     ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_114497907_   3120 CCATACTGTCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGCTA 3169
                          v     vi     v i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_114497907_   3170 CCA-CTGACTTTCTTCACAGAATTAGATAAAACT-ACTTTAAATTTCATA 3217
                            -   v    i  -i     v v  i  i-  - iii    v      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr1_114497907_   3218 TGGAACCAAAAACGAGCCTGCATTGCCAAGACAATCCTAAGCAAGAAGAA 3267
                              viiv  iv  v  v v  v     i      i i iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_114497907_   3268 CAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTGTACTATAAGGCTA 3317
                              i      vv   vi  v  ii i      viv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_114497907_   3318 CAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGATATATAGACCAA 3367
                               i   i    ii           iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_114497907_   3368 TGGAACAGGACAGAGGCCTCGGAAATAATGCCGCACATCTACAACCATCT 3417
                              i  i iv   ivii i       vv  ii    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_114497907_   3418 GATCTTTGATAAACCTGACAAAAAGAAGCAATGGGGAAATGATTCCCTAT 3467
                            i  i  i  ivv  v   i vv vv           vi  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_114497907_   3468 TTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAA 3517
                          i  i        i     v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_114497907_   3518 TTGGACCCCTTCCTTACAACTTCTACAAAAATTGACTCAAGATGGATTAA 3567
                                   v   i   v v v          i      i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_114497907_   3568 AGACTTAAAGGTAAAACCTAAAACCATAGAAACCATAGAAGAAAACCTAA 3617
                             i    v    i v       i   i  vi v           v  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_114497907_   3618 GCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAAC 3666
                          ?i- v i -   iv   v v  vv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_114497907_   3667 ACCAAAAGCAATGGCAACAAAGGCCAAAATTGACAAATGGGATCTAATTA 3716
                                   vvi        i vv     v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_114497907_   3717 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACACG 3766
                           v v  i i   i  ii vv    i  v    i  vv i      v vi
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_114497907_   3767 CAACCTACAGAATGGAAGAAAATTTGTGCAATCTATCTATCTGACAAAGG 3816
                              i         i       v v     vii  v       i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_114497907_   3817 GCTAATATCCAGAATCTATAAGAAACT--TA-AATTTA-CAAGAAAAA-- 3860
                         i  vi          v     ii    --  -  i i -i  v     --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_114497907_   3861 -AAACAACCCCATCGAAAAGTGGGCAAAGGATATGAACAGACACTTCTCA 3909
                         -   i     v  i?    i            v    i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_114497907_   3910 AAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTCATCATC 3959
                                 i  vi vi       i  i  i       i v     v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_114497907_   3960 ATTGGTCAT 3968
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.30 (13 / 10)  


3151 27.34 0.66 0.55  chr1_114558156_114564532     4978  5884 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_114558156_   4978 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5027
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_114558156_   5028 CGCCATACTGCCCAAGGTAATTTGTATATTCAATGCCATCCCCATCAAGC 5077
                         v  v     v     iv i  i ii v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_114558156_   5078 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTCA 5125
                          v   iivi i  i  ii     -   -- v  i  - iii i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_114558156_   5126 TACGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5175
                           i    viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_114558156_   5176 AACAAAGCCGGAGACGTCACGCTACCTGACTTCAAACTATACTACAAGGC 5225
                                ii    ivv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_114558156_   5226 TACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGACC 5275
                                 i   i     i         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_114558156_   5276 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACTGCATATCTACAACT 5323
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_114558156_   5324 AACTGATATTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5373
                           i    v  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_114558156_   5374 CTGTTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAAAAAGCT 5423
                           v  i  i   i          v      v  ?   i   i    iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_114558156_   5424 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATCCAAGATGGA 5473
                            ii    i    v   i     v              ii   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_114558156_   5474 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5523
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_114558156_   5524 CTAGGCA-ATACCATTCAGGGCATAGGCATGGGCAAGGACTTCATGTCTA 5572
                         v    ?i- v i -   iv i v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_114558156_   5573 AAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTA 5622
                         vi            vvii         vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_114558156_   5623 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5672
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_114558156_   5673 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5722
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_114558156_   5723 CAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTATGAGAAA 5772
                         vi  i  vi          v  i  v      vv    v iv  i v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_114558156_   5773 AAAACAAACAACCCCATCAAAAAGTGGCCAAAGGGTATGAACAGACCCTT 5822
                           i     i     v  i?    i   v      i v    i    vi  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_114558156_   5823 CTCAAAAGAAGACATTTATGCAGCCAA-AAACACATGAAAAAATGCTCAT 5871
                            v        i  vi viii     -  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_114558156_   5872 CATCACTGGCCAT 5884
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


 558 30.00 11.92 1.15  chr1_114845522_114847597.rev      495   754 (1322)    L1M4_orf2#LINE/L1      133   420 (488)  

  chr1_114845522_    495 CCAACCATAAAATTTAATTGTATGTACAAAGGGCCAAGAATAGCCAAGGC 544
                          ii i v       i vv  v vi i   i  i  v           ii 
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr1_114845522_    545 ACTC-----AAAAAAGAACAAGACTGGAAGGCTTGCACTACTAGACATCA 589
                          v  -----   i        iii    i i  ii    v ivi iv   
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_114845522_    590 AAAATTATTATAAAG--ATAGTAATTAAGATAGTTTGGTTTTGGTGCA-G 636
                            v   i  i    -- i      i    i   v    vi   iii - 
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_114845522_    637 AA-------ATAGAGCAATAGAA-AGAATACAGAGTGCA----------T 668
                         i -------     v    i   -     vv     v  ----------i
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_114845522_    669 ATACAT--AAGGAAACTTGATTTGTGTCA---GAGCCAGCGTTGTGTATC 713
                               -- v  vv v       vi v  --- v    iviiii ---  
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT---TC 379

  chr1_114845522_    714 AGTGGAAAAAGGATGGACCATTTAATAAATGATACTAGGGC 754
                          i   ii    i  i v iv  i  i     i i  i  i 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

Transitions / transversions = 1.89 (51 / 27)
Gap_init rate = 0.03 (9 / 288), avg. gap size = 3.78 (34 / 9)  

 999 25.44 4.08 5.83  chr1_114845522_114847597.rev     1071  1585 (491)    L1M4_orf2#LINE/L1      403   908 (0)  

  chr1_114845522_   1071 AATAAATGATACTAGGACAATTGG-TCTCTATATG-AAAAAAATGAATAT 1118
                           i     i i  i      i   - v? i i   -    i      vv 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_114845522_   1119 GGATCTACACCTCACAC--TATACAGAAAATTAATTCCAG-TGAATTTAA 1165
                            i ivi         --      -        i  v i-  i  i- ?
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACA-AAAATTAACTCAAAATGGATC-AW 500

  chr1_114845522_   1166 AGACTTAAATGTTAAAAGC-AAAGCTTTTGAAAATATTTTTAAAAGAA-- 1212
                             i       -  i   -   i  v --    i-- i   i     --
  L1M4_orf2#LINE/    501 AGACCTAAATGT-AAGAGCTAAAACTAT--AAAAC--TCTTAGAAGAAAA 545

  chr1_114845522_   1213 --TAGAAGAAAATATTTTATGTC----AATAAAACAGTGGTGGGGTTCTT 1256
                         --   i? v    -i  ii  v ----ii v ii  i    ----     
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGT----TTCTT 590

  chr1_114845522_   1257 AAAAATACGGCACAAAGAGCAGAGACCATAAAGGAAAAGACAGGTTAATT 1306
                          i --  i i   v  i    v ii v i   i     i i  i v    
  L1M4_orf2#LINE/    591 AGA--TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_114845522_   1307 TGACTGTGTTAAATCTTTACATTTTCTTTTCGTCAAGGGACACCATGGA- 1355
                         v    vii i   -v  v v vi  i v v v    i      i  vi -
  L1M4_orf2#LINE/    639 GGACTTCATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_114845522_   1356 AAAGAGATTTTAAAAACTAGTTACAGACTAGGTGAAGATATCTTGAATAT 1405
                             v  ----   i  v vii     v i  v   i    -   v v  
  L1M4_orf2#LINE/    688 AAAGTGA----AAAGACAACCCACAGAATGGGAGAAAATAT-TTGCAAAT 732

  chr1_114845522_   1406 -ATATAACTATCAAATGAATAGTGTCTAGAATTTATTTTTTTAAAAAACA 1454
                         -     v  ivi  iv  v v  i  i     v   ------   i   v
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATAT------AAAGAACT 776

  chr1_114845522_   1455 CCTGCAAATCAGTAAGAAAAAGATAAACAATCCAATAGAAAAATGAGGAA 1504
                          i i   v   i   v       i   i  i     v?       i v  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_114845522_   1505 AAGATAGGAACAAACATT----CAAAGAAGA-AGAAACATGATAAGCCCA 1549
                          i   vv   i i     ----         - v v v   ----   v 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG----GCCAA 872

  chr1_114845522_   1550 TAAATAATTGAAGAGACATGCAACCTCACTACATCA 1585
                            ii vv    i   iiiv    v   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (76 / 51)
Gap_init rate = 0.05 (24 / 506), avg. gap size = 2.12 (51 / 24)  


2009 22.65 6.78 5.08  chr1_114891584_114894257      889  1537 (1137)    L1M4_orf2#LINE/L1       22   681 (227)  

  chr1_114891584_    889 TGGCTAGGAATATTCAACTTTGTTACTATAAAAAATTA-TCTCAAAATTG 937
                            v v    v i i  iv      vv  iiv  --  -  i v      
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAA--TACTCCCCAAATTG 69

  chr1_114891584_    938 ATCTACAGATTCAACACAATCTCCAGATTGTTGAATCTGTAGATTCAACA 987
                                        i     i i -------------------    --
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTA-------------------TCAA-- 98

  chr1_114891584_    988 AAATCACAGCAGGTTTTGCTGTAGAAATTGACAAGTTGATTTTCAAGTTT 1037
                         -    v    v vi   vi  i             i    ii v  i  i
  L1M4_orf2#LINE/     99 -AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_114891584_   1038 ATAAGGAAAGGCAAAGAATCTAGATTAGCCTAAATAATTTTCAAAACGAA 1087
                            v     v    i i i i   v     v   i   i  v    v   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_114891584_   1088 GAATAAAGCTGGAGGGCATAGACTACCTGATTTTAAGACTTAT---AAAA 1134
                            i    i      i vi v   v  ii    i  i     i---   i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_114891584_   1135 CTA-AGTAATCACAACAATGTA-TATTAGTTGACAGGACAGACAAAAGGA 1182
                            -        vi   i   i-  i i ivv -    i     v vi  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATA-AGGATAGACATATAGA 296

  chr1_114891584_   1183 TCAGCAGAAGAGCAC--AGAGTCCAGAAATGAACCCACATATATATAGTC 1230
                            iii   v  v i--             i      i i  v   i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_114891584_   1231 AATTGATTTCC-ACAAAG---C-------------TGGGGAAAGAATAAT 1263
                                  i -    i --- -------------             i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_114891584_   1264 CTTTTCAATAAATGGCATCAGAACAAATAGGTATCTATCTGTAAAAAAAA 1313
                                 i      iiiii i    v i i  ? i iv  i    i  -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA- 445

  chr1_114891584_   1314 ATGAACCTCAACCTTTACC-CATAACATTTACAAAATTTAAGTTGAAATA 1362
                         -    vi vi   ii    -  i v   v       v    v ii    i
  L1M4_orf2#LINE/    446 -TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_114891584_   1363 GATCATAAACCTAACTACTAAGAGCTAAAACCACAAACTTTCTGGAAGAA 1412
                              ? i      v i-             i i   vi ii i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATG-TAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_114891584_   1413 AA---------AAATCTTCACGACCTTGAGGAAGAAAAAGATGTCTTAG- 1452
                           ---------        ii       i vv  iv  v i v      -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_114891584_   1453 ---GACAC--AAAACACATTAACCATAAAGAAAAAGAATGGATACATTGG 1497
                         ---     --   i    -- i v i   ii    -   i    v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACA--AGCAACAAAAGAAAA-AATAGATAAATTGG 640

  chr1_114891584_   1498 ACTTCATCAAAATTAAAACCTTCTGCTCACTT---AAGACATT 1537
                                           v   i  i--i   --- i    i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGT--GCTTCAAAGGACACT 681

Transitions / transversions = 2.02 (97 / 48)
Gap_init rate = 0.03 (22 / 660), avg. gap size = 3.50 (77 / 22)  

 549 19.75 6.69 9.55  chr1_114891584_114894257     1869  2182 (492)    L1M4_orf2#LINE/L1      604   908 (0)  

  chr1_114891584_   1869 AAAAAAAAAGAAAGAAAAGAAAGAATATATAGACAGAAAATCAGTAAATA 1918
                            iv v   v  v        i    v   i iv i vv   vi   - 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA-A 652

  chr1_114891584_   1919 TATAAAGACTTGAATATCACTATCAATCAACTTGACTTAATTGGCAAGAA 1968
                          -    i    v-- i -i  -    vvi  ---   --  ---      
  L1M4_orf2#LINE/    653 T-TAAAAACTTT--TGT-GCT-TCAAAGGAC---ACT--AT---CAAGAA 689

  chr1_114891584_   1969 ACAAAGAAATAAATGGCAAGCCACAGACTGGGAAAAAATATCTGCCATAC 2018
                          vvi i  ------ i   v       v     i       i   v vv 
  L1M4_orf2#LINE/    690 AGTGAAAA------GACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_114891584_   2019 ATATATCTGATGAGG-ACTTAAATCCAGAATA----AAAAATTATTACAC 2063
                                    i   -    iv          ----  i  i v     v
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_114891584_   2064 CT-------AAAAAGTCAAACAACACAACTAAAATATGAGTAA--GATTT 2104
                           -------      v    i   v   i ?   v   i i  --     
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_114891584_   2105 GAACA-------CTTTACAAAAGATTTATGAGTAGCCAATAAGCACAATA 2147
                            i -------  ii v i     v  ii i i             ---
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA--- 880

  chr1_114891584_   2148 AAGCACATGAAAAGATGCACACCATCCTGAGTCAC 2182
                         -------           v  v    v????????
  L1M4_orf2#LINE/    881 -------TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.03 (31 / 30)
Gap_init rate = 0.05 (15 / 305), avg. gap size = 3.40 (51 / 15)  


2783 26.82 1.76 0.94  chr1_115038930_115047095.rev     6464  7313 (853)    L1M4_orf2#LINE/L1        4   860 (48)  

  chr1_115038930_   6464 AAAAAAATTCCATGCTCATGGATAGGAAGAATTGGTATCATGAAAATGGC 6513
                            i v  i     i        v      v  ii   ii v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_115038930_   6514 CATACTATCCAAAGTAATTTATAGATTCACTGCTATTCCCATCAAGCTAC 6563
                         v     vi     v i  i  i       vi  v  i  i     iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_115038930_   6564 CATTGACTTTCTTCACAGAACTAGAAAAAACT-ACTTTAGATTTCATATG 6612
                           vivi i  i  ii     v v  v  i-  - iii  i v        
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATG 152

  chr1_115038930_   6613 GAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAA-AAGAACA 6661
                            viiv  ii  v  viv        i      i i iv  -       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_115038930_   6662 AAGCTGGAGGCATCACACTACCTGATTTCAAACTATACTACAAGGCTACA 6711
                            i      vv       v  ii        viv        i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_115038930_   6712 GTAACCAAAACAGCATGGTACTGATAGCAACACAGATATATAGACCAATG 6761
                             i   i    ii        ii vv iv i   i       i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_115038930_   6762 GAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCTGA 6811
                            i    iv   ivii         vv   i    i  iiii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_115038930_   6812 TCTTCGGCAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTACTT 6861
                          i    i   ivv  v   i v  vv            i  vvi  vi i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_115038930_   6862 AATAAATGGTGATGGGAAAACTGGCTAGCCATATGCAGAAAACAGAAACT 6911
                           i        v     v      v  ?   i     i  i vv   ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_115038930_   6912 GGGCCCCTTCCTTATGCCTTAAACAAAAATTAACTCAAGGTGGATTAAAG 6961
                           i     v   i ii  v  v                ii     i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_115038930_   6962 ACTTAAACATAAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTA--A 7009
                           i    ii   i v       i      vi i           v  --?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_115038930_   7010 GTAATATCATTCAGGACATAGGCATGGGCAAAGACTTC--AAGTCTAAAA 7057
                             -   -   iv   v v  vv i     v ii   -- ii v i --
  L1M4_orf2#LINE/    553 GTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-- 598

  chr1_115038930_   7058 CACCAAAAGCAATTTCAGCCGCA---GCCAAAATTGACAAATGGGATCTA 7104
                                    ---iv   vi  --- vv     v  i    v   ii v
  L1M4_orf2#LINE/    599 CACCAAAAGCA---CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_115038930_   7105 ATTAAA-CTAAGAGCTTCTGCTCAGCAAAAGAAACTATCGTCAGTGTGAA 7153
                           i   -i   i i   i  iv vv    i  v      ivv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_115038930_   7154 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCGTCTGACA 7203
                         v  i     i                 v       vii  vii     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_115038930_   7204 AAGGGCTAAACTCCAGAATCTAAAAGGAACTTAAACAAATTTACAAGAAA 7253
                          i  i  vivv        v  v  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_115038930_   7254 AA---AAA-AACCCAATCAAAAAGTGG-CAAAGGATATGAACAGACACTT 7298
                           ---   -        i?    i   -        v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_115038930_   7299 CTCAAAAGAAGACAT 7313
                            v        i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATAT 860

Transitions / transversions = 1.41 (131 / 93)
Gap_init rate = 0.02 (14 / 857), avg. gap size = 1.64 (23 / 14)  


2643 24.29 3.08 3.55  chr1_115079174_115081001      492  1335 (492)    L1M4_orf2#LINE/L1       69   908 (0)  

  chr1_115079174_    492 GGTTCACAGATTTAATACAATTCCTATAAAAATCCCAG-TGAATTTTTT- 539
                          i ii       i  ii    i     v          -  vv      -
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG 118

  chr1_115079174_    540 TAGCAATAGACAAGCTTATATTGAAAGTTACATGGAAAAAGCACAAGTCC 589
                         i  v   v        v  vi i   v i i       v-   vii v  
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT-GCAAGGGACC 167

  chr1_115079174_    590 TAGAAAAATTAAAATAATCATGACAAAGAAGAATAAAATGGGAGAAATCC 639
                         i    v iii    i    v   v         i   i v    i v  v
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr1_115079174_    640 CTCTACTTAATACTATGGCTTACTGTAGAGCTATAGTAATCAAAACAGCA 689
                          v  v ii   vii vii      ii i     i         i    --
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG-- 265

  chr1_115079174_    690 AAACTGTATAGTGCTGGTGGAGAGACAGACACATAGAACAATGGAAGAGA 739
                         ------ i i  i    iiv ii  i     i     v        v   
  L1M4_orf2#LINE/    266 ------TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_115079174_    740 ATAGAGAATCCAAAAATTGGCCCACATGAATATTTCCAACTGAATTTTGA 789
                           v    i    i    vii    i iivv   vvi   i   v   i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_115079174_    790 CAAGGGTGCAAAAGCAATTTAATGGAGGAAGGATCACCTTTTTGAACAA- 838
                                  v  ii v   i     i i   i  vii     i-     -
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC-AACAAA 408

  chr1_115079174_    839 TGATGCTGGAGCAATTGGTTGGATACCAATAGGCGAAAAAAAATAAGAAA 888
                           i      ii   i   ----   ? v i v  --    i   ------
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGG----ATAKCCACATGC--AAAAGAAT------ 446

  chr1_115079174_    889 AGAAAAAGAACCTTAAGACTCACTCTCACTCTTTATAAAAATATTAACTA 938
                         -   ivv i   ------ ii  -     v iv    v   v       v
  L1M4_orf2#LINE/    447 -GAAGTTGGACC------CCTAC-CTCACACCATATACAAAAATTAACTC 488

  chr1_115079174_    939 AAAATGAATCATAGACTTAAATGTAAAAGTTAATA-TATAAAGCTTTTAG 987
                               i    ?    i         i  i   v -      i  i    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_115079174_    988 AAAAAAA-ATCAGAGAAAATCTTCAGGAT-TTGGACTAGGGAAAGAGTTC 1035
                           i    -  vi ? v        iv  i-    ii    v  v iv   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_115079174_   1036 TTAAATTAAACATCAAAAGTAGAATCCATAAAAGAATAAATTGATACATT 1085
                            i  vvi   i      i v  v v i       v    v    v   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_115079174_   1086 AGACTGCATAAAAATGAAAAACTTTCACTTTGCAAAAGACCCTCTGAAGA 1135
                         i    v   v     v         iiivi v    i   v  v v    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_115079174_   1136 AGATG----GATAAGCTACAGACTGGGA-AAAATATTTGCAAATCATATA 1180
                          ii  ----  i  v i     v     -                     
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_115079174_   1181 TGCAACAAAAGACTAGGAACTAGAATATATAAAAAG-----GCAAC---- 1221
                          vii i  ii    v v v i            i i-----i    ----
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_115079174_   1222 -AGTAAAAAGATAA-----CCAATTGGAAAATGAGAAAAAGACATGAATA 1265
                         - i        i  -----      ?i      i v   i  iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_115079174_   1266 GACATTTCCCCACAGAGGATATATAAATGGCAAATAAACACATTAAAAAA 1315
                                 i   v   i      i       v     i     v    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_115079174_   1316 TGTTTAGCATTATTAGCCAT 1335
                           i i i   i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (124 / 77)
Gap_init rate = 0.02 (19 / 840), avg. gap size = 2.95 (56 / 19)  


 724 21.65 0.69 11.34  chr1_115120597_115125562.rev      233   523 (4443)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr1_115120597_    233 AAAATTAAAAACTTCTACTCTACAAAAGAGAATGTCAAGAGAATGAGAAT 282
                                       i iiv  v    i  v v i      i i   i  v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_115120597_    283 ACAAGCCACAGACTGGGAGAAAATGTCTGCAAAAGAAACATCTGATGAAG 332
                             v       v           i i      vv v i       i i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_115120597_    333 GACTGTTATCTATAATATACAAAGACTCAAATATTATTAAGTCTTTTCTC 382
                             vv    i v      i     -------------- -------   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGA--------------A-------CTC 777

  chr1_115120597_    383 TTATTGTTGATTAAAATTCAACATTAAGAAAACAAGCAATTTGATTAAAA 432
                            i----------  i    i v   i  i    ii  iiii   ?   
  L1M4_orf2#LINE/    778 TTAC----------AACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_115120597_    433 AATGGGCCAAAGACCTTAACAGACACCTTACAAAAGGAGACATATGGATG 482
                                v  i  ii v  i     ii iv v    i   i   iii   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_115120597_    483 GCAAATAATCATATAAAAAGAGTAGCT--ATATTAATTTCAGA 523
                           v     v  i  i      - -   -- i  i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGA-T-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (42 / 20)
Gap_init rate = 0.02 (6 / 260), avg. gap size = 5.83 (35 / 6)  

3062 20.14 2.56 9.71  chr1_115120597_115125562.rev     3499  4476 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115120597_   3499 TAGAGAAAGATTCCATGATCATAGATAGGAAGATTCAATATTGTCAAGAT 3548
                          i  i i v  i     v    i   v      i i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115120597_   3549 GTCAATCCTTCCCAACTTGATCTACAGATTCAATGCAATCCCAATAAAAA 3598
                          v    v  i     v                 i        v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115120597_   3599 TCTCAGCAAGTTATATTGTGGATATCTACAAACTGATTCTAAAGTTTATA 3648
                           i    vivi v v   ii  v  iv    i     i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_115120597_   3649 TGGTGAGGCAAAAGACTCAGAAGAGCGAACACGATATTAAAGGAGAAGAA 3698
                            vi v    ii   i     v   v  v  i  v  i  ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_115120597_   3699 CAAAGTTGGAGAACTGATACTATTCAAATTCAAGACTTACTATAAAGCTA 3748
                                    i   v i   vii   v     i        i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_115120597_   3749 CAGTAATCAACATAGTGAGGGATTTGTGGGGGAAAAGGACAAAGAAATCA 3798
                                   v i    v  v i v iivii i v  -   v v i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG-ACATATAGATCA 299

  chr1_115120597_   3799 AGGGAACAAAATAGAGAGTCCAGAAACAGACCCA-ATATATATAGTCAAC 3847
                          v    i i   v             i i     - i  v   i     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_115120597_   3848 TGATCTTTGACAAAGGAGTAACAAATAGACCCAAACAAATATAGTCAACT 3897
                             i  i     i  v i--   ---    -------------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGC--CAA---GACC------------------- 375

  chr1_115120597_   3898 GATATTTGACAAAGGAGTAACAGCTATAAAATAGAGAAAAGATGGTCTTT 3947
                         ---   i----------------------   i i    ii  i      
  L1M4_orf2#LINE/    376 ---ATTC----------------------AATGGGGAAAGAATAGTCTTT 400

  chr1_115120597_   3948 TCAACAAATGATGCTGAAACAAGTGGACATCTGCATGCAAAAAAAAAAAA 3997
                                   i     ii    v    i ? ii         i  v----
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT---- 446

  chr1_115120597_   3998 AGAATCTGGACACAGATCTTACACCCTTAACAAAAATTAACTCAAAATTT 4047
                         -   vi     v vv i  i     v vv                   vv
  L1M4_orf2#LINE/    447 -GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_115120597_   4048 ATCATAGACCTAAATGTAAAA--TACAAACCATAAAACTCC---AAGATA 4092
                             ?              i --  -    i         i---    v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAA 544

  chr1_115120597_   4093 A-ATAGGAGAAAACCTGGATGATCTTGGGTATCACGATGACTTTTTTTTT 4141
                          -     ? v   i  vvi   i       vvvi i   i------   i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG------TTTC 588

  chr1_115120597_   4142 TTAGATA--------------CAATCCATGAAAGAAAGAAATA-ATGAGC 4176
                                --------------   v v ii       -     -  i ii
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAAT 637

  chr1_115120597_   4177 TGGACTTCATTAAAATTAAAAACTTCTGCTCTCCAAAAGATAATGTCAAG 4226
                                   i              i  iv  i    i  i v i     
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_115120597_   4227 AGAATGAGAATACAAGCCGCAGACTGGGAGAAAATGTCTGCAAAAGAAAC 4276
                          i i   i  v    v  i    v           i i      vv v i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_115120597_   4277 ATCTGATAAAGGACTGTTTTCTATAATATACAAAGA-CTCAAAATTGTTA 4325
                                  i     vv v  i v      i     -   ----------
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC---------- 777

  chr1_115120597_   4326 AGTCTTTTTTCTTATTGTTGATTAAAACTCAACAATAAGAAAACATGCAA 4375
                         ---------------------   v       i     i  i   vii  
  L1M4_orf2#LINE/    778 ---------------------TTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_115120597_   4376 CCTGATTAAAAAATGGGACAAAGACCTT-AACAGACACCTTACCAAAGGA 4424
                           ii   ?         -     ivi  -  i     ii iv      i 
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGG-CAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_115120597_   4425 GACATACAGATGGCAAATAATCACATGAAAAGATTCCCATCAT-ATGTCA 4473
                           i     i     v     v             v i  v   - ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_115120597_   4474 TCA 4476
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.57 (118 / 75)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 6.00 (120 / 20)  


3441 25.52 0.66 1.31  chr1_115171897_115176164.rev     2865  3777 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_115171897_   2865 GGAAAGACACTACGTGTTCACGGACTGGAACAATCAATACTGTTAAAATG 2914
                                i iiv i      i   i     v v i    i      i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_115171897_   2915 TCTGTACTACCCAAAGCAGTCTACAGATTCAATGCAATCTCTATCAAAAT 2964
                         v vi    v      viii             i      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_115171897_   2965 ACCAATGACATTATTCACAGAAATAGAAGAATCAATCCTAAAATTTATAT 3014
                         v   iivi v  v  ii       v  vi iiii           i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_115171897_   3015 AGAACCACAAAAGACCCAGAATAGCCCAAGATATTCTGGGCAAA-AAGAA 3063
                         i   vii   ii              -  i i v   v iv   -     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCC-AAAACAATCTTGAAAAAGAAGAA 200

  chr1_115171897_   3064 CAAAACTAGAGGAATTACATTACCTGATTTCAAAATGTACTACCTAGCTA 3113
                             ii i     v i   i v  ii         iv      vv     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_115171897_   3114 TAGTAACCAAAACAGCATGGCATTAGCATAAAAACAGAAATATAGACCAA 3163
                         i     i   i    ii   i i i      ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_115171897_   3164 TGAAACAGAACAGAGAACTCACAAACAAATCCATTCATCTGCAGTGAACT 3213
                           i  i    iv    iii  v   i   i    v   i iii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_115171897_   3214 CATTTTTGACAAAGGTGCCAAGATCACACATTGGGGAAAGGATAGTCT-- 3261
                         v     i     i          i  iv  v         i       --
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_115171897_   3262 -CGATACACAGTGCTGGGAAAACTGGATATCCATATATCCATATGCAGAA 3310
                         - i i v ii         v         ?   i  --------   i  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACAT--------GCAAAA 442

  chr1_115171897_   3311 GAATGAAACTAGACCCCTATCTCTTGCCATATATAAAAATCAAATCAAAA 3360
                                ii i        i   vii       i      i  v      
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_115171897_   3361 TGGATCAAGGACTTAAATCCAAGATCTCAAGCTATGAAATTACTAAAAGA 3410
                                ?i   i     vi    v  v  i    i   i vi  i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_115171897_   3411 AACCGTCGAGGAAACTCTCCAGGACATTGGACTGGGCAAAGATTTCTTGA 3460
                           v i v i? v  v   i iv   v    ii i     v i      ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_115171897_   3461 GTAATATCCCACAATTACAGACAACCAAAGCAAAAATAGATAAGTCAGAT 3510
                         i  vv iv   v  vi   ii    v    v            i ii  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_115171897_   3511 CACATCAA-GTTAAAAAGCTTCTGCACAGAAAAAAAAAA-ATCAACAAAG 3558
                         iv      -i       -   i  ii vvv   ii v v-     v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_115171897_   3559 GGAGGACACAACCCACAGCATGGGAAAAAATATTTGTAAACTATCCATCT 3608
                         v  ii v           v      i          i   ii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_115171897_   3609 GACAAGGGATTAATACACACAATATATAAGGGGCTCAAAAAACTCTATGG 3658
                           i      i vi  iv  v         i ii   vv v     v  ii
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_115171897_   3659 GAATAAGTCTAATAATCCTATGGGAAAAAATGGGCGAAAGATCTAAATAG 3708
                         v  v   v v     i  v  --v?          i  i   i i     
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAAT--TWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_115171897_   3709 GCATTTTTCAAAAGAAGACATACCAATGGCAAACAGGTATATGAAAAGGT 3758
                         i     i  v        i    v      v  i i i i        i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_115171897_   3759 GATCAACATCATTGATCAT 3777
                          v         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (149 / 80)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 2.25 (18 / 8)  


1170 26.70 4.81 2.84  chr1_115186604_115192971        7   463 (5905)    L1M4_orf2#LINE/L1      376   841 (67)  

  chr1_115186604_      7 ATTCAATGGAGAGAAATGAAAGTCTTT-CAACAAATGAT-TTGGAATAAC 54
                                  i  i i -- v       -         i -i   i i   
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGA--ATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_115186604_     55 CAGATATTCATATGGGAAAGAAAAAAAACAAACCTTGACCCTTACATCAG 104
                         ii    ?i  i   vi      vi  i------i v     i   v   v
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAG------TTGGACCCCTACCTCAC 467

  chr1_115186604_    105 ATCATATACAAACATTAATTTTAAATGGGTTATAGGCATACAAT------ 148
                          i          v     i iv      i i ?  i v  -   ------
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA-AATGTAAGA 516

  chr1_115186604_    149 -CTTGAACTCTGAAGTCTTCAGAAGAAAACGTAGGAGGGTACTTTCATGG 197
                         -  vi    v i  iiii i          i    ? viv ii   i  i
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_115186604_    198 CCA-AGGTCAG-CAAAGATTTCTTAG----GGCA--AAGA----AAGCAA 235
                           v-i   i  -   v i        ---- i  --  i ----      
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_115186604_    236 TATTCTTAACATGTCAAATAAGTTAGACTACATCAAAACTTGAAAGATCT 285
                         i vvvvv  v -i - i    i  i    v        i vi   vv i 
  L1M4_orf2#LINE/    617 CAAAAGAAAAA-AT-AGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_115186604_    286 GTTTATCAAAAGGCATTATTAAGCAAATGAATAGACAAGGTACAAAGAAA 335
                           viv     i i  i   i   v  i    v      vvi   i ivii
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_115186604_    336 AAGAAAACACTGACTAAACATTTATTTGACAGATGACATGTATCCAGAAT 385
                         i      i i vi v  v   v   i   i iiv   v            
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_115186604_    386 ATATAAATAACTCTTGAAACTCAATAATAAAAAAATAAATATCTCAACTC 435
                                v       iv                i i     v i   i ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_115186604_    436 AAAA-TAGGCAAAAGACTGTAAAATAAAC 463
                             - i      i  i - i  -  i  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATT-TGAA-TAGAC 841

Transitions / transversions = 1.88 (77 / 41)
Gap_init rate = 0.03 (16 / 466), avg. gap size = 2.19 (35 / 16)  

3252 26.40 0.77 0.88  chr1_115186604_115192971     4967  5875 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115186604_   4967 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAAGATCATGAAAAT 5016
                              ii i  i     i        v      v i  v  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115186604_   5017 GGCCATACTGCCCAAGGTAATTTATAGGTTCAATGCCATCCCCATCAAGC 5066
                            v     v     iv i  i  i  i     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115186604_   5067 TACCAATCACTTTCTTCACAGAA-TTGGAAAAAACT---CCTTTAAAGTT 5112
                          v   iiii i  i  ii     -   -- v  i  ---   --   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCT--AAAATT 146

  chr1_115186604_   5113 CATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATTCTAAGCGAAA 5162
                                  viiv  ii  v  v v  v     i     ii i ivi i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_115186604_   5163 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 5212
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_115186604_   5213 GCTACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGA 5262
                                   i   i    ii       v i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_115186604_   5263 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAA 5310
                         i        i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_115186604_   5311 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 5360
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_115186604_   5361 CCCTATTTAATAAATGGTGCTTGGAAAACTGGCTAGCCATATGTAGAAAG 5410
                         vi  v  i  i          v   v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_115186604_   5411 CTGAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATG 5460
                         v    ii    i    v   i i   v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_115186604_   5461 GATTAAAGACTTAAATGTTAGACCTAAAATCATAAAAACCCTAGAAGAAA 5510
                            i ?    i       v   v      ii      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_115186604_   5511 ACCTAGGCG-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGAC 5559
                           v    ? - v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_115186604_   5560 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5609
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_115186604_   5610 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5659
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_115186604_   5660 AACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGA 5709
                           v  i     i                 v   i   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_115186604_   5710 CAAATGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 5759
                         i  iv i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_115186604_   5760 AAAAAATCAAACCACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACA 5809
                             i -    iv    v  i?    i    ii      v    i     
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_115186604_   5810 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAGATGCT 5859
                         i     v        i  vi viii     i ii                
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_115186604_   5860 CATCATCACTGGCCAT 5875
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2961 25.67 2.46 1.12  chr1_115218288_115225277.rev     5604  6499 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115218288_   5604 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATACCATGAAAAT 5653
                               i i  i     i        v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115218288_   5654 GGCCATGCTGCCCAAAGTAATTTACAGATTCAATGCTATCCCCATCAAGC 5703
                            v  i  v      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115218288_   5704 TACCATTGACTTTCTTCATAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5752
                          v   vivi i  i  iii    v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_115218288_   5753 ATGGAACAAAAAAGAGCCCATA-TATCCAAGACAATCCTAAGCCAAAAGA 5801
                               vviv  i ii    v -  v    i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_115218288_   5802 ACAAAGCTGGAGGCATCATGCTACGTGACTTCAAACTATACTACAAGGCT 5851
                               i      vv   ii  v vii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_115218288_   5852 -CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGG----------- 5889
                         -      i   i    ii         i iv ii i  i-----------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_115218288_   5890 ATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACCA 5937
                               i    i--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_115218288_   5938 TCTGATCTTTGACAAACATGACAAAAACAAGAAATGGGGAAAGGATTCCC 5987
                         vi    i  i     ivi  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_115218288_   5988 TATTTAATAAATGGTATTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 6037
                          v  i  i       ii     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_115218288_   6038 AAACTGGACCCCTTCCTTACATCTTATACAAAAATTAACTCAAGATGGAT 6087
                           ii         v   i   i v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_115218288_   6088 TAAAGACTTAAACTTAAGACCTAAACCCATTAAAAACCCTAGAAAAAAAA 6137
                         i ?    i    iv     v     v i  --     i  vii  i    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT--AAAACTCTTAGAAGAAAA 545

  chr1_115218288_   6138 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATAACT 6186
                          v    ?i- v i -   iv   v v  vv i     v ii   v  iv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_115218288_   6187 AAAACACCAAAA--ACAATTGCAACAAAAGCCAAAATAGACAAATGGGAT 6234
                          vi         --    --          vv        i    v   i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_115218288_   6235 CTAATTAAA-TGAAAGAGCTTCTGCACAGCCAAAGAAACTATCATCAGAG 6283
                         i v  i   - v   i -   i  ii vv v  i  v       vv i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_115218288_   6284 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 6333
                             v  i     i                 v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_115218288_   6334 GACAAAAGACTAGTATCCAGAATCTACAAGGAACTTAAACAAATTTACAA 6383
                           i  ii    v           v  i  i     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_115218288_   6384 GAAAATAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAAGAGAC 6433
                         v    vi     i     v  i?    i            v    v    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_115218288_   6434 ACTTCTCAAAAGAAGACATTTTTGCAGCCAACAA--ACATGAAAAAAAAG 6481
                          i     v        i  vivviii     i  --         i v- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-G 890

  chr1_115218288_   6482 CTCATCATCACTGATCAT 6499
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (133 / 93)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.00 (32 / 16)  


4127 18.38 3.24 0.35  chr1_115245394_115248194     1436  2300 (501)    L1M4_orf2#LINE/L1        1   890 (18)  

  chr1_115245394_   1436 TGGAAAGACATCCTATGTTTATTGATAGAAAGACTAAATATTGTTAAGAT 1485
                                 i    i     i  v   v i      v              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115245394_   1486 GTCAGTGGTACCCAAAT----CTCCAGATTCAATGCAATTTCTATAAAAA 1531
                          v  i iv v       ----  v         i     ii    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115245394_   1532 TTCCAACAATTTTTTTTGCATAAATGGAAAAA---ATACTCAAATTAATG 1578
                          i   i viii         v    v  v  i---  v  v     v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_115245394_   1579 TGGAATTGCAAAGGGCCCCAAAAGGCTAAAACAATCTTGAAAAATAAGGA 1628
                              v     i  i   vi  vi  i                 v   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_115245394_   1629 TAGAGTTGGAGGACTCACAGTTCCTAACTTTGAAACTTACTACAAAGCTA 1678
                         i i                v    i  i  ii                  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_115245394_   1679 --GTAATTAAAACAGCATAGTACTTGTATAAGGTCAGACAGGCAGACCAA 1726
                         --     i  i    ii i     v i      vi     vii   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_115245394_   1727 TGGAATAGAATAGAGAGCCTAGAGATAAACCCTCACATACATAGTCAGTT 1776
                                    v     i i   i        vi    vi  i    i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_115245394_   1777 GATTTTTGACAAGAGTGCCAAGACCATTCAATGGGGAAGGAACATTTTTT 1826
                               i      i                        i   i v i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_115245394_   1827 TCAACATATGGTGCTGGGAAAACTG----TCCACATGTCAAAAGAATTAA 1872
                               v            v     ----?       -         v  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAATGAA 449

  chr1_115245394_   1873 GTTGGATCCTT----TATATCATATA-AAAAAT-GACTCAAAATGGATGA 1916
                               i  i ----i i i      -      -i             v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_115245394_   1917 AAGACCTAAACTTAAGAGCTAAAACTATAAAACTAT-AGACGAAAACACT 1965
                         ?         iv                      v -   v       iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_115245394_   1966 GTCA-AAATCTTCATGACACTGGATTTGGCAGCAACTT-TTATGGATGAC 2013
                          v?i-        i    vi   i  v    iiiii  -   viv     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_115245394_   2014 ACCAAAAGCACAGGTAATGAAAGAAAAAA-AGATAAATTGGACTGCATCA 2062
                                     i i  ii          -              v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_115245394_   2063 AAATTAAGAACTGTTGTGAATTAAAGGAGACTATCAAGAAAGTGAAAAGA 2112
                                i    v     vv i      v                     
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_115245394_   2113 CAAGGTAAATAGTGAGAGGAAATATTTAAAAATCATATATATGACAAGGG 2162
                            vvi v v i  i   i        iv           v   i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_115245394_   2163 ATTGATATCTAGGATATATAAAGAACTCCCACAATT-AATAACCACAAAA 2211
                          i vi    i  i               ii    i -     iv v  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_115245394_   2212 --AGT--CCCAATTGAAAAGTGGGGAGAAAAGATTCGAATAGCCATTTCT 2257
                         -- i --       ?    i    v --  i    i      v       
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCA--AAGGATTTGAATAGACATTTCT 847

  chr1_115245394_   2258 CCAAAGATGAAACATAAATGGCCTATAAACACATGAAAAGATG 2300
                                v  v i i        v    i              
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

Transitions / transversions = 1.63 (96 / 59)
Gap_init rate = 0.02 (16 / 890), avg. gap size = 1.94 (31 / 16)  


 583 30.15 0.50 1.01  chr1_115268964_115275352.rev      189   387 (6002)  C L1M4_orf2#LINE/L1   (149)   759   562  

C chr1_115268964_    387 CATGATTTATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCA 338
                          i   ii - i  i- i     v ii   v ivv  vi            
  L1M4_orf2#LINE/    562 CGTGACCT-TGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

C chr1_115268964_    337 ATGGCAACAAAAGCCAAAATTGACAA-TGGGATCTAATTAAACTCAAGAG 289
                         vvi          vv     v  i  - v   ii v  i   v i  i i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

C chr1_115268964_    288 CCTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAG 239
                          i i  ii vv    i  v    i  vv i      v  i     i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

C chr1_115268964_    238 AATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAAGGCTAATGTCC 189
                                      v       vii ivi      i  ii i  vi i   
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

Transitions / transversions = 1.61 (37 / 23)
Gap_init rate = 0.02 (3 / 198), avg. gap size = 1.00 (3 / 3)  

3203 27.09 0.55 0.55  chr1_115268964_115275352.rev     4991  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115268964_   4991 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5040
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115268964_   5041 GGCCAGACTGCCCAAGGTAAATTATAGATTCAATGCCATCCCCATCAAGC 5090
                            v v   v     iv i vi  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115268964_   5091 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_115268964_   5139 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5188
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_115268964_   5189 AACAAAGCCAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5238
                                iii    vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_115268964_   5239 TACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5288
                             i   i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_115268964_   5289 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACTGCATATCTACAACT 5336
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_115268964_   5337 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5386
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_115268964_   5387 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5436
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_115268964_   5437 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 5486
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_115268964_   5487 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5536
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_115268964_   5537 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAACGACTTCATGTCTT 5585
                         v    ?i- v i -   iv   v v  vv i     i ii   v ivv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_115268964_   5586 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5635
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_115268964_   5636 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5685
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_115268964_   5686 CAGGCAACCTACAGAATGGGAGAACATTTTTGCAACCTACTCATCTGACA 5735
                         v  i     i              v  v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_115268964_   5736 AAGGGCTAATATCCAGAATCTACAAGGAACTCAAACAAATTTACAAGAAA 5785
                          i  i  vi          v  i  i      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_115268964_   5786 AAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTT 5835
                           i     i     v  i? v  i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_115268964_   5836 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5885
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_115268964_   5886 CCTCACTGGCCAT 5898
                          v   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 673 24.05 12.32 7.62  chr1_115280106_115282067.rev      481   821 (1141)    L1M4_orf2#LINE/L1      205   561 (347)  

  chr1_115280106_    481 GTTGAAAATCTTACTGAATCGCTGATTTCAAGA--TGGTA--AACCTATG 526
                             i iiv  i  -- v iv ii       i -- iv  --  v   ii
  L1M4_orf2#LINE/    205 GTTGGAGGACTCAC--ACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_115280106_    527 GTAATTAAGAAAGTG--GTGTTA----------AGACA----GATCATTG 560
                              i    v    --  ii i----------     ----     v  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_115280106_    561 GAACAAAAT--ATGGTCCAGTAATAAACCTGTACACATGTGGTCAAATTA 608
                            i i   -- vi      v        ii    iv i       v v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_115280106_    609 TTTTCAAGAAAGGTG--AAAACAAAATTGAGTAGAAAATAAATAGTATTT 656
                              i v  i    --  i  v --  v i i ii  vi      v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCA--TTCAATGGGGAAAGAATAGTCTTT 400

  chr1_115280106_    657 TCAACAAATGGTGCTGGAACAATTCGTTATCCATATATAAAAATAAATAC 706
                                          i    i v v  ?   i  ii    i-------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG------- 443

  chr1_115280106_    707 TTTTTAAAAATAAATAAATAACTTCAATACATATCTTGCATTATATACAA 756
                         ------------   i  v---  vi iv v  i  ii  ii        
  L1M4_orf2#LINE/    444 ------------AATGAAG---TTGGACCCCTACCTCACACCATATACAA 478

  chr1_115280106_    757 ATATTAAC-----ATG------------AAATATAAAAACTAAAATTCTA 789
                          v      -----   ------------    i   i i      i v  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_115280106_    790 ACATTTCTAGAAGAAAGCAT-GGAATAAAACTT 821
                          v i ii         i   -  ?i    v   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

Transitions / transversions = 1.96 (53 / 27)
Gap_init rate = 0.04 (14 / 357), avg. gap size = 4.86 (68 / 14)  

1024 20.36 6.08 2.43  chr1_115280106_115282067.rev     1143  1471 (491)    L1M4_orf2#LINE/L1      568   908 (0)  

  chr1_115280106_   1143 CTTGAATTAGGCAAAACTTTCTTAGATATAACACCAACAGCATGATCCAT 1192
                             ii        viv            i       v    ii v v -
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA- 616

  chr1_115280106_   1193 TTTCAAAA-----AAT-GATAAATTGGACTCCATCAGAATTAAGAACTTC 1236
                         ---     -----   -             i     i      i     i
  L1M4_orf2#LINE/    617 ---CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_115280106_   1237 TCT-CTTCGAAAGGCATTGTTAA--AAG---AACGACATACCACAAACTG 1280
                          v -    i  i i  i i i  --   ---  v    vv     i v  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_115280106_   1281 AAAGAAAAGAAACTTGCAAATTATATATAAGATAAAGAACTTGTATACAG 1330
                         ii      v --i        i      vv     i i        v   
  L1M4_orf2#LINE/    714 GGAGAAAATA--TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_115280106_   1331 AATATATGAAGAACCTGCTATA-CTCAATTATAAGAAAA-AAATTATCCA 1378
                                i      - vi  i -      v    i  i -    v i   
  L1M4_orf2#LINE/    762 AATATATAAAGAAC-TCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_115280106_   1379 ATTTTTTAAATAAGCAAATG-TTTGAATAGACATTTCACAAAAT----TA 1423
                            ?vv-    ii     v -                v v   v----  
  L1M4_orf2#LINE/    811 ATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_115280106_   1424 TGTAGATGGGAAGTAAACAGATGAAAA-ATTTTCATCATTAGTCTCAGA 1471
                          ii i    vv i   i  v       -  vi   v   i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (38 / 28)
Gap_init rate = 0.04 (14 / 341), avg. gap size = 2.00 (28 / 14)  


3275 23.92 1.08 3.23  chr1_115400120_115408254      775  1702 (6433)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115400120_    775 TGGAAAAACATCCCATGCTTATGGATCAGAAGAATTAATATTGTTAAAAT 824
                               i i        i i      ii     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115400120_    825 GACCATACTACCCAAAGCAATAAACAGATTCAATGCATTCCCTATCAAAA 874
                          i v     v      vii  vv          i   v            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115400120_    875 TACCA--TGCCATTTTTCACAGAATTAGTAAAAAG--AATCCTAAAATTC 920
                          v   --    -     ii     -- v i v   --i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chr1_115400120_    921 ATATGGAACAACAACAACAACAAAAAAAACAGCTCAAATAGCCACAGCAA 970
                                 -------- ii-   iii vv   ----        v i   
  L1M4_orf2#LINE/    148 ATATGGAA--------ATG-CAAGGGACCCAG----AATAGCCAAAACAA 184

  chr1_115400120_    971 TCTTTAAGCAAAAAGAACAAAGCTGGAGGCATCACATTTTCTGACTTCAA 1020
                             v  i-  i          i      vv     i  i ii i     
  L1M4_orf2#LINE/    185 TCTTGAAA-AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_115400120_   1021 ATTGTACTACAAGGCTATAGTAACCAAAACAGCATGGTGCTGGTATAAAA 1070
                          viv        i    i     i   i    ii    i    i    ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_115400120_   1071 ATAGACAAATCAATCAATAGAAAAGACTAGAATACCCAGAAATAAATTTG 1120
                                v  vi      i   v   v v  ivii           iiii
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_115400120_   1121 CATATTTACAGCCAACTGATCTTTGACTAAGTTGATATGAACATACACTG 1170
                         i i     ii i   i    i  i   v i v  vi v  v   v  v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_115400120_   1171 GAGAAAGGACACCCTTTTCAACTAATG-TGCTGGGA-AGGTGGACTTGCC 1218
                          i     i i vi         v    -        - iv    - v?  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA-TAKCC 432

  chr1_115400120_   1219 ATATACAAAAGAATGAAACTGGATCTCTATCTCTCGCCATGTACAAAAAT 1268
                          i  i            ii    i i   i   v i    i         
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_115400120_   1269 CAACTCAAGATGGATAAAAGACTTAAATGTGAAACCTGAAATCATAAAAG 1318
                         i       i      v ?    i       i i v  i   ii      v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_115400120_   1319 TAAAAGAAGAAAACCTGAGGAAAACTCTTCTGGACATTGGTCTAGGCAAA 1368
                          vvv          v ii ?iv  v     vv   v    vi       v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_115400120_   1369 GAATTCATGACTAAAACCTCAAAAACACAGGCAATAAAAACAAAAATAGA 1418
                          iv   v iiv  vi  vi     i    i    i    iv         
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_115400120_   1419 CAAATTAGACTTAATTAAACTAAAAAGCTTCTACACAGCAAAAGAAATAA 1468
                         i     i     v  i   v v    i   i iii vv    i  v iv 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_115400120_   1469 TCAACAGAGTC----GACAACCTGTGGAGCAGGATAAAATATTTGCAAAC 1514
                             v i   v----       iiii  iii   v              -
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA- 731

  chr1_115400120_   1515 TATGCATTCTATACATCTGACAGGAGACTAATATCCAGAATTGACAAGGA 1564
                         -------  -   i      i i i    vi          vv i  i  
  L1M4_orf2#LINE/    732 -------TC-ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_115400120_   1565 ACTCAAACAACTCAGTGACAACAGAACCCCCAATAATCCCGTTAAAAAGT 1614
                             vv        i i i  v ii  v---     i  vi  ?    i 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACA---AATAACCCAATTWAAAAAT 820

  chr1_115400120_   1615 GATCAAAGAACATCAGTGGACATTTTTCAAAAGAAGACATATAAATGGCC 1664
                          iv     i iv v i i       i  v        i   i        
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_115400120_   1665 AACAGACATATGAAAAAATGCTCAACATCATAAATCAT 1702
                           i ii  i       i             ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (140 / 78)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  

3287 26.76 0.44 0.44  chr1_115400120_115408254     6735  7642 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115400120_   6735 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 6784
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115400120_   6785 GGCCAGACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 6834
                            v v   v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115400120_   6835 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6882
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_115400120_   6883 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 6932
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_115400120_   6933 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6982
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_115400120_   6983 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 7032
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_115400120_   7033 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 7080
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_115400120_   7081 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 7130
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_115400120_   7131 CTATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGCT 7180
                           v  i  i          i   v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_115400120_   7181 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 7230
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_115400120_   7231 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 7280
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_115400120_   7281 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 7330
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_115400120_   7331 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 7380
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_115400120_   7381 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 7430
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_115400120_   7431 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 7480
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_115400120_   7481 AGGGCTAATATCCAGAATCTACAATTAACTCAAACAAATTTACAAGAAAA 7530
                         i  i  vi          v  i  vv     vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_115400120_   7531 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 7580
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_115400120_   7581 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 7630
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_115400120_   7631 ATCACTGGCCAT 7642
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2553 24.19 6.68 2.42  chr1_115417551_115419610.rev      702  1569 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_115417551_    702 AGAAGTATACCATGTTCATGGTTTAAAAGACTCAATATT-TT-----GTC 745
                          i ii   v            v  ii      i      -  ----- v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_115417551_    746 AGT-TTCCTTAGATTGACCTGTATATTTAACACAATCTCAATGAAAATCC 794
                          i -i   ii i     i  ii v   i   i     i v  v       
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_115417551_    795 TCAAAGACATTTTTTTTTTAGAAATTGACAAGCTGATTCTAAAATCTATA 844
                         i---  viiii      vi                  i       ii   
  L1M4_orf2#LINE/    104 C---AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_115417551_    845 TGGAAAC-------ATT---AATAATCAAAACAATCTTCGAAAA----AA 880
                               i------- ii---    ii            vi    ----  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_115417551_    881 CAAACTCTGAGAACTTACTCTACATGACTTCAAGACTTATTATAAACCCA 930
                             v iv   i   i  v  v vii i     i     i  i   v i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_115417551_    931 CTGTGATTAAGACAGTGTTGTA---GCATAAAGATAAACAGATAG-TCAA 976
                          v  i  i          v   ---      i    i   v    -    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_115417551_    977 CTAGATCAATAGAATAAGCAGAGTCCAAAAATAGACCCATGT-TATATGG 1025
                         - i  ---       vi--        i     i      ii- v     
  L1M4_orf2#LINE/    301 -TGGA---ATAGAATTG--AGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_115417551_   1026 TCAATTAATATTTTACCAATGTGCCAAAACAGATGAATGAGGAAAGGGAA 1075
                               i  v  iv  v iv       i  viv v    i      iiv 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_115417551_   1076 ATCTTTTTAACAAATGGTGCTAGAAAGATCGCCTA-CTATAGCTGAAAAA 1124
                         i      i             i i vi ii vv  - i i vvii   i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_115417551_   1125 AAGAA------------CCTCAACCCATACATAAAA-TGGATTATAGATG 1161
                          v   ------------     vv     i i    - vi i vv i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_115417551_   1162 GATTACATAACTAAATGCAAAAGCTAAAACTATAAAGCTTTTGGAAGACA 1211
                            i ? v v       i  i               i  i  i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_115417551_   1212 ACATAGGAGAAAAGCTTTGCAATCTTTGGTTAGATAA------CTAAAAA 1255
                                ? v   v   i ii i   v      ii  ------  v ---
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA--- 591

  chr1_115417551_   1256 AAGATAGGACTCAGAAAGTAGTAATTATAAAAGACAAAACTTGATAAATT 1305
                         --    v   v vi    i vv iiv i      v    - v        
  L1M4_orf2#LINE/    592 --GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATT 638

  chr1_115417551_   1306 A-ATTATAGCAAAATTTAAAAACTTCTGCTCATCAAAAGGCACTATGAAA 1354
                         i- i vi v       -        i  iv v     i i      v  i
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_115417551_   1355 AAAATGAAAAG-CAAG--ACAGACTGAAAGGAAATATTCACAACT----- 1396
                            i       -   v--     v  ii  i       ii   v -----
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_115417551_   1397 -TCTGACAAAGGACATGT--TAAGAATATATTTTTGATACACTTGCAACT 1443
                         -     i  i    v   --iv         vvv-  -  v   i     
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAA-GA-ACTCTTACAACT 785

  chr1_115417551_   1444 CAACAATAAAAATATAAACAATCCATTTTTCTTTAAATGGGCAAAAGATT 1493
                            i        v i   i  i   v  ?vv---           i    
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAA---AAATGGGCAAAGGATT 832

  chr1_115417551_   1494 TGAATATATACTTGACAAATGATGATCTGTAAATGATTAGTAAGTACATG 1543
                               v i i  vv v  v  v   v ii     iii i    i     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_115417551_   1544 AAAAGATACTCAAGATCATTAGCCAT 1569
                                i     v    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (127 / 80)
Gap_init rate = 0.03 (28 / 905), avg. gap size = 2.82 (79 / 28)  


2960 25.20 2.79 1.56  chr1_115454547_115457577     1642  2538 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115454547_   1642 TGGAAATACATCCCATGTTCATGTACTGGAAGAATTAGTGTCATAAAAAT 1691
                               v i              v i       v   i i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115454547_   1692 GACTATATTGCCCAAAACAATTTACAGATTTAATGCAATTTCTTTCAAAA 1741
                          i v   i v      vii  i        i  i     ii  v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115454547_   1742 TACCAACATCATTCTTCACAAAATTAGAAAAAAAAATCCTAAAATTCATA 1791
                          v   i vv v  i  ii  i  v v  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_115454547_   1792 TAGGACCAAAAAAGAGCCTGAATAGCCAAACCAATCCTAAGCAAGCAAAA 1841
                          i i viiv  ii  v  v           v     i i iv   v i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_115454547_   1842 TGAATCTGGAGGCATCATATTACTTGACTTCAAA--TTA-TATAAGGCTA 1888
                         ii  vi      vv   i i v iii i      --   -  i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_115454547_   1889 TAGTAACCAAACCAACATGGTACTGGTCTAAAAATAGGTACGTAG-TCAA 1937
                         i     i   iv  iii         iv   ii    ii ii   -    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_115454547_   1938 ATGGAATAGAATAGAGAAGCCAGAAATAAAGCCAAACAC----AACCAAC 1983
                         -           v    iv           v   v   i----iii   i
  L1M4_orf2#LINE/    301 -TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_115454547_   1984 TGATCTCTGACAAAGCATACAAAAACACA---AACTAGGGAAAGCACACC 2030
                             i ii     i -i i v  i  -  ---  - i       v i vi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGAC-CATTCAA-TGGGGAAAGAATAGT 396

  chr1_115454547_   2031 CTTTTCAATAAATGGTGCTGGGAAATTTGGATAGCCACATGTGAAA-AAT 2079
                                 i              v vi      ?       ii   -   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_115454547_   2080 GAAACTGGATCCCTATCTCTCACCATGGATAAAAATTAATTCAAGTTGAA 2129
                            ii    i     i   v      iv i         i    iv  i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_115454547_   2130 TTAAAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAAAAAAC 2179
                          i ?    i     v     v  i    i      v ii     i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_115454547_   2180 CTAGGAAAAATTTTTCTGGACCTTGTCCTAGGCAAAGAATTTAT-GATGA 2228
                         v    ?iv  v i   vv       vvi       v iv  iv -   - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr1_115454547_   2229 AGACCTCCAAAGCAAATGCAACAAAAAGAAAGGTAGACAAACAGGACTTA 2278
                         v   vi v      v v         ii   ii    i   iv      v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_115454547_   2279 ATTAAACTAAAAAGCTTCTGCACAGAAAAAAAAAAAAAAATTATCAG--- 2325
                           i   v v    i   i  ii vvv   ii v ------i     i---
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA------CTATCAAGAA 689

  chr1_115454547_   2326 AGTAAGCAGACAGCCTACAGAATGGGAGAAAATATTTGCAAACTATATAC 2375
                            i iv     i  i                          ii     i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_115454547_   2376 ACAACAAAGGACTAATATCCTGAATCTACAAGGAAATCAAACAATCAGCA 2425
                         vii i  i     vi     v    v  i  i   v  vv    ii--  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--CA 787

  chr1_115454547_   2426 AGAA-AAAAAAACAAATAATCCCATTAAAAAGTGGGTAAATGACATAAAT 2474
                          v  -     i        i  v   ?    i    i   v  iv i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_115454547_   2475 AGACATTTCTCAAAAGAAGATATACAAA-AGCCA-------TATGAAAAA 2516
                                    v                -i    -------i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_115454547_   2517 AATGCTTAACACCATGAATCAT 2538
                          -    i    i  ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (141 / 81)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.05 (39 / 19)  


 499 25.15 2.40 3.59  chr1_115459587_115462033      768   934 (1513)    L1M4_orf2#LINE/L1        6   170 (738)  

  chr1_115459587_    768 AGGTATAAACCAATGTTCCCAGATGAGACGACTCAATATTGTTAAAATGG 817
                           i   ---  v      vii   vi  v    i           i    
  L1M4_orf2#LINE/      6 AGATAT---CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_115459587_    818 CAGTTCCCCCCAAAT-GGTCCACAGATGCAATGCAATCC-TACCAACAAT 865
                           i v i        - i  i      v   i       -  i   -   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-AAT 101

  chr1_115459587_    866 CCCAGAATGTTTTCCATTGCAAACTATG-CAATATAGTTCTAATATTT-T 913
                              v-  ii  ii-     i vvv  -   vv ii i    v   i- 
  L1M4_orf2#LINE/    102 CCCAGC-TGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_115459587_    914 ACAGGACAGCAAAGGACTGAG 934
                          ii i vv    i    iv  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAG 170

Transitions / transversions = 1.62 (26 / 16)
Gap_init rate = 0.05 (8 / 165), avg. gap size = 1.25 (10 / 8)  

1847 26.47 4.89 3.88  chr1_115459587_115462033     1260  1954 (493)    L1M4_orf2#LINE/L1      175   876 (32)  

  chr1_115459587_   1260 GCCAA--TAATTTTTAAAA-GAGAAAGAAATTCAGAGGATTAA-ACTACT 1305
                              --i   i  v    -  ii  v   v ii     i v -   v i
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr1_115459587_   1306 TGATTTTAATACTGTGAAGCTATAGTAAACTGTGAAGCTATAGTAAATAA 1355
                         ii    i  v   ------------  --  iii      i     vi  
  L1M4_orf2#LINE/    225 CAATTTCAAAACT------------TA--CTACAAAGCTACAGTAATCAA 260

  chr1_115459587_   1356 GACAGTGTGATATTGATGTAAGGATAGATAAATATGCCAATGAGACAAAA 1405
                                  i  i  iii          i v   vii     ii i i  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_115459587_   1406 CAGAAAATTCGGAAACAGACCCCACACATTCATGGTTGATTGATTTTTAC 1455
                         iv  i i i i    i i    - i     i     ii         iiv
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCC-ATACATTTATGGTCAATTGATTTTCGA 359

  chr1_115459587_   1456 CAAAGGCATCAAGATAATTCAATAAGAATAGG-TAGTCTTTTCAACAA-T 1503
                            i  iii     iv       ii i v  i-               - 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_115459587_   1504 GGTGTTGGAACAATTGGCTATCCATTTTTTAAA-AATAAACCTCAGCATT 1552
                             i   i    i   v  ?   iv viv   -   i  vi vii vii
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_115459587_   1553 TAACTTATTCCTTACATAAATATTATCTTGAAATTAATCTTAGATCTGAA 1602
                           v  i iv  v  i i   v    v  ii    vi   v?   i  i  
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_115459587_   1603 AGTAAAAGCTAAAACCATAAAACTTCTACAAGAGAACACTGAGGAAAATC 1652
                         v    i         i        ii  v    i    iv i? v     
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_115459587_   1653 TTTGCAAACTCAAGATAAGCAAAAAATTTTATAGATA--AAATTAAAATA 1700
                           i ii v  iii v  i    viiv  i -      -- v ii    vv
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCT-TAGATATGACACCAAAAGC 608

  chr1_115459587_   1701 ACTGTGAACCATG---AAAATTGTTAAACATTGTTTCGTTTTCA-CAAAC 1746
                           vivv   v vi---     v v    --   ---- vi    -    -
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAA--TTG----GACTTCATCAAA- 651

  chr1_115459587_   1747 ATTAAAAACTTTTGCTCTTT----GTCATTGTTAAGAAAATGAAAAAGGC 1792
                                       iv   i---- v  i i i      i      - i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GAC 700

  chr1_115459587_   1793 AAACCACAGACTGGAAGGAAATATTTGTCTCA---CATGTATCTGACAAA 1839
                           v       v   i  i         ---  ---   i       i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTG---CAAATCATATATCTGATAAG 747

  chr1_115459587_   1840 AAACTTCTATTTGAAATATATAAAGAATTCTTACAGTTCTGTAATAAAAA 1889
                         ii    v   iiii             i       ii  vi         
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_115459587_   1890 GACAAATGATCCAAT-------------AAAGATTTTAACAC-CACTTCA 1925
                                i i     -------------  i     v  i v-  i   v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_115459587_   1926 CAAAGGAAAATATACAAATAGACTCTAAG 1954
                          v  i   i          i v vv    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAG 876

Transitions / transversions = 2.07 (122 / 59)
Gap_init rate = 0.03 (22 / 702), avg. gap size = 2.77 (61 / 22)  


1189 28.40 10.65 3.79  chr1_115506507_115508433      594  1438 (489)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_115506507_    594 AGACATATCATGGTCACAGACAGGAAGACTGACCATTGTAAAAGTTATTA 643
                            i  vi    v   ii  iv        v vi     v  - v ivi 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA-GATGGCA 54

  chr1_115506507_    644 ATTTTCCCCAAATCAATCCACAGGTTCAATATAATTCTAAT-AAAATTCT 692
                           vi         ii   i    i     iii   i iv  -     i i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_115506507_    693 GAAGTAAGATTGT--GAAGAATTTGAC----TATTTTTAAAGTTTATATG 736
                         --  ivivv  v -- v    v     ---- iv ii    i  i     
  L1M4_orf2#LINE/    105 --AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_115506507_    737 GATGAT-CAAA--ATGCAGTACA--CAATATACTCCC---AGAGAAAAAT 778
                           -i  -   i-- iv   v i --   v i v  ii--- i    i  i
  L1M4_orf2#LINE/    153 GA-AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_115506507_    779 GTTAGATAGGAAGACTTGCTCTACCAAAT--CAAGTCTTATTTCAA-GCT 825
                         i-- ii v   i    ii v  v  v   --   iv    i v   -   
  L1M4_orf2#LINE/    202 A--AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_115506507_    826 ATCATAATTAAAA--GTGTGGTTTGAGTGCAGAGATAGGAAGAAAGCCCA 873
                          ivi    i  i --       vivi iii ii     iv v v  vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_115506507_    874 ATGGAACAGAAT--AGAGCCCAAAGACAGACGCATACAT--------AAC 913
                               i     --    i   i i i i  v       --------  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_115506507_    914 TGATGAAAGCCATTACAGGAAGAGCTGGCATTGACGAT--AAGCTGGGAA 961
                             --------  v iiv   i -  v  v-   v  --  --    i 
  L1M4_orf2#LINE/    350 TGAT--------TTTCGACAAGGG-TGCCAA-GACCATTCAA--TGGGGA 387

  chr1_115506507_    962 AAGACTAACCATTT-AACAGATGACATTAAGACAACTGC-TCGTC-TATG 1008
                             v  ii v   -    i   iiii ii        v- v?i -i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_115506507_   1009 TGGGGGAA--AAACTGGATCCCTGCCACAGACACACATTCTAAA--TAAG 1054
                         iiiii   --  ii    i    i  v  v  -  i  v v   --   v
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACAC-CATATACAAAAATTAAC 486

  chr1_115506507_   1055 TGTAA--GGATT-----CC--ACTGAAAAAGG-AAAACTACAAAATGTTT 1094
                          vv  --    i-----  -- v  v  i  v-       i    ivi  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_115506507_   1095 AATGAAAAATATAGA---AAATAGCTTT-TAATTTTGGGAGTGGGAAAGA 1140
                          ivii    i    i---    --   i- i ii     -v i  v  vi
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGG-TTAGGCAATG 583

  chr1_115506507_   1141 ATGCCTTAAACA--ATATT-----CATATG--AGGAAATCCTTATAAAAT 1181
                         i vi    i i -- i ii-----  i v -- vi   -----iv    v
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA-----GAAAAAA 628

  chr1_115506507_   1182 TAGATTATAAATTTGACTGCATCATAATCAAAAACTTCTTTCTTTCAAAA 1231
                              ---     v    v     v   i        i v vi      i
  L1M4_orf2#LINE/    629 TAGAT---AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_115506507_   1232 GACACCATAAAGAAA----AGAGATAAGCCCCAAATTGTTAGAAAATAGT 1277
                              i  v      ---- i   i  v  v  i v  vv        v 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_115506507_   1278 TGCAA--CATATTAACTAATAAATAATTAATATCTAT--TATAGAACAAA 1323
                              --     - v  i    ivi i vi    i v--    v  - i 
  L1M4_orf2#LINE/    726 TGCAAATCATAT-ATCTGATAAGGGACTTGTATCCAGAATATATAA-AGA 773

  chr1_115506507_   1324 ACTCT-GTGAATTAATAAGAAAAAGA-----AAC-----------ATGGG 1356
                              -iii v i     v       -----   -----------     
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_115506507_   1357 CCAAACATATGAACAAGCCTTTCGC-AGAGAAGAAATAGGACTGGTTAAT 1405
                          v  iv  v    i ii v    v - i      v   vi v   ii   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_115506507_   1406 AA--ATGTGAAAAGATGTTCAACTACATAAGTAAT 1438
                           -- ii          i     vv  ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.06 (50 / 903), avg. gap size = 2.44 (122 / 50)  


3180 27.64 0.44 0.44  chr1_115638261_115644632.rev     4974  5881 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115638261_   4974 TGGAAGAATTTTCCATGCTCATAGATAGGAAGAATTAATATCATGAAAAT 5023
                              ii  v i     i    i   v      v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115638261_   5024 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 5073
                            v     v     iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115638261_   5074 TACCAATCACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5121
                          v   iiii i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_115638261_   5122 TATGGAACCAAGAAAGAGCCTGCATGGCCAAGACAATCCTAAGCAAAAAG 5171
                                viivi ii  v  v v  i     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_115638261_   5172 AACAAAGCTAGAGGCATCACATTACCTGACTTCAAACTATACTACAAGGC 5221
                                i i    vv     i v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_115638261_   5222 TACAGTAACCAAAACAGGATGGTACTGGTACCCAAACAGATACATAGACC 5271
                                 i   i    vi         i ivvii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_115638261_   5272 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5321
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_115638261_   5322 CTGATCTTTTACAAACATGAGAAAAACAAGAAATGGGGAAAGGATTCTGT 5371
                         i    i  iv    ivi  vv  i v  vvv           i  vv v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_115638261_   5372 ATTTAATAAATGGTGCTGGGAAAACTGGCTATCCATATGTAGAAAGCTAA 5421
                         v  i  i              v      v  ?   i   i i  iiv i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_115638261_   5422 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5471
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_115638261_   5472 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5521
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_115638261_   5522 AGG--TAATACCATTCAGGACATAGGCATGGGCAAGGACTTTATGACCAA 5569
                            --   - i -   iv   v v  vv i     v ii  iv iivi v
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_115638261_   5570 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5619
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_115638261_   5620 TTAAACTAAAGAGCTTCTGCACGAATAAAGAAACTACCATCAGAGTGAAC 5669
                          i   v v  i i   i  ii vvvv  i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_115638261_   5670 AGGCAACCTACAGAATGGGAGAAAATTCTTGCAATCTACCCATCTGACAA 5719
                           i     i                 vi      vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_115638261_   5720 AGAGCTAATATCAAGAATCTACAAAGAACCTAAACAAATTTACAAGAAAA 5769
                         i ii  vi    v     v  i       iivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_115638261_   5770 AAATAAACAACCCCATCAAAAAGTAAGCAAAGGATATGAACAGACACTTC 5819
                          i i   i     v  i?    i ii         v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_115638261_   5820 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5869
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_115638261_   5870 ATCACTGGTCAT 5881
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (154 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


4381 16.44 3.72 1.46  chr1_115670872_115672827      576  1463 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115670872_    576 TGGAAAGCCATCCCATGCTCATGG-TCAGAAATTTTAATATTGTTGATAT 624
                                vi        i      - ii   ivi           i v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115670872_    625 GGCAATACTCCCCACACTGATGTACAGATTCAACATAATCCCTATCAAAA 674
                                       v i    v            ii              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115670872_    675 TCCTAGCTTTCTTTTTTGGTTTCCAAGAATTACCAAGCTGATCCTAAAAT 724
                            i    vi        -----  ii    iv                 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-----CAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_115670872_    725 TTATAGAGATAT-CAAGGAACCTAGAATAACCAAAACAATCTTGAAAAAG 773
                          i   vi  v  -     i   i      i                    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_115670872_    774 AA---CAAAGTTGGAGAACTCATACTTCCCAATCTCAAAACTTACTACAG 820
                           ---           i     i          i               i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_115670872_    821 TGCTATAGTAATTAAAACAGAGTGAT-CTGGTATAAGAATGGATATATAG 869
                         v    i      i  i    v   i -    i     i  i  i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_115670872_    870 CTTAGTGGAACAGAATTGATAGTCTAGAAATAAATCC-TAAGTTTATGGT 918
                         v i i     i        v    i         i  -  vi        
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_115670872_    919 CAATTGATTTTCAGCAAAG------AGACAATTCAATGTGGAAAGAATCA 962
                                     ii   i ------    v        v         vi
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_115670872_    963 TCTT--AAACTAATGAAGCTCTGACAACTGGATATTCACATGCAAATGGA 1010
                             --v   v    iv   vv            ?i          v i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_115670872_   1011 TGAAACTGGACCCCTACCTCAAGCCATATACAAAAACTGACTAGGAATGG 1060
                             ii               vi             i i   vii     
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_115670872_   1061 ATCACGGACCTAAATGTAAGAGTGAAAACTCTAAAATTCTTAGAAAAAAA 1110
                             ?i                iv      v     i        i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_115670872_   1111 -ATAGGCATA--TCTTTGTGACTTTGGATGATACAATGGT--CTTAGACA 1155
                         -     ?i  --    i     i    i v vi       --      i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_115670872_   1156 TGACATCCAAAATACAAGCATACACACACAAAAAA---ATGCACTGGGTT 1202
                              i v   ii       -   - v v      ---  iv i   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCA-ACA-AAAGAAAAAATAGATAAATTGGACT 643

  chr1_115670872_   1203 TCATCAAAAATTAAAAACTTTTGTGCTTCAAAGGGCACCATCAAGAAAGT 1252
                                  -                        i   i           
  L1M4_orf2#LINE/    644 TCATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_115670872_   1253 -AAAAGACA-CTCAAAGAATAGAAAAAAATATATATTTACAAATCATATA 1300
                         -        - i  v     i i i       ----  i           
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATAT----TTGCAAATCATATA 738

  chr1_115670872_   1301 TCTAGTGACGGACCTAT-TCTAGAATATTTGAAGAACATTTATGATTCAA 1349
                            ii i v    i i -  i       v i      vi   ii i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_115670872_   1350 CAAATAAAAGACAAATAACCTAATTAAGAAAATGAAC-------TTGAAT 1392
                         i  vv               i    ? -      ii -------      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAAT 837

  chr1_115670872_   1393 AGAAATTTATCCAAAAAAGATATGCAGATGGTTAATAAACTCATAAAAAG 1442
                            v    v      i       i  i    ii     i v   i     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_115670872_   1443 ATACCCAACATCATTAATCAT 1463
                           i i        ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (100 / 42)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.19 (46 / 21)  


2506 28.04 2.07 3.37  chr1_115675134_115678512.rev     1969  2888 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115675134_   1969 TGGAGAGACATACAGTGTTCATGAATTGAATGACGCAACTTAGTAAAGAT 2018
                             i   i  v vi        i    i v   vi  iv v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115675134_   2019 GTCAGT-TTTCCAAAATTGATATACACGTTTAATATAATTTATATCAAAT 2067
                          v  i -i i  v        v    vi  i  iii   iiv       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115675134_   2068 TCTCTGCCAGAATTTTTGTAGATATGCAGAATATTACTCTAAAATTTATT 2117
                           i v  iivvv      i   v  vv v  vv v ii        i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_115675134_   2118 TTGAAATTCAAAGGAACTGGGATAGCTAAAACCATTTTTAAAAAGAA--- 2164
                          v     v   i   v ii i     i     v  i  v        ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_115675134_   2165 TAAAATATAAGGAATC-CATCTACACAATTTTATGACTTATTATATAGC- 2212
                         i   i vvi    v  -  -  v v      i vi     i  i v   -
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACA-CTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_115675134_   2213 -CAGCCTAATCAAGACTGTGAAGTGTCGGTAGGAGATTAGATACATAGAT 2261
                         -   --          v   vi  iii  i vi  iv    i i      
  L1M4_orf2#LINE/    250 ACAG--TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_115675134_   2262 CAACAGATGAGAAAAGAAAACCCAGAAATAGACCCACACTAACATGTCCA 2311
                            ii  vv    vv  i ii         i     i  vvvi   vi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_115675134_   2312 ACTGATTTTTGACAAAATTGCAAAAGCAATCCAATAAAGAAAAGATAGCC 2361
                          i       i     iiv   v  ii v  i    iii    ii    i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_115675134_   2362 TTTTAAACAA----TGCCGGGGCAATTGGTCATCCATGGGCAAAATAATG 2407
                             v     ----   i   i   i   vi ?   iiv      v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_115675134_   2408 AACTCTGACCTAAGTCTCACAACTTATACAAATGTAAGTTCAAAACGGAT 2457
                           v iv    ivvii      v v        vi v ii      i    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_115675134_   2458 CAAGTTCTTAAACGTAAAACACAAAACTATGAAACATTTATTTTAAAAAA 2507
                           ?ivv i    i    i vvi        i    vi   vvvv    v 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_115675134_   2508 GAGAA--AAATCTTTGGAATTTGGGGCTGGGCCAAG--TTCTTAGACTTG 2553
                         v  i?--       i vi ii v   i i   v v --        iv  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_115675134_   2554 ACACTAAAAGCATCAACCATACAAGAAAA--TTGATAAAATGGGTTTTAT 2601
                             i       iv i v i v       -- v      v   ii  i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_115675134_   2602 CAAAATTAAAAACTTTTCT-TTGCAAAATACTCTATAGAGGGAATTAGT- 2649
                                          v -i v    iv  v    vi  ii i v iv-
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_115675134_   2650 GATGAGCTGCAGACTGGGAAAAAATATTTGCAAACCACATATGCAACAAA 2699
                           ii v ii    v     i              i  i    vii i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_115675134_   2700 GTAGTAGTGTCTTAGAATATATGAGGAACTCTCAAAACTTAGAATATATA 2749
                          v v v  i  i----------------------------          
  L1M4_orf2#LINE/    748 GGACTTGTATCC----------------------------AGAATATATA 769

  chr1_115675134_   2750 AAGAATTCTCAAAATTTAATAGTAAAAAACAAAACAATGCAATTAGAAAA 2799
                              i   i v  i i    i      ivv   i  iv     ?i    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_115675134_   2800 TAGGCAAGATATATGAACAGATATTTCACTGAAAAGGATATACAGATGAC 2849
                          i     iiv  v    i   i     v ii  i i        i   i 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_115675134_   2850 AAATAAACACATGAAAAGTTGTTCAATATCATAAGTTAT 2888
                         v     i           v  i    i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (147 / 107)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.85 (50 / 13)  


3142 26.85 1.10 0.77  chr1_115833144_115840141.rev     5603  6507 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115833144_   5603 TGGAAGAACATTCCCTGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5652
                              ii i  i  v  i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115833144_   5653 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCTCATCAAGC 5702
                            v     v     iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115833144_   5703 TACCA-CTGACTTTCTT-CACAGATTTGGAAAAAACT-ACTTTAAATTTC 5749
                          v   -   v    i  -  v i   ---i v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chr1_115833144_   5750 ATATAGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAA 5799
                             i   viiv  ii  v  viv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_115833144_   5800 GAACAAAGCTGGAGGCATCACACTATCTGACTTTGAACTATACTACAAGG 5849
                                 i      vv       vi ii i  ii  viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_115833144_   5850 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGAGATAG 5899
                                  i   i    ii         i i--  iv v   v v    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAG 295

  chr1_115833144_   5900 ACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCAGACATCTACAAC 5949
                          i        i    iv   ivii         vv   v    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_115833144_   5950 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAAGATTC 5999
                           vi    i  i     ivv  v   i v  vv           ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_115833144_   6000 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAACC 6049
                         i  v  i  i              v      v  ?i  i   i i  ivv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_115833144_   6050 TGAAACTGGATCCTTTCCTTATGCCTTATATAAAAATTAATTCAAGATGG 6099
                             ii    i  i v   i ii  v    i         i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_115833144_   6100 ATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 6149
                           i ?    i           v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_115833144_   6150 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACT 6198
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_115833144_   6199 AAAATACCAAAAGCAATGGCAACAAAAGCCAAAATTCACAAATGGGATCT 6248
                          vi i          vvi          vv     vv i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_115833144_   6249 ------AATTAAAGAGCTTCTGCAGAGCAAAAGAAACTATCATTAGAGTG 6292
                         ------       i -   i  iivvv    i  v       vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_115833144_   6293 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 6342
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_115833144_   6343 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 6392
                         i  i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_115833144_   6393 TAAAAATAAACAAACCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 6442
                         v   i i   i  v  v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_115833144_   6443 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATCAAAAAATGCTC 6492
                              v        i  vi viii     i ii  i  v    i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_115833144_   6493 ATCATCACTGGCCAT 6507
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


2481 26.14 0.44 0.29  chr1_115856305_115857979.rev      504  1184 (491)    L1M4_orf2#LINE/L1      227   908 (0)  

  chr1_115856305_    504 ACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGG 553
                          i      viv        i          i   i    ii         
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr1_115856305_    554 TACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAA 601
                         i iv ii i   v                i    i--    i  --    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAA 324

  chr1_115856305_    602 ATAACGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAA 651
                             vv  ii i  i  iiiii vi    i  i     ivv  vv  i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_115856305_    652 CAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACT 701
                           vv            i  vvi  v  i  i              v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_115856305_    702 GGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTAT 751
                           v  ?   i   i i  iiv    ii    i    v   i     v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_115856305_    752 ACAAAAATTAATTCAAGATGGATTAAAGACTTAA-CGTTAGACCTAAAAC 800
                                    i    i      i ?    i   -i  v   v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_115856305_    801 CATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCA 850
                         i      vi i           v    ?i v viv   iv   v v  vv
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_115856305_    851 TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCC 900
                          i     v ii   v ivv  vi            vvi          vv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_115856305_    901 AAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 950
                              v  i    v   ii v  i   v v  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_115856305_    951 AGAAACTACCGTCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTT 1000
                         i  v    i ivv i      v  i     i   i             v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_115856305_   1001 TCGCAACCTACTCATCCGACAAAGGGCTAATATCCAGAATCTACAATGAA 1050
                          i    vii ivi   i  i  i  i  vi          v  i  v   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_115856305_   1051 CTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGC 1100
                            vv    v iv i  v     i     i     v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_115856305_   1101 AAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 1150
                               iv    i     i     v        i  vi viii     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_115856305_   1151 AACACATGAAAAAATGCTCACCATCACTGGCTAT 1184
                          i          i       v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (102 / 72)
Gap_init rate = 0.00 (3 / 682), avg. gap size = 1.67 (5 / 3)  


3001 27.36 1.67 0.67  chr1_115888391_115895090.rev     5311  6209 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_115888391_   5311 TGTAAAAACATTC-ATGCTCATGGATAAGAAGAATCAATATTGTGAAAAT 5359
                           v   i i  i -   i        vi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_115888391_   5360 GGCCATACTGCCCAAAGTAATTTGTAGATTTAATGCTATCCCCATCAAGC 5409
                            v     v      v i  i ii     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_115888391_   5410 TACCATTGACTTTCTTCACAGAATTAGAAAGAACT-ACTTTAAATTTCAC 5458
                          v   vivi i  i  ii     v v  v - i  - iii    v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr1_115888391_   5459 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCT-------AAGC 5501
                               viiv  ii  v  viv        i      i -------   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_115888391_   5502 AAAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5551
                          v    i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_115888391_   5552 ACCTACAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGATATATAG 5601
                           ----     i   i    ii       i i iv ii i   i      
  L1M4_orf2#LINE/    250 AC----AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_115888391_   5602 ACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATGTACAAC 5651
                          i        i    iv   ivii         vv   i    v  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_115888391_   5652 CCTCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5701
                          vvi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_115888391_   5702 ACTATTTAATAAATGATGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 5751
                         v  v  i  i     i  i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_115888391_   5752 TGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGGTGG 5801
                             ii         v   i     v                   ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_115888391_   5802 ATTAAAGATTTAAACGTAAGACCTAAACCCATAAAAATCATAGAAGAAAA 5851
                           i ?   ii    i      v     v i      v  v          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_115888391_   5852 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGAAA-GACTTCATGACT 5899
                          v    ?i- v i -   iv   v v  vv i  v  - ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_115888391_   5900 AAAATACCAACAGCAATGGCAACAAAAGCCAAAATTCACAAATGGGATCT 5949
                          vi i     v    vvi          vv     vv i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_115888391_   5950 GATTAAACTAAAGAGCTTCTGCACAGCGAAAGAAACTACCATCAGAGTGA 5999
                         v  i   v v  i i   i  ii vv i  i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_115888391_   6000 AAAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 6049
                             i     i                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_115888391_   6050 AAAGGGCTAATATCCCGAATTTACAAGGAACTTAAACAAATTTACAAGAA 6099
                           i  i  vi     v    v  i  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_115888391_   6100 AAAAACAA----TCCCATCAAAAAGTGGGTAAAGGATATGAACAGACACT 6145
                            i    ----i  v  i?    i    i       v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_115888391_   6146 TCTCAAAAGATGACATTTATGCAGCCAACAAACATATAAAAAAAAGCTCA 6195
                             v     v  i  vi viii     i  i  i  i    i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_115888391_   6196 TCATCACTGGTCAT 6209
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (141 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.33 (21 / 9)  


2062 26.70 3.98 1.62  chr1_116000748_116003177.rev      898  1575 (855)    L1M4_orf2#LINE/L1        6   699 (209)  

  chr1_116000748_    898 AGACATACCATATTCATGAATTGGAAGAC--AACATAGTAAATATGTCAC 945
                            i  v    i      i          --  i  v  v  v   v  v
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_116000748_    946 T-CTCCCCAAGTTTATACACAGATTTAATGCAATTGCTATCAAAATTCTA 994
                          -        i  v  vi       i  i     iv          i i 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_116000748_    995 GTAATATTTTTTTTTGTGTATAAA----CAAGATTATTCTGAAGTTTATA 1040
                          i-- iii      --- i v   ----    v v  i  i  i  i   
  L1M4_orf2#LINE/    106 GC--TGCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_116000748_   1041 CAAAAATGCTAAAGGACT-AGGATAGTTAAAGCAATTTAGAAAAATAAAG 1089
                         iii      -  i    i-  i    ii   i    i v      -i   
  L1M4_orf2#LINE/    151 TGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA-GAAG 198

  chr1_116000748_   1090 AATAAAGTGAAAAGAGATAGTCTACCTGCTTTCAGATATACTTGATCCTA 1139
                           i     vii i  vvi vv  v  iiv     i ---    iv v v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA---ACTTACTACAA 245

  chr1_116000748_   1140 -GCTACTGCAATCAAGACTATGTGGTGTTGGCAGAGGAACAGACATATAG 1188
                         -     v i         vi      ii     v i i i          
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_116000748_   1189 AGCAATGGAACAGAATCGAGAAACCACAAATAGACCCACATGAATATG-C 1237
                          v        i     i    iv   v     i     i iivv    -i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_116000748_   1238 CAACTGATTTTTGACAAAGTTACAAAAGCAATTGAATGGATGAAAGA-CA 1286
                            i       i     i v i v  ii v   v     i-      -i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATA 394

  chr1_116000748_   1287 GCCTTTTCACCAAAAAATATCGGAACAGTCGGACATCTATTGGCAAAAAA 1336
                          i       v    vii iii  i   iii   i ? i ivv      i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_116000748_   1337 A-GAAAAAGGA-----ACCTCA-ACC-TATCTTAAATTTTA-TCAAAGTG 1377
                          -   ivv   -----      -   -   viv   v  v -     i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_116000748_   1378 AATCACGAACTTAAATATAAAATGAAAAACTATAAAATTTTTAGAAAAAA 1427
                         i    ?ii  i     i   i vvv            i i      i   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_116000748_   1428 ---TAAGAG--AAT--TCAGGATCTGAGGCTAGACAAAGAGTTCTTGGAC 1470
                         ---  i ? --   --  iv  i  vi  i   i   v iv     i  i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_116000748_   1471 TTAATATCAAAAGTACAATCCATGAATGAAAAAAGTGATCAACTGGACTT 1520
                         v i i i      i    v v ii  v       vv   v  i       
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_116000748_   1521 CATCAAAATTGACAATTTTTGTTCTGTGAAAGATCCTATTAAGAAGATGA 1570
                                   i v  i      v  vii  i  iv    i     ii   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_116000748_   1571 AATGA 1575
                           v  
  L1M4_orf2#LINE/    695 AAAGA 699

Transitions / transversions = 1.78 (114 / 64)
Gap_init rate = 0.03 (21 / 694), avg. gap size = 1.81 (38 / 21)  

 667 24.55 5.45 2.27  chr1_116000748_116003177.rev     1722  1941 (489)    L1M4_orf2#LINE/L1      682   908 (0)  

  chr1_116000748_   1722 ATCAAAAAAGAAGATGAAATAACACACATACAGAGTAAAAAAAAATGCTT 1771
                              i    ----     vi   -  vi     i iii i     ii  
  L1M4_orf2#LINE/    682 ATCAAGAAAG----TGAAAAGACA-ACCCACAGAATGGGAGAAAATATTT 726

  chr1_116000748_   1772 GTAAACCATATATCTGAAAAAGGACTGGTATTTA--------AAAAAACT 1813
                          i   i           v  i     v    ii --------   i    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_116000748_   1814 CTCAAAATTCAACAGCCAAAAAGCAA----TCCAGTTGAAAAATGAGCAA 1859
                           i v  i    i iiv    ii   ----i   i  ?       i    
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_116000748_   1860 AAGATGTGAACAGGCATTTCATAGTAGAGAACATACACATGGCAAATCAG 1909
                          i   v    i  i      viviv   ii i     v     v   v  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_116000748_   1910 GACATTTAAAAATGCTCAACATTGTTAGCCAT 1941
                         v    vv   i           ii????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (37 / 16)
Gap_init rate = 0.02 (4 / 227), avg. gap size = 4.25 (17 / 4)  


3216 27.47 0.33 0.55  chr1_116033835_116035931      695  1604 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_116033835_    695 TGGAAGAACATTCCATGCTCATGGATAGAAAGAATCAGCATTGTGGAAAT 744
                              ii i  i     i        v i    v i ii     vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116033835_    745 GGCCATACTGCCCAAGGTAATTTTTAGATTCAATGCCATCCCCATCAAGC 794
                            v     v     iv i  i vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_116033835_    795 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAATTTCAT 843
                          v   iivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_116033835_    844 ATGGAACCAAAAAAAAGAGTCCTTATAGCCAAGACAATCTTAAGCAAAAA 893
                               -- viv  ii  vi vvv        i        i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_116033835_    894 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATTACAAGG 943
                                 i      vv   ii  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_116033835_    944 CTACAGTAACCAAAACAGCATGTTACTGGTACCAAAACAGATATATAGAC 993
                                  i   i    ii  v      i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_116033835_    994 CAATGGAACAGAAC--AGAGTCCTCAGAAATAACACCACACATCTGCAAA 1041
                                 i    i--       --        vv   i    i iiiiv
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_116033835_   1042 CATCTGATCTTTGACAAACCTAACAAAAAGAAGAAATGGGAAAAGGATTC 1091
                           vi    i  i     ivv iv   i vv vvv      i    i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_116033835_   1092 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1141
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_116033835_   1142 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCACGATGG 1191
                             ii    i    v   i     v              i   vi    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_116033835_   1192 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1241
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_116033835_   1242 CTTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGGCTTCATGACTA 1291
                          v    ?i v viv   iv   v v  vv i     v  i   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_116033835_   1292 AAATGCCAAAAGCAATGGCAACAAAAGCAAAAATAGACAAATGGGATCTA 1341
                         vi ii         vvi          v         i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_116033835_   1342 ATTAAACTAAAGAGCATCTGCACAGCAAAAGAAACTACCATCAGCACGAA 1391
                           i   v v  i i v i  ii vv    i  v    i  vv ivii   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_116033835_   1392 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCTATCTGGCA 1441
                         v  i     i                 v       vii iv      ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_116033835_   1442 AAGGGCTAATATCCAGAATCTACAAAGGACTCAAACAAATTTACAAGAAA 1491
                          i  i  vi          v  i    i    vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_116033835_   1492 AAATCAAACAACCCCATCAAAAAGTGGGCAAGGGATATGAACAGACACTT 1541
                           iv    i     v  i?    i       i    v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_116033835_   1542 GTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 1591
                         v  v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_116033835_   1592 CATCACTGGTCAT 1604
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2643 25.63 3.83 4.38  chr1_116039977_116044263     2882  3794 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_116039977_   2882 TGAAGCAATACACCATGCTTATGGATTGGAAAATTCCATTTTGTTAAGAC 2931
                           i ivi   iv     i i           i i iv  v         i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116039977_   2932 TTTAATTCTCAACAAACTGGACTATATGTTCAATATAATCCTAATGAAAA 2981
                         vvi   v   vv    i  iv   i vi     iii     iv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_116039977_   2982 TCTCAGAAATCATTTTTATAGAAATTGGCAAACTGACTTTAAAATTTATA 3031
                           i   vvii v     ii        i   i    iii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_116039977_   3032 TGGAAATAAAAATGATCACCACTAGTCAGAAGACTTTTGAAATAGAA--- 3078
                                iv  iv  i vvv v   i  i  v v i      v    ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_116039977_   3079 ---AGCTTGAGGACCTACCCTACTTGATTTCAAGACTTACTGTAAAGCTA 3125
                         ---  i v      ii  v  v iii       i       ii       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_116039977_   3126 CATTAAAGAAGATAGTATTATATTGGCATAAGCCTAGACA-------CAA 3168
                           v   vv    i   i vi  i         vv      -------   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_116039977_   3169 TGTAACAAAACAGAG-GTCTGAGAGCAGACTCAAATGAATATGATGAATT 3217
                           v  i i  iv   -   iiii ii i  i  v iivv    i v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_116039977_   3218 GATTTTCAACAATGTTGTCAAGATAATTCAATGGGGAAAAGATAGT--TT 3265
                                i    v v  i     iv              ii     --  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_116039977_   3266 TCAA-AAATAGCCTTGAAAAAATTGGATATCCCTGTGCAAAATAATTAAA 3314
                             -    i ivi  ii v  i      ?  vii       v   v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_116039977_   3315 CTTAAACCTTGCTTCATGCTATACACAAAAATTAAATTAAAATTCCTTGC 3364
                         i vi v  i i i   ii i   i           v i     vvv ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_116039977_   3365 AGTCCTAAATGTAAGAGCTAAAAAATAATGATACTTTTAGTT----ATGT 3410
                           v                    --iv  i v   i    vv---- ii 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAA--CTATAAAACTCTTAGAAGAAAACAT 548

  chr1_116039977_   3411 GACAGAAAATATTTGTGACTGTGAATTGGGCAAAGTCTTCTTAGGTAGAA 3460
                         iiv? v    v  i     iv  ii  i     v vi       i  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_116039977_   3461 CAT-AAAAATA-AAG-AACCAC-TAAAAAGT-GATAAATTGGACCTCATT 3505
                           i-    ii -   -   v v-v     i -            i    i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_116039977_   3506 AAAATTAAAAACCTTTTAT-CTTTAAAGGATATTCAACCTCATTAAAATT 3554
                                     -    i -   i      i i -------------  i
  L1M4_orf2#LINE/    649 AAAATTAAAAAC-TTTTGTGCTTCAAAGGACACT-------------ATC 684

  chr1_116039977_   3555 AAAAACCTTTGATCTTTAAAGGATATCATTGAGAAAATGAAAGCCATAGA 3604
                           i  --------------  --------   i  i i--  v   i   
  L1M4_orf2#LINE/    685 AAGAA--------------AG--------TGAAAAGAC--AACCCACAGA 710

  chr1_116039977_   3605 CTGCATGAACATATTTGCAAAATATATATCTGATCAATAACTTGCACCCA 3654
                         v  viv   v           vi           v ivi     i i   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_116039977_   3655 GAATATACAAGTAATTTTTACAA-----TAATAA---GACACATAATCCA 3696
                                i  iv  i i      -----      ---    v    i   
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_116039977_   3697 ATTAATAATTGAGCAAAATATTTGAATGAACACTTCACCAAAGAAGATAC 3746
                            ? v  v  i     iv        ii   i   v            i
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_116039977_   3747 ATGAATGGTGAATAAACATGTGAAACAATGCTTAACATCACTAATCAT 3794
                          ii     iv     i  ii     vi     i       ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (145 / 85)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.75 (75 / 20)  


2532 24.35 3.30 0.00  chr1_116106852_116110751.rev     2186  2760 (1139)    L1M4_orf2#LINE/L1        1   594 (314)  

  chr1_116106852_   2186 TGGAAAGACATCCCATGCTCATGGATCAGAAGAATTACTATTGTTAAAAT 2235
                                 i        i        ii     v   v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116106852_   2236 GGCCATACTACACAAAACAATCTATAGATTTAATGCATTCCCTATCAAAA 2285
                            v     v v    vii     i     i  i   v            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_116106852_   2286 TACCAGTGACATTCTTCACATAAATAGAAAAG--AATTCTAAAATTTGTA 2333
                          v    ivi v  i  ii  v    v  v   --i  i        ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_116106852_   2334 TGGAACCACAAAAGACCTCAAATAGCCAAAGCAATCCTAAGCAAAAAGAA 2383
                              vii   ii    ivi          i     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_116106852_   2384 CAAAGCTGGAAGCATCATACTACCTTACTTCAAAATATACTACAAAGCTA 2433
                              i    i vv   i   v  iv i       iv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_116106852_   2434 TAGTAACCCAAACAGCATAGTATTAGTATAAAAATCGATACATAGGCCAA 2483
                         i     i v i    ii i   i i i    ii  v  i i    ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_116106852_   2484 GGGAACAGAACAGAGAACCCAGAAATAAATCCACATATTTACAGCCAATT 2533
                         v    i    iv    ii           i   i i     ii i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_116106852_   2534 GATTTTTGACTAAAGTGCCATGAACATACACTGGGGAAAGAACACCTTCT 2583
                               i   v ii      v  v   v  v           i vii i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_116106852_   2584 TCAATAAATGGTGCTGGGGAAACTGGATATCCACATGCAGAAGGATGAAA 2633
                             i             iv         ?         i   i     i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_116106852_   2634 CTAGACCCTTGTCTCTCACCATATACAAAAGTCAACTTAAAATGGATTAA 2683
                         i i     i ii   v              i i    i         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_116106852_   2684 AGACTTAAAGATAAGATCCAAAA-----------------GAAAACATAG 2716
                             i    vi     v i    -----------------          
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_116106852_   2717 GGGAAATTCTGTAGGACATTGGACTACGTGAAGATTTTATGGAT 2760
                          ? v  v   viiv   v    ii  v ii v i   iv i   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

Transitions / transversions = 2.19 (94 / 43)
Gap_init rate = 0.00 (2 / 594), avg. gap size = 9.50 (19 / 2)  

1024 24.54 2.76 4.91  chr1_116106852_116110751.rev     3085  3410 (489)    L1M4_orf2#LINE/L1      590   908 (0)  

  chr1_116106852_   3085 TAACTAAGACTTTAAAAGCATGGGCAACAAAAACAAAAACAGACAGAAAA 3134
                           iv  v   vii       iii         iv     i   i i vvi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_116106852_   3135 GACTATATTAAGCTAAAAAGGTTCTGCACTGCAAAAGAAACAATTGATAA 3184
                             vi  i  iv v    iv  i  ii  v    i  v  v  ii v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_116106852_   3185 AG-----AGGCAACTTGTACAATGGGAGAAAATATTTGCAAACTATTCAT 3229
                           -----  i    iiii v                      ii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_116106852_   3230 CTGACAAGGAACTGATATCTAGAATATACAAGGAACTC----AACTCAAC 3275
                             i    i   vi    i        i  i      ----       i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_116106852_   3276 AGCAACAAAACAAAACAAAACAAAAGCCAGTAATCCCATTAAAAAGCGGG 3325
                          ii  v  i     ----------------   i  v   ?    ii   
  L1M4_orf2#LINE/    790 AATAAAAAGACAAA----------------TAACCCAATTWAAAAATGGG 823

  chr1_116106852_   3326 CAACAGATGTGAATAGACATTTCTCATAAGAAGACATATAAATGGCCTAC 3375
                            vi   v                vv       i   i        v i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_116106852_   3376 AGACATGTGAAAAAATGTTCAACGTTGCTAATCAT 3410
                          ii  ii      i   i     i ii????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (55 / 24)
Gap_init rate = 0.01 (3 / 319), avg. gap size = 8.33 (25 / 3)  


1005 29.96 8.21 3.15  chr1_116150187_116151905.rev      502  1232 (487)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_116150187_    502 AAAAGTTATGTGGAAGAATA-AAGGGATCAAAATTAGCCAAGA-AAT-TT 548
                             v i  i     --  i-      i v i v       i -   -  
  L1M4_orf2#LINE/    141 AAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_116150187_    549 AAAGGAGTAAGAATGAGGAAGATGGACTTATACTACCAGATATCAAGACT 598
                         i  ii  -     ii i vv iv     i i   v  vi  v    i   
  L1M4_orf2#LINE/    189 GAAAAAG-AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_116150187_    599 CA-TAAGCAGCTATA----TTAAGATAGGGTGTTACTAGTGTAGACACAA 643
                         i -  viv     i ---- i    i  v   v    i ii  iiv i i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_116150187_    644 AC---TGG-TCAATGGATTAGAATAGAGAACCCAGAAAGAGACCCTTGAA 689
                           --- i -        v      v    ii       v i    v iv 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_116150187_    690 TATATAG--AACTTTGATATTTGAGATAGCTGGTATGGAAGGTCAGTAGG 737
                          v   i --  --     v  i  v vi v  vi v ivviv   i i  
  L1M4_orf2#LINE/    338 TTTATGGTCAA--TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_116150187_    738 GAAAAAAGA--CAATTTAATAAATTAACCTGGGGGACGGGGGAAAAGAAT 785
                             i  v -- vv  i  i    -------  v vi   iv  vv i  
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAAT-------GGTGCTGGGACAACTGGAT 428

  chr1_116150187_    786 AGCTACGGG-AAAAAAGTGAAATTAGTTCTTAAGTTCACACCACACACAA 834
                          ? i  iv -    i i    i  i vi iiv vi        i i    
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_116150187_    835 AAAT-AATTACAGATTACTCAGGGATAACTAA---CAAAAGCTAAGCTTC 880
                             -  i vv i  viv   ?i  i--    ---i  i      ivi v
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGAC--CTAAATGTAAGAGCTAAAACTA 526

  chr1_116150187_    881 TATCTTTTTTTAAGGAGCGAAGATAAGTAAATATCCTTCTAATCTTGAGA 930
                           vvvi i  --  i  vi  v   i ?iv v   i iv i i    i v
  L1M4_orf2#LINE/    527 TAAAACTCTT--AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_116150187_    931 TAAGAAA---------AAATTTAGCAACAAAAATGCTAACCATAAAATTA 971
                           i v  --------- i  v ii  v     iii v i v i    vv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_116150187_    972 ACAATTGATAAAT-G----TTATTATA-TTAAAAACTTCTGTTCATCAAC 1015
                          v   v       - ---- i  i v -          i   v v    -
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA- 673

  chr1_116150187_   1016 AGAACCTTAT---GAATGTGAAA-GACAACTTACAAATTGGATTAGAAAA 1061
                           i  vi   ---   v      -      ii   i v   i--      
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG--AGAAAA 721

  chr1_116150187_   1062 AGATATTTTCAATACATGTAACTGATGATGAATTTATATC-AGGATCATA 1110
                         ---     v   vv   i  v     i v i i  i    -  i  -   
  L1M4_orf2#LINE/    722 ---TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT-ATA 767

  chr1_116150187_   1111 TTAAAAACTCCTTCAAAGTTGTCACAAACA-ACAGACATTCCAGAAGAAA 1159
                          v  i     i v   vvivi v i   v -   i i vi   ivv?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_116150187_   1160 AATAG-CAAAAGCCATACATAGGCATTTTACAGAAGAGGA---------- 1198
                            i -    i viv iv    i     iv vi    i  ----------
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_116150187_   1199 ---AATAA--ACATAAAAAGATGTTCAG--TCAGAGGGAAT 1232
                         ---     --    i        i   i--   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (124 / 91)
Gap_init rate = 0.04 (34 / 768), avg. gap size = 2.44 (83 / 34)  


2979 26.67 1.44 0.56  chr1_116217014_116222205     3807  4706 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_116217014_   3807 TGTAAACACATCCCATGCTCATGGATAGGTAGAATCAATATTGTGAAAAT 3856
                           v   v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116217014_   3857 GACCACACTGCCAAAAGCAATCTACAAATTCATTGCAATCCCCATCAAAA 3906
                          i v i   v  v   vii       i     vi        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_116217014_   3907 TACCACCATCATTCTTCACAAAATTAGAAAAAACAATTCTAAAATTCATA 3956
                          v   v vv v  i  ii  i  v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_116217014_   3957 TGGAGCCAAACAAGAG-CCCACA-TACCCAAAGCAAGTCTAAGCAAAAAG 4004
                             i-- vi    i -    v -  v     i   vii i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_116217014_   4005 AACAAATCTGGAGGCATCACACCACCTGATTACAAACTATACTGTAGGGC 4054
                               vi      vv      iv  ii   v    viv    ii ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_116217014_   4055 CATAGTCAACAAGCCAGCATGGTACTGGTATAAAAATGG-TACATAGATC 4103
                         i i   v v    v   ii         i    ii  i -i i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_116217014_   4104 AATGGAACAGGATAGAGAACCCAGAAATAAACCCAAATACTTACAGCAAA 4153
                                i  i  v    ii               v i i   ii iv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_116217014_   4154 CTGGTCTTCAAGAAAGCAAACAAAATCATAAAGTGGGGAAAGGACACCCT 4203
                         i  i i   i v  i vviv   i i   vv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_116217014_   4204 TTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGGGAATGA 4253
                                              i  i   v  ?       i iii      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_116217014_   4254 AACTGGATCCTCATCTCTCACCTTACATAAAAATCAACTCAAGATGGATT 4303
                          ii    i  ii i   v    v  i i      i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_116217014_   4304 AAGGACTTAAATCTAATGCCTGAAACTATAAAAATTCTAGAAGACAACAT 4353
                          ?i   i     v   viv  i           v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_116217014_   4354 TGGAA-AAACCATTCTAGACATTC--TTAGGCAAGGATTTCATGACCAAG 4400
                         v  ?i-   i -   vv   v  v--        v i    v iivi v 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_116217014_   4401 AATCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGTTGAGACTTAAT 4450
                          vv         v v    i    iv   i   i   iv vi     v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_116217014_   4451 TAAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAGACA 4500
                         i   v v  i i      ii vv    i iv  vi   iv i   ii v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_116217014_   4501 GACAATCCACAGAGTGGGACAAAATCTTCACAATCTGTACATCTGACAAA 4550
                              i       i     v     v  ii   viii  i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_116217014_   4551 GGACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGTAA-GAAAA 4599
                              vi          v  i  v      vv    v   i   -i    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_116217014_   4600 CACAA----TCGCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCT 4645
                         v    ----i vv  i?    i     v     iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_116217014_   4646 CAAAATAAGGACAAACAAATGGCCCAACAA--ACAAGAAAAAATGCTCCC 4693
                          v   v   - i v          -  i  --   v     i      vv
  L1M4_orf2#LINE/    848 CCAAAGAAG-ATATACAAATGGCC-AATAAGCACATGAAAAGATGCTCAA 895

  chr1_116217014_   4694 CAGCACTTTGGGA 4706
                           v  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (136 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


 394 25.18 6.47 5.04  chr1_116296776_116301649     2797  2935 (1939)    L1M4_orf2#LINE/L1        6   146 (762)  

  chr1_116296776_   2797 AGAT-TACCATGCTTATGGACCAGAAGA--------TATTAAGATATCAG 2837
                             - v     i i     iii     -------- i       iv  i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_116296776_   2838 CACTCCCCAAACTGATTTATCTTCATTCAGTGTGATATCAGTAAAATTTC 2887
                         i          i    i  ivv--     ii ii  vi vi v   v i 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAG--ATTCAACGCAATCCCTATCAAAATCC 103

  chr1_116296776_   2888 CATCAGTCTTCTTTTGGTGATAGAAATTGACAAGTTAATACTAAAACT 2935
                           v v i   -     ----i             i i  v      i 
  L1M4_orf2#LINE/    104 CAGCTGCCTT-TTTTG----CAGAAATTGACAAGCTGATCCTAAAATT 146

Transitions / transversions = 2.18 (24 / 11)
Gap_init rate = 0.04 (5 / 141), avg. gap size = 3.20 (16 / 5)  

 432 24.77 0.92 0.92  chr1_116296776_116301649     3231  3339 (1535)    L1M4_orf2#LINE/L1      132   240 (668)  

  chr1_116296776_   3231 GCCAATACTAAAATTTTTATGGAAATTCAAAGGATCTGGACTATCCAAAA 3280
                           ii  v        iv         v   i   i ii  v  v      
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_116296776_   3281 TAATTTTATCAAGGAAAAACAAAGTTGAAGAACTTA-ACTTACCTGATTA 3329
                         i   i  ivv  i   i          i  i   i -    -  ii   v
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT-CCCAATTT 230

  chr1_116296776_   3330 TAAGACTTAC 3339
                         i  i      
  L1M4_orf2#LINE/    231 CAAAACTTAC 240

Transitions / transversions = 2.38 (19 / 8)
Gap_init rate = 0.02 (2 / 109), avg. gap size = 1.00 (2 / 2)  

 508 20.17 5.04 0.00  chr1_116296776_116301649     3643  3761 (1113)    L1M4_orf2#LINE/L1      232   356 (552)  

  chr1_116296776_   3643 AAGACTTATAATGAAGTTACATTAATCAAGACAGTACAGTATTGGCATAG 3692
                           i     iv ii   i    v             iii   i       i
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_116296776_   3693 GAATGTCTCTATAGAT-AATGGAACAGAATTGAGTAT---GAAATAGAAC 3738
                          i  ivviv       -       i         vi ---      i v 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_116296776_   3739 CA--CATATATGGTCAATTGATTTT 3761
                           --   v                 
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 2.00 (6 / 3)  

2004 22.43 6.07 1.29  chr1_116296776_116301649     3838  4381 (493)    L1M4_orf2#LINE/L1      339   908 (0)  

  chr1_116296776_   3838 TCATGGTCAATTAATTTTTGATGAAAATGACATGTTAATTCAATGAGGAA 3887
                          i          i     i  ii iii  v  v viv        i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_116296776_   3888 AACATAACCTTTTTAAAAAACGGTGCTGAAATAACTGGATCTCCATATAC 3937
                          iv   ii     i  v   i       ii i        v?   i  i 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_116296776_   3938 AAAA-AATATAACTTCAACCTGTAAATCACATTATATGCAGTAATAAACT 3986
                             -   i-  v  vi   iv  vv     ii    i  iv   v    
  L1M4_orf2#LINE/    439 AAAAGAATG-AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_116296776_   3987 TGAAATGGTTGTTTAACTGAAATGTAAATGCTAAAACTGTGTTGTACAAC 4036
                         ii      v vv?vi  iv        iv         i ----- v   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-----AAAAC 532

  chr1_116296776_   4037 TACTAGAAGAGAACATAGGAGAAAAATCTTAGTGACTTTGAGTTAGGCAA 4086
                          vi       i        ? v   -    v     i   i         
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_116296776_   4087 ATATTTCTTAACTAGGACACCAAAAGCACAAA----AAGAAAAAAAATTC 4132
                         vvi       iv  v                i----  i i       vv
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_116296776_   4133 ATGACCTAGACTTCAT-AAAGTTAAAAACTTTTGCTTTTTAAAAGACTCT 4181
                           i vi i        -   i             ivi  i   i   v  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_116296776_   4182 ATTACAGAAATGAAAAG-TAAGACACAAACTGGGAGAAAATATCTGTAAA 4230
                           i vii  i       -i  vv    i v             i  i   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_116296776_   4231 ACATGTATCTGATAAAAGACTTGTATCCAGAATATAGAAAGGACTCT--- 4277
                         v   i          ii                   v    i     ---
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_116296776_   4278 -----AATAATAAGGA-----------------AAAAATAGGCAAAAGAT 4305
                         -----        ii -----------------      i      i   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_116296776_   4306 TTGAATGGATGCTTCTCCAAA-AAGATATAAAAATGGCAAATAAATATGG 4354
                               i  iii         -        v       v     ii iiv
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_116296776_   4355 GGAAAGTTGTTCAACATCATCAGACAT 4381
                          i    v  i         ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (76 / 43)
Gap_init rate = 0.02 (10 / 570), avg. gap size = 4.00 (40 / 10)  


3220 27.31 0.44 0.44  chr1_116307248_116312481     3834  4741 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_116307248_   3834 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3883
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116307248_   3884 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3933
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_116307248_   3934 TACCAATGACTTTCTTCACACAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3981
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_116307248_   3982 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 4031
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_116307248_   4032 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4081
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_116307248_   4082 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4131
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_116307248_   4132 AATGGAACAGAAC--AAAGCCCTCAGATGTAACGCCGCATATCTACAACT 4179
                                i    i-- i  i  --   vi   vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_116307248_   4180 ATCGGATCTTTGACAAAGCTGAGAAAAACAAGACATGGGGAAAGGATTCC 4229
                          viv   i  i     i v  vv  i v  vvvv          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_116307248_   4230 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTACAAAGCT 4279
                           v  i  i              v      v  ?   i v i v  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_116307248_   4280 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4329
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_116307248_   4330 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACGCTAGAAGAAAAC 4379
                          i ?    i    i  v   v       i      vivi           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_116307248_   4380 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4429
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_116307248_   4430 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4479
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_116307248_   4480 TTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGTGAAG 4529
                          i   v v  i i   i  ii vv       v    i  vv i      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_116307248_   4530 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4579
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_116307248_   4580 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4629
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_116307248_   4630 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 4679
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_116307248_   4680 TCAAAAGAAGACATTTATGTAGCCAACAGACACATGAAAAAATGCTCATC 4729
                           v        i  vi vi i     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_116307248_   4730 ATCACTCGCCAT 4741
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2642 25.13 2.36 4.83  chr1_116340741_116345064.rev     2903  3833 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_116340741_   2903 TGAAAACACATCCCATACTCATGGATTGGAAGAATCAATATTGTGAAAAT 2952
                           i   v i       ii               v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116340741_   2953 GACCATACTGCCGAAAGCAATCTACAGATTCAATGCAATTCCCATCAAAA 3002
                          i v     v  v   vii              i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_116340741_   3003 TACTCACATTG---TTTTCACAGAACTAGAAAAAA-AATCCTAAAATTCA 3048
                          - i  -ii  ---    ii     v v  v  iv-i             
  L1M4_orf2#LINE/    101 T-CCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_116340741_   3049 TATGGAGCCAAAAAAGAGCTCAAGTAGCCAAAAAGAATCCTAAGCAAAAC 3098
                               iviiv  ii  v ivi i         v-    i i -------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AATCTTGA------- 190

  chr1_116340741_   3099 AAACAAAAAAAACACACACAAAACAAAACAAAACAAACAAACATCTGGAG 3148
                         ----    i  i--------------      ii-----------     
  L1M4_orf2#LINE/    191 ----AAAAGAAG--------------AACAAAGT-----------TGGAG 211

  chr1_116340741_   3149 GCATCACATTGCTGGACTTCAAGTTATACCACAAGGCTATAGTTACCAAA 3198
                          vv     i v ivi i     iviv   i    i    i   v i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_116340741_   3199 ACAGCATAGCACTGGTATAAAAGTAGGCACACAGACCAATGGAACAGAAT 3248
                             ii i i     i    iii   i  i i   i        i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_116340741_   3249 AGAGAATGCAGAAAGAAAGCCAGATACTTACAACCAACTAATCTTCAGCA 3298
                         v    i v      v   v   v i i   iiii   i i  i   ii  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_116340741_   3299 AAGCATACAAAAAC-ATAAATTGGGGAAGGAACACCCTACTTAATACATG 3347
                          i -i i v  i  -  vv v       i   i vi  vi i  i v   
  L1M4_orf2#LINE/    362 AGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_116340741_   3348 GTGCTGGGAAAACTGGCTAGCCGCCTGCTGAAGAATGAAACTAGATTTCT 3397
                                  v      v  ?  i v   vi         ii i  iii  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_116340741_   3398 ATCTCAC-CC-TATACAAAAATCGACTTAAGATGGATCAAAAATTT---- 3441
                          i     -  -           ii   i  i        ? i ii ----
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_116340741_   3442 -TAAGACCTGAAATCATGAAAAGTCT-AGAAGATAACCTTGGAAAAAGTC 3489
                         -     v  i   ii  -    v   -      v   v v  ?iv  i  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_116340741_   3490 TTC-TGGCCAATGGCCTAGGCAAAGATT-CTTGACTAACACCCCAAAAGA 3537
                            -  i  v-   vi       v i  -   iiv  vv  v       v
  L1M4_orf2#LINE/    560 TTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_116340741_   3538 AAATGGAACAAAAATAAAAATAAATAAATGGTACCTGATTAAACTAAAAA 3587
                          v v v       iv       i      v v  i v  i   v v    
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_116340741_   3588 GTTTCTGCATAGCAAAAGAAATAATCATCAGAGTAAACAGACAACCCACA 3637
                         ii  i  iiivv    i  v iv    vv i   i  v            
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_116340741_   3638 AAATGGGAGAAAATATTTACAAACTATGCATTCAACAAAGGACTATTATC 3687
                         i                 i    ii  ii  iii i  i     vv    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_116340741_   3688 CAGAATCTATAAGAAACTC----AAATCATCAAGAAAAAAA--AATAACC 3731
                               v     ii     ----  v   vi  v     i --       
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_116340741_   3732 CA-TTTGCAAGTGTGCAAATGACATGAATAGACATTTATCAAGAGAAGAT 3780
                           -  ?iv  i  v     v  iv             v  v i       
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_116340741_   3781 ACGCAAATGGGGAAGAAAAATGTGAAAAAAAAAAGCTCAACATCACTAAT 3830
                          ii       vv  v  iv ii      i v---           ?????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGAT---GCTCAACATCAZZZZZ 905

  chr1_116340741_   3831 CAC 3833
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.67 (144 / 86)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.05 (67 / 22)  


3705 22.97 1.67 0.45  chr1_116442537_116444806.rev      883  1779 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_116442537_    883 TGGAAAGATATTCCATGTTCATGGATTGGAAGAATAAATATTGTTAAAAT 932
                                    i                     v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116442537_    933 ATCCTTACTACCCAAAGCAATTTACAGATTCAATGCAATCCCTATCAAAA 982
                         iv vv    v      vii  i           i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_116442537_    983 TACCAATAACGTTCTTCACAGAAATAGAGAAAAACT-ATCCTAAAATGCA 1031
                          v   iivi v  i  ii       v  v  i--  -          v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_116442537_   1032 TATGTAACCCCAAAAGACTCAGAGTAGCCAAAGCTATCCTGAGCAAAAAG 1081
                             v  viv   ii   i    i        i v   i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_116442537_   1082 AATAAAACTGGCAGAATCACATTACCTGACTTCAAATTATACTATA---- 1127
                           i   ii   vi  v     i v  ii i      viv     i ----
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_116442537_   1128 -----TAACCGAAA-AGCATGGTACTGGCATAAAAACAGACTCATAAACC 1171
                         -----   i i i -  ii              ii i    vi   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_116442537_   1172 ACTGGAACAGAACACAGAACTCAGAAACAAATCCATACATTTATAGTGAA 1221
                          v     i    ivv   iii      i   i            i  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_116442537_   1222 CTCATTTTTGACAAAGGTGCCAAAAACATACATTGGGGAAAGGA--GTCT 1269
                         i v     i     i        i v   v  v         i --    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_116442537_   1270 CTTCAATAAATGCTGCTGAGAAAACTGGATATACATATGCAGAAGAATGA 1319
                         i     i     v     i  v         ?v  i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_116442537_   1320 AACTAGACCTCTATCTCTCATCATATATAAAAATCAAATCAAAATGTATT 1369
                          ii i    i   i   v  i      i      i  v        v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_116442537_   1370 AAAGACTTAAATCTAAGATCTCAAACTATGAAACTACTAAAAGAAAACAT 1419
                          ?    i     v     v  v       i     vi  i          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_116442537_   1420 TGGGGGAAACTCTCTAGCACTTTGGAGTAGGCAAAAATTTCTTGAGTAAT 1469
                         v  ? v   -   iiivv  i    iv       vii      iii  vv
  L1M4_orf2#LINE/    549 AGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_116442537_   1470 ACCTCACAAGTACAGAAAACCAAACCAAAAATTGACAAATGAGATCACAT 1519
                           vi  v   i   iiv   v   vv      v  i    vi  iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_116442537_   1520 CAAG-TTAAAAAGCTTCTGCACAGCAAAAGAAACAATCAACAAAGTGAAA 1568
                            i-       -   i  ii vv    i  v  v     v         
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_116442537_   1569 AGACAATCTACAGAATGGGAGAAAATATTTGCAAACTATCCGTTTGACAA 1618
                               i i                          ii  vii i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_116442537_   1619 GGGATTAATAATCAGAATATATAAGGAGCTCAAACAACTCTATAGGAAAG 1668
                             i vi  vi            i  i   vv       v   iv   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_116442537_   1669 AATCTAATAATCTGATT-AAAAATGGGCAAAATATCTGAATAGACATTTC 1717
                          iv v     i ii   -             iv  i              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_116442537_   1718 TCAAAAGAAGACATACAAATGGCAAATAGGTATAGAAAAAGGTGCTCCAC 1767
                           v        i           v    i i i vi     i     v  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_116442537_   1768 ATCACTGATCAT 1779
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (125 / 78)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


2660 18.97 1.68 16.82  chr1_116535142_116539705.rev     3004  4073 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_116535142_   3004 TAGAAAGACATCCCATCCTCATGAATTGGAAGACTTAATATTGTTAAAAT 3053
                          i      i       vi     i                       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116535142_   3054 GACAATACTACCCAGA-----CAACAGATTCAACACCATCCCTATCAAAA 3098
                          i       v    i ----- v           i v             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_116535142_   3099 TACCAAGGACATTGTTCACAGAAATAGAAAAAAAATTTTTTTTTTTAAAT 3148
                          v   ivvi v  v  ii       v  v  i-----i vv ii v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAAT 145

  chr1_116535142_   3149 TTGCATGGAAACACAAAGGACTCGGAAAGGATAGCTAAAGCAAACCCGGG 3198
                          iii       ii   i    i i   ----    i   i   v ii i-
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAA----TAGCCAAAACAATCTTGA- 190

  chr1_116535142_   3199 CTAAAAGAATAAAGCCAGAGGTATCACTACCAGACCTCAAAATATACTTT 3248
                         --       v  -------------------------    i -------
  L1M4_orf2#LINE/    191 --AAAAGAAGAA-------------------------CAAAGT------- 206

  chr1_116535142_   3249 AGGTCAGGTGCAGTGGCTCATGCCTGTACTTTCAATACTTTGGGAGGCCA 3298
                         --------  v  - i    ------------------------------
  L1M4_orf2#LINE/    207 --------TGGAG-GACTCA------------------------------ 217

  chr1_116535142_   3299 AGGCAGGGGGATCATTTGATCCTAAGAGTTTGAGACCATCCTGGGCAACA 3348
                         ------------  i  ---------------------------------
  L1M4_orf2#LINE/    218 ------------CACTT--------------------------------- 222

  chr1_116535142_   3349 TAGTGTGACCCTGTCTCTATTACAAAAAATTTTTAAATTAGTTTTTAAAA 3398
                         --------   ----------------     ------------------
  L1M4_orf2#LINE/    223 --------CCC----------------AATTT------------------ 230

  chr1_116535142_   3399 ACAAAACAAAATATACTACAAAGCTGTAGTAACCAGAATAGCATAGTACT 3448
                         ------     iv            ii     i  ii i  ii i     
  L1M4_orf2#LINE/    231 ------CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_116535142_   3449 GGCACAAAAACAAGTACACAGACCAATGGAATACA---GAGAATCCAGAA 3495
                             i  ii i iii i i   i          v ---    i       
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_116535142_   3496 ATTAATT--TACATGTATCAAGCAACTGATTTTTGACAAAGGTGCCAAGA 3543
                           v  ii--     v   -iiv   i       i     i          
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTAT-GGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_116535142_   3544 ACAATCATTGCAGAAAGGACAGTCTCTTCAATAAGCAGTGCTGGGAAAAC 3593
                         v  v   v  vi     i i     i     i  iii         v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_116535142_   3594 TGGATATCCACACGCAGAAGGATAAAACTACACCCCCACCTCTCACCCTA 3643
                               ?     i   i   i  i  ii iv     i     v    v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_116535142_   3644 TAGAAAAATTAACTCAAAATAGATCAAAGACCTAAATGTAAGACCTGAAA 3693
                           v                 i     ?                v  i   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_116535142_   3694 CAATAAAACTTCTAGAAAGAAACACAGGGG-AAGTGTTTCAGGTTATTGG 3742
                          v        ii     ii     i   ? -  i -i   iv viv    
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGG 572

  chr1_116535142_   3743 TCTGGGAAAATATTTTATGAATAAGACCTCAAAAGCACAAGCAACACAAG 3792
                         vi i  v  vvi   iv ii   v   vi                 v   
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_116535142_   3793 GAAAAATAAATGAAATTATACT------AAATGAAAAAGCTTCTACACAG 3836
                         i       i  -     iv   ------    v     -   i iii vv
  L1M4_orf2#LINE/    623 AAAAAATAGAT-AAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTT 670

  chr1_116535142_   3837 CAAAGGAAACAATCAACAGAGTAAGAAGACAACCTACAGAATATGAGAAA 3886
                                v  v     v i   i i         i       iv      
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_116535142_   3887 ATATATGCAAACTACTCATCCAACAGGGGATTAACATCCAGAATATGCAA 3936
                             v      ii ivi   ii i i    i vii           ii  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_116535142_   3937 GGAACTCAATCATCTCAACAGGAAAAAAATAAACCATCAAATTGAAAAAT 3986
                         i      vvv  v     i iv     i i   iv i v    ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_116535142_   3987 GGGTGAAAAATTTGAATAGACATTTCTCAAAAGAAGACATACAATTGGCC 4036
                            ii  ii                   v        i      v     
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_116535142_   4037 AACAAATACATGGAAA-ATGCTCAACATCATTAATTAT 4073
                           i  ii     i   -             ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (135 / 64)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 9.90 (198 / 20)  


4238 15.73 4.83 2.81  chr1_116558502_116560728.rev      847  1736 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_116558502_    847 TGGAAAGATGTACTGTGCTCATGGATTAGAAGGCT-AATATT---AAGAT 892
                                  i v ii  i         i    i  -      ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116558502_    893 AGTAATATTCCCAAAATTGATCTTCAGGTTCAGTGCAATCTCACTCAAAG 942
                         i i    i    v          v   i    ii      i vv     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_116558502_    943 TCCCAGCTGCCTGTTTTTTGTTTTTTTTTTTAAAAAAAACATATATAGAC 992
                                     --      i------------- i   ------ v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT--TTTTTGC-------------AGAAA------TTGAC 129

  chr1_116558502_    993 AAGCGAATTCCTCAACTTCATATGGAAGTTCAAGAGACCCAGAATAGTCA 1042
                             vi  -   v  v           i v    i            i  
  L1M4_orf2#LINE/    130 AAGCTGAT-CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr1_116558502_   1043 ATGCAATCTTGAGAAATAAGAACAAAGTTGTAGGACTCATATGTCCTGAT 1092
                          vi         i   v             v        i iv   ii  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_116558502_   1093 TTCAAAACGTACTACAAAGCTATAGTAATGAAGACAGTATGGTACTAAAA 1142
                                 v             i      v        i       iiv 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_116558502_   1143 TAAGCATAGACACATAGATTAATGGAATAGAATTCACAGTCCAAAAAAAA 1192
                             v       i      i              v v      i   v  
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_116558502_   1193 GTCCCTTACATTTATGGTCAATTGATTTTTGGCCTGGCTGAAAAG-CCAG 1241
                         i-   v                       i i vv  v  vv   -   -
  L1M4_orf2#LINE/    329 A-CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA- 376

  chr1_116558502_   1242 TTCAGTGGGGGAAATAATATTCTTTTTAACAAATA-TGCTGGGACAACTG 1290
                             i     -   v    v      i       i-              
  L1M4_orf2#LINE/    377 TTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_116558502_   1291 GATATTCACACACAAAAGAATAAAGTTGGGTCCCTACCTCACACCATATA 1340
                             ?i    ii         i       ii                   
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_116558502_   1341 --AAAGTTGATTAAAAATGGATCATATACCTAA-TGTTAGAGCTAAAAGT 1387
                         --   i  i i v           ? v      -   v          v 
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_116558502_   1388 ATAAAACTCTTAGAAGGAAACATATTTGTAA-TCTTTGTGATCTTAAATT 1436
                                         i       vv?    -    i    i   iii  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_116558502_   1437 AGGTGATTTGTTTTTAGATATGAAATCAAAAGTACAAGCAACAAAAGAAA 1486
                            ii  vvv  i          v i      i                 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_116558502_   1487 AA-TAAGTAAAT------------AAGTTAAAAATGTTGGTGCTTAAAAG 1523
                           -  ii     ------------  i       iv  v      v    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_116558502_   1524 AACACTTTTAAAAAAGTAAAAAGTTCACTCACTAAAT------------T 1561
                         i     v i  i     i     viv  i   vi   ------------ 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_116558502_   1562 TGCAAATTATATCTTTGATAAGGGACTTAGTTCTAGAATATATAAAGAAC 1611
                                i    v i             ivv  i                
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_116558502_   1612 TCTTACAACTCAACAATGAAAAGACAA----TCTAATT---AAATGAGCA 1654
                                      i   i         ----i i    ---     i   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_116558502_   1655 AAGGATACAAACAGACATTTCTTCAAAGAAGATATGCAAAAGGC-AATAA 1703
                               vii  i          i            i    v   -     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_116558502_   1704 GCACATGAAAAGATACTCAATATCATTCACTAC 1736
                                       i     i    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (86 / 51)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.40 (68 / 20)  


 275 19.18 21.92 0.00  chr1_116604029_116607123     1601  1673 (1422)    L1M4_orf2#LINE/L1        1    89 (819)  

  chr1_116604029_   1601 TGGAAACACATCTCATGTTCATGGATTAAAAGA--------TGT------ 1636
                               v i   i              ii    --------   ------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116604029_   1637 --CAATACCACCCAAAGCAATGTACAAATTCAATGCTAT 1673
                         --      iv      vii  v    i      i  v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.02 (2 / 89), avg. gap size = 8.00 (16 / 2)  

 249 19.61 0.00 0.00  chr1_116604029_116607123     1676  1726 (1369)    L1M4_orf2#LINE/L1       37    87 (821)  

  chr1_116604029_   1676 AAAATTATTAAGGTGTCAATACTACCCAAAGCAATGTACAGATTCAATGC 1725
                           v   i     i  v       v      vii  v           i  
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chr1_116604029_   1726 A 1726
                          
  L1M4_orf2#LINE/     87 A 87

Transitions / transversions = 1.00 (5 / 5)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.00 (0 / 0)  

3489 18.49 4.00 4.00  chr1_116604029_116607123     1727  2602 (493)    L1M4_orf2#LINE/L1       33   908 (0)  

  chr1_116604029_   1727 ATTGAAAATTGTTAAGGTATCAATATCACCCAAAGCAATGTACAGATTGA 1776
                          i v  v         i iv     iiv      vii  v        v 
  L1M4_orf2#LINE/     33 ACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCA 82

  chr1_116604029_   1777 ATGCAATCCCTGTCAAAATATCAATGATGTTTTTTGCAGAAATAGGAAAA 1826
                          i         i       vi  iiviiv              -v  v  
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAA 131

  chr1_116604029_   1827 CCCCATGTAAAAACTCATATGGCATCTCAAGGGACCATGAATAGCTGAAA 1876
                         v iv  viv    i        v viv         vv       ii   
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_116604029_   1877 CAATCTTAAGGAAAAAGAACAGAGCTGGAGGAATCATACTTTCTGATTTC 1926
                                i ii  i       i  i       v   i    i ii     
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_116604029_   1927 AAAACT-ACTACAAAGCTACAGTAATCAAAGCAACGTGATATTGACACAA 1975
                               -                      ii  ii   i  i  i  i  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_116604029_   1976 G-ACAGACATATAGACCAATGAAAAAAAATAAAGAGCCCAGAAATAAACT 2024
                          - i           i     i  v i   vi    i            i
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_116604029_   2025 CTTGAATAAATGGTTAAATTACTTTTGACAA---TGCCAAGACCATTCAA 2071
                          v iv  vv     i  v v i   i     ---                
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_116604029_   2072 TGGGGAAAGTACAGTCTTTTCAACAAATGCTGCCAGGGAAACTGGATATC 2121
                                  v i                 v   ii  iv         ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_116604029_   2122 CAAATACAAAAAAGAAAAGAAAAGAAAAGAAACTGGACCATTACTTGACA 2171
                           v  i     i ------------- v   ii      vi   i v   
  L1M4_orf2#LINE/    432 CACATGCAAAAGA-------------ATGAAGTTGGACCCCTACCTCACA 468

  chr1_116604029_   2172 TCATAT-CAAAAAGTTAATTCAAAGTGGATCAAAGACCTAAATTTAAGAC 2220
                         i     -      -    i     i       ?          v     v
  L1M4_orf2#LINE/    469 CCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_116604029_   2221 CTAAAACTATAAAACTCTTAGAA---AACACAAATGGCAAAACTTCACAA 2267
                                                ---    i ii? -i   v    iii 
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG-TAAATCTTCGTGA 566

  chr1_116604029_   2268 CATTGGATTTGGCAATGAATTCTTGAATATGACACCAAAGGCACAAATAA 2317
                          v    i  v       iv     ii             i      ii  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_116604029_   2318 CAGAAGAAAAAATAGACAAATAGAACTTCAT-AAAATTTTTTAAAA---T 2363
                           i             i    v i       -      ----    --- 
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT----AAAAACTT 662

  chr1_116604029_   2364 TTATACT-CAAAAGAGAATATCAACAGGGTGAAAAGGAAAGCCACAGAAT 2412
                           i i  -    i  v v      v ii        iv  v         
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_116604029_   2413 GGGAGAAAATATTTGCAAATTGTGTATCTGATAAGGGTTTAATATTCAGA 2462
                                             ii i             vi vi   i    
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_116604029_   2463 A---------AACTCCTAAAACTCAATAACAACAAAAATATGACAAATAT 2503
                          ---------     i  v          i  ---   ---        -
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAA---AAA---GACAAATA- 805

  chr1_116604029_   2504 AGTAAAAAACTCAACC-AAAATTAGGCAAAGGACTTATATAAGCATTTC- 2551
                         --------  i   ii-    v i         i  iv   ii      -
  L1M4_orf2#LINE/    806 --------ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_116604029_   2552 ---------ATATACAAATGGATAATAATCATATGAAAAGATGCTCAA-A 2591
                         ---------            vi     v  i                - 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_116604029_   2592 TCACTAATTAT 2602
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.84 (103 / 56)
Gap_init rate = 0.02 (20 / 876), avg. gap size = 3.50 (70 / 20)  


 761 34.19 4.68 3.67  chr1_116612024_116613921.rev      514  1411 (487)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_116612024_    514 GAAAAGA---CCTAAATAAATGACTAGGGCAATTTATTGTTGCTATTATG 560
                          i     ---  i vi vv   iv v  ivi i   v i   i  vv   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_116612024_    561 TCATTTGTCTCCAGATTGTTTTATGTATTTCATGACAATTCCAATCAAAA 610
                         v  v vv  i   i    v i  iiv   iv i -    i  v       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACG-CAATCCCTATCAAAA 100

  chr1_116612024_    611 TCACAGTAGGAATTTCTG---AAATTATGGTAAACTGATTTTAAATTTTA 657
                           v   iv vvv   i  ---     -- ii  i     ii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr1_116612024_    658 TAAGAAAGCATAAAGGCTCTTGAGTAACTAAG-CAATTTTGAAAAAGAAC 706
                           v i  iiii  i  vi iv  i  i i  i-    i           v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_116612024_    707 AAAAGAAT---AGAAC---CATTTTACTAGAAAAT---GAGATTTG--AG 745
                           v i i ---  i  ---  i  iv -----   ---i i i  i-- v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCC-----AATTTCAAAACTTACTAC 243

  chr1_116612024_    746 AAAGACATAGTAACTGATGTTATAAAGTTTAGGTGCA-GAATAAGCAAAG 794
                             vi i     iii viivi ivi  viv  iii - i   ii  v v
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_116612024_    795 AGACGAAAGGGA-AAAATGAAAAGTCCCCAAATCAAACTGTGCATCTGTG 843
                            iv  v  i - i   vi i     vv    v  v ii i   i i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_116612024_    844 AAAAATAAGTAAT----GATGGGGACAGCTTGACAAGTGCATAGCAAAAG 889
                         ivv   --- i  ----  iii  iiiv vv   v v vv  i vi    
  L1M4_orf2#LINE/    344 GTCAAT---TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_116612024_    890 AAAAGGCCAATTTAGAAAATACTTCAGAGAAAA--GTATTACTATAGGGA 937
                           v  v iv-  i iv    iv v v i  v  -- v  v? i i v v 
  L1M4_orf2#LINE/    391 AATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_116612024_    938 GAAAAATACAGTTGAATCCCTATATTGAC-CCATTTAAAAAAAA-AGCTC 985
                         i  i   iv     i i     iv i-  -    v  v     v- i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTC-ACACCATATACAAAAATTAACTC 488

  chr1_116612024_    986 AAAATGGAGTA-ATTTCAAAATGTGAAAGG-AAACCTGTAAAGTGAATAG 1033
                                 vi - vvi v      i i  v-   v  i    iivvv   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_116612024_   1034 AAGAAAATGTAGGGGAATATCTGTTTGCCCTTGGGTGGTAGAAAAA---T 1080
                                ii    ? v v    viv  v        --   iv  v--- 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT--TAGGCAATGGTT 586

  chr1_116612024_   1081 TATTAAATAAAGCCTCATATGCTCAAGCTGTCAAGAAATAAATTGACGAA 1130
                          v   i   vii vi  v v  v     viiv  ii  v    v  ii  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_116612024_   1131 TTGTACACTAATCAAAAATGAAAGACTT--GTG-TTCAATGAAGGGCATC 1177
                            v  -i v       - v   i    --   -     ---   i  ii
  L1M4_orf2#LINE/    637 TTGGAC-TTCATCAAAA-TTAAAAACTTTTGTGCTTCAA---AGGACACT 681

  chr1_116612024_   1178 GTGAACAAAGTTAACAGTGACAAGTGACTGG-TGACATTCTAGAAGTCTT 1226
                         i v  v     v  v  --    viv  v i-  iv ----ii  i v  
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAG--ACAACCCACAGAATGGGA----GAAAATATT 725

  chr1_116612024_   1227 TGCAATGCCTAAAACTTTAAAGGTATCAATAGCTAGAATGTACCAGAGAT 1276
                              vv v  v v  vvv    v iivi  v i     i  iv iii i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_116612024_   1277 TAATGCAGGTCAGCAATAATAAAGATAGAAAAAAGTGATAGAAAAAAAGA 1326
                          vv i  iv   ii     -     i -  v  vvii  v?     vi i
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAA-AAAGACA-AATAACCCAATTWAAAAATGGG 823

  chr1_116612024_   1327 C----GATGCGGATAGGCAATTCACAGAAGGGGA-ATCCTGAGTGGTTTA 1371
                          ----   vi i    i  v   v vi   ii  -  v -i i   iiv 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC-AAATGGCCAA 872

  chr1_116612024_   1372 TAATCTCCTGAAGACATAGATACTCAACCTAACCATCAAT 1411
                            v v v    i ----   i      v v ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAA----GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (163 / 141)
Gap_init rate = 0.04 (37 / 907), avg. gap size = 2.03 (75 / 37)  


3585 23.52 2.16 0.68  chr1_116780118_116783012.rev     1517  2396 (499)    L1M4_orf2#LINE/L1        1   893 (15)  

  chr1_116780118_   1517 TGGAGAGATATTCTATGTTCATAGATAGGAAGACTCCTTATTGTGAAGAT 1566
                             i      i i        i   v        ivv      v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_116780118_   1567 GTCAGTTATTTCCAATTTACTCTATAAATTCAGTGCAATCCCAAGCAAAA 1616
                          v  i vv ii    v  iv    i i     ii        v v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_116780118_   1617 TATCAGAAGTCATTTGTG--GATATCAGCAAACTGATTTTAAGGTTAA-A 1663
                          vi   vv i v   v  --  v  iii   i     ii   ii  v - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_116780118_   1664 TGGGCAGGCAAAAGACC-AGAATAGCCAGCAAAATATTGAA---GGAGAA 1709
                            iv v    ii    -          iv v   v     --- i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_116780118_   1710 CAAAATTGTAGGACTGATACTACTCAACTTCAAGACTTACTATAAAGCTA 1759
                             i   v      v i   v i   i     i        i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_116780118_   1760 CAGTAGTCAACATAGTGTGGTACTGGTGGAAAAATAAAAGACAAATAGAT 1809
                              i    v i             iiv  ii   ---    v      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA---GACATATAGAT 297

  chr1_116780118_   1810 CAGTGAATCGGAATAGAGAGCCCAGAAATAAACCAACATAAATATGGTCA 1859
                           i  i vii    v     i             v i i vv        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_116780118_   1860 ACTGATCTTTGACAAAGGAGCAAAGGCAATACAATGGAGCAAAGATGATC 1909
                          i    i  i     i  v  v   i v  v      i v  ii  ii  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_116780118_   1910 TTTTCAACAAATAGTGCTGTAACAACTGGACATCCACATGCAAAAAAATG 1959
                                     i      vi         i ?            i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_116780118_   1960 AATCTAAACACAGACCTTATGCCCTTCACAAAATTTTACTCAAAATGGAC 2009
                           vi ii  v vv    i ii  v vi      v  v            i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_116780118_   2010 CATAGATCTAAATGTAAAATGC-AAAACCATAAGACTCCTA-----AAAC 2053
                           ?   i          i -  -     i    i    i  -----    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_116780118_   2054 ATAAGAGAAAACCTAGATAACTTTGGAT---ATGATGACTTTTTAGATAC 2100
                            i ? v   i  vvi i  i    i ---iii   ii  i       i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_116780118_   2101 AACACCAAAGACATGATTCATGAAAGAAAGAATTGGTAAGCTGTACTTCA 2150
                         i        ii  ii viv ii       i   v i   ii  v      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_116780118_   2151 TTAAAATTAAAAACATT---GCTCTATGAAAGACAATTTCAAGAGAATGA 2197
                          i            v  ---   ii --  i    v v      i i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAAAGTGA 694

  chr1_116780118_   2198 GAAGCCAAGCCACAGACTGGGAGAAAATATTTGCAAAAGACACATCTGAT 2247
                         i   v   v       v                    vv i i       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_116780118_   2248 AAAAGACTGTTATCCAAAATATACAAAAAACTTTTAAAACTCAACAAGAA 2297
                           ii    vv      i      i   i    i   v       i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_116780118_   2298 AAACACAAACAACCCAATTAAAAAATGAGTCAAAGATCTCATCACACACT 2347
                            v     i         ?       i iv  i   i v vi v   i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_116780118_   2348 TCTCCAAGGAAGGTATACAGATGGCAAATAGGGATATAAAAAGATACTC 2396
                                i    i      i     v    i v i  i       i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.74 (129 / 74)
Gap_init rate = 0.01 (11 / 893), avg. gap size = 2.27 (25 / 11)  


2971 27.08 1.17 0.00  chr1_117040174_117045777     4259  5111 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_117040174_   4259 AAAATGGCCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCAT 4308
                           i     v     v  v   vii       i      i     i  i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_117040174_   4309 CAAGATACCACCATCATTCTTTGCAGAACTAGAAAAAAAAATCCTAAAAT 4358
                            i  v   v vv v  i         v v  v  ivvi          
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_117040174_   4359 TCAT---GACCCAAAAAAGACTCA---TAGCCAAAGCAAGACTAAGCAAA 4402
                             ---  vviiv  ii   i  ---        i   vvi i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_117040174_   4403 AAGAACAAATCTGGAGGCATTACATTACCCGACTTCAAACTATACTATGA 4452
                                  vi      vv i   i v   i i      viv     ii 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_117040174_   4453 GACCATAGTCACCAAAACAGCATGGCACTGGTATAAAAACAGACATATAG 4502
                         ii i i   v i   i    ii   i     i    ii i          
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_117040174_   4503 ACCAATGGAACAGAATAGAGAACTCAGAAATAAAGCCAAATACTTACAGT 4552
                          i        i     v    iii          v   v i i   ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_117040174_   4553 CAACTGATCTTCAACAAAGGAAACAAAAACATAAAGTGAGAAAAAGACAC 4602
                            i    i   i    i  viv   i v   vv i  i i   ii i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_117040174_   4603 CCTATTCAACAAATGATGCTGTGATAATTGGCTAGCCACATGTAGAAGAA 4652
                         i  v           i     v  i  i   v  ?       i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_117040174_   4653 TGAAACTGGATCCTCATCTTTCATCTTATACAAAAATCAACTCAAGATGG 4702
                             ii    i  ii i  iv  i v           i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_117040174_   4703 ACCAACGACTTAAATCTAAGACCTGAAACCATAAAAGTTCTAAAATGTAA 4752
                          i  ?v   i     v     v  i    i      v ii  i  viv  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_117040174_   4753 CGTTGGAAAAACTCTTCTAGATATTGGCTTAGGCAATGACTTCATGACCA 4802
                          i v  ?iv  v     vv  iv    v          ii   v iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_117040174_   4803 AGAACCCAAAAGCAAACACAACAAAAACAAAGATAAACAGATGAGACTTA 4852
                         v  vv         v vi        iv   i   i i i  vi     v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_117040174_   4853 ACTAAACTAAAAAGCTTCTGCACAGCAACAGAAATAATCAGCAGAGTAAA 4902
                          ii   v v    i   i  ii vv   vi  v iv    iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_117040174_   4903 AAGACAATCCACAGAGTAGGAGAAAATCTTTGCAATCTATATATCCAACA 4952
                                i       i i         v       vii       ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_117040174_   4953 AAGGACTAATATCCAGAATCTACAAGGAACTTAAACAAATCAGCAAGAAA 5002
                          i     vi          v  i  i     ivv    v   ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_117040174_   5003 AAAACAA----TCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATG 5048
                           i    ----i  v  i?    i     v     iv          v v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_117040174_   5049 CTCAAAAGAAGATATACAAATGGCCAACAAATACAAGAAAAAGTACTCAA 5098
                            v                       i  ii   v     ii i     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_117040174_   5099 TATCACTAATTAT 5111
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (140 / 87)
Gap_init rate = 0.00 (3 / 863), avg. gap size = 3.33 (10 / 3)  


3180 26.56 1.56 0.67  chr1_117228903_117235289     4995  5894 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_117228903_   4995 TGGAAGAACATTCCATCCTCATGGATAGGAAGAATCAATATCATGAAAAT 5044
                              ii i  i    vi        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_117228903_   5045 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5094
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_117228903_   5095 TACCAATGGCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5142
                          v   iiv  i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_117228903_   5143 TATGGCACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5192
                              v viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_117228903_   5193 AACAAAGCTGGAGGTATCACGCTGCCTGACTTCAAACTATACTACAAGGC 5242
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_117228903_   5243 TGCAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGACC 5292
                          i      i   i    ii    i    i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_117228903_   5293 AATGGAAAAGAAC--AGAGCCCTCAAAAATAATACCACACATCTACAACT 5340
                                v    i--    i  -- i      vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_117228903_   5341 ATCTGATCTTTGACAAACCTGAGAAAAACAAGACATGGGGAAAGGATTCC 5390
                          vi    i  i     ivv  vv  i v  vvvv          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_117228903_   5391 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5440
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_117228903_   5441 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5490
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_117228903_   5491 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5540
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_117228903_   5541 CTAGGCAGTA--CCATTCAGGACATAGGCATGGGCTAGGACTTCATGTTT 5588
                         v    ?-   --i -   iv   v v  vv i   v v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_117228903_   5589 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 5638
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_117228903_   5639 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5688
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_117228903_   5689 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACTCATCTGAC 5738
                          v  i     i                 v      ivii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_117228903_   5739 AAAGGGCTAATATCCAGACTCTACGAAGAACTC----AAATTTACAAGAA 5784
                           i  i  vi        v v  ii        ----  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_117228903_   5785 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAGCAGACACT 5830
                            i    ----   v  i?    i            v   ii     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_117228903_   5831 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAACGCTCA 5880
                             v        i  vi viii     i ii          i i     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_117228903_   5881 TCATCACTGGCCAT 5894
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


3356 26.21 0.55 0.55  chr1_117471760_117478177     5018  5925 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_117471760_   5018 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5067
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_117471760_   5068 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5117
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_117471760_   5118 TACCAGGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5165
                          v    vvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_117471760_   5166 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTGAATCCTAAGCCAAAAG 5215
                                viiv  ii  v  v v  v     ivv    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_117471760_   5216 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAATGC 5265
                                i      vv    i  v  ii i      viv        v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_117471760_   5266 TACAGTAACCGAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5315
                                 i i i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_117471760_   5316 AATGGAAAAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACC 5363
                                v    i--    i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_117471760_   5364 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5413
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_117471760_   5414 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5463
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_117471760_   5464 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5513
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_117471760_   5514 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5563
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_117471760_   5564 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGGCTTCATGTCTA 5612
                         v    ?i- v i -   iv   v v  vv i     v  i   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_117471760_   5613 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTTACAAATGGGATCTC 5662
                         vi            vvi          vv     vv i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_117471760_   5663 ATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGAA 5712
                           i   v v  i i   i  iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_117471760_   5713 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTTGTCTGACA 5762
                         v  i     i                 v       vii iv i     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_117471760_   5763 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5812
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_117471760_   5813 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5862
                           i     i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_117471760_   5863 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5912
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_117471760_   5913 CATCACTGGCCAT 5925
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3205 27.42 0.44 0.44  chr1_117607479_117613888.rev     5012  5919 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_117607479_   5012 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCCATATTGTGAAAAT 5061
                              ii i  i     i      i v      v iv       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_117607479_   5062 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 5111
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_117607479_   5112 TACCAGGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5159
                          v    vvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_117607479_   5160 CATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5209
                         i      viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_117607479_   5210 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5259
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_117607479_   5260 TACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGAGATATAGATC 5309
                                 i   i   iii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_117607479_   5310 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5357
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_117607479_   5358 ATCTGATCTTCGACAAACCTGAGAAAAACAAGACATGGGGAAAAGATTCC 5407
                          vi    i        ivv  vv  i v  vvvv         ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_117607479_   5408 CTATTTAATAAATGGTGCTGGGTAAACTGGCTAGCCATATGTAGAAAGCT 5457
                           v  i  i             vv      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_117607479_   5458 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5507
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_117607479_   5508 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAGACCCTAGAAGAAAAC 5557
                          i ?    i       v   v       i     ivi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_117607479_   5558 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5607
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_117607479_   5608 AACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5657
                         i    v       vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_117607479_   5658 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAAT 5707
                          i   v v  i i   i  ii vv    i  v    i ivv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_117607479_   5708 GAGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5757
                         iii     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_117607479_   5758 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5807
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_117607479_   5808 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 5857
                          i     i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_117607479_   5858 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5907
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_117607479_   5908 ATCATTGGCCAT 5919
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 711 29.42 12.61 3.19  chr1_117632962_117634596.rev      471  1160 (475)    L1M4_orf2#LINE/L1      154   908 (0)  

  chr1_117632962_    471 AAATGCTTATGAAAGAGCTTAGAATTAAGAGC-AAAA-AATTTTGAA--- 515
                               -----  i ii ii     ----   -    -   i     ---
  L1M4_orf2#LINE/    154 AAATGC-----AAGGGACCCAGAAT----AGCCAAAACAATCTTGAAAAA 194

  chr1_117632962_    516 ---GAGCAAGGTAGAAGAGCCCACACTATCTGATGTCAAGATATATCTA- 561
                         ---  i   i  v i  ii i      vi ii  v    i iv  -   -
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTAC 243

  chr1_117632962_    562 AAGGCTATACTTAACAAAACGGCACGTTATTC-CA-----ACAGAAATAT 605
                           i    i v v v   i  i iii v  i v-  ----- i   v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_117632962_    606 A---CAAAAGAACC-AAGTGAAA--TCATAAACAAATCTATGAATATATG 649
                          ---   vi   iv-  v   i --i  v   i   i i  iv  v    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_117632962_    650 A-AAATTTATATT--GCAGAAATGACATTACAAATCCATGAGAAAAAAAC 696
                         i-v    v  v  --i  iiii  v  vv  v v  v   i i   i  i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_117632962_    697 AGACTCTTCAATAAGTCACACAGGGACAACTAGATACCCATACGGAAAAA 746
                           v  i     i  i viii v         i    ?   i i v    i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_117632962_    747 TATAAATTCAGTCCCC-ACCTCAT--CATACACAAAAATCAAC---AAGT 790
                         v  i  v ii v    -      i--    i        i   ---  i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_117632962_    791 AGATTAAATCCCTAGGTGTGAAAAACAAAACTTTACAACTATCAGAACTG 840
                         i   i ? vv    ii   i i ivi      v  v    v i    -- 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA--G 541

  chr1_117632962_    841 AAAATACAGG---AAA-CT--GTTACTTCAGAGTAG-------------A 871
                             i i   ---   -  --  v  i ii iv   ------------- 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_117632962_    872 GA-------CCA-------------TAAATGAAAACATTAACAATTTTAA 901
                           -------   -------------i   v     v  vi i  v  vi 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_117632962_    902 ATATATTAAAATTTCAAACTTGTGTAAAACTAAAAACATCATAATCAAAA 951
                         v vi  i      vv      v   ivvv v  ii   ii  v vv   i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_117632962_    952 TTAAAAAATAAGGTATTCACAG-----GAGGAAATGT--GTAATGCATAT 994
                          v    i i  ----ii     -----   i    i -- i  vv     
  L1M4_orf2#LINE/    692 TGAAAAGACAA----CCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_117632962_    995 ---TAACACAGAATTC--ATCCAGAATGTACAAATAACTTCTACAAATAA 1039
                         --- i i vi i i i--         i  i   v    ii     v v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_117632962_   1040 ATAAGAAAAAGGCAA-CAACCCAAA-AGAAAACTGGCAAAAAACT-GAAC 1086
                             v      i   -i       v-?i    iv      ii i -   i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_117632962_   1087 AAGTAACTC---AAAGATTAAGAAACTCAAATAGTCAATAAATATGTTGA 1133
                          iii vi  ---     ---   v iv     i i      ii ii -  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGA---AGATATACAAATGGCCAATAAGCACAT-GA 883

  chr1_117632962_   1134 AAATACGTGTTTCACCTCTAGTAATCA 1160
                            v --  i iv  v  v????????
  L1M4_orf2#LINE/    884 AAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (126 / 74)
Gap_init rate = 0.05 (36 / 755), avg. gap size = 3.03 (109 / 36)  


3213 27.02 1.00 0.44  chr1_117636101_117638910.rev     1417  2319 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_117636101_   1417 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 1466
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_117636101_   1467 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1516
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_117636101_   1517 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1564
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_117636101_   1565 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1614
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_117636101_   1615 AACAAAGCTGGCGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1664
                                i   v  vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_117636101_   1665 TACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1714
                                 i   ii   ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_117636101_   1715 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1762
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_117636101_   1763 ATCTGATCTTCGACAAACCTGAGAAAAACAAGACATGGGGAAAGGATTCC 1812
                          vi    i        ivv  vv  i v  vvvv          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_117636101_   1813 CTATTTAATAAATGGTGCTGGGTAAACTGGCTAGCCATATGTAGAAAGCT 1862
                           v  i  i             vv      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_117636101_   1863 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1912
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_117636101_   1913 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1962
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_117636101_   1963 CTAGGCATTA-CATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2011
                         v    ?i v -iv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_117636101_   2012 AACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 2061
                         i    v       vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_117636101_   2062 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAAC 2111
                          i   v v  i i   i  ii vv    i  v    i ivv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_117636101_   2112 GAGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 2161
                         iii     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_117636101_   2162 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2211
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_117636101_   2212 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 2257
                          i    ----   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_117636101_   2258 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 2307
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_117636101_   2308 ATCACTGGCCAT 2319
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2693 23.75 8.91 1.07  chr1_117676839_117678762.rev      592  1433 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_117676839_    592 TGGAGAGATATACCATTATTCATGGACTGAAA----CAATACTGTGAAGA 637
                             i      v    -i        i  i  ----i    i   v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_117676839_    638 TGTCAA-ATCACTCAAA---ATTTATA-----------ATCCCAGTTAAA 672
                           v   - iiv i    ---  i  i -----------     vi i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_117676839_    673 ATCTCAGTAGA---TTTTATAGAAACCAACAAGTTGATTCTAAAATTTAT 719
                            i   iv v---    ii     iii     i    i        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_117676839_    720 ACAAAAAGGAAAAGTAACTAAAACAGCCACAACAATTTTGAAAAGGAA-- 767
                          iii   v v  i v v i i  i     v      i       i   --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_117676839_    768 -TAAAGTTGGAGGACTCACACAACCTGATTTCAAGACTTTCTATAAAGCC 816
                         -i                   vv  ii       i    v   i     i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_117676839_    817 ATAATAATGAATACAATGTGGTAGTACCA--AAGACAGACACATAAATCA 864
                          i i    v  v   i       v iv  -- i  i     i   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_117676839_    865 AGAGAACAAAACAGAATGTCTAGAG-TAGACCCACACATACCTAATCAAC 913
                          vi   i i  iv  iv   i   i-  i     i    viv ii    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_117676839_    914 TGATTTTCAACAAAGGTACAAAG-TCAATTAATG---AAAAAGTAGTCTT 959
                                 i    i   i v   -i  v i    ---   i i       
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_117676839_    960 TTCAACA-----------------------TCCATATGGAAAAAAGTAGA 986
                                -----------------------?   i   v    i i ii 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_117676839_    987 CTTCAACTTATACCTCACAGCATATATAGGATTTAACTCAAAATCAATTA 1036
                         v  vi  iiv         v      i ii v            vi  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_117676839_   1037 CAGACTTAAAAGTACAAATAAAG-TAAAGCTATAATAGTTTTGGAAGAAA 1085
                         ?    i    v   ----- i  -    i      v v i  i       
  L1M4_orf2#LINE/    500 WAGACCTAAATGTA-----AGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_117676839_   1086 ACTTAAGAGAAAATCTTTGTGATGTTGGATTAGGCAAACATTTCTTAAAC 1135
                           v  i ? v       i    iv    i        vvi       i i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_117676839_   1136 AAAATACCAAATGCATGAACCATAAAAGACAAAATTAGTAAATTGTACTT 1185
                          vi i      v   ii i v i      v     vii       v    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_117676839_   1186 C--CAGA-TTAACAACATCAATTCTTCAAAAGATACTGTTAAATCACTGG 1232
                          --  i -    v   v ivi v       i  i   i i  ivv v  i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_117676839_   1233 AAAGACAAGCCACAGA-TAG-AGAAAATAATTGCAAAT-GTATAGATTAT 1279
                                 v       - i -        v        -i    vv v  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_117676839_   1280 AAAAGACCTATGTCCAAAATATGTAAAGAACTATCACAATTTAATAATTC 1329
                           ii   i i i    i     i         v i    i i      --
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-- 792

  chr1_117676839_   1330 AAAAAAAACAAA------AATTTTTAAATGGGCAAGGGATTTGAGCAGCT 1373
                         -     i     ------    ?vv          i        ii  vi
  L1M4_orf2#LINE/    793 -AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_117676839_   1374 AATTC---AAAAAA----TACATATGACAAATAAACATAGGAAAAGATGC 1416
                          v   ---   i  ----    v   i v     i  i v          
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_117676839_   1417 TCAACATCACTTGTCAT 1433
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (129 / 67)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.65 (84 / 23)  


1982 24.73 6.97 3.55  chr1_117732346_117734068.rev      502  1233 (490)    L1M4_orf2#LINE/L1      152   908 (0)  

  chr1_117732346_    502 GAAAATGCAAAGGACCTAGAG-AGCAAAAACAACTATTGAGAAAGAA--- 547
                          i        i     i   i-   v       - v    i      ---
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAA 200

  chr1_117732346_    548 CAAATTTGGAAGGCTAACACTATTTGACTTCA---TTTATAATAAATCTA 594
                             v     i i  v     viiii i    ---i   iv i   v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_117732346_    595 CACTCATCAAAACAGGATGGTAC--ACACTGTGTTGATTGTGTAGATTTA 642
                           v v     i    vi      --i  iviv v iivii i     i- 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC-A 299

  chr1_117732346_    643 ATAACAAACAGAAT--AGAGTCTAAAAATAAAC--ATACACTTAAATGTA 688
                           ii--  i     --      i i        --     i   --  vv
  L1M4_orf2#LINE/    300 ATGG--AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA--TGGT 345

  chr1_117732346_    689 CAACTGATTCTTAACAAAGCTGCAAAGGCAATGCAGTGAAAAAAGGAAAG 738
                            i     i ii    i v   v   i v  v  i  iii    i v  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_117732346_    739 CCTTTTCAACCAATGATGCTGAAATAATAGAATATTTATATGTAAAAAAA 788
                         i         v    i     ii i  iv i   ?ii i   i    i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_117732346_    789 ATAAACTTTGATCCCTA------------TAGAAAAATCAACTCAAAATG 826
                         - i  v  v  i     ------------  v      i           
  L1M4_orf2#LINE/    446 -TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_117732346_    827 TCTCACAGATGTAAATACAAAACCCGAATCTATAAA-CTTTTAGAAGAAA 875
                         vv   ?   iv     ii  i v ii  v       -  i          
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_117732346_    876 ACATAGGAAGAAATCTTTGTGTGCTTGGGTTAGGCGTGCTTGAGTTAGGC 925
                                ?iv       i   vv            ---------------
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC--------------- 579

  chr1_117732346_    926 AAAGATTTCTTAGATATGACAT--AAAATATAATTCATAAAAAGCAAATT 973
                           v i                i--   ii i  viv i    iiv   v 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_117732346_    974 GGAAAAAT-GGACTTCCT---AATTAGAATCTTCTGCTTTTCAA----CA 1015
                         i  v    -       v ---     i  v   i  ivi     ----  
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_117732346_   1016 CTATTAAGAGAATTAAAAGATG-----------GGGTGAAAATACCTTCC 1054
                             i    i i v      ii-----------   v       ii v v
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_117732346_   1055 AAGAATATATCTGATATAGGAATTGTATCCAGAATATATACTGAAATCTC 1104
                           vv            vi   v                  vv   v   i
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_117732346_   1105 AAAACTCAACAATTAAGA---AAATAATGTTTTTAATAGGCAGTAGACAA 1151
                          v       i   v  i ---      ivivv  ? v --- i i i   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA---AATGGGCAA 826

  chr1_117732346_   1152 GAGATTTGATCAGATAATTCATCAAAGAAGATAAATGGATAGCAAA-GAG 1200
                         ii       vi   i v   vi           v iii  i  v  -i  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_117732346_   1201 TATATAAAAAAGATGTTCAACATCGTTAGTCAT 1233
                         i i  i    -    i        i????????
  L1M4_orf2#LINE/    877 CACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (112 / 65)
Gap_init rate = 0.03 (23 / 757), avg. gap size = 3.35 (77 / 23)  


2982 25.97 1.08 3.23  chr1_117736633_117739089.rev     1039  1966 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_117736633_   1039 TGGAAGAATATTCCATGCTCATTGATAGGAAGAACCACTATCATGAAAAT 1088
                              ii    i     i    v   v      vii v   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_117736633_   1089 GGCCATATTGCCCAAAGTAATTTATAGATTCAATGCCATCTCCATCAAGC 1138
                            v   i v      v i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_117736633_   1139 TACCAATGACTTTCTTCACAGAAATGGAAAAAACT-ACTTTAAAGTTCAT 1187
                          v   iivi i  i  ii       v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_117736633_   1188 ATGGAACCAAAAATGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAGA 1237
                               viiv  iv  v  v v  v     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_117736633_   1238 ACAAAGTTGGAGACATCACGCTACCTGACTTCAAACTATACTATAAGGCT 1287
                                     ivv    i  v  ii i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_117736633_   1288 ACAGTAACCAAAACAGCATGGTATTGGTACCAGAACAGATATATAGACCA 1337
                                i   i    ii     i   i iv  i i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_117736633_   1338 ATGGAACAGAA---AGAGGCCTCAGAAATAACACCACACATCTACAACCA 1384
                               i    ---    v  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_117736633_   1385 TCTGACCTTTGACAAACCTGACAAAAACAAGAAATGGAGAAAGGATTCCC 1434
                         vi   ii  i     ivv  v   i v  vvv     i     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_117736633_   1435 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTA 1484
                          v  i  i              v      v  ?   i   i i  iiv i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_117736633_   1485 AAACTGGATGCCTTCCTTACATCTCATACAAAAATTAATTCAAGATAGAT 1534
                           ii    iv   v   i   i vi             i    i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_117736633_   1535 TAAAGACTTAAACCTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1584
                         i ?    i    iv     v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_117736633_   1585 TAGGCAGTA--CCATTCAGGATATAGGCATGGG-AAGGACTTCATGACTA 1631
                             ?-   --i -   iv  iv v  vv i  -  v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_117736633_   1632 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 1681
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_117736633_   1682 ATTAAACTAAAGAAGTTCTGCATGGCAAAAGAAACTACCATCAGAGTGAA 1731
                           i   v v  i  v  i  iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_117736633_   1732 CAGGCAACCTACAGAATGAGAGAAAAGTTTTGCAATCTACCCATCTGACA 1781
                         v  i     i        i       vv       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_117736633_   1782 AGCGGCTAATATCCAGAATCTACAAATAACTGAAACAAATTTACAAGAAA 1831
                           v i  vi          v  i   v    vvv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_117736633_   1832 AA---AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1878
                           ---   i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_117736633_   1879 CTCAAAACAGTCTTCTTTTGAGACATATATATATGTCTGTATATGCAGCC 1928
                            v   v -----------   --    i v   ------------   
  L1M4_orf2#LINE/    846 CTCCAAAGA-----------AGA--TATACAAATG------------GCC 870

  chr1_117736633_   1929 AACAGACACATGAAAAAATGCTCATCGTCACTGGTCAT 1966
                           i ii          i       v i   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.33 (40 / 12)  


3121 27.28 0.55 0.66  chr1_117974838_117981246     5008  5916 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_117974838_   5008 TGGAAGAACATTCCATGCTCATGGGTACGAAGAATCAATATCGTGAAAAT 5057
                              ii i  i     i      i vv     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_117974838_   5058 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5107
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_117974838_   5108 TACCAATGACTTTCTTCACATAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5155
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_117974838_   5156 TATGGAACCAAAAAAGAGCCCACATGGCCAAGTCAATCCTAAGCCATAAG 5205
                                viiv  ii  v  viv  i     iv     i i ivv v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_117974838_   5206 AACAAAGCCAGAGGCATCACGCCACCTGACTTCAAACTATACTACAAGGC 5255
                                iii    vv    i iv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_117974838_   5256 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGATC 5305
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_117974838_   5306 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCATGTATCTACAACC 5353
                                i    i--    i  --        vv    ii  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_117974838_   5354 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5403
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_117974838_   5404 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5453
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_117974838_   5454 GAAACTGGATCCCTTCCTTTCACCTTAGACAAAATTTAATTCAAGATGGA 5503
                            ii    i    v   iv    v  v      v    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_117974838_   5504 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5553
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_117974838_   5554 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAGGGACTTCATGTCTA 5602
                         v    ?i- v i -   iv   v v  vv i    iv ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_117974838_   5603 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5652
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_117974838_   5653 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5702
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_117974838_   5703 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5752
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_117974838_   5753 AAGGGCTAATATGAAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5802
                          i  i  vi   vv     v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_117974838_   5803 AAAACAAACAACCCCATCAAAAAGTGGGTGGAAGGATATGAACAGACACT 5852
                           i     i     v  i?    i    ii-      v    i     i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCA-AAGGATTTGAATAGACATT 844

  chr1_117974838_   5853 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5902
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_117974838_   5903 TCATCACTGGCCAT 5916
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3013 18.60 4.92 8.86  chr1_117990257_117992524.rev      872  1785 (483)    L1M4_orf2#LINE/L1       31   908 (0)  

  chr1_117990257_    872 AAATTCAATATTGTTAACATGTCAATTCACTGCAAATTGATCTACAGATT 921
                          i i i           v   v    v v iv                  
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chr1_117990257_    922 TAACATAATCTCAATCAAAATCCCATTAGGCTTCTTTTTTTGTAAAAATT 971
                         i   ii    i v            ----   v i       i i     
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCA----GCTGCCTTTTTTGCAGAAATT 126

  chr1_117990257_    972 AACGAGCTTATTATAAAATTTATATAAGAATACAAATGAGCTAGGATAAC 1021
                         i  i    v  iv       i    iii   i   iv  v i  i   i 
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr1_117990257_   1022 CAAAACAATTTTAAGAAGAGGGGAACAATATTGGAGGGCTTACA-TTCCT 1070
                                  i  i i  -  ii      vi       i  i   -    i
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAA-AGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr1_117990257_   1071 GATT-CAAGATTTATTATAAAGCTACAGTCATCAAGACAATGTGGTATTG 1119
                         i   -   i i   i  i           v         i       i  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_117990257_   1120 ACATCAAGATATACAAATAGATCAATGGAATCCCATGGAGAATCCAGAAA 1169
                         i   v i    v   v               vvv  v    i        
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_117990257_   1170 TACATCCAAATAAATATGGTCAACTGATTTTCAA-AAAAATGCAAAGACA 1218
                           v i   v i vv         i        i -  iii   v     v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_117990257_   1219 ATTCAGTGGAGAAAGAATA-TCTCTTCAACAAATGGTGCTGAAACAATTG 1267
                              i   i         -   i                 ii    i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_117990257_   1268 GATATCTACATAAAACAACAAATAACTTCAATCCACACCTCACACTATAT 1317
                             ? i    iv  -  v  vv  v  vi i  vi         i    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAA-AAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_117990257_   1318 TCAGAATTAATTCAAAAATTAACTCAAGATCTAGCTGATCTAAGTCTAAA 1367
                         --------- --               i  --- --    ----------
  L1M4_orf2#LINE/    475 ---------A--CAAAAATTAACTCAAAAT---G--GATC---------- 498

  chr1_117990257_   1368 AGATATAAATATATAATAAAGATCTAAATAATGTAAATTTAAATGATCCA 1417
                         ----------------- ?   i      ---    --------------
  L1M4_orf2#LINE/    499 -----------------AWAGACCTAAAT---GTAA-------------- 514

  chr1_117990257_   1418 AAAGATCTAAAGCTAAATCTAAAACTATGTAACTTCCAGAAGAAAATCTA 1467
                         ---  v     i   ----       ------   --         iv  
  L1M4_orf2#LINE/    515 ---GAGCTAAAACTA----TAAAACT------CTT--AGAAGAAAACATA 549

  chr1_117990257_   1468 GGGGAAAATCTTTGTGACACTGGATTAGACAAAGATTTCTTGGATA---- 1513
                           ? v       i     vi   i    i   v i      i    ----
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_117990257_   1514 --CAA---------CAACAAAGGAAA-----------CTG-ACTTTGTCA 1540
                         --   ---------       i    -----------i  -    ii   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_117990257_   1541 AAGTCAGTCAGGTCTGCTCTTCAAAAGACACTACTAAAAGAATAAAAAG- 1589
                           i i ivv vv i  iv       i       ii  i i i i     -
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_117990257_   1590 ----CCACAGACTGGGAGAAAATATTTGAAAGTCACATACCTAATAAAGG 1635
                         ----       v                v  i   i   i  i    i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_117990257_   1636 ACTTGTATCCAGA-TATAAAAGGAACTCT-AAAACTCAATAATAAGAAAA 1683
                                      -    v  i       - v             i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_117990257_   1684 CAAA------ATTTTTAAAATAGGCAAAAGATTTGAACAAGTATTTTATC 1727
                             ------ v  ?v     i      i        i iii    ivi 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_117990257_   1728 AAAAAAGATA-ATGGATAGCAAATAAGCACATAAAAAGATACTTTATTGC 1776
                            i      - iii  i  v           i       i  iv ivv 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_117990257_   1777 ACACCATGA 1785
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.07 (112 / 54)
Gap_init rate = 0.03 (26 / 878), avg. gap size = 4.85 (126 / 26)  


2983 26.46 2.48 0.23  chr1_117996264_118000535.rev     2894  3781 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_117996264_   2894 TGGAAATACATCTCATGCTCTTGGATGGGTAGAATTAATATTGTGAGAAT 2943
                               v i   i    i  v     v  v   v          v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_117996264_   2944 GACCATACTGCTCAAAGCAATCTACAAATTAAATGCAATTCCCATCAAAA 2993
                          i v     v i    vii       i   v  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_117996264_   2994 TACCACCATCATTCTTCACAGAACTAGACAAAAAAATCCTAAAATTCATA 3043
                          v   v vv v  i  ii     v v     ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_117996264_   3044 TGGAACCAAAAAAGAGGCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 3093
                              viiv  ii  vv v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_117996264_   3094 CAAATCTGGAGGCATCACAATACCTGATTTCAAACTATACTATAGGGCCA 3143
                             vi      vv     v v  ii        viv     i ii  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_117996264_   3144 TAGTCACCAAAACAGCATGGTCCTGGAATAAAAATAGTCGCATAGACCGA 3193
                         i   v i   i    ii    v    v    ii    v ii     i i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_117996264_   3194 TGGAACAGAATAGAGAACCCAGAAACGAAGCCAAA----TACAGCCAACT 3239
                              i     v    ii       ii  v   v ----  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_117996264_   3240 GTTCTTCAACAAAGAAAACCAAAAC-ATAAAATGGGGAAAAAACAACCTA 3288
                          v i   i    i ivi-    i  -  vv          i  i ii  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_117996264_   3289 TTCAACTAATGGTGTTGGGATAATTGGCAAGCCACATGTAGGAGAATGAA 3338
                               v       i     i  i   vv ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_117996264_   3339 ACTGGATCCTCATCTCTGACCTTATACAAAAATCAACTCAAGATGGACCA 3388
                         ii    i  ii i   vv   v           i       i     i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_117996264_   3389 AAGATTTAAATCTAAGACGTGAAACTATAAACATTCT-AGAAGATAACAT 3437
                         ?   ii     v     vv i          - i   -      v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACAT 548

  chr1_117996264_   3438 TGGAAAAACCCTTCTAGTCATTGGCTTAGGCAAGGATTTCATGACCAAGA 3487
                         v  ?iv  vi    vv v v    v        v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_117996264_   3488 ACCCAAAAGGAAATGCGACAAAAACAAAGATAAATAGCTAGGACTTAATT 3537
                         vv       v v v  i      iv   i   i   iv v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_117996264_   3538 AAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAA--- 3584
                            v v  i i      iiivv    i iv  vi   iv i   i  ---
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_117996264_   3585 -CAGCCTACAGAGTCGGAGAAACTCTTCACAATCTATACATCTGACAAAG 3633
                         -  i  i     i v       v v  ii   vii   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_117996264_   3634 GACTAATATCCA-AATCTACAAGGAACTCAAACAAATCAGCAAGAAAAA- 3681
                             vi      -   v  i  i      vv    v   ii  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_117996264_   3682 ----ACAATCCCATCAAAAAGTAGGCTAAGGAC----ATAGACAATTCTC 3723
                         ---- i  i  v  i?    i i   v     i----       v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_117996264_   3724 AAAAGAAGATATACAAATGGCCAACAA--ACATAAAAAAATGCTCAACGT 3771
                         v                       i  --    i    i         i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_117996264_   3772 CACTAATGAT 3781
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.33 (132 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.40 (24 / 10)  


3170 27.88 0.77 0.33  chr1_118018890_118025257.rev     4974  5877 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118018890_   4974 TGGAAGAACGTTCCATACTCATGGTTAGGAAGAATCAATATTGTGAAAAT 5023
                              ii ii i    ii      v v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118018890_   5024 GGCTATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5073
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118018890_   5074 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5121
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_118018890_   5122 TATGGAACCAAGAAAGAGCCCGCATTGCCAAGACAATCCTAAGAAAAAAG 5171
                                viivi ii  v  v v  v     i      i i i   i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_118018890_   5172 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAGCTATACTACAAGGC 5221
                                i      vv   ii  v  ii i     iviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_118018890_   5222 TACAGTAACAAAAACAGCGTGGTACTGGTCCCAAAACAGATATACAGACC 5271
                                 iv  i    i          iviv ii i   i   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_118018890_   5272 AATGGAACAGAACAGAGGCCTCAGAAATAACACTACACATCTACAACTAT 5321
                                i    iv   ivii         vv i i    i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_118018890_   5322 CTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCT 5371
                         i    i  i     ivv  vv  i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_118018890_   5372 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTAA 5421
                         v  i  i              v      v  ?   i   i i  iiv i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_118018890_   5422 AACTGGATCCCTTCCTTACACCTTATACAAAAATTATTTCAAGATGGATT 5471
                          ii    i    v   i     v             vi    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_118018890_   5472 AAAGACTTAAATGTTAGACCTACAACCATAAAAACCATAGAAGAAAACCT 5521
                          ?    i       v   v   v   i      vi v           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_118018890_   5522 AGGCA-ATACCACTCAGGACGTAGGCATGGGCAAGAACTTCATGACTAAA 5570
                            ?i- v i -i  iv   v v  vv i     viii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_118018890_   5571 ATACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGAGATCTAAT 5620
                          i          vvi          vv        i    vi  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_118018890_   5621 TAGACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGGGTGACCA 5670
                         i i v v  i i   i  ii vv    i  v    i  vv ii    vv 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_118018890_   5671 TGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5720
                         vi     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_118018890_   5721 GGGCTAATATCCAGAATCTACAAAGAACTTAAATAAATTTACAAGAAA-- 5768
                           i  vi          v  i        ivv i  v iv i  v   --
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_118018890_   5769 --CAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5816
                         --    i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_118018890_   5817 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5866
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_118018890_   5867 TCACTGGTCAT 5877
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.58 (152 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


 218 30.30 11.19 8.51  chr1_118189279_118191168      544  1401 (489)    L1M4_orf2#LINE/L1        4   884 (24)  

  chr1_118189279_    544 AGAGATATAATCCATGTTCTTGAATGGGAAGACAAGGTATTGAAAAGATG 593
                          i      --i        v  i  v       vvii     vv      
  L1M4_orf2#LINE/      4 AAAGATAT--CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_118189279_    594 GTAGTGTTTTCTAA-TTGATTTATATAGCTAAAGCTATGTTTAGACATAT 642
                          i i ii ii i  -     i  i v vii  v  v  vii  -------
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA------- 94

  chr1_118189279_    643 GTTTATATAGATAC-AGATATATTT-------AAATAGATATCTTAAAGG 684
                         -- i --- i  v -  v iiv   -------    v  i ---------
  L1M4_orf2#LINE/     95 --TCA---AAATCCCAGCTGCCTTTTTTGCAGAAATTGACA--------- 130

  chr1_118189279_    685 TTTTAGTTGTTACTTAGAACTTGACCTAATATGGAAAAGCAAAGGAATTG 734
                         ----  i  v - i  i  i i------         v    i   viii
  L1M4_orf2#LINE/    131 ----AGCTGAT-CCTAAAATTC------ATATGGAAATGCAAGGGACCCA 169

  chr1_118189279_    735 GAAACACTAAAA---TTTGGGAAGAAAAGAATAATAAAACAGGGG----- 776
                            vvi i    --- i v i  i i     i  -- ivii i  -----
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAA--AGTTGGAGGACTCA 217

  chr1_118189279_    777 ---TTTTAGATATTAAAATGTCATATAAACCCATAAT--TTAAGA-AGTA 820
                         ---  iivi  v i    iv vv  i   v i i i -- i    -   i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_118189279_    821 TCATATTGATACTTCAATGCAAGTACCAATGCAAAATAGATTATTGCAAC 870
                          vi  i  ii i--------   v ivi i--- v      i v  v  i
  L1M4_orf2#LINE/    268 TGGTACTGGCAT--------AAGGATAGAC---ATATAGATCAATGGAAT 306

  chr1_118189279_    871 CAAATGGAAATCTCAGAAACACATCCATGATTACATTCCTAATTAGTATA 920
                         vi   v  i vii      i v i    ----     iv ii i i vv 
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCAT----ACATTTATGGTCAATTGA 352

  chr1_118189279_    921 TTTT----AAAG-----ACGACATTTTAATAAGTAGAAAAATGATAGATT 961
                             ----  i ----- v   vv  i   ii --    i --    vi 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGG--GAAAGA--ATAGTCT 398

  chr1_118189279_    962 ACTTATAAAACAGTCCTTAGACAATTGGCTATTTG-A-GCGAAATTTTTA 1009
                         vi i vv   ii  v  vi     i   v  ?iii- -  i   vvv v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_118189279_   1010 AATTAAAGCTTTACCTCATGCTATATACCAAAATGAAA-CAAA---GATT 1055
                          i  ii v ii       ii i      v     v  v-    ---   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_118189279_   1056 AAAGACTTAACTATTAAAAAATAGCATTTTAAAG----TAAACTAGAAAA 1101
                          ?    i   v i -  i iv  iv i v    i----  i --      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGA--AGAAAA 545

  chr1_118189279_   1102 TATGTAAGTAAATATCCGATAGC---AAGGTAGAAAAGGACTTTATTAG- 1147
                         i  ivi?      v i  - ii ---ii v   iv  v i-   v    -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGG-TTTCTTAGA 593

  chr1_118189279_   1148 --------CAAAGAAATAAATTAAAAAAGGAAACTGTTGGTAGATTGGA- 1188
                         --------    iiv i  iiv v     i   v-i v i  i      -
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGAC 642

  chr1_118189279_   1189 ---AT----ACTTGAAACATTTGTACATTAAAA-ACA----------AGT 1220
                         ---  ---- i vi    v     i v i   i-   ----------   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_118189279_   1221 CAGAGGACA-CTGAAAAAGTTAAAATATTTAATATTTTCAA--TATAAA- 1266
                         v i i    - iv v i i vii iv ---       v   --i   v -
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAA---AATATTTGCAAATCATATAT 739

  chr1_118189279_   1267 --AAGAAAGGATTAGTATCATTCATCTATTAATAACT--TACAG-TCAA- 1310
                         --i v  i   i v     vvvv  v   v  v    --    i-    -
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_118189279_   1311 -ATAAGA-GATGA------CACTCTAAGAATGATAGACAAAAGAAAGTCA 1352
                         -    i -  ii ------  v i?  i    --- i    i  --- i-
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATG---GGCAAAGGA---TT- 832

  chr1_118189279_   1353 TGAATTGGCAATTC-----AAAAGAGATACTTTATGGCCAATAATCACCA 1397
                              v i  v   ----- i    v    vv-           v   - 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAA-ATGGCCAATAAGCAC-A 880

  chr1_118189279_   1398 TAAA 1401
                          i  
  L1M4_orf2#LINE/    881 TGAA 884

Transitions / transversions = 1.56 (156 / 100)
Gap_init rate = 0.06 (52 / 881), avg. gap size = 3.25 (169 / 52)  


3241 26.25 1.11 0.55  chr1_118253743_118260109.rev     4974  5876 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118253743_   4974 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5023
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118253743_   5024 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5073
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118253743_   5074 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTTA 5121
                          v   iivi i  i  ii     -   -- v  i  - iii    i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_118253743_   5122 TATGGAACCAAGAAAGAG-CCCACATT-GCCAAGACAATCCTAAGCAAAA 5169
                                -- v v   i -    v v -     i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_118253743_   5170 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 5219
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_118253743_   5220 GCTACAGTTACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGA 5269
                                 v i   i    ii         i  v ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_118253743_   5270 CCAATGGAACAGGACAGAGGCCTCAGAAATAACACCACACATCTACAAAC 5319
                         i        i  i iv   ivii         vv   i    i  iiiv 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_118253743_   5320 ATCTGATCTTTGACAAACCTGACAAAAATAAGAAATGGGGAAAGGATTCC 5369
                          vi    i  i     ivv  v   i vi vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_118253743_   5370 CTGTTTAATAA-TGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5418
                           v  i  i  -  i        v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_118253743_   5419 GAAACTGGATCCCTTCCTTACACCTTAGACAAAAATTAATTCAAGATGGA 5468
                            ii    i    v   i     v  v           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_118253743_   5469 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5518
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_118253743_   5519 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGTACTTCATGACTA 5567
                         v    ?i- v i -   iv   v v  vv i     vvii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_118253743_   5568 AAACACCAAAAACAATGGCAACAAAAGCCAAAATAGACAAATGAGATATA 5617
                         vi         i  vvi          vv        i    vi  iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_118253743_   5618 ATTAAACTAAAGAGCTGCTGTACGGCAAAAGAAACTACCATCAGAGTGAA 5667
                           i   v v  i i  vi   i vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_118253743_   5668 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5717
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_118253743_   5718 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5767
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_118253743_   5768 AAAACAA----CCCCATCAAAAAGTGGGCACAGGATATGAACAGACACTT 5813
                           i    ----   v  i?    i      v     v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_118253743_   5814 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5863
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_118253743_   5864 CATCATGGTCATC 5876
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2538 22.38 3.20 2.33  chr1_118304637_118306305      503  1190 (479)    L1M4_orf2#LINE/L1      215   908 (0)  

  chr1_118304637_    503 TCACACTACCTGATTTCAAAATGGTTAGCTATAAAGCTATGCTAATCAAG 552
                                v  ii         i--   -   i       iiv        
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAAC--TTA-CTACAAAGCTACAGTAATCAAG 261

  chr1_118304637_    553 ACACCATGGTACTGGCATAA------ACACAGAGATCAATGGAATACAAT 596
                            vii              ------   i v              v   
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_118304637_    597 AGAGGGCCCATAAATAAATCCACACATGTACAGTCAATTCATATTCAGCA 646
                         v   i i   v       i   i    v  ii       v  v   ii  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_118304637_    647 TAGATGCCAAGAACACAAAATTGAGGAAGACCAAGTTTTTCAATAAATGG 696
                         vi i        v  ivv   v i i    vi ivi       i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_118304637_    697 TGCTGGGAAAACTGGATATCCACATGCAAAAGAATGAAATTAGACTCTAA 746
                                 v         ?                   i  i   i iv 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_118304637_    747 TGTG----CATGCACAAAAAC-AACACAAAATGGATTAAAGACTTAAATG 791
                         iv v----   ii       i-   v          i ?    i      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_118304637_    792 TACGTCCTGAAATTATGAAACTACTTACTAGAAGAAAACACAAGAG-AAA 840
                           v vv  i   i   i     -    ---          i i ? -   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACT-CTTA---GAAGAAAACATAGGNGTAAA 557

  chr1_118304637_    841 TCTCTGTCACATTGTTCTGGGCAGTGATGTTTTGAATATAACCTCAAAAG 890
                            ii  v  v   vvi i    i  i v i  ii    i  vi      
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_118304637_    891 CACAGGCAACAAAAACAAAAATAGACAAAT-GG----CATCACGTTAGAC 935
                             i         iv         i    -  ----     ---- i i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA----AAAT 653

  chr1_118304637_    936 TAAAACCTTCTGCACAACAAAGAAAACAATCAACAAAGCGAAGAAATAAC 985
                              v   i  ii vv     i v  v     v    i   i i i   
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_118304637_    986 CTATGGAATAGGACATAATATTTGAAAACC-TGCAACTGATAAGGAGTTA 1034
                          i ii    i   v v        v   i - ii v         iii v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_118304637_   1035 ATATCTAAAAATATACCTAAGGAACTC----AACTCAGTAGCAAGGAAAC 1080
                         i    i i  -    --   i      ----      i  ii  ii i  
  L1M4_orf2#LINE/    754 GTATCCAGAA-TATA--TAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_118304637_   1081 AAATAACCCAATTAAAAAATGAGCAAAGGACCCGAGCAGACATTTCTCAA 1130
                                      ?       i        iii  ii           v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_118304637_   1131 AAGAAGGCTTACAAATGTCCCACAGGTTCATGAAAAAAAATGCCTGGCAT 1180
                               iiv        v  v i i iv        i --   iiii   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAACAT 898

  chr1_118304637_   1181 AACTAATCAG 1190
                         v ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.06 (101 / 49)
Gap_init rate = 0.02 (16 / 694), avg. gap size = 2.38 (38 / 16)  


3422 23.07 2.91 1.34  chr1_118430399_118435017     3235  4127 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_118430399_   3235 GAAAAGATATCCCATGCTCATGGATTGGAAGAATTAATACTGTGAAAATA 3284
                          i              i               v      i   v  i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_118430399_   3285 TCCATACTATCCAAAATAATTTACAG-TT--ATGCAATCCCTATTAAAAT 3331
                         v v     vi     v i  i     -  -- i           i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_118430399_   3332 ACTAATGACGGTCTTCACAGAAATAGAAAAAA-AATCCTAAAATTTACAT 3380
                         v i iivi vv i  ii       v  v  iv-i           i i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_118430399_   3381 GGAACCACACAAAACCCAGGAGAACCAAAGGATTCTTAAGCAAAAAGAGC 3430
                             vii  viii      i v i     iv v    i iv  i    i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_118430399_   3431 AAAGCTAGAGGCATCAAACT----GATTTCAAAA-------------TAT 3463
                             i i    vv   v   ----i         -------------  i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_118430399_   3464 AGTAAACAAATCTGCATGGGACTCACATAAAAATGGACACATAGACCAAT 3513
                              v   iv v ii   v   vi     ii  i    i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_118430399_   3514 GGAACAGAATAGAGCACTCAGATATAAATACACGAATTTGTAGTAAACTC 3563
                             i     v   viii    v     iv  iiv    i i  v  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_118430399_   3564 ATTTTCAACAGCAGTGCCAAGAGCTTACAATAGG-AAAGGACAGTCTCTT 3612
                               i   ivi         v v v    i  -    i i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_118430399_   3613 CAATAAATGGGAAATAAATGCTGGGAAAACTGGATATCCATATGCAGAAG 3662
                            i      --------        v         ?   i     i   
  L1M4_orf2#LINE/    402 CAACAAATGG--------TGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_118430399_   3663 AATGAAACTAGACCCCTGTCTCTCTCCATAAACAAAAATCAAATCAAAAT 3712
                               ii i       ii   v v     v        i  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_118430399_   3713 GGATTGCAGACTTAAATCTAATACCTGAAACTATGAAATTATTAGAAGAA 3762
                             ii?    i     v   v v  i       i   i v         
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_118430399_   3763 AACATTGGAG-AAATGTTTCAGGACATTGGTCTAGGCAAGTATTTTTTTG 3811
                              v  ? -    -i   iv   v    vi       - iv   i  i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA 591

  chr1_118430399_   3812 TGTAAGACCTCAAAAGCATATGCAACCAAAGCAAAAATAGAGAAGTGGGA 3861
                         vi  v   vi        i v     v    v         v  i v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_118430399_   3862 TCATATCAAG-TTAAAAAGCTCTGCACAGCAAAGAAAACAATCAACAAAG 3910
                         iivi     i-       vi i  ii vv     i v  v     v    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_118430399_   3911 TGAAAAGACAACTCATGGAGTGGGAGAAGATATTTGCAAATTATCCATCT 3960
                                     i  ii  i        i            i  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_118430399_   3961 GACAAGGGATTAATAACCAGG-TATTTAAGGAGCTCAAACAACTAAATAG 4009
                           i      i vi  v    i-   v   i  i   vv      v    i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_118430399_   4010 GAAAAAACCCCAAATAATCTGATTTAAAAATAGGCAAAGGATTCAAATAG 4059
                         v     iv --      i ii   ?      i           ii     
  L1M4_orf2#LINE/    792 TAAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_118430399_   4060 ACATTTCTC-AAAAAAGATGTACAAATGACCAAAAGGTATATGAAAAGAT 4108
                                  -   i     i        i    v i i i          
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_118430399_   4109 GCTCAACATCGCTAATCAT 4127
                                   i????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (125 / 77)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 2.71 (38 / 14)  


2400 23.76 13.68 2.86  chr1_118446636_118448431      500  1303 (493)    L1M4_orf2#LINE/L1       18   908 (0)  

  chr1_118446636_    500 TTTATGGGCTGAAAGAATTAATATTGTTAAAATGTCCGTACTACCCAAGG 549
                           i    ii  i    v             i   v vi    v     iv
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr1_118446636_    550 TGACCTAAAGATTCAGTGCAATCCCTATCAAAATTCCAGTGGCATTCTTC 599
                            i   v       ii                 i    iv  v  i  i
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr1_118446636_    600 ACAGAAATAGAAAAAAAAAATCCTAAAATTTATATGAAACCACAAAAGAC 649
                         i       v  v  ivvi -          i     i  vii   ii   
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGA-TCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr1_118446636_    650 TCTGAATTGCTGTAAAGCAACCCCAAGCAAAAAGAATAGAGACAGAGGTA 699
                         i v    v  i--   i   i iii iv  i     i i  vii    - 
  L1M4_orf2#LINE/    167 CCAGAATAGCC--AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-A 213

  chr1_118446636_    700 TTAATATTACCTTACCTGACTTTAAACTAAACTACAAAGTTATAGTAATC 749
                         i v i ----   -  ii i  i   vivv         i  i       
  L1M4_orf2#LINE/    214 CTCACA----CTT-CCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_118446636_    750 AAAACAACATGGTACTGGCATAA----AAACACATAGACCAATGAAACAG 795
                           i   iii              ---- i   i     i     i  i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_118446636_    796 AATAGAGAACCCAGATACAAATCCATGTATTTACAGTGAACTTATTTTCA 845
                            v    ii     v i   i    ii     ii  v  i v      i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_118446636_    846 ACAAAGGCTGCAAAAAC-ATACCCTGGAGAAAGGACAGTCTCTTCAATAA 894
                             i  -   v  i  -  v vv   i     i i     i     i  
  L1M4_orf2#LINE/    359 ACAAGGG-TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_118446636_    895 ATGGCACTGGGAAAACTGGACAACCAC----------------------- 921
                             ii      v       i ?    -----------------------
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_118446636_    922 -------------------------------------------------- 921
                         --------------------------------------------------
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_118446636_    922 ----------------------------TAGAATAAAACATTGGAG-AAA 942
                         ----------------------------     v       v  ? -   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_118446636_    943 TGCTTTGGAACACTGGCCTAGGCAAAGATTTCTTGAGTAGGACCTCAAAA 992
                          -   i vi  vi   vi       v i      iii  v   vi     
  L1M4_orf2#LINE/    558 T-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_118446636_    993 GCACAGGCAACAGAAGCAAAAAGGGATAAATGTGATCTTATTAAG-TTAA 1041
                              i      i   v     vi       vv  ii i  i  i-    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_118446636_   1042 AAAGCTTCTGCACAGCAAATGAAACAGTCAATA--GTGAAGAGACAACCC 1089
                            -   i  ii vv    v  v  vi    v --     i         
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_118446636_   1090 ACAGAATGAGAGAAAATATTTGCAAACTATTTAAATGACAAGAGATTGTT 1139
                                 i                 ii  v  vv   i   i  i vv 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_118446636_   1140 AGCTAAACTATATAAAGAACACAAACTACTCAATAGCAAAAAAAATTTTT 1189
                          v i i v            v vv  v        ii     i ------
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA------ 799

  chr1_118446636_   1190 AATGTCAAATAATTGGATTAAAATGTGAGCAAAAGATCTGAATAGACATT 1239
                         -----       iivi   ?   vi  i     i   i            
  L1M4_orf2#LINE/    800 -----CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_118446636_   1240 TCTCAAAAGAAGGCATACATATGGTCAACAGGTATATGAAAAATTGTTCC 1289
                             v       ii     v    i   i i i i       iv  i  v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_118446636_   1290 ACATCACCAAACAT 1303
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (123 / 65)
Gap_init rate = 0.02 (15 / 891), avg. gap size = 8.87 (133 / 15)  


2617 20.99 7.21 9.47  chr1_118466906_118469656.rev     1335  2263 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118466906_   1335 TGGAATGACTTTCCATGTTCATGGATTGGGAGAATCAATATTGTTAAAAT 1384
                              v  iv i                 i   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118466906_   1385 GCCCATACTACCTAAAGCAATCTAAAGATTCAATGCAATCCCTATCAAAA 1434
                          v v     v  i   vii     v        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118466906_   1435 TACCTATGACATTTTTTCACAAAAATTGAAATAAATAATTCTAAAATGTA 1484
                          v  viivi v      -i  i       v - iv i  i       vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chr1_118466906_   1485 TGTGGAACAACAACAGACCTAGAATACCCA-------------------G 1515
                          i     vvi   vi    i      v   ------------------- 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_118466906_   1516 AACAAAACTGGAGGCATCACATTACCTACATCT--AAATTATACTACAAA 1563
                               ii      vv     i v  i -  i --   i -         
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACT-TACTACAAA 246

  chr1_118466906_   1564 GCTATAACCACCAAAACAGCATGATACTGGTATAAAAACAGACACA--GA 1611
                             i iiv i   i    ii  i      i    ii i     i --  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_118466906_   1612 CCAATGGAACAGAA-------------AATAAAT-------TTTACAGTG 1641
                         i        i    -------------      i-------    ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_118466906_   1642 AATTTATCTTCAATGAAGGCCCCAAAAACATACTTTTGGGAAAGGTCATT 1691
                             v  i   i ii i  iv    i v   v vv v       ivi v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_118466906_   1692 CTCTTCAATAAATGGTGCTGGGAAAACTGGACAACCATATGCAGAAGAAT 1741
                           i     i              v       i ?   i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_118466906_   1742 GAAACTAGATTCCTTTCTCTTACCATATATAAAATATATAAAATAAAAAT 1791
                            ii i  ii   -------   --------------------------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCT-------ACC-------------------------- 463

  chr1_118466906_   1792 ATATAAAAATAGACTCAAACATATATAAAACATATAAAATAAACATAAAC 1841
                         --------------   v  ------------------------------
  L1M4_orf2#LINE/    464 --------------TCACAC------------------------------ 469

  chr1_118466906_   1842 TCAAACATATATAAAAATAAACTCAAAATGGATTAAAGACTTAAATTTAA 1891
                         -----      i      v              i ?    i     v   
  L1M4_orf2#LINE/    470 -----CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_118466906_   1892 GACCTGAAACTATGAAACTACTATTAGAAAACACTGGGG--AATTACTCC 1939
                           v  i       i     vi  vv        iv  ? --   --  i 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTC 562

  chr1_118466906_   1940 AGGACATTAGTTTGGGCAATGATTTCTTTAGTAAGACTTCAAAAGCACAG 1989
                         iv   v  i v  i       i      vii  v   vi          i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_118466906_   1990 GCAACCAAAGCAAAAATGAATAAATGGGATCATATCAAG-CTAAAAGCTT 2038
                              v    v      ii      v   iivi     i-i     i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_118466906_   2039 CTGCACAACAAAGAAAAC----AACAAAGTGAAGAGACAACCCACAGAAT 2084
                         i  ii vv     i v  ----  v        i                
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_118466906_   2085 AAGAGAAAATATTTGCTAACAATTCAACTGGCAAACGATT---------A 2125
                         ii              v  iv  vi v   ii  iv  i --------- 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_118466906_   2126 ATA-ATAAGGAGCTCAAACAATT------TAAACAGAAAAATAATCTGAT 2168
                            -    i  i   vv    i ------    v   v      i ii  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_118466906_   2169 TTAAAA-TGGGTAAAAGATCTGCATAGATATTTCTCAAAAGAAGACATGC 2217
                          ?    -    i   i   i  v     i       v        i  i 
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_118466906_   2218 AAATAGCCAACAGGTGCATGGAAAAATGCTCATCACTAGTCATCAG 2263
                             i     i i ii    i   i       v  ii ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (123 / 68)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 7.75 (155 / 20)  


 955 26.38 11.66 0.00  chr1_118489473_118495944     2818  3143 (3329)    L1M4_orf2#LINE/L1        1   364 (544)  

  chr1_118489473_   2818 TGGAAACACATCCCAAGCTCATGGAT-GGGTGAATCAATATTGTAAAAAT 2866
                               v i      v i        -  iv  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118489473_   2867 GACCATACTGTCAAAAGAAATCTACAAATTCAATGTAATTCCCATCAAAA 2916
                          i v     vi v   vvi       i      i i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118489473_   2917 TACCATCATCATTCTTCACAGAACTAGAAAAAACAATCCAAAAATTCATA 2966
                          v   v vv v  i  ii     v v  v  ivii    v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_118489473_   2967 TGAAA----------CCAAAAAGAGCC---------TTCATAAA------ 2991
                           i  ----------  v i  v    ---------  v v   ------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_118489473_   2992 CAAAG------------CATCACCTGACTACAAACTACACTATAAGGCCA 3029
                              ------------  iiv  ii i v    vivi    i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_118489473_   3030 TAGTCACCAAAACAGTATGGTACTGGTATAAAAACAGGCACATAGACCAA 3079
                         i   v i   i     i         i    ii i  i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_118489473_   3080 TGAAACAGAATGGAGAACCCAGAAATAAAGCCAAATACTTACAGCCAACT 3129
                           i  i     v    ii           v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_118489473_   3130 GATTTTCAACAAAG 3143
                                i    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG 364

Transitions / transversions = 1.69 (54 / 32)
Gap_init rate = 0.01 (5 / 364), avg. gap size = 7.60 (38 / 5)  

1671 24.96 2.79 3.78  chr1_118489473_118495944     5371  5979 (493)    L1M4_orf2#LINE/L1      306   908 (0)  

  chr1_118489473_   5371 TAGAACTGTGAGTC---AATTAAACCTCTTTCCTTTATAAACTACCAAGT 5417
                              i  v     ---  v      - v v v     ii----i   --
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACC-CATACATTTATGG----TCAA-- 348

  chr1_118489473_   5418 CTTGAATATTTCTTCATAGCAGCATGAGAACGGACTCATACA-TGAGAAA 5466
                         -    ----  i iv i --  vi  vv  --   -   v  -  i i  
  L1M4_orf2#LINE/    349 -TTGA----TTTTCGACA--AGGGTGCCAA--GAC-CATTCAATGGGGAA 388

  chr1_118489473_   5467 AGAACATGCTATTCAACAAACGGTGCTGGGACAATTGGCAAGCCACATGT 5516
                             i vv  v         i             i   vv ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_118489473_   5517 AAAAGAATGAAATTGGATCCTCATCTCTCACCTTATACAGAAATCCACTC 5566
                                    i     i  ii i   v    v      i    iv    
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_118489473_   5567 AAGACAGATCAAAGACTTGAATCTAAGACCTGAAACCATAAAGATTCTAG 5616
                           i ii     ?    i i   v     v  i    i     iv ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_118489473_   5617 AAGAAAACATTGGAA-AAAGCCTTGTAGACATTGGCTTAGACAAAGACTT 5665
                                   v  ?i-   v i i  -   v    v    i   v ii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTT 587

  chr1_118489473_   5666 TGTGACCAAGAACCCAGAAGCAAATGCAACAAAAAGAAAGATAAATAGAT 5715
                         iv iivi v  vv   i     v v         ii   i   i   i  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_118489473_   5716 GGGATGGGACTGAATTAAACTAAAAAGCTTCTGCACAGCAAAATAAATAA 5765
                         ----   -   vv  i   v v    i   i  ii vv    iv v iv 
  L1M4_orf2#LINE/    638 ----TGG-ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_118489473_   5766 TCAGCAGAATTAACAGAAAACCCCCAGAGAGGGAGAAAATCTTCACAGTC 5815
                            iv i i v  v   v     v    iv          v  ii  ivi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_118489473_   5816 TACACATCCAACAAAGGACTAATACCCAGAATCTACAAATAACTC--A-A 5862
                         i i i   ii i  i     vi  i       v  i   v     -- - 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_118489473_   5863 ACTGAG----AAAAAAA-----AATCCCATAAAAAAGTTGGCTAAGGACA 5903
                            v i----     i -----  i  v  v?    i v   v     iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_118489473_   5904 CAAATAGCCAATTCTCAAAAGAATATATACAAATGGCCAACAAGTACATG 5953
                         ii     v  v     v      v                i   i     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_118489473_   5954 GGAAAATGCTGAACATCACTAATTAT 5979
                         ii  i     v       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (84 / 64)
Gap_init rate = 0.03 (17 / 603), avg. gap size = 2.35 (40 / 17)  


3125 26.88 1.00 0.55  chr1_118535053_118541326     4878  5781 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118535053_   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118535053_   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCAGCAAGC 4977
                            v     v     iv i  i           i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118535053_   4978 TACCAAG-GCATTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5024
                          v   iv-  v   i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_118535053_   5025 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5074
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_118535053_   5075 GAACAAAGCTGGAGGCATCACACTACTTGACTTCAAACTATACTACAAGG 5124
                                 i      vv       v iii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_118535053_   5125 CTACAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGATATAGAT 5174
                                  i   i    ii           iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_118535053_   5175 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5222
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_118535053_   5223 TATCTGATCTTTGACAAACCTGAGAAAAACAAGACATGGGGAAAGGATTC 5272
                         i vi    i  i     ivv  vv  i v  vvvv          i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_118535053_   5273 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACAAGTAGAAAGC 5322
                         i  v  i  i              v      v  ?     v i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_118535053_   5323 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5372
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_118535053_   5373 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5422
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_118535053_   5423 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5472
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_118535053_   5473 AAACACCAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGGGATCTA 5522
                         vi            vvi          iv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_118535053_   5523 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAA 5572
                           i   v v  i i   i  ii vv    i  v    i  vv i i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_118535053_   5573 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5622
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_118535053_   5623 AAGGGCTAATATCCAGAATCTGCAATGAACTCAAACCAATTTACAAGAAA 5672
                          i  i  vi          v ii  v      vv  v v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_118535053_   5673 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5718
                           i    ----   v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_118535053_   5719 CTCAAAAGAAGACATTTATGCAGCCAAAAAAAACATGAAGAAATGCTCAT 5768
                            v        i  vi viii     v  iv       i i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_118535053_   5769 CATCACTGGCCAT 5781
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (138 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3334 26.32 0.77 0.77  chr1_118603550_118609322     4373  5280 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118603550_   4373 TGGAAGAACGTTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4422
                              ii ii i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118603550_   4423 GGCTGTACTGCCCAAGGTAATTTATAGATTCAACACCATCCCCATCAAGC 4472
                            vi    v     iv i  i  i         i v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118603550_   4473 TACCAATGACTTCCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4520
                          v   iivi i ii  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_118603550_   4521 TATGGGACCAAAAAAGAGTCTGCATTGCCAAGTCAATCCTAAACCAAAAG 4570
                              i viiv  ii  vi v v  v     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_118603550_   4571 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4620
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_118603550_   4621 TACAGTTACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGATC 4670
                               v i   i    ii         i  v ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_118603550_   4671 AGTGGAACGGAA--GAGAGCCCTCAGAAATAATACCACACATCTACAACT 4718
                          i     ii   --     i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_118603550_   4719 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGGAAGGAT--T 4766
                          vi    i  i     ivv  v   i v  vvv       i   i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_118603550_   4767 CCCTAATTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 4816
                          ii -- i                 v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_118603550_   4817 CTGAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATG 4866
                         v    ii    i    v   i   i v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_118603550_   4867 GATTAAAGACTTAAATGTTAGACTTAAAACCATAAAAACCCTAGAAGAAA 4916
                            i ?    i       v   vi      i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_118603550_   4917 ACCTAGGCA-ATACCATTCAGGACACAGGCGTGGGTAAGGACTTCATGTC 4965
                           v    ?i- v i -   iv   viv  vv i  i  v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_118603550_   4966 TAGAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAGAAATGGGATC 5015
                           vi            vvi          vv     v  v    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_118603550_   5016 TAATTAAACTAGAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5065
                          v  i   v vi i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_118603550_   5066 AACAGGAAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGA 5115
                           v  iv    i                 v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_118603550_   5116 CAAAGGGCTTGTATCCAGAATCTACAATGAACTCCAACAAATTTACAAGA 5165
                         i  i  i              v  i  v      iv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_118603550_   5166 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5215
                             i     i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_118603550_   5216 TTCTCAAAAGAAAACATCTATGCAGCCAACAGACACATGAAAAGATGCTC 5265
                              v      i i  vi viii     i ii                 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_118603550_   5266 ATCATCACTGGCCAC 5280
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (145 / 90)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


1654 27.21 7.30 3.89  chr1_118609664_118611573.rev      563  1411 (499)    L1M4_orf2#LINE/L1        1   878 (30)  

  chr1_118609664_    563 TGGAGGGATATTTTATGACCATGCATCAGAAGTCTCAGTACTGTAAAGAC 612
                             ii     iii   vi    v  ii    v  i i  i   v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118609664_    613 AACAAT--TCTTCAGCAATTTATTAACAGATTGAATGCAATCTCAATTAA 660
                         ii    --  ii  --    v  iv       v  i      i v  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCA--AATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_118609664_    661 --TACCAA-TGTCAATTTTAATGTAAATTGGCAATATAATTCTAAAATTC 707
                         -- v   i-  i vv    ivv -      i   vv i  i         
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAG-AAATTGACAAGCTGATCCTAAAATTC 147

  chr1_118609664_    708 ATATAGAAACATAAG---CTAAAAATAACCAAAGAAAATCTTGAAGAAAA 754
                             i    iii   --- iv i    i     - v         i  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGA 196

  chr1_118609664_    755 TAAACAAAATTGGAAGTCTAACACCACTAGATATCCAACTATATTTATTA 804
                         vi      i     i v  v    iv ivi  v  v  ---- i   i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACTTACTA 242

  chr1_118609664_    805 CAAAGCTGTAATATTTGATACA-------ACTGGTATAAA---------A 838
                                ii i  v ii v   -------     i    i--------- 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_118609664_    839 TAAATAAATAAGACAGA-----GATTCCAGAAA-ACAATCACACATATAT 882
                           i  v   iii i   -----  v        - v vi  i    v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_118609664_    883 GAAAATTTTATTTATGACAAAGATGCAGTTTCAGAGCA----GTGAGGAA 928
                          ivv v  v    vi     i i   ----iv   v  ----i  i    
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGC----CAAGACCATTCAATGGGGAA 388

  chr1_118609664_    929 ATGACAGTCTTTATTTAAATAAAGGGTGCTTATGTAATTGGTTATGCATG 978
                          vi i       --- v  i   v      vivii  i   v  ?v  ii
  L1M4_orf2#LINE/    389 AGAATAGTCTTT---TCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_118609664_    979 TG-AAAAAAGTGTGTCTTGGCCCCTATCTCACACCTTACCCTCCAAAATT 1027
                           -    i i  vivi v i      i        v  iv --v      
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC--AAAAATT 483

  chr1_118609664_   1028 AACTGTAGATGACTTGATACATCTTAATGTACAAGATACGAGGGCT-CAA 1076
                             vv i   iv i- ? v i  v      vi  v  vi ---  -i  
  L1M4_orf2#LINE/    484 AACTCAAAATGGATC-AWAGACCTAAATGTAAGAGCTAAAA---CTATAA 529

  chr1_118609664_   1077 GATT-TCAGCATATAACAT-GCAGAATACCTTCATGGCCTTTCAGGTTAG 1124
                         i i - i  v v v     - v? v v i    i  i    --i      
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT--GGGTTAG 577

  chr1_118609664_   1125 -CAAAGATTTTTTAAACTA-GACACAAAGGG---GAGTAATCATGAAGAA 1169
                         -   v i   i   i -  -     v  ii ---i  i  iv --     
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAA--AAGAA 624

  chr1_118609664_   1170 AACAATTTATATCTTGGACTACATTAAAATTAAATA--TATCTGCTTACC 1217
                           -   vv   vv       v   i         v -- v v     -- 
  L1M4_orf2#LINE/    625 AA-AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--C 671

  chr1_118609664_   1218 AAATGATACCATTAGAAGAGAGGTAAGAGAAGCCAAAGG-TGGGAGACAG 1266
                            v  i  i  i ii i  v iv    v  v   v  i-       v i
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_118609664_   1267 TATTTGCTA--CATGTATTATTAACAAATGAATTATATCTAGAATA---- 1310
                                v --   i   i-- i i  iv  v  i    i      ----
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATC--TGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_118609664_   1311 AAGAACTTCTACAACTCAG-AA--AAAAGATATACAATCTACTTTTTAAA 1357
                                ii         i-  --      i v i  i i v  ?--   
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW--AAA 817

  chr1_118609664_   1358 AATT--TAAA-----TGAATAAATGTTTCATAAAAGAAGACATTCCAATG 1400
                            v--i   -----      i ii    viv        i  v v    
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_118609664_   1401 GTCAATAAGTA 1411
                          i       i 
  L1M4_orf2#LINE/    868 GCCAATAAGCA 878

Transitions / transversions = 1.44 (134 / 93)
Gap_init rate = 0.05 (40 / 878), avg. gap size = 2.38 (95 / 40)  


1762 25.98 11.83 2.80  chr1_118612039_118616016     2702  3521 (457)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr1_118612039_   2702 ATGTTTACATATTGCAAGATTGAATATTGCTGAGATTTCTATTCACCTGA 2751
                              i iiv    v    i v       i i    vv v  v v  iv 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_118612039_   2752 AATT-ATCTGTAGATTCAGCCTGATTTCAATAAAAAATCTCAGCTGTTCC 2800
                             -    ii       i vii  ii v  v    -  i      iiii
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCCAGCTGCCTT 113

  chr1_118612039_   2801 TTTTGTAGAAATATCCAAGTTAATCTCAAAATCTATATGGAA-CACAAAG 2849
                              i      vvv    i i   ii     ii        -ii   i 
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_118612039_   2850 AACCTACACTAGCCAAAACAACCTATGAAACAAGAA----AAAGCTGAAG 2895
                         i   i v v            i  -     -     ----    i  i  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCT-TGAAA-AAGAAGAACAAAGTTGGAG 211

  chr1_118612039_   2896 AACCTGTACTATCTGTCTTTAAGTCTTTTTATAAAACCACAACAAT---- 2941
                         i  iiii   vi iivi  i  iv   vi  i   i i   ii   ----
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_118612039_   2942 ---------TATTAATGCACAGATAAACAAATAGGTCAGTGAAACAGAAT 2982
                         ---------  i iiiii vi    i   v    i   i  i  i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_118612039_   2983 GGTAAGTCGAGAGA--GACCTA------------CAAT-GATTTT-GTCA 3016
                         v vi    v   i --i   i ------------    -      - v  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_118612039_   3017 TAGGCACAAAG-CAATTCAATGAGGAAAGGAAAGCCAATTCAACAAAAGG 3065
                         vi  ii v   - v        i      i v  i vv         v  
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_118612039_   3066 CACTGAAACAACTGGAAAGCCACAT-----AGAAAGAAAC--AACTCCTA 3108
                         ii   ii         v ?      -----    v   ii--i  i    
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_118612039_   3109 TTTCATGCCACATATAAAA-TTAATTCAAGATATACCATAGCTCTAAAGA 3157
                         ii   ii   i   i    -    i    i  iv i  ?  vi     vi
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_118612039_   3158 TAAAAACTACAACTATAAAGCT--TAGAAGAAAA----GGAGAATATCTT 3201
                            i i   v         i  --          ----  ? v v     
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_118612039_   3202 CAAAGCCCTTGA------CAATACCTTCTTAGAT-TCATCTCAGAAAGCA 3244
                          iv- v     i------    ivi         - v ivi  -      
  L1M4_orf2#LINE/    562 CGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA-AAAGCA 609

  chr1_118612039_   3245 CTAACCATAAAAGAAACAAAATTCATAAAGTGGACCTTTTCAAAATTCAC 3294
                          v i v i        --    vv     v     i iv        v v
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAA--AAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_118612039_   3295 AACTT--ATGCT-CATTGGAATTTATCATTAAGAAAATTTGTATCAGAT- 3340
                              --i    -  vv   ---i ii  i      i -- v -v   i-
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGA---CACTATCAAGAAAGT--GAA-AAGACA 701

  chr1_118612039_   3341 -----CAAATATCAGGAAAAATGTTT-----TCA-ATACCT-ATA----- 3373
                         -----  i -  vi ii     i   -----   -   i  -   -----
  L1M4_orf2#LINE/    702 ACCCACAGA-ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_118612039_   3374 ----TAT--------TATAAAGGCCTTTTA-AA---AATAATAACAAAGA 3407
                         ----   --------       iv  i   -  ---        -     
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AAAGA 799

  chr1_118612039_   3408 CAAACAATCTCATT--AAAATGCATAACAAATTTGAACAGGCACTTCATA 3455
                             i  i iv   --      vii  vii       i  i  i   viv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_118612039_   3456 AAAGGAAATATAAAAATGGTCAGTTAATGTGTCAAAAGGGAGATGCAAAT 3505
                             i i     v      i  i v iiiii v     ----    ----
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG----ATGC---- 891

  chr1_118612039_   3506 TCAA-ATCAAAACAGCA 3521
                             -    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (141 / 69)
Gap_init rate = 0.05 (41 / 894), avg. gap size = 2.93 (120 / 41)  


4013 18.76 6.45 0.35  chr1_118623127_118625375.rev      906  1758 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_118623127_    906 AAAGACATCCTATGTTCATGGATAGGAAAACCTAATATTATTAAAATGTT 955
                              i    i            v    i  i       i    i   vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_118623127_    956 AATACTCCCTAAATTGATCTACAGACTTAAGTGTAATCTCTGTCAAAATC 1005
                                  i               i i  -i i    i  i        
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAAATC 102

  chr1_118623127_   1006 TCCACTCCTTTTTTTCTGCAAAAAT-GGCAAGCAGAACCTAAAATTCATA 1054
                         i vi  v i      --   i    - i     v  v             
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_118623127_   1055 TGGAAATTCAAACATCCCAGAATAGT-AAAAC-----TAGAAAAGGATAG 1098
                                v   iviv          i-     ----- ii     i v i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_118623127_   1099 CAAAATTGAAGGACTCACACTTTCTGATTTCAAAATTT--TACTCAGTTT 1146
                             i   i             i ii         i  --   vv  i v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_118623127_   1147 CAGTAATTAGGACTGTGTGTTACTGGCATAAGGATGGATATATAGGTCAA 1196
                                i i   v     v               i  i      i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_118623127_   1197 TGGAATAGAATTGAGAGCCTGGAAATAAACCTTTCTACTTACAATCAATT 1246
                                          i ii          iv vi i   iii      
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_118623127_   1247 GATTTTCAACAAGAGCACCAAGATAATCCAATGAAGAA-GACTAATCTTT 1295
                                i     i ii      iv  i     ii   -  v  i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_118623127_   1296 TCAACAAGTAACACTGGGACAACTGGATTTCGACATGCAAAAGAATGAAG 1345
                                i iiii               v? v                  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_118623127_   1346 CTAGACACCTTCCTAGCAATATACACAAAAATGAATTCAAAATGGGTCAG 1395
                         i i   v   v   vi  vi   i        v  i         i   ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_118623127_   1396 AGACCTAAATTTAAAAGTTAAAACTGTAAAATCCTTAGAGGAAAGCATA- 1444
                                   v   i  i       i     ii      i    i    -
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_118623127_   1445 -------TC--------CCTGGATTAGGC--TG------TAGA------- 1464
                         -------  -------- i   i      --  ------    -------
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_118623127_   1465 ----AAG-----GCAACAAAATAAAAAATAGATAGATTGAACTTCATCAA 1505
                         ----   -----         v            i    i          
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_118623127_   1506 AATTGAAAACTTTTGTTCGGCAAATGATGCCATCAAAAAAGTGGAAAGAC 1555
                             i           v vv    v  ii i     i      i      
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_118623127_   1556 AATTGACAAAATGGGAAAAAGTATTTGCAACTCACATATCTGATAAGAGA 1605
                           iiv   i       i   i         v   i            i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_118623127_   1606 CTGATGTACAGAAAACATAATGAGTTCTCACAACTCAATAATAACAAGAC 1655
                           vi i v     v i    v  ii   i               v     
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_118623127_   1656 AA----CTCAATT-AAAAATGGGTAATTGATTTTTATAAGCACCTATCCA 1700
                           ---- i     -         i  vv     vv   ii  ii v    
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_118623127_   1701 AAGAACATATACAGATGACCAATGAATATATTAAGAAATGCTCAACATCA 1750
                              v       i   i     i ii i  v  i i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_118623127_   1751 TTAGCCAC 1758
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.43 (112 / 46)
Gap_init rate = 0.02 (15 / 905), avg. gap size = 3.87 (58 / 15)  


2857 26.60 0.85 4.06  chr1_118659101_118663725     3197  4132 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_118659101_   3197 GAAAAACATTCCATGCTCGTGGATAGGAAGAATCAATATTGTGAAAATGG 3246
                             i i  i     i  i     v      v i        v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_118659101_   3247 GCATACTATCCAAAGTAATGTATAGATACAATGCTATCCCCATCAAG--- 3293
                         vv     vi     v i  v  i    v   i  v     i     i---
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_118659101_   3294 CCGTTGTTGATTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 3342
                           i-- i  vi   i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    103 CCA--GCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_118659101_   3343 TATGGAAACAAAAAAAGAGCCCATA-TAGTCAAGACAATCCTAAGCAAAA 3391
                                 iiv  i-- ii    v -   i   i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_118659101_   3392 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 3441
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_118659101_   3442 GCTACAGTAACCAAAACATCATGGTACTGATGCCAAAACAGATATGCAGA 3491
                                   i   i   vii        iiiiv ii i   i  ii   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_118659101_   3492 CCAATGGAACATAACAGAGGCCTCAGAAATAACACTACACATCTACAACC 3541
                         i        i v  iv   ivii         vv i i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_118659101_   3542 ATCTGATCTTTGACAACCCTGACAAAAACAG-CAATGGGGAAAGGATTCC 3590
                          vi    i  i     vvv  v   i v  v-            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_118659101_   3591 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACC 3640
                           v  i  i              v      v  ?   i   i i  i vi
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_118659101_   3641 GAAACTGGACCCCTTCCTTAAACCTTACACAAAAATTAACTCAAGATGGA 3690
                            ii         v   i v   v  i                i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_118659101_   3691 TTCAAGACTTAAATGTAAGACCGAAAATCATAAAAACCCTAGAAGAAAAC 3740
                          iv?    i           v v    ii      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_118659101_   3741 CTAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAAGACTTCATGACT 3788
                         v    ?-   --i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_118659101_   3789 AAAACACCAAAAGCAATGGCAACACAAGCCAAAATTGACAAATGGGATCT 3838
                          vi            vvi      v   vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_118659101_   3839 AATTAAACTAAAGAGCTTCTGCACAGCAAAAAAAAAAAAAAAAAAAAAAA 3888
                         v  i   v v  i i   i  ii vv    ii v ---------------
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA--------------- 679

  chr1_118659101_   3889 AAAAAAAAAAAAAACCTATTGTCAGAGTGAATAGGCAACCTATAGAATGG 3938
                         ---------------    iivv i      v  i     i i       
  L1M4_orf2#LINE/    680 ---------------CTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_118659101_   3939 GAGAAAATTTTTTCAATCTATCCATCTGACAAAGGTCTAATATCCAGAAT 3988
                                 v   v   vii  vi      i  i  v  vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_118659101_   3989 CTACAAGGAACTTAGACAAATTTACAAGAAAAAAACAAACAGCCCCATCA 4038
                         v  i  i     ivv    v iv i  v     i     i i   v  i?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_118659101_   4039 AAAAGTGGGCTAAGGGTATGAACAGACACTTCTCAAAAGAAGACATTTAT 4088
                             i     v    i v    i     i     v        i  vi v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_118659101_   4089 GCAGCCAACAAACATATGTAAAAAAGCTCTTTATCACTGGTCAT 4132
                         iii     i  i  i   v   i v    vvi    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 3.83 (46 / 12)  


3598 20.59 4.32 1.02  chr1_118667520_118669506.rev      618  1496 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118667520_    618 TGAAAAGACATCT-GTGTTCAAGAATTGAAAGGCTTAATATTGTTAAGAT 666
                           i     i   i-i      v i    i   i                 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118667520_    667 ATCAATACTATCCAAAATGATTGACAGATTTAATGCAATCTCTA-CAAAA 715
                         iv       vi     v    iv       i  i      i   -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118667520_    716 ATACAACAACATTTCT-GCAGAAATAGAAGAAGC--ATCCTAAAATTCAT 762
                         viv  i vi v   i -        v  v-    --              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr1_118667520_    763 TTCAAATCTCAAGAGACCCTGGAGAGCTAAAACAATC----AAAAGAAGA 808
                         v vi  viv    i     v i v   i         ----         
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_118667520_    809 ACAAAGCTAGAGTTCTCACATTTCCTGATTTTAAAACTTACTACAAAGCT 858
                               i i   vv      i    ii    i                  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_118667520_    859 ACAGTAATCAAAGCAGTGTGGTACTGACAAAGAAACAGACATA--GACCA 906
                                    ii             i  v iii i       --  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_118667520_    907 ATGGGATAGAATAGAGAGACAAAAAATAAATTCCGGCATATATAATCAAA 956
                             i       v     v v i       ii vvi   v   ii    v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_118667520_    957 CGTTTCTTGACAAAAATGTAAAGACCACTTAATGGGGAAAGGACAGTCTC 1006
                         i v  i i     iii  iv       i i           i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_118667520_   1007 TTCAAAAAATG---TTGGGAAAACTGGACATCTACATTCAAGATTATGAA 1053
                              v     ---i     v       i ? i    v   i vv     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_118667520_   1054 GCTGGACCCTTACCTTATACAAAAAAAAAAAAAAAAACAACTCAGAGTGG 1103
                          i       i     i i  v v v v     v----i      i i   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAAT----TAACTCAAAATGG 495

  chr1_118667520_   1104 ATCAATGACTTATACACAAG-GCCAGAATTATAAAACCCTTTGAAGAAAA 1152
                             ?v   i  v iii   -  i i  i        i   v        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_118667520_   1153 CATAGGGG-AAAGCTGTATGATATTGGATTTATCAAT---TTCTTGGATA 1198
                               ? -   v  vii   iv    i  viv    ---     i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_118667520_   1199 TGACACCAAAGGCAAAGGTAACAAAAATAAAAATAGACAAGTTAGACTAA 1248
                                   i   v i i       iv         i  i  i    vv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_118667520_   1249 ATCAAAATTTAAAACTTCTGTGTATCAAATGACACAATTAACAGAGTGAA 1298
                                  v       i    iv     v     v  i  v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_118667520_   1299 AACGCAACCTACAGAATTGGAGAAAATATTTGCAAGTGATATATCTGATA 1348
                           vi     i       v                 i v            
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_118667520_   1349 AGTGGTTAATATCCAGAATATATAAAGACCTACTACAACCCAAGCAAAAA 1398
                           v ii vi                   v  vi      i   -i  v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA-TAATAA 794

  chr1_118667520_   1399 ACATATATATAACCCATTTTTTTAAAA--GGGCAAAGGATTTGAATAGAC 1446
                          v v i v        v  ?---    --                     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTW---AAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_118667520_   1447 ATTTATCTAAATAATATATCTAAATTGTCA-----------------TGC 1479
                             v  i   v  v    vi    v i  -----------------   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_118667520_   1480 TCAACATCAGTAGTCAC 1496
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (104 / 73)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.94 (47 / 16)  


3582 19.83 1.48 5.20  chr1_118720019_118722344      891  1833 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118720019_    891 TGAAAATATATCTCATATTCATTGATTGAAAGACAATATTATAATATTGT 940
                           i   v     i   i     v     i     ----   --       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC----TTA--ATATTGT 44

  chr1_118720019_    941 CAGAATGTCAAGACTGCCCTG-TCGGCAGTCTTATACAGATTTAATGCAA 989
                         i ii   v   v   v   vi- i i---   ---       i  i    
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGA---TCT---ACAGATTCAACGCAA 88

  chr1_118720019_    990 TATTGATATACATATCAGCAACATTTTTTGATTAAATGAGATTAAAATAA 1039
                          viiv  vv v  vi    vi v       --i ---  i   i --i  
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTG--CA---GAAATTGA--CAA 131

  chr1_118720019_   1040 ACCCATCCCCAAAATTACGTAGAAACTTAAGGACCCCA-AATAATCAAAA 1088
                         i iv    iv   v i ii i    ivi    iv    -    ii     
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_118720019_   1089 CAATTTTGAAAAAAAAAAAAAAAGAACAAAGT-GTAGGACTCTCACTTTC 1137
                             i        i  -------         - v       v     i 
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAA-------GAACAAAGTTGGAGGACTCACACTTCC 224

  chr1_118720019_   1138 AGATTTGAAAACTTACTACAAAGCTATGGTAATTAAAGCAATGTGGCACT 1187
                         vi    v                   ii     i  ii  i     i   
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_118720019_   1188 GGCATAAACACAGACATATATACCAATGGAGTGGAATATACCAATAGAAA 1237
                                iv i         v i       i i    ------- -  i 
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAAT-------T-GAGA 316

  chr1_118720019_   1238 GCCCAGACATAAGCACTCACATATATGGTCAAATGATTTTTGGAAAAGGT 1287
                          i     v    i v vi    v         v       i iv  i   
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_118720019_   1288 GTCAAGACCATTCAATGGGGAAAGGACAGTCTTGTCAACAAATTGTGCTA 1337
                          i                      i i      v         v     i
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_118720019_   1338 GGAAAACTGGATGTTTACACGTAAAA-AATTAATTTTGATGCTTACCTAA 1386
                            v        i?ii   i i    -   v  v  v  iv i     v 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_118720019_   1387 CATCATATACAAAA-TTAACTCAAAATGGGTGAAAGACCTAAACATAAGA 1435
                           i           -              i v ?         ii     
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_118720019_   1436 GCTGACA-TATAAAAACTTTTAGAATGAAACATAGGGAAAAAGCTATATG 1484
                            i v -       -  i      vi         ?iv   v  vii  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_118720019_   1485 ACACTTCATTT-GGTAATAATTTCTTGGATATGACTTTAAAGGCACATGC 1533
                           -   viv  -  i   ii      i        vii   i     v  
  L1M4_orf2#LINE/    566 AC-CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_118720019_   1534 AACAA--TAAAAAGTAGACAAACTAGACTTCATAACAATTAAAGACTTTT 1581
                              --v     i    i   i i        v v       i      
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_118720019_   1582 TTGCATCAAAGGAAATATTCAACAGAGTGAAAAGGCAATCTACCTACTAC 1631
                         v   v        v ivv    v i         i   i i  vv -- i
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA--AT 712

  chr1_118720019_   1632 AGGCTTCAAGAAAATGTTAACAAATCATATATCTGATAAGAGGTTGATAT 1681
                         i  -----       i  vi                    i ii vi   
  L1M4_orf2#LINE/    713 GGG-----AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_118720019_   1682 CCACAATATATAGATAACTCCTGAAACTCAACAACAA-----CAAAAAAC 1726
                            v        i v     i iv       i  i  -----    v   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_118720019_   1727 CCAGAACTGATACAAATATGGGCAAAGAACTTGGATAGACATTTCTCCAA 1776
                            ------  v?   v          i i   i                
  L1M4_orf2#LINE/    808 CCA------ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_118720019_   1777 AGAAAATATACAAATGGCCAGAAAGCATATGAAAAGATGCTCAACCTCAC 1826
                             i               iv     i                 v   ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_118720019_   1827 TAATTTT 1833
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.61 (113 / 70)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.62 (63 / 24)  


3015 21.92 1.83 9.38  chr1_118766702_118774735.rev     1173  2153 (5881)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_118766702_   1173 GGAATAATATTCTGTGTTCAGAGACTGGAAGAATTAATATAGCTAAAACG 1222
                             vi    i ii      vi  i       v       v i   i i 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_118766702_   1223 TCCATACTACCCAAAAATATCAACAGATTTAATGCAATCTCTATCAAAGT 1272
                         v v     v      vvv   v       i  i      i        i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_118766702_   1273 CACAATGACATTCTTCACAGAAATAGAAAAA--AGTCCTAAAATGTGTAG 1320
                          v  iivi v  i  ii       v  v  i--ii         vii  v
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_118766702_   1321 GGGAACCACAAAAGACCCTTAGTACTCAAAACCATCTTCAACATAAATAA 1370
                           i  i-i   ii     vv i  vi      v     v  v vi  v  
  L1M4_orf2#LINE/    152 GGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_118766702_   1371 CAAAGCTGGAGGCATCATATTGCCTTATGTGAAAGTATACTATATCCATC 1420
                              i      vv   i i v  iv  v v   ----------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA---------------- 234

  chr1_118766702_   1421 ATGACTTGTCAAAAAAGAATTTTTTTAAAAGTATACAAAGTTATAGTAAC 1470
                         ---    ii------------------------       i  i     i
  L1M4_orf2#LINE/    235 ---ACTTAC------------------------TACAAAGCTACAGTAAT 257

  chr1_118766702_   1471 CAA-ACAGCATGATACTGGCATAAAAACAGACATATAGACCAATGGAACT 1519
                            -    ii  i           ii i           i        iv
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_118766702_   1520 GACCAGAGAGCCCAAATAGAAATCCATGCATTTATATCCAACTCATTTTT 1569
                           viv     i   i v v   i    i       ivi   i v     i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_118766702_   1570 GACAAAGATGTCAAGAACATACA-TTGAGAAAGGAGAGTCTCTTCAATAA 1618
                              i i  i     v   v  - v i     i v     i     i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_118766702_   1619 ATGGTTTTGGGAAAACTGGATATCCACATTCAGAAGAATGAAATTAGACC 1668
                              vi     v         ?      v  i         i  i    
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_118766702_   1669 CTTATCTCTCACCATATTCTCACCATATTAAAAAATCAACTCAAAATGGA 1718
                          i  i   v        ----  -------      i             
  L1M4_orf2#LINE/    458 CCTACCTCACACCATAT----AC-------AAAAATTAACTCAAAATGGA 496

  chr1_118766702_   1719 TTAAAGACTTAAATTTAAGACTTGAAACTATAAAACTATATAACTATAAA 1768
                          i ?    i     v     ----------------------i   ----
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGA----------------------GCTA---- 520

  chr1_118766702_   1769 ACTCGAAACTATAAAACTCCTGGAAGAAAACATTGG-GTAAATAAATGCT 1817
                         -----              i i           v  -      -----  
  L1M4_orf2#LINE/    521 -----AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-----CT 560

  chr1_118766702_   1818 TTATAACATTGGTGTGGACAGTAATTTTTCAAA---GACCTCAAAAGCAC 1864
                          ii i  v    vv i i  i ii   i i i ---   vi         
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_118766702_   1865 AGGCAGCAAATGCAAAAATAGACAAATCATATTACGTCAAA-TTG----T 1909
                          i   i    v v         i    iiv i v i     -  i----i
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_118766702_   1910 CTCTGAACAGCAAAGGAAAC----AACAGAGTGAATAGATAACCTACAGA 1955
                         i i  vi vv       v  ----  v i      v   i    i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_118766702_   1956 ATAAGAGAAGATATTTGCAAATTATATATCTGACAAGAGGTTAATATCCA 2005
                           ii     i            i          i   i ii vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_118766702_   2006 AAATATCTAAGGAACACAAATAACTCAGTAGCAAAAAATCCAAACAATTT 2055
                         i     v   i    v vv i      i  ii     i-v    i  iii
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAG-ACAAATAACCC 809

  chr1_118766702_   2056 GACTTAAAAATAAGCAAAAAATATGAATAGACACTTCTCCAAAGAAGACA 2105
                         i i ?      ii     ii  v          i              i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_118766702_   2106 TACAAATGGCTAACAGGTAAATGAAAA-ATGCTTTATGTCGGGGGTGTT 2153
                                   i  i i i v       -     iv ii  i????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (140 / 72)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 6.11 (110 / 18)  

2879 27.27 1.88 1.22  chr1_118766702_118774735.rev     6642  7543 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118766702_   6642 TGGAAGAATATTCCACGCTTATAGATAGGAAGAATCAATATTGTGAAAAT 6691
                              ii    i   i i i  i   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118766702_   6692 GGCCATACTGCCCAAAGTAATTTATAGACTCAACGCCATTCCCATCAAGC 6741
                            v     v      v i  i  i   i       v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118766702_   6742 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTACAGTTCA 6789
                          v   iivi i  i  ii     -   -- v  i  - iii  v i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_118766702_   6790 TATGGAACCAAAAAAGAGCCCTCATTGCCAAGACAATCCTAAGCAAAGAG 6839
                                viiv  ii  v  vvv  v     i      i i iv  ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_118766702_   6840 AACAAAGCTGGAGGCATCACGCTACCTGACTTTAAACTATACTACAAGGC 6889
                                i      vv    i  v  ii i  i   viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_118766702_   6890 TACAGTAACCAAAACAGCATGGTACTGGTACCTAA--ACAGATACATAGA 6937
                                 i   i    ii         i --   -- i   i i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATAGA 296

  chr1_118766702_   6938 CCAGTGGAACAGAACAGAGACCTCAGAAATAACACCACACTTCTACAACC 6987
                         i  i     i    iv    vii         vv   i  v i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_118766702_   6988 ATCTGATTTTTGACAAACCTTGCAAGAACAAGAAATGGGGAAAGGATTCC 7037
                          vi       i     ivv vv     v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_118766702_   7038 CTATTTAATAAATGGTCCGGGGAAAATTGGCTAGCGATATGTAGAAAGCT 7087
                           v  i  i       v v    v  i   v  ? v i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_118766702_   7088 GAAACTGGATCCCTTTCTTACACCTTATACAAAAATTAATTCGAGATGAA 7137
                            ii    i    vi  i     v              i  i i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_118766702_   7138 TTAAAGACTTAAATATTAGATCTAACACCATAAAAAACCCTAGAATAAAA 7187
                          i ?    i     i v   v    v  i      v-i i     v    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chr1_118766702_   7188 CCTAGGCAGTA--CCATTCAGGACACAGGCATGGACAAGGACTTCGTGTC 7235
                          v    ?-   --i -   iv   viv  vv i i   v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_118766702_   7236 TAAAACACCGAAAGCAATGGCAACAAAAGCCAAAATTGACAAAGGTGATC 7285
                           vi     i      vvi          vv     v  i   vvv  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_118766702_   7286 TAATTAAACTAAACAGCTTCTACATGGCAAAAGAAACTACCATCAGAGTG 7335
                          v  i   v v  v i   i iiiivv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_118766702_   7336 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 7385
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_118766702_   7386 CAAAGGGCTAATATCCAGAATCTACAAGAAACTCAAACAA----AT--TT 7429
                         i  i  i  vi          v  i  ii     vv    ----  -- v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_118766702_   7430 ACAAGAGAAAAAACCCA-TCAAAAAGTGGGCAAAGCATATGAAGAGATAC 7478
                          v    v   v      - i?    i         v  v    v   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_118766702_   7479 ATCTCAAAAGAAGACTTCTCTGCA----GCCAACAGACACATGAAAAAAT 7524
                         v    v        ---- v i  ----     i ii          i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_118766702_   7525 GCTCATCATCACTGGTCAT 7543
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (140 / 102)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  


3030 27.29 1.90 0.34  chr1_118797532_118803040     4123  5016 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118797532_   4123 TGGAAGGACATTCCATGCTCATCAATAAGAAGAATCAATATTGTGAAAAT 4172
                              i  i  i     i    vi  vi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118797532_   4173 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGC---------TAACA 4213
                            v     v      v i  i  i        i  ---------i  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118797532_   4214 T------TGACTTTCTTCACAGAATTGGAAAAAATGACTTTAAAGTTCAC 4257
                          ------  v    i  -i     v v  v  iv   iii    i    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_118797532_   4258 ATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAATA 4307
                               viiv  ii  v  viv        i      i i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_118797532_   4308 ACAAAGCTGGAGGCAC-CACGCTACCTGACTTCAAACTATGCTGCAAGGC 4356
                               i      -  -   i  v  ii i      viv i  i   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_118797532_   4357 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 4406
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_118797532_   4407 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATATACAACCAT 4456
                                i    iv   ivii         vv   i    v  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_118797532_   4457 ATGACCTTTCACAACCCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 4506
                         v   ii  iv    vvv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_118797532_   4507 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 4556
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_118797532_   4557 AACTGGACCCCTTGCTTACATTGTACACAAAAATTAACTCAAGATGGATT 4606
                          ii         vv  i   iii  i                i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_118797532_   4607 AAAGACTTAAATGTAAGACCGAACACCATAAAAACCCTAGAAGAAAACCT 4656
                          ?    i           v v  v  i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_118797532_   4657 AGGCA-ATACCACTCAGGACATAGGCATGGGCAAAGCCATCATGACTAAA 4705
                            ?i- v i -i  iv   v v  vv i     v viv  v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_118797532_   4706 ACACCAAAAGCAATGGCAATAAAAGCCAAAATTGACAAATGGGATCTAAT 4755
                                     vvi    i     vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_118797532_   4756 TAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTATCATGAGAGTGAACA 4805
                         i   v    i i   i  ii vv    i  v       v  i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_118797532_   4806 GGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTACCCATCTTACAAA 4855
                          i     i       i         v       vii ivi    v i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_118797532_   4856 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAGGAAGAA 4905
                           i  vi          v  i         vv    v iv i iv  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_118797532_   4906 AACAATTAACCCCATCAAAAAGTGGGCAAAGGCTATGACCAGACACTTCT 4955
                         i    v      v  i?    i          v v   vi     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_118797532_   4956 CAAAAGAAGACATTTATGCAGCCAACAGACATATGCAAAAATGCGCATCA 5005
                          v        i  vi viii     i ii  i   v   i    v  v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_118797532_   5006 TCACTGGTCAT 5016
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.86 (20 / 7)  


 342 18.42 0.00 0.00  chr1_118806029_118809215      168   243 (2944)  C L1M4_orf2#LINE/L1   (0)   908   833  

C chr1_118806029_    243 TGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATG 194
                             i     i     v        i  vi viii     v  i      
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

C chr1_118806029_    193 AAAAAATGCTCATCATCACTGGCCAT 168
                             i       v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.00 (0 / 0)  

3148 26.83 1.11 0.44  chr1_118806029_118809215     1793  2694 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118806029_   1793 TGGAAAAACATGCCATGCTCACGGATCAAAAGAATCAATATCATTAAAAT 1842
                               i i  v     i   i    iii    v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118806029_   1843 GGCTATACTGCCCAAATCAATTTACAGATTCAATGTTATTCCTATCAAAC 1892
                            v     v       ii  i           i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118806029_   1893 TACTAAAGAAATTCTTTACAGAAATAGAAAAACT-ACCTTAAAATTCATA 1941
                          v i ivvivv  i   i       v  v  i  - i i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_118806029_   1942 TGGAACCAAAAAAGAGCCCAAATAGCCAAGGCGATTCTAAGCAAAAAGAA 1991
                              viiv  ii  v  vi         ii i  ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_118806029_   1992 CAAAGCTGGAGGCATCACATTACCCAACTTCAAACTATACTACAAGGCTA 2041
                              i      vv     i v     i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_118806029_   2042 CAGTTACCAAAACAGCATGTCACTGGTACAAAAACAGGCACAGAGACCAA 2091
                             v i   i    ii  vi     i i  ii i  i  i v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_118806029_   2092 TGCAACATAATAGAGAGCTCAGAAATAAAGCCATACATCTACAATCATCT 2141
                           v  i v   v     ii          v        i  iii   vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_118806029_   2142 GACATTTGACAAAGCTGACAACAACAAGCAATGGGAAAAAGACTCCCTAT 2191
                           iv  i     i v  v   v v  vv       i   ii ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_118806029_   2192 TCAATAAATGGTTCTGGAATAACTGATTAGCCATATGCAGAAGATTGAAG 2241
                             i       v    i i     iv  ?   i     i    v     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_118806029_   2242 CTGGACCCCTTCCTTATACTGTACCCAGAAATCAACTCAAGATAGATTAA 2291
                         i         v   i i  ii  iv  i    i       i  i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_118806029_   2292 AAACTTAAATGCAAAACCCAAAACTATAAAAACCCTGGAGGACAACTTGG 2341
                          i  i      i  i v i            vi i i  i  v   v i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_118806029_   2342 CAATACCATCCT-G-GACATAGGAACAGGCAAAGATTTCATGACAAAGAC 2389
                         v?i  v-   i - -   v v  ivi      v i    v iivv v   
  L1M4_orf2#LINE/    551 GNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_118806029_   2390 ACCAAAAGTAGCAGCAACAAAAGCAAAAATTGACAAGTGGGATCTAATTA 2439
                                 i vv           v      v  i  i v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_118806029_   2440 AACTTATGAGCTTCTGCAAAACAGAAAAAACTTATCAACAGAGTAAACTA 2489
                           v   vi i   i  iivvv  i ii v   -     v i   i  vvi
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGAAAGTGAAAAG 698

  chr1_118806029_   2490 ACAACCCACAGAATGGGAGAAAATATTTGCAAACTATGCTTCTGATAAAA 2539
                                                          ii  iiv        ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_118806029_   2540 GTCTAATATCCAGCATCTATAAAGA--TCTTAAACAAATTTACAAGAGAA 2587
                          v  vi       v  v        --     --   v iv i  v i  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAAA 796

  chr1_118806029_   2588 AAACAA----CCTCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTC 2633
                          i    ----  iv   ?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_118806029_   2634 TCAAAAGAAGACATACATGCAACCGACA-GCATATGAAAAAAAGTTCAAT 2682
                           v        i     viiii  i i -   i       i v i    i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_118806029_   2683 ATCATTGATCAT 2694
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (150 / 88)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


 393 26.15 7.18 2.05  chr1_118823149_118829415.rev      236   430 (5837)  C L1M4_orf2#LINE/L1   (240)   668   464  

C chr1_118823149_    430 TCATAGCATACACAAAA-TTAACTGAAGGTGAATTCCAGTCATAAA-ATA 383
                            i v    i      -      v  ii  i  iv?  v v    -i  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

C chr1_118823149_    382 -----TAAAATCATATCAATGTTA--AGATAAACATAGGAGAGTGTCTTT 340
                         -----     ii   vv v v   --   -         ? vivi    i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGA-AAACATAGGNGTAAATCTTC 562

C chr1_118823149_    339 GTCGTTATTGAGC-AAGCAATGATTTCTTAGCTAGGCCATACCAAGGAC- 292
                           - viv   i i- i      i        v  v -- i     iii -
  L1M4_orf2#LINE/    563 GT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG--ACACCAAAAGCA 609

C chr1_118823149_    291 TAAATA-CAAAAGGAACAATTG-TAAATTGGATCTGCTTAAAAT-AAAAA 245
                         i  ii -      i  v   v -         ii vv i     -     
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

C chr1_118823149_    244 CTTATTTGC 236
                            v v   
  L1M4_orf2#LINE/    660 CTTTTGTGC 668

Transitions / transversions = 1.33 (28 / 21)
Gap_init rate = 0.06 (12 / 205), avg. gap size = 1.50 (18 / 12)  

3225 26.36 1.22 0.66  chr1_118823149_118829415.rev     4874  5776 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118823149_   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4923
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118823149_   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAAC 4973
                            v     v     iv i  i           i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118823149_   4974 TACCAATGACTTTCTCCACAGAATTGGAGAAAACT-ACTTTAAAGCTCAT 5022
                          v   iivi i  i iii     v v  v  i-  - iii    ii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_118823149_   5023 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTGAGCCAAAAGA 5072
                               viiv  ii  v  v v  v     iv     i   ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_118823149_   5073 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5122
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_118823149_   5123 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5172
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_118823149_   5173 ATGGAACAGAAC--AGAGCCCTCAGAAGTAACGCCACATATCTATAACTA 5220
                               i    i--    i  --    i   vv   i i  i   iiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_118823149_   5221 TCTGATCTTCGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5270
                         vi    i        ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_118823149_   5271 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5320
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_118823149_   5321 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5370
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_118823149_   5371 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5420
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_118823149_   5421 TAGGCAT---TCCCATTCAGGACATAGGCATGGGCAAGTACTTCATGTCT 5467
                             ?i ---  ---   iv   v v  vv i     vvii   v ivv 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_118823149_   5468 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGGCAAATGGGATCT 5517
                          vi            vvi          vv     v ii    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_118823149_   5518 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5567
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_118823149_   5568 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5617
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_118823149_   5618 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5667
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_118823149_   5668 AAA-----ACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5712
                            ----- i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_118823149_   5713 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTAA 5762
                             v        i  vi viii     v  i          i     v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_118823149_   5763 CCATCACTGGCCAA 5776
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.43 (17 / 7)  


3597 22.40 2.80 1.12  chr1_118861536_118865586.rev     2670  3562 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118861536_   2670 TAGAAAGACATCCCAT---CATGGATTGGAAGACCTAATATTATTGAAAT 2716
                          i      i       ---               i       i  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118861536_   2717 GTCAACGTTATACAAAGCTATCTGCAGATTTAATGCAATCCTTAATAAAA 2766
                          v   iii viv    viv    i      i  i       i  vi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118861536_   2767 TCCAAGTGGCTTTTTTTTGTAGAAATAGAAAGAAAAGACATTTAAAATTC 2816
                            v  iv  i      - i      v  v - ivv  i-ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACA-AGCTGAT-CCTAAAATTC 147

  chr1_118861536_   2817 ATGTGAAATCTG-AAAAGATCCCTAATAACCATAACAAACTTGAGAAAGA 2865
                           i  i  -v  -  ii  i  vv    i   v     v     i     
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_118861536_   2866 AAAATAAAGCTGTGGGTCTTATACTTCCTGCTCTCAAAACATATTACAAA 2915
                          i  i    i  vi  v  i i      iiv i       v  i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_118861536_   2916 GTTATAGTTATCAAAACAGTGTGATACTGGTATAAAGACAAACATATAGT 2965
                          i  i   v     i        i      i    i  i i        v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_118861536_   2966 CCAATGGAAAACAATAGAGAACTCGGAAATAAATTGACAAATACATGGTC 3015
                         i        v v   v    iii i        iiv i v  vi      
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_118861536_   3016 AACTGATCTTTCATAAGGGTGTCAAGAACACACAATCGGAAGAAAATTGT 3065
                           i    i  iv i       i     v  iv    v  i i i   v  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_118861536_   3066 CTCTTCATCATATGGTATTGAGGAAAACTGAATATCCACATGCACAAAAA 3115
                           i    v  v     ii  -   v     i   ?         ---   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCA---AAA 442

  chr1_118861536_   3116 AAATAAAGTTGGAGTCTTACCTCACACCATATTTAAAAATTTAATTAAAA 3165
                         i   i        vi i               vi       v v i    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_118861536_   3166 TTGAATTAAAGTCCTAAGTGTAATACGC-AAAACTATAAAAACCCAAAAA 3214
                          - i  i ?  v     i     v -  -            vi iv i  
  L1M4_orf2#LINE/    493 T-GGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAA 540

  chr1_118861536_   3215 CTAAACATAGGGGAAAAGTTTTCTGACATTGGATTTGGCACTGATTTATT 3264
                         vv         ? v   vi  iv    v    i  v    v  i   v  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_118861536_   3265 GGATATGACACCGAAAGCA---------------AAAATAGACAAATGGG 3299
                         i           i      ---------------        i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_118861536_   3300 ACTACATCTAACTTAAAAACTTCTGCATAGCAAAGGAAAC----AACAGA 3345
                            v    v  v          i  iiivv       v  ----  v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_118861536_   3346 GTAAAAAGGCGATCTACAGAATGGGAGAAAATAATT-TAAACCATTAATC 3394
                           i     i i i i                  v  -i   i   vv   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_118861536_   3395 TGATAAAGGATTAACATCCAGAATTTATAAGGAACACCTACAACTCAATA 3444
                               i   i vii         v     i    v i            
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_118861536_   3445 GCCAAAACCCAAATAACCCAATTAAAAAATAGGCAAAGGCATTGAATAGA 3494
                         iiv    vv              ?      i        vv         
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_118861536_   3495 CATTTCTCCAAAGAAGACATACAAATGATCAACAGGTGTATGAAAAGGTG 3544
                                          i         ii   i i iii        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_118861536_   3545 TTCAGCATTGCTAATCAT 3562
                         i   i   ii????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (123 / 73)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.50 (35 / 14)  


3388 25.22 1.33 0.44  chr1_118866597_118869281.rev     1296  2195 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118866597_   1296 TGGAAAGATATTCCATGTTCATGGATTGGAAAAATCAATATTGTTAAAAT 1345
                                    i                   i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118866597_   1346 GTCCATACTACCCAAAGCAACCTACAGGTTCAATGTAATCCATATCAAAA 1395
                          v v     v      vii i      i     i i     v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118866597_   1396 TACCAA-TGAAATTTTTTCACAGCAAAAGAAAAAACAACCCTAGGTTGTA 1444
                          v   i-  v--i     ii   v  vv  v  ivii i    iiv vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_118866597_   1445 TATAGAATCACAAAAGACCCAGAACAGTCAAAGCTATCCTAAGCAAAAAG 1494
                            i   vii   ii         i  i    i v   i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_118866597_   1495 AACAAAACTGGTGGAATCATATTACCCGACTTCAAA--TTA-TACAGAGC 1541
                               ii   v   v   i i v   i i      --   -    i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_118866597_   1542 TATAATAACCAAAACAGCATGGTACTGGCATAGAAACAGATACAT-TACA 1590
                           i i   i   i    ii             iii i   i i  -v iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_118866597_   1591 AACTAAACACAATAGAGTACCCAGAAACAAATCTATACACCTACAGTGAA 1640
                           ivi  i v   v   vii       i   i i     ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_118866597_   1641 CTCATTTTTGACAAAGTTGCCAAGAACATCCACTGGGGAAA----AGTGT 1686
                         i v     i     i v        v   i  v        ----   v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_118866597_   1687 ATATC--CAAATGGTGCTAGGAAAACTGGATATTCATATGCAGAAGAATG 1734
                         v -  --           i   v         ?i  i     i       
  L1M4_orf2#LINE/    399 TT-TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_118866597_   1735 AAACTAGACCTCTATCTGTTGCCATATACAAAAATCAAATCAAAATGGAT 1784
                           ii i    i   i  vvii              i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_118866597_   1785 TAAAGACTTAAATCTAAGACCTCAAACTATGAAGCAGCTAAAAGAAAACA 1834
                         i ?    i     v     v  v       i  i vvi  i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_118866597_   1835 ATGGGGACACTCTCCAGGACATTGGTATACAAAACAATTTCCTGAGTAAT 1884
                         vv  ? vv v   i iv   v    vv  viv  iii    i iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_118866597_   1885 ACCCCAAAGGTACAGGCAACCAAAGCAGAAATGGACAAATGTGATCATAT 1934
                           v     i i   i     v    v i    i  i    vv  iivi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_118866597_   1935 CAAG-TTAAAAAGCTTCTGCACAGCAAATAAAATAATCAACAAAGTGAAA 1983
                            i-       -   i  ii vv    vi v iv     v         
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_118866597_   1984 AGACAATCCACAGAACTGGAGAAAATATTTGCAAACTATCCACTTGACAA 2033
                               i        iv                  ii  vi ii   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_118866597_   2034 GGGATTAATAACCAGAATATACAAGCAGCTTAAACAACTCTATAGGAAAA 2083
                             i vi  v          i  iv i  ivv       v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_118866597_   2084 AAATTAATAATCCAATTTTAAAATGGGCAAAAGGTTTGAATAGACATTTC 2133
                          i iv     i      ?v            i i                
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_118866597_   2134 TTAAAAGAAGACATACAAATGATAAACAGGCATATGAAAAAGTGCTCAAC 2183
                          iv        i         iiv  i i   i       ii        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_118866597_   2184 ATCTTTGATTAT 2195
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (141 / 82)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2260 25.76 7.49 0.89  chr1_118875399_118879873.rev     2140  2927 (1548)    L1M4_orf2#LINE/L1        1   840 (68)  

  chr1_118875399_   2140 TGAAGAGATATACCACGTTAATAGATAGGAAGTCTCAATATTGTTAAGAT 2189
                           i i      v   i   v  i   v     v  i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118875399_   2190 GTCAGTTCTCTCCAAATTGATCTACATATTTAAAGCATTCCTAATCAAA- 2238
                          v  i v   i               v   i  v   v   iv      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118875399_   2239 TTCCATTAAGCTTTTTAAAAGGTGAAAATTGGCAAGCAAATTCTAAAAGT 2288
                          i   viviv      viv  ----      i     vi  i      v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG----AAATTGACAAGCTGATCCTAAAATT 146

  chr1_118875399_   2289 C-TA---------AAAGGACCTAGAATAGCCAAAATGA-CTTCAAACA-A 2326
                          -  ---------  i     i             ii -   v   v - 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_118875399_   2327 AGAACAAAATCAAAGCATTAACAGTACCTGATCTCAAGAAATACTATAAA 2376
                                 i iii  v i v   v v  ii  i    i vv     i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_118875399_   2377 ACTACAATAATCAAGATAGTGTGGCATTGGCAAAAAGATAAACAACTAGA 2426
                         i     i         i       i i     v  i    i   vv    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_118875399_   2427 TCAATAAAACAGAATAGACAATCCAGAAAGAGACCT-CACATATAGCAGC 2475
                              ii  i     v  v i        v i   i-i    v  vviv 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_118875399_   2476 AAATGATTTTCAACGAGGATGCAAAGAAAATTCAGCAGAGA--------- 2516
                           v        i  i   i   v    vv     iii i  ---------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_118875399_   2517 -TGTGC------TGGTGCTGAAACACTTGAATAGCCATAAGCAACAAATA 2559
                         - v v ------        ii   vi  i   ?   i v    v i - 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-A 445

  chr1_118875399_   2560 TAAATTTTGATCTATACCTCATGCCATATA-AGAAATTAATCCAAAATAT 2608
                          i  v  v  i iv       ii       - i       ii      iv
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_118875399_   2609 ATTATAAATCTAAATACAAAACCTAAAACTATAAGATT-TTAGCAGAAA- 2656
                           i ? i i      ii  i v            i i -    v     -
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_118875399_   2657 TATGGAAAAATATATTAGTGACATAGAGTTTGATAAAGATTTCTTAGATA 2706
                         i  i i?iv v  v  v     v v i   v ii  v i           
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_118875399_   2707 CATTACCAAAAGCATGATCCTTAAAA-----AACTGATAAATCGAACTTT 2751
                         iivi          ii v vvi    -----  iv       i i    i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_118875399_   2752 ATTAAAATTAAAATAAGTATT---TTTTGAAAGACACTTT----AAAATT 2794
                           i          -- v v  ---i  ii  i      v ----   i v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAA--ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_118875399_   2795 AAAAAACAAGTCGTAGA--GCAAAAAAAT-TTTGAAAAGCATATATCTAA 2841
                             i    vi ii   -- vi i     -    v   v         i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_118875399_   2842 TGAAGGACTTATA--CAAAATACAAAAAGAATTCTCAAAACTCAAGAATA 2889
                          i i      i  --  i    i v      i   i v       v    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_118875399_   2890 ----TTCCAATAATCCCAT----GACTGGGTATAGG-TCCAAATAAA 2927
                         ----vv v     i  v  ----i v    i v   - iii    i 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

Transitions / transversions = 1.50 (120 / 80)
Gap_init rate = 0.03 (23 / 840), avg. gap size = 2.87 (66 / 23)  

 329 20.20 0.00 5.05  chr1_118875399_118879873.rev     3889  3987 (488)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_118875399_   3889 AAAAAAAGGCAAAATATTTGATCAGACGTTTCACTAAAGAAAAGAAAATA 3938
                              vi      iv      vi    i    v i      i -----  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA-----TA 859

  chr1_118875399_   3939 AACACGTGGTAAATAAGCATTTGAAGAGATGCTCAACAATATTGTTTAT 3987
                         v   vi   iv        iv    i            vi ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 5.00 (5 / 1)  


 290 34.19 3.23 0.00  chr1_118880672_118882355      119   273 (1411)    L1M4_orf2#LINE/L1       16   175 (733)  

  chr1_118880672_    119 TGTTTATTAATTGTAAGATTTAACAATGTCAAGATATCAAGTCTCCCCAA 168
                             i  vi    v    i    i v   i     iv   vv        
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_118880672_    169 ATCAATCTGTAAGTT-AATGAAATTTCAATGAAATTTAAAAAT----TTT 213
                           ii    ii ii  -  i v   ii v  v   v ivv iv ----   
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_118880672_    214 TTATGAAAGTAGAAACTCTGATTCTTAAATCTATATGTAAGACTAAGTGT 263
                           iiii  i v  v vv     i  v    ii     v  ivvi   v v
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_118880672_    264 CTAAGACTAG 273
                          iv   v   
  L1M4_orf2#LINE/    166 CCCAGAATAG 175

Transitions / transversions = 1.12 (28 / 25)
Gap_init rate = 0.01 (2 / 160), avg. gap size = 2.50 (5 / 2)  

 424 31.58 10.23 6.29  chr1_118880672_118882355      500  1183 (501)    L1M4_orf2#LINE/L1      175   885 (23)  

  chr1_118880672_    500 GCCAAAGACAATTCTGAAAAAGAAGA------TTGG-GAATTTG-GCTTA 541
                               -     ii            ------    - i i ii-i   v
  L1M4_orf2#LINE/    175 GCCAAA-ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr1_118880672_    542 GCATATATCAAGA--TGGTAGAAGGCAATAGCAATTAAGATCATTTGCGT 589
                         v  -  v    i -- iv  v  i  v i  i   i    ivi v  -  
  L1M4_orf2#LINE/    224 CCA-ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG-GT 271

  chr1_118880672_    590 ATTATTGCAT--GGATACAGAAAAAGATCAGTGGAACAAAACAGGGAAGC 637
                          i i--    --     v v v v      i     i i  iv i  iv 
  L1M4_orf2#LINE/    272 ACTG--GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_118880672_    638 CAGAAGTAGCTCTTATTGTATACAAAATTT--GGTTAAC--ATATT--AT 681
                              i  ivi i------     ---   --   i  i--  v  -- i
  L1M4_orf2#LINE/    320 CAGAAATAAACCC------ATACA---TTTATGGTCAATTGATTTTCGAC 360

  chr1_118880672_    682 AGAAATACCACTACAAATCAGTTATAAAAGGATGGAATTAGTTAACAAAT 731
                          iiii i   vv  v v   i vivi    i  i vv  -v i       
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-TTCAACAAAT 409

  chr1_118880672_    732 GCCGCTCAGACAGTTGCCT-TCCTTTTAGGAAAAATATG----------- 769
                          vi   vi    ii  vv -?  viv - v    iv   -----------
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAATGAAGTTGGACCC 458

  chr1_118880672_    770 ------TACACAATA----------AATTCTATGTGGTTTACTGATCTAA 803
                         ------i    v   ----------  i  v vi   v i ?v  i    
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_118880672_    804 GT-----AGCCTAGGA----AAAGCTTTTAGCAACAATTCTATGAGAATA 844
                         i -----   -  ii ----   i  i    v iv  viv  v ? v v 
  L1M4_orf2#LINE/    509 ATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_118880672_    845 TCTTTATGACCCTATTGTAGAAAAAAATGTTTTAGACATAAAACAAAAGG 894
                             ii     i ivvv   iv  vii v i     i  i v  v   i 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_118880672_    895 CTCATCTTACAAAG------ATTAATAAATTTGTTTATATAAATATGTAA 938
                          v  vviv     i------  vi       v vi vi  v  v  vv  
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_118880672_    939 ATCTTCTGTTATATAAAAGAACATCATAAACATGGAGAAAACATGAGACA 988
                          v   i   vv - v    i   ii  v  v vi v     v ii vv  
  L1M4_orf2#LINE/    658 AACTTTTGTGCT-TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_118880672_    989 CAAACTGAGAGAAGATATTTGAAACTTGTATA-------AAGAATTGGTA 1031
                           i v  i     i       v  v ii    ------- i i i v   
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_118880672_   1032 TTAATTTAAAAATGTGTTTATGAA-AGTTCTACCAAACCGCACCCCAGCC 1080
                          i----i i  ----- v   i  - ii   vv   ------- i  ---
  L1M4_orf2#LINE/    757 TC----CAGAA-----TATATAAAGAACTCTTACAA-------CTCA--- 787

  chr1_118880672_   1081 AAAAGAAAAACTAAAAGATAAA-AACCAAATGGGAAAAAGGGCAAAGGTT 1129
                         ------ v  iv      i   -    v   v?i    v         v 
  L1M4_orf2#LINE/    788 ------ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_118880672_   1130 TTGAGCAGAAAATTCATAGAAGAGGAAACCTGGATAGTTAACAAACATAC 1179
                             ii   v v   vivi    i  v iviii  i ii  i  i  i i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_118880672_   1180 AAAA 1183
                         i   
  L1M4_orf2#LINE/    882 GAAA 885

Transitions / transversions = 1.23 (117 / 95)
Gap_init rate = 0.04 (31 / 711), avg. gap size = 3.65 (113 / 31)  


2934 28.63 0.33 0.33  chr1_118884683_118888940.rev     2863  3770 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118884683_   2863 TGGAAACACATCCCATACTCATGAATGGGTAGAATCAATATTGTCAAAAT 2912
                               v i       ii     i  v  v   v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118884683_   2913 GACCATACTTCCAAAAGCAATCTACAAATTCAGTACAATTCCCATCAAAA 2962
                          i v     i  v   vii       i     iii    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118884683_   2963 TACTATTTTTATTCTTCACAGAACTAGAAAACACAATTCTAAAATTCATC 3012
                          v i vi viv  i  ii     v v  v  vvii  i           v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_118884683_   3013 TGGAACCTAAAAAGAGCCTGCATAGCCAAGGCAAGACTAAGCAAAAAGAA 3062
                              vivv  ii  v  v v        ii   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_118884683_   3063 CAAATCTGGAGCCATCACATTACGTGACTTCAAA-TATACTGTTAAGGCT 3111
                             vi     vvv     i v vii i      -iv    i-i  i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA-CAAAGCT 249

  chr1_118884683_   3112 ATAGTCAGTCAA-ACAGCATGGTACTGGCATAAAAATAGGCACACAAACC 3160
                          i   - i    -    ii              ii    i  i i i i 
  L1M4_orf2#LINE/    250 ACAGT-AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_118884683_   3161 AATGGAACAGAATAAAGAACCCAGAAATAAAGCCAAATACTTGCAGCCAA 3210
                                i     vi   ii           v   v i i  iii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_118884683_   3211 CTGATCTTTGACAAATCAAACAAAAACATTAAGTGGGGAAAGGACACCCT 3260
                         i    i  i     ivvviv   i v    v i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_118884683_   3261 ATTTAACAAATGGTGCTAAGATAATTGGCAAGCCACATATAGAAGAATGA 3310
                         v  i             ii  i  i   vv ?      ii i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_118884683_   3311 AACTGGGTCCTCACGTCTCACCTCATACAAAAATCAACTCAATATGGATC 3360
                          ii   ii  ii  v  v    vi          i       v       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_118884683_   3361 AATGATTTAAATCTAAGACCTGAAACCTTAAACATTCT-GGAAGACAACA 3409
                          ?v  ii     v     v  i    iv    - i   -i     v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chr1_118884683_   3410 TCAGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCATGACCAAG 3459
                          vi ?iv  vi    vv   v    v        v ii   v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_118884683_   3460 AACTCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGCCTTAAT 3509
                          vvi        v v         iv   i   i   i  v  v   v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_118884683_   3510 TAAACTAAAAAGCTTCTGCACAGCAGAAGAAATAATCAGTAGAATAAACA 3559
                         i   v v    i   i  ii vv  i i  v iv    iv i i i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_118884683_   3560 GACAACCCACAGAATGGGCAAAAATCTTCATAATCTATACGTCTGACAAA 3609
                                           vi     v  iii  vii   ii     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_118884683_   3610 GGAGTAATTCCCAGAATATACAAGGAACTCAAACAAATCAGCAAGAAAAA 3659
                            v vi vi          i  i      vv    v   ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_118884683_   3660 ATTGAGTAATCCCATCAAAAAGTGGGCTGAGGACATGAATAGACAATTCT 3709
                         ivii i   i  v  i?    i     vi    iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_118884683_   3710 CAAAAGAAGATATACAAATAGCCAAAAAACATGAAAAAAAATGCTAAACA 3759
                          v                 i     v  i  iivi    i     v    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_118884683_   3760 CTAATTATCAG 3770
                         ii ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (155 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.00 (6 / 6)  


3077 28.32 0.55 0.44  chr1_118891919_118898329     5015  5918 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_118891919_   5015 AAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGC 5064
                           ii i  i     i      i v      v i     i  v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_118891919_   5065 CATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTAC 5114
                         v     vi    iv i  i  i        i  v     i     iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_118891919_   5115 CAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATAT 5162
                            ivi i  i  ii     -   -- v  i  - iii    i       
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATAT 151

  chr1_118891919_   5163 GGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCATAAGCGAAAATAAC 5212
                             viiv  ii  v  viv  v     iv     v i ivi i  v   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_118891919_   5213 AAAGCTGAAGGCATCATGCTACGTGACTTCAAACTATACTACAAGGCTAC 5262
                             i  i   vv   ii  v vii i      viv        i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_118891919_   5263 AGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGACCAAT 5312
                              i   i    ii       v i iv ii i   v       i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_118891919_   5313 GGAGCAGAACAGAGCCCCCAGAAATAATGCCACATATCTACAACTATCTG 5362
                            ii    iv   vvi          vv   i i  i  iiiii vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_118891919_   5363 ATCTTTGACAAACCTGACTAAAACTAG-CAATGAGGAAAGGATTCCCTAT 5411
                           i  i     ivv  - i  i  i v-     i      i  vvi  v 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_118891919_   5412 TTAATAAATGGTGCTGGGGAAACTGGCTAACCATATGTAGAAAGCTGGAA 5461
                          i  i             iv      v  ?   i   i i  iiv  i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_118891919_   5462 CTGGATCCCTTCCTTACACCTTATGCAAAAATTAATTCAAGATAGATTAA 5511
                         i    i    v   i     v   i          i    i  i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_118891919_   5512 AGACTTACATGTTAGACCTAAAGCCATAAAAACCCTAGAAGAAAACCTAG 5561
                             i  v    v   v     i i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_118891919_   5562 GCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAAC 5610
                          ?i- v i -   iv   v v  vv i     v ii   v ivv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_118891919_   5611 ACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATCTAATTA 5660
                                   vvi          vv   i v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_118891919_   5661 AACTAAAGAGCTTCTGCACAGCAGGAGAAACTACCATCAGAGTGAACAGG 5710
                           v v  i i   i  ii vv  iii  v    i  vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_118891919_   5711 CAACCTACAGAATGAGAGAAAATTTTTGCAACCTGCTCATCTGACAAAAG 5760
                              i        i        v       viiiivi      i  ii 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_118891919_   5761 GCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA-A 5809
                         i  vi          v  i  v      vv    v iv i  v     - 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_118891919_   5810 CAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCTCA 5859
                             i     v  i?    i    ii      v    i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_118891919_   5860 AAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATC 5909
                                 i  vi viii     v  i          i       v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_118891919_   5910 ACTGGCCAT 5918
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.62 (156 / 96)
Gap_init rate = 0.01 (8 / 905), avg. gap size = 1.12 (9 / 8)  


3204 22.76 3.20 2.87  chr1_118981756_118983895      745  1649 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_118981756_    745 TGGAAAGATATTCTGTGTTCATGGTTTAAAAAA-TTAACATTATTAAAGT 793
                                    i ii         v  ii  i -    i   i    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_118981756_    794 GTTCATAATACCCAAAGTAATCTACAAATTTAATGCAATTCCTACAAAAA 843
                          viv   v v      v i       i   i  i     i    iv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_118981756_    844 CCCCCATGATATTTTTCACAGAAATTTATTTAA----ATCCTGAAGTTTT 889
                         i   viiviiv     ii        v i--  ----     i  i  iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chr1_118981756_    890 TATGGAACCACAGAAAAACCCA-AATAGCCAAAGCAGTCTTGAACAAAAT 938
                                vii  - iii     -          i  i       v  i v
  L1M4_orf2#LINE/    149 TATGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_118981756_    939 GAACAAAGCCAGAGGCATCACACTACCTGATTTAAAAATCCACTACAAAA 988
                                 iii    vv       v  ii    v    iii        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_118981756_    989 CTATAGTAATCAAAACAGTATGGTACCAACATAAAAACAGATACATAGAC 1038
                            i         i     i      iii     ii i   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_118981756_   1039 CAATGGAACAAAATAGAAAGCCCAGACATAAATC-ACACATAGATGGTCA 1087
                                 i i   v  i  i     v     i - i    vv       
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_118981756_   1088 ACTTATCTTTGATAACAGTGTCAAGAACACACAATGAAGAAAACATAGTT 1137
                          i v  i  i  i  vi   i     v  iv     ii    iv     i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_118981756_   1138 TCTTCATCAAATGGTGTTGGGAAAAATGGATATACACATGCAAAAAAAAA 1187
                          i    v         i     v  v      ?v           i  --
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-- 445

  chr1_118981756_   1188 AGTGAAATGGGACCCC-A--TTACATCATACACAAAAATCAACTCAAAAT 1234
                         --    i v       - -- i   i    i        i          
  L1M4_orf2#LINE/    446 --TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_118981756_   1235 GTATTAAATTCCTAAAAATAAGACCTGAAACTATAAAACTACTACTAGAA 1284
                          v  i ? vv      vi     v  i             -  --     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CT--TAGAA 540

  chr1_118981756_   1285 AAAAGAAACAGAGGAAAACCTCCATGACAGTGGTCTGAATAATGATTTTT 1334
                         i   - v i  i? v   i  i i    vv   vi iiii    i   i 
  L1M4_orf2#LINE/    541 GAAA-ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_118981756_   1335 TGTGTATGACCCCAAA-GCATGAACAAAAAAAAAGCAAAAATAGACAAAA 1383
                          ivi      v     -   ii i   v    i --         i   -
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGA--AAAAATAGATAAA- 636

  chr1_118981756_   1384 ATCAAATTACCTCAAA-CTAAAAAC-------CTTCAACAGAGAAAACAA 1425
                         - iii i v v     -i       -------      ---  i v  --
  L1M4_orf2#LINE/    637 -TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA---AGGACAC-- 680

  chr1_118981756_   1426 AATTATCAACAGAGTGAATAGA--ACCTACGGAATGGGAAAAAATATTTG 1473
                         ---      v i      v   --   i  i        i          
  L1M4_orf2#LINE/    681 ---TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_118981756_   1474 CAAACCATACATCTGATAAGGGTTTAATATCCA--------AAGGAATCT 1515
                             i    i            vi vi      --------  i   -  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CT 776

  chr1_118981756_   1516 CTTACAGCTACATAGCAAAAAGAAACAAATAAACCAATTAAAATACAGGC 1565
                               i  vv   ii       --       v      ?   v ii   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGC 824

  chr1_118981756_   1566 AAAGGACTTGGACAGACATATCTCCATGGAAGATGTACAAATACCTACCG 1615
                               i   i i      v      vi      i       iv i vii
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_118981756_   1616 TGTGTATGAAAGGATGCTCAACATTGATAATCAT 1649
                         v iii      i            ii????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.26 (140 / 62)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.39 (55 / 23)  


3180 24.13 3.02 1.79  chr1_119017649_119019744      737  1631 (465)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_119017649_    737 GAATGACATCCCATGTTCCTATACTAGAAGACTCAATATTGTTAAAATGT 786
                            v  i           v iv i i       i           i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_119017649_    787 CCATACTAACTAAAGCAATGTATGGATTCAATGCAATCCCTATCAAAATT 836
                          v     vv i   vii  v  ii       i                 i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_119017649_    837 CCAATGGCATTTTTTACAGAAATAAAGAAAGCAATTCTCTAAT--ATATG 884
                            iiv  v      i       vi v  ivii  i  vv   --     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_119017649_    885 GAAGCACAAAGGACCCACTAATAGCCAAAACTATCTTGAGAAAGCAGAAC 934
                            iii   i       v-            v       i    v     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAG-AATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_119017649_    935 AATGGTGGAGGCATCATATTGCATTATTTCAAAATATATTACAAAGCTAC 984
                           v v      vv   i i v viv         iv  i           
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_119017649_    985 AGTAATCAAAACAGTATGGTACTCATGTGAAGACAGACATATAGATTAAT 1034
                                  i     i       viii i i  i            i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_119017649_   1035 CGAACAGAATACAAAGCCCAGAAATAAATCTACACATATATGGTCAACTG 1084
                         v   i     vv i  i           i i i    v         i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_119017649_   1085 ATTTGTGACAAGGGTACCAAGGGTGCCCCAAAGGGAAAGGATAGTCTCTT 1134
                             vi         i     iviiii v vi       i       i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_119017649_   1135 CAATATCCTGGGAAATATTGGGAGAATTGAATATACATATGCAAAGGAAT 1184
                            i -vv   ---- ii     v  i  i   ?v  i       i    
  L1M4_orf2#LINE/    402 CAACA-AATGG----TGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_119017649_   1185 GAAATTGGTTGCCTATATTAGACTACACAAAAAAATTA---CAAAACGGA 1231
                            i    viv    iv i v  i i i v        ---     i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_119017649_   1232 TTAAAGACTTAAACATAAGACGTGAAACAGTAAAAATCCTAGA-GAAAAC 1280
                          i ?    i    ii     vv i    vi     v  i    -      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_119017649_   1281 ATAGGG--AAAGCTTCATGGCATTGGTCCTAGCAATGATTTCATTGGA-A 1327
                              ?--   v    i  i v    viivi      i    -  i  - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATA 595

  chr1_119017649_   1328 TGACACCAAA-GCACGGGTAATAAAAGCAAAAAGTCGACAAGTGGAACTA 1376
                                   -    ii i  i     -     i v  i  i v i   v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTT 644

  chr1_119017649_   1377 CA----AACTAAAAAGCTTCTGCACAACAAAGGAAAAAATCAAGAGAATG 1422
                           ----  i      -   i  ii vv       v vv       i i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_119017649_   1423 AAA-GCCAACCTATGAGATGGGAGAAAACATTTGCAAACCATATACTTGA 1471
                            - v     i iiii           i         i      ii   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_119017649_   1472 TAAGGG-TTAATTTCCAAAATATATAAGAAAATT-----ATTCAA----- 1510
                               -i vi v    i         ii  v i----- i    -----
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_119017649_   1511 -AGAAATGAATAATCTAAATTTAAAATAGGCTAAGAACACAAATACACAT 1559
                         - i i ii     i i  v ?v     i   v   i ivii    v    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_119017649_   1560 TTCTACAAAGTACACAAACAGATGGCCAACAGGTATCAGTAATTGTCAAT 1609
                             v     v v i v   i        i i i -  vv  -----  v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCA-CATGAA-----AAG 887

  chr1_119017649_   1610 ATTGCTTAATGTCACTAATTGT 1631
                           -   i  ii   ????????
  L1M4_orf2#LINE/    888 AT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (135 / 77)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 2.15 (43 / 20)  


1208 20.00 8.86 4.30  chr1_119050559_119055058.rev       98   492 (4008)  C L1M4_orf2#LINE/L1   (0)   908   496  

C chr1_119050559_    492 ATCAGAACACCTAAATATATAAAGCAAATATTAATAGATTACAATTGTTA 443
                             ? i-        i  - i   v  v i  ------  v  i v   
  L1M4_orf2#LINE/    496 ATCAWAG-ACCTAAATGTA-AGAGCTAAAACTA------TAAAACTCTTA 537

C chr1_119050559_    442 GAACTTCCTAATTAAT-TGGGA--AAAGCTTCTTGACATTGCTCTGGATA 396
                            v-----  --  i- i  ?--   v    v    v   vvi i ii 
  L1M4_orf2#LINE/    538 GAAG-----AA--AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

C chr1_119050559_    395 ATAATTTTTTAGATGTGACCCCAAAAACACAGGCAACCAAAGCAAAAG-- 348
                           ii   i      i    v      i    i     v    v    i--
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

C chr1_119050559_    347 -----------CT-----AAAACTAAACAGCTTCTGCACAGTGAAGGAAA 314
                         -----------  -----    i    - i   i  ii vvii     v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACA 679

C chr1_119050559_    313 C--------AAGTGACTACACAACCTACGGAATAGGAGAAAATATTTGTA 272
                          --------      vv v      i  i    i              i 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

C chr1_119050559_    271 AACCATATATCTGTTAAGGGATTAATATTCAAAATAGATAAGAAACTCCT 222
                           i          v       i vi   i  i    v    ii     i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

C chr1_119050559_    221 ACAACTCAATAGCAAGAAAGA-AAATAACCCAATTTAAAAATGGGCAAA- 174
                                    ii  -     -             ?             -
  L1M4_orf2#LINE/    780 ACAACTCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

C chr1_119050559_    173 --CCTGAATAGATATTTCTCCAAAAAA-ATATACAAATGGTCAGCAGGAG 127
                         --ii        i           i  -            i  ii i vi
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

C chr1_119050559_    126 TTTGAGACAATGC-CAACATCATTAATCAT 98
                         iv   i vi    -        ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (51 / 25)
Gap_init rate = 0.04 (16 / 413), avg. gap size = 3.25 (52 / 16)  

3090 25.73 2.79 0.12  chr1_119050559_119055058.rev     3143  4001 (499)    L1M4_orf2#LINE/L1        7   888 (20)  

  chr1_119050559_   3143 GATATCA-ATGTTAATGGATTGCAAGGATTAATATTGTTAAAATGTTCAT 3191
                               v-     v        v   iv             i   viv  
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_119050559_   3192 ATTACCTAATGTAATCTACAGATTCAA-----TTTCTATCAAAATCCCAG 3236
                          i v  i  vv i              ----- ii               
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_119050559_   3237 TATCAATTTTCACAGAAA----CAAAAAAATCCTAACATTTGTATGGAAA 3282
                         ivv vv    ii      ----   ivvi       v   ii        
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_119050559_   3283 CAGAAAAGATCTTGAATAGTCAAAGCAATCTTGAGCAAACAGAGCAAAGT 3332
                         iiv  ii  i iv      i    i         iv  iv   i      
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_119050559_   3333 TGGAAGCATCACACTGGTTGATTTTCAAA-----TATAAAGCGATTATAA 3377
                             i vv       vviii    iv   -----  i     v ivi   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_119050559_   3378 TGAA-ACAACATGGTACTGATATAAAAATAGATACATCAACCAATGGAAT 3426
                          v  -   iii        ii    ii     i i  vi i         
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_119050559_   3427 GGAATAAAAAGCCCATTAATAAACCTAAGTATTTATGCTCAGTTGATTTT 3476
                         i    vi i  i   vv        i vii       v   i        
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_119050559_   3477 CAGCAAAGGTGCTAAGAACACACAATGGGAAATGGACAGTCTCTTCAATA 3526
                          ii   i     i    v  iv       i  v i i     i     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_119050559_   3527 AA-AGTGTTGGAAAAACTGGATAACCCCATGCAGAGGA-TGAAATTGAAC 3574
                           -i   i   i v         ?  v      i i  -    i   i  
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_119050559_   3575 TC-TATGTCACACCATAGA-GAAAATCAAC-AGAAACGAATTAAAGATTT 3621
                         i -  iv          v -i     i   -vi   i i  i ?   ii 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_119050559_   3622 AAATGTAAGACCTAAAACCATAAAGCTACTAGAGGAAAGCA-AGGAAGAA 3670
                                   v       i     i  vi    i    i  -   ?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_119050559_   3671 G-CTCCACTACTTTAGTCTGGGCAATGACTTCTTCGATAGGAT-TTGAAA 3718
                         i-  i iiv  i  i vi i       ii     v    v  i-iii   
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_119050559_   3719 GCACATGCAACAAAAGCAAAAATAAACAAATGGGAATGCATCAGACTAAA 3768
                              v          v       i i    v   v v     i v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_119050559_   3769 AAGTTTCTGCACAGTGAAAGAAACAATGAACAAAGTGAAGAGACAGCCCA 3818
                           ii  i  ii vvii  i  v  v  v  v        i     i    
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_119050559_   3819 GGGATTGAGAGGAGATATTTGCAAACCATAACTCAGATAAGGAACAAATA 3868
                         vi  v  i   i i           i    vv  v       i  vvi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_119050559_   3869 TCCAAAAGACATAAAAAACTAAAACAACTCAACAGCAGAAAAAACAAATA 3918
                             i  v i     i    vvv         i ii -    i       
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATA-AAAAGACAAATA 805

  chr1_119050559_   3919 ACCCAGTGAAAAAATAGGCAAATGATCTGAACAGACATTTCTAAAAGGAA 3968
                              i v?      i      v   i    i          vv  i   
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_119050559_   3969 GAAATGTAAATGGCCAATAGCTATATGAAAAAA 4001
                           v  ii            ivi i       i 
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.75 (138 / 79)
Gap_init rate = 0.02 (14 / 882), avg. gap size = 1.79 (25 / 14)  


2186 27.66 4.22 0.95  chr1_119072971_119075103      500  1233 (900)    L1M4_orf2#LINE/L1       73   830 (78)  

  chr1_119072971_    500 TACAGATTCAATGCTATTCCTATCAAACTACCAACATCATTCTTTACAGA 549
                                    i  v  i         v v   i vv v  i   i    
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chr1_119072971_    550 ATTAGAAAAAA-AATTCTAAAATTCATATGGGACCAAAAGGGAGCCTGAA 598
                          v v  v  iv-i  i               i viiv      v  v   
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr1_119072971_    599 TAGCCAAAGAAGTCCT-------AAGCAC--------------CACACTA 627
                                 iv i  i -------   v  --------------      v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_119072971_    628 CCTGAATTCAAACTATACTATAGAGCCACAATAACCAAAACAGCTTGGTA 677
                           ii v      viv     i i   i   i   i   i    iv     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_119072971_    678 CTGGTACAAAAACAGACAAATAGACCAATGGAACAGAATAGAAAAATCAG 727
                             i i  ii i     v     i        i     v  i ivi   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_119072971_    728 AAGTAAAGCCACATACCTACAACCATCTGATCATCCATAAGGCTGACAAA 777
                           i    v   i i ii  iiii  vi    iv  v i    v  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_119072971_    778 AACAAGCAATGGGGAAAGGAC--TCCTTATCAATAAATGGTGCTCGGAAA 825
                          v  vv            i i--  i  -    i          v   v 
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTT-TCAACAAATGGTGCTGGGACA 421

  chr1_119072971_    826 ACTATTAATAGCTCGGCATATCCAGAAGATTGAAACCAGACTCCTACCTC 875
                            i--i   ? ----  i  v  i    v    iiii   i        
  L1M4_orf2#LINE/    422 ACTG--GATAKC----CACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_119072971_    876 TTACCATATATAAAAACTAACTCAAACTAAATTAAATATTTAAATGTAAG 925
                         vi        i     i         v ii  i ? v ii          
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_119072971_    926 ATCTCAAACTATAAAAATACTGGAAGGCAACCTAGGAAATACTCTTCTCA 975
                          v  v           v vi i    iv   v    ?ivv v     vii
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_119072971_    976 ACATCAGCCTTGGTGAAGAATTTTTGCCTAAGTCCCCAAAAGCAATTGCA 1025
                           v ii vi v  ii v iv  i  ivv  v v v         vvv   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_119072971_   1026 ACAAAAACAAAAATAGACAAGTGGGGCCTAATTAAACTAAAGAGCTTCTG 1075
                               iv         i  i v  i i v  i   v v  i i   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_119072971_   1076 CACAGCAAAAGAAACTATGAACAGAGCAAACAGACA-------GAACAGG 1118
                         ii vv    i  v     v  v i  ii  v     -------   ii  
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_119072971_   1119 AGAAGATATTTGCAAATTATGCATCCAACAAAGGCCTAATACCCAGAATG 1168
                             i            i  ii   ii i  i  v  vi  i       i
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_119072971_   1169 TATAGACAACTTAAACAAATCAATGAGCAAAAAACAAATAACCCAATGAA 1218
                             i v    ivv    v     i vv    i              v? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_119072971_   1219 AATATGGGCAAAAGA 1233
                           v         i  
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGA 830

Transitions / transversions = 1.37 (115 / 84)
Gap_init rate = 0.01 (8 / 758), avg. gap size = 4.75 (38 / 8)  

 334 19.47 3.54 2.65  chr1_119072971_119075103     1528  1640 (493)    L1M4_orf2#LINE/L1      795   908 (0)  

  chr1_119072971_   1528 AAAAACAACAACAAC--AA--AAAAAAAAGGCAAAAGACATGAACAGACA 1573
                            i    -- i   --  --?     vi      i  iv    i     
  L1M4_orf2#LINE/    795 AAAGACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_119072971_   1574 CTTCTCAAAAGAAAGCGTACATGTGGCCAACAAACATATGAAAAAAATGC 1623
                         i     v      iiii    vi       i  i  i       i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chr1_119072971_   1624 TCAGCATCATTAATCAT 1640
                            i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.25 (17 / 4)
Gap_init rate = 0.04 (4 / 114), avg. gap size = 1.75 (7 / 4)  


3243 27.09 0.44 0.44  chr1_119085604_119091999     4996  5903 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_119085604_   4996 TGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5045
                           i  ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119085604_   5046 GGCCATACTGCCCAAGGTAATTCATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v     iv i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119085604_   5096 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_119085604_   5144 TATGGAACCAAAAAAGAGCCTCCATTGCCAAATCAATCCTAAGCCAAAAG 5193
                                viiv  ii  v  vvv  v      v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_119085604_   5194 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACCACAAGGC 5243
                                i      vv   ii  v  ii i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_119085604_   5244 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATC 5293
                                 i   i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_119085604_   5294 AATGGAACAGAAC--AGAGCCCTCAGAAGTAACGCCACATATCTACAACT 5341
                                i    i--    i  --    i   vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_119085604_   5342 ATCTGATCTTCGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5391
                          vi    i        ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_119085604_   5392 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5441
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_119085604_   5442 GAAATTGGATCCCTTCCTTACACCTTATACAAAAATGAATTCAAGATGGA 5491
                            i     i    v   i     v           v  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_119085604_   5492 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5541
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_119085604_   5542 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5591
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_119085604_   5592 AACACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATCTAA 5641
                         i            vvi          vv   i v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_119085604_   5642 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5691
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_119085604_   5692 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5741
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_119085604_   5742 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5791
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_119085604_   5792 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5841
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_119085604_   5842 TCAAAAGAAGACATTTATGCAGCCAAAACACACATGAAAAAATGCTCACC 5891
                           v        i  vi viii     v vi          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_119085604_   5892 ATCACTGGCCAT 5903
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3323 26.76 0.44 0.44  chr1_119106517_119112795     4879  5786 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_119106517_   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119106517_   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119106517_   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_119106517_   5027 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_119106517_   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_119106517_   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_119106517_   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_119106517_   5225 ATCTGATCTTTGACAAACCTGAGAAAAGCAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_119106517_   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAGGCT 5324
                           v  i  i              v      v  ?   i   i i   iv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_119106517_   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_119106517_   5375 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_119106517_   5425 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_119106517_   5475 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5524
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_119106517_   5525 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5574
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_119106517_   5575 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5624
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_119106517_   5625 AGGTCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  v  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_119106517_   5675 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_119106517_   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5774
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_119106517_   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3204 26.83 1.11 0.44  chr1_119274797_119281055     4865  5766 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_119274797_   4865 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4914
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119274797_   4915 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4964
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119274797_   4965 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5012
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_119274797_   5013 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5062
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_119274797_   5063 AACAAACCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5112
                               vi      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_119274797_   5113 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5162
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_119274797_   5163 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5210
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_119274797_   5211 ATCTGATCATTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5260
                          vi    iv i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_119274797_   5261 CTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5310
                           v  v  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_119274797_   5311 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCATTTCAAGATGGA 5360
                            ii    i    v   i     v           i vi    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_119274797_   5361 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAAC 5410
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_119274797_   5411 CTAGGCATTACCATTCAGGACAT------GGGCAAGGACTTCATGTCTAA 5454
                         v    ?i v viv   iv   v ------i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_119274797_   5455 AACACCAAAAGCAATGGTAACAAAAGCCAGAATTGACAAATGGGATCTAA 5504
                         i            vvi i        vv i   v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_119274797_   5505 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5554
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_119274797_   5555 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5604
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_119274797_   5605 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5654
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_119274797_   5655 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5704
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_119274797_   5705 TCAAAAGAAGACATTTATGCAGCCAAAAACCACATGAAAAAATGCTTACC 5754
                           v        i  vi viii     v  v          i     i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_119274797_   5755 ATCACTGGCCAT 5766
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.33 (14 / 6)  


1794 26.35 20.09 0.00  chr1_119311274_119315295.rev      879  1580 (2442)    L1M4_orf2#LINE/L1       66   908 (0)  

  chr1_119311274_    879 ATTGATCTATAGACTTCTCACAATCGCAATGAAAATTTCAACATACATTT 928
                                  i   i ivv i     v v  v     ii  i vvv v   
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_119311274_    929 TTATATAAACTGACACACTGAATCTGAAATGTATAAGGCCATGCAAAGTG 978
                           ii v   i     vi    vi  i    vi   v  vv      i vi
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_119311274_    979 TTTAGAATACTCAAAACAGCTTTGAAAAAGAA-AACACAACTAGAGGACT 1027
                         iii      vi       iii           -    v ii i       
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_119311274_   1028 TATACTGCC---TTTTGAAGCTTATTATACAGCTATAATAATTGAGA--G 1072
                         i i   v  ---   ii  i    i  i v     i i    ii   -- 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_119311274_   1073 TGTGGTATGGACATA------GACTTACAGGTCACTGAAA---------- 1106
                                iv i    ------   v  i  i   v  i  ----------
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_119311274_   1107 -----AGAAAT--------------------------------------G 1113
                         -----      -------------------------------------- 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_119311274_   1114 TA------------------GAAAG-----------------------CT 1122
                          i------------------     -----------------------  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_119311274_   1123 GA---AACTGGAT----------------------------CCCTTCCTT 1141
                          i---        ----------------------------    v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_119311274_   1142 ACACCTTATACAAAAATCAATTCAAGATGGATTAAAGACTTAAACGTTAG 1191
                              v           i  i    i      i ?    i    i  v  
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_119311274_   1192 ACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGG 1241
                          v       i      vi i           v    ?i v viv   iv 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_119311274_   1242 ACATAGGAATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCA 1291
                           v v  iv i     v ii   v ivv  vi            vvi   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_119311274_   1292 ACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTG 1341
                                vv     v  i    v   ii v  i   v v  i i   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_119311274_   1342 CACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGG 1391
                         ii vv    i  v    i  vv i      v  i     i   i      
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_119311274_   1392 AGAAAATTTTCACAACCTACTCATCTGACAAAGGGCTAATATCTAGAATC 1441
                                v  ii   vii ivi      i  i  i  vi    i     v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_119311274_   1442 TACAATGAACTCAAACAAATTTACAAGAAAAAAACAA----CCCCATCAA 1487
                           i  v      vv    v iv i  v     i    ----   v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_119311274_   1488 AAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATG 1537
                            i     i     iv    i     i     v        i  vi vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_119311274_   1538 CAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCAT 1580
                         ii     v  i          i       v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (107 / 75)
Gap_init rate = 0.01 (11 / 843), avg. gap size = 12.82 (141 / 11)  

1677 23.23 4.65 2.63  chr1_119311274_119315295.rev     2327  2821 (1201)    L1M4_orf2#LINE/L1      309   813 (95)  

  chr1_119311274_   2327 AATAGGGAATCAAGAAGTAGACCCACATATATATGGTCAAAT-ATTTTCA 2375
                            v i  i  v    i  i     i i  v         v -      i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_119311274_   2376 ATGAAGGGT-TCAAAGCAGTTCAGTGGGGGAAAAAATAGTCTTTTCAGCA 2424
                          i-      -i   ii vi    i     -   i             i  
  L1M4_orf2#LINE/    359 AC-AAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACA 406

  chr1_119311274_   2425 GAGGGTGTTAGGTCTCCAGCTAGATGTCCATGTGAGGGAGAACATGAACC 2474
                         i v    i i  ---v  i  i   i?   ii  viii    --    vi
  L1M4_orf2#LINE/    407 AATGGTGCTGGG---ACAACTGGATAKCCACATGCAAAAGAA--TGAAGT 451

  chr1_119311274_   2475 TTGACTCTCACCTCATACCATTCACAAAAAAGATCAACTTAAAACC-ACC 2523
                          v   i ii      i     vi       --- i    i    iv- i 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAA---TTAACTCAAAATGGATC 498

  chr1_119311274_   2524 ACAGACTTAAATGTAAAATCTGAAGCTATGAAACTTCTGAAAGAAAATAT 2573
                          ?    i         i v  i  i    i     ii ii       i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_119311274_   2574 -GGGGAAAATTTTCCAGGCCTTTAGGATAGGCCAAGATTTCTTA-ATAGT 2621
                         -  ? v    i   vv i    -i  v     v v i       -   vv
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTT-GGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_119311274_   2622 ACAC-AAAATCAC--TTAATATAAGAGAAACTATTGATACATTTGATTTC 2668
                             -    v   --vi  i v    i   v  --    v   v  i   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTC 645

  chr1_119311274_   2669 ATCAAAAGATAAAGCCTCTGTTCTTCAAAA-ACACCATTAAGAAAATGAA 2717
                                vvv   i i i   v       i-    i  i      i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_119311274_   2718 AAGGTAACCCATAAAGTGGGAGCAAATATTCACAGTACATATATCTGGCA 2767
                            ii      i i i      v       ii  ivv          ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_119311274_   2768 AGG--CTTTTATCCAGC-TGTATAAAAAACTCTTA-------ATAATAAG 2807
                            --   v       v- i      i        -------       i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_119311274_   2808 GAGACAA----CCTAATT 2821
                         i      ----  i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATT 813

Transitions / transversions = 2.11 (76 / 36)
Gap_init rate = 0.04 (19 / 505), avg. gap size = 1.89 (36 / 19)  

 275  4.44 6.67 0.00  chr1_119311274_119315295.rev     3487  3531 (491)    L1M4_orf2#LINE/L1      861   908 (0)  

  chr1_119311274_   3487 ACAAATGGCTAATAAGCACATGAAAAG---TTCAACATCATAGTCGTC 3531
                                  i                 ---i         ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (2 / 0)
Gap_init rate = 0.02 (1 / 48), avg. gap size = 3.00 (3 / 1)  


2941 28.56 0.22 0.11  chr1_119373216_119377469     2855  3761 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_119373216_   2855 TGGAAACACATCCCATGTTCATGAATGGGTAGAATCAATATTGTAAAAAT 2904
                               v i              i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119373216_   2905 GACCATACTGCCAAAAGCAATCTATAAATTCAATGCAATTCCCATCAAAA 2954
                          i v     v  v   vii     i i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119373216_   2955 TACCACCAACACTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCATA 3004
                          v   v vi vi i  ii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_119373216_   3005 TGTAAGAAAAAAAAAGCCCACATAGCCAAAGCAAGACTAGGCAAAAAGAA 3054
                           v  iviv  iii v  viv         i   vvi iiiv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_119373216_   3055 CAAATCTGGAGGCATCACATTACCCAGCTTCAAACTATACTACAAGGTTA 3104
                             vi      vv     i v    ii      viv        i i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_119373216_   3105 TAATTACCAAAACAGCACAGTACTAGTATAAAAACAGGCACGTAGTACAA 3154
                         i i v i   i    iiii     i i    ii i  i  ii   vv   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_119373216_   3155 TGGAAAGGAATAGAGAACCCAGAAATAAAGCTTAATACTTACAGCCAACT 3204
                              vi    v    ii           v ivv i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_119373216_   3205 GATCTTCAAGAAAGCAAACAAAATCATAAAGTGAGGAAAGGACACCCTAT 3254
                            i   i v  i vviv   i i   vv i  i      i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_119373216_   3255 TCAACAAATGATGCTGGGATAATTGGCAAGCCACATATAGAATAACGAAA 3304
                                   i        i  i   vv ?      ii i  v  i   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_119373216_   3305 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATTGATCAA 3354
                         i    i  ii i   v    v           i       i  v     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_119373216_   3355 AGACTTAAATCTGAGACCTCAAACC-TAAAAATTCTAGGAGATAACATCA 3403
                             i     v i   v  v    i-     v ii   i   v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_119373216_   3404 GAAAAATTCTCCTAGATACTGGCCTAGGCAAAGAATTCATGAGCAAGTGC 3453
                          ?iv  v   i vv  ivi   vi       v iv   v iiii v vvv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_119373216_   3454 CCAAAAGCAAATGCAATGAAAACCAAGACAAATAGATGGGACTTAATTAA 3503
                                  v v    ii   ivv  i i i   i  v      v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_119373216_   3504 ACTAAAAAGTGCCTGCACAGCAAA-AACAATAATCAGCAGAGTAAACAGA 3552
                          v v    iivii  ii vv    -i   v -    iv i   i  v   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGAAAGTGAAAAGA 699

  chr1_119373216_   3553 CAACTCACAGTATGGAAGAAAATCTTCAGAATCTATATACCTGACAAAGG 3602
                             i     v    i       v  iiv  vii     i    i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_119373216_   3603 ACTAATATCCAGAATCTACAAAGAACTCAAACAAATCAGCAAGAAAAAAG 3652
                            vi          v  i         vv    v   ii  v     ii
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_119373216_   3653 CAATCAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCA 3702
                            vi  i  v  i?    i     v     iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_119373216_   3703 AAAGAAGATATACAAACGGCCAACAAGCACATGGAAAAATGCTCAATATT 3752
                                         i      i         i   i        i  i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_119373216_   3753 ACTAATTAT 3761
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.48 (152 / 103)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.00 (3 / 3)  


1506 27.82 0.96 0.96  chr1_119405852_119412582.rev     4994  5410 (1321)    L1M4_orf2#LINE/L1        1   417 (491)  

  chr1_119405852_   4994 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCATGAAAAT 5043
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119405852_   5044 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5093
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119405852_   5094 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5141
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_119405852_   5142 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAACCAAAAG 5191
                                viiv  ii  v  viv  v     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_119405852_   5192 AACAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATACTACAAGGC 5241
                                i      vv   ii  v  ii        viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_119405852_   5242 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 5291
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_119405852_   5292 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5339
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_119405852_   5340 ATCTGATCTTTGACAAACCTGACAAAAGCAAACAATGGGGAAAGGATTCC 5389
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_119405852_   5390 CTATTTAATAAATGGTGCTGG 5410
                           v  i  i            
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGG 417

Transitions / transversions = 1.97 (77 / 39)
Gap_init rate = 0.01 (5 / 417), avg. gap size = 1.60 (8 / 5)  

1839 25.69 0.20 0.20  chr1_119405852_119412582.rev     5735  6240 (491)    L1M4_orf2#LINE/L1      403   908 (0)  

  chr1_119405852_   5735 AATAAATGGTGCTGGGAAAACTGGCTAACCATATGTAGAAAGCTGAAACT 5784
                           i              v      v  ?   i   i i  iiv    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_119405852_   5785 GGATCCCTTTCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAG 5834
                            i    vi  i     v              i    i      i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_119405852_   5835 ACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAATCTAGGC 5884
                           i  v    v   v       i      vi i          iv    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_119405852_   5885 A-ATACCATTCAGGACATAGGCATGAGCAAGGACTTCATGTCTAAAACAC 5933
                         i- v i -   iv   v v  vv ii    v ii   v ivv  vi    
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_119405852_   5934 CAAAAGCAATGGCGACAAAAGCCAAAATTGACAAATGGGATCTAATTAAA 5983
                                 vvi  i       vv     v  i    v   ii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_119405852_   5984 CTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTCAATAGGCA 6033
                         v v  i i   i  ii vv    i  v    i  vv i   v  v  i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_119405852_   6034 ACCTACAGAATGGGAGAAAACTTTTGCAATCTACTCATCTGACAAAGGGC 6083
                            i                iv       vii ivi      i  i  i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_119405852_   6084 TAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAACACA 6133
                          vi          v  i  v      vv    v iv i  v     v   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_119405852_   6134 AACAACCCCATCAAAATACGGGCAAAGGATATGAACAGATACTTCTCAAA 6183
                           i     v  i?   v i           v    i   i i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_119405852_   6184 AGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCAC 6233
                               i  vi viii     v  i          i       v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_119405852_   6234 TGGCCAT 6240
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.21 (69 / 57)
Gap_init rate = 0.00 (2 / 506), avg. gap size = 1.00 (2 / 2)  


2944 26.95 3.40 0.57  chr1_119465776_119468003      853  1735 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_119465776_    853 TGGAAAAAAATTCCATGCTTGTGGACAGGAAGAATCAATATCATGAAAAC 902
                               i v  i     i ii    iv      v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119465776_    903 GGCTATACTGCCCAAAGTAATTTATAGATTCAATGCTGTCCCCATCAAGC 952
                            v     v      v i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119465776_    953 TACCATTGACTTTCTTCACAGAACTAGAAAAAACT-ACTTTAAATTTCAT 1001
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_119465776_   1002 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCCAAAAGA 1051
                               viiv  ii  v  viv        i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_119465776_   1052 ACAAAGCTGGAGGCATCATGCTACCTGAC------------------GCT 1083
                               i      vv   ii  v  ii i------------------   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_119465776_   1084 ACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATAGAGACCA 1133
                                i   i    ii  i      i iv ii i   i   v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_119465776_   1134 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACAGCTACAACCATC 1183
                               i    iv   ivii         vv   i   vi  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_119465776_   1184 TGATCTTCTACAAACCCAACAAAAACAAGCAATGGGGAAAGGATGCCCTG 1233
                             i   v    ivviiv   i v  vv            i  ivi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_119465776_   1234 TTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGCAGAAAACAGAA 1283
                           i  i              v  i   v  ?   i     i  i vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_119465776_   1284 ACTGGACCCCTTCCTTACACCATATACAAAAATTAACTCAAGATGGATTA 1333
                         ii         v   i                         i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_119465776_   1334 AAGACTTAAATGTAAAACCTAAAATCATAAAAACTCT-AGAAGAAAACCT 1382
                         ?    i         i v      ii      -    -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr1_119465776_   1383 AGACA-ATACCATTCAGGACATTGGGATACACAAAGACTTCATGACTAAA 1431
                           i?i- v i -   iv   v     v  vi   v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_119465776_   1432 ACACCAAAA--ACAATTGCAATAAAAGTGAAAATTGACAAATGGGATCTA 1479
                                  --    --    i     vi     v  i    v   ii v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_119465776_   1480 ATTGAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATCATCAGAGTGAA 1529
                           ii  v v  i i   i  iv vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_119465776_   1530 CAGGCAACCTACAGAATGGGAGGAAATTTTTGCAATCTATCCATCTGACA 1579
                         v  i     i            i    v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_119465776_   1580 AAGGGCTAATATCCAGAATATACAAAGAACTTAAACAAATTTACAAGAAA 1629
                          i  i  vi             i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_119465776_   1630 AAAACAA------CA-TGAAAAAGTGGGCAAAGGATATGAACAGGCACTT 1672
                           i    ------  - v?    i            v    i  i  i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_119465776_   1673 CTCAAAAGAAGACATTTATGTGGCCAACAAACATGGGGAAAAAAGCTTGT 1722
                            v        i  vi vi       i  i  iiv i   i v   iiv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_119465776_   1723 CAACACTGGTTAT 1735
                           v  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (144 / 90)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.18 (35 / 11)  


 974 26.30 9.98 3.17  chr1_119525706_119528336      996  1436 (1195)    L1M4_orf2#LINE/L1       18   488 (420)  

  chr1_119525706_    996 TCCATAGATTGGAAGACTCAATAGTGCAAAAATATTAAGTCTCCTCAAAT 1045
                          i   i            i    v  iv  i  ivi  vv    i     
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr1_119525706_   1046 TGATCTATACATTCAATGCAATCTCAATTAAAATTCCAACAGATGTTCTT 1095
                                i v      i      i v  i     i   i ---  iii  
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC---TGCCTTT 114

  chr1_119525706_   1096 TTT--AAAAGTAGATAAATTTGTG-TGGAATTACATATAGAAATGTACAA 1142
                            -- i  i v  i  ii vi v- ii    -     i      i - i
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATT-CATATGGAAATGCA-AG 162

  chr1_119525706_   1143 TGAT--AGCAATAGGTAAGAGAATCTTTAA---GAAGATTAGAGTTTGAA 1187
                         v  i--  -     vi  i v      v  ---     vi i    v  i
  L1M4_orf2#LINE/    163 GGACCCAG-AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_119525706_   1188 CACTTA----TCCTATTATATACAATAATTATTATCAAA-------TAAT 1226
                         v   i ----   i --  v -   v v   i  -    -------    
  L1M4_orf2#LINE/    212 GACTCACACTTCCCA--ATTT-CAAAACTTACTA-CAAAGCTACAGTAAT 257

  chr1_119525706_   1227 TAATACAATGCAAATAGAGGCACAAAAATAGACAAATAGACCAATGGAAC 1276
                         i  v   i  iii-  vv    i  ii       v     i        i
  L1M4_orf2#LINE/    258 CAAGACAGTGTGG-TACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_119525706_   1277 ACAATAGAAAGTCTAGAATCAGACCCACACGTATATGGACACCATTGGTC 1326
                          v   v  i    i    vi i     i  i v     v  --    i i
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA--ATTGATT 354

  chr1_119525706_   1327 -----CA----TGCAGAG------CAGTGGGAAAAAGACACTATTTT-AA 1360
                         -----  ----   vi  ------  i    i   ii i v v    -  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_119525706_   1361 TTAATGGT-------CAATTGGATATCCATATGAGAAAAAACAATCTTG- 1402
                         iv      -------   i      ?   i   vi   i  ii vv   -
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_119525706_   1403 ACTCCTGTC-CATACGTTATGTAAAGAACCAATTC 1436
                           i   ii -  i  vv   ii   -  ii  i  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAA-AATTAACTC 488

Transitions / transversions = 2.03 (77 / 38)
Gap_init rate = 0.05 (23 / 471), avg. gap size = 2.52 (58 / 23)  

 320 27.25 17.20 2.91  chr1_119525706_119528336     1761  2138 (493)    L1M4_orf2#LINE/L1      477   908 (0)  

  chr1_119525706_   1761 AAAAATCATTTCCAGGTG-ATTTTAGATCAAAAAATGATATGTAAAATAG 1809
                               i vi  v ii  -  iv?   i v   vi i v vv     ivi
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_119525706_   1810 TAAAGTTTCTAAAAAATAACATAGAATGATATTTT-GTATGCCTGGAGCA 1858
                             ii ii  i  i v       i?vv v  i  -  ivv i   ivi 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_119525706_   1859 GGCAAGGATTTCTTAAATAAGA----AATAACATT-----CCTAAAAAAA 1899
                              v i       i   v  ----  v i  iv----- vv  i    
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_119525706_   1900 ATTAAA-ATATTGG----CAT--------------TTTCTGTTTATAAAA 1930
                          v  i - v     ----   --------------   v  i  -i   i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT-CAAAG 675

  chr1_119525706_   1931 GACACCATTATGAGAAGGAAAAGA-AAGTTATAGAATGGAAGAAAATGTA 1979
                              i  i v  i iv       -  vii i       i       i v
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_119525706_   1980 TGTATAAAAATATTATAT---ATAAAATGACAT---TTCA-----TATAA 2018
                           i ----   vv     ---    ii-   v --- i  -----     
  L1M4_orf2#LINE/    726 TGCA----AATCATATATCTGATAAGG-GACTTGTATCCAGAATATATAA 770

  chr1_119525706_   2019 AT--TTTTCACAATT------TAAAAAGTCAGAAAACCTAGT--AAAAAT 2058
                          v--i i i    i ------       v  i v    i i --      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_119525706_   2059 TGG---ATGCT----AT-----TTTCTTCACAAAACAGAATATCCACATT 2096
                         v  --- v v ----  -----     i  v i  ---i    v  v  v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA---GATATACAAATG 867

  chr1_119525706_   2097 GCCAATAAGCATTTTTTTAAAG-TGCTCAACCTCATTAGCTAT 2138
                                    iv vv--    -        v   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGA--AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (55 / 46)
Gap_init rate = 0.05 (23 / 432), avg. gap size = 3.30 (76 / 23)  


2434 20.51 6.09 0.48  chr1_119560166_119561776.rev      499  1122 (489)    L1M4_orf2#LINE/L1      250   908 (0)  

  chr1_119560166_    499 ACAGTAATCAAGACAATGTGGTATTGGTATAAAGATAAACAGATAAACTG 548
                                        i       i   i    i    i   v   i iii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_119560166_    549 ATGGAATAGAATAGAGAGACTAAATAGCAAAGTACACACAT--ATGGACA 596
                                     v     v i i - ii   vi-  i    --    v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGA-AATAAACC-CATACATTTATGGTCA 347

  chr1_119560166_    597 AGTGATTTCC-ACAAACGT-CCAATGGCAGAAAGTAGTGAGAAAATAGTC 644
                          v      i -    iv  -    viv  vvv i i v  i i       
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_119560166_    645 TTTTATACAA-------TAGATTAATTGGATATCCATATGCAAAA--ATG 685
                             vv    ------- i ivi  i      ?   i        --   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_119560166_    686 AACTTTGATCCATACCTCTCACCATATACAAAAATTAACTCAAAATGGAT 735
                           v  v  i  v      v                               
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_119560166_    736 CATAGACATAAATGCAAATCCTAAAACTATAAAATTTCTAGAAGAAATCA 785
                           ?    v      i  ivv              i ii         v  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_119560166_    786 TTAGAGTAAACCTTTGTTATCTTGGGTTTAGCAAAGATTTCTTAGTTATA 835
                          vi ?     i   i  v i        vi    v i        v   i
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_119560166_    836 ATATCAAAAGCATGATCCAGAAGAGAACAGATTGATAAGTTGGACTT--- 882
                          i i        ii v v v  i    v i  v     i        ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_119560166_    883 ---AAT--AAAAGTTTTA------AAAAGACA-------GAGAATGAACA 914
                         ---   --    v    i------   i    -------  i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_119560166_    915 GACAAACCATAGACTGTGAGTAAATATTTGCAAAGCATATATCTAATAAG 964
                              v   i   v  v   v             v         i     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_119560166_    965 TGACTTATACTCAGAATTTAGAAAGAACTGTAAAAAACCCGACAATAACA 1014
                         v     i  ii      v  v        v v v  - i i i     v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAAA 796

  chr1_119560166_   1015 AAACAA----CATAATTTTAAAATGGACGAAAGATGTTAACAGACATTTT 1060
                          i    ---- vi    ?v       i i  i   v v  i        i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_119560166_   1061 GCCAATGTAGATATACAGATGGCAAATAAGCACATGAAAAGATGCTCAAC 1110
                         v    v v         i     v                          
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_119560166_   1111 ATAATTAGTCAC 1122
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (67 / 57)
Gap_init rate = 0.02 (13 / 659), avg. gap size = 3.15 (41 / 13)  


2982 27.47 2.35 0.56  chr1_119654257_119658637.rev     2999  3890 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_119654257_   2999 TGGAATAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3048
                              vi i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119654257_   3049 GGCCATGCTGCGCAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 3098
                            v  i  v v   iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119654257_   3099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTTA 3146
                          v   iivi i  i  ii     -   -- v  i  - iii    i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_119654257_   3147 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAGAAG 3196
                                viiv  ii  v  v v  v     iv     i i ivv     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_119654257_   3197 AATAAAGCTGGATGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3246
                           i    i    v vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_119654257_   3247 TACAGTAATCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATC 3296
                                     i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_119654257_   3297 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 3344
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_119654257_   3345 ATCTGATCTTTGACAAAC-TGACAAAA-----------AGAAGAAATTCC 3382
                          vi    i  i     iv-  v   i -----------i   ii   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_119654257_   3383 CTATTTAATAAATGGTGCTGGGAAAACCGGCTAGCCATGTGTAGAAAGCT 3432
                           v  i  i              v   i  v  ?   ii  i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_119654257_   3433 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3482
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_119654257_   3483 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 3532
                          i ?    i  v    v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_119654257_   3533 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3581
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_119654257_   3582 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGTGATCTA 3631
                         vi            vvi          vv     v  i    vv  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_119654257_   3632 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGCGTGAA 3681
                           i   v v  i i   i  ii vv    i  v  i i  vv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_119654257_   3682 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 3731
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_119654257_   3732 GAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 3781
                         ii  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_119654257_   3782 AAAA-AAAT--CCCA-TCAAAAAGTGGGCAAAGGATATGAACAGACACTT 3827
                           i -    --    - i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_119654257_   3828 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 3877
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_119654257_   3878 CATCACTGGCCAC 3890
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.17 (26 / 12)  


1181 23.28 6.62 0.74  chr1_119751813_119758231        1   408 (6011)    L1M4_orf2#LINE/L1      477   908 (0)  

  chr1_119751813_      1 AAATATTCTCTCAAAATGGGTTATAGGCCTAAATTTCAG-GCGTAAACCA 49
                            v   vv          i i ?  i       v v  -  vv    i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_119751813_     50 TACACTTCTTCGAAGAAAACATAAAT-TAACATGTTCATGACCTTAAATA 98
                           v vi    v            ii?-   -  v   i       iii v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTT 575

  chr1_119751813_     99 AAGAAAAAAATCTTTT---TCTG---CTAAA--------CAAAAAAAGTT 134
                          i v  vii- i i  --- v  --- i   --------   v     vv
  L1M4_orf2#LINE/    576 AGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_119751813_    135 AAAA-----AAATGAGACATGATCAAAACTAAAAACATTTGCTCTTTAAA 179
                             -----    vi   v v       i       v    iv   i   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_119751813_    180 AGACATCAATAAGAAAATGAAAAGACAAGCCACAGAATGAGAAAAAATAT 229
                         i    ii vi      i           v          i  i       
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_119751813_    230 ---CAAAACGTATATTTGGTAAAGGACTTCTATCCAGAATATA--AAATA 274
                         ---    v i     i  i   i      v             --  iv 
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_119751813_    275 CAATTACAACTAAAGAACACAAGGATAAATGACTCAATTTTAAAATCAGC 324
                          vv        v  v  i v  i  i    i  i     ?v     vi  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_119751813_    325 ACAATATTTGAATAGTCACTTAACCAAAAATG-TGTAACAATGGCCAATA 373
                          v iv          v  i  vv     i v - i  vv           
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_119751813_    374 AAGTACACGAAAAGACAGTCAGCATCACCAGTCAG 408
                          - i   i       iiv   i     ????????
  L1M4_orf2#LINE/    875 A-GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (48 / 44)
Gap_init rate = 0.03 (12 / 432), avg. gap size = 2.50 (30 / 12)  

3126 27.53 0.55 0.55  chr1_119751813_119758231     5019  5926 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_119751813_   5019 TGGAATAACATTCCATGCTCATGGGTAGGAAGAATCAATGTCTTGAAAAT 5068
                              vi i  i     i      i v      v i   i iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119751813_   5069 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5118
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119751813_   5119 TACCAATGACTTTTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5166
                          v   iivi i     ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_119751813_   5167 TATGGAAACAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5216
                                 iiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_119751813_   5217 AACACAGCCAGAGGCAACACGCTACCTGACTTCAAACTATACTAAAAGGC 5266
                             v  iii    vvv   i  v  ii i      viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_119751813_   5267 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5316
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_119751813_   5317 AATGGAACAGAACAGAGACCTCAGAAATAATGCCACATATCTACAACTAT 5366
                                i    iv    vii         vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_119751813_   5367 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5416
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_119751813_   5417 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAGCTGA 5466
                         v  i  i              v      v  ?   ii  i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_119751813_   5467 AACTGGATTCCTTCCTTACACCTTATATGAAAATTAATTCAAGATGGGTT 5516
                          ii    ii   v   i     v    ii        i    i    i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_119751813_   5517 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACTT 5566
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_119751813_   5567 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5615
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_119751813_   5616 ACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCT-AC 5664
                                     vvi          vv i   v  i    v   ii - i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_119751813_   5665 TGAAACTAAAGAGCTTCTGCACAGCAGGAGAAACTACCATCAGAGTGAAC 5714
                         ii   i    i -   i  ii vv  iii  v    i  vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_119751813_   5715 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTCCT-CATCTGACA 5763
                           i     i   i             v  ii   v-  v -i      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATA 745

  chr1_119751813_   5764 AAGGGCTAATATCCAGAATCTACAATGAACCCAGACAAATTTACAAGAAA 5813
                          i  i  vi          v  i  v    i vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_119751813_   5814 AAAACAAACAACCCCATAAAAAAGTGGGCAAAGGATATGAACAGACACTT 5863
                           i     i     v  v?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_119751813_   5864 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5913
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_119751813_   5914 CATCACTGGCCAT 5926
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


3087 28.11 0.55 0.44  chr1_119776022_119780228     2808  3714 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_119776022_   2808 TGGAATAACATTCCATGCTCATGTGTAGGAAGAATCAATGTCGTGAAAAT 2857
                              vi i  i     i     vi v      v i   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119776022_   2858 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2907
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119776022_   2908 TACAAATGACTCTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 2957
                          v v iivi ii i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_119776022_   2958 TGGAACCAAAAAAGAGCCTGCAT-GCCAAGTCAATCCTAAGCCAAAATAA 3006
                              viiv  ii  v  v v  -     iv     i i ivv i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_119776022_   3007 CAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTACACTACAAGGCTA 3056
                              i      vv    v  v  ii i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_119776022_   3057 CAGTAACCAAGACAGCATGATACTGGTACCAAAACAGAGATATAGACCAA 3106
                               i        ii  i      i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_119776022_   3107 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCAT 3154
                              i    i--    i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_119776022_   3155 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 3204
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_119776022_   3205 ATTTAATAAATGATGCTGGGAAAACTGGCTACCTATATGTAGAAAGCTGA 3254
                         v  i  i     i        v      v  ? i i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_119776022_   3255 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCATGATGGATT 3304
                          ii    i    v   i     v              i   vi      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_119776022_   3305 AAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGGAGAAAACCT 3354
                          ?    i       v   v       i      vi i   i       v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_119776022_   3355 AGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 3402
                            ?-   --i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_119776022_   3403 AACACCAAAAGCAATGGCTACAAAAGCCAAAATTGACAAATGGGATCTAA 3452
                         i            vvi  v       vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_119776022_   3453 TTAAACTAAAGAGCTTGTGCACAGTAAAAGAAACTACCATCAGAGTGAAC 3502
                          i   v v  i i   v  ii vvi   i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_119776022_   3503 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3552
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_119776022_   3553 AGGGCTAATATCCAGAATCCACAAAGAACCTAAATAAATTTAGAAGAAAG 3602
                         i  i  vi          vi i       iivv i  v iv v  v   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_119776022_   3603 AATCAAACAATTCCATCAAAAAGTGGGCAAAGGATGTGAACAGACACTTC 3652
                          iv    i  ii v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_119776022_   3653 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGTTCATC 3702
                           v        i  vi viii     i ii          i   i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_119776022_   3703 ATCACTGGCCAT 3714
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (148 / 103)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3134 27.31 0.44 0.44  chr1_119828046_119834768     5323  6230 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_119828046_   5323 TGGAAGAATGTTCCATGCTCATGGATAGGAAAAATCAATATCATGAAAAT 5372
                              ii  i i     i        v    i v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119828046_   5373 GGCTATACTGCCCAAGGTAATTTATAGATTCAATACTATCCCCATCAAAC 5422
                            v     v     iv i  i  i        ii v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119828046_   5423 TACCA-CTGACTTTCTT-CAAAGAATTGGGAAAAAAATACTTTAAATTTC 5470
                          v   -   v    i  -  i -     iv  ivvi  v  --   v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCT--AAAATTC 147

  chr1_119828046_   5471 ATATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAA 5520
                                 viiv  ii  v  viv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_119828046_   5521 GAACAAAGCTGGAGGCATCACGCTATCTGACTTCAAACTATACTATAAGG 5570
                                 i      vv    i  vi ii i      viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_119828046_   5571 CTACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGACATGCAGAC 5620
                                  i   i    ii       v i iv ii i      ii   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_119828046_   5621 CAATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCA 5670
                                 i    iv    vii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_119828046_   5671 TCTGATCTTTGACAAACCGGACAAAAACAAGCAATGGGGAAAGGATTCCC 5720
                         vi    i  i     ivvv v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_119828046_   5721 TATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5770
                          v  i                 v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_119828046_   5771 AAACTGGATCCTTTCCTTACACCATGTACGAAAAATAACTGAAGATGGAT 5820
                           ii    i  i v   i       i   i    v     v  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_119828046_   5821 TAAATACTTAAATGTAAGACCTAACACCATAAAAACCCTAGAAGAAAACC 5870
                         i ? v  i           v    v  i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_119828046_   5871 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5919
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_119828046_   5920 AACACTAAAAGCA-ATGCAGCAAAAGCCAAAATTGACAAATGAGATCTAA 5968
                         i    i       - v   i      vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_119828046_   5969 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 6018
                          i   v v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_119828046_   6019 AGGCAAACTACAGAATGGGAGAAAATCTTTGCAATCTACCCATCTGACAA 6068
                           i   v i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_119828046_   6069 AGGACTAATATCCAGAGTCGACAAAGAACTTAAACAAATTTACAAGAAAA 6118
                         i     vi        i vv i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_119828046_   6119 CAACAAATCACCTCATGTAAAAGTAGACAAAGGATATGAACAGATACATC 6168
                         vi      v   iv  v?    i i i        v    i   i iv  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_119828046_   6169 TCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTCATC 6218
                           v        i  vi viii     i ii  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_119828046_   6219 ATCACTGGTCAT 6230
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


3325 26.57 0.55 0.44  chr1_119946010_119952683.rev     5277  6183 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_119946010_   5277 TGGAAGAATGTTCCATGCTCATGGATAGGAAGAATGAATATTGTGAAAAT 5326
                              ii  i i     i        v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_119946010_   5327 GGCCATACTGCCCAAGGTAATTTACAGATTCGATGCCATCCCCATCAAGC 5376
                            v     v     iv i  i         i i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_119946010_   5377 TACCAATAACTTTCTTCACAGAA-TTGGAATAAAGT-ACTTTAAAGTTTC 5424
                          v   iivi i  i  ii     -   -- i  iv - iii    i  iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_119946010_   5425 TGTGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5474
                          i     viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_119946010_   5475 AACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGGC 5524
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_119946010_   5525 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5574
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_119946010_   5575 GATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5624
                         i      i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_119946010_   5625 CTGATCTTTGACAAACATGACAAAAACAGGAAATAGGGAAAGGAT-GCCT 5673
                         i    i  i     ivi  v   i v  vvv   i       i  - i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_119946010_   5674 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGATG 5723
                          -  i  i              v      v  ?   i     i  ii   
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_119946010_   5724 AAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAATATGGAT 5773
                           ii    i    v   i i   v              i    v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_119946010_   5774 TAAAGACATAAATGTTAGGCCTAAAATCATAAAACCCT-AGAAGAAAAGC 5822
                         i ?    v       v  iv      ii       i  -         vv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_119946010_   5823 TAAGCA-ATACCATTCAGGACATAGGCATAGGCAAGGACTTCATGACTAA 5871
                           i ?i- v i -   iv   v v  vv       v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_119946010_   5872 AACACCAAAAGCAAAGGCAACAGAAGCCAAAATAGACAAATGGGATCTAA 5921
                         i            v i      i   vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_119946010_   5922 ATAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAATGAAC 5971
                         vi   v v  i i   i  iiivv    i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_119946010_   5972 AGGCAACCTATAGAATGGGAGAAAATCTTTGCAATCTACCCATCTGACAA 6021
                           i     i i               v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_119946010_   6022 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 6071
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_119946010_   6072 AAACAAATCACCCCATCAAAAAGTAGACAAAGGATATGAACAGACACTCC 6121
                          i      v    v  i?    i i i        v    i     i i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_119946010_   6122 TCAAAAGAAGACATCTATGCGGCCAACAGACACATGAAAAAATGCTCATC 6171
                           v        i  vi vii      i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_119946010_   6172 ATCACTGGCCAT 6183
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (146 / 91)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


2556 26.17 0.85 0.28  chr1_120129301_120130994      499  1201 (493)    L1M4_orf2#LINE/L1      202   908 (0)  

  chr1_120129301_    499 AAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTATAAGGCTAC 548
                             i      vv   ii  v  ii i      viv     i  i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_120129301_    549 AGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATGTATAGACCAAT 598
                              i   i    ii         i iv ii i   ii      i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_120129301_    599 GGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACGACCATCTG 648
                             i    iv   ivii         vv   i    i  i ii  vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_120129301_    649 ATCTTTGATAAACCTGACAAAAACAAGCAATGGAGAAAGGATTCCCTATG 698
                           i  i  i  ivv  v   i v  vv      i     i  vvi  v v
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_120129301_    699 TAATAAATGGTGTTGAGAAAACTGGCTAGCCATATGCAGAAAACTGAAAC 748
                         i  i        i  i  v      v  ?   i     i  i v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_120129301_    749 TGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAACATGGATTAAA 798
                                  v   i     v                   v      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_120129301_    799 GACTTAAAAGTAAGCCCTAAAATTATAAAAACTCT-AGAAGAAAACTTAG 847
                            i    v     vv      i       -    -          v   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAG 550

  chr1_120129301_    848 GCA-ATACCATTCAGGACATAGGCATGGGGAAAGACTTCATGACCAAAAC 896
                          ?i- v i -   iv   v v  vv i  v  v ii   v iivi vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_120129301_    897 ACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAATTA 946
                                   vvi          vv        i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_120129301_    947 AACTAAAGAGCTTCTGCACGGCAAAAGAAACTGTCATCAGAGTGAACAGG 996
                           v v  i i   i  ii vv    i  v   i   vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_120129301_    997 CAACCTACAGAATGGGAGAAAATTTTTGCAATCTGTCCATCTGACAAAGG 1046
                              i                 v       viii vi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_120129301_   1047 GCTAATATCCAGAATCTAAAAAGAACTTAAACAAATTTACAAGAAAAACA 1096
                         i  vi          v  v        ivv    v iv i  v     v 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_120129301_   1097 CAA----CCCCATCAAAAAGTGGGAGGAGGATATGAAGAGATATTTCTCA 1142
                            ----   v  i?    i    vii     v    v   i       v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_120129301_   1143 GAAGAAGGCATTTATGCGGCCAACAAACATATGAAAAGAAGCTCATCATC 1192
                         i      ii  vi vii      i  i  i         v     v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_120129301_   1193 ACTGGTCAT 1201
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.34 (103 / 77)
Gap_init rate = 0.01 (5 / 707), avg. gap size = 1.60 (8 / 5)  


 230 10.53 2.63 0.00  chr1_120390588_120392328      464   501 (1240)  C L1M4_orf2#LINE/L1   (752)   156   118 *

C chr1_120390588_    501 GCAGAAATTGACAAGTTGATTCTAAAATTCAT-TAAAAA 464
                                        i    i           - ii   
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

Transitions / transversions = 1.00 (4 / 0)
Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1)  

3444 14.71 5.67 3.64  chr1_120390588_120392328      500  1240 (501)    L1M4_orf2#LINE/L1      132   887 (21)  

  chr1_120390588_    500 GCTGCTCTTAAAATGTATATGGAAATGCATGGGACTCATAAAAGCCAAAA 549
                             v  i      vi             v     i  v  v        
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_120390588_    550 CAAT---------GAAGAACAAAGTTGGTGGATTCACACTTCCCAATTTC 590
                             ---------               v   i                 
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_120390588_    591 AAAACTTACAACAAAACTACAGTAACAAAGACAGTGTGTTACTGACAGAA 640
                                  v     i         iv           v     i  v  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_120390588_    641 GGATAAACATACAGATCAATGGAACAGAATTGAGAATC-ACAAATAAACC 689
                              i     i            i          i  - v         
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_120390588_    690 CTAACAGTTACAATCAATTGATTTTCAACGAAAGAGCCAAGACAATTCAA 739
                          vv   v   iii             i  i ii v        v      
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_120390588_    740 TGGGGGAAAAAAAATGGTCTTTTCAACAAGTGGTGCTGGG-CAACTGGAT 788
                              ---   i   i             i          -         
  L1M4_orf2#LINE/    382 TGGGG---AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_120390588_    789 ATCCACATGCAAAAGAATTAATTTGGACCCCTA----AGATTGTACACAA 834
                          ?                v  v           ---- v iii  i    
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_120390588_    835 TAATTAACTCAAAGTGAATCATAGGCCTAAATGTAGAAGCTAAAA-TATA 883
                         v            i  i    ?  i          ii        -    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_120390588_    884 AAACTTTTAGAAGAAAACTAACTCTTTTGACCTGAGTTAAGCAGTAAATC 933
                              i            ---------------- --  i ?-       
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAAC----------------A--TAGGN-GTAAATC 559

  chr1_120390588_    934 TTTGTGACTTTGAGTTAGGCAGTAATTTCTTTGATGCAACATCAAGAGCA 983
                           i     i   i        i ii      v   iii   i   i    
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_120390588_    984 CAAATAATAAAAGAGAAAAAAGTTGATAAGTTGAACTTAATCAAAATAAA 1033
                            ii  i      i    v  ---    i   i    v        v  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAG---ATAAATTGGACTTCATCAAAATTAA 656

  chr1_120390588_   1034 AAACTTCTGTGCTTCAAAGGACACCAACAAG----TGAAAGAACAGCCCC 1079
                               i                 i v    ----     ii   i   -
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC- 705

  chr1_120390588_   1080 ACAGAATCAGAGAGCATATTTGCAAATTATACTATCTGTTAAGGGACT-- 1127
                                vi    iv            i   -      v         --
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATA-TATCTGATAAGGGACTTG 754

  chr1_120390588_   1128 -----AGAATATA--AAAAAC----ACAAATCAATAA-GAAATGACAAAT 1165
                         -----        --  i   ----    v       -i   v       
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_120390588_   1166 GATCTAAGTTGGGAATGGGCAAAGGATTACAA--GATATTTTTCAAGAGA 1213
                         i i i  v ?iii               vv  --  i    i  v i   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_120390588_   1214 AAA-ATAT-----GCAAATAAGCACATGAAAAG 1240
                          i -   i-----  v                 
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAG 887

Transitions / transversions = 2.00 (70 / 35)
Gap_init rate = 0.03 (20 / 756), avg. gap size = 3.45 (69 / 20)  


2775 26.29 3.36 1.79  chr1_120402757_120405457.rev     1317  2210 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_120402757_   1317 TGGAAAAAGATTCCATGCTCATGGATAGGAAGAATTAGTGTTGTTAAAAT 1366
                               i v  i     i        v      v   i i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_120402757_   1367 GGCTGTACTTCCCAATGCAGTTTATGGATTCAATGCTATTCCTATGAAAC 1416
                            vi    i     vviii i  ii       i  v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_120402757_   1417 TACCAGTGACATACTTCACAGAATTAGAAAAAAAAACTTCTAAAATTCAT 1466
                          v    ivi v vi  ii     v v  v  ivvi - i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_120402757_   1467 ATGGAACTTAAAAAAGAGCCTGAATAGCCATAACAATCTTAAGCAAAATG 1516
                               v -iv  ii  v  v         v         i iv  i v 
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_120402757_   1517 AACAAAGCTGAAGGCATTACACTACCCAATTTCAA--CTATAATACAAGG 1564
                                i  i   vv i     v           --  -  v     i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_120402757_   1565 CTTCGGTAACCAAAACAGCAGGGTACTGGTACAAAAACAGACACATAGAC 1614
                           v i    i   i    iiv        i i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_120402757_   1615 CAATGGAACAGAA--AAGAGCCCAGAAATAATGCTGCACACCTATGATC- 1661
                                 i    --i    i          vv iii   ii    i  -
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_120402757_   1662 --TGATATTTGAAAAAAGTTGACAAAAACAAGCAATGAGAAAAGGACTCC 1709
                         --    v  i  v  ii  - v   i v  vv     i i    i ivvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_120402757_   1710 CTATTCAATAAATGGTGCTGAAATAAGTGGCTAGCCATATGCATAAGATT 1759
                           v     i           ii i  v   v  ?   i     v    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_120402757_   1760 GAAACTGGACCCCTTCCCTTTGCCATATACAAAAATCAACTCATA-TGAA 1808
                            ii         v  iivii              i      v -  i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_120402757_   1809 GTAAAGACTTAGATATAAAACCTAAAACTATAAAAGCCGTGGAAGATAGC 1858
                         vi ?    i  i  i   i v              vi v i     v i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_120402757_   1859 CTGGGAAATACTATTC-TGGAATAGGACCTGGCAAAGATTTCATAACAAA 1907
                         v i  ?ivv v v   -  ivv v  iiiv     v i    v  ivv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_120402757_   1908 GATGCCAAAAACAGTTGCAACTAAAACAAAAATTGACAAATGGAATCT-- 1955
                           ii      i  vvv     v   iv      v  i    v i ii --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_120402757_   1956 ----AATTAAAGAGCTTTAACATAGCCAAAAACAAACAAACAAAACAGTG 2001
                         ----       i -    viiiivv v  ii   -- v v   i v    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA--CTATCAAGAAAGTG 693

  chr1_120402757_   2002 AACACGGTAAACAGATAACCTACAGAATGAGAGAAAATATTTGCAAACTA 2051
                           -------  --  i    i        i                 ii 
  L1M4_orf2#LINE/    694 AA-------AA--GACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_120402757_   2052 TGCATCCTAGAGAAGTCTAATATCCAGAATTTATAAGGAACTTT------ 2095
                          ii   iv v iii v  vi          v     i     i ------
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_120402757_   2096 ---ATAAGCAAAAAACAA----CCTCATTAAAAAGTGGGCAAATGACACG 2138
                         ---    vv    i    ----  iv   ?    i        v  ivi 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_120402757_   2139 AACAGACATTTTTC--AAAAAGACATACATGTGGCCAAGAAGCATATGAA 2186
                           i        i  --  i    i     vi       v     i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_120402757_   2187 AAAATGTTCCACATCACTAATAAT 2210
                           i   i  v      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.71 (46 / 17)  


3120 26.59 1.67 0.67  chr1_120754850_120761119     4879  5777 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_120754850_   4879 TGGAAGAACATTGCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  iv    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_120754850_   4929 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_120754850_   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_120754850_   5027 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCT----AAGCCA 5072
                                viiv  ii  v  viv  vi    iv     i ----   -- 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG--A 196

  chr1_120754850_   5073 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5122
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_120754850_   5123 TCTACAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5172
                         v         v   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_120754850_   5173 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAA 5220
                                  i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_120754850_   5221 CTATCTGATCTTTGACAAACATGAGAAAAACAAGCATTGGGGAAAGGATT 5270
                         ii vi    i  i     ivi  vv  i v  vv  v         i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_120754850_   5271 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA-- 5318
                         vi  v  i  i              v      v  ?   i   i i  --
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_120754850_   5319 ----AGCTGAATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5364
                         ----  i  i i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_120754850_   5365 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5414
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_120754850_   5415 ACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCT 5464
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_120754850_   5465 AAAACACCAAAAGCAATGGCAATAAAAGCCAAAATTGACAAATGGGATCT 5514
                          vi            vvi    i     vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_120754850_   5515 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5564
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_120754850_   5565 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGGC 5614
                          v  i     i   i             v  i    vii ivi     ii
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_120754850_   5615 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5664
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_120754850_   5665 AAA-ACAAACAACCCCATCAAAAAGTGGGCAGAGGACATGAACAGACACT 5713
                            -     i     v  i?    i      i    iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_120754850_   5714 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATCCTCA 5763
                             v        i  vi viii     v  i          i  v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_120754850_   5764 CCATCACTGGCCAT 5777
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.33 (21 / 9)  


2981 25.77 3.47 0.50  chr1_120790614_120795117     2831  3637 (867)    L1M4_orf2#LINE/L1        1   831 (77)  

  chr1_120790614_   2831 TGGAAAGGTATTTTATGTTCATGAATTGGAAGAATTAATATTGCTAAAAT 2880
                                i   iii         i         v         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_120790614_   2881 GGCCGTACTACCCAAAGCAATCTACAGATTCAATGCAATCCATGTCA--- 2927
                            vi    v      vii              i       v i   ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_120790614_   2928 ------------------CAGAAATAAAAAAAAACT-ATTCTAAAATTTA 2958
                         ------------------       vi v  i--  -  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_120790614_   2959 TATGGAATCACAAATTACCCAGAGTAGCTAAAGCTATCCTAAGCAAAAAG 3008
                                vii   ivv       i    i   i v   i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_120790614_   3009 AATAAAACTGAAGGAATTACATTACCTGACTTCAAATTATACTACAGAGC 3058
                           i   ii  i    v i   i v  ii i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_120790614_   3059 TATAGTAACCAAAATAGCATGGTATTGGCATAAAAACAGGCACATACACC 3108
                           i     i   i i  ii     i        ii i  i  i   v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_120790614_   3109 AATGGAACAGAATAGAGAACCCAGAAACAAATCCACACACCTATAGTGAA 3158
                                i     v    ii       i   i   i   ii   i  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_120790614_   3159 CTCGTTTTTGACAAAGGTGCCAAGAATATAAATTGAGGAAGAGACAGTCT 3208
                         i vi    i     i          vi  vv v  i    iii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_120790614_   3209 CTTCAGTAAATGGTACTGGGAACACTAGATATCCATATGGTGAAGAATGA 3258
                         i    ii       i      vv   i    ?   i   vvi        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_120790614_   3259 AGCTAGATCTCTATCTCTTGCCACATAAAAAAATCAAATAAAAATGGATT 3308
                           i i  i i   i   vii   i   v      i  v v         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_120790614_   3309 AAAGACTTAAATCGAAGACCTAAAGCTATGAAACTACTATGAGAAAACTT 3358
                          ?    i     vv    v     i    i     vi  vi       v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_120790614_   3359 TGGGGAAACTCTCTAGGACATTGGTTTGGGCAA-AATTTCTTGAGTAATA 3407
                         v  ? v  v   iiiv   v    v  i     -ii      iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_120790614_   3408 CCCCACA-GCACTGGCAAGCGAAGTCAAAATGGACAAATGAGATCACATC 3456
                          v   v -    vi    vvi   vv     i  i    vi  iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_120790614_   3457 AAG-TTAAAAAGCTTCTGCACAACAAAGGATACAATCAC-AAAGTGAAGA 3504
                           i-       -   i  ii vv       i  v    v-        i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_120790614_   3505 G-CACCCCACAGAATGGGAAAAAATATTTGAAAACTATCCATCTAATAAG 3553
                          -  v              i          v   ii  vi    i     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_120790614_   3554 AGATTAACAACCAGAATATGTAAGGATTCCTAACAACTCTATAA-GAAAA 3602
                         i  i vii v         i   i  vii  v       v    -i    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_120790614_   3603 GACTTAATACTCTGCTTAAAAAATAAGCAACAGAT 3637
                            v-    vi iiv  ?      ii    vi   
  L1M4_orf2#LINE/    798 GACA-AATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.87 (133 / 71)
Gap_init rate = 0.01 (11 / 831), avg. gap size = 2.91 (32 / 11)  

 345 14.81 0.00 12.96  chr1_120790614_120795117     3932  4039 (465)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_120790614_   3932 AAAAAAAAGCAACAGATTTGATTAGACATTTTTCAAAAGAAGACATACAA 3981
                              vii    vi       v         i  v        i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_120790614_   3982 ATAGCAAGCAATTATATGTAAATAGGCATATGATGAGGTGCTGAACATCA 4031
                           i  ---    ----------- i   i    vi  i    v       
  L1M4_orf2#LINE/    865 ATGGC---CAAT-----------AAGCACATGAAAAGATGCTCAACATCA 900

  chr1_120790614_   4032 TTAAACAT 4039
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 7.00 (14 / 2)  


3214 26.57 0.77 0.66  chr1_120830465_120836864     5001  5907 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_120830465_   5001 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5050
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_120830465_   5051 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCGCCATCAAGC 5100
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_120830465_   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTCA 5148
                          v   iivi i  i  ii     -   -- v  i  - iii i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_120830465_   5149 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAA 5198
                                viiv  ii  v  viv  v     iv     i i ivv i  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_120830465_   5199 AGCAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5248
                          i     i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_120830465_   5249 TACAGTAACCAAAACAGTATGGTACTGGTATCAAAACAGAGATATAGACC 5298
                                 i   i     i         i  v ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_120830465_   5299 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGTCACATATCTACAACT 5346
                                i    i--    i  --        vvi  i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_120830465_   5347 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5396
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_120830465_   5397 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAACT 5446
                           v  i  i              v      v  ?i  i   i i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_120830465_   5447 GAAGCTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGA 5496
                             i    i    v   i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_120830465_   5497 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAAC 5546
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_120830465_   5547 CTAGGCA-ATACCATTCAGGACATAGGCATGGGTAAGGACTTCATGTCTA 5595
                         v    ?i- v i -   iv   v v  vv i  i  v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_120830465_   5596 AAACAACAAAAGC-CATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5644
                         vi   v       -  -i          vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_120830465_   5645 AATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTGCCATCAGAGTGA 5694
                         v  i   v v  i i   i  ii vv    i  v   ii  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_120830465_   5695 ACAGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTACTTGTCTGAC 5744
                          v  i     i       i         v       vii iv i     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_120830465_   5745 AAAGGGCTAATATCCAGAATCTAGAAAGAACTCAAACAAATTTAGAAGAA 5794
                           i  i  vi          v  v         vv    v iv v  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_120830465_   5795 AAA-ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5843
                            -     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_120830465_   5844 TCTCAAAAGAAGACATTTATGCATCCAAAAGACACATGATAAAATTCTCA 5893
                             v        i  vi viiiv    v ii       v  i  v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_120830465_   5894 TCATCACTGGCCAT 5907
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3260 26.22 1.11 0.66  chr1_120886325_120892601.rev     4882  5785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_120886325_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_120886325_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_120886325_   4982 TACCAATGACTTTCTTCCCAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  iv     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_120886325_   5030 TATGGAACCAAATAAGAG-CCC-GCATCGCCAAGTCAATCCTAAGCCAAA 5077
                                -- vii   i -   - v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_120886325_   5078 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5127
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_120886325_   5128 GCTACAGTAACCAAAACAGCCTGGTACTGGTACCAAAACAGAGATATAGA 5177
                                   i   i    iv         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_120886325_   5178 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 5225
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_120886325_   5226 CTATCTGATCTTTGACAAACCTGAGAAAAGCA----ATGGGGAAAGGATT 5271
                         ii vi    i  i     ivv  vv  i v  ----          i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_120886325_   5272 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5321
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_120886325_   5322 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5371
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_120886325_   5372 GATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5421
                            i ?   ii    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_120886325_   5422 ACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCC 5471
                           v    ?i v viv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_120886325_   5472 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5521
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_120886325_   5522 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5571
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_120886325_   5572 ACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5621
                          v  i     i   iv            v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_120886325_   5622 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5671
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_120886325_   5672 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5721
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_120886325_   5722 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5771
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_120886325_   5772 TCATCACTGGCCAT 5785
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


3199 27.43 0.88 0.44  chr1_120927630_120934010     4985  5888 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_120927630_   4985 TGGAAGAACATTCCATGCTCAAGGGTAGGAAGAATCAATATCGTGAAAAT 5034
                              ii i  i     i   v  i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_120927630_   5035 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5084
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_120927630_   5085 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5132
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_120927630_   5133 TATGGAACCAAGAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 5182
                                viivi ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_120927630_   5183 AACAAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGGC 5232
                                i      vv   i   v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_120927630_   5233 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5282
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_120927630_   5283 AATGGAACAGAGC--ACAGCCCTCAGAAATAACGCTGCATATCTACAACT 5330
                                i   ii-- v  i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_120927630_   5331 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAGTGGGGAAGGGATTCC 5380
                          vi    i  i     ivv  vv  i v  vv  i       i i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_120927630_   5381 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5430
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_120927630_   5431 GAAATGGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGA 5480
                            i v   i    v   i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_120927630_   5481 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAAC 5530
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_120927630_   5531 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTTATGTCTAA 5580
                         v    ?i v viv   iv   v v  vv i     v ii  iv ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_120927630_   5581 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5630
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_120927630_   5631 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5680
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_120927630_   5681 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5730
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_120927630_   5731 AGGGCTAATATCCAGAATCTACAATGAACTC--AAATTTCGA--AGAAAA 5776
                         i  i  vi          v  i  v      -- v vi  i -- v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_120927630_   5777 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5826
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_120927630_   5827 TCAAAAGAAGACATGTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5876
                           v        i  ii viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_120927630_   5877 ATCACTGGCCAT 5888
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (150 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


3202 26.47 1.45 0.44  chr1_120935264_120941944.rev     5292  6190 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_120935264_   5292 TGGAAAAACATTCCATGTTCATGGATAGGAAGAATCAATATCATGAAAAT 5341
                               i i  i              v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_120935264_   5342 GGCCATACTGCCCCAAGTAATTTATAGATTCAATGCTGTCCCCATCAAGC 5391
                            v     v   v  v i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_120935264_   5392 TACCA-TTGACTTTCTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 5438
                          v   -i  v    i ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_120935264_   5439 TATGGAATCAAAAAAGAGCCCACATAGTCAAGCCAATCCTAAGCAAAAAG 5488
                                viiv  ii  v  viv    i   iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_120935264_   5489 AACAAAGCTGGAGGCATCACGCTACTTGACTTCAAACTATACTACAAGAC 5538
                                i      vv    i  v iii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_120935264_   5539 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATA--GACC 5586
                                 i   i    ii         i iv ii i   v   --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_120935264_   5587 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCATGTATCTACAATCAT 5636
                                i    iv   ivii         vv    ii  i  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_120935264_   5637 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGAGGAAAGGATTCCCT 5686
                         i    i  i     ivv  v   i v  vvv    i      i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_120935264_   5687 ATTTTATAAATGGTGTTGGGAAAACTAG----CCATATGCAGAAAGCTGA 5732
                         v  iv i        i     v    i ----   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_120935264_   5733 AACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGCATT 5782
                          ii    i    v   i     v  i           i    i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_120935264_   5783 AAAGACTTAAATGTTAGATCTAAAACCATAAAAGCCCTAGAAGAAAACCT 5832
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_120935264_   5833 AGGCA-ATACCATTCAGGACACAGGCACAGGCAAAGATTTCATGATTAAA 5881
                            ?i- v i -   iv   viv  vvi      v i    v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_120935264_   5882 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5931
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_120935264_   5932 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 5981
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_120935264_   5982 GGCAAACCTACAGAACGGGAGAAAATTTTTGCAATGTGTCTATCTGGCAA 6031
                          i   -  i      i          v       vvii v      ii  
  L1M4_orf2#LINE/    698 GACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_120935264_   6032 AGGGCTAATATCCAGAATCCACAAAGAATTTCAACAAATTTACAAGAAAA 6081
                         i  i  vi          vi i      i iiv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_120935264_   6082 A---AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 6128
                          ---   i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_120935264_   6129 TCAAAAGAAGACATTTATGCAGCCAACAGGTACATGAAAAAATGCTCATC 6178
                           v        i  vi viii     i i i         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_120935264_   6179 ATCACTGGCCAT 6190
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


 518 20.00 0.00 0.00  chr1_120950177_120951777.rev      380   484 (1117)    L1M4_orf2#LINE/L1        5   109 (799)  

  chr1_120950177_    380 AAGTTATCCAGTGCTCTTGAGTTGGAAGAATTAATAGTGTTAACTTGTCC 429
                            v     vi  i  v  ii        v      v      vv  v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_120950177_    430 GTACTACCCAAAGTGTTCAACAGATTCAATGCAATCCCCATCAAAATTCC 479
                         i    v      v  v  v          i        i        i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_120950177_    480 AGCTG 484
                              
  L1M4_orf2#LINE/    105 AGCTG 109

Transitions / transversions = 0.62 (8 / 13)
Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.00 (0 / 0)  

2304 24.13 4.16 0.17  chr1_120950177_120951777.rev      502  1102 (499)    L1M4_orf2#LINE/L1      271   895 (13)  

  chr1_120950177_    502 TACTGAAGTTAAAACAGAAATATAGATCAATGGAACAGAATAGACAGCCC 551
                              ivi v ii i   v                i     v  v  i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_120950177_    552 AGAAATAAAATCATGCATATACAACCAACCAATCTTCAAAAAGTGTGCCA 601
                                  vi   i   v  iiii   iii  i   i v   v      
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_120950177_    602 AGAATACACAATGGGGTAAAAAAT-GTCTCTTCCACAAATAGTGTTAGGA 650
                            vi iv        -   i   -    i   v      i   i i   
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_120950177_    651 AAACCAGATACTCACATGCAGAAGAATAAA-TTGGACTCTCCTCTCACAC 699
                         v   ii    ?i        i      i  -      i iivi       
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_120950177_    700 CATATATAAAAATCACCTCAAAAT-----AAAGACTTAAATGTAAGACCC 744
                               i      i v        ----- ?    i           v i
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_120950177_    745 CAGACTGTAAAACTCTTAGTACA---CATAGGGGGAAAGCTTCTGGATGT 791
                         v i   i            v v ---      ? v   v    vv  iv 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr1_120950177_    792 CGGTCTTGACAATGATTTCTTGTATATGACA---AAAGCCCAGGCAATAA 838
                         i  vi v i     i      iv        ---     v  i    i  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_120950177_    839 CAACAAAAATGAACAAGTGAAACTCCTTTAGACTAAATAGCTTCTGTATA 888
                         v iv      ii i  i vii   i v i i v v  v i   i   iiv
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_120950177_    889 GCAAAAGAACCAATCAACAGAGTGAAAAGGCAGCCTATAGAATGGGTTAA 938
                         v    i  vv v     v i         i  i  i i        vv  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_120950177_    939 AATATTTGCAAACCACATATCCAATAATGGGTTAATCTCCA-AATATATA 987
                                     i  i     ii    v  ii vi v    -        
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_120950177_    988 AGGAACTTCTACAACTCATTATCAAAAA-----ATAATTT--TT----AA 1026
                          i     ii         v  vi     -----    iii--  ----  
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_120950177_   1027 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGATGACATACAAATGGC 1076
                                                            v  i           
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_120950177_   1077 CAAAAAATATATAAAAAAGCATTCAA 1102
                            v  ii i  i    iiiii    
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.84 (92 / 50)
Gap_init rate = 0.02 (10 / 625), avg. gap size = 2.60 (26 / 10)  


3118 27.31 0.66 0.66  chr1_120952284_120958659.rev     4978  5885 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_120952284_   4978 TGGAAGAAAATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5027
                              ii v  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_120952284_   5028 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5077
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_120952284_   5078 TACCAATGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5125
                          v   iivi i  i   i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_120952284_   5126 TATGGAACCAAAAAAGAGTCCGCATTGCCAAGTCAATCCTAAGTCAAAAG 5175
                                viiv  ii  vi v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_120952284_   5176 AACAAAGCTGGATGCATCACCCTACCTGACTTCAAACTATACTACAAGGC 5225
                                i    v vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_120952284_   5226 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5275
                          i      i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_120952284_   5276 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5323
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_120952284_   5324 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5373
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_120952284_   5374 CTATTTAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5423
                           v  i ii              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_120952284_   5424 GAAACTGGATCCCTTCCTTATGCCTTATACAAAACTTAATTCAAGATGGA 5473
                            ii    i    v   i ii  v         v    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_120952284_   5474 TTAAAGACTTAGATGTTAGACCTAAAACCATAAAAACCCTAGAAGAATAC 5523
                          i ?    i  i    v   v       i      vi i        v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_120952284_   5524 CTAGGCA-ATACCATTCAGGAGATAGGCAT-GGCAAGGAATTCATGTCTA 5571
                         v    ?i- v i -   iv  vv v  vv -     v iv   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_120952284_   5572 AAACACCAAAAGCAATGGCCACAAAAGCCAAAATTGACAAATGGGATCTA 5621
                         vi            vvi  v       vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_120952284_   5622 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5671
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_120952284_   5672 CAGGCAACCCACAGAATGGGAGAAAATGTTTGCAATCTACTCATCTGACA 5721
                         v  i                       i       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_120952284_   5722 AAGGGCTAATATCCAGAATCTAAAAAGAACTCAAACAAATTTACAAGAAA 5771
                          i  i  vi          v  v         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_120952284_   5772 AAAACAAAAAAATCCCATCAAAAAGTGGGTGGAGGATATGAACAGAGACT 5821
                           i     v  -i  v  i?    i    iii     v    i   v i 
  L1M4_orf2#LINE/    796 AAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_120952284_   5822 TCTTGAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5871
                            iv        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_120952284_   5872 TCATCACTGGCCAT 5885
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3283 26.40 0.55 0.66  chr1_141494753_141500444.rev     4293  5201 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_141494753_   4293 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4342
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_141494753_   4343 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4392
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_141494753_   4393 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4440
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_141494753_   4441 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGGCAAAAG 4490
                                viiv  ii  v  v v  v     iv     i i iiv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_141494753_   4491 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4540
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_141494753_   4541 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4590
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_141494753_   4591 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATACCTACAACT 4638
                                i    i--    i  --        vv   i i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_141494753_   4639 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4688
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_141494753_   4689 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4738
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_141494753_   4739 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4788
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_141494753_   4789 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4838
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_141494753_   4839 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 4888
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_141494753_   4889 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 4938
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_141494753_   4939 T-AAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4987
                          -    i    i -   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_141494753_   4988 CAGGCAAACTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5037
                         v  i   v i   iv            v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_141494753_   5038 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5087
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_141494753_   5088 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACT 5137
                           i -    i     v  i?    i    ii     iv    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_141494753_   5138 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5187
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_141494753_   5188 TCATCACTGGCCAT 5201
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1991 26.21 4.25 1.76  chr1_142178405_142180079.rev      502  1184 (491)    L1M4_orf2#LINE/L1      209   908 (0)  

  chr1_142178405_    502 GAGGTTTGGCACT-ACCAACTTCAGGACTTAC-ATTAAGCTACAGTAACC 549
                             vi vi    -v    i    ii      - iv            i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_142178405_    550 CAAATAGTGTGAAGTTGGTGAAAAGAGAAAACACACACATATAGATGCAT 599
                         v i i      ivii   iiv  i  v i -------         vv  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGA-------CATATAGATCAAT 301

  chr1_142178405_    600 GGAAAAGAATACGGAGCCCAGAAGCAGGCC--TACAT--ACAGTCCACTG 645
                             v     vvi   i      ii ii  --     -- ii   v i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_142178405_    646 ATCTTCCATGGAGGTTTAGAGACAATTTAAAACAGCAAAGATAGCCTTTC 695
                           i   v iiii   vivi    v   i  vivi v  ii    i    i
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_142178405_    696 CAACTAGTGGTGCTAGAACAGCTGGACAACCACATGCAAAAAAATAAA-- 743
                             v i       i i   i     i ?            i   i  --
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_142178405_    744 TAAATCCAGGTATGCATGTTATATACCC---TTTAT--AAAATAAATCTT 788
                          ii i  vviiv -  iiii      vv---  v i--     ii   v?
  L1M4_orf2#LINE/    452 TGGACCCCTACCT-CACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_142178405_    789 ACATGTAAATGTAAGGTGC-AAAACCATAAGAATCCTAAGAGATAAAATA 837
                          v iv          i-  -     i    i v  i  ii   v  v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_142178405_    838 GGAGAAAATCTGAGGGATCCTGGGTTCAATGATGGCTTCTTAGATACAAA 887
                           ? v      vv v  i i      viiii    i          ii v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_142178405_    888 ACCAAAAGCACAATCTACTAATGAAAAAA-AATTAAGTTGAGCCTCATTA 936
                                      v v  v  v       - iv   i   ii i    i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_142178405_    937 AAATTAAAAACTTCTGTTGTGTGAAAGACACTGTTAAGAGAATGGAAAAA 986
                                      i   vv vii  i      i i    i i  i   i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_142178405_    987 GCAAGTCACAGACTGGGAGAAAATATTTACAAA--ATA-ATCTGATGGAA 1033
                         -   vi      v               i    --   -       i- i
  L1M4_orf2#LINE/    700 -CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA-AG 747

  chr1_142178405_   1034 AAACTGCTGTCCAAAATATATGAAGAATTCTGAGAACTAAACAACACAAA 1083
                         ii   vv i    i       i     i   v v    v  i  i v   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_142178405_   1084 G-CAAAAAA---AA--AAAAAAAAGGTGAAAGATCTGAA----CACCTCA 1123
                          -    v  ---  --?     vi  ii  i   i    ----  ii  v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_142178405_   1124 TTAA-TAAGATATACAGATGGCAAATAAGCATATGAGAAAGATGCTCAAA 1172
                         ii  -v          i     v        i    -            v
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTCAAC 896

  chr1_142178405_   1173 ATCATTTGTTGT 1184
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (113 / 62)
Gap_init rate = 0.03 (22 / 700), avg. gap size = 1.86 (41 / 22)  


3131 26.85 0.88 0.55  chr1_142331850_142338237     4991  5895 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_142331850_   4991 TGGAAGAACATTCCATTCTCATGGAGAGGAATAAACAATATCGTGAAAAT 5040
                              ii i  i    vi       vv    v vvi     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_142331850_   5041 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5090
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_142331850_   5091 TACCAATGACTTTCTTCACA-AAATTAGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii  -     i-- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_142331850_   5139 TATGTAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5188
                             v  viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_142331850_   5189 AACAAAGCTGGAGGCATCACACTACCTGACTTTAAACTATACTACAAGGC 5238
                                i      vv       v  ii i  i   viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_142331850_   5239 TACAGTAAACAAAACAGCATGGTACTGGTACCAAAACGGAGATACAGACC 5288
                                 v   i    ii         i iv ii ii  v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_142331850_   5289 AATGGAACAGAAC--AGAGCCCTTAGAAATAACACCACACATCTACAACT 5336
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_142331850_   5337 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5386
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_142331850_   5387 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 5436
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_142331850_   5437 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGGTGGA 5486
                            ii    i    v   i   i v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_142331850_   5487 TTAAAGACTTAAATGTTAGATGTAAAACCATAAAAACCCTAGAAGAAAAC 5536
                          i ?    i       v   vv      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_142331850_   5537 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5585
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_142331850_   5586 AAACACCAAAAGCAATAGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5635
                         vi            vv           vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_142331850_   5636 ATTAAACTAAAAAGCTTCTGCACAGCAAAACAAACTACCATCAGAGTGAA 5685
                           i   v v    i   i  ii vv    iv v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_142331850_   5686 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5735
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_142331850_   5736 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAGGAAA 5785
                          i  i  vi          v  i         vv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_142331850_   5786 AA---AAACAACCCCATCAAAAAGAGGGCAAAGGATATGAACAGACACTT 5832
                           ---   i     v  i?    iv           v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_142331850_   5833 CTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTCAT 5882
                            v        i  vi viii     i ii  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_142331850_   5883 CATCACTGGTCAT 5895
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2445 24.22 10.72 1.33  chr1_142441497_142443853.rev     1037  1866 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_142441497_   1037 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATATCATTAAAAT 1086
                               i i  i     i               v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_142441497_   1087 GGCCATATTGCCGAAGGTAATCTACAGATTCAACACTATTCCTGTCAAAC 1136
                            v   i v  v  iv i               i v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_142441497_   1137 TACCAA-TGTC--------------------------------ATTCAT- 1152
                          v   i-  i --------------------------------      -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_142441497_   1153 --------CAAATGACC----------------------------AAGAT 1166
                         --------   iv    ----------------------------    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_142441497_   1167 CAAAGCCAGAGGCATCACACTATCCAACTTCAAACTATACTACAAGGCTA 1216
                              iii    vv       vi    i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_142441497_   1217 CAGTTGCCAAAACAGCATGTTGCTGGAAAAAAAAAAAGACACATAGACCA 1266
                             vii   i    ii  v i    v v  ii v -    i     i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGATCA 299

  chr1_142441497_   1267 ATGGAAGCAAATAGAGAACCCAAAAATAAAGCTACACACCTACAG-CAAT 1315
                               vvi   v    ii   i       v i i   ii  ii -    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_142441497_   1316 CTGATCTTCGACAAAATCAACAAAAATAAGCAGTGGGGAAAGCACTCCCC 1365
                         -    i        iiviiv   i vi vv  i         v - vvi 
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTC 397

  chr1_142441497_   1366 TATTCGA----TGGTGGTGGGATAGATAACTGGCTAGCCATATGCAAAAG 1411
                          v   i ----     v     i ----     v  ?   i         
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACA----ACTGGATAKCCACATGCAAAAG 443

  chr1_142441497_   1412 AATGAAACTGGGCCCCTACCTTTCAGCACATATAAAAATTAACTCAAGAT 1461
                               ii   i         iv  v  i   i              i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_142441497_   1462 GGAGTAAAGATGTAAATGTAAGACCTCAAACTATAAGAATCCTAGAAGAA 1511
                            vi ?   iv           v  v         i v  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_142441497_   1512 AACCCAAGAA-ACACCATTCTGGACATTGGCCTCAGGAAT------TTAT 1554
                            vi i ?i- v i -   vv   v    vi vi v   ------   -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA- 591

  chr1_142441497_   1555 GACTAAGTCCTCAAAAGCAATTGCAACAAAAACAAAAAGAGACAAGTCGG 1604
                           -  v v vi        vvv         iv     v   i  i i  
  L1M4_orf2#LINE/    592 GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_142441497_   1605 ATTT-ATTTAAACTAAAGAGTTTTGCACAGCAAAAGAAACTATCAACAGA 1653
                          i  -  iv   i    i v     ii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_142441497_   1654 GTAAACAGACAACCTGTAGAATCTAAAAAAAT--TTGCAACT-A-GCATC 1699
                           i  v        iii     vvi i     --      v - -ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_142441497_   1700 TGAAAAGGGTCTAATATCCAGAATCCATAAGGAATT-TAACAATTGAACA 1748
                            v     v  vi          vi    i   i - v    i v  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_142441497_   1749 ATGAAAA-ACAAATAACCCCATTAAAAAAATGAGCAAAAGGCATGATCAA 1797
                           i    -           v   ?     -  i     i iiv   vi i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAG 839

  chr1_142441497_   1798 ACACTTTTCAAAAGAAGACATACAAATGCCCACCAAATATATGAAAAATT 1847
                            i  i  v        i         v   vi  ii i       iv 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_142441497_   1848 GCTCCACATCACTAATCAT 1866
                             v      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (115 / 82)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.55 (100 / 22)  


3031 27.17 0.76 2.07  chr1_142536359_142542752     4982  5901 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_142536359_   4982 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATCAATATCGTGAAAAT 5031
                              ii i  i     i       iv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_142536359_   5032 GGCCATGCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5081
                            v  i  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_142536359_   5082 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5129
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_142536359_   5130 TATGGAACCAAAAAAGAACCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5179
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_142536359_   5180 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5229
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_142536359_   5230 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATTTTTGGT 5279
                                 i   i    ii         i iv ii i   v  -------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT------- 291

  chr1_142536359_   5280 AAACAAAACAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCC 5327
                         ------- i   i        i    i--    i  --        vv  
  L1M4_orf2#LINE/    292 -------ATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCC 332

  chr1_142536359_   5328 ACATATCTATAACCATCTGATCTTTGACAAACCTGATAAAAACAAGCAAT 5377
                          i i  i   iii  vi    i  i     ivv  vi  i v  vv    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_142536359_   5378 GGGGAAATGATTCCCTATTTAATACACGGTGCTGGGAAAACTGGCTAGCC 5427
                                vi  vvi  v  i  i v i          v      v  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_142536359_   5428 ATATGTAGAAAGCTGAAACTAGATCCCTTCCTTACACCTTATACAAGAAC 5477
                          i   i i  iiv    ii i  i    v   i     v       i  i
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_142536359_   5478 TAATTCGAGATGTATTAAAGACTTAAATGTTAGACCTGAAACCATAAAAA 5527
                            i  i i   v  i ?    i       v   v  i    i      v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_142536359_   5528 CCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAA 5576
                         i i           v    ?i- v i -   iv   v v  vv i     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA 581

  chr1_142536359_   5577 GGACTTCATGTCTAAAACACCAAAAGCAATGGCAAGGAAAGCCAAAATTG 5626
                         v ii   v ivv  vi            vvi    vi    vv     v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_142536359_   5627 ACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAGAAAACT 5676
                          i    v   ii v  i   v v  i i   i  ii vv     i v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_142536359_   5677 ACCATCAGAGTGAACAGGC--CCTACAGAATGGGAGAAAATTTTTGCAAT 5724
                          i  vv i      v  i --  i                 v       v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_142536359_   5725 CTACTTATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAAC 5774
                         ii iv       i  i  i  vi          v  i  v      vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_142536359_   5775 AAATTTACAAGAAAAAAACAAACAACCCCATCAACAAGTGGGCGAAGGAT 5824
                           v iv i  v     i     i     v  i? v  i     i      
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_142536359_   5825 ATGAGCAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACAG 5874
                         v   ii     i     v        i  vi viii     i ii    v
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_142536359_   5875 GAAAAAAGGCTCATCATCACCGGCCAT 5901
                              i v     v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.89 (26 / 9)  


2198 20.06 2.96 16.24  chr1_142558996_142560613       79  1125 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_142558996_     79 TGAAATAATATGTCATGTTCATGCATCAGAAGACCCAATGTTGTTAAGAT 128
                           i  vi    vi          v  ii      ii   i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_142558996_    129 ATCAATTCTCTATAAGTTGATCTATAGACTCAATGTGACCCCAATCAAAT 178
                         iv    v   ivi  i        i   i    i ii i   v      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr1_142558996_    179 ACCCCA-CTGGCTTTTT-GTCTACATTTACAAGTGAATTCTGAAATGTAT 226
                          i    -   v      - ivv v   v     ivi  i  i    vi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_142558996_    227 ATGGAAATTCAAAGAACCTAACACAATGAAAACAATTTTGAACAAGAAGA 276
                                 v   i i   i iv i iiv        i     v       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_142558996_    277 GCAAAGCTCAAGAATTTG-ACTACGTGATTTCAAAACGTAT---AAAGCT 322
                         i     i vi  i i ii-   v vii          v  i---      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_142558996_    323 ACTGTAACCAAATCAGTTTGGTATTAGTCTAAAGATGGATA-AGGGAGGC 371
                           v    i   iv    v     i i iv   i   i  i - vi  ---
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA--- 296

  chr1_142558996_    372 TGAGGCAGTAGAATTGCTTGAACCCAGGAGGCGAAGGTTGCCGTGAGCCA 421
                          ----  i i    ----------------------------------- 
  L1M4_orf2#LINE/    297 T----CAATGGAAT-----------------------------------A 307

  chr1_142558996_    422 AGATTGTGCCACTGCACTCCAGCCTGGGCAACAGAGTTAGACTCCATCTC 471
                         ii    --------------------------     i------------
  L1M4_orf2#LINE/    308 GAATTG--------------------------AGAGTC------------ 319

  chr1_142558996_    472 AAAAAAAGAAAAAGGAAAAAAAAAAGGCAGATAAATAAATCAGTCAAACA 521
                         ---------------------------    --      -----------
  L1M4_orf2#LINE/    320 ---------------------------CAGA--AATAAA----------- 329

  chr1_142558996_    522 CAATAGAAACCCAGATACAGACGATTATATATGTGGTCAATTGATTTG-A 570
                         ---------    ------------  i  v i              v-i
  L1M4_orf2#LINE/    330 ---------CCCA------------TACATTTATGGTCAATTGATTTTCG 358

  chr1_142558996_    571 ACAAAGGTGCTAAGGCAATTAAATGGAAAAAGGATAGTGCTCTTAACAAA 620
                             i     i   i v   v     ii    i     vi i i      
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_142558996_    621 CAGTGTTAGAACAACTGTACATCTACATGCAAAAAAAAAAAAAAGATAAA 670
                         ii   i i i       v i ? i          i  --------- i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA---------TGAA 449

  chr1_142558996_    671 AAAGAAAAAAAAAAACACCTTGATCACA--ATATACAAAAGTTAACTCAA 718
                         ivv i --------- v   vvv     --          i         
  L1M4_orf2#LINE/    450 GTTGGA---------CCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_142558996_    719 A-TGGATCATAGGCCTAAATGTAAAAATGC-AAAACTATAAAACTTCTAG 766
                          -       ?  i           i --  -              ii   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGA--GCTAAAACTATAAAACTCTTAG 538

  chr1_142558996_    767 AAAAAAATA---GAATA--TTTTTGTAATCT-GGATTAAGTAATGATTTC 810
                           i    i --- ?i  -- i  i  i i  -  i   i i    i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_142558996_    811 TTAGATATGACATTAAAAGCAGAACCA-TAAAAGAAAAAACTGATAATGT 859
                                     ii       v  v  -i           iv     ---
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA--- 635

  chr1_142558996_    860 TTATTT-ACCACAGCAAAATTTTAAAATGTCTGGTCTTCAAAAGACACTG 908
                         --   v-  iv  v       v-    iv i  vv       i      i
  L1M4_orf2#LINE/    636 --ATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_142558996_    909 TTACTAAAATGGAAAGACAATCTGCACAGTGGGAGAAAATATTTGCAAAG 958
                          i vv   i  i        i ii  v i                    v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_142558996_    959 AACATATATAATAAA--ACTTGCATTTAGAATATGAAATGAACCCAATGA 1006
                         v i    v i    i--     i  ii       iv  v    i vvvv 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_142558996_   1007 ACTCAGTGA----AACCCAAACAACTCAAT-GGAAAATGGGCAAAATATT 1051
                              i i ----  vv    i   i    -?i            iv   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_142558996_   1052 TCAACAGACACTTTACCAAAAA---TATGTAGATAAT-AATCAAGCTCAT 1097
                          v  i     i  iv     i ---   ii i  iii-   -    v   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCACAT 881

  chr1_142558996_   1098 GAAAAAAAAGCTCAATATCATTAATCAT 1125
                              i v-      i    ????????
  L1M4_orf2#LINE/    882 GAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (138 / 68)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 5.74 (201 / 35)  


3580 15.73 4.57 8.82  chr1_142572891_142574939.rev      618  1558 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_142572891_    618 ATGTTCCACATTCATGGATTGGAAGACTTAACAGAGTTAAGATGGCAGTA 667
                           i i   ii                     i vv            i  
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_142572891_    668 ATCCC-AAATTGATCTATAGATTTGTTGCAATCTCTATCAAAATCCCAGC 716
                         v    -           i     iivi      i                
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr1_142572891_    717 AGGATCTCTCTCTCTCTCTTTTTTTTTTTTTTTTTTTTTTTGTGTGTGGC 766
                         v --------------- i      -----------------------  
  L1M4_orf2#LINE/    108 TG---------------CCTTTTTT-----------------------GC 119

  chr1_142572891_    767 AGAAATTGACAAGCTGCTCTTAAAATTCAGGTAGAAAAGCAAAGGACCCA 816
                                         v  i         vi i    v    i       
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_142572891_    817 GAATAATTAAAACCATCTTTAAAA-GAAGGAAAAAGGTGTGAGAAGGACT 865
                              iii     v     v    -    i v    v  ----i      
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG----GAGGACT 215

  chr1_142572891_    866 CATACTTCT-GATTTCAAAACTTAATAACAAGCAACA-TAATTAAGACAG 913
                           i     i-i             v  vv    v   -    i       
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_142572891_    914 TGTGGTATTGAAATCAGAATAGACATACAGGTCAATGGAATATAATTGAG 963
                                i  iv  v  i         i  i           v       
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_142572891_    964 AGTCCCAAAAATAAACACATGCATATATGGTC---TAATT------AAA- 1003
                              - i        v   i   v       --- i   ------  i-
  L1M4_orf2#LINE/    316 AGTCC-AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_142572891_   1004 -----AAAA------AATAAGGAAAGGAGAGTATTTTCAACAAATGATG- 1041
                         -----  i ------   ii      i v   v             i  -
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_142572891_   1042 TGTGACAACTGGATATTCACATGCAAAATGATGA---TGGGCTCTTACAT 1088
                           v            ?i           vi    ---   i i i   v 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_142572891_   1089 CACACTATATATAAAAATTATCTCAAAATGGATTGTCAACCTA--TG--- 1133
                              i     i        v            ii?vi     --  ---
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_142572891_   1134 -AGCTAAAACTATATATCTCTTTGAATGAAACACAGGAATAAATCTTTGT 1182
                         -             v v     v   vi     i   ?i        i  
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_142572891_   1183 GACCTTTGATCCAGCA-TGGTTTCCTAGCTATGACACCAAAAGTACAAGC 1231
                               v i ivi   -       i   v              i      
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_142572891_   1232 TGCAAAAGAAAAAAATAGATAAAA-AGACTTCACCAAAATTTAAAACTTA 1280
                         vi            -        v-i       i       v       v
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_142572891_   1281 TTTTCTTCAAAAAGCAC----AAGAAAGTGAGAGGACAACCCTCAAAGTG 1326
                          v v       iii   ----          i i        v  i i  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_142572891_   1327 GGACAAAATACTTGCAAATCATAT--CAGGTAAAGGAATTGCATCCAGAA 1374
                            v      i             -- v i   i   v   i        
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_142572891_   1375 CACACACACACACACACACACACACACACACACACACACACACACACCCC 1424
                         i i i v v -----------------------------------  i -
  L1M4_orf2#LINE/    764 TATATAAAGA-----------------------------------ACTC- 777

  chr1_142572891_   1425 TTACAACTCAGTAATAAAATAAGAACAAACAACCCAATTGAAAAATAGGC 1474
                                   i        --   -    i         ?      i   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAA--AGA-CAAATAACCCAATTWAAAAATGGGC 824

  chr1_142572891_   1475 AACAAATTTGAAAAAATGTTTCTCCAATGAAGATATACAAATAAATACTA 1524
                           vii       v i ii         v              iivi v  
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_142572891_   1525 AATACAAGACAAGATGCTCAACATTATTAGCTAG 1558
                          ii   v  v              i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (90 / 54)
Gap_init rate = 0.03 (25 / 901), avg. gap size = 5.04 (126 / 25)  


2773 25.95 3.58 2.01  chr1_142611137_142613835     1313  2206 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_142611137_   1313 TGGAAAAAGATTCCATGCTCATGGATAGGAAGAATTAGTGTTGTTAAAAT 1362
                               i v  i     i        v      v   i i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_142611137_   1363 GGCTGTACTTCGCAATGCAGTTTATGGATTCAATGCTATTGCTATGAAAC 1412
                            vi    i v   vviii i  ii       i  v  iv    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_142611137_   1413 TACCAGTGACATACTTCACAGCATTAGAAAAAAAAACTTTTAAAATTCAT 1462
                          v    ivi v vi  ii   v v v  v  ivvi - ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_142611137_   1463 ATGGAACTTTAAAAAGAGCCTGAATAGCCATAACAATCTTAAGCAAAATG 1512
                               v vi  ii-  v  v         v         i iv  i v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_142611137_   1513 AACAAAGCTGAAGGCATTACACTACCCAATTTCAA--CTATACTACAAGG 1560
                                i  i   vv i     v           --  -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_142611137_   1561 CTTCGGTAACCAAAACAGCAGGGTACTGGTACAAAAACAGACACATAGAC 1610
                           v i    i   i    iiv        i i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_142611137_   1611 CAATGGAACGGAA--AAGAGCCCAGAAATAATGCTGCACACCTATGATC- 1657
                                 ii   --i    i          vv iii   ii    i  -
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_142611137_   1658 --TGATATTTGAAAAAAGTTGACAAAAACAAGCAATGAGAAAAGGACTCC 1705
                         --    v  i  v  ii  - v   i v  vv     i i    i ivvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_142611137_   1706 CTATTCAATAAATGGTGCTGAAATAAGTGGCTAGCCATATGCATAAGATT 1755
                           v     i           ii i  v   v  ?   i     v    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_142611137_   1756 GAAACTGGACCCCTTCCTTATGCCATATACAAAAATCAACTCATA-TGAA 1804
                            ii         v   i ii              i      v -  i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_142611137_   1805 GTAAAGACTTAGATATAAAACCTAAAACTATAAAAGCCGTGGAAGATAGC 1854
                         vi ?    i  i  i   i v              vi v i     v i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_142611137_   1855 CTGGGAAATACTATTC-TGGAATAGGACCTGGCAAAGATTTCATAACAAA 1903
                         v i  ?ivv v v   -  ivv v  iiiv     v i    v  ivv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_142611137_   1904 GATGCCAAAA--ACAATTGCAACTAAAACAAAAATTGACAAATGGAATCT 1951
                           ii      --    --     v   iv      v  i    v i ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_142611137_   1952 ------AATTAAAGAGCTTTAGCATAGCCAAAAACAAACAAACAAAACAG 1995
                         ------       i -    v iiivv v  ii   -- v v   i v  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA--CTATCAAGAAAG 691

  chr1_142611137_   1996 TGAACACGGTAAACAGATAACCTACAGAATGAGAGAAAATATTTGCAAAC 2045
                             -------  --  i    i        i                 i
  L1M4_orf2#LINE/    692 TGAA-------AA--GACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_142611137_   2046 TATGCATCCTAGAGAAGTCTAATATCCAGAATTTATAAGGAACTTT---- 2091
                         i  ii   iv v iii v  vi          v     i     i ----
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_142611137_   2092 -----ATAAGCAAAAAACAA----CCTCATTAAAAAGTGGGCAAATGACA 2132
                         -----    vv    i    ----  iv   ?    i        v  iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_142611137_   2133 CGAACAGACATTTTTC--AAAAAGACATACATGTGGCCAAGAAGCATATG 2180
                         i   i        i  --  i    i     vi       v     i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_142611137_   2181 AAAAAATGTTCCACATCACTAATAAT 2206
                             i   i  v      ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.63 (50 / 19)  


4104 19.22 1.74 3.15  chr1_143124029_143126723     1282  2202 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_143124029_   1282 TAGAAAGACATCCTGTGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 1331
                          i      i    ii                                   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_143124029_   1332 ATGAATTCTTCCCAAAGCGATCTACAGATTCAACAGAATACCTATCAAAA 1381
                         ivv   v  i      vi                iv   v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_143124029_   1382 TCCCAACAGCATTTTTTTTGCA--AATAGA-AGTTTCATCCCAAAATTAA 1428
                              i v  --i         --   v  - ivi v    i      v 
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_143124029_   1429 TTTGGAATCTCACGTTACCCCTAATAGCCAGAACAGTTTTCAAAAAGAAA 1478
                          v     viv  v vv    vv        i    i i  v        i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_143124029_   1479 AACAAAGCTGGAGGACTCAAACTTTCTGATTTCAAAATATATTACTAAGC 1528
                                i           v    i ii         iv  i   v    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_143124029_   1529 TATGGTAATAAAACTAGTGTGGTACTGGCATAACAACAGACATATAGA-C 1577
                           ii     v  ivi                  vi i           - 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_143124029_   1578 AATGGAATAGA-----GACTCCAGAAATAAACCCTTGCATATGTGGTCAG 1622
                                    -----  v               v i   v i      i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_143124029_   1623 ATGATCTTGGACAGAGGTGCTAGGACCCCTCTGTGGAGCAAGGACAGTCT 1672
                         v    i  v    ii     i i    vi  vi   i v   i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_143124029_   1673 CTTCAGCAAACAGTGTTGGGAAAACTGGACTTTCACATACAAAACAA-AA 1721
                         i    i    ii   i     v       iv?i     i     v  -i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_143124029_   1722 ATTTGGACTCATATTTTACACTATATATAAAAATAAACTCAAAGTGGATT 1771
                          v      i v  ii i    i     i      v        i     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_143124029_   1772 AAAGACCTAAATATAAGACCTAAAACTGTAAAACTCCTAAAAGAAAACTT 1821
                          ?          i     v        i        i  i        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_143124029_   1822 AGAGGAAAGGCTTATAACTTAAAACTTAGAGGAAAGGCTTTATAACTTTG 1871
                           i? --------------    --- ----------   ii i  i   
  L1M4_orf2#LINE/    549 AGGNG--------------TAAA---T----------CTTCGTGACCTTG 571

  chr1_143124029_   1872 GATTTGGCAGTGATTTCTGGCATATGACACCATAAGCACAGGCAACAAAA 1921
                          i  v    i  i     viv           v       i         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_143124029_   1922 GGAAAAATAGGCAAATGGGACTGCATCAAACTTAAAAACTTTGGTGCATC 1971
                          i        ii    v     v       v           v    v  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_143124029_   1972 AATGAACACAATCAAC---TTGAAAAGGCAACCTGTGGAATGGGAGAAAA 2018
                           v i    v     v---v       i     iiii             
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_143124029_   2019 TGTTTGTAAATTGTGTATCTGTTAAAGTATTAATATCCAGAATGTAGAAA 2068
                          i    i    ii i      v   i v i vi          i  v   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_143124029_   2069 GAACA---ACAACTCAACAACAAAAAATCAAATAAACAGATTAAAAAATA 2115
                             v---         i  i     iv       v vi   ?      i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_143124029_   2116 GGCAAATGACTTGAATAGTCATTTCTCCAAAGATGATAAACCAATGGTCA 2165
                               v  i        v              v    v  v     i  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_143124029_   2166 AGACACATTTGAAAAGATGTTCAACATCACTAATCAT 2202
                          v vi  iv          i         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (102 / 71)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 4.09 (45 / 11)  


3166 25.80 1.10 1.43  chr1_143267702_143273858     4760  5670 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_143267702_   4760 TGGAAAAACACTCCATGCTCCCAGATAGGAAGAATCAATATCATGAAAAT 4809
                               i i ii     i  vii   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_143267702_   4810 GGCCATACTGCCCAAAGTAATTTATAAATTCAGTGCTACTCCCATTAAAC 4859
                            v     v      v i  i  i i     ii  v ii  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_143267702_   4860 TACCATTGACATTCTTCCCAGAATTAGAAAAAAACT-ATTTTAAAATTCA 4908
                          v   vivi v  i  iv     v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_143267702_   4909 ATATGGAAGCAAAAAAGAGCCCGTACAAGTCAAGACAACTGTAAGCAAAA 4958
                         -       iiiv  ii  v  v v i - i   i    iiv i iv  i 
  L1M4_orf2#LINE/    149 -TATGGAAATGCAAGGGACCCAGAATA-GCCAAAACAATCTTGAAAAAGA 196

  chr1_143267702_   4959 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 5008
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_143267702_   5009 GTTACAGTGACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGA 5058
                          i      i i   i    ii         i i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_143267702_   5059 CCAATGGAACAGAATAGAGAACTCAGAAATAAGACCGCACATCTACAGCC 5108
                         i        i     v    iii         iv  ii    i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_143267702_   5109 ATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5158
                          vi    i  i     i v  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_143267702_   5159 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5208
                           v  i  i              v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_143267702_   5209 GAAACTGGAACCCTTCTTTACACCTTATACAAAAATTAACTCAAGATGGA 5258
                            ii    v    v i i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_143267702_   5259 TTAAAGACTTAAATGTAAAACCCCAAACTATAAAAAACCTAGAAGAAAAT 5308
                          i ?    i         i v iv           vv i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_143267702_   5309 CTAGGCA-ATACCATTCAGGACAT--GGTACAGGCAAAGGTTTC------ 5349
                         v    ?i- v i -   iv   v --   -i      v      ------
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr1_143267702_   5350 ATGACAAAAATGTCAAAAGCAATTGCCACAAAAGCAAAAATTGACAAATG 5399
                               ------i        vvv  v       v      v  i    v
  L1M4_orf2#LINE/    595 ATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_143267702_   5400 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCTAAAGAAACTATCATCA 5449
                            ii v  i   v v  i i   i  ii vv v  i  v       vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_143267702_   5450 GGGTGAACAGACAACCAACAGAATGGGAGAAAATTTTTGCAATCTATCCA 5499
                         ii     v        v                 v       vii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_143267702_   5500 TCTGACAAAGGCCTAATATCCAGAATCTACAAGGAACTTAAAGAAATTTA 5549
                              i  i  v  vi          v  i  i     ivv v  v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_143267702_   5550 CAAGAAAAAAATCAAACAACCCCATTAAAAAGTAAGCAAAGGACATGAAC 5599
                         i  v     i -    i     v   ?    i ii        iv    i
  L1M4_orf2#LINE/    789 TAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_143267702_   5600 AGACAATTCTCAAAAGAAGACATTTATGTGGCCAACAAACGTATGAAAAA 5649
                              v     v        i  vi vi       i  i ii       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_143267702_   5650 AAGCTCAAGCTCAGTATCACT 5670
                          v      vv   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


1075 24.05 5.70 0.32  chr1_143282665_143285613.rev      675   990 (1959)    L1M4_orf2#LINE/L1        6   338 (570)  

  chr1_143282665_    675 AAATAAACCATGTTAATAGATTGGAAGACTTGA-ATAGTAATGATGTTAA 723
                          i   vv       v  i             i -  v  v v    vi  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_143282665_    724 TTCTCCCCAAATTGGTATACAAATTTAATGTTATTCATTTCAAAATCCCA 773
                          v            i v    i   i  i iv  i v v           
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_143282665_    774 GCAAGATTTATTTGTAGATATACACAAAATTATTCTAAAATTTGTACAGA 823
                           -v vi  v    i   v  vv    iv v  i        ii  ii  
  L1M4_orf2#LINE/    106 GC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_143282665_    824 AAGGCAAAATAACTAGAATAGTTAATACAATTTTTAAAAAGAA---CAGT 870
                           v    iiv v i       ii  v     i  v        ---  iv
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_143282665_    871 ATGAGAGGAATTCCTCTACCTGATCTTTAAACATATTATATAGCTACAGT 920
                         i vi     v iv v  v  ii  i iv    v  i  i v         
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_143282665_    921 AATCAAGAC--TGTGGTACTGG--------TAGACATA--GATCACTGGA 958
                                  --           --------        --     v    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_143282665_    959 ACAGAAAAGAGAACCCAGAAATA--CCGACACAT 990
                          i    vv    ii         --  v i    
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

Transitions / transversions = 1.00 (38 / 38)
Gap_init rate = 0.02 (7 / 333), avg. gap size = 2.71 (19 / 7)  

 435 33.95 2.47 0.62  chr1_143282665_143285613.rev     1297  1458 (1491)    L1M4_orf2#LINE/L1      321   485 (423)  

  chr1_143282665_   1297 AGAAATA--CTGACACAAATACACCCAGCTAATTTTTGACAAAGATGCAA 1344
                                -- iv i   vv  iivi  ii i     i     i i   v 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_143282665_   1345 AAGCAGTTCAGTGGAGGAAAGATAACCTTT-CACCAAATGGTGCTAGAGC 1393
                          ii vi    i   i i  ii   ii    -  v           i ii 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_143282665_   1394 AATTAGGCGTCCATAGGTTTAAAAAATGAATCTAAATCTAAGTCTTACAC 1443
                           i i iii?   i v iv-   i      vi ii i ivvii  i    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCA-AAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_143282665_   1444 CTTATATAAAA-TTAA 1458
                          v    i    -    
  L1M4_orf2#LINE/    470 CATATACAAAAATTAA 485

Transitions / transversions = 3.15 (41 / 13)
Gap_init rate = 0.02 (4 / 165), avg. gap size = 1.25 (5 / 4)  

 473 26.40 7.61 0.51  chr1_143282665_143285613.rev     1748  1944 (1005)    L1M4_orf2#LINE/L1      477   687 (221)  

  chr1_143282665_   1748 AAAAA--AAATTAAAACAGATAATAGACTAAAATGTAA-------AACTA 1788
                              --  v i    ii   v ?    iv        -------     
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_143282665_   1789 TAAAACTTTCAGAAAAAAAAA-AAAAG--AATCTTTGGAATCAAGGGCTA 1835
                                i i    i    v - ii? --      i vi i vv   i  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_143282665_   1836 CACAAAAAGTTCTTTACT-TGATACCAAAAATAAAATCCATGAAAGGAAA 1884
                         vi   viiv     viv -   i       ii v  v v ii    -   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAA 625

  chr1_143282665_   1885 AAATGGATAAATTGGGCTCCATCAAAATTTAACACTTTCGCTCTGTAAAA 1934
                             i          i  i          v  v     i iv  vi   i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_143282665_   1935 GAC--TGTTAAG 1944
                            -- i i   
  L1M4_orf2#LINE/    676 GACACTATCAAG 687

Transitions / transversions = 1.63 (31 / 19)
Gap_init rate = 0.03 (7 / 211), avg. gap size = 2.29 (16 / 7)  

 664 25.56 6.73 0.45  chr1_143282665_143285613.rev     2238  2460 (489)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr1_143282665_   2238 AAAAAATACTGTTAAGAGGATGAAAAGATAAGCTACCCACTGGGAGAAAA 2287
                            ii i   i i    iii        i  v i  vv v          
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_143282665_   2288 TATTTGCAAGCCACTTATTTGAGAAAGCACTAGTATCTAGAATA----AA 2333
                                  ii  iv   i   v  i v   v     i      ----  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_143282665_   2334 AAACATTCAAAGCTTACATT-TAAAAA---AAATG---CAGTTAGAAAAT 2376
                         i   vi i v i  i -  v-      ---    i---  i  ?i     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCA-ATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_143282665_   2377 AAGCAAAAA---TGA-TGAACATTTTATTGTAGAGGATATGCAAATGGCA 2422
                         ii     ii---   - ii      iviiiv   i     i        v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_143282665_   2423 CATAACCACATGAAAAGGTGTTCAACATTGTTAGCCAT 2460
                         v    v           i  i       ii????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (40 / 16)
Gap_init rate = 0.03 (7 / 237), avg. gap size = 2.29 (16 / 7)  


1067 24.37 5.70 0.32  chr1_143361239_143364180      668   983 (1959)    L1M4_orf2#LINE/L1        6   338 (570)  

  chr1_143361239_    668 AAATAAACCATGTTAATAGATTGGAAGACTTGA-ATAGTAATGATGTTAA 716
                          i   vv       v  i             i -  v  v v    vi  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_143361239_    717 TTCTCCCCAAATTGGTATACAAATTTAATGTTATTCATTTCAAAATCCCA 766
                          v            i v    i   i  i iv  i v v           
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_143361239_    767 GCAAGATTTATTTGTAGATATACACAAAATTATTCTAAAATTTGTACAGA 816
                           -v vi  v    i   v  vv    iv v  i        ii  ii  
  L1M4_orf2#LINE/    106 GC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_143361239_    817 AAGGCAAAATAACTAGAATAGTTAATACAATTTTTAAAAAGAA---CAGT 863
                           v    iiv v i       ii  v     i  v        ---  iv
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_143361239_    864 ATGAGAGGAATTCCTCTACCTGATCTTTAAACATATTATATAGCTGCAGT 913
                         i vi     v iv v  v  ii  i iv    v  i  i v    i    
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_143361239_    914 AATCAAGAC--TGTGGTACTGG--------TAGACATA--GATCACTGGA 951
                                  --           --------        --     v    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_143361239_    952 ACAGAAAAGAGAACCCAGAAATA--CCGACACAT 983
                          i    vv    ii         --  v i    
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

Transitions / transversions = 1.03 (39 / 38)
Gap_init rate = 0.02 (7 / 333), avg. gap size = 2.71 (19 / 7)  

 435 33.95 2.47 0.62  chr1_143361239_143364180     1291  1452 (1490)    L1M4_orf2#LINE/L1      321   485 (423)  

  chr1_143361239_   1291 AGAAATA--CTGACACAAATACACCCAGCTAATTTTTGACAAAGATGCAA 1338
                                -- iv i   vv  iivi  ii i     i     i i   v 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_143361239_   1339 AAGCAGTTCAGTGGAGGAAAGATAACCTTT-CACCAAATGGTGCTAGAGC 1387
                          ii vi    i   i i  ii   ii    -  v           i ii 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_143361239_   1388 AATTAGGCGTCCATAGGTTTAAAAAATGAATCTAAATCTAAGTCTTACAC 1437
                           i i iii?   i v iv-   i      vi ii i ivvii  i    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCA-AAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_143361239_   1438 CTTATATAAAA-TTAA 1452
                          v    i    -    
  L1M4_orf2#LINE/    470 CATATACAAAAATTAA 485

Transitions / transversions = 3.15 (41 / 13)
Gap_init rate = 0.02 (4 / 165), avg. gap size = 1.25 (5 / 4)  

 480 26.02 8.16 0.51  chr1_143361239_143364180     1743  1938 (1004)    L1M4_orf2#LINE/L1      477   687 (221)  

  chr1_143361239_   1743 AAAAA--AAATTAAAACAGATAATAGACTAAAATGTAA-------AACTA 1783
                              --  v i    ii   v ?    iv        -------     
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_143361239_   1784 TAAAACTTTCAGAAAAAAAAAAAAG----AATCTTTGGAATCAAGGGCTA 1829
                                i i    i    v v i ----      i vi i vv   i  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_143361239_   1830 CACAAAAAGTTCTTTACT-TGATACCAAAAATAAAATCCATGAAAGGAAA 1878
                         vi   viiv     viv -   i       ii v  v v ii    -   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAA 625

  chr1_143361239_   1879 AAATGGATAAATTGGGCTCCATCAAAATTTAACACTTTCGCTCTGTAAAA 1928
                             i          i  i          v  v     i iv  vi   i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_143361239_   1929 GAC--TGTTAAG 1938
                            -- i i   
  L1M4_orf2#LINE/    676 GACACTATCAAG 687

Transitions / transversions = 1.50 (30 / 20)
Gap_init rate = 0.03 (6 / 211), avg. gap size = 2.83 (17 / 6)  

 673 25.11 6.73 0.45  chr1_143361239_143364180     2229  2451 (491)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr1_143361239_   2229 AAAAAATACTGTTAAGAGGATGAAAAGATAAGCTACCCACTGGGAGAAAA 2278
                            ii i   i i    iii        i  v i  vv v          
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_143361239_   2279 TATTTGCAAGCCACTTATTTGAGAAAGCACTAGTATCTAGAATA----AA 2324
                                  ii  iv   i   v  i v   v     i      ----  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_143361239_   2325 AAACATTCAAAGCTTACATT-TAAAAA---AAATG---CAGTTAGAAAAT 2367
                         i   vi i v i  i -  v-      ---    i---  i  ?i     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCA-ATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_143361239_   2368 AAGCAAAAA---TGA-TGAACATTTTATTGTAGAGGATATACAAATGGCA 2413
                         ii     ii---   - ii      iviiiv   i              v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_143361239_   2414 CATAACCACATGAAAAGGTGTTCAACATTGTTAGCCAT 2451
                         v    v           i  i       ii????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.44 (39 / 16)
Gap_init rate = 0.03 (7 / 237), avg. gap size = 2.29 (16 / 7)  


3140 26.13 0.99 1.32  chr1_143373000_143379068.rev     4674  5584 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_143373000_   4674 TGGAAAAACACTCCATGCTCCCAGATAGGAAGAATCAATATCATGAAAAT 4723
                               i i ii     i  vii   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_143373000_   4724 GGCCATACTGCCCAAAGTAATTTATAAATTCAGTGCTACTCCCATTAAAC 4773
                            v     v      v i  i  i i     ii  v ii  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_143373000_   4774 TACCATTGACATTCTTCCCAGAATTAGAAAAAAACT-ATTTTAAAATTCA 4822
                          v   vivi v  i  iv     v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_143373000_   4823 ATATGGAAGCAAAAAAGAGCCCGTACAAGTCAAGACAACTGTAAGCAAAA 4872
                         -       iiiv  ii  v  v v i - i   i    iiv i iv  i 
  L1M4_orf2#LINE/    149 -TATGGAAATGCAAGGGACCCAGAATA-GCCAAAACAATCTTGAAAAAGA 196

  chr1_143373000_   4873 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACCAG 4922
                                  i      vv    i  v  ii i      viv      v i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_143373000_   4923 GTTACAGTGACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGA 4972
                          i      i i   i    ii         i i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_143373000_   4973 CCAATGGAACAGAATAGAGAACTCAGAAATAAGACCGCACATCTACAGCC 5022
                         i        i     v    iii         iv  ii    i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_143373000_   5023 ATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5072
                          vi    i  i     i v  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_143373000_   5073 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5122
                           v  i  i              v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_143373000_   5123 GAAACTGGAACCCTTCTTTACACCTTATACAAAAATTAACTCAAGATGGA 5172
                            ii    v    v i i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_143373000_   5173 TTAAAGACTTAAATGTAAAACCCCAAACTATAAAAAACCTAGAAGAAAAT 5222
                          i ?    i         i v iv           vv i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_143373000_   5223 CTAGGCA-ATACCATTCAGGACAT-GGCACAGGCAAAGGTTTC------A 5264
                         v    ?i- v i -   iv   v -  vvi      v      ------ 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_143373000_   5265 TGACAAAAATGTCAAAAGCAATTGCCACAAAAGCAAAAATTGACAAATGG 5314
                              ------i        vvv  v       v      v  i    v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_143373000_   5315 GATCTAATTAAACTAAAGAGCTTCTGCACAGCTAAAGAAACTATCATCAG 5364
                           ii v  i   v v  i i   i  ii vv v  i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_143373000_   5365 GGTGAACAGACAACCAACAGAATGGGAGAAAATTTTTGCAATCTATCCAT 5414
                         i     v        v                 v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_143373000_   5415 CTGACAAAGGCCTAACATCCAGAATCTACAAGGAACTTAAACAAATTTAC 5464
                             i  i  v  vii         v  i  i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_143373000_   5465 AAGAAAAAAATCAAACAACCCCATTAAAAAGTAAGCAAAGGACATGAACA 5514
                           v     i -    i     v   ?    i ii        iv    i 
  L1M4_orf2#LINE/    790 AATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_143373000_   5515 GACAATTCTCAAAAGAAGACATTTATGTGGCCAACAAACGTATGAAAAAA 5564
                             v     v        i  vi vi       i  i ii       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_143373000_   5565 AGCTCAAGCTCAGTATCACT 5584
                         v      vv   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


2003 25.89 5.18 1.63  chr1_143539492_143541159      500  1175 (493)    L1M4_orf2#LINE/L1      209   908 (0)  

  chr1_143539492_    500 GAGGTTTGGCACT-ACCAACTTCAGGACTTAC-ATTAAGCTACAGTAACC 547
                             vi vi    -v    i    ii      - iv            i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_143539492_    548 CAAATAGTGTGAAGTTGGTCAAAAGAGAAAACACACACAAATAGATGCAT 597
                         v i i      ivii   -  v   i------ i v   v      vv  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGG-CATAAGG------ATAGACATATAGATCAAT 301

  chr1_143539492_    598 GGAAAAGAATACGGAGCCCAGAAGCAGGCC--TACAT--ACAGTCCACTG 643
                             v     vvi   i      ii ii  --     -- ii   v i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_143539492_    644 ATCTTCCATGGAGGTTTAGAGACAATTTAAAACAGCAAAGATAGCCTTTC 693
                           i   v iiii   vivi    v   i  vivi v  ii    i    i
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_143539492_    694 CAACTAGTGGTGCTAGAACAGCTGGACAACCACATGCAAAGAACTAAA-- 741
                             v i       i i   i     i ?           ii v i  --
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_143539492_    742 TAAATCCAGGTATGCATGTTATATCC-----TTTAT--AAAATAAATCTT 784
                          ii i  vviiv -  iiii    v -----  v i--     ii   v?
  L1M4_orf2#LINE/    452 TGGACCCCTACCT-CACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_143539492_    785 ACACGTAAATGTAAGCGC-AAAACCATAAGAATCCTAGGAGATAACATAG 833
                          v  v          v  -     i    i v  i   i   v       
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_143539492_    834 GAGAAAATCTCGGGGATCCTGGGTTCAATGATGGCTTCTTAAATACAAAA 883
                          ? v      iv v  i i      viiii    i      i   ii v 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_143539492_    884 CCAAAAGCACAATCTACTAATGAAAAAA-AATTAAGTTGAGCCTCATTAA 932
                                     v v  v  v       - iv   i   ii i    i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_143539492_    933 AATTAAAAACTTCTGTTCTGTGAAAGACACTGTTAAGAGAATGGAAAAAG 982
                                     i   v  vii  i      i i    i i  i   i -
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA- 699

  chr1_143539492_    983 CAAGTCACAGACTGGGAGAAAATACTTACAAA--ATA-ATCTGATGGAAA 1029
                            vi      v            i  i    --   -       i- ii
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA-AGG 748

  chr1_143539492_   1030 AACTGCTGTCCAAAATATATGAAGAATTCTGAGAACTAAACAACACAAAG 1079
                         i   vv i    i       i     i   v v    v  i  i v    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_143539492_   1080 -CAAAAAA--------AAAAA-AGGTGAAAGATCTGAA----CACCTCAT 1115
                         -    v  --------     -i  ii  i   i    ----  ii  vi
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_143539492_   1116 TAA-TAAGATATACAGATGGCAAATAAGCATATGAGAAAGATGCTCAAAA 1164
                         i  -v          i     v        i    -            v 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTCAACA 897

  chr1_143539492_   1165 TCATTTGTGAG 1175
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.87 (112 / 60)
Gap_init rate = 0.03 (22 / 700), avg. gap size = 2.09 (46 / 22)  


3062 26.88 1.11 0.66  chr1_143702398_143712771     5014  5917 (4457)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_143702398_   5014 TGGAAGAACATTCCATGCTCATGGAGAGGAATAAACAATATCGTGAAAAT 5063
                              ii i  i     i       vv    v vvi     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_143702398_   5064 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5113
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_143702398_   5114 TACCAA-TGACTTTCTT-CAAAGAATTAGAAAAAACT-ACTTTAAAGTTC 5160
                          v   i-  v    i  -  i -    i-- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_143702398_   5161 ATATGTAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAA 5210
                              v  viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_143702398_   5211 GAACAAAGCTGGAGGCATCACACTACCTGACTTTAAACTATACTACAAGG 5260
                                 i      vv       v  ii i  i   viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_143702398_   5261 CTACAGTAAACAAAACAGCATGGTACTGGTACCAAAACGGAGATACAGAC 5310
                                  v   i    ii         i iv ii ii  v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_143702398_   5311 CAATGGAACAGAAC--AGAGCCCTTAGAAATAACACCACACATCTACAAC 5358
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_143702398_   5359 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGCGGAAAGGATTC 5408
                         i vi    i  i     ivv  v   i v  vvv    v      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_143702398_   5409 CCTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGCTGAAAGC 5458
                         i  v  i                 v      v  ?   i    vi  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_143702398_   5459 TGAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGGTGG 5508
                             ii    i    v   i   i v              i    ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_143702398_   5509 ATTAAAGACTTAAATGTTAGATGTAAAACCATAAAAACCCTAGAAGAAAA 5558
                           i ?    i       v   vv      i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_143702398_   5559 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5607
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_143702398_   5608 AAAACACCAAAAACAATGGCAACAAAAGCCAAAATTAACAAATGGGATCT 5657
                          vi         i  vvi          vv     vi i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_143702398_   5658 CATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5707
                            i   v v    i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_143702398_   5708 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5757
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_143702398_   5758 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 5807
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_143702398_   5808 AAAAACAA----CCCCAGCAAAAAGTGGGCAAAGAGTATGAGCAGACACT 5853
                            i    ----   v vi?    i         ii v   ii     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_143702398_   5854 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGACAAAATGCTCA 5903
                             v        i  vi viii     i ii       v  i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_143702398_   5904 TCATCACTGGCCAT 5917
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  

3158 25.47 1.10 0.99  chr1_143702398_143712771     8975  9881 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_143702398_   8975 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 9024
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_143702398_   9025 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 9074
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_143702398_   9075 TACCA-CTGACTTTCTTCACAGAACTGGAAAAAAAACT-ACTTTAAACTT 9122
                          v   -   v    i  -i     v v  v  i---  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chr1_143702398_   9123 CATATGGAACCAAAAAAGGGCCCTC--ATAGCCAACATAATCCTAAGCAA 9170
                                  -- viv     v  iv--        v i    i i iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_143702398_   9171 AAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACA 9220
                         i          i      vv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_143702398_   9221 AGGCTACAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 9270
                          i          v   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_143702398_   9271 GACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACGTCTACAA 9320
                           i        i    iv   ivii         vv   i  i i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_143702398_   9321 CTATCTGATCTTTGACAAAA-TGACAAAAACAAGCAATAGGGAAAGGATT 9369
                         ii vi    i  i     ii-  v   i v  vv    i       i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_143702398_   9370 CCCTATTTAATAAATAGTGCTGGAAAAACTGGCTAGCCATACGTAGAAAG 9419
                         vi  v  i  i    i       i v      v  ?   i i i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_143702398_   9420 CTGAAACTGGATCCATTCCTTACACCTTACACAAAAATTAACTCAAGATG 9469
                         v    ii    i  v v   i     v  i                i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_143702398_   9470 GATTAAAGACTTAAATGTAAGTCATAACACCATGAAAACCCTAGAAGAAA 9519
                            i ?    i          vvv   v  i  i   vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_143702398_   9520 ACCTAGG--TAATACCATTCAGGACATAGGCATGGGCAAAGACTTCAT-G 9566
                           v    --   - i -   iv   v v  vv i     v ii   v - 
  L1M4_orf2#LINE/    545 ACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_143702398_   9567 ATCAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 9616
                           - vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_143702398_   9617 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAG 9666
                         ii v  i   v v  i i   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_143702398_   9667 AGAACAGGCAACCGACAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 9716
                         v   v  i     v                 v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_143702398_   9717 GACAAAGGGCTAATATCCAGAATCTACAAAGAACTTCAACAAATCTACAA 9766
                           i  i  i  vi          v  i        iiv    v  v i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_143702398_   9767 GAAAAAAA-AAA-AACCCCATCAAAAAGAGGGCAAAGGATATGAACAGAC 9814
                         v     i -   -     v  i?    iv           v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_143702398_   9815 ACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGC 9864
                          i     v        i  vi viii     i ii  i       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_143702398_   9865 TCATCATCACTGGTCAT 9881
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.36 (19 / 14)  


3254 26.11 1.11 0.66  chr1_143759774_143766177     5008  5911 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_143759774_   5008 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5057
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_143759774_   5058 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 5107
                            v     v     iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_143759774_   5108 TACCAATGGCTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTCA 5155
                          v   iiv  i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_143759774_   5156 CATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCAAAAAG 5205
                         i      viiv  ii  v  v v  v     iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_143759774_   5206 AACAAAGCCAGAGGCGTCACGCTACCTGACTTCAAACTATACTACAAGGC 5255
                                iii    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_143759774_   5256 TACAGTAACCAAAACAGAATGGTACTGGTACCAAAACAGACATATAGATC 5305
                                 i   i    vi         i iv ii i             
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_143759774_   5306 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5353
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_143759774_   5354 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5403
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_143759774_   5404 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTACAAAGCT 5453
                           v  i  i              v      v  ?   i   i v  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_143759774_   5454 GAAACTGGATCCCTTCCTTACACCTTATACAAAAGTTAACTCAAGATGGA 5503
                            ii    i    v   i     v         i         i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_143759774_   5504 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAAACCTAGAAGAAAAC 5553
                          i ?    i  v    v   v       i      vv i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_143759774_   5554 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5602
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_143759774_   5603 AAACACCAAAAGC-CATGGCAACAAAAGCCAAAATTGACAAATGGGATTT 5651
                         vi           -  -i          vv     v  i    v   i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_143759774_   5652 AATTAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5701
                         v  i  iv v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_143759774_   5702 ACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAAACTACTCATCTGAC 5751
                          v  iv    i                 v        ii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_143759774_   5752 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5801
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_143759774_   5802 AAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5847
                            i    ----   v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_143759774_   5848 TCTCAAAAGAAGACATTTATGCAGCCGAAAAACACATGAAAAAATGCTCA 5897
                             v        i  vi viii   i v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_143759774_   5898 TCATCACTGGCCAT 5911
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


1126 29.12 6.94 6.94  chr1_143831190_143833227.rev      661  1539 (499)    L1M4_orf2#LINE/L1        8   886 (22)  

  chr1_143831190_    661 ATATATTATGTTCATGGATTGGAAGACTCCATTTTGTTAGGAT------- 703
                             vii                     iv  v      i   -------
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_143831190_    704 --------ATT-----ACA---TCAACATAATTCTGATTAATAACTTTAA 737
                         --------   -----   ---     ii   i iv  i  -  iiii i
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-AATCCCAG 106

  chr1_143831190_    738 TAGTAGTTTTTAGAGAAATTTAAAAGCTAATTTCAAAATGTATTTAAAAA 787
                         iv ivv     iv       v v     i  iii     vi  v ii   
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_143831190_    788 T-CAAAGAATCTAGAACAGGCAAGCCAGTCTT---AAAGCGGCAATAAA- 832
                          -   i i i i    i  v   iv  i    ---    vi -  i   -
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG-AACAAAG 205

  chr1_143831190_    833 TTGGAGGACTTACTCTGCTATATTTTAAAACTCATTTTAAAGCTACAATG 882
                                   i  v  v ivv    i      i i vi         i i
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_143831190_    883 ACTTAAAA-ATTATACTACTGGTGTAAGTATACATAAATATATCAAAGTA 931
                          - i  i - v i iv      ii    v   v i v   v     v v 
  L1M4_orf2#LINE/    256 A-TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_143831190_    932 AAAGAATGCAGTTTCAAACAATATGCCCACATATGTACAGTTATTTAAAT 981
                          v     vv  vv  v iv    vi    i i  v  ii  i v  i --
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA-- 352

  chr1_143831190_    982 TTTTTAAAAACAAGTACGCTAATGCCCTTAATTGAGGAAATGAA-AGACT 1030
                             ii ---    vii  i  vi  v  v v  i     -   -  v  
  L1M4_orf2#LINE/    353 TTTTCGA---CAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCT 398

  chr1_143831190_   1031 TTTCAATAAAAAAGTTCTTGAGTAAAATAATATTTGT-TGTTTTAAAAAT 1079
                               i   vi-  v  v iii  vvvi   ?iiii-  i---    iv
  L1M4_orf2#LINE/    399 TTTCAACAAATG-GTGCTGGGACAACTGGATAKCCACATGC---AAAAGA 444

  chr1_143831190_   1080 TTAATATTA-ACAACCACTTTCCACAATACATTAAATTTAACTTAAGATG 1128
                         v i vi  i-  vv i  i iv   v   i iv   v      i  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_143831190_   1129 -----------------TGAAAGTTAAAATTAGAAGTCTTGTAAAAGAAA 1161
                         ----------------- i i  i     i  v  iv  iv  i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_143831190_   1162 A-ATAGAAA-ATATTTTCATGAACTTGACATAGGAAAATATTTCTTATAC 1209
                          -    i?i- v  i   i   v    ivv    v  vvi       v i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_143831190_   1210 CAGATACTGTA-GCAC--TCATCACAGTGAGAAATAAATTAAATTGTACT 1256
                         vv  i  iiv -    --v  v  v ivi i     i  -      v   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT-AAATTGGACT 643

  chr1_143831190_   1257 TTATTT---TTAAAAAGCTTCTGCTTATTACAGGTTATTGTTTAACAAGT 1303
                          i  iv---       -   i  iviv i v   vi i i iv iv    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_143831190_   1304 TAAAAG-CTATCTGTAAACCAGGACTAATTATTTGCAACATATGTATATG 1352
                         v     - v i iii i vii   vv  v         ---  ---i  i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA---AT---CATA 736

  chr1_143831190_   1353 TATATGTATATGTATGTGTATATACACATATATGGACTCATTCATTTGAA 1402
                            v  -   v ---------------------     ii ---------
  L1M4_orf2#LINE/    737 TATCTG-ATAAG---------------------GGACTTGT--------- 755

  chr1_143831190_   1403 ATGGACTCATTCAAAATATATAAAGAACT---ATAGATCACAAAGAAAAT 1449
                         --------  i  i               --- i iv   vv  v    v
  L1M4_orf2#LINE/    756 --------ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_143831190_   1450 GACAAACAACCCAGTATATCAATGAGCAGAAAAATTTGAAAAGACCCTTT 1499
                               i      i v? vv    i   -  ii       v    vi  i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCA-AAGGATTTGAATAGACATTTC 846

  chr1_143831190_   1500 ACATAAAAATATATCTAAATGACCAATAGGCATGTGAAAA 1539
                         v vv  i  v    vi     i      i   ii      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.34 (145 / 108)
Gap_init rate = 0.04 (34 / 879), avg. gap size = 3.59 (122 / 34)  


3175 22.23 4.63 2.14  chr1_143837564_143841478.rev     2539  3424 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_143837564_   2539 TGGAAAGATAT-----------GGTATGGAAGAATAAATATTGTTAAAAT 2577
                                    -----------  vv       v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_143837564_   2578 GCCTGTACTGCCCTAATGTGGTCTACAAATTCAAAGCAATCCCTATCAAA 2627
                          v vi    v   v   -  i      i      v               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_143837564_   2628 ATTCCAATAGCATTTTTCGCAGAA-TAGAGAAA---ACCTCTAAATTTGT 2673
                           i   iiv  v     i      - v  v  i--- i iiv     ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_143837564_   2674 ATGTAATCAT-CAAAAG-CCCAGAATAGACACAGCAGTCCTGAGAAAGAA 2721
                            v  --  -   ii -          v  v i  i  i   i      
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_143837564_   2722 AAGCAGAGTTGAAGCTTTCATACTATGTAGTTTCAAATTATATTACAAAG 2771
                         i i  i     i  vvi   i   vivi i       viv  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_143837564_   2772 CTATAGTAATCAAAACTCTATGGGACTGGCATTAAAACAGACACATAGAC 2821
                            i         i  vv i   v        v ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_143837564_   2822 CA--GAAACAGAATAGATAGCCCAGAAATAAACCCAGGTACAT--ACAGT 2867
                           -- i  i     v  v  i               --     -- ii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGT 345

  chr1_143837564_   2868 CTACTACTTTTTGACCATGTCCCCAAGAACACAAAATGGGGAAAGGATAG 2917
                          v i iv    i   v v viv      v  ivv           i    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_143837564_   2918 TCTCTTAAACAAATGGTGCTTGGAAAACTGGATATCCACATGCAAAACAA 2967
                            i  v             v   v         ?            v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_143837564_   2968 TGAAATTGGACACATAC---A-A--ATACACAAAAATCAACTCAAAATGG 3011
                             i      v v   --- - --   i        i            
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_143837564_   3012 ATTAAAGACTTATGTGTAGAATGTGAAATCATAAAATTTCTAGAAGAAAA 3061
                           i ?    i  vi    ii vv i   ii      i ii          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_143837564_   3062 CATAGGGGAAAAGCTCCTTGACATTGGTCTTGGCAATAATTCTTTTGATA 3111
                               ? v   v  i v    v    vi v      ii  ii  v    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_143837564_   3112 GGACATCAAAAGCA--------AAAATAAACAAATAAACAAATGGGACTA 3153
                         v    i        --------    v   -     i i    v     v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTT 644

  chr1_143837564_   3154 CATCAAACCAAATAGCTTCTGCACAGCAAAAAAAAAAAAAAAAAAAAAAA 3203
                                viv  v i   i  ii vv    ii v vv ------------
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA------------ 682

  chr1_143837564_   3204 ATCAACAACATGAAAAGGCAGCCTACTCATTTGGAGAAAATATTTGCAAG 3253
                         -    v  vi       i  i  i  vv v v                 i
  L1M4_orf2#LINE/    683 -TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_143837564_   3254 CCATATATCTGTCAAAGGGTTTATATCCAAAATA-A-AAAGAACATATAG 3301
                         i          vi  i  ii  i      i    - -       viv  v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_143837564_   3302 AATTCAATCACAAA----TAAATAACTTGACTAAAAAATGTACAAAGGAC 3347
                           i     v i   ----i       iii i ?       vi       i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_143837564_   3348 CTGAATAGATATTTCTCCAAAGAGGGCATACAAATGGCCAACATGTATAT 3397
                         i        i             i ii              i v i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_143837564_   3398 GAAAAGTTGTTCAATATCACTAATCAT 3424
                               v  i    i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (113 / 80)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.16 (60 / 19)  


2957 22.28 9.08 0.97  chr1_143995056_143999271     2898  3723 (493)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr1_143995056_   2898 TGTTGATAGATTGGAAAA---AGTATTGTTATAAAATGTCTATACTACCC 2944
                             v  i        i --- i        -- i   v v     v   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTA--AGATGGCAATACTCCCC 63

  chr1_143995056_   2945 AAAGCAATCTAAAG------TACAATCCCTATCAAAGT------------ 2976
                            vii     v  ------ii              i ------------
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr1_143995056_   2977 -------GAAATAGAAAAAA-AATGCTAAA-TTTGTATTGAACCACGGAA 3017
                         -------     v  v  iv-i  v     -  ii   v   vii iiii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_143995056_   3018 GATCCTGAATAACCAAAGCAGTCTTGAGCATAAAGAACAAAGCTGGAAAT 3067
                           i  v     i     i  i      iv vi          i    ii-
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG- 212

  chr1_143995056_   3068 AC-CACATTATCTGACTTCAAAATGTACTACAAAGCTGTAGTAACTCAAA 3116
                           -    i vi ii i       iv            ii     iiv i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_143995056_   3117 CAGCATGGTACTGGCATAAGAACAGACATA--GATCAATGGAACAGAATA 3164
                            ii               i i       --           i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_143995056_   3165 GAGAGAC--GAAA--AATTCATGCATTTACAGTAAATGGATTCTTTACAA 3210
                              v --    --  ii   i      ii  v   v    i iv    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_143995056_   3211 AGGCACCAAGAATACACAATGAGGAAAGGACAATGTCTTCAATAAATGAT 3260
                         i  ii      vi iv     i      i i i v i     i     i 
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_143995056_   3261 GCTGGGAAAACTGGATA-CCACATGTAGAAGAATGAAATTAAACTCT--- 3306
                                v         -       i i         i  ii  i i---
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_143995056_   3307 CTCATCTTTTATAAGAAAAAATCAATTCAAAATGGATTAAAGACCT---- 3352
                             iviiv    v--      i  i           i ?      ----
  L1M4_orf2#LINE/    463 CTCACACCATATAC--AAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_143995056_   3353 -------C--AAACTGTGAAACTTCTAGAAGAAAACATAGGGGGAGAGCT 3393
                         ------- --     i i     ii                ? v i v  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_143995056_   3394 TCATGACATTGGTCCAGGCAATG---------ATATGAC-CTAAATAGCA 3433
                           i    v    vii        ---------       - i   -    
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA-AGCA 609

  chr1_143995056_   3434 TAAGTAACAAAAGCAAAAATAGACAAATGGAATTACATCACA-CTGAAAA 3482
                         i   i        v         i    v i i v     v -i i    
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_143995056_   3483 CTTT----CTGCACAGCAAGCGATCAACAGGGTGAAGACATACCCTACAA 3528
                             ----  v  v  v vi v     v ii     i v i v  i   i
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_143995056_   3529 AATGGGAGAAAATGTTTGCAAAGTATGTATTTGATAAGGGATTAATATCC 3578
                                      i        vi  i   i          i vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_143995056_   3579 AAAATATATAAGGAACTGAAATAATGCAATAG-----AAACAAATAACTG 3623
                          i         i     vvv i  iv     i----- i         iv
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_143995056_   3624 GATTTTTTAAATGGGCCAAAGACCTCAATAGCCATTTCTC-AAAGAAGAC 3672
                         i   ?vv-        v  i  ii v     v        -        i
  L1M4_orf2#LINE/    810 AATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_143995056_   3673 ATATAAATGGCCAACAGGTATATGAAAAAAATGCTCAACATCACTAATCA 3722
                            i          i i i i       i -            ???????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZ 907

  chr1_143995056_   3723 T 3723
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.12 (123 / 58)
Gap_init rate = 0.03 (25 / 893), avg. gap size = 3.32 (83 / 25)  


2508 24.30 2.37 0.56  chr1_143999578_144001285      500  1215 (493)    L1M4_orf2#LINE/L1      180   908 (0)  

  chr1_143999578_    500 AGCAATCCTGAGCAAAAAGAACAAAACTGGAGACATCACATAACCTGACT 549
                          i     i   iv  i         ii     ivv     ivv  ii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_143999578_    550 TCAAAATATGTTACAAAGCTATAGTAACCAAAACATCATGGTATTAGTAT 599
                               iv ii          i     i   i   vii     i i i  
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_143999578_    600 AAAAATAAACACATAGACCAATGGAACAGAATAGAGGATCCAGAAATAAA 649
                           ii   i   i     i        i     v   ii            
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_143999578_    650 GCCATGTATTTGCAGCCAGCTGATCTTCAACAAAGCCAACAAGATCTTAC 699
                         v    ii    iii i  ii    i   i    i viiv     i v v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_143999578_    700 ACTGGGGAAAAAAGACTATCTTCAACAAATAGTGCTGGGAAAATTGGATG 749
                          v        i  v v v i          i         v  i     i
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_143999578_    750 GCCACATGCAGAAGAATGAAACTGGACCCCTTACCTCTCACCATACACCA 799
                         ?         i         ii         -     v       i  v 
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCT-ACCTCACACCATATACAA 478

  chr1_143999578_    800 AG-TAAATTCAAAGTGCATTAAAGACTTTAAATATAAGACCCAAAACTAT 848
                          i- v  i     i  v  i ?    i -    i     v i        
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCT-AAATGTAAGAGCTAAAACTAT 527

  chr1_143999578_    849 AAAAATACTAGAAGCAAATCTAGGGAAAACTCTCTTG-GATATTGTTCTA 897
                             v vi      v   iv    ?iv  v   - i -  iv   vvi  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCT-TCGTGACCTTGGGTTA 576

  chr1_143999578_    898 GGCAAAGAATGTATGACTTAAGACCTCAAAAGTACAGGGAACAAAACCAA 947
                              v i- v v v vv  v   vi      i   i v       vv  
  L1M4_orf2#LINE/    577 GGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_143999578_    948 AAACAGAAAAATGGGACTTAATTAAACTAAAAAGCTTCT---CTACAGCA 994
                            i   v    v      v  i   v v    i   i ---  v  ivi
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_143999578_    995 GA----AT-AAGTGAGTGAAGAGACAACCTATTAAATGGGAGAAAATATT 1039
                           ----  -   vi      i        i ivi                
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_143999578_   1040 TGCAAGCCATTCATTTGACAGGTGACTAATATCCAGAATACACAAGGAAC 1089
                              ii   vi  i   i i v    vi           i i  i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_143999578_   1090 TCAAACAACTCAACAGTTAACA-ACAAA-AG---AATAAAAAAGTGGACA 1134
                           vv         i i v  v -     - i---   v?    i   i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_143999578_   1135 AAGGACAT-AATAGACAACTCTCAAAAGAAGACATACAAATGGCCAAGAG 1183
                              iv -        vi    v        i              v i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_143999578_   1184 GTGAAAGAAAA-ATGCTTAACACCACTAATCAT 1215
                          iiv v     -     i    i  ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (104 / 66)
Gap_init rate = 0.02 (14 / 729), avg. gap size = 1.50 (21 / 14)  


3163 26.99 1.00 0.55  chr1_144018588_144027028      492  1395 (7046)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_144018588_   1395 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1346
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_144018588_   1345 GGCCATACTGCCCAAGGTAATTTACAGATTCAGTGCCATCCCCATCAAGC 1296
                            v     v     iv i  i          ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_144018588_   1295 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1248
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chr1_144018588_   1247 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1198
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr1_144018588_   1197 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATTCTACAAGGC 1148
                                i      vv       v  ii i      viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr1_144018588_   1147 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1098
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr1_144018588_   1097 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1050
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chr1_144018588_   1049 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTTC 1000
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chr1_144018588_    999 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 950
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chr1_144018588_    949 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGAA 900
                            ii    i    v   i     v           i  i    i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chr1_144018588_    899 TTAAAGACTTAAACTTTAGACCTAACACCATAAAAACCCTAGAAGAAAAC 850
                          i ?    i    iv v   v    v  i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chr1_144018588_    849 CTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 800
                         v    ?v v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chr1_144018588_    799 AACACCAAAAGC-CATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 751
                         i           -  -i          vv     v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chr1_144018588_    750 ATTAAACTAAAGAGCTTCTGCACAGCTAAAGAAACTACCATCAGAGTGAA 701
                           i   v v  i i   i  ii vv v  i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chr1_144018588_    700 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 651
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chr1_144018588_    650 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 601
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chr1_144018588_    600 AAAACAA----CCCCATTAAAAAGTGGGCGAAGGACATGAACAGACACTT 555
                           i    ----   v   ?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chr1_144018588_    554 CTCAAAAGAAGACGTTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 505
                            v        ii vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chr1_144018588_    504 CATCACTGGCCAT 492
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  

2579 27.03 4.47 0.80  chr1_144018588_144027028     7077  7949 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_144018588_   7077 AAAAACATTCCATTTTCATGGA-----ATATTCAATATTGTGAAAATGGC 7121
                            i i  i    v        ----- v i i        v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_144018588_   7122 CATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAACTAT 7171
                         v     v      v i  i  i        i  v  i  i      --  
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA--AT 101

  chr1_144018588_   7172 CCTTGAGA--TTCTTCACAGAA-TT-AGAA---------AAAACTTA-AT 7207
                           iv vvi--  i  ii     -  - v  ---------    i i -  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_144018588_   7208 --AAATG-AAG--ACCCCGTTTTGCCAAGACAGTCCAAAGCAAAAAGAAC 7252
                         --     -   --    v vv v     i   i  ivi iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_144018588_   7253 AAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAAGCGAT 7302
                             i      vv   ii  v  ii i      viv           v i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_144018588_   7303 AGTAACAAAAACAACATGGTACTGGTACCAAAACAGTCATATATACCAAT 7352
                              iv  i   iii         i iv ii i  v      v i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_144018588_   7353 GGAACAGAATAGAGACCTCAGAAATAACGCTACACATCTACAACCATCTG 7402
                             i     v    vii         vv i i    i  iiii  vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_144018588_   7403 ATCTTCAACAAACCTAACAAAAACAAGCAATGGGGAAAG----GCCTCCT 7448
                           i   i    ivv iv   i v  vv            ---- i  i--
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-- 399

  chr1_144018588_   7449 ATTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATACAGAAAACTGA 7498
                         -     i              v      v  ?   i  i  i  i v   
  L1M4_orf2#LINE/    400 -TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_144018588_   7499 AACTGGACCCCTTCCTTACACCTTGGACAAAAATTAACTCAAGATGGATT 7548
                          ii         v   i     v iv                i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_144018588_   7549 AAAGACTTAGATGTAAAACCTCACATTATAAAAACCCTAGAAGAAATC-T 7597
                          ?    i  i      i v  v v i       vi i         v - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_144018588_   7598 AGGCA-ATACCAGTCAGGACATAGGCTTGAGCAAAGACTTCAT-GATGAA 7645
                            ?i- v i -v  iv   v v  v  ii    v ii   v -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr1_144018588_   7646 AACGCTAAAAGCTATTGCAACAGAAGCCAAGTT-GACAAATGGGATCCAA 7694
                         i  i i      vvvv      i   vv  iv -  i    v   iiiv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_144018588_   7695 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCACCAGAGTGAAC 7744
                          i   v v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_144018588_   7745 AGGCAACCTACAGAATGGGTGAAATTTTTTGCAACCTACCCATCTGATGA 7794
                           i     i          v    v v       vii ivi       i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_144018588_   7795 AGGGCTAATATCCAGAATTTACAAGGAACTTAAACAAATTTACAAGAAAG 7844
                         i  i  vi          v  i  i     ivv    v iv i  v   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_144018588_   7845 AAACAA----CTCCATCAAAAACTAGGTCAAGTACATGAACAGACACTTC 7890
                          i    ---- i v  i?    v i  iv   v iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_144018588_   7891 TCAAAAGAAGACACTTACACAGCCAACA--CACGTGAAAAAAAGTTCAAC 7938
                           v        i ivi v ii     i --   i      i v i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_144018588_   7939 AT-ACTGATCAT 7949
                           - ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (136 / 96)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 2.19 (46 / 21)  


3155 27.42 0.55 0.55  chr1_144039064_144045433     4971  5878 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144039064_   4971 TGGAAGAACATTCCATGCTCATGGGTAGTAAGAATCAATATTGTGAAAAT 5020
                              ii i  i     i      i v v    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144039064_   5021 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5070
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144039064_   5071 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5118
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_144039064_   5119 TATGGAACCAAAAAAGAGCCCACGTCACCAAGTCAATCCTAAGCCAAAGG 5168
                                viiv  ii  v  vivi vi    iv     i i ivv i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_144039064_   5169 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5218
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_144039064_   5219 TACAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGAGATATAGACC 5268
                                 i   i    ii       i i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_144039064_   5269 AATGGAACAGAAC--AGAGCCCTCAGAAACAATATCACACATCTACAACC 5316
                                i    i--    i  --     i  vvi  i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_144039064_   5317 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGTATTCC 5366
                          vi    i  i     ivv  v   i v  vvv           v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_144039064_   5367 CTATTTAACAAATGGTGCCGGGAAAACTGGCTAGCCATATATAGAAAGCT 5416
                           v  i            i    v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_144039064_   5417 GAAACTGGATCCCTTCCTTACACGTTATACAAAAATTAATTCAAGATGGA 5466
                            ii    i    v   i    vv              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_144039064_   5467 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAAC 5516
                          i ?    i  v    v   v       i      vi i   i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_144039064_   5517 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5565
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_144039064_   5566 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5615
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_144039064_   5616 GATAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5665
                         ivi   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_144039064_   5666 CAGGCAACCAATAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5715
                         v  i     v i               v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_144039064_   5716 AAGGGCTAATATCCAGAATCTACAATGAACTCAAGCAAATTTACAAGAAA 5765
                          i  i  vi          v  i  v      vvi   v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_144039064_   5766 AAAATGAACAACCCCATCAAAAAGTGGGCTAGGGATATGAACAGACATTT 5815
                           i ii  i     v  i?    i     v i    v    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_144039064_   5816 CTCAAAAGAAGACATTTATGTAGCCAAAAGACACATGAAAAAATGCTCAT 5865
                            v        i  vi vi i     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_144039064_   5866 CATCGCTGGCCAT 5878
                             i????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3067 12.96 3.06 21.33  chr1_144048696_144050349.rev       53  1163 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144048696_     53 TGGAAAGACATTCTGTGTTTATGGATTGGAATAATTAATATTGTTAAGAT 102
                                 i  i ii    i           v v                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144048696_    103 GGCAGTATTATCCAAATTGAACTACAGATTTAACAC---CTTTATTAAAA 149
                             i  i vi         v         i   i --- ii   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144048696_    150 TACCAGCTGCTTCCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 199
                          v        ----                                    
  L1M4_orf2#LINE/    101 TCCCAGCTGC----CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_144048696_    200 TACATGAAAAAGCGAAGGACCCAAGATG---------ATACTGAAAAAGA 240
                         i i   i   v  i i       ii  i---------  vi         
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_144048696_    241 AGAACAAA-TTGGAAAGCTCACACTTTGTGATTCCAAAACTTATTACAAA 289
                                 -     iii         ivii   i         i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_144048696_    290 GCTACGATAAGCAAGCTATTTAAATCAATGTTAGCAGTGCGTGGGGGTGT 339
                              ii   v    ------------------i     --   ------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAG------------------ACAGTG--TGG------ 270

  chr1_144048696_    340 GTGCCTGTAGTCCTAGCTACTAGTCCTAGGCTGGGGCAGGAGGATCGCCT 389
                         -----------------    -------------    vi     -----
  L1M4_orf2#LINE/    271 -----------------TACT-------------GGCATAAGGAT----- 285

  chr1_144048696_    390 GAGCCCAGGAGTTTGAGGCTGCAATGAGCTGTGATTGTACCACTGCACTC 439
                         --------------------------------------------------
  L1M4_orf2#LINE/    286 -------------------------------------------------- 285

  chr1_144048696_    440 CAGCCTGGGTGACAGAGCAAGATCTTGTTCAAAAATCAATCAACCAATCG 489
                         -------------------   i---------------  ------  v 
  L1M4_orf2#LINE/    286 -------------------AGAC---------------AT------ATAG 295

  chr1_144048696_    490 ATCAGTCAATCCATGGAATAGAATTGAGAATCCAGAAACAAGTTCATACG 539
                             --------                 i        i  iii     i
  L1M4_orf2#LINE/    296 ATCA--------ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_144048696_    540 TTTACGATCAATTGACTTTCAACAAGGGTACTAAGATAATTCAAAGGAGG 589
                             i i        i    i        i i    iv      v  -  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GG 386

  chr1_144048696_    590 AAAGAATAGTCTTTTCAACAAATGTTGCTGGAACAACTGAATAGCCACAT 639
                                                 v      i       i   ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_144048696_    640 GCGAAAGAATAAAATTTGACACCTATTTCACAGAATATACAAAAATTAAT 689
                           i       i  i  v   v    ii     vv               i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_144048696_    690 TTAAAATGGATCCAATTTCATATAATAGACAAAAATTAATTTAAAATGGA 739
                          i          ------------ ?    ----------i    -----
  L1M4_orf2#LINE/    487 TCAAAATGGATC------------AWAGAC----------CTAAA----- 509

  chr1_144048696_    740 TGAAATTTCATATAATATACAAAAATTAATTTAAAATGGACCTAGATATA 789
                         ---------- i   -----------------------  v   ------
  L1M4_orf2#LINE/    510 ----------TGTAA-----------------------GAGCTA------ 520

  chr1_144048696_    790 AGAAAACTATACAACTCTTAGAATAAAATATAGATGTAAATCATCATGGC 839
                         ---        v           v    i    i?       v  i  i 
  L1M4_orf2#LINE/    521 ---AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_144048696_    840 CTTGGATTATACAATGGATTCTCAAATATAACATCAAAAGCA-AAGCA-C 887
                              i   vi      v    i i    i   i        -     - 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_144048696_    888 AATCAAGAAAAAAATGCATAAATCAGACTTCCTAAAAATTGAAAGCTTTT 937
                           --         - iv      ii      v v      i   i     
  L1M4_orf2#LINE/    618 AA--AAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_144048696_    938 GTGTTACAAAGAACACTATTAAGAA-GCAAGAAGACAACCCACAGGAATG 986
                            i v     i       i     - ii i              -    
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG-AATG 713

  chr1_144048696_    987 G-AGAAAATATTTTCCAATCACATATGTGATAAGA-------AT---GAA 1025
                          -           v v     i    v       i-------  ---   
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_144048696_   1026 TACATA------CCTTAAAATTCA-CAATTAAAGAACAAATAACGCAATT 1068
                           i   ------i    v  i   -i   v   ii         v     
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_144048696_   1069 TAAAAATGGACAAAATAGCTGAATAAATATTTCTCTAAAGCAGATATATA 1118
                         ?        i    iv vi      i i       i    v       i 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_144048696_   1119 GATGGACAATAAGCATATGTAAATCTGTACAACATCATTAGCCAT 1163
                         i    v         i   v   vv  iv        ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (98 / 42)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 9.34 (271 / 29)  


2567 26.83 9.10 0.36  chr1_144063795_144066357.rev     1238  2072 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144063795_   1238 TGGAAAAACATTCCCTACTCATGGATCGAAAGAATCAATATTGTTAAAAT 1287
                               i i  i  v ii        i i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144063795_   1288 GGCCATACTGCCCAAAGCGATCTACAAATTCAACACTATTATCTATTAAA 1337
                            v     v      vi        i       i v  i-i    i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC-CCTATCAAA 99

  chr1_144063795_   1338 CTACCAA-TGTCATTTCTCACAGGATTTAAAAAACT-ATTCTAAAAGTAA 1385
                         v v   i-  i -   i ii   i v  i v  i  -  i      v v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_144063795_   1386 CATGGAATCAAAAAAGAGCCTGGATAGCCAAAA----------------- 1418
                         i      viiv  ii  v  v i          -----------------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_144063795_   1419 ----AAGTT------------------------------TACAGTAAGGC 1434
                         ----     ------------------------------   vii  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_144063795_   1435 TACAATAATGAAAGCAGCATCGCACTGACACAAAAACAGACACACAGACC 1484
                             i    v  ii   ii v i    i  i  ii i     i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_144063795_   1485 AATGAAATATAATAGAGAACTCAGATGTAAAGCTGCATACCTACAACCAT 1534
                             i    v   v    iii    vi    v iii i ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_144063795_   1535 CTGATCTTTGACAAAGCTGTCAAAACTAAGCAATGGGGAAAGGACTGCCT 1584
                         i    i  i     i v  i   i  i vv            i iv i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_144063795_   1585 ATTCAATGGATGGTGCCGGGAGAACTGGCTAGCCATATGCAGAAGAATGA 1634
                         v     iii       i    v      v  ?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_144063795_   1635 AACGGGACTTGCTACTTTTCACTATATACAAAAATTAACTCAAGATGGAT 1684
                          iiv    ii-    i iv   i                    i      
  L1M4_orf2#LINE/    449 AGTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_144063795_   1685 TAACGATTTAAATGTAAGACCTCAAGCTATAAAAATCTTAGAAGAAA--- 1731
                         i ?v  ii           v  v  i        v            ---
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_144063795_   1732 TAG-------CCTTTG-GACATCAGCCTTGACAAAGAATTTATGACTAAG 1773
                            -------i   i -   v ii vi v i   v iv  iv iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_144063795_   1774 TTGTCAAAAGCAATTGCACCAAAACCAAAAATGGACAAATAGAACCTAAT 1823
                         viii        vvv   v     vv      i  i    v i  i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_144063795_   1824 TAAA-CTAAAGAGCTTCGCACAGCAAAAGAAGTTATCAACAGAGTAAACT 1872
                         i   -i    i vi  i ii vv    i  vii      v i   i  vv
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_144063795_   1873 GACAACCCAAAGAATGGGAGAAAATATTTGCAACCGATGCATCTGACAAA 1922
                                  v                       viv  ii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_144063795_   1923 AGTATAATATCCAGAGTTTATAAGGAACT-TAACAAGCCAA------AAA 1965
                         i vv vi        i v     i     - v    vi   ------   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_144063795_   1966 GA--AGTATCTCCATTAAACAGTGGGCAAAAAACATGGACAGACAATTCT 2013
                           -- i  v i v   ?  v i        ii iv  i i     v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_144063795_   2014 CAAAAGAAGACATACAAGCAGCTAACAA--ACATGAAAAAATGCTCAACA 2061
                          v        i      iii  i  i  --         i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_144063795_   2062 CCAGTAATCAT 2072
                         i  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.91 (145 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 5.27 (79 / 15)  


1689 24.62 14.85 0.89  chr1_144082283_144085414.rev     1854  2641 (491)    L1M4_orf2#LINE/L1       11   908 (0)  

  chr1_144082283_   1854 TTCAATGTTTTTGGATTGGAAAACTCAATATTGTTTAAGATGGCAATTTT 1903
                          i v     iv          i   i         -           vi 
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAGATGGCAATACT 59

  chr1_144082283_   1904 TTCCAAATTGATCTATGGGTTTGGTGCCAT-----TCAAAATTCCAGTAG 1948
                         ii             ii i  iiii  v  -----       i    iv 
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_144082283_   1949 A-TTTTGTGTGGAGACAAACAAGCAGATTCTAAAAATTCTGTGAAAACTC 1997
                         v-    v  ii  i ivi      v   i      v iv i  i   iv 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_144082283_   1998 AAAAGACTCAGAATAGCAGAAACTATTTTAAAAAA-----ACAAAGCTGG 2042
                           ii   i         vi    v  i  i     -----      i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_144082283_   2043 -GAATTTG-----------TTCA---TGTA-TAGGAAGACTCCA-TA-TT 2074
                         - i i ii-----------    ---iv  -  vi   -  v  -  - i
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG-CTACAGTAATC 258

  chr1_144082283_   2075 AA--CA-TGT--TACTTATCTCCAAATTGTTCTATAGATTCTATATAATA 2119
                           --  -   --    viiv vvii  v viv       - v  iv    
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT-CAATGGAATA 307

  chr1_144082283_   2120 CCATTCAAAAT-----AATAG---CAGGGTTTT----TCTCTTT-TTTTT 2156
                         vv   v i i -----    i---  vivv   ----  vv  v-    i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_144082283_   2157 AAAAAAGATGACAA-----TTTGATACTAAAA--------TTT------- 2186
                         i v  i i  v   -----  ii  ivvi   --------   -------
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_144082283_   2187 ATG----TGGAA-ATTTGAAAAACC---TAGAATAGCTAATGAAATT--- 2225
                            ----   i - vi  i v ?  --- iv  v  --      i  ---
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG--AATGAAGTTGGA 455

  chr1_144082283_   2226 --TCTGTGT---ACTACATA-----GT---CTTGTAATCAATCATAGACC 2262
                         --i  iiv ---  i i   -----i ---  iiv   vi    ?     
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_144082283_   2263 TAAATATAAAATCTAAAACTATTAAAGTTCTACAA--AAATATAGGAG-A 2309
                              i   i v          v   v ii  v  --   i     ? - 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_144082283_   2310 AATTTTAATGACATTGG-TGAGGCAAAGATTTCATAGATAAGACACTAAA 2358
                            i  vi    v    - v      v i    v      v     i   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_144082283_   2359 AGCATGAG-----ATAGAAAATACTCATATATTTGCCATCATCAAAATTT 2403
                             ii  ----- v      v ivv   v   v v v           -
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT- 654

  chr1_144082283_   2404 AAAAACTTTTGCTCTTCAAGAAGATACTCTAATGGAAGTGAAAAGCAAAG 2453
                                    iv      - i  i   v v v i          vv  v
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAA-AGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_144082283_   2454 CCACAGATTGGGAGAAAATATCTGCTAA-CAGATATCCAAAAAAGGACTT 2502
                                v             i   v  -  v     ii v  i      
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_144082283_   2503 GTATCTAG----TACAAAAAAATGT-ACAGTTCAACTATAA---GACAA- 2543
                              i  ----  i   i  v v -   ii    iv    ---     -
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_144082283_   2544 ---CCAAATTTAAAAATAGTTAAA---TTTGAACAGACATTTCACCAAAG 2587
                         ---  v    ?      i vi   ---      i         v      
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_144082283_   2588 AAGATGTATAAGTAGCAAATAAGTATATGAAA-TATGCTCAACATCATTA 2636
                              i  i  i i  v      i i      -v             ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_144082283_   2637 TTCAT 2641
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.29 (107 / 83)
Gap_init rate = 0.05 (43 / 898), avg. gap size = 2.88 (124 / 43)  


1895 26.33 12.01 1.82  chr1_144090919_144092852.rev      637  1460 (474)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144090919_    637 TGGAAGAGCATAT---GTGTTCATGGATTGA-----TTAATATAGTCA-- 676
                              -  -    ---i             i-----       v  i --
  L1M4_orf2#LINE/      1 TGGAA-AG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_144090919_    677 -TATCAGTTCTCTCCAAATTGATATTTACAGGTTTAATACATTTTCCATC 725
                         - iv  i v   i          --i     i  i  ii  v ii i   
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGAT--CTACAGATTCAACGCAATCCCTATC 96

  chr1_144090919_    726 AAAATCCCAGTAAGATTTTTTAACAGATATAGACAAGATTATTCCAAAAT 775
                                   ivivv      i-    v  v      v v  i i     
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_144090919_    776 TTAAATGAAAAGGTAAAGGAACTAGAATAGCTAAAGCAATTATGTTTTAA 825
                          i v   i   v i  i   v i        i   i    iv  ----  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG----AA 191

  chr1_144090919_    826 AAA----AATAAAATGGGAAAA------------AGT------ACTGTAC 853
                            ----  i   i v   ii ------------ i ------   -   
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TAC 240

  chr1_144090919_    854 C------TTACAA----CAAGACTGTGTAGTATTAGTGTAAGGATAAGAC 893
                         i------i    i----      v    i   i i ii        -   
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GAC 289

  chr1_144090919_    894 ACTTGGATCAATGGAACAGAATAAACAACCTAGAAGTAGACTCAATGCGG 943
                          iv i           i     vi v ii i    i  i  i  - i iv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACAT 338

  chr1_144090919_    944 C-ATGGGTAACTAATTTAAGATGAAAGTGT-AAAA----TCAATT----- 982
                         i-    vi  i i    vv  ii ii   i-  i ----     v-----
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_144090919_    983 ----TAGTCTTTCAAGTAAATGGTGATGAAGAATTTAGATATCCATAT-T 1027
                         ----        iv ii        v  iiiv vi i    ?   i  -i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_144090919_   1028 AAAAAAAC-----TAAACCTCAACCTTACAGTTTATACTAAAATTAACTC 1072
                             i  i----- ii   i v    i   viv     v           
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_144090919_   1073 AAAATGCATCATATATTTAAACTTAAACCATAAAACTATAAAACTTTTAT 1122
                               v    ? v ii    iv   ivvv               i   v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_144090919_   1123 GGAAAAGCATAGGAGTAAATTTT-GTGGACCAGTGATTTGGTGAACACAT 1171
                         iii   i      ?      i  -   -   vvv i  v  ii vviiv 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTT 587

  chr1_144090919_   1172 TTTAGACATAATGCCAAAGGCTTGATCCATAAAAGGAAAAAAATAG-TAA 1220
                         i     i  i ii     i  vii v v i     --         -   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAG--AAAAAATAGATAA 635

  chr1_144090919_   1221 ATTG-ACATCACCAAAATTTAAAACTTTTTCTCTGTGGAAGA-----TCA 1264
                             -  v   i       v         viv  viii i  -----   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_144090919_   1265 -GAGGACAAAAAAACAAGATACAGATCTGGAGAAAATATTTTCAAACCAT 1313
                         -  iiiii    i    vvi     viv             v    i   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_144090919_   1314 ATATCTGACAGAGGACTC--ATCTAGAAT-TATAAAGAACTCTCA-AACT 1359
                                 i ii     i--   i     -             i -    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_144090919_   1360 TAACAATAAAAA--------ATCAAATTAGAAAATTGTCAATATACACAA 1401
                         i  i        -------- i v    ?i     v v   viv ivii 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_144090919_   1402 GGAGACATTTCATAAAATAAGTTATATAGATAAC-AAT------------ 1438
                         iv         viv   v   v    i i  ii -   ------------
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_144090919_   1439 -GATATTCAGTATCACTAGCCAT 1460
                         -   ii   ii    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (142 / 71)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 3.26 (114 / 35)  


3203 27.20 0.55 0.55  chr1_144098431_144104827     4997  5904 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144098431_   4997 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5046
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144098431_   5047 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCTCATCAAGC 5096
                            v     v     iv i  i           i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144098431_   5097 TACCAATGACTTTCTTCACAGAA-TTGGGAAGAACTGCTT-TAAAGTTCA 5144
                          v   iivi i  i  ii     -   iv   --   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_144098431_   5145 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5194
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_144098431_   5195 AACAAAGCTGGAGGCATCACGCTACCTGGCATCAAACTATACCACAAGGC 5244
                                i      vv    i  v  iiiiv     viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_144098431_   5245 TACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5294
                             i   i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_144098431_   5295 AATAGAACAGAACAGAGCACTCAGAAATAATGCCGCATATCTACAACTAT 5344
                            i   i    iv   viii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_144098431_   5345 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5394
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_144098431_   5395 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTACAAAGCTGA 5444
                         v  i  i              v      v  ?   i   i v  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_144098431_   5445 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5494
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_144098431_   5495 AAAGACTGACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5544
                          ?    iv v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_144098431_   5545 AGGCA-ATACCATTCAGGACAT--AGTCATGGGCAAGGACTTCATGTCTA 5591
                            ?i- v i -   iv   v --i  i --     v ii   v ivv  
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATA 595

  chr1_144098431_   5592 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5641
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_144098431_   5642 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGTGTGAA 5691
                           i   v v  i i   i  ii vv    i  v    i  vv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_144098431_   5692 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5741
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_144098431_   5742 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGATA 5791
                          i  i  vi          v  i  v      vv    v iv i  v v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_144098431_   5792 AAAACAAACAACCCCATCAGAAAGTGGGCAAAGGATATGAACAGACTCTT 5841
                           i     i     v  i?i   i            v    i    vi  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_144098431_   5842 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5891
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_144098431_   5892 CATCACTGGCCAT 5904
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3146 27.75 0.44 0.44  chr1_144119262_144125541     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144119262_   4880 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4929
                              ii    i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144119262_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCTCATCAAGC 4979
                            v     v     iv i  i           i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144119262_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_144119262_   5028 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_144119262_   5078 AACAAAGCTGGAGGCATCACGCTACCTGGCATCAAACTATCCTACAAGGC 5127
                                i      vv    i  v  iiiiv     viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_144119262_   5128 TACAATAACCAAAACAGCATGGTACTGGTACCGAAACAGAGATATAGATC 5177
                             i   i   i    ii         i iviii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_144119262_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_144119262_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_144119262_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTACAAAGCT 5325
                           v  i  i              v      v  ?   i   i v  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_144119262_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_144119262_   5376 TTAAAGACTGACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?    iv v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_144119262_   5426 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_144119262_   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_144119262_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATTAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_144119262_   5576 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_144119262_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_144119262_   5676 AAACAAACAACGCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i   v v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_144119262_   5726 TCAAAAGATGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5775
                           v     v  i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_144119262_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1516 22.35 2.29 0.29  chr1_144138251_144142144.rev      815  1163 (2731)    L1M4_orf2#LINE/L1        2   357 (551)  

  chr1_144138251_    815 GGAAATATGTCTTAAGTTCATTGATAGAAAGACTTAACTTTGTTA---T- 860
                              v  i  ii v      v   v i         iv      --- -
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_144138251_    861 -CACTACTACCCAAAGTGATCTACAGATTCAATGAAATCCATATCATA-T 908
                         -  v    v      v                i v     v     v - 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_144138251_    909 TCCAGCAGCCATTTTCATAGAAATGTAAAAGCCCCTCCTCAAATTTGTAT 958
                         i     v   v    iii      vv v    ivv    v     ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_144138251_    959 GGAATTGCAAGGGGCCCCGGATAGCCAAAATAACCTTGAAAAGGAAGAAT 1008
                             v        i   v i          i  i        i      i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_144138251_   1009 AAAGTTAGAGGACTCATACTTCCTGGCTTTGCAACTTACAATAACGATAC 1058
                               i         i      iiii  iiv       v i  v v   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_144138251_   1059 ACTAAACTGAAACAGTATGGTACTGTAATAAGAACAGTCATA--GACTGA 1106
                          v   v -i i     i        vv     i i  v    --  iii 
  L1M4_orf2#LINE/    252 AGTAATC-AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_144138251_   1107 TGGGATAGACCAGAGAGCTCAGAAATCAACCTCCACATATATGGTTAATT 1156
                            i     viv     ii       v    ivi    v      i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_144138251_   1157 GATTTTC 1163
                                
  L1M4_orf2#LINE/    351 GATTTTC 357

Transitions / transversions = 1.23 (43 / 35)
Gap_init rate = 0.01 (5 / 356), avg. gap size = 1.80 (9 / 5)  

3053 27.73 1.34 0.33  chr1_144138251_144142144.rev     1904  2801 (1093)  C L1M4_orf2#LINE/L1   (0)   908     2  

C chr1_144138251_   2801 GGAAGAACATTCCATGCTCCTGGATAGGAAGAATCAATATCGTGAAAATG 2752
                             ii i  i     i  v     v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

C chr1_144138251_   2751 GCCATACTGCCCTAGGTAATTTATAAATTCAATGCCATCCCCATCAAGCT 2702
                           v     v   v iv i  i  i i      i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

C chr1_144138251_   2701 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAAAGTTTAT 2654
                         v   iivi i  i  ii     -   -- v  i  -  ii    i  i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

C chr1_144138251_   2653 ATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGA 2604
                               viiv  ii  v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

C chr1_144138251_   2603 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 2554
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

C chr1_144138251_   2553 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACCA 2504
                                i   i    ii         i iv ii i   v   i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

C chr1_144138251_   2503 ATGGAACAGAACAGAGCACTCAGAAATAATACCACACATTTAAAACCATC 2454
                               i    iv   viii         vv   i       viii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

C chr1_144138251_   2453 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGAGAAAGGATTCCCTA 2404
                             i  i     ivv  v   i v  vvv     i     i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

C chr1_144138251_   2403 CTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 2354
                         i    i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chr1_144138251_   2353 ACTGGATCCCTTCCTTACACCTTATACAAAACTCAATTCACAATGGATTA 2304
                         ii    i    v   i     v         v i  i   v       i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chr1_144138251_   2303 AAAACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAACCTA 2254
                         ? i  i       v   v       i      v  i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

C chr1_144138251_   2253 GGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 2205
                           ?i- v i -   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

C chr1_144138251_   2204 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAATT 2155
                                    vvi          vv     v  i    vi  ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

C chr1_144138251_   2154 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGTGTGAACAG 2105
                            v v  i i   i  ii vv    i  v    i  vv iv     v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

C chr1_144138251_   2104 GCAACCTAAAAAATGGGAGAAAATTTTTGCAAGCTACTCATCTGACAAAG 2055
                         i     i v i             v       iii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

C chr1_144138251_   2054 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 2005
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

C chr1_144138251_   2004 ACAA----CCCCATCAACAAGTGGACGAAGGATATGAACAGACACTTCTC 1959
                             ----   v  i? v  i   i i      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

C chr1_144138251_   1958 -----AAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 1914
                         -----    i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

C chr1_144138251_   1913 CACTGGCCAT 1904
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 2.14 (15 / 7)  

2345 19.96 3.42 1.44  chr1_144138251_144142144.rev     2875  3430 (464)    L1M4_orf2#LINE/L1      342   908 (0)  

  chr1_144138251_   2875 TGGTTAATTGATTTTAAACATGCATGTCAAGTCTATTCAATGGGGAAAGA 2924
                             i          vi   v vi  i    v i                
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_144138251_   2925 ACAGTTTTTCCAGAAAATGGTCCTAAGAAAACTATATATCCACATGCAAG 2974
                          i   i   i  iv       v  ii  v    iv   ?          i
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_144138251_   2975 AGAATGAAGTGGGGCCCTTAACTTACACTATATACAAAA-TTAACTCAAA 3023
                                   v  i   i  v  i    i          -          
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_144138251_   3024 ATTGATCAAAGACCTAAATATAAGAGCTAAAACTGTCAAAGTCTCAGAAA 3073
                           v     ?          i              i v   v   i    i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_144138251_   3074 AAAA--TTGGGGACAATCTTCATGTCATTGGATTTGAATTTGGATTATTA 3121
                             -- v  ? vv       i  v v    i  -------i iiv  vi
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTT-------AGGCAATGG 584

  chr1_144138251_   3122 TTTCATAGAAATAACACCAAAAGTACAGACAACAAAAGAAAAAGTAGGTA 3171
                             v    v  i          i   ii              i   i  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_144138251_   3172 ACATTT-ACTTCGTTGAAATTAAGAAAGT--GTCATCCAAAGGATGCCAT 3218
                          -   v-     i ii       i  vv --  vv i       ii i  
  L1M4_orf2#LINE/    635 A-ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_144138251_   3219 CAATAAAGTGAAAAGACAATCTGTAGAATGGAAGAAAATATCTGCAAATC 3268
                            v               i iii       i         i        
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_144138251_   3269 AGAAATCTAGTAATGCATTAATATTCATAATATA--AAGAACTCCTACAA 3316
                          v v    ii   v v i vi   i  v      --        i     
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_144138251_   3317 CTCAACAACAGTAATAAAAACCAACCAATTCAAACGTGGACACTGGAC-- 3364
                              i  i iv  v v   iv v      ?   vi   i  vv   i--
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_144138251_   3365 --ATAGACATTTCTCCAGAGAAGATATACAAAT-------AAGGGCCTGA 3405
                         --               i               -------   vi v   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_144138251_   3406 AAAGATGCTCAACACCATTAGTCAT 3430
                                       i  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (63 / 44)
Gap_init rate = 0.02 (9 / 567), avg. gap size = 3.00 (27 / 9)  


3036 28.38 0.33 0.44  chr1_144159567_144164592.rev     3627  4535 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144159567_   3627 TGGAAAAACATTTTATGCTCATGGATATTAAGAAAAAATATCAGTAAAAT 3676
                               i i  iii   i        vvv    vvv     iiv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144159567_   3677 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGTTATTCCTATCAAAC 3726
                            v     v      vii  i           i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144159567_   3727 TACCAAAAACATTCTTCACAAAACTAGAAAAAACAATTTAAAAATTTATA 3776
                          v   ivvi v  i  ii  i  v v  v  ivii  iiv      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_144159567_   3777 TGGAACCAAAAAAGAGCCCAAATAGCCAAGGAAATCCTAAGCAAAAAGAA 3826
                              viiv  ii  v  vi         iiv    i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_144159567_   3827 CAAAACTGGAGGCATCACATTACCTGAATTCAAACTATACTACAGGGCTA 3876
                             ii      vv     i v  ii v      viv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_144159567_   3877 CAGTAATCAAAACAGCATGATAATAGCACGAAAATAGACACATAGACCAA 3926
                                   i    ii  i  v i   ii ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_144159567_   3927 TGGAACAGAATAGAGAGCCCAGAAATAAGGTTGCACACCTATGACCACCT 3976
                              i     v     i          iviiii   ii    ii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_144159567_   3977 GATCTTTGACAAAGCTAACAAAAACAAATAATGCAGAAAAAACTTATCTC 4026
                            i  i     i v iv   i v  vvi    vi    i  - vi   i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTT 399

  chr1_144159567_   4027 TAGTCAATAATTGGTGCTGGGATAACTGGCTAGCCATTTGCAGAAGAC-- 4074
                          --    i  v           i      v  ?   iv    i    v--
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_144159567_   4075 AAGCTGGATCCCTTTCTTACACTGTATACAAAAATCAACTCAAGATGGAT 4124
                            i    i    vi  i    ii           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_144159567_   4125 TAAAGACTTAAATGTAAAACCCCAAACCATAAAAACCCTGGAAGACAACC 4174
                         i ?    i         i v iv    i      vi i i     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_144159567_   4175 TAGGCAATAATATCCTGGACATAGGAATGGGCAAATATTTCATGACAAAG 4224
                             ?ivv   v i vv   v v  iv i     vvi    v iivv v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_144159567_   4225 ATACCAAGAGCAATCTCAACAAAAGCAAAAATTGACAAATAGGATCTAAT 4274
                          i     i    vvvv         v      v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_144159567_   4275 TAAATTTAAGAGCTTCTGCATAGAAAAAGAAACTATCAACAGAGTAAACA 4324
                         i   v    i i   i  iiivvv   i  v        v i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_144159567_   4325 GACATCTTACACAATGGGAGAAAAT-TTTGCAAAGTATGCATCTGACAAA 4373
                             v ii   v             -        vi  ii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_144159567_   4374 GGTCTGATATCCAGCATGTATGAGAAACTTAAACATCTCTACGAGAGAAA 4423
                           v  vi       v  i   i ii    ivv   v   v ii v i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_144159567_   4424 AACAAACAACCCCATTGAAAAGTGGGCAAAGGACATGAGCAGATACTTTT 4473
                         i     i     v   ?    i           iv   ii   i i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_144159567_   4474 CAAAAGAAGACATAGTTTGTGGCCAACAAGCATATGAAAAAAAGCTCAGT 4523
                          v        i   -ivvi       i     i       i v     ii
  L1M4_orf2#LINE/    848 CCAAAGAAGATATA-CAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_144159567_   4524 ATCACTCATCAT 4535
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (154 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


 276 12.77 0.00 0.00  chr1_144380446_144385831     3477  3523 (1863)    L1M4_orf2#LINE/L1        1    47 (861)  

  chr1_144380446_   3477 TGAAAAGATATTCTGTGTTCATGGATTGGAAGAATTAATATTATTAA 3523
                           i        i ii                  v        i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

Transitions / transversions = 5.00 (5 / 1)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.00 (0 / 0)  

3020 20.96 1.86 7.86  chr1_144380446_144385831     3978  4893 (493)    L1M4_orf2#LINE/L1       48   908 (0)  

  chr1_144380446_   3978 GATGAAGACACCACCCAAAGCAATCCACAGATTCAGTGCAATCTCTATTA 4027
                             ivi i  iv      vii   i         ii      i    i 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_144380446_   4028 AAATTTTAATGACATTTTTCACAGAAATAGGAAAA--AAACCTAAAATGT 4075
                             iii iivi v     ii       v iv  i--i v        vi
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_144380446_   4076 ATATGGAACCATAAAAGACCCCAAGACCCCAAGACCCCAAATAGCCAAAC 4125
                                 --  i--------    i------     vi          v
  L1M4_orf2#LINE/    148 ATATGGAA--ATG--------CAAGG------GACCCAGAATAGCCAAAA 181

  chr1_144380446_   4126 CAATTCTGAGCAAAACGAACAAAGCCAGAGGCATCACACTACTTGCTTTG 4175
                             ii   iv  i v        iii    vv       v iiiv   v
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_144380446_   4176 AAAATTTACTACCAAACTAGAAGAATCAAAAGTGTATTGTGCTGGTATAA 4225
                             i       v  i   v iv      i vv  i v  i    i    
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_144380446_   4226 AAACAGACACATAGACCAATGAAATGGAATAGAGAGCTCAAAAATAAATC 4275
                         ii i     i     i     i   i    v     ii  i       i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_144380446_   4276 CATGCATTTATAGTCAATTGATTTTTGACAAAGTTGCCAAGAACACAAAA 4325
                            i       i             i     i v        v  ivv  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_144380446_   4326 TGGAGAAAGAATA-TCTTCTTCAATAAATGGTGCTAGGGAAACTGGATAT 4374
                            i         -    -     i          i  iv         ?
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_144380446_   4375 CCACATGCAGAAGAATAAAATTAGACCCTCATCTCACACCATATATTTAT 4424
                                  i      i  i  i     ii i             i----
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC---- 476

  chr1_144380446_   4425 ACAAAATTAACTCAAAATGAATTAAAATCTTAAATGTAAAACTTGAGACT 4474
                          -                 i  i ? iv i         i vi i i   
  L1M4_orf2#LINE/    477 A-AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_144380446_   4475 GTAAAA---TCAGCAGAC--CA-------AAATCTCCATGACATTGGTCT 4512
                         i     --- i  v   v--  -------      i i    v    vi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_144380446_   4513 GGGCAAAGATTATTTTGATATGACCCCAAAAGCAAAAGCAACAAAAGTGA 4562
                         i     v i  vi  v        v         v            vi 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_144380446_   4563 AAGTAGACAGATGAAATTACATCAAACTAAAAAACTTCTACATAGCAAAG 4612
                           i    i i  vii i v       v v        i iiiivv     
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_144380446_   4613 GAAACAATCAACAGAGTGAAGAGACAACATATAGAATGACAGAATATATT 4662
                           v  v     v i      i       vi i      iv    v     
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_144380446_   4663 TGCAAGCCATACATCCAATAAGAGGTACAAAATATAAAATATAAAAGCAA 4712
                              ii    i   ii     i --  ------ ---- i  -------
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGG--AC------T----TGTA------- 756

  chr1_144380446_   4713 CAAATACAAAGCAAAAAAAATACAAAAAAATACAAAATATA-AAAGCAAC 4761
                         ------------------------------ v  i      -    -   
  L1M4_orf2#LINE/    757 ------------------------------TCCAGAATATATAAAG-AAC 775

  chr1_144380446_   4762 TCAAACAACTCAATAGTAAGAAAACAAATAACCCAAATAAAAAATGGGCA 4811
                           vv           i   i  i             v ?           
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_144380446_   4812 AGGGACCTGAATAGACATTTTTCAAAGGAAGACATATAGATATCCAATA- 4860
                          i   ii             i  v  i     i   i i  iv      -
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_144380446_   4861 GTATATGAAAAAATGCTCAATAACACCAATCAG 4893
                          i i       i        i v  ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (128 / 61)
Gap_init rate = 0.02 (18 / 861), avg. gap size = 4.94 (89 / 18)  


3156 27.38 0.33 0.88  chr1_144402191_144409301.rev     5707  6619 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144402191_   5707 TGGAAGAACATTCCAGGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5756
                              ii i  i   v i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144402191_   5757 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATAAAGC 5806
                           iv     v     iv i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144402191_   5807 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTCA 5854
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_144402191_   5855 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAAG 5904
                                viiv  ii  v  viv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_144402191_   5905 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTTCAAGGC 5954
                                i      vv   ii  v  ii i      viv    v   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_144402191_   5955 TACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGATATAGATC 6004
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_144402191_   6005 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACCACACATCTACA 6054
                                i    iv   ivii         -   ----  i    i  ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAA-ACC----CATACATTTATG 343

  chr1_144402191_   6055 ACTGTCTGATCTTTGACAAACATGACAAAAACAAGAAATAGGGAAAGGAT 6104
                         iiiivi    i  i     ivi  v   i v  vvv   i       i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_144402191_   6105 TCCCTATTTAATAAATGGTGCTGGGAAAATGGGCTAGCCATATGTAGAAA 6154
                         vvi  v  i  i              v  iv  v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_144402191_   6155 GCTGAAACTGGATCCCTTCCTTAAACCTTATACAAAAATTAATTCAAGAT 6204
                         iv    ii    i    v   i v   v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_144402191_   6205 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 6254
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_144402191_   6255 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 6303
                            v    ?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_144402191_   6304 CTAAAACAACAAAAGCAATGGCAACAAAAGTCAAAATAGACAAATGGAAT 6353
                         v  vi   v        vvi          vv        i    v i i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_144402191_   6354 CTAATTGAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 6403
                         i v  ii  v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_144402191_   6404 GAACAGGCAACCTAGAGCATGGGAGAAAATCTTTGCAATCTATCCATCTG 6453
                            v  i     i v  v            v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_144402191_   6454 ACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAG 6503
                          i  i  i  vi          v  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_144402191_   6504 AAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 6553
                              i     i     v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_144402191_   6554 CTTCTCAAAAGAAGACATTTATGCTGCCAACAGACAGATGAAAAAATGCT 6603
                         i     v        i  vi viiv     i ii  v       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_144402191_   6604 CATCATCACGGTCATC 6619
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


2975 25.53 3.49 1.35  chr1_144523713_144528662.rev     3571  4459 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144523713_   3571 TGGAAACACATCCCCTGTTCATGGATGGGTAGAATCAATATTGTGAAAAT 3620
                               v i     v           v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144523713_   3621 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCAT-AAAA 3669
                          i v     v  v   vii       i      i        i  -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144523713_   3670 TACCACCATCATTCTTTTCAGAATTAGAAAAAAAAATT-TAAAATTCATA 3718
                          v   v vv v  i   v     v v  v  ivvi  i-           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_144523713_   3719 TGGAGCCAAAAAAGAGCCCTCATGGTCAAAGCAA----------AAAGAA 3758
                             iviiv  ii  v  vvv  i i    i   ----------i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_144523713_   3759 CAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGCCA 3808
                             vi      vv       v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_144523713_   3809 TAGTCACCTAGTCACCAAAACAGCGTGGTGGTGGTATAAAAATAGGCACA 3858
                         i   ----- i   --- i    i     iv   i    ii    i  i 
  L1M4_orf2#LINE/    251 CAGT-----AATCA---AGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_144523713_   3859 TAGACCAGTGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTAC 3908
                             i  i     i     v    ii               v i i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_144523713_   3909 ATCCAACTGATCTT-----AAAGCATAAAG-----TTAA---GGAAAGGA 3945
                         ivi   i    i  ----- ii iiiv   ----- i  ---      i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_144523713_   3946 CACCGTTTTCACCAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGA 3995
                         i viv      v               i  i   v  ?       i ii 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_144523713_   3996 GAATGAAACTGGATCCTCATCTCTCACCCCATACAAATATCAACTCAAGG 4045
                                ii    i  ii i   v    vi       v  i       ii
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_144523713_   4046 TGGATTAAGGACTTAAATCAAAGACCTGAAACTATAAAAATTCTAGAAGA 4095
                              i ?i   i     vv    v  i           v ii       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_144523713_   4096 TAACATTGGAAAAACCCTTCTAGACACTGGCTTAAGCAAGGATTTCATGA 4145
                         v     v  ?iv  vi    vv   vi   v   i    v i    v ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_144523713_   4146 CCAAGAACTCAAAAGCAAATGCAACAAAAACAAATTTAAATAGTGGGGAC 4195
                         vi v  vvi        v v         iv   vv  i   ivvv    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_144523713_   4196 CTAATTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGT 4245
                         i v  i   v v  i i      iiivv    i iv  vi   iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_144523713_   4246 AAACGGACAACCCACAGAGTAGGAGAAAATCTTCATAATCTATAAATCTG 4295
                         i  vi             i i         v  iii  vii   v     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_144523713_   4296 ACAAAGGACTAATATCCAGAATATACAACAAAA-----ACAAATCAGCGA 4340
                          i  i     vi             i  - i  -----    v   --- 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAA-AGAACTCTTACAACTCA---A 788

  chr1_144523713_   4341 GAA-AAAAAAACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATA 4389
                         v  -     i     i  i  v  i?    i     v     iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_144523713_   4390 GACAATTCTCAAATGAAGATATACAAATGGCCAACAGACATATGAAGAAA 4439
                             v     v  v                    i ii  i     i i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_144523713_   4440 TGCTCAACATCACTAATGAT 4459
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (131 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.58 (43 / 12)  


3095 27.58 0.44 0.66  chr1_144551026_144557670     5243  6152 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144551026_   5243 TGGAAAAACACTCCATGCTCCCAGACAGGAAGAATCAATATCATGAAAAT 5292
                               i i ii     i  vii  iv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144551026_   5293 GGCCACACTGCCCAAAGTAATTTATAAATTCAATGCTACACCCATTAAAC 5342
                            v i   v      v i  i  i i      i  v iv  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144551026_   5343 TAACATTGACATTCTTCACAGAATTAGAAAAAACT-ATTTTAAAATTCAT 5391
                          vv  vivi v  i  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_144551026_   5392 ATGGAAGCAAAAAAGAGCCTGTACAGTCAAGACAATTGTAAGCAAAAAGA 5441
                               iiiv  ii  v  v v i  i   i     iv i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_144551026_   5442 ACAAAGCTGGAGGCATTACACTACCTGACTTCAAACTATACTACAAGTTT 5491
                               i      vv i     v  ii i      viv        ivi 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_144551026_   5492 ACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGACACATAGACCA 5541
                                i   i    ii         i iv ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_144551026_   5542 GTGGAACAGAATAGAGACTC-AGAAATAAGACCGCACATCTACAGCCATC 5590
                         i     i     v    v  -        iv  ii    i  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_144551026_   5591 TGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5640
                             i  i     i v  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_144551026_   5641 TTTAATAAATGGTGCTGGAACA-CTGGCTGGCCATGTGCAGAAAATCAAA 5689
                           i  i            i   -    v i?   ii    i  i vii  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_144551026_   5690 ACTGGTACCCTTCTTTGCACCTTATACAAAATTTAACTCAAGATGGATTA 5739
                         ii   vv    v i ii    v         v         i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_144551026_   5740 AAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5789
                         ?    i           v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_144551026_   5790 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAAAA 5838
                           ?i- v i -   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_144551026_   5839 CACCAAAAAAAAAATGGTAACAAAAGCCAAAATTGACAAATGAGATTTAG 5888
                                 iv v  -- i        vv     v  i    vi  i  vi
  L1M4_orf2#LINE/    599 CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_144551026_   5889 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTCTCATCAGAGTGAAC 5938
                          i   v v  i i   i  ii vv    i  v   v   vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_144551026_   5939 AGGCAACCTATAGAATGGGAGAAAATTTTTGCAAACTATCCCTCTGACAA 5988
                           i     i i               v        ii  viv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_144551026_   5989 AGGGCTAATATCCAGAATCTACAAGGAACTTAGACAAATTTACAAGAAAA 6038
                         i  i  vi          v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_144551026_   6039 AAACAAACAACCTCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 6088
                          i     i    iv  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_144551026_   6089 TCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAAAGCTCA 6138
                           v        i  vi viii     i  i  i       i v--     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT--GCTCA 894

  chr1_144551026_   6139 CCATCATTGGTCAT 6152
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  

 642 22.94 0.59 0.00  chr1_144551026_144557670     6189  6358 (287)    L1M4_orf2#LINE/L1      738   908 (0)  

  chr1_144551026_   6189 ATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTT 6238
                               i  i  i  vi          v  i         vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_144551026_   6239 ACAAGAAAAA-ACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAAC 6287
                          i  v     -     i     v  i? v  i    ii      v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_144551026_   6288 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGACAAA 6337
                              i     v        i  vi viii     i ii       v  i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_144551026_   6338 ATGCTCATCATCACTGGCCAT 6358
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (23 / 15)
Gap_init rate = 0.01 (1 / 171), avg. gap size = 1.00 (1 / 1)  


3159 25.61 1.77 1.55  chr1_144558087_144564458     4974  5879 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144558087_   4974 TGGAAGAACATTCCATGCTCATGGATAGGAA---TCAATATCATGAAAAT 5020
                              ii i  i     i        v    --- i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144558087_   5021 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCC-ATCAAGC 5069
                            v     v     iv i  i  i        i  v     -     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144558087_   5070 CACCAATGACTTTCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCA 5117
                         iv   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_144558087_   5118 TATGGAACCA-AAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAG 5166
                                vii-  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_144558087_   5167 AGCAAAGCTGGAGGCATCATGCTACCTGACTTTAAACTATACTACAAGGC 5216
                          i     i      vv   ii  v  ii i  i   viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_144558087_   5217 TACAGTAATCAAAGCAGCATGGTACTGGTACCAAAACAGATATATAGATC 5266
                                     ii   ii         i iv ii i   i         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_144558087_   5267 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACTGT 5316
                                i    iv   ivii         vv   i    i  iiiiiiv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_144558087_   5317 CTGAACTTTGACAAATCTTACAAAAACAAGCAATGGGGAAAGGATTCCCT 5366
                         i   vi  i     ivv vv   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_144558087_   5367 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5416
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_144558087_   5417 AACTGGATCCCTTCCTTACACCTTATACAAAAGTTAACTCAAGATGGATT 5466
                          ii    i    v   i     v         i         i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_144558087_   5467 AAAGACTTAAATGTTTGACCTAAAACCATAAAAACCCTGGAAGAAAACCT 5516
                          ?    i       vv  v       i      vi i i         v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_144558087_   5517 AGGCA-ATACCATTCAGGACATATGCATGGGCAAGGACTTCATGACTAAA 5565
                            ?i- v i -   iv   v vv vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_144558087_   5566 ACACCAAAAAAAAAAAAAAAATGGCAACAAAAGCTAAAATAGACAAATGG 5615
                                  iv v  --------          vv        i    v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA--------GCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_144558087_   5616 GA-TCCAGTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTCTCATCA 5664
                           - i  viv   i    i -   i  ii vv    i  v   v   vv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_144558087_   5665 GAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAA--CATACC 5712
                         i      v  i     i                 v       --    i-
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT- 737

  chr1_144558087_   5713 CATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTCCAACAAATT 5762
                         -      i  i  i  vi          v  i         iv    v i
  L1M4_orf2#LINE/    738 -ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_144558087_   5763 TACAAGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATAT-AA 5807
                         v i  v     i    ----   v  i?    i            v -  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_144558087_   5808 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAA 5857
                         i     i     v        i  vi viii     i ii          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_144558087_   5858 AATGCTCATTATCACTGGTCAT 5879
                         i       vi    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (142 / 86)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.00 (30 / 15)  


 985 20.64 2.75 1.38  chr1_144576920_144579910.rev     1299  1516 (1475)    L1M4_orf2#LINE/L1        1   221 (687)  

  chr1_144576920_   1299 TGAAGAGATATATCATGTTCATGGATTGGAAGAATCAGTATTGCTAAGAT 1348
                           i i      vi                    v i i     i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144576920_   1349 GCCCATTCTCTCCAAATTGATCTGTAGATTCAGTGCAATCCCAATCAGAA 1398
                          v v  v   i            ii       ii        v    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144576920_   1399 TCCTAGAAGATTTTTTAAATGTA--AATTGACATTTTGATTCTAAAATAT 1446
                            i  vv vi     ---  i --        vvi    i       vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT---TGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_144576920_   1447 ATGTGGACATGCAAAGGACTT-TAATAGTCAAAACAATTTTGAAAAAGGA 1495
                           i    v      i    ii-v     i         i         i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_144576920_   1496 ---CAAATTTGGAGAATTTTCATT 1516
                         ---    v      i i iv  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACT 221

Transitions / transversions = 1.81 (29 / 16)
Gap_init rate = 0.02 (4 / 221), avg. gap size = 2.25 (9 / 4)  

2018 24.59 3.00 2.40  chr1_144576920_144579910.rev     1834  2500 (491)    L1M4_orf2#LINE/L1      238   908 (0)  

  chr1_144576920_   1834 TATTTTAAAACTATAGTAATTAAGACAATGTAGTATTGATGTAAACACAG 1883
                           i vi   i   i      i      i   i   i  iii   iv i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_144576920_   1884 AAAAAAATAGATGAATGGAACAGAATATAGAGTCCAGAAAGAGAT--ATA 1931
                          v v --     v       i     vv            v i i--   
  L1M4_orf2#LINE/    288 ACATA--TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_144576920_   1932 CATATATGATCAATCGATTTTTGACAAA----TCAACAACTCAAATCAGT 1977
                            v    i     i      i     i----i   -i  i-- v   i 
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACC--ATTCAAT 382

  chr1_144576920_   1978 AGAGGAAACGAA-AACCTTTCCC-CATATGGTGCTGAAACACCTGAATAA 2025
                         i -     -   - ii    i v-  v         ii   v   i   ?
  L1M4_orf2#LINE/    383 GG-GGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_144576920_   2026 ATGTATG-AAAAATATGAAACTTTACCCTTACCCCATATTACTACACAAA 2074
                         viii   -    iv     ii vv    i    i  i ii -  i     
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA-TATACAAA 479

  chr1_144576920_   2075 A-TTAATTTGACATGGCTCATAGACCTAAACATAAAATTTAAAACTATAA 2123
                          -    i ii v    v   ?         ii   i vi           
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_144576920_   2124 AACTTCTAGAAGAAACCTTCAGAGAATATTTTTTTGTGATCTTGGGATGG 2173
                             ii         v v -  - ?i  vv i  i    i      v i 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACAT-AG-GNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_144576920_   2174 AAAATA-TTTTTTAAAGAGGTCACAAAATACACTAACCAATAATAAAAAA 2222
                         iv   i-   i   i v v v   v   vi   -  v   i  -  i   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCAC-AAGCAACAA-AAGAAA 625

  chr1_144576920_   2223 AAGTTGATAAACTAGATTT-ATCAAAGTCCAAAACTTCTGCTCATCAAAA 2271
                           i v      i i  i  -      i iv       i  iv v     i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_144576920_   2272 GATGTCACCATTAAAATGAAAAAGCCAGCCACAGTCTAGGAAAAAAATAT 2321
                           iiii i  vv   i      ii v v      vv i   i    -   
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TAT 724

  chr1_144576920_   2322 TTGTAAAATATAGATTTGACACAGAATTCCT-TTCACA-TATATAAAGAA 2369
                            i   vi   v  i   i vi i i iv - i  v -           
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_144576920_   2370 CTTTTACATATCAATCATAGAAAGA----TAATCCAAC--AAATATAATG 2413
                           i     vv     v   i     ----   i    i--   ---    
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA---AATG 821

  chr1_144576920_   2414 GGCAAAAGATCTGAATAGAGACTTCACAAAAGAAGATACATGAATGACTA 2463
                               i   i        v i   v v          i ii    i i 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_144576920_   2464 ATAAGCACATAAAAATGTGTTCAACATCACTAGTCAC 2500
                                   i    vi  i         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (107 / 54)
Gap_init rate = 0.04 (24 / 671), avg. gap size = 1.50 (36 / 24)  


1067 24.37 5.70 0.32  chr1_144658206_144661148      668   983 (1960)    L1M4_orf2#LINE/L1        6   338 (570)  

  chr1_144658206_    668 AAATAAACCATGTTAATAGATTGGAAGACTTGA-ATAGTAATGATGTTAA 716
                          i   vv       v  i             i -  v  v v    vi  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_144658206_    717 TTCTCCCCAAATTGGTATACAAATTTAATGTTATTCATTTCAAAATCCCA 766
                          v            i v    i   i  i iv  i v v           
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_144658206_    767 GCAAGATTTATTTGTAGATATACACAAAATTATTCTAAAATTTGTACAGA 816
                           -v vi  v    i   v  vv    iv v  i        ii  ii  
  L1M4_orf2#LINE/    106 GC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_144658206_    817 AAGGCAAAATAACTAGAATAGTTAATACAATTTTTAAAAAGAA---CAGT 863
                           v    iiv v i       ii  v     i  v        ---  iv
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_144658206_    864 ATGAGAGGAATTCCTCTACCTGATCTTTAAACATATTATATAGCTGCAGT 913
                         i vi     v iv v  v  ii  i iv    v  i  i v    i    
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_144658206_    914 AATCAAGAC--TGTGGTACTGG--------TAGACATA--GATCACTGGA 951
                                  --           --------        --     v    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_144658206_    952 ACAGAAAAGAGAACCCAGAAATA--CCGACACAT 983
                          i    vv    ii         --  v i    
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

Transitions / transversions = 1.03 (39 / 38)
Gap_init rate = 0.02 (7 / 333), avg. gap size = 2.71 (19 / 7)  

 435 33.95 2.47 0.62  chr1_144658206_144661148     1291  1452 (1491)    L1M4_orf2#LINE/L1      321   485 (423)  

  chr1_144658206_   1291 AGAAATA--CTGACACAAATACACCCAGCTAATTTTTGACAAAGATGCAA 1338
                                -- iv i   vv  iivi  ii i     i     i i   v 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_144658206_   1339 AAGCAGTTCAGTGGAGGAAAGATAACCTTT-CACCAAATGGTGCTAGAGC 1387
                          ii vi    i   i i  ii   ii    -  v           i ii 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_144658206_   1388 AATTAGGCGTCCATAGGTTTAAAAAATGAATCTAAATCTAAGTCTTACAC 1437
                           i i iii?   i v iv-   i      vi ii i ivvii  i    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCA-AAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_144658206_   1438 CTTATATAAAA-TTAA 1452
                          v    i    -    
  L1M4_orf2#LINE/    470 CATATACAAAAATTAA 485

Transitions / transversions = 3.15 (41 / 13)
Gap_init rate = 0.02 (4 / 165), avg. gap size = 1.25 (5 / 4)  

 480 26.02 8.16 0.51  chr1_144658206_144661148     1743  1938 (1005)    L1M4_orf2#LINE/L1      477   687 (221)  

  chr1_144658206_   1743 AAAAA--AAATTAAAACAGATAATAGACTAAAATGTAA-------AACTA 1783
                              --  v i    ii   v ?    iv        -------     
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_144658206_   1784 TAAAACTTTCAGAAAAAAAAAAAAG----AATCTTTGGAATCAAGGGCTA 1829
                                i i    i    v v i ----      i vi i vv   i  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_144658206_   1830 CACAAAAAGTTCTTTACT-TGATACCAAAAATAAAATCCATGAAAGGAAA 1878
                         vi   viiv     viv -   i       ii v  v v ii    -   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAA 625

  chr1_144658206_   1879 AAATGGATAAATTGGGCTCCATCAAAATTTAACACTTTCGCTCTGTAAAA 1928
                             i          i  i          v  v     i iv  vi   i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_144658206_   1929 GAC--TGTTAAG 1938
                            -- i i   
  L1M4_orf2#LINE/    676 GACACTATCAAG 687

Transitions / transversions = 1.50 (30 / 20)
Gap_init rate = 0.03 (6 / 211), avg. gap size = 2.83 (17 / 6)  

 673 25.11 6.73 0.45  chr1_144658206_144661148     2230  2452 (491)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr1_144658206_   2230 AAAAAATACTGTTAAGAGGATGAAAAGATAAGCTACCCACTGGGAGAAAA 2279
                            ii i   i i    iii        i  v i  vv v          
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_144658206_   2280 TATTTGCAAGCCACTTATTTGAGAAAGCACTAGTATCTAGAATA----AA 2325
                                  ii  iv   i   v  i v   v     i      ----  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_144658206_   2326 AAACATTCAAAGCTTACATT-TAAAAA---AAATG---CAGTTAGAAAAT 2368
                         i   vi i v i  i -  v-      ---    i---  i  ?i     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCA-ATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_144658206_   2369 AAGCAAAAA---TGA-TGAACATTTTATTGTAGAGGATATACAAATGGCA 2414
                         ii     ii---   - ii      iviiiv   i              v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_144658206_   2415 CATAACCACATGAAAAGGTGTTCAACATTGTTAGCCAT 2452
                         v    v           i  i       ii????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.44 (39 / 16)
Gap_init rate = 0.03 (7 / 237), avg. gap size = 2.29 (16 / 7)  


3140 26.13 0.99 1.32  chr1_144669972_144676141.rev     4775  5685 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_144669972_   4775 TGGAAAAACACTCCATGCTCCCAGATAGGAAGAATCAATATCATGAAAAT 4824
                               i i ii     i  vii   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_144669972_   4825 GGCCATACTGCCCAAAGTAATTTATAAATTCAGTGCTACTCCCATTAAAC 4874
                            v     v      v i  i  i i     ii  v ii  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_144669972_   4875 TACCATTGACATTCTTCCCAGAATTAGAAAAAAACT-ATTTTAAAATTCA 4923
                          v   vivi v  i  iv     v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_144669972_   4924 ATATGGAAGCAAAAAAGAGCCCGTACAAGTCAAGACAACTGTAAGCAAAA 4973
                         -       iiiv  ii  v  v v i - i   i    iiv i iv  i 
  L1M4_orf2#LINE/    149 -TATGGAAATGCAAGGGACCCAGAATA-GCCAAAACAATCTTGAAAAAGA 196

  chr1_144669972_   4974 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACCAG 5023
                                  i      vv    i  v  ii i      viv      v i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_144669972_   5024 GTTACAGTGACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGA 5073
                          i      i i   i    ii         i i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_144669972_   5074 CCAATGGAACAGAATAGAGAACTCAGAAATAAGACCGCACATCTACAGCC 5123
                         i        i     v    iii         iv  ii    i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_144669972_   5124 ATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5173
                          vi    i  i     i v  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_144669972_   5174 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5223
                           v  i  i              v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_144669972_   5224 GAAACTGGAACCCTTCTTTACACCTTATACAAAAATTAACTCAAGATGGA 5273
                            ii    v    v i i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_144669972_   5274 TTAAAGACTTAAATGTAAAACCCCAAACTATAAAAAACCTAGAAGAAAAT 5323
                          i ?    i         i v iv           vv i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_144669972_   5324 CTAGGCA-ATACCATTCAGGACAT-GGCACAGGCAAAGGTTTC------A 5365
                         v    ?i- v i -   iv   v -  vvi      v      ------ 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_144669972_   5366 TGACAAAAATGTCAAAAGCAATTGCCACAAAAGCAAAAATTGACAAATGG 5415
                              ------i        vvv  v       v      v  i    v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_144669972_   5416 GATCTAATTAAACTAAAGAGCTTCTGCACAGCTAAAGAAACTATCATCAG 5465
                           ii v  i   v v  i i   i  ii vv v  i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_144669972_   5466 GGTGAACAGACAACCAACAGAATGGGAGAAAATTTTTGCAATCTATCCAT 5515
                         i     v        v                 v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_144669972_   5516 CTGACAAAGGCCTAACATCCAGAATCTACAAGGAACTTAAACAAATTTAC 5565
                             i  i  v  vii         v  i  i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_144669972_   5566 AAGAAAAAAATCAAACAACCCCATTAAAAAGTAAGCAAAGGACATGAACA 5615
                           v     i -    i     v   ?    i ii        iv    i 
  L1M4_orf2#LINE/    790 AATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_144669972_   5616 GACAATTCTCAAAAGAAGACATTTATGTGGCCAACAAACGTATGAAAAAA 5665
                             v     v        i  vi vi       i  i ii       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_144669972_   5666 AGCTCAAGCTCAGTATCACT 5685
                         v      vv   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


 446 29.88 3.05 0.00  chr1_144870730_144872747.rev      502   665 (1353)    L1M4_orf2#LINE/L1      188   356 (552)  

  chr1_144870730_    502 TGAAAAAGAAGAA---AACCAGAGGACTTGCACAACCTGAGTTTCAGACT 548
                                      --- iiii       ii   vv  ii v  iv i   
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_144870730_    549 CACT-CTAAGCTGTTATAATCAAGGCAGTGTGCAAGTGGCATTGGGAGAC 597
                         i   - v     iivi        i       vv v      vi   v v
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_144870730_    598 ACAAATACATCAACAGACT-GACTTTGGAGTCCTGAAACTGACCCACAGC 646
                            v   v     ii  v -  v  vi      v    ivi     i vv
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_144870730_    647 TATAAGGTTCATAGGTTTT 665
                          v  v   iv  v i    
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTT 356

Transitions / transversions = 0.96 (24 / 25)
Gap_init rate = 0.02 (3 / 169), avg. gap size = 1.67 (5 / 3)  

 516 25.55 7.67 11.07  chr1_144870730_144872747.rev      946  1532 (486)    L1M4_orf2#LINE/L1      342   908 (0)  

  chr1_144870730_    946 TGGCCA-TAGGTTTTCAATAAAAG---CAG-----TTTAATGGGGCAAAG 986
                            i  - v i     i i  ii ---  i-----  i       -    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAG 390

  chr1_144870730_    987 GAAATAGT---TTCAATTAATTGC-CTTTCATAAA-GGAGA---AGGGGT 1028
                         --      ---     iv   v i-  vvv i  v-   v --- viv i
  L1M4_orf2#LINE/    391 --AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_144870730_   1029 AGACGAACAAGGTT--ATTTCTCCCTCACACTACACTTGAAAGT-AACTT 1075
                          i v   ii i   -- iii  v        i i ivii   i -    i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_144870730_   1076 GAGACACATTATAGACCAAAATATAAAAGCCAAAGATATAAAGCATTTCG 1125
                         i i iiv  i ?     v    i   i   i   iv      i vi  v 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_144870730_   1126 AGGA-----TA---------CTTTGTGACTTGTTGG--TAGACAGAGATT 1159
                          i  -----  ---------   i     i --   --   i  iv i  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCT--TGGGTTAGGCAATGGTT 586

  chr1_144870730_   1160 TATTAAATAGGGCACAGAAAAAA-ATGTA-TAAAGGAAAGGCTTGATACA 1207
                          v   i   v i   vi   iv - v i -i   i    iiv v    v 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_144870730_   1208 TTAGACTTCATCAAATATTAGCCATATCTTCT---CATCAAAAGAGGCAA 1254
                           i            -    --- v v   i --- v     i  vi v 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAA-ATTA---AAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_144870730_   1255 CAAAGAAAGTGAAGAAATGAGACAGCCT-CAGACAGGGAGAAAATAGTCA 1303
                         iv           i -----    i  i-    vv           ----
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAA-----GACAACCCACAGAATGGGAGAAAATA---- 723

  chr1_144870730_   1304 CGAAACTTATCTGACCCCCAAACCCTGTAACT-ATAAAGTATGCTGAGAT 1352
                         --------- i  -----    i v i  v  -    i --------  -
  L1M4_orf2#LINE/    724 ---------TTTG-----CAAATCATATATCTGATAAGG--------GA- 750

  chr1_144870730_   1353 CTTCTTACCTGGTAATTAAAACA-ACAAGGACAACAACAACAACAACAAC 1401
                         ---   -----   vii i  i - i  i  -----  vviv     v- 
  L1M4_orf2#LINE/    751 ---CTT-----GTATCCAGAATATATAAAGA-----ACTCTTACAACT-C 786

  chr1_144870730_   1402 AACAACAACAACAACAAACCAATCAACCCAAGTATGCTAGATGGGTAAAA 1451
                           i  i  v  -i     i-----       v ?vi-- i     i   i
  L1M4_orf2#LINE/    787 AATAATAAAAA-GACAAAT-----AACCCAATTWAA--AAATGGGCAAAG 828

  chr1_144870730_   1452 GACTTGAACAGATACATAAGAATAAAAGGTACACACATGGTCAACAAAGC 1501
                           i     i   i iv vvvv v i   i  i   v    i   i  -  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA-GC 877

  chr1_144870730_   1502 ATAT-ACAATATGTTTAGCTCTCAGGAAAATG 1532
                          i  - v  v   i i i -v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (93 / 55)
Gap_init rate = 0.07 (37 / 567), avg. gap size = 2.97 (110 / 37)  


 420 30.49 3.05 0.00  chr1_144885463_144887480      500   663 (1355)    L1M4_orf2#LINE/L1      188   356 (552)  

  chr1_144885463_    500 TGAAAAAGAAGAA---AACCAGAGGACTTGCACAACCTGAGTTTCAGACT 546
                                      --- iiii       ii   vv  ii v  iv i   
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_144885463_    547 CACT-CTAAGCTGTTATAATCAAGGCAGTGTGCAAGTGGCATTGGGAGAC 595
                         i   - v     iivi        i       vv v      vi   v v
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_144885463_    596 ACAAATACATCAACAGACT-GACTTTGGAGACCTGAAACTGACCCACAGC 644
                            v   v     ii  v -  v  vi   v  v    ivi     i vv
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_144885463_    645 TATAAGGTTCATAGGTTTT 663
                          v  v   iv  v i    
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTT 356

Transitions / transversions = 0.92 (24 / 26)
Gap_init rate = 0.02 (3 / 169), avg. gap size = 1.67 (5 / 3)  

 516 25.55 7.67 11.07  chr1_144885463_144887480      944  1530 (488)    L1M4_orf2#LINE/L1      342   908 (0)  

  chr1_144885463_    944 TGGCCA-TAGGTTTTCAATAAAAG---CAG-----TTTAATGGGGCAAAG 984
                            i  - v i     i i  ii ---  i-----  i       -    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAG 390

  chr1_144885463_    985 GAAATAGT---TTCAATTAATTGC-CTTTCATAAA-GGAGA---AGGGGT 1026
                         --      ---     iv   v i-  vvv i  v-   v --- viv i
  L1M4_orf2#LINE/    391 --AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_144885463_   1027 AGACGAACAAGGTT--ATTTCTCCCTCACACTACACTTGAAAGT-AACTT 1073
                          i v   ii i   -- iii  v        i i ivii   i -    i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_144885463_   1074 GAGACACATTATAGACCAAAATATAAAAGCCAAAGATATAAAGCATTTCG 1123
                         i i iiv  i ?     v    i   i   i   iv      i vi  v 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_144885463_   1124 AGGA-----TA---------CTTTGTGACTTGTTGG--TAGACAGAGATT 1157
                          i  -----  ---------   i     i --   --   i  iv i  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCT--TGGGTTAGGCAATGGTT 586

  chr1_144885463_   1158 TATTAAATAGGGCACAGAAAAAA-ATGTA-TAAAGGAAAGGCTTGATACA 1205
                          v   i   v i   vi   iv - v i -i   i    iiv v    v 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_144885463_   1206 TTAGACTTCATCAAATATTAGCCATATCTTCT---CATCAAAAGAGGCAA 1252
                           i            -    --- v v   i --- v     i  vi v 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAA-ATTA---AAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_144885463_   1253 CAAAGAAAGTGAAGAAATGAGACAGCCT-CAGACAGGGAGAAAATAGTCA 1301
                         iv           i -----    i  i-    vv           ----
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAA-----GACAACCCACAGAATGGGAGAAAATA---- 723

  chr1_144885463_   1302 CGAAACTTATCTGACCCCCAAACCCTGTAACT-ATAAAGTATGCTGAGAT 1350
                         --------- i  -----    i v i  v  -    i --------  -
  L1M4_orf2#LINE/    724 ---------TTTG-----CAAATCATATATCTGATAAGG--------GA- 750

  chr1_144885463_   1351 CTTCTTACCTGGTAATTAAAACA-ACAAGGACAACAACAACAACAACAAC 1399
                         ---   -----   vii i  i - i  i  -----  vviv     v- 
  L1M4_orf2#LINE/    751 ---CTT-----GTATCCAGAATATATAAAGA-----ACTCTTACAACT-C 786

  chr1_144885463_   1400 AACAACAACAACAACAAACCAATCAACCCAAGTATGCTAGATGGGTAAAA 1449
                           i  i  v  -i     i-----       v ?vi-- i     i   i
  L1M4_orf2#LINE/    787 AATAATAAAAA-GACAAAT-----AACCCAATTWAA--AAATGGGCAAAG 828

  chr1_144885463_   1450 GACTTGAACAGATACATAAGAATAAAAGGTACACACATGGTCAACAAAGC 1499
                           i     i   i iv vvvv v i   i  i   v    i   i  -  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA-GC 877

  chr1_144885463_   1500 ATAT-ACAATATGTTTAGCTCTCAGGAAAATG 1530
                          i  - v  v   i i i -v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (93 / 55)
Gap_init rate = 0.07 (37 / 567), avg. gap size = 2.97 (110 / 37)  


2258 25.17 5.67 2.21  chr1_144935501_144937148      433  1155 (493)    L1M4_orf2#LINE/L1      161   908 (0)  

  chr1_144935501_    433 AGAAACCCAA------CAAAGTTCTCATGGAGAAGATCAGAA-AAAATCC 475
                           ii     i------    iivv  v  i i    --    -   i iv
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA--AGAACAAAGTTG 208

  chr1_144935501_    476 CCGAGGATTGGCACTGCC-AACTTCA--------------GCTACAGTAA 510
                         --     i vi    v  -  i    --------------          
  L1M4_orf2#LINE/    209 --GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_144935501_    511 CCAAAACAGTATGGAGTTGGTGAAAAAATGTAAAACAGACTCATAGATCA 560
                         i   i     i   vii   iiv  ii  -------    vi        
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGAT-------AGACATATAGATCA 299

  chr1_144935501_    561 ATGGAAAAGAAAACAGAGCCCAGAAATAGACCTACATAAATATAATAAAC 610
                               v    vvv    i         i   i i i vv   ii v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_144935501_    611 TGATCTTTGATAAAGGTGCAAAGACAATTTAACAGAGCAAGGATGGCCTT 660
                             i  i  i  i     v     v   i  ii i v   i  i i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_144935501_    661 TTCAACAAATGGTGCGAAAACACCTGGACAACCACATG--AAAAAATAAA 708
                                        viii   v     i ?       --   i   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_144935501_    709 --TAAATG--TACATACAGATCTTATA----ACTT---TCACAAGTGGAT 747
                         -- ii iv--   v -  v i v    ---- v  ---   -  i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCT-CACACCATATACAAAAATTAACTCA-AAATGGAT 497

  chr1_144935501_    748 CTTATAACTACCTGTAAGGTTCAAAACCACAGGACTCCTAGGAGATAACA 797
                          v? v v   vv      ivii     i i ii    i   i   v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_144935501_    798 CAGGAGAAAAGCTAGGTGACCTTGGGTTTGGTGATGATTTCTTAGAAACA 847
                         i   ? v   v  vv             v  ii   i         v ii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_144935501_    848 GCATTAAAAGCGCAATCCATGGAAGAAACAAAATTGAAAAGTTGAACTTC 897
                         i  ii      i   v v iii      --    v  v  i   i     
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAA--AAATAGATAAATTGGACTTC 645

  chr1_144935501_    898 ATTACAATTAAAACCTTCTGCTCTGTGAAAGACACTGTTAAGAGAATGAA 947
                           i v        v   i  iv  vii  i      i i    i i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_144935501_    948 AAAACAAGTCA-AGACTGAGAGAAAATATTTGCAAAATACAGATCTGATG 996
                           i    vi  -   v  i                 vi i v       i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_144935501_    997 AAGGGCTGGTGCCCAAAATAAATGAAGAACTCTTCAAACTCAATAATAAG 1046
                          i  i  v  ii   i    v  i          vv             i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_144935501_   1047 AAAGTGAACAACCCAATTTAAAAGTAGGCAAAAGATCTGAA----CACCT 1092
                           iiii  i         ?    i i      i   i    ----  ii 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_144935501_   1093 CACTGAA-AAGATATACAGATAACAAATAAGTATATGAAAGAGACACTCA 1141
                          v ii  -          i  ii v      i i      -   ii    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATGCTCA 894

  chr1_144935501_   1142 AAGTCATTTGTCAT 1155
                          vi   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (120 / 58)
Gap_init rate = 0.03 (19 / 748), avg. gap size = 3.00 (57 / 19)  


1973 26.71 3.48 1.89  chr1_145343008_145344688.rev      502  1190 (491)    L1M4_orf2#LINE/L1      209   908 (0)  

  chr1_145343008_    502 GAGGTTTGGCACT-ACCAACTTCAGGACTTAC-ATTAAGCTACAGTAACC 549
                             vi vi    -v    i    ii      - iv            i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_145343008_    550 CAAATAGTGTGAAGTTGGTGAAAAGAGAAAACACACACATATAGATGCAT 599
                         v i i      ivii   iiv  i  v i -------         vv  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGA-------CATATAGATCAAT 301

  chr1_145343008_    600 GGAAAAGAATACGGAGCCCAGAAGCAGGCC--TACAT--ACAGTCCACTG 645
                             v     vvi   i      ii ii  --     -- ii   v i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_145343008_    646 ATCTTCCATGGAGGTTTAGAGACAATTTAAAACAGCAAAGATAGCCTTTC 695
                           i   v iiii   vivi    v   i  vivi v  ii    i    i
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_145343008_    696 CAACTAGTGGTGCTAGAACAGCTGGACAACCACATGCAAAAAAATAAA-- 743
                             v i       i i   i     i ?            i   i  --
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_145343008_    744 TAAATCCAGGTATGCATGTTATACCC-----TTTAT--AAAATAAATCTT 786
                          ii i  vviiv -  iiii   iv -----  v i--     ii   v?
  L1M4_orf2#LINE/    452 TGGACCCCTACCT-CACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_145343008_    787 ACACGTAAATGTAAGGTGC-AAAACCATAAGAATCCTAGGAGATAACATA 835
                          v  v          i-  -     i    i v  i   i   v      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_145343008_    836 GGAGAAAATCTGAGGGATCCTGGGTTCAATGATGGCTTCTTAGATACAAA 885
                           ? v      vv v  i i      viiii    i          ii v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_145343008_    886 ACCAAAAGCACAATCTACTAATGAAAAAAAAATTAAGTTGAGCCTCATTA 935
                                      v v  v  v       v iv   i   ii i    i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_145343008_    936 AAATTAAAAACTTCTGTTCTGTGAAAGACACTGTTAAGAGAATGGAAAAA 985
                                      i   v  vii  i      i i    i i  i   i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_145343008_    986 GCAAGTCACAGACTGGTAGAAAATATTTACAAA--ATA-ATCTGATGGAA 1032
                         -   vi      v   v           i    --   -       i- i
  L1M4_orf2#LINE/    700 -CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA-AG 747

  chr1_145343008_   1033 AAACTGCTGTCCAAAATATATGAAGAATTCTGAGAACTAAACAACACAAA 1082
                         ii   vv i    i       i     i   v v    v  i  i v   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_145343008_   1083 GCAAAAAAAAAAAAAAAAAAAAAAAGGTGAAACATCTGAA----CACCTC 1128
                          - v   v  vvv  vv?     vi  ii  iv  i    ----  ii  
  L1M4_orf2#LINE/    798 G-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_145343008_   1129 ATTAA-TAAGATATACAGATGGCAAATAAGCATATGAGAAAGATGCTCAA 1177
                         vii  -v          i     v        i    -            
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTCAA 895

  chr1_145343008_   1178 AATCATTTGTTGT 1190
                         v    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (112 / 68)
Gap_init rate = 0.03 (19 / 700), avg. gap size = 1.95 (37 / 19)  


2565 25.37 6.31 2.64  chr1_145450946_145453695.rev     1389  2259 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_145450946_   1389 AAACACCTTACACCCATGAATTGGACGATTTGATATTGT---------AG 1429
                          i i i ii iiii    i      v  i  i       --------- i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_145450946_   1430 TACTTTACAATTTGAACTACAGATTTGATGAAATCCCTG-CAAGTATCCC 1478
                             iiv   v    v         ii i v       i-   i-     
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA-ATCCC 104

  chr1_145450946_   1479 AACAGACTTGTGTCTAGAAACTGACAAGCTGATTCTAAAATACACATGAA 1528
                          i v v   v v vi     i            i       v  i   i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_145450946_   1529 ATTGTAAGGGACTCAAAATAGCCAAAATAATCTTGAAGAAAGAAAACATA 1578
                          v  i       i  i           i         i  ii i    v 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_145450946_   1579 TTAGGATAATTCACAC--CCCATGCTCCAAACCTTACTGCAAAGTATCAG 1626
                         v v   vi i      --    -ii i    v      i     ivv   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_145450946_   1627 TAATCAAGACAACACAACATTGATG-AAGGAAAAATATATAGATTGATGG 1675
                                    iiiiiii i  iii-     v i i        ii    
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_145450946_   1676 AAGAGAATTGAGAGTCCATATATAAAACTATGTGTCTACAGTCAATGGAT 1725
                           v               v v     v i  iii i  ii      v   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_145450946_   1726 TCTTAA-AGTGGTGCCATGTGCAATTCAATGAGGAAGAGACAGTCTTTG- 1773
                          i ii - iv       v -i v        i    iii i       v-
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_145450946_   1774 AACACA-----CTGGGTCAACAACGTACACGTGGATCACCACTTGCAAAA 1818
                             v -----     ---     -------     v?    v       
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGG---ACAAC-------TGGATAKCCACATGCAAAA 442

  chr1_145450946_   1819 TAATAAATTAGAACCCTTACCCCAAAGCATACAAAAATATTAACTCAAA- 1867
                         v   i  v v i    i    i  v v    i v   v           -
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_145450946_   1868 TGAATTAAAGACACACATGCAAGAGGTA-----------------GAATA 1900
                           i  i ?    vi v   i     v  -----------------   v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_145450946_   1901 AAGCATATGGGAAAATCTTCAGGATTTTGGATCTAGCAAAGA---AATAG 1947
                           i    v ? v        iv  ii    i ivi    v i---vv   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_145450946_   1948 CTGTAACCCCAAAAACATGAGCAACAGAATAAAAATTAGATATTTAAAAT 1997
                         v i i  v      i  ii       i  v     v      vv vii i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_145450946_   1998 TTCTTAAAAATTAAAGACATCGGTGTTTCAGAGGACA--ACCAAGCAAGT 2045
                            v v         i  v iv   i    i      -- i    v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_145450946_   2046 CAAAAGGCAGCTC-CAAAATTGTGAGAAGATATTTGAAAAACACGTATCT 2094
                         v     i  i i -  i   v -     i       v   v  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGG-GAGAAAATATTTGCAAATCATATATCT 741

  chr1_145450946_   2095 -ATATGTCTGTATATATATATGTATCTTGAATATAGAAA-AATTGGTTTA 2142
                         -   v ---------iv iv      iv       v   -  i vv vi 
  L1M4_orf2#LINE/    742 GATAAG---------GGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_145450946_   2143 ACTCCGTCA--------CAAATATCCCAACTCAAAACTGA-TAAATGATA 2183
                             vi v --------      v     i ?    v  i-i   v   v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_145450946_   2184 GGAATAGATGTGTTTCCCAAGAAGATACATGAACGGTCAATAATCCCATA 2233
                         v       ii v i   v         i ii  i  i      v v   i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_145450946_   2234 AAAATATACTCAACAGCATCACTCTT 2259
                             v  i       v  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (130 / 87)
Gap_init rate = 0.03 (23 / 903), avg. gap size = 3.39 (78 / 23)  


2565 25.37 6.31 2.64  chr1_145612856_145615606.rev     1390  2260 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_145612856_   1390 AAACACCTTACACCCATGAATTGGACGATTTGATATTGT---------AG 1430
                          i i i ii iiii    i      v  i  i       --------- i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_145612856_   1431 TACTTTACAATTTGAACTACAGATTTGATGAAATCCCTG-CAAGTATCCC 1479
                             iiv   v    v         ii i v       i-   i-     
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA-ATCCC 104

  chr1_145612856_   1480 AACAGACTTGTGTCTAGAAACTGACAAGCTGATTCTAAAATACACATGAA 1529
                          i v v   v v vi     i            i       v  i   i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_145612856_   1530 ATTGTAAGGGACTCAAAATAGCCAAAATAATCTTGAAGAAAGAAAACATA 1579
                          v  i       i  i           i         i  ii i    v 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_145612856_   1580 TTAGGATAATTCACAC--CCCATGCTCCAAACCTTACTGCAAAGTATCAG 1627
                         v v   vi i      --    -ii i    v      i     ivv   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_145612856_   1628 TAATCAAGACAACACAACATTGATG-AAGGAAAAATATATAGATTGATGG 1676
                                    iiiiiii i  iii-     v i i        ii    
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_145612856_   1677 AAGAGAATTGAGAGTCCATATATAAAACTATGTGTCTACAGTCAATGGAT 1726
                           v               v v     v i  iii i  ii      v   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_145612856_   1727 TCTTAA-AGTGGTGCCATGTGCAATTCAATGAGGAAGAGACAGTCTTTG- 1774
                          i ii - iv       v -i v        i    iii i       v-
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_145612856_   1775 AACACA-----CTGGGTCAACAACGTACACGTGGATCACCACTTGCAAAA 1819
                             v -----     ---     -------     v?    v       
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGG---ACAAC-------TGGATAKCCACATGCAAAA 442

  chr1_145612856_   1820 TAATAAATTAGAACCCTTACCCCAAAGCATACAAAAATATTAACTCAAA- 1868
                         v   i  v v i    i    i  v v    i v   v           -
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_145612856_   1869 TGAATTAAAGACACACATGCAAGAGGTA-----------------GAATA 1901
                           i  i ?    vi v   i     v  -----------------   v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_145612856_   1902 AAGCATATGGGAAAATCTTCAGGATTTTGGATCTAGCAAAGA---AATAG 1948
                           i    v ? v        iv  ii    i ivi    v i---vv   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_145612856_   1949 CTGTAACCCCAAAAACATGAGCAACAGAATAAAAATTAGATATTTAAAAT 1998
                         v i i  v      i  ii       i  v     v      vv vii i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_145612856_   1999 TTCTTAAAAATTAAAGACATCGGTGTTTCAGAGGACA--ACCAAGCAAGT 2046
                            v v         i  v iv   i    i      -- i    v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_145612856_   2047 CAAAAGGCAGCTC-CAAAATTGTGAGAAGATATTTGAAAAACACGTATCT 2095
                         v     i  i i -  i   v -     i       v   v  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGG-GAGAAAATATTTGCAAATCATATATCT 741

  chr1_145612856_   2096 -ATATGTCTGTATATATATATGTATCTTGAATATAGAAA-AATTGGTTTA 2143
                         -   v ---------iv iv      iv       v   -  i vv vi 
  L1M4_orf2#LINE/    742 GATAAG---------GGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_145612856_   2144 ACTCCGTCA--------CAAATATCCCAACTCAAAACTGA-TAAATGATA 2184
                             vi v --------      v     i ?    v  i-i   v   v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_145612856_   2185 GGAATAGATGTGTTTCCCAAGAAGATACATGAACGGTCAATAATCCCATA 2234
                         v       ii v i   v         i ii  i  i      v v   i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_145612856_   2235 AAAATATACTCAACAGCATCACTCTT 2260
                             v  i       v  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (130 / 87)
Gap_init rate = 0.03 (23 / 903), avg. gap size = 3.39 (78 / 23)  


3320 21.27 4.01 3.23  chr1_145677385_145680030.rev     1258  2155 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_145677385_   1258 AACGATATCCCCAAGTTTGTGGATTGGAAGA----ATATTGTTAAAATGT 1303
                           v        - v   ii            ----          i   v
  L1M4_orf2#LINE/      4 AAAGATATCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_145677385_   1304 CCATACTATCCAAAGTGATCTACAGATTCAATGCAATCCCTATCAAATTT 1353
                          v     vi     v                i               v i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_145677385_   1354 CCAAAGGCATTTTTTACAAAAATAGAAAACACAATTCTAAAATTTGTATT 1403
                            ivv  v      i  i    v  v  vvii  i        ii   v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_145677385_   1404 AAATCATAAAAGACCCTGAATAGCCAAAAGAATCTTGAGAAAGAAAAACA 1453
                         i  viii  ii     v            v        i      i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_145677385_   1454 AAGTAGAAGGTATCACACTACCTGATTTCAA--CTTATATTACAAAGTGA 1501
                             v i   vv       v  ii       --    i--       iv 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGCTA 250

  chr1_145677385_   1502 TAGTTATCAAAAC-GTATGGTACTGGCATAAAAGCAGACACATGGATCAA 1550
                         i   v     i  -  i              iiii     i  i      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_145677385_   1551 TGGAACTGAATACAGAGCCCAAAAATAAACCCAAACATATATTATGAGCT 1600
                              iv    vv    i   i           v    v   vi v ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_145677385_   1601 GATTTTTGACAAG--T-CCAATAAGATACAATAGGGAAAAGATGGTGTCT 1647
                               i      -- -    v vv  v    i      ii  i  v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_145677385_   1648 TCAATAAGTAGTGGTAAGAAAACTAGATATCTATATGCAAAAGAATGAAA 1697
                             i  i i   v ii  v    i    ? i i               i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_145677385_   1698 CTGGACCTGATGCCTATCTTACACATCATACATAAAAAGCAACTCAAA-T 1746
                         i      -----    i  i    --    i i     vi        - 
  L1M4_orf2#LINE/    451 TTGGACC-----CCTACCTCACAC--CATATACAAAAATTAACTCAAAAT 493

  chr1_145677385_   1747 AGATTAAATACCTAAC------ACCTGAAACCATAAAACTCCTAGAAGGA 1790
                         i   i ? v      v------ v  i    i         i      i 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_145677385_   1791 AATATAGGAGAAAAACTCCTTAATATCCTC---CTTGACAATGATTTTTT 1837
                           i     ? v   v  i v i ---   i---i v i     i   i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGA---CCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_145677385_   1838 GGATATCACACCAAAAGCTCAGGCAGCAAAAGCAAAAATAAGCAAGTGGG 1887
                         i     v           v  i   i      v       iii  i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_145677385_   1888 ACTACATCAAGCAAAT---AAGCTTCTG-----CATAG--CAATA--AAA 1925
                            v      ---   ---  i   i  -----  v  --  v  --  i
  L1M4_orf2#LINE/    641 ACTTCATCAA---AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_145677385_   1926 AAAACATGGGGTAAAAAGGTAGCACAGGGATTAGGGGAAAATATTGGCAA 1975
                            -------  i     ii i v  vi  v i  i         v    
  L1M4_orf2#LINE/    688 AAA-------GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_145677385_   1976 ACCACACATCTGATAAGGGGTTAAAATCCAAAACATATAAGGAACTCACA 2025
                          i  i i            ii viv     i  i      i      vi 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_145677385_   2026 CAACTCAGTAGCAAAAAAAAATCCCCAAATAACTGGATTTTAAAATAGGC 2075
                                i  ii     i ------        ivi   ?v     i   
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGA------CAAATAACCCAATTWAAAAATGGGC 824

  chr1_145677385_   2076 AA-GGACCTGAATAGCCATTTTTCCAAAGT---CACACAAATGGTCAAAT 2121
                           -   ii       v     i       v---i i        i   vv
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_145677385_   2122 GGTATATGAAAAGATGCTCAATATCATAATCATG 2155
                         i i i                i    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (121 / 66)
Gap_init rate = 0.02 (22 / 905), avg. gap size = 2.95 (65 / 22)  


2565 25.37 6.31 2.64  chr1_145791129_145793879     1388  2258 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_145791129_   1388 AAACACCTTACACCCATGAATTGGACGATTTGATATTGT---------AG 1428
                          i i i ii iiii    i      v  i  i       --------- i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_145791129_   1429 TACTTTACAATTTGAACTACAGATTTGATGAAATCCCTG-CAAGTATCCC 1477
                             iiv   v    v         ii i v       i-   i-     
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA-ATCCC 104

  chr1_145791129_   1478 AACAGACTTGTGTCTAGAAACTGACAAGCTGATTCTAAAATACACATGAA 1527
                          i v v   v v vi     i            i       v  i   i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_145791129_   1528 ATTGTAAGGGACTCAAAATAGCCAAAATAATCTTGAAGAAAGAAAACATA 1577
                          v  i       i  i           i         i  ii i    v 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_145791129_   1578 TTAGGATAATTCACAC--CCCATGCTCCAAACCTTACTGCAAAGTATCAG 1625
                         v v   vi i      --    -ii i    v      i     ivv   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_145791129_   1626 TAATCAAGACAACACAACATTGATG-AAGGAAAAATATATAGATTGATGG 1674
                                    iiiiiii i  iii-     v i i        ii    
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_145791129_   1675 AAGAGAATTGAGAGTCCATATATAAAACTATGTGTCTACAGTCAATGGAT 1724
                           v               v v     v i  iii i  ii      v   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_145791129_   1725 TCTTAA-AGTGGTGCCATGTGCAATTCAATGAGGAAGAGACAGTCTTTG- 1772
                          i ii - iv       v -i v        i    iii i       v-
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_145791129_   1773 AACACA-----CTGGGTCAACAACGTACACGTGGATCACCACTTGCAAAA 1817
                             v -----     ---     -------     v?    v       
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGG---ACAAC-------TGGATAKCCACATGCAAAA 442

  chr1_145791129_   1818 TAATAAATTAGAACCCTTACCCCAAAGCATACAAAAATATTAACTCAAA- 1866
                         v   i  v v i    i    i  v v    i v   v           -
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_145791129_   1867 TGAATTAAAGACACACATGCAAGAGGTA-----------------GAATA 1899
                           i  i ?    vi v   i     v  -----------------   v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_145791129_   1900 AAGCATATGGGAAAATCTTCAGGATTTTGGATCTAGCAAAGA---AATAG 1946
                           i    v ? v        iv  ii    i ivi    v i---vv   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_145791129_   1947 CTGTAACCCCAAAAACATGAGCAACAGAATAAAAATTAGATATTTAAAAT 1996
                         v i i  v      i  ii       i  v     v      vv vii i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_145791129_   1997 TTCTTAAAAATTAAAGACATCGGTGTTTCAGAGGACA--ACCAAGCAAGT 2044
                            v v         i  v iv   i    i      -- i    v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_145791129_   2045 CAAAAGGCAGCTC-CAAAATTGTGAGAAGATATTTGAAAAACACGTATCT 2093
                         v     i  i i -  i   v -     i       v   v  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGG-GAGAAAATATTTGCAAATCATATATCT 741

  chr1_145791129_   2094 -ATATGTCTGTATATATATATGTATCTTGAATATAGAAA-AATTGGTTTA 2141
                         -   v ---------iv iv      iv       v   -  i vv vi 
  L1M4_orf2#LINE/    742 GATAAG---------GGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_145791129_   2142 ACTCCGTCA--------CAAATATCCCAACTCAAAACTGA-TAAATGATA 2182
                             vi v --------      v     i ?    v  i-i   v   v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_145791129_   2183 GGAATAGATGTGTTTCCCAAGAAGATACATGAACGGTCAATAATCCCATA 2232
                         v       ii v i   v         i ii  i  i      v v   i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_145791129_   2233 AAAATATACTCAACAGCATCACTCTT 2258
                             v  i       v  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (130 / 87)
Gap_init rate = 0.03 (23 / 903), avg. gap size = 3.39 (78 / 23)  


3189 27.53 0.44 0.44  chr1_145832612_145838885.rev     4876  5783 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_145832612_   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4925
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_145832612_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_145832612_   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_145832612_   5024 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_145832612_   5074 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGC 5123
                                i      vv       v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_145832612_   5124 TACAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGATATAGATC 5173
                                 i   i    ii           iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_145832612_   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCTTACCTACAACT 5221
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_145832612_   5222 ATCTGATCTTTGACAAACCTGAGAAAAACAAACAATGGGGAAAGGATTCC 5271
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_145832612_   5272 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5321
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_145832612_   5322 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5371
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_145832612_   5372 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5421
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_145832612_   5422 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5471
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_145832612_   5472 AACACCAAAAGCAACGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5521
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_145832612_   5522 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5571
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_145832612_   5572 AGGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5621
                           i     i   iv            v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_145832612_   5622 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5671
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_145832612_   5672 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5721
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_145832612_   5722 TCAAAAGAAGACATTTATGCAGTCAAAAAACACATGAAAAAATGCTCGTC 5771
                           v        i  vi viii i   v  i          i      iv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_145832612_   5772 ATCACTGGCCAT 5783
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3088 26.08 1.55 1.22  chr1_145851766_145858180.rev     5020  5924 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_145851766_   5020 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5069
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_145851766_   5070 GGCCATACTACCCAAGGTAATTTATAGATTCATTGCTATCCCCATCAAGC 5119
                            v     v     iv i  i  i       vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_145851766_   5120 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAAAATACTTTAAACTTC 5167
                          v   -   v    i  -i     -   iv  ivvi  v  --   v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCT--AAAATTC 147

  chr1_145851766_   5168 ATATGGA--TCCAAAAAAGAGCTCCCA---TAGCCAAGACAATCCTAAGC 5212
                                -- v   iii -----    ---       i      i i iv
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-----CCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_145851766_   5213 CAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTA 5262
                         v i          i      vv   ii  v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_145851766_   5263 CAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATA 5312
                            i          i   i    ii         i iv ii i   v   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_145851766_   5313 TAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCT 5360
                             i        i    i--    i  --        vv   i    i 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTT 340

  chr1_145851766_   5361 ACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAG 5410
                          iiii  vi    i  i     ivv  v   i v  vv            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_145851766_   5411 GATTCCCTATTTAATGAATGGTGCTGGGGAAACTGGATAGCCATATGTAG 5460
                         i  vvi  v  i  ii            iv         ?   i   i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_145851766_   5461 AAAGCTGAAACTGGATACCTTCCTTACACCTTACACAAAAATTAACTGAA 5510
                           iiv    ii    iv   v   i     v  i             v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_145851766_   5511 GGTGGATTAAAGACTTAAATGTAAGATGTAACACCATAAAAACCCTAGAA 5560
                         ii     i ?    i           vv   v  i      vi i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_145851766_   5561 GAAAACCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAAGACTTCA 5609
                               v    ?i- v i -   iv   viv  vv i     v ii   v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_145851766_   5610 TGATTAAAACACCAAAAGCAATGGCAACGAAAGTCAAAATAGACAAATGG 5659
                          iiv  vi            vvi     i    vv        i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_145851766_   5660 GATCCAATTAAACTAAAGAGATTCTGCACAGCAAAAGAAACTGTCATCAG 5709
                           iiiv  i   v v  i iv  i  ii vv    i  v   i   vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_145851766_   5710 AGTGAACAGGCAACCTACGGAATGGGAGAAAATTTTTGCAATCTATCCAT 5759
                               v  i     i  i              v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_145851766_   5760 CTGACAAAGGGCTAATATCCAGCATCTAGAAAGAACTTAAACAAATTTAG 5809
                             i  i  i  vi       v  v  v        ivv    v iv v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_145851766_   5810 AAGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAG 5855
                           v     i    ----   v  i?    i            v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_145851766_   5856 ACACTTCTCAAAAGAAGACACTTATGCAGCCAACAGACATAGGAAAAAAG 5905
                            i     v        i ivi viii     i ii  i v     i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_145851766_   5906 GCTCATCATCACTGGTCAT 5924
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.08 (25 / 12)  


1937 25.99 3.38 2.79  chr1_145905874_145907551      505  1185 (492)    L1M4_orf2#LINE/L1      224   908 (0)  

  chr1_145905874_    505 CCAACTTCAGGGCTTA-TATTAAGCTACAGTAGCCCAAATAGGGTGAAGT 553
                             i    iii    -  iv           ii v i i  v   ivii
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_145905874_    554 TGGTGAAAAGAGAAAACACACACAAATAGATCCATGGAAAAGAATACAGA 603
                            iiv  i  v i -------  v       v      v     vv   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGA-------CATATAGATCAATGGAATAGAATTGAGA 316

  chr1_145905874_    604 GCCCAGAAACAGACCTACACAC----AGTCCACTGATCTTCCATGAAGGT 649
                          i       i i   i i   i----i   v i    i   v ii i   
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_145905874_    650 TTAGAGACAATTTAAAACAGCAAAGATAGCCTTTCCAACTAGTGGTGCTA 699
                         vivi    v   i  vivi v  ii    i    i    v i       i
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_145905874_    700 GAACAGCTGGACAACCACATGCAAATGTATATAGATAGATAGATCCAGGT 749
                          i   i     i ?           v v  ---  -  v i  i  vvii
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAAT---GA-AGTTGGACCCCTAC 462

  chr1_145905874_    750 GTGCATGTTCTACCC-----TTTAT--AAAATAAATCTTACATGTAAATG 792
                         v -  iiiiv  iv -----  v i--     ii   v? v iv      
  L1M4_orf2#LINE/    463 CT-CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_145905874_    793 TAAGGTGC-AAAACCATAAGAATCCTAGGAGATAACATAGGAGAAAAATC 841
                             i-  -     i    i v  i   i   v        ? v   -  
  L1M4_orf2#LINE/    512 TAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TC 559

  chr1_145905874_    842 TCGGGGATCTTGGGTTCGATGATGGCTTCTTAGATACAAAACCAAAAGCA 891
                          iv v  i        v iii    i          ii v          
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_145905874_    892 CAATCTACTAATGAAAAAA-AATTAAGTTGAGCCTCATTAAAATTAAAAA 940
                            v v  v  v       - iv   i   ii i    i           
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_145905874_    941 CTTCTGCTCTGTGAAAGACACTGTTAAGAGAATGGAAAAAGCAAGTCACA 990
                            i  iv  vii  i      i i    i i  i   i -   vi    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA-CAACCCACA 708

  chr1_145905874_    991 GACTGGCAGAAAATATTTACAAA--ATA-ATCTGATGGAAAAACTGCTGT 1037
                           v   v           i    --   -       i- iii   vv i 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATA-AGGGACTTGTAT 757

  chr1_145905874_   1038 CCAAAATATATGAAGAATTCTGAGAACTAAACAACACAAAGCAAAAAAAA 1087
                            i       i     i   v v    v  i  i v    - v   v  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG-ACAAATAA 806

  chr1_145905874_   1088 AAAAAAAAAAAAGTAGGTGAAAGATCTGAA----CACCTCATTCA--TAA 1131
                         vvv  vv?    i i  ii  i   i    ----  ii  - i  --v  
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC-TCCAAAGAA 855

  chr1_145905874_   1132 GATATACAGATGGCAAATAAGCATATGAAAAAGATGCTCAAAATCATTTG 1181
                                 i     v        i       -         v    ????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZ 904

  chr1_145905874_   1182 TCGT 1185
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.66 (108 / 65)
Gap_init rate = 0.03 (21 / 685), avg. gap size = 2.00 (42 / 21)  


 324 32.30 3.11 1.24  chr1_145931347_145933335      500   660 (1329)    L1M4_orf2#LINE/L1      193   356 (552)  

  chr1_145931347_    500 AAAAAGAACAAAACCAGAGGACTTGCACAACCTGACATTCAGACTCACT- 548
                           i         iiii       ii   vv  ii iv iv i   i   -
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_145931347_    549 CTAAGCTGTTATAAACAAGGCAGTATGCAAGCGGCATTGGAAGACACAAA 598
                          v     iivi   v    i    i  vv vi     vi i v v   v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_145931347_    599 TACATCAACAGACT-GACTTGGGAGATCTGAAACTGACC---ACAGCTGT 644
                           v     ii  v -  v   i   vi v    ivi   ---   -- v 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA--TTT 340

  chr1_145931347_    645 AAGGTCCATAGGTTTT 660
                          v    v  v i    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTT 356

Transitions / transversions = 1.17 (28 / 24)
Gap_init rate = 0.02 (4 / 164), avg. gap size = 1.75 (7 / 4)  

 626 26.73 9.48 8.46  chr1_145931347_145933335      913  1503 (486)    L1M4_orf2#LINE/L1      312   908 (0)  

  chr1_145931347_    913 TGGGATTACAGGCATGAACC---AC---CATGACCAGTCACAGGTTTTCA 956
                           i  v v   iv  i    ---  ---i   ii  i i--- i     i
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT---GATTTTCG 358

  chr1_145931347_    957 ATAAAAG---CAG-----TTCAATGGGGCAAAGGAAATAGT---TTCAAT 995
                          i  ii ---  i-----          -    --      ---     i
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGG-AAAG--AATAGTCTTTTCAAC 405

  chr1_145931347_    996 TAATTG-ACTTTCACAAA-GAAGA---AAGGGGAGATGAACAAGGTT--A 1038
                         v   v -i  vvv    v- i v --- viv v i v   ii i   -- 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_145931347_   1039 TTTCTCCCTCACACTACACTTGAAAGT-AACTTGAGGCACATTATAGACC 1087
                         iii  v        i i ivii   i -    ii iiiiv  i ?     
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_145931347_   1088 AAAACTTAAAAGCTAAAGATATAAAGCATTT-----------CAAGGATA 1126
                         v   iv   i       iv      i vi  -----------i i ?i  
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_145931347_   1127 ---CTTTGTGACTTGTTGG--TAGACAGAGATTTATTAAACAGGGCACAG 1171
                         ---   i     i --   --   i  iv i   v   i i v i   vi
  L1M4_orf2#LINE/    556 AATCTTCGTGACCT--TGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_145931347_   1172 AAAAAAAATGTA-TAAAGGAAAGACTTGATAAATTAGACTTCATCAATAT 1220
                            iv v v i -i   i    i v v        i           v  
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_145931347_   1221 TAGCCATATCTTCT---CATCAAAAGATGCCACAAAGAACTTGAAAAAAT 1267
                           --- v v   i --- v     i  ii i iv     vv      i i
  L1M4_orf2#LINE/    654 TA---AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_145931347_   1268 GAATCAGCCTCAG----GGAGAAAATAGTCACAAA--ACCTATCTGACCC 1311
                         i vi  ----   ----          v ii    -- iv       i--
  L1M4_orf2#LINE/    701 AACCCA----CAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT-- 744

  chr1_145931347_   1312 CCAAAC--CCTGTAACTATAATGTATGGTGAGATCTTCTTACCTGGTAAC 1359
                         --  iv-- i    v i v   i   ii--   v  -     -----   
  L1M4_orf2#LINE/    745 --AAGGGACTTGTATCCAGAATATATAA--AGAACT-CTTAC-----AAC 784

  chr1_145931347_   1360 GAAAACAACAACAACAAAACAAAAACAAAAAATAATCAACCCAAGTATGC 1409
                         v-------   i  i    --- i     -------i       v ?---
  L1M4_orf2#LINE/    785 T-------CAATAATAAAA---AGACAAA-------TAACCCAATTW--- 814

  chr1_145931347_   1410 TAGAA--GGGTAAAAGACTTGAACAGATACATAAGAATAAAAGGTACACA 1457
                         - i  --   i   i  i     i   i iv vvvv v i   i  i   
  L1M4_orf2#LINE/    815 -AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_145931347_   1458 CATGGTCAATAAAGCACAT-ACAATATGTTTAGTTATCAGGAAAATG 1503
                         v    i      -      - v  v   i i ii-    ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAA-GCACATGAAAAGATGCTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (100 / 55)
Gap_init rate = 0.06 (36 / 597), avg. gap size = 2.94 (106 / 36)  


 623 24.18 0.65 0.65  chr1_146080018_146085558     3854  4006 (1535)    L1M4_orf2#LINE/L1        1   153 (755)  

  chr1_146080018_   3854 TGGGAAAACATTCCATGCTTGTGGACTGGAAGAATCAATATTGTTAAAAT 3903
                            i  i i  i     i ii    i       v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_146080018_   3904 GACCATTCTATCCAAAGCAATCTAAAGATTCAACGCAATTCCTATCAAGT 3953
                          i v  v  vi     vii     v              i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_146080018_   3954 TACCAA-TGTCATTTTTTACAGAATTTAAAAAAAAAATTATAAAATTCTT 4002
                          v   i-  i -      i     v  i v  ivvi  iv        v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_146080018_   4003 ATGG 4006
                             
  L1M4_orf2#LINE/    150 ATGG 153

Transitions / transversions = 1.64 (23 / 14)
Gap_init rate = 0.01 (2 / 153), avg. gap size = 1.00 (2 / 2)  

2555 24.03 3.62 0.54  chr1_146080018_146085558     4304  5048 (493)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_146080018_   4304 AAAATCCCCATGGAACCAAAAAACGGCCCA-AATAGTCAAG-CAATCCAA 4351
                              i vi      viiv  ii- i    -     i   i-     ivi
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTG 189

  chr1_146080018_   4352 AGCAAAAAGAACAAATCCAGAGGCATCACATTACCTAACTTCAAACTATA 4401
                          iv  i         viii    vv     i v  i  i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_146080018_   4402 CTACAAGGCTATAGCAACAAAAACAGCAAGGTACCGACACAAAAATAGAC 4451
                               i    i  i  iv  i    iiv     i i  i  ii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_146080018_   4452 ACATGAATCAATGGATAAGAATAGAGAACCCAGAAATAAAGTCACACACC 4501
                          i  ii         vv     v    ii           vi  i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_146080018_   4502 TACAACCAACTGATCTTTAACAAAGTTGACAAAAATAAACAATGAGGAAA 4551
                           iiii   i    i  ii    i v  v   i vi vv     i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_146080018_   4552 ATGATACCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAAATGC 4601
                         i-i   vi  v  i  i              v      v  ?   v    
  L1M4_orf2#LINE/    390 G-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_146080018_   4602 AGAAGAATGAAACTGGACCCCTACCTCCCACCATATACAAAAATTAATTC 4651
                          i         ii              v                   i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_146080018_   4652 AGA-TGGTTTACAGACTTAAATATAGGACGTCAAACTATAAAAATGCTAG 4700
                          i -   v i ?    i     i  i  vv v           v vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_146080018_   4701 AAGAAAACCTAGGAAAACCTCTTCTTGACATTGGCCTA-----TGACT-- 4743
                                 v    ?iv vv     v    v    vi  -----  ii --
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_146080018_   4744 ------AAGACCTCAAAAGCAAATGCAACAAAAACGAAAATTGACAAATG 4787
                         ------ v   vi        v v         ivi     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_146080018_   4788 GGACTT----AAACTTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAAC 4833
                               ----   v       -   i  ii vv    i  v iv     v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_146080018_   4834 AGAGTAAACAGACAACCTACAGAATGGGAGAAAATATTTGAAAACTATGC 4883
                          i   i  v        i                      v   ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_146080018_   4884 ACCTGACAAAGGACTAATATCCAGACTCTATAAGGAACTT----AAATCA 4929
                          i    i  i     vi        v v     i     i----  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_146080018_   4930 ACAAGACAAAACCAAATAACCCTATTTAAAAAATGGGCAAAGGACATGGC 4979
                          i  v v   iv          v   ?     -           iv  iv
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chr1_146080018_   4980 TAGACACTTATCAAAAGAACACATACAAGCGGCCAACAAACATATGAAAA 5029
                               i  v  v      v i      ii      i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_146080018_   5030 AATGC---ACATCACTAATCAT 5048
                         i    ---      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (106 / 69)
Gap_init rate = 0.02 (12 / 768), avg. gap size = 2.58 (31 / 12)  


1719 28.28 6.03 1.85  chr1_146143944_146145582.rev      502  1148 (491)    L1M4_orf2#LINE/L1      235   908 (0)  

  chr1_146143944_    502 ACTTACTATTAAGCTGTTTATTACTATAAACAAAACAGTGTGAATGTGGC 551
                                 iv     -------  vi   v   i        ivvv    
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCT-------ACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_146143944_    552 AAAAGGATACACATATTGATAAATGAAACTGAAGTGAGACACCTAAAACA 601
                          v       v      v   v    i  iv   v     vv  vi   i 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_146143944_    602 GATCCTTGT-TATATGGTCAATTGATTTTTTTTTCAAAAAAGGTACTAAA 650
                         i i  v ii- v                 ----- i v  i   i i  i
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTT-----CGACAAGGGTGCCAAG 372

  chr1_146143944_    651 GTAATACAATGGGGAAGAAGT-GTCATTTCAACGAGTAGTGCTGGACCAA 699
                         iiv  v          ii i -   v       i i i       iv   
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_146143944_    700 CTAGATATCTACTAGTGAGGAAAAAAATCTCAATCCCTACCTCACAACAT 749
                           i    ? i  vv ii iii  vi  vi vi i            v   
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_146143944_    750 ACACAAAAGCTAATTTGAGTTGGATCACAGAACAAACCATA----C--AA 793
                          i      ii   i ii iv       ?   v v  vii  ---- --  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_146143944_    794 ACTATGAAGTT-TTAGAAGAAAATGCATGAAAATGTCTTTAAGACTTGGC 842
                              i  ii -           iii v ?iv vi    iiv   i v v
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_146143944_    843 AGAAAGCAAATATTTTCTAAATATTACACAGAGAA-ATAAATAA-AACAG 890
                         ivv i    vvi   ii  i    v    vi i i- i  ii  -  v  
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_146143944_    891 AAAAA-T-GATAAATTAGGCTTTGTTGATATGAAATATGTCTTTTCATCC 938
                              - -        i i   ii ii v  v   v iv i v v v  v
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_146143944_    939 AAAGACACCATTAAGTAACTGAAAAGGCAAGCCATGGACGAGGAGAAAAT 988
                           i     i  i   v  v       i   v   ii  vvi         
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_146143944_    989 ATTCACAA--CACATATTTGACCAAGAACCTGTATCCAGAGTATACAATT 1036
                            ii   --  i    i   iv i i  i          i    i  vv
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_146143944_   1037 AGCTCCTACA-CCCATT----------------------TTTAAAAATGG 1063
                          i   i    - i  v ----------------------  ?        
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_146143944_   1064 GCAAAAG-CTTAAACAGACATTTCAGAGAAGAAAATATACTAGTGGCCAG 1112
                              i -i  i  i         vvvi     i      v i      i
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_146143944_   1113 TCAGTTCATAAAAGAGTGCTCAATATCATTAGTTGT 1148
                          v  iv   i   iii       i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (111 / 68)
Gap_init rate = 0.02 (15 / 674), avg. gap size = 3.40 (51 / 15)  


1254 30.34 10.55 2.28  chr1_146171908_146173952      719  1552 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_146171908_    719 AGATACATTAAGTTTATGGTTTAGAAGACTCAATGTCATTAAG-TACAAA 767
                              ivii v   i    v  i       i   i ii     - ivv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_146171908_    768 TTTTCTTCAAATTTGTTTACATATTCAATGTAA-----ATCTAAATCCCA 812
                          vi  ii      vi i    v      i i  -----   v        
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_146171908_    813 ACAAATAC------TA-AGAAAGCTGACAACTTGATTC---AATGTGTAC 852
                         i --- i ------ i-     -i      vi    i ---   vii  i
  L1M4_orf2#LINE/    106 GC---TGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_146171908_    853 ATTAATGAGCAAAAATCCAAGAATAACTATGAAAATCCTGA----GATGA 898
                         ivv    --   iiiv  v      i i vi v    i   ----  v  
  L1M4_orf2#LINE/    152 GGAAATG--CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_146171908_    899 TTAA----GGAG-ATGTGCACTACCATATATAAGGATGTATTATAAAGCT 943
                         vi  ----    - ivii    v  vv  v v ii iv  i  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_146171908_    944 ATAATA-TTAAGACAATGTGGTATTGAGACAAAGATAAGCAAATTGCT-G 991
                          i i  - i      i       i  iv i  i    ii  v  v v -i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_146171908_    992 GTCAAATAGC-CTAAGC-TCTAAAAACA----CATATAT--ATGA--AAC 1031
                         i vi     v-i i  v-  i i   i ----    i  --   i--  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_146171908_   1032 T---TTGTGATAGAATTGTCA-GTTCATATCAAAAACAGGATGATTAGGT 1077
                          ---  vi  i iiiv  i  - vi   -    vii-i i v  v   - 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGG-GGAAAGAATAG-T 396

  chr1_146171908_   1078 CTTTT----AAATGGTACTGACACAACTGCTTATACACAAGGGAAAAAAA 1123
                              ----       i   iv       vv  ?v    -v v    i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGAA 445

  chr1_146171908_   1124 AGAAATTAGATACCTGCTTCACATCACCTACAGACATGGACTTAA----- 1168
                         v   i  i  iv   i i     i  iv    i v  vi   i  -----
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_146171908_   1169 ------GACTTAATTGTAAAAGGCAAAACTTTAATACTTTTAGAAGAAAA 1212
                         ------   i   v     i  vi      v   v   i           
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_146171908_   1213 TA-------------------CTTTGGAATCAGCAAAGATTTCATAAGCA 1243
                         i ------------------- i    iv vi    v i    v  iii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_146171908_   1244 AGACA---AAAATACTAATCATAAAATAAAATACTGACAAATTAAACCTC 1290
                         v    ---   ii  v iiv i    v    v iv  i     ii  i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_146171908_   1291 ATCAAAATTAAGAACTTTTGTACATGAAAAGACAACATAAAGAAAGTCAG 1340
                                    i         i v v   i    vi  v        v i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_146171908_   1341 GAAATGAGTTGCCAATCAGAAAAAAATAATTTCAA--CAGAAGTAAGCCA 1388
                         i i ii viii vi vii i i      v  v   --  v vi vv -- 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG--A 743

  chr1_146171908_   1389 TGAGGG-TTTGTATCAGACTAAATTTTTAAA---CCTTTATAAACCAATA 1434
                          i    -i       --- vi   v v    --- ii   i  vi     
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATC---CAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_146171908_   1435 AGAGATAGACAAAAGTGCACACTATGAACAAAAT----AAAAGCCACAAA 1480
                          v i v       -- i-  v v  v? -     ----   i vivii  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAA--TA-ACCCAATTWA-AAAATGGGCAAAGGATTTGAA 836

  chr1_146171908_   1481 CAGATATTTCATGGAAGAAACTGCATAAATGGTAAATTAACATATGAAAA 1530
                         i   i     vivi     iv ii i      iv   v i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_146171908_   1531 AGGACTCAACCTCATCAGTAAT 1552
                         iivi      v   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (155 / 96)
Gap_init rate = 0.04 (37 / 903), avg. gap size = 2.89 (107 / 37)  


 623 24.18 0.65 0.65  chr1_146499033_146504561     3848  4000 (1529)    L1M4_orf2#LINE/L1        1   153 (755)  

  chr1_146499033_   3848 TGGGAAAACATTCCATGCTTGTGGACTGGAAGAATCAATATTGTTAAAAT 3897
                            i  i i  i     i ii    i       v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_146499033_   3898 GACCATTCTATCCAAAGCAATCTAAAGATTCAACGCAATTCCTATCAAGT 3947
                          i v  v  vi     vii     v              i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_146499033_   3948 TACCAA-TGTCATTTTTTACAGAATTTAAAAAAAAAATTATAAAATTCTT 3996
                          v   i-  i -      i     v  i v  ivvi  iv        v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_146499033_   3997 ATGG 4000
                             
  L1M4_orf2#LINE/    150 ATGG 153

Transitions / transversions = 1.64 (23 / 14)
Gap_init rate = 0.01 (2 / 153), avg. gap size = 1.00 (2 / 2)  

2533 23.95 4.47 0.54  chr1_146499033_146504561     4298  5036 (493)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_146499033_   4298 AAAATCCCCATGGAAC--CAAAAAACAGCCCGAATAGTCAAG-CAATCCA 4344
                              i vi      v--   iii  --  v      i   i-     iv
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTT 188

  chr1_146499033_   4345 AAGCAAAAAGAACAAATCCAGAGGCATCACATTACCTAACTTCAAACTAT 4394
                         i iv  i         viii    vv     i v  i  i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_146499033_   4395 ACTACAAGGCTATAGCAACAAAAACAGCAAGGTACCGACACAAAAATAGA 4444
                                i    i  i  iv  i    iiv     i i  i  ii     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_146499033_   4445 CACATGAATCAATGGATAAGAATAGAGAACCCAGAAATAAAGTCACACAC 4494
                           i  ii         vv     v    ii           vi  i   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_146499033_   4495 CTACAACTAACTGATCTTTAACAAAGTTGACAAAAATAAACAATGAGGAA 4544
                         i  iiiii  i    i  ii    i v  v   i vi vv     i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_146499033_   4545 AATGATACCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAAATG 4594
                          i-i   vi  v  i  i              v      v  ?   v   
  L1M4_orf2#LINE/    389 AG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_146499033_   4595 CAGAAGAATGAAACTGGACCCCTACCTCCCACCATATACAAAAATTAATT 4644
                           i         ii              v                   i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_146499033_   4645 CAGA-TGGTTTACAGACTTAAATATAGGACGTCAAACTATAAAAATGCTA 4693
                           i -   v i ?    i     i  i  vv v           v vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_146499033_   4694 GAAGAAAACCTAGGAAAACCTCTTCTTGACATTGGCTTA-----TGACT- 4737
                                  v    ?iv vv     v    v    v   -----  ii -
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_146499033_   4738 -------AAGACCTCAAAAGCAAATGCAACAAAAATGAAAATTGACAAAT 4780
                         ------- v   vi        v v         ivi     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_146499033_   4781 GGGACTT----AAAA-----AGCTTCTGCACAGCAAAAGAAATAATCAAC 4821
                         v      ----    ----- i   i  ii vv    i  v iv     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_146499033_   4822 AGAGTAAACAGACAACCTACAGAATGGGAGAAAATATTTGAAAACTATGC 4871
                          i   i  v        i                      v   ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_146499033_   4872 ACCTGACAAAGGACTAATATCCAGACTCTATAAGGAACTT----AAATCA 4917
                          i    i  i     vi        v v     i     i----  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_146499033_   4918 ACAAGACAAAACCAAATAACCCTATTTAAAAAATGGGCAAAGGACATGGC 4967
                          i  v v   iv          v   ?     -           iv  iv
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chr1_146499033_   4968 TAGACACTTATCAAAAGAACACATACAAGCGGCCAACAAACATATGAAAA 5017
                               i  v  v      v i      ii      i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_146499033_   5018 AATGC---ACATCACTAATCAT 5036
                         i    ---      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (105 / 68)
Gap_init rate = 0.02 (12 / 768), avg. gap size = 3.08 (37 / 12)  


1880 28.17 2.53 2.09  chr1_146529446_146531108.rev      502  1172 (491)    L1M4_orf2#LINE/L1      235   908 (0)  

  chr1_146529446_    502 ACTTACTATTAAGCTGTTTATTACTATAAACAAAACAGTGTGAATGTGGC 551
                                 iv     -------  vi   v   i        ivvv    
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCT-------ACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_146529446_    552 AAAAGGATACACATATTGATAAATGAAACTGAAGTGAGACACCTAAAACA 601
                          v       v      v   v    i  iv   v     vv  vi   i 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_146529446_    602 GATCCTTGT-TATATGGTCAATTGATTTTTTTTTTCAAAAAAGGTACTAA 650
                         i i  v ii- v                 ------ i v  i   i i  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTT------CGACAAGGGTGCCAA 371

  chr1_146529446_    651 AGCAATACAATGGGGAAGAAGT-GTCATTTCAACGAGTAGTGCTGGACCA 699
                         ii v  v          ii i -   v       i i i       iv  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_146529446_    700 ACTAGATATCTACTAGTGAGGAAAAAAATCTCAATCCCTACCTCACAACA 749
                            i    ? i  vv ii iii  vi  vi vi i            v  
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_146529446_    750 TACACAAAAGCTAATTTGAGTTGGATCACAGAACAAACCATA----C--A 793
                           i      ii   i ii iv       ?   v v  vii  ---- -- 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_146529446_    794 AACTATGAAGTT-TTAGAAGAAAATGCATGAAAATGTCTTTAAGACTTGG 842
                               i  ii -           iii v ?iv vi    iiv   i v 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_146529446_    843 CAGAAAGCAAATATTTTCTAAATATTACACAGAGAA-ATAAATAA-AACA 890
                         vivv i    vvi   ii  i    v    vi i i- i  ii  -  v 
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_146529446_    891 GAAAAA-T-GATAAATTAGGCTTTGTTGATATGAAATATGTCTTTTCATC 938
                               - -        i i   ii ii v  v   v iv i v v v  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_146529446_    939 CAAAGACACCATTAAGTAACTGAAAAGGCAAGCCATGGACGAGGAGAAAA 988
                         v  i     i  i   v  v       i   v   ii  vvi        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_146529446_    989 TATTCACAA--CACATATTTGACCAAGAACCTGTATCCAGAGTATACAAT 1036
                             ii   --  i    i   iv i i  i          i    i  v
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_146529446_   1037 TAGCTCCTACAATTCAGTATTAGAAATGGAAACA-CCCATTTTTAAAAAT 1085
                         v i   i     i   i  v  i   viv   i -    v  ?-      
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAAT 820

  chr1_146529446_   1086 GGGCAAAAG-CTTAAACAGACATTTCAGAGAAGAAAATATACTAGTGGCC 1134
                                i -i  i  i         vvvi     i      v i     
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_146529446_   1135 AGTCAGTTCATAAAAGAGTGCTCAATATCATTAGTTGT 1172
                          i v  iv   i   iii       i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (114 / 71)
Gap_init rate = 0.02 (15 / 674), avg. gap size = 2.07 (31 / 15)  


1284 30.35 10.16 2.27  chr1_146556839_146558906      739  1575 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_146556839_    739 AGATACATTAAGTTTATGGTTTAGAAGACTCAATGTCATTAAG-TACAAA 787
                              ivii v   i    v  i       i   i ii     - ivv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_146556839_    788 TTTTCTTCAAATTTGTTTACATATTCAATGTAAATC--ATCTAAATCCCA 835
                          vi  ii      vi i    v      i i  vi --   v        
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_146556839_    836 ACAAATAC------TA-AGAAAGCTGACAACTTGATTC---AATGTGTAC 875
                         i --- i ------ i-     -i      vi    i ---   vii  i
  L1M4_orf2#LINE/    106 GC---TGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_146556839_    876 ATTAATGAGCAAAAATCCAAGAATAACTATGAAAATCCTGA----GATGA 921
                         ivv    --   iiiv  v      i i vi v    i   ----  v  
  L1M4_orf2#LINE/    152 GGAAATG--CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_146556839_    922 TTAA----GGAG-ATGTGCACTACCATATATAAGGATGTATTATAAAGCT 966
                         vi  ----    - ivii    v  vv  v v ii iv  i  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_146556839_    967 ATAATA-TTAAGACAATGTGGTATTGAGACAAAGATAAGCAAATTGCT-G 1014
                          i i  - i      i       i  iv i  i    ii  v  v v -i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_146556839_   1015 GTCAAATAGC-CTAAGC-TCTAAAAACA----CATATAT--ATGA--AAC 1054
                         i vi     v-i i  v-  i i   i ----    i  --   i--  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_146556839_   1055 T---TTGTGATAGAATTGTCA-GTTCATATCAAAAACAGGATGATTAGGT 1100
                          ---  vi  i iiiv  i  - vi   -    vii-i i v  v   - 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGG-GGAAAGAATAG-T 396

  chr1_146556839_   1101 CTTTT----AAATGGTACTGACACAACTGCTTATACACAAGGGAAAAAAA 1146
                              ----       i   iv       vv  ?v    -v v    i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGAA 445

  chr1_146556839_   1147 AGAAATTAGATACCTGCTTCACATCACCTACAGACATGGACTTAA----- 1191
                         v   i  i  iv   i i     i  iv    i v  vi   i  -----
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_146556839_   1192 ------GACTTAATTGTAAAAGGCAAAACTTTAATACTTTTAGAAGAAAA 1235
                         ------   i   v     i  vi      v   v   i           
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_146556839_   1236 TA-------------------CTTTGGAATCAGCAAAGATTTCATAAGCA 1266
                         i ------------------- i    iv vi    v i    v  iii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_146556839_   1267 AGACA---AAAATACTAATCATAAAATAAAATACTGACAAATTAAACCTC 1313
                         v    ---   ii  v iiv i    v    v iv  i     ii  i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_146556839_   1314 ATCAAAATTAAGAACTTTTGTACATGAAAAGACAACATAAAGAAAGTCAG 1363
                                    i         i v v   i    vi  v        v i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_146556839_   1364 GAAATGAGTTGCCAATCAGAAAAAAATAATTTCAA--CAGAAGTAAGCCA 1411
                         i i ii viii vi vii i i      v  v   --  v vi vv -- 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG--A 743

  chr1_146556839_   1412 TGAGGG-TTTGTATCAGACTAAATTTTTAAA---CCTTTATAAACCAATA 1457
                          i    -i       --- vi   v v    --- ii   i  vi     
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATC---CAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_146556839_   1458 AGAAATAGACAAAAGTGCCCACTATGAACAAAAT----AAAAGCCACAAA 1503
                          v   v       vi-i    --  v? -     ----   i vivii  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATA-ACCCA--ATTWA-AAAATGGGCAAAGGATTTGAA 836

  chr1_146556839_   1504 CAGATATTTCATGGAAGAAACTGCATAAATGGTAAATTAACATATGAAAA 1553
                         i   i     vivi     iv ii i      iv   v i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_146556839_   1554 AGGACTCAACCTCATCAGTAAT 1575
                         iivi      v   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (156 / 96)
Gap_init rate = 0.04 (37 / 903), avg. gap size = 2.81 (104 / 37)  


3217 27.10 0.77 0.33  chr1_146737287_146743643.rev     4963  5866 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_146737287_   4963 TGGAAGAACATTTCATGCTCTTGGATAGGAAGACTCAGTATCGTGAAAAT 5012
                              ii i  ii    i  v     v        i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_146737287_   5013 GGCCATACTGCCCAAGGTAATTTATAGACTCAGTGCCATCCCCATCAAAC 5062
                            v     v     iv i  i  i   i   ii  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_146737287_   5063 CACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTCCA 5110
                         iv   iivi i  i  ii     -   -- v  i  - iii    i i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_146737287_   5111 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5160
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_146737287_   5161 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5210
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_146737287_   5211 TGCAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATATAGACC 5260
                          i      i   i    ii     i   i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_146737287_   5261 AATGGAACAGAACAGAGCCTTCAGAAATAATACCACACATCTACAA-CAA 5309
                                i    iv   vv i         vv   i    i  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_146737287_   5310 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5359
                          -    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_146737287_   5360 TATTTTATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCTG 5409
                          v  iv i              v      v  ?   i v i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_146737287_   5410 AAACTGGATCCCTTCCTTACACCTTATAAAAAAGTTAACTCAAGATGGAT 5459
                           ii    i    v   i     v    v    i         i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_146737287_   5460 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5509
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_146737287_   5510 TAGGCAATACCCTTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 5559
                             ?ivv vi    iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_146737287_   5560 ACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAAT 5609
                                     vvi          vv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_146737287_   5610 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAACA 5659
                         i   v v  i i   i  ii vv    i  v  i i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_146737287_   5660 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5709
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_146737287_   5710 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAA---AGTTATAAGAA 5756
                           i  vi          v  i        ivv    --- i v    i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_146737287_   5757 AA-AATCAACCCCATCAAAAAGTGGGCGAAGCATATAAACAGACACTTCT 5805
                         i -  vi     v  i?    i     i   v  v i  i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_146737287_   5806 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5855
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_146737287_   5856 TCACTGGCCAT 5866
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2470 25.29 3.96 5.24  chr1_146836528_146839317     1056  1913 (877)    L1M4_orf2#LINE/L1        1   847 (61)  

  chr1_146836528_   1056 TGGAAAAACATCCCATGCTCATGGATAGGAAGAACCAATGTCATTAAAAT 1105
                               i i        i        v      vii   i ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_146836528_   1106 GGTCATATTGCCCAAAGCAATTTACAGATAAAATGTTATTCCTATCAAAC 1155
                           iv   i v      vii  i       vv  i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_146836528_   1156 TACCAATAACATTCTTCACAGAA-TTAGGAAAAACT-ATTTTAAAATTCA 1203
                          v   iivi v  i  ii     -  --  v  i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr1_146836528_   1204 TATGGAACTAAAAAAGAGCCCAAATAGC-AAAGC---C------AAAAAG 1243
                                v iv  ii  v  vi      -   i --- ------  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_146836528_   1244 AACAAACCTGGAGGCATCACATTACCTGACTTCAAA-----CTATA---C 1285
                               vi      vv     i v  ii i      -----   i --- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_146836528_   1286 TACAGTGGCCAAAACAGCATGGTACTGGTAAAACAAACAAACAAACAAAC 1335
                               iii   i    ii         i v  -----------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAA----------------- 281

  chr1_146836528_   1336 GAAAACAAAAAACAAAAAAAAAAAAACAGGCACATAGACCAATGAAACAG 1385
                         -----------------------ii i  i  i     i     i  i  
  L1M4_orf2#LINE/    282 -----------------------GGATAGACATATAGATCAATGGAATAG 308

  chr1_146836528_   1386 AATGCAGAGTCCAAAAATAAGGCCACACACCTATGACCATCTGAACTTCA 1435
                            vv        i      iv   i   ii    ii  vi   vi   i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_146836528_   1436 ACAAAGCTGACAAAAACAAGCAATAGAGAAAAGACTCCCTAGTCAATACA 1485
                             i v  v   i v  vv    i i    ii ivvi  vv    i v 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_146836528_   1486 TGGTGCTGGGATAACTGGCTAACCATATGCAGAAGATTGAAACTGGACTC 1535
                                    i      v  ?   i     i    v    ii     i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_146836528_   1536 CTTCTTTACACCATATACAAAAATCAACTCAAGATGGAATAAATACTTAA 1585
                           v i i                 i       i     vi ? v  i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_146836528_   1586 ATATAAAACCCAAAACTATAAAAACCCTGGAAGACAACCTAGGC---AAT 1632
                           i   i v i            vi i i     v   v    ?---   
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_146836528_   1633 ACTATCCTGGACTTAGGAACAGGTGAAGATTTCATGACAAAGATGCTAAA 1682
                         -  -  v  -  i v  ivi   ii v i    v iivv v  ii i   
  L1M4_orf2#LINE/    559 -CT-TCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_146836528_   1683 AGCAATCGCAA--------AAAATTGACAAATGGGATCTAATTAAACTTA 1724
                             vvv    --------     v  i    v   ii v  i   v   
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_146836528_   1725 AGAGTTTTTGCACAGCAAAATAAACTATCAACAGAGTAAACAGACAATCT 1774
                          i ii     ii vv    iv v        v i   i  v      i i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_146836528_   1775 ACAGAATGGGAGAAAATATTTTCAAACTATGCATCTGACAAAGGTCTAAT 1824
                                              v    ii  ii      i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_146836528_   1825 ATCCAGCATCTATAAGGAACTTAAACGAATTTACAAGAGAAAAACAACTA 1874
                               v  v     i     ivv  i v iv i  v i   i    v  
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_146836528_   1875 CCCCA-TTAAAAAGTGGGCAAAGGACATGAACA--CTTTTCT 1913
                         v    -  ?    i           iv    i -- v     
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

Transitions / transversions = 1.63 (132 / 81)
Gap_init rate = 0.02 (16 / 847), avg. gap size = 4.94 (79 / 16)  

 285 26.32 0.00 0.00  chr1_146836528_146839317     2222  2297 (493)    L1M4_orf2#LINE/L1      833   908 (0)  

  chr1_146836528_   2222 TGAACAGACACTTTCCAAAAGAAGGCATATATGCAGCCAACGGACATATG 2271
                             i     i  ii v       ii   i viii     iiii  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_146836528_   2272 AAAAAAAGCTCAATATCACCGATCAT 2297
                             i v      i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 5.67 (17 / 3)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.00 (0 / 0)  


2272 24.33 2.68 1.01  chr1_146884200_146887043     1324  1919 (925)    L1M4_orf2#LINE/L1        1   606 (302)  

  chr1_146884200_   1324 TGGAAA-ACATCCCATGCTCATGGATAGGAAGAATCAATATCATTAAAAT 1372
                               - i        i        v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_146884200_   1373 GGCTATACTGCCCAAAGCAGTTTACAGATTCAGTGCTATTCCTATCTAAC 1422
                            v     v      viii i          ii  v  i      v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_146884200_   1423 TACCAATGACATTCTTCACAGAACTAGAAAAAATTATTTTAAAATTCATA 1472
                          v   iivi v  i  ii     v v  v  iv v  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_146884200_   1473 TGGAACCA-AAAAAACGCCAAAATAGCCAAGGCAATCCTAAGCAAAAAGA 1521
                              vii-  iii  -   i         ii     i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_146884200_   1522 ACAAAGCTGGAAGAATCACGTTACCCAACTTCAAACTATACTACAAGGCT 1571
                               i    i  v    ii v     i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_146884200_   1572 ACAGTGACCAAAACAGCATGGTATGGGTACAAAAACAAGCACATAGACCA 1621
                              i i   i    ii     iv  i i  ii i ii  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_146884200_   1622 ATGGAACAGAATAGAGAGCCCAGAAATAAGGCCTCACATCTATGACCATC 1671
                               i     v     i          iv  vi    i    ii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_146884200_   1672 TGATCTTTGACAAAGCTGATAAAAACAAGCAATGGGGAAA----AGACTC 1717
                             i  i     i v  vi  i v  vv           ----  v  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_146884200_   1718 ATTCAATAAATGGTGCTGAAATAACTGACTAGCCATATGCAGAAGATTGA 1767
                         -     i           ii i     iv  ?   i     i    v   
  L1M4_orf2#LINE/    400 -TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_146884200_   1768 AGCTGGACCCCTTCCTTACACGGTATACAAAAATTTCAACTCAAGATTGA 1817
                           i         v   i    vi            --       i  v  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATT--AACTCAAAATGGA 496

  chr1_146884200_   1818 TTAAAGAC--AAATGTAAAACCCAAAATTATAAAAACCCTGGAGGACAAC 1865
                          i ?    --        i v i    i       vi i i  i  v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_146884200_   1866 CTAGG--TAATACCATTCTGGACCTAGGAACAGGCTAAGATTTC------ 1907
                         v    --   - i -   vv     v  ivi    v v i    ------
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_146884200_   1908 ATGACAAAAAAA 1919
                               vv    
  L1M4_orf2#LINE/    595 ATGACACCAAAA 606

Transitions / transversions = 1.86 (93 / 50)
Gap_init rate = 0.02 (11 / 606), avg. gap size = 2.00 (22 / 11)  

 225 26.97 7.87 0.00  chr1_146884200_146887043     1922  2010 (834)    L1M4_orf2#LINE/L1      734   829 (79)  

  chr1_146884200_   1922 ATGCATCTGAGAAAGGTCTAATATCCAGCATCTATAAAGAACTTAAACAA 1971
                           ii      v  i  v  vi       v  v           ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_146884200_   1972 ATTTACAAGAGAAAAACAA----CCTCATTAAAATGTGG---AAGG 2010
                         v iv i  v i   i    ----  iv   ?   vi   ---    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 0.92 (11 / 12)
Gap_init rate = 0.02 (2 / 96), avg. gap size = 3.50 (7 / 2)  

 395 22.34 0.00 0.00  chr1_146884200_146887043     2258  2351 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_146884200_   2258 AAAAGTGGGCAAAGGACATGAACAGCTACTTCTCAAAAGAAGACATACGT 2307
                             i           iv    i  vi i     v        i    iv
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_146884200_   2308 GCAGCCAACAAGCATATGAAAAAAAACTCAGTATCACTGATCAT 2351
                         iii     i     i       i vi    ii    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.20 (16 / 5)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


2807 25.72 6.14 0.93  chr1_146889813_146892168     1001  1863 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_146889813_   1001 TGGAAAAACATCCCATGCTTATGGATTGGAAGAATCAATATT---AAAAT 1047
                               i i        i i             v i      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_146889813_   1048 GATCATATTACCCAATGCAATCTACAGATTCAACACAATTCCTATCAATT 1097
                          iiv   i v     vvii               i    i        vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_146889813_   1098 TACCAACATCATTCTTCACAGAATTAGGAAAAAGAATCCTAAAGTTGATA 1147
                          v   i vv v  i  ii     v v iv  ivvi        i  v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_146889813_   1148 TGGAACCAGAAGAAAGCCTGAATAGCCAAGGTGCTCCTAAGCAAAAA--A 1195
                              viiv   ii v  v          iiiiv  i i iv  i  -- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_146889813_   1196 CAAATCCAGAG---TCACATTGCCTGACTTCAAATTATATTATAAGGCTA 1242
                             viii   ---     i v  ii i      viv  i  i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_146889813_   1243 CAGTAACTAAAACAGCATGGTACTGGTACAAAAACAGACACATAGATCAA 1292
                               ii  i    ii         i i  ii i     i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_146889813_   1293 TGGAACAGAATAGAGAACCCAGAAATAAAGCCACATACCTACAACCAACT 1342
                              i     v    ii           v   i i ii  iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_146889813_   1343 GATCTTCAATAAAGTCGATAAAAATAAACAATGGGGAAAGAACACCCCAC 1392
                            i   i i  i vi vi  i vi vv              i vi ivi
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_146889813_   1393 TCGATAAATTATGCTGGGAAAATTGGCCAGCCATATGCAGAAAAATGAAA 1442
                           i i    vi        v  i   vi ?   i     i  i      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_146889813_   1443 TTGGACCCCTATCTCTTAACCATATACAAAAATTAACTCAAGATGGATTA 1492
                                    i   vi -                      i      i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACA-CCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_146889813_   1493 AAGGCCTAGATGTGGGACCTGAAACTGTGAAAGTCCTAGATGAAAACCTA 1542
                         ?  i    i    ii  v  i     i i   v  i    v      v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_146889813_   1543 GGAAAAACTCTTCTGGACATTGGCCTAGGCAAAGAATT------TATGAC 1586
                           ?iv  v     vv   v    vi       v iv  ------      
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_146889813_   1587 AAAGATCCCAAAAGCAAATGCAACAAAAACAAAAGTAGACAAGTAGGACT 1636
                          ------         v v         iv    i    i  i v     
  L1M4_orf2#LINE/    600 A------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_146889813_   1637 TAATTAAACTAAAGGGCTTCTGCACAGCAAAAGAAATAACCAACAGAATA 1686
                          v  i   v v  iii   i  ii vv    i  v iv i   v i i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_146889813_   1687 AACAGACAACCTACA-----------AATA----------ATGCCTCCAA 1715
                           v        i   -----------    ----------  iiv  ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_146889813_   1716 CAAAGGACTACCATCCACATCCTACAAGGAACGC---------AATAAGT 1756
                         i  i     vvi     v viv  i  i    v ---------     - 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-T 792

  chr1_146889813_   1757 AAAAA------CAACCCCATTAAAAACTGGGCAAACGACATGAAAAGACA 1800
                              ------i     v   ?    v        v  iv    v     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_146889813_   1801 TTTCTCAAAAGAA--T-TACAAGTGGCCAAAAAACGCTTGAAAAAATGCT 1847
                               v      -- -     i       v  i i v      i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_146889813_   1848 CAACATTACTGATCAT 1863
                               i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (138 / 80)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.69 (61 / 13)  


 252 20.83 0.00 6.94  chr1_147101204_147105407.rev      488   559 (3645)    L1M4_orf2#LINE/L1      253   319 (589)  

  chr1_147101204_    488 GTAATGTGTAAGACACAGTGTGGTACTGGCGTAAGAACAGGCAGGTAAAC 537
                              ---i      --             i    i i  i  vi  i i
  L1M4_orf2#LINE/    253 GTAAT---CAAGACA--GTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_147101204_    538 CAACAAAAGAGAATAGAGGGTC 559
                            iii  v     v   i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC 319

Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.03 (2 / 67), avg. gap size = 2.50 (5 / 2)  

 242 16.33 2.04 0.00  chr1_147101204_147105407.rev      856   904 (3300)    L1M4_orf2#LINE/L1      307   356 (552)  

  chr1_147101204_    856 AGAATAGAGAGCCCAGAA-TAAACACTCACATATATGGTCAGCTGATTTT 904
                              v     i      -     v vi    v        ii       
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 1.00 (4 / 4)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1)  

1066 18.67 0.00 4.44  chr1_147101204_147105407.rev     1775  1999 (2205)    L1M4_orf2#LINE/L1      312   526 (382)  

  chr1_147101204_   1775 TGGGATTACAGGCATGAGCCCCTGCACCTGGCCATGGTCAGCTGATTTTT 1824
                           i  v v   iv  i i   v i  ii ----       ii       i
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTT----ATGGTCAATTGATTTTC 357

  chr1_147101204_   1825 GACAAAGGTGCCAAGGCTATTCAATGTGGAAAGGACAGTCTGTTTAACAA 1874
                              i         i i        v      i i     v  i     
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_147101204_   1875 ATGATGCTGGGAAAAGCAGATATCCACAAACATAAGAGTTAAATTGGACC 1924
                            i        v  vii    ?     vi  v    i v  i       
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_147101204_   1925 CCCTACCTCATACCGTATACAAAAATTAATTCAAAATGGATCTAAGACCT 1974
                           -       i   i              i            v?      
  L1M4_orf2#LINE/    458 CC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_147101204_   1975 AAATTTAAGAAATATACAAAAACTA 1999
                             v     iv  -----      
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTA-----AAACTA 526

Transitions / transversions = 1.86 (26 / 14)
Gap_init rate = 0.01 (3 / 215), avg. gap size = 3.33 (10 / 3)  

1465 16.82 2.49 3.74  chr1_147101204_147105407.rev     3010  3330 (874)    L1M4_orf2#LINE/L1      497   813 (95)  

  chr1_147101204_   3010 TCAAAAAATGCCTAAAACTAAGGAGCAATAACTGTAAAACTCTTAGAGGA 3059
                            ? i ---      vv    -   v v    i             i  
  L1M4_orf2#LINE/    497 TCAWAGA---CCTAAATGTAAG-AGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_147101204_   3060 AAACACAGGAGAACAGGAGTGTATCTTTTTGACATTGGATTTGGCGATAA 3109
                              i   ? -------- iv     iv    v    i  v   i  ii
  L1M4_orf2#LINE/    543 AAACATAGGNG--------TAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_147101204_   3110 TTTCTTGGATATGATGCCAAACATACAGGCAAACAAAGGAAAAACAGATG 3159
                               i       ii     vii   i    vv    i     i    i
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_147101204_   3160 AATTGGACTTCATCAAAATTTAAAG-TTTTGTGCATTAAATGACACTATC 3208
                                             v   i-        v i   v         
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_147101204_   3209 AACAGAATGAAAAGGCAACCCACAGAATGTGAGAGAATATTTGCAAGTCA 3258
                           v i i       i              v    i           i   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_147101204_   3259 TATATCTGATAAGAGATTAATATCCAGAATATATTAAGAACACTTACAAC 3308
                                      i  i vi              v      v        
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_147101204_   3309 TCAACAACAAAA-------CAACCTAATT 3330
                             i  i    -------i    i    
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATT 813

Transitions / transversions = 1.74 (33 / 19)
Gap_init rate = 0.02 (5 / 317), avg. gap size = 4.00 (20 / 5)  

 438 19.63 0.93 0.00  chr1_147101204_147105407.rev     3607  3713 (491)    L1M4_orf2#LINE/L1      801   908 (0)  

  chr1_147101204_   3607 AAACAACCTAATTCAAAAACAGGTAAAACACTTGAATATATGTATGTTCA 3656
                            i    i    ?     ii  i   iv i       v ii v v i  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_147101204_   3657 AAGAAGACA-AAAAATGGCAAATAAGCACATGGAAAGATGCTCCACAGCA 3705
                                i - v       v            i          v   v  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_147101204_   3706 TTAGTTAT 3713
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.50 (12 / 8)
Gap_init rate = 0.01 (1 / 108), avg. gap size = 1.00 (1 / 1)  


 340 20.22 0.00 6.74  chr1_147142494_147145952      484   572 (2887)    L1M4_orf2#LINE/L1      189   271 (637)  

  chr1_147142494_    484 GAAAAAAAAAAAATCCAATAGAGTTGAAGGACTGACATTACCCAACTTTG 533
                               i  i  ---   ---     i      v   i v     i  ii
  L1M4_orf2#LINE/    189 GAAAAAGAAGAA---CAA---AGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_147142494_    534 AGAATTACTGTAAAGCTACAGTAATGAAGGTGGTGTTGT 572
                          i v     ii              v   iii    v  
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.02 (2 / 83), avg. gap size = 3.00 (6 / 2)  

 771 23.96 15.62 1.04  chr1_147142494_147145952     1174  1461 (1998)    L1M4_orf2#LINE/L1      261   590 (318)  

  chr1_147142494_   1174 GGTAGTATAGTATTGGT-----GAAAGA---ATAGATCAGTGGAACAGAG 1215
                          ii   i i   i   i-----  v   ---        i     i   i
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_147142494_   1216 TAGAGA-TCACAGAGATAGACTCACATA------GTCAACTGCTCTTTGA 1258
                          v    -  -    i   i  i  i i ------     i  v i  i  
  L1M4_orf2#LINE/    311 TTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_147142494_   1259 TAAAGGAGCAAAAGCAATATAA--AGGAGAGA-TAATCTTTTTTAAAAAT 1305
                         i  i  v  v  ii v  vi  --i   i   -  i      iv v    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_147142494_   1306 TGGTGTTGGAACAACTGGATGTTCACATGCAAAAAAGTGAA--------- 1346
                         -    i   i          i?i           i i    ---------
  L1M4_orf2#LINE/    410 -GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_147142494_   1347 -----TC------TAGACACAAATTAACTCAAAATAGGTAACAGACCTAA 1385
                         -----  ------  v   v               i i v ?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_147142494_   1386 ATGTAAAATGC-AAACCTGTAAAGTACCTAGTAGATAACAGA-----AAA 1429
                               i -  -   v  i    iiv i   v   v    v -----   
  L1M4_orf2#LINE/    509 ATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_147142494_   1430 TGTAGCTGACTTGGGGTT-GGCCTTGACTTTTT 1461
                          v vvv    i v     -   vv  ii  i  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.79 (43 / 24)
Gap_init rate = 0.04 (14 / 330), avg. gap size = 3.43 (48 / 14)  

 492 24.49 5.44 1.36  chr1_147142494_147145952     1731  1877 (1582)    L1M4_orf2#LINE/L1      547   699 (209)  

  chr1_147142494_   1731 ACAGGTGTGAGCCACCGTGCCC---AGCCAGCCT-TGACTTTTTAGAAAC 1776
                          i   ?  i ii vi    v  ---i ii  v v-  ii  i     v i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_147142494_   1777 AACACCAAAGGCATGATCTATGAAAGAAAAAAT-TATAAACTGGACTTAA 1825
                         i        i   ii v v ii           -v     i       v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_147142494_   1826 TTAAAATGAAAAATTCTGCTGTGC---AAAAGACACTGTCAAGAAAATGA 1872
                          i     v     i i --     ---   i      i        i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTT--TGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_147142494_   1873 AAAGA 1877
                              
  L1M4_orf2#LINE/    695 AAAGA 699

Transitions / transversions = 2.50 (25 / 10)
Gap_init rate = 0.03 (5 / 153), avg. gap size = 2.00 (10 / 5)  

 563 21.23 2.74 0.00  chr1_147142494_147145952     2149  2294 (1165)    L1M4_orf2#LINE/L1      674   823 (85)  

  chr1_147142494_   2149 AAGACTCCATCACCAAAA-AAAAAGA-AGGCCTCATACTGGAAGAAAATA 2196
                          i   v i    vv   i-i      - iv  v  v v   i        
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_147142494_   2197 TTTGCAAAAGATGTATCTGATAAAGGACTT--ATCCAAAATATACAAAGA 2244
                                 vv  i          i      --     i      i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_147142494_   2245 ACTCCTAAAACTCAACACTAAGAAAATGAACAACTCAATTAAAAAGTGGG 2294
                             i  v       i v   i  i ii  i   i     ?    i    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

Transitions / transversions = 1.73 (19 / 11)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 1.33 (4 / 3)  

 361 21.05 0.00 1.05  chr1_147142494_147145952     2872  2966 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_147142494_   2872 AAAAGTGGGCCGAAGACCTTAACGGACACATCATCAAAAAAAGATACAGA 2921
                             i     vi i  ii v  ii    iv  -  v   i      i v 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTC-TCCAAAGAAGATATACA 863

  chr1_147142494_   2922 GATGGCAAATAAACATATGAAAAGATGCTCCACATCAGGCTGGGC 2966
                         i     v     i  i              v      ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


2575 13.66 12.90 0.76  chr1_147579534_147581630.rev      505  1031 (1066)    L1M4_orf2#LINE/L1       39   629 (279)  

  chr1_147579534_    505 TGTTGTTAATATGGCAATAATCTCCAAATTGATCTACAGAATTAACACAA 554
                          i       v         v  i                 v i   i   
  L1M4_orf2#LINE/     39 TATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAA 88

  chr1_147579534_    555 TTTGTATTAAAATCTCAGCTGGCTTTCTTGCAGAAATTGGCAAGCTGGCT 604
                          iiv   i      i      v    i            i       iii
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chr1_147579534_    605 CTAAGATTCATATGGACATTCAAGGGCTTCAGAATAGCCAAAACAACCTT 654
                             i           v  v      vii                 i   
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_147579534_    655 GAAAAAGAA---CAAAGTTGGAGGACTTGCACTTCTCAATTTCAAAACTT 701
                                  ---               ii      i              
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_147579534_    702 AACTTCAAACCAATAGTAGTCAAGGCA----------------------- 728
                          -  v    v v i    i     i  -----------------------
  L1M4_orf2#LINE/    239 A-CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_147579534_    729 ---TACAGATCAATGGAATAGAATTAAGGGTGTAGAAATAAACC---ACA 772
                         ---  i                   i  i  vi           ---   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_147579534_    773 TT------CAATTGA-------CATGGGGTGCCAAGACAATTCAAGGTGG 809
                           ------       -------  -i            v      v -  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACA-AGGGTGCCAAGACCATTCAATG-GG 385

  chr1_147579534_    810 GAAAGAATAGTCTTTTCAAAAAGTCATGCTGG-ACAACTGAATAACAACA 858
                                            v  i vi      -       i   ? v   
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_147579534_    859 TGGAGAAGAATGAAGTTGGAACACTACTCCACCTCATATA-AAAAATTAA 907
                           v i               v v    ii   vi      -         
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_147579534_    908 TTCAAAATGGCT-AAAAACCTAAAGGTAAGAGCTAAAACT--------CT 948
                         i         v - ? i       v               --------  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_147579534_    949 TAGAA---AACACAGGGGTAAATCTTCCTGACCTTGAATTAGGCAGTGGT 995
                              ---    i   ?          v        ii       i    
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_147579534_    996 T--------ATGACACCACA-GCACAAGAAAGAACAACAAAAAAT 1031
                          --------         v -       v  v  -  v       
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAA-AAGAAAAAAT 629

Transitions / transversions = 1.46 (41 / 28)
Gap_init rate = 0.03 (16 / 591), avg. gap size = 4.50 (72 / 16)  

1290 14.39 4.91 1.75  chr1_147579534_147581630.rev     1322  1606 (491)    L1M4_orf2#LINE/L1      615   908 (0)  

  chr1_147579534_   1322 AAAAAAAGAAAAAAGTTAGATAAATTGGACTTCTGTCAAAATTAGAATTT 1371
                           v           --                 -i         i  vi 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAA--TAGATAAATTGGACTTC-ATCAAAATTAAAAACT 661

  chr1_147579534_   1372 TTTTGTCCACCAAAGGACACTATTAAGAGAGGGTAAAGACAAC--ACAGA 1419
                            -  v vi             i    i  v v         --     
  L1M4_orf2#LINE/    662 TTT-GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_147579534_   1420 ATGGGAGAAGATATCCACAAGTTATATATCTGATGAAAGAATTAATATCC 1469
                                  i    iii   i i           -  i i i vi     
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGAT-AAGGGACTTGTATCC 759

  chr1_147579534_   1470 AAAATATTCAAAGAACTCCCACAACTCTACAATAAGAAAA---------- 1509
                          i     vi         ii       v i     i  i ----------
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_147579534_   1510 -ATT-AAAAATGGGCAAAGGACTTGAATACATATTTCACCAAAACAGATA 1557
                         -   -                i       v i     v     iv     
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_147579534_   1558 TACAAATGGTGAATAAGCACATGAAAATATGCTCAACATCACTAGCCTA 1606
                                  iv                v             ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (27 / 14)
Gap_init rate = 0.02 (7 / 294), avg. gap size = 2.71 (19 / 7)  


1856 19.85 13.24 6.76  chr1_147612970_147614640.rev      502  1181 (490)    L1M4_orf2#LINE/L1      185   908 (0)  

  chr1_147612970_    502 TCTTGAAAACAAAGAACAAAG----AGAATTTACACTACCTGATT-CAAC 546
                                  vi          ----  i i i     v  ii   -   v
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_147612970_    547 ACTAACTATAAAGCTA---TTACCAAGACACTGTGGTGTTGGTGTAAGGA 593
                            v    i       --- v i       v      ii   ii      
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_147612970_    594 TAGATATATAGATCAATAGACCAGAAT--AAGGTCTA--------TTCTT 633
                             i            i  vi     -- ii   i --------ii v 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_147612970_    634 ATACTT---GTCAACTAATTTTCAGCAAAGGTGACAAGACAATTCAATGG 680
                          i i  ---     i i      ii   i    v      v         
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_147612970_    681 ATAAAATA-AATATTTCTAACAAATGG------AACAATTGGATATCTGT 723
                         iv   iv - i v   ii         ------i    i      ? iii
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_147612970_    724 ATGCAAAAAAAAAAAAAAACAAAAAAAAAACCACACCCAAAAATGAAAAC 773
                                 i  --------------------------------    iv-
  L1M4_orf2#LINE/    435 ATGCAAAAGAA--------------------------------TGAAGT- 451

  chr1_147612970_    774 ACATAGATCT-TACCTCATACAATTTACAAAAATCAGCTTAGA------- 815
                         --- i  i i-       i  v  v         i i  i i -------
  L1M4_orf2#LINE/    452 ---TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_147612970_    816 ---GGCCTAAATGTGTAAGAGCTAAAGTTACAAATAAACTCCTAGGAGAA 862
                         --- i         --          ii  i   ---    i   i    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGT--AAGAGCTAAAACTATAAA---ACTCTTAGAAGAA 543

  chr1_147612970_    863 AA------------TCTTTGTGATTTTGAGTTAGGCAAAAGATTTCTTA- 899
                           ------------    i    ii   i         vi -       -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAG 592

  chr1_147612970_    900 ------CACTAAAAGCATGATTCACAGAAGAAAAAAAATTATAAATTGGA 943
                         ------   i       ii viv   i         v v-          
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG-ATAAATTGGA 641

  chr1_147612970_    944 TTTAATTGTAATTAAAA---TTTGCCCTCTTTAAAGGATATTATTAAGAA 990
                         i  v  iiv        ---    iv  -- i      i i   i     
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTATCAAGAA 689

  chr1_147612970_    991 AATGAAAAGACCAGACATA-AATGGAGAGAAAATAGTTACAAGTCATATA 1039
                          i         v vv  i -     -         v  i   i       
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGG-GAGAAAATATTTGCAAATCATATA 738

  chr1_147612970_   1040 CCTGAAAGAGGATTTGTACCAGGAATATATAAA---------CAACTCAT 1080
                         i    v ii   i     i vi           ---------       v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_147612970_   1081 TAA------GACAAACAGCTGG--TAAAAAA-GAGCATAAGACTTGA--- 1118
                            ------      i i ivi-- ?     - i   v i  i    ---
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_147612970_   1119 --CATTTGACTGAAGAATAAATATGCATT-----TATGCACATGAAAAGA 1161
                         --     vv ii     v v   iiv  v-----  v             
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_147612970_   1162 TGCTCAACATCTTTTTACCA 1181
                                    v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (92 / 41)
Gap_init rate = 0.04 (28 / 724), avg. gap size = 4.86 (136 / 28)  


1043 24.30 4.98 3.43  chr1_148793720_148795716.rev      502   822 (1175)    L1M4_orf2#LINE/L1      209   534 (374)  

  chr1_148793720_    502 GAGAACTGACACTGCC-AACTTCAGTACTAATTATAAAGCTAAAGTAACC 550
                            i   v     v  -  i    iv   v i  i       v     i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_148793720_    551 AAAACAGTGTGGAATTGGTGAAGAAAGAAAAAACAGACAAATAGGTTACT 600
                           i         v i   i-- v  i  -----i     v    i i v 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGC--ATAAGGA-----TAGACATATAGATCAAT 301

  chr1_148793720_    601 GGAAAAGAACACAGAGCTCAGAAATAGTCC--TACATAAATAGTCAACTG 648
                             v    ivv    ii        iv  --     vv  i     i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_148793720_    649 ATCTTTGAGAAAGGCACAAAAGCAATTTAACAGGGCAAGGATAGTCTTTT 698
                           i  i  v  i  ii v  ii v   i  ii   v   i          
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_148793720_    699 CAACAAACGGTGCTAGAATGACTAGACATCCACATGCGAAAAATAAATAA 748
                                i      i i ii   i  i ?        i   i ---  i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA---ATGA 448

  chr1_148793720_    749 ATCTAGGCACAGATTTTACACC-T---------TTCACT--AAATGGATC 786
                          vi i i v vv ii i     - ---------  v   --         
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_148793720_    787 TTACACCTGAATGTAAGGTGC-AAAACTGTAAGACTC 822
                         v? v    i        i-  -      i   i    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTC 534

Transitions / transversions = 1.92 (50 / 26)
Gap_init rate = 0.03 (10 / 326), avg. gap size = 2.70 (27 / 10)  

1667 20.16 2.62 0.79  chr1_148793720_148795716.rev     1125  1506 (491)    L1M4_orf2#LINE/L1      520   908 (0)  

  chr1_148793720_   1125 AACACTGTAAGACTCCTAGACAATAACATAGGGGAAAATCTAGGTGACTT 1174
                           v   i   i    i    vi v        ? v      vv     i 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr1_148793720_   1175 TGGGTTTGGTGATGACTTCTTAGATACAATGACAAAAGCACAATCCAGGA 1224
                               v  ii   ii          ii iiv           v v vi 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_148793720_   1225 AACAAAAAATTGATAAGTTGAACTTCATTAAAATTAAAAACTGCTTTGTG 1274
                           v       v     i   i       i             --      
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT--TTTGTG 667

  chr1_148793720_   1275 -----AAAGACACTGTTAGGAGAATGAATAAACATGTTATAGTCTGGGA- 1318
                         -----  i      i i i  i i    v i   vvii i  vv     -
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_148793720_   1319 AAAATATTTGCAAAATACAGATTTGATGAAAGACTGGTGTCCAAAATATA 1368
                                       vi i v  i    i ii    v  i    i      
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_148793720_   1369 TAAAGAACTCTTAAAACTCAATAATAAAAAAGCAAACAACCCAATTCAAA 1418
                                      v                ii    i         ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_148793720_   1419 AATAGACAAAAGATCTG----GACACTTCACCGGAAAAGATATATGGATG 1464
                            i i    i   i  ----    i   v  ii i        iii   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_148793720_   1465 GCAAATAAGCATATGAAAAAGATGCTCAAAATCATTTGTCAC 1506
                           v        i       -         v    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (50 / 25)
Gap_init rate = 0.01 (5 / 389), avg. gap size = 2.60 (13 / 5)  


2967 21.64 1.70 10.72  chr1_149016749_149020055.rev     1819  2816 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149016749_   1819 TGGGAAAATATCCCATGCTCATGGATTAGAAGAATTAATATTGTTAAAAT 1868
                            i  i          i         i     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149016749_   1869 GTCCATACTACTCCAAGAAATCTATAGATTCAATGCAATCCCTATGAAAA 1918
                          v v     v i v  vvi     i        i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149016749_   1919 TACCAATGACATCCTTCATAGACATAGAAAAAAGC-ATTCCTAAAATTTG 1967
                          v   iivi v ii  iii   v  v  v  --  -iv          ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr1_149016749_   1968 TATGAAACCACAAAAGACCCCAAATAGCCAAAGCAATCTTGAGCAAAAAG 2017
                             i  vii   ii     vi          i         iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_149016749_   2018 AAGAAAGCTGGAGGCATCACACTACTTGACTTCAAATATACTACAAGTCA 2067
                           v    i      vv       v iii i      --------------
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-------------- 234

  chr1_149016749_   2068 CACCAACATGGCACATTTATACATATGTAACACACCTGCACATTGTGCAC 2117
                         --------------------------------------------------
  L1M4_orf2#LINE/    235 -------------------------------------------------- 234

  chr1_149016749_   2118 ATGTACCCTAAAACTTAAAGTATAATTAAAAATATATATTTACTACAAGT 2167
                         ------------------------------------- i         iv
  L1M4_orf2#LINE/    235 -------------------------------------ACTTACTACAAAG 247

  chr1_149016749_   2168 CTATTATAATCAAAACAGCATGGTATTGACACAAAAACAGACACATAAAC 2217
                            ivi       i    ii     i  i  i  ii i     i   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_149016749_   2218 CAGTGGAACAGAATACAGAACTCAGAAATAAATCCACATATTTATAGCCA 2267
                           i     i     vv   iii          i   i i      i i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_149016749_   2268 AATCATTTTC-ATAAATGTGCCAAGAACATACATTGGGGAAAGAATATCT 2316
                          v v      - i  iv         v   v  v             vii
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_149016749_   2317 TTTTCAATAAATAGTTCTGGGAAAACTGGATATCCATATGCAGAAGAATG 2366
                                i    i  v      v         ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_149016749_   2367 AAACTAGACCCCTATGTCTCACTATATACAAAAGTCAACTCAAAATGGAT 2416
                           ii i        iv  v   i          i i              
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_149016749_   2417 TAAAGACTTAAATGTAATACCTAAAACCAGGAGACTGCTGACAGCAAACA 2466
                         i ?    i         v v       i vi i   vi iiv  v     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_149016749_   2467 TTGGGGAAACACTTTCA-GACATTCATCTAGGCAA--ATTTTTTGGGGGG 2513
                          v  ? v  - ii   i-   v  vivi       --i   i  i i---
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA--- 593

  chr1_149016749_   2514 TAAGACCTCAAAAGGACAGGCAACAAAAGTAAAAATAGATAAATGGAACT 2563
                           v   vi      v   i          v              v i   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_149016749_   2564 ATATTGAA-TTAAAAAGTTCTGCACAGCAAAGGAAACAATCAACATAATG 2612
                         vi  ii  -       v  i  ii vv       v  v     v v i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_149016749_   2613 AAGAGACAGCCTGCAGAATGGGAAGAAATATTTGCAAACTATCCATCTGA 2662
                           i     i  ii          ii             ii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_149016749_   2663 CAAGGGATTAATAACCATTACTTATAAGGAAACCAAACAGCTCAACAGCA 2712
                         i      i vi  v   vv iv     i   vi vv   i     i ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_149016749_   2713 AA--GAAAAA------AATTAAAAAGTGAGCAAATTAGCTGAATAGATAT 2754
                           --  v   ------    ?    i  i     vv vi        i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_149016749_   2755 TTCAC---AAAAGACATTTAAGTGGTCAAAATGCATAGGAAGAAATGCTC 2801
                            v --- i    i  vi  i   i   v v   i v   i i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_149016749_   2802 AACATCACTAATTAT 2816
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (133 / 79)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 10.33 (124 / 12)  


3137 27.01 0.66 0.55  chr1_149049494_149052707     1815  2721 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149049494_   1815 TGGAAGAACATTCCATGCTCATGGGTAGAAAGAATCAATATCGTGAAAAT 1864
                              ii i  i     i      i v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149049494_   1865 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGTGATCCCCATCAAGC 1914
                            v     v     iv i  i           i ii     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149049494_   1915 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTCCA 1962
                          v   iivi i  i  ii     -   -- v  i  - iii    i i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_149049494_   1963 TATGGAACCAAAAAAGAGCACGCATTGCCAAGTCAATCCTAAGCCAAAAG 2012
                                viiv  ii  v vv v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_149049494_   2013 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 2062
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_149049494_   2063 TACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 2112
                              i  i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_149049494_   2113 AACGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 2160
                           i    i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_149049494_   2161 ATCTGATCTTTGACAAACATGACAAAAACAAGCAATGGGGAAAGGATTGC 2210
                          vi    i  i     ivi  v   i v  vv            i  v i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_149049494_   2211 CTATTTAATAAATGGTGCTGGGAAAAATGGCTAGCCATATGTAGAAAGCT 2260
                           v  i  i              v  v   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_149049494_   2261 GAAACCGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2310
                            iii   i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_149049494_   2311 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2360
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_149049494_   2361 CTAAGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTA 2409
                         v  i ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_149049494_   2410 AAACAGCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2459
                         vi   v        vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_149049494_   2460 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 2509
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_149049494_   2510 CAGGCAACCTACAGAATGG-AGAAAATTTTTTCAACCTACTCATCTGACA 2558
                         v  i     i         -       v   v   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_149049494_   2559 AAGGGCTAATATCCAGCATCTACAAAGAACTAAAACAAATTTACAAGAAA 2608
                          i  i  vi       v  v  i        vvv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_149049494_   2609 AAAACCAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTT 2658
                           i  v  i     v  i? v  i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_149049494_   2659 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 2708
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_149049494_   2709 CATCACTGGCCAT 2721
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2772 24.27 6.50 1.05  chr1_149063928_149073761     3632  4492 (5342)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149063928_   3632 TGGAAACACATCC-ATGCTCATGGATGGGTAGAATTAATATTGTGAAAAT 3680
                               v i    -   i        v  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149063928_   3681 GTCCATACTGACAAAAGCAGTCTACAAATTCAATGCAATCCCCATCAAAT 3730
                          v v     vv v   viii      i      i        i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr1_149063928_   3731 ATCCCA--T-CATTCTTCACATAA----------------TAAAG----- 3756
                               -- - v  i  ii  v  ----------------    i-----
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_149063928_   3757 -----AATG--AG---CCCACAA-AGCTAAAGCAAAACTAAGCAAAAAGA 3795
                         -----    --  ---    v  -   i   i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_149063928_   3796 ACCAATCTGGAGG-CATAAACTACCTGATTTCAAACTATACTATAAGGCC 3844
                           v  vi      - vi v   v  ii        viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_149063928_   3845 ATAGTCACCAAAACAGCATGGTACTGCTATAAAAATAGGCATATAGACCA 3894
                          i   v i   i    ii        vi    ii    i        i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_149063928_   3895 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAGTACTTACAGCCAAC 3944
                               i     v    ii               vii i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_149063928_   3945 TGATCTTTGACAAAG----CAAATAAACCATAAAGTGGGGAAAGGGCAGC 3990
                             i  i     i ----   i---     vv i         iii  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAG---ACCATTCAATGGGGAAAGAATAGT 396

  chr1_149063928_   3991 CTTTTCAATGAATGATGCTGGCATAATTGGCTAGCCATATGTAGGAGAAT 4040
                                 ii    i      v i  i   v  ?   i   i ii     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_149063928_   4041 TAAACCGGATCCTCATCTCTCACTTTATACAAAAATCAACTCAGGATAGA 4090
                         v  iii   i  ii i   v   iv           i      ii  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_149063928_   4091 TTAAAGACTTAATCCTAAGACCTGAAACTATAAAAATTCTAGAAGATAAT 4140
                          i ?    i   viv     v  i           v ii       -  -
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA-AA- 544

  chr1_149063928_   4141 AACATTGGAAAAACCCTTCTAGACATTGCCTTAGTCAAGGATTTCATGAC 4190
                         -    v  ?iv  vi    vv   v   vv    v   v i    v iiv
  L1M4_orf2#LINE/    545 -ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_149063928_   4191 CAAGAACCCAAAAACAAATGCAATAAAAACAAAGATAAATAGCTGGGACC 4240
                         i v  vv      i  v v    i    iv   i   i   iv v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_149063928_   4241 T------AATTAAAGAGCTTTTACATGATAAAAGGA-AC-ATCAGCAGAG 4282
                          ------       i -     iiiiv- v      -  -    iv i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCT-TCAAAGGACACTATCAAGAAAG 691

  chr1_149063928_   4283 TAAAAAGACAACCCATAGTGTGGGAGAAAATCTTCACAACCTATACATCT 4332
                          i             i  vi           v  ii   vii   i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_149063928_   4333 GACAAAGGACTAATATCCAGAATCTGCAATGAACTCAGACAAATCG-TAA 4381
                           i  i     vi          v ii  v      vv    v  i-   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_149063928_   4382 GAAAAA----AATATCTCA-TCAAAAAGTGGGCTAAGGACATGAATAGAA 4426
                         v     ----    v i  - i?    i     v     iv        v
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_149063928_   4427 AATTCTCAAAAGAAGATATACAAATGGCCAAGAAACATATAAAAAAA-AC 4475
                          v     v                       v  i  i  i    i -i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_149063928_   4476 TCAACATCACTAATGAT 4492
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (126 / 79)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.83 (65 / 23)  

2557 27.50 3.37 1.46  chr1_149063928_149073761     8451  9341 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149063928_   8451 TGGAAAAACATTCTATGCTCATGGATAGAAAGAATCAATATTGTTAA-AT 8499
                               i i  i i   i        v i    v i           -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149063928_   8500 GGCTATACTACCCAAAGCAATTTATAGATTCAGTGCTATTACTATCAAAC 8549
                            v     v      vii  i  i       ii  v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149063928_   8550 TTCCAATGACATTCTTCATAGAA-TTAAAAAAAT-ATTTTAAGTATTC-T 8596
                          i   iivi v  i  iii    -  i v  iv -  ii   i-    - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA-ATTCAT 149

  chr1_149063928_   8597 ATGGAACCAAAAAAAGAGCCCA-AATAGCCAAGGCAATACTAACCAAAAA 8645
                               -- viv  i ii    -         ii    vi i vv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_149063928_   8646 GAATAAATGTGGAGACATCACATTAACCAACTTCAAACTATGCTACAAGG 8695
                            i   vv     ivv     i vv    i      viv i      i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_149063928_   8696 TTA------TCAAAATAGCATAGTGCTGATACAAAAATAGACACATAGGC 8739
                         i  ------    i i  ii i  i   ii i  ii       i    ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_149063928_   8740 CAACAAAGCAGAATACCGAGCCCAGAAATAATGCCACATACCTGCAACCA 8789
                            iii ii     vvv   i          vv   i i ii iiiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_149063928_   8790 TCTGATCTCTGACAAAGTCAACAAAAACAAGCAATGGGGAAAGGA--GTC 8837
                         vi    i ii     i viiv   i v  vv            i --   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_149063928_   8838 CCTATTCAGCTA-TGCTAGCTGGTGTAACTGGCTAGCCCTAAACAGAAGG 8886
                         -- v    i v -  v -     vii      v  ?  vi vi  i   i
  L1M4_orf2#LINE/    398 --TTTTCAACAAATGGT-GCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_149063928_   8887 TTGAAACTGGACCCTTTCCTTACACCATATACAAAAATCAACTCAAGATT 8936
                         v    ii       i v   i                 i       i  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_149063928_   8937 GATTAAAGACTTAAATGTAACACCTGAAACTATAAAAATGTTGGAAGATA 8986
                            i ?    i         v v  i           v v  i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_149063928_   8987 ATCTAGG---AAATACCATGCTGGACACATGCCCT-GGCAAAGATTTTAT 9032
                          iv    ---    - ivi i--   - v  vvi -     v i   iv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGT--GAC-CTTGGGTTAGGCAATGGTTTCTT 590

  chr1_149063928_   9033 -GATGAAGACACGTAA--CACAGTTGCAACAAAAACAAACATTGACAAAT 9079
                         -   - v     vv  --    i--         iv   v  v  i    
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAAT 637

  chr1_149063928_   9080 GGGACCTAATTAAACTAAAGAGCTTCAG-----CAAAATAAGCTATCAAC 9124
                         v    i v  i   v v  i i   iv -----    iv vi       v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_149063928_   9125 AGAATAAACAGACAACGTACAGAAGGGGAGGAAATATGTATAACCTATGC 9174
                          i i i  v       vi      v     i      v ii  vii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_149063928_   9175 ATCCAACAAAAGTCTAATATCCAGAATATATAAGGAATTTAAACAAATTA 9224
                            ii i  ii v  vi                i   i ivv    v i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_149063928_   9225 ATCAGCAAGAAATAAACAACCCCATTAAAAACTGGGCAAAGGACATGAA- 9273
                           v vv  i i i   i     v   ?    v           iv    -
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_149063928_   9274 ---CATTTTTCCAAAGAAGACACCCACATGGCCAACAAATATATGAAAAA 9320
                         ---     i           i iv  v        i  ii i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_149063928_   9321 ATGCTCACCATTACTAATCAT 9341
                                v   i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (151 / 91)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.87 (43 / 23)  


3032 27.89 0.66 0.55  chr1_149073872_149076670.rev     1402  2308 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149073872_   1402 TGGAAGAACATTCCATGCTCATGGGTAGGAGGAATCAATATCATGAAAAT 1451
                              ii i  i     i      i v   i  v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149073872_   1452 GGCCATACTGCACAAGGTAATCTACAGATTCAATTCCATCCCCATCAAGC 1501
                            v     v v   iv i              iv v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149073872_   1502 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1549
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_149073872_   1550 TATGGAACCAAAAAAGAACCTGCATTACCAACACAATACTAAGCAAAAAG 1599
                                viiv  ii  v  v v  vi    v     vi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_149073872_   1600 AAGAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTGCAAGGC 1649
                           v    i      vv   ii  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_149073872_   1650 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1699
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_149073872_   1700 AATAGAACAGAAC--AGAGTCCTCAGAAATAAGACTACACGTCTATAACC 1747
                            i   i    i--       --        iv i i  i i   iii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_149073872_   1748 ATCTGATCTTTGACAAACCTGACAAAAATAAGCACTGGGGAAAGGACTCC 1797
                          vi    i  i     ivv  v   i vi vv  v         i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_149073872_   1798 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1847
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_149073872_   1848 GAAACCGGATCCCTTCCTTACACCTTATACAAAAATTAATTCCGA-TGGA 1896
                            iii   i    v   i     v              i  vi -    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_149073872_   1897 TTAAAGACTTAAATGTTAGACCCAAAACCATAAAAACCCTAGAAGAAAAC 1946
                          i ?    i       v   v i     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_149073872_   1947 CCAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACCTCATGTCTA 1995
                         vi   ?i- v i -   iv   v v  vv i     v iii  v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_149073872_   1996 AAACAGCAAAAGCAAAGGGAACAAAAGCCAAAATTGACAAATGGGATCTA 2045
                         vi   v        v i v        vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_149073872_   2046 ATTAAACTAAAGCGCTTCTGCACAGGAAAAGAAACTACCATCAGAGTGAA 2095
                           i   v v  ivi   i  ii vvv   i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_149073872_   2096 TAGGCAACCTATAGAATGGGAGAAAATTTTTGCAACCTACTCCTCTGACA 2145
                         v  i     i i               v       vii iviv     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_149073872_   2146 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 2195
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_149073872_   2196 AAAACAATCAATCCCATCAAAAAGCGGGCAAAGTATATGAACAGACACTT 2245
                           i    vi  i  v  i?    ii        v  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_149073872_   2246 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 2295
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_149073872_   2296 CATCACTGCCCAT 2308
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1282 28.96 13.50 2.09  chr1_149105325_149109591     2964  3778 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149105325_   2964 TGGACAATATATAGCTTGTTTATGAACTGAAAGTCTAAATAGCATTAAGA 3013
                             -  v    vv v    i   i i  i   v  v    vii      
  L1M4_orf2#LINE/      1 TGGA-AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_149105325_   3014 TATCAAATCTCCTTAAATTCATTTATAGATGCAATGAAATCCCATTCTGA 3063
                          iv   vv    ii     v  i  i    v   i v      -- v v 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC--TATCA 97

  chr1_149105325_   3064 ATATCTGAAGT---TTTTTTAAAAAATAAAGATTAATAAGGTGATTTCTA 3110
                          v   iv iv ---      iv i  -----   i i   v    i-   
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAA-----ATTGACAAGCTGATC-CTA 141

  chr1_149105325_   3111 AAATTTATATGAAAATGTAGAGGGCTAAGATTAGGTAAGACCATCTTTAA 3160
                              i     i     i ii  i iv   v   vi  i  v     v  
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_149105325_   3161 GAAGA----CTAAGTTGGAAGAC--ATAC---CAGATAGCAAGGTGTGTT 3201
                         i    ---- v        i   -- i  --- vi  vv   iiiv ii 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_149105325_   3202 ATAAAG-----G-----AAGAAAATATGGCA-TGATGCAAGGCTAAACAA 3240
                          i    ----- -----    v i i   i -  iiii    v  i   v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_149105325_   3241 ATGGAATGATAAAAGATAAT----AGTATAAAGTCAGTCTTATATCACTC 3286
                           i  vii  ii  v v   ----   vi i ivi iv ii   -  i i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTT 340

  chr1_149105325_   3287 -TGGACATTTGGTTAATGGCAAAGATGGTAGTGTAGGTCAGTAGAGAAAG 3335
                         -   v  v   i  vvi i   i i  vi iviiviv   i i i     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_149105325_   3336 AATAGTCTTG--AATAAATGGTGCTGGGTTAATTGAATTTTCAAATGGAA 3383
                                  v--  i             vi  i  i  v?i  v   v  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_149105325_   3384 AAAAA-ATAGTT----------------------------------TCCA 3398
                           i  -iv    ----------------------------------  v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_149105325_   3399 GGTTGATT------TTACATGTAAGAG--------ATAAA-C-----GAA 3428
                         ii v   i------i  v         --------     - -----   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_149105325_   3429 GATAACATTGGAGAATATCTTCAGGACCTCGGGGTGGGGAAA---TACTT 3475
                           v     v  ? v v      iv     i   v i  v  v--- v   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_149105325_   3476 AAATAAAATTCAAAAAGTACTAATTAATAAGAAAAAGACT-GATAAATTG 3524
                          i   vi iv v     i  -  vi  i  i i   i v -         
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCAC-AAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_149105325_   3525 TACTGCATTAAAAGTAGGAATGTTTATTCTTTTAAAGATAGCATTAG--A 3572
                         v   v   i    v  ii  iv   i v   iv  i  i vi  i i-- 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_149105325_   3573 AGAGAGATGTACAAGCCACACAGTGGGAGGATATA----CAAAACACATT 3618
                           v  i v -    v     v i      i v   ----    v  i  v
  L1M4_orf2#LINE/    690 AGTGAAAAG-ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_149105325_   3619 TAACCAATAAAGGAATC-TGTCCTGAATATAAAAATAGCTTCTATAAATC 3667
                          -- ii    i   v i- i   v       v   v i  ii  i  v  
  L1M4_orf2#LINE/    739 T--CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_149105325_   3668 AATAA--AAAATACAGTTAACTCAATGGAAAAATGAATACCTTAGGA--- 3712
                              --    v   iv    i    v?       iii v---    ---
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA---AGGATTT 833

  chr1_149105325_   3713 ------ACGTTAC--AGAAAAGGATATCCAAATGGCCAATAAACATATCA 3754
                         ------  i  v --vi  i i     v              i  i  v 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_149105325_   3755 AAAC-TTCTCAACCTTGTTATGCAC 3778
                            v- v      v ii????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (133 / 100)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 3.74 (127 / 34)  


1115 31.28 6.62 2.97  chr1_149121823_149124259.rev     1076  1951 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149121823_   1076 TGGAGTGACATTCCATAT-CTTGGGGGAGATGACTTAATATTATAAACAT 1124
                             iv  i  i    i - v   ivvi  v           i v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149121823_   1125 GTCAGT-----TCATATTAATCTATACATTCAACACAATCACAAATACTT 1169
                          v  i -----i  v   i     i v       i     v ---  -- 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC---TA--T 95

  chr1_149121823_   1170 CAAAATATTTGTGTTGAATTTCTTG-AGAAGTT--CAA--TAA-CCTCAA 1213
                               viiv i--  vv   i   -    i  --   -- i -   v  
  L1M4_orf2#LINE/     96 CAAAATCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_149121823_   1214 GTTTTTATGGAAGAATAAAG-ATCCACGAACAGGTAAGTCAACATTTCAA 1262
                         i  iv       ivii  i - i   -   i  vi  iv   i-i  v  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAAT-CTTGAA 191

  chr1_149121823_   1263 GAAAAAGG-CAAAGAATGG-GTACTTGCCCTTCCAAGTATTAAGACATAC 1310
                         i  i   i-     v-   - v   ii v     v i v i  i  v   
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_149121823_   1311 TACACAGTCA-AGTAATAATAACAATGTGATATTATTGCA-----AT-GA 1353
                             v  ii -      v vi   i    i  i i--   -----  -  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTG--GCATAAGGATAGA 288

  chr1_149121823_   1354 CAAAAAGATCAGTGAAACATGATAAGGAGCTTAGAAATTAA---GTATGT 1400
                           v v      i  i  i vi  vii   iii      v  ---i  ii 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_149121823_   1401 TTATATGGGAACTTAATATATAGTAAAGTGGGTACCA----TATATCAAT 1446
                             --  vv v  i  v viiii  ---    i   ----i  -     
  L1M4_orf2#LINE/    339 TTAT--GGTCAATTGATTTTCGACAA---GGGTGCCAAGACCAT-TCAAT 382

  chr1_149121823_   1447 GGGAAAAGGGCAGATT----AATAGAAGGAGTTGCAA-ACCTGGCTCAT- 1490
                            i    iii  vi ----  i i v  v i  vi - v    ---  -
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG---ATA 429

  chr1_149121823_   1491 GCCATAGATAAAA--ACAAAATTGGATATTTACCTAAAGTCACATACAAA 1538
                         ?   i vii    -- ii  i     ivii     v vii  i       
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_149121823_   1539 GATAGACTGCAAATGAAATAAATATCTGAATGTGA-AGCTTAAAACAACA 1587
                         i  vi   vv     i vi ? v i  i     i -    -     v i 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATA 528

  chr1_149121823_   1588 AAGTAAAGAGAAGAAAATATGGGAAAATACCTTAGTAATCTCAGCACAGG 1637
                           iivvvv         i  i  ?iv v i   v  i i  ii vvi   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_149121823_   1638 AAAGAACATTGTAGATAGAACTTTACAGGCACACATAATACAA----AAC 1683
                         v  viiiv iv      vi  vii v i     vii  i v  ----  v
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_149121823_   1684 TAGTGATGACTTTTATTACATCATAATTAAAGATTTCTGTTCAGTGAAAG 1733
                            --  i v  vv i v     v       i i  i   v vvii  i 
  L1M4_orf2#LINE/    629 TAG--ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_149121823_   1734 ACACCACGAACAAAGTTAACAGAGAGAAGACACATTG----AAATTATTT 1779
                             i iv  v     v  v   v ivvv   v v  ----   v     
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_149121823_   1780 GCAGTGTC-TAAAAATAACAATGTACTAACGTCTAGAACATACAATGAAC 1828
                            i-i  -  v vv i i  v v   viii  i    i   i  v    
  L1M4_orf2#LINE/    727 GCAA-ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_149121823_   1829 TTCT-TAA---AGTAA--AAAAGAAAATTAAC--AG---AAAAATGGACA 1867
                          ii -i  --- i   --      v  v    -- i---        i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_149121823_   1868 AAGTATTTGAACAGGCAATGTATAGAATAGGGTAATCAAAATGGCTTACA 1917
                            v       i  i  v vivivi  v i i  - vv       iv i 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATA-TACAAATGGCCAATA 874

  chr1_149121823_   1918 AATATACATAAAGATGTTCAAACTCATGGATAAG 1951
                          ii i iiv       i    vv   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (157 / 114)
Gap_init rate = 0.05 (42 / 908), avg. gap size = 2.00 (84 / 42)  


2825 21.44 4.18 9.21  chr1_149155782_149158679     1450  2405 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149155782_   1450 TGAAGAGTCATCCT-TGTTCATGGACTAGAAGACTTAATATAATTAAGTT 1498
                           i i  vi    i-          i i             vi     v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149155782_   1499 GTCAAT-TTCCCCCAATT-AT-TAGAAATGCAACAACATCCTAATAAAAA 1545
                          v    -i     v    -  -  v i  v    ivv    iv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149155782_   1546 TTCTAATGGTCTTTTTCTTTAATGGTCTGTTTTATATTAATGGGCAAACT 1595
                          i i iiv i      ---------------- ii vv   v i   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT----------------TGCAGAAATTGACAAGCT 134

  chr1_149155782_   1596 GATTCTAAGATTTAAAGGGAAAGGGAAAGGAACTGGAATAGCCAAAACAA 1645
                            i    i   i v v     v v  i   v ii               
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_149155782_   1646 CAT-----AAGAA-AACAGAATCGGAAGACTCACACTGGTTGTCTTTAAG 1689
                         iv -----     -    i i i   i          vviiivi  i  i
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_149155782_   1690 ACTTAGTATAAAGCTGCAGTAATCGAGAAAGTGTTTCATTAGCA-AAGTT 1738
                              v  i      i        i   v     vvi i i   -   vv
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_149155782_   1739 TAGTCACTTAGAACAATGGAATAAA-------GTTCATAAATAGACCCAT 1781
                            v  iv    v          i -------  i  v     i      
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_149155782_   1782 GCTGATATGTTCAGGTAATTTTCAACAGATGTACAAAGGC-ACTAATTGG 1830
                         i vvv    v   iv i      i   iiv  i v   i - i v v   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_149155782_   1831 GGAATGA-TAATCTTTTCAACATACGGAACTGGAACAATTGGATAGCCAT 1879
                             v  -  i           v i  vi    i    i      ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_149155782_   1880 ATGCCAGAAAGAGAGAGAGAGAGGGAGACAGAAGGAGAGAGAGAGAGAGA 1929
                             ----------------------------------------------
  L1M4_orf2#LINE/    435 ATGC---------------------------------------------- 438

  chr1_149155782_   1930 ACAAAAAGAATGAAAAAGAGCTTTGTTCCATATTTTGCACCGTATACAAA 1979
                         ---           i------  v vi  v  ii ii    i        
  L1M4_orf2#LINE/    439 ---AAAAGAATGAAG------TTGGACCCCTACCTCACACCATATACAAA 479

  chr1_149155782_   1980 AATTACCTTAAAATGAATCGTAGACCTAAATGTCAAACCTCAATGAATAA 2029
                              v  i      i   i?            v i v  v  vvv    
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_149155782_   2030 AATATGATTAGAAGAAAACATAGGAAAAAATCTTTGGGACCTTGAGCTAT 2079
                           ivi--                 ?iv       i v       i i  v
  L1M4_orf2#LINE/    530 AACTC--TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_149155782_   2080 ACAAGGTTTCTGAGATTGATTTCTTAGATTTGACATTGAAAGCACAATTC 2129
                         i   ------------  i          v     iii         viv
  L1M4_orf2#LINE/    578 GCAA------------TGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_149155782_   2130 ATAAAAGAATAAAAAATTGAAAAATCGAACATCATAAAAATTTAGAATTT 2179
                          i       ---     v  v    i i  v    v      v i  i  
  L1M4_orf2#LINE/    616 ACAAAAGAA---AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_149155782_   2180 -----CTTTGAAAGATACTATTATGAGGATGATAAAATAAGCCACAGATT 2224
                         -----   ii  i  i     i v  iii   v  i i  v       v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_149155782_   2225 GGGA-----TATTTGCAAATCACGTATCTGTTAAAAGGCTTGTATCCAGA 2269
                             -----             ii      v   ii i            
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_149155782_   2270 ATATATTAAGAACTCTTAAAACTCAATAACGAGAAAATAAACAACTCAAT 2319
                               v           v          ii i  i i   i   i    
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_149155782_   2320 GAATAAATGGGCAAAAAATTCGAATAGACATTTCACCAAAGAAGATATAT 2369
                         v? v           ii   i             v              i
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_149155782_   2370 TAATGTTAAATGTGCA----------TGTTCAACATCACTGGTCCT 2405
                         v    viv   iv   ----------  i         ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (119 / 82)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 6.74 (128 / 19)  


2308 24.59 3.80 0.33  chr1_149181289_149182880      494  1099 (493)    L1M4_orf2#LINE/L1      282   908 (0)  

  chr1_149181289_    494 GGTTGGACATA--GACCAATGGAATAGAACAGTGAACTCAGAGATAAGTT 541
                           v i      --  i             iv v  iii    i    iii
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_149181289_    542 TACATATTTACAGCCAGTTGATTTTTCAGCAAAGTTACCAAGAACATACA 591
                         i i i     ii i  i        - ii   i v i      v   v  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTT-CGACAAGGGTGCCAAGACCATTCA 380

  chr1_149181289_    592 CTAGGGAAAGGACACCCTCTTCCATAAATAGTGCTGGGAAACCTGGATAA 641
                         v i       i i vi  i   v i    i         v v       ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_149181289_    642 CCATTTACAGAAGACTGAAACTAGACCCCTATCTTTTACCGTATATGAAA 691
                            iv i  i    v    ii i        i  ivi   i    ii   
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_149181289_    692 ATCAACTCAAACTGGATTAAAGACTTAAACATAAAACTCAAAGCTATAAA 741
                           i        v     i ?    i    ii   i vii   i       
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_149181289_    742 ACTACTGAAAGAAAACA---GGGAAAATATTTCAGGACATTGGTCTGAAC 788
                            vi ii         --- ? v    -i   iv   v    vi iii 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGC 579

  chr1_149181289_    789 AAAGATTTTATGGCTAAGACTTCAAAAGGACAAGCAACTAAATCAAAAAT 838
                           v i   iv i v  v   vi      v         v   vv      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_149181289_    839 AGGCAAATGGCACTATGTTAAACTAAAAAGCTTCCGCGCAGCAAAGGAAA 888
                           ii    v v   vii i   v v    i   ii i  vv       v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_149181289_    889 C----AAAAGAGTAAAAAGACAACGTGTAGAAGGGGAGAAAATATTTGCA 934
                          ----  i i   i          viii    v                 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_149181289_    935 AACTATTCA-CTGATAGGGGACTAATATCCAAAGCATACAAGGAACTC-- 981
                           ii  vi -      i      vi      i ii   i  i      --
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_149181289_    982 --AACTCAACAA--------CAAATAATCCTATT-AAAAATGGGCAAAGG 1020
                         --       i  --------       i  v   -               
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_149181289_   1021 ATCTGAATAGACATTCCTCAAAAGGAGACAGACAAATGGCTAACAGCTAT 1070
                           i            i   v    i   i v         i  i ivi i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_149181289_   1071 ATGAAAAAATGCCCAACATCACTAGTCAT 1099
                                i    i        ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (100 / 46)
Gap_init rate = 0.01 (9 / 627), avg. gap size = 2.78 (25 / 9)  


3187 26.74 0.88 0.55  chr1_149186002_149187858.rev      462  1366 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149186002_    462 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATGAATATCGTGAAAAT 511
                              ii    i     i      i v      v v     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149186002_    512 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 561
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149186002_    562 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 609
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_149186002_    610 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 659
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_149186002_    660 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTCTACTACAAGGC 709
                                i      vv   ii  v  ii i      vii        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_149186002_    710 TACAGTAACCAAAACAGCATGGTACTGGTAACAAAACAGAGATATAGATC 759
                                 i   i    ii         i vv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_149186002_    760 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAACT 807
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_149186002_    808 ATATGATCTTTGACAAAGCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 857
                          vv    i  i     i v  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_149186002_    858 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAAGTAGAAAGCT 907
                           v  i  i              v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_149186002_    908 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 957
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_149186002_    958 TTAAAAACTTAAACGTTAGACCTACAACCATAAAAACCCTAGAAGAAAAC 1007
                          i ? i  i    i  v   v   v   i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_149186002_   1008 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1057
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_149186002_   1058 AACACCAAAAGCAATGGCAACAAAAGCCAACATTGACAAATGGGATCTAA 1107
                         i            vvi          vv  v  v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_149186002_   1108 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1157
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_149186002_   1158 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 1207
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_149186002_   1208 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1257
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_149186002_   1258 AAA--AATGACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 1305
                          i --   i    v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_149186002_   1306 TCAAAAGAAGACATTTA--TGAGCCAAAAAACACATGAAAAAATGCTCAC 1353
                           v        i  vi --  -     v  i          i       v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATG-GCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_149186002_   1354 CATCACAGGCCAT 1366
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3262 26.65 0.55 0.55  chr1_149217012_149221960.rev     3551  4458 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149217012_   3551 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 3600
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149217012_   3601 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3650
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149217012_   3651 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3698
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_149217012_   3699 TACGAAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 3748
                           i i  viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_149217012_   3749 AACAAAGCTGGAGGCATCACACTACCAGACTTCAAACTATACTACAAGGC 3798
                                i      vv       v  vi i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_149217012_   3799 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3848
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_149217012_   3849 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3896
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_149217012_   3897 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3946
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_149217012_   3947 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3996
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_149217012_   3997 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGGTGGA 4046
                            ii    i    v   i     v           i  i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_149217012_   4047 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4096
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_149217012_   4097 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4145
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_149217012_   4146 AAACACCAAAAGCAATGGCAACAAAAGCCAACATTGACAAATGGGATCTA 4195
                         vi            vvi          vv  v  v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_149217012_   4196 ATTAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4245
                           i   v    i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_149217012_   4246 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 4295
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_149217012_   4296 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4345
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_149217012_   4346 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 4395
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_149217012_   4396 CTCAAAAGAAGACATCTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 4445
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_149217012_   4446 CATCACTGGCCAT 4458
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2905 24.15 6.77 0.82  chr1_149238423_149240659.rev      890  1746 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149238423_    890 TGGAAAAACATTTCATGCTCATGGATAGGAAGAATCAATATTGTTAAAAT 939
                               i i  ii    i        v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149238423_    940 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 989
                            v     v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149238423_    990 TACCAGG-GTC--------AGAATTAGAAAAAA-AATTCTAAAATTCATG 1029
                          v    v- i --------    v v  v  iv-i  i           i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_149238423_   1030 TAAAACAAAAAAAAAAAAAGCCCA-AATAGCCAAAACAATCCTAGGCAGA 1078
                          ii  ----- viv  iiii    -                i iiiv ii
  L1M4_orf2#LINE/    151 TGGAA-----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_149238423_   1079 AAGAAGAAACCTGGAGGAATCATATTATCTGACTTCAAACTGTACTATAA 1128
                              v   vi       v   i i vi ii i      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_149238423_   1129 GGCTACAGTAACCAAAACAACATGGTACAGG--TAAAAATAGACACATAG 1176
                         i          i   i   iii      v  --   ii       i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_149238423_   1177 ACCAAAGGAACAGAATAGAGAGCCCAGAAATAAAGCTACACAGCTACAAC 1226
                          i   v    i     v     i           v i i   vi  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_149238423_   1227 TATCTGATCTTCAAC--------------CATTTA--------------- 1247
                         i vi    i   i  --------------    i ---------------
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_149238423_   1248 --TCTTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATACAGAAGAT 1295
                         -- i     i              i      v  ?   i  i  i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_149238423_   1296 TGAAACTAGACCCCTTCCTTACACCATATATAAAAATCAACTCAAGATGA 1345
                             ii i       v   i          i      i       i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_149238423_   1346 ATTAAAGACATCAATGTAAAACCTAAAACTATAAACACCCTT-GAAGAAA 1394
                           i ?    v v       i v             -  i   -       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAA 544

  chr1_149238423_   1395 ACCTAGGAAATACTATTCTGGACATAGGCCCTGGCAAAGATTTTATGACA 1444
                           v    ?ivv v v   vv   v v  viiv     v i   iv iivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_149238423_   1445 AAGACACAAAAAGCAATTGCAACCAAAACAAAAATTGGTAAGTGGAACCT 1494
                          v     v       vvv     v   iv      v i   i v i  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_149238423_   1495 AATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCAACAGAGTAA 1544
                         v  i   v v  i i   i  iiivv    i  v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_149238423_   1545 ATAGACAACCAACATAATAGGAGAAAATATTTGCAAACTATGCATTTGAC 1594
                          v        v   v   i                  ii  ii  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_149238423_   1595 AAAGGTCTAATATCCAGAATCTATAAAGAA--------ATT-AACAAGCA 1635
                           i  v  vi          v         -------- i -  i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_149238423_   1636 AAAAACAA----CCCCATTAAAAAATGGGCAAAGGACATGAACAGACAAT 1681
                            i    ----   v   ?                iv    i     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_149238423_   1682 TTTCAAAAGAAGACATATACATGGCCAAAAAGCATATGAAAAAAATATTC 1731
                          i  v        i   i v        v     i       i - ii  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chr1_149238423_   1732 ATCATCACTAGTCAT 1746
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (123 / 80)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.64 (65 / 14)  


3086 26.06 4.00 0.23  chr1_149313058_149317313.rev     2891  3765 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149313058_   2891 TAAAAAAAAATTCCATGCTCATGGATAGAAAGAATCAATGTCATTAGAAT 2940
                          ii   i v  i     i        v i    v i   i ii   ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149313058_   2941 GTCCATACTTCCCAAAGAAATTTACAGATTCAATGCTATTCCTATCAAAC 2990
                          v v     i      vvi  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149313058_   2991 TACCAATGGCATTTTTCACAGAACCAGAAAGAACT-ATTTTAAAATTCAT 3039
                          v   iiv  v     ii     viv  v - i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr1_149313058_   3040 ATGGAG----------CCCA-AATAGCCAAAGCAAGCCTAAGCAAAAAGA 3078
                              i----------    -          i   v i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_149313058_   3079 ACAAAGCTGGAGGCATCATGTTACCTGACTTCAAACTACACTACAGGGCT 3128
                               i      vv   iii v  ii i      vivi      ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_149313058_   3129 ACAGTAACCAAAACAGCACAGTACTGGTACAAAAACAGACACATAGACCA 3178
                                i   i    iiii       i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_149313058_   3179 ATGAAACAGAATAGGGAGCCAAGAAATAAGGCCACAAACCTATGATCATC 3228
                            i  i     v i   i v        iv   i v ii    i   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_149313058_   3229 TGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGACTCTCTA 3278
                             i  i     i v  v   i v  vv            i ivv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_149313058_   3279 TTCAGTAAACGGT---------------TACCCATATGCAAAAGATTAAA 3313
                             ii   i   ---------------  ?   i          v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_149313058_   3314 ATGGGACCCCTTCCTCTCACCATATACAAAACTCAATTCAAGATGGATTA 3363
                         i v        v    v              v i  i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_149313058_   3364 AAGATTTAAATGTAAAACCCTAAACTATAAAAACCCCAGAAGACAACCTA 3413
                         ?   ii         i v iv           vi ii      v   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_149313058_   3414 GGCA-ATACCATTCAGGACGTAGAAACAGGCAAAGATTTC------ATGA 3456
                           ?i- v i -   iv   v v iivi      v i    ------    
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_149313058_   3457 TGCCAAAAGCAATTTCAACAAAAGCAAAAATTGATAAATGGGATCTGATT 3506
                         ii         vvvv         v      v       v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_149313058_   3507 AAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCAACAGAGTAAACAG 3556
                            v v  i i   i  iiivv    i  v        v i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_149313058_   3557 ATAACCTACAGAATGGGAGAGAATATTTGCAAACTGTCCACCTGACAAAG 3606
                          i    i             i            iii vi i    i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_149313058_   3607 GTCTAAAATCCAGCATCTATAAGGAACTTAAATAAATTTACAAGAAAAAA 3656
                          v  viv      v  v     i     ivv i  v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_149313058_   3657 GCAAACACCCCA-TTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTC 3705
                         i    i v    -  ?    i           iv    i     i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_149313058_   3706 AAAAGAAGACATACATGTGGCCAACAAGCATATGAAAGAAAGTTCAGTAT 3755
                         v        i     vi       i     i      ii v i   ii  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_149313058_   3756 CACTGATCAT 3765
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.73 (142 / 82)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 4.11 (37 / 9)  


3158 27.72 0.55 0.66  chr1_149333588_149339967.rev     4981  5889 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149333588_   4981 TGAAAGAACATTCCACATTCATGGACAGGAAGAATCAATATCATGAAAAT 5030
                           i  ii i  i   ii        iv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149333588_   5031 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 5080
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149333588_   5081 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5128
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_149333588_   5129 ATATGGAACCAAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCCAAAA 5178
                                 viiv  ii  v  vvv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_149333588_   5179 GAACAAAGCTGGAGGCATCACGCTAACTGACTTCAAACTCTACTACAAGG 5228
                                 i      vv    i  vv ii i      vii        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_149333588_   5229 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5278
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_149333588_   5279 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5326
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_149333588_   5327 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5376
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_149333588_   5377 TCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5426
                            v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_149333588_   5427 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAAGCAATTCAAGATGG 5476
                             ii    i    v   i     v          vi  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_149333588_   5477 ATTAAAGATTTAAATGTTAGATGTACAACCATAAAAACCCTAGAAGAAAA 5526
                           i ?   ii       v   vv  v   i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_149333588_   5527 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAA-GGTCTTCATGTCT 5575
                          v    ?i v viv   iv   v v  vv i     -   -   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGAT 594

  chr1_149333588_   5576 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5625
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_149333588_   5626 AATTAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTGA 5675
                         v  i   v    i i   i  ii vv    i  v    ii vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_149333588_   5676 ACAGGCAACCTATAGGATGGGAGAAAATGTTTCCAATCTACTCATCTGAC 5725
                          v  i     i i  i            i   v   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_149333588_   5726 AAAGGGCTGATATCCAGAATCTACAATGAGCTCAAATAAATTTACAAGAA 5775
                           i  i  vi          v  i  v  i   vv i  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_149333588_   5776 AAAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACT 5825
                            i     i     v  i? v  i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_149333588_   5826 TCTCAAAAGAAGACATTTATGCAGCTAAAAAACACATGAGGAAATGCTCA 5875
                             v        i  vi viii  i  v  i       ii i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_149333588_   5876 TCATCACTGGCCAT 5889
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


 454 26.72 0.86 0.00  chr1_149376725_149381254.rev     2834  2949 (1581)    L1M4_orf2#LINE/L1       15   131 (777)  

  chr1_149376725_   2834 ATGTTCATGGTTTGAAAAAGTTAACATTGTTAAAATGTTCATATTACTCG 2883
                                   v   i  i v    i        i   viv   i v i i
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_149376725_   2884 AAGTGATCTGTAGATGCAATACAACTTACATCAAAATTCCA-TTGCCATT 2932
                           v      ii    v   ii   iiivi        i   -i    v  
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr1_149376725_   2933 TTCACAGAAATAGAAAA 2949
                           ii       v  v  
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAA 131

Transitions / transversions = 1.82 (20 / 11)
Gap_init rate = 0.01 (1 / 117), avg. gap size = 1.00 (1 / 1)  

2759 24.13 2.70 2.70  chr1_149376725_149381254.rev     3261  4039 (491)    L1M4_orf2#LINE/L1      130   908 (0)  

  chr1_149376725_   3261 AAAATAATCTTTAAATTCACGTGAAAGCACAAAAGACCACAAACAGTTCA 3310
                           iv i   i v       ii  i  iii   ii    vvi  i  i-  
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC-CA 178

  chr1_149376725_   3311 AGGCAATCTTGAACAAAAATAACAAAGCTGG-GGATATCACCTGACCTAT 3359
                          ii          v  i  v       i   -   i-    vivv  i v
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAA 227

  chr1_149376725_   3360 TTTTGAAATCTACTACAAAGCTACAGTAGTAAAAACAGCACAGTGCTTGC 3409
                            ii   ii                  i v  i    iiii  i  v  
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_149376725_   3410 ATAAAAACAGACACATAGACAAATGGAACAATTTAGTAGAAAGCCAGGGA 3459
                             ii i     i     iv       i i--- i v  i  i vi i 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAG---AATTGAGAGTCCAGAA 324

  chr1_149376725_   3460 ATAAACCTAAGCGTTCACAGTCGATTGACTTTTGACAAAGGTACCAAGAA 3509
                                i vi i  i ii   i     i   i     i   i      v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_149376725_   3510 CACACAATGGGTAAAGGACAGTCTCTTCAATAAGTAGTGCTGGGAAAACT 3559
                           iv       v    i i     i     i  i i         v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_149376725_   3560 GGTTATC---ATGCATAAAAGTGAAATTAGACCTTTATTTTGCAGCATAC 3606
                           v  ? ---     v  i i    i  i    ii  ii ii  v    i
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_149376725_   3607 ACAAAAATAAACTCAAAATGGATTAAAGACATAAACATAATACCTGAAAC 3656
                                 v              i ?    v    ii   v v  i    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_149376725_   3657 TTTAAAACTATTAGAAGAAAACATAGGGGGAAAGCTCCATGACATTGCTC 3706
                          v       v                 ? v   v  i i    v   ---
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG--- 571

  chr1_149376725_   3707 GG---GGCAATAATTTTTTGAATATGACCCTGAAAGCTCAGGCAACGAAA 3753
                           ---      ii   i  ii       v ii     v  i     i   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_149376725_   3754 GCAAAAATAGAAAAATTGGATTGCTTTTGTTAGTTAAACTAAAAACCTTC 3803
                          v         v        i ---- ii i ---   i       i  -
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACT----TCATCA---AAATTAAAAACTTT- 663

  chr1_149376725_   3804 TGCACAGCCAAAGAAC-CAATTAACAAAGTGAACAGACAACCCACAGAGT 3852
                           ii -vi     i  - v  i  v        v              i 
  L1M4_orf2#LINE/    664 TGTGC-TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_149376725_   3853 GGAAAAAAA-ATTTGCAAACCATATATCTGATAAAGGGTTAATATCCAAA 3901
                           i i    -         i              i  ii vi      i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_149376725_   3902 ATATGTAATGAACTC----AACTCAGTAGCAAGAAAA-AAA-------AT 3939
                             i   v      ----      i  ii  i  i -   -------  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_149376725_   3940 TTGAACATGGGGAAAGAACTTTAACAGACACTTCTCAAACAAAGACCTAG 3989
                          ?i  v     v    i i  v  i     i     v  vi    iv  v
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_149376725_   3990 GGATGACCAACGGGTTTAGGAAAAAAAAAAAACTCAGCATCACTAATTAT 4039
                         ii   i    iii ivi v     i vi----    i     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATG----CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.54 (132 / 52)
Gap_init rate = 0.02 (17 / 779), avg. gap size = 2.47 (42 / 17)  


2289 23.63 2.82 1.41  chr1_149419273_149421280      465  1103 (905)    L1M4_orf2#LINE/L1      166   813 (95)  

  chr1_149419273_    465 CCCTGAAC--CCAAAATAA------AAGATAAAAATTAAAAAACTAGAGG 506
                            v   i--      i  ------  i v  i  i---   ii i    
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC---AAAGTTGGAGG 212

  chr1_149419273_    507 AATCATATTACCTGACTTCAAATTATACTACAGAGCTATAGTAACCAAAA 556
                          v   i i v  ii i      viv       i     i     i   i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_149419273_    557 CCGTATGGTATTGGCATAAAAACAGACATATAGACCAATGGAATCAAATA 606
                          v  i     i        ii i           i         vi   v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_149419273_    607 GAAAATCCAGAAATAAATTCATATATCTCCAGTAAACTCATTTTTGACTA 656
                           i i            ii    i  i vii  v  i v     i   v 
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_149419273_    657 AGGTGCTAAGAATATACATTGAGGAAAGGACAGTCTCTTCAATAAGTGGT 706
                         i     i    vi  v  v  i      i i     i     i  i    
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_149419273_    707 GCTGCAAAAACTGGATATCCATATGCAGAAGAATGAAACTCAACC--TAT 754
                             vi v         ?   i     i         ii vi   --  i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_149419273_    755 CTATGGCCATATA-AAAAATCAAATCAAAATGGACTA-AGACTTGA-TGG 801
                           vvvi       -      i  v          ii -    i i -  v
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_149419273_    802 ACTTAGACCTCAAAATATGAAACTACTATAAGGAAACATTGGGGAAACTC 851
                          ---   v  v   v   i     vi  v   i      v  ? v  v  
  L1M4_orf2#LINE/    513 A---AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_149419273_    852 TCTAGGATGTTGATCTGGGCAAAGATTTCTTAAGTA--ATATCCCAAAGC 899
                          iiiv  iv   ivi i     v i       ii  -- i -  v     
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA-CCAAAAGC 608

  chr1_149419273_    900 ACAGGCAACAAAAGCAAAA-TGGACAAATTGGATCACATCAAA-TTAAAA 947
                            i          v    - i  i        iiv       -      
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_149419273_    948 AGCTTCTGCACAGCAAAGGA-ACAATCAATGAAGTGAAGAGACAACCCAC 996
                          -   i  ii vv       -  v     vi       i           
  L1M4_orf2#LINE/    659 A-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_149419273_    997 AGAATGGGAGAATATATTTGCAAACTATCCATCTGACAAGAGATTAGTAA 1046
                                     v           ii  vi      i   i  i v   v
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_149419273_   1047 CAACAATATATAAGGAACTCAAAAAACTGTATAGGGAAAAAGTCTAATAA 1096
                          v v         i      vv v    vv   iv-      v v     
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAAAAGACAAATAA 806

  chr1_149419273_   1097 TCTGATT 1103
                         i ii   
  L1M4_orf2#LINE/    807 CCCAATT 813

Transitions / transversions = 1.61 (92 / 57)
Gap_init rate = 0.02 (15 / 648), avg. gap size = 1.80 (27 / 15)  

 426 21.30 0.00 0.93  chr1_149419273_149421280     1414  1521 (487)    L1M4_orf2#LINE/L1      802   908 (0)  

  chr1_149419273_   1414 AATAACCCGTTTTTAAAATTGGGCAAAAGACATGAATAGACATTTATCAA 1463
                                 i-v  ?    v        i  iv             v  v 
  L1M4_orf2#LINE/    802 AATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_149419273_   1464 AAGCAGATACACAAATGTCAAACAGGCATATGAAACGGTACTCATCGGCG 1513
                            v     i       v v  i i   i      v i i    v iv i
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_149419273_   1514 CTTGTTAG 1521
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.00 (11 / 11)
Gap_init rate = 0.01 (1 / 107), avg. gap size = 1.00 (1 / 1)  


2795 24.28 0.72 0.29  chr1_149500306_149501993      500  1195 (493)    L1M4_orf2#LINE/L1      210   908 (0)  

  chr1_149500306_    500 AGGCATCACACTACCTGACTTTAAAATATACTACAAAGCTATAGTAACTG 549
                            vv       v  ii i  i    iv             i     iii
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_149500306_    550 AAACAGCATGGTACTGGCATAAAAACAGACACATAGACCAATGGAACAGA 599
                          i    ii              ii i     i     i        i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_149500306_    600 ATAGGGAACCCAGAAATTAATCCATATATTTGCTATCAACTGATCTTTGA 649
                           v i  ii        v  i     i    iivi    i    i  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_149500306_    650 CAAAGGTGCCAAGAACACACAATAGGGAAAGGAAAGTCTCTTGAATATGT 699
                            i          v  iv    i       i v     i  v  i vi 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_149500306_    700 GGTACTGAAAAAACTGGGTATCCTCATGAAGAAGAATGAAATAAGATGCT 749
                            i   ii v      i  ?  v    v i         i vi  iv i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_149500306_    750 TATCTCACACTGTATACAAACATCAACTGAAAAATGAATTCAAAATGTAA 799
                           i       ii        v  i    v    -  i  iv? i iv   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAA-TGGATCAWAGACCTAA 508

  chr1_149500306_    800 ATTTAAGATTCAAAACTATGAAACTACTAGGAAAAAA-ACAGGGGAAAAG 848
                           v     vii        i     vi   i i    - i   ? v   v
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_149500306_    849 CTCCATGACATTGGTCTGGGCAAGGATTTTTTGAATATGACCTCAAAAAC 898
                           i i    v    vi i     v i   i  ii       vi     i 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_149500306_    899 ATAGACAACAAAAGCAGAAACTGACAAATAAGATTAAATCAAG-TTAAAA 947
                          i ii         v i   iv  i    vi  i vv     i-      
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_149500306_    948 TGCTTCTGTACAGAAAAGGAAATAAGCAACAGAGTAAAGAGACAACCTAC 997
                         -i   i   i vvv      v iv v   v i   i  i        i  
  L1M4_orf2#LINE/    659 -ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_149500306_    998 AAAATC--AGAAAACATTTGCAAACTATACATCTGATAAGGAGTTAATAT 1045
                          i   v--      i         ii   i           iii vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_149500306_   1046 CCAAAATATATAAGGAACTCAAACAACCCAATAGAAAGAACACAAATATC 1095
                            i         i      vv     i     iv  i  v       v 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_149500306_   1096 CCAATT-AAAAATGGGCAGAGAATCTGAATATACATTTCTCAAAAGAAGA 1144
                               -           i  i  i      v         v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_149500306_   1145 CGTACAAATGGCCAACATGTCTAGAAAAAAATGCTCAATATCACTAATCA 1194
                         ii             i v ivi vi    i        i    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_149500306_   1195 C 1195
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.07 (112 / 54)
Gap_init rate = 0.01 (6 / 699), avg. gap size = 1.17 (7 / 6)  


 315 26.25 1.25 0.00  chr1_149576764_149579113      495   574 (1776)    L1M4_orf2#LINE/L1      166   246 (662)  

  chr1_149576764_    495 CCTCAAATAGCCAAACCAATGCTGAAGAAGAAAAATATAGTTAGAGT-CA 543
                           ivi          v    vi    i     i  i v    i   v- v
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_149576764_    544 CATACTTCCTGACTTTAAAACTTATCACAGA 574
                           i      ii i  i        ii   i 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAA 246

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.01 (1 / 81), avg. gap size = 1.00 (1 / 1)  

 370 19.16 7.78 8.98  chr1_149576764_149579113      689   855 (1495)    L1M4_orf2#LINE/L1      192   356 (552)  

  chr1_149576764_    689 AAAAAAAAATAAAAGTAAA---TTAACAC-----AATTT-A----TTACA 725
                            i  i  i   iv ii ---i v    -----     - ----    v
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_149576764_    726 ACAAAGCAACCATAATGAAAATAATGTGTTATTGGCATAAAGATAGACAT 775
                                v  vi    v  i i i    v  i        i         
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_149576764_    776 ATAGGTCAATGAAATAGAATAGAAGAGTAGCAGAGAAACTTAAAATAAAT 825
                             i      i        v  -    v-    -------------   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGA-GAGTC-CAGA-------------AAT 326

  chr1_149576764_    826 AAACCTTCATATATATGGTCAAATTATTCT 855
                              ivi i  v         v v   i 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 1.46 (19 / 13)
Gap_init rate = 0.04 (7 / 165), avg. gap size = 4.00 (28 / 7)  

 938 19.89 0.55 0.00  chr1_149576764_149579113      988  1168 (1182)    L1M4_orf2#LINE/L1      347   528 (380)  

  chr1_149576764_    988 AAATGATTCTTGATAAGGGTGCCAATACCACTCAATGGAGAAAGGACAAT 1037
                           v     i i  i           v    i       i     i i i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_149576764_   1038 CTTTTCAACAGGTGGTGTTGGGAAATTTAGATATGCACATGCAAAAGCAT 1087
                                   ii     i     v vi i    ?v            v  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_149576764_   1088 GAAGCTGGACCCTCAGGTTACACCATACACAAAAATTAACTCATTAAGGA 1137
                             i       ii vv i        i               vv v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_149576764_   1138 TCAAAGACATAAACATA-GAGTTAAAACTACA 1168
                            ?    v    ii  -   i        i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

Transitions / transversions = 1.83 (22 / 12)
Gap_init rate = 0.01 (1 / 182), avg. gap size = 1.00 (1 / 1)  

1460 25.00 2.83 1.09  chr1_149576764_149579113     1398  1857 (493)    L1M4_orf2#LINE/L1      441   908 (0)  

  chr1_149576764_   1398 AAGATCATGCAACTGCACTCCAGCCTGCACGACAGA-GCAAGACTCCATC 1446
                             --   v ii  v  i  vi   -   iv  v -i   i v iv - 
  L1M4_orf2#LINE/    441 AAGA--ATGAAGTTGGACCCCTACCT-CACACCATATACAAAAATTAA-C 486

  chr1_149576764_   1447 TCAAAATAAAT-AAATAAATAAAT----------AAACTACAAAATTTCT 1485
                                ii  - ? v vv     ----------      i    i ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_149576764_   1486 AAAAGGAAACATAGGAGGAAATCTTCATGACATTGGATTTGACAATGATT 1535
                          i   i         ? v        i    v    i  v i     i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_149576764_   1536 TCTTAACTATGATACCAAAAGCACAGGCAACAAATGTAAAAATAGATAAA 1585
                              iv     i            i        v v             
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_149576764_   1586 TTAGACTACATAAACATTAGAAATGTATGTGAATCAGTGAACAAAGTCAA 1635
                           i    v   v  v    i   iv v    vv   iv i   vvi    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_149576764_   1636 TACCATGAAAAGGAAATCTTTGTTATGGGAGCAAATATTAGCAAATCGTG 1685
                         v vvi       iv  i iviivv       v       v       i i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_149576764_   1686 TATCTGGTAGTGGGTTGCTATACAAAATATGTAAAGAACCCCCACAATTA 1735
                               i  iv  ii vv   v  i     i        i ii    i v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_149576764_   1736 AACAACAAGTAAACAAACAACCTTATT-AAAAATGGAAAAAAAAACTTGA 1784
                           i  i  iv i     i    iv   -        iv   ii -i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA-TTTGA 835

  chr1_149576764_   1785 ATAGACACTTATCCAAAAGAAATTTACAAATAGCCAAAAGACACATGAAA 1834
                                i  v      ii i  v       i     v ii         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_149576764_   1835 GTATGCTCAACACCATTCATAAT 1857
                         iv          i  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (66 / 47)
Gap_init rate = 0.02 (8 / 468), avg. gap size = 2.25 (18 / 8)  


 420 31.96 8.59 6.41  chr1_149594427_149596469      670  1542 (501)    L1M4_orf2#LINE/L1        1   892 (16)  

  chr1_149594427_    670 TAAAGAGATATACCATATTTATGGGTGAGTAGAAAA---AA-ATTATAAT 715
                          ii i      v    i  i    i --- i   i ---  -   i -- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT---TGGAAGACTTAATATTGT--T 45

  chr1_149594427_    716 AAAATAAAATAATTCTTCATAAATTAATGCATATTCTCAATGATGTTTTC 765
                           i  ii--i   v  i vi     i  vi i vvi    i vvi iiii
  L1M4_orf2#LINE/     46 AAGATGG--CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr1_149594427_    766 ATCAAAATTCTAATAATGATTTGTTTTGCTTCATCTTCATTGTGTAGGAT 815
                                 i i ---------------   v --   --  v  i  i v
  L1M4_orf2#LINE/     94 ATCAAAATCCCA---------------GCTGC--CTT--TTTTGCAGAAA 124

  chr1_149594427_    816 GTGACAAACTGGCTCTAATGTTTATATA-AAATGACAAAGGTTTAATAAT 864
                         v      i   iii    vi  i    i-     -   i  viiv v   
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATG-CAAGGGACCCAGAAT 173

  chr1_149594427_    865 CACCAAGACAATCTT---AAGGAATGATGAAACCTGTGTGATTTAGATAC 911
                         vi    i        ---  i   -  vv   vi  viv  i i v ivi
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAA-GAACAAAGTTGGAGGACTCACACTT 222

  chr1_149594427_    912 CGCAATTG--------ATTATACACCTATGGTAATTAAGGCAGCAGGATG 953
                          v     v-------- i  i v v   ii     i   i   iiv i i
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_149594427_    954 TTCTCAGAGGTGTTGACAAATTGG-CAATGACA-AGAATTGTTCACCCAA 1001
                         i vv  v i vi v    v  v i-     iv -       vvvii   i
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_149594427_   1002 TTATAAATCTACGGAAATGTGAAAAATTGATTCT-GACCCATAGGTATTT 1050
                         vv     i i iiv vv i  ivv        i -   -- vi   iii-
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGAC--AAGGGTGCC- 369

  chr1_149594427_   1051 CAGA----TGAGTGGGGGAAAATGGAAAATTTGATTA-CAA----TACTA 1091
                         v   ---- v i     i  i --- v i i vv i -   ---- i  i
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGA---ATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_149594427_   1092 AGACAATTGGTTATCCA--TTCAGAAAAATG--TTTAAAA---TAT---A 1131
                         i     i   v  ?   -- v  i  i    --v  ii v---  i--- 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_149594427_   1132 TAAAATGTACAAAAATTCCTTTCTTGATTGAATAAAAACCTTCATTTTTA 1181
                         i vv  i          vvi - vvi  v  vi ? i    vv  v ---
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACT-CAAAATGGATCAWAGACCTAAATGT--- 512

  chr1_149594427_   1182 AAAAGAAAAAATTTTCAACTTTTTA-AAGA-----TAGGGAAAAGATTTC 1225
                           i  vv    i v v  vi i   -    -----    ?iv  ivi   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_149594427_   1226 -TAAACTTACAAATGGTTGAG-----ATTTATTAAA-AT--CATGAAAAT 1266
                         - i v   i-----    ii -----i   v   i -  --  iv    v
  L1M4_orf2#LINE/    563 GTGACCTTG-----GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_149594427_   1267 TGCAAACAATATAGTTATTGTTGCAGAAATTCAACTATGTTAAAAATAAA 1316
                         ii   i   i v ivv vviv iv v     vi   vii i    v    
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_149594427_   1317 A-CACTAGTTCATCAAATGACACCATTAAAA---TGCAAACAAGAACATA 1362
                          - vi v  v v     v     i  i  i ---  v   -i v   vi 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GACAACCCA 706

  chr1_149594427_   1363 TTTGTTTGGAAAAGATATTCACAA----CACATTTAATAGCAGTACATTA 1408
                         ivviv v   i  i     ii   ----i i  i i   ivi --- i v
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG---ACTT 753

  chr1_149594427_   1409 GTAACTAGAATATGTAAAGAACATTTACAAAT-ACTAACAAAAGGA--GA 1455
                            v i       i        vi      v - v   i    i  --i 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_149594427_   1456 TAAACAAATTGAAAAACATTTTCGAGAAAAAG-------CAGACAAGTCA 1498
                            v v    ?     i------ i v   i -------i     vv  v
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAAT------GGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_149594427_   1499 C---AGAAGGGAAACCTCAATTAACCAA-AAATACATTAAAAGATGCT 1542
                          ---     iv v  ---  v ii    -  ii    v          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATAC---AAATGGCCAATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.33 (157 / 118)
Gap_init rate = 0.05 (47 / 892), avg. gap size = 2.79 (131 / 47)  


 784 30.07 8.41 6.57  chr1_149607810_149609618.rev      481  1348 (461)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr1_149607810_    481 ATAGAAAGA---AACATTGTCTTAAAAACGTCAATTTTCTGCAAGTCAAC 527
                           v i    ---  i     i---  i i v    vi  iv   i ii i
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTT---AAGATGGCAATACTCCCCAAATTGAT 71

  chr1_149607810_    528 CTGTGGATTCCATGTAATTCTAATGAAAACCACAAGAGAGAGTTCAACAG 577
                           iii     v i i   i iv  v    i v  ivv vvvv  ivi   
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAG 121

  chr1_149607810_    578 AACTTAATGAGCTGATTCTACGACTCAAATCAAACAGCAAGAGGCCCAGA 627
                           v  i ii       i   vi i   v  vi  vv     i i      
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr1_149607810_    628 ATAGACAGGATAACCATGAA---GAAGAATACA--TGG-GAACTTAT--C 669
                             v  ii i  i v    ---      i v --   - i   i i--i
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_149607810_    670 TCACAAAACACCAAGAATAATTATAAAGCAATTGTCGTTCAGAC--TGTG 717
                           v   --ivi   i v v i  i     v iv  vi iv    --    
  L1M4_orf2#LINE/    222 TCCCAA--TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_149607810_    718 ATTTATTGAT-TAAGGAACAATGTGACAGGTTA-TA----AGAACTAAAA 761
                         i -- i  ii-      vvi ii - i  i i - i----    i i i 
  L1M4_orf2#LINE/    270 GT--ACTGGCATAAGGATAGACAT-ATAGATCAATGGAATAGAATTGAGA 316

  chr1_149607810_    762 GTC---------ATTCATTCATGTATGAACCCCTGAAATGTGTCAGAGG- 801
                            --------- ii   v   v    iv vvi   vv vi v  ii  -
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_149607810_    802 --CAGGATTACAGAAAAGTGGGTTAGGAGTAATCAGTTCAGTAAATGATA 849
                         --  i  ii ivv  ---    vv i  i  i  vv    ii     i i
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAA---TGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_149607810_    850 CCATACCAACTGTTTATTCATTTGGGCAATA-AATAAA--TG--CCTCTA 894
                          iiviv      vv  ?i  iv  --   v -   i  --  --  i   
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATG--CAAAAGAATGAAGTTGGACCCCTA 461

  chr1_149607810_    895 CTTCACACCATATAATTAAAATAAATTCCA--TAAATCAAAGATCTAA-T 941
                          i            -iv     v  i  v -- ii    ?   i    - 
  L1M4_orf2#LINE/    462 CCTCACACCATATA-CAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_149607810_    942 GTAGTAAACAAAACTTTAGAAATATATTTAAAATTTTCAAAAATGATTTA 991
                            iv ivi      v  i  v ---i   i  -----i    i------
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACT---CTTAGAA-----GAAAAC------ 546

  chr1_149607810_    992 ATAGAA-TAA--CCTTATGGACTTTTGAT--GGAAAAGATTTCCTAAATA 1036
                             i?-   -- i ii  -  i  v i --  v  v i    i  i   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_149607810_   1037 ATATACATGTGTTCACATCAGAGACAAACACATTACAAACAAACAAA--- 1083
                         ---------  ---   i  i ii  v vi  --     vi  v   ---
  L1M4_orf2#LINE/    596 ---------TG---ACACCAAAAGCACAAGCA--ACAAAAGAAAAAATAG 631

  chr1_149607810_   1084 ---AACCCTTGAGTTTGGTTATA-TTAAA---TTTT---CTTTAACCAGA 1123
                         ---  ---   iii  vi i v -     ---    ---   i  --  i
  L1M4_orf2#LINE/    632 ATAAA---TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA--AGG 676

  chr1_149607810_   1124 AAAC-ATCACAAAAGATGAAAA-------TACAGATTATGAAAAGATATT 1165
                          v  -    vi    -      -------i     v iv  i  i     
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAG-TGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_149607810_   1166 TGCAACACATATAATTGACAACAAATTAGTATCTAAA-----TAAATAAC 1210
                              vv      vi   i  vii i v     i i -----    v   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_149607810_   1211 CCT-ACAAATCAGTGAGAAGAAAGCAA-TGACCCAAAGGAAAAATGAGAA 1258
                         i  -    v   i i v  i  ii   - i      vv?       i v 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_149607810_   1259 AAACACATGAAAATTGATTTC-CAGAAGTGAAAACCTGAATAACCAATAA 1307
                           iv iv    v vvv     - vi   vii v ivii   ii       
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_149607810_   1308 CCAATATGTTTTTGAAAAAGCTTTTCAACCTTGCTAGGAAT 1348
                         v  -i   -------     v vi     v ii????????
  L1M4_orf2#LINE/    876 GCA-CATG-------AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (157 / 100)
Gap_init rate = 0.05 (48 / 884), avg. gap size = 2.71 (130 / 48)  


3113 26.98 0.66 0.66  chr1_149615334_149621675     4942  5849 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149615334_   4942 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4991
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149615334_   4992 GGCCATACTGCCCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 5041
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149615334_   5042 TACCAA-TGCCTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTC 5088
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_149615334_   5089 ATATGGAACCAAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCCAAAA 5138
                                 viiv  ii  v  vvv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_149615334_   5139 GAACAAAGCTGCAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5188
                                 i  v   vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_149615334_   5189 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATACAC 5238
                                  i   i    ii         i iv ii i   v     v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_149615334_   5239 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5286
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_149615334_   5287 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5336
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_149615334_   5337 CCCATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGC 5386
                         i iv  i  i          i   v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_149615334_   5387 TGAAACTGGATCCATTCCTTACACCCTATACAAAAATTAATTCAAGATGG 5436
                             ii    i  v v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_149615334_   5437 ATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5486
                           i ?    i  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_149615334_   5487 CCTAGGCA-ATACCATTCAGTACATAGGCATGGGCAAGGACTTCATGTCT 5535
                          v    ?i- v i -   ivv  v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_149615334_   5536 AAAACACCAAAAGCAATGGCAACAAAAGCCGAAATTGACAAATGGGATCT 5585
                          vi            vvi          vvi    v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_149615334_   5586 AATTAAACTAATGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAATGA 5635
                         v  i   v v vi i   i  ii vv    i  v  i i  vv i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_149615334_   5636 ACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAACCTACACATCTGAC 5685
                          v  i     i                vv       vii i i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_149615334_   5686 AAAAGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5735
                           ii i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_149615334_   5736 AAAAACAAACAACCCCATCAAAAAGTCGGCGAAGGATATGAACAGACACT 5785
                            i     i     v  i?    i v   i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_149615334_   5786 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5835
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_149615334_   5836 TCATCACTGGCCAT 5849
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2785 27.04 3.51 0.79  chr1_149771798_149775457     2284  3167 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149771798_   2284 TGGAAAGATATCTTATGTTCATGGACTAGAAGAATTAATATTGTTAAAAT 2333
                                     ii           i i     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149771798_   2334 GACCATACCACCCAGAGCAATCGATAGATTCAATACAATCCTTCTCGAAA 2383
                          i v    iv    i vii   v i        ii      i v  i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149771798_   2384 GTCCA--TGATATTTTCAAAGAAATAGAAAAAACAATCCTTAAATTCACA 2431
                         vi   --  viv    iiv      v  v  ivii     v       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_149771798_   2432 TGGAATCACAGAAGACCCAAAATTGTCAAAGCAATATTGAACAAAAAGAA 2481
                              vii  iii      i   v i    i    v     v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_149771798_   2482 CAAACCTTGAAGCATCACACTACCTTACTTCAAAATATGCTACAAAGCTA 2531
                             vi v  i vv       v  iv i       iv i           
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_149771798_   2532 TAGTAACAAAAAAAGGCATGGTATTGGCAGAAAAAAACAAACACTA-AAA 2580
                         i     iv  i v  -ii     i     v  ii --i i   -  - i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAG-TGTGGTACTGGCATAAGGA--TAGACA-TATAGA 296

  chr1_149771798_   2581 CCAATGTAACAGA-TAAAGCACTCATAAATAAATCCACGTATTCACATCC 2629
                         i     v  i   - vi  viii  v       i   iii   i iivi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_149771798_   2630 AACTGGCTCTCAAAAATGGCCCCAAGAACATAAACTGGGGAAAAGACAAT 2679
                           i  ii i  i v  v  iv      v   vv v        ii i i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_149771798_   2680 CTCTTCAATAAATTAT-CTGGGAAAACATGG-CATCCATACGCAGAGGAA 2727
                           i     i    vi -      v   -   -i ?   i i   i i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAAC-TGGATAKCCACATGCAAAAGAA 445

  chr1_149771798_   2728 TGAAAATAGATTCCTGTCTTTCACCACATACAAAAATCAACTCGAGATGG 2777
                             iv i  ii   ii  iv     i          i     i i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_149771798_   2778 ATTAAAAACTTAAATATAATA--TGAAACTACAA--------GAAGAAAA 2817
                           i ? i  i     i   v -- i      i  --------        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_149771798_   2818 CATTGGGG-AAATGCTGCAGGACATTGGTGTGGACAAAGATTT-TTGGAG 2865
                            v  ? -    -  v iv   v    vv i i   v i   -  i  v
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_149771798_   2866 AAGAACTCAAAAGCATAGGCAACAAAAGCAAAAATAGACAAATGGAATTA 2915
                          v  vvi        i i          v         i    v i i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_149771798_   2916 TATCAAGCTAAAAAGCTTTTGAGCAGCAAAGAAAGCAATTAACAAAATGA 2965
                         i     iv v    i      v  vv     i vi v  i  v   i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_149771798_   2966 AGAGTCAGCCTACAGAATGGGAGGAAATATTTGCAGACTATCCATCCAAC 3015
                          i  v  i  i            i           i ii  vi   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_149771798_   3016 AAGAGATTAATAACCAGAATACATAAGAAGCTCAAACTATTTGCTAGCAA 3065
                            i  i vi  v        i    ii i   vv  v i iiv  ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_149771798_   3066 AAA---AAAT----TGATT------TGAGCAAAAGACATGAGCAGACATT 3102
                            ---    ----ii   ------  i     i  iv   ii       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_149771798_   3103 TCACAAAGGAAGACATACAAATGGCCCAAAAGATATATTTAAAAATGCTC 3152
                           v v  i     i            v v   -i i  vv   i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTC 893

  chr1_149771798_   3153 AGTGTCACTAATCAT 3167
                          iii   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (154 / 82)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.11 (38 / 18)  


1837 27.33 12.33 2.54  chr1_149778738_149780847      792  1618 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149778738_    792 TGGAGAGA----CCACTGTGCTTATCTGTTAGATGATTCAACATGGTAAA 837
                             i   ----   ---  i i  vvi  i  v  i i  i  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCA---TGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chr1_149778738_    838 GATGTCAATGCTTTTAAAATTGATCTATAGCTTTAATACAATTCTTATGA 887
                             v    i  iiiv           i  v  i  ii    i i   v 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_149778738_    888 AAA-----------------------ATT--------------AAAAT-- 898
                            -----------------------   --------------     --
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_149778738_    899 ----------------GGCCTAGAATAGCCAAAACA---TT-AAAAGCAA 928
                         ---------------- i  i               ---  -    iv  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_149778738_    929 GAATAGAAT----AGATTCATTCTTTCCAATATTAAGGATTACTCTATAC 974
                            i i i ----i  i   iv   i     v i  iiv     vi v v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_149778738_    975 CTCCATTAATCAAGGTGGCACAGCACTAGGGAAAGGACAGACACACAGAT 1024
                           v  v        iii iiii i   i viv     i     i i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_149778738_   1025 CAATGGAGCAGAA---AACATACACTCTGAAAT----CCACACAA--ATG 1065
                                ii    --- ivi v  ----     ----   i   v--   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCA----GAAATAAACCCATACATTTATG 343

  chr1_149778738_   1066 TTCCAATTATTTTTTTAATACAAGG---TTAAAGCAATACAATGAAGGAG 1112
                         v  -    iv    iv ---     ---ii  ii v  v     i-   i
  L1M4_orf2#LINE/    344 GTC-AATTGATTTTCGA---CAAGGGTGCCAAGACCATTCAATGG-GGAA 388

  chr1_149778738_   1113 AGGCCACTTTTTCAATAAATAAATGGTGTTAGAACAATTGTACTGCCATA 1162
                           ivi v i   --- v  i        i i i    i  v iv?   i 
  L1M4_orf2#LINE/    389 AGAATAGTCTTT---TCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_149778738_   1163 GGTAAAATATTTAACTTCAATCTAAACATTACTCCTTACACAAAAATTAA 1212
                         v i    v v v  v  vi i ivv  v i  v  v  i           
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_149778738_   1213 CTCAAAATGGACAATGGGCTTAA-T-TAAAAACATGAAACTATAT--TTT 1258
                                    iv ?i i i   - -   i i - i        v--i i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTC 534

  chr1_149778738_   1259 TTACAA------ACAGGAA-AAATCTTTGAGACTTAGGACTAAGTAAAGA 1301
                            v  ------ i   ?i-       i v   i v  ii  i i  v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_149778738_   1302 CTTTTTAGACTTGGCACCAAAAGCACAATTCCAAAAAGAAAACAAAAAT- 1350
                         i  i     iv  i              v--   v  i i  --     -
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAG--CAACAAAAGAA--AAAATA 630

  chr1_149778738_   1351 GATAAGTTGGAATCCATCAAAATTAAATAATTTCTGCTTTGTAAAAGACC 1400
                              i     v i             -  i  i  ivi vi   i   v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACA 679

  chr1_149778738_   1401 CTGTTAAGACAATAGAAAGACAAATTATAGACAGGTAGAAAATATTTCCA 1450
                           i i    v i ii        vii i   vv  v           v  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_149778738_   1451 GATCACTTATTCAACAAAGGACTTATATACAGAATACATAAAATGCCCTC 1500
                         i    iv   iii i  i      i   v       i     ivi i  i
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_149778738_   1501 AAAACTTAACAATAAAAA--------ATCCCATTAGAAAATGTACGAATG 1542
                          v    i  i        -------- i  v   ?i      vi i  v 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_149778738_   1543 TCATGAGCAGACATTTC---ATGGAAGACATACAGATGGCATATAAACAC 1589
                         viv   ii         --- vi     i     i     vv    i   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_149778738_   1590 ACAGAAAGACATTCAACATCCTCAGCCAT 1618
                          iii     iii        v????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (146 / 76)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 4.24 (123 / 29)  


3352 20.75 4.42 4.19  chr1_149799366_149803597.rev     2836  3741 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149799366_   2836 TGGAAAGACATCT-GTGTTCATGACCTGGAAGACTTAACATTGTTAAGAT 2884
                                 i   i-i        ivi            i           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149799366_   2885 GTCAATGCTACCCAAAGCGATCTACAGATTCAGTGTAATCTCTATCAAAA 2934
                          v    i  v      vi              ii i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149799366_   2935 TCCCAATGATGTTTATTGTAGAAATATGA-AAACCCATCCTAAAATCCAT 2983
                              iiviiv   v   i      -   -  i iv          i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_149799366_   2984 CTGGAATCTCAAGGGATCCTGAATAGCCAAAAGAATCTTGAAAAATAAGA 3033
                         v     viv       i  v            v            v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_149799366_   3034 GCAAAGCAGAAAGAGTCACACCTGTTAATTTCAAAACTTACTATGAATCT 3083
                         i     iv i i  v      i vii                 ii  v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_149799366_   3084 CTAATAATCAAAA--GTGTGGTATTGGCATGAATACAGACATTTAAACCA 3131
                         vi i       i --        i      i iv i      v  i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_149799366_   3132 GTAGAATACAACTGAGAGCCCAGAAATAAACT-ATCAAATACATGATACA 3180
                         i i     v  i      i            i-  - v  vi   i -  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGGT-CA 347

  chr1_149799366_   3181 GTT-ATTTTTGA----------------------------AAGGACAGCC 3201
                         i  -     i  ----------------------------   i i  i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_149799366_   3202 TTTTCAACAAATGGTGCTGGGAAAACTGGATATCCACATGCAAAAGAATA 3251
                                               v         ?                i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_149799366_   3252 AGGTTGGACTCTTGCCTAAGACCGCATATAAAAATTAAACTCAAGGTGGA 3301
                          i       i i i   v v   ii   i         -     ii    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAA-CTCAAAATGGA 496

  chr1_149799366_   3302 TTCATGACCTAAATGTAAGACCTGAAACTATAAAGCTCTTCAAAGAAAAC 3351
                          iv?v               v  i          i     vi        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_149799366_   3352 ATAGGGTAAAAACTTTACAACACTGAATTTAGCAATGATTTTTTTGGATA 3401
                              ?vv   v   iiii  vi  ii  vi      i   i  -i    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATA 595

  chr1_149799366_   3402 TGACACCAAAGGTAGAGACAACAACA--AATAATAGATAAATTGGACTTA 3449
                                   i i v ii      v --  v                  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_149799366_   3450 GT--AAATTAAAAAGTAATGTATACT-AAAAGAATGTCTTCAACACTG-A 3495
                         i --          v -- v i i  -v    i iiiiv    v vv -i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACT--TTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_149799366_   3496 AAAAGGGAACTCACTGAATGGGAAAATATATTTGCAAGTCATATATATCG 3545
                              iv   i   v        i  v          i        v vi
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_149799366_   3546 TATGGGATTAATATCCAAAAGGCATAGAGAAGTCCTGAAACTCAACAACC 3595
                           v    i vi      i  vii   i    v  i iv       i  iv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_149799366_   3596 AACAAAACCAAATGTCCCAATTAAAAAAATAGGAAAACTAGGTAAATAAC 3645
                           -  i  -    iv       ?     ---------- i  i   vi i
  L1M4_orf2#LINE/    794 AA-AAGAC-AAATAACCCAATTWAAAAA----------TGGGCAAAGGAT 831

  chr1_149799366_   3646 TTGCCTAAGCATTTATTTAAATAAGTTCAGAAAACATTGGCCAAGGTATA 3695
                            vv  ii     v ii   --------   i i  ---v   ------
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAA--------GAAGATAT---ACAA------ 864

  chr1_149799366_   3696 CCATGGCCAATAAGAACATGAAAAGATACTGAACATCACTAACCAT 3741
                         --            v            i  v       ????????
  L1M4_orf2#LINE/    865 --ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (118 / 66)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.55 (78 / 22)  


2655 28.84 1.67 0.67  chr1_149836662_149840188     2137  3034 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_149836662_   2137 GGGAGCACACTCCGTGCTCATAAATAGGAAGAATCAATATCATTAAGATG 2186
                           i iv i ii  i  i    ii  v      v i     ii        
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_149836662_   2187 ACCATATTGCCCAA-----TTTACAGATTCAATGTGATTCCTATCAAACC 2231
                         i v   i v     ----- i           i ii  i         vi
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_149836662_   2232 ACCAAAGACATTCTTCACAGAACTAGAAAAAAAACT-ATCCTAAAATTCA 2280
                         v   ivvi v  i  ii     v v  v  i---  -             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCA 148

  chr1_149836662_   2281 TATAGAACCAAAACTGAGCCCAAATAGCCAAGGCAATCCCTAAGCAAAAA 2330
                            i   viiv  vv  v  vi         ii     i- i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT-TGAAAAAGAA 197

  chr1_149836662_   2331 GAAAAAAACTAGAGGCATCACACTACCTGATTTCAAACTATACTACAAGT 2380
                            v   ii i    vv       v  ii        viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_149836662_   2381 CTACAGTAACCAAAACAGCATGGCACTGGTACAAAAACAGACACACA--C 2428
                                  i   i    ii   i     i i  ii i     i i --i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_149836662_   2429 TGATGCAACAGAATAGGGAAGCCAGAAATAAAGC-ATCACACCTGTAACT 2477
                         ii   v  i     v i  iv           v -  -   ii i iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGGTC 346

  chr1_149836662_   2478 ATCTGATCATCTAAAAAGGTGACAAAAACAAACAATGGGGAAAGGACTCC 2527
                          vi    iv  v v  i    v   i v  vv            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_149836662_   2528 CTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGATT 2577
                           v     i              i      v  ?   i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_149836662_   2578 GAAACTGGATGCCTTCCTTACACCATATATAAAAATCAACTCAAGATGGA 2627
                            ii    iv   v   i          i      i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_149836662_   2628 TTAAAGACTAAAACGTAGAACCCATAACCATAAAAACTTTGAAAGACAAC 2677
                          i ?    iv   i   ii v i v   i      vii  ii    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_149836662_   2678 CTAGGCA-ATACCATTCTGGACATAGAGACAGGCAAAGATTTCATGAATA 2726
                         v    ?i- v i -   vv   v v i vi      v i    v ii   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_149836662_   2727 AGATGCCAAAAGCAATTGCAACAAAAACAAAAATTGGCAAGTAGGATCTA 2776
                         v  ii         vvv         iv      v ii  i v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_149836662_   2777 ATTAAACTAAAGAGCTTCTACAAAGCAAAGGAAACCGTCAAAAGAGTAAA 2826
                           i   v v  i i   i iiivvv       v  ii    i i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_149836662_   2827 CAGACAACCTATAGAATGGGAGAAAATTGTTGCAAACTATGCATATTATA 2876
                         v        i i               vv       ii  ii  v v   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_149836662_   2877 AAGGTGTAATATCTAGCATCTATAAGGAATTTAAAGAAATCCACAAGAAA 2926
                          i  vv vi    i  v  v     i   i ivv v  v  v i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_149836662_   2927 AA---AAACAGCCCTATTAAAAAGTGGGAAAAGGACAGGAACAGACGCTT 2973
                           ---   i i   v   ?    i    v      ivv   i    ii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_149836662_   2974 -TAAAAAGAACACATATGTGTGGTACACAAGCATATTAAAAAA-GCCCAA 3021
                         - vv      v i   iivi   ivv i     i  v    i -  i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_149836662_   3022 TATCACTGATCAT 3034
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (154 / 101)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 1.75 (21 / 12)  


3054 27.82 1.56 0.11  chr1_149968519_149975155.rev     5252  6146 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_149968519_   5252 TGGAAAAAC-TTCCATGCTCATGGACAGGAAGAATCAAT----------- 5289
                               i i- i     i       iv      v i   -----------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_149968519_   5290 GGCCATACTGCCTAAAGTAATTTAGAGATTCAATGCTATTCCCATCAAGC 5339
                            v     v  i   v i  i  v        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_149968519_   5340 TATCATTGATTTTCTTCACTGAATTAGAAAAAAGTACTTTAAATTTCATG 5389
                          vi  viviii  i  ii v   v v  v  ivvv iii    v     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_149968519_   5390 TGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAAGAA 5439
                              viiv  ii  v  viv        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_149968519_   5440 TAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5489
                         i    i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_149968519_   5490 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 5539
                               i   i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_149968519_   5540 TAGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCATCT 5589
                          i   i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_149968519_   5590 GATCTTTGACAAACCTGACGAAAACAAGCAATGGGGAAGGAATTCCCTAT 5639
                            i  i     ivv  v i i v  vv          i    vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_149968519_   5640 TTAATAAAAGGTGCTGGAA-AACTGCCTAACCACATGTAGAAAGCTGAAA 5688
                          i  i   v        i -     vv  ?       i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_149968519_   5689 CTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAA 5738
                         i    i    v   i     v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_149968519_   5739 AGACTTAAATGTAAAATCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5788
                             i         i v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_149968519_   5789 GCA-ATACCATTCAGGACATAGGCATGTGCAAAGACTTCATGACTGAAAC 5837
                          ?i- v i -   iv   v v  vv iv    v ii   v iiv ivi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_149968519_   5838 ACTAAAAGCAATTGCAACAAAAGCCAAAATTGGCAAATTGGATCTAATTA 5887
                           i       vvv          vv     v ii        ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_149968519_   5888 AACTAAAGAGCTTGTGCACAGCAAAAGAAAATATCATCAGAGTGAACAGG 5937
                           v v  i i   v  ii vv    i  v v     vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_149968519_   5938 CAACCTGCAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGG 5987
                              ii                v       vii  vi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_149968519_   5988 TCTAATATCCAGAATCTACAAGGAATTTAAATAAATTTACAAGAAAAAAA 6037
                         v  vi          v  i  i   i ivv i  v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_149968519_   6038 CAAACAACCCCAACAAAAAGTGGGCAAAGGATATGAACAGACACTTGTCA 6087
                             i     v vi?    i            v    i     i  v  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_149968519_   6088 AAAGAAGACATATATGTGGCCAACAAACACATGAAAAAAAGCTCATCATC 6137
                                 i   i vi       i  i          i v     v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_149968519_   6138 ACTGGACAT 6146
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 3.00 (15 / 5)  


3107 23.99 5.68 0.46  chr1_150068784_150071104      968  1830 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_150068784_    968 TGGAGAGATATATTCTGTGTTCAGAGATTAGAAGACACAGTACTGTTAAG 1017
                             i      --i ii      vi    i      vi i  i       
  L1M4_orf2#LINE/      1 TGGAAAGATAT--CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_150068784_   1018 ATGTCAA--CTCACCCAAATTAACCTATAGATTTAACGCAATCCCAATCA 1065
                            v   --   -        i i   i     i           v    
  L1M4_orf2#LINE/     49 ATGGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_150068784_   1066 AAATCCTAGCAAGGTATTTTACAGATCTTGACAGAATGATACTAAAATTT 1115
                               i   vivv v    i    vv      iiv    v        i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_150068784_   1116 ATATGGAAAGGCAAAAGACCTAGAATAAC----ACAGTACTGCAGGAGAC 1161
                                  v    ii    i      i ----   i vi  v ii   v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_150068784_   1162 AAACAAAGTTCGAAGACTCACATCACCTGATTTCAAGACTTACTATAAAG 1211
                         i         v  i        iiv  ii       i        i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_150068784_   1212 CTATAATAATAAATACTGTGTGGTATTGGTGAAAGAATAGACATATATAT 1261
                            i i    v  v  v        i   iiv   i           v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_150068784_   1262 CAATGGA----------GAGCCCAC---TGGGCC-------TTA--GTGA 1289
                                ----------   i   v--- iii  -------   --  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_150068784_   1290 ACTTACCTTTAACAAAGG----AA-------CAA--GGAAAAGGA--GTC 1324
                          i v ii  ii    i  ----  -------   --  i    i --   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_150068784_   1325 ATTTTAAGAAATTGTGCTAAAATCATTGGGTGACCTATTTG-AAAAAACT 1373
                         v   i  v    v     iii iv i   i - ? i iv  -    i v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCAAAAGAAT 446

  chr1_150068784_   1374 GAACCTAGACATAGACTTTACGCCTTTCACAAAAATGAACACAAA-TG-A 1421
                            vi i   vivv  i i  i  v vi        v   v    -  - 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_150068784_   1422 TCATAGACGTAAATGTAAAATGTAAAACTATACAGCGTCTAGAAGAAAAC 1471
                            ?    v         i vv          v i vii           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_150068784_   1472 ATAGGAGGAAATCTAGGTAACCTTGGGTATGATAATGAGTTCTGAAATAC 1521
                              ? v      vv  i         vv ii    iv    v i   i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_150068784_   1522 AACACCAAAAGCACAATTCATGAAAGAAAAGTTA-ATAAATTGGACTTCA 1570
                         i               viv ii        iv  -               
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_150068784_   1571 TTAAAATTAATAACTTCTGCTCTGTACGTGGTAACGTTAAGAGAATGAAG 1620
                          i        v     i  iv  vi viv ii vii i    i i    i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_150068784_   1621 AGACAAGCCATAGACTGGGA-AAAATATTTGTAAAACACA-ATCTAATAA 1668
                               v   i   v     -          i   v  i -    i    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_150068784_   1669 AGCACTTATATCCAAAATATGCAAAGATCTTTTAACACTCAACAATAAAA 1718
                         i v    i      i     ii     v  i   vv      i       
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_150068784_   1719 AAACAAACAACTTAATTACGAAACAGACAAAACATTTAAGCAGACATCTC 1768
                          i     i   ii    ?vi   ii i    iv    i ii      i  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_150068784_   1769 ACCAAATAAGAAATGCAGATGGCAAATAAACATATGAAAAGATGCTAAAT 1818
                         v     v    v  i  i     v     i  i             v  i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_150068784_   1819 ATAATTTGTCAT 1830
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (127 / 76)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.79 (53 / 19)  


3103 25.72 1.78 0.67  chr1_150100071_150106615.rev     5157  6054 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_150100071_   5157 TGGAAGAACATTCCATGCTCATGGATAGAAGGAATCAATATCATGAAAAT 5206
                              ii i  i     i        v i i  v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_150100071_   5207 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGC------TATCAAGC 5250
                            v     v      v i  i  i        i  ------      iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_150100071_   5251 TACCA-CTGACTTTCTTCACAGAATTGGAGAAAACT-ACTTTAAAGTTCA 5298
                          v   -   v    i  -i     v v  v  i-  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_150100071_   5299 TGTGGAACCAAAAAAGAGCCCTCATAGCCAAGACAATCCTAAGCAAAATG 5348
                          i     viiv  ii  v  vvv        i      i i iv  i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_150100071_   5349 AACAAAGCCGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5398
                                ii     vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_150100071_   5399 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGACC 5448
                                 i   i    ii       v i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_150100071_   5449 AATGGAACAGAACAGAGCCTTCAGAAATAACACCACACATCTACAACCAT 5498
                                i    iv   vv i         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_150100071_   5499 CTGATTTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5548
                         i       i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_150100071_   5549 ATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATAT--AGAAAGCTGA 5596
                         v  i  i  i           v      v  ?   i  -- i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_150100071_   5597 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAAATCAGA-TGGATT 5645
                          ii    i    v   i     v              v   i -     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_150100071_   5646 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACTCC-AGAGGAAAACC 5694
                          ?    i           v       i      -   i-   i      v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr1_150100071_   5695 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAATACTTTAT--GACT 5741
                             ?i- v i -   iv   v v  vv i     - iv   v --  - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA-T 594

  chr1_150100071_   5742 AAAATACCAAAAGCAATGGCAACAAAAGCCAAAATCGACAAATGGGATCT 5791
                          vi i          vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_150100071_   5792 AATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCAGCAGAGTGA 5841
                         v  i   v v  i i   i  ii vv    iv v       iv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_150100071_   5842 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTATCCATCTGAC 5891
                          v  i     i                 v   i   vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_150100071_   5892 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5941
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_150100071_   5942 AAA-ACAAACAACCCCATCATAAAGTGGGCAAAGGATATGAACAGACACT 5990
                            -     i     v  i?v   i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_150100071_   5991 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATCTTCA 6040
                             v        i  vi viii     v ii          i  vi   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_150100071_   6041 TCATCACTGGTCAT 6054
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.47 (22 / 15)  


3205 26.13 0.88 0.77  chr1_150192040_150198441     5003  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_150192040_   5003 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5052
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_150192040_   5053 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 5102
                            v     v     iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_150192040_   5103 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAAACT-ACTTTAAAATTC 5150
                          v   iivi i  i  ii     -   --- v  i  - iii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_150192040_   5151 ATATGGAACCAAAAAAGAGCCCTCATTGCCAAGACAATCCTAAGCCAAAA 5200
                                 viiv  ii  v  vvv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_150192040_   5201 GAACAAAGTGGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5250
                                  v     vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_150192040_   5251 CTACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGGTATAGAG 5300
                                      i    ii         i iv ii i   vi      v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_150192040_   5301 CAATGTAACAGAAC--AGAGCCCTCAGAAATAATACCACACAACTACAAC 5348
                              v  i    i--    i  --        vv   i   vi  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_150192040_   5349 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5398
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_150192040_   5399 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAACCCATATGTAGAAAG 5448
                         i  v  i  i              v      v  ?  - i   i i  ii
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC-ACATGCAAAAGA 444

  chr1_150192040_   5449 CTGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAAATCAAGATG 5498
                         v    ii    i    v   i     v  i           v    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_150192040_   5499 GATTAAAGACTTAAATGTTAGACCTAAAACCATAGAAACCCTAGAAGGAA 5548
                            i ?    i       v   v       i   i  vi i      i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_150192040_   5549 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTC 5597
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_150192040_   5598 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5647
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_150192040_   5648 TAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTG 5697
                          v  i   v v  i i   i  iiivv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_150192040_   5698 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 5747
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_150192040_   5748 CGAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5797
                         ii i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_150192040_   5798 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5847
                             i     i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_150192040_   5848 TTCTCAAAAGATGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5897
                              v     v  i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_150192040_   5898 A---TCACTGGCCAT 5909
                          ---   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (135 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2481 26.66 0.29 0.29  chr1_150227470_150229152      497  1190 (493)    L1M4_orf2#LINE/L1      215   908 (0)  

  chr1_150227470_    497 TCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACA 546
                                v  ii i      viv        i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_150227470_    547 GCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC--A 594
                          ii         i iv ii i   v                i    i-- 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_150227470_    595 GAGCCCTCAGAAATAACGCCGCATACCTACAACTATCTGATCTTTGACAA 644
                            i  --        vv  ii i ii  iiiii vi    i  i     
  L1M4_orf2#LINE/    315 GAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_150227470_    645 ACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGT 694
                         ivv  vv  i v  vvv           i  vvi  v  i  i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_150227470_    695 GCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTC 744
                                v      v  ?   i   i i  iiv    ii    i    v 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_150227470_    745 CTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTTAAAAGT 794
                           i     v           i  i    i      i ?   ii    v  
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_150227470_    795 TAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTC 844
                         v   v       i      vi i           v    ?i v viv   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_150227470_    845 AGGACATAGGCATGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATG 894
                         iv   v v  vv i     v ii   v ivvi vi            vvi
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_150227470_    895 GCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTT 944
                                    v     v  i    v   ii v  i   v v  i i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_150227470_    945 CTGCACAGCAAAAGAAACTACCATCAGACTGAACAGGCAACCTACAAAAT 994
                         i  ii vv    i  v    i  vv i v    v  i     i   i   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_150227470_    995 GGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGA 1044
                                   v  i    vii ivi      i  i  i  vi        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_150227470_   1045 ATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCAT 1094
                           v  i  v      vv    v iv i  v     i     i     v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_150227470_   1095 CAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTT 1144
                         i?    i     i     iv    i     i     v        i  vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_150227470_   1145 ATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCAT 1190
                          viii     v  i          i       v     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (106 / 75)
Gap_init rate = 0.00 (2 / 694), avg. gap size = 2.00 (4 / 2)  


 703 17.32 1.12 9.50  chr1_150690534_150692954      497   675 (1746)    L1M4_orf2#LINE/L1      117   280 (628)  

  chr1_150690534_    497 TGTGAAAA--GAAAAACCCATCCTAAAATTCATATGGCATCTCAAGGAAG 544
                           iii   --  v  i iv                  v viv     i v
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr1_150690534_    545 CCCAAACAGCCAAAACAATTTTGGAAAAAAAAAAAAAAAAAAAAAAGAAC 594
                           vi  i            i   ---------------     i      
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTG---------------AAAAAGAAGAAC 201

  chr1_150690534_    595 AAAGTCAGACGACTCATTCTTCCTGATTCCAAAACTTACTACGTAACTAC 644
                              ii  v      iv     ii   i             iv i    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_150690534_    645 AGTAATCAAAACAGTGTGGTAGCCCGGCATA 675
                                  i           -- i      
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTA--CTGGCATA 280

Transitions / transversions = 2.10 (21 / 10)
Gap_init rate = 0.02 (3 / 164), avg. gap size = 6.33 (19 / 3)  

1496 14.65 13.62 2.83  chr1_150690534_150692954     1540  1928 (493)    L1M4_orf2#LINE/L1      478   908 (0)  

  chr1_150690534_   1540 AAAA--AACACAAAATAAATGAAAGAC-TAAACAGAAGAGCTAA--C--- 1581
                             --   v      ii  v ?    -    iiv         -- ---
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_150690534_   1582 ---ACTCTTAGATG-----------------CTTCATGATGTTGGACTTG 1611
                         ---         v -----------------    i   iv    ii v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_150690534_   1612 ACAATGATTTATTAGA-----CACCAAAAGCACAGGCAAAAAAGGAAAAA 1656
                         i     i   v     -----             i    v   i      
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_150690534_   1657 AAAACAACAGATAAACTGGACTTCATCAAAATTAAAT-TTTTTGTGCATC 1705
                          ------i       i                    v-i        v  
  L1M4_orf2#LINE/    628 A------TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_150690534_   1706 AAAGGACACTAC----AGAGTGAAAGGGCAACCCACTGAATGAGA----- 1746
                                    i---- i       i i        v     i  -----
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_150690534_   1747 ---------ATCATATATGTGGATAATGGATTAAAATCCAGAATATACAA 1787
                         ---------         v  -    v   i viv            i  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTG-ATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_150690534_   1788 AGAACTCCTACAACTTAGAAACAAAAACAACAACAAA-AACCCAATTAAA 1836
                                i       i iv  i     ----i     -         ?  
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAA----GACAAATAACCCAATTWAA 816

  chr1_150690534_   1837 AACTAAGCAAAGGATCTGAATAGACATGTCTCCAAAGGAAATATACGAAT 1886
                           v ii         i           v         i i      i   
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_150690534_   1887 AGCCAATAAGCACCTGAAAAGATGATCAACATCACTAATCTT 1928
                         i            v          v         ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (35 / 20)
Gap_init rate = 0.03 (13 / 431), avg. gap size = 4.92 (64 / 13)  


2271 15.33 6.37 0.47  chr1_150870099_150873085      954  1377 (1610)    L1M4_orf2#LINE/L1        3   451 (457)  

  chr1_150870099_    954 GAAAGACAT-CCATGTTCATAAATCAAAAGGC--AATATTATCAAAATGG 1000
                               i  -          ii  iii   i --      i i  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_150870099_   1001 CAATACTCCTCAAACTGATCTACAGATTCAATGCAATCCCTATCAAAATC 1050
                                  i    i                i                  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_150870099_   1051 TCTGCTGGCTTT------------GACAAGCTGACCCTAAAAATTTATGT 1088
                         i v    v    ------------          i       -  i  i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCATAT 151

  chr1_150870099_   1089 GGAAATGCAAGGGACCCAGAATAGCCAAAATAATATTGAAAAAGAA---C 1135
                                                       i   v           --- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_150870099_   1136 AAAGTTGCAAAATTCATACTTCCCAACCTCAAAACTTACTACAAAACTAC 1185
                                v ii i   i         ii                 i    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_150870099_   1186 AGTGATCAAGACAGTGTGGTACTGACATAAAGAT----GTATAGATTAAT 1231
                            i                    i     i   ----i       i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_150870099_   1232 -----AGATTTTAGAGTCCAAAAATAAACTCTCATGTTTATGGTTAACAG 1276
                         -----   v  v        i        i vi ii        i  iv 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_150870099_   1277 ATTTGCAACAAGAGTGCCAAGACAACTCAAGGTATAAGAAATAATCTTTT 1326
                             v i     i          v i    v viv  ii    i      
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_150870099_   1327 AAACAAATGGTGCTGTGTCAAGTGGATACCAACATGTAAAAAAAATGAAG 1376
                         v              v v   v      ? v     i    i  -     
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAG 450

  chr1_150870099_   1377 T 1377
                          
  L1M4_orf2#LINE/    451 T 451

Transitions / transversions = 2.56 (46 / 18)
Gap_init rate = 0.02 (8 / 449), avg. gap size = 3.62 (29 / 8)  

1375 13.31 1.52 3.80  chr1_150870099_150873085     1716  1978 (1009)    L1M4_orf2#LINE/L1      438   694 (214)  

  chr1_150870099_   1716 CACAATAATGAAGTTAGATCCCTACCTCACACCATA----AAAATGAACT 1761
                           v  v         i  i                 ----     v    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_150870099_   1762 CAAAGTGGATCAGAGAGCTAAATGTAAGAGTTAAAACTATAAAACTCATA 1811
                             i       ?   v             i                v  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_150870099_   1812 GAATAAATCAAAGGCATAAATCTTCATGCCCTTGGATTAGGCAATGATTT 1861
                            v   v  v   ?i         i  v      i          i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_150870099_   1862 CTTAGATTAGATATGACACCAAAAGTACAAACAACAACCATAGTAACAAA 1911
                                -----             i    i      ---- iv  -   
  L1M4_orf2#LINE/    588 CTTAGAT-----ATGACACCAAAAGCACAAGCAACAA----AAGAA-AAA 627

  chr1_150870099_   1912 ATTGATAAATTGGGATTCATCAAAGTTAAAAACTTTTGTGCTTCAAAAGA 1961
                           v          iv         i                      i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_150870099_   1962 TGTCATTAGAAAAGTGA 1978
                         iiii  i ii       
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGA 694

Transitions / transversions = 1.75 (21 / 12)
Gap_init rate = 0.02 (4 / 257), avg. gap size = 3.50 (14 / 4)  

1078 13.92 5.49 2.11  chr1_150870099_150873085     2259  2495 (492)    L1M4_orf2#LINE/L1      664   908 (0)  

  chr1_150870099_   2259 TGTGTCTTAAAAAA-------AAAAAAGT-AAAAGATAACCCATGTGATG 2300
                             ii i   ii -------  i     -      i      iivi   
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_150870099_   2301 AGAGAACATTTTTGCAAATCATATATCTGAAAAGAGACTTGTATGTAGAC 2350
                         i     v  v                    v   i         vi   -
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA- 762

  chr1_150870099_   2351 TATATGAAATGAAGAACTCTTGCAACTCAATAA---AAAGACATATAGTT 2397
                         -    ---  i          i           ---       v   iii
  L1M4_orf2#LINE/    763 -ATAT---ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_150870099_   2398 CAATT-AAAAATTGGCAAAGGATCTGAATATACATTTGTCAAAAGAAGAT 2446
                              -      v          i      v      v  v         
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_150870099_   2447 ATACAAATGGCCAGTAAGCACATAAAAAGATACACAACAT-AGGCCAGGC 2495
                                      i         i       i v      - ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (22 / 11)
Gap_init rate = 0.03 (7 / 245), avg. gap size = 2.57 (18 / 7)  


 706 27.36 13.87 7.98  chr1_151414040_151417723.rev     1803  2566 (1118)    L1M4_orf2#LINE/L1        3   811 (97)  

  chr1_151414040_   1803 GAAAGTTATCCCTTGCTTATGGA-----AGACTCAGAATCAT-AAAATGT 1846
                              v      v  i i     -----     i iv  ii -  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_151414040_   1847 CAATTCTCTCCAAATTTATATATTAGTTATTTATTATTCAATGCAATGCC 1896
                             v   i       v  v  i-  ---------      i     v  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTAC-AG---------ATTCAACGCAATCCC 92

  chr1_151414040_   1897 AACAGGTTTTTGTTGTTGTTACTGCTGCGTGTGTGTGTGTGCAACTTGTT 1946
                         ---------- i iivvi iv v     ----------------   v  
  L1M4_orf2#LINE/     93 ----------TATCAAAATCCCAGCTGC----------------CTTTTT 116

  chr1_151414040_   1947 TGTGTGTGCAACTTGAGATGCTTGCCTTAAAAT----ATGGGAAAACTAA 1992
                           ii--- v  -    v v   vii i      ----    i  vi v i
  L1M4_orf2#LINE/    117 TGCA---GAAA-TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr1_151414040_   1993 AGACCAAGCATAGCCCAAAAAAA----GAAGATGGATGAAGAATAAAAG- 2037
                         i    v  v      -    v  ----   i --- -      i   iv-
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCC-AAAACAATCTTGAAAA---A-GAAGAACAAAGTT 207

  chr1_151414040_   2038 GGAGATTTTGCACTACTAAATATCAAGACTTTTTATAAAGCTGTGGTAAT 2087
                             ivi ii    v iv   v    i    vi  i      iii     
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_151414040_   2088 TAA-ATAATGTGGTGTTGACATCAAGATAGACAAATTTTCCAGTGGAAGA 2136
                         i  - i i      ii  i   v i        v  vvvi  i     v 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_151414040_   2137 GAATAGATAGATCAGAAATAGACCCATA-AGTAACTGG--AATGTTGATA 2183
                             v  v  vi        i       - v v -   --   --    v
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAAT--TGATT 354

  chr1_151414040_   2184 TATAACAAAGTTGGGAAAGGTGGGAAAGTTGGGAAAGGTGGGGCTAGTCA 2233
                          vii    i v  vv  iiviivvv  - v       ivvi v  vv   
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCA 403

  chr1_151414040_   2234 ATAAACAAACCTGGGGAAAAATAAAGGTCATTTGTATGTAAAA-AGTAAA 2282
                          i   iiivv     - v  v ---  vi ?iiii   i    - i i  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGG-ACAACT---GGATAKCCACATGCAAAAGAATGAA 449

  chr1_151414040_   2283 ATGGGATCCCTACCTCACACCATATACAAAAGTAAATTCCAGAGAGAATA 2332
                         i v   i                        i v  i  v i vi  vi 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_151414040_   2333 AGGATTTAAA--------------------GATTTTTAGGAG------TA 2356
                         ?i  ii    --------------------i i i    i  ------  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_151414040_   2357 AGAGTAA------GTGA--------------AT--------AAATATTA- 2377
                         i ?    ------    --------------  -------- i    v -
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_151414040_   2378 -----GGGTACGGGGAA---AAGAAAAACAGGATAAAT---A-TTAAT-- 2413
                         -----ii i  ii v  ---        vvi       --- -  v  --
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_151414040_   2414 AAATTCAAAGTT-----------AAGAACATCTACCAAAATAGAAAATGA 2452
                              v   ii -----------   i   -   i   ----    i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAA----GAAAGTGA 694

  chr1_151414040_   2453 AAGGATA---CATA---TGGAAGGATAAATTTGCAACACATATAACTGAT 2496
                           i  i ---  i ---   i  i v v        vv      v     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_151414040_   2497 GAAGAATCAGTGCCCTAAGTTTGTGAATAATGTAGCAAACAATCCACTAA 2546
                         i i i iiv  ii  vi i v i i  v  i- -- vv    ii  v   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAAC-T--CTTACAACTCAATAA 791

  chr1_151414040_   2547 AACAATAATAAAAGACTCAA 2566
                         v v  vi i   vi  i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAA 811

Transitions / transversions = 1.40 (120 / 86)
Gap_init rate = 0.05 (40 / 809), avg. gap size = 4.17 (167 / 40)  

 219 23.94 0.00 1.41  chr1_151414040_151417723.rev     3123  3193 (491)    L1M4_orf2#LINE/L1      839   908 (0)  

  chr1_151414040_   3123 GACATTTCACAGAAGAGAAACTACAGATGGACAATACATATTTAAAAGAG 3172
                                 v vi    ii vv    i    v     vii iv i   -  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AG 887

  chr1_151414040_   3173 ATGCTTAACCTCAATAAGGGC 3193
                              i   v   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1)  


1452 17.95 10.83 2.85  chr1_151433953_151435820.rev      480   830 (1038)    L1M4_orf2#LINE/L1      250   628 (280)  

  chr1_151433953_    480 ACAATGAACAAGAAAAAAAAGTGTGTGGGCCTGGTAT---GATAGACA-- 524
                            i i v     v -------      vv    i  ---        --
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACA-------GTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_151433953_    525 -------GTGGAATAAAATTAACAGTCCAGAAATACACCCTTACATGTAT 567
                         -------i       i    i v            v    v     v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_151433953_    568 GGTTAACTGATTTTTGACAAAAGCACTATCACAATTCGATGAAGAAA-AA 616
                            i  i       i     ii ii i vv  v    i   ii    -  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_151433953_    617 TCATCTTTTCAACAAATAGTACTGGGATAACTGAATATCTATATCCGAAC 666
                          vi              i  i      i     i   ? i i  v i  v
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_151433953_    667 AGATGAAGCTGGATCCCCTACCTCATACCATACACTAAA-CTAACTCAAA 715
                         ii      i    -           i      i  v   -i         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGA-CCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_151433953_    716 ATGGATCATAGACCTAAATGTAGGAGTTAAATCTATGAAACTCTTAGAAG 765
                                 ?             i   i    v    i             
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_151433953_    766 AAATCATAGG--------------ACC--AGA--AGGCAATATTTTTTTT 797
                            v      --------------   --i i--       iv   i  -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT- 590

  chr1_151433953_    798 TACGTATGGCACCAAAAGTG------ACAAAAGAAAAAA 830
                         - vi    i         ii------             
  L1M4_orf2#LINE/    591 -AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

Transitions / transversions = 2.21 (42 / 19)
Gap_init rate = 0.03 (11 / 379), avg. gap size = 4.36 (48 / 11)  

1082 18.18 5.33 5.33  chr1_151433953_151435820.rev     1096  1414 (454)    L1M4_orf2#LINE/L1      590   908 (0)  

  chr1_151433953_   1096 TAAGCATGAGCCACCA----CATCAAGC--CAGAAAAAAAAATGTTGATA 1139
                           iii    --     ----  -     --  i  i       i--    
  L1M4_orf2#LINE/    590 TAGATATGA--CACCAAAAGCA-CAAGCAACAAAAGAAAAAATA--GATA 634

  chr1_151433953_   1140 ACTCAGACTTTATCAAAATACCAAGTTTTTGAGCTTCAGAGAACATCACG 1189
                          v ii     i        vvv  ii     v      i  i   ii iv
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_151433953_   1190 AGGGAAGTGAAAAGACAACCCACAAGCTGGGAGGAAATATTTGCAAATAA 1239
                          i i                    iiv      i              v 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_151433953_   1240 TATATCTGAT-------TTAAATTCAGAGTAT-TAAATAACTCTTATAAT 1281
                                   -------  iv  i    i   -    v        i  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_151433953_   1282 TCAATAG---GAAGACAAATAGCTCAATTAAAACCATAGGTAACAATTTT 1328
                               i---i          i i     ?   v-  i  i  viiv   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGGATTT 833

  chr1_151433953_   1329 GAATAAACATTTCTCCAAAGAAGATATACAAATATCCAACATCAGTAGTA 1378
                              i                           iv    i -----  i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA-----AGCA 878

  chr1_151433953_   1379 TCAATTAGAAAAATGCAAATCAAAACCACAATGAGA 1414
                         -  -- ii   i    ---    v i  ????????
  L1M4_orf2#LINE/    879 -CA--TGAAAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.80 (42 / 15)
Gap_init rate = 0.04 (13 / 319), avg. gap size = 2.62 (34 / 13)  


1086 26.95 9.09 3.03  chr1_151525789_151527397.rev      502  1128 (481)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr1_151525789_    502 AAGGCTACAG-----AGAATACTGTAATA-TAACTTCAGGGTTAGACAAA 545
                           i       ----- ii i v   ii  - ii v v   i -     v 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATA 292

  chr1_151525789_    546 TAGACCAATGGAACAGAATAGAGAACCAAGAAATAGTACCACTTCCACAT 595
                             i        i     v    ii v       i-   - v v  iv 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA-ACC-CATACATTT 340

  chr1_151525789_    596 ATAATTTAT-GA-----GACAGAGGGAGCATTGAAAGCTAGT-A--GGAG 636
                           ii iv  -  -----    -    v  v---  ii i v - --  i 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACA-AGGGTGCC---AAGACCATTCAATGGGG 386

  chr1_151525789_    637 AAAGGATGGTCTGCACATTAAGTGAAACTGAGATAATTGCTTACCCATGT 686
                             i  i    viv  vi  i  ivi   i  i  i  vv  ?   ii 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_151525789_    687 G-AAAAAAATGAAGTTGTATCCCTGCCTCACACCATATGCAAAA-TCAAT 734
                          -    i          v i    i             i     - i  i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_151525789_    735 TCCAGGCAAATTGAAGACTTAGA---AAG-GC---AAC------ATTTT- 770
                           v iiiii  ii?    i  i ---   -  ---   ------ i i -
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_151525789_    771 -----AAAATAT--GTAAAAATGTT-ACAATCTCAGGG-AGGGAATGATT 811
                         -----    i  -- ?iv    v  -iii i  ii  v-   v    i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_151525789_    812 TCTGCAA----AAACCAAATAACTGCTAATTATAAATTAAAGGAT-GATA 856
                            vvi ---- v      - i -i v iiv i   vv   ii  -    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAA-AGC-ACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_151525789_    857 AAGTCACCTACAGTAAAATTTAAAACTTCTATTCATCAAAA-ATACTGT- 904
                           v viv  v  vi      v       i i v v     i- i   i -
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_151525789_    905 -AGAGA---AAAAGGCAAGGCACACACTGGAAGAAGATATTTGCAACACA 950
                         -   i ---     i   vv    v v   i    i          vv  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_151525789_    951 CAAA-CTGACAAAATTCTTATTATCTAGAATATATAAATAACTTTTAGAA 999
                         i v -    i  iivv   i -   i            v    i   v  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_151525789_   1000 -TCAATGAGAAAAAACAAAAACAAGCCAATAGAAAAGTGGACAAAAGTCA 1048
                         -     i v     i- v   i  v     v?    i   i    i viv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_151525789_   1049 TGAAT-GACA---CGCCACAGAAGAGAAAGTATGAATGACAAAGAAACAT 1094
                              -    --- v   v      v ---  ii    i v  v  i  i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATA---TACAAATGGCCAATAAGCAC 879

  chr1_151525789_   1095 ATGAAAGGCTACTTAAGCTTTTATCATGGAAACG 1128
                               i v i  i  -----i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAA-----CATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (102 / 63)
Gap_init rate = 0.05 (36 / 665), avg. gap size = 2.11 (76 / 36)  


 650 30.27 8.77 4.10  chr1_151547491_151549171.rev      502  1208 (473)    L1M4_orf2#LINE/L1      169   908 (0)  

  chr1_151547491_    502 AGAATAGCTTAACTTTTTTTGAAAGAGAAGACCA---TTGAGGGGGCTTT 548
                                 iv  vivv i      i      v  ---   - i  i  iv
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG-GAGGACTCA 217

  chr1_151547491_    549 CTCTACTAGATATTAAAATGTATTATAAAACTGAAAGTAATTAAGTCCCT 598
                          v  v ivi  v i    iv  i  i   i  - v      i   v vv 
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCT-ACAGTAATCAAGACAGT 266

  chr1_151547491_    599 CTGGCATTACTG----AAAAATCAATAATGACAGATCAATGAAACCTAAT 644
                         v   ---     ----  ii  vi i - - i         i  ivv   
  L1M4_orf2#LINE/    267 GTGG---TACTGGCATAAGGATAGACA-T-ATAGATCAATGGAATAGAAT 311

  chr1_151547491_    645 GGAAAACACTGAAATAAACCC-TAC---TATGTTAGAACCCAATATACGA 690
                         v  i iiv v           -   ---    v vi --iii  v v   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA--TTGATTTTCGA 359

  chr1_151547491_    691 GAAAG-----AAAACCA---ACTGGGAAGCGA-TAGATTATTCAATAAAT 731
                         v  i -----  i    --- v    i iv  -   vi v     i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_151547491_    732 GGTAATGGAGAAATTGGAAGCTTGGATG---AAAAATCAAATTGGAACCC 778
                            iv   iiv  i    vi?iiiv   ---  i   v  i     v   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_151547491_    779 TAGCTCTCACCAGCCACCAAAATAAATTCCAGGTGGATTAAAAAGTCAGA 828
                           v   v     vvi  v     v  i  v ii     i ? i vii i 
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_151547491_    829 TGTAAAAGAAGAAACCATGAGCAAGCTCC----AGAAAACA---AAGTGA 871
                              i  vvi    i  i --- i   i----        ---i?  i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAA---AACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_151547491_    872 ATATTTAATCAGCCCTGAG--AGGAGAAAGAACTGTTAAGCATAAAATC- 918
                           v  ii--iii  i  i --   v-  v ivi v   iii  i v i -
  L1M4_orf2#LINE/    557 ATCTTCG--TGACCTTGGGTTAGGC-AATGGTTTCTTAGATATGACACCA 603

  chr1_151547491_    919 ---TCAGAAGAAACATGAAGGAAAAAACTGGTGTGTTTGATTACATCATA 965
                         ---v  v   v    --  i       iv i ivi  v  i ---    -
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACA--AAAGAAAAAATAGATAAATTGGACT---TCAT- 647

  chr1_151547491_    966 CACACAATTTTAGATTTCAGTCCCTCAAAAAA---TATGAACTTATTTAA 1012
                         --  v    vv i i  iv  v i     ii ---   v  vvv v v  
  L1M4_orf2#LINE/    648 --CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_151547491_   1013 AGAGCAA---ATGTTATGCTAGAAAAAGTATTTGCAG--CAAACAT--GA 1055
                          iii   --- iivv   --i  i   i        i--  v i  --  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATG--GGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_151547491_   1056 CAAGAGGTAAATATCCCTATTATACAAAGCAGTCTTAGAA---ACTAATC 1102
                         i   i iivvi     vv v    i    v v     v  --- v    v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_151547491_   1103 AGAAGAACTTATCTCCCCAGTGAAAAAAATAGGCTGAAGAT---AA-GGC 1148
                          i    - vv  vv   v v --?      i   vi i   ---  -i v
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATT--WAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_151547491_   1149 CAA--CTACAAAGGAAGAAATACAAAAAGCCAATAAA---ATAAAA---C 1190
                           v--  v     -    v       vi        i---  i   ---i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_151547491_   1191 ACACAACA-CATATTCAGT 1208
                         i v     -  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (114 / 96)
Gap_init rate = 0.05 (39 / 740), avg. gap size = 2.33 (91 / 39)  


3593 20.62 2.36 4.83  chr1_151940122_151942079      535  1465 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_151940122_    535 TAGAAAGATATTCCATGTTCCTGGATTGGAAGTATCAATATTGTTAAAAT 584
                          i         i        v           vv i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_151940122_    585 GTCTATACTACCCAAAGCAATCTACAGATTCAAAGAAATCCCTATCAAAC 634
                          v v     v      vii              v v             v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_151940122_    635 TACCAATGACATTCTTCACGAAAATAGACAAAACAATCCTAAAAGTTGTA 684
                          v   iivi v  i  ii ii    v     ivii         v ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_151940122_    685 TGGAATCACAAAAGATCCAGGATAGCCAAAGCTATCTTGAGCAAAAAGAA 734
                              vii   ii  i    i         i v       iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_151940122_    735 CAAAACTGGAGGAATCACATTACCTGACTTCAAATTACACTACAGAGCTA 784
                             ii       v     i v  ii i      vivi      i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_151940122_    785 TAGTATGCAAAACAGCATGGAACTGGCATAAAAACGAACACATAGACCAA 834
                         i    vv   i    ii   v          ii iii   i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_151940122_    835 TGG--CAGAATAGAGAACCCAGAAACAAATTTATACACCTATGGTAAACT 882
                            --i     v    ii       i   iii     ii      v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_151940122_    883 CATTTTTGACAAAGGTGCCAAGAACATACACTGGGGAAAAAAACATTCTC 932
                         v     i     i          v   v  v        i  -i v   i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTT 399

  chr1_151940122_    933 TTTAATAAATGGTGCTGGGATAACTAGATATTCATATGCAGAAGAATGAA 982
                           i  i              i    i    ?i  i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_151940122_    983 ACAAGGGAGGCAGATTGCACAGGAAAAAAAAATGGATGAAACTTGACCCC 1032
                         i-------------   ---------------------------      
  L1M4_orf2#LINE/    450 G-------------TTG---------------------------GACCCC 459

  chr1_151940122_   1033 TGTCTCTCGCCATATACAAAAATCTAA-TCAAAATGGATTAAAGTCTTAA 1081
                          ii   v i              -   -           i ?  v i   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAAT-TAACTCAAAATGGATCAWAGACCTAA 508

  chr1_151940122_   1082 ATCTAAGACCTCAAACTATGAAACTGCTACAAGAAAACATTGAGG-AAA- 1129
                           v     v  v       i     vi  v          v i? -   -
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_151940122_   1130 CTCCAGGACATTGGTCTGGGCAAAAATTTCTTGAGTAATATACCATAAGA 1179
                           i iv   v    vi i     vii      iii  vv i    v   v
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_151940122_   1180 ACAGGCAACTAAAGCAAAAATGGACAAATGAGATCACATCAAG-TTAAAA 1228
                            i     v    v      i  i    vi  iiv      i-      
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_151940122_   1229 A-------GCATAACAAAGGAAA-TAACAACAAAGTGAAGAGACAACCCA 1270
                          -------  v --       v -  v   v        i          
  L1M4_orf2#LINE/    659 ACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_151940122_   1271 CAGAATGGAAGAAAATATTTGCAA--------TCTGATAAGGGATTAATA 1312
                                 i               --------            i vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_151940122_   1313 ACCAGAATATATAAGGAGCTTAAACAACTCTTTAGGAAAAAAATCTAATA 1362
                         v             i  i  ivv       vv  iv     i - v    
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATA 805

  chr1_151940122_   1363 ATCTGATTTTAAAATGGGCATAAGATTTGAGTAGACATTTCTCAAAAGAA 1412
                          i ii   ?v          v i       i            v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_151940122_   1413 AACATACAAATGGCAAACAGACATATGGAAAGGTGCTCAACGTCATTGAT 1462
                         i i           v  i ii  i   i    i        i   ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_151940122_   1463 CAT 1465
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.72 (119 / 69)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.79 (67 / 14)  


1877 27.33 1.36 1.55  chr1_152168374_152171396.rev      747  1262 (1761)    L1M4_orf2#LINE/L1        1   515 (393)  

  chr1_152168374_    747 TGGAAAAATATTCCATGCTTATGGATTGGAAGAATAAATACCGTTAAAAT 796
                               i    i     i i             v v    ii     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_152168374_    797 GGCCATATTGCCCAAAGCAATTTATAGATTCAATGCTATTCCCATTAAAC 846
                            v   i v      vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_152168374_    847 TACCATTGAAATTCTTCATAGAGCTAGAAAAAAACT-ATTTTAACATTCA 895
                          v   vivivv  i  iii   iv v  v  i--  -  ii   v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_152168374_    896 TATGGAACCAAAAAAGAACCTAAATAGCCAAGGCAATCCTACACACAAAA 945
                                viiv  ii  v  vi         ii     i i--- -    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG---A-AAAA 194

  chr1_152168374_    946 AAAGAACAAAGCTGAAGGCATCATGCTACCTGACTTCAAACTATACTACA 995
                         i          i  i   vv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_152168374_    996 GGGCTACAGTAATCAAAACAGCATGGTACTGATACAAGAGCAGACACATA 1045
                         ii              i    ii        ii i   iii     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_152168374_   1046 GACCAGTGAAACAGAATAGAGAACCCAGAAATAAGACTGCACACCTACAA 1095
                           i  i  i  i     v    ii          iv iii   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_152168374_   1096 CTGCGTGATCTTTAACAAACCTGACAAAAACAAGCAATTGGGTAAGGATT 1145
                         iiivv    i  ii    ivv  v   i v  vv    v   v   i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_152168374_   1146 CCCTATTCAGTAAATGGTGCTGGGATAACTGGTTAGCCATATGCAGAAGG 1195
                         vi  v    ii              i      v  ?   i     i   i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_152168374_   1196 TTGAAACTGGACCCCTTCCTTACAGCATATACAAAAA------CAAAATA 1239
                         v    ii         v   i   v            ------      -
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT- 493

  chr1_152168374_   1240 TGGATTAAAAACTTCAATGTAGG 1262
                         -    i ? i  i v      i 
  L1M4_orf2#LINE/    494 -GGATCAWAGACCTAAATGTAAG 515

Transitions / transversions = 2.09 (94 / 45)
Gap_init rate = 0.01 (6 / 515), avg. gap size = 2.50 (15 / 6)  

 606 27.54 11.30 1.45  chr1_152168374_152171396.rev     1498  1842 (1181)    L1M4_orf2#LINE/L1      450   828 (80)  

  chr1_152168374_   1498 GCTGCACTCCAGCCTGGGCAACACA-GCAAAACTCTGTCTCAAAAAAAAA 1546
                          i  v  i  vi   vi-  v  i -i     v - iv       vii v
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCA-CACCATATACAAAAAT-TAACTCAAAATGGAT 497

  chr1_152168374_   1547 AAAAGACTTAATTGTAAAACCCAAAACTATAAAAACCCTGAAAGACAATC 1596
                         v ?    i   v     i v i            vi i ii    v  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_152168374_   1597 TAGGCAGTA--CCATTCAGGACATAGGCACAGGCAAAGACTTCATG---A 1641
                             ?-   --i -   iv   v v  vvi      v ii   v i--- 
  L1M4_orf2#LINE/    548 TAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_152168374_   1642 CGATGCCAAAAGCAATTGTAACAAAAGCAAAAATGGACAAATAG------ 1685
                         i  ii         vvv i        v      i  i    v ------
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_152168374_   1686 --------TATGAACTTCTGCGCAGCAAAATAAACTATGAACAGAGTAAA 1727
                         --------  vi     i  i  vv    iv v     v  v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_152168374_   1728 ----CAACCTATAAAATGGGAGAAAAATTTTGCAAAC--TGCTTCTGACA 1771
                         ----     i i i            vv        i-- iiv     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_152168374_   1772 AAGATCTAATATCCAGCATCTATAAGGAACT--TA---------AATATA 1810
                          i iv  vi       v  v     i     --  ---------    - 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA-A 794

  chr1_152168374_   1811 CAAGAAAAAAAACC--ATTGAGAAGTGGGCAAGG 1842
                         v    v   v    --   ? i  i       i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.14 (49 / 43)
Gap_init rate = 0.04 (14 / 379), avg. gap size = 3.14 (44 / 14)  

 297 20.00 4.62 0.00  chr1_152168374_152171396.rev     2460  2524 (499)    L1M4_orf2#LINE/L1      815   882 (26)  

  chr1_152168374_   2460 AAAAATGGGCAAGGGACATGAACAGACACTTCTC---AAAAGACATATAC 2506
                                     i   iv    i     i     --- i    i   i v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_152168374_   2507 GTGGCCAACAATCATATG 2524
                         i       i  v  i   
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATG 882

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.01 (1 / 68), avg. gap size = 3.00 (3 / 1)  


2351 24.26 5.92 0.99  chr1_152229986_152231686.rev      502  1210 (491)    L1M4_orf2#LINE/L1      165   908 (0)  

  chr1_152229986_    502 ACCCAGAATAGCCAAAGCTATTTCTAAGCTGAA------AG--GGAGAAA 543
                                         i v  i iv  ivv   ------  --    i v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_152229986_    544 TAACTTTACCTGACTTCAG---TTATGCTACAGAGCTATGATAACCAAAA 590
                          v  vi v  ii i    i---   --     i     iii   i   i 
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTA--CTACAAAGCTACAGTAATCAAGA 262

  chr1_152229986_    591 CAGCATGGTACTAGCATAAAAATAGACACATAGACCAGTGGAACAGGAGA 640
                            ii       i      ii       i     i  i     i  i vv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_152229986_    641 GAGAACCCAGAAACAAATCCACACACCTACAGTGAACTTATTTTTGACAA 690
                             ii       i   i   i   ii  ii  v  i v     i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_152229986_    691 AGGTCCCAAGAGCAT---------AAAG-----TCTCTTCAATAAATAGT 726
                         i   v      v   ---------    -----   i     i    i  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_152229986_    727 GCTGGGAATACTGGATATTCATATGCAAAAGAA--AAACTTGACCCCTGT 774
                                vv        ?i  i           --  ii v       ii
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_152229986_    775 CTCTCAGCACATACAAAAACTGAAATCAAAATGGATGAAAGGCTTAAATC 824
                            v  v  i         i -  v           v ?  i i     v
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATT-AACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_152229986_    825 TAAGATCTCAAAAGTATGAAACTACTATAAGAGAACATTGGGAAAACTCT 874
                              v  -    v   i     vi  v    i     v  ?iv  v   
  L1M4_orf2#LINE/    512 TAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_152229986_    875 CCCGGATATTGATCTGAACAAAAATTTATGAGCAAT-ACCCCACAGGCAC 923
                         i vv  iv   ivi iii   vii   v v  vv  -  v   v i    
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_152229986_    924 AGGCAGCCAAACAAATA-TGGATAAATGTGATCAAATCAAG--TAAAAAA 970
                          i   i v   v   v - i       vv  iivv     i--      -
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA- 659

  chr1_152229986_    971 GCTTCTGCACAGCAAAGTATACAATCAATAAAGTGAAGAGACAACCCACA 1020
                         -   i  ii vv     v i  v     v        i            
  L1M4_orf2#LINE/    660 -CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_152229986_   1021 GAATGGGAGAAAATATTTGCAAACTACACATCTGACAAAGTGTTCATAAC 1070
                                                ii i i      i  i vii ii  v 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_152229986_   1071 CAGAATATGTAAA---TTCAAACCACTCTATAGGTAAAAGTCTAATAATC 1117
                                 i    ---i  vv  v    v   ivv     v v     i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_152229986_   1118 TGTTTAAAAAATGGACAAAAGACT-GAAGAGATATTTCTCAAAAGAAGAT 1166
                         iiv  ?        i    i  i -   v   i       v         
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_152229986_   1167 GCTACAAATGGC-AACAGGCATA------GGTATTCAACATCATTGATTA 1209
                         i-          -  i i   i ------ i ii         ???????
  L1M4_orf2#LINE/    859 A-TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_152229986_   1210 T 1210
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.58 (103 / 65)
Gap_init rate = 0.02 (18 / 744), avg. gap size = 2.72 (49 / 18)  


1092 19.31 3.43 0.00  chr1_152298748_152301991     1086  1318 (1926)    L1M4_orf2#LINE/L1        4   244 (664)  

  chr1_152298748_   1086 AAAGACATCCCACATTCCTGGATTTCAAGACTTCATATT---AAGATGAC 1132
                              i      ii   v      vv       v     ---      i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_152298748_   1133 AACACTACCTAAAGTGATCTGTAGATTCAATGTAATTTCTATCAAAATCC 1182
                           i   v  i   v      ii        i i   ii            
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_152298748_   1183 CAACATTATTGTTTAAAGAAACAGAAAACCCCATCCTAAAATCCATATGG 1232
                           i vviv  v   iv     iv  v  v iv          i       
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_152298748_   1233 AATCTCAAGGAACCCCAAATAGCCAAAACAATTTTGAAAAATAA---CAA 1279
                           viv     i    vi               i        v  ---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_152298748_   1280 AGTTGGAGGACTCACACTTTCTGACTTCAA--CTTACTACA 1318
                                            i ii i     --         
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

Transitions / transversions = 1.37 (26 / 19)
Gap_init rate = 0.01 (3 / 241), avg. gap size = 2.67 (8 / 3)  

 639 15.57 0.82 0.82  chr1_152298748_152301991     1787  1908 (1336)    L1M4_orf2#LINE/L1      234   355 (553)  

  chr1_152298748_   1787 AACTTACTACAAAGCTACAGTAATGAAAACAGTGTGGTACTTGCAGAAAG 1836
                                                 v  i             v   v  i 
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_152298748_   1837 ACAGACATATGGACCAATGGAATGGAAAGGAAGAGTCCTAAAATAAACTC 1886
                          i        i  i         i   vv -       vi        i 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTG-AGAGTCCAGAAATAAACCC 332

  chr1_152298748_   1887 TCACATATATGGCCAAT-AATTT 1908
                         vi    v     i    -i    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTT 355

Transitions / transversions = 1.38 (11 / 8)
Gap_init rate = 0.02 (2 / 122), avg. gap size = 1.00 (2 / 2)  

2224 18.52 7.04 2.22  chr1_152298748_152301991     2212  2751 (493)    L1M4_orf2#LINE/L1      343   908 (0)  

  chr1_152298748_   2212 GGCCCAATAATTTCTTTAACAAAGTTGCCAAAACCATTCAATGAAGAAAA 2261
                           i v v i    -- ii    i v      i           ii    i
  L1M4_orf2#LINE/    343 GGTCAATTGATTT--TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_152298748_   2262 GATACTCTCTTCAAGAAACGATGCTGAGAAAACTGAATATC---ATGTAA 2308
                         i   v   i     v   i i     i  v     i   ? ---   i  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_152298748_   2309 AGGAATGAAGCTGGACCCTTACTTTAAACCATATACAAAACTTAAATACA 2358
                          i        i       i   i i v             v    v -  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT-CA 489

  chr1_152298748_   2359 AAACGGATCACAGATCTAAACATAAGAGCTAAAACGATAAAACCCTCAG- 2407
                            i      ?   i     ii             v       i  i  -
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_152298748_   2408 -GAAAACATAGGGGGAAGACTTTCACAACATTGGATTTGGCAGTGATTTC 2456
                         -           ? v  - ii   iii  v    i  v    i  i    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_152298748_   2457 TAGGCTATGACACTAATAATACAGGTAATAAAGGAAAAAATA----AACT 2502
                          vi v        i  v ii   i i  i   i         ----  i 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_152298748_   2503 GGACCTGGTTTTCATCAAAATTGAAAACTTTTTTTTGCATCAGAGGACAC 2552
                             ------            i         v --  v   i       
  L1M4_orf2#LINE/    639 GGAC------TTCATCAAAATTAAAAACTTTTGT--GCTTCAAAGGACAC 680

  chr1_152298748_   2553 AA--AAGGAAATTAAAAGACTATCCACAGAATGAGAGAAAATATTTTTAA 2600
                         v --   i  i v       v i          i            vi  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_152298748_   2601 A------ATCC-----------TATATACAGATTATATAAAGAACCTGGA 2633
                          ------   i----------- i   v    v            iivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_152298748_   2634 CAATTCAACAACAAAA---CA-------CAATTCAAAAGTAGTCAAATAA 2673
                            i    i  i    ---  -------     ?    i i v    vi 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_152298748_   2674 TTTGAACAAACATTTCTTCAAAGAAGATACACAAATGGCCAATAAGCACA 2723
                               i i        i           i                    
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_152298748_   2724 TGAAAAATTGTTCAACATCATTAGTTGT 2751
                               iv  i         ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (67 / 29)
Gap_init rate = 0.02 (13 / 566), avg. gap size = 3.85 (50 / 13)  


 233 18.60 0.00 0.00  chr1_152357724_152361448.rev      500   542 (3183)    L1M4_orf2#LINE/L1       92   134 (774)  

  chr1_152357724_    500 CTATCAAAATCCCAGCAATCTTTTTGGTCAAAATTGTCAAGCT 542
                                         vii      v ivi      v      
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

Transitions / transversions = 1.00 (4 / 4)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.00 (0 / 0)  

1704 15.76 15.76 0.00  chr1_152357724_152361448.rev      840  1188 (2537)    L1M4_orf2#LINE/L1      130   533 (375)  

  chr1_152357724_    840 AAGCTGATCTCAAAATTCATATGGAAATGCCATAGACCTAGAATAGCCCA 889
                                  ii                   v vi    i         v 
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr1_152357724_    890 AGCATTCTTGAAAAATAA---CAAATTTAAAGGACTCATACATCTTGATT 936
                          i  v          v  ---    v  ii        i  v  iii   
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_152357724_    937 CCAAAACTTACGATAAAGCTACAGTAATCAAGATAGTCTGGTACTGGCAT 986
                         i          v i                   i   v            
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_152357724_    987 A------------------------------------------------- 987
                          -------------------------------------------------
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_152357724_    988 CGCTTACA-TCATGGTCAACTGATTTTCAACATGGATGCCAAGACACTTC 1036
                          v v    - i        i        i   v  i         vv   
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_152357724_   1037 AATGAAGAAAGAATAGTCTCTTCAACAAATAGTGCTGGGACAACCTGATA 1086
                             ii             i          i             iv    
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_152357724_   1087 --CTCATGCAAAAGAATGAAAATGGACCCCTACCTTACATTATACACAAA 1134
                         -- v                iv             i   ii   i     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_152357724_   1135 CATGAATGCAAAATAGCTCATAGACCTAAATGTAAGAGCTACAGGTATAA 1184
                         v  v  iv      i v   ?                    v iv     
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_152357724_   1185 AACT 1188
                             
  L1M4_orf2#LINE/    530 AACT 533

Transitions / transversions = 1.35 (31 / 23)
Gap_init rate = 0.01 (4 / 404), avg. gap size = 13.75 (55 / 4)  

 538 19.83 0.00 0.86  chr1_152357724_152361448.rev     1847  1962 (1763)    L1M4_orf2#LINE/L1      517   631 (277)  

  chr1_152357724_   1847 GCTCAGCCTCTAATTTTCTATAGCAGAAAATACAGGAGTAAATCTTCATT 1896
                            v iv  v   vvi   -   v      i i   ?          i v
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCT-TAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_152357724_   1897 ATCGTGTGTTATGCAATGGTTTCTTAGATATAACATCAAAAGCACAAGCA 1946
                          i v  v    v                   i   i              
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_152357724_   1947 AAAGAACTAAAAATAG 1962
                          v i  vv        
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAG 631

Transitions / transversions = 0.69 (9 / 13)
Gap_init rate = 0.01 (1 / 115), avg. gap size = 1.00 (1 / 1)  

 799 15.35 6.98 3.72  chr1_152357724_152361448.rev     2249  2463 (1262)    L1M4_orf2#LINE/L1      602   823 (85)  

  chr1_152357724_   2249 CAAAAACA-AAACAGAACAAAACAAAAAAACTATAAATAGATAACGAATT 2297
                              i  -  i  --      v      ----  i   i  --i i i 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCA--ACAAAAGAAAAAA----TAGATAAAT--TGGACT 643

  chr1_152357724_   2298 GTATCCAAATCAGACACTT--GTACTTCAAAGGATACCATCAAGTAAGTG 2345
                         vi   v    i i v    --  i          i  i      v     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_152357724_   2346 GAA-GACAACCCACAGGATGGGAGAAAATATTTGCAAATCACATA---GA 2391
                         i  -            i                        i   ---  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_152357724_   2392 -ACTTAACTTATCTCCATAATATATAAAGAACATTTACAACT---TAATA 2437
                         - vvvi    i v    v              vi        ---     
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_152357724_   2438 AAAAGGCAA----CTCAATTTAAAAATGGG 2463
                              i   ---- i     ?         
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGG 823

Transitions / transversions = 1.91 (21 / 11)
Gap_init rate = 0.05 (10 / 222), avg. gap size = 2.30 (23 / 10)  

 525  8.16 1.02 5.10  chr1_152357724_152361448.rev     3137  3234 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_152357724_   3137 AAAAAAAGGCAAAAGATTTGAGCAGGCATTTCTCCAAAGTATAAAAGTTA 3186
                              vi      i       ii  i             -----   v  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG-----AAGATA 859

  chr1_152357724_   3187 TACAAATGGCCAATAAGCACATGAAAA-ATGCTCAACATTATTAGTCAT 3234
                                                    -           i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 3.00 (6 / 2)  


1384 24.09 1.55 1.55  chr1_153601768_153604731.rev      935  1320 (1644)    L1M4_orf2#LINE/L1        1   386 (522)  

  chr1_153601768_    935 TGGAAACACAGTCCATCCTCATGGATGGTAAGAATCAATATTGTGAAAAT 984
                               v i vi    vi        v v    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_153601768_    985 GACCATACTGCCCAAAGCAATCTACAGATTCAATGCAATTTCCAACAAAA 1034
                          i v     v      vii              i     ii i v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_153601768_   1035 TACCTTCATCATTCTTCACAGAACTATAAAAAAC-AATCCTAAAATTCAC 1083
                          v  vv vv v  i  ii     v - i v  i -i             i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_153601768_   1084 ATGGAACCAAAAAAGAGCCCATATAGCCAAAGCAATACTATGCAAAA--A 1131
                               viiv  ii  v  viv         i    -  -  v    -- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGAA 197

  chr1_153601768_   1132 GAACAAATCTGGAGGCATCACATTATCCAACTTCGAA--TTAAACTACAA 1179
                                vi      vv     i vi    i   i  --   --      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAA 245

  chr1_153601768_   1180 GGCTATAGTTATCAAAACTGCATGGTACTGGTATAAAAATAGGCATGTAG 1229
                         i    i   v     i  v ii         i    ii    i   i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_153601768_   1230 ACCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACATACAGC 1279
                          i        i     v    ii           v   v i iv  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_153601768_   1280 CAATTGATCTTTGACAAAGCATACAAAAAC-ATACATTGGGG 1320
                                 i  i     i -i i v  i  -  v  v     
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGG 386

Transitions / transversions = 1.45 (55 / 38)
Gap_init rate = 0.02 (9 / 386), avg. gap size = 1.33 (12 / 9)  

1310 28.14 0.70 0.70  chr1_153601768_153604731.rev     1625  2054 (910)    L1M4_orf2#LINE/L1      381   810 (98)  

  chr1_153601768_   1625 ATTGGGGAAGGACACCCTATTCAATAAATGGTGCTGAGTAAACTGGCAAG 1674
                           v   i   i i vi  v     i           i vv      vv ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_153601768_   1675 CCACATGTAGAAGAATGAAACTGGTTCCCCATCTCTCTCCTTATACAAAA 1724
                                i i         ii   vi   i i   v v  v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_153601768_   1725 ATCAACTCAAGATGTATTAAAGACTTAAATCTCAGGGCTGAAACCATAAA 1774
                           i       i   v  i ?    i     v v  i   i    i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_153601768_   1775 AATTCTAGAAGATAACATCCAAAAAACTCTTCTGGACATTGGCTTAGGCA 1824
                          v ii       v     vvi?iv  v     vv   v    v       
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_153601768_   1825 AAGAATTCATGACTAAGACCCCAAAAGCAAATGCAACAAGAACAAAAATA 1874
                          v iv   v iiv  v   v         v v       i iv       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_153601768_   1875 AATAGATGGGGAACTAATTAAACTAAAAAGCTTCTGCATAGCAAAAAAAA 1924
                         i   i  v  - vi v  i   v v    i   i  iiivv    ii v 
  L1M4_orf2#LINE/    631 GATAAATTGG-ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_153601768_   1925 GTAATCAGCAGAGTAAACAGACAATCCACAGAGTGGGAGAAAACATTCTC 1974
                         v  -   iv i   i  v      i       i          i   iv 
  L1M4_orf2#LINE/    680 CTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_153601768_   1975 AAGCTGTGCATCCAACAAC--ACCCAGTGCCCAGAATCT-CAAGGAACTC 2021
                           iiii ii   ii i  v--  ii-  ii       v -i  i      
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTT-GTATCCAGAATATATAAAGAACTC 777

  chr1_153601768_   2022 AAACAAATCAGGAAGAAAAAAACAAATAGGCCA 2054
                         vv    v   iv  v     i       iv   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCA 810

Transitions / transversions = 1.23 (65 / 53)
Gap_init rate = 0.01 (5 / 430), avg. gap size = 1.20 (6 / 5)  

 453 17.73 5.67 0.00  chr1_153601768_153604731.rev     2333  2473 (491)    L1M4_orf2#LINE/L1      760   908 (0)  

  chr1_153601768_   2333 AAAATA-ATAAAAA-----TAAAAATAAA-AATAAAAAAATAA-TAATCC 2374
                          i    -     i -----  v  v v  -        i i  -   i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_153601768_   2375 CATCAAAAAGTGAGCAAAGGACATGAATAGACATTTCTCAAAAGAAAGTA 2424
                         v  i?    i  i        iv                v      ii  
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_153601768_   2425 TACAAACAGCCAACAAACATATGAAAAAATGCTCAACACCACAATCATC 2473
                               ii     i  i  i       i          i  ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (18 / 6)
Gap_init rate = 0.03 (4 / 149), avg. gap size = 2.00 (8 / 4)  


3272 14.94 2.51 3.99  chr1_153757672_153759327.rev      492  1167 (489)    L1M4_orf2#LINE/L1      243   908 (0)  

  chr1_153757672_    492 CAAATGTCAGAGTAATCAAGACAGTATAATACTGGTTCAAGGATAGACCT 541
                             - ii v               i ii      ivi          v 
  L1M4_orf2#LINE/    243 CAAA-GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_153757672_    542 GTAGATGAATGGAATAGAATTCACATGCCAGAAATTAACCCATACATCTA 591
                         i     v              v v vv        v           i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_153757672_    592 TGGTCAATTGATTTTCAACAAAGGTACCAAGACAATTCAATGGAGAAAGA 641
                                         i    i   i       v         i      
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_153757672_    642 ATAGTATTTTCAACAAATGGTGCTAGGACAACTGGATATCTACATACAGA 691
                              v                  i             ? i    i  i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_153757672_    692 -TACTTAATTTGGACCCTTACCTCATACAGTAAACAAAATTTAACTCAAA 740
                         -v v v  v        i       i  vi  v      v          
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_153757672_    741 GTGGA-CAAAGACTTAAATGTAAGAGCCAAAACTATTTTTAAAAACTGTA 789
                         i    -  ?    i             i        ------------- 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-------------A 528

  chr1_153757672_    790 AAACTCCTAGAAAAAATTTTAGGTGGGAGTAAATCTTCATGACCTTGGAT 839
                               i     i   ---- vi i  ?          i         i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAA----ACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_153757672_    840 TGGGCAGTGGTTTCTTAGATATGACACCAAAAGCATAACCTCCCCCCAAA 889
                          i    i                            i  v vv vvvvi  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_153757672_    890 AAAATAG-----TTGGATTTCATCAAAATTTAAAGCTTGTATATGTCAAA 934
                                -----     i            v   i   v i iiv     
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_153757672_    935 GGATTCTATCAAGAAAGT--AAAGACAACCCATAGAAGAAATGGGGAAAA 982
                            iv             --            i    ----    ii   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA----TGGGAGAAA 720

  chr1_153757672_    983 ATATTTACAATTCAAGTATCTGATAAGGATCTAATG-CCAGAATATATAA 1031
                               i   v   vi            iv  vi i-             
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_153757672_   1032 AGGACTCTTAAAAGCTCAGCAATAAAAAGACAA----CCCAATTTAAAAA 1077
                           i       v  -    ii             ----       ?     
  L1M4_orf2#LINE/    771 AGAACTCTTACAA-CTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_153757672_   1078 CTTGCAAAGGATTTGAATAGACAGT-CTCTAAAGAAGACAGACATACAAA 1126
                         ivv                    v -   i        i ----      
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA----TACAAA 865

  chr1_153757672_   1127 TGGCCAATAAGCA--TGGGAAGATGCCCAGCATTGTTATTCAC 1167
                                      --  ii       i  i   ii????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (59 / 38)
Gap_init rate = 0.02 (14 / 666), avg. gap size = 3.14 (44 / 14)  


4701 13.55 5.05 0.80  chr1_153792555_153795105     1188  2058 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_153792555_   1188 TGAAAAGACATCC-ATGTTTACAGAGTGGAAGATTTAAGATAGTTAAGAT 1236
                           i     i    -     i ii  v       i    v  v        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_153792555_   1237 GGCAACATTCCACAAATTGATCCACAGATTAAATGAAATCCCTATTAAAA 1286
                              i i   v          i       v  i v         i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_153792555_   1287 TCTCAATT---TTTTTTG---AAATTGAGAAGTTGACCCTAAAATTCATA 1330
                           i  ii ---       ---       v   i   i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_153792555_   1331 TGAAAATG------------AATAGCTAAAACAATCCTGAGAAAGAA--- 1365
                           i     ------------      i         i   i      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_153792555_   1366 TCAAGTTGGTGGACTCATAATTCCTGATTTCAAGATCTACCAGAAAGCTA 1415
                         iv       v       i v    ii       i ii   i v       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_153792555_   1416 CAGTAAGCAAGTCAGTATGCGACTGGCATAAGGATAGACATA--GATCAA 1463
                               v    v    i  vv                     --      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_153792555_   1464 TAAAACAGAAC-----ATCCAGAAATAAACTCTCACATTTAGGGTCAATT 1508
                          ii  i    i-----i             i vi       v        
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_153792555_   1509 CATTTT-GACAACAGTGCCAGGACAATTCAGTGGAGAGGTAATAGACTTT 1557
                         v     -     vi      i   v     i   i  iiv     v    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_153792555_   1558 TCAATAAATGGTGCTAAGACAACTGGATATCCACATGCAAAATAATGAAG 1607
                             i          ii            ?            v       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_153792555_   1608 CTAGACCCCTGCCTCACATCATATACAAGAATTAACTCAA---GAATTA- 1653
                         i i       i       i         i           --- i  i -
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_153792555_   1654 --ACTCAAAATGGATCACTGACCTAA--CTGTAAAACTCTTAGAAGAAAA 1699
                         --  - v     v -- --  v    --  i                   
  L1M4_orf2#LINE/    501 AGAC-CTAAATGTA--A--GAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_153792555_   1700 CATAGGAATAAATCTTTGTGACCTTGAGTTAGGCAGTGGTTTTCTAGATA 1749
                               ?i        i         i        i      ii      
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_153792555_   1750 TGACACCAAAAGCATACGCAAAAAAAGAAAAAATATATAAAAACTGGACT 1799
                                       i v    v             v     --i      
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA--TTGGACT 643

  chr1_153792555_   1800 TCATCAAAATAAAAAACCTTTGTGCTTCAAAGGATGCCATCAAGAAAGTG 1849
                                   v      i                ii i            
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_153792555_   1850 AAAAGACAGCCCAGAGGATGGGAGAAAATATTTGCAAACCACATATCTGA 1899
                                 i    v  i                     i  i        
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_153792555_   1900 TAAGGGACTTGTAACCAGAATATATAAAGAACTCTTACAAATCAACAATA 1949
                                      v                          v    i    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_153792555_   1950 AAAAGACAA----CACAATTAAAAAATGGGCAAAG-ATCTGAAAAGATAC 1994
                                  ---- v     ?              -  i    v   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_153792555_   1995 TTCTCCAAAGAAGACATACAAATGGCCTATATGCATATGGAA-GAGGCTC 2043
                                       i            v   v   i   i  -  v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_153792555_   2044 AATATCATTAGTTAT 2058
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (77 / 38)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.83 (51 / 18)  


4665 15.12 4.70 0.69  chr1_153804151_153806765     1250  2122 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_153804151_   1250 TAGAAAGACATCC-ATGTTTATGGGTTGGAAGGTTTAAAATTGTTAAGAT 1298
                          i      i    -     i    i       ii    v           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_153804151_   1299 GATACTACTCCACAAAGTTATCTACAGATTTGATGCAATCCCTATCAAAA 1348
                          ii v      v    v v           ii i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_153804151_   1349 TCTCTGTTGATTTTTTAATAGAAATTGACAAGCTGATCCTAAAATTCATA 1398
                           i v i  vi     vii                               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_153804151_   1399 TGGAAATATAAGTGACCCAGAACGGCCATAATAGTCTTGAAAAAAACT-- 1446
                                ii   v         ii    v  i i          i vv--
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_153804151_   1447 CAAAGTTGGAGAACTCACACTTTCTGATTTCAAAACCTATTACCAAGCT- 1495
                                    i          i ii          i  i   v     -
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_153804151_   1496 ------TCA-----GTGTAGTACTGGCATAATGACAGA------GATCAA 1528
                         ------   -----    i            v  i   ------      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_153804151_   1529 TGGAATGGAACTGAGAAACCAGAAATAGGCC-ATCACATTTATGGGTCCA 1577
                               i   i     iv         ii  -  -          -  v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGG-TCAA 348

  chr1_153804151_   1578 CTGATTTTTAACAAAGGTGCCAAGACAATTAAATGGAGAAAGAATAGTTT 1627
                         i       ii    i           v   v     i           i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_153804151_   1628 TTTCAACAAATGGGGCTGGGACAATCAGAAATCCATAAGCAAAAGTACGA 1677
                                      v          iii  v ?   i v       v i  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_153804151_   1678 AGTTGGACCCCTACCTCATACCATACATAAAAATTAACTCAAAATGGACC 1727
                                           i      i i                    i 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_153804151_   1728 ATAGAC-----TATATGAGTTAAA-CTATGAAACTCTTAGAAGAAA-CAT 1770
                          ?    ----- i  v   i    -    i                -   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_153804151_   1771 GAGAGTAAATCTTCGTGACTTTTGAGGTAGGCAATGGTTTATCAGACATG 1820
                         ii ?               i  - i v             v i   i   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTT-GGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_153804151_   1821 ACACCAAAAGCATA-GCAACAAAAGAAA-----------TTAGACATAAT 1858
                                     i -             -----------  i   v v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_153804151_   1859 TAAAATTAAAACGTCTTGTGTGTCAAAAGACACTATCAATAAAAGTGGAA 1908
                         i          vv i     iv     i           -i      i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA-GAAAGTGAAA 696

  chr1_153804151_   1909 AGACAATCCATGAGATGGGAGAAATTATTTGCCAATCATATGTCTCTGAC 1958
                               i   iiii          v       v        i   --  i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT--GAT 744

  chr1_153804151_   1959 AAGGGTCTAGTATACAGAATCTATAAAGAACTCTTAAAACTCAACAATAA 2008
                              v  v    v      v               v       i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_153804151_   2009 AGGGACGAATAACTTAAATAAAAAATGGGCAAAGGACGTGAACAGATATT 2058
                          ii   i      ii  v ?                iv    i   i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_153804151_   2059 TCTCTAACCAAGATATACAAATGACCAATAAGCACATAAAAAGATGCTCA 2108
                             i  vv              i             i            
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_153804151_   2109 ACATCATTAGTCAT 2122
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (87 / 41)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.94 (47 / 16)  


3860 14.93 7.07 5.16  chr1_153839739_153841845.rev      726  1616 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_153839739_    726 TGGAAAGACATCCCATGTCTATGGGTTAGAAGAC--AATATTGTTAAGGT 773
                                 i         ii    i  i      --            i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_153839739_    774 GCCAATACTACCCAAAGCAATCTACAGAATCAATGCAGTCCCTATCAAAA 823
                          v       v      vii         v    i   i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_153839739_    824 TCTCAAGGGAGTTTGTTTGTTTCAGGGTTTTTGGTGGAAATAGAAAAACT 873
                           i  i----------i  ii -----      -ii     v  v  i  
  L1M4_orf2#LINE/    101 TCCCAG----------CTGCCT-----TTTTTG-CAGAAATTGACAAGCT 134

  chr1_153839739_    874 TATCATAAAATT-ATTTGGAATTTCAAGGGATCCCAAATAGCCAAAACAA 922
                         v   v       -  v     v v       i  vi              
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_153839739_    923 TCTCAAAAAAGAA---CAAAG----ATGACTCAAACTCCTCAATTTCAAA 965
                            ii        ---     ---- v      v   i i          
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_153839739_    966 ACTTACTACAAAGCAACAGTA--------------GTACTGGCATA---- 997
                                       v      --------------           ----
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_153839739_    998 TAGACATATAGACCAATAGAATAGAATAGAGACCCAAGAAATAAACCCTC 1047
                                     i    i         v    vi v            vi
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_153839739_   1048 ATATATATGTTCAATTGATGTTTGACAAGCATATCAAGACCATTCAATGA 1097
                          i  v    v         v  i      vi ii               i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_153839739_   1098 GGAAAGG-CAATCTTTTAAACAAATAGGACTGGGAAAAATAGATATTCAC 1146
                               i-i i      v       i vi      v  v i    ?i   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_153839739_   1147 ATGCAAAAGAAAGAAGTTGGACTAAATCTCACAACTTTTCATGATAAAAC 1196
                                    v          ----------------------------
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGAC---------------------------- 456

  chr1_153839739_   1197 CCTTACCTTACACCATATATAAAAATTAGAT-AAAATGAATCAAAAAACT 1245
                           i     i          i        iv -      i    ? i v  
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_153839739_   1246 AAGTTTAAGAGGCAAAACTATAAAACTTGTAGGAGAAAACAGACAGGAAT 1295
                           i v      vi              iv   i        --i   ?i 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA--TAGGNGT 554

  chr1_153839739_   1296 A--TCTTCATGACTTTGGATTTGGCAATGGTTTCTTAGATATGATAATAA 1343
                          --     i    i    i  v                      i vi  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_153839739_   1344 AAGCACAGGCAATGAAAGAAAACATAGATAAATTGGGCTTAATCAAAATT 1393
                                i    ii        v             i   v         
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_153839739_   1394 AGACACCTCAATGCATCAAATGACACT--CAC--AAGTGAAAAGCCAACA 1439
                          i v  i ivi   v     v      --  v--          v    v
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_153839739_   1440 CACAGAATGGGAGGCAACATTTGAAAATCATATATCTGAC---GGAATTA 1486
                                      iv  i     v               i---   v  i
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_153839739_   1487 TATCCAGAATAAATAAAGAAC------AACTCATCAACAACAAAACAA-- 1528
                                    v         ------      vi  i  v  i    --
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_153839739_   1529 --TCCAATTCAAAAATGGGCAAAG--------------TTTCTCCAGAGA 1562
                         --i      ?              --------------        i   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_153839739_   1563 AGATATACAAATGGCCAGTGAGCACATGAAAAGATATTCAACATCATTTG 1612
                                          i i               ii         ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_153839739_   1613 TCAT 1616
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.58 (79 / 50)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 5.45 (109 / 20)  


3643 22.41 2.82 0.79  chr1_154004621_154007406.rev     1408  2295 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_154004621_   1408 GAAAGGTATCA-GTGTTTATGGATTGGAAGAATTCATATTGTTAAAATGT 1456
                              i    v-i    i             v  v          i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_154004621_   1457 TTATACTACAGAAAATTATCTACAGATTTAATGCAATCTATATCAAAATT 1506
                         iv     v vv   v v           i  i      iv         i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_154004621_   1507 CTAA-TGACTTTTTCACAGAAATAAAAAAACCAATCCTAACATTTTTATG 1555
                          i i-  v      ii       vi v  i ii       v   iv    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_154004621_   1556 GAATCACAAAGAACCCTGAACAGTCAAAGCAATCTTGAGCAAAAAGAACA 1605
                            vii   i i    v   i  i    i         iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_154004621_   1606 AAGCTGGACACATGATACCACTTGATCTCAAAATATACTACAAATCTGTA 1655
                            i    vivv v i  iv iii  i      iv         v  ii 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_154004621_   1656 GTAACCAAAACAGCATGGTACTAGC-CAAAAACAGACACATAGACCAATG 1704
                             i   i    ii       i  -i  ii i     i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_154004621_   1705 GAACAGAACAGAGAGGCCAGAAGTAAGTCCATGCATTTACAGT-----GA 1749
                            i    iv     v      i   ii    i      ii  -----  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_154004621_   1750 TTTTTGATATCAGTGCCAAGAACACACACTGGGGAGAGAGCAGTATTTTC 1799
                             i  i vvi         v  iv  v      i   ii   v     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_154004621_   1800 AATAAATGGTTTTGGGAAAACTTGATATCTACCTGCAGAAGAATGAA-TA 1848
                           i       vi     v    v    ? i  v    i         - v
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_154004621_   1849 GAACTCTTATCTCACACCATGTACAAAAATCAACTCAAAATGGATTAAAG 1898
                          i  i i  i          i         i              i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_154004621_   1899 ACTTAAAATGTAAGACTTGAAACTATAAAGTTACTAGAAGAAATTATAGG 1948
                           i    -       vi i          ii vi         vi     
  L1M4_orf2#LINE/    503 ACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_154004621_   1949 ACAAAAAGTCTATAATATTGGTCTTGGCAATGATTTTTTTGGATATGAGC 1998
                         ?vv   vv iii i iv    vi v       i   i  -i       vv
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACA 600

  chr1_154004621_   1999 CCAAAAGCACAGAAAACAAAAGCAAAAATGAACAAATGGGACTATAT-AA 2047
                                    iiv        v      ii i    v     vi  -  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_154004621_   2048 AGCTAAAAAGTTT----CTTCACCACCAAGAAAACAATTAGCACAGTGAA 2093
                          ii      v   ----     -----   i v  v  i iv v      
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCA-----AAGGACACTATCAAGAAAGTGAA 695

  chr1_154004621_   2094 GAGACAACTTACAGAATGGGAGAAAATATTTGCAAATCATACATTCGATT 2143
                         i       ii                               i  ii   v
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_154004621_   2144 GGGG-TTAATATCCAAAATATATAACAAACGC---------AATAGCAAG 2183
                         i   -i vi      i         vi   v ---------    ii  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_154004621_   2184 AAAACAAATAATTCAATTTTAAAATGGACAAAGGATCTGAATAGACAATT 2233
                           i        ii     ?v       i        i          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_154004621_   2234 CTCAAAAGAAGATACACAAATGACCAACAGGTATATCAAAA-ATGCTCAA 2282
                            v          i       i    i i i i  v    -        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_154004621_   2283 CATCATTAATTAT 2295
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (127 / 68)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 2.46 (32 / 13)  


3303 26.10 0.66 0.66  chr1_154036271_154042678     5008  5915 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_154036271_   5008 TGGAAGAGCATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5057
                              iiii  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154036271_   5058 GGCCATACTACCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5107
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154036271_   5108 TACCAATGACTTTCTTTACAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 5155
                          v   iivi i  i   i     -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_154036271_   5156 TATGGAACCAAAAAAGAGCCTGTATTGCCAAGTCAATCCTAAGCCAAAGG 5205
                                viiv  ii  v  v v  v     iv     i i ivv i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_154036271_   5206 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5255
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_154036271_   5256 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5305
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_154036271_   5306 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5353
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_154036271_   5354 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5403
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_154036271_   5404 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTTGAAAGCT 5453
                           v  i  i              v      v  ?   i   ivi  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_154036271_   5454 GAAACTGGATCCCTTCCTTAAACCTTACACAAAAATTAATTCAAGATGGA 5503
                            ii    i    v   i v   v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_154036271_   5504 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 5552
                          i ?    i  v    v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_154036271_   5553 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5601
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_154036271_   5602 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5651
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_154036271_   5652 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5701
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_154036271_   5702 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5751
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_154036271_   5752 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5801
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_154036271_   5802 AAAAACAAACAACCCCATTAAAAAGTGGGCGAAGGATATGAACAGACCCT 5851
                            i     i     v   ?    i     i      v    i    vi 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_154036271_   5852 TTTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5901
                          i  v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_154036271_   5902 TCATCACTGGCCAT 5915
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2941 28.32 0.66 0.22  chr1_154076848_154083002     4759  5662 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_154076848_   4759 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4808
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154076848_   4809 GGCCATACTGCCAAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4858
                            v     v  v   v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154076848_   4859 TACCATTGACACTCTTCACAGAATTAGAAAAAGCT-ACTTTAAATTTCAT 4907
                          v   vivi vi i  ii     v v  v  -   - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_154076848_   4908 ATGGAACCAAAAGAGAGCTCGTATAGCTAAGACAATCCTAAGCAAAGAGA 4957
                               viiv   i  v iv v     i  i      i i iv  ii   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_154076848_   4958 ATAAACCTGGAGGCATCACACCACCTGACTTCAACCTATACTACAAGGCT 5007
                          i   vi      vv      iv  ii i     vviv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_154076848_   5008 ACCATAACCAAAACAGCATGGTACTTGTACCAAAACAGATATATAGACCA 5057
                           vi   i   i    ii       v i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_154076848_   5058 ACGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCATC 5107
                          i    i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_154076848_   5108 TGATCTTTGACAAACCTAACAAAAACAAGCCATGAGGAAAGGATTTCCTA 5157
                             i  i     ivv iv   i v  vv v   i      i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_154076848_   5158 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATACAGAAAACTGAA 5207
                           i  i              v      v  ?   i  i  i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_154076848_   5208 ACTGGACCCCTTCCTTACACATTATAGAAAAATTAACTCAAGATGGATTA 5257
                         ii         v   i    vv    v              i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_154076848_   5258 AAGACTTAAATGTAAGACCTAAATC-ATAAAAATCCTAGGAGAAAACCTA 5306
                         ?    i           v     v -      v  i   i       v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_154076848_   5307 GCCA-ATACCATTCAGGACACAGGCATGGGCACAGACTTCATGACTAAAA 5355
                          v?i- v i -   iv   viv  vv i    vv ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_154076848_   5356 TACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATTTAATT 5405
                         i          vvi          vv     v  i    v   i  v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_154076848_   5406 AAACTAAAGAGCTTCTGCACAGCAAGAGAAACTATCATCACAGTGAACAG 5455
                            v v  i i   i  ii vv   ii  v       vv v      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_154076848_   5456 GCAACCTACAGAATGGAA-AACATTTTTGCAATCTATCCATCTGACAAAG 5504
                         i     i         i -  v  v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_154076848_   5505 GGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAT 5554
                          i  vi          v  i        ivv    v iv i  v     v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_154076848_   5555 ATGAACAACCCCATAAAAAAGTGGGCAAAGGATAGGAACAGACACTTCTC 5604
                          ii  i     v  v?    i            vv   i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_154076848_   5605 AAAAGAAGACATTTTTGCAGCCCACAGACATAAATAAAAAT--TCATCAT 5652
                         v        i  vivviii   v i ii  i viv   i  --   v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_154076848_   5653 CACTGGTCAT 5662
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.27 (141 / 111)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


3018 28.63 0.33 0.33  chr1_154097630_154107107     6126  7033 (2445)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_154097630_   6126 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 6175
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154097630_   6176 GGCCATAGTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 6225
                            v   v v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154097630_   6226 TACCAATGACTTTCTTCACAGAACTGGAAACAATTACTTTAAATTTCATA 6275
                          v   iivi i  i  ii     v v  v viv v iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_154097630_   6276 TGGAACCAAAAAAAGAGCCCACA-TAGCCAAGACAATGCTAAACAAAAAG 6324
                              -- viv  i ii    v -       i     vi i  v  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_154097630_   6325 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6374
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_154097630_   6375 TACCATAACCAAAACAGCATGGTAGTGGTACCAA-ACAGATATATAGACC 6423
                            vi   i   i    ii     v   i iv i- i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_154097630_   6424 AATAGAAAAGAACAGAGGCCTCAGAAATAACACCACACATCTATAACCAT 6473
                            i   v    iv   ivii         vv   i    i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_154097630_   6474 CTGATCTTTGACAAAGCTGACAAAAACAGAAAATGGGGAAAGGATTCCCT 6523
                         i    i  i     i v  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_154097630_   6524 ATTTAATAAATGGTGCTGGGAAAGCCAGCTAGCTGTATGTAGCAAGCTGA 6573
                         v  i  i              v i ii v  ? iii   i iv iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_154097630_   6574 AACTGGATCCCTTCCTTACACCTTTTACAAAAATTAACTCAAGATAGATT 6623
                          ii    i    v   i     v v                 i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_154097630_   6624 AAAGACTTAAAAGTAAGACCTAAAACCATAAAAACCTTAGAAGAAAACTT 6673
                          ?    i    v      v       i      vi             v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_154097630_   6674 AGGCA-ATACCATTCAGGACATAGGCATGAGCAAAGACTTTATGACTAAA 6722
                            ?i- v i -   iv   v v  vv ii    v ii  iv iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_154097630_   6723 ACACCAAAAGCAATGGCAACGAAAGCCAGAATTGACAAATGGGATCTAAT 6772
                                     vvi     i    vv i   v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_154097630_   6773 TAAACTAAGGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 6822
                         i   v v ii i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_154097630_   6823 TGCAACCTACAGAATGGGAAAAAATTTTTGCAATCTATCCATCTGACAAA 6872
                         vi     i           i     v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_154097630_   6873 GGGCTAACATTCAGAATCTACAAGGAACTTAAAAAAATTCACAAGTAAAA 6922
                           i  vii  i      v  i  i     ivv v  v iv i  vv    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_154097630_   6923 AACAAACAACCTCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 6972
                         i     i    iv  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_154097630_   6973 CAATAGAAGACATTTATGCAGCAGGCGGACAAATGAAAAAATGCTCATCA 7022
                          v v      i  vi viii  viiiiii  v       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_154097630_   7023 TCACTGGTCAT 7033
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (152 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  

3078 21.98 6.04 2.85  chr1_154097630_154107107     8108  8985 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_154097630_   8108 GAAAAATCATGACGTGCTTATGAATGAGGAGATTTAATATTGCTAAGATG 8157
                             i  -  vv i  i i   i  vi i   i         i       
  L1M4_orf2#LINE/      3 GAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_154097630_   8158 ATAATATTTCCCCAATTCATCTACCAATTCAATGCAATCCCTATCAAAGT 8207
                         ii    i i   v    v      vi      i               i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_154097630_   8208 CCAGGTGAATTTTTTTGTAGGAATTGACAAAGTAGTCCAGAAATTACTAG 8257
                           vi ivivi       i  i         iv ii   vi     vv  v
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_154097630_   8258 AGAAATGC------CATATGAATAGCCAAAA--ATTTTGAAAAAGAGGAA 8299
                         i       ------ vi -            --  i          i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_154097630_   8300 TAAAAATGGAAGACTCACACTTTACAGTTTCAAATCTTACTACAATGCTG 8349
                         i   iv    i           iv  i       v          v   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_154097630_   8350 ----AATCAAG-CAGTGTAGTACTGACATGATGA---------AAATCAC 8385
                         ----       -      i      i   i v  --------- i    v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_154097630_   8386 TGGAATAAAATTGAAAGTTTGGTAATGAACCCACACATCAACTATAAATT 8435
                                i      i   iii v   i      i    iv ivi v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_154097630_   8436 TGTTTTCAACAAGGATGCCCAGACAATTAAATGGGGAAAAATAGTGTTGA 8485
                         vi     i      i    v    v   v          ---------  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA---------GA 391

  chr1_154097630_   8486 ATAGTGTTTTCAATGCATGGTGCTGGGAAAAATGGATCCATACATGTGAA 8535
                              v       iiv            v  v     v?vi     ii  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_154097630_   8536 AGAATGAGGCTGAGCCTTTATCCCAGAACCATAAACAAAAATTGACTCAA 8585
                                i i  ii  ii  i i  v -     v         i      
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACA-CCATATACAAAAATTAACTCAA 490

  chr1_154097630_   8586 AATGCATTAAACACTGAGTTATTCAAGCTAAAACTGAGAGCTACCTCTTT 8635
                             v  i ? v  iv iv i vvi          ivi --- v     v
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA---AACTCTTA 537

  chr1_154097630_   8636 AAGG------TAGGTGAACGTATTCAT----TTC--TTAGTCAATGGTCT 8673
                         i i ------    ? v vi v   i ----  v--    v       i 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_154097630_   8674 CTGAAATATGACACCT------CAAACAACCAAAGAAAAAACAGATAAGT 8717
                           v i          v------   i    v          i      i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_154097630_   8718 TAAACTTCAACAAAATTAAAAACGTTTGTGCATAAAAGAACACTATCAAG 8767
                          ii      v             v       v v    i           
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_154097630_   8768 AAAGCCAAT-GATGAGCCAGAGAATGGGATGAAATATTTGTCCATTTTAC 8816
                             iv  v-  ii v   v         vi         ivv  -----
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT----- 732

  chr1_154097630_   8817 CATATACCTGGTAAGAATCTAGTATCTGGAAACTATCAAGAACACTTATA 8866
                               i   i    iiv  v     ii   vv   v      v    i 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_154097630_   8867 CCTC--CAGTAGAAAGACAAATAATTCAATGTGTTTAA---TGA-CAAAG 8910
                         v   --i i  i            ii    ---- ?  ---  i-     
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAAT----TWAAAAATGGGCAAAG 828

  chr1_154097630_   8911 GAGTTGAGTAGACAT-----CAAAGGACTTATAAAAATGGCCAATAAAGT 8955
                           v    i       -----     i vv    v             - i
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA-GC 877

  chr1_154097630_   8956 A-ATAGAAAGATACACCAGATCATTAGTCAT 8985
                          -  ii      i v v v    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (110 / 79)
Gap_init rate = 0.03 (23 / 906), avg. gap size = 3.39 (78 / 23)  


3134 28.16 0.33 0.44  chr1_154120276_154128707.rev     3906  4814 (3618)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_154120276_   3906 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 3955
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154120276_   3956 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4005
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154120276_   4006 TACCAATGACTTTCTTTACAGAATTAGAAAAAAACT-ACTTTAAAGTTCA 4054
                          v   iivi i  i   i     v v  v  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_154120276_   4055 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 4104
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_154120276_   4105 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4154
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_154120276_   4155 TACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGATATAGACC 4204
                                 i   i    ii       v i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_154120276_   4205 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCGCATATCTACAACT 4252
                                i    i--    i  --    i   vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_154120276_   4253 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4302
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_154120276_   4303 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATCTATAGAAAGCT 4352
                           v  i  i              v      v  ?   iv ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_154120276_   4353 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4402
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_154120276_   4403 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4452
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_154120276_   4453 CCAGGCATTACCATTCAGGACATAGGCATGGGCGAGGACTTCATCTCTAA 4502
                         vi   ?i v viv   iv   v v  vv i   i v ii   v vvv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_154120276_   4503 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4552
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_154120276_   4553 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 4602
                          i   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_154120276_   4603 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTGCTCACCTGACAA 4652
                           i     i   i             v  i    viiiivi i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_154120276_   4653 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 4702
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_154120276_   4703 AAACAAACAACCCCTTCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 4752
                          i     i     vv i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_154120276_   4753 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCGCC 4802
                           v        i  vi viii     v  i          i      iv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_154120276_   4803 ATCACTGGCCAT 4814
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (152 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.75 (7 / 4)  

3018 27.05 1.44 0.78  chr1_154120276_154128707.rev     7040  7941 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_154120276_   7040 TGGAGAAACATTCCATGCTCATAGATAGGAAGAATCAATATCATGAAAAT 7089
                             i i i  i     i    i   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154120276_   7090 GGCCATACTGCCCAAAGTAATTTAGAGATTCAATACTATTCTCATCAAGC 7139
                            v     v      v i  i  v        ii v  i ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154120276_   7140 TACCATTTACTTTCTTCACAGA--TTTAGAAAAAAACT-ACTTTAAATTT 7186
                          v   vi i i  i  ii    --  ----i v  i  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT----GACAAGCTGATCCTAAAATT 146

  chr1_154120276_   7187 CATATGAAACTGAAAAAGAGCTCATATAGCCAAGACAATCTTAAGCAAAA 7236
                               i  v  v  ii  v iviv        i        i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_154120276_   7237 AGAACAAAGCTGAAGGCATCACACTACCTGACTTCAAACTACACTGCAAG 7286
                                  i  i   vv       v  ii i      vivi   i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_154120276_   7287 GCTACAGTAACCAAAACAGCATGGTACTGGTATCAA-ACAGATATATAGA 7335
                                   i   i    ii         i  v i- i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_154120276_   7336 CCAATGGAA-------GAGAGCCCTCATTAATAATGCCATACATCTACAA 7378
                         i        -------     i  vv --     vv        i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGA--AATAAACCCATACATTTATGG 344

  chr1_154120276_   7379 CCATGTGACCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 7428
                         i  vv   ii  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_154120276_   7429 CCCTATTCAATAAATAGTGCTGAGAAACCCAGCTAGCCATATGCCAAAAA 7478
                         vi  v     i    i      i  v v ii v  ?   i    v   i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_154120276_   7479 CTGAAACTGGACCCTTTCCTTACACCTTACATAAAAATTAACTCAAGATG 7528
                         v    ii       i v   i     v  i i              i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_154120276_   7529 AATTAAAGACTTAAATGTAAGACATAAAACCATAAAAACCCTAGAAGAAA 7578
                         i  i ?    i           vv      i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_154120276_   7579 ACCCAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTTATGAC 7627
                           vi   ?i- v i -   iv   v v  vv i     v ii  iv iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_154120276_   7628 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 7677
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_154120276_   7678 TAATTAAACTCAAGAGCTTCCACACAACAAAAGAAACAATCATCACAGTG 7727
                          v  i   v i  i i   iiiii vv    i  v  v    vv v    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_154120276_   7728 AACAGGCAACCTAAAGAATGGGAAAAAAAATT-GCAACCTATCCATCTGA 7776
                           v  i     i v         i    v   -    vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_154120276_   7777 CAAGGGGCTAATATCCAGAGTCTATAAGGAACTTAAACAAATTTACAAGA 7826
                         i     i  vi        i v     i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_154120276_   7827 AAAAAACGAACAACCCCATCAAAAAGTGGGCAAAGTACATGAACAGACAC 7876
                             i  i  i     v  i?    i         v iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_154120276_   7877 TTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAGAAGCTC 7926
                              v        i  vi viii     i  i  i         v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_154120276_   7927 ATCATCACTGGTCAT 7941
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


1871 28.20 5.32 3.17  chr1_154336089_154339173.rev     1718  2600 (485)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr1_154336089_   1718 GATATTGTATGTTTATGGATTGGGAGACTAAATCTTTTCTAATTT----A 1763
                              ivi     i         i     v   v  v -   vv ---- 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGT-TAAGATGGCAA 55

  chr1_154336089_   1764 TAC-----AAATTAACTTATAAATCCAATGCAATCCCAGTTATTAAAAAT 1808
                            -----     i ii  i i  i   i        ---   i    vi
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCC---TATCAAAATC 102

  chr1_154336089_   1809 CTACTAGGCTTTTGGGGAGAGAGGGGACAGGAATTGACAAGGTGATTTTT 1858
                          i viv v     vv -----------   i          v    ii v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTG-----------CAGAAATTGACAAGCTGATCCTA 141

  chr1_154336089_   1859 AAATGTATAGAAAAATTCAAAAAGCCAAAAATAGCCATAACAATTTTGAA 1908
                             vi   vii    v   iiii  v i        v      i     
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_154336089_   1909 ---GAAGAACAGCATTTTATGACTTAAACTATCAGTTAAT---AAGAGTT 1952
                         ---        ivi  vv v    i v   -  --ii   ---  i v  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACT-TC--CCAATTTCAAAACTT 238

  chr1_154336089_   1953 ATTATAAAGCCACAATAATTAGAAGAGTGTGGTATTGGCATGAGGATAGA 2002
                          i  i     i   i    i ii v         i      i        
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_154336089_   2003 CAAAATAGACTAATGGACAAGAAAGGAGTTTCCAAAAATAGACC--TACA 2050
                           v -    ii      vv    vv   vv    i     i   --    
  L1M4_orf2#LINE/    289 CATA-TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_154336089_   2051 T----GGCTTTTTGTTTTATAACAAAGGTG---AAATTGCACTGTACTGT 2093
                          ----  iivv   v   vii    i    --- i i--  i -i v  v
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC--CATT-CAATGG 384

  chr1_154336089_   2094 GGAAAAAATCAACTTT-CAATAAATAGGGC-AGGATAAAT---TATCTGT 2138
                              i   viv    -   i    i v  -i   i  v ---  ? iii
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_154336089_   2139 ATTTAAGTTAAAAGTGAATATAAAC----AC-TCAAACTGTACACAAAAA 2183
                           vi  ---  i i    vv ii  ----  -   v  ii  i       
  L1M4_orf2#LINE/    435 ATGCAA---AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_154336089_   2184 TCAATT-GCAATGCTCTTATAAATATAAA-ATAAATGGTAAAAA-ATAAA 2230
                          i  i -iv    v-v i ? i iv    -i   iv v     v-     
  L1M4_orf2#LINE/    482 TTAACTCAAAATGG-ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_154336089_   2231 GTTTCTAGAAGATAACCTGGGAGAGTATCTTTATGATCTTGGAGTAGACT 2280
                         ii ii       v   v i  ? viv     ii   i     iv   i -
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC- 579

  chr1_154336089_   2281 AAC--TTTCTTAGAAGGGATGCAAAAATCTCTAACCACAAAGGAGAAGAC 2328
                           i--         viv  ii v    v v v i v     i  i  i i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_154336089_   2329 TGATAAACTGGACTATGTCAAAGTTAGAA-TGGTTGTTCATCAAAAGGCA 2377
                         v      i      vii     i   i  -ivv    v v     i i  
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_154336089_   2378 CTATCAATGA-GCAAAGAAGCAAGCCACAGATTGAAGGAAGACATTTGCA 2426
                                vi - ii  i ii   v       v  iii   i i       
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_154336089_   2427 ATACATATATCCAACAAAAGGTTTATATTCAGGGTTTA-AAATAACT--- 2472
                          vv        ii i  ii ii  i   i   ii v  -   v    ---
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_154336089_   2473 ACAAAACAGGAAAAGAAAGACTGA-AAGTTAAGAGAAAAATGAGGAAAT- 2520
                             vv  iv  v i      vi -  vii  vv?       i v   v-
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_154336089_   2521 ATTTGAACAGAGATTGCACATAAAAAGGATATCTACATCACCAATTAGAC 2570
                                i   v   v v -i   i i     vi v  vi     v  vv
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTC-CAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_154336089_   2571 TATGAAAAAATGCTCATTCTCAAATTCACC 2600
                         i       i       viv   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.04 (34 / 902), avg. gap size = 2.21 (75 / 34)  


3153 27.77 0.66 0.22  chr1_154468286_154470560      879  1782 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_154468286_    879 TGGAAAAATATTGCATGCTCATAGATTGGAAGAATTAATATTGTTAAAAT 928
                               i    iv    i    i          v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154468286_    929 GGCCATACTGCCCAAAGAAATTTACAGATTCAATATTATTCCTATCAAAT 978
                            v     v      vvi  i           iiiv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154468286_    979 TACCAATATCATTCTTCACAGAATTAGAAAAATCTATTTTAAAATTCATA 1028
                          v   iivv v  i  ii     v v  v  iiiv  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_154468286_   1029 TGGAACCAAAAAAGAGCCCAAATAGCCAAAGCATTCCTAAGCAAAGACAG 1078
                              viiv  ii  v  vi          i  v  i i iv  ii v i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_154468286_   1079 CAAAGCTGAAGGCATCACACCTCACAACTTCAAACTATACTATAAGCCTA 1128
                              i  i   vv      i  v   i      viv     i  iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_154468286_   1129 CAGTAATCAAAATAGTATAGTACTGATACAAAAACAGACACATAGACCAA 1178
                                   i i   i i      ii i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_154468286_   1179 CGGAATGGAATAGAAAACTCAGAAATAAAGATTCACACCTACAACCATCT 1228
                         i     i    v  i iii          vvivi   ii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_154468286_   1229 GATCTTTGCCAAGGCTAACAAAAAGAAGCAATGGGGAAATGACTGTCTAT 1278
                            i  i v     v iv   i vv vv           vi iv    v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_154468286_   1279 TCAATAAATGGTGCTGGGATAACTTGCTAGCCATATTCAGAAAACTGAAA 1328
                             i              i    v v  ?   i  v  i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_154468286_   1329 CTAGACCCCTACTTTTCACCATATACAAAACTTAATTCAGGATGGATCAA 1378
                         i i         i iv              v    i   ii        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_154468286_   1379 AGATTTAAATGTAGGACTCCAAACTATAAAATTCCTAGAGGAAAACCTAG 1428
                            ii        i  viiv           i  i    i      v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_154468286_   1429 GAAATACAATCCT--TGACATCAGCTTTGGCCAAGAATTTTTGGCTAAGT 1476
                          ?i-  -    i --    v ii v  v   v v iv  i  i v  v v
  L1M4_orf2#LINE/    551 GNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_154468286_   1477 TCCCAAA-GCAATTGCAACAAAAACAAAAATTGACAAGTGTGACTTAATT 1525
                         iv     -   vvv         iv      v  i  i vv     v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_154468286_   1526 AAACTAAAGAGCTTCTGCACGGCAAAAGAAATTATCAACAGAGTAAACAG 1575
                            v v  i i   i  ii vv    i  v i      v i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_154468286_   1576 GCAACCTATAGAATGGGAGAAAATATTAGGAAACTATGCATCTGACAGAA 1625
                         i     i i                  v v   ii  ii      i iii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_154468286_   1626 GTCTAATGTTGAGACC-TGTAAGGAACTTAAACAAATCAACAAGCAAAAA 1674
                          v  vi i iv   vi- i   i     ivv    v    i  vv    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_154468286_   1675 CCAAATAACCCCATTAAAATATAAGTGAAGGACATGAACAGCCACTTCTC 1724
                         v          v   ?   v  ii ii     iv    i  v  i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_154468286_   1725 AAAAGAAGTCAAGCAAGCAGCCAACAA--ACATAAAAAAATGCTCAACAT 1772
                         v       vi vi   iii     i  --    i    i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_154468286_   1773 CACTAATCTC 1782
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2812 26.81 2.34 1.33  chr1_154509866_154511990      734  1632 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_154509866_    734 TGGAAACACATCCCATGCTCATGGATTGGAAGAATGGTTATTTTCACAAT 783
                               v i        i               v viv    v i vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154509866_    784 TTTGTGAT--TGCCCAAAGTCACCTACAGATTTCATGCAAATTATATCAA 831
                         v-- ii  -- v      v v i         iv i    viiv      
  L1M4_orf2#LINE/     51 G--GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_154509866_    832 AATACCATCACCATTTTTCACAGAC-TTAAAAAA--AATCTTAAAATTCA 878
                            v   v vv v     ii    v-  i v  i--i   i         
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_154509866_    879 TATGGAACAACAACAAAAAAAGCCCA-AATAGCCGAAGCAATCCTAAGCA 927
                                ----- iiv  iiii    -       i  i     i i iv 
  L1M4_orf2#LINE/    149 TATGGAA-----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_154509866_    928 AAAAGAACAAACCTGGAGGTATTACAAGACTTGAATTTA-----TACTAC 972
                          i         vi      vv i   vvv iii v  i -----      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_154509866_    973 AAGGCTATAGTTACTAAAACAGCATGGGCACTGGTATAAAAGTAGGCATA 1022
                           i    i   v ii  i    ii   -i     i    iii   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGG-TACTGGCATAAGGATAGACATA 292

  chr1_154509866_   1023 TCGTAACCAATGGAACAGAACAGAAAATCCAGAAATAAAGCCAAATGCTT 1072
                          v -- i        i    iv  i i            v   v iii  
  L1M4_orf2#LINE/    293 TAG--ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_154509866_   1073 ACAACGAACTGATGTTCAACAAAACATACAAAAAC-ATAAATTGGAGAGA 1121
                          iiiiv  i    v   i    ii-i i v  i  -  vv v   i  i 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAA 389

  chr1_154509866_   1122 GGACACCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACGTGTA 1171
                          i i vi  v  i  i              v      v  ?    i  i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_154509866_   1172 GAAGAATAAAACTGGATCCCTATCTCTCATCTCATACAAAAATCAACTTA 1221
                         i      i  ii    i     i   v  i vi          i    i 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_154509866_   1222 GGATGAGTCAAAGACTTAA-TCTAAGACCTGAAACCATAAAAATTCTAGA 1270
                         ii   ii   ?    i   - v     v  i    i      v ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_154509866_   1271 AGATGACCTTGGAAAAACTCTTCTGGACATTGACCTAGGCAAAGAATTTA 1320
                            vi  v v  ?iv  v     vv   v   ivi       v iv  iv
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_154509866_   1321 TAACTAAGACCTCAAAAGCAAATGCAACAAAAACAAGGATAAATAAATGG 1370
                           iv  v   vi        v v         iv  ii   i      v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_154509866_   1371 GACCTAATTAAACTAAAAAAGCTTCTGCACAGCAAAAGCAATAATCATCA 1420
                            i v  i   v v     -   i  ii vv    i vv iv    vv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_154509866_   1421 GAGCAAACAGACAACCCACAGACTGGGAGAAAATATTTGCAAACTATCCG 1470
                         i  ii  v              v                    ii  vii
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_154509866_   1471 TCTGACAAAGGACTAATATTTAGAAC-TACAAGGAACTCAGACAAATCAG 1519
                              i  i     vi   ii    i-  i  i      vv    v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_154509866_   1520 CAAGAAAAAAA------ACTCA-TGAAAAAGTGAGCAAATGACATGTATA 1562
                         i  v     i ------  i  - v?    i  i     v  iv  v   
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_154509866_   1563 GACATTTCTCAAAAGAAGATATGCAAAAGGCCAACAAATATATGAAACAA 1612
                                   v           i    v      i  ii i      vi 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_154509866_   1613 TGATCAACATCACTAATCAT 1632
                           v         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.06 (33 / 16)  


1956 26.17 2.80 4.27  chr1_154524759_154526499.rev      502  1250 (491)    L1M4_orf2#LINE/L1      171   908 (0)  

  chr1_154524759_    502 AATAGCTAGTAAAATGAGTTTTGAGAGAAATTACTAAAGTGGGAGAAATT 551
                               i ---   ii - i    i i i vv vi     v    i v i
  L1M4_orf2#LINE/    171 AATAGCCA---AAACAA-TCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr1_154524759_    552 ATTCTTCCTGATGTTAAGGATTATTATATAGCTACAGTAATAATGACAGG 601
                          iv     ii  v i  iiv   i  i v            v v     v
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr1_154524759_    602 ATGTTACTGGTGGAAGGATAGACACATAGGTCAGTGGAACAGAACACAGA 651
                         i  v      iiv           i    i   i     i    ivv   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr1_154524759_    652 ACTCCAAAACAGACCTACACAAATATGCTCAAATGATTTTTGACA---GT 698
                         iii vi   i i   i i   vv    v    v       i    ---  
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_154524759_    699 -CTATAAAGCAATCGAAAGGAGGAAGGGTAATCTTTTCAATAAATAGTAC 747
                         - i - i v  v  -  v  i i   ii  i         i    i  i 
  L1M4_orf2#LINE/    367 GCCA-AGACCATTC-AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_154524759_    748 TCAAGA-GATTGGACATCCATAAGCAAAGGAAATGAACCTTAACTTAAGT 796
                          -ii  -i i    i ?   i v     i   -    vi vi  iivvii
  L1M4_orf2#LINE/    415 T-GGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCTAC 462

  chr1_154524759_    797 CTCACATCCTATATAAAAATTAATTCAAAATGGATCACATGCTTAAGTGT 846
                               i v    i         i             ? vi i   i   
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_154524759_    847 AACATGTAAAAATTTAGTAAATT--TAGAGAAAAACATGTGAAAAAAATC 894
                           v vv     v v  --   i --    ii       i- i?iv     
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATA--AAACTCTTAGAAGAAAACATA-GGNGTAAATC 559

  chr1_154524759_    895 TTTGGGATGGCATAAGGTTAGGTAAAGAGGTCTTAGAGTTGACACTAAAA 944
                           i ---  i v vi       i  v ivv       vv      i    
  L1M4_orf2#LINE/    560 TTCG---TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_154524759_    945 TAAAGAATAGAAAACATTTATAAAAGAAAAAGTCACTGAATTGGATCTCT 994
                         ---- v i --- i  --- i          i viv i       ii  v
  L1M4_orf2#LINE/    607 ----GCACA---AGCA---ACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_154524759_    995 TCAAAATTAAAAA-TCTTACTCTGTAAGAGATCCTGTTAATAGAATGAAA 1043
                                      - i  iiv  vi  ii  iv  i i  v i i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_154524759_   1044 AAGCAATTTAAAGGTTTAGATAAAACATTTGTA--TCCAATATCCAACAA 1091
                          ii   iii v  iv vi  v    i     i --  vv     ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_154524759_   1092 ATGACTTGTATCTAGACAT-TATCAAGAGCTATCA-AATGCAACAGTAAA 1139
                         iv          i   -  -   v    i  v i -  iv   i i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGA-ATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_154524759_   1140 AA--TAAACAATCCAATTTAAAAATGGACAAA--ACGTGAACA-----CT 1180
                           --i   i  i      ?        i    -- iv    i -----i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_154524759_   1181 CTCCAAAGAGGATTTAAATACAGAAAATAGATAATAAGCACATGAAAAGT 1230
                                  i   ----     ---   i vi                 v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGAT----ATACA---AATGGCCAATAAGCACATGAAAAGA 888

  chr1_154524759_   1231 TATTCAACATTAGCCATTAG 1250
                          ii       i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (127 / 65)
Gap_init rate = 0.04 (26 / 738), avg. gap size = 2.04 (53 / 26)  


1384 25.10 12.86 2.90  chr1_154540748_154543070      605  1086 (1237)    L1M4_orf2#LINE/L1        1   530 (378)  

  chr1_154540748_    605 TGAAAAAATATTCCATGCTCATGGATAGGAAGAATCAGGGTTGTTAAAGT 654
                           i   i    i     i        v      v i ivi       ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154540748_    655 GGCCACACTCTTCAAAGCTATTTACAGATTCAAGGCTATTCTTAGCAAAC 704
                            v i    ii    viv  i           v  v  i i  v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154540748_    705 TACCAATGACATTGTTTGCAAAATTAGAAAAAAAAATC-TAAAATTCATT 753
                          v   iivi v  v      i  v v  v  ivvi   -          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_154540748_    754 TGGAACCAAAAAAGAGCCCAAATAGCCAAAGCAGTCCCAAGCAAAAAAAA 803
                              viiv  ii  v  vi          i  i  iii ----------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---------- 190

  chr1_154540748_    804 AAAAAAAAAAAAAACAAAGCTGGAGGGCTAACACTATACAACTTCGAACT 853
                         ----    i  i       i      i  v     viv   i   i  vi
  L1M4_orf2#LINE/    191 ----AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_154540748_    854 ATATGACAAGGCTACAATAACCAA-----------------ATAAG---- 882
                         v  iv    i      i   i   -----------------     ----
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_154540748_    883 ------------------------------------AAATAAAGCCATAC 896
                         ------------------------------------       v      
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_154540748_    897 ATCTACAACCATCTGATCTTCTACAAAGCTGATAAACACAAGCAATGGGG 946
                           i  iiii  vi    i   v    i v  vi  ivv  vv        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_154540748_    947 AAAGGA----CTCTCTAATAAATGCTGATGGGATAACTGGCTAACCATAT 992
                             i ----  i ii  i     v  v     i      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_154540748_    993 GCAGAATATTGAAACTGGACAACTACCTTTCACCATATACAAAAATCAAC 1042
                            i  v v    ii     vv      iv                i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_154540748_   1043 TCAAGATGGATCAAATTCTTAAATGTAAAACCTAAAACTATAAA 1086
                             i        ? vv i         i v             
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

Transitions / transversions = 1.38 (69 / 50)
Gap_init rate = 0.01 (5 / 530), avg. gap size = 15.20 (76 / 5)  

 984 24.24 3.79 3.03  chr1_154540748_154543070     1435  1830 (493)    L1M4_orf2#LINE/L1      510   908 (0)  

  chr1_154540748_   1435 TGTGAGAAC--AGACTAATACAAAACTCT-AGAAGAAAACCTAGG---AA 1478
                            i   i -- i    ---i        -          v    ---  
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTA---TAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_154540748_   1479 ATACCGTTCTGGACATTGG-CCAAGAAAAGCCTTCAT-GATGAAGACTCC 1526
                           -- -   vv   v    -ii i v  v vi   v -   - v   v  
  L1M4_orf2#LINE/    557 AT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACC 602

  chr1_154540748_   1527 AAAA--ACAATTGCAATAAAAACAAAAAATTGACAAATGGGACCTAATTA 1574
                             --    --    i    i-       v  i    v    i v  i 
  L1M4_orf2#LINE/    603 AAAAGCACAA--GCAACAAAAG-AAAAAATAGATAAATTGGACTTCATCA 649

  chr1_154540748_   1575 AACTAAAGAGCTTCTTCACAACAAAAGAAACTAACAA---AGTAAATAAA 1621
                           v v  i i   i vii vv    i  v    v   ---   i  v i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_154540748_   1622 CAATCTATAGAATGGAAGAAGATATTTGCAAACTGAGCATCCAACAAAG- 1670
                            i i i       i    i           iiivii   ii i  i -
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_154540748_   1671 -CTTTAATACCTAGAATCTACTAGGAACTCAAGCAAATCAATAAGTGAAA 1719
                         -   --i  i i     v  iv i      vvi   v       vvi   
  L1M4_orf2#LINE/    750 ACTT--GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_154540748_   1720 ACCAAACAACACTATTTAAAAATGGGCAAAGGACATGAACAGACACTTCT 1769
                         iv    i   v v   ?                iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_154540748_   1770 CCAGAAAAGACATATATGCAGCCAAAAATCATATGAAAAAGTGTTCAATA 1819
                            i i    i   i viii     v  v  i       ii  i    i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_154540748_   1820 TCACTAACCAT 1830
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.64 (59 / 36)
Gap_init rate = 0.04 (15 / 399), avg. gap size = 1.80 (27 / 15)  


2057 21.34 13.48 9.38  chr1_154569873_154574180     2963  3815 (493)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr1_154569873_   2963 ATGGATTGAAATAATTAGTATTGTTAAAATGTCCATAATACCCAAAGAGA 3012
                                 i  v v   i         i   v v   v v      vv  
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr1_154569873_   3013 TCTACAGATTTAATGTAATCCCTATTAAATTTTGAATAATATTTTTAACA 3062
                                   i  i i         i   v iiv iiviiv     vi  
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr1_154569873_   3063 AACATAGAAAAA--AATTCTAAAATTTGTGTGGAACCACAAAAGGCCCCA 3110
                         i v  v  v  i--i  i        ii i     vii   ii i   --
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC-- 168

  chr1_154569873_   3111 ATACAAAA-AGCAACTTCGCAAACCAATTCTGCTAAAATTTAATGCCATT 3159
                         ---- i  -   -------    v    ----------------------
  L1M4_orf2#LINE/    169 ----AGAATAGC-------CAAAACAAT---------------------- 185

  chr1_154569873_   3160 TAATTTGGCATAGTGAAATTTGTTCTTGAGAAGAAATAACAAAGCTAGAG 3209
                         ------------------------     i  ii  v       i i   
  L1M4_orf2#LINE/    186 ------------------------CTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_154569873_   3210 GCATCACATTACCTAATTTCAAAATGTACT-CAAAGCT-TAGTAATCAAA 3257
                          vv     i v  i          iv    -       -i         i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_154569873_   3258 TGAGTATGACAATGGCATAAAAACAGAAATATAGACCAATAGAACAGAGT 3307
                         vv   i  ii v        ii i   v       i    i   i   i 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_154569873_   3308 AGAAAGCCCGGAAATAATTTCACAAATTTATGCTCAAGTGATTTTTGACA 3357
                         v  i  i  i       vii  i v       v    v       i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_154569873_   3358 AAG-TACACACAAGAACAGGAACAAGAACACACAATGGGGAAAGGGCAGT 3406
                          i - i ---------------     v  iv            iii   
  L1M4_orf2#LINE/    362 AGGGTGC---------------CAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_154569873_   3407 CTTTCCAATAAATGGTGTTGGGAAAACTGGATATCTACATGCTGAAGAAT 3456
                             i   i        i     v         ? i      vi      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_154569873_   3457 AAAATTGGATCCTTATCCTACACCATACACAAAAATCAACTTAAAA---- 3502
                         i  i     i  i  i ii        i        i    i    ----
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_154569873_   3503 ------ACTTAAATGTTAAGACTTGAAACTGTAAAATACT--GGAGGAAA 3544
                         ------  i       -    vi i     i     iv  -- i  i   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_154569873_   3545 CATAAGGAAAAA-CTTCTTGACTTCAATCTTGACAAAGATTTTTTGGATC 3593
                             i ?iv   -    v    i iiivi v i   v i   i  i   v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_154569873_   3594 TGATCCCAAAA--------------------------------------- 3604
                            iv      ---------------------------------------
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_154569873_   3605 -----------------TTATG--------GGCA-----AAGAAA---AA 3621
                         -----------------  i  -------- i  -----      ---  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_154569873_   3622 AAGACAA-------------------TATTTGCAAACCATATATCTGACA 3652
                                -------------------          i           i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_154569873_   3653 AGAG-TTAGTATGCCAAATATATAA-GAAC-CT--CAGGTCAACAACAAG 3697
                           i -i v    v vi         -    -  --  iv    i  i  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_154569873_   3698 GAAACAAATAATTCAGTTAAAATATAGGCAAAGAACCTGAATAGATATTA 3747
                         i i        ii  i  ?   v  i       i ii        i   v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_154569873_   3748 CTCAAAAGAAGACATACAAATGTCCAGCAGATATATAAAACAGGTATATG 3797
                            v        i         v   ii iii i  i   -  ----   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AG----ATG 890

  chr1_154569873_   3798 TTAAACATTACTAATCAT 3815
                         i v     i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (125 / 54)
Gap_init rate = 0.03 (24 / 888), avg. gap size = 8.12 (195 / 24)  


3261 23.03 3.21 2.88  chr1_154596971_154601279     2914  3816 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_154596971_   2914 GAAAGATATCACATGTTCATGGATTGGAAGAATAAATACTGTTAAAATGT 2963
                                   v                    v v    i      i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_154596971_   2964 CAATACTACCCAGAATCATCTACAGATTCAATGCAATCTCTATCAAAATA 3013
                                v    i v v              i      i          v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_154596971_   3014 CCAATGACATTGTCTTCAGAAATAGAAAAAGCAATCCTAAAATTTGTATG 3063
                            iivi v  v i v       v  v  ivii           ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_154596971_   3064 GAACTAAAAACAAATAAACAAACAGAAAACCCTGAATAGCCCAAACAACC 3113
                            ----------  i------  iiii    v        v      i 
  L1M4_orf2#LINE/    153 GAA----------ATG------CAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_154596971_   3114 TTGAAGAA-AAGAA--AAGCTTCAGGTATTATACTACCTGACTTCAAAAA 3160
                              i  -     --   i vv   vv i i   v  ii i       -
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA- 235

  chr1_154596971_   3161 CTCTAATAATCTACAAACCTATAATAATCAAAACAGCATTGTACAGGCAC 3210
                         --  --  --       v   i i       i    ii v    v    i
  L1M4_orf2#LINE/    236 --CT--TA--CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_154596971_   3211 AAAAACAGACACATAGACCAATGAAACAGAATAGAGAGCCCGGAAATAAA 3260
                           ii i     i     i     i  i     v     i  i        
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_154596971_   3261 TCCACACATTTATAGCCCACTGATTTTCAACAAAGGTGTTAAGAATACAC 3310
                         i   i        i i v i        i    i    ii    vi iv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_154596971_   3311 GATGTGGAAAGGACAGTGTCTTCACTAAATAGTATTAAGAAAACTGGATA 3360
                         i   v      i i   v i    vi    i  ii ii  v         
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_154596971_   3361 TCCACTTATAGAAGAATGAAATTAGATTCTTATCTCTCACCATAGACAAA 3410
                         ?    v ii i         i  i  ii i  i   v       v     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_154596971_   3411 AATCAACTCAAAATGGATGAAAGACTTAAATGTATGACCCTGAACTG--A 3458
                            i              v ?    i        v  v ivi    i-- 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_154596971_   3459 AACTACTAGGAGAAAACATTGGGG-AAAGCTCTATGTCACTGATTTGGGC 3507
                             vi   i         v  ? -   v  iii  v vi  iv  i   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_154596971_   3508 AGTGATTTTTTTGGCTAGGACCTCAAAAGCAAAAGCAATAAAAGCAAAAA 3557
                          i  i   i  -i v  v   vi        v      i     v     
  L1M4_orf2#LINE/    580 AATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_154596971_   3558 TAGACAAACGGGATTACA-CACAACCAAAAGGCTTCAGCATAGTAAAAGA 3606
                             i   iv   i v  -  v  ii    i-   iv iiivvi   i  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

  chr1_154596971_   3607 AACAATCAACAGAGTGAAGAGACAACCTATGAAATAGGAAAAAGTACTTG 3656
                         v  v     v i      i        i iii   i   i   i  i   
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_154596971_   3657 CAG-TCAATACATCTGAGAAAAAGTTAATATCCAGAATATATAAGAAACT 3705
                           i-   -  i      v  iiiii vi                ii    
  L1M4_orf2#LINE/    728 CAAATCA-TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_154596971_   3706 CAAACAACTCAATAGTGAGAAAACAA----CCCTATT-AACAATGGTCTA 3750
                          vv           i i i  i    ----   v   -  v     v v 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_154596971_   3751 A----------------TTCTCAAAAGAAGAAATGCAAATGGCCAACAGG 3784
                          ----------------     v        v  i           i i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_154596971_   3785 TATATGAAAAAATGCCCAATATCACTAATCAA 3816
                         i i       i    i   i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (135 / 70)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 3.24 (55 / 17)  


1076 24.06 5.22 2.03  chr1_154640410_154642510      404   748 (1353)    L1M4_orf2#LINE/L1        1   356 (552)  

  chr1_154640410_    404 TGGGGAGTTATACCTTATTTGTAGATAGGCATATTCAAAAATGTTAGGA- 452
                            ii  v   v  v i  ii i   v  v v i i  v v     i  -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154640410_    453 ATCTATTCTCCCTAAATTGATCTATAGATTTAGTGCAATCCATACTGAAA 502
                         iv v  v     i           i     i ii       v  iii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154640410_    503 TTCCAGTATGC-TTTTTTGAACATATTGAATAGCTAATTCTAAAATTTAT 551
                          i    i-   -       v v v     vv    i  i        i  
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_154640410_    552 TT--AAATGCAAAGG-TTTAGAATATCCAAAATAATTTTAAGAAAATAAG 598
                         v --        i  -iii      v      i   i  i -    v   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAG 198

  chr1_154640410_    599 AA--ATGT-GTAAAACGTCTTCAACACT--CTGATTTCAAGACTTATTAC 643
                           -- v  - v ii  ----   -    -- ii       i     i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGAC----TCA-CACTTCCCAATTTCAAAACTTACTAC 243

  chr1_154640410_    644 ----C----GTAATGAAGACAGTATGGTATTGACATAATGATGTACAAAT 685
                         ---- ----     v        i     i  i     v   iv   v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_154640410_    686 AGATCAATGGAACACAACAGAGAATTTGGAAATAAAACCACATATAAACA 735
                                     i v  iv    i iii        v   i i  vv ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_154640410_    736 ATCAGTTGATTTT 748
                         i   i        
  L1M4_orf2#LINE/    344 GTCAATTGATTTT 356

Transitions / transversions = 1.68 (52 / 31)
Gap_init rate = 0.04 (13 / 356), avg. gap size = 1.92 (25 / 13)  

1057 27.43 8.77 3.73  chr1_154640410_154642510     1074  1609 (492)    L1M4_orf2#LINE/L1      346   908 (0)  

  chr1_154640410_   1074 CAGTTGATTTTTTTTTTAAACCAAGCTGCCAAGTCAATGCACTGAGGAGA 1123
                           i        i------i  v i v       v v  v  v  i   - 
  L1M4_orf2#LINE/    346 CAATTGATTTTC------GACAAGGGTGCCAAGACCATTCAATGGGGA-A 388

  chr1_154640410_   1124 AGAA-AGACTTATCAGCAAATAGTGCCACGTCAACTGCATATCTGTATGG 1172
                             -  v   v   i     i    iiv v      v   ? iii   v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_154640410_   1173 AACA-AATGAACCTTGGAATTTTTTCTGAATATAATA-ATAATAATAATA 1220
                           v -      v-     viii vi  v -i iv   - i  v   --  
  L1M4_orf2#LINE/    439 AAAAGAATGAAG-TTGGACCCCTACCTCA-CACCATATACAAAAAT--TA 484

  chr1_154640410_   1221 ACAATTGAGATAGATCACAGACTTAAGCACAAAACACAGTTCCATAAAGC 1270
                           -- ii i  i     ?    i   iiii  i vvi ivv i     i 
  L1M4_orf2#LINE/    485 AC--TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_154640410_   1271 TTCTAGAGGAAAACATAGGAAAATGTCTTGCTGGCCTAAGGATAAACAGA 1320
                          ii    i           ?iv vi    vv  i   vi  v  ii  iv
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_154640410_   1321 GATTTCTTAAAAAGGAAACAAAAAGCTTTAC--TCATTTAAAGCAAT--T 1366
                          i       i v v  v  v      ---  --v  viv    v  v-- 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGC---ACAAGCAACAAAAGAAAAAAT 629

  chr1_154640410_   1367 TGATAAATTGGTCTTCATCAAAATTAA---TTTTTTTCTTTTAAAGGACA 1413
                         v          v               ---i    v vi  i        
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_154640410_   1414 CAATT------TTTAAAAGAGTAGCC---AGAATAGAAAAAA-------- 1446
                          v  i------v v      -i i  ---     i i i   --------
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGA-CAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_154640410_   1447 -------------GATA-----CTTGTCCCTTGACTATTACAAAAAATTC 1478
                         -------------    -----     vi iv  v   - i   i  i  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATAT-ATAAAGAACTC 777

  chr1_154640410_   1479 CTACAAAACAAAGGTAAAAGATTATGAGCAATTCAGTT-AAAAGTGG-CA 1526
                         i     vv   vii     ii-- ii ii  ii  i  -    i   -  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAG--ACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_154640410_   1527 AAACCTTTGAACAGACACTTCACAAAAGAAGATGTGTGAATGTTCAATAA 1576
                           ivv      i     i   v v         i iii    vi      
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_154640410_   1577 GCACGTGAAAAGTTACTTAACCTCGTTCGTCAA 1609
                             i       v i  i   v  i????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (85 / 59)
Gap_init rate = 0.04 (22 / 563), avg. gap size = 3.05 (67 / 22)  


3163 27.69 0.89 0.33  chr1_154685859_154690605     3352  4254 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_154685859_   3352 TGGAAGAACATTCCATGCTCATGGTTGGGAAAAATCAATATCGTGAAAAT 3401
                              ii i  i     i      v v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154685859_   3402 GGCTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 3451
                            v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154685859_   3452 TACCAATGACTTTCTTCACATAATTGGAGAAAACT-ACTTTAAAATTCAT 3500
                          v   iivi i  i  ii  v  v v  v  i-  - iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_154685859_   3501 ATGGAACCAAAAACAGCCC-GCATTGCCAAGACAATCCTAAGCAAAAAGA 3549
                               viiv  ivii   - v  v     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_154685859_   3550 ACAAAACTGGAGGCATCACACTACCTGAATTCAAACTATACTACAAGGCT 3599
                              ii      vv       v  ii v      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_154685859_   3600 ACAGTAACCAAAACAGTGGGGTACTGGTACCAAAACAGAGATATAGAACA 3649
                                i   i      v        i iv ii i   v       v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_154685859_   3650 ATGGAACAGAACAGAGGCCTCAGAAATAA-----CACATCTACAACCATC 3694
                               i    iv   ivii         -----i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_154685859_   3695 TAATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 3744
                          i  i  i     ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_154685859_   3745 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 3794
                           i  i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_154685859_   3795 ACTGGATCCCTTCCTTACATCTTATACAATGATTAATTCAAGATGGATTA 3844
                         ii    i    v   i   i v       vi     i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_154685859_   3845 AAGACTTAAATGTTAGACCTAAAACCATAAAAACCCCAGAAGAAAACCTA 3894
                         ?    i       v   v       i      vi ii          v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_154685859_   3895 GGCA-ATACCATTCAGGACATAGGCATGGGCAAGAACTTCATGACTAAAA 3943
                           ?i- v i -   iv   v v  vv i     viii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_154685859_   3944 CACCAAAAGCAATGGCAACAAAAGCCGAAATTGACAATTGGGATCTAATT 3993
                                    vvi          vvi    v  i  v v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_154685859_   3994 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTGAACAG 4043
                            v v  i i   i  ii vv    i  v   ii  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_154685859_   4044 GCAACCTACAGAATGGGAGAAAATTTTTGCAAACTACCCATCTGACAAAG 4093
                         i     i                 v        ii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_154685859_   4094 GGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAA 4143
                          i  vi          v  i        ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_154685859_   4144 ATCAAACAACCCCATCAAAAAGTGAGCAAAGGACATGAACAGATACTTTT 4193
                          -    i     v  i?    i  i        iv    i   i i  i 
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_154685859_   4194 CTAAAGACGACATTTATGCAGCCAACAGACACATGAAGAAATGCTCATCA 4243
                          i     v  i  vi viii     i ii        i i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_154685859_   4244 TCACTGGTGAT 4254
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.59 (151 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


 612 15.24 0.95 0.00  chr1_154694941_154698369     1742  1846 (1583)    L1M4_orf2#LINE/L1        1   106 (802)  

  chr1_154694941_   1742 TGGAGAGACATTCCATTTTTAT-CATTGGAAGACTTAGTATTGTTAAGAT 1790
                             i   i  i    v  i  -v             i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154694941_   1791 GTCAATACAACCCAAAGCAATCTACAGATTCAGTACAATCCCTATCAAAA 1840
                          v      vv      vii             iii               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154694941_   1841 TCCCAG 1846
                               
  L1M4_orf2#LINE/    101 TCCCAG 106

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.01 (1 / 106), avg. gap size = 1.00 (1 / 1)  

3152 21.39 3.42 0.63  chr1_154694941_154698369     2147  2936 (493)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr1_154694941_   2147 AAAATTTCATATACACTTTTTTGAAGATACAGAAAAATCCATCCTAAAAT 2196
                              ii  vv i -        v   v iv  v  iiiv          
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_154694941_   2197 TTGTATGGAATCTCAAGAGATCCCAAATAAGCAAAACAACATTGAAAA-- 2244
                          ii       viv    i  i  vi    iv        iv       --
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_154694941_   2245 --GAACAAAGTTGCAGCTCTTAGATATCCTGGTTTTAAAACTTACTACAA 2292
                         --           v  vv  i v iv   iii   i              
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_154694941_   2293 AGCTACAAGCAATCCAAACAGTATGGTATGAGCATAAACACAGACATACT 2342
                                - i    v i     i     ivi      iv i       iv
  L1M4_orf2#LINE/    246 AGCTACA-GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_154694941_   2343 GACAAGTGGAATAGAATAGATATCCCAGAAATAAACCCTTATGTATACAG 2392
                           iv i           v  v vi              v  ii v  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_154694941_   2393 TCAAATGACTTTCAACA-GGGTGCCAAGAACATTCAATGGGGAAAAGATA 2441
                             v   i    i   -           v               ii   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_154694941_   2442 GTCTGTTTAACAAATGACATTGAAA-AACTAGATATCCACACATAAA-TA 2489
                             v  i        iiii  ii -    i    ?     iii   -v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_154694941_   2490 ATGAAGTTAGATC---A--TTACAGCATATATAAAAAT-AATTCAAAATT 2533
                                 i  i --- -- i   v      i      -  i       v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_154694941_   2534 GATCAAAGACTTAAACATAAGAACTAAAATTACAAAAAATCCTA-----A 2578
                              ?    i    ii     i      i  i    v-  i  ----- 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAA 543

  chr1_154694941_   2579 TATATAGGAAAAAAGCTTAATTGCATTGGATTTGTCAATAATT-CTTGGA 2627
                         v i     ?iv   v   vi vi v    i  v v    ii  -   i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_154694941_   2628 TATGACACCAAAACCACAGGCAACAAAAGAATAAA--GATAAATTATAGT 2675
                                      v    i            v   --        iv v 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_154694941_   2676 ATATCAAAGTTTACAATTTCTATGCATCAAAGGTCACAATCAACA--GTG 2723
                         vi      i  v v  i  i i   v       v   v     v --   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_154694941_   2724 AAAAGACAACTCATGGAATGAGAGAAGATATTTGCAAATTGTATATCTGA 2773
                                   i  ii     i     i            ii         
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_154694941_   2774 TAAGGGATTAATATCCAGAATATATGTATATAACTTTTACAATTTAACA- 2822
                                i vi              -- v v    i      i i  i -
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATAT--AAAGAACTCTTACAACTCAATAA 791

  chr1_154694941_   2823 TAAAATGA---ACAATGTAATTTTAAAATGAGCAAAGAATTTAAATAGGC 2869
                              v  --- i  ivi    ?v      i      i    i     i 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_154694941_   2870 ATTTCTCCCAATAAGATATACACATGACCAGTTAGCATATGAAAAGATGC 2919
                                 v  v          v   i   i v    i            
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_154694941_   2920 TCAATATCAATATCACT 2936
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (102 / 63)
Gap_init rate = 0.02 (17 / 812), avg. gap size = 1.88 (32 / 17)  


 421 34.26 10.43 3.17  chr1_154718074_154720169.rev      502  1038 (1058)    L1M4_orf2#LINE/L1       63   638 (270)  

  chr1_154718074_    502 CAAATTAATCTATAAATGTAATAAAATCCCAATAAAAAGTTCACCTGGAT 551
                               i     i i  vi  iiv      v  v    vii  v   vv 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_154718074_    552 TTTTTTTAGCCATTTAATATACTTACTCTAAAATTT-TATAGAA-TAATA 599
                              vi  vv   -i i vi  v ii        i-   i   - ivv 
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_154718074_    600 AAAATCTATGAA-AGTCCAGGTTAACTTTGATAAAAAAGAACAAAG--AG 646
                         iii i i -   -  -   iivi  ii    v   i          --i 
  L1M4_orf2#LINE/    162 GGGACCCA-GAATAG-CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_154718074_    647 TGGTTTTATATTATCAGATATTAAGGTAGATCAGAAGTCCAGGGCAATTA 696
                         v  vi i i i vi vi  v i  iiivv ii v  iv i vi i   i 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_154718074_    697 AGTCAGTACAATGTATGTGCAAGATCAAATAAATAAATCAGTGGAACAGA 746
                           v    iiii iivv iii   ivi i i v   i    i     i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_154718074_    747 GTAGAGAGATCA----TAGACCTTGGGTGCACACACACACACACACACAC 792
                         i v     vi  ----  i   -------  i   ivi iivv  - ivv
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACC-------CATACATTTATGGTCA-ATTG 351

  chr1_154718074_    793 ACTT-----AAGGTTGACATCACAAAATAATGGGGAGTGCATGACCTGGC 837
                          i  -----    v  v  vv  v vvi        iv v  i----- i
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-----GT 396

  chr1_154718074_    838 CTATTTAGTACATGGTGCTAG-ATTACT------CTA-AGGGAAAACAAT 879
                           v  i ii v        i - iv   ------ i - v v    v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_154718074_    880 ----TTGGACTTATACCTAATATCAAATGTAAAGTTGGACTCCAAA-AGA 924
                         ----      iiv     v i i  v  ii   iv vi    v   -i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_154718074_    925 TCCAATGCATAAA---AAG---TAAAACTATAAAA---TTAAGGGAA--- 962
                           v? vi v    ---   ---             ---   iii   ---
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_154718074_    963 ------GT-----TTTGCGATTTTGG---AGTCAAGAGGGACT-AAACAA 997
                         ------  -----  i i  ii    ---  v   vi vvv  - i i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_154718074_    998 AACTCTAAAAACATATGT--TAAAAGCAAAAATTGGATGAGTT 1038
                         i  v i    i  i v i--i     v      -i   i i  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAATT 638

Transitions / transversions = 1.54 (111 / 72)
Gap_init rate = 0.05 (26 / 576), avg. gap size = 2.81 (73 / 26)  

 356 28.11 6.45 3.69  chr1_154718074_154720169.rev     1381  1597 (499)    L1M4_orf2#LINE/L1      672   894 (14)  

  chr1_154718074_   1381 AAAAGACACTATGGACAAAGTTGACTGATGGT----AGAGTAGGAGGTAA 1426
                            i        vi v     vi vv  iiii----   i i    iv  
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_154718074_   1427 TGTTTGCAAAGCCTAAAACAAGCAAGAAACTTATAT--AGAA-----AAA 1469
                          i        v v  v v viii   ii    i   --    -----   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_154718074_   1470 GCAGTAGCTCCTATATACCAAATAGGAAAAACCAGAAATTAT---ATTAA 1516
                          ---- i   i  i -  iv    iv     v- v    v i---   ? 
  L1M4_orf2#LINE/    772 G----AACTCTTACA-ACTCAATAATAAAAAG-ACAAATAACCCAATTWA 815

  chr1_154718074_   1517 CAAAATGGGCAAAGGGCACAAAATGGTTATTTCATAGAAGAGGAAACTCA 1566
                         -              iivii  - i vi     vivi    i  v iv  
  L1M4_orf2#LINE/    816 -AAAATGGGCAAAGGATTTGAA-TAGACATTTCTCCAAAGAAGATATACA 863

  chr1_154718074_   1567 AAAGGCTAACAAGCACATGCAAAGATGCTTA 1597
                           v   i  i         v         i 
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.50 (36 / 24)
Gap_init rate = 0.04 (9 / 223), avg. gap size = 2.44 (22 / 9)  


3305 26.07 0.77 0.88  chr1_154998917_155005310.rev     4995  5903 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_154998917_   4995 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5044
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_154998917_   5045 GGCCATACTGCACAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 5094
                            v     v v   iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_154998917_   5095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5142
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_154998917_   5143 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAA 5192
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_154998917_   5193 GAACAACACTGGAGGCATCACACTACCTGACTTCAAACTATGCTACAAGG 5242
                               vii      vv       v  ii i      viv i      i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_154998917_   5243 CTACAGTAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGATATAGAC 5292
                                  i   i    i          i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_154998917_   5293 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5340
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_154998917_   5341 TATCTGATCTTTGACAAGCCTGACAAAAACAAGCAATGGGGAAAGGATTC 5390
                         i vi    i  i      vv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_154998917_   5391 CCTATTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5440
                         i  v     i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_154998917_   5441 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5490
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_154998917_   5491 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5540
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_154998917_   5541 CCTAGGCA-ATACCATTCAGGACAT--AGTCATGGGCAAGGACTTCATGT 5587
                          v    ?i- v i -   iv   v --i  i --     v ii   v iv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAG 592

  chr1_154998917_   5588 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAATTGGGAT 5637
                         v  vi            vvi          vv     v  i  v v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_154998917_   5638 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5687
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_154998917_   5688 GAAAAGACAACCTACAGAATGGGAGAAATTTTTTGCAACCTACTCATCTG 5737
                                     i               v v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_154998917_   5738 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 5787
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_154998917_   5788 AAAAAAACAAACAGCCCCGTCAAAAGGTGGGCAAAGGACATGAGCAGACA 5837
                              i     i i   vi i?   ii           iv   ii     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_154998917_   5838 CTTCTCAAAAGAAGACATTCATGCAGCCAAAAAACACATGAAAAAATGTT 5887
                         i     v        i  v  viii     v  i          i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_154998917_   5888 CATCATCACTGGCCAT 5903
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3091 28.38 0.22 0.34  chr1_155017424_155025271     1810  2704 (5144)    L1M4_orf2#LINE/L1        1   894 (14)  

  chr1_155017424_   1810 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATAGTTAAAAT 1859
                              ii i  i     i      i v      v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155017424_   1860 GGCCATACTACCCAAGGAAATTTATAGATTCAATGCCATCCCCATCAAGC 1909
                            v     v     ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155017424_   1910 CACCAATGACTTTCTTCACAGAATTGGAAAAAAAGTACTTTAAAGTTCAT 1959
                         iv   iivi i  i  ii     v v  v  ivv - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chr1_155017424_   1960 ATGGAACCAAAAAAGAGCCTGCATCTCCAAGTCAATCGTAAGCCAAAAGA 2009
                               viiv  ii  v  v v  vv    iv     v i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_155017424_   2010 ACAAAGCTGGTGTCATCACGCTACCTGATTTCAAACTATACTACAAGGCT 2059
                               i   v vvv    i  v  ii        viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_155017424_   2060 ACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 2109
                                    i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_155017424_   2110 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACTA 2157
                               i    i--    i  --        vv iii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_155017424_   2158 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAACGGATTCCC 2207
                         vi    i  i     ivv  v   i v  vv          v i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_155017424_   2208 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 2257
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_155017424_   2258 AAACTGGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAGATGGAT 2307
                           ii    i    v   i     v    i         i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_155017424_   2308 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 2357
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_155017424_   2358 TAGGCATTACTATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 2407
                             ?i v v v   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_155017424_   2408 ATACCAAAAGAAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 2457
                          i        v vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_155017424_   2458 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 2507
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_155017424_   2508 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCGGACAAA 2557
                          i     i   i             v  i    vii ivi   v  i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_155017424_   2558 GGGCTAATATCCAGAATCTACAATGAACTCAGACAAATTTACAAGAGAAA 2607
                           i  vi          v  i  v      vv    v iv i  v i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_155017424_   2608 AACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCT 2657
                         i     i     v  i?    i    ii     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_155017424_   2658 CAAAAGAAGACATTTATGCAGCCAAAAAACACATTAAAAAATGCTCA 2704
                          v        i  vi viii     v  i     v    i       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.34 (143 / 107)
Gap_init rate = 0.00 (3 / 894), avg. gap size = 1.67 (5 / 3)  

3163 27.31 0.55 0.55  chr1_155017424_155025271     6448  7355 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155017424_   6448 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTAAAAAT 6497
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155017424_   6498 GGCCATACTGCCCAGGGTAATTTACAGATTCAATGCCATCCCCATGAAGC 6547
                            v     v    iiv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155017424_   6548 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6595
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_155017424_   6596 TATGGAACCAAAAAAGAGCCCACAAC-GCCAAGTCAATCGTAAGCCAAAA 6644
                                viiv  ii  -    v  i-     iv     v i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_155017424_   6645 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 6694
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_155017424_   6695 CTACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 6744
                                  i v i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_155017424_   6745 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAAC 6792
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_155017424_   6793 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 6842
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_155017424_   6843 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGGCATATGTAGAAAGC 6892
                         i  v  i  i              v      v  ?v  i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_155017424_   6893 CGAAACTGGATGCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 6942
                         i   ii    iv   v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_155017424_   6943 ATTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 6992
                           i ?    i     i v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_155017424_   6993 CCTAGGCATTACTATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 7042
                          v    ?i v v v   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_155017424_   7043 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 7092
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_155017424_   7093 ATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 7142
                           i   v v  i     i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_155017424_   7143 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCACCTGACG 7192
                         v  i     i   i             v  i    vii ivi i    ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_155017424_   7193 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 7242
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_155017424_   7243 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAGCAGACACTT 7292
                           i     i     v  i?    i           iv   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_155017424_   7293 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAGAAAATACTCAC 7342
                            v        i  vi viii     v  i       i  i  i    v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_155017424_   7343 TATCACTGGCCAT 7355
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3109 24.74 4.74 0.69  chr1_155092370_155096665.rev     1669  2533 (1763)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr1_155092370_   1669 TATTTTATGTTCACAGATTGAAATAATTGGCATTGTTAAAATGCCCATAC 1718
                            iii       ii     i  v v  iii        i   v v    
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr1_155092370_   1719 TACCCAAAGCAATCTACAGATTCAATGTAATCTCTATCAAAATACCAATG 1768
                          v      vii              i i    i          v   iiv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr1_155092370_   1769 ACATACTTCATAGAAATAGAAAAGATGATTCTAAA-TTAATATTGAACCA 1817
                         i v vi  iii      v  v   v    i     -  v    v   -- 
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA--A 156

  chr1_155092370_   1818 T-CAAAGACCCCAAAA--GCCAAAGTAATCTTGAGCAAAAAGGGCAAATC 1864
                          -   i iv    i  --      ii        iv  i   ii    vi
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_155092370_   1865 TGTAGAAATCACACTACCTGATTTCAAAATATACTACAAAACTATAGTAA 1914
                           v  i v       v  ii         iv         i   i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_155092370_   1915 CCAAAACAGCATGGTACTGGTATAAAAACAGATACATAGATCAGCGGAAC 1964
                         i   i    ii         i    ii i   i i        ii    i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_155092370_   1965 AGAATATATAACCCAGAAATAAATCCATGCCTTTACAGCCAACCTATTTT 2014
                              vv v ii           i    i v    ii i   iiv     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_155092370_   2015 TAACAAAAGTGCCAAGACACA--CATTGGGGACAGAACAGTCTCTTCAAT 2062
                         ii    ii          -  --  v      v    i     i     i
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_155092370_   2063 AAATAGTGCTGGGAAAACTGAATATCCATATGCAGAAGAACAAAACTAGA 2112
                             i         v     i   ?   i     i     ii  ii i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_155092370_   2113 GCCCTATATCTCACCATATACAAAA-TCAAATGAAGATGGGTTAAAGACT 2161
                         v     iv  v              - i  v v  i    i i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_155092370_   2162 TAAATGTAAGACCCAAAATTGTGAAACTACAAGAAGAAAATATAGGGG-- 2209
                                    v i    i i i     viv         i     ? --
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_155092370_   2210 AATGCTTCATG---TTGGTCTGGGAAAAGATTT--TCGATAAGACCTCAA 2254
                            -    i  ---    vi i  v  v i   -- v    v   vi   
  L1M4_orf2#LINE/    556 AAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_155092370_   2255 AAGCACTGGTAATACAAAACAAAATAGACAAATGAAATTTTATCTAA-CT 2303
                               vi i  i v  i v        i    vii i  i   v  -i 
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_155092370_   2304 AACAAGCTCTGCACAGCAAAGGA--------------------AATAAGC 2333
                           v  vi i  ii vv       --------------------i i  v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_155092370_   2334 TACAGAATGGTAGAAAATATCTGCAAACTACGTATCCAA--AGGGATTAA 2381
                         i         v         i      ii ii    ii --     i vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_155092370_   2382 GATCCAGAATATATAAGGAACTCAAAGAGCTCAATGGCAAAAAAGTAAGT 2431
                         v               i      vv v i      iii     iii  i 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_155092370_   2432 TATTTAAATTTTAAA---GGGCAAAAGACCTGATTAGACAACTCTGAAAA 2478
                         v iii  --  ?   ---       i  ii   v      vi   vv   
  L1M4_orf2#LINE/    805 AACCCAA--TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_155092370_   2479 GAAGACATACGAATGACCAATAGGTAAAT-ATAATATGCTCAACATGACT 2527
                              i    i    i      i i v  - v  v           v ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_155092370_   2528 AATCAG 2533
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 2.04 (141 / 69)
Gap_init rate = 0.02 (17 / 900), avg. gap size = 2.76 (47 / 17)  

2244 26.17 2.72 2.59  chr1_155092370_155096665.rev     3073  3844 (452)  C L1M4_orf2#LINE/L1   (0)   908   136  

C chr1_155092370_   3844 ACCCTAAAACTTAACGTATAATAATAAAAAAAAAAGAGTCTGAACACCCA 3795
                          i       i i ---   iiv   iv  ii----  vi v   i v   
  L1M4_orf2#LINE/    136 ATCCTAAAATTCA---TATGGAAATGCAAGG----GACCCAGAATAGCCA 178

C chr1_155092370_   3794 AAGCAATCTTAAGCAAAAAGAACAAAGCTGGAAGCAC-CACACTATCTGA 3746
                           i       i iv  i          i    i -  -      vi ii 
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAA 227

C chr1_155092370_   3745 CTTCAAACTATAGTACAAGGCTACAGTAACCAAAACAGCATGGTACTAGT 3696
                         i      viv  v     i          i   i    ii       i i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

C chr1_155092370_   3695 AGAAAAACAAACACATAGATAAATG-AACAGGTTAGAGAACCCAGAAATA 3647
                          v  ii i i   i      v    -  i  iv v    ii         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

C chr1_155092370_   3646 AATCTGCACACCTTACAACCATCTGATCTTTGACAA---TGTCAA---CA 3603
                           i iii   i-   iiii  vi    i  i     ---  i   ---  
  L1M4_orf2#LINE/    328 AACCCATACAT-TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

C chr1_155092370_   3602 GTAAGAAGCAATGGGGTGAAGACT--TCCTATTCAATAAATGGTGTTGTG 3555
                         v ------        -i    v --  i -     i        i  v 
  L1M4_orf2#LINE/    377 TT------CAATGGGG-AAAGAATAGTCTT-TTCAACAAATGGTGCTGGG 418

C chr1_155092370_   3554 CTAACTGGCTAGCCATATGCAGAATATTGAAAATTTACATCTTCCTTTCA 3505
                         vi      v  ?   i     i  v v    iv vv  vi  v   iv  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

C chr1_155092370_   3504 CCACATACAAAAGTTAATTCAAGATGGATTAAAGACTTAAATGTAAAACC 3455
                            i        i    i    i      i ?    i         i v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

C chr1_155092370_   3454 TAAAACTACAGAAATCTTGGAAGAAAACCT--GTGAAATTCCATTCTGGA 3407
                                 i i  v    i         v -- ? v  v  --   vv  
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC--TTCGTGA 566

C chr1_155092370_   3406 CATAGGCCCTGGCAAGGATTTCAT-GATGAAGACTTCAAAAGAAACTGCA 3358
                          v v  viiv     v i    v -   - v   vi      v vvv   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCA 615

C chr1_155092370_   3357 ATGTAAACAAAAAT---TAAATGGAACTTAATTAAACTAAAGAGTTTCTG 3311
                          iiv  iv      ---     v i    v  i   v v  i ii  i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

C chr1_155092370_   3310 CACAGCAAACAAAATTGTCAACAGAATAAACAGACAACTTACAGAATGGA 3261
                         ii vv    vi v i i    v i i i  v       ii         i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

C chr1_155092370_   3260 AGAAAATACTTGCAAACTATGTGTATGACAAAGATCTAATACCCAGCATC 3211
                                 i       ii  i i v   i  i iv  vi  i    v  v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

C chr1_155092370_   3210 TATAAGGAACTT----AAATTAACAAGCAAAAAACCA-CAACCTCCTTAA 3166
                              i     i----  v i  i  vv    i  v -i    ivv  ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

C chr1_155092370_   3165 AAAATAGGCAAAGAATATCAACAGACACTTCTCAAAAGAAGACATATACA 3116
                              i       i  v v  i     i     v        i   i v 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

C chr1_155092370_   3115 TAGCCAACAAGCATATTTAAAAATTCTCAACATCACTAATCAT 3073
                          i     i     i  vv   i  v          ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (121 / 77)
Gap_init rate = 0.02 (19 / 773), avg. gap size = 2.16 (41 / 19)  


3213 25.36 1.32 1.21  chr1_155097771_155104048.rev     4881  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155097771_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4930
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155097771_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155097771_   4981 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACTATTTTTAG--TTC 5026
                          v   i-       i  -i     -   -- v  i  iv ii  i--   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_155097771_   5027 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCGTAAGCCAAAA 5076
                                 viiv  ii  v  v v  v     iv     v i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_155097771_   5077 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5126
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_155097771_   5127 CTACAGTAACCAAAACAGCATGGTACTGGAACCAAAACAGAGATATAGAT 5176
                                  i   i    ii         v iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_155097771_   5177 CAATGGAACAGAAC--AGAGCCCTCAAAATTAATGCCACATATCTACAAC 5224
                                 i    i--    i  -- i  v   vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_155097771_   5225 TATCTGATCTTTGACAAACCTGAGAAAAACCAG-CAATGGGGAAAGGATT 5273
                         i vi    i  i     ivv  vv  i -   v-            i  v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATA 394

  chr1_155097771_   5274 CCCCATTTAATAAATGGTGCTGGGATAATTGGCTAGCCATATGTAGAAAG 5323
                         vi iv  i  i              i  i   v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_155097771_   5324 CTGAAACTGGATCCCTTCCTTACACCTCATACAAAAATTAATTCAAGATG 5373
                         v    ii    i    v   i     vi             i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_155097771_   5374 GATTAAAGACTTAAACGTTAGAGCTAAAACCATAAAAACCCTACAAGAAA 5423
                            i ?    i    i  v           i      vi i  v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_155097771_   5424 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5472
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_155097771_   5473 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5522
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_155097771_   5523 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5572
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_155097771_   5573 AACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 5622
                           v  i     i   i             v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_155097771_   5623 CAAAGGGCTAATATCGAGAATCTACAATGAACTCAAACAAATTTACAAGA 5672
                         i  i  i  vi    v     v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_155097771_   5673 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACAC 5722
                             i     i     v  i?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_155097771_   5723 TTCTCAAAAGAAGACCTTTATGCA----GCCAAAAAACACATTAAAAAAT 5768
                              v        ----   i  ----     v  i     v    i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_155097771_   5769 GCTCATCATCACTGGCCAT 5787
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (133 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


3214 27.09 0.55 0.55  chr1_155118461_155124847     4987  5894 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155118461_   4987 TGGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5036
                              ii i  ii    i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155118461_   5037 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCATCAAAC 5086
                            v     v     iv i  i  i        i  v    ii      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155118461_   5087 TACGAGTGACTTTCTTCACAGAA-TTGGAAAGAACT-ACTTTAAAGTTCA 5134
                          v v  ivi i  i  ii     -   iv   --  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_155118461_   5135 TATGGAACTAAAGAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAATAG 5184
                                v iv iii  v  v v  v     i      i i ivv iv  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_155118461_   5185 AAAAAAGCTGGAGGCATCATGCTACCTTACTTCAAAGTATGCTACAAGGC 5234
                           v    i      vv   ii  v  iv i      iiv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_155118461_   5235 TACAATAACCAAAACAGCATGGTACTGGCACCAAAACAAAGACATAGACC 5284
                             i   i   i    ii           iv ii i i v i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_155118461_   5285 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5332
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_155118461_   5333 ATCTGACCTTTGACAAAGCTGACAAAAACAAGAAATGGGGAAAGGATTCT 5382
                          vi   ii  i     i v  v   i v  vvv           i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_155118461_   5383 CTATTTAATAAATGGCTCTGGGAAAACTGTCTAGCCATATGTAGAAAGCT 5432
                           v  i  i      iv      v     vv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_155118461_   5433 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5482
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_155118461_   5483 CTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5532
                         ii ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_155118461_   5533 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5581
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_155118461_   5582 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5631
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_155118461_   5632 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5681
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_155118461_   5682 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5731
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_155118461_   5732 AAGGGCTAATATCCAGAATCGACAATGAACTCAAACAAATTTACAAGAAA 5781
                          i  i  vi          vv i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_155118461_   5782 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5831
                           i     i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_155118461_   5832 CTCAAAAGAAGATCTTTATGTAGCCAACAGACACATGAAAAAATGCTCAT 5881
                            v         v vi vi i     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_155118461_   5882 CATCATTGGCCAT 5894
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2352 28.26 5.03 1.37  chr1_155157553_155161778     2860  3733 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_155157553_   2860 GAAAAATATCCTATTTTCACATATCAGAAGGATTAATATCCTTAAAATAA 2909
                             i      i  v    iiv  ii    iv       iv    i  ii
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_155157553_   2910 CCATATTGCCCCAAAT-AATCTACAGATTCAATGCAATCTTTGTGAAAAT 2958
                          v   i -        -i              i      ii i v     
  L1M4_orf2#LINE/     53 CAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_155157553_   2959 ACAAA-TGTCATTCTTTATAGTATCAGAGAAAACAATCCTAACATTCATA 3007
                         v v i-  i -  i   ii  v viv  v  ivii       v       
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_155157553_   3008 TGGATCCAAAAAAGAGCCTAAATTGCTGAAGCAAGCCTGA---------- 3047
                             vviiv  ii  v  vi   v  ii  i   v i   ----------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_155157553_   3048 -----CTGGAGGCATCACATTATGTGACTTCAAAATGTATCACAAGGCTA 3092
                         -----i      vv     i vivii i       iv  ii    i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_155157553_   3093 TCATAATGAAAAACAGCATGAAATTTTTATAAATATATAAACACAGACCA 3142
                         ivi    v  i -   ii  iv i vvi    iv   v v i i   i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_155157553_   3143 GTGGAGCTAATAAAA----AAACTCAGAACTAAAGGCATATGTTAATAGC 3188
                         i    ----   i  ----i iii     v    vv    ii  v  i i
  L1M4_orf2#LINE/    300 ATGGA----ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_155157553_   3189 AAACTAATCTTCTACAAACCTGACAAGAACTTACATTGGGGAAAAGACAC 3238
                         v  i i  i   v    ivv  v     v v v  v        ii i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_155157553_   3239 CCTATTCAATAAATGGTGCTGAGAAAATTGGATAGCCACATGTGGAAAAA 3288
                         i  v     i           i  v  i      ?       iii  i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_155157553_   3289 TAAAACTGGATCACTGTCTCTCATCTTAT-TAAAA--CAACTCAAGATGG 3335
                          i  ii    i v  ii   v  i v   -i    --i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_155157553_   3336 GGATTAAAGACTTAAACATAAACCCCAAAACTATAAAAATACTAGA-GAA 3384
                         --  i ?    i    ii   ivv i            v vi    -   
  L1M4_orf2#LINE/    496 --ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_155157553_   3385 AAC-----------TCTCC-TGTACATTGGTTTAGGCAAATAATTTATCA 3422
                            -----------   i -  -  v    v        - ii   v i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAA-TGGTTTCTTA 591

  chr1_155157553_   3423 C-TAAGACCTTAAATGCACAGGTGACAAAAATAAAAATAGACACATGGGA 3471
                         v-  v   vii   v     i ii      iv         i v  v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_155157553_   3472 CTATATTAAACTAAAGAGATTCTGCATAGAAAAAGAAAT----AACAAAG 3517
                           vi  i   v v  i iv  i  iiivvv   i  v i----  v    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_155157553_   3518 TGTAGAGACAATCTGTTAAATGGGAGAAAATATTTGCAATCTACTCATCT 3567
                           v i      i iiivi                     vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_155157553_   3568 GGCAGGGGACTAATATCCAGAATATACAAGGAACTCAAACAACTCAACAG 3617
                          ii i      vi             i  i      vv         i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_155157553_   3618 GCAAAAGA-AAATAATCTCATGAAAAAGTGGGCAAAGAACATGAATAGAC 3666
                         vv      -      i iv  v?    i         i iv         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_155157553_   3667 ATTTTTCAAAAGAAGACATACAAATGGGTAACAGG-ATTTGAAAAAAAAG 3715
                             i  v        i          vi  i i - iv      i v- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-G 890

  chr1_155157553_   3716 TTTAACATCACCAATCAC 3733
                         i i       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (152 / 92)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 2.67 (56 / 21)  


3165 26.93 0.99 0.77  chr1_155210130_155216863.rev     5338  6243 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155210130_   5338 TGAAAAAGTATTCCATGTTCATGAATAGGAAGAATCAATATGGTGAATAT 5387
                           i   ii   i           i  v      v i     v  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155210130_   5388 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5437
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155210130_   5438 TACCAGTGACTTTCTTCACAGAATTAGAAAAAACTACTTGATCTT----- 5482
                          v    ivi i  i  ii     v v  v  i-----i     i -----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAAT 145

  chr1_155210130_   5483 TCATATGGAACTGAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAA 5532
                                   v  v  ii  v  viv        i      i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_155210130_   5533 AAGAACAAAGCTAGAGGAATCACACTATCTGACTTCAAACTATATTACAA 5582
                                   i i     v       vi ii i      viv  i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_155210130_   5583 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAG 5632
                         i          i   i    ii         i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_155210130_   5633 ACCAATGGAACAGAACAGTGGCCTCAGAAATAACGCCACCTACCTACAAC 5682
                          i        i    iv v ivii         vv   ivi ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_155210130_   5683 CATCTGATCTTTAACAAAACTGACAAGAACAAGCAATGGGGAAAGATTC- 5731
                           vi    i  ii    iiv  v     v  vv             v v-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_155210130_   5732 CCTATTTAATAAATGGCACTGGGAAAACTGGCCAGCCATATGCAGAAAAC 5781
                         i  v  i  i      ii      v      vi ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_155210130_   5782 TGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGGTGG 5831
                             ii         v   i     v                   ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_155210130_   5832 ATTAAAGACTTAAATGTAAGACCTAAAACCATTAAAACC--TAGAAGAAA 5879
                           i ?    i           v       i  -     i--         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAA 544

  chr1_155210130_   5880 ACCTAGGCA-ATACCATTCAGGACACAGGCACATGCAAAGACTTCATGAC 5928
                           v    ?i- v i -   iv   viv  vvi v    v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_155210130_   5929 TAAAACACCAAATGCAATGGAAACAAGAGCCAAAATTGACAAATGGGATC 5978
                           vi        v   vvi v     i  vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_155210130_   5979 TAATTAAACTAAAGAGCTTCTGCACAGCAAATGAAACTATCATCAGAGTG 6028
                          v  i   v v  i i   i  ii vv    v  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_155210130_   6029 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGA 6078
                           v  i     i                 v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_155210130_   6079 CAAAGGGCTAATATCCAGAATCTGCAAAGAACTTAAATAGATTTACAAGA 6128
                         i  i  i  vi          v ii        ivv i iv iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_155210130_   6129 AAAAAACAAACAATCCCATCAAAAAGTGGCCAAAGTTTATAAACAGACAC 6178
                             i     i  i  v  i?    i   v     vv v i  i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_155210130_   6179 TTCTTAAATGAAGGCATTTATACGGCCAACAAACATATGAAAAAAAGCCC 6228
                             iv  v    ii  vi v i      i  i  i       i v  i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_155210130_   6229 ATCATCACTGGTCAT 6243
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


1404 26.84 1.60 9.42  chr1_155233191_155237094     2296  2921 (983)    L1M4_orf2#LINE/L1        5   581 (327)  

  chr1_155233191_   2296 AAAAAATCCCAAGGTTATGGATTAAAATAATCAATATTGTTAAAATAATC 2345
                           i v      v v i       ii  v v i           i  iiiv
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_155233191_   2346 ATCATGCTAAAAGCAATCTATAGATTCAATGCAATTCCTATTAAATTACC 2395
                           vv v iv   vii     i        i     i     i   v v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_155233191_   2396 AAG-GTCTTCTTTCCAAGAATTAGAAAAAC--ATTCTGAAGTTCATGTGA 2442
                          iv- i   i   v  ii    -  v  i --  i  i  i     i  i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCATATGG 153

  chr1_155233191_   2443 AACCATAAAGAGCCT-GAACAGCCAAAGCAATCCTACAAAAAGAACAAAT 2491
                           viii  i ii  i-   i       i     i i-        -----
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-AAAAAGAA----- 197

  chr1_155233191_   2492 AATGTGATGCCTCTGTATTTGTTCCGTTTTTAGAAATTTTTTAAAAAAGA 2541
                         ------------------------------------------------  
  L1M4_orf2#LINE/    198 ------------------------------------------------GA 199

  chr1_155233191_   2542 ACAAATACAGAGGCATCACATTATCTGACTTCAAA--TTACCCTACTAGG 2589
                              vvii    vv     i vi ii i      --    --   v i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAG 247

  chr1_155233191_   2590 CCATAGTAAATAAAATGACACAATACTGGTACGAAAATAGACACATCAAA 2639
                          i i     vi  i iiiiiiii      i ii ii       i  vi v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_155233191_   2640 CAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACATACAACCA 2689
                                 i     v    ii           v   v i iv  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_155233191_   2690 ACTGATGTCCAACAAAGTCAACAAA--CATAAACAATGGAGAAAGTACAT 2737
                          i    v i i    i viiv   i--   v--      i     v i v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATT--CAATGGGGAAAGAATAG 395

  chr1_155233191_   2738 TCTATTCAATAAATGGTGCTGGGAAGATTAGCCAGTCATATACAGAATAA 2787
                            v     i              vi i i vi ?i  i  i  i  v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_155233191_   2788 TGAAAGTAGATTCCTAGCTTTCAACATATA-AAAAATTAAATGAAGATAA 2836
                             iv i  ii    v  iv  v      -         v v  i  ii
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_155233191_   2837 ATTAAAGACTTAAATGTAAAACCTGAAAGTATAAAAATCCTAGAAGAAAA 2886
                           i ?    i         i v  i   v       v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_155233191_   2887 CCCAGAAA-AACTCTTCTAGACATTGGCCTAGGGAA 2921
                          vi  i?i-  v     vv   v    vi    v  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

Transitions / transversions = 1.95 (109 / 56)
Gap_init rate = 0.02 (12 / 577), avg. gap size = 5.75 (69 / 12)  

 526 29.39 6.42 0.00  chr1_155233191_155237094     3119  3414 (490)    L1M4_orf2#LINE/L1      594   908 (0)  

  chr1_155233191_   3119 TAAGATCCCAAAAGCAAATATGACTAAACCAAAAATAGACATATAGGACT 3168
                           v  iv         v viii  v   vv         i v  v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_155233191_   3169 TAATTTAACTAAAAAGCTTCTGCACAGCAAAATAAATAATCAACAGAGTA 3218
                          v  iv  v v    i   i  ii vv    iv v iv     v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_155233191_   3219 AACAAAAAACCTACAGAATGAAATAAAATATTT-----T----------- 3252
                           v i v    i        ii v         ----- -----------
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_155233191_   3253 TAAAAGACTAATATGCAGAATCTACAAGAAACTCAAACAATTCAACAATG 3302
                            ii    vi   v      v  i  ii     vv    i    i   i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_155233191_   3303 AAACAAAAAACAACCCCAATAAAAACTGGGCAAAAGACACGAACTGACAT 3352
                            vi v   i     v v ?    v        i  ivi   iv     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_155233191_   3353 CTCCCAAGAGAAGACATGCAAATATATGACAAACATAAAAAAAAAT---C 3399
                         i  i v i      i  i     ivvii i  i  i vi    i  --- 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_155233191_   3400 AACAGTACTAATCAT 3414
                             vi ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (47 / 39)
Gap_init rate = 0.01 (3 / 315), avg. gap size = 6.33 (19 / 3)  


1195 27.84 9.85 1.02  chr1_155281446_155283064.rev      543  1131 (488)    L1M4_orf2#LINE/L1      268   908 (0)  

  chr1_155281446_    543 TAGTATTAGTATAAAGATGAACAAATAGATTAATGGAACAAAACAGAACA 592
                          i   i i i    i   ii   v      i       i i  iv  ivi
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_155281446_    593 CTCAGAAATAGAAACACATATGTAT----AATTAATTTTCTACAAAGCC- 637
                         ii        i vv  i i  v   ----    i      v    i vi-
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_155281446_    638 TCAAGGCAATTTAATGGTAGAAGAATACTCTTTCCAATAA-TAATGC--- 683
                         i    i v   i     vii       v     i   i  - ii   ---
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_155281446_    684 ---ATTTGGATAG--------AAAAGAATC---TTGAAATTTT--TTCAC 717
                         --- vi      ?--------        v---   i viii --i    
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_155281446_    718 ACCATTTACAAAAATTAACTAGAGATGAATCACAT-CCTGCTTGTAAGAA 766
                              v              vi i   i    ? v-   ivv       i
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_155281446_    767 CTAATATTATTAAA-------AAGAACAT-TAGATA-GAACCTTAGTGAG 807
                             v i   v   -------     v i-   i?i-i  i   v    v
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_155281446_    808 CTTGAATTTTTCAGAAACTTATTAAGTATGACA--GAAAACACTTGAACT 855
                             ii  vvv  iviii  v   ii       --i   i   --i i v
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC--AAGCA 615

  chr1_155281446_    856 ATAAAAGTCAAAGTCAATAAGTTGGACTTTATCAAAACCAAAGGAAACTT 905
                          i     vv   i vi    i        i       ii   ---     
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA---AACTT 662

  chr1_155281446_    906 CTGCTCTTCAAAAGACATGGT--AGAAAATTAAAAG-CAAGTTACAATAT 952
                         i  iv       i    ivi --     i v     -   vii   iv  
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_155281446_    953 AGT-GAAAATATTTGCGTAATATACAAGTAACAAAAATATATATACCTGG 1001
                         i v-            iv vi   i vv i i  iii- iv i  i ii 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGG-ACTTGTATCCAG 761

  chr1_155281446_   1002 AAAACATAAAGAACTCTTACATTTCAATTATGAA--GACAAAGGAACTAA 1049
                           v i                vi     v  i  --      vi v i  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_155281446_   1050 TTAAAATATTGG-AAAGAA---GAA--AATATGCCTCTAACTGAGG---- 1089
                           ?   v  v  -    i ---   --i i  vi   i  vvi  i----
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_155281446_   1090 --AATGGACAA-AAG-ATCTGAAAAGACGCTCAAC-TAAAAAATATG 1131
                         --     v   -   - iv        i       - v ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (103 / 57)
Gap_init rate = 0.04 (26 / 641), avg. gap size = 2.46 (64 / 26)  


2072 28.24 2.59 1.04  chr1_155314113_155315873.rev      500  1271 (490)    L1M4_orf2#LINE/L1      125   908 (0)  

  chr1_155314113_    500 TTAAAAAACT-ACTCTAATATTCATATGAAACTAAAAAAAAACCTGAGTA 548
                           i v  i  - ii    v         i  v iv  iii v  v  i  
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr1_155314113_    549 GACAAAACAATCCTAAACAAAAATAACAAAGCCAGAAGCCTCACATTACC 598
                          v          i i  v  i  v       iii  i v      i v  
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr1_155314113_    599 AGACTTCAA--TTTATGCAACAAGGCTACAGTAACCAAAACAGCACGATT 646
                         vi i     --i   -- v    i          i   i    iii i v
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTA--CTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_155314113_    647 CTGATACAA----AAACACA--GCCTCACAGAACATAACAGATAACCCAG 690
                            ii i  ---- i   i -- viiv ii   i v  iv  v ii    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_155314113_    691 AAATAAAGCCACATATCTACAACCATCTCTTTTTTGACAAAGTTGACAAA 740
                                v   i i  i  iiii  vi vv    i     i v  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_155314113_    741 AATAAACAATAGGGAAAGAACTCCCTATTCAATAAATGGTGCTGGGACAA 790
                          vi vv    i         ivvi  v     i                 
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_155314113_    791 ATGGATAGCCATATGAAGAAGAAAAAAACTGGACCTCGATTTATTACAAT 840
                         v      ?   i   v i     vi  ii      i v ii vvi  v  
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_155314113_    841 AAACACATATTAACTCAAGATGGGTTAAGGACTTACATGTGAGACCTCAA 890
                          v   v v          i    i i ?i   i  v    i   v  v  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_155314113_    891 ACTATAAAAATCCTAGGAGAAAACCTAGG---AAATACCATTCTGGACAT 937
                                  v  i   i       v    ---    -- -   vv   v 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCT 569

  chr1_155314113_    938 TAGCCGT--GGCAAAGAATTTATGACTATGTCTCCCAAATTAATTGCAAC 985
                          i --  --     v iv  iv iiv    v v  v   vi vvv     
  L1M4_orf2#LINE/    570 TGG--GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_155314113_    986 AAACACAAAAATTGAAAAGTGGGTACTG-ATTAAACTAAAGAACTTTTGC 1034
                            viv      v  v  i v  -   v-  i   v v  i        i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGG-ACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_155314113_   1035 ACAGCAACAGAAATTATCAACAGAGTAAATAAGCAACCTACAGAATGGTA 1084
                         i vv   vi  v i      v i   i  v ii     i         v 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_155314113_   1085 GAAAAGATTTTCAAATTATGCATCTGACAAAGGTCTAATATCCAAAATCT 1134
                              v    v     i  ii      i  i  v  vi      i   v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_155314113_   1135 ACAACAAACTTAAACAATTAAAGGAGCAAAAAACAA----CCTCACTAAA 1180
                          i  vi    ivv    i v  vi vv    i    ----  iv i ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_155314113_   1181 AGGTCAA-AAAGGACATAAACAGACACTTTTCAAAAGAAGACATACATAT 1229
                          ii vii-      iv i  i     i  i  v        i     v  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_155314113_   1230 GGCCAACAAGCATATGAAAAAATGCTCAATATCTCTAAACAT 1271
                               i     i       i        i   v????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (122 / 93)
Gap_init rate = 0.02 (14 / 784), avg. gap size = 2.00 (28 / 14)  


2026 27.45 2.28 6.15  chr1_155375101_155376955      486  1363 (492)    L1M4_orf2#LINE/L1       65   908 (0)  

  chr1_155375101_    486 AATGGATAAACAATTTTAGTGCTATTCCTACCAAACTACCAGAT-CATTC 534
                            v   vv   iv  i ii  v  i    i    v v    v - v  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr1_155375101_    535 TTCACAGAA-TTGGTAAAAAAGT--ATTCCAAAATTCATGTGGAACCAAA 581
                           ii     -   ---- v   i--  i i         i     viiv 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTG----ACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr1_155375101_    582 ACAAGATCACAAATAGTCAAAGGAAT-TTGAAGTAAAAAGACAAAGCTGG 630
                          -ii  i vvi     i    iv   -     iv i  ii      i   
  L1M4_orf2#LINE/    161 A-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_155375101_    631 AGGCATTACAACACCAAACCTCAAACTATACTATAAAACTATAAGACTAT 680
                            vv i   viv  v  ii     viv     i   i   i -------
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA------- 252

  chr1_155375101_    681 AAGAATCTAGTAACCAAAGAATCATGGTGCTGGTATAAAAACAGACACAC 730
                         ---------    i   iiv vii    i    i    ii i     i i
  L1M4_orf2#LINE/    253 ---------GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_155375101_    731 AGATGAATGGAACAGAAAAAAAAAAAACTCAGAAATAAAGCCTCACACCT 780
                             v       i    vvi i i---ii          v  vi   ii 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAG---TCCAGAAATAAACCCATACATTT 340

  chr1_155375101_    781 ACAACCATATGATCTTTGACAACACTAACAAAAACAAGCAACGGGGAAAG 830
                          iiii  vv    i  i     viv iv   i v  vv   i        
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_155375101_    831 GACTCCCTGTTAAACAAATGGTGCTGGGATAACTAGCTAGCCATATGCAG 880
                         i ivvi  v  v                 i    i v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_155375101_    881 AACATTGAAACTGGACTCTTACTTTTCACCACATATAAAAATCAACTAAA 930
                           v v    ii     i i   i iv     i   i      i    v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_155375101_    931 GATGAATTAAGGGTTTAAAGGTGAGACCCAAA-CTATAAAAATCCCAGAA 979
                         i   i  i ?i iii    v  i   v i   -        v  ii    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_155375101_    980 AAAATC-TAGGAAATAACCCTTGTGATACTGGCCTGGGCAAATAATTT-T 1027
                         i   v -    ?ivv  i i i    ivi   vi i     - ii   - 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chr1_155375101_   1028 TGGCTAAGTCACCAAAAGCAGTTTCAACGAAAACAAAAATGGACAAAT-G 1076
                          i v  v v           vvvv    i   iv      i  i    - 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_155375101_   1077 GGCCTAATTAAACT--AGAGTTTCTGCACAGCCAAAAAATAAAATAAAAT 1124
                          i i v  i   v -- i ii  i  ii vv ------------------
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTC------------------ 671

  chr1_155375101_   1125 AAAAAACACTATAAATAGAGTACACAGATAACCTACTGAGACCTACTGCA 1174
                            ii       v  v i   iv v   i    i  --   -------- 
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC--AGA--------A 711

  chr1_155375101_   1175 TGGGAGAAAATATTCACAAAGTATGTATCAGACAAAAGCCTACTATCTAA 1224
                                       ii    vi  i    v  i  ii v  vv    i i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_155375101_   1225 AAATCTATAAGGAACTTAAACAAGTCAATAAGCAGAAAACA--TA----- 1267
                           - v     i     ivv    v       vv i  i   --  -----
  L1M4_orf2#LINE/    762 AA-TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_155375101_   1268 --TTAAAAATAAGCAAAGAACATGAACTGATACTTCTCAAAAGAAGACAT 1315
                         -- ?      ii      i iv    iv  i i     v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_155375101_   1316 ACAATTTGCCAATTAACATATGAAAAAATGCTCAGCATCGCTAATTAT 1363
                             v v      v i  i       i       i    i????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (149 / 88)
Gap_init rate = 0.02 (20 / 844), avg. gap size = 3.70 (74 / 20)  


2461 25.92 2.89 1.18  chr1_155382068_155385415     2096  2855 (493)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_155382068_   2096 ATACTAAAATTTATATAAAGCCCCAAACAAGCCTGAACAGCTAATGCAAT 2145
                           v        i    ii iviv   ivi v  v   i   i  vi    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_155382068_   2146 TCAGGGCAAAAAGAACAAAGCTGGAGGCATCACATTACCTGACTTCAAAA 2195
                         iiv iiv  i          i      vv     i v  ii i       
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_155382068_   2196 TGTATTACAAGGATATAGTACCCAATACAGCATGCTGTTG-TAGAAAAAT 2244
                         iv  i     i v  i    vi   v    ii  v ii  -i v  ii  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_155382068_   2245 AGACACA-AAATCCCATGGAATAGAATAGAAATTCCAGAAAGAAAGTCAC 2293
                              i - i   v-            v  i v        v   vi  i
  L1M4_orf2#LINE/    286 AGACATATAGATCA-ATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_155382068_   2294 ATACTTAGAGCCAACTGATCTTCAACAAAG---CCAATGAGAACTTACAT 2340
                          i i   vi i   i    i   i    i ---    ---  v v v  v
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA---GACCATTCAA 381

  chr1_155382068_   2341 TGAAGACAGGACATGTTCTTCAATTTATGGTGCTGGAAAAATTGGATAGC 2390
                           ii  v  i i vvi i     ivv          i v  i      ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_155382068_   2391 CACATGCAGAAGAATGAAATTAGACCCCTATTTCTCACCATA-------- 2432
                                 i         i  i        ii  v       --------
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_155382068_   2433 --AACTCAAAATTGATTAAGGACTTAAACATAAGACCTTAAATAATAAAA 2480
                         --          v   i ?i   i    ii     v  v   iv      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_155382068_   2481 C-ATTAGAACAAAACCTAGAGAAATATTTCCTGGACATTGGTTTAGGCAA 2529
                          -v      v     v   i?iv v  i i vv   v    v        
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_155382068_   2530 ATAATTTAT--GACTAGGACATCAAAAGAACAGGTGACAACA---ACAAC 2574
                         - ii   v --  -  v    i      v   i ii    v --- v  i
  L1M4_orf2#LINE/    582 -TGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_155382068_   2575 AAAAAAGTGGGACCACATTAAACTAAAAAGCTTCTGCACAGTAAAGGAAA 2624
                          i v  i v    iv   i   v v    i   i  ii vvi      v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_155382068_   2625 CAATCAACAAAGCAGAGAG-CAATCTTTTGAATGGGAGAAAATATTTGCA 2673
                          v     v    iii i  -   i iviv                     
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_155382068_   2674 AAATATTTGTCTTGCAGGGAAATTATATCCAGAATATACAAGAAACTCAA 2723
                           vi  v i   vii i  i v  i             i  ii     vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_155382068_   2724 ACAACTCAGCAGGAAAAAAAACCCAAATAAACCCATTAAAAAGTGGGCAA 2773
                                 ii iv     i ---       v  v   ?    i       
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGA---CAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_155382068_   2774 AGAATATGAATAAACATTTTTCAAAAGAAGACATACAAATGGCTAACAAG 2823
                           i  v      i      i  v        i           i  i   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_155382068_   2824 TATATGAAAAAATGGTCAACATCAAAAATCAT 2855
                         i i       i   v         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (116 / 77)
Gap_init rate = 0.02 (13 / 773), avg. gap size = 2.38 (31 / 13)  


3410 22.71 3.28 0.68  chr1_155411082_155414251     1793  2677 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155411082_   1793 TGGAAAAATATTCTGTGTTCATGGATTAGAAGATTTAATATTGTTAAAAT 1842
                               i    i ii            i     i             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155411082_   1843 GTGAATACTACCCAAAGTGATGTACAAGGTCAATGAAATCCCTATTAAAA 1892
                          vv      v      v    v    iiv    i v         i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155411082_   1893 TCCCAATGACATTTTTTACAGAAATAGAAAAATCAATTCTAAAATTTATA 1942
                              iivi v      i       v  v  iiii  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_155411082_   1943 TGGAATCAGAAAAGACCACAAATAGTCAAATCAATATTGACAAAGAAGAA 1992
                              viiv  ii    vvi     i    v    v    v         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_155411082_   1993 CAAAGCTGAAGGAATCACACTTCCTGATTTTAAAATACAGTAAAAAGCTA 2042
                              i  i    v          ii    i    ivi v  v       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_155411082_   2043 CAATAATTAAGA--GTATGGTACTGGCATAAAAACAGACATA--GATGAA 2088
                           i    i    --  i              ii i       --   v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_155411082_   2089 TGAAACAGAATAGAGAGTCCAGAAATAAACCCATGTATATGTAGTTAACT 2138
                           i  i     v                      ii  v i i  i  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_155411082_   2139 GGTCTTTGACAAGGGTGCCAAAAATATACAATGGAGAATAGACAGCTTCT 2188
                          i i  i              i vi  v      i   vii i  ii i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_155411082_   2189 TTAACAAATAGTGCTGGGAAAACTGCTT-TTCACTTGCAGAATAATGAAA 2237
                          i       i         v     vv -?i   v    i  v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_155411082_   2238 TAAGACCCTTATGCCATACC-----CAAGAATCAACTCAAAATTGTTTAA 2282
                          vi     i  ivi  i   -----   i   i          v v i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_155411082_   2283 AGACTTAAATGTAAGTCTTGAAACTATAGAACTCCTGAAAGAAAAGGTAG 2332
                             i          vvi i        i     i ii       vi   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_155411082_   2333 GGTAAAATCTTCATGATACTGGTCTTGGCAATGATTACATAAATATGACA 2382
                          ?vv        i   ivi   vi v       i  v v  i        
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_155411082_   2383 CTAAAAGCACAGGCAACAAAAAGAAAAAATAAACAAATGGGAGTATAT-A 2431
                          i         i         -         i i    v   v vi  - 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_155411082_   2432 AAGCTAAAA-CTTCTGCACAGCAAAGGAAACAATCAACAGAGTGAAAAGG 2480
                           ii     -   i  ii vv       v  v     v i         i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_155411082_   2481 CAGCCCACTGAATGAGAGTTAATACTTATAAATGATTTCCCTAATAAGGG 2530
                           i     v     i   vv    i  ii    v  v vi  i       
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_155411082_   2531 GTTAATCTCTAAAATATATAAGGAACTAATATAACTCAATACTAAAAAG- 2579
                         ii vi v  i i         i     vv  i         v       -
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_155411082_   2580 TAAATAA---AAAATAAAAATA---AAAG----TAAA-AAAC-----CCC 2613
                         i      ---  vv?      i---    ---- i  - i  -----i  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_155411082_   2614 TAATAACTTGATTTAAAAATGGGCTAAAAACAAACATGAAAAAATGTTCA 2663
                         v  v  ---   v  v      v v v  i  --        i   i   
  L1M4_orf2#LINE/    850 AAAGAA---GATATACAAATGGCCAATAAGCA--CATGAAAAGATGCTCA 894

  chr1_155411082_   2664 ATATCACTAATTAT 2677
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (122 / 75)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.33 (35 / 15)  


 357 26.53 0.00 3.06  chr1_155571950_155574147.rev      493   590 (1608)    L1M4_orf2#LINE/L1       13   107 (801)  

  chr1_155571950_    493 CCATATCACTCATGAATTAAAAAAATTAATACTATTAAAATGTCAAAGCT 542
                             i ---     i   ii  i v      i i    i   v   vi  
  L1M4_orf2#LINE/     13 CCATGT---TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_155571950_    543 ATCTAAAGCAATCTGTAGATTCAATAAAATCCCTATCAAAGGCCCGGC 590
                         vi i   vii    ii        iiv             iv   i  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

Transitions / transversions = 2.71 (19 / 7)
Gap_init rate = 0.01 (1 / 95), avg. gap size = 3.00 (3 / 1)  

2868 26.43 0.37 0.49  chr1_155571950_155574147.rev      887  1707 (491)    L1M4_orf2#LINE/L1       89   908 (0)  

  chr1_155571950_    887 TCCCTATCAAAATACCAATTGATATTCTTCACAGAAACAGAAAAAAACAA 936
                                      v   ii  vi-  i  ii      iv  v  ivvv v
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGAT 137

  chr1_155571950_    937 CCTAAAGTTTATATGGAACCAGAAAAGACCCCAAATAGCCAAAGCAGTTT 986
                               i  i        viiv  ii     vi          i  i i 
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_155571950_    987 TGAACAAAAAGAACAAAGCTAGATATATCACAGTACTTGAATTCAAAATA 1036
                             v  i          i i  vivv     v v iii v       iv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_155571950_   1037 TACTACAAAAGTATAGCAAGCTAAACAGCATGGTACTGACATAACAACAG 1086
                                  iv  i  i  v v i    ii        i     vi i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_155571950_   1087 ATACATAGAGTAATGGAACAGAAAAGAGAATCCAAAAATGAATACACACA 1136
                          i i     vi       i    vv    i    i    i  iv  i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_155571950_   1137 TTTACAGCCAACTCATTGTTGACAAATACACCACGAACATACATTGAGGG 1186
                             ii i   i v   v i     iviii   v  v   v  v  i  i
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_155571950_   1187 AAGAACAGTCTCTTCCATAAATGGTGCAGGAAAAACTAGATGACTATATG 1236
                              i     i   v i         v  i v    i   i? i i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_155571950_   1237 AAGAAGAATGAAACTAGACTCCTTTCTCTCACAACATAAAAACATTAAAT 1286
                         v i         ii i   i   vi   v   v i   v   v     v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_155571950_   1287 CAAAATGCATTAAAGACTTAAATCTAAGACTTCAAATGACAAAACTATCA 1336
                                v  i ?    i     v     vi v   iv i      v i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_155571950_   1337 GAAGAAAACATTGGAG-AAATACTTCAGGGCATTGGCCTGGGCAAAGATT 1385
                                    v  ? -    -    iv i v    vi i     v i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_155571950_   1386 T-TTGTGTAAGACTTCAAAAGCACAGGCAACAAAAACAAAAATAGCCAAG 1434
                          -  ivi  v   vi          i         iv        vi  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_155571950_   1435 TGGAATTATATGAAGCTAAAAAGCTTCTGTACAGCAAAGGAAACAATCAA 1484
                          v i i vi  v  iv v    i   i   i vv       v  v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_155571950_   1485 CAAAGTGAAGAGACAACCCACACAATGGGAGAAAATATTTGCAAACTATC 1534
                         v        i            v                      ii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_155571950_   1535 TATCTGACAAAGGGTTAATGACCAGACTATATCTGGAACTCAAATAACTC 1584
                                i  i  ii vi iv     v     vvi      vv i     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_155571950_   1585 CATAGTAAGAAAACAGATAATCCAATTTTTAAATGGGCAAAAAAATCTGA 1634
                         v   i   i  i   i    i      ?vv           ii - i   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA-TTTGA 835

  chr1_155571950_   1635 ATGGATATTTCTCAAAAGAATATATATAA-TGGCTAGGAGTTATAGAAAT 1683
                           i  i       v      v     i  -    i iv ivi i vi  -
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA- 884

  chr1_155571950_   1684 AAAAAGCTCAACCTCACTATTGAT 1707
                           i v       v   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (124 / 89)
Gap_init rate = 0.01 (7 / 820), avg. gap size = 1.00 (7 / 7)  


2824 23.74 2.74 3.42  chr1_155616518_155620994.rev     2864  3739 (738)    L1M4_orf2#LINE/L1        1   870 (38)  

  chr1_155616518_   2864 TGGGAAGGCATCT-GTGTCCAGGGGTTAGAAGACTTGATACTGTTAAGGT 2912
                            i   ii   i-i   i  v  i  i        i   i       i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155616518_   2913 GTCAATACCCAAGGAACTGCATATGCAATGCAATTTGCAATGTAATCTGT 2962
                          v      i vvvi  i  -  v i  i----   --   i i    iv 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG-ATCTACAG----ATT--CAACGCAATCCCT 93

  chr1_155616518_   2963 AATGCAAAATCCCAGAAGTGTTTTTTACACGAACACAAAAATTTGTCTTA 3012
                          - -           vv iv      i  vi  ivv v  ii vi  i  
  L1M4_orf2#LINE/     94 A-T-CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr1_155616518_   3013 AAATTCATGTAGAATTTAAAGGTACTTTAAATAGCCTTTTTTAATCTTGA 3062
                                 i i   v vv    v  iivi       vvvvi-        
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AATCTTGA 190

  chr1_155616518_   3063 AAAC-AAGAACA----TGGAGGTTTCAGACTTCCTGCTTTCAAAACTTGT 3107
                            v-       ----      vi   v      iiv           ii
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_155616518_   3108 TATAAAGACACAATAATCAAAACAGTGTGGTATTGGCATAAAGACAGACA 3157
                           i    vi   i       i           i        i  i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_155616518_   3158 TAAAGAACAATGGAATATGATAGATAGCATAGAAATAAACCCTGAGAAAT 3207
                           v   v          vi  v  v  ivi            vv v vv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_155616518_   3208 ATGGCTTATTGATTTTTGACATGGACGTCAAGGCTGTTTAATGAG-AAAG 3256
                             iiv         i    v  ii i    i ii  i    i -    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_155616518_   3257 AACAGTCTTTTCAA-AAATGCTGTTGGG-CAATTGTGACATCTGTATACA 3304
                           i           -     v  i    -   i  -  i ? iii  i  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTG-GATAKCCACATGCA 439

  chr1_155616518_   3305 AAA------AGTTGAACCCTTACCT-ACATCATATACAAAATGTAACTCA 3347
                            ------     i    i     -   i           vv       
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_155616518_   3348 AAGTATATCAAATATCTAAATGTAGGAATTAAAACTATGAAACTCTCAGA 3397
                           i iv    ? v i         i  ii         i       i   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_155616518_   3398 ATAAAACAAAAGGGAAAGGCTCCATGACATTGGATTTGGCAATGGGTTTC 3447
                          v      v i ? v  iv  i i    v    i  v        -    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTC 588

  chr1_155616518_   3448 TTGGACATGACACCGATGGCACAGGCAACAACAACAACAATAAAATAGAT 3497
                           i  i        i vi     i       ----  v  -         
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAA----AAGAA-AAAATAGAT 633

  chr1_155616518_   3498 AAATTAGACTACAACAACATTTAATTTTTATATACATCAAAG-ACACAAT 3546
                              i    v  v   v   v  vvi  v i i v      -    v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_155616518_   3547 TAACAGAGTAAAAAAGGGAACCTAGAGAATGAGAGAAAATATTCACACTT 3596
                         i  v i   i    - iv    i v      i           ii  vv 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_155616518_   3597 TATATATTTGATGAGTGCTTTATATCCAGAATATACAGCCAACTCCTACA 3646
                         i      i    i  v vi  i             i ivv     i    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_155616518_   3647 AATCAACTCCAACAACAACAGAATCCAAACAGTGTGAT--AAAAATTGAT 3694
                          v    i---  i  -  -   ---    i iivii  --      v ii
  L1M4_orf2#LINE/    783 ACTCAAT---AATAA-AA-AGA---CAAATAACCCAATTWAAAAATGGGC 824

  chr1_155616518_   3695 AAACACGG---TGAA--ACCCCTTCTCTACTAAAAATACAAAAATTAGCC 3739
                            ---  ---    --iv vi     i vvi  i   i v    -i   
  L1M4_orf2#LINE/    825 AAA---GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT-GGCC 870

Transitions / transversions = 1.53 (124 / 81)
Gap_init rate = 0.03 (29 / 870), avg. gap size = 1.86 (54 / 29)  

 497 15.96 0.00 0.00  chr1_155616518_155620994.rev     3897  3990 (487)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_155616518_   3897 AAAAATTGATAAAGGACTTGAATAGACATTTCTTCAAAGGTGCTATACAA 3946
                               v ii      i                i     iv v       
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_155616518_   3947 ATGGCCAATAAGCACATATGAGTATGCTCAACGGCAATAATCTT 3990
                                          ivi iv         iv  ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


2908 25.96 2.30 2.85  chr1_155632929_155637902     1594  2506 (2468)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155632929_   1594 TGAAAAAATATTTCATGCTCATGGATTGGAAGAATCAATATTGTTAAAAT 1643
                           i   i    ii    i               v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155632929_   1644 GACTATACTGCCCAAAGCAATTTACAGAGTTAATGCTACTCCTATTAAGC 1693
                          i v     v      vii  i      v i  i  v ii     i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155632929_   1694 TACCAA-TGTCATTCTTCACAGAATTAGAAAATGCCTATTTTAAAATTTA 1742
                          v   i-  i -  i  ii     v v  v  -  iv  ii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr1_155632929_   1743 TATGGAACCAAAAAAGAGCCCAAATAGCCAAAGCAATCCTAAGCAAAAAG 1792
                                viiv  ii  v  vi          i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_155632929_   1793 AACAAAATTGGAGGCATTACATTACCCAACTTCAAACTCTACTATAAGAC 1842
                               i       vv i   i v     i      vii     i  ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_155632929_   1843 TACAGTAATCAAAACTGCATGGTACTGGTGCAAAAACAGACACA--GACC 1890
                                     i  v ii         iii  ii i     i --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_155632929_   1891 AATGGAGGAGAATAGAAAATTCTGAAATAAAGCTGAACACTTATAACCAT 1940
                               iv     v  i i i v        v iiv   i    iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_155632929_   1941 CTGATATTTGACAAGGTGGACAAAAACAAACAAGAGGGAAAGGACTCTCT 1990
                         i    v  i       vv v   i v  vv   vi       i ivv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_155632929_   1991 GTTCAGTAAGTGAACTCCCTATTCAGTAAATTCAGTAACTGACCAGCCAT 2040
                         v    ii  i  i------ ii vi --------ii     ivi ?   i
  L1M4_orf2#LINE/    399 TTTCAACAAATGG------TGCTGGG--------ACAACTGGATAKCCAC 434

  chr1_155632929_   2041 ATGCAGAACAATGAAACTAGACACTTACCTTTCAACATGTATAAA--TTA 2088
                              i  v      ii i   v i     iv  v   i  i   --   
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_155632929_   2089 ACTCAAAATGGATTAAAGATTTCAGTGTAAGACCTCAAACTACAAAAATC 2138
                                      i ?   ii v i       v  v      i    v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_155632929_   2139 CTGGAAGAAAACCCAGG---AAATACCCCTCTTAACATCCACCTTGAAT- 2184
                         i i         vi   ---    --- i  v i  ------    ii -
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT---CTTCGTGAC------CTTGGGTT 575

  chr1_155632929_   2185 ----AA--ATTTTTTAGTTAAGTTCCTAAACGCAATTGCAACAAAAACAT 2228
                         ----  --i   i    v  v viv i   v   vvv         iv -
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA- 624

  chr1_155632929_   2229 AAAAT-GATAAGTAGGATCTAATTAAACTAAAGAGGTTCTATGCAGCAAA 2277
                              -     i v   ii v  i   v v  i iv  i i   vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_155632929_   2278 AGAAACTGTCAACAGGGTAAACAGAGAATCTACAAAATGGGAGAAAATAT 2327
                         i  v   i    v ii  i  v   v  i i   i               
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_155632929_   2328 TCACAAACTATGCATCTGACAAAGGTCTAATATCCAGAATCTATAAGGAA 2377
                          ii    ii  ii      i  i  v  vi          v     i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_155632929_   2378 CT--TAAAAT--AACAAGCAAAAAACAACAAACTCCATT-AAAAATGGGC 2422
                           --  v  i--  i  vv    i    vv   i v   -          
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_155632929_   2423 AAAGGACATGAATAGTCACTTATCAAAAGAAGACATACGAGTAGCCAACA 2472
                               iv       v  i  v  v        i    i i i     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_155632929_   2473 AACATATGAAATAATGCTCATCATCACTGTTTAT 2506
                          i  i      vi       v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (149 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.76 (47 / 17)  

1914 28.03 5.38 2.97  chr1_155632929_155637902     3621  4494 (480)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr1_155632929_   3621 CATGTTTGTCGGCTAAAAGATTCAAAAGGTTTTAGATGTGCATT-TTCCT 3669
                               ii v ii ii    i i  v vvv  v     -   v -i   i
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG-GCAATACTCCC 62

  chr1_155632929_   3670 CAAATTGATCTATAAATTCAAGGAAATCCTAGTCACAATCACAAAAGGCT 3719
                                     i i      v v     ivi   v    v  ivv v  
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_155632929_   3720 TTTTGGTACAAATTGACAGGCTGAATATGAAATGTATATGAAAATGCAAG 3769
                             v i v         i     viv i    vi     i         
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr1_155632929_   3770 GGATCTAGAATAGCCAAAGCAACTTCAAAACATAAACACAAAACTGGATA 3819
                            i i            i   ii ii   v v  iv     ii    vi
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr1_155632929_   3820 ATTTGTACTCACTGATTTCATGACTTATTATAAAGCTATAAAGATAAAGG 3869
                          i iii   iv ii      vi     i  i       i ivi  v   i
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_155632929_   3870 CACTGTGATAATAGCAGAAATAAAAACATATTGGTCATTAAAATAGAACA 3919
                           v    i  v i   v  iv v i      v i   v ii       iv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_155632929_   3920 GAGAGTCCAGAAATGGATG-ATTCATAAATGATCAATTGGTGTTTTATGA 3968
                                       ii iv-  v   vv   i       i v  iv ii 
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_155632929_   3969 AATAGCCACTGGA--ATTTAATAGCAGTAAGA-TAGTCTTTTCAAAAAAT 4015
                         iivv    --i  --   i   i -i v    -            v    
  L1M4_orf2#LINE/    363 GGGTGCCA--AGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_155632929_   4016 GGTGCTGAAA--AC---ATA-----ATG----AGCATTGACTTGAACTTC 4051
                                ii --  ---   -----   ----  v  vi v   i  ii 
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_155632929_   4052 -ATCCCACAC---AGAAAAATATTAATT-GAAGTGAGATAATAGAT-TAA 4095
                         - i i     --- v v   v     i -i  i  -   v ?   i-   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATG-GATCAWAGACCTAA 508

  chr1_155632929_   4096 ACATGAAACCCAGAACTATAA----TTCAGTATTAACACAGAGGAGAAAA 4141
                          ii i i v i i        ----i i  v v-  v   v   ? v   
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAG-AAAACATAGGNGTAAA 557

  chr1_155632929_   4142 TCTGCGTGAACCTGGGATAGACTACAATTT-TTA-ACATGTAAATAACAG 4189
                            v     v i    v   i v iii   -   - i   vv vi  v  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_155632929_   4190 TAAATGGAA---AAGAAAAGTTA-ATGACTTGGATGTCATCAAAATTTAA 4235
                         i v v v  ---       iv  -  i v     iv           v  
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_155632929_   4236 AATGTCAGTTCTTCAAAAGACATATTTAAGAAAAGAAAACAACAAACTCC 4285
                           iv iv  v       i    ivv i      ivi   vi    v iv 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_155632929_   4286 AAACTGGAATTAACTATTCTCAA--CACATATTTGACAAAAAATTTGTAA 4333
                          i v   i vv  v    iv   --  i    i   i  iii i     v
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_155632929_   4334 CTAGCATATGCAAAGGATTCTTAGAATCCTTCAATTCTATCAATGCTTCA 4383
                          i  v    ii    i i     --------   i  ----   ----- 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTA--------CAACTC----AAT-----A 790

  chr1_155632929_   4384 ACGAAAAGGCAGCAAACAACTCAATGTAAAA-TGA-CACAATATATGAA- 4430
                          ii     i  ---  i   i    v?    -  i-  v iv  v    -
  L1M4_orf2#LINE/    791 ATAAAAAGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_155632929_   4431 ---CATT---CTACAGAAGATGCGCGGATTATAAATAAGCACATGAAAAT 4474
                         ---    --- i v       iii ii  viiv                v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_155632929_   4475 -TGTTTAGAATCTTTAGTTAT 4494
                         -  i i iv   v????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.04 (32 / 895), avg. gap size = 2.28 (73 / 32)  


2791 26.17 7.16 0.59  chr1_155646751_155653428     5334  6185 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155646751_   5334 TGGAAGAACATTCCATGCTCATGGATAAGAATAATCAATATCATGAAAAT 5383
                              ii i  i     i        vi   v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155646751_   5384 GGCCATACTGCCCAGGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5433
                            v     v    iiv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155646751_   5434 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5480
                          v   -   v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_155646751_   5481 ATATGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAATAA 5530
                                 viiv  ii  v  v v        i      i i iv  v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_155646751_   5531 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5580
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_155646751_   5581 CTACAGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5630
                                  i   i v  ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_155646751_   5631 CATTGGAACAGAACAGAGGCCTCAGGAACGACACCACATATCTACAATCA 5680
                           v     i    iv   ivii   i  ii vv   i i  i  iii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_155646751_   5681 TCTAATCTTTGACAAACCTGACAAAAGCAAGGAATGGGGAAAGGATTTCC 5730
                         vi i  i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_155646751_   5731 TACTTAATAAATCATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5780
                          vi i  i    vi        v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_155646751_   5781 AAACTGGATCCCTTCCTTAGACCATATACAAAAATTAACTCAAGATGGAT 5830
                           ii    i    v   i v                       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_155646751_   5831 TGAAGACTTAAATATAAGACCTAACACCATAAAAACCCTAGAAGAAAACC 5880
                         ii?    i     i     v    v  i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_155646751_   5881 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5929
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_155646751_   5930 AACACTAAAAGCAATGGCAACAAAAGCTAAAATAGACAAATGGGATCTAA 5979
                         i    i       vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_155646751_   5980 TTAAA-TTAAAGAGCTTCTGCACCACAAAAGAAACTATCATCAGAGTGAA 6028
                          i   -     i -   i  ii iv    i  v       vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_155646751_   6029 CAGGCAACCTACAGAATGGGAGAAAATCTTTGCAA--------TCT---- 6066
                         v  i     i                 v       --------   ----
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_155646751_   6067 ----------ACCCA------------------------TCA-------- 6074
                         ---------- i   ------------------------   --------
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_155646751_   6075 --GACAAACAATCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 6122
                         --      i  i  v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_155646751_   6123 CTCAAAGGAAGACATTTATGCCACCAACAGACATATGAAACAATGCTCAT 6172
                            v  i     i  vi viivi    i ii  i      vi       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_155646751_   6173 CATCACTGGTCAT 6185
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (136 / 83)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 5.08 (66 / 13)  


3290 26.54 0.44 0.44  chr1_155668467_155674742     4876  5783 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155668467_   4876 TGGAAGAACATTCCATGCTCATTGGTAGGAAGACTCAATATCATGAAAAT 4925
                              ii i  i     i    v i v        i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155668467_   4926 GGCCAAACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v v   v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155668467_   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_155668467_   5024 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_155668467_   5074 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTTCAAGGC 5123
                                i      vv       v  ii i      viv    v   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_155668467_   5124 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATC 5173
                                 i   i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_155668467_   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5221
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_155668467_   5222 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5271
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_155668467_   5272 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5321
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_155668467_   5322 GAAACTGGATCCCTTCCTTACACCTTCTACAAAAATCAATTCAAGATGGA 5371
                            ii    i    v   i     v v         i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_155668467_   5372 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5421
                          i ?    i       v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_155668467_   5422 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5471
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_155668467_   5472 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5521
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_155668467_   5522 TTAAACTAAAGATCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5571
                          i   v v  i v   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_155668467_   5572 AGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5621
                           i         i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_155668467_   5622 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5671
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_155668467_   5672 AAACAAACAACCCCATAAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5721
                          i     i     v  v?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_155668467_   5722 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5771
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_155668467_   5772 ATCACTGGCCAT 5783
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3255 26.76 0.55 0.55  chr1_155735104_155741380     4877  5784 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155735104_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155735104_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155735104_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_155735104_   5025 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGGCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_155735104_   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_155735104_   5125 TACAGTAACCAAAACAACATGGTACTGTTACCAAAACAGAGATATAGATC 5174
                                 i   i   iii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_155735104_   5175 AATGGAACAGAAC--AGAGCCCGCAGAAATAATGCCGCATATCTACAACT 5222
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_155735104_   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAATC- 5271
                          vi    i  i     ivv  vv  i v  vv            -   v-
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAG 395

  chr1_155735104_   5272 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5321
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_155735104_   5322 TGAAACTGGATCCCTTCCTTACACCTTCTACAAAAATCAATTCAAGATGG 5371
                             ii    i    v   i     v v         i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_155735104_   5372 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5421
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_155735104_   5422 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5471
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_155735104_   5472 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5521
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_155735104_   5522 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5571
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_155735104_   5572 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5621
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_155735104_   5622 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5671
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_155735104_   5672 AAAACAAACAACCCCATCAGAAAGTGGGTGAAGGACATGAACAGACACTT 5721
                           i     i     v  i?i   i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_155735104_   5722 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5771
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_155735104_   5772 CATCACTGGCCAT 5784
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2632 27.27 2.55 1.88  chr1_155764259_155769224.rev     3574  4475 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155764259_   3574 TGGAAAGACATTTCATTCTCATGGATAGGAAGAATCAATATTGTTAAAAT 3623
                                 i  ii   vi        v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155764259_   3624 GGCTATATTCTCCAGAGCAATTTACAGATTCAATGTTATTCTGATCAAAC 3673
                            v   i  i   i vii  i           i iv  i iv      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155764259_   3674 TACCAA-TGTCATTTTTCACAGAATTAGAAAAACT-ATTCTAAAATTTAT 3721
                          v   i-  i -     ii     v v  v  i  -  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_155764259_   3722 ATGGAACCCAAAAAAGATCCCAAATAACCAAAATAATCCTATGCAGAAAC 3771
                               vi-iv  ii  i  vi    i      i    i iviv ii  v
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_155764259_   3772 CACAAAGCTGGAGGCATCACACTATCCAAATTCAAACTATACTACAAAGT 3821
                         v      i      vv       vi    v      viv          i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_155764259_   3822 TACAGTCACCAAAGTAGCATGGTGCTAGAACAAA-ACAGATACATAGACC 3870
                               v i   iii  ii    i  i v i  i- i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_155764259_   3871 AATGGAACAGGTTAGAGAACCCAGAAATAAAGCTGCACACCTACAACCAT 3920
                                i  iv v    ii           v iii   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_155764259_   3921 TGGATCTTCAACAAAGTTGACAATAACAAGTAATGG--AAACAGTACTTC 3968
                          v   i   i    i v  v   v v  vvi     --   v i  v --
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT-- 396

  chr1_155764259_   3969 CTATTCAACAAGCAGTGTCAGGATAACTGGCTGGTTATATACAGAAAATT 4018
                           v        iii   iii   i      v i?ii i  i  i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_155764259_   4019 AAAACTGGAACCCTTCCTTTCACCATATA-AAAAATCTACTCAATATAAA 4067
                         i  ii    v    v   iv         -      iv      v  ii 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_155764259_   4068 GTTAAAAAAAACTTATATATGTAAAACCTAAAACTGTAAATGCCCTAGAA 4117
                         - i ? i --- i  - -      i v        i    vvi i     
  L1M4_orf2#LINE/    497 -TCAWAGA---CCTA-A-ATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_155764259_   4118 GAAATC-TAGGAAATACTATTCTGGACATTAGCCTTGGCAAAGACTTCAT 4166
                             v -    ?ivv v v   vv   v  i vi v     v ii   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_155764259_   4167 GACAAAGACTCCAAAAGCAAATGTAGCAACAACAACAAAAATTGACAAGT 4216
                         iivv v   v         v ---        v iv      v  i  i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACA---AGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_155764259_   4217 GAGATCT------AATTAAAGATCTTCTGTACAGCAAATTAGACTATCAA 4260
                         vi  ii ------       i -   i   i vv    vv v        
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_155764259_   4261 CAGAATAAAAAGATAGTCTACAGAATGGGAGAAAGTATTTGCAAACTATG 4310
                         v i i i      i ii i               i          ii  -
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT- 735

  chr1_155764259_   4311 ATTTCTGAGAAAGGTCTAATATCTAGACTCTATAAGGAACTT----AAAT 4356
                           v     v  i  v  vi    i   v v     i     i----  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_155764259_   4357 CAACAAGCAAAAACCAAACAGTTTCATT-AAAAATGGTTAAAAGCCATGA 4405
                            i  vv    iv    i iiiiv   -        vi   i viv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_155764259_   4406 ATAGATCTTTCTCAAAAGAGGATCCATGCAA----CTAACAAGCATGTGA 4451
                              iv      v     i   --  i   ---- i  i     ii   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGAT--ATACAAATGGCCAATAAGCACATGA 883

  chr1_155764259_   4452 AAA-ATGCTCAATATCACTAATCAT 4475
                            -        i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (149 / 94)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.82 (40 / 22)  

 322 31.33 0.00 0.00  chr1_155764259_155769224.rev     4629  4711 (255)  C L1M4_orf2#LINE/L1   (426)   482   400  

C chr1_155764259_   4711 TTCAGCAAATAGCATCAGGATCACTGGCTAGCTGTATGAAGAAAATTAAA 4662
                             i     i iiiii   iv     v  ? iii   v i  i v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chr1_155764259_   4661 ACTGGACCTCTTCCTTTCACCATATAAAAAAAT 4629
                         ii      i  v   iv         v      
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAAT 482

Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.00 (0 / 0)  


3062 28.30 0.78 0.22  chr1_155776980_155778768.rev      404  1304 (485)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_155776980_    404 GAAAAACATTTCACGCTCATGGATAAGAAGAATTAATTTCACTAAAATGT 453
                             i i  ii  i i        vi     v     v iii   i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_155776980_    454 CCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAATTA 503
                          v     v      vii  i           i  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_155776980_    504 CCATTGACATTCTTCACAGAACTAGAAAAATCTACTCTAAAATTAATATG 553
                            vivi v  i  ii     v v  v  iiiv ii        v     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_155776980_    554 GAATCAAAAAAGAGCCCGAATAGCCAAGACAATCCTAAGCAAAAGGAATA 603
                            viiv  ii  v  v          i      i i iv  i i   i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_155776980_    604 AAGCTGGAGGCATCATGTTACCTGACTGCAAA-CATACTACAGGGCTACA 652
                            i      vv   iii v  ii i v    - v       ii      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_155776980_    653 GTAACCAAAGCAGCATGGCATTGGTACAAAAACAGATACACAGACCAGTG 702
                             i   ii   ii   i i   i i  ii i   i i i   i  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_155776980_    703 GAACAGAATAGATAGCTCAGAAATAAGGCCGTACACCTACAACCATCTGA 752
                            i     v  v  ii         iv  i    ii  iiii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_155776980_    753 TCTTTGGCAAAGCTGACAGAAGCAAGCAATGGGGAAAGGACTCCCTTTTC 802
                          i  i i   i v  v  ii v  vv            i ivvi      
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_155776980_    803 AATAAATGGTGCTAGGAGAACTGGCTACCCATACGAACAAGATTGAAACT 852
                           i          i   v      v  ?   i i v v    v    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_155776980_    853 AGACCTCTTCCTTATACCATATACAAAAATCAACTCAAGCTGGATTAAAG 902
                         i    i  v   i i               i       iv     i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_155776980_    903 ACTTAAATGTAAAACCCAAAACTATAAAAATCCT-GACGACAACTTAGGC 951
                           i         i v i            v  i -  v  v   v    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_155776980_    952 A-ATACCATCTGGACATAGGAACGGTCAAAGATTTCATAACAAAGATGCC 1000
                         i- v i v  vv   v v  ivii v   v i    v  ivv v  ii  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_155776980_   1001 AAAAGCAATCA--TAACAAAAGCAAAAATTGAAAAATGGAATCTAATTAA 1048
                                --  --i        v      v  v    v i ii v  i  
  L1M4_orf2#LINE/    603 AAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_155776980_   1049 ACGTAAGAGCTTCTGTACAGCAAAAGAAACTATCAACAGAGTAAACAGAC 1098
                          vv   i i   i   i vv    i  v        v i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_155776980_   1099 AATCTATAGAATAAAAGAAAAT-TTTGCAAACTATGCATCTGACAAATGT 1147
                           i i i     iii       -        ii  ii      i  iv v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_155776980_   1148 CTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAAAAAC 1197
                           vi       v  v     i     ivv    v iv i  v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_155776980_   1198 AAACAACCTTGTTGAAAAGCGGGCAAAGAATGTGAACAGATGTTTTTC-A 1246
                            i    ivi  ?    ii        i  v    i   ii   i  - 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_155776980_   1247 AAGAAGACATATGTGTGGCCAAAAAGCACATGAGTAAAAGCTCAATAGGA 1296
                                i   iivi       v          iv i v      i vv 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_155776980_   1297 CTGATCAT 1304
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.67 (157 / 94)
Gap_init rate = 0.01 (7 / 906), avg. gap size = 1.29 (9 / 7)  


1472 27.02 3.00 2.63  chr1_155843633_155845601.rev      503  1035 (933)    L1M4_orf2#LINE/L1      227   761 (147)  

  chr1_155843633_    503 ATTTAGAAATATTTTA-AAAGGTATAGAAATAATAACACAATTTTGTGTT 551
                             vi   iv vi  -    v  i  v   --i  v   i ---   v 
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAAT--CAAGACAGT---GTGGT 271

  chr1_155843633_    552 ATTGGAGAAAGAATAAGCATAAAGCCCAATGGAA---AACTAGAGAG-CC 597
                          i   viv   i   ii    v  vi        ---  i -     -  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT-GAGAGTCC 320

  chr1_155843633_    598 AAAACTAGGCTTGCACATTTACAGTCTATTGATTT-CTACAAAAGTAC-A 645
                          i  v  ii iiii       ii   v        - v    ii  i - 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_155843633_    646 ACACAGTTCAGTGGAGAAAAGACTAA-------AAAAAAAGCTACAACAA 688
                          v  vi    i   i    -  v  i-------  v   v v i vivi 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_155843633_    689 CAATTAGATATCCATACTTAAAAAAATGAATCTGAGCCATT-CCTCACTC 737
                            i i    ?   i ivi    i      vi  ii  vi -      v 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_155843633_    738 TTTATACAAAAATAAACTCCAAACAGATCATTGGCTTTTCATA-AACAGC 786
                         iv           v     v   ii     ?v i i v-v  i-  v   
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTA-AATGTAAGAGC 518

  chr1_155843633_    787 TAAAACCATAAAACTTCTACAAGAAAACATGGGAGAAAATCTGTGTGATC 836
                               i        ii  v          i  ? v      vi    i 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_155843633_    837 TTGGTGTAGGCAAAGATTAAAGATTTAGATATCACACCAAAAGCACAATC 886
                             vv       v i  v----i        v               v 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTT----CTTAGATATGACACCAAAAGCACAAGC 614

  chr1_155843633_    887 TACATAACATAAATGCTTAATAATTTGAACTTCATCAAAATGAAGAACTT 936
                         v   v  v v   --v vi    v   i             v  i     
  L1M4_orf2#LINE/    615 AACAAAAGAAAAA--ATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_155843633_    937 CTGTTCTTCAAAAGGTACCATTAAGAGCATTGAAAGGCAAACCATAGATT 986
                         i   v       i ii  i  i    ivi vi    i   v   i   v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_155843633_    987 GGGGCTTAATATTTGTTAGTCACACAGCTGCTGAAGACCCTGTATCCAG 1035
                            ivvv        iv i   i i v   v i i iv i         
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

Transitions / transversions = 1.27 (79 / 62)
Gap_init rate = 0.03 (15 / 535), avg. gap size = 2.00 (30 / 15)  

 351 23.24 16.20 0.70  chr1_155843633_155845601.rev     1338  1479 (489)    L1M4_orf2#LINE/L1      745   908 (0)  

  chr1_155843633_   1338 AAAGATCCTGTATCCAGAATTTATAAAGAACACTCAAAATTCAATAATTG 1387
                           i iv i            v          v  i v  i        vi
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_155843633_   1388 CAGAACAACCAATTAAATGTTTAAAATGGGCAAA---------------- 1421
                         v ii    vi  iiv   - ?v            ----------------
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_155843633_   1422 -------AAGATGATACATGGATGTCAAATAAGCACATAAAAATACACTC 1464
                         -------    v    i iii   v v           i    v ii   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_155843633_   1465 AACATAATTCATCTT 1479
                              v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (18 / 14)
Gap_init rate = 0.01 (2 / 164), avg. gap size = 12.00 (24 / 2)  


2968 25.98 0.98 2.28  chr1_155889936_155893181     1834  2753 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_155889936_   1834 TGGAAACACATCCCATGCTCAGGGATGGGTAGAATTAAAATTGTGAAAAT 1883
                               v i        i   v    v  v   v    v     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_155889936_   1884 GACCATGCTGCCAAAAGCAACCTACAAATTCAAT-CAATTCCCATTCAAA 1932
                          i v  i  v  v   vii i     i      i-    i  i  iv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_155889936_   1933 TACCA-CCACCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCAT 1981
                          v   - ii  -  i  ii     v v  v  ivii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_155889936_   1982 AAGGAAC--CAAAAAACAGCTCACATAGCCAAAGCAAGACTAAGCAAAAA 2029
                          v    v--   iii  -- iviv         i   vvi i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_155889936_   2030 GAACAAATATGAAGGCATCAATATTACCTGATTTCAAACTATACTATAAG 2079
                                vv  i   vv   -i i v  ii        viv     i  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_155889936_   2080 GCCATAGTCACCAAAACAGCATACCAGTACAGCATACTCTACTGGTATAA 2129
                           i i   v i   i    ii i---    ------------   i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTG---GTAC------------TGGCATAA 281

  chr1_155889936_   2130 AAATAGGCACATAGAGCAATGGAACAGAATAGAGAACCCAGAAATAAACC 2179
                         ii    i  i     v        i     v    ii             
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_155889936_   2180 CAAATACTTACAGCCAACTGATCTTCAACAAAGCAAACAAAAACACAAAG 2229
                           v i i   ii i   i    i   i    i vviv   i v  ivv i
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_155889936_   2230 TGGGGAAAGGACACCCTATTCAACAAATGGTACTGGGCTAATTGGCTAGC 2279
                                  i i vi  v             i     vi  i   v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_155889936_   2280 CACATGTAAGAGAATGAAACTGGATCCTCATCTCTCACCTTATACAAAAA 2329
                               i  i        ii    i  ii i   v    v          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_155889936_   2330 TCAACTCAAGATGGATTAAGGACTGAAATCTAAGACCTGAAACTATAAAA 2379
                          i       i      i ?i   iv    v     v  i           
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_155889936_   2380 ATTCTAGAAGATAACATTGGAAAAAACCCTTCTAGACATTGCCTTAGGCA 2429
                         v ii       v     v  ?iv   i -   vv   v   vv       
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chr1_155889936_   2430 AGAATTTCATGATTAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATC 2479
                          vii    v iiv  v  vv         v v    i    iv   i  v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_155889936_   2480 AATAGGTGGGATTTAATTAAACTAAAGGGCTTTTGCACAGCAAAAGGAAC 2529
                         i   ii v   i  v  i   v v  iii      ii vv    i iv  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_155889936_   2530 AGTCAGCAGAGTAAATAGACAACCCACAGAGTGGGAAAACAATCTTTACA 2579
                         vi   iv i   i  v              i     i  -   v   i  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA-AATATTTGCA 729

  chr1_155889936_   2580 ATCTATACAACTGACAAAGTGCTAATATCCAGAATCTACAATGAACTCAA 2629
                          vii   i v    i  i vi  vi          v  i  v      vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_155889936_   2630 ACAAATCAACAAGAAAAAAA-----AATTCCATCAAAAAGTGGGATAAGG 2674
                             v    i  v     i -----  ii v  i?    i    vv    
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_155889936_   2675 ATATGAATAGACAATTCTCAAAAGAAAATATACAAATGGCCAACAAACAT 2724
                           v          v     v      i                i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_155889936_   2725 ATGAAAAAATGCTCAGCACCACTAATGAT 2753
                                i       i  i  ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.73 (30 / 11)  


 753 30.84 7.25 6.10  chr1_155941601_155943457.rev      502  1370 (487)    L1M4_orf2#LINE/L1       30   908 (0)  

  chr1_155941601_    502 AAGATTCATTGTGGTAAAGATGGTAAT-TT-------TTAATTTATAAAT 543
                             i i v i v  v       i   -i -------  i  i  i i  
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGAT 79

  chr1_155941601_    544 TTGATGCAATAC-TATGCTAAATTCCAATAAGATATTTTATGGAACTTGA 592
                          ii i     v -   - v    i   iivivv v    iii   v    
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTAT-CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chr1_155941601_    593 CTAGCCTATTCTAACATTCCCTTGGAAGATAAAGTCAAGAG---TA-AAT 638
                          v   iv  i    v    viv     -  i----    i ---i -   
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAA-ATG----CAAGGGACCCAGAAT 173

  chr1_155941601_    639 AGCCATAAT--TTTTTAAACACATGGGGCTAAGGGGGAGGATG---ATTT 683
                              v  i-- i  v   v v -i ii v   vv      iv--- i  
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGA-AGAACAAAGTTGGAGGACTCACACTT 222

  chr1_155941601_    684 TCTAGCTATCCTAAGCAACTT----TAAAATTATAGCAATTAAAACA-TG 728
                         i i ---  iii  --     ----i   ii  i  i   i  i   -  
  L1M4_orf2#LINE/    223 CCCA---ATTTCAA--AACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_155941601_    729 AAATCTTGGCACAGGAATACATAAATAGAACCATGGAGCAGAAGAGAGAG 778
                         vii vi     i i i   v i v     v v     ii    vv     
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_155941601_    779 TGTAGTTACAAACC-A---ACTT--GGAAATTTAGTGTATGA--AGAGTG 820
                          vi  vv i     - --- i  --  vv v  ii v vi  --  i   
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_155941601_    821 CTACCTTCATTATATACTACACTTCTAATCAGTGACTAGAGGGTTGTACT 870
                          i ---------- v  i i--------   i  ivv i  ii v  -  
  L1M4_orf2#LINE/    368 CCA----------AGACCAT--------TCAATGGGGAAAGAATAGT-CT 398

  chr1_155941601_    871 GTTTAA-A---GACATTAGAATAATTGGTTATCTGTTTGTCAGTTGGTAT 916
                         v  i  - --- iiii i i i  i   v  ? iiiv  iv i--i v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA--AGAAT 446

  chr1_155941601_    917 GGGATAGGTTTAGCCTTTCCTTATGCCATATACGACAATATATTTCAGGT 966
                          iii v  --- v  i v   i ii        i v   vv i iv ii 
  L1M4_orf2#LINE/    447 GAAGTTGG---ACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_155941601_    967 GGACTTGTG--CTAAATTTTATAAACCAAACAACACTAAAAATGTTTGCA 1014
                            iiv?v --      v v -i i i   --  vv     v v  v v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAA-GAGCTAAA--ACTATAAAACTCTTAGAA 540

  chr1_155941601_   1015 AAAACTGTCGAA--AAATATACTTAATCTTAGAGTGGGAAAGACCTTCCT 1062
                         i   vii v i?--    v v v i i   i iv i  v  vivi   i 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_155941601_   1063 AAGCAAGACAC----AACACCTAGAGTCGATAAAGGAAAGGACCGATAAG 1108
                          iii v     ---- i   ---i  - i i   i    ii iv     -
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCAC---AAG-CAACAAAAGAAAAAATAGATAA- 635

  chr1_155941601_   1109 ATTT-ACTGCAT-AATTTTTAAAACTGATATAATTGCA---GAC-CCATA 1152
                            v-   v   -  vv  v      vv i iv  -  ---   - i  v
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT-CAAAGGACACTATC 684

  chr1_155941601_   1153 GACAAAATGTAAAAGTAAGTCACAGACTGGGAAGATTTTATTTGCAA--- 1199
                         i v   i  v   iii  vi      v     -  vvv         ---
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGA-GAAAATATTTGCAAATC 733

  chr1_155941601_   1200 -TATATATGCCAAAG------TATC-AAAATTGCTAACATGCAAAATAGT 1241
                         -     v  vi  i ------    - i   ----- i  iv i  ivv 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAAT-----ATATAAAGAACTCT 778

  chr1_155941601_   1242 CAGCAAATAAACATAAAAAAGACAAACAGTCCAAGAGAAAATTGGGCAAA 1291
                         i -   v v  i vv           i ii    vv?    v        
  L1M4_orf2#LINE/    779 TA-CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_155941601_   1292 GGATATGAGTATGA-ATT-CTCAGAAAAAAA-ATACAGTTGTCTAATAAA 1338
                             v   i  -  -   -   vi  i  i -     iv  v i     i
  L1M4_orf2#LINE/    828 GGATTTGAATA-GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_155941601_   1339 CATTTGAAAAGATGATCAACGGCATTTGGATT 1370
                           iv          v     iv  ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (153 / 111)
Gap_init rate = 0.06 (49 / 879), avg. gap size = 2.37 (116 / 49)  


3360 24.52 2.02 0.34  chr1_156024475_156028966.rev     3111  4003 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_156024475_   3111 TGGAAAGATATATGATGTTTATGGTTTGGAAGA-TTAATGTTGTTAAAAT 3159
                                    viv     i    v        -     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_156024475_   3160 GTTTATACTACACAAAGTGATCTACAGATGTAATGGAATCCCTATCAAAA 3209
                          viv     v v    v            vi  i v              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156024475_   3210 CTCCAA-TGTGATTTTTCACAGAAATAGAAAAA---ATTCTAAAATT-GT 3254
                         ii   i-  iv-     ii       v  v  i---  i        -i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_156024475_   3255 -TTGAACCACAGAAAACCCTGAATAACCAAACCAATTGTGCATAAAAAGG 3303
                         - v   vii  iiii    v     i     v    iv  v v  i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_156024475_   3304 ACAAAGCTGGAGGTGTCATACTACCAGACTTTAAACTACATGACAAAACT 3353
                               i      vv   i   v  vi i  i   vivi iv     i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_156024475_   3354 ATAGTAATTAAAACAACATGGTATCACCATAAAAATAGACACATAAA--A 3401
                          i      i  i   iii     iiiv     ii       i   i -- 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_156024475_   3402 A-AGAACAGAATAGATAGCCCAAAAAATGAACTCATGAAATTATGGTCAA 3450
                          -i   i     v  v  i   i   - i   i   iv v          
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGTCAA 348

  chr1_156024475_   3451 TTAATTTTCAGAAAGGGTCCCA-GAATACACAATGGGAAAAGGACAGTCT 3499
                           i      iiv      v   -  vi iv       i    i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_156024475_   3500 CTTCAATAAAGGATATTGGGAAAACTGGATATCCACATGTTAAAGAATAA 3549
                         i     i   v i ii     v         ?       iv       i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_156024475_   3550 AATTGGACCTTTATCTCATATCATGTACAAAAATTAAGTCAAAATGGATT 3599
                          i       ii  i    i i   i            v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_156024475_   3600 AAAGACTTAAATGTAAGACCTGAAACTGTAAATCTACTAGATGAAAACAT 3649
                          ?    i           v  i     i    v  vi    v        
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_156024475_   3650 AGGTTAAAAACTATATGATATATGTCTAGGCAATGATTTTTTAGATATGA 3699
                            ?vv   v  vii   iv vv vi         i   i          
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_156024475_   3700 CCCCAAAAGCTCAGGCAACAAAACCAAAAATAGACAAATGGAATTACATC 3749
                          v        v  i         vv         i    v i i v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_156024475_   3750 AAACTAAAAAGTTTCTGCACAGCAAAGAAAGCAATTAACAAAGTGAAGAA 3799
                            v v    ii  i  ii vv     i vi v  i  v        i i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_156024475_   3800 GCAACCTATGGAATGAAAGAAAATGTTTGTAAACTATGTATATGATAAGG 3849
                         i     i ii     ii       i    i   ii  i   v        
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_156024475_   3850 GGTTAAAATTTAAAATATATAAGGAACTCAAACAACTCAGTAG----AAA 3895
                          ii viv  ii i         i      vv        i  i----  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_156024475_   3896 ACAAATAACCATATT--AAAATGGGCACTGAACCTGAAATAGACATTT-T 3942
                                   vv   --          vv i ii    -         - 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA-TAGACATTTCT 847

  chr1_156024475_   3943 CAAAAGAACTCATAGAAACGGCCAACAGATACATGAAGAACTGCTCAATA 3992
                          v      vvi   v   i      i iii       i iv       i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_156024475_   3993 TTTCCAATTAT 4003
                          iv????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.70 (136 / 80)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


3097 27.34 0.55 0.44  chr1_156051678_156057315     4244  5150 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_156051678_   4244 TGGAAAAGCATTTCTTGCTCATGGATAGGAAAAATCAATATCGTGAAAAT 4293
                               iii  ii v  i        v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_156051678_   4294 GGCCATACTGCCCAAAGTAATTTATATATTCTATGCTATTCCCATCAATC 4343
                            v     v      v i  i  i v    v i  v  i  i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156051678_   4344 TATCAGTGGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 4392
                          vi   iv v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_156051678_   4393 TATGGAACCAAAAAAGAGCTTGTATAGCCAAGACAATCCTAAGCAAAAAG 4442
                                viiv  ii  v iv v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_156051678_   4443 AACAAAGCTGGCGGCATCACGCTACCTGTCTCCAAACCATACTACAAGGC 4492
                                i   v  vv    i  v  iivi i    v v        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_156051678_   4493 TACAGTAACCGAAACAGCATAGTACTGGTACCAAAACAGACACATGGACC 4542
                                 i i i    ii i       i iv ii i     i  i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_156051678_   4543 AATGGAACAGAACAGAGACCTCAGAAATAACACCACACATTTACAACCAT 4592
                                i    iv    vii         vv   i       iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_156051678_   4593 CTGATCTTCAACAAACCTGACAAAAAAAG-CAATAAGGAAGGGATTCTGT 4641
                         i    i   i    ivv  v   i vv v-    ii    i i  vv v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_156051678_   4642 ATTTAATAAATGGTGCTGGGAAAATTGGCTAGTCATATGCAGAAAATTGA 4691
                         v  i  i              v  i   v  ?i  i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_156051678_   4692 AACTGGACCCCTTCCTTACACT-TATACAAAAATTAACTCAAGATGGATT 4740
                          ii         v   i    i-                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_156051678_   4741 AAAGACTTAAATGTAAAACCCAAAACCATAAAAATCTTAGAAGAAAACGT 4790
                          ?    i         i v i     i      v              i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_156051678_   4791 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 4839
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_156051678_   4840 ACACCAAGAGCAATTGCAACAAAAGCCAGAACTGACAAATGGTACCTAAT 4889
                                i    vvv          vv i  iv  i    v v  i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_156051678_   4890 CAAA-TGAAAGAGCTTCTGCACAGCAAAAGGAACTATCATCAGAGTGAAC 4938
                             - v   i -   i  ii vv    i iv       vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_156051678_   4939 AGACAACCTACAGAAGGGAGGAAAATTTTTACAAGCTACCCATCTGACAA 4988
                                 i      v  ii      v   i   iii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_156051678_   4989 AGGTCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5038
                         i  v  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_156051678_   5039 AAACCAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5088
                          i  v  i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_156051678_   5089 TCAAAAGAAGGCATTAATATGGTCAACAAACATATGAAAAAAAGCTCATT 5138
                           v       ii  vv v    i   i  i  i       i v     vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_156051678_   5139 GCCACTCATCAT 5150
                         ii  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.00 (9 / 9)  


3236 27.12 0.66 0.55  chr1_156106000_156113323     4179  5085 (2239)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_156106000_   4179 TGGAAGAACATTCCATGCTCATAGGTTGGAAGAATCAATATCATGAAAAT 4228
                              ii i  i     i    i i        v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_156106000_   4229 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4278
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156106000_   4279 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4326
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_156106000_   4327 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4376
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_156106000_   4377 AACAACGCTGGAGGCATCACACTATCTGACTTCAAACTATACTACAAGGC 4426
                              v i      vv       vi ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_156106000_   4427 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4476
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_156106000_   4477 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACTGCATATCTACAACT 4524
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_156106000_   4525 ATCTGATCTTTGACAAACTTGACAAAAACAAGCAATGGGGAAAGGATTCC 4574
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_156106000_   4575 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4624
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_156106000_   4625 GAAACTGGACCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4674
                            ii       i v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_156106000_   4675 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCCAGAAGAAAAC 4724
                          i ?    i       v   v       i      vi ii          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_156106000_   4725 CTAGGCA-ATACCATTGAGGACATAGGCATTGGCAAAGACTTCATGTCTA 4773
                         v    ?i- v i v i v iv v i  i- v     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr1_156106000_   4774 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4823
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_156106000_   4824 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAA 4873
                           i   v v  i i   i  ii vv    i  v    i ivv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_156106000_   4874 CAGGCAGCCTACAAAATGTGAGAAAAT-TTTGCAACCTACTCATCTGACA 4922
                         v  i  i  i   i    v        -       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_156106000_   4923 AAGGGCTAATATCCAGAATCTATAATGAACTCAAACAAATTTACAGGAAA 4972
                          i  i  vi          v     v      vv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_156106000_   4973 AAAACAAACAACCCCATCAAAAAGTGGGCAAAAGACATGAACAGACACTT 5022
                           i     i     v  i?    i        i  iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_156106000_   5023 CTCAGAAGAAGACATTTATGCAGCCATAAAACACATGAAAAAATGCTCAT 5072
                            vi       i  vi viii    vv  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_156106000_   5073 CATCATTGGCCAT 5085
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  

3044 26.30 1.10 0.77  chr1_156106000_156113323     5927  6831 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_156106000_   5927 TGGCAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTAAAAAT 5976
                            v  i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_156106000_   5977 GGCCACACTTCCCAAGGTGATTTATAGATTCAGTCCTATTCCCATTAAAT 6026
                            v i   i     iv    i  i       iiv v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156106000_   6027 TACCA-TTGCAATTCTTCACA-AAATTAAAAAAA-AATACTTTAAAATCC 6073
                          v   -i   v-  i  ii  -     i v  iv-i  v  --     i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTC 147

  chr1_156106000_   6074 ATATGAAACAAAAAAAGAGCCCGTATAGCCAAGACAATCCT---AAGCAA 6120
                              i  vviv  ii  v  v v        i      i ---  iv  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_156106000_   6121 GAACAAACCTGGAGGCATCACACTACCTGACTTCAAATCATACTACAAGG 6170
                                vi      vv       v  ii i      v v        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_156106000_   6171 CTACAGTAACCAAAACAGCATGGTATTGGTACAAAAACAGACACATGGAC 6220
                                  i   i    ii     i   i i  ii i     i  i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_156106000_   6221 CAATGGAACAGATAAGAGAACTCAGAAATTAGACTACACATCTACAACCA 6270
                                 i   vvv    iii       v iv i i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_156106000_   6271 TCTGATCTTCAACAAACCTGACAAAAACAAACAATGGGGAAAGGATTCCC 6320
                         vi    i   i    ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_156106000_   6321 TGTTTAATAAATCGGT-CTGGGACAACTGGCTAGCCATATGCAGAAAACT 6369
                          v  i  i    -   -             v  ?   i     i  i v 
  L1M4_orf2#LINE/    398 TTTTCAACAAAT-GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_156106000_   6370 GAAACTGGACTCCTTCCTTACACCTTGTACAAAAATTAACTCAATATGGC 6419
                            ii     i   v   i     v i                 v    v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_156106000_   6420 TTAAAGACTTAAATGTAAATCCCAAAATTATAAAAACCCTAGAAGAAAAG 6469
                          i ?    i         ivv i    i       vi i          v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_156106000_   6470 CTAAGCA-ATACCATTCAGGACATAGGCATGGGCAATAATTTCAT-GATG 6517
                         v  i ?i- v i -   iv   v v  vv i      ii    v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr1_156106000_   6518 AAAACATCAAAAGTAATTTCAATAAAAGCAAAAATTGACAAATGGGATCT 6567
                          vi   i      i vvvv   i     v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_156106000_   6568 GATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCATCAGAGTGA 6617
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_156106000_   6618 ACAGACAACCTACAGAATGGGGGGAAGTTTTCGCAATCTATCCA-CTGAC 6666
                          v        i          i i  i v  i    vii  vi -    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_156106000_   6667 AAAGTTCTAATATTCAGAATCTACAAGGAACTTAAACAAATTTACAAGAA 6716
                           i vv  vi   i      v  i  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_156106000_   6717 AGAAACCAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACAC 6766
                          i i  -   i     v   ?    i           iv    i     i
  L1M4_orf2#LINE/    795 AAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_156106000_   6767 TTCTCAAAAGAAGACATTTATGTGGACTATAAACATATGAAAAAAAGCTC 6816
                              v        i  vi vi   v v    i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_156106000_   6817 AACATCACTGATCAT 6831
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.21 (17 / 14)  


3152 25.22 1.21 1.32  chr1_156182583_156186888     2906  3813 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_156182583_   2906 GGAAAAAGATTCCATGTTTATGGGT-GGAAGAATCAATATTGTTAAACTA 2954
                              i v  i       i    i -      v i           iv i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_156182583_   2955 TTTATAGTACCCAAAGCTG-TCTACAGATTCAATGCAATCCCTATAAAAA 3003
                         viv   v v      -i  -             i           v    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156182583_   3004 TACCAATGATATTCTCCACAGAAATAGAAAAACCAATCATAAAATTTATA 3053
                          v   iiviiv  i iii       v  v  i ii   v       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_156182583_   3054 TGGAATCACAAAAGACTCAGAATAGCCAAAGCTAGCCTAAGCAAAAAGAA 3103
                              vii   ii   i             i v v i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_156182583_   3104 CAAAACTGGAAGAATCACATTACCTGACTTCAAATTATACCACAGAGCTA 3153
                             ii    i  v     i v  ii i      viv   i   i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_156182583_   3154 CAGTAACCAAAACAGCATACTAGTGTCATAAAAACAAACACATAGACGAA 3203
                               i   i    ii iv  v  v     ii i i   i     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_156182583_   3204 TTGAACAGAATAGAGAACCCACAAACAAATCCACACACCTACAATGAACT 3253
                          v   i     v    ii   v   i   i   i   ii  iii v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_156182583_   3254 CATTTTAAACAAAGGTACCTAGAACA--CAAACTAGGGGAA-AAGACTCT 3300
                         v     vi    i   i  v   v  --   -- i   i  -  v v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTCT 398

  chr1_156182583_   3301 CTTCAATAAATGGTGCTGGGAAAACTGGGTATACATATGCACAAGGATTA 3350
                         i     i              v      i  ?v  i     v   i  v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_156182583_   3351 AACTAGACCCCTATCTCTCACCATGCACAAAAATCAAATCAAAATGGATT 3400
                          ii i        i   v      ii        i  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_156182583_   3401 AAAGACTTAAATCTAGGGCCTCAAACCATGAAACTGCTACAAGAAAACAT 3450
                          ?    i     v  i iv  v    i  i     vi  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_156182583_   3451 TGGGGAAAATCTCTAGGACATTA--TTAACCTGGGCAAAAATTTCTTGAG 3498
                         v  ? v      iiiv   v  i--   -----     vii      -  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTA-----GGCAATGGTTTCTT-AG 592

  chr1_156182583_   3499 CAATAAC-CCACAAACACAGGCAACCAAATCAAAAGTGGACAAATGGGAT 3547
                         vv  i  -   v  i    i     v   vv    i i  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_156182583_   3548 CACATCAAG-TTAAAAAGCTTCTTCATAGTAAAGTATACATTCGACAAAG 3596
                         iv      i-       -   i viiivvi    v i  vv  i v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_156182583_   3597 TGAAGAGACAACCCACAGAATGGAAGACAATATTCTCAAACGATCCACGT 3646
                             i                  i   v      iv    iv  vi iv 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_156182583_   3647 GACAAGGGATTAATAAACCAAATGTGTAAGGAGCACAAACAACTCTATA- 3695
                           i      i vi  vv vi   i i   i  i v vv       v   -
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_156182583_   3696 TGAAAACAATCTAATAATCTGATC-AAAAATAGGCAAAAGATTTGAATAG 3744
                          i    v -- v     i ii  i-      i      i           
  L1M4_orf2#LINE/    792 TAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_156182583_   3745 ACATTTCTCAAAAGAAGACATACAAATAGCATGCAGGCATATGAAAATGT 3794
                                  v        i        i  vvii i   i       vi 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_156182583_   3795 GCTCAACGTCATTGATCAT 3813
                                i   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (140 / 86)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 1.53 (23 / 15)  


3103 26.45 1.86 0.46  chr1_156197195_156203705.rev     5159  6020 (491)    L1M4_orf2#LINE/L1       35   908 (0)  

  chr1_156197195_   5159 TTCATATCATTAAAATTACCATATTGCCCAAAGTGATCTATAGATCCAAT 5208
                           v    ii    i  vi v   i v      v       i    i   i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr1_156197195_   5209 GCAATCTCCATTCAAATATCAA-TGTCATATTTCACAGAATTAGAAAAAG 5257
                               i i  iv    vi  i-  i v -   ii     v v  v  iv
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGC 133

  chr1_156197195_   5258 CAATCCAAAAATTTGTATGGAACCAAAAAAGAGCTTGAATAGCCAAAGCA 5307
                         ii    v      ii       viiv  ii  v iv           i  
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr1_156197195_   5308 ATCTTGAGCACAAACAACAAAGCTAGAGGCATCACCTGACCTGACTTCAA 5357
                                iv vi  v       i i    vv    vivv  ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_156197195_   5358 AATGTGTTACAGGGCTATCATAACCAAAATAGCATGGTATTAGTATAAAA 5407
                           iv ii    ii    ivi   i   i i  ii     i i i    ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_156197195_   5408 ACAGACACACAGGCCAGTGAAACAGAATAGAGAATTCAGAAATGCATTCA 5457
                          i     i i  ii  i  i  i     v    i i       iv ii  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_156197195_   5458 TTTATTCACAGTCAACTGATTTTAGACAAAGGCACTAAGAACATGCATTG 5507
                          vi   i ii     i       v     i  ii i    v   v  v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_156197195_   5508 GGAAAAGGATACCTTCTTCAATAAGTGGTACTGGGAAAATTGGATGTCCA 5557
                           i    i   vii i     i  i    i      v  i     i?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_156197195_   5558 TATGCAGAAGAATAAAAGTGGGCTTCTATCTCTCACCATATAAAAAAATC 5607
                         i     i      i  iv   i ii   i   v         v      i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_156197195_   5608 AACTCAAGATGGATCAAAGACTTGAATGTAAGACCCAAAACTATGAAATA 5657
                                i        ?    i i         v i        i   iv
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_156197195_   5658 ACTAGAAGAAAACGTAGGGAAAACCCTTCAGAATACTGATGCAGGCAAAG 5707
                         vi           i    ?iv  vi    ivi ivi  ivvi      v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_156197195_   5708 ATTTAT---GTATAATG--AAGATCGCAAAAGCATAGATAAAAACAAACA 5752
                         i   v ---i   i ii--  i --   v     - v v  i  v   i 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAA--GCACAAGCA-ACAAAAGAAAAAATA 630

  chr1_156197195_   5753 GATAAATTGAACTCTATTAAACTAAATAGCTTCTTCACAGCAAAGGAAAC 5802
                                  i   ii  i   v v  v i   i vii vv       v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_156197195_   5803 AATCAA--AAGTTGAGAAACAACACATTGAATGGGAGTATATATTTGCAA 5850
                         v     --    vi i i     v  iv         v v          
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_156197195_   5851 ACTATTCATCCCACAAGGGACTAATATCCAGAATATACAAGGAACTC--A 5898
                          ii  vi   iv i        vi             i  i      -- 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_156197195_   5899 C--CTCAACAGTAAAAA--TAAA-AATCCAATTAAAAAGTGGGCAAAGGA 5943
                          --     i i      --i   -  i      ?    i           
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_156197195_   5944 CAAGAATAGACATTTTTCAAAAGAAGATATACAAATGACCAACCA-TACA 5992
                         ivv            i  v                  i    iv -i   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_156197195_   5993 TGAAAAAATGCTTAATATCACTAATCAT 6020
                               i     i  i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (150 / 74)
Gap_init rate = 0.01 (12 / 874), avg. gap size = 1.67 (20 / 12)  


 269 16.33 0.00 0.00  chr1_156235317_156241587      445   493 (5778)    L1M4_orf2#LINE/L1        6    54 (854)  

  chr1_156235317_    445 AGATATTTCATGTTCTTGGATTGAAATAGTCAATATTGTTAAGATAGCA 493
                               ii       v       i  v v i              i   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.00 (0 / 0)  

3200 26.76 0.77 0.77  chr1_156235317_156241587     4871  5778 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_156235317_   4871 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGCGAAAAT 4920
                              ii i  i     i      i v      v i     i iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_156235317_   4921 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4970
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156235317_   4971 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5018
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_156235317_   5019 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCGATCCTAAGCCAAAAG 5068
                                viiv  ii  v  v v  v     iv i   i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_156235317_   5069 AACAAAGCTGGAGGCATCACACTACTTGACTTCAAACTATGCTACAAGGC 5118
                                i      vv       v iii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_156235317_   5119 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5168
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_156235317_   5169 AATGGAACAGAAC--AGAGCCCTCACAAATAACGCCGCATATCTACAACT 5216
                                i    i--    i  -- v      vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_156235317_   5217 ATCTGATCTTTGACAAACCTAAGAAAAACAAGCAATGGGGAAAGGATTCC 5266
                          vi    i  i     ivv ivv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_156235317_   5267 CTATTTAATAAGTGGTGCTGGGAGAACTGGCTAGCCATATGTAGAAAGCT 5316
                           v  i  i  i           v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_156235317_   5317 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5366
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_156235317_   5367 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTT-GAAGAAAA 5415
                          i ?    i    i  v   v       i      - i   -        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_156235317_   5416 CCTAGGCTTTACCATTCAGGACATAGGGATGGGCAAGGACTTCATGTCCA 5465
                          v    ?v v viv   iv   v v   v i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_156235317_   5466 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5515
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_156235317_   5516 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5565
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_156235317_   5566 CAGGCAACCTACAACATGGGAGAAAATTTTCGCA--TCCTACTCATCTGA 5613
                         v  i     i   iv            v  i   --  v  i--      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chr1_156235317_   5614 CAAAGGTCTAATATCCAGAATCTATAATGAACTCAAACAAATTTACAAGA 5663
                         i  i  v  vi          v     v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_156235317_   5664 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACAC 5713
                             i     i     v  i?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_156235317_   5714 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTC 5763
                              v        i  vi viii     v  ii         i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_156235317_   5764 ATTATCACTGGCCAT 5778
                          vi    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


 493 25.87 1.40 3.50  chr1_156303351_156307854.rev     2830  2972 (1532)    L1M4_orf2#LINE/L1        1   140 (768)  

  chr1_156303351_   2830 TGGAAAAA-GTCCCATGCTCATGAATCAGG-GAATTAACATTGTTAGAAT 2877
                               i -i       i     i  ii i-  v    i       ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_156303351_   2878 GACCATACTGCCCAAAGCAATGTACAGACTCAATGCAATCCCTATGAAAC 2927
                          i v     v      vii  v      i    i           v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156303351_   2928 TACCAACATCATTTTTTTTTTCACAGAATTAGGAAAAATAATCTT 2972
                          v   i ----- vii     ii     v v iv  iv i   i 
  L1M4_orf2#LINE/    101 TCCCAGC-----TGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 1.85 (24 / 13)
Gap_init rate = 0.02 (3 / 140), avg. gap size = 2.33 (7 / 3)  

2074 25.89 5.89 1.51  chr1_156303351_156307854.rev     3280  4009 (495)    L1M4_orf2#LINE/L1      130   891 (17)  

  chr1_156303351_   3280 AAAATAATCTTAAAATTCATCTG-AAATGAAAAAAGAGCCAGAGTAGCCA 3328
                           iv i   i          v  -     v  ii-  v     i      
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGG-GACCCAGAATAGCCA 178

  chr1_156303351_   3329 AAGCAATCTTAAGCAAAAAGAACAATGCTGCAGGAATCACATTACCTGAC 3378
                           i       i iv  i        v i  v    v     i v  ii i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_156303351_   3379 CTCAAATTATGCTATAAAGCTGGCCAGTAAGCAAAACAGCACGGTATTGG 3428
                         i     viv i   i      i--      v   i    iii    i   
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTA--CAGTAATCAAGACAGTGTGGTACTGG 276

  chr1_156303351_   3429 TATAAAAATGGACACATAGATCAATGAAACAGAATGAAAAAAAAACCATA 3478
                         i    ii  i    i           i  i     vi i iv---   v 
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT---CCAGA 323

  chr1_156303351_   3479 AATAAAGCCACATATCTTTAGGTAACTGACCTTTG-CAAAGTTGAGAAAA 3527
                               v   i i  i v i vi  i   ii  i -   i v  vv  i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_156303351_   3528 ACATACACTGGGGAAAGGACACTCTTTTCAATAAATGGTGCTAGAAAAAT 3577
                         v   v  v         i i v         i          i i v  i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_156303351_   3578 TATATTACTGTATGCAGAATAATAAAACTGGATC--TGTCTTTCTCCATA 3625
                          iv  v? iii     i  v   i  ii    i -- ii  iv v     
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_156303351_   3626 TACAAAA-TCAACTCAAGATGGATGAAAAAGTTAAATTTAAGACCTAAAA 3674
                                - i       i      v ? i vi     v     v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_156303351_   3675 TTATAGAGCTACTAGAAGAAAACCTATGG--AAATTATTTTAGACATAGG 3722
                         i    i i  vi           v  v ?--    iv iv -   v v  
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACCTTGG 572

  chr1_156303351_   3723 TCTAGGCAAAGAATTTATGACTGTGACA---AAAGCACAAGGAAGAAAAA 3769
                         vi       v iv  iv iiv i     ---          v  v    i
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_156303351_   3770 TAAAAATAAACAAATAAAA----ATTAAGCTAAAAAGTTTCTGCACAGCA 3815
                         v       i i    vii ----  i  iv v    ii  i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_156303351_   3816 ACAGAACA---------GAGTGAACAGACAATC--------AGGAGAAAA 3848
                          -  i   ---------i      v      i --------i        
  L1M4_orf2#LINE/    673 A-AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_156303351_   3849 TATTTATAAACTATGCATCCAACAGGGGACTGATATCCAGAAT---TAAA 3895
                              ii   ii  ii   ii i i      vi          ---    
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_156303351_   3896 CAA----TA-AA---AACAACAAAAAC-CAAATTACCACATTAAAAAGTG 3936
                         v  ----  -  ---  i  i     v-     v   vv   ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_156303351_   3937 GGCAAAAGACATGAATAGACTTCTTTTTCAAAAGAAGACATACAAATGGC 3986
                               i  iv         --v   i  v        i           
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGAC--ATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_156303351_   3987 CAACAAGATTATAAAAAAAATGC 4009
                            i   vvi  i    i -   
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGA-TGC 891

Transitions / transversions = 1.76 (118 / 67)
Gap_init rate = 0.03 (21 / 762), avg. gap size = 2.57 (54 / 21)  


2554 24.01 6.44 1.24  chr1_156349646_156351961     1017  1824 (492)    L1M4_orf2#LINE/L1       59   908 (0)  

  chr1_156349646_   1017 TTCCCAACTTGATCTGTAGATTTAAGGCAATCACAATCAAAATTTTAGC- 1065
                          i     v       ii     i  v      v v        iii   -
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr1_156349646_   1066 AAATTATTTGTGTATATTAACAAACTGGTTTTGAAGTTTATATAGAAA-G 1114
                         ivv  v    iiv v   i    i   i ii i  i  i    i    - 
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr1_156349646_   1115 AAGAAGACCCTGAATAGCCAACCCAATCCTGAAGGGGAACAAGAAAATCC 1164
                         v iii     v          vv     i    iii   v  v   i --
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT-- 206

  chr1_156349646_   1165 TAGAG---TCAACACT-----ATT-CAAGACTT--TA-------ACAA-- 1194
                          i   ---   -    -----   -   i    --  -------   i--
  L1M4_orf2#LINE/    207 TGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_156349646_   1195 ---AAAATGATGTGGTACTAGAAAAAGAACAGACAAGTGGATCAATGGAA 1241
                         ---  i iii         i v v   i i     vi i           
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_156349646_   1242 TGGAAT-AAGAGTCCAGAAATAGACCTACACA-----AATAAACCGATCT 1285
                          i    -i              i   i i   -----ii v  ii   i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_156349646_   1286 TTAACAAAGGGGCACAGGTAAGTCAATGGAGAAAGGATCATC-----AAA 1330
                          ii    i  v  vv  iiv v       i     i  vi  -----  v
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_156349646_   1331 ATATGGAGCTAAAACAACTTGCTAACTACAT----AAGACTACATGGATC 1376
                          v    v   iii      v v  ? i    ----    ----   i vi
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA----ATGAAGT 451

  chr1_156349646_   1377 TAGACACAAAACACATACCTTTCACAAAAAAATTAACT-AAAATGAGTTA 1425
                          i   v vv v v  i   v vi       --      -      ii i 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAATGGATCA 499

  chr1_156349646_   1426 AAAACCTAAATGTAAAACACAAAACCATAAAATTTATAGATGATAATAAA 1475
                         ? i            i vvi     i      i iv    v  v  i v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_156349646_   1476 GGAG-AAGTTTAGGTGACTTTGGGTTTGAGAATGACTTTTTAGATAAAAC 1524
                           ? -  i i vv     i       v iv    ii  i       vi  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_156349646_   1525 ACTAGAAGTATAATC--CAA--GAAAAAATTGATG--TTAGACTTTATTA 1568
                           i i   i i  v --   --        v   i--  i     i  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_156349646_   1569 AAATTATAAACATTTGCTCTGTAAAATACTTTGTTGAGTAAGTGAAAAGA 1618
                               v    v    iv  vi   iv  vi i ii  v           
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_156349646_   1619 CAAGCCACAGCCTGGTAGAGTATATTTACAAAACACATATCTCATAAAGG 1668
                            v      vv   v   iv      i    v  i      v    i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_156349646_   1669 ACTTCTATTAAAAATATACAAAGAACTCTTAAAATTCAACAATAAGAAAA 1718
                             v   iv i      i            v  i    i     i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_156349646_   1719 TAAACAACCCAATT-AAAAATGGGCAAAAGATCTGAATAAACACTTCACC 1767
                         i   i         -             i   i      i   i   v  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_156349646_   1768 AAAGAAG-TATTCACATGGCAAATAAGCATATAAAAAAGATACTCAACA- 1815
                                -   v  v     v        i  i    -   i       -
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAACAT 898

  chr1_156349646_   1816 -ATGTGTCTC 1824
                         - ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.65 (119 / 72)
Gap_init rate = 0.03 (25 / 850), avg. gap size = 2.48 (62 / 25)  


3071 28.11 0.55 0.44  chr1_156352065_156358467.rev     5006  5912 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_156352065_   5006 TGGAAGAACATTCCATGCTCAAGGGTAGGAAGAATCAATATCATGAAAAT 5055
                              ii i  i     i   v  i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_156352065_   5056 GGCCACACTTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5105
                            v i   i     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156352065_   5106 TACCAATGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTAAAGTTCA 5153
                          v   iivi i  i  ii    i-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_156352065_   5154 TATGGAACCGAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAACG 5203
                                vi v  ii  v  v v  vi    iv     i i ivv i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_156352065_   5204 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGGC 5253
                                i      vv   ii  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_156352065_   5254 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACACAGATATAGATC 5303
                                 i   i    ii         i iv ii i v v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_156352065_   5304 AGTGGAACAGAAT--AGAGCCCTCAGAAATAACACCACATATCTACAACT 5351
                          i     i     --    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_156352065_   5352 GTCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5401
                         ivi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_156352065_   5402 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCT 5451
                           v  i  i              v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_156352065_   5452 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5501
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_156352065_   5502 TTAAAGACTTAAATATCAGACCTAAAACCATAAAAGCCCTAGAAGAAAAC 5551
                          i ?    i     i v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_156352065_   5552 CTAGGCATTACCATTCAAGACATAGGCATGGTCAAGGACTTCATGTCCAA 5601
                         v    ?i v viv   iv   v v  vv i v   v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_156352065_   5602 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5651
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_156352065_   5652 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5701
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_156352065_   5702 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5751
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_156352065_   5752 AGGGCTAATATCCAGAATCGACAATGAACTCAAAGAAATTTACAAGAAAA 5801
                         i  i  vi          vv i  v      vv v  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_156352065_   5802 A-ACAAACAACCCCGTCAAAAAGTGGGCAAAGGACGTGAACAGACACTTC 5850
                          -     i     vi i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_156352065_   5851 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACT 5900
                           v        i  vi viii     v  i          i       vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_156352065_   5901 ATCACTGGCCAT 5912
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (150 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3231 27.42 0.44 0.44  chr1_156386126_156392516     4991  5898 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_156386126_   4991 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATTAATATCGTGAAAAT 5040
                              ii i  i     i      i v      v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_156386126_   5041 GGCCATACTGCCCAAAGTAATTTATGTATTCAATGCCATCCCCATCAAGC 5090
                            v     v      v i  i  iiv      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156386126_   5091 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_156386126_   5139 TATGGAACCAAAAAAGAGCCCGTATCGCCAAGTCAATCGTAAGCCAAAAG 5188
                                viiv  ii  v  v v  v     iv     v i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_156386126_   5189 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5238
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_156386126_   5239 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGATC 5288
                                 i   i    ii         i iv ii i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_156386126_   5289 AATGGAACAGAAT--AGAGCCCTCAGAAATAACTCCGCTTATCTACAACT 5336
                                i     --    i  --        vi  iivi  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_156386126_   5337 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGGTTCC 5386
                          vi    i  i     ivv  v   i v  vv            ii vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_156386126_   5387 CTATTTAATAAATGGTGCTGGGAAGACTGGCTAGCCATATGTGGAAAGCT 5436
                           v  i  i              vi     v  ?   i   iii  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_156386126_   5437 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 5486
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_156386126_   5487 TTAAAGACTTAGATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5536
                          i ?    i  i    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_156386126_   5537 CCAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAA 5586
                         vi   ?i v viv   iv   viv  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_156386126_   5587 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5636
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_156386126_   5637 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTCAAC 5686
                          i   v v  i i   i  ii vv    i  v    i  vv i   v  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_156386126_   5687 ACGAAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5736
                          viv    i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_156386126_   5737 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5786
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_156386126_   5787 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5836
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_156386126_   5837 TCAGAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5886
                           vi       i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_156386126_   5887 ATCACTGGCCAT 5898
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2830 25.94 0.63 5.65  chr1_156398445_156405197     5305  6260 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_156398445_   5305 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5354
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_156398445_   5355 GGCCCTACTGCCCAAAT--ATATACA--CTCAGTGCTATTCCCATCAAGC 5400
                            vv    v       --  v    --i   ii  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156398445_   5401 TACCATTGACTTCCTTCACAGAATTATAAAAAACT-ACTTTAAATTTCAT 5449
                          v   vivi i ii  ii     v - i v  i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_156398445_   5450 GTGGAATCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 5499
                         i     viiv  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_156398445_   5500 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATGCTATAAGGCT 5549
                               i      vv       v  ii i      viv i   i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_156398445_   5550 ACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5599
                                i   ii   ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_156398445_   5600 ATGGAAAAGAACAGAGGACTCAGAAATAACACCACATGTCTACAACCATC 5649
                               v    iv   iiii         vv   i ii i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_156398445_   5650 TGATCTTTGACAAACCTGACAAAAACAAACAATGGGGAAAGGATTCCCTA 5699
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_156398445_   5700 CTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACAGAA 5749
                         i i  i        i     v      v  ?   i     i  i vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_156398445_   5750 ACTGTACCCTTTCCTCATACCTTATACAAAAATTAACTTGAGATGGATTA 5799
                         ii  v    i v     i   v                ii i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_156398445_   5800 CAGACTTAAACATAAGACCTAAAACCATGAAAACCCTAGAAGAAAACCTA 5849
                         ?    i    ii     v       i  i   vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_156398445_   5850 GGCA-ATACCATTCAGGACATAGGGATGGGCAAAGACTTCATGACTAAAA 5898
                           ?i- v i -   iv   v v   v i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_156398445_   5899 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAGTGGGATCTTAAT 5948
                                    vvi          vv     v  i  i v   ii i vi
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_156398445_   5949 AAACTAAAGAGCTTCTGCACAGAAAAATAAACTATCATCAGAGTGAACAG 5998
                            v v  i i   i  ii vvv   iv v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_156398445_   5999 GCAACCTACAGAATGGGAGAAAATTTTTGCAAGTTACCCATCTGAGAAAA 6048
                         i     i                 v       i i ivi      v  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_156398445_   6049 GTCTAACATCCAGAATATACAAAGAACTTAAACGAATTTACAAGAAACTT 6098
                          v  vii            i        i--------      ----  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTC--------TTACAA----CTC 786

  chr1_156398445_   6099 AAACAAAGGAACTTAAACAAACAAGGAACTTAAACAACTTTACAAGAAAA 6148
                           -----------   --------------    ---------    ---
  L1M4_orf2#LINE/    787 AA-----------TAA--------------TAAA---------AAGA--- 799

  chr1_156398445_   6149 AATCGAACAACCGCATCAAAAATTGAGTGAAGGATATGAACAGACACTTC 6198
                         --- i  i    vv  i?    v  i ii      v    i     i   
  L1M4_orf2#LINE/    800 ---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_156398445_   6199 TCAAAAGAAGACAGTTATGCTGCCAACAAACATATAAATAAAAGCTCATC 6248
                           v        i vvi viiv     i  i  i  i  v i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_156398445_   6249 ATCACCGGTCAT 6260
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (150 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 5.00 (60 / 12)  


 483 31.97 15.00 3.82  chr1_156418650_156420397.rev      502  1261 (487)    L1M4_orf2#LINE/L1       64   908 (0)  

  chr1_156418650_    502 AAGTCAATCCATAAATTTAGAGTCATCTG-ATTAAA-TCACCAACAGGAC 549
                           i ii   i i i   i iv iv   iv-  i   -  -   i v -- 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC-CCAGCTG--C 110

  chr1_156418650_    550 TTTCTTTTGCAGTAA--AGCAAACTGTTTCTAAAATTCGTAGAGAAAAGT 597
                         i  -        v  --ii   i   v i         i  vi    v i
  L1M4_orf2#LINE/    111 CTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_156418650_    598 TAAAAAGCAAGAATGGCCAAGGAAATTTCTACTATTAAACATAAAGTT-- 645
                         v iii v v     i     iiv   i iv vv vv  iv i      --
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_156418650_    646 -------ATAC-----AAATTCAAA----------------TAGTA---- 663
                         ------- i  -----  v      ----------------i    ----
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_156418650_    664 -----GTATGATA---GCACA----TAAACA----GACCAATGTATCAGA 697
                         -----  i  i  ---   i ----  i   ----  i     v vi   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_156418650_    698 AT--AGAGTCCAGACATGGACCTAAATGCATATGGGAATTTAGGGTCTGA 745
                           --          v  ii   i v iiiv     vv v  iivv ii  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_156418650_    746 TGAAGGCATCATTTTAAAACAGT-AGTGGAAAGGAAGAATAGTC------ 788
                         ii i  iii  ---- i v  v - i   ii --          ------
  L1M4_orf2#LINE/    360 CAAGGGTGCCA----AGACCATTCAATGGGGA--AAGAATAGTCTTTTCA 403

  chr1_156418650_    789 -------------AGACATCTGGGTAGCCATCTGGAATCAAA-AAGGTTG 824
                         -------------i    v    i  ?   iv  v  vvi  -i i    
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_156418650_    825 CATCATATACACTGAACATTCTAGACCAAAATGGTTTCCAAGTGGATTAA 874
                         v i vi-   -  v -  iiv  v  v     vivi  v  i     i ?
  L1M4_orf2#LINE/    454 GACCCC-TAC-CTCA-CACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_156418650_    875 AAATGCAAATGTAAAAATCTATCTTGTTATAGA-TGATTAG--GAAGAT- 920
                          i ivi        i i-   vv--ii    i -ivv    --   i i-
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAG-CTAAA--ACTATAAAACTCTTAGAAGAAAACA 547

  chr1_156418650_    921 TAAGGG--AGTGTTTAAGAATAATTCTGG-TTAGGAGAATTATT-CTTAA 966
                           i ? -- i v  ii---- i iii   -     v-   vi  -    i
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCG----TGACCTTGGGTTAGGC-AATGGTTTCTTAG 592

  chr1_156418650_    967 ACATGCCACAAAATGCAACAGTCATGGTCATGAAAATATTGATAAATTCA 1016
                          i   v   v   v   vv  iv iii-- v     v  v        vi
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAA--AAGAAAAAATAGATAAATTGG 640

  chr1_156418650_   1017 AC--CAT----ATTAAACA---TTGT--TT--------ATTATAAAACCA 1047
                           --   ----      v ---    --  -------- i   v  i-- 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG--A 688

  chr1_156418650_   1048 AAGTCAAAAGACAA---ATGATGTAAGAAAAAGTATTTACAGGTCATGT- 1093
                             v         --- iiivi ii  i   i     i  ii    i -
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_156418650_   1094 --TAAAAAAGACTGAGTTTTGTACA----ATATGAGTGATTTTTACAGAT 1137
                         -- i v  i ---  v  v i v  ----    i ivi i i     iv 
  L1M4_orf2#LINE/    739 TCTGATAAGG---GACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_156418650_   1138 TGCTTGGAAAGAGACCAACAGCCCACTAGAAATATAGGCAAAAGGCATAA 1187
                         iiv viv   i    v  i i    v v?   v  i      i iiv i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_156418650_   1188 ATAAGTAGTTCAGAGGAAAAGACATATCAGCAGCTCATTAAACTCATTAA 1237
                            iii v   vvvii i    i   iv iii  -  v   i v   v  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGC-CAATAAGCACATGAA 884

  chr1_156418650_   1238 AAGATGGGCAACTTTCTTTATAAT 1261
                               vv    v iv????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.05 (44 / 845), avg. gap size = 3.25 (143 / 44)  


3300 26.32 0.55 0.55  chr1_156512813_156519186     4974  5881 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_156512813_   4974 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATTAATATCGTGAAAAT 5023
                              ii i  i     i      i v      v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_156512813_   5024 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5073
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156512813_   5074 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5120
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_156512813_   5121 GTATGGAATCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 5170
                         i       viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_156512813_   5171 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5220
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_156512813_   5221 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATCTAGAT 5270
                                  i   i    ii         i iv ii i   v  v     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_156512813_   5271 CAATGGAACACAAC--AGAGCCCTCAGAAATAATGCTGCGTATCTACAAC 5318
                                 i v  i--    i  --        vv iiiii  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_156512813_   5319 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGAATTC 5368
                         i vi    i  i     ivv  vv  i v  vv               vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_156512813_   5369 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5418
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_156512813_   5419 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5468
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_156512813_   5469 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5518
                           i ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_156512813_   5519 CCTAGGCATTACCATTCAGGACATAGGCATGGTCAAGGACTTCATGTCTA 5568
                          v    ?i v viv   iv   v v  vv i v   v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_156512813_   5569 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5618
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_156512813_   5619 ATTAAACTAACGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5668
                           i   v v vi i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_156512813_   5669 CAGGCAACCTATAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5718
                         v  i     i i i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_156512813_   5719 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5768
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_156512813_   5769 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5818
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_156512813_   5819 CTCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5868
                            v           vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_156512813_   5869 CATCACTGGCCAT 5881
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2537 19.67 2.98 15.93  chr1_156749079_156751666.rev     1056  2097 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_156749079_   1056 GGCAAGATATTCCATGTTCATGGATTGGAAAAGTTAATACTGTTATAATG 1105
                           v       i                   i v      i     vi   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_156749079_   1106 TCCATATTAACCCAAAACAATCTACAGATTCAAGGCAATCTCTATTAAAA 1155
                         v v   i v-      vii              v      i    i    
  L1M4_orf2#LINE/     52 GCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_156749079_   1156 TTCCAA-TGCCACTCTTCGC-GAAATAGAAAAAC-AATCCTTAAGTTCGT 1202
                          i   i-    -i i  i  -     v  v  i -i     v  i   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_156749079_   1203 AGGGAACAACAAAAGACCACAAATGGCCAAAACAATTTTGAGCAAAAATA 1252
                          v    vvi   ii    vvi   i           i    iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_156749079_   1253 ACAAAGCTGGAGGCATCACACGACCTGACTTTAAAGTATATTATAAGGAA 1302
                               i      vv      vv  ii i  i   iiv  i  i  i vv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_156749079_   1303 ATTGTAATCAAA---------TACTGGCATAAAAACAGATCCATCAACCA 1343
                          iv        i---------           ii i   ivi  vi i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_156749079_   1344 ATGGAA--------------CAGAAATAAACCAATGCATTTATAGTTGAT 1379
                               --------------            v  i       i  ii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_156749079_   1380 TGATTTTTGACAAAGGTTCCAAAAGCCTACAATGAGGAAAGGACAATCTA 1429
                                i     i   v    i v v v     i      i i i   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_156749079_   1430 TTCAATAAATGGTG-TGGGAAAACTGGTTATCCACATTCAGAAGAATGAA 1478
                              i        -     v      v  ?      v  i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_156749079_   1479 ATTAGATCTTTATCTTACACCATGCATAAAAATCAACTCAAGGGAGGGAT 1528
                         i  i  i ii  i  i       ii i      i       ---------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA--------- 490

  chr1_156749079_   1529 AGCATTAGGAGAAATAACAAATGTAAGACAAGTTGATGGGTGCAGCAAAC 1578
                         -------------------    -----------   -------------
  L1M4_orf2#LINE/    491 -------------------AATG-----------GAT------------- 497

  chr1_156749079_   1579 CAACATGGCACATGTATACCTGTGTAACAAACCTGCACATTGTACACATG 1628
                         --------------------------------------------------
  L1M4_orf2#LINE/    498 -------------------------------------------------- 497

  chr1_156749079_   1629 TACCCTAGAAGTTAAAGTATAATAAAAAAAACTCAAAACGGGAAAGACTT 1678
                         ---------------------------------  ? --------   i 
  L1M4_orf2#LINE/    498 ---------------------------------CAWA--------GACCT 506

  chr1_156749079_   1679 TAATGTAAGACTTGACACTATAAAACTACTAGAAGAAAGCATAAGGGGAA 1728
                         v         vi i v           vi         i    i ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_156749079_   1729 ACCCTCATTACATTGGTTTGGACAAGAATTTTTTGGATTTGACTCTGACA 1778
                          i i  i v  v    v  i i   vii   i  i   v    v ii v 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_156749079_   1779 CCTCAGGTAACAAAAGCAAAAATAAACAAATGGGATTGCAT-AAAACTAA 1827
                         v v  i i        v       i i    v   i v   -    i   
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_156749079_   1828 AAAGTTT-ATGCATAGCAAAACAAAAACAAAAACAAACAAAAAAACAAAA 1876
                            v   -i   v --    i----i   ---- v v   i   iii   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTT--CAAAG----GACA----CTATCAAGAAAGTGAAA 696

  chr1_156749079_   1877 ACAACAAAGTGAACAGACCCACAGAATGGGAAAAAATATTTTCAAACTAT 1926
                          -i    ----------              i         v    ii  
  L1M4_orf2#LINE/    697 A-GACAA----------CCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_156749079_   1927 ACATCTGATAAGGAGTTAAAATCCAAAATATATGAGGAATCCAAACAACT 1976
                          i           iii viv     i       i i   ii vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_156749079_   1977 CATTAGCAAGAAAACAAGTAAT--GATTAAAAAATGGGCAAATGACTAGA 2024
                           v  ii  i  i    i   i--i   ?             v  i v  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_156749079_   2025 ACAGACACTTCTCAAAAGAAGGCATACAAATGGCTAACAGGTTCATTAAA 2074
                          i     i     v       ii           i  i i iv   v   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_156749079_   2075 AAATGCTCAGGATCAGTAATCAC 2097
                          i       iv    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (131 / 70)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 9.85 (197 / 20)  


 337 25.93 1.48 8.15  chr1_157081991_157087267     3285  3419 (1858)    L1M4_orf2#LINE/L1        9   134 (774)  

  chr1_157081991_   3285 TATACCAAGTTCACAGATTAGGAAACTGAACACTGTAAGGACTGTAAAGA 3334
                            v   v     ii    i i i   v  i i   --------   -  
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGT--------TAA-GA 49

  chr1_157081991_   3335 TGACAGTTATCCCCCAACTGATGTAGAGAATTAATGCAATTCCAAACGAA 3384
                           i  i vv     v  i    v  v   v i  i     i  v v i  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_157081991_   3385 ACCACAA--ACTTTTTTTGTGTGGAATTTCACAAGTT 3419
                          i v  i--i i       ii--   v  v     i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCA--GAAATTGACAAGCT 134

Transitions / transversions = 1.50 (21 / 14)
Gap_init rate = 0.03 (4 / 126), avg. gap size = 3.25 (13 / 4)  

 985 27.64 14.62 3.47  chr1_157081991_157087267     4094  4784 (493)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_157081991_   4094 AAAACTTACGTGAGAAGGCAAAATTTACTTGAAAATACCCTAACGACTTT 4143
                             i i ii  ii  v    iiv--  ii- i    v  v  vv v i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGG--ACCC-AGAATAGCCAAAACAATCT 187

  chr1_157081991_   4144 TAAAAAATAA--ACAAAATAGGATCAAAGGA---AAAGTTGTACCAGATG 4188
                          i     v  --     i v   -----   --- v v  ---  vi  v
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGA-----GGACTCACACTT---CCCAATT 229

  chr1_157081991_   4189 TGAAGATTTATCATAAAGCTACATTATTTAAGACAGTGTGGAATTAGAGC 4238
                          v  i i   ii i         v  v i            v i i vii
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_157081991_   4239 AGAGATAGACA----GACCACAT---------TTGA------------AA 4263
                          ii        ----  i  -  ---------    ------------  
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCA-ATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_157081991_   4264 AC--ATG-ATTTATGTATAACAAA-----GACGAGACTGC--AGA--A-- 4299
                           --  i-       vvi  ivi -----   i  iv   --   -- --
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_157081991_   4300 CAATGGAGAAAGAACGGTCTTTTCAATAA-TGCTGCTGGG-CAATTGAGT 4347
                               i       ii          i  -  v       -   i  ii 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_157081991_   4348 GTCCTTATGGAAAA-AGTGGGATTGAGCTTTCTATACCTCACACCATACA 4396
                         i?  vi   v    - i  iii   ii --- iv              i 
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGAC---CCCTACCTCACACCATATA 475

  chr1_157081991_   4397 TAACTATCAATGTCAGGTAGATTATAGACCTAGATATAAAAAGCAAAGTT 4446
                         i  vv  i  iviv ii i   i ?       i  i   i ivi   ii 
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_157081991_   4447 ACAATGTTTTTACAGAAGAATACAGAAGAATGG--CTTTATGAT-TTGGG 4493
                          i  vii i   --      v   v i ?i ii--   ii   i-     
  L1M4_orf2#LINE/    526 ATAAAACTCTTA--GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_157081991_   4494 --AGTCAATAAATATTTTAAAAATAGGATGAAACCTAATATCCATAAAAG 4541
                         --  v    iiv - i   i v  iiv iv   vvi vv v v i     
  L1M4_orf2#LINE/    574 TTAGGCAATGGTT-TCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_157081991_   4542 ATAAAGATTCATAAACTCAACTACATTGAAATTAAGA----CTGTTCATT 4587
                          -   i  vv     i vi   v   ii       i ----i   v v i
  L1M4_orf2#LINE/    623 A-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_157081991_   4588 AAAGGATACCATAAAGAAAATCAGAAGACATGCTACAAAAGAGGAGATAC 4637
                               i  i  v      i v i      vv i   i  vi     - -
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA-A- 719

  chr1_157081991_   4638 TAATATTTGCAA--CATGTAGCTCTGACAAAGGACTGACATGCA------ 4679
                         -           --   i  --     i  i     vii  v  ------
  L1M4_orf2#LINE/    720 -AATATTTGCAAATCATATA--TCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_157081991_   4680 --------------------------AAAAAGAAAGATAAT---AT---A 4697
                         --------------------------       v i    i---  --- 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_157081991_   4698 AAATAGATTAAAGATTTGAACAGA-ATT-CACATAAGAGGAAATCCTACT 4745
                             i iiv  i        i   -   - v vv    i  v  v v v 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_157081991_   4746 GG---ATGGCCAGATGAAAAGGTGCTCAATCTCATTAGGAAA 4784
                           ---  iiv  v        i       iv   ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (118 / 70)
Gap_init rate = 0.05 (37 / 768), avg. gap size = 3.38 (125 / 37)  


3089 27.29 1.90 0.34  chr1_157167727_157174393.rev     5283  6176 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_157167727_   5283 TAGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5332
                          i   ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_157167727_   5333 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5382
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_157167727_   5383 TACAGATTACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5430
                          v viii i i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_157167727_   5431 TATGGAACCAAAAAAGAGCCCATATTGCCAAGGCAATCCTAAGCAAAAAG 5480
                                viiv  ii  v  viv  v     ii     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_157167727_   5481 AACGAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGGC 5530
                            i   i      vv   i   v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_157167727_   5531 TACAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGATCTAGACC 5580
                                 i   i    ii           iv ii i   v  v    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_157167727_   5581 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAGCCAT 5630
                                i    iv   ivii         vv   i    i  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_157167727_   5631 CTGATCTTTAACAAACCTGACAAAAACAAGAAATGGGGTAAGGATTCCCT 5680
                         i    i  ii    ivv  v   i v  vvv       v   i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_157167727_   5681 ATTTAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAATGCTGA 5730
                         v  i ii              v      v  ?   i   i i  viv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_157167727_   5731 AATTGGGTCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGATT 5780
                          i    ii    v   i     v              i    ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_157167727_   5781 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCCAGAAGAAAACCT 5830
                          ?    i       v   v       i      vi ii          v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_157167727_   5831 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 5879
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_157167727_   5880 ACATCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAAT 5929
                            i        vvi          vv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_157167727_   5930 TAAACTAAAGAGCTCCTGCACAGCAAAAGAAAGTACCATCAGAGTGAACA 5979
                         i   v v  i i  ii  ii vv    i  v v  i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_157167727_   5980 GG-AGT-----GAATGGGAGAAAATTTTTGCAATCTACGCATCTGACAAA 6023
                          i- ii-----              v       vii iii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_157167727_   6024 AGGCTAATATCCAGAATCTACAATAAA---TTA-AATTTA-TAAGAAAAA 6068
                         i i  vi          v  i  vi  ---   -  i i -   v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_157167727_   6069 AACAAAGAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACATTTCT 6118
                         i     v     v  i?    i            v    i          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_157167727_   6119 C---AAAAGACATTTATGCCGCCAACAGACACATGAAAAAATGCTCATCA 6165
                          --- i    i  vi viiv     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_157167727_   6166 TTACTGGTCAT 6176
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.67 (150 / 90)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


1655 25.21 7.51 1.84  chr1_157226209_157227794.rev      502  1100 (486)    L1M4_orf2#LINE/L1      276   908 (0)  

  chr1_157226209_    502 GTATAAAATTAGATACATAGACCAGTGGAAAAGAATAGAGACCCCAGAAA 551
                          i    iiv    i i     i  i     v     v    vi       
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_157226209_    552 TAAAGCCAAATGCTTACAACCAACTAACCTTTGACAAAGCAGACAAAAAC 601
                             v   v iii   iiii   i i ii  i     i vv v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_157226209_    602 ATAAATTAGGGAAAGGTCACCCTATTCAATAAATGGTGCTGGGAAAATTG 651
                           vv v i       ivi vi  v     i              v  i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_157226209_    652 GATTGCCACATGTAGAAGAATGAAACTGCATCGCTATCTCTCACCATATA 701
                            v?       i i         ii  v i v   i   v         
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_157226209_    702 CAAAAGTTATCTCAAGATGGATCAAAGAC-TAAAT--------------- 735
                              i   v     i        ?    -     ---------------
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_157226209_    736 ---------CTAGATGATAACCTAGGAAAAACTTTTCTCAACATTGACCT 776
                         ---------i    v  v   v    ?iv  v i   vii  v   ivi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_157226209_    777 AGGTAAAGAATTTATGACAAA-GACCCCAAAAGCAAATGCAACAAAA--- 822
                            i  v i-   v v v v -   v         v v         ---
  L1M4_orf2#LINE/    576 AGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_157226209_    823 ---ATAAATAAAT--GACGTCTAATTAAACTAAAAAGCTTCTG--CTTAG 865
                         ---   i      --   v  --  i   v v    i   i  --   --
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTC--ATCAAAATTAAAAACTTTTGTGCTT-- 670

  chr1_157226209_    866 CAAAAGAAATAATCATCAGAGTAAA-------CCTACATAATGGGAGAAA 908
                             i  v iv    vv i   i  -------  i   v           
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_157226209_    909 ACATTTGCAAACTATGCATCCAACAAAGGCCTAATATCTACAAGGAATCT 958
                          i         ii  ii   ii i  i  v  vi    i ----    v 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA----GAATAT 766

  chr1_157226209_    959 ACAA-GAACTTAAACAAATCAGCAAGAAAAAAACAAATAATCCCAT-AAA 1006
                          i  -     ivv    v   ii  v     i        i  v  -?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_157226209_   1007 AAGTGGGCAAATGACACGAATAGACATTTATCAAAAGAAGGCATACAAAT 1056
                           i        v  ivi            v  v       ii        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_157226209_   1057 GGCTAACAAACATGAAAAAAAAAAAGCTCAATGCTGTTAATCAT 1100
                            i  i  i  i-- vi    i v      iiiii????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCAC--ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (87 / 60)
Gap_init rate = 0.02 (14 / 633), avg. gap size = 4.00 (56 / 14)  


3192 24.12 0.55 3.84  chr1_157248017_157250375.rev      947  1858 (501)    L1M4_orf2#LINE/L1        1   882 (26)  

  chr1_157248017_    947 TGGAAAGACATCCCATGCTCATTAATCAGAAGAATTAATGTTGTTAAAAT 996
                                 i        i    vi  ii     v     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_157248017_    997 GACTATACAACCCAAAGCAATCTACAGATTCAATGTAATTCCTAACAAAA 1046
                          i v    vv      vii              i i   i    v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_157248017_   1047 TACCAATGACATTCTTCACAGAAATTAAAAAAAGAAATCTTAAAATTCAT 1096
                          v   iivi v  i  ii        i v  ivvi -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_157248017_   1097 ATGGAAGTACAAAA-ATCCTGAATAGCCAAAGCAATCCTGAAGAAGGGGG 1145
                               i i   ii- i  v           i     i    i   ----
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG---- 195

  chr1_157248017_   1146 AAAAATGCAAAGCTGTAGTCATCACACTACCAGACTTCAAAATATACCAC 1195
                           i  --     i  v  vvv       v  vi i       iv   i  
  L1M4_orf2#LINE/    196 AAGAA--CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_157248017_   1196 AAAGCTATAGAAACCAAAATAGCATGGTGCTGTCATTTAAAAAAAAAAAA 1245
                                i  v  i   i i  ii    i   v   --------------
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-------------- 279

  chr1_157248017_   1246 AAAAAAAAAAAAAGACACATGGGCTAATGGAACAGGATAAAGAACCCAGA 1295
                         ------  ii v     i  i iii       i  i  vi   ii     
  L1M4_orf2#LINE/    280 ------AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_157248017_   1296 AATTAATCTGCATATCTATAGCTAACTGATTTTTGACAAAGCCTCCAAGA 1345
                            v  i iii i  i   i ii  i       i     i viv      
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_157248017_   1346 ATACTCACTGGGGAAACTACAGTCTCTTCAATAAATGGTGTTAGAAAGAC 1395
                         vi i   v        vv i     i     i        i i i vi  
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_157248017_   1396 TGAATATACTTATGCAAAAGAATGAAATTAGACCCCCACCTCTCACCCTG 1445
                           i   ?v vi               i  i      i     v    v i
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_157248017_   1446 TACAAAAATTAACTCAAAATGAATCAAAGACCTAAATGCAAGACCTGAAA 1495
                                              i    ?           i    v  i   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_157248017_   1496 CCATAAAACTACTAGAAAAAAAAACATAGAGG-AAATACTTCTGGACATC 1544
                          i        vi     i    --     i? -    -    vv   v i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAAT-CTTCGTGACCTT 570

  chr1_157248017_   1545 AGTTTGAGAAAAAATTGTATGAATAAGACCTCCAAACCACAGGCAACAAA 1594
                         i v  ii v  vii  viv ii   v   vi v   v    i        
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_157248017_   1595 AGCAAAAATTTTGAAATGGGATTATATCAAACTGAAAAGCTTCTTCACAG 1644
                           v      vvvv    v   i vi      v v    i   i vii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_157248017_   1645 CAAAGGAAACAATCAACAGAGTGAAAAGACAATATATAGGATGGGAGAAA 1694
                                v  v     v i             ivi i  i          
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_157248017_   1695 ATATTTGTAAAGTATTCATCTGACAGGGGATTAATATCCAGAATATACAA 1744
                                i   vi  vi      i i    i vi             i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_157248017_   1745 GGTACTCAAACATCTCAACAGCAAAAATCTCAAAAACCCACAATTTGATT 1794
                         i v    vv   v     i ii     vviv  v      --   ?i --
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA--ATTWAA-- 816

  chr1_157248017_   1795 AAAATGGGCAAATGATTCAAGCAGTCCTTT-TCCAAAGAAGACATACAAA 1843
                         -           v    ii ii  v v   -           i       
  L1M4_orf2#LINE/    817 -AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_157248017_   1844 TGACCAACA--CATATG 1858
                           i    i --  i   
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATG 882

Transitions / transversions = 1.67 (135 / 81)
Gap_init rate = 0.01 (12 / 882), avg. gap size = 3.33 (40 / 12)  


3289 26.87 0.44 0.44  chr1_157258419_157264814.rev     4998  5905 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_157258419_   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5047
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_157258419_   5048 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5097
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_157258419_   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_157258419_   5146 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5195
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_157258419_   5196 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_157258419_   5246 TACAGTAACCAAAACAGCATGGTACTGGTAGCAAAACAGAGATATAAATC 5295
                                 i   i    ii         i vv ii i   v     i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_157258419_   5296 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5343
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_157258419_   5344 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5393
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_157258419_   5394 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5443
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_157258419_   5444 GAAACTGGATCACTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5493
                            ii    i v  v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_157258419_   5494 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5543
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_157258419_   5544 CTAGGCATTACCATTCACAACATAGGCATGGGCAAGGACTTCATGTATAA 5593
                         v    ?i v viv   iii  v v  vv i     v ii   v iv   v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_157258419_   5594 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5643
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_157258419_   5644 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5693
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_157258419_   5694 AGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCACCTGACAA 5743
                           i         i             v  i    vii ivi i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_157258419_   5744 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5793
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_157258419_   5794 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5843
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_157258419_   5844 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5893
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_157258419_   5894 ATCACTGGCCAT 5905
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3037 25.93 1.80 1.01  chr1_157281179_157283072.rev      513  1403 (491)    L1M4_orf2#LINE/L1       11   908 (0)  

  chr1_157281179_    513 TTCCATGCTCATGGATTGGAAGAATCAACATCGTTAAAATGGCCATACCA 562
                          i     i               v i  i  i     i     v    iv
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chr1_157281179_    563 CACAAAGCAATTTCTAGATTCAGTGCTATTCCTATCAAACTACCAA-TGT 611
                          v    vii  i vi       ii  v  i         v v   i-  i
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr1_157281179_    612 CATTCTTCACAGAATTAGAAAAACC-ATTCTAAAATTCATATGGAACCAA 660
                          -  i  ii     v v  v  i i-  i                 -- v
  L1M4_orf2#LINE/    111 C-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA--AT 157

  chr1_157281179_    661 AAAAAGAGCCCA-AATAGTCAAAGCAATTCTAAGCAAAAACAAAAAATCC 709
                         iv  i ii    -     i    i    ii i iv  i  v  v   vii
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_157281179_    710 AGAGACATCACACTATCTGACTTTGAACCATACCATAAGACTATAGTAAC 759
                         i   ivv       vi ii i  ii  v v   i i  ii   i     i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_157281179_    760 CAAAACAGCATGGTACCGTTACACAAACAGACACATAGA-CAACTGGAAG 808
                            i    ii      i vi i vii i     i     -   -     v
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA-TGGAAT 306

  chr1_157281179_    809 AGAACAAAAAACTCAGAAATAAAGCCACACCCTTACAACCATCTGATTTT 858
                             ivi i iii          v   i  vi   iiii  vi       
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_157281179_    859 TGACAAGGCCAACAAAAGCGAGCAATGGGGAAAGGACTCCCTGTTCAATA 908
                         i       viiv   i v ivv            i ivvi  v     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_157281179_    909 AATGGTGCTGG-ATAACTGGCTAGCCATATGCAGAAGATTGAAACTGGAC 957
                                    - i      v  ?   i     i    v    ii     
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_157281179_    958 CCTTACCTTTAACCATATACGAAAATTAACTCAAGATGGATCAAATATTT 1007
                           i     ivv         i             i        ? v ii 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_157281179_   1008 AAATGTAAAACCTCAAGCTATAAAAATCCTAGAAAAAAA--TAGG---AA 1052
                                 i v  v  i        v  i     i    --    ---  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_157281179_   1053 ATACCCTTCTTGACACTGGCCTTGGCAAAGAATTTTTGGCTAGGTCCCCA 1102
                           ---    v    vi   vi v     v iv  i  i v  v v v   
  L1M4_orf2#LINE/    557 AT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_157281179_   1103 AAAGCAATTGCAACAAAAACGAAAATTGACAAGTGGAACCTAAGTAAACT 1152
                               vvv         ivi     v  i  i v i  i v vi   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_157281179_   1153 ATAGAGCTTCTGCACAGCAAAAGAAACTATCATTACCGTAAACAGACATC 1202
                         vv i i   i  ii vv    i  v       vv vv  i  v     v 
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_157281179_   1203 TTACAGAATGAGAGAAAATATTTGCAAACTATGTACCCAACATAAGGTCT 1252
                         ii        i                 ii  i  i ii i - i  v  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA-AGGGACT 752

  chr1_157281179_   1253 AATATCCAGAATCTATAAGGAGCT--TA-AAC-CAATAAGCAAAAAGACG 1298
                         vi          v     i  i  --  -   -      -i        i
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAGACA 801

  chr1_157281179_   1299 AATAACCCCATTAAAAAATGGGCAAAGGACATGAACAGGCACTTCTTAAA 1348
                                 v   ?                iv    i  i  i    iv  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_157281179_   1349 TGAAGATATACAAGCACTCAGCAA--ACATGAAAAAATGCTCAGCATCAG 1396
                         v            iiivi  ii  --         i       i     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_157281179_   1397 TAATCAT 1403
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.71 (144 / 84)
Gap_init rate = 0.02 (17 / 898), avg. gap size = 1.47 (25 / 17)  


2922 26.51 1.42 1.97  chr1_157294865_157300634     4365  5277 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_157294865_   4365 TGGAAAAATATTCTGTGCTCATGGATAGGAAGAATCAACATCATGAAAAT 4414
                               i    i ii  i        v      v i  i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_157294865_   4415 GACCATACTGCCCGAAGTAATTAATAGATTCACTACTATTCCCATTAAAC 4464
                          i v     v   i  v i  iv i       vii v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_157294865_   4465 TATCATTGACATTTTTCACA-AAATTAGAAAAAACT-ATTTTAAAATTTA 4512
                          vi  vivi v     ii  -     i-- v  i  -  ii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_157294865_   4513 TATGGAACCAAAAAAGGG-CTCATA-TAGCCAAGACAATCCTAAGCAAAA 4560
                                -- viv     - i  v -       i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_157294865_   4561 GGAACAAAGCTGGAGGCATCATGCTACTGGACTTCAAACAATACTATAAG 4610
                         i        i      vv   ii  v ivi i      vvv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_157294865_   4611 GCAGCAATAACCAAAACAGCACGGTACATGGTACTGGTACAAA-ACAGAC 4659
                           vi  i   i   i    ii-------         i i  i- i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTG-------TGGTACTGGCATAAGGATAGAC 289

  chr1_157294865_   4660 ACATAGACCAATGGAACAGAATAGAGAACCCATAAATAAGACTGCACATC 4709
                          i     i        i     v    ii   v      iv iii    i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_157294865_   4710 TACCACTATCTGATCTTCAAAAAACGTGACAAAAACAAGCAATGGGGAAA 4759
                           iviii vi    i   i v  iv   v   i v  vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_157294865_   4760 GGATTCACTATTTAATAACTGGTGCTGGGAGAACTGGCTATCCATATGCA 4809
                          i  vvv  v  i  i  v           v      v  ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_157294865_   4810 GAAAATTGAAACTGGACCCCTCCCTCACACCTTATACAAAAATTAACTCA 4859
                         i  i v    ii         v         v                  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_157294865_   4860 AGATAGATTAAAGACTTAAATGTAAAACTCAAAACTATGAAAACCCTAGA 4909
                          i  i   i ?    i         i vii        i   vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_157294865_   4910 ATACAATCTAGGC---AATGCCATTCAGGACATAGGCATGGGCAAAGATT 4956
                          v v  iv    ?---   -- -   iv   v v  vv i     v i  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_157294865_   4957 TCAT---TATGAAATCACTGAAAGCAATTGCAACAAAAGCAAAAATTGAC 5003
                           v ---     ---   ii      vvv          v      v  i
  L1M4_orf2#LINE/    587 TCTTAGATATGA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_157294865_   5004 AAATGGGATCTAGTTAAACTGAAGAGCTTCTGCATAGCAGAAGAAACTAT 5053
                             v   ii vi i   v v  i i   i  iiivv  i i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_157294865_   5054 TATCAGAGCCAAGAGGCAACCTACAGAGTGGGAGAAAATTTTTGCAATCT 5103
                         i vv i  iv  i  i     i     i           v       vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_157294865_   5104 ATTCATCTGTTAAAGGTCTAATATCCAGATTCTACAAGGAACTCAAACAA 5153
                           vi     v   i  v  vi        v v  i  i      vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_157294865_   5154 ATTTACAAGAAAAAAATCAAACAACCCCATTAAAAGGCGAGCAAAGGACA 5203
                         v iv i  v     i -    i     v   ?   iii i        iv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_157294865_   5204 TTAACAGACACTTCTCAAAAGAAGACATTCATGCAGCCAACAA--ACATG 5251
                          v  i     i     v        i  v  viii     i  --     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_157294865_   5252 AAAAAAAGCTCAACATCACTGATCAT 5277
                             i v           ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.07 (31 / 15)  


2930 27.96 0.99 0.66  chr1_157306774_157313210.rev     5042  5946 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_157306774_   5042 TGGAAAACCATTCCATGCTCATAGATAGGAAGAATCAATATCATGAAAAT 5091
                               ivi  i     i    i   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_157306774_   5092 GGCCATATTGCCCAAAGTAATTTATAGGTTCAATGCTATTTCCATCAAAC 5141
                            v   i v      v i  i  i  i     i  v  ii i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_157306774_   5142 TACTATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5190
                          v i vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_157306774_   5191 ACAGAACCAAAAACGAGCCCATATAGCCAAGACAATTGTAAGCCAAAAGA 5240
                          ii   viiv  iv  v  viv        i     iv i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_157306774_   5241 ACAAAGCTGGAGGCAGCACGCTAACTGACTTCAAACTATACTACAAGGCT 5290
                               i      vvv   i  vv ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_157306774_   5291 GCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5340
                         i      i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_157306774_   5341 ATGGAGCAGAACAGAGGCCTCAGAAATAACATCACACATCTACAACCATC 5390
                              ii    iv   ivii         vvi  i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_157306774_   5391 TGATCTTTGACAAACCTAACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5440
                             i  i     ivv iv   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_157306774_   5441 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCAATTATGCAGAAAACTGA 5490
                           i  i        i     v      v  ? v i-     i  i v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCAC-ATGCAAAAGAATGA 448

  chr1_157306774_   5491 AACTGGTTCCCTTCCTTATACCTTACACAAAAATTAACTCAAGATGGATT 5540
                          ii   vi    v   i i   v  i                i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_157306774_   5541 AAAGACTTAAATGTTAGACCTAAAACCACAAAAACCCCAGAAGAAAACCT 5590
                          ?    i       v   v       i i    vi ii          v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_157306774_   5591 AGGCA-ATACCATTCAGGACAAAGGCATGGGCAAAGACTTC---AATACT 5636
                            ?i- v i -   iv   vvv  vv i     v ii   ---i   i-
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT- 596

  chr1_157306774_   5637 AAAACATCAAAATCAATGGCAACAAAAGCCAAAATTGACAAATGGGACCT 5686
                         --i   i     v  vvi          vv     v  i    v    i 
  L1M4_orf2#LINE/    597 --GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_157306774_   5687 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5736
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_157306774_   5737 ACAGGGAACCTACAGAATGGGAGAAAATTTTTGCAGTCTATCCATTTGAC 5786
                          v  iv    i                 v      ivii  vi  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_157306774_   5787 AAAAGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 5836
                           ii i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_157306774_   5837 AAAAAAAAAAACCCCAAC-AAAAAGTGGGCAAAGGATATGAA--GACACT 5883
                            i v   v v     i-?    i            v    --    i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_157306774_   5884 TCTCAAAAGAAGACATTTATGCGGCCAAGAAACATATGAAAAAA-GCTCA 5932
                             v        i  vi vii      v  i  i       i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_157306774_   5933 TCATCACTGGTCAT 5946
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2748 26.33 1.52 2.72  chr1_157340469_157346364     4485  5403 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_157340469_   4485 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4534
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_157340469_   4535 GGCCATACTGCCCAAAGTAATTTATAGATTCTAAGCTATTCACATTAGAC 4584
                            v     v      v i  i  i      v v  v  i vi  i i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_157340469_   4585 TACTATTGACATTCTTCATAGAATTAGAAAAAACT-ACTTTAAAATTCAT 4633
                          v i vivi v  i  iii    v v  v  i-  - iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_157340469_   4634 ATGGA--TGAAAAAGAGCCTGAATAGCCAAGACAGTCCTAAGCAAAAAGA 4681
                              --  v  ii  v  v          i   i  i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_157340469_   4682 ACAAAACTGGAGGCATCACACTACCCAACTTCAAACTATACTACAAGGCC 4731
                              ii      vv       v     i      viv        i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_157340469_   4732 AAGGTAACCAAAACAGCACGGCACTGGTACAAAAACAGACACATAGACCA 4781
                          vi    i   i    iii  i     i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_157340469_   4782 ATGGAACAGAATAAAGAACTCAAAAATAAGACCACACACC---AG-CAAT 4827
                               i     vi   iii  i      iv   i   ii---i -    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_157340469_   4828 TATCAGATTTTCGACAAACCTGACAAAA--A--CAATGGGAAAAGGATTC 4873
                          ----            ivv  v   i -- --       i    i  vv
  L1M4_orf2#LINE/    350 T----GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_157340469_   4874 CCTATTTAA-AAATGGTGCAGGGAGAACTGGCTAGCCACATGCAGAAAAT 4922
                         i  v  i  -         v    v      v  ?         i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_157340469_   4923 TGAAACTGGACCACTCCCTTATACCTTAAACAAAAATTAATTCAAGGTGA 4972
                             ii      v  v   i i   v  v           i    ii  i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_157340469_   4973 ATTAAAGACTTAAATGTAAAGCCCCAAAGTATAAAAACCCTATAAGAAAA 5022
                           i ?    i         iiv iv   v       vi i  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_157340469_   5023 TCTGGGCA-ATACCATTCAGGACATAGGCACGGGCACAGATTTCAT-GAT 5070
                         iv i  ?i- v i -   iv   v v  vvii    vv i    v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_157340469_   5071 GAAAATGTCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATC 5120
                         - vi iii        vvv          v      v  i    v   ii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_157340469_   5121 TGATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 5170
                          v  i   v v  i i   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_157340469_   5171 AACAAACAACCTACAGAATGGGAGAAAATTTTTCCAGTCTATCCATCTGA 5220
                           v i      i                 v   v  ivii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_157340469_   5221 CAAAGGTCTAATATCCAGAGTCCACAAGGAACTTAAACAAACGTTTAAGG 5270
                         i  i  v  vi        i vi i  i     ivv    ---i i  v-
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA---CTCAAT- 789

  chr1_157340469_   5271 AAAAAACAAACAGAAAAAAAACCACACACAGCCCCATTAAAAACTGGGCA 5320
                         ----  i   v   v   v    -----  -----   ?    v      
  L1M4_orf2#LINE/    790 ----AATAAAAAGACAAATAACC-----CA-----ATTWAAAAATGGGCA 825

  chr1_157340469_   5321 AAAACCATGAACAGACACTTCTCAAAAGAAGACATTCATGCAGCCAACAA 5370
                           iiviv    i     i     v        i  v  viii     i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_157340469_   5371 ACATGTGAAAAAAAGCTAAACATCACTGATCAT 5403
                         i  ii      i v   v       ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.29 (39 / 17)  


2702 15.03 1.20 23.65  chr1_157654087_157657564.rev     1818  2988 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_157654087_   1818 TGGAAAGACATCTCATGTTTATGGATTGAAAGGCTTAATATTGTTAAGAT 1867
                                 i   i      i        i   i                 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_157654087_   1868 GTCAATACTACCCAAAGTGATTTATAGATTCAATGCAATATCTATCAAAA 1917
                          v       v      v    i  i        i     vi         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_157654087_   1918 TCCCAATGATATTTATTTGCAGAAATAGAAAAACCCATTTTAAAATTCAT 1967
                              iiviiv   -           v  v  i iv  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_157654087_   1968 ATGGAATCTCAAGAGACTCCAAATAGCCAAAACCACCATGAAAAAGAA-- 2015
                               viv    i   i vi            v i v          --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_157654087_   2016 -CTAAGCTTGAAGACTCAGATATCCAGATTTCAAGACTTGCTACAAAGTT 2064
                         - v   i v  i      v iv   vi       i    i        i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_157654087_   2065 ACAGTACACAAAGCAGTGTGCTACTGGCATAAGATCAGACATACAAACTA 2114
                               vv   ii       v            ivi       i i ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_157654087_   2115 ATACAATAGAATAGAGAGCCCAGAAAGAAACCC-TAGCATATATGGCCAA 2163
                           iv        v     i       v      -  -   v     i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGTCAA 348

  chr1_157654087_   2164 ATGATATTTGACAAGGTTGCCAAGACCATTCAATGGGGAAAGGGCAATGT 2213
                         v    v  i       v                         iii i v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_157654087_   2214 TTTCAAACAAATGATACTGAGAAGACTGAATATCCACATGTAAAAGAATA 2263
                               -      i i   i  vi    i   ?       i        i
  L1M4_orf2#LINE/    399 TTTCAA-CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_157654087_   2264 AAAGTTGAGGCTGGGCGTGGTGGCTCATGCCTGTAATCCCAGCAGTTTGG 2313
                           -    -------------------------------------------
  L1M4_orf2#LINE/    448 AA-GTTG------------------------------------------- 453

  chr1_157654087_   2314 GAGGCCAAGGCGGGTGGATTATGAGATCAGGAGTTTGAGAGCAGCCTGAC 2363
                         -----------------------------------------------   
  L1M4_orf2#LINE/    454 -----------------------------------------------GAC 456

  chr1_157654087_   2364 CAACATGGTGAAACCCTGTCTCTACTAAAAACACAAAAATTAGCCAGGTG 2413
                          -------------   ii   --------    ----------------
  L1M4_orf2#LINE/    457 C-------------CCTACCTC--------ACAC---------------- 469

  chr1_157654087_   2414 TGGTGGCGCATGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGA 2463
                         --------   i--------------   ---------------------
  L1M4_orf2#LINE/    470 --------CATA--------------TAC--------------------- 476

  chr1_157654087_   2464 ATCACTTGAACCCAGGAGGCAGAAGTTGCAGTGAGCCGAGACTGCGCCAC 2513
                         --------------------------------------------------
  L1M4_orf2#LINE/    477 -------------------------------------------------- 476

  chr1_157654087_   2514 TGCACTCCAGCCTGGGTGACAGAGTGAGACTCCATCTCAAAAAAAAAAAA 2563
                         --------------------------------------------------
  L1M4_orf2#LINE/    477 -------------------------------------------------- 476

  chr1_157654087_   2564 AAAAAAATTAACTCCAAATAGACCCATGACTCAAATGTAAGACCTAAA-C 2612
                         --            v    i  i v?v   ii          v     - 
  L1M4_orf2#LINE/    477 --AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_157654087_   2613 TATGAAACTCTTAGATCAAAA--TAGGACAGAAGCATCACAGCACTGGAT 2660
                            i           vv    --    ?vvi  v v  iiii vi   i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_157654087_   2661 TTGGCAATAATTTCTTGACTATGACAACAAA-GCATAGGCAACAAAAGAA 2709
                          v      ii      iiv       v    -   i i            
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_157654087_   2710 AAAAATGAACAAATTGTGCTTTATGAAAGTTTAAAAATGTTGTGCACCTA 2759
                             - ii i      vi   i  v   i  v    v v      vi v 
  L1M4_orf2#LINE/    625 AAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_157654087_   2760 AACACACTATCAACAAAGTAAAAA-----CCCACAGA-TGGGAGAAAATA 2803
                          iv          v     i    -----        -            
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_157654087_   2804 TTTTCAAATCATGTATCTTATAAAGAATTAATATCCAGACTATGTAGATA 2853
                            v        i     v    i i i vi        v   i  i v 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_157654087_   2854 ACTCCCAAAATTCAACAACAAAATACCAAACAACCCAATTCAAAAATGGG 2903
                             ii v  i    i  i    viv    i         ?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_157654087_   2904 CAAAGGACTTGAATAGACCTTTTTCCAAACAAGATATACAAATGCCTAAT 2953
                                i          v   i      v              v i   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_157654087_   2954 ATGCATATGAAAAAACGCTTAGCATCCCTAATCAT 2988
                          v   i       i i   i i    v????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (104 / 68)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 16.17 (291 / 18)  


3057 26.92 1.56 0.56  chr1_158393808_158404113     5304  6202 (4104)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_158393808_   5304 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5353
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_158393808_   5354 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATGAAAC 5403
                            v     v      v i  i  i        i  v  i  i  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_158393808_   5404 TACCATTGACTTTCTTTGCAGACTTAGAAAAAACT-ACTTTAAATTTCGT 5452
                          v   vivi i  i        vv v  v  i-  - iii    v   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_158393808_   5453 GTGGAACCAAAAAGCAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAGA 5502
                         i     viiv  i v v  v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_158393808_   5503 ACAAAGCTGGAGGCATCATGCAACCTGACTTCAAACAAAACTACAAGGCT 5552
                               i      vv   ii vv  ii i      vvvv       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_158393808_   5553 ACAGTAACCAAAAT-GCATGATACTGGTACCAAAACAGATATGTAGACCA 5601
                                i   i i- ii  i      i iv ii i   i  i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_158393808_   5602 ATGGAACAGAACAGAGACCTTAGAAATAATGCCACACATCTATAACCATC 5651
                               i    iv    viii        vv   i    i   iii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_158393808_   5652 TGATCTTTGACAGACCTGACAAAAACAAACAATGGGCAAAGGATTCCCTA 5701
                             i  i    iivv  v   i v  vv       v    i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_158393808_   5702 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACAGAA 5751
                           i  i              v      v  ?   i     i  i vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_158393808_   5752 ACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCGAGATAGATTA 5801
                         ii         v   i     v                 i i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_158393808_   5802 AAGACTTAAATGTAAAAATCTAAAACCATAAAAACCCTAGAAGAAAACCT 5851
                         ?    i         i i-       i      vi i           v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAG-CTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_158393808_   5852 AGGC---AATGCCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5898
                            ?---   -- -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_158393808_   5899 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5948
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_158393808_   5949 ATCAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCACCAGAGTGAA 5998
                               v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_158393808_   5999 CAGGCAACCTACAGAATGGGAGAAAAGTTTTGCAAGCTACCCATCTGACA 6048
                         v  i     i                vv       iii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_158393808_   6049 AAGGTCTAATATCCAGAATCTACAAGGAGCTTAAACAAATTTACAAGAAA 6098
                          i  v  vi          v  i  i  i  ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_158393808_   6099 AAAACAA---------TCAAAAAGTGGGCGAAGGTTATGAACAGACACTT 6139
                           i    --------- i?    i     i    v v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_158393808_   6140 CTCAAAAGAAGACATTTATGGGGCCAACAAACATATTTTAAAAAGCTCAT 6189
                            v        i  vi viv      i  i  i  vvv  i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_158393808_   6190 CATCACTGGTCAT 6202
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  

 502 27.94 2.94 0.00  chr1_158393808_158404113     8384  8519 (1787)    L1M4_orf2#LINE/L1        1   140 (768)  

  chr1_158393808_   8384 TGAAGAGAAATGTTGTTTTCATGGATCAGAAGATTTGGTATTGTTATGGT 8433
                           i i   v  viii v         ii     i  ii        v i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_158393808_   8434 GTGAATTCTTTCCAAACTGATCTATAGAATCAAGGTAATCCTAGTCAACG 8483
                          vv   v  ii     i       i   v    v i     ivi    vi
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_158393808_   8484 TCCCAGCAGGCTT----AAAAAAATTGACATGCTGATTTT 8519
                                v v   ----iv i         v      ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 1.53 (23 / 15)
Gap_init rate = 0.01 (1 / 140), avg. gap size = 4.00 (4 / 1)  

1191 23.63 4.90 2.59  chr1_158393808_158404113     8926  9272 (1034)    L1M4_orf2#LINE/L1      304   658 (250)  

  chr1_158393808_   8926 AACAAAGTTGAGGAAGAACGTCTAGAAATAGGATCAAATATATATGATCA 8975
                           i i i     i------   i       iivi  v i  v    i   
  L1M4_orf2#LINE/    304 AATAGAATTGAGA------GTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_158393808_   8976 ATTGATTTTTGATAAAGATGCTAAGGCAATTCAATAAGGGAAGTATAATC 9025
                                  i  i  i i   i   i v       ii  i   v   i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_158393808_   9026 TTTTCAACAAATCGGTGCTGGAACAATTGG-TAGCCATATGTAAAA-ATT 9073
                                     -        i    i   -  ?   i   i    - v 
  L1M4_orf2#LINE/    398 TTTTCAACAAAT-GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_158393808_   9074 AAACCTCAACCCTTAACTCACATCATATATGAAAATTTACCTGAAATGAA 9123
                         i  vi vi    i  v      i      ii      v  iii     i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_158393808_   9124 TCATATATTTAAATGTAAGAGCTAGACCTGTA------------GAAAAT 9161
                            ? v ii               i v  i  ------------     i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_158393808_   9162 GGTAGG---AAATCTTAGTAACCTCAGCTTTGGGAGAGATTTATTAAATA 9208
                         i-    ---       v  i    ii v  v  v iv i   v   i   
  L1M4_orf2#LINE/    547 A-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_158393808_   9209 GGAAACAAAAATCATGATCTGTTAAAGAAGAAATTGATTAATTGGACTTC 9258
                         v  v  v    v  ii v viiv      i    v   v           
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_158393808_   9259 ATAAAAATGTAAAA 9272
                           v     -     
  L1M4_orf2#LINE/    646 ATCAAAAT-TAAAA 658

Transitions / transversions = 1.86 (52 / 28)
Gap_init rate = 0.02 (8 / 355), avg. gap size = 3.25 (26 / 8)  

 671 23.43 5.44 2.51  chr1_158393808_158404113     9576  9814 (492)    L1M4_orf2#LINE/L1      663   908 (0)  

  chr1_158393808_   9576 TTGTTTTTTAAAAGATAATGATAAGAAAATGACAACACAAGTCACAGACT 9625
                             vi  i   i  i v ivi      i   v  v    vi      v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_158393808_   9626 GAGAGAAAATATTTGCAGAACATCTATCTAACAAAGGACACATATCTAGA 9675
                          i               i v   v     i i  i    vii    i   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_158393808_   9676 ATTTTTTTTTAAAAAAC-CT--CAACTCAATAA------GA-AAACAACC 9715
                           v v ----   i   -  --           ------  -   i    
  L1M4_orf2#LINE/    763 ATATAT----AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_158393808_   9716 CAGTTTTTAAACACTGGCAAAAGATTTGAATTGATTCTACCCCAAAATAT 9765
                           i  ?--   v iv      i         v  ivi v i     iv v
  L1M4_orf2#LINE/    809 CAATTW--AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_158393808_   9766 ATATGCAGTTAGTAAATAAATACATGAAAAAATA---AACATCCTTATTC 9812
                             i  iv i iv     ii         i  i---      v??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_158393808_   9813 AT 9814
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.50 (33 / 22)
Gap_init rate = 0.03 (7 / 246), avg. gap size = 2.71 (19 / 7)  


1083 26.86 10.05 7.56  chr1_158798116_158800456.rev      975  1860 (481)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_158798116_    975 TGAAGAGATAAAGCCATATTCATGGACTAAAAGACTAAATATCATAAAGA 1024
                           i i     vv-    i        i ii      v     ii v    
  L1M4_orf2#LINE/      1 TGGAAAGATATC-CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_158798116_   1025 TGTCATTAATCTCAAAAATTATTCTATAAATTCAACATGATTCTGATTAA 1074
                           v  v  v  i v   -  iv    i i       iii  i iv  i  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_158798116_   1075 AAATCTCAACCCAAAAAGACAAATAAAGAAAAAAAACGAATAAATATAAA 1124
                           -  i  i ----------------------------------------
  L1M4_orf2#LINE/     99 AA-TCCCAGC---------------------------------------- 107

  chr1_158798116_   1125 TATACCTATTTTAAAGAACTTACTAAACTGATTCTAACATTTATATGAGA 1174
                         -- i   v    iv    v  ivi  i     i    v   i     ii 
  L1M4_orf2#LINE/    108 --TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_158798116_   1175 AAGCAAAGGGAGGCCCAAGAATAGCCAAGACCAT---------------- 1208
                          v    -    --    -          i  v  ----------------
  L1M4_orf2#LINE/    156 ATGCAA-GGGA--CCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_158798116_   1209 AAGGTT--AGGAATCATCCCGCTAGATCGCAAGACTAAA-ATAGAGCTAT 1255
                           i   --    v   iv iv ivi  iv   i   v v- i i     i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_158798116_   1256 AATAATTAAGATAGAG--GTTCTAA-ATGAAGGAGAGATCAACAGACCAA 1302
                          i    i    i  v --  v  ii-  -     v   ivv i   i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATCAA 300

  chr1_158798116_   1303 TAGAACTGAAT---AAACCTTGAAATGGACCTCCACACATATA----CAC 1345
                          i   iv    ---i ii iv     ii   --  i    v  ----  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCAA 348

  chr1_158798116_   1346 TTGACACATGACAG------CAACAACATGGTAAAAGTGGTGAACAGACA 1389
                             ivivi    i------   v v   -- v  --   v   vii i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCAT--TCAA--TGGGGAAAGAATA 394

  chr1_158798116_   1390 G-------AATGAA--GTGCTTCAGAACCACTGGTTATCTACATAGAGAA 1430
                          -------  ii  --     --i i  v     v  ? i    iv -  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCT--GGGACAACTGGATAKCCACATGCA-AA 441

  chr1_158798116_   1431 AAAACAAAATTAGAATCTTATTTCAAACCATGCATAAAAATAAATTCCAG 1480
                          i  ii  i  i  vi i  ii   v     ii i      v  i  v i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_158798116_   1481 ATG-----------CAAATGTGAAAGGCAAA-CTTTAAAAC-CTTAGAAG 1517
                            -----------i      i i  vi   -  v      -        
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_158798116_   1518 A---TATAGAAGAACACTATTATGATCACAGATTACAGAAAATG----TT 1560
                          ---i    i? v v iiv ii   i vii i   -- iv    ----i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA--GGCAATGGTTTCT 589

  chr1_158798116_   1561 GAAACA-GACAAAGAAAACACAAATAA--AAAGGAAAGATA--TACATT- 1604
                         v i i -    vvi   i     ii  --    i   i   --  v   -
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_158798116_   1605 --TTACATTTAAATCTTAAAGTTCCATACATCAGAAGATACCATAAAGAC 1652
                         --i v   iv    ivv   v  iii i v   i i  i  i  v    v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_158798116_   1653 AGTGAAAACAGCAGCCACATAGTGGAA-AAGACAATTGTTATACACATAA 1701
                                 v vv v     v i   i -  i i v   iv vv  i   v
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_158798116_   1702 CTGA-----GAC-------CAGCATTTAGATAGAATGCCTATAAGTTAAC 1739
                             -----   -------   v  v  v v    iv i  i  v i  i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_158798116_   1740 AAGGAAAAGACAAAAGAACTCAGCTTAAAAATGGGCAAGAGATATGAAGA 1789
                           vi          -v   i  ii ?            ii   v    v 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_158798116_   1790 GGCAAT-CGCATAAGAGGGAAAAACATAATGACCAATA--CACATAGAAA 1836
                          i  v - v vv    i - v v   -    i      --     ii   
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAG-ATATACA-AATGGCCAATAAGCACATGAAAA 886

  chr1_158798116_   1837 CTGATGGTTTAAC-TCACTAGTAAT 1860
                         --    -i i   -   ????????
  L1M4_orf2#LINE/    887 --GATG-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.05 (44 / 908), avg. gap size = 3.55 (156 / 44)  


2845 27.15 0.87 1.85  chr1_158800523_158807412.rev     4377  5293 (1597)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_158800523_   4377 TGGAAAAACATTCCATCCTCATGGATAGGTAGAATCAATATCATAAAAAT 4426
                               i i  i    vi        v  v   v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_158800523_   4427 GCCCAAAGTACATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCC 4476
                          ------ i -     v      v i  i  i        i  v  i  i
  L1M4_orf2#LINE/     51 G------GCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr1_158800523_   4477 ATTAAACTACCATTGACATTCTTCACTGAATTAGAAAAAGCT-ATTTTAA 4525
                           i   v v   vivi v  i  ii v   v v  v  -   -  ii   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAA 142

  chr1_158800523_   4526 AATTCACATGTAACTGAAAAAGAACCCAAATAGCCAAGACAATCCTAAAC 4575
                               i   v  v  v  ii  v  vi         i      i i  v
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_158800523_   4576 AACAATAACAAGACTGGAGGCATCATGCT----AACTTCAAACTATACTA 4621
                           v  v     iii      vv   ii  ----  i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_158800523_   4622 CAAGGCTCCAGTAATCAAAACAGCATGGTACTGGTACAAGAACAGACATA 4671
                            i   v          i    ii         i i   i i       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_158800523_   4672 TAGACCAATGGAACAGAATAGAGAACTCAGAAAGAAGACCACACACTTAC 4721
                             i        i     v    iii      v  iv   i   i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_158800523_   4722 AACCATCTGATCTTCAACAAACCTGACAAAAACAAACAATGGGGAAAAGA 4771
                         iii  vi    i   i    ivv  v   i v  vv           ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_158800523_   4772 TTCCCTATTTAATAAATGGTGCTGGTTGAACTGGCCAGCCATATGTAGAA 4821
                          vvi  v  i  i            vvv      vi ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_158800523_   4822 AACTGAAACTGGACCCCTTCCTTACACCATATAAAAAAATTAACTGAAGA 4871
                         i v    ii         v   i          v           v  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_158800523_   4872 TGGATTAAAGACTTAAATCTAAAACTCAAAACTACAAAAACCCTAGAAGA 4921
                              i ?    i     v   i vii       i    vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_158800523_   4922 AAATCTAGGCA-ACACCATTCAGGACATAGGCACAGGAAAAGGTTTCAT- 4969
                            iv    ?i- v i -   iv   v v  vvi   v  v      v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_158800523_   4970 GATGAAAAGGCCAAAAGCAATTGCAACAGAAGCAAAACTTGACAAATGGG 5019
                            - vi vi         vvv      i   v    v v  i    v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_158800523_   5020 ATCTAATTAAACTAAAGAGCTTCCGCAAAGTGAAAGAAACTATCATCAGA 5069
                          ii v  i   v v  i i   ii iivvvii  i  v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_158800523_   5070 GTAAAGAGAGAACCTAGAGAATGGGAGAAAATTTTTGCAATCTATTCATC 5119
                           i  i   v    i v               v       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_158800523_   5120 TGACAAAGATCTAATATCCAGAGTCTATGAGGAACTTAAACAAATTTACA 5169
                            i  i iv  vi        i v   i i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_158800523_   5170 AGAAAAAAACAAATGACCTAATTAAAAAGTGACCAAAGGACATGAACATA 5219
                          v     i      i   i    ?    i  iv       iv    i v 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_158800523_   5220 CACTTCTCAAAAGAAAACATACATGCAGCCA-TAGGCATGGGCAAGGACT 5268
                           i     v      i i     viii    -  i   iiv v  i  --
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-- 888

  chr1_158800523_   5269 TCATGTCTAAAACACCAAAAGCAAT 5293
                         ---  iii  --  i  ????????
  L1M4_orf2#LINE/    889 ---TGCTCAA--CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.08 (25 / 12)  

1045 26.01 0.00 0.00  chr1_158800523_158807412.rev     5295  5590 (1300)    L1M4_orf2#LINE/L1      613   908 (0)  

  chr1_158800523_   5295 GCAACAAAAGCCGAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTT 5344
                                   vvi    v  i    v   ii v  i   v v  i i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_158800523_   5345 CTGCACAGCAAAAGAAAATACCATCAGAGTGAACAGGCAGCCTACAGAAT 5394
                         i  ii vv    i  v v  i  vv i      v  i  i  i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_158800523_   5395 GGGAGAAAATTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGA 5444
                                   v       vii ivi      i  i  i  vi        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_158800523_   5445 ATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCAT 5494
                           v  i  v      vv    v iv i  v     i     i     v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_158800523_   5495 CAAAAAGTGGGTGAGGGATATGAACAGACACTTCTCAAAAGAAGACATTT 5544
                         i?    i    ii i    v    i     i     v        i  vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_158800523_   5545 ATGCAGCCAAAAAACGCATGAAAAAATGCTCATCATCACTGGCCAT 5590
                          viii     v  i i        i       v     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (44 / 32)
Gap_init rate = 0.00 (0 / 296), avg. gap size = 0.00 (0 / 0)  

 211 15.87 0.00 6.35  chr1_158800523_158807412.rev     6337  6399 (491)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_158800523_   6337 AAAGAAAACATACATGCAGCCAATAATCATATGAAAATAAAAAAGCTCAA 6386
                               i i     viii        v  i       ----i v      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAA----GATGCTCAA 895

  chr1_158800523_   6387 CATCACTGATCAT 6399
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 4.00 (4 / 1)  


1832 20.84 6.52 10.49  chr1_159004376_159006415.rev      447  1228 (812)    L1M4_orf2#LINE/L1      137   887 (21)  

  chr1_159004376_    447 TCCTAAAAGTGA-ATGGATG-GAAAAAGACATACGATA-CTAATACTAAT 493
                                 v v -     vi- v  ii   vi vi   - i  v  -   
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AAT 185

  chr1_159004376_    494 --TGAATAAAAAAACTTTTTTAAAAAAGAAAGAAGACTATTACTACCTGA 541
                         --    -   i  i-------  v    vvi  i    vvi   v  ii 
  L1M4_orf2#LINE/    186 CTTGAA-AAAGAAG-------AACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_159004376_    542 TTTCAAGAATTATTA---AACTATGGTAATCAAGACAGTGTGGTACTAGT 588
                               i v   i  --- i   ii                      i i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_159004376_    589 GTCAAGACAGACAATTAGACAAATAGGACAGAATAAAGAGTCCAGAAATA 638
                         i v i  i     vv    iv   i i i     vi              
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_159004376_    639 AACCT-CACAGAGACGGATAACTGATGTTTAGCAAAGGC------ACTAT 681
                             i-i   vvv i  vi  i    v  iii   i  i------  i  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_159004376_    682 --AGTGGAGAAAGAACAGTCTTTTCAACAAACAGGGCTAGAACAACTGGA 729
                         -- i   i       i               ii v   i i         
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_159004376_    730 CATCCATTTGCAGAGAGGGAGGGAGAGAGGAACAGAGAGAAGGAAGAAGA 779
                         i ?   iv    i ----------------------------------- 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAA-----------------------------------A 442

  chr1_159004376_    780 GAAGGAAGAGGAGGAGGAGAAGGAGAACTTTAATCTATTCCTCATACCAC 829
                            v    --------------------  vi i iv v     i    i
  L1M4_orf2#LINE/    443 GAATGAAG--------------------TTGGACCCCTACCTCACACCAT 472

  chr1_159004376_    830 ATA-AAAAATTGAATCAACTTGGATTATACACATAAACTTAAAACCTAAA 878
                            -       i v    vv     i ? v  v    iv   i v     
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_159004376_    879 --TTTAAACTTCATGCTTTAGAAGAAAACAGAA----AAATCTTTGTGAC 922
                         -- v    vi  -----             v i----       i     
  L1M4_orf2#LINE/    523 ACTATAAAACTC-----TTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_159004376_    923 CTTGAGTTAGGTACAGATTTCTTAGCTATGACACCAAAAGCACAATCAAT 972
                             i      i vv i        v                   v   i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_159004376_    973 AAAATTTTAAAAATTAACAAATTGGACTCCATCAGAATTTAAAACTTTTG 1022
                             vv--      vi i          i     i    v          
  L1M4_orf2#LINE/    618 AAAAGA--AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_159004376_   1023 CTCTTTAAAAGACACTATTTAAAAAAAAAAAAAAAAAAAAAAGACAAGCC 1072
                         iv   i   i        i----------  i   ivi         v  
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATC----------AAGAAAGTGAAAAGACAACCC 705

  chr1_159004376_   1073 A--GACTTGGAGAAAATGTTTGTAAACCATGTATTTGACAAAAAGTCTTA 1120
                          --  v v         i    i   i   i   i   i  ii- v   i
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG-GACTTG 754

  chr1_159004376_   1121 CATCCATAATTTATAAAGAACTCT--CAA---GATTATGAAAA--CAAA- 1162
                         i     v   v             --   ---i  v  i    --    -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_159004376_   1163 --------------ATGGGCTAAAGATTTGAACAGA---TGCTTAAAAAT 1195
                         --------------      v  i        i   --- v  iv   iv
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_159004376_   1196 ATATATACAAATGGCATGTAAGATCAAGAGAAG 1228
                          v             vvi    vv  v  i   
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAG 887

Transitions / transversions = 1.40 (94 / 67)
Gap_init rate = 0.03 (26 / 751), avg. gap size = 5.12 (133 / 26)  


 877 27.49 5.69 5.69  chr1_159129286_159132248     1374  1795 (1168)    L1M4_orf2#LINE/L1      121   542 (366)  

  chr1_159129286_   1374 GAAAATGACAAAACGATTCTAAAATTTATATAGAAATGAAAATAGTCACT 1423
                             v      ivi   i        i    i      v  i-i v v v
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG-GGACCCA 169

  chr1_159129286_   1424 GC-TAGTCAAGACACTCTTGAAGAAGAAA----------GGGGACTTA-A 1461
                          v-   i   i   v       i     i---------- i     i - 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_159129286_   1462 CTAATTCTAAAGATATTAAAATCTATTATAAAGCTACTAAAATTATGACA 1511
                           -- i i  --- v i    ii  i  i        viv   i v    
  L1M4_orf2#LINE/    220 CT--TCCCAA---TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_159129286_   1512 GTGTGGTTATAGCACAAGAAAGGCCAAATAAACCAATGGAACAAAATTAA 1561
                                vv i   i   i vi v  v   i i        i i    i 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_159129286_   1562 AGTTCCAGAAATACACACTATTATATGTACA--CACTCAGTCTGTGACAA 1609
                         iiv          v  - i  - i  v  ii--  v iii i vi     
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAAC-CCAT-ACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_159129286_   1610 AGGAGATACTACAGAGC-T---ATGGAGAAATGACAATTTTTTTGACAAA 1655
                         i  --- i i -   v - ---    i    vi i i i    ii     
  L1M4_orf2#LINE/    363 GGG---TGCCA-AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_159129286_   1656 TGGTGCTGCGTCAATTAGACATTCATTCAGTGTGGAAAAAAATGAAACTC 1705
                                 v v   i i  i ?i  --  ---  v    i      ii v
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCA--CA---TGCAAAAGAATGAAGTTG 453

  chr1_159129286_   1706 ACACCTTACTTCACACTTTACATCTCCAAA------TTCCAAGTATATTG 1749
                         ivv  i   i      ----   v v    ------i  v  i iv  ii
  L1M4_orf2#LINE/    454 GACCCCTACCTCACAC----CATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_159129286_   1750 AAGACCCTCATGTGACATGTAAATTTTTTTAAAATCTTCTAAAAGA 1795
                         ?     ivv    i v vv    vi v --    -  ii  i    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT--AAAA-CTCTTAGAAGA 542

Transitions / transversions = 1.78 (73 / 41)
Gap_init rate = 0.05 (19 / 422), avg. gap size = 2.53 (48 / 19)  

 452 26.74 7.52 3.90  chr1_159129286_159132248     2120  2478 (485)    L1M4_orf2#LINE/L1      537   908 (0)  

  chr1_159129286_   2120 AAAAAAAAAAAGAAGAGTATCTGAATTCTGTGTGATCTTGTGGTAGGGAA 2169
                          i  i    v v i ?   ----   -  vi    i    v v    v  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTA----AAT-CTTCGTGACCTTGGGTTAGGCAA 581

  chr1_159129286_   2170 AGAATTCTTAAACAGAACA--AAAAAAAAAAGAAAGGCTAACCCTAAAAG 2217
                         v iv      i i vi   --    iv v   v  -- v  ---- i  i
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAA--CAAA----AGAAA 625

  chr1_159129286_   2218 AAAT-GATGA--TGTACTAAATTAATCTTAAGAAATTCCACTTATCAAAA 2264
                             -   i --  v   vv  i  vv    i  v  iiiiviv     i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_159129286_   2265 GAC--CGTTAA-AAAGTAAAGAGACAAAGCACAGAATAGGAGAGAAGATT 2311
                            --ii i  -     i  i      vv        i     i  v   
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_159129286_   2312 TGCAACACATAAAAC--AAAAAGCTCTTATCCCCAAAATATATA--GAAT 2357
                              vv    v v -- v  i vv   i vi   i        --   i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_159129286_   2358 TGT-ACAAATCAAAAGGAAAATGACAGACAACTCAATCGAGAAATTAGCA 2406
                          v -    v    v iv    v    i i   i    i? i    vi   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_159129286_   2407 AAAAACTTGAAAAG-CATTTC---AAA---------CAA-TAACCAATAA 2442
                           ii i     v  -      ---   ---------   - ii       
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_159129286_   2443 ACATTTTTAAAGGTATTCAATCGTATTAGTAATCAG 2478
                         i  iv vv    i ii    i---  i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAAC---ATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (52 / 42)
Gap_init rate = 0.05 (17 / 372), avg. gap size = 2.41 (41 / 17)  


1356 23.38 3.94 1.13  chr1_159181659_159183674      459   813 (1203)    L1M4_orf2#LINE/L1      141   505 (403)  

  chr1_159181659_    459 AAAATTT-TATAGCAAT--AAATGCCTACATCAAAA-AACTAGAAAAACC 504
                               i-   i v   --  iv ---  -i  i  - i i i  v  i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGG---AC-CCAGAATAGCCAAAACAATC 186

  chr1_159181659_    505 T-AAAAAAAAAAAAAAAAGTCG---------TATTACCTGACTTCAAATT 544
                          -i     i  i  v     i ---------i i v  ii i      vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_159181659_    545 ATACTACAGAACTATAGTAACCCAAACAGCATGGTACTAGCATAAATATG 594
                         v       i i   i     i v i    ii       i      iv  i
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_159181659_    595 GACACATAGACCAATACAACAGAATAGAGAACCCATAAATAAATCCACAC 644
                             i     i    iv  i     v    ii   v       i   i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_159181659_    645 ATTTACAGTAAACTCATTTTTGACAAAGGTGCCAAGAACATACATTGGGG 694
                              ii  v  i v     i     i          v   v  v     
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_159181659_    695 AAAGAACAGTCTCGTCAATAAATTGTGCTGAGAAAACTGGATATCCATAT 744
                               i     iv    i    v      i  v         ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_159181659_    745 ACAAAAGAATGAAACTAGACCCCTATCTTTTGCCATATACAAAATTGAAA 794
                         i            ii i        i  ivii            v v  v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_159181659_    795 TCAAAATGGATTAAAGGCC 813
                                    i ?  i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACC 505

Transitions / transversions = 2.38 (57 / 24)
Gap_init rate = 0.02 (7 / 365), avg. gap size = 2.57 (18 / 7)  

1402 23.30 4.98 2.04  chr1_159181659_159183674     1082  1523 (493)    L1M4_orf2#LINE/L1      454   908 (0)  

  chr1_159181659_   1082 GACTCC-ATCTCA-ACAACA-ACAACAATGAA---AAA---GATTAAAGA 1122
                            i  - i    -  v i -    v   v  ---   ---   i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_159181659_   1123 CTTAAATCTAAGGCCTGAAACTATAAAACTACTAAGAGAAAATGTTGGC- 1171
                          i     v    iv  i             vi  ii      ii v  ?-
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_159181659_   1172 TAAACACTCTGGGACATTGATCTGGACAAAGATTTCTTGAGTAATACCTC 1221
                             i-  ii v   v   ivi i i   v i      iii  vv  vi 
  L1M4_orf2#LINE/    554 TAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_159181659_   1222 AAAAGCATAGGCAACTGAAGCAAAAATGGACAGAT-----------GAAG 1260
                                i i     vi   v      i  i i  -----------i  i
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_159181659_   1261 CTAAGAAGCTTTTGCACAGCAATGGAAACAATCAACACAATAAAGAGACA 1310
                         i   i  -      ii vv   v   v  v     v v i i  i     
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_159181659_   1311 ACCCACAGAATGGGAGAAAATGTTTGCAAACTACCCATCTGAAAAGGGAT 1360
                                              i        ii ivi      v      i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_159181659_   1361 TAATAACCAGAATATATAAGGAGCTCAAACAACTCATTACGAAAAAAAAA 1410
                          vi  v             i  i   vv        v  ------ v   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA------ATAAA 795

  chr1_159181659_   1411 AAAACAAATAATCCA-TTAAAAAGTAGGCAAAAGATCTGAATAGATGTTT 1459
                           i        i   -  ?    i i      i   i        ii   
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_159181659_   1460 CTCAAAAGAAGACATGTAAATGATCAACAGGTATAAAAAGAAAATGCTCA 1509
                            v        i  ii     ii   i i i i vi  -  i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGATGCTCA 894

  chr1_159181659_   1510 ACATCACTAATCAC 1523
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (67 / 33)
Gap_init rate = 0.03 (12 / 455), avg. gap size = 2.58 (31 / 12)  


2255 24.84 2.47 0.82  chr1_159211991_159214033.rev      508  1115 (928)    L1M4_orf2#LINE/L1      160   777 (131)  

  chr1_159211991_    508 AAGGACACCCTAAATAGCCAAAATAATCTTGAGAAAAAAGAACAAGGCTG 557
                             i-    vi           i        i   i        i i  
  L1M4_orf2#LINE/    160 AAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_159211991_    558 GAAGCACT-ATACTACCTGACTTCAAAAAAGTT-CTATGAAGCTACAGTA 605
                           i -   - i   v  ii i       --v  -   ii           
  L1M4_orf2#LINE/    209 GAGG-ACTCACACTTCCCAATTTCAAAA--CTTACTACAAAGCTACAGTA 255

  chr1_159211991_    606 ACCAAAACAGCATGGTATTGATATGAAAACAGACACACAGACTGATGAAA 655
                          i   i    ii     i  ii  i ii i     i i   iii   i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_159211991_    656 CAGATCAGAGAGCCCAGGGAAAAA--AAAATATTTACAACCAACTGATTT 703
                         i   viv     i    ii v   --v v i     iiii   i      
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_159211991_    704 TCAACAAAGGTGCCAAGAAAACACAATGGGGAAAGGACAGTATTTTCAAT 753
                           i    i          vv iv            i i   v       i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_159211991_    754 AAACGGTGCTGGGAAAAACTGGATATTAACACGCCAAAGAATAAAATTAA 803
                            i          v  -       ?iv   i  v       i  i  ii
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_159211991_    804 ACCCTTATCTCTGACC-TACACAAAAATCAACTCAAAATGGATTAACAAT 852
                             i  i   vv   -  i        i              i ?vi i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_159211991_    853 TTAAATGTAAGACCCAAAACTA--------CTAGAAGAAAACA--AGAGA 892
                         i           v i       --------i            --i ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_159211991_    893 AAAGCTGCACAACATTGTTCTGAGCACTGAATTTTTGAATATAACTTCAA 942
                            v  v iii  v   vvi ii   v  iv  i  ii    i  vi   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_159211991_    943 CAGCACAAGCAACAAAAACAAAAACAGACAAATGGGATTATATCAAACTA 992
                         v                iv     i   i    v   i vi      v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_159211991_    993 AAATCCTTCTGCACAGCCAAGGAAACAATGAACAGGGTGAAGAGACAACT 1042
                            vv   i  ii vv v     v  v  v  v ii     i       i
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_159211991_   1043 TACAGAATGGGAGAAAATATTTACCAACTATACATCTGCTAGGGGAGTAA 1092
                         i                     i v  ii   i     v  i    v vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_159211991_   1093 TATACAAGATATATAAGGAACTC 1115
                            v  ii        i      
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTC 777

Transitions / transversions = 2.08 (100 / 48)
Gap_init rate = 0.02 (10 / 618), avg. gap size = 2.00 (20 / 10)  

 544 21.01 1.45 0.00  chr1_159211991_159214033.rev     1416  1553 (490)    L1M4_orf2#LINE/L1      769   908 (0)  

  chr1_159211991_   1416 AAAGAGCTCAAATAACTTTATAGCAAGGAAACAAATAGCCCAATTAAAAA 1465
                              i   vv i    iv   ii  ii i       i       ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_159211991_   1466 ATGGGCAAAAGACCTGAACAAACATTTCTCAAAAGAACACATAAAAATAG 1515
                                  i  ii    i i         v      v i   v    i 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_159211991_   1516 CCAACA-GTATATGAGAA-ATGCTCAATATCGCTAATCAA 1553
                             i - i i    i  -        i   i????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.67 (22 / 6)
Gap_init rate = 0.01 (2 / 140), avg. gap size = 1.00 (2 / 2)  


2192 25.35 2.66 3.08  chr1_159380834_159382539.rev      502  1215 (491)    L1M4_orf2#LINE/L1      198   908 (0)  

  chr1_159380834_    502 GAACAAACCAGGAGGTATCATGTTACTCGACTTAACTTCAAAGTATACTG 551
                                viv     vv   i---   i-- ii  i      iiv    i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCAC---ACTT--CCCAATTTCAAAACTTACTA 242

  chr1_159380834_    552 CAGGGCTGTAGTAACCAAAACAGCATGGTGCTGATACAGAAACAGACATA 601
                           ii   ii     i   i    ii    i   ii i iii i       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_159380834_    602 TAGACCAATGTAATTGAATAGAGAGCCCAGAAATAATGCTGCATACTTAC 651
                             i     v   v    v     i          vv iii i i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_159380834_    652 AACCATCTGATCTTCAACAAAATCAACAAAACCAAGCACTAGGAAAAGGA 701
                         iii  vi    i   i    iiviiv   i    vv  v i  i    i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_159380834_    702 CTCTCCATTCAATAAATGATATTGAGATAGCTGGCTAGCCATATGCAGAA 751
                         ivv  iv     i     i ii  i  i i    v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_159380834_    752 GATTGAAACTGGACCCCTATCTTATATACCACATACGAAAATCAACTCAA 801
                           v    ii          i  i i --   i    i     i       
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACA--CCATATACAAAAATTAACTCAA 490

  chr1_159380834_    802 GATGGATTAAAGACTTAAATGTAAAACCTAAAACCATAGAAACT-TTGGA 850
                         i      i ?    i         i v       i   -     -  i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGA 539

  chr1_159380834_    851 AGATAACCTAGG---AAATACCATTCTGGACATAGGACTTGGCAAAGATT 897
                            v   v    ---    -- -   vv   v v  ii v     v i  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_159380834_    898 TCGT-GATGAAGACACCAAAAGCAATTGCAACAAAAACAGAAATTTACCA 946
                           v -   - v             vvv         iv i    vv iv 
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_159380834_    947 ATGAGAACT------AATTAAAAAGATTTTGCACAGCAAAAGATACTATT 990
                           vi  vi ------         v-     ii vv    i  i     i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATC 684

  chr1_159380834_    991 AACA--GTAAA----TAACCTACAGAATGGGAGAAAATATTTGCAAACTA 1034
                           v --  i  ----i    i                          ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_159380834_   1035 GGAGGGGAACAACAGACAAAG-ACTTAATGTCCAGAATCTATAAGGAACT 1083
                         v------- i v v  i  i -    i- i        v     i     
  L1M4_orf2#LINE/    735 T-------ATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACT 776

  chr1_159380834_   1084 TGAACAAATTTACAAGGAAAAACCAAACAACCCCATTAAAAAGTGGGCAA 1133
                         ivv    v iv i  vi    iv    i     v   ?    i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_159380834_   1134 AGAACATGAACAGACATTT-TCAAAAAAAGACGTACATGCGGCCAACAGG 1182
                           i iv    i        -  v   i    ii    vii      i i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_159380834_   1183 CATACGAAAAAAATACTTGACATCACTAATCAT 1215
                           i i     i - i  ii      ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (119 / 59)
Gap_init rate = 0.03 (19 / 711), avg. gap size = 2.16 (41 / 19)  


2781 23.12 4.84 2.66  chr1_159446040_159453356      492  1317 (6000)  C L1M4_orf2#LINE/L1   (0)   908    65  

C chr1_159446040_   1317 AATTGAA--ACGGATTCACAACTGATTGCATTTCAAAATCTCAGTGACAT 1270
                               v--  i      --  vv v v v v        i   ivi v 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCA--ACGCAATCCCTATCAAAATCCCAGCTGCCT 112

C chr1_159446040_   1269 TTGTTACAGAAATTATTTTGAAATAATTTTAAACCCTAAAATTTATATGG 1220
                           v  i        i------- i  vi --i i         i      
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTG-------ACAAGCT--GATCCTAAAATTCATATGG 153

C chr1_159446040_   1219 AACCACAAAAAGTTTCAAAATATCCAAAGCAATGTTGAAAAAGAAGAAAT 1170
                           vii   ii- vii  i    v     i    v              vv
  L1M4_orf2#LINE/    154 AAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

C chr1_159446040_   1169 CAGTCAGAAGTATCACACGTCCTAATTTCAAAATATTTTAGAAAGTTAC- 1121
                         v   ii  i vv      v   i          iv vi  v    i   -
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

C chr1_159446040_   1120 ----TTAAAACAGTATGGTACCTGA---AAAAACAGACATATAGACCAAT 1078
                         ---- i  i     i      -  i---  ii i           i    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTAC-TGGCATAAGGATAGACATATAGATCAAT 301

C chr1_159446040_   1077 AGGACAGAATAGAGAGCCTGGAAGTCA-CCCACACA-----GGTCAACTG 1034
                         i i i     v     i ii   i v -    i   -----      i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

C chr1_159446040_   1033 ATCTTCAACAAGAGTGTCAAAAATAAACAATGGGCAAAAAAAAAAATCTC 984
                           i   i     i   i   i vi vv       --i   i  v i   i
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGG--GAAAGAATAGTCTT 399

C chr1_159446040_    983 ATTAATAAATGGTGTTGGGAAAACTGGATATCCACATGCAAGATAATAAA 934
                         v i  i        i     v         ?          i v   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chr1_159446040_    933 ATTAAACTATTATCATACATTGTACCCAAAAATCAACTCAAAATGGATTA 884
                         i  ii  ivi  i vi   iii  iv       i              i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chr1_159446040_    883 AAGATTTAAACATGATATCTAAAAGTATAAAACTCCTGGAAGAAGATACA 834
                         ?   ii    ii i v v      v          i i      i i i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

C chr1_159446040_    833 TGAAAAAA--------ACATTGGTCTAAGCAATGATTTCTTGGATATGAT 792
                         v ?iv   --------  v    vi  i      i      i       i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

C chr1_159446040_    791 ACCAAACACATAAGCAACAAAAGCAAAAACAGGCGGAACTACAATTGAAC 742
                               vi  i            v     i  i------  -     i  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGA------TA-AATTGGAC 642

C chr1_159446040_    741 AACAACAA---CAAAAACTTCCGCACAGCAAAGGAAACAATGAACAAAGT 695
                         vv  v   ---i        ii ii vv       v  v  v  v     
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

C chr1_159446040_    694 GAAAAGAC---CTTTGGAATGAGAGAAAATATTTGCAAATTATATATTTG 648
                                 --- ivii     i                  i      i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

C chr1_159446040_    647 A--AGG--TTAATATCCAAGATATATAGGGAACTCATACAACTTGATAGG 602
                          --   --i vi      ii       ii      v       ii   iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

C chr1_159446040_    601 AAACAAA-AAATA---TGATTTTAAAGTGGTCAAAGAAGTTGAATAGACA 556
                            v i -     ---ii   ?v   i   v     i v           
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

C chr1_159446040_    555 TTTCTTCAAAGAAGACATACAAATGGCCAA--GTTACACGAAAAGGTGTT 508
                              i         i              --ivi   i      i  i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

C chr1_159446040_    507 CAACATCACTAATCAT 492
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (124 / 63)
Gap_init rate = 0.02 (21 / 844), avg. gap size = 2.95 (62 / 21)  

3245 26.18 0.77 0.88  chr1_159446040_159453356     5916  6824 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_159446040_   5916 TGGAAGAACATTCCATGCTCGTGGGTAGGAAGAATCAATATCGTGGAAAT 5965
                              ii i  i     i  i   i v      v i     i  vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_159446040_   5966 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCCATCAAG 6015
                            v     v     iv i  i  i        i  v     i-     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT-ATCAAA 99

  chr1_159446040_   6016 CTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 6063
                         v v   iivi i  i  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_159446040_   6064 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAA 6113
                                 viiv  ii  v  v v  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_159446040_   6114 GAACAAAGCTGGAGGCATCACACTACTTGACTTCAAACTATACTACAAGG 6163
                                 i      vv       v iii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_159446040_   6164 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 6213
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_159446040_   6214 CAATGGAACAGAAC--ACAGCCCTCAGAAATAATACCACACATCTACAAC 6261
                                 i    i-- v  i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_159446040_   6262 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 6311
                           vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_159446040_   6312 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAAGC 6361
                         i  v  i  i              v      v  ?   i i i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_159446040_   6362 TGAAATTCGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 6411
                             i  v  i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_159446040_   6412 ATCAAAGACTTAAATGTTAGACCCAAAACCATAAAAACCCTAGAAGAAAA 6461
                             ?    i       v   v i     i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_159446040_   6462 CCTAGGCA-ATACCATTAAGGACATAGGCATGGGCAAGGACTTCATGACT 6510
                          v    ?i- v i -  viv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_159446040_   6511 AAAACACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 6560
                          vi         i  vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_159446040_   6561 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 6610
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_159446040_   6611 ACAGGCAACCTACAGAATAGGAGAAAATTTTTGCAATGTACCCATCTGAC 6660
                          v  i     i       i         v       vvi ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_159446040_   6661 AAAGGGCTAATATCCAGAGTGTACAAAGAACTTAAACATTT--ATAAGAA 6708
                           i  i  vi        i i  i        ivv   vi --    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_159446040_   6709 AAAAAATCAAACAACCCCATCAAAAAATGGGCAAAGAATATGAATAGAAA 6758
                            i --    i     v  i?              i  v        v 
  L1M4_orf2#LINE/    795 AAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_159446040_   6759 TGTCTCAAAAGAAGATATTTATGCAGCCAACAGATACATGAAAAAATGCT 6808
                          v    v           vi viii     i iii         i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_159446040_   6809 CATCACCACTGGTCAT 6824
                           v  i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3120 26.53 1.66 0.89  chr1_159508673_159513327.rev     3264  4164 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_159508673_   3264 TGGAAGAACATTCCATGCTCATAGATAGGAAGAATCAATATCATGAAAAT 3313
                              ii i  i     i    i   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_159508673_   3314 GGCCATACTACCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3363
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_159508673_   3364 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 3411
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_159508673_   3412 TATGGAACCAAAAAAGGGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 3461
                                viiv  ii iv  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_159508673_   3462 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3511
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_159508673_   3512 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3561
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_159508673_   3562 AATGGAACAGAAC--ACAGCCCTCAGAAATAATGCTGCATATCTACAACC 3609
                                i    i-- v  i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_159508673_   3610 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 3659
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_159508673_   3660 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3709
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_159508673_   3710 GAAACTCGATCCCTTCCTTACACCTTATACAAAAATTAATTCGAGATGGA 3759
                            ii v  i    v   i     v              i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_159508673_   3760 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3809
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_159508673_   3810 CTAGGCAATACTATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 3859
                         v    ?ivv v v   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_159508673_   3860 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3909
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_159508673_   3910 TTAAACTAAAGAGCTTCTGCAAAGCAAGAGAAACTACCATCAGAG---GA 3956
                          i   v v  i i   i  iivvv   ii  v    i  vv i  ---i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_159508673_   3957 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 4006
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_159508673_   4007 AGGGCTAATATCCAGAATCTACAATGAACTC----AAATTTACAAGAAAA 4052
                         i  i  vi          v  i  v      ----  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_159508673_   4053 AAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTTC 4102
                          i     i     v  i? v  i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_159508673_   4103 TCAAAAGAAGACATTTATGCAAG----CAAAAGACACATGAAAAAATGCT 4148
                           v        ----   i   i----   v ii          i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_159508673_   4149 CATCATCACTGGCCAT 4164
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.56 (23 / 9)  


3110 16.47 9.33 1.75  chr1_159527329_159529006.rev      502  1187 (491)    L1M4_orf2#LINE/L1      171   908 (0)  

  chr1_159527329_    502 AATAGCCAAAGAAACCTTGAAAAAGAA---CAAAGTTGGAGATCTCATTT 548
                                   iv  i            ---           iv    ---
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA--- 217

  chr1_159527329_    549 CACATTCCCTGATTTCAAAATTTACTAGAAAGCTATTGTAATTAAAACAG 598
                         --  i i  ii         i      v       iv     i  i    
  L1M4_orf2#LINE/    218 --CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_159527329_    599 TGTGGTGTGCTA-CATAA----AGACAGATAGACCAAAAGAATAGAATAT 643
                               i--  i-     ----     v     i   vi         - 
  L1M4_orf2#LINE/    266 TGTGGTA--CTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT-T 312

  chr1_159527329_    644 AGACAGCACAGAAGTAAATCCTTGCACATTTGGTCAAACGATTT--GACA 691
                         -  v  iv     i    i  v i  iv v       vi     --    
  L1M4_orf2#LINE/    313 -GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_159527329_    692 AAGGTGCCAAGACCATTCAGTGGGAAGAAAGGACAGTCTTTTCAACAAAT 741
                          i                 i    --     i i                
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGG--GAAAGAATAGTCTTTTCAACAAAT 409

  chr1_159527329_    742 GGTGTTGAGAAAACTGGATATCCACAAGCTAAAGAAAGAAGTTG-ACCTT 790
                             i  i  v         ?     v  v      v       -   ii
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_159527329_    791 TATCTTATCCCATATGCAAAAAAGTAACTGAAATTGG-TCAAAAACCTAA 839
                           i  i iv      i      -v     v   v   -   ? i      
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_159527329_    840 ACATAAATGCT--------------------------------------- 850
                          ii   iv   ---------------------------------------
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_159527329_    851 ------------GGATTTGGCAATGATTTCTTGGATATGACACCAAAAGC 888
                         ------------  i  v       i      i                 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_159527329_    889 ACAGGCAGCAAAAGAAAAAATAGTTAAGTTGGACTCTATCAAAATTAAAA 938
                            i   i               v   i       ii             
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_159527329_    939 ACTTTTGTGCATCAAAGGACACTATTAATACAGTGAAAAGGCAACCCACC 988
                                   v              i  v v         i        v
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_159527329_    989 AACTGGTA-AAAATTTTTGCAAATCACTTACCAGATAAGGGGTTAATATC 1037
                         i v   v -     v           iv  i v        ii vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_159527329_   1038 CAGAATACATAAAGAACTACTACATCTCTACAACAAAGAAACAAGCAACC 1087
                                i          vi    v   v i  i   i i    ii    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_159527329_   1088 CATTCCAAAAATGGGCAAAAGACTTGAATAGACATTTCTCCAGAGAAGGT 1137
                           v i?             i  i                   i     i 
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_159527329_   1138 ATACAAATGACCAATCAGTACAGGAAAGGATGCTCAATGTCACTAGTCAT 1187
                                  i     v  i   v    i         ii   ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (71 / 39)
Gap_init rate = 0.02 (14 / 738), avg. gap size = 5.43 (76 / 14)  


2232 27.30 3.55 2.77  chr1_159566556_159569287     1354  2254 (478)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_159566556_   1354 TGAGGAGATATATCATGTTTATGG-CTAGAATCCTAAGTATT-TTAGACT 1401
                           iii      vi      i    -i i   vv  v i    -   iiv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_159566556_   1402 GCCAATTCTTCTAAAAATTATCTGTAGATTTAA-----TCATGATCAAAA 1446
                          v    v  i iv   v v    ii     i  -----  viv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_159566556_   1447 CCCTAGCAGACTTTTTTTTTCTGGCAAATA-----AAGGTGACTCTAAAA 1491
                         i  i   v v       ------   i v -----   v   ii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT------GCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_159566556_   1492 TTCAAGTGGTAATACAAATGACTTACAGTAGTCAAAATAATTTTGAAAAG 1541
                             vi   v   i   iv   ii v i   i     i   i       i
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_159566556_   1542 AATGAACAAATTATATAGGACTTAATATTATCTGATTTCGAGACTTATTC 1591
                         i v       v - iv      i -i i vi ii     i i     i v
  L1M4_orf2#LINE/    195 GAAGAACAAAGT-TGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTA 242

  chr1_159566556_   1592 TAATGCTATAGTCAATAAGATTGTGTAGTGTTGGTATAAAGGTGAACATG 1641
                         i  v    i   v vi    iv    i  ii   i    i i ii    i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_159566556_   1642 TAGGATCACTACCACAGAG--GAGACTTTAGAAGTAAACTCACACATTTA 1689
                            -    v ivv i   i--    v ii    i     i  i       
  L1M4_orf2#LINE/    293 TAG-ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_159566556_   1690 --GTCAGTTTATTTTAGAAAGAAACACCAATATAATTTAATGGGGGGGAA 1737
                         --    i  v     v  v iiiiii    v iv   i       ---  
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG---AA 388

  chr1_159566556_   1738 AGAATATTCTTTTTA-CAAGTAGTATTGGAACAA-TGGGTATCTATGTGG 1785
                               v      i -   i i  ii   i    -   i  ? i ii  v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_159566556_   1786 AAAAGAAATCAAATTTCAATTTTTATGTTATCCCCTACACAAAAATTATT 1835
                                --ii  v  vi iiii  iv i iv  v  i          vi
  L1M4_orf2#LINE/    439 AAAAGAA--TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_159566556_   1836 TTAAAATTGATTATATACCTTAACATGCTGGCAAAAACTACAAAACTTCT 1885
                          i     v   i ? v    v  ii ivvi  v       i      ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_159566556_   1886 AGAAGAAAA-ATAAGAAAAGAAAATTTTTGTAAACTTGAGTTTGGCAAAG 1934
                                  -   i ?--- v    i  i  i v    i   v     v 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGN---GTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_159566556_   1935 ATTTCTTATATAGCAGAAAAAAAGACCAAACTATAAAAGAAAAAATTTGA 1984
                         i       v   vv v vv     vv   i v i            v-  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GA 632

  chr1_159566556_   1985 TAAAATTGACTTAATAAAAATTAAAACCTTCTGTTCTTAAAAAAACACTA 2034
                             v v     v  v          v   i   v   v   ii      
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_159566556_   2035 CGAGGGAAAACAAAAGGCAAGC-A-AGAACCTGTTGGAATATATTGACAA 2082
                         iv i i  ivv     i   v - -    --  vvi   v     vi   
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAA--TGGGAGAAAATATTTGCAA 730

  chr1_159566556_   2083 CGCAAAAAAACCTAACCAAAAAACTC-TATCTA---TATCTAAATAACAC 2128
                         vv  v v --i  i i-  iii   i-    i ---   v    v   v 
  L1M4_orf2#LINE/    731 ATCATATA--TCTGAT-AAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_159566556_   2129 CAACAACTTAACATTAAGGACACAAATAACTCTATTTAAAAATG--CAAA 2176
                         iv      i  i v   ii v         i v   ?       --    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_159566556_   2177 AAATACTTGAATAGACA---ATCCAAAAGA-ATATACAAATGGCCAATAA 2222
                         ii  --           ---v      ii -                   
  L1M4_orf2#LINE/    828 GGAT--TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_159566556_   2223 ACAAATGAATATACATTTAAT-TTAATTAGTCA 2254
                         i  v     v v iii i  i- i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 1.97 (57 / 29)  


2362 21.58 3.65 2.58  chr1_159696570_159698177      471  1128 (480)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr1_159696570_    471 AAAGTTGAAAATAATTCCAAAA-AGCATTATATTGGCAACAGAATAAACA 519
                             i - v i    --   i -  ii vi  i     vv  i   i   
  L1M4_orf2#LINE/    244 AAAGCT-ACAGTAAT--CAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_159696570_    520 CATAGACCAGTGGAACAGACTTGAGAATCCAGAAATAGGCCCAC-CAAAT 568
                         i     i  i     i   v      i          ii    i-  vv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_159696570_    569 ATAGTCAACTGATCTTCCACAAGTGAGCAAAGGCAATTCAGCGGAAAAAG 618
                           i     i    i   v     v v  v   i v     ii  ii    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_159696570_    619 GATAATCTATCTTTTCAACAAATGGTGCTGGAACAACTGAAAATCCATAT 668
                         i   i   ----                   i       i v ?   i  
  L1M4_orf2#LINE/    391 AATAGTCT----TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_159696570_    669 TCTCCCAAAAAAGCATG----TAGACTCAAACCTTACACCATTCAAAAAA 714
                         v ------     v   ---- i   i vv    i       vi v    
  L1M4_orf2#LINE/    437 GC------AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_159696570_    715 ATTAACTCAAAATGGATCATAGACCTAAATGTAAAATGC-AAAACTATAA 763
                                            ?              i -  -          
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAA 529

  chr1_159696570_    764 CATTTCTAGAAGACAGCACAGGAGAAAATCTG-GTGACCTTAGGCTTGGT 812
                         v i ii       v i  i   ? v      v-        i  i v  i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_159696570_    813 GATAAATTTTTATGTACAACAGCAAATACATGATCCATGAAAGAAAAAAA 862
                         i  iiv  i   vi  ii   v    vi  ii v v ii          -
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA- 628

  chr1_159696570_    863 TTGATAAGCTGGACTTCATGAAAATTAAAATATTTTTG---------AGA 903
                          v     ii          v          - i     ---------i  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGA 677

  chr1_159696570_    904 CACTGTTAAGAGAATGAAAAGACAAGAAACAGACTGAGGTAAAATACTTG 953
                             i i    i i           vvv     v  i iv      i   
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_159696570_    954 CAAAACACATATCTGATAGAGGACTGGAATCCCAAATATACAGA---CTT 1000
                             v  i          ii     v v    vi      i i ---  i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_159696570_   1001 TTAAAGCTCAACAATAGAAAAGCAAACCACCCTATTAAAAAATGGGCAAA 1050
                            v i     i    i   ii    iv    v   ?             
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_159696570_   1051 AGATCTGAACAGATATTTCACCAAAAAGAATATACAGATGGAAAAT--TC 1098
                         i   i    i   i     v     i ii       i    vv   --v 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_159696570_   1099 ACATAAAAA-AT-CTTAATCATTAGACATCAT 1128
                             i    -  -  i  -   i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (90 / 48)
Gap_init rate = 0.03 (18 / 665), avg. gap size = 2.28 (41 / 18)  


1413 26.65 4.56 1.14  chr1_159713172_159715613.rev      755  1193 (1249)    L1M4_orf2#LINE/L1        4   457 (451)  

  chr1_159713172_    755 AAACACATCCCATGCTCACGGATGGGTAGA---------------ATGAC 789
                            v i        i   i    v  v   ---------------   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_159713172_    790 CATACTGCCAAAAGCAATCTAAAAATTCAATGCAATTCCCATCAGAATAC 839
                         v     v  v   vii     v i      i     i  i    i   v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_159713172_    840 CACCATCATTCTTCACAGAAATAGAAAAAAACAATTCTAAAATCTGTATG 889
                           v vv v  i  ii       v  v  -ivii  i       iii    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATG 152

  chr1_159713172_    890 GAACAAAAAAGAGTACTCAG---GGCCAAAGCAAGACTAAGCAAAAAGAA 936
                            - viv   i -  i   ---i      i   vvi i iv  i     
  L1M4_orf2#LINE/    153 GAA-ATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_159713172_    937 CAAATTTGGAGGCATCACATTACCTGACTTCAAA-CTATCTGATAAGGCC 985
                             v       vv     i v  ii i      -  vv  - i  i  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT-ACAAAGCT 249

  chr1_159713172_    986 ATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACACAGACCA 1035
                          i   v i   i    ii         i    ii    i  i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_159713172_   1036 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAAC 1085
                               i     v    ii               v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_159713172_   1086 TGATCTTTGGCAAAACAAACAAAAGCA-TAAATGGGGGAAAAGACACCCT 1134
                             i  i i   iivviv   i v  - v       i  i - i vi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCT 398

  chr1_159713172_   1135 ATTCAACAAATGGTGCTGGGATAGTTGGCAAGCCACATGTAGAAGAATGA 1184
                         v                    i ii   vv ?       i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_159713172_   1185 ATCTGGGCC 1193
                          vi   i  
  L1M4_orf2#LINE/    449 AGTTGGACC 457

Transitions / transversions = 1.90 (76 / 40)
Gap_init rate = 0.02 (9 / 454), avg. gap size = 2.78 (25 / 9)  

1432 24.20 1.49 1.70  chr1_159713172_159715613.rev     1482  1952 (490)    L1M4_orf2#LINE/L1      439   908 (0)  

  chr1_159713172_   1482 AAAAGAATGAATCTGGATACTCATCTCTCACCTTATACAAAAATCAACTC 1531
                                    vi    iv ii i   v    v           i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_159713172_   1532 AAGATGAATCAAGGACCTAAATCTAAAACCTGAAACCATAAAAATTCAAG 1581
                           i   i    ?i         v   i v  i    i      v iiv  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_159713172_   1582 AAGATGACTTCAGAAAAAAACCCTTCTAGATATTGGTTTAGGCAAAGGCT 1631
                             vi  v -  i?iv   i -   vv  iv    v        v  i 
  L1M4_orf2#LINE/    539 AAGAAAACAT-AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_159713172_   1632 TCATACCAAGAAC-CCAAAAGCAAATGCAACAAAACCAAAAATAAATAGA 1680
                           v  vvv vi  -         v v         vv       i   i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_159713172_   1681 TGGGACTTAATTAAACTAAAAAGCTTCTGCAAAGCAAAAGAAACAATCAG 1730
                          v      v  i   v v    i   i  iivvv    i  v  v    i
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_159713172_   1731 CA----GAATAGACAACTCACAGAGTGGGAAAAAGTCTTCACAATCTATA 1776
                         v ----   v       i      i     i   i v  ii   vii   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_159713172_   1777 CATCTGACAAAAGGACTAATATCCAGAATCTACAAGGAACGCCAACAAAT 1826
                         i      i  i-     vi          v  i  i    v iv    v 
  L1M4_orf2#LINE/    737 TATCTGATAAG-GGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_159713172_   1827 CAGGAAGAAAACAAACAAACAAACAATCCCATCAAAAAGCGGGCTAAGGA 1876
                           iv  v    ----- i     i  i  v  i?    ii    v     
  L1M4_orf2#LINE/    786 CAATAATAAAA-----AGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_159713172_   1877 CATGAATAGAAAATTCTCAAAGGAAGATATACAATTGGCCAAGAA--ACA 1924
                         iv        v v     v  i            v       v  --   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_159713172_   1925 TGAAAAAATACTCGACATCTAATGATCA 1952
                               i  i   i     v????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.06 (57 / 54)
Gap_init rate = 0.01 (7 / 470), avg. gap size = 2.14 (15 / 7)  


3113 25.70 1.47 1.35  chr1_159716649_159720251.rev     2225  3111 (491)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr1_159716649_   2225 ATAAATGGAAAGATATATCACTGTTGTTAAAATGTTCATACTGACCAAAG 2274
                           ii  v i    i--- i v i       i   viv     vv     v
  L1M4_orf2#LINE/     21 ATGGATTGGAAGAC---TTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr1_159716649_   2275 CAATCTACAGATTCAATGCAATCCTTATCAAAATTCCAA-TGTCATTTTT 2323
                         ii              i       i         i   i-  i -     
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTT 116

  chr1_159716649_   2324 CCCAGAAATAGGAAAAC-AATTGTAAACTCTGTATGGAATCACAAAGGAC 2372
                         iv       v iv  i -i  iv    v iii       vii   i    
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr1_159716649_   2373 CCCCAAATAGTCAAAACAATTTTGAGCAAAAAGAAGAAAGCTGGAGGCAT 2422
                           v-i     i         i    iv  i     v    i      vv 
  L1M4_orf2#LINE/    167 CCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_159716649_   2423 CACACCCCCTGATTTCAAAATATATTATAAAGCTATTGTAATGAAAACAG 2472
                              ii  ii         iv  i  i       iv     v  i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_159716649_   2473 CATAGCACTGGCAAAAAAACAGACACATTGATCAATGGAGCAAAATATAA 2522
                         ii i i       v  ii i     i  v          ii i   vv i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_159716649_   2523 AACTGAGAAATAAATACACACATCAATTTAGTCAATAAATTTGCAAGAAA 2572
                          iiiv         iv  i    iv  --i      vi    v i v  i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTAT--GGTCAATTGATTTTCGACAAG 363

  chr1_159716649_   2573 GGTGCCAAGAACATACAATGGAGACAGAACAGTGTTTTTAATCATTGGTT 2622
                                   v   v      i  v    i   v    i  iv v    v
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_159716649_   2623 TTGGTAAAACAGAATATCTTCATGAAGAAGAGTAAAATTAGATCCTTATC 2672
                         i   v v   v i   ? iv    v i    i i  i  i  i  i  i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_159716649_   2673 TCACACTATATACAAAAATTAAGTCAAAATGGATTACAGACTGAAATATA 2722
                               i               v           i ?    iv    i  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_159716649_   2723 AGACCTGAAGCTGTAAAACTACTAGAAGAAA-CATAGAAGAAAAGTTTTA 2771
                            v  i  i  i       vi         -     i? v   vi  ii
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_159716649_   2772 TGATATCAATCTGGAGAATAATTTCTTTGGTTATGACCTCAAAAGCACAG 2821
                            iv iiivi i iv   ii      v i -     vi          i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAA 612

  chr1_159716649_   2822 ACAACAAAAGCAAAAATAGACAAACGGGATTACGTCAAACTAAAAAGTTT 2871
                         i         v         i   iv   i v i     v v    ii  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_159716649_   2872 CTGCACAGTAAAGAAGACAAACAACTGAGTGAAGAAACAACCTACAGAAT 2921
                         i  ii vvi    i v  v v   vvi      i i      i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_159716649_   2922 GGGAGAAAGTGTTTGCAAATCATACTGCTGATGATGAAAAGTTAATATTC 2971
                                 i i             ivv     i v i ---i vi   i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA---CTTGTATCC 759

  chr1_159716649_   2972 AAAATATATAAGAAACTCAAACAACTAAACAACACAAAAA-AAAT---CT 3017
                          i         ii     vv      v  i  i v   i -    --- i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_159716649_   3018 GAT-----AACAAGCAAAGGACCCAAATAGACATTTCTCTAAAAAAGAC- 3061
                         i  -----  iii        iiii              i   i    i-
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_159716649_   3062 TAGCAAATGACCAACAGCTATATGAAAAAATGCTCAACATCATTAATTAT 3111
                           -      i    i ivi i       i             ????????
  L1M4_orf2#LINE/    860 TA-CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (150 / 75)
Gap_init rate = 0.02 (14 / 888), avg. gap size = 1.79 (25 / 14)  


 619 27.89 16.95 5.65  chr1_159788709_159790787.rev      779  1592 (487)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_159788709_    779 GAAGGA-ATACGATGTTCATAAACAGGAATA-TTGATATTA--AATATGT 824
                            i  -  v v        ii iv    v -  i     i--  v   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_159788709_    825 CAATTAGCTTCAAATGAATTCGTAAGTATAATTCAATTCCAGTTAAAATT 874
                             vvv ii     vi  iiii ii vi  iv    i  vi i     i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_159788709_    875 TTAGCCAAGGTATTAAGAATTGTTCATCAAAATTTCTTGGAGAATCTGCC 924
                         ii   ---------------  ii--------   i   v    vi  v 
  L1M4_orf2#LINE/    103 CCAGC---------------TGCC--------TTTTTTGCAGAAATTGAC 129

  chr1_159788709_    925 AAGCTAATTCCAAGGGTGAT--GGAAGAATAAGGACTCAAAAATAACCAA 972
                              i  i i  iiv v  --    ivii    ivi v i    i    
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr1_159788709_    973 GACACTCCTTAAAACAAAAAAAAAAAAGCTTGAGGG------------AA 1010
                         i   v  -  i   -  i  i  v    i v    i------------  
  L1M4_orf2#LINE/    180 AACAATC-TTGAAA-AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_159788709_   1011 T---------------GAGGTTA---------GGAAAG-GTGG------- 1028
                          ---------------i i i  ---------i  v  -    -------
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_159788709_   1029 ATAA--ATAAACA-AT---CCAATGGAATAGAAT----ATTCCAGATATA 1068
                             --   i   -  ---i              ---- v      v   
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_159788709_   1069 AATCCTTATTCTTATGG-CAATTTAATTTATGACA----CACCTAACACT 1113
                           i  v  ivi      -     -i    vi    ----ii  -  v  -
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATT-GATTTTCGACAAGGGTGCC-AAGAC- 374

  chr1_159788709_   1114 CACACCTAGTGTCGAGTGAATGGATTTTTCAGTAAATGTTAC-------- 1155
                         --  iii i  vv  iv    i vi      ii     v i --------
  L1M4_orf2#LINE/    375 --CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_159788709_   1156 CTGGATA----CATGCAAAAGAA--AATCTTAATCAACTACTTCA----- 1194
                                ----            --  vi vi i v-    i   -----
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC-CTACCTCACACCA 471

  chr1_159788709_   1195 TGAAAAAAAATCAATTTCCTGTGGATTAAAGGTGTTATTATATATGAAAG 1244
                          iv v      i  i ivvvi     i ?  ii----i  v  i i i  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGAC----CTAAATGTAAGAG 517

  chr1_159788709_   1245 GCATAGGTATATAATTTT--GAA-AACATATAGGAAAAAATATATATGAT 1291
                         vi v iv    v  i i --   -  v i     ?iv    v vii   i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_159788709_   1292 CTTAGCATTA-------------TAGATA----------------AACCA 1312
                            i -i   -------------      ---------------- i v 
  L1M4_orf2#LINE/    568 CTTGG-GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_159788709_   1313 TAAAAGGAAAACT-GATGTATTCGGCTACCTTAAAAT-GAAAATTTCTGT 1360
                         i     i    v -   iv   v i  v v i     -i    i  i   
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_159788709_   1361 TCATTAAAAGA---TATCATAAATATTTGGAAAAAACAAGAAACAAAAAC 1407
                         v v i   i  ---     vi  vi ---     i    vvv   i  --
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGT---GAAAAGACAACCCACAGAA-- 711

  chr1_159788709_   1408 TGGAAGAAAATGTGTGTAATATGTACAACTGACAATGAATTAGCATCTAC 1457
                            i       i v  i  vvii  i v    i  v i i v i   i v
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_159788709_   1458 GATATATAGA-AATTTTTAAAAATCATTATTTAATAAAAC--CAAATAG- 1503
                         i       i -  i i   v  v   --  --       v--      i-
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCA--AT--AATAAAAAGACAAATAAC 807

  chr1_159788709_   1504 --AA---AAAAATGGACAAAA-ACTGAAACAGCTACTTTGCAGAAGAAAA 1547
                         --  ---        i    i- i vi  i  vi i  iv vi     i 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_159788709_   1548 -ATCACAAA--GCAAGGAAACA----AAAAGATGTGCAACGTTTGTTATC 1590
                         -  -     --  v iv  i  ----        iv    i iv??????
  L1M4_orf2#LINE/    858 TAT-ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_159788709_   1591 AG 1592
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.68 (141 / 84)
Gap_init rate = 0.05 (49 / 906), avg. gap size = 3.76 (184 / 49)  


2535 20.81 3.18 4.34  chr1_159973151_159974842.rev      502  1193 (499)    L1M4_orf2#LINE/L1      182   865 (43)  

  chr1_159973151_    502 CAATTTTTATAAAGAAAAATAA--TTGG-TGATTTATACTACCAAATTCC 548
                             i  v v      i  i  --    -v  i i i   v  v    i 
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_159973151_    549 AAAACTTATCATAAAGCTGTAGTAATAAAAATAGTGTGGTACTAGCATAA 598
                                 ii i      ii      v  i i           i      
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_159973151_    599 AGATAGGTATATAGATCAATGAAAAAGAGTTGAGATCAGTGGAACAGAAG 648
                         i     ii             --------------------   i    v
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATG--------------------GAATAGAAT 311

  chr1_159973151_    649 TGAGAGCCCAGAAATAAACCCATATATCTATGGTTAGTTAATTTTCAGCA 698
                               i                 i  i      i i  i      ii  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_159973151_    699 ACAGTGCCAAGACAATTCAAAGGGGAAAGGATAACTTCTTTTTTAACAAA 748
                          vi          v      v        i   i--      i-      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAG--TCTTTTC-AACAAA 408

  chr1_159973151_    749 TGATGAAGGAATAATTAAATATAAACCACA-ACAAAAAAA---ACTTAGG 794
                           i  vv  i i  i ii   ?---     -i     i  --- v  i i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAK---CCACATGCAAAAGAATGAAGTTGGA 455

  chr1_159973151_    795 CCCCTACCTTATGTTCTATTCAAAAATTAACT-AAAATGAGTCATAGAGC 843
                                  i iiiiv   v            -      ii   ?   v 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_159973151_    844 TAAATATAAAAGTTAAATCTATAAAATTCA-AGAGTAAATCATAGGAGGA 892
                              i   i  i    v        i  v-   iv   v      ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_159973151_    893 CATCTTTGTGACTTTGGGTTAGCCAAAAAGTTCGTACATAAGATGACCAA 942
                         v     i     i         v   viiv   v  v   v  i-     
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC-ACCAA 604

  chr1_159973151_    943 A-GCAGAAGCCATACAAGAAAAAAATTAG-TGAATTTTATTTCATTAAAA 990
                          -   v    v i v         --   - i    vv i     i    
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAA--TAGATAAATTGGACTTCATCAAAA 652

  chr1_159973151_    991 TTGAGAACTTTTGTGCCTCAAAGGATACCATGAAGAAAAGGAAAAGATAA 1040
                           i i           i        i  i  v      iv       i  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_159973151_   1041 ACTTCACACTAGCAGAAGATATTTGCAAAGTACAAAACTGA-AAAGGACT 1089
                         v iv  v v i v    i           vi i v v    -  i     
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_159973151_   1090 TGTATCCAGCATACATA-----TCTTTATAACTCAATA-TAAAGAAGGTA 1133
                                  v   i   -----iii   i         -    -   ii 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGACA 801

  chr1_159973151_   1134 AACAATCTAA----AACATAGGCAAAAGGTAGGCATAGACATTTTACCAA 1179
                           i  i i  ----  v  i      i i vv v          iv    
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_159973151_   1180 AAAAGATATATGAA 1193
                          i        ii  
  L1M4_orf2#LINE/    852 AGAAGATATACAAA 865

Transitions / transversions = 1.88 (92 / 49)
Gap_init rate = 0.03 (19 / 684), avg. gap size = 2.74 (52 / 19)  


2046 26.26 1.88 4.04  chr1_159982625_159984295      486  1178 (493)    L1M4_orf2#LINE/L1      231   908 (0)  

  chr1_159982625_    486 CAAACCATATCA-AGAACTATAGTAACCAAAAGATCATGGCATTAGTATA 534
                             v v  ii - i i   i     i   i v vii   i i i i   
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_159982625_    535 AAAACAGATACATTGACTAATCGAACAGCATGGAGAACCCCCAAATAAAT 584
                          ii i   i i  v  ii   v   i  v  v    ii  vv       i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_159982625_    585 CCATGTTTGTACAGTCAACTTATTTTGGACAAAGGTATCATTAACACACA 634
                             iiv v  ii     i v     v     i   ii  vv v  iv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_159982625_    635 TTGGGAAAAGGACAGTGTCTTCAATAAATCATGCTGGGAAAGCTGGATAT 684
                         v    i    i i   v i     i    vi        v i       ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_159982625_    685 CCACACGCATAAGAATGAAACTAGACCCCTATTTCTAACCATATACAAAA 734
                              i   v         ii i        ii  vv             
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_159982625_    735 ATCAACTCTCAGAGTGAATTAAAGAATTAAA-----GACCTGAAACTATA 779
                           i     -- i i  i  i ?   vi    -----  v  i        
  L1M4_orf2#LINE/    481 ATTAACTC--AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_159982625_    780 AAACTACTAGAAGAAAACAAAAGGA-AAATGCTTTAGAATATTGTTGTAG 828
                              vi            v i ?i-    -   iivi iv   vvv   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAG 577

  chr1_159982625_    829 GCAAAGATATTATGGGTGAGACTTCAGAAGTGCACGCGCGCGCACACACA 878
                             v i v iv i i iv   vi  i   ------------------  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAG------------------CA 609

  chr1_159982625_    879 CACACACACACAAACAAAAATAGACATATAGGACTATATCACA-CTAAAA 927
                           vi  -   v  iv         i v  v     vi    v -i     
  L1M4_orf2#LINE/    610 CAAGCA-ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_159982625_    928 AGCTCTGTACAGCAAAGAAAGCCATCTATGGCATGAAGAGACAACTTGTA 977
                          vi i   i vv     i vi i   v viivi    i       iiii 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_159982625_    978 GAATGGGAGAAAATATTTGCAAACTATTCATTTGACAAGCGACTATCAAT 1027
                                                ii  vi  i   i   v    - --i 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT-T--GT 755

  chr1_159982625_   1028 ATCCAGAATATACGAACAACTC----AACTCAACAGCAAACAAACAAATA 1073
                                     ii  v     ----       i ii   v i       
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_159982625_   1074 AAAATCTGATTTTAAAATAGA-AAAAGATTTGAATAAACATTTCTCAAAG 1122
                          ---i ii   ?v     i i-   i          i         v  i
  L1M4_orf2#LINE/    806 A---CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_159982625_   1123 GAAGACATATAAATGATCAACAAGTATATTTTAAAATGTTCAACATTACT 1172
                              i   i     ii   i   i i  vvv  i   i       i ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_159982625_   1173 AATCAT 1178
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.87 (116 / 62)
Gap_init rate = 0.02 (13 / 678), avg. gap size = 3.15 (41 / 13)  


3242 21.08 6.91 0.59  chr1_160195922_160197793      526  1379 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160195922_    526 TGGAAAGATATTCCATGTTTATGCATTGGAATAATTAAT---GTTAACAT 572
                                    i       i   v       v v     ---     v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160195922_    573 GTTCATACTACCCAAAGCAATTTACATATTCAATGCAATCTCATTCAGAA 622
                          viv     v      vii  i    v      i      i vv   i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160195922_    623 TTCAAAAGGCATTTTTGACAGAAATAGA-AA----------AAATTC--- 658
                          i v ivv  v     vi       v  -  ----------      ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_160195922_    659 TGAAAA-------GACCCTGACTAGCCAATGCAATCTTGAGAAA-AATAA 700
                           i   -------     v  v       vi         i   -  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_160195922_    701 CAAAAGCTGGAGGCATCACACTATCTGATTTTAAATTGCACTACAAATCT 750
                             - i      vv       vi ii    i   vivi        v  
  L1M4_orf2#LINE/    201 CAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_160195922_    751 ATAGTAATCAAAATAGCATGATATTGGCATAAAAACAGACATATAAATCA 800
                          i         i i  ii  i  i        ii i         i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_160195922_    801 ATGGAATAGAATCTAGAGTCCAGAAATAAAACCACACATTTATGGTCAAA 850
                                     iv                v   i              v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_160195922_    851 TGATCATCAATAAAGCTACCAAGA--------------AAGGCTAGTCTC 886
                             iv  i i  i v i      --------------   iv      i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_160195922_    887 TTCAATAAATGGTGTTGGAAAAACTGGATATCCACATGTAGAATAATAAA 936
                              i        i   i v         ?       i i  v   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_160195922_    937 TTTGGAGCCTTATCTTATGCCATACA-AAAAATCAACCCAAACTAGATTA 985
                         v     v  i  i  i ii     i -      i   i    v i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_160195922_    986 AAGACTTAAAAGCAAGACCAGAAACTA--AAACTACTAGAAGAAAACATA 1033
                         ?    i    v i    v vi      --     vi              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_160195922_   1034 GGAA-AAATGCTTCATGACATTGA-TCAGGGCAATGATTT-TTAGATGTG 1080
                           ?i-    -    i    v   i- i   -     i   -      i  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTAGATATG 597

  chr1_160195922_   1081 ACTCCAAAG-----------AAAAGTAAAAATAGAAAAATGGGATTGCTT 1119
                           v     i-----------     v         v    v   i v v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_160195922_   1120 CTAACTAAAATGCTTCTGAGTAACAAAGGAAACAAT-AAGCAAAATGAAA 1168
                          v  v v   vi   i  v ivv       v  v  -   -   i     
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAA 696

  chr1_160195922_   1169 AGGCATCCAATGAAATGAGAGAAAATATTTGCAAACTATACATCTGATAA 1218
                           i  v  v iii    i                 ii   i         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_160195922_   1219 GGGCTTAATATTCAAAATATATAAAGAACTCATACAACTCATTAGCGAGA 1268
                            vi vi   i  i                v         v  iii i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_160195922_   1269 AAACAAATAATCAAATT-AAAAGTGGGGTAAGTTCCTGA-TAGACAGTTC 1316
                          i        i v    -    i    vv   vvii   -      v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_160195922_   1317 TCAAAAGAAGACATACAAATTAGTCAACAGGTATATGAAAAAGTGCTCAG 1366
                           v        i        -i i   i i i i       ii      i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAAT-GGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_160195922_   1367 TATCACTAACCAT 1379
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (106 / 71)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.05 (64 / 21)  


1675 23.28 15.27 3.45  chr1_160227056_160229955      492  1303 (1597)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_160227056_   1303 TGGAAGGACATCCCATGTTTATGAGTTTGAAAGAATTAATATTGTTAAAA 1254
                              i  i          i   - v   i    v             i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATG-GATTGGAAGACTTAATATTGTTAAGA 49

C chr1_160227056_   1253 TCATTGTACTGCCCAAAGGAATCTACAGATCTAATGCAATATCTATCAAA 1204
                          viivi    v      vvi          ii  i     vi        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

C chr1_160227056_   1203 ATACAAATGACATTCTTCACAAAAATATAAAAA----ATTCTAAAATGTA 1158
                           v v iivi v  i  ii  i    - i v  ----  i       vi 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

C chr1_160227056_   1157 TATGGAACCACAAAAGACCGCAAATAGCCCAAAGCAATCTTGTA------ 1114
                                vii   ii    vvi       -   i        v ------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCC-AAAACAATCTTGAAAAAGAA 197

C chr1_160227056_   1113 ---TATTTTTGGGTGACAACTATATAT---AATGAAATCCTAAACATTCC 1070
                         ---i vvv    iv   --ii i iv ---   ---- i v    -  v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGAC--TCACACTTCCCAAT----TTCAAAAC-TTAC 240

C chr1_160227056_   1069 T-TAGAGTCTTACA-TATT--ACACA------TA-TGGGAAAAGTTTAGA 1031
                          -i i  i--    -  v -- v   ------  -   v v   vv    
  L1M4_orf2#LINE/    241 TACAAAGC--TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

C chr1_160227056_   1030 CA-ACAACTGTTTGTACAACACATTT-----TCC-----TATAACCAATA 992
                           - i i--i ivi iv  i v v  -----   -----  -    v   
  L1M4_orf2#LINE/    289 CATATAG--ATCAATGGAATAGAATTGAGAGTCCAGAAATA-AACCCATA 335

C chr1_160227056_    991 ----TGTGGTGACACTTTGGTATGTTATGAAGATACCTGAAGCAGT-AAT 947
                         ---- i    --  v  - i v viv ii i i i  vii v  v -   
  L1M4_orf2#LINE/    336 CATTTATGGT--CAATT-GATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

C chr1_160227056_    946 CTGGA----------TTTTCAA--AAT----TT------ACTG-ATGTCT 920
                         vv   ----------       --   ----i ------    -  i? i
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

C chr1_160227056_    919 ATCTTTAATGCCATCAGCTTAATACCATT--CTCCTTCTATATCC----- 877
                          iv vi  vivv  v iv  ii-   vi --   viv i    v -----
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGG-ACCCCTACCTCACACCATATACAAAAA 481

C chr1_160227056_    876 ----CTCAATACCCCTG--TTGCAG-CCTGAATTCAAAAGCTTAGGC-AT 835
                         ----     v ----  -- ii?  -   i   vi  i    v ii -  
  L1M4_orf2#LINE/    482 TTAACTCAAAA----TGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

C chr1_160227056_    834 TG--CTCT--GAAGAGTTACGTAAAAATAAA------------------- 808
                         vi--    --     iv-  i  ii?i    -------------------
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAA-ACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

C chr1_160227056_    807 -GCA-----------GATCATGACATCAAAAGCATACACAAAAAAGAGAA 770
                         -   -----------   -      i        i vi   v   -    
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAA-AGAA 624

C chr1_160227056_    769 ACAATAAATACATTGGACATCATCAAAATTAAAAACCCTTATGTTCCAAA 720
                          v    i   v       v                 ii  i  i i    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

C chr1_160227056_    719 GGATATTATCAAGAAAGAGAAAAGACAATCCACAGAATGAGAGAGCATTT 670
                            i i           v          i          i    iv  v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

C chr1_160227056_    669 TTGCAAATCATATATCTGACAAGGGACTTGTATCTAGAATATATAAAAGA 620
                                            i              i            ii 
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

C chr1_160227056_    619 CTCCTACAACTCAATAA---AAAGACCAATCACCCAAT--AAAAATGGTC 575
                            i             ---      v   v       --        v 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

C chr1_160227056_    574 AAGAGATCTAAATAGATATTTCTCTAAAGAATATATTCACAAA--GCCAA 527
                           ii   i i      i       i      v    --     --     
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT--ACAAATGGCCAA 872

C chr1_160227056_    526 AAAACACATACAAAG-TGTTCAGCATTAGCCATCAC 492
                         v  i     iv    -  i   i   i ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (111 / 75)
Gap_init rate = 0.05 (48 / 908), avg. gap size = 3.17 (152 / 48)  

2425 23.82 2.76 3.82  chr1_160227056_160229955     1648  2407 (493)    L1M4_orf2#LINE/L1      157   908 (0)  

  chr1_160227056_   1648 TGCAAGCAGGGA---AAATTTGCTAAAGCAATCCTGAGTGAAAAGAATAA 1694
                               ---   --- i v v  i   i     i   ivi i     i  
  L1M4_orf2#LINE/    157 TGCAAG---GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_160227056_   1695 CATTGTAGGCATCACACTACCTGACCTCAAAATATATTATAAAGCTATAA 1744
                         vi   v   vv       v  ii ii      iv  i  i       i i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_160227056_   1745 TAACCAAAACAGCATGGTACTGACATGAAAATAGACACATAGACCAATGG 1794
                            i   i    ii        i   i ii       i     i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_160227056_   1795 AACAGAAA-GAGAACCCAGAAATAAATCCACATACTTACAGACACCTGAT 1843
                           i    v-    ii           i   i i i   ii v  vi    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_160227056_   1844 TTTCAACAAAGATGCGAAGAACATACATTGAGGAAAGGACATTCTCTTTA 1893
                             i    i i   v    v   v  v  i      i i v   i  i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_160227056_   1894 ATGAATAATGCCGGAAAAACCAAAATATTCATATGCAGAGGAATGAAACT 1943
                          ii   ii   i  i v   iii -  ?i  i     i i       ii 
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGA-TAKCCACATGCAAAAGAATGAAGTT 452

  chr1_160227056_   1944 AGGCCTCTATC----ACCACATCCAAAAGTCAATTCAAAATGGATTAAAG 1989
                         i i  i   i ----    i  v     i i  i           i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_160227056_   1990 ACCTAAAT-------CTCAAACTATGAAAATACTAGAAGAAAACTTAGGA 2032
                                 -------  v       i   v vi           v    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_160227056_   2033 G-AAATGCTTCAGGACATCAGTCTAGGCAGATATTTTTATGGAGAAGACC 2081
                          -    -    iv   v ii vi      -  iv   iv i  v v   v
  L1M4_orf2#LINE/    553 GTAAAT-CTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAGATATGACA 600

  chr1_160227056_   2082 TTAAAAAAGACAATAAAAAGGACAACAAAAGCCAAAATAGACAAATGAGA 2131
                         ii    iv-    --------i         vv        i    vi  
  L1M4_orf2#LINE/    601 CCAAAAGC-ACAA--------GCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_160227056_   2132 TTATATCAAATTAAAAAACTTTGGCATAGCAAAGGAAAC-ATTGACAGGG 2180
                         i vi      v v         v iiivv       v  -  ii v ii 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_160227056_   2181 T-AAAGGACAACCTGCAGAATGGGAGAAAATATTTGCAAATTATTTATCC 2229
                          -   i       ii                          i  v    i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_160227056_   2230 AACAAGGGAACAATACTCAGAATATTCAAACAACTCA-ACAGC-CAACAC 2277
                         i i      vivi  ii        vi   v     v-   i -   i -
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA- 790

  chr1_160227056_   2278 ACACACACACACACACACACACACACAATGCAATTCAAAA-TGGGCAAAT 2326
                         ------------ i v v v   v i  iv     ?    -        v
  L1M4_orf2#LINE/    791 ------------ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_160227056_   2327 GATATGAATAGACATTTCTCAAAAGAAGGCATACAAATGTTCAAGAAGTA 2376
                            v                v       ii         vi   v   i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_160227056_   2377 TATGGAAAAAATGCTGAACATCACTAATCAT 2407
                         i   -    i     v       ????????
  L1M4_orf2#LINE/    879 CATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (117 / 60)
Gap_init rate = 0.02 (18 / 752), avg. gap size = 2.78 (50 / 18)  


2787 25.28 2.95 1.70  chr1_160250876_160254031.rev     1784  2665 (491)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr1_160250876_   1784 TGTTTATTGATTAGAAAACTGAATATTATACAAATGTTATTCAGTTCCTT 1833
                             i  v    i   i   v      i vv i   vi v - v i  --
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT-ACTCCC-- 62

  chr1_160250876_   1834 CAATATTGATGCATA-ACTCAACACCATCTCAATTAAAATTCTAGCAGG- 1881
                            -      vi i - i     i v   i v  i     i i   v v-
  L1M4_orf2#LINE/     63 CAA-ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr1_160250876_   1882 -TTTTTGTGGAAATGAGTAAGTTGATTCTGAAATGTATCTATAAATGCAC 1930
                         -      ii     viii   i    i  i    vi  v iv       v
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_160250876_   1931 AGAACCTAGAATATTTCCAATATCCATGAACAA-AAGAATAAAGCTGGAT 1979
                         i i   i      viivv  i vi v    v  -     i    i    v
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_160250876_   1980 GACTCACACAATCTTGTTTCAATACTTATTATAAAGCCACATTAATCAAG 2029
                                  vvi ivi      v     i  i     i   v        
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_160250876_   2030 ACAATATAGTATTGATGTAAATACAGACACATG----AGTGTAATAGACT 2075
                            i i i   i  iii   iv i     i  i---- i  v      v 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_160250876_   2076 AGAGAGTCCAGAAATAGACCCACCC--TTACAATCAATGGACTTTTTCTA 2123
                         v               i     iv --   iii     v  --     v 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA--TTTTCGA 359

  chr1_160250876_   2124 CAAAGGTGCAAAGATAATTCAGTGTAGAACAGATAGCATTATCAACAAAT 2173
                            i     v    iv     i  vi   vii    iv  v         
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_160250876_   2174 GAGGTTGCAACAATTGCATCTCCACAAGTAAAA-AGTAAACTTCAATCTT 2222
                          iv i  vi    i  v  v?     v i    - i i  v  vi i ii
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_160250876_   2223 TATTTTGTGACATGTTCAAAAATTAATTCAAGATGGATCATATGCCTAAA 2272
                           ii iiiiv   i v          i    i        ? vi      
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_160250876_   2273 GATACTACTTAAAATTACAAAACTTCTAAAAGACAACATAGAAAACAAAA 2322
                         vi  vv vi     i  i      ii  i    v       i?i-i   v
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG-TAAAT 558

  chr1_160250876_   2323 TTTTGTGACTTTGGGCTAGGCAAAGATTTCTTAGATATAATACAAAAAGC 2372
                         i  i     i     i       v i            i i  v      
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_160250876_   2373 ACAAAC--CAAAAGAGAAAAATTAATCAAGTTGACTTCATACAAAATTAA 2420
                             i --       -      vi  v  v v        -         
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCAT-CAAAATTAA 656

  chr1_160250876_   2421 AA-CTTTTG--CTCTGAAATACAATGTTAAGAAAATGAA--GGCAATCC- 2464
                           -      --  iii  iv   v i i      i    -- i   i  -
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_160250876_   2465 CA-ACTGGAAGGAATTGTTT-CAAAGCATATATCTATCTAATAAATAACT 2512
                           - v   i  i  v i   -    v         i----    ivi   
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTG----ATAAGGGACT 752

  chr1_160250876_   2513 AGTATCAAAAATACATAAAGAAAT-TGAAAATGTAATAATAAGAAAACAA 2561
                         v     v i    i        v - v v  ivi        i  i    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_160250876_   2562 A-AAC---ATGTAACATAATAGAGAAAAGATTTGAATAGACACTTCACCA 2607
                          -   ---  v?  - -   i iv   i              i   v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAA-A-AATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_160250876_   2608 GTGATGATATATGGATAGTGAATAAGCTCAAGAAAAGATGCTCAACATCA 2657
                         iv  v      iii  i iv       v  v                   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_160250876_   2658 TTAGTGAT 2665
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.61 (135 / 84)
Gap_init rate = 0.03 (26 / 893), avg. gap size = 1.58 (41 / 26)  


 878 29.77 8.75 3.79  chr1_160267450_160270345.rev     1647  2412 (484)    L1M4_orf2#LINE/L1      105   908 (0)  

  chr1_160267450_   1647 AGCTG--TTATCTACAGGTATTTTTCAAGCGGATTCTACTATTTGTATCT 1694
                              --  v i i   iv   vv-     v   i   vv   ii   vv
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATATGG 153

  chr1_160267450_   1695 AAGAATAAA--ACTTTAAAAATAGCCAGTACATTAATGCAGAAGAATGAC 1742
                           ivii  i--  ii-- i        iv   v vv  v i     vi  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCC--AGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_160267450_   1743 AAAGTTGTGGATCTGGCTGTAATCAAT-----AATTATTATTGTAAAGTC 1787
                                vi iv  vi vv vvi    -----  i --  i ii    ii
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT--TACTACAAAGCT 249

  chr1_160267450_   1788 ----TGAT-AAGACAGTGTAGTTTTGGGATAGAAACAGGTAAATACACTA 1832
                         ---- i  -          i  vi   v   iii i  ii v   v ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_160267450_   1833 ATGCAATCAAATGAAGA-TCT-----------CATGTATTTAGAAAC--T 1868
                            v   vi   vi   -  i-----------   ii     viiv -- 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_160267450_   1869 TGATAAATGACA--GATCTAGCTTTGAAAATCAGTGAAT------AAAAT 1910
                             vvvi    -- i ---  i---  i i  v v   ------ i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGT---GCC---AAGACCATTCAATGGGGAAAGAAT 393

  chr1_160267450_   1911 AGACTCTGTTCAATAAGTAATATGGAAAAAATTAGTGGCCCATATGTAAA 1960
                           --   v     i  i ii iiv ii v  i i vvi?   i   i   
  L1M4_orf2#LINE/    394 AG--TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_160267450_   1961 AATATGAAATTGGATACATATTTC---CTATTTGCAAATATCAGTTGTGC 2007
                          iv     i     iv v  ii  --- i  v i    v  i ii --- 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT---C 488

  chr1_160267450_   2008 TAA---GATTAT-GACCTTAATGAAAAAGGCAAAATT-TAAAACTTTTT- 2051
                         v  ---   i ?-     v    v  i  vi    i -       i  v-
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_160267450_   2052 ----AAATATAGAAG-A---CTTTGTGGCTTTAGAAT-GGAAAAGATTTG 2092
                         ----   i    i? - ---   i   i i  i iv -  v  v i   v
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_160267450_   2093 TTAAACTA-GACTCAAAAAGCAAAATTTATTT--TAAAAAATGAATAGAT 2139
                            i -  -   v v       v  viv ivv--v       ii   i  
  L1M4_orf2#LINE/    589 TTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_160267450_   2140 TCAACTATATTAAAATTAAAG---TTTGC-CTTCAACAAATGATACCATA 2185
                          vi   vi  i         i---    i-      --- v  i  i  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA---AGGACACTATC 684

  chr1_160267450_   2186 AAGAAAGTGAAAGAGGCAAGCCACAAAGTAGGAAAATAATGTTTGCAA-- 2233
                                     -  i   v     i i i   i  -   i       --
  L1M4_orf2#LINE/    685 AAGAAAGTGAAA-AGACAACCCACAGAATGGGAGAA-AATATTTGCAAAT 732

  chr1_160267450_   2234 CACATATCATAATAATGGATTTACGTTCAGGAGAAAAAAACAAAAACAAA 2283
                           i     - i    v   i  iii i   i v v v   -i  vv vv 
  L1M4_orf2#LINE/    733 CATATATC-TGATAAGGGACTTGTATCCAGAATATATAAA-GAACTCTTA 780

  chr1_160267450_   2284 AAACT-AA-AATACGAAAAGAAATAAAATACTAATAGGAAAATTGGCAAA 2331
                         v    -  -    vi  i v      v--- i   v?i     v      
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAAC---CCAATTWAAAAATGGGCAAA 827

  chr1_160267450_   2332 CCGTCATGACCGAGCATTT-TCAAGAGGAGAGACTGTCAATGGTCAATAA 2380
                         vvi i-   viiii     -  v i  i   v - iiv     i      
  L1M4_orf2#LINE/    828 GGATT-TGAATAGACATTTCTCCAAAGAAGATA-TACAAATGGCCAATAA 875

  chr1_160267450_   2381 ACATATGAGAAGATACT-AATCTCATTAGTTAT 2412
                         i  i    i     i  -  iv   ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (134 / 90)
Gap_init rate = 0.05 (43 / 804), avg. gap size = 2.23 (96 / 43)  


1464 27.48 2.33 0.21  chr1_160341659_160347929.rev       31   503 (5768)    L1M4_orf2#LINE/L1      341   823 (85)  

  chr1_160341659_     31 ATAATCAACTGATCTTTGACAAGGAATTAAAGACAATGCAATGCAACAGA 80
                           ii    i    i  i       ivviv     v  v     viiv ii
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_160341659_     81 GATAGTCTTTTCAACAAATGGTTCTGGAACAATTGAACATCTACATGCAA 130
                         i                     v    i    i  i i ? i        
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_160341659_    131 AACAATAAATCTAGACACAGGCCTTACAC--TTTACATAAATTAACTCAA 178
                           v   i  vi i   v vvi   i    -- v    v            
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_160341659_    179 AATGGAAAATAAACCTAAGTGTAAAATTAAAAACCATATAAACTCCAAGA 228
                               vv ? i      i     i viv     i   -      iv   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGA 539

  chr1_160341659_    229 AGAAAACATTGGATAAAATCTAGATGATCTAGGGTTTGGCAATAACATTT 278
                                  v  ?vv      vvi   i  v     v      iiiv i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_160341659_    279 TAGATACAACACCAAAGGCATGATACATAAAAGAAAAAATTGAGAAGGAG 328
                               ii        i   ii vvv i            v  v  ivv 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_160341659_    329 GATTTTATTAAAATTAAGAATTTCTTCTCTGTGAA----ACT--TAAGA- 371
                           i  i  i        i  i  i viv  vii  ----   --i    -
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_160341659_    372 --TAAAAAGAGAAGCCTCAAACTGAGAAAGAATATTTTCAAAATACAAAC 419
                         -- i      v  v  v  i v  i  i i       v    vi i v i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_160341659_    420 CTGTTAAAAGACTGTTCTCCAAAATATACAAAGAATACTTAAAACTCAAC 469
                            v   ii    vv v    i      i      iv    v       i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_160341659_    470 AATAAGAAAAGAAAAATTCTGCTTAAAAAATCGG 503
                              i  i v   v vi iiv  ?      v  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

Transitions / transversions = 1.25 (70 / 56)
Gap_init rate = 0.01 (5 / 483), avg. gap size = 2.40 (12 / 5)  

3233 27.02 0.78 0.22  chr1_160341659_160347929.rev     4878  5780 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160341659_   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160341659_   4928 GGCCATACTGACCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     vv    iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160341659_   4978 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 5022
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_160341659_   5023 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5072
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_160341659_   5073 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5122
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_160341659_   5123 CAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATCAA 5172
                               i   i    ii        vi iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_160341659_   5173 TGGAACAGAAT--AGAGCCCTCAGAAATAATGCCGCATACCTACAACTAT 5220
                              i     --    i  --        vv  ii i ii  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_160341659_   5221 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5270
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_160341659_   5271 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5320
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_160341659_   5321 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5370
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_160341659_   5371 AAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5420
                          ?   ii    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_160341659_   5421 AGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAA 5470
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_160341659_   5471 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5520
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_160341659_   5521 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5570
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_160341659_   5571 GCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5620
                         i     i   iv            v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_160341659_   5621 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5670
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_160341659_   5671 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5720
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_160341659_   5721 AAAAGAAGACATTTATGCAGCCAAAAAACACATTAAAAAATGCTCATCAT 5770
                         v        i  vi viii     v  i     v    i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_160341659_   5771 CACTGGCCAT 5780
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.25 (9 / 4)  


3674 21.08 4.81 0.80  chr1_160383063_160385415      989  1861 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160383063_    989 TGGAAAGACATCCTATGTTTATGGACTGGAAGACTTAATATTGCTAAGAA 1038
                                 i    i     i     i                 i     v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160383063_   1039 ATCAATACTAACTAAAACAATTTATAGATTCAACACAATCCACATCAAAA 1088
                         iv       vv i   vii  i  i         i      vi       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160383063_   1089 TCTCAAGTGTCTTTTTTTTGCAGAAATAGCAAAAAATCATCCTATAATGA 1138
                           i  iv  i       --        v - v  iv v      v   vv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--GCAGAAATTG-ACAAGCTGATCCTAAAATTC 147

  chr1_160383063_   1139 ACATGGGATCTCAGGAAACCTTGAATAGCTAAAATAATCTTGAAAAAGTA 1188
                          i    i viv  i ii   iv       i    i             v 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_160383063_   1189 AAACAAAGTTGAAGGATTTATGCTTCCTGATTTGAAAAC--ATTACAAAG 1236
                         i          i    i i ii     ii    v     -- i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_160383063_   1237 CTATTACAGTCAAAATAGTATGATACTCGTGTGAAGGCAGACATATAGAT 1286
                            ivii i    i i   i  i    v ii i i ii            
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_160383063_   1287 TAATGAAATAGAAT--AGAGTCCAGAAACAAACCTA-------------A 1321
                         i    i        --            i     i ------------- 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_160383063_   1322 AT-----------GAGGGTGCCAAGATCAGTCAATGGG-AAAGA---GTC 1356
                           -----------i            i  v        -     ---   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_160383063_   1357 TCTTCAACAAATGGTATTCAGAAAACTGGATATGCACATGCAAAATAATG 1406
                          i             ii vi  v         ?v           v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_160383063_   1407 AATTTGGAGCCTTATTTTATACCATATACAAAAATTAACTCAAA-TATAT 1455
                           v     v  i  ii i i                        - iv  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_160383063_   1456 TAAAGGCTTAAATGTAAAATCCAAAAATGTAAAACTCCCAGAAGA---CA 1502
                         i ?  i i         i v i    v i        ii      ---  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_160383063_   1503 TATGAAAAAAATCTTCATGATATTAGATTTGCCCATGATTT-TCATACAT 1551
                           - i?iv        i   iv  i i  v v v   i   - i v i  
  L1M4_orf2#LINE/    548 TA-GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_160383063_   1552 AACACCAAAAGCACAGGTAACAAAAGAAAAAATAGACAAAAGGGACTATG 1601
                         i              i i                  i   vv     vii
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_160383063_   1602 TCAAATTTAAAACTTTTTGTTCATCAAAGGACACAATCAATTGAGTGAAA 1651
                              v      vi      v v           v     vvi       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_160383063_   1652 GG-TGGCCTACCGAATAGGAGAAAATATTTGCAAATCATGTATCAGCTGA 1700
                         i -iii  i  v    i                      i    v v i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_160383063_   1701 GGGGTTAATATCTAACATATATAAAGAACTACTATAACTCAACAACAACA 1750
                            ii vi    i iv              vi  i       i  i  --
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-- 794

  chr1_160383063_   1751 AAAAATCAAATTACTC----TAAAAATGAGTGAAGGACTTGAATATACAT 1796
                            i -     v  i ----?       i ii     i       v    
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_160383063_   1797 TTCTTCAAAGATGATATGCAAATGTCCAATAAGCATATGTGAAAATGCTA 1846
                             i      v     i      v          i   vi  i     v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_160383063_   1847 GATATCCCTAATCAT 1861
                         i i   v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (120 / 60)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.06 (49 / 16)  

 272 31.87 10.71 0.82  chr1_160383063_160385415     1967  2330 (23)    L1M4_orf2#LINE/L1      161   560 (348)  

  chr1_160383063_   1967 AGGGATATGGAGAAGTTAGAATA-CCATGCAAAAAATGCTCAATGATGGG 2015
                              ivii  iv  ii i  i -i v  v    i v vv   v v   i
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_160383063_   2016 GGGCTATCCCTAACAAATACTACAACATATTCTAAACGCTCTAA-AAT-- 2062
                           i  vv v  vv v   vii v   v  i vi   -   vi i-   --
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAA-GCTACAGTAATCA 259

  chr1_160383063_   2063 AAACA---TAGCA-TGGCACATGGATAGACAGACTGAGCAATGAAACA-- 2106
                          i   --- i i -     i v         v iv  v     i  i --
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_160383063_   2107 AT--AAAGTACATAAATAGATTGTTGAAATT-TGG-CAAATGAT------ 2146
                           -- i   v  v     i iivv iv v  -   -   v    ------
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_160383063_   2147 -AAAGGCAGCATATTTAATCATTGGGGAAACACGA--CCTATTAAGAAAC 2193
                         -  i  iiv  vivii v   v        v vv -- i v i  v   i
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_160383063_   2194 AATGTTGAGAAAACTAGATAGCCATTTAGTAAAAGA-TAAAATTG-ACAA 2241
                         ii  i  i  v    i    ?   iv - i      - i  i   -  vv
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAATGAAGTTGGACCC 458

  chr1_160383063_   2242 ATA--TCACA--ATGT-CAGAAAA-AATTCCACATTAATCAGATATCTAA 2285
                         v  --     --  i -  i   v-  i  v v  vi    ? v i    
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_160383063_   2286 AATGGAAAA----AAATTATAAAAAG--TATCAGAAAATAT--GAGTAAA 2327
                          -  v  i ----   i       vv--  vv      i  -- ?     
  L1M4_orf2#LINE/    509 A-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_160383063_   2328 TTT 2330
                          i 
  L1M4_orf2#LINE/    558 TCT 560

Transitions / transversions = 1.02 (57 / 56)
Gap_init rate = 0.06 (23 / 400), avg. gap size = 1.83 (42 / 23)  


 578 27.60 3.65 0.52  chr1_160415077_160416727.rev        1   192 (1459)    L1M4_orf2#LINE/L1      100   297 (611)  

  chr1_160415077_      1 ATCTCAGCAAGGTTTTTGGTAGAAATAAACAA-CTCTTTCTAAAATTTTT 49
                            i    vivv     v i      vi    -  vv i        iv 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_160415077_     50 AGGGAAAGACAGATAAATTAGAATAGTCCAAACAATTTTTGAAAAAGAA- 98
                          v     vi  iivi vii       i v       i  -         -
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT-GAAAAAGAAG 198

  chr1_160415077_     99 ---AATGTCAGAAAACTCACAAC-ACTGATTTCAAGACTTACTATAAAGT 144
                         ---  v  ii  ii       vi-v ii       i        i    i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_160415077_    145 TACAGTAACTAA-ACAGTGCAGTATTGTCAAAAGAATTAGTATATATAT 192
                                 ii  -      ii   i  v  v   i  viii     v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

Transitions / transversions = 1.65 (33 / 20)
Gap_init rate = 0.03 (5 / 198), avg. gap size = 1.60 (8 / 5)  

1600 22.15 4.40 10.02  chr1_160415077_160416727.rev      502  1160 (491)    L1M4_orf2#LINE/L1      287   908 (0)  

  chr1_160415077_    502 GATATATATATCAATGAAATAGCACAAAGAGTATAGAAATAGACCCATAC 551
                           i     v       i     v ivi     vi       i        
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_160415077_    552 AACTATAGTCTATTGATTTTCAA-AAAGGTGCAAAGGAAATCCAATGGAG 600
                          vi   i   v          i -  i     v   ivv  i      i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_160415077_    601 AAAGGATAGGCTTTAAAACAAATGGTGT---ATCAATTGAAAGACTCTAT 647
                             i    v    vv           i---iv   i  i vi? ivi  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_160415077_    648 GCAAAAGAAGAAAGAAAAAGAGTAAAACTGGAGGAGAGGGTGGGGAAGAA 697
                                  ------------- i  ii    ------------------
  L1M4_orf2#LINE/    437 GCAAAAGAA-------------TGAAGTTGGA------------------ 455

  chr1_160415077_    698 GGGAGGAAGAGGAGAAAGAACTTTCATGCATACCTCATGACTTATACAAA 747
                         -----------------------i --- v       iiv v        
  L1M4_orf2#LINE/    456 -----------------------CC---CCTACCTCACACCATATACAAA 479

  chr1_160415077_    748 AATTAATATAAAATGAAT---AAATCTCAATGTAAAATGTAAACCTATAA 794
                               ivi      i  --- i i  v       i vv    v      
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_160415077_    795 AATTTCTGAATGAACACATAGGAGAAAATCTTTATCAGCTTGGGTAAGGC 844
                           i ii ii v   v       ? v       ii v v       v    
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_160415077_    845 ACGTATAA---CTTGGATGTTACACCAAAAGCATGATCCATAAGTGAAAA 891
                          ---  ii---   i   i v            ii v v i  iv     
  L1M4_orf2#LINE/    580 A---ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_160415077_    892 TGTTGATAAATTAGACTTTATTAAAATTAAAAACTGATGCTTTTTGAAAG 941
                         vi v        i     i  i             vv  ivi  ii  i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_160415077_    942 GCACTATCAAGAGACTCAATGGACAAACCAGAGAAGAGAGGGAAAAATTT 991
                         i           i v v  vi     v   v    vi ii i   v    
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_160415077_    992 TTAAAGCACATAGCTAATAAAGGACTTTTACCCAAAATA---------CT 1032
                         vi   v  i   v  i    i      v  i   i    ---------  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_160415077_   1033 CTCAAAACATAACAATAAA----TAAACAACCTAATTTTTTAAATGTGCA 1078
                           i v   vi  i      ----i   i    i    ?vv-     v   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCA 825

  chr1_160415077_   1079 AAAGATTTGAAATGAC---TCTTTATTTTATAAGATATATAAAT---CAA 1122
                           i        vv   ---   ii v--- v        i    ---   
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAA---AGAAGATATACAAATGGCCAA 872

  chr1_160415077_   1123 AGTAAGCATACGAGAAGATGGTCAACCTCATTAGTCAT 1160
                         --      i i  i      v     v   ????????
  L1M4_orf2#LINE/    873 --TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (83 / 60)
Gap_init rate = 0.02 (15 / 622), avg. gap size = 6.33 (95 / 15)  


3198 24.63 2.92 0.79  chr1_160440065_160444289.rev     2848  3736 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160440065_   2848 TGGAAAGATATTTTATGTTCATGGATTGAAAGAATCAATATTGTTAAAAT 2897
                                    iii              i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160440065_   2898 GTCCAGATTACTCAATGCAATCTACAGATCCAATGCAATCCCTATCAAAA 2947
                          v v v i v i   vvii          i   i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160440065_   2948 TGCC-GATGAC------ACAGAAGTAAGAAAAGT--ATCCTAAAATTTAT 2988
                          v  - v  v ------i     i v-  v   i--           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chr1_160440065_   2989 ATAGAACTGCAAAAGACCCAGAATAGCCTAAGGTATCCTGAGCAAAAATA 3038
                           i   v     ii              v  ivv   i   iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_160440065_   3039 ACAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTACTAAGCT 3088
                              ii       v     i v  ii i      viv      v     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_160440065_   3089 ATAGTAACCAAAGCAGCATGATATTGGCATAAAAACAGACACATAGACAA 3138
                          i     i   ii   ii  i  i        ii i     i     iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_160440065_   3139 ATGGAACAGAATGGGGAACCCAGAAACAAATCTATACATCTGCAGTGGAC 3188
                               i     v i  ii       i   i i      i iii  vi i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_160440065_   3189 TCATTTTTGATGAAGGGGCCAAGAACAG-AAATTGGGGGAAAGGTCATTC 3237
                          v     i  ii i  v       v  v-v   --        ivi v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAAT--GGGGAAAGAATAGTC 397

  chr1_160440065_   3238 TCTTCAATAAATGA--CTAGGAAAACTG-ATATTCATATGCAGAAGAATA 3284
                          i     i     i--  i   v     -   ?i  i     i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_160440065_   3285 AAACTAGACCCCTATCTCTTGCCTTATATAAAAATTAAATCAAAATGGAC 3334
                           ii i        i   vii  v    i         v          i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_160440065_   3335 TAAAGACTTAAATCTAAGACCTAAAATTATGAAACTACTACAAGAAAACA 3384
                         i ?    i     v     v      i   i     vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_160440065_   3385 TAGGGGAAACTCTACAGGACATTGGTCTGGGAAAAAATTTATTGAGTAAT 3434
                             ? v  v   v iv   v    vi i  v  vii   v  iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_160440065_   3435 ATCCTACAAGAATAAGCAACCAAAACAAAAATTGA------------CAT 3472
                          iv i v   v i       v   iv      v  ------------   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_160440065_   3473 CAAG-TCAAAAGGTTTCTGTACAGAAAAGGAAACAATCAATAAAATGAAG 3521
                            i- i    iv   -   i vvv      v  v     v   i    i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_160440065_   3522 ATAACACACACAGAATGGGAGAAAACATTATCAAACTATCCATCTGACAA 3571
                          v vv  v                 i   vv    ii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_160440065_   3572 GGAATTAATAATCAGAATATATAAGGAGCTCAAACAATTCTATAGGAAAA 3621
                           i i vi  vi            i  i   vv    i  v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_160440065_   3622 AAAACTAACAATCTGATTTTAGAATGGGCAAAAGATCTGAATAGACATTT 3671
                          i - v  i  i ii   ?v i          i   i             
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_160440065_   3672 TACAAAAGAAGACATACAAATGGCAAACAGGCATATATGAAAATGTGTTG 3721
                         iv v        i           v  i i   i  --     vi  i v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACAT--GAAAAGATGCTC 893

  chr1_160440065_   3722 AACATAATTGATGAT 3736
                              v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (129 / 86)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.54 (33 / 13)  


3220 26.54 0.66 0.66  chr1_160451378_160457653.rev     4878  5785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160451378_   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCTTGAAAAT 4927
                              ii i  i     i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160451378_   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160451378_   4978 TACCAATGACTTCCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi i ii  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_160451378_   5026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_160451378_   5076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACAAC--ACTACAAG 5123
                                i      vv       v  ii i      --  --       i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAA 246

  chr1_160451378_   5124 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5173
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_160451378_   5174 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACGTATCTACAA 5221
                                  i    i--    i  --        vv   iii  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_160451378_   5222 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5271
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_160451378_   5272 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAACCATATGTAGAAAG 5321
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_160451378_   5322 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5371
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_160451378_   5372 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5421
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_160451378_   5422 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5471
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_160451378_   5472 AAAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCT 5521
                          vi            vvi     v    vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_160451378_   5522 AACTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5571
                         v ii   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_160451378_   5572 ACAGGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5621
                          v  i     i   iv            v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_160451378_   5622 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5671
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_160451378_   5672 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5721
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_160451378_   5722 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5771
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_160451378_   5772 CCATCACTGGCCAT 5785
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2767 26.44 2.18 3.37  chr1_160460734_160465113     2969  3887 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160460734_   2969 TGGAAAAACATTCCATCCTCATAGATAGGAAGAATCAGT--TATGAAAAT 3016
                               i i  i    vi    i   v      v i i -- i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160460734_   3017 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGTTATTCCCATTAAAC 3066
                            v     v      v i  i  i        i iv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160460734_   3067 TACTATTGACATTCTTAACAGAATTCGAAGAAACT-ACTTTAAAATTTAT 3115
                          v i vivi v  i  vi     v i  v-  i  - iii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr1_160460734_   3116 ATGGAACCAAAAAAAGAAAAAAGAAAAAAAGCCCACATAGCCAAGGCAGT 3165
                               -------------- v v  iii v  viv        ii  i 
  L1M4_orf2#LINE/    150 ATGGAA--------------ATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_160460734_   3166 CCTAAGCAAAAAGAACAAAGCTAGAGGCATTACACTACCTGACTTCAAAC 3215
                          i i iv  i          i i    vv i     v  ii i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_160460734_   3216 TATAGTCCAAGG-TACAGTAACCAAAACAGCAAGGTACTAGTACCAAAAC 3264
                         iv  v v   i -        i   i    iiv      i i iv ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_160460734_   3265 AGGCATATAGACCAATGGAACAGAATAGATACCTCAGAAATAAGACCACA 3314
                           i        i        i     v  v vii         iv   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_160460734_   3315 CATCTACAG-CAATCTGATCTTTGACAAACTGGTCAAAAACAAGCAATGG 3363
                            i  ii -    -    i  i     ivvv i   i v  vv      
  L1M4_orf2#LINE/    336 CATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_160460734_   3364 GGAAAGGATTCCCTATTTAATAAATGGTGCTGGGTAAACTGGCTAGCCAT 3413
                               i  vvi  v  i  i             vv      v  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_160460734_   3414 ATGCAGAAAACTGAAACTGGGCCCCTTCCTTACACCTTATACAAAAATTA 3463
                              i  i v    ii   i     v   i     v             
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_160460734_   3464 ACTCAAGATGGATTAAAGACTTAAATATAAAACCCCAAACCGTAAAAACC 3513
                               i      i ?    i     i   i v iv    ii     vi 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_160460734_   3514 CTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAG 3562
                         i           v    ?i- v i -   iv   v v  vv i     v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chr1_160460734_   3563 ATTTTATGAAGAAATTTG----CAAAAGCAATTGTAACAGAAGCTATAAT 3608
                         i   iv ---- i  v  ----        vvv i    i   vv v   
  L1M4_orf2#LINE/    584 GTTTCTT----AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_160460734_   3609 TGATAAATGTGATCTAATTAAACTAAAGAGCTTCCACATGGCAAAAGAAA 3658
                         v       vv  ii v  i   v v  i i   iiiiiivv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_160460734_   3659 CTATTATGAGAGTGAACAGGCAACCTACAGAATAGGAGAAAATTTTTGCA 3708
                             i v  i      v  i     i       i         v      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_160460734_   3709 AACTACCCATCTGACAAAGGACTAATATTCAGAATTTACAAGGAACT--T 3756
                           ii ivi      i  i     vi   i      v  i  i     -- 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_160460734_   3757 A-AATTTA-CAAGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAGGG 3800
                          -  i i -i  v     i    ----   v  i?    i       i  
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_160460734_   3801 ATATGAACAGAGGGAGGTCATTCATTCTTAAAAGAAGACATTTGTGTGGC 3850
                           v    i   -------    ---   iv        i  viivi    
  L1M4_orf2#LINE/    830 ATTTGAATAGA-------CATT---TCTCCAAAGAAGATATACAAATGGC 869

  chr1_160460734_   3851 TGACAAAC-TATTAAAAAA-GCTCAACATCACTGATCAT 3887
                         ii i  i -i  v    i -           ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (148 / 91)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.68 (51 / 19)  


3399 21.00 8.59 0.24  chr1_160484003_160486212      880  1717 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160484003_    880 TGGAAAAACATCTCATAGTCATGGATCATAAGTCTTAAT-TTGTTAAGAT 928
                               i i   i   iv        iiv   v      -          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160484003_    929 GGTGATATTTTC-AAATAAATCCACATATTTAACTCAATTCCTATTAAAA 977
                           ii   i ii -    vi   i   v   i   v    i     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160484003_    978 TCTCAGCTACCTTTTTTTCAGATAT---CAA----------------ATA 1008
                           i     i        v    v  ---   ----------------   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_160484003_   1009 TGAATATG-----AATCCTGAATAGCCAAGACAACCTAGGTAAAGAAGAA 1053
                           i v   -----i i  v          i    i  v iv         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_160484003_   1054 CAAAGTTGGAGAAGTCACACTTTCAAATTTGAAGATGTATTCCAAAGCTA 1103
                                    i v        i v     v  i iv  i v        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_160484003_   1104 TAGTAATCAAAGCAGTTTGATATTAGCATATGAA--GACACATAGGTTAA 1151
                         i         ii    v  i  i i     v i --    i    i i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_160484003_   1152 CATAATAGAATTGTAAGTTCAAAAATAAACCCTTAC-TTTATGGCCAATT 1200
                         iiv          vi   i  i          v   -       i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_160484003_   1201 TATTTTCAACAAGAATGCCAAAAAAATTCAATGAGGAAAGAATGATCTTT 1250
                         v      i     ii      i vv        i         ii     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_160484003_   1251 TTCAACAAATGTTCCTAGAATCACTGGATATCCA---------AAATCAA 1291
                          -         v v  i i iv        ?   ---------i   v  
  L1M4_orf2#LINE/    401 T-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_160484003_   1292 AT----------------ATCATGTGCCAAAAATTAAGCCAAAATAGATC 1325
                         i ---------------- i   i i -         vi      i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAAATGGATC 498

  chr1_160484003_   1326 ACAGACCTAAATATCAGAGCTAAAATTATGAGATT--TAGAAGAAAAAAT 1373
                          ?          i v          i   i i i --          v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_160484003_   1374 AGGTATAAATCTTTGTTAGTTTCACTTAAA----GATTTCTTAGATATGG 1419
                            ?i        i  v vi  viv   ii---- i             i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_160484003_   1420 CAT-ACAAATACAAGTGATAAAAGAAAGAATAGATAATTTGGACTTGATA 1468
                           i- v  ii     ii i        i         v        v  v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_160484003_   1469 TAAATTAAGAACTTT-GTCTTATGAAAAATACCATCAAGGAAGTAAAAAA 1517
                         v       i      -  vi vii  ii i  i      i    i    i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_160484003_   1518 ACAACCCACAGT-TGGGAGAAAACACTTACAAACCATATATCTGATAAGA 1566
                                    v-          i i  i    i               i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_160484003_   1567 GGCTCATAAGCAGAATATATAAAAAATTCTTACAACTCAATAATAAAGAG 1616
                          i  ii  vv             i  i                    i  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_160484003_   1617 ATAAGCAACCCAATT-AAAAACAGGCAGCAGACCCGAACAGACATTTCTC 1665
                          i  ii         -     ii    ivi  iii   i           
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_160484003_   1666 AGAAGAATGTATATAAA--------AAGCATAAGAAAAGATACCCAGCCT 1707
                         vi     vi    i   --------     i v        i i  i v 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_160484003_   1708 CATTAGTTAT 1717
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.39 (122 / 51)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.11 (74 / 18)  


2652 23.09 1.39 6.70  chr1_160515711_160517568.rev      502  1367 (491)    L1M4_orf2#LINE/L1       89   908 (0)  

  chr1_160515711_    502 TCCCCATCAAAATACCA-CCACCATTCTTCGTAGAGTTAGAAAAAGCAAT 550
                             i        v   - ii  -  i  i i   iv v  v  ivii  
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGAT 137

  chr1_160515711_    551 TCTAAAATTCATATGAAACCAAAAAAGAGCCTGCATAGCCAAAGCAAAAC 600
                         i              i  viiv  ii  v  v v         i   v- 
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-C 186

  chr1_160515711_    601 TAGGCAAAAAAGAAAAACAAAAACAACAACAACAACAACAACAAAAAAAA 650
                          v ---        i      i----------------------------
  L1M4_orf2#LINE/    187 TTG---AAAAAGAAGAACAAAG---------------------------- 205

  chr1_160515711_    651 AACCTGGAGGCATCACACTACCTGATTTTAAACTATACTATAAGGCCATG 700
                         ---i      vv       v  ii    i   viv     i  i  i ii
  L1M4_orf2#LINE/    206 ---TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_160515711_    701 GTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCAATT 750
                           v i   i    ii         i    ii    i  i     i    v
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_160515711_    751 GAACAGAATAAAGAACCCAGAAATAAAAACCCAGAAATAAACCCAAATAC 800
                            i     -------------- i i ii               v i i
  L1M4_orf2#LINE/    303 GAATAGAAT--------------TGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_160515711_    801 TTACAGCCAACTAATCTTTGACAAAGCAAACAAAAACATAAAGTGGTGAT 850
                            ii i   i i  i  i     i vviv   i v   vv i   v  v
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_160515711_    851 AGGACACCGTTTTCAATAAATGATGCTGGGATAACTGGCTAGCCACATGT 900
                           i i viv       i     i        i      v  ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_160515711_    901 AGGAGAAGGAAACTGAATCCTCATCTCTCTCCTTATACAAAAATGAACTC 950
                          ii    v   ii  i i  ii i   v v  v           v     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_160515711_    951 AAGATGGATTAAGAACTTAAACCTAAGACCTGAAACTGTAAACATTCT-A 999
                           i      i ?ii  i    iv     v  i     i    - i   - 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTA 537

  chr1_160515711_   1000 GAAGAAAACATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTT 1049
                                    v  ?iv  vi    vv   v    v        v i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_160515711_   1050 C------ATGACCAAAAACTCAAAAGCAAATGCAATAAAAACAAAGATAA 1093
                          ------     -----  -        v v    i    iv   i   i
  L1M4_orf2#LINE/    588 CTTAGATATGAC-----AC-CAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_160515711_   1094 ATAGTTGGGACCTAATTAAACTAAAGAGCTTTTGCACGGCAAGAGGA-AC 1142
                            iv v    i v  i   v v  i i      ii vv   -    -  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACAC 680

  chr1_160515711_   1143 AGTCAGCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCACAA 1192
                         vi   iv i   i  v              i           v  ii   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_160515711_   1193 TGTATACATCTGACAAAGGACTAATATCCAAAATCTACAATGAACTCAAA 1242
                         vvi   i      i  i     vi      i   v  i  v      vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_160515711_   1243 CAAATAAGTAAGAAAAAAATCAAT--CCCA-TCAAAAAGTGGGCTAATGA 1289
                            v v i   v     i iv   --    - i?    i     v  v  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_160515711_   1290 CATGAATAGACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATA 1339
                         iv          v     v                       i  i  i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_160515711_   1340 TGAAAAAATGCTCAACATCACTAATGAT 1367
                               i             ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (120 / 76)
Gap_init rate = 0.02 (15 / 820), avg. gap size = 4.67 (70 / 15)  


3229 26.98 0.55 0.55  chr1_160549567_160551493.rev      529  1436 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160549567_    529 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 578
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160549567_    579 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 628
                            v     v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160549567_    629 TACCAATGACTTTCTTCACAGAATTGGAAAAGACT-ACTTTAAAGTTCAT 677
                          v   iivi i  i  ii     v v  v   -  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_160549567_    678 ATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGA 727
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_160549567_    728 ACAAAGCTGGAGGCATCATGCTACCTGGCTTCAAATTATACTACAAGGCT 777
                               i      vv   ii  v  iiii      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_160549567_    778 ACAGTAACCAAAACGGCATGGTACTGGTACCAAAACAGAGATATAGACCA 827
                                i   i  i ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_160549567_    828 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTA 875
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_160549567_    876 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 925
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_160549567_    926 TATTTAATAAATGGTGCTGGGAAAACTGGCTGGCCATATGTAGAAAGCTG 975
                          v  i  i              v      v i?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_160549567_    976 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 1025
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_160549567_   1026 TAAAGACTTAAATGGTAGACCTAAAACCATAAAAACCCTAGAAGAAAACT 1075
                         i ?    i      vv   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_160549567_   1076 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1124
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_160549567_   1125 AACACCAAAAGCA-ATGTCAACAAAAGCCAAAATTGACAAATGGGATCTA 1173
                         i            - v -         vv     v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_160549567_   1174 ACTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1223
                          ii   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_160549567_   1224 CAGGCAACCTACAATATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 1273
                         v  i     i   iv            v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_160549567_   1274 AAGGGCTAATATCCAGAATTTACAATGAACTCAAACAAATTTACAAGAAA 1323
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_160549567_   1324 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1373
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_160549567_   1374 CTCAGCAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1423
                            viv      i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_160549567_   1424 CATCACTGGCCAT 1436
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


1333 25.78 1.70 0.85  chr1_160603436_160608327.rev     3184  3536 (1356)    L1M4_orf2#LINE/L1        1   356 (552)  

  chr1_160603436_   3184 TGAAAAGATATTTCATGTGCATGAATTGGAAGAATTAATATTCTTAAAAT 3233
                           i        ii     v    i         v        v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160603436_   3234 AACAATACTACCCAAAGCAATTTATAG--CCAATGTAATCCCTATCAAAA 3281
                         ii       v      vii  i  i  --i   i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160603436_   3282 TACCAATGACGTTTTTCAGAAAAATAGAGAACACAACCCTAAAATTTATA 3331
                          v   iivi v     iiv i    v  v  vvii i         i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_160603436_   3332 TGGAATCACAAAAGAACTCAGA-TAGCCAAAGCAATCCTGAGCAGAAAGA 3380
                              vii   ii  - i    -        i     i   iv ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_160603436_   3381 ACGAAGTTGG--GAATCACACTACATGACTTCAAAATATATCACAAGGCT 3428
                           i       --  v       v vii i       iv  ii    i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_160603436_   3429 GTAGTTACCAAATCAGCATGGTAATGGCATAAAAACAGATACATAGGCTA 3478
                         ii   v i   iv   ii     v        ii i   i i    iii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_160603436_   3479 GTGGAACAGAATAGCGAACACAGACACATAAATCCATGCATTTACAGCCA 3528
                         i     i     v v  iiv    - -     i    i      ii i  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGA-A-ATAAACCCATACATTTATGGTCA 347

  chr1_160603436_   3529 ACT-ATTTT 3536
                          i -     
  L1M4_orf2#LINE/    348 ATTGATTTT 356

Transitions / transversions = 2.64 (66 / 25)
Gap_init rate = 0.02 (7 / 356), avg. gap size = 1.29 (9 / 7)  

1675 22.98 4.39 5.26  chr1_160603436_160608327.rev     3832  4401 (491)    L1M4_orf2#LINE/L1      344   908 (0)  

  chr1_160603436_   3832 GCCAACTCATTTTTGA--ATGGTGCCAAGAACATAGAATGTGAAAAGAAC 3879
                          i   i v     i  -- v          v   vv    v i      i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_160603436_   3880 AGTCCCTTCAATAAATTGTGTTGGAAAAACTAG----CCATATGTAGAAG 3925
                             ii     i    v   i   i v    i ----   i   i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_160603436_   3926 AATGAAGCTAGATCTCTATCTCTCACCATATGCAAAATCAAACT-GAACT 3974
                                i i  i i   i   v        i     viv    -i  v 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_160603436_   3975 GGATTCAAGATTTTAATATAAGACCTGAAACTATAAAACTCCTAGAAGAA 4024
                             iv?   ii v   i     v  i              i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_160603436_   4025 ACCATTGGAA-AAGTGCTCTAAAACACTGATTTGTGCAAAGATTTTGTGT 4073
                          v   v  ?i-  i -  iiivi  vi  iv  iv    v i   iv iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_160603436_   4074 GTGTAAGACCTCAAAAGCACAGACAACCAAAGCAAAAACAGACAAATGGG 4123
                         i i --   vi          ii    v    v     i   i    v  
  L1M4_orf2#LINE/    593 ATAT--GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_160603436_   4124 ATTACATCAAGCTAAAAAAAAAAAAAAAAAAAAAAAAAACTGCTAAGC-- 4171
                          i v      --------------------  vv       vi iv  --
  L1M4_orf2#LINE/    641 ACTTCATCAA--------------------AATTAAAAACTTTTGTGCTT 670

  chr1_160603436_   4172 -AAAGTA-A--ATCAACAAAATGAAGAGACA-------GAATTGGA---A 4207
                         -    v - --     v   i    i     -------    v   --- 
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_160603436_   4208 ATATTTGCAAACTATCCATCTGGCAAAAGATTAATAACCAGAATAAATAA 4257
                                    ii  vi     ii  ii  i vi  v        v    
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_160603436_   4258 GGAACTCAAACAACTCAATAATTAAAAAAAAGAAAACAGATATTTTGACT 4307
                         i      vv             ----       ---  i   viiii i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAAT----AAAAAGA---CAAATAACCCAATT 813

  chr1_160603436_   4308 AATAAATGAGCAAAATATCTAAACAGACATTTCTCAAAAGAAGACATACA 4357
                         ? v     i     iv  i i  i           v        i     
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_160603436_   4358 AATGGCCAAAAAGTATATGAGAA-ATGTTTAATGTCACTAATCAT 4401
                                  v   i i    i  -   i i  ii   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (81 / 47)
Gap_init rate = 0.03 (15 / 565), avg. gap size = 3.67 (55 / 15)  


2489 18.41 4.49 4.64  chr1_160609965_160611599      494  1183 (452)    L1M4_orf2#LINE/L1      220   908 (0)  

  chr1_160609965_    494 CTTCCTATTTGTAAAA-TGATTACAAAGCAACTATAATCAAGACACTCTA 542
                              i v  vi    - v i        v  vi           v v i
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_160609965_    543 CCACTGGAGAAAGAATAGGCATATAAATTAATGGAAATTAATGGGATAGA 592
                         vi     viv   i    i      i  i       ----------    
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAA----------TAGA 309

  chr1_160609965_    593 ATAGAGATTCAAGAAATAAAGCCATTTACCTATAATCAGCTTATTTTAGT 642
                           v    v  v         v    vi ii   ii   ii v     v v
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_160609965_    643 CAAGGATTCTAA-ACCATCCAATGAAGAAATAATAGTTCTTTTTTACAAA 691
                              i v i  -     i     ii    v      -     iv     
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT-CTTTTCAACAAA 408

  chr1_160609965_    692 AAGTGCTGGGATAACTGCATAGCCACATGCAAAC-AGTG----------C 730
                         vi         i     v   ?           v- i  ---------- 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_160609965_    731 TTACCTCACGCCACATATAGAAATGTATACAAAATTGATCAAAGACCTAA 780
                         i        i   i   i i    vv iv      v     ?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_160609965_    781 GTGTAAAAGTGAAAACTTTAAAACTCTTAGTAGAAAACAAAGAGGTAAAC 830
                         i     i  iv      v            v        v  i?     i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_160609965_    831 CTTCATGACCTTGGGTTTTGCAAAGGATTCTTAGGTATGACACTAAAAGC 880
                             i            vv    v  v       i        i      
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_160609965_    881 TTATGCAATGACAATAACAATAACAACAAAAAAATAGG-AAATCAGACTT 929
                         ----------    --i   i  -  -i         i-    ii     
  L1M4_orf2#LINE/    609 ----------ACAA--GCAACAA-AA-GAAAAAATAGATAAATTGGACTT 644

  chr1_160609965_    930 CACCAAAGTGGAAAACTTTTCTACTTCAAAGGACACCA-CAAAAAAGTGA 978
                           i    i vi         v i             i -   i       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_160609965_    979 AAAGACAACC-AGAGAAATGAGATAAAATATTGGCACATCATGTATCTTG 1027
                                   - v    -  i  v        v   v     i     vi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_160609965_   1028 TATGTGACTTGTATCCAAAATATGTAAAGAATTCTTACTACTCAATAATA 1077
                           v v            i     i       i      v           
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_160609965_   1078 AAAAGACAA-----CCAAATCAAACATGGGTAAATCAGAT--GAATAAAT 1120
                                  -----    v ?   v     i   --i   --     i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAA--GGATTTGAATAGAC 841

  chr1_160609965_   1121 GTTTCTTCAA-GAAGCTCAACAA-----CATTAATCATCAGGAAAA--TA 1162
                         i     i   -    v vv    -----  v   v  -  v     -- i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA-CATGAAAAGATG 890

  chr1_160609965_   1163 CAAATTAAAACCACAATGAGG 1183
                          --- i  v i  ????????
  L1M4_orf2#LINE/    891 C---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (68 / 55)
Gap_init rate = 0.03 (22 / 689), avg. gap size = 2.86 (63 / 22)  


3154 25.95 2.01 0.45  chr1_160665600_160670392     3407  4300 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160665600_   3407 TGGAA---TATATTATGTTCACTGACTGTAAGAATCAATATTGTTAAAAT 3453
                              ---   vii       iv  i  v    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160665600_   3454 GTCTATACTACTCAAAGCAGTCTATAGATTCAATGAAATCCCCATTAAAA 3503
                          v v     v i    viii    i        i v      i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160665600_   3504 TATCAATGACATTCTTCACAGAAATAGATAAAATAATCTTAAAATTTATA 3553
                          vi  iivi v  i  ii       v  i  iv i   i       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_160665600_   3554 TGGAACCACAAAAGACTCAGAATACCCAAAGCTAACCTGAGCAAAAAGAA 3603
                              vii   ii   i       v     i v v i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_160665600_   3604 CACAACTGGAAGAATCACATTATCTGACTTCAAATTATACTACAAAGCTA 3653
                           v ii    i  v     i vi ii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_160665600_   3654 ACATAACCAAAATAGCATGGTGCTGGCATGAAAACAGACACATAGAGCA- 3702
                         vvi   i   i i  ii    i       i ii i     i     v  -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_160665600_   3703 --GAACAGCATAGAGAACCCAGAAACAA-TCCACGCACATACAGTGAACT 3749
                         --   i  v  v    ii       i  -i   ii  iv  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_160665600_   3750 CATTTTCAACAAAGAGGCCAAGAACATACACTGAGGATGGGACAGCTTTT 3799
                         v      i    i iv       v   v  v  i   vi i i  ii   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_160665600_   3800 TCAATAAATGGTGCTGAGAAAACTGGATGTCCATATGCAGAAGAATTGAA 3849
                             i           i  v        i?   i     i      -   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT-GAA 449

  chr1_160665600_   3850 ACTAGACCCCTATCTTTCACCATATA-GAAAATCAAATTAAA-TTTATTA 3897
                         ii i        i  iv         -i     i  v i   - vv  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_160665600_   3898 AAAACTTAGATCTAAGACCTCTGACTATGAAACTATTAAAAGAAAACATT 3947
                         ? i  i  i  v     v  vvi     i     v   i          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_160665600_   3948 TGTGAAACTTTCCAGGA--TTGGACTGGGGAAAATGTTTTTGAGTGATAA 3995
                         v ? v  v i i iv  --    ii i  v  vi-    i v  vv  i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTAGATATGA 598

  chr1_160665600_   3996 CGC-ACAAGAATAATCAACCTAAGCTAAAATGGACAGATGGAATTACGTC 4044
                          i - v   v i  v    vv   vv     i  i i  v i i v i  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_160665600_   4045 AAG-TTAAAAAGCTTTG-GC---AAAGCAAACAAATAA-AAAGTGAAGAG 4088
                           i-       vi    -  ---    v v  v vi  -        i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_160665600_   4089 ACAACCCACAGAATGGGAGAAAATATTTGCAAACTATGCATATGACAAGG 4138
                                                          ii  ii  v   i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_160665600_   4139 GATTAATAACCAGAATATATATAAGTAGTCTAAACAATTCAATAGGAAAA 4188
                           i vi  v            -   v v   v -   i      iv    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATA-AAGAACTCTTA-CAACTCAATAATAAAA 796

  chr1_160665600_   4189 AAACTAATAATCTGATTTAAAAATAGGCAAAGAATCCAAATAGATATTTC 4238
                          i  v     i ii   ?      i       i  iii      i     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_160665600_   4239 TCAAAAGAAGACATACAAATGGCAAACAGATATATGAAAAAATCCTTCAC 4288
                           v        i           v  i iii i       i  v  iv  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_160665600_   4289 ATTATTGATCAT 4300
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (145 / 83)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.47 (22 / 15)  


2653 25.35 3.26 4.46  chr1_160701009_160704282     1863  2781 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160701009_   1863 TGCAGAAATATTTTATGCTCATTAATGGGAAGAATTAATATTGTTAAAAT 1912
                           v i i    iii   i    vi  v      v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160701009_   1913 GGCCACACTACCCAAAGCAATTTACAGATTCAATGCTATTCTTATCAAAC 1962
                            v i   v      vii  i           i  v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160701009_   1963 TATCAACATCATTTTTCACAGAATTAGAAAATACT-ATTCTAAAGTTCAT 2011
                          vi  i vv v     ii     v v  v  -i  -  i     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_160701009_   2012 ATGGAA---TAAATAACCT-GAATTGCCAGAAAAAAAAATCTACTCAAAA 2057
                               ---i  ivi   i-    v    ----   v     -- v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCA----AAACAATCT--TGAAAA 193

  chr1_160701009_   2058 AGAA---TCAAGCCAGAGGTATCACACTACCTAACTTCAAACTATACTAC 2104
                             ---iv   iii    vv       v  i  i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_160701009_   2105 AAGGCTATAGTAACCAAAACAGCATGGTACTGGCACAAAAACAGACACAT 2154
                           i    i     i   i    ii           i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_160701009_   2155 AGACCAATGGAACGGA-TAGAGGACCCAGAAATAAAGTCACACACTTACA 2203
                            i        ii  - v   iii           vi  i   i   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_160701009_   2204 ACCACCTTATCTTTGACAAAGTTGACAATAAAAAATAATGAAGGAAGCAC 2253
                         ii  vi v  i  i     i v  v   v vv vvi    ii i   v i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_160701009_   2254 TCCCTATTCAATAAACGGTGCTGGGAAAA-TGGCTAGACATCTGCAGAAG 2302
                         vvi  v     i   i          v  -   v  ?v  iv    i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_160701009_   2303 ATTGAAACTGGACTGCTTCTTTTCACCATATACAAAAATTAACTCAAAAT 2352
                          v    ii     iv  v i iv                           
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_160701009_   2353 GGATTAAAGACTTGAA-------------ACAATAAAAACTCT-AGAAGA 2388
                             i ?    i i  -------------  v      -    -      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGA 542

  chr1_160701009_   2389 AAACCTAGGAAATACTATTCCAGACATTGGCCTTGGCAAAGAATTTATGA 2438
                             v    ?ivv v v   vv   v    vi v     v iv  iv ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_160701009_   2439 CTGAGTCCTCAAAAGCA-ATGCAACAAAAACAAAAATTGGTAAGTAGGAC 2487
                         v iv v vi        - v         iv      v i   i v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_160701009_   2488 CTAATTAAACTCACGAGCTTCTGCACAGCAAAACAACAACAACAACAAAA 2537
                         i v  i   v i vi i   i  ii vv    i-----------------
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAG----------------- 675

  chr1_160701009_   2538 ACAAACAAACAAACAAAAAACTATCAACAGAGTAAACTGACAACCTACAG 2587
                         -----------i   -----       v i   i  vv       i    
  L1M4_orf2#LINE/    676 -----------GACA-----CTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_160701009_   2588 AATGGGAGAAAATATTTACAAACTATGCATCTGACACAGGTCTGATATCC 2637
                                          i    ii  ii      i vi  v  vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_160701009_   2638 AGAATCCATAAGGAACTT----AAATCAGCAAGCAGAAAGCAAATAAACT 2683
                              vi    i     i----  v   ii  vv i  ii       v i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_160701009_   2684 TATTATAAAATGAGCTAAGGACATGAACAGACACTTCTCAAAATAAGACA 2733
                         v   ?v      i  v     iv    i     i     v   v    i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_160701009_   2734 TACGTGTGGCCAACAAATATATGAAA-TATACTCAGAATCACAAATCAT 2781
                            ivi       i  ii i      -v  i    iv    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (133 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.18 (71 / 17)  


2488 21.06 1.22 15.26  chr1_160768159_160772954.rev     2975  3957 (839)    L1M4_orf2#LINE/L1        4   848 (60)  

  chr1_160768159_   2975 AGAAACATTCCATGTTCATGGGTTGAAAAAATTAATATTGTTAAAATGTC 3024
                          i i i  i            i   i  i v             i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_160768159_   3025 TATGCTACCTAAGA-AAGCTATAGATTTAATGCAACCCCTATCAAAATAC 3073
                         v  i  v  i  iv-i v   i     i  i    i            v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_160768159_   3074 CAATGACATTCTTTACAGAAATAGAAAAAAAAATCCTAAAATGTATGTGG 3123
                           iivi v  i   i       -------------------------  -
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAAT-------------------------TG- 127

  chr1_160768159_   3124 AACCACAAAAGATCCAGAATAGCCAAAGATATCCTGAGTAAAAAAACAAG 3173
                         ----    i------------------------    -------------
  L1M4_orf2#LINE/    128 ----ACAAG------------------------CTGA------------- 136

  chr1_160768159_   3174 AAAAACAAACAACAACAAAAAATCCTAAAATGTATATGGAGCCACAAAAG 3223
                         ----------------------         vi       ivii   ii 
  L1M4_orf2#LINE/    137 ----------------------TCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_160768159_   3224 ATCTGGAATAGCCAAAGCTATCCTGAGCAGAAAAACAAGAACAACAAACA 3273
                          i ii           i v   i   -----    v        ------
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGA-----AAAAGAAGAACAA------ 203

  chr1_160768159_   3274 AACTAACTAAAAAACAACACCCCCCCTCTTCCCTTCCAAAGAAAACTGGA 3323
                         ------------------------------------------- ii    
  L1M4_orf2#LINE/    204 -------------------------------------------AGTTGGA 210

  chr1_160768159_   3324 GAAATCACATTACCTGACTTCAAATTCTACTACAGAGCTATAGTGACCAA 3373
                          i v     i v  ii i      vii       i     i   i i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr1_160768159_   3374 AACAGCATGGTACTGGCATAAAAATAGACACACAGCCCAATAGAACAGAA 3423
                         i    ii              ii       i i  vi    i   i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_160768159_   3424 TTCAGAACCCAGAAACAAATCCACACACCTATAGTGAACTCATTTTTGAC 3473
                           v   ii       i   i   i   ii   i  v  i v     i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr1_160768159_   3474 AAAGATGCCAAGAACATACATTGGGGAAAAGACAGTCTCTTCAATAAATG 3523
                           i i        v   v  v        ii i     i     i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_160768159_   3524 GGACTGGGAAAACTAGATATTCATATGCAGACGAATAAAACTAGATCCCT 3573
                          vi      v    i    ?i  i     i v    i  ii i  i    
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_160768159_   3574 --CTCAC--CATATACAAAAATCAAATCAAAATTGATTAAACATTTACAT 3619
                         --     --             i  v       v   i ? v ii  v  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_160768159_   3620 TTAAGACCTCAAACTATGAAAATAATACTATAAAACATCAAGGAAACTAT 3669
                         v     v  v       i   v vv  vv v       vii? v  v v 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_160768159_   3670 CCAGGTCATTGGTCTGTGCAAAGATTTCTTGAGCAGTACACCACAAGCAC 3719
                         i iv v v    vi iv    v i      iiii vv      v      
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_160768159_   3720 AGGTAACCAAAGCAAAAATAAACAAATGAGATCACATCAAG-TTAAAAAA 3768
                          i i   v    v       i i    vi  iiv      i-       -
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA- 659

  chr1_160768159_   3769 GTTTCTGCACAGCAAAGGAAACAATCAACAAAATGAAGAGACTACTCACA 3818
                         -i  i  ii vv       v  v     v   i    i    v  i    
  L1M4_orf2#LINE/    660 -CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_160768159_   3819 GAATGGGAGAAAATATTTGCAAACTACTTCTCTGACAAGGGATTAATAAC 3868
                                                ii iv v     i      i vi  v 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_160768159_   3869 CAGAATATATACGGAGTTCAAATATCTC-----TAAAGGGAAAAATCTCA 3913
                                    vi  ii  vv i v   -----    ii  v    ----
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT---- 804

  chr1_160768159_   3914 CAATCTAAT-AAAAAATGGGCAAAAGATCTGCACAGACATTTCTC 3957
                         -  i i   -?             i   i  v i           
  L1M4_orf2#LINE/    805 -AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

Transitions / transversions = 1.82 (131 / 72)
Gap_init rate = 0.02 (14 / 845), avg. gap size = 11.57 (162 / 14)  

 356 16.18 0.00 0.00  chr1_160768159_160772954.rev     4238  4305 (491)    L1M4_orf2#LINE/L1      841   908 (0)  

  chr1_160768159_   4238 CATTTCTTAAAAGAAGGCACACAAATGGCAAATAGGCATGTGAAAAGCTG 4287
                                iv       ii i         v    i   ii       v  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_160768159_   4288 CTCAACACCATTGATCAT 4305
                                i  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.00 (0 / 0)  


3175 26.73 2.13 0.56  chr1_160867674_160872735     3676  4569 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160867674_   3676 TAGAAGAACATTCCATGCTCATGTATAGGAAGAATCAGTATCATGAAAAT 3725
                          i   ii i  i     i     v  v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160867674_   3726 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3775
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160867674_   3776 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTAA 3823
                          v   iivi i  i  ii     -   -- v  i  - iii    i  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_160867674_   3824 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 3873
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_160867674_   3874 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3923
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_160867674_   3924 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3973
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_160867674_   3974 AATGGAACAGAACAGAGACCTCACAAATTAACACCACACATCCACAACCA 4023
                                i    iv    vii  v    v   -   i    ii iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTTATGGTCA 347

  chr1_160867674_   4024 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 4073
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_160867674_   4074 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGAAAGCTG 4123
                          v  i  i              v      v  ?  ii   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_160867674_   4124 AAACTAGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 4173
                           ii i  i i  v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_160867674_   4174 TAAAGACTTAGATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4223
                         i ?    i  i    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_160867674_   4224 CAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGACTA 4271
                         i   ?i- v i -   i- i  v i  i- i     v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr1_160867674_   4272 AAATACCAAAAGCAATGGCAACAAAAACCAAAATAGACAAATGGGATCTA 4321
                         vi i          vvi         ivv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_160867674_   4322 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCTTTAGAGTGAA 4371
                           i   v i  i i   i  ii vv    i  v    i vvv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_160867674_   4372 CAGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTACCCATCTGACA 4421
                         v  i     i              v  v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_160867674_   4422 AAGGGCTAATATCCAGAATCTACAAAGAACT---------------TAAA 4456
                          i  i  vi          v  i        ---------------    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_160867674_   4457 AAAACAGACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAGTT 4506
                           i   i i     v  i?    i            v    i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_160867674_   4507 CTCAAAAGAAGACATTTATACAGCCAACAGACACATTAAAAAATGCTCAT 4556
                            v        i  vi v ii     i ii     v    i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_160867674_   4557 CATCACTGGCCAT 4569
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (149 / 86)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  


3290 27.01 0.55 0.44  chr1_160916417_160922830     5015  5921 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160916417_   5015 TGGGAGGACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5064
                            i i  i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160916417_   5065 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGT 5114
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160916417_   5115 GACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5162
                         vv   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_160916417_   5163 TGTGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5212
                          i     viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_160916417_   5213 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5262
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_160916417_   5263 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5312
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_160916417_   5313 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5360
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_160916417_   5361 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5410
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_160916417_   5411 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 5460
                           v  i  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_160916417_   5461 GAAACTGGATCCCTTCCTTATGCCTTATACAAAAATCAATTCAAGATGGA 5510
                            ii    i    v   i ii  v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_160916417_   5511 TTAAAGACTTAAACGTT-GACCTAAAACCATAAAAACCCTAGAAGAAAAC 5559
                          i ?    i    i  v-  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_160916417_   5560 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5609
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_160916417_   5610 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTCA 5659
                         i            vvi           v     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_160916417_   5660 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAG 5709
                          i   v v  i i   i  ii vv    i  v    i  vv i      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_160916417_   5710 AAGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCCTCTGACAA 5759
                          ii     i   i             v  ii   vii iviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_160916417_   5760 AGGGCTAATATCCAGAATCTACAATGAACTCAGACAAATTTACAAGAAAA 5809
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_160916417_   5810 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5859
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_160916417_   5860 TCAAAAGAAGACATTTATGCAGCCAACAAACACATGAAAAAATGCTCACC 5909
                           v        i  vi viii     i  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_160916417_   5910 ATCACTGGCCAT 5921
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2437 27.05 4.79 1.14  chr1_160923079_160925333      887  1762 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160923079_    887 TGGAAACACATCCCATGCAGGTGGATAGGTAGAATTAATATTGTGAAAAT 936
                               v i        ivvi     v  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160923079_    937 GACCATACTGCCAAAAGCAAACTGCAGATTCAATGTAATACCCATTGAAA 986
                          i v     v  v   vii v  i         i i   v  i  ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160923079_    987 TACCATCATCATTCTTCACAGAACTAGAAAAAAAAAATTCTAAAGTTCAT 1036
                          v   v vv v  i  ii     v v  v  ivvi - i     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_160923079_   1037 ATGGAACCAAAAAAGAACCCACACAACCAAAGCAATACTAAGCAACAGGA 1086
                               viiv  ii  v  viv i i     i    vi i iv  v i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_160923079_   1087 ACAAATCTGGAGGCATCAGATTACTCAACTTCAAATTATACTACAAGGCT 1136
                              vi      vv   v i v i   i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_160923079_   1137 ----TAA-----------------------AAAAATAGGCACTTAGACAA 1159
                         ----   -----------------------  ii    i  iv    iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_160923079_   1160 ATAGAAAAGAATAAAGAACCCAAAAGTGAAGCCAAATACTTACAGCCAAC 1209
                           i   v     vi   ii   i  i i  v   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_160923079_   1210 TTATCTTTGACAAAGCATAC-AAAACC-TTAAAGTGGGGAAAGGAGACCC 1257
                          v  i  i     i -i i -  i   -  v  -         i v vi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAA-TGGGGAAAGAATAGTC 397

  chr1_160923079_   1258 TATTCAATAAATGGTGCTGGGATAACTGCCAAGCCACATATAGAAGAATG 1307
                          v     i              i     vvv ?      ii i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_160923079_   1308 AAACTAGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGAAT 1357
                           ii i  i  ii i   v    v           i       i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_160923079_   1358 CAAAGGCTTAAATTTAAGACCTGAAACCATAAAAATCCTAGAAGATAACA 1407
                           ?  i i     v     v  i    i      v  i       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_160923079_   1408 T---CATAAAAACTCTTCTAGACATTGGCTTTGGCAAAGAATTC--AGGA 1452
                          ---?i    ---     vv   v    v  v     v iv   --  i-
  L1M4_orf2#LINE/    548 TAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA- 593

  chr1_160923079_   1453 CTAAGAACCCAAAAGCA-----AATAAAACAAAAA-TAAATAAAT-GGAC 1495
                         -  v  vv         -----  i    v     -  i      -    
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_160923079_   1496 CTAATTAAACTAAAAATCTTCTGCACAGCAAAAGAAATAATTAGCTGAGT 1545
                         i v  i   v v    v   i  ii vv    i  v iv  i ivvi   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_160923079_   1546 AAACAGGCAACTCAGAGAG-GGGAGAAAATCTACACAAACTGTGCATCCA 1594
                         i  v  i    i  v   i-          v vii    iii ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_160923079_   1595 ACAAAGGACTAATATTCAGAATCTACAAGGAACTCAAACAAATCAGCAAG 1644
                          i  i     vi   i      v  i  i      vv    v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_160923079_   1645 ATAAAAACAAATAATCCCATTGAAAAGTGGGCAAAAGACATGAATAGTCA 1694
                          v   i        i  v   ?    i        i  iv       v  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_160923079_   1695 ATTCTCAAAAGAAGATATACAAACAACCGACACACATAGGGAAAAAAATG 1744
                         v     v                iii  i i vi  i v --    i   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG--AAAAGATG 890

  chr1_160923079_   1745 TTCATCTTCAGTAGTTTT 1762
                         i   v v   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (134 / 99)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.25 (52 / 16)  


4254 19.76 1.21 0.99  chr1_160966450_160968409      562  1467 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160966450_    562 TAGAAAAACTTCCTGTGTTCATGGATAATAAAACCTAATATTGGTAAGAT 611
                          i    i iv   ii           viv  i  i        v      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160966450_    612 GTTAATGCTACCCAAAGTAATCTACAGATTCAGTGTAATCTTTATCAAAA 661
                          vi   i  v      v i             ii i    ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160966450_    662 TTCTAACAGCCATTTTTGCATATATGAAAAAGTCAATCCTTAAATTCATA 711
                          i i i v   v        v v  vi v   iii     v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_160966450_    712 AGGAACTGAAAGGTGCTCTGAATAGTCAAAACAATATTGAAAAAAGAAAA 761
                         v    v  v    vi i v      i         v        ii i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_160966450_    762 CAAAGTTGGGGATCTCATCCTTCCCAATTTCGCAACTTACTCCAAAGCTA 811
                                  i iv    iv            iv        v        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_160966450_    812 CAGTACATAAGCCAGTGTAGTACTGACATTAAGAAAGATATATAGACCAA 861
                              vvi   v      i      i   v i  v   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_160966450_    862 TGGAAGGAAATTGAGAGTTATATATGGAATATAAACCAATGTATCTATAA 911
                              vii          i-----ii   -       v  ii  i   ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-----CAGAA-ATAAACCCATACATTTATGG 344

  chr1_160966450_    912 CTAATTGATTTTTGACAAAAGTGATGAGTTCATTCAATGGGGAAAGAAGA 961
                         ii          i     ii   vii  vi                  v 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_160966450_    962 GTCTCTTCAACAAA-GGTACTGGGACAAATGGATTTTCAT-CACATGAAA 1009
                             i         -   i         v     v?i  i-ii  vi i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_160966450_   1010 ACAGAGTTGAATCCTTAGTTCACAGCATATACAAAAAAATTAATTCAAAG 1059
                          iii     i i  i  vi     v            --    i     -
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAA- 491

  chr1_160966450_   1060 ATGGATCAACGGCTGAAATATAAGAGCTAAAACCACAACATGATTAAAAG 1109
                                 ?v i iv    i             i i  v ivv   i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_160966450_   1110 AAAACC--AAAGTAAATCTTCATTACCTTAGATTTGGTAATGAAGACTTA 1157
                              v--ii?          i v     i i  v  i    ivvv    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_160966450_   1158 GATATAACACCAAAAGCATGAGCAATGAAAGGAAAAATATATAAATTGAA 1207
                              i            ii     ii    i       v        i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_160966450_   1208 CTTCATCAAAATTAAGAACTTTTATGCATCAAAGGACACTATCAAGAAAG 1257
                                        i       i   v                      
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_160966450_   1258 TGAAAAGATAGCCTTTAGAAAGGGAGAAAGTATTTGCAAATAATATATGT 1307
                                 i i  ivi    v        i           v      v 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_160966450_   1308 --TAAGGGTTTAATATCCGGAATATATAAAGAACTCCTACAACTCAACAA 1355
                         --      vi vi     i                 i          i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_160966450_   1356 CACAA-GACAAAAAAA--AATTTAAA--TAGGTAAAGGACTTAAATAGAC 1400
                         i v  -      v  v--    ?   -- i  i      i  i       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_160966450_   1401 ATTTCTCCCAAGAAGATATACAAATAGCCAATAAGCACATGAAAAGATGT 1450
                                 v                i                       i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_160966450_   1451 TCAACATCATCAATCAT 1467
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (113 / 62)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


2252 19.51 3.43 17.03  chr1_160974453_160976635      640  1690 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160974453_    640 TGGAAAGATATCT-GTGATAATGAGTCAGAA---TTCATATTGTTTAAGT 685
                                     i-i  v v   ii ii   ---  v        v ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160974453_    686 ATTCATACTACCCAAAGTAGTCTATAGATTCCATGCAATCCCTCTCAAAA 735
                         iviv     v      v ii    i      v i         v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160974453_    736 TTTAAATGGCATTTTT--CACAAATAGAGAAAAAAGTTCTAAAATTCATG 783
                          iiv iiv  v     --  v    v  v  ivvii i           i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_160974453_    784 TAAAACTACAAAAGACTCCAAAATAGCCAAAGTAATCTTGAGTTAAAAAC 833
                          ii  v i   ii   -   i          ii        ---------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGA--------- 190

  chr1_160974453_    834 AAAAAAAAAAAGCTGGCGGCATCACATTACTTAATTTAAAATGATATTAC 883
                         -    i  i  -------------------------------------- 
  L1M4_orf2#LINE/    191 -AAAAGAAGAA--------------------------------------C 201

  chr1_160974453_    884 AAAGACTACAAATTGGGTTCAGTGTATATTGCTCGAGTGATGGGTGCACC 933
                             --------    ----------------------------------
  L1M4_orf2#LINE/    202 AAAG--------TTGG---------------------------------- 209

  chr1_160974453_    934 AAAATCTCACAACTCACCACTGAAGAACTTACTGATGTAACCAAATACCA 983
                         -----------------------  i   i  ----------------- 
  L1M4_orf2#LINE/    210 -----------------------AGGACTCAC-----------------A 219

  chr1_160974453_    984 CCTGTTCCCCAAAAACATATAGAAATTTAAAAAAAGTTTTAATTATATTA 1033
                          ---     --------------     v    ----i   ------i  
  L1M4_orf2#LINE/    220 C---TTCCC--------------AATTTCAAAA----CTTA------CTA 242

  chr1_160974453_   1034 CAAAGCTATAGTAGTAATCAAAACAGCATAGTGCCAGCCTAAAAACTGAT 1083
                                 i    ---     i    ii i  i ii  v   ii iv  i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTA---ATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_160974453_   1084 ATACTGACCAATGGAGCAGAATAGAGAGTCCAGAAATAAACTCACACAAA 1133
                            iv  i       ii     v                  i  i   vv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_160974453_   1134 CAAAATTAACTAATATCTGACCAGGGTGCCAAGAATACACAATGGTGAAA 1183
                         i vii i  i i  v ii   v            vi iv      v    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_160974453_   1184 GAATAGTCTCTTCACTAAATGGTGTTGGGAAAACTGAATAACCACTTGCA 1233
                                  i    vi        i     v     i   ?    v    
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_160974453_   1234 AAACAATAAAATTGGATCCCT----TATACCATTCAAAAAAAT-AATTTG 1278
                            v   i  i     i    ----i i     vi v      -  i ii
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_160974453_   1279 AAATGGTTTAAGGACCAAGAATTTAAGACCTAAAGCCATAAAACTCTTAG 1328
                               v i ?i    v -   v     v     i i             
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTA-AATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_160974453_   1329 AAAAAAAAAAAAAAAACACATAGAAG-----CTCATTAACATTTGTCTTA 1373
                           i    -----------     i? -----  ivv i  -i   vv   
  L1M4_orf2#LINE/    539 AAGAAAA-----------CATAGGNGTAAATCTTCGTGAC-CTTGGGTTA 576

  chr1_160974453_   1374 G-CAGTGATTTTTTTGGGGGTATAACACCAAA-GTACAAGCAACCAAAAA 1421
                          -  i  i   i  ---i i   i        - i         v   i 
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTT---AGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_160974453_   1422 ---------TAAACTGAGACTACATCAAACTAAAAAGATTCTGCACTAAC 1462
                         ---------    i  -    v       v v    iv  i  ii  v- 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTG-GACTTCATCAAAATTAAAAACTTTTGTGCTT-C 671

  chr1_160974453_   1463 AAAGGAAATAATCAACAAAATGAAAAGTCAACCTACAGAAGGGGAGAAAA 1512
                               v iv     v   i       v     i      v         
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_160974453_   1513 TATTCTCAAATCATACATCTAATAAAGGGTTAATACTCAAACTATA-AAG 1561
                             iv         i    i    i  ii vi  ii  i v    -  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_160974453_   1562 GAACTCCTATAACTCAATAGCAAACAAATAAGTAATTTG-TTTAAAAA-- 1608
                               i  i         ii   v i i  i   iiii-  ?     --
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_160974453_   1609 -----AGGATCTGAATAGACAATTTTCCCAGGAAGACATACAAATGAACC 1653
                         -----     i          v  i   v i     i         iv v
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_160974453_   1654 ACAGGTACATTAAAAGGTGCTCAACGTCACTAATTAT 1690
                          i i i    v     i        i   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (135 / 66)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 7.41 (215 / 29)  


2785 25.68 4.00 0.34  chr1_160977733_160981237     2137  3012 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_160977733_   2137 TGGAAAAACATTTCATGCTCATGGATTGGAAGAATCAATATTGTTAAAAT 2186
                               i i  ii    i               v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_160977733_   2187 TTCCATACTGCTCAAAGGAATCTACAGATTCAATGCAATCCTTATCAAAT 2236
                         vv v     v i    vvi              i       i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_160977733_   2237 TACCAACATCATTCTTCATA-AAATTGGAAAACAAATTCTAAAATTCATA 2285
                          v   i vv v  i  iii -      iv  i vi  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_160977733_   2286 TGGAAC--CAAAAGAGCTCGACTAGCCAAAGCTATCCTAAGCAA-AAGAA 2332
                              v--   ii  v iv  v        i v   i i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_160977733_   2333 CAAATATGGAGGCATCACATTACTCAACTTCAAGCTACACTACAAAGCTA 2382
                             vv      vv     i v i   i     ivivi            
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_160977733_   2383 CAGTTACCAAAACAGCATGGTACTTGTGCA-AAAAATAAATGCAGAGACC 2431
                             v i   i    ii       - -   -  ii   i iii v   i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACT-G-GCATAAGGATAGACATATAGATC 298

  chr1_160977733_   2432 AATGGAACAGAATAAGGAACTCAGAAAATAAGCCACACATCTACGAACAG 2481
                                i     vii  iii      vv  v   i    i  i iv  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_160977733_   2482 CTTATCTTTGCCAAAGCTGACAAAAGTAAACAATGGGGAAAGCCAACTCT 2531
                         i v  i  i v   i v  v   i vi vv            vvv v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_160977733_   2532 ATTCACTAAATGTTGCTAGAAAAACTGGCTAACCATGTGCAGAAGAATGA 2581
                         v    vi     v    i i v      v  ?   ii    i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_160977733_   2582 AACTGAACCCCTACCTCTAACCATATACAAAAATTAACTCAAGATGGATT 2631
                          ii  i           vv                       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_160977733_   2632 AAAGACTTAAATTTAAGACCTCAAATTCTAAAAATCTTACAAGAAAACA- 2680
                          ?    i     v     v  v   i v     v     v         -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_160977733_   2681 GGAAATAC-TCTTCTGGACATTGGCCTAGGCAAAGAATTTATGACTAAGT 2729
                         i i?i  v-     vv   v    vi       v iv  iv iiv  v v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_160977733_   2730 CCTCATA-GCAAATGTAACAATA----AAACTGACAAATGGGATCTAATT 2774
                          vi  v -   v v i     v ----   iv  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_160977733_   2775 AAGCCAAAGAGCTTCTGCACAGCAAAAGAAACTATCAGCAGAGTAAA--- 2821
                           iviv  i i   i  ii vv    i  v       iv i   i  ---
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_160977733_   2822 -CAACCTACAGAAAGGGAGAAAATATTTGCAAACTATGGATCTGACAAAG 2870
                         -     i      v                   ii  iv      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_160977733_   2871 GCCTAATACCCAGACTCTACAG-GAACTT----AAATCAA---------- 2905
                          v  vi  i     v v  i i-     i----  v    ----------
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_160977733_   2906 -CCAACAACCCCAATAAAAAGAGGGCAAAGTACGTGAACAGAAACTTCTC 2954
                         - v  i     v v ?    iv        v iv    i   v i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_160977733_   2955 AAAAAAAAGACATACAAGTGGCCAAAAA--ACATGAAAA-ATGGTCATCA 3001
                         v   i  -  i      i       v  --         -   v   v  
  L1M4_orf2#LINE/    849 CAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_160977733_   3002 ACACTAATCAC 3012
                         v  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.17 (119 / 102)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  


2940 24.25 3.58 2.35  chr1_161052688_161057049     2975  3869 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_161052688_   2975 GAAAAA-AGTCCATATTTATAGACAGGAACCATTAATAGTATTAAAATAT 3023
                             i - vi    i  i  i  iv    vvv      v i    i  iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_161052688_   3024 TCATAATATACAAAGTGATTTA--------ATACAACCCCTATTAAAGTT 3065
                         iv   v viv    v    i  -------- ii   i      i   i i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_161052688_   3066 TAAAATGGCATTTTTTACAGAAATAGAAAAAATAATAATCTTAAAATTCA 3115
                         iv iv  v -      i       v  v  iv i  --- i         
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGAT---CCTAAAATTCA 148

  chr1_161052688_   3116 TATGAAACCACAAAAAA---AAACTGTTATAGCCAAAGCAATCTTGAGTA 3162
                             i  vii   iii --- i -----         i         iv 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGA-----ATAGCCAAAACAATCTTGAAAA 193

  chr1_161052688_   3163 AAAAGAACACAGCTGGAGGCATTACACT----AATTTCAAAATATAGTAC 3208
                          i       v  i      vv i     ----          iv  v   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_161052688_   3209 AAAGCTATAGTAATCAGAACACTATGCGACTGACATAAAAATAGACATAT 3258
                                i        ii   v i  vv    i     ii          
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_161052688_   3259 ACACCAATGGAACAGAATAGAGAGCCCAGAAGTAAATCCACATATTTACA 3308
                          v i        i     v     i      i    i   i i     ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_161052688_   3309 GACAATTGACCTTCATAAAAAGGTGCCAAGATTACACAATACAGAAAGGA 3358
                          v       ii   i- v  i          ii iv    ivi     i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_161052688_   3359 CGGTCTCCTAAATAAATGTTGTTGTGAAAACTAGATATACACATACAGAA 3408
                         ii    ii v  i     v  i  v  v    i    ?v     i  i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_161052688_   3409 GAATGAAAGTAAAC----ACTT-ATACCATGTACAAAAATTAACTCAAAA 3453
                                iv ii  ----  i - i     i                   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_161052688_   3454 TACATTAACGGTTTCAATGTAAGACATAAAACTATAATATTCCCTGAAAA 3503
                          iv  i ?v iii v         vv           v i  iiv   i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_161052688_   3504 AAACATAGAAGAAAAGTTTCTTGATATTGACCTGGGAAATGATTTTTTAA 3553
                                 i? v   vi   v   iv   ivi i  v    i   i   i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_161052688_   3554 AAATATATAACCCTAAAAGCACAGGAGACAAAAGCAAAATTATACAAATA 3603
                          ----   i  v i         i vi       v    v  v i    v
  L1M4_orf2#LINE/    593 A----TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_161052688_   3604 TGATTGCATCAAATTTAGAAGCTT-----CTTCACAGGAAAGAAAAAAAA 3648
                         v  i v       v   i  i   -----     v    v vv vv  i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_161052688_   3649 CAGATTAAAGAGACAACCTATGGAA-GGGGGAAATGATATTTTCAAACCA 3697
                         v  -- i  i        i ii   -   i    --      v    i  
  L1M4_orf2#LINE/    689 AAG--TGAAAAGACAACCCACAGAATGGGAGAAA--ATATTTGCAAATCA 734

  chr1_161052688_   3698 TAAATTTGATAAAGAGTTAATATCCAAAATATATTAGGAACTC----AAC 3743
                           v  i      i iii vi      i       v i      ----   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_161052688_   3744 TCAATAGCAAAAAGACAAATAACCTAATTAAAGAATGAGCAAAGGACCTG 3793
                               ii                i    ?  i    i        ii  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_161052688_   3794 A-TAGACATTTCTCAAAAGAAGACATATAAATGGTCATTTATGGGTATAT 3842
                          -            v        i   i      i  ---  ii i i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCA---ATAAGCACAT 881

  chr1_161052688_   3843 GAAAAAATGTTTCATATCACTACTCAA 3869
                              i   i iv i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (138 / 75)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 2.94 (53 / 18)  


 638 23.08 8.65 1.92  chr1_161108773_161112821.rev     2359  2566 (1483)    L1M4_orf2#LINE/L1        1   222 (686)  

  chr1_161108773_   2359 TGGAAACACACCTCATGTTCATGAATTAGAAAGTTTA-TAT--------- 2398
                               v i i i          i   i   iii   -   ---------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_161108773_   2399 --CAATACTACTCAAAGTAGTCTAAAGATTCACTGCAATCACTGTCAAAA 2446
                         --       v i    v ii    v       vi      v  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_161108773_   2447 TCCCAAA-GACTTTTTTTCAGAAAT-AAAAAATCCATGCTAACAGTTATA 2494
                              iv- v       v       -i v  iiiv  v    v v i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_161108773_   2495 TGGAATCTCAAGAAAAACTGAATAGCCAAA-CAATCTCAGAAAACAA--- 2540
                              viv    ii vv v           -      iii    v  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_161108773_   2541 CAAAGCTGGCTGGATAACTCACACTT 2566
                              i   ---- vi          
  L1M4_orf2#LINE/    201 CAAAGTTGG----AGGACTCACACTT 222

Transitions / transversions = 1.29 (27 / 21)
Gap_init rate = 0.03 (7 / 222), avg. gap size = 3.14 (22 / 7)  

2751 20.86 1.71 2.29  chr1_161108773_161112821.rev     2864  3563 (486)    L1M4_orf2#LINE/L1      213   908 (0)  

  chr1_161108773_   2864 ACTCACACTTCTTAATTTCAAAACTTACTCCAAAGCT---GTAATGAAAA 2910
                                    ii                v       ---     v  i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_161108773_   2911 AAGTGTCATGCTAGCATAGACATTAGACACAAATAGACAGATGGAATAGT 2960
                         v     vi i  i     iiv  -     i --    ivi         v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGAT-AGACATA--TAGATCAATGGAATAGA 309

  chr1_161108773_   2961 GTGGGGAGACCAAAAACAAACCCTTACATACGTGATCAAATGATTTTTGA 3010
                         i v i   v   i   i      v     vii  i    v       i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_161108773_   3011 TAAAGGTGCCAAG--CATTAAATGGGGAAGGA-CAGACTTTTCACAAAAT 3057
                         i  i         --    v         i  -i  v       vv    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_161108773_   3058 GGTACTGGCAAAACTGGATATCCACATACATAAGAATAAAATTGGACCTT 3107
                            i    v v         ?      i  v      i  i       ii
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_161108773_   3108 TATCTAATACCATATATAAAAAG-AATTCAAAATGTATCAAAGACCTTAA 3156
                           i  v i        i     v-  i        v    ?      v  
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_161108773_   3157 TGTAATACCTAAAATTATAAAACTCCTAGAAGAAA-CATAGGACAAAAAC 3205
                              v v      i          i         -      ?vv   v 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_161108773_   3206 TTTACAACATTGGATTTGGAATTGATTTCTTGAAGATGGCACCAAAGGTA 3255
                           iiii  v    i  v  v v  i      ii v   i       i i 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_161108773_   3256 CAGGCAACAACAACAAAAAAAATAGACATATTAGACTGTGTGAAAATTGA 3305
                           --- i      v i          i v   i    vii v      i 
  L1M4_orf2#LINE/    610 CA---AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_161108773_   3306 AAAAATTTGTGCATCAAAACACAATATCAATAGAGTAAAAAGGCAATCCA 3355
                            vv       v     iv   v      v i   i     i   i   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_161108773_   3356 TAGAATGTGAGAAAATAGCTGGAAAATCATATATACGATAAAAGAATGAT 3405
                         i      v         vi  v   -        vi     ii  v vi 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATAAGGGACTTGT 755

  chr1_161108773_   3406 ATCCAGAATATATAAAGAACTCCTAAAATCCAACAACAACAACAACAACA 3455
                                               i  --------    v-   i  i  v 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTA--------CAACT-CAATAATAAAA 796

  chr1_161108773_   3456 AAACAAACAACCCAATTAAAATATGGTTGAAACACTTGACCAGAGATTTC 3505
                          i     i         ?   v    vii  iv i    vi   v     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_161108773_   3506 TCTAAAGA---TCTACAAATAACCAATGGGCTCATCAAAGAATGCTTAG- 3551
                           i     --- v       ii     ii  v   v   ii     i i-
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_161108773_   3552 ATCACTAATCAG 3563
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (83 / 59)
Gap_init rate = 0.02 (13 / 696), avg. gap size = 2.15 (28 / 13)  


 678 16.78 0.00 0.00  chr1_161159599_161165896      323   465 (5833)    L1M4_orf2#LINE/L1      766   908 (0)  

  chr1_161159599_    323 TAAAAGGAACACTTATAACTCAATAATAAAAAGATAAATAACCCAATTGT 372
                           v  i    v    i                  i             ?v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_161159599_    373 AAAATGGACACAGGATCTGAAGAGATAGTTCTCTAAAGAAGACACACGAA 422
                                i  v     i    v   i v     i        i i  i  
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_161159599_    423 TGTCCAATAACCACATTGAAATATGGTCAGCATCATTAGAAAA 465
                           v       v     vi   v   v   i     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (12 / 11)
Gap_init rate = 0.00 (0 / 143), avg. gap size = 0.00 (0 / 0)  

3405 25.66 0.55 0.55  chr1_161159599_161165896     4898  5805 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_161159599_   4898 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4947
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_161159599_   4948 GGCCATACTGCCCAAGGTAATTTACAGACTCAATGCCATCCCCATCAAGC 4997
                            v     v     iv i  i      i    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_161159599_   4998 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5045
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_161159599_   5046 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5095
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_161159599_   5096 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5145
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_161159599_   5146 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5195
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_161159599_   5196 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5243
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_161159599_   5244 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5293
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_161159599_   5294 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5343
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_161159599_   5344 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5393
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_161159599_   5394 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTT-GAAGAAAA 5442
                          i ?    i       v   v       i      - i   -        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_161159599_   5443 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5492
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_161159599_   5493 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5542
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_161159599_   5543 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5592
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_161159599_   5593 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5642
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_161159599_   5643 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5692
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_161159599_   5693 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5742
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_161159599_   5743 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5792
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_161159599_   5793 CATCACTGGCCAT 5805
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3692 21.23 2.19 2.84  chr1_161642860_161649052.rev     3037  3950 (2243)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_161642860_   3037 TGCAAAGACATGCCATGTTCAGGGATTGGAAGAATTAATATTGTTAAAAA 3086
                           v     i  v         v           v             i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_161642860_   3087 GTTCATACTACCCAAAGTGATTTACAGATTCAATGCAATCCCTATCAAAA 3136
                          viv     v      v    i           i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_161642860_   3137 GCCCAATAATACTTTTTGCAGAAATAGAAAAAACAATCCTAAAATTCATA 3186
                         v    iiviivi             v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_161642860_   3187 CGGAACCACAAAG-ACTCTGAATAGCCAAAGCCATTTTGAGCAAGAAGAA 3235
                         i    vii   i -  i v           i v  i    iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_161642860_   3236 CAAATCTGGAGACATTGTACTTCATGATTTCAAAATAGATTACAAA-CTA 3284
                             vi     ivv iii     vii         ivv i      -   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_161642860_   3285 TAGTAATCAAAACATTATGGTACT-----AAAAGCAGACATACAGAGCAA 3329
                         i         i   v i       -----  iiii       i   v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_161642860_   3330 TGAAACAGAATGGACAGCCCAGAAATAAACCCATGTGTATATGGTCAACT 3379
                           i  i     v  v  i                iii v         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_161642860_   3380 GGTCTTTGACATGGGTGCCAAGAATATGCAATGAGGAAATGATAGTTTTT 3429
                          i i  i    v           vi  v     i     vi     i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_161642860_   3430 TCAACAAATTGTGTTGGGAAAACTGGATATCCACATGCAAAACAATGAAA 3479
                                  v   i     v         ?            v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_161642860_   3480 TTGGATCCTTATTTTACACTATATACAAAAATCAAC-CAAAATAGATTAA 3528
                              i  i  ii i    i            i   -      i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_161642860_   3529 AGACTTAAATGCCAGATTTGAAACTGTAAAATCTGCAGAAGAAAACATAG 3578
                             i      iv   vi i     i     iiivi              
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_161642860_   3579 AGA-AAATGCTTTCTGACATTGGCCTTGGGCAATGATTTCCTAGGATATT 3627
                         i?i-    -   iv    v    v-  i       i    i   -    v
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAG-ATATG 597

  chr1_161642860_   3628 ATACCAAAC-CGAAGGCAACAAAAGCAAAAATAGACAAACTAAGAAAAAA 3676
                          i      v- iv i          v         i   i ii-------
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG------- 640

  chr1_161642860_   3677 ACTAAAAGAAAA--AGAAACATCCGCACCACAAAGGAAATAATCAACCAA 3724
                            vv vv    -- i    v ii ii iv       v iv     vv  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_161642860_   3725 ATG------CAAACTACAGAAAAGGAGAAAATATTTGCAAGCCATGTATC 3768
                         i  ------   v i      vi                 ii   i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_161642860_   3769 TGATAAAGAGTTAATGTCCAAGATAAATGAA--ACTCCTATAACTTAATA 3816
                               i iii vi i    ii   v  i  --    i  i    i    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_161642860_   3817 ATAAATGTTAAAAACAAAAACAAATAACCTGATTGAAAAATGGACAAAGG 3866
                              -----------  i          ii   ?        i      
  L1M4_orf2#LINE/    791 ATAAA-----------AAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_161642860_   3867 AACTGAATAGGCATTTTTCCAAAAAAAAAAAAACATACAAATGACCAGCC 3916
                          vi       i     i      i  i -----i         i   iiv
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGA-----TATACAAATGGCCAATA 874

  chr1_161642860_   3917 AGTATCTGAAAAGCTGCTCAACATCACTAATCGG 3950
                           i iv       v            ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (125 / 65)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.07 (46 / 15)  

2636 24.52 5.22 2.50  chr1_161642860_161649052.rev     4822  5702 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_161642860_   4822 AAATACATTCCATGTTCATGGATTGGAAGAATCAATATCATGAAACTGAA 4871
                            v i  i                     v i     ii v  iv  iv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_161642860_   4872 CATACTGCCCAAAGCAAACTAGAGACTCAACGCAATTCCTATCAAAAT-- 4919
                         v     v      vii v   v   i          i           --
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_161642860_   4920 ------------------------ACAA----ATCCTAAAATTCATATGG 4941
                         ------------------------    ----                  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_161642860_   4942 AATTTTAAAGAGCCCA-AACAGCCAAAACAATTCTAAGCAAAAATAACAA 4990
                           v vi  i ii    -  i            ii i iv  i  v     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_161642860_   4991 ATCTGGAAGCATCACATTACCCAATTTCAAATTATACTATCAGGCTATAG 5040
                          vi    i vv     i v            viv     iv i    i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_161642860_   5041 GAAACAAACAAACAAAAAAAACCAGCATGACA-TGGTATAAAAGTAGACA 5089
                         --------i  v   i -----   ii  ii -   i    iii      
  L1M4_orf2#LINE/    254 --------TAATCAAGA-----CAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_161642860_   5090 CATAGACCAACGGAATAGAATAGAGAACGAAGAAATAAAGCCAAATACTT 5139
                         i     i   i          v    iivv         v   v i i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_161642860_   5140 ACAATCAAC--ATCTTCAACAAAACATACAAAAAT-ATAAACTGGGGAAA 5186
                          iii    i--  i   i    ii-i i v  i i-  vv v        
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAA 389

  chr1_161642860_   5187 GGATACCCTAGTCAATAAACGGTGCTGGGAAAATTGGGTAGCCACATGTA 5236
                          i   vi  vv    i   i          v  i   i  ?       i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_161642860_   5237 GAAGAATGAACCTTGATCCTAATCTCTCACCATATACTAAAATGTATATG 5286
                         i         vi v  i  iv i   v          v     ---  --
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT---TA-- 484

  chr1_161642860_   5287 GATCTCAAGATGGATCCAAGACTTAAATCTGTGACCTGAAAACATAAAAT 5336
                         - -     i       v?    i     v iv  v  i   vi      i
  L1M4_orf2#LINE/    485 -A-CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_161642860_   5337 TTCTAGAAGAAAACCTAGAAAGAACTCTTCTGGACATTAGCCTAGGCAAA 5386
                          ii           v   i?iv  v     vv   v  i vi       v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_161642860_   5387 GAATTTATGACTAAGACCCCAAAAGCAAATGCAAGAAAAACAAAAATAAA 5436
                          iv  iv iiv  v   v         v v    v    iv       i 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_161642860_   5437 TAAATGAGACCTAATTAAACTAAAACACTTGTGCACAGCAAAGTATGTAA 5486
                              vi   i v  i   v v   v    v  ii vv     v iiiv 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_161642860_   5487 TCATCAGAGTAAACAGACAATC-ATAGAATGGGAGAAAATAGTTGTGAAT 5535
                            vv i   i  v      i - i                v   ii   
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_161642860_   5536 TATGCATCAGACAGAGGACTAATATCCAGAATCTACAAGGAACTCAAACA 5585
                         i  ii   v  i ii     vi          v  i  i      vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_161642860_   5586 A-TCAGCAAGAAAAA---AAA-AACTCA-TCAAAAAGTGGACAAATGACA 5629
                          -   ii  v     ---   -   i  - i?    i   i    v  iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_161642860_   5630 TGAA----CACTTCTCAAGTGAAGTTATACAAATGGCCAACAAATATATG 5675
                             ----  i     v iv    v               i  ii i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_161642860_   5676 AAAAAATTGCTCAAGATCACTAATCGT 5702
                             i  -      v    ????????
  L1M4_orf2#LINE/    883 AAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (124 / 88)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 3.58 (68 / 19)  


1998 20.81 3.13 1.79  chr1_161703476_161706797     1438  1884 (1438)    L1M4_orf2#LINE/L1        4   456 (452)  

  chr1_161703476_   1438 AAAAACATTCTGTGTTCATGAATTGCAAAACTCGATATTATTAAAATGAC 1487
                            i i  i ii        i    v  i   ii     i    i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_161703476_   1488 AATAATTTCCAAATTGACATGCAGATTCACTGCAATCCCCATCACAACTT 1537
                             v ii         iv i        vi        i    v  iii
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_161703476_   1538 CAGAGACCCTTTTTGCACAAATGGAAGAGGGTAATCTTAAAATTCATACA 1587
                            vvi  i        v    v  vi  v- i   i           ii
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATG 152

  chr1_161703476_   1588 GAATTGCAAGGGACCTCAAGTAGCCAAAACAATCTTGGAAAAGAAAAACA 1637
                            v           ivi i                 i       i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_161703476_   1638 ------GATGACTTACACTTTCTTTGAGTTGAAAA-TTACTACAAAGCTA 1680
                         ------  v    i      i i--i v  v    -              
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCC--AATTTCAAAACTTACTACAAAGCTA 250

  chr1_161703476_   1681 CAATAATCAAAGCATTATGTTGCTGGCATAAGGCTGGACATACAGAT--- 1727
                           i       ii  v i  v i           v i      i    ---
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_161703476_   1728 -GAAATAGAATTGAAAGTCCATTTTTTAAATC--CCCATTTATCTATGGT 1774
                         - i           i      v-----    v--     vi  i      
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAG-----AAATAAACCCATACATTTATGGT 345

  chr1_161703476_   1775 TAACTGAGTTTTTACAAGGCTGTCAATACCATTCAATAGTGAAAAAATAG 1824
                         i  i   v   iv      v  i   v          i v    i     
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_161703476_   1825 ACTCTTCTACAAAAGGTGCTGGAA-ATCTGGATACTTACACGCAAAAGAA 1873
                         v  i   v     v        i - v       ?ii   i         
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_161703476_   1874 TGAAATTGAAC 1884
                             i   i  
  L1M4_orf2#LINE/    446 TGAAGTTGGAC 456

Transitions / transversions = 1.97 (61 / 31)
Gap_init rate = 0.02 (8 / 453), avg. gap size = 2.75 (22 / 8)  

2243 14.03 3.39 1.36  chr1_161703476_161706797     2392  2833 (489)    L1M4_orf2#LINE/L1      458   908 (0)  

  chr1_161703476_   2392 CCTATGTCACACCATATA--AAAATGGGCTCAAAATGGATCAAACACTTT 2439
                             iv            --     vii              ? v  i -
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT- 506

  chr1_161703476_   2440 TAGA-GTAAGAG--AAAACTATAAAACTCTTAGAAGAAAACATAGGAATA 2486
                         - i -       --                                ?i  
  L1M4_orf2#LINE/    507 -AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_161703476_   2487 AATCTTTATAACCTTGAATTTAGCAATGGTTTCTTAGATATGACACCAAA 2536
                               ii i      ii  vi                            
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_161703476_   2537 AGCA---ACAAT----GAAAAAATAAATAAATTAGAATTTCATCAAAATT 2579
                             ---i   i----         i       i  -i            
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA-CTTCATCAAAATT 654

  chr1_161703476_   2580 AAAAACTTTTGTGCTTCAAAGGGCACCATCAAGAAAGTGGAAAGATAACC 2629
                                               i   i            i     i    
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_161703476_   2630 CATAGAATGGAAGGAAATATTTGCAAAT--TATATCTGA-AAGGGTCTAG 2676
                           i       i  i              --         -     v  v 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_161703476_   2677 CATACCCAAGATTTCTAAAGAACTGTTACAATCCAACTATAAAAATACAA 2726
                         i  --   ii  v v         v      ii   iv       v    
  L1M4_orf2#LINE/    755 TAT--CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_161703476_   2727 ATAACCCAACAGAAAAAATGGGTAAAGAATTAGAATACATACCTTTCTAT 2776
                                  i-v?         i    i   v     v i ii i  i v
  L1M4_orf2#LINE/    803 ATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_161703476_   2777 GAAAGATATACAAGTGGCCAATAAGCACATGAAAACATGCTCAACTTTAT 2826
                         ii           i                     v         v i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_161703476_   2827 TAGTCAT 2833
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.47 (42 / 17)
Gap_init rate = 0.02 (11 / 451), avg. gap size = 1.91 (21 / 11)  


3132 26.85 1.10 0.77  chr1_161785361_161791753     4996  5900 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_161785361_   4996 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5045
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_161785361_   5046 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_161785361_   5096 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_161785361_   5144 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAACCCTAAGCCAAAAG 5193
                                viiv  ii  v  viv  v     iv   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_161785361_   5194 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5243
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_161785361_   5244 TACAGTAACCAAAACAGCATGATACTGGTACGAAAACAGAGATATAG-TC 5292
                                 i   i    ii  i      i ii ii i   v      -  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_161785361_   5293 AATGGAACAG---TGCAGAGCCCTCAGAAATAATGCCACATATCTACAAC 5339
                                i  ---  -    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTG-AGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_161785361_   5340 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5389
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_161785361_   5390 CCTGTTTAATAAATGGTGCTGGGA-AACTGGTTAGCCATATGTAGAAAGC 5438
                         i  v  i  i              -      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_161785361_   5439 TGAAACTGGATCCTT-CCTTACACCTTATACAAAAACTAATTCAAGATGG 5487
                             ii    i  i -   i     v          i   i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_161785361_   5488 AATAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5537
                          vi ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_161785361_   5538 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTA 5587
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_161785361_   5588 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5637
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_161785361_   5638 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAACGGAGTGAA 5687
                           i   v v  i i   i  ii vv    i  v    i   vii      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_161785361_   5688 CAGGCAACCTACAAAATGGGAGAAAATCTTTGCAACTTACTCATCTGACA 5737
                         v  i     i   i             v       v i ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_161785361_   5738 GAGGGCTAATATCCGGAATTTACAATGAACTCAAACAAATTCACAAGAAA 5787
                         ii  i  vi     i    v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_161785361_   5788 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5837
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_161785361_   5838 CTCAAAAGAAGACATTTA--TGCACCAAAAAAACACATGAAAAAATGCTC 5885
                            v        i  vi --  -i    v  i-          i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG-GCCAATAAG-CACATGAAAAGATGCTC 893

  chr1_161785361_   5886 ACCATCACTGGCCAT 5900
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (148 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


3024 25.75 2.22 1.44  chr1_161797159_161801633     3082  3982 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_161797159_   3082 TGGAAAACTATCCCATGTTCATGCATTAGAAGAATTAATACTGTTAAAAT 3131
                               iv               v   i     v      i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_161797159_   3132 ATCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCTCTATCAAAA 3181
                         iv v     v      vii              i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_161797159_   3182 TAT-AGATAATATTCTTCACAGAAATAGAAAAAA-AATCCTAAAATTCTT 3229
                          vi-  v ivi-  i  ii       v  v  iv-i            v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_161797159_   3230 A--GAACCACAAAAGACCCTAAATAGCTGAG-CAA------AAAGAAAAA 3270
                          --   vii   ii     vi      ii i-   ------   ii  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_161797159_   3271 ATGAAGCTGGAGGCATCACATTATCTGACTT-AAAATATATCACAAAGCT 3319
                          ii   i      vv     i vi ii i  -    iv  ii        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_161797159_   3320 ATAGTAACTTAAACTGCATGATACTAACATAAAAA-AGAAACATAGACCA 3368
                          i     iiv i  v ii  i    ii     ii -   v i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_161797159_   3369 ATGGAGCAAAAC--AGAATA-AAAAATAAATCCAAATATTTACATCCACC 3415
                              ii i  i--   i v- i       i   v i     iivi  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_161797159_   3416 TGATTTTTGACAAAGCCACTAAGCACACACATTGGGGAAAGGGCAATTTA 3465
                                i     i vii i   vv  iv  v         iii i i v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_161797159_   3466 TTTAATAAATGATGCTGGGAAAACTGGATATCCACATGCAGAAGAGTGAA 3515
                           i  i     i        v         ?         i    i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_161797159_   3516 ACTAGACCCCTACCTCTAACCATAAGCAAAAATCAGCTCAATAAGGATTA 3565
                         ii i            vv      vi       i i     v v    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_161797159_   3566 AATACTTAAATTTAAGACCCAAAACTATGAAACTACTAGAAGAAAACATA 3615
                         ? v  i     v     v i        i     vi              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_161797159_   3616 GGGA-AAATGCTTAATGATATTGGTCTGGGTAAGAATTTTTTTAATAGGA 3664
                           ?i-    -   vi   iv    vi i  i  vii   i  vi   v  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_161797159_   3665 CCTTAAAAACATAGATAATTAAACCAAAAATAGACAAAATAG---TCATC 3711
                          vii    i  i iii  iv   vv         i   v i ---     
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_161797159_   3712 AAACTGCAAAGCTTCTGCTTATCAAAATAAACAATCAGTAGAACAAAAAG 3761
                            v vv   i   i  iviv     iv v  v    iv i iii     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_161797159_   3762 ACAACCTACAGAATGGGATAAAATACTTGCCAAGTATGCATCTAACAAAA 3811
                               i           v      i    v  vi  ii    i i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_161797159_   3812 GGTTAATATCTAAAATACTTAAGCACCTCAAACAATTCAATAACAAAATA 3861
                          ii vi    i i    iv   iv v   vv    i       i    --
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA-- 796

  chr1_161797159_   3862 TAATAATAATACAAATAATTCAATTTTTAAAATGAGCAAAAGACTTGAAT 3911
                         -------- v        ii     ?v-      i     i  i      
  L1M4_orf2#LINE/    797 --------AGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAAT 837

  chr1_161797159_   3912 AGACATTTCTCAAAAGAAAACATACAAATGGCCAACAGGTATATGAAAAA 3961
                                    v      i i              i i i i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_161797159_   3962 ATTCTCAGCATCACTAATCAT 3982
                           v    i     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (152 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


3036 27.23 1.56 0.22  chr1_161804376_161811101.rev     5339  6234 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_161804376_   5339 TGGAAGAACATTCCATGCTCA---ATAGGAAGAATCAATATTGTGAAAAT 5385
                              ii i  i     i   ---  v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_161804376_   5386 GGTCATACTGCCCATGGTAATTTAAAGATTAAATGCCACCCCCATCAAGC 5435
                           iv     v    viv i  i  v     v  i  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_161804376_   5436 TACCAACGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTACATTTTA 5483
                          v   i vi i  i  ii     -   -- v  i  - iii  v v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_161804376_   5484 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAAG 5533
                                viiv  ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_161804376_   5534 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAGGGC 5583
                                i      vv       v  ii i      viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_161804376_   5584 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACG 5633
                          i      i   i    ii         i iv ii i   i       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_161804376_   5634 AATGGAACAGAACAGAGGGCTCAGAAATAACACAACACACCTACAAACAT 5683
                                i    iv   i ii         vv v i   ii  iiiv  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_161804376_   5684 CTGATCTTTGTCAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5733
                         i    i  i v   ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_161804376_   5734 ATTTCATAAATGGTGCTGGGAACACTGGCTAGCCATATGTAGAAAGCTGA 5783
                         v  iv i              vv     v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_161804376_   5784 GACTGGATCCCTTCCTTACACTTTACACAAAAATTAACTCAAGACGTATT 5833
                         iii    i    v   i    iv  i                i i v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_161804376_   5834 AAAGACTTAAATGTAA-ACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5882
                          ?    i         - v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_161804376_   5883 AGGCAATACTATTCAGGACATAGGCATAGGCAAAGACTTCATGACTAAAA 5932
                            ?ivv v v   iv   v v  vv       v ii   v iiv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_161804376_   5933 CATCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAATT 5982
                           i        vvi          vv        i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_161804376_   5983 AAACTAAAGAGCTTCTGCACAACAAAGAA-ACTATCATCACAGTGAACAG 6031
                            v v  i i   i  ii vv     i -       vv v      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_161804376_   6032 GCAACTTACAGAATGGGAGAAAATCTTTGCAATCTATCCATCTGACAAAG 6081
                         i    ii                 v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_161804376_   6082 GGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA- 6130
                          i  vi          v  i        ivv    v iv i  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_161804376_   6131 --AAA-AAC---ATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 6174
                         --   -   ---  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_161804376_   6175 AAAAGAAGACATTTATGCACCCAACAGACATATGAAAAAATGCTCATCAT 6224
                         v        i  vi viiiv    i ii  i       i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_161804376_   6225 CACTGGTCAT 6234
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


3045 24.80 2.40 1.49  chr1_162219575_162221815.rev      888  1762 (479)    L1M4_orf2#LINE/L1       26   908 (0)  

  chr1_162219575_    888 TTGGAAGAATTAATATTGTTAAAATGGCCATACTGCCCAAAACAATCTAT 937
                                 v             i     v     v      vii     i
  L1M4_orf2#LINE/     26 TTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chr1_162219575_    938 A--TTCAGTGCTGTTCTTATCAAATTACTAATTATCATTTTTCACAGAAT 985
                          --    ii  vi i i       v v i ii ii -     ii     v
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAA 124

  chr1_162219575_    986 TAGAAAAAAACT-ATTTTAAA-TTCATATGGAATCACAAAAGAGCCTGAA 1033
                          v  v  i--  -  ii    -           vii   ii  v  v   
  L1M4_orf2#LINE/    125 TTGACAAG--CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr1_162219575_   1034 TAGCCAAAGCAATTCAAAGCAAAAAGAACAAAGCCAGAGACATCACATTA 1083
                                 i    iivi iv  i          iii   ivv     i v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_162219575_   1084 ACTGACTTCAAACTGTATTATCAGGCTATAGTAACCAATACAGCATGGCA 1133
                         v ii i      viv  i  iv i    i     i   v    ii   i 
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_162219575_   1134 CTGG--TAAAAACAGACACATAGACCAATGGAATAGAAGAGAGAACTCAG 1181
                             --   ii i     i     i             vv    iii   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_162219575_   1182 AAACAAAGCCAGACAC----AACCATCTGATCTTTGACAAGGTTGGCAAG 1227
                            i   v   v   i----iii  vi    i  i       v  v    
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_162219575_   1228 AATAGCCAATGGGAAAAGGACTGCCTATTCAATAAATGGTGCTGGTGTAA 1277
                          vi vi       i    i iv i  v     i            vii  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_162219575_   1278 CCAACTAGCCATATGCAGAAGAATGAAATTGGACCCCTACATTTCATCAC 1327
                          iiiv  ?   i     i         i            v iv  i  i
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_162219575_   1328 ATACAAAAATTAATTCAAGATGGATTAAAGATTTAAATCTAAGACTTCAA 1377
                                      i    i      i ?   ii     v     vi v  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_162219575_   1378 ACTATAAAAATCCTAGAGGAAAACCTAGG---AAATACCCTTCTGGACAT 1424
                                  v  i    i      v    ---    ---    vv   v 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCT 569

  chr1_162219575_   1425 TAGATTTGAGAAGGAATTTATGAG---TAACTCCTCAAAAGCAATTGCAA 1471
                          i i  v iv  v i-   v v  --- i  v  --       vvv    
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGG-TTTCTTAGATATGACACC--AAAAGCACAAGCAA 616

  chr1_162219575_   1472 AAAAAAAAAAAAATAAGACAAATGGGACGTAATTAAACTAAACAGCTTTT 1521
                         v    i      -  -  i    v    v v  i   v v  v i     
  L1M4_orf2#LINE/    617 CAAAAGAAAAAA-TA-GATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_162219575_   1522 GCATAGCAAAAGAAACTATGAAGAGGGTAAACAGATAGCCGACATAGTGG 1571
                          iiivv    i  v     v    ii  i  v   i i  v   v i   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_162219575_   1572 GAGAAAATATTTGCAA-CAATGTATCCGACAAGGGGTCTAATATCCAAAA 1620
                                         -iv  i    i  i     i-  vi      i  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGA-CTTGTATCCAGAA 763

  chr1_162219575_   1621 ATCTATAAGGAACTTAAACAATTCAACAAGCAAAAAACATATAACCCTAT 1670
                         - v     i     ivv    i    i  vv    i   v       v  
  L1M4_orf2#LINE/    764 -TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_162219575_   1671 TAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC---AGAAGACATAC 1717
                          ?    i           iv    i     i     ---      i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_162219575_   1718 AAGCAGCCAACAAACATGTGAAAA-ATGTTTCATATCACCAATCAT 1762
                           iii     i  i  ii      -   i iv i    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (134 / 80)
Gap_init rate = 0.02 (19 / 883), avg. gap size = 1.79 (34 / 19)  


3571 19.02 4.25 2.80  chr1_162276430_162278376      564  1457 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_162276430_    564 GGAGAAACATTTCAT--TCATATACTGGAAG-CTCAGTATTGTTAAGGTA 610
                            i i i  ii   --    iv i      -  i i          i i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_162276430_    611 CCAATAATTCCCCCCAAATTGATCTATAATATT-------ATCCC-AGCA 652
                         v     --- i               i i-   -------     - v  
  L1M4_orf2#LINE/     52 GCAATA---CTCCCCAAATTGATCTACAG-ATTCAACGCAATCCCTATCA 97

  chr1_162276430_    653 GGTTTT----TTTTTTTTTTGCAGAAATTGAAAAGTTGATTCTAATACTT 698
                         iiv ii---- vii                 v   i    i    v i i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_162276430_    699 ACATGGAAATACAAAGGACTCAGAGTAGCCAAAACAATTTGGAAATAAAA 748
                          i        i   i    i    i             i v    -  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGA 196

  chr1_162276430_    749 AGAA---AGTTGGAAGACTTATAATT---AATTGCAAAATGTATCATAAA 792
                             ---       i    i i v  ---    v     iv  ii i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_162276430_    793 GCTACAGTAATCAACACAGTGTAGTACTGACTATAAAGATAAACATATAA 842
                                       v       i      i -    i    i       i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGACATATAG 295

  chr1_162276430_    843 ATCACTGGAACAAAATTGAGAGTCCAGAAATAATCCCTTATATTTATGGT 892
                             v     i i                    v   v  i         
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_162276430_    893 GAATTGATTTTCAACAAAGGCACCAAGACAATTCAAAGGGGAAAGGATAA 942
                         v           i    i  ii       v      v        i   i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_162276430_    943 TCTTTGCAAAAAATAGTGTTGGAACAAATGGATATCTACACACAAAAAGA 992
                              v   v    i   i   i    v      ? i   ii     ii 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_162276430_    993 TTAATGTACACCCCTGC-TCACATCATACAGAAAAAATAACTCAAAATTA 1041
                          v  vv iv      i -     i    i v     v           vi
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_162276430_   1042 ATCACACGCTTAAATGTAAGAGCTAAAGCTATAAAAGTATTAGAAGAAAA 1091
                             ? vi i                 i        v v           
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_162276430_   1092 TCTAAAATCTCCTAAAATCTAGAAGAAAGTCTTCTTGATCTTGGGT-AGG 1140
                         i---------------  --  i? v  i     v   i       -   
  L1M4_orf2#LINE/    546 C---------------AT--AGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_162276430_   1141 CAAATATTTCTTAAATAGAACACTAAAAGTATGACTCAAAAAGGAAAAAA 1190
                            vvi       i   vi    i     i ii viv v   i       
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_162276430_   1191 -AAATCACATGTGGACTTCATCAAACTTAATCACTTC-GAGCTTCAAAAG 1238
                         - i  v -  -              v    vv    i- v        i 
  L1M4_orf2#LINE/    629 TAGATAA-AT-TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_162276430_   1239 AAACCATTAAGAAAGTGAAAGAACAAGCCAC----TG--AGAAAATATTT 1282
                          v  i  i            ii    v    ----  --           
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_162276430_   1283 GCAAATCATATATCTAAAAATGTACTT--ATTCAGAATTTGTAAAGAACT 1330
                                        i v  v v    --  i      v i         
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_162276430_   1331 CTTACAACTAAATAATAA---GACAAG-AAACCAATCTGAAAATGAATAA 1376
                                  v        ---     i-  v     i?i      iii  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_162276430_   1377 AAGAGTTGAAGAGATATTTAGACAGAGGAGATATATAAATGACAAATAAT 1426
                          i  v     v   i    vvv  i  i       i     i v     v
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_162276430_   1427 CCCATGAAAAAATGC-CAACAGTATTCATTAT 1457
                          v        i    -     vi ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (105 / 61)
Gap_init rate = 0.03 (25 / 907), avg. gap size = 2.52 (63 / 25)  


1767 17.60 5.36 2.81  chr1_162475556_162478161      809  1200 (1406)    L1M4_orf2#LINE/L1        1   402 (506)  

  chr1_162475556_    809 TGGAATGACGCACTGTGTTCATAGATTGAAACAGTTAATATT---AAGAT 855
                              v  iiiv ii       i     i  v v        ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_162475556_    856 GTTGATACTACTCAAAGTGATCTACAGATTCATTAGGTAATCCCTGTCAA 905
                          vii     v i    v               -- v i       i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCA--ACGCAATCCCTATCAA 98

  chr1_162475556_    906 AATCCCAG-TGACTTTTTTTCAGAAATAGAAAAATTCATCCTAAAATGTA 954
                                 -  v       v       v  v  ii v          vi 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_162475556_    955 TATGAAAACTCAGAGTACCCCAAATAGCCAAA-CAATTTTGCAAGAGAA- 1002
                             i   iv  ii v    vi          -    i   v  i    -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_162475556_   1003 --CAAAGTTGAAGGTCTCATGCTTCCTGATTTCAAAATTTAACTATAAAG 1050
                         --        i   v    ii     ii         i   -   i    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAAAG 247

  chr1_162475556_   1051 CTACAGTAATCAAAACACTGTAGTCCTAGCATAAAGACAGACATATAGA- 1099
                                      i   v   i  v  i      i  i           -
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_162475556_   1100 -------ATAAA-----GAACCCAGAACTAAACCCTCACATATATGGTCA 1137
                         -------   i -----  ii      v       vi    v        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_162475556_   1138 ATTGATTTTTGACAAGGTTGTCAAGACCAGTCAATCAATGGAGAAAGGAT 1187
                                  i       v  i        - ---       i     i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCA-T---TCAATGGGGAAAGAAT 393

  chr1_162475556_   1188 ATCCAGTTTTCTC 1200
                          ----  i  i  
  L1M4_orf2#LINE/    394 A----GTCTTTTC 402

Transitions / transversions = 1.76 (44 / 25)
Gap_init rate = 0.03 (11 / 402), avg. gap size = 2.91 (32 / 11)  

 318 21.92 0.00 4.11  chr1_162475556_162478161     1178  1250 (1356)  C L1M4_orf2#LINE/L1   (443)   465   396 *

C chr1_162475556_   1250 TCTTTTAAATACATGGTGTTGGGAAAACTGGATATCCACATGTAAAAATG 1201
                               v  i v      i     v         ?       i    -- 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA--G 443

C chr1_162475556_   1200 GAGAAAACTGGATATCCTTTCTC 1178
                         i vi  ii    i-i   vi   
  L1M4_orf2#LINE/    444 AATGAAGTTGGAC-CCCTACCTC 465

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.50 (3 / 2)  

 231 12.50 0.00 2.50  chr1_162475556_162478161     1656  1695 (911)  C L1M4_orf2#LINE/L1   (466)   442   404  

C chr1_162475556_   1695 ATAAATCGTGTTGGGAAAACTGGATTATCCACATGCAAAA 1656
                          i    v   i     v        - ?            
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCAAAA 442

Transitions / transversions = 1.00 (2 / 2)
Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1)  

1717 16.63 8.56 0.98  chr1_162475556_162478161     1707  2115 (491)    L1M4_orf2#LINE/L1      469   908 (0)  

  chr1_162475556_   1707 CCACATGCAAAA-TTAACTCAAAATGGATCAAAGACTTAAATGAAAGTGC 1755
                            i  i     -                  ?    i      v   v  
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_162475556_   1756 TAAAACT--------CTTAGATGAAAACA--GGA--AAACCTTCATGACA 1793
                                --------      v       --  ?--   i    i    v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_162475556_   1794 TTGGATTTGGCAATGATTTATTGAATATAACACCAGAAGCAAAGGCAACA 1843
                             i  v       i   v  ii    i      i     v i      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_162475556_   1844 AAAAA---------TAAATTGGACTTTATCAAAATTAAAAATGTTTATTC 1884
                            i ---------            i              iv   i v 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_162475556_   1885 ATCAAAGGACAC----AACAGAGTGAAAAGGAAACTCATGGAATGGGAGA 1930
                         v           ----  v i         iv   i  ii          
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_162475556_   1931 AA-TATTTACAAAGCATATATCTGGTAAGGGATTAAAATCCATTATAAAT 1979
                           -     i    v          i       i viv     vv   v  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_162475556_   1980 ACATTTTAAAATCCTTCAACTCACCAA-------ATAAA-ATCCCAATTC 2021
                          v ----i  v  i v       vi  ------- i   - v       ?
  L1M4_orf2#LINE/    769 AAA----GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_162475556_   2022 AAAAATGGGCAAAGGACTTAAACAAAGGTTTCTCCAAAGAAGATAAGCAA 2071
                                         i  i  i i vi                 vi   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_162475556_   2072 ATGGCTGATAAGCCCATGAAAAGATGGTCAACATAACTAACTAG 2115
                              ii      v            v       v ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (37 / 28)
Gap_init rate = 0.02 (10 / 440), avg. gap size = 3.90 (39 / 10)  


3285 26.71 0.55 0.55  chr1_162479184_162485548.rev     4969  5874 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_162479184_   4969 GAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGG 5018
                            ii i  i     i      i v      v i     i  v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_162479184_   5019 CCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 5068
                          v     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_162479184_   5069 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 5116
                            iivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr1_162479184_   5117 TGCAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAGAA 5166
                           v  viiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_162479184_   5167 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5216
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_162479184_   5217 CAGTAACGAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGACCAA 5266
                               iv  i    ii         i iv ii i   v  i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_162479184_   5267 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACCAT 5314
                              i    i--    i  --        vv   i i  i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_162479184_   5315 CTGATCTTTGACAAACCTGACAAAAATAAGAAATGGGGAAAGGATTCCCT 5364
                         i    i  i     ivv  v   i vi vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_162479184_   5365 ATTTTATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5414
                         v  iv i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_162479184_   5415 AACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGACT 5464
                          ii    i    v   i     v  i           i    i     ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_162479184_   5465 AAAGACTTAAATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAACCT 5514
                          ?    i       v   v  i    i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_162479184_   5515 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5563
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_162479184_   5564 ACACCAAAAGCAATGGCAACAAAAGCCAAACTAGATAAATGGGATCTAAT 5613
                                     vvi          vv   v         v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_162479184_   5614 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5663
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_162479184_   5664 GGCAACCTACAGAATGGGAGAAGATTTTTGCAATCTACTTATCTGACAAA 5713
                          i     i              i  v       vii iv       i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_162479184_   5714 GGGCTAATATCCAGAATCTACAATGAACTCCAACAAGTTTACAAGAAAAA 5763
                           i  vi          v  i  v      iv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_162479184_   5764 AACAAACAACCCCATCAAAAAGTGGGAGAAGGATATGAACAGACACTTCT 5813
                         i     i     v  i?    i    vi      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_162479184_   5814 CAAAAGAAGACATTTATGCAACCAATAGACACATGAAAAAATGCTCATCA 5863
                          v        i  vi viiii      ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_162479184_   5864 TCACTGGCCAT 5874
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (7 / 906), avg. gap size = 1.43 (10 / 7)  


1316 21.04 6.49 4.16  chr1_162499769_162505370      501   885 (4717)    L1M4_orf2#LINE/L1       61   454 (454)  

  chr1_162499769_    501 CTCAAAACGATCTACATATGAAAC--AATCCCTATCAAAATTCCAATGGC 548
                          i    vi        v  vv   --               i   iiv  
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr1_162499769_    549 ATTTATTTTGCAGAAAT----AAA---AT-----AATTCATACAAAATCT 586
                         v   --           ----  i---  -----        iii  viv
  L1M4_orf2#LINE/    111 CTTT--TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr1_162499769_    587 CAAGGAATCTCAAATAGCCAAAACAATTTAAAAAAAAAGAAGAGCAAGTT 636
                              i i ivi               i vi     --     i   iv 
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA--GAAGAACAAAGT 206

  chr1_162499769_    637 TAAAAGATTCAAACTTCAAAATCTTCAAAAGATTTCAAAGCATGTTTCAA 686
                          ii i  i   v     -------i   ----       i v ii v   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTC-------CCAA----TTTCAAAACTTACTACAA 245

  chr1_162499769_    687 AGCTACAGTAATTAAAACAGTGTGGTACTGACATAAGCAT-GTCAAGTAG 735
                                     i  i              i      v  - v  vi   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_162499769_    736 ACCAATGGAATAA----GACAACCAAGAAATAAACCCTCCCATAGGTGGC 781
                          i          i----  v ii v            viv   vvi   i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_162499769_    782 CAAATAATCTTAAACAAGGGTGCCAAGAACACTCAATGGGGCAAAGACT- 830
                            v i  i  vi               v  i         -     v -
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chr1_162499769_    831 --CTCTTCAA---ATAGTGTTGGGAAAACTGAATCTTCACATGTCAAGGA 875
                         --  i     ---  i   i     v     i  v?i      iv  i  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_162499769_    876 ATTATGTTGG 885
                           v v     
  L1M4_orf2#LINE/    445 ATGAAGTTGG 454

Transitions / transversions = 1.50 (48 / 32)
Gap_init rate = 0.03 (13 / 394), avg. gap size = 3.15 (41 / 13)  

1312 16.86 0.00 0.78  chr1_162499769_162505370     1248  1502 (4100)    L1M4_orf2#LINE/L1      496   748 (160)  

  chr1_162499769_   1248 ATTAAGGATCTAAATATAAGACCTAAAATTAATAAACTCCTAGAAGAAAA 1297
                           i ?i  i      i     v      i  vv      i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_162499769_   1298 TGTGGGGGGAAAGCTTCATAACATTGGACTTGGCAATGATTTCTAGGATA 1347
                         ii i  ? v   v    i i  v    ii v       i     vi    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_162499769_   1348 TAACACCAAAAGCACAGACAACAAAAGCAAAAATAGACAAATGGGACTAC 1397
                          i              ii         v         i    v     v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_162499769_   1398 ATCAAACTTAAAAACTTTTGTGTATCAAAGGACACAATTAACAGAGTGAA 1447
                               v               iv           v  i  v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_162499769_   1448 AAAGGCAACCTACAGAATGGGAGAAAAAAATTTGCAAATCATATATTTGA 1497
                           - i     i                v -                i   
  L1M4_orf2#LINE/    696 AA-GACAACCCACAGAATGGGAGAAAATA-TTTGCAAATCATATATCTGA 743

  chr1_162499769_   1498 TAAGG 1502
                              
  L1M4_orf2#LINE/    744 TAAGG 748

Transitions / transversions = 1.56 (25 / 16)
Gap_init rate = 0.01 (2 / 253), avg. gap size = 1.00 (2 / 2)  

 397 18.95 4.21 0.00  chr1_162499769_162505370     1936  2030 (3572)    L1M4_orf2#LINE/L1      757   855 (53)  

  chr1_162499769_   1936 TCCAAAATATATAAAGTACTCCTATAATTCAACAACAAAAAGTAATATAA 1985
                             i           v    i  i  i    i  i      vv v    
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_162499769_   1986 CCCCATTAGAGAATGGGCAAAGCAGTT---TGGAGATTTC-CCAAAGAA 2030
                            v   ?i i           v v  --- i  v     -        
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.02 (2 / 99), avg. gap size = 2.00 (4 / 2)  

3126 25.69 1.43 1.32  chr1_162499769_162505370     4203  5109 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_162499769_   4203 TGGAAAAACATCCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4252
                               i i        i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_162499769_   4253 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4302
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_162499769_   4303 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACCTTAAAGTTCAT 4351
                          v   vivi i  i  ii     v v  v  i-  - i i    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_162499769_   4352 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGA 4401
                               viiv  ii  v  v v  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_162499769_   4402 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGCT 4451
                               i      vv       v  ii i      vivi       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_162499769_   4452 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGAGAGACCA 4501
                                i   i    ii         i iv ii i   v v v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_162499769_   4502 ATGGAACAGAACAGA-AGCCTCAGAAATAACACCACACATCTACAACCAT 4550
                               i    iv  -  i -         vv   i    i  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_162499769_   4551 CTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAGTATTCCCT 4600
                         i    i  i     ivv  v   i vi vv            v  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_162499769_   4601 GTTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 4650
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_162499769_   4651 AATTGGACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 4700
                          i          v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_162499769_   4701 AAAGACTTAAACAAAAGACCTGAAACCATAAAAGCCCTAGAAGAAAACCT 4750
                          ?    i    iiv    v  i    i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_162499769_   4751 AGGCA-ATACCATTCAGGACATAAGCATTGGCAAAGACTTCATGACTAAA 4799
                            ?i- v i -   iv   v vi vv v     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_162499769_   4800 ACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCT--- 4846
                                     vvii         vv     v  i    v   ii ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_162499769_   4847 ---AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGACTGAAC 4893
                         ---       i -   i  ii vv    i  v       vv i v    v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_162499769_   4894 AGACAACCTACAGAATGGGAGAAAATTTTTGTAATCTATCCATCTGACAA 4943
                                 i                 v    i  vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_162499769_   4944 AGGGCTAATATCCAAAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 4993
                         i  i  vi      i   v  i  i     ivv    v ---   v  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATA 793

  chr1_162499769_   4994 AACAAACAAACAAAAAAACCCCATCAAAAAGTGGGTGAAGCAT----ACA 5039
                           v i     i  -----   v  i?    i    ii   v  ---- i 
  L1M4_orf2#LINE/    794 AAAAGACAAATAA-----CCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_162499769_   5040 GACACTTCTCAAAAGAAGACATTTATGTGGCCAACAAACATATGGAAAAA 5089
                             i     v        i  vi vi       i  i  i   i   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_162499769_   5090 AGCTCATTGTCATTGGTCAT 5109
                         v     vii   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (133 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.27 (25 / 11)  


2985 26.62 1.90 0.34  chr1_162677741_162682854.rev     3730  4623 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_162677741_   3730 TGGAAACACATCCCATGCTCATGGATGGGAAGAATCAATATTGTGAAAAA 3779
                               v i        i        v      v i        v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_162677741_   3780 GACCATACTGCCAAAAGCAATCTACAAGTTTAATGCAATTTCCATCAAAA 3829
                          i v     v  v   vii       ii  i  i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_162677741_   3830 TGCCATCATCATCCTTCACAGAACTAGAAGAAAACAATCATAAGATTCAT 3879
                          v   v vv v ii  ii     v v - v  ivii   v   i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr1_162677741_   3880 ATGAAACCAAAAAAGATCCCACATAGCCAAAGGAAAACTAAGCAAAAAGA 3929
                            i  viiv  ii  i  viv         iv  vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_162677741_   3930 GCAGATCTGGAGGCATCACATTACCCAACTTCAAACTATATTATAAGGCT 3979
                         i  i vi      vv     i v     i      viv  i  i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_162677741_   3980 ATAGTCACCAAAACAGCACAGTACTGGTATAAAAATGGGCACATAG---- 4025
                          i   v i   i    iiii       i    ii  i i  i    ----
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_162677741_   4026 ---GAACAGAATAGAGAACCCAGAATTAAAGCCAAATACTTACAGCCAAC 4072
                         ---   i     v    ii      v    v   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_162677741_   4073 TGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACTCTA 4122
                             i   i    i vviv   i v   vv i         i i v   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_162677741_   4123 TTCAAGAAATGTTACTGGGATAATTGGCAAGCCACGTGTAGAAGAATGAA 4172
                              v     v i      i  i   vv ?    i  i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_162677741_   4173 GCTGGATCCTCATCTCTCACCTTATTCAAAAATCAACTCAAGATGGATCA 4222
                          i    i  ii i   v    v   v       i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_162677741_   4223 AGAACTTAAATCTAAGACCAAAAACCATGAAAACT---AGAAGACAGCAT 4269
                         ?ii  i     v     v v     i  -      ---      v i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chr1_162677741_   4270 CAGAA-AAACCATTCCAGACATTGGCTTAGGCAAAGACTTCATGACCAAG 4318
                         vi ?i-   i -   vv   v    v        v ii   v iivi v 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_162677741_   4319 A-ACCCAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGACTTAAT 4367
                          -   v      v v         iv   i   i   i  v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_162677741_   4368 TAAACTAAAAAGCTGCTGCACAGCAAAAGAAACAATCAGCAGAGTAAACA 4417
                         i   v v    i  vi  ii vv    i  v  v    iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_162677741_   4418 GACAACCCACAGAGTGGGAGAAAATCTTTGCAATCTATACATCTGACAAA 4467
                                      i           v       vii   i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_162677741_   4468 GGACAAATATCCAGAATCTACAAAGAACTCAAACAAATTATCAAGAAAAA 4517
                             vvi          v  i         vv    v i vi  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_162677741_   4518 AA-----AATCCCTTCAAAAAGTGGGCTAAGGACATGAACAGACAATTCT 4562
                         i -----  i  vv i?    i     v     iv    i     v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_162677741_   4563 CAAAAGAAGACATACAAATGGCCAACAAATATATGAAAAAGTGCTCAATG 4612
                          v        i              i  ii i       ii       ii
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_162677741_   4613 TCACTAATGAT 4623
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.50 (20 / 8)  


3142 26.79 0.77 1.21  chr1_162702636_162708900.rev     4868  5774 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_162702636_   4868 AAACATGCCATGCTCATGGATAAGAAGAATCAGTGTCATTTAAATGACCA 4917
                          i i  v     i        vi     v i i i ii  v i   i v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_162702636_   4918 TACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACTACCA 4967
                             v      vii  i           i  v  i         v v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_162702636_   4968 ATGACATTCTTCACAGAACTAGAAAAAAACT-ATTTTAAAATTCATATGG 5016
                         iivi v  i  ii     v v  v  i--  -  ii              
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATATGG 153

  chr1_162702636_   5017 AACCAAAGAAGAGCCTGAATAGCCAAGACAATCCTAAGCAAAAAGATCAA 5066
                           viiv iii  v  v          i      i i iv  i    v   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_162702636_   5067 AGCTGGAGGCATCACGTTACCCACCTTCAAACTATACTATACTGCAGGGC 5116
                           i      vv    ii v    vi      ----   -    i  ii  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAA----ACT-TACTACAAAGC 248

  chr1_162702636_   5117 TACAGTAACCAAAACAGTGTGGCACTGGAACAAAAACAGGCACATAGACC 5166
                                 i   i         i     v i  ii i  i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_162702636_   5167 AGTGGAACAGAACAGAAAGCCTGGAAATAAGGCCACACACCTACAA-CAT 5215
                          i     i    iv  i  i ii       iv   i   ii  iii-  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_162702636_   5216 CTGATCTTCTATGAAGCTGACAAAAACAAGCAATGGGGAAAAGACTCCCT 5265
                         i    i   v ii i v  v   i v  vv           ii ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_162702636_   5266 ATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAAATTGA 5315
                         v     i              i      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_162702636_   5316 AACTGGACCCCTTCTTTACACCATATACAAAAATCAACTCAAGATGGATT 5365
                          ii         v i i                 i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_162702636_   5366 AAAGACTCTGATGTAAAATCCAAAACTATAAAAACCT-GGAAGACATCCC 5414
                          ?    iivi      i v i            vi  -i     v v vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_162702636_   5415 AGGC---AATATGATCCTGGACATAGGCATGGGCAAAGATTTCATGACAA 5461
                            ?---   v --  v  iv v i  i- i     v i    v iivv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCT--TCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr1_162702636_   5462 AGACACCAAAAGCAATTGCAACCAAAGGAAAAATTGACAA-TGAGATCTA 5510
                         v             vvv     v    i      v  i  - vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_162702636_   5511 ATTAAACTTAAGAGCTTCTGCACAGCACAAGAAACTATCAACAGAGTAAA 5560
                           i   v    i i   i  ii vv  v i  v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_162702636_   5561 CAGATGACCTACAGAATGAGAGGAAATATTTGCAGACTATGCATCTGACA 5610
                         v   ii   i        i   i           i ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_162702636_   5611 GAGGTCTAATATCCATCATCTATAAGAAGCTTAAACAAATTTATAAAAGA 5660
                         ii  v  vi      vv  v     ii i  ivv    v iv    v i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_162702636_   5661 AAAGCAAACAACCCTCATTAAAAAGTAGGCAAAGGACATGAATGGACACT 5710
                           ii    i     -v   ?    i i         iv     i    i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_162702636_   5711 TTTCAAAAGAAGACATACATGCAGCCAACAAGCATATGAAAAAAAGCTCA 5760
                          i  v        i     viii     i     i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_162702636_   5761 ATATCATTAGAGAA 5774
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (154 / 85)
Gap_init rate = 0.01 (11 / 903), avg. gap size = 1.64 (18 / 11)  


3210 26.43 0.88 0.88  chr1_162800600_162807012     5013  5920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_162800600_   5013 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATCGTGAAAAT 5062
                              ii i  i     i      i v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_162800600_   5063 GGCCATACTGCCCAAGGTAATTTATAGATTTAATGCCATCCCTATCAAGC 5112
                            v     v     iv i  i  i     i  i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_162800600_   5113 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5160
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_162800600_   5161 TATGGAACTAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCAAAAAG 5210
                                v iv  ii  v  v v  v     iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_162800600_   5211 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGG 5260
                                i      vv   ii  v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_162800600_   5261 TAGAGTAACCAAAACAGCATGGTACTGGTACCTAA--ACAGACATATAGA 5308
                           v     i   i    ii         i --   -- i           
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATAGA 296

  chr1_162800600_   5309 CCAATGGAACAGAAC--AGGGCCCTCAGAAATAATGCCACATATCTACAA 5356
                         i        i    i--  i i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_162800600_   5357 CTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5406
                         ii vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_162800600_   5407 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5456
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_162800600_   5457 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5506
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_162800600_   5507 CATTAAAGACTTAAATGTTAGACCCAAAACCATAAAAACCCTAGAATAAA 5556
                         v  i ?    i       v   v i     i      vi i     v   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_162800600_   5557 ACCTAGGCA-ATACCAGTCAGCACATAGGCATGGGCAAGGACTTCATGTC 5605
                           v    ?i- v i -v  ivv  v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_162800600_   5606 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5655
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_162800600_   5656 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5705
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_162800600_   5706 AACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGA 5755
                           v  i     i                 v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_162800600_   5756 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAACTTA-CAAG 5804
                         i  i  i  vi          v  i  v      vv    -  i -i  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAAT 792

  chr1_162800600_   5805 AAAAAAGCAAACAACCCCATCAACAAGTAGGCGAAGGATATGAACAGACA 5854
                              ii    i     v  i? v  i i   i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_162800600_   5855 CTTCTCAAAAGAAGACATGTATGCAGCCAACAGACACATGAAAAAATGCT 5904
                         i     v        i  ii viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_162800600_   5905 CATCATCACTGGCCAT 5920
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3026 28.74 0.44 0.44  chr1_162912372_162915128.rev     1359  2266 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_162912372_   1359 TGGATGAACATTCCATGCTTATGTGTAGGAAGAATCAATATCATGAAAAT 1408
                             vii i  i     i i   vi v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_162912372_   1409 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1458
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_162912372_   1459 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAAAGTTCA 1506
                          v   iivi i  i  ii     -   -- v  i  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_162912372_   1507 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATTCTAAGCAAAAAG 1556
                                viiv  ii  v  v v  v     iv    ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_162912372_   1557 AACAAAGCCATGGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1606
                                iiivi  vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_162912372_   1607 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAGCAGAGATATAGGTC 1656
                                 i   i    ii         i iv iiii   v      i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_162912372_   1657 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACTTATCTACAACT 1704
                                i    i--    i  --        vv   ivi  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_162912372_   1705 ATCTGATCTTTGAGAAACCTGAGAAAAACAAGCAACGGGGAAAGGATTCC 1754
                          vi    i  i  v  ivv  vv  i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_162912372_   1755 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCT 1804
                           v  i  i              v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_162912372_   1805 GAAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1854
                            ii    i i  v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_162912372_   1855 TTAAAGATTTAAACGTTAGTCCTAAAACCATAAAAACCCTAGAAGAAAAC 1904
                          i ?   ii    i  v  vv       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_162912372_   1905 CTAGGCATTACCATTCAGGACATAGGCATGGGCGAGGACTTCATGTCTAA 1954
                         v    ?i v viv   iv   v v  vv i   i v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_162912372_   1955 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAG 2004
                         i            vvi          vv     v  i    v   ii vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_162912372_   2005 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2054
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_162912372_   2055 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 2104
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_162912372_   2105 AGGGATAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2154
                         i  iv vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_162912372_   2155 AAACAAACAACCCCATCAAAAAGTGGGCAAATGACATGAACAGACACTTC 2204
                          i     i     v  i?    i        v  iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_162912372_   2205 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTAACC 2254
                           v        i  vi viii     v  i          i     v v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_162912372_   2255 ATCACTGGCCAT 2266
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (153 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 364 31.25 0.00 0.00  chr1_162922019_162926365.rev     2806  2901 (1446)    L1M4_orf2#LINE/L1        1    96 (812)  

  chr1_162922019_   2806 TAGAAAAACATTCCCTGCTCACGAATAGAAAGAGTCAATATCATTAAAAT 2855
                          i    i i  i  v  i   i i  v i    v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_162922019_   2856 GGCCATACTGCTCAAAACAACTCGTAGATTTAATGCTATTCCTATC 2901
                            v     v i    vii iiiii     i  i  v  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

Transitions / transversions = 3.29 (23 / 7)
Gap_init rate = 0.00 (0 / 96), avg. gap size = 0.00 (0 / 0)  

2717 26.67 1.32 0.96  chr1_162922019_162926365.rev     3021  3856 (491)    L1M4_orf2#LINE/L1       70   908 (0)  

  chr1_162922019_   3021 ATCTCCTCATCCAATGATTCTATTCCTATCAAACTACCAATGACATTCTT 3070
                             v vv  i   i --- v  i         v v   iivi v  i  
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACG---CAATCCCTATCAAAATCCCAGCTGCCTTTTT 116

  chr1_162922019_   3071 CACAGAATTAGAAAACACT-ATTTTAAAATTCATATGGAATGAAAAAAGA 3119
                         ii     v v  v  -i  -  ii                vviv  ii  
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAA-GCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_162922019_   3120 GCCTGAATAGCCACGACAATCCTAAGCAAAAAGAACAAAGCTGGAGGCAT 3169
                         v  v         vi      i i iv  i          i      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_162922019_   3170 CACATTATCCAAGTTCAAACTATACGACAGGGCTAGAGTAACCAAAACAG 3219
                             i vi    v      viv   v   ii    v     i   i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_162922019_   3220 CATGGTACTGGTACAAAAACAGACATAGAGACCAATGGAACAGAATAGAC 3269
                         ii         i i  ii i       v   i        i     v  v
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_162922019_   3270 AGCCCAGAAATAAGGCCCTACATCTACAACCATCTGATCTTCAGCAATGT 3319
                           i          iv  v     i  iiii  vi    i   ii   v v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_162922019_   3320 TGACAAAAACAAGCAATGGGGAAAGGACTTCCTATTCAATAAATGGTCCT 3369
                           v   i v  vv            i ivvi  v     i       v  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_162922019_   3370 GGGGTAATTGGTTAGTGATATATAGAAGATTGAAACTGGACTTCTTCCTT 3419
                            ii  i   v  ?iv i  ii i    v    ii     ii  v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_162922019_   3420 ACACCATGTACAAAAGCCAACTCAATGTGTATTA-AAACTTAAATGTAAA 3468
                                i       iii       vi  v  i - i  i         i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_162922019_   3469 GCCTAAAATGATAAAAATCCTGGAA-ACAACCTAGG---AAATACCATCC 3514
                         iv      iv      v  i i   - v   v    ---    -- v  v
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCG 563

  chr1_162922019_   3515 TGGACATAGGCCCTGGCAAAGATTTTATGAGAAA-GACTCCAAAAACAAT 3563
                           -  v v  viiv     v i   i- v   v -   v      i  vv
  L1M4_orf2#LINE/    564 TG-ACCTTGGGTTAGGCAATGGTTTC-TTAGATATGACACCAAAAGCACA 611

  chr1_162922019_   3564 GGAAACAAAAACAAAAATTGGCAAATGGGACCTAATTAAACTAAATATCT 3613
                         i v       iv      v ii    v    i v  i   v v  v v  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_162922019_   3614 TCTGCACAGCAAAATAAACAATTAATAGAGTAAACAGACATCCTACAGAA 3663
                          i  ii vv    iv v  v  i  v i   i  v     v  i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_162922019_   3664 TGGGAGAAAATATTTGCAAACTATGC-CCTAACAAAGGTCTAATATCCAG 3712
                                             ii  ii-i  i i  i  v  vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_162922019_   3713 AATCTATAAGGAACTTAAACAAAT---TTACAAGAAAACAAACAACCCTT 3759
                            v     i     ivv    v --- v i  i  i     i     vv
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_162922019_   3760 TTAAAAAGTAGACAAAGTATGTGAACAGACACTTTTCAAAAGAAGACATG 3809
                           ?    i i i     v  v    i     i  i  v        i  i
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_162922019_   3810 CATATGGCCACCAAGTATATGAAAAAATGCTCAACATCACTAATCAT 3856
                           v       vi   i i       i             ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (125 / 96)
Gap_init rate = 0.01 (12 / 839), avg. gap size = 1.58 (19 / 12)  


2786 28.89 0.77 0.66  chr1_162928801_162934407.rev     4210  5116 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_162928801_   4210 TGGAAAAACATTCCATGCTCATGAATAGGAAGAATCAGTGTCATGAAAAT 4259
                               i i  i     i     i  v      v i i i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_162928801_   4260 GGCCATACTGCCTGAAGCAATTTACAGATTCAATGCTATTCCTATGAAAC 4309
                            v     v  ii  vii  i           i  v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_162928801_   4310 TACCATTGACATTCTTCACAGTATTAGAAGAAACC-ATTTTAAAGTTCAT 4358
                          v   vivi v  i  ii   v v v  v-  i i-  ii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr1_162928801_   4359 ATGGAACCAAAAAAGAGCCCAAATAGCCAAAGCAATCCTAAGCAAGAAGA 4408
                               viiv  ii  v  vi          i     i i iv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_162928801_   4409 ATAAAGCTTGAGGCATCACACTACCTGACTTCAAACTATACTATAGCAAT 4458
                          i    i v    vv       v  ii i      viv     i iviv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_162928801_   4459 ACAGTAATCAGAATAGCATGATACTGGTATAAGAATAGCAACATACACCA 4508
                                   ii i  ii  i      i     i    vv i   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_162928801_   4509 ATAGAACAGAATAGAGAACCTAGAAATAGGACCACACACCTACAATTATC 4558
                           i   i     v    ii i       iiv   i   ii  iii i vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_162928801_   4559 TGATCTGTGACAAACCTTACAAAAACAAGCAATTGGAAAAGGATTCCCTA 4608
                             i vi     ivv vv   i v  vv    v  i    i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_162928801_   4609 TTTAATAAATGATGCTGGGAGAACTGGCTAGCCATACGCAGAAAATTGAA 4658
                           i  i     i        v      v  ?   i i   i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_162928801_   4659 ACCAGATCCCTTCCTTATACCATATACAAAAATCAAATCAAGATGGATTA 4708
                         iiii  i    v   i i               i  v    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_162928801_   4709 AAGACTTAAATGTAAATCCCAAAACTATAAAAATCTTAGAAGAAAACCTA 4758
                         ?    i         ivv i            v              v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_162928801_   4759 GGCAATACAAT--TCAGGACATAGGCACAGGCGAAGATTTCATGAGGAAG 4806
                           ?i-  -   --  iv   v v  vvi    i v i    v iiiv v 
  L1M4_orf2#LINE/    550 GGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_162928801_   4807 AAGCCCAAAGCATTTGCAACAAAAGCAAATATGGACAAGTTAGATCTAAT 4856
                          vi  v      ivv          v   v  i  i  i  i  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_162928801_   4857 TAAACTTAAGAGCTTCTATATAGCAAAAGAAACTGTCAACAGAGTAAACA 4906
                         i   v    i i   i i iivv    i  v   i    v i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_162928801_   4907 GA-ACCCTACAGAATGGGAAAAATTTTTTACAATCTATCCTTCTGACAAA 4955
                           - v  i           i   v v   i   vii  viv     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_162928801_   4956 GTTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAAC 5005
                          vv  vi       v  v     i     ivv    v iv i  v    -
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA- 796

  chr1_162928801_   5006 AAACAAACAACCCCATTAAAAAGTGGCCAAAGGACACGAACAGAC--TCT 5053
                          i     i     v   ?    i   v       ivi   i    -- ii
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_162928801_   5054 TCAAAAGAAGAAATGCGTGAGGCCAAAATATTAACAAAAAAAAA-GCTCA 5102
                           v        v  i iviv      --  vvv   vi    i -     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAA--TAAGCACATGAAAAGATGCTCA 894

  chr1_162928801_   5103 ACGTCACTGATCAT 5116
                           i   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (152 / 106)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3290 26.54 0.55 0.55  chr1_162944201_162950479.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_162944201_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_162944201_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_162944201_   4981 TACCAA-TGACTTTCTT-CAAAGAATTGGAAAAAACT-ACTTTAAAGTTC 5027
                          v   i-  v    i  -  i -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_162944201_   5028 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5077
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_162944201_   5078 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5127
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_162944201_   5128 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5177
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_162944201_   5178 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5225
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_162944201_   5226 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5275
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_162944201_   5276 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5325
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_162944201_   5326 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5375
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_162944201_   5376 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5425
                           i ?   ii    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_162944201_   5426 CCTAGGCATTACCATTCAGGGCATAGGCGTGGGCAAGGACTTCATGTCCA 5475
                          v    ?i v viv   iv i v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_162944201_   5476 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5525
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_162944201_   5526 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5575
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_162944201_   5576 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5625
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_162944201_   5626 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5675
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_162944201_   5676 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5725
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_162944201_   5726 CTCTAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCAT 5775
                            i        i  vi viii     v  i        i i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_162944201_   5776 CATCACTGGCCAT 5788
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1301 18.38 0.00 1.10  chr1_162978104_162980733.rev       73   344 (2286)    L1M4_orf2#LINE/L1      640   908 (0)  

  chr1_162978104_     73 GACTGCATCAAAACTTAAAACTTTTATACATCAAAAGACACAATGAACAG 122
                             v        i v         i i v     i     v  v  v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_162978104_    123 AGTGGAAAAGTGACATACAAAATGGGAGAAAATATTTGCAAATTATATAT 172
                             i   iiii  vi   i                       i      
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_162978104_    173 CTGATTGAGGAATTGATATCCAGAATATATAAAGAACTCCTACAACCCAA 222
                              -i   i i vi                       i      i   
  L1M4_orf2#LINE/    740 CTGAT-AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_162978104_    223 CAATGAAAAAAACCAAATACCTTGATTTAAAAATAGGCAAAGGACTTCAA 272
                         i   i    i --      v iii   ?      i         i  v  
  L1M4_orf2#LINE/    789 TAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_162978104_    273 CAGACACTTCTCCAAAAAAGATACACAAATAGCCAACAAGTATATAAAAA 322
                         i     i         i      i      i     i   i i  i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_162978104_    323 CATGTTCAATATCACTAATTAT 344
                         v   i    i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.45 (38 / 11)
Gap_init rate = 0.01 (2 / 269), avg. gap size = 1.50 (3 / 2)  

3007 26.25 1.55 1.00  chr1_162978104_162980733.rev     1237  2139 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_162978104_   1237 TAGAAAAACATTCCATGCTCACAGATAGGAAGAATCAATATCATTAAAAT 1286
                          i    i i  i     i   ii   v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_162978104_   1287 GGCCAGACTGCCCAAAGCAATTTAAAGATTCAATGCTATTCCTATCAAAC 1336
                            v v   v      vii  i  v        i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_162978104_   1337 CACCAG-TGTCATTCTTCACAGAGCTAGAAATAACT---TTTAAAATTCA 1382
                         iv    -  i -  i  ii    iv v  v - i  ---ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chr1_162978104_   1383 CATAGAACAAAAAAAGGAGCTCA-AATAGCCAAGGCAATCCTAAGCAAAA 1431
                         i  i   -- viv    ii i  -         ii     i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_162978104_   1432 AGAACAAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAGG 1481
                                  i      vv   i   v  ii i      viv       ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_162978104_   1482 TCTACAGTAACCAAAACAGAATGGTACTGGTACAAAAACAGACATATAGA 1531
                         v         i   i    vi         i i  ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_162978104_   1532 CCAATGGAACAGAATAGAGGGCCCAGAAATAAGGCTGCACACCTACAACC 1581
                         i        i     v   i i          iv iii   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_162978104_   1582 A-CTGACCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGACTCC 1630
                          -i   ii  i     i v  v   i v  vv            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_162978104_   1631 CTGCTCAATAAATGGTGCTGGGAT--CTGGCTAGCCATATGCAGAAGATT 1678
                           vi    i              i--    v  ?   i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_162978104_   1679 GAAACTGAACCCCTTCGTTACATCATGTACAAAAATCAACTCAAGATGGA 1728
                            ii  i      v v i   i   i         i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_162978104_   1729 TTAAAAAACTTAAATGTA-GAACTCAAAACTATAAAAACCCTAGAAGAAA 1777
                          i ? i - i        -  i  -            vi i         
  L1M4_orf2#LINE/    497 TCAWAGA-CCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAA 544

  chr1_162978104_   1778 ACCTGGGCA-ATACCATCCTAGATATAGGAATGAGCAAAGATTTCATGAC 1826
                           v i  ?i- v i v  v -  iv v  iv ii    v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_162978104_   1827 AAAGACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAGTGGGATC 1876
                         v v             vvv          v      v  i  i v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_162978104_   1877 TAATTAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAAAGCA 1926
                          v  i   v    i i   i  ii vv    i  v        v    ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_162978104_   1927 AATCGTCAACCTACAGAATGGGAGAAAACTTTTGCAACCTATGCATTTAA 1976
                           vv v     i                iv       vii  ii  i i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_162978104_   1977 CAAAGGTCTAACATCCAGCAACTATAAGGAACTTAAAGAAATTTACAAGA 2026
                         i  i  v  vii      v vv     i     ivv v  v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_162978104_   2027 AAAAAAACAAACACCCCTATTAAAAAGTGGG-AAAGGACATGAACAGGCA 2075
                             i -    i v   v   ?    i    -      iv    i  i  
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_162978104_   2076 ---CTACAAAAGAAGACATACATGTGGCCAAGAAACATATGAAAAAAAGT 2122
                         ---  v    -     i     vi       v  i  i       i v i
  L1M4_orf2#LINE/    843 TTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_162978104_   2123 TGAATATCACTGATCAT 2139
                          v  i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (147 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.35 (23 / 17)  


3011 26.90 0.55 1.98  chr1_163009981_163018422.rev     4998  5904 (2538)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr1_163009981_   4998 ATGCTCATGGGTAGGAAGAATCAATATCATGAAAATGGCCATACTGCCCA 5047
                            i      i v      v i     ii v  i     v     v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_163009981_   5048 AGGTAATTTATAGATTCAATGCCATCCCCATCAAGTTACCAATGACTTTC 5097
                          iv i  i  i        i  v     i     iv v   iivi i  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr1_163009981_   5098 TTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATATGGAACAGAAAAGA 5146
                           ii     v v  v  i  - iii    i           vv v  i i
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_163009981_   5147 GCCC-GCATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGTA 5195
                         i   - v  v     iv     i i ivv i          i      vv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_163009981_   5196 TCATGCTACCTGACTTTAAACTATACTACAAGGCTACAGTAACCAAAACA 5245
                            ii  v  ii i  i   viv        i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_163009981_   5246 TCATGGTACTGGTACCAAAACAGCGATATCGACCAACGGAACAGAACAGA 5295
                         vii         i iv ii i  vv    v  i   i    i    iv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_163009981_   5296 CCAAG--CAGAAATAATGCCACATATCTACAGCTATCTGATATTTGACAA 5343
                         --i  --         vv   i i  i  ii ii vi    v  i     
  L1M4_orf2#LINE/    315 --GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_163009981_   5344 TCCTGACTAAAACAAGAAATGGGGAAAGGATTCTGTATTTAATAAATGGT 5393
                         vvv  v v i v  vvv           i  vv v v  i  i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_163009981_   5394 GCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCTGAAACTGGATCTCTTC 5443
                                v      v  ?   i v i i  iiv    ii    i i  v 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_163009981_   5444 CTTACACCTTATACAAAAATTAATTCAAGATGGATTATTCAAGATGGATT 5493
                           i     v              i    i      i ?------------
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAW------------ 500

  chr1_163009981_   5494 ACAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5543
                         --    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    501 --AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_163009981_   5544 AGGCG-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5592
                            ? - v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_163009981_   5593 ACACTAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5642
                             i       vvii         vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_163009981_   5643 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5692
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_163009981_   5693 GGCAACCTACAGAATGGCAGAAAATTTTTGCAATCTACTCATCTGACAAA 5742
                          i     i         v       v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_163009981_   5743 GGGCTAGTATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5792
                           i  v           v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_163009981_   5793 AATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5842
                         i -    i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_163009981_   5843 TCAAAAGAAGATATTTATGCAGCCAAAAGACATGTGAAAAAATGCTCATC 5892
                           v           vi viii     v ii  ii      i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_163009981_   5893 ATCTCTGGCTAT 5904
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (135 / 105)
Gap_init rate = 0.01 (8 / 894), avg. gap size = 2.88 (23 / 8)  

3470 23.23 1.18 3.55  chr1_163009981_163018422.rev     7022  7951 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163009981_   7022 TGGAGAGATATTCTATATTCATGGAGAGGAAGATAAAATATTGTTAAAGC 7071
                             i      i i  i        vv      ivv           iii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163009981_   7072 ATCAGTTCTTTCCCACTTGATCTATAGATTCAACACAATCCTAAACAAAA 7121
                         iv  i v  ii  v v        i         i      iv v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163009981_   7122 TCTCAGCAAGTTATTTTGTGGATATCAACAATTATG-TTCTAAACTTTAT 7170
                           i    vivi v     ii  v  ii    vi-  - i     v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_163009981_   7171 ATAGAGATGCTAAAGACCCAGAACAGCCAACGCAATAT------AGAAGA 7214
                           i  i    v ii         i      vi    v ------      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_163009981_   7215 ACAAAGTCAGAGGACTGACACT-CTGAACTCCAAGACCTACTAAAAAGCT 7263
                                ii       v     - iv  i i   i  i     v      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_163009981_   7264 ACAGTAATCAAGACAGTGTGATATTGGTCCAAGAATAGACAAATATATCA 7313
                                             i  i   ivi   i       v   v    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_163009981_   7314 ATGAAACATAATAGAAAAGCTAGAAATAAGTGCACATAAACATGGTCAAC 7363
                            i  i v   v  i iv i        iiv  i i vvi        i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_163009981_   7364 TGATGTTTAACAAAGGAGCAAAGGCAATACA-TGGATAAAAGATAGTCTT 7412
                             v  ii    i  v  v   i v  v  -   iv   ii        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_163009981_   7413 TTCAACAAATGGTGCTGGAACAATTACACATCCAAATGCAAAAAAAAAAA 7462
                                           i    i iv i ?   v        i  v---
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT--- 446

  chr1_163009981_   7463 AAAAAAAAGAAGAAGAAGAATTTAGCCACACCTTATACCACTCAAAAAAA 7512
                         -----------    vv i i----  vi    i i    ivi v     
  L1M4_orf2#LINE/    447 -----------GAAGTTGGAC----CCCTACCTCACACCATATACAAAAA 481

  chr1_163009981_   7513 GCTTTTCCTGCATTTAACTCAAAATGGATCACAGACATGAATGTAAAATG 7562
                         -------------                  ?    v i       i - 
  L1M4_orf2#LINE/    482 -------------TTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-G 517

  chr1_163009981_   7563 C-AAAACCATAAAACACTTACAAGATAGCATAGAAGAAAACCTAGATGAC 7611
                          -     i       v    v    v i     i? v   i  vvi    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_163009981_   7612 CCTAGATGTGGTGATGATTTTTTAGGTCCAACACCAAGC-CACAGTCCAT 7660
                          i i i vv  ii   i   i    i vii       iv-    iv v i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_163009981_   7661 GAAAGAGATAATTGATAAGCTGGACTTCATTAAAATTAAAAACTTCTGCT 7710
                         i     i v   v     ii          i              i  iv
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_163009981_   7711 TTGCAAAAGATATTGTCAGGAGAATGAGAAGACAAGCCACAGACTGGGAG 7760
                         i v    i  i i i   i  i i   i       v       v      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_163009981_   7761 AAAATATTTGCAAAAGACATATCTGATAAAGTGCTGTTATCCAAAATATA 7810
                                       vv i           i vi  vv      i      
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_163009981_   7811 CAAAGCTCTCTTAAAACTCAACAATAAGAAAACCAACATCTTGATTAAAA 7860
                         i    vv      v       i     i  i  v  i v iii   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_163009981_   7861 AATAGGCAAAAGGCCTGAATAGATACCTTGCCAATGAAGATATACAGGTG 7910
                            i      i iii        i ii iv    v           ii  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_163009981_   7911 GCAAATAAGCATATGAAAAGATGCCCAAAATCATATGTAAT 7951
                           v        i            i   v    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (134 / 78)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 4.00 (44 / 11)  


2637 25.00 1.18 5.04  chr1_163100911_163103160.rev      828  1759 (491)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr1_163100911_    828 CTATTTTCATGAATGAGGAAAC--AATATTATTGAGATGTTTTATTGAAT 875
                          i  v      i  vi i i  --      i  i     vi------   
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC------AAT 56

  chr1_163100911_    876 -CTATAGATCCAAATTCATCTATGGATTCAATAAAATCCTAATTAAAGTC 924
                         -  vi----       v     ii       iiv     iv  i   i  
  L1M4_orf2#LINE/     57 ACTCC----CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_163100911_    925 CCAGTAGG--TGTTTATAAAAATCAACAAGATGATTCCAAAATTTATAGG 972
                             iv v-- v   ii i    ii     v    i i      i   v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_163100911_    973 GAAAGGCAAAGTAACTAGAAGAGCCAAAACAATTTTAGGAGTTGGGGGAA 1022
                             v    i v v i    v            i  iii i-----i   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA-----AGAA 197

  chr1_163100911_   1023 GAACAAAGTTGGAGTACACACATTACTTTACTTCAAGATTTATTATAAAG 1072
                                       v  v    i v iiv i     i i   i  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_163100911_   1073 CAAAAATAACCAA-ACAATGTCCTAATGACTGAAAGATATATAAACAAAT 1121
                          v v i   i   -   i   vv  v  i vv  i    v i v i i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_163100911_   1122 CAGTGAAACAGAATAGAAAGTCCAAAAATGAAAACACACAAATATGGTCA 1171
                           i  i  i     v  i      i    i  vv  i   vv        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_163100911_   1172 ATTGAATTTTGACAAAAATGTGTGGACAAATCACTGGAGAAAGCATAATA 1221
                              v   i     iii  ivvi   v v   v   i     v   i v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_163100911_   1222 TTTTCAACAAATGCAAAGGAGGAGGAGGAGGAGGAAGAGGAGGAAGGGGA 1271
                                      ----------- v vv  iiv  vv   v- ?vviv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATG-----------GTGCTGGGACAACTGGAT-AKCCACA 435

  chr1_163100911_   1272 AGAAGAAGAGGAGGAGGAAGAAGAGGGGCTGCTGG-TCACACATTGCAGA 1320
                         v v i    -------- v    vv  i iv  iv-      vv ii v 
  L1M4_orf2#LINE/    436 TGCAAAAGA--------ATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_163100911_   1321 AAGATTAAGTCAAAATATATCACAGACCTGAATGTGAAATATAAAGCTAT 1370
                           i     v       iv    ?      i     i i vv    i    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_163100911_   1371 AAGACTTTTAAAAGAAAACATGAAAAAATATCCCTGTGATCTTAA-TTAG 1419
                           i   i   i          iii?iv v   iii    i   ii-    
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_163100911_   1420 GCAAAGAATCCTTAGATATGACA--AAAAGCCTGATCCATAAAACAAAAA 1467
                             v iv i             --      vii v v i    v     
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_163100911_   1468 AATGATAAATTGGACTTCCTCAAAATTTTAAAAACCTTTGCTCTGTAAAG 1517
                          vv               v        --      i    iv  vi    
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATT--AAAAACTTTTGTGCTTCAAAG 675

  chr1_163100911_   1518 GATACTCTTAAGAAAATGATTAAAAAACATACACCACAGAATAGGAGAAA 1567
                           i   v i      i   ---   i   -  -         i       
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGA---AAAGACA-AC-CCACAGAATGGGAGAAA 720

  chr1_163100911_   1568 ATATTTGCAAATCACATATCTGACAAAGAACTTGTGTCCAATATATATGC 1617
                                       i        i  i i      i    iv      iv
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_163100911_   1618 GCAGCTCTCA-AACTAAATAGCAAGAAAACAAGCAACCCAGTTGGAAAAT 1666
                         iv i    i -    v    ii  i  i    ii      i  ?i     
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_163100911_   1667 ATAAGGAGCAAAATATCTAAACAGGCACATCACAAAAGAAAATATATGTA 1716
                         ----- i     iv  i i  i  i  iv  v v      i     iiv 
  L1M4_orf2#LINE/    821 -----GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_163100911_   1717 TGGCAAATAAGCACAAGAAAACATGTTGAGCACCATTAATCAT 1759
                             v          v     v   i v i  i  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.02 (19 / 896), avg. gap size = 3.05 (58 / 19)  


3092 26.79 0.77 0.66  chr1_163112445_163118833.rev     4992  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163112445_   4992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5041
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163112445_   5042 GGCCATACTGCCCAAGATAATTTATAGATTCAATGCCATCTCCATCAAGC 5091
                            v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163112445_   5092 TGCCA--TGACTTTCTTCACTGAA-TTGGAAAAAAAATACTTTAAAGTTC 5138
                          v   --  v    i  -i v   -   iv  ivvi  v  --   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCT--AAAATTC 147

  chr1_163112445_   5139 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAACCCTAAGCCAAAA 5188
                                 viiv  ii  v  v v  v     i    i i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_163112445_   5189 GAACGAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5238
                             i   i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_163112445_   5239 CTAGAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGACATATAGAC 5288
                            v     i   i    ii i       i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_163112445_   5289 CAATGGAACAGAGC--AGAGCCCTCAGAAATAATACCACATATCTACAAC 5336
                                 i   ii--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_163112445_   5337 CATCTGATCTTTGACAAACATGACAAAAACAAGAAATGGGGAAAGGATTC 5386
                           vi    i  i     ivi  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_163112445_   5387 CCTATTTAATAAATGGTCCTGGGAAAACAGGCTAGCCATATGTAGAAAGC 5436
                         i  v  i  i       v      v   v  v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_163112445_   5437 TGAAACTGGATCCCTTCCTTACACCTTACAGAAAAATTAATTCAAGATGG 5486
                             ii    i    v   i     v  i v         i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_163112445_   5487 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5536
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_163112445_   5537 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5585
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_163112445_   5586 AAAACACCAAAAGCAATGGCAACAAAACCAACA-TAGAAAAATGGGATCT 5634
                          vi            vvi         vv  v -    v    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_163112445_   5635 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5684
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_163112445_   5685 ACAGGCAACCTACAGAATGGCAGAAAATTTTTGCAATCTACTTATCTGAC 5734
                          v  i     i         v       v       vii iv       i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_163112445_   5735 AAAGGGCTAATATCCAGAATCTACAAAGAACACAAACAAATTTACAAGAA 5784
                           i  i  vi          v  i       v vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_163112445_   5785 AAAATCAAACAACCCCATCAACAATTGGGCGAAGGATATGAACAGACATT 5834
                            iv    i     v  i? v  v     i      v    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_163112445_   5835 TCTCAAAAGAAGACATTTATGCAGCCAAAATACACGTGAAAAAATGCTCA 5884
                             v        i  vi viii     v vi   i      i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_163112445_   5885 TCATCACTGGTGAT 5898
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (135 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


3082 27.04 0.77 0.55  chr1_163124603_163130747.rev     4749  5654 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163124603_   4749 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGACAAT 4798
                               i i  i     i        v      v i     ii v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163124603_   4799 GGCCATAGTGCCCAAGGTAATTTATAGATTCAGTGCTATTCCCATCAAGC 4848
                            v   v v     iv i  i  i       ii  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163124603_   4849 TACCA-TTGACTTTCTT-CACCAAATTAGAAAAAAAATACTTTAAATTCC 4896
                          v   -i  v    i  -  v-     iiv  ivvi  - i v      -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG-AAATTGACAAGCTGAT-CCTAAAATTC- 147

  chr1_163124603_   4897 ATATGGAACCAAAAAAGATCCTGGATAGC-AAGACAATCCTCAGCAAAAA 4945
                                 viiv  ii  i  v i     -  i      i v iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_163124603_   4946 GAACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGG 4995
                                 i      vv   vi  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_163124603_   4996 CTACTGTAACTAAAACATCATGGTACTGGTACCAAAACAGATATATAGAC 5045
                             v    ii  i   vii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_163124603_   5046 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCATACTTCTACCACCA 5095
                                 i    iv   ivii         vv      v i  ivii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_163124603_   5096 TCTGATCTTTGACAAAACTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5145
                         vi    i  i     iiv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_163124603_   5146 TGTTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5195
                          v  i  i        i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_163124603_   5196 AAACTGGATCCCTTCCTTACACCTTATACAAA--TGAACTCAAGATAGAT 5243
                           ii    i    v   i     v        -- v       i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_163124603_   5244 TAAAGACTTAAATGTAAGACCTAAAACCATAAAAACTCT-AGAAGAAAAC 5292
                         i ?    i           v       i      -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr1_163124603_   5293 AGAGGCA-ATACCATTCAGAACATAGGCATGGGCAAAGACTTCATGACTA 5341
                          v   ?i- v i -   ivi  v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_163124603_   5342 AAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTT 5391
                         vi            vvv          vv     v  i    v   ii i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_163124603_   5392 ATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCATCAGAGGGAA 5441
                           i   v v  i i   i  ii vv    i  v       vv i  v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_163124603_   5442 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCATCTGAAA 5491
                         v  i     i                 v       vii  vi      v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_163124603_   5492 AAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAA 5541
                          i  i  vi          v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_163124603_   5542 GAAATGAACAACCCCATCAAAAAATGGGCCAAGTATATGAACAGACACTT 5591
                         i i ii  i     v  i?          v   v  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_163124603_   5592 CTCAAAAGAAGACATTTATGTGGCCAGCAAACATGAAAAAAAAAGCTCAT 5641
                            v        i  vi vi      ii  i  iivi    i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_163124603_   5642 TATCACTGGTCAT 5654
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.09 (12 / 11)  


3427 24.17 1.32 1.10  chr1_163139647_163142403.rev     1363  2268 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163139647_   1363 TGGAAATATATTCCATGTTCATGGATTGGAAGAATCAGTGTTGTTAAAAC 1412
                               v    i                     v i i i       i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163139647_   1413 GATCACACTACCCAAAGCAATCTACAGATTCAATGCAGTCTCTATCAAAA 1462
                          iiv i   v      vii              i   i  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163139647_   1463 TACTAATAACAATCTTCACAGAAATAGAAAAAACAATCCTAAAATTTAAA 1512
                          v i iivi vv i  ii       v  v  ivii           i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_163139647_   1513 TGGAACCACAAAAGACCCAGAATAGCCAAAGCAATTCTGAGCAAGAACAA 1562
                              vii   ii                 i    ii   iv     v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_163139647_   1563 CAAAACTGGAGAAATCATATTACCTGACATTAAGTGATACTACAGAGCTA 1612
                             ii     i v   i i v  ii iv i  ivvv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_163139647_   1613 CAGTAACCAAAACAGCATGGTACTGGCATAA---TTGACACATAGACCAA 1659
                               i   i    ii              --- v    i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_163139647_   1660 TGGATCAGAATAGACAACCGAGAAATAAATCCATACAGCCCTAGTGAACT 1709
                             vi     v  v ii v         i       viiv i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_163139647_   1710 CATTTTTGAAAAAGGTTCCAAGAACATAT-ATTGGGAAAGGGCAACCTGT 1758
                         v     i  v  i   v      v   vi-  v       iii ii  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_163139647_   1759 TCAATAAATGGTGCTGGGAAAACTGGATACCCATATGCAGAAGAATGAAG 1808
                             i              v         ?   i     i          
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_163139647_   1809 TTAGACCCCCTGCTATCTCTCACCATATACAAAAATCAAATTACAATGCA 1858
                           i      ----  i   v                i  v i v    v 
  L1M4_orf2#LINE/    451 TTGGACCCC----TACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_163139647_   1859 TCAAATACTTAAGTCGAATACCTCAAACTATGAAACTACTACAAGAAAAC 1908
                            ? v  i   i vv  v v  v       i     vi  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_163139647_   1909 ACTGAGGAAACTCTCTAGGACATTGGACTGAGCAAAGATTTCTTGAATA- 1957
                          iv i? v  v   iiiv   v    ii ii    v i      ii   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_163139647_   1958 AACCCCACAAGCACAGACAACCAAAGCAAAAATGGACAAATGGGATCACA 2007
                         i  v   v       ii    v    v      i  i    v   iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_163139647_   2008 TTAA-GTTAAAAAGCTTCTTCACAGCAAAGAAAACAATTAACAAAGTGAA 2056
                          i  -i       -   i vii vv     i v  v  i  v        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_163139647_   2057 GAAACAACCCACA-AATGGGAGAAAATATTTTCAAAAGACTTCATAT--- 2102
                         i i          -                 v    -----      ---
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-----TCATATATC 740

  chr1_163139647_   2103 -GACAAGCGATTAATAACTAGCATACATAAGGAATTCAAACAACTCTATA 2151
                         -  i   v  i vi  v i  v   i    i   i  vv       v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_163139647_   2152 GGAAAAAACCCAATAATCCAATCCAAAA-TGAGCAAAAGATCTGAACAGA 2200
                         iv     iv v     i     i?    -  i     i   i    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_163139647_   2201 CATTTATCAAAAGAAGATATAGAAGTGATAAATAGATATATGAAAAGGTG 2250
                              v  v            v  i  iiv    iii i        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_163139647_   2251 CCCAATATTGTTGATCAT 2268
                          i   i  ii????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (132 / 83)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.20 (22 / 10)  


2928 25.49 1.19 2.71  chr1_163199298_163201265      554  1475 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163199298_    554 TGGAAAAAAATTCCATGTTCATGGATAGGAAGAATCAGTATCGTGAAAAT 603
                               i v  i              v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163199298_    604 GGCCATACTGCCCAAAGTAATTTATAAATTCAATGCTATTCTCATCAAGC 653
                            v     v      v i  i  i i      i  v  i ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163199298_    654 TACCA-CTGACTTTCTTCAAAGAAAAAGAAAAAGCT-ACTTTAAATTTCA 701
                          v   -   v    i  -iv     vv  v  -   - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr1_163199298_    702 TATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAG 751
                                viiv  ii  v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_163199298_    752 AACATCCTAAGCAAAAATACTAAGCAAAAAGGCATCACGCTACCTGACTT 801
                             -----------------   ivii i i -    i  v  ii i  
  L1M4_orf2#LINE/    199 AACA-----------------AAGTTGGAGGAC-TCACACTTCCCAATTT 230

  chr1_163199298_    802 CAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTATC 851
                             viv        i          i   i    ii         i  v
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_163199298_    852 AAAACAGATATATAGGCTAATGGAACAAGACAGA-AGCCTCAGAAATAAC 900
                          ii i   i      iii       i ii iv  -  i -         v
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAA 329

  chr1_163199298_    901 ACCACACATCTACAAACATCTGATCTCAGACAAACCTGACAAAAACAAGC 950
                         v   i    i  iiiv  vi    i iv     ivv  v   i v  vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_163199298_    951 AATGGGGTAAAGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGGTA 1000
                                v  ii  vvi  v  i  i              v      i  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_163199298_   1001 GCCATAGGTAGAAAGCA-GAAACTGGACCCCTGCTT-ACATCTTATACAA 1048
                         ?   i v i -    v -   ii         i i -   i v       
  L1M4_orf2#LINE/    430 KCCACATGCA-AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_163199298_   1049 AAATTAGCTCAAGATGGATTAGAGACTTATATGTAAAACCTAAAACCATA 1098
                               i     i      i ?    i  v      i v       i   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_163199298_   1099 AAAACCCTAGATGAAAACCTAGGCA-ATACCAGTCAGGACATAGGCATGG 1147
                            vi i    v      v    ?i- v i -v  iv   v v  vv i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG 577

  chr1_163199298_   1148 GCAAAGACTTCAT-GAT-TGAATCACCAAAAGCAATTGCAACAGGAGCCA 1195
                             v ii   v -   -   --           vvv      ii  vv 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGA--CACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_163199298_   1196 AAATTGACAAATGGGATTTAATTAAACTAAAGAGCTTCCGTTCAGCAAAT 1245
                             v  i    v   i  v  i   v v  i i   ii  v vv    v
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_163199298_   1246 GAAACAATCAG---AGTGAACAGACAACCTACAGAATGGGAGAAAGTTTT 1292
                           v  v    i---      v        i               i v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_163199298_   1293 TGCAATCTATCCATCTGACAAAGGGCTAATATCGAGAATCTACAAGGAAC 1342
                              vii  vi      i  i  i  vi    v     v  i  i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_163199298_   1343 TTAAACAAATTTACAAGAAAAAAGCAAACAACCCCATCAAAAAGTGGGCA 1392
                          ivv    v iv i  v     ii    i     v  i?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_163199298_   1393 AAGTATATGAACAGACACTTCTCAAAAGACGACATTTAAGAGGCCAACAA 1442
                            v  v    i     i     v     v  i  vi  iv      i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_163199298_   1443 ACATGTGAAAAAAAGCTCATCATCACTGGTCAT 1475
                         i  ii      i v     v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (133 / 98)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


3076 28.27 0.22 0.33  chr1_163247269_163253717.rev     5050  5958 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163247269_   5050 TGGAAAAACATTCCATGCTTATGGATAGGAAGTATCAATATCAGGAAAAT 5099
                               i i  i     i i      v     vv i     iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163247269_   5100 ATCCATACTGTCCAAAGTAATTTATAAATTCAATGCTATCCCCATCAAGC 5149
                         iv v     vi     v i  i  i i      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163247269_   5150 TACCATTGAATTTCTTCACAGAATTAGAAAAAACT-ACTCTAAATTTCAT 5198
                          v   vivivi  i  ii     v v  v  i-  - ii     v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_163247269_   5199 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 5248
                               viiv  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_163247269_   5249 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACCACAAGGCT 5298
                               i      vv   ii  v  ii i      viv   i    i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_163247269_   5299 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5348
                                i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_163247269_   5349 ATGGAACAGAACAGAGGCCTCAGAAATAATGCTACACATCTACCACCATC 5398
                               i    iv   ivii         vv i i    i  ivii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_163247269_   5399 TGATCTTTGACAAACCTGACAATAACAAGCAATGGGAAAAGGATTCCCCA 5448
                             i  i     ivv  v   v v  vv       i    i  vvi iv
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_163247269_   5449 TTTAATAAATAGTGTTGGGAAAACTGGCTAACCGTATGCAGAAAACTGAA 5498
                           i  i    i   i     v      v  ?  ii     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_163247269_   5499 ACTGGACTCTTTCCCTTACACTTTACACAAAAATTAACTCAAGAAAGATT 5548
                         ii     i i -v   i    iv  i                i vi   i
  L1M4_orf2#LINE/    450 GTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_163247269_   5549 AAAGATTGAAACATAAGAGCTAAAACCATAAAAACCCTAGAAGAAAACCT 5598
                          ?   iiv   ii             i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_163247269_   5599 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAGTAAA 5647
                            ?i- v i -   iv   v v  vv i     v ii   v iii  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_163247269_   5648 ACACCAAAAGCAATGGCAACAAAAGCCATAATAGACAAATGGGATCTGAT 5697
                                     vvi          vv v      i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_163247269_   5698 TAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATCATCAGAATGAACA 5747
                         i   v v  i i   i  iv vv    i  v       vv i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_163247269_   5748 GACAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCTATCTGACGAA 5797
                                i                 v       vii  v       ii i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_163247269_   5798 GGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTAACAGGAAAAA 5847
                           i  vi          v  i  i     ivv    v i  i iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_163247269_   5848 AACAAACAACCCCACTAAAAATTGGGGGAAGGAAATGAACAGACACTTCT 5897
                         i     i     v i ?    v    vi     vv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_163247269_   5898 CAAAAGAGGACATCTATGCAGCCAACAAACATATGAAAAAAAGCTCATCA 5947
                          v     i  i  vi viii     i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_163247269_   5948 TCACTGGTCAT 5958
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (153 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


1609 28.36 8.45 3.36  chr1_163315983_163319195.rev     1860  2723 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163315983_   1860 TAGAGAGAGATACTAT-TACATAAATGAGATGACTCAGCATTATTACAAA 1908
                          i  i   v  v i  - v   ii  vi  v    i ii   i   - i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGA 49

  chr1_163315983_   1909 TT-TAATCCTTTCCAACTACATCCATAAAGCCAATGCAATCCCAAATAAT 1957
                          v-i   v  ii    v vv   i i i vi   i        v vi  v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_163315983_   1958 ATTCCAGCAGATATTTTTGT-GAAATTGACA-GCTATTTCTAAAACTTAT 2005
                           i     v viv      i-          -   iv i      i i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_163315983_   2006 ATTAAAATGTAGAGATCCTTGAA-AATTAAAGAAAATACTT-ATGAAGAA 2053
                           vi     i ii iv  iv   - iii   - v   -   - vi     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAA-ACAAT-CTTGAAAAAGAA 197

  chr1_163315983_   2054 AAACAAA---------------------AATACCAAACTTTACTATAAAG 2082
                         i      ---------------------   vi    vi      i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_163315983_   2083 ATACAGCAAT---GAT------------GCAT--GGATAGAAACATGGAC 2115
                         v     i   ---  i------------    --       v i  i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_163315983_   2116 CAGTGAAACAGACT--A------AGAAACAAACTCACACATAAACAGCCA 2157
                           i  i  i   v -- ------     i    i  i    vv ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_163315983_   2158 CCAAATTTCCAAAAATGAATGAATAAATAAAAGGCACTATTGTAACTCAA 2207
                         vivi    i i v  - ii  vv-------   --  i   ------   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAA-GGGTGCC-------AAG--ACCATT------CAA 381

  chr1_163315983_   2208 TGGGGGAAATAATGGTCTTTTCAATAAATGGTGCTATATCCACTGGATAT 2257
                              -   v   i          i          iviv v        ?
  L1M4_orf2#LINE/    382 TGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_163315983_   2258 CCGTATGTGGGAAAAATGAA-CGGGATCCTTATATCTCACCATACACAAA 2306
                           ii   iii-  i      -iv   i  i  iv  v       i     
  L1M4_orf2#LINE/    431 CCACATGCAA-AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_163315983_   2307 AAGTAATTCAAAATGGATCATAAATCCAAACATTAAAGGTACAGCAATAA 2356
                           v   i             ? i i i   ii v i  v  v i v    
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_163315983_   2357 CAGTTCT--GAAGGAAATACAAGAAACCATCTTCAGGACTTTGGGATAAA 2404
                         - ii   --    i   i i i ?ivvv      iv   i     v  ii
  L1M4_orf2#LINE/    530 -AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_163315983_   2405 TAAAAGTTTCTTATCTATAATACAAATAATTACAAACCATTAAA---AAA 2451
                         i  vi        vv   i i  v  -  vi    i v iv   ---   
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAA-AAGCACAAGCAACAAAAGAAAAA 627

  chr1_163315983_   2452 CTGGATAAAGTGGGCTTCATTAAAATCTTGAGCCTCTGT----CAAAAGT 2497
                         v i      v   i      i     ivvi i i i   ----    i -
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG- 676

  chr1_163315983_   2498 TATACTATCTTTATGACAATAAAAACACATAACACATACTAGGAGA---T 2544
                         - i      --- v  v i i    v   vvv    v v i     --- 
  L1M4_orf2#LINE/    677 -ACACTATC---AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_163315983_   2545 ATTCACAACAAATGCATGCAACAAAAGACTCATATACAAAATATAAAAAA 2594
                            ii   vvv  ii  vii i  ii    ii   v  i      v   i
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_163315983_   2595 CAATTCTTAC----CAAAGA-AAAAAGATAGACGAATTAGATTGACAATG 2639
                         -  i      ----   vi -       i i ii vii iv ?i v    
  L1M4_orf2#LINE/    773 -AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_163315983_   2640 GACAGAAGACTTGAACAAAT-TTTTAACAAATGAGA-ATATCTATG-CCA 2686
                          i  i i  i     i i i-   ivv    vi   -   ivv   -   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_163315983_   2687 ATAAGCATATTACAAGATGTTCAGCATCTGTACGCAT 2723
                                i  v v      i   i    v????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (152 / 89)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 2.83 (102 / 36)  


 887 27.57 5.14 2.70  chr1_163341747_163346441      499   868 (3827)    L1M4_orf2#LINE/L1      129   507 (401)  

  chr1_163341747_    499 CAAACTAATT-TAAACTTCATGTGGAACCACAAAAGAGCCTGAATAGCCA 547
                            i  i  i-    v     i     vii   ii  v  v         
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr1_163341747_    548 AAGCAATCATAAGCAAAAAGAACAAAGATAAAGGCATCAC---------- 587
                           i     v i iv  i          v ii   vv    ----------
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_163341747_    588 --CAAAATAGATGGTACTGGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 635
                         --     i--- --    i-i   ivv v iv  vv  i v iviviiv 
  L1M4_orf2#LINE/    229 TTCAAAAC---T--TACTA-CAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_163341747_    636 --AAAAAAAAGACAGGCACATAGACCAATGAAACAGAATAGAGAACCCAA 683
                         --iiv v  i  i  i  i     i     i  i     v    ii   i
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_163341747_    684 CAATAAAGCCACACACCTACAGTCATCTGATCTCCCACAGGGCCAACAAA 733
                         v      v   i   ii  ii    vi    i i v   i  viiv   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_163341747_    734 A--AT--AAGATTAAGGAAAGGACTTCCTATTGAATAAATGGTGCTGGGA 779
                          --  --  --- ii      i ivvi  v  v  i              
  L1M4_orf2#LINE/    373 ACCATTCAA---TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_163341747_    780 TAGCCGGCTAGCCAATATGCAGAAGAATGAAACTGGACCCCTACCTTATA 829
                         i i i  v  ?   -i     i         ii             i i 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCA-CATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_163341747_    830 CCACATACAAAAATTAACTCAAGATGGATTAAAGACTTA 868
                            i                  i      i ?    i  
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

Transitions / transversions = 2.03 (67 / 33)
Gap_init rate = 0.03 (10 / 379), avg. gap size = 2.90 (29 / 10)  

1205 27.87 1.47 0.24  chr1_163341747_163346441     1169  1577 (3118)    L1M4_orf2#LINE/L1      495   908 (0)  

  chr1_163341747_   1169 GATTAAAGGTTTAAATGTAAGACTTCAAAATATAAGAATTCTAGAAGAAA 1218
                            i ?  iii           vi v   v     i v ii         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_163341747_   1219 ACCTAGGAA-ACACCATTCTGGACATTGGCCTTGGAAAAGAATTTATGAA 1267
                           v    ?i- v i -   vv   v    vi v  v  v iv  iv ii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_163341747_   1268 TAAGTCCTCAAAAGCAATTGCAACAAAAATAGAAATTGACAAGTAAGACC 1317
                           v v vi        vvv         iv i    v  i  i vi   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_163341747_   1318 TAATTAAACTAAAGAGTTTCTTCACAGCAAAAGAAATCATCAACAGAGTA 1367
                          v  i   v v  i ii  i vii vv    i  v ii     v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_163341747_   1368 AACAGACAACTTACAGAATGGGAGAAAATATTCAAAAACTATGCACCTGT 1417
                           v       ii                    iiv   ii  ii i   v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_163341747_   1418 TAAAGGTATAGTATCCAGAATCTATAAGGAGCTT----AATTCAATAAGC 1463
                            i  vv v           v     i  i  i----  i       vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_163341747_   1464 AAAAC-CAAATAAGCCCATTAAAAAATAGGCAAAGGACATAAACAGACAC 1512
                             v-       v  v   ?      i         iv i  i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_163341747_   1513 CCATCAAAAGAAGACATACAAGTGTTCAACAAACATATGGAAAAATGCTC 1562
                         iiv  v        i      i  vi   i  i  i   i   i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_163341747_   1563 AACATCATTAATCAT 1577
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (63 / 48)
Gap_init rate = 0.01 (4 / 414), avg. gap size = 1.75 (7 / 4)  

2806 27.12 3.62 1.02  chr1_163341747_163346441     3318  4202 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163341747_   3318 TGAAAAAACATTCCGTGCTCATGGATTAGAAGAATTTATATTGTCAAAAT 3367
                           i   i i  i  i  i         i     v  v       i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163341747_   3368 GACCATATTACCTAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 3417
                          i v   i v  i   vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163341747_   3418 TACCAA--GATTGTTCTGCTCAGAAATAGAAAAAAACAATTCTACAATTC 3465
                          v   i-- vi v  i   --      v  v  iv-ii  i   v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGC--AGAAATTGACAAGC-TGATCCTAAAATTC 147

  chr1_163341747_   3466 ATGAGGAATAAAAAAAGAGCTCA-AATAGCCAAAAACAATTCTGAGCAAA 3514
                           iv    - viv  i ii i  -           -    ii   iv  i
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAG 195

  chr1_163341747_   3515 AAGAACAAAGCTGAAAGCATCATGTTACTTGACTTCAAAATATATTGCAA 3564
                                   i  i i vv   iii v iii i       iv  i i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_163341747_   3565 GGCTATAGTAACCAG--CAG---GGTATTAGTATAAAAATAGATACATAG 3609
                         i    i     i  i--   ---    i i i    ii     i i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_163341747_   3610 ACCAATGAAACAGAATAGATAATCCAGAAATAAAACCAGATATTTACAGC 3659
                          i     i  i     v  v i            v   v i     ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_163341747_   3660 CAATTGATCTTTGACAAAGTTGGCAAGAACTTATGCTGGGGAGAGGACAC 3709
                                 i  i     i v  v     v v viiv      i  i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_163341747_   3710 CCTTTTCAATAAGTTGTGCTGGGAAAATTCAACAGTCACATGTAGAAGAG 3759
                         i        i  i v         v  i vi i ?i      i i    i
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_163341747_   3760 TAAAACTGGACCCCTATGTCTCGTCATATTAAAAAAAT---CTCAAAATC 3806
                          i  ii          iv  v ii     - v      ---        v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATG 494

  chr1_163341747_   3807 TATTGCAATCTTAAACATAAGACTCAAAAGTATAAAAATGT---GAGAAA 3853
                         v  ii? iv i    ii     vii    v       v v ---i     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_163341747_   3854 ATCTAGGGAAAAAAATCCCTGAACATTTGTCTAGGCAA--ATAACTTATA 3901
                          iv    ?iv   vv i v   v -  v vi       --i vv    v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_163341747_   3902 ACTAACAGCTCAAAAGCACATTCAACGAAAACAAAAATAAACAAATGGAG 3951
                         vv i   --i          vv    i   iv       i i    v ii
  L1M4_orf2#LINE/    594 TATGACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_163341747_   3952 CTTAGTCAAACAAAAAAGCTTCTTCACAGCAAAAGAAGTAATCAATAGAG 4001
                            vi     vvv    i   i vii vv    i  viiv     v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_163341747_   4002 TGAAGAGATAATCTGTTGAATGGGAAAAAATATTTGCAAAGTATTCATCC 4051
                             i   i  i iiiv        i              vi  vi   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_163341747_   4052 AACAGGGGACTAATATTCAGACTATACAAGGAACTC---------GACAG 4092
                         i i i      vi   i    v    i  i      ---------i i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_163341747_   4093 GAAAAA-------AATCCCATTAGAAAGTGGGCAAGGGACATAAATTGAC 4135
                         v     -------  i  v   ?i   i       i   iv i   v   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_163341747_   4136 ATTTCTTGAAAGAAGACATACAAATGGACAACAGGTGTAAGAAAAAATGC 4185
                               iv        i          v   i i iii v     i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_163341747_   4186 TCAACATCACTGATCAT 4202
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (153 / 83)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.56 (41 / 16)  


2187 25.65 3.69 1.08  chr1_163386735_163388394.rev      509  1159 (501)    L1M4_orf2#LINE/L1      193   860 (48)  

  chr1_163386735_    509 AAAAAGAACAAAGCCAGAAAGATTACATTACCTGACTTCAAACTATACTA 558
                           i          iii  iiiv i   i v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_163386735_    559 CAAGGCTATAGTAACCAAAAGAGCATGGTACGGGTACAAAAACAGACACA 608
                            i    i     i   i v  ii      v  i i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_163386735_    609 TAGACCAATGGAACAGCATAGAGAACCCAGAAATAAAGCCACACACCTAC 658
                             i        i  v  v    ii           v   i   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_163386735_    659 AGCCATCTGATCTTCGACAAAGGTACAAAAAATAATTAATGGGGAAAGAA 708
                         i i  vi    i        i   i v  i vi v i             
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_163386735_    709 CTTCCTATTTAACAAATGGTGCTGGGATAGCTGGCTAGCCATATGGAGAA 758
                         ivvi  v  i                 i i    v  ?   i   v i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_163386735_    759 GATTTAAACTGGACCCCTACCTATCATTATGTACAAAAATTAACTCAAGA 808
                           v v  ii             vv  ii  i                 i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_163386735_    809 TGGATTAAAGACTTAAATGTAAGACCTCAAACTA--AGAGTCCTAGAAGA 856
                              i ?    i           v  v      -- i v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_163386735_    857 AAACCCAGG---AAATACCTTTCTCAATGTTGGCCTTGGCAAAAAATTTG 903
                             vi   ---    ---i   vii iv    vi v     viiv  iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_163386735_    904 TGGCTAAGTCCTCAAAA--ACAATTGGAACAAAAACAAAAAATTGACAAG 951
                          i v  v v vi     --    -- v       i-       v  i  i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAA--GCAACAAAAG-AAAAAATAGATAAA 636

  chr1_163386735_    952 TGGGATCT-ACTGAAACTAAAGAACTTCTACACAGCAAA----ACTATCA 996
                          v   ii - iii   i    -     i iii vv    ----       
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_163386735_    997 -GTAAGTAAACAGACAACCTACAGAATGAGAGAAAATTTTCAAAAACTAT 1045
                         - v    i  v        i        i        v  iiv   ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_163386735_   1046 GCATCTGACAAAAG-------TCCAGAATCTATAAGGAACTTAAACAAAT 1088
                         ii      i  ii -------        v     i     ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_163386735_   1089 CAACAAGCAAAAAACAA----CCCCATTAAAATGCAGGCAAAGGACATGA 1134
                            i  vv    i    ----   v   ?   viii         iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_163386735_   1135 GCAGACACTTCTCAAAATAAGACAT 1159
                         ii     i     v   v    i  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.88 (107 / 57)
Gap_init rate = 0.02 (12 / 668), avg. gap size = 2.58 (31 / 12)  

 418 21.05 0.88 0.00  chr1_163386735_163388394.rev     1351  1464 (196)    L1M4_orf2#LINE/L1      794   908 (0)  

  chr1_163386735_   1351 AAAAATCCAACAACCTCAT-AAAAAATGGGCAAAGAACATGAACAGACAC 1399
                             iv v  i    iv  -?              i iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_163386735_   1400 TTTTCAAAAGAAGACATACACGTGGCCAACAATCATATGAAAAAAACTTC 1449
                           i  v        i     vi       i  v  i       i vvi  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_163386735_   1450 AACATCACTGATAAT 1464
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.01 (1 / 115), avg. gap size = 1.00 (1 / 1)  


2594 26.49 3.82 1.31  chr1_163431794_163437068     3566  4403 (872)    L1M4_orf2#LINE/L1        1   859 (49)  

  chr1_163431794_   3566 TGGAAAAACCTTTCATGTTCATGGATTGGAAGAATCAAAATCATTAAAAT 3615
                               i iv ii                    v i  v  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163431794_   3616 GGCCATATTACCCAAAGCAATTTACAGATTCAGCACTATTCCTCTCAAAC 3665
                            v   i v      vii  i          i i v  i   v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163431794_   3666 CACCAA-TGCCGTTCTT-CAAAGAATTAGTAAAAACTG-TACTAAAATTC 3712
                         iv   i-    v  i  -  i -    i-- v  i   - v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_163431794_   3713 ATATGTAACCAAAAAAAGAGCCTGAATAGCCAAAGCAATTCTAAGCAAAA 3762
                              v  viiv  ii-  v  v           i    ii i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_163431794_   3763 AGAAAAAA--------ACT-ATATAT---GACTTCAAA-CATATTATAAA 3799
                             v   --------   - i iv ---i i      - v  i  i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_163431794_   3800 ACTATGGTAACTTAAACAGCATGATACTGGTACAAAAACAGACACATAGA 3849
                         i   ii    iiv i    ii  i      i i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_163431794_   3850 ACAATGGAACAGAATAGAAAACTCAGAAATAAAGCCACACAC----AACC 3895
                         v        i     v  i iii          v   i   i----iii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_163431794_   3896 ATCTGATCTTCAACAAGACCAACAAGAATAAGCAATGAGGAAAGGA--GT 3943
                          vi    i   i     iviiv     vi vv     i      i --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_163431794_   3944 CCCTTTTCAATACACGGTGCTCGGATAACTGGCTAGCCATATGCAGAAGA 3993
                          --       i v i      v   i      v  ?   i     i    
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_163431794_   3994 ATGAAACTGGACCTTAACTTT-CACCATACATAAAAATTTAACTCAAGAT 4042
                              ii      iiv  i i-       i i       -       i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AACTCAAAAT 493

  chr1_163431794_   4043 GGATTAAAAATTTAAATGTAAGACCTCAAACTCTAAGAATCCTAGAAGAA 4092
                             i ? i ii           v  v     v   i v  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_163431794_   4093 AATTTAGG---AAATACCCTTAGCAATATTGGTCTTGGCAAAGAATTTAT 4139
                           iv    ---    ---   v ii iv    vi v     v iv  iv 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_163431794_   4140 GACTAAGTCCCTAAAAGCAATTGCAACAAAAACAAAAATTGAAAAGTGGA 4189
                         iiv  v v v i       vvv         iv      v  v  i v i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_163431794_   4190 ACCTAATTAAACTAAAGAGATTTTGCACAGCAAAATAAACTATCAATAGA 4239
                           i v  i   v v  i iv     ii vv    iv v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_163431794_   4240 GTAAGCAGACAGTCTACAGAATGGGAGGAAATATTTACAAACTGCAGAT- 4288
                           i iv     ii i            i        i    iiii v  -
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_163431794_   4289 -GACAAAGGTCTAATATCCAGAATCCATAAGGAACTT----AAGTCAACA 4333
                         -  i  i  v  vi          vi    i     i----  v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_163431794_   4334 AGCAAAAAACAAAGAATCTCATTTAAAAATGGGCAAGAGATATGGACAGG 4383
                          vv    i     v  i iv   ?            ii   v  i i  i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_163431794_   4384 CACTTCTCAAAAGACAGATA 4403
                           i     v     -     
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGA-AGATA 859

Transitions / transversions = 1.74 (139 / 80)
Gap_init rate = 0.02 (20 / 859), avg. gap size = 2.15 (43 / 20)  

 206 20.73 14.63 0.00  chr1_163431794_163437068     4701  4782 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_163431794_   4701 AAAAATAAATAAAAGAC------AGACACTTCTC----AAAAACATACAT 4740
                               iiii   i  i------     i     ----i  i i     v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_163431794_   4741 GCAGCCAACAA--ACATGAAAAAATGCTCATCATCACTAATCAT 4782
                         iii     i  --         i       v     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 7.50 (15 / 2)
Gap_init rate = 0.03 (3 / 94), avg. gap size = 4.00 (12 / 3)  


3025 27.27 2.13 0.22  chr1_163452781_163457092     2929  3819 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163452781_   2929 TGGAAAAACATCCCATGATCATGAATAGGAAGAACTGATATCATTAAAAT 2978
                               i i        v     i  v      vi i    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163452781_   2979 GGCCATATTGTCCAAAGCAATTTACAGATTCAATGCTATTCCTATGAAAC 3028
                            v   i vi     vii  i           i  v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163452781_   3029 TACCAACAACTTTCTTCACAGAACTAAAAAAACT-ATTTTAAAATTCATA 3077
                          v   i vi i  i  ii     v vi v  i  -  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_163452781_   3078 TGGAACCAAAATAGAGCCCAAATAGCCAAGACAATCCTAAGCAAAAAGAA 3127
                              viiv  vi  v  vi         i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_163452781_   3128 CAAAGCTGAACACATCATGTTACCCAACTTCAAACTATACTACAGGGCTA 3177
                              i  i vivv   iii v     i      viv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_163452781_   3178 TAGTAACCAAAATAGCGTAGTACTGGTACAAAAGCAGACACACAGACCAA 3227
                         i     i   i i  i  i       i i  iiii     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_163452781_   3228 TGGAACAGAATGGGGAGCCCAGAAATAAGGCTGCACACCTATGACCATCT 3277
                              i     v i   i          iv iii   ii    ii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_163452781_   3278 TATCTACAACAAAGCTGACAAAAACAAGCAATGGGGAAAAAAATCCCTAT 3327
                         v  i v i    i v  v   i v  vv           i  vvvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_163452781_   3328 TTAATAAATGGTGCTGGGATAACTGGCTAGCCACATACAGAAAAATGAAG 3377
                          i  i              i      v  ?      i  i  i       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_163452781_   3378 CTGGATACCTTCCTTGCATCATATACAAAAATCAACTCAAGATGGATTAA 3427
                         i    iv   v   ii  i             i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_163452781_   3428 AGACTTCAACGTAAAATACAAAACTATAAAAACCCTGGAAGACAATCTAG 3477
                             i v  i    i vvi            vi i i     v  iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_163452781_   3478 GCAATACCATCTAC---ACATAAGGACAGGCAAAGATTTTGTGACAAAGA 3524
                          ?i-  v-    v ---  v vi  vi      v i   iv iivv v  
  L1M4_orf2#LINE/    551 GNG-TAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_163452781_   3525 CACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAA-------TTAATT 3567
                                    vvv          v      v  i  -------  v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_163452781_   3568 AAACTTAAGAGCTTCTGCACAGCAAAAGAAACTATCTATAGAGTAAACAC 3617
                            v    i i   i  ii vv    i  v      v v i   i  v v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_163452781_   3618 ACAGCCTACAGAATGTGACAAAATGTTTTCAAAGTATGTAAATGACAAAG 3667
                            i  i        v  v     i   v    vi  i  vv   i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_163452781_   3668 GTCTAAAATCCAGCATCTATAAGGAAC----ATAAGTTTACAAGAGAAAA 3713
                          v  viv      v  v     i    ---- i  v iv i  v i   i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_163452781_   3714 ACAA----CCCCATTAAAAAGTAGGCAAAGGATATGAACAGACCCTTTTC 3759
                             ----   v   ?    i i          v    i    vi  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_163452781_   3760 AAAAGAAAACATGCATGTGGTCAAAAAGCATATGAAAAACAGCTCGATAT 3809
                         v      i i  i  vi   i   v     i       ivv    i i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_163452781_   3810 CACTGATCAT 3819
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.00 (21 / 7)  


3251 26.46 0.77 0.66  chr1_163479711_163486686.rev     5579  6485 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163479711_   5579 TGAAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5628
                           i   i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163479711_   5629 GGCCTTACTGCCTGAAGTAACTTGTAGATTCAATGTTATCCCCATCAAGC 5678
                            vv    v  ii  v i ii ii        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163479711_   5679 TACCA-CTGCCTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAACTT 5725
                          v   -        i  -i     -   --- v  i  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr1_163479711_   5726 CATATGTAACCAAAAAGAGCCCACA-TAGCCAAGACAATCCTGGGCAAGA 5774
                               v  viiv  i ii    v -       i      i  iiv    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_163479711_   5775 AAAACAAAGCTGGAGGCATCACGCTACCTGGCTTCAAACTTTACTACAAG 5824
                          i       i      vv    i  v  iiii      vi         i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_163479711_   5825 GCTACAGTAACCAAAACAGCATGGGACTGGTGCCAAAACAGGTATATAAA 5874
                                   i   i    ii   v     iiiv ii i  ii     i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_163479711_   5875 CCAATGGAACAGAACGGAGGCCTCAGAAATAACACCACACATCTACCACC 5924
                         i        i    iv   ivii         vv   i    i  ivii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_163479711_   5925 ATCTGATCTTTGACAAAACTGACACACACAAGCAGTGGGGAAAAGATTCC 5974
                          vi    i  i     iiv  v  vivv  vv  i        ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_163479711_   5975 CTATTTAATAAATGGTGTTGGGAAAATTGGCTAGCCTTATACAGAAAACT 6024
                           v  i  i        i     v  i   v  ?  vi  i  i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_163479711_   6025 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGATGGA 6074
                            ii         v   i     v           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_163479711_   6075 TCAAAGACTTAAATGTAAGACCTAGAGCCATAAAAATCCTAGAAGAAAAC 6124
                            ?    i           v   i i i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_163479711_   6125 CT--GAGCAATACCATTCAGGACACAGGCATGGGCAAAGACTTCATGTCT 6172
                         v -- ? i  - i -   iv   viv  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_163479711_   6173 AAAACACCAAAAGCAACGGCAACAAAAGCCATAATTGACAAATGGGATCT 6222
                          vi            vvi          vv v   v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_163479711_   6223 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 6272
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_163479711_   6273 ACAGGCAACCTACAGAATGGGAGAACATTTTTGCAATCCATCCATCTGAC 6322
                          v  i     i              v  v       vi   vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_163479711_   6323 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 6372
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_163479711_   6373 AAAAGCAAACAACCCCATC-AAAAATGGGCAAAGGATATGAACAGACACT 6421
                            ii    i     v  i-                 v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_163479711_   6422 TCTCAAAAGAAGACATTTATGCAGCCAACAGACTTATGAAAAAATGCTCA 6471
                             v        i  vi viii     i ii vi       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_163479711_   6472 TCATCACTGGTCAT 6485
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (145 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3192 26.57 0.77 0.66  chr1_163500191_163504311.rev     2724  3630 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_163500191_   2724 TGGATTAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 2773
                             vvi i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163500191_   2774 GGCCATACTGCCCAAGGTAATTTATAGATCAAATGCCATCCCCATCAAGC 2823
                            v     v     iv i  i  i    iv  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163500191_   2824 TACCA-CTGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2870
                          v   -        i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_163500191_   2871 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAA 2920
                                 viiv  ii  v  viv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_163500191_   2921 GAACAAAGCTGAAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 2970
                                 i  i   vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_163500191_   2971 CTACAGTAACCAAAACAGCCTGGTACTGGTACCAAAACAGAGATATAGAC 3020
                                  i   i    iv         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_163500191_   3021 CAATTGAACATAAC--AGAGCCCTCAGAAATAGTACCACACATCTACAGC 3068
                             v   i v  i--    i  --       ivv   i    i  ii i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_163500191_   3069 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 3118
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_163500191_   3119 CCTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAGC 3168
                         i  v  i  i  i           v      v  ?   ii  i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_163500191_   3169 TGAAACCGGATCCTTTCCTTACGCCTTATACAAAAATTAATTCAAGATGG 3218
                             iii   i  i v   i  i  v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_163500191_   3219 AT-AAAGACTTAAATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAA 3267
                           - ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_163500191_   3268 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 3316
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_163500191_   3317 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3366
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_163500191_   3367 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3416
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_163500191_   3417 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 3466
                          v  i     i                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_163500191_   3467 AAAGGGCTAATATCCAGAATCTACAAAGAATTTAAACAAATTGACAAGAA 3516
                           i  i  vi          v  i      i ivv    v ii i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_163500191_   3517 AAAATCAAACAACCCCATTAAAAAGTGGGCAAAGGATATCAACAGAAACT 3566
                            iv    i     v   ?    i            v v  i   v i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_163500191_   3567 TCTCAAAAGAAGACGTTTATGCAGCCAACAGACACATGAAAAAATGTTCA 3616
                             v        ii vi viii     i ii          i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_163500191_   3617 TCATCACTGGCCAT 3630
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


 762 16.41 12.82 5.13  chr1_163724684_163728209      479   673 (2853)    L1M4_orf2#LINE/L1      246   455 (453)  

  chr1_163724684_    479 AATTACAGTGCATTAATAAAA-GTGGTCTTAAGTATGAGGACAGATGTAT 527
                          ii      i-  i  v v i-     vi -i i  i    i   ii   
  L1M4_orf2#LINE/    246 AGCTACAGTA-ATCAAGACAGTGTGGTACT-GGCATAAGGATAGACATAT 293

  chr1_163724684_    528 GTAAATCATTGGAATAGAATTGAGAGTCTATTCCAGAAATAAACTCATGT 577
                         -- i    v                   -----           i   ii
  L1M4_orf2#LINE/    294 --AGATCAATGGAATAGAATTGAGAGTC-----CAGAAATAAACCCATAC 336

  chr1_163724684_    578 ATCT------------------------GTGCCAAGACCATTCAATGGAG 603
                           i ------------------------                    - 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-G 385

  chr1_163724684_    604 GGAAGAATAGTCTTTAAAACAGATGGTTCTAGGGCAACTGGATATCCACA 653
                          i             vv    i     v  i  i          ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_163724684_    654 TGCAAAATAATGAATTTAGA 673
                                v      v  i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGA 455

Transitions / transversions = 2.44 (22 / 9)
Gap_init rate = 0.03 (7 / 210), avg. gap size = 5.00 (35 / 7)  

1837 14.29 6.61 5.76  chr1_163724684_163728209     1047  1515 (2011)    L1M4_orf2#LINE/L1      436   908 (0)  

  chr1_163724684_   1047 TACAAATGGACTGAGACAGGGACCCTACCTAACAC-------AAAAATTA 1089
                          i    -i  v   iiiv  iv        v    -------        
  L1M4_orf2#LINE/    436 TGCAAA-AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_163724684_   1090 GTTCAAAATGGATTAAAGACCTAA-TGTAAGAGCTAAAATTATGCAACTG 1138
                         ii           i ?        -              i   iv    v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_163724684_   1139 TTAGAGGAAGAAAATACAAGTGTAAATCTTCATGACCTTAGATGAGGAAA 1188
                              ---      i i i ?          i       i i v   v  
  L1M4_orf2#LINE/    535 TTAGA---AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_163724684_   1189 CAGTCTCTTA-ATAGGACACCAAAAGAACAAACAA-----GAAAAAATA- 1231
                         ii  i     -   v           v    i   -----         -
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_163724684_   1232 AT---TTGGAATATATCAAAACTAAGTCCTAAAAAGCAGACTTGTGTGTT 1278
                           ---     v vi       i   ------------ i    v    i 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAA------------AAACTTTTGTGCT 669

  chr1_163724684_   1279 --AAAAGATACTATCAAGAAAGTGAAAAAGACAACACACAGAATGGGAGA 1326
                         --   i  i                   -      v              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAA-GACAACCCACAGAATGGGAGA 718

  chr1_163724684_   1327 AAGTATTTACAAATCATTTATCTGATAAAGGTCTAGTATACAGAGTA-AT 1375
                           i     i        v          i  v  v    v    i  -  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_163724684_   1376 AAAGAACTCTTA--AC--AATAA--AAAAGACGA----CCCGGTTTCTAA 1415
                                     --  --     --       i ----   ii  ?vv  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_163724684_   1416 ATAGGCAAAAGATTTGAAAAGATATTTCAAATATCTGTTCCAAAGAAGAA 1465
                           i      i        v   i     ----------           v
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTC----------TCCAAAGAAGAT 858

  chr1_163724684_   1466 ATACAAATGGCCAATAAGCATACAAAAAGATGTGCAACATCATTAATCAT 1515
                                             i ii        iv        ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (41 / 23)
Gap_init rate = 0.04 (17 / 473), avg. gap size = 3.41 (58 / 17)  

2059 25.68 3.91 0.00  chr1_163724684_163728209     2446  3033 (493)    L1M4_orf2#LINE/L1      298   908 (0)  

  chr1_163724684_   2446 CAGTGAAACAGAATAGAGAATCCAGAAATAAACCCAAATACTTACAGCCA 2495
                           i  i  i     v    i                v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_163724684_   2496 ACTGATCTTTGACAAAGCAAACAAAAACGTAAAGTGGGAAAAGGACACCC 2545
                          i    i  i     i vviv   i v i vv i    i    i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_163724684_   2546 TATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGGGGAATT 2595
                          v                    i  i   vv ?       i iii    v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_163724684_   2596 AAACTGGATCCTCATCTCTCACTTTTTACAAAAATCAACTCAAGATGGAT 2645
                           ii    i  ii i   v   iv v         i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_163724684_   2646 CAAGGACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGAGAACA 2695
                           ?i   i     v     v  i           v ii       i    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_163724684_   2696 TTGGAAAAACCCTTCTAGATACTGGCTTAGGCAAGGATTTCATGACCAAG 2745
                          v  ?iv  vi    vv  ivi   v        v i    v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_163724684_   2746 AACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGA----AT 2791
                          vv         v v    i    iv   i   i   iv v   ----  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_163724684_   2792 TAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAA-- 2839
                         i   v v  i i      iiivv    i iv  vi   iv i   i  --
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_163724684_   2840 -------CACAGAGTGGGAGAAAATCTTCACCATCTATACATCTGACAAA 2882
                         -------      i           v  ii v vii   i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_163724684_   2883 GGACTAATTTCCAGAATCTACAACAAACTC----AAATTAGCAAGAAAAA 2928
                              vi v        v  i  vi     ----  v i ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_163724684_   2929 ---AAAT--CCCA-TCAAAAAGTGGTCTAAGGACATGAATAGACAATTCT 2972
                         ---    --    - i?    i   v v     iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_163724684_   2973 CAAAAGAAGATATACAAATGGCCAACAAATATATGAAAAAATGCTCAACA 3022
                          v                       i  ii i       i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_163724684_   3023 TCACTAATGAT 3033
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (89 / 58)
Gap_init rate = 0.01 (6 / 611), avg. gap size = 3.83 (23 / 6)  


2508 23.77 2.15 0.46  chr1_163738253_163739896.rev      502  1153 (491)    L1M4_orf2#LINE/L1      246   908 (0)  

  chr1_163738253_    502 AGCTATAGTAACCAAAACAGCATGGTATTGGTATAAAAATAGACACATAG 551
                              i     i   i    ii     i   i    ii       i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_163738253_    552 ACAAATGGAACAGAATGGAGAACTGAGAAATAAAGCCATGTATTTACAGC 601
                          iv       i     v    iiiv         v    ii     ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_163738253_    602 CAACTGACCTTTTACAAAGCCAACAAGAACTTACATTGGAGAAAGGATAC 651
                            i   ii  iv    i viiv     v v v  v   i     i   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_163738253_    652 TCTCTTCAATAAATTGTGCTGGTAAAATTAG----CCACATGCAGAAGAA 697
                            i     i    v       v v  i i ----         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_163738253_    698 TGAAACTGGACTCCTAGCTCTCACCATATACAAAAATCAATTCAAAATGG 747
                             ii     i    v   v                i  i         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_163738253_    748 ATTAAAGCCTTAAACATAAGACCTGAAACTATAAAAATACTAGAAGAAAA 797
                           i ?  v i    ii     v  i           v vi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_163738253_    798 CCTAG-AGTAAA-CTCTAGGACATTGGTCTATGCAAAGAATTTATGACTA 845
                          v   -?     -  iiiv   v    vi  v    v iv  iv iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_163738253_    846 AGACCTCAAAAGCACAGGCAACAAAACCAAAAATAGACAAATGGGACCTA 895
                         v   vi          i         vv         i    v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_163738253_    896 ATTAAA-CTAAAAACTTTT-TGCCCAGCAAAATAAATAATAAACAGAGTG 943
                           i   -i           -   ii--    iv v iv  v  v i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTG 693

  chr1_163738253_    944 AAGGGACAACTTGTTGAATGGGAGAAAATGTTTGCAAACTACCCATCTGA 993
                           ii      iiiiv              i        ii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_163738253_    994 CAGGGTACTAATATCCAGAATATAAAAAGAACTCAAACAACTCAACAG-- 1041
                         i i  v   vi             v         vv         i i--
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_163738253_   1042 AAAAAACAA----CTCCATTAAAAAGCAAGCAAAGAATGTGAATAGCTAT 1087
                             i    ---- i v   ?    iiii      i  v       vi  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_163738253_   1088 TTCTTAAAATAAGGCATACAAATGCTCAACAGGTATATGAAAAAAATGTT 1137
                             iv   v   ii         vi   i i i i       i -  i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr1_163738253_   1138 CAACATCACTATCAGA 1153
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (98 / 54)
Gap_init rate = 0.01 (9 / 663), avg. gap size = 1.89 (17 / 9)  


1878 26.09 5.60 1.05  chr1_163992836_163996075     1550  2120 (1120)    L1M4_orf2#LINE/L1        1   597 (311)  

  chr1_163992836_   1550 TAGAAGCACAACTCATGCTCATGGACTGGAAGAATCAATATTGT------ 1593
                          i   iv i v i    i       i       v i        ------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_163992836_   1594 -GC---------CAG-TTGA----CAGATTCAATGCAGTCCCTATCAAAA 1628
                         -  ---------  i-    ----         i   i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_163992836_   1629 TACCAACATCATTTTTCATGGAATTAGAAAAAT--ATCCTAAAATTCATA 1676
                          v   i vv v     iiii   v v  v  ii--               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_163992836_   1677 TGGAACCAAAAAAGAGCTCAGG-TAGCCAAAGGTAATTGTAAACAAAAAG 1725
                              viiv  ii  - i   i-        i-i   iv i  v  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAG 198

  chr1_163992836_   1726 AACAAATCTGGAGGCATCACCCACTACGGGATTTCCAGTTATACTACAAG 1775
                               vi      vv    --   v vvi     v iviv        i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCAC--ACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_163992836_   1776 GCTGTAGTTACCAAAGCAACATGGTACTGGTATAAAAGTCGGCATGTAGA 1825
                            ii   v i   ii  iii         i    iii v i   i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_163992836_   1826 CCAATGGAACAGGACAGAGAACTCAGAAATAAAGCCAAATATGTATAACC 1875
                         i        i  i iv    iii          v   v i  v   iii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_163992836_   1876 AACCTGATCTTCAATAAAGCATACAAAAA--AGTAAATTAGGAAAGGACA 1923
                           i-    i   i i  i -i i v  i -- v v   vi      i i 
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_163992836_   1924 CCCTATTTAATAAATGGTGCTGGGAGAACTGGTTAGCCACATGAAGAAGA 1973
                         vi  v  i  i              v      v  ?       v i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_163992836_   1974 ATGAAACTGGATTCCTATCTCTCACCTTATACAAAAGTCAATTCAAGATG 2023
                              ii    ii    i   v    v         i i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_163992836_   2024 GATCAAAGACTTAAATCTAAGACTCAAAACTG--GAACT---AGAAGATA 2068
                              ?    i     v     vii      i--i    ---      v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_163992836_   2069 ACCTTGGAAAACCTCTTC-TGACATTGGCCTAGGCAAAGAATTCATGACT 2117
                           v v  ?iv vv     -    v    vi       v iv   v iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_163992836_   2118 ATG 2120
                            
  L1M4_orf2#LINE/    595 ATG 597

Transitions / transversions = 1.70 (92 / 54)
Gap_init rate = 0.03 (15 / 597), avg. gap size = 2.53 (38 / 15)  

 991 24.10 2.28 0.98  chr1_163992836_163996075     2441  2747 (493)    L1M4_orf2#LINE/L1      598   908 (0)  

  chr1_163992836_   2441 ACCCCAGAAGCAAATGCAACAAAA----ACATAAATAAATGGGACCTAA- 2485
                           v   i     v v         ---- v   i      v    i v -
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_163992836_   2486 CGGAATCAAAAAACTTCTGCACAGCAAAAGAAATAATCATCCGAGTACAC 2535
                          ii   i     -   i  ii vv    i  v iv    vvvi   iv v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_163992836_   2536 AGACAACCCACAAAGTGGGAGAAAATATTTGCAAACTATACATCTGACAA 2585
                                     i i                    ii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_163992836_   2586 AGGACTAGTATCCAGAATCTACAAGGAACTCAAACAAATAAGCAGGAGAA 2635
                         i     v           v  i  i      vv    v v ii -- v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA--ATAA 794

  chr1_163992836_   2636 AAACACAAATAATTCCATCAAAAAGTGAGTAGATGACAGGAGTAGACATT 2685
                            v        ii v  i?    i  i i i v  ivv  i        
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_163992836_   2686 TCTCAAAATAAGATATACAAGTGGTCGACAA--ACATGAAGAAGTGCTTG 2733
                             v   v           i   i i i  --       i ii    ii
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_163992836_   2734 GAATCATTAGTCAT 2747
                         iv    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (43 / 30)
Gap_init rate = 0.02 (5 / 311), avg. gap size = 2.00 (10 / 5)  


1506 24.47 10.40 8.51  chr1_164055182_164057027.rev      502  1347 (499)    L1M4_orf2#LINE/L1       34   895 (13)  

  chr1_164055182_    502 CTCAATATTGTAAAAATGTCAGTTCTCCCCAAACTGACCTATGGATTCAA 551
                           i        v  i   v  i v         i   i   ii       
  L1M4_orf2#LINE/     34 CTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAA 83

  chr1_164055182_    552 AGTAAATTCATATGAAAATCTCAATAAATTATTTTCTCTCTGTCTTTTTT 601
                         v i  - i v   v      i  i---------------   i       
  L1M4_orf2#LINE/     84 CGCAA-TCCCTATCAAAATCCCAG---------------CTGCCTTTTTT 117

  chr1_164055182_    602 TTGGAGCAGAGGGGTAGAACTTAACAAGTTGATTCTAAAATTTACATAGA 651
                         ------------- i    v  i     i    i        i i  i  
  L1M4_orf2#LINE/    118 -------------GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_164055182_    652 ATGGCATGGG----------GCCAAGATGTTCTTTAAAA-------CA-- 682
                          vv   v   ----------     i iiv    v    -------  --
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_164055182_    683 --TGGAG-ACGTGGATTATCAAGATATTAACATTTAG---AGAGCAATAA 726
                         --     -  viiv i vi v -  v i  v i   v--- i   v i i
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_164055182_    727 TAATTGAGGCAGTGTGGTATTAGCATAGGGATCAACACATATACCAGTG- 775
                             ii  i          i i     i    vi   i   v i  i  -
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_164055182_    776 --CAGAGTCTAGAG-ACAGAGGTA----CACACACCTATGAACACTTGAA 818
                         --i   i iv    -v    ii  ----  i   ii    iv  v    v
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_164055182_    819 ACATGACAGAGGTGAGGAAGGGATGAAAGATGACAGATCAATGAGGAAAG 868
                         vivi    ii    vv----------    iv i---      i      
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCC----------AAGACCAT---TCAATGGGGAAAG 390

  chr1_164055182_    869 GGTGGAGTTTTTAATAAA-------GGGGTAGCTGGGTATCTATTTAAAA 911
                         ii i vv    i  i   -------   ii i    i  ? i iv i---
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG--- 437

  chr1_164055182_    912 AACAAAAAACAAAAAACTAGAC----ACATTACACTATACTAAAAAAAAA 957
                         --     i - vi  ii i   ----  v i    i   i----------
  L1M4_orf2#LINE/    438 --CAAAAGA-ATGAAGTTGGACCCCTACCTCACACCATAT---------- 474

  chr1_164055182_    958 AAAAGAAAGAAAAATGAAAATTTCAGAA-GGATTAAAAGCCAAAATGTGA 1006
                         ------- v      v  ---i   i  -    i ? ii  v      i 
  L1M4_orf2#LINE/    475 -------ACAAAAATTAA---CTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_164055182_   1007 AATGC-AAAACTATAACATTCTTAGAAGATAACATAAAAGAATATCATTC 1055
                         i -  -          v i          v      ii? v v   v iv
  L1M4_orf2#LINE/    515 GA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_164055182_   1056 TAACCTTGGGAAAGTGAAGAATTTCTT---TAT-------------CAAG 1089
                          i        vv  vv  vii      ---   -------------    
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_164055182_   1090 AACCAAAAGATGAAAACACATAAATTTAACTACTTTAAAATTAAAAGCT- 1138
                         v v       -i    i v       vi   v v i          i  -
  L1M4_orf2#LINE/    614 CAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_164055182_   1139 -----CATCAAAGGGC--TAC--ATAAAGTGAATTGA--------AAAA- 1170
                         ----- v       i --  i-- v        vv  -------- i  -
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_164055182_   1171 ---AGAAAATATTTACAATCCATACAAACAACAAAGGATTAGTATTCAGA 1217
                         ---           i   vi    i vvii i  i   i v    i    
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_164055182_   1218 ATACACAAAGAACTCCTATGAGTCAATAAGAAAAAGTCAA----CCCAAC 1263
                            i i         i  ii v       v      v   ----     i
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_164055182_   1264 AGAAAAAATAGGCAAGATAAATGAACAGGAATTTAACAAAGGAAGAAACA 1313
                         -v?      i     iiv vv    i  iv    vv v  i     v i 
  L1M4_orf2#LINE/    813 -TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_164055182_   1314 CAGATGGCCCATAAACACAGGAAAAGATGTTCAA 1347
                           i      v    i    v         i    
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.57 (124 / 79)
Gap_init rate = 0.04 (33 / 862), avg. gap size = 4.85 (160 / 33)  


2426 24.62 4.27 4.92  chr1_164060333_164063267.rev     1531  2444 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_164060333_   1531 TAGAAAATAATTCCATGAGCGAGGGTTGGAAAAATCAATACCTTTAAAAT 1580
                          i    ivv  i     vv iv  i      i v i    iiv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_164060333_   1581 GTCTATACTGCCCAAAGCAATCTACAGATTCAACACTAGTCTTATCAAAT 1630
                          v v     v      vii               i v vi i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_164060333_   1631 TACCAACATCATTTTTTTTACATAATTAGAAAAAAACT-ATTCTAAAATT 1679
                          v   i --iiii      i  v  v v  v  i--  -  i        
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT 146

  chr1_164060333_   1680 CATATAGAACCA-AAAAGAGCCTGAATAGCCAAGGCAATCCTAAACAAAA 1728
                              i   vii-  ii  v  v          ii     i i  -   i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAG 195

  chr1_164060333_   1729 AAGAATAAAGCCAGAAGCATCACATTACCTGACTTCAAGCTATACTACAA 1778
                              i    iii  i vv     i v  ii i     iviv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_164060333_   1779 GGCTAC-TTAATGAA-ACAGCATGGTACTGGTACAAAAATAGATACACAG 1826
                         i     -v    v  -    ii         i i  ii     i i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_164060333_   1827 ACCAATATAACAGAGTAGAGACCTCTAAAATAAAGCCCCACACCTACACC 1876
                          i    iv  i   i v    vii vi       v  vi   ii  iivi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_164060333_   1877 CAACTGATCTTTGACACAG---TCAAGAAAAATAAACAATGGGGAACAGG 1923
                            i    i  i    vi ---i     vv v ---          viii
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAAGAA 392

  chr1_164060333_   1924 CACCCTAT------AACGGTGCTGGGAAAACTGGCTGACCATATGCAGAA 1967
                         i vi  v ------  i          v      v i?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_164060333_   1968 GAATGAAACTGGACCGCTACGTCTCACTATATACAAAAATTAACTCAAGA 2017
                                ii      v    v  v   i                    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_164060333_   2018 TGGATTAAATACTTCCATGTAAGACCACAAACTGTAAAAACCCCAGAAGA 2067
                              i ? v  i vv        v vv     i     vi ii      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_164060333_   2068 AAACCTAGGAGATACTCTT-GTAAACATTGGCCTAAGCAAAGAATT---- 2112
                             v    ? vv v    -  i v -    vi  i    v iv  ----
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTA 591

  chr1_164060333_   2113 --TATGACTAACTACTCAAAAGCAAACGCAACAAAAATAAAAACAGACAA 2160
                         --      -----  -        v v         iv     i   i  
  L1M4_orf2#LINE/    592 GATATGAC-----AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_164060333_   2161 CTTGGATTTAATTAAACTAAAGAGACAGGACTGAGGAGATAGGTACACTG 2210
                         v     i  v  i   v v  i ------   ------- vv  i viii
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAA------ACT-------TTTGTGCTTCA 672

  chr1_164060333_   2211 AGGGCCAAAACCAACTATCAAAAGAAACTATCAACAGAATAAACAACCTA 2260
                          i  -----  --        --    v -------   v i      i 
  L1M4_orf2#LINE/    673 AAGG-----AC--ACTATCAA--GAAAGT-------GAAAAGACAACCCA 706

  chr1_164060333_   2261 CAGAATAGGAGAAAATATTAGCAAACTGTGCATCCAAAAAAGGACTAATA 2310
                               i            v     iii ii   ii v  i     vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_164060333_   2311 TCCAAAATCTATAAGGAACTT----AAATCAACAAGAAAAAAA------A 2350
                             i   v     i     i----  v    i  v     i ------ 
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_164060333_   2351 CTTCATTAAAAAGCAGGCAAAG-------ACAGACACGTCTCAAAAGAAG 2393
                          iiv   ?    iii       ------- i     iv    v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_164060333_   2394 ACATACAAGCAAGTCAACAA--ACATGAAAAAATGCTCAACATCACTAAT 2441
                          i      iii- i   i  --         i             ?????
  L1M4_orf2#LINE/    857 ATATACAAATG-GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_164060333_   2442 CAT 2444
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.63 (137 / 84)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.23 (84 / 26)  


2633 21.50 11.71 2.05  chr1_164085019_164087402     1073  1900 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_164085019_   1073 TAGAAAGAAGTAATATGTTCATGAATCAGAAGACTTAAGTTAAATGTTAA 1122
                          i      vi vvi         i  ii          --  v-      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAA--TAT-TGTTAA 47

  chr1_164085019_   1123 AATGTCAGTTTTTCCCAAATTGACCTCTAGATTCAAC--AGTCTCAACCA 1170
                         i   v  i vi i          i  vi         -- i  i v i  
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_164085019_   1171 ATA-CCTAGCAGGCTTTTTTGTAGAAATTTGCATACTGTTTCTAACATTT 1219
                          v -  i   v v        i       vi  vi   v i    v   i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_164085019_   1220 ATATAGAACTGTAGAAAACACAGAATAACCAAA-CGATTTTGA----GAA 1264
                             i   v  i iiii  v       i     - i  i    ----   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_164085019_   1265 GAA---AATTGAAGGACT---ACT----GATGTCAAGAATAATTATAAAA 1304
                            --- i   i      ---   ----i  v    i v v i  i   i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_164085019_   1305 CTCAAGTAATGAAGACAGTGTAATACTGGCATATGGATAGAAATAGAGAT 1354
                           vv      v          ii          v       v   v    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_164085019_   1355 CAGTGGAACAGAATAGAAGGTCCAG---TAGATCCACATGTATATGGCCA 1401
                           i     i     v  ii      ---  i i   i ii v     i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_164085019_   1402 ACTGATTTGC--CAAAGGTGCCAAAGGAT--TTCAATGGGAAAAAAAAAG 1447
                          i      v --   i        --  i--         i   i  v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAA--GACCATTCAATGGGGAAAGAATAG 395

  chr1_164085019_   1448 TCATT-CAAAAAATGCAGCTGAAACAATAGG----------GAAAAAAAA 1486
                           v  -   v     vv    ii    iv  ---------- v    i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_164085019_   1487 TAAAAAACCTTGACTATTATTTCACACCATGTACAAAGATTTGTTTGA-- 1534
                          i  i---i v   ivi  ii         i      i   vii ii --
  L1M4_orf2#LINE/    446 TGAAG---TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_164085019_   1535 TGGGTCATAGACCTAAACTTA-GAG--AAAA-----AAGCT--TGGAAAA 1574
                            i   ?         iv  -   --    -----  i  -- i   i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_164085019_   1575 AAA------------TCTTTGTGTCCTTGGGTTAGGCAAGGATTTCTTAA 1612
                            ------------    i   v               v i       i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_164085019_   1613 ATAGGACACAAAAAGCAC------CATAA--AATAATGGATAAATTTAAT 1654
                            v     v        ------  v  --  v   i        vi i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_164085019_   1655 TTCATAAAAATCAAAAGCTT-----------------CTCTCAAGTGAAT 1687
                              v     i    i   -----------------  v     vi i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_164085019_   1688 GAAAAGAAAACC-ACAGATGGGGAGAAAATATTTATGAA--ACATATCTG 1734
                                v    -     vv              iii  -- i       
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_164085019_   1735 ATAAAACATTTGTGTTCAGAATGTCTAAAGAACTCATTCAAGTTAATAAT 1784
                             iiv i    i i      i v          v v   v i      
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_164085019_   1785 AA---GACAA----TCTGATTTAAAGGAATGGGCAGCAAAAAAATTGGA- 1826
                           ---     ----i ii   ?   --        ---  ii v   i -
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAA--AATGGGCA---AAGGATTTGAAT 837

  chr1_164085019_   1827 -GATACGTCACCAAAGATGATATGTAAATGTCCAGCAGGCATATGAAAAG 1875
                         -  i iv  v       v     ii     v   ii i   i        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_164085019_   1876 ATGCTCAAAAACCGTTAGTGATCAG 1900
                                 ---- i i ????????
  L1M4_orf2#LINE/    888 ATGCTCAA----CATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (113 / 63)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.45 (114 / 33)  


 275 21.88 0.00 1.56  chr1_164107727_164109535       50   113 (1696)    L1M4_orf2#LINE/L1        8    70 (838)  

  chr1_164107727_     50 ATATTCCATGTTCATGTTTTGGAAGACTAAGCATTCTTAAGATGACAGTT 99
                             i           vv          v ii   v        i  i -
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT- 56

  chr1_164107727_    100 TTTCTCCAGCTTGA 113
                         vi  i   iv    
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGA 70

Transitions / transversions = 1.33 (8 / 6)
Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1)  

3225 20.69 6.98 3.30  chr1_164107727_164109535      500  1316 (493)    L1M4_orf2#LINE/L1       62   908 (0)  

  chr1_164107727_    500 CCAGCTTGATTTATAGATTCAACAAAATCATAGTAAAAATTCCAACAGGT 549
                            iv     i  i         iv    vivi v     i   i ----
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC---- 107

  chr1_164107727_    550 TTTTTCTTTGTTTTGTTTTAAAGAAATCGATAAACT----CT-------- 587
                         --------  ii  -    iv      i  i  i  ----  --------
  L1M4_orf2#LINE/    108 --------TGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_164107727_    588 --TGGAA------GGGACCAAGAATAGCCAAAACAATTTTGAGAAAGAG- 628
                         --     ------      v                 i    i     i-
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_164107727_    629 --TGAAATCAGAGGATTTTCATGTCCTAATTTCAAAGTTTACTGTAAAGC 676
                         --ii  i ii     i iv  iv   i         ii     ii     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_164107727_    677 AACAATAATCAAAGCAGTGTATTACTGGTATACATATAGATATATAGATT 726
                         v   i       ii      iv      i   viv     i        i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_164107727_    727 AAATGGAACAAAATTAAGAGTCCAGAAGCAAAACTTTAAATTTATGCTTT 776
                           -     i i    i           ii   v iv  v       v iv
  L1M4_orf2#LINE/    299 AA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_164107727_    777 ATTGATTTTTGACAGAGGTGCCAAGGCAATTCAATAGGGAAAGGACAGTC 826
                                  i    ii         i v       i       i i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_164107727_    827 TT--CAACAAATGGTTCTAGGACAACTGGATATCCATATGCAGAAAGAGG 874
                           --           v  i             ?   i     i  ---- 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA----G 443

  chr1_164107727_    875 AATAGAGGAATTTAGATCCTTACCTTACACCGTGCATAAAAATTAACT-G 923
                            ----   v  i  i  i     i     i ii i           -i
  L1M4_orf2#LINE/    444 AAT----GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_164107727_    924 AAATGGATCAAAGGCCTAAATATAAGAGCTGAAACTATAAAGTTGCTAGT 973
                                   ?  i       i        i          ii vi   v
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_164107727_    974 AAATAAAGTAGGACAAAATCTTTGTGACCTTGGGTTAAGCACAGAGTTCA 1023
                          i v  vi    ?vv       i              i   vv iv   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_164107727_   1024 TATACACAGCACCAAGAGAACGATCCATAAAAGAAAAAAAAATTAG-TAA 1072
                           v i iii      i  v  i v v i           ----   -   
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA----TAGATAA 635

  chr1_164107727_   1073 ATTCAGCTTCATCAAAAGTAAAATCTTTTGTGCTTCAAAAG--------- 1113
                            vii           v     v               i ---------
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_164107727_   1114 ------------------CCACAGACTGAGAGAAAACATTTGCAGATCAC 1145
                         ------------------       v  i       i       i    i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_164107727_   1146 ATATCCAATAAAGAAATTGTGTCTAGAATGTATAAACAACTCTTACAACT 1195
                              ii    i i v    i  i     i      v             
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_164107727_   1196 CAATAGTAAGAATATAAACAACTCAGATTTTTAAATGGACAAATG-TT-- 1242
                              i   i  v i   i   i  -   ?vv      i    v -  --
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTG 834

  chr1_164107727_   1243 AGTAGACATTTTACCAAGGAAGATATAGGAGTGACTAGTAAGCACATGGA 1292
                          i         iv    i         vi i  i i i          i 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_164107727_   1293 GAGATATGTGACATTAGCATTACT 1316
                         i    iivii    i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.44 (117 / 48)
Gap_init rate = 0.02 (17 / 847), avg. gap size = 4.94 (84 / 17)  


2193 26.30 5.36 0.16  chr1_164585962_164591359.rev     2056  2671 (2727)    L1M4_orf2#LINE/L1        3   650 (258)  

  chr1_164585962_   2056 GAAAGATATTCCATGCTTATAGATTGGAAGA---------------ATGT 2090
                                  i     i i  i          ---------------   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_164585962_   2091 TCATACTACCCAAAGCAATCTACAGATTCAATGCAATACCTAACAAAATA 2140
                         iv     v      vii              i     v    v      v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_164585962_   2141 CCAATGACATTCTTCACAGAAATAGAAAAAAAAAATTCTAAAATTTACAT 2190
                            iivi v  i  ii       v  v  ivvi - i        i i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATAT 151

  chr1_164585962_   2191 GGAACCACAAAAGACCCAGAGTAGCCAAAGCTATCTGAAGCAAAAAGAAT 2240
                             vii   ii        i        i v    vi iv  i     i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_164585962_   2241 AAATCAGGAGGAATCATATTATCTGACTTCAAATTATACCACA--GCTAT 2288
                            viv      v   i i vi ii i      viv   i   --    i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_164585962_   2289 AGCAACCCAAATAGCATAGTACTGGCATGAAAACAGACACATAGACCAGT 2338
                           i  i v i i  ii i          i ii i     i     i  i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_164585962_   2339 GGAACAGAATAGAGAAACAAGAAATAAACTCATACATCTACAGTGAACTA 2388
                             i     v    iv v          i       i  ii  v  i i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_164585962_   2389 ATTTTTGACAAAAGAGCCAAGAATAT--AA--AGGAAAAGACAATCCCTT 2434
                              i     ii v       vi  --  --i     ii i i  ii  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_164585962_   2435 CAATAAATTGTGCTGGGAAAACTGGATATCCATATGCAGATGAATGAAAC 2484
                            i    v         v         ?   i     i v       ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_164585962_   2485 TAGACTCCTATCTCTTGCTATATACAAAAATCAAGTCAAAATGGA----- 2529
                          i   i    i   vii i            i  v          -----
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_164585962_   2530 --CTT-----TGAGACATCAAACCATGAAACTACTACAAGAAAACATTGG 2572
                         -- i ----- i   vv v    i  i     vi  v          v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_164585962_   2573 GGAGACTCTCAAGGACATTGGAGTGGGCAAAGATTTCTTGAGTAATACCC 2622
                         ? vi v   iviv   v    iv i     v i      iii  vv  v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_164585962_   2623 CACAAGCACAGGCAACCAAAGCAAAAATGGACAGATGGGATAACATCAA 2671
                           v       i     v    v      i  i i  v   ivv      
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

Transitions / transversions = 1.81 (103 / 57)
Gap_init rate = 0.01 (7 / 648), avg. gap size = 4.86 (34 / 7)  

3054 28.29 0.77 0.44  chr1_164585962_164591359.rev     3500  4404 (994)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_164585962_   4404 TGGAAGAACATTCCATGCTCATGGATAGGAAAAATCAATATCATGAAAAT 4355
                              ii i  i     i        v    i v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_164585962_   4354 GGCCATACTGCTCAAGGTAATTTATAGATTCCATGCCATCCCCATCAAGC 4305
                            v     v i   iv i  i  i      v i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_164585962_   4304 TACCAATGACTTTCTTCACAGAATTGGAAAAATCTACTTTAAAGTTCATA 4255
                          v   iivi i  i  ii     v v  v  iiiv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr1_164585962_   4254 TGGAACCAAAAAAGAGCCTGCATTGTCAAGATAATCCTAAGCAAAAAGAA 4205
                              viiv  ii  v  v v  v i   i i    i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chr1_164585962_   4204 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 4155
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chr1_164585962_   4154 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGACCAA 4105
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

C chr1_164585962_   4104 TGGAATGGAAC--AGATCCCTCAGAAATAATACCACACATCTACAACCAT 4057
                               i   i--   vi  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

C chr1_164585962_   4056 CTGATCTTTGACAAACCTGAAAAAGACAAGAAATAGGGAAAGGATTCCCT 4007
                         i    i  i     ivv  vv  iiv  vvv   i       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

C chr1_164585962_   4006 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3957
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

C chr1_164585962_   3956 AACTGGATCCCTTCCTTCCACCTTATACAAAAATTAATTCAAGATGGATT 3907
                          ii    i    v   iv    v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

C chr1_164585962_   3906 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAACC-T 3858
                          ?    i       v   v       i      vi i         v - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

C chr1_164585962_   3857 AGGCA-ATACCATTCAGTACATAGGCATGGGCAAGGACTTCATGACTGAA 3809
                            ?i- v i -   ivv  v v  vv i     v ii   v iiv ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

C chr1_164585962_   3808 ACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAACAGGATCCAAT 3759
                                     vvi         ivv     v  i   iv   iiiv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

C chr1_164585962_   3758 TAAACTAAAGAGCTTCTGAACAGCAAAAGAAATCATCAG---AGTGAACA 3712
                         i   v v  i i   i  vi vv    i  v ii    i---      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

C chr1_164585962_   3711 GGCATCCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACAAA 3662
                          i  v  i                 v   i   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

C chr1_164585962_   3661 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTGCAAGAAAAA 3612
                           i  vi          v  i        ivv    v ivii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

C chr1_164585962_   3611 AATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 3562
                         i -    i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chr1_164585962_   3561 TCAAAAGAAGACATTTATGCAGCCAACAGACAGATGAAAAAATGTTCATC 3512
                           v        i  vi viii     i ii  v       i   i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chr1_164585962_   3511 ATCACTGGCCAT 3500
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (155 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  

 260 26.67 0.00 0.00  chr1_164585962_164591359.rev     4476  4550 (848)    L1M4_orf2#LINE/L1      764   838 (70)  

  chr1_164585962_   4476 TATATAAGAAGCTGTAACAGCTCTATAGAAAAAAATCTAATAATCTGATT 4525
                                ii i  v v   i   v   iv     iv v     i ii   
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_164585962_   4526 AAAAAATGGGTAAAAGGTCTGAATA 4550
                         ?         i   i i i      
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATA 838

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.00 (0 / 0)  

 331 14.74 0.00 11.58  chr1_164585962_164591359.rev     4837  4931 (467)    L1M4_orf2#LINE/L1      825   908 (0)  

  chr1_164585962_   4837 AAAAGATCGAAATAGACATTTCTCAAAGGAAGACATACAAATGGCAAACA 4886
                            i   ivi              v  i     i           v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_164585962_   4887 AGTATGTGAAAAATATGTGAAAAGGTGCACAACATCACCAATCAT 4931
                           i ii      ----------- i   v        ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAA-----------GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (10 / 4)
Gap_init rate = 0.01 (1 / 84), avg. gap size = 11.00 (11 / 1)  


2319 25.64 12.58 1.71  chr1_164644957_164649536.rev     3271  4089 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_164644957_   3271 TGGAAAAACATCCCATGATCACTGGATATTCAGAAGA----ATATCATTA 3316
                               i i        v   -     ---ii     ----    ii   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCA-TGGAT---TGGAAGACTTAATATTGTTA 46

  chr1_164644957_   3317 AAATGACCATACTGTACAAAGCAGCCTACATATTCTATACAATCCCTATC 3366
                          i   i v     viv    viiii     v    v ii           
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_164644957_   3367 AAAATACCAAGTTAATTTTTTGCAAAATTAGAAAAAACAATCCTAAAATT 3416
                              v   iv vvv         i  v v  v  ivii           
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_164644957_   3417 CATATGGAACCAAAAAGAAGCCCCAATAGCCAAAGCAATGCTGAGCAAAA 3466
                                  viiv  i i v  vv          i    vi   iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_164644957_   3467 AGAATAAAGCTAGAGGCATCACATTATCTAACTTCAAATTATATTACAAG 3516
                             i    i i    vv     i vi i  i      viv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_164644957_   3517 ACTATACTAACCAGAACAGCAGGTTACTGGTATAAAAATAAGACACACAG 3566
                         i   i v   i  ii    iiv v      i    ii   -    i i  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAG 295

  chr1_164644957_   3567 GTCAATGGAACAGCATAGAGAACCCAGAAATAAAGCCGCATACTTGCAGC 3616
                         i         i  v  v    ii           v  ii i i  iii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_164644957_   3617 CAACTGATGTTTGACAAAGCCGACAAGAACATACACTGTGGAAACGAA-A 3665
                            i    v  i     i vi v     v   v  v  v     -   - 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATA 394

  chr1_164644957_   3666 CCCTCTTCAATCAATGGTGCTGAGAAAATTAGATATCCATATGCAGAAGA 3715
                         vi  i     iv          i  v  i i    ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_164644957_   3716 ATGCAATTGAACTCTTATCTCTCACTAATACATAAAAATCAACTCAAGGT 3765
                            v i   i  i i  i   v   i -  i i      i       ii 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCA-TATACAAAAATTAACTCAAAAT 493

  chr1_164644957_   3766 GGATTAAAGACTTAAGTGTAAGACCCAAAACTATAAA------------- 3802
                             i ?    i   i       v i           -------------
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_164644957_   3803 -------------------------------------------------- 3802
                         --------------------------------------------------
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_164644957_   3803 ---GATACTAGAA--------------------AACAGACAAATGGGACT 3829
                         ---  i  i i  --------------------  i   i    v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_164644957_   3830 CAATTAAACTAAAAAGCTTCTGCATGGCAAAAGAAAT----AACAGATTG 3875
                         iv  i   v v    i   i  iiivv    i  v i----  v i v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_164644957_   3876 AAGAGACAACCAATCCTGTTGAATGACAGAAAATATCTGCAAATTATTCA 3925
                           i        v iv-----     iv         i       i  vi 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACA-----GAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_164644957_   3926 TCCAACAGGGGACTAATATCCAGACTACACAAGGAACTCAAACGATTCAA 3975
                           ii i i      vi        v  i i  i      vv  i i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_164644957_   3976 CAACCAAAAAAATCTAACAATCCTATTAAAAAGTAGGCAAAACACATGAA 4025
                         i  i-     i - v  i  i  v   ?    i i      iv iv    
  L1M4_orf2#LINE/    789 TAAT-AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_164644957_   4026 TAGACATTTTTCAAAAGCA--TACAC------CCAACAGGTATATGAAAA 4067
                                  i  v    v --  i  ------    i i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_164644957_   4068 AATGCTCAACATTACCAGTCAT 4089
                         i           i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (137 / 70)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 7.80 (117 / 15)  


3161 14.93 3.37 4.25  chr1_164658282_164659956.rev      502  1184 (491)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr1_164658282_    502 AAAACTTATTACAAAACTACAGTAATCAAGACTGTGTGGCACTGGCAAAA 551
                                 i      i                v      i       v  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_164658282_    552 ACAAACACATACAGATCAATGTAATGGAATTAAGAGTTCAGAAATAAACT 601
                         iv v v     i         v   i     i     i           i
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_164658282_    602 CTTCTATTTATGGTCAAGTGATTTTTTGACAAGAGATCCAAGACCATTCA 651
                          v vi            v       i-      i vv             
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTC-GACAAGGGTGCCAAGACCATTCA 380

  chr1_164658282_    652 ATG---AAAGAAAAGTCTTTTCACCAAATGGTGCTGAGACAACTAGATAA 698
                            ---      v          v            i       i    -
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA- 429

  chr1_164658282_    699 TCGCCACCAAAAAAAAAACAAAAAAAAACACCTTGGACCCCTACTTTATA 748
                         --?    vviv    i  ii  i---------            i i i 
  L1M4_orf2#LINE/    430 --KCCACATGCAAAAGAATGAAG---------TTGGACCCCTACCTCACA 468

  chr1_164658282_    749 CCATATA--AAAATTAACTGAAAATAGATCAAATATCTAAACAGAAGAGC 796
                                --          v     i     ? v i     iiv      
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_164658282_    797 TAAAACTATACAACTCTTAGAAGAAAACA--GGTATAAATCTTCACGACC 844
                                   v                  --  ?i         ii    
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_164658282_    845 AGTGATTAAGCAA--GTTTCTTAAATACGGCACCAACAGCCCAAGCAA-- 890
                         vvv i   i    --        i   i i      v   v       --
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_164658282_    891 ACAGCAAAAA--GA--AATTAGACTTCACCAAAATTAAAAACTTTTGTAC 936
                          v  v     --  --    i       i                   i 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_164658282_    937 ATTAAAGGACACTATGAGGAAGGCAAAAAGACAACCCATAGAATGAAGGG 986
                         v i            v i   i ii             i      iii i
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_164658282_    987 AAATATTTGCAAATCATATATCTGATAAGAGTCCCATGACAAGAGTCCCA 1036
                                                      i v iii i--------i   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTA--------TCCA 760

  chr1_164658282_   1037 GAATATACAAA-------CACAACTCAACAACAAAAAGACAAACAATCCA 1079
                                i   -------i         i  i           i  i   
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_164658282_   1080 ATT-AAAAATAGGTAAAGGATTTAAATAGACATTTCTCCAAAGAAGGTAT 1128
                            -      i  i         i                      i   
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_164658282_   1129 GTAAATGACTCATACCTTCATATGCACATAGAAAGATGCTCAACATCATT 1178
                         ii     i -  -------   v      ii                 ??
  L1M4_orf2#LINE/    861 ACAAATGGC-CA-------ATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_164658282_   1179 AGTCAT 1184
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 2.19 (68 / 31)
Gap_init rate = 0.02 (15 / 677), avg. gap size = 3.47 (52 / 15)  


 213 20.00 0.00 0.00  chr1_164660027_164661680.rev      170   214 (1440)    L1M4_orf2#LINE/L1      214   258 (650)  

  chr1_164660027_    170 CTGACACTACCCAACTTCAAGACTTACTATAAAGTGCCTGTAATC 214
                           v     v     i     i        i    ivv v      
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

Transitions / transversions = 0.80 (4 / 5)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.00 (0 / 0)  

1981 23.38 4.98 2.87  chr1_164660027_164661680.rev      502  1164 (490)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr1_164660027_    502 AAATTTTACTGTAAGGCTACACCAAATAAGACAGTGTGGTATTGGCAAAA 551
                            vi     ii  i      vi  vi              i     v  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_164660027_    552 GAGCAGACAAACAGAT-AACTAAACAGAATTCAGAGCCCAGAAACAGACC 600
                          iii     v i    -  ivi  i      v    i       i i   
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_164660027_    601 CACATAAACACGATCATCGGACCTTTGACAAAGGAGTAAAGTCAATACAA 650
                           i i vvi i i   viv  ii  i     i  v iv   v v  v   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_164660027_    651 TGCAGA-----TAGTCTTTTCAACAAATGGTGCTGCTACAACTGGATATT 695
                           vi  -----                        vv           ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_164660027_    696 CACATGCAAAAAAAATAAAAATAAAAATAAAATCTAGACACATAACTTAC 745
                                    i  ------------- i  i - i   v v  v  i  
  L1M4_orf2#LINE/    432 CACATGCAAAAGAA-------------TGAAGT-TGGACCCCTACCTCAC 467

  chr1_164660027_    746 ACCCTTCACAAAAATTAATTCAAAATAGATCACAGACCTAAATATAAACA 795
                            v vi           i       i     ?          i   ivi
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_164660027_    796 C-AAAACTATAAACCTCTGAGAAGATAACATAGGGAAAAAACTCAGATGA 844
                          -           v    v      v        ?iv   v  iv -   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG-TGA 566

  chr1_164660027_    845 CCTTGGGTATGGTGATAATTTATTAAGTACAATACCAAG-GCAAGATCCA 893
                                 vv  ii  ii   v   ii  ii i     i-   vi v v 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_164660027_    894 TAAAAGAAATCATTGATAAGACTG-ACTTCATTAAAATTAAAAACTTCCA 942
                         i        vv  v     - i  -       i              iii
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAA-ATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_164660027_    943 CCCTGCAAAAGACAATGTCAAGAAAACAAGAAGACAAG--ACAG---GGG 987
                         iv  v    i    v i        iii i       v--    ---   
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_164660027_    988 A---AATACTTTCAAAAGACACATCTGATAAAGTAATGTTATCTAAAATA 1034
                          ---    i  v    vv i i         i v v vv    i i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_164660027_   1035 AATAAAGAACTCTTAAAACACTACAATAAGAA-ACA-----TCTAA---- 1074
                         v              v   v v i     i  -   -----i i  ----
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_164660027_   1075 GAAATGAGCCAAAGGCCAT---AACAGGCA---CCTCAGCAAAGATACAC 1118
                         i     i  -     --  ---  i  i  --- ii  ivi      i  
  L1M4_orf2#LINE/    816 AAAATGGGC-AAAGG--ATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_164660027_   1119 AGATTGCAAACGAGCATATGAAAAGATAATCCACATCCTATGTTAT 1164
                          i  v  v  ii    i          iv  v     v????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (91 / 61)
Gap_init rate = 0.03 (19 / 677), avg. gap size = 2.74 (52 / 19)  


2609 20.85 1.74 14.09  chr1_164856468_164861370.rev     3377  4412 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_164856468_   3377 TGGAAAAA-ATCC-ATGCTCATGGATCAGAAGAATTAATATTGTTAAAAT 3424
                               i -    -   i        ii     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_164856468_   3425 TACCCTACTACACAAAATTATCTATAGGTTTAATGCAATCCCTACCAAAA 3474
                         vi vv    v v    v v     i  i  i  i          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_164856468_   3475 TCCCAATGGCATTATTTACAGAAATAGAAAACACAATCTTAAAATTCATA 3524
                              iiv  v  v   i       v  v  vvii   i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_164856468_   3525 TGGAACCACAAAAGCCTCTGAATAGCCAAAGCCATCCTAAGCAAAAAGAA 3574
                              vii   ii v i v           i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_164856468_   3575 CAGTGCTGCAGGCATCCA-ACTACTAAACTTCAAACTACACTACAAAGCT 3623
                           iv i  v   - ii  -   v iv  i      vivi           
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_164856468_   3624 GTAGTAACCAAAACAACACATAGTACTGGCATAAAAAACAGAAACAGACA 3673
                         ii     i   i   iii-- i            ii -------i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTG--TGGTACTGGCATAAGGA-------TAGACA 290

  chr1_164856468_   3674 CATAGGCTGGGAGCGGTGGCTCATGTCTGTAATCCTAGCACTGCACTCCA 3723
                         i    i--------------------------------------------
  L1M4_orf2#LINE/    291 TATAGA-------------------------------------------- 296

  chr1_164856468_   3724 GTCTGCGTGACAGGAGCAAGACTCCATCTCAAAAAATAAAAATAAAAAAC 3773
                         ----------------------------    ------------------
  L1M4_orf2#LINE/    297 ----------------------------TCAA------------------ 300

  chr1_164856468_   3774 CCAGAAACACAAACTGATGGAGCAGAATAGAGAACCCAGAAACTAATCCA 3823
                         -----------------    ii     v    ii       iv  i   
  L1M4_orf2#LINE/    301 -----------------TGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_164856468_   3824 TGTATCTACAACCAACTAACTTTAGACAAAGGTGCCAAAAC-ATACACTG 3872
                          ii  i  iiii   i i i   v     i        i  -  v  v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_164856468_   3873 GGGAAAAGACAGTCTCTTTAATAAATAAACCATTTGGTACTGGGAAAACT 3922
                               ii i     i  i  i    ---------   i      v    
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAAT---------GGTGCTGGGACAACT 424

  chr1_164856468_   3923 GGATATTCATATGCAGAAGAATGAAACTAG-CTCTTACCCTACAC----- 3966
                              ?i  i     i         ii i - i i    ii    -----
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_164856468_   3967 ---AAAATCAACTCAAAATGGATGAAAAACCTAAATTTAAGATCCAAAAT 4013
                         ---     i              v ? i        v     v i    i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_164856468_   4014 GATAAAACTACTAGAAGAAAATATAGGGGAAACACTTCAGGACATTGGTC 4063
                         v        vi          i     ? v  vv    iv   v    vi
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_164856468_   4064 TGGGGAAAGATTTTATGAATAAGATCTCAAAAGCATAGGCAACAAAAGCA 4113
                          i  v  v i   iv ii   v  ivi        i i          v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_164856468_   4114 AAAATAAACACATAGGATTATATCCAACTACAAAGCTTCTGCACAGCAAA 4163
                               i i v  v   i vi   v  v vv   i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_164856468_   4164 GGAAA--A--AATAGAGTGAAAGGACAACCTGCAGAATGAGTGAAAATAT 4209
                            v -- --  v i       i       ii       i v        
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_164856468_   4210 TTGCAAACTATTAATCTGACAGGGGATTAATATCCAGAATATACAAGGAA 4259
                                ii  vv      i i    i vi             i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_164856468_   4260 CTCAAATACTTCAATAGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4309
                            vv i vi      -------------------- v     i v   v
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATA--------------------ATAAAAAGACAAAT 804

  chr1_164856468_   4310 AATCCCACTAAAATATGGGCAAATGATCTGAACAGACATTTCTCAAAAGA 4359
                           i  v i ?   v         v   i    i           v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_164856468_   4360 AGACATACAAACGACCAACATTTACGAGAAAA-ATGTTCAACATCACTAA 4408
                            i       i i    i vvi  iv     -   i         ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_164856468_   4409 TCAT 4412
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.75 (135 / 77)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 10.25 (164 / 16)  


1476 24.56 8.77 1.32  chr1_165050011_165056275.rev       43   498 (5767)    L1M4_orf2#LINE/L1        1   490 (418)  

  chr1_165050011_     43 TGGAAAAACATTCTATGCTCAGGGATTAAAAGAATCAATATCTTTAAGAT 92
                               i i  i i   i   v     ii    v i     iv       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165050011_     93 GGCCAAACTGCCCAAAGCAATTAACAGATTCAATGCTATTCCTATCAAAC 142
                            v v   v      vii  iv          i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165050011_    143 TACCACCATGC----TTCACGGAATTTGAAAAAAGCT-ATTCTAAAATTC 187
                          v   v -   ----  ii i   v    v  --   -  i         
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTC 147

  chr1_165050011_    188 ACATGGAATAAAAAAAGAGCCTGAATAGGCAAGGCAATCCTAAGCCAAAA 237
                          i      vviv  ii  v  v      v   ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_165050011_    238 GAACAAAGCTGGAGGCAC-CACACTACCTGACGT-GAAACTGTAATATAA 285
                                 i      -  -      v  ii iv -i     -  v  i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chr1_165050011_    286 GGTTACAGAAACCAAAGCAGCATGGTACTGGTACAAAAACAGACACATAG 335
                         i i     v  i   ii   ii         i i  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_165050011_    336 GCCAATGGAACAGAAGAGAAAATTCAGAAATAAAGCCACACACCTACAG- 384
                         ii        i    vv  i i i          v   i   ii  ii -
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_165050011_    385 CAATCTAATCTTGCACAAGGCCAACAAAACAAG-CAATGGAGAAAGGACT 433
                             - i  i  vv      viiv   i  v v-      i     i iv
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_165050011_    434 CCCTTT-------------------------------CATATGCAGAAGA 452
                         vi    -------------------------------  i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_165050011_    453 ATGAAACTGGACTCTTACCTTTCACCATATACAAAAATTAACTCAA 498
                              ii     i i     iv                        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

Transitions / transversions = 1.95 (74 / 38)
Gap_init rate = 0.02 (12 / 490), avg. gap size = 3.83 (46 / 12)  

3301 27.09 0.22 0.22  chr1_165050011_165056275.rev     4867  5774 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165050011_   4867 TGGAAGAAAATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4916
                              ii v  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165050011_   4917 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4966
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165050011_   4967 TACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 5016
                          v   iivi i  i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_165050011_   5017 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5066
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_165050011_   5067 CAAAGCTTGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5116
                              i v    vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_165050011_   5117 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5166
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_165050011_   5167 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT 5214
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_165050011_   5215 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5264
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_165050011_   5265 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5314
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_165050011_   5315 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5364
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_165050011_   5365 AAAGACTTACATGTTAGACCTAAAACCTTAAAAACCCTAGAAGAAAACCT 5414
                          ?    i  v    v   v       iv     vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_165050011_   5415 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5464
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_165050011_   5465 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5514
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_165050011_   5515 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5564
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_165050011_   5565 GCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAG 5614
                         i     i   i             v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_165050011_   5615 GCCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5664
                          v  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_165050011_   5665 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAAACACTTCTC 5714
                              i     v  i?    i     i     iv    i i   i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_165050011_   5715 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 5764
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_165050011_   5765 CACTGGCCAT 5774
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


 660 29.97 14.57 2.15  chr1_165219621_165221190.rev      480  1083 (487)    L1M4_orf2#LINE/L1      230   908 (0)  

  chr1_165219621_    480 TTAACACTTGGTTTAAAGGCA-GGTAATTAAGACAGTGTGCTATCAGGA- 527
                          i  v    iv vi    vi -i     i           v  iii v -
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_165219621_    528 AGGAATAGGCAAACTGACCCATGGAGCAGAGA-AAGAGTGTGGACACAGA 576
                          i i    i  v iv  i v     ii   iv-i     vii  v i i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_165219621_    577 CCCACTTA-ATCTAT----AACTG------GCCAGGCATTGT--AGA--- 610
                             --  -  i   ----  i  ------ v  i vi - i--   ---
  L1M4_orf2#LINE/    330 CCCA--TACATTTATGGTCAATTGATTTTCGACAAGGGT-GCCAAGACCA 376

  chr1_165219621_    611 -TCAGTGGAGAAAGAACAGACAATTAAATAAGTGCTTCTGGATCTAGTGT 659
                         -   i   i       i  v vv  v  i  i  v v    iv v v  v
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_165219621_    660 TCAACCACACAGAGGGAAATGAAATAAGGTCCCTATCTCACA------AC 703
                         vi ?     iiv iiii      i vi ii     i      ------  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_165219621_    704 AA--------------TGAA-----GA----AATGTGGGGGAAAAAAATA 730
                           --------------  i -----  ----     ii i vv    v  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_165219621_    731 AAAGACTTGTAGAAGAAAATATGGAAG---ATCTTTATGAC-------TA 770
                         v  i   iv          i  i i? ---     ii    -------  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_165219621_    771 A-CAA----------------ACACACAAAAACTAAAACCCTAAAGAAAA 803
                         i-   ----------------    -     i vv  i vvi   ii   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACAC-CAAAAGCACAAGCAACAAAAGAAA 625

  chr1_165219621_    804 AGATTGATAAATTTAATGACATTTAAATTAACAACTTCTGCTCATTTAAA 853
                          i  v        vi ivv   iv       v     i  iv v iv  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_165219621_    854 GATG-TATAAACAGGGC-AAAATACAAGACACC-ATTAGGAAGAAATATT 900
                           ii-   v  v ii i-    v    vv   v- v i   ii       
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_165219621_    901 TGCTA--CACATATGAGAAAAAAAAATTTATATCCAGAAAA---AAATAC 945
                            v --  i    vv  v  iii -i  i         v ---   v v
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGA-CTTGTATCCAGAATATATAAAGAA 774

  chr1_165219621_    946 TTCCTACAATT-AGTTTTTTTAAAAAAAAGACCAAAAA---AATCTTGAA 991
                         i  i     i - i ------  v        v  v  ---   - ?i  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAAT------AATAAAAAGACAAATAACCCAAT-TWAAA 817

  chr1_165219621_    992 AATGGGCAAAATCTATGAACAGGTGTTTCATAGAAGAGGAAACACAAAGA 1041
                                   ivv v    i  iii    vivi    i  v i     vi
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_165219621_   1042 ACCCATAAATTAAATGAAAACGTGCTTAACTTTAACCTCATT 1083
                         i  v    ii- v       vi    i   v i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGC-ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (105 / 73)
Gap_init rate = 0.04 (30 / 679), avg. gap size = 3.37 (101 / 30)  


2052 27.34 0.70 2.93  chr1_165240149_165241876      503  1219 (509)    L1M4_orf2#LINE/L1      160   860 (48)  

  chr1_165240149_    503 AAAAGAGTCTGCATTGCCAAGACAATCCTAAGCCAAAAGAACAAAGCTGG 552
                           ii  vi v v  v     i      i i ivv i          i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_165240149_    553 AGGCATCAGGTAGTTGAAGCTACCTGACTTCAAACTATACTACAAGGCTA 602
                            vv   --i v  -------  ii i      viv        i    
  L1M4_orf2#LINE/    210 AGGACTCA--CACTT-------CCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_165240149_    603 CAGTAACCTTGTAGTATACTACAGCATGGCACTAGTACCAAAACAGAGAT 652
                               i v---  ------    ii   i   i i iv ii i   v  
  L1M4_orf2#LINE/    251 CAGTAATCA---AG------ACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_165240149_    653 ATAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATC 700
                              i        i    i--    i  --        vv   i    i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATT 339

  chr1_165240149_    701 TACAACCATCTCATCTTTGACAAACCTGAAAAAAACAAGAAGTGGGGAAA 750
                           iiii  vi v  i  i     ivv  vv  i v  vvv i        
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_165240149_    751 GGATTCCCTATTTAATAAATTGTGCTGGGAAAACTGGCTAGCCATATGTA 800
                          i  vvi  v  i  i    v         v      v  ?   i   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_165240149_    801 GAA-ACTGAAGAGGGATCCATTCTTTACACCTTATACAAAAATCAATTCA 849
                         i  - v     vv   i  v v i i     v           i  i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_165240149_    850 AGATGGATTAAAGAATTAAATGTTAGACGTAAAACCATAAAAACCCTAGA 899
                          i      i ?   vi       v   vv      i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_165240149_    900 AGAAAACCTAGGCA-ATACCATTCAGGACATACGCAAGGGCAAGGACTTC 948
                                v    ?i- v i -   iv   v vv vvvi     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_165240149_    949 ATGACTAAAACACCAAAAGTAATGGCAACAAAAGCCAAAATAGACAAATG 998
                         v iiv  vi          i vvi          vv        i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_165240149_    999 GGATCTAATTAAACTAAAGAGCTTCTGCACACCAAAATAAACTACTATCA 1048
                            ii v  i   v v  i i   i  ii vi    iv v    ii vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_165240149_   1049 GAGTGAACAGGCAACCTACAGAATGGGAGAACATTTTTACAATCTACCCA 1098
                         i      v  i     i              v  v   i   vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_165240149_   1099 TCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTA 1148
                              i  i  i  vi          v  i        ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_165240149_   1149 CAAGAAAAAATCAAACAACCCCATC-AAAATTTGGCAAAGGATATGAACA 1197
                         i  v     iv    i     v  i-    v v          v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_165240149_   1198 GGCACTTCTCAAAAGAAGATGT 1219
                          i  i     v         i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.22 (106 / 87)
Gap_init rate = 0.01 (10 / 701), avg. gap size = 2.60 (26 / 10)  


 647 25.89 4.85 3.24  chr1_165246954_165251346      260   568 (3825)    L1M4_orf2#LINE/L1      595   908 (0)  

  chr1_165246954_    260 ATGACATTGGTCTAAGCAAATAAAGGAAACAAAGGCAAAAACAGACAAAT 309
                               ----- i  --  ii v i v      i v     i   i    
  L1M4_orf2#LINE/    595 ATGACA-----CCAA--AAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_165246954_    310 AGAATTACGTCTAACTAAAAAGCCTCTGCACAGCAAAGGAAATAATCAAC 359
                         v i i v i  v  v v    i i i  ii vv       v iv     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_165246954_    360 AGAGGTAGAAGACCGCTTATGAAACGGGAGAAAATATTTACAAACTATAC 409
                          i  vv i     vi ii iii  i              i    ii   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_165246954_    410 ATCTGATAAGGAATTAATATGCAAAATATATGAAGAACTCAAGGAACTCA 459
                                    i i vi   v  i       i        vviv      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_165246954_    460 TTAGCAAGAAAACAA----CACAATTTAAAAATGGGCAAAAGAGTGTAA- 504
                         v  ii  i  i    ---- v     ?             i  v vv  -
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_165246954_    505 AAACATGCC-------AAGTTATAAAGACCACCAAT--GC-TAGGAAGAA 544
                          i    vi -------   v    v i ivi     --  -i v   i i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_165246954_    545 ACTGCATCAACTATCAAGCAAAAT 568
                          -   -     -    ????????
  L1M4_orf2#LINE/    888 A-TGC-TCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (48 / 31)
Gap_init rate = 0.03 (10 / 314), avg. gap size = 2.50 (25 / 10)  

2987 25.92 1.19 3.13  chr1_165246954_165251346     2975  3900 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165246954_   2975 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 3024
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165246954_   3025 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3074
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165246954_   3075 TACCAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTTCA 3122
                          v   iivi i  i  ii  -      -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_165246954_   3123 TATGGAAC--CAAAAAACAGCCTGCATTGCCAAGACAGTCCGAAGCCAAA 3170
                                v--   iii  --  v v  v     i   i  ivi ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_165246954_   3171 AGAACAAAGTTGGAGGCATCACACTCCCTGACTTCAAACTATACTACAAT 3220
                                         vv       i  ii i      viv        v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_165246954_   3221 GCTACAGTAACCAAAACAGCATGGCGTTGGTACCAAAACAGCATGGCGCT 3270
                                   i   i    --  ----      ---------------- 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAG--TG----TGGTAC----------------T 274

  chr1_165246954_   3271 GGTACCAAAACAGAGATATAGACCAGTGGAACAGAAC--AGAACCCTCAG 3318
                           i iv ii i   v       i  i     i    i--   ii  --  
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AG 322

  chr1_165246954_   3319 AAATAATACCACACATCTACAACCATCTGATCTTTGACAAACCTGACAAA 3368
                               vv   i    i  iiii  vi    i  i     ivv  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_165246954_   3369 AACAAGAAATGGGGAAAGGATTCCCTGTTTAATAAATGGTGCTGGGAAAA 3418
                          v  vvv           i  vvi  v  i  i              v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_165246954_   3419 CTGGCTAGCCATATGTAGAAAGCTGCAGCTGGATCCCTTCCTTCCACCTT 3468
                             v  ?   i   i i  iiv  v  i    i    v   iv    v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_165246954_   3469 ATACAAAAATTAATTCAAGTTGGATTAAAGACTTAAATGTTAGACCTAAA 3518
                                      i    iv     i ?    i       v   v     
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_165246954_   3519 ACCATAAAAACCCTAGAAGAAAATCTAGGCA-ATACCATTCAGGACATAG 3567
                           i      vi i          iv    ?i- v i -   iv   v v 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chr1_165246954_   3568 GCATGGGCAAAGACCTCATGACTAAGACTCCAAAAGCAATGACAACAAAA 3617
                          vv i     v iii  v iiv  v   v         vvii        
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_165246954_   3618 GCCAAAATAGACAAATGGGATGTAAGTAAGCTAAAGAGCTTCTGCACAGC 3667
                          vv        i    v   iv v vi  iv v  i i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_165246954_   3668 AAAAGA-ACCATCAG---AGTGAACAGGCATCCTACAGAATGGGAGAAAA 3713
                            i  -  i    i---      v  i  v  i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_165246954_   3714 TTTTTACAATCTACCCATCTGACAAAGGGCTAATATCCAGAATCTACAAA 3763
                          v   i   vii ivi      i  i  i  vi          v  i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_165246954_   3764 GAACTTAAACAAATTTACAAGAAAAAATCAAGCAGCCCCATCACAAAGTG 3813
                              ivv    v iv i  v     iv   ii i   v  i?v   i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_165246954_   3814 GGCAAAGGAGATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCA 3863
                                  vv    i     i     v        i  vi viii    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_165246954_   3864 ACAGACACACAAAAAAATGCTCATCATCACTGGCCAT 3900
                          i ii    ii    i       v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.86 (40 / 14)  


2400 23.14 3.57 0.93  chr1_165260107_165261742      500  1143 (493)    L1M4_orf2#LINE/L1      248   908 (0)  

  chr1_165260107_    500 CTACAGCAATCAAGACAGTGCGGTATTGGTAAAACAACAGACAAATAGAT 549
                               i             i    i   i v  vi i     v      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_165260107_    550 TGGTCAAACAAAACAGAGAGCTCAGAAATTGACCCACACAAATATGGTCA 599
                         iii vi  i i  iv     ii       vi     i   vv        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_165260107_    600 ACTGGTCTTTGACAAATAAGTAAAGGCAATTCAAT-----------AGTC 638
                          i  i i  i     iviv iv   i v       -----------    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_165260107_    639 TTTTCAACAAATGGTTCTGAAACAA---GACATCAACAT-----AAAATA 680
                                        v   ii    ---  i ? v    ----- i   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_165260107_    681 AATTTAGAAACAGATCTTTTACCTCTTACAAAAATGAACTCAAAATGCAT 730
                           v  i  vv vv i  ivi   viv         v           v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_165260107_    731 CATAGGCCTAAGTGTAAAATACAAAACTATTAAACACCTAGAAGATAACA 780
                           ?  i     i     i vvi        v    v i       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_165260107_    781 TAGGAAAAAATCTAGATGTGTTTGGGTTTGGAGATGGTTCTTTAGATATG 830
                             ?iv      vvi  vvi       v  vi      ii         
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_165260107_    831 TCACCAAATGCACT-GTATACATGAAAGAAAAGTT-GATACATTGGACTT 878
                         v       v    v- i -   --        iv -    v         
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCA-ACA--AAAGAAAAAATAGATAAATTGGACTT 644

  chr1_165260107_    879 CATTAAAATTAAATATTTTTGTTCTGTGAAAGACACTGTCAAGAGAATGA 928
                            i         v i      v  vii  i      i      i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_165260107_    929 GAAG-TAAGCTACAGAGTGGGAGAAA-TATTTTCAAAAGATATATCTGAA 976
                         i   -i  v i     i         -     v    vv          v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_165260107_    977 AGAGGACTTGTTACCCCAAATATAGAAGGAACTCTTAAAGCTCAGCGATA 1026
                          ii        - i  vi      v  i         v i    iii   
  L1M4_orf2#LINE/    745 AAGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_165260107_   1027 AGAAAACAAACAACCTGATTAAACAACCAGGGTAAAAAATCTGAACAGAC 1076
                          i  i     i    ii   ?  v  i--   i   ii  i    i    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAAT--GGGCAAAGGATTTGAATAGAC 841

  chr1_165260107_   1077 ACCTAACCAAAGAAGATATACACATGACAAATAAGCATATGAAAAGATAG 1126
                          ii vv                v   i v        i          iv
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_165260107_   1127 TCTACATTATACCTCAT 1143
                           v    i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (86 / 59)
Gap_init rate = 0.02 (11 / 661), avg. gap size = 2.64 (29 / 11)  


2880 25.83 2.44 1.77  chr1_165379430_165385174.rev     4353  5254 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165379430_   4353 TGGAAAAACATTTTATCCTCATGAATAGGAAGAATTAATATCATGAAAAT 4402
                               i i  iii  vi     i  v      v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165379430_   4403 GGCCTTACTGCCAAAAGTAATTTATAGGTTAAATGCTATTCCCATCAAAC 4452
                            vv    v  v   v i  i  i  i  v  i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165379430_   4453 TACTATTGGCATTCTTTACAGAATTAGAAAAAAATACTTTAAATTTCATA 4502
                          v i viv  v  i   i     v v  v  ivvv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_165379430_   4503 TGGAACCAAGAAAAAGCCAATATAGCAAAGACAATCCTAAGCAAAAAAAA 4552
                              viivi iii v   iv     v  i      i i iv  i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_165379430_   4553 CAAAGCTGGAGGCATCACTCTACCTGACTTCAAATTTTACTACAAGTCTA 4602
                              i      vv    v  v  ii i      vi         iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_165379430_   4603 CAGTAACCAAAACAGCATGGTGCT--CATACCAAAACAGACATATAGATC 4650
                               i   i    ii    i  --    -- ii i             
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATATAGATC 298

  chr1_165379430_   4651 AATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAT 4700
                                i    iv    vii         vv   i    i  iiii  -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA- 347

  chr1_165379430_   4701 CTACAAACATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAA 4750
                         --------  -    i  i     ivv  v   i v  vv          
  L1M4_orf2#LINE/    348 --------AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_165379430_   4751 AGGATTCTCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGC 4800
                           i  vv   v  i  i              v      v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_165379430_   4801 AGAAAACTGAAACTGAACCCTTTCCTTACACCTTATACAAAAATTAACTC 4850
                          i  i v    ii  i    i v   i     v                 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_165379430_   4851 AAGATGAATTAAAGACTTCAATGTGAAACCCAAAATTATGAAAACCCTAG 4900
                           i   i  i ?    i v     i i v i    i   i   vi i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_165379430_   4901 AATAAAACCTAGGCA-ATACCACTCAGGACAT------AGGCA------- 4936
                           v     v    ?i- v i -i  iv   v ------     -------
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_165379430_   4937 --TAGACGAAAATGCCAAAAGCA-ATGTCAACAAAAGCCAAAATTGACAA 4983
                         --    i- vi ii         - v -         vv     v  i  
  L1M4_orf2#LINE/    588 CTTAGAT-ATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAA 635

  chr1_165379430_   4984 ATGGGATCTAATTAAACTAAAGAGCATCTGCATAGCAAAAGAAACTATCA 5033
                           v   ii v  i   v v  i i v i  iiivv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_165379430_   5034 TCAGAGTGAACAGGCAACCTGCAGAATGGGAGAAAATTTTTGCAA-TC-T 5081
                         vv i      v  i     ii                v       -  - 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_165379430_   5082 ACCATCTGACAAAGGTCTAATATCCAGAATCTACAAGGAACCTAAACAAA 5131
                          i-      i  i  v  vi          v  i  i    iivv    v
  L1M4_orf2#LINE/    736 AT-ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_165379430_   5132 TTTACAAGAAAAA-ACAAACAACCCCATCTGAAAGGGGGCAAAGTATATG 5180
                          iv i  v     -     i     v  i?i   iv        v  v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_165379430_   5181 AAAAGACGCTTCTCAAAAGAAGACATTTACATGGCCAACAAACATATGCA 5230
                           v    ii     v        i  vi v        i  i  i   v 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_165379430_   5231 AAAAAGCTCAACATCACTGATCAT 5254
                           i v           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (133 / 96)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.53 (38 / 15)  


2509 26.04 2.25 2.13  chr1_165450443_165452283.rev      506  1350 (491)    L1M4_orf2#LINE/L1       63   908 (0)  

  chr1_165450443_    506 CAAATTAA-----AAATTCAATGCATTTCCCATCAAAATACCAAAATACC 550
                               i ----- i      i   v i  i        v   iv- i  
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCC 111

  chr1_165450443_    551 ATCATTCTTCACAGAACTTGAAAAAACAATCCTAAAATTCATATAGAACC 600
                         ----  i  ii     v    v  ivii                i   vi
  L1M4_orf2#LINE/    112 ----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_165450443_    601 AAAAAAGTACCTTCATAGCTGAAGCAACACTAACCAAAAAGAGCAAATCT 650
                         iv  ii vv  vvv     ii  i   ivi i vv  i    i    vi 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_165450443_    651 AGAGGCATCACATTACCCAACTTCAAACTATACTAGCAAAGACTATAGTC 700
                         i    vv     i v     i      viv     -     -   i   v
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTA-CAAAG-CTACAGTA 255

  chr1_165450443_    701 ACCAAAACAGCATGGTACTGGTATAAAAACAGGCACACAGAATAATGGAA 750
                          i   i    ii         i    ii i  i  i i   vi       
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_165450443_    751 CAAAATAGAGAA-CCAGCAATAAAGCCAAATACTTACACCCAACTAGTAT 799
                         i i   v    i-    v      v   v i i   iivi   i ii v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_165450443_    800 TTGACAAAGCAAACAAAAACGTAAAGTGGGGAAAGGACACCCTATTCAAC 849
                          i     i vviv   i v i vv i         i i vi  v      
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_165450443_    850 AACTGGTGCTGGGATAATTGGCAAGCCATATGTAGAGGAATGAAACTGGA 899
                           v           i  i   vv ?   i   i i i       ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_165450443_    900 GTCTCATGTCTCATCTTATAAAAATATCAACTCAAGGTGGATCAAAGACT 949
                         vi ii iv  v  i v    v   v  i       ii       ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_165450443_    950 TACATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACAGTGGAA-A 998
                           v  v     v  i    i      v ii       v    vv  ?i- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_165450443_    999 AACCTTCTAGACAGTGACTTAGGCAAAAACTTCATGACTAAGAACCCAAA 1048
                           i    vv   vv  iv        viii   v iiv  v  vv     
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_165450443_   1049 AGCAAATGCAACAAAAACAAAAATAAATAAATGGGACCTAATTAAGGAAA 1098
                             v v         iv       i      v    i v  i  ---  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA---AA 652

  chr1_165450443_   1099 TTAAAGAAAAAGCTTCTGTGCAGCAAAAGAAATAATCAGGAGAGTACACA 1148
                              i -----   i     vv    i  v iv    i  i   iv v 
  L1M4_orf2#LINE/    653 TTAAAAA-----CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_165450443_   1149 GACAACCCACAGAATGGGAGAAAAATTTTGCAATCTATGCATCTGACAGA 1198
                                                 vv       vii  ii      i ii
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_165450443_   1199 GGACTAATATCCAGAATCTAAAAAGAACTCAAACAAATCAGCAAGAAAAA 1248
                              vi          v  v         vv    v   ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_165450443_   1249 AATAC-TAATCCA---------TGTCCCCTAAGGACATGAATAGATAATC 1288
                         i i v-   i   ---------  vv v--     iv        i v i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCA--AAGGATTTGAATAGACATTT 845

  chr1_165450443_   1289 CTCAAAAGAGGATATATAAATGGCCAAGAA--ACATGAAAAACATGCTCA 1336
                            v     i      i          v  --         i-       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG-ATGCTCA 894

  chr1_165450443_   1337 ACATCACTAATGAT 1350
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (123 / 94)
Gap_init rate = 0.02 (14 / 846), avg. gap size = 2.64 (37 / 14)  


1074 25.50 4.70 1.01  chr1_165496713_165498854.rev      502   799 (1343)    L1M4_orf2#LINE/L1       46   354 (554)  

  chr1_165496713_    502 AAGGTGTCAATTTTCCCCAAAGTGGTGTATAGATTCCATAGGATCCCGTT 551
                            i  v    vi        v  i v  i      v iivi     vv 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_165496713_    552 CAA-GTCCCAGTAGATATTTTTGCAGAAATTGTCAAGATGATTCTAACAT 600
                            -i      iv viv               v    v    i    v  
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_165496713_    601 TTATATGAAAATTCAAAGGACCTAGGATAGCCAATACAACTATGAAAAAG 650
                          i     i    v   i     i  i        v    iiv        
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_165496713_    651 A----TAAAATTGGAGGACTTATCCTACTACCTGACTTTAAAAATTATTT 696
                          ----i   i          i ---i   v  ii i  i    v   i v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCA---CACTTCCCAATTTCAAAACTTACTA 242

  chr1_165496713_    697 TAAAGCTATGAAAATCAAGATGAAGTAGCATTGCTGAAATGGTAGGCAAA 746
                         i       iiiv        iiiv  i i i  viiv  v i   i  v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_165496713_    747 TAGATCATTGAAACAG-------CGTCCAGACGTAAAGCCA--CATATAT 787
                                v  i  i  -------v       vi    v   --   v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_165496713_    788 AGTCAATTGATT 799
                         i           
  L1M4_orf2#LINE/    343 GGTCAATTGATT 354

Transitions / transversions = 1.45 (45 / 31)
Gap_init rate = 0.02 (5 / 309), avg. gap size = 3.40 (17 / 5)  

1908 24.07 5.00 0.56  chr1_165496713_165498854.rev     1112  1651 (491)    L1M4_orf2#LINE/L1      345   908 (0)  

  chr1_165496713_   1112 TCAATTGATTTTTGACAAAAGTGAAAGGGTAATTCAATGGAGAAAGAATA 1161
                                     i     ii   vv i iiv         i         
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_165496713_   1162 GTTTTTCCTGTAAATTCTGCTGGAATAGCTGGTTATTCCTATGCAAAACA 1211
                           i   i vii    vv      i i i    v  ?i vi        v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_165496713_   1212 GTGAACTTAGATTCACAACTTATGGCATATACAAAAATTAACTCAAAGTG 1261
                         i    v  i  ii vi v  i iiv                      i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_165496713_   1262 GATTATATACCTACATGTAAAA-CTAAAACTGTAAATTCCCTATAAGAAG 1310
                            i ? v     v      i -        i    vii i  v     i
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_165496713_   1311 AAAAAGAGAAAAATTATTGTGCCCTTGGGTAAGGCAAATATTTCTTAGAT 1360
                          v v  i?iv    iv i   v        v      vvi          
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_165496713_   1361 ATTATACCAAAGGCACAAATCATAAAA-----ATTTGATGATTTGAACTT 1405
                           v i      i      iiv i    ----- v v   i v   i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_165496713_   1406 GATAAAAATGAAAAACTATTACTATGTGACAAA---CACTATTAAGAGAA 1452
                         v  v     v       -  -- i  ivv    ---      i    i i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACT-TT--TGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_165496713_   1453 TGAAAAGACAAGCCATAGTCTGAGAGAAAATATTTGCAAGTAAAATATCT 1502
                                    v   i  vv  i                i v v      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_165496713_   1503 GTTAATGGTCTTGTATTCAGAACATGTAAAGAACTCTTAAAACTCAATTT 1552
                          v   v  v       i     i  i             v        vv
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_165496713_   1553 TTAAAAAA----------------AGGATGGAAAAAAGACTTGAGCAAA- 1585
                          v    i ---------------- ii    iv   i  i    ii i -
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_165496713_   1586 ATTTTACCACAAAAGATACATGGATGGTAAATAAGCACATGAAA-TATAT 1634
                             iv   v i      i iii    iv               -v  ii
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_165496713_   1635 TCAATATTATTTATTAG 1651
                             i  i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (75 / 52)
Gap_init rate = 0.01 (8 / 564), avg. gap size = 3.75 (30 / 8)  


3152 27.81 0.55 0.33  chr1_165585157_165587481.rev      929  1834 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165585157_    929 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 978
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165585157_    979 AGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1028
                         i  v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165585157_   1029 TACCAATGACTTTCTTCACAGAATTGAAAAAACT-ACTTTAAAGTTCATA 1077
                          v   iivi i  i  ii     v vi v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_165585157_   1078 TGGAAC--CAAAGAAGAGCCCACATT-GCCCAGTCAATCCTAAGCCAAAA 1124
                              v--   i i ---    v v -   v iv     i i ivv i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_165585157_   1125 GAACAAAGCTGGAGGCATCACGCTACGTAACTTCAAACTATACTACAAAG 1174
                                 i      vv    i  v vi  i      viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_165585157_   1175 CTACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAGATATAGAC 1224
                                  i   ii   ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_165585157_   1225 CAATGGAACAGAACAGAACTCTCAGAAATCATGCCGCATATCTACAACTA 1274
                                 i    iv  ivvii       v vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_165585157_   1275 TCTGATCTTTGACAAATCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 1324
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_165585157_   1325 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAACTG 1374
                          v  i  i              v      v  ?   i  ii i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_165585157_   1375 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 1424
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_165585157_   1425 TAAAAACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1474
                         i ? i  i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_165585157_   1475 TAGGCATTACCATTCAGGACATAGGCATGGG-AAGGACTTCATGTCTAAA 1523
                             ?i v viv   iv   v v  vv i  -  v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_165585157_   1524 ACATCAATAGCAATGGCAGCAAAAGCCAAAATTGACAAATAGGATCTAAT 1573
                            i   v    vvi   i      vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_165585157_   1574 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATTAGAGTGAACA 1623
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_165585157_   1624 GGCAACCTACAGAATGGGAGAAAAGTTTTGCCATCTACTCATCTGACAAA 1673
                          i     i                vv     v vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_165585157_   1674 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAGAA 1723
                           i  vi          v  i         vv    v iv i  v  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_165585157_   1724 AGCAAACAATCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 1773
                         ii    i  i  v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_165585157_   1774 CAAAAGAAGACATTTATGCAGCCAACATACACATGAAAAAATGCTCATCA 1823
                          v        i  vi viii     i vi          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_165585157_   1824 GCACTGGCCAT 1834
                         v  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 201 11.90 2.38 0.00  chr1_165628272_165631334      453   494 (2569)  C L1M4_orf2#LINE/L1   (0)   908   866  

C chr1_165628272_    494 TAGCCAACAAACATATGAAAAAA-GCTCAACATCACTGATCAT 453
                          i     i  i  i       i -           ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (5 / 0)
Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1)  

2699 26.96 1.41 1.17  chr1_165628272_165631334     1710  2562 (501)    L1M4_orf2#LINE/L1        1   855 (53)  

  chr1_165628272_   1710 TGGAAAAACATTTCATCCTCATGGATAGGAAGAATCAATATTGTGAAAAT 1759
                               i i  ii   vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165628272_   1760 GGCCCTATTGCCTACAGTCATTTACAGATTCAATGCTATTCCCATTAAA- 1808
                            vv  i v  i v v v  i           i  v  i  i  i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165628272_   1809 --CTAGCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAAATT 1855
                         -- i   --  v -  i  ii     v v  v  i-  - iii       
  L1M4_orf2#LINE/    101 TCCCAGC--TGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chr1_165628272_   1856 CAAGTGGAACCAAAAAAGAGTCCACATAGCCATGACACTCCTAAGCAAAA 1905
                           vi     viiv  ii  vi viv       vi   v  i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_165628272_   1906 ATAACAAAGCTGGAGGTAC-CACAATACCCCACTTCAAACTACACTACAA 1954
                          v       i      -  -    v v   v i      vivi       
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_165628272_   1955 GTCTACAGTAACCAAAACAGCTTGGTAATGGTACAAAAACAGACACACAG 2004
                         iv         i   i    iv     v   i i  ii i     i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_165628272_   2005 ACCAATGGAACAGAATAGAGATCTCAGAAATAAGACCACACATCTGCAAC 2054
                          i        i     v    vii         iv   i    i --- i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT---AT 342

  chr1_165628272_   2055 AAACATCTGATCTTCGACAAACTTGACAA----ACGCAATGGGGAAAGGA 2100
                         iiv  vi    i        ivv  v   ---- iv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_165628272_   2101 TTTCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAA 2150
                          vvi  v  i  i              v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_165628272_   2151 AATTGAAACTGGACCTCTTCCTTATATCTTATACAAAAATTAACTCAAGA 2200
                         i v    ii      i  v   i i i v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_165628272_   2201 TGTATTAAAGACTTAAATGTAAAAGCCAAAACTATAAAAATCCTAGAAGA 2250
                           v  i ?    i         i   i            v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_165628272_   2251 AAATCTAGGCA-ATATCATTTAGGACATAGGCATGGGCAAATATTTCAT- 2298
                            iv    ?i- v   -  iiv   v v  vv i     vvi    v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_165628272_   2299 GATGAAAATGTCAAAAGCAATGACAGAAAAAGCAAAAATTGACCAAAGGA 2348
                            - vi iii        vvii  iv     v      v  iv  vv i
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_165628272_   2349 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCA-TCAA 2397
                          ii v  i   v v  i i   i  ii vv    i  v       -vv  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_165628272_   2398 GTGAACAGACAACCTACAGAGTGGGAGAAAAATTTTGCAATCTATCCACC 2447
                              v        i     i          vv       vii  vi i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_165628272_   2448 TGACAAAAGTCTAATATCCAGAATCTACAGGGAACTTAAACAAATTTACA 2497
                            i  ii v  vi          v  i ii     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_165628272_   2498 AGAAAAAAACAAACAACCCCATTAAAACATGGGCAAAGGACATAAAAAGT 2547
                          v     i     i     v   ?   v            iv i  v  v
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_165628272_   2548 CACTTCTCAAAACAA 2562
                           i     v   v  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAA 855

Transitions / transversions = 1.28 (127 / 99)
Gap_init rate = 0.02 (14 / 855), avg. gap size = 1.57 (22 / 14)  


 434 15.46 20.62 0.00  chr1_165688815_165691708     1201  1297 (1597)    L1M4_orf2#LINE/L1        1   117 (791)  

  chr1_165688815_   1201 TGGAAAGATATCCTATG-----------GAAGAATTAATATTGTTAAAAT 1239
                                      i   -----------     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165688815_   1240 ----AT-----CTAAAGTGATCTGCAGATTTGATGCAATTCCTATCAAAA 1280
                         ----  ----- i   v      i      ii i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165688815_   1281 TTCCAGTAACTTTTTTT 1297
                          i    ivi i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT 117

Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.03 (3 / 117), avg. gap size = 6.67 (20 / 3)  

2947 23.86 1.73 2.10  chr1_165688815_165691708     1593  2401 (493)    L1M4_orf2#LINE/L1      103   908 (0)  

  chr1_165688815_   1593 CCAATAACATTTTTAACAAAAATTTTTAAA--AATTCTAAAATTTGTATA 1640
                            iivi v     vi  i     vvi  i--i  i        ii   i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_165688815_   1641 GAATCACAAAAGACCCTGAATAGCTGAAGCAATCTTGAGAAAAAA----A 1686
                            vii   ii     v       ii  i         i   i  ---- 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_165688815_   1687 AAACTGAAGG-TATACACTT----ATTTCAAAATATATTACAAAGCTGTA 1731
                           ii  i   -ivi      ----         iv  i         ii 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_165688815_   1732 GTACTCAAAACAGCATTATAAGGGCATAAAAACAGACATATAGATCAATG 1781
                            v    i    ii vi  vv       ii i                 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_165688815_   1782 AAACAAAATAGAGAGCCCAGAAATAAATCCTCACATATATGGTCAAGTAA 1831
                         i  i i   v     i           i  vi    v         v i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_165688815_   1832 TATTTGACAAATGTGCTAAGAATACACAAGGGGGAAAAGACATTCTCTTC 1881
                          v  i     iv    i    vi iv   v       ii i v   i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_165688815_   1882 AATAAATGGTGTTTGGAAAACAGGACATCTACATGTAAATGAATAAAATT 1931
                           i        i v   v   v   i ? i     i   v    i  i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_165688815_   1932 GGACCCCTCTCTTACACCACACACTAAAATTAACTTAAAATCAATTAAAG 1981
                                 vi  i      i i  v          i     vi  i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_165688815_   1982 ACTTAAATATAACACCTGAAACCATAAAACACCTAGAAGAAAACATAAGG 2031
                           i     i   v v  i    i       v i              i ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_165688815_   2032 AAAAAGCTCATTGACATTTGTCTTGACAATT-TTTTTTAGATATGACACC 2080
                         iv   v  ivv    v  v vi v i    v-   i              
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_165688815_   2081 AACATCATAAGCCCCAAATGCAAAAATAAACAAGTGGGACTGTATCAAG- 2129
                           v v  i    vv    v v       i i  i v     vi     i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_165688815_   2130 CTAGAAAGTTTAATACAGCAAAGGAAACAATCACCAAAATGAAAGG-TAA 2178
                         i  i   v   vi i vv       v  v    vv   i     i -i  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_165688815_   2179 CCTCAAGATTGGGAGAAAATATTTACAAACCATATGCCTGATAAGAGGTT 2228
                           ivv   v               i    i     ii        i ii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_165688815_   2229 AATATCCAAAACATATGAGGAACTCATGCAACTCAGCAAAAACAAAACAA 2278
                         vi      i  i    i i      v i       ii  v  --------
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-------- 794

  chr1_165688815_   2279 AACAAAAACAAACACAAATATTCCAATTAAAAACTAGGCAAAGAAACTGA 2328
                         ---------   v       vi      ?    v i       i vi   
  L1M4_orf2#LINE/    795 ---------AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_165688815_   2329 ATAGAAATTTCACTAAAGAAGACATAGAAATGGCCAACAGGTATATGAAA 2378
                              v     v i        i   v          i i i i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_165688815_   2379 ATATGCTCAACATCACCAATCAT 2401
                          v             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (117 / 72)
Gap_init rate = 0.01 (8 / 806), avg. gap size = 3.88 (31 / 8)  


3100 26.59 1.33 0.33  chr1_165693788_165700417.rev     5241  6139 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165693788_   5241 TGGAAAAACATTCCATGGTAATGGAT---AAGAATCAATAGTGTGAAAAT 5287
                               i i  i     v v      ---    v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165693788_   5288 GGCCATACTACCCAAAGTAATTTGTAGATTCAGTGCTATCCCCATCAAGC 5337
                            v     v      v i  i ii       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165693788_   5338 TACCA-TTGACTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5385
                          v   -i  v   i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_165693788_   5386 ATGGAACAGAAAGAAGGCCCATA-TAGCCAAGACAATCCTAAGCAAAAAG 5434
                               vv v   i- i    v -       i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_165693788_   5435 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGC 5484
                                i      vv       v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_165693788_   5485 TACAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGATATAGACC 5534
                                 i   i    ii           iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_165693788_   5535 AATGGAACATAATAGAGGCCTCAGAAATAACGCCACACATATACAACCAT 5584
                                i v   v   ivii         vv   i    v  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_165693788_   5585 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGCAAAAGGATTCCCT 5634
                         i    i  i     ivv  v   i v  vv      vi    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_165693788_   5635 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5684
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_165693788_   5685 AACTGGACCCCTTCGTTACACCTTATACAAAAATTAACTCAAGATGGATT 5734
                          ii         v v i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_165693788_   5735 AAAGATTTAAACAGAAGACCTAAAACCATAAAAACCCCAGAAGAAAACCT 5784
                          ?   ii    iiv    v       i      vi ii          v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_165693788_   5785 AGGCA-ATACCATTCAGGACATAGGCAGGGGCAAAGACTTCATGACTAAA 5833
                            ?i- v i -   iv   v v  vvvi     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_165693788_   5834 ACACCGAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5883
                              i      vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_165693788_   5884 TAAGCTAACGAGCTTCTGCACAGCAAAAGAAACTATCATCGGAGTGAACG 5933
                         i  iv v vi i   i  ii vv    i  v       vvii      vi
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_165693788_   5934 GGCAACCTACAGAATGAGAGAAAATTTTTGCAATCTATCCATCTGACAAA 5983
                          i     i        i        v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_165693788_   5984 GGACTAATATCCAGAATCTACAAGGAAGTTAAACAAATTTACAAGAAAAA 6033
                              vi          v  i  i   v ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_165693788_   6034 AA-----AACCCCATCAAAAAGTGTGTGAAGGATATGAACAGACACTTCT 6078
                         i -----     v  i?    i  v ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_165693788_   6079 CAAAAGAAGACATTTACACAGCCAACAAACATATGAAAAAAAGCTCATCA 6128
                          v        i  vi v ii     i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_165693788_   6129 TCACTGGTCAT 6139
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.33 (134 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3414 24.81 1.10 0.99  chr1_165738566_165742837     2873  3779 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165738566_   2873 TGGAA---TATCTTTCCACGTCCATGGATTAGAAAAATTAATACTGTTAA 2919
                              ---    ---   i  i        i   i v      i      
  L1M4_orf2#LINE/      1 TGGAAAGATATC---CCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chr1_165738566_   2920 AATGACAATACTACCCAAAGCAATTTACAGATTCAATGCAACCTCTATCA 2969
                         i   i       v      vii  i           i    i i      
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_165738566_   2970 AAATATCAATGACATTCTTTACAGAAATAGAAAAAGAAATCTTAACATTT 3019
                             vi  iivi v  i   i       v  v  ivvi   i   v   i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_165738566_   3020 ATATGAAACCACCACAGAAGACCCCAAATAGCCAAAGCAATTCTGAACAA 3069
                              i  -- i-i  iii     vi          i    ii    v  
  L1M4_orf2#LINE/    148 ATATGGAA--AT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_165738566_   3070 AAAGAATAAAGCTGGAGGCATCACACTACTTGACTTCAAAATGTACTATA 3119
                         i     i    i      vv       v iii i       iv     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_165738566_   3120 AAGCTATAGTAACCAAATCAGGGTGGTACTGGCATAAAAACAGACA---- 3165
                               i     i   iv   v               ii i     ----
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_165738566_   3166 GGCCAGTGGAACAGAATAGAGAACCCAGACATAAATCTACACATTTACAG 3215
                          ii  i     i     v    ii     v     i i i       ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_165738566_   3216 CCAACTCCATTTCAGCAAAAGTGTCAAGAACACACTATGAGGAAAAGACA 3265
                         i   i vvv    ii   ii   i     v  iv v   i     ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_165738566_   3266 GTCTCTTCAATAAATGTTTCTGGGAAAACTAGATAACTGTATGCAGAAAA 3315
                             i     i     v v      v    i    ? iii     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_165738566_   3316 ATGAAACTAGACCCCCTATCTCTCACCTTAAACAAATATCAAATAAAAAT 3365
                              ii i      -  i   v    v  v     v  i  v v     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_165738566_   3366 ATATTA--GACTTAAATCCACGACCTGAAATTATAAAACTACTAGAAGAA 3413
                         iv  i --   i     vi v  v  i   i         vi        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_165738566_   3414 AACATTGGGAAAACATTCCAGGACATTGGTCTGGGCAAAGACTTTTTGTG 3463
                              v  ?iv  vvi i iv   v    vi i     v ii  i  ivi
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_165738566_   3464 GAAGACCTCAAAAGCTCAAGCAACCAAAGCAAAAATTGACAAATGGGATT 3513
                         v v   vi       v        v    v      v  i    v   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_165738566_   3514 ACATCAAGCTAAAATGCTTCTGCACAGCAAAGGAAACAATTAGCAAAGTG 3563
                         v      iv v   vi   i  ii vv       v  v  i iv      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_165738566_   3564 AAGAGACAACTCACAGAATGGGTGAAAACATTTACAAACTACCCATCTGA 3613
                           i       i           v     i    i    ii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_165738566_   3614 CAAAAGTTTAATAATCAGAATATATAAGGAGCTCAAACAACTCAACAGCA 3663
                         i  ii vi vi  vi            i  i   vv         i -- 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA--A 791

  chr1_165738566_   3664 AAAAAAAAAAAAGAGTCCAATTTTAAAACGGGCAAAA-ATCTGAATAGAC 3712
                         v     i v   v ii      ?v    i       i-  i         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_165738566_   3713 ATTTCTCAAAAGAAGACATACAAATGGCCAACAGGTATATGAAAAAAGGA 3762
                                v        i              i i i i       i v v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_165738566_   3763 TCAACATCACTAATCTT 3779
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (141 / 81)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


3232 16.72 1.74 0.95  chr1_165897893_165899511      493  1126 (493)    L1M4_orf2#LINE/L1      270   908 (0)  

  chr1_165897893_    493 GTACACATGGCACAAAGATAGACATATGGATTAATGGAATAGAATTGAGA 542
                             ---     i  i           i   i                  
  L1M4_orf2#LINE/    270 GTAC---TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr1_165897893_    543 GCTCAGAAATAAATATATACATCCACTTTCAACTGATTTTCAACAAAGTT 592
                          ii          ivi      ii ivv    i        i    i v 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_165897893_    593 GCCAAGGCCAACCAATGGGGGAAATAATAATCTTTTCAACAAATAATGTT 642
                               i   vi        -   v    i              ii  i 
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_165897893_    643 TCAACAGCTGGATAGCAATGTGCAAAAAAATGAAGTTCAATCCTTACCTC 692
                         vvi   i       ? v ii       i         vi i  i      
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_165897893_    693 ACACCATATACAAAAATTCACTCAAAATGAATAAAAGGCCTAAAAGCAAG 742
                                           v          i  v ?  i      v i   
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_165897893_    743 ACCTACAATTTTAGAACTCTTAGAAGACAACATAGGAGTAAAACCTTTAT 792
                          v   v  i v  i             v        ?     -i   ii 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGT 564

  chr1_165897893_    793 GATGCTGGCTTTGACAAAGGATTCTCAGATATGACACCAAAAGTATAAGC 842
                           ivi   v  v i   v  v    i                 i i    
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_165897893_    843 AATAAAAGCAAAAAATAGATAAATTAGACTTAATCTAAGTTAAAAAACTT 892
                           i     -                i     v   v  i       vi  
  L1M4_orf2#LINE/    615 AACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_165897893_    893 CCTGCTTCAAAGGACACCAACAAGAAAAGTAACAGACAGCCCACAGAATG 942
                         iv               i v       ivv  v     i           
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_165897893_    943 GGAGAAAATATTTGCAAATTATATCTCTGATAAGGGACTTTTATTGATAA 992
                                            i    v               v   iv v  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_165897893_    993 CATATAA----CTCTTACAAGTCAATAATAAAAA------TGACTTAATT 1032
                         i      ----         v             ------ i  ii    
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_165897893_   1033 TAAAAATAGGCAAAGAACT-GAATAGGTATTTCTCCATGGAAGATATACA 1081
                         ?      i       i i -      ii         vi           
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_165897893_   1082 AATGGCCAATAAGCACATAAAAAGATACTCGATATCACTAGTCAA 1126
                                           i       i   i i    ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (66 / 36)
Gap_init rate = 0.01 (7 / 639), avg. gap size = 2.43 (17 / 7)  


3270 27.20 0.33 0.33  chr1_165948631_165958987.rev     4882  5789 (4568)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165948631_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165948631_   4932 GGCCATACTGCCCAAGGTAATTTATAGAATCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165948631_   4982 TACCAA-TGCCTTTCTTCACAGAATTGGAAAAATCTACTTTAAAGTTCAT 5030
                          v   i-       i  -i     v v  v  iiiv iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_165948631_   5031 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGA 5080
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_165948631_   5081 ACAAAGCTGGAAGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5130
                               i    i vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_165948631_   5131 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5180
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_165948631_   5181 ATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACTA 5228
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_165948631_   5229 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5278
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_165948631_   5279 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5328
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_165948631_   5329 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5378
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_165948631_   5379 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5428
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_165948631_   5429 TAGGGATTACCATTCAGGACATAGGCATAGGCGACGACTTCATGTCTAAA 5478
                             ?i v viv   iv   v v  vv     i i ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_165948631_   5479 ACACCAAAAACAATGGCAGCAAAAGACAAAATCGACAAATGGGATCTAAT 5528
                                  i  vvi   i       v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_165948631_   5529 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5578
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_165948631_   5579 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCTTCTGACAAA 5628
                          i     i   i             v  i    vii iviv     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_165948631_   5629 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTTTAAGAAAAA 5678
                           i  vi          v  i  v      vv    v ivv   v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_165948631_   5679 AACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCT 5728
                         i     i     v  i?    i    ii     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_165948631_   5729 CAAAAGGAGACATTTATGCTGCCAAAAAACACATGAAAAAATGCTCATCA 5778
                          v    i   i  vi viiv     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_165948631_   5779 TCACTGGCCAT 5789
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  

2860 24.37 2.43 2.32  chr1_165948631_165958987.rev     8960  9866 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165948631_   8960 TGGAAACACATCCCATGCTCATGGATTGGAATAATCAATATCATGAAAAT 9009
                               v i        i             v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165948631_   9010 GACCATACTACCCAAAGCAATCCACTGATTCAGTGCAATTCCTATCAAAA 9059
                          i v     v      vii   i  v      ii     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165948631_   9060 TACCAACATCATTTTTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 9109
                          v   i vv v     ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_165948631_   9110 TGAAACCAGAAAAAGAACCTGAATAGCCAAAGCAATCCTATGCAAAAAAA 9159
                           i  vi- v  ii  v  v           i     i i---     i 
  L1M4_orf2#LINE/    151 TGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTG---AAAAAGA 196

  chr1_165948631_   9160 CAAACAAACAAGAAAACAGACGTAGAGGCATCACATTATCAGATGTTTGC 9209
                         vi      vvv i i---   vi v -- v  v  v v   i -ii  i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAG---GACTCACA--CTTCCCAATTTCAAA-ACTTAC 240

  chr1_165948631_   9210 CACAAGGCTGTAGTTACAAAAATAGTG-----CTGGTATAAAAGTAGGCA 9254
                         i    i   ii   v iv  i i    -----    i    iii   i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_165948631_   9255 CATAGAGCAGTGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTT 9304
                         i     v  i     i     v    ii           v   v i i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_165948631_   9305 ACAACCAACTGATCTTCAACAAAGCATAGAGAAACACAGGC--TGAGGAA 9352
                          iiii   i    i   i    i -i ivvi i  -  vv --  i    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGG-GTGCCAAGAC-CATTCAATGGGGAA 388

  chr1_165948631_   9353 AGGACACCTTATTTAATAAATAATGCTGGGAAAACTGGATAACCACATGT 9402
                           i i vii v  i  i    ii        v         ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_165948631_   9403 AGAAGAATGAAACTGGATGCTTATCCCTTACCTTATACAAAAATCATCTC 9452
                          i         ii    iv i  i i vi   v           i v   
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_165948631_   9453 AAGATGGTTCAAAGATGTAAATCTAAGACATGAAACTATAAAAATTATAG 9502
                           i    v   ?   iv     v     vv i           v iv   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_165948631_   9503 AAGATAACCTAGGAAAAACTATTCTGGACATTGGCTTAGGCAAATAATTC 9552
                             v   v    ?iv  v v   vv   v    v        - ii  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTT 587

  chr1_165948631_   9553 GTGAG-TAGGACCCCAAAAGCAAATGCAACTAAAATAAAAATAAATAAAT 9601
                         v v  -  v   v         v v     v   iv       i      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_165948631_   9602 AGGACCTAATTAAA--TAAAAGAAACTTCAGTACATTAAAAGAAATAACT 9649
                         v    i v  i   --     ---    iv  i v i   i  v ---  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAA---ACTTTTGTGCTTCAAAGGACA---CT 681

  chr1_165948631_   9650 ATCA-GAA--TAAATAGACAACCCACAGAGTGGGAGAAAATATCTGCAAA 9696
                             -   -- i  v              i             i      
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_165948631_   9697 CTATACATCTAGCAAAGGACTAATATCTAGAATCTACAATGAACTCAAGT 9746
                         ii   i    iii  i     vi    i     v  i  v      --v 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--TT 779

  chr1_165948631_   9747 ACA--TCAACAAGAAAAAAA-----AATCCCATCAAAATGTGGGCAAATA 9789
                            --    i  v     i -----  i  v  i?   vi        vi
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_165948631_   9790 ACATGAATAGACATTTCTCAAAAGAGGATATAAGAATGGTAAAGAA-CAT 9838
                          iv                v     i      vi     iv  v  -  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_165948631_   9839 ATGAAAA-ATGCTAAACATCACTGATCAT 9866
                                -     v       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (126 / 91)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.05 (43 / 21)  


2850 25.92 1.84 3.78  chr1_165963488_165969595     4690  5615 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165963488_   4690 TGTAAGAACATTCCATGCTCTTAGATGGGAAGAATCAATATCATTAAAAT 4739
                           v  ii i  i     i  v i   v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165963488_   4740 GGTCATACTGCCTAAAGCAATTTACAGATTCAATGCTATTCCTTTCCATG 4789
                           iv     v  i   vii  i           i  v  i   v  v vi
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165963488_   4790 TACCAGTGACATTCTT--CACAAACTGGAAAAAAACT-ATTTTAATGTTC 4836
                          v    ivi v  i  --  v   i  --- v  i  -  ii   vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_165963488_   4837 ATATTGAACCAAAAAAGAGCCTGAATTGCCAAGGGAACCCTAAGCAAAAA 4886
                             v   viiv  ii  v  v    v     iiv  i i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_165963488_   4887 GATCAAAGCTGGAGGAATCATATTGTCCAACTTCACACTGTAGTACAAGG 4936
                           v     i       v   i i vi    i    v viv  v     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_165963488_   4937 CTACAGTAACCAAAAACAACATGGTACTGGTATAAAAACAGACACACAGA 4986
                                  i   i -  iii         i    ii i     i i   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_165963488_   4987 CCAATGGAGCAGGATAGAGAGCCCAGATATAAACCCACACACCTACAACC 5036
                         i       ii  i  v     i     v         i   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_165963488_   5037 ATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGACTCC 5086
                          vi    i  i     i v  v   i v  vv            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_165963488_   5087 CTATTCAATAAATGATTCTGGGATAACGGGCTAGCTATATACAGAAGACT 5136
                           v     i     i v      i   v  v  ? i i  i  i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_165963488_   5137 AAAACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGA 5186
                         i  ii         v   i                 i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_165963488_   5187 TGAAAGACCTAAATGTAAAACCTAAAACCTAAATAAAACCTAAAACCTAA 5236
                          v ?              i v       i---       i----------
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACT---ATAAAACT---------- 533

  chr1_165963488_   5237 ATAAAAACCCTAAAGGATAACCTAGGAA-ATATCATTTTGT-ACATAGGA 5284
                         -------- i  i i  v   v    ?i- v   --  i  -  v v  i
  L1M4_orf2#LINE/    534 --------CTTAGAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGG 573

  chr1_165963488_   5285 ACTGGCAAAGATTTC------ATGACAAAAATGCCAAAAGCAATTGCAAC 5328
                         viv     v i    ------      ------         vvv     
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAAC 617

  chr1_165963488_   5329 AAAAGCAAAAATTGATAAATCAAA----AATAAGCTAAAGAGCTTTTGCA 5374
                              v      v       iii ---- vi  iv v  i i      ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_165963488_   5375 TAGCAAAAGAAACTATGAACAGAGTAAACAGACAACCTACAGAATGAGAG 5424
                         ivv    i  v     v  v i   i  v        i        i   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_165963488_   5425 AAAATATTTGCTAACTATACGTCTGACAGAGGTCTAACATCCAGAATCTA 5474
                                    v  ii   ii     i ii  v  vii         v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_165963488_   5475 TGAGGAACTTAAACAAATTTACAGGAAAAAAATAAAAACAACCCCATAAC 5524
                          i i     ivv    v iv i iv     i i   --i     v  v?v
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAA--TAACCCAATTWA 815

  chr1_165963488_   5525 ACAGTGGGTGAAGGACATGAACAGACAATTTTCAAAAGAAGACACACATG 5574
                          v i    ii     iv    i     v  i  v        i i   vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_165963488_   5575 CAGCCAACAA-C-CATGAAAAAAAGCTCAATATCACTGATCAT 5615
                         ii     i  - -        i v      i    ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (146 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.47 (52 / 15)  


1455 26.80 3.09 0.82  chr1_165974613_165985758.rev       44   528 (10618)    L1M4_orf2#LINE/L1      413   908 (0)  

  chr1_165974613_     44 GCTGGGAGAACTG-ATAGCCACATGGAGAAAATTGACACGGGACCCCTTC 92
                                v     -   ?       v i  i v   viiv        v 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_165974613_     93 CTTATACCGTATACAAAAATTAACTTAAGATGAATTAAAGACTTAAATGT 142
                           i i   i                i  i   i  i ?    i       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_165974613_    143 AAAACCCAAAACTATAAAAACCCTAGTAGAAAATCTAG---TCAATAGCA 189
                           i v i            vi i   v      iv   --- v   -- -
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C- 559

  chr1_165974613_    190 TTCAGGACATAGGCATGGGCAACAATTTTGTGAACAAAATGTGAAAAGCA 239
                            iv   v v  vv i     iii   iv ii i vi iiiv       
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_165974613_    240 ATTACAACAAAAACAAAAATTGCCAGATTGGATCTAATTAAACTAAAGAG 289
                         vvvi        iv      v vi i      ii v  i   v v  i i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_165974613_    290 CTTCTGTACAGCAAAATGA-ACTATCATCAGAGTGAACAGACAACCTACA 338
                            i   i vv    i-  -       vv i      v        i   
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_165974613_    339 GAATGAGAGAAAATTTTTGCAATCTATCCATTTCACAAAGGTTTAATATC 388
                              i        v       vii  vi  i v i  i  vi vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_165974613_    389 TGGAATCTACAAGGGACT--TA-AATTTA-CAAGAAAAA-----ACAACC 429
                         ii    v  i  i i   --  -  i i -i  v     ----- i    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_165974613_    430 TCATTAAAAAGTGGTCAAAGGACATGGACAGACCCTTCTCAAAAGAAGAC 479
                         iv   ?    i   v       iv  i i    vi     v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_165974613_    480 ATTCATGCACCCAACAAACACATGAAAAAAAGCTGAA-GTCAAATTGCTA 528
                           v  viiiv    i  i          i v   v  -i   ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (76 / 51)
Gap_init rate = 0.02 (11 / 496), avg. gap size = 1.73 (19 / 11)  

3002 27.78 1.44 0.56  chr1_165974613_165985758.rev     3759  4658 (6488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165974613_   3759 TGGGAAAACATTCCATGCTCATGGATAGGAAGAATCAGTATCACGAAAAT 3808
                            i  i i  i     i        v      v i i   iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165974613_   3809 GGCCATATTGCTGAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 3858
                            v   i v iv   v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165974613_   3859 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAACTTC 3906
                          v   vivi i  i  ii     -   --- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_165974613_   3907 ATATGGAACCAAAAAAGAGCCTGCGTAGCCAAGACAATCTTGGGCATGAA 3956
                                 viiv  ii  v  v vi       i         iiv v   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_165974613_   3957 GAACAAAGCTGGAGGCATTATGCTACCTGACTTCTAACTATACTACAAGG 4006
                                 i      vv i ii  v  ii i   v  viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_165974613_   4007 CTACAGTAACCAAAACAGCATGGTACTTATACCAAAACAGATATGTAGAC 4056
                                  i   i    ii       vii iv ii i   i  i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_165974613_   4057 AAAAGGAACAGAATGTAGGCCTCAGAAATAACACCACACAGCTACAACCA 4106
                         v  v    i     vv  ivii         vv   i   vi  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_165974613_   4107 TCTGATCTTTGACAAACCTGACACACACAAGCAATGGGGAAAAGATTCCC 4156
                         vi    i  i     ivv  v  vivv  vv           ii  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_165974613_   4157 TATTTAATAAATAGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 4206
                          v  i  i    i   i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_165974613_   4207 AAACTGGACCCCTTCCTTACACCTTTTACAAAAATCAACTCAAGATGGAT 4256
                           ii         v   i     v v         i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_165974613_   4257 CAAAGACTTTAAT--AAGACCTAGGACCATAAAAATCTTAGAAGAAATCC 4304
                           ?    i v   --    v   ii  i      v            v v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_165974613_   4305 TTGGCA-ATACCATTCAGGACATAGGAATGGGCAAAGACTTTATGTCTAA 4353
                          v  ?i- v i -   iv   v v  iv i     v ii  iv ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_165974613_   4354 AACACCAAAAGCAATGGCAACAAAAGCCATAATTGACATATGGGATCTAA 4403
                         i            vvi          vv v   v  i v  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_165974613_   4404 TTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 4453
                          i   v v  i ii  i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_165974613_   4454 AGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTATCCATCTGACAA 4503
                           i     i       i         v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_165974613_   4504 AGGGCTAATATCTAGAATCTACAAAGAATGTAAACAAACTTA-CAAGAAA 4552
                         i  i  vi    i     v  i      ivivv    -  i -i  v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAA 795

  chr1_165974613_   4553 AAAACAAACAACCCCATCAAAAAATGGGCAAAGGATATGAACAGACACTT 4602
                           i     i     v  i?                 v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_165974613_   4603 CTCAAAAGAAG---TGCA----GCCAACAGACATATGAAAAAATGCTCCT 4645
                            v       --- i  ----     i ii  i       i      vv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_165974613_   4646 CATCCCTGGTCAT 4658
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (143 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  

3186 26.76 0.66 0.66  chr1_165974613_165985758.rev     9748 10655 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_165974613_   9748 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCGTGAAAAT 9797
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_165974613_   9798 GGCCATACTGCCTAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 9847
                            v     v  i  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_165974613_   9848 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTC 9894
                          v   i-       i  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_165974613_   9895 ATATGGAACCAAAAAAGAGCCCACATCGCCAACTCAATCCTAAGCCAAAA 9944
                                 viiv  ii  v  viv  v     vv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_165974613_   9945 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 9994
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_165974613_   9995 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGAT 10044
                                  i   i    ii         i iv ii i   v v      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_165974613_  10045 GAATGGAACACAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 10092
                         v       i v  i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_165974613_  10093 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGAAAAGGATTC 10142
                         i vi    i  i     ivv  vv  i v  vv       i    i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_165974613_  10143 CCTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 10192
                         i  v  i  i  i           v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_165974613_  10193 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 10242
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_165974613_  10243 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 10292
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_165974613_  10293 CCTAGGCA-ATACCATTCAGGACATAGGCATAGGCGACGACTTCATGTCT 10341
                          v    ?i- v i -   iv   v v  vv     i i ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_165974613_  10342 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATCT 10391
                          vi            vvi          vv     v  i i  v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_165974613_  10392 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 10441
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_165974613_  10442 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCTTCTGAC 10491
                          v  i     i   i             v  i    vii iviv     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_165974613_  10492 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 10541
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_165974613_  10542 AAAAACAAACAACCCCATCAAAAAGTGGACAAAGAATATGAACAGACACT 10591
                            i     i     v  i?    i   i     i  v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_165974613_  10592 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 10641
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_165974613_  10642 TCATCACTGGCCAT 10655
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3048 25.53 2.22 1.66  chr1_166051696_166055208     2120  3020 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_166051696_   2120 GAAAGAT--TCCATGTTTATGGA----AAGAATCAATATTGTTAAAATGT 2163
                                --i       i     ----    v i           i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_166051696_   2164 CCATACTACCTAAAGCAATCTACAGATTCAATGCAATCACTATCAAAATA 2213
                          v     v  i   vii              i      v          v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_166051696_   2214 TCAATGATATTCTTCAAAGAGTAGAAATAGAAAAAACAATCCTAAAATTT 2263
                         i  iiviiv  i  i----- i      v  v  ivii           i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT-----GCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_166051696_   2264 ATA---AAA-------GACTCAGAATAGCCAAAACCATCCTAAGTAAAAA 2303
                            ---   -------   i               v   i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_166051696_   2304 GATGAAAACTGAAAAAAATCACACTATCTGACTTCAAATTATACTACAGA 2353
                           vv   ii  i ii v-       vi ii i      viv       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_166051696_   2354 GCTATAGTAACCAAAACAGCGTGGTACTGGCATAAAAACAGACACATAGA 2403
                             i     i   i    i               ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_166051696_   2404 TCAATGGAACAGAATAGAGAACCCTGAAACAAATCCATACATCTACAATG 2453
                                  i     v    ii  v    i   i        i  iii v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_166051696_   2454 AACTCATTTTCAACAAAGTTTCCAAGAACATATATTGGAGAAG--ACAGC 2501
                           i v      i    i v v      v   vi v   i   i-- i  i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_166051696_   2502 CTCTTCAATAAATGGTACTGGAAAAACTGGGTATTTATACACAGAAGAAT 2551
                           i     i       i    i v      i  ?ii i ii  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_166051696_   2552 GGAACAAGACCCCTTTCTCTGGTCATATACAAAAATAAAATCAAAATGGA 2601
                          i iivi       vi   vvii             v  v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_166051696_   2602 TTTGGATTAAAGACTTAAATTTAATACCTCTAACTATGAAACTACTACAA 2651
                          i------ ?    i     v   v v  vv      i     vi  v  
  L1M4_orf2#LINE/    497 TC------AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_166051696_   2652 GAAAACATTGAGGAAAATTCCCAAGGTATTGGTCTGGGCAAAAATTTCTT 2701
                                 v i? v    iii iv iiv    vi i     vii      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_166051696_   2702 GACCACCACCACACAGGCACAGGCAACCAAAGCAATCATGGATAAATTGG 2751
                         iivi iv  vv  v i     i     v    v  vv  i          
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_166051696_   2752 GGCACATCAAG-TTAAAAAGCTTCTGCATAGCACAGGAAACAATCAACAA 2800
                         iviv      i-       -   i  iiivv  v    v  v     v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_166051696_   2801 AGTCAAGAGACAACCCACAGAATAGGACAAAATATTTGCAAACTAACCAT 2850
                            v  i                i   v              ii vvi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_166051696_   2851 CTAACAAGACATTAATAATCAGAATACACAAGGAGCTCAAACAACTCTAC 2900
                           i i   iv i vi  vi       i i  i  i   vv       v i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_166051696_   2901 AGGAAAAAAAATCTAATAATCTGACTAAAAATTGGGCAAAAAATCTCAAT 2950
                          iv     i -- v     i ii i ?    v        ii  i v   
  L1M4_orf2#LINE/    790 AATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_166051696_   2951 ATACGTTTCTCAAAAGAAGACA-ACCAGTGGCAAACAGGGATATGAAAAG 2999
                          v  i      v        i -  v i    v  i i v i        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_166051696_   3000 TTGCTCAATATCATTGATCAT 3020
                         v       i    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (140 / 86)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 2.92 (35 / 12)  


2976 26.56 2.57 1.23  chr1_166101088_166107454     4979  5874 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166101088_   4979 TGGAAGAACATTCCATGTTCATAGATAGTAAGAATCAATATCGTGAAAAT 5028
                              ii i  i          i   v v    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166101088_   5029 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5078
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_166101088_   5079 TATCAATGACTTTCTTCACAGAA--TGGAAAAAACT-ACTTTAAAGTTCA 5125
                          vi  iivi i  i  ii     --  -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_166101088_   5126 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAAG 5175
                                viiv  ii  v  viv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_166101088_   5176 AACAAAGCTGGAGGCATCACGCTACCTGACTGCAAACTACACTGCAAGGA 5225
                                i      vv    i  v  ii i v    vivi   i   i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_166101088_   5226 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5275
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_166101088_   5276 AGTGGAACAGAAC--AGAACCCTCAGAAATAATACCACATATCTACAACC 5323
                          i     i    i--   ii  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_166101088_   5324 ATCTGATCTTTGACAAACCTCACAAAAACAAGAAACGGCGGAAGGATTCC 5373
                          vi    i  i     ivv vv   i v  vvv  i  v i   i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_166101088_   5374 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5423
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_166101088_   5424 GAAACTGGATTCCTTCCTTACGCCTTATACAAAAATTAATTCAAGATGGA 5473
                            ii    ii   v   i  i  v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_166101088_   5474 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAG 5523
                          i ?    i       v   v       i      vi i          v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_166101088_   5524 CTAGG---AAATACCATTCA-GGCCACAGGCATGGGCAAAGACTTC---- 5565
                         v    ---    -- -   i- i  vii  i- i     v ii   ----
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAG 592

  chr1_166101088_   5566 --ATGACTAAAACAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGG 5613
                         --     --- v        vvi          vv     v  i    v 
  L1M4_orf2#LINE/    593 ATATGAC---ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_166101088_   5614 GATCTAATTAAAATAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG 5663
                           ii v  i     v  i i   i  ii vv    i  v    i  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_166101088_   5664 AGTGAACAGGCAACCTACAGAATGGGGGAAAATTTTTACAATCTACCCAT 5713
                               v  i     i          i      v   i   vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_166101088_   5714 CTGACAAAGGGCTAATATCCAGAATTTACAAAGAGCT--TA-AATTTA-C 5759
                             i  i  i  vi          v  i     i  --  -  i i -i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_166101088_   5760 AAGAAAAAAACAA----CCCCATCAAAAAATGAGTGAAGGATATGAACAG 5805
                           v     i    ----   v  i?       i ii      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_166101088_   5806 ACACTTCTCAAAAGAAGACATTTATGCAGCCAACATACACATGAAAAAAG 5855
                            i     v        i  vi viii     i vi          i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_166101088_   5856 GCTCATCATCACTGGCCAT 5874
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (151 / 84)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.12 (34 / 16)  


3068 26.42 1.55 0.78  chr1_166108023_166114676     5261  6161 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166108023_   5261 TGGAAAAACATTCCATGCTCATGGACAGGAAGAATCAATATTATGAAAAT 5310
                               i i  i     i       iv      v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166108023_   5311 GGCCATACTGCCCAAAGTAATTTACTGATTCAATGCTATCCCCATCAAGC 5360
                            v     v      v i  i   v       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_166108023_   5361 TACCATTGACGTTCTTCACAGAATTAGAAAAAACT--TCTTTAAAGTTCA 5408
                          v   vivi v  i  ii     v v  v  i-  --  i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCT-AAAATTCA 148

  chr1_166108023_   5409 TATGGAACAAAAAAAGAGCCTGCATAGCCAAGATAATCTAAAGCAAAAAG 5458
                                vviv  ii  v  v v        i i     vi iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_166108023_   5459 AACAAAGCTGGAGGCATCATGGAC---CTGACTTCAAACTATACTACAAG 5505
                                i      vv   i--  --- ii i      viv        i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCAC--ACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_166108023_   5506 GGTACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGATATATAGA 5555
                          v        i v i    ii         i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_166108023_   5556 CCAGTGGAACAGAACAGAGGACTCAGAAATAATGCCACCCATCTACAACC 5605
                         i  i     i    iv   iiii         vv   iv   i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_166108023_   5606 ACCTGATCTTCGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT--T 5653
                          vi    i        ivv  v   i v  vvv           i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_166108023_   5654 CCTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAA 5703
                          i  -- i  i              v      v  ?   i     i  i 
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_166108023_   5704 CTGAAACTGTACCCCTTCCTTACATCTTATACAAAAATTAACTCAAGATG 5753
                         v    ii  v      v   i   i v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_166108023_   5754 GATTAAAGATTTAAACAGAAGACCTAAAACCATAAAAACCCTAGAAGAAA 5803
                            i ?   ii    iiv    v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_166108023_   5804 ACCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAAGACTTTATGAC 5852
                           v    ?i- v i -   iv   viv  vv i     v ii  iv iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_166108023_   5853 TAAAACACCAACAGCAATGGCAACAAAAGCCAACATTGACAAATGGGATC 5902
                           vi       v    vvi          vv  v  v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_166108023_   5903 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 5952
                          v  i   v v  i i   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_166108023_   5953 AACAGGCGACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCACTAGA 6002
                           v  i i   i                 v       vii  vi iiv  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_166108023_   6003 CAAAGGGCTAATATCCAGAATCTACAAGGAACT--TA-AATTTA-CAACA 6048
                         i  i  i  vi          v  i  i     --  -  i i -i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_166108023_   6049 AAAA-ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAA 6097
                             -     i     v  i?    i            v    i     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_166108023_   6098 TTCTCTAA-GAAGACATTTATGCAGCCAATAGACATATGAAAGAAAGGTC 6146
                              i  -     i  vi viii       ii  i      ii v v  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_166108023_   6147 ATCATCACTGGTATT 6161
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


3541 18.51 4.99 4.32  chr1_166132992_166135601     1216  2117 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166132992_   1216 TGGAAAGCTATCCCTTGTTAATGGATTGGAGGAC--AATATTATTAAGAT 1263
                                v      v    v          i   --      i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166132992_   1264 GTCAGTATTACCCAAAGTAGATATGCAGATTCAATGTAATACCTATCAAA 1313
                          v  i  i v      v -   v i         i i   v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATT-GATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_166132992_   1314 ATCTCAGAAAA-------GCAGAAAT----AAATCCATCCTAAAATTTGT 1352
                            i   vviv-------        ----  iiiv           ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_166132992_   1353 ATGTAATTTCAAGGAACCCCAAA-AGCCAAAAGAGTCTTGAAAAAGAA-- 1399
                            v  v v     i    vi  -        v i             --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_166132992_   1400 -CAAAGTTGGAGCACTAATACTTCCTGATTTCAAAACTTACTATAAAGCT 1448
                         -           v   v i      ii                i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_166132992_   1449 AAAATAATTTAAACTATGTGGTACTG-CATAAAGACAGCTTTATAAACCA 1497
                          v i    iv i  vi          -     i  i  viv    i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_166132992_   1498 ATGGAATCAAATTTAGAGGTCATAAATAAACTCTCACATATATGGTCAAA 1547
                                vi    v    vi  v        i vi    v         v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_166132992_   1548 TGATTTTTCACAAGGGTTTTATGAAAC--TCCGA-GGGGAAAGGATATCA 1594
                                iv        vii -- i  -- i i -        i   --i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCA--AGACCATTCAATGGGGAAAGAATA--G 395

  chr1_166132992_   1595 TCTTT-CAACAAATGGTTCTGGGAAAACTGGATATCCACATGCAAATGAA 1643
                              -           v      v         ?           v   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_166132992_   1644 TTAGGTTGGACCCTTACCTCGCACCATATTCAAAAAT------AAAATGG 1687
                          v i         i      i        v       ------       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_166132992_   1688 ATCAAAGATGTAAATGTAAGAACTAAAACTATGAA-CTCTTATAAGGAAA 1736
                             ?   iv           i          i  -      v   i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_166132992_   1737 CAGAGCAATAG--CTTTGCCACATTGGATTTGACAATAATTTCTTAGATA 1784
                           v  v?i  i--   i iv  v    i  v i    ii           
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_166132992_   1785 TGACAGCAAAAGCACATGCAA---------AAGTAAACAAATTGGACTGC 1825
                              v          v    ---------  i  i i          v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_166132992_   1826 A-CAAATATTAAGTACTGTTGCATTTTAAATACTTTTGCTCACTAGACAT 1874
                          -    -     iv   v   iii  i   --------------i    i
  L1M4_orf2#LINE/    646 ATCAAA-ATTAAAAACTTTTGTGCTTCAAA--------------GGACAC 680

  chr1_166132992_   1875 TATCAGCAGAATGAAAAGGCAACCTATGAAATGGGAGAAAATATTCGCAA 1924
                              iv i i       i     i iii                i    
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_166132992_   1925 ATGATATATCTAATGTTCATAGGTATCCAAGGTATTAATATCCATAACAA 1974
                           v        i  --------------    v i vi      v  i v
  L1M4_orf2#LINE/    731 ATCATATATCTGAT--------------AAGGGACTTGTATCCAGAATAT 766

  chr1_166132992_   1975 ATAGAGACCTTCTA-AACTCAACAACAATTATAAAAACAAACACTCCAAT 2023
                            i   v  ii  -       i  i  ----   i     i vi     
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAA----AAAGACAAATAACCCAAT 812

  chr1_166132992_   2024 TCAAAAAATGGACAAACAACTTGATTAGACATTTCTCC---GAAAATACA 2070
                          -?        i    vi i    v             ---   i   i 
  L1M4_orf2#LINE/    813 T-WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_166132992_   2071 TGAATTGCCAGGAAACATATGAAAAGATGCTAACTATCACTAATTAT 2117
                         ii   v    iv  i  i             v vi    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (99 / 64)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.50 (84 / 24)  


2581 24.13 3.57 5.30  chr1_166232228_166235052     1409  2332 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166232228_   1409 TGGAAAAACATTCTATGCTTATGTATTGGAAGAATCAGTATTGTTAAAAT 1458
                               i i  i i   i i   v         v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166232228_   1459 AGCCATTGTGCCCAAAGCAATCTACAGATTCAACACTATTTTTTAACAA- 1507
                         i  v  vv v      vii               i v  iii - v   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT-ATCAAA 99

  chr1_166232228_   1508 ---CTA-CTGGAATCATTTTCCTCAGGATTAGACAAAGCT-ATTCTAAAA 1552
                         --- i -   ---- v    iiv   i v v     -   -  i      
  L1M4_orf2#LINE/    100 ATCCCAGCTG----CCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAA 144

  chr1_166232228_   1553 TTCATATGGAATCAAAAAAGAGCCTGAATAGCCAAAGCAATCCTAAGCAA 1602
                                    viiv  ii  v  v           i     i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_166232228_   1603 AAAGAACAAATCTGGAGGTATCACAGTACCTGACTT-GAAACTATACTAT 1651
                         i         vi      vv     v v  ii i  -i     -     i
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTAC 243

  chr1_166232228_   1652 AAAGTTACAATAACCAAAATAGCATGGTACTGATACAAAAACAGACACAT 1701
                             i    i   i   i i  ii        ii i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_166232228_   1702 AGGCCAATGAAACAGAATAAAGAACCCAGAAATAAAGCCACACACTTACA 1751
                           ii     i  i     vi   ii           v   i   i   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_166232228_   1752 ACCACCTGAACTTTGACAAAGTCAACAACAACAGCAACAACAACAACAAA 1801
                         ii  vi   vi  i     i ------------ iiv   v v  vi---
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGG------------GTGCCAAGACCATT--- 378

  chr1_166232228_   1802 AAACAAGGGGAAAAGGAC--TCATATTTAATAAATGGTGCTGGAATAGCC 1849
                         ---   v   i    i i--  v -  i  i            i i i i
  L1M4_orf2#LINE/    379 ---CAATGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACT 424

  chr1_166232228_   1850 GGCTACCCATATGTGGAAGAATGAAACTGAACCCCAATGAATCCAATGAA 1899
                           v  ?   i   iii         ii  i     v i---ii  -----
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC---CTCA----- 466

  chr1_166232228_   1900 ACTGGATTCATCATATACAAAAATTAACTCAAAATGGATTAAAGATTTAA 1949
                         --------  i                            i ?   ii   
  L1M4_orf2#LINE/    467 --------CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_166232228_   1950 ATGTCAGACCTCAAACTATAAGAATCCTAGAAGAAAAACCTAGGAA-ACA 1998
                             v   v  v         i v  i          - v    ?i- v 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGTAAA 557

  chr1_166232228_   1999 CCATTCTGGATATCAGCCTTGGGAAAGAATTTAT--GAC-TAATTCCTCA 2045
                         i -   vv  iv ii v-  i  v  vii   v --  i- i -- vi  
  L1M4_orf2#LINE/    558 TC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGA--CACCA 603

  chr1_166232228_   2046 AAAGCATT-TCAACAAAAGCAAAAATTGACAAATT-----------AAAC 2083
                               iv-v         v      v  i     -----------   i
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_166232228_   2084 TAAAGAGCTTCTGCTCAGCAAAAGAAGCTATCTACAGAGTGAACAGACA- 2132
                             i -   i  iv vv    i  vi     v v i      v     -
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_166232228_   2133 ----CAGAATAGAA-AAAATATTCACAAAGTATGTATCTGACAAAGGTCT 2177
                         ----      i i -        ii    vi  i       i  i  v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_166232228_   2178 AATATCCAGAAACTATAAGATAGTTAAACAATTGAACAAGCGAAATACAA 2227
                         vi         vv     iiv v ivv    i v  i  vvi   v    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_166232228_   2228 ATAACCCCATTAAAAAGTGGGCAAAAGACATGAACAGATACTTATCAAAA 2277
                                v   ?    i        i  iv    i   i i  v  v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_166232228_   2278 GAAGACATACAAATAGCCAACAA--ATGTGAAAAAAATGCTCAACATCAC 2325
                              i        i     i  -- ii      i -            ?
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZ 901

  chr1_166232228_   2326 TAATCAT 2332
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.84 (142 / 77)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.93 (82 / 28)  


2887 21.25 0.98 12.24  chr1_166336055_166338849     1296  2316 (479)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_166336055_   1296 GAAAGATATCCCATATTTATGAATTTGAAAAATTAATATTGTTAAAATGT 1345
                                       i  i   i   v   i v             i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_166336055_   1346 CTATACTACCCAAAGCAGTCTGCAGATTCAATGTAATTCCTATCAAAATT 1395
                          v     v      viii   i         i i   i           i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_166336055_   1396 TCAATGGCATTTTTCAGAGAAATAAAAAATAACAATCTTGAAATTCATAT 1445
                         i  iiv  v     iiv      vi v  -ivii   i i          
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATAT 151

  chr1_166336055_   1446 AGAACCACAAAAAAATCCTGAATAGCCAAAGCAATCTTAAGCAAAAAGAA 1495
                         i   vii   iii -i  v           i       i iv  i     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_166336055_   1496 CAAAGCTAGAAGCAGCACACTGCCTGATTTCAAAATATACTACAAAGCTA 1545
                              i i  i vvv      v  ii         iv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_166336055_   1546 TAGTAATTCAAACAGCAT---ACTGGCATAAAAATAGATACTTAGACCAA 1592
                         i      iv i    ii ---          ii     i iv    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_166336055_   1593 TGAAACATAGTAGAAAGATAAGGAATAGATTCATGCATTTACAGTCAATT 1642
                           i  i v i v  i  viv  i    i ii   i      ii       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_166336055_   1643 GATTTTTGATAAAGATGCCAAGAACATTCAATGGTGAAAGGAGGGTCTCT 1692
                               i  i  i i        v          v     i vi    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_166336055_   1693 TTAATAAATGATATTGGGAAAACTGGATATCTATATAAAGAAGCTTGAAA 1742
                          i  i     i ii     v         ? i i  iv i   vv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_166336055_   1743 TTGGATTCTTGTCTCACA-----TACATAAATCAAAGGAAAATGGATTAA 1787
                              ii i ii      -----    v    i  vvv         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_166336055_   1788 AGACTTAAATATAAGTCCTGAAACTATAAAACGATTAGAAGAAAACACAC 1837
                             i     i    vv  i            vv             i v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_166336055_   1838 ATAAAAAGCTCCATGACAGCTTGCAGTGAGCCGAGATCACGCCACTGCAC 1887
                         i?iv   v  i i    --    -i  v  --------------------
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGAC--CTTG-GGTTAG-------------------- 577

  chr1_166336055_   1888 TCCAGCCTGGGCGACAGAGCAAGACTCCGTCTCAAAAAAAAAAAAAAAAA 1937
                         ------------------    ----------------------------
  L1M4_orf2#LINE/    578 ------------------GCAA---------------------------- 581

  chr1_166336055_   1938 AAAAGCTCCATGACATTAATCTTGGCAACGACTTTGTATATGACCACAAA 1987
                         ----------  i--  --    i ------------       vv    
  L1M4_orf2#LINE/    582 ----------TGG--TT--TCTTAG------------ATATGACACCAAA 605

  chr1_166336055_   1988 AGCACAGGCAACAAAAGCAAAAATAAACAAATGGGATAACTTCAAACTAA 2037
                               i          v       i i    v   ivv v     v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_166336055_   2038 AAAGCTTTT-TCCAAAGCAAAGGAAACAATTGACAGAGTGAAGAGACAAC 2086
                            i     - v v--v       v  v  ii v i      i       
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCT--TCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_166336055_   2087 CTATGGAGCTGAAGAAAATATTTACAAACCATGTATCTGATAGAAGATTA 2136
                          i ii  iiv i           i    i   i         iii  i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_166336055_   2137 ATATGCAAAATATGTAAGAAACTCAATTGCAAAATGCACACACACACTCG 2186
                         i   v  i     i   ii     --  i   --------------   i
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTC--TTACAA--------------CTCA 787

  chr1_166336055_   2187 CGTACACACACACACACACACATATAACTCAATTTAAAAATGGGCAAAGA 2236
                         ------- i - i v v v   v     i     ?              i
  L1M4_orf2#LINE/    788 -------ATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_166336055_   2237 ACCTGAATAGACATTTCTCCAAATAAGACATATAAATGGCCAACAGGTAT 2286
                          ii                    v    i   i          i i i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_166336055_   2287 ATTTAAA-ATATTTGACTAATCATCAGGGAA 2316
                           vv   -  ii ii  --    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAAC--ATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (143 / 70)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 7.11 (135 / 19)  


 633 27.33 0.00 0.00  chr1_166349813_166352025      547   696 (1517)    L1M4_orf2#LINE/L1        3   152 (756)  

  chr1_166349813_    547 GAAAGATATTTCATGTTTACGAGTAGGAAGACTCAATGTTATTAAGATAT 596
                                  ii      i i ii v        i   i  i       iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_166349813_    597 CAATTCCTCCCAACTTGATCTTTAGATTTAATGCAACCTCAATCAAAATC 646
                             v ii     v       vi     i  i    i i v         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_166349813_    647 CCAACAAGTTATTTCGTCAATATCAACAAACTGATTCTAAAGTTTATTTG 696
                            i vivi v   i ivi v  ii    i     i     i  i  v  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

Transitions / transversions = 2.42 (29 / 12)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.00 (0 / 0)  

2346 25.83 3.47 0.56  chr1_166349813_166352025     1001  1720 (493)    L1M4_orf2#LINE/L1      168   908 (0)  

  chr1_166349813_   1001 CACAATATTGCCAACACAATATTGAAGGAGAAGAACAACGTTGAAGTACC 1050
                           v    --     v     v     ii          v    i  v  i
  L1M4_orf2#LINE/    168 CAGAATA--GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_166349813_   1051 AATACTACCCAACTTCAAAAGTTACTATAAAGCTACAGTAATCAAGGAAG 1100
                         v i   v     i       v      i                  iv  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_166349813_   1101 TGCAGTATTGGTGAAAAAGTGCACAAATAGATCAATGGAATAGATTAGAG 1150
                           ii   i   iiv  iii iv   v                  v v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_166349813_   1151 AGCCCAGAAATAGACCAACA----TAAAGTCAACTGATCTTTGATAAAGG 1196
                           i         i   v i ----  vi     i    i  i  i  i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_166349813_   1197 AACAAAGGCAATACAATGGGGCAAAGATAGTCTTTTGCACAAATGGAGCT 1246
                         vi v   i v  v        v  ii          vv        v   
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_166349813_   1247 GGAACATCTGAACATCTACACGCATAAAAGAT----CTGGACATAGACTT 1292
                           i   v   i i ? i   i   -   ii  ----i     vivv  i 
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCA-AAAGAATGAAGTTGGACCCCTACCT 464

  chr1_166349813_   1293 TACACACTTCACAAATTTTAACTCAAAATGGA----------AAATTTAA 1332
                         i    vv vi     vv               ----------    v   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_166349813_   1333 T-GC-AAAACTATAAAACTCCTAGAAGATAACA--GGAAAAAACCTAGAT 1378
                         v-  -               i       v    --  ?iv   i  vvi 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_166349813_   1379 AACCTTAGATATAGTGATGACTTTGTAGCTACAACACCAAAGGCACAATA 1428
                         i     i i vvi ii   ii  iv   v  ii        i      vv
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_166349813_   1429 CATGAAACAAATCATTGATTAAGACGGACTTCATTAACTTTAAAAACTTC 1478
                         v ii   v   vv  v   -  ivi         i  vv          i
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGAT-AAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_166349813_   1479 TGCTCTGTGAAAGACAATGTCAAAGAAATGAAAAGACAAGCCGCAGGCTG 1528
                           iv  vii  i    v i    ii  i           v  i   iv  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_166349813_   1529 GGAGAAAA-ATTTGCAGAAGATGCACGTGAGAAAGCACTGTTATCCAAAA 1577
                                 -       i vv  ii iv   v  i v   vv      i  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_166349813_   1578 TATAAAAAGA-TATTTAAAACTTAACATTGAGAA-ACAAACCACTCAGTT 1625
                             v     -ivi   v    i  i v i i  -     iv  i  i  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_166349813_   1626 AAAAAGTGGGTCAAAGATCTTACAAGACACCTCACCAAAGAATGTGTGCA 1675
                         ?    i    iv  i   i v vv     ii  v        vi i i  
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_166349813_   1676 GCTTACAAATGATCACATGAAAAGATGCTCTGCATCATGTGTTAT 1720
                         iv vi v   i v                 vi     ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (102 / 81)
Gap_init rate = 0.02 (12 / 741), avg. gap size = 2.42 (29 / 12)  


1648 25.32 2.60 3.41  chr1_166372735_166374358      516  1131 (493)    L1M4_orf2#LINE/L1      298   908 (0)  

  chr1_166372735_    516 CAATGGAACAGAATACAGAGGCCAGAAATAATGCTGAACACTGACAACCA 565
                                 i     vv    v          vv iiv   i v iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_166372735_    566 TCTGATCTTTGACAAAA-TCCACAAAAACAAGCAATGGAGAAAGGACTCC 614
                         vi    i  i     ii- v -   i v  vv      i     i ivvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_166372735_    615 CTATTCCATAA-TGGTGCTGGGATAACTGTCTAGCTATATACAGAAGATT 663
                           v   v i  -           i     vv  ? i i  i  i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_166372735_    664 GAACCTGGGCCCCTTCCTTACATCATATACAAAAAATAACTCAAGATGGA 713
                            vi   i     v   i   i            v        i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_166372735_    714 GTAAAGACTTAAATCTAAAACCAAACACTATAAAAACCCTGGAAGATAGC 763
                         vi ?    i     v   i v v  v         vi i i     v i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_166372735_    764 CTGGG---AAATACCATTCTGGACATAGGACCTGGCAAAGACTTCAT-GA 809
                         v i  ---    -- -   vv   v v  iiiv     v ii   v -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_166372735_    810 CAAGACACCAAAAGCAATAGCAACAAAA-ACCAAATTGACTAATGAAACT 858
                         i v             vv          - vv    v  iv   vii   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_166372735_    859 -AATGAAACTCTTTAGTTGTACAACAGATAGTTTATCTGTACAACAAAAT 907
                         -v  v   v ---  ----- v   ------   ---   i vv    iv
  L1M4_orf2#LINE/    644 TCATCAAAAT---TA-----AAAAC------TTT---TGTGCTTCAAAGG 676

  chr1_166372735_    908 AAACTATCAACAGAGTAAA----CAACCTACAGAATGGAA-AAATTTTTT 952
                          v        v i   i  ----     i         i -   v v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_166372735_    953 GCAAACTATGCATCTGACAAAGGTCTAATATCCAGAATCTATAAGGAATT 1002
                              ii  ii      i  i  v  vi          v     i   i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_166372735_   1003 TAAACAAATTTACAAGCAAAA---AAATGACCTCATTAAAAAGTGGGCAA 1049
                         ivv    v iv i  vv    ---    i   iv   ?    i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_166372735_   1050 AGGACATGAACAGATGCTTTTCAAAATAAGACATTCACACATCCAACAAC 1099
                             iv    i   iii  i  v   v    i  v  v iiv    i  v
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_166372735_   1100 CATATGAAAAGATGTTTAACATCACTAATCAT 1131
                           i           i i       ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (80 / 73)
Gap_init rate = 0.03 (16 / 611), avg. gap size = 2.31 (37 / 16)  


3120 26.73 0.88 1.42  chr1_166413131_166416187     1652  2564 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166413131_   1652 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1701
                               i i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166413131_   1702 GACCATACTGCCCAAGGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 1751
                          i v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_166413131_   1752 TACTA-CTGACTTTTTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTC 1799
                          v i -   v       -i     v v  v  i--  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr1_166413131_   1800 ATATGGAACCAAAAAAGAGCTTGTATAGCCAAGACAATCCTAAGCAAAAA 1849
                                 viiv  ii  v iv v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_166413131_   1850 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 1899
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_166413131_   1900 CTATAGTAACCAAAACAGCATGGTGCTGGTACAAAAACAGATATATGGAC 1949
                            i     i   i    ii    i    i i  ii i   i    i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_166413131_   1950 CAACGGAACAGAACAGAGGCATCAGAAATAACACCACACATCTACAACCA 1999
                            i    i    iv   ivvi         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_166413131_   2000 TCTGATCTTTGACAAAGCTGACAAAAAGAAGCAATTGGGAAAGGATTCCC 2049
                         vi    i  i     i v  v   i vv vv    v       i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_166413131_   2050 CATTTAATAAATGATGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 2099
                         iv  i  i     i  i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_166413131_   2100 AAACTGGATCCCTTCCTTACACCTTATATAAAAATTAACTCAAGATGGAT 2149
                           ii    i    v   i     v    i              i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_166413131_   2150 TAAAGACTTAAATGGAAGACCTAAAACCATAAAAATTCTAGGAGAAAACC 2199
                         i ?    i      v    v       i      v ii   i       v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_166413131_   2200 TAGGCA-ATACCATTCAGGACGTAGGTATGGGCAAAGACTTCATGACTAA 2248
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_166413131_   2249 AACACCAAAAGCAACAGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 2298
                         i            vv           vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_166413131_   2299 TTAAACTAAAGAGCTTCTGCACAGTAGAAAAAAAAAAACTATCATCAAAG 2348
                          i   v v  i i   i  ii vvi -----  ii v       vv    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCA-----AAGGACACTATCAAGAAAG 691

  chr1_166413131_   2349 TGAACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCACCT 2398
                             v  iv    i                 v       vii  vi i  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_166413131_   2399 GACAAAGGGCTAATATCCAAAATCTACAAGAAACTTAAACAAATTTACAA 2448
                           i  i  i  vi      i   v  i  ii    ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_166413131_   2449 GAAAAA-ACAAACAACACCATCAAAAAGTGAGTGAAGGATATGAACAGAT 2497
                         v     -     i   v v  i?    i  i ii      v    i   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_166413131_   2498 GCTTCTCAAAAGAAGAAGTTTATGCA----GTCAACAAACATATGAAAAA 2543
                         ii     v        ----   i  ---- i   i  i  i       i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_166413131_   2544 AAGCTCATCATCACTGGTCAT 2564
                          v     v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (148 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


2746 26.34 4.22 0.68  chr1_166539810_166542677.rev     1508  2384 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166539810_   1508 TGGAAAAACATTCCATGCTCATAGATTGGAAGAGTCAGTATCATTAAAAT 1557
                               i i  i     i    i          v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166539810_   1558 GGCCATACTGCCCAAAGCAATCTACAGATTCAATGCTTTTCCTACCAAAC 1607
                            v     v      vii              i  vv i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_166539810_   1608 TATTGACACCATTTTTCACAGAATTAGAAGAAACT-ATTCTAAAATTCAT 1656
                          viiii vv v     ii     v v  v-  i  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr1_166539810_   1657 ATGGAATCAAAAAAGAGCCTGAATAGCCAAAGTAATCCTAAGCAAAATGA 1706
                               viiv  ii  v  v           ii    i i iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_166539810_   1707 AGAAGGCCAGAGGCATCACGTGACTTGACTT-GAAACTATACTATAAGAC 1755
                          v  i iii    vv    iivv iii i  -i     -     i  ii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr1_166539810_   1756 TACAGTAACCAAAACATCATGATACAGGTACAAAAACAGA-A-ATGGATC 1803
                                 i   i   vii  i   v  i i  ii i   - -  i    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_166539810_   1804 AATGAAACACAATAGAGAACCTACAAATAAAGCCACATACCTACAGCCAT 1853
                             i  i v   v    ii i v       v   i i ii  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_166539810_   1854 GTGATCATTGAAAAAGTCAACAAAAACAAGCAACAGAGAAAGGAC--TCC 1901
                         v    iv i  v  i viiv   i v  vv   ii i     i i--  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_166539810_   1902 TATTCAATAAATGGTGCTGGGATAGCTAGCTAGCCTACATGCAGAAGAAT 1951
                          -     i              i i  i v  ?  -       i      
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCC-ACATGCAAAAGAAT 446

  chr1_166539810_   1952 GAAACTGGATAGCCACCTTTCAGCATATACAAAAATTAACTCAAGATGGA 2001
                            ii    ivv i    iv  v                     i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_166539810_   2002 TTAAAGATTTAAATATAAGACCTCAAACTATAAGAATCCTAGGAAAAAAC 2051
                          i ?   ii     i     v  v         i v  i   i i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_166539810_   2052 CTAGG---AAAC-------ACCATT---CTAGACATCAGCCT-TGAGAAA 2087
                         v    ---   i-------   -  ---i   i  vii ii - v   v 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_166539810_   2088 -GACACCAATAGCAATTGTAATGAAAACAAAAATTGACAAGTGGGACCT- 2135
                         -        v    vvv i  ii   iv      v  i  i v    i -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_166539810_   2136 -----AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAAAGTAA 2180
                         -----       i -   i  ii vv    i  v        v     i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_166539810_   2181 ACAGACAACCCATAAAATGGGAGAAAATACTTGCAAACTATGCATGTGAC 2230
                          v          i i              i       ii  ii  v   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_166539810_   2231 AAAGGTCTAATATCCAGAATCTATAAGGAACTTAAACACCTGAACAAGTA 2280
                           i  v  vi          v     i     ivv   v  v  i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_166539810_   2281 AAAAACAA----CCCCATTAGAAAATGGGCAAAAGACATGAACAGACGCT 2326
                            i    ----   v   ?i            i  iv    i    ii 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_166539810_   2327 TCTCAAAACAAGACACACAAGAGGCCAACCATCATATGAAAAA--GCT-- 2372
                             v   v    i i    iv      iv v  i       i--   --
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_166539810_   2373 --ATCAGGGAAATG 2384
                         --    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (147 / 81)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.15 (43 / 20)  


1598 25.30 10.37 1.52  chr1_166729991_166731632      494  1149 (493)    L1M4_orf2#LINE/L1      195   908 (0)  

  chr1_166729991_    494 GAATAA-AAAATTGGTAGGGCTAAAAGCACCCAATATCAACATTTTCCAT 542
                            v  -   i    -   i  v v viv      v    v i  v i i
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGG-AGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_166729991_    543 AA-GCTATGGTAATGAAGACACTGTGCTATTGGCATCAAAAACACACAAA 591
                           -    ii     v      v    v  i      -  ii i v   v 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATA 292

  chr1_166729991_    592 AGTGATGGATAGAACAAAATAGAAA-CCCAAAAATAGGCATGACACATT- 639
                         vi-   vi  i   i i   v  i -i   i     ii vi- i     -
  L1M4_orf2#LINE/    293 TA-GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC-ATACATTT 340

  chr1_166729991_    640 --GGACAAATGGTTCT-GACAAAGATAT-AAATCAATTCAGTAGATAAAA 685
                         --  v   v  i  i -     i i ii-  iv v     i i iv   i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_166729991_    686 GATAGTGTTTTCAA-AAGTAGTACTTAAATAATTAGCTATTTATATGCAA 734
                         i     v       -  i i  i  vii i  i i v  ?ii i      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_166729991_    735 AAAGAATGAAGAACTTTGATCCATTCCTCACCCCATATACAAAAATTAAC 784
                           -        ---  v  i  v v      v                  
  L1M4_orf2#LINE/    441 AA-GAATGAAG---TTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_166729991_    785 TCAAAATATATTATAGCCTTAACT--AAACTCTGAGACTATACAACTTCT 832
                                iv  i ?  v i   v --  ivv  i i      v    ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_166729991_    833 AGAAGAAAACATATTAGAAAATAATTGTAACCTTTAGTTAGGAAAGGATT 882
                                      vv? v    vv i  i     vi      v  v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_166729991_    883 TCTTAGACACAATACCAAAACCATGATC--CAAAAAACAC------TAAG 924
                                i ii i       v  ii v --     i v v------   i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_166729991_    925 TTGGAATTCATAAAAATGTAAAA--TTCTGCTCTTAAAAAGATACT-TTA 971
                              v     v     -     --  i  iv   v   i  i   - i 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_166729991_    972 GGAGA--------ACAA----------------AAATTTCTGCAAATCAT 997
                         i  i --------    ----------------    v i          
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_166729991_    998 GTATCTGATAAATG-CTTATATCCAAAACATATAAAGAATGGATACAA-- 1044
                         i          iv -   i      i  i          ivvv     --
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_166729991_   1045 ----------------AACTATCCAATTTAATAATAAGGCAAAAGTTATG 1078
                         ----------------  iv i      ?  v   i-      i v v  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATG-GGCAAAGGATTTG 834

  chr1_166729991_   1079 AAGGCACA---CTTCAATAAACATAAAGAGATGGCAGATAAGCACATCAG 1125
                           viv   ---  i   vi  v   v v i     vi          v i
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_166729991_   1126 GAGATGCTCAACATTAATCAGTCA 1149
                         i             i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (94 / 68)
Gap_init rate = 0.04 (25 / 714), avg. gap size = 3.12 (78 / 25)  


2653 26.87 2.20 2.20  chr1_166748837_166755555     5320  6227 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166748837_   5320 TGGAAAAACATCCCATCCTCATGGATAGGAAGA---AA-------AAAAT 5359
                               i i       vi        v      ---  -------  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166748837_   5360 GGCCATACTGCTCAA---GGTTTATAAATTCGATGCTATTCCCATCAAG- 5405
                            v     v i   --- i i  i i    i i  v  i  i     i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_166748837_   5406 --CTAGCATTGATTTTTTTCACAGAACTAGGAAAAAT-ACTTTAAATTTC 5452
                         -- i   --  vi      -i     v v iv  iv - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_166748837_   5453 ATATGGAACAAAAAAAGAGCCCATA-TAGCCAAGACAGTTCTAAGCAAAA 5501
                                 - viv  i ii    v -       i   i ii i --    
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAA 194

  chr1_166748837_   5502 AACAAAACAAAACAAAAAAAAACCCAAAGCATCATGCTACCTGACTTCAA 5551
                         i - i      iivii ii --------- -   ii  v  ii i     
  L1M4_orf2#LINE/    195 GA-AGAACAAAGTTGGAGGA---------C-TCACACTTCCCAATTTCAA 233

  chr1_166748837_   5552 ACTATACTACAAGGCTACAGTAACCAAAATAGCATGGTACTGGTATCAAA 5601
                          viv        i          i   i i  ii         i  v ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_166748837_   5602 ACAGGGATAAAGACCAATGGAACAGAACAGAGACTC-AGAAATAACACCA 5650
                          i  iv   v   i        i    iv    v  -        vv   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_166748837_   5651 CACATCTACAACCAACTAACCTTCGACAAATCTGACAAAAACAAGAAATG 5700
                         i    i  iiii   i i ii        ivv  v   i v  vvv    
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_166748837_   5701 GGGAAAGGATTTCCTATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCA 5750
                                i  vvi  v  i  i              v      v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_166748837_   5751 TTTGTAGAAAACAGAAACTGGACCCCTTCCTTACACCTTATCCAAATGTT 5800
                         iv  i i  i vv   ii         v   i     v   v    vi  
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_166748837_   5801 AACCCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAGCCATAAAAAC 5850
                            i   i      i ?    i         i v i   i i      vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_166748837_   5851 CCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGACAAG 5899
                          i           v    ?i- v i -   iv   v v  vv i i   v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chr1_166748837_   5900 GACTTCATGACTAAAACACCAAAAGCAATGGAAACAAAAGCTAAAATTGA 5949
                          ii   v iiv  vi            vvi v        vv     v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_166748837_   5950 CAAATGGGATCTAATTAAACTAAAGAGCCTCTGCACAGCAAAAGAAACTA 5999
                         i    v   ii v  i   v v  i i i i  ii vv    i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_166748837_   6000 ACATCAGAGTGAACAGGAAACCTACAGAATGGGAGAAAATTTTTTGCAAT 6049
                         v  vv i      v  iv    i                 v   -    v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAA 731

  chr1_166748837_   6050 CTACCCATCTGACTAAGGTCTAATATCCAGAATCCACAAGGAACTTAAAC 6099
                         ii ivi      iv i  v  vi          vi i  i     ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_166748837_   6100 AAATTTACAAGAGAAAAAACAAACAACCCCTTCAAATAGTGGGCAAAGGA 6149
                           v iv i  v -    i     i     vv i?  v i           
  L1M4_orf2#LINE/    782 AACTCAATAATA-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_166748837_   6150 TATGAACAGACACTTCTCAAAAGAAGACATTTATGCGGCCAAGAAACACA 6199
                          v    i     i     v        i  vi vii      v  i    
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_166748837_   6200 TGAAAAGAAGCTCATCATCGGTCATTAG 6227
                                 v     v    i????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.22 (40 / 18)  


3370 25.55 0.66 0.66  chr1_166790223_166796500.rev     4880  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166790223_   4880 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i i    i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166790223_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_166790223_   4980 TACCAA-TGCCTTTCTTTACAGAA-TTGGAAAAAACT-ATTTTAAAGTTC 5026
                          v   i-       -   i     -   -- v  i  -  ii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_166790223_   5027 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5076
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_166790223_   5077 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5126
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_166790223_   5127 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5176
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_166790223_   5177 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAAC 5224
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_166790223_   5225 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5274
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_166790223_   5275 CCTATGTAATAAATGGTGCTGGGAAAACTGGCTAGGCATATGTAGAAAGC 5324
                         i  v vi  i              v      v  ?v  i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_166790223_   5325 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5374
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_166790223_   5375 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5424
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_166790223_   5425 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5473
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_166790223_   5474 AAAACACCAAAAGCAATGGCAACAAAAGCTAAAATTGACAAATGGGATCT 5523
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_166790223_   5524 AATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGA 5573
                         v  i   v v  i i   i   i vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_166790223_   5574 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5623
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_166790223_   5624 AAAGGGCTAATATCCAGAATCTACAACGAACTTAAACAAATTTACAAGAA 5673
                           i  i  vi          v  i  v     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_166790223_   5674 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACGTGAACAGACATT 5723
                            i     i     v  i?    i           iv    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_166790223_   5724 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5773
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_166790223_   5774 TCATCACTGGCCAT 5787
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2460 27.02 5.13 1.60  chr1_166803963_166808247.rev     2918  3794 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166803963_   2918 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 2967
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166803963_   2968 GTCCATACTGCCCCAAGTAATTTATAGATTCAATGCCAACCCCATCAAGC 3017
                          v v     v   v  v i  i  i        i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_166803963_   3018 TAC-AACTGACTTTCTT-CACAATATTGGAAAAAAT-ACTTTAAACATCA 3064
                          v - i   v    i  -  v  -    - v  iv - iii    vv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTG-ACAAGCTGATCCTAAAATTCA 148

  chr1_166803963_   3065 TATGGAACCAAAAAAGAGCCCTCATAGCCAAGACAATCCTGGGCAAGAA- 3113
                                viiv  ii  v  vvv        i      i  iiv     -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_166803963_   3114 --CAAATCTGAAGGAATCACACTACCTGACTTCAAACTATACTACAAGTC 3161
                         --    vi  i    v       v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_166803963_   3162 TACGGTAACCAAAACAGCATGGTACTGGTA---------ACA-------- 3194
                            i    i   i    ii         i ---------   --------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_166803963_   3195 --------------GAGGCCTCAGAAATAACACCACACATCTACTACCAT 3230
                         --------------   ivii         vv   i    i  ivii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_166803963_   3231 CTGATCTTTGACAAACCTGACATGAACAAGCAATGGGGAAA-AATTCCCT 3279
                         i    i  i     ivv  v  v  v  vv           -   vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_166803963_   3280 ATTTAATAAATGTTATTGGGAAAACTGGCTAGTCATATGCAGAAAACTGA 3329
                         v  i  i     v ii     v      v  ?i  i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_166803963_   3330 AACTGGAACCCTTCCTTACACCTTATACAAAAATCAACTCAAGATGGATC 3379
                          ii    v    v   i     v           i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_166803963_   3380 AAAGGCTTAAATGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAACCT 3429
                          ?  i i           v   ii  i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_166803963_   3430 GAGAAATACCTGAGCAATACCATTCAGGACATAGGCATGGGCAAAGACTT 3479
                         -  i?i  -------   -- -   iv   v v  vv i     v ii  
  L1M4_orf2#LINE/    549 -AGGNGTA-------AAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_166803963_   3480 CATGTCTAAAGCACCAATAGCAATGGCAACAAAAACCAAAATTGGCAAAC 3529
                          v ivv  vii      v    vvi         ivv     v ii   i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_166803963_   3530 GGGATCCAATTAAACTAAAGAGCA---GCACAGCAAAAGAAATTATCATC 3576
                         v   iiiv  i   v v  i i v--- ii vv    i  v i     vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_166803963_   3577 AGAGTGAACAGGTAACCTAAAGAATGGGAGATAAAT-TTTGCCATCTATC 3625
                          i      v  ii    i v           -    -     v vii  v
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGA-AAATATTTGCAAATCATA 736

  chr1_166803963_   3626 CATCTGACAAAGGACTAATATCCAGAATCTACAAGGAACGTCAACAAATT 3675
                         i      i  i     vi          v  i  i    viiv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_166803963_   3676 TACAAGAAAAA---AAACAACACCATCAAAAAGTGGGCAAAGGGTATGAA 3722
                         v i  v     ---   i   v v  i?    i          i v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_166803963_   3723 CAGAAACTTCACAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAA 3772
                         i   v i   v v        i  vi viii     i ii  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_166803963_   3773 AATGCTCATCGTCACTGGTCAT 3794
                         i       v i   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (130 / 103)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.47 (59 / 17)  


3323 26.54 0.44 0.44  chr1_166808528_166815081.rev     5156  6063 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166808528_   5156 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATGAATATTGAGAAAAT 5205
                              ii i  i     i      i v      v v       vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166808528_   5206 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCGCCATCAAGC 5255
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_166808528_   5256 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5303
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_166808528_   5304 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5353
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_166808528_   5354 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5403
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_166808528_   5404 TACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5453
                                 iv  i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_166808528_   5454 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACC 5501
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_166808528_   5502 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5551
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_166808528_   5552 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5601
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_166808528_   5602 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5651
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_166808528_   5652 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5701
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_166808528_   5702 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5751
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_166808528_   5752 AACACCAAAAGCAATGGCAACAAAAGCTAAAATTGACAAATGGGATCTAA 5801
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_166808528_   5802 TTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5851
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_166808528_   5852 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5901
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_166808528_   5902 AGGGCTAATATCCAGAATCTACAACGAACTCAAACAAATTTACAAGAAAA 5951
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_166808528_   5952 AAACAAACAATCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 6001
                          i     i  i  v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_166808528_   6002 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 6051
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_166808528_   6052 ATCACTGGCCAT 6063
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2451 23.86 5.06 2.53  chr1_166823859_166825858.rev      680  1509 (491)    L1M4_orf2#LINE/L1       58   908 (0)  

  chr1_166823859_    680 CTCCCTACCATATCGATT--CAGATTCAACACAATCTCAATCAAAATCCC 727
                              ---  v  i   i--          i     i v           
  L1M4_orf2#LINE/     58 CTCCC---CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_166823859_    728 AGCTCCCAGCATGCTTTTAAATATACATTGACAAAGTGATGAGAACATAT 777
                             ----  ---     vvii v v        iv    vvv  v  vi
  L1M4_orf2#LINE/    105 AGCT----GC---CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_166823859_    778 ATATGAAAATCACAAAGGATCTAAAATAGCCAAAACAATCTTCAAAACAA 827
                              i    -i   i   i i i                  v    vi 
  L1M4_orf2#LINE/    148 ATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_166823859_    828 AGAATAACATTGGAGAACTCATACTACCTTATTTGAAAACTTTTT-TAAA 876
                             i  vi      i     i   v  iv    v       vi -i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_166823859_    877 GCTACAGTAATCAAAAGAGTGTGCCACTGGTGAAAGGATAGA----TAGA 922
                                       i v      vi     iiv         ----    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_166823859_    923 -AAATAGAACAGAAGAGAGAGTCCTGAAATGGATCCACACATGTACGGTC 971
                         -v   i   i    vv        v     ii i   i    v  i    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_166823859_    972 AAGTTATTTTT-ACAAACGCACTGAAATAATTCAACTGGGAGTGAAAAAT 1020
                           v v     i-    iv ii ii i iv      iv    iv   v i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_166823859_   1021 GTCTTCAACAAATGGAGCTAGAATAACTGGATAATCATATGAGCAAAA-- 1068
                         v i            v   i i i         ?i  i   --     --
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG--CAAAAGA 444

  chr1_166823859_   1069 ---AACCTGGACTCCCCCGTTCCCTCAATGCACAAAAATTAAT--GAGAT 1113
                         ---  vi     i  iv -i  v v v  ii           i--i i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTAC-CTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_166823859_   1114 TCATCATAGAACTAAATAGAAAAGCTAAAACCATGAAGTTTCTAGAA-AA 1162
                         vv    ?   v      iv  i         i  i  ii ii     -  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_166823859_   1163 AACAGCAGAAGAAAGTATCTTTATGACTTTTG--TAGGCAAAGATTGCTT 1210
                             -i  i? v  --     ii    i  v --       v i  v   
  L1M4_orf2#LINE/    544 AACA-TAGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_166823859_   1211 AGAGTGGACAAAGAAAGCATGAATTACAAAGAGAAGAAATA-ATAAATTG 1259
                            vvv    vvi      ii iiv     -    i     -        
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAA-AGAAAAAATAGATAAATTG 639

  chr1_166823859_   1260 GGATTCATCAAATTTTTAAAACCTTCTGCTCATTGAAAAATTCCAGTAAG 1309
                          iv         v  --    v   i  iv v ii  ii iv i vi   
  L1M4_orf2#LINE/    640 GACTTCATCAAAATT--AAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_166823859_   1310 TAAATGAAAAGGCAAGCCATAGACTGA-AGAAAATATT--CA---TATAT 1353
                         v  i       i   v   i   v  i-          --  ---i    
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_166823859_   1354 ATCTG-CAAGAGAATTACATATAAAATATATGAA-AAC----ACAACTCT 1397
                              -i   i  v  ii  vi i       i  -   ----       v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_166823859_   1398 ATAACAAAACAA-AAACAAC--AA--AAAAAATGATTAAAAGACTTGAGC 1442
                             i    vi -   i   --  --?       ivi   i  i    ii
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_166823859_   1443 AAACGCTTAACT---GAAGATATACAAGTGGT--ATATAGCACATAAGAA 1487
                          i  ii  vv i---            i   i--   -       i i  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATA-AGCACATGAAAA 886

  chr1_166823859_   1488 AGTCTTCAACATCATTAGTGAT 1509
                         ii vi         ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (121 / 73)
Gap_init rate = 0.04 (32 / 851), avg. gap size = 1.97 (63 / 32)  


 744 28.12 11.22 4.27  chr1_166841229_166842820.rev      483  1115 (477)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr1_166841229_    483 AAAATCTACTTCAGGAAG--A-AGGAATTAATACAGGGTGTTATTAGCAC 529
                             ii    v  --   -- -  v   i  v    v   v  i i   i
  L1M4_orf2#LINE/    232 AAAACTTACTACA--AAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_166841229_    530 AGGAATAGGTAAAAAGATTAATAAAACAGAATACACATAGAACTACA-AA 578
                          i i    ii v v    i   ii  i     ----- iii v v  -  
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAAT-----TGAGAGTCCAGAA 324

  chr1_166841229_    579 ACAAATCTATTCATATATGGTAAGTTGACATAAGACAGAGAT----AG-- 622
                          i   i i  v   v      v i    iv vv    ii i ----  --
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_166841229_    623 TATTGCAGTAGAGAAAAGATA---TTTTCAACAT-TGGTCCTGGTGC--- 665
                         i   -  i i i    ii   ---         v-    v    vi ---
  L1M4_orf2#LINE/    375 CATT-CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_166841229_    666 TGG-------CAT------------AATTGGGTCCCCATCTCACATCATG 696
                            -------   ------------ i    ii   i i      i   i
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_166841229_    697 CACAAAT-CTAACCCAGG-CAGATTGAAGATTTAAATGTGAAAAGC-AAA 743
                         i     v-i    i  ii-ii   ii?   ii       -  i   -   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAA 522

  chr1_166841229_    744 ACTCCAAAATTCTTTGAACGTCTTATGGGAAAACATCTTTATGATAACAG 793
                            vi    i    v   vivvvi  i  ?iv v     ii   ivvii 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_166841229_    794 AGTAAAAGAAGGATAACTTTTTTAA----GATTCAAAAAGCA-AA--AAC 836
                         iv  iivi v  -----   i   i----  iv v       -  --   
  L1M4_orf2#LINE/    573 GTTAGGCAATGG-----TTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_166841229_    837 TAAAGAAAAAGTATAATTAATTAGACTACATTGAAATTAGAATGGTGAAC 886
                         v         i  -i  v    i    v   ii      i  ------  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATA-GATAAATTGGACTTCATCAAAATTAAAA------AC 660

  chr1_166841229_    887 TTTTGTTTATCAAAAGAAACCAT--------TGAA----CAA-------- 916
                               viv     i  v  i  --------    ----   --------
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_166841229_    917 ATGGGTAAGAAATACTTGTACCACCA-ATAATTAATCAGAAATTAGTATA 965
                              - ii     i   i v- i  -   vi i  v  ii i v    v
  L1M4_orf2#LINE/    711 ATGGG-AGAAAATATTTGCAA-ATCATATATCTGATAAGGGACTTGTATC 758

  chr1_166841229_    966 CTAAATATATGAAGAGTTTCTATGAATAAATAAGAATAATACAAACAATT 1015
                          vi       i    ii ii  ii v v     v  v  v     i  ii
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_166841229_   1016 CTATAGAAAAATTGAAAAAAGACATTAACAGGTAGTTC-ACAGAGAAGTA 1064
                          v  v?      v iv   i  iv v  i  ii v   -v  i     - 
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG-A 857

  chr1_166841229_   1065 AATAAAAATA-CAAATGAAACAT-TAAAAAAAGGCT-AACCCATTAATCA 1111
                         v   v    i- v   -  i  i- i    i v   -   --  i ????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAAT-AAGCACATGAAAAGATGCTCAAC--ATCAZZZZ 904

  chr1_166841229_   1112 CCTA 1115
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.78 (112 / 63)
Gap_init rate = 0.05 (36 / 677), avg. gap size = 2.72 (98 / 36)  


2928 26.93 1.21 0.99  chr1_166886583_166892626.rev     4648  5553 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166886583_   4648 TGGAAAAACATTCCATGCTCATGGATAGGAAAAATCAGTATTGTGAAAAC 4697
                               i i  i     i        v    i v i i      v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166886583_   4698 AGCCATACTGCCCAAAGCAATTTATAAATTCAATGTTATTCCCATTAAAC 4747
                         i  v     v      vii  i  i i      i iv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_166886583_   4748 TACT-GTTGACATTCTTCACAGAA-TTAGGAAAAACT-ATTTTAAAATTC 4794
                          v i- i  v -  i  ii     -  --  v  i  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTC 147

  chr1_166886583_   4795 ATATGAAAATGAAAAAGAGCTTGAATAGCCAAGACAATCCCAAGCAAAAA 4844
                              i     v  ii  v iv          i      iii iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_166886583_   4845 CAACAAAGCTGGAGGCATCACAATATCTGACTTCAAACTATACTACAGGA 4894
                         v       i      vv     v vi ii i      viv       iii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_166886583_   4895 CTACAGTAACCAAAACAGCATGGAACTGGTACAAGAACAGACACATAGAA 4944
                                  i   i    ii   v     i i   i i     i     v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_166886583_   4945 CACTAGAACAAAACAGAGAACCCAAAAATAAGACCACACAGCTGCAACCA 4994
                           v i   i i  iv    ii   i      iv   i   vi iiiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_166886583_   4995 TCTGATCTTCAACAAACCTGACAAAAACAAGCAATAGGGAAAGGATTTAA 5044
                         vi    i   i    ivv  v   i v  vv    i       i  -- i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT--AG 395

  chr1_166886583_   5045 TATTT--AATAATTGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAAT 5092
                          v   --  i  v           v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_166886583_   5093 TAAAACAGGACCCCTTCCTTACATCATATACAAAAATCAACTCAAGATGG 5142
                          i  iiv        v   i   i             i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_166886583_   5143 ATTAAAGACTTAAAGGTAAAATGC-AAAACTATAAAAATCCTAGATGAAA 5191
                           i ?    i    v    i -  -            v  i    v    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_166886583_   5192 ATCTAGGC---AATGCCATTTAGGACACAGACACAGTCAAAGATTTCATG 5238
                          iv    ?---   -- -  iiv   viv ivvi  v   v i    v i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_166886583_   5239 GTGAAAATGCCAAAAGCAGTTGCAACAAAAGCAAAAATTGACAAATGGAA 5288
                          vv vi ii         vvv          v      v  i    v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_166886583_   5289 TCTAATGAAACTAAAGAGCTTCAGCACAGCAAAAGAAACTATCATCAGGG 5338
                         ii v  v   v v  i i   iv ii vv    i  v       vv ii 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_166886583_   5339 TGAAGAGACAACCTACAGAATGGAAGAAAATTTTTGCAATCTATCCGTCT 5388
                             i        i         i       v       vii  vii   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_166886583_   5389 GACAAAATCCTAATATCTAGCATCTACAAGGAACTGAAACAAATTTATGA 5438
                           i  iivv  vi    i  v  v  i  i     vvv    v iv  i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_166886583_   5439 GAAAAAAACAAATAACCCCATTAAAAAGTGGGCAAAGGACATGGACAAAC 5488
                         v     i           v   ?    i           iv  i i i  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_166886583_   5489 ACTTCTCAAAAGAAGACATACGTGGGACAAACAA--ACATGAAAAAAAGC 5536
                          i     v        i    iviv i v  i  --         i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_166886583_   5537 TCAACATCACTGATCAT 5553
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


3253 25.60 0.98 2.49  chr1_166893086_166896463.rev     1969  2890 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166893086_   1969 TGAAAAGACATCCCACGTTTTTTGGAAGAATTTGAAGATTGGAAGATTTA 2018
                           i     i      i   i---------  ----i          i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTC---------AT----GGATTGGAAGACTTA 37

  chr1_166893086_   2019 ATATCATTAAAATGACCATACTGCCCAAAGCAACCTACAGATTCAATGCA 2068
                             ii    i   i v     v      vii i            i   
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chr1_166893086_   2069 ATCTCTATCAAAATATGAATGAAATTATTCACAGATGTAGAGAAAC-AAT 2117
                            i          viv iivivv  v  ii    vi v  v  i -i  
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chr1_166893086_   2118 CCAAAAATTTGTATAGAACCACAGAATAGCTCAAACAGCCAAAGCAATAC 2167
                           v      ii   i   vii  iiiv v ivi  i       i    vi
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_166893086_   2168 TGAGCAAAAAGAAGAAAGCTGGAGGTGTCGTACTACCTGACTTCCAGATA 2217
                            iv  i     v    i      vv  ii   v  ii i   v i iv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_166893086_   2218 TACTGCAGAGCTATAGTAACCAAAAGAGCATGACATTTGTATAAAAACAG 2267
                             i  i     i     i   i v  ii  ii i v i    ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_166893086_   2268 ACATGTAGATAAAACTGAACGGAATAAAGAACCCCCAAATAAGTCCACAT 2317
                             i     v  -iv   ii    vi   ii  vv      ii   i i
  L1M4_orf2#LINE/    288 ACATATAGATCAA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_166893086_   2318 GTTTACAGCCAATTGATTTCTGACAAAGGTGCCAAGAACATACCCTGGGG 2367
                         i    ii i          ii     i          v   v vv     
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_166893086_   2368 AAAGAACACCCTCTTCAATAAATGATGCTGAGAAAACTGGAAATACATAT 2417
                               i vi  i     i     i     i  v       v ?v  i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_166893086_   2418 ACAGAAGAATGAAACTAGACCCCAAACTCACACTGTATACAAAGAATCAA 2467
                         i  i         ii i      v v       ii        -   i  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA-AATTAA 485

  chr1_166893086_   2468 CTCAAAATGGATTACAGGCTTAAATGTAAGACTTGAAACTATAAAACCAC 2517
                                     i ?  i i           vi i            ivi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_166893086_   2518 TAGAAGAAGATATAGGGG-AAATGCTCTGGGACATTGATCTAGACAAAGA 2566
                                 i i     ? -    -  ii v   v   ivi   i   v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_166893086_   2567 T--CTTAGGGAGGGCTAAGATCTCAAAAGCACAGGCAGTGGGAAAAAAAA 2614
                          --     i------  v  ivi          i   iiiii i      
  L1M4_orf2#LINE/    585 TTTCTTAGA------TATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_166893086_   2615 T-GACAAATTAGACTATATTAAA-TTAAAACTCTTCTGCACGGCAGAGAA 2662
                          -  i     i    vi  i   -      v-   i  ii vv  i  i 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

  chr1_166893086_   2663 AACAATCAACAGAGTGAACAAATAGCCTGTTGAATAGGAGAAAATATTTG 2712
                         v  v     v i      v i i i  iiiv    i              
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_166893086_   2713 CAAACTATTCTTCTGACAGGGGGCTAACATCCAGAATATACAAGAAGCTC 2762
                             ii  viv     i i   i  vii            i  ii i   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_166893086_   2763 AAACAACTCAACAGCAAAAA-ACAAATAATCTCATT--AAAATGGGCAAA 2809
                         vv         i ii     -        i iv   --            
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_166893086_   2810 GAATCTGAGAAGACATATCTCAAAAGAAAACATACAAATGGCCAAGCAGT 2859
                          i  i   iv      v    v      i i              vv  i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_166893086_   2860 ATATGAAAAAATGCTCAACACTATTAATCAT 2890
                          i       i          ii ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (163 / 70)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.29 (32 / 14)  


3308 25.83 0.88 0.66  chr1_166979938_166984246     2911  3816 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_166979938_   2911 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATGAATATTGTGAAAAT 2960
                              ii i  i     i      i v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_166979938_   2961 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3010
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_166979938_   3011 TATCAA-TGTCTTTCTTCACAGAA-TTGGAAAAAACTA--CTTTAAGTTC 3056
                          vi  i-  i    i  -i     -   -- v  i  i-- i v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_166979938_   3057 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 3106
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_166979938_   3107 GAACAAAGCTGGAGGCATCACACTACCTGACTCCAAACTATACTACAAGG 3156
                                 i      vv       v  ii i i    viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_166979938_   3157 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 3206
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_166979938_   3207 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAAC 3254
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_166979938_   3255 CATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGTATTC 3304
                           vi    i  i     ivv  vv  i v  vv            v  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_166979938_   3305 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGC 3354
                         i  v  i  i              v      v  ?   i  ii i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_166979938_   3355 TGAAATTGGATCCCTTGCTTATACCTTATACAAAAATCAATTCAAGATGG 3404
                             i     i    vv  i i   v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_166979938_   3405 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3454
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_166979938_   3455 C-TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 3502
                          -    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_166979938_   3503 AAAATGCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3552
                          vi ii         vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_166979938_   3553 AATTAAACTGAAGACCTTCTGCACAGCAAAAGAAACTACCATCAAAGTGA 3602
                         v  i   v v  i v   i  ii vv    i  v    i  vv       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_166979938_   3603 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 3652
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_166979938_   3653 AAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTATAAGAA 3702
                           i  i  vi          v  i  v      iv    v iv    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_166979938_   3703 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACT 3752
                            i     i     v  i?    i    ii     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_166979938_   3753 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 3802
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_166979938_   3803 TCATCACTGGCCAT 3816
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (135 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2848 26.84 3.45 2.34  chr1_167062341_167066577.rev     2849  3746 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167062341_   2849 TGAAAAGATATCCCATCTTCACGGATAAACAAAAACTAATACCCTTAAAA 2898
                           i             v    i    vii-  i vi     iiv    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGG-AAGACTTAATATTGTTAAGA 49

  chr1_167062341_   2899 TAACCATACTGCCCAAAGCAATCTACAAATTTAATGAAATCTCTATCAAA 2948
                          ii v     v      vii       i   i  i v    i        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_167062341_   2949 ACATCA------TTTTTTACAGAAATAGAAAAAACAGTCATAAAATTCAT 2992
                          ivi  ------      i       v  v  iviii  v          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_167062341_   2993 ATGGCACCAAAAAAGAGCCAGAATAGCCAAAGCAATTCTGAGCAA-AAGA 3041
                             v viiv  ii  v              i    ii   iv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_167062341_   3042 ACCAAGTCAGAGGCATCATATTATGTGACTTCAAAATATATTACAAGGCC 3091
                           v    ii    vv   i i vivii i       iv  i     i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_167062341_   3092 ATAGTAACCAAAACAGCATGGTATTGGTACAAAAACAGACATTTAGACCA 3141
                          i     i   i    ii     i   i i  ii i      v    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_167062341_   3142 ATGGAATAGA-------GTTCAGAAATAAATATATGTATTTACAGCCATC 3184
                                   -------  i          ivi  ii     ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_167062341_   3185 TGATTTTCAGTTAAGGCATCAAGAACATACACTGAGAAAAGA-TACCCTT 3233
                                 iiiv i  iii     v   v  v  i i     -  vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_167062341_   3234 TGCATTAAATGGGGTTGGGAAAATTGAATACCTATATGCAGAAGAATGAA 3283
                          v  vi      v i     v  i  i   ? i i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_167062341_   3284 ACTGGACCTATATCTC-CTCCACATACAAAAATTATATCAGA-TGGATTG 3331
                         ii      iv  i   - v   i            vv   i -     ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_167062341_   3332 AAGACTTAAATACAAAACCTGAAACTATAAAATTGCCAG--GAAAAAAAA 3379
                         ?    i     ii  i v  i           i vii  --     v v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_167062341_   3380 GAACTTAAAAAATATTTCAAGATGTCAGTCTCGGGAAAGATTTCGTGGCT 3429
                          i?v ----    -i   iv  iv ii vi v  v  v i    v i v 
  L1M4_orf2#LINE/    550 GGNGT----AAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_167062341_   3430 A---------AAGCACAGACAAATATAATGAAATTAGACAAATAAAACTA 3470
                          ---------       ii   vv v ivi   v    i    vii   v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_167062341_   3471 TATTAAC-CTAAAAGCTTCTGCACAGCAAAGGACACAGTCAATAGAGTGA 3519
                         i  i  v-i     i   i  ii vv          vi    v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_167062341_   3520 AGAGATGACCTGCTGGATGGGAGGAAATATTTGCAAATTACTCATCCAAC 3569
                          i   ii   ii v i       i              i ivi   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_167062341_   3570 AAGGGACTAACATCCAGATTATACAAGGAATTCAAACAGTTCAACAGTAA 3619
                                 vii       v    i  i   i  vv   ii    i i   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_167062341_   3620 AAAAAAAAATAGTTTTTCAACTATTAGCCCCATTAAAAAGTGGGCTAAGG 3669
                            i v     i---------------   v   ?    i     v    
  L1M4_orf2#LINE/    795 AAAGACAAATAA---------------CCCAATTWAAAAATGGGCAAAGG 829

  chr1_167062341_   3670 ACCTGAATAGACATTTCTCAAGTGAAGACATA--AATGACCAACAGGTAT 3717
                          ii                v iv     i   --    i    i i i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_167062341_   3718 ATGACAAAATACTCAACATTACTAATCAT 3746
                             v  i  i        i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (160 / 77)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.71 (52 / 14)  


2277 23.34 4.44 8.55  chr1_167080126_167084382.rev     2820  3766 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167080126_   2820 TGGAAAAGTATTCCATGTTCCTGGATTGGAAGAATCAATATTGTTAAAAT 2869
                               ii   i        v            v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167080126_   2870 GTCTGTACTACACAAAGCAATCTACAGATTTCATGCAATCCCTATCAAGA 2919
                          v vi    v v    vii           iv i              i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167080126_   2920 TATGAGTGACATTCTTCACAGAAATGAAAAAAC-AATCCTATTATAAAAT 2968
                          viv  ivi v  i  ii       vi v  i -i      -----    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA-----AAAT 145

  chr1_167080126_   2969 TTATATGGAACCACAAAAGACCCAGAATACCCAAAGCTATCCCGAGCAAA 3018
                          i        vii   ii           v     i v   ii  iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_167080126_   3019 AAGAACAAAACTGGAGGAATCACATTACCAGACTTCAAAGTATACTACAG 3068
                                  ii       v     i v  vi i      iiv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_167080126_   3069 AGCTGTCGTAACCATAACAGCATGGTATTGGCATAAAAACAGATATATAG 3118
                             iiv    i  vi    ii     i        ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_167080126_   3119 ATAAATGGAGCAGAATAGAGAACTCAGAAACAAATGCACATACCTACAGT 3168
                           v      ii     v    iii      i   iv  i i ii  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_167080126_   3169 GAACTCATTTTTCACAAAGGTGCCAAGAACCTACACTGGGGCAGAGA--- 3215
                         v  i v     iv    i          v v v  v     - i   ---
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chr1_167080126_   3216 -------CA-------GTGCTTGAGGGAA-TGGATACCC-CATTCTCCAT 3249
                         -------  -------     - i iv  -      ?  -   v vvv v
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_167080126_   3250 GATG----TG----CTTATTTCACACTGTATGCCTGTATCAAAACATCTC 3291
                         i   ----  ---- i  ii      ii   i -------    ------
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATAC-------AAAA------ 480

  chr1_167080126_   3292 ATGTACCCCATAAATATAT---ACACTTACTATGTACTCACAAAAATAAA 3338
                           -  v i  -    iv  --- v  i  v-     ----- i iv    
  L1M4_orf2#LINE/    481 AT-TAACTCA-AAATGGATCAWAGACCTAA-ATGTA-----AGAGCTAAA 522

  chr1_167080126_   3339 AATAAAAATGACACTATCAACAGAGTAAAAAGGCAACCCAGAATAGAAAA 3388
                          v  v   ----   v i i------  i  ---   -----    i?iv
  L1M4_orf2#LINE/    523 ACTATAAA----ACTCTTAG------AAGAA---AAC-----ATAGGNGT 554

  chr1_167080126_   3389 GGATACTTGCAAACAAATTGAGCTAA-CATATGAGCTCTTCAATAAATGG 3437
                         ii  vi i ii v ---   i i  i-  -   ivi    vi   --  i
  L1M4_orf2#LINE/    555 AAATCTTCGTGACC---TTGGGTTAGGCA-ATGGTTTCTTAGATA--TGA 598

  chr1_167080126_   3438 TGCTGGGAAAACTGGATATCCATATGCAGAAG-AATGAAACTGGACCCTT 3486
                         ii i---    --------------   v   -  ii   ---  -----
  L1M4_orf2#LINE/    599 CACC---AAAA--------------GCACAAGCAACAAAA---GA----- 623

  chr1_167080126_   3487 GTCAAACATGAACAAATGGGATCACATCAAG-TTAAAAAGCTTCTGCACA 3535
                         ---   v  ii i    v   iiv      i-       -   i  ii v
  L1M4_orf2#LINE/    624 ---AAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCT 669

  chr1_167080126_   3536 GCAA-GGATACAATCAACAAAGTGAAGAGACAACCCACAAAATGGGAGAA 3584
                         v   -   i  v     v        i            i          
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_167080126_   3585 AATATTTCCAAACTACCCATCTGACAAGGGATTAATATGCCAAATATATA 3634
                                v    ii ivi      i      i vi   v vi        
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_167080126_   3635 AGGAGCTGAAACAACTCTATAGGAAGAAATCTAATAATCTAATC----AA 3680
                          i  i  vvv       v   iv  i  iv v     i i   i----  
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_167080126_   3681 TGGGCAAAAGATTTGAATAGACATTTTT---AAAAAGACATACAAATGGC 3727
                                 i                 i ---  i    i           
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_167080126_   3728 AGAGAGACATATGAAACAGTGCTCAGCCTCATTCATCAT 3766
                         vi v ii  i      vii      i v   ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (142 / 77)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 3.51 (123 / 35)  


2746 26.12 1.82 4.60  chr1_167100172_167102513      916  1849 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167100172_    916 TGCAAAAATATTCTATGCTCATGGATTGGAAGGATTAATATCACTAAAAT 965
                           v   i    i i   i              iv       iii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167100172_    966 GGCCACACTGCCCAAAGAAATCTACAGATTCAATGCTATTACTATCAAAC 1015
                            v i   v      vvi              i  v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167100172_   1016 TACCAA-TGTCATTTTTTACAGAATTGGAAAAATCTATTCCAAAATTTAT 1064
                          v   i-  i -      i     v v  v  iiiv  i i      i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_167100172_   1065 ATGGAACCAAAAAAGAGCTA-AATAGTCAAAGCAATCCTAAGCAAAAAAA 1113
                               viiv  ii  v i -     i    i     i i --    i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAA 197

  chr1_167100172_   1114 TAACAAAGCCAGAGACATCATGTCTCCTGACTTCAAACTATAGTATAAGG 1163
                         v       iii   ivv   iiii   ii i      viv  v  i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_167100172_   1164 CTACAGTAATCAACACAACATGGTACTACTACAAAAACAGACACATAGAC 1213
                                      v   iii       ivi i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_167100172_   1214 CAATGAAACAGATTAGAGAACCCAGAAATAAAGCTGCACATTTACAACCA 1263
                              i  i   v v    ii           v iii       iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_167100172_   1264 TCTGATCTTTGACAAAGTTAGTAAAAATAAGCAATTAAGAAAAGACTTTC 1313
                         vi    i  i     i v ivi  i vi vv    vii    ii ivv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_167100172_   1314 TAATCAATAATTGGCACTGGGATAACTGGCCAGCCATATGCGGAAGAATG 1363
                          vv    i  v   ii      i      vi ?   i    ii       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_167100172_   1364 AAACTGGATCCCTATTTC-CACCATGTAGTTTTATAGTTCGGATTCTTAT 1412
                           ii    i     ii  -      i  ----------- ii -------
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATA-----------CAAA------- 479

  chr1_167100172_   1413 ATTTACATCTTTAATTAAAGATTTAATAT---TTAAAGATTTATATATAA 1459
                         ------------      ---i i  v  --- i ?   ii  v  i   
  L1M4_orf2#LINE/    480 ------------AATTAA---CTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_167100172_   1460 GACCCCAAACTATAAAAATCTTAGAAGAAAACCTAGG---AAATACCATT 1506
                           v iv           v              v    ---    -- v i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTC 562

  chr1_167100172_   1507 GTGGACATCAGCCTTAGCAAAGAATTTATGACTAAGTCCTCAAAA--ATA 1554
                            -  v ii vi vi    v iv  iv iiv  v v vi     -- i 
  L1M4_orf2#LINE/    563 GTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_167100172_   1555 ATTGAAACAAAAACAAAATTTGATAAGTGGGACCTAATTAAACTTAAAGA 1604
                          -- v       iv    v v     i v    i v  i   v     - 
  L1M4_orf2#LINE/    612 A--GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA-A 658

  chr1_167100172_   1605 ATTTTTGTGCAGCAAAATGA-ACTATCAACAGAATAAACAGACAACTTAT 1653
                          i        vv    i-  -        v i i i  v       ii i
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_167100172_   1654 AGAATGGGAGGAAATATTTGCAGACTATATGTTTGACAAAAGTCTAATAT 1703
                                   i           i ii    i i   i  ii v  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_167100172_   1704 CCAGAATCTATAAGGAACTT----AATTCAACAAGCAGAAAACAAAGAAT 1749
                                v     i     i----  i    i  vv i  i     v  i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_167100172_   1750 CCTGTTTAAAAGTGGGCAAAGGACATTAACAGATAATTCTC-AAAGAAAA 1798
                           vi  ?    i           iv v  i   i v     -      i 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_167100172_   1799 CATACAAGCAGCTAACAAACATAGAAAAAAATGCTCAACACCACAAATTA 1848
                         i      iii  i  i  i  i vi    i          i  ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_167100172_   1849 G 1849
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.01 (161 / 80)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.16 (60 / 19)  


1540 27.42 3.23 0.60  chr1_167126470_167133132        1   496 (6167)    L1M4_orf2#LINE/L1      322   830 (78)  

  chr1_167126470_      1 GACATAAGGCTGCACACCTACAACCGTCTGATCTTTGACAAAGCCAACAA 50
                           v    iv iii   ii  iiii ivi    i  i     i viiv   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_167126470_     51 AAACAAACAATAGGAAAAGAACTCCCTATTCAATAAATGATACTGGGATA 100
                         i v  vv    i  i      ivvi  v     i     i i      i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_167126470_    101 ACTGTCTAGCTACATGCAGAAGATTGAAACTGGATCCCTTCCTTACAGCA 150
                             vv  ? i       i    v    ii    i    v   i   v  
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_167126470_    151 TATACAAAAATCAACTCAAGACAGATTAAAGACCTAAATGTAAAACCTAA 200
                                    i       i ii   i ?              i v    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_167126470_    201 AACTATAAAAACCCTGGAAGACAGCCTAGG---AAATACCATTCTAGACA 247
                                   vi i i     v i v    ---    -- -   vv   v
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACC 568

  chr1_167126470_    248 TAGGAGTGGGCAAAAATTTCATGACCAAGATGCCAAAAGCAGTTGCAACA 297
                          v  iv i     vii    v iivi v  ii         vvv      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_167126470_    298 AAACCAAAAATTGACAAATGGGCTCTAATTAAACTAAAGAGCTTCTGCAC 347
                            vv      v  i    v  vii v  i   v v  i i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_167126470_    348 AGCAAAAGAAACTATCAACAGAGTAAACAGACAAC----AGAATGGGAGA 393
                         vv    i  v        v i   i  v       ----           
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_167126470_    394 AACTATTTGCAAACTATGCATCTGACAAAGATCTAATATCCAGCATCTAT 443
                           v          ii  ii      i  i iv  vi       v  v   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_167126470_    444 AAGGAACT--TAAATTTC--CAAGAAAAAAA-----AATCCCATTAAAAA 484
                           i     --  v vi  --i  v     i -----  i  v   ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_167126470_    485 GTGGGCAAAAAA 496
                         i        ii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGA 830

Transitions / transversions = 1.46 (79 / 54)
Gap_init rate = 0.01 (7 / 509), avg. gap size = 2.71 (19 / 7)  

2749 26.42 2.33 1.55  chr1_167126470_167133132     5270  6170 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167126470_   5270 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5319
                               i    i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167126470_   5320 GGCCATACTGCCCAAAGTAATTTATAGACTCAATGCTATTCCCATCAAGC 5369
                            v     v      v i  i  i   i    i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167126470_   5370 TACCA-TTGACTTTCTT-CAGAGAATTTGAAAAAAATG-TTTTAAATTTC 5416
                          v   -i  v    i  -    -    --i v  iv  - ii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATT--GACAAGCTGATCCTAAAATTC 147

  chr1_167126470_   5417 ATATGCAACCAAAAAAGAGCCTATATAGTCAAGACAATCCTAAGCAAAAA 5466
                              v  viiv  ii  v  viv    i   i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_167126470_   5467 GAACAAAGATGGAGGCAACATACTACCTGACTTCAAACTATACTACAAGA 5516
                                 v      vvv  i   v  ii i      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_167126470_   5517 TTACAGTAACCAAAACAGCATGGTACTGATACTAAAACAAATATATAGAC 5566
                         i        i   i    ii        ii iv ii i i i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_167126470_   5567 CAATGGAACAGAACAGAGACCTCAGAAATAACACCACACACACATCTACA 5616
                                 i    iv    vii         -   ---  i    i  ii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAA-ACC---CATACATTTATG 343

  chr1_167126470_   5617 ACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATAGGGAAAGGAT 5666
                         ii  vi    i  i     ivv  v   i v  vv    i       i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_167126470_   5667 GCCCTATTTAACAAATGGTGCTGAGAAAACTGGCTAGCCATATGCAGAAA 5716
                         ivi  v  i              i  v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_167126470_   5717 ACAGAAACTGGATCCCTTCCTTGTGCCTTATACCAAAATTAACTCAAGAT 5766
                          vv   ii    i    v   iiii  v     v             i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_167126470_   5767 GGATTAAAGTCTTAAATGTAAAACCCCAAACCATGAAAACTCT-AGAAGA 5815
                             i ?  v i         i v iv    i  -        -      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGA 542

  chr1_167126470_   5816 ACACCTAGGCA-ATACCATTCAGGATATAGGCATGGTCAAAGACTTCACG 5864
                          v  v    ?i- v i -   iv  iv v  vv i v   v ii   vii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_167126470_   5865 ACTAAAACACCAAAAGCAATGGCAACGAAATCCAAAATTGACAAATGGGA 5914
                         iv  vi            vvi     i   vvv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_167126470_   5915 CCTAATCAAACTAAAGAACTCCTACATAGCAAAAGAAACTA--AAATCAG 5962
                          i v      v v  i    ii iiiivv    i  v    --  i-- i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG--AA 689

  chr1_167126470_   5963 AGTGAACAGGCAACCTACAAAATGGGAGAAAATTTCTGCAATCTACCCAT 6012
                               v  i     i   i             v i     vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_167126470_   6013 CTGACAAAGGTCTAATTGCCACAATCTACAAGGAACT-TCACCA---AAT 6058
                             i  i  v  vi vv   v   v  i  i     - i  v ---   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_167126470_   6059 T-TAAAAGAAAAAATAACCCCATCAAAAAGTGGGCCAAGGAC------AG 6101
                         v-     ii v         v  i?    i     v     i------  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_167126470_   6102 A-ACTTCTCAAAAGAAGACATTTATGTGGCCAACAA--ACATGAAAAAAA 6148
                          - i     v        i  vi vi       i  --         i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_167126470_   6149 AAATCTCACCATCACTGGTCAT 6170
                         i---    v     ????????
  L1M4_orf2#LINE/    890 G---CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.75 (35 / 20)  


2796 24.77 4.91 1.26  chr1_167140698_167143513     1448  2323 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167140698_   1448 TGGAGAGAGATATTGTATTTGTGAGTAGAGAAAATCAATATAGTTAAGAC 1497
                             i   v  viii i  ii  ii v ii i v i     v       i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167140698_   1498 ATCAAATCTCCCCAAATTGATCTATAGATTCAATA-GAT-----TCAAAC 1541
                         iv   vv                 i        ii-i  -----     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167140698_   1542 TGCCAACAGGCCCTTTTAAAAAAATAGACAAGCTGAGTATAAAATTCACA 1591
                          v   i v v ii    iv i    v          viv         i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_167140698_   1592 TGAAATTGCAAAGAACATAAAATAAACAAAACATCTTTGGAAGAGAA--- 1638
                           i  v     i i  vi i    iv       vii   i  i    ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_167140698_   1639 TAAAGTT-------------TT---AAAGTCAGGACTTATT-TACAGCTA 1671
                         i      -------------  ---  vv   ii     i -i v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_167140698_   1672 CATAAATCATGACAGTGTGGTATTCTCATAAAGATATAAAAATAAATGAA 1721
                           vv     v            i vv     i    v v v   i  v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_167140698_   1722 TGAAAAATAAT--AGAGTTCAAAAATAGATACACACATATATAGACAACT 1769
                           i  v v   --     i  i     i iv  i    v   i v   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_167140698_   1770 GATTTTCTACAAAGATTTCCAAGGCAATTCTGCAGAGAAGGGATA--CTG 1817
                                v    i i v-     i v    viii i   i i   --  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_167140698_   1818 TTCAACAACTGGTTCAGGAGCAGTTGAATATTCAAATGCAAA-GTATGAC 1866
                                 v    v v  ii  ii  i   ?i  v       - v    v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_167140698_   1867 TATT--ATCAC-ACTTTTTATCATATGTATAAA----CTCAAAAATGATC 1909
                         -i  -- i v -  i ivi i     ii v   ----       vv    
  L1M4_orf2#LINE/    450 -GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_167140698_   1910 ACAGACCTAAATGTAAATACTAAAACTATAGAACTTTCTGAAGAAAAAAG 1959
                          ?              ivi           i    i iv        v -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA- 547

  chr1_167140698_   1960 TAGATGAAAATCTTTGTGACCTTGGATTACGCTAAGATTTGTTAGGTAGG 2009
                            i? v       i          i   v  v v i   v    i  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_167140698_   2010 AAACCAAAATCATGATCCATAAAACAGGCCCCCAAAAGT-GATAGATTGT 2058
                          v       v  ii v v i    v -------    i -    i    v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGA-------AAAAATAGATAAATTGG 640

  chr1_167140698_   2059 ACTTCATGAGAATTAAATATTTCTGCTCTTTGAAAGACACTGTTAAGAAC 2108
                                v i       v i  i  iv   ii  i      i i     v
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_167140698_   2109 ATGAAAAGACAAGCCACGGAATGGGAGAAAATATTTGCAAATCATACATC 2158
                         i           v    i                            i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_167140698_   2159 TAAAAAAGAATTAGTATCCAGTATCTATAAAGATCATGTAAAACTCGGTA 2208
                          i v  i i i v        v  v        v viv  v     ii  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_167140698_   2209 GTAAGAAAACAAACAACGTAATTTTAAAAATGAGGAAAG-ATTTGAACAG 2257
                         i   i  i     i   vi    ?-       i v    -       i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAG 839

  chr1_167140698_   2258 ACACTTCATCAAAGA---TATCTGTGTGGCAAATAAGAACACAAAAAGAT 2304
                            i   vi      ---   viivi    v      v   ii       
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_167140698_   2305 ACTCAATATCATTAGTCAT 2323
                         i     i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (125 / 88)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.70 (54 / 20)  


2842 27.82 0.99 1.53  chr1_167152796_167159829.rev     5631  6543 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167152796_   5631 TGGAAAAGCATTCCATGCTCATGGATAAGAAGAATCAGTTTCGTGAAAAT 5680
                               iii  i     i        vi     v i i v i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167152796_   5681 GGCCATACTGCAGCCCAATGTAATTGATAGATTCAATGCTATTCCCATGA 5730
                            v     v --  v   - i  iv i        i  v  i  i  v 
  L1M4_orf2#LINE/     51 GGCAATACTCC--CCAAAT-TGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_167152796_   5731 AGCTACCATTGACTTTCTTCACAGAATTAGAAAAAAACT-ACCTTAAATT 5779
                          iv v   vivi i  i  ii     v v  v  i--  - i i    v 
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAAT 145

  chr1_167152796_   5780 TCATATGGAACCAAAAAAGAGCTCATATAGCCAAGACAATCCTAAACAAA 5829
                                   viiv  ii  v iviv        i      i i  v  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_167152796_   5830 AAGAACAAAGCTGGAGGCATCACACCACCTGACTTCAAACTATACTAGAA 5879
                                   i      vv      iv  ii i      viv     v  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_167152796_   5880 GGCTACCGTAACCAAAACAGCATGGTACTGGTACTAAAACAGAGATATAG 5929
                         i     v    i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_167152796_   5930 ACCAGTGGAACAGAACAGAGGCCTCAGAAATAACACTACACATCTACAAC 5979
                          i  i     i    iv   ivii         vv i i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_167152796_   5980 CATCTGATCTTTGAAAAACCTGAACAAAG--CAAGCAATAGGGAAAGGAT 6027
                           vi    i  i  v  ivv  -- v   --  vv    i       i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTG--CCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_167152796_   6028 TCCCTATTTAATAAATGGTATTGGGAAAACTGGCTAGCCATATGCAGAAA 6077
                         vvi  v  i  i       ii     v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_167152796_   6078 ACTGAATCTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGAT 6127
                          v    vi         v   i     v                   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_167152796_   6128 GGATGAAATACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAA 6177
                             v ? v  i           v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_167152796_   6178 AACCTTGGCA-ACACCATTCAGGACAAAGGCATGGGCAAGGACTTCATGA 6226
                            v v  ?i- v i -   iv   vvv  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_167152796_   6227 CTAAAACACTTAAAGCAACGGCAACAAAAGCCAAAATTGACAAATGGGAT 6276
                         v  vi    iv      vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_167152796_   6277 CTAATTAAA-TTAAAGGGCTTCTGCACAGCAAAAAAAAAAAAACTGTCAT 6325
                         i v  i   -     ii-   i  ii vv    ii v -----  i   v
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA-----CTATCAA 686

  chr1_167152796_   6326 CAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATC 6375
                         v i      v  i     i                 v       vii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_167152796_   6376 CATCTGACAAAGGGCTAACGTCCAGAATCTACAAGCAACTTCAACAAATT 6425
                         i      i  i  i  viii        v  i  iv    iiv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_167152796_   6426 TACAAGAAAAAAGCAA----TCCCATGAAAAAATGTGGGAAGGATATGAA 6471
                         v i  v     ii   ----i  v  v?       v vi      v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_167152796_   6472 CAGAAACTTCTCAAAAGAAGACATTTATGCAGCCAACAAATATATGAATA 6521
                         i   v i     v        i  vi viii     i  ii i     v 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_167152796_   6522 AAAGCTCATCATCACTGGTCAT 6543
                         i v     v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (144 / 106)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


3235 26.54 0.66 0.66  chr1_167164185_167170582     4998  5905 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167164185_   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5047
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167164185_   5048 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5097
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167164185_   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_167164185_   5146 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5195
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_167164185_   5196 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_167164185_   5246 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5295
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_167164185_   5296 GATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 5343
                         i      i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_167164185_   5344 ATCTGATCTTTGACAAACCTGACAAAAACAGGAAATGGGGAAATGATTCC 5393
                          vi    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_167164185_   5394 CTATTTAATAAATGGTGCTGGGAAAACTAGCTAGCTACATGTAGGAAGTT 5443
                           v  i  i              v    i v  ? i     i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_167164185_   5444 GAAACTGGATCCCGTCCTTACACCTTATACAAAA-TTAATTCAAGATGGA 5492
                            ii    i   vv   i     v         -    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_167164185_   5493 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5542
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_167164185_   5543 CTAGGCATTACCATTCAGGACATAGGCATAGGCAAGGACTTCATGTCTAA 5592
                         v    ?i v viv   iv   v v  vv       v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_167164185_   5593 AACACCAAAAGCAATGGCAACAACAGCCAAAATTGACAAATGGGATCTAG 5642
                         i            vvi       v  vv     v  i    v   ii vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_167164185_   5643 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5692
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_167164185_   5693 AGGCAACCTACAGAACGGGAGAAAATATTTGCAA-TCAACTCATCTGACA 5741
                           i     i      i                  -   vv -      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATA 745

  chr1_167164185_   5742 AAGGGCTAATATCCAGAATCTACAAGGAACTCAAACAAATTTACAAGAAA 5791
                          i  i  vi          v  i  i      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_167164185_   5792 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGCATATGAACAGACACT 5841
                           i -    i     v  i?    i    ii   v  v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_167164185_   5842 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5891
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_167164185_   5892 TCATCACTGGCCAT 5905
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3291 26.00 1.11 0.66  chr1_167269732_167275924     4797  5700 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167269732_   4797 TGGAAAAACATTCCATGCTTATGGATAGGAAAGATCAATATTGTGAAAAT 4846
                               i i  i     i i      v    iiv i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167269732_   4847 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4896
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167269732_   4897 TACCA-TTGACTTTATTCCCAAAATTAGAAAAAACT-ACTTTAAATTTTA 4944
                          v   -i  v    v  v vi     i-- v  i  - iii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_167269732_   4945 TACGGAA---CAAAATACAGCCCGTATAGCCAAGGCAATCCTAACCAAAA 4991
                           i    ---   iiv  --  v v        ii     i i vv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_167269732_   4992 AGAACAAAGCTGGGGGCATCATGCTACCTGACTTCAAACTATGCTACAAG 5041
                                  i   i  vv   ii  v  ii i      viv i      i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_167269732_   5042 GCTACAGTAACCAAAACAGCATGTTACTGGCACCAAAACAGATATACAGA 5091
                                   i   i    ii  v        iv ii i   i   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_167269732_   5092 CCAATGGAACAGAACAGAAACCTCAGAAATAACACCACACATCTACAGCC 5141
                         i        i    iv  i vii         vv   i    i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_167269732_   5142 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCG 5191
                          vi    i  i     ivv  v   i v  vv            i  vvv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_167269732_   5192 CTATTTAACAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5241
                           v  i           i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_167269732_   5242 GAAACTGGACCCCTTGCTCACACCTTATACAAAAATTAACTCAAGATGGA 5291
                            ii         vv        v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_167269732_   5292 TTAAAGATTTAAATATAAGACCTAAAAGCATAAAAACCCTAGAAGAAAAT 5341
                          i ?   ii     i     v      vi      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_167269732_   5342 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTG 5390
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_167269732_   5391 AAACACCAAAAGCAGTGGCAACAAAAGCCAAAAAT-GACAAATGGGATCC 5439
                         vi            vvi          v-      -  i    v   iii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTT 644

  chr1_167269732_   5440 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5489
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_167269732_   5490 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 5539
                          v  i     i                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_167269732_   5540 AAAGGGCTAATATCCAGAATCTGCAAAGAACTTCAACAAATTTACAAGAA 5589
                           i  i  vi          v ii        iiv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_167269732_   5590 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATTTGGACAGACGAT 5639
                            i     i     v  i?    i    ii         i i    iv 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_167269732_   5640 TTTCAAAAGAAGACATTTATGCAGCCAACAAACATTTGAAAAAATGCTCA 5689
                          i  v        i  vi viii     i  i  iv      i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_167269732_   5690 ---TCACTTTTCAT 5700
                         ---   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (141 / 90)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3133 26.91 1.11 0.55  chr1_167309285_167316280.rev     5603  6505 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167309285_   5603 TGGAAAAACATTCCAGGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5652
                               i i  i   v i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167309285_   5653 GGCCATAATGCCCAAAGTAATTTATAGATTCA-TGTTATTCCCATCAAAC 5701
                            v   v v      v i  i  i       -i iv  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167309285_   5702 TACCATTCACTTTCTTCACAGAATTAGAAAAATCTACTTTAAATTTCATA 5751
                          v   viii i  i  ii     v v  v  iiiv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_167309285_   5752 TGGAAGCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGAA 5801
                              iiiv  ii  v  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_167309285_   5802 CAAAGCTGGAGGCATCACGCTACCTGACATCAAACTATACTGCAAGGCCA 5851
                              i      vv    i  v  ii iv     viv    i   i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_167309285_   5852 CAGTAACCAAAACAGCATGTTACTGGTACCAAAACAGATATATAGACCAA 5901
                               i   i    ii  v      i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_167309285_   5902 TGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCATCA 5951
                              i    iv   ivii         vv   i    i  iiii  viv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_167309285_   5952 GATCTTTGACAGATTTGACAAAAACAAGCAAGGGGGAAAGAAT--TCCTT 5999
                            i  i    iivv  v   i v  vv   v           --  i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_167309285_   6000 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGCTGAAAACTGA 6049
                         -- i  i              v      v  ?   i i  vi  i v   
  L1M4_orf2#LINE/    401 --TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_167309285_   6050 AATTGGACCCCTTCCTTACACCTTACACAAAAATTAACTCAAGGTGGATT 6099
                          i          v   i     v  i                ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_167309285_   6100 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 6149
                          ?    i           v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_167309285_   6150 AGA--TAATACCATTCACAACATAGGCATGGGCAAATACTTCATGACTAA 6197
                           i--   - i -   iii  v v  vv i     vvii   v iiv  v
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_167309285_   6198 AACACCAAAGGCAATGGCAACAAAAGCCAATATTGACAAATGGGATCTAA 6247
                         i        i   vvi          vv  v  v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_167309285_   6248 TTACACTAAAGAACTTTTGCACAGCAAAAGAAATGATCATCAGAGTGAAC 6297
                          i v v v  i        ii vv    i  v iv    vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_167309285_   6298 AGGCAACCTACAGAACGGGAGAAAATTTTTGCAA-TCAATCCATCTGACA 6346
                           i     i      i          v       -   - vi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGATA 745

  chr1_167309285_   6347 AAGGGCCAACATCCAGAATCTACCAGGAACTTCAACAAATTTACAAGAAA 6396
                          i  i ivii         v  iv i     iiv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_167309285_   6397 AAAACAA----CCCCATCAAAAAGCGGGCAAAGGATATGAACAGACACTT 6442
                           i    ----   v  i?    ii           v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_167309285_   6443 CTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGTTCAT 6492
                            v        i  vi vi       i  i  i       i v i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_167309285_   6493 CATCACTGGTCAT 6505
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2631 25.36 4.73 0.97  chr1_167498640_167500454      500  1323 (492)    L1M4_orf2#LINE/L1       54   908 (0)  

  chr1_167498640_    500 AATTTTCTGCACATTGATCAAGAGATTTAGTGCAATTTCAGTAAAATTCC 549
                            vi  iv  v       v v     i ii     ii vi v   v   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_167498640_    550 CAAGAGAATTTTTCTTGTAGAAATGGACAGATTTATTCTAAAATTTATAT 599
                           ivv --ii   i   i      v    iii v  i        i    
  L1M4_orf2#LINE/    104 CAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_167498640_    600 GAAAAT-CATAAGGATCTAGAATAGCTAACATAATTTTGTAAAAAGAGCT 648
                          i    -  - i   i i        i  v i   i   -       ivv
  L1M4_orf2#LINE/    152 GGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTG-AAAAAGAAGA 199

  chr1_167498640_    649 ATAAAGTTGGATGA-TAACACTAGCCCCAGTTT-AAGACTTAATATATGG 696
                          i         v  - v     --i    i   -  i     v  i vi 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACT--TCCCAATTTCAAAACTTACTACAAAG 247

  chr1_167498640_    697 CT---GTGATC-------T----TATTTACAGAGTGATAGACTCATAGAT 732
                           ---  i   ------- ----  i vi  v iv       vi      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_167498640_    733 TAATGAAACAGAATAGAGAGTACAGAAGGGGACCCACCAAATTCTGACCA 782
                         i    i  i     v      v     ivii     ivv v  v  ii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_167498640_    783 ATTGATCTTTGACAAAGGTAAAATGGTAATTCAATAAAGGAAAGAACAGT 832
                               i  i     i   ivv v iiv       ii-        i   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGT 396

  chr1_167498640_    833 CTTTTTAATAAAGAGT--TA----AATTGTCCATTAATATGCAAAA--AT 874
                              i  i   vi  -- i----  i  vvi ?iv i        --  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_167498640_    875 GAA------CTTTAACCTCACACCTGTTACAAAAATGAACCCAAATTGGA 918
                            ------ iiiv          vvv         v   i    v    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_167498640_    919 TCATAGATCTAAATGGAAAATGGAAAATTATAAAGCCTTCAGAAGAAAAC 968
                            ?   i       v  i vvv    i      i ii i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_167498640_    969 ATGGAAGAAAATCATTGTAAACTGGGATTAGGCAAAGAATTCTTAGACAT 1018
                           i i? v     v i  i v  v  i        v iv        i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_167498640_   1019 TATGCCAAATGCATGATCCATTAAATATAAAAATGGATAAACTGGACTTC 1068
                         v ii     v   ii v v iv   v -      i      i        
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTC 645

  chr1_167498640_   1069 ATCCGACCTTAAAACGTTTGTTCTGCAAAAGAT-TTGTTAAGACAATGTA 1117
                            vi vi v     v     v  v    i  i-i i i    v i  v 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_167498640_   1118 AATACAAACTACAGACTGGAA-AAAATATATGCAGATTACATATTTGACA 1166
                           v    v i     v   i -       v    i  i i    i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_167498640_   1167 AAGGAATTGAATCCAGAATATATACAGAGCACTCAAAACTCAACCACCAG 1216
                          i   v   v              v   i v  i v       iv iv i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_167498640_   1217 AACACAA----CCCAATTTAAAAATGGGCAAAAGGTTGGAATAGATGCTT 1262
                           v    ----       ?             i i  v       iii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_167498640_   1263 CACCAAAGAGGATATATTGATGGCAAA-AAACACATTAAAA-ATGTTCAA 1310
                          v       i      ivi     v  -  i     v    -   i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_167498640_   1311 CATCCTGAACAAT 1323
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (119 / 86)
Gap_init rate = 0.02 (21 / 855), avg. gap size = 2.24 (47 / 21)  


3167 27.28 0.44 0.55  chr1_167511054_167517472     5018  5926 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167511054_   5018 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATAAATATCATGAAAAT 5067
                              ii i  i     i        v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167511054_   5068 GGCCATACAGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAAC 5117
                            v    vv     iv i  i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167511054_   5118 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAGGTCCA 5165
                          v    ivi i  i  ii     -   -- v  i  - iii i ii i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_167511054_   5166 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGTAAAAAG 5215
                                viiv  ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_167511054_   5216 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5265
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_167511054_   5266 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGATC 5315
                                 i   i    ii         i iv ii i   i         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_167511054_   5316 AATGGAACAGAATACAGGCCTCAGAAATAACAGCACACATCTACAACCAT 5365
                                i     vv  ivii         vvv  i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_167511054_   5366 CTGATCTTTGAAAAATTTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5415
                         i    i  i  v  ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_167511054_   5416 ATTTAATAAATGGTGCTGAGAAAAACTGGCTAGCCATATGTAGAAAGCTG 5465
                         v  i  i           i  v  -    v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATG 447

  chr1_167511054_   5466 GAACTAGATCCCTTCCTTACTCCTTATACAAAAATTAATTCAAGATGGAT 5515
                         i ii i  i    v   i  v  v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_167511054_   5516 TAAAGACTTAAATATTAGACCTAAATCCATAAAAACTCT-AGAAGAAAAC 5564
                         i ?    i     i v   v     v i      -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr1_167511054_   5565 CTAGGCA-ATACCATTCAGGACATAGACATGGGCAAAGACTTCATGACTA 5613
                         v    ?i- v i -   iv   v v ivv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_167511054_   5614 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 5663
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_167511054_   5664 ATTTAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5713
                           iv  v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_167511054_   5714 CAGGCAACCTGCAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5763
                         v  i     ii                v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_167511054_   5764 AAGGGCTAATATCCAGAGTCTACAAAGAACTCAAACAAATTTACAAGAAA 5813
                          i  i  vi        i v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_167511054_   5814 TAAACAAACAACCCCATCAAAAAATGGACAAAGGATACAAACAGACACTT 5863
                         v i     i     v  i?        i        vii  i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_167511054_   5864 CTCAAGAGAAGACATTTATGCAGCCAACGGACACATGAAAAAATGCTCAT 5913
                            v i      i  vi viii     iiii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_167511054_   5914 CATCACTGGCCAT 5926
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (149 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


2394 24.43 1.68 0.92  chr1_167569908_167571554      500  1154 (493)    L1M4_orf2#LINE/L1      249   908 (0)  

  chr1_167569908_    500 TACAATAACCAAAACAGCATGGTACTGGTACAAAAACTGGCATATAGACC 549
                             i   i   i    ii         i i  ii iv i        i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_167569908_    550 AATGGAACAGAATAGAGAACTCAGAAATAAAACCATATATCTACAATCAC 599
                                i     v    iii          v     i  i  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_167569908_    600 TTGATCTTTGACAAACCTGAAAAAAACAAGCAACGGGGAAAGGACTTCCT 649
                              i  i     ivv  vv  i v  vv   i        i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_167569908_    650 ATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGACTGA 699
                         v  i  i              i      v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_167569908_    700 AACTGGATCTCTTCCTTACATCTTATTCAAAAATTAACTCAAGATAGATT 749
                          ii    i i  v   i   i v   v               i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_167569908_    750 AAAGACTTAAATGTAAAACCCAAAGCTATAAAAACCCTAGAA-AAAGTTT 798
                          ?    i         i v i   i        vi i     -   iiv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_167569908_    799 AGGCAGTA--CCATTCAGGGAATAGGCATGGGCAAAGATTTTATGAGGAA 846
                            ?-   --i -   iv ivv v  vv i     v i   iv i--  v
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA--GAT 594

  chr1_167569908_    847 AT--CACCGAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCT 894
                           --    i      vvv          v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_167569908_    895 ------AATTAAAGAGCTTCTGCACAGCAAACGAAACTATCATCAGTGTG 938
                         ------       i -   i  ii vv    v  v       vv iv   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_167569908_    939 AACAGACTACCTACAGAATGGAAGAAAATTTTTGCAATCTATCCATCTGA 988
                           v    v   i         i       v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_167569908_    989 CAAAGGTCTAATATCTAGAATCTACAAGGAACTTAAACAAATTTACAAGA 1038
                         i  i  v  vi    i     v  i  i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_167569908_   1039 AATAAAACAAACAACCCCATTAAAAAGTGGACAAAGGATATGAACAGACA 1088
                           -  i     i     v   ?    i   i        v    i     
  L1M4_orf2#LINE/    794 AA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_167569908_   1089 CTTCTCAAAAAAAGACATACACGTGGCCAACAAACATATGAAAATAAGCT 1138
                         i     v   i    i     vi       i  i  i       v v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_167569908_   1139 CAACATCACTGATTAT 1154
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (93 / 63)
Gap_init rate = 0.01 (9 / 660), avg. gap size = 1.89 (17 / 9)  


2413 24.25 3.01 1.72  chr1_167655077_167658943.rev      503  1199 (2668)    L1M4_orf2#LINE/L1      164   869 (39)  

  chr1_167655077_    503 GACCTCCAATAGCCAAAACAATCTTAAGAAAGAA---CA----TGGAGGT 545
                             ivv                  i i      ---  ----      v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_167655077_    546 CTTACAGTTAT-GATTTCAAGCTATAATACAAA-----AGTAATTAAAAT 589
                           i   v  vi-i       iviv  v      -----      i  i i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_167655077_    590 TGTAGGG-ACTGCTATAAAAACAGACTCATAGACAAATTGAATGAAATAA 638
                         v  iv  -    vi    ii i    vi     iv   v    ii   vi
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_167655077_    639 AAAGCCCAGAAATAAATCTATTAATATATGGTCAAGTAATCTTTGATAAG 688
                          i  i           i i  vv  v         v i  i  i  i   
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_167655077_    689 GGAGACAAGA--ATTCACAATGGGCAAAGGACAGTCTCTTCAATAAATGA 736
                           v v     --     --     v    i i     i     i     i
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCA--ATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_167655077_    737 TGTTGGGAAAACTGAATGTCCATAAGCAAATAAATGAAATGGGACCCTTA 786
                           i     v     i  i?   i v     vi      i v      i  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_167655077_    787 TCTTTTACCATATACAAAAGTTGATTTGAAATGGGTTAAAGAC--AAATG 834
                         i  ivi             i  i i ii      i i ?    --     
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_167655077_    835 TAAAGAAGTGAAACTGTAAAACACCTAGAAGAAAACATAGGGAAAGAGCT 884
                            -  iv i     i      v i                ?iv i v  
  L1M4_orf2#LINE/    512 TAA-GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_167655077_    885 TATTTACATTAGTTTCGGTGAAGATTTTTTGGATATGACGTAAAAAGCAC 934
                          vv v  v  i v  v  ii v i   i  i        iiv        
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_167655077_    935 AGGCAACAAAAGCAAAATTAAACAAGTGGGACTACATCAAACTAACAAGC 984
                          i          v    v  i i  i v     v       v v v  i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_167655077_    985 TTCTGCACAGCAAAGAGAACAATTAATAAAATTAGAAAGACAACCTATGG 1034
                           i  ii vv     iiv  v  i  v   i v -          i ii 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA-AAAGACAACCCACAG 709

  chr1_167655077_   1035 AATGGGATAAAATATTTGTAAAACATAAATCAGATAAGGGGTTAATATCC 1084
                                v          i   v    v   v        ii vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_167655077_   1085 AAAATGTATAAGAAACTC--ATGATTCAATGGCAAAAAAAAAAAAAAGCA 1132
                          i   i     ii     -- ii i     --------  v     ii  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAAT--------AATAAAAAGACA 801

  chr1_167655077_   1133 GATAATCCAATT-ACAAATGGGCAAAAGACCTGAATAAAACTTTTTCCAA 1181
                         i    i      - v           i  ii      i vv   i     
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_167655077_   1182 AAAATACATACAAAAAGC 1199
                          i  v i       vi  
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGC 869

Transitions / transversions = 1.63 (103 / 63)
Gap_init rate = 0.02 (13 / 706), avg. gap size = 2.54 (33 / 13)  

3460 25.53 0.67 0.00  chr1_167655077_167658943.rev     1683  2583 (1284)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_167655077_   1683 GGAAACATATCCCATGCTCATGGATGGGTAGAATCAACATTGTGAA-ATG 1731
                              v          i        v  v   v i  i     v  -   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_167655077_   1732 ACCATACTGCCAAAAGCAATCTACAAATTCAACGCAATCCCCATAAAAAT 1781
                         i v     v  v   vii       i               i  v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_167655077_   1782 ACCACCAACATTCTTCATAGAATTAGAAAAAAAAATTCTAAAATTCATAT 1831
                         v   v vi v  i  iii    v v  v  ivvi  i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_167655077_   1832 GGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGGCTAAGCAAAAAGAAC 1881
                             viiv  ii  v  viv         i   vvi i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_167655077_   1882 AAATCTGGAGGCATCACATTATCTGATTTCAAGCTGTACTATAAGGCCAT 1931
                            vi      vv     i vi ii       iviv     i  i  i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_167655077_   1932 AGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCAAT 1981
                            v i   i    ii         i    ii    i  i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_167655077_   1982 GGAACAGAATAGAGAATCCAGAAATAAACCCAAATGCTTACAGCCAACTG 2031
                             i     v    i                v iii   ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_167655077_   2032 ATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTTTT 2081
                           i  i     i vviv   i v   vv i         i i vi     
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_167655077_   2082 CAACAAATGGTGCTGGGATAATTGGCTAGCCACATGCAGGAGAATGAAAC 2131
                                           i  i   v  ?         ii        ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_167655077_   2132 TGGATCCTCATCTCTTACCTTATACAAAAATCAACACAAGATGGATTAAG 2181
                             i  ii i   vi   v           i   v   i      i ?i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_167655077_   2182 GACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATTGG 2231
                            i     v     v  i           v ii       v     v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_167655077_   2232 AAAAACCCTTCTAGACGTTGGCTTAGGCAAAAATTTCATGACCAAGAACC 2281
                         ?iv  vi    vv   v    v        vii    v iivi v  vv 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_167655077_   2282 CAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATTAAA 2331
                                 v v    i    iv   i   i   iv v      v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_167655077_   2332 CTAAAGAGCTTTTGTACGGCAAAAGGAACAGTCAGCAGAGTAAACAGACA 2381
                         v v  i i       i vv    i iv  vi   iv i   i  v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_167655077_   2382 ACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGAAC 2431
                                  i           v  ii   vii   i      i  i i  
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_167655077_   2432 TAATATGCAGAATCTACAACAAATTCAAACAAATCAGTAAGAAAAAAACA 2481
                          vi   v      v  i  vi  i  vv    v   i   v     i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_167655077_   2482 A----TCTTATCAAAAAGTGGGCCAAG-ACATGAGTAGACAATTCTCAAA 2526
                          ----i iv  i?    i     v   - iv   i      v     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_167655077_   2527 AGAAGATATACAAATGGCCAACAAACATATGAAAAAATGTTTAACATCAC 2576
                                              i  i  i       i   i i       ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_167655077_   2577 TAATGAT 2583
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.43 (133 / 93)
Gap_init rate = 0.00 (3 / 907), avg. gap size = 2.00 (6 / 3)  

 203 20.69 1.72 0.00  chr1_167655077_167658943.rev     3319  3376 (491)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_167655077_   3319 AAAAAAGGCATATAAACGGTGAATAGGAACGTGAAAA-ATGCTCAATATT 3367
                            i   ii   i   i  iv    i v  i      -        i  i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_167655077_   3368 ATTAATATA 3376
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 5.00 (10 / 2)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1)  


2893 25.80 3.86 0.68  chr1_167728104_167733304.rev     3831  4710 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167728104_   3831 TGGAAAGACATTCCATCCTCATGGATAGGAAGAATCAATATTGTGAAAAT 3880
                                 i  i    vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167728104_   3881 GGCCATACTGCCCAAGTTAATTTATAGATTCAGTACTATTCCCATCAAAC 3930
                            v     v     i  i  i  i       iii v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167728104_   3931 TACCATTGACATTCTTCACAGAA-TTAGGAAAAACT-ATTTTGGATTTCA 3978
                          v   vivi v  i  ii     -  --  v  i  -  ii ii v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr1_167728104_   3979 CATGTAA-TGAAAGAAGACCCCATATAGCCAAGAGAATCCTAAGCAGAAA 4027
                         i   v  -  v   i-     viv        i v    i i iv ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_167728104_   4028 GAACAAAGCTGGAGGCATTGTGGTGCCTGGCTTCAAACTATACCACAAGG 4077
                                 i      vv iiiiv v  iiii      viv   i    i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_167728104_   4078 CTACAGTAATCAAAACAACATGGTACTGGTACCAAAGCAGATACATAGAC 4127
                                      i   iii         i iv iiii   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_167728104_   4128 AAATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAATCA 4177
                         v       i    iv    vii         vv   i    i  iii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_167728104_   4178 TCTGATTTTCGACAAACCTGCTAAAAACAAGCAATGGGGAAAGGATCTCC 4227
                         vi             ivv   i  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_167728104_   4228 TATTCAGTAAATGGTGCTGCGAAAACTGGCTAGCCATATGCAGGAAACTG 4277
                          v    ii           v  v      v  ?   i     ii i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_167728104_   4278 AAACTAGACGCTTTCCTTACACCTTATACAAAAATTAAC--AA---GGCT 4322
                           ii i   v i v   i     v               --  ---  v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_167728104_   4323 TAAAGACTTAA-TGTAAAACCCCAAACCCTCAAAACCCT-AGAAGAAAAC 4370
                         i ?    i   -     i v iv    iv -     i  -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAAC 546

  chr1_167728104_   4371 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTCATGACAA 4419
                         v    ?i- v i -   iv   v v  vv i     v i    v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_167728104_   4420 AAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATAGGGTCTA 4469
                         vi            vvv          vv     v  i    v  iii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_167728104_   4470 ATTAAA-TTAAACAGCTTCTGCACAGCAAAAGACA-----AAGAC--TGA 4511
                           i   -     - i   i  ii vv    i    -----    v--   
  L1M4_orf2#LINE/    646 ATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_167728104_   4512 ACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACCCATCTGAC 4561
                          v  i     i                vv       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_167728104_   4562 AAAGGTCTAATATCCAGAATCTACAAG---------TAACTTAACAACAA 4602
                           i  v  vi          v  i  i---------i    i  i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_167728104_   4603 AAA-----ACAACCCCCTCAAAAAGTGGGCAAAGGATATGAATAGACACT 4647
                            ----- i     vv i?    i            v          i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_167728104_   4648 TCTGAAAAGAAGACATTTACATG-CCAACAAGCATATGAAAAAAAGCTCA 4696
                            vv        i  vi v   -    i     i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_167728104_   4697 ACATCACTGATCAT 4710
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (132 / 91)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.11 (40 / 19)  


3505 24.28 1.33 0.67  chr1_167743036_167747609.rev     3182  4083 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167743036_   3182 TGAAAAAAAATTCCAAGTTCATGGATTGGAAGAATCAATTTTGTTAAAAT 3231
                           i   i v  i   v                 v i   v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167743036_   3232 GTCCATACTACACAAAGCAATCTACAGATTAAATACAATCCCTATCAAAA 3281
                          v v     v v    vii           v  ii               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167743036_   3282 TAAATACCAATGACATTCTTTATATAAATAGAAAATACT-ATTCTAAAAT 3330
                          ----v   iivi v  i   ii v    v  v  -i  -  i       
  L1M4_orf2#LINE/    101 T----CCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAAT 145

  chr1_167743036_   3331 GTATATGAAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAACCAA 3380
                         vi     i  vii   ii                 i v   i i  vv i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_167743036_   3381 AAAAACAAAACTGGAGGAATCACATTACCTGATTTCAAATTATACTACAG 3430
                           i      ii       v     i v  ii        viv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_167743036_   3431 AGCTATAATAACCAAAACAACATGGTACCGGCATAAAAACAGACACACAG 3480
                              i i   i   i   iii      i       ii i     i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_167743036_   3481 ACCAATGGAACAGAATAGAGAACCCAGAAAGAAATCCACACACCCACAGT 3530
                          i        i     v    ii       v   i   i   iii ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_167743036_   3531 AAACTCATTTTTGACAAAGATGACAAGAACAT----------AAAAGCAG 3570
                         v  i v     i     i i  v     v   ----------  i ii  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_167743036_   3571 TCTCTTCAATAAATGGTGCTGGAAAAACTGGATATCCATGTGCAGGAGAA 3620
                            i     i            i v         ?   ii    ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_167743036_   3621 TGAATCTAGACCCCCATCTCTTGTCATATACAAGAATCAAGCCAAAATGG 3670
                             vi i      i i   viii         i   i  vi        
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_167743036_   3671 ATTAAAGGCTTAAATCTAGGACCTCAAAATATACACCTATTACAAGAAAA 3720
                           i ?  i i     v  i  v  v   v    v v  v   v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_167743036_   3721 CATTGGGGAAAACCTCCAGGACATTGGTCTGGGCAAAGATTTCTTGACCA 3770
                            v  ? v   i  i iv   v    vi i     v i      iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_167743036_   3771 ATACCTCACAAGCACAAACAACCAAAGCAAAAATGGACAAATGAAATCAC 3820
                         vv  vi  v        i    v    v      i  i    vii iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_167743036_   3821 CTC-AAGTTAAAAAGATCTGGACAGCAAAGGAAGCAATCAACAAAGTGAA 3869
                         v  -  i       vv i  vi vv       vi v     v        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_167743036_   3870 GAGACAACCCACACAATGGGAGAAAATGTTTGCAAACTACTTATCTGACA 3919
                         i            v             i        ii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_167743036_   3920 AGAGGTTAATAACCAGAATATATAAGGAGTTCAAACAACTCTATAGGAAA 3969
                           i ii vi  v             i  ii  vv       v   iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_167743036_   3970 AACATCTAATAATCAGATCAAAAGATGAGCAAAAGATTTGAATAGACATT 4019
                           v - v     i vi  i?   i   i     i                
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_167743036_   4020 TCTAAAAAGAAGACATACAAATGGCAAACAGGTATATGAAAAGATGTTCA 4069
                            vv        i           v  i i i i           i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_167743036_   4070 ACATCACTGATCAT 4083
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (134 / 81)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 3.00 (18 / 6)  


1724 25.86 6.16 0.68  chr1_167754488_167756063      500  1083 (493)    L1M4_orf2#LINE/L1      293   908 (0)  

  chr1_167754488_    500 TAGACCAATGAAGCAGAATAGAGAACCCAGAAATAAAGTAAAA----TAC 545
                             i     i ii     v    ii           viv v ----  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_167754488_    546 AGCCAACTGATGTTCGACAAAGCAAACAAAAATATAAAGTGGGGATATGA 595
                         i i   i    v        i vviv   i vi  vv i      v vi 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_167754488_    596 CACCCTATTCAACAAATTGTGCTGGGATAATTGGCAAGCCACATGTAGAA 645
                         i vi  v          v         i  i   vv ?       i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_167754488_    646 GAATGAAAAGTGGATTCTCATCTCTCACCTTATACAAAAATTAACTCAAG 695
                                i-v    ii ii i   v    v                   i
  L1M4_orf2#LINE/    443 GAATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_167754488_    696 ATGGATCAGAGACTTAACTCTAAGACCTGAAACCATAAAAATTCCAGAAA 745
                                 ?    i   v v     v  i    i      v iii    i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_167754488_    746 AATAGCATCAGAA-AAACCTTTCTAGGCATTGGCTTAGGCAAAGACTTCA 794
                           - i   vi ?i-   i   iv - i v    v        v ii   v
  L1M4_orf2#LINE/    542 AA-AACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_167754488_    795 TGACCAAGAACCCAAAAGCAAATGCAACAAAATTAAGA-TAAACAGATGG 843
                          iivi v  vv         v v         vv  i -  i i i  v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_167754488_    844 GACTT------AACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCA 887
                              ------  i      -   i  ii vv    i  v iv    iv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_167754488_    888 GAGTAAAGCAACAACC-ACAGAGTGGGAGAAAATCTTCACAAACTATGCA 936
                         i   i  ivi      -     i           v  ii    ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_167754488_    937 TCCAA---------------CATAATCTACAAGGAACTC----AAATCAG 967
                           ii ---------------  v   v  i  i      ----  v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_167754488_    968 CAAGAAAGAAACAA----TCCTATCAAAAAGTGGGCTAAGGACATGAATA 1013
                         i  v   i i    ----i  v  i?    i     v     iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_167754488_   1014 GATAATTCTCAAAAGAAAATATACAAATGGCCAACAAACCTATGAAAATA 1063
                           i v     v      i                i  i vi       v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_167754488_   1064 TGCTCCACACCACTAATTAT 1083
                              v   i  ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (88 / 59)
Gap_init rate = 0.02 (12 / 616), avg. gap size = 3.33 (40 / 12)  


2619 25.05 2.53 7.05  chr1_167758294_167762415      867  1816 (2306)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_167758294_    867 GGAAAAACATTCCATCCTCATGGATAAGAAGAATCAATATCGTGAAAATG 916
                              i i  i    vi        vi     v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_167758294_    917 GCCATACTGCCCAAAGTAATTTATAGATTCAATGTTATTCCCATCATACT 966
                           v     v      v i  i  i        i iv  i  i    v v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_167758294_    967 ACTATTGACATTCTTCATA-AAATTAGAAAAAAAAACTAGTTTCAT--TT 1013
                         v i vivi v  i  iii -     i----- v  i  ii iii v--  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG-----ACAAGCTGATCCTAAAATT 146

  chr1_167758294_   1014 CATATATGATCAAAAAAGATCCCATATGGCCAAGACAATCCTAAGCAGGA 1063
                              ivi viiv  ii  i  viv  i     i      i i iv i  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_167758294_   1064 AGAACAAAGCTGGAGGCATCATGTTACCTGACTTTA-----TACTACAAG 1108
                                  i      vv   iii v  ii i  i -----        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_167758294_   1109 GCTACAGTAACCACAACAACATGGTACTGGTACAAAAACAGACATATAGA 1158
                                   i  vi   iii         i i  ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_167758294_   1159 CCAATGGAACAGAAAAGAGACCTCAGAAATAACACTACACATCTACAACC 1208
                         i        i    vv    vii         vv i i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_167758294_   1209 ATCTGACCTTCGACAAACCTGACGAAAACAAGCAATGGGGAAAGGATTTC 1258
                          vi   ii        ivv  v i i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_167758294_   1259 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACT 1308
                           v  i  i              v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_167758294_   1309 GAAACTGGACCCTTTCCTTACACCTTATACAAAAATTAACTCAACATGGC 1358
                            ii       i v   i     v                   v    v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_167758294_   1359 TTAAAGACTTAAATGTAA-ACCCCAAACCACAAAAACCCTAGAAGAAAAC 1407
                          i ?    i         - v iv    i i    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_167758294_   1408 CTAGGCA-ATACCATTCAGGGCATATGCATGGGCAAAGACTTC------A 1450
                         v    ?i- v i -   iv i v vv vv i     v ii   ------ 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_167758294_   1451 TGACAAAAATGCCAAAAGCAATCA--CAACAAAAGCCAAAATTGACAAAT 1498
                              ------         --  --         vv     v  i    
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_167758294_   1499 GGGATCT------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAT 1542
                         v   ii ------       i -   i  ii vv    i  v       v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_167758294_   1543 TAGGGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACC 1592
                         v ii     v  i     i                 v      ivii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_167758294_   1593 CATCTGAGAAAGGTCTAATATCCAGAATCGACAAGAAACTTAAATAAATT 1642
                         i      v  i  v  vi          vv i  ii    ivv i  v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_167758294_   1643 TACAAGAAAAAAACAAGTATCAATAGCTGAATCAACCAAGTGGAAGAAAG 1692
                         v i  v     i    ------   i --------    v ?--------
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAA------ATAAC--------CCAATTW-------- 814

  chr1_167758294_   1693 AATATCAGAGTCTGAAGTGGGCAAAGTAACAAAAGTGGGCAAAGGATATG 1742
                         ------------------------------    i            v  
  L1M4_orf2#LINE/    815 ------------------------------AAAAATGGGCAAAGGATTTG 834

  chr1_167758294_   1743 AACAGACACTTCTCAAAAGAAGACTTTTACATGGCCAACAAACTTATGAA 1792
                           i     i     v        iv vi v        i  i vi     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_167758294_   1793 AAAAAGTGCAACATCACTGATTAG 1816
                           i v iv        ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 5.69 (91 / 16)  

1490 28.89 10.53 3.55  chr1_167758294_167762415     2805  3621 (501)    L1M4_orf2#LINE/L1        7   880 (28)  

  chr1_167758294_   2805 GATATATTATGCTCATTGATTGAAAGATTAAATATTATGATGATGTCAGT 2854
                              vii   i    v     i    i v      i v v    v  i 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_167758294_   2855 TCTCCCCAAATTGATCTGTATAGATTCAATGTATTCCCAAACAATATCTC 2904
                         v                -- i        i i v    v v   v   i 
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCT--ACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_167758294_   2905 A-CTGGGTATTTTGGGTGTGTGTATGAAATGTGACAAGCTGATTATAAAC 2953
                          -   vv -    -------  i -     -            iv    v
  L1M4_orf2#LINE/    105 AGCTGCCT-TTTT-------TGCA-GAAAT-TGACAAGCTGATCCTAAAA 144

  chr1_167758294_   2954 TTTATATTAAAACTTAAGTGTTCAAGAATAGCCAAGATAATTT----AAA 2999
                           i    vi   ivi   v vi v           i i   i ----   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_167758294_   3000 GAGGAACTAGAGTTGAAGGACTTATACCATGGGATATCAAGATGCATTAC 3049
                           i    - i     i      i i  ivivvi  v    i ivi i   
  L1M4_orf2#LINE/    195 GAAGAAC-AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_167758294_   3050 A------CA----TTAAGGTCATGTCGTAGTGACACAATGATAGACA--- 3086
                          ------  ---- i   iivi   v   v  i  i  v        ---
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_167758294_   3087 ---------GAATAGAAT-------CAAGACATTGACCACACACAATTTA 3120
                         ---------         ------- v   v  vi   -  i   -    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC-CATACA-TTTA 341

  chr1_167758294_   3121 CGTCTAGGTGAC-----AC-----TGCCGAA------CAGTAAGGTAAGA 3154
                         i vii iv   i-----  -----    i i------  i ii  v    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_167758294_   3155 ACGAT-TTTTCTCTTAACGGTGCAGTATCAACTATACAGGTATAT----A 3199
                          iii -     vviv  i     v viv     iv i ?vi i  ---- 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_167758294_   3200 AAAAT--ATCTTGACCCCAACTTCATGCTGTATA---------ACTCCAG 3238
                          i   -- vi v      v  i   ii ii    ---------    v i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_167758294_   3239 ATGGATGGTATATATAAGCATAAAAGGTAAAATAGTAAAGCTTCCAGAAG 3288
                               vi? v iv   iii   i  v     ivi    i  iii     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_167758294_   3289 TAAATATAGGAGAATATCTTTATGGC-TTAAGACAAGCAAACATTTCCTG 3337
                         v   i     ? v v     ii  i -  ii vi i    vvi    i i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_167758294_   3338 AACAGGACCTCAAAATTAACTGACCATAAATGTAAAGAT-GATGAGTTCA 3386
                         i i v   vi     vi - vii v i   v v   i  -   i i  vi
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_167758294_   3387 ACTACATTGAAATTAGGGG--TTTGTGTTAATTAAAAAACA-----AATG 3429
                            v   ii      iiii--      i -- i   ii   -----  - 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTATCAA-G 687

  chr1_167758294_   3430 CAAATGGAAAAATTTAGCCATGAGATAAGAGAAGATATT-GTAAG--ATA 3476
                         v  i  i   i iv- v   iiii  ii     i     - i  i--   
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACA-ACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_167758294_   3477 TGCACCATTTTA-AACAGATTAGTACTTAGAACTT-TAAA--ACGTCTAC 3522
                          -----  i v -  vi  i v   iii    iv -    --  vii   
  L1M4_orf2#LINE/    737 T-----ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_167758294_   3523 AAGTAACTAAGAAAAAGA----TAACTCAATATATACACCGGCAAGAGAC 3568
                           v v v   v       ----    i    v? v v iv     ii  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_167758294_   3569 TTATCTGAATAAGCATTTCACAAAAGAAGACATCCAAATGGCCAGTAAAT 3618
                           ----     ii      v v        i  v          i   ii
  L1M4_orf2#LINE/    832 TT----GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_167758294_   3619 ACA 3621
                            
  L1M4_orf2#LINE/    878 ACA 880

Transitions / transversions = 1.70 (146 / 86)
Gap_init rate = 0.04 (37 / 874), avg. gap size = 3.11 (115 / 37)  


2835 25.40 5.66 0.81  chr1_167794514_167796471.rev      602  1467 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167794514_    602 TGGTAAAACATCTCATGCTCATGGATTGGAAGGGCCAATATCATTAAAAT 651
                            v  i i   i    i              ivii     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167794514_    652 AACCATA-TGCCCAAA---------AGACTTAATGCAATTTCTAACAAAA 691
                         ii v   - v      ---------   i i  i     ii   v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167794514_    692 TATCAA-TGCCATTTTTTACAGAATTAGAACAA-----TTCTAAAAATTC 735
                          vi  i-    -      i     v v  -   ----- i      -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAA-TTC 147

  chr1_167794514_    736 ATATGGAAC--CAAAAAAGCCCAAATAACCTCAGCAATTCTAAGCAAAAA 783
                                 v--   iii v  vi    i  vv i    ii i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_167794514_    784 GAACAAAACTGGAGGCATCATATTACCTGACTTCAAATTATACTACAAGG 833
                                ii      vv   i i v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_167794514_    834 CTATAGTAATTAAAATAGCATGGTACTGGTATAAACATAGACACATAGAT 883
                            i      i  i i  ii         i    iv       i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_167794514_    884 CAGTGGAACAGAATAGAGAAGTCAGAAATAAAGCCTCATCCCTATAGCCA 933
                           i     i     v    ivi          v  vi ivii   i i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_167794514_    934 ACTGATCTTCAGCAAAGTTGACAATAGCATATGCTGGGGAAAGGACACCC 983
                          i    i   ii   i v  v   v v   viiv         i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_167794514_    984 TATTCAGTACATTGTGCTTGGAAAATTAGATAGCCATACGCA---GAATG 1030
                          v    ii v  v     v   v  i i    ?   i i   ---     
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_167794514_   1031 AAAGTGGACCCCTATCTCTCACCATATACAAAAATGAACTCAAGAGAGAT 1080
                           iv          i   v                v       i vi   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_167794514_   1081 TAAAGACTTAAATGTAAGATCTGAAACTATAAAAATTCTAGAAAAAAA-- 1128
                         i ?    i           v  i           v ii     i    --
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_167794514_   1129 TAGGTAAAACTCTT--TTACCT-AGGCTATGACTAAGAATTTATGACTAA 1175
                             ?iv  v    -- v    -i  i  - i v v iv  iv iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATAT 596

  chr1_167794514_   1176 GGCCTCAAAAGCAAATGTAATAAAA------ATAGACAA--------TC- 1210
                          i vi        v v i  i    ------     i  --------  -
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_167794514_   1211 -------TAAAAATCTTTTTCGCATAAAGAGAAATAATTAACAGAGTGAA 1253
                         -------      -     vi  v v  ii  v iv  i  v i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_167794514_   1254 CAGACTACCTTCAGAATGGGAGACAATATTTGCAAGCTATGCATTCAACA 1303
                         v    v   iv            v           iii  ii  iii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_167794514_   1304 AAAGACAAATATC-AGAATTTATAAGGAACTCAAGCAACTCAATTTTAAA 1352
                          ii   vvi    -     v     i      vvi         vv    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_167794514_   1353 GAAGCACAGATAACACCATTACAAAGGGGAAAAAGGAGATAAATAAGCAT 1402
                         -   -   i     v v   ?v   iv  iv      vv i    ii   
  L1M4_orf2#LINE/    796 -AAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_167794514_   1403 TTTTCAAAAAAAGACATACCAATGGCCAATAAACATATGGGAAAATGCTT 1452
                           i  v   i    i    v            i  i   ii  i     i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_167794514_   1453 AACATCACGAATTAC 1467
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (135 / 81)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.80 (56 / 20)  


2787 27.90 2.47 0.34  chr1_167938282_167944024     4362  5250 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_167938282_   4362 TGGAAAAACATTCCATCCTCATGGATAGGAGGAATCACTATCATGAAAAT 4411
                               i i  i    vi        v   i  v i v   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_167938282_   4412 GGCCATACCGCCCAAAATAACTTACAGATTCAATGCTATTCCCATTGATA 4461
                            v    iv      v i ii           i  v  i  i  ii v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_167938282_   4462 TTC-----------TTCACAGAATTTAAAAAATT-ATTTTAAACTTTATA 4499
                          i -----------  ii     v  i v  ii -  ii    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_167938282_   4500 -AGAAAT-CAAAGAAGACCCGGTATAGCCAAGACAATTGTAAGCAAAAAC 4547
                         -i     -   i --     i v        i     iv i iv  i  v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_167938282_   4548 AACAAAGCTAGAAGAAACACACTACCTGACTTCAAACTATACTACAAGGC 4597
                                i i  i  vv      v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_167938282_   4598 TACAGTAACCAAAATAGCATGGTATTGGTACCAAAACAGGCATATAGGCC 4647
                                 i   i i  ii     i   i iv ii i  i       ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_167938282_   4648 AATGGAGTAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAT 4697
                               i     iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_167938282_   4698 CTGATCTTTGACAAACCTGCCAACAACAAGCAATGGGGAAAGGATCTCCT 4747
                         i    i  i     ivv      v v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_167938282_   4748 ATTCAGTAAACGGTGCTGGGAAAACTGGCTAGCCATAGGCAGAAAACAGA 4797
                         v    ii   i          v      v  ?   i v   i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_167938282_   4798 AAGTGGACACTT--CTTAAGCCTTATACAAAAATTAACTCAAGTTGGATT 4845
                          iv     v i --  i vi  v                   iv     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_167938282_   4846 AAATACTTAAATGTAAAACCACAAACCTTAAAAACCCTAGAAGAAAACCT 4895
                          ? v  i         i v vv    iv     vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_167938282_   4896 AGGCA-ATACCATACAGGACATAGGCATGGGCAAAGACCTCATGACTAAG 4944
                            ?i- v i v - iv   v v  vv i     v iii  v iiv  v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_167938282_   4945 ACGCCAAAAGCAATTGCAACAAAAGCCAAAATTGATAAATGGGATCTAAT 4994
                           i         vvv          vv     v       v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_167938282_   4995 TAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATTATCAGAGTGAACA 5044
                         i   v v  i i   i  ii vv    i  v     i vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_167938282_   5045 GGTAACCTAGAGAATGGGAGAAAATTTCTGCAATCTATCCATCTGACAAA 5094
                          ii    i v               v i     vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_167938282_   5095 GCTCTAACATCCAGAATCTACGAGAAACTTAAACAAATTTACAAGAAAAA 5144
                          vv  vii         v  ii ii    ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_167938282_   5145 ---AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5191
                         ---   i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_167938282_   5192 CAAAAGAAGACATTTATGCAGCTAACAA--ACATGAAAACAATCTCCACA 5239
                          v        i  vi viii  i  i  --         v vv   v   
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_167938282_   5240 TCACTGATCAT 5250
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.50 (25 / 10)  


2086 26.10 0.55 0.74  chr1_168059518_168066552     5330  5873 (1162)    L1M4_orf2#LINE/L1        1   543 (365)  

  chr1_168059518_   5330 TGGAAAAACATTCCATGCTCATGGATAGAAAGAATCAATATTTTGAAAAT 5379
                               i i  i     i        v i    v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168059518_   5380 GGCCATACTGCCCAAAGGAATTTATAGATTCAATTCTATCCTCATCAAGC 5429
                            v     v      vvi  i  i        iv v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168059518_   5430 TACCATTGACTTTCTTCACAGAATTAGAAAAAAACACTTTAAATTTCAAA 5479
                          v   vivi i  i  ii     v v  v  ivvv iii    v    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_168059518_   5480 GGGAACCAAAAAAGAGCCCATATAGTCAAGACAATCCTAAGCAAAAAAGA 5529
                         v    viiv  ii  v  viv    i   i      i i i-   i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chr1_168059518_   5530 ACAAAGCTGAAGGCATCTTGCTACCTGACTTCAAACTATATTGCAAGGCT 5579
                               i  i   vv  vii  v  ii i      viv  i i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_168059518_   5580 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACCA 5629
                                i   i    ii         i iv ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_168059518_   5630 ATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCACC 5679
                               i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_168059518_   5680 TGATCTTTGACAAACCTGACAAAACCAAGCAATGGGGAAAGGAT--TCCT 5727
                             i  i     ivv  v   i    vv            i  --  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_168059518_   5728 TATTTAACAAATGGTGTTGGGAAAACTGGCTAGCCATCTGCAGAAAACTG 5777
                          -- i           i     v      v  ?   iv    i  i v  
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_168059518_   5778 AAACAGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 5827
                           iiv        v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_168059518_   5828 TAAAGACTTAAATGTAAGACCTAAAACCATTAAAACCCTT-GAAGAA 5873
                         i ?    i           v       i  -     i   -      
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAA 543

Transitions / transversions = 1.64 (87 / 53)
Gap_init rate = 0.01 (5 / 543), avg. gap size = 1.40 (7 / 5)  

1061 24.05 4.05 1.08  chr1_168059518_168066552     6173  6542 (493)    L1M4_orf2#LINE/L1      528   908 (0)  

  chr1_168059518_   6173 AAAACTCT-AGAAGAAAACCCAGGCA-ATACCATTCAGGACATAGGCATG 6220
                                 -          vi   ?i- v i -   iv   v v  vv i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTA 576

  chr1_168059518_   6221 GGCA--GACTTCATGACTAAAACACCAAAAGCAATGGCAACAGAAGCCAA 6268
                             -- ii   v iiv  vi            vvi      i   vv  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_168059518_   6269 AATTGACAAATGGGACCTAATTAAACTAAAGAGCTTCTGATCAGCAAAAG 6318
                            v  i    v    i v  i   v v  i i   i  vv vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_168059518_   6319 AAA-TATCATGAGAATGAACAGGCAACCTACAGAATGGGAAAAAAT-TTT 6366
                          v -     v  i i    v  i     i           i     -   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_168059518_   6367 CCCAATCTATTCATCTGACAAAGGGCTAATATCCAGACTCTACAAAGAAC 6416
                         v v    -  vi      i  i  i  vi        v v  i       
  L1M4_orf2#LINE/    727 GCAAATC-ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_168059518_   6417 T--TA-AATTTA-CAAGAAAAAAACAA----CCCCATCGAAAAGTGGGCA 6458
                          --  -  i i -i  v     i    ----   v  i?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_168059518_   6459 AAGGATATGAACAGATACTTCTCAAAAGAAGGCATTTATGTGGCCAACAA 6508
                               v    i   i i     v       ii  vi vi       i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_168059518_   6509 ACATATTTTAAAAAA-GCTCATCATCACTGGTCAT 6542
                         i  i  v--    i -     v     ????????
  L1M4_orf2#LINE/    876 GCACATG--AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (47 / 40)
Gap_init rate = 0.03 (13 / 381), avg. gap size = 1.46 (19 / 13)  


3219 26.61 1.00 0.33  chr1_168073884_168080123     4846  5747 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_168073884_   4846 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4895
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168073884_   4896 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4945
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168073884_   4946 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 4990
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_168073884_   4991 TGGAACCAAAAAAGTGCCCACA-TCACCAAGGGAATCCTAAGCCAAAAGA 5039
                              viiv  ii -i    v - vi    iiv    i i ivv i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_168073884_   5040 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5089
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_168073884_   5090 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5139
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_168073884_   5140 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACTA 5187
                               i    i--    i  --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_168073884_   5188 TCTGATCTTTGACAAACTTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5237
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_168073884_   5238 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5287
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_168073884_   5288 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5337
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_168073884_   5338 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAAACCTAGAAGAAAACC 5387
                         i ?    i    i  v   v       i      vv i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_168073884_   5388 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAA 5437
                             ?i v viv   iv   v v  vv i     v ii   v ivvi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_168073884_   5438 ACATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCAT 5487
                            i        vvi          vv     v  i    v   ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_168073884_   5488 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5537
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_168073884_   5538 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5587
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_168073884_   5588 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5637
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_168073884_   5638 AACAAACAACCCCATC-AAAAAGGGGCGAAGGACATGAACAGATACTTCT 5686
                         i     i     v  i-     v    i     iv    i   i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_168073884_   5687 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5736
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_168073884_   5737 TCACTGGCCAT 5747
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2648 28.50 0.36 0.48  chr1_168107113_168112970     3803  4637 (1221)    L1M4_orf2#LINE/L1        1   834 (74)  

  chr1_168107113_   3803 TGGAAACACATCCCATGCTCATGGATGGGTAGAGTCAATATTGTGAAAAC 3852
                               v i        i        v  v   v i        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168107113_   3853 GATCATATTGCTAAAAGCAATCTACAAATTCAATGCAATTTCCATCAAAA 3902
                          iiv   i v iv   vii       i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168107113_   3903 TACCATCATTATTCTTCACAGAACTAGAAAAAA-AATCCTAAAATTCATA 3951
                          v   v vviv  i  ii     v v  v  iv-i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_168107113_   3952 CATAACCAAAAAAGAGCCAGCCAGCATAGCCAAAGCAAGACTAAGCAAAA 4001
                         iiv  -- viv   i v --    v         i   vvi i iv  i 
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_168107113_   4002 AGAATAAATCTGGAGACATTATATTACCCAATTTCAAACTGTACTACAAA 4051
                             i   vi     ivv i i i v            viv         
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_168107113_   4052 GC-ATAGTTACCAAAACAGCATGGTACTGGTATAAAAACAAGCAAATAGA 4100
                           - i   v i   i    ii         i    ii i ii  v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_168107113_   4101 CAAATGGAACATAATAGAGAAACCAGAAATAAAGCTAAATACTTACAGCC 4150
                         iv       i v   v    iv           v i v i i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_168107113_   4151 AACTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGAAACC 4200
                           i    i   i    i vviv   i v   vv i         i v vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_168107113_   4201 CTATTCAACAAACAGTGCCGAGATCATTGGCAAGCCACATATAGAAGAAT 4250
                           v         ii    i i  iv i   vv ?      ii i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_168107113_   4251 GAAACTGGATCCTCGTCTCTCACTTTATACAAAAATCAACTCAAGATGGA 4300
                            ii    i  iiii   v   iv           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_168107113_   4301 TCAAAGACCTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAAT 4350
                            ?          v     v  i    i      v ii       v  i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_168107113_   4351 ATTGGAAAAACCCTTCTAGACATTGGCCTAGGCAAAGAGTTCATGACCAA 4400
                           v  ?iv  vi    vv   v    vi       v iv   v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_168107113_   4401 GAACCCAAAAGCAAGTGCAACAAAAACAAAGATAAATAGCTGGGACTTAA 4450
                           vv         viv         iv   i   i   iv v      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_168107113_   4451 TTAAACTAAAATGCTTCTGCACAGCAAAAGAAATAATCAGCAAAGTAAAC 4500
                          i   v v   vi   i  ii vv    i  v iv    iv     i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_168107113_   4501 AGAAAACCCATAGAGTGGAAGAAAATATTTACAAACTATGCATCCAACAA 4550
                            v      i   i   i           i    ii  ii   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_168107113_   4551 AGGACTAACATTCAGAATTTACAAGGAACTCAAGCAAATCAGCAAGAAAA 4600
                         i     vii  i      v  i  i      vvi   v   ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_168107113_   4601 AAACAAATAATCCCATCAAAAATTAGGCTAACG-TTTG 4637
                          i        i  v  i?    v i   v  v -    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.01 (5 / 834), avg. gap size = 1.40 (7 / 5)  

 287 13.51 1.35 2.70  chr1_168107113_168112970     5292  5365 (493)    L1M4_orf2#LINE/L1      836   908 (0)  

  chr1_168107113_   5292 ATAGACAATTCTTAAAAGAAGATATACATATGACCAACAAACATATTTTA 5341
                                v    iv              v   i    i  i  i  --v 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT--GA 883

  chr1_168107113_   5342 AAAAATGCTCA-CATCACTAATTAT 5365
                            i       -     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (6 / 4)
Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.50 (3 / 2)  


 427 33.33 2.42 0.97  chr1_168145353_168147790      458   664 (1774)    L1M4_orf2#LINE/L1       81   290 (618)  

  chr1_168145353_    458 CAGCCCACTCTC---CAGGACTCCAGCTGGATTTTGAGGGGAATGTGACA 504
                           i v  v  i ---  ii ii       vv    vv vi   vv     
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA 130

  chr1_168145353_    505 AATTGATTCTGAAATGAACAAAGAATAGCTAAG-ACGCA-AATAACTAAA 552
                          ii    i  i    vv i vi   vv  v i -  v  -    i i   
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr1_168145353_    553 CTAATTTTGAGAAAGAAGAGCAAAGATAGAGGACTTTTTCTACCAAATAT 602
                         vi   i    i        i     v i       iviv  v  v   v 
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_168145353_    603 TAAGATAAATCAATCACATTCACAGAAATAAAAACAATTTAATACTGCCA 652
                         i  i ivv ii --  v vii    v   v  i   i v ii     v  
  L1M4_orf2#LINE/    231 CAAAACTTACTA--CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_168145353_    653 CAAGAACAGATA 664
                         i   i i   i 
  L1M4_orf2#LINE/    279 TAAGGATAGACA 290

Transitions / transversions = 1.23 (38 / 31)
Gap_init rate = 0.02 (4 / 210), avg. gap size = 1.75 (7 / 4)  

 530 32.48 5.14 6.97  chr1_168145353_168147790      903  1447 (991)    L1M4_orf2#LINE/L1      284   818 (90)  

  chr1_168145353_    903 ATAGATCAATAGATCAGTAGAACAAAATAAGGAGCCCCGAAACAAACCCA 952
                              ivv        i i   i i   vii   i  v    i       
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_168145353_    953 TGTGCATATTGAAACTTCATATATCATAGAAATGGCATCTTTAATCAATG 1002
                          iiiiv   v vv v  v  v viv i iiii  v  vvvii v      
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_168145353_   1003 AAGAAAGAAGGATAGATTTTTTTTTTTTTTTTAGTGAATGACGTTGGGGG 1052
                         ii       ---   ---------- i    i iii    ii i    iv
  L1M4_orf2#LINE/    384 GGGAAAGAA---TAG----------TCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_168145353_   1053 AGCTAG-----TACATGGAGAAAAACCCAGTTGTATTCCTGCCTCATACC 1097
                          i  i -----i     v i  i  ivv     v ii   i     i   
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_168145353_   1098 ATATACAAATGTTAACT-GTAATGGATTA----CTTCCATCTGAAATGGA 1142
                                  vi      -iv       i ---- i vv  v i i vvv 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_168145353_   1143 AATCAGTGAAGAT----AAGGAAAGTAGAGAAGAATATCTTTGTGACTTT 1188
                           v vi i  iv ----i i    ii v  i? v v     i     i  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_168145353_   1189 GAAATGGA----GGTGT--TAG-TAAGAAAGGCCTGAAAATCTTA--CCA 1229
                          iiv i i----   v --   -  v  v --  --    v vi -- v 
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACA--CC--AAAAGCACAAGCAA 616

  chr1_168145353_   1230 TAAAGGGGGAAATTTGTGGATTTAAATACAAAAACAAAAACACGCACAAA 1279
                         i   i iii    vvi ii   vi v v  v---     vi --------
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCAT---CAAAATTA-------- 655

  chr1_168145353_   1280 AAAACACCAGGGTTTCT-TTTCAAAGAAGACTATCATAAATAAAGTTAGG 1328
                              ------v   v -i       i v       --- v     v ii
  L1M4_orf2#LINE/    656 AAAAC------TTTTGTGCTTCAAAGGACACTATCA---AGAAAGTGAAA 696

  chr1_168145353_   1329 GGGCAAGTGATAGCCTAGAAGAGTATATTTGCCACCTATGCAACTCA--- 1375
                         i i   viv i  vv i i   iv        v vii  ii v  v ---
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_168145353_   1376 -GGAATTGTTATGTAGAATATACAGAGAAATTCTGTAGATCAAGAAGCAA 1424
                         -   v    -  vi        i i    v ii ii iv    v  vv  
  L1M4_orf2#LINE/    747 GGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_168145353_   1425 AAGACGTGAAGTCCAATAGAAAA 1447
                              iviv ii     v?    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAA 818

Transitions / transversions = 1.33 (100 / 75)
Gap_init rate = 0.04 (19 / 535), avg. gap size = 3.47 (66 / 19)  


2468 26.27 1.41 0.42  chr1_168152193_168153892.rev      502  1209 (491)    L1M4_orf2#LINE/L1      194   908 (0)  

  chr1_168152193_    502 AAAAGAACAAAGCTGGAGGTATTATGCTACACAACTTCAAACTCTGCTAC 551
                          i          i      vv i ii  v v   i      vii i    
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_168152193_    552 AAGGCTACAGTAACCAAAACAGCATGATACTGGTACAAGAACAGACACAT 601
                           i          i   i    ii  i      i i   i i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_168152193_    602 AGACCAATGGGACAGAATAGTGAACTCATAAATAAGACTGGACACCTACA 651
                            i      i i     v v  iii  v      iv iiv   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_168152193_    652 ACCATCTGATCTTTGGCAAACCTGACAAAAACAAGCAATAGGGAAGAGAT 701
                         ii  vi    i  i i   ivv  v   i v  vv    i     iii  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_168152193_    702 TTCCTGTTTAATAAATGGTGCTGGGATAACTAGCTAGCCATATGCAGAAA 751
                         vvi  v  i  i              i    i v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_168152193_    752 ATTGAAACTGGACCCCTTCCTTACACTATATACAAAAATTAACTCAAGAT 801
                          v    ii         v   i    i                    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_168152193_    802 GGACTAAAGACTTAAATGGAAAATCTAAAACTACAAAAACCCTAGAAGAA 851
                            ii ?    i      v  i v         i    vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_168152193_    852 AATCTAGGCA-ATACCACTCAGGACATAGGTGTCGGCAAAGATTTCAT-G 899
                           iv    ?i- v i -i  iv   v v  vv v     v i    v - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_168152193_    900 ATAAAAATGCTAAAAGCAATTGCAACAACAGCAAAAATTGACAAATGGAA 949
                            vi -ii i       vvv       v  v      v  i    v i 
  L1M4_orf2#LINE/    593 ATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_168152193_    950 TCT------AATTAAAGAGCTTCAGCACAGCAAAATAAACTATCATCAGA 993
                         ii ------       i -   iv ii vv    iv v       vv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_168152193_    994 GTAAACAGACAACCTACAGAATGTGAGAAAATTTTTGCAATCTATCCATC 1043
                           i  v        i        v        v       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_168152193_   1044 TGACAAAGGTCTAATATCCAGAGTCTACAAAGAACT-TAAGAAATTTACA 1092
                            i  i  v  vi        i v  i        - v v  v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_168152193_   1093 AGAAAAAAAGAAACAACCCA-TTAAAAAGTGGTCAAAGGACATGAACAAA 1141
                          v     i v   i      -  ?    i   v       iv    i i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_168152193_   1142 CACTTCTCAAAATAAGACATACATGTGACCAACAAACATATGAAAAAATG 1191
                           i     v   v    i     vi  i    i  i  i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_168152193_   1192 TTCAACATCACTAATCAT 1209
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (112 / 70)
Gap_init rate = 0.01 (8 / 715), avg. gap size = 1.62 (13 / 8)  


2488 23.58 8.21 4.16  chr1_168204371_168206946.rev     1227  2091 (485)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr1_168204371_   1227 TATGCCATGTTCATGGATCACAAGACCCAATATT---AAGATGTCAATTA 1273
                            v              iiv     ii      ---      v    vv
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr1_168204371_   1274 TTTTCAAGTTTATCTACAGATTCAAAGCAATCCCCAACAAAACCTCAGAA 1323
                          iii   i  v              v        i v     i i   vv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr1_168204371_   1324 GAAATTTATTGGAGGACAAAAGTTGTCAAGCTGATTCTAAAATTTATAAA 1373
                          vvv   -   -----  i  i   v         i        i   vi
  L1M4_orf2#LINE/    109 GCCTTTT-TTG-----CAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_168204371_   1374 GAAATGGACTGGCTCTAGAACAGCACCACCCACCCCCTACCCTCCACCCC 1423
                               v vv  vi i    i   ------  ------------- ----
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGC------CA-------------A---- 179

  chr1_168204371_   1424 GCCAGCTTTGAAAA----GAATGAAATTGGAAGGTGAATACTACTTGCTT 1469
                         iv  iii       ----   ii  i     i iivv i   v iiiv  
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_168204371_   1470 TCAAGACTTA-----AGGC-ACAGCAATGAAGACAGTGTGGTACTGGTGT 1513
                             i     ----- i  -    i   v                  ii 
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_168204371_   1514 AAAAATAAGACAAATAGTTCAGTGGAGCAGAAT--AGAGTCTAGAAATAT 1561
                           ii   -    v    v   i    ii     --      i       -
  L1M4_orf2#LINE/    280 AAGGATA-GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA- 327

  chr1_168204371_   1562 AA---ATACAC--ATAAGCATTTGATTTTTGACAAA--TGCAAAGAA-AT 1603
                           ---     i--  iiv  v        i     i--   v    v-  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_168204371_   1604 TCAGTGGATAAAGGACAGTCTTCCCAA-AAATGATACTGGAGCAATTATG 1652
                            i   iv    i i      ii   -     i i    ii   i ivi
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_168204371_   1653 TGTACATAATATTAAAAACTTAACACTGATTCATACCTTACACCATATAT 1702
                          i?v  i - iiv   i v v  vviv  ii v     i          i
  L1M4_orf2#LINE/    428 TAKCCACA-TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_168204371_   1703 GAAACTCAACTCAAAAATGAACCATAGACA-AAATGTAAAACCTGAAACT 1751
                         i   v i         -  i i  ?    v-        i v  i     
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAA-TGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_168204371_   1752 GTAAAACTTCCAGA-GAAAACATAGA---AAATCTTTGTGACACTGGGTT 1797
                         i       iii   -          i---       i     vi      
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_168204371_   1798 TAGATAAGGACTTCTTAGATATAACACCAAAAGCACAATCTATAAAAAAT 1847
                         -  ii  v ii           i               v v i    i v
  L1M4_orf2#LINE/    576 -AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_168204371_   1848 GAAATTTATAAACTGGACTT------------------TTGCTTTTTGAA 1879
                         i    vv     i       ------------------   ivi  ii  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_168204371_   1880 AGATAATGTTGAGAA--CTAAAGGACAAACTAGAGTCTGGAAAAAAA-AT 1926
                         i  i v i ii    --iv   i     v i v  vv   i i    -  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_168204371_   1927 TGTCAAATCATAGATCTGAGAAAGAACTTTTATCAAGAATACATACAAAA 1976
                          vv         v      v  i i    v    v      i   v i  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_168204371_   1977 CTCTCATAAC----------------AACCAACCCAGTTTTTAAAAATCG 2010
                             i i   ----------------  vi      i  ?--      v 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW--AAAAATGG 822

  chr1_168204371_   2011 GCAGGAGATTTGAAGAGACACTTCACCAGACA---TATACAAATGGTAAG 2057
                            iii        v     i   v   i v ---           iv i
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_168204371_   2058 TAAGCATATGAA--GATACTCAGTGATATGGTTTGG 2091
                               i     --   i    iiivi ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (129 / 72)
Gap_init rate = 0.03 (30 / 900), avg. gap size = 3.57 (107 / 30)  


3155 27.54 0.77 0.33  chr1_168251513_168257852.rev     4946  5849 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_168251513_   4946 TGGAAGAACATTCCATGCTCATGGATAGAAAGAATCAGTATCGTAAAAAC 4995
                              ii i  i     i        v i    v i i   i  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168251513_   4996 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCTCCATCAAGC 5045
                            v     v     iv i  i           i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168251513_   5046 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5093
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_168251513_   5094 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGATAATCCTAAACAAAAAG 5143
                                viiv  ii  v  v v  v     i i    i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_168251513_   5144 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGTC 5193
                                i      vv   ii  v  ii i      vivi       iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_168251513_   5194 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 5243
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_168251513_   5244 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACCCATCTACAACCAT 5293
                                i    iv   ivii         vv   iv   i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_168251513_   5294 CTGATTTTTGGCAAACCTGACAAAAACAAGAAATGGAGAAAGGATTCCCT 5343
                         i       i i   ivv  v   i v  vvv     i     i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_168251513_   5344 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5393
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_168251513_   5394 AACTGGATCCCTTCCTTACACCTTATACAAAAACTAATTCAAGATGGATT 5443
                          ii    i    v   i     v          i   i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_168251513_   5444 AAAGACTTAAATGTTAGACCTAAAACGATAAAAACCCTAGAAGAAAACCT 5493
                          ?    i       v   v       v      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_168251513_   5494 AGGC-CATACCATTCAGGATATAGGCATGGGAAAGGACTTGGTGACTAAA 5542
                            ?-i v i -   iv  iv v  vv i  v  v ii  vv iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_168251513_   5543 ATACCAAAAGCAATGGCAACAAAAGCCAAAACAGACAAAAGGGATCTAAT 5592
                          i          vvi          vv    i   i   vv   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_168251513_   5593 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5642
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_168251513_   5643 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5692
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_168251513_   5693 GGGCTAATATCCAGAATCTACAATGAACT--TA-AATTTA-CAAGAAAAA 5738
                           i  vi          v  i  v     --  -  i i -i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_168251513_   5739 ATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTTT 5788
                         iv    i     v  i?    i            v    i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_168251513_   5789 CAAAAGAAGACATATACGCAGCCAGCAGACACATGAAAAAATGATCATCA 5838
                          v        i   i viii    ii ii          i   v   v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_168251513_   5839 TCACTGGTCAG 5849
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.63 (152 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


3249 26.71 0.66 0.44  chr1_168389883_168397718.rev     6440  7345 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_168389883_   6440 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 6489
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168389883_   6490 GGCCATACTGCCCAAGGTAATTTACAGATTTAATGCCATCCCCATCAAGC 6539
                            v     v     iv i  i        i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168389883_   6540 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6587
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_168389883_   6588 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 6637
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_168389883_   6638 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6687
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_168389883_   6688 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGATC 6737
                                 i   i    ii         i iv ii i             
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_168389883_   6738 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 6785
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_168389883_   6786 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 6835
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_168389883_   6836 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6885
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_168389883_   6886 GAAAT--GATCCCTTCCTTACACCTTATACAAAAATCAATTTAAGATGGA 6933
                            i --  i    v   i     v           i  i i  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_168389883_   6934 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 6983
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_168389883_   6984 CTAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAA 7033
                         v    ?i v viv   iv   v v  vv i i   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_168389883_   7034 AACACCAAAAGCAATGACAACTAAAGCCAAAACTGACAGATGGGACCTAA 7083
                         i            vvii    v    vv    iv  i i  v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_168389883_   7084 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 7133
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_168389883_   7134 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 7183
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_168389883_   7184 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 7233
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_168389883_   7234 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 7283
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_168389883_   7284 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATCCTCACC 7333
                           v        i  vi viii     v  i          i  v    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_168389883_   7334 ATCACTGGCCAT 7345
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3379 25.22 0.77 0.77  chr1_168420973_168423964     1592  2499 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_168420973_   1592 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 1641
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168420973_   1642 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 1691
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168420973_   1692 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1739
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_168420973_   1740 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 1789
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_168420973_   1790 AACAAAGTTGGAGGCGTCACGCTACCTGACTTCAAACTATACTACAAGGC 1839
                                       vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_168420973_   1840 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1889
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_168420973_   1890 AATGGAACAGAAT--AGTGCCCTCAGAAATAATACCAGACATCTACAACC 1937
                                i     --  v i  --        vv   v    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_168420973_   1938 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATAGGGAAAGGAATC- 1986
                          vi    i  i     ivv  v   i v  vvv   i       -   v-
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAG 395

  chr1_168420973_   1987 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2036
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_168420973_   2037 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 2086
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_168420973_   2087 ATTAAAGACTTAAATGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAA 2136
                           i ?    i       v i v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_168420973_   2137 CCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGATTTCATGAAT 2185
                          v    ?i- v   -   iv   v v  vv i     v i    v ii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_168420973_   2186 AAAACACCAAAAGCA-ATGTCAACAAAAGCCAAAATTGACAAATGGGATC 2234
                          vi            - v -         vv     v  i    v   ii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_168420973_   2235 TCATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 2284
                             i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_168420973_   2285 AACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGA 2334
                           v  i     i                 v   i   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_168420973_   2335 CAAAGGGCTAGTATCCAGAATCTACAAAGAACGTAAAGAAATTTACAAGA 2384
                         i  i  i  v           v  i       vivv v  v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_168420973_   2385 AAAAATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 2434
                             iv    i     v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_168420973_   2435 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 2484
                              v        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_168420973_   2485 ATCATCACTGACCAT 2499
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


4709 16.46 3.16 0.79  chr1_168561349_168563288      561  1447 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_168561349_    561 TGGAAAGATATCCTATGTTCATGAACTTGAAGACTTAAG--TGTTAAAAT 608
                                      i         i i v          v--      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168561349_    609 GGCAACACACCTCAAATCAATCTGCAGACTTAATGAAATTCCTATCAAAA 658
                              i  v  i     ii    i    i i  i v   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168561349_    659 TTCCAGATGCCATTTTTGTGCAGAAATTGACAAACTGATCTTAAAATTTT 708
                          i    v    -     -               i      i       iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_168561349_    709 TATGGAGTTGCATAGGATTCAGAATGGCCAAAACAATGTTGAAAGCAAAA 758
                               iv    vi   ii      i           v      --  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA--AAGA 196

  chr1_168561349_    759 CAAAACAA-GTTGAAGGACTCACACTTCCCAGTTCTAAAACTTACTACAA 807
                         - i     -    i                 i  ii              
  L1M4_orf2#LINE/    197 -AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_168561349_    808 A----------TCA-----GTGTAATACTGGTGTAAATATACACATACTA 842
                          ----------   -----    ii      ii   iv   v     -  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TA 294

  chr1_168561349_    843 AATGAATGGAATAGACTTGAGAGTCCAGAAATAAACTGTTACATTCGTGG 892
                         i  v           v                    ivv      ii   
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_168561349_    893 TCAATTGATTTTTAACAAAAGTACCAAGATAATTCAATGGAGGAAAGAGT 942
                                     ii    ii  i      iv         -       i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAAT 393

  chr1_168561349_    943 AGCCTTTTCAACAAATGGTACTGGGACAGCAGTATATCCATGTGCAAAAG 992
                           i                i        i v v   ?   ii        
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_168561349_    993 AATACATTGGGGCCCCTACCTCACATCATATATACAGATTAACTCAAAAT 1042
                            iv v v  i             i      i v i             
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_168561349_   1043 GGATCAAAGACCTAAATGTAAGAGCTAAAGCTACAAAATTTTTAGAAGAA 1092
                               ?                      i   i    i i         
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_168561349_   1093 AACACAAGTATAAATCTTGGTGATTTTAGATTAGACAGTAGTTTCTTAGC 1142
                             i i ?i        v    ii  i i    i  i i         v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_168561349_   1143 TACGATACCCAAAGCATAAGTGACAAAATAAAAAATAGTTAAAGTGAACA 1192
                           i  i   v      i   ii      v         v    v  i  v
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_168561349_   1193 ACATCAAAATTAAAAACTTTTGTGCTTCAAGGGACACTATTAAGGGTATG 1242
                         v                             i         i   iivi  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_168561349_   1243 AAAAGATAACCCAGAGAATGGGGGGAAATTTTTGCAAATTATATATGTGA 1292
                               i      v        i i    v         i      v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_168561349_   1293 TAGGGAACTAGCATCCTGAATACAAAAGGAACTCTTATAACACAACAATA 1342
                           i  i   v i    v     i v  i         i   v   i    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_168561349_   1343 AAAAGACAAATAACCCAATTAAAAATTAGGCAGAAGACTTGA-------- 1384
                                             ?    v i    i i  i    --------
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_168561349_   1385 TTTTCTAAAGAA--TGTATAAATAGCTAATATGCACATAGAAAGATGCTC 1432
                           i  i      -- i  i    i  i    v      ii          
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_168561349_   1433 AACATCAGTAGTCAG 1447
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.55 (102 / 40)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.92 (35 / 12)  


3386 26.18 0.33 0.44  chr1_168595685_168597979.rev      896  1804 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_168595685_    896 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 945
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168595685_    946 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 995
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168595685_    996 TACCAATGACTTCCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1043
                          v   iivi i ii  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_168595685_   1044 TATGGAACCAAAAAGGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAG 1093
                                viiv  i   v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_168595685_   1094 AACAAAGTTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1143
                                       vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_168595685_   1144 TACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1193
                            i    i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_168595685_   1194 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACCCATCTACAACCAT 1243
                                i    iv   ivii         vv   iv   i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_168595685_   1244 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 1293
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_168595685_   1294 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1343
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_168595685_   1344 AACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGATT 1393
                          ii    i    v   i   i v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_168595685_   1394 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1443
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_168595685_   1444 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 1492
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_168595685_   1493 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1542
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_168595685_   1543 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1592
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_168595685_   1593 GGCAACCTACAAAATGGGAGAAAAATTTTGCAATCTACCCATCTGACAAA 1642
                          i     i   i            vv       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_168595685_   1643 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 1692
                           i  vi          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_168595685_   1693 AATCAAAAAATCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 1742
                         i -    v  i  v  i?    i            v    i     i   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_168595685_   1743 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAATAAATGCTCATC 1792
                           v        i  vi viii     i ii        v i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_168595685_   1793 ATCACTAGTCAT 1804
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


1769 18.46 3.86 0.55  chr1_168623563_168628033.rev      502   864 (3607)    L1M4_orf2#LINE/L1      128   502 (406)  

  chr1_168623563_    502 ACAAGCTCATTCTGAAATTCATATTGAACTTCAAGAGACCCAGGATAGCC 551
                                v  i  i          v   v v    i       i      
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr1_168623563_    552 AAAACAATCCTGAAAAAAAA---TAAAGTAGAAGGACTTGCAATTCTCAA 598
                                  i       i  ---i     v i      ii  v   i   
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_168623563_    599 TTT-GAAACTTACCACAAAGCAAGGGTAATTAAGAGAGTATGCTATTGGC 647
                            -i        i       v vi     i    v   i  v  i    
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_168623563_    648 CCAAGGATAGACATAAATATCAGTCGAAAAGAACTGAGAGTCCCAAAATA 697
                         vi             v v    i v   v    i         vi     
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_168623563_    698 AACCTGTATTTCTCTGGTCAACAGATTTTTGACAAAGGGGCCAAGATCCT 747
                             ii  iv i v       iv      i     i  v       i v 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_168623563_    748 ACAGTGAGGAAAGAATAGTCTTTTCAACAAATTGTGCTGGGACTAGTGGA 797
                         v  i  i                         v          v v    
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_168623563_    798 TATCCACATGCAGAA-AATAAAGTTTGACACTTA---------GTGCATA 837
                           ?         i  -   i     v   v i  ---------i ii i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_168623563_    838 AAATTATTAACTCAAAATGGATCAAAG 864
                            --                   ?  
  L1M4_orf2#LINE/    478 AAA--ATTAACTCAAAATGGATCAWAG 502

Transitions / transversions = 1.41 (38 / 27)
Gap_init rate = 0.01 (5 / 375), avg. gap size = 3.20 (16 / 5)  

3078 23.44 0.96 1.79  chr1_168623563_168628033.rev      875  1710 (2761)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr1_168623563_    875 TGGAAAAACATCCCATGCTCATGGATTGGAAGAATCAATATGGTTAAAAT 924
                               i i        i               v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168623563_    925 GACTATACTGCCCAAAGCAATCTACAGATTCTATGCAATTCCTATCAAAT 974
                          i v     v      vii            v i     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168623563_    975 TACCAACATCATCTTTCACAGAATTAGAAAAAACAATACTAAAATTAATA 1024
                          v   i vv v i   ii     v v  v  ivii  v        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_168623563_   1025 GGGAACCAGAAGAGAGCCCAAATAGCCAAAGCAATCCTAAGCAAAAAGAA 1074
                         v    viiv   i  v  vi          i     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_168623563_   1075 CAAAGCCAGAGGCATCACATTACCCAACTTCAAACTACTCTATACTAAAC 1124
                              iii    vv     i v     i      --   ---     ---
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACT---TACTA--- 242

  chr1_168623563_   1125 TATACAAGGCTATAGTAACCAAAACAGCATGGTACTTGTATGAAAATAGA 1174
                         ----   i    i     i   i    ii       v i  i ii     
  L1M4_orf2#LINE/    243 ----CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_168623563_   1175 CACATAGATCAATGTAAAAGAACAGAGAACTCAGAAGTAAAGCCACATAT 1224
                           i           v  v    iv    iii     i    v   i i  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_168623563_   1225 TTTCAACCAACACGTCTTCCACAAAGTCAACAAAA--A--CAATGAGGAA 1270
                           viiii   ivvi i   v    i viiv   i -- --     i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_168623563_   1271 AGAACATCCTACTCAATAAATGGTGTTGGGAAAACTGCCTAACCATATGC 1320
                             i vi  vi    i        i     v     vv  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_168623563_   1321 AGAAGAATATAACTGGACCCCTATCTCTCACCATATACAAAAATTAACTC 1370
                          i      iv ii          i   v                      
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_168623563_   1371 ATGATGGATTAAAGACTTAAATGTAAGTCCTCAAACTATAAAAATTCTAG 1420
                          vi      i ?    i          vv  v           v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_168623563_   1421 AAGAAAACCTAGGAAAAACTTCTCCAGACATCAGCCTAGGAAAAGGACTT 1470
                                 v    ?iv  v ii  vv   v ii vi    v  v  -i  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTT 587

  chr1_168623563_   1471 CTCAC-TAAGACCCCAAAAGCA-ATGCAACAAAAACAGAAATAGACAAAC 1518
                           i v-  v   v         - v         iv i       i   i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_168623563_   1519 GGGACTTAA-CTAAACTAAAGACATTATGCACTGCAAAAGAAACTACCAA 1567
                         v      v - v   i    i  v  -  ii  v    i  v    i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAA 686

  chr1_168623563_   1568 CAGAGTAAACAGACGATCTACAGGATGAGAGAAAATTTTTGCAAACTATG 1617
                         v i   i  v    i i i    i   i        v        ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_168623563_   1618 CATCCAATAAAGGACTAATATCCAGAATCTATAA-GAACTTTAAACAAAT 1666
                         i   ii    i     vi          v     -     i v -   v 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACT 785

  chr1_168623563_   1667 CAACAAGAAAAAAACAAATAACCCCATTAAAAAGTGGGCAAAGG 1710
                            i  v     i           v   ?    i          
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.46 (114 / 78)
Gap_init rate = 0.01 (12 / 829), avg. gap size = 1.92 (23 / 12)  

 345 18.95 0.00 1.05  chr1_168623563_168628033.rev     2338  2432 (2039)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_168623563_   2338 AAAAGTGGGCAAAGGACAGGAACAGACAATTCTCAAAAGAATACATAAAA 2387
                             i           ivv   i     v     v      v i   v  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_168623563_   2388 GCAGCCAACAAACATAAGAAAACAATGCTCAACATCATTAATCAT 2432
                         iii     i  i  i v     -i             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (11 / 7)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  

1791 16.90 3.05 1.64  chr1_168623563_168628033.rev     3556  3981 (490)    L1M4_orf2#LINE/L1      477   908 (0)  

  chr1_168623563_   3556 AAAAATTAGTAATTTTAAAAAATGGATCAAAGACCTAAGTGGAAGATC-A 3604
                                 --- i i---           ?        i  v    v - 
  L1M4_orf2#LINE/    477 AAAAATTA---ACTC---AAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_168623563_   3605 AAGCTATAAATCTCCTAGAAGAAAACATAGAA-TAAAGTTTTATAACCTT 3653
                           i       v   i               i?-    vi  ii i     
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_168623563_   3654 GGTTTTGGCAAAGGATTCTTAGATAT-ATACAAAAATAACGAGAAATGAA 3702
                           v  v     v  v           - i  v    vv  i  v  ii  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_168623563_   3703 AGAAAAAAGTAGATAAATTGGACTTCACCAAAAT-AAAAAATCTTGTGCT 3751
                                 -                  i      -     v i       
  L1M4_orf2#LINE/    621 AGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_168623563_   3752 TCAAAGGACACTGCCAAGAAAATGAAAAGG--GCCTATAAAATAGAAAAA 3799
                                     ii       i       i--i  i i i   i i i  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_168623563_   3800 AAAAAT-GCAAATCAAATATCTGATATGGGACTTGTATTTAATATATAT- 3847
                           v v -        v          v           ii iv      -
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_168623563_   3848 -----CTGTTACAATTCAGTAATACAAAGGCAAATAACCAAATTTAAAAC 3892
                         -----  v      i   i     v    i         v    ?    v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_168623563_   3893 TAGGCAAAGGAAATGAATACACATTTATCTAAATAATATATACAAATGAT 3942
                          i         vv      v      v  i   v  v           ii
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_168623563_   3943 CATTAAGCACATGAAAAGATGCTCAGTATCTTTAGTCAT 3981
                           v                      ii   v????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (39 / 30)
Gap_init rate = 0.02 (10 / 432), avg. gap size = 2.00 (20 / 10)  


 553 22.41 9.77 3.45  chr1_168708252_168709853.rev      315   488 (1114)    L1M4_orf2#LINE/L1      326   510 (398)  

  chr1_168708252_    315 TAAAC--ATACAT--------AATTGGTTTCAGACAAAAGATGCCCATGT 354
                              --      --------     i   iv     ii -    v vii
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG-TGCCAAGAC 374

  chr1_168708252_    355 AATTCCATGGAGAAAGGACAGTCCATTCAAACTAAATGATGGTACTGGAG 404
                         v    v    i     i i    iv     --i     i  ---    ii
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAA--CAAATGGTG---CTGGGA 419

  chr1_168708252_    405 TAATTACATATCCATATGAAAAATAATGAACTTTGACTCTTACTTCACAC 454
                         i  i iv   ?   i   v    v      v  v   i i   i      
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_168708252_    455 CATATACAAAAA-------AAAAAAAATTGCAGACCTAAAT 488
                                     -------    vii  ii?          
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

Transitions / transversions = 2.08 (25 / 12)
Gap_init rate = 0.03 (6 / 185), avg. gap size = 3.83 (23 / 6)  

2121 26.21 2.09 0.80  chr1_168708252_168709853.rev      490  1111 (491)    L1M4_orf2#LINE/L1      279   908 (0)  

  chr1_168708252_    490 TAAGGCTAAA-AC-TAGACCAATGGAACAAAATAGAGAACACAGAAATAA 537
                              v  i - i-    i        i i   v    iiv         
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_168708252_    538 ATCCACGCAC----AGCCAACTGATTTTTGACGAAGGCACAAAGAACACA 583
                          i   ii  i----i i   i       i   i i  ii v    v  iv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_168708252_    584 CATTGGAGAAGAGACAGTCTCTTCAATAAATGGTGCTGAAAAAACTAGCT 633
                           v   i   iii i     i     i           ii v    i v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_168708252_    634 TTCCACATCCAAAAGTATGAAATTAGACTCTGATCTCTCACCATATGCAA 683
                         v?      v      v     i  i   i iv i   v        i   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_168708252_    684 AAATCAATTCCAAATAGATTAAAGACTTAAATGTA-TACCCAAAATTATA 732
                             i  i  v    i   i ?    i        -v v i    i    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_168708252_    733 AAAAACTACTCGAAGAAAACAGAGGAGAAACTCTTCGTGACATTGATCTA 782
                            --  vi v          v   ? v  v          v   ivi  
  L1M4_orf2#LINE/    529 AAA--CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_168708252_    783 GATAAAGATTTTTTGGATAAGA-ATAAGAAAGTACAGGCAACAAAAGCAA 831
                          ii  v i   i  i    v  - iv -    i   i          v  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCA-AAAGCACAAGCAACAAAAGAAA 625

  chr1_168708252_    832 AAACAGACAAATGAAATTACATCACACTAAAAAACTTCTGCATACCGGAG 881
                            i   i    vii i v     v v v        i  iiivi ii  
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_168708252_    882 GAAACAACAGAGAAAG-----AGACAACCTACAAAATAGAAAAAAAAAAT 926
                           v  v ivi      -----        i   i   i i i    v - 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA-T 724

  chr1_168708252_    927 TTGCAAACTGTGCATCTGACAAGATGGTAATATCCAGAATATACAAGGAA 976
                                iii ii      i   iviv vi             i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_168708252_    977 CTCAAACAACTCAATAGCTGACAAACAAACCATCTGACTTTAAAATGGGC 1026
                            vv           iivi v i     iv i ii i ?v         
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_168708252_   1027 AAAAGACCCGAATAGATGTTTCTCAAAAGAAGACGTACAAATAGCTAACT 1076
                            i  iii       ii      v        ii       i  i  iv
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_168708252_   1077 GATATATGAAAAAAATGCTCAACGTCAATAATTAT 1111
                         iii i       i -        i   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (110 / 49)
Gap_init rate = 0.02 (10 / 630), avg. gap size = 1.80 (18 / 10)  

 645 24.01 8.44 6.07  chr1_168708252_168709853.rev     1224  1602 (0)    L1M4_orf2#LINE/L1      445   832 (76)  

  chr1_168708252_   1224 ATGA--TTGCATCACTGCACTC-CAGTATATGTAAAGAGCAATACCCTGT 1270
                             --   v i v  i -   -  vi    ii   i vi  --------
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTAC-CTCACACCATATACAAAAATTAA-------- 485

  chr1_168708252_   1271 CTCAAATAAATAAATTA--AACTTT--TTTAAAACCTAAAACTACAAAAT 1316
                               ---  ii  i --i  i v-- v   i v         i    i
  L1M4_orf2#LINE/    486 CTCAAA---ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_168708252_   1317 TTCTAGATAAAAGCATAAAAGAAAAAATCTCTGCAAACTTGGGTTAGGCA 1366
                          ii    vi   i    ii? v   --   ii ii v             
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCA 580

  chr1_168708252_   1367 AAG---TCT--AATGTGAT--TATGGGCATAATCAA-AAGAGCCATATAA 1408
                          v ---   --i  i   i--i vii   i  v   -  i  ------  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG------AA 624

  chr1_168708252_   1409 AAACTTGATAAATTGGGCATAATCAAAAGTAAAA---TTTGCTCTTCAAA 1455
                            v v          i v v       v     ---    iv       
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_168708252_   1456 AGATACAGTTAAAGAATATGAGAAAATAAACTATAGA-TG--AGAAAGCA 1502
                         i  i  vi i  -   vi   i  i i  v i i   -  --     ii 
  L1M4_orf2#LINE/    675 GGACACTATCAA-GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_168708252_   1503 TTAG-AAAT-ATATA----ATGAAAGATTTGTATC-AGAA-ATATTTTTA 1544
                           v -    -     ----  i ii  i       -    -    vvvv 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_168708252_   1545 ACTC--ATTACTTAATCCTAAGAAGACGAACACAACTCAATTTAAAA-TA 1591
                             -- iv   i   vv   i     i  i --  i     ?    - i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATA--ACCCAATTWAAAAATG 821

  chr1_168708252_   1592 GGCAAAAGATT 1602
                               i    
  L1M4_orf2#LINE/    822 GGCAAAGGATT 832

Transitions / transversions = 1.97 (59 / 30)
Gap_init rate = 0.06 (25 / 388), avg. gap size = 2.20 (55 / 25)  


2786 25.20 5.02 1.48  chr1_168714846_168719530.rev     3318  4194 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_168714846_   3318 TGAAGAGCTATTTACATGTTAACAAGTAGAAAGACTCAATATTGCAAAGA 3367
                           i i  v   ii-      v iiii v i      i       iv    
  L1M4_orf2#LINE/      1 TGGAAAGATATCC-CATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_168714846_   3368 TATTAGTTCTTCCCAACTTAATCTATAGATTCAATGAAATCTCAATCAAA 3417
                          ivi i v  i     v  i     i        i v    i v      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_168714846_   3418 ATCCCAGTCAGTTATTTTGTGGATATCAACAAACTGATTCTAAGTTTTGT 3467
                                iiivi v     ii  v  ii    i     i    iv  ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_168714846_   3468 ATGGAGAAGCAAAGAGCCCAGGATAGCCAACACAATAT---AAAAGAAGA 3514
                              i v    i ii     i        v     v ---         
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_168714846_   3515 ACAAAGCTGGAGGACTGACACCTCT-GACTTTAAGACTTACAATAAAGCT 3563
                               i         v    i  i-i i  i  i      v i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_168714846_   3564 GCAGTAATCAACACAGTGTAGTACTAGTGAAAGAATAGACATGTAAAACA 3613
                         i          v       i     i iiv   i        i  i v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_168714846_   3614 ATAAAATAGA-------GCCCAGAAACAGACCCATATAAATACAGTCAAC 3656
                           ii      ------- i       i i       i vv  ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_168714846_   3657 AGATCCTTGACAAAGATACAAAGGCAAT---ATGGTGGAGCAAAGAGTTT 3703
                         v   ii i     i i i v   i v  ---    -   ivi  v   i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCT 398

  chr1_168714846_   3704 TTTCAAAAAATTTTGCTGAAAAAACTGGACACCTACATGCTAAAAGATGA 3753
                               v    vv     ii v       i ? i      v   ii    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_168714846_   3754 ATATAGACACAAACCTCACACTCCTA-ATAAAAATTAACTCAAGGTGGGT 3802
                          vv i   v vv         - v  - i              ii   i 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACAC-CATATACAAAAATTAACTCAAAATGGAT 497

  chr1_168714846_   3803 AATAGACCCACA-----AAGCTGAAA-----AGACTCCTAAAAGTTAACA 3842
                         v ?     i v -----i    i   ----- i    i  i   vv    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_168714846_   3843 TAGGATAAAAACCTACATCACCCTGG--TACAGCAATAACTTTCTAGACA 3890
                             ?-iv   i  v i v   i   --  -i     iii  ii    i 
  L1M4_orf2#LINE/    548 TAGGN-GTAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATA 595

  chr1_168714846_   3891 CAACACCAAAGACATGATCCATGAAAGAAATAATCAATAAGG-GGACTTT 3939
                         ii        ii  ii v v ii       v   vi    iv-      i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_168714846_   3940 ATTAAAACTTAAAAGCTCT---GCT-CAGAAAAAAAAATTAA-AAAGTGA 3984
                           i    -      i  i ---   -  i ii v vv  i  -       
  L1M4_orf2#LINE/    646 ATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_168714846_   3985 GAAAACAAGTCACAGACTAGAAGAAAACAATTGCAAAAGAAACCCCACAT 4034
                         i  i    vi      v i i      i v       -----i vi i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-----TCATATAT 739

  chr1_168714846_   4035 CTTATAAAGAACTGTTATCCAAAATACACAAAAATACTCTTAAAACTCAA 4084
                           v    i i   vv      i    i i   i -       v       
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGA-ACTCTTACAACTCAA 788

  chr1_168714846_   4085 CAA------GA--AACAACTCAATTAAAAAATGAGAAAAATACCTGAACA 4126
                         i  ------  --  i   i     ?       i v   iv ii    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_168714846_   4127 GCC---TTACCAAAGAGGATAAACAGATGACAAGTAAGCCTATGAAAAAG 4173
                          v --- iv       i    v   i   i v i     vi       - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-G 887

  chr1_168714846_   4174 ATGTTCAACATCATATTACAT 4194
                            i         ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (148 / 69)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.38 (57 / 24)  


3163 26.39 1.22 0.55  chr1_168724815_168732110     5902  6803 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_168724815_   5902 TGGAAAAACATTCCATGCTCCTGGATAGGAAGAATCAATATCATGAAAAT 5951
                               i i  i     i  v     v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168724815_   5952 GGCCATAGTGTCCAAAGTAATTTATAGATTCAGTGCTACCTCTATCAAGC 6001
                            v   v vi     v i  i  i       ii  v i i       iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168724815_   6002 TACCA-CTGACTTTCTT-CAAAGAATTAGAAAAAACT-ACTTTAAATTTC 6048
                          v   -   v    i  -  i -    i-- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_168724815_   6049 ATATGGAAACCAAAAAGAGCCCATGTAGCCAAGACAATCCTAAGCAAAAA 6098
                                  ivv  ii  v  vivi       i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_168724815_   6099 GAACAAAGCTGGAGGCCTCATACTACCTGACTTCAAATTATACTACAAGG 6148
                                 i      v    i   v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_168724815_   6149 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 6198
                                  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_168724815_   6199 CAATGAAACAGAACAGAGGCCTCAGAAATAACGCCAGACATCTACAACCA 6248
                              i  i    iv   ivii         vv   v    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_168724815_   6249 TCTGATCTTTGACAAACCTGACAAAAACAAGCAAGGGGGAAAGGATTTCC 6298
                         vi    i  i     ivv  v   i v  vv   v        i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_168724815_   6299 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 6348
                          v  i  i        i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_168724815_   6349 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACCCAAGATGGAT 6398
                           ii         v   i     v               i   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_168724815_   6399 TAAAGACTTAAATGTAAGACCCAAAACCATAAAAACCATAAAAGAAAACC 6448
                         i ?    i           v i     i      vi v  i        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_168724815_   6449 CAGGCA-ATACCATTCAGGACAT------GGGCAAAAACTTCATGACTAA 6491
                         i   ?i- v i -   iv   v ------i     viii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_168724815_   6492 AACACCAAA-GCAATGGCAATAAAAGCCAAAATTGACAAATGGGATCTAA 6540
                         i        -   vvi    i     vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_168724815_   6541 TTAAACTAGAGAGCTTCTTCACAGCAAAAGAAACTATCATCAGAGTGAAC 6590
                          i   v vi i i   i vii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_168724815_   6591 AGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTACCCATCTGACAA 6640
                           i     i       i         v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_168724815_   6641 AGGGCTAATATCCAGAATCTACAAAGAACATAAACAAATTTACAAGAAAA 6690
                         i  i  vi          v  i       vivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_168724815_   6691 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGTTATGAACAGACACTT 6740
                          i -    i     v  i?    i          v v    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_168724815_   6741 CTCGAATGAAGACATTTATGTAGCCAACAAACATATGAAAAAAAGCTCAT 6790
                            v  v     i  vi vi i     i  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_168724815_   6791 CATCACTGGTCAT 6803
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2413 26.53 1.17 0.29  chr1_168736674_168738348      497  1182 (493)    L1M4_orf2#LINE/L1      217   908 (0)  

  chr1_168736674_    497 ACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGC 546
                           i  v  ii i      viv        i          i   i    i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr1_168736674_    547 ATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGA 594
                         i         i iv ii i   v                i    i--   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr1_168736674_    595 GCCCTCAGAAATAACGCCGCATATCTACAACTGTCTGATCTTTGACAAAC 644
                          i  --        vv  ii i  i  iiiiiivi    i  i     iv
  L1M4_orf2#LINE/    317 GTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_168736674_    645 CTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGC 694
                         v  vv  i v  vv            i  vvi  v  i  i         
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_168736674_    695 TGGGAAAACTGGCTAGCCATAGGTAGAAAGCTGAAACTGGATCCCTTCCT 744
                              v      v  ?   i v i i  iiv    ii    i    v   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_168736674_    745 TACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTA 794
                         i     v              i    i      i ?    i    i  v 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_168736674_    795 GACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGACATTACCATTCAG 844
                           v       i      vi i           v   i?i v viv   iv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_168736674_    845 GACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGC 894
                            v v  vv i     v ii   v ivv  vi            vvi  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_168736674_    895 AACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCT 944
                                 vv     v  i    v   ii v  i   v v  i i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_168736674_    945 GCACAGCAAAAGAAACTAGCATCAGAGTGAACAGGCAACCTACAAAATGG 994
                          ii vv    i  v    v  vv i      v  i     i   i     
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_168736674_    995 GAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAAT 1044
                                 v  i    vii ivi      i  i  i  vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_168736674_   1045 CTACAATGAACTCAAACAAATTTACAAGAAAAAAACAA----CTCCATCA 1090
                         v  i  v      vv    v iv i  v     i    ---- i v  i?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_168736674_   1091 AAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGAGATTTAT 1140
                             i           iv    i     i     v        v  vi v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_168736674_   1141 GCAGCCAAAAA--ACATGAAAAAATGCTCACCATCACTGGCCAT 1182
                         iii     v  --         i       v     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (102 / 76)
Gap_init rate = 0.01 (4 / 692), avg. gap size = 2.50 (10 / 4)  


3385 25.77 0.55 0.55  chr1_168756127_168762406     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_168756127_   4880 TGGAAGGACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              i  i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168756127_   4930 GGCCATACTGCCCAAGGTAATTCACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  ii          i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168756127_   4980 TACCAA-TGCCTTTTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5026
                          v   i-          -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_168756127_   5027 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 5076
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_168756127_   5077 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5126
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_168756127_   5127 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5176
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_168756127_   5177 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5224
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_168756127_   5225 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5274
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_168756127_   5275 CCTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGC 5324
                         i  v  i  i              v  i   v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_168756127_   5325 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5374
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_168756127_   5375 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5424
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_168756127_   5425 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5474
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_168756127_   5475 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5524
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_168756127_   5525 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5574
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_168756127_   5575 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5624
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_168756127_   5625 AAGGGCTGATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5674
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_168756127_   5675 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5724
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_168756127_   5725 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5774
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_168756127_   5775 CATCACTGGCCAT 5787
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (136 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2962 27.11 1.56 0.78  chr1_168775367_168778767.rev     2011  2910 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_168775367_   2011 GAAAAAACATCCCTTGCTCATGGATAGGAAGAATCAATATTGAAAAAATG 2060
                          i   i i     v  i        v      v i       vv  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_168775367_   2061 GCAATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCC-TCAAGCT 2109
                                 v      v i  i  i        i  v     i-    iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_168775367_   2110 ACCA-TTGACTTTCTT-CACAGATTTAGAAAAAACT-ACTTTAAATTTCA 2156
                         v   -i  v    i  -  v i   ---i v  i  - iii    v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTCA 148

  chr1_168775367_   2157 TATGAAACCAAAAAAGAGCCCATATAGCCAAGACAAGCGTAGGCAAAAAG 2206
                             i  viiv  ii  v  viv        i    v v iiiv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_168775367_   2207 TACAAAGCTGGAGGCATCATGCTGCCTGACTTCAAACTATACTACAAAGC 2256
                         v      i      vv   ii  v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_168775367_   2257 TTTGGTAACCACAACAGCATGGTACTGGTACCAAAACCGATATACAGACC 2306
                          vii    i  vi    ii         i iv ii iv  i   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_168775367_   2307 AATGGAATAGGACAGAGGCCTCAGAAATAATGCCACACATCTACAACCAG 2356
                                   i iv   ivii         vv   i    i  iiii  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_168775367_   2357 CTGATCTTTGACAAATCTGACCAAAAAAAAGCAATGGGGAAAGGATTCCC 2406
                         i    i  i     ivv  -    i vv vv            i  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_168775367_   2407 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAGACTG 2456
                          v  i  i        i     v      v  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_168775367_   2457 AAACTGGACACCTTCCTTACACCTTATACAAAAATTGACTCAGGATGGAT 2506
                           ii     v   v   i     v            i     ii      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_168775367_   2507 TAAAGACTTAAACACAAGACCTAAAAGCATAAAAACCATAGAAGGAAACC 2556
                         i ?    i    iii    v      vi      vi v      i    v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_168775367_   2557 TAGGCA-ATACCATTCAGGACATAGGCATGGAGAAAGACTTCATGACTAA 2605
                             ?i- v i -   iv   v v  vv i iv  v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_168775367_   2606 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTAA 2655
                         i            vvi          vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_168775367_   2656 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAA 2705
                          i   v v  i i   i  ii vv    i  v       vv i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_168775367_   2706 AGGCAACCTATAGAATGGGAAAAAAATTTTTGCAATCTACCCATCTGACA 2755
                           i     i i         i    - v       vii ivi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATA 745

  chr1_168775367_   2756 AAGGGCTAATATCCAGAATTTACAAAGAACGTATACAAATTTACCAGAAA 2805
                          i  i  vi          v  i       viv     v iv iv v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_168775367_   2806 AA---AAA------AATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 2846
                           ---   ------   i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_168775367_   2847 CTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAAGCTCA 2896
                            v        i  vi viii     i  i  i       i v-     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCA 894

  chr1_168775367_   2897 TCATCACTGGTCAT 2910
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 1.75 (21 / 12)  


3312 24.92 0.99 0.99  chr1_168896966_168901941.rev     3590  4496 (480)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_168896966_   3590 GAAAAAACATCCCATGCTCATGGATAGGAAGAATTGATATCATTAAAATG 3639
                          i   i i        i        v      v  i    ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_168896966_   3640 GTTATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACT 3689
                          iv     v      vii  i           i  v  i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_168896966_   3690 ACCAATGACATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCATG 3738
                         v   iivi v  i  ii     v v  v  i-  -  ii          i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr1_168896966_   3739 TGGAACCAAAAAAGACCCTGAGTAGCCAAGGCAATCCTAAGCAAAAAGAA 3788
                              viiv  ii     v  i       ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_168896966_   3789 CAAAGCTGGAGGCATCATGTTACTCAACTTCAAACTATATTACAAGGCTA 3838
                              i      vv   iii v i   i      viv  i     i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_168896966_   3839 CAGTAACCAAAACAGCATGGTACTGATACAAAAACAGGCACATAGACCAA 3888
                               i   i    ii        ii i  ii i  i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_168896966_   3889 TGGAACAGAATAGAAAGCCAGGAAATAAGGCTACACATCTATAA-CAATC 3937
                              i     v  i  i vi       iv i i    i   ii-    -
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT- 349

  chr1_168896966_   3938 TGATCTTCGACAAAGCTGAAAAAAAGAAGCAATGGGGAAAAGACTCCCTA 3987
                             i        i v  vv  i vv vv           ii ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_168896966_   3988 TTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGACTGAA 4037
                              i              i      v  ?   i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_168896966_   4038 GCTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGGTGGATTA 4087
                          i         v   i                 i       ii     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_168896966_   4088 AAGATTTAAATGTAAAACCCAAAACAATAAAAACTCT-AGAATACAACCT 4136
                         ?   ii         i v i     v      -    -    v v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr1_168896966_   4137 AGGC---AATGCTATCCTGGACATAGGAAAAGGCAAAGATTTTACAACTA 4183
                            ?---   -  -  v  -  v v  ivv      v i   ivi iv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CT-TCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_168896966_   4184 AGACACCAAAAGCAATCA--CATCAAAAGCAAAAATTGACAAGTGGGATC 4231
                         v             --  --  v      v      v  i  i v   ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_168896966_   4232 TAATTAAACTTAAGAGCTTCTGCATAGCAAAAGAAAATATCAACAGAACA 4281
                          v  i   v    i i   i  iiivv    i  v v      v i iii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_168896966_   4282 AATGGACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCTGA 4331
                           vi       i                          ii  ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_168896966_   4332 CAAAGGTCTAATATCCAACATCTATAAGGAATTTAAACAAATTTACAAAA 4381
                         i  i  v  vi      iv  v     i   i ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_168896966_   4382 GAAAAACAAACAACCCCCATTTAAAAGTGGACAAAGGACATAAACAGAGA 4431
                         i   i     i     v-   ?    i   i       iv i  i   v 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_168896966_   4432 CTTCTCAACAGAAGACATACATCTGGTCAATAAACATATAAAAAAAGG-T 4480
                         i     v v      i     vv   i      i  i  i    i v - 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_168896966_   4481 GAATATCACTGATGAC 4496
                         v  i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (140 / 82)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 1.29 (18 / 14)  


2986 25.75 5.17 0.80  chr1_168932329_168936555     2865  3734 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_168932329_   2865 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 2914
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_168932329_   2915 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2964
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_168932329_   2965 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 3012
                          v   iivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_168932329_   3013 TATGCAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 3062
                             v  viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_168932329_   3063 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATATTACAAGGC 3112
                                i      vv    i  v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_168932329_   3113 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3162
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_168932329_   3163 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACAGATCTACA-CC 3209
                                i    i--    i  --        vv   i v  i  ii-i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_168932329_   3210 GATCTGATCTTCGACA---------------------------------- 3225
                         i  -    i       ----------------------------------
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_168932329_   3226 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3275
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_168932329_   3276 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 3325
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_168932329_   3326 ATTAAAGACTTAAATGCTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3375
                           i ?    i      iv   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_168932329_   3376 CCTAGGCAGTA--CCATTCAGGACACAGGCATGGGCAAGGACTTCATGAC 3423
                          v    ?-   --i -   iv   viv  vv i     v ii   v iiv
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_168932329_   3424 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATC 3473
                           vi            vvi          vv    iv  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_168932329_   3474 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 3523
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_168932329_   3524 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 3573
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_168932329_   3574 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 3623
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_168932329_   3624 AAAAAACAA----CCCCATCAACAAGTGGGCAAAGGATATGAGCAGACAC 3669
                             i    ----   v  i? v  i            v   ii     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_168932329_   3670 TTCTCAAAAGAAGACATTTATGCAGCCGAAAGACACGTGAAAAAATGCTT 3719
                              v        i  vi viii   i v ii   i      i     i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_168932329_   3720 ATCATCACTGGTCAT 3734
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (137 / 83)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 4.33 (52 / 12)  


3037 26.47 1.55 1.00  chr1_169004039_169008583     3150  4052 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169004039_   3150 TGGAAGAACATTCCATGTTCATGGATAGGAAGAATCAATATTTTGAAAAT 3199
                              ii i  i              v      v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169004039_   3200 GGCCATACTGCCCAAGGTAATTTATAGGTTCAATGCCATCCCCATCAAGC 3249
                            v     v     iv i  i  i  i     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169004039_   3250 TAACAATGACTTTCTTCACAGAA-TTGGAAAAAAACC-ACTTTAAAGTTC 3297
                          vv  iivi i  i  ii     -   --- v  i i- iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_169004039_   3298 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAA 3347
                                 viiv  ii  v  v v  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_169004039_   3348 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 3397
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_169004039_   3398 CTACAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 3447
                                  v   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_169004039_   3448 CAATGGGACAGAACAGAGGCCTCAGCAATAACACCACACATCTACAACCA 3497
                               i i    iv   ivii   v     vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_169004039_   3498 -TC--TCTTTGACAAACCTGACCAAAACAAG-CAATGAGGAAAGGATTCC 3543
                         - i-- i  i     ivv  -    i  v v-     i      i  vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_169004039_   3544 CTATTTAATAAATGGTGCTGGGAAAACTGGGTAGCCATATGTAGAAATCT 3593
                           v  i  i              v      i  ?   i   i i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_169004039_   3594 GAAACTGGATCCCTTCCTTACACCTTATAGAAAAATTAATTCAAAATGGA 3643
                            ii    i    v   i     v    v         i          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_169004039_   3644 TTAAATACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3693
                          i ? v  i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_169004039_   3694 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3742
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_169004039_   3743 AAACACCAAAAGCAACCACAACAAAAGCCAAAATTGACAAATGGGATCTA 3792
                         vi            vvvi         vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_169004039_   3793 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3842
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_169004039_   3843 CAGGCAACCTACAGAGTGGGAGAAAAATTTTGCATTCTACCCATATGACA 3892
                         v  i     i     i          vv      vvii ivi  v   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_169004039_   3893 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTTACCAGAA 3942
                          i  i  vi          v  i        ivv    --i i -- v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CTCA--ATAA 791

  chr1_169004039_   3943 AAAATAAACAAACAACCCCATCAAAAAGTGGGCAAAGCATATGAACAGAT 3992
                         v   v i     i     v  i?    i         v  v    i   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_169004039_   3993 ACTTCTCAAAAGAAAACATTTA--TG-----CAGACACATGAAAAAATGC 4035
                          i     v      i i  vi --  -----i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_169004039_   4036 TCATCATCACTGATCAT 4052
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


3143 27.08 1.33 0.55  chr1_169014544_169020940     5004  5904 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169014544_   5004 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCATGAAAAT 5053
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169014544_   5054 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5103
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169014544_   5104 TACCAATGACTTTCTTCACAGAC-TTGGAAAAAACT-ACTTTAAAGTTCA 5151
                          v   iivi i  i  ii    v-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_169014544_   5152 TGTGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5201
                          i     viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_169014544_   5202 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5251
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_169014544_   5252 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5301
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_169014544_   5302 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5349
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_169014544_   5350 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGAGGAAAGGTTTCC 5399
                          vi    i  i     ivv  vv  i v  vv     i      iv vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_169014544_   5400 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5449
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_169014544_   5450 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5499
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_169014544_   5500 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5549
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_169014544_   5550 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5599
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_169014544_   5600 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAA 5649
                         i            vvi          vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_169014544_   5650 TTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5699
                          i   v v  i ii  i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_169014544_   5700 AGGCAA-------AATGGGAGAAAATTTTTGCAA-CCTTCTCATCTGACA 5741
                           i   -------             v       -i v v -      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATA 745

  chr1_169014544_   5742 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5791
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_169014544_   5792 AAAACAAACAACCTCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5841
                           i     i    iv  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_169014544_   5842 CTGAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5891
                           vv        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_169014544_   5892 CATCACTGGCCAT 5904
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


1963 28.75 2.97 2.41  chr1_169041275_169043310      772  1477 (559)    L1M4_orf2#LINE/L1        1   710 (198)  

  chr1_169041275_    772 TGGAAGCAAATTCCATACTTATGGATAGGAATAATCAATATCATTAAAAT 821
                              iv v  i    ii i      v    v v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169041275_    822 GGCCATACTGCCTAAAGCAATTTGTAGACTCAATGCTATTCCTATTAAAC 871
                            v     v  i   vii  i ii   i    i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169041275_    872 TACCAGTAGTATTCTTCACAGAATTGGAAAAATCTAGTATAAAATTCAGA 921
                          v    iv iv  i  ii     v v  v  iiiv viv         v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_169041275_    922 TAAACCAA---AAATGATCCTGAATAGCCAAGGCCATCCTAAGCAAAAAG 968
                          ii --  ---  iv  i  v          ii v   i i iv  i   
  L1M4_orf2#LINE/    151 TGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_169041275_    969 AATAAAGCTGGATGCATCATGTTACCCAACTTCAAGCTATACTGCAGGGC 1018
                           i    i    v vv   iii v     i     iviv    i  ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_169041275_   1019 TACAGTCATCAAAACGGCATTGTACTGGTACAAAAACAGACGTATAGACT 1068
                               v     i  i ii v       i i  ii i    i      ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_169041275_   1069 AATGGAACAGAATAGAGAGCCCAGAAATAATGCTGCACACCTTCAGCCAT 1118
                                i     v     i          vv iii   ii vii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_169041275_   1119 CTAATTTTCAACAAAGCTGATAAAAGCATT----GGGGAAAGGACTCCCT 1164
                         i i      i    i v  vi  i v    ----        i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_169041275_   1165 ATTCCCTAACTGGACCTAGGATAACTGGCTAGCTATATGCAGAAGATTGA 1214
                         v   vvi  v   vv  i   i      v  ? i i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_169041275_   1215 AATTGGGCCCCTTCTTT-CACCATAAACGAAAATTAACTCAAGATGGATT 1263
                          i    i     v i i-       v  i             i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_169041275_   1264 AAAGACCTAAATGTAAAATCTATAAGTATAAAAACCCTGGAAGATAACTT 1313
                          ?              i v   v  v       vi i i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_169041275_   1314 AGGCG-ATACCATTCTGGACATAGGAATTTGCAAATATTTCCTGACGAAG 1362
                            ? - v i -   vv   v v  iv vv    vvi    i iivv v 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_169041275_   1363 ACGCCAAAAGCAATTGCAATAAAACCAAACCAGTGTCTATAAGGAACTTC 1412
                           i         vvv    i    vv   -- i ivv  v vv i     
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAA--AATAGATAAATTGGACTTC 645

  chr1_169041275_   1413 TTAAACAAATTTACAAGCAAAAAC----------CAAACAATCCCATTAA 1452
                         v ---    v   ------     ----------    vi iv i  i  
  L1M4_orf2#LINE/    646 AT---CAAAATTA------AAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_169041275_   1453 -AAAGTACACAAAGGACA-CACACAGA 1477
                         -     i---   i    - v      
  L1M4_orf2#LINE/    687 GAAAGTG---AAAAGACAACCCACAGA 710

Transitions / transversions = 1.33 (114 / 86)
Gap_init rate = 0.02 (13 / 710), avg. gap size = 2.92 (38 / 13)  

 311 13.64 3.03 0.00  chr1_169041275_169043310     1478  1543 (493)    L1M4_orf2#LINE/L1      841   908 (0)  

  chr1_169041275_   1478 CACTTCTCAAAAGAAGATA--CATCCAGCCAATAAGCATATGAAAAAATG 1525
                           i     v          --  vvii           i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_169041275_   1526 TTCAACATCACTAATCAT 1543
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (6 / 3)
Gap_init rate = 0.01 (1 / 68), avg. gap size = 2.00 (2 / 1)  


3177 26.44 1.33 0.88  chr1_169131919_169138296     4982  5885 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169131919_   4982 TGGAAGAACATTCCATGTTCATGGATAGGAAGAATCAGTATCATGAAAAT 5031
                              ii i  i              v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169131919_   5032 GGCCATACCGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATGAAGC 5081
                            v    iv     iv i  i  i        i  v   i i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169131919_   5082 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5129
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_169131919_   5130 TATGGAACCAAAAAAAGAGCATGCATTGCCAAGACAATCCTAAGTAAAAA 5179
                                viiv  ii-  v vv v  v     i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_169131919_   5180 GAACAAAGTTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGG 5229
                                        vv    v  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_169131919_   5230 CTACAGTAAGCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGAC 5279
                                  v   i    ii        ii iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_169131919_   5280 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5329
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_169131919_   5330 TCTGATCTTTGACAAACCTGACCAAAACAAG-CAATGGGGAAAGGA--AT 5376
                         vi    i  i     ivv  -    i  v v-            i --i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_169131919_   5377 CCTGATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAG 5426
                          i --  i  i              v      v  ?   i v i i  ii
  L1M4_orf2#LINE/    397 CTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_169131919_   5427 CTGAAACTGGATCCCTTCCTTATACCTTACACAAAAATTAATTCAAGATG 5476
                         v    ii    i    v   i i   v  i           i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_169131919_   5477 GATTAAAGACTCAAATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAA 5526
                            i ?    ii      v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_169131919_   5527 GC-TAGG--TAATACCATTCAGGATATAGGCATGGGCAAGGACTTCATGA 5573
                         i -    --   - i -   iv  iv v  vv i     v ii   v ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_169131919_   5574 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGAT 5623
                         v  vi            vvi          vv        i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_169131919_   5624 CTAATTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAGT 5673
                         i v  i   v v  i i   i  iiivv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_169131919_   5674 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTG 5723
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_169131919_   5724 ACAGAGGGCAAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAG 5773
                          i ii  i vvi          v  i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_169131919_   5774 AAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 5819
                              i    ----   v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_169131919_   5820 CTTCTCAGAAGAAGACATCTGTGCTGCCAACAGACACATGAAAAAATGCT 5869
                         i     vi       i  viiviiv     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_169131919_   5870 CATCATCACTGGTCAT 5885
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (148 / 88)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


4661 15.72 2.79 1.56  chr1_169158340_169160749     1021  1917 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169158340_   1021 TGGAAAGA-ACCCCATGTTTATAGATTGGAACACTTAATATTGTAAAGAT 1069
                                 - i        i  i        v            v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169158340_   1070 GAATATACTCCGCCAAACTGATCTACATATTTAATGTAATCC---TCAAA 1116
                          ivv       -     i         v   i  i i     ---     
  L1M4_orf2#LINE/     51 GGCAATACTCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_169158340_   1117 ATCCCAGATGCCATTTTTATAGAAATTTGCAATCATATCTTAAAATTTAT 1166
                                v    v     ii       vi   v vv   i       i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_169158340_   1167 ATTAAAATGCAAGAGATCCAGGATAGCCAAA-CAATCTTTAAAAAGAAGA 1215
                           vi         i  i    i         -       v          
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_169158340_   1216 ACGAAGTTGGAGGTCTCATACTTCTTGATTTTAAAACTAACTACAAAGCT 1265
                           i          v    i     iii    i      v           
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_169158340_   1266 ATGGT---CAGGACTGTGTGGTACTGCCATAAAGATAGACAAATAGATAA 1312
                          ii  ---  i   v           v     i        v      v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_169158340_   1313 ATGGAATAAAATTGAAAGTTCAGAAGTAAATTCTTATGTTTATAAACAAT 1362
                                 i      i   i     i    ii v  ii     iiv    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_169158340_   1363 TGATTTTTGACAAAGGCACCAAGACAGTTCAATGAGGAAAGAATAGTATT 1412
                                i     i  ii       vi       i            v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_169158340_   1413 TTCAATAAGTGGTACGGGGGCAGCTGCATAGATACATGCAAAAGAATGAA 1462
                              i  i    i v   i  i   v   ?vi                 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_169158340_   1463 TTTGTACCTCTTCCTCACACCATGTACAAAAAT-AACTCAAAATAGGTCA 1511
                         v   v   i  v           i         -          i i   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_169158340_   1512 AAGAGCTAAATGTAAGACCTAAAACCATAAAACTCTTAGAAGAAAACATA 1561
                         ?   v            v       i                        
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_169158340_   1562 GGTATAAAGCTTCATGACCTTGGATAAGGCAATGGTTTCTAAGATAGGAC 1611
                           ?i    v    i         i v              v     v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_169158340_   1612 ACCCAAAGCACAAACAACAAAAGGATA--TAGATAAATCAGTCTTCATAA 1659
                            v         i         i v --         ii v      v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_169158340_   1660 AAATTTTAAACTTTTGTTCCACAAAGAACACCATCAAGAACACGAAAAGA 1709
                              vv          v iv     i    i        vii       
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_169158340_   1710 CAACCCA-------------AATATTTGCAAATCAACAGATGAAGGATTA 1746
                                -------------               -------------  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCA-------------TA 736

  chr1_169158340_   1747 TGTCAGATAAGGGACTAGTATCTGGAATATATAAGGAACACTTAAAACTC 1796
                          i  v           v     ii          i    v    v     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_169158340_   1797 AACAATAAAAAGGCAAACACTCTAGTTGAAAAGTGAGCAAAAAGTTTCAA 1846
                           i         i    i vi i i  ?    i  i     iii   v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_169158340_   1847 TAGACATT-CTCTAAAGAAGATCTACAAATGACCAATAAACACATGAAAA 1895
                                 -   i         v        i       i          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_169158340_   1896 GATACTCAACATTATTTGTTGT 1917
                            i        i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (86 / 51)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.90 (39 / 10)  


3149 26.66 1.11 0.66  chr1_169292328_169298716.rev     4995  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169292328_   4995 TGGAAGAACATCCCATGTTCATGGGTAGGAAGAACCAATATCGTGAAAAT 5044
                              ii i               i v      vii     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169292328_   5045 GGCCATACTGCCCAAGATAATTTATAGATTCAATGCTATCCCCATCAAGC 5094
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169292328_   5095 CACCAATGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5142
                         iv   iivi i  i   i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_169292328_   5143 TAAGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAAG 5192
                           v    viiv  ii  v  viv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_169292328_   5193 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5242
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_169292328_   5243 TACAGTAACAAAAACAGCATGGTAATGGTACCAAAACAGAGATATAGACC 5292
                                 iv  i    ii     v   i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_169292328_   5293 AATGGAACAGAAC--AGAACCCTCAGAAATAATACCACACATCTACAACC 5340
                                i    i--   ii  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_169292328_   5341 ATCTGATCTTTGACAAACCTGACCAAAACAAG-AAATGGGGAAAGGATTC 5389
                          vi    i  i     ivv  -    i  v v-v           i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_169292328_   5390 CCTATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGC 5439
                         i  v  i  i          i   v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_169292328_   5440 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5489
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_169292328_   5490 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5539
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_169292328_   5540 CCTAGGCA-ATACCATTCAGCACATAGGCATAGGCAAGGACATCATGACT 5588
                          v    ?i- v i -   ivv  v v  vv       v iiv  v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_169292328_   5589 AAAACACCAAAAGCAATGGCAACAAAAGCTGAAATTGACAAATGAGATCT 5638
                          vi            vvi          vvi    v  i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_169292328_   5639 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5688
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_169292328_   5689 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5738
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_169292328_   5739 AAAGGGCTAATATCCAGAATCTACGAAGAACT---GAAATTTA-CAAGAA 5784
                           i  i  vi          v  ii       ---iv  i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_169292328_   5785 AAAATCAAACAACCCCATCAAAAAGTAGGGAAAGGATATGAACAGACACT 5834
                            iv    i     v  i?    i i  v       v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_169292328_   5835 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAGAAAATGCTCA 5884
                             v        i  vi viii     i ii       i  i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_169292328_   5885 TCATCACTGGTCAT 5898
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3184 26.46 2.13 0.34  chr1_169482932_169487144.rev     2831  3722 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169482932_   2831 TGGAAAGATATTCCATTTTCGTGGACTGGAAGAATCAATATTGTTAAAAT 2880
                                    i    v   i    i       v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169482932_   2881 GTCCATACTATCCAAAGTAATCTAAAGTTTCAATTCAACCTCTATCAAAA 2930
                          v v     vi     v i     v  v     iv   i i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169482932_   2931 TATCAATGACATTCTTCACAGAAATAGAAAAA--AATCCTCAAATTTATA 2978
                          vi  iivi v  i  ii       v  v  i--i     v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_169482932_   2979 TGGAACCACAAAAGACCCAGAATAGTCGAAACCATCCTAAGCAAAAGGAA 3028
                              vii   ii            i i    v   i i iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_169482932_   3029 CAAAACTGGACGAATCACATTATCTGACTTCAAATTATATTACAGAGCTA 3078
                             ii    v  v     i vi ii i      viv  i    i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_169482932_   3079 TAGTAACCAAAACAGCATGGTAATGGCATGAAAACAGACACATAGA-CAA 3127
                         i     i   i    ii     v      i ii i     i     -   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_169482932_   3128 TG-AACAGAATAGAGAACTCAAAAACTAATCCACACACCTACAATGAACT 3176
                           -  i     v    iii  i   iv  i   i   ii  iii v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_169482932_   3177 CATTTTTGACAAATATGCCAAGAATATACACTGAGGGAAAGACAGTCTCT 3226
                         v     i     ivi        vi  v  v  i  i  ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_169482932_   3227 TCAATA---GGGACTGGAAAAACTAAATACTCATATGCAAAATAATGAAA 3273
                             i ---  vi    i v    ii   ?i  i        v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_169482932_   3274 CTTGACCCATATCTCTTGCCATGTA-AAAAATCAGATCAAAATGGATTAA 3322
                         i v     v  i   vii    i  -      i iv           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_169482932_   3323 AGACTTTAATCAAAGACCTCAAACTATGAAACTACTACAAAAAAACATTG 3372
                             i v   vv    v  v       i     vi  v  i       v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_169482932_   3373 GAGAAACTCTCCCGGACATCGGTCTGGGTGGAAATTTCTTGGGTA--ATA 3420
                          ? v  v   i vv   v i  vi i  iiivii      i i  -- i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_169482932_   3421 TCCCACACACAGGCAACCAAAGCAAACATGGACAAACGGGATCCCATCAA 3470
                         i vv vi    i     v    v   v  i  i   iv   iii      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_169482932_   3471 G-TTAAAAAGCTTCTGTACAGCAAAGAAAACAATAAACAAAGTGAAGAGA 3519
                         i-       -   i   i vv     i v  v  v  v        i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_169482932_   3520 CAACCCACAGAATAGGAGAAGATACTTGCAAACTACCCATTTGATTAACA 3569
                                      i      i   i       ii ivi  i    v ivi
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_169482932_   3570 AC-------CAAAATATATAAGGAGCTGAAACAACTCCATAAGAAAAAAA 3612
                           -------  i         i  i  vvv       v    v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_169482932_   3613 ATCTAATAATCTGATTTAAAAATGGGCAAAAGATTTGAATGGACATTTCT 3662
                         -- v     i ii   ?             i         i         
  L1M4_orf2#LINE/    800 --CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_169482932_   3663 A-AAAGAAAACTTGCAAATGTCAAAGAGGTGTATGGAAAGGTACCCAACA 3711
                         v-      i iv i      v v  v i iii   i    i i i     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_169482932_   3712 TCATTGATCAT 3722
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.86 (151 / 81)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


3906 17.83 4.48 2.69  chr1_169492481_169496063.rev     2201  3092 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169492481_   2201 TGGAAAGATATCCCACATTCATGGATCAGAAAACTTGATATTGTTAAAAT 2250
                                        ii         ii   i    i          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169492481_   2251 GGGGATACTCCTCAAATTAATTTATGGATTCAATATAACGCCTAATAAAA 2300
                           vi       i      i  i  ii       iii  iv    vi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169492481_   2301 --ACAGCT---TTTTTCCCAGAAATTGACAAACTGA-CTTAAAAAAAAAA 2344
                         --v     ---     iv             i    - i     ------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA------ 144

  chr1_169492481_   2345 AACTCAT--GGAAATGAAAAAGTAGTAGAATAGCTAAAACAATCATCAAA 2392
                         --i    --       v  ii vvvi        i         v v   
  L1M4_orf2#LINE/    145 --TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_169492481_   2393 AAGAA---CAAAATTGGGGGACTTAC--TTTACTATTTCAAAATCTTACT 2437
                              ---    i    i     i  --  iv v         -      
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA-CTTACT 241

  chr1_169492481_   2438 GCAAAGCTACAGTAATTAAGACAGTGTGATACAGGCATCAGGATAAGCAT 2487
                         i               i           i   v     v      ii   
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_169492481_   2488 ATAGATCAATGGAATAGAAATGAGAGTCTAGAAATAAACCTTTACATTTA 2537
                                            v        i           iv        
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_169492481_   2538 CAGTTAACTGATTTTTGACAAGTGTATCACGACAATTCAAAGCAAACTAA 2587
                         ii  i  i       i      v  ii  v   v      ----------
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA---------- 381

  chr1_169492481_   2588 ATGAGGACAGAATAGTTTGTTTCAACAAATGGTGCCCGGACAACTAGCTA 2637
                         -  i   v        i -                iv        i v  
  L1M4_orf2#LINE/    382 -TGGGGAAAGAATAGTCT-TTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_169492481_   2638 ACCACATGTAACAGAATTACATTGGACGCTTCCCTCACA----------A 2677
                         ?       i  v     v vi      v i v       ---------- 
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_169492481_   2678 AGTTAATTCAAAAAGTATAATAGACCTAAATATAATGGTTAATACCCTAA 2727
                          i    i      v v  v ?          i   vi i   v  iv   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_169492481_   2728 CATTATTAGGAGAAAACAAAGGATTGAACCCTCATGGCCTTAAATCTAGG 2777
                         v i v    i        v   ?v i  i i  i  i    iii -    
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGG 578

  chr1_169492481_   2778 CAATAGATTTCTAGATGTGACTCCAAAAGCATGAGCAA-AAAAGACAAAA 2826
                             i v  ii     i    v         ii     -      -    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAA 627

  chr1_169492481_   2827 ACAGATAAATTGGGCTTTATTGAAATTTAAAGCATATGTGCTTCAG-GAA 2875
                          i           i   i  ii     v   i v v         i- i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_169492481_   2876 AACAATCAAGACA-TGAAAAGACAAC--AAAAAGTAAGATAAAATATTTG 2922
                         v  v       v -            -- v i i ii  v          
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_169492481_   2923 CAAGTTGT-TATCTCATAAGGAACTTGTACCTTGAATATATAAAGAACTT 2971
                            i ii -     v      i       i iv                i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_169492481_   2972 TTACAACTCAATAATAAAAAGACAAGTAACCCAAT-----------CAAA 3010
                                                  i         -----------    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_169492481_   3011 GTTATATAAATACATATTTCTCCAAGAAACATATAAAAATGGCCAATAAG 3060
                          v-  v i    v i          ii  v     v              
  L1M4_orf2#LINE/    828 GG-ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_169492481_   3061 CACATGAAGGAATGCTCAACATTAGTCAATAA 3092
                                 iii           i ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (101 / 55)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.20 (64 / 20)  


2920 23.96 2.42 3.19  chr1_169568995_169570921      525  1434 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_169568995_    525 AGATATACTATGTTTATGGATCAGAAGATTCAATATTTAAAAGATATCAA 574
                               v i     i      ii     i i      vvv     iv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_169568995_    575 TTATACAAAAATTGATATATTGATTCTGTGTTATCTCAATCAAAATCTTA 624
                          vv v vv        v  iv     vii iv   i v         ii 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_169568995_    625 GTGAAATTTTTCGTAGAAACTGACAAGCTGATTCTAAAATTTACATATAA 674
                          ivivv     i i     i            i        i i  iv  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_169568995_    675 ATGCAAAAGATTGAGAATAGCCAA--CAATTTTTAAAAAGAAGAACAAAG 722
                               ii  iiv           --    i  v                
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_169568995_    723 TTGGAAGACTCATATTACCTGATTTTAAAAATGATATAGCTATAAAGCTA 772
                              i      i i v  ii    i    ---------  -  ---   
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAA---------CT-TA---CTA 242

  chr1_169568995_    773 TGATCATAAAGCTACAGTAATAAAGACAATAGAGTATTGATCTAAGGAGA 822
                         i------              v      i ivi   i  iiv      v 
  L1M4_orf2#LINE/    243 C------AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_169568995_    823 GACCTATAGAT-AATGGAATAAACAAGATAATTCAGAAATACACCTGCTT 871
                            v       -         i vvv  v i i        v   -- v 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CAT 334

  chr1_169568995_    872 TTATATATAATCAATTGATTTTCAGCAAAAGATGCCAAGGCAACTTAATA 921
                         vi  v   ii             ii   ii -       i v i i   i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGG-TGCCAAGACCATTCAATG 383

  chr1_169568995_    922 AGAAAATAATACACTTTTTAAACAAGTAGTCCCAGAACCATTGGTTATCC 971
                         i i   v    vv     i  -   i i  v ii i  v i   v  ?  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAA-CAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_169568995_    972 TTATGTAATAAG--TGAACTTTGACTTTTACCTTACACCATACACAGTAA 1019
                         vi   i  -   --    v  v   iii     i        i   iv  
  L1M4_orf2#LINE/    433 ACATGCAA-AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_169568995_   1020 TTAACTCTAAATGGATCACAGATCTAAAGGGAGAAGTTAAAACTATAAAA 1069
                                v          ?   i     v v ii  i             
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_169568995_   1070 TTCTCAAAGAAAATATATAAGAGAAAATCTACATGAATTTTTATTTGGCA 1119
                         i   i i ii   - i   i ? v      v i   vi  vvi  v    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAA-ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_169568995_   1120 GTAACTT-TTATATACAAAACCAAAAGCATAATCAATAAAAGAAAAAGTA 1168
                         i iii  -   v   ii v          i  v   i          i  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_169568995_   1169 AATCAA----ACTTTATTTAAATTAAAAGTTTT---GCTTTGTGAAAAAT 1211
                         i  v  ----    i  iv         ii   ---    ii--  ii i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGAC 678

  chr1_169568995_   1212 ACTGGTAAGCAAATGAAAAGAAAACTCACAGACTGGGAGAAAATATTTTC 1261
                            ivi   v  i        v   i      v               v 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_169568995_   1262 CAATTAAATATCTGATAA----TTTATTTCTAGAATATACGAAACAACTT 1307
                         v   i v           ----i  i v  i        i-   v    i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT-AAAGAACTC 777

  chr1_169568995_   1308 TTAAAATTCAACAA-AAGGGAACAAATATCCTAATTTTTAAAATGGTCAA 1356
                            v  i    i  -  iiii       v  i    ?v-       v   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAA 826

  chr1_169568995_   1357 AAGATCTTAACATATACTTCACCAAAGAAAATATGTGGATGGCAAATAA- 1405
                          i   i v  i v i i   v        i    iiii     v     -
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_169568995_   1406 -ACATAAAAA--TGCATGATATCACTAGTTAG 1434
                         -    i    --   vii i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (136 / 78)
Gap_init rate = 0.02 (22 / 903), avg. gap size = 2.32 (51 / 22)  


 253 24.59 1.64 7.38  chr1_169577817_169582883.rev      379   500 (4567)    L1M4_orf2#LINE/L1      717   831 (77)  

  chr1_169577817_    379 GAAAACATTTTAAAACTATATGCCTGATAAAGGGTTAAGAGACAAAATAT 428
                              i    vv   ii    ii       i  ii viv vv  i     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_169577817_    429 TTAAAGTACTGCTACCACTCAGCAGCAATAAACAAACAAA-AACACACTT 477
                         v     v   vi   v     ---ii      v i     -   ------
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCA---ATAATAAAAAGACAAATAAC------ 807

  chr1_169577817_    478 CCACTTAAAAAGCAGG-AAAGGAT 500
                            v  ?    iii  -       
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.42 (17 / 12)
Gap_init rate = 0.03 (4 / 115), avg. gap size = 2.75 (11 / 4)  

2287 27.65 2.65 1.39  chr1_169577817_169582883.rev     1827  2618 (2449)    L1M4_orf2#LINE/L1        2   803 (105)  

  chr1_169577817_   1827 GAAAAAACACTTCATGCTTATAGATTAGAAGAATCAATATAGTTAAAATG 1876
                          i   i i iii    i i  i    i     v i     v     i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_169577817_   1877 GTCATACTACCCAAAGAAATGTACAAATTCAGTGCTATTCCTATAAAACA 1926
                          iv     v      vvi  v    i     ii  v  i     v   vv
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_169577817_   1927 ACCAGTATCATTTTGCACAGAAATAGAAAAAAACTC-TCCTAAAATTCAT 1975
                         v    ivv v    vii       v  v  i--  v-             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCAT 149

  chr1_169577817_   1976 ATGGAAC--CAAAAAATAAAACAAATAGTTAAAACAATACTACACAA-AA 2022
                               v--   iii ivv i--     ii        vi iv v  -  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAG--AATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_169577817_   2023 GAACAAAGCCAGAGGCATCACACTACCCGACTTTAAATTATACTATAAGG 2072
                                 iii    vv       v   i i  i   viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_169577817_   2073 CTACAGTAACCAAAACAGCATGGTGCTGGTACAAAAACAGACACATAAAC 2122
                                  i   i    ii    i    i i  ii i     i   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_169577817_   2123 CA-TGGAACAGAAAAGAAAACTCATAAATAAAGCTGCACACCTATAACCA 2171
                           -     i    vv  i iii  v       v iii   ii   iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_169577817_   2172 TCTGATCTTTGACAAGGCTAACAAAAACATGCAATAGGGAAAGA-T-GCC 2219
                         vi    i  i       v iv   i v   v    i        - - i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_169577817_   2220 TTATTCAATAAGTGGTACTACAATAACTGGCTACCCATATGCAGAAAAAT 2269
                           -     i  i    i  ivi i      v  ?   i     i  i   
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_169577817_   2270 AAAACTGGACCCACACCTTTCACCATATGCAAAAATTAACTCACGATGGA 2319
                         i  ii       vi    iv        i              vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_169577817_   2320 ATAAAGATTTAAATGTAAGACATCAAACTATAAAAATCCTAGAAGAAAAC 2369
                         vi ?   ii           vv v           v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_169577817_   2370 CTAGG---AAATACCCCATCTCAACATCAGCCTTGGCAAAGAATTTTTGG 2416
                         v    ---    - ii i ---i  v ii vi v     v iv  i  i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGT---GACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_169577817_   2417 CCAAGTTCCCAAAAGCAACTGCAATAAAAACAAAAGTTGACAAGTGAGA- 2465
                         vi v viv         vvv    i    iv    i v  i  i vi  -
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_169577817_   2466 ---A-CAAA--TGAAAGAGCTTGTGCATAGCAAAATAAACTATCAACAGA 2509
                         --- -    -- i   ivvi      v --    iv v        v i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAA 690

  chr1_169577817_   2510 GTAAACAGACAACCTACAGAATGGGAGAAAATATTTTCAAACTATGCATT 2559
                           i  v        i                     v    ii  ii  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_169577817_   2560 CAACAAATTTCTAATATTTAGAATCTACAAGGAACTT----AAATCAACA 2605
                         ii i  ivvv  vi   ii     v  i  i     i----  v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_169577817_   2606 ACTGAAAAACAAA 2618
                          ivi   i     
  L1M4_orf2#LINE/    791 ATAAAAAGACAAA 803

Transitions / transversions = 1.71 (137 / 80)
Gap_init rate = 0.02 (17 / 802), avg. gap size = 1.88 (32 / 17)  

3246 26.73 0.44 0.55  chr1_169577817_169582883.rev     2802  3710 (1357)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169577817_   2802 TGGGAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2851
                            i ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169577817_   2852 GGCCATACTGCCCAAGGTAATTTATAAATTCAATGCCATCCCCATCAAGC 2901
                            v     v     iv i  i  i i      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169577817_   2902 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 2950
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_169577817_   2951 ATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAGA 3000
                               viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_169577817_   3001 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 3050
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_169577817_   3051 ACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 3100
                                iv  i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_169577817_   3101 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACCA 3148
                               i    i--    i  --        vv   i i  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_169577817_   3149 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 3198
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_169577817_   3199 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 3248
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_169577817_   3249 AAACTGGATCCCTTCCTTACACCATATACAAAAATTAATTCAAGATGGAT 3298
                           ii    i    v   i                    i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_169577817_   3299 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 3348
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_169577817_   3349 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 3397
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_169577817_   3398 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3447
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_169577817_   3448 TTAAACTAAAGAGCTTCTGCACAGCAAAACAAACTACCATCAGAGTGAAC 3497
                          i   v v  i i   i  ii vv    iv v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_169577817_   3498 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3547
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_169577817_   3548 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3597
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_169577817_   3598 AAAACGAACAACCCCATCAAAAAGTGGACAAAGGATATGAACAGACACTT 3647
                          i - i  i     v  i?    i   i        v    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_169577817_   3648 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 3697
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_169577817_   3698 CATCACTGGCCAT 3710
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  

 323 22.31 1.65 3.31  chr1_169577817_169582883.rev     4456  4576 (491)    L1M4_orf2#LINE/L1      790   908 (0)  

  chr1_169577817_   4456 AATAAATAAATAAGTAAATAAAT--AAAAATGGGCAAAGGACATGAACAG 4503
                               v i i  i   viv   --                iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_169577817_   4504 ATACTTCTCAAAAAAAAAAAAAATGCAAGCAGCCAAAAGGACATATGACA 4553
                          i i     v   i  i v --- i   iii     v i -  i    v 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATA---TACAAATGGCCAATAAG-CACATGAAA 885

  chr1_169577817_   4554 AAATGTTCATCATCACTAATCAT 4576
                          i   i   v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (18 / 9)
Gap_init rate = 0.03 (3 / 119), avg. gap size = 2.00 (6 / 3)  


2125 28.19 3.37 0.14  chr1_169608515_169610217      498  1210 (493)    L1M4_orf2#LINE/L1      173   908 (0)  

  chr1_169608515_    498 TAGCCAAGGCAATCCTAAGCAAAAACAACAAAGCAGGGGGCATCATGCTA 547
                                ii     i i iv  i  v       iv  i  vv   ii  v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_169608515_    548 CCTAACTTCAAACTATACTACAGGGCTACAGTAAACAAAACAACATGGTA 597
                           i  i      viv       ii          v   i   iii     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_169608515_    598 CTAGTACAAAAACAGACACATAGAAAAATGGAACAGAATAGAGGGCCCAC 647
                           i i i  ii i     i     vv       i     v   i i   v
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_169608515_    648 AAATAAGCCTACATAGTTGCAACCATCTGATCTTCAACAAAG-TGACAAA 696
                               i  i i i v  iiiii  vi    i   i    i -  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_169608515_    697 AACAAGCAATGGAGAAAAGACTCCCTATTCAATAAATAGTGCTGGGATAA 746
                          v  vv      i    ii ivvi  v     i    i         i  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_169608515_    747 CTGACTAGCCATATGCGGAAGATTGAAACTGAACCCCTTCCTTATACCAT 796
                            iv  ?   i    ii    v    ii  i      v   i i     
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_169608515_    797 ATACAAAAATCAACTCAAGATGAATTAAATACTTAAATAGAAAACCCAGA 846
                                   i       i   i  i ? v  i     iv  i v i i 
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_169608515_    847 ACTATAAAAACCCT-GAACAATACCAT---------TCT--G-AACATAG 883
                                  vi i -   v  - v   ---------   -- -i  v v 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAA-AACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_169608515_    884 GAATGGGCAAAGATTTCATGACGAAGATGCCAAAAGCAATTGTAACAAAA 933
                          iv i     v i    v iivv v  ii         vvv i       
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_169608515_    934 GCAAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGC 983
                          v      v  i    v   ii v  i   v v  i i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_169608515_    984 AAAAGAAACTGCTGAG----CGAACAGACAACCTACAGAATGGGAGAAAA 1029
                            i  v   iiii  ----i   v        i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_169608515_   1030 TTTTAGGAAACTATGCATTGGACAAAGGCCTAATAACCAACATCTACAAG 1079
                          v  v v   ii  ii  iv  i  i  v  vi  v   iv  v  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_169608515_   1080 GAACT--TA-AACTTA-CAGGAAGAAAACAAACAACCCCAT-AAAAAGTG 1124
                              --  -    i -i iv  i  i     i     v  -?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_169608515_   1125 GGCAAAGAACATGAACAGACACATTTCAAAAGAAGACATACATGCAGCTA 1174
                                i iv    i     iv i  v        i     viii  i 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_169608515_   1175 GAAAGCCTACGAAAAAA-GCTCAATATCACCGATCAT 1210
                         iv    vi i     i -      i    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (129 / 69)
Gap_init rate = 0.02 (12 / 736), avg. gap size = 2.08 (25 / 12)  


3220 26.93 0.66 0.44  chr1_169682325_169687827.rev     4107  5012 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169682325_   4107 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4156
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169682325_   4157 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4206
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169682325_   4207 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4253
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_169682325_   4254 ATATGGAACCAAAAAAGAGCCCGCATCACCATGTCAATCCTAAGCCAAAA 4303
                                 viiv  ii  v  v v  vi   viv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_169682325_   4304 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 4353
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_169682325_   4354 CTACAGTAACCAAAACAAAATGGTACTGGTACCAAAACAGAGATATAGAT 4403
                                  i   i   ivi         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_169682325_   4404 CAATGGAACAGAACAGAGCTCTCAGAAATAACGCCGCATACCTACAACTA 4453
                                 i    iv   vvii         vv  ii i ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_169682325_   4454 TCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCC 4503
                         vi    i  i     ivv  vv  i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_169682325_   4504 TATTTAATAAATGGTGCTGGGAAAACTGGATAGCCATATGTAGAAAGCTG 4553
                          v  i  i              v         ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_169682325_   4554 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 4603
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_169682325_   4604 TAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4653
                         i ?   ii    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_169682325_   4654 TAGGCATTACCATTCAGGACATAGGCGT---GCAAGGACTTCATGTCCAA 4700
                             ?i v viv   iv   v v  -  ---    v ii   v ivvi v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATAT 596

  chr1_169682325_   4701 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATTGGATCTAA 4750
                         i            vvi          vv     v  i        ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_169682325_   4751 TTAAACTAAAGAGCTTCTGCACAGCAAAACAAACTACCATCAGAGTGAAC 4800
                          i   v v  i i   i  ii vv    iv v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_169682325_   4801 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4850
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_169682325_   4851 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 4900
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_169682325_   4901 AATCAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 4950
                          iv    i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_169682325_   4951 TCAAAAGAAGACATATATGCAGCCAAAAAATACATGAAAAAATGCTCATC 5000
                           v        i   i viii     v  ii         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_169682325_   5001 ATTACTGGCCAT 5012
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2671 27.56 3.37 1.24  chr1_169726452_169730064.rev     2234  3122 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169726452_   2234 TGGAAACACATTCCATGATCACGGATAGGAAGAATCAATATTGTTAAAAT 2283
                               v i  i     v   i    v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169726452_   2284 GGCCATACTTCCAAAGCATG-TC-ATAGATTGAATGCTATTCCTATCAAA 2331
                            v     i  v  ii-  -  - i     v  i  v  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_169726452_   2332 TTACCAATGACATTTTTCATAGAA-TTAGGAAAAAATTATTCTAACATTT 2380
                         v v   iivi v     iii    -  --  v  iv v  i    v   i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTC 147

  chr1_169726452_   2381 ATTTAAAACCAAAAAAAGAGCTCA-AATAGCCAAGACAACCCTATGCCAA 2429
                           v ii  -- viv  i ii i  -         i    i i ivivv i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_169726452_   2430 AAGAACAAAGCTGGAGATATCACATTACTCAACTTCAAACTATGCTACAT 2479
                                   i     ivv     i v i   i      viv i     v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_169726452_   2480 GGCTACAGTAACTAAAACAACATGATATTGATACAAAAACAGAGATATAG 2529
                         i          ii  i   iii  i  i  ii i  ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_169726452_   2530 ACCAATGGAAT-GCATT-AGTTAACCCAGAAATAAAGTTGTACCCCCACA 2577
                          i         - v   -  -- ii           viii   viii ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAG--AGTCCAGAAATAAACCCATACATTTATG 343

  chr1_169726452_   2578 ACCATCTGATTTTTGACAAAACCAACAAAGAAAAGCAATGCGGAAGTGAC 2627
                         ii  vi       i     iiviiv   iivv vv     v    ivi i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_169726452_   2628 TCCCTATTCAATAAATGGTGCTAGGCTAACTGGCCAGCCATATGCAGAAG 2677
                         vvi  v     i          i  vi      vi ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_169726452_   2678 AATAGAACTGGATCTGTACCTTTCACCATATACAAAAATCAACTAAAAAT 2727
                            ii ii    i iv     iv                i    v     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_169726452_   2728 GAATTGAAGACTTAAATGTACAACCTAAAACTAAAAAAATTCTAGAAGAA 2777
                          i  ii?    i        vi v         v    v ii        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_169726452_   2778 AACCTAGGA-TACACCATTCTGGACATTGGCCCTGGCAAAGACTTCCTGA 2826
                            v    ?-  v i -   vv   v    viiv     v ii   i ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_169726452_   2827 GGAAGACTCCAAAAGCAATTGCAA--AAAAACAAATTTGACAATTTGGAC 2874
                         iv v   v         vvv    --   i v   v v  i  v      
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_169726452_   2875 CT------AATTGAAAGAGTTTCTGCATAGGGAAAGAAATAATCAACGGT 2918
                         i ------    i   ivv   v   v vi--  i  v iv     viiv
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAAA 690

  chr1_169726452_   2919 GTAACCAGATAATCTACAGAATAGGAGAAAATATTTGCAAACGACGCATC 2968
                           i vv   i  i i       i                  iv iii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_169726452_   2969 TAACAAAGGCCTAATATCCAGAATCTATGAGGAACT-------------- 3004
                          i i  i  v  vi          v   i i     --------------
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_169726452_   3005 -TAAACAAATCAAACAACCCCATTTAAAAATGGGCAAAGGATATAAACAG 3053
                         -    v i -    i     v   ?                 v i  i  
  L1M4_orf2#LINE/    791 ATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_169726452_   3054 ACACTTCTCAAAAGAATACATACACACAGCCAACAAGTATATGAAAAATT 3103
                            i     v      v i     v ii     i   i i       iv 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_169726452_   3104 GCTCAATATCACTAATCAT 3122
                               i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.41 (41 / 17)  


2818 27.98 0.98 1.75  chr1_169731314_169736568     3848  4762 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169731314_   3848 TGGAAAAACATTCCATCCTCATGGACAGGAAGAATCAATATCATAGAAAA 3897
                               i i  i    vi       iv      v i     ii vi i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169731314_   3898 GACCAGAGAGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 3947
                          i v v vvv      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169731314_   3948 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 3996
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_169731314_   3997 ATGGAACCAAAAAAGAGCCCGTATATGTCTTGGATATCCAAGACAATCCT 4046
                               viiv  ii  -   i---------- i   v    i      i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCA----------GAATAGCCAAAACAATCTT 188

  chr1_169731314_   4047 AAGCAAAAAGAACAAAGCTGGAGTCCTCACACTACTTGACTTCAAAGTAT 4096
                         i iv  i          i     vv        v iii i      iiv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_169731314_   4097 ATTACAAGGCTACAGTAACCAAAATATCATGGTCCTGGTACCAAAATAGA 4146
                          i     i          i   i i vii    v    i iv ii     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_169731314_   4147 CATGTAGAACAATGGAACAGAACAGAGGCCTCAGAAATAACACCACATAT 4196
                            i    v        i    iv   ivii         vv   i i  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_169731314_   4197 CTACAACCATTTGATCTTTGACAAACTTGACAAAAACAAGCAACGGGGAA 4246
                         i  iiii  v     i  i     ivv  v   i v  vv   i      
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_169731314_   4247 AGGATTCCCTATTTAATAAATGATATTGGGAAAACTGGCTAGCCATATGC 4296
                           i  vvi  v  i  i     i ii     v      v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_169731314_   4297 AGAAAACAGAAACTGGACCCCTTTCTTAGGCCTTATACAAAAATTAACTC 4346
                          i  i vv   ii         vi  i vi  v                 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_169731314_   4347 AAGGTTGATTAAAGACTTAAATGTAAGACCTAAAACCATACAAACCCT-A 4395
                           ii v   i ?    i           v       i   -    i  - 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTA 537

  chr1_169731314_   4396 GAAGAAAACTTA--TGTAATATCATTCAGGACATAGGCATAGGCAAAGAC 4443
                                  v  --?    -   -   iv   v v  vv       v ii
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_169731314_   4444 TTCATGACTAAAACGCCAAAAGCAATTACAGCAAAAGCCAAAATTGACAA 4493
                            v iiv  vi  i         vvvi  i      vv     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_169731314_   4494 ATGGGATCTAATTAAACCAAAGGGCTTCTGCACAGCAAAACAAACTGTCA 4543
                           v   ii v  i   viv  iii   i  ii vv    iv v   i   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_169731314_   4544 TTAGAGTGAACAGGCAGCCTACAAAATGGGAGAAAATTTTTGCCGTCTAT 4593
                         vv i      v  i  i  i   i             v     vivii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_169731314_   4594 CCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAAT 4643
                         vi      i  i  i  vi          v  i  i     ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_169731314_   4644 TTACAAGAAAAAAACAAACAACCCTATCCAAAAGTAAGCAAAGGATATGA 4693
                         iv i  v     i     i     v  i?    i ii         v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_169731314_   4694 ACAGATACTTCTCAAAAGAAGATATTTA--TGCACCAACAAACATATGAC 4741
                          i   i i     v           vi --  -i    i  i  i    v
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATG-GCCAATAAGCACATGAA 884

  chr1_169731314_   4742 A---TACTGGTCATTAGAGAAATG 4762
                          --- i  viv   i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (152 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.08 (25 / 12)  


 654 21.93 4.39 5.70  chr1_169770155_169774934.rev      163   390 (4390)  C L1M4_orf2#LINE/L1   (524)   384   160  

C chr1_169770155_    390 AAGGGA-----AATAGCCAAAACAATATTGAGATA-AAGAATGAAGCTGA 347
                               -----               v    i v -     ii   i  i
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

C chr1_169770155_    346 AAGCATTACACAAGTTAATTTCAAATTATATTACAAAGCTATAGTAATAA 297
                          i vv i    vvvii         viv  i          i      v 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

C chr1_169770155_    296 AAACAGTATGATACTCGCATAAAAAGAGGTATATAAGCCAATGGAAAAGA 247
                          i     i  i    v      ii v  ii     iii        v   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

C chr1_169770155_    246 ATAGAGAAATCAATTAATCAATAGGAATTCACACATTTACAGTCAATTTT 197
                           v    ivi  i--  ---   --  ii  i       ii       vv
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAG--AA---ATA--AACCCATACATTTATGGTCAATTGA 352

C chr1_169770155_    196 TCTTTAACA-GGGTGAAGCCAAGATGGCCA---AATGG 163
                          i  ii   -     ---      ---   ---     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTG---CCAAGA---CCATTCAATGG 384

Transitions / transversions = 1.94 (33 / 17)
Gap_init rate = 0.04 (9 / 225), avg. gap size = 2.56 (23 / 9)  

3158 26.66 1.00 0.55  chr1_169770155_169774934.rev     3386  4289 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169770155_   3386 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3435
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169770155_   3436 GGCCATACTGCCCAAGGTAATTTATAGATTCACC---ATCCCCATCAAGC 3482
                            v     v     iv i  i  i       v ---     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169770155_   3483 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 3530
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_169770155_   3531 TATGGAACCAAAAAGAGCCC-GCATTGCCAAGTCAATCCTAAGCCAAAAG 3579
                                viiv  i ii   - v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_169770155_   3580 AACAAAGCTGGAGGCATCACGCTATCTGACTTCAATGTATACTACAAGGC 3629
                                i      vv    i  vi ii i     viiv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_169770155_   3630 TACAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGACATAAAGACC 3679
                                 v   i    ii         i iv ii i       v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_169770155_   3680 AATGGAAAAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 3727
                                v    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_169770155_   3728 ATCTGATCTTTGACAAACCTGACAAAAATAAGAAATGGGGAAAGGATTCC 3777
                          vi    i  i     ivv  v   i vi vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_169770155_   3778 CTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3827
                           v  i  i   i          v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_169770155_   3828 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTATTTCAAGATGGA 3877
                            ii    i    v   i     v             vi    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_169770155_   3878 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3927
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_169770155_   3928 CTAGGCA-ATACCATTAAGGACATAGGCATGGGCAAGGACTTCATGCCTA 3976
                         v    ?i- v i -  viv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_169770155_   3977 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTA 4026
                         vi            vvi          vv     v  i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_169770155_   4027 ATTAAACTAAATAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4076
                           i   v v  v i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_169770155_   4077 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 4126
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_169770155_   4127 AAGGGCTAATATCGAGAATCTACAATGAAGTCAAACAAATTTACAAGAAA 4176
                          i  i  vi    v     v  i  v   v  vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_169770155_   4177 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 4226
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_169770155_   4227 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 4276
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_169770155_   4277 CATCACTGGCCAT 4289
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


 462 29.61 0.66 0.00  chr1_169781590_169784318     1068  1219 (1510)    L1M4_orf2#LINE/L1        1   153 (755)  

  chr1_169781590_   1068 TGGAAA-ACATTCCATGTTGATAGCTAGGAAGAATAAATATTGTTAAAAT 1116
                               - i  i       v  i v v      v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169781590_   1117 GGCCATACGGCCCAAAGCAATTTACAGATTCGATTCTATTCCTATCAAAC 1166
                            v    vv      vii  i         i iv v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169781590_   1167 TACCAATTACATTCTTCACATAACTAGAAAAAACTATTTAAAAAATTGTA 1216
                          v   ii i v  i  ii  v  v v  v  iviv  iiv    v ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_169781590_   1217 AGG 1219
                         v  
  L1M4_orf2#LINE/    151 TGG 153

Transitions / transversions = 0.96 (22 / 23)
Gap_init rate = 0.01 (1 / 153), avg. gap size = 1.00 (1 / 1)  

2078 24.82 9.58 0.73  chr1_169781590_169784318     1548  2236 (493)    L1M4_orf2#LINE/L1      159   908 (0)  

  chr1_169781590_   1548 CAAAGAGTCT-GAATAGCCAAAGCAATACTATACAAAAAGAACAAAGCTG 1596
                            i iii i-           i    vi iv v  i          i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_169781590_   1597 GAGAAATTACATTATCCAACTTCAAACTTTACTACAGAGCTACAGTAA-C 1645
                            i v i   i vi    i      vi        i           - 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_169781590_   1646 AAAA---------------------ACAGACACACAGACCTACGGAACAG 1674
                           i --------------------- i     i i   i v i    i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_169781590_   1675 AATACAGAGTCT----------------------------TTG---TTTG 1693
                            vv      i----------------------------   ---  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_169781590_   1694 ACAAAGTTGACAATAACAAAGAATGAGGAAAGGACCTCCTGTTCAATTAA 1743
                             i v  v   v v  vvv    i      i ivvi  v     iv  
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_169781590_   1744 TGGTGCTGGGAAAGCTGGTTAGCCAAGTGCAGAAGATTGAAACTGGATGC 1793
                                    v i    v  ?   vi    i    v    ii    iv 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_169781590_   1794 CTTCCTTACAC-ATACACAAAAATCAACTCAAGATGCATTAAAGACATAA 1842
                           v   i    -   i        i       i   v  i ?    v   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_169781590_   1843 ATGCAAAACCTAAAACTATAAAATGCT-GCAAGAAAACCTAGAAAATAAG 1891
                            i  i v              iv  -iv        v   i?i-   i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG-TAAA 557

  chr1_169781590_   1892 TTTCTG-GACATTGGCCCTGGCAAAGAGTTCATAATGAAGACCCCGAAG- 1939
                          i ii -   v    viiv     v iv   v  ivv v   v  i  i-
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_169781590_   1940 -ACAATTGCAACAGAAACAATAATTGA-GAATGGGACCTAATTAAACTAA 1987
                         -    --      i  iv  v   v  -i   v    i v  i   v v 
  L1M4_orf2#LINE/    608 CACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_169781590_   1988 AGAGCTTCTGCACTGCAAAAGAAACTATCAACAGACTAAATAG----TCT 2033
                          i i   i  ii  v    i  v        v i v i  v  ----i i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_169781590_   2034 ACAGAATGGGAGAATATATTTGCAAATTATGGATCTGACAAAGGTCTAAT 2083
                                       v            i  iv      i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_169781590_   2084 ATCCAGAATCTATACGGAACT--TAATCAAATTATCAAGCAAAATACAAA 2131
                                  v    vi     --  --   v i vi  vv    v     
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAAAAGACAAA 803

  chr1_169781590_   2132 CAATCTCATTAAAAAGTGAGCAAAGGACATAAACAGACACATTTCAAAAG 2181
                         i  i iv   ?    i  i        iv i  i     iv i  v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_169781590_   2182 AAGACATACACATGGCCAACAAGCATATGAAAAAATACTCAACATCATTA 2231
                             i     v        i     i       i  i          ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_169781590_   2232 ATCAC 2236
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.39 (97 / 70)
Gap_init rate = 0.02 (15 / 750), avg. gap size = 4.73 (71 / 15)  


2327 21.20 10.02 0.83  chr1_169785794_169787384      500  1098 (493)    L1M4_orf2#LINE/L1      255   908 (0)  

  chr1_169785794_    500 AATAAAAACAGTATGGTAATGGCATAAAGGTCAATGTAAAGACCAGTGAA 549
                            v  i     i     v        i i vi ii  v   i  i  i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_169785794_    550 ACACAAT-GCAGGCAGAGCCCAGAAATAAATCCTCACATATTTG---AAT 595
                          i v   - -----    i           i  vi    v v  ---   
  L1M4_orf2#LINE/    305 ATAGAATTG-----AGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_169785794_    596 -GGTCTGTGACAAGATTGCCAAAGCTAC---------------------- 622
                         - i i vi      iv      ii i i----------------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_169785794_    623 ----ACAA-TGGTGTTAGGAAAACCAGACATCCATATGCAAGAGAATGAA 667
                         ----    -     i i   v   ii  i ?   i      i        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_169785794_    668 TTTAGACTCTTACTTTACATCATATACAAAATTTAACTTAAAACAAATGA 717
                         v  i   i i   i i   i           v      i    iii  v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_169785794_    718 AAGACCTAAATATAGAAGCTAAAACCATCAAACGCTTAAGAGAAAACA-A 766
                         ?          i  ii         i  v    v    ii        - 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_169785794_    767 AGGGCAAAACTTCATGATATTTGATTTAGAATTGATTTCTTGGATATGAC 816
                         i ? i   v    i   iv  v i  vi v v  i      i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_169785794_    817 ACTAAAAGCACAGGCAACAAAAGAAAAA-TAGACAAATTCGACTT----- 860
                           i         i               -    i     v     -----
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_169785794_    861 ---------------GTGCATCAAAGAATAATATCAACAGAATAAAAAGG 895
                         ---------------    v      i i v      v i i i     i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_169785794_    896 CAACCAATAAAATGGGAGAAAA-ATTTGCAAATCATACACTTGATAAGAA 944
                              v i i            -              i ii       ii
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_169785794_    945 ATTAGTATCCAGAGTGTATAGAAAACTCCTAAAATTCAACAATGAAAAAG 994
                          i v         i i    i i     i  v  i    i   i    ii
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_169785794_    995 CAA-----CCAACTCAAAAATAATCAAAAGACTTGAATAGACATTTCTCC 1039
                            -----    i ?      iiv    i  i                  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_169785794_   1040 AAAGAAGATATATGAATGGTTAAAAAGTACATGAAAAGATGCTCAATTTC 1089
                                     ii     ii  v   i                  iv  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_169785794_   1090 ACTAATTAT 1098
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.84 (91 / 32)
Gap_init rate = 0.02 (11 / 654), avg. gap size = 5.91 (65 / 11)  


2789 25.00 2.46 5.45  chr1_169790249_169792218.rev      544  1479 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169790249_    544 TGGAAAAGCATTCCATGCTCATGGATAGGAAGAATCAATACCATTAGAAT 593
                               iii  i     i        v      v i    iii   ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169790249_    594 GATTATACTGCCCAAAGCAAGTCACAGATTCAATGCTATTCCTGTCAAAT 643
                          iiv     v      vii vii          i  v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169790249_    644 TACCAATTACGTTCTTCACAGAACTAGAAAAAACT-ATT-TAAAATTTGT 691
                          v   ii i v  i  ii     v v  v  i-  -  i-       ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_169790249_    692 ATGGGACCTACCGTTTACTGCAAGTCCAGCAAAATAATTCATATGGAGTC 741
                             i ---------- -      --------------------   vi 
  L1M4_orf2#LINE/    150 ATGGAA----------A-TGCAAG--------------------GGACCC 168

  chr1_169790249_    742 AAGAAAGAGCCTGAATAGCCAAGGTAATCCTAAGCAAAAAGAACAAAGCT 791
                          -----------          iii    i i iv  i          i 
  L1M4_orf2#LINE/    169 A-----------GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_169790249_    792 GGAGACATCA-ATTTAACTGACTTCAAACTGTACTACAGCGCTACAGTAA 840
                             ivv   - i  v- ii i      viv       iv          
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTC-CCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_169790249_    841 CAAAAACAGCATGGTAGTGGTACAAAAACAGACACATAGACCAGTGGAAC 890
                         iv  i    ii     v   i i  ii i     i     i  i     i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_169790249_    891 AGAATAGAGAGCCAAGAAATAAGGGCACATACCTATGACCATCGGATCTT 940
                              v     i v        ivv  i i ii    ii  viv   i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_169790249_    941 TGACAGG---------------CAATGGGGAAAATATTCCCTATTCAATA 975
                         i    i ---------------           iv  vvi  v     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_169790249_    976 AATGGCACTGGGATAACTGGCTAGCCATATACAAAAGATTGAAACTGGAC 1025
                              ii      i      v  ?   i  i       v    ii     
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_169790249_   1026 CCCTTTCTTACCCCATATACAAAAATTAACTCAAGTTGGATTAAAGACTT 1075
                             vi  i  v                      iv     i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_169790249_   1076 AAGTGGATAACCCAAAACTATAAAAACACTGGAAGATCACCTAGGTAATA 1125
                           i  v vi v i            vivi i     vv  v    ?ivv 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_169790249_   1126 ATATCCTAGACATAGGAACAGGCAAAGATTTCATGACAAAGACACCAAAA 1175
                           v i vv   v v  ivi      v i    v iivv v          
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_169790249_   1176 ACAATCA--CAACAAAAGCAAAAATTGACAAATGGGATCTAATTAAA-TT 1222
                         i  --  --         v      v  i    v   ii v  i   -  
  L1M4_orf2#LINE/    607 GCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_169790249_   1223 AAAGAGCTTCTTTCTGTACAGTGAAAGAAATTATCAACATAGTCAACAGG 1272
                            i ----    -   i vvii  i  v i      v v   v  v  i
  L1M4_orf2#LINE/    655 AAAAA----CTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_169790249_   1273 TAACCAACAGAATGAGAGAAAATATTTGTAAACTATGTGTCTGAAAATGG 1322
                         i    v        i             i   ii  i i     v  v  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_169790249_   1323 TCTAATATCCAGCATCTATAGAGAAAT-TAACAAATTTATAAGAGAAAAA 1371
                         v  vi       v  v    i    v - v    v iv    v i   i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_169790249_   1372 CAAACAATCCTATTAAAAAGTGGGCAAAGGACATGGACAGACACTTTTT- 1420
                             i  i  v   ?    i           iv  i i     i  i i-
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_169790249_   1421 AAAGAAAACATACATGTGGCCAACAAGCATATGATGAAAAGTTTAATATC 1470
                               i i     vi       i     i    vi i v i i  i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_169790249_   1471 ACTGATCAT 1479
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.64 (143 / 87)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.35 (74 / 17)  


3108 27.35 0.78 0.55  chr1_169843214_169848348.rev     3742  4644 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_169843214_   3742 AAAAATCATCCCCTGCTCATGGATAGGAAGAATCAATATCGTTAAAACGG 3791
                            i  -     v  i        v      v i     i     i i  
  L1M4_orf2#LINE/      4 AAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_169843214_   3792 ---TACTATCTAAAGGGATTTACAGATTCAGTGCTATTCCTATCAAGCTA 3838
                         ---    vi i   vv   i          ii  v  i        iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_169843214_   3839 CCAATGACATTCTTCAAAGAACTAGAAAAATATATTTTAAAATTTATATA 3888
                            iivi v  i  iiv    v v  v  iivv  ii       i    i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_169843214_   3889 GAATCAAT--AAAGAGCCCA-AATAGCCAAGGCAATCTTAAGCAAAAAGT 3935
                            ---  --  i ii    -         ii       i iv  i   v
  L1M4_orf2#LINE/    153 GAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_169843214_   3936 TCAAAGCTGGAGCCATCATGTTACCCAACTTCAAACTATACTACAGTGCT 3985
                         v     i     vvv   iii v     i      viv       iv   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_169843214_   3986 ACAGTAACTGAAACAGAATGATACATGTACAAAGACAGACACATAGGCCA 4035
                                iii i    vi  i   vv i i  i  i     i    ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_169843214_   4036 ATGGAACAGAATACAGAACTCAGAAATAAGGCCACACAGCTACAACCATC 4085
                               i     vv   iii         iv   i   vi  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_169843214_   4086 TGATCTTTGACAAAGCTGATTAAAACAAGCAATGGAAAAAAGACTCACTA 4135
                             i  i     i v  viv i v  vv      ii   ii ivvv  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_169843214_   4136 TTCAATATATGGTGCTGGGATAACTGCCTAACCATATGCAGAATATTGAA 4185
                              i v            i     vv  ?   i     i  v v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_169843214_   4186 ACCTGACCCCTTCCTTACCCCATATACAAAAATCAACTCAAGATGGATTA 4235
                         iiiv       v   i  v              i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_169843214_   4236 AAGACTTAAATGGAAAACCTAAAGCTATAAAAACCCTAAAAGACAACCTA 4285
                         ?    i      v  i v     i        vi i  i    v   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_169843214_   4286 GGCA-ATACCATCCTGGACATAAGAATGGGCAAAGATTTCATGACAAAGA 4334
                           ?i- v i v  v  -  v vi iv i     v i    v iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_169843214_   4335 CACAAAAAGCAATTGCAACAGAAGCAAAAACTGATAAGTGGGATCTAATT 4384
                            v       vvv      i   v     iv     i v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_169843214_   4385 AAACTTAAGAGCTTCTGCACTATGAAAGAAACTATCAACAGAGTCAACAG 4434
                            v    i i   i  ii  vii  i  v        v i   v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_169843214_   4435 ACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCTGACAAAG 4484
                               i                          ii  ii      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_169843214_   4485 ATCTTATATCCGGCATCTATAGGGAACTTAAACAACTTTGCAAGAGAAAA 4534
                         iv   i     i v  v    ii     ivv      ivii  v i   i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_169843214_   4535 ACAAACCACCGCATTAAAAAGTGGGCAAAGGATATGAACAGACACTTATC 4584
                              iv   vv   ?    i            v    i     i  v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_169843214_   4585 TAAAGAAGACATACACGTGGCCAACAAGCATATGAAGAAAAGTTCAATAT 4634
                         i        i     vi       i     i     i i v i    i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_169843214_   4635 CACTGATCAT 4644
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (7 / 905), avg. gap size = 1.71 (12 / 7)  


3242 26.57 0.77 0.66  chr1_169854041_169860453     5014  5920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169854041_   5014 TGGAAGAACATTCCATGCTCATGAGTAGGAAGAATCAATATCGTGAAAAT 5063
                              ii i  i     i     ii v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169854041_   5064 GGCCATACTGCCCAAGGTAATTTATAGATTCAATATCATCCCCATCAAGC 5113
                            v     v     iv i  i  i        iiiv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169854041_   5114 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTCA 5161
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_169854041_   5162 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTTAATCCTAAGCCAAAAG 5211
                                viiv  ii  v  v v  v     ivi    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_169854041_   5212 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATACTACAAGGC 5261
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_169854041_   5262 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5311
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_169854041_   5312 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 5359
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_169854041_   5360 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5409
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_169854041_   5410 CTATTTAAGAAATGGTGCTGGGAAAACTAGG-AGCCATATGTAGAAAGCT 5458
                           v  i  v              v    i i- ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_169854041_   5459 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5508
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_169854041_   5509 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5558
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_169854041_   5559 CTA--CGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5606
                         v  --? i  - i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_169854041_   5607 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5656
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_169854041_   5657 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5706
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_169854041_   5707 ACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAGGCTACTCATCTGAC 5756
                          v  i     i                 v  i   iiii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_169854041_   5757 AAAGGGCTAATATCCAGAATCTACAAAGAACCCAAACAAATTTACAAGAA 5806
                           i  i  vi          v  i       i vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_169854041_   5807 AAAAACAAACAGCCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5856
                            i     i i   v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_169854041_   5857 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5906
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_169854041_   5907 TCATCACTGGCCAT 5920
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2759 22.85 10.53 2.27  chr1_169866455_169868310.rev      530  1365 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_169866455_    530 AAAGATATCCCATGTTTATTGGATCTGAGGAATCAATATTGTCAAAATAT 579
                                         i  -    iv  i  v i        i  i  iv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCAT-GGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_169866455_    580 CTATGCTACTCCAAGTTC-TCTAGAGATTCAATGCAATCCCTACCAAAAT 628
                          v  i  - i    i  v-    v        i          i      
  L1M4_orf2#LINE/     53 CAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_169866455_    629 TCCAA-TGGAATTTTCACAGAAATATAAAAAATAATCCTAAAATTAATAT 677
                         i   i-  vvv    ii       vv v  iv i           v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_169866455_    678 GGAATGACAAAAGACCCCAAATAGCTAAAGCAATCTGGAGCAACAAGAAC 727
                             vvi   ii     vi      i   i      v  iv  v      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_169866455_    728 AAAGCTGGAGGCATCACTCTTTTTCAATTT-AAAATTATATTACACACCT 776
                             i      vv    v   ii-      -    i -  i    v v  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCC-CAATTTCAAAACT-TACTACAAAGCT 249

  chr1_169866455_    777 CTAGTACTCAAAACAATATAGTACTGGCATAAAAATGAACACATAAACCA 826
                         vi    v    i   i i i            ii  ii   i   i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_169866455_    827 ATGAAACAGAATAGAAAGCCCAGAAATAAATCCACACATATATGGTCAAC 876
                            i  i     v  i  i           i   i    v         i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_169866455_    877 TAATCTTTGACAGAGGCTCATTGTCAAAGTATGCCTAGAATATATAATGA 926
                          i  i  i    ii  ---------------    v   vi  vi    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGG---------------TGCCAAGACCATTCAATGG 384

  chr1_169866455_    927 GGAAA-AATAATCTCTTCAATAAATGGTGTTGGGAAAACTGGATATCCAT 975
                              -    i   i     i        i     v         ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_169866455_    976 ATGCAAAAAGAGGAAACTGAGTTCTTAC--------------AATAATAG 1011
                                 ii v   ii  iiii i   --------------  v   vi
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_169866455_   1012 ACTCAAAATGGATTACAGA-----------------------------TT 1032
                                      i ?   ----------------------------- i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_169866455_   1033 TT---------CATA-----------TCG-----------------ATAT 1045
                           ---------    -----------   -----------------  iv
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_169866455_   1046 TTTTTTGTATATGACATCAAAAGCACAGGCAAGAAAAGTGAAAATAAACA 1095
                            i  iv        i          i    v     vi      i i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_169866455_   1096 AGCGGTACTATATTAAATTGAAAAGTTTCTGCACAGGAAAGAAAAAAATC 1145
                          iiv v   vi  i   v v    ii  i  ii vvv    i v vv   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_169866455_   1146 AATAAAATTAAAAAGCAACCCTAGGAATGG---AAAATATTTGTAAATCA 1192
                           v   i v    ii      vvi      ---          i      
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_169866455_   1193 TATATCTGATAAGGAGGTAATATCCAAAATATATAAAGACCTCATACAAC 1242
                                       iiv vi      i            v   v      
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_169866455_   1243 TCAATAGTAAAAAATCAAATAACCCAATT-AAAAATGGGGAAAGGACCTG 1291
                               i      iv              -         v      ii  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_169866455_   1292 AATAAATATTTTCCTAAGGAATAAATACAAATAGCTAACTGTTCTATAAA 1341
                             i i    ii i  i   v v        i  i  ivivivi  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_169866455_   1342 AAAGTGTTTGACATCAGTAATCAT 1365
                           ii  i ii      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (123 / 66)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 6.69 (107 / 16)  


2858 25.53 2.33 1.55  chr1_169937697_169939953      870  1770 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169937697_    870 TGTAAGAATATTTCATGCTCATTGATAGGAAGAATCAATATCATTAAAAT 919
                           v  ii    ii    i    v   v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169937697_    920 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 969
                            v     v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169937697_    970 TACCAATGACATTCTTCACTGAACTAGAAAAAACT-ATCCTAAAATTCAT 1018
                          v   iivi v  i  ii v   v v  v  i-  -              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_169937697_   1019 ATGGAACCAAAAATGAGCCAGAATAGCCAAGGCAATCCTAAACAAAAAGA 1068
                               viiv  iv  v             ii     i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_169937697_   1069 ACAAAGCTAGGGTAATCACATTGCCCAACTTCAAACTGTACTACAAGGCT 1118
                               i i i v v     i v     i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_169937697_   1119 ACAGTAACCGAAACAGCATGGTACTGGTATAAAAACAGACACATAGAACA 1168
                                i i i    ii         i    ii i     i     v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_169937697_   1169 ATGGAACAGAATAGACAGCCCAGAAATAAAGCTACACACCTACAACCATC 1218
                               i     v  v  i           v i i   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_169937697_   1219 TGATCTTTGACAAAGGTGACAAAAACAAGCAATGGTAAAAGGATTTCCTA 1268
                             i  i     i    v   i v  vv      vi    i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_169937697_   1269 TTCAATAAATGGTGCTGGGAAAACAGCCTAGCCATATGCAGAAGATTGAA 1318
                              i              v   v vv  ?   i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_169937697_   1319 A----ATCTC---CTTACACCATATCGAAAAATCAACTCAAGATAAATTA 1361
                         i---- i i ---  i         vv      i       i  ii  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_169937697_   1362 AAGACCTAAATGCAAAACTTAAAAATTTAAAAACCCTCGAAGATAACCTA 1411
                         ?           i  i vi     v v     vi i v     v   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_169937697_   1412 GGTG-ATACCATGCTGGACATAGAAAATGGCAAAGATTTCACAACAAAAA 1460
                           ? - v i v vv  iv v i ivv -     v i    vi ivv vi 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATATGA 598

  chr1_169937697_   1461 TGCCAAAAGCAATTGCAATAAA-GCAAAAATTGGCAAATGGGACCCTAAA 1509
                         ii         vvv    i   - v      v ii    v    iii --
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA-- 646

  chr1_169937697_   1510 GAAGCTCTTGAACTAACAAGCTTCTTCACAACAAAAGAAACTGTCAG--- 1556
                         -----  v-i  i   -  i   i vii vv    i  v   i   i---
  L1M4_orf2#LINE/    647 -----TCA-AAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_169937697_   1557 AGTAAACAGGCAACCTACAGAATGGGAGATAAATATCTGCAAACTCTACA 1606
                            i  v  i     i             -      i      iiv  i 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGA-AAATATTTGCAAATCATATA 738

  chr1_169937697_   1607 TCTGACAAATGTCTAATATCCAGAATGTACAAGAAACT--TA-AAC--AA 1651
                              i  iv v  vi          i  i  ii    --  -   --  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_169937697_   1652 ACATACAAGCAAAAACACTACCCCTTTAAAAAGTGGGCAAAGGACATGAA 1701
                         vv   v  iv v   i --    vv  ?    i           iv    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATA--ACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_169937697_   1702 CAGACACTTTTCAAAAGAAGACATACATGCGGCCAACAA--ACATGAAAA 1749
                         i     i  i  v        i     vii      i  --         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_169937697_   1750 -ATACTCAATATTACTAATCAT 1770
                         -  i     i  i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.94 (35 / 18)  


1973 28.64 4.70 3.13  chr1_169986381_169988292      527  1420 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169986381_    527 TGGAAGAGTATAATATGCTCATGAATTACAAAACTCAAAATTGTTACAAT 576
                              iii   vvi   i     i   iv  i   i  v       vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169986381_    577 GTCATTTCACCTCATATAGTTCTATAGACTCAGTTCAATCCCAACTTAAG 626
                          v  v v v  i  v  v v    i   i   iiv       v - i  i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAAA 99

  chr1_169986381_    627 AACCCAGCTAAGATTTGATTTGTTTTGTTTTGTA--AATTGAGAAGCAAA 674
                          v       ------------ ii  -     i --      v    vi 
  L1M4_orf2#LINE/    100 ATCCCAGCT------------GCCTT-TTTTGCAGAAATTGACAAGCTGA 136

  chr1_169986381_    675 TTCTAAAATGTATATAGAAATGTAAGAGACCTAGAAAAGCCAAGACAATC 724
                          i       vi    i      i   i    i    v      i      
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_169986381_    725 T---AACAGAAGAAAAAAACTGGCAGACATACACTGTCTGACTTCAAACC 771
                          ---  v       v   ii   vi   vi     vi ii i      v 
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_169986381_    772 --ATTATGAAACTGAAGAAATTAAGATACTGTGTAATATTGGCACAAGAA 819
                         -- i  ii  i  iv  v   i    i --    ii  i     i   i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACA--GTGTGGTACTGGCATAAGGA 284

  chr1_169986381_    820 TGGAGCA-ATGGTACA---GAATAGCTATTAAG---CAAGAAATATACCT 862
                          i  -  -  i vv  ---      v-   i  --- v       v   i
  L1M4_orf2#LINE/    285 TAGA-CATATAGATCAATGGAATAGA-ATTGAGAGTCCAGAAATAAACCC 332

  chr1_169986381_    863 ACACATATACAGTCACCTGATTTGTGTCAAAGACACTAA-----TTCAGT 907
                          i    v  ii    vi      vi v   i iii i  -----    i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_169986381_    908 CAGGAAAGTACAGTCAATTCAATAGATAGTGATGGATTCAGTGGATATCC 957
                         vi      v i    vv     i i  i   v   iviv v      ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_169986381_    958 ATTTTTGAAAT--TAACTTTAGACTCA-ATCT-GTGCTACATGCAAAAAC 1003
                          iv vii   v-- i vv  i   i v- i  -iii i i  i      i
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_169986381_   1004 TTATTCCAAATGAACCATAGACCTAAACGTGAAAGTTAAAACAATAAATA 1053
                          v i  v     i i  ?         i  i i  i      v     - 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-A 531

  chr1_169986381_   1054 TTCTAATAGAAAAAAATAAAAGAATC--TCTTTCTGAACTTGGGAAAGAC 1101
                         i   --     i    i v i ?i v--    iv   v      vv  i 
  L1M4_orf2#LINE/    532 CTCT--TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_169986381_   1102 AAACATTTCTTAAACAGGACATAAAATGCACTAACCATAAAA--AAAGAT 1149
                           vvi       i i v    iv   v    v i v i    --   i  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_169986381_   1150 TAATATATTGGACTTTCTTAAAATCAAGCA----TGTGTTGATCAAAAGA 1195
                         vi   v         iv i     i  iv ----    i --     i  
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGGA 677

  chr1_169986381_   1196 CACTATTAAGATAATGAAAATGCAAGAAACACAA--AAATAAGACAGTTT 1243
                               i    v i      vi   vvv   v  --ii v  i i -   
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA-TTT 726

  chr1_169986381_   1244 CCATA-CGTACATCTAACAAAGAATTATTATTTAGAATATATCTTCAACA 1292
                         v  v - i  i    i i  i i i vv   ii         vvvv   -
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC- 775

  chr1_169986381_   1293 TTTTATAAATTGGTATGGAAAAGAGAAAAAAATCCAAT--------GGAC 1334
                          i   i  v iii  vvi      v   v  -i     --------  i 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAA-CCCAATTWAAAAATGGGC 824

  chr1_169986381_   1335 AAAAAAGCCAAATCTAGTCATTTAATAAAAAAAGACATTGAAATAACTAA 1384
                            ii viii   --  v     vviv   i    i  vv    ii i  
  L1M4_orf2#LINE/    825 AAAGGATTTGAAT--AGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_169986381_   1385 TAAATATATTAAAATGTGCCCAGCATCCATAGTCAT 1420
                            ii i  v    vi   i  i    v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (153 / 100)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.41 (70 / 29)  


2654 27.30 4.78 1.48  chr1_169990415_169995171     3386  4264 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_169990415_   3386 TGGAGAAATATTCCATGCTCATGGATAGGAAGAATCAGTATTGTTAAAAT 3435
                             i i    i     i        v      v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_169990415_   3436 GGCCATACTGCCCAAAGCAATTTACTGATTTAATAGTATTCATATCAAAC 3485
                            v     v      vii  i   v    i  iivv  i v       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_169990415_   3486 TACCAA-TGTCATTTTTCACAGAA-------------------------T 3509
                          v   i-  i -     ii     ------------------------- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_169990415_   3510 ATGGAGTGAAAAAAGAGCCAAAA--GCCAAGGCAATCCTAAGCAAATAGA 3557
                              ivviv  ii  v   i  --     ii     i i iv  iv   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_169990415_   3558 ACACAGCCAAAGACATCATACTACCCAACTTCAAACTATACTATAAGGCT 3607
                            v  iiii  ivv   i   v     i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_169990415_   3608 ACAGTAACCAAAACAGCATAGTATTGGTATTTAATACAAAAACAGACCCC 3657
                                i   i    ii i   i   i  -------  ii i    vi-
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCAT-------AAGGATAGACAT- 291

  chr1_169990415_   3658 ACAGACCAACGGAACTGCATAGAAAACTTTGAAATAAAGCTGCACACCTA 3707
                          i   i   i    iv v  v  i iiiiv        v iii   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_169990415_   3708 CAACCATCTGATCATCAACAACACTGACAAAAACAAGCAATGAGGAAA-- 3755
                         iiii  vi    iv  i    viv  v   i v  vv     i     --
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_169990415_   3756 --AGACTCTTCAATAAATGGTGCTGGGATTACTGGCTAGCCATATGCAGG 3803
                         --  v  i     i              iv     v  ?   i     ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_169990415_   3804 AGATTGAAACCGGACCCCTACTTT-CACCTTATACAAAAATCAACCCAAG 3852
                            v    iii          i i-    v           i   i   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_169990415_   3853 ATAAATTAAAGACTTAAATTTAAGACCTGAAACTCTAAAAATCCTAGAAG 3902
                           ii  i ?    i     v     v  i     v     v  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_169990415_   3903 AAAACCTAGG---AAATACCATTCTGGACACTAGTCTTAGCAAAGAATTT 3949
                              v    ---    -- -   vv   vi i vi vi    v iv  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_169990415_   3950 ATGACTAAGTCCCCAAAAGCAATTGCGATAAAAATGAAAATTGACACATG 3999
                         v iiv  v v v         vvv  i i    ivi     v  i v  v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_169990415_   4000 GGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACA 4049
                             i v  i   v v  i i   i  ii vv    i  v        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_169990415_   4050 GAGTCAACAGGCAACCTACAGAATGGGAGAAAATATCTGCAAACTATGCA 4099
                         i   v  v  i     i                   i      ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_169990415_   4100 TCTGACAAAGGTCA-ATATTCAGAATCTATAAGGAACTT----AATGCAT 4144
                              i  i  v v-i   i      v     i     i----  iv  v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_169990415_   4145 CAAGCAGAAAAACAAATAACCCTGTGAAAAAATGGGTAAAGGACATGAAT 4194
                         i  -i i   i           vi v?         i      iv     
  L1M4_orf2#LINE/    789 TAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_169990415_   4195 GGACACCTCTC-AAAAAAGACACACATGAAGCCAACAAATATATTTAAAA 4243
                         i    ii    -   i    i i   vivi     i  ii i  vv   i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_169990415_   4244 ATGCTCAACATCACTAACTAT 4264
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (150 / 87)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.67 (55 / 15)  


2999 27.37 1.79 0.34  chr1_170020294_170029061     1343  2237 (6531)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170020294_   1343 TGGAAAAACATTTCATGCTCATGGATAGGAAGAATCCGTATTGTGAAGAT 1392
                               i i  ii    i        v      v ivi      v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170020294_   1393 GGTCATGCTGCCCAAAGTAATTTATAGATTCATTGCTATTCCCAATAAGC 1442
                           iv  i  v      v i  i  i       vi  v  i  i vi  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170020294_   1443 TACCAGTGACTTTCTTCCCAGAATTAGAAAAAAGCT-ACTTTAAATTTCG 1491
                          v    ivi i  i  iv     v v  v  --   - iii    v   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr1_170020294_   1492 TATGGAACCAAAAAAGAGCCCATATAGCCAAGAAAATCCTAAGCAAAAAG 1541
                                viiv  ii  v  viv        i v    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_170020294_   1542 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1591
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_170020294_   1592 TACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGATATATAGACC 1641
                                 i   ii   ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_170020294_   1642 AAAGGAACAGAACAGAGGCTTCAGAAATAACACCACACATCTACAAACAT 1691
                           v    i    iv   iv i         vv   i    i  iiiv  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_170020294_   1692 CTGATCTTTGACAAACCTGTCAGAAACAAGCAATGGG-AAAGGATTCCCT 1740
                         i    i  i     ivv  i  ii v  vv       -    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_170020294_   1741 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 1790
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_170020294_   1791 AACTAGACCCCTTCTTTATACCTTATACAAAAATTAATTCAATATGGATT 1840
                          ii i       v i i i   v              i    v      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_170020294_   1841 AAAGACTTAAATGTAAAACCCAAAACCCTAAAAACCCTAGAAGAAAACCT 1890
                          ?    i         i v i     iv     vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_170020294_   1891 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGAGTTCATGACTAAA 1939
                            ?i- v i -   iv   v v  vv i     v iv   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_170020294_   1940 ACACCAAAAGCAATAGCAACAAGAGCCAAAATTGACAAATGGGATCTAAT 1989
                                     vv        i  vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_170020294_   1990 TAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTATCATCAGAATGAACA 2039
                         i   v v  i i   i   i vv    i  v       vv i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_170020294_   2040 GGCAACCTACAGAATGGGAGAAAATTTTTGCAAGATACCCATATGACAAA 2089
                          i     i                 v       ivi ivi  v   i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_170020294_   2090 GGTCTAATATACAGAATCTACAAAGAACT--TA-AATTTA-CAAGAAAAA 2135
                           v  vi   v      v  i        --  -  i i -i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_170020294_   2136 ---AAA-AACC--ATCAGAAAGTGGGCAAAGGATATCAACAGACATTTCT 2179
                         ---   -    --  i?i   i            v v  i          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_170020294_   2180 CAGGAGAAGAGATTTATGCAGCCAATAGATATA-AAAAAG--GTTCATCA 2226
                          vii      v  vi viii       iii i -i     -- i   v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_170020294_   2227 TCACTGGTCAT 2237
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  

3140 26.88 2.02 0.34  chr1_170020294_170029061     7383  8275 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170020294_   7383 TGGAAGAACATTCCATACTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 7432
                              ii i  i    ii      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170020294_   7433 GGCCATACTGCCCAAGGTAATTTATAGAATCAATGCCATCCCCATCAAGC 7482
                            v     v     iv i  i  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170020294_   7483 TACCAATGACTTTCTTCACAGAATTGAAAAAACT-ACTTTAAAGTTCATA 7531
                          v   iivi i  i  ii     v vi v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_170020294_   7532 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 7581
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_170020294_   7582 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 7631
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_170020294_   7632 TAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATATAGACCAA 7681
                         i     i   i    ii i       i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_170020294_   7682 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 7729
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_170020294_   7730 CTGATATTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 7779
                         i    v  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_170020294_   7780 ATTTAATAAATGGTGCTGGGAAAACTGGAAAGC--------------TGA 7815
                         v  i  i              v       v ? --------------   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_170020294_   7816 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 7865
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_170020294_   7866 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 7915
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_170020294_   7916 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 7964
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_170020294_   7965 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 8014
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_170020294_   8015 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 8064
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_170020294_   8065 GGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 8114
                          i     i                 v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_170020294_   8115 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 8164
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_170020294_   8165 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTTT 8214
                         i     i     v  i?    i            v    i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_170020294_   8215 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCCCATCA 8264
                          v        i  vi viii     v  i          i    i  v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_170020294_   8265 TCACTGGCCAT 8275
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 3.50 (21 / 6)  


2910 26.82 2.79 1.34  chr1_170211711_170217483.rev     4388  5282 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170211711_   4388 TGGAAAAACATTCCATGCTTATGGATAGGAAGAATCAATAGTGTGAAAAT 4437
                               i i  i     i i      v      v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170211711_   4438 GACCATACTGCCCAAAGTTATTTATAGATTCAATGCTATTTCCATCAAAC 4487
                          i v     v      v v  i  i        i  v  ii i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170211711_   4488 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTCAT 4536
                          v   vivi v  i  ii     v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_170211711_   4537 ATGGAACCAAAAAAGAGCCCACATAGACAAGACAATCGTAAGCAAAAAGA 4586
                               viiv  ii  v  viv    v   i      v i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_170211711_   4587 ACAAAGCTGGAGGCATCACGCTAGCTGACTTCAAACTATACCACAAGGCT 4636
                               i      vv    i  vv ii i      viv   i    i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_170211711_   4637 ACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGACATATGGACCA 4686
                                i   i i  ii         i iv ii i        i  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_170211711_   4687 ATGGAACAGAACAGAGGCCTCAGAAATAACCCTACACATATACAACTACC 4736
                               i    iv   ivii         v  i i    v  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_170211711_   4737 TCATCTTCGACAAACCTGATAAAAACAAGCAATGGGGAAAGGATCTCCTA 4786
                          v  i        ivv  vi  i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_170211711_   4787 TTCAGTAAATGGTGTTGGGAAAACTGGTGAGCCATATGCAGAAAACCAAA 4836
                             ii        i     v      vv ?   i     i  i vii  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_170211711_   4837 ACTGGACCCCTTCCTTACACCTTATACGTAAATTAACTCAAGATGGATTA 4886
                         ii         v   i     v     iv            i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_170211711_   4887 AAGACTTACATGTAAAACCCAAAATCATAAAAACCCTAGAAGAAAACCTA 4936
                         ?    i  v      i v i    ii      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_170211711_   4937 GGCA-ATACCACCCAGGACATAGGCATGGGCAAAGACTTC------ATGA 4979
                           ?i- v i -ii iv   v v  vv i     v ii   ------    
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_170211711_   4980 CAAAAATGCCAAAGGCAATTGCAACAAAAGCCTAAATTGACAAATGAGAT 5029
                           ------     i   vvv          vvv    v  i    vi  i
  L1M4_orf2#LINE/    599 CA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_170211711_   5030 CT------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATTAGAG 5073
                         i ------       i -   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_170211711_   5074 TGAACAGGCAGCCTACAGAATGGGAGAAAGTTATTGCAATCTACCCATCT 5123
                             v  i  i  i               i vv      vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_170211711_   5124 GACAAAGGTCTAATATCCGGAATCTACAAGGAACTTAAACAAATTTACAA 5173
                           i  i  v  vi     i    v  i  i     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_170211711_   5174 GAAAAA---------CCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 5214
                         v     ---------   v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_170211711_   5215 ACCTTTCAAAAGAAGACAATTTACG--TAGCCAACAAACATATGAAAAAA 5262
                          ii i  v        i ---   i-- i     i  i  i       i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATA---TACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_170211711_   5263 AGCTCAACATCACTGATTAG 5282
                         v           ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.36 (37 / 11)  


3083 28.68 0.00 0.22  chr1_170241192_170245565     2972  3881 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170241192_   2972 TGGAAGAACATTTCATGCTCATAGATAGGAGGAATCAATATCGTGAAAAT 3021
                              ii i  ii    i    i   v   i  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170241192_   3022 GGCCATACTGCCCAAGGCAATTTATAGATTCATTGCCATCCCCACCAAGC 3071
                            v     v     ivii  i  i       vi  v     i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170241192_   3072 TACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 3121
                          v   iivi i  i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_170241192_   3122 TGGAACCAAAAAAGAGTCTGCCTTGCCAAGACAATCCTAACCAAAACTAA 3171
                              viiv  ii  vi v vv v     i      i i vv  i vv  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_170241192_   3172 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 3221
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_170241192_   3222 CAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGAAGTATAGACCAA 3271
                               iv  i    ii         i iv ii i   vi      i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_170241192_   3272 TGGAACAGAACAGAGGCATCAGAAATAACACCACACATCTACAACCATCT 3321
                              i    iv   ivvi         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_170241192_   3322 GATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 3371
                            i  i     ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_170241192_   3372 TTAATAAATGGTGCTGGGAAAGCTGGCTAGCCATACGTAGAAAGCTGAAA 3421
                          i  i              v i    v  ?   i i i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_170241192_   3422 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 3471
                         i    i    v   i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_170241192_   3472 AGACTTAAATGTTAGACCTAAAAACCATAAAAAACCCAGAAGAAAACCTA 3521
                             i       v   v      - i      vv ii          v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACATA 549

  chr1_170241192_   3522 GGCAATACTATTCAGTACATAGGCATGGGCAAGGACTTCATGACCAAAAC 3571
                           ?ivv v v   ivv  v v  vv i     v ii   v iivi vi  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_170241192_   3572 ACCAAAAGCAATGGCAATAAAAGCCAAAATTGACAAATGGGATCTAATTA 3621
                                   vvi    i     vv     v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_170241192_   3622 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGG 3671
                           v v  i i   i  ii vv    i  v    i  vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_170241192_   3672 CAACCTACAGAATGGGAGAAAGTTTTTGCAATCTACCCATCTGACAAAGG 3721
                              i               i v       vii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_170241192_   3722 GCTAATATCAAGAATCTCCAAAGAACTTAAACAAATTTACAAGAAAAAAA 3771
                         i  vi    v     v vi        ivv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_170241192_   3772 TCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGCCACTTCTC 3821
                         -    i     v  i?    i            v    i  v  i     
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_170241192_   3822 AAAAGAAGACACTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 3871
                         v        i ivi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_170241192_   3872 CATTGGTCAT 3881
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.38 (149 / 108)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 1.00 (2 / 2)  


3004 26.52 1.40 0.35  chr1_170322219_170324666      748  1603 (845)    L1M4_orf2#LINE/L1        1   865 (43)  

  chr1_170322219_    748 TGGAAAAACATTCCATGCTCATGGACAGGAAGAACTAATATTATGAA-AT 796
                               i i  i     i       iv      vi       i v  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170322219_    797 GACCATACTGCCCAAAGTAATTTAAAAATTCAATGCTATTCCCATTAAAC 846
                          i v     v      v i  i  v i      i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170322219_    847 TGTCATTGACATTCTTCACAGAATTAGAATAAACT-ATTTTAAAATTCAT 895
                          vi  vivi v  i  ii     v v  -i  i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr1_170322219_    896 ATGGAATAAAAAAAGAGCCTGAATAGCCAAGACAATCCTAAGCAAAAAGA 945
                               vviv  ii  v  v          i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_170322219_    946 ACAAAGCTGGAGGCATCATGCTACCCAACTTTGAACTATACCACAAGGCT 995
                               i      vv   ii  v     i  ii  viv   i    i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_170322219_    996 ACAGTAACAAAAACAGCATGGTATTGGTACAAAAACAGACACATAGACCA 1045
                                iv  i    ii     i   i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_170322219_   1046 ATGGAAAAGAATAGAGAACTCAGAAATCAGACCACACACCTACAACCATC 1095
                               v     v    iii       v iv   i   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_170322219_   1096 TGATCTTCAACAAACCTCACAAAAACAAGTAATGGAGAAAGGATTCCCTA 1145
                             i   i    ivv vv   i v  vvi     i     i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_170322219_   1146 TTTAATAAATGGTGTTGGGAAAACTGGTTAGCCATATGCAGAAAATTGAA 1195
                           i  i        i     v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_170322219_   1196 ACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATAGATTA 1245
                         ii         v   i     v                   i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_170322219_   1246 AAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGAAAATCAA 1295
                         ?    i         i v i            vi i          ivv 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_170322219_   1296 GGCA-ATACCATTCAGGACATAGGTGCAGGCAACGATTTCATGAGTAAAA 1344
                           ?i- v i -   iv   v v  vvi      i i    v iii  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_170322219_   1345 CACCAAAAGCAATTGCAACAAAAGGAAAAATTGACAAATAGGATCTAATT 1394
                                    vvv          i      v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_170322219_   1395 AAACTAAAGAGCTTCTGCACAGCAAAAGAGACTATCATCAGAGTGAACAG 1444
                            v v  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_170322219_   1445 ACAACCTACAGAA--------AATTTTTGCAATCTATTCATCTGACAAAG 1486
                               i      --------   v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_170322219_   1487 GTCTAATATCCAGAGTCTACAAGGAACTTATACAAA-CATACAAGCAAAA 1535
                          v  vi        i v  i  i     iv     v-  - i  vv    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-ATAATAAAAA 797

  chr1_170322219_   1536 AACAAACAACCCCATTAAAAAGTTGGCAAAAGACACGAACAGACACTTCT 1585
                         i     i     v   ?    i v      i  ivi   i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_170322219_   1586 CAAAAGAAGACATTCAAA 1603
                          v        i  v    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAA 865

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.01 (8 / 865), avg. gap size = 1.88 (15 / 8)  


3504 21.69 3.26 1.24  chr1_170331261_170335535     2893  3782 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170331261_   2893 TGGAAAGACATTCCATGTTCATAGATTGGAAGAATCAATATTGTTAAAAT 2942
                                 i  i          i          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170331261_   2943 GCTCATACTACCCAAAGCAATGTACAGATTCAATGCA-TTGGTATCAAAA 2991
                          viv     v      vii  v           i   - ivv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170331261_   2992 TACCAACGACATGCTTCACAGAAATAGAAAAAACAATACTAAAATTTTTA 3041
                          v   i vi v vi  ii       v  v  ivii  v        iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_170331261_   3042 TGGAACCACAAAAGCCCCAGAATAGCCAAAGACA-TCCTGAGCAAAACAA 3090
                              vii   ii v               -   -  i   --    v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGA--AAAAGAA 197

  chr1_170331261_   3091 AAACATAAAAACTGAAGGAATCACATTACTTGACTTCAAATTATACTACA 3140
                         i    ---  ii  i    v     i v iii i      viv       
  L1M4_orf2#LINE/    198 GAACA---AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_170331261_   3141 GAGCTATAGTAACCAAAACAGCATGGGACTGGCCTAAAAATAGACACATA 3190
                         i     i     i   i    ii   v      v   ii       i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_170331261_   3191 GACCAATGGAACAGAATGGAGAACCCAGAAATAAATCTATAAATCT---- 3236
                           i        i     v    ii           i i   v  i ----
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_170331261_   3237 -CA-----CTTTTGACGAAGGTGCCAAGAACATACATTGGGGAAAGGACA 3280
                         -  -----i   i   i i          v   v  v         i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_170331261_   3281 GTCTCTTCAATAAATGGTGCTGGGAAAACTGGATATCCATAAGCAGAAGA 3330
                             i     i              v         ?   i v   i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_170331261_   3331 ATGAAACTCGACCCC-ATCTCTCACCATATACAAAAATTAAATCAAACTG 3379
                              ii v      - i   v                   v     v  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_170331261_   3380 AATTAAAGACTTAAATATAAGACCTCAAACTATGAAACTACTGTAAGAAA 3429
                         i  i ?    i     i     v  v       i     vi iv      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_170331261_   3430 ACATTTGGGAAAGTCTCCAGGATATTGGTCTGGGCAAAGATTTTTTCAGT 3479
                             vv ? v  i   i iv  iv    vi i     v i   i  vii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_170331261_   3480 AATACCCTACGAGCAGAGGCAACCAAAGAAAAAATCGACAAATGGGATT- 3528
                          vv  v i vi    v i     v           v  i    v   i -
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_170331261_   3529 -ATTACG-TTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACGAAGTG 3576
                         -  i vi-       -   i  ii vv       v  v     vi     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_170331261_   3577 AAGAGGCAACCCACAGAATGGAATAAAAC---TAC---TCATAT----GA 3616
                           i  i               i v    i--- i ---      ----  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_170331261_   3617 CAAGGGATTAATAACCAGAATATATAAGCAGCTCTAACAACTCAATAGGA 3666
                         i      i vi  v             iv i    v           iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_170331261_   3667 AAAAAATCTAATAATCCTATTTTTTTAAATGGGCAAAAGATGTGAATGGA 3716
                             i - v     i  v   ?vv--           i   v     i  
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAA--AAATGGGCAAAGGATTTGAATAGA 840

  chr1_170331261_   3717 CATTTCTC---AAAAGACATACAAAATGGCAAACCAGTATATGAAAAGGT 3763
                                 --- i    i       -    v  iv  i i        i 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACATGAAAAGAT 889

  chr1_170331261_   3764 GATCAACATCACTGATCAT 3782
                          v         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (112 / 77)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.22 (40 / 18)  


3153 27.59 0.66 0.44  chr1_170351145_170357531.rev     4993  5898 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170351145_   4993 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5042
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170351145_   5043 GGCCATACTGCTCAAGGTGATTTATAGATTCAATGCCATCCCCATCAAGC 5092
                            v     v i   iv    i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170351145_   5093 TACCAATGACTTTCTTCACACAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5140
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_170351145_   5141 TATGGAACCAAAAAAGACCCTGCATTGCCAAGACAATCCTAAGCAAAAAG 5190
                                viiv  ii     v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_170351145_   5191 CCAACAAAGCTGAAGGCATCATGCTACCTAACTTCAAACTATACTACAAG 5240
                         --       i  i   vv   ii  v  i  i      viv        i
  L1M4_orf2#LINE/    199 --AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_170351145_   5241 GCTACAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5290
                                   v   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_170351145_   5291 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAATC 5340
                         i        i    iv   ivii         vv   i    i  iii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_170351145_   5341 ATCTGATCTTTGACAAACCCGACAAAAACAAGAAATGGGGAAAGAATTCC 5390
                          vi    i  i     ivvi v   i v  vvv              vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_170351145_   5391 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAACCT 5440
                           v  i  i              v      v  ?   i   i i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_170351145_   5441 GAAACTGCATCCCTTCCTTACACCTTATGCTAAAGTCAATTCAAGATGGA 5490
                            ii  v i    v   i     v   i v   i i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_170351145_   5491 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5540
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_170351145_   5541 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5590
                         v    ?i v viv   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_170351145_   5591 AACACCAAAAGCAATGGCAACAAAAGCCCAAATCGACAAACAGTATCTAA 5640
                         i            vvi          vvv    v  i   iv v ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_170351145_   5641 TTAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTACCATCAGAGTGAAC 5690
                          i   v v  i i   i  iv vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_170351145_   5691 AGACAACCTACAGGATGGGAGAAAATTTTTGCAATCTGCCCATCTGATAA 5740
                                 i    i            v       viiiivi         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_170351145_   5741 AGGGCTAATATCCAGAATCTGCAAAGAACTTAAACAAATTTAAAAGAAAA 5790
                         i  i  vi          v ii        ivv    v iv v  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_170351145_   5791 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5836
                          i    ----   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_170351145_   5837 TGAAAAGAAGACATTTCTGCAGCCAAAAGACACATGAAAAAATACTCATC 5886
                          vv        i  vivviii     v ii          i  i    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_170351145_   5887 ATTGTTGGTCAT 5898
                           ii????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (143 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.00 (10 / 5)  


1601 27.66 3.68 0.97  chr1_170397099_170402376        4   520 (4758)  C L1M4_orf2#LINE/L1   (287)   621    91  

C chr1_170397099_    520 CTCATCAAAGTCAT-----CCTCTATTTGAATAGAAA-----AAACT-AT 482
                          ii      i  vi-----   i -    --i     -----  i  -  
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTT-TTTG--CAGAAATTGACAAGCTGAT 137

C chr1_170397099_    481 TCTTAAATTCATATGAAACCAAAAAAGAGCCCTAATAGCAAAAGCAATCC 432
                         i  v           i  viiv  ii  v  vv      v   i     i
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

C chr1_170397099_    431 TAAGCAAAAAGAACAAAGCTGGATGCATCACATTACTCAACTTCAAACTA 382
                          i iv  i          i    v vv     i v i   i      viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

C chr1_170397099_    381 TACTACAAGGCTACAGTAACCGAAACAGCATGGTATTGGT-CAAAAACAG 333
                                 i          i i i    ii     i   i-i  ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

C chr1_170397099_    332 ACCCATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCACACA 283
                           vi     i        i     v    ii           v   i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

C chr1_170397099_    282 CCTACAACCACCTGATCTTTGACAAAATCAGCAAAAACAAACAATGAGAA 233
                         ii  iiii  vi    i  i     iiviiv   i v  vv     i i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

C chr1_170397099_    232 AAGGGCTCCCTATTCAGTAAATGGTACTGGGATAACTGGCTAGCCCTAAG 183
                            iiivvi  v    ii       i      i      v  ?  vi v 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

C chr1_170397099_    182 CAGATGATTGAATCTGGAATCCTATGTTTCACCATAGACAAAAATTTACT 133
                           i v  v    vi    vi    iv iv       v         v   
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

C chr1_170397099_    132 CAAGATGGATTAAAGGCTTAAATGTGAGACCTAAAACTATAAAAATCCTA 83
                            i      i ?  i i       i   v              v  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

C chr1_170397099_     82 GAAGAAAGGA--AATGTCATTCT--G-GACACTGGCCTTGGCAAATAATT 38
                                iv --ii?  v v   -- -   vi   vi v     - ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTT 586

C chr1_170397099_     37 TAT--GACTAAGTCCTCAAAAGCAATTGTAACAAGA 4
                          v --  -  v v vi        vvv i     i 
  L1M4_orf2#LINE/    587 TCTTAGA-TATGACACCAAAAGCACAAGCAACAAAA 621

Transitions / transversions = 1.64 (87 / 53)
Gap_init rate = 0.02 (12 / 531), avg. gap size = 2.00 (24 / 12)  

3160 26.99 1.11 0.66  chr1_170397099_170402376     3882  4785 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170397099_   3882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 3931
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170397099_   3932 GGCCATACTGCCCAAGGTAATTTATAGACTCAATGCCATCCCCATCAAGT 3981
                            v     v     iv i  i  i   i    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170397099_   3982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_170397099_   4030 TATGGAATCAAAAAAGAGCTTGCATTGCCAAGACAGTCCTAAGCCAAAAG 4079
                                viiv  ii  v iv v  v     i   i  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_170397099_   4080 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATTCTACAAGGC 4129
                                i      vv   ii  v  ii i      viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_170397099_   4130 TACAGTAACCAAAACAGCATGGGACTGGTACCAAAACAGAGATATAGACC 4179
                                 i   i    ii   v     i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_170397099_   4180 AATGGAACAGAACAGAGGCATCAGAAATAATGCCACATATCTACAACCAT 4229
                                i    iv   ivvi         vv   i i  i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_170397099_   4230 CTGATCTTTGGACAACC-TGACAAAAACAAGAAATGGGGAAAGGA--GTC 4276
                         i    -   v     vv-  v   i v  vvv           i --   
  L1M4_orf2#LINE/    349 TTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_170397099_   4277 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAACC 4326
                         -- v  i  i              v      v  ?   i   i i  ivv
  L1M4_orf2#LINE/    398 --TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_170397099_   4327 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 4376
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_170397099_   4377 ATTTAAGACTTAAATGTTAGACCTAAAACCACAAAAACCCAAGAAGAAAA 4426
                           iv?    i       v   v       i i    vi iv         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_170397099_   4427 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGTAAGGACTTCATGACT 4475
                          v    ?i- v i -   iv   v v  vv i  i  v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_170397099_   4476 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATAGGATCT 4525
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_170397099_   4526 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 4575
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_170397099_   4576 ACAGGCAACCTACAGGATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 4625
                          v  i     i    i            v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_170397099_   4626 AAAGGGCTAATATCCAGAATCTACAAAGAACTTATACAAATTTACAAGAA 4675
                           i  i  vi          v  i        iv     v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_170397099_   4676 AAAAGCAA----CCCCATCAAAAAGTGGGCAAAGGATATGAGCAGACACT 4721
                            ii   ----   v  i?    i            v   ii     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_170397099_   4722 TTTCAAAAGAAGACATTTCTGCAGCCAGCAGACACATGAAAAAATGCTCA 4771
                          i  v        i  vivviii    ii ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_170397099_   4772 TCATCACTGGCCAT 4785
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3165 27.32 1.00 0.55  chr1_170426061_170432424     4968  5871 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170426061_   4968 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5017
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170426061_   5018 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5067
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170426061_   5068 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5115
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_170426061_   5116 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5165
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_170426061_   5166 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5215
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_170426061_   5216 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGACC 5265
                                 i   i    ii         i iv ii i   v  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_170426061_   5266 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5313
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_170426061_   5314 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5363
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_170426061_   5364 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTGTATGTAGAAACCT 5413
                           v  i  i              v      v  ? iii   i i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_170426061_   5414 GAAACTGGATCCCTTCATTACACCTTATACAAAAATTAATTCAAGATGGA 5463
                            ii    i    v v i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_170426061_   5464 TTAAAGACTTAAATATTTGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5513
                          i ?    i     i vv  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_170426061_   5514 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5562
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_170426061_   5563 AAACACCAACAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTA 5612
                         vi       v    vvi   i      vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_170426061_   5613 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAA 5662
                           i   v v  i i   i  ii vv    i  v    i  vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_170426061_   5663 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5712
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_170426061_   5713 AAGGGCTAATATCCAGAATCTACAATGAACTCGAACAAATTTACAAGAAA 5762
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_170426061_   5763 AAAACAA----CCCCATCAAAAAGTGGGCAGAGGATATGAACAGACACTT 5808
                           i    ----   v  i?    i      i     v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_170426061_   5809 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5858
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_170426061_   5859 CATCACTGGCCAT 5871
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3039 23.79 3.25 1.35  chr1_170437274_170442021.rev     3367  4257 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170437274_   3367 TGGAAACACATCTCATGCTCATGAATGGGTAGAATCAATATTGTGAAAAT 3416
                               v i   i    i     i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170437274_   3417 GTCTATACAGCCAAGAG-AATCTATAAATTCAATGCAATTCCCATAAAAA 3465
                          v v    vv  v i v-i     i i      i     i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170437274_   3466 TACCACCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCATA 3515
                          v   v vv v  i  ii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_170437274_   3516 TGGAA----------CCAAAAATGAGCCCACATACCC----AAAGGAAGG 3551
                              ----------  v i   -    v v i vi ----   i    -
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAAT-AGCCAAAACAATCTTGAAAAAGAAG- 198

  chr1_170437274_   3552 CTAAGCAAATCTGGAGGCATCACATTACCTAATTTCAAACTATTT--TAC 3599
                         --- i    vi      vv     i v  i         -- i  --   
  L1M4_orf2#LINE/    199 ---AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTAC 243

  chr1_170437274_   3600 AAGGCTATAGTCACCAAAACAGCATGATACTGGCATAAAAATAGGTACAT 3649
                           i    i   v i   i    ii  i           ii    ii i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_170437274_   3650 AGACCAATGGAA-AGAATAGAGAACCCAGAAATAAAGCCAAATAGTTAAA 3698
                            i        -     v    ii           v   v i v   vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_170437274_   3699 GCCAACTGATCTTTGACAAAGCAAACAAAAACAT--AATGTGGGGAAAGG 3746
                          i   i    i  i     i vviv   i v   --    --       i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG--GGGAAAGA 391

  chr1_170437274_   3747 ACACCCTATTCAGCAAACAGTGCTGGGATAATTGGCAAGCCACATGTAGA 3796
                          i vi  v    i    ii         i  i   vv ?       i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_170437274_   3797 AGAATGAAACTGAATCTTCATCTCTCACCTTATACAAAAACCAACTCAAG 3846
                                 ii  i i iii i   v    v          ii       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_170437274_   3847 ATGGATCAAAGACTTAAATCTAAGACATGAAACCATAAAAATTCTAGAAG 3896
                                 ?    i     v     vv i    i      v ii      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_170437274_   3897 ATAACATTGGAGAAACCCTTCTAGACATTGGCTCAGGCAAAGAGTTCAT- 3945
                          v     v  ? v  vi    vv   v    v i      v iv   v -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_170437274_   3946 GATCAAGA-ACCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGA 3994
                            - v  -          v v         iv   i   i   i  v i
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_170437274_   3995 ACTT-----AAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAG 4039
                             -----   i      -   i  ii vv    i  v iv    iv i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_170437274_   4040 AGTAAATAGACAACCCACGGAGTGGGAGAGAATGTTTGCAAACTACAGAT 4089
                            i  v           i  i       i   i        ii i v  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_170437274_   4090 CCAACCACAGACTAATATCCAGAATCTACAAGGAATTCAAACAAATCACC 4139
                          ii iv vi    vi          v  i  i   i  vv    v   vi
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_170437274_   4140 AAGGAAAAAAACAAATAATTCCATCAAAAAGTGGGCTAAAGACC--AATA 4187
                           v-     i        ii v  i?    i     v  i  ii--    
  L1M4_orf2#LINE/    790 AAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_170437274_   4188 GACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAA 4237
                             v     v                       i  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_170437274_   4238 TGCTCAACATCACTAATGAT 4257
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (123 / 85)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.41 (41 / 17)  


3183 25.92 1.68 0.22  chr1_170460377_170465432     3669  4563 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170460377_   3669 TGGAAACACTTCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3718
                               v iv       i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170460377_   3719 GACCATATTGCC-AAAGCAATCTACAAATTCAATGCAATCACCATCAGAA 3767
                          i v   i v  -   vii       i      i      v i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170460377_   3768 TACCACCATCATTCTTCACAGAATTAGAAAAAAACAATTATAAAGTTCAT 3817
                          v   v vv v  i  ii     v v  v  iv-ii  iv    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_170460377_   3818 ATGGAACCAAAAAAGAGCCCACATAGCCAAAGCAATACTAAGCAAAAAGA 3867
                               viiv  ii  v  viv         i    vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_170460377_   3868 ACAAATCTGGAGGCATCACACTACCTGATTTCAGACTATATTATAGAGCC 3917
                              vi      vv       v  ii      i viv  i  i i   i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_170460377_   3918 ATAGTCACCAAAACAGTGTGGTACTGGTATAAAAACAGGCACATAGACCA 3967
                          i   v i   i               i    ii i  i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_170460377_   3968 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAACACTTACAGCCAAC 4017
                               i     v    ii               v   i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_170460377_   4018 TGATCTTCAACAAAGCAAACAAAAACATAAAGGGGGGCAAGAACACTCTT 4067
                             i   i    i vviv   i v   vv iv    v     i v    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_170460377_   4068 TTCAACAAATGTTGCTGGGATAATTAGCTAGCCACATGTAAGAAAACGAA 4117
                                    v        i  i i v  ?       i  i i  i   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_170460377_   4118 ACTGGATCCTCAGCTCTCACCTTATACAAAAATCAACTCAAGATGTATTA 4167
                         ii    i  ii v   v    v           i       i   v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_170460377_   4168 AGGACTTAAACCTAAGACCTGAAACTGTAAAAATTCTAGAAGATAACATT 4217
                         ?i   i    iv     v  i     i     v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_170460377_   4218 GGAAAAACCCCTCTTGACATTGGCTTAGGCAAGGATTTCATGACCAAGAA 4267
                           ?iv  vi i  v    v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_170460377_   4268 CCCAAAAGCAAATGCAATAAAAAAAAAAAAAAAACAGCTGGGACCTAATT 4317
                         v         v v    i    i      v i -i iv v    i v  i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGA-TAAATTGGACTTCATC 648

  chr1_170460377_   4318 AAACTAAAGAGCTGTTGCATGGCAAAAGTAACAGTCAGCAAAGTAAACAG 4367
                            v v  i i  v   iiivv    i vv  vi   iv     i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_170460377_   4368 ACAATCCACAGAGTGTGAGAAAATCTTCACAA-TC-TACATCTGACAA-- 4413
                             i       i  v        v  ii   -  -  i      i  --
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_170460377_   4414 --CTAATATCCAGAATCTACAGTGAATTC----AAGTCAGTGAGAAAAAA 4457
                         --  vi          v  i iv   i  ----  v   i i v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_170460377_   4458 ACAA----TCCTATCAAAAAGTGGGCTAAGGACGTGAATAAACAATTCTC 4503
                             ----i  v  i?    i     v     iv      i   v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_170460377_   4504 AAAAGAAGATGTACAAATTGCCAACAAACATATGAAAAAATGCTCAACAT 4553
                         v         i       v     i  i  i       i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_170460377_   4554 CACAATGATC 4563
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.38 (132 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


3668 22.62 2.13 0.45  chr1_170476481_170480509.rev     2647  3539 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170476481_   2647 TGAAAAGACATTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 2696
                           i     i  i                     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170476481_   2697 GTCCATGCTATCCAAAACAATCTACAGATTCAATGCAATCCCTACCAAAA 2746
                          v v  i  vi     vii              i          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170476481_   2747 TACCAATGACAGTCTTCACAGAAATAGAAAAAATAATCCTAAAATTGATA 2796
                          v   iivi vv i  ii       v  v  iv i           v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_170476481_   2797 TGCAACCACAAAG-ACCCAGAATAGCCAAAGCTATCTTGAGCAACAAGAC 2845
                           v  vii   i -                i v       iv  v    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_170476481_   2846 CAAAACTGGAGGAATCACATTATCTGACTTCAAATTATACTAAAGAGCTA 2895
                             ii       v     i vi ii i      viv     v i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_170476481_   2896 CAGTAACTAAAACGGTATGAGACTAGAATAAAAACAGACACATAGACCAA 2945
                               ii  i  i  i  iv   i v    ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_170476481_   2946 TGGAACAGAATGGAGAACCCAGAAATAAACCTATACATCTACAGCGAACT 2995
                              i     v    ii             i      i  ii iv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_170476481_   2996 GTTTTTTTGACAAAGGTGCTAGGAACGTATATTGGGGAAAGGACAATCTC 3045
                          v    i-     i     i i  v i vi v         i i i   i
  L1M4_orf2#LINE/    351 GATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_170476481_   3046 TTCAATTAACAGTGCTGGGAAAACCAGGTAACTATATGCA---GAATGAA 3092
                              iv  ii         v   ii i  ? i i     ---       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_170476481_   3093 ACTAGACCCC-ATTTTTTGCCATATACAAAAATCAAATTAAAATGAATTA 3141
                         ii i      - ii ivii              i  v i      i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_170476481_   3142 AAGACTTAAATCTAAGGCCTCAAACAATGAAACTGCTAAAAGAAAACACT 3191
                         ?    i     v    iv  v    v  i     vi  i         iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_170476481_   3192 GGGGAAACTCTCCAGGACATTGGTCTGGGCAAAGATTTTTTTCAG-TAAT 3240
                           ? v  v   i iv   v    vi i     v i   i  --  -  vv
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--AGATATG 597

  chr1_170476481_   3241 ACTCCACAAGCACAGGCAACCAAAGAAAAAATAGACAAATGGGATCACAT 3290
                           v   v       i     v              i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_170476481_   3291 TAAG-TCAAAAAGCTTCTGCACAGCAAAGGAAACAACCAACAAAGTGAAG 3339
                         i  i- i     -   i  ii vv       v  v i   v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_170476481_   3340 AGACAACCCACAGAATGGGAGAAAAC---TAC---TC-T---TCTGACAA 3379
                                                  i--- i ---  - ---     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_170476481_   3380 GGGATTAATAACTAGAATATATAAGGG-CTCAAACAACTCAATAG-AAAA 3427
                             i vi  v i           i i-   vv           i-    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_170476481_   3428 AAACTAATAATCCAATTAAAAAGTGGGCAAAAGATCTGAATAGACCTTTC 3477
                          i  v     i      ?    i        i   i         v    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_170476481_   3478 TCCAAAGAAGACATAAAAATAGCAAACAGGTATATGAAAAGGTGCTCAAC 3527
                                    i   v    i  v  i i i i        i        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_170476481_   3528 ATCTGATCATTA 3539
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (129 / 69)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


2231 26.73 1.38 1.38  chr1_170511993_170518711     4999  5649 (1070)    L1M4_orf2#LINE/L1        1   651 (257)  

  chr1_170511993_   4999 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5048
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170511993_   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170511993_   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_170511993_   5147 TACGGAAACAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAAG 5196
                           i     iiv  ii  v  viv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_170511993_   5197 AACAAAGCTGGAGGCATCATGCCACCTCGC--TTT--AAACTATACTACA 5242
                                i      vv   ---   i  v --   --     -       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCA---CACTTCCCAATTTCAAAACT-TACTACA 244

  chr1_170511993_   5243 AGGCCACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 5292
                          i  i       i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_170511993_   5293 GACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAA 5342
                           i        i    iv   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_170511993_   5343 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAACGGGACAAAGATT 5392
                         i  vi    i  i     ivv  v   i v  vvv  i   iv  ii  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_170511993_   5393 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCTTATGTAGAAAG 5442
                         vi  v  i  i              v      v  ?  vi   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_170511993_   5443 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5492
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_170511993_   5493 GATTAAAGATGTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5542
                            i ?   iv       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_170511993_   5543 ACCGAGGCACTATCAATC---AGGACACAGGCATGGGCAAGGACTTCATG 5589
                           vv   ?i-  --    ---iv   viv  vv i     v ii   v i
  L1M4_orf2#LINE/    545 ACATAGGNG-TA--AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_170511993_   5590 ACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGA 5639
                         iv  vi            vvi          vv        i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_170511993_   5640 TCTAATTAAA 5649
                         ii v  i   
  L1M4_orf2#LINE/    642 CTTCATCAAA 651

Transitions / transversions = 1.63 (106 / 65)
Gap_init rate = 0.02 (10 / 651), avg. gap size = 1.80 (18 / 10)  

 824 22.30 5.23 1.74  chr1_170511993_170518711     5940  6226 (493)    L1M4_orf2#LINE/L1      612   908 (0)  

  chr1_170511993_   5940 AGAAAAAAAAGAAAGCAAAAAAATAAAT------------AAAT-AAATA 5976
                           v  v        --   v i      ------------    -   v 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAA--AAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_170511993_   5977 CTGTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAATCTACA 6026
                           - i  ii vv    i  v    i  vv i      v  i   i i   
  L1M4_orf2#LINE/    660 CT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_170511993_   6027 GAATGGGAGAAAATTTTTGCAATCTACCCATCAGACAAAGGGATAATATC 6076
                                       v       vii ivi   v  i  i  iv vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_170511993_   6077 CAGAATCTAAAAAGGACTTAAACAAATTTACAAGAAAAAAACAAACAACC 6126
                               v  v    i   ivv    v iv i  v     i     i    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_170511993_   6127 CCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTTTCAAAAGAAGAC 6176
                          v  i?    i            v    i     i  i  v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_170511993_   6177 ATTTATGAA--GCCAACAAACACATGAAAAAATGCTCTTCATCACTGGTC 6224
                           -- ii  --     i  i          i      vv     ??????
  L1M4_orf2#LINE/    859 AT--ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_170511993_   6225 AT 6226
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.25 (35 / 28)
Gap_init rate = 0.02 (6 / 297), avg. gap size = 3.33 (20 / 6)  


2058 25.05 1.39 0.20  chr1_170755187_170759331.rev      500  1002 (3143)    L1M4_orf2#LINE/L1       82   590 (318)  

  chr1_170755187_    500 AATGCAATTGCTATCAAAATATCAATGACATTCTTCACAGAAATAGAAAA 549
                           i     iv          vi  iivi v  i  ii       v  v  
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

  chr1_170755187_    550 AAAAATCTTAAAATTTATGTGGAACCACAAAAGACCCTGAATAGCCAAAG 599
                         ivvi   i       i  i     vii   ii     v           i
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_170755187_    600 CAATCCTGAGCAAAAAGAACAAAGGTGCAGGCACCATATTACCTTGACTT 649
                              i   iv  i          v  v   vvi  i i v  -ii i  
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC-CAATTT 230

  chr1_170755187_    650 CAAAATTTACTACAAAGCTATAGCAACCAAATCAGCATTGGAGTGGCATA 699
                              i              i  i  i   iv   ii v v v       
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_170755187_    700 AAAACAGACACATGGACCAATGGAAT-GTATAGAGAACCCAGATACAAAT 748
                          ii i     i  i  i         - v  v    ii     v i   i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_170755187_    749 CCATGCATTTACAGGCAACT-----CTGACAAAAGTGCCAAGAATATACA 793
                             i      ii v   i -----ii     ii         vi  v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_170755187_    794 ATTGCGAAAGGACAGTCTCTTCAATAAATGGTGCTGAGAAAACTAGATAA 843
                           v v     i i     i     i           i  v    i    ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_170755187_    844 CCATATGCAGAAGACTGAAACTAGACCCCTGCCTCGTACCATATACAAAA 893
                            i     i    v    ii i       i    ii             
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_170755187_    894 -TCAAATCAAAATGAATGAAAGACCTAAATGTAAGACCTGAAACTATGAA 942
                         - i  v        i  v ?                v  i       i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_170755187_    943 GCTACTAGAAGGAAACTTTGGGGAAAAACTCCAGGACATTGGTATGGGCA 992
                         i  vi      i    v v  ? v   v  i iv   v    vv i    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_170755187_    993 AAGATTTTTT 1002
                          v i   i  
  L1M4_orf2#LINE/    581 ATGGTTTCTT 590

Transitions / transversions = 1.86 (80 / 43)
Gap_init rate = 0.01 (4 / 509), avg. gap size = 2.00 (8 / 4)  

1044 23.86 0.00 0.76  chr1_170755187_170759331.rev     1305  1568 (2577)    L1M4_orf2#LINE/L1      577   838 (70)  

  chr1_170755187_   1305 GGCAAAGATTTTTAGGATAAGACCGCAAAGGCACAGGCAACCAAAGCAAA 1354
                              v i   i vi    v   vv    i     i     v    v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_170755187_   1355 AATAGATAAATGGGATTGCCTCAAGTTTAAAAGCTTCTGTACAGCAAAGG 1404
                                    v   i v v    iv      i   i   i vv      
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_170755187_   1405 AAACAACCAATAAAGTGGAAAGATAACCTACAGAATGGGAGAAAATATAT 1454
                          v  v i   v      i     i    i                   --
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT-- 724

  chr1_170755187_   1455 TTGCAAACTACCCATCTGACAATAGTCTAATAACCAGAATATATAAGGAG 1504
                                ii ivi      i  vi v  vi  v             i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_170755187_   1505 CTTTAATAACTCAATAGCAAAAGAAGAAATAATCTGATTAAAAAGTGGTT 1554
                           i v i         ii    ii v      i ii   ?    i   vi
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_170755187_   1555 AACAGACCTGAATA 1568
                           vi  ii      
  L1M4_orf2#LINE/    825 AAAGGATTTGAATA 838

Transitions / transversions = 1.48 (37 / 25)
Gap_init rate = 0.00 (1 / 262), avg. gap size = 2.00 (2 / 1)  

 429 17.86 0.00 0.00  chr1_170755187_170759331.rev     3571  3654 (491)    L1M4_orf2#LINE/L1      825   908 (0)  

  chr1_170755187_   3571 AAAAGATCTAAATAGACATTTCTCAAAAGAAGACATACAAACAGCTAATA 3620
                            i   i i              v        i       ii  i    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_170755187_   3621 GGTATATGAAAAAATGCTCAGTGTCACTAATCAT 3654
                         i i i       i       iii   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 14.00 (14 / 1)
Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.00 (0 / 0)  


2737 21.02 1.10 4.67  chr1_170779630_170781350      501  1228 (493)    L1M4_orf2#LINE/L1      207   908 (0)  

  chr1_170779630_    501 TGGGGGCATCGCATCATCTGACTTTAAAATCTGCTACAAAGCTATAGTAA 550
                            i  vv  i  iivi ii i  i    ii i           i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_170779630_    551 GCAAAACAGCATGGTAGTGGCATAAAAACAGACACATAGACCAATGGAAC 600
                         v   i    ii     v        ii i     i     i        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_170779630_    601 AGAATAGAGAACTCAGAAATAAATCCATACATTTATAGCCAATTCATTTT 650
                              v    iii          i            i i     v     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_170779630_    651 CGACAAAGGCACCAGAAACATACATTAGGGAAAAGACAGTCTCTTCAATA 700
                               i  ii   ii v   v  v i      ii i     i     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_170779630_    701 AATAGTACTGGGAAAACTAGATAACCATATGCAGAATAGTGAAACTAGAC 750
                            i  i      v    i    ?   i     i  v i    ii i   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_170779630_    751 CCCTATCTCTTTTGACCATATACAAAAATCTAA-TCAAAATGAATCAAAG 799
                              i   vi---               -   -        i    ?  
  L1M4_orf2#LINE/    457 CCCTACCTCAC---ACCATATACAAAAAT-TAACTCAAAATGGATCAWAG 502

  chr1_170779630_    800 ACTTCAATGTAAGACCTGAAACTATGAAACTACTAGAAGAAAACATTGGG 849
                           i v         v  i       i     vi             v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_170779630_    850 G-AAATACTCCAGGTCATTGGTCTGGGCAAAGATTTTTTGAGTAAGATTT 898
                          -    -  i iv v v    vi i     v i   i  iii  v  ivi
  L1M4_orf2#LINE/    553 GTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_170779630_    899 CAAAAACACAGGCAACCAAAGCAAAAATACACAAACGAGATTACATCAAG 948
                              i    i     v    v       v i   ivi  i v      -
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA- 650

  chr1_170779630_    949 CTAAAAAACAAACAAACAAAAAACCCTTCTAAACAGCAAAGGAAAT---- 994
                         --------------  iv      --  i ivi vv       v i----
  L1M4_orf2#LINE/    651 --------------AATTAAAAAC--TTTTGTGCTTCAAAGGACACTATC 684

  chr1_170779630_    995 AACAGAGTGAAGAGACAACCTACAGAATGGGAGAAAAT--TTGCAAACTA 1042
                           v i      i        i                 --       ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_170779630_   1043 TCTATCTGATGACACATTAATAACCAGAATATGTAAGGAACTCAAACAAC 1092
                          v        i viv i vi  v         i   i      vv     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_170779630_   1093 TCAATAGCAAAAACAACAACAATGAAACCAAATATCTGATTTGAAAATGG 1142
                               ii     -i    --  --    v   ------- ?i       
  L1M4_orf2#LINE/    785 TCAATAATAAAAA-GACAA--AT--AACCCAAT-------TWAAAAATGG 822

  chr1_170779630_   1143 GCAAATAAGCTGAATAGACATTTCACAAAAGAAGACATACAAATAGCCAA 1192
                              vi vi              v v        i        i     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_170779630_   1193 CAGGTAAATGGAAAAATGCTCAACATCACTAGTCAT 1228
                         i i i v   i   i             ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (101 / 48)
Gap_init rate = 0.02 (13 / 702), avg. gap size = 3.23 (42 / 13)  


3152 24.14 2.10 1.55  chr1_170826514_170832325.rev     4419  5321 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170826514_   4419 TGGAAAAACATTCCAACCTCATGGATAGGAAGAGTCCATATCTTGAAAAT 4468
                               i i  i   vvi        v      v iv    iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170826514_   4469 GGCCATACTGCCCAAAGTAGTTTATAGATTCAATGCTATCCCCATCAAAT 4518
                            v     v      v ii i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170826514_   4519 TACCA-CTGACATTCTTCACAGAATTAGATAAAACT-ACTTTAAATTTCA 4566
                          v   -   v -  i  ii     v v  i  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_170826514_   4567 TATGGAA-T-CAATGAAGTCCCTGTATAGCCAAGACAATCCTAAGCAAAA 4614
                                - -   v i --   v v        i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_170826514_   4615 AGAACAAAGGTGGAGGCATCGCGCTACCTGACTTCAAACTATACTACAAG 4664
                                  v      vv  i i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_170826514_   4665 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGA 4714
                                   i   i    ii         i iv ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_170826514_   4715 CCAATGGAACAGAACAGAGACCTCAGAAATAATGTCATACATCTACAACC 4764
                         i        i    iv    vii         vvi       i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_170826514_   4765 ATCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGATCTC 4814
                          vi    i   i    ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_170826514_   4815 CTATTCAATAAATGGTGCTGGGAAAACTGGCTACCCATATGCAGATAATT 4864
                           v     i              v      v  ?   i     i vi v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_170826514_   4865 GAAACTGGATCCCTTCCTTTCGCCTTATACAAAAATTAACTCAAGATGGA 4914
                            ii    i    v   iv i  v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_170826514_   4915 TTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTT-GAAGGAAA 4963
                          i ?    i         i v i     i      - i   -    i   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_170826514_   4964 CGTAGGCAGTA--CCATTTAGGACATAGGCATGGGCAA-AACTTC----- 5005
                          i    ?-   --i -  iiv   v v  vv i     -iii   -----
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_170826514_   5006 -ATGACAAAAATGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAAT 5054
                         -      ------         vvv          vv     v  i    
  L1M4_orf2#LINE/    594 TATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_170826514_   5055 GGGATATAAT-AAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCAT 5103
                         v   iv v  -    i    i -   i  ii vv    iv v       v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_170826514_   5104 CAGTGTAAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATTTACC 5153
                         v iv  i  v  i     i                 v       v i iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_170826514_   5154 CATCTGACAAAGGTCTGATATCCAGAATTTACAAGGAACTTAAACAAATT 5203
                         i      i  i  v  vi          v  i  i     ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_170826514_   5204 TACAAGAAAAA---AAA-AACCCTATCAAAAAGTGGGCAAGGGTTATGAA 5249
                         v i  v     ---   -     v  i?    i       i  v v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_170826514_   5250 CAGACACTTCTCAAAAGAAGATTTTTATGCATCCAACAAACATATGAAAA 5299
                         i     i     v         v vi viiiv    i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_170826514_   5300 AAAGCTCAACATCAATGATCAT 5321
                         i v           ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (122 / 92)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.74 (33 / 19)  


2691 26.90 0.41 0.28  chr1_170843875_170850296     4681  5405 (1017)    L1M4_orf2#LINE/L1        1   726 (182)  

  chr1_170843875_   4681 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4730
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170843875_   4731 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 4780
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170843875_   4781 TATCATTGACTTTCTTCACAGCA-TTAAAAAAAATACTTTAAATTCCATA 4829
                          vi  vivi i  i  ii   v -  i v  ivvv iii    v i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_170843875_   4830 TGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGAA 4879
                              viiv  ii  v  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_170843875_   4880 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 4929
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_170843875_   4930 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 4979
                               i   i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_170843875_   4980 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5029
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_170843875_   5030 GATTTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 5079
                               i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_170843875_   5080 TTAATAAATGGCATTGGGAAAACTGGCTAGCCATATGCAAAAAACTGAAA 5129
                          i  i      iii     v      v  ?   i        i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_170843875_   5130 CTGGACTCCTTCCTCACACCTTATACAAAAATTAACTCAAGATGGATTAA 5179
                         i     i   v         v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_170843875_   5180 AGACTTAAACATTAGACCTAAAACCATAAAAACCCTAAAAGAAAACCTAG 5229
                             i    ii v   v       i      vi i  i        v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_170843875_   5230 GCAGTA--CCATTCAGGATATAGGCATGGGCAAAGACTTCATGAATAAAA 5277
                          ?-   --i -   iv  iv v  vv i     v ii   v ii   vi 
  L1M4_orf2#LINE/    551 GN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_170843875_   5278 CACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5327
                            v       vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_170843875_   5328 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAATAG 5377
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_170843875_   5378 GCAACCTATAGAATGGGAGAAAATTTTT 5405
                         i     i i               v   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTT 726

Transitions / transversions = 1.46 (114 / 78)
Gap_init rate = 0.01 (4 / 726), avg. gap size = 1.25 (5 / 4)  

 753 22.22 2.02 1.01  chr1_170843875_170850296     5732  5929 (493)    L1M4_orf2#LINE/L1      709   908 (0)  

  chr1_170843875_   5732 GAATGGGAGAAAATTTTTGCAATCTATCTATCTGACAAAGAGCTGATATC 5781
                                       v       vii  v       i  i ii  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_170843875_   5782 CAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAACAA----CC 5827
                               v  i  i     ivv    v iv i  v     i    ----  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_170843875_   5828 CCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGAC 5877
                          v  i?    i            v    i     i     v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_170843875_   5878 ATTTATGCAGCCAACAAACATATGAAAAAAAAAGCTCATCATCACTGGTC 5927
                           vi viii     i  i  i       i --v     v     ??????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAACATCAZZZZZZ 906

  chr1_170843875_   5928 AT 5929
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.53 (26 / 17)
Gap_init rate = 0.01 (2 / 200), avg. gap size = 3.00 (6 / 2)  


3011 27.04 1.10 0.88  chr1_170877527_170879671.rev      749  1654 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170877527_    749 TGGAAAAACAGTCCATACTCACGGATAGGAAGAATCAATGTCGTGAAAAT 798
                               i i vi    ii   i    v      v i   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170877527_    799 GGCCATA-TGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 847
                            v   - v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170877527_    848 TACCATTGACTTTCTTTGCAGAATTAGAAAAAACT-ACTTTAAATTTCAT 896
                          v   vivi i  i         v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_170877527_    897 ATGGAAC--CAAAAAACAATCCATA-TAGCCAAGACAACCTTAAGCAAAA 943
                               v--   iii  ---   v -       i    i   i iv  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_170877527_    944 AGAACAAAGCTGGAGGCATCATGCTACCTGCCTTCAAACTATACTACAAG 993
                                  i      vv   ii  v  iivi      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_170877527_    994 GCTACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGATATACAGA 1043
                                   i   i    ii        vi iv ii i   i   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_170877527_   1044 CCAATGGAACAGAATAGAGACCTCGGAAATAACACCACACATCTACAACC 1093
                         i        i     v    vii i       vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_170877527_   1094 AGCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGAATTCC 1143
                          ii    i  i     ivv  v   i v  vv               vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_170877527_   1144 CTACTTAATAAATGGCGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 1193
                           vi i  i      i i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_170877527_   1194 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTAAAGATGGA 1243
                            ii         v   i     v                v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_170877527_   1244 TTAAAGACTTAAATGTAAAACCCAAAATCATAATAACCCT-AGGAAAAAA 1292
                          i ?    i         i v i    ii    -   i  -  i i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAA 545

  chr1_170877527_   1293 CCTAGGC---AATGCCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 1339
                          v    ?---   -- -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_170877527_   1340 CTAAAACGCCAAAAGCAATTTTAATAAAACCCAAAATTGACAAATGGGAT 1389
                         v  vi  i         vvvvi  i    vvv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_170877527_   1390 CTAATTAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 1439
                         i v  i  iv v  i i   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_170877527_   1440 GAATAGGCAACCTACAGAACGGGAGAAAATTTTTGCAATCTACCCATCTA 1489
                            v  i     i      i          v       vii ivi    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_170877527_   1490 ACTATGGTCTAATATCCAGAATCTACAAGAAACTTAAACAAATTTACAAG 1539
                          iv v  v  vi          v  i  ii    ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_170877527_   1540 AAAAAAACAAACAATCCCATC-AAAAGTAGGCGAAGGATATGAACAGACA 1588
                              i     i  i  v  i-    i i   i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_170877527_   1589 CTTCTCAAAAGAAGACATTTATGCGGCCAACAAACATAAGAAAAAAAGCT 1638
                         i     v        i  vi vii      i  i  i v     i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_170877527_   1639 CATCATCACTGGTCAT 1654
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


3012 25.09 1.47 1.35  chr1_170913132_170916877     2012  2828 (918)    L1M4_orf2#LINE/L1        1   818 (90)  

  chr1_170913132_   2012 TGGAAAGATATTCCATGTTCATGGGTTGGAGGAACCAATATTGTTAAAAT 2061
                                    i            i     i  vii           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170913132_   2062 GTCCATACTTACCCAAAGCAATCTATAGATTAAATGTAATCCATATCAAA 2111
                          v v     i-      vii     i     v  i i     v       
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_170913132_   2112 ATAACAATGACATTCTTCACAGAAATAGAAAAAAAAGTCCTAAAATTTAT 2161
                           vv  iivi v  i  ii       v  v  ivvii          i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_170913132_   2162 ATGAAACTACAAAAGACCCAGAATAGCCAAAACTATCCTAAGCAAAAAGA 2211
                            i  v i   ii                   v   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_170913132_   2212 ACAAAGCTGCAGCAATCACATTATTTGCTTTTAAATTATGCTCCATAGCT 2261
                               i  v  v v     i viiiiv   i   viv i  v  v    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_170913132_   2262 ATAGTAACCAAAACAGCAAAAACCAGTACTAGCA--AGAA---ACACATA 2306
                          i     i   i    ii-----ii     i   --  i ---   i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTG-----TGGTACTGGCATAAGGATAGACATATA 294

  chr1_170913132_   2307 GACCAGTGGAACATAATAGGGAACCCAGAGATAAATCTGTACATCTATGG 2356
                           i  i     i v   v i  ii     i     i ii     i     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_170913132_   2357 TGAACTCAGTTTTGACTAAGCTGCTAAGAACATAACACTGGGGAAAGGAC 2406
                          v  i v v   i   v i v   i    v   v-  v         i i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAAT 393

  chr1_170913132_   2407 AGTCTGTTCAATAAATGGTGCTGGGAAGAATGGATATCCATATACAGAAG 2456
                              v     i              vi v      ?   i  i  i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_170913132_   2457 GATGAAACTGGACCCCTGTATCTCATCATGTACAAAAACAAAATTAAAAT 2506
                         i     ii         iiv  v  i   i        iv  v i     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_170913132_   2507 ACATTGAAGACTCAAATATAAGACCTCAAACTATGAAGCTACTAAGAGAA 2556
                         iv  ii?    ii    i     v  v       i  i  vi  ii    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_170913132_   2557 ATTATTGGGA-AACTCTCCAGGACGTTGGACTGGGCAAAGATTTATT-GA 2604
                          vi  v  ?i-  v   i iv   v    ii i     v i   v  -  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_170913132_   2605 -GTGATACCCTAAAAGCATGGGCAAAAAAAGCAAAAATGGACAAATGGTA 2653
                         -i   i   --       iii    v     v      i  i    v v 
  L1M4_orf2#LINE/    594 TATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_170913132_   2654 TCACATCAAG-TTAAAAAGGTATCTGCACAACAAAGAAAACAATCAACAA 2702
                         iiv      i-       --iv i  ii vv     i v  v     v  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_170913132_   2703 AGTGAAGAGACAACCCACAGAATGGGAGAAAATATTTTCAAACTACCTAT 2752
                               i                              v    ii iv   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_170913132_   2753 CTGACAAGGGATTAATAACCAGAATATATAAGGAGCGCAAACAACTCTAT 2802
                             i      i vi  v             i  i v vv       v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_170913132_   2803 AGGAAAAAGTC---TAATCTAATTAAAAA 2828
                          iv      v ---   i i    ?    
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAA 818

Transitions / transversions = 1.68 (126 / 75)
Gap_init rate = 0.01 (12 / 818), avg. gap size = 1.92 (23 / 12)  

 573 15.00 1.67 0.00  chr1_170913132_170916877     3134  3253 (493)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr1_170913132_   3134 AATAATAATAAAATAAA--ATCTAATTTAAAAATGGACAATAGATTTGAA 3181
                                 v  i i   -- i i    ?        i   vi        
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_170913132_   3182 TAGACATTTCTCAAAAGAAGATATACAAATGGCAAAAAGGCATATGAAAA 3231
                                     v                    v  v i   i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_170913132_   3232 GGTGCTTAGCAACACTGATCAT 3253
                          i    i i  v  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 2.00 (2 / 1)  


3224 27.97 0.22 0.22  chr1_170934312_170940588.rev     4879  5786 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_170934312_   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4928
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_170934312_   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_170934312_   4979 TACCAATGACTTTCTTCACAGAATTGGAAAAAACCACTTTAAAGTTCATA 5028
                          v   iivi i  i  ii     v v  v  iviv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_170934312_   5029 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAG 5078
                              viiv  ii  v  v v  v     iv     i i ivv i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_170934312_   5079 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5128
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_170934312_   5129 CAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGATATAGATCAA 5178
                               i   i    ii   i     i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_170934312_   5179 TGGAACAGAA--AAGAGCCCTCAGAAATAATGCCGCATACCTACAACTAT 5226
                              i    --i    i  --        vv  ii i ii  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_170934312_   5227 CTGATCTTTGACAAACCTGAGAAAAAGAAGCAATGGGGAAAGGATTCCCT 5276
                         i    i  i     ivv  vv  i vv vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_170934312_   5277 ATTTAATAAATGGTGCTGGGAAAACTGGATAGCCATATGTAGGAAGCTGA 5326
                         v  i  i              v         ?   i   i ii iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_170934312_   5327 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5376
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_170934312_   5377 AAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5426
                          ?   ii    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_170934312_   5427 AGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAA 5476
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_170934312_   5477 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5526
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_170934312_   5527 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5576
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_170934312_   5577 GCAACCTACAAAATGGAAGAAAATTTTCACAACCTACTCATCTGACAAAG 5626
                         i     i   i     i       v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_170934312_   5627 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5676
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_170934312_   5677 ACAAACAATCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5726
                              i  i  v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_170934312_   5727 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 5776
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_170934312_   5777 CACTGGCCAT 5786
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.55 (152 / 98)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


 201 28.17 1.41 1.41  chr1_170982683_170985268.rev      975  1045 (1541)    L1M4_orf2#LINE/L1       46   116 (792)  

  chr1_170982683_    975 AAAACAGCAACTCTTCCCAAAATCATTTACATATTCAG-GCATTCTCAGT 1023
                           i ii    iv  i      v v  i    v     i-   v  i vi 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_170982683_   1024 CAAAATCTGGGAATGCATTTTT 1045
                                ivi v-   v     
  L1M4_orf2#LINE/     96 CAAAATCCCAGC-TGCCTTTTT 116

Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2)  

2125 22.44 10.53 1.64  chr1_170982683_170985268.rev     1365  2095 (491)    L1M4_orf2#LINE/L1      113   908 (0)  

  chr1_170982683_   1365 TTTTTCTACAAACTGACAAACTAATCCTAAAATTCAGATGGAAATGCAAA 1414
                              vi v   i      i  i             v            i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr1_170982683_   1415 GAACTCGCAACAAATAAAAC-----TAAGAATGA-GAA--AGGTTGGGAA 1456
                          i  i iv  i ivi     ----- i i  v  -   -- i     iii
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr1_170982683_   1457 GCTTACAA--CACAGACTTTAATACATAATATAAAGTTATAATGAGCAAG 1504
                         i  i   v-- v  - i  i  v  v  v  i    i  i i i v    
  L1M4_orf2#LINE/    213 ACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_170982683_   1505 ACTGTGTGGTACT--CA----------CATAGAGTTCAATGGAAGAGAAA 1542
                           v          --  ----------    v  v         v    v
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_170982683_   1543 T-AGTGTCCCAGAAACAGACTTATACATCTACAGTCAATTAATTTTAGAC 1591
                          -  v    -     i i  ii      i  ii       i     v   
  L1M4_orf2#LINE/    312 TGAGAGTCC-AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr1_170982683_   1592 AAA----CTAA-----TTCTATAGATAAA--AGAGTCTTTTCAACAAATG 1630
                           i---- i  -----   v  i iv   -- v                 
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_170982683_   1631 ATGCTGGAACAACTGTATACCCACATGAGAGAGGTGTGGGAAGATG-ACC 1679
                         i      i       v   ?       vi i  i-i  --   v  -   
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGA-ATG--AAGTTGGACC 457

  chr1_170982683_   1680 TCAAGCCTTCATGCCATACATACAAATTAACAGAAAATAGGTAATAGGCC 1729
                         i v -- i   ii     i i v        vv     i i v ?  i  
  L1M4_orf2#LINE/    458 CCTA--CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_170982683_   1730 TGAA-------------ACTATAAAGTCTTTACAGGAAAACATAAAGA-A 1765
                          i  -------------        iiii   v i         ii?i- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_170982683_   1766 CATCTTCACAACCTTGAGGTAGGCAAAATTTCCTTAGATAGGACACAAAA 1815
                         v      iii      i v       viv  i        v     v   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_170982683_   1816 AAAGCAAAAACAATAAAATAAAATATTAATA---TG-ACTTCATCGAAAT 1861
                          --   v  i   i    v    v  vi   ---  -        i    
  L1M4_orf2#LINE/    606 A--GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_170982683_   1862 GTAAAACTTCAGTTCTTCAAGAGACATTAT---GAAAATAAAAAGGCAAG 1908
                         vv       iv  v      ii    i   ---    i i     i   v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_170982683_   1909 CCACTGTCAGGAAGAAACTATTTG-AAATATGTGTATCTGACAAAAGAAA 1957
                             v vvv  i     v      -    -ii i       i  ii  vv
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAAT-CATATATCTGATAAGGGACT 752

  chr1_170982683_   1958 ATATATTCAGAAAATATAAACAACTCTTGCAACTCAGTAA------GACA 2001
                         - i   i     v       v       i       i   ------    
  L1M4_orf2#LINE/    753 -TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_170982683_   2002 AACAA---------AAAGTGGACAAAA-ATTT---TAGACATTT-TATAA 2037
                           i  ---------   i   i    i-    ---         - vi  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_170982683_   2038 AGAAGATATATGAATGATTAATAACCATAAGAAAAAAATGCTCAAAATCA 2087
                                   ii    iii     v  i v     i -       v    
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCA 900

  chr1_170982683_   2088 TTACTCAA 2095
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.73 (102 / 59)
Gap_init rate = 0.04 (31 / 796), avg. gap size = 2.87 (89 / 31)  


2710 23.26 1.42 1.42  chr1_171012639_171016826.rev     2994  3698 (490)    L1M4_orf2#LINE/L1      204   908 (0)  

  chr1_171012639_   2994 AGTTCAAGAA-TCACAA---CTGACTTCAAACTATACTACAGAGCTATAG 3039
                             vi  i -     v--- ii i      viv       i     i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_171012639_   3040 TAACCAAAACAGCATGGGACTGGCATAAAAACAGACACATAGACCAATGG 3089
                            i   i    ii   v          ii i     i     i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_171012639_   3090 AACTGAAGAGAGAACCCAGAAATAAATCCATACGTCTACAGTGAAATATT 3139
                           iv   vv    ii           i      i i  ii  v  v iv 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_171012639_   3140 TTTTGACAAAGGTGCCAAAAACAGACATTGGAGAAAGAACAGTCTCTTCA 3189
                            i     i        i v  vv  v   i       i     i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_171012639_   3190 ATAAATGGTTCTGGGAAAACTGAATATCCATATCCAGAAGGATGAAACTA 3239
                          i       v      v     i   ?   i  v  i   i     ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_171012639_   3240 ATCCCCT--CTCAC--CATATACAAAAATCAAAACAAAACGGATTAAAGA 3285
                         iv     --     --             i  vv     i    i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_171012639_   3286 CTCAAGTATAAGACCTCAAACTATAAAACTACTATAAGAAA-CACTGGGG 3334
                          ii  i i     v  v             vi  v      -  iv  ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_171012639_   3335 AAAATCTCCAGGACATTGGTCTAGGCAAAAATTTCATGGGTAATACCCTA 3384
                         v      i iv   v    vi       vii    v i i  vv  v i 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_171012639_   3385 CAAACACAGGCACCCAAAGCAAACATGAACAAATGAGACCGTATCAAG-T 3433
                         v  i    i   v v    v   v  ii i    vi   ivi     i- 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_171012639_   3434 TAGAAAGCTTCTGCACAGCAAAGGATGCAATTAACAAAGTGAAGAGATAA 3483
                           i   -   i  ii vv       ii v  i  v        i   i  
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_171012639_   3484 CTCACAGGATGGGAGAAAATATTTGTAAACTACCTATCTGACAAGGGATT 3533
                          i     i                 i   ii iv       i      i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_171012639_   3534 AATAACCAGAAAATATAAGGAACAGCTCAAACATCTCTGTAGGAAAAAAA 3583
                         vi  v      v      i    ---  vv   v   vi  iv     i 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAAC---TCTTACAACTCAATAATAAAAAGA 799

  chr1_171012639_   3584 TCGAATAATCTGATTAACACACGGGCAAAAGATTTGAATAGACATTTCTC 3633
                         - i     i ii   ? v v i       i                    
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_171012639_   3634 AAGAAAAAAAAAGACATACAAATGGCAAACAGGCATATGAAAAGATGCTC 3683
                         v -----  i    i           v  i i   i              
  L1M4_orf2#LINE/    849 CA-----AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_171012639_   3684 AACATCTTTGATCAT 3698
                               v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (100 / 60)
Gap_init rate = 0.01 (10 / 705), avg. gap size = 2.00 (20 / 10)  


3063 24.68 7.05 0.59  chr1_171027933_171032842     3567  4417 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_171027933_   3567 GAAAGATATATCATGTTCATGGATGGTAAGAATTAATATTTTTAAAATGT 3616
                                  vi             v v    v        v    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_171027933_   3617 CTATACTACCCAAAGCAATCTACAGATTCAGTGCAATTTCTATCAAAATT 3666
                          v     v      vii             ii     ii          i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_171027933_   3667 CCAATGACATTCTTCACAGAAATAGAAAAAAAAATTT--AAATTCATATG 3714
                            iivi v  i  ii       v  v  ivvi  ii--           
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_171027933_   3715 GAGCCACAAAAGACCCTAAATAGGCCAAGCAATCTTGAGCAAAAAGAACA 3764
                           ivii   ii     vi     v v  i         iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_171027933_   3765 AAGCTGGAGACATCATGCTACCTGATT-CAAAATCTACTACAAAGGTATA 3813
                            i     ivv   ii  v  ii   -     ii          v  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_171027933_   3814 TTAGCCAAAACAGTATGGCATTGGCATAAAAAATAGACGCATAGACCTAT 3863
                         v  ii   i     i   i i        ii -     ii     i v  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAAT 301

  chr1_171027933_   3864 GGAACAAAATAGAGAGTCCCGAAATAAATTCAGGCATTTACAGCCAACTG 3913
                             i i   v        v        ii  vi      ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_171027933_   3914 ATGTTTATGAAAGGTGCCAAGAACACACAATGGGGAAAGAACAGTTTTTT 3963
                           v  iivv  i          v  iv              i   i    
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_171027933_   3964 CAGTAAATGGAACTGGGAAAACTGGATAGCTACATGTAAAAGAATGAAAC 4013
                           ii      vi      v         ? i     i           ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_171027933_   4014 TAGGCCCCTCTCTCTCTCTGTATGTAAG--TCAATTCAAAA-GGATTAAA 4060
                          i i     vi   v v ii   ii  i-- i  i      -    i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_171027933_   4061 TACTTAAATGTGAGACTTGAAACTATGAAATTGCTAGAAGAAAACACAGG 4110
                         v  i       i   vi i       i   i vi            i   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_171027933_   4111 AGAAACACTGTAAGTGA--TTGGTCTGGACAAAGATTTATTTTAGACAAG 4158
                         ? v  vv  vi--    --    vi i i   v i   --i     i v 
  L1M4_orf2#LINE/    552 NGTAAATCTTC--GTGACCTTGGGTTAGGCAATGGTTT--CTTAGATATG 597

  chr1_171027933_   4159 ACCTCAAAAATAAGAGCAACAAAAGCAAACATAAATGGAT----CTACAT 4204
                           vi     ii vi           v   v   i  ii  ----  v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_171027933_   4205 CACACTAAAAAGCTCCTGCACAGCAA-GGAAAAAATCAACAA--TGAAGA 4251
                           v v v    i  ii  ii vv   -   v vv     v  --    i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_171027933_   4252 GACAGCCTATGACATT--AGAAAATATTTGCACATTAT------------ 4287
                             i  i iiiv  v--              v  i  ------------
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_171027933_   4288 ------GCATTCA--ATA-GCAAAAAACCC-------------------- 4308
                         ------ i  i  --   -ii   i   i --------------------
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_171027933_   4309 --CAAATAGTCTGATTTAAAAATGGGCAAAAGATCTGAATAGATATTTCT 4356
                         --      ii ii   ?             i   i        i      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_171027933_   4357 CCAAAGATGACATACAAATAGTCAACAGGTTTATGATAAAACGCTCAACA 4406
                                v  i        i i   i i ivi    v  i i        
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_171027933_   4407 TCACTATCAGG 4417
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.99 (137 / 69)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 4.06 (65 / 16)  


2721 27.20 1.87 2.09  chr1_171062827_171066022.rev     1798  2705 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_171062827_   1798 GAAAAACATTCCATGCTCATATACAGGAAGAAGCAATATTGTGAAAATGG 1847
                             i i  i     i    iv iv      vvi        v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_171062827_   1848 CCAAACTGCCCAGTGCAATTTACATATTCAATGCTATTTCTATTAAACTA 1897
                          v v   v    ivvii  i    v      i  v  ii    i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_171062827_   1898 CCATTGACATTCTTCAAAGAACTACAAAAAAACT-ATTTTAAAATTCATA 1946
                            vivi v  i  iiv    -- ivi v  i  -  ii           
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_171062827_   1947 TGGAACCCCAGAAAAGCTTGAATAGCCAAGGCAATCCTAAGCAAAAAGAA 1996
                              viv  iiii v iv          ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_171062827_   1997 ACAAAGCTGGAGACATCATGCTACATTACTTCAAACTATACTACAGGGCT 2046
                         -     i     ivv   ii  v viv i      viv       ii   
  L1M4_orf2#LINE/    201 -CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_171062827_   2047 ATGGTAACCAAGACAGCATGGCACTGATATAAGAACAGACACATAGACCA 2096
                          ii    i        ii   i    ii     i i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_171062827_   2097 ATGGAACAGAATAGAGAACCCAAGAATAAGACCACACATCTA----CAAC 2142
                               i     v    ii   ii     iv   i    i  ----   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_171062827_   2143 T-ATCTGCAACAAACCTGACAAAAACAAGCAATGGGGAAACGATTCCCTA 2191
                          -  i v i    ivv  v   i v  vv           vi  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_171062827_   2192 TTCAATAAATGGCACTGGGATAACTGGCTAGCCATATGCAGAAGATTAAA 2241
                              i      ii      i      v  ?   i     i    v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_171062827_   2242 ACTGGACCCCTTCCTTACACCATGCACAAAAATCAACTCAAGATAGATTA 2291
                         ii         v   i       ii        i       i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_171062827_   2292 TTGACTTAAATGTAAAACCCAAAACTATAAAAATCCTTGAAAACAACCTC 2341
                         ?v   i         i v i            v  i v   i v   v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_171062827_   2342 AGCA-ATACCATTCGAGACATCGGC----ACAAATATTTCAT-GATGAAG 2385
                         i ?i- v i -    v   v i  v----i   vvi    v -   - v 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr1_171062827_   2386 ATGCCAAAAGCAACTGCAACAGAAGCAAAAATTGATAAATGGTATCTAAT 2435
                          ii         vvv      i   v      v       v v ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_171062827_   2436 TAAACTAAAGAGCTTCTGGCACAGCAAAAACAACAACAACAAAACACTAT 2485
                         i   v v  i i   i  -ii vv    ii-------------       
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTG-TGCTTCAAAGG-------------ACACTAT 683

  chr1_171062827_   2486 CAACAGAGTAAACAGACAATTTACAGAATGGGAGAACATTTTTGCAATTT 2535
                            v i   i  v      iii              v  v       v i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_171062827_   2536 ATGCATCTGACAAAAGTCTAATATCCAGCATCTATAAGGAACTTAAATAA 2585
                           ii      i  ii v  vi       v  v     i     ivv i  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_171062827_   2586 ATTTACAAGAGAAAAACAA----CCCCATTAAAAAGTGGGCAAAGGACAT 2631
                         v iv i  v i   i    ----   v   ?    i           iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_171062827_   2632 GAACGAACATCTCTCAAAAAAAGACATACATGGGGCCAAGAATCA-ATGA 2680
                            iii    i    v   i    i     viv      v  v  -    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_171062827_   2681 AAGAAACCTCAACAACACTGATCAT 2705
                           ii vv       v  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 2.57 (36 / 14)  


3232 26.76 0.66 0.66  chr1_171078832_171085110.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_171078832_   4881 TGGAAGAACATGCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  v     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171078832_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171078832_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_171078832_   5029 TATGGAAC--CAAAAAACAGCCCGCATCGCCAAGTCAATCCTAAGCCAAA 5076
                                v--   iii  --  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_171078832_   5077 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5126
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_171078832_   5127 GCTACAGTACCCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5176
                                  vi   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_171078832_   5177 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAA 5224
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_171078832_   5225 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGGTT 5274
                         ii vi    i  i     ivv  vv  i v  vv            ii v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_171078832_   5275 CCCTATTTAATAAATGGTGCTGGGAAAACTCGCTAGCCATATGTAGAAAG 5324
                         vi  v  i  i              v    v v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_171078832_   5325 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5374
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_171078832_   5375 GATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5424
                            i ?   ii    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_171078832_   5425 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCC 5474
                           v    ?i v viv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_171078832_   5475 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5524
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_171078832_   5525 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5574
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_171078832_   5575 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5624
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_171078832_   5625 AAAGGACTGATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5674
                           i     vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_171078832_   5675 AAAAACAAACAATCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5724
                            i     i  i  v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_171078832_   5725 TCTCAAGAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5774
                             v i      i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_171078832_   5775 TCATCACTGGCCAT 5788
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


1534 26.51 2.13 6.71  chr1_171109111_171112978.rev     1300  1910 (1958)    L1M4_orf2#LINE/L1        5   587 (321)  

  chr1_171109111_   1300 AAAAAATTCCACGATCATGGATTGGAAGAATCAATTTCATTAAAGTGGCC 1349
                           i v  i   i v               v i   v ii    ii    v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_171109111_   1350 ATACTGCCCAAAGAAAGCAAGAGATTGAATGCTATTTCTATTCAACTACC 1399
                              v      vvi v v v     v  i  v  ii    iv  v v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_171109111_   1400 AACATTAGTTTTCACAGAACTAGAAAAAAACT-ATTCTAAAATTCATATG 1448
                          i vvivv    ii     v v  v  i--  -  i              
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATATG 152

  chr1_171109111_   1449 GAACCAAAAAATGGCCCA-AATAGCCAAAGCATTCT-AAGCAAAAAGAAC 1496
                            viiv  ii- i    -          i  v   -i iv  i      
  L1M4_orf2#LINE/    153 GAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_171109111_   1497 AAAGCTGGAGGCATCACATTACCTGAATTCATACTATA-TATAAGGCTAC 1545
                             i      vv     i v  ii v    v viv  -  i  i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_171109111_   1546 AGTAACCAAAACAGCATGATAATTGGTACAAAAACAGATACATAAACCAA 1595
                              i   i    ii  i  -i   i i  ii i   i i   i i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTA-CTGGCATAAGGATAGACATATAGATCAA 300

  chr1_171109111_   1596 CAAAATAAA-----GAACGCAGAAATAAAGCCACACACCTACAGCCATCT 1640
                         iii    i -----  iiv          v   i   ii  ii i  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_171109111_   1641 GATCCTCAACAAAGTCAACAAAAATAAGCAATAGGGAAAGGGC--TCCTT 1688
                            ii  i    i viiv   i vi vv    i       iii--  i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_171109111_   1689 ATTCAATAAATGGTGAAAAGACTTAGCCACACATTATCCCTGCTATTACG 1738
                         --    i        ------------------------   --------
  L1M4_orf2#LINE/    401 --TCAACAAATGGTG------------------------CTG-------- 416

  chr1_171109111_   1739 GGATAGTTGGCTAGCCATATGCAGAAGAAAGAAACTGGACCCTTATCTGT 1788
                            i ii   v  ?   i     i     v   ii       i  i  vv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_171109111_   1789 CACCATACACAAAAATTAACTCCAGATGAATTAAAATTTTTAAATGTAAG 1838
                                i              v i   i  i ? ivii -         
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT-AAATGTAAG 515

  chr1_171109111_   1839 ACCTCAAACTCTAAAAATCT-AGAAGAAAACCTAGGGA-ACACCATTCTG 1886
                          v  v     v     v   -          v    ?i- v i -   vv
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGT 564

  chr1_171109111_   1887 GACATCAGCCTTGGGAAATAATTT 1910
                            v ii v-  i  v   ii   
  L1M4_orf2#LINE/    565 GACCTTGGG-TTAGGCAATGGTTT 587

Transitions / transversions = 1.69 (100 / 59)
Gap_init rate = 0.03 (17 / 583), avg. gap size = 3.18 (54 / 17)  

 873 23.97 1.89 2.52  chr1_171109111_171112978.rev     3061  3377 (491)    L1M4_orf2#LINE/L1      594   908 (0)  

  chr1_171109111_   3061 TATGAC--TAAACCCTCAAA-AACAATTGCAAGAAAACATAAATTAACAA 3107
                               --i   vv v   i-     ----       v   i  ----  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAA----AAGAAAAAATAGAT----AA 635

  chr1_171109111_   3108 GTAGGACCTAATTAAACTGAAGAGCTTCTGCACAGGAAAAGAAACTATCA 3157
                         i v    i v  i   v v  i i   i  ii vvv   i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_171109111_   3158 ATAGAGTAAACAGAAAACCTACAGAATAGGAGAACATACTCAGAAACTAC 3207
                          v i   i  v   v    i       i      v   i iiv   ii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_171109111_   3208 GTATCTGACAAAGGTCTAACATT-AGAATCTATAAGGAACTTAAAAAATT 3256
                         i       i  i  v  vii  i-     v     i     ivv v  i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_171109111_   3257 CAACAAGCACAAAACAAATAACACCATTAAAAAGCAGGCAAAAGATATGA 3306
                            i  vv v  i         v v   ?    iii      i   v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_171109111_   3307 ATAGACACTTCTCAAAAGAAGACAAACAAGCAGCCAACAA--ACATGAAA 3354
                                i     v        i v    iii     i  --        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_171109111_   3355 AAATGCTCAACATCACTAATCTG 3377
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (44 / 31)
Gap_init rate = 0.02 (6 / 315), avg. gap size = 2.33 (14 / 6)  


 590 28.61 2.72 6.27  chr1_171135031_171136930.rev      453   819 (1081)    L1M4_orf2#LINE/L1      232   585 (323)  

  chr1_171135031_    453 AAAACTTA-----AAG-TATAATAATAATAAAAAAAAGAGTTAAGATCTT 496
                                 -----   -  i i    --i  i v iv v v  ----  v
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAAT--CAAGACAGTGTGGTA----CTG 275

  chr1_171135031_    497 GCATAAAGAATATACAAAATGATCAGTGAGA-AGAA--GAAAGTCTAAAA 543
                               i  -  v   v vv     i  ii -    --  i    i i  
  L1M4_orf2#LINE/    276 GCATAAGGA-TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_171135031_    544 ATAAACCCACACTTATATGGTCAACTGAATTTCAATTAAAAATTCTAAAA 593
                                  i  v v         i   v    i i-  iii v i  i 
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGAC-AAGGGTGCCAAGA 373

  chr1_171135031_    594 CAAATCAA-GGAAAAAGGAAAATTTTCTCAGTAAATGGTATTAGAAAAAT 642
                          v v    -  ii    i v i i  i   ii       ii i i v  i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_171135031_    643 TTGAATAATCTTCTGGGGAAAAATTAACTTAGACCATGTCCTCACAATAT 692
                          - i   ?i viv  vii  i   v  v  i    vivv       vi  
  L1M4_orf2#LINE/    424 T-GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_171135031_    693 ATAGAAAAATTTAAATGATATGGATCATAGATCTAAACAAAAAAAAATTG 742
                            v       v vvii v        ?   i     iiv  i i--i i
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG--CTA 520

  chr1_171135031_    743 AAACTGCAAATATATAGCTTCTAAAGGAAAACATTCTAGAAGAAGAATGT 792
                              ------   v i  ii  i i        ---  i? v i --- 
  L1M4_orf2#LINE/    521 AAACT------ATAAAACTCTTAGAAGAAAACAT---AGGNGTAAA---T 558

  chr1_171135031_    793 CTTCATAACTTAAGGATAGACAAAGAT 819
                             i i  i vi  v   i   v i 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGT 585

Transitions / transversions = 1.76 (65 / 37)
Gap_init rate = 0.04 (14 / 354), avg. gap size = 2.36 (33 / 14)  

 774 23.93 10.16 0.66  chr1_171135031_171136930.rev     1106  1410 (490)    L1M4_orf2#LINE/L1      575   908 (0)  

  chr1_171135031_   1106 TAGACAAAGACTTATTAG----GATACTGGAAGCA---ATAACTATAAAA 1148
                            i   v ii  v    ----  i  iii     ---ii   v v i  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_171135031_   1149 AAGTTTAATAAAATATACTT----AAAAT-AAA---TGTTCTGCTTAGCA 1190
                           iv vi     v iv    ----     -   --- v  v     --  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CA 672

  chr1_171135031_   1191 AAAGACATCATTAAGAAAATCAG----CAAGCCA--------AAGACAGT 1228
                           i    ii  i      i v i----   v   --------i   v i 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_171135031_   1229 ATTAGCAAAACATATGTCTAACAAAGGAGTTGCATCCAAAATATATAACT 1278
                            v     v     i   i i  i   v   i     i         vv
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_171135031_   1279 GACTCCTACAATTTGTTAATATGAATACAAATAATCCAATT--AAAATGG 1326
                         i    i     i iiv     vi  v        i      --       
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_171135031_   1327 TGAAAAAACTGGAA--GACACTTCACAAAAGAAGATATACAAATAACCAT 1374
                         vv   ii i v   --    i   v v                 ii   v
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_171135031_   1375 TAAGAAAATGAAAAAATGCTCAGCACCCACAGTCAT 1410
                             v v       i       i  i v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (43 / 30)
Gap_init rate = 0.03 (10 / 334), avg. gap size = 3.30 (33 / 10)  


2850 25.47 6.54 0.47  chr1_171184449_171187646.rev     1852  2707 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_171184449_   1852 TGGATAGATATTTCATGTCCGTGTATCGGAAGACTCAATCTTGTTAAAAT 1901
                             v      ii     i i  v  i        i   v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171184449_   1902 GTCCATATTACACAAAGCAATCAACAGATTCAGTGCAATCCCTATCAAAA 1951
                          v v   i v v    vii   v         ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171184449_   1952 TACCAAAGATATTCTTCACAGAAATAGGGAAAACAATCCTGAAATTTACA 2001
                          v   ivviiv  i  ii       v iv  ivii     i     i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_171184449_   2002 TGACA--GCACAGAAACTCAGAATAGCCAAAGTTATCCTAAGCAAAAAGA 2049
                           iv --   -  ii  i             iiv   i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_171184449_   2050 ACAGAACTGGAAGAATCACA-TTACTGACTTCAAATTATATGACAGAGCT 2098
                            i ii    i  v     -  v ii i      viv  iv   i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_171184449_   2099 ACA-TAACCAAAAC-----------GGCACA------------------- 2117
                            -   i   i  -----------    i -------------------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_171184449_   2118 ---GAATAGA-----GAACCTAGAAATAAACCCACACATCTACAATGAAT 2159
                         ---       -----  ii i             i    i  iii v   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_171184449_   2160 TCATTTTTGACAAAGTTGCTCAGAAAATACATTGGGGAAAGGACAGTCTC 2209
                          v     i     i v   iv   vv  v  v         i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_171184449_   2210 TTCAATAAATGTTGTTGGGAAAACTGATTATCCATATGCAGAAGAA---- 2255
                              i     v  i     v     iv  ?   i     i     ----
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_171184449_   2256 -------CCCTATCTCTCACCATATACAAATATCAAATCAAAATGGATTA 2298
                         -------     i   v             v  i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_171184449_   2299 AAGACTTAAATCTAAGGTCTCATATTATAAAACCACTACAAGAAAATATT 2348
                         ?    i     v    iv  v v i        ivi  v       i  v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_171184449_   2349 GGGGAAACTTTTAAGGACATTAGCCTGGGCAAAAATTTCTTGAGTA--AT 2396
                           ? v  v i  viv   v  i vi i     vii      iii  -- i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_171184449_   2397 ACCACACAAGCACAGGCAACCAAAGCAAACATGGACAAATGGGATCACAT 2446
                             - -       i     v    v   v  i  i    v   iiv   
  L1M4_orf2#LINE/    600 ACCA-A-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_171184449_   2447 CAAGGTAAAAATCTTCTGCATAGCAAAGGAAACAATGTACAAAGTCAAGC 2496
                            ii v    v   i  iiivv       v  v  vv v     v  iv
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_171184449_   2497 AACAACCCACAGAATGGGAGAAAATATCTGCAAACGACCCATCTGACAAG 2546
                         i                          i      iv ivi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_171184449_   2547 GGATTAATAACCAGAATCTATAAGGTTCTCAAACAACTCTATAGAAGAAA 2596
                            i vi  v       v     i vv   vv       v   iv i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_171184449_   2597 AATCTAACAATCTTATTAAAAAATGGG-AAAACATCTGAATAAACATTTC 2645
                         i - v  i  i iv   ?         -   iv  i      i       
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_171184449_   2646 TCCAAAGATGACATACGAATGACACACAGGTATATGTAAAGGTAATCAAT 2695
                                 v  i    i    i vv i i i i   v    i iv    i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_171184449_   2696 ATCACTGATCAT 2707
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (127 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.62 (60 / 13)  


 444 18.07 0.00 0.00  chr1_171203987_171206409      682   764 (1659)    L1M4_orf2#LINE/L1        1    83 (825)  

  chr1_171203987_    682 TGGGAATATATCCTGTGTTCATAGATTAGAAGAATTAATATTGTTAAAAT 731
                            i  v      ii       i    i     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171203987_    732 GTCCATACTACCTAAAACAATCTACAGATTCAA 764
                          v v     v  i   vii              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA 83

Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.00 (0 / 0)  

2857 22.99 2.92 5.60  chr1_171203987_171206409     1080  1936 (487)    L1M4_orf2#LINE/L1       75   908 (0)  

  chr1_171203987_   1080 CAGACTCAACAC--CCTTTATCAAAATTCCAATAACTTTTTTCACAGAAA 1127
                             i     i --i ii         i   iivi i     ii      
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr1_171203987_   1128 TAGAAAAAATAACCCTAAAACTTGTTTTAGGATTGTTTAAATCTTATTTG 1177
                          v  v  iv i i       i ii v --   -------   ------- 
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATAT--GGA-------AAT-------G 158

  chr1_171203987_   1178 TTTAAATCCTGTTTAGACCCTGAATAGCCAAAGCAAACTTGAGGGAAAAA 1227
                         i--  i--------i     v           i   v     -----   
  L1M4_orf2#LINE/    159 C--AAG--------GGACCCAGAATAGCCAAAACAATCTTGA-----AAA 193

  chr1_171203987_   1228 AAAAAAACCAAACAAATAAAAACAAAGCTGGAAGCATAACACAACCTGAC 1277
                          i  i   ---------------    i    i vv v    vv  ii i
  L1M4_orf2#LINE/    194 AGAAGAAC---------------AAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_171203987_   1278 TTCAAAATACAATACACAGGTATAATAACCAAAACGGCATGGTACTGGCA 1327
                                ivi v    v  v  i i   i   i  i ii           
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_171203987_   1328 CAAAAACAGAACCATAGACCAATAAAACAGAAGAGAGGGCCCAGAAGTAA 1377
                         i  ii i   vvi     i    ii  i    vv   i i      i   
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_171203987_   1378 A----TACATTTATAGTCAATTGATTTTTGACAACTATGCCAAGAACACA 1423
                          ----         i             i     vvi        v  iv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_171203987_   1424 CAAGATGGAAAAGACAGTCTCTTCAATAAATGGTCCTAGGAAAACTGGAT 1473
                            viv     ii i     i     i       v  i   v        
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_171203987_   1474 ATCCATGTGCAGAATAATGAAATTAGAGCCTCATTTCATACCATATACAA 1523
                          ?   ii    i  v      i  i  v  ii ii   i           
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_171203987_   1524 AAATTCAAGTCAAAATGAA-----GACTTAAATGTAAAACCTGAAACTGT 1568
                              -  v        i -----   i         i v  i     i 
  L1M4_orf2#LINE/    479 AAATT-AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_171203987_   1569 AAAACTACTAGAAGACAGTGTAGGGGAAAAGCTCCATGACATTGGTCTGG 1618
                               vi       v iii    ? v   v  i i    v    vi i 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_171203987_   1619 GCAATGATGTTTTAGATATAATTCCAAAAGCACAAGCAACAGAAGCAAAG 1668
                               i v i        i iv                  i   v   i
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_171203987_   1669 GTAGACAAATAGAATTGAATCAAA-TGAAAAAGCTTCTGCACAGCAAAAG 1717
                         i    i    v i i vv      - v     -   i  ii vv    i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGG 676

  chr1_171203987_   1718 AAAC----AACAGGGTGAGGAGTCATCCTACAGAATGGGTGCAAATATTT 1763
                          v  ----  v ii    ii  v  v  i          v v        
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_171203987_   1764 GCCAACCATACATCTGATAAGGGGTTAATATCCAAAATATATAAGGAAT- 1812
                           v  i    i            ii vi      i         i   i-
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_171203987_   1813 ----CAATTCAATTGTAAGAAAACAA----CCTGATTTAAAAATGGGCAA 1854
                         ----   i     vi   i  i    ----  ii   ?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_171203987_   1855 AATACCTGAATAGACACTTCTCAAAAGAAGACATAAAAATGGCCAGCAGG 1904
                          iv ii          i     v        i   v         ii i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_171203987_   1905 TATATAAAAAAATGTTCAGTGCTATAAGAGGA 1936
                         i i  i    i   i   iiiii ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (135 / 59)
Gap_init rate = 0.02 (16 / 834), avg. gap size = 4.56 (73 / 16)  


 832 21.21 2.53 0.00  chr1_171224699_171229477.rev     2465  2662 (2117)    L1M4_orf2#LINE/L1      706   908 (0)  

  chr1_171224699_   2465 ACAGCACAACAGACAATATTTGCAAACTATTCATCCAACAAAGGACTAAT 2514
                             v iiiv   v            ii  vi   ii i  i     vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_171224699_   2515 ACCCAGAATATGCAAGAAACTC-----AGTCGACAATAGAAAAACAAATA 2559
                          i         ii  ii     ----- v  i i    i   i       
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_171224699_   2560 ATCCCATTAAAACATGGGCAAAGGACATGAATAGACAATTCTCAAAAGAA 2609
                          i  v   ?   v            iv          v     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_171224699_   2610 GACATACAAATGACCAATGGGTATATGAAAAAATGTTCAACATCACTAAT 2659
                           i         i     ii i i       i   i         ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_171224699_   2660 CAT 2662
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.73 (30 / 11)
Gap_init rate = 0.00 (1 / 203), avg. gap size = 5.00 (5 / 1)  

3060 26.48 2.01 0.56  chr1_171224699_171229477.rev     3394  4288 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_171224699_   3394 TGGAAAGACAACCCATGCTCATGGATCAGAATAATTAGTATTGTTAAAAT 3443
                                 i v      i        ii   v v   i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171224699_   3444 GACCATACTGCCCAAAGCAATCTA-AAATTTAATTCGATCCCTAT-AAAA 3491
                          i v     v      vii     - i   i  iv i        -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171224699_   3492 TTACAA-TGTAATTTTTCACAGAGTTAGTAAAAAG--AATTCTAAAATGT 3538
                          iv  i-  iv-     ii    i-- v i v   --i  i       vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chr1_171224699_   3539 TTATGGAACCAAAAAAGAGCCAGGATGGCCAAAGCAATCCTGAGCAAAAA 3588
                         v       viiv  ii  v    i  i      i     i   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_171224699_   3589 GAACAAAGCTGGAGGTAGCACACTACCTGACATCACATTATATTACAAGA 3638
                                 i      vvv      v  ii iv   v viv  i     ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_171224699_   3639 CCATAGTAACCAAAACAGCATGGGAATAGCACAACAACAGACAAAAAGAC 3688
                          i i     i   i    ii   v v i   i  vi i     v v   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_171224699_   3689 GAATGGAACAAAATAGAAAAGACAGAAATAAATCCACCTATTTACAACTA 3738
                         v       i i   v  i ivv          i   ivi     iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_171224699_   3739 ACTGATTTTTGACAAAGGCACCAAGAACATATGCTGGGAAAAGGACACAC 3788
                          i       i     i  ii      v   viiv    i    i i vv 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_171224699_   3789 TCTTCAATAAATGGTGCTGGGAAAATCGGATATCCATATGCCAAAGAATG 3838
                          i     i              v  ii     ?   i    v        
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_171224699_   3839 AAACTGGACCATTATCTCTCATCACATACAAAAATCAATTCAAGATGGGT 3888
                           ii      vi  i   v  i  i          i  i    i    i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_171224699_   3889 TAAAGACTTAAAAGTAAGACCCAAAACTATGAAACTAATAGAAGACAACA 3938
                         i ?    i    v      v i        i     vv       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_171224699_   3939 TAG-TG-AAATTACTTCAGAACACTGGTCCAGGCAAAGATTTTACAGCTA 3986
                            -? -    --    ivi  vi   vii      v i   ivi  v  
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_171224699_   3987 AGACCTTAAAAGCACAAAAAACTAAAACAAAAATAAACAAGG-GGACTAT 4035
                         v   vii          iv   v   iv       i i  iv-     vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_171224699_   4036 ATTAAACTAATAAGCTTCTGCACAGCAAAGGAAATAATCAACATAGTGAA 4085
                           i   v v v  i   i  ii vv       v iv     v v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_171224699_   4086 GAGACAACTTGTTGAACAGGAGAAAATATCTGCAAACTATTCATTCAACA 4135
                         i       iiiiv   ii           i      ii  vi  iii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_171224699_   4136 AGGGATTAATATTCAGAATATCCAAGGAACTC---------AAGAATGAA 4176
                              i vi   i        vi  i      ---------  v   i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_171224699_   4177 AAAACAAATATCCCA-TTAAAAAGTGGGCAAATGACACAAATAGACAATT 4225
                           i       v    -  ?    i        v  ivii        v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_171224699_   4226 CTCAACAGAAGACATACAAATGACGAACAGGTATATAAAAAAATGTTCAA 4275
                            v v      i         i v  i i i i  i    i   i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_171224699_   4276 CATCACTAATCAT 4288
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (150 / 83)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


3211 26.98 0.55 0.55  chr1_171240339_171247016.rev     5280  6187 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_171240339_   5280 TGGAAGAACATCCCATGCTCGTGGATAGGAATAATCAATATTTTGAAAAT 5329
                              ii i        i  i     v    v v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171240339_   5330 GTCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5379
                          v v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171240339_   5380 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5427
                          v    ivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_171240339_   5428 TATGCAACCAAAAAAGAACCCACATTGCCAAGACAATCCTAAACAAAAAG 5477
                             v  viiv  ii  v  viv  v     i      i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_171240339_   5478 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGAC 5527
                                i      vv    i  v  ii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_171240339_   5528 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5577
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_171240339_   5578 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 5625
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_171240339_   5626 ATCTGATCTCTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5675
                          vi    i ii     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_171240339_   5676 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAAGCT 5725
                           v  i  i              v      v  ?   i i i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_171240339_   5726 GAAACTGGATCCCTTCCGTATACCTTATACAAAAATTAATTCAACATGGA 5775
                            ii    i    v  vi i   v              i    v     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_171240339_   5776 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGGGGAAAAC 5825
                          i ?    i       v   v       i      vi i   ii      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_171240339_   5826 CTAAGCA-ATACCATTTAGGACATTGGCATGGGCAAGGACTTCATGACTA 5874
                         v  i ?i- v i -  iiv   v    vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_171240339_   5875 AAACACCAAAAACAATGGCAACAAAAGCCAAAATAGATAAATGGGATTTA 5924
                         vi         i  vvi          vv             v   i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_171240339_   5925 ATTAAACTAAAGAGCTTCTGCACAACAAAAGGAACTACCCTCAGAGTGAA 5974
                           i   v v  i i   i  ii vv    i iv    i vvv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_171240339_   5975 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACA 6024
                         v  i     i                 v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_171240339_   6025 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 6074
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_171240339_   6075 AAATCAAACTACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 6124
                           iv    iv    v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_171240339_   6125 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTTAT 6174
                            v        i  vi viii     v ii          i     i v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_171240339_   6175 CATCACTGGCAAT 6187
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3358 26.54 0.44 0.44  chr1_171291397_171297674.rev     4880  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_171291397_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171291397_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171291397_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_171291397_   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_171291397_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_171291397_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAAGAGAGATATAGATC 5177
                                 i   i    ii         i iv ii v   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_171291397_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5225
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_171291397_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_171291397_   5276 CTATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATGTAGAAAGAT 5325
                           v  i  i              i      v  ?   i   i i  ii  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_171291397_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_171291397_   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_171291397_   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_171291397_   5476 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5525
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_171291397_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_171291397_   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_171291397_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_171291397_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_171291397_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_171291397_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3266 26.54 0.55 0.55  chr1_171311101_171317523.rev     5025  5932 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_171311101_   5025 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5074
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171311101_   5075 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5124
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171311101_   5125 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5172
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_171311101_   5173 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5222
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_171311101_   5223 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5272
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_171311101_   5273 TACAGTAACCAAAACAGCATGGTAGTGGTACCAAAAGAGAGATATAGACC 5322
                                 i   i    ii     v   i iv ii v   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_171311101_   5323 AATGGAACAGAAC--AGAGCCCTCAGAAGTAACACCACATATCTACAACT 5370
                                i    i--    i  --    i   vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_171311101_   5371 ATCTGATTTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5420
                          vi       i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_171311101_   5421 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAGCT 5470
                           v  i  i              v      v  ?   ii  i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_171311101_   5471 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5520
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_171311101_   5521 TAAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5570
                          v ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_171311101_   5571 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5619
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_171311101_   5620 AAACACAAAAAGTAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5669
                         vi    v     i vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_171311101_   5670 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5719
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_171311101_   5720 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5769
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_171311101_   5770 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5819
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_171311101_   5820 AAAACAAACAACCCCATCAAAAAATAGGCAAAGGACATGAACAGACACTT 5869
                           i     i     v  i?      i         iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_171311101_   5870 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5919
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_171311101_   5920 CATCACTGGCCAT 5932
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3147 25.16 1.10 1.32  chr1_171346256_171350912.rev     3259  4168 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_171346256_   3259 TGGAAAAACATTCCATGCTCATGGATAGAAAGAATTAATATTGCAAAAAT 3308
                               i i  i     i        v i    v         iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171346256_   3309 GGTCATACTGCCCAAAGCAATCTTTAGATTCAATGCTATCCCCATCAAGC 3358
                           iv     v      vii    vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171346256_   3359 TACCA-CTGACACTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCT 3406
                          v   -   v -i i  ii     v v  v  i-  - iii    v   -
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC- 147

  chr1_171346256_   3407 CATGTGGAAC--CAAGAAAGCCTGTATAGCCAAGACAATCCTAAGCAAAT 3454
                         -  i     v--    ii v  v v        i      i i iv  iv
  L1M4_orf2#LINE/    148 -ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_171346256_   3455 AGAACAAATCTGGAGGCATCATGCTACTTGATTTCAAACTATAATACAAG 3504
                                 vi      vv   ii  v iii        viv  v     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_171346256_   3505 GCTACAGTAACGAAAACAGCATGGTACTGGTATCAAAACAGATATATAGA 3554
                                   iv  i    ii         i  v ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_171346256_   3555 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAAC 3604
                         i        i    iv   ivii         vv   i    i  iiiv 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_171346256_   3605 ATCTGATATTTGACAAACCTGACAAAAACTAGCAATGGGGAAAG--TATT 3652
                          vi    v  i     ivv  v   i v vvv            --  v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_171346256_   3653 CCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 3702
                          i -  i  i        i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    397 CTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_171346256_   3703 TGAAACTAGACCCCTTACTTAAATCTTATACAAAAATTAACTCAAGATGG 3752
                             ii i       vv  i v i v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_171346256_   3753 ATTAAAGACTTAAACATAAGACCTAAAACCATAAAAATCCTAGAAGAAAA 3802
                           i ?    i    ii     v       i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_171346256_   3803 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAATACTTCATAACT 3851
                          v    ?i- v i -   iv   v v  vv i     vvii   v  iv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_171346256_   3852 AAAACACCAAAAGCAATAGCAACAAAAGCTAAAATTGATGAATGGGATCT 3901
                          vi            vv           vv     v   i   v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_171346256_   3902 AATTAAA-TGAAAGAGCTTCTGCACAGCAAAAGAAACTTATCATCA--GT 3948
                         v  i   - v   i -   i  ii vv    i  v   -    vv --  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT-ATCAAGAAAGT 692

  chr1_171346256_   3949 GAACAGGTAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTG 3998
                            v  ii    i                 v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_171346256_   3999 ACCAAGGGCTAATATCCAGAATCTACAATGAACTTAATTAAACAAATTTA 4048
                          iv i  i  vi          v  i  v     i--   --   v iv 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTC--TTA--CAACTCAA 788

  chr1_171346256_   4049 CAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACA 4098
                         i  v     i     i     v  i?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_171346256_   4099 GACACTTCTTAAAGGAAGATATGTATGTGGCCAACAAACATATGAAAAAA 4148
                             i    iv  i        ii vi       i  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_171346256_   4149 AGCTCATTATAATTGGTCAC 4168
                         v     vi  v ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (128 / 97)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.38 (22 / 16)  


2976 25.37 0.81 0.27  chr1_171369161_171373563.rev     2641  3381 (1022)    L1M4_orf2#LINE/L1        1   745 (163)  

  chr1_171369161_   2641 TGGAAAGATATCCCATGTTCATGGACTGAAAAAATTAATATTGTTAAAAT 2690
                                                  i  i  i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171369161_   2691 GCCCATATAGTCCAAAGTGACCCATGTATTCAATGGAATCCCCATAAAAA 2740
                          v v   ivvi     v   i i iiv      i v      i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171369161_   2741 TACCAATGACATTATTTACAAAAATAGAAAAATAAATCTTTAAGATTTAT 2790
                          v   iivi v  v   i  i    v  v  iivi   i -  i   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAATTCAT 149

  chr1_171369161_   2791 ATTGAACCACAAAAGACCTTGAATAGCCAAAACAATCTTCAGCAAAAAGA 2840
                           v   vii   ii    iv                   v iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_171369161_   2841 ACAAAGCTGGAAGCATCACATGACTTGGCTTCAAAATACACTACAAAGCT 2890
                               i    i vv     ivv iiiii       ivi           
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_171369161_   2891 ATAGTAACCCAAACAGCATGGGATTGGCATAAAAACAGAAAGCTAGACCC 2940
                          i     i v i    ii   v i        ii i   v vv    i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_171369161_   2941 AAGAAACAGAATAGAGGGCCTGGAAATAAATTCACACATTTACAGCCAAC 2990
                          v i  i     v   i i ii        ii  i       ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_171369161_   2991 TGATTTTCAACAAAGGTACTAAGAACATACAATGTGGAAAGAACAGTCTC 3040
                                 i    i   i i    v   v     v        i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_171369161_   3041 TTCAATACATGGTTCTGAGAAGACTGCATATCCACATGCAGAATAATAAA 3090
                              i v     v   i  vi    v   ?         i  v   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_171369161_   3091 GCTAGACCCTTATCTCTCACCATTTGCAAAAATAAACTCTAAATGGATTA 3140
                          i i     i  i   v      v i       v     v        i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_171369161_   3141 AAGATGT-----TAAGACTTGAAACTATGAAACTACCAGAAGAAAATA-A 3184
                         ?   iv -----     vi i       i     vii         i - 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_171369161_   3185 AGAGAAAACGCTCAAGGACATTGGTCTGGGCAATGATTTTTTGGATATGA 3234
                         i ? v   ivi  i-v   v    vi i       i   i  i       
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_171369161_   3235 CTTCAAAGGCACAGACAACAAAAGTAAAAATAGACAAATGTGATTGCATC 3284
                          vi    i     ii         v         i    vv  i v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_171369161_   3285 AAACTAAAAAGCTTCTGCATAGCAAAGAAAACAACCAACAGAGTGAAGAG 3334
                            v v    i   i  iiivv     i v  v i   v i      i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_171369161_   3335 ACAACCTACAAAATGGGATAAATTATTTGCAAACTATACATCTAATA 3381
                               i   i       v   v          ii   i    i   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

Transitions / transversions = 1.72 (117 / 68)
Gap_init rate = 0.01 (4 / 745), avg. gap size = 2.00 (8 / 4)  

 552 22.93 3.18 0.64  chr1_171369161_171373563.rev     3748  3904 (499)    L1M4_orf2#LINE/L1      730   890 (18)  

  chr1_171369161_   3748 AATAAAACATCTGATGAGGGGTTAACAATGAAAATTATATGAGGAACTC- 3796
                            v v i       i    ii vii viv i  -     i i      -
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAA-TATATAAAGAACTCT 778

  chr1_171369161_   3797 ---AAATCAATAGCAAGAAAACAAACAACCCAATTTAAAA-TGAGCAAAA 3842
                         ---  v      ii  i  i     i         ?    -  i     i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_171369161_   3843 GATGTGAATAGACATGCCTTAAAAGAAGACGTACAAATGGCCAACAGGAA 3892
                            v           vi  iv        ii             i i v 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_171369161_   3893 TATGAAAAAATG 3904
                         i       i   
  L1M4_orf2#LINE/    879 CATGAAAAGATG 890

Transitions / transversions = 2.50 (25 / 10)
Gap_init rate = 0.02 (3 / 161), avg. gap size = 2.00 (6 / 3)  


 527 23.28 0.86 0.00  chr1_171429236_171431018       44   159 (1624)    L1M4_orf2#LINE/L1        1   117 (791)  

  chr1_171429236_     44 TGAAAAAACATTTCTTGTTCATGGATTGGAAGAATCGGTATCATTAATAT 93
                           i   i i  ii v                  v iii   ii    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171429236_     94 GGCCATACTGTGCAAAGTAACCTACAGATACAATGCTATTCCTATCAAAC 143
                            v     viv    v i i        v   i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171429236_    144 TACCAG-TGTCTTTTTT 159
                          v    -  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT 117

Transitions / transversions = 1.45 (16 / 11)
Gap_init rate = 0.01 (1 / 117), avg. gap size = 1.00 (1 / 1)  

2627 25.97 2.13 1.00  chr1_171429236_171431018      501  1297 (486)    L1M4_orf2#LINE/L1      103   908 (0)  

  chr1_171429236_    501 CCAG-TGTCATTTTTGACAGAACTAAATAAAACTATTCAAAAAATTCGTA 549
                             -  i v      -     v vi i  i-  iv  vv       i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTG-CAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr1_171429236_    550 TGGA--CCCAAAAGAGCCCAAATAGCCAAAGCAATCCAAAGCAAAAAGAA 597
                             --iv   ii  v  vi          i     ivi iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_171429236_    598 CAAAGCTGGAGGCGTCACATTACCTGTCTTCAAA-TATACTGTAAGGCTA 646
                              i      vv     i v  iivi      -iv    ii  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_171429236_    647 TATAGTAATCAAAACAACGTGGTACTGGTACAAAAATAGACACATAGACC 696
                         i --        i   ii          i i  ii       i     i 
  L1M4_orf2#LINE/    251 CA--GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_171429236_    697 AAAGGAACAGAATAGAGAACCCAGAAATAAAGATGCACACTTACAACTAT 746
                           v    i     v    ii           vviii   i   iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_171429236_    747 CTGATCTTTGACAAAGTCGACAAAATTCAGCAATGGAGAAAGGACTCCCT 796
                         i    i  i     i vi v   i iivvv      i     i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_171429236_    797 ATTCAATAAATGATGCTGGGATAGTTGGCGAGCCATATGCAAAAGAATGA 846
                         v     i     i        i ii   vv ?   i              
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_171429236_    847 AACTGGACCCCTACCTGTCACCATATACAAAAATTAACTCAAGAAGGATT 896
                          ii             vv                        i v    i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_171429236_    897 AAAGATTTAAATGTGACATCACAAACTATAAGAATCCTAGAAGAAAATCT 946
                          ?   ii       i v v vv         i v  i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_171429236_    947 AGGAA-ACACCATTCTGGACATCAGCCTTGGGAAAGAATTTATGACTAAG 995
                            ?i- v i -   vv   v ii vi v  v  v iv  iv iiv  v 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_171429236_    996 TCCTCAAAAGCAATTGCAACAAAAACAAAAAATTGACAAGTGGAACCT-- 1043
                         v vi        vvv         i-       v  i  i v i  i --
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCA 646

  chr1_171429236_   1044 ----AATTAAAGAGCCTCTGCACAGCAAAAGAAATTATCAACAGAGC--- 1086
                         ----       i - i i  ii vv    i  v i      v i  i---
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_171429236_   1087 -AGACAACCTACAGAATGGGAGATGATATTTGCAAAGCATGCATCTGACA 1135
                         -        i             vi           v   ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_171429236_   1136 AAAGTCTAATACATAGAATCTATAAGGAACTTAAACAGTTGAACAAGCAA 1185
                          ii v  vi  ivi     v     i     ivv   ii v  i  vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_171429236_   1186 AAAACAAATAACCCCATTTAAAAAATGGACAAAGGACACGAACAGACACT 1235
                           i           v   ?     -   i       ivi   i     i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATT 844

  chr1_171429236_   1236 TCTCAAAAGAAGACATACAAGCAGCCAA-AAG-ACATGAAAAAATGCTCC 1283
                             v        i      iii     -   -         i      v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_171429236_   1284 ATATCACTAATCAT 1297
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (125 / 78)
Gap_init rate = 0.02 (15 / 806), avg. gap size = 1.67 (25 / 15)  


 331 29.20 1.77 1.77  chr1_171441115_171443068.rev      502   614 (1340)    L1M4_orf2#LINE/L1      274   386 (522)  

  chr1_171441115_    502 TGGTATAAAAGTAGCCACATAGACCAGTAGAACAAAACAGAGAACTCAGA 551
                            i    iii   v  i     i  i i   i i  iv    iii    
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_171441115_    552 AATAAAGACACATAGTTACAGCCAACTGATCTTCAACAAAGCCAACAAGA 601
                               vv  i i v   ii i   i    i   i    i viiv     
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_171441115_    602 --ATTTATACTGGGG 614
                         --   i - -     
  L1M4_orf2#LINE/    374 CCATTCA-A-TGGGG 386

Transitions / transversions = 3.71 (26 / 7)
Gap_init rate = 0.03 (3 / 113), avg. gap size = 1.33 (4 / 3)  

1730 23.77 1.83 3.11  chr1_171441115_171443068.rev      917  1463 (491)    L1M4_orf2#LINE/L1      369   908 (0)  

  chr1_171441115_    917 CAAAAACTTACACTGGGGAAAGGACAATCTCTTCAATAAACGGTGCTGGG 966
                            i v v v  v         i i i   i     i   i         
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_171441115_    967 AAAATTGTATAGCCA--TGCAGAAGAATGTAACTGGACCATTATCTCAC- 1013
                          v  i  v   ?   --    i       v ii      vi  i     -
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_171441115_   1014 -CATATACAAAAATGAACTCAAAGTAGATTAAAGACTTAAAAGTAAAACC 1062
                         -             v        i i   i ?    i    v    i v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_171441115_   1063 TGATACTATAGAAATATTAGAAGAAAAAATCTAGGGAACCCTCTCCTGGT 1112
                          i v      i  v v           v  vvi? v  vi  -  v  ii
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT-TCGTGAC 567

  chr1_171441115_   1113 TGTTGGTTTAGGCAAAGAATTTGTTACAAA-GGCCTCAAAAGATCAGGCA 1161
                         i-    v        v i-   v   v v - i vi      vv  i   
  L1M4_orf2#LINE/    568 C-TTGGGTTAGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_171441115_   1162 ACAAAACCAAAAATAAGTGATTGGGAATTAATTAAACTAAAAAGCTCCCA 1211
                               vv       ii i v v   v  v  i   v v    i  iiii
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_171441115_   1212 CACACAAAAAAAAAAAAACAAAACAAAAAAATCAACAGAGTGAAGAGACA 1261
                         ii viv   ii ------  --- v -----    v i      i     
  L1M4_orf2#LINE/    666 TGCTTCAAAGGA------CA---CTA-----TCAAGAAAGTGAAAAGACA 701

  chr1_171441115_   1262 ACCTGCAGAATGGGATAAAATATTTGCAAATTATTTATCCAACA-GGAAC 1310
                            ii          v               i  v    ii i -  i  
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_171441115_   1311 TAATATATAGAACAGATAAGGAACTC----AACTCAACAGGAAAAAAACA 1356
                          vi   vi    i v    i      ----       i iv     i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_171441115_   1357 AATAATCCCATTCATACTTGGGCAAAGTATATGAATAGCCATTTCTCAAA 1406
                              i  v   ? v vv         v  v       v        v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_171441115_   1407 AAAATAAATACAAACAGCCAACAGGTATATGAAAAAATGTTCAACCTCAT 1456
                          i  v v       ii     i i i i       i   i     v   ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_171441115_   1457 GAATCAT 1463
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.21 (69 / 57)
Gap_init rate = 0.02 (11 / 540), avg. gap size = 2.45 (27 / 11)  


3223 27.10 0.88 0.44  chr1_171544274_171550538.rev     4871  5774 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_171544274_   4871 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4920
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171544274_   4921 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4970
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171544274_   4971 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5018
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_171544274_   5019 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5068
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_171544274_   5069 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTTCAAGGC 5118
                                i      vv    i  v  ii i      viv    v   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_171544274_   5119 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5168
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_171544274_   5169 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5216
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_171544274_   5217 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5266
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_171544274_   5267 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5316
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_171544274_   5317 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5366
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_171544274_   5367 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5416
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_171544274_   5417 CTAGGCATTACCATTCAGGACATAGGTGTGGGCAAGGACTTCATGTCCAA 5466
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_171544274_   5467 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5516
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_171544274_   5517 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5566
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_171544274_   5567 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5616
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_171544274_   5617 AGGGCTAATATCCAGAATCTACAATGAACTCGAACAAATTTACAAGAAAA 5666
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_171544274_   5667 AAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5712
                          i    ----   v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_171544274_   5713 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5762
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_171544274_   5763 ATCACTGGCCAT 5774
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2206 18.88 5.79 2.80  chr1_171615685_171617581.rev      502  1036 (861)    L1M4_orf2#LINE/L1      279   829 (79)  

  chr1_171615685_    502 TAAAGAGAGACATATAGATTAACAGAACAGAATTGAGAGTTCAGACATAA 551
                            i  v            i  ii   i            i    v    
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_171615685_    552 ACCC------TTATGGTCATCTGACTTTCAACAAAGTTGCCAGGGAAATT 595
                             ------         vi   i    i    i v     i ivv   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_171615685_    596 CAATAGGGGAAAGAATAATCTTTTCAACAAATAGTGCTGGGATAATTGGA 645
                             -            i              i         i  i    
  L1M4_orf2#LINE/    379 CAAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_171615685_    646 TAGCCCTATACAAAAAAAAAATGTACATAGACCCTTACCTCATACCATAC 695
                           ?  vi  i     i  vi v  --- i     i       i      i
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGT---TGGACCCCTACCTCACACCATAT 474

  chr1_171615685_    696 CAAAAAAAAAAAAAAAACTAAAGAAAAATTTATTATAGACTTAAATATAA 745
                         ---------- v     i   vvv     vv  i ?    i     i   
  L1M4_orf2#LINE/    475 ----------ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_171615685_    746 CAGTGAAAACTATAAAACATTTAGAAGAAAACATAAGAGAAAGTCTTTGC 795
                         v  iv             vi               i ? v  i    i i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_171615685_    796 AGTCTTGGATTAGGCCAAGATTTATTAGAT--GACACCAAAAGCATAATC 843
                         iii     i      v v i   v      --             i  v 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_171615685_    844 CATAAAAGAAAAAAATGGCTAAGTT-------------ATTAAAA-CCTT 879
                         v i           - i v   i  -------------       - i  
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_171615685_    880 TGCTTTTCAAAACACACCATTAATTT-TTAAAAAG-----CCACAGATTG 923
                           ivi      iv    i  i  vvv-v i     -----       v  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_171615685_    924 GGAAAAAATATTTATAAATCATATATGTCATAAAGGACTTATTTCTATAA 973
                            i         ii           v v    i      i v  i v  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_171615685_    974 TATATAAAGAACTCTCATGACTCAATAG---GAAGACAAATAACCCAATT 1020
                                        i ii        i---i                  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_171615685_   1021 TAAAAATGGGCAAAGG 1036
                         ?               
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGG 829

Transitions / transversions = 1.69 (61 / 36)
Gap_init rate = 0.02 (11 / 551), avg. gap size = 4.18 (46 / 11)  

 310 16.67 11.90 0.00  chr1_171615685_171617581.rev     1323  1406 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_171615685_   1323 AAAAAAGGGCAAAAACTCTGAACAGACATTTTACCAAAGAAAATATATAA 1372
                              v       iiv i    i        iv        i     i  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_171615685_   1373 AGGGC----------ATGAAAAGGGGCTCAACACCATTAGAAAA 1406
                          v   ----------        iv        i  ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 10.00 (10 / 1)  


2557 26.94 0.68 0.14  chr1_171757523_171759231      482  1216 (493)    L1M4_orf2#LINE/L1      170   908 (0)  

  chr1_171757523_    482 GAATCACCACA-CTATCTTAGCAAA-AAGAACAAAGCTGGAGGCATCATG 529
                             vi   v - v     iiv   -          i      vv   ii
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_171757523_    530 CTACCTGACTTCAAACTATACTACAAGGCCACAGTAACCAAAATAGCATG 579
                           v  ii i      viv        i  i       i   i i  ii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_171757523_    580 GTACTGGTACCAAAACAGATATATAGACCAATGGAACAGAACATAGGCCT 629
                                i iv ii i   i       i        i    ivv  ivii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_171757523_    630 CAGAAATAACACCACACATCTACAACCATCTGATCTCTGACAAACCTGAC 679
                                  vv   i    i  iiii  vi    i ii     ivv  v 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_171757523_    680 AAAAGCAAGCAATGGGGAAAGAATTCCCTATTTAATAAATGGTGTTGGGA 729
                           i v  vv               vvi  v  i  i        i     
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_171757523_    730 AAACTGGATAGCTATATTCAGAAAACTGAAACTGAACCTGTTCCTTACAC 779
                         v         ? i i  v  i  i v    ii  i   iv v   i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_171757523_    780 CTTATACAAAAATTAACTCAAGATGGATTGAAGACTTAAATGTAAGACCT 829
                          v                   i      ii?    i           v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_171757523_    830 AAAACCATAAAATCCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACA 878
                              i      ii i           v    ?i- v i -   iv   v
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACC 568

  chr1_171757523_    879 TAGGCATGGGCAAAGACTTCATGACTAAAACACCAAAAGCAATTGCTACA 928
                          v  vv i     v ii   v iiv  vi            vvv  v   
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_171757523_    929 AAAGCCAAAACTAACAAATGGGATGTTATTAAACTAAAGAGCTTCTGCAG 978
                             vv    ivi i    v   iv i  i   v v  i i   i  iiv
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_171757523_    979 AGCAAAAGAAACTAGCATCATAGTGAACAGGCAACCTACAGAATGGGAGA 1028
                         vv    i  v    v  vv v      v  i     i             
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_171757523_   1029 AAAATTTTGCAATCCATCCATCTGACAAAGTATTAATATCCAGAATCTAC 1078
                            vv       vi   vi      i  i v i vi          v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_171757523_   1079 AAGGAACTTAAACAAATTTACAAGAAAAA-ACAAACAACCCCATCAAAAA 1127
                           i     ivv    v iv i  v     -     i     v  i?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_171757523_   1128 GTGGGTGAAGGATATGAACAGGTACTTCTCAAAAGAAGACATTTATGTGG 1177
                         i    ii      v    i  ii i     v        i  vi vi   
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_171757523_   1178 CCAAAAAACATATGAAAAAA-GCTTATCATCACTGGTCAT 1216
                             v  i  i       i -   i v     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (112 / 82)
Gap_init rate = 0.01 (6 / 739), avg. gap size = 1.00 (6 / 6)  

1523 17.39 7.45 1.24  chr1_171757523_171759231     1388  1709 (0)    L1M4_orf2#LINE/L1      350   691 (217)  

  chr1_171757523_   1388 TGATTTTCAACAGGAAAGAATGCCAGGACAATTTAATGTGGAAAGAAGAG 1437
                                 i   ----  ii     i   v   i    v        v  
  L1M4_orf2#LINE/    350 TGATTTTCGACA----AGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_171757523_   1438 TCCTCCCCAAAAATGCTCCTGGGACAATTGGATATCCACATGCAAAAGGA 1487
                           i ii v v     v v         i      ?             i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_171757523_   1488 TAGAGTTGGATTCTTGTCTCATGTCATATGCAAAAATTAACTCAAAGTGG 1537
                          ii       ii i ii    iii     i                i   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_171757523_   1538 ATCACTGGCTTAAGTGTTAAAGCTAAAACTATAA--C----------AAA 1575
                             ?v i i   i   v i              -- ----------   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_171757523_   1576 CTT----GTAAATCT-CATAACCCTGGATTAGTCAATGGTTTCTTATATA 1620
                          v ----        - i i   i   i    v             v   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_171757523_   1621 TGACACCTAAAGCACAAGAAACAAAGGAAAAAA---AT---TTTGACCTT 1664
                                v          v      i       ---  ---  v   i i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_171757523_   1665 ATTAAA-TTAAAAATTATGGTGCTTCAAAAGACATTATCAAGAAAG 1709
                           i   -       i v v          i    i           
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

Transitions / transversions = 2.18 (37 / 17)
Gap_init rate = 0.02 (8 / 342), avg. gap size = 3.50 (28 / 8)  


 427 27.50 3.33 0.00  chr1_171810400_171813661.rev     1228  1347 (1915)    L1M4_orf2#LINE/L1        1   124 (784)  

  chr1_171810400_   1228 TGGAAATATATCCTATGTCTATGAATGGGAAGA----ATATTGTAAAAAA 1273
                               v      i    ii   i  v      ----       v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171810400_   1274 AATTGTACTCCCAAAAGCAATCTATAGATTCAATGCAATCTGTATCAAAA 1323
                         iiivi       v   vii     i        i      iv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171810400_   1324 TATCAATGACATTCTTTAGAAAAA 1347
                          vi  iivi v  i   iv i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA 124

Transitions / transversions = 1.75 (21 / 12)
Gap_init rate = 0.01 (1 / 124), avg. gap size = 4.00 (4 / 1)  

3006 23.12 0.89 2.17  chr1_171810400_171813661.rev     1989  2771 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_171810400_   1989 ATTCTAAAATTCATATGGAACCACAGAAGACCCCAAATAGCCAAAGAAAT 2038
                           i                 vii  iii     vi          iv   
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_171810400_   2039 CCTGAGCAAAAATAACAAAGCTGGAGGCATCACATGAGCTGACTCTAATA 2088
                          i   iv  i  v       i      vv     ivvv ii i ii  v 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_171810400_   2089 TGTACTACAAAGCTACAGTAACCAAAACAGCTTGGACCTGGCATAAAAAC 2138
                         iv                   i   i    iv   vv         ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_171810400_   2139 GGACACATAGGCACAATGGAACAGAATAGAGAACCCAGAAATAAATCCAC 2188
                         i    i    ii-        i     v    ii           i   i
  L1M4_orf2#LINE/    286 AGACATATAGAT-CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_171810400_   2189 ATATTTACTGCCAACTGATTTTTGACAAGTA-ACCAAGAACATTCAATGG 2237
                          i     iv i   i       i      vi-i      v          
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_171810400_   2238 GGAAAGAACAGGCTCATCAATAAATAGTTCTAGGAAAATTGAATATCCAT 2287
                                 i  v  iv    i    i  v  i   v  i  i   ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_171810400_   2288 ATGCAGAAGAATAAAACTAGACCTCTATTTCTCACCGTATTCAAAAATTA 2337
                              i      i  ii i    i   ii  v    i   v         
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_171810400_   2338 AATTAAAGTGGATTAAAGAATTAAATGTAAGACCTGAAACTATGAAACTA 2387
                          v i   i     i ?   vi           v  i       i     v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_171810400_   2388 C-AGAAGAAAACATTGGTGAAACACTTTAGAACATTGGTCTAGGCA--GA 2434
                         i-            v  ? v  vv   iivi  v    vi      -- i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_171810400_   2435 TATTTTGGGTAAGACTGCAAAAGCACAGGCAACAAAAGCAAAAATAGACA 2484
                          v i  i i  v   vv          i          v         i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_171810400_   2485 AATGGAAATACATCAAGCTGAAAAGCTTTTGCACAGCAAAGGAAATAATC 2534
                            v i v v      iv v    i      ii vv       v iv   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_171810400_   2535 GACAGAATGCAGAGACAACCTACATAATGGGAGAAACTATTTGCAAGCTG 2584
                         i v i i  v i        i   v           v         iiii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_171810400_   2585 TCTATGTGATAAAGTATTAATAAACAGAATACATAAGGAGTTC--A-AAC 2631
                          v   v      i v i vi  vv       i    i  ii  -- -   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_171810400_   2632 TCAATAGCAAAATAATAATAACAATCATCATCATCATCTTATTTTAAAAT 2681
                               ii    vi i  -- i  i --------  ----   ?v     
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAA--ATAACC--------CA----ATTWAAAAAT 820

  chr1_171810400_   2682 GGGCAAATGATCTAAATAGACATTTCTCAAAAGAAGACATACAAATGACC 2731
                                v   i i              v        i         i  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_171810400_   2732 AACAAACATTTACGAAAAAATGTTCAACATCACTAATCAT 2771
                           i  i  i-- i     i   i         ????????
  L1M4_orf2#LINE/    871 AATAAGCAC--ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (113 / 64)
Gap_init rate = 0.01 (10 / 773), avg. gap size = 2.40 (24 / 10)  


3633 24.48 0.33 0.44  chr1_171913430_171915124.rev      298  1204 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_171913430_    298 GAAAGATATTCCATGTTCATGAATTGGAAGAATTGATATTGTTAAAATGT 347
                                  i           i         v  i          i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_171913430_    348 TCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAATA 397
                         iv     v      vii              i                 v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_171913430_    398 CCAATGACAGTCTACACAGAAATAGAAAAAACAATCTGAAAATTTATATG 447
                            iivi vv i vii       v  v  ivii   iv      i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_171913430_    448 GAACCAGAAAAGACCCAGAATAGCCAAAATTATACCAAGAAAAAAAAAAA 497
                            viiv  ii                  iv  viii i   i  i  v 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_171913430_    498 AACTTGTAGAAACCGCATTACCTGACTT-AAAATTATGGTACAGAACTAT 546
                           v   v  i vi i  i v  ii i  -    i - iv    i i   i
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTAC 251

  chr1_171913430_    547 AGTAACCAAAACAGTATGGCACTGGCATAAAAATCAACACATAGACCAAT 596
                              i   i     i   i          ii  vi   i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_171913430_    597 GGAACAGAATAGAGAACCCAGAAACAAATCCACACACCCACAATGAACTA 646
                             i     v    ii       i   i   i   iii iii v  i i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_171913430_    647 ATTTTCAACAAAGGAGCCAAGAATATACGCTGGGGAAAAGACAGTCTCTT 696
                               i    i  v       vi  v iv        ii i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_171913430_    697 CAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAG-TTGAAAC 745
                            i              v         ?   i     i   -v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_171913430_    746 TAGACCCCTATCTCTCACCATATACAAAAATCAAATCAAAATGGATTAAA 795
                          i        i   v                i  v           i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_171913430_    796 GACTTAAGTTGATGACCTCAAACTATGAAACTACTACGAGAAAACATTGA 845
                            i   i vv v  v  v       i     vi  vi         v i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_171913430_    846 GGAAAATCTCCAGGATGTTGATCTGGGCAAAAATCTCTTGAGCAATACTC 895
                         ? v      i iv  iv   ivi i     vii i    iiii vv  v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_171913430_    896 CATAAACATAGGCAACTAAAGCAAAAATAAACAAATGGGATTGCACCAA- 944
                           v  i  i i     v    v       i i    v   i v  i   -
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_171913430_    945 GTTAAAAAGCTTCTGCTCAGAAAAGGATACAATCAACAAAGTAAAGAGAC 994
                         i       -   i  iv vvv      i  v     v     i  i    
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_171913430_    995 AACCCACAGAATTGGAGAAAATATTTGTAAACTACACATCTGACAAGGGA 1044
                                     v              i   ii i i      i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_171913430_   1045 CTAATAACCAGAATACATAAGGAGCTCAAACGACCCTGTAGGAAAAAAAA 1094
                           vi  v        i    i  i   vv  i  i vi  iv     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA- 799

  chr1_171913430_   1095 TCTAATAATTAGATTTACAAATGGGGAAAAGATTTGAATAGACATATATC 1144
                         - v     iivi   ? v       v   i               v v  
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_171913430_   1145 AAAAGAAGACATACAGATGGCAGACAGGCATATAAAAAGGTGCTCAACAT 1194
                         v        i     i     vi i i   i  i     i          
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_171913430_   1195 CATTGATCAT 1204
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.83 (141 / 77)
Gap_init rate = 0.01 (6 / 906), avg. gap size = 1.17 (7 / 6)  


3163 25.08 2.00 1.22  chr1_171936073_171941176     3717  4617 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_171936073_   3717 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3766
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171936073_   3767 GATCATACTGCCAAAAGCAATCTACAAATTCA-CACAATCCCCATCAAAA 3815
                          iiv     v  v   vii       i     - i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171936073_   3816 TCC--ACCATCATTCTTCACAGAGTTGGAAAAAACAATTCTAAAAATCAT 3863
                            --i iii -  i  ii    iv v  v  ivii  i      v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_171936073_   3864 ATGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAAACTAAGCAAAAAGA 3913
                               viiv  ii  v  v v         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_171936073_   3914 ATAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGCC 3963
                          i   vi      vv       v  ii        viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_171936073_   3964 ATAGTCACCAAAACAGTGTGGTACTGGTATAAAAATAGGCACCTAGACCA 4013
                          i   v i   i               i    ii    i  iv    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_171936073_   4014 ATGGAACAGAATAGAGAAACCAGAAATAAACCCAAATATTTACAGACAAC 4063
                               i     v    iv               v i     ii v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_171936073_   4064 CAATCTTCAACAAAGCAAACAAAAATATAAAGTGGGGAAAGCACACCCTT 4113
                         ii  i   i    i vviv   i vi  vv i         v i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_171936073_   4114 TTCAACAAATGGTGCTAGGATAATTGGAAAGCCACGTGTAGGAGAATGAA 4163
                                         i   i  i    v ?    i  i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_171936073_   4164 ACTGAATCCTCATCTCTCACCTAATACAAAAATCAACTCAAGGTGGATAA 4213
                         ii  i i  ii i   v    vv          i       ii     v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_171936073_   4214 AGGACTTAAACCTAAGATCTGAAACTATAAAAATTCTAGAAGATAACATT 4263
                         ?i   i    iv     v  i           v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_171936073_   4264 AGAAAAACCCTTCTAGACATGGCCTTAGGCAAGGATTTC------ATGAC 4307
                         i ?iv  vi    vv   v v vv        v i    ------     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_171936073_   4308 --CAAAAACCCAAAAGTAATTGCAATAAAAACAAAGATAAATAGCTGGGA 4355
                         --     i v   --------    i    iv   i   i   iv v   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAA--------GCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_171936073_   4356 CCTAATTAAACTGAAGAGCTTTTGCATGGCAAAAGGAACAGTTAGCAGAG 4405
                          i v  i   v v  i i      iiivv    i iv  vi i iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_171936073_   4406 TAAACAGACAATCCACAGAGTGGGAGAAAATCTTCATAATCTATACATCT 4455
                          i  v      i       i           v  iii  vii   i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_171936073_   4456 GACAAAGGACTAATATCCAGAATCTACAACAAACTC----AAATAAGTAA 4501
                           i  i     vi          v  i  vi     ----  v v i   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_171936073_   4502 GAAAAAAACCAATTAATCCAATC-AAAAATGGGCTAAAGACATGAATAGA 4550
                         v     i  v   -  i     i-          v  i  iv        
  L1M4_orf2#LINE/    792 TAAAAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_171936073_   4551 CAATTCTCAAAAGAAGATATACAAATGGCCAACAA--ACATGGAAAAATG 4598
                           v     v                       i  --     i   i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_171936073_   4599 CTCAAAAATCACTAATGAT 4617
                              v -   ????????
  L1M4_orf2#LINE/    891 CTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.64 (29 / 11)  


3094 27.64 1.11 0.33  chr1_171957148_171960583.rev     2045  2945 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_171957148_   2045 TGGAAAAACATTCCATGCACATGGATAGGAAAAATCAATACCGTGAAAAT 2094
                               i i  i     iv       v    i v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_171957148_   2095 GGCCATACTTCCCAAGGTACTTTATAGATTCAATGCTATCCCCATCAAGC 2144
                            v     i     iv iv i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_171957148_   2145 TACCATTGACTTTCTTCACAGAATTGGAAAAATCTAATT-TAAATTTCAT 2193
                          v   vivi i  i  ii     v v  v  i-  i  i-    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_171957148_   2194 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 2243
                               viiv  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_171957148_   2244 ACAAAGCTGGAGGTATCACGCTACCTGACTTCAAACTATACTACAAGGCT 2293
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_171957148_   2294 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACCGATATATAAACCA 2343
                                i   i    ii         i iv ii iv  i     i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_171957148_   2344 ATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCATC 2393
                               i    iv    vii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_171957148_   2394 TGATCTTTGACAAACCTGATGAAAGCAAGCAATGGGGAAAGGATTCCCTA 2443
                             i  i     ivv  vii i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_171957148_   2444 TTTAATAAATGGTGTTGGGAAAATGGGCTAGCCATGTGTAGAAAGCTGAA 2493
                           i  i        i     v  iv  v  ?   ii  i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_171957148_   2494 ACTAGATCCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGGATTA 2543
                         ii i  i    v   i     v  i                i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_171957148_   2544 AAGACTTCAATGTAAGACGTAAAACCATAAAAACCCTAGAAGAAAACCTA 2593
                         ?    i v         vv      i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_171957148_   2594 GGCA-ATACCACTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 2642
                           ?i- v i -i  iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_171957148_   2643 CACCAAAAGCAATGGCAATGAAAGCCAAAATTGACAAATGGGATCT---- 2688
                                    vvi    ii    vv     v  i    v   ii ----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_171957148_   2689 --AATTAAAGAGCTTCTGCAAAGCAAAAGAAACTAGCATCAGAGTGAACA 2736
                         --       i -   i  iivvv    i  v    v  vv i      v 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_171957148_   2737 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 2786
                          i     i                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_171957148_   2787 GGGCTGATAACCAGAAACTACAAAGAACTTAAACAAATTTACAAGAAAAA 2836
                           i  vi  v      vv  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_171957148_   2837 --CAAACAACCTCAACAAAAAGTGGGCAAAGGATATGCACAGACACTTCT 2884
                         --    i    iv vi?    i            v  v i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_171957148_   2885 CAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTCATCA 2934
                          v        i  vi viii     i ii  i       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_171957148_   2935 TCACTGGTCAT 2945
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3260 26.46 0.66 0.55  chr1_172136800_172141079     2881  3787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_172136800_   2881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2930
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_172136800_   2931 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2980
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_172136800_   2981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_172136800_   3029 TATGGAACAAAAAATGAGCCCTCATTGCAAAGTCAATCCTAAGCCAAAAG 3078
                                vviv  iv  v  vvv  v  v  iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_172136800_   3079 AACAAAGCTGGAGGCATCACGCTATCTGACGTCAAACTATACTACAAGGC 3128
                                i      vv    i  vi ii iv     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_172136800_   3129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3178
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_172136800_   3179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_172136800_   3227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_172136800_   3277 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACT 3326
                           v  i                 v      v  ?   i   i i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_172136800_   3327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3376
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_172136800_   3377 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3426
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_172136800_   3427 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3475
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_172136800_   3476 AAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTA 3525
                         vi            vvi          vv    iv  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_172136800_   3526 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3575
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_172136800_   3576 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCATCTGACA 3625
                         v  i     i                 v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_172136800_   3626 AAGGACTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAA 3675
                          i     vi          v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_172136800_   3676 AA-ACAAACAACCCCATCAGAAAGTGGGCGAAGGATATGAACAGACACTT 3724
                           -     i     v  i?i   i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_172136800_   3725 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAGTGCTCAT 3774
                            v        i  vi viii     v  i          ii      v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_172136800_   3775 CATCACTGGCCAT 3787
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1785 17.63 0.81 27.70  chr1_172498223_172500627      671  1912 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_172498223_    671 TGGGAAGATCTCCCAAGTTCACAGATTGGAAGAATTAATGTGGTTAAAAT 720
                            i     v     v     ii          v     i v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_172498223_    721 GTTCACACTTCCCAAATTAATATACATTTTCACTGCAATCCCTATCAAAA 770
                          viv i   i        i  v    vv    vi                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_172498223_    771 TTTCAATGGCATTTTTTCACAGAAATAGAAAAAACAATTTTAAAATTTGT 820
                          ii  iiv  v      -i       v  v  ivii  ii       ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_172498223_    821 ATGGAACCACAAAAGACCCAAAAGAATCTTGAAAATGTAGCCAAAACACT 870
                               vii   ii      i  --------------           v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAA--------------TAGCCAAAACAAT 185

  chr1_172498223_    871 CTTGAGAAAGAAAAACAAAGTTGGAGACATTATACCTTCTGATTTCGAAT 920
                              i      i             ivv i i  i i ii     i  v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_172498223_    921 TATATTACGAAGCTATATTAATTAAAATAGCATGGTACTGGCACATAAAC 970
                         iv  i   i      i v    i  i i  ii           i vii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_172498223_    971 AGACACATAGACCAATGAAACAGAATAGAGAGCCCAGAAATAAACTTAAG 1020
                              i     i     i  i     v     i            ii vi
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_172498223_   1021 CATACATGGTAAGCTAATTTTCAACAAGGCTACCAAGAAGACACAATGGG 1070
                            vi     v ii i      i      v i      ------------
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA------------ 373

  chr1_172498223_   1071 CTGGGCATGGTGGCTCATGCCTGTAATGCTAGCACTTTAGGAGGCCAAGA 1120
                         --------------------------------------------------
  L1M4_orf2#LINE/    374 -------------------------------------------------- 373

  chr1_172498223_   1121 TGGGCAGATCATGAGGTCAAGAGATCGAGACCATCCTGGCCAACATGGTG 1170
                         ------------------------------    i --------------
  L1M4_orf2#LINE/    374 ------------------------------CCATTC-------------- 379

  chr1_172498223_   1171 AAACCTGTCTCTACTAAAAATACAAAAATTATCTGGGCATAGTGCCACGC 1220
                         --------------------------------------------------
  L1M4_orf2#LINE/    380 -------------------------------------------------- 379

  chr1_172498223_   1221 ACCCGTAATCCCAGCTACTTGGGAGGCTGATGCAGGAGAATCGCTTGAAC 1270
                         --------------------------------------------------
  L1M4_orf2#LINE/    380 -------------------------------------------------- 379

  chr1_172498223_   1271 CCGGGAAGTGGAGGTTACAGTGAGCCAAGATCATGCCACTGCACTCCAGC 1320
                         --------------------------------------------------
  L1M4_orf2#LINE/    380 -------------------------------------------------- 379

  chr1_172498223_   1321 CTGGCAACAGAGCAAGATTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAGA 1370
                         --------------------------------------------------
  L1M4_orf2#LINE/    380 -------------------------------------------------- 379

  chr1_172498223_   1371 CACAATGAGCAAAGAATGGTCTCAAGAATAGTCTCTTAAATAACTGATGT 1420
                         ---    i ----   --------          i  v  i  v  i  i
  L1M4_orf2#LINE/    380 ---AATGGG----GAA--------AGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_172498223_   1421 TAAGGAAACTGGATATCCACATGCAAAAAAATAAAACTGGACCC-TGTCT 1469
                          ii iv         ?            i   i  ii       - ii  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_172498223_   1470 TACAGCATACACAAAAATCAACTCAAAATGGGTTAAAGATACGAAACGGA 1519
                         i   v    i        i            i i ?   i- v   i v 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC-CTAAATGTA 513

  chr1_172498223_   1520 AACACCTAAAACTGTAAAACTTTTAATAAAAATCATAGGGGAAAAGTTCC 1569
                          i- v        i       i   iv i   v      ? v   vi i 
  L1M4_orf2#LINE/    514 AG-AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_172498223_   1570 TTGATGTATGCCTAGGCAAATATATTTTTGATATCTCACCAAAAGCACGG 1619
                         v   iv vv vi       vvi v i  v     vv            ii
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_172498223_   1620 GCAA---AAGCAAAAATAAACAAGTGAGACT--AT--AAACTAAAAGCCT 1662
                             ---   v       i i  i vi    --  --   i     i i 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_172498223_   1663 TTTTGGCAGCAAAGGAAACAATCAACAAATTAAAAAC-CAGCCAATGGAT 1711
                           v  - vv       v  v     v   v i    v-  i  v ii  v
  L1M4_orf2#LINE/    663 TTGTG-CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_172498223_   1712 TGGAAGAAAATATTTGCAACTCATATATTAGATGAGTGGTTAATATCCA- 1760
                            i               v        iv   i  v ii vi      -
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_172498223_   1761 AATATATAAGAAATGCAAACAATTCAATAGCAAAACAAATAAACAAACAA 1810
                                  ii  iv vv    i      ii    ----- i     i  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAA-----AGACAAATAA 806

  chr1_172498223_   1811 CTTGATTAAGAAATGAGCAAAGAACCTGAATAGACATTTCTCTAAAGAAA 1860
                          iii   ? i     i      i ii                i      i
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_172498223_   1861 ACATAAAAATGTCCAACAGATATATGAAAACGTGCTCAAAGTCACGAATC 1910
                          i   v     v    i iii i       vi       vi   ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_172498223_   1911 AT 1912
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.95 (142 / 73)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 22.12 (354 / 16)  


3206 26.79 0.66 0.55  chr1_172692550_172698953     5005  5911 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_172692550_   5005 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCCTGAAAAT 5054
                              ii i  i     i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_172692550_   5055 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5104
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_172692550_   5105 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 5152
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_172692550_   5153 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5202
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_172692550_   5203 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5252
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_172692550_   5253 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5302
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_172692550_   5303 AATGGAACAGAAC--ACAGTCCTCAGAAATAATGCCGCGTACCTACAACT 5350
                                i    i-- v     --        vv  iiii ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_172692550_   5351 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5400
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_172692550_   5401 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5450
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_172692550_   5451 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5500
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_172692550_   5501 TTAAAGACTTAAATGTTAGACCTAAAACCAAAAAACCCT-AGAAGAAAAC 5549
                          i ?    i       v   v       i v     i  -          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_172692550_   5550 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5598
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_172692550_   5599 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5648
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_172692550_   5649 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5698
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_172692550_   5699 TAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5748
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_172692550_   5749 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5798
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_172692550_   5799 AAAACAAACAACCCCATGAAAAAGTGGGCGAAGGGAATGAACAGACACTT 5848
                           i     i     v  v?    i     i    ivv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_172692550_   5849 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5898
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_172692550_   5899 CATCACTGGCTAT 5911
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3226 25.64 1.44 0.67  chr1_172703401_172709660.rev     4869  5769 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_172703401_   4869 TGGAAGAACATTCCATGCTCATGGGTTGGAAGAATCAATATCCTGAAAAT 4918
                              ii i  i     i      i        v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_172703401_   4919 GGCCATACTGCCCAGGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4968
                            v     v    iiv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_172703401_   4969 TACCAAC-GCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTC 5015
                          v   i -      i  -i     -   -- v  i  - iii v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_172703401_   5016 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 5065
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_172703401_   5066 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5115
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_172703401_   5116 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGAT 5165
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_172703401_   5166 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACGTATCTACAAC 5213
                                 i    i--    i  --        vv   iii  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_172703401_   5214 TATCTGATCTCTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5263
                         i vi    i ii     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_172703401_   5264 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5313
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_172703401_   5314 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5363
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_172703401_   5364 ATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5413
                           i ?    i  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_172703401_   5414 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5462
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_172703401_   5463 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5512
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_172703401_   5513 AATTAAACTAAAGAGCTTCTGCACAGCGAAAGAAACTACCATCAGAGTGA 5562
                         v  i   v v  i i   i  ii vv i  i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_172703401_   5563 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5612
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_172703401_   5613 AAAGGGCTAATATCCAGAATCTAGAATGAACTCAAACAA----AT--TTA 5656
                           i  i  vi          v  v  v      vv    ----  -- v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_172703401_   5657 CAAGA-AAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5705
                         v    -   i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_172703401_   5706 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5755
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_172703401_   5756 TCATCACTGGCCAT 5769
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (133 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


2599 26.30 3.22 2.44  chr1_172776772_172780195     2031  2931 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_172776772_   2031 TGGAAAATCCTTCCATAAGCATGATTTGGAAGAATCGATATTGCTAAAAT 2080
                               iviv i    ivv    iv        v ii      i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_172776772_   2081 GGCAATATTGTTCAAAGCAATTTACAGATCCAATGTTATCCTTA---AAA 2127
                                i vii    vii  i       i   i iv    i  ---   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_172776772_   2128 TACCAACGTCATTTTTCACAGAATTAGAAAAAAACT-ATTCTAAAATTCA 2176
                          v   i vv v     ii     v v  v  i--  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_172776772_   2177 CATGGAACAAAAAAAGAGCTTGAATGGCCAAAGCAGTCCTAAGCAAAATG 2226
                         i      vviv  ii  v iv    i      i  i  i i iv  i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_172776772_   2227 AACATACCTGGAGGCATCACACTACCCAACTTCAATTTATACTATCAGGC 2276
                             v vi      vv       v     i     vviv     iv i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_172776772_   2277 TACAATAACCAAAACAGTATGGCACTGGTAGGTACAAAAACAGACATA-A 2325
                             i   i   i     i   i     i ----i  ii i       - 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA----TAAGGATAGACATATA 294

  chr1_172776772_   2326 GACCAATGGAATAGAATACAGAACCCAGGCATAAAGCTGTAAACCTACA- 2374
                           i              vv   ii    iv     v ii  v ii  ii-
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_172776772_   2375 CCATCTGATCTTTGACAAAATCAACAAAAACAAGCAATGGGGAAAGGACT 2424
                         i  vi    i  i     iiviiv   i v  vv            i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_172776772_   2425 CCCTATTCAATCAATGGTGCTTGGATAACTAGCTAGCCATGTGCAGAAGA 2474
                         vi  v     iv         v   i    i v  ?   ii    i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_172776772_   2475 ATAAAACTGGACCACTACTTTTCACCATATACAA----TAACTCAAGATC 2520
                           i  ii      v    i iv            ----        i  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_172776772_   2521 AATCA-AAACTTAAGTCTAAGACCTCAAACTATAAAAATCCTAGAAGGAA 2569
                         i    - i  i   i v     v  v           v  i      i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_172776772_   2570 AGCTAGG---AAATATCCTTCATGACACAGGCTTTGGCAAATAATTTAT- 2615
                          vv    ---    ---    i    viv  v  v     - ii   v -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTT 590

  chr1_172776772_   2616 GGCTAAGTCTTCAAAAGCAATTGCAAAAAAAAAAACAAAAATTGACAAGT 2665
                         i v  v v vi        vvv    v    i   ---    v  i  i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAA---AAATAGATAAAT 637

  chr1_172776772_   2666 GGGACCTAATTAAA-TTAAAGAGCTTCTGCATAGCAGAAGAAATTGCCAA 2714
                         v    i v  i   -     i -   i  iiivv  i i  v i ii   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_172776772_   2715 CAGAGTAAACAGACAGCCTAGGGAATGGGTGAAAGTATTTGCAAACTATG 2764
                         v i   i  v     i  i vi       v    i          ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_172776772_   2765 CATCTGACAAAGGCCTAATCTCTAAAATCTACAAGAAACT--TAAAA--- 2809
                         i      i  i  v  vi v  i i   v  i  ii    --  v  ---
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_172776772_   2810 AAAAATCAACCTGTGAAAAACAAAAAAATCCAAT-AAAAAATGAG---AA 2855
                           v   -  ------   i     v  -i     -?       i --- i
  L1M4_orf2#LINE/    787 AATAAT-AA------AAAGACAAATAA-CCCAATTWAAAAATGGGCAAAG 828

  chr1_172776772_   2856 GAC----ACAGACACTTCTCAAAAGAAGACATACAAGTCGCCAACAAGCA 2901
                           i---- i     i     v        i      i v     i     
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_172776772_   2902 TATGAAAAAACACTCAGCATCACTAATCAT 2931
                         i       i ii    i     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (145 / 90)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.22 (51 / 23)  


1508 25.97 13.35 3.16  chr1_172842872_172846553     2366  3189 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_172842872_   2366 TAGAGGGAAGTACCACATTCACAGATTAGAAGACTGAATACTGTAAATAC 2415
                          i  ii  vi v   ii    ii    i       v    i   v  v i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_172842872_   2416 A-CAGT-CTCCC-AGATTTATCTAGTCAAATT------AATCCCAATAAA 2456
                         i-  i -     - i   v     --  i   ------      v  v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTA--CAGATTCAACGCAATCCCTATCAA 98

  chr1_172842872_   2457 AAGCACAG-TAAGTTTACCATGGAAACGTACTAGCTGATTCTAAAATTTA 2505
                           v v   - ivv   viiiii    ivv  v       i        i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_172842872_   2506 TACTGAAATGCAGACAGCCAGGAATATCCCAGAC--TTT----AAAGAAG 2549
                           iv        iivii  vi     v  v i  -- i ----       
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_172842872_   2550 AACAG------------CA-ACTT---AATT-------------CAAAGC 2570
                             i------------  -    ---    -------------      
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_172842872_   2571 TCTAGTATTTAATACAAGGTGGTATTGCGAAAA------------AGACC 2608
                          vi    v i  v   iv      i  vv v  ------------   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_172842872_   2609 AGTGAAGCAGAAAAGAGGACCTAGAAACAGACCCACACATACATGGACAC 2658
                          i  i ii    vv   iii i     i i     i    vi    v  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_172842872_   2659 ATGATATATGACAAAGGTG---AAAC--TTCAGAGTGATGAAGAAAGAAT 2703
                         v    v vi     i    --- i  --    -----   ii        
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCA-----ATGGGGAAAGAAT 393

  chr1_172842872_   2704 GGACTTTTTAATAAAGGATGCTTGGGCAGCTAGATATCCATATG----AA 2749
                         i v     i  i   v i    v  i  i  i    ?   i   ---- i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_172842872_   2750 AAT--------ATCTCTATACCTCACATTATACACAAAAATAAATCTTCA 2791
                            -------- i i   --       ii   i        v  -  iv 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAA-CTCAA 490

  chr1_172842872_   2792 AGT-----ATAGATCTAAATATGAAAGATAAAAGAATAAAGCTTCAAATA 2836
                          i ----- ?   i      i i i  v     vv     i  iiv i--
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG-- 538

  chr1_172842872_   2837 AAGAACAGCATAGAAAAATGTCTTCATGACCACAGGT--GGAAAAGACTT 2884
                              - i     i?iv vi     i     vii   --  v  v ii  
  L1M4_orf2#LINE/    539 AAGAA-AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_172842872_   2885 CTTTAA-GTGACACAAAACACACTAAGTA-TAACAGATAA----GATAAA 2928
                            vi -i      v   vi   -   i -i  v   v  ----      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCAC-AAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_172842872_   2929 TTTCACTCTATTAATATCAGAAACTTCTGGTCATCAAATGACACCATTAA 2978
                           vv   ii  i  v  i i      i  vv v     v     i  i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_172842872_   2979 GATAATGAAAAGAATGCAACCCAATTAGA--GGGA-AAGATATTTGTGAT 3025
                           v i        ---       --i   --    -  i       ii v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGA---CAACCCA--CAGAATGGGAGAAAATATTTGCAAA 731

  chr1_172842872_   3026 AGATAGATCTGACAAG--ATGTATATCTAGAATATATAAA-------TAT 3066
                         vv   v      i   -- iv i    i            -------  -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA- 780

  chr1_172842872_   3067 CAAACCATTAAGAAAAAT-CAAACAA---------AAAATGTA-AAAAGT 3105
                            vi  v   v     v-    i  ---------      vi-   i v
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_172842872_   3106 TTTAAACAATTACTTCACACACAAACATAAAAAAACCCAAATGGCCAATC 3155
                            i  i ivi i   v ---    ---i  i v iv            v
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTC---CAAA---GAAGATATACAAATGGCCAATA 874

  chr1_172842872_   3156 AATGTAGTACTAGGTGCTCAACCTCATAAGTCAT 3189
                          iiii vv vv  i        v   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (127 / 84)
Gap_init rate = 0.04 (40 / 908), avg. gap size = 3.40 (136 / 40)  


2281 24.48 8.62 2.80  chr1_172897997_172900153      813  1670 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_172897997_    813 TGGAGAAATATACTATGTTCATGATTCAAAAGA--TAATATT---AAGAT 857
                             i i    v i         iv iii    --       ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_172897997_    858 GTCA-T-CTTCCCAAATGAAATCACAGATTCAAAGTAACCAACATTAAAA 905
                          v  - -  i       vi vii          v i  i vvi  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_172897997_    906 TCCTACAT-CCTTTTTTATAGAAATTGGCACGCTAATCCTAAGATTTATG 954
                            i vv -        ii        i  v   i       i   i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_172897997_    955 TGGAAATGCAAAGAACATA-AATAATCAAAACAACTTTGAAATA-AAGGA 1002
                                    i i  vi -    ii        ii      v -   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_172897997_   1003 TAAA--------AATTACACTACCTGATTTCAAGATGTACTATAATAATA 1044
                         i   -------- v i     v  ii       i iv     i  viv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_172897997_   1045 CCATAATCAAAACAGTGTGGCACTTGTGTAGGGATAAACATATATACACC 1094
                          vi       i         i   v ii  i     i       v i-- 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT--C 298

  chr1_172897997_   1095 AACGGGACAGAATAAAAATTGCAGAAATAAACTCATATAT--ATGGTTAA 1142
                           i  i i     vi i v v           i    i  --     i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_172897997_   1143 TT----TTTGAGAAAGGTGCCAAGAAAATTCAATGAACAGAGA-TGATCT 1187
                           ----  i  v  i          vv        iiv i   - ii   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_172897997_   1188 TTTCAACAAATGATGTT---ATAA-----TATT------------AATGA 1217
                                     i  i --- i  -----  ?i------------     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_172897997_   1218 AGCCTTCAACCCTTACCAAACACAGTGTATAAAAACTAACTTGAAGTGGA 1267
                           --  vi    i    vv    vi i  i     i     ii  i    
  L1M4_orf2#LINE/    449 AG--TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_172897997_   1268 TCATA-ACC-----ATAAGA----AAACTATAAATCTTCTAGTAGAAAAT 1307
                            ? -   -----i     ----          v  ii   v      i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_172897997_   1308 ATACAAGAGAATGTTTTCTAATTTCATGTTAGATAAC---TTCTTAGCTA 1354
                            vi? vi   -i  iv i ii iiv     ii  i---       v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_172897997_   1355 GAACACAAAAATTAAAAATAATAAAAATCAATTTGGACTTAAAACTGAAA 1404
                         vi    v    vi v  ii  i    ivv  vv i  i---   i  i -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT---AAATTGGA- 641

  chr1_172897997_   1405 ACTTTATCGATACATTAGAAAAAAGAAAAAACTTTTGCACTTTAAAAAAT 1454
                         -   i   ------------    vv           ii   i   ii i
  L1M4_orf2#LINE/    642 -CTTCATC------------AAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_172897997_   1455 --TATTAAGAAAATGAAAAGATAAGCAACAGACTAAGAGAAAATACC-AC 1501
                         --   i      i        i  v v     v ii         ii-i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_172897997_   1502 AATACACAGGTCTGACAAAAGA--TGTATGCAGAATACATAAAGAACACT 1549
                           vv  i vi     i  ii  --     v       i         v  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_172897997_   1550 TACAACGCAA-GAT-----GACATGCAATTTTAAGGGAAAAAATGGGCCA 1593
                               v   -i  -----    vii  iii-- ivv?          v 
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCC--AATTWAAAAATGGGCAA 826

  chr1_172897997_   1594 AAGATCAAAACAGACATTTCAC---AAAAGATATGCAAATGAAAAATAAG 1640
                          i   ivi  i         v --- i       i      ivv      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_172897997_   1641 CACATAAAAATATGTT--ACATAACAATGTGA 1670
                              i    v   i --    v ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (138 / 68)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 3.06 (98 / 32)  


 500 25.74 4.41 0.00  chr1_172936918_172942111.rev     3534  3669 (1525)    L1M4_orf2#LINE/L1        1   142 (766)  

  chr1_172936918_   3534 TGGAGAAATATTCTATGTTCATATATTAAAAGACTCAAAATTGTTAAGAT 3583
                             i i    i i        iv   ii      i  v           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_172936918_   3584 -----TTCTCCTAACA-TGATCTATAGATTCAGTGTAATTTCAATCAAAA 3627
                         ----- v    iv v -       i       ii i   ii v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_172936918_   3628 TTCCTGCAATCTATATTGTAGATATTGATGAAATGATTCTAA 3669
                          i  v  vii  v v   i   v     ii iv    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

Transitions / transversions = 1.92 (23 / 12)
Gap_init rate = 0.01 (2 / 142), avg. gap size = 3.00 (6 / 2)  

2367 23.99 3.77 2.23  chr1_172936918_172942111.rev     3984  4700 (494)    L1M4_orf2#LINE/L1      134   861 (47)  

  chr1_172936918_   3984 TGATTCTAACATTTATACG-AAATGACAAACAAACCTATAACAGCAAAGA 4032
                             i    v   i   i -     -   i-ii   i v  i   v  i 
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATG-CAAG-GGACCCAGAATAGCCAAAA 181

  chr1_172936918_   4033 CAATACTGAA---GAAGAACAAAGTTGGAGGATGCACACTCTCTGATTTC 4079
                             vi    ---                   iv      ii ii     
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_172936918_   4080 AAGTCATTCTACAAAGTGACTAGTAACCAAAACAGTGTGATATTGGGGAA 4129
                           iv v v        iv  -     i   i        i  i   v---
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTAC-AGTAATCAAGACAGTGTGGTACTGGC--- 277

  chr1_172936918_   4130 AAAAAAAAAAATAGACACATAGATCAATGGAACAGAAACAACAGAGCCCA 4179
                         ---- v  ii       i              i    vii --   i   
  L1M4_orf2#LINE/    278 ----ATAAGGATAGACATATAGATCAATGGAATAGAATTGA--GAGTCCA 321

  chr1_172936918_   4180 GAAATATGCCCACACAAATATCATCAACTGATATTTGACAAAAGAGTAAA 4229
                               vi    i   vv   vi    i    v  i     ii v iv  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_172936918_   4230 GGCAATCGAATAGAGAA------GTCTTTTTAACAAATGGTGCTGCAACA 4273
                          i v  iv   i i   ------       i              vi   
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_172936918_   4274 ATTTAATGTCCACATGTAAAAATAATAAACCTAGACACAGACCTTACACC 4323
                          i vi  i?       i    i-   i  vi i   v vv    i     
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAG-AATGAAGTTGGACCCCTACCTCACACC 470

  chr1_172936918_   4324 TTACATAAAAATTAACTCAAAATGGATCATA-----AAATGTAAAACACA 4368
                         v  i i                       ? -----        i vvi 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_172936918_   4369 AAACTATATAACTCCTAGAAGTTAATATAGGAGAAAATATAGGTGACCTT 4418
                                 v     i      vv  i     ? v    v vv        
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_172936918_   4419 TGGTTTGGCAATGAAATTTTTGATAAAACACCAAAAGAATGGTCCATT-- 4466
                         v    v       ivv i  v    vi          v iiiv v iv--
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_172936918_   4467 -TAAAAAGTTGATGCATTGGACTTCATTAAAATTTAAAACTACTG--CTC 4513
                         -v     i v   iv            i      v      vi  --  i
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_172936918_   4514 CATGAAAGACACTGTTAAGGGGCTAAAAAGATAAGTTAAAGA-CAGGA-A 4561
                           --  i      i i   iiiv i      i  vii v   -ii   - 
  L1M4_orf2#LINE/    671 CA--AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_172936918_   4562 AAATATTTGCAAAAACACATTTCTAAGAAAAGATTTGTATTCATAATATA 4611
                                      v-  i  v   i v  ii  i      i  v      
  L1M4_orf2#LINE/    719 AAATATTTGCAAAT-CATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_172936918_   4612 TGAAGAACTCCTA-AATGCAACAATAAGAAAACAA----CTGTATTTTTT 4656
                          i        i  -  iv   i     i  i    ---- ivv   ?vvv
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_172936918_   4657 AATGGGCAAAAGATCTAAACAGACCCCTCTCCAAAGAAGGTACA 4700
                                   i   i i  i    vii            i  i 
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

Transitions / transversions = 1.55 (102 / 66)
Gap_init rate = 0.02 (18 / 728), avg. gap size = 2.39 (43 / 18)  


3283 26.98 0.44 0.44  chr1_172957130_172960583.rev     2056  2963 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_172957130_   2056 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2105
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_172957130_   2106 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2155
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_172957130_   2156 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2203
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_172957130_   2204 TATGGAACCAAAAAAGAGCTCGCATCACCAAGTCAATCCTAAGCCAGAAG 2253
                                viiv  ii  v iv v  vi    iv     i i ivv     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_172957130_   2254 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 2303
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_172957130_   2304 TACAGTAACCTAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2353
                                 i v i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_172957130_   2354 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 2401
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_172957130_   2402 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2451
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_172957130_   2452 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2501
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_172957130_   2502 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 2551
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_172957130_   2552 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2601
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_172957130_   2602 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 2651
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_172957130_   2652 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 2701
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_172957130_   2702 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2751
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_172957130_   2752 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 2801
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_172957130_   2802 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2851
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_172957130_   2852 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 2901
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_172957130_   2902 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 2951
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_172957130_   2952 ATCACTGGCCAT 2963
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2330 26.42 1.57 6.60  chr1_172983252_172987591.rev     2896  3849 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_172983252_   2896 GAAAAACATTCCATGATCATAGATAGGAAGACTCAATATTGCTTAAATGG 2945
                             i i  i     v    i   v        i       i v i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_172983252_   2946 CA-TACAGCCTAAAGCAGTTTACAGATTCAATGCTATTTCTATTAAATTA 2994
                           -   vv  i   viii i           i  v  ii    i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_172983252_   2995 CCAATGACATTCTTCACTAGTACTCTAATGGTATTCTAAACAGAATTAGA 3044
                            iivi v  i  --------------  ----------     v v  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTT--------------TG----------CAGAAATTGA 128

  chr1_172983252_   3045 AAAAAAAACTG-TTCTGAAATTCACATGGAACCAAAAAAGGGCCTAAAGA 3093
                         v  i----   - i  i       i      viiv  ii iv  vi  v 
  L1M4_orf2#LINE/    129 CAAG----CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr1_172983252_   3094 GCCAAAACTATCCTAAGCAAAAAAATAAAAATAAAATAAAATAAACAAAA 3143
                                 v   i i --    i  -----------------i      -
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGA--AAAAGAA-----------------GAACAAA- 204

  chr1_172983252_   3144 AATTAAAAGCTGGAGGCATCACATTATCTGACTTCAAACTATACTACATG 3193
                         -------- i      vv     i vi ii i      viv       vi
  L1M4_orf2#LINE/    205 --------GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_172983252_   3194 GCTACAGTAACTAAAACAGCATAATATTGGTACAAAAATAGACACA--GA 3241
                                   ii  i    ii ii  i   i i  ii       i --  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_172983252_   3242 CCAATGAAACAGACTAGAGAGCCCCAAAATAAAGCCACATACCTACAACC 3291
                         i     i  i   v v     i  vi       v   i i ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_172983252_   3292 ATCTGATCTTCAACAAAGTCAACAAAAACAAGCAATGGGCAAAGGACTCC 3341
                          vi    i   i    i viiv   i v  vv       v    i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_172983252_   3342 CTATTTAATAAATGTTGCTGGGATAACTGGAAGGCCATATGCAGAAGATT 3391
                           v  i  i     v        i       vi?   i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_172983252_   3392 GAGACTGGATGCCTTCCTTACATCATATATAAAACCTAACACAAGATGGA 3441
                           iii    iv   v   i   i      i    vi    v   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_172983252_   3442 TTAAAGACATAAATGTAAAACCTAAAACTATAAAAATGCTT-GAAGAAAA 3490
                          i ?    v         i v              v -   -        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAA 545

  chr1_172983252_   3491 CCAAAGAAATACCACTCTG-GACATAGATCCTGGCAAAGATTTCATAACA 3539
                          - v  i?i  vvv  ii -   v v iviiv     v i    v  ivv
  L1M4_orf2#LINE/    546 C-ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_172983252_   3540 AAGATGCCAACAGTACTTGCAA---AAAAAAAAATGGGCAAATGGAGCCT 3586
                          v  ii    v  i  vv    ---  i       i ii    v ii i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_172983252_   3587 AATTAAACCAAAGACCTTCTGCCCAGCAAAAGAAACTTTCAACAAAGTAA 3636
                         v  i   viv  i v   i  iv vv    i  v   v    v     i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_172983252_   3637 ACAGACAACCCACAGAATCATAGGAAGTATTTGCAAACTGAGCAAAGCTC 3686
                          v                viv  i  i          i----  v vv  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT----CATATATC 740

  chr1_172983252_   3687 TGACAAAGGTCAAATATCCCAAATCTATAAGGAACTTAAACAAATGAACA 3736
                            i  i  v vvi     vi   v     i     ivv    v v  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_172983252_   3737 AGCAAAAAACAAACAACTCTATTAAAAAGTGGGCAAAGGACATCCACAGG 3786
                          vv    i     i   i v   ?    i           iv vv i  i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_172983252_   3787 TACTTTTCAAAACACATTTGTGCA----GCCAATAAGCACATAAAAA--T 3830
                         i i  i  v   v - vv i i  ----              i    -- 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_172983252_   3831 GTTCAACATCACTAATCAT 3849
                          i         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 4.33 (78 / 18)  


2598 27.12 2.12 1.42  chr1_172989188_172991034.rev      509  1356 (491)    L1M4_orf2#LINE/L1       55   908 (0)  

  chr1_172989188_    509 ATACTACCTAGTAGT--ATCTATAGGCTCAATGCAATATTCATCAAAATA 556
                              v  i -- i --     i  ii    i     viii        v
  L1M4_orf2#LINE/     55 ATACTCCCCA--AATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_172989188_    557 CCAATGATATTCTGCACAGAAGTAGGAAAAA-AACCTTAAAATTTATATG 605
                            iiviiv  i vii     i v iv  iv-i i i       i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_172989188_    606 GAACTACAAAATACACAGAATAACCACAGACATCTTTGAGGGAAAAAAAA 655
                            v i   iiv  v       i   - i   vii    ii-  i  i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCA-AAACAATCTTGAAA-AAGAAGAA 200

  chr1_172989188_    656 TGAAACTGGAGAAATCACATTATCTGCCTTCAAATTATACTACAGAGCTA 705
                         ii  ii     i v     i vi iivi      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_172989188_    706 TAAGAACAAAAACATCATTGTACTGGTGCAAAAATAGGCACAAAGACCAA 755
                         i iv  iv  i   vii v       iii  ii    i  i v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_172989188_    756 TGGTATGGAA--GAAAATAACCCATAAATAAATCCACAAATCTGGGGTAA 803
                            v  i   --  i i ---   v       i   i v  i iv   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGT---CCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_172989188_    804 ACTCAGTCTTGACAAAAGTGCCAGGAGCATACATTGGAGAATGGAGAATA 853
                          i v v i i     ii      i  v   v  v   i   v i v i v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_172989188_    854 TCTTCAATAAATGGTGCTGAGAAAACTGGATGTCCATAGGCAGAAGAATG 903
                          i     i           i  v        i?   i v   i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_172989188_    904 AAACTAGACAGCTATCTCTTGCTGTATACAAAAATCAAATCAAAATGGAT 953
                           ii i   vv   i   vii ii           i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_172989188_    954 CAAAGACTTAAATAGAAGACCTCAAACTAAGAAACCACTAAAATAAA-CA 1002
                           ?    i     iv    v  v      vi    ivi  i  v   -  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_172989188_   1003 TTGAGGAAACTCTCCAGGACATTGGCCTGGGCTGAGATTTCTTGAGTAAT 1052
                          v i? v  v   i iv   v    vi i   viv i      iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_172989188_   1053 ACCCCACAAGCACAGGCAACCAATGAAAAAATGGACAAATGTAA--TCA- 1099
                           v   v       i     v  v        i  i    vvi --   -
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_172989188_   1100 CAATAACTTAAAAAGCTTTTGCACAGCAAAAGAGACAATCAACAAAGTGA 1149
                            -  -       -      ii vv    i  v  v     v       
  L1M4_orf2#LINE/    648 CAA-AA-TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_172989188_   1150 AGATACAACCTACAGAATGGGAGAAAATATTTGTAAACTATCAATCTGTC 1199
                          i v      i                      i   ii  vv     vi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_172989188_   1200 AAGGGATTAATAACCCAG----TAAGAAAAATTA--ATAACTCAATAGGA 1243
                               i vi  -i    ----  vi  i  i v-- i         iv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTA-TCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_172989188_   1244 AAAAAATCTAAAAATCCAATGAAAAAATAGGCAAAAAATCTGAATAGACA 1293
                             i - v  v  i     v?      i      ii  i          
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_172989188_   1294 TTTCTC---AAAAGCTGTACAAACGGCAAACAGGTATATGAAAATGTGCT 1340
                               --- i   v i      i   v  i i i i       vi    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_172989188_   1341 CAACATTATTGATCAC 1356
                               i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (143 / 83)
Gap_init rate = 0.02 (18 / 854), avg. gap size = 1.67 (30 / 18)  


3318 26.54 0.44 0.44  chr1_173009423_173015703.rev     4883  5790 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_173009423_   4883 TGGAAGAACATTCCATGTTCATGGGTAGGAAGAATCAATATCATGAAAAT 4932
                              ii i  i            i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_173009423_   4933 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4982
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_173009423_   4983 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5030
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_173009423_   5031 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAGAAG 5080
                                viiv  ii  v  v v  vi    iv     i i ivv     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_173009423_   5081 AACAAAGCTGGAGGCATCACGCTACATGACTTCAAACTATACTACAAGGC 5130
                                i      vv    i  v vii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_173009423_   5131 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5180
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_173009423_   5181 AATGGAACAGAAC--AGAGTCCTCAGAAATAATACTGCATATCTACAAAT 5228
                                i    i--       --        vv iii i  i  iiivi
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_173009423_   5229 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5278
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_173009423_   5279 CTATTTAAGAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5328
                           v  i  v              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_173009423_   5329 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5378
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_173009423_   5379 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5428
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_173009423_   5429 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5478
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_173009423_   5479 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5528
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_173009423_   5529 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5578
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_173009423_   5579 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5628
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_173009423_   5629 AGGGCTAATATCCGGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5678
                         i  i  vi     i    v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_173009423_   5679 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5728
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_173009423_   5729 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5778
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_173009423_   5779 ATCACTGGCCAT 5790
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3348 25.61 0.88 0.66  chr1_173056737_173062550     4416  5321 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_173056737_   4416 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4465
                              ii    i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_173056737_   4466 GGCCATACTGCACAAGGTAATTTACAGATTCAATGCCATCCCC-TCAAGC 4514
                            v     v v   iv i  i           i  v     i-    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_173056737_   4515 TACCAATAACTTTTTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 4562
                          v   iivi i     ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_173056737_   4563 TATGGAATCAAAAAAGAGACT--GCATAGCCAAGACAATCCTAAGCCAAA 4610
                                -- viv   i   i-- v        i      i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_173056737_   4611 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTCTACTACAAG 4660
                                  i      vv    i  v  ii i      vii        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_173056737_   4661 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGACAGA 4710
                                   i   i    ii         i iv ii i   v v i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_173056737_   4711 CCAATGGAACAGAACAGAG-GTCTCAGAAATAACACCACACATCTACAAC 4759
                         i        i    iv   -   -         vv   i    i  iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chr1_173056737_   4760 CATCTGATCTTTGACAAATCTGACAAAAACAAGAAATGGGGAAAGAATTC 4809
                           vi    i  i     ivv  v   i v  vvv              vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_173056737_   4810 CCTGTTTAATAAATGGTGCTGGAA-AACTGGCTAGCCATATGTAGAAAGC 4858
                         i  v  i  i            i -      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_173056737_   4859 TGAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGG 4908
                             ii    i    v   i i   v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_173056737_   4909 ATTGAAGACTTAAATGTAAGACCTAAAACTGTAAAAACCCTAGAAGAAAA 4958
                           ii?    i           v        i     vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_173056737_   4959 CCTAGGCA-ATACCGTTCAGGACATAGTGATGGGGAAAGACTTCATGACT 5007
                          v    ?i- v i -   iv   v v v v i  v  v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_173056737_   5008 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5057
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_173056737_   5058 AATTAAACTAAAGAGCTTCTGTACAGCAGAAGAAACTACCATCAGAGTGA 5107
                         v  i   v v  i i   i   i vv  i i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_173056737_   5108 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5157
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_173056737_   5158 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5207
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_173056737_   5208 AAAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACACT 5257
                            i     i     v  i? v  i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_173056737_   5258 TCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAGTGCTAA 5307
                             v        i  vi viii     i ii  i       ii    v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_173056737_   5308 TCATCACTGGTCAT 5321
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (139 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


2501 26.07 2.96 5.15  chr1_173071975_173074544.rev     1168  2080 (490)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr1_173071975_   1168 TGTTCATGGATTGGAAGAATTAATATTGTAAAAATGACCATATTACCAAA 1217
                                           v          v  i   i v   i v  v  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_173071975_   1218 AGCAATCTACAGATTCAATGAACTCC--ATCAAAATACCGATGATACTCT 1265
                          vii              i v v   --        v  iiiviivi i 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_173071975_   1266 TCACAGAAATAGAAAAAGAACAATTCTAAAATTCATACGGAACCACAAAA 1315
                          ii       v  v  iv--ii  i            i    vii   ii
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGC--TGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_173071975_   1316 GACTCCAGA-TAGCTAACACAATTCTGAGCAAAAAGAACAATGCTGGAGA 1364
                            -     -    i  v     ii   iv  i        v i     i
  L1M4_orf2#LINE/    164 GAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr1_173071975_   1365 CATCACATTACATTACATCACATCACATTACCTGACTTGAAAATATACTA 1414
                         vv     i v viv iv   v v vi i   vvii  -- v i  - ii 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT--ACAGTA-ATCA 259

  chr1_173071975_   1415 AAA--GCATGATACCGGCATAAAAACAGATACACAGACCAATAGAACAGA 1462
                          i -- ii  i   i       ii i   i i i   i    i   i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_173071975_   1463 ATATAGAACTCAGAAATGAATCAGCATATTTATAGCCATCTGATTTTTGG 1512
                           vv   iii       i  i vii i      i i  vi       i i
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_173071975_   1513 CAAAGGCTCCAAGAACATTTGCTCAGGAAAGGACCGTCTCTTTAATTAAT 1562
                            i  iv      v    iiv vi      i iv    i  i  iv   
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_173071975_   1563 AGTGCTGGGAAAACTGAATATCCATATGTAGAAGAATAAAATTAAACTCC 1612
                         i         v     i   ?   i   i i      i  i  ii  i  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_173071975_   1613 TATCTCTCATCATCTACAAAACATCAACTCAAAATAAATTAAAGACCCAA 1662
                           i   v  i   v       -  i          ii  i ?     i  
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAA-ATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_173071975_   1663 A--------------CTATGAAACTACTGGAAGGAAACATAGGGAAAACA 1698
                          --------------    i     vi i    i         ?iv  vv
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_173071975_   1699 CATCAGGACAT-GGGTCTGGACAA-GATTCTATCAACAAAACCACAATAG 1746
                          v  iv   v -    - i i   - i  iiv vi i vi  vv   v  
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_173071975_   1747 CATAAGCAACAAAAGCAAAAATAGCCAAATGGGATTACATCAAACTAAAA 1796
                           i            v        vi    v   i v       v v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_173071975_   1797 AACTGCTACACAGCAAAGGAAAC----AACACACTGAAGAAACAACATGC 1842
                             vi iii vv       v  ----  v v v    i i     vii 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_173071975_   1843 AGAATGGGAAGAAAATACTTGCAAACTATTCATCCAACAAGGGACTAATA 1892
                                  -       i       ii  vi   ii i        vi  
  L1M4_orf2#LINE/    708 AGAATGGGA-GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_173071975_   1893 TATGGAATACA--AGGAATTAAAAAAACTCAACATCAAAACACACAGACA 1940
                          vii     i -- i   i vvv v       i vi    --------- 
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA---------A 797

  chr1_173071975_   1941 GACACACACACACACACACACACACACACACAATAATCTGACTGAAAAGT 1990
                             ---------------------------     i ii i ?    i 
  L1M4_orf2#LINE/    798 GACA---------------------------AATAACCCAATTWAAAAAT 820

  chr1_173071975_   1991 GAGCAAAGGATCTGAATAGACATTTCTTAAAAGAAGACATATGAATGGCC 2040
                          i         i               iv        i   ii       
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_173071975_   2041 CACAGGTATATGAAAAAAATTGCTTAACACCCCTAATCAT 2080
                         v i i i i       i --    i    i v????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (153 / 81)
Gap_init rate = 0.02 (18 / 893), avg. gap size = 4.11 (74 / 18)  


3347 24.94 1.22 0.55  chr1_173098924_173103202.rev     2887  3788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_173098924_   2887 TGGAAA--CATTTCATGTACATGGATTGGAATAACCAATATT---AAAAC 2931
                               --i  ii     v            v vii      ---  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_173098924_   2932 GCCTATACTACCCAAAGCAATCTATTGATTCAATGTAATCTCTATCAAAA 2981
                          v v     v      vii     iv       i i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_173098924_   2982 TACTAATGACATTCTTCACAGAAATAGAAAAAA-AATCCTAAAATTTATA 3030
                          v i iivi v  i  ii       v  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_173098924_   3031 TGGAACTAAAAAAGACCCAGAATAGCCAAAGCTATTCTAACCAAAAAAGA 3080
                              v iv  ii                 i v  ii i v-   i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chr1_173098924_   3081 ATAAAACGGGAGGAATCACATTACCTAACTTCACATTGTACTACAGAGCT 3130
                          i   iiv      v     i v  i  i    v viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_173098924_   3131 ATAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACATATAGACCA 3180
                          i     i   i    ii              ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_173098924_   3181 ATGGATCAGAACACAGAACCTAGAAACAAATCCACACACCTACAGTGAAC 3230
                              vi    ivv   ii i     i   i   i   ii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_173098924_   3231 TCATTTTTGACAAAGTTGCCAAGTACATACACTGGGGAAAAGACAGCCTC 3280
                          v     i     i v       vv   v  v        ii i  i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_173098924_   3281 TTCAATAAGTGGTGCTGAGAAAACCAGACATTCAGACGCAGAAGAATAAA 3330
                              i  i        i  v   ii  i ?i  v i   i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_173098924_   3331 ACTAGATGCCTATTTATCACCACATACAAAAATAAAATCAAAATGAATTA 3380
                         ii i  iv    ii vv     i          v  v        i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_173098924_   3381 AAAACTTAAATCTAAGACCTCAAACTATGAAACTGCTACAAAAAAA-ATT 3429
                         ? i  i     v     v  v       i     vi  v  i    -  v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_173098924_   3430 GAGGAAAATCTCCAAGACATTGATTTGGGCAAAGATTTATTGAGCAATAC 3479
                          i? v      i iv   v   iv  i     v i   v  iiii vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_173098924_   3480 CCCTTAAGCACAGGCAACCAAAGCAAAAAATGGACAAATGGGATCACATC 3529
                         v  vv       i     v    -       i  i    v   iiv    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCATC 648

  chr1_173098924_   3530 AAATTTAAAAGCCTTTGTGTAGTAAAGCATACAATTAACAAAGTAAAGAA 3579
                            v      i i      ivvi    v i  v  i  v     i  i i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_173098924_   3580 ACAACCCACAAAATGGGATAAAATATTTA-AAACTACCCATCTGAAAAGG 3628
                                   i       v         i-   ii ivi      v    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_173098924_   3629 GA--TAAATCACTCA-ACTATAAAAGGAGCTCAAACAACTCTATAGGAAA 3675
                           -- iv   ---  - v    v  i  i   vv       v   iv   
  L1M4_orf2#LINE/    749 GACTTGTATC---CAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_173098924_   3676 AAGTCTAATAATCTGATCAAAAAATGGGCAAAAGATTTGAATAGACATTT 3725
                            v v     i ii  i?             i                 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_173098924_   3726 CTCAAAAGATGACATACAAATGGCAAACAGGCATACGAAAAGGTCTTCAA 3775
                            v     v  i           v  i i   i i      i vi    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_173098924_   3776 CATCACTGGTCAT 3788
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (138 / 83)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2840 25.76 2.58 1.12  chr1_173103547_173106187.rev     1258  2150 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_173103547_   1258 GAGAAACATTCCATACTCATGGATAGGAAGAATCAATATCATGAAAATGG 1307
                           i i i  i    ii        v      v i     ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_173103547_   1308 CCATAATGCCCAAAGCAGTTTATATATTCAATGCTATTCCCATTTAACTA 1357
                          v   v v      viii i  i v      i  v  i  i  iv  v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_173103547_   1358 CCATTGACATCCTTCACAGAATATTTTAATAA-CT-ATTTTAAAATTCAT 1405
                            vivi v ii  ii     -   --i i  -  -  ii          
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAA-ATT--GACAAGCTGATCCTAAAATTCAT 149

  chr1_173103547_   1406 AGGGAACCAAAAAAGAGCCCGAAGAGCCAAGTCAATCCTAAGCAA-AAGA 1454
                          v    viiv  ii  v  v   v      iv     i i iv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_173103547_   1455 ACAAAGCTGAAGGCATCACACTACCCAACTTCAAACTATCCTACAAGGCT 1504
                               i  i   vv       v     i      viv v      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_173103547_   1505 ACTGTAAACAAAAACAGCATGGTACTGGTACAAGAACAGACACATAGACC 1554
                           v    v   i -   ii         i i   i i     i     i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_173103547_   1555 AATGGAACAGAATAGAGAACTCAGAAATAAGACTGTACACCAATAGCCAT 1604
                                i     v    iii         iv ii    iiv  i i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_173103547_   1605 CTGATCATCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 1654
                         i    iv  i    ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_173103547_   1655 ATTTAATAAATGGTGCTGGGAAAATTGGTTAGCCATATGCAGAAAATCGA 1704
                         v  i  i              v  i   v  ?   i     i  i vi  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_173103547_   1705 AACTGGAACCCTTCCTTACAATATATATAAAAATTAACTCAAGATGGATT 1754
                          ii    v    v   i   vi     i              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_173103547_   1755 AAAGACTTAAATGTAAAACTCAAAACTATAAAAACCCTAAAAGAAAATCT 1804
                          ?    i         i vii            vi i  i       iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_173103547_   1805 AGGCAATATAA---TTCAGGATATAGGCATGGGCAAAGGTTTCATGACAA 1851
                            ?i---   ---   iv  iv v  vv i     v      v iivv 
  L1M4_orf2#LINE/    549 AGGNG---TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_173103547_   1852 AGATACCAAAAGCAATTACAACAAAAGCAAAATT-GACAAATGAGATCTA 1900
                         v  i          vvvi         v    v -  i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_173103547_   1901 ATTAAA-CTAAAGA-------GCATCA--GCACAGCA--AAAGAAATAAA 1938
                           i   -i    i -------  v   -- v   vi --  ii  i i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_173103547_   1939 GAGACAACCTACAGAATGAGGGAAAATTTTTGCA--TCTATCCATCTGAC 1986
                         i        i        i i      v      --  -  vi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGAT 744

  chr1_173103547_   1987 AAAGGACCAGTATCCAGAATCTATAAGGAACTTGAACAAATGTACAAGAA 2036
                           i    iv           v     i     ivv    v vv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_173103547_   2037 AAAAAAAAA-AACCCCACTAAAAAGTGGGCAAAGGACATAAACAGACACT 2085
                            i v   -     v i ?    i           iv i  i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_173103547_   2086 TCTCAAAAGAAGACATACAT-TGCAGCCAACAAACTTATGAAAAAAATCT 2134
                             v        i     v-  --     i  i vi       i vv  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCT 892

  chr1_173103547_   2135 CAACATCACTAGTTAC 2150
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 1.83 (33 / 18)  


2936 26.13 1.65 1.54  chr1_173120224_173125346.rev     3726  4632 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_173120224_   3726 TGGAAAAACATCTCAGGCTCATGGAAAAGAAGAATCAATATCATTAAAAT 3775
                               i i   i  v i       vvi     v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_173120224_   3776 GGCTATACTGCCTAAAGTAATTTACAGATTCAACGATAATCC-TGTTAAA 3824
                            v     v  i   v i  i             -i     - i i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACG-CAATCCCTATCAAA 99

  chr1_173120224_   3825 CTACCAATGACATTCTTCACAGAACTAGAAAAAAAAAACT-ATTTTAAAA 3873
                         v v   iivi v  i  ii     v v  v  i-----  -  ii     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAA 144

  chr1_173120224_   3874 TCCATAGAGA---GCCAAAAAAGAACCCA-AATAGCCAAGGCAATCCTAA 3919
                          i    vi  ---  ----  i i     -         ii     i i 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_173120224_   3920 GCAAAAAGAACAAAGCTGGAGGTATCACATTACCCAATTTCAAACCATAC 3969
                         iv  i          i      vv     i v            v v   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_173120224_   3970 CATAACACTACAGTGACCAAAACAACATGGTACTAGTACAGAAACAGACA 4019
                         i i  vi       i i   i   iii       i i i iii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_173120224_   4020 CATAGACCAATGGAACAGAATAGAGAGTCCAGAAATAAGGATGCACACCT 4069
                         i     i        i     v                ivviii   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_173120224_   4070 ATGACCATATGATCTTTGACAAAGCTGACAAGAACAAGCAATGTAGAAAA 4119
                            ii  vv    i  i     i v  v     v  vv     vi    i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_173120224_   4120 GACTCCCTATTCAATAAATGGTGCTGAAATAACTGGCTAGCCATATGCAG 4169
                         i ivvi  v     i           ii i      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_173120224_   4170 AAGATTGAAACTGGAATACTTTTTTACACCATATACAAAAATTAACTCAA 4219
                             v    ii    viv  vii i                         
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_173120224_   4220 TATGGATTAAAGGCTTAAATGTAAAACCAAAAACTATAAAAACCCTGGAA 4269
                         v      i ?  i i         i v v            vi i i   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_173120224_   4270 GACCACTTAGGCAATAGGAATCCT-G-GACATAAGAATAGGCAAAGATTT 4317
                           vv  v    ?i-  --    i - -   v vi iv       v i   
  L1M4_orf2#LINE/    541 GAAAACATAGGNG-TA--AATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_173120224_   4318 CATGACAAAGACACCAAAAGCAATGGCAACAAAAGTAAAAATTGACAAAT 4367
                          v iivv v             vvi          v      v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_173120224_   4368 GGAAACTAATTAA--CTAAAGAGCTTCTGCACAGTAAAAGAAACTGTCAA 4415
                         v i vi v  i  --i    i -   i  ii vvi   i  v   i    
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_173120224_   4416 CAGAGTAAACAGACAACTTACAGAATAGGAGAAAACTTTTGCAAACCATG 4465
                         v i   i  v       ii       i        iv        i   i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_173120224_   4466 CATCTGAAAAAAGTCTAATATCCAGCATCTCTAAGGAACTTAAGCAAATT 4515
                         i      v  ii v  vi       v  v v   i     ivvi   v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_173120224_   4516 TACCAGAGAAAAACAA----CCCCATTAAAAAGTGGGCAAAGAACAT-AA 4560
                         v iv v i   i    ----   v   ?    i         i iv -  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_173120224_   4561 CAGACAATTTTCAAAAAAAGACATACGTGTAGCCAAGAAGTATATTTAAA 4610
                         i     v  i  v   i    i    ivi i     v   i i  vv   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_173120224_   4611 AAAACTCAACATCACTGATCAT 4632
                         i vi          ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.93 (29 / 15)  


 550 30.63 7.85 4.19  chr1_173155306_173157056      500  1263 (488)    L1M4_orf2#LINE/L1      117   908 (0)  

  chr1_173155306_    500 TGAAGAAAT-GACCTAGAGCTTAATCTACAATTTATATGGATTAA--CAA 546
                           v      -   ---i    v vi   v    i       --  --   
  L1M4_orf2#LINE/    117 TGCAGAAATTGAC---AAGCTGATCCTAAAATTCATATGGA--AATGCAA 161

  chr1_173155306_    547 CTG-CCCATAAACCACTAAGTCAAATTTGAAAA-GAGGAGCAAA-CAGGG 593
                         vv -    -i  ivi i  iv   vi       -  i  i    -iv  i
  L1M4_orf2#LINE/    162 GGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_173155306_    594 AGAGTCACTCTGACAGATATAGAACCATACTATAAACATACATGCAATAA 643
                         i  v    v  vv vi  v vi  v v     i   vv    - i   v 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA-GTAATCA 259

  chr1_173155306_    644 ACACTGTGTAATATATGTAAAAGAATAGGGAAATAAATCCATGTCACCGA 693
                          v  v    ii  ivv i v   i    iv v   i   v   vv iv  
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_173155306_    694 AGAAAGAGTT-AAAGGCAGACCCGTG--TTTATTTGGAAACCTGGCATAT 740
                          vvi     i- i iii i    i i--     --  vv vi  iiv vi
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTAT--GGTCAATTGATTTTC 357

  chr1_173155306_    741 AATAGGTGTGGCATCACAAATATATATGTCAA---TAGATTATTTAATGT 787
                         i i i v   v  vv  v v vv  iv vv  ---   vi v  i  iiv
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_173155306_    788 CTGGTATTAGGGAAATCAG---GCCACTATCTGGATAAA--AAACTG--- 829
                         v    ii i  iv  iii ---?    -  viii vi  --  ii  ---
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCAC-ATGCAAAAGAATGAAGTTGGAC 456

  chr1_173155306_    830 TCATATTCTTATAAGACAT-TAAAAATTAATCTTTCAGAA-GGAT----- 872
                         i v  i-  i i vv i  -i         i---   i  -    -----
  L1M4_orf2#LINE/    457 CCCTAC-CTCACACCATATACAAAAATTAAC---TCAAAATGGATCAWAG 502

  chr1_173155306_    873 ---TAAATGTGAA---TGGAACTATAAAGCTAATGG--GAAA-------- 906
                         ---       i i--- ii         i  vv i --    --------
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_173155306_    907 -TAATATCTTTGTGAGTTTGGAGTGAGG-AA-GGTCTTCTTAAATAAGAA 953
                         -   -     i    vi    -  v   -  -   -      i   v  v
  L1M4_orf2#LINE/    553 GTAA-ATCTTCGTGACCTTGG-GTTAGGCAATGGT-TTCTTAGATATGAC 599

  chr1_173155306_    954 AACCAAACCACAATT--CAAGAGGAAAACAGGGTGATGTATTTGACTACA 1001
                          v v   v     vi--   i  i    vvi i i ---   v    v  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA---ATTGGACTTCA 646

  chr1_173155306_   1002 ATCAAATTAGATTATTTCT---TTTCAATAAA-AGTATGATAGATCAAAT 1047
                         viv      i v- i  i ---i     vii - v   v -   ---  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCA-AGA---AAG 691

  chr1_173155306_   1048 TCATTAGACTGATGACAGACTGGGAAAAGATATTTTGCATGAACCATAAC 1097
                          v vv    viviv     v     i  i      -   --  i    vv
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCA--AATCATATA 738

  chr1_173155306_   1098 AAAAATAAGGAACTGATATCTAGATTAGAAAAAGAATTGTTAAAATTCAA 1147
                         vvvi      i   vi    i   v  v v      i v   v  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_173155306_   1148 CAACACAGTTTGACAAA---CTCCAT--AGAAATGGTTGAAGAATAGGAA 1192
                         i  i v iv--      --- i v  -- i      vii   i  vv   
  L1M4_orf2#LINE/    789 TAATAAAAA--GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_173155306_   1193 TAGACAATTC---AGAGAAGAGAGATCTGAAAGGTTAACGAGTATATGAA 1239
                               v   --- i      v v i--i  v  ii  ii  i i     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATAC--AAATGGCCAATAAGCACATGAA 884

  chr1_173155306_   1240 AATTTACTCAAACTCATAAATAAG 1263
                           vv i     vv   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.04 (119 / 114)
Gap_init rate = 0.06 (44 / 792), avg. gap size = 2.09 (92 / 44)  


3124 25.37 3.28 0.45  chr1_173281025_173285926.rev     3529  4411 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_173281025_   3529 TGAAAAGACATCTCATATTAATGGATTTAAAGA----ATATTGTGAAAAT 3574
                           i     i   i   i  v       vi    ----       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_173281025_   3575 GACCATGCTAACAAAAGCAATCTACATAT-CAATGCAACCCCTATCAAAA 3623
                          i v  i  vv v   vii       v  -   i    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_173281025_   3624 TACCAATGACATTCTTCATAAAAATAGAAAACACCATCCTAAAATTT-TG 3672
                          v   iivi v  i  iii i    v  v  vviv           i- i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_173281025_   3673 CAGGCTACTGCAAAAGACCTCAAATAGCCAACACAATCCCGAGCAAAAAG 3722
                         ii i-- v     ii    ivi         v      ii  iv  i   
  L1M4_orf2#LINE/    151 TGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_173281025_   3723 AACAAAGCTGGAGGCATCACACCACCAGACTTTAAAATTTACTACAAAGC 3772
                                i      vv      iv  vi i  i    i            
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_173281025_   3773 TATAGTAACCAAAATAGCATTGTACTGGCATAAAAATAGGCAAATAGACC 3822
                           i     i   i i  ii v            ii    i  v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_173281025_   3823 AGTGGAACATAATAGAGAACCCAGAAATTAATCCATGTATCCACAA-CAA 3871
                          i     i v   v    ii        v  i    ii  ii iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_173281025_   3872 CTGATTTTTGACTAAGGTACCAAGTACATTGATTGCGGAAGGGAAAATCT 3921
                         i       i   v i   i     vv    v v  v    i i v i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_173281025_   3922 TTTCAATAAATGGTGCTCAGAAAACTGGATACCCATATGCTGAACAAGGA 3971
                               i          vi  v         ?   i    vi  v  v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_173281025_   3972 AATTAGACTCCCACCTCTCACCCTATTAAAAAAAATT---TCAAAATGGG 4018
                          i  i   i  i     v    v   -- v       ---         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATAT--ACAAAAATTAACTCAAAATGGA 496

  chr1_173281025_   4019 TTAAAGACCTAAATGTAAGACACAAAACGACAAAGCTGCTAGAAGAAAAT 4068
                          i ?                vvi     v i   i  vi          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_173281025_   4069 ATAGGGGAAACACTTCAGGATGTTGGTTTGGGAAAAGATTTTATGAATAA 4118
                              ? v  vv    iv  iv    v  i  v  v i   iv ii   v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_173281025_   4119 GACTTCAACAGCACAGGCAACAAATGAAAAAAC---TA--TTGAACT--- 4160
                            vi   v      i        v       i---  --   i   ---
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_173281025_   4161 --------AAAAGCTTTTGCACAGCAAAAGAAACAACTGAAAGAGTGAAA 4202
                         --------    i      ii vv    i  v  v iii i i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_173281025_   4203 AGACAATCTAAAGAATGGGAGAAAATAGTTGCAACT-ATTCATCCAACAG 4251
                               i i v                v      v -  vi   ii i i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_173281025_   4252 TGGTTTAATATCCAGAATATGCAAAAAATGCAAACATTTCAATGGCAAAA 4301
                         v  vi vi            ii   i  iv vv   vi     iii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_173281025_   4302 GTACAAATAATCAGATGAAAAAATGAGCAA-TGATCTGAACAGATATTTC 4350
                         iv        i vi  v?       i    -v   i    i   i     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_173281025_   4351 TCAAAAGAAGACATACAA-TAGCCAACAAATATATGAAACACTGCTCAAC 4399
                           v        i      - i     i  ii i      viv        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_173281025_   4400 ATTATTAATTAT 4411
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (136 / 84)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.54 (33 / 13)  


 498 24.83 1.34 2.68  chr1_173287331_173289772.rev      921  1069 (1373)    L1M4_orf2#LINE/L1        1   147 (761)  

  chr1_173287331_    921 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAATATTGTGAAAAT 970
                               i i  i    vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_173287331_    971 GGCCATACGGCCCAAAGTAATGTATAGATTCAATGCTACTCCCATCAAAT 1020
                            v    vv      v i  v  i        i  v ii  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_173287331_   1021 TACT-GTTGACATTCTTCACAGAATTAGAAAAAAAACT-ATTTTAAATTT 1068
                          v i- i  v -  i  ii     v v  v  i---  -  ii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chr1_173287331_   1069 C 1069
                          
  L1M4_orf2#LINE/    147 C 147

Transitions / transversions = 1.18 (20 / 17)
Gap_init rate = 0.03 (4 / 147), avg. gap size = 1.50 (6 / 4)  

2442 25.52 1.94 1.81  chr1_173287331_173289772.rev     1180  1951 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_173287331_   1180 ATTTTAAATTTCATATGGAA-T-CAAAGAAGACCCTGTATAGCCAAGACA 1227
                           ii    v           - -   i --     v v        i   
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACA 183

  chr1_173287331_   1228 ATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAA 1277
                            i i iv  i          i      vv    i  v  ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_173287331_   1278 ACTATAGTACAAGTCTACAGTAACCAACACAGCATGGTCCTATTACCAAA 1327
                          viv  v     iv         i   v    ii    v  ivi iv ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_173287331_   1328 ACAGACATAAAGACCAATGGAGTAGAACAGAGACCTCAGAAATCACACCA 1377
                          i       v   i       i     iv    vii       v vv   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_173287331_   1378 CACATCTACAACCATCTGAT---CAACAAACCTGTCAAAAACAGGGAATG 1424
                         i    i  iiii  vi    --- i    ivv  i   i v  vvv    
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_173287331_   1425 GGGAAAGGATCTTCTATTCAGTAAATGGTGCTGGGAAAACTGGCAAGCCA 1474
                                i  vv   v    ii              v      vv ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_173287331_   1475 TAGTCAGAAAACTGAAACTGAACCCCTTCCTTACAACTTACACAAAAATT 1524
                         i vv  i  i v    ii  i      v   i   v v  i         
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_173287331_   1525 AACTCAAGATGGATTAAAGACTTAAATGTAAAACCCCAAACCATAAAAAC 1574
                                i      i ?    i         i v iv    i      - 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-C 532

  chr1_173287331_   1575 TCT-AGAAGAAAACCTAGGCATTACCATTCAGAACATAGGCATGGGCAAA 1623
                            -          v    ?i v viv   ivi  v v  vv i     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_173287331_   1624 GACTTC------ATGACA--AAAATGGCAAAAACAATTGCAACAAAAACC 1665
                          ii   ------      --    --   ----   --         ivv
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAA--GCA----CAA--GCAACAAAAGAA 624

  chr1_173287331_   1666 AGAATCAACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 1715
                          i   vi i    v   ii v  i   v v  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_173287331_   1716 AGAAACTATCATCAGAGTGAGCAGCCAACCTAAAAAATGGTTGAAAATTT 1765
                         i  v       vv i     iv  v     i v i     vv      v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_173287331_   1766 TTGCAGTCTATCCATCTGACAAAGGTCTAATATCCAGAATTTATGAGGAG 1815
                              ivii  vi      i  i  v  vi          v   i i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_173287331_   1816 CTTAAGCATATTTACAAGAAAAAAAAAACAAACAACCCA-TCAAAAAGTG 1864
                           ivvi  - i --   v  v     i     i      - i?    i  
  L1M4_orf2#LINE/    775 CTCTTACA-ACT--CAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_173287331_   1865 GGCCAAGGGTATGAACAAACACTTCTCAAAAGAAGACATTTAAGTGGCCA 1914
                            v    i v    i i   i     v        i  vi  i      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_173287331_   1915 ACAAACATATGAAAAAAAGCTCAACATCACTGATCAT 1951
                          i  i  i       i v           ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (109 / 84)
Gap_init rate = 0.02 (14 / 773), avg. gap size = 2.07 (29 / 14)  


3376 24.33 0.75 3.43  chr1_173347454_173351648.rev     2772  3704 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_173347454_   2772 TGGAAATATATTTCAAGCTTATGGATTGGAAGAATTAATGTTGTTAAAAT 2821
                               v    ii  v i i             v     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_173347454_   2822 GACTAGAC-----AAAGCAATAGACAGATTCAATGCAATTTCTACCAAAA 2866
                          i v v  -----   vii  vv          i     ii   i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_173347454_   2867 TACCAATGACATTCCTCACAGAAATAGAAAAAG-AATCCTGAAATTTATA 2915
                          v   iivi v  ii ii       v  v  iv-i     i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_173347454_   2916 TGGAACCTCAAAAGACCCCAAATAGCCAAAGCAATTCTGAGCAAAAGGAA 2965
                              viv   ii     vi          i    ii   iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_173347454_   2966 CAAAGCTGGAGGCCTCAAAATACCTGATTTCAAAATACACTACAAAGTTA 3015
                              i      v    v v v  ii         ivi         i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_173347454_   3016 TAGCAGCCAAAATGGCATGTTACTGGCAAGGAAAAAAACAAACAAAGAAA 3065
                         i  i ii   i ii ii  v        v----  ii i i   v v i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCAT----AAGGATAGACATATAGA 296

  chr1_173347454_   3066 CAAACAAAAAACATTAACCATTGACAGTTGGAACAAAGTAGAGAACCCAG 3115
                         ------------- i  -----------     i i i v    ii    
  L1M4_orf2#LINE/    297 -------------TCAA-----------TGGAATAGAATTGAGAGTCCAG 322

  chr1_173347454_   3116 ATATTAATCCTTGCATTTATAGCCAACTCATTTTTGACAAAGGTACCAAA 3165
                          v  v  i  v i       i i   i v     i     i   i    i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_173347454_   3166 AACATACAATAGGGAAAGGACAGTCTCTTCAATAAATAGTGCTGGGAAAA 3215
                          v   v    i       i i     i     i    i         v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_173347454_   3216 CTGGATAACCATATGCAGAAGAATAGAACCAGACCCCTATCTCTTACCAC 3265
                                ?   i     i      ii iiii        i   vi    i
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_173347454_   3266 ATACAAAAAATAAAATCAAAATGGATTAAAGACTTAAATGTAAGGCCTCA 3315
                                  v   v-           i ?    i          iv  v 
  L1M4_orf2#LINE/    473 ATACAAAAATTAAC-TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_173347454_   3316 AACTATGAAACTGCTACAAGTAAACATTGACAAAATTTTTCATGGCATTG 3365
                               i     vi  v   v      v i?iv  v i   i  i v   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_173347454_   3366 GACTGGGCTAAGATTTCTTGAGTCACACCCCACAGGCACAGGCAACCAAA 3415
                          ii i   v v i      iii vvv  v   v i     i     v   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_173347454_   3416 ACAAAACTGGACAAATGAGATCATATCAAG-TGAAAAAGCTTCTGCATAC 3464
                         iv    v i  i    vi  iivi     i- v     -   i  iiivi
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTT 670

  chr1_173347454_   3465 CAAAGGAAACAATCAACAAAGTGAAGAGATAACCCACAGAATGGGAGAAA 3514
                                v  v     v        i   i                    
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_173347454_   3515 ATATTTGCAAACTACCCATCTGACAAGGGATTAATAACCAGAATATATAC 3564
                                    ii ivi      i      i vi  v            v
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_173347454_   3565 GGAGCTCAAACAACTCAATTGGAAAAAAAATCCAATAATCCAACTAGAAA 3614
                         i  i   vv          viv     i -- v     i    i ?i   
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAA 818

  chr1_173347454_   3615 ATGGACAAAACACCTGAATAGACATTTATCAAAAGAGGACATACAAATGG 3664
                             i    iv ii             v  v     i  i          
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_173347454_   3665 CAAACAGGTATGTGAAAAGGTGCTCAACATCACTGATCAT 3704
                          v  i i i ii       i            ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (146 / 77)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 4.33 (39 / 9)  


2740 25.25 2.51 3.28  chr1_173703147_173706533     1980  2894 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_173703147_   1980 TGGGAACACCTCCCATGCTCATCAATTGGAAGAACCAATATCATGAAAAT 2029
                            i  v iv       i    vi         vii     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_173703147_   2030 GACCATACTGCCCAAAGCAACCTACAGATTCAATGAAATTC-TGTCAAAA 2078
                          i v     v      vii i            i v   i - i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_173703147_   2079 TATCAAGAACTTTTTTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 2128
                          vi  ivvi i     ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_173703147_   2129 TGGAACAACAACAACAACAACAAAAGCCCGAATAGCCAAAGCAATCCTAA 2178
                              vvi   ----------iii v  v           i     i i 
  L1M4_orf2#LINE/    151 TGGAAATGCAA----------GGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_173703147_   2179 GTAAAAATAACAAATCTTGATGCATCATATTACCTGATCTCAAA--TTA- 2225
                         iv  i  v      vi v  v vv   i i v  ii  i     --   -
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_173703147_   2226 TACAAGACTATCATAACCAAAATAGCATGGTACTGGTATAAAAGTAGATA 2275
                              ii   ivi   i   i i  ii         i    iii    i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_173703147_   2276 TACAGGCCAAAGGAACAGAATAGAGAACCCAGAAATAGAGCCAAATACTT 2325
                           i  ii   v    i     v    ii         i v   v i i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_173703147_   2326 ACAACCATATGATCTTTGACAAAA-CACACAAAAACAAAAACCAAGGAAA 2374
                          iiii  vv    i  i     ii-ii -   i v  vvv viii     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAA 389

  chr1_173703147_   2375 GGACACCCTATTCAATAAATGGTACTGAGAAAGCTGGATAGCCACATGCA 2424
                          i i vi  v     i       i   i  v i       ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_173703147_   2425 GAGGAATTAAACGGGATCCCTATCCCTCACCATACATAAAAATTAACTTA 2474
                         i i    v  iiv   i     i i v       i i           i 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_173703147_   2475 AGATGGATTAAAGGCTTAAATCTAAGATCTGAAACCATAAAAATTCTAGC 2524
                          i      i ?  i i     v     v  i    i      v ii   v
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_173703147_   2525 AGAAAACCTAGGGA-AAACCATCTGGACATTGGCCTAGGCAAATAATTTA 2573
                                v    ?i-   i v  vv   v    vi       - ii   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTC 588

  chr1_173703147_   2574 T--GACTAAGACCCCAAAAGTAAATGCAAAAAAACCAAAAACAAATCAAT 2621
                          --  -  v   v       i v v    v    vv     i i  v   
  L1M4_orf2#LINE/    589 TTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_173703147_   2622 GGTACTTAACTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACAACCATC 2671
                         v v    v ii   v v    i   i  ii vv    i  ----------
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA---------- 677

  chr1_173703147_   2672 TTATTTCATAATCAAGA--GTAAACAGACAACCTACAGAATGGGAGAAAA 2719
                         ------  iv       --  i  v        i                
  L1M4_orf2#LINE/    678 ------CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_173703147_   2720 TATTTGCAAAACATGCATCTG-CAAAGGACTAATATCCAAAATCTACAAG 2768
                                   v   ii     -i  i     vi      i   v  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_173703147_   2769 GAATTCATATAAATCAGCAA-GAAAAGA-----AATCCCATTAAAAAATA 2812
                            i  v  i  v   ii  -i      -----  i  v   ?      i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_173703147_   2813 GGCAAAGGACATGAATTGACATATTT--AAAAAAAATA--CAAATGGCCA 2858
                                  iv     v     v i --   i  i   --          
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_173703147_   2859 GAGAA--ACATGTAAAAATGCTCAACATTATTAATCAT 2894
                         - v  --     v   i           i ????????
  L1M4_orf2#LINE/    872 -ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (142 / 85)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.79 (53 / 19)  


3238 15.44 0.85 6.09  chr1_173792547_173794243.rev      502  1207 (490)    L1M4_orf2#LINE/L1      240   908 (0)  

  chr1_173792547_    502 CTACAAAGCTACAGCAATAAAAACAGTGTGGTACTAGCATAAGCACAGAT 551
                                       i   v  i             i       v i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_173792547_    552 ATATAGAAATGGGTTAGTATTGAATGTCTAAAATAAAAAACCCAATGAGA 601
                                ------ i --  v    ---- i   -----------     
  L1M4_orf2#LINE/    290 ATATAGA------TCA--ATGGAAT----AGAAT-----------TGAGA 316

  chr1_173792547_    602 TATCACTTTACAGCCTAGAAGTAAACCCTTATATTTACAGACAATTCATT 651
                         ------------ i i    i       v  i     ii v     v   
  L1M4_orf2#LINE/    317 ------------GTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_173792547_    652 TTTGGCAAGAGTGCCAAGACAATTCAATGAGGGAAATCATAATTTTGTCA 701
                           i i    i          v        -      vv   i i  v   
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTTCA 403

  chr1_173792547_    702 AAAAA-AGTGCTGGGACAACTGCAAACTGCCTATC-ACATG-GAAACAAT 748
                          v   -i               v -------  ? -     -i   v   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGA-------TAKCCACATGCAAAAGAAT 446

  chr1_173792547_    749 GAAGTTGGACCTTTACCCCATGCCATATACCAAAATGAACCCCAAATGGA 798
                                    ii    i  ii        v     v   i v       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_173792547_    799 TCAAACACCTAAATGTAAGTGCCAAAAATATGAAACTATTAGAAGACAAT 848
                            ? v             v  i    v   i     v        v  i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_173792547_    849 ATAGGTGTAAATTTCTGTGATCTTGGATTAAGCAATGGAT-CTTAAATAT 897
                              ?      i ii    i     i   i       v -    i    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_173792547_    898 GACACCAAAAGCAAAAGCGACAAAAGAAAAC-TAGGTAAATTTGACTTCG 946
                                      v    i           v-   i      v      i
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_173792547_    947 TCAAAGTTTGTAACTTTTGTGCTTCAAAATTCACCATCAGGAAAGTAAAA 996
                              i  viv                 ivv   i    i      i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_173792547_    997 ATACAACCCACAGTATGGGAGAAAATATTTGTAAATCATGTATCTGATAA 1046
                          v           v                 i       i          
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_173792547_   1047 AGGTTTTGTAGTCAGTATGTATAAAGAACTCCTACAACTCAACAATAAAA 1096
                         i  vi     vi   v  i            i          i       
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_173792547_   1097 AGACAAGTATTCTAGTTAAGCATTGGTCAAAG-ATTTGAACAGACATTTC 1145
                               i  vi i i  ? iv v   v     -       i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_173792547_   1146 TCTAAGGAAGATACAGAAATGACCAACAAGCAGATGAAAAGATGCTCAAC 1195
                           i  i       i v     i    i     v                 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_173792547_   1196 ATCCTTAGTCAT 1207
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (64 / 41)
Gap_init rate = 0.02 (13 / 669), avg. gap size = 3.77 (49 / 13)  


4375 18.71 0.88 1.53  chr1_173990716_173992967.rev      848  1761 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_173990716_    848 TGAAAAGACATTCTGTGTTCACAGATCAGAAAACTTAATATTGTTAAGAT 897
                           i     i  i ii      ii   ii   i                  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_173990716_    898 AAAAACAGTCCCCAGATTGATTCACAGATTCTACACAATTGCTATTAAA- 946
                         iiv  i v      i      ii        v  i    iv    i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_173990716_    947 TCCCAGCTGTCTTTGTTTAGCAGAATTTGATTAACTAAACTTAAAATTTA 996
                                  i    -   -      v    iv i  i v i       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTT-GCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_173990716_    997 TATGAAAATGCAAGGGACCCAGAATAGCCAAAA-AATCATGACAAGGAAA 1045
                             i                            -    v   v  i   i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_173990716_   1046 AACAAAGTTAAAGGATATACGTTTCCTGATTTCAAAATGTACTACAAAGA 1095
                                  ii    ivi  ii    ii         iv          v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_173990716_   1096 TACAACAATAAAGACAATGCCTTTTTTGTAGTGGTATAAAAATAGACACA 1145
                             ii   v      i  ------ v   v   i    ii       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTG------TGGTACTGGCATAAGGATAGACATA 292

  chr1_173990716_   1146 TAGATCAATAAAATAGAATTGAGGGGCTGGAAATCAAGCCATACATTTAT 1195
                                  ii            i v ii     v  v            
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_173990716_   1196 GGTCAATCGATTTT-GATACATGTGCCAAGAAAATTCCACAAGGGAAGA- 1243
                                i      -  i viv         vv    v iii  i    -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_173990716_   1244 -GGGCTTTTCAACAAATGGTGCTGAGACAACTGGACATCCATGTGCAAAA 1292
                         -i v                    i          i ?   ii       
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_173990716_   1293 TAATAAAGTTGGACCCCAATCTTATACCATATACAGTAATTAAAACAAAA 1342
                         v   i            v i  i i          iv      vv     
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_173990716_   1343 TGGATCAAAGGCCTTAAACTAAGAGATACAACTATGAAACTCTCAAAATA 1392
                                ?  i   v  vv      v  v      i       i i  v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_173990716_   1393 AAACACAGACATAAATCTTTGTGACCTTCGATTTGGCAATGCTTCCTAAG 1442
                              i  i?i        i        v i  v       v  i  v  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_173990716_   1443 ATATGACACCAAAAGTATAAACAGCAACA-AAAAGGTAGAAAAATTGATC 1491
                                        i i  i  i   v -    ii    v      iv 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_173990716_   1492 TTCATCAAAACTTAAAACTT--ATGGTCCAAAGGGCACTATCAAGAAAGT 1539
                                   i v       --i  v i      i               
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_173990716_   1540 AAAAGAACTATTCACTCAATGGGAGAAAATATTTATAAACCATATATCTG 1589
                         i   ii  v ii   vv                 ii   i          
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_173990716_   1590 ATAAAGTTCTTGTATGCAGAATATATAAAGAAAGAACTCCTAGAACTGAA 1639
                             i vv       v                ----   i  v    v  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAA----CTCTTACAACTCAA 788

  chr1_173990716_   1640 CAGTAAAAAGAAAAGTAGCCCATTTAAAAAGATGAAAAAAATATTTAAAT 1689
                         i i        v  i  i    v  ?    -   iiv   iv    i   
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAAT 837

  chr1_173990716_   1690 AGACATTTTTTCCAAAGAAGGTATACAAATGACCAATAAGCATATGAAAT 1739
                                 i -         i          i          i      v
  L1M4_orf2#LINE/    838 AGACATTTCT-CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_173990716_   1740 GATGCTCAATATCACTAGTTGT 1761
                                  i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (110 / 57)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


2935 27.47 1.67 0.67  chr1_174079960_174085589.rev     4241  5139 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174079960_   4241 TGGGAAAACATTCCATGCTCATGGGTAAGAAGAATCAATATTGTGAAAAT 4290
                            i  i i  i     i      i vi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174079960_   4291 GGCCATACTACCCAAAGTAATTTATAGATCCAATACCATTCCCATTAATC 4340
                            v     v      v i  i  i    i   ii v  i  i  i  vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174079960_   4341 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAAATTCAC 4389
                          v   vivi v  i  ii     v v  v  i-  - iii         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_174079960_   4390 ATGAAACCAAAAAAGAGCTCATATAGCCAAGACAATCCTAAGCAAAAAGA 4439
                            i  viiv  ii  v iviv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_174079960_   4440 ACAAAACTGGAGCCATCATGCTACCTGACTTCAAACTATACTAAGAGGCT 4489
                              ii     vvv   ii  v  ii i      viv     vi i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_174079960_   4490 ACAGTAACCAAAACAGTATGGTACTGGTACAAAAACAGACACATAGACCA 4539
                                i   i     i         i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_174079960_   4540 ATGGAACAGAATAGAGATCTCAGAAATAAGACTGCACATCTATAACCATC 4589
                               i     v    vii         iv iii    i   iii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_174079960_   4590 TGATCGTTGACAAATCTGACAGAAATAAGCAATGGGGAAAGGATTCCCTA 4639
                             iv i     ivv  v  ii vi vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_174079960_   4640 TTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACAGAA 4689
                           i                 v      v  ?   i     i  i vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_174079960_   4690 ACTGGACCCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGGTTTA 4739
                         ii         v   i     v  i                i    v i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_174079960_   4740 CAGACTTAAATGTAAAACCCAAAACTATAAAACCTCTAGAAGAAAATCTA 4789
                         ?    i         i v i             iii          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_174079960_   4790 GACA-ATACCATTCAGGACATAGGCACAGGCAAAGATTTCATGATGAAAT 4838
                          i?i- v i -   iv   v v  vvi      v i    v i--  v  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA--GATAT 596

  chr1_174079960_   4839 GAT--CAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATAGGATCTAA 4886
                           i--        vvv          v      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_174079960_   4887 TTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTATTAACAGAGTGAAC 4936
                          i   v v  i i   i iii vv    i  v     i  v i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_174079960_   4937 AGACATCCTACAGAATGGGA-AAAATTTTTTCAATCTATCCATCTGACAA 4985
                              v  i           -     v   v   vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_174079960_   4986 AGGTCTAACATCCAGGATCGACAAGAAACTTAAACAAATTTACAATTAAA 5035
                         i  v  vii      i  vv i  ii    ivv    v iv i   v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_174079960_   5036 AAA------ACCCA-TTAAAAAGTGGGCAAAGAACATGAACAGACACTCC 5078
                          i ------     -  ?    i         i iv    i     i i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_174079960_   5079 TC---AAAAGACATTTATGCGGCCAACAAACATATGAAAAAAAAAACTCA 5125
                           --- i    i  vi vii      i  i  i       i vi--    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG--CTCA 894

  chr1_174079960_   5126 ACATCAATGATCAT 5139
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (150 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.91 (21 / 11)  


3326 25.50 0.88 0.66  chr1_174101963_174108234.rev     4876  5781 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174101963_   4876 TGGAAGAACATTCCATGGTCATGGATAGGAAGAATCAATATCGTGAAAAT 4925
                              ii i  i     v        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174101963_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174101963_   4976 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTC 5022
                          v   i-       i  -i     -   -- v  i  - iii i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_174101963_   5023 ATATGGAACCGAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5072
                                 vi v  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_174101963_   5073 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5122
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_174101963_   5123 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5172
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_174101963_   5173 CAATGGAAGAGAAC--AGAGTCCTCAGAAATAATGCCGCATATCCACAAC 5220
                                 v    i--       --        vv  ii i  ii iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_174101963_   5221 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5270
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_174101963_   5271 CCTATTTAATAAATGGTGCTGGGA--ACCGGCTAGCCATATGTAGAAAGA 5318
                         i  v  i  i              --  i  v  ?   i   i i  ii 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_174101963_   5319 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCGAGATGG 5368
                             ii    i    v   i     v           i  i  i i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_174101963_   5369 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5418
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_174101963_   5419 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5467
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_174101963_   5468 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5517
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_174101963_   5518 AATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGA 5567
                         v  i   v v  i i   i   i vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_174101963_   5568 ACAGGAAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCTTCTGAC 5617
                          v  iv    i   i             v  i    vii iviv     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_174101963_   5618 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5667
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_174101963_   5668 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5717
                            i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_174101963_   5718 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5767
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_174101963_   5768 TCATCACTGGCCAT 5781
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (134 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2701 27.83 1.55 0.89  chr1_174154205_174156288.rev      692  1593 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174154205_    692 TGGAAACTCCTTCCATGCTCATGGATAGAAAGAATCAATATAGTTAAAAT 741
                               vviv i     i        v i    v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174154205_    742 AGCCATATTCCCAAAAACAATTTATAGATTCAAGGCTATTCCTATCAAAC 791
                         i  v   i    v   vii  i  i        v  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174154205_    792 TACCAATAATATTCTTCATACAAATAGAAAAAACT-ATATTAAAATTCAT 840
                          v   iiviiv  i  iii v    v  v  i-  -  vi          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_174154205_    841 ATGGAACTGAAAAACAGCCTGAATAGCCAAAGCAAGCCTAAGCAAAAAGA 890
                               v  v  iiv v  v           i   v i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_174154205_    891 ACAAAGCAGGAAGCACT-ACA-TTACCGACTTCAAACTATACAACAGGTC 938
                               iv   i -   -   -  v  i i      viv   v   iiv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_174154205_    939 TACAGTAACAAAAACAGCATGGTACTGATACAAAAACAGACACATAGACC 988
                                 iv  i    ii        ii i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_174154205_    989 AATGGAACAGAAAAGAGAACCCAGAAATAAGGCCGCACACCTACAA-CAA 1037
                                i    vv    ii          iv  ii   ii  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_174154205_   1038 TCTGACCTTTTACAAAGCTGACAAAAAGAAGCAGTGGGGAAAGGATTCGC 1087
                          -   ii  iv    i v  v   i vv vv  i         i  vvv 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_174154205_   1088 CACTCAATAAATGGTGCTGGGATAGCTGGGTGGCCAGATGCAGAAGACTG 1137
                         ivi    i              i i    i i?   v     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_174154205_   1138 AAACTCAAATCCTTCCTTACACTACATAAAAAAATCAACTCAAGGTGGAT 1187
                           ii vi vi   v   i    i i   v      i       ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_174154205_   1188 TAATGACTTAAACGTAAAACATAAATCTATGAAAAGCCTGGGAGATAACC 1237
                         i ?v   i    i    i vv    v    i   vv i i i   v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_174154205_   1238 TAGG---AAATATTATTTTG-GACATAGGACTTGGCAAAGATTTCAC-GA 1282
                             ---    ----i  i -   v v  ii v     v i    vi-  
  L1M4_orf2#LINE/    548 TAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_174154205_   1283 TGAAGACGCCAAAAGCAATTGCAACACAAACAAAAATTGACAAATGGGAC 1332
                          - v   i         vvv      v  iv      v  i    v    
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_174154205_   1333 ATAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAATGTATCAACAGAGT 1382
                         v v  i   v v  i i   i  iiivv    i  vvv      v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_174154205_   1383 AATCAGACAATCTACAGAATGGGAGAAAATAGTCACAAACTGTGCATCCA 1432
                         i vv      i i                  v ii    iii ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_174154205_   1433 ACAGAGGTCTAATATCCAGA-TCTATAAGGAACT--TA-AGCACATTTAC 1478
                          i ii  v  vi        - v     i     --  - i v  v v i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_174154205_   1479 GAGAAAA-AAACAATCTCATTATAAACTGGGCAGAGGACAAGAACAGACA 1527
                         i i  i -   i  i iv   ?v   v      i    ivv   i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_174154205_   1528 CTTTTCAAAAGAAGACATATATGTGGCCAACAAGCATATGAAATAATGCT 1577
                         i  i  v        i   i vi       i     i      vi     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_174154205_   1578 CAACATCACTAATCAA 1593
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.38 (22 / 16)  


2411 26.37 1.30 0.43  chr1_174209914_174211607.rev      502  1195 (499)    L1M4_orf2#LINE/L1      172   871 (37)  

  chr1_174209914_    502 ATAGCCAAGACAATCCTAAACAAAAAGAACAAAGCTGGAGGCATCACGCT 551
                                 i      i i  v  i          i      vv    i  
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_174209914_    552 ACCTGACTTCAAACCATACTACAAGGTTACAGTAACCAAAAACAGCATGG 601
                         v  ii i      v v        i i        i   i -   ii   
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGG 270

  chr1_174209914_    602 TACTGCAACCAAAACAGATTTATAGACCAATGGAACAGAACAGAGACCTC 651
                              vv iv ii i   iv      i        i    iv    vii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_174209914_    652 AGAAATAACACCGCACATCTACAACCATGTGATCTTTGACAAACCTGACA 701
                                 vv  ii    i  iiii  vv    i  i     ivv  v  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_174209914_    702 AAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAA 751
                          i v  vv            i  vvi  v  i  i              v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_174209914_    752 AACTGGCTAGCCATATGCAAAAAACTGAAACTGAACCTCTTCCTTATACC 801
                               v  ?   i        i v    ii  i   i  v   i i   
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_174209914_    802 TGATACAAAAATTAATTTAAGATGGATTAAAGACTTAAATGTAAAACCTA 851
                         vv             i i  i      i ?    i         i v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_174209914_    852 AAACCATAAAAACCCTAGAAGAAAACCTAGG--TAATACCATTCAGCACA 899
                             i      vi i           v    --   - i -   ivv  v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATC-TTCGTGACC 568

  chr1_174209914_    900 TAGGCATGGGCTAAGACTTTATGACTAAAATGCCAAAAGCAATTGCAACA 949
                          v  vv i   v v ii  iv iiv  vi ii         vvv      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_174209914_    950 AAAGCCAAAATTGACAAATGGAATCTAATTAAACTAAAGAGCTTCTGCAC 999
                             vv     v  i    v i ii v  i   v v  i i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_174209914_   1000 AGCAAAAGACACTATCATCAAATTGAACAGGAAACCTACAGAATGGGAGA 1049
                         vv    i          vv   v    v  iv    i             
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_174209914_   1050 AAATTTTTGCAATCTATCCATCTGACGAAGACCTAATATCCAGAATCTAC 1099
                             v       vii  vi      ii i iv  vi          v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_174209914_   1100 AAGGAACTTAAACAAATTTACAAGAAAAA-----ACAACCCCATCAAAAA 1144
                           i     ivv    v iv i  v     ----- i     v  i?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_174209914_   1145 CTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGACATATG--CGG 1192
                         v     i      v    i     i     v        i   ii--i  
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_174209914_   1193 CCA 1195
                            
  L1M4_orf2#LINE/    869 CCA 871

Transitions / transversions = 1.34 (103 / 77)
Gap_init rate = 0.01 (6 / 700), avg. gap size = 2.00 (12 / 6)  


2539 25.58 6.83 1.74  chr1_174235858_174241109     3896  4759 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174235858_   3896 TGGAAAAACATGCCATGCTCATGGATAGGAAGAATAAATATTGTTAAAAT 3945
                               i i  v     i        v      v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174235858_   3946 GGCCATGCTGCC--AAGCAATTTGCAGATCCAATGCTATTCCTATCAAAC 3993
                            v  i  v  --  vii  i i     i   i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174235858_   3994 TACCAATGACATTCTTTACAGAATTAGAAAAACCTATTTTAAAATTCATA 4043
                          v   iivi v  i   i     v v  v  i iv  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_174235858_   4044 TGAAAC--CAAGAAATAACCTGAATAGCCAAGGCAATCCTAAGCAAAAAG 4091
                           i  v--    ii i--  v          ii     i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_174235858_   4092 AATAAAGTTAGAGGCATCACATTACCTGACTTCAAACC--A-TACAAGGT 4138
                           i      i    vv     i v  ii i      v -- -     i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_174235858_   4139 TACAGTAACCAAAACAGAATGGTG-TGGTACAAAAATGGAACCGCAGACC 4187
                                 i   i    vi    i-   i i  ii  i  vviii   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_174235858_   4188 AATGGAACAAAAT----AGCACAGAAATAAGGCTGCACATCTACAAGCAT 4233
                                i i   ----  iv         iv iii    i  iiiv  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_174235858_   4234 CTGATCTTTGACAAAACTGACAAAAATGAGAAACGGGGAAAGGACTTA-- 4281
                         i    i  i     iiv  v   i viivvv  i        i --  --
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA--TAGT 396

  chr1_174235858_   4282 TTATTCAATAAACAGTACTGGGA--------------------------- 4304
                         i v     i   ii  i      ---------------------------
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_174235858_   4305 ---ATTGGACCCCTTCCTTATACCATATA-AAAAATCAACTCAAGGTGGA 4350
                         ---i          v   i i        -      i       ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_174235858_   4351 TTAAAGACTTAAAGGGAGAATCTAAAACCATCCAAATCCTGAAAGATAAT 4400
                          i ?    i    v v ii v       i  vv  v  i ii    v  i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_174235858_   4401 CTACAAAATACCATTCTCAATACAGGACCT-------GGCAAAGATTTTA 4443
                         v  -ii?i  -- v   i---- iv     -------     v i   i-
  L1M4_orf2#LINE/    547 ATA-GGNGTA--AATCTT----CGTGACCTTGGGTTAGGCAATGGTTTC- 588

  chr1_174235858_   4444 TTACAAAC-ACACTAAAAGAAATGGCAACAAAACCAAAAATTGACAAATG 4492
                            v v i-    i     v vvi         vv      v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_174235858_   4493 GGATCTGAT-AAAACTAAAGAACTTCTGCACAGCAAAAGAAATTATCAAC 4541
                            ii v  -    i    -     i  ii vv    i  v i      v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_174235858_   4542 AGAATGAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAAACTATGC 4591
                          i i    v        i                 v        ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_174235858_   4592 ATCTGACAGAGATCTAATATCCAGAATCTATAAGGAACT--TA-AATTTG 4638
                               i ii iv  vi          v     i     --  -  i --
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT-- 785

  chr1_174235858_   4639 CAA-AACAAAAATCCAA-CAACCTCACTAAAAAGTGGGCAAAGGACATGA 4686
                            -  i     vv   -i    iv i ?    i           iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_174235858_   4687 ACAGGAAATTTTCCAAAGAAGACATACACTTGGCCAACAAGTATATGAGA 4736
                          i  iv v  i           i     vv       i   i i    i 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_174235858_   4737 AAATGCTCAAAATCACTAATAAT 4759
                          i        v    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (141 / 77)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.08 (74 / 24)  


3665 18.38 2.98 4.06  chr1_174326375_174328403      699  1536 (493)    L1M4_orf2#LINE/L1       80   908 (0)  

  chr1_174326375_    699 TCAACACAATTTCTACCAAAATTTCAAAAGC-TTTCTTACACAAATGGAA 747
                              i    ii   i      ii  ivv  -   i  i  v    v  v
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chr1_174326375_    748 AAGCCATTCTTCAAATTCATATGGAATTGCAAGAGTCCCTGGATAGCCAA 797
                             iiv  i v              v      i v   v i        
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr1_174326375_    798 ACACTCTTGGTCTTGAAAAAGAAACGT---GTTAGAGTACTCACATTTCT 844
                          -  ----ii             ivii---   i   v       i   i
  L1M4_orf2#LINE/    180 A-AC----AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr1_174326375_    845 CCATTTTAAAATTTACTACAAAACTATAGTAATCAAAACAATATGGTACT 894
                          v    i    i          i   i         i   i i       
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_174326375_    895 AGCATAAAGATACACATATACACCG-TGAAGTAGAACACAGAGTCCAGAA 943
                         i      i    v       v i i-  i i     ivv           
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_174326375_    944 ATAAACCAGATGTATAAATTATTTATACATCTGTAAGTAATTTATTTT-G 992
                                ----------------i      i i iivi    v     - 
  L1M4_orf2#LINE/    325 ATAAACC----------------CATACATTTATGGTCAATTGATTTTCG 358

  chr1_174326375_    993 AGAAGGGTGCCAAAACCATTTATTGGGGAAAGAATGGTCTCTTCAACAAA 1042
                          v           i      i v            i    i         
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_174326375_   1043 TGGTGGTGGAACAAGTTGATTTCTATATGTCAAAGAATAAAGTTTCACCC 1092
                              v   i    v v   v? i i   iv       i     vv    
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_174326375_   1093 CCACCTCACACCATATACAAAAATTAACTTGAAATGGATGAACAACCTAA 1142
                          i                           ii        v ?vi      
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_174326375_   1143 ATATAAGAGCTAAAGCCAGAAAATTCTTAGACAGAAACATGGGGATAAAT 1192
                           i           i i v    i       vii      i  ?i     
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_174326375_   1193 CTTCATGACCTTGGATTTGGCA---------------TGACACTAAAAGT 1227
                             i         i  v    ---------------      i     i
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_174326375_   1228 ATGTACAACAAAAGAAAAAAATCAATAAATTGTTCTTCAACAAAATTTTT 1277
                          iivi               - vi        vv     v       ---
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATT--- 654

  chr1_174326375_   1278 AAAA----TTGTAAACATCAAAGAATATTATGAGGAAAGCTTTTAAAAGT 1323
                             ----    i-- v      i i i   v i     --- v     -
  L1M4_orf2#LINE/    655 AAAAACTTTTGTG--CTTCAAAGGACACTATCAAGAAAG---TGAAAAG- 698

  chr1_174326375_   1324 GTAACCTTTTACAGACTGGGAGAAAATATTGGTGAATCACATATCCAATA 1373
                         ii    i---     v              v ii     i     ii   
  L1M4_orf2#LINE/    699 ACAACCC---ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_174326375_   1374 AAGGTTTAATATCCAGAATATATAAAGAACTTCTGCAACTCAACAGCAAA 1423
                          i  vi vi                      ii i        i ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_174326375_   1424 AAGACAAACAACTCAATTTTAAAATGGGCAAAGGGCTTGAATAGAGATTT 1473
                                 i   i     ?v              ii         v    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_174326375_   1474 CTCCAAAGTAGATATATAAATGGCCAATAAGCAAATAAAAAGATGTTCAA 1523
                                 v       i                v  i        i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_174326375_   1524 CTTCATTAGTCAT 1536
                          v   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (100 / 50)
Gap_init rate = 0.02 (15 / 829), avg. gap size = 3.93 (59 / 15)  


2645 24.70 4.65 4.10  chr1_174328770_174330969      806  1708 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174328770_    806 TGGAGATAACATATTATGTTCTTGAAATTAAAGACTTAACATAGTAAAAA 855
                             i -i i  vii      v  i v vi         i  v  v  i 
  L1M4_orf2#LINE/      1 TGGAAA-GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_174328770_    856 TGCCAATTCTTCCTAAATTGATATATAGGTTTAATGCAATTTCCATTAAA 905
                           v    v  i  i        v  i  i  i  i     ii i  i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_174328770_    906 ATCCAAGCAAAGTATTTTTT--AGATATAGACAAGTTTATTGTACAATTT 953
                             v   v-- iv      --   v  v      i v  iv  v    i
  L1M4_orf2#LINE/    100 ATCCCAGCT--GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_174328770_    954 ACATGGAAAAATAAAGGAACTAGAACAGTAAAAACAATTC----AAATAA 999
                          i       vii  i   v i    i  iv        ii----   v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_174328770_   1000 GAATAAAGTAGGAGGA---ATACTTCTACATGATTCTAAAACTTTGACTA 1046
                            i     v      --- i     i-  --   ii       --    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCC-CA--ATTTCAAAACTT--ACTA 242

  chr1_174328770_   1047 CAA--CTACAGTGATCAAGACTATGTGGCATTGGTGGGGGAATAGAAATA 1094
                            --       i        vi     i i   iivii i     v   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_174328770_   1095 TAGGCCACTGGAATAGAA--GA---CCCAGATATATACTCACACGAATAT 1139
                            ii  v          --  ---i     v   v  i  i  ivv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_174328770_   1140 GCCCAACTTATTTTT-ATAAAGGTGCAAAGGCAATTCAATGAAGGAGAGA 1188
                          vi   i v     i- i  i     v   i v        ii i iii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_174328770_   1189 TAGCCTTTTTAACAAATGTTGCTGGATCAATTAGACACCCATTGGCCTAA 1238
                            i     i        v      iv   i i  i ?   i--------
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC-------- 434

  chr1_174328770_   1239 ACAAATAACAACAAAAAGAACTTTGATGCAGGTCTCACACTTTATACAAA 1288
                         ----  i-   v i  v   v  v  iv vvii       iv        
  L1M4_orf2#LINE/    435 ----ATG-CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_174328770_   1289 ATGTAACTCAAAATAGATCATAGACTGAAATGCAAAATGTAAAACTCCAA 1338
                          vv           i     ?    iv     i  i vv       vi  
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_174328770_   1339 AGTTTTGAGAGTCTTTAGAAAACCACATAGGAACAG--CTTCAGAATCTA 1386
                          ii i v   ------       ---     ?ii i--    ivi i  v
  L1M4_orf2#LINE/    530 AACTCTTAGA------AGAAAAC---ATAGGNGTAAATCTTCGTGACCTT 570

  chr1_174328770_   1387 GGGCTAGGAAAATCGTT-CTTAGACTTGACACCAAA-GCACAATATATAA 1434
                            i    v  - v   -      iv          -      vvv i  
  L1M4_orf2#LINE/    571 GGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_174328770_   1435 AAGGAAAAATA----------------TCAAA-TTAAAAACTTGCCCTCT 1467
                            i       ----------------     -          viviv  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_174328770_   1468 ATAAAAGATGCTGTTAAGAGAATGAAAAGACAAGCTAAGCTACATGCTGG 1517
                         vi   i  ii  i i    i i           - ---- i   viv   
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAA-C----CCACAGAATGG 714

  chr1_174328770_   1518 GAGAAAATATGTGCAAACCACATATCCAGTGAAAAACTAGTACCTAGAAT 1567
                                   v      i  i     iii i iii   v   i i     
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_174328770_   1568 ATATAAGGCACTCTTG--ATTCAACAGTGAAAA--CAAAAGATTGCAATT 1613
                               i v      i-- i    i i i    --    vi ii-     
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC-CAATT 813

  chr1_174328770_   1614 AGATAATGGGCAAAAGACATAAAAAGACATTTCATTAAAGAGGAACTGTA 1663
                         ?i v          i  iv i  v         vii     i  vv ii 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_174328770_   1664 GATGACAAATAAACATGTGAAAAGATGTTCAACATCCTTAGCCAT 1708
                         i   i v     i  ii          i        v????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (142 / 77)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.93 (79 / 27)  


3392 26.43 0.33 0.33  chr1_174334220_174340490     4871  5778 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174334220_   4871 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4920
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174334220_   4921 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4970
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174334220_   4971 TACCAGTGACTTTCTTCACACAATTGGAGAAAACT-ACTTTAAAGTTCAT 5019
                          v    ivi i  i  ii  v  v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_174334220_   5020 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGA 5069
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_174334220_   5070 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5119
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_174334220_   5120 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5169
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_174334220_   5170 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTA 5217
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_174334220_   5218 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5267
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_174334220_   5268 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5317
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_174334220_   5318 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5367
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_174334220_   5368 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5417
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_174334220_   5418 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5467
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_174334220_   5468 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5517
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_174334220_   5518 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5567
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_174334220_   5568 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5617
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_174334220_   5618 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5667
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_174334220_   5668 AACAAATAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCT 5717
                         i           v  i?    i     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_174334220_   5718 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5767
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_174334220_   5768 TCACTGGCCAT 5778
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


 901 30.56 11.49 4.65  chr1_174363508_174365317      500  1317 (493)    L1M4_orf2#LINE/L1       35   908 (0)  

  chr1_174363508_    500 TTAATATCATAAAGATGTCATTTCTCCTCCAAATTAATTTATAAATTTGA 549
                                ii v      v  v v    -       i  i  i i   ii 
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCC-CCAAATTGATCTACAGATTCAA 83

  chr1_174363508_    550 TACAATCTCATTTAAAATATCAGTTAGAATTT--AGAGGAATTCAATAAA 597
                         ii     i vv i     vi   i ivvv   --iv  i    -i i  i
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT-GACAAG 132

  chr1_174363508_    598 CTCATTTGAAAGTTTTATATGGAAAAGTAAAG-ATCCA------------ 634
                           v  iiv   i  i-         v i  i - i   ------------
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTC-ATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_174363508_    635 ----CTTAAAAATAGTAG-------------------------------- 648
                         ----   i    -  v  --------------------------------
  L1M4_orf2#LINE/    182 CAATCTTGAAAA-AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_174363508_    649 ------------TAAATCCATAGTAATGAAAGCAAGGTGATATTGGCACA 686
                         ------------i   v i i      v  ii  iv   i  i     i 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_174363508_    687 AGAACAAAT-TATGGACCA-TGGAACAGCATTGTCCCATTGAGAACAGCC 734
                           i i i i-   i  i  -     i  - -------       ------
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAG-A-------ATTGAGA------ 316

  chr1_174363508_    735 ATAGTTCAGAAAGGGAGCCGTGTATGTATGAGGACTTAATGTAGGATAAT 784
                         ---  i      vii v  i ii  v    ivv v  i  v vv  i  v
  L1M4_orf2#LINE/    317 ---GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_174363508_    785 GATGGCACCCCAAATCAAAGTGGAAACAACTGTTATTT-AGGGAGTAGGG 833
                          i  v  vvv v v    v v     v  iv  iv   - ivi i i v 
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_174363508_    834 CTGGGGAAACTAGCTCATTACATGAAGAAAAGTGAAACTGGGTATCTATT 883
                              iv    i v v?ii     v i  i i    ii   iivi   ii
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_174363508_    884 TAATGCCTCATACAAAGCTGAAAAGTAGATGGAATAAAGAGCTAAACATA 933
                          v ii  vi       iv v  vvvv i     vi ?   v     ii  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_174363508_    934 AAAGGTATTTTTATAAAGTTAAGC--AGAAAAAAAACTGTAGGAG-AATT 980
                          i  v  vvvi      ii --- --    i    --ii    ? -  v 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACT---CTTAGAAGAAAA--CATAGGNGTAAAT 558

  chr1_174363508_    981 CTTTATGTGCCTAGCTGTGAAGACA--GACTTCTTAAA----ATTCCAAA 1024
                            ii  vv i i --  v i -  -- ii      i ---- iv     
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGG--GTTAGG-CAATGGTTTCTTAGATATGACACCAAA 605

  chr1_174363508_   1025 -GCACAAGTAGTAAAACAAATAA-ACATAAA--AGGTTTGATTCAAAATT 1070
                         -       i ii    v   v  - v     --i ii  v  -       
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT-CAAAATT 654

  chr1_174363508_   1071 AAATATTTTTTCATTCTACAAAGGATATAACAAAGTAAATAAAGAAATAA 1120
                            v i    --i v  v       i iv iv   v  i i  i i i  
  L1M4_orf2#LINE/    655 AAAAACTTTT--GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_174363508_   1121 -----AGAATAGGAGAATATATTTATGCCTCAAACA------AAAAAAAT 1159
                         -----     i      v      iiivv   v i ------  iii v 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_174363508_   1160 C--ATCTGGCATATACAAGAAATTCCTACAAGTCAACATTTTAAAAAAAA 1207
                         i--   ii v     i  ii  i  i     v    -----   v     
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAA-----TAATAAAAA 797

  chr1_174363508_   1208 TACAGA-AACATCAATTTGCAAATGAGCAAAA-ATAGGAACATGCAATTC 1255
                         v   i -   -i     ?iv     i     i-  vv   i vi  v   
  L1M4_orf2#LINE/    798 GACAAATAAC-CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_174363508_   1256 ACAGAAAAGGAAACCTAAATGGCTATGAAATATATGAAGAAATGTTCAAA 1305
                         v vi  i i  v ivi       i vv  ii i     i i   i    v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_174363508_   1306 ATTATTAGTAAT 1317
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (150 / 96)
Gap_init rate = 0.04 (34 / 874), avg. gap size = 3.88 (132 / 34)  


 338 25.77 4.29 2.45  chr1_174372857_174379238.rev       15   177 (6205)    L1M4_orf2#LINE/L1      677   842 (66)  

  chr1_174372857_     15 ACACCATCAAAA---TTAAAAGACCAATCC-CACACTGGAAGAAA-TATT 59
                             i     i --- v       -  i  -  v v   i     -    
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGAC-AACCCACAGAATGGGAGAAAATATT 725

  chr1_174372857_     60 TGCAGCACATGTAATAGATAAAGGGATGCTCTCCTCAATGCATAGAGGCC 109
                             ivv   i  viv     i  iv vv v   vv   ii   i  iv 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_174372857_    110 ATTTAAAAATCATTAAAGAAAAAGATAAACAACC--ATGTAGAAATATTG 157
                         vi   v  v   v   -v       i   i    --  v? i    i-- 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATG--G 822

  chr1_174372857_    158 GCAAAGGACTTAAAAAGACA 177
                                 i  i  v     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACA 842

Transitions / transversions = 0.95 (20 / 21)
Gap_init rate = 0.04 (7 / 166), avg. gap size = 1.57 (11 / 7)  

3173 27.64 0.55 0.55  chr1_174372857_174379238.rev     4984  5891 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174372857_   4984 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCCTGAAAAT 5033
                              ii i  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174372857_   5034 GGCCACACAGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5083
                            v i  vv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174372857_   5084 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5131
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_174372857_   5132 TATGGAACCAAAAAAGAGCCCACATTGCCATGTCAATCCTAAGCCTAAAG 5181
                                viiv  ii  v  viv  v    viv     i i ivvvi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_174372857_   5182 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5231
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_174372857_   5232 TACAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5281
                                 v   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_174372857_   5282 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5329
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_174372857_   5330 ATCTGATCTTTGATGAACCTGACAAAAACAAGCAATGGGGAAGGGATTCC 5379
                          vi    i  i  ii ivv  v   i v  vv          i i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_174372857_   5380 CTATTTAATAATTGGTGCTGGGACAACTGGCTAGCCATATGTAGAAAGCT 5429
                           v  i  i  v                  v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_174372857_   5430 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCCAGATGGA 5479
                            ii    i    v   i     v              i  v i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_174372857_   5480 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5529
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_174372857_   5530 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5578
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_174372857_   5579 AAACACCAAAAGCAATGGCAACAAAAGTCACAATTGACAAATGGGATCTT 5628
                         vi            vvi          vv v   v  i    v   ii i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_174372857_   5629 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 5678
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_174372857_   5679 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5728
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_174372857_   5729 AAGGGTTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5778
                          i  ii vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_174372857_   5779 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5828
                           i     i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_174372857_   5829 CTCAAAAGAAGACATTTATGCAGTCAAAAGACACATGAAAAAATGTTCAT 5878
                            v        i  vi viii i   v ii          i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_174372857_   5879 CATCACTGGCTAT 5891
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3100 27.50 0.55 0.66  chr1_174392822_174399212     4990  5898 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174392822_   4990 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCCTGAAAAT 5039
                              ii i  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174392822_   5040 GGCCATACAGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5089
                            v    vv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174392822_   5090 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5137
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_174392822_   5138 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5187
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_174392822_   5188 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAA--CTACAGTACGAG 5235
                                i      vv   ii  v  ii i      --i   --   i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAA 246

  chr1_174392822_   5236 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5285
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_174392822_   5286 CCAATGGATCAAAACAGAGGCCTCAGAAATAATACCACACATCTACAACT 5335
                         i       vi i  iv   ivii         vv   i    i  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_174392822_   5336 ATCTGATCTTTGATAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5385
                          vi    i  i  i  ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_174392822_   5386 CTAGTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5435
                           vv i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_174392822_   5436 GAAACTGGACCCCTTCCTTACACCTCATACAAAAATTAATTCAAGATGGA 5485
                            ii         v   i     vi             i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_174392822_   5486 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAATAAAAC 5535
                          i ?    i       v   v       i      v  i     v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_174392822_   5536 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5584
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_174392822_   5585 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACTAATGGGATCTC 5634
                         vi            vvi          vv     v  iv   v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_174392822_   5635 ATTAAACTAAAAAGCTCCTGCACAGCAAAATAAACCGTCATCAGAGTGAA 5684
                           i   v v    i  ii  ii vv    iv v  ii   vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_174392822_   5685 CAGGCCACCTACAGAATGGGAGAAAATTTTTGCTATCTACTTATCTGACA 5734
                         v  i v   i                 v     v vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_174392822_   5735 AAGGGCTAATATCCACAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5784
                          i  i  vi      v   v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_174392822_   5785 AAAAAAAAACAATCCCATCAACAAGTGGGCGAAGGATATGAACAGACACT 5834
                           i v   -i  i  v  i? v  i     i      v    i     i 
  L1M4_orf2#LINE/    796 AAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_174392822_   5835 TCTCAAAAGAAGACATTTATGCAGTCAAAAGACACATGAAAAAATGCTCA 5884
                             v        i  vi viii i   v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_174392822_   5885 TCATCACTGGCCAT 5898
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3203 27.12 0.55 0.44  chr1_174459696_174466085     4991  5897 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174459696_   4991 TGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5040
                           i  ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174459696_   5041 GGCCATACAGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5090
                            v    vv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174459696_   5091 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_174459696_   5139 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5188
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_174459696_   5189 AACAAAACTGGAGGCATCACGCTACCTGACTCCAAACTATACTACAAGGC 5238
                               ii      vv    i  v  ii i i    viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_174459696_   5239 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5288
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_174459696_   5289 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5336
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_174459696_   5337 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGAATTCC 5386
                          vi    i  i     ivv  vv  i v  vv               vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_174459696_   5387 CTATTTAA-AAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5435
                           v  i  -              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_174459696_   5436 GAAACTGCATCCCTTCTTTACACCTTATACAAAAATCAATTCAAGATGGA 5485
                            ii  v i    v i i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_174459696_   5486 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5535
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_174459696_   5536 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5585
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_174459696_   5586 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATGAATGGGATCTCA 5635
                         i            vvi          vv     v   i   v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_174459696_   5636 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAACATCAGAGTGAAC 5685
                          i   v v  i i   i  ii vv    i  v    v  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_174459696_   5686 AGGCAACCCACAAAATGGGAGAAAATTTTCACAACCTGCTCATCTGACAA 5735
                           i         i             v  ii   viiiivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_174459696_   5736 AGGACTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 5785
                         i     vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_174459696_   5786 AAACAAATAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5835
                          i           v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_174459696_   5836 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5885
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_174459696_   5886 ATCACTGGCCAT 5897
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3205 26.43 0.99 0.99  chr1_174686325_174692737     5013  5920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174686325_   5013 TGGAAGAACAGTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5062
                              ii i vi     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174686325_   5063 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 5112
                            v     v     iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174686325_   5113 TACCAATGACTTTCTACACAGAA-TTGGAAAAAACTAATT-TAAAGTTCA 5160
                          v   iivi i  i vii     -   -- v  i  i  i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_174686325_   5161 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAG 5210
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_174686325_   5211 AACAAAGCTAGAGGCATCACTCAACCTGACTTCAAACTATACTACAAGGC 5260
                                i i    vv    v vv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_174686325_   5261 TACAGTAACCAAAACAGCCTGGTACTGGTACCAAAACAGATACATAGACC 5310
                                 i   i    iv         i iv ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_174686325_   5311 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACGTCTACAACCAT 5360
                                i    iv   ivii         vv   i  i i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_174686325_   5361 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAGGGATTCCCT 5410
                         i    i  i     ivv  v   i v  vv          i i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_174686325_   5411 ATTTGATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAGCTGA 5460
                         v  ii i              v      v  ?   ii  i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_174686325_   5461 AACTGGATCCCTTCCTTACACCTTATACAAAAATTCATTCAAGATGGATT 5510
                          ii    i    v   i     v            v i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_174686325_   5511 AAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAAAAGAAAACTT 5560
                          ?   ii       v   v       i      vi i  i        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_174686325_   5561 AGGC---AATACGATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5607
                            ?---   - --   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT-C--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_174686325_   5608 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 5657
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_174686325_   5658 ATTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAGTGAA 5707
                           i   v v  i i   i  iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_174686325_   5708 CAGGCAACCTACAGAATGGGAGAAAATTTGTGCAATCTATCCAACTGACA 5757
                         v  i     i                 v v     vii  vi v    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_174686325_   5758 AAGGTCTAATATCCAGAATCTACAAAGGACTCAAACAAATTTACAAGAAA 5807
                          i  v  vi          v  i    i    vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_174686325_   5808 AAAACAAACAACCTCATCAAAAAGTGGGTAAATGATAAGAACAGACACTT 5857
                           i     i    iv  i?    i    i   v   vv   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_174686325_   5858 CTCAAAAGAAGACTTTTATGCA----GCCAACAGACACATGAAAAAATGC 5903
                            v        ----   i  ----     i ii          i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_174686325_   5904 TCATCATCACTGGTCAT 5920
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.25 (18 / 8)  


2732 19.63 4.21 0.93  chr1_174708903_174710536      500  1141 (493)    L1M4_orf2#LINE/L1      246   908 (0)  

  chr1_174708903_    500 AGCTACAGTAATCAAGGCAGTGTGATATTGGTGAAAGAATAGACAAACAG 549
                                         i       i  i   iiv   i       v i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_174708903_    550 ATCAATGGAATAGAATAGAGAGCCCAAAAATAGACCCATACAAATATAGT 599
                                         v     i   i     i         vv   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_174708903_    600 TAACTGATCTTTGACCAAAGAACAAAG-CAATTCAATGGAGACAGAATAG 648
                         i  i    i  i   v ii vi v   - v         i  v       
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_174708903_    649 TCTTT-CAACAAATGGTGCTGGAAAAACTGCACAGCCACATGCAAAAATA 697
                              -                i v     v i ?            iv 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_174708903_    698 TGAATCTAGATACAGACCTTATACTCTTCACAAAAAAAAACCTTAAAATG 747
                             vi i  iv vv    i i  iv vi       vv   - i      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC-TCAAAATG 494

  chr1_174708903_    748 GATCATAGACCTTAAATGTAAAATGC-AAAACTATAAAACTTCCAGAAGA 796
                              ?      -        i -  -              iii      
  L1M4_orf2#LINE/    495 GATCAWAGACCT-AAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_174708903_    797 AAATATAGCGAAAAATCTAGGTCACCTTGGTTTAG-CAATGAGTTTTTAG 845
                            i    v?iv      vv  v       v    -     iv  i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_174708903_    846 ATACAGCACCAAAAAAGCACAATCCATGAAA-AAAAAATGGGTAAGT-AG 893
                            iii        --      v v ii   -       i i   i -i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAA--GCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_174708903_    894 TCTTCATTAAAGTTAAAAACTTATGCTCTGCAGAAGACACTGTTAAAAGA 943
                         v      i   i          v  iv  v  i i      i i  i i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_174708903_    944 ATAAAAAGACAAGCCACAGTCTGGGAGAAAAATCTCTGCAAAACATATAT 993
                         i i         v      vv          - v i      v       
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATAT 739

  chr1_174708903_    994 CTGACAAAGGATGTGTATCTAAAATATACACAGAATTCTTAAAACTTAAC 1043
                             i  i   iv      i i      i v    i     v    i  i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_174708903_   1044 AATAAAAAG-CA--------------------GGCAAAAGATCTGAACGG 1072
                                  -  --------------------      i   i    ii 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_174708903_   1073 ACACTTCACCAAAGAAGATATACAGATGGCAAATCAGTATATAAAAAGAT 1122
                            i   v                i     v   v  i i  i       
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_174708903_   1123 GCCCAACATCATATGTCAC 1141
                           i        ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (78 / 45)
Gap_init rate = 0.02 (13 / 663), avg. gap size = 2.54 (33 / 13)  


3213 24.73 0.88 1.53  chr1_174713745_174718056.rev     2908  3821 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174713745_   2908 TGGAAACATATCCCATGCTCATGGATGGGAACAATCAATATTGTGAAAAT 2957
                               v          i        v    v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174713745_   2958 GACCATGCTGCCCAAAGCAATCTACAGATTCAATGCAATTGCTATCAGAA 3007
                          i v  i  v      vii              i     iv      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174713745_   3008 TACCAGCATCATTCTTCACATAACTGGAAAAAACAATCCTAAAATTCATA 3057
                          v     vv v  i  ii  v  v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_174713745_   3058 TGGAACCAAAAAAGAGCCCACATAGCCAGAGCAATACTAAGCAAAAAGAA 3107
                              viiv  ii  v  viv       i i    vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_174713745_   3108 CAAATCTGGAAACATCACATTACCCAACTTCAAATTATAGTACAAGGCCA 3157
                             vi    iivv     i v     i      viv  v     i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_174713745_   3158 TAGTTACCAAAACAGCATGCTACTGGTTTAAAAATAGGCACATAGACCAA 3207
                         i   v i   i    ii  v      iv   ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_174713745_   3208 TGGAACAGAATAGAGAGCCCAGAAATAAAGCCCA-ATTCTTACAGCCAAC 3256
                              i     v     i           -    - ivi   ii i   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTCAAT 349

  chr1_174713745_   3257 TGACTTTCAACAA-ATCACACAAAAACATAAATTGGGGAAAGGACACCCC 3305
                            i    i    -ivii -   i v   vv v         i i vi i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_174713745_   3306 ATTCAATAAATGGTGCTAGGAAAACTGG-CAGGCACATCTAGAAGAAACA 3354
                         v     i          i   v      -i ?v     vi i     vv 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_174713745_   3355 AACTGGATCCCTATCGCTCACCTTATACAAAAATCAACTCAAGAACTCAA 3404
                          ii    i     i v v    v           i       i ------
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA------ 492

  chr1_174713745_   3405 GATGGATCAAATACTTAAATATAAGACCTGAAACCATAAAAATTCTAGAA 3454
                         --       ? v  i     i     v  i    i      v ii     
  L1M4_orf2#LINE/    493 --TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_174713745_   3455 GATAACATCAGAAAAACTCTTCTAGACATTGGCTTAGGCAAAGAATTCAT 3504
                           v     vi ?iv  v     vv   v    v        v iv   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_174713745_   3505 GACTAAGACCCCAAAAGCAAATGCAACAAAAACAAAAAATAAATAGATGG 3554
                         iiv  v   v         v v         i-        i   i  v 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTG 639

  chr1_174713745_   3555 GACCTAATTAAACTAGAAAGCTTCTGCACAGCAAAAGAAATAATTAGCAG 3604
                            i v  i   v vi   i   i  ii vv    i  v iv  i iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_174713745_   3605 AGTAAACAGACAACCCACGGAGAGGGAGAAAATATTTGCAACCTATGCAT 3654
                            i  v           i  iv                  vii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_174713745_   3655 CTGACAAAGGACTAGTATCCAGAATCTACAAGGAACTC----AAATCAGC 3700
                             i  i     v           v  i  i      ----  v   ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_174713745_   3701 AAGAAAAAAAAACAAATAGTTCCATC-AAAAGTGGGGGAAGGACATGAAT 3749
                           v     i --      iii v  i-    i    vi     iv     
  L1M4_orf2#LINE/    790 AATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_174713745_   3750 AGACATTTCTCAAAAAGAGATATACAAACAGCCAACAAACGTATGAAAAA 3799
                                    v   ii           ii     i  i ii       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_174713745_   3800 AATGCTCAGCATCACTAATAAT 3821
                          -      i     ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (132 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


2702 22.32 3.94 4.92  chr1_174884344_174887716.rev     1969  2882 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_174884344_   1969 AGAGAAATTCTAAATTCATGGATTGGAAGACTCAATTTTGAAAAGATT-C 2017
                          i   v  i i vi                  i   v   vv     v- 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_174884344_   2018 AATTCTTCCCTATTTGTTCTATATATTCAACACAATCTCAATTAAATTTC 2067
                            v  i   v v   v    i v       i     i v  i   v i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_174884344_   2068 CAGCAAGTTGTTTTGTGGA---TAACAAATTATCCCTAAAGTTTATATGA 2114
                             vivi v     ii  --- i    ii ivi      i  i     i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_174884344_   2115 AATAGGAAAAGACCTAGAATAACCAACACAATACTGAAAAAGAA---CAA 2161
                           vv v  ii    i      i    v     vi          ---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_174884344_   2162 AGTTGAAGGA-TCACACTGTAGCAGATCTTAAGACCTACTACAAAGCTAC 2210
                              i    -       - vv  -  i i  i  i              
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACT-TCCCA-ATTTCAAAACTTACTACAAAGCTAC 251

  chr1_174884344_   2211 AGTAATCAAGAGAGCATAGTATCTACA-AAGAACAGA-A---AAAGCAAT 2255
                                    v  ii i   iivi  -   i i   - --- i v    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_174884344_   2256 GAAACAGAATAGAGAGACTGGAAAAAGAC--ACACATTTATATAGTTAAC 2303
                          i  i     v     v ii    v i  -- i        i--  i  i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG--GTCAAT 349

  chr1_174884344_   2304 TGGTTTTTGACAAAAGGAAACAAG-TAATTCAATGGAGAAAGAATAGTAT 2352
                           i    i     i-  viv    -iv         i           v 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAG-GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_174884344_   2353 TT-CAACAAATAATGCTGAAACA-TTGGATGCCTGTATGTAAAACTATGA 2400
                           -        ii     ii   -i     i? iii   i    vv    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_174884344_   2401 ACCTAAACACAAACCTAACATCTTTCACAAAATAAACTAAAAATGGAACA 2450
                          vi ii  v vv    v   i ---------   v  -      ------
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACC---------ATATAC-AAAAAT------ 482

  chr1_174884344_   2451 CAGATCTAAATGTAAATAAACTAAAAATGGAACATAGATCTAAATGTAAA 2500
                         ----------------   -  v        v  ?   i          i
  L1M4_orf2#LINE/    483 ----------------TAA-CTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_174884344_   2501 ATGTAAAAGTATAAAACTTCTTTAAAAAAAAAAACAGGAAAAATTATACG 2550
                          vv     v         i--   i  i    v i   ?iv  v v v  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTC--TTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_174884344_   2551 TGACCT-GGATTTTG--ATGAGTTTTTGGATGTAACACCAAAAGCATACT 2597
                               -  i  vv --   iv  i  i   i i            i vv
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_174884344_   2598 CCAT----GAAAAAAT---TAATTTGCAGGATTTAATTAAAATTAAA--- 2637
                          v i----        ---   v   ---  i  v  i         ---
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTG---GACTTCATCAAAATTAAAAAC 660

  chr1_174884344_   2638 TTCTTTGC---AAAACACACTGGTAAGAGAGTCAAAAGACAAGATATAAA 2684
                           i v   ---   iv     ivi    i   v         vvi i i 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_174884344_   2685 CTGGAAGAAAATATCTGCAAAACACATATCTGACAAAGGACTTGTATCCA 2734
                         v   i         i      v  i        i  i             
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_174884344_   2735 AAATATACAAAGA-CTCTATAAAGTTCACCAATATAAAAACAGATAACTC 2783
                         i      i     -    -  v ii   vi    v   i   i     i 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCT-TACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_174884344_   2784 AATTTTAAAAATGGGCATAAGGTCTGAATGGGCAGCTTACCAAAGAAAAT 2833
                             ?-           v i i i     i i  vi iv        i  
  L1M4_orf2#LINE/    810 AATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_174884344_   2834 ACACAGATAGCAAATATGCATACAAAAA-ATGATCAACATCATCTTTCAT 2882
                          i   i  i  v    v   i ii    -   v         ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (123 / 77)
Gap_init rate = 0.03 (31 / 905), avg. gap size = 2.61 (81 / 31)  


3079 25.42 2.12 0.89  chr1_174945620_174951991.rev     4985  5881 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_174945620_   4985 TGGAAAAAAATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5034
                               i v  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_174945620_   5035 GACCATACTGCCCAAAGTAATTTATAAATTCAATGCTATTCCTATCAAGT 5084
                          i v     v      v i  i  i i      i  v  i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_174945620_   5085 TACCA-CTGACTTTCTTCACAGAACTAGAAAAAATGACTTTAAATTTCAT 5133
                          v   -   v    i  -i     v v  v  iv   iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_174945620_   5134 ATGGAACCAAACAAGAG--CCTGTATAGCCAAGACAATCCTAAGCAAAAA 5181
                               -- vi    i --  v v        i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_174945620_   5182 GAACAAAGCTGGAGGCATCATGCTACCCGACTTCAAACTATACTACAAGG 5231
                                 i      vv   ii  v   i i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_174945620_   5232 CTACAGTAACCAA-ACACCATGGTAGTGGTACCAAAACAGATATATAGTC 5280
                                  i   -   vii     v   i iv ii i   i      vi
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_174945620_   5281 CAATGCAACAGAACAGAG-GTGTCAGAAATAACACCACACATCTACAACC 5329
                              v  i    iv   -  -i         vv   i    i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGT-CCAGAAATAAACCCATACATTTATGGTC 346

  chr1_174945620_   5330 ATCTGATCTTTGACAAACCTGACCAAAAAAAG-CAATGGGGAAAGGATTC 5378
                          vi    i  i     ivv  -    i vv v-            i  --
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAAT-- 393

  chr1_174945620_   5379 CGTATTTT--ACAAATGGTGCTGGGAAAACTGGCTAGCCGTATGCAGAAA 5426
                         v  v    --                v      v  ?  ii     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_174945620_   5427 ACAGAAACTGGACCCCTTCCTTGCACCTCACACAAAAATTAACTCAAGAT 5476
                          vv   ii         v   ii    vi i                i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_174945620_   5477 GGATTAAATAATTAAATGTAAAACCTAAAACCGTAAAAACCCTAGAAGAA 5526
                             i ? v vi         i v       ii     vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_174945620_   5527 AACCTAGGCA-ATATCATTCAGGACAT------AGGCAAAGACTTCATGA 5569
                            v    ?i- v   -   iv   v ------      v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_174945620_   5570 CTAAAACACCAAAAGCAACTGCAACAAAAGCCAAAACTGACAAATGGGAT 5619
                         v  vi            vvv          vv    iv  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_174945620_   5620 CTAATTAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATCATCAGAGT 5669
                         i v  i   v v  i i   i  iv vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_174945620_   5670 GAATAGGCAACCTACAGAACGGGAGAAAATTTTTGTAATCTACCCATCTG 5719
                            v  i     i      i          v    i  vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_174945620_   5720 ACAAAGAACTGATACCCAGAATCTACAAGGAACTTAAACAAATTTACAAG 5769
                          i  i i   vi  i       v  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_174945620_   5770 AAAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACA 5815
                              i    ----   v  i?    i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_174945620_   5816 CTTCTCAAAAGAAGACATTTATGGAGCTGACAAACATATGAAAAAAAGCT 5865
                         i     v        i  vi vivi  ii i  i  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_174945620_   5866 CATCATCACTGGTCAT 5881
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (130 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.80 (27 / 15)  


3324 26.76 0.44 0.44  chr1_175015833_175022110.rev     4880  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_175015833_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_175015833_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_175015833_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_175015833_   5028 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_175015833_   5078 AACAAAGCTGGAGGAATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i       v       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_175015833_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_175015833_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAGCT 5225
                                i    i--    i  --        vv  ii i ii  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_175015833_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_175015833_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 5325
                           v  i  i              v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_175015833_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_175015833_   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_175015833_   5426 CTAGGCATCACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_175015833_   5476 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5525
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_175015833_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_175015833_   5576 AGGCAACCTACAAAATGGGAGAAAGTTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   i           i v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_175015833_   5626 AGGGCTAATATCCAGAATCTACAGTGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i iv      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_175015833_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_175015833_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5775
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_175015833_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 205 25.51 3.06 6.12  chr1_175055464_175057143      153   250 (1430)    L1M4_orf2#LINE/L1        8   102 (806)  

  chr1_175055464_    153 ATATACTACGTTTCTGGAGTTGGAAAACT-GGT-TTGT-ATGGTGTTAAC 199
                             v i i   iv    -      i   -ii -    - v i  vi  i
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGA-TTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_175055464_    200 TTTTACCCTAAATTCCTTTATAGATTCAATGTAATTCCAGTTTTAAAAAT 249
                         vi --   i     vv i  i        i i   i  --- v v     
  L1M4_orf2#LINE/     57 ACT--CCCCAAATTGATCTACAGATTCAACGCAATCCC---TATCAAAAT 101

  chr1_175055464_    250 C 250
                          
  L1M4_orf2#LINE/    102 C 102

Transitions / transversions = 1.78 (16 / 9)
Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.50 (9 / 6)  

1257 28.32 10.12 3.18  chr1_175055464_175057143      500  1191 (489)    L1M4_orf2#LINE/L1      169   908 (0)  

  chr1_175055464_    500 AGGATAGCCAAAA-ACTCTTTTAGAA----ACCTAATTTAGGAGGACTTG 544
                           i          - v    vv i  ---- v v  v  -        ii
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT-GGAGGACTCA 217

  chr1_175055464_    545 CTCTGTCAGCTATTAAGGCTCTTTATAAAACTATATTAATTGAGACAAAG 594
                          v  vi viv v i  ii  ivi  i   i   i v    ii     iv 
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_175055464_    595 TGGTATTAGTGTTAGAA-------ATAGACCAATGGAACAGAATAAAGAG 637
                              i i ii v  i -------     i        i     vi    
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_175055464_    638 TCCAAAAACAGACCTGTGCATATATGTACATTTTACTTATGATAAAATTG 687
                             i   i i   ii i   v    vv  v  v i  vi  i  iiv  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_175055464_    688 ACACTGCAGAGTG----GTGGGGAAATTAAGATCTTTTCAATAAATGATC 733
                         v  ----   vii----i        vv vii         i     i v
  L1M4_orf2#LINE/    368 CCA----AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_175055464_    734 CTGGCTCATCTGGAGATCCATATGGAAAA--ATAAAGTGGAAGTGGATTA 781
                             vv  v     v ?   i   v    --  i    -----    iiv
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT-----TGGACCC 458

  chr1_175055464_    782 TTTCTTAACAATTTACATAAAAATGAATTCCATCTAAATTGTAGACCTAC 831
                         i v i v   viv  i i      v  i  v vv ii  ii?       v
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_175055464_    832 GTGTAAAACACCAAATAGTAATAATACCACTTTTAGAATATATTATAGC- 880
                         i     i -i i   ----- iv   vv   i      v v vi    v-
  L1M4_orf2#LINE/    509 ATGTAAGA-GCTAAA-----ACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_175055464_    881 ----ATCTTCATGACCTGAGGATAAAGAA--GTAATTATTAAATCAAATA 924
                         ----      i      vi  v  iiv  --  --  v   i  vvi i 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGT--TTCTTAGATATGACA 600

  chr1_175055464_    925 GAAAAAGCACCAATTATAAAGAAGAAAAAGGTGATAA--TG---TTTATT 969
                         vv        v iiv i   --       ivv     --  ---  i  i
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAA--AGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_175055464_    970 AATATTAATAACTTCTGTTTGTCAAAAGACACTACT--GAAAGTGCAAAA 1017
                           v     v     i   viv     i       ii--       --   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG--AAA 696

  chr1_175055464_   1018 AGTCAAGCTA---------------TAT----AAACCA--------ACAA 1040
                           v   v i ---------------   ----   i  -------- i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_175055464_   1041 AGAAATTATA-CCAGAATATTTCAAGCATCCCGACAAATTGA-----GAA 1084
                         i i v  i  -         v v   v ii iv    v ii -----i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_175055464_   1085 AGACAAA--GCCCAATAGAAAAATGGGCAGAGACTT--AATAGGCACTTC 1130
                                --i      v?           i  iv  --     i  i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_175055464_   1131 ACAAAAGAATATAACCAAATGGCTG-TATACATTTAAAGAGGTGCTCAGC 1179
                         v v      v   vv        ii-  vi  iv i  i  i      i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_175055464_   1180 CTTATCAAGGAA 1191
                         v i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (108 / 85)
Gap_init rate = 0.04 (26 / 740), avg. gap size = 3.54 (92 / 26)  


1113 27.82 6.18 6.00  chr1_175397734_175399906.rev      524  1073 (1100)    L1M4_orf2#LINE/L1        1   551 (357)  

  chr1_175397734_    524 TGGAAAGACATACTAT-TTTATGTTTTAGAAGTCCCAAT-TTCATAAGCA 571
                                 i  v i  -  i   vv  i    v ii   -  vv    - 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-A 49

  chr1_175397734_    572 TGTAAGTTCTACCCAAATTATTCTAAAAATTCAATGTAATTTCAATCAAA 621
                           vv i v  v        iv    v i      i i   ii v      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_175397734_    622 ATGACAACACAGGGTTTTTTTTTTTTTGTTTTGGAATTTAATAAGCTAAT 671
                           ----- v   ----i vii       i---i   v  i i     i  
  L1M4_orf2#LINE/    100 AT-----CCCAG----CTGCCTTTTTTGC---AGAAATTGACAAGCTGAT 137

  chr1_175397734_    672 TTAAAAAT--ATAT----ATACA--GGAACTAG--TGGCCAAGAATAGTC 711
                         iiv     --    ----  i  --   v i  -- i     -  i i  
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA-AACAATC 186

  chr1_175397734_    712 T----GAAGAAAAACATAGTTGGAGG--TAGGGCAGGGTAACTGCCTTAT 755
                          ----i     i    v         -- ----  v----   v  i---
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACT----CAC----ACTTCCC--- 225

  chr1_175397734_    756 AAGATAGCAAGACTTATTATGAAGCCGAAGTAATTAGGA--GTGTGGTGT 803
                         --i  vv   i     i  ii    iiv      i i  --       ii
  L1M4_orf2#LINE/    226 --AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_175397734_    804 TAGTTTGGGAATAGAAAAATTGGCCAATAAAATAGAATAAAGAACCTATA 853
                          i iv ii i     v v  v ii    ii        vi   ii i v 
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_175397734_    854 AACAGATCCACATAGATGTGAAAAACTGAATTATGTCAGCACTGTCAGTG 903
                           i i i   i i vv i  ivv  i   v  vi v  iviv  i  ivi
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_175397734_    904 CAGGTCA-TGGGAAA------------TCAATAAGTGGTACTGGGACAAT 940
                          viv   -    i  ------------    i  i    i         i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_175397734_    941 TGTTTACCCATAAG-GGAATAATTAATTTGGACCTCTACCTCATACCGTA 989
                           vv  ?   i v -ii  v   v  v       i        i   i  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_175397734_    990 CCCCACCCCCCTAATCAATTCCAGGTGGATTATATACTTAAAAGTAAAAG 1039
                         iv v v------   i  i  v ii     i ? v  i    v    i  
  L1M4_orf2#LINE/    474 TACAAA------AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_175397734_   1040 GCAAAACTATACAACTTATAGAAAATAATATAGG 1073
                         vi         v    iv     i v  i     
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

Transitions / transversions = 1.60 (93 / 58)
Gap_init rate = 0.04 (21 / 551), avg. gap size = 3.19 (67 / 21)  

 374 30.43 17.08 1.24  chr1_175397734_175399906.rev     1365  1686 (487)    L1M4_orf2#LINE/L1      536   908 (0)  

  chr1_175397734_   1365 TAAATAAATACATAAATACGTAATGTCTTCACAATCTCAGTGTAGGGAAG 1414
                           i vi  v     ii?--    -i     iii i  ii vv    v  v
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGN--GTAA-ATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_175397734_   1415 AATTTCTTGAACCAGACTTTAAAATCACAAACT-CAAAAGAAAAAATTAA 1463
                         ii      ii ivv   vii    v     i v-             vi 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_175397734_   1464 TATTTTTAATTATATATATATTTGAAACCCTGGT-----------CATTA 1502
                           vv  vi i vi  vv v   vi    ii v  -----------  i  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_175397734_   1503 -------------AAGACGAGCCACAAACTTGGAGAACAAATCTGTAAAA 1539
                         -------------     i v     i v v      v v  i  i   v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_175397734_   1540 CATAACAGCAAATAA----TTTATAATCAGAATGTA--AACAACTCTTAC 1583
                             -i v vi    ----i  i  vi      i  --  v         
  L1M4_orf2#LINE/    733 CATA-TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_175397734_   1584 AA---------------------AGCTTGATATAAAAAAGGGAAAAACAT 1612
                           --------------------- i iii  v?     v   v   iv  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_175397734_   1613 TAGAATAGGAA---CTTCACAGAAGGAACCTGAATGCTCAGTAAAAACAT 1659
                          v      iv ---  i  v     iv ivii    vi  i   iv    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_175397734_   1660 GAAAAGATGCTTAACTTTATTAGTAAT 1686
                                    i   v i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (53 / 43)
Gap_init rate = 0.03 (10 / 373), avg. gap size = 5.90 (59 / 10)  


2308 22.49 4.29 4.44  chr1_175442071_175447616     3854  4529 (1017)    L1M4_orf2#LINE/L1        3   677 (231)  

  chr1_175442071_   3854 GATAGATACTCTTTGTTTATGGGTGAGAAGACTCG---TTGCTAAGAAGA 3900
                           v     ii iv    i    i vi       ii---   i     v i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_175442071_   3901 CAATTATCCCTAAATTGATC---------AATGTGATTCCAGTCAAAATG 3941
                             vv    i         ---------  i ii  i  vi       v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_175442071_   3942 CCAGCAGGCTTTCTTTTTTGGCGGTGGGGTGGGGGAATAGAAATTGGCAA 3991
                              v ----i        -----------------i        i   
  L1M4_orf2#LINE/    103 CCAGCTG----CCTTTTTTG-----------------CAGAAATTGACAA 131

  chr1_175442071_   3992 GCTGATTCTAAAATTCGTGTGGAAATGTAAAGGACGTAGAATAGCCAAAA 4041
                               i         i i        i  i    vi             
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_175442071_   4042 CAGCTTTGTAAAAAGAAGAACAAAGTTGGAGGTCTAATGCTATCTGATAT 4091
                           iii   -                       v  v ii  vi ii  v 
  L1M4_orf2#LINE/    182 CAATCTTG-AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_175442071_   4092 CACAATTTATTATAAATCTGAAGTAGTCAAAACAATGTTGTATTTGTATA 4141
                           v  i   i  i   v  iv    i    i   i   v   i v i   
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_175442071_   4142 AGGAT-GATGAAATAGATCAATGGAATAGAAC--AGAGTCCAGAAGTAAG 4188
                              -  i- v                   i--           i   i
  L1M4_orf2#LINE/    281 AGGATAGAC-ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_175442071_   4189 CCAGTACATAAATGGACAACTGAATTTTGACAAGG-TGCAAAGGCAGTTC 4237
                           vi     vv    v   i   v   i       -   v   i vi   
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_175442071_   4238 AGCAGAGAAAGGATAGTCTATTCAACAAATAATGCTGGCACAAAATGGAT 4287
                          iii i     i       v          ii      v    v-     
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC-TGGAT 428

  chr1_175442071_   4288 ATCCAAATGCAAACAAATGAACTTCAGTCTGTATCTTGCACTGTATGGGA 4337
                          ?   v       vi      v  viii iv  i  ii   ii   ivi 
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_175442071_   4338 AAATGAGCTCAAAATGAATCAAAGACCTAAATGGTCAAGA-CTTAAATTA 4386
                             v i         i    ?           --i    -  v   i  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATG--TAAGAGCTAAAACTA 526

  chr1_175442071_   4387 CAAA-CTTTTGGCA--AAAT-TAGGACAAAATCTTTAT---CTTGAGTCA 4429
                         i   -  i  i v --   i-    ?vv       ii ---    i  i 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_175442071_   4430 AGCAAAATTATTTTTAGTTACAACACCAAAAGCATGATCCTTAAAATAGC 4479
                         i    viv -  i    v  ii            ii v vvi    v iv
  L1M4_orf2#LINE/    577 GGCAATGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_175442071_   4480 ACATTGATAAAATGATTTTTTATCAAA-TTGAAAA----TGTGCTATTCA 4524
                          v  v      v  ivi  i-      -  i    ----      --   
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTC-ATCAAAATTAAAAACTTTTGTGCT--TCA 672

  chr1_175442071_   4525 AAAGA 4529
                           i  
  L1M4_orf2#LINE/    673 AAGGA 677

Transitions / transversions = 1.81 (96 / 53)
Gap_init rate = 0.03 (21 / 675), avg. gap size = 2.81 (59 / 21)  

 603 21.05 12.92 2.87  chr1_175442071_175447616     4852  5060 (486)    L1M4_orf2#LINE/L1      679   908 (0)  

  chr1_175442071_   4852 ATTCTTAAGAGAATGAAAAGACCGGCTGCAGGATGGCAGAAAATACTTGC 4901
                          i v i    i i         viv ii   i    v        i    
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_175442071_   4902 AAATCAAATATGTGATTAAGGTCTTGTATATAGAATATATACTAATGAAC 4951
                               v    v    v i  v       vi          --  -    
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA--AA-GAAC 775

  chr1_175442071_   4952 TCT--CAAC--------------ACCAACAATCCAACTTTTTGAAATCTG 4985
                            --    --------------  v  i  i    --  ?vi    vv 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAA--TTWAAAAATGGG 823

  chr1_175442071_   4986 CAAAATATTTGA-TAGATACCTCACCACAGAAGATACGC----------T 5024
                             iv      -    i ii  v   v        ii ---------- 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_175442071_   5025 AAGTATATGAAAAGATGTTTAGTCCTTATATATATT 5060
                            i i           i i i- v i ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (26 / 17)
Gap_init rate = 0.03 (8 / 230), avg. gap size = 4.12 (33 / 8)  


3088 24.18 1.63 3.38  chr1_175456232_175461455.rev      935  1852 (3372)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr1_175456232_    935 GATATTGCATATTAACGGACTCAAAGAATCAATATTTTTAACTTGTCTGC 984
                              iv   i  v i   i vi    v i      v    vv  v vii
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_175456232_    985 ACT-----AACTAATCTACAGATTCAAGGCAATGCAATCCCTATCAACAT 1029
                            -----  i i              -----i              v  
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAA-----CGCAATCCCTATCAAAAT 101

  chr1_175456232_   1030 ACCAATAATATTCTTCATGGAAATAGAAAAAACAATCCTAAAATTTATAT 1079
                         v   iiviiv  i  iiii     v  v  ivii           i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_175456232_   1080 GGAACCACAGAAGACACAGAATAGCTAAAGCAATCTTGGGCAAAAAAAAA 1129
                             vii  iii   v         i   i        ------------
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG------------ 189

  chr1_175456232_   1130 AAAAAAAAGAACAAAACTG-AGGAATCCTATTACTTGACTTCAAATTATA 1178
                              i         ii  -    v  vi i v iii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_175456232_   1179 CTATAGAGTTACAGTAACCAAAACAGCATG-TACTGGCATAAAAACATAG 1227
                            i i  i        i   i    ii  -           ii i v v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_175456232_   1228 AAATAGACCAATTGAACAGAACAGAGAATCCAGAAACAAATCCACACACC 1277
                          v     i    v   i    iv    i        i   i   i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_175456232_   1278 TACAGTAAACTCATTTTCAACAAAGGTGCCAAGAACATTCATTGGCAATG 1327
                           ii  v  i v      i    i          v      ------   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA------ATG 383

  chr1_175456232_   1328 GGAAAAGGACAGTCTCTTCAATAAACAGGGCTGGGAAAACTAGATATCCA 1377
                           i    i i     i     i   ii v       v    i    ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_175456232_   1378 TGTATAGAAGAATGGAACTAGACCCCTAACTCTCACCTTATACAAAAATC 1427
                         ii ii i       i ii i        v   v    v           i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_175456232_   1428 AAACCAAAATGGATTACAGACTTAAATCGAAGACCTGAAACAATGAAACT 1477
                           vi          i ?    i     vv    v  i    v  i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_175456232_   1478 ACTACAAGAAAACACTTGGA--AAACCCTCCAGAGCATTGGTCTGGGAGA 1525
                         vi  v         - v  ?--   i i  vv  v -    vi i  vi 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACA-TAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAA 581

  chr1_175456232_   1526 AAATCTATTGAATAACACCCCACAAGCACAGGCAACCAAAGCAAAAATGG 1575
                         vii i v  ii   vv  v   v       i     v    v      i 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_175456232_   1576 ACAAATAGGATCACATCAAG-TTAAAAAGCTTTTGCGCAACAAAGGAAAC 1624
                          i    v   iiv      i-       -      i  vv       v  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACAC 680

  chr1_175456232_   1625 AATCAACAAAG-----AGACGACTTACAGAATGGAAGAAAATATTTGCAG 1669
                         v     v    -----    i  ii         i              i
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_175456232_   1670 CCTACCCATCTGAGAAGGGATTAATAACCAGAACATATAAGGAGCTCAAA 1719
                         vii ivi      v      i vi  v      i      i  i   vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_175456232_   1720 CAACTCTACAGGAAAAAAAAAATCTAATACTCTGATTTTTTAAATGGGCA 1769
                               v i iv     i v  ----   vi ii   ?vv-         
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAA----ATAACCCAATTWAA-AAATGGGCA 825

  chr1_175456232_   1770 AAAGATCTGACTAGACATTTCTCCAAAGAAAACATATAACTGGTAAAGAG 1819
                           i   i   v                   i i   i  v   iv  v i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_175456232_   1820 GCATATGAAAAAGTTCTCAACATCACTGTAAGT 1852
                            i       ii v          ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (136 / 82)
Gap_init rate = 0.02 (14 / 902), avg. gap size = 3.29 (46 / 14)  

2410 26.17 5.52 1.68  chr1_175456232_175461455.rev     3902  4734 (490)    L1M4_orf2#LINE/L1       44   908 (0)  

  chr1_175456232_   3902 TTAAAATGGCCACACTGCTCAAAGCAATCTGCAGATTCAATACTATTCCT 3951
                             i     v i   v i    vii    i         ii v  i   
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr1_175456232_   3952 AT-AAAGCTACAA--ACATTTTTCACAGAACCAGAAAAAAACT-ACTCTA 3997
                           -   iiiv  i--i v     ii     -- vvi v  i  - ii   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTA 141

  chr1_175456232_   3998 AAATTCATATGGAACCAAAAAAGAACCTGAGTAGCCAAGGCAATCCTAAG 4047
                                       viiv  ii  v  v  i       ii     i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_175456232_   4048 CAAAAAGAACAAAGTGTGATGCATCACACTACCTGAGTTCAAACTATACC 4097
                         v  i           vv  v vv       v  ii v      viv   i
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_175456232_   4098 ATAAGGCTACAGTAAGTAACCAAAACAGCACGGTTCTAGTACAAA-ACAG 4146
                          i  i          ----i   i    iii   v  i i i  i- i  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAA----TCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_175456232_   4147 ACATACAGACCAATGGAACAGAATGGAGAACCCAGAAATAAAGCCA-ACA 4195
                              i   i        i     v    ii           v   -   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_175456232_   4196 GCTACAGCCATCTGATCTTGTATAAAGTTAACAAAAATGAGCAATGGGAA 4245
                         vi  ii i  vi    i  vv i  i v iv   i viivv       i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_175456232_   4246 AAG-----TCTTCCTATTAAATAAATAGTGCTGGGATAGCTGGCTAGCCA 4290
                            -----    ----  v  i    i         i i    v  ?   
  L1M4_orf2#LINE/    388 AAGAATAGTCTT----TTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_175456232_   4291 TATGCAGAACAATGAAATTATACCCCTACCTTTTACCATATACAAAAATT 4340
                         i     i  v      i  iv          ivi                
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_175456232_   4341 AAC--AAGATGGATTAAAGATTTAAATGTAAAACCTAAAATTATAAGAAC 4388
                            --  i      i ?   ii         i v      i     i vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_175456232_   4389 CCTAGAAAAAAACCTAGGAA-ACACCATTCTGGACATGTGCCTTGGGAAA 4437
                          i     i     v    ?i- v i -   vv   v -  vv  i  v  
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT-TGGGTTAGGCAA 581

  chr1_175456232_   4438 TAACTTAT--GACTAAGTCCTCAAAAGCAAATGTAACAAAAACAAAAATT 4485
                          iii  v --  -  v v vi        v v i       iv      v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_175456232_   4486 GACAAGTGGGACCT------AATTAAAGAGCTCTTCCAC----AAGAAAA 4525
                           i  i v    i ------       i -  i  vii ----   i v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA 679

  chr1_175456232_   4526 CAATCAACAGGGTCAACAGACAACCTATAGAATGGGAGAAAATACTGACC 4575
                          v     v ii  v  v        i i                i vi v
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_175456232_   4576 AACTATGCATCTGACAAAGGTCTAATACCCAAAATTTATAAGGAATGTAA 4625
                           ii  ii      i  i  v  vi  i   i   v     i   ivivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_175456232_   4626 ACAATTGAACAAGCAAAA-ACAAA-----------------GGACAAAAG 4657
                             i v  i  vv    -     -----------------  i    i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_175456232_   4658 ATACAAACAGACACTTCCCAAAAGAAGACATACAAGTGGCCAAGAAACAT 4707
                           vii  i     i   i v        i      i       v  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_175456232_   4708 ATAAAAA--TGTTCAACATCGCTAATCAT 4734
                           i    --  i        i????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (136 / 79)
Gap_init rate = 0.02 (21 / 865), avg. gap size = 2.86 (60 / 21)  


3285 26.87 0.44 0.44  chr1_175477452_175479597      746  1653 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_175477452_    746 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATGGTGAAAAT 795
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_175477452_    796 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 845
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_175477452_    846 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 893
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_175477452_    894 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGGCAATCCTAAGCCAAAAG 943
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_175477452_    944 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 993
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_175477452_    994 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1043
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_175477452_   1044 AATGGAACAGAAC--AGAGCCCTCGGAAATAACACCGCATATCTACAACT 1091
                                i    i--    i  --i       vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_175477452_   1092 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAAGGATTCC 1141
                          vi    i  i     ivv  vv  i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_175477452_   1142 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1191
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_175477452_   1192 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1241
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_175477452_   1242 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1291
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_175477452_   1292 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1341
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_175477452_   1342 AACACCAAAAACAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 1391
                         i         i  vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_175477452_   1392 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1441
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_175477452_   1442 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 1491
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_175477452_   1492 AGTGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1541
                         i vi  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_175477452_   1542 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 1591
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_175477452_   1592 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 1641
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_175477452_   1642 ATCACTGGGCAT 1653
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1244 25.19 10.54 0.26  chr1_175516625_175519193.rev      643  1031 (1538)    L1M4_orf2#LINE/L1        4   432 (476)  

  chr1_175516625_    643 AGAAATAAACCATGTTTGTGGATTGAAAGTCTTAATGTTGTTA---T--C 687
                          i i   vv       ii       i   v      i      --- -- 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_175516625_    688 AATTCTTCCCAAAGTGATCTATAAATTCAATAAAACCTCAATCAAAAATG 737
                            v  i      v       i i      iiv  i i v       - v
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TC 102

  chr1_175516625_    738 GAAGCAGGCCATGTTGTAGAAATTGACAAGCTACTTCTAAAATTTCCACA 787
                         vv   v v iv v   i               iv i        ivi ii
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_175516625_    788 GATATAAAATGGAGATAGCATAGCCAAGACAATCTTGAAGAAGAAAAA-A 836
                           v  iv  v   vvi  v        i           i     i  - 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_175516625_    837 AAATTAGA------ACACTATCAGATTGCAAGGCTTACTACAAAGCTACA 880
                           i  i  ------     vi vi   v   ii                 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_175516625_    881 GTAATTAAGACAAAGAGATATTGGAATAAGAATAGACAAATAAATCAAAG 930
                              i      iv v i  i   v     i       v   i     v 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_175516625_    931 GAA--------------CAGAAATATACCTACACGTATTTGATCAAGTGA 966
                            --------------        v   i i  i v v  i    v   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_175516625_    967 TTTTCAACCAAAATGTCAAAGCAGTTAAACAGAGAAA----AG------- 1005
                              i  v iii  i   ii vi  v  ii i    ----  -------
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_175516625_   1006 ----AATGGAGTTAGCACAATTAGATATTC 1031
                         ----     v i i v    i i    ?i 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCC 432

Transitions / transversions = 1.49 (58 / 39)
Gap_init rate = 0.02 (8 / 429), avg. gap size = 5.25 (42 / 8)  

1040 23.61 5.84 2.92  chr1_175516625_175519193.rev     1702  2078 (491)    L1M4_orf2#LINE/L1      521   908 (0)  

  chr1_175516625_   1702 AAACTATAATACTTCTAGGAGTGATCAAAGGAAAATGTCTTTATGACCCT 1751
                                  v   ii   i  vi v  v   ?iv vi    ii     i 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_175516625_   1752 GGATTAAGAAAAGATTTATTAAACAAGACAC--AAAACACAGTAACCACA 1799
                           i   i v  v i   v   i i v     --   i    -- i v   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA--AGCAACA 618

  chr1_175516625_   1800 AAGATAAAAATA-ACAAATGGGACTTCATTAAAATTGAACAGTTCTGCTC 1848
                           iiv       - i    v         i      i  v v  i  i--
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT-- 666

  chr1_175516625_   1849 ACTAACCAAAAGACAGCATTAAAA---TAAAAACGCAAGGCATAGACTAG 1895
                         i  --i    i    vi  i  i --- i    vi   vv  i   v i 
  L1M4_orf2#LINE/    667 GCT--TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_175516625_   1896 GAAAAAATACTT---------ATTTCTGAAAAGGG-TTTGTATTCAGAAT 1935
                           i      i  ---------  v     v     -i      i      
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_175516625_   1936 ACATTAAAAAAATCCCTACAACTTGATAA------GACAAACAATCCTAT 1979
                          i  --   i  ii i       ii    ------      i  i  v  
  L1M4_orf2#LINE/    765 ATAT--AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_175516625_   1980 TAAAAATATGGGTAAAAGATTTGAAAGGATAGTATCACAAAACAAAATAT 2029
                          ?    -     i   i        vi  i v -  v v   v  i    
  L1M4_orf2#LINE/    813 TWAAAA-ATGGGCAAAGGATTTGAATAGACATT-TCTCCAAAGAAGATAT 860

  chr1_175516625_   2030 CCAAATGGTCCACATACATATGAAAAGATACTCAACCATCACTATCATC 2078
                         v       i v i vi  i          i      -    ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (56 / 31)
Gap_init rate = 0.03 (13 / 388), avg. gap size = 2.54 (33 / 13)  


 906 26.87 1.32 0.00  chr1_175527287_175529972      674   900 (1786)    L1M4_orf2#LINE/L1        1   230 (678)  

  chr1_175527287_    674 TGGAAGGATATCCTGTGTTTGTGCATTGGAAGAATTCATATTGTTAAAAT 723
                              i       ii    ii  v         v  v          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_175527287_    724 ATCCATACAGCCCAAAGCAATCTACAGATTCAGTGCAGTCACTATCAAAA 773
                         iv v    vv      vii             ii   i  v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_175527287_    774 TTTCAATGACATTTATCACAGAAATAGAAAAAACAATTCTAAAATTCACA 823
                          ii  iivi v   v ii       v  v  ivii  i          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_175527287_    824 TGGAATCACAAACATCTCAGAATAGCCAAAGCAATCTTGA---GCAACAA 870
                              vii   iviv i             i         ---iv  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_175527287_    871 CAAAGCTAGAGACATCATACTCTCTGATTT 900
                              i i   ivv   i   ii ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTT 230

Transitions / transversions = 1.77 (39 / 22)
Gap_init rate = 0.00 (1 / 230), avg. gap size = 3.00 (3 / 1)  

2265 23.36 4.49 0.56  chr1_175527287_175529972     1196  1730 (956)    L1M4_orf2#LINE/L1      212   767 (141)  

  chr1_175527287_   1196 GGCCCATACTCTCTGATTTTAAAATACACTGTGAAGCTATAGTAATCAAA 1245
                          i i  i   ii ii    i    ivi   iii      i         i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_175527287_   1246 ATATTGTGGT--TAGCATAAA-ATAGACATGTAGACCAATGGACCAAAAT 1292
                          i v      -- i      i-        i    i       vi i   
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_175527287_   1293 AAAGGGCCCAGAAATAAATACACACATTTACAGTCAATTGATCCTCAACA 1342
                         vi  i i           iv  i       ii          ii  i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_175527287_   1343 AAGATAACAAGAACACACAATGGGGAAATGGTAGTTTCTTCAATAAATTG 1392
                          i i iv     v  iv           vii    i i     i    v 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_175527287_   1393 TGTCAGAAAAACTGGATGTCCGCATGCAAAAGAATGAAACTGGACCCTTA 1442
                           iii i v        i?  i                ii       i  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_175527287_   1443 TCTCATACCATCTGCAAAAATGAACTCAAAATATA-CTTAGTACTTAAAC 1491
                         i    i     v i       v          iv - v?  -  i    i
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG-ACCTAAAT 510

  chr1_175527287_   1492 ATGAGACCTGAAACTGTAAAACTACTAGAAGAAAACACACGGGAAAAGCT 1541
                         i i   v  i     i       vi            i v ? v   v  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_175527287_   1542 TCTTGACAGTGGATCTGGACAATAATTTTTTGGCTATGACCCCAAAAGTA 1591
                           v    vv   i - i i    ii   i  i v      v       i 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_175527287_   1592 CAAGCAACGAAAGCAAAAATATACAAAATGGGATTGCATCAAACTAAAAA 1641
                                 i    v       v i   - v   i v       v v    
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAA-TTGGACTTCATCAAAATTAAAA 658

  chr1_175527287_   1642 GCTTTTGTACAGCAAAGGA--------------------GACAGTCTATG 1671
                         i       i vv       --------------------    ii i ii
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_175527287_   1672 GAATGGGAGAAGATATTTGCAAATAATACATCTGATAAGGGGTTAATATC 1721
                                    i            v   i            ii vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_175527287_   1722 CAAAATACA 1730
                           i    i 
  L1M4_orf2#LINE/    759 CAGAATATA 767

Transitions / transversions = 2.49 (87 / 35)
Gap_init rate = 0.01 (7 / 556), avg. gap size = 3.86 (27 / 7)  

 626 19.44 2.78 0.00  chr1_175527287_175529972     2051  2194 (492)    L1M4_orf2#LINE/L1      761   908 (0)  

  chr1_175527287_   2051 GACTGTATAAGGAACTCAGACAATGTGATAACAAGAAAACAA----CCCA 2096
                           v i     i      vv    ivii    i  i  i    ----    
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_175527287_   2097 ATTAAAAAATGGGCAAAGGATCTGAATAGACATTTCTCAAAAGAAAACAT 2146
                            ?                 i                v      i i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_175527287_   2147 ACACAAGTCCCACAGGTATATCAAAAGGTGCTCAACATCGCTAATCAT 2194
                            v v v  v i i i i  v     i           i????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 4.00 (4 / 1)  


3352 26.54 0.44 0.44  chr1_175537840_175544206     4967  5874 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_175537840_   4967 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5016
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_175537840_   5017 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5066
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_175537840_   5067 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5114
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_175537840_   5115 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5164
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_175537840_   5165 AACAAAGCTGGAGGAATCACACTACCTGACTTCAAACTATACTACAAGGC 5214
                                i       v       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_175537840_   5215 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5264
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_175537840_   5265 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAGCT 5312
                                i    i--    i  --        vv  ii i ii  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_175537840_   5313 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5362
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_175537840_   5363 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 5412
                           v  i  i              v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_175537840_   5413 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5462
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_175537840_   5463 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5512
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_175537840_   5513 CTAGGCATCACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5562
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_175537840_   5563 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5612
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_175537840_   5613 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5662
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_175537840_   5663 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5712
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_175537840_   5713 AGGGCTAATATCCAGAATCTACAGTGAACTCAAACAAATTTACAAGAAAA 5762
                         i  i  vi          v  i iv      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_175537840_   5763 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5812
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_175537840_   5813 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5862
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_175537840_   5863 ATCACTGGCCAT 5874
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2764 25.32 2.38 4.11  chr1_175608971_175614183.rev     3811  4734 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_175608971_   3811 TGGAAAAGCATTCCATGCTCATGGATTGGAAGAATCAATACTGTTAA-AT 3859
                               iii  i     i               v i    i      -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_175608971_   3860 GTCCATATTGTCCAAACCAACCTACAGATTCAATGCTATTCTTATCAAAC 3909
                          v v   i vi     iii i            i  v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_175608971_   3910 TACCAATGACATTCTTCAAAGAATTAGAAAAAACCATTAGAAAATTCATA 3959
                          v   iivi v  i  iiv    v v  v  iviv  ivv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_175608971_   3960 TGGGAACAACAACAACAACAACAACAACAAAAG-CCCA-AATAGCTAAAG 4007
                            i  ii-------------------   ii -    -      i   i
  L1M4_orf2#LINE/    151 TGGAAATG-------------------CAAGGGACCCAGAATAGCCAAAA 181

  chr1_175608971_   4008 CAATTCTAAGTAAAAAGAACAAAGCTGAAGGCATCACACTACCTGACTTC 4057
                             ii i iv  i          i  i   vv       v  ii i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_175608971_   4058 AAACTATACTACAAGACTACAGTAACCAAAAAATAGCATGGTACTGGTAC 4107
                            viv        ii         i   i --i  ii         i i
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGA--CAGTGTGGTACTGGCAT 279

  chr1_175608971_   4108 AAAAACAGATACCAATGGAACAGGATAGAACCAATGGAACAGTATAGAGA 4157
                           ii i   i i------------     -i        i  v  v    
  L1M4_orf2#LINE/    280 AAGGATAGACAT------------ATAGA-TCAATGGAATAGAATTGAGA 316

  chr1_175608971_   4158 GCCCAGAAATAATGCCTCACACCTACTACCATCTGATCTTTGACAAAGCT 4207
                          i          vv  vi   ii  ivii  vi    i  i     i v 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_175608971_   4208 GACAAAAACAAGCAATGGGGAAAAGGCTCCCTATTCAATA--TGCTGCTA 4255
                          v   i v  vv           iiiivvi  v     i --  v    i
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_175608971_   4256 GGATAACTGGATAGCCATATACAGAAGATTAAAACTGGACCCCTTCCTTA 4305
                            i         ?   i  i  i    v i  ii         v   i 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_175608971_   4306 CACTGTATACAAAAATCAACTCAAGATGGATTAAAGACTTAAATGCAAAA 4355
                            ii           i       i      i ?    i      i  i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_175608971_   4356 CCTAAAACTATAAAAACCCTGAAAGATAACCTAGGA-TATACCATTCTGG 4404
                         v              vi i ii    v   v    ?-  v i -   vv 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTG 565

  chr1_175608971_   4405 ACACAGGCCCTGGCAAAGACTTCAT-GATGAAGACTCCAAAAGCAGTTGC 4453
                           viv  viiv     v ii   v -   - v   v         vvv  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGC 614

  chr1_175608971_   4454 AACAAAAACAAAAACTGACAAACAGGACCT------AATTAGAGAGCTTC 4497
                                iv     iv  i   iv    i ------     i i -   i
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTT 663

  chr1_175608971_   4498 TGCAGAGCAAAAGAAACTATCAGCAGAATAAACCAACATTCCTAGAGAAT 4547
                           iivvv    i  v       iv i i i  vvi   vi  - v     
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC-ACAGAAT 712

  chr1_175608971_   4548 GGGAGAAAATATTTTCAAACTGTGTATCTGAAAAAGGTCTAATATCTAGA 4597
                                       v    iii i       v  i  v  vi    i   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_175608971_   4598 ATCTATAAGAAACT--TA-AATTTA-CAGGCAAAAAACAA----CCCCAT 4639
                           v     ii    --  -  i i -i ivv    i    ----   v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_175608971_   4640 TAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAGAGAAGAAATAC 4689
                          ?    i           iv    i     i     v i      v    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_175608971_   4690 ACATGGCCAACAAGCATTTGAAAA-ACGGCCAATATCACTAATTGC 4734
                          v        i     iv      - i vi   i    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (145 / 85)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.00 (60 / 20)  


3530 18.06 9.57 0.96  chr1_175624759_175627668     1582  2417 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_175624759_   1582 TGGAAACATATCACCTGCTCCTGGATTGAAAGAC--AATATCGTTAAGAT 1629
                               v     v v  i  v       i     --     i        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_175624759_   1630 GTCAGTACTACTCAAATCAATATATAGATTCAATACAATCCCTATTG--- 1676
                          v  i    v i     ii  v  i        ii          ii---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_175624759_   1677 ---TAG-TG--TTTTTTACAGAAATAGAAAACCCCATTCAAAAATTCATA 1720
                         ---i  -  --      i       v  v  v iv  i v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_175624759_   1721 TGGAATCTCAAGGGACCCCTAATAACCAAAACA-TCTTGAAAAAGAA--- 1766
                              viv          vv    i        -             ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_175624759_   1767 CAAAGCTAGAAGACTTAT--TTCCTGATTTCAAAACTTACTACAAAGCTA 1814
                              i i  i    i i--    ii                        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_175624759_   1815 CAGTAATCAAAGTACTGTGGTACTTGCGTAA----AAACATA--AACCTA 1858
                                   iii v         v  i   ---- i     --i i v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_175624759_   1859 CGGGATAGA-----GAGCCCAGAAATAAACCCTCGCATATATGGTCAAAT 1903
                         i  i     -----   i              vii   v         v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_175624759_   1904 GATTTTTGACA-GGGTGCCAAGAC-ACCCA-TAAGGAAAGGA--GTCTTT 1948
                               i    -            - ii  - ii      i --      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_175624759_   1949 TCAG---ATGGCGCTGGGG-AACTGTATCTCCACATGCAAAAGAATGAAG 1994
                            i---    i      i-     v  v?                    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_175624759_   1995 TTGTATCCTTACCTAACACTGTATACAAAAATTAACTCAAAATGAATCAA 2044
                            v i  i     v    ii                       i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_175624759_   2045 AGACCTTAATGTAAGACCTAAGCCTGTAAG--TCTTACTGAAGATAACAT 2092
                               v         v    iv  i   i--     --     v     
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA--GAAGAAAACAT 548

  chr1_175624759_   2093 AGGGCAAAAGCTTCACATCGTTGAATTTGGCAGTGACTTTATAGGTATGA 2142
                            ?vv   v    iiiv v   ii  v    i  ii  iv   i     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_175624759_   2143 CACTAAAGGCACAGGCAACAAAGGGAAAAACAGAT----TGGACTTAATG 2188
                            i   i     i        i i     i    ----       v  v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_175624759_   2189 AAAATTTAAGA----TGTGTGTCATAG-ACAATAT-----AAACAGAAAG 2228
                               v  i ----    iv   v  -   v   -----  iiii    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_175624759_   2229 -CAACCCACAGAATGGGAGAAAGCATATGCAAATTATCTAGCTGATAAGG 2277
                         -                     ii  v       i  v  v         
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_175624759_   2278 GATTAATATCCAGAATGTATAGAGAACT---GAAACTCAGCAACAGAAA- 2323
                           i vi          i    i      ---iv      ii  i i   -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_175624759_   2324 ----------TAATTCAGAAATGGGCAAAGAACTTGAATACACATTTCTC 2363
                         ----------i    ? i            i i       v         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_175624759_   2364 TGAAGAAGAT-------TG-CCAATAAATACATTTTTTAGAA----TGCT 2401
                         ii        -------  -       ii    ------   ----    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACAT------GAAAAGATGCT 892

  chr1_175624759_   2402 TAATATCAGGACTAAT 2417
                         i  i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (98 / 49)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 3.03 (88 / 29)  


2723 22.76 4.37 5.49  chr1_175679425_175684283     3467  4358 (501)    L1M4_orf2#LINE/L1        1   882 (26)  

  chr1_175679425_   3467 TGAAAATACATCCCATGCTCATGGATTGGAAAAATTAATATTATCAAAAT 3516
                           i   v i        i             i v        i i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_175679425_   3517 G-----ACT----AAAGCAATTTACAGGTTCAATGTAATCTCTATCAACA 3557
                          -----   ----   vii  i     i     i i    i       v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_175679425_   3558 TACCAG--ACATTCTTCATGGGAATAGAAAAAC-AATCCTAAAATACATA 3604
                          v    --i v  i  iiii i   v  v  i -i          v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_175679425_   3605 TGGAACCACAAAAGACCTCAAATAGCTAAAGCAATATATATAGAAAAAAA 3654
                              vii   ii    ivi      i   i    v vv v i i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_175679425_   3655 AATAGCAGGAGGCATCATACTACCTGACTTCAAAATACACGACAAAGCTA 3704
                         v v  iv     vv   i   v  ii i       ivi  v         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_175679425_   3705 TAGAGGTATAGTAACCAAAACAGCATAGTATTGGTATAAAAACAGACACA 3754
                         i  --------   i   i    ii i   i   i    ii i     i 
  L1M4_orf2#LINE/    251 CAG--------TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_175679425_   3755 TAGAACAATGGAACAGAATAGAGAATCCAGAAAT----CCACATATTTAA 3800
                             v        i     v    i         ----   i i     v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_175679425_   3801 AGCCAACTAATTTTTGACAAAGGCACCAAGAACATACATTGGGAAAAGGA 3850
                         i i   i i     i     i  ii      v   v  v    i    i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_175679425_   3851 CACCTTCTTCAATAAATGGTGCTGGGAAATATTGAAGAAGGACACCTTCT 3900
                         i vii i     i              -----------------------
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGA----------------------- 419

  chr1_175679425_   3901 TCAAAAAACGGTGCTGGG-AACTATATGCAGAAGAATGAAACTAGACCCT 3949
                         -   ---------    i- ? i i     i         ii i     i
  L1M4_orf2#LINE/    420 -CAA---------CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_175679425_   3950 TAT-TCTCACCATATACAAAAATCAACCCAAAATGGATTAAAGACTGAAA 3998
                           i-  v                i   i          i ?    iv   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_175679425_   3999 AGTAAGACCCAAAACTATAAAAACGCTAGAAGAAAACATAAGGA-AAATG 4047
                         v      v i            vivi              i ?i-    -
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT- 558

  chr1_175679425_   4048 TGCTTCA-GCCCATTGGTCTAAGCAAAGATTTTATGTCTAAGGCTTCAAA 4096
                         --    i- v  -    vi  i    v i   iv ivv  v i vi    
  L1M4_orf2#LINE/    559 --CTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_175679425_   4097 AGCACAG----CTAAAGAAAA--TAGATAAATGAGACTATATTAAACTAA 4140
                               i---- v        --         vi    vi  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_175679425_   4141 AAACCTTCTCCCCAGCAAAGGAAACAATCAAGAGAGTGAAGAGACAACCT 4190
                            v   i viv vv       v  v       i      i        i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_175679425_   4191 ACAGAATGGGAGAAAATATGTGCAAGCTACTCATTTCGCAAGGGA-TAAC 4239
                                            v     iii ivi  i vii      - vii
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_175679425_   4240 ATCTAGAATATACCAGGAACTC---------AACACTAAAAAAAAAAAAA 4280
                            i        iv i      ---------  i v      i v   v 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_175679425_   4281 AACCA-CTAAAAAGTGGAGAAAGAATCTAGAATTATAGACATTCCTCAAA 4329
                          v   -i ?    i   iv    i  i -    ---       i   v  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTT-GAAT---AGACATTTCTCCAA 851

  chr1_175679425_   4330 AGAAAATATACAAATGACCAA--AGAATATG 4358
                             i           i    --  v i   
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATG 882

Transitions / transversions = 1.93 (131 / 68)
Gap_init rate = 0.02 (22 / 882), avg. gap size = 4.00 (88 / 22)  


3156 27.80 0.22 0.44  chr1_175688639_175694865.rev     4827  5736 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_175688639_   4827 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCCTGAAAAT 4876
                              ii i  i     i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_175688639_   4877 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4926
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_175688639_   4927 TACCAATGACTTTCTCCACAGAATTGGAAAAAAGTACTTTAAAGTTCATA 4976
                          v   iivi i  i iii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_175688639_   4977 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5026
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_175688639_   5027 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGACTA 5076
                              i      vv       v  ii i      viv        ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_175688639_   5077 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5126
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_175688639_   5127 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5174
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_175688639_   5175 CTGATCTTTGACAAACCTGAGAAAATCAAGCAATGGGGAAAGGATTCCCT 5224
                         i    i  i     ivv  vv  i i  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_175688639_   5225 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5274
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_175688639_   5275 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGCATT 5324
                          ii    i    v   i     v           i  i    i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_175688639_   5325 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5374
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_175688639_   5375 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCACGTCTAAAA 5424
                            ?i v viv   iv   v v  vv i     v ii   viivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_175688639_   5425 CACCAAAAGGAATAGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5474
                                  v vv           vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_175688639_   5475 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5524
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_175688639_   5525 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5574
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_175688639_   5575 TGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5624
                         vi  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_175688639_   5625 ACAAACAACCCCATCAACAAGTGGGCGAAGGACATGAACAGACACTTCTC 5674
                              i     v  i? v  i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_175688639_   5675 TCAAAAGAAGACATTTATGCAGCCAAAAAACACAAGAAAAAATGCTCATC 5724
                         i--        i  vi viii     v  i    v     i       v 
  L1M4_orf2#LINE/    849 C--AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_175688639_   5725 ATCACTGGCCAT 5736
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (145 / 104)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 2.00 (6 / 3)  


2991 15.01 14.46 3.31  chr1_176019488_176021701.rev      274   999 (1214)    L1M4_orf2#LINE/L1        4   810 (98)  

  chr1_176019488_    274 AAAGACATCCCATATTCATTGACTAGAAGATTTAATATTGTTAATATGGC 323
                              i       i     v  i i     i             v     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_176019488_    324 AGTGCTCCCCAATTTT-TCTATAGATTTAAAGCAATACTCACTAAAATTT 372
                          i i        v  v-    i     i  v     v ii ii     ii
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_176019488_    373 CACCTGGCTTCTTTGCAAAAATTGACAAGCTGATCCTAAAATTCATATAG 422
                           v   v   i      i                              i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_176019488_    423 AAATTCAAGA-ACACAGAATAGCCATACAAATCATGAAAAAAAAAATAAC 471
                             v    i-  v           v vv    v       i  i --  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA--AC 201

  chr1_176019488_    472 AAAGCTGGAAAACTCACACTTCCCAATTTTAGA----------------- 504
                             i    ii                  i i -----------------
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_176019488_    505 -------------------------------GATAGACACATAGATGATC 523
                         -------------------------------        i      --- 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT---C 298

  chr1_176019488_    524 AATGTAAAAGAACTGAGAGTCCAGAAATAAACATTCACCTTTATGATTAT 573
                             v  v    i                   vivi  v      i i -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA- 347

  chr1_176019488_    574 TAATAATTGATTTTCGAAAAGGGTGCCAAGAA-A---AATGCGGAAAGAT 619
                         -----            v             v- ---    v       v
  L1M4_orf2#LINE/    348 -----ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_176019488_    620 TCTTCTTTTCAACAAATGGAGCTGGGACAACTGAATAGCCACATGAAAAA 669
                          vv                v             i   ?       v    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_176019488_    670 GCATGAAGATGGACCTGGAACTCACACCATATGTAGAAACTAACTCAAAA 719
                          v      v      ivv v            ii i   i          
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_176019488_    720 AGGATCAAATACCTAAAAATA----------------------TAGAAGA 747
                         v      ? v       vi  ----------------------       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_176019488_    748 AAACA-----------------GGCCTTGGACTAGACAATGACTTCTTAA 780
                              ----------------- i      ii   i     ii      i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_176019488_    781 A-----CACCAAAAGAACAATCAAGATTAGAAAATATAGAAAAACTATAT 825
                          -----         v    v   v vv      v     v   ----- 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA-----T 637

  chr1_176019488_    826 TGATAGATTCTATCAAAATTTAAGTCACTTTTGTGCTACAAAGAACACCA 875
                           ---  i ii         v  i--           v     i    i 
  L1M4_orf2#LINE/    638 TG---GACTTCATCAAAATTAAAA--ACTTTTGTGCTTCAAAGGACACTA 682

  chr1_176019488_    876 TCAAGAAAGTAAAACGACAACCCATAGAATGGGAAAAAAAAAAATTTGCA 925
                                   i   v         i         i    v ---      
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA---TTTGCA 729

  chr1_176019488_    926 AATC-------TGATTAGGGACTTGTATCCAGAATACATAAAGAACTCTT 968
                             -------    v                    i             
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_176019488_    969 ACAACTCAACATTAAAAAGACAAATAGGCCA 999
                                  i v              iv   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCA 810

Transitions / transversions = 1.18 (58 / 49)
Gap_init rate = 0.02 (16 / 807), avg. gap size = 8.06 (129 / 16)  

 252 21.59 6.82 0.00  chr1_176019488_176021701.rev     1636  1723 (490)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_176019488_   1636 AAAAAAAGGCAAAGTAACTGAACAGATATTTCTTTTAAAAAAA-----AA 1680
                              vi       v vi    i   i      iiv  i  i -----  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_176019488_   1681 A-GCCCAATAACCACACAAAAAGACACTCAACATCCCTGGCCAT 1723
                          - v       v    ii      ii         v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 3.00 (6 / 2)  


 823 27.65 0.46 0.00  chr1_176117380_176124749.rev     2639  2855 (4515)    L1M4_orf2#LINE/L1      147   364 (544)  

  chr1_176117380_   2639 CATAGAGAACCACAAAAGACCCCAAATAACCAAAGCAATCTTGTGCAAAG 2688
                             vi   vii   ii     vi    i     i        viv  ii
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_176117380_   2689 AGAACAAAGCAGGAGGCATCACACTACCTGACTTCGAAATTTACTACGAA 2738
                                  iv     vv       v  ii i   i   i       i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_176117380_   2739 GCCATAGTAAACAAACCAGCATGGTAATGGCATAAAAGCAGACATATAGA 2788
                           i i     v   iv   ii     v        iiii           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_176117380_   2789 CCAATGCAATAAAATATAGAACCTGGATATAAATTCATGCATATATAGCC 2838
                         i     v    i   vv   ii ii  v     ii   i   v   i i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_176117380_   2839 AACC-ATCTTTGACAAAG 2855
                           ii-  i  i     i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGG 364

Transitions / transversions = 2.53 (43 / 17)
Gap_init rate = 0.00 (1 / 218), avg. gap size = 1.00 (1 / 1)  

2332 23.27 17.65 1.53  chr1_176117380_176124749.rev     6098  6879 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176117380_   6098 TGGAAATATATTCCATGCTCATGGACTGGAAGAACTAATATTGTTAA-AT 6146
                               v    i     i       i       vi            -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176117380_   6147 GGCAATACTACCCAAAGAAATTTGCAGATTCAATGCCAGCCCTCTTAAAA 6196
                                  v      vvi  i i         i  v v    v i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176117380_   6197 TACCAATGGCATTCTTCACAGAATTTTTTTTTTAAATCCTAAAATCTATA 6246
                          v   iiv  v  i  ii     v  vvivvvivi          ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_176117380_   6247 TGGAACCACAAAAGGCCCCAAATAACCAAAGCAATCCTGTGCAAAAAGAA 6296
                              vii   ii i   vi    i     i     i  viv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_176117380_   6297 CAAAGCAGGAGGCATCACACTACCTGACTTCAAAATTTAGTACAAAGCCA 6346
                              iv     vv       v  ii i       i   v        i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_176117380_   6347 TAGTAAACAAATCGGCATGGTAATGGCATAAAAGCAGACACACAGACCAA 6396
                         i     v   iv i ii     v        iiii     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_176117380_   6397 TG-------------------------------------------CAA-- 6401
                           -------------------------------------------   --
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_176117380_   6402 -------------------------------------------------- 6401
                         --------------------------------------------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_176117380_   6402 -CAATAAA-------------ACTAGAC---------------------- 6415
                         -   i   -------------   i  i----------------------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_176117380_   6416 -----CCCCTATTTCTCACCATATACAAAAATCAAATCAAAATGGATTAA 6460
                         -----      ii  v                i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_176117380_   6461 AGACTTAATTCTAAGACCTGAAACTAAAACAACTCCTTGAAGAAAACGTT 6510
                             i   v v     v  i      v  -     i v         i v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACATA 549

  chr1_176117380_   6511 GGGGAAACACTCTAGGACATTGGTTTGGGCAAAGATTTTCCGTGTAAGAC 6560
                           ? v  vv  iiiv   v    v  i     v i   iiiivi  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_176117380_   6561 CTCAAAAGCACAGGCAACCAAAGCAAAAAGAAAGAAAAAGCAATTACATC 6610
                         vi          i     v    v     v i v   vv v v  -    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATC 648

  chr1_176117380_   6611 AAGCTACAAACCTTCTGCATGGTAAAGGAAACAATCAACAAAGTGAAGAG 6660
                           iv vv   v   i  iiivvi      v  v     v        i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_176117380_   6661 AAAACCTACAGAGATAG-AGAAAATATTTGCAAACTATCTATCTGATAAG 6709
                          v    i     -  i -                ii  v           
  L1M4_orf2#LINE/    699 ACAACCCACAGA-ATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_176117380_   6710 GGAGTTACAACCAGAATTTATAAGGAGCTCAAACAACTCAATAGCAAAAA 6759
                            v  ii v       v     i  i   vv           ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_176117380_   6760 AAAAAAAAGAGGAGATAGTCTGATTTTAAAATGGGCAAAAGATCTGAATA 6809
                         i v   ---------  ii ii   ?v            i   i      
  L1M4_orf2#LINE/    798 GACAAA---------TAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_176117380_   6810 GATATTTCTCCAAAGAAGACATACAAATGGCAAACAGGTATGTGAAAAAA 6859
                           i                i           v  i i i ii      i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_176117380_   6860 TGCTCAACATCAGTAATCAT 6879
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (104 / 75)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 15.00 (150 / 10)  


3073 27.92 0.66 0.55  chr1_176161094_176167547.rev     5058  5963 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_176161094_   5058 GGCAGAACACTCCATGTTCATGGATAGGAAGAATCAATATCGTGAAAATG 5107
                           v ii i ii              v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_176161094_   5108 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 5157
                           v     v     iv i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_176161094_   5158 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 5205
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr1_176161094_   5206 ATGGAACCAAAAAATAGCCCACATTGCCAAGACAATCCTAAGCAAAATGA 5255
                               viiv  iiv v  viv  v     i      i i iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_176161094_   5256 ACAAAGCTGGAGGCATCATGCTACCTGACTTCGAACTATACTACAAGGCT 5305
                               i      vv   ii  v  ii i   i  viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_176161094_   5306 ACAGTAACCAAAACAGCATGGTATTGCTATCAAAACAGATATATAGACCA 5355
                                i   i    ii     i  vi  v ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_176161094_   5356 ATGGAACAGGAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCA 5403
                               i  i i--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_176161094_   5404 TCTGATCTTTAAGAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5453
                         vi    i  ii v  ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_176161094_   5454 TATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAACCTG 5503
                          v  i  i              v     iv  ?   i   i i  ivv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_176161094_   5504 AAACTGGATCCCTTCCTTACACCTTATACAAAA-TTAATTCAAGATGGAT 5552
                           ii    i    v   i     v         -    i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_176161094_   5553 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5602
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_176161094_   5603 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGAACTTCATGACTAA 5651
                             ?i- v i -   iv   v v  vv i     viii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_176161094_   5652 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAA 5701
                         i            vvi          vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_176161094_   5702 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5751
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_176161094_   5752 AAGCAACCTACAGAATGGGAGAAAATTTTTAGAATCTACCCATCTGACAA 5801
                          ii     i                 v   iv  vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_176161094_   5802 AGGGCTAATATTCAGAGTCCACAAAGAACTTAAACAAATTTACAAGAAAA 5851
                         i  i  vi   i    i vi i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_176161094_   5852 AAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTTG 5901
                          i     i     v  i? v  i     i      v    i     i  v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_176161094_   5902 TCAAAAGAATACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5951
                           v      v i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_176161094_   5952 ATCAGTGGTCAT 5963
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (152 / 97)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 1.38 (11 / 8)  


2598 19.66 2.78 12.61  chr1_176194633_176200130      492  1498 (4000)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_176194633_   1498 TGAAGAGATAGACCATGTTCACAGATTTAAAGACTCCATATTGTTAAGAT 1449
                           i i     vv         ii    vi      iv             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_176194633_   1448 ATCAATTCTCCACAAACTGATCAATAGAT-----ATAATATCAATTAAAA 1404
                         iv    v    v    i     v i    -----ii   vi v  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_176194633_   1403 TCTCAGCAAGGTTTCTTGAGGAAATTGATAGGCTAATTATAAAAT----A 1358
                           i    vivv   i   vi        i i   i  iv      ---- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr1_176194633_   1357 TGGAAA-GCAAAGGACCTAGAATAGCC----TGATCTTGAAAAAAAA--- 1316
                               -    i     i         ----ii           i  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chr1_176194633_   1315 CAAATTTGGAGGATTTATATTACCTGATTTTAAAACTTATTACAAAACAA 1266
                             v        i i i i v  ii    i        i      i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chr1_176194633_   1265 TAGTAATGAAGGCAGTTTGGAGACGGTGACAATGTT-GACAAATGGATCA 1217
                         i      v   i    v   vivi  i- i  v v -    v  i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGACATATAGATCA 299

C chr1_176194633_   1216 ACAGAACACAACAGAATGTCCAGAA-TAATACCAAGACATATATGGTTAA 1168
                          ii   i v  iv  iv        -   -   v v    v      i  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCAA 348

C chr1_176194633_   1167 AAGGTTTTCAATCAAGATACAAAGGC-ATCTCAATAGAGAAAGTACAGCC 1119
                         vv i     i iv i i i v   i -  -     i i     v i  i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGTC 397

C chr1_176194633_   1118 TTTTCAGCAAATGGTGCTAAAACAATTGGATATCCAAATGCCACAAAATG 1069
                               i           iii    i      ?   v    v v i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chr1_176194633_   1068 AACTTGAATCCA-ACCCCAGCACCATATTTTTAAAAGTTAACTCAAAATG 1020
                           v   i i  v-   i  -        vi--    i             
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCA-CACCATATAC--AAAAATTAACTCAAAATG 494

C chr1_176194633_   1019 GGTCATAGACTTGAATATAATGCCTAAAACTCTAAAACTTCTAGAAGAAA 970
                          i   ?    i i   i   viv        v       ii         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chr1_176194633_    969 ACATAGGAGAAAATCTTTATGATGTTG--TTATGCAAAAATTTCTTTAGA 922
                                ? v       ii   iv   --   v    vii      -   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGA 593

C chr1_176194633_    921 TAGAATACCAAAAGCA-AGGTCTATAAAAGAAAAAAAATCAGAGATTGAA 873
                           vi i          - i - v i           v v- v i    i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAG-ATAAATTGGA 641

C chr1_176194633_    872 CTTCATCAAAATTAAGAACTTCTCTCTTTGAAAGACACTATAACTGGGCA 823
                                        i     -----------------------------
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTT----------------------------- 662

C chr1_176194633_    822 TGAGGTTCATGTCTGTAATCCTGGCTACTCTGGAGACTGAGGTGGGAAGA 773
                         --------------------------------------------------
  L1M4_orf2#LINE/    663 -------------------------------------------------- 662

C chr1_176194633_    772 TCACTTGAGCTCAGGAGTTCAAGTCCAGCCTACGCAACATAGTAAAATAC 723
                         ----   v   -------    --------------------- ii i  
  L1M4_orf2#LINE/    663 ----TTGTGCT-------TCAA---------------------AGGACAC 680

C chr1_176194633_    722 TATCTTAGGAAAAAAAAAAAAAGACAAATCACAGACTGAGAGAAGATATT 673
                             -----  i   ivi         vi      v  i     i     
  L1M4_orf2#LINE/    681 TATC-----AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

C chr1_176194633_    672 TTAAAATCATGTATCTGATAAAAGACTTGGTATCGAGAAAA-A-AAACAG 625
                          vv       i          ii      -    v    v - -   v i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAA 774

C chr1_176194633_    624 CTGTCTA-AACTCAATAATAAGGAAACAAACAAATCAAT-ACTAAACGGG 577
                           v -  -             ii i     i  vi    -?vv   i   
  L1M4_orf2#LINE/    775 CTCT-TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

C chr1_176194633_    576 TCAAAGATTTGAACAGACATTACACCACAGAAAATACATGGATTACAAAT 527
                         iv  i        i       v v   v    i   i iii  vi v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

C chr1_176194633_    526 ACACACATGAAAAGAAGTTCAACATCATTGGTCAT 492
                          vi            v i         ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (119 / 75)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 5.34 (155 / 29)  

2325 25.82 11.03 0.97  chr1_176194633_176200130     4181  5005 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176194633_   4181 TGGAAAAACATTTCATGCTCATGGATAAGAAGAATCAATATCATAAAAAT 4230
                               i i  ii    i        vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176194633_   4231 GGCCATACTGCCCAAAGCAGTTTATAAATTCGGTTCTATTCCTATCAAAC 4280
                            v     v      viii i  i i    iiiv v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176194633_   4281 TATCAA-TGTCATTCTTCACAGAATTTGAAAAA--AATATTAAAAGTTCA 4327
                          vi  i-  i -  i  ii     v    v  i--i  vi     -    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCA 148

  chr1_176194633_   4328 TATGGAACTGAAAGAGAGCCCAAATAGCCAAAGCAGTCCTGAGCAAAAGG 4377
                                v  v   i  v  vi          i  i  i   iv  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_176194633_   4378 AACAAAGCTGGAGGCATCACACTACCTTACTTCAAA-----CTATATAA- 4421
                                i      vv       v  iv i      -----   i v i-
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_176194633_   4422 TAAAGTAAACAAAACAGCATGGTACTGGTACAAAAACAGACATGTAGACT 4471
                           v     v   i    ii         i i  ii i      i    ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_176194633_   4472 AATGGAACATAATAGAAAACTTAGAAATATGGCTTCACACCTACCAACCA 4521
                                i v   v  i iiii       viv ivi   ii  i-iii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT-GGTCA 347

  chr1_176194633_   4522 TCTGATCTTCAACAATGCTGACAAAAACTAGCAAGGGGGAAAAGACTCCC 4571
                         vi    i   i    v v  v   i v vvv   v       ii ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_176194633_   4572 TATTCATTAAATGGTGCTGGGATAA------------------------- 4596
                          v    vi              i  -------------------------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_176194633_   4597 --------------------------------------------ATGGAT 4602
                         --------------------------------------------      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_176194633_   4603 TAAAGATTTAAATGTAAGACATCAAACTATAAAAATCTGGGAAAACAAGA 4652
                         i ?   ii           vv v           v   vi   i v  v 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_176194633_   4653 CTGGAAAATATTCTTCTTGACATTGACCTTGGCAAATAATTT-TTGGCTA 4701
                         iv  ?iv v  -    v    v   ivi v     - ii   -  i v  
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATA 595

  chr1_176194633_   4702 AATCTCCAAAAGCAGTAGCAACAAAAACAAAAATAGACAAGTGGGTCCT- 4750
                         viv v         vv          iv         i  i v  v i -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_176194633_   4751 -----AATTAAAGAACATCTGCACAG-AAAGGAAACTGTCATTGGAAA-- 4792
                         -----       -   v i  ii vv-      v   i   --i    --
  L1M4_orf2#LINE/    646 ATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCA--AGAAAGT 692

  chr1_176194633_   4793 -AACAGAAAACCTCCAGAATAGGGGAAGATATTTGCAAACTATGTGTCTG 4841
                         -  v   v    iv      i  i   i           ii  i i    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_176194633_   4842 ACAAAGGCCTAATATCTAGAATCTATAGGGAACTCAAACAAATCAACAAG 4891
                          i  i  v  vi    i     v    ii      vv    v    i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_176194633_   4892 CAAAAACCAAATAACCCACTT-AAAAATGGGCAAAGGATATGAACAGATA 4940
                         v    iv           v  -                 v    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_176194633_   4941 TTTCTCAAAAGAAGATACACAG-TGGCCAACAAACATATGAAAAAATTCT 4989
                               v          i   i-       i  i  i       i  v  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_176194633_   4990 CAGCATCACTAATCAT 5005
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (125 / 86)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 5.50 (99 / 18)  


 666 27.55 12.24 1.70  chr1_176201422_176203505      505   798 (1286)    L1M4_orf2#LINE/L1       94   418 (490)  

  chr1_176201422_    505 ATCAAGTTTCCAACAGTTTTTTTTTCA--ACTTGACAAACTGTCTCTAAA 552
                              iv i   i v ii      v  -- v       i   vii     
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_176201422_    553 AGCTGTTTTGGATATTCAAAGAACCAAGAATAGCTAACACACTTTTGAAA 602
                          -i vv v    v  v   i i   v        i  v   v i      
  L1M4_orf2#LINE/    144 A-TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_176201422_    603 A-------TAAGGTGAGAGGACTCAT-CCTCCCATATTTTAAA-CTTCTT 643
                          -------i  i  vi         i- i     -    i   -   vi 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACT 241

  chr1_176201422_    644 GTAAAGCTA----AACTGAAACAGCATGGTGTTAGTTCAAAGATGGACAA 689
                         ii       ----  iii i    ii    ii i ivi  i   i    v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_176201422_    690 CTATGTCAATGGAATCAAA---AAA---CAGAA------CCAAAAATTTA 727
                         v  vi          vi  --- i ---     ------   v v     
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_176201422_    728 TGGCC------TTTTATATAAGCATGGCATACAGA--ATT-AATGAGGAA 768
                            i ------    vv i   vi  v  ---   --   -    i    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCA---AGACCATTCAATGGGGAA 388

  chr1_176201422_    769 ATGATGAACTTTCCAATTAAAAATACTAGG 798
                          vi  iiv    i   iv  vii i  i  
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGG 418

Transitions / transversions = 1.70 (51 / 30)
Gap_init rate = 0.04 (14 / 325), avg. gap size = 2.93 (41 / 14)  

1213 28.45 5.94 0.85  chr1_176201422_176203505     1121  1591 (493)    L1M4_orf2#LINE/L1      414   908 (0)  

  chr1_176201422_   1121 CTAGGAATATTGGCTATCTATATAGGAGAGA-TGAAATGAGACTTTTACT 1169
                           i   vv i   v  ? i i  ivi i   -    i vi   iii   i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_176201422_   1170 TCACAC-------AAAAATCAATTCCAAATGGACTAGAAACCTACATGTG 1212
                               -------      i  i  v       ii ? i     v    i
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_176201422_   1213 AAAGTCAAAATTATAAAGCTTTTAGAAGACAATATC----TAA------- 1251
                          i  ii    i      i  i        v  i  v----   -------
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_176201422_   1252 -GATCTTGGGGGTAGGAAAATTTTTTTTAAGTAAGAGATAAGAAGCACTA 1300
                         -  i      v-    v  vvv   i   ii  v  v iv i      v 
  L1M4_orf2#LINE/    564 TGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_176201422_   1301 ACT-CAAAGGGAAAAGGTTCATAATTTTGATTACCTTAAATTTAAGAATT 1349
                         i v-    i i    i- vv    v  v  i v v i   v    i  i 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_176201422_   1350 ATTTTTG--TCAAGAAAATACCATTAAAACA-----AAAACAATCCACAA 1392
                         -   v  --    - ii i  i  i  i v -----  i    i     i
  L1M4_orf2#LINE/    662 -TTTGTGCTTCAA-AGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_176201422_   1393 AATGGGAGACTGTATTTGCAACACTTATAACTGACAAAGGACCAGTATCC 1442
                                  vvi         vv v    v    i  i    iv      
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_176201422_   1443 AGAATAGAAAATGACCTTCTAGGAATCAATATTATAAAAATACACAACCC 1492
                               v v  v  v  ii  vi v      v  v   i i v i     
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_176201422_   1493 AATAGAAAAATGGGCAAAAAGCCTGAATGTATACCTCACCAAAGAGAAAA 1542
                            v?             iiiii     iv i ii  v       ii v 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_176201422_   1543 TCCCAATGGTTGACATACTTATGAAAAGCTGCTCAATTTCATAAGTGAT 1591
                          v v     iii i vi vi        v       iv   ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (77 / 54)
Gap_init rate = 0.02 (11 / 495), avg. gap size = 2.91 (32 / 11)  


3172 26.90 0.33 0.22  chr1_176212106_176216387.rev     2885  3791 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176212106_   2885 TGGAAACACACCCCAAGCTCACGGATGAGTAGAATCAATACTGTGAAAAT 2934
                               v i i    v i   i    vi v   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176212106_   2935 AGCCATACTGCTAAAAGCAATCTACAAATTCAATGCAATCCCCATCAGAA 2984
                         i  v     v iv   vii       i      i        i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176212106_   2985 CACCA-CTATCATTCTTCACATAATTAGAAAAAAAAATTCTAAAATTCAT 3033
                         iv   -  ii -  i  ii  v  v v  v  ivvi  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_176212106_   3034 ATGAAACCAAAATAGAGCCCGCATAGCCAAAGCAAGACTAAGCATGAAGA 3083
                            i  viiv  vi  v  v v         i   vvi i iv v     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_176212106_   3084 ACAAATCTGAAGGCATCGCACTACCTGATTTCAAACTATACTATAAGGCC 3133
                              vi  i   vv  i    v  ii        viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_176212106_   3134 ATAGTAACCAAAACAGCATGGTACTGGTATAAAAACAGGCATATAGACCA 3183
                          i     i   i    ii         i    ii i  i        i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_176212106_   3184 ATGGAACAGAATAGAGAACCCAGAAATAAATCCAAATACTTATAGCCAAC 3233
                               i     v    ii           i   v i i    i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_176212106_   3234 TGATCTTCAACAAAGCAAACAGAAACATAAAGTGGGGAAAGGACACCCTT 3283
                             i   i    i vviv  ii v   vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_176212106_   3284 TTAAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAACGAA 3333
                           v                 i  i   v  ?       i ii    i   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_176212106_   3334 ACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTA 3383
                         ii    i  ii i   v    v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_176212106_   3384 AGGACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAC-ATAACATT 3432
                         ?i   i     v     v  i           v ii    v- v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_176212106_   3433 GGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGATTTCATGACCAAGAA 3482
                           ?iv  vi    vv   v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_176212106_   3483 CCCAAAAGCAAATGCAATAAAACAAAGA-TAAATAGCTGGGGCTTAATTA 3531
                         v         v v    i    v   i -  i   iv v  i   v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_176212106_   3532 AACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAGA 3581
                           v v  i i      ii vv    i iv  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_176212106_   3582 CAACGCACAGAGTGGGAGAAAATCTTCACAATCTTTACATCTGACAAAGG 3631
                             v      i           v  ii   viiv  i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_176212106_   3632 ACTAATATCCAGAATCTAAAACAAACTCCAACAAATCAGCAAGAAATGAA 3681
                            vi          v  v  vi     iv    v   ii  v   -i i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAG 798

  chr1_176212106_   3682 ACAAACAATCACATCAAAAAGTGGGCTAAGGACATGAATAGACAATTATC 3731
                              i  i vv  i?    i     v     iv          v  v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_176212106_   3732 AAAAGAAGAGACACAAATGGCCAACAAATATATGAAAAAAAGCTCAGCCT 3781
                         v        v i            i  ii i       i v     i v 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_176212106_   3782 CACTAATGAT 3791
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


3127 27.23 1.79 0.45  chr1_176236266_176242753.rev     5102  5997 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176236266_   5102 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5151
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176236266_   5152 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCTATCCCCACCAAGT 5201
                            v     v     iv i  i ii        i  v     i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176236266_   5202 TGCCACTCACTTTCTTCACAGAATTGGAAAAATCTATTTTAAATTTCATA 5251
                          v   viii i  i  ii     v v  v  iiiv  ii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_176236266_   5252 TGGAACCAAAAAAGAGTGCACAGA---GCCAAGACAAGCCTAAGCAAAAA 5298
                              viiv  ii  --- v    ---     i    v i i iv  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_176236266_   5299 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5348
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_176236266_   5349 CTACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5398
                             i    i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_176236266_   5399 CAACGGAACAGAACAGAGGCCTCCGAAATAACACCACACATTTACAACCA 5448
                            i    i    iv   ivii v       vv   i       iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_176236266_   5449 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATTCCC 5498
                         vi    i  i     ivv  v   i v  vv      i     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_176236266_   5499 TATTTAATAAACGGTGTTGGGAAAACTAGCCAGCCATATGCAGAAAGCTG 5548
                          v  i  i   i    i     v    i vi ?   i     i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_176236266_   5549 AAACTGGATCTCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 5598
                           ii    i i  v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_176236266_   5599 TAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAATAAAACC 5648
                         i ?    i           v       i      vi i     v     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_176236266_   5649 TAGGCA-ATACCACTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5697
                             ?i- v i -i  iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_176236266_   5698 AACACCAAAAGCAATAGCAACACAAGCCAAAAGAGACAAATGGGATCTAA 5747
                         i            vv       v   vv    v   i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_176236266_   5748 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAGCAGACTAAA- 5796
                          i   v v  i i   i  ii vv    i  v       iv i v i  -
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_176236266_   5797 ----------CAGATTGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 5836
                         ----------    v           v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_176236266_   5837 AGGGCTAATATCCAGAATCTACAAAGAACTTCAACAAATTTACAAGAAAA 5886
                         i  i  vi          v  i        iiv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_176236266_   5887 AAGCAAACAACACCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5936
                          ii    i   v v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_176236266_   5937 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAA-ATGCTCATT 5985
                           v        i  vi viii     i ii          -       vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_176236266_   5986 ATCACTGGTCAT 5997
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (148 / 92)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 3.33 (20 / 6)  


3126 27.51 0.77 0.44  chr1_176266611_176273489.rev     5484  6388 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176266611_   5484 TGGGAGAACATTCCATGCTCATAGATAGGAAGAATCAATATCATGAAAAT 5533
                            i ii i  i     i    i   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176266611_   5534 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5583
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176266611_   5584 TACCAATGACTTTCTTCACAGAACTTGAAAAAACT-ACTTTAAAGTTCAT 5632
                          v   iivi i  i  ii     v    v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_176266611_   5633 ATGGAACCAAAAAAAGAGCCCACATT-GTCAAGACAATCCTAAGCAAAAG 5681
                               -- viv  i ii    v v - i   i      i i iv  i i
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_176266611_   5682 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5731
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_176266611_   5732 CTACAGTAACCAAAACAGCATGGTATTGCTACCAAAACAGAGGTATAGAC 5781
                                  i   i    ii     i  vi iv ii i   vi      i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_176266611_   5782 CAATGGAACAGAACAGAGGCCTCAGAAATAACACAACACATCTACAACCA 5831
                                 i    iv   ivii         vv v i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_176266611_   5832 TCTGATCTTTGACAAACCCAACAAAAACAAGCAATGGGGAAAGGATTCCC 5881
                         vi    i  i     ivviiv   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_176266611_   5882 TATTTAATAAATCGTGCTGGGAAAACTGGCTACCCAAACATAGAAAGCTG 5931
                          v  i  i    v         v      v  ?   v iii i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_176266611_   5932 AAACTGGATCCCTTCCTTACACCTTACACAAAAATTGATTCAAGATGGTT 5981
                           ii    i    v   i     v  i         i i    i    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_176266611_   5982 TAAAGACATAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 6031
                         i ?    v       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_176266611_   6032 TAGGCA-ATACCGTTCAGAACATAGGCATGGACAAGGACTTCATGACTAA 6080
                             ?i- v i -   ivi  v v  vv i i   v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_176266611_   6081 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 6130
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_176266611_   6131 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAGCAGAGTGAAC 6180
                          i   v v  i i   i  ii vv    i  v       iv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_176266611_   6181 AGGCAACCTACAGAATGGGAGAAGATTTTTGCAATCTACCCATCTGACAA 6230
                           i     i              i  v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_176266611_   6231 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 6280
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_176266611_   6281 AAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 6326
                          i    ----   v  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_176266611_   6327 TCAAAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAATACTCATC 6376
                           v        i  vi viii     i ii          i  i    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_176266611_   6377 ATCACTGGTCAT 6388
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (153 / 92)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


 680 21.97 3.14 5.83  chr1_176297344_176300975.rev     1673  1895 (1737)    L1M4_orf2#LINE/L1        5   221 (687)  

  chr1_176297344_   1673 AAGATATACCATGCTTTTGAATCAGCAGACTTGATACTGTTAAGATGTCA 1722
                                v     i iv  i  ii v      i   i          v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_176297344_   1723 TTTTCCCCCCAAACATATCTATAGATCCAATGTGATTCTAATGAAGATCA 1772
                         v v- i       ivv     i    i   i ii  i iv  v  i   v
  L1M4_orf2#LINE/     55 ATA-CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_176297344_   1773 CAATCTTATTTATTTCTGGCAGAAACTGACAAGTTGATTTGTATCAAATT 1822
                           i-  vvi  v   ---       i       i    ii-  --     
  L1M4_orf2#LINE/    104 CAG-CTGCCTTTTTT---GCAGAAATTGACAAGCTGATCC-TA--AAATT 146

  chr1_176297344_   1823 AAATGTATCTGCAAATGCAA---ACCTAGAATATCCAAAGCACTTTTGAA 1869
                         -----i  v  v        ---   i      v     i  v i     
  L1M4_orf2#LINE/    147 -----CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_176297344_   1870 AAATAA---CAAAGTTGCAAGACTTA-ACT 1895
                            v  ---        v i    i -   
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACT 221

Transitions / transversions = 1.45 (29 / 20)
Gap_init rate = 0.04 (9 / 217), avg. gap size = 2.22 (20 / 9)  

 507 25.24 26.86 0.65  chr1_176297344_176300975.rev     2243  2551 (1081)    L1M4_orf2#LINE/L1      238   627 (281)  

  chr1_176297344_   2243 TATTATAAAGCTACAGGAATAAAGATAGTACAGTATTGGCA--AAAACAG 2290
                           i  i          v   v    i   iii   i     -- ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_176297344_   2291 AAATGTAGATAAATGGACCTGAAC--AGAGTCTCAAAATAGAACTACACA 2338
                          v  i     v      viv   i--      ivi     i v i i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_176297344_   2339 TGTGTGAGGTGAATGGA-----------GGTGCCAA----ATT-AATAAG 2372
                          v i  --  v   v  -----------        ----   -   ii 
  L1M4_orf2#LINE/    338 TTTATG--GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_176297344_   2373 GAA-------------------------------TAACTG----TCTATA 2387
                            -------------------------------i     ----? i i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_176297344_   2388 TGCAGAA-----AACTTTGATCCATGCCTGGTACCTTAGGCAAAT-CTGG 2431
                             i  -----  v  v  i  v i   vii   v  vi    v-i ii
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_176297344_   2432 CTTGAAATGGATAATATACCTAAATATAAGAACTGAAAACATAAAACTTC 2481
                           ii        v ? v        i     i  i   vi        ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_176297344_   2482 AAGAA--AAACGTAGGAGAAAAACTT-GTAAC-TTCGATTAA--AAT--- 2522
                         v    --    i    ? v   v   -  i  -  v i   i--   ---
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_176297344_   2523 CCATTAGATAGG------------CAAG-AATAAAAGAAAAA 2551
                         iiv       v ------------    -  i          
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

Transitions / transversions = 1.78 (48 / 27)
Gap_init rate = 0.04 (17 / 390), avg. gap size = 5.00 (85 / 17)  

 952 20.85 6.36 1.06  chr1_176297344_176300975.rev     2859  3141 (491)    L1M4_orf2#LINE/L1      611   908 (0)  

  chr1_176297344_   2859 AAGAAAAGAAAGAAAAATATGAATAAATTAGACTGTATCAAAATTAAAGA 2908
                            v  vi         -  ii       i    vi            i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_176297344_   2909 CTTTT---CCACAACAGACAGGATTAAGGAAATGAAGAAGCAAAC-ATCG 2954
                              --- iv   vi    vv  i   i  i    i ii   v - iv 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_176297344_   2955 GCCAGGAGAAAATATTTACAAAACACGCCTCTGATAAGG-ACTTACATCT 3003
                         ivii             i    v  iiiv          -    ii   i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_176297344_   3004 AGAATATGTAAA---TTTTTCCAATTCAATAC---AATGACAA----CAC 3043
                                i    ---i i  v   i      v---  v     ---- v 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_176297344_   3044 AGTTTTATAAAATGGGCAAAATATTTGAATAGACA---CTTCAAAAAGGA 3090
                          i  ?- -            iv             ---  i    i i  
  L1M4_orf2#LINE/    810 AATTW-A-AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_176297344_   3091 AATACAAATGGCAAACACGCATGTGAAAAGATGCTCAACATTATCATTAG 3140
                         v           v  i v   ii                  i ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_176297344_   3141 A 3141
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.90 (38 / 20)
Gap_init rate = 0.03 (10 / 298), avg. gap size = 2.10 (21 / 10)  


3001 23.15 3.88 3.43  chr1_176306483_176308790.rev      915  1817 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_176306483_    915 GGATAATTATTCCATGTTCATGGATAGAAAAACTCAATATTGTCCAGATG 964
                            v iv   i              v i  i   i        iv     
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_176306483_    965 TTAGCTCTTCCCAACTTGATTTATAGATTCTATTCAATCCCAAACAAAAT 1014
                         vi iiv  i     v     i  i      v iv       v v      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_176306483_   1015 CTCAGCAAGTAATTTTGTGAATATCAACAAACTGATTCTGAAGTTTATAT 1064
                          i    vivivv     iii v  ii    i     i  i  i  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_176306483_   1065 AGGAG-GCAAAAGATCCAGAATAGCCAACAAAATATTGAA------GAAT 1107
                         i i i-    ii  i             v v   v     ------   i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_176306483_   1108 AAAGCCAGAGGATTGACACTACCCAACTTCAAGACTTATTGAAAAAGCTA 1157
                             iii     i v     v     i     i     i - v       
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT-ACAAAGCTA 250

  chr1_176306483_   1158 CAGTAACCAA-ATAGTGTGGTACTGGTG-AAAGA---ACAAATAGACCAG 1202
                               i   - i             ii-  i  ---   v     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_176306483_   1203 TGGAACAGACTAGAGAACCTAGACATAGACTCACATAAATACAGTGAACT 1252
                              i   v v    ii i   v   i  i  i i vv  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_176306483_   1253 GATCTTTGATAAAGGAGC-AAAAGCAACCAATGAATCAAACATAGTCTTT 1301
                            i  i  i  i  v  -  i v  vi     iivv  iv         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_176306483_   1302 TCA-CAAATGGTACTAG---AATTGAACATCCACTTGCAAAAAAACCCAC 1347
                            -        i  i ---  i  i i ?    v       i  i----
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT---- 446

  chr1_176306483_   1348 AAAAACGACCCCACACACACATATCTAGACCTTACACCCTTCACAAACAT 1397
                         i  ivi iv   ------------   --   i     v vi     v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCC------------CTA--CCTCACACCATATACAAAAAT 482

  chr1_176306483_   1398 TAACTTAAAATGGATCATAGACCTAAATGTGAAATTCAAAACTATAAAAC 1447
                              i           ?            i i vii             
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_176306483_   1448 TCTTTGAAGATAACATAAGA-TAACACTAGCTGACTTTGGATAAGGCGAT 1496
                             v     v      i ?-   vv  vvv    i    i v    i  
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_176306483_   1497 GAGTTTCT-AGAAACAACACCAAAGGCACAATACATGAAAGAAATAATTG 1545
                          -      -   v ii        i      vvv ii       v   v 
  L1M4_orf2#LINE/    583 G-GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_176306483_   1546 ATTGCCTGGTCTT----AAGATTAAAAACTACTT---CTCTGTAAGACAA 1588
                           vivi   v   ----  i          -i  ---  iiiv i    v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACT-TTTGTGCTTCAAAGGACAC 680

  chr1_176306483_   1589 -GTCAAAAGATTGAGAA-ATAAGCCACAGAATAGAAGAAAATATTTGCAA 1636
                         -i    i i v   i  - i  v         i i               
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_176306483_   1637 G--ACACATCTGATAAAAGACTATTATTAAAAACAAAACAAAACAAAGAA 1684
                         i-- i i         ii    vv   i-----  i  i v -i      
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATC-----CAGAATATA-TAAAGAA 774

  chr1_176306483_   1685 CTCTTAAAACTCAGCAATAAGAA-----ACAATCCAATTTTTAAAAAATG 1729
                               v      ii     i  ----- i  i      ?---       
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW---AAAAATG 821

  chr1_176306483_   1730 GGCAAAATACCTGAACAGACCTCTCACTAAAGAAGATATACCAGATGGCA 1779
                               iv ii    i    v i  v i             - i     v
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC-AAATGGCC 870

  chr1_176306483_   1780 AGTAAGCATATGAAAAGATGTTCAATATCATGTCATGA 1817
                          i      i           i    i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (134 / 71)
Gap_init rate = 0.03 (26 / 907), avg. gap size = 2.54 (66 / 26)  


 530 24.74 18.56 0.00  chr1_176356477_176358717.rev      664   857 (1384)    L1M4_orf2#LINE/L1        1   230 (678)  

  chr1_176356477_    664 TGGGGAGATACACCATGTTCATGGACT--AAAGC---AT----------- 697
                            ii     iv             i --  ii ---  -----------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176356477_    698 --CAACTTTCCTCAAAATTATCTATATATATAACACAACTCCAATCAAAA 745
                         --   ivi   i    v v     i v  vi   i   ii  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176356477_    746 TCTCAGGT---------------ATAGATAAGCTGATTCTAAAATTTACA 780
                           i   v ---------------  v  i        i        i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_176356477_    781 AGGAAAGAAAAAGGAACCAAAATATTAAAAACAATTTTGAAAAAGTA--- 827
                         v     viv  i   v   i    viv        i         v ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_176356477_    828 TAAAATAGGAGGAATCATACTACCTGATTT 857
                         i   i v      v   i   v  ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTT 230

Transitions / transversions = 1.53 (29 / 19)
Gap_init rate = 0.02 (5 / 230), avg. gap size = 7.20 (36 / 5)  

1816 23.70 17.82 1.01  chr1_176356477_176358717.rev     1156  1750 (491)    L1M4_orf2#LINE/L1      214   908 (0)  

  chr1_176356477_   1156 CCCATACTACCTGATTTTAAGAGGTACTATGTAAGTCTACAGTAATCAAG 1205
                          i  i   v  ii    i  i vv     ii-   -              
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACA-AAG-CTACAGTAATCAAG 261

  chr1_176356477_   1206 ACAATGTGGTAGTGATGAAGAGACAAACATATAGGTCACTGGAGAAGAAT 1255
                            i       v  iiiv ii  i i        i   v    iv     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_176356477_   1256 ATAGAGTCTAGAAATAGACTTACAGAAATATGGACAATTGATTTTTGATA 1305
                         vv      i       i  ii i v vv     v           i  i 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_176356477_   1306 AGGCTTCAAAGACAATTCAATGGAGATAGGATAGTCTTGTCAACAAAGGA 1355
                            v v v     v         i  v  i        v        v i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_176356477_   1356 TGCTGGATCAGTTGGACATCCACATGTAACAAAATGAAACCTAACCTAAA 1405
                               iv  ii    i ?       i  v i      iiivi   ivv 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_176356477_   1406 TTTCATGCCTTATACTAAAATTAACTCAAGATG----------------- 1438
                         ii   ii  v     v             i   -----------------
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_176356477_   1439 ---------------------TCTT------------------------- 1442
                         ---------------------    -------------------------
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_176356477_   1443 -----------------------------------GATACTGGAAACACT 1457
                         -----------------------------------  i  iii  i   v
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_176356477_   1458 GTCCATAATAGAAAACAAGTTGATACGTTAGGTTTTTTCAAAATTAAAAA 1507
                         iv v i  v      -- i v    vi  i ii  iv             
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAA--AATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_176356477_   1508 CTTCTGTAT---GAAAGACACTATCAAGAGAATGAAAAGACAAGCTACA- 1553
                            i   ii---i  i             i i           v i   -
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_176356477_   1554 AGTGAGAAAATATTTTTGAAAATCACATTATTTGACAAAGAACTAGTATC 1603
                          i  i  i  v  v    v      i  -  i   i  i i   v     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGGGACTTGTATC 758

  chr1_176356477_   1604 CTGAATATATAAAGAACTCTCAAAACTCAAGAGTAAGAAAACAA----CC 1649
                          v                  i v       v i   i  i    ----  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_176356477_   1650 CAATCAAAAAAATGGGAAAAAGACTTCAACAGAAATTTCACCAAGAATTG 1699
                             i?     -    v   i  i  v  i   v     v    ii vvi
  L1M4_orf2#LINE/    809 CAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_176356477_   1700 TGTATAGATGACAACTAAGCACATGAAAAGATGTTCAACATCATTAATCA 1749
                          i  i i   i v v                  i         ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_176356477_   1750 C 1750
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.78 (89 / 50)
Gap_init rate = 0.01 (10 / 695), avg. gap size = 11.20 (112 / 10)  


3063 16.77 7.70 0.15  chr1_176365323_176366976.rev      502  1163 (491)    L1M4_orf2#LINE/L1      197   908 (0)  

  chr1_176365323_    502 AGAA-AAAGTTTGAGGACTCAGATTTCCTGACTTCAAAACTTATTAAATA 550
                             -      v         v i    ii i           i  v v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_176365323_    551 GCTAGAGTAATCAAGACAATGTGACGCTGGTATAGGAACAGACACATAGA 600
                             v             i    iii    i   i i i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_176365323_    601 ------GAATAGGATTAAGAATCCAGAAATAAACCC-TATCTTTATG-TC 642
                         ------      i   i   i               -  iv      -  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_176365323_    643 AGCTGATTTTCAATAAGGATGCCAAGACAATTCA-TGGGGAAAGAATCAT 691
                          ii        i i    i         v     -            vi 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_176365323_    692 CGTTTCAACAACTAGTGCTGGTACAGCTGAATGTCCACATGCAAAAGAAT 741
                          v         v i       v   i   i  i?                
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_176365323_    742 AAAGATGGACTC-TATCTCACACCATA-ACAAA--TTAACTCAAAATGGA 787
                         i   v     i -  i           -     --               
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_176365323_    788 TCAAAGGCCTAAATGTAAGAGCTAAAATTATAAAATGCTTAGGTGAAAAC 837
                            ?  i                    i       iv     iv      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_176365323_    838 ACAAGTGTAAATCTTTGTAACTTTTGGTCAGACAATGGCTTATTAGGG-- 885
                          i i ?         i  i  i  v   i  i      i  v    iv--
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_176365323_    886 GAGACCAAGAGCTCAAGCAACCAAATAAAAAA---ATCGATTGGATTTTA 932
                           v     i   v        v   v      ---  vi      i  i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_176365323_    933 TTAAAA--ACAAACTTTTGTGCTGCAATGGACACCATTAAG----TGAAA 976
                          i    -- v             v   v      i  i   ----     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_176365323_    977 AAGAAAA---ACAGAAGAGTAGAAAAT--TTGAAAATAATATATCTCATA 1021
                          -  v  ---      vi v       --   v    v        v   
  L1M4_orf2#LINE/    697 A-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_176365323_   1022 AGGGACTTGTA--------ATATGATATTTTCTTATATCTGAATAACAAA 1063
                                    --------    i vivvi     i v  v     i   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_176365323_   1064 A-GACAA----CCTACTTTTAAAATGGGCAAAGGATCTGAATA----TCT 1104
                          -     ----  i v  ?v                i      ---- i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_176365323_   1105 TGTCAGAGAAGATA----AATCACCAATAAGCACATGAAAAGACACCCAA 1150
                         ivi  i        ----   vi                    ii i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_176365323_   1151 CATCATTAGCCAT 1163
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (67 / 40)
Gap_init rate = 0.03 (20 / 712), avg. gap size = 2.60 (52 / 20)  


3060 25.70 2.82 0.45  chr1_176370954_176377681.rev     3646  4532 (2196)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176370954_   3646 TGGAAACACATCTCATGCTCGTGGATGGGTAGAATCAATATTGTGAAAAT 3695
                               v i   i    i  i     v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176370954_   3696 GATCATACTGCCAAAAGCAATCCACAAATTCAGATCAATTCCCATCAAAA 3745
                          iiv     v  v   vii   i   i     ivv    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176370954_   3746 TACTACCATCATTCATCACAGAACTAGAAAAAACAATCTTAAAATTCATA 3795
                          v i v vv v  iv ii     v v  v  ivii   i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_176370954_   3796 TGGAACCAAAAAAGAGCCCACATAGCCAAAACAAGACTAAGCAAAAAGAA 3845
                              viiv  ii  v  viv             vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_176370954_   3846 CAAATCTGGAGACATCACATTACCTGACTTCAAACTATACTATAAGGCCA 3895
                             vi     ivv     i v  ii i      viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_176370954_   3896 TAGTTACCAAAACAGCATGGTACCGGCATAAAGATAGGCACATAGACCAA 3945
                         i   v i   i    ii      i       i     i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_176370954_   3946 TGGAACAGAATAGGGAACCCAAAAACAAAGCCAAATACTTACAGCCAACT 3995
                              i     v i  ii   i   i   v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_176370954_   3996 GATTTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTAT 4045
                               i     i vviv   i v   vv i         i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_176370954_   4046 TCAACAAATGGTGCTAGGATAATTGGCAAGCCACATGTAGAAAAATGAAA 4095
                                        i   i  i   vv ?       i i  i      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_176370954_   4096 TTAGATCCTCATCTCTCACCCTATATAAAAATCAACTCAAGATGGATCAA 4145
                           i  i  ii i   v    v    i      i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_176370954_   4146 AGACTTAAATCTAAGACCTGAAACCTTAAAAATTCTAGAGTATAACATTG 4195
                             i     v     v  i    iv     v ii    iv v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_176370954_   4196 GAAAAACCCTTCTAGACATTGGCTTAGGCAAATAATTCAT--GATCAAGA 4243
                          ?iv  vi    vv   v    v        - ii  iv --   - v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT-ATGA 598

  chr1_176370954_   4244 ACCCAGAAGCAAATTCAACAAAAACAAACATAAATAAATGGGACTTAATT 4293
                         vv   i     v vv        iv   v   i      v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_176370954_   4294 AAACTAAAAAGCTTCTGTACAGCAAAAGAAATAATCAGCAGAGTTAACAA 4343
                            v v    i   i   i vv    i  v iv    iv i   v  -  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA-AA 697

  chr1_176370954_   4344 GACAACCCACAGAATGGGAGAAAATCTTCACAATCTATACATCCAACAAA 4393
                                                  v  ii   vii   i   ii i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_176370954_   4394 GGACTAATATCCAAAAATCTACAAAGAACTC---------AGCAAGAAAA 4434
                              vi      i  - v  i         --------- ii  v    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAA-TATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_176370954_   4435 AATGAAACAATCC--------------CAAAGGACTTGAATAGACAATTC 4470
                          ivv   i  i  --------------       i           v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_176370954_   4471 CCAAAAGAAGATATACAAATGGTCAACAAGCATATGGAAAAATGCTCAAC 4520
                         i v                   i   i     i   i   i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_176370954_   4521 ATCACTAATTAT 4532
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (133 / 92)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 4.14 (29 / 7)  

2643 22.55 10.78 1.49  chr1_176370954_176377681.rev     5433  6239 (489)    L1M4_orf2#LINE/L1       27   908 (0)  

  chr1_176370954_   5433 TGGATAGACTTAATATTGTTAAGATGAGAATTCTCCTCAAATTGATCTAC 5482
                             -                     iv   v    i             
  L1M4_orf2#LINE/     27 TGGA-AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chr1_176370954_   5483 AAACTTAAATTTAAAAAATCAGATCAAAATCTTAGCAGGCTTTGT-GCAG 5531
                          i i i  vvi----  vi vv         ii   v v    v -    
  L1M4_orf2#LINE/     76 AGATTCAACGC----AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAG 121

  chr1_176370954_   5532 ATACTGACAAGCTAATTCTAAAATTTATGTGAAAAT-CAAAGGACCTATA 5580
                          v i         i  i        i  i  i    -   i     i v 
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr1_176370954_   5581 ATAGC-AAAACAA-CTTGA----GAAAAAGAAAGTTGGAGGACTAACATT 5624
                              -       -     ----   i  v              v   i 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_176370954_   5625 ATGTGATTTCAAGACTTATTATAAAGCCATGGTAATTAAGATAGTA--GT 5672
                         vivii       i     i  i     i ii     i    i   i--  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_176370954_   5673 AC------AAAAACAGACATATAGACCAAGAGGACAAAATGGAAATTTTA 5716
                           ------  ii i           i   vi i i i   v  i v ii 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_176370954_   5717 GAAACAGATCCTCACAAATACAGCCTATTGACTTTTGGCAAAGGTGTCAA 5766
                             i i i  vi   vv  ii i v     i   i i   i    i   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_176370954_   5767 GGCAATTTACTGGAGA-----TAGTCTTTTCAACAAATGGTGCTGGAACA 5811
                          i v   i v   i  -----                         i   
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_176370954_   5812 AATGGACATTCAGATGCAAACAAAATAAACATTGATCCTCACATCATACC 5861
                          v    i ?i  v       - i   i  vv v  i  ii  v   i   
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAA-AGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_176370954_   5862 CTATACAAATATTAACTTGAATTGGATCTCAGACTTAAA----------- 5900
                         v        v       ii  v      v?    i    -----------
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_176370954_   5901 --ACTACAAAAATTTTATAAGAAAATGTAGGAGAAAATCTTAGTTAT-TT 5947
                         --    i    v i   v       ii    ? v       v  v i-  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_176370954_   5948 GAGTTAAA----GATTTCT-AAACAAGATACACAAAGCTCAAATTGTAA- 5991
                          i    ii---- i     - i i v  i  vv     v   --- i  -
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA---GCAAC 617

  chr1_176370954_   5992 AGAGAAAAAAATCAATAAACTGGACTT----------GAAAACTTTTGCT 6031
                          i ii       vi     i       ----------i          iv
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_176370954_   6032 CTTCCAAAGATACTA------------AAAGGCAAGCCACAGACTGGAGG 6069
                             v  i  i    ------------    i   v       v   ii 
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_176370954_   6070 AA--TATTT---------ATACCTGACAAAGAATGTGTATACAGAACA-- 6106
                           --     ---------   i    i  i i iv     v     i --
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_176370954_   6107 --AAGAACTTCTACAG----GTAGGTAAGAAGA----TAACCCAATTTAA 6146
                         --       ii    i----i  i-   i    ----          ?  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAA 816

  chr1_176370954_   6147 AAAGTAAATAAAT-ACTTGAACAGGCACTTAGCTAAAGAAGATATATGAA 6195
                            - iiii   v- i     i  i  i  vv i            ii  
  L1M4_orf2#LINE/    817 AAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_176370954_   6196 TGGCAAATAAGCACACAAAAAAGATGGTGAACATTGTGGTAAAC 6239
                             v          ii    -    v v     ii????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (121 / 57)
Gap_init rate = 0.03 (28 / 882), avg. gap size = 3.54 (99 / 28)  


3137 27.41 1.00 0.22  chr1_176385091_176391492.rev     5011  5911 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176385091_   5011 TGGAAGAACAATCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAC 5060
                              ii i vi     i        v      v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176385091_   5061 GGCCATACTGCCCAAGGTAATTTATAGAGTCAATGCCATCCCCATCAAAC 5110
                            v     v     iv i  i  i   v    i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176385091_   5111 TACCAATGACCTTCTTCACAGAATTGGAAAACACT-ACTTTAAAGTTCAT 5159
                          v   iivi    i  ii     v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_176385091_   5160 ATGGAACCAAAACAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGA 5209
                               viiv  vi  v  v v  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_176385091_   5210 ACAAAGCTGGAGGCTTCACGCTACCTGACTTCAAACTATAC--CAAGGCT 5257
                               i      vi    i  v  ii i      viv   --   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_176385091_   5258 ACAATAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGATATAGACCA 5307
                            i   i   i    i          i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_176385091_   5308 ATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATCTATAACCATC 5357
                               i    iv   ivii         vv   i    i   iii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_176385091_   5358 TGATCTTAGACAAACCTGACACAAACAAGAAATGGGGAAAGGATTCCCTA 5407
                             i  v     ivv  v  vi v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_176385091_   5408 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 5457
                           i  i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_176385091_   5458 ACTGGATCCCTTCCTTACACCTTATACAAAAACTAATTCAAGATGGATTA 5507
                         ii    i    v   i     v          i   i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_176385091_   5508 AAGACTTAAATATTTGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5557
                         ?    i     i vv  v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_176385091_   5558 GGCA-ATACCATTCAGGGCATAGGCATGGGCAAGGACTTCATGTCTAAAA 5606
                           ?i- v i -   iv i v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_176385091_   5607 CACCAAA-GCAACGGCAACAAAAGCCAAAATTGACAAATGGGATCTAACT 5655
                                -   vvi          vv     v  i    v   ii v ii
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_176385091_   5656 AAACTAAAGAGCTTCTGCACAGCAAAAGAGACTACCATTAGAGTGAACAG 5705
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_176385091_   5706 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAG 5755
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_176385091_   5756 GGCTAATATCCAGAGTCTACAAAGAACTTAAATAAATTTACAAGAAAAAA 5805
                          i  vi        i v  i        ivv i  v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_176385091_   5806 TCAA----CCCCATCAAAAAGTGGGCAAAGCATATGAATAGACACTTCTC 5851
                         v   ----   v  i?    i         v  v          i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_176385091_   5852 AAAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAATGTTCAGCAT 5901
                         v        i  vi viii     i ii          i   i   i   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_176385091_   5902 CACTGGCCGT 5911
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3176 25.42 2.81 0.67  chr1_176394355_176400983     5248  6136 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176394355_   5248 TGGAAAAATATTCCATGCTCGTGGATAGGAAGAATCAATGTTGTGAAAAT 5297
                               i    i     i  i     v      v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176394355_   5298 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5347
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176394355_   5348 TACCA-TTGACTTTCTT-CACGAATTATAAAAAACT-ACTTTAAATTTTA 5394
                          v   -i  v    i  -  vi    i-- v  i  - iii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_176394355_   5395 TATAGAACCAAAAAAGAGCCCTTATAGCCAAGACAATCCTGAGCCAAAAG 5444
                            i   viiv  ii  v  vvv        i      i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_176394355_   5445 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5494
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_176394355_   5495 TACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGATATATAGACC 5544
                                 i   i    ii        vi iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_176394355_   5545 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACAGCTACAACCAT 5594
                                i    iv   ivii         vv   i   vi  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_176394355_   5595 CTGATCTTTGACAAACCTGACAAAAGCA----ATGGAGAAAGGATTCAGT 5640
                         i    i  i     ivv  v   i v  ----    i     i  --   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT--AGT 396

  chr1_176394355_   5641 ATTT--AATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5688
                         v   --  i        i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_176394355_   5689 GAAACTGGACCCCTTCCTTGTATCTTATACAAAAATTAACTCAAGATGGA 5738
                            ii         v   iii i v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_176394355_   5739 TTAAAGACTTAGATGTAAGACCTAAAACCATAAAAATCCTAGAAGAAAAC 5788
                          i ?    i  i        v       i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_176394355_   5789 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5837
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_176394355_   5838 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT- 5886
                         vi            vvi          vv     v  i    v   ii -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_176394355_   5887 -----AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5931
                         -----       i -   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_176394355_   5932 ACAGGCAACCTACAGA-TGGGAGAAAAATTTTGCAATCTATCCACCTGAC 5980
                          v  i     i     -          vv       vii  vi i    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_176394355_   5981 AAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAA--G 6028
                           i  i  vi          v  i  i     ivv    v iv i  --i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_176394355_   6029 AAAGA------ACCCCATCAAAAAGTGGGTGAAGGATATGAGCAGACACT 6072
                              ------    v  i?    i    ii      v   ii     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_176394355_   6073 TCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGTACAAAAGCTCA 6122
                             v        i  vi viii     i  i  i   v v i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_176394355_   6123 TCATCACTGGTCGT 6136
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (134 / 88)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.21 (31 / 14)  


 265 22.03 0.00 0.00  chr1_176416736_176418847.rev      137   195 (1917)    L1M4_orf2#LINE/L1      172   230 (678)  

  chr1_176416736_    137 ATAGCTAAAGCAATCTAGATAAAGAAGAGCAAAGCTGCAAGCATCACACT 186
                              i   i      v  v        i     i  v i vv       
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_176416736_    187 TTCTAAATT 195
                          i i  v  
  L1M4_orf2#LINE/    222 TCCCAATTT 230

Transitions / transversions = 1.17 (7 / 6)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  

3834 22.62 1.11 0.44  chr1_176416736_176418847.rev      720  1621 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176416736_    720 TGGAAAGATATCCCATGTT-ATGGATTGGAAGACTTAATACTGCAAAAAT 768
                                            -                    i  iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176416736_    769 GTCCATACTACCCAAAGTGATCTACAGATTTAACATAATCTTCATCAAAA 818
                          v v     v      v             i   ii    iii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176416736_    819 TTCCAATGACGTTTTTCACAAAAATAGA-AAATAAATTCTAAAATGTATA 867
                          i   iivi v     ii  i    v  -  iivi  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_176416736_    868 TGGAACCACAAAAGACCCCAAATAGCTAAAGAAATCTAGATAAAGAAGAG 917
                              vii   ii     vi      i   iv     v  v        i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_176416736_    918 CAAAGCTGGAAGCATCACAGTTCCTGATTTTGAATTATATTACAAAGCTA 967
                              i    i vv     v    ii    ii  viv  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_176416736_    968 CAGGAATCAAAACAGTATGGAATTGGCACAAAAACAAACACATAGATCAG 1017
                            v      i     i   v i     i  ii i i   i        i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_176416736_   1018 TGGAACAGAATAGACAGCTCAAAAATAAAGCCATACATATACAGTCAACT 1067
                              i     v  v  ii  i       v        v  ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_176416736_   1068 AATCTTTGACAAAGGTGCCAAGGATACACAATGAGAAAAGGATAGCCTTT 1117
                         i  i  i     i         ivi iv     i i    i    i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_176416736_   1118 TCAATAAATGGTGTTGGGAAAACTGAATAGCTAAGTGCAAAAGAATAAAA 1167
                             i        i     v     i   ? i vi           i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_176416736_   1168 TTGGAGCCTTATCTTACACTATACACAAGAGTCAACACAAAATGGATTAA 1217
                              v  i  i  i    i   i    i i i   v          i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_176416736_   1218 AGACTTAAATGTAAGACTTGAAACTGTAAAACTCCTAGAAGAAGACATAG 1267
                             i           vi i     i        i        i      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_176416736_   1268 GGAAAAATCTT---GACACTGATCTTGGCAATGATTTATTGGATGTGACA 1314
                          ?iv       ---   vi  ivi v       i   v  i   i     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_176416736_   1315 CCAAAAGCACAGGTCACAAAAGTAAAAATAGACAAGTATGACTACATTAA 1364
                                    i iv       v         i  i vv    v   i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_176416736_   1365 ACTAAAAAGCTTCTGCACATTAAAGGAAACAATCAGTGGCATGAAAAGGC 1414
                          v v    i   i  ii v i      v  v    iviivi       i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_176416736_   1415 AACTTTTGGAAAGAGAGAAAATATTTGCAAGCCATATATTTGATAGGGG- 1463
                            iivii   v i                ii       i     i   -
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_176416736_   1464 -CAATATCCAAAATATATA-GGAATTAACATAATAGCAAAAAAATAAAAA 1511
                         -ivi      i        -i   i -- v - i i vv  v        
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACT--CTT-ACAACTCAATAATAAAAA 797

  chr1_176416736_   1512 ATAAAAATAA-AAAATAAAAAAATGAGCAAAAGACCACAATAGACATTTT 1560
                         i- v      -vv   v?       i     i  iivv           i
  L1M4_orf2#LINE/    798 G-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_176416736_   1561 TCCTAAGAAGACATACAAATGGCCGACAA-TATATGAAAAGATGCTCAAC 1609
                            v       i            i i  -i i                 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_176416736_   1610 ATCACTAATCAT 1621
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (136 / 64)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


4482 15.53 2.17 3.20  chr1_176419768_176421635      500  1375 (493)    L1M4_orf2#LINE/L1       42   908 (0)  

  chr1_176419768_    500 TGTTAAGATGCCAATACTTTTCAAATTGATCTACACATTCAATGCAATCC 549
                                   v       iii              v      i       
  L1M4_orf2#LINE/     42 TGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chr1_176419768_    550 TTATCAAAATCCCAGCTGGCTTTTT-GTGGAAATTGACAAGCTGATCCTA 598
                         i                 v      - ii                     
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr1_176419768_    599 AATTTCATATGTAAATACAAGGGACACTAAATAGCCAAAACAATCTTGGA 648
                           v        v    i        v vi                   i 
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_176419768_    649 AAGAACAAAAAAGGAACAAAGTTAGAGGACTCATACTTTCAGATTTCAAA 698
                           ------- i i          i         i    i vi        
  L1M4_orf2#LINE/    192 AA-------AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_176419768_    699 ACTCTCTATAAATCTACTGTAATCAAGACTGTGTGGTACTTGTATAGAGA 748
                            iv   i   v    v           v          v i   ii  
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_176419768_    749 TAGACATATAAAACAATGGAATAGAATTAATGGTCTAGAAGTAAACCCAT 798
                                   i v               i vi   i    i         
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_176419768_    799 ACATTTA----CAATTAATTTTTGACAAGGGTATCAAGATTATTCA-TGG 843
                                ----     i     i         ii     ii     -   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_176419768_    844 GAAAAGGGTCATTTTTTCAACAAATGGTTCTGAAACAAATGGATAGACAC 893
                          i    ii vi i               v   ii    v      ?v   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_176419768_    894 ATGCAAAAGAAGGAAGTTGGACCC-TATCACACACTATATGTAAAA-TTA 941
                                    v            -  i v     i    ii    -   
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_176419768_    942 ACTAAAAATTGATCAATAACTTAA------GAGCTGAAACTGTACAACTC 985
                            v     v     ?vi  i   ------     i     i  v     
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_176419768_    986 TTAGGGAAAAAAGTGAGCATAAATCTTTGTGATTTTGGATTTGACAATTA 1035
                             iii    vi ii ?i        i    ii    i  v i    vi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_176419768_   1036 TTTCTTGGTTATGACACCAAAAATGCAGGCAACAAAAGAAAAATTAGGAC 1085
                               i v             iii  i               v   ---
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG--- 631

  chr1_176419768_   1086 TTCAAAAGAAAAAATACATAAATTGGACTTCACCTAAATTAGTAACTTTC 1135
                         -----------------               i v      iv      i
  L1M4_orf2#LINE/    632 -----------------ATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_176419768_   1136 ATGCTTCAAAAAGATACCTTCAAGAAAGTGAAAAGACAGCCCACAGAATG 1185
                         i         i-  i  iv                   i           
  L1M4_orf2#LINE/    665 GTGCTTCAAAG-GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_176419768_   1186 GGAGAGAATTTTTGCAAGTCATATATATGATAAGGAACTTGCATATAAAA 1235
                              i   v       i        v        i     i  vi i  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_176419768_   1236 TATATAAAGAACTCTTATAACTCAATAA---AAAGACAAATAGCTCCATT 1282
                                          i          ---           i i v   
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_176419768_   1283 --AAAATGGACAAATAATATGAATAGACATTTCTCCAAAAGAGATAAACA 1330
                         --       i    vi  v                    ii     v   
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_176419768_   1331 AATGTCCCACAAACACATGAAAAGGTGCTGAACATTATTAGTCAT 1375
                             v  v i  i           i    v     i ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (90 / 43)
Gap_init rate = 0.01 (11 / 867), avg. gap size = 4.27 (47 / 11)  


1789 23.87 7.85 5.74  chr1_176439061_176441069      493  1154 (855)    L1M4_orf2#LINE/L1       87   762 (146)  

  chr1_176439061_    493 AATTTATATCAAAATATCAATGAGAATTTTTGTATTAATAGATATAGAGG 542
                            iiv         vi  iivivvv      i vv   v  i ------
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA------ 130

  chr1_176439061_    543 AGATTATTCTAATATTTAAACAGAAAGGCAAAGGAACTAGAAGAGCTAAA 592
                           v v  i    v   i v ii    v    i   v i    v   i   
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr1_176439061_    593 ACAATTTTGAATAGAAGGAATAAAGTGGGCAGAATCAGACTACCCAGTTT 642
                              i     v ii i   i     v  vi  v   v   v    i   
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_176439061_    643 CAAGATTTATTATATAGCTTCAGTAATCAAGACTGTATGGTATTGGTGGA 692
                            i i   i  i v    v             v  i     i   iiv 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_176439061_    693 GGGATAGACACATAGATCAATGGAATGGAATAGAGAATCCAAAAATAAAC 742
                         i         i               i    v    i    i        
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_176439061_    743 CCACACAACTATGCCCAGCTGATTCTTGACAAAGGTGCAAAAGCAATTAA 792
                            i   vi    vi  ii     i i     i     v  ii v   v 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_176439061_    793 ATGG----------------TTAACAAATGATGCCAGAGCAACTGGA--- 823
                             ---------------- i        i   ii ii        ---
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_176439061_    824 CCTTATTAGGCAAGAAGAAGAAGGAGAAGAAGGAGAAGGAGAAGGAGCTG 873
                           vi  ---    -------------     v  -----  vv   v --
  L1M4_orf2#LINE/    431 CCACAT---GCAA-------------AAGAATGA-----AGTTGGACC-- 457

  chr1_176439061_    874 CTCAACCTAGCCCTCACATCTTATACAAAAATTAACTTATGATGGATTAC 923
                         -----    --       i v                i vi      i ?
  L1M4_orf2#LINE/    458 -----CCTA--CCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_176439061_    924 CAAC---------AGAACATGAAAC-AGAAAA-------AAAAAAA-ATT 955
                         vi  ---------   i - i    - v    -------  i    -  v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_176439061_    956 GGAGAAAACCTTTGGGGTTTAGGGCTAGCCAGAAAGTTCTTAGTCTTGAC 1005
                           ? v   i   i v iii v   i   v  iviiv       viv    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_176439061_   1006 ACCAACAACATGCTCCATAATAGAAAAAATAGTAAAATTAGACCTTATCA 1055
                              v i  iivv v i  v           vv     i   i i    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_176439061_   1056 AAATTTAAAAATTTCT---CTACAAAGTGCA-TGTAAAGAGGATGAAAAG 1101
                              -     i  i ---  v     vi  - i v    iii       
  L1M4_orf2#LINE/    650 AAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_176439061_   1102 AC-----------TGGGGGAAAATACTTGCAAGCCACAGATCTGAAAAAG 1140
                           -----------    i       i      ii  i v      v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_176439061_   1141 GACCAGGATCTAGA 1154
                            iv v   i   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGA 762

Transitions / transversions = 1.44 (92 / 64)
Gap_init rate = 0.03 (17 / 676), avg. gap size = 5.29 (90 / 17)  

 424 19.77 1.16 11.63  chr1_176439061_176441069     1386  1557 (452)    L1M4_orf2#LINE/L1      755   908 (0)  

  chr1_176439061_   1386 TATCTAGACTATATAGAGAACTCTGAAAATTCAACAGTCAAAAAGACAAA 1435
                             i   v      i        v v  i    i i -           
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAAAAGACAAA 803

  chr1_176439061_   1436 ACAATCCAATTAGCAAATGACCAAAAGACGTAAACAGAGATTTCACCAAA 1485
                         -i  i      ?iv     iv    i  iv i  i   v     v     
  L1M4_orf2#LINE/    804 -TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_176439061_   1486 GATTGCATATAGGTGGAAATAAGGATGGCAAGTAAGCACGAGCCCCTGAA 1535
                           --------  i ----   vii     v i       i------    
  L1M4_orf2#LINE/    853 GA--------AGAT----ATACAAATGGCCAATAAGCACA------TGAA 884

  chr1_176439061_   1536 --GACGTCTGACATCAGTAGTCAT 1557
                         --  i iiii      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.30 (23 / 10)
Gap_init rate = 0.04 (6 / 154), avg. gap size = 3.67 (22 / 6)  


 459 26.92 3.85 7.69  chr1_176554447_176556763      686   893 (1424)    L1M4_orf2#LINE/L1        4   203 (705)  

  chr1_176554447_    686 AAAAATATC--ATG--CATAGACAAATAAGACTCAAAACCATT--GATGC 729
                            i     --   --   i  ivii-      i  v iii  --    v
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGG-AAGACTTAATATTGTTAAGATGG 52

  chr1_176554447_    730 CAATTTTCTCCAAATTAATCTACAAATTTAATGCAATTTGAAACAAAATC 779
                             vi  i       i       i   i  i     iivv v       
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_176554447_    780 TCAA--GTTTTTTGATTATTGTTGGTTTCTAGTGAAATGGAAAAGTGGGT 827
                         i  i-- ii    -----   i--------  --    v  v   iv i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTT-----TTGC--------AG--AAATTGACAAGCTGAT 137

  chr1_176554447_    828 CCTAAAATTCACAAAGAGCAGCAAAGGATCAAGAAGAGTCAGCATAATTC 877
                                    i vi  ivv    i   i v    v  i  iv i   ii
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_176554447_    878 TAAAGAAGGGGGGCAA 893
                          i  i   ii ii   
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAA 203

Transitions / transversions = 2.50 (40 / 16)
Gap_init rate = 0.04 (8 / 200), avg. gap size = 3.00 (24 / 8)  

 864 28.67 13.15 1.35  chr1_176554447_176556763     1224  1816 (501)    L1M4_orf2#LINE/L1      233   895 (13)  

  chr1_176554447_   1224 AAACAAACAAAAAACTTAAAGTAATAAAAGCAATGGAACACTAGCACACG 1273
                             vv  v v   vi  v      v  ii  i  viii   i   i v 
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_176554447_   1274 AATAGACAAACAGTAT-------ACAGAATAGAGAGTCAAGAAATATATG 1316
                         i       v i  -  ------- i     v       v       v iv
  L1M4_orf2#LINE/    283 GATAGACATATAG-ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_176554447_   1317 CATACATACATAAGGAAATTG---------------GCCAAT-TCA--CA 1348
                                vi  i- vv     ---------------     v-i  --  
  L1M4_orf2#LINE/    332 CATACATTTATG-GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_176554447_   1349 AAAGGGAAATAATGAATTAGTGAATAAATAGCGTGGGGACAACTGACTAT 1398
                          vi      v   iivi vv v  i    i i iv          iv  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_176554447_   1399 TCAAATA-GGGGGAA--AAATTAGATTTCTGTCTC---CTATTCATATAA 1442
                         i  v  i-iiii   --  i  i  iii  ii   --- i  --   i  
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT--ATACAA 478

  chr1_176554447_   1443 AAATCAACTCCA----GATTAAAGACCTAAATGTAAACAGC-AAAACTTT 1487
                             i     v ----   i ?              i-   -      v 
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG-AGCTAAAACTAT 527

  chr1_176554447_   1488 TAAACTTTGAGAATATCAAATA--------TCTTTATAACT--------- 1520
                         v     i v    v vv v   --------    ii i  i---------
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_176554447_   1521 GCAAGGGTTTCTTAAATAAGATATACAATACACAAACCA-GAAAGGAAAA 1569
                             v         i   v  i ivv  vi     i v -i    i    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_176554447_   1570 TTTGACAAATGTGACCCTAT------TAAAAAATTTTAATTTCTACACAA 1613
                         v v  i    vv   iii  ------      v    i-- v  v  -  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG--TGCTTCA-AA 674

  chr1_176554447_   1614 GG----TATCAAAA---TTAAAAGGTAAGTCTCTGACTAGAA--AAACAT 1654
                           ----      i --- v     ii  vi v v  v i i --   i  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_176554447_   1655 CTGCAACACATAAAACCAGTAAGGAATTAATATTGAGAACACATAAAGAA 1704
                         i     vv    v v iii     i i vi   iv    i i        
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_176554447_   1705 TTCC-ACAAATCAGTAA----AAGACAAATAATGCTAT-GAAAAGTGGGT 1748
                         i  i-    v   i   ----           iv v  -?    i    i
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_176554447_   1749 AAAGGGAT-GAATAAGCAGTTCAACAAAGAGGAAATATGAAAACCTAATG 1797
                              iv -     ii  v   vv      i  v   ii  viv i   i
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_176554447_   1798 A--ATATTAAAAAACAGTCAA 1816
                          -- i  v    i iiv    
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.35 (96 / 71)
Gap_init rate = 0.04 (27 / 663), avg. gap size = 3.19 (86 / 27)  


2491 24.62 3.39 4.05  chr1_176663354_176665715.rev      958  1871 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176663354_    958 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAAAATT--TAA-AT 1004
                               i i  i     i               v i  v   --   -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176663354_   1005 GACCATACTGCCCAAAACAATCCAAAAATTCTA-----TTCCCATCAAAT 1049
                          i v     v      vii   i v i    v ----- i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_176663354_   1050 TAGCAAC-ATCATTTTT-CACAAATTAGAAAAAACAATTCTAAAATTCAT 1097
                          vv  i -ii v     -  v     -  v  ivii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chr1_176663354_   1098 ATGGAACCAAAAAAGAGCCTGAATAGCCAA---------GCAAAA--AGA 1136
                               viiv  ii  v  v          --------- v    --   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_176663354_   1137 ACACAGCAGGAGGCATCACATTACCCAACTTCAAACTATACTACAAGGAT 1186
                            v  iv     vv     i v     i      viv        i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_176663354_   1187 ATCCTAACCAAAACAGCATGTTACCAATACAAAAACAGACATCTGTATCA 1236
                          ivv   i   i    ii  v   iiii i  ii i      v iv    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_176663354_   1237 ATGTAACAGAATAGAGAACCCAGAAATAAAGCCATACACCTATAACCAGT 1286
                            v  i     v    ii           v       ii   iii  i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_176663354_   1287 TGATCTTGAACAAAGCTGACAAAAGCAA-AAATGGGGAAAGGACA-CCTA 1334
                             i  vi    i v  v   i v  v-v           i i -i  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_176663354_   1335 TTCAATAAACAGTGCTAAAAAGAAAAAAAAACCCAAAAAACACACAAAAA 1384
                              i   ii     iii ------------------------   ---
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGA------------------------CAA--- 422

  chr1_176663354_   1385 AACTGGCTAGC-ATGTGCAGAAGAATGAAACTGGACCCCCTACCTTTCAC 1433
                         --    v  ? - ii    i         ii        -     iv   
  L1M4_orf2#LINE/    423 --CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC-TACCTCACAC 469

  chr1_176663354_   1434 CACATACAAAAATTAACTCAAGACGTATTAAAGACTTAAACATAAAACCT 1483
                           i                  i i v  i ?    i    ii   i v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_176663354_   1484 CAAACTATAAAGATCCTATTTTAAAAAACCTAGGAAAAACTCTTC-TGCA 1532
                         v          iv  i  vv-- i     v    ?iv  v     -  vv
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGA--AGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_176663354_   1533 CATGGGCCTAGGCAAAGAATTTATGACTAAAACCTCAAAGGCAAATGCAA 1582
                          v    i-       v iv  iv iiv  vi  vi    i   v v    
  L1M4_orf2#LINE/    568 CTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_176663354_   1583 CAAAACAAAAATTC-ATAAACAAGATTTAATTAAACTAAAAAGCTTCTAC 1631
                              v     v v-     ivi  i  v  i   v v    i   i ii
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_176663354_   1632 ATAGCAAAAGA----ATCAACAAAGTAAAGAGGTAACCTAAAGAATGGGA 1677
                         iivv    i  ----     v     i  i  ii    i v         
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_176663354_   1678 AAAAAATATTTGCAAACTGTACATCTGACAAAGGACTAGGATCCAGAATC 1727
                         i    -          iii  i      i  i     v v         v
  L1M4_orf2#LINE/    717 GAAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_176663354_   1728 TACAAGGAATCTCAAACAAATGAACAAGAAAAAAA-AAATAACTCCATTA 1776
                           i  i   -   vv    v v  i  v     i -       i v   ?
  L1M4_orf2#LINE/    766 TATAAAGAA-CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_176663354_   1777 AAAAGTGAGCAATGGACATAAACGGATACTTCTCAAAAGAAGACATACAA 1826
                             i  i    v   iv i  ii  i i     v        i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_176663354_   1827 GTGGCCAACAAACATATGAAAAAAATGCTCAGAATCACTAATCAT 1871
                         i       i  i  i       i -      iv    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.96 (68 / 23)  


2059 23.12 3.77 4.79  chr1_176738926_176741353.rev      638  1221 (1207)    L1M4_orf2#LINE/L1        1   578 (330)  

  chr1_176738926_    638 TAGAAAAATATATCATGTTCATGAATTAGAAAAGGCAACACTGTTAAGAT 687
                          i    i    vi          i   i   i vvi  i i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_176738926_    688 GTGAATTCTCCCCAGACTGACTAACCTACAGATTCAATACCATTCTAATG 737
                          vv   v       i i   i----            ii v  i iv  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT----CTACAGATTCAACGCAATCCCTATC 96

  chr1_176738926_    738 AAAATCCTACCAGGCTTTTTGTTGTTGTTGTTGTTGAAACTAACAAACTG 787
                                i v v v      -----------  iv    i i    i   
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTT-----------TGCAGAAATTGACAAGCTG 135

  chr1_176738926_    788 ATTCTAAAAGTTACACGGAAATGCAAAAAACCTAGAATAGCCAAAATCAT 837
                           i      v i i i          iii   i             iv  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_176738926_    838 CTTTGAAAAAAAGAAACAAAGTTGGAGGAATTATG--TCTTGATTTCAAA 885
                            -      i ii               v i ii--  iii        
  L1M4_orf2#LINE/    186 CTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_176738926_    886 ACTCACTAAAAAGCCATAGTAATAAAGACAATATGGTACTGACATTACAG 935
                            i    v     i i      v      i i        i   - vi 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGG 283

  chr1_176738926_    936 ATAGATGAATAGATTAATGGAA---AAT---GAGTCTAGAAATAGATCTA 979
                              iiv      i       ---   ---     i       i i i 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_176738926_    980 CACATAATTGATCACTTAATCATTGATAAAGGCACCAAGGTAATTTAA-- 1027
                         i    vvv  i   v  i  iv i  i  i  ii     iiv   i  --
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_176738926_   1028 -----------GTCTTTTTAATAAAATGGTGCTGGAACAATTGAATATCC 1066
                         -----------       i  i   -         i    i  i   ?  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCC 432

  chr1_176738926_   1067 ATACTAGAGAAAAAGAAACTTTGACTCTCTTCCTCACATCAAATCCAAAA 1116
                          i - iv i  i  vi  v  v   i -  v       i  v  v     
  L1M4_orf2#LINE/    433 ACA-TGCAAAAGAATGAAGTTGGACCC-CTACCTCACACCATATACAAAA 480

  chr1_176738926_   1117 ATTAACTTGAGAAGGATTACACACTTAAATATGAAAGATAAAATTATAAA 1166
                                ii i v    i ? v  i     i i i  v     i      
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_176738926_   1167 GCTTTTGGAAAAAAACGTAAGAGAATGTTAAGATATCTTAGT-ATCTTAG 1215
                         i  i  i   i     i  i ? -----   ---     v  - i   i 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNG-----TAA---ATCTTCGTGACCTTGG 572

  chr1_176738926_   1216 GGTAGG 1221
                          v    
  L1M4_orf2#LINE/    573 GTTAGG 578

Transitions / transversions = 2.47 (94 / 38)
Gap_init rate = 0.02 (14 / 578), avg. gap size = 3.57 (50 / 14)  

 897 19.61 9.80 1.96  chr1_176738926_176741353.rev     1632  1937 (491)    L1M4_orf2#LINE/L1      579   908 (0)  

  chr1_176738926_   1632 CAAAGATTTCTTAGA----AAATTAAAGGTTCTACCA-CAAAAGAAAGAA 1676
                            v i         ---- v ii   i iv v v  -         i  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_176738926_   1677 ---ATTAAAACTGGATTTCATCAAAATTTAAAACTTCTATTCCTCAAAAG 1723
                         ---  --   i    i            v       i i v i     i 
  L1M4_orf2#LINE/    629 TAGAT--AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_176738926_   1724 ACACAGTTTAAAAAGTGAAAAGATAAGCCA-AGACCTGGAATACAATATT 1772
                             vi iv i            i  v   -   v-   i v v      
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAA-TGGGAGAAAATATT 725

  chr1_176738926_   1773 TCCAA----TACATCTGA-AAAGGACTTGTTTCCAGAATATATGAAGAAC 1817
                          v   ----  i      -  i        v            i      
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_176738926_   1818 TCCTATAAAATCAATAATTAAAAAGACAA-T--CCCA--TAATGAAGGGG 1862
                           i  i  v-        -          - --    -- ? -i  iv  
  L1M4_orf2#LINE/    776 TCTTACAAC-TCAATAAT-AAAAAGACAAATAACCCAATTWA-AAAATGG 822

  chr1_176738926_   1863 GTAAAAGATTTGAACAGATATT----CACAAAAGA-------ATGCTCAA 1901
                          i   i        i   i   ----  v i    -------   vi   
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_176738926_   1902 TAAATACACAAAAAGACAATCAGTCTCATCAGTAAT 1937
                            ii   ii      iiv   iiv   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (38 / 21)
Gap_init rate = 0.05 (16 / 330), avg. gap size = 2.25 (36 / 16)  


1367 21.43 1.79 4.76  chr1_176847056_176849407      512   847 (1505)    L1M4_orf2#LINE/L1      232   557 (351)  

  chr1_176847056_    512 AAGACTTACTATGATGCTATAGTAATCAAGGCAGTGTGATACCAGCACAA 561
                           i        ii v    i          i       i   ii   i  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_176847056_    562 GGATACCATATGTGTCATATACACATGTATTTTAGTGGAACAGAATTGGG 611
                              -------- v      v -------- i i     i       i 
  L1M4_orf2#LINE/    282 GGATA--------GACATATAGA--------TCAATGGAATAGAATTGAG 315

  chr1_176847056_    612 --TCTAGAAATAGATTCACACATATATGGTAAATTACTTTTTGAAAACTC 659
                         --  i       i ii  i    v      v    iv    i  v  vvv
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_176847056_    660 TGCCAAGGCAGTTCCATAAGGAAAAGATAGTCCTTTCAATAAATGTTGCT 709
                                i vi   v  ii     ii      i      i     v    
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_176847056_    710 AAGACAACTGGATATTTCTATGGAGATAAATGAACTTTGACCCTTACCCT 759
                         ii            ?iivi   v i vi      v  v     i    ii
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_176847056_    760 ----TATATACAAAAATTAACTTGATATGAATCAAAGACCTAAATGTAAG 805
                         ----i                 ii v   i    ?               
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_176847056_    806 AGTTAAAACTATAAAATTTATAAAAGAAAACATACAAGAAAA 847
                           i             i iv  i           vi? v   
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

Transitions / transversions = 2.14 (47 / 22)
Gap_init rate = 0.01 (4 / 326), avg. gap size = 5.50 (22 / 4)  

 507 21.60 4.32 3.09  chr1_176847056_176849407     1144  1305 (1047)    L1M4_orf2#LINE/L1      537   700 (208)  

  chr1_176847056_   1144 AAAAGAAAACATACAAAAACATCTTTGTGGCCTTGGAATAAGCAAAGATT 1193
                          i           vi?iv v     i   i      iv  i    v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_176847056_   1194 TCTTAG----GACACAAAAAGTGCAAACCACAATAGAAAAAAAAAAAGAT 1239
                               ----     v     ii   i v    ---  i      v    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAA---AAGAAAAAATAGAT 633

  chr1_176847056_   1240 AAAT-AGATTTCATAAAAA-CAAAAACCTTC-TGCTTATCAAGAGATACC 1286
                             -i  i     v    -i      i  i-     --   ii  i  i
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACT 681

  chr1_176847056_   1287 ATTAAGAAAATGAATAGGC 1305
                           i      i    v  i 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGAC 700

Transitions / transversions = 2.40 (24 / 10)
Gap_init rate = 0.04 (6 / 164), avg. gap size = 2.00 (12 / 6)  

 492 18.53 3.86 17.37  chr1_176847056_176849407     1606  1864 (488)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_176847056_   1606 AAGAAAATTAATACACAAGCTATTGACTGAGAGAAAATGTTTGCAAAACA 1655
                               i v  v v    v i iv  v  i        i        v  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_176847056_   1656 TACATCTGACAAAGGATTTGCATCCAGCATATATATGTATATATGTAAAT 1705
                           i      i  i   i   i      v       ---------------
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATA--------------- 769

  chr1_176847056_   1706 TTAAGTACATATATACCTATACATACAGAACTCTTACAATTCGGTAATAA 1755
                         --   -----------------------           i  ii      
  L1M4_orf2#LINE/    770 --AAG-----------------------AACTCTTACAACTCAATAATAA 794

  chr1_176847056_   1756 ---GACAA----CCTAACTTTTTAAAAGGAGCAAAAGATTTCAACAGATA 1798
                         ---     ----  i  --  ?v    v i     i     v  i   i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAA--TTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_176847056_   1799 CTTCAC--ACACACACACACGAATATTTAAGAATAGC-CATGAAAAGATG 1845
                         i   v -- viv v i i  i   ivii  v  --  -            
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAA--GCACATGAAAAGATG 890

  chr1_176847056_   1846 TTTAACTGTTAGTTACCAG 1864
                         i i   -i i ????????
  L1M4_orf2#LINE/    891 CTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (30 / 17)
Gap_init rate = 0.04 (9 / 224), avg. gap size = 6.11 (55 / 9)  


2904 22.66 7.05 2.08  chr1_176991763_176995023.rev     1912  2776 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_176991763_   1912 TGGAAAGAGATACCATTGTTCATGGATCAAAAGACTCAGTATTGTTCAGC 1961
                                 v  v    -          iii      i i       v  v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_176991763_   1962 TGTCCATTCTTTCCAAATTGATTCATAGATTCAGCGGGGTCCCAATCAGA 2011
                           v v  v  ii          ii i       i  vii    v    i 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_176991763_   2012 ATCCCAGCAGGATCTTT-GTAAAAACTTATAAGTTGATTCTAAAATTTAT 2060
                                 v vv i   - i i   i v i   i    i        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_176991763_   2061 ATGGAAAAGCAAAGGACCTAGAATAATCAAAACAACTTTGAAAAAGAA-- 2108
                                v    i     i      ii        ii           --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_176991763_   2109 -TAAAGTTGGAGGCCCCACACT----GGTTTCAGGACTTACTATAAAG-T 2152
                         -i           v i      ----ii     ii        i    - 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_176991763_   2153 ACAGAAATCAAGCCAATGTTGTATTGGTATAAGAATAGGTATATAGATCA 2202
                             v       v  i   v   i   i     i    ii          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_176991763_   2203 AAGGAACATGATAGATAACCTAGAAATAGATCCAATCACAAATGGTCAGC 2252
                          v    i vi  v  v ii i       i i   vv  ivv       ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_176991763_   2253 TGATTTTTGACAAAAATGCCAACATAAAATTCAGTGGAGGGAAGACTAGC 2302
                                i     iii      v iv --    i   -  i    v   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCA--TTCAATGG-GGAAAGAATAGT 396

  chr1_176991763_   2303 CTTTTCAACGTATAGAGCTGTAACAATTGGACATCAAAATGCAAAACAAA 2352
                                  iv  i v    vi    i    i ? v v        --i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA--GA 444

  chr1_176991763_   2353 ACAAAAAGGTGAGCC------TGAAGCC-TACTCAAAAATTAACTGGGAA 2395
                          ii  -- v  ii  ------ v vi  -  iv            vii  
  L1M4_orf2#LINE/    445 ATGAA--GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_176991763_   2396 GGTAAGATCTTAGATGTATATGTAAGAGGAATAATGATAAAGAACT---A 2442
                         v ---    v?   iv  v         vv v  iv     --   --- 
  L1M4_orf2#LINE/    493 TG---GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA--ACTCTTA 537

  chr1_176991763_   2443 GAAGAA----TA--------TCTTTGTGATCTTGGTGTAGGCAAAGTTTT 2480
                               ----  --------    i    i     vv       v v   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_176991763_   2481 TTTTAGATGGAACAC---AAGCACAAACTATAAAAGAAAAAATA----AA 2523
                         i  -    ivi    ---        i v i             ----  
  L1M4_orf2#LINE/    588 CTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_176991763_   2524 TTGCACTTTATCAAAATTTAAAAATTCCACTCTTCAA--GATACTCTTAA 2571
                            v    i         v    v  iiiiv      --  i   v i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_176991763_   2572 AAAAAATGAGAAG-----TCATATACTGGGAGAAAATATTTATAAAACAT 2616
                         i   i-   i   -----i  i v v               ii   v   
  L1M4_orf2#LINE/    687 GAAAG-TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_176991763_   2617 ATATTTGGAAAAAAAAATTTTGTGTCCACAACATATAAAGACCTCTTA-- 2664
                             i  iv  iii ---i    i    v  i         v      --
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGA---CTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_176991763_   2665 ------TAAGAAAATGACAA----CCTTATTAACAAATGAACAAAAGATT 2704
                         ------   v    v     ----  iv   ? v     ii    i    
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_176991763_   2705 TGAACAGATAAATCACCAAAGA---TAGATAGTTGGCAGATAAGCACATG 2751
                             i   i vv  v       ---  v i iv    vi           
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_176991763_   2752 AGAA-ATGTTCATTGTTAGACATTAG 2776
                          i  -   i   vii i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (118 / 75)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.93 (79 / 27)  


3098 26.52 1.10 0.77  chr1_177004039_177006805     1370  2274 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_177004039_   1370 TGGAAGAACATTCCATGCTCATGG-TAGGAAGAATCAATATCATGAAAAT 1418
                              ii i  i     i      - v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177004039_   1419 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1468
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177004039_   1469 TACAAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1516
                          v v iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_177004039_   1517 CATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 1566
                         i      viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_177004039_   1567 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1616
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_177004039_   1617 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1666
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_177004039_   1667 AATGGTACAGAAC--AGAGCCCTCGGAAATAATGCCACATATCTATAACC 1714
                              v i    i--    i  --i       vv   i i  i   iii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_177004039_   1715 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 1764
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_177004039_   1765 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATA---GAAAGC-T 1810
                           v  i  i              v      v  ?i  i ---i    v- 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_177004039_   1811 GAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGA 1860
                            ii    i    v   i    iv              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_177004039_   1861 TTAAAGACTTAAATGATAGACCTAAAACCATAAAAACCCTAGATTAAAAC 1910
                          i ?    i      vv   v       i      vi i    vv     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_177004039_   1911 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1959
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_177004039_   1960 CAACACCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 2009
                         ii     -       vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_177004039_   2010 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 2059
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_177004039_   2060 ACAGGTAACCTACGGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 2109
                          v  ii    i  i              v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_177004039_   2110 AAAGGGCTAATATCCAGAATCTATAATGAACTCAAACAAATCTACAAGAA 2159
                           i  i  vi          v     v      vv    v  v i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_177004039_   2160 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATCAATAGACAC 2209
                            i -    i     v  i?    i            v v        i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_177004039_   2210 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 2259
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_177004039_   2260 ATCATCACTGGCCAT 2274
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


2976 24.83 0.98 0.00  chr1_177020547_177025539.rev     3310  4026 (967)    L1M4_orf2#LINE/L1        1   724 (184)  

  chr1_177020547_   3310 TGGAAAGATATTCCATATTCATGGATTGGAAGAATCAATATTGTTAAAAT 3359
                                    i    i                v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177020547_   3360 GTCCATACTACCCAAAGTAATCTATAAATTCAGTGCAATTTCTATGAAAA 3409
                          v v     v      v i     i i     ii     ii    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177020547_   3410 TACCAATGACATTCTTCACAGAAGTAGAAAAAC-AATCCTAAAATTTATA 3458
                          v   iivi v  i  ii     i v  v  i -i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_177020547_   3459 TGGAACTACAAAAGACCCAGTATAGCCAAAGCTATGCTGAGCAAAAAGAA 3508
                              v i   ii       v         i v  vi   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_177020547_   3509 CAAAACTGGAAGGGTCACATTATCTGACTGCAAATTATACTACAAAACTA 3558
                             ii    i iv     i vi ii i v    viv         i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_177020547_   3559 TAGTAACAAAAACTGCTTGGTATTGACATAAAAATAGAGAGATAGATGAA 3608
                         i     iv  i  v iv     i  i     ii     v v      v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_177020547_   3609 TGGAACAGAATAGAGAACCCAGAAACAAATCTATACACCTATAGTGAACC 3658
                              i     v    ii       i   i i     ii   i  v  ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_177020547_   3659 CTTTTTCAACAAAAGTACCAAAAACATACATTGGGGAAAAGACAGCCTCT 3708
                         vv     i    ii  i    i v   v  v        ii i  i  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_177020547_   3709 TTAATAAACGGTGCTGGGAAAACTAGATACCCGTATGCAGAAGAATGAAA 3758
                          i  i   i          v    i    ?  ii     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_177020547_   3759 CTAGACCCCTGTCTCTCACCATGTACAAAAGTCAAACCAAA-TGGATTAA 3807
                         i i       ii   v      i       i i  vi    -     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_177020547_   3808 AGACTTAGATCTGAGATCTCAAACTATGAAACTACTACAAGAAAACATTG 3857
                             i  i  v i   v  v       i     vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_177020547_   3858 GGGAAACTCTCCAGGACTTTGGTCTCTGTAAAAATTTCTTAAA----ACC 3903
                          ? v  v   i iv   i    vi vv i  vii       i ----  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_177020547_   3904 CCACAAACACAGGCAACCAAAGCAAAAATGAACAACTGAGATCACATCAA 3953
                            v  i    i     v    v      ii i  v vi  iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_177020547_   3954 GTTGAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAAA-GAC 4002
                         iv v    i   i  ii vv       v  v     v         -   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_177020547_   4003 AACCCACAGAATGGGAGAAAATAT 4026
                                                 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATAT 724

Transitions / transversions = 1.73 (111 / 64)
Gap_init rate = 0.01 (4 / 724), avg. gap size = 1.75 (7 / 4)  

 474 15.89 0.93 0.93  chr1_177020547_177025539.rev     4396  4502 (491)    L1M4_orf2#LINE/L1      802   908 (0)  

  chr1_177020547_   4396 AATAATCAGATTTTAAAATGGGCAAATGATTTGAATAGATCTTTCTCAAA 4445
                              i vi   ?v            v            iv      v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_177020547_   4446 AGAAGACATAAAAATGGC-AATCAGTTATATGAAAAGGTGGTCAATATCA 4494
                               i   v       -   v  -i i        i  v    i    
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCAACATCA 900

  chr1_177020547_   4495 TTGATCAT 4502
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.00 (8 / 8)
Gap_init rate = 0.02 (2 / 107), avg. gap size = 1.00 (2 / 2)  


3249 25.11 1.10 1.54  chr1_177033864_177040234     4967  5878 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_177033864_   4967 TGGAAGAACATCCAAACAAATGCTCATGGATAGGAAGAATCAATACCGTG 5016
                              ii i    ---  --  i        v      v i    ii  v
  L1M4_orf2#LINE/      1 TGGAAAGATATCC---CA--TGTTCATGGATTGGAAGACTTAATATTGTT 45

  chr1_177033864_   5017 AAAATGGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCAT 5066
                           i     v     v     iv i  i  i        i  v     i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_177033864_   5067 CAAGCTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAA 5114
                            iv v   iivi i  i  ii     -   -- v  i  - iii    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAA 143

  chr1_177033864_   5115 GTTCATATGGAACCAAAAAAAGAGCCCACATT-GCCAAGTCAATCCTAAG 5163
                         i           -- viv  i ii    v v -     iv     i i i
  L1M4_orf2#LINE/    144 ATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_177033864_   5164 CCAAAAGAACAAAGCTGGAGGAATCACACTACCTGACTTCAAACTATACT 5213
                         vv i          i       v       v  ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_177033864_   5214 ACAAA----CAGTAACCAAAACAGCATGGTACTGGTATCAACACAGAGAT 5259
                              ----      i   i    ii         i  v iv i   v  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_177033864_   5260 ATGGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATC 5307
                           i  i        i    i--    i  --        vv   i    i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATT 339

  chr1_177033864_   5308 TACAACTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAA 5357
                           iiiii vi    i  i     ivv  v   i v  vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_177033864_   5358 GGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTA 5407
                          i  vvi  v  i  i              v      v  ?   i   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_177033864_   5408 GAAAGCTGAAACTGGATCCCTTCCTTACACCTTCTACAAAAATTAATTCA 5457
                         i  iiv    ii    i    v   i     v v            i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_177033864_   5458 AGATGGATTAAAGACTTAAATGTTAGACCTAAAATCATAAAAACCCTAGA 5507
                          i      i ?    i       v   v      ii      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_177033864_   5508 AGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTC 5556
                                v    ?i- v i -   iv   v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_177033864_   5557 ATGTCTAAAACACCAATGGCAATGGCAACAAAAGCCAAAATTGACAAATG 5606
                         v ivv  vi       vi   vvi          vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_177033864_   5607 GGATCTAATTAAAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAC 5656
                            ii v  i    -i    i -   i  ii vv    i  v    i  v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAA-TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_177033864_   5657 CAGAGTGAATAGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTACT 5706
                         v i      v  i     i                 i       vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_177033864_   5707 CATCTGACAAAGGGTTAATATCCAGAATCTACAAAGAACTCAAACAAATT 5756
                         i      i  i  ii vi          v  i         vv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_177033864_   5757 TATAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGGTATCAA 5806
                         v    v     i     i     v  i?    i          i v v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_177033864_   5807 TAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAA 5856
                               i     v        i  vi viii     v ii          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_177033864_   5857 GATGCTTATCATCACTGGCCAT 5878
                               i v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (136 / 89)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.71 (24 / 14)  


 509 26.81 11.26 3.75  chr1_177075124_177077374      640  1012 (1239)    L1M4_orf2#LINE/L1        1   401 (507)  

  chr1_177075124_    640 TGGAAAGACACCCTATATTCTTGTATTGGT-GACTCAATATTATAAAGAT 688
                                 i i  i  i   v  v     v-    i      i v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177075124_    689 GTCAGTTTTCCCTAACTT-----ATAAATTCAATGCAATCCCAATAAAAA 733
                          v  i vi    i  v  ----- i i      i        v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177075124_    734 TACCAATAAGCTATTTTATGGAGTTACATAAACT-ATTATGAAACTTCAT 782
                          v   iiviv  v    iii  iv vv i  i  -  iv i   -     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCAT 149

  chr1_177075124_    783 AT-----TTCAAAGAGTGCA--ATAACCAGGAAAACA--CTT-AAAAAGA 822
                           ----- v   i iiiv  --   i   ---     --   -       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCA---AAACAATCTTGAAAAAGA 196

  chr1_177075124_    823 AAAACTA---TGAAAGAGAAATACCTATTCTAGACATTAATACCTATTAT 869
                          i   v ---  i i  vvv i  ---   ivi iv i  v  i  i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACAC---TTCCCAATTTCAAAACTTACTAC 243

  chr1_177075124_    870 AAAGCCTT-TTAATTAAAATAATGT---ACATGCACAAA---AGA----- 907
                              ivi-v    i  i i i   ---  vv   i  i---   -----
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_177075124_    908 AG--CAGTGGAAGAGGTTATGA-AGTCCAAAATTAAACCCCAAACAT--A 952
                           --  i     v  iv -   -      i  v       - v    -- 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAAT-TGAGAGTCCAGAAATAAACCC-ATACATTTA 341

  chr1_177075124_    953 AGG-AAATACAATATAAGACAAAGGTGGCATCTCAAATCAT--GA-GGGA 998
                         v  -v   -ii  v vv     i    v  ---- i i   --i -   i
  L1M4_orf2#LINE/    342 TGGTCAAT-TGATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGG 386

  chr1_177075124_    999 ACAGACT-GTTTTTT 1012
                          v   v -  i    
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTT 401

Transitions / transversions = 1.38 (58 / 42)
Gap_init rate = 0.06 (26 / 401), avg. gap size = 2.15 (56 / 26)  

 834 26.58 11.60 2.11  chr1_177075124_177077374     1295  1768 (483)    L1M4_orf2#LINE/L1      390   908 (0)  

  chr1_177075124_   1295 GAATAGACTTTTAAATAAATGGTGCCAGGACAACAGGTAAGCCACTTGGA 1344
                               v     v  i         ii       v  vv ?    v  v 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_177075124_   1345 AGAAGACAAAATTAGATCCACATCTCCAATCATACA------TT---TCA 1385
                          i ii ii  i  i  i  vi i   vv i    i ------  ---   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_177075124_   1386 GAAT-----------CTAAGTGTAAA--CTATGAAACCATACGAGTACTA 1422
                         i   -----------    i     i--   --    i   vi v vi  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTA--AAACTATAAAACTCTTA 537

  chr1_177075124_   1423 GAAGAAAATATGG-----AATCTCT-----CTTGA-------AAAGGCTT 1455
                                 i  i -----     ii-----    i-------  v  i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_177075124_   1456 -TTAATTATGACTTAAAATCCAGAGGCAATAAAATGAC---TA-ATAAAT 1500
                         -   iv      viv   vv  v i    i    vi v---  -      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_177075124_   1501 TTGATTATATAAAAATAAAAAGTTCTTGCATGATGAAAGATACCATAAAC 1550
                          v  i vi  v     v    ii i   iiivvii  i  i  i  v  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_177075124_   1551 AAAATCAACAGACAAATGAAACA-AAAATGGGCGAAAATATCTACAA--C 1597
                            i v  v      vi----  - i      v        i i   -- 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACC----CACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_177075124_   1598 ATATACC--ACAAAGGGTTAATATCCATGGTATATAAAGAACTCTGAAAA 1645
                              i -- i  i  ii vi      vii               v v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_177075124_   1646 AACTGAGTCACAAAAGGCCAAA-AACCTGATAGAAAAATGGGGAAAA-AT 1693
                         --  v i v i    i v    -    ii  v?         v   i-  
  L1M4_orf2#LINE/    784 --CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_177075124_   1694 GTGAACAGATAGTTCACCAAAACCAGGATATAAAAATAGCCCTGAAATAC 1743
                         v    i   i v   v     i-- i      v    i   vvv  ii  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAG--AAGATATACAAATGGCCAATAAGCAC 879

  chr1_177075124_   1744 ATAAAAATAAG---AAC-TCACTCATAAT 1768
                           i    v v ---   -   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (72 / 52)
Gap_init rate = 0.04 (21 / 519), avg. gap size = 3.10 (65 / 21)  


3482 24.24 3.04 0.68  chr1_177080004_177085708     4326  5212 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_177080004_   4326 TAGAAAGACATGCCATGCTCATGAGTTAGAAGA----ATACTGTTTAAAT 4371
                          i      i  v     i     ii  i     ----   i    v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177080004_   4372 GACCACACTGCCCAAAGTAATCTACAGATTCAATGCAACCCCTATCAAAA 4421
                          i v i   v      v i              i    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177080004_   4422 TATTGACGTCATTTTTCACAGAAATAGAAAAAATAATTGTAAAATGTGTA 4471
                          viiii vv v     ii       v  v  iv i  iv      vii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_177080004_   4472 TGGAACCAGAAAAGAGCCCAAATAGCTAAAGCAATCCTGAGCAAAAAGAA 4521
                              viiv  ii  v  vi      i   i     i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_177080004_   4522 CAAAGCTGGAGGCATCACACTGTCTGACTTCAAAATATATTATAATGCTA 4571
                              i      vv       vi ii i       iv  i  i  v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_177080004_   4572 TAGTAACCAAGAAAGCATGGTATTGGTATAAAAACAGACACACAGACCAG 4621
                         i     i     v  ii     i   i    ii i     i i   i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_177080004_   4622 TGGAACAGAATAGGGAATCCAGAAGTAAATCTAGGTATTTAGAGTCAACT 4671
                              i     v i  i       i    i i vii     vi     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_177080004_   4672 GATACTCAACAAAGATGCCAAGAATATACATTGAGGGAAGGCCATCCTTT 4721
                            vi  i    i i        vi  v  v  i  i   ivi vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_177080004_   4722 TCAATAAATGGTGCTGGAAAAACTGGATATCCATATGCAAGGGAATAAA- 4770
                             i            i v         ?   i      ii    i  -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_177080004_   4771 CTGGATCCCCATCTCTCACCATATATAAAAATCAACTCAAGATGAATCAA 4820
                         i    i   i i   v         i      i       i   i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_177080004_   4821 ATACCTAAATACAAGGCCTGCAACTATAAAACTACTAGATGAAAACATAG 4870
                          v        ii   iv  iv            vi    v          
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_177080004_   4871 G-------------GAACTTGGTCTAGACAATGGTTTTATGGCTAAGACT 4907
                          -------------  v     vi   i         iv i v  v   v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_177080004_   4908 TTGAAAGCAGAGATTAAAAAAAAAAAACAAAAATAGCTAAATGAGACTAT 4957
                         iii      -----i  iv  v    iv        v     vi    vi
  L1M4_orf2#LINE/    601 CCAAAAGCA-----CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_177080004_   4958 ATTAAACTACAAAGCTTCTG-----CACAGCAAACAATCAAAAGAGTAAA 5002
                           i   v vv   i   i  -----  v  v v  v     i i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_177080004_   5003 GAGTCAACCTATAGAATGTGAAGAAATATCTGCAAAT----TATCTGACA 5048
                         i  v     i i      v  ii      i       ----       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_177080004_   5049 AGGGACTAATATCCAGAATATACAAGAAACTCAAACCATTCAATAGTTAA 5098
                                vi             i  ii     vv  v i      i v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_177080004_   5099 AAAAATAATAATCCTATTAAAAAATGAGTAAAGGATGTGAATAGACATTT 5148
                           i vv     i  v   ?       i i       v             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_177080004_   5149 CTCAAAAGTAGACAAACAAATAGCTAACAGCTACATGAAAGAAATGCTTA 5198
                            v    v   i v      i  i  i ivi        - i     i 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATGCTCA 894

  chr1_177080004_   5199 ACATCACTAATCAT 5212
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (137 / 75)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 4.71 (33 / 7)  


 402 20.24 10.71 0.00  chr1_177089033_177092855      685   768 (3055)    L1M4_orf2#LINE/L1        1    93 (815)  

  chr1_177089033_    685 TGGGAAGGCATCATGTATTCATGGA--------CTTAATATT-TTAAGAT 725
                            i   ii   vii i        --------         -       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177089033_    726 GGTACTATTCCCCAAGCTGATCTATAGATTCAATGCAATTTTT 768
                           i v  i       ii       i        i     iii 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

Transitions / transversions = 7.50 (15 / 2)
Gap_init rate = 0.02 (2 / 93), avg. gap size = 4.50 (9 / 2)  

3238 27.86 0.22 0.22  chr1_177089033_177092855     1504  2411 (1412)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_177089033_   2411 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 2362
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_177089033_   2361 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2312
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_177089033_   2311 TACCAATGACTTTCTTCACAGAATTGGGAAAACCTACTTTAAAGTTCATA 2262
                          v   iivi i  i  ii     v v iv  i iv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr1_177089033_   2261 TGGAACCAAAAAAGAGCCTGCATCTCCAAGTCAATCCTAAGCCAAAAGAA 2212
                              viiv  ii  v  v v  vv    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chr1_177089033_   2211 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 2162
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chr1_177089033_   2161 CAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGATATAGATCAA 2112
                               i   i    ii   i     i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

C chr1_177089033_   2111 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCGTATCTACAACTAT 2064
                              i    i--    i  --        vv  iiii  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

C chr1_177089033_   2063 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 2014
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

C chr1_177089033_   2013 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1964
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

C chr1_177089033_   1963 AACTGGATCCCTTCCTTACACCTTCTACAAAAATTAATTCAAGGTGGATT 1914
                          ii    i    v   i     v v            i    ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

C chr1_177089033_   1913 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1864
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

C chr1_177089033_   1863 AGGCATTACCATTCAGGACATAGGCATGGGCAAGAACTTCATGTCTAAAA 1814
                            ?i v viv   iv   v v  vv i     viii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

C chr1_177089033_   1813 CACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATAGGATCTAATT 1764
                                    vvi          vv i   v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

C chr1_177089033_   1763 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTGAACAG 1714
                            v v  i i   i  ii vv    i  v    ii vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

C chr1_177089033_   1713 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 1664
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

C chr1_177089033_   1663 GGCTAATATCCAGAATCTACAATGAACTCAAACCAATTTACAAGAAAAAA 1614
                          i  vi          v  i  v      vv  v v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

C chr1_177089033_   1613 ACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 1564
                              i     v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

C chr1_177089033_   1563 AAAAGAAGTCATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 1514
                         v       vi  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

C chr1_177089033_   1513 CACTGGCCAT 1504
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  

3814 16.90 5.17 0.50  chr1_177089033_177092855     2538  3330 (493)    L1M4_orf2#LINE/L1       79   908 (0)  

  chr1_177089033_   2538 TTCA-CACAATTCTTATTAAAATCTTCACTGCCTTTTTAGCAAAAATGAA 2586
                             - i    i i   i      iivi          v   i    vi 
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chr1_177089033_   2587 CACACTGATCCTAAAATTCACATGGAAATTCACGGGGCCCAGAATAGCCA 2636
                           vi                i        v  v   i             
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr1_177089033_   2637 AAACAACTTTGAAAAA---------AGGCGGAAGAATAACACTTCTCAAT 2677
                               ii        ---------  vi   i  v v       i    
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_177089033_   2678 TTCAAAACTTAACTACAAAGCCATAGTAATCAAGACTGTGTGGTATTAAC 2727
                                    -         i i            v        i ii 
  L1M4_orf2#LINE/    229 TTCAAAACTTA-CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_177089033_   2728 ATAAGGAAAGACATACTGATCAATGGAATAAAATTAAGAATCTAGAAATA 2777
                                v       iv             i    i   i  i       
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_177089033_   2778 AACCCTCATATTTATAAACAAATTTATTTTTGACAAGAGTGCTACAATGA 2827
                              vi i      iiv   -  v     i      i    i vi iv 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAA-TTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_177089033_   2828 CTTAATGGGGGAAAGAACAGTCTTTTCAATAA-TGGTGGTGAAACAACTG 2876
                         i i       -      i           i  -     v  ii       
  L1M4_orf2#LINE/    377 TTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_177089033_   2877 GATATCCATATGTAAAAGAATGAAGTTAGACCCCTACTTCACACTCTACC 2926
                             ?   i   i              i         i      iv  iv
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_177089033_   2927 CAA---TTAACTCAAAATA-ATCAAAGACTTCAATGTAAGAGATAACACT 2972
                            ---            i-    ?    i v          v   v   
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_177089033_   2973 ATAAAATTCTTAGAAGAAAA---AGGCTTAA-TCATCATGATCTTTGATT 3018
                               i             ---   ?v   -  v  i   i   v i  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_177089033_   3019 AGACAATGATTTCTTA------------AAACCACAAACAACAACAACAA 3056
                           i     i       ------------   v     i      v iv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_177089033_   3057 AAATAAATAA----GA--TCATAAAAATTTAAAACTTTTATGTTTTAAAG 3100
                              i    ----  --    v      v         i  i  i    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_177089033_   3101 GACACTATCAAGCAAGTAAAAACACAATTCAATGAACTGAAGAAAGTATC 3150
                                     v    i    v    ii  vv   iv i     i   i
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_177089033_   3151 TGCAAATCACACATCTGAAACGAGACTTGTATCCAAAACATATAA----C 3196
                                  i i      v v i            i  i      ---- 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_177089033_   3197 TCTTATAACTCAATAATAAAGAGACAAATAACACAATTTTAAAAATAAGC 3246
                              i              i           v     ?-      ii  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGC 824

  chr1_177089033_   3247 ACAAAATCTGAATAGAAATTTCCACAATGAACATATACAAATGACCAATG 3296
                          v ii  i        v     iv   v   v           i     i
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_177089033_   3297 AGTACATGAAAAGATGCTCAATATCATTAACCAT 3330
                           i                  i    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (86 / 44)
Gap_init rate = 0.02 (15 / 830), avg. gap size = 3.00 (45 / 15)  


2891 26.53 3.40 0.45  chr1_177160684_177166714     4657  5538 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_177160684_   4657 TGAAAAAACACCCCATGCTCATGGACAGGAAGAATCAATATCATTAAAAT 4706
                           i   i i i      i       iv      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177160684_   4707 GGTTACACTACCCAAAGCAATTTACAGATTAAATGCTATTCCTATCAAAC 4756
                           iv i   v      vii  i        v  i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177160684_   4757 TACCAATGACATTCTTCAAAGAACTAAAAAAATT-ATTTTAAATTTTATA 4805
                          v   iivi v  i  iiv    v vi v  ii -  ii    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_177160684_   4806 TGGAACCAAAAAGAGGGCCCA-AATAGCCAAGACAATCCTAAGCAAAAAG 4854
                              viiv  i -- i    -         i      i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_177160684_   4855 AAAAAAGCCAGAGAAATCACATTACCCAACTT-GAAACTATACTACAAGG 4903
                           v    iii   i v     i v     i  -i     -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_177160684_   4904 CTACAGTGACCAAAACAGCATGGTACTTGTATAAAAACAGGCATATAGAC 4953
                                i i   i    ii       v i    ii i  i        i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_177160684_   4954 CAATGGAACCGAATAGAGAGCCCAGAAATAAGGCCTCATATCTATGACCA 5003
                                 iv    v     i          iv  vi i  i    ii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_177160684_   5004 ACTGATCTTTGACAAAGCTGACAAAAGCA----ATGAGGAAAAGACTCCC 5049
                          i    i  i     i v  v   i v  ----   i     ii ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_177160684_   5050 TATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATATAGAAGATTG 5099
                          v     i              i      v  ?   i  ii i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_177160684_   5100 AAGCTGAACCCCTTCCTTACATCGTACACAAAAATCAATTCAAGATGGAT 5149
                            i  i      v   i   i i  i        i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_177160684_   5150 TAAAAACTTAAATGTAAAACCCAAAACCATAAAAACCCTGGAAGACAACC 5199
                         i ? i  i         i v i     i      vi i i     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_177160684_   5200 TCGGC---AAT----GCCATCCTGGACACAGCAAAGATTTCATGACAAAG 5242
                          v  ?---   ---- iv i i   iivvi    v i    v iivv v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_177160684_   5243 AAACCAAAAGCGATTGCAACGAAAGCAAAACTTGACAAAAGGGATCTAAT 5292
                          v         ivvv     i    v    v v  i   vv   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_177160684_   5293 TAAACTTAAGAGCTTCTGCACAGAAAAATAAACTATCAACA----GAAAA 5338
                         i   v    i i   i  ii vvv   iv v        v ----     
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_177160684_   5339 -----TCTACAGAACGGGAGAGAATATCTGAAAACTATACATCTGACAAG 5383
                         -----i i      i      i     i  v   ii   i      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_177160684_   5384 CT-CTAATATCCAGCATCTATAAGGAACTTAAACAGATCAACAAGCGAAA 5432
                         vv-  vi       v  v     i     ivv   iv    i  vvi   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_177160684_   5433 AACCA----CCCCATTAAAAAGTAGGCAAAGGACATGAAAAGACACTTTT 5478
                         i  v ----   v   ?    i i         iv    v     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_177160684_   5479 CAAAAGAAGACATACATGTGGCCAAGAAGGA--TGAAAGAAAAGCTCAAC 5526
                          v        i     vi       v   v --     - i v       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATGCTCAAC 896

  chr1_177160684_   5527 ATCACTGATCAT 5538
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (144 / 86)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.43 (34 / 14)  


3374 22.37 6.67 0.35  chr1_177357383_177362668.rev     3942  4795 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_177357383_   3942 TGGAAAGATATTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 3991
                                    i                     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177357383_   3992 GTCCATATTACCCAAAGCAATCTACAGATTCAATGCAATCTCTATCAAAA 4041
                          v v   i v      vii              i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177357383_   4042 TATCAATGACATTCTTCACAGAAATAGAAAAAA-AATCCTAAAATTTATA 4090
                          vi  iivi v  i  ii       v  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_177357383_   4091 TGAAACCATAAAAGACTCAGAATAGCCAAAGCAATCCTGAGCAAAAAGAA 4140
                           i  viii  ii   i             i     i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_177357383_   4141 ---AACTGGAGGAATCACATCACCTGACTTCAAATTATACTACAGAGCTA 4187
                         --- ii       v     iiv  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_177357383_   4188 TAGTGACCAAAATAGCATGGTACTAGCATAAAAACAGACACACAGAACAA 4237
                         i   i i   i i  ii       i      ii i     i i   v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_177357383_   4238 TGGAAAAGAATAAGGAATCCAGAAACAAATCCATACATCTAAACTGAACT 4287
                              v     vii  i        i   i        i  viv v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_177357383_   4288 CATTTTCAACAAAGGTGCCAAGAACATACATTGGAGAAAGGACAATCTCT 4337
                         v      i    i          v   v  v   i     i i i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_177357383_   4338 TCAGTAAGTGGTACTGGGAAAACTGGATATACCCATGCAGAAGAACAAAA 4387
                            ii  i    i      v         ?v v      i     ii  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_177357383_   4388 CTAGACCCC-ATCTCTCACCATATACAAAAATCAAATAAAAGTGGATTAA 4436
                         i i      - i   v                i  v v   i     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_177357383_   4437 AGGCTTAAATCTAAAACCTCAACCTATGAAACTACTAAAAGAAAACACTG 4486
                           i i     v   i v  v  v    i     vi  i         iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_177357383_   4487 AGGAAAGTCTCCAGGACACTGAACTAGGCTAAGATTTCTTGAATA---CC 4533
                         i? v  i   i iv   vi  iii     v v i      ii   --- v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_177357383_   4534 CCACAAGCACAGGCAACCAAAGCAAAA-TGGACAAATGGGATCACATCAA 4582
                            v       i     v    v    - i  i    v   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_177357383_   4583 G-TTAAAAATCTTCTGCACAGCAAAGGAAACAATCAACAAAATGAAGAGA 4631
                         i-       -   i  ii vv       v  v     v   i    i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_177357383_   4632 CATCCCACAGAATGGGAAAAAATATTT----------------------- 4658
                           v              i         -----------------------
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_177357383_   4659 --------CC------TATAA----------TAACTCTATAGGAAAAAAA 4684
                         --------  ------     ----------i     v   iv     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_177357383_   4685 ATCTAATAATCCAATTAAGAAATGGACCAAAGATCTGAACAGACATTTCT 4734
                         -- v     i      ? i      i v  i   i    i          
  L1M4_orf2#LINE/    800 --CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_177357383_   4735 CAAAAGAAGAAATGCAAATGGCAAACAGGCATATGAAAAGGTGCTCAACA 4784
                          v        v  i        v  i i   i        i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_177357383_   4785 TCACTGATCAT 4795
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.97 (124 / 63)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 5.45 (60 / 11)  


3255 23.40 0.96 4.57  chr1_177395439_177399738.rev     2870  3809 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_177395439_   2870 GAAAGATATCCCATGCTCATGGGTCAGAAGAATTAATAGCATTAAAATGA 2919
                                        i      i ii     v      vii    i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_177395439_   2920 CCACACTACCCAAAGCAATCTACAGATTCAATACAATCCCTATCAAAATG 2969
                          v i   v      vii              ii                v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_177395439_   2970 C-AATGATATTCTTCACAGAAATAGAAAAAAAAATCCCAAAATTTGCATG 3018
                          - iiviiv  i  ii       v  v  ivvi    i      iii   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_177395439_   3019 GAACCACAAAAGACTCCGAATAACCAAAGCAATCCCAAGCAAAAAGAACA 3068
                            vii   ii   i v     i     i     iii iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_177395439_   3069 GAGCTGAAGGCATCACACTACCTGACTTCAAAGTATACTACAAAGCTATA 3118
                         i  i  i   vv       v  ii i      iiv             i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_177395439_   3119 GTAACCAAAATAGCAAGATACTGGACTAACTACATACACACAGGCCATTG 3168
                             i   i i  iiv i      vv   vv i v   i i  ii  v  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_177395439_   3169 GAACAGAATAAAGAATCCAAAAATAAACCCACATATTTACAGAAAACTGA 3218
                            i     vi   i    i           i i     ii vv  i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_177395439_   3219 CTATCAACAAAGGCTCCA-GAACATACACTGGAGAAAGAACAACCTCTTC 3267
                         i v  i    i  iv   -  v   v  v   i       i ii  i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_177395439_   3268 AAAAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAAAATGAAACT 3317
                           v              v         ?   i     i  i      ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_177395439_   3318 AGATCCCCCTCTCTCACCACACACAAAAATCAACTCAAAATGGACAGAAG 3367
                         i  i   ivi   v     i i        i             ivi?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_177395439_   3368 ACTTAAATGTAAGACCTGAAACTATAAAACTACCAGAAGAAAACAAAGGG 3417
                           i           v  i             vii           v   ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_177395439_   3418 ATATGT-TTCAGAACATTGGTCTGAGAAAACATTTCATGACTAAGACTTC 3466
                         i  vi -   ivi  v    vi ii v  vvi    v iiv  v   vi 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_177395439_   3467 AAAAGCGCAGGCAACAAAAGCGCGCGCGTGCGCGCGCATACACACACACA 3516
                               i  i          ------------------------------
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAG------------------------------ 622

  chr1_177395439_   3517 CACACACACACACACACACACAAATGGGACTACATTAAACTAAAAGGCTT 3566
                         --------- v v - i v i    v     v   i   v v   ii   
  L1M4_orf2#LINE/    623 ---------AAAAA-ATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_177395439_   3567 CTGCACAGCAAAGGAAACAATCAACAGAGTGAA--GACAGCACCTGCAGA 3614
                         i  ii vv       v  v     v i      --    --   ii    
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA--ACCCACAGA 710

  chr1_177395439_   3615 GTGGGAGAAAATATCTGCAAACTATTCATCTGAAAAGCAAATAGTATCCA 3664
                         i             i      ii  vi      v   vi v v       
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_177395439_   3665 GAATACCCAAGGAACTCAAACAACTCAATAATGAAAAAGCAA----TCCC 3710
                              ivi  i      vv             i    ii   ----i  v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_177395439_   3711 ATTACAAAGTGGGCAAAGGATTTGAATGGACATTTCTCAGAAGAAGACAT 3760
                            ?v   i                  i          vi       i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_177395439_   3761 ACAAATGGCCAATAGGTATATGAAAAAAGTGCTCAATATCACTAATCAT 3809
                                       i i i       i -       i    ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (140 / 76)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 5.78 (52 / 9)  


2402 25.11 2.68 0.99  chr1_177429946_177431638.rev      494  1202 (491)    L1M4_orf2#LINE/L1      188   908 (0)  

  chr1_177429946_    494 TGAAAGTCAAGAACTTGAAACTTAGAGGCATCCTATTACCTAACTTCAAA 543
                              ivv      ---   v  i    vv  vi i v  i  i      
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAAC---AAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_177429946_    544 CTATACAATGAGGCTACAGTAAACAAAACAGCATGGTACTGGTACAAAAG 593
                         viv   v ii i          v   i    ii         i i  iii
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_177429946_    594 CAGACACAGAGATCAATGGAAGAGAATAGAGAGCCCAGAAATAAAGCTGC 643
                         i     i v            v     v     i           v iii
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_177429946_    644 ACACCTACACTCT-CTGATCTTTGACAAAGTTGACAAAAACAAGCAATGG 692
                            ii  iiv  v-i    i  i     i v  v   i v  vv      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_177429946_    693 GGAAAGGATTCCCTATTCAATAAATGGTGCTAGGATAACTGGGTAGCCAT 742
                               i  vvi  v     i          i   i      i  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_177429946_    743 ACGCAGAAGACTGAAACTGGACTCCTTCCTAACACCATATATAAAA-TCA 791
                          i   i    v    ii     i   v   v          i    - i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_177429946_    792 ACTCAAGATGTATTGCAGACTTATATGTAAAACCTAAAACAATAAAACCC 841
                               i   v  ii?    i  v      i v       v       i 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_177429946_    842 CTGGGAGATAACCTAGG---AAATACCATTCTGGACATAGACCCCGGCAA 888
                         i i i   v   v    ---    -- -   vv   v v iviiv     
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAA 581

  chr1_177429946_    889 AGATTTCAT-GCTGAAGGTGCCAAAAGCAATTGCAACAAAATCAAACACT 937
                         v i    v - v - v iii         vvv         vv   v iv
  L1M4_orf2#LINE/    582 TGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_177429946_    938 GCCAAATGGGACTT-----AAACTAAGAGCTTCTGCACAGCAGAAGAAAA 982
                          vi    v      -----   i   i i   i  ii vv  i i  v v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_177429946_    983 TATAAACAGAGTAAA----TAACTTAGAGAATGGGAGAAAATATTTGCAA 1028
                            v  v i   i  ----i   ii v                       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_177429946_   1029 ACTATGCATCCAACCAAAGTCTAATATCCAGAATCTATAAGGAACT--TA 1076
                          ii  ii   ii iv ii v  vi          v     i     --  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_177429946_   1077 -AATTCA-CAAGCAAAAAACAAATAATCCCATTAAAAAGTGGGCAAAGGA 1124
                         -  i   -i  vv    i        i  v   ?    i           
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_177429946_   1125 CATGAACAGACACTTTACAAAAGAAGATATACACATGGCCAACAAGTATA 1174
                         iv    i     i  iv v              v        i   i i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_177429946_   1175 TGAAAAAATACTCAACATTACCACTCAT 1202
                               i  i        i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (104 / 71)
Gap_init rate = 0.02 (13 / 721), avg. gap size = 2.00 (26 / 13)  


2486 22.21 4.83 7.40  chr1_177438947_177441989.rev     1621  2552 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_177438947_   1621 TGGAGACACTTTCCATAATCATGTATTGGAAGCCAAAATGCAGTAAAGAT 1670
                             i v iv i    iv     v        v vv   iiv  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177438947_   1671 GTCAATTCTCCCTAAATTGATCTACAGATTTAACACAGTTCTAATTGATA 1720
                          v    v     i                 i   i  i i iv  ii v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177438947_   1721 TGCCAGAAATATTTTTTCATAGATATAGACAAACGGAGTCTAAATTTTAT 1770
                          v    vviiv      -ii   v  v     i v  vi     v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_177438947_   1771 ATTAGGCAAAATATAAAGGCAAAATAACTAGAATAACTGGATAAAAAGGC 1820
                           --  --    ii  i  ------ v i      i ------------ 
  L1M4_orf2#LINE/    150 AT--GG--AAATGCAAGGG------ACCCAGAATAGC------------C 177

  chr1_177438947_   1821 AAAAGCCAATAGAAAGACAAAAGAATGAAAATAGCCATAAAATTTTTGAA 1870
                             --    ------------------------- v i   ------  
  L1M4_orf2#LINE/    178 AAAA--CAAT-------------------------CTTGAAA------AA 194

  chr1_177438947_   1871 AAACAATAAAGTCAGAGAAATCACCCTAGACAATTTTAAGACATA--ATT 1918
                         i  v  i     ii   i v    v  vvv      i  i  v  -- iv
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_177438947_   1919 AAGACAAAGTG-----GGCACTGTGGTATTTGGCAAAGGAACAGACATAT 1963
                            vi v   i----- i  v       i -    v i i i        
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACT-GGCATAAGGATAGACATAT 293

  chr1_177438947_   1964 AAACTAATGAAACAGAATAGACAGTCCAGAAATAGACCCAAACAAATACG 2013
                          i ii    i  i     v  v            i     v   vv  i 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_177438947_   2014 GTAAATTGATTTTTGACAAAGGTGCACAGGCAATTCAAAGGAGAAGGGAG 2063
                           v          i     i     vv  i v      v  i   i i v
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_177438947_   2064 AGAGACTCTTTTTTAACAAATTATGTTATAACAACTGGATGTCCATATCT 2113
                           ----      i-       vi  i ivi          i?   i  vi
  L1M4_orf2#LINE/    394 AG----TCTTTTC-AACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_177438947_   2114 AAGAAAATGAA-CTGG-TCTAAACCCCACACCTTTTACAAAAATTAACTC 2161
                           i i      -i   -i ivv   i      v v               
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_177438947_   2162 AAAATGGATGACAGAGCGAAATG-AAAATTTAAAACTATAAAACTTTTAG 2210
                                  v ?   v v     -  i vi               i    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_177438947_   2211 AAGAAAACAAAGGAGAAAATCTTTGTGACCATAGGTTAGACAAAAAGATC 2260
                                  v   ? v       i      v i      i   viivv  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_177438947_   2261 TTAGGCATGACATCAAAA----------TGAAA--AAAAACTGATAAATT 2298
                             ii      i     ----------ii   --     iv        
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_177438947_   2299 GAACTTAATCAAAACAAAAAAACTT-GTGCTATGTGAAGGCCACTGTTAA 2347
                          i    v       iv     vi  -     - -ii    v    i i  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCT-T-CAAAGGACACTATCAA 686

  chr1_177438947_   2348 AAGAATGAAAAAACTATAATCTACAGACTTGGACAAAATGTTTGCAAGTC 2397
                         i i i      i  ---  i i     v v   v     i       i  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGAC---AACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_177438947_   2398 ACAAAATCAACAAAAGGACTTGTATCTAGAATATATAA-GCACTCTCAAA 2446
                          i v viii i  i-           i           - v     i v 
  L1M4_orf2#LINE/    734 ATATATCTGATAAG-GGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_177438947_   2447 ACTCAAGAGTGAGAACACAGAAAAGCCAAATTTAAAAATGGACAAAAGAC 2496
                               v i i i  v   i v  v    -  ?        i    i  i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAA-TTWAAAAATGGGCAAAGGAT 831

  chr1_177438947_   2497 TGG------------------GAA---ATACTAATGGCAAAGAAGCATAT 2525
                          v ------------------   ---    v      v  v     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_177438947_   2526 AAAAAGATGTTTAATACCATGAGCCCA 2552
                         i        i i  i i  ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (119 / 84)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 4.22 (114 / 27)  


3196 18.10 3.29 4.81  chr1_177456683_177458464.rev      502  1291 (491)    L1M4_orf2#LINE/L1      131   908 (0)  

  chr1_177456683_    502 AGCTGATGCTAAAATACATATGGAAATGCAAGGAACCCAAAAGAGCCAAA 551
                                v       v                 i     i  v       
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr1_177456683_    552 ATAATTTTGAAAAAGAAGAGTAAAGTTGATGAATTAATACTTCCTGATTT 601
                          i   i             ii       iv i i v i      ii    
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr1_177456683_    602 TAAAACTTACCATAAAGCTATAATA-TCATGATAGCATAGTACTGATGTA 650
                         i         i i       i i  -   v  i  ii i      iii  
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_177456683_    651 AGAATAAACATA--GGTCAACGAAAAAGAATTGAGAGTCCAGAAATAAAC 698
                           i   i     -- i    i i  v                        
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_177456683_    699 TCTCACACTTGTGTTCAACTGATTTTCAACAAAGGTGACAAGATAATTCA 748
                         i vi   i  i  v    i        i    i    v     iv     
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_177456683_    749 ATGTGAGAAAGACTAGTCTTTTCAACAAATGGTGGTGGGACAACTGAATA 798
                            - i      v                     v           i   
  L1M4_orf2#LINE/    381 ATG-GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_177456683_    799 TC-ATATGCAAAAGAATGAAGGGAGAGTCTT-TCT---ATCATGTGCGAA 843
                         ? - i                vvi  vi i -i  --- i   i i i  
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_177456683_    844 AATTAATTCAAAATGGAGCAAAGACCTTCCTCTTTTTCCAGTATCGTTTT 893
                               i          v  ?      -----------------------
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCT----------------------- 506

  chr1_177456683_    894 CATTACTAAGTATCACCCACAATGCTATCATTACATTGCTCTTAGAAAAT 943
                         -------  i i v -----i -    vv i  i vvi         i -
  L1M4_orf2#LINE/    507 -------AAATGTAA-----GA-GCTAAAACTATAAAACTCTTAGAAGA- 542

  chr1_177456683_    944 AAAAATAAGA--AAATCTTCATGACTGAAGATAAGACAAACCTCTCTTAC 991
                            v   i ?--        i    ivvi i v  i   vvv i     v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_177456683_    992 ATATGACATTAAAAGCACAATGAATGAAAGAAAAATGAGATAAATTAGAC 1041
                                 ii          vv  ii         vv         i   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_177456683_   1042 TTTATCAAAATTTATAACTTTTGTTATTCAAAGGACACCATCAATAACAT 1091
                           i         v v         vv            i     v  vi 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_177456683_   1092 GAAAAGGTAAAC-ATAGAATGGGAGAAAATATTTGCCAAT---ACAACTG 1137
                               ii  v - i                     v   --- i v   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_177456683_   1138 ACGAAGGACTTGTATT-------TATAAGGAACTCTTATAATGCAATAAT 1180
                          ii i          i-------     i         i  iv       
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_177456683_   1181 ATAAAGAC---TA-CACAATTTTAAAATGGGCAGAGGATGTGAATAGACT 1226
                          v      ---  - v     ?v          i     v         v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_177456683_   1227 TATC-CCAAAGAAGAAATAAAAATGGCTAATAAGCATATGAAAATATGCT 1275
                          v  -          v   v       i        i       v     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_177456683_   1276 CAACAGCATTACCCAG 1291
                              v  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (85 / 54)
Gap_init rate = 0.02 (17 / 778), avg. gap size = 3.76 (64 / 17)  


 404 27.81 1.78 4.73  chr1_177507318_177509999     1039  1207 (1475)    L1M4_orf2#LINE/L1        3   166 (742)  

  chr1_177507318_   1039 GAGAGAGATGCTATGTTCATGGGTATATTGCACACACCCAGTATTTTAAA 1088
                           i   v  v i          ----    v - v  ii i    v v  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGG----ATTGGA-AGACTTAATATTGTTAA 47

  chr1_177507318_   1089 GATACGTTGTTTCTTCCTGAGGTGATTTATAGATATAATACGTTCCAGCT 1138
                            -- viiv v  i  ii iv    i  i    vi  ii iv   vvv 
  L1M4_orf2#LINE/     48 GAT--GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_177507318_   1139 CAGAAATCTCAGAAGACTTCTTTGTA-AAATTGATAAGCAGATTTAAAAA 1187
                           -     i   vv v   i    i -       i    v   iiv    
  L1M4_orf2#LINE/     96 CA-AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_177507318_   1188 TTTATATGGAG--GCCAGGCAC 1207
                           i       i--  v   v  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGAC 166

Transitions / transversions = 1.14 (25 / 22)
Gap_init rate = 0.04 (6 / 164), avg. gap size = 1.83 (11 / 6)  

2246 22.57 10.30 1.97  chr1_177507318_177509999     1481  2189 (493)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_177507318_   1481 AAAAGT-ATATGGAAAGGCAGAGGACCTAGAATAGCCAAAGCAACTTTG- 1528
                             v -         v   ii     i            i   ii   -
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_177507318_   1529 -------GAACATAAATTGAAGGATTAACATTACCTTATG--AAAGCTTA 1569
                         -------     -  i   i    i v   i v  iv  v--   i    
  L1M4_orf2#LINE/    191 AAAAGAAGAACA-AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_177507318_   1570 TTA--AAGCTGCAGTAATCAAGAGAGTGTGGTAATAGTGTCATGGTAGGC 1617
                         i  --     i            v         v i ii v v i   i 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_177507318_   1618 AAAT-GATCAATGGACCAGAATAGAGTGTCCAAAAATAGACTAACATATT 1666
                          v  -          vi     v   v     i     i  iv i i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_177507318_   1667 -ACGAACAACAGATATTTGATAAAGATATAAAGCAGATT-AGTGGAGAAG 1714
                         - i iv   iv   v  i  i  i i iiv   vvv   - i   i   i
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_177507318_   1715 GG-TAGCATTTTCAACTAAGGATGCTGAAACAGTTGAAT-TCCATATACC 1762
                          i-   iv        v  v i     ii   ii  i  -?   i  i -
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC- 438

  chr1_177507318_   1763 AAAAAAAAAAAAAAATGAGCTTTCATCCATACTTCACA--ACATACAG-- 1808
                         --------    i     iv  vv i  v   i     -- i     i--
  L1M4_orf2#LINE/    439 --------AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_177507318_   1809 -----TTCTAAATGTACCATAGATCTAAATG--AAAACTGGAAACTACAA 1851
                         -----i  v     v i  ?   i       -- i i  i-      i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAA 529

  chr1_177507318_   1852 ATTTCT-AGAAGAAAATATAGAAGAAAGTCCTAATGACTTTGGGTTATGC 1900
                          vi   -         i    i? v  i  i vi    i        v  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_177507318_   1901 AAAGATTTCTTAGAAATGACACCAAAAGCAC------------------- 1931
                           v i         v                -------------------
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_177507318_   1932 -------------CTCATCAAAATTAAAAAACGTATGCTCTTCAAAAGAC 1968
                         -------------i                - v v  iv       i   
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chr1_177507318_   1969 A-TATTAAGAGAATGAAAAGAAAAGCAAGAGACTAGCAGAAAATATTTAT 2017
                          -   i    i i        v  v v v   v i v           ii
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_177507318_   2018 AAA--ACATATCTGTTAAAGGTCTTATATTTAGAATATATAAAGAACTCC 2065
                            -- i       v   i  v   i   ii                  i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_177507318_   2066 AATA-CTCAATAGAAGGAAAACAATCAACCCAACTTTTAAAAATGGGCAA 2114
                         v i -       iv ii  i    vi       --  ?            
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAA--TTWAAAAATGGGCAA 826

  chr1_177507318_   2115 AAGACCTGAACAG----TTCTTCACAGA---TGTACAGGTGGCAAATTAG 2157
                          i  ii    i  ----    i  v   --- i    ii    v   v  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_177507318_   2158 CATGTGATAAAATGCTCAATATCATTAGGCAT 2189
                           ii   v  i        i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (101 / 55)
Gap_init rate = 0.03 (24 / 768), avg. gap size = 3.62 (87 / 24)  


4273 19.03 3.06 0.34  chr1_177521114_177523237.rev      753  1635 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_177521114_    753 GAAAAGA-ATCCTGTGTTCATGGATTTAAAGATTTAATATTGTTAAGACG 801
                          i     -    ii            vi    i               i 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_177521114_    802 GCAATACTACCCAAAGCAATCTACAGATTTAATGCAATCCCTATCAAAAT 851
                                 v      vii           i  i                 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_177521114_    852 TCCAATGGCTTTTTTT-CAGAACTGAAAAAGTCAATCCTTAAATTCATAT 900
                         i   iiv  i      -     v vi v   iii     v          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_177521114_    901 GGAATTCCAAGAGGTCCCAAATAGCTAAAACAATAATGAAAAA--AGAAC 948
                             v v    i ii  vi      i        vv       --     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_177521114_    949 AAAGTTAG-GGACTCATACTTTGTCATTTTAAAACTTACTACAAAGCTAT 997
                               i -       i    iviv    i                   i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_177521114_    998 AGTAATCAAAACATTGTGGCACTGGTATGAAAACAGACATATAGATGAAT 1047
                                  i   v     i     i  i ii i            v   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_177521114_   1048 GGAATAGCACTGAGAATCCAGAGATAAACCTATACATCGATGGCTGATTG 1097
                                v i     i      i       i      iv    iii    
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_177521114_   1098 ATTTTCAACATGAGTGCCAACACCATTCAGTGGA-AAAGAATATTCTCTT 1146
                               i   v i       v        i   i-        v   i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_177521114_   1147 CAACAGCTTAGTCCTGTGACAACTGGATATTCACATGCAAAAAAGTGAAG 1196
                              iv -i  v   v            ?i           i i     
  L1M4_orf2#LINE/    402 CAACAAAT-GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_177521114_   1197 TTGGTCCCTTGTCTCACAGCATACACAAAGATTAATTCAAAACTCATTGA 1246
                             v   i ii      v    i     i     i      ivv  ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_177521114_   1247 TGACTTCAATATAGGAATTCAAACCATAAAACTCC--AAAGAAAACATAA 1294
                         v   i v   i  i  ii v    i         i--i           i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_177521114_   1295 TGATAAATCTTCATGACCTTGAATTTGGCAATAGATTCTTAGGTATCACA 1344
                         v?i         i        ii  v      i v       i   v   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_177521114_   1345 ACAAAAGTACATGAAACAAAAGGAAAAACAGATAAATGAGACTTCATCAA 1394
                         v      i   v v        i     i        vi           
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_177521114_   1395 AATTTAAAACATCAGTA--------GACATTATCAAGAAAGTAAAAAAA- 1435
                             v     v iv  i--------    i            i    i -
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_177521114_   1436 -------AAAA-GGGAGGAA-TATTTGCAAATCATTTATCTAATATAAGG 1476
                         ------- i  -     i  -              v     i   --   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA--AGG 748

  chr1_177521114_   1477 GTCTAGTATCTAGAACACATGAAGAACTCTTACAACTTAACAATGGAACA 1526
                          v  v     i    i i  i                i  i   ii  vi
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_177521114_   1527 ATGAACAACCCAATTAAAATA-GGGCTAAGAACCTGGATAGACATTTGTC 1575
                          ii  i         ?   v -    v   i ii  i          v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_177521114_   1576 CAAAATATATATATAAATGGCCAATGAGCACATGAAAAGATGCTTAATAT 1625
                             iv v     i           i                  i  i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_177521114_   1626 AATTAGTCAT 1635
                         v ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.09 (111 / 53)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 2.31 (30 / 13)  


3312 26.87 0.44 0.44  chr1_177567857_177574136.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_177567857_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177567857_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177567857_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_177567857_   5030 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_177567857_   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_177567857_   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_177567857_   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5227
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_177567857_   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_177567857_   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_177567857_   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_177567857_   5378 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_177567857_   5428 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_177567857_   5478 AACACCAAAAGTAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5527
                         i          i vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_177567857_   5528 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_177567857_   5578 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5627
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_177567857_   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_177567857_   5678 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_177567857_   5728 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5777
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_177567857_   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2174 23.08 2.99 5.27  chr1_177679593_177681565      421  1122 (851)    L1M4_orf2#LINE/L1      175   860 (48)  

  chr1_177679593_    421 GTCAACAGAAACCTGAAAAAAGAAAAAAAGACTGAAAAAAAACCTGGCAC 470
                          i   v v  v i       ii i  v  iii  i ii ----  vi   
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA----CTCACAC 220

  chr1_177679593_    471 AGAATATTCCAGAAATGTGGAACAACTATAAGACTTACCATAA-----CA 515
                         ------    ------------   i vi  i      i i  -----  
  L1M4_orf2#LINE/    221 ------TTCC------------CAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_177679593_    516 TCAATCAAGATAATGTAGTATTAG---GAAAATAGACAAGCAGATCAATG 562
                         vi        i i   i   i i ---i ii       vii         
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_177679593_    563 GAACAGAC-----AGTCCAGAAATAGGCTGACATAAATACAGTCAACTGA 607
                            i   v-----            ii iv i i vv  ii     i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_177679593_    608 TCTTTCACAAAGGAGC-AAGTGCAATACAACAGAGCAAAGAGAGTCTTTT 656
                          i  iv    i  v  -   -i v  v   ii i v  ii v        
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_177679593_    657 CAACAAATGGTGCTGAAACAACTGGACATCCA--TGCCAAAAAAATGAAG 704
                                        ii         i ?   --   -    i       
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-AAAAGAATGAAG 450

  chr1_177679593_    705 TTGGAGGCAGACTTTACACCTTA-ACAAAAATTAACTCAAAATGTATCCA 753
                              vv vv  i i     v  -                    v   - 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC-A 499

  chr1_177679593_    754 CAGACCTAAATGTAAAATGC-AAAATTATCAAACTCCTGGAAGAAAACAC 802
                         ?              i -  -    i   v      i i          i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_177679593_    803 AGGAGAAAACCTAGATGACCTTGGGTATGGCAATGACTTTTTAGATGCAA 852
                            ? v   i  vvi           vv       ii  i      iii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_177679593_    853 CACCAAAGACACTATATATCCATGAAATAAATAATTGA--AATTGGGATG 900
                                ii   --- - v v ii   v   v   v  --      - iv
  L1M4_orf2#LINE/    599 CACCAAAAGCAC---A-AGCAACAAAAGAAAAAATAGATAAATTGG-ACT 643

  chr1_177679593_    901 TCATTAAAATTAAAAACTTATGCTCTGTGAAGT-CACTGTCAAAAGAATG 949
                             i              v  iv  vii   v-    i    i i i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_177679593_    950 AGAAGACAAGCCACAGATTGGGGTAGAATATTTGCAAAAGATTCATCTGA 999
                          i       v       v    iv i            vv  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_177679593_   1000 TAAAGGACTGTTGTCCAGAATGTATTATACAAAGAATTTTTAAAACTCAC 1049
                            i     vv i        i   -----      i i   v      v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATAT-----AAAGAACTCTTACAACTCAA 788

  chr1_177679593_   1050 CAGTATGAAAACTAACAGCTTGATTTTAAAAATGGGCAAAAGACCTGAAC 1099
                         i i  vi  i  v  i i iii   ?-             i  ii    i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAAT 837

  chr1_177679593_   1100 AGACACCTCATCAAAAAAGAGAT 1122
                              ii  vi    i    v  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.93 (104 / 54)
Gap_init rate = 0.03 (21 / 686), avg. gap size = 2.76 (58 / 21)  


 758 29.77 11.65 3.07  chr1_177857439_177859048      500  1117 (493)    L1M4_orf2#LINE/L1      238   908 (0)  

  chr1_177857439_    500 TATTATAAACCTACAATAAATAAAATAGTGTAG----------------G 533
                           i  i   v     i   vi  i i     i ---------------- 
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_177857439_    534 ACATCTTGGAGT--TGGAAT-GAGATAAGACGTCCAGAAATAAACCAAAA 580
                             v -i  vi--      -  iv i   -               v v 
  L1M4_orf2#LINE/    288 ACATAT-AGATCAATGGAATAGAATTGAGA-GTCCAGAAATAAACCCATA 335

  chr1_177857439_    581 C--TTATTGGGAGTTTAGCTTCTGATAATGATGGCATTTCAAATCATTCA 628
                          --    v vv i  v vi   -  i  v i  v  ---- i i      
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTC-GACAAGGGTGCCA----AGACCATTCA 380

  chr1_177857439_    629 --GGAAAAGAAATGAATTATTCAATAAATGGTGTTGAGACAACTGGGTAG 676
                         --  ii  ii   iivi v     i        i  i         i  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_177857439_    677 CCATCTGGAAAAAAATTAAGTTGGATTCAGATCTCACTTCTTATATTAGG 726
                            iv  v    i   v        ii vv i     vi v    iv ii
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_177857439_    727 ATACATACCAGGAGAAGTCAGTGATTTAAATGT----TTCAAAATGATAG 772
                           vv i-i  ii viii   ?v  ii       ----vii    iv   -
  L1M4_orf2#LINE/    481 ATTAAC-TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA- 528

  chr1_177857439_    773 AAACAAGTTTGGGAGAGTAAAAAAGG-----ATCT-AATGACCATGTTGG 816
                             --vi  i i   i-  v v   -----    -vi     ---    
  L1M4_orf2#LINE/    529 AAAC--TCTTAGAAGAA-AACATAGGNGTAAATCTTCGTGACC---TTGG 572

  chr1_177857439_    817 AACAGGGAAGAACTTCCAAAGTATGACACTAAAAACAGAAGCCATAGAGA 866
                         ivi   v  viii   iv ii        i    i  v    v i i ii
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_177857439_    867 AAAAAACA-ATAACTTCTATTGCATTAAAATTA----------TGCAT-- 903
                               i -    v  vv i v   i       ----------   v --
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_177857439_    904 -GGGAAA-----AAGAAC---AAAAGTCAGTTCA--GAA---GAGTAA-T 938
                         -i   v -----     v---     v  iii  --   ---   v  - 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_177857439_    939 GT---CAAACCAGAAA---AATTATG--CTAATATTCCTAATGCATAATG 980
                         i ---    i  v v ---i  v v --  vi   i vv   ii    v 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_177857439_    981 ACCTTCTCTT-CA--TCAACAAGAAAAATGACATACTATACAGTAAGAAC 1027
                          v  ---   -  --    i  v     -    v iv iv  i v?i  v
  L1M4_orf2#LINE/    773 AACT---CTTACAACTCAATAATAAAAA-GACAAATAACCCAATTWAAAA 818

  chr1_177857439_   1028 ATTTGCAAAAGGTATGAACAGAGAGTTCGTAGAAAAAGGAACACAAGTGT 1077
                           vv     i i v    i   v v   vivi  i   iv i    i  v
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_177857439_   1078 TTTATGAACATATACAAAGCTGCTTCACATTACTCATAGT 1117
                         iiv  i i  i  iv    v    iv    i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (104 / 77)
Gap_init rate = 0.05 (32 / 671), avg. gap size = 2.84 (91 / 32)  


3199 26.52 0.88 0.55  chr1_177897737_177902292     3159  4063 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_177897737_   3159 TGGAAGAAAATTCCATGCTTATGGATAGGAAGAATCAATATCGTGAAAAT 3208
                              ii v  i     i i      v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177897737_   3209 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATAAAGC 3258
                            v     v      v i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177897737_   3259 TACTA-CTGACTTTCTTCACCGAATTGGAAAAAATTACTTTAAAGTTCAT 3307
                          v i -   v    i  -i v   v v  v  iv v iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_177897737_   3308 ATGGAACCAAAAAAGAGCCTGAATTGCCAAGACAATCCTAAGCAAAAAGA 3357
                               viiv  ii  v  v    v     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_177897737_   3358 ACAAAGCTGGAGGCATTACATTACCTGACTTCAAACTATACTACAAGGCT 3407
                               i      vv i   i v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_177897737_   3408 ACAGTAACCAAAACAGCATGGTACTGGTATGAAAACAGATATATAGACCA 3457
                                i   i    ii         i  i ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_177897737_   3458 ATGGAACAGAAC--AGAGCCCTTAGAAATAACACCACACATCTACAATCA 3505
                               i    i--    i  --        vv   i    i  iii   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_177897737_   3506 TCTGATCTTTGACAAACCTGATTAAAAACAAGAAATGGGGAAAGGATTCC 3555
                         vi    i  i     ivv  -ii  i v  vvv           i  vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_177897737_   3556 CTATTTAACAAAGGGTGCTGGGAAAACCTGCTACCCATATGTAGAAAGCT 3605
                           v  i      v          v   iv v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_177897737_   3606 GAACCTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3655
                            vi    i i  v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_177897737_   3656 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3705
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_177897737_   3706 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 3754
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_177897737_   3755 AAACACCAAAAGCAATAGCAACACAAGCCAAAAGAGACAAATGGGATCTA 3804
                         vi            vv       v   vv    v   i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_177897737_   3805 ATTAAACTAAAGAGCTTCTGCGCAGAAGAAGAAATTACCATCAGAGTGAA 3854
                           i   v v  i i   i  i  vvv i i  v i  i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_177897737_   3855 TAGGCAAACTACAGAATGGGAGAAAATTTTTGCAATCTACCCGTCTGACA 3904
                         v  i   v i                 v       vii ivii     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_177897737_   3905 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 3954
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_177897737_   3955 AAAACAAC--ACC--ATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 4000
                           i    v--   --  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_177897737_   4001 CTCAAAAGAAGACATCTATGCAGCCAACAGAGGCATGAAAAAATGTTCAT 4050
                            v        i  vi viii     i iivi        i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_177897737_   4051 CATTACTGGCCAT 4063
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2904 27.48 0.49 0.49  chr1_177926416_177928239      500  1314 (510)    L1M4_orf2#LINE/L1       46   860 (48)  

  chr1_177926416_    500 AAAATGGCCATACTACCCAAGGTAATTTACAGATTCAATGCCATCCCCAT 549
                           i     v     v     iv i  i           i  v     i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_177926416_    550 CAAGCTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAA 597
                            iv v   iivi i  i  ii     -   -- v  i  - iii    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAA 143

  chr1_177926416_    598 GTTCATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCC 647
                         i           viiv  ii  v  v v  v     iv     i i ivv
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_177926416_    648 AAAAGAACAAAGCTGGAGGAATCACACTACCTGACTTCAAACTATACTAC 697
                          i          i       v       v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_177926416_    698 AAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAT 747
                           i          i   i    ii         i iv ii i   v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_177926416_    748 AGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTA 795
                                     i    i--    i  --        vv  ii i ii  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chr1_177926416_    796 CAACTGTCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGG 845
                         iiiiiivi    i  i     ivv  vv  i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_177926416_    846 ATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGG 895
                           vvi  v  i  i              v      v  ?   i   i ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_177926416_    896 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAG 945
                          iiv    ii    i    v   i     v           i  i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_177926416_    946 ATGGATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAG 995
                               i ?   ii    i  v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_177926416_    996 AAAACCTAGGCATTACCATTCAGGACTTAGGCATGGGCAAGGACTTCATG 1045
                              v    ?i v viv   iv   i v  vv i     v ii   v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_177926416_   1046 TCCAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGA 1095
                         vvi vi            vvi           v     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_177926416_   1096 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 1145
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_177926416_   1146 TGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCT 1195
                             v  i     i   i             v  i    vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_177926416_   1196 GACAAAGGGCTAATATCCAGAATCTACAGTGAACTCAAACAAATTTACAA 1245
                           i  i  i  vi          v  i iv      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_177926416_   1246 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGAC 1295
                         v     i     i     v  i?    i     i     iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_177926416_   1296 ACTTCTCAAAAGAAGGCAT 1314
                          i     v       ii  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.59 (135 / 85)
Gap_init rate = 0.01 (5 / 815), avg. gap size = 1.60 (8 / 5)  


3102 26.90 0.77 0.66  chr1_177966898_177972147.rev     3853  4759 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_177966898_   3853 TGGAAGAACACTCCACACTCATGGATAGGAAGAATCATTATTGTGAAAAT 3902
                              ii i ii   iii        v      v i v      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177966898_   3903 TGTCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAA-- 3950
                         v iv     v      v i  i  i        i  v     i     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177966898_   3951 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 3997
                          v   -   v    i  -i     -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr1_177966898_   3998 CATATGGAACCAAAAAAGAGTCCACATAGCCAAGATAATCCTAAGCAAAA 4047
                                  viiv  ii  vi viv        i i    i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_177966898_   4048 AGAACAAAGCCGGAGGCATCACGCTACCTGACTTCAAACTATACTACGAG 4097
                                  ii     vv    i  v  ii i      viv      i i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_177966898_   4098 GCTACAGTAACCAAAACAGCATGGTACTGTTGCCAAAACAGATATATAGA 4147
                                   i   i    ii        viiiv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_177966898_   4148 CAAATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACC 4197
                         iv       i    iv    vii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_177966898_   4198 ATCTGATCTTCGACAAACCTGACCAAAACAAG-AAACGGGGAAAGGATTC 4246
                          vi    i        ivv  -    i  v v-v  i        i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_177966898_   4247 CCTATTTAATAAATGGTATTGGGAAAACTGGCTAGCCATATGCAGAAAAC 4296
                         i  v  i  i       ii     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_177966898_   4297 TGAAACTGGATCCCATCCTTACACCTCATACAAAAATTAACTCAAGATGA 4346
                             ii    i   vv   i     vi                  i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_177966898_   4347 ATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4396
                           i ?    i           v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_177966898_   4397 CCTAGGCA-ATACCACTCAGGACATAGGCAAGGGCAAAGACTTCATGACT 4445
                          v    ?i- v i -i  iv   v v  vvvi     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_177966898_   4446 GAAACATCAAAAGCAATCGCAACAAAAGCCAAAATAGACAAATGAGATCT 4495
                         ivi   i        vvv          vv        i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_177966898_   4496 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAGCAGAGTGA 4545
                         v  i   v v  i i   i  ii vv    i  v       iv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_177966898_   4546 ACAGGCAGCCTACAGATTGGGAGAAAATTTTTGCAATCTATCCATCTGAC 4595
                          v  i  i  i     v           v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_177966898_   4596 AAAGGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAGAA 4645
                           i  i  vi          v  i   v    ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_177966898_   4646 AAAAACAAACAACCCCATCAAAAAATGGCCAAAGGCTATGAACAGACACT 4695
                            i     i     v  i?        v      v v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_177966898_   4696 TCTCAAAAGCAGACATTTATGCAGCCAACAAACTTATGAAAAAATGCTCA 4745
                             v    v   i  vi viii     i  i vi       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_177966898_   4746 TCATCACTTGTCAT 4759
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3164 27.20 0.55 0.55  chr1_177976156_177982534     4981  5888 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_177976156_   4981 TGGAAGAACACTCCATGCTCATAGGTAGGAATAATCAATATCGTGAAAAT 5030
                              ii i ii     i    i i v    v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_177976156_   5031 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5080
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_177976156_   5081 TACCAATGAATTTCTTCACAGAA-TTGGAAAAAACTACTTTTAAG-TTCA 5128
                          v   iivivi  i  ii     -   -- v  i  iv ii   i-    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_177976156_   5129 TATGGAACCAAAAAAGAACCCACATTGCCAAGTCAATCCTTAGCCAAGAG 5178
                                viiv  ii  v  viv  v     iv     i v ivv ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_177976156_   5179 AACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTATACTACAAGGC 5228
                                i     ivv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_177976156_   5229 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5278
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_177976156_   5279 AATGAAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5326
                             i  i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_177976156_   5327 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5376
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_177976156_   5377 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAATCT 5426
                           v  i  i              v      v  ?   i   i i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_177976156_   5427 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5476
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_177976156_   5477 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5526
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_177976156_   5527 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5575
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_177976156_   5576 AAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGAGATCTC 5625
                         vi            vvi          vv    iv  i    vi  ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_177976156_   5626 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5675
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_177976156_   5676 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5725
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_177976156_   5726 AAGGGCTAATATCCAGAATTTATAATGAACTCAAACAAATTTACAAGAAA 5775
                          i  i  vi          v     v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_177976156_   5776 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5825
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_177976156_   5826 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5875
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_177976156_   5876 CATAACTGGCCAT 5888
                            v ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 362 29.43 8.05 6.90  chr1_178002166_178004896.rev     1806  2240 (491)    L1M4_orf2#LINE/L1      469   908 (0)  

  chr1_178002166_   1806 CTGTATTCCAGAATGAATTCCAAACAGATCTGAGATTTAAATATTAAAAA 1855
                          ii   v v i   v  i  v   ii    v?   ii     i -  i i
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAG 517

  chr1_178002166_   1856 ATGAAACCA-ACAAATATTTGGAGAAAACATGGGTG-AGTTCCTCTATAA 1903
                         v i    i - v  v v  v i         i  ? - iv  i  -i i 
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGA 566

  chr1_178002166_   1904 TCTTGCAGTAGGAAAAACCTTCCTA----TGAC-TCAAACCCAGAAGCAA 1948
                         i    viv    v  vivi   i  ----    -i    vv  v      
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_178002166_   1949 TT---TTAAAAATTGATAAATTTTATTACATACATTTTTTTAACTTTTGC 1995
                         iv---vv      v        vv i v   vv vv  vvv        i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_178002166_   1996 ATGGCAAA----------AAAAAAGAAAAAAGACAAATGGCAAAATAGGA 2035
                         iivv    ----------  i    vi         vivi  i   i   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_178002166_   2036 AAAACTGTTCACAATTTATTCATA---AACAAAAGGTTACTGTTCTTAAT 2082
                         i   v i  ii   v i  --   ---i i  ii ii vv i i vv   
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCAT--ATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_178002166_   2083 ATATGAAGACCTTCTA-AA------AATAAAGAGGCCAAAACATTTTTAA 2125
                             i    v  ii  -  ------      i  i --   ------   
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGAC--AAA------TAA 806

  chr1_178002166_   2126 TTTAATATACAATATATAATAAAATGTAATGTATAATAAAGATATGAACT 2175
                         iii   ------------- ?   ---    vii  -- i   v    iv
  L1M4_orf2#LINE/    807 CCCAAT-------------TWAAA---AATGGGCAA--AGGATTTGAATA 838

  chr1_178002166_   2176 GATAGTTCAT--AGGAAAAAATGCAAATAGCTCCTAA---TATGAAAAGA 2220
                           i v   vi-- i   i v  i     i  ivv   ---i         
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_178002166_   2221 TGTTCATCCTCAGTCATAAT 2240
                           i   v v   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (70 / 55)
Gap_init rate = 0.04 (19 / 440), avg. gap size = 3.42 (65 / 19)  


3447 24.25 2.35 0.89  chr1_178038716_178040721.rev      621  1515 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_178038716_    621 TGGAAAGATTTCCCATGTTTCTGGGTTAGAAGAATTAATATTGTTAAAAT 670
                                  v         iv   i  i     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178038716_    671 GGTCACACTGCCCAACGTGATACACAGATTCAGCACAATCCCTATCAAAA 720
                           iv i   v     vv    vi         i i               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178038716_    721 TTCCAATGGTACTTTTCACACAAATAAAAAAAC-AATTCTAAAATCTGTA 769
                          i   iiv ivi    ii  v    vi v  i -i  i       iii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_178038716_    770 TGGAATCATATAAG--ATCCTGAATAGCCAAAGCAATCTTGAAAAAGAAA 817
                              --  ii   -- i  v           i                i
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_178038716_    818 AATAAAGTTGGAAGCATCATACTTCCTGATTTCAAATTATATTACAAAAT 867
                           i         i vv   i      ii        viv  i      ii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_178038716_    868 TATAATAATCAAAACAG----ACACATAGGCATAAAAACAGACACATAAA 913
                           i i       i    ----ii  - -       ii i     i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTAC-T-GGCATAAGGATAGACATATAGA 296

  chr1_178038716_    914 CCAATGGAACAGAATAGAGAGCCTAGAAATAATTCGAAGCATAGACAGTC 963
                         i        i     v     i i        vi v vi   vv ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_178038716_    964 AACTAATTTTTGACAAGGCCACCAAGAATACATAATGGAGAGAGGACAGT 1013
                           i i     i       vii      vi ivi     i  i  i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_178038716_   1014 CTCTTCAATTAATTGTGCTAGAAAAACTGTATATCCACAGGCAAAAAAAA 1063
                           i     iv   v     i i v     v   ?     v      i  -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA- 445

  chr1_178038716_   1064 ATGAAACTGGACCCTTAATTTACACTATACACAAAAATCATCTCAAAATG 1113
                         -    ii       i  vi i    i   i        i v         
  L1M4_orf2#LINE/    446 -TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_178038716_   1114 GATTAAAGACCAAAACATAAGACCTGAAATCATAAAAATGCTGGGAAAAA 1163
                            i ?     v   ii     v  i   ii      v -  vi   i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAA 543

  chr1_178038716_   1164 AGAAATAAGGGAAAAGCTCTTTGATAGTGGCCTTGGCAATAATTTTTTGA 1213
                          - v   i ? v   v  iiv   ivv   vi v      ii   i  ii
  L1M4_orf2#LINE/    544 A-ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_178038716_   1214 ATATCACACCAAAAGCTTAGGTAACAAAAGCAAAAATAAACAAGTGGTAC 1263
                             v           vi i i        v       i i  i v v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_178038716_   1264 TGCATCAAACTAAAAAGCTTCTGAACAGCAAAGGAAAAT-CCAACAAAAT 1312
                          v       v v    i   i  vi vv       v v -i   v   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_178038716_   1313 TAAAAGACAGCCTACTTATTGGTAGAAAATATTTGCAAACTACATATCTG 1362
                         v        i  i  vv v   v                ii i       
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_178038716_   1363 ACAAAGAGTTAATATTTAAAGTATATAAAGAACTCACACAACTTAGCCAC 1412
                          i  i iii vi   ii i i              vi      i iiv i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_178038716_   1413 AAAAAAA-AAA------------AAAATGGGTAAATGACCTGAATAGACA 1449
                              i -   ------------        i   v  ii          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_178038716_   1450 TTTTTCCAAAGAAGACACATAGATGGCCAAGAGGTGCATAAAAAGGTGCT 1499
                            i           i i i i        v i ii   i     i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_178038716_   1500 CGACATCACTAATCAT 1515
                          i      ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (144 / 70)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  


2208 25.67 1.48 2.97  chr1_178071317_178075686.rev     2651  3324 (1046)    L1M4_orf2#LINE/L1        2   665 (243)  

  chr1_178071317_   2651 GAAAAAATATTTTATGCTCATGTACAGGAAGAATCAATATCATTATAATG 2700
                          i   i    iii   i     v iv      v i     ii   vi   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_178071317_   2701 GCCATACTGCTCAAAGCAATTTACATATTCAGTGCTATTCCTACCGAACT 2750
                           v     v i    vii  i    v     ii  v  i    i i  v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_178071317_   2751 ACCAA-TGTCATTTTTCACAGAATTATAAGAAACT-ATTCTAAAATTCAT 2798
                         v   i-  i -     ii     v - i v  i  -  i           
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_178071317_   2799 ATGGAACCAAAAAGAAGCCCAAATACCCAAAGTAATCCCAAGCAAAAAGA 2848
                               viiv  i i v  vi    v     ii    iii iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_178071317_   2849 ACAAAGGCATCACATTACCTGAGGTATCACGTTACCCAACTTCAAACTAT 2898
                               --------  i---    vv    ii v     i      viv 
  L1M4_orf2#LINE/    200 ACAAAG--------TTG---GAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_178071317_   2899 ACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGA 2948
                                i          i   i    ii         i i  ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_178071317_   2949 TACATAGACTAATGGAACAGG-TTAACGAACCCAGAAATAAAGTCACATG 2997
                         i i     ii       i  i-  i -  ii           vi  i ii
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACA 337

  chr1_178071317_   2998 CCTACAACCATCTGATTTTCCACAAAGTTGACAATAACAAGCAATGGGGA 3047
                         ii  iiii  vi        v    i v  v   v v  vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_178071317_   3048 AGGACTC-CCTATTCAATAAGTGGTGCTGGGATAAATGGCTAGCCATATG 3096
                          i  v v-i  v     i  i           i  v   v  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_178071317_   3097 CAGAAGATTGAATCTAGATCCCTTCCTTTCACTACATAGAAAAATCAACT 3146
                           i    v    vi i  i    v   iv   i i   v      i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_178071317_   3147 CAAAATAAATTAAAGACTTAAATGTAAAACCTAAAACTATAAAAACCCTA 3196
                               ii  i ?    i         i v              vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_178071317_   3197 ATAGAAAACCTAGG---AAATACCATTCTGAACATAGGCCTTGGCAAAGA 3243
                         iv       v    ---    -- v iv   v v i  i- v     v i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGT-TAGGCAATGG 584

  chr1_178071317_   3244 TTTCATA---ATGAAGTCTCCAAAAGCAATTGCAACAAAAACAAAAATAG 3290
                             v  ---    --- v         vvv         iv        
  L1M4_orf2#LINE/    585 TTTCTTAGATATGA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_178071317_   3291 ATAAGTAGGACCTAATTAAACTAAAGAGCTTCTG 3324
                             i v    i v  i   v v  i i   i  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.71 (108 / 63)
Gap_init rate = 0.02 (14 / 664), avg. gap size = 2.14 (30 / 14)  

 772 25.09 4.88 1.74  chr1_178071317_178075686.rev     3593  3879 (491)    L1M4_orf2#LINE/L1      613   908 (0)  

  chr1_178071317_   3593 GCAATGGCAAAAAATAAAAATAAACTAAATTTAAA---AATAAAATAAAG 3639
                             ---     i -       i -      vi v--- vi     v  i
  L1M4_orf2#LINE/    613 GCAA---CAAAAGA-AAAAATAGA-TAAATTGGACTTCATCAAAATTAAA 657

  chr1_178071317_   3640 AGCTTCTGCACAGCAAAAGAAGACATCAA-----TAAACAGACAACCTAC 3684
                          i   i  ii vv    i  vivi     ----- i  v        i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_178071317_   3685 AAAATG--AGAAAATATTCATGAACTATGCATTCAGCAAAGATCTAATAT 3732
                          i    --          iiii  ii  ii  iiiii  i iv  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_178071317_   3733 TCAGAATCTATAAGGAATTTAAACAAATCAATAGCTGAAAAACAA----C 3778
                         i      v     i   i ivv    v      iivi   i    ---- 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_178071317_   3779 CCCATTTAAAAATGGGCAAAGGACATGAACAGACACTGCTCAAAAGAAGA 3828
                           v   ?                iv    i     i v   v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_178071317_   3829 CATACGTGCAGCCAACAAGCATATGAAAAAATGCTCAACATCACTAGTCA 3878
                         i    iviii     i     i       i             ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_178071317_   3879 T 3879
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.38 (50 / 21)
Gap_init rate = 0.02 (7 / 296), avg. gap size = 2.71 (19 / 7)  


1147 27.06 15.95 2.88  chr1_178163860_178166074.rev      960  1724 (491)    L1M4_orf2#LINE/L1       44   908 (0)  

  chr1_178163860_    960 TTAAATATGGCAAGGCTCCCTTAGGTTAATCTATCCATTTA-TTCCATTT 1008
                             i-       vi     i- ii  i     ivv   i -iv v  ii
  L1M4_orf2#LINE/     44 TTAAG-ATGGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCC 91

  chr1_178163860_   1009 CAATTAAAATCTAA----TCTTTTTAGT-GAAATGTGACAAGGTGATCCT 1053
                          v  i      iv ----i      v i-     -       v       
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCT 140

  chr1_178163860_   1054 AAAAATCATATGATGAAT--AAAGAGCC---AATAGCCAAGACAATTTGG 1098
                             v       i-i   --  i ii  ---         i     i v 
  L1M4_orf2#LINE/    141 AAAATTCATATGG-AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_178163860_   1099 -----GGAGAATTAA-----------TATAC----------CAAAACT-- 1120
                         ----- i    iv  -----------i i  ----------       --
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_178163860_   1121 --ACAAAGTTATAAAAACTAAATTAGTGAGACATGGGTGAGAGGGATATA 1168
                         --      i  i iv  ii  ivi    v ii iv  i- v i     v 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGA 288

  chr1_178163860_   1169 CAAATAGACCAGTGGAATAAAATAAAGTGCCCAGAAACA----------- 1207
                           v     i  i       i   vi  v i       i -----------
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_178163860_   1208 ----------------------------GC--AGAT-------------A 1214
                         ----------------------------  --   i------------- 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_178163860_   1215 AGAATTGCCTACTCACTAAATGGTGTTGAGTCAAAGGACTAATCATA-GC 1263
                              v i  vi   vi        i  i v   vv iv  ?i  i -  
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_178163860_   1264 AGAGAAAAAATAGATAAAATTAGAGCCC-ACCTCACACTATACACAAAAA 1312
                          ---   i   i----  i  i  v   -         i   i       
  L1M4_orf2#LINE/    439 A---AAAGAATG----AAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_178163860_   1313 TTAATTCCAGATAGATTAAAAGAGCCAAATGTGATATGC-AAAACTGTAA 1361
                             i  v i  i   i ? -  v i      i v -  -      i   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWA-GACCTAAATGTAAGA-GCTAAAACTATAA 529

  chr1_178163860_   1362 AAAATGTTATTTAAAAAATATAAATG-ACTTCTTTTTTATCTCAGTATGT 1410
                           v- v   vv- i    i   ii? - vv    iv v i  ii ---  
  L1M4_orf2#LINE/    530 AAC-TCTTAGA-AGAAAACATAGGNGTAAATCTTCGTGACCTTGG---GT 574

  chr1_178163860_   1411 --GGAAGGAATTTTTTA---ATGAGAGAAGATGAACAAA-AATCATCAAA 1454
                         --  v ivii   i   ---    v vv i v v    i-  iv vvi  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_178163860_   1455 AAAATGCAGATACATTTTACCACACTAAAATTAATAACTCT-GTATGACA 1503
                              --     v   vv  iv  ii        v    i -  iivv  
  L1M4_orf2#LINE/    625 AAAAT--AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_178163860_   1504 AAAAGCACCATAAACAAAGTGAAAAAGACAAGTCAT-GTGGGGGAGAAGA 1552
                           iii   i  v  v          -     vi  i- viv       i 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAA-GACAACCCACAGAATGGGAGAAAA 721

  chr1_178163860_   1553 TACTGACAACTCAC-------------GAATTCTATCTAGAACATATACA 1589
                           i vi   v   i-------------  v  v    i    i     v 
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_178163860_   1590 AGATTCTCAGAAATCA-TAAGAAAAACACATACTACCTCATAGAAATATG 1638
                         ii i   i v  v   -   v     v   v iv   iv  v?   v   
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_178163860_   1639 GGCAGAGGATAGGAATCTACAGTTCACACAAGAGGAAATCCAAATGGCCA 1688
                             i     vv    vv   v   v vv    i  v  v          
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_178163860_   1689 ACAAACATATGTTCAG-TGCTCAATTTCATTAGTAAT 1724
                          i  i  i   vvv  -       iv   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (113 / 90)
Gap_init rate = 0.04 (38 / 865), avg. gap size = 3.79 (144 / 38)  


2496 28.43 4.19 1.36  chr1_178391855_178394344     1117  1999 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_178391855_   1117 TGGAAAAATATTTTATGCTCATGAATTGGAAGAGTCAGTATTGTTAAAAT 1166
                               i    iii   i     i         v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178391855_   1167 GGCCATACTGCCCAAA--G-----------CAACACTATTTCAATCAAAC 1203
                            v     v      -- -----------    i v  ii v      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178391855_   1204 TACAAA-TGTCACTTTTCACAGAATTAGAAAAAACT-ATTCTAAAATTTA 1251
                          v v i-  i -i    ii     v v  v  i-  -  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_178391855_   1252 CATGGAGCTAAAAAAGGGCCCA-AATAGCCAAAGCAATCCTAAGTAGCAG 1300
                         i     iv iv  i-  i    -          i     i i iv iv i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_178391855_   1301 GAACAAAGCCAGTGACATCACACTACCTGATTTCAAACTATATTATAAGA 1350
                                 iii v ivv       v  ii        viv  i  i  ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_178391855_   1351 CTACAGTAACCCAAACAGCATGGTCTTGGTACAGAAACAGAAACATAGAC 1400
                                  i v i    ii    vi   i i iii i   v i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_178391855_   1401 CAATGAAACAGAATAGGGAACCCAGGCATAAGGCTGCAAACCTACAGCCA 1450
                              i  i     v i  ii    iv    iv iii v ii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_178391855_   1451 TCTGATCTTCAACAAAGTTGACAGAATTAAGCAATGGGGAAAGGA--ATC 1498
                         vi    i   i    i v  v  ii ii vv            i --i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_178391855_   1499 CCTGCTCAATAAACAATGCTGGGATAGCTGGTTAGCTAGATGCAGAAAAA 1548
                         ii --    i   iii        i i    v  ? i v     i  i  
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_178391855_   1549 TGAAACTGGACCCTTACCTCTCAATATATGCAAACATTAA-----GATGA 1593
                             ii       i      v  vi    i    v     -----i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_178391855_   1594 ATTAAAAATTTGAATATAAGACCTCAAACTATGAGAATCCAAGAAATACA 1643
                           i ? i ii i   i     v  v       i i v  iv    iv v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_178391855_   1644 CCTAGGAA-ACACCATTTTG-GACATCAGCCTTGAGAAGGATTTAT--GA 1689
                          v    ?i- v i --  i -   v ii vi v iv  v i   v --  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_178391855_   1690 CTAAGTCCTCAAAAGCAATTGCAATAAAA--AACAATTGACAAGTGGGAC 1737
                         -  v v vi        vvv    i    --  v   v  i  i v    
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_178391855_   1738 CTAATTAAA-CTAAAGAGCTCTGTATGGCAAAAGAAGTTATCAACAGAGT 1786
                         i v  i   -i    i vi i   iivv    i  vii      v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_178391855_   1787 AAACAGACAACCTACAGAATGAGAATGCAAAATATTTGCAAACTATGCAT 1836
                         i  v        i        i  i---              ii  ii  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAG---AAAATATTTGCAAATCATATAT 739

  chr1_178391855_   1837 CCAACAAAGGTCTAATATCCAGAATCTCTAG-GAACATAAACAATTCAAC 1885
                          ii i  i  v  vi          v v  i-    vivv    i    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_178391855_   1886 AAGCAAAAAACAAACAACCCCATTAAAAAATGGGCAAAGGACATGAAAAG 1935
                           vv    i     i     v   ?                iv    v  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_178391855_   1936 -CACTTTTT---AAAAGATACACAAGCAACCAACAA--ATGTGAAAAAAA 1979
                         -  i  i i--- i      i    iiii    i  -- ii      i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA- 888

  chr1_178391855_   1980 TGCTCAACATTGCTAATTAT 1999
                                   ii????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (167 / 80)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.04 (49 / 24)  


3728 17.72 7.65 0.24  chr1_178538964_178540829      547  1370 (496)    L1M4_orf2#LINE/L1        1   885 (23)  

  chr1_178538964_    547 TGGAAAAACATCCCATGTTCATGAATTGGAAGAC--AATAGCATGAAGAT 594
                               i i              i          --    vii v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178538964_    595 GTCAATACTACCCAAAGTGCTTTACAGATTTAATTCAATCACTATCAAGG 644
                          v       v      v  v i        i  iv     v       ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178538964_    645 TCCCAATGACATTTTTTGAAGAAATAGAAAAACTCATTCTAAAATTTATA 694
                              iivi v       v      v  v  i  v  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_178538964_    695 --GATTTCCAAAGGACTCTGAATAGCCAAAACAATCCCAAAAAAGAACAA 742
                         --  vv v   i    i v                 iii        v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_178538964_    743 TAAAGCTGGAGGACTCACATTTCCTGATGTCAAATCTTACCACAAATCTA 792
                         i    i             i    ii  v     v     i     v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_178538964_    793 CAGTAATCAAAA--GTGTGGTACTAGTATA----CAGACATATAGACCAA 836
                                   i --          i i   ----i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_178538964_    837 TGGAATAGAATAGAGAGTCCAGAAATAAAC-----------------ATT 869
                                    v                  -----------------   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_178538964_    870 GA------ATA---GTGCCAAGACCATTCAATGGGAAAAGGAAAGTCTTT 910
                           ------ i ---                     i    i v       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_178538964_    911 CCAACAAA-GGTGCTGA---------ATATCCATATGCAAAAGAGTGAAG 950
                         i       -       i---------   ?   i          i     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_178538964_    951 GTAAACTGTTACCTAACACCATACCCAAAAATTAACGTGAAATGAATCAA 1000
                         v ii  ivi     v        iv           vii     i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_178538964_   1001 AGACCTAAACATAAGAGCTAAA-CTATAAAACTCTTGGAAGAAAACATAA 1049
                                  ii           -             i            i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_178538964_   1050 GGCAAAATATTAATACCACTGGATTTGGCAATGATTTCTGACATATGACA 1099
                          ?vv    v  vi iv vi   i  v       i     v v        
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_178538964_   1100 TCACAAAAACCAGCAATAAAAGAAAAAC------AATTGGACTTCAT-AA 1142
                         i  v  iv  v     i          v------             -  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_178538964_   1143 AA----AAATTTGAATGTGCATCAAAAAACTCTATCAG---AGTAAAAAG 1185
                           ----   i  v--     v     ii  v      i---   i     
  L1M4_orf2#LINE/    651 AATTAAAAACTTT--TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_178538964_   1186 GAAACCCACAGAATGGAAGAAAATATTTGCAAATAATATATCTGATAGGG 1235
                         iv              i                 v            i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_178538964_   1236 AATTGATATGCACAACATATAGAGAATTCCTACAACT-ACTAAACAAAAA 1284
                         i i vi   v  v  i     i    i  i       - v   vv    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_178538964_   1285 TCAAACAACCTGAATAAAGAATGGTCAAAGT-CTTGAACAGACATTCCTC 1333
                         v    i    ii v ?  i     v     v-i     i       i   
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_178538964_   1334 CCAAGAAGATATACGAATGGCCAATAAGCACACGAAA 1370
                          v            i                 i    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

Transitions / transversions = 1.45 (84 / 58)
Gap_init rate = 0.02 (17 / 885), avg. gap size = 3.82 (65 / 17)  


2806 26.34 2.01 0.67  chr1_178550229_178555769     4153  5048 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_178550229_   4153 TGGAAAAACATTCCATCCTCATTGATAAAAAGAATCAATATCATGAAAAT 4202
                               i i  i    vi    v   vii    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178550229_   4203 GGCCATACTGCTCAAAGTAATTTACAGGTTCAATGCTATTCCAATCGAAC 4252
                            v     v i    v i  i     i     i  v  i  v   i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178550229_   4253 TACCA-CTGACATTCTT-CATGGAATTAGAAAACACT-ATTTTAAATTTC 4299
                          v   -   v v  i  -  - i    -  v  -i  -  ii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATT-GACAA-GCTGATCCTAAAATTC 147

  chr1_178550229_   4300 ATATGGAA-TCAAAGAAGAACCCTGTATAGCCAAGAGAAGTATAAGCAAA 4348
                                 - vv   -- i    v v        i v  viv i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_178550229_   4349 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATTACAA 4398
                                   i      vv   ii  v  ii i      viv  i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_178550229_   4399 GGCTACAGTAACCAAAACAGCGTGGTACTTGTACCA----AAACACATAG 4444
                         i          i   i    i        v i iv ---- i   i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_178550229_   4445 ACAAATGCGGCAGAACAGAGACTTCAGAAATAACACCACATATCTACAAC 4494
                          iv    viii    iv    v i         vv   i i  i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_178550229_   4495 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATCT 4544
                           vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_178550229_   4545 CCTATTCAATAAATAGTACTGGGAAAACTGGCAAACCATATGCAGAAAAC 4594
                         i  v     i    i  i      v      vv ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_178550229_   4595 TGAAACCGGACCCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGG 4644
                             iii        v   i     v  i                i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_178550229_   4645 ATTAAAGACTTAAGTGTAAAAACCAAAACGATAAAAACCCTAGAAGAAAA 4694
                           i ?    i   i     i i i     v      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_178550229_   4695 CCTAGACA-ATACCATTCAGGGAATAGGCATAGACAAAGACTTCATGACT 4743
                          v   i?i- v i -   iv ivv v  vv   i   v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_178550229_   4744 AAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTAACAAATGGGACCT 4793
                          vi            vvv          vv     vi i    v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_178550229_   4794 AATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTATCATCAGAGTGA 4843
                         v  i   v v  i i   i  ii vv       v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_178550229_   4844 ACGGGCCATCTAAAGAATGGGAGAAAAATTTTGCAATCTACCCATCTGAC 4893
                          vi i v i i v              vv       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_178550229_   4894 AAAGGTCTAATATCCAGAATTTACAAGGAACT--TA-AAC---ATATTTA 4937
                           i  v  vi          v  i  i     --  -   ---   v v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_178550229_   4938 CAAGAAAAAAAAACCA--TCAAAAATGGGCAAAAGACATGAACAGACAAT 4985
                         v    v   v  v   -- ?             i  iv    i     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_178550229_   4986 TCTCAAATGAAGACATTTACATGGCCAA-AAACATATGAAAAAAAGCTTA 5034
                             v  v     i  vi v        -  i  i       i v   i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_178550229_   5035 ACATCACTGATCAT 5048
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (127 / 105)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.50 (24 / 16)  


3321 26.19 0.89 0.11  chr1_178574009_178578982     3581  4481 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_178574009_   3581 TGGAAATACATCCCATGCTCATGGATGGGTAGAATCAGTATTGTGAAAAT 3630
                               v i        i        v  v   v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178574009_   3631 GATCATACTGCCAAAAGCAATGTGCAAATTCAACCCAATCCCCATCAAAA 3680
                          iiv     v  v   vii  v i  i       v       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178574009_   3681 TACCA-CTACCATTCTTTACAGAATAGGAAAAAACAATTCTAAAATTCAT 3729
                          v   -  i  -  i   i     vvv  v  ivii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_178574009_   3730 ATGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGA 3779
                               viiv  ii  v  viv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_178574009_   3780 AAAAATCTGAAGGCATAACACCACCTGATTTCAAACTATACTATAAGGCC 3829
                          v   vi  i   vv v    iv  ii        viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_178574009_   3830 ATAGTCACCAAAACAGCATGACCCTGGTATAAAAATAGGCACATAGACCA 3879
                          i   v i   i    ii  iiv    i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_178574009_   3880 ACGGAACAGAATAGAGAACCCAGAAATAAAGGCAAATACTTACAGCCAAC 3929
                          i    i     v    ii           vv  v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_178574009_   3930 TGGTCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACAGCCTT 3979
                           i i  i     i vviv   i v   vv i         i i  i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_178574009_   3980 TTTAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAA 4029
                           i                 i  i   v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_178574009_   4030 ATTGAATCCTCATCTCTCACCTTACACAAAAATCAATTCAAGATGGATCA 4079
                         i   i i  ii i   v    v  i        i  i    i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_178574009_   4080 AGGACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAATATAGCATT 4129
                         ?i   i     v     v  i           v ii     v v i   v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_178574009_   4130 GGAAAAACCCTTCTAGGCATTGGCTTAGGCAAGGATTTCATGATTAAGAA 4179
                           ?iv  vi    vv i v    v        v i    v iiv  v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_178574009_   4180 CCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATTA 4229
                         v         v v    i    iv   i   i   iv v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_178574009_   4230 AACTAAAGAGCTTTTGCACTGCAAAAGGAACAGCCAGCAGAGTAAACAGA 4279
                           v v  i i      ii  v    i iv  vii  iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_178574009_   4280 CAACGCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGG 4329
                             v      i           v  ii   vii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_178574009_   4330 ACTAATATCCAGAATCTACAAGAAACTC----AAATTAGTAACAAAAA-A 4374
                            vi          v  i  ii     ----  v i i   i     - 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_178574009_   4375 CAAACAATCCCACTGAAAAGTGGGCTAAGGGCATGAATAGACAAGTCTCA 4424
                             i  i  v i ?    i     v    iiv          vv    v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_178574009_   4425 AAAGAAGACATACAAATGGTCAACAA--ACATGAAAAAATGCTCAACATC 4472
                                 i          i   i  --         i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_178574009_   4473 ACTAATAAT 4481
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.55 (141 / 91)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.80 (9 / 5)  


2200 26.78 1.08 0.31  chr1_178592562_178594199      500  1145 (493)    L1M4_orf2#LINE/L1      258   908 (0)  

  chr1_178592562_    500 CAAAACAGCATGATACTGGTACCAAAACAGATATACAGACCAAAGGAACA 549
                            i    ii  i      i iv ii i   i   i   i   v    i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_178592562_    550 AAACAGAGACCTCAGAAATAACACCACACATTTACAACCATCTGATCTTT 599
                         i  iv    vii         vv   i       iiii  vi    i  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_178592562_    600 GACAAACCTGATGAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAA 649
                              ivv  vii i v  vvv           i  vvi  v  i  i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_178592562_    650 ATGGTGCTGGGAAAACTGGTTAGCCCTATGCAGAAAACTGAAACTGGACC 699
                                     v      v  ?  vi     i  i v    ii      
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_178592562_    700 CCTCCCTTACACCTTATACAAAAATTAACTCAAGATGAAGTAAAGACTTA 749
                            v   i     v                   i   i vi ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_178592562_    750 AATGTAAAACCTAAAACCATAAAAACTCT-GGAAGAAAACCTAGGCA-AT 797
                                i v       i      -    -i         v    ?i- v
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_178592562_    798 ACCATTCAGTACATAGGCATGGGCAAAGACTTCATAACTAAAACACCAAA 847
                          i -   ivv  v v  vv i     v ii   v  iv  vi        
  L1M4_orf2#LINE/    557 ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_178592562_    848 AACAATGGCAACAAAAGCTGAAGCTGACAAATGGGGTCTAATTAAACTAA 897
                          i  vvi          vvi  iiv  i    v  iii v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_178592562_    898 AGAGCTTCTGCACAGCAAAAGAGACTATCATCAGAGTGAAAAGGCAACCT 947
                          i i   i  ii vv    i  v       vv i         i     i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_178592562_    948 ACAGAATGGGAGAAAGTTTTTGCAATCTATCCATCTAACAAAGGGCTAAT 997
                                        i v       vii  vi    i i  i  i  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_178592562_    998 ATCCAGAATCTACAAGGAACT--TA-AATTTA-CAAGAAAAAAA-AAATA 1042
                                  v  i  i     --  -  i i -i  v     i -     
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_178592562_   1043 ACCCCATCAAAAAGTGAGTGAAGGATATGAACGGACACTTCTCAAAATAA 1092
                             v  i?    i  i ii      v    ii    i     v   v  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_178592562_   1093 GACATTTATGCGGCCAACAAACATATGAAAAAAAGCTCATCATCACTGAT 1142
                           i  vi vii      i  i  i       i v     v     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_178592562_   1143 CAT 1145
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.60 (104 / 65)
Gap_init rate = 0.01 (8 / 651), avg. gap size = 1.12 (9 / 8)  


 250 13.48 3.37 15.73  chr1_178657154_178663641.rev        4    92 (6396)  C L1M4_orf2#LINE/L1   (828)    80     3  

C chr1_178657154_     92 GAAAAATA--CCATATTCATGGACTGGAATAGTTAACATTGTTAAATTTA 45
                             i   --    i        i     v v    i        -----
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA----- 47

C chr1_178657154_     44 AGATGTTAAATTTAC-CCCCAGGTGACTGATCCAATCAAATT 4
                         -    vi  ---   -     ii ---     i --  i   
  L1M4_orf2#LINE/     48 -GATGGCAA---TACTCCCCAAAT---TGATCTA--CAGATT 80

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.08 (6 / 78), avg. gap size = 2.83 (17 / 6)  

 366 23.53 5.23 0.65  chr1_178657154_178663641.rev      340   492 (5996)    L1M4_orf2#LINE/L1      671   830 (78)  

  chr1_178657154_    340 CAAAAGAAACAATCAACAGAGTGAAAAGATAACCTATAGAATGAAAGAAA 389
                             i  v  v     v i          i    i i      ii     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_178657154_    390 ATACTTGAAAACTATTCATCCAACA--GGATTAATATCCAGAACATATAA 437
                            i   v   ii  vi   ii i --   i vi         i      
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_178657154_    438 AAAACTGAGACATCGCAA-AAGAAAAAAA-AAAT---CCAACTAACATAA 482
                          i    vvv   v v   -  v     i -    ---    i ? v -  
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA-AA 819

  chr1_178657154_    483 CAGG-AAAGGA 492
                         ii  -      
  L1M4_orf2#LINE/    820 TGGGCAAAGGA 830

Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.04 (6 / 160), avg. gap size = 1.50 (9 / 6)  

2595 25.36 4.21 3.65  chr1_178657154_178663641.rev     5095  5997 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_178657154_   5095 TGGAAAAATATTCCATCCTCATGGATAGGAAGAATCAATGTC------AT 5138
                               i    i    vi        v      v i   i i------  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178657154_   5139 G------------AAAGTAATTTATAGATTCAGTAGTATCCCCATCAAGG 5176
                          ------------   v i  i  i       iiivv     i     ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178657154_   5177 TAC-AACTGACTTTCTTCACA-AAATTAGAAAAAACT-ACTTTAAATTTT 5223
                          v - i   v    i  -i  -     i-- v  i  - iii    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_178657154_   5224 ATATGGAACCAAAAAAAAGAAAAAGGCCT-GTATAGCCAAGATAATCCTA 5272
                                 -------- v v  ii i  i- v        i i    i i
  L1M4_orf2#LINE/    148 ATATGGAA--------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_178657154_   5273 AGCAAAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATA 5322
                          iv  i          i      vv    i  v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_178657154_   5323 CTGCAATGCTACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGAT 5372
                           i   v          i   i    ii         i iv ii i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_178657154_   5373 ATATACACCAGTGGAACAGAATAGA-AGCCTCAGAAATTACACCACACAT 5421
                              v i  i     i     v  -  i -       v vv   i    
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACAT 338

  chr1_178657154_   5422 CTACAACCATCAGATTTTTGACAAACCTGACAAAAACAAGCAATGGGGAA 5471
                         i  iiii  viv      i     ivv  v   i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_178657154_   5472 ACAATTACCTATTTAA--AATGGTGTTGGGAAAAGTGGCTAACCATATGC 5519
                          v   vii  v  i  --       i     v  v   v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_178657154_   5520 AGAAAACTAAAACTGGACCCCTTCCTTACACTTTATAAAAAAATTAACTC 5569
                          i  i v i  ii         v   i    iv    v            
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_178657154_   5570 AAGGTGGATTAAAGAATGAAATGTAAAACTTAAAACCATAAAAACCCTTA 5619
                           ii     i ?   viv        i vi      i      - i    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTA 537

  chr1_178657154_   5620 GAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACT 5668
                                  v    ?i- v i -   iv   v v  vv i     v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_178657154_   5669 TCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAA 5718
                           v iiv  vi            vvi          vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_178657154_   5719 TGGGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAAAAAAAAAAAA 5768
                          v    i v  i   v v  i i   i  ii vv    ii v -------
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA------- 679

  chr1_178657154_   5769 AAAAAAGAAAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAG 5818
                         ------------   i  vv i      v  i     i            
  L1M4_orf2#LINE/    680 ------------CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_178657154_   5819 AAAATTTTTGCAATCTGTCCATCTGACAAAGGGCTAATATCTAGAATCTA 5868
                              v       viii vi      i  i  i  vi    i     v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_178657154_   5869 CAAGGAACTTAAACAAATTTACAAGAAAAA-------AACCCA-TCAAAA 5910
                         i  i     ivv    v iv i  v     -------      - i?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_178657154_   5911 AGTGGGCAAATAATA-GAACAGACACTTCTCAAAAGAAGACATTTATGTG 5959
                          i        vi  v-   i     i     v        i  vi vi  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_178657154_   5960 GCCAACAAACATATGCAAAAAAGCTCA---TCACTGGTCAT 5997
                              i  i  i   v   i v     ---   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.55 (71 / 20)  


1715 27.02 0.44 0.22  chr1_178706625_178713599     3896  4354 (2621)    L1M4_orf2#LINE/L1        1   460 (448)  

  chr1_178706625_   3896 TGGAAAAACATCCCATGCTCATGGATGGATAGAATCAATATGATGAAAAT 3945
                               i i        i        v iv   v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178706625_   3946 GACCATACTGCCAAAAGGAATATACAAATTTAAAACAATTCCTATCAAAA 3995
                          i v     v  v   vvi  v    i   i  vi    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178706625_   3996 TACCATCATCATTCTTCACAGAATTAGAAAAAC--ATCCTAAAATTCATA 4043
                          v   v vv v  i  ii     v v  v  i --               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_178706625_   4044 TGGAACCAAAAGAGAACCTGCATAGCCAAAGGAAGATTAAGTAAAAAGAA 4093
                              viiv   i  v  v v         iv  vv  i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_178706625_   4094 CAAATCTGGAGGCATCACATTACCTGACTTCAAACTACACTACAAGACTA 4143
                             vi      vv     i v  ii i      vivi       ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_178706625_   4144 TAGTCACCAAAATAGTATGGTACTGGCATAAAAATAGACACACAGACCAG 4193
                         i   v i   i i   i              ii       i i   i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_178706625_   4194 TGAAACAGAATAGGGAGCCCAGAAATGAAGCCAAATACTTGCGGCCAACA 4243
                           i  i     v i   i        i  v   v i i  ii  i   iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_178706625_   4244 GATCTTTGACAAACTAAGCAAAAACATTTAAGTGGAGAAGGGACACCCTA 4293
                            i  i     ivvviv   i v    i  -   i   i i i vi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTT 399

  chr1_178706625_   4294 TTCAACAGATGGTGCTGGGATAACTGGCAAGCCACATGTAGAAGAATGAA 4343
                                i            i      vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_178706625_   4344 ACTGGCTCCCT 4354
                         ii   vi    
  L1M4_orf2#LINE/    450 GTTGGACCCCT 460

Transitions / transversions = 1.46 (73 / 50)
Gap_init rate = 0.00 (2 / 460), avg. gap size = 1.50 (3 / 2)  

1264 27.09 3.52 0.00  chr1_178706625_178713599     6030  6483 (492)    L1M4_orf2#LINE/L1      439   908 (0)  

  chr1_178706625_   6030 AGAAGAATGAAACTGGATCCTCAGCTCTCACATTAAACAAAAATCAACTC 6079
                          i         ii    i  ii v   v   vv  v        i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_178706625_   6080 AACACGGACCTTAAATCT-----TAAGACCTGAAACCATAAAAAATCTAG 6124
                           v i   i v? i i  -----     v  i    i      vvii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_178706625_   6125 AATATAACATCAGAAAAACTCTTCTAGACATTGACTTAGGCAAAGACTTC 6174
                           v v     vi ?iv  v     vv   v   iv        v ii   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_178706625_   6175 ATGACCAAGAACCCAAAAGAAAATGCAACAAAAACAAAGATAAATAGATG 6224
                         v iivi v  vv       v v v         iv   i   i   i  v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_178706625_   6225 GGACTTAATTAAACTAAAAGGCTTCTGAAGAGCAAAAGAAATAATCAGCA 6274
                               v  i   v v   ii   i  vivvv    i  v iv    iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_178706625_   6275 GAGTAAACAGACAACTCATAGAGTGGGAGAAAATATTTGCAAACAATGCA 6324
                         i   i  v       i  i   i                    iv  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_178706625_   6325 TCCGACAAAGGACTAATACCCAGAATCTACAAGGAATTCAAACAAATCAG 6374
                           i  i  i     vi  i       v  i  i   i  vv    v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_178706625_   6375 CAAGAAAAAAA-AAAT--CTC-ATCAAAAAGTGGCCTAAGAACATGACTA 6420
                         i  v     i -    -- i -  i?    i   v v   i iv   v  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_178706625_   6421 GACAATTCTCAAAAGAAGTTATACAAGTGGCCA-------TATGTAAAAA 6463
                             v     v       v       i      -------i   v   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_178706625_   6464 TGCTAAACATCTCTAATTAT 6483
                             v      v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.07 (62 / 58)
Gap_init rate = 0.01 (5 / 470), avg. gap size = 3.20 (16 / 5)  


4531 17.47 1.79 0.11  chr1_178776772_178778826      670  1562 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_178776772_    670 TGGAAACACAACTCATGTTTATGGATTGGAAGAC---ATATTATTAAGAT 716
                               v i v i      i              ---     i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178776772_    717 GTAAATACTACCCAAAGCAATCTACCAATTTAATATAATTCCTATCAAAA 766
                          vv      v      vii      vi   i  iii   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178776772_    767 TCCCAATAACCATTTTTGTAGAAAT-GAAAAA---ATCTTAAAATTTTTA 812
                              iivi  v      i      -  v  i---   i       iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_178776772_    813 TGGAATCTCAAGGGACTCAAAATAGCCAAAACAATTTTGAAAAAGAAAAA 862
                              viv        i  i               i           i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_178776772_    863 ACATAGTTGGAGGACTCACACTTCCTAATTTCAAAACTTATTACAAAGCT 912
                         -  v                     i              i         
  L1M4_orf2#LINE/    201 -CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_178776772_    913 ACAGTAATCAAAAC--TGTGATACTGGCATAAAGACAGACATA--GA-CA 957
                                    i  --    i           i  i       --  -  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_178776772_    958 ATGGAATAGAATAGAGAGCCTAAAAGTAAACCCTTGCATATATGGTCAAA 1007
                                     v     i i i  i       v i   v         v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_178776772_   1008 TTATTTTTGAGAAGGATGCCAAGACCATTCAATAGG-ATAGGATAGCCTT 1056
                          v     i  v    i                 i  - v  i    i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_178776772_   1057 TTCAAATAATGGTGCTAGGAAAACTGGGCCTGCACCTACAAAATATTGTA 1106
                              vv         i   v      iiv?v   v i     v v  v 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_178776772_   1107 GTTGGACCCTTACTTAATGCCATATACAAAAATCAACTCAAAATGGATCA 1156
                                  i   i v ii              i                
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_178776772_   1157 AAGATATAAATATAAGAGCTAAAACTGTAAAACTC--AGAAGAAGACATA 1204
                         ?   iv     i              i        --       i     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_178776772_   1205 GGACAAAAGCTTTACAACATGGAATTTGTCAATACATTCTTGAATAGGAC 1254
                           ?vv   v   iiii  v v ii  v v    ivv     ii   v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_178776772_   1255 ACCAAAGACTTGGGGAACACAAGAAAACATAGACAAACTGGACTTCA-CA 1303
                               ii viii v    v       v     i   i         -  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_178776772_   1304 AAATTAAAAACTTCTGTGCATCAAAGAACACTATCAACAGAATGAAAAAG 1353
                                      i     v      i          v i i      ii
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_178776772_   1354 CAACCTACGGAATGGGAGAAAATACTTCCAAATGATATATCTGATAAGAG 1403
                              i  i               i  v     v              i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_178776772_   1404 AATAACATTCAGAATACATAGAGAACTCCAGAAACTCGACAACAAAAAAC 1453
                          v vii  i       i   i       iviv     i i  i     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_178776772_   1454 CAAACAACCTTATTACAAAATTGGCAAAGGACTTGAATAGACATTTCTCC 1503
                             i    iv   ?v     v         i                  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_178776772_   1504 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACGTC 1553
                                                                        i  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_178776772_   1554 ACTAATTAT 1562
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.62 (94 / 58)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


2960 25.80 1.76 1.65  chr1_178799247_178801887.rev     1246  2152 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_178799247_   1246 TGGAAAAACATCTCATGCCCATGAATTGAAACAATCAATATTATGAAAAT 1295
                               i i   i    ii    i    i  v v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178799247_   1296 GACCATACTGCCCAAAGCAATCTACAAATTTAATGTAATTCCTATCAAAC 1345
                          i v     v      vii       i   i  i i   i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178799247_   1346 TACCAATATCATTTTTCACATAATTAGAAAAAGCAATCCTAAAATGTATA 1395
                          v   iivv v     ii  v  v v  v  ivii          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_178799247_   1396 TGGAATCAAAAAAGAGCTGGAATTGCCAAAGCAATCCTAGATAAAAAGAA 1445
                              viiv  ii  v ii    v      i     i ii v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_178799247_   1446 CCAATCTGAAGGCATCACATAACCCAACTTCAAATTATATTACAAAGATA 1495
                          v  vi  i   vv     ivv     i      viv  i       v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_178799247_   1496 TAGTAACCAAAACAGCATGGTACTGCGATAAAAGTAGACACATAGACCAG 1545
                         i     i   i    ii        vv    iii      i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_178799247_   1546 TGGAATGGAATAGAGAACCTAGAAATAAAGCCAAATACTTACAACCAACT 1595
                               i    v    ii i         v   v i i   iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_178799247_   1596 GATATTTGACAAAGATCAACAAGGC--------AGACAAAAACACACACT 1637
                            v  i     i i -iv    i --------i iv   i - i vv  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGA-ATAGTCT 398

  chr1_178799247_   1638 GTTCAATAAATGGTGCTGGGAAAACTGGATTACCATATACAGAAGAAGGA 1687
                         v     i              v        v?   i  i  i     v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_178799247_   1688 AACTGGATCCCTATCTCTAACCATATATAAAAATTAACTCAAGCTGAATT 1737
                          ii    i     i   vv        i              iv  i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_178799247_   1738 AAAAGACTTAAATTAAATTTAAGACCTGAAACCATAAAAATTCTAGAAGG 1787
                          ? -   i     v-----     v  i    i      v ii      i
  L1M4_orf2#LINE/    499 AWA-GACCTAAATG-----TAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_178799247_   1788 ATATCTAGGA--AAACCTCTCTGGACGTTGGCCTATGCAAAGAATTTATG 1835
                          v iv    ?--   i  -  vv   v    vi  v    v iv  iv i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_178799247_   1836 ACTAAGACCCCAAAAGCAAATGCAACAAAATAAACACAAAAATAAATAAA 1885
                         iv  v   v         v v         v   -----     i     
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAA-----AAATAGATAAA 636

  chr1_178799247_   1886 TGGAACATAATTAAACTAAAAAGCTTTTGCACACCAAAATAAATAATCAA 1935
                          v i  v v  i   v v    i      ii vi    iv v iv     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_178799247_   1936 CAGAGTAAATAGATAACCTATAGGATGGGAGAGAATATTGGCAAACTCTA 1985
                         v i   i  v   i    i i  i        i      v     iiv  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_178799247_   1986 CATCTGACAAAGGACTAATATCCAGAATCCACAAGGAACTCAAACAAATC 2035
                         i      i  i     vi          vi i  i      vv    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_178799247_   2036 AGCAAAGGAAAAAAAAAT--CCCA-TTGAAAAGTGGGCAAATGACATGAA 2082
                          ii  vii   i v    --    -  ?    i        v  iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_178799247_   2083 CAAACATTTTTCAAAAGAAGATATACAAATGGCCAAATAA---CATGAAA 2129
                         i i      i  v                       -   ---       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGAAA 885

  chr1_178799247_   2130 AAATGCTTGATATTCCTAATCAT 2152
                          i     ii i  iv????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


 249 14.29 0.00 0.00  chr1_178823570_178826573     1318  1359 (1645)    L1M4_orf2#LINE/L1        1    42 (866)  

  chr1_178823570_   1318 TGAAAAGATATCCTTCATTCATGGATTGGAAGAATTAATATT 1359
                           i          ivii                v        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT 42

Transitions / transversions = 2.00 (4 / 2)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.00 (0 / 0)  

3057 24.48 3.58 1.27  chr1_178823570_178826573     1646  2511 (493)    L1M4_orf2#LINE/L1       23   908 (0)  

  chr1_178823570_   1646 GGCCTGGAAGAATTAATATTCT--AAATGTTCATACTACCCAAAGCAATC 1693
                           vi       v        v -- i   viv     v      vii   
  L1M4_orf2#LINE/     23 GGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATC 72

  chr1_178823570_   1694 TACAGATTAAATGTAATCTTTATCAAAATTCCAATGGCATTCTTCATAGA 1743
                                 v  i i    ii         i   iiv  v  i  iii   
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chr1_178823570_   1744 AATAGAAAAAACAGTTCTAAAATTTGTATGGAACCACAGAAGACCCTGAA 1793
                            v  v  iviii i        ii       vii  iii     v   
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr1_178823570_   1794 TCACCAAACCAATTCCAAGAAAGAAAAAACATAGTTGGGGCAC-CACACT 1842
                          vi     v    iiii i      i  -  v      i v  -      
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAA-CAAAGTTGGAGGACTCACACT 221

  chr1_178823570_   1843 ACTTCACTT-AAAATTATATTATACAGTTACAGTAATTTTAAAA------ 1885
                         v iiv i  -    i -  i  i v  i         i--  i ------
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATC--AAGACAGTGT 268

  chr1_178823570_   1886 AGTACTGGTATAAAAACAGGCACATAGACCAATGGAACAGAATAGCGAGC 1935
                         i       i    ii i  i  i     i        i     v v   i
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_178823570_   1936 CCAGCAATAAACACAAGCATATATGGTTAACTAACTTTTGACATGGCCTC 1985
                             v       v  vi   v      i  i i i   i    v  viv 
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_178823570_   1986 CAAGAGAATACAGTGAGGAAAGAATA----TTTCATGTGAAAATAAAGGG 2031
                              vv  v  i  i          ----     ------- i   v  
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA-------ACAAATGG 411

  chr1_178823570_   2032 -GCTGGAAAAACTAAATTTCCACATGCAGAGGAATCCAATTGGAATT-TG 2079
                         -     i v    ii  v?         i i    vv i     vii- i
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_178823570_   2080 TCTCACAC-ATACACAAAAATAAACTCAAATTGGATAAAAGGCCCAGATG 2128
                         i       -   i        v        v     v ?  i  i i   
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_178823570_   2129 TAAGACCTGAAACCA-AAATCTCCTAGAAGAAAACATAGGGAAAAAGCTC 2177
                              v  i    i -   v   i                ?iv   v  i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_178823570_   2178 CTTGACATTCACTTTGGCAAGGATTTTTTAGATATCACACCAAAAACTCA 2227
                          v    v  viv  v     v i   i        v         i v  
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_178823570_   2228 GGCTATAAAAGCGAAAATAAATA----GGACTGCATCAAACTAAAAAGCT 2273
                         i  v i     vi      i   ----     v       v v    i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_178823570_   2274 TTGGCAAAGCAAAGAAAATAATCAACAAGATGAAAAGTCAGCCTATAGAT 2323
                           v iivvv     i v iv     v  ii       v  i  i i   v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_178823570_   2324 TGGGAGAAAATATTTGCAAACCATATATCTGATATGGAGTTAATATACAA 2373
                                             i             v  iii vi   v  i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_178823570_   2374 AA-ATATAAAGAACTTGTACAACTCAGTATCAGAAAAATAAATAACTTGA 2422
                           -            iv         i  vi i   i i       iii 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_178823570_   2423 TCAAAAAATAGAC-------CTGAATATACTTTTCTCCAAAAAAGACATA 2465
                          i?      i i -------i      v  v          i    i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_178823570_   2466 AAGATGACTA-CAGGTATATGAAAAGATGTTCAACATCACTAATCAT 2511
                         v i   i i -i i i i           i         ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (131 / 77)
Gap_init rate = 0.02 (17 / 886), avg. gap size = 2.47 (42 / 17)  


4603 17.09 1.68 0.22  chr1_178858397_178861608.rev     1827  2721 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_178858397_   1827 TGGAAATACATTTCATGTTATTGAATTGGAAGACTTAATATTGTTAAGAT 1876
                               v i  ii      vv  i                          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178858397_   1877 GGCAATACTACCAAAAGCAATCTACAAATTCAATGCAATCACTTTCAAAA 1926
                                  v  v   vii       i      i      v  v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178858397_   1927 TCCAAAA-ACGTTTTTTGTAGAAATAGAAGAGCCTATCCTAAAATTCACA 1975
                            v iv-i v       i      v  vi   iv             i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_178858397_   1976 TGGAGTTTTAAGGGATCCTGAATAGTCAGAATAATCTTGAAAAAGAA--- 2022
                             iv vi      i  v      i  i  i               ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_178858397_   2023 CAAATCTAGAGGACTCATATTTCCTGATTTCAAAATTTACCACAAATCTG 2072
                             vi i         i i    ii         i    i     v  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_178858397_   2073 CAGTAATCAAAACAGTGTGGTACTGGCATAAAGACAGACATACAGATCAA 2122
                                   i                    i  i       i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_178858397_   2123 TGAAATAGAATCGTGAGCCCAGAAGTCAGTCCTCACATATATGGTCAAGT 2172
                           i        i v   i      i v ii  vi    v         v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_178858397_   2173 GATTTTTGACAAGGGTGACAGGATCATTCCATG-AAAAAGGACAGTATTT 2221
                               i          v  i  i     v   -ii    i i   v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_178858397_   2222 TCAACAAATGATGTGGGAAAAACTGGATATCCACATGCAAAATAATGAGG 2271
                                   i  iv  i v         ?            v     i 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_178858397_   2272 TTGAATCCTTACCTAACACTATATACAAAAATTAACTCAGAATAGATCAA 2321
                            i i  i     v    i                   i   i     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_178858397_   2322 AGATCTTAATATAAGACCTAAAACTATGAAACTCTTATAAGAAAACATAG 2371
                            i  v   i     v          i         v            
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_178858397_   2372 G-GCAAATCCTTCCTGACTTTGGGTTTGGCACTGAATTCTTGGATATGAC 2420
                          - i     -   v    i       v    v  iv     i        
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_178858397_   2421 ACCAAAA-CACAGGCAATAGAAGAAAAAATTAGACAA-TTGGACCTTACG 2468
                                -    i    i i          -   i  -      i i iv
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAATTGGACTTCATC 648

  chr1_178858397_   2469 AAAATTTAAAAATTTTGTACATCAGAAGATGCTATCAACTTAGTAGAAAT 2518
                               v    v      i v   i i  ii       vvv   ii   v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_178858397_   2519 GTGGTCCACAGAATGGGA-AAAATATTAGCGAATAGTATACCTG-T-AGA 2565
                         iiiii             -        v  i   vi    i   - -  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_178858397_   2566 GA-TTGTATCCAGACTATATAGAACACTCCTAAAACTCAATGA--AAAAG 2612
                           -           v      i iv    i  v        i --     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_178858397_   2613 -CAAATAACCAAATTCAAAAATGGGCAAAAGACTTTAATAGACATTTCTC 2661
                         -         v    ?             i  i  v              
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_178858397_   2662 CAAAGAAGATATACAAATGGCCAATAAGCATATGAAAAGATTTTTAACAT 2711
                                                       i          vi i     
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_178858397_   2712 CACTAATCAT 2721
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.78 (96 / 54)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.21 (17 / 14)  


2861 26.79 1.43 1.32  chr1_178918761_178925917     5758  6664 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_178918761_   5758 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5807
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_178918761_   5808 GGCCATACTGCCCAAAGTGATTTACAGATTCAATGCTATCCCCATCAAGC 5857
                            v     v      v    i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_178918761_   5858 TAACATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5906
                          vv  vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_178918761_   5907 ATGGAACCAAAAAAAGAGCCTGTATAGCTAAGACAATCCTAAGCCAAAAG 5956
                               viiv  ii-  v  v v     i  i      i i ivv i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_178918761_   5957 AACAAAACTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 6006
                               ii      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_178918761_   6007 TACAGCAACCAAAACAGCATGGTACTGGTACTGGTACCACAGCAGATATA 6056
                              i  i   i    ii         i ----  -- viii   i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA----TA--AGGATAGACATA 292

  chr1_178918761_   6057 TACACCAATGGAACAGAACAGAGACATCAGAAGTAACACCACACATCTAC 6106
                           v i        i    iv    vvi     i   vv   i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_178918761_   6107 AACCATCTGATCTTTGACAAACCTAACAAAAACAAGCCATGGGGAAAGGA 6156
                         iii  vi    i  i     ivv iv   i v  vv v          i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_178918761_   6157 TTTCCTATTTAATAAATGATGTTGGGAAAAGTGGCTAGCTATATGCAGAA 6206
                          vvi  v  i  i     i  i     v  v   v  ? i i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_178918761_   6207 AACTGAAACTGGACCCCTTTTCTTACAGCTTATACAAAAATTAACACAAG 6256
                         i v    ii         vi-  i   v v               v   i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTAC-CTCACACCATATACAAAAATTAACTCAAA 491

  chr1_178918761_   6257 ATGGATTAAAGACTTAAACATAAGATTTAAA-CCATAAAAACCCTAGAAG 6305
                               i ?    i    ii     vi    - i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_178918761_   6306 AAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGCCAAAGACTTCAT 6354
                              v    ?i- v i -   iv   v v  vv i v   v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_178918761_   6355 GACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGA 6404
                         iiv  vi            vvi          vv     v  i   iv i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_178918761_   6405 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGA 6454
                          ii v  i   v v  i i   i  ii vv    i  v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_178918761_   6455 GCGAACAGGCGACCTACAGAATGAGAGAGAAACTCTG-AAATCTATCCAT 6503
                          i   v  i i   i        i    i  vv i  -     -  vi  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATAT 739

  chr1_178918761_   6504 CTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTGAAACAATCTTAC 6553
                             i  i  i  vi          v  i        vvv    iiiv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_178918761_   6554 AAGAAAAAAACAA----CCCCATTAAAAAGTGGGCAAACGATATGAACAG 6599
                           v     i    ----   v   ?    i        v   v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_178918761_   6600 ACATTTCTCAAAAGACATTTATGCA----GCCAACAAACATATAAAAAAA 6645
                                  v     - vv   i  ----     i  i  i  i    i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_178918761_   6646 -GCTCATCATCACTGGTCAT 6664
                         -     v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


2110 23.45 9.73 1.03  chr1_178927064_178928727.rev      502  1179 (485)    L1M4_orf2#LINE/L1      172   908 (0)  

  chr1_178927064_    502 ATAGCCATTTAAGTACTCTTGAGCAAAAAGAACAAAGCTGGAGGCATCAC 551
                                ---  ii v      iv  i          i      vv    
  L1M4_orf2#LINE/    172 ATAGCCA---AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_178927064_    552 ATTACCTGATTTCAAATTATAGTACAAAGCAAGAATAACCAAAACCGCAC 601
                          i v  ii        viv  v        v v i   i   i  v iii
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_178927064_    602 AGTACTGGCATAAAATGAGACA----GAC-----GAACAGAATAGGGAAT 642
                         i            iivv     ----  i-----   i     v i  i 
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_178927064_    643 CCGGAAATAAATC-ATGCATTTACGGTCAACTCATTTTTGACAAAGGTGT 691
                           i        i -  i      i      i v     i     i    i
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_178927064_    692 CAAGGACC-TACACTGGGGAAGGGACAGACTCTTCAGTAAGAGGTGCTAA 740
                             -   - v  v       i i i  v  i    ii  iv      ii
  L1M4_orf2#LINE/    369 CAAG-ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_178927064_    741 CAGAACTGGATATCCACATACAGAAGAATGAAACTAGACTCCTATCTCTT 790
                         v v         ?      i  i         ii i   i    i   vi
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_178927064_    791 GCCATATACAAAAATCAACTCCAAATGGATTAAAGACTTAACCTTAAAAC 840
                         i              i     v        i ?    i   viv   i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_178927064_    841 CTGAGACTATGAAACTACTAGAAGAAAACATTGGG--AAACACTCCAGGG 888
                           i i     i     vi             v  ?--   i-  i iv i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGA 566

  chr1_178927064_    889 CATTAGTCT-GGCAAAGATTT--TGAGTAAGACCTAAAAAGCAGAGGAAA 935
                          v  i vi -     v i   -- iii  v   viv       v i v  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_178927064_    936 CCAAAACAAAAATGGACAAATGGGATTGCATCAAG-CTAAAA----TGGT 980
                          v   iv      i  i    v   i v      i-i     ---- v  
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_178927064_    981 TCTTCG--------TATCAA---AG-GAAA---CAAC-----GA------ 1004
                         v    i--------      ---  -    ---    -----  ------
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_178927064_   1005 -------TTTGCAAACTACCCATCTGATGAGAGATTAATAACTAGAATGT 1047
                         -------        ii ivi       i  i  i vi  v i     i 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_178927064_   1048 -TAG-GAGGTC----AA----ATAATAGCAA-ACAAACAATCCTATT-AA 1085
                         -  i-  iv  ----  ----      iv  -     i  i  v   -  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_178927064_   1086 AAATGGGCAAAACAGCTGAATAGACATTTCTGAAAAGAAGACATACAAAT 1135
                                    iv vi               vv        i        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_178927064_   1136 GGCTAACAGGTATATGAAAAAATTCTCCACTAGTCATCAAAATA 1179
                            i  i i i i       i  v   v  --i   ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAAC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (101 / 55)
Gap_init rate = 0.03 (25 / 737), avg. gap size = 2.92 (73 / 25)  


2736 21.95 2.16 0.62  chr1_178951479_178953118      501  1147 (493)    L1M4_orf2#LINE/L1      252   908 (0)  

  chr1_178951479_    501 AGTAACCAGAACAGCATGGTCCTGGCATAAAAACAGACACATAGACCAAT 550
                              i  ii    ii    v         ii i     i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_178951479_    551 GGAACAGAATAGAGAACCCAGAAATAAATCCATGCACTTACAGCCAACTC 600
                             i     v    ii           i    i  i   ii i   i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_178951479_    601 ATTTTTGACAAAAACCCCAAGAACATT----GGAGAAAGAATGGCCTCAT 646
                              i     iiiiv      v    ----  i        i i  iv 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_178951479_    647 TAATAAATGGTTTTGGGAAAACTGGATATCCATATGCAGAATAATGAAAC 696
                         i  i       vi     v         ?   i     i  v      ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_178951479_    697 TAGATCCTCATTTT-TACCATATACAAAAATCAACTCAAAATGGATTAAA 745
                          i  i  ii ii i-i               i              i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_178951479_    746 GACTTAAGTGTAAGACCTTAAACTATAAAACAACTAAAAGAAAAACACTG 795
                            i   i       v  v            vvi  i       -  iv 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATAG 550

  chr1_178951479_    796 GGG-AGATGGTACAGGACATCGGTTTGAGCAAAGATTTATCTGCATAAGG 844
                          ? - i  vv - iv   v i  v  ii    v i   v iv -   v i
  L1M4_orf2#LINE/    551 GNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAG-ATATGA 598

  chr1_178951479_    845 CCTCAGAAGCACAGGCAATAAAAGCAAAAATGGCCAAATGAGATTACATC 894
                          vi  i       i    i     v      i vi    vi  i v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_178951479_    895 AAGCTAAAAAGCTTCTGCACAACAATGGAAACAATCAACAAAGCAAAAAG 944
                           iv v    i   i  ii vv   v   v  v     v    ii     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_178951479_    945 ACAACCTACAGAATGGGAGAAAAATATTTGTAAACTATCCACCCGACAAG 994
                               i                -      i   ii  vi i i  i   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAG 747

  chr1_178951479_    995 GGATTTGTAACCAGAATATAGAAGGAACTCAAACAACTCAATAGCAAAA- 1043
                            i     v          v  i      vv           ii    -
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_178951479_   1044 GACAAATAATCCAATTTGAAAATGGGCAAAAGACCTGAATAGACATTTCT 1093
                                  i      ?i            i  ii               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_178951479_   1094 CAAAAGAAGATATACAAATGGCCAACAGGTATA-------ATGCCCAACA 1136
                          v                       i i i i -------    i     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_178951479_   1137 TCAATCATTAG 1147
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.29 (96 / 42)
Gap_init rate = 0.01 (9 / 657), avg. gap size = 2.00 (18 / 9)  


1997 25.73 7.70 1.39  chr1_179120832_179122863.rev      477  1125 (907)    L1M4_orf2#LINE/L1      102   791 (117)  

  chr1_179120832_    477 CCCAGCTATTAAAATTTTT---AAAAATGAAAAAGGT-ATTCTAAAAT-C 521
                                iii----     --- i    vi v   v -  i       - 
  L1M4_orf2#LINE/    102 CCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_179120832_    522 ATATGTAACAAAAAAGAACTCA-AATAGCCGAAGCAA----------AAT 560
                              v  vviv  i i  i  -       i  i   ----------i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_179120832_    561 GAACAAAGCTGGAGGTATCACATTACCTGACTT-AAAGTTATACTATAAG 609
                                 i      vv     i v  ii i  -   ii -     i  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr1_179120832_    610 GCTACAGTAACCAAAACAG----------------------ACACATAGA 637
                                   i   i    ----------------------   i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_179120832_    638 CCAATGGAACAGAATAGAGAACCGAGGAATAAAGCCACACAGCTGCAATC 687
                         i        i     v    ii v  i      v   i   vi iiii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_179120832_    688 ATCTGACTTT-AACAAAGTTGGCAAAAATAAGCAATGGGAAAAGGAC-TT 735
                          vi   i   -i    i v  v   i vi vv       i    i i-v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_179120832_    736 CTTATTTAATAAATGGTGCTGGGATAGCTGGCTAGCCATATGCAGATGAA 785
                            -  i  i              i i    v  ?   i     i v   
  L1M4_orf2#LINE/    397 CTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_179120832_    786 TGAGACTGGACCCCTACCTTTCACCATATACAAAAATTAACTCAAGATGG 835
                            iii             iv                        i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_179120832_    836 CTTAAAGATTTAGATGTAAGACCTCAAACTATAAAAGTCCCAGAAAAAAA 885
                         v i ?   ii  i        v  v           v  ii    i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_179120832_    886 CCTAGG---AAATACAATTCTGGATATTGGCCTTGGCAAAGAATTCCTGA 932
                          v    ---    - --   vv  iv    vi v     v iv   i ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-C--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_179120832_    933 CTGAGTCCTCAAAAGCAATGGCAACAAAATCAAAAATTGATAAATGAGAC 982
                         v iv v vi        vvi         vv      v       vi   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_179120832_    983 CT------AATTAAAGAGCTCCGCACAGCAGAATAAACTATCAACACAGT 1026
                         i ------       i vi ii ii vv  i iv v        v v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_179120832_   1027 AAACAGGCAACCTAAAAGATGGGAGAAAATATTTATAAACTATGCATCCA 1076
                         i  v  i     i v ii                ii   ii  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_179120832_   1077 ACAAAGGTCTAATATCCAGAATCTATGAGGAAGTTGAACAATTCAACAA 1125
                          i  i  v  vi          v   i i   v ivv    i    i  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

Transitions / transversions = 1.66 (103 / 62)
Gap_init rate = 0.02 (16 / 690), avg. gap size = 3.69 (59 / 16)  

 384 21.90 1.90 0.95  chr1_179120832_179122863.rev     1443  1547 (485)    L1M4_orf2#LINE/L1      803   908 (0)  

  chr1_179120832_   1443 ATAACCCTATTAAAATGTGGACAAAGGACATGAACAGACACTTCCCAAAA 1492
                                v   ?   vi   i       iv    i     i   i v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_179120832_   1493 CAAGACATACA--TGAGCCAAGAAACGTTTAAAAGAATGCTCAATGTCAC 1540
                         v    i     --  -     v  i iiv i   ii        ii   ?
  L1M4_orf2#LINE/    853 GAAGATATACAAATG-GCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_179120832_   1541 TAATCAT 1547
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.14 (15 / 7)
Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.50 (3 / 2)  


1067 19.84 6.35 1.59  chr1_179165910_179170713     1587  1838 (2966)    L1M4_orf2#LINE/L1       16   279 (629)  

  chr1_179165910_   1587 TATTTATGGACTGGAAAACTTAATGTTGTTAACATGCCAATACAACCCAA 1636
                          i  i     i     i       i       v   v      vv     
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_179165910_   1637 AACAATGTACAGATTCA-TGCAATCTCTATCAAAATCTCAATGACATCTT 1685
                          vii  v          -i      i           i  iivi v i  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_179165910_   1686 TTGCAGAAATAGAAACGTCAATCCTAAAATT----------TCCAAGGAA 1725
                                   v  v v iii           ---------- v     i 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_179165910_   1726 CTCCAAACAGCCATAACAATTTTGAAAAAATTTCAAAAA---AGCTGCAG 1772
                          i vi  i     v      i        i----  i  ---  i  v  
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAG----AAGAACAAAGTTGGAG 211

  chr1_179165910_   1773 GACTCAC-CTTCT-GATTTCAAAACTTACTACAAGTTTACAGCAATCAAC 1820
                                -    i-i                   ivi     i      v
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_179165910_   1821 ACAGTGTGGTGCAAGCAT 1838
                                   i vi    
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCAT 279

Transitions / transversions = 1.78 (32 / 18)
Gap_init rate = 0.02 (6 / 264), avg. gap size = 3.33 (20 / 6)  

3144 27.31 0.66 0.66  chr1_179165910_179170713     2012  2919 (1885)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_179165910_   2012 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2061
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_179165910_   2062 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2111
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_179165910_   2112 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACTGCTT-TAAAGTTC 2159
                          v   iivi i  i  ii     -   --- v  i   v i-    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_179165910_   2160 ATATGGAACCAAAAAAGAGCCCTCATCGCCAAGTCAATCCTAAGCCAAAA 2209
                                 viiv  ii  v  vvv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_179165910_   2210 GAACAAAGCTGGAGGCATCATGTTATCTGACTTCAAACTATACCACAAGG 2259
                                 i      vv   iii vi ii i      viv   i    i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_179165910_   2260 CTACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 2309
                                      i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_179165910_   2310 CAACGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 2357
                            i    i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_179165910_   2358 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAGGGATTC 2407
                         i vi    i  i     ivv  v   i v  vvv         i i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_179165910_   2408 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGC 2457
                         i  v  i  i              v      v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_179165910_   2458 TGAAACTGGATCCCTTTCTTACACCTTATACAAAAATTAATTCAAGATGG 2507
                             ii    i    vi  i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_179165910_   2508 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAA-TCCTAGAAGAAAA 2556
                           i ?    i       v   v       i      -  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_179165910_   2557 CCTAGGCA-ATACCATTCAGAACATAGGCATGGGCAAGGACTTCATGTCT 2605
                          v    ?i- v i -   ivi  v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_179165910_   2606 AAAACACCAAAAGCAATGGCAATAAAAGCCAAAATTGACAAACAGGATCT 2655
                          vi            vvi    i     vv     v  i   iv   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_179165910_   2656 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 2705
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_179165910_   2706 ACAGGCAACCTACGGAATGGAAGAAAATTTTTGCAATCTACTCATCTGAC 2755
                          v  i     i  i      i       v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_179165910_   2756 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAC 2805
                           i  i  vi          v  i  v      vv    v iv i  v v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_179165910_   2806 AAAAACAAACAGCCCCATCAACAAGTCGGCAAAGGCTATGAACAGACACT 2855
                            i     i i   v  i? v  i v        v v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_179165910_   2856 TCTCAAAAGAAGACATTTATGTAGCCAAAGACAACATGAAAAAATGCTCA 2905
                             v        i  vi vi i     vi vv         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_179165910_   2906 TCATCACTGGCCAT 2919
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  

2669 18.89 3.41 2.79  chr1_179165910_179170713     3677  4322 (482)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr1_179165910_   3677 AAAACAGTGTGGT---GGCATAAATGCAGACATATGGAAAGACAGAGTAG 3723
                           i          ---       ivii        i  vvi ii  i   
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_179165910_   3724 AATAAAAAGCCTGGAAATAAACCCTCACATATATGGTAAAATGATTTTTG 3773
                            vi i  i ii           vi    v      v  v       i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_179165910_   3774 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGGACCATCTTTTCAACAAA 3823
                                                         i ivi             
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_179165910_   3824 CAGTCCTGGGTAAACTGGATGTCCACGTGCGAAATAATGAAATTGGACCC 3873
                         ii  v     vv        i?    i   i   v      i        
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_179165910_   3874 TTACATAACACCCTATATGAAAATTAACTCAAAATGGATTGAAGACCTAA 3923
                         i   v v     v    ii                    ii?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_179165910_   3924 ATTTAAG-GCATAAAACTATAAAACTCATGAAAAAACTTATGGAGGACAA 3972
                           v    -  -                v ii  i  vvi  --   ?vv 
  L1M4_orf2#LINE/    509 ATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACAT--AGGNGTA 555

  chr1_179165910_   3973 AATGTTCACAACATTGGATTTGGCAGTGATGTCTTGGATATGACAGGAAA 4022
                            v   iii  v    i  v    i  i v    i         vv   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_179165910_   4023 GGAAGAAGCAACAACAAAGAA----------TTGGGCTTCATAAAAAATC 4062
                         i v v         v i i  ----------    i      v    v -
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT- 654

  chr1_179165910_   4063 AAAAAACTT--GTGCATCAAAAGATACTATCAA--AAGTAAAAAGGCAGC 4108
                         -        --    v     i  i        --    i     i  i 
  L1M4_orf2#LINE/    655 -AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_179165910_   4109 CTAAAGAATGGAAGAAAATACTTCAAAATCATATATCTGAGAAAGGATTG 4158
                          i v       i        i  vv               v  i   i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_179165910_   4159 ATATCCAGAATATATGGAGAACACCTAAAACTCAACAACAACAAAGA--- 4205
                         i              ii     v i  v       i  i  -     ---
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AAAGACAA 802

  chr1_179165910_   4206 GCAACATGATTCAAAAATAGGGAAAAGACTTAATTAAACAAAACATTCCT 4255
                         ii   vii   ?      i  v   i  i  i v  i   -----  i  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA-----TTTCT 847

  chr1_179165910_   4256 CCAAAGAAGATATACAGATAGCCAATA-GCACATGAAAAGATGCTCTACG 4304
                                         i  i       -                  v  -
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC- 896

  chr1_179165910_   4305 GGACTAATCATTAGGGAA 4322
                         ------    ????????
  L1M4_orf2#LINE/    897 ------ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (73 / 45)
Gap_init rate = 0.02 (13 / 650), avg. gap size = 3.08 (40 / 13)  


1511 26.78 4.50 0.71  chr1_179211001_179213410.rev      735  1156 (1254)    L1M4_orf2#LINE/L1        1   438 (470)  

  chr1_179211001_    735 TGAAAGGTTACTCCATGCTCATG-ACTGGAAGAATTAATACTGTTAAAAT 783
                           i  i v  ii     i     - i       v      i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_179211001_    784 GACAATACTATCCAGAGTAATTTATAGATTCA-------TCCTATCGAAA 826
                          i       vi   i v i  i  i       -------i      i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_179211001_    827 CACCAATGACATTCTTCAGAGAAATTTTTTAA---ATCCTGCAATTTATA 873
                         iv   iivi v  i  iiv       vviv i---     iv    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_179211001_    874 TGAAATCACAAAAGACCCCCAAATAGCCAAAGCAATCCTAAGCAAAAAGG 923
                           i  vii   ii     v-i          i     i i iv  i   i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_179211001_    924 ACAAAACTAAAAGCATCATACTACCTGGTTTCAAAATTTACTACAAAGCT 973
                              ii ii i vv   i   v  iii        i             
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_179211001_    974 ACAGTAACCAAATCAGC-----AC---CATGGAAACAGATACATAGACCA 1015
                                i   iv   i-----  ---   iiii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_179211001_   1016 ATGGGACAGAACACAGAGCCCAGATATAAATCCATGCCTTTACAGCCAAC 1065
                             i i    ivv    i     v     i    i v    ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_179211001_   1066 TCATCTTCAACAAATGTGCAAAGAAGATACAATGGGGAAATAACAGTCTC 1115
                          v  i   i    iv    v    vv  v           v  i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_179211001_   1116 TTCAATAAATGGTGCTAAGAAAGCTGGATAACTGGACAGGC 1156
                              i          ii  v i       ? i--   v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCC--ACATGC 438

Transitions / transversions = 2.50 (80 / 32)
Gap_init rate = 0.02 (7 / 438), avg. gap size = 3.14 (22 / 7)  

1528 24.67 1.97 2.18  chr1_179211001_179213410.rev     1456  1913 (497)    L1M4_orf2#LINE/L1      421   877 (31)  

  chr1_179211001_   1456 AGCTGGATAACTATATGGAGAAGAATGAAACTAGACCTCTATCTCTCATC 1505
                          i       ? i i   v i         ii i    i   i   v  i 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_179211001_   1506 ATATACAAAAATCAAATAAAAATGTATTAAAGACAAAAATCTAAGACCTG 1555
                                     i  v v      v  i ?    vv    v     v  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_179211001_   1556 AAACTATAAAACTATTAGATGAAAACATTAGGG-AAATGCTCCAGGACAT 1604
                                      v     v        vi ? -    -  i iv   v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCT 569

  chr1_179211001_   1605 TGGTCTGGGCAAAGACTTTTTGTGTAAGACTTCAAAAGAAAAAAAAGCAC 1654
                            vi i     v ii  i  ivi  v   vi      ---------   
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG---------CAC 610

  chr1_179211001_   1655 CAGCAACCAAAATAAAAATATACAAATAGGATTACATCCTAAT-----AT 1699
                         v      v   iv       v i    v   i v    vv   ----- i
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_179211001_   1700 TTATTCACAGTAACAAAAACAATTATCAAAATAAACAGGCAACACATAGA 1749
                           v vii vvi  vii v  v  i vv   i i  v  i    v  i   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_179211001_   1750 CTGGGAGAAAATATTTGCAGACTATCCACCTGAAAAGGGATTCATAACCA 1799
                         v                  i ii  vi i    v      i ii  v   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_179211001_   1800 GAATATATAAGAAGCTCAAACAACGCAATAGCAAAC---CAAATAATCCA 1846
                                   ii i   vv     v     ii   v---       i   
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_179211001_   1847 ACTTAAAAATGGGCAAAAGCTCTGAATAGACGTTTCTCAAAAGAAAACAT 1896
                          i ?             i v i         i      v      i i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_179211001_   1897 ACAAATAGTCAATAGGC 1913
                               i i     i  
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGC 877

Transitions / transversions = 1.27 (61 / 48)
Gap_init rate = 0.01 (5 / 457), avg. gap size = 3.80 (19 / 5)  


3382 24.80 2.02 0.34  chr1_179242121_179246317.rev     2816  3706 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_179242121_   2816 GAAGTATATTCCATGCTCATGGATTGGAAAACATAATATTATTAAAATGT 2865
                            iv    i     i             i  v       i    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_179242121_   2866 CTACACTAACCAAAGAAATTTATAGATTCAGTGCAATCCCTATCAAAATA 2915
                          v i   vv     vvi  i  i       ii                 v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_179242121_   2916 CCAATGGCATTCTTCACAGAAATAGAAAAAAAAATCCTAAAATTTACACG 2965
                            iiv  v  i  ii       v  v  ivvi           i i i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_179242121_   2966 GAACCACAAAAGACCCTGAATAGTCAAAGCAATCCTGACCAAAAAGAACA 3015
                            vii   ii     v      i    i     i   vv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_179242121_   3016 AAGCTGGAGGCATCACTCTAGCTGACCTCAAAAGATACTACAAAGCTATA 3065
                            i      vv    v  vv ii ii      vv             i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_179242121_   3066 GTAACGAAATCAGCATGGTGCTGGCATAAAAACAGACACATAGACCTGTG 3115
                             iv  iv   ii    i         ii i     i     i vi  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_179242121_   3116 GAACAGAATAGACAATTCAGATATAAATCCATGCCTTTGCAGCCAACACA 3165
                            i     v  v i i    v     i    i v   iii i   ivv 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_179242121_   3166 CTTTTGACACAGGTGGCAAGAATGCGCAATGGGGGAAAGGACCGTCTCTT 3215
                         i   i    vi    v     viiiv        -    i iv    i  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTT 401

  chr1_179242121_   3216 CAATAAATGGTGATAGGAAAACTGAATGTCCATATGCAGCAGAATGAAAC 3265
                            i        v i   v     i  i?   i     iv        ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_179242121_   3266 CAGACACCTATCTCTCACCATATACAAAAATCAAATAAAAATGTACTAAA 3315
                         ii   v    i   v                i  v v      v ii ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_179242121_   3316 GGCTTAAAT-------CTAAAACTCTGAAGCTACTGGAAGAAAACATTGG 3358
                          i i     -------        v i  i  vi i           v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_179242121_   3359 GG-AAACATGGCAGGACATTGGTTTGGGCAAAGGTTTTT---GTGTAA-- 3402
                         ? -   iv v- iv   v    v  i     v     i ---i i i --
  L1M4_orf2#LINE/    552 NGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_179242121_   3403 ---GAAGCATAGGGAGCCAAAGCAGAAACACACAAAT-GGATCACATCAA 3448
                         ---i     i i v i v    v i   i v i    -   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_179242121_   3449 GCTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTAAAGAGAC 3498
                         iv v    i   i  ii vv       v  v     v     i  i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_179242121_   3499 AACCCTCAGAATGGGAGAAAATATTTGCAAACTATCCATCTGACAAGAGA 3548
                              v                         ii  vi      i   i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_179242121_   3549 TTAATAACCAGAATATATAAGGAGCTCAAACATCTCAATAACAAAAAACC 3598
                         i vi  v             i  i   vv   v        i     iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_179242121_   3599 CAAATAATCTGATTTTTTAAAGTGCAAAAGATCTGAATAGACATTTCTCA 3648
                         -      i ii   ?vvv  v v     i   i                v
  L1M4_orf2#LINE/    801 -AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_179242121_   3649 AAGGAAGATATACAAATGCCCAACAGGTATATGAAAAACTGCT-AAGATC 3697
                           i               v    i i i i       iv    -  v   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_179242121_   3698 ACAAATCAT 3706
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.52 (131 / 86)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 2.33 (21 / 9)  


4397 16.83 1.94 3.99  chr1_179266153_179268075.rev      506  1432 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_179266153_    506 TGGGAAGACATCCTATGTTCATGGATTGAAAGACTTAGTACTGTTAAGAT 555
                            i    i    i              i        i  i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_179266153_    556 GACAATACACTCTAAGTTGAACTCCAGAGTCAATGCAATCTTGATCAAA- 604
                          i      v i i  i    v  v    v    i      iiv      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_179266153_    605 -TCCAGCTGACATTTGTTTATTTACCTATTTACTTATTTAGCAGAAATT- 652
                         -i       ----------------------- i v   v         -
  L1M4_orf2#LINE/    101 TCCCAGCTG-----------------------CCTTTTTTGCAGAAATTG 127

  chr1_179266153_    653 --AAGCTGATCCTAAAAT----ATGGAAATACAACAGCCCCAACTTAGCC 696
                         --                ----        i   vi v    ivv     
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr1_179266153_    697 AAAACAATCTGGAAAAAGAAAAAAACAGAACAAA-TTGGAGGACTCTCAC 745
                                   v         -------       -           v   
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAA-------GAACAAAGTTGGAGGACTCACAC 220

  chr1_179266153_    746 TTCCTGATGTCAAAACCTATTACAAAGCCACAATAATTAA-ATAGTGTGG 794
                             ii  v       i  i        i   i    i  - i       
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr1_179266153_    795 TACTGGCATAGGAACAGACATGTAGATTAATGAAATAAAACTGAGAGTTC 844
                                   i i i      i     i    i    i  i       i 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_179266153_    845 AGATATAAACCTTTACGTTGGTCATAAGCTGATTCTTTGCCAGGAGTATG 894
                            v       iv   i  vi vi v ii     -  i v  i i  iiv
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATT-TTCGACAAGGGTGCC 369

  chr1_179266153_    895 GAAGACAATTCTATGGGGGAAAGAATAGTCTTTTCCACAAATGGAGGTGG 944
                         -     v    v      -                v        v v   
  L1M4_orf2#LINE/    370 -AAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_179266153_    945 GATAACTGGATATACACATGCAAAAGAATGAAATCGATACCCCT-CCTCA 993
                           i         ?v                  i i i-      -     
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG-ACCCCTACCTCA 466

  chr1_179266153_    994 CACCATACACAAAAATTAACTCAAAATGAATAATACACTTAAATATAGGA 1043
                                i                    i  v ? v  i     i  i  
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_179266153_   1044 GCTAAAACTATAAAACCTTCAGAAGAAAACATAGGAGTAAATTTTTGTGG 1093
                                         ii i               ?      i  i   i
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_179266153_   1094 TTTTTGGTTAAGCAATGGTTTTTTAGATATAAGACCAAATGTACAACTTA 1143
                         ii  v     i          i        i v      v i    viv 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_179266153_   1144 CAAAAGAAAAAATAAGAAAATTG-ACTATATCAAGGCTTGAAAG--TTTA 1190
                                       iiv      -   vi     ii-  i   i--   i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA-TTAAAAACTTTTG 665

  chr1_179266153_   1191 TGCTGCAAATAACGCTA---AGAAAGTGTAAAAACAACCTACAGAATGGG 1237
                             v    vi  i   ---        v   i      i          
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_179266153_   1238 AGAAAATATTTGCAAATCACATATCTGATAAGAAACTTGTATCTAGAATA 1287
                                            i            ii         i      
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_179266153_   1288 TATAAAAAGCATTTACAACTTAAAAATGAAAAACTAAAAATAATCCAACT 1337
                               i i vi        i  v   i    i-- v      i    i 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAG--ACAAATAACCCAATT 813

  chr1_179266153_   1338 TAGAAATGGGCAAGGGATTTGAACAGACATTTGTCTAAAGAAGATGCACA 1387
                         ? i          i         i        v  i         ii   
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_179266153_   1388 AACAACCAGTATGCATACATAAAGACGTTCAACATCATTAGCCGT 1432
                           iii   i  v   i iiv     i i         ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (107 / 45)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.24 (55 / 17)  


3061 25.31 1.25 0.80  chr1_179277815_179279683      500  1376 (493)    L1M4_orf2#LINE/L1       28   908 (0)  

  chr1_179277815_    500 GGAATAACTAATATTGTTAAAGTGATCACCCCGCCCAAAGCAATCTACAG 549
                             v vi            ii  iiv iv iv      vii        
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chr1_179277815_    550 ATTCAATGCAATCCCTATCAAAATACCAACATCATTTTTCACAGAATTAG 599
                               i                 v   i vv v     ii     v v 
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chr1_179277815_    600 AGAAAA-AATCCTAAAATTCACATGAAACCAAAAAAGAGCCCAAATAGCC 648
                          v  iv-i             i   i  viiv  ii  v  vi       
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr1_179277815_    649 ACAGGCATCTTAAGGAAAAAAAAACAAAGTTGGAGGCATCACATTATGAT 698
                          v ivv     i i-   i  i              vv     i - vvi
  L1M4_orf2#LINE/    178 AAAACAATCTTGAA-AAAGAAGAACAAAGTTGGAGGACTCACACT-TCCC 225

  chr1_179277815_    699 ATACCTCCAA--TTATTGTGCAAGGCTAAGATAACCAAAACAGCACAGTA 746
                          - ii  v  --   i i--   i    vii   i   i    iiii   
  L1M4_orf2#LINE/    226 A-ATTTCAAAACTTACTA--CAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_179277815_    747 CTGGTATAAAAATAGACACATAGATCAATGGAACAGAATACAGAAGCCAC 796
                             i    ii       i              i     vv   iv   v
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_179277815_    797 AAATAAAGCCACATATCTACAACCAACTGATCTTAGACAAAGTCGGCAAA 846
                                v   i i  i  iiii   i    i  v     i vi v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_179277815_    847 AACATACACTGGGAAAAAGACACCCTATTCAGTAAGTGGTGCTGGGAAAA 896
                          v   v  v    i   ii i vi  v    ii  i           v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_179277815_    897 TTAGACTGCCATATGTAGAAGATTAAAACTAGACCTCTCTCTCTCAGTGT 946
                         i i  iv?   i   i i    v i  ii i    i  vi   v  vii 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_179277815_    947 ATACAAAAATCAACTCAAGATGGATTAAAGACTTAAATGTAAGACCTGAA 996
                                   i       i      i ?    i           v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_179277815_    997 ACTATAAAAATACTAAAAGAAAACCTAGGAAAAACTCTTCTGGACATTGG 1046
                                  v vi  i        v    ?iv  v     vv   v    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_179277815_   1047 TCTAGGCAAAGAATTCATGACTAAGACCCCAAAAGCACAAGCAATGAAA- 1095
                         vi       v iv   v iiv  v   v                ii   -
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_179277815_   1096 -ATAAAGAAACAGATGGGGTTTAATTAAA-CTAAAAACTTCTGCGCAGCA 1143
                         - v   v i i i  v  ii  v  i   -i         i  i  vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_179277815_   1144 AAAGAAA-TA--AACAGAGTGAACAAACAACCTGCAGCATGGGAAAAAAA 1190
                           i  v -  --  v i      v i      ii   v      i    -
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA- 721

  chr1_179277815_   1191 ATATTTGCAAACTATGCATCCAACAGAGGATTGATATCCAGAATTTACAA 1240
                         -          ii  ii   ii i ii   i vi          v  i  
  L1M4_orf2#LINE/    722 -TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_179277815_   1241 GGAACTCAAACAACTTAACAATAAAAA-ATAA-TAACACCATTAAAAAGT 1288
                         i      vv      i  i        - i  -    v v   ?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_179277815_   1289 GGGCAAATGACAAGAATAGACATTTCTCAAAAGAAGACGTACAAATTGCC 1338
                                v  ivv               v        ii       v   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_179277815_   1339 AAAAAGCATATGAAAAAATGCTTAACATCACTAATCAT 1376
                           v     i       i     i       ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (134 / 84)
Gap_init rate = 0.01 (13 / 881), avg. gap size = 1.38 (18 / 13)  


2790 25.48 5.41 0.72  chr1_179594304_179596879      878  1709 (867)    L1M4_orf2#LINE/L1        1   871 (37)  

  chr1_179594304_    878 TGGAAACATATCCCATGCTCATGGATGGGTAGAATTAATATTGTGAAAAT 927
                               v          i        v  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_179594304_    928 GACCATACTGCCAAAAGCAATCTATAGATTTAGTGCAATTCCCATCAAAA 977
                          i v     v  v   vii     i     i ii     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_179594304_    978 TACTATCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCATA 1027
                          v i v vv v  i  ii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_179594304_   1028 TGGACCCAAA---AAAGG--CCGGCACAGCCAAAGCAAGACTAAGTGGAA 1072
                             ----  ---  i  --  i v i       i   vvi i iviii 
  L1M4_orf2#LINE/    151 TGGA----AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_179594304_   1073 AGAACAAATCTAGAGGCATCATATTAGCTGACTC--AAACTATACTACAA 1120
                                 vi i    vv   i i vv ii i i--     -        
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chr1_179594304_   1121 GGCTATAGTTACCAAAACAGCATGGTACTGGTATAAAAAAAAGGCATGTA 1170
                         i    i   v i   i    ii         i    ii v - i   i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATA 294

  chr1_179594304_   1171 GACCAATGGAACAGAAT-----ACCCAGAAATAAAGCCAAATATTTACAG 1215
                           i        i     -----ii           v   v i     ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_179594304_   1216 CCAACTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGATA 1265
                         i   i    i  i     i vviv   i v   vv i         i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_179594304_   1266 CTGCATTCAACAAATGGTGCTGAGATAATTGGCAAGCCACAGGTAGAAGA 1315
                         v viv                 i  i  i   vv ?     v i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_179594304_   1316 ATGAAACTGGATCCTCATCTCTCACCTTATATAAAAATCAACTCAAGATG 1365
                              ii    i  ii i   v    v    i      i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_179594304_   1366 GATCAAAGACTTAAATCTAAGACCTGAGACCATAAAAATTCTAAAAGATA 1415
                              ?    i     v     v  i i  i      v ii  i    v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_179594304_   1416 ACATCGGAAAAACTCTTCTAGATATTGGCTTAGGCAAAGAGTTCATGACC 1465
                             v  ?iv  v     vv  iv    v        v iv   v iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_179594304_   1466 AAGAACCCAAAAACAAATGCAACAAAAACAAAAATAGATG----GGACCT 1511
                          v  vv      i  v v         iv          i----    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_179594304_   1512 AATTAAACTAAAAAACTTCTGCACAGCAGAAGAAATAATCAGCTTAGTAA 1561
                         v  i   v v        i  ii vv  i i  v iv    ivvv   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_179594304_   1562 ACAGACAGTCCACAGAGTGGGAGAAAATATTTGCAAACTATGCATCCAAC 1611
                          v     ii       i                    ii  ii   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_179594304_   1612 AAAGGTCTAATATCCAGAA-----------CTC----AAATCAGCAAGAA 1646
                           i  v  vi         -----------   ----  v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_179594304_   1647 AAAAA-----------ATCAAAAAGTGGGCTAAGGACATGAATAGACAAT 1685
                            i -----------  i?    i     v     iv          v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_179594304_   1686 TCTCAAAAGAAGTTATACA---GGCCA 1709
                             v       v      ---     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.42 (122 / 86)
Gap_init rate = 0.01 (12 / 871), avg. gap size = 4.25 (51 / 12)  

 310  7.02 1.75 0.00  chr1_179594304_179596879     2027  2083 (493)    L1M4_orf2#LINE/L1      851   908 (0)  

  chr1_179594304_   2027 AAAAAGATATACAAATGGCCAAGAAACATATGAAAA-ATGCTCAACATCA 2075
                           i                   v  i  i       -             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_179594304_   2076 CTAATTAT 2083
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 3.00 (3 / 1)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1)  


2821 22.37 6.94 5.37  chr1_179634734_179636999.rev      882  1775 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_179634734_    882 TGGAGAGATATCTTATGTTCTTGGATTGGAAGACCCAATATTTTAAAAAT 931
                             i       ii      v             ii      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_179634734_    932 GTCAGTTCTTCCCAACTTGATCTGTAGATCCAGTGCAATCCCAGTGAAAT 981
                          v  i v  i     v       ii    i  ii        vi v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_179634734_    982 TCATAGCAAAATATTTTGTAGATATTGGCAAACTGTTTCTAAAACTCATG 1031
                           vi   vivv v     i   v    i   i   v i      i    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_179634734_   1032 TGGAAAGGCAGGAAACCTAGAATAGCCAAAA------------------- 1062
                               v   i ii   i             -------------------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_179634734_   1063 ---AGTAGAAGGACTCATACTACTCGATTTTAAGACTTACTATGAAGCTG 1109
                         ---   v i        i   v i i    i  i        ii     i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_179634734_   1110 TAGTAATCAAGACAGTATGGTATAAGTCAAAGAATAGATTAATGGAAGAG 1159
                         i               i     ivi ivv   i     ------------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA------------ 288

  chr1_179634734_   1160 ACAGATAGAACAGTGAAAGGAAATAGAGTCCATAAATAGAGTCCTTATAT 1209
                         -  v     v  i  i  -----    --------  v   ---------
  L1M4_orf2#LINE/    289 -CATATAGATCAATGGAA-----TAGA--------ATTGAG--------- 315

  chr1_179634734_   1210 AGTCCAGATTAGAGAGTCCATAAGATCCACACAT--AGAGTAGACTGACT 1257
                                 ------ ----    - i   i    -- vi  vi i   i 
  L1M4_orf2#LINE/    316 AGTCCAGA------A----ATAA-ACCCATACATTTATGGTCAATTGATT 354

  chr1_179634734_   1258 T--GACAAAGG-GCAAAAGAAATGTAATAGAAAAAGGATATTCTCTTCAA 1304
                          --     i  -  v  iivv  vi   i ii    i   v   i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_179634734_   1305 CAAATGGTGCTGGAATAATTGAATATCTATATCCAAAAACGTGAACCTAG 1354
                                      i i  i  i   ? i i  v     ivi    vi i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_179634734_   1355 A----TAC---AGACCTTTCACAAAAATTAACTCAAAGTGGTCCATAAAC 1397
                          ----   --- v   v vi                 i   vi  ? i  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_179634734_   1398 CTAAACATAAAACTCAAAACTATAAGACTCATAG--GAAATTATAGA--- 1442
                              ii   i vii          i    v   --    vi    i---
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_179634734_   1443 ---------TAATCTTGTGTTTGGCAGTGGGTTTTTAGGTACCACAACAA 1483
                         --------- i i    v   v    i   v  i    i  iv   v   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_179634734_   1484 TACTGTATGTTATGTGAGAGAAAAAAGTCATAAGTTGGACTTTGTTAAAA 1533
                         v viii v iv iivi   i    v  --    i        ii i    
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAG--ATAAATTGGACTTCATCAAAA 652

  chr1_179634734_   1534 TTGAAAACT---GCTCTGAAAAATACACTATTAAGAGAATGAAGAAACTA 1580
                           i      --- iv  vv   iv       i    i i    i i  v 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_179634734_   1581 GCCACAGATTAGGAGAAAATATTTGCATAATGCATATCTGATA---GACT 1627
                         v       v i                v viii          ---    
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_179634734_   1628 TGTATCTAAAATATACAAAGAGCTCATAAAACTCAAACATAA-----CAA 1672
                               i i      i     i   v  v       vv    -----   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_179634734_   1673 ACAACCCAATT-AAAAATGGGCAAAG-ATCTGAATAGACACCTTACCGAA 1720
                          i         -              -  i          ii iv  i  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_179634734_   1721 GAAGACACACAGACAGAAAA-AAGCATATAAAGAGATGCTCAACCTCATT 1769
                              i i   i ii vv  -     i  i  i           v   ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_179634734_   1770 TGTCAT 1775
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.83 (128 / 70)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 5.00 (110 / 22)  


3320 22.05 1.81 2.17  chr1_179954630_179956952.rev      596  1425 (898)    L1M4_orf2#LINE/L1        3   829 (79)  

  chr1_179954630_    596 GAAAAGTATTTCATGCTCATGGATCAGAAAAGTTAATATTGCTAAAATGT 645
                             ii   ii    i        ii   i v         i   i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_179954630_    646 CCATGCTACCTAAAGAAATATAAAGATTTAATGAAATACCTATCAAAATC 695
                          v  i  v  i   vvi  v  v     i  i v   v            
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_179954630_    696 CCAATGGCAGCATTCATACTTCACAGAAATAGAAAAATCAACCCTAAAAT 745
                            ---  v  v  i----  ii       v  v  iiii i        
  L1M4_orf2#LINE/    103 CCA---GCTGCCTTT----TTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_179954630_    746 GTGCTCAGAACTGCAAAAGACCCTGAATAGCCAAAGCAATTATGAGAAAA 795
                         viiivii   v     ii     v           i    iv   i   i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_179954630_    796 AA----AAAGTTGGAGGCATCACACTTCTTCATTT-AAAATTATATTACA 840
                           ----           vv         iiv    -    i -  i    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACA 244

  chr1_179954630_    841 AAGCTGTAGTAATCAAAACAGTATGGTACTGGCATAAAAGCAGACACATA 890
                              ii         i     i              iiii     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_179954630_    891 GAGCAGTGGAACCGAATAGTGAGCCCAGAAATAAATTCAAACATATATGG 940
                           v  i     iv    v v   i           ii  v    v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_179954630_    941 TCAACTGATTTTTGACAAAGGTACCAAAAAAGCACAATAAAGAGAGGACA 990
                             i       i     i   i    i vviiv    iii  i  i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_179954630_    991 GTCTCTTCAATAGATGGTGCTGGAAAAACTGGATTTCTACAGGCAAAAGA 1040
                             i     i i          i v        v? i   v        
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_179954630_   1041 ATGAAATTGGACCT-TATCTCACACCAGTCACAAAAATCAGCTCAAAATG 1089
                              i       i-  i         vvi        i i         
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_179954630_   1090 GATAAAGAACCTAAGTGTAAGATCTGAAACAGTAAACAAAAAC----AGA 1135
                            v ?ii      i       v  i    vi    -----  ----   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-----ACTCTTAGA 539

  chr1_179954630_   1136 AGAAAACATAAAGGAAAATCTCCTTGACATTGGTCTTGGCAATTATGTCT 1185
                                   ii? v      i v    v    vi v      vi v   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_179954630_   1186 TGGATGCCACACTGAAAGCACAGGCTACAAAAGCAAATAAATAAATAAAT 1235
                          i   iiv    ii        i  v       -   -     i      
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAG-AAA-AAATAGATAAAT 637

  chr1_179954630_   1236 GGGACTTCA----AACTAAAAAGCTTCTGTACAGCAAAGGAAACAACCAA 1281
                         v        ----  i      -   i   i vv       v  v i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_179954630_   1282 CAAAATGAAAAGGCAACCTAGGGATTGAGAAAAAATATTTTCAAATCATA 1331
                         v   i       i     i vi  v  i  i         v         
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_179954630_   1332 TATCAGATA-GGGATTAATATCCAAGATTTATAAAGAACTTACACAACTC 1380
                             v    -    i vi      ii  v           ivi       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_179954630_   1381 AAAATAGCAAGAAAACATATTACTCAACTAAAAACTGGGCAAAGG 1425
                           --  ii  i  i   v  v  i   i ?    v          
  L1M4_orf2#LINE/    787 AA--TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.80 (115 / 64)
Gap_init rate = 0.02 (14 / 827), avg. gap size = 2.36 (33 / 14)  

 345 25.40 0.00 0.79  chr1_179954630_179956952.rev     1707  1832 (491)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_179954630_   1707 CTCAAAAAGCAAACAAACAAACAAACAAACAAACAAAACACCAGAAGATT 1756
                              v  -i   v i     i  v v  iv? v   vviv  i i    
  L1M4_orf2#LINE/    784 CTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_179954630_   1757 TGAGTAGACATCTCTCCAGAGATGACATAAAAATTGCTAACAGGTGCATA 1806
                            i       i      i   v  i   v    v  i  i i ii   i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_179954630_   1807 AAAAGATGCGCAACATTACTAATCAC 1832
                                  v      i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (18 / 13)
Gap_init rate = 0.01 (1 / 125), avg. gap size = 1.00 (1 / 1)  


3185 27.53 0.55 0.55  chr1_180097594_180102618     3625  4532 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_180097594_   3625 TGGAAGAACATTCCATGCTTATGGATAGGAAGAATCAATATCGTGAAAAT 3674
                              ii i  i     i i      v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_180097594_   3675 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3724
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_180097594_   3725 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGCTCA 3772
                          v   iivi i  i  ii     -   -- v  i  - iii    ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_180097594_   3773 TATGGAAGCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 3822
                                iiiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_180097594_   3823 AACAGAGCTGGAGGCATCATGCTACCTGACTTCACACTGTACTACAAGGC 3872
                             i  i      vv   ii  v  ii i    v viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_180097594_   3873 TACAGTAACCGAAACAACATGGTACTGCTACCAAAACAGAGATATAGACC 3922
                                 i i i   iii        vi iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_180097594_   3923 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACATATCTACAATC 3970
                                i    i--    i  --        vv   i i  i  iii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_180097594_   3971 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4020
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_180097594_   4021 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4070
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_180097594_   4071 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4120
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_180097594_   4121 CTAAAGACTTAAACGTTAGACCTAAAACCACAAAAACCCTAGAAGAAAAC 4170
                         ii ?    i    i  v   v       i i    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_180097594_   4171 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTAATGACTA 4219
                         v    ?i- v i -   iv   v v  vv i     v ii  vv iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_180097594_   4220 AAACATGAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4269
                         vi   iv       vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_180097594_   4270 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTTAA 4319
                           i   v i  i i   i  ii vv    i  v   ii  vv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_180097594_   4320 CAGGCAACCTACAGAATGAGAGAAAATTTTTACAATCCACCCATCTGACA 4369
                         v  i     i        i        v   i   vi  ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_180097594_   4370 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 4419
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_180097594_   4420 AAATCAAACAACCCCGTCAAAAAGTGGGCAAAGGATATGAACAGACACTT 4469
                           iv    i     vi i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_180097594_   4470 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 4519
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_180097594_   4520 CATCACTGGCCAT 4532
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (153 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3249 27.20 0.44 0.44  chr1_180358360_180364766     5007  5914 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_180358360_   5007 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATAAAAAT 5056
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_180358360_   5057 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5106
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_180358360_   5107 TACCAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5154
                          v   iivi    i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_180358360_   5155 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5204
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_180358360_   5205 AACAAAGCTGGAGGCATCACGCTACCTGAGTTCAAACTATACTACAAGGC 5254
                                i      vv    i  v  ii v      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_180358360_   5255 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGATC 5304
                                 i   i    ii         i iv ii i   v i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_180358360_   5305 AATGGAACAGAAC--AGAGCCCTCACAAATAACGCCGCATATCTACAACT 5352
                                i    i--    i  -- v      vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_180358360_   5353 ATCTGATCTTTGACAAATCTGAGAAAAATAAGCAATGGGGAAAGGATTCC 5402
                          vi    i  i     ivv  vv  i vi vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_180358360_   5403 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5452
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_180358360_   5453 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5502
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_180358360_   5503 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5552
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_180358360_   5553 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5602
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_180358360_   5603 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5652
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_180358360_   5653 TTAAACTAAAGAGTTTTTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5702
                          i   v v  i ii     ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_180358360_   5703 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5752
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_180358360_   5753 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5802
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_180358360_   5803 AAACAAACAACCCCATCAAAAAGTGGACGAAGGATATGAGCATACACTTC 5852
                          i     i     v  i?    i   i i      v   ii v   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_180358360_   5853 TTAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5902
                          iv        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_180358360_   5903 ATCACTGGCCAT 5914
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2882 26.35 4.95 0.46  chr1_180380259_180386335.rev     4718  5586 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_180380259_   4718 TGGAAAAACATTCCATGCTTAGGGATAGGAAGAATCAATATCGTGAAAAT 4767
                               i i  i     i i v    v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_180380259_   4768 GGCCATACTGCCCAAAATAATTTATAGATTCAATGCTATCCCTAACAAGC 4817
                            v     v      v i  i  i        i  v       v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_180380259_   4818 TACCATTGATTTTCTTCACAGAATCAGAAAAAAACT-ACTTTAAATGCCA 4866
                          v   viviii  i  ii     -- vvi v  i  - iii    vvi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr1_180380259_   4867 TATGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAG 4916
                                viiv  ii  v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_180380259_   4917 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAAGTGTACTACAAGGC 4966
                                i      vv    i  v  ii i      iiv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_180380259_   4967 TATAGTAACCAAAACAGCATGGTACCGGTACCAAAACAGATATATAGACC 5016
                           i     i   i    ii      i  i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_180380259_   5017 AATGGAACAGAACAGAGGCCTCAGAAATAACGCCACACA----------- 5055
                                i    iv   ivii         vv   i   -----------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_180380259_   5056 -------------AG-----------CATT----GGGGAAAGGATTCCCT 5077
                         -------------  -----------    ----        i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_180380259_   5078 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAACTGA 5127
                         v  i  i        i     v      v  ?   i   i i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_180380259_   5128 AACTGGGCCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 5177
                          ii   i     v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_180380259_   5178 AAAGACTTCAACATAAGACCTAAAAC-ATAAAAACCCTAGAAGAAAACCT 5226
                          ?    i v  ii     v       -      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_180380259_   5227 AGGCA-ATACCATTCAGGACACAGGCATGGGAAAAGACTTCATGACTAAA 5275
                            ?i- v i -   iv   viv  vv i  v  v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_180380259_   5276 ACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGGAATCTAAT 5325
                                     vvi         ivv     v  i    v i ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_180380259_   5326 TAAACTAAAGAGCTTCTGGACAGCAAAAAAAACTATCATTGGAGTGAACA 5375
                         i   v v  i i   i  vi vv    ii v       vvii      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_180380259_   5376 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGATAAA 5425
                          i     i                 v       vii  vi         i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_180380259_   5426 GGGCTACTATCCAGAATGTACAAGGAAGTAA-ACAAATTTACAAGAAAAA 5474
                           i  vv          i  i  i   v vv-    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_180380259_   5475 AACAAACAACCCCATCAAAAAGTGGGCAAATGATATGAACAGACACTTCT 5524
                         i     i     v  i?    i        v   v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_180380259_   5525 CAAAAGAATACATTTATGCGGCCAACAAACATATGAAAAAAAAGCTCATC 5574
                          v      v i  vi vii      i  i  i       i v-     v 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAAC 896

  chr1_180380259_   5575 ATCACTGGTCAT 5586
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (133 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 4.70 (47 / 10)  


2340 23.40 9.86 3.68  chr1_180428738_180430664      593  1434 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr1_180428738_    593 ATGTTTATAGATTGGAAGACCTGAAATTGT---GATTTCAGT--TCCTCG 637
                              i  i           i i v     ---   vv  i --   i i
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_180428738_    638 AATTGATTTATAGATTTGATGACATTCCAATAAAAATCC-AGAT---TTT 683
                                i  i     ii i vv  i  v  v       -  v ---   
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr1_180428738_    684 CTTATAGAAATGTTCAAGCCATTTCTAAAACCTA------AATGC----- 722
                         i  ii      vvv     iiv i      iii ------     -----
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_180428738_    723 --TTAGAATAACCAAAACAATTTTGAGAAAGAA---CAAAGTTAGAACAC 767
                         --ii      i          i    i      ---       i  iv  
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_180428738_    768 TTAAACTTACTGGCTTTAACACTTACTGTAAAGATACAGCAATCAAGTTG 817
                          i v    v iiii  i  v       ii    v     i       vii
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_180428738_    818 GTGTGTTATTGGCATA-GTTTTGACACATAGATCAATTAAACACAATCGA 866
                              v  i       - vv v    i          vi  i v   i  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_180428738_    867 GAACCCAGAAATAGACGAGCATGTGTATGGCCAATTGATTTCTGACAAAG 916
                           ii         i  vvii ii v     i          ii     i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_180428738_    917 ATGCCAAGGTAATTCAATATGGAAAGGAATA-CCTTTTCAACAAATGGT- 964
                         i       iiv       iv      -    -i                -
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTG 413

  chr1_180428738_    965 CTTGAACAACTTGTTATCCACATTTAAATAAATTAACATCAACCCTTACT 1014
                           v i      v v  ?      vi   vi   v  vv vi    i   i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_180428738_   1015 TTATG--GTACACAA-------CT------GGATAAT---CTTAAATGTA 1046
                          i ii--i  i    -------  ------    v ?--- i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_180428738_   1047 AATGCTAAAACTATACAACTTCTGGAAGAAA--------------CTTTA 1082
                          iv            v    ii i       --------------   ii
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_180428738_   1083 TAACCTTCACGTAGGCAAAGATTTCTTAAACAGGACACAAAATAGCATAA 1132
                          i     vivv       v i       i i v     v   -    i  
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA-AGCACAA 612

  chr1_180428738_   1133 ACATAAAAAGTATAAAAAATTTATAAATTGGGCTACATCAAAATTTAAAA 1182
                         i  vv     ---       vv         i  v          v    
  L1M4_orf2#LINE/    613 GCAACAAAAG---AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_180428738_   1183 CCCGTTTAT------AAGAAAAT------GCAAATGCAAAGGTAGACCTC 1220
                          i--   i ------   i v i------ v  i  v    ii iv  v 
  L1M4_orf2#LINE/    660 CT--TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_180428738_   1221 AGACAGATAAAATATATATGTGTGTGTGTGTGTGTGTGTGTATACTATTT 1270
                            vv iv i  v    v  iivi ---------------i   -   i 
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAAT---------------CATA-TATCT 741

  chr1_180428738_   1271 TATATTATAAGGACTGATATCTAGAATATATAAAGAAGTCTTTCAACTCA 1320
                         v   ---- i     vi    i               v    v       
  L1M4_orf2#LINE/    742 GATA----AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_180428738_   1321 CTGATAGAA---CCAATTATAAAGTCAAT---AAAATGGACACA---TTT 1361
                         v i   i  --- v   ----  vi    ---       i  v ---   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAAT----AACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_180428738_   1362 GAACAAAC--TTTACCAAAGAAGATACACAGATAGCCAATATATCCATGA 1409
                            i i  --  iv            i   i  i       viiv     
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_180428738_   1410 CTAGATGCTCAATATCATTCATCAT 1434
                         vv          i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (118 / 77)
Gap_init rate = 0.03 (29 / 894), avg. gap size = 3.93 (114 / 29)  


2564 21.08 0.54 2.34  chr1_180501544_180503888.rev      514  1068 (1277)    L1M4_orf2#LINE/L1        1   545 (363)  

  chr1_180501544_    514 TAGAAAGACATCCCGTGTTTACGGGTTGAAAGACTTAATAT-GTTAAAAT 562
                          i      i     i    i i  i   i            -     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_180501544_    563 GTCCATATTATCCAAAACTT--TCTGCATATTCAATGCAATCCCTTCCGA 610
                          v v   i vi     --  --   i  v      i         vi i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_180501544_    611 AATCCCAAGTGTATTTTTGACAGAAATAGCAAAAATAACCTTAAAATTCA 660
                                iv  iv     vi       v vv  iv i i i         
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_180501544_    661 AATGGAACTACGAAGGATCCTGAATAATCAAAGCAATCTTGAAAAAGAAG 710
                         v      v i i i   i  v     ii    i                 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_180501544_    711 AGTAAAGCTGGAGATCTCATGCTTCTTGATTTGAAAACATATTACAAAGC 760
                          ii    i     iv    ii    iii    v     v  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_180501544_    761 CACAGTAATCAAAACTTTATGGTACCGGCATAAAGACAGACACACAGATC 810
                         i           i  vv i      i       i  i     i i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_180501544_    811 AATGGAACAGAACAGAAAGCCCAGAAATAAACCCAAGCATATGTGGTCAA 860
                                i    iv  i  i               vi   v i       
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_180501544_    861 CTGATCTTCAATAAGGATGCCAAGAATATACAACAAGGAAAAGATAATCT 910
                         i    i   i i    i        vi  v   iii     ii   i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_180501544_    911 CTCCAACAAATGGTGCTGGGAAAACATTTGTACAAAAACTAGATCACATG 960
                         i i                  v   ---  v -------  ?-i      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAAC---TGGA-------TAK-CCACATG 437

  chr1_180501544_    961 TAAAAGAATGAAATTGGACATTTATTTTACACCATACACAAAAATCAATT 1010
                         i           i      vii  ii i        i        i  i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_180501544_   1011 CAAAATGGATTGCAGACTTAAACATAAGACCTGAAACTATAAAACTCCTT 1060
                                   ii?    i    ii     v  i              i v
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_180501544_   1061 AAAGAAAA 1068
                         i       
  L1M4_orf2#LINE/    538 GAAGAAAA 545

Transitions / transversions = 2.83 (85 / 30)
Gap_init rate = 0.01 (6 / 545), avg. gap size = 2.67 (16 / 6)  

1548 22.49 1.63 0.00  chr1_180501544_180503888.rev     1486  1854 (491)    L1M4_orf2#LINE/L1      534   908 (0)  

  chr1_180501544_   1486 CTTAGATAAAAATATAGGGGGAAAGCTTTATTATATTGGCCTTGGCAATG 1535
                               vi    i     ? v   v   ii v iv    vi v       
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_180501544_   1536 ATTTCTTGGATATCACACCAAAAGCACAGGCAAGAAAATTAAAATTAGAG 1585
                         i      i     v              i    v    vv    v    v
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_180501544_   1586 AAGTGAAAGTACATCAAACTAAAAAGCTTCTGTGCAGCAAATGAAACAAT 1635
                           i vii v v       v v    i   i     vv    v  v  v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_180501544_   1636 CAATAGAGTGAATAAATGACCTATGGAATGGGAGAAAATATTTGCAAATC 1685
                            v i      v i ii   i ii                         
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_180501544_   1686 ATGTATCTAATAAGGGGTTAATACCCACAATATTTTAAGAGCTTCTACAA 1735
                           i     i       ii vi  i   v     v v    i  ii     
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_180501544_   1736 CTGAATAG-AAAAAAA-----AACCCAATTTAAAAATGGGCAAAACACCC 1779
                           v    i-     i -----         ?             iv iii
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_180501544_   1780 GAATAGATATTTTTCCTAAGAAGACATACAAACGACCAACACATATATGA 1829
                                i    i   v       i       i i    i vii i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_180501544_   1830 GAAAGTGCTCAACATCACTAATCAT 1854
                         i  ii            ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (48 / 33)
Gap_init rate = 0.01 (2 / 375), avg. gap size = 3.00 (6 / 2)  


 714 22.38 17.14 0.48  chr1_180766046_180768439.rev      736   945 (1449)    L1M4_orf2#LINE/L1        1   245 (663)  

  chr1_180766046_    736 TGGAGAGATAGTCCATGTTCCTGGAT------AC---------------- 763
                             i     vi        v     ------  ----------------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_180766046_    764 --CAATTCTTCTCAATGTGATCTACAAGT-----GCAATCCCATTCAAAA 806
                         --    v  i i   vv         ii -----        vv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_180766046_    807 TCCCAGC-ACGTTGTTTTGTAGATATTGACAAGCTGATTGTAAAATTGAT 855
                                -i v  -     i   v              iv       v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_180766046_    856 ATGGAAAGGCAAAAGAGTCAGAATATCCAACAAAGTGTTAAA------GA 899
                                v    ii  vi       v    v v i v  i  ------  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_180766046_    900 ACAAAGTGAGAGGACTGATTTTATCTGACTTTAAGGCCTATTACAA 945
                                vi       v ivi vi ii i  i  ii i  i     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

Transitions / transversions = 1.24 (26 / 21)
Gap_init rate = 0.02 (6 / 245), avg. gap size = 6.17 (37 / 6)  

2546 21.88 4.78 0.46  chr1_180766046_180768439.rev     1255  1903 (491)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr1_180766046_   1255 AAGACCTATTGTAAAGCTATAGTAATCAAGATCATGTGGTATTGGT-TAA 1303
                           i  i  i ii       i           ivi       i   i-   
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_180766046_   1304 GGAATAGATGAATAGGTCAATGGAATAGAATAGAGAGCTCAGAATTGA-C 1352
                            -    iiv    i               v     ii     v i - 
  L1M4_orf2#LINE/    282 GGA-TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_180766046_   1353 TCA--CATAAATAGTCAATTGATCTTTGACCAAAAAAAAAAAGGCAATTT 1400
                         i  --   vv  i          i  i   -  iiivivv   i v   i
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGAC-AAGGGTGCCAAGACCATTC 379

  chr1_180766046_   1401 GATGAAGAAATAAACATCTTTTCAACAAATGGTGTTAGAGTAACTGGATA 1450
                         i   ii    v  vvi                  i i iii         
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_180766046_   1451 TTCACCTGGAAAA-AATCAATCTAAACACTGACCTTATATCCTTCATAAA 1499
                         ?i   v  v    -   v  vi ii  v iv    i i i v vi i   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_180766046_   1500 AATTAACTAAAAATGGATCACAGACCTTAATGTAAAATGC-AAAACTATA 1548
                                 v           ?      v       i -  -         
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATA 528

  chr1_180766046_   1549 AAACTTCTAGAAGACAAAATAGGA-----------TG-CCTTGGATTTGG 1586
                              ii       v  v     ?-----------  -      i  v  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_180766046_   1587 TGATGAGTTTTTAGATAAAATACCAAAAGCATGATC--CAGGA-AAAAAA 1633
                         ii   iv  i       vi i          ii v --  ii -      
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_180766046_   1634 T---TATATCAGATTCTATTAAAATTTAAAACTTCTGTTCTGCAAAATAC 1680
                          ---  v  ii  i ii  i      v       i   v  v    iv  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_180766046_   1681 AATGTTAAGATAATGAAAATATAAGCCATGGACTGGGAGAAAATATTTGT 1730
                          v i i    v i      v i  v   ii  v                i
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_180766046_   1731 AAAACACATATCTGATAAAGGACTTGCATTCAAAATATACACAGAAGTCT 1780
                            v  i           i       i  i  i      i v    v   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_180766046_   1781 TGAAACT---TATCAAAAAGA-AAA---CCCAATTTAAAAATGGGCAAAA 1823
                          iv    ---  vi       -   ---       ?             i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_180766046_   1824 AATCTGAACAGACACCTCACCAAAGGAGATATACAGGTGGCAAATAAGCA 1873
                         i  i    i     ii  v      i         ii    v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_180766046_   1874 TATGAAAAGATGCTCAACATCATATGTCAT 1903
                         i                     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (92 / 46)
Gap_init rate = 0.02 (16 / 677), avg. gap size = 2.12 (34 / 16)  


3173 27.53 0.55 0.55  chr1_180827882_180838048.rev     5037  5944 (4223)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_180827882_   5037 TGGAAGAACATTCCATGCTCGTGTGTAGGAAGAATCAATGTCGTGAAAAT 5086
                              ii i  i     i  i  vi v      v i   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_180827882_   5087 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5136
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_180827882_   5137 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5184
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_180827882_   5185 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTTAATCCTAAGCCAAAAG 5234
                                viiv  ii  v  v v  vi    ivi    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_180827882_   5235 AACAAAGCCAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5284
                                iii    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_180827882_   5285 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5334
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_180827882_   5335 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACC 5382
                                i    i--    i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_180827882_   5383 ATATGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGTAAGGATTCC 5432
                          vv    i  i     ivv  v   i v  vv        v   i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_180827882_   5433 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5482
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_180827882_   5483 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5532
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_180827882_   5533 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5582
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_180827882_   5583 CTAGGCA-ATACCATTCAGGGCATAGGCATGGGCAAGGACTTCATGTCTA 5631
                         v    ?i- v i -   iv i v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_180827882_   5632 AAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTA 5681
                         vi            vvi          vv    iv  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_180827882_   5682 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5731
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_180827882_   5732 CAGGCAATCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5781
                         v  i   i i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_180827882_   5782 AAGGGTTAATATCCAGAATCTACAATGAACGCAAACAAATTTACAAGAAA 5831
                          i  ii vi          v  i  v    v vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_180827882_   5832 AAATCAAATAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTT 5881
                           iv          v  i? v  i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_180827882_   5882 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5931
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_180827882_   5932 CATCACTGGCCAT 5944
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

3320 20.20 4.43 1.97  chr1_180827882_180838048.rev     8437  9248 (919)    L1M4_orf2#LINE/L1        1   832 (76)  

  chr1_180827882_   8437 TGGAGTTATATTTCATGTTCATAAATTGGA-GATTCAATCTTTTTAAGAT 8485
                             ivv    ii         ii      -  i i   v  v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_180827882_   8486 AGCAATTCTCCCCAGAATGAAGTATAGATTCAACACAATCCCTATAAAAT 8535
                         i     v       i v   vv  i         i          v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_180827882_   8536 TTCTAGCAGAGCAATTTCTTTGGTAGACATTGATAAGCTCATTCTAAAAT 8585
                          i i   v -----ii i   v i   v     i     v  i       
  L1M4_orf2#LINE/    101 TCCCAGCTG-----CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_180827882_   8586 GCGTATGAAAATGCAAAGAACCTAGAATAGCTGTAATAATCTTGAAAAA- 8634
                         v i    i        i i   i        iiv  i            -
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_180827882_   8635 -AGAACAAAGCTGGAGAACTTACACTCCCCAATTTCGAAG-TTATAATAA 8682
                         -         i     i   i     i         i  i-   iv i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_180827882_   8683 AGGTACAATAATCGAGACAATATAGTATTGGCACA-GGATAGGTACATAG 8731
                           v    i     i     i i i   i     i -      ii i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_180827882_   8732 ATCAATAGAATAGAATTGAGAGTCCAGAAATAAATTCTTCCATTTATGGT 8781
                               i                           ii v v          
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_180827882_   8782 CAGTTGATTTTTGACAAGTGT---AAGGCAATTCAATTCGGGAAAGGACA 8828
                           i        i      v  ---   i v       v-       i i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATA 394

  chr1_180827882_   8829 GTGTTTTCAACTAATGTTTGTGAGACAGTTGGATATACATGTACAAAACA 8878
                           v        v    v vv  i    ii      ?v  ii i     --
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-- 442

  chr1_180827882_   8879 TAAAGAAAAAAGAACATAGAC----ACCTCATAGTATACACAAAAATTAA 8924
                         ----   vi   v--- i   ----      i vi   i           
  L1M4_orf2#LINE/    443 ----GAATGAAGT---TGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_180827882_   8925 CTCAAAATGGATCATTGACTTAA-TGTCTAAG-TAAAATTATAAAACTTT 8972
                                       ?v   i   -   vvi  -     i         i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_180827882_   8973 TAGAAGAAAACA--GGGGAAAAA--TAGTGACATTGA-TTAGGCAAAGAA 9017
                                     --  ? v   v-- v     v   i-        v iv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_180827882_   9018 TTCTTAGATATGACAACAAAAGCATAATCCACAAAAGAAAAAA------- 9060
                                        v        i  v v             -------
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_180827882_   9061 ------CTTAAACAAAATTAACG-TTTTTGCTCTTCTAAAAA-ATCATTA 9102
                         ------   v v         vi-i     iv    v  ii - ii  i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_180827882_   9103 -GACAATGAAAGGGCAAGGCAAAAACTGGGAGAAAA-GTTTATGAATCAT 9150
                         -  v i     i i   vv  v i v          -i   iii      
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_180827882_   9151 ACATCTGATAAAGGAATTTGTATCCGGAATACATAAATAACTAATATAAC 9200
                          i         i   -i        i     i     v    vv  i   
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGA-CTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_180827882_   9201 TCAATAACAAGAAGACAAGCAGCCTAATTTGAAAATGGCCAAAAGGTT 9248
                                i  i       ii i  i    ?i       v    i i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

Transitions / transversions = 1.76 (102 / 58)
Gap_init rate = 0.03 (21 / 832), avg. gap size = 2.48 (52 / 21)  

 334 17.83 0.78 5.43  chr1_180827882_180838048.rev     9548  9676 (491)    L1M4_orf2#LINE/L1      786   908 (0)  

  chr1_180827882_   9548 CAAAAATAAACAAACAAAAAACAACAACAAAAACAAAAGAATGGCCAAAA 9597
                            v      v i     v   v-   iv?   ------     v    i
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACC-CAATTWAAA------AATGGGCAAAG 828

  chr1_180827882_   9598 AAGTTGAAAAGACATTTCTCCAAATGAAATACAGAAATAACTAATAAACA 9647
                         i v     v               vi i   i v    ii i     i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_180827882_   9648 CATGAAAAAATGCTCA-CATCACTAGTCAT 9676
                                 i       -     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (12 / 10)
Gap_init rate = 0.02 (3 / 123), avg. gap size = 2.67 (8 / 3)  


3418 24.05 0.76 2.82  chr1_180868705_180871749.rev     1632  2554 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr1_180868705_   1632 AAGATATTCTACATTCATGGATTGGAAGACTCAATTTAGTTAAAATGTCT 1681
                                i i ii                  i   v v     i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_180868705_   1682 CTAGTACCCTAAACAATCTACAGATTCAATGCAATCCCTACCAAAATACC 1731
                         v  v v   v  vii              i          i      v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_180868705_   1732 AATGACATTCTTCATAGAAATAGAAAAAAC-ATC-TAAAATTTATATGGA 1779
                          iivi v  i  iii      v  v  ivi-   -       i       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_180868705_   1780 ACCAAAAAAGACCCAGAATAGCCAAAGCCATCCTGAGCAAAGAGAACAAA 1829
                          viiv  ii                 i v   i   iv  ii        
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_180868705_   1830 ACTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCTATAGT 1879
                         ii       v     i v  ii i      viv       i     i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_180868705_   1880 AACCTAAATAGCATGGTGCTGACTTAAAAACAGACATATAGGGCAATGGA 1929
                           i v i i  ii    i   i v   ii i          iv       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_180868705_   1930 AAAGAATAGAGAA-CCAGAAATAAGTCCACACATTTACAGTCAATTCATA 1978
                          v     v    i-          ii   i       ii       v  v
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_180868705_   1979 TTTTACAAAGGTGCCAAGAATGTACATTGGAGAAAAGACAGTCTCTTCAA 2028
                           iv    i          vii v  v   i    ii i     i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_180868705_   2029 TAAATGGTGCTGGGGAAACTGGAGATCCATATGCAGAAGAATGAAACTAG 2078
                         i             iv       v ?   i     i         ii i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_180868705_   2079 ACTCCTATCTCTCACCATACTAGACTCCTATCTCTTGCCATATACAAAAA 2128
                           i    i   v       -----------------------        
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATA-----------------------TACAAAAA 481

  chr1_180868705_   2129 TAGAAATCAAAATGGACTATATAATTAATTCTAAGA-CTAAAACTATACA 2177
                          -v  v          ii ? v vi   v v     -           v 
  L1M4_orf2#LINE/    482 T-TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_180868705_   2178 ACTAATAGAGGGAAACATTAGGGAAGCACTCCAGGACATTGGTCTGGACA 2227
                            vv    i i      vi ? v ivv  i iv   v    vi i i  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_180868705_   2228 AAGATTTCTTGAGTGAGACCTCAGAAGCACAGGTGATAAAAGCAGAAATG 2277
                          v i      iii iv   vi  i       i ii i     v i    i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_180868705_   2278 GACAAATGGGATCATATCAAGTTAAAAAACTTCTGCACTGCGAAGGAAAC 2327
                           i    v   iivi     iv v        i  ii  v i     v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_180868705_   2328 AATCAACACAGGTAGGAGACAACCCACAAAATGGGAGAAAATATTTGCAA 2377
                         v     v v  vv ii            i                     
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_180868705_   2378 CCTACCCATCTGATAAGGGATTGATAACCAGAATATATAAGAAGCCCAAA 2427
                         vii ivi             i vi  v             ii i i vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_180868705_   2428 CAAC--AATAGGAAAAAAAAAAACATAATCTGATTTTAAAATGGGCAAAC 2475
                             --    iv     i v   --   i ii   ?v            v
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAA--TAACCCAATTWAAAAATGGGCAAAG 828

  chr1_180868705_   2476 TATCTAAATACACATTTCTTTAAAAAATACATAAAAATGGCTGATAGGAA 2525
                         v  i i    v        ii   i  v i   v       ii   i v 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_180868705_   2526 TATGAAAA-ATGCTCAACATCATTAATCAT 2554
                         i       -             ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (135 / 83)
Gap_init rate = 0.01 (9 / 904), avg. gap size = 3.67 (33 / 9)  


3233 25.89 1.67 0.78  chr1_180929989_180936679.rev     5301  6200 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_180929989_   5301 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5350
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_180929989_   5351 GGTCATACTGCCCAAGGTAAGTTATAGATTCAATGCCACCCCCATCAAGC 5400
                           iv     v     iv i vi  i        i  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_180929989_   5401 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAATTC 5448
                          v   iivi i  i  ii     -   --- v  i  - iii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_180929989_   5449 ATATGGAACCAAAAAAGGCCCACA-TCGCCAAGTCAATCCTAAGCCAAAA 5497
                                 viiv  ii i    v - v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_180929989_   5498 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5547
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_180929989_   5548 CTACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5597
                                  i   i i  ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_180929989_   5598 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTA---- 5641
                                 i    i--    i  --        vv   i i  i  ----
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_180929989_   5642 CAACT-----TTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5686
                            i ----- i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_180929989_   5687 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5736
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_180929989_   5737 TGAAATTGGATCCCTTCCTTACACCTTATACAAAAATTAATTGAAGATGG 5786
                             i     i    v   i     v              i v  i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_180929989_   5787 ATTAAAGACTTAAATGTTAGACCTAAAACCACAAAAACCCTAGAAGAAAA 5836
                           i ?    i       v   v       i i    vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_180929989_   5837 CCTAGGCA-ATACCATTCGGGACATAGGCATGGGCAAGGACTTCCTGTCT 5885
                          v    ?i- v i -    v   v v  vv i     v ii   i ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_180929989_   5886 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5935
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_180929989_   5936 AATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGA 5985
                         v  i   v v  i i   i   i vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_180929989_   5986 ACAGGCAACGTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 6035
                          v  i    vi                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_180929989_   6036 AAAGGGTTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 6085
                           i  ii vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_180929989_   6086 AAAAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACGC 6135
                            i -    i     v  i? v  i     i      v    i    ii
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_180929989_   6136 TTCTCTAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 6185
                              i        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_180929989_   6186 ATCATCACTGGCCAT 6200
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


3439 24.27 1.68 0.22  chr1_181004741_181009046.rev     2922  3815 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_181004741_   2922 GGAGAGAGATCCCATGTTCATGTACTGGAAGAATCAATACTGTTAAAATG 2971
                            i   v              v i       v i    i      i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_181004741_   2972 TCCATACCATCCAAAGCAATCCCACAGATTCAATGAAATTCCTATCAAAA 3021
                         v v    ivi     vii   i-          i v   i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCT-ACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_181004741_   3022 TACCAATGACATTCTTCACAAAAATAGAAAAAAATATCCTAATATTTATA 3071
                          v   iivi v  i  ii  i    v  v  ivvv       v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_181004741_   3072 TGAAACCACAAAAGACCCAGAATAGCCAAAGCTATTCTAAGTAAAAAGAA 3121
                           i  vii   ii                 i v  ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_181004741_   3122 CAAATCTGGAGGAATCACAT-----AACTTCGAATCATATCACAGAGCCT 3166
                             vi       v     i-----  i   i  v v  ii   i   iv
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_181004741_   3167 TAGTAACCACAACAGCATGGTACTGGCATAAGAACAGTCACAAAGACCAA 3216
                         i     i  vi    ii               i i  v  i v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_181004741_   3217 TGGAACACAATAGAATACCCAGAAATAAATTCACATACCTACAGTAAACT 3266
                              i v   v  ivii           ii  i i ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_181004741_   3267 CATTTTTGACATAGGTGTCAAGAACATACACTGGGAAAAAGACAGTCTCT 3316
                         v     i    vi    i     v   v  v    i   ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_181004741_   3317 TCAATAAATGGTGTTGGGAAAACTGGATCTCCATATACAAATGAATGAAA 3366
                             i        i     v        v?   i  i    v       i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_181004741_   3367 CTAGACCCCTATCTCTAACCATACACAAAAATAAAACCAAAATGGATTAA 3416
                         i i        i   vv      i        v  vi          i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_181004741_   3417 AGACCTAAATCTAAGACCTAAAATGATGCGACAACTAAAAGAAAACACGA 3466
                                   v     v      iv  ivi  vvi  i         iii
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_181004741_   3467 GGGAAACTCTCTAGGATGTTGGACTGGGCAAAGTTTTCTTAAATAATAC- 3515
                          ? v  v   iiiv  iv    ii i     v v       i   vv  -
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_181004741_   3516 CCACAGGCACAGGTGACCAAAGCAAACATGGATGAATAGGATCACATCAA 3565
                            v i     i ii  v    v   v  i   i   v   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_181004741_   3566 G-TTAAAAACCTTCTGCACAGCAAAGCAAGTAATCAACAAAGTGAAGAGA 3614
                         i-        i  -  ii vv     v viiv     v        i   
  L1M4_orf2#LINE/    651 AATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_181004741_   3615 CAATGCACAGAATGGGAGAAAATATTTGCAAAC----TCTCTGACAAGGG 3660
                            iv                           i---- v     i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_181004741_   3661 ATTAATAACCAGAATATAAAAAGAGCTCAAGCAACTCTATAA--AAAAAT 3708
                          i vi  v          v     i   vvi      v    --    iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_181004741_   3709 CTAATAATCCAATC-AAAAATGGGCAAAAGATTTGAAAAGACATTTCTCA 3757
                          v     i     i-             i        v           v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_181004741_   3758 AAAGAAGACACACAAATGAC-AACAGGCATATCAAAACGTGCTCAACATC 3806
                                 i i       i -  i i   i  v    vi           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_181004741_   3807 ACTGATTAT 3815
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.55 (130 / 84)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 1.89 (17 / 9)  


3029 19.39 2.42 0.30  chr1_181238508_181240159.rev      502  1161 (491)    L1M4_orf2#LINE/L1      235   908 (0)  

  chr1_181238508_    502 ACTTAATTACAAAATTACAATAATCAAAACAGTGTGGTACTGACATAAAG 551
                             - i      ii    i       i              i     i 
  L1M4_orf2#LINE/    235 ACTT-ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_181238508_    552 GTAGACATATAAA---ATGAAATAGAATGGAGAACTCAGAAATACACTTT 598
                         i          i ---   i        v    iii        v  iiv
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_181238508_    599 TGTATATATGGTCAAATGATTTTTGACAAGGTTGCCAAGACCATTCAATG 648
                          ii  v         v       i       v                  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_181238508_    649 GAGAAAAGAGAGTCTTTCCAACAAATGGTGCTGGAAAAACTGGACACCAA 698
                          i    ii v       i                i v       i ? v 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_181238508_    699 TATGCAAAAGAATGACATT--ACTCTTACTTAATACTATGTACAAAA-TG 745
                         i              vi  --  i i   i v i  i  i       - v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_181238508_    746 ACCTCAAAATGGATCAAAGATCGAAACATAGGA-CTAAAACTATAAAGCT 794
                          v              ?   i v   ii  i  -             i  
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_181238508_    795 GTTATTAGAAAGCATAAGGCAAAAGCTTCATGACATTGCATTTGACAGTG 844
                         v   vv     i    i ?vv   v    i    v   vi  v i  i  
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_181238508_    845 ATTTATTGGCAATGACACCAAAGTCACAGGCAACAAAAGAAAAAA----- 889
                         i   v  i vv           iv    i                -----
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_181238508_    890 -AATTGGATTTCATGAAAATGAAAAG-TTTTGTTCATCAAAAGATATGAG 937
                         -       i     v     v    i-      v v     i  i iv v
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_181238508_    938 TGATAGAATAAAAAGGCAACCTACGGAATGAGAAAGAATATTTG-AAATC 986
                         ii v i i i     i     i  i     i  i i        -     
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_181238508_    987 GCATATCTATTAAGGGATTAATATC-AAAATATATATAGAATTCCTAAAA 1035
                         ii      iv       i vi    - i        v    i  i  v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_181238508_   1036 CTTAACAAGAAAAGAAGCAAACAACTAAATTGAAAGATTGGAAAAGGACT 1085
                           i  i  v    - ii    i   iv    ?   i  v  v      i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_181238508_   1086 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCTAATAAGCACATG 1135
                                                              i            
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_181238508_   1136 AAAAGATGTTCAACCTCACTAAATCA 1161
                                 i     v   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (81 / 43)
Gap_init rate = 0.01 (10 / 674), avg. gap size = 1.80 (18 / 10)  


 230 21.15 3.85 0.00  chr1_181374827_181377594      522   573 (2195)    L1M4_orf2#LINE/L1       56   109 (799)  

  chr1_181374827_    522 TACTACCCAAAGCAATC--CAGGGTCAATGCAATCCCCATCAAAATACTG 569
                             v      vii   --   iv    i        i        v ii
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_181374827_    570 GCTG 573
                             
  L1M4_orf2#LINE/    106 GCTG 109

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 2.00 (2 / 1)  

2143 25.32 4.49 0.32  chr1_181374827_181377594      944  1567 (1201)    L1M4_orf2#LINE/L1      164   813 (95)  

  chr1_181374827_    944 GACCCCAAATAGTCAAAGCAATCCTGAGCAAAAAGAACAAACCTAGAAGC 993
                              vi     i    i     i   iv  i         vi i  i v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_181374827_    994 ATTGTACTATCAGACTTCAAAATATACTACAAAGGTGTGGTAACCCAAGA 1043
                         v iii   vi vi i       iv          v iii    i -    
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC-AAGA 262

  chr1_181374827_   1044 -AATATGGTACTGGCATAAAAACAGACACAAAGACCAATGGAACAGAAAA 1092
                         - i i              ii i     i v   i        i    vv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_181374827_   1093 GAGAACCCAGAAATTAATTCACATATCTACAGCCAACCGATTTTTGACAA 1142
                             ii        v  ii  i i  i  ii i   ii      i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_181374827_   1143 AAGTGCTAAGAGCATTCACTGGTGAAAGGATAATTTCTTCAATAAAAGGT 1192
                         ii    i    v      v   v     i   i i i     i   v   
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_181374827_   1193 GCTGGGAAAACTGGATATCCATAAAGAGAAGACTGAA-----ACC---AC 1234
                                v         ?   i viv i    v    -----   ---  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr1_181374827_   1235 CTCTCATCCTATAAAAAAATCAACTCAAAATGGATCAAAGAC-TAAATGT 1283
                            v  i v    v      i                ?    -       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_181374827_   1284 AAGACCCCAAACTATAAAATTAATAGAAGGAAATATAGGGG-AAATGCTT 1332
                             v iv           i vv      i   i     ? -    -   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTT 561

  chr1_181374827_   1333 CAGCACATTGATCT-GGAAAAGACTTTATGAATAAAACCTCAAAAGTACA 1381
                          ivv  v   ivi -  v  v ii  iv ii   vi  vi      i   
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_181374827_   1382 GGCAATAAAAGCAAAAACAAACAAGTAGGATTATATCAACG--AAAAGGC 1429
                         i    i     v     i i i  i v   i vi     vi--    ivi
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_181374827_   1430 TCTGCACAGCAAAGGAAACAATCAGCAAGGGGAAAAGACAATCTAAAGAA 1479
                          i  ii vv       v  v    iv  i v          i i v    
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_181374827_   1480 TGGGAGAAAATATTTGTAAGCTATTCATCTGACAAGGGCTTAATATCCA- 1528
                                         i  iii  vi      i     vi vi      -
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_181374827_   1529 AATATACAAGCAACT---GCAA----------ACAAGTTAAATAATCCAA 1565
                               i  iv    ---i   ---------- v   vi      i    
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_181374827_   1566 TT 1567
                           
  L1M4_orf2#LINE/    812 TT 813

Transitions / transversions = 1.82 (100 / 55)
Gap_init rate = 0.02 (12 / 650), avg. gap size = 2.50 (30 / 12)  

 444 14.41 0.00 7.63  chr1_181374827_181377594     2179  2296 (472)    L1M4_orf2#LINE/L1      800   908 (0)  

  chr1_181374827_   2179 CAAATAATCCAATTTTAAAAGGGGCAAATGATCTAAACAGACATTTCTCA 2228
                                i      ?v    v       v   i i  i           v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_181374827_   2229 AAAGAAGACATACAAATGGCCAACAAATAAATGGAAAAAAAAAAAAAAAG 2278
                                 i              i  ii v   ---------    i v 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATG---------AAAAGATG 890

  chr1_181374827_   2279 CTCAACAACACCAATCAT 2296
                                v  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (9 / 7)
Gap_init rate = 0.01 (1 / 109), avg. gap size = 9.00 (9 / 1)  


3254 27.20 0.44 0.44  chr1_181549494_181552182     1289  2196 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_181549494_   1289 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1338
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_181549494_   1339 GGCCATATTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1388
                            v   i v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_181549494_   1389 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1436
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_181549494_   1437 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1486
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_181549494_   1487 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1536
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_181549494_   1537 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1586
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_181549494_   1587 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATGTCTACAACT 1634
                                i    i--    i  --        vv  ii ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_181549494_   1635 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1684
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_181549494_   1685 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1734
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_181549494_   1735 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1784
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_181549494_   1785 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1834
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_181549494_   1835 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 1884
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_181549494_   1885 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1934
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_181549494_   1935 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1984
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_181549494_   1985 AGGCAACCTACAACATGGGAGAAAATTTTCACAACCTAGTCATCTGACAA 2034
                           i     i   iv            v  ii   vii vvi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_181549494_   2035 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2084
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_181549494_   2085 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 2134
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_181549494_   2135 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 2184
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_181549494_   2185 ATCACTGGCCAT 2196
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3227 24.47 0.50 0.88  chr1_181622794_181626333.rev     1829  2625 (915)    L1M4_orf2#LINE/L1        2   795 (113)  

  chr1_181622794_   1829 GGAAAGATATTCCATGTTCATGGGTTGGAATTATTAATATTGTTAAAATA 1878
                                   i            i      vvv             i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_181622794_   1879 TCCATACCACCCAACCCAAAGCAATCTACAGATTCAATGCAATCCTTATC 1928
                         v v    i-   ----    vii              i       i    
  L1M4_orf2#LINE/     52 GCAATACT-CCC----CAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_181622794_   1929 AAAATACCAATGACATTCTTCACAGAAATAGAAAAGACAATCCTAAAATT 1978
                              v   iivi v  i  ii       v  v   vii           
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_181622794_   1979 TATATGGAACCACAAAAGACCCAGGATAGCCAAAGCTATCATGAACAAAA 2028
                         i        vii   ii       i         i v   v    v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_181622794_   2029 AGAACAAAACTGGAGGAATCACATTACCTGACTTCAAATTGTAGTACAGA 2078
                                 ii       v     i v  ii i      viv  v    i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_181622794_   2079 GCTATAGTAACCAAAACAGCATGGTGTTGGCATAAAACCAAACACATACA 2128
                             i     i   i    ii    ii        iivi i   i   v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_181622794_   2129 CCAATGGAACAGAATAGAGAACCCAGAA-TAAATCTATATATCTACAGTG 2177
                         i        i     v    ii      -    i i   i  i  ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_181622794_   2178 AACTTATATCCCACAAAGGTAACAAGAGCATACTTTGGAGAAGGGACAGT 2227
                           i v  v i v    i   iv     v   v vv   i   i i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_181622794_   2228 CTCTTCAGTAAATGGTGCTAGGAAAGCTGGAGGTCCATACGCAGAAGAAT 2277
                           i    ii          i   v i     vi?   i i   i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_181622794_   2278 GAAACTAGACCCCTACCTCTTGCCATATACAAAAACCAAATCAAAATAGA 2327
                            ii i            vii             ii  v       i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_181622794_   2328 TTAAAGACTTAAATCTAAGATGTCAAAGTATGAAACTACTAAAATAAAAC 2377
                          i ?    i     v     vv v   v   i     vi  i  v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_181622794_   2378 ATTAGGGAAACTCTCTAGGACATTGGACGGAGCAAAGGTTTCTTGAGTAA 2427
                           vi ? v  v   iiiv   v    iivii    v        iii  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA- 595

  chr1_181622794_   2428 TGTC-CCATAAGCATGGGCAACAAAAGCAAAAATGGACAAATGGGATCCC 2476
                           v -   v     iii          v      i  i    v   iii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_181622794_   2477 ATCAAG-TTAGAAGGCTTCTGCACAGCAAATGAAACAATCAACAAAGTGA 2525
                              i-   i  i-   i  ii vv    v  v  v     v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_181622794_   2526 AGAGACAACTGACAGAATGGGAGAAAATATTTGCAAACTATCCATCTGAC 2575
                          i       iv                          ii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_181622794_   2576 AGGGG-CTGATAACCAGAATGTATAAGAAGCTTAAACAACTCTATAAGAA 2624
                          i   -  vi  v       i     ii i  ivv       v    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_181622794_   2625 A 2625
                          
  L1M4_orf2#LINE/    795 A 795

Transitions / transversions = 1.78 (123 / 69)
Gap_init rate = 0.01 (8 / 794), avg. gap size = 1.38 (11 / 8)  

 352 20.35 8.85 0.00  chr1_181622794_181626333.rev     2942  3054 (486)    L1M4_orf2#LINE/L1      786   908 (0)  

  chr1_181622794_   2942 CAAAAACAAAAAAACAAA--AC--------AAAAGGGACAAAAGATCTGA 2981
                            v  i     i     --  --------    v  i    i   i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_181622794_   2982 ATAGATATTTCTCAAAAGAAGACAACCAAATAGCAGACAGGTACATGAAA 3031
                              i       v        i vv     i  vi i i i        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_181622794_   3032 AGGTGCCCAAAGTGAGACCTTTG 3054
                           i   i   vi v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.02 (2 / 123), avg. gap size = 5.00 (10 / 2)  


3225 27.20 0.44 0.44  chr1_181701820_181708091     4872  5779 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_181701820_   4872 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4921
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_181701820_   4922 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4971
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_181701820_   4972 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5019
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_181701820_   5020 TATGGAACAAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5069
                                vviv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_181701820_   5070 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5119
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_181701820_   5120 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5169
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_181701820_   5170 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCTCATATCTACAACT 5217
                                i    i--    i  --        vv  vi i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_181701820_   5218 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5267
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_181701820_   5268 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5317
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_181701820_   5318 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATCAATTCAAGATGGA 5367
                            ii    i    v   i i   v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_181701820_   5368 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5417
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_181701820_   5418 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5467
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_181701820_   5468 AACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTAA 5517
                         i            vvi     i    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_181701820_   5518 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5567
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_181701820_   5568 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5617
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_181701820_   5618 AGGGCTAATATCCAGAATCTACAATGAAATCAAACAAATTTACAAGAAAA 5667
                         i  i  vi          v  i  v   v  vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_181701820_   5668 AATCAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5717
                          iv    i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_181701820_   5718 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5767
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_181701820_   5768 ATCACTGGCCAT 5779
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2021 24.24 5.72 0.51  chr1_181729438_181731014      493  1086 (491)    L1M4_orf2#LINE/L1      284   908 (0)  

  chr1_181729438_    493 ATGGACA-----ATCAATGGAACAGAATAGAGATCCCAGAAATTCACCCA 537
                           i    -----          i     v    vi        vv     
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_181729438_    538 CATAAGCAGATTCAACTGATCTTTGAGAAAGGAGCAAAGGCAATACAACA 587
                         i i vvi viv    i    i  i  v  i  v  v   i v  v   ii
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_181729438_    588 GAGCAAAGACAATCTTTTTAACAAATGGTGCTGGAACA-CTGGACATCCA 636
                          i v  ii i i      i               i   -     i ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_181729438_    637 C--GTAAAGAAAAGAAATCTAAACACAGATCTTACACCCTTCACAACAAA 684
                          -- i   ii  v   i - ii  v vv i  i     v vi    v  v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_181729438_    685 TAACTCCAAATGGATCACAAACCTACTTTTAAAACACAAAACTATAGAAC 734
                               v          ? i     vv v   i vvi         i   
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_181729438_    735 TCTTAGAAGATAACA--AGAG-AAATCCTAAATGACCTTGG--TATGGTG 779
                                   v    --i ? -     i vi-         --  -  ii
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTA-GGCA 580

  chr1_181729438_    780 ATG---------ATACAACACCAAGGGCATGATCCATGAA--------TT 812
                            ---------   ii       ii   ii v v ii  -------- v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_181729438_    813 GATAAGCTAAACTTTATTAAAATTAAAAACTCATGTTCTGTGAAAGACAT 862
                              ii ii    i  i             iv   v  vii  i    i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_181729438_    863 TATCAGGAGAATGAGAAGATAAGCCAGAGACTGAGTTA---TCTTTGCAA 909
                              i  i i   i    i  v   v   v  i vv --- v       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_181729438_    910 AAGACATATCTGATAAAGGACTATTATCTAAAATATATAAAGAACTATTG 959
                          vv i           i     vv    i i               v  i
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_181729438_    960 AAACTCAATAATAAGAAAATAAACAACCCAATT-AAAAATAGGCAAATGA 1008
                         v             i  i i   i         -      i      v  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_181729438_   1009 CCTGAACAGAAACCTCACAAAAGAAGATATGTAGATGGCAAATAAGCATA 1058
                         ii    i   v ii  v v           ii i     v        i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_181729438_   1059 TGAAAAGATGCTTAATATTGTATGTCAT 1086
                                     i  i  ii????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (88 / 53)
Gap_init rate = 0.02 (13 / 625), avg. gap size = 2.85 (37 / 13)  


2616 15.33 12.07 1.47  chr1_181803433_181805037.rev      502  1114 (491)    L1M4_orf2#LINE/L1      231   908 (0)  

  chr1_181803433_    502 CAAAATTTATTACAAAGCTAAAGTAATCAAAATAGTGTAGTACTGGCATA 551
                              i   i          v         i i     i           
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_181803433_    552 AGGACAAACATATAGACCAATGGAATACAAC-----ATCCAGAAATAAAC 596
                             i i         i          v  i-----i             
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_181803433_    597 CCTCACAT--ATG--------ATTTAGAACAAGAGCACCAAGATCATTCA 636
                           vi    --   --------    vvi     i ii      i      
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_181803433_    637 GTGGAGAAA----AG-----------------GCTAAGAAAACTGGATAT 665
                         i   i    ----  -----------------   ii  v         ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_181803433_    666 CCAAATACAAATGAACAAAGCTGGACACTGACCTTTCACCATATACAAAA 715
                            v  i    v   ii   i     v iv    iv              
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_181803433_    716 -----CTCACAATGGATCAAAGAC-------TAAGAGCTAAAACTATAAA 753
                         -----    v         ?    -------                   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_181803433_    754 ACTCTTAAAAGA-------GGA--AAATCTTCATGACATTGGGTTTGGCA 794
                                i    -------  ?--        i    v       v    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_181803433_    795 AT--CTTCTTGAATATGACACCAATAGCATA-GC--CAAAAGAAAAAAGA 839
                           --i     ii            v    i -  --            --
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-- 628

  chr1_181803433_    840 CAGATACACTAGACTTCACCAAAATAAAAAAAATTCTGTACATCAAAGGA 889
                         i     v i i       i      v     v-  i   i v        
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGA 677

  chr1_181803433_    890 CACTATCAAGGGAATCAAAAGAAAACCCAAAGAATGGGAGAAAATATTTG 939
                                   ii i v      v      v                    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_181803433_    940 CAAATCATGTATCTGATAATGGATTACTAACTAGAATA----AAGAATGC 985
                                 i          v   i vv  v i      ----     iv 
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_181803433_    986 CCACAACTCAACAATAA-----CAGA--ACCCAGTC-AAAAATGGGTGAA 1027
                         ii         i     -----  i --     i i-         ii  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_181803433_   1028 GGACTTGAATACACATACACATTTCTCCACAGAAAATACACAAATGGCCA 1077
                            i       v    ------       v    i   i           
  L1M4_orf2#LINE/    828 GGATTTGAATAGACAT------TTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_181803433_   1078 GCAAGTACAGAAAAAGATGCTCAGCATCACAAGCTGT 1114
                         ii   i   vi            i     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (61 / 30)
Gap_init rate = 0.03 (19 / 678), avg. gap size = 4.37 (83 / 19)  


3084 26.85 1.90 0.34  chr1_181896038_181902443.rev     5022  5915 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_181896038_   5022 TGGAAAAACATTCCATGCCCATGGATAGGAAGAATCAGTATTGTGAAAAT 5071
                               i i  i     ii       v      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_181896038_   5072 GGCCACAATGCCCAAAGTAATTTATTGATTCAATGCTATCCTGATCAAGC 5121
                            v i v v      v i  i  iv       i  v    iv     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_181896038_   5122 TACCATTGGCTTTCTTCACAGAATTAGAAAAACT-ACTTTAAATTTCATA 5170
                          v   viv  i  i  ii     v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_181896038_   5171 TGGAAAGAAGAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAAAGAGAA 5220
                               vivi ii  v  v v        i      i i iv  ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_181896038_   5221 CAAAGCTGGAGGCATCACATTACCTGACTTCAAACTCTACTACAAGGCCA 5270
                              i      vv     i v  ii i      vii        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_181896038_   5271 CAGTAACAAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGACCAA 5320
                               iv  i     i         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_181896038_   5321 TGGAACAGAACAGAGGCCTCAGAAATAA-------CATCTACAACCATGT 5363
                              i    iv   ivii         -------   i  iiii  vv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_181896038_   5364 GATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 5413
                            i  i     ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_181896038_   5414 ATAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAGACTGAAA 5463
                         vi  i        i     v      v  ?   i     i    v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_181896038_   5464 CTGGAACCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGGATTAA 5513
                         i    v    v   i     v  i                i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_181896038_   5514 AAACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5563
                          i  i    i      v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_181896038_   5564 GCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAAC 5612
                          ?i- v i -   iv   v v  vv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_181896038_   5613 ACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTAATTA 5662
                                   vvi          vv    iv  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_181896038_   5663 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGGGTTAACAAG 5712
                           v v  i i   i  ii vv    i  v       vv ii  v  v ii
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_181896038_   5713 CAACCTACAGAATGTGAGAAATTTTTTGCAA--CCTATCATTTGACAAAG 5760
                              i        v      v v       -- v   -  i   i  i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGG 748

  chr1_181896038_   5761 GGCTAATATCCAGAATCGACAAAGACCTTAAACAAATTTACAAGAAAAAA 5810
                          i  vi          vv i     v  ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_181896038_   5811 ACAA----CTCCATCAAAAAGTGGGCAAATGATATGAACAGACACTTCTT 5856
                             ---- i v  i?    i        v   v    i     i    i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_181896038_   5857 AAAAGAAGACATTTA--TGTGTCAACAAACATATGGAAAAAGGCTCATCA 5904
                         v        i  vi --  - i   i  i  i   i   i v     v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATG-GCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_181896038_   5905 TTACTGGTCAT 5915
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (136 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


3385 25.99 0.55 0.55  chr1_181952822_181959094.rev     4875  5782 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_181952822_   4875 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4924
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_181952822_   4925 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4974
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_181952822_   4975 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5021
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_181952822_   5022 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAA 5071
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_181952822_   5072 GAACAAAGCTGGAGGTATCACGCTACCTGACTTCAAACTATACTACAAGG 5121
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_181952822_   5122 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5171
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_181952822_   5172 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5219
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_181952822_   5220 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5269
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_181952822_   5270 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5319
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_181952822_   5320 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5369
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_181952822_   5370 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5419
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_181952822_   5420 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5469
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_181952822_   5470 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5519
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_181952822_   5520 ATTAAACTCAAGAGCTTCTGTACAGCAAAAGAAACTACCAACAGAGTGAA 5569
                           i   v i  i i   i   i vv    i  v    i   v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_181952822_   5570 CAGGCAACCTACAAAATGGGAGAAAATTTTCATAACCTACTCATCTGACA 5619
                         v  i     i   i             v  iii  vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_181952822_   5620 AAGGGCTAATATCCAGAATCTACAATGAACTCAAGCAAATTTACAAGAAA 5669
                          i  i  vi          v  i  v      vvi   v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_181952822_   5670 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5719
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_181952822_   5720 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5769
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_181952822_   5770 TATCACTGGCCAT 5782
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (140 / 92)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2482 26.40 6.28 0.70  chr1_182059729_182065952     4872  5731 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_182059729_   4872 TGGAAAAACATTGCATGCTCATGGACAGGAAGAATCAATATTGTTAAAAA 4921
                               i i  iv    i       iv      v i           i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_182059729_   4922 GGCCACAGTGCCAGAAGCAATGTACAGACTCAATACTATTCCTTTCAAAC 4971
                            v i v v  vi  vii  v      i    ii v  i   v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_182059729_   4972 TACCAACATCATTTTTCATAGAATTAGAAAAA--ACTTCAGAAATTCACA 5019
                          v   i vv v     iii    v v  v  i--iv i vi       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_182059729_   5020 TGGAACAAAAAATGAGCCCA-AATAGCCAAAGCAATCCTAAGCAAAAAGA 5068
                              - viv  v ii    -          i     i i iv  i    
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_182059729_   5069 ACAAAGCCAGAGAAC-----------------AAAAC------------- 5088
                               iii   i  -----------------     -------------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_182059729_   5089 --------CAAAACAGCATGGTAGTTGTACAAAAACAGACACATAAACCT 5130
                         --------   i    ii     v v i i  ii i     i   i i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_182059729_   5131 ATAGAACAGGTTAGAGAACCCAGAAACCAAGCTGCACAGCTACGACCATC 5180
                           i   i  iv v    ii       iv  v iii   vi  i ii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_182059729_   5181 TGATCTTCAACAAGC-TGACAATAACAAGCAACAGGGAAAGGACTCCCTA 5229
                             i   i     v-  v   v v  vv   ii       i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_182059729_   5230 TTCAATAAATCGTGTTGGGATAACTGGCTGGTCATATGCAGAAGATTGAA 5279
                              i    v   i     i      v i?i  i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_182059729_   5280 TCTGGACCTATTCCTTTCACTATATGCAAAAATCAACTCCAAATGGATTA 5329
                         vi      iv v   iv   i    i       i     v        i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_182059729_   5330 AAGACTTAAATATAAGACCTAAAACTA-AAAACGCT-AGAAGAAAACCTA 5377
                         ?    i     i     v         -     v  -          v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_182059729_   5378 GGAA-ATATCATTCTGGACCTAGACCTTGGCAAAGATTTCAT-GATAAAG 5425
                           ?i- v   -   vv     v ivi v     v i    v -    v- 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-G 597

  chr1_182059729_   5426 ACTCTAAAAGCAATTGCAACAAAAATAAAAATTGACAAGTAGGACCT--- 5472
                           v i       vvv         iv      v  i  i v    i ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_182059729_   5473 ---AATTAATGACCTTTTGCACAGCAAAAGAAACTATCAATACAGTAAAC 5519
                         ---      -i v      ii vv    i  v        v v   i  v
  L1M4_orf2#LINE/    648 CAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_182059729_   5520 AGACAACCTACAGCATGGGAGAAAATATTCTCAAACTTTACATGTAACAA 5569
                                 i    v               iv    iiv  i  v i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_182059729_   5570 AGGTCAAATATCCAGAATTTGTAAGGAACTTAAGCAAATCAGCAGGTAAA 5619
                         i  v vvi          v i   i     ivvi   v   ii i-    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAA 795

  chr1_182059729_   5620 AAAACAAACAATCCCATTTCAAAAATAGGAAAAGGACATAAACAGACACT 5669
                           i     i  -    v  ?      i  v      iv i  i     i 
  L1M4_orf2#LINE/    796 AAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_182059729_   5670 TCTCAAAAGAAGACACACATGCAGCCAACGA--ACATGAAAAAATGCTCA 5717
                             v        i i   viii     ii --         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_182059729_   5718 ACATCACTAATCAT 5731
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (129 / 94)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.53 (60 / 17)  


3156 27.20 0.55 0.55  chr1_182079641_182086028.rev     4990  5897 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_182079641_   4990 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5039
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_182079641_   5040 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5089
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_182079641_   5090 TACCAATGACTTTCTTCCCAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5137
                          v   iivi i  i  iv     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_182079641_   5138 TATGGAACCAAAAAAGAGCCCTCATCGCCAAGTCAATCCTGAGCCAAAAG 5187
                                viiv  ii  v  vvv  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_182079641_   5188 AACAAAGCCAGAAGCATCACGCTACCTGACTTCGAACTATACTACAAGGC 5237
                                iii  i vv    i  v  ii i   i  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_182079641_   5238 TACAGTAACCAAAACAGCCTGGTACTGGTACCAAAACAGAGATATAGACC 5287
                                 i   i    iv         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_182079641_   5288 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5335
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_182079641_   5336 ATCTGATCTTTGACAAACCTCACAAAAACAAGCAATGGGGAAAGGATTCC 5385
                          vi    i  i     ivv vv   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_182079641_   5386 CTATTTAATAAATGGTGCTGGGAAAAATGGCTAACCATATGTAGAAAGCT 5435
                           v  i  i              v  v   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_182079641_   5436 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5485
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_182079641_   5486 TTAAAGACTTACATGTTAGAGCTAAAACCATAAAAACCCTAGAAGAAAAA 5535
                          i ?    i  v    v           i      vi i          v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_182079641_   5536 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5584
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_182079641_   5585 AACCACCAAAAGCAACGGCAGCAAAAGCCAAAATTGACAAATGGGATCTA 5634
                         viv           vvi   i      vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_182079641_   5635 ATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5684
                           i   v v  i     i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_182079641_   5685 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5734
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_182079641_   5735 AAGGGCTAATATCCAGAATCTACAATGAACTCCAGCAAATTTACAAGAAA 5784
                          i  i  vi          v  i  v      ivi   v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_182079641_   5785 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5834
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_182079641_   5835 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5884
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_182079641_   5885 CATCACTGGCCAT 5897
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2983 27.62 2.71 0.34  chr1_182286700_182293062     4984  5870 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_182286700_   4984 TGGAAGAACATTCCATGCTCATGGATAGGAGGAATCAATATCATAAAAAT 5033
                              ii i  i     i        v   i  v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_182286700_   5034 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAAC 5083
                            v     v     iv i  i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_182286700_   5084 TACCAATGACTTTCTTCACAGAATTGGAAAAAAATACTTTAAAGTTCATA 5133
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_182286700_   5134 TGGAACCAAAAAAGTGCCCGCATAGCCAAGACCATCCTAAGGCAAAAGAA 5183
                              viiv  ii vv  v v        i  v   i i iiv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_182286700_   5184 CAAAGCTGGAGGCATCACGCTACCTGACTT---------------GGCTA 5218
                              i      vv    i  v  ii i  ---------------i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_182286700_   5219 CAGTAGCTAAAACAGCATGGTGCTGGTACCAAAACAGCGATATAGA-CAA 5267
                              iii  i    ii    i    i iv ii i  vv       -   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_182286700_   5268 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATGT 5317
                              i    iv   ivii         vv   i    i  iiii  vv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_182286700_   5318 GATCTTTGACAAACTTGACAGAAATAAGAAATGGGAAAGGGAT--TCCAT 5365
                            i  i     ivv  v  ii vi vvv      i  i i  --  -- 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC--T 398

  chr1_182286700_   5366 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5415
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_182286700_   5416 AACTGGATTCCTTCTTTACGCCTTATACAAAAATTAATTCAAGATGGATT 5465
                          ii    ii   v i i  i  v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_182286700_   5466 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5515
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_182286700_   5516 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATAACTAAA 5564
                            ?i- v i -   iv   v v  vv i     v ii   v  iv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_182286700_   5565 ACACCAAAAGCAAGGGCAACAAAAGCCAAAATAGACAAATTGGATCTAAG 5614
                                     vii          vv        i        ii v v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_182286700_   5615 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5664
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_182286700_   5665 GGCAACCTACAGAATGGGAGAAAATTTTTGCACTCTGCCTGTCTGACAAA 5714
                          i     i                 v      vviiiiv i     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_182286700_   5715 GGACTAACATCCAGAATCTACAAAGAACT-TAAGAACTTAA-ATTTAAAA 5762
                              vii         v  i        - v v    i  - v v    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_182286700_   5763 GACAAA--ACCGCATCAAAAAGTGGGCAAAG-ATATGAACAGATACTTCT 5809
                               --   vv  i?    i         -  v    i   i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_182286700_   5810 TAAAAGAAGACATTTATGCAGCCAACAGAAACATGAAAAAATGCTCATCA 5859
                         iv        i  vi viii     i iiv         i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_182286700_   5860 TCACTGGTCAT 5870
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.70 (27 / 10)  


3312 24.12 0.53 4.04  chr1_182312614_182315509.rev     1465  2405 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_182312614_   1465 TGGGAAGATATTCCATGTTCATGGACTAGAAAACTCAATATTGTTAACAT 1514
                            i       i             i i   i   i           v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_182312614_   1515 GTTTATACTACCCAAAGCAATCTACAGATTCAGTGCAATCACAATAAAAA 1564
                          viv     v      vii             ii      v v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_182312614_   1565 TATCAAGGACATTCATAACAAAAATAGAAAAAATTATCCTAAAACATATA 1614
                          vi  ivvi v  iv vi  i    v  v  iv v         ivi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_182312614_   1615 CAGAACCACAAAAGACCCTGAATAGCCAAAGTCATCCTGAGCAAAAAGAA 1664
                         ii   vii   ii     v           iiv   i   ---       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAA 197

  chr1_182312614_   1665 AAATAAAACTGGAGAAATCATATTATCTGACTTCAGATTATACTACAGAG 1714
                         i  i   ii     i v   i i vi ii i    i viv       i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_182312614_   1715 CTATAGTAACCAAAAAAGCATGACACTGGCATAAAAACAGACATGTAGA- 1763
                            i     i   i v  ii  ii          ii i      i    -
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_182312614_   1764 CAATGGAACAGAATAGAGAACCCAGAAATAAATCCATACATCTACAATGA 1813
                                 i     v    ii           i        i  iii v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_182312614_   1814 ACTAATTTTCAACAAAGGTTTCAAGAACACTCATTGGGGAAAGGAGAGTC 1863
                          i i      i    i   vi     v  i   v         i v    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_182312614_   1864 TCTTCAATAAATGGTGCTGGGAAAACTGGATATTCATATGCAGCAGAATT 1913
                          i     i              v         ?i  i     iv     v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_182312614_   1914 AAATGAGACCCCTATCTCTTGCTACGAACAAAA-TAAAATCAAAATGGAT 1962
                           i vi        i   vii i iiv      - v  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_182312614_   1963 TACAGACTTAAATCTAAGACCTAAAACTACACAACAAATTTTGTATTTGT 2012
                         i ?    i     v     v         i v   --- i  --------
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC---TCTT-------- 536

  chr1_182312614_   2013 CATATACAAATACAAAAAGAAAGCTTTGAGGAAACTCTCCAGGACATTGG 2062
                         -------------- i      i v v i? v  v   i iv   v    
  L1M4_orf2#LINE/    537 --------------AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_182312614_   2063 TCAAGGTAAAGATTTCTTGAGTAATACCTCCAAAGCACAGGGAACCAAAG 2112
                         viv   i  v i      iii  vv  vi v        i v   v    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_182312614_   2113 CAAAAATGGACAAATGGGATCATATCAAGTTGAAAAGCTTCTGCACAGCA 2162
                         v      i  i    v   iivi     iv v    i   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_182312614_   2163 AAGGAAACAATCAACAAAGTGAAGAGGCAACCCACAGAATGGGAGAACAT 2212
                              v  v     v        i  i                    v  
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_182312614_   2213 ATCTGTAAACTAGCCATCTGACAAAGAA--TGCATACCAGAATACATACA 2260
                           i  i   ii vvi      i  i i --  i  -        i   v 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTAT-CCAGAATATATAAA 771

  chr1_182312614_   2261 GAGCTCAAACAACTCAATAGAAAAAAATCTAATAATCTTATTTTAAA-TG 2309
                           i   vv           iv     iv v     i iv   ?v   -  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_182312614_   2310 GGCAAAAGATCTGTATAGACATTTCTAAAAAAAAACACAAACAAACATAC 2359
                               i   i  v            vv   i  i--------- i    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG---------ATATAC 862

  chr1_182312614_   2360 AAATGGTAAACGGGTATATAAGAAGATGCTCAACATCATTGATCAT 2405
                               iv  iii i i  i i                ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (139 / 84)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 4.78 (43 / 9)  


 390 25.00 0.96 0.96  chr1_182320687_182322539      228   331 (1522)  C L1M4_orf2#LINE/L1   (531)   377   274  

C chr1_182320687_    331 TGGCTAAAGAATAGACACATAGATCAGTGGAACAGAATAGAGAGCCTAGA 282
                             vv   i       i        i     i     v     i i   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

C chr1_182320687_    281 ATTTGACCCACATAAATATAGTTAACTGATCTCTGACAAAAGAGC-AAAA 233
                          v vi     i i vv   i  i  i    i ii     ii v  -  i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

C chr1_182320687_    232 CACAT 228
                          -   
  L1M4_orf2#LINE/    374 C-CAT 377

Transitions / transversions = 2.25 (18 / 8)
Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2)  

3328 23.81 1.39 1.16  chr1_182320687_182322539      500  1360 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_182320687_    500 AAGATTCCAATTCTTCCCAACTTGATCTATAGAGTCAATGCAATCCCAAT 549
                              vv    v  i     v        i   v    i        v  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_182320687_    550 CAAAATCCCAG-TATGTTATTCTGTGAATATTGACAGACTGATTTTAAAG 598
                                    - iiv  -  i  iii v       ii     ii    i
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_182320687_    599 TTTATTTTAAGAGGGAAAAGGCCCAGAATAGCCAAAGAGCTACTTTAATA 648
                           i  v vi i v v  ii i               i-- v ii  i v 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA--CAATCTTGAAA 192

  chr1_182320687_    649 TTCAAGAAGAATTAAAGTGGAGGACTGGCTCT--ACAATTTTTGAAGACT 696
                         ---        iv  iv         vi v  --v      i--  i   
  L1M4_orf2#LINE/    193 ---AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC--AAAACT 237

  chr1_182320687_    697 TACTGTAAAGCTAGAGTAATCAAGACAATGTACTATTGGCTAAACAATAG 746
                             ii       v             i   iv  i    vv  vi    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_182320687_    747 ACACATAGATCAGTGGAATAGAATAGAGAGCCTAGAATCTGACCAACGTA 796
                            i        i           v     i i    vivi   v iii 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_182320687_    797 AATATAGTTAACTGATCTCTGACAAAAGAGCAAAGGCAATTCAATGGAGT 846
                         vv   i  i  i    i ii     ii v  v   i v         i v
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_182320687_    847 AAACGTAGTCTTTTCAACAAATGGCACTGAAACAACTGGACATCCACATG 896
                           ivi                   ii   ii         i ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_182320687_    897 CAAGAAAAATGAATCTAGACACAAGCTTTACACCTTTCACAAAAA----C 942
                            -  i      vi i   v vvi i i     v vi       ---- 
  L1M4_orf2#LINE/    438 CAA-AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_182320687_    943 TCAGAATGAATCACAGACCTAAATGTAAAATGC-ACAACTAAAAAACTAT 991
                            i    i    ?              i -  - v     v      v 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCT 535

  chr1_182320687_    992 TAGAAGATAACATAGGAGAAAATCTAGATGACCTTGGGGTTGGAGATGAC 1041
                                v        ? v      vvi          v v  vi   ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_182320687_   1042 TTTTTAGATACAAGACCAAAGGCATGATCCATGAAAGAAAGACTTGATAA 1091
                           i       ii v      i   ii v v ii       i v v     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_182320687_   1092 GCTGGACTTCCTTAAAATTAAAAATTTCTATACTGTGAAAGACACTGTCA 1141
                         ii        v i           i  i i i  vii  i      i   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_182320687_   1142 AGAGAATGGGAAGACAAGCCACAGATGGAGAGAAAATATTTGCAAA--AA 1189
                            i i  ii       v       vv i                 -- v
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_182320687_   1190 ACAGCTGATAAAGGAGTGCTATCCAACACATACAAAGAACTCTTGAAACT 1239
                          i v       i   v vv      iv i   i           iv    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_182320687_   1240 CAAAAATAAGGAAACAAA-AACTTGATCAAAAAA-ATACCAAAGCTGTCA 1287
                            v     ii i     -   iii  i?     -ivi v  i v v v 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_182320687_   1288 ACAGACACTTCACCAAAGAAGATAAATAGATGGCAAATAAGCATATGAAA 1337
                          i     i   v            v i i     v        i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_182320687_   1338 AGATGCTCCGTATCATACAGTAT 1360
                                 vii    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (123 / 78)
Gap_init rate = 0.02 (13 / 863), avg. gap size = 1.69 (22 / 13)  


2997 27.11 1.21 1.54  chr1_182337943_182344605     5260  6170 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_182337943_   5260 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5309
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_182337943_   5310 GGCCAAGGTACTGGCCAAGGTAATTTATAGATTCAATGCCATCCCCATCA 5359
                            -  --    vv    iv i  i  i        i  v     i    
  L1M4_orf2#LINE/     51 GGC-AA--TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_182337943_   5360 AGCTACCAATGACTTTCTTCACAGAATTGGAAGAAAACCA--CTTTAAGT 5407
                          iv v   iivi i  i  ii     v v  v--  i ii-- i v  i 
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAAT 145

  chr1_182337943_   5408 TCATATGGAACCAAAAAAGAGCCCGCCCACATT-GACAAGTCAATCCTAA 5456
                                   viiv  ii  -----    v v - v   iv     i i 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGA-----CCCAGAATAGCCAAAACAATCTTGA 190

  chr1_182337943_   5457 GCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATAC 5506
                         ivv i          i      vv       v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_182337943_   5507 TACAAGGCTACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGA 5556
                              i          i   i    ii       v i iv ii i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_182337943_   5557 TACAGACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCGCATATCT 5606
                           i   i        i    iv   ivii         vv  ii i  i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_182337943_   5607 ACAACCATCTGATCTTTGACAAACCTGACAAAAGCAAGCAATGGGGAAAG 5656
                          iiii  vi    i  i     ivv  v   i v  vv            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_182337943_   5657 GA--GTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGT 5704
                         i --   -- v  i  i              v      v  ?   i   i
  L1M4_orf2#LINE/    391 AATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_182337943_   5705 AGAAAGCTGAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATGC 5754
                          i  iiv    ii    i    v   i i   v              iv 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_182337943_   5755 AAGATGGATTAAAGACTTACATGTTAGTCCTAAAACCATAAAAACCCTGG 5804
                           i      i ?    i  v    v  vv       i      vi i i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_182337943_   5805 AAGAAAACCCAGGCAATACTATTCAGGACAT--AGTCATGGGCAAGGACT 5852
                                 vi   ?ivv v v   iv   v --i  i --     v ii 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA--GGCAATGGTT 586

  chr1_182337943_   5853 TCATGTCTAAAATACCAAAAGCAATGGCAACAAAAGCCAAAATTAACAAA 5902
                           v ivv  vi i          vvi          vv     vi i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_182337943_   5903 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAT 5952
                          v   ii v  i   v v  i i   i  ii vv    i  v    i  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_182337943_   5953 CAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACT 6002
                         v i      v  i     i                 v       vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_182337943_   6003 CATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATT 6052
                         i      i  i  i  vi          v  i  v      vv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_182337943_   6053 TACAAGAAA----CAAACAACCCCATCAAAAAGTGGGCAAGGGATATAAA 6098
                         v i  v   ----    i     v  i?    i       i    v i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_182337943_   6099 CAGACACTTCTCAAAAGAAGACATTTATGCAGTCAAAAAACACATGAAAA 6148
                         i     i     v        i  vi viii i   v  i          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_182337943_   6149 AATGCTCATCATCACTGGCCAT 6170
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.27 (25 / 11)  


3343 26.76 0.44 0.44  chr1_182407687_182414117     5031  5938 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_182407687_   5031 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5080
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_182407687_   5081 GGCCACATTGCCCAAGGTAATTTATAGATTCAATGCCGTCCCCATCAAGC 5130
                            v i i v     iv i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_182407687_   5131 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5178
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_182407687_   5179 TATGGAACAAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGACAAAAG 5228
                                vviv  ii  v  v v  v     iv     i i i v i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_182407687_   5229 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5278
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_182407687_   5279 TACAGTAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGATATAGATC 5328
                                 i   i    i          i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_182407687_   5329 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5376
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_182407687_   5377 ATCTGATCTTTGACAAACCTGTGAAAAACAAGCAATGGGGAAAGGATTCC 5426
                          vi    i  i     ivv  iv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_182407687_   5427 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5476
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_182407687_   5477 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5526
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_182407687_   5527 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5576
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_182407687_   5577 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGAACTTCATGTCTAA 5626
                         v    ?i v viv   iv   v v  vv i     viii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_182407687_   5627 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATTGGATCTAA 5676
                         i            vvi          vv        i        ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_182407687_   5677 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAGCTACCATCAGAGTGAAC 5726
                          i   v v  i i   i  ii vv    i  vi   i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_182407687_   5727 AGGCAACCTACAAAATCGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5776
                           i     i   i   v         v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_182407687_   5777 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5826
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_182407687_   5827 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5876
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_182407687_   5877 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5926
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_182407687_   5927 ATCACTGGCCAT 5938
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3401 25.88 0.44 0.44  chr1_182479386_182485790.rev     5007  5914 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_182479386_   5007 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5056
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_182479386_   5057 GGCCATATTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 5106
                            v   i v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_182479386_   5107 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5154
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_182479386_   5155 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAACCAAAAG 5204
                                viiv  ii  v  v v  v     i      i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_182479386_   5205 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5254
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_182479386_   5255 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGGCC 5304
                                 i   i    ii         i  v ii i   v      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_182479386_   5305 AATGGAACAGAACAGAGCTCTCAGTAATAATACCACACATCTATAGCCAT 5354
                                i    iv   vvii   v     vv   i    i   i i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_182479386_   5355 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGAAAAGGATTCTCT 5404
                         i    i  i     ivv  v   i v  vvv      i    i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_182479386_   5405 ATTTAATAAATGGTCCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5454
                         v  i  i       v      v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_182479386_   5455 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5504
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_182479386_   5505 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAACT 5553
                          ?    i       v   v       i      -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr1_182479386_   5554 TAGGCA-ATACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCTAA 5602
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_182479386_   5603 AACCCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5652
                         i  v         vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_182479386_   5653 TTAAACTCAAGAGCTGCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5702
                          i   v i  i i  vi  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_182479386_   5703 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5752
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_182479386_   5753 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5802
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_182479386_   5803 AAACAAACAACCCCACCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 5852
                          i     i     v ii?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_182479386_   5853 TCAAAAGAAGACATTTATGCAACCAACAGACACATGAAAAAATGCTCATC 5902
                           v        i  vi viiii    i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_182479386_   5903 ATCACTGGCCAT 5914
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (135 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


2115 27.22 1.56 0.31  chr1_182530287_182531921.rev      502  1144 (491)    L1M4_orf2#LINE/L1      258   908 (0)  

  chr1_182530287_    502 CAAAACAGCATGGTAGTGGTACCAAAACAGACATATAGACCAATGGAGCA 551
                            i    ii     v   i iv ii i           i       ii 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_182530287_    552 GAA---------CAGAGATAACACCACACATCTACAACCATCTGCTCTTC 592
                            ---------    i    vv   i    i  iiii  vi  v i   
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_182530287_    593 TGCAAGCCTGACAAGAACAAGCAATGTGGAAAGGATCTCCTATTCAGTAA 642
                         vi    vv  v     v  vv     v      i  vvi  v    ii  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_182530287_    643 ATGGTGCTGGGAAAACTGCCTAGCCATATGCAGAAAACTGAAATTGAACC 692
                                     v     vv  ?   i     i  i v    i   i   
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_182530287_    693 CCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAAAAACTTC 742
                            v   i     v                   i      i ? i  i v
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_182530287_    743 GATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-AAA 791
                         i      i v i     i      vi i           v    ?i-   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_182530287_    792 CCATTCAGGACATACGGCACGGGCAAAGCCTTCATGACAAAAACGCCAAA 841
                         i -   iv   v vv  i-ii     v vi   v iivv vi  i     
  L1M4_orf2#LINE/    558 TC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_182530287_    842 AGCAATTGCAACTAAAGCCAAAATTGACACATGATATCTAATTAAACTAA 891
                             vvv     v    vv     v  i v  viv ii v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_182530287_    892 AGAGCTTCTGCAAAGCAAAAGAAACTATCATCAGAGTGAACAGGTAATCT 941
                          i i   i  iivvv    i  v       vv i      v  ii  i i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_182530287_    942 ACAGAATGAGAGAAAATTTTTGCAATCTACCCATCTGACAAAGGTCTAAT 991
                                 i        v       vii ivi      i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_182530287_    992 ATCCAGGATTTACAAGGAACTTAAACATATTTACAAGAAAAAAACAAACA 1041
                               i  v  i  i     ivv   vv iv i  v     i     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_182530287_   1042 ACTCTATCAAAAAGTGGGCAAAGGATATGAATAGACACTTCTCCAAAGAA 1091
                           i v  i?    i            v          i            
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_182530287_   1092 GACATTTATGCAGCCAAAAAATACATGAAAAAAAGCTCAACATCACTAAT 1141
                           i  vi viii     v  ii         i v           ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_182530287_   1142 CAT 1144
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.28 (96 / 75)
Gap_init rate = 0.01 (4 / 651), avg. gap size = 3.00 (12 / 4)  


2508 23.33 2.93 8.26  chr1_182576952_182579018.rev      621  1576 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_182576952_    621 AAAAATCATCCTGTGCTCGTGGATTAGAAGAATCAATATTGTTAAAATGC 670
                            i  -    ii  i  i      i     v i           i   v
  L1M4_orf2#LINE/      4 AAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_182576952_    671 CCATAATGCCCAGAGCAATATGCAGATTCAATGTAATTTCTATCTAACTA 720
                          v   v v    i vii  v i         i i   ii     v  v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_182576952_    721 CCAATGTTG--TTTTTCACAGAATTAGAAAAAA-AATCCTGAAATTAATA 767
                            -- i  --     ii     v v  v  iv-i     i     v   
  L1M4_orf2#LINE/    103 CCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_182576952_    768 TTGAACCAAAAAAGAGCCCT--ATAGCCAAAGTAATCCTAAACAAAAAGA 815
                          v   viiv  ii  -   v--         ii    i i  v  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_182576952_    816 ACAAAACTAGAGGCATCACATTACCTGACTTCAAA--TTA-TACAA---- 858
                              ii i    vv     i v  ii i      --   -     ----
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_182576952_    859 --------CAAGGCGAGCATGGTACTGGTAAAAAAAAAAAAAAAAAAAAA 900
                         --------    i -  ii         i v  i----------------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGAC-AGTGTGGTACTGGCATAAG---------------- 282

  chr1_182576952_    901 AAAAAAAAAGAAAGACACATAGATCAATGAAATAGAATGGAGAATCCAGA 950
                         ---------  v     i           i        v    i      
  L1M4_orf2#LINE/    283 ---------GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_182576952_    951 AATTAAGCCACATACTCCCAGCCAACTGATCTTCAACAAAGTCAACAAAA 1000
                            v  v   i i i ivii i   i    i   i    i viiv   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_182576952_   1001 ATATACAATGGAGAGAGGATACTCTATTTAATAAATGCTCTTTCCAGGAC 1050
                         vi  v      i  i  i   v   v  i  i     -------------
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG------------- 410

  chr1_182576952_   1051 TGTTATTAAATAAATAAATATTTAGTAATAGTCCTGGGAAAATTGGATAG 1100
                         ------------------------------  v      v  i      ?
  L1M4_orf2#LINE/    411 ------------------------------GTGCTGGGACAACTGGATAK 430

  chr1_182576952_   1101 CCATATGCAGAAAAATGAAATTAGACCCTTTGTATCTCTTACAATATACA 1150
                            i     i  i      i  i     i --- i   vi  v       
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCT---ACCTCACACCATATACA 477

  chr1_182576952_   1151 AAAATCAACTCAAGATGGGTTAAATACTTAAATGTAAGACCTGAAACTAT 1200
                              i       i    i i ? v  i           v  i       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_182576952_   1201 AAAAATTCTAGAAGCAAACTTAGGAAAAGCTCTTCTAAACCTTGATCTAG 1250
                             v ii      v    v    ?iv iv     vvi      ivi   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_182576952_   1251 GCAAAGAATTTATGACTAAGAACTCAAAAGCAAATGTAA-AAATCCAAAA 1299
                             v iv  iv iiv  v  vvi        v v i  -   vvv    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_182576952_   1300 ATAGATAAATGGGACTTAAACAAAAT----ACCTCCTGCAGAGCAAAAGA 1345
                                   v      v v      ---- v  ii  iivvv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_182576952_   1346 AATAACTAGTGGAGTAAACAAGAAAACCAATAGAAAGGGAGAAAATATTT 1395
                         v iv ii ivii   i  -    v    v i    v              
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAA-AAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_182576952_   1396 GTAAATTTTACATCTGACAAAGGACTAACATCCAGATTCTAGAAATAACT 1445
                          i    iv  i      i  i     vii       v v  v   v    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_182576952_   1446 CAAACAACTCAACAAGAAGAAAAAAAAGTGGGCACATTAAAATGTGGACA 1495
                          vv         i  v  i  i v   - iiv vv   ?   vi   i  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCA 825

  chr1_182576952_   1496 AAGGATATGAACAGATAGTTCTCCAAAGA---TATACAAATGGCCAACAA 1542
                               v    i   i v           ---               i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_182576952_   1543 ACATATGAAAAAAATGTTCATCATCACTAATCAT 1576
                         i  i       i -  i   v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (128 / 91)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 5.63 (107 / 19)  


3267 26.54 0.55 0.55  chr1_182588348_182594623.rev     4878  5785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_182588348_   4878 TGGAAGAACATTCCATGCTCATGGGTAGAAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_182588348_   4928 GGCCATACTGCCTAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v  i  iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_182588348_   4978 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5024
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_182588348_   5025 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5074
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_182588348_   5075 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5124
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_182588348_   5125 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGAT 5174
                                  i   i    ii         i iv ii i   v v      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_182588348_   5175 CAATGGAACACAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5222
                                 i v  i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_182588348_   5223 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5272
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_182588348_   5273 CCTCTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5322
                         i  i  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_182588348_   5323 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5372
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_182588348_   5373 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAAAAGAAAA 5422
                           i ?    i    ii v   v       i      vi i  i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_182588348_   5423 CCTAGGCATTACCATTCAGGACATACGCATGGGCAAGGACTTCATGTCTA 5472
                          v    ?i v viv   iv   v vv vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_182588348_   5473 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5522
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_182588348_   5523 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5572
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_182588348_   5573 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5622
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_182588348_   5623 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5672
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_182588348_   5673 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5722
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_182588348_   5723 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5772
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_182588348_   5773 CATCACTGGCCAT 5785
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 801 26.98 9.75 6.07  chr1_182692323_182693977.rev      462  1169 (486)    L1M4_orf2#LINE/L1      175   908 (0)  

  chr1_182692323_    462 GTTAAAATAGTTTTAAAGGATAGGGG--AGGCTAGGTAGAC-----CTAC 504
                          ii    i i i  i  ii v i ii-- i i -  vi   -----  v 
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTT-GGAGGACTCACACTTC 223

  chr1_182692323_    505 CTAGTACCAAGATTTCTTATACAGCTA----AGTCAAATGCAGAGTGCTC 550
                          i i vi   i i  vi  i v     ---- i    i-i   v   v v
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG-ACAGTGTGGTA 272

  chr1_182692323_    551 TTGGCCCAG----AGACATGCAAATGAATA-AATAG--TTAAGGACAGAG 593
                         i    vi i----      ii i  v   i-     --  i  -----  
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG-----AG 317

  chr1_182692323_    594 TCCTCCAGAAA--GACCTAAGCATATTTGAAAACTCAACATGTAATATGT 641
                            ---     --i   i vi   v v  i----    i--- i  v vi
  L1M4_orf2#LINE/    318 TCC---AGAAATAAACCCATACATTTATGG----TCAAT---TGATTTTC 357

  chr1_182692323_    642 AACATCAGAGGTGATATTACAA---AAAGTAAGGAAAGTATTGACTATTC 688
                         i   --  -    vi vv  v ---  -- ii      v  v v  v   
  L1M4_orf2#LINE/    358 GACA--AG-GGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTCTTTTC 402

  chr1_182692323_    689 AA--AGTGATGTCGGG-CAACTGGCTCTCCAAATGGAAAAATAAAGATAT 735
                           -- i  i  ii   -       v v?   v   v    -----  -  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-----GA-AT 446

  chr1_182692323_    736 AAAATTAGAGCACTACCTGATATTATTTACAAAATTTAAAATTCAGA-TA 784
                         i  i  i  v v      v i ii  v       v    --i   i - i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA--CTCAAAATG 494

  chr1_182692323_    785 GATTGAAGTCCAAAATGTGAAAAAGAAAACT-TAAAA-TATTAGAATTAA 832
                            ii?  v  v      i i ivv      -     - v      vv  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_182692323_    833 ACATTGAAG---------GTTAT----GTTTA--TAAT--TTTCTTCATG 865
                             v i? ---------  v i---- v   --i   --      - - 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-A-G 592

  chr1_182692323_    866 TTAAGATACAAAAAGTGCA--CATCTGAAAAAGAACAGATTAATACACTG 913
                         v  v  i  v     ii  --  v ---       v i  vi   v i  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAAC---AAAAGAAAAAATAGATAAATTG 639

  chr1_182692323_    914 TGCTCCTTAAAAACTGAAACCTTCTGTACAACAAAAGACACCA-CACATA 962
                         vi  i v v    i i   v   i   i vv    i     i -  - v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA-AGA 688

  chr1_182692323_    963 AACTT----GACA--CCACAGAAATAGACTGAGAGAAGATATTTTCAACA 1006
                           v v----    --        ------  i     i      v   vv
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAA------TGGGAGAAAATATTTGCAAAT 732

  chr1_182692323_   1007 CATATAAAAGACAAAAGATTATTATCAAAAATAAAGACCAAATTTCTACA 1056
                               vvv  i  ii  i vv    v i    v v vvi  i ii    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_182692323_   1057 -TTCAATAAGAGAAAGACAAGTCACC-AG---AAAACTGTGCAACAGATT 1101
                         -i       v i        i v   - i---    v  v    vi    
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_182692323_   1102 T--ACAGGTTATTCACCAA------TACCACAAATGGCCAACAAACACGT 1143
                          -- i  iivv   v    ------  i-            i  i   i 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATAT-ACAAATGGCCAATAAGCACAT 881

  chr1_182692323_   1144 AAAAGTGTTCTCAGT-TCACTTGAAGT 1169
                         i   ivi v    ii-   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (106 / 82)
Gap_init rate = 0.06 (45 / 734), avg. gap size = 2.49 (112 / 45)  


3224 26.76 1.45 0.22  chr1_182858481_182864849.rev     4982  5878 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_182858481_   4982 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5031
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_182858481_   5032 GGCCATACTGCCCAAGGTAATTTATAGATTCGATGCCATCCCCATCAAGC 5081
                            v     v     iv i  i  i      i i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_182858481_   5082 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 5126
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_182858481_   5127 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5176
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_182858481_   5177 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5226
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_182858481_   5227 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5276
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_182858481_   5277 TGGAACAGAAC--AGAGCCCTCTGAAATAATGCCACATATCTACAACTAT 5324
                              i    i--    i  v--       vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCA--GAAATAAACCCATACATTTATGGTCAA 348

  chr1_182858481_   5325 CTGATCTTTGACAAACCTCCCAGAAACAAGCAATGGGGAAAGGACTCCCT 5374
                         i    i  i     ivv v   ii v  vv            i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_182858481_   5375 ATTTAATAAATGGTGCTGGAAAAACTGGCTAGCCATATGTAGAAAGCTGA 5424
                         v  i  i            i v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_182858481_   5425 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5474
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_182858481_   5475 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5524
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_182858481_   5525 AGGCATTACCATTCAGGACATAAGCACAGGCAAGGACTTCATGTCTAAAA 5574
                            ?i v viv   iv   v vi vvi      v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_182858481_   5575 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5624
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_182858481_   5625 AAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATGA--GTGAACAG 5672
                           iv v  i i   i  ii vv    i  v    i  v  --     v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_182858481_   5673 GCAACCTACAGCATGGGAGAAAATTTTCGCAACCTACTTATCTGACAATG 5722
                         i     i    v            v  i    vii iv       i  v 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_182858481_   5723 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5772
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_182858481_   5773 ACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5818
                             ----   v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_182858481_   5819 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 5868
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_182858481_   5869 CACTGGCCAT 5878
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.50 (15 / 6)  


3029 25.06 3.30 0.46  chr1_182869438_182871368      561  1438 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_182869438_    561 AAACATTCCATGTTCATGGATAAGAAGAATCAATATTGTGAAAATGGCCA 610
                          i i  i              vi     v i        v  i     v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_182869438_    611 TACTTCCCAATTTAATTTACAGATTCAATGCTATCCCCATCAAGCTACCA 660
                             i     v  i  i           i  v     i     iv v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_182869438_    661 ATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTTATGTGGA 709
                         iivi i  i  ii     v v  v  i-  - iii    v  i  i    
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGA 154

  chr1_182869438_    710 ACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAGAACAAA 759
                          viiv  ii  v  v v        i      i i iv  i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_182869438_    760 GCTGGAGGCATCACACTACCTGACTTCAAACTATATTACAAGGCTACAGT 809
                          i      vv       v  ii i      viv  i     i        
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_182869438_    810 AA-CAA-ACAGCATGGTACTGGTACCAGAATAGATATACAGACAAATGGA 857
                           -   -    ii         i iv  i     i   i   iv      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_182869438_    858 ACAGAACAGAGGCCTCAGAAATAACACC---ACATCTACAACCATCTGAT 904
                          i    iv   ivii         -   ---    i  iiii  vi    
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCAATTGAT 353

  chr1_182869438_    905 CTTTGACAAACCTGACA----CAAGCAATGGGGAAAGGATTCCCTATCTA 950
                         i  i     ivv  v  ----  vv            i  vvi  v ii 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_182869438_    951 ATAAATGGTG---AGAAAACTGGCTAGCCATATGCAGAAAACTAAAACTG 997
                          i        ---i  v      v  ?   i     i  i v i  ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_182869438_    998 GACACCTTCCTTACACCTTATACAGAAATTAACTCAAGATGGGTTACAGA 1047
                            v   v   i     v      i            i    i i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_182869438_   1048 CTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA 1097
                          i    i      v       i      vi i           v    ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_182869438_   1098 -ATACCATTCAGGACACAGGCATAGGCAAAGACTTCATGACTAAGACACC 1146
                         - v i -   iv   viv  vv       v ii   v iiv  v      
  L1M4_orf2#LINE/    554 TAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_182869438_   1147 AAAAGCAATGGCAACAAAAGTCGAAATTGACAA--TGCGATCTAATTAAA 1194
                                vvi          vvi    v  i  --  -  ii v  i   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG-GACTTCATCAAA 651

  chr1_182869438_   1195 CTAAAGAGCTTCTGCACAGCAGAAGAAACTATCAG---AGTGAACAGGCA 1241
                         v v  i i   i  ii vv  i i  v       i---      v  i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_182869438_   1242 ACCTACAAAATGGGAGAAAATTTTTGCAATCTATCCACCTGACAAAGGGC 1291
                            i   i             v       vii  vi i    i  i  i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_182869438_   1292 TAATATCCAGAATCTACAAGGAACT--TA-AATTTA-CAAGAAAAAAA-A 1336
                          vi          v  i  i     --  -  i i -i  v     i - 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_182869438_   1337 AA-AACC--ATCAAAAAGTGGTCAAAGGATATGAACAGACACTTCTCAAA 1383
                           -    --  i?    i   v        v    i     i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_182869438_   1384 AGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAAGCTCATCATCAC 1431
                               i  vi viii     i  --         i v     v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_182869438_   1432 TGGTCAT 1438
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.67 (135 / 81)
Gap_init rate = 0.02 (20 / 903), avg. gap size = 1.65 (33 / 20)  


1274 20.33 23.68 0.84  chr1_182900063_182902268.rev      502   860 (1346)    L1M4_orf2#LINE/L1       59   499 (409)  

  chr1_182900063_    502 TTCCCAAATTGATCTACAGATTGGATGAAATTTCTATCAAATTACCACAA 551
                          i                    vi i v   ii        v v   vvv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr1_182900063_    552 GCCCTTTT-GCAGAAATTGATAAA---ACCCTAAAATTTTTATGGAGATG 597
                            i    -           i  i--- i         iv      i   
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr1_182900063_    598 CAAGGGACCCAGTGTAGCCAAAATATTTTTGAAAAAGAAAAAACAAAGTT 647
                                     vi         i v i           i  -       
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA-CAAAGTT 207

  chr1_182900063_    648 AGAGGACT-ACCTTTTCTAATTACAAAACTTATTCTAAAGTTACAGTAAT 696
                         i       -  vi  i i    v         i vi    i         
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_182900063_    697 CAA----------------------------------------------- 699
                            -----------------------------------------------
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_182900063_    700 ------------------------------TTTATAGTCAATTGATTTTT 719
                         ------------------------------     i             i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_182900063_    720 AACAAAAGTGCCAAGGCAATTCAATGGGAAAAAAATAGACTTTTCCA-AA 768
                         i    ii        i v          i   i     v      v -  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_182900063_    769 ATAATGCTGGGGCAATTGGATGT--ACATGGTCAATATGATGAATTTAGC 816
                           ii       i   i     i?--     --   v vi     v  i v
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATG--CAAAAGAATGAAGTTGGA 455

  chr1_182900063_    817 TCTTTCCCCTACATTGTACACAAAAGTTAAATAGAAATGTATCA 860
                         i ii v  ii   iii  i      i    v vi     v    
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

Transitions / transversions = 2.00 (48 / 24)
Gap_init rate = 0.02 (8 / 441), avg. gap size = 11.00 (88 / 8)  

1592 18.37 3.15 0.79  chr1_182900063_182902268.rev     1335  1715 (491)    L1M4_orf2#LINE/L1      519   908 (0)  

  chr1_182900063_   1335 TAAAATGCTATAA--CTTTAATAAGAAAACATAAGAGAAAATCTTTGTGA 1382
                              --      --  i v v           i ? v       i    
  L1M4_orf2#LINE/    519 TAAAA--CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_182900063_   1383 CCTTGTGTTAAGACAAAGATTTCTTAGCTAGAACACCAAATGCACAATCC 1432
                              v    i -   v i        v  vi        v      v v
  L1M4_orf2#LINE/    567 CCTTGGGTTAGG-CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_182900063_   1433 ATTAAAGAAAACATTGATAAAATGGACTT----AAAAATGAAAACCTCTG 1478
                          iv        v  v      v       ----    v i     i i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_182900063_   1479 TACTTCAAAAGACACAATTAAGAAAATGAAAAGATAAGCCACAGC-TGGA 1527
                          i       i     v  i      i        i  v      v-   i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_182900063_   1528 AAAGCATATTGACAAATCAGTTATCTGATAAAGAACCTGGATCTAGAATA 1577
                          i iv     vi       vv          i i  i  v   i      
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_182900063_   1578 TATAAATAATTCTTACAA---AACAACAAAAAGAGAGACAACACAGCTTG 1624
                               v  i        ---  i  i       v i i   v  ii ?i
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_182900063_   1625 AAA-TGGGCAAATTATATGAATAGACATCTCCCCAGAGAAGATATCCCAA 1673
                            -        vv  v           i  i   i         v v  
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_182900063_   1674 TGGCCAATA-GCACATAAAAAGATACTCAACATTATTAGTCAT 1715
                                  -      i       i        i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (37 / 31)
Gap_init rate = 0.02 (8 / 390), avg. gap size = 1.88 (15 / 8)  


3030 26.21 1.54 1.65  chr1_182957636_182960581.rev     1548  2455 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_182957636_   1548 GGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATCGTGAAAATG 1597
                             ii i  i     i i    i v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_182957636_   1598 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGCT 1647
                           v     v     iv i  i  i        i  v     i  i  iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_182957636_   1648 ACCAATGCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAG 1695
                         v   --  --  v    i  -i     -   -- v  i  - iii    i
  L1M4_orf2#LINE/    102 CCCA--GC--TGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAA 144

  chr1_182957636_   1696 TTCATATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAACCCTAAGCCA 1745
                                    viiv  ii  v  v v  v     iv   i i i ivv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_182957636_   1746 AAAGAACAAAGCTGAAGGCATCATGCTACCTGACTTCAAACTATACTACA 1795
                         i          i  i   vv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_182957636_   1796 ATGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 1845
                          v          i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_182957636_   1846 GACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTAC 1893
                           i        i    i--    i  --        vv  ii i  i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chr1_182957636_   1894 AACCATCTGATCTTTGACAAAGCTGACAAAAACAAGAAATGGGGAAATGA 1943
                         iii  vi    i  i     i v  v   i v  vvv          vi 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_182957636_   1944 TTCCCTCTTTACTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 1993
                          vvi  i  i vi              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_182957636_   1994 AGCTGAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGA 2043
                         iiv    ii    i    v   i i   v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_182957636_   2044 TGGATTAAAGACATACATGTTAGACCTAAAACCATAAAAACCCTAGAAGA 2093
                              i ?    v  v    v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_182957636_   2094 AAACCTAGGCA-ATACCATTCAGGATACAGGCATGGGCAAGGACTTCATG 2142
                             v    ?i- v i -   iv  iviv  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_182957636_   2143 TCCAAAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 2192
                         vvi vi    v       vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_182957636_   2193 TCTAATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 2242
                         ii v  iv  v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_182957636_   2243 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCT 2292
                             v  i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_182957636_   2293 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTATGA 2342
                           i  i  i  vi          v  i  v      vv    v iv  i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_182957636_   2343 GAAAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGAC 2388
                         v     i    ----   v  i?    i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_182957636_   2389 ACTTCTCAAAAGAAGACATTTGTGCAA-----CAAAAAGACACATGAAAA 2433
                          i     v        i  ----i   -----   v   -          
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATAT----ACAAATGGCCAATAAG-CACATGAAAA 886

  chr1_182957636_   2434 AATGCTCATCATTACTGGCCAT 2455
                         i       v   i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 2.07 (29 / 14)  


3592 19.91 2.89 5.67  chr1_183167853_183169995      717  1650 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_183167853_    717 TGTAAAGACATCCCATTTTCCTAGAGTGGAAGATTTAATAATGTTAAAAT 766
                           v     i       v   v i  v       i      v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183167853_    767 TTTAATACCACCTAAACCAATCTACAGGTTGTATTTAATCCTTATCAATA 816
                         vvi     iv  i   iii        i  vv ivi     i      - 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-A 99

  chr1_183167853_    817 ATCCAA------TTTTTTATATAAATAGGAAAAACAATCCTAAAATTCA- 859
                             v ------      ii v    v iv  ivii             -
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_183167853_    860 ---------CAAAGGACCCCAAATACCCTAAACTGTCTTTAGAAAGAA-- 898
                         ---------   i      vi    v  v    vi    v i      --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_183167853_    899 -CAAAACTGTAGGCATAACACTTCCTGATTTCAAAGTTGATTGCAAAGCT 947
                         -    ii  v   vv v        ii        ii v i i       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_183167853_    948 ACAGTAATTAACGTAGTATGGTACCCACATAAAGACAGACACATATAGCA 997
                                 i  vii   i      ivi     i  i     i   v v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_183167853_    998 ATGCAACAGAATAAAGTGTCCAGAAATAATCCCACACATATATGGTCAAC 1047
                            v  i     vi  v            v    i    v         i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_183167853_   1048 TGATTTATAACAAGGGTGCCAAGAACACATGATGGGGAAAGAACAGTTTT 1097
                               vii               v  ivii            i   i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_183167853_   1098 TTTCAACAAAATGGTGTTGGGA-AAGTGGAT-TCCACATGTAAAAGAATG 1145
                           -       -     i     -  v     -?       i         
  L1M4_orf2#LINE/    400 TT-CAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_183167853_   1146 AAATGAGACCTTTATCTTACACCGTATACAAAA-TCAACTCAAAATGGAT 1194
                           i vi    ii  i  i     i         - i              
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_183167853_   1195 TAAAGACTTAAATATAAAACCTGAAACTGTAAAAATCCTAGAAGAAAACA 1244
                         i ?    i     i   i v  i     i     v  i            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_183167853_   1245 --GGGGAAAA-CTTTGTAACATTAGTCTTGGCAATGATTTCTTGGATATG 1291
                         --  ? v   -   i  i  v  i vi v       i      i      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_183167853_   1292 TCACCAAAAGCACAGGCAACAAAAGTGAAAATAGACAAATGATACTACAT 1341
                         v             i          vi        i    viv   v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_183167853_   1342 CAAACTAAAAAGTTTCTGCAAG-CAAAGGAAACATTTAACGTAATGAAAA 1390
                             v v    ii  i  iivv-       v  vv i  viv i      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_183167853_   1391 GCCAACCCATGAAGTGGAAGAAAATATTTGCAGGCCACTTATCTAATTAG 1440
                          v       iii i   i              iii  iv     i  v  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_183167853_   1441 GGGTCAATATCTAAAATATATAAGGAACTCCTTCAACTCAATAGCAAAAA 1490
                           iiivi    i i         i      i v          ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_183167853_   1491 G-CACATAACCTTATTAAAAAGTTGAAACCTTTGCAGAGCAGTAGTAAAT 1539
                          -  v      i-----------------------------------   
  L1M4_orf2#LINE/    798 GACAAATAACCC-----------------------------------AAT 812

  chr1_183167853_   1540 TGAAAAAATAAAAAATAAAAACTGGACAAAGGATTTGAACAGACATTTCT 1589
                          ?     ---------------   i             i          
  L1M4_orf2#LINE/    813 TWAAAAA---------------TGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_183167853_   1590 TCAAAGAAGACATACAAATGGCCAATAAGTATATGAAAAGATGCTGAACA 1639
                         i         i                  i i             v    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_183167853_   1640 TTATCTGGGAA 1650
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.72 (115 / 67)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 5.33 (80 / 15)  


3120 25.20 2.35 0.67  chr1_183207432_183213607.rev     4793  5685 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_183207432_   4793 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAA-AT 4841
                              ii i  i     i        v      v i     i  v  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183207432_   4842 GGTCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4891
                           iv     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_183207432_   4892 TACCATTAACTTTCTTCACAGAA-TTAGGAAAAACT-ACTTTAAATTTCA 4939
                          v   vivi i  i  ii     -  --  v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr1_183207432_   4940 TATGGAACAAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAAAAG 4989
                                vviv  ii  v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_183207432_   4990 AATAAAGCTGGAGGCATCATGCTACCTGACTTCAAAGTATACTACAAGGC 5039
                           i    i      vv   ii  v  ii i      iiv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_183207432_   5040 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGA--GACC 5087
                                 i   i    ii         i iv ii i   v v --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_183207432_   5088 AATGGAACAGAACAGAGGCCTCACAAATAAAACCACACATCTACAACCAT 5137
                                i    iv   ivii  v       v   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_183207432_   5138 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGAGGAAAGGATTCCCT 5187
                         i    i  i     ivv  v   i v  vvv    i      i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_183207432_   5188 ATTTAATAAATGGTGCTGGGAAAACAGGCTAGCCATATGCAGAAAGCTGA 5237
                         v  i  i              v   v  v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_183207432_   5238 AACTGGAGCCCTTCCT-ACACCTTATACAAAAATTAATTCAAGATGGATT 5286
                          ii    v    v   -     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_183207432_   5287 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTATAAGAAAACCT 5336
                          ?    i           v       i      vi i  v        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_183207432_   5337 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 5385
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_183207432_   5386 ACACCAAAAGCAATGGCAACAAAAACCAAAATAGACAAATGGGATCTAAT 5435
                                     vvi         ivv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_183207432_   5436 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 5485
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_183207432_   5486 GGCAACCTACAGAATGGGAGAACATTTTTGCAA-TCA---ATCTGACAAA 5531
                          i     i              v  v       -   ---      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_183207432_   5532 GGGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTA-CAAGAAAAA 5577
                           i  vi          v  i        --  -  i i -i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_183207432_   5578 AA--ACCAACCTCATCAAAAAGTAGGTAAAGGATATGAACAGACACTTCT 5625
                         i -- vi    iv  i?    i i  i       v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_183207432_   5626 CAAAAGAAGAAATTATGCA----GCCAACAAACGTATGAAAAAAAGCTCA 5671
                          v        ---   i  ----     i  i ii       i v     
  L1M4_orf2#LINE/    848 CCAAAGAAGA---TATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_183207432_   5672 TCATCACTGGTCAT 5685
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.69 (27 / 16)  


3140 25.53 2.58 1.01  chr1_183226881_183232986.rev     4723  5615 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_183226881_   4723 GAAAAAAAATTTCATGATCATGGATAGGAAGAATCAATACTGTGAAAATG 4772
                          i   i v  ii    v        v      v i    i   v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_183226881_   4773 GCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATTCCCATTAAACT 4822
                           v     v      v i  i           i  v  i  i  i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_183226881_   4823 ACCATTGACATTCTTCACA-AAATTAGAAAAAACT-ATTTTAAAATTCAT 4870
                         v   vivi v  i  ii  -     i-- v  i  -  ii          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr1_183226881_   4871 ATGGAACCAAAAAAGAGCCCAAATAACCAAGACAATCCTAAGTAAAAAGA 4920
                               viiv  ii  v  vi    i    i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_183226881_   4921 ACACAGTTGGAGCCATCACATTACC------------TTACTACAAGGCT 4958
                            v        vvv     i v  ------------         i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_183226881_   4959 ATAGTAACCAAAACAGCATGGTACTGGTACAAGAACAGACATACAGACCA 5008
                          i     i   i    ii         i i   i i       i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_183226881_   5009 ACGGAACAGAATTGAGAACTCAGAAATAAGACTGCACACCAGCAACCATC 5058
                          i    i          iii         iv iii   iiviiiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_183226881_   5059 TGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAATTATTTTCTA 5108
                             i   i    ivv  v   i v  vv           vv  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_183226881_   5109 TTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATACAGAAAATCGAA 5158
                           i  i              v      v  ?   i  i  i  i vi   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_183226881_   5159 ACTGGGCCCCTTCCTTACATAATATACAAAAATCAACCCAAGATGGATTA 5208
                         ii   i     v   i   iv            i   i   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_183226881_   5209 ATGACTTAAATGTAAAAGCCAAAACTATAAAAC-CTTAGGAGAAAATCTA 5257
                         ?v   i         i   i             -     i      iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_183226881_   5258 GGCA-ATACCATTCAGGACATAGGCATTGGTAAATATTTC------ATGA 5300
                           ?i- v i -   iv   v v  vv v  i  vvi    ------    
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_183226881_   5301 CAAAAATGCCAAAAGCAATGGCAA-AAAAGCAAAAATTGACACATGGGAT 5349
                           ------         vvi    -     v      v  i v  v   i
  L1M4_orf2#LINE/    599 CA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_183226881_   5350 CTAATTAAACTAAAGGGCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 5399
                         i v  i   v v  iii   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_183226881_   5400 GAAAAGACAATCTGCAGAATAGGAGAAAATTTTTGCAATCTATTCATCTG 5449
                                   i ii      i         v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_183226881_   5450 ACAAAGGTCTAATATCCAGAGTCTACATGGAACTTAAACAAATTTACAAG 5499
                          i  i  v  vi        i v  i vi     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_183226881_   5500 AAAAAAACAAACAACCCCATTAAAAAGTGGGCAAAGGACATAAACAGACA 5549
                              i     i     v   ?    i           iv i  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_183226881_   5550 CTTCTCAAAAGAAGACATACATGCAGCCAACAAACATAGGAAAAAAAGCT 5599
                         i     v        i     viii     i  i  i v     i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_183226881_   5600 CAACATCACTGATCAT 5615
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (137 / 87)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 3.20 (32 / 10)  


3074 28.10 0.55 0.88  chr1_183246338_183252729.rev     4991  5901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_183246338_   4991 TGAAAGAACATTCCAAACTCATGGATAGAAAGAATCAATATCATGAAAAT 5040
                           i  ii i  i   vii        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183246338_   5041 GGCCATACTACCCAAAGTAATTTATAGATTCGATGCCATCCCCATCAAGC 5090
                            v     v      v i  i  i      i i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_183246338_   5091 CACCAATGACTTTCTTTACAGAA-TTGGAAAGAAAACT-ACTTTAAAGTT 5138
                         iv   iivi i  i   i     -   iv   ----  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chr1_183246338_   5139 CATATGGAACCAAAAAGAGCAC-GCATTGCCAAGACAATCCTAAGCAAAA 5187
                                  viiv  i ii v - v  v     i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_183246338_   5188 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAGCTATTCTACAAG 5237
                                  i      vv   ii  v  ii i     iviv v      i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_183246338_   5238 GCTACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATACAGA 5287
                                   i   i    ii  i      i iv ii i   i   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_183246338_   5288 CCAATAGAACAGAACAGAGGCCTCAGAAATAAAACCACACATCTACAACC 5337
                         i    i   i    iv   ivii          v   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_183246338_   5338 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGAGGAAAGGATCCC 5387
                          vi    i  i     ivv  v   i v  vvv    i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_183246338_   5388 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5437
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_183246338_   5438 GAAACTGGATCTCTTCCTTACACCTTACACAAAAGTTAATTCAAGATGGA 5487
                            ii    i i  v   i     v  i      i    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_183246338_   5488 TTAAAGACTTAGATGTTAGACCTAAAACCATAAAAACCCTAAAAGAAAAC 5537
                          i ?    i  i    v   v       i      vi i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_183246338_   5538 CTAGGCA-ATACCATTCAGGACATAGACATGGGCAAGGACTTCATGACTA 5586
                         v    ?i- v i -   iv   v v ivv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_183246338_   5587 AAATACCAAAAGCAATGGCAGCAAAAGCCAAAATGAACAAATGGGATCTA 5636
                         vi i          vvi   i      vv     ii i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_183246338_   5637 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGTGAA 5686
                           i   v v  i i   i  ii vv    i  v    i  vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_183246338_   5687 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTATCCATCTGGCA 5736
                         v  i     i                 v      ivii  vi     ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_183246338_   5737 AAGGGCTAATACCCAGAATCTACAAAGAACTTAAACAAATGTACAAGAA- 5785
                          i  i  vi  i       v  i        ivv    v ---   v  -
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAAT 792

  chr1_183246338_   5786 AAAAAAACAAACAATCCCATCAAAAATTGGGCAAAGGATATGAACAGACA 5835
                              i     i  i  v  i?    v            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_183246338_   5836 CTTCTCAAAAGAAGAGATTTATGCAGCTAACAGACACATGAAATAATGCT 5885
                         i     v        v  vi viii  i  i ii         vi     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_183246338_   5886 CATCATCACTGGTCAT 5901
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (161 / 91)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3657 23.61 0.66 1.42  chr1_183298818_183303086.rev     2864  3778 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_183298818_   2864 TGTAAAGAT-TTTCATGCTGATGGTTTAGAACACTTAATATTGTTAATAT 2912
                           v      - ii    i v    v  i   v               v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183298818_   2913 ATCCATACTTTCCAAAGTGATCTACAGATTTAATGCAAGCCCCATCAAAA 2962
                         iv v     ii     v             i  i    v   i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_183298818_   2963 TGCCAATGACATTCTTCACAGAAATAGAGGAAAAAAAATCCTAAAATTTG 3012
                          v   iivi v  i  ii       v  v--  ivvi           ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chr1_183298818_   3013 TATGGAACCATAAAAGCTCCCAAATAGCCAAAGCAATCCTGAGTAAAAAG 3062
                                viii  ii vi  vi          i     i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_183298818_   3063 AACAAAGCTGTAGGCATCACACTATCCAATTTCAAACTATACTACAAAGC 3112
                                i  v   vv       vi           viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_183298818_   3113 TATTATAACCGAATCAGCATGGTAGTGGCATAAAAGCAGACACATAGACC 3162
                           ivi   i i iv   ii     v        iiii     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_183298818_   3163 AATGGAACAGAATAGAGAACCCCAAAATAAACCCATGCATTTACAGACAA 3212
                                i     v    ii  vi            i      ii v   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_183298818_   3213 CTCATTTTCAACAAAGGTACCAAGAACATACACCGGGGAAAGAACAGTCT 3262
                         i v      i    i   i      v   v  vi          i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_183298818_   3263 CTTCAGTAAATGATGTTGGGAAAATTGGATAACCATATGCAGAAGAATGA 3312
                         i    ii     i  i     v  i      ?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_183298818_   3313 AACTAGATCCCTACCTCTCACCTTATGTAAAAATCAAATAAAGATGTATT 3362
                          ii i  i         v    v   ii      i  v v  i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_183298818_   3363 AAAGACTTAAATGCAAGATCTGAAACACTATGAAATTACTAGAAGAAAAC 3412
                          ?    i      i    v  i    --   i   i vi           
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAAC--TATAAAACTCTTAGAAGAAAAC 546

  chr1_183298818_   3413 ATGAGAGAACTACACCTTAG-GACATTGGTCTGGGCAATTTTTTTTTTTT 3461
                           ii ? ---  v i   v -   v    vi i      vv   i  v--
  L1M4_orf2#LINE/    547 ATAGGNG---TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-- 591

  chr1_183298818_   3462 TTGGTAAGTCATTAAAAAGCACAGACAACAAAAGCAAAATTACACAAATG 3511
                         -- i  v v  ii    -     ii         v    v  v i    v
  L1M4_orf2#LINE/    592 --GATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_183298818_   3512 GGATTATATCAAGCTGAAAAGCTTCTGCACACCAAAAGAAACAATCAGCA 3561
                            i vi     iv v    i   i  ii vi    i  v  v    iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_183298818_   3562 AAGTGAAAAAAACAACCTATAGAATGGAAGAAAATATTGGCAAAC----T 3607
                                  i -     i i       i          v     i---- 
  L1M4_orf2#LINE/    689 AAGTGAAAAGA-CAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_183298818_   3608 ATCTAAGATGAGATTAATAATTAGAATATATATGGAACTCAAACAACTCA 3657
                             i v v i  i vi  vii          vi      vv        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_183298818_   3658 ATAGCAAAAAATCAAATAATTCAAATAAAAAATGTGCAAGAGATCTGAAT 3707
                            ii     iv       ii   v ?       v    ii   i     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_183298818_   3708 AGACATCCCTCAAAAGAAGACATACAGATGGCCAATAGGTATACGAAAAA 3757
                               ii   v        i     i          i i i i     i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_183298818_   3758 ATTTTCAACATCACTAATCAT 3778
                           vi         ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (135 / 77)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


3195 27.53 0.44 0.44  chr1_183337621_183343897     4877  5784 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_183337621_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183337621_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_183337621_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_183337621_   5025 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_183337621_   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAGGGC 5124
                                i      vv       v  ii i      viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_183337621_   5125 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 5174
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_183337621_   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACTGCATATCTACAACT 5222
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_183337621_   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_183337621_   5273 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_183337621_   5323 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i   i v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_183337621_   5373 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_183337621_   5423 CTAGGCATTACCATTCAGGACATAGGCATGGGCGAGGACTTCATATCTAA 5472
                         v    ?i v viv   iv   v v  vv i   i v ii   v  vv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_183337621_   5473 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5522
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_183337621_   5523 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_183337621_   5573 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5622
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_183337621_   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACGAATTTACAAGAAAA 5672
                         i  i  vi          v  i  v      vv  i v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_183337621_   5673 AAACAAACACCACCATCAAAAAGTTGGCGAAGGACATGAACAGACACTTC 5722
                          i     i v v v  i?    i v   i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_183337621_   5723 TCAAAAGAAGACGTTTATGCAGCCAAAAACCACATGAAAAAATGCTCATC 5772
                           v        ii vi viii     v  v          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_183337621_   5773 ATCACTGGGCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 578 27.92 0.00 0.00  chr1_183387880_183391612     2023  2176 (1557)    L1M4_orf2#LINE/L1        1   154 (754)  

  chr1_183387880_   2023 TGGAGAGATATTACATGTTCATAGCTAGAAAGACTCATGATTGTCAAGAT 2072
                             i      iv         i v v i      i vv     i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183387880_   2073 TTCAGTTCTTCTTAAATTAATCTATAGATACAACATAATTTCAATAAAAA 2122
                         vv  i v  i ii     i     i    v    ii   ii v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_183387880_   2123 TTCCAGCATATTGTGTTGTGGATGTTGACAAACTTATTCTAAAGTTTATA 2172
                          i     vvvi v v   ii  vi       i  v  i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_183387880_   2173 TGGA 2176
                             
  L1M4_orf2#LINE/    151 TGGA 154

Transitions / transversions = 1.39 (25 / 18)
Gap_init rate = 0.00 (0 / 154), avg. gap size = 0.00 (0 / 0)  

2586 23.07 1.27 4.06  chr1_183387880_183391612     2463  3251 (482)    L1M4_orf2#LINE/L1      142   908 (0)  

  chr1_183387880_   2463 AAGTTTATGTGGGAAGGCAAAAGACCCAAAAAAGCCAACTCATTACTGAA 2512
                           i  i  i   i  v    ii      i  v      vv  v vi    
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_183387880_   2513 GGAGAAGAACAAAGTTGCAGGACTGACACTATCTTACTTCAAGACTTACT 2562
                         ii               v      v     vi iv i     i       
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_183387880_   2563 ATAAAGCTACAGTAGTCAAGACAGCATAGTATTTGCAAAAGAATCGACAA 2612
                          i            i         ii i   i v   v   i  v    v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_183387880_   2613 ATAGATCAATAGAATAGA-T--AGGGTCCAGAAATAGGCCCACATAAATA 2659
                                   i       - --  i           ii    i i vv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_183387880_   2660 TAGTCAATTAATTTTTGACAAGGGATACATGGCAATACAATGGAACAAAG 2709
                          i       i     i        vvv  v i v  v      iiv  ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_183387880_   2710 ATAGCATTTTCAACAAATGGTGCTAGAAAAACTGAACATCAACAAGCAAA 2759
                             iv                  i i v     i i ? v   v     
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_183387880_   2760 ACAAAAAAATAAAAAATAAAAAAGTCTCTTGATACAGACTTTACACTTTT 2809
                          v  vi  i ------ ii ----- i i -------  i i    iv -
  L1M4_orf2#LINE/    442 AGAATGAAGT------TGGA-----CCCCT-------ACCTCACACCAT- 472

  chr1_183387880_   2810 AATAAAAAAGTTAACTCAAAATAGGTTATAGACCTAAATGTAAAATGTAA 2859
                         -   v    i            i i i ?              i vv   
  L1M4_orf2#LINE/    473 -ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_183387880_   2860 AATTATAAAAGTCTTAGATGATAACATAGAAGGAAATCTAGACGGATTTG 2909
                           i       v       v  v       i? v      vvii ivi   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_183387880_   2910 GGTATGGCAATGATTTTTTTTTAGATA---CAC-AAGGGCATGATTCATG 2955
                            vv       i   i  ---     ---   -  ii   ii viv ii
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTT---AGATATGACACCAAAAGCACAAGCAACA 618

  chr1_183387880_   2956 AAAAAAGTAATTGACAATTTGGACTTCAGTAAAATTAAAAACATCTG--C 3003
                            i  iv   v  i  v          vi            v i  -- 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_183387880_   3004 TTCACAAACTCACTGTCAAAAACGAATGGGAAGACAAGTCCCAGACAGGG 3053
                             -  ivv    i    i  -- i  ii       vi v    vv   
  L1M4_orf2#LINE/    669 TTCA-AAGGACACTATCAAGAA--AGTGAAAAGACAACCCACAGAATGGG 715

  chr1_183387880_   3054 AGAAAATATTTGCGAAAAACATTTCAGATAAAGGACAGTTATCCAAAATA 3103
                                      i  vv i  v  v     i    vvv      i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_183387880_   3104 TACAAAGATGTCTTAAAACTCAAAAATAGGAAAACAAACAATCCAGTTAA 3153
                           i     vv     v       v    ii  i     i  i   i  ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_183387880_   3154 AAAATAAGTCAAAGG-CCTGAATAGACACAGTGCCAAAGAATACACATGT 3202
                              ii -      -ii          ivviv        v i i i--
  L1M4_orf2#LINE/    816 AAAATGGG-CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC-- 862

  chr1_183387880_   3203 AATACATGGCAAATAAGCATATGAAAAGATTTACCACAACACATGTCTT 3251
                           ---     v        i          viv v   v  ????????
  L1M4_orf2#LINE/    863 AA---ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (103 / 75)
Gap_init rate = 0.02 (16 / 767), avg. gap size = 2.62 (42 / 16)  


3108 25.46 0.65 1.96  chr1_183424879_183432244.rev     5957  6875 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_183424879_   5957 GGAAAAACATTCCATGCTCATGGATAGGAAGAATAAATACTGTGAAAAAT 6006
                              i i  i     i        v      v v    i   v  i - 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-T 50

  chr1_183424879_   6007 GGCCATACTGCCCAAAGTAATTTATAGAATCAATGCTATCCATTGACTTT 6056
                            v     v      v i  i  i   v    i  v    ---------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC--------- 91

  chr1_183424879_   6057 CCATTAAGCTACCATTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTT 6105
                          i  i  iv v   vivi i  i  ii     v v  v  i--  - iii
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCC 139

  chr1_183424879_   6106 TAAATTTCATATGGAACCAAAAAAGAACCCGCACAGCCAAGACAATCCTA 6155
                             v           viiv  ii  v  v v i      i      i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_183424879_   6156 AGCAAAAAGAACAAAGCTGGAGGCATTATGCTACCTGACTTCAAACTATA 6205
                          iv  i          i      vv i ii  v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_183424879_   6206 CTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAG 6255
                               i          i   i    ii         i iv ii i   v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_183424879_   6256 ATATAGACCAATGGAACAGAACAGA-AGCCTCAGAAATAATACCGCACAT 6304
                                i        i    iv  -  i -         vv  ii    
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACAT 338

  chr1_183424879_   6305 CTACAACCATCTGATCTTTGACAATCCTGACAAAAACAAGCAATGGGGAA 6354
                         i  iiii  vi    i  i     vvv  v   i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_183424879_   6355 AGGATTCTCTATTTAATAAATGGTGCTGGGAAAACTGGCTAACCATATGC 6404
                           i  vv   v  i  i              v      v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_183424879_   6405 AGAAAACTGAAACTGGACCCCTTCCTTGCACCTTATACAAAAATTAACTC 6454
                          i  i v    ii         v   ii    v                 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_183424879_   6455 AAGATGGATTAAAAACTTAAATATAAGACTTAAAACCATAAAAACCCTAG 6504
                           i      i ? i  i     i     vi      i      vi i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_183424879_   6505 GAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGACAAAGACTT 6553
                         i       v    ?i- v i -   iv   v v  vv i i   v ii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_183424879_   6554 CATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAT 6603
                          v iiv  vi            vvi          vv     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_183424879_   6604 GGGATCTAATTAAACTAAAGTACTTCTGAACAGCAAAAGAAACTATCATC 6653
                         v   ii v  i   v v  iv    i  vi vv    i  v       vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_183424879_   6654 AGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCCATCTATGC 6703
                          i      v  i     i                 v     v vii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_183424879_   6704 ATCTGACAAAGGGATAATATCCAGAATCTACAAGGAACTTAAACAAATTT 6753
                               i  i  iv vi          v  i  i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_183424879_   6754 ACAAGAGAAAAACAAAAAAAAGCCCA-TTAAAAAGTGGGCAAAGGATATG 6802
                          i  v i   i     v  ---    -  ?    i            v  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAA---CCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_183424879_   6803 AACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAA 6850
                           i     i     v        i  vi viii     i  --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_183424879_   6851 AAAAAAGCTCATCATCACTGGTCAT 6875
                           i v-     v     ????????
  L1M4_orf2#LINE/    885 AAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (133 / 97)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 2.00 (24 / 12)  


2799 26.81 1.86 2.74  chr1_183720409_183724846     3032  3945 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_183720409_   3032 GAAAAATTGTTCATGCTCATGAATAAGAAGAATCAATATTATTAAAATGG 3081
                             i  vvii    i     i  vi     v i      i    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_183720409_   3082 CCATACTGCCCAAAGCAATTTACAGATTCAATGTTATTCCTATCAAACTG 3131
                          v     v      vii  i           i iv  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_183720409_   3132 CCAG-TGTAATTTTT-CAAAGTATTAGAAAAAAAAGTCTTAAAATGCACA 3179
                             -  ivv     -  i i-   -  v  ivvii  i      v  i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAA-ATT-GACAAGCTGATCCTAAAATTCATA 150

  chr1_183720409_   3180 TGGAATCAAAAAAGAGCCAAAATACCCAAGGCAATCCTAAGCAAAAAGAA 3229
                              viiv  ii  v   i    v    ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_183720409_   3230 CAAAACTGGAGGCATCACATTACCCTACTTCAAAGTATACTACACAGCTA 3279
                             ii      vv     i v   v i      iiv       v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_183720409_   3280 CAGTAACCAAAACAGCACGTTACTGGAA-AAGAAAAAAAAAAAAAGTCAT 3328
                               i   i    iii v      v -   i v i ------------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA------------ 288

  chr1_183720409_   3329 ACAATCTCACACAGCTCAATGGAACAAAATAAGAAGCTTAGAAATAAAGC 3378
                         -------  i i  v         i i   viii  iii         v 
  L1M4_orf2#LINE/    289 -------CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_183720409_   3379 CATACACCTACAACCATCTGATCTTTGATGAAACTGACAAAAACAAGCGA 3428
                               ii  iiii  vi    i  i  ii iiv  v   i v  vv i 
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_183720409_   3429 TAGGAAAAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGGTTAGC 3478
                          i  i    i ivvi  v     i              i      v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_183720409_   3479 CATATGCAGATGATTGAGTCTAGACCTCTTCCTTTCACTAAATA-AAAAA 3527
                           i     i v  v   ivi i    i  v   iv   i v   -     
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_183720409_   3528 TTAAATCAAGAAGGGTTAAGGATTTAAATGTGTAACCTAAAACTATAAAA 3577
                             v    i v  i i ?i  ii       ivi v              
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_183720409_   3578 ACCCTGGGAGATAACATTGG---AAATAC-CATACTGGACATAGGCCCTG 3623
                         vi i i i   v     v  ---    vi- i ----   v v  viiv 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGT----GACCTTGGGTTAG 577

  chr1_183720409_   3624 GCAAAGATTTTATGACAAAGACACCAAAAGCAATTGCAACAAAACCAAAA 3673
                             v i   iv iivv v             vvv         vv    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_183720409_   3674 ATTGACAAATGGGACCTAAATAAGCTAAAGAGCTTCTGCACCACAAAAGA 3723
                           v  i    v    i v vi  iv v  i i   i  ii iv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_183720409_   3724 AACTATCAGCAGAGTAAACACACAACCTACAGAATGGGAGAAAATATTTG 3773
                         v       iv i   i  v v      i                      
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_183720409_   3774 CAAACTGTGCATCTGACAATATTCTAGTATCCAGAATCTATAAGGAACT- 3822
                             iii ii      i  vivv  v           v     i     -
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_183720409_   3823 -TA-AATTTACAAGCAAAAAAGT------CTCCATTAATAAATGGGCAAA 3864
                         -  -  i i vv ii     iii------ i v   ? v           
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_183720409_   3865 GGCCATGAATAGACACTTTTCAAAAGAAGACATACAAGTGGCCAGCAAGC 3914
                           viv          i  i  v        i      i      ii    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_183720409_   3915 ATATGAAAAAATGCTCAGCATCACTAATCTA 3945
                          i       i       i     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 3.23 (42 / 13)  

1427 24.74 1.53 0.26  chr1_183720409_183724846     4046  4437 (1)    L1M4_orf2#LINE/L1      452   848 (60)  

  chr1_183720409_   4046 TGGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGATGGATTAAA 4095
                                  v   i     v           i       i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_183720409_   4096 GACTTAAATGTAAGACCTAAAACCATAAAAATCCTAGAAGAAATCCTAGG 4145
                            i           v       i      v  i         v v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_183720409_   4146 CA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAAAACA 4194
                         ?i- v i -   iv   v v  vv i     v ii   v ivv  vi   
  L1M4_orf2#LINE/    552 NGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_183720409_   4195 CCAAAAGCAAAGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAA 4244
                                  v i          vv     v  i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_183720409_   4245 ACTAAAGAGCTTCTGCACAGCAAAAGAAGCTATCATCAGAGTGAACAGGC 4294
                          v v  i i   i  ii vv    i  vi      vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_183720409_   4295 AACCTACAGAATGGGAGAAAATTTTTGCAATGTACTCATCTGACATAGGG 4344
                             i                 v       vvi ivi      i vi  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_183720409_   4345 CTAATATCCAGAATCTATGAAGAACTTAAACAAATTTACAAGAAAAAAA- 4393
                           vi          v   i       ivv    v iv i  v     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_183720409_   4394 ----ACCCCCATCAAAAAGTGGGCAAAGTATATGAACAGACGCTTCTC 4437
                         ---- v   v  i?    i         v  v    i    ii     
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

Transitions / transversions = 1.00 (47 / 47)
Gap_init rate = 0.01 (3 / 397), avg. gap size = 2.33 (7 / 3)  


2143 29.42 2.21 2.32  chr1_183758096_183760767.rev     1281  2184 (488)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_183758096_   1281 AGCTATCCAATGCTCATGTACTAGAGGACACCATACTGTTAAGATATCTA 1330
                           v     v   i     v i i  i   viv   i         iv v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_183758096_   1331 TTCTTTTCCAAAATTATCTATACACTTATCACAACCCCAAATAAA-TATC 1379
                          v  ii-     v v     i v i i v i   i   v vi   - vi 
  L1M4_orf2#LINE/     56 TACTCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_183758096_   1380 AGCATGATATTTTTGTGTGGAAAGAGACAAGCCAATTCTAAAACGTATAT 1429
                            -  vi-     -  ii    vv       ii  i      ivi    
  L1M4_orf2#LINE/    105 AGC-TGCC-TTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_183758096_   1430 GGAAATTCAAAGGATCTAGAATCATAAAAACAATTTTGCAAAATAAAAAC 1479
                               v   i   i i     viiv        i   v    v  i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_183758096_   1480 AAGGTTGGAAAGCTTACATTGCAGCCTGATGTTAAGAGTTACTATAATAA 1529
                           i      iii  i   i v --- ii  v i  i v      i  viv
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTC---CCAATTTCAAAACTTACTACAAAGC 248

  chr1_183758096_   1530 TACAGTAATCAAGATGGCGTGGTATTGTGAAAAGGATGGACAAATAAAAA 1579
                                       ii i      i  vv v      i    v   i --
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA-- 296

  chr1_183758096_   1580 TCAATACAATGGAATAGAAAGTTCATAAAGAGATGCACACATATAAAATC 1629
                              iv   i    v  i   i  v   v i iv  i    v  vii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_183758096_   1630 AGCTGAAATTAGTGAAAGGCAGCAAAACAATTCAGTGGGG---GAAT-GT 1675
                          ii   vv  v vv  i  iiv   i  v     i     ---    -  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_183758096_   1676 AACGTTTTAACAAATAGTGCTGGAATAGATAAATATCCTAATGTGAAAAA 1725
                         -- v   i       i       i i iv ii   ?  -- ii  v    
  L1M4_orf2#LINE/    397 --CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC--ACATGCAAAA 442

  chr1_183758096_   1726 GAAATGAGACTTGACCC-TACCTGATTTCATACACGAAAAACAAGTTAAC 1774
                            -   iii v     -     v ivi    i  i    vi  v i  v
  L1M4_orf2#LINE/    443 GAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_183758096_   1775 ATACACCATGAACCTAAACATAA-AGC-AGAACTATAAAGCTTCTAAAAA 1822
                           iv i  ?ii       ii   -   - i         i  ii  i  i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_183758096_   1823 GTTACTTAGATGAGTATCTTCAAAACCTTGGAGTTGACAAAGAATTTTAA 1872
                         ivv  v   i? viv      ivi       iv v i   v iv  i v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_183758096_   1873 AACAGAACTGCAGAAGTGCAAACCATAAAAAAAGTAAAT-GATAAATTGG 1921
                         i i vi  vv  i   ii   i v i    i  i-    -          
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGG 640

  chr1_183758096_   1922 ATTTCATTAAA-TTAAAAATCATTGCACATTAAAATATACCATTAAGATA 1970
                          i     i   -       iiv   ii v i   iv i  i  i    - 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA-A 689

  chr1_183758096_   1971 ATTATAACAGGGAAACCACACACTAGGAAAAAGTTTTTGCAA--CACATA 2018
                          v i-  v  iv  v     v v i   i   i v       --  i   
  L1M4_orf2#LINE/    690 AGTG-AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_183758096_   2019 TCTGACAAATGATTTGTATATAAAATACACAAAAAATCTCTTCAAAATCA 2068
                              i  iv  i      vi i    i i   i  -     vv  v   
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCA 787

  chr1_183758096_   2069 ACAATAAATTAAAAAATGG-------AAAAAATACTAAACTAAAATCTTA 2111
                          i      vvi v    ii-------?      i---ii v  iivi  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATG---GGCAAAGGATTTG 834

  chr1_183758096_   2112 AACACTCATTTTACAAAAGAAGATAAACAGATAACTACTAGACCC-TGTA 2160
                           i vv     iv v          v   i  ii i v  ii v -  v 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_183758096_   2161 AAGTTTCTCAACAGTATTAATCAC 2184
                            v v       vi ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (159 / 103)
Gap_init rate = 0.03 (25 / 903), avg. gap size = 1.64 (41 / 25)  


3462 24.75 2.59 0.45  chr1_183832413_183836863     3070  3958 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_183832413_   3070 TGGAAAGATATCCCATGTGCAGGGACTGGAAAAATTACTATTGTTAAAAT 3119
                                           v  v   i     i v   v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183832413_   3120 GGTCATACTACCTAAAGTAATCTATAGATTTAATGAAACCTCTATCAAA- 3168
                           iv     v  i   v i     i     i  i v  i i        -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_183832413_   3169 TATAAATGGCATTCTTGACATGAATAGA-AA--TAATTCTAAAATTCATA 3215
                          viv iiv  v  i  vi  vi   v  -  -- i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_183832413_   3216 TGGAACCACAAAAGACCCTGAATAGCAAATGCAACCCTGAGCAAAAAGAA 3265
                              vii   ii     v       v  vi   i i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_183832413_   3266 CAAAGCTGGAGACATCACATTACCTGATTTCAAAATATGCTACCAAGTTA 3315
                              i     ivv     i v  ii         iv i    v   i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_183832413_   3316 TAGTAACCAAAAGAGGATGATACTGGCATAGAAATAGGCACATAGGCCAA 3365
                         i     i   i v  vi  i          iii    i  i    ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_183832413_   3366 TGGAACAGAATAGAAAGCCCAGAAATAAATTCATGCACCTACAGTCAACT 3415
                              i     v  i  i           ii   i  ii  ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_183832413_   3416 GATTTCCAACGAAGGTGGCAAGAAAACACATTTGGGAAA---TA----TC 3458
                              i i  i i    v     vv iv  v v      ---  ---- i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_183832413_   3459 TCAGTAAATAGTGCTGGGAAAATTAAATATCCATATGCAGAAGAATGAGA 3508
                            ii    i         v  i ii   ?   i     i        ii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_183832413_   3509 TTAGACTCCCAACTCTCACCATATACAAAAATCAACTCAATGTGGATTAT 3558
                           i   i  i v   v                i       vi     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_183832413_   3559 AGGTTTCAACGTAAAACCCAAAACTATGAAACTGCTAGAACAAAATTTAG 3608
                           iii v  i    i v i        i     vi     v    iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_183832413_   3609 GGGAAACACTTCATAGCATTAGGCTGAGGAAGAGTTTTTTTTACATAATG 3658
                          ? v  vv    i ii v  i  i ii v  vi    i  vv i  i ii
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_183832413_   3659 CCTCAAAAGCACAGGCAACAAAAGAAAAG-TAGACC--TTGGGGTTATAT 3705
                           --         i              i-    iv--    iv  -i  
  L1M4_orf2#LINE/    601 CC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CAT 647

  chr1_183832413_   3706 CAAAATAAAAAGCTTCTGCACAGCAAAGAAAAC-------AGAGTGAAGA 3748
                               v    i   i  ii vv     i v  ------- i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_183832413_   3749 GACAACCTACTGAAATGGGAGAAAATATTTGCAAACTGTACATCTGTCCA 3798
                                i  v   -                    iii  i     viv 
  L1M4_orf2#LINE/    698 GACAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_183832413_   3799 GGGCTTAATATTCAGAATATGTAAGAAACTCAAACAACTCAATAGCAAAA 3848
                            vi vi   i        i   ii     vv           ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_183832413_   3849 AAACAAATAATCTGATTTTAAA-TGAGCTAAAGATCTAAATAGACTTTTC 3897
                          i        i ii   ?v   -  i  v  i   i i       v    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_183832413_   3898 TCAAAAGAAGACATACAAATGTCCAAAAGGTATATGGAAAAA-ATTCAAT 3946
                           v        i         v    v i i i   i   i -ii    i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_183832413_   3947 ATCATTAATCAT 3958
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (146 / 70)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.08 (27 / 13)  


3328 23.18 1.85 3.05  chr1_183846137_183853134.rev     2889  3807 (3191)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_183846137_   2889 TGGAAAAATATTTTATGTTTAGGGATTTGAAGAACCAATATTCTTAAAAT 2938
                               i    iii     i v     v     vii      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183846137_   2939 ATCCATACTACCCAAAGCAATCTGCAAACTCAGTGTAATCCCTATCAAAA 2988
                         iv v     v      vii    i  i i   ii i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_183846137_   2989 TAATGACAGTCTTC---ACAGAAACAGAAACGACT-ATCCTAAAATTTAT 3034
                          vviii v i   i---i      iv  v v -  -           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_183846137_   3035 ATGGAACCACAAAA-ACCCATCATAGCCAAAGCTATCCTAAGCAATAAGA 3083
                               vii   ii-     vv         i v   i i iv  v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_183846137_   3084 ACAAAATGGAAGGAATTACATTACCTGACTTTAAAA---ACTACAGAGCT 3130
                              i v i    v i   i v  ii i  i    ---      i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_183846137_   3131 ATAGTAACCAA-ACAGCATGGTACTGCCATGCAAACAGACACATAGACCA 3179
                          i     i   -    ii        v   ivii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_183846137_   3180 ATGGAGCAGAATAAAGAACCCAGAAACGAATCCACATACCTATAGTGAGT 3229
                              ii     vi   ii       ii  i   i i ii   i  v i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_183846137_   3230 TCATTTTCAACAAAGGTGCCAAGATCATACACTGTGGAAAAGAGAGTCTC 3279
                          v      i    i          i   v  v  v     ii v     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_183846137_   3280 TTCAATCAAATGGTGCTTGGAAAACTGGATATCTATATGCAGAAAAATGA 3329
                              -           v   v         ? i i     i  i     
  L1M4_orf2#LINE/    400 TTCAA-CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_183846137_   3330 AATGAATGAAACTAGATCCCTATGTCTTCTCATATACAAAAATCAAGTCA 3379
                          i --------- i  i     iv  vivi             i  v   
  L1M4_orf2#LINE/    449 AGT---------TGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_183846137_   3380 AAATGAATTAAAGACTTAAATTTAAGACCTCAAACTATGAAACTACCTCA 3429
                              i  i ?    i     v     v  v       i     --  i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT--CTTA 537

  chr1_183846137_   3430 --AGGAAACATTGAGGAAAATCTTCAGGACATTTGTCTGGGCAAATATTT 3477
                         --  i      v i? v        iv   v  v vi i     vvi   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_183846137_   3478 CTTGAGATGCTTTGATCTCATTACCCACAAACACAGGCAACCTAAGCAAA 3527
                            -    i---   ---  ----   v  i    i     vv   v   
  L1M4_orf2#LINE/    588 CTT-AGATA---TGA---CA----CCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_183846137_   3528 AGTGAACAAATGGGA--TCAAGTCAAG--TGAAAGGGTTTCTGCATAGCA 3573
                          i ii i    v   --   --    i-- i   ivv   v   v --  
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCA--TCAAAATTAAAAACTTTTGTGCTT--CA 672

  chr1_183846137_   3574 AAGGTTACAGTCAACAAAGTGAAGAGACAACTCATGGAATGCAAGAAAAT 3623
                             vi  vi    v        i       i  ii     vi       
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_183846137_   3624 ATTTGCAAACTACCCATCTGACAAGGGATTAATAACCAGAATATACAAGG 3673
                                  ii ivi      i      i vi  v          i  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_183846137_   3674 ATCTCAAACAACTCTATAGGAAAATATCTAATAATCCAATC--AAATTGG 3721
                          v   vv       v   iv    viv v     i     i--   v   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_183846137_   3722 GCAAAAGATTTGAATAGACATTTCTCAAAAGAAGACATAAAAATGGCAAA 3771
                              i                    v        i   v       v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_183846137_   3772 CAGGCATATAAAAAGGTGCCCAATATCACTGATCAT 3807
                         i i   i  i     i   i   i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (133 / 77)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.37 (45 / 19)  

1238 26.75 6.51 2.41  chr1_183846137_183853134.rev     5018  5432 (1566)    L1M4_orf2#LINE/L1       13   444 (464)  

  chr1_183846137_   5018 CTATGTTCACAGATAGGAAGAGTCAGCATTGTCAATATGTCAATTCATCC 5067
                          i       ii   v      v i ii     i  v   v    v vi  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_183846137_   5068 CAACTTGATCTATAGATTCAATGTAATTCCCAATCAAAATACCAGCAAGT 5117
                            v        i        i i   -   v        v     vivi
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAAT-CCCTATCAAAATCCCAGCTGCC 111

  chr1_183846137_   5118 TAAGTTGTGGATATCAACAAACCAATTCTAAAGTTTCTACAGAGAAGCAA 5167
                          vvv   ii  v  ii    i ii  i     i  iv  ii  i v    
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_183846137_   5168 AAGACCCAGGATAGCCAAAACAATGGTGAAAGAGAATGAAAAAAAATGTC 5217
                         ii       i              vv     i    -   v   ---  i
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GAACAAA---GTT 207

  chr1_183846137_   5218 GGAGGCCTGACACTACCCTACTTTAA-------------GCCATA----T 5250
                              v  v     v   v i  i  -------------  i i ---- 
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_183846137_   5251 CG-----GTGTTACGCTGGCAAAAGG-TAGATAAACAGCTTGGTGTAACA 5294
                          i-----    viii      v    -    i v i  v iii  v  i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_183846137_   5295 GAATAGAGAGCCCAGAAATAGACTTGTACACAGATATAATTAACTGGTCT 5344
                             v     i         i  iii    iv--   ii i  i  i i 
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAATTGATTT 355

  chr1_183846137_   5345 TTGACAAAAACACAAAGGCAAAACAATGGAGCAAAGA----TCATTTTAA 5390
                          i     iiiii v   i v vv      i -     ----  -    v 
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTC-TTTTCA 403

  chr1_183846137_   5391 ACAAATGGTGCTAGAATTATGGGACATTCACATGTTAAAAGA 5432
                                     i i iv iv   i ?i      i-      
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGC-AAAAGA 444

Transitions / transversions = 1.89 (72 / 38)
Gap_init rate = 0.03 (12 / 432), avg. gap size = 3.08 (37 / 12)  

 602 29.44 0.43 2.60  chr1_183846137_183853134.rev     5712  5942 (1056)    L1M4_orf2#LINE/L1      440   665 (243)  

  chr1_183846137_   5712 AAAAAATAAATCTAGTCACAGAAGTTACATTCTTCACAAAAATTAACTCC 5761
                            i   i  vi i v v vv vv i   iiv vi              v
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_183846137_   5762 AAATTGATCATAGACCTAAATGCAGCACACAAAACTTTAAATAAGAACTC 5811
                             v     ?           i iv vvi      ----    -     
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT----ATAA-AACTC 534

  chr1_183846137_   5812 CTAATAGACAACGTAAGAG-AAATCCTAGATGACCTTGAGTATGAGGGTG 5860
                         i  iv   v   i  i ? -     i v -        i  vv ivii  
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATG 583

  chr1_183846137_   5861 ACTTTTTAGATACAACATAAAAGGCATGATTCATGAAAGAAATAATTAAT 5910
                         ii  i       ii   iv   i   ii viv ii       v   vi  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_183846137_   5911 AAGCTTGATTTCAGTAAAATTAGAAACTTCTG 5942
                           ii v  i    vi       i      i  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.44 (39 / 27)
Gap_init rate = 0.02 (4 / 226), avg. gap size = 1.75 (7 / 4)  

 583 22.66 2.88 9.35  chr1_183846137_183853134.rev     6230  6507 (491)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr1_183846137_   6230 AAAATTAGAAGCTTCAGCTATGTGAAAGACA--AT--AGAA--TGATAAG 6273
                                i  i   iv ivv vii  i    --  --    --   v   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_183846137_   6274 ACCAACTGTAGACTGGGAAAAAATATTTGCAAAAGACACTTGTGATAAAG 6323
                           v v iii   v     i              vv i iv v      i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_183846137_   6324 GACTGTTATTTGAAACATACAACACACTCTTAAAACTTCACAGTAAAAAA 6373
                             vv   iiii  i   i  viv       v    ---  i   v   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAAA 795

  chr1_183846137_   6374 AAAAAAAAAAAAACAAGAAAAGAAAACAAAAAAAACTGATTGAAAAGTGG 6423
                           i ---------   ------ v   -------- ii   ?    i   
  L1M4_orf2#LINE/    796 AAGA---------CAA------ATAAC--------CCAATTWAAAAATGG 822

  chr1_183846137_   6424 CCAAAGGCCTT-AACAGATACCACATCAAAGAAGATACACAGATGGCAAA 6472
                         v      vi  -  i   i iiv vi           i   i     v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_183846137_   6473 TGAGCATAT-AAAAGATGCTCCATATCATATGTTAT 6507
                          i    i  -           v i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (37 / 25)
Gap_init rate = 0.03 (9 / 260), avg. gap size = 3.78 (34 / 9)  


2759 27.57 2.22 0.58  chr1_183881338_183885527     2834  3689 (501)    L1M4_orf2#LINE/L1        1   870 (38)  

  chr1_183881338_   2834 TGGAATGATATTTCATGCTAATGGTTTGGAAGAATTAAT--TGTTTAAAT 2881
                              v     ii    i v    v        v     --    v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183881338_   2882 ATCCATACTACCGCAA-----TCTACAGATTCAACACAACTCCTATCAAA 2926
                         iv v     v  -   -----              i   ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_183881338_   2927 ATGCCA--TGACTGTCTCTACAGAAATAAAAAAAAAATCAACCTTAAAAT 2974
                           v   --  v  - i i i       vi v  i---iii i i      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCT-TTTTTGCAGAAATTGACAAG---CTGATCCTAAAAT 145

  chr1_183881338_   2975 CCATAGGTAACCACAAAAGACCCTGATTAGCCAAATCAATCATGTGCAGA 3024
                         i    v v  vii   ii     v  v        v     v  viv ii
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_183881338_   3025 AATAACAAAACTGAAGGCTTTACATGACCTATCTTCCAAATATTCTACAA 3074
                           v      ii  i   vi i   ivv  i vi   v   iv v      
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_183881338_   3075 AGCTAAATTAACCAAAATAGCATAATACTAGAATAAAAACAGACACATAG 3124
                              v v   i   i i  ii ii    i v    ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_183881338_   3125 ACAAACGTAAAAGA-TAGATAGCCCAGAAATAAGTCCA--CATATAAAGT 3171
                          iv  i v  v   - v  v  i          ii   --   v  vi  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_183881338_   3172 CAATTTCTGTTTGACAAAAATATCAAGGACACATATTGGGCAAAAA---- 3217
                              vv v  i     iii ii    iv  ivi v    v   i ----
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_183881338_   3218 TCTCTTTAATAAACAGTGGTTGGAAAACTGGTT--TCATATGCATAAGAA 3265
                            i  i  i   ii   v v   v      v --i  i     v     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_183881338_   3266 TGAAACTAGATTCCTATCTCTCATCATACACAAACATTACATCAAAATGA 3315
                             ii i  ii    i   v  i    i     v    vv        i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_183881338_   3316 ACTAAAGAC-TAAATGTAAGACATGAAACTATGAAGCTACCAGAAGAAAA 3364
                          ii ?    -           vv i       i  i  vii         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_183881338_   3365 CATTGGAAAAATTCTTGCCAGGCTTGGACTGGGCAAAAATCTTCTGGGTA 3414
                            v  ?iv  v    vviiiv     ii i     vii i ii i i  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_183881338_   3415 AGACCTCATAAACATAAGCAACAAAAGCAAAAATAGAGAAATCGGATTAT 3464
                         v   vi  v  i  i            v         v    i   i vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_183881338_   3465 GTCAAGTTTAAAAGCTCCTGTTCAGCAAAAGTAACAATCATCAGAGTGAA 3514
                         i    iv      i  ii   v vv    i vv  v    vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_183881338_   3515 GAGATAATCTAAAGAATGGGATAAAATACTTGCAAACTATCCATCTGCCA 3564
                         i   i  i i v         v      i       ii  vi     vi 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_183881338_   3565 GGGAATTAATAACTAGAATATATAATGAACTCAAACAACTCAATAGCAAA 3614
                         i  i i vi  v i           v      vv           ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_183881338_   3615 ACACCACATAATCCAATTTAAAAATGGGCAAATTATCTGAATATGCATTT 3664
                          viv  v    i      ?             vv  i      vi     
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_183881338_   3665 CTCAAAAGATAGCATACAAATGGCC 3689
                            v     viii            
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCC 870

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.01 (11 / 870), avg. gap size = 2.18 (24 / 11)  


2406 27.56 3.94 1.80  chr1_183898880_183900946.rev      688  1576 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_183898880_    688 TGGAGTAACATTTCATGCTCATAGGTAGAAAGTAAC--AATATTGTTAAA 735
                             ivi i  ii    i    i i v i   --  --           i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAG--ACTTAATATTGTTAAG 48

  chr1_183898880_    736 ATGACCATACTGCCCAAAGCAGTTTACAGATTCAATGCTATGTCCATGAA 785
                            i v     v      viii i           i  v  vi i  v  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_183898880_    786 ACTACCAA-TGTCATTTTTCACAGAATTAGAAAAAACT-ATCCTGAAACA 833
                          v v   i-  i -     ii     v v  v  i-  -     i   iv
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chr1_183898880_    834 CATATGAAACAACAACAACAAAAACCTGAATACCCAAAACAATTCTAACA 883
                               i  vvi   ----iii v  v     v          ii i v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAA----GGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_183898880_    884 AA-AAGAGAAAAGCCAGAAGCTTCACACCACCTAACTTCAAGCTATACTA 932
                           -    iv    iii  i vi      iv  i  i     iviv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_183898880_    933 CAAGAATATAGTAACCAAAACAGCATGATACTGGTACACAAACAGACATA 982
                            iiv  i     i   i    ii  i      i i vii i       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_183898880_    983 TAGACAAATGGAACAGGATAAAGAATT--GACATGAGGCCACACACCTAC 1030
                             iv       i  i  vi   i i--  v  i iv   i   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_183898880_   1031 AACCATCTGATCTTCAACAAAGTTGGTAA--CAAGTAAATGGGGAAAGTA 1078
                         iii  vi    i   i    i v  vi  -- v v v           v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_183898880_   1079 CTCTCTATCTAATAAGTGGTGATGGGATAATTGGCTAACTATATGCAGAA 1128
                         ivv   v ii  i  i     v     i  i   v  ? i i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_183898880_   1129 GATTTAAACTAGACCCTTTCTTT-CATCATATACCAAAATTAGATCAAGG 1177
                           v v  ii i     i v i i-  i       v       iv    ii
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_183898880_   1178 AGGGTTAAAGATTTAAATGTAAGACCTAAAATCCTA-AAAACACT-AGAA 1225
                         v  i i ?   ii           v      --   -     v  -    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAA--CTATAAAACTCTTAGAA 540

  chr1_183898880_   1226 GAAAACCTAGG---AAATACCATTCTGGACATGGGCCACAGCAAAGAGTT 1272
                               v    ---    -- v iv  iv v    ii -i    v iv  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTA-GGCAATGGTTT 587

  chr1_183898880_   1273 TATGACCAAGTCTCCAAAAGCAATTGCAACAGAAACAAAAGTTGACAAAT 1322
                         iv iivi v v v         vvv      i  iv    i v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_183898880_   1323 GTGACCT------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCCA 1366
                         vv   i ------       i -   i  ii vv    i  v      v 
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_183898880_   1367 TAGAGTAAACAGACAACCTACAGAATGGGAAAAGATATTTACAAACTACA 1416
                         v i   i  v        i           i  i      i    ii i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_183898880_   1417 CATCTGACAAAGG---TGTAAC----GTACATAAT---CTGTAACAAGCC 1456
                         i      i  i  ---    v ----i  i    v---  v v    vi 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_183898880_   1457 AACAAGCAAAA--CA--TAACCGCATTAAGAAGTGGGCAAAGGACACGAA 1502
                           i  vv    --  --     vv   ? i  i           ivi   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_183898880_   1503 CAGACACTTCTCAAAAGATGACTTGCATGTGGTCAAAAAGTATATGGGAA 1552
                         i     i     v     v  iv i  vi   i   v   i i   --  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG--AA 884

  chr1_183898880_   1553 AAAATGCTCAAAATCACTAATCAT 1576
                           i        v    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (150 / 92)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.04 (51 / 25)  


3298 25.14 0.54 1.74  chr1_183918753_183923002.rev     2841  3759 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_183918753_   2841 TGAAAAAATATTTTATGTTCATTGACTGGAATAATCAATATTGTTAAAAT 2890
                           i   i    iii        v  i     v v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183918753_   2891 GTTTATACTATACAAAGCAATCTACAGATTCAGTGCAATCCCTCTTAAAA 2940
                          viv     viv    vii             ii         v i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_183918753_   2941 TACCAATGATATATTCTTCACACAAATAGAAAAAATAAACCCTAAAGTTC 2990
                          v   -- v iiv  i  ii  v    v  v  iv i -i      i   
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTC 147

  chr1_183918753_   2991 ATATGGAAACACAAAAAGACTCATAATAGCCAAAGCTATCTGAGGCAAAA 3040
                                  ii   ii-   i  v          i v    viiiv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_183918753_   3041 AGAACAAAACTAGAGAAATCATATTACCTAACCACAAATTATACTAAAGA 3090
                                 ii i   i v   i i v  i  iiv    viv     v i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_183918753_   3091 GCTGCAGTTACCAAAACAGCATGGTTTTGGCATGAAAACAGACACAGAGA 3140
                            i    v i   i    ii    vi      i ii i     i v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_183918753_   3141 CCAATGGAACAGAATAGAGAACAAAGAAACAAATCTACATGTCTACAGTT 3190
                         i        i     v    iivv     i   i i i ii i  ii  i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_183918753_   3191 AGTTCATTTT-GACAAGTGTGCCAAGAGGGTACACTGGGGAAAAGACAGC 3239
                          i  v     -      v         vvi v  v        ii i  i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_183918753_   3240 CTCTTCAATAAATGGTGCTGGGAAAACTAGATATTCATATGCAGAAGAAT 3289
                           i     i              v    i    ?i  i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_183918753_   3290 AAAACTAGACCCCTATCTCTGGCCATATAAAAAAATCAAGGAAAAATGGA 3339
                         i  ii i        i   vvi       v      i  vvv        
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_183918753_   3340 TTAAAGATTTAAATCTAAGACCTCAAACTATGAAAGTACTACTACAAAAA 3389
                          i ?   ii     v     v  v       i   ---  vi  v  i  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA---CTCTTAGAAGAA 543

  chr1_183918753_   3390 AAAAAATTGGGGGAAAATCTCCTGGACATTAATCTGGGCAAAAATTTCTT 3439
                           v --- i  ? v      i vv   v  iivi i     vii      
  L1M4_orf2#LINE/    544 AACA---TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_183918753_   3440 TAG---CAACACCCTACAAGCACAGGCAACCTAAGCAAAAATGAACAAAT 3486
                         -  ---ii     -- v       i     vv   v      ii i    
  L1M4_orf2#LINE/    591 -AGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_183918753_   3487 GGGATCACATTAGG-TTACAAAGCTTTTGCACACCAAAGGAAGCAATCAA 3535
                         v   iiv   i ii-   -   i      ii vi       vi v     
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_183918753_   3536 CAAATTGAAAAGACAACCCACAGAATGGGAGAAAACATTTGCAAACTACA 3585
                         v   v                              i         ii i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_183918753_   3586 TATCTGACAACCGGTTAATAACCAGAAAATATAAGGAGCTCAAACAACTC 3635
                                i  vv ii vi  v      v      i  i   vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_183918753_   3636 TATAGGAAAAAAAATCTAATAATCTGATCAGAAAATGTGCACATGATTTG 3685
                         v   iv     i -- v     i ii  i?i      v   v v      
  L1M4_orf2#LINE/    787 AATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_183918753_   3686 AATAGACATTTCTCAAAAGAAAACACACAAATGGCAAACAGGCATATGAA 3735
                                       v      i i i         v  i i   i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_183918753_   3736 AAGGTGTTCAACATCACTGATCAT 3759
                            i  i         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (144 / 83)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


2844 23.36 2.19 7.51  chr1_183947496_183949487      541  1499 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_183947496_    541 TGGGAAGATGTTCCATGTTCATGGATTGAAAG--TTAATATTGTTAAAAT 588
                            i     i i                i   --             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_183947496_    589 GTGCATACTACCCAAAGCAATCTGTAAATTCCACTACCCAAAATGATCTA 638
                          ---------------     -----------   v      v       
  L1M4_orf2#LINE/     51 G---------------GCAAT-----------ACTCCCCAAATTGATCTA 74

  chr1_183947496_    639 CAGAGTTAATGCAGTTTCTTTCAAAATTTTAATGTTG--TTTTCCACAGC 686
                             v i  i   i ii  v       iii -- i  --    iii   v
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCA--GCTGCCTTTTTTGCAGA 122

  chr1_183947496_    687 CAT--ACAAAAT-ATTCTAAAATTTGTTTAGAACCAGAAAATTTGTTTAA 733
                         v  --    iv -  i        ii v i   viiv  ii-------i 
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG-------GA 165

  chr1_183947496_    734 CCTA-AATAGCTAAAACAGTCTTGAAAAAAAAGAAGAAAGCTGGAGGCAT 782
                           i -      i      i          i     v    i      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_183947496_    783 CACACTCCTTAATTTCAAAATATATGACAAAGCTGTAGTTATCAAAACAG 832
                               i ii          iv  iv        ii   v     i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_183947496_    833 TATAGTACTACCATAAAAAGAGACACATATGAATATGTGTCTGCCAACGA 882
                          i i     iv     ii v     i   --i  ----------   i i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATA--GAT----------CAATGG 303

  chr1_183947496_    883 AGCAGAATAGAGAGCCTAGAAATGGATCCGTACATATCTGGTCAACTAAC 932
                          ii     v     i i      ii i  i     v v       i i i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_183947496_    933 CTTTGACAAGGGCACTACGACTACACAATGGAGAAAAGATAATCTCTTCA 982
                         i  i        ii i v   i iv      i    ii   i   i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_183947496_    983 ATGAATGGTGTAAGGAAAACTGAAAATCAAAAAATCA-ACAACATTTTAA 1031
                          ii       ivi   v     i v ? v -----  -i   ------  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCA-----CATGCAA------AA 442

  chr1_183947496_   1032 AAATGAAATCAGACCCTTATTTTACAACATGCATGAAAAGTAACTTTAAA 1081
                         i      i ii     i  ii i   v   ii ii    v     iv   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_183947496_   1082 TTGATTAAATACTTACATCTTTAAGTCTTAAAGATCTAAAACCATAATAC 1131
                          v   i ? v  i  v  ------  ----    v       i    v  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAAT------GT----AAGAGCTAAAACTATAAAAC 532

  chr1_183947496_   1132 TTCTAGAAGAAAACATAGAAAAAAAATCTCCTTGACTTTGTTCTTGGCAA 1181
                          ii               i?iv   -   i v    i   vvi v     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_183947496_   1182 TGTCTTTTTTGATATGACATCAAAAGCACAGGCAACTAAAACAAAATTAA 1231
                           vi  i  v         i          i     v   iv    v  i
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_183947496_   1232 ACAAGTGGGAC--CATCAAACTGAAAAGCTTCCACATAGCAAAGGAAATA 1279
                          i  i v    --       v v    i   iiiiiivv       v iv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_183947496_   1280 ATCAAGAAAGTGAAAAAACCATACATGAAATGAAAGAATATATTTGCAAA 1329
                                         i  v iv  iii    ii    v           
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_183947496_   1330 CCAAACATCTGATTAGAGATTAATATTCAAAATATAAAAGGACCTCACAC 1379
                         i  v i       v  i  i vi   i  i      v  i  v   vi  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_183947496_   1380 AACTCAA-AACAGACAAAAATATAACAAAAAATTTTAAAAAGGATCAAAA 1428
                                -  i i v i v v     vv  ---  ?     v iv    i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAA---TTWAAAAATGGGCAAAG 828

  chr1_183947496_   1429 CACCTGAGTAAATATTTTTCCAAA-AAGAT--------GGACAAGAGGTA 1469
                         v ii   i  i i    i      -     --------  v   v i i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_183947496_   1470 TGTGAAAAGATGCTTAACATCACTAAACAT 1499
                         ii            i       ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (149 / 71)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.23 (93 / 22)  


2578 27.06 3.69 1.91  chr1_183974494_183976579.rev      746  1584 (502)    L1M4_orf2#LINE/L1        3   856 (52)  

  chr1_183974494_    746 GAAAAACCTTCCGTGCTCATGGATAGGAAGAATCAATATTGTGAAAACGG 795
                             i iv i  i  i        v      v i        v  i i  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_183974494_    796 CCATACTGCCCAAAGCAATTTACAGATTCAATGCTAATCTC-ATTAAA-- 842
                          v     v      vii  i           i  -    i -  i   --
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAAAAT 101

  chr1_183974494_    843 -----CTGCCATTTTTCTAACTATTGACAGAATTAGCAAAAAATATTTTA 887
                         -----     v     vi ivv       -----   vi ----- ii  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACA-----AGCTGA-----TCCTA 141

  chr1_183974494_    888 AAATTCATATGAAACCAAAAAAGAGCTCACATAGACATGACAATCCTAAG 937
                                    i  viiv  ii  v iviv    v  vi      i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_183974494_    938 CAAAAAGAACAAAGCTGGAGGCATTAGGCTATCCGACTTCAAACTATACT 987
                         v  i          i      vv i vi  vi  i i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_183974494_    988 ACAAGTCCACAGTAACCAAAACAGCATGGCACTGGTACAAAAACAGGCAC 1037
                             iv i       i   i    ii   i     i i  ii i  i  i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_183974494_   1038 ATAGACCAGTGGAACAGAATAGAGAATTCAGAAATAAAACCACACTTCTA 1087
                              i  i     i     v    i i          v   i  v i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_183974494_   1088 CATTCATCTGATCTCTGGCAAATATGATGAAAACAAGCAATGGGGAAAGG 1137
                         iiv   vi    i ii i   ivi  vii i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_183974494_   1138 ATTCCCTATTCAATAAATGGTGCTGGGAGAACTGGCTAGCCATAGGCAGA 1187
                           vvi  v     i              v      v  ?   i v   i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_183974494_   1188 AAATTGAATCTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAG 1237
                          i v    vi    i    v   i     v                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_183974494_   1238 ATAGATTAAAGAGTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAG 1287
                           i   i ?   vi         i v i            vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_183974494_   1288 AAAGTCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTTAT 1336
                            iiv    ?i- v i -   iv   v v  vv i     v ii  iv 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_183974494_   1337 G---ATGAATTCGCCAAAAGTAATTGCAACAAAAGCAAAAATTGACAAAT 1383
                         i---    --- i       i vvv          v      v  i    
  L1M4_orf2#LINE/    591 AGATATGA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_183974494_   1384 GGGATCTAATTGAACTAAAGTGCCTCTGCATAGCCAACGAAACTATTATC 1433
                         v   ii v  ii  v v  ivi i i  iiivv v  v  v     i vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_183974494_   1434 AGAGTGA--------------GAGTGGGAGAAAATTTTTGCAATCTATCT 1469
                          i     --------------  i           v       vii  v 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_183974494_   1470 ATCTGACAAAAGTCTACTATCCAGAATCTACAAGGAACT--TA-AGCCGA 1516
                               i  ii v  vv          v  i  i     --  - i iv 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_183974494_   1517 TTTACAAGAAAA-AAACAACCCCATTATAAAGATGG-CAAAGAATATGAA 1564
                         v v i  i  i -   i     v   ?-   i    -     i  v    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAA 836

  chr1_183974494_   1565 CAGACACTTCTCAAAAACAG 1584
                         i     i     v   iv  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAG 856

Transitions / transversions = 1.48 (133 / 90)
Gap_init rate = 0.02 (15 / 854), avg. gap size = 3.13 (47 / 15)  


1713 24.65 3.30 4.24  chr1_183993327_183994954      500  1136 (492)    L1M4_orf2#LINE/L1      278   908 (0)  

  chr1_183993327_    500 ATAAAGACAGACTTATTGGCCA-TGGAACATAATAGAAAGCCCAGAAATA 548
                             i  i    v   v ii  -     i v   v  i  i         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_183993327_    549 AATCTACACATATAGAGTCAACTGATCTTCAGAAAAGATGCCAAGAATAC 598
                           i i i    v  vi     i    i   iiv  i i        vi i
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_183993327_    599 ACAATAGGGAAACGACTGTTTCTTCAACAAATTGGGCTGGGAATACTAGA 648
                         v    i      vi iv  i i          v v       vv   i  
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_183993327_    649 TAGCCACATCCAAAAGAATGTAATTGGATCCCTATCTGACACCAGACACA 698
                           ?      v          v i     i     i  v      v i   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_183993327_    699 AAAATCAACTCCAAATGGGGGTAAAGACTGAAATGTAACATCTGAGTCTT 748
                              i     v      iv-i ?    iv        v v  i iv  v
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGAT-CAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_183993327_    749 TGAAACTCTTAGAAAAAAATTTAGGGGGAAATCTT---GACAATGGTCTT 795
                          i            i    iv    ? v       ---   vv   vi v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_183993327_    796 GGAAATTATTTCTTTGATCTGACACCAAAAGCACAGGCAACTAAAGCAAA 845
                           v   vi      v   v                i     v    v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_183993327_    846 AATAGACCAG--GGACTTATTATCAAACTCAAAAGCATCTGCTATGCAAA 893
                               iv i--      --i      v i    i v i  ivv v    
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTT--CATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_183993327_    894 GGAAACAATTAACAGAGTGAAATT-TATCTGATAAA--GGGTTAATATA- 939
                            v  v  i  v i       vv-i v iv i i --   vv  v   -
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_183993327_    940 ---CAAA--ATATATAAGACA---GTCCTGTAACTCAGTAGCAAATACAC 981
                         ---    --      vv  i --- v i    v -   -----    i i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATC-CAG-----AATATAT 768

  chr1_183993327_    982 ACACACACACACACACACACACACACACACAGAGGGAGAGAGAGAGAGAG 1031
                          v v -------  v vi   -  v  - i ------- v i i   v i
  L1M4_orf2#LINE/    769 AAAGA-------ACTCTTACA-ACTCA-ATA-------ATAAAAAGACAA 802

  chr1_183993327_   1032 AGAG---ATTTTAAGAATAGGCAAAAGTCCTGAACATACATTTCCCCAAA 1078
                          v i--- v  ?  i   i      i vii    i v       i     
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_183993327_   1079 GAAAACACACACAAATGGTCACCAGATATATGAAAAAATGCTCAGCATCG 1128
                            i i i   --     i  vi iii i       i       i    i
  L1M4_orf2#LINE/    853 GAAGATATACA--AATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_183993327_   1129 CTAATCAT 1136
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.19 (83 / 70)
Gap_init rate = 0.03 (18 / 631), avg. gap size = 2.67 (48 / 18)  


 872 28.47 10.12 3.43  chr1_184002622_184004191.rev      502  1084 (486)    L1M4_orf2#LINE/L1      287   908 (0)  

  chr1_184002622_    502 GACAAATAGACCAGTAGAATAGA-----GAATCCAACAAGTGACCCAGAT 546
                             v     i  i i       -----  i    iv  vvi     v i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_184002622_    547 ATATGAGGTTCCA--TGAATTATAACTAAGGTGACACTAAAGTAG-AGAG 593
                           v iv   --  --   v  vii  v i    v  -- i vi v-vi v
  L1M4_orf2#LINE/    337 ATTTATGGT--CAATTGATTTTCGACAAGGGTGCCA--AGACCATTCAAT 382

  chr1_184002622_    594 GGGGAGAAGATGGTCTTTTTGCTAAACAGTTCTGGGTCTAGGTCAGTTGG 643
                              i ii  i       iivi   ii  v     --- ---  ii   
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG---A---CAACTGG 426

  chr1_184002622_    644 CTAAACATATGAAGCAAAAAAGTTACCTTG-ATTCCTACCTTGTACCATG 692
                         v  ?v  i   ---     i i v vv   - ii       iii     i
  L1M4_orf2#LINE/    427 ATAKCCACATG---CAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_184002622_    693 TATAAAAAC-ATTTCCAAGTGAATCATA--CATAAATGTGAATGGTAAAT 739
                           i     i- vi  v  i  i    ? -- v       i iv v    v
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_184002622_    740 TGACAAAGCTTTTGGGAAAAAAAGTAGGCAAATATCTTCA-------GGA 782
                         iv i   i  i  i i i    vi    ?iv v      i-------  i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_184002622_    783 TTA-----TGA------AGATA---CA--AAAGGTGCTAACTCCAAATGA 816
                            -----  i------     ---  --   i ii v i vv    v  
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_184002622_    817 AATCATTGATTATAAGATTACAGTT--TTAACTTTAAAAATCTGTTTA-T 863
                           vv  v   ---- i   iv v  -- i  vv       ii v v i- 
  L1M4_orf2#LINE/    624 AAAAATAGAT----AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_184002622_    864 TCACAG-ACACCATTAAGA----GAAAAGGCAAACCACAGAGCAGGAGAA 908
                            v  -    i  i    ----      i   v       iii      
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_184002622_    909 AATAGTTGCAACACATAGATCCAATAA---------ATCCAGAATGTACA 949
                             v      vv    v   ii    ---------         i  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_184002622_    950 AATGACTCCTACCAATTTAG----AAAAAGTCATACAAGTCAATGCAAAG 995
                           vi    i   -  i i i----      v  v i  vi    v?   i
  L1M4_orf2#LINE/    770 AAGAACTCTTAC-AACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_184002622_    996 -TTGTCAAAAACCTTCTATAGGACTTTTATAACAAAGAAAAC-TA-AAAT 1042
                         - v v    iivi  vv    -  v   v v-       i i-  -    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAG-ACATTTCTC-CAAAGAAGATATACAAAT 866

  chr1_184002622_   1043 GACAAATAAATATAAGAAAAATGGCTCAAGGTCCAGGCACGG 1084
                          i v     ii i v     ivv      vi  v????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (92 / 70)
Gap_init rate = 0.05 (29 / 622), avg. gap size = 2.72 (79 / 29)  


3151 27.25 1.33 0.33  chr1_184032736_184035359.rev     1235  2133 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184032736_   1235 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1284
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184032736_   1285 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1334
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184032736_   1335 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 1379
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_184032736_   1380 TGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGAA 1429
                              viiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_184032736_   1430 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 1479
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_184032736_   1480 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACACAGATATAGACCAA 1529
                               i   i    ii         i iv ii i v v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_184032736_   1530 TGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCGCATATCTACAACTAT 1577
                              i    i--    i  --    i   vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_184032736_   1578 CAGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAGGATTCCCT 1627
                         iv   i  i     ivv  v   i vi vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_184032736_   1628 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1677
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_184032736_   1678 AACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGATT 1727
                          ii    i    v   i i   v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_184032736_   1728 AAAGACTTACATGTTAGACTTAAAACCATAAAAACCCTAGAAGAAAACCT 1777
                          ?    i  v    v   vi      i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_184032736_   1778 AGGCA-ATACCATTTAGGACATAGGCATGGGCAAGGACCTCATGTCTAAA 1826
                            ?i- v i -  iiv   v v  vv i     v iii  v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_184032736_   1827 ACACCAAAAGCAATGGCAACATAAGCCAAAATTGACAAATGGGATCTAAT 1876
                                     vvi      v   vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_184032736_   1877 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATTAGAGTGAGCA 1926
                         i   v v  i i   i  ii vv    i  v    i  vv i     iv 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_184032736_   1927 GGCAACCTACAGAATGAGAGAAAATTTTTGCAACTTACTCATCTGACAAA 1976
                          i     i        i        v       v i ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_184032736_   1977 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 2026
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_184032736_   2027 AACAA----CCCCATCAAAAAGTAGGCAAAGGATATGAACAGACACTTCT 2072
                         i    ----   v  i?    i i          v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_184032736_   2073 CAAAAGAAGACATTTATGCAGCCAAAAAACACAGGAAAAAATGCTCATCA 2122
                          v        i  vi viii     v  i    v     i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_184032736_   2123 TCACTGGCCAT 2133
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.14 (15 / 7)  


3237 27.20 0.44 0.44  chr1_184044806_184051083.rev     4880  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184044806_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATCGTGAAAAT 4929
                              ii i  i     i      i v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184044806_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184044806_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_184044806_   5028 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_184044806_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_184044806_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_184044806_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_184044806_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_184044806_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_184044806_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_184044806_   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_184044806_   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_184044806_   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_184044806_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_184044806_   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_184044806_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_184044806_   5676 ACACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          v     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_184044806_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_184044806_   5776 CTCACTGGCCAT 5787
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 662 28.47 9.49 1.82  chr1_184055383_184058093      920  1193 (1518)    L1M4_orf2#LINE/L1        6   300 (608)  

  chr1_184055383_    920 AAATATACCATGATCCTGGATGGCAAGAGTCGGTGTTGTTCAGA---CAC 966
                          i    v     v  v     v v    v iii i     v   ---  v
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_184055383_    967 TACTTGTCCCCAAATTGTTCTATGAATTTATCATAATTCACTG--AAAAT 1014
                             ---          v    iii   i v ii   i -  i--     
  L1M4_orf2#LINE/     56 TACT---CCCCAAATTGATCTACAGATTCAACGCAATCC-CTATCAAAAT 101

  chr1_184055383_   1015 CTCAACAGTTTTTTTTCATATGAACCATCATGTTGATTCTAAAATTTATA 1064
                          i  i v ii      -ii vi  iiiv  v i    i        i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_184055383_   1065 AGGAAAATCACGGAATTTTCATTGGCCACAACAATTGTGAAAAAG----- 1109
                         v     vv  v  i iiivv v i    v      iv        -----
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_184055383_   1110 -----TTGAAGTATGCACACTATCTGATGTCAAGACTTTC-------CTA 1147
                         -----   i  v iv      vi ii  v    i    v -------   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_184055383_   1148 CAGTAATTAAGACAGCAT---ATTCACAATAGCAAAGACATGGA-ATCAA 1193
                                i       ii --- i vi  vv  v v      iv -     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

Transitions / transversions = 1.29 (44 / 34)
Gap_init rate = 0.03 (9 / 295), avg. gap size = 3.44 (31 / 9)  

1392 27.26 7.58 1.61  chr1_184055383_184058093     1599  2218 (493)    L1M4_orf2#LINE/L1      252   908 (0)  

  chr1_184055383_   1599 AGTTATTAAAA-AGTGTAATATTGGTGAAAGAATAGATACATAGGTCAAT 1647
                            v  i  i -     ii  i   iiv   i     i i    i     
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_184055383_   1648 GGAACAAA-------GTGCAAAACAGAACTTGCATATATATAGTTCATTG 1690
                             i i -------  v  i  vvi   iiii i  v   i  iv    
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_184055383_   1691 ATTTTTGACAAAGACTCAAAGGCAATTCAATGCTAAATGA-TAACCTTTT 1739
                              i     i iiv v   i v        vvi  v  -  ii     
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_184055383_   1740 CAACAGA--GTGCTGAAACAACTAGACATCCATATTTAAAA--AGGAACT 1785
                              i --      ii      i  i ?   i  vi    -- v   v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_184055383_   1786 TCAAATCATACCTTGCAGCATTT-TAAAATTTAA------ATGGATCCTA 1828
                          vi vi v     ii  v   v -i    v    ------       v? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_184055383_   1829 AACCTAAATAATAAACCCAAAGCTGTAACATTTCTAGGCTATGTCATAGA 1878
                         i        ivv i v i   i  i   v i ii   ivv viv     i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_184055383_   1879 AGAAAAACTTTGGTACTCTAGGTTAGAAAATGTTTTCTTAAGTAGTACAC 1928
                         ? v   v   i vv  ii i      iv    v       ii  vv    
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_184055383_   1929 -AAAAACACAACTCATAAAAGAAAAAAT-GATCAATAGGAATATATCAAA 1976
                         -    i     viv i            -   v   v   v vi      
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_184055383_   1977 ATCAACAGCTG--ATGCT-CAAATGACCATATTAAAAAA-TAAAACCATA 2022
                           i  v i  v--i    -    v   vv   i  i   - i   vv i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_184055383_   2023 AGCTACAGATTGAGA-AAAATATTGTTAAAT-ATATATCTGATACAAGTC 2070
                          v i     v  i  -        vvi    -            vii v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_184055383_   2071 T-G---CTGAGATTT-TAAAGT-TTCTTAAAACTCAACCGCAATAATAAT 2114
                          - --- iiii  v -     v-i     v       ------      v
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAA------TAATAAA 795

  chr1_184055383_   2115 TTTTAAAACAG-TAAG------AAAAAATGGGCAAAAGAT------GGCC 2151
                         ----  i   i-   v------?             i   ------i v 
  L1M4_orf2#LINE/    796 ----AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_184055383_   2152 CATTCACCTAAGGAGATAGACATTTGGCCAATAAATAGATGAAAAGATAT 2201
                         vv   v  v   i     v   vv          ii v          ii
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_184055383_   2202 TAACCATCACTATTCAC 2218
                          v v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (91 / 74)
Gap_init rate = 0.04 (23 / 657), avg. gap size = 2.48 (57 / 23)  


3114 26.82 1.68 0.34  chr1_184098429_184102018     2215  3109 (481)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_184098429_   2215 GGAAAAACATTCCATGCTCATGGAAAGGAAGAATCAATATCATGAAAATG 2264
                              i i  i     i       vv      v i     ii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_184098429_   2265 GCCATACTGCCCAAAGTAATTTATAGATTCAATGTCATCCCCATCAAGCT 2314
                           v     v      v i  i  i        i iv     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_184098429_   2315 AACAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTCGT 2362
                         vv  iivi i  i  ii     -   -- v  i  - iii        i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr1_184098429_   2363 ATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATTCTAAGCAAAAAGA 2412
                               viiv  ii  v  viv        i     ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_184098429_   2413 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGGCT 2462
                               i      vv   ii  v  ii i      vivi       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_184098429_   2463 ACAGCAACAAAAACAGCATGGTACTGGTACCAAAACACAGATATAGACCA 2512
                             i  iv  i    ii         i iv ii i v v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_184098429_   2513 ATGGAACAGAAAAGAGACTTCAGAAATAACACCACACATCTATAACCACC 2562
                               i    vv    v i         vv   i    i   iii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_184098429_   2563 TGATCTTTGACAAACCTGATAAAAACAAGCAATGGGGAAATGATTCCCTA 2612
                             i  i     ivv  vi  i v  vv           vi  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_184098429_   2613 TTGAATAAATGGTGTTGGGAAAATTGGCTAGCCATATGCAGAAAGCTGAA 2662
                           v  i        i     v  i   v  ?   i     i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_184098429_   2663 ACTGGATCCTTTCCTTACACCTTATACAAAAATTAACTCAAGATGTATTA 2712
                         ii    i  i v   i     v                   i   v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_184098429_   2713 AAGACTTAAATGCAAGACCTGAAACCATAAAAATCCTAGAAGAAAACCTA 2762
                         ?    i      i    v  i    i      v  i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_184098429_   2763 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 2811
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_184098429_   2812 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 2861
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_184098429_   2862 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 2911
                            v v  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_184098429_   2912 CCAACCTACAAAATGGGAGAAAATGTTTGCAGTGTATCCATCTGACAAAG 2961
                         v     i   i             i      ivvi  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_184098429_   2962 GGCTAGTATGCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA- 3010
                          i  v    v      v  i        ivv    v iv i  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_184098429_   3011 ACAAACAATCCA-TCAAAAAGTGGGTGAAGGATGTGAACAGACACTTCTC 3059
                              i  i   - i?    i    ii      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_184098429_   3060 CAAAGAAGACATGTATGCAGCCAACAA--ACATCA--------TCATCAT 3099
                                  i  ii viii     i  --    v --------   v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_184098429_   3100 CACTGGTCAT 3109
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 2.00 (18 / 9)  


2533 22.01 5.79 2.70  chr1_184139191_184142399.rev     1942  2718 (491)    L1M4_orf2#LINE/L1      108   908 (0)  

  chr1_184139191_   1942 TATCTTTTTTAAATAGAAATTGACCAGCTA-----------------GAA 1974
                          ii       i--i          v    i-----------------   
  L1M4_orf2#LINE/    108 TGCCTTTTTTG--CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_184139191_   1975 ATACAAAGAACCTAGAATAGCCAAA-CAATTTTGAAGAAAGAAGAATAAA 2023
                           i   i i   i            -    i     -         i   
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAACAAA 204

  chr1_184139191_   2024 TTTAGAAGAC--ATATGACCTGGTT-CAACAGCTTCCCTGGAAGCT---G 2067
                         v  i  i   -- i ivv  iii  -   - i   v ivvi     --- 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAA-AACTTACTACAAAGCTACAG 253

  chr1_184139191_   2068 TAATCAAGA--GTGTGGTACTGGCATAAAGGTAGACACATAGATCAATGG 2115
                                  --                 i i      i            
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_184139191_   2116 AACAGAA---------CAGAAATAAACACATATATATAAGATTAATCGAT 2156
                           i    ---------           v    i  v  v i i   i   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_184139191_   2157 CTGCAACACAATTGCCAACATAATTAAATGGGGGAAAAGATAGTATAT-A 2205
                         i v i   viiv      v iv   v       i  i -     v v -v
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTTC 402

  chr1_184139191_   2206 AAAAAATGGTTCTAGAGTAATTGAAGATTCACGTTGTAGGGAAAAGGCAA 2255
                           v       v  i iii  i  i v ?i   i ----- v     ----
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACAT-----GCAAAAG---- 443

  chr1_184139191_   2256 GAATAAGCATGGACCCTTACCTCACACCACAAAGAAAAAT-GACTTGTAA 2304
                         -   i ivv       i            i v v      -i   iiv  
  L1M4_orf2#LINE/    444 -AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_184139191_   2305 TAGGAT-ATAGCCCTAAATTTAAGTG-TAAAACCATACAACTTCTTAGA- 2351
                          -    - ?  v       v    v -      i   v    -      -
  L1M4_orf2#LINE/    493 T-GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAA 540

  chr1_184139191_   2352 TAAAGCATAGAAGATAATCCTTGTGACTTTGGATTAAGAAAAAAATTCTT 2401
                         v   i     i? vv    i i     i    i   i v  viiv     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_184139191_   2402 GGATATAAGGCAAAAAGCATAATACCTAAAACAAATAAAAATA-ATAAAC 2450
                         i     i vi v       i  -i --  v v  iv       -     i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAA-GC--AACAAAAGAAAAAATAGATAAAT 637

  chr1_184139191_   2451 CAGACTTCATAAGAATTTAAATCTCTTGTTTTTCAAAAGACACTATTGAG 2500
                         ii        v i    v   v  i    vi      i        ii  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_184139191_   2501 AAAATGAAAAGATAAGCCACAGAGAAGCAAAAAGTACCTGCAAAACATAT 2550
                            i        i  v       ivi v i   i  ii      v     
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_184139191_   2551 TTCTGATAAAAGACTTTTATCCAAAATATATAATACATTCTTACAACTCA 2600
                         v        ii     v      i         viv i            
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_184139191_   2601 ACCATAACAGGACAA----TCTAATTAGAAAATGGACAAAAATATTTGAA 2646
                          iv    v i     ----i i    ?i       i    ii-       
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG-ATTTGAA 836

  chr1_184139191_   2647 TGAACACTTAACCAAATAAGATATACAAATGGCAAATATGCACATGAAGA 2696
                          ii   i  vv     v                v    v         i 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_184139191_   2697 GGCCCTAAACATCATTAGTCAT 2718
                          iiv  v       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (103 / 64)
Gap_init rate = 0.03 (25 / 801), avg. gap size = 2.64 (66 / 25)  


3094 23.00 3.50 4.05  chr1_184193152_184195508.rev      962  1874 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184193152_    962 TGTAAAGATACCCTGTGTTCATGGATTGGAAAAATTACTGTTGTTAAAAT 1011
                           v       i  ii                i v   v i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184193152_   1012 GGCCATATTACTCAAAGTGATCAACGAATTCAATGTACTCCCTATAAAAA 1061
                            v   i v i    v     v  ii      i i v       v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184193152_   1062 CTCCAATGGCATTTCTCACATAAATAGAAAAAACAATCCTAAAATTGGTA 1111
                         ii   iiv  v   i ii  v    v  v  ivii           vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_184193152_   1112 TAAAACCATAAAATACT----GCAACTAAATCAATCTTGAGAAAGAA--- 1154
                          ii  viii  iiv  i----ii i i   v         i      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_184193152_   1155 CAAAGCTGAAGGCATCACGCTTTCTGACTCCAAGCTATATTAAAAAGCCA 1204
                              i  i   vv    i   i ii i i   iviv  i  v     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_184193152_   1205 TAGTAATCAAAACACTG--GTACTGGCACTAAAAAAAAAAAAAAAAAAAA 1252
                         i         i   v  --         i----------------  ii 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCAT----------------AAGGA 284

  chr1_184193152_   1253 CAGGCACATACACCAATGGAACAAAATAGAGAGATCAGAAATAAATGCAT 1302
                         i  i  i   v i        i i   v     vi          iv   
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_184193152_   1303 ACATATATGGTATACTATTGTGTGACAAGGGCATCAATAATATACAATGG 1352
                             v      vv i iv v vi        iii   v vi  v      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_184193152_   1353 GGAGAG-----TCGCTTCAATAAACAGTGTTCGGAAAAATGAATACCCAC 1397
                            i  -----  vi     i   ii   i v   v  v  i   ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_184193152_   1398 ATGTAGAAGAATGAAATTGGATCCCCATTTTACACCATGCACAAAAATTA 1447
                            i i         i     i   i ii i       ii          
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_184193152_   1448 ACTCAACAAGGATTAAAGACTTAAATGTAAGACCTGAAACTGTAAAACTC 1497
                               v v    i ?    i           v  i     i        
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_184193152_   1498 TTA-AAGAAAAAATAGAAAAAAACTTCCTTGAAATTGGTCTTGGCAATGA 1546
                            -       v    i?iv   ii i v   vv    vi v       i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_184193152_   1547 TTTTTTAAATATGACACCAAAAACACAGACAACAAAAGTAAAATTAAACA 1596
                            i   i              i    ii         v    v  i i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_184193152_   1597 GTTAGGACTATAT-AAAACTAAAAAGCTTCTGTA-TGCAAAGGAAACAAT 1644
                         iv v     vi  -    i      -   i   i- v       v  v  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chr1_184193152_   1645 -------ATAAAAAAGCAACTTACTGAATGGGAGAAA-----TGCAAACC 1682
                         -------i i    ii    ii  v            -----      i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_184193152_   1683 ATATATCTGATAAGAGATTACTGTCCTAAATATATAAGGAACTCATACAA 1732
                                       i  i vv i   vi         i      v     
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_184193152_   1733 CTCAATAGCAAAAAATCAAAAACAAAAACAACCATGAATACTGCAATT-A 1781
                                ii     i------     --i    ----------     - 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAG------ACAAA--TAACC----------CAATTWA 815

  chr1_184193152_   1782 AAAATGGGCAAAGGATCTGAAAAAAAACATTT-TCTAAAGTAGACATACA 1830
                                         i    v i --     -  i    v   i     
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGA--CATTTCTCCAAAGAAGATATACA 863

  chr1_184193152_   1831 AATGGATATCAGGTACTTGAAAAGGTGC-AAATACTACAAAATGC 1874
                              vi vi i i  v       i   -v  i ii ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (136 / 71)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.83 (69 / 18)  


3262 27.09 0.44 0.44  chr1_184297961_184304236     4876  5783 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184297961_   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184297961_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184297961_   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_184297961_   5024 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_184297961_   5074 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5123
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_184297961_   5124 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5173
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_184297961_   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5221
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_184297961_   5222 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5271
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_184297961_   5272 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5321
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_184297961_   5322 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5371
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_184297961_   5372 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5421
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_184297961_   5422 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5471
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_184297961_   5472 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5521
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_184297961_   5522 CTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5571
                         ii   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_184297961_   5572 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5621
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_184297961_   5622 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5671
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_184297961_   5672 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5721
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_184297961_   5722 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5771
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_184297961_   5772 CTCACTGGCCAT 5783
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3027 25.00 1.95 0.26  chr1_184440579_184443200      981  1748 (874)    L1M4_orf2#LINE/L1        9   789 (119)  

  chr1_184440579_    981 TATCCTGTGTTCATGGATTTGAAGAATTAATATTCTTAAAATGTCCATAC 1030
                              ii            v     v        v    i   v v    
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr1_184440579_   1031 TATCTAATGCGAGCTACAGACTCAATGCAATTTCTATCAAAACCTCAA-T 1079
                          vi i  vvi  v       i    i     ii         i i  i- 
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr1_184440579_   1080 GGCATTTTCCCAGAAATAGAAAAAAATAACCCCCAAATTCATATGGAACC 1129
                          v v    iv       v  v  iv- i i  iv              vi
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATGGAAAT 157

  chr1_184440579_   1130 CCCAAAATTCCCAAATAGCCAAAGCATTTCTGAGAAAGAAGAACAAACTT 1179
                         v v iiivi  vi          i  v ii   i             v  
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_184440579_   1180 GGGGGCATTGCATTTCCTGATTTCAAAATATATAACAAAGCTACAATAAT 1229
                           i  vv ii  i    ii         iv  iv           i    
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_184440579_   1230 TAGGAAAGTATAGTACTGGCATAAAAAGAGAAATGTAGACCAATGGAAAA 1279
                         i i  v   i i            ii v   v  i    i        v 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_184440579_   1280 GAATAGAGAGCTCAGAAATAAATTCATACATCTACAGTCAACTGATCTTT 1329
                             v     ii          ii       i  ii     i    i  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_184440579_   1330 GGGAAGGATGCCAAAAACACATAATAGGGACACAACAGTCTCTTTAA--- 1376
                          iv    i      i v  ivi   i    v v  i     i  i  ---
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_184440579_   1377 -TGGTGTTGCCAAAACTGGATATCAACAGGCAGAAGAGTGAAACTGAAAC 1425
                         -     i  vv v         ? v   v   i    i    ii  i v 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_184440579_   1426 TTTAACTCACACCATATACAAAAGTCATCTCAAAATGGATCACAAAC--A 1473
                         ii  v                  i i v              ? i  -- 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_184440579_   1474 AACATAAGACCTGAAATCATAAAACTATTAGAAGAAAACATAGCTA-AAA 1522
                           ii     v  i   ii        v                v?i-   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_184440579_   1523 CATTTTTTAC-TTGGTCTGGGCAATGATTT-TCAGATACGATACCAAGAG 1570
                         iv  iv v  -    vi i       i   - i     i  i     i  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_184440579_   1571 CATAGGCAATTAAAGCAAAAATAGATGA----GACTATGGTAAACTAGAG 1616
                           i i    iv    v          i ----    viivi   v vi i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_184440579_   1617 AGCTTCTTCACAGCAACAGAAGCAATCAGCAGAGTAGAAATATAACCTGC 1666
                          i   i vii vv   vi  vi v    iv i   ii   v i    ii 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_184440579_   1667 AGAATGGGAGAAAATATTTGCAAACTATATATCTGATA-GGGATTTAATA 1715
                                                 ii            -    i  i-  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG-TA 756

  chr1_184440579_   1716 TCCAAAATATATAAGGGTCTCATGCAAATCAAT 1748
                             i         i iv   v i   v     
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAAT 789

Transitions / transversions = 1.74 (120 / 69)
Gap_init rate = 0.01 (10 / 781), avg. gap size = 1.70 (17 / 10)  

 279 20.55 0.00 1.37  chr1_184440579_184443200     2058  2130 (492)    L1M4_orf2#LINE/L1      837   908 (0)  

  chr1_184440579_   2058 TAAACATTTCTTAAAAGAAGAAATAAAAAATGGCCAATAGATATATGAAA 2107
                           i        iv        v   v   -         iii i      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACATGAAA 885

  chr1_184440579_   2108 AGGTTCTTAGCTTCGCTATTAGG 2130
                           i v  i i v  i????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1)  


3128 27.78 0.44 0.33  chr1_184457570_184460583.rev     1617  2523 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184457570_   1617 TGGAAGAACATTCCGTGCTCATGGATAGGAAGAATCAATATC-TGAAAAT 1665
                              ii i  i  i  i        v      v i     i- v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184457570_   1666 GTCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1715
                          v v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184457570_   1716 TACCAATGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTAAAGTTCA 1763
                          v   iivi i  i  ii    i-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_184457570_   1764 TATGGAACTAAAAAACAGCCCGCATTGCCAAAACAATCCTAAGCCAAAAT 1813
                                v iv  iiv v  v v  v            i i ivv i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_184457570_   1814 AACAAAGCTGGAGGCCTCATGCTACCTGACTTCACACTATACTACAAGGC 1863
                                i      v    ii  v  ii i    v viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_184457570_   1864 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1913
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_184457570_   1914 AATGGAACAGATCAGAGACCTCAGAAATAATACCACACATCTACAACCAT 1963
                                i   viv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_184457570_   1964 CTGATCTTTGACAAACCTGACAAAAGCAAGAAATGGGGAAATGACTCCCT 2013
                         i    i  i     ivv  v   i v  vvv          vi ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_184457570_   2014 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 2063
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_184457570_   2064 AACTGGATCCTTTCCTTACACCTTATACAAAACTTAATTCAAGATGGATT 2113
                          ii    i  i v   i     v         v    i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_184457570_   2114 AAAGAATTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 2163
                          ?   vi    ii v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_184457570_   2164 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 2212
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_184457570_   2213 ACAGCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAAT 2262
                            v        vvi     v    vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_184457570_   2263 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 2312
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_184457570_   2313 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 2362
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_184457570_   2363 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAA 2412
                           i  vi          v  i         vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_184457570_   2413 AACAAACAACCCTATCAAAAAGTGGGCGAAGGATATGAACAGACACATCT 2462
                         i     i     v  i?    i     i      v    i     iv   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_184457570_   2463 CAAAAGAAGACATTTATGCAGCCAACGGACACATAAGAAAATGCTCATCA 2512
                          v        i  vi viii     iiii     i i  i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_184457570_   2513 TCACTGGCCAT 2523
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


3164 27.64 0.44 0.44  chr1_184504976_184509787.rev     3414  4321 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184504976_   3414 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3463
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184504976_   3464 GGCCATACTGCCTAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3513
                            v     v  i  iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184504976_   3514 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3561
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_184504976_   3562 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 3611
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_184504976_   3612 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAATTATACTACAAGGC 3661
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_184504976_   3662 TATAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 3711
                           i     i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_184504976_   3712 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGGTGCATATCTACAACT 3759
                                i    i--    i  --        vvviii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_184504976_   3760 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3809
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_184504976_   3810 CTATTTAATAAATGGTGCTGGGAAAACAGGCTAGCCATCTGTAGAAAGCT 3859
                           v  i  i              v   v  v  ?   iv  i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_184504976_   3860 GAAACTGGATCCCTTCCTTGCACCTTACACAAAAATCAATTCAAGATGGA 3909
                            ii    i    v   ii    v  i        i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_184504976_   3910 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3959
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_184504976_   3960 CTAGGCATTGCCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4009
                         v    ?i viviv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_184504976_   4010 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 4059
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_184504976_   4060 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4109
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_184504976_   4110 AGGCAACCCACAAAATGAGAGAAAATTTTCACAACCTACTCATCTGACAA 4159
                           i         i    i        v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_184504976_   4160 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4209
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_184504976_   4210 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGTCACTTC 4259
                          i     i     v  i?    i           iv    i  v  i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_184504976_   4260 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 4309
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_184504976_   4310 ATCACTGGCCAT 4321
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2335 26.86 1.70 5.31  chr1_184534091_184536474      952  1893 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184534091_    952 TGGAGAGGTATTCTATGTTCATGGATAGGAAGATTCAATATTGTTGAGAT 1001
                             i  i   i i            v      i i         i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184534091_   1002 ATCATT-CTTCCCAACTTCATTTATAAATTCGTTGCAATCCCAATCAAAA 1050
                         iv  v -  i     v  v  i  i i    ivi        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184534091_   1051 TTGAAGCAGGGTAGTTTCTAGATATTGATGAAATAATCATAAAATGTATA 1100
                          ivv   v vv vv   vi   v     ii iv i   v      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_184534091_   1101 TAAATAGACAAAAGACCTAAAATTATCAACAAAATACTGAACATGATAAA 1150
                          ii v vi   ii    i i   vii   v v   vi    v v  vi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_184534091_   1151 GAAATTTGGAGGACTGGCATGAATCACTTTGTAGACTTTATACAAGACTA 1200
                         v   v          vi  ivvvi  v   vv i    vv     ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_184534091_   1201 CTGTAACTGAGTATTGTATTGTTTTGTGTTGTATTGTATTGTATTGTATT 1250
                          v    iii  ----ii -------    v   i  --------- i  -
  L1M4_orf2#LINE/    251 CAGTAATCAAG----ACA-------GTGTGGTACTG---------GCAT- 279

  chr1_184534091_   1251 GGTGAAAGA-AAATAAA-AGAGCAGTGCAATAGAATAGAGAGCCCAGGTA 1298
                         ----  i  - i i v -   v  i  v        v     i    iv 
  L1M4_orf2#LINE/    280 ----AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_184534091_   1299 TAGATCCA-GCAAATATAGTCAAGTTATCTTTTACAAAAG-ATTAAAAGT 1346
                           i i   -i  vv   i     v v  i  iv    ii -iii  i vi
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_184534091_   1347 AACTCAGTGGAGAAAGTATAGTCTTTTTAGCAAATATTTCCAGAATAAAT 1396
                          -i   i   i     v          i i     iv v ii i i  v 
  L1M4_orf2#LINE/    376 A-TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_184534091_   1397 GGAAAGCTACATGTAAAAATATGAAACTATATACAAGCCTTA-GCCTTTC 1445
                            v ? i     i    iv     ii iv iv vvi   i -i  v vi
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_184534091_   1446 ATAAAAATGAACTCAAAAGGTATAGGAGACTTGAGCATAAAATGTAAAAC 1495
                          i      v         v v  vi?    i -------        i v
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCT-------AAATGTAAGAG 517

  chr1_184534091_   1496 CTGTCTTCCATTCTAGACTATAGAATGTCTAGAAGACAATATAGTAGAAA 1545
                           i----------- i      i  ivii       v  i    v? v  
  L1M4_orf2#LINE/    518 CTA-----------AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_184534091_   1546 ATGTAGATGACCTTACAGTT-GATAATGACTTTTTTTTTAGATGCAACAC 1594
                           v vvi       i-i   - ii    i----   i      iii    
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTG-GGTTAGGCAATGG----TTTCTTAGATATGACAC 601

  chr1_184534091_   1595 TAAAAGCATGATTTATGAAAGAAAAAGTTGATAAATTGGACTACGTTACA 1644
                         i       ii viv ii         i v             v i i v 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_184534091_   1645 ATTTAAAACTTCTGCACTTTGAAAGTCATTACTAAGAGAATGAAGAGACA 1694
                            v       i  ii   ii  i v  i  ii    i i    i     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_184534091_   1695 AGCCAGATTCTGTGAGAAAATATTTGCAAAACTTTTATCTGATAAAGGAC 1744
                          v   v vvv  v                 v v v          i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_184534091_   1745 TGGTAT--AGAAAATATGCAAAATTCTTTAAAACTCAA-AAGAAGAA-AT 1790
                          v    --    v    iv i  i    - v       -  v  i  - i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTT-ACAACTCAATAATAAAAAGAC 800

  chr1_184534091_   1791 ATACAACACACTTAAAA----GGCAAAA-ATCTGAAATGATACCTCATCA 1835
                          v i   v  v  ?   ----      i-  i    vv  i ii  vi  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_184534091_   1836 AAGATGATATACAGATGGCAAAAAAGCATATGAAAAGATGCTCAACATGA 1885
                             v        i     v  v     i                   v 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_184534091_   1886 TGTCATTA 1893
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.33 (142 / 107)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.00 (66 / 22)  


1116 26.76 0.33 0.33  chr1_184702711_184705620.rev     1216  1514 (1396)    L1M4_orf2#LINE/L1        1   299 (609)  

  chr1_184702711_   1216 TGGAAACATATCCCATGCTCATTGATAGGAAGAATCAATATTGTGAAAAT 1265
                               v          i    v   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184702711_   1266 GACCATACTGCCCAAATTAATCTACAGATTCAATGCAATTCC-ATCAAGA 1314
                          i v     v        i              i     i  -     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184702711_   1315 TGCCATCATCATTTTTCACAGAACTAGAGAAAAACAATCCTAAAACTCAT 1364
                          v   v vv v     ii     v v  v  -ivii         i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_184702711_   1365 ATCGTACCAAAAAAGAGCCAGCATAGCCAAGGCAATACTAAGCAAAAAGA 1414
                           v v viiv  ii  v    v        ii    vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_184702711_   1415 ACAAATCTGGAGGCATTGCATTATCAGACTTCTAATTATACTACAAGGTT 1464
                              vi      vv ii  i vi vi i   v  viv        i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_184702711_   1465 ATAGTTACAAAAACGGTATGGTACTGGTATAAAAATAGGCACATAGGCCA 1514
                          i   v iv  i  i  i         i    ii    i  i    ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

Transitions / transversions = 1.35 (46 / 34)
Gap_init rate = 0.01 (2 / 299), avg. gap size = 1.00 (2 / 2)  

1971 24.92 3.93 0.49  chr1_184702711_184705620.rev     1810  2419 (491)    L1M4_orf2#LINE/L1      278   908 (0)  

  chr1_184702711_   1810 ATAA--ATAGGCATATAGACCAATGGAATAGAATAGAGAACCCAGAAATA 1857
                             --    i        i              v    ii         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_184702711_   1858 AAGTCAAATACTTACAGCCAATTGATCTTTAAAAAGCATGCAAAAAC-AT 1906
                           vi  v i i   ii i        i  ii v   vi   v  i  -  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_184702711_   1907 AAAGTGGAGAAAGGACATCCTATTAAATAAATGTTGCTGGGAAAACTGGC 1956
                         vv i   i     i i vi  v  v  i     v        v      -
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG- 426

  chr1_184702711_   1957 ATA-CCACAAGTCAAAGAATAAAACTGGATACCCATCTCCCATTTTCTAC 2005
                            -     v iv       i  ii    iv  i i   v  iiv v   
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_184702711_   2006 AAAAATCAACTCAAGATGGATCAGTGACTTAAATCTAAGACCTGAAATCA 2055
                               i       i        ?v   i     v     v  i   ii 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_184702711_   2056 TAAAAATTCTAGAAGATAGCATTGGGAAAGATTTTTTTGGACATTGGCCT 2105
                              v ii       v i   v  ?iv i  i  iv  -  v    vi 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTT 575

  chr1_184702711_   2106 CAGCAAAGCATTCATAACTAAGACCCCAAAAGAAAATGCAGCAAATAAAT 2155
                         vi    v vv   v  iv  v   v       v v v   i    vi  v
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_184702711_   2156 AAATAAATAAATGAGACCTAAT-----TTAAAAAGCTTCTGCACCGCAAA 2200
                              i      vi   i v  -----       -   i  ii iv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAA 674

  chr1_184702711_   2201 AGAAATAATCAGCAGAGTAAACAGACAACTCACAGAGTCGGGGGAAATAT 2250
                         i  v iv    iv i   i  v       i      i v  i i      
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_184702711_   2251 TTGCAAACTACGCATTGGACAAAGGGCTAGTATCCAGAATCTACAA-GAA 2299
                                ii iii  iv  i  i  i  v           v  i  -   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_184702711_   2300 -----ACAAATCAGCAAGAAAAA---AAAT--CCCA-TCAAAAAGTGGAC 2338
                         -----    v   ii  v     ---    --    - i?    i   i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_184702711_   2339 AATGGACACGAATAGACATTTCTC---ACAAGATATACAAACAGCCAACA 2385
                           v   ivi               --- v            ii     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_184702711_   2386 AACATAGAAAATAATGTTCAACATCACTTATCAT 2419
                          i  i vi   vi   i         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (89 / 60)
Gap_init rate = 0.02 (13 / 631), avg. gap size = 2.08 (27 / 13)  


 359 21.74 1.45 0.00  chr1_184751036_184752655.rev      430   498 (1122)  C L1M4_orf2#LINE/L1   (321)   587   518  

C chr1_184751036_    498 CTAAAATTATAAAATTCCTAGGAGAAAACATAAGCGCAAAT-TCTGTGAC 450
                               i       i  i   i          i ? i    - ii     
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

C chr1_184751036_    449 TTTGGATTTGACAACAGTTT 430
                         i    i  v i   ii    
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTT 587

Transitions / transversions = 13.00 (13 / 1)
Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1)  

1805 21.99 15.51 2.06  chr1_184751036_184752655.rev      503  1134 (486)    L1M4_orf2#LINE/L1      192   908 (0)  

  chr1_184751036_    503 AAAGAC-AACAAATTTGGAGGACTCACATTTTCTGATTTTAAAACTTACT 551
                              v-      v              i  i ii    i          
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_184751036_    552 GTAAAGCTACAATAATCCATATTCTGTGTTACTGACATAAAAATAAACAT 601
                         ii         i     v v ivv    v     i     ii   i    
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_184751036_    602 -------------------TT-------------------------TTCA 607
                         -------------------  -------------------------  i 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_184751036_    608 TG-----------------AAGGGTGCTAAGATAAATCAATAGTGAAAAA 640
                           -----------------        i    iv v     i v    i 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_184751036_    641 GTA---TTTTCAACAAATAGTCATGAAA--------TACTCACATCCAAA 679
                         i  ---            i  vv  ii --------  ?i     v    
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_184751036_    680 AACATGAAGTTGTATTCCGACCTTGCCCTGTTT-CAAAAATTAATTAAAT 728
                          iv         v ii  v    ii v ii v -          i v  v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_184751036_    729 GTGTATCAGTGAACTAAATGTTACCACTAAAAGTATAAAATTCTTGGGAG 778
                         i  v    ?v  v        v vvi      v       i    i i  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_184751036_    779 AAAACAGAAGTGCAAGCTCTGGTTCTGTGATCTTAGATTTGGCAATAGTT 828
                               v i ? i  i-   ---  -    i   i i  v      i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAA-TCT---TC-GTGACCTTGGGTTAGGCAATGGTT 586

  chr1_184751036_    829 TATTAAATAGGATGTATAAAGCAAAAACTACCAAAGAAGGAAAAAAATAG 878
                          v   i   v  iiivv      v  i v  v      -----       
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA-----AAAATAG 631

  chr1_184751036_    879 TTAAATGGGACCTTATCAAAAATTTTCAAAA----TGTGCCTCAATGTGT 924
                         v     v    i i       ---  v    ----     i    v vii
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAA---TTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_184751036_    925 GCTAT-GAGAAAGTAAAACGATAACTCATATAATGAAAGAGAATATTTGC 973
                         i    -i       i   v  i   i  i v    ii   i         
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_184751036_    974 AAAT---ATATCTAGTAAGGATCTAGTATTAAAAACATATAACAAAC--- 1017
                             ---      ii     iv  v    iv i  i      vi   ---
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_184751036_   1018 -ACGACTCAATAC----AAAACAAATAATCCAATT--AAAATTAGCTATA 1060
                         -  i        v----  i        i      --     vi  v vi
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_184751036_   1061 ATTTTGAATAGAC--TTCTTCTAAAAAGATA----AATGGCCAATAAACA 1104
                         iv           --    i v  i      ----            i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_184751036_   1105 CAGAAAAAGATGCTCAAATTTACACTTTTA 1134
                           vi             vv i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (80 / 56)
Gap_init rate = 0.03 (20 / 717), avg. gap size = 5.55 (111 / 20)  


2389 28.39 4.90 1.37  chr1_184759817_184767959.rev     4674  5550 (2593)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184759817_   4674 TGTAAAAACATCTCATGTTCATTGATAAGATGAATCGATTTTCTTAAAAT 4723
                           v   i i   i         v   vi  v  v ii  v  v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184759817_   4724 GGCCATACTTCCCAAAGCAATTTACAGATTCAGTGCTATTCTTAGTAAAC 4773
                            v     i      vii  i          ii  v  i i  vi   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184759817_   4774 TACCAATGACATTCTTGACAGAATTAGAATAAACTATTTTTTTAAATTCA 4823
                          v   iivi v  i  vi     v v  -i  i  iv ii v-       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTA-AAATTCA 148

  chr1_184759817_   4824 TGTGGGACCA-AAAAGAGCCTGAATAACAAAGGCCATCTTAAGCAAAATG 4872
                          i   i vii-  ii  v  v     i v  ii v     i iv  i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_184759817_   4873 AACAAAGCTGGAAGCATTC-CATTACCCAACTTTAAA--CTACTACAAGG 4919
                                i    i - i  -  i v     i  i   --i        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_184759817_   4920 CTACAATAACCAAAACAGCATGGTACTGTTACAAA-ACAGGCACATAGTC 4968
                              i   i   i    ii        vi i  i- i  i  i    vi
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_184759817_   4969 CAATGGAACATAATAGAGAGGCTAGAAATAATGCTACATACCTATAACCA 5018
                                 i v   v     v i        vv i i i ii   iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_184759817_   5019 TCTGATCTTCATTAAAG-------------TCAACAAAAACAAGTACTGC 5055
                         vi    i   ivi  i -------------    iiiii -   v iv i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATAGT 396

  chr1_184759817_   5056 TCATTCAATAAATGGTGATGTGATAACTGGACACCTATATGCAGAAGATT 5105
                         iiv     i        v  v  i       i ? i i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_184759817_   5106 GAAACTGGAGCCCTTCCTTATACCAAA-ACAAACATTGACTCAAGATGAA 5154
                            ii    v    v   i i    v -     v   i      i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_184759817_   5155 TTAAAGA--TAAATGTAAAACCTAACACTATAAAAACCCTGGAAGATAAC 5202
                          i ?   --         i v    v         vi i i     v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_184759817_   5203 CTAAGAG-ATACCATTCTGGATGTAGAACTTGGCAAAGGCTCC------A 5245
                         v  i ? - v i -   vv  iv v iii v     v  i i ------ 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_184759817_   5246 TGACAAAAACTCCAAAAGCAATTGGAAAAAACACAAAAACTGACAAATGG 5295
                              ------         vvv v  v   viv     iv  i    v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_184759817_   5296 CACCTCATTAA--CTAAAGAAATTCTG-----CACAGAAAA--ATGAACA 5336
                         v  i    i  --i    -  v  i  -----  v  i v --  v  v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_184759817_   5337 GAGTAAACAGACAACCTACAGAATGGGAGGAAATATTTGTAAACTATGCA 5386
                         i   i  v        i            i         i   ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_184759817_   5387 TTTGACAAAGGTCTAATATCCTGAATATATATAAAACT---A-AAC--AA 5430
                          i   i  i  v  vi     v         v i    --- -   --  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_184759817_   5431 AAAGCAAAAAACAAACTACTTGATTTAAATGTGAGCAAAGAACAGGAATG 5480
                         v  vv    i     iv  iii   ?   vi  i      i ivv    i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_184759817_   5481 GACACTTTTTAAGAAAAGACGTACATGCATCCAACAAGCATATGAAAAAG 5530
                             i  i iv i i    ii    viiiv    i     i       ii
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_184759817_   5531 TACTCAACGTCACTAATCAT 5550
                          i      i   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (156 / 89)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.50 (55 / 22)  

2642 26.22 4.31 1.82  chr1_184759817_184767959.rev     6772  7652 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_184759817_   6772 AGACATCCCATACTCAAGGATCAAAAGAATTAATGTCATTGAAAACGAGC 6821
                            i       ii   v    iii    v     i ii  -  i i ivv
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAGATGGCA 54

  chr1_184759817_   6822 ATGCTCCTCAAAGAAATCTACAGATGCAATGCAATCCTTAACAAAATAGT 6871
                           i    i    vvi          v   i       i  v      vvi
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_184759817_   6872 AACATCATTTTTCACAGAATTAGAGAAAGTAATCCTAAAATTTGTATGGA 6921
                          i vv v     ii     v v  v  iv i           ii      
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_184759817_   6922 ---GCCCAAAAAGACCCCAAATAGCCAAAGCAATCCTGAGCAAGAAGAAC 6968
                         ---  ---  ii     vi          i     i   iv         
  L1M4_orf2#LINE/    155 AATGC---AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_184759817_   6969 AAAACTGGAGGTATCACATTACCTGACTTCAAAATATATTACAAAG---- 7014
                            ii      vv     i v  ii i       iv  i       ----
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_184759817_   7015 -GTAGCCCAAACAGCAGGATATTGGTAAAGAAACAGACACAGAGATTAAT 7063
                         -   ii v i    iiv i  i   i v iii i     i v    i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_184759817_   7064 GGAACAGGAT--AGAGTCCAGAAATGAATCCATATACTTACATCTAAATG 7111
                             i  i  --             i  i     i i   iivii  v  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_184759817_   7112 ATTATTTTTAAAAGCACCAAGAGCCTACTC--TTGGGAAAGAACACTATC 7159
                            v ivvi  ii ii      -- i i  -- v         i v v i
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGA--CCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_184759817_   7160 TTCAATCAATGGTACTAGGAGACATTGGATATCTGAATACAGAAGATTGA 7209
                              iv      i  i   v - i      ? iiv  i  i    v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACA-ACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_184759817_   7210 AAATGGATGCCTATCTCTCCTCACATACAAAAATCAACCCATGATGGGTT 7259
                          iv    iv    i   v vi  i          i   i  vi    i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_184759817_   7260 AAAGACTTAAACATAAGACCTGAAAGTATTAAACTAGGTAGAAAAACA-A 7308
                          ?    i    ii     v  i   v   v     vv-     i  v - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAACA 547

  chr1_184759817_   7309 CAGGAA-AAATACTTCAAAGGTG-TTTTAGGTCTAGGCAAAGATTTCATG 7356
                         i   ?i-    -    ----   -ii  i   -       v i    v i
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTC----GTGACCTTGGGT-TAGGCAATGGTTTCTTA 591

  chr1_184759817_   7357 TCTAAGA-ACTAAAAAGCACAAACAACTCTAACAAAAATAAGGGAATGAA 7405
                         vv  v  -  i    -      i    vvv iv       iivi   vii
  L1M4_orf2#LINE/    592 GATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_184759817_   7406 ACTATATTAAACTAAAAAGCTTCTGTACAGCAAAAGAAACTATCAA---- 7451
                            vi  i   v v    i   i   i vv    i  v        ----
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_184759817_   7452 ---------CAACTTGTTAAATGGAATAAAATATCTGCAAACTATTTATC 7492
                         ---------    iiiivi     i v       i      ii  v    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_184759817_   7493 TAATAATGGACTAATATACAGAACATACAAGCAACTCAAACAACTGAACA 7542
                          i    v     vi   v     i   i  iv     vv      v  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_184759817_   7543 ATTAAAAAA------ACTCA--TTAAAATTGGGCTAAAGACATGAACAGA 7584
                           v    i ------  i  -- ?    v     v  i  iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_184759817_   7585 CATTGCACAAAAGAAG-CATACAAATGGCCAATAGGTATATGAAAAATAT 7633
                             v v v       -i                i i i       i-  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG-AT 889

  chr1_184759817_   7634 GCTCAATATCACTAAGCAT 7652
                               i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (143 / 84)
Gap_init rate = 0.02 (22 / 903), avg. gap size = 2.45 (54 / 22)  


2273 26.41 2.24 5.54  chr1_184774397_184777088.rev     1263  2201 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184774397_   1263 TGAAAAAACAT---ATGCTTATAGATAGGAAGAATCAATGTTCCTAAAAT 1309
                           i   i i  ---   i i  i   v      v i   i  vi   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184774397_   1310 GGCCATCATGCCCCACAA--AATTTATAGATTCAGTGTTATTCCTATCAA 1357
                            v  - iv     -  --i  i  i       ii iv  i        
  L1M4_orf2#LINE/     51 GGCAAT-ACTCCCCA-AATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_184774397_   1358 ACTACTAAAAACTTTTTATTCACAGAA-TT-ACAAAACAATACTATAAAA 1405
                          v v i ivvi i    -- ii     -  -    ivii  v   --   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTT--TTGCAGAAATTGACAAGCTGATCCTA--AAA 144

  chr1_184774397_   1406 TTCATTTGGAACCAAATAAAACCCA-AATAGCCAAAGCAATCCTCAGTGA 1454
                              v     viiv viii     -          i     i v ivi 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_184774397_   1455 TAAGAACAAAGCTGAAGGCATCACATTACTCAACTTCAAACTATACAACG 1504
                         v          i  i   vv     i v i   i      viv   v  i
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_184774397_   1505 AAGCAACAGTAACCAAAACAGCATAGTACTAGTACAAAAGCAGACACATA 1554
                             v       i   i    ii i     i i i  iiii     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_184774397_   1555 CACCAATGGAACAGTTTAGAGAATGTAAATATAAAGCT-TACAACTACAA 1603
                         v i        i  vv v    i vi i v     v i-    vi  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_184774397_   1604 CCATCTAATCTTCAAAAAAGTGAGCAAAGGCAAG-CAATGGTGAAAGGAT 1652
                         i  vi i  i   i v  i - v  v   i v v-      v     i  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_184774397_   1653 TGCTCATACACTAAATGATGATGGGATAACTGGCTACCCATATGCAGAAT 1702
                         v iiiv v  vi     i  v     i      v  ?   i     i  v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_184774397_   1703 ACTGAAATTGGGCCC-TACCTTTTACCATACATACAAATCAACTCAAGTT 1751
                          v    i    i   -     ivi      i i v    i       iv 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_184774397_   1752 GGATTAAAGACTTAAAGGCAAAACCTAAAACTTTAAAACCCTT-GAAGAA 1800
                             i ?    i    v i  i v        v      i   -      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_184774397_   1801 AATCTA----TAACATACCATTCTGGACATTGG-CCAGGCAAAGACTTCA 1845
                           iv  ----   --- i -   vv   v    -ii      v ii   v
  L1M4_orf2#LINE/    544 AACATAGGNGTAA---ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_184774397_   1846 TGACGAAGACTCTAAAAGCAATTGCAAAAAAAATAAAAATTGACAAATGG 1895
                          iivv v   v i       vvv    v    iv      v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_184774397_   1896 CACCTAATTAAACTAGAGAGCTTCTGCACAATTAAAAAAAGCAAGAAAAG 1945
                         v  i v  i   v vi i i   i  ii --  v   ii -  -------
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGC--TTCAAAGGA-CA------- 679

  chr1_184774397_   1946 AAAAGAAAAAATAACCAACAGAGTATACAGACAACTTACAGAATGGGAGA 1995
                         -----------iv i   v i   iv v       ii             
  L1M4_orf2#LINE/    680 -----------CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_184774397_   1996 AAATATTCACAAGCTATACATCCGATATAGGCCTAATTTCCAGAATTCAT 2045
                                ii   iii   i   i    vi  v  vi v        vi  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_184774397_   2046 AAAGAACTTAAACAAATTACCAATCAAGAACTTAAACAAATTACCAATCA 2095
                                 i-------    v v    v  --    v i i---------
  L1M4_orf2#LINE/    769 AAAGAACTC-------TTACAACTCAATAA--TAAAAAGAC--------- 800

  chr1_184774397_   2096 AAAACAACTTCATTTACAAGTGGGCAAAGGAC----ACAGACATTTTTCA 2141
                         -   i   iiv   ? v  i           i---- i        i  v
  L1M4_orf2#LINE/    801 -AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_184774397_   2142 AAAGAAGTCATACATGTGGCAAACAAGCATATGAAAAAAATACTCAATAT 2191
                                vi     vi    v  i     i       i - i     i  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACAT 898

  chr1_184774397_   2192 CACTAATCAC 2201
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.55 (149 / 96)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.81 (73 / 26)  


2344 26.46 5.49 3.70  chr1_184831474_184833945     1088  1979 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184831474_   1088 TGAAAAAGGATTTCATGCTCATGGATTGAAAAAATCAATATTGCTAAAAT 1137
                           i   iiv  ii    i          i  i v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184831474_   1138 GGCCATACTTCCAAAAGCAGTCTACTGATACAATGCTATTCCTATCAAAG 1187
                            v     i  v   viii     v   v   i  v  i         i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184831474_   1188 TACCAA-TGTCATTTTTCACAGAATTAGAAAAATACT-ACTCTAAGGTTC 1235
                          v   i-  i -     ii     v v  v  i--  - ii    ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr1_184831474_   1236 ATATGGAA---CAAACACCCCA-AGTAGCCCAAACAATCCTAAGCAA-AA 1280
                                 ---   iviv    - i     v        i i iv  -  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_184831474_   1281 GAACAAAGCTAGACATATCACATTACCTGACTTTAAACTATGCTCTAAGG 1330
                                 i i  vivv     i v  ii i  i   viv i  vi  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_184831474_   1331 CTACAGTAACCAAAACAACATGGTGTTTGTACAGAAACAGACACATAGAC 1380
                                  i   i   iii    ii v i i iii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_184831474_   1381 CAATGGAGCAGAACAGAGAACCCAGAAATAAAGCCTCACATCTACAACCA 1430
                                ii    iv    ii           v  vi    i  ------
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA------ 341

  chr1_184831474_   1431 TCTGATCTTTGACATCTACAACCATCTGATCTTTGACAAAGTTGATAATA 1480
                         --  i  ------------  i----    i  i     i v  vi  v 
  L1M4_orf2#LINE/    342 --TGGTC------------AAT----TGATTTTCGACAAGGGTGCCAAGA 373

  chr1_184831474_   1481 GCAAGCAATGGGAAATCGAT--TCCTTATTGAATAAATGATGCTGAGATA 1528
                         v  vv       i  vvi  --  i  -- v  i     i     i  i 
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACA 421

  chr1_184831474_   1529 TCTGGCGAACCATATGCAGAAGATTGAAAATGGACTACTACTTTTCACCA 1578
                         v    vv ?   i     i    v    iv     iv    i iv     
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_184831474_   1579 TA-ACGAACATTAACTCAAGATGAATTA-AGAGTTGAAAGGTAAGAACAC 1626
                           -  i  v          i   i  i -   vi -   v      i vv
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCT-AAATGTAAGAGCTA 520

  chr1_184831474_   1627 AAACTACAAGAATCTGAGAAGAAAACCTAGAAAATATTCTTTGGGACATT 1676
                               i  i v   v          v   i?ivv v    i v   v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_184831474_   1677 GGTCTTAGGAAA-GATTTTTTGACTAAGTCCTCAAAAGCAATTGCAGCAA 1725
                           v-     v  - i   i  iiv  v v vi        vvv   i   
  L1M4_orf2#LINE/    571 GGG-TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_184831474_   1726 AAGCAAAAATTGACAAGTGGGACCTAAATAGACTAAAGAACTTCTGTACA 1775
                            v      v  i  i v    i v vi i v v  i     i   i v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_184831474_   1776 GCAAAATAAACTATCAACAAAGTAAGCAGACAACCTACAGAATGGGA-AA 1824
                         v    iv v        v     i iv        i           -  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_184831474_   1825 AACATTTGCAAACTATCCATCTGACAAAGATGTAATATACA---TATCCA 1871
                           i         ii  vi      i  i ivv vi   v  ---   -- 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT--A 767

  chr1_184831474_   1872 TAAGGAAATTAAACAATTCAACCAGCAAAA-----ACAACCCCATT---- 1912
                            i   v ivv    i    iv vv    ----- i     v   ----
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_184831474_   1913 --------------------AAACACTCCTC----AAAGACCTGCAGGCA 1938
                         -------------------- i   i i   ----i    iv i  iiii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_184831474_   1939 GCCAACAAACATATGAAAAAATGCTCCACATCACTAATCAT 1979
                              i  i  i       i      v      ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.57 (82 / 23)  


 578 24.68 1.30 0.65  chr1_184939858_184942051      646   799 (1394)    L1M4_orf2#LINE/L1        1   155 (753)  

  chr1_184939858_    646 TGGAAAGACATCC-ATGGTCACGGATTGGAAGATTGACTGTTGTTAAGAT 694
                                 i    -   v   i           i v v i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184939858_    695 GCCAATATTACTCAAAACAATCTA-ATATTTAATGCAATCTCTATCAAAA 743
                          v     i v i    vii     - v   i  i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184939858_    744 TCCCAATGGCATGTTTTTTGGAAATAGAAAAAATCCATCTTAAATTGTAC 793
                              iiv  v v    vii     v  v  iv v-   i    v vi i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chr1_184939858_    794 ATAAAA 799
                           ii  
  L1M4_orf2#LINE/    150 ATGGAA 155

Transitions / transversions = 1.24 (21 / 17)
Gap_init rate = 0.02 (3 / 155), avg. gap size = 1.00 (3 / 3)  

2586 23.61 3.58 1.33  chr1_184939858_184942051      949  1702 (491)    L1M4_orf2#LINE/L1      138   908 (0)  

  chr1_184939858_    949 CCTAAATTGTATATAAAATCTCCAGGCATTCTGAGAAGCCAAAATATTCT 998
                               v vi    ii  viv v   v ii v  iv        i v   
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_184939858_    999 TAAAAAGAAATAACA---TTG-AGTCCTCACAATTCCTGATTTCAAAACT 1044
                          i    ii  v    ---   -  vv      v    ii           
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_184939858_   1045 TATTACAAAGCTTTAGTAATTAA-ATTGTGTGTTATGGACATAAACACAT 1093
                           i         vi      i  - iv     v  iv i     iv i v
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_184939858_   1094 ACATATAGAACAAATGAAAAAAGTAAAAAGCCCAGAAATAAACCATTGCA 1143
                                  v   vv   v i i vi i  i             vv i  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_184939858_   1144 TATAGGGTCAAATGATTTCTGACAAGAGTGCCAAGAATATTCAATAGAGA 1193
                          v  v      v      ii      i         vi       i i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_184939858_   1194 ATGGACAGTCTTTT-AACATACGATGTTGGAAAAACTGGATACCCACATG 1242
                          v i i        -    v i i  i   i v         ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_184939858_   1243 CAAAAGAATGAAGTTAGATCCTGACCTTATACCACATACAAAATGTAACT 1292
                                        i  i  iv    i i    i        vv     
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_184939858_   1293 CAAAATGAACCAAATACCTAAATGTAAAAGCTACAACTATTATATTATTA 1342
                                i i  ? v            i     v      v v i v   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_184939858_   1343 CAA-AAATCACAGGGAAACAAACTTTATGACACTCGAT---GCAATAATG 1388
                         v  -   v  i   ?iv -  v   ii    vi v i ---     ii v
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_184939858_   1389 TATTGAATATCATCCCCAAATTACAGACAACATAAGAAATAAGAGCTAAG 1438
                          v  ii    v iv  v   vi   ii     v      v  v  v   i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_184939858_   1439 TCGAACTACGCCAAAATGAAAAAAACTTTCATGAGTCAAATGACACACTC 1488
                          i i   v ii      v     --    ii  vv     v     vv  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATC 684

  chr1_184939858_   1489 AACAG-GTGAAAAGGCAACCCATGAAATGGTAAAACATATTTTCAAATT- 1536
                           v i-        i       iii     v i  v      v     i-
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_184939858_   1537 ---------TAAGGGTTTAATATCCAAAATGTGTAACTAACTCATATGAC 1577
                         ---------      vi vi      i   i i   vv     v  ii  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_184939858_   1578 TCATCAATAACAACAACAAA--ACCTGGTTCAAATATGAAAATGGACAAA 1625
                            vi     v  -i     --   iii  ?   ------     i    
  L1M4_orf2#LINE/    785 TCAATAATAAAAA-GACAAATAACCCAATTWAAA------AATGGGCAAA 827

  chr1_184939858_   1626 GG-TT--AAGAGATATTTCTTGAAAGCAAACATACAAATGGCCAATAAGC 1672
                           -  --  v   i      iv    v i i                   
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_184939858_   1673 ACATGAAAA-ATGCTCAGCATCGCTGACCAT 1702
                                  -       i    i????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (96 / 78)
Gap_init rate = 0.02 (16 / 771), avg. gap size = 2.31 (37 / 16)  


3082 26.46 0.88 0.77  chr1_184954555_184958424.rev     1681  2587 (1283)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_184954555_   1681 TGAAAACACATTCCGTGCTC-TTGATAGGTAGAATCAATATTGTGAAAAT 1729
                           i   v i  i  i  i  - v   v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_184954555_   1730 GGCCATACTGCCAAAAGCACTCTACA--TTCAACACAATCCCCATCAAAA 1777
                            v     v  v   viiv      --      i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_184954555_   1778 TACCATCATCATTCTTCACAAAATTAGAAAAGAACAATTCTAATATTCAT 1827
                          v   v vv v  i  ii  i  v v  v   v-ii  i    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_184954555_   1828 ATGGAACCAAAGAAGACCCCACATAACCATAGCAAGACTATGCAAAA--A 1875
                               viiv iii     viv   i   v i   v-  -  v    -- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGAA 197

  chr1_184954555_   1876 GAGTAAATCTGTAGGCATCACACTTCCTAATTTCAAACTATACTACAAGG 1925
                           ii   vi  v   vv          i         viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_184954555_   1926 CCATAGTCACCAAAACAGCATGCTACTGCTATAAAAATAGGCACACAGAC 1975
                          i i   v i   i    ii  v     vi    ii    i  i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_184954555_   1976 CAATGGAACAGAATAGAGAACCTGGAAATTAACCCAACTACTTACAGCCA 2025
                                 i     v    ii ii     v      vvi i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_184954555_   2026 CCTGATCTTCGACAAAGCAAACACAAACATAAAGTGGAGGAAACGACACT 2075
                         vi    i        i vviv  vi v   vv i   -     vi i v 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGT 396

  chr1_184954555_   2076 CTTTTCAACAAATGTTGCTGAGATAACTGGCTATTCACATGTATGAGAAT 2125
                                       v     i  i      v  ?i      i vi     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_184954555_   2126 AAAATTGGATCCTCATCTTTCACCCTACACAAAAATCAACTGAAGATGAA 2175
                         i  i     i  ii i  iv    v  i        i    v  i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_184954555_   2176 TTAAGGACTTAAATCTAAGA-CTGAAACTATAAAAATTCTAGAAGATAAC 2224
                          i ?i   i     v     -  i           v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_184954555_   2225 ATTGGCAAAACCCTTCTAGACATTGGTTTAGGCAAGGATTTCATGACCAA 2274
                           v  ?iv  vi    vv   v    v        v i    v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_184954555_   2275 GAAACTGAAAGCAAATGGAATATAAACAAAAATTAATAGTTGAGACTTAA 2324
                           v  ii      v v v  i v  iv      vi   iv vi     v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_184954555_   2325 TTAAACTAAAGAGCTTTTGCATAGCAAAAGGAACACT--CAGCAGAGTAA 2372
                          i   v v  i i      iiivv    i --     --  iv i   i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGG--ACACTATCAAGAAAGTGA 694

  chr1_184954555_   2373 ACAGACAACCCACAGAGTGGGAGAAAATTTTCACAATCTATACATCTGAC 2422
                          v              i           v  ii   vii   i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_184954555_   2423 GAAGGGCTAATATCCAGAATCTACAATGAACTCGAACAAATCCATAAGAA 2472
                         i i  i  vi          v  i  v      vv    v  v    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_184954555_   2473 AAAAACAAACAATCCCATCAAAAAGTGGGCTAAGAATATGAATAGACAAT 2522
                            i     i  i  v  i?    i     v   i  v          v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_184954555_   2523 TCTCAAAAAGAAGATATACAAATGGCCAATGGACATATAGAAAAATGCTC 2572
                             v   -                     iii  i  ii   i      
  L1M4_orf2#LINE/    845 TCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_184954555_   2573 AGCATCACTAATGAA 2587
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (134 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  

1348 28.10 3.92 1.88  chr1_184954555_184958424.rev     2743  3379 (491)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr1_184954555_   2743 AAAACAGTGTGATGAT--TATA----TACTTACATAGATAAATGTTATTG 2786
                           i        i iv --i   ----  vvi i      v    vv  v 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_184954555_   2787 CAAAGAAATCCCAGAAGTCATCTCACAACTACAGAGTCAACAGAATTTTG 2836
                         v vv  i vi      i v v i  i vv vi vi     iv  v   i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_184954555_   2837 ACAACTA-GCAAAGACAATTCAA-GGAGAACGTATAGTC-----AGCAAA 2879
                             vvi-  v     v      -  i   v v      ----- i    
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_184954555_   2880 CAGTGCTGGAATACTTGGGCATCCATAAGCAAAA-AATGAACCTAGAC-- 2926
                         ii       i i vi   ii ?   i v      -      vi i   --
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_184954555_   2927 --AGTCCACATTCATTTCACAAATATTAACTCACAATAGATCAAACACCT 2974
                         -- vii    i-   v -     v         v   i     ? v    
  L1M4_orf2#LINE/    459 CTACCTCACAC-CATAT-ACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_184954555_   2975 AAAAGTAAAATGC-ATAATTATAAAACTTCTGGAAAAAAATCACAGGGTT 3023
                            v    i -  - v  i         ii i   i    -  i   ?v 
  L1M4_orf2#LINE/    507 AAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGT 554

  chr1_184954555_   3024 AAATATACATTTACTTGGATTTGGTAGTGAAATTTTACATACAAAGCAC- 3072
                             v v i vvv     i  v  i i  ivv i   v   ii --   -
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA--CACC 602

  chr1_184954555_   3073 -AAAACAAAAATGACCCATGAACAAAAAACATGACAAAATGGATTTTAAT 3121
                         -   i  v  iii  -- -i  v      i -  i   v    i  i vi
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAAC--A-AAAGAAAAAATA-GATAAATTGGACTTCATC 648

  chr1_184954555_   3122 ACAATTAAAATCTTCTACTGTATGAAAGAA-A-TGTTGAAAAATT-AATG 3168
                          v        v   i i-  iv v    i - - i ii i   v -  vi
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_184954555_   3169 TACAAGCCACAGACAAGGAGAACATATTTGCAAAATATGTATCTTTTACA 3218
                         v    v       vvi      v           vi  i     vv  vi
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_184954555_   3219 GGGCTTGCTTACAAAATGTACAAATAACTATTGAAACTCAACAATAGGAA 3268
                           i    iv v  i   i  i   v    v  iv       i    ii  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_184954555_   3269 -AGAAATGACCTAATTTTAAAAATGGGCAAACTATCTGAACAGACACCTT 3317
                         - v    i   i    ?-             vv  i    i     ii i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_184954555_   3318 ATCGAAGAAGATATACTCATAATAAATATTCATATAAAAAGATATTAAGC 3367
                         vi i            vv  iiiv    vv  i  i       ii v i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_184954555_   3368 ATCATTTGACAT 3379
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (96 / 79)
Gap_init rate = 0.04 (23 / 650), avg. gap size = 1.61 (37 / 23)  


2468 24.64 5.39 5.50  chr1_185031813_185036078.rev     2867  3775 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_185031813_   2867 TAGAAAAATATTCTATTTTCATGGATTGGGAGAATCAATATTGTTAAAAT 2916
                          i    i    i i  v            i   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_185031813_   2917 CCCCATACTACCCAA-----TCTACAGATTCAATGCAATCCCTATCAAAA 2961
                         vv v     v     -----             i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_185031813_   2962 TATCAATGATATTCTTCAATGACATAGAAAAAATAATTCCAAAATTTATA 3011
                          vi  iiviiv  i  iivv  v  v  v  iv i  i i      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_185031813_   3012 TGCAAACACACAAAAAACAAGAATAGCTATTCTAAACTCTCCTAAACAAA 3061
                           v   ii  - iii v v        i ----    vv  i i  v  i
  L1M4_orf2#LINE/    151 TGGAAATGCA-AGGGACCCAGAATAGCCA----AAACAATCTTGAAAAAG 195

  chr1_185031813_   3062 AAGAACAAAAGAAGAGCTATCCAAAACTATCCTAATAATAATAATAAAAA 3111
                                  i----------------------------------------
  L1M4_orf2#LINE/    196 AAGAACAAAG---------------------------------------- 205

  chr1_185031813_   3112 AACTGGAGAAATCACA-TTACTGTCTTCAAACCATAGTA--GAGTGATAG 3158
                         --i     i v     -  v iivi      v v  v  --i  iv i  
  L1M4_orf2#LINE/    206 --TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_185031813_   3159 TAACCAAAACAGTACTATACTG-CATAAAAACAGACACAAAG-CCAATGG 3206
                            i   i     iivi     -     ii i     i v  -i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_185031813_   3207 AACAGAATAGAGAATGCAGGAACAAATCCACACAACTACACTGAACTCAT 3256
                           i     v    i v   i  i   i   i   vi  iiv v  i v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_185031813_   3257 TTTCAGTAAAGGTCTTAAGAAAATGCACTAAGGAAAAGGCCGTCTTTTTA 3306
                             iii  i   vii    vv  v  v ii     iiiiv       i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_185031813_   3307 ATAACTGGTTCTGGGAAAACTGGATATCCATATGCAGAAGAAAAGAACTG 3356
                          i  v    v      v         ?   i     i     vii ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_185031813_   3357 -ACCCCTATTTGACA---TATACAAAAATCAAATCAAAATGGATTAAAGA 3402
                         -       ii v   ---           i  v           i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_185031813_   3403 CTTAAATCTAAGACCTCAAAAC-ATGAAACTACACAAATAAAATATTGGG 3451
                          i     v     v  -     -  i     vivvi  v    i  v  ?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_185031813_   3452 GAAAACCTCCAGGACACTGATCTGGGCAAAAATTTTTGAGCAATATGCCA 3501
                          v   i  i iv   vi  ivi i     vii   i v  --     v  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG--ATATGACA 600

  chr1_185031813_   3502 C---AAGCACAGGCAAGCAAAGCAAAAATGAACAACTGAAA--TCAT--- 3543
                          ---       i    vv    v      ii i  v vii --    ---
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_185031813_   3544 -ATTAGG----TTTACGG--CCAAGGATACAATCAA---AGTGAAGTGAC 3583
                         -    ii----   ii v-- v     i  v     ---      iv   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_185031813_   3584 AACTCACACAATGGGAGAAAGTATTTGCAAACTACCTATCTCATAAGGGA 3633
                            i    v           i          ii iv     v        
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_185031813_   3634 TTAACAACCAGAATGTATAAGGAGCTCAAACAGCTCTACAAGAAAAAT-C 3682
                         i vii v       i     i  i   vv   i   v i  v     v- 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_185031813_   3683 TAATAATCTGATCAAAAGATGGGCAAAAGAGTTAAGTAGATATTTCTC-- 3730
                         v     i ii  i?   i         i  v  i i    i       --
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_185031813_   3731 -------TATA------GCAAACAGGCATATGAAAAGGTGCTCAACATCA 3767
                         -------    ------  v  i i   i        i            
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_185031813_   3768 TTGATCAT 3775
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.62 (136 / 84)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.50 (99 / 22)  


2689 25.41 3.43 3.43  chr1_185098195_185102436     2845  3749 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_185098195_   2845 AAATATGTGTTATGTCCATGGATTGGAACAATTTATAATGTGAAAATAAC 2894
                            v  i vii    i            v v  v   v   v  i  ii 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_185098195_   2895 CAAATTACCAAAG---------AGATTCTATGCAAACTCTATCAAAATAC 2935
                         v v i v  v  i---------      v i    v i          v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_185098195_   2936 CAA-TGCAATTCTTCACAGAAATAGTAAAATCAATCCTGAAATTTGAATG 2984
                           i-   v-  i  ii       v vv  iiii     i     iiv   
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_185098195_   2985 CAACGACAAAAGATGCTGAATAGTCAAAGAAATACTGAGAAAAAAAGAAC 3034
                         v  vvi   ii  iv v      i    iv   vi   -    i      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAGAAC 201

  chr1_185098195_   3035 AAAGTTGGAGACATCACACTACTTGACTTCAAAACATACTACAAAGCTA- 3083
                                   ivv       v iii i        v             -
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_185098195_   3084 GGTAACCAGAACAGCATTTTACTGGCATATAAACAGATACATAGGTCAGT 3133
                         i    i  ii    ii vv          vii i   i i    i   i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_185098195_   3134 A-AACAGAATAGATAATCTAGAAATAAATCCATGTATTTATAGCCAAGTA 3182
                         i-  i     v  v i  i         i    ii      i i   v i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_185098195_   3183 ATTT--GACAACCATGCCAAGAACCTACATTGGAGAAAGG-CAGTCTCTT 3229
                             --     vvi        v v v  v   i     i-i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_185098195_   3230 CAATAAATGGTGCTGGTAACACCGGATATCCACATGTAGAAAAATGAAAT 3279
                            i            v vv  i     ?       i i  i      i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_185098195_   3280 TGATATATAAAATGATTTTATATAGGATTTTCCCTATCTCCTACCATATA 3329
                           -----------------------  i---     i   vi        
  L1M4_orf2#LINE/    452 TG-----------------------GAC---CCCTACCTCACACCATATA 475

  chr1_185098195_   3330 TAAG--TCAATTCAAAATGGATTACATACTTAAATGTAAGACCTGAA-CT 3376
                         i  i-- i  i           i ? v  i           v  i  -  
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_185098195_   3377 ATGACACTACTAGACAAAAACACAGGGG-AAATGTTTCAGGACATTGGTC 3425
                           i v   vi    vi      i   ? -    -i   iv   v    vi
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGT 574

  chr1_185098195_   3426 TGTGCAAATATTTTATGGAGAAGACCTTATAAATACAGGAAACAAA-GCA 3474
                          iv    vvi   iv i  v v   vii v  ii   i v      - v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_185098195_   3475 AAAATAGACA----GGATTATATCAAG-CTAAAAAGTCT-GTGCATAGCA 3518
                                 i ----   i vi     i-i      v i -    v --  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CA 672

  chr1_185098195_   3519 AAAGAAAC----AACAAATTGAAGAGACAACCTGCAGAAGGGGAGAAAAT 3564
                           i  v  ----  v   v    i        ii     v          
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_185098195_   3565 ATTTGAAAA-CTTTCATTTAACAAGAGATTAACATTCAGAGTACATAAGG 3613
                              v   - v vi  i i i   i  i vii  i    i  i    i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_185098195_   3614 AGCACAAATGACTCAACAGCAAAATAACTAATAATATGATTAAAATATGG 3663
                          i v vv ii      i ii    vi  v     ivii   ?   v    
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_185098195_   3664 GCAAATGAGCTAAATAGATATCTCTCAAAAGAAAATATACAAATGACCAA 3713
                              v  vi i      i  i    v      i           i    
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_185098195_   3714 CAGGTATATATAGAAATGCTCAACATCACTAATCAT 3749
                         i i i i  iv i i             ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (140 / 86)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 2.95 (62 / 21)  


1764 26.93 9.40 1.40  chr1_185206122_185207826.rev      502  1214 (491)    L1M4_orf2#LINE/L1      139   908 (0)  

  chr1_185206122_    502 CTAAAGTTTATGTGGAAAGACAAAAGTCTTTTAATAGCTAACATTATTCT 551
                              i  i  i      vi   ii v iivv      i  v iv  ii 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_185206122_    552 AAAAAAGAC---CGAAGTAGGAGATCTAACACTATCTGACTTTAAGAC-- 596
                         i       v--- i    v    iv  v     vi ii i  i  i  --
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_185206122_    597 ATTATGAAGCTACAGATATCGAGACAAAGTGATATTGGCAAAACAAAAGA 646
                          i  ii         vv   i     iv   i  i     v  vi v   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_185206122_    647 GAAATAGATCAATTGAACTGATATGAGAGTTCAGAAATAGATCTATGCAA 696
                         v v          v   iv  vv       i        i i i  i  v
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_185206122_    697 ATATAGTCAACAGATCTTTGACAAAGGAGCAAAGAC-----AATGGTGGA 741
                         v   i     iv   i  i     i  v  v     -----     v i 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_185206122_    742 AGGATAATACTTTTAAACAAACGATG----AACAGCTGAATATCTATGTG 787
                           i   i -     v      i i  ----i   i   i   ? i ii  
  L1M4_orf2#LINE/    389 AGAATAGT-CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_185206122_    788 CAAAA-AATA---TTAGACAAAAACTGTATGTCA----CAAAAGTT---- 825
                              -   i---  i   vvvv  ivi iii  ----     i  ----
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_185206122_    826 CAAAATGGATCACAGACCTAAATGTAA-AGCATAAAACTATCAAAATTTG 874
                                     ?              -   -         v   v i v
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTT 536

  chr1_185206122_    875 AGGAGGTAACA---GGATAA-TCTAGGTTACCTTGAGTTTGATGATGACA 920
                           i  iv    --- ?i   -   vv  v      i   v iii   iiv
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_185206122_    921 TTTTACATACCACACCAGAAGCATA-----CATAAAAAAAAATTGATAAA 965
                          i   v   iv      i     i -----  v  i       v      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_185206122_    966 T-------------AGTTGGCAATTTCTGCTCTGTAAAAGATTTCATTCA 1002
                          ------------- i  iiv  i  i  iv  vi   i  ivii  iv 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_185206122_   1003 GAGAATGAAAGAACAAGTCACAAACTAGAAGAATATATTCACAAAACCTT 1052
                           i i     ii    vi    i v i i    v     ii    v v v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_185206122_   1053 TTTCTGATAAAAGACTTGTGTCTGTGTTTCTAAAATATAACAAGAATGG- 1101
                          v        ii       i  i-------- i      vv     ivv-
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCC--------AGAATATATAAAGAACTCT 778

  chr1_185206122_   1102 -ACAATATA-TATTTAAAA---AAATAAT---------AAATGAGCAAAA 1137
                         -    ivi -  v v    ---      i---------     i     i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_185206122_   1138 TATATAAACAGACA---CCTCAAAAAAGATATACAGTTAGCAAATAAGCA 1184
                         v  v i  i     --- ii    i          iv i  v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_185206122_   1185 TATCAAAAGATGCTAAACATTATATGCCAT 1214
                         i  v          v     i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (116 / 73)
Gap_init rate = 0.03 (21 / 770), avg. gap size = 3.67 (77 / 21)  


2903 21.45 3.25 4.88  chr1_185269923_185271837      500  1422 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_185269923_    500 TGAAAAGCTATCTCATGTTTATAGATGGGAAGACTTAATATTAT-AAAAT 548
                           i    v    i      i  i   v               i -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_185269923_    549 GATGATACTCTACAAATTGATCTTTGTATTTAACATAATTCCTATTAAAA 598
                          iii      iv           viiv   i   ii   i     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_185269923_    599 TCTCAGCTACATCTATCTATTTTTATTTTGGAGAAAATAAAATAACTTTT 648
                           i     i ---------i    ---   v     v i v - i  vv 
  L1M4_orf2#LINE/    101 TCCCAGCTGC---------CTTTT---TTGCAGAAATTGACA-AGCTGAT 137

  chr1_185269923_    649 CCTAAAATGCTTTTAAAAATACAAAAGACTCAA-----CCTAAACAA-CT 692
                                 v v v ii    i   ii   i  i-----  v      -  
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_185269923_    693 TGAAAAATAATAACAAACTTAGAAGACTTACTCTTAGCAATTTAATAACT 742
                                v  v      v  i  i    i  v   vv      v v    
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_185269923_    743 AAC-ATGCAGCTACAGTAACCTAAGAT-TTGTGGTACTGACACATGAGTA 790
                         v  - iiv           i -    i-v          i  i v ii  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATC-AAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_185269923_    791 GACATAGAGATCAATGGAGTAGAACTGAAATGCCAGCAGTAATTCTATAA 840
                               v           i     i   i vv    v i   vi i   v
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_185269923_    841 ATTTATGGTCAGTTAATTTTCTATAAGGGAGCCAAGACAATCTAAAGGAG 890
                                    i  i      v i     v        v  ii  v  i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_185269923_    891 AAAAGACTAGCCCTTTAAGCAAACAGTCCTAGTGTTTAAGTGGATGTCTA 940
                            -  v   i i   v i    ii  v  i vii--  v     i? i 
  L1M4_orf2#LINE/    387 AAA-GAATAGTCTTTTCAACAAATGGTGCTGGGAC--AACTGGATAKCCA 433

  chr1_185269923_    941 CCTGCAAAAGAAACAAATTAGTCTCCAACCTCATATCACATACAAAA-TT 989
                          v          vv  i  i v i  v      i i  i        -  
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_185269923_    990 AACTCAAATAGAAAAAACAACAACACTTAAACAGTGTCTAAAGAGGTAAG 1039
                                 --- vii v  ?-- v  i    ---   ---     v   -
  L1M4_orf2#LINE/    484 AACTCAAA---ATGGATCAW--AGACCTAAA---TGT---AAGAGCTAA- 521

  chr1_185269923_   1040 AGGAACAACTAAAATTCTACGAAGAAAACA-AAGGGTAAATCTTCCTGAT 1088
                         ---   v -     i   vv          - i ?          v   i
  L1M4_orf2#LINE/    522 ---AACTA-TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_185269923_   1089 CTTGGACTTGGCAATAGTCTCTTA----TGACAGCAAAAACACA-TTAAT 1133
                              ii v      i  i     ----     v     i    -vi  i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_185269923_   1134 CAAAGAAACAA--GAAAAAT-GAACTTTTT--AAACTGAAAACTT--ATG 1176
                         v       v  --  v    - i    iv --   i i       --i  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_185269923_   1177 CT----AGAATAATCTCATCAATTAAGTGAAATGACATCTCACAGAATAG 1222
                           ----  i i --  -     vv        v    v i        i 
  L1M4_orf2#LINE/    668 CTTCAAAGGACA--CT-ATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_185269923_   1223 -AGAAAATATCTGGCAAATCATGTACTTGACAAAGGTCTGGTAGGCAGAA 1271
                         -         i  -        i  ii   i  i  v  v   vv     
  L1M4_orf2#LINE/    715 GAGAAAATATTTG-CAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_185269923_   1272 GATATAAAGAAATGTTATGATGTAAAAACGAGAACAACAAAATGAATAAC 1321
                         v          v v   ii ivi  ------v  i  v  i ii      
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAA------TAATAAAAAGACAAATAAC 807

  chr1_185269923_   1322 CCAATTTAAAAAGTGGCCAAAAGATTTTAATGGACAATTTTACAAGGAAG 1371
                               ?     -   v    i     v   i    v  i v   i    
  L1M4_orf2#LINE/    808 CCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_185269923_   1372 ATATACAAATGACCAATA--CACATGTAACAATCACTGACCATCATTAGT 1419
                                    i      --      v  vi  -i  v v     ?????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACATCAZZZZZ 905

  chr1_185269923_   1420 CAT 1422
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.34 (111 / 83)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 2.21 (75 / 34)  


2474 26.77 2.07 3.26  chr1_185313983_185316293      934  1852 (459)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_185313983_    934 TGGAAATACAGCCCTATAT-AATGGATTGAAAAAATTCATATTGTTAAAA 982
                               v i v   -  i -v        i  i v  v          i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_185313983_    983 TATCCATACTATCTAAAATGATGTATAAACTCTGTGCAATCT-TGTTAAG 1031
                          iv v     vi i   v    v  i i i  vii      i- i i  i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_185313983_   1032 ATCCCA-TTGAATTATTTATAGAAATAGGAAAAAAATAACAACACTAATA 1080
                               -i  vv  v   ii      v -- v  iv i i-- -    v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGAT--C-CTAAAA 144

  chr1_185313983_   1081 TTTATATGTAACCACAAAAGTATACT----ATTGCCAAAGAGATCCTGAG 1126
                           i     v  vii   ii ---  i----  v      ivi   i   i
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGG---ACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_185313983_   1127 CAAGAA---CACAGCTGAAGGCATTACACTTCCCTTTGTGTGAATATACT 1173
                         v     ---  v  i  i   vv i         vv v vvi  iv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_185313983_   1174 ACTAAGTGAAAATAATCAAAACAGCATGGTACTAGAATAGAAACAGACAT 1223
                           v   iv v i       i    ii       i v   iii i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_185313983_   1224 ATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAATCCACATATTTG 1273
                              i        i     v    ii           i   i i    i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_185313983_   1274 TATATAACTGATCTTCAACAAGGGTTTTAAGAACACACAATGGGTGAAAG 1323
                          ivvi  i    i   i        vii    v  iv       -     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAG 390

  chr1_185313983_   1324 A-TAGTCTTCTCAATAAATAGTACTGGGAAAACTGGATATTTACATGCAG 1372
                          -       i    i    i  i      v         ?ii       i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_185313983_   1373 ATGAATGAAACTGGATCATTATCTTACACCACATACAAAAATCAATTCAA 1422
                          v       ii    i vi  i  i      i          i  i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_185313983_   1423 AATGGACTAAAGACATAAATATTTGACCTGATAC-ATAAAACTACTCA-- 1469
                               ii ?    v     i vv  v  i v  -        -  i --
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGA 539

  chr1_185313983_   1470 AGAAGACATAAGAA-AAACATGTATGACATTGTCCTGGGTAATGATTTTT 1518
                             i     i ?i-   iv vii    v   vvi i  i    i   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_185313983_   1519 ATATATATATAATCCCAAAGCCACAGATAACAAAACCCAAAATAGA-AAG 1567
                         ---  v    i iv     iv    iii       vvv        -  i
  L1M4_orf2#LINE/    590 ---TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_185313983_   1568 TAGTATTACATCAGTCTATAATAAAAAGCTTCCACACAGTAAAATAAACA 1617
                          v v i v     i-----   v    i   iiiii vvi   iv v  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAA-----AATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_185313983_   1618 TTCAACAGAATGAGTAGACAGTCTATGGAACTGGAGAAAGTATTTTCAAA 1667
                         v    v i i   iv     ii i ii   iv       i     v    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_185313983_   1668 TTATATATCTGATAAGAGGATAATATACA-AATATATGAAATATCCGTAT 1716
                          i              i iv vi   v  -       i  iv ii v  i
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_185313983_   1717 ATTTTTGTTACAAGAAACTAAA-AACTCAATGGGAAAAACAGGCAAAGTC 1765
                          vi ivi v i  i  ivi   -   i    v?-     ii       vv
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGA 830

  chr1_185313983_   1766 CTTGAATAGACATTTTCCCAAAGAAGTTATAAAAAGTTCCCAACAACATT 1815
                         i              ii         v    v   - vv    ------ 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAA------T 873

  chr1_185313983_   1816 AAGCATCAGACAA-ATGCAAATCAAAACCACAATGAAA 1852
                              ivv  v  -    ---    v i  ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 1.88 (49 / 26)  


2475 27.57 3.10 2.55  chr1_185396137_185398212.rev      683  1585 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_185396137_    683 TAGAAAAGCATCTTATGGTCATGGA---GCAGAATTAATGTCACTAAAAT 729
                          i    iii   ii   v       --- v   v     i iii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_185396137_    730 GGTCATATTTCGCAAAGCAATCTACAGATTTAATTCAATCTCTATAAAAA 779
                           iv   i i v    vii           i  iv     i    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_185396137_    780 T----GCTCTCATTATTTTACACAAA--GATAAAAAAAATCTAGAACTAA 823
                          ----   vi -  -    i  v   --  i  ivvi vi   i  i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_185396137_    824 TATAAAACAAAGCAAAACAAAAAAGAGCCCA-AATAACCAAAGCATTCCT 872
                            ii  -- v    i-------- ii    -    i     i  v  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAG--------GGACCCAGAATAGCCAAAACAATCTT 188

  chr1_185396137_    873 GAGCAAAATGGACAAATCTGGAAGCATCATATTACCTAACTTCAAAATAT 922
                           iv  i v i     vi    i vv   i i v  i  i       iv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_185396137_    923 ATTACAAGGCCATAGTAACCAAAGCAGCATAGTATTTGTATAATAATAGA 972
                          i     i  i i     i   ii   ii i   i v i    vi     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_185396137_    973 TACATAGACCAATGGAACAGTATAGAGAACCCTGAAATAAGGCCACATAT 1022
                         i i     i        i  v  v    ii  v       iv   i i  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_185396137_   1023 TTACAGCCAACTAATCTTTGACAAATCTGACAAGAACTTACACTGGGGAA 1072
                            ii i   i i  i  i     ivv  v     v v v  v       
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_185396137_   1073 AATATACTCTCTTCAGTAAATG-TGCTAAGAAAATTGGCTA--------C 1113
                          iv   v   i    ii     -    ii  v  i   v  -------- 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_185396137_   1114 AGAAGAATAAAACTGAACTCTTATCTCTCATCGTATA--GACATTAACTC 1161
                          i      i  ii  i  i i  i   v  i i    --i v        
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_185396137_   1162 AAAATAAATTAAAGATTTAAATATAAGACCTGAAAGTATAAAAATACTAG 1211
                              ii  i ?   ii     i     v  i   v       v vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_185396137_   1212 TAGACAACTAAAGCAAAACTCTTCCGGACATTGATCTAGGCAAAGGATTT 1261
                         v   v   vv i ?iv  v     vv   v   ivi       v  -   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTT 587

  chr1_185396137_   1262 ATTAC-TAAGACCTCAAAAGCACAGGCAACAAAAACAAAAACAGACAAAT 1310
                         v   v-  v   vi          i         iv     i   i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_185396137_   1311 AGAAAGGACTTAATTAAACTAAATAGGTTCTGCAAAGCAAAATAAATAAC 1360
                         v ----     v  i   v v  v iv  i  iivvv    iv v iv i
  L1M4_orf2#LINE/    638 TG----GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_185396137_   1361 CGAGA--GTGAAAAAACTATATGTTGAATGTGAGAAAATATCTGCACACT 1408
                          i   --       i  v iviiiv     v          i    v ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_185396137_   1409 AT-TAGTCTGACAGGGGGCTAATATTTA---TATTTGAGGAACTCAAACA 1454
                           -  -     i i   i  vi   ii ---   v i i      vv   
  L1M4_orf2#LINE/    734 ATATA-TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_185396137_   1455 TCTCAATAAATTACAAAAAACAACCCCAATCCTGTTAAAAAGTGTGCAGA 1504
                         v        --  -    i    vi--  i  vi  ?    i  v   i 
  L1M4_orf2#LINE/    783 ACTCAATAA--TA-AAAAGACAAAT--AACCCAATTWAAAAATGGGCAAA 827

  chr1_185396137_   1505 GGACATGAATAGACATTTCTGAAAAGAAGACATGCAAATGATCAACAGGT 1554
                            iv               vv        i  i      ii   i i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_185396137_   1555 ATACAAAAAAAAGCTTCACATCACTAATCAT 1585
                          i ii    i v   iv      ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (154 / 92)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.43 (51 / 21)  


2813 27.94 0.89 0.44  chr1_185418971_185421835.rev     1473  2374 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_185418971_   1473 GAAACACATCCCATGCTCATTGATGGGTAGAATCAATATTGTGAAAATGA 1522
                             v i        i    v   v  v   v i        v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_185418971_   1523 CCATACTGCCAAAAACAGTCTACAAATGCAATGCAATTCCCATCAAATTA 1572
                          v     v  v   viii      i  v   i     i  i      v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_185418971_   1573 CCATCATCATTCTTCACAGAA-TTAAAAAAAAAATCCTAAAATTTATATG 1621
                            v vv v  i  ii     -  i v  ivvi           i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_185418971_   1622 GAACCATAAAGTGCC-GGCATAGCCAAAGCAAGACTAAGCAAAAAGAACA 1670
                            viii  i vi  -i v         i   vvi i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_185418971_   1671 AATCTGAAGGCATCACATTCCCCGACTTCAAACTATACCACAAGACTGTA 1720
                           vi  i   vv     i i   i i      viv   i    ii  ii 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_185418971_   1721 GTCTCCACAACACCAAGGTACTGGTAATAAAAATAGGTACATAGACCAAT 1770
                           vvi  vi   viiv        i -   ii    ii i     i    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATCAAT 301

  chr1_185418971_   1771 GGAACAGAATAAAGAACCCAGAAGTAAAGTCAAATACTTACAGCCAATTG 1820
                             i     vi   ii      i    vi  v i i   ii i      
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_185418971_   1821 ATCTTCAAGAAAGCAGACAAAAACATAAAGTGTG-AAAGGACACCGTATT 1869
                           i   i v  i vv v   i v   vv i  v -    i i viv v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_185418971_   1870 CAACAAACGGTGCTGGGATAATTGGCAAGCCACATGTAGAAGAATGAAGC 1919
                                i          i  i   vv ?       i i          i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_185418971_   1920 TGAATCCTAATTTCTCACCTTATATAAAAAGCCACTTAACATGGATCAAA 1969
                           i i  iv ii  v    v    i     viv   i  v        ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_185418971_   1970 GACTTAAATCTAAAACCTGAAACCATAAACATTCT-GCAAGACAACATCA 2018
                            i     v   i v  i    i     - i   -iv    v     vi
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAG 550

  chr1_185418971_   2019 GAAAAAGTATTCTAGACATTGGCTTACGCAG-AGTTTAT--GATCAAGAA 2065
                          ?iv  i v   vv   v    v   v   i-i    v --   - v  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGAC 599

  chr1_185418971_   2066 CCCAACAGCAAATACAACAAAAACCAAAATAAAGAGATGAGACTTAATTA 2115
                         v    v    v vi        ivv      i v i  vi     v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_185418971_   2116 AA-TCAAAAAGCTTTTATGTAGCAAAAGAAATTATCAGGAGAGTAAACAG 2164
                           - i     -     i  ivv    i  v i     i  i   i  v  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_185418971_   2165 ACAACCCACAGATTGGGAGAAAATTTTCACCAACTATGCATTTAACGAAT 2214
                                     v           v  ii v  ii  ii  i i ii iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_185418971_   2215 AACCAATATCCAGAATCTACAAGGAGCTCAAACAAATCAGCAATAAAATA 2264
                         i  ivi          v  i  i  i   vv    v   ii       vi
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_185418971_   2265 ATAAATAATTTCAACAAAAAGTGTGCTAAAGACACAAATAGACAATTCTC 2314
                          i      iiiv vi?    i  v  v  i  ivii        v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_185418971_   2315 AAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACAT 2364
                         v                       i  i  i       i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_185418971_   2365 CACTAATTAT 2374
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.09 (12 / 11)  


3283 26.15 0.77 0.99  chr1_185453275_185459548.rev     4874  5783 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_185453275_   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATAAAAAT 4923
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_185453275_   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4973
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_185453275_   4974 TACTAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5020
                          v i i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_185453275_   5021 ATGTGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCGAAAA 5070
                           i     viiv  ii  v  v v  v     iv     i i ivi i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_185453275_   5071 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5120
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_185453275_   5121 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5170
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_185453275_   5171 TAATGGAACAGAGCAGAGACCTCAGAAATAATGCCGCATATCTACAACTA 5220
                         i       i   iiv    vii         vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_185453275_   5221 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGGTTCCC 5270
                         vi    i  i     ivv  vv  i v  vv            ii vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_185453275_   5271 TATTTAATAAATGGTGCTGGTAAAACTGGCTAGCCATATGTAGAAAGCTG 5320
                          v  i  i            v v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_185453275_   5321 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5370
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_185453275_   5371 TAAAGACTGAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5420
                         i ?    iv   i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_185453275_   5421 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5470
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_185453275_   5471 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATTTAAT 5520
                                     vvi          vv     v  i    v   i  v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_185453275_   5521 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAGA 5570
                         i   v v  i i   i  ii vv    i  v    i  vv i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_185453275_   5571 GGCAACCTACAAAATGGGAGAAAATTTTTGCAAGCTACTCATCTGACAAA 5620
                          i     i   i             v       iii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_185453275_   5621 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5670
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_185453275_   5671 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5720
                         i -    i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_185453275_   5721 TCAAAAGAAGAACATTTATGCA----GCCAAAAAACACATGAAAAAATGC 5766
                           v        -----   i  ----     v  i          i    
  L1M4_orf2#LINE/    847 TCCAAAGAAGA-----TATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_185453275_   5767 TCATCATCACTGGCCAT 5783
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


2786 26.93 1.99 1.77  chr1_185469690_185475577     4490  5395 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_185469690_   4490 TAAAAAAAAATTCCATACTCATGGATAGGAAGGATCAATATTGTGAAAAT 4539
                          ii   i v  i    ii        v     iv i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_185469690_   4540 GGCA-TACTTTCCAAAGCAATTTATAGATTCAATGCTATTCCCATTAAAT 4588
                             -    ii     vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_185469690_   4589 TACCATTGTTG--TTCGTCACAGAAAGAAAAAAAAAGCATTTTAAAATTC 4636
                          v   -- i  --  iv ii      vvi v  ivv -  ii        
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTC 147

  chr1_185469690_   4637 ATATG--AACGCCAAAAAGAGCTCATT-TAGCCAAGACAATCCTAAACAA 4683
                              --  i  ---  i ii i  vv-       i      i i  v  
  L1M4_orf2#LINE/    148 ATATGGAAATGC---AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_185469690_   4684 AAAGAACAAAACTGGAGGCATC-TGTTATGCAACTTCAAACTATACTACA 4732
                         i         ii      vv  -iii viv   i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_185469690_   4733 AGGCTGCAGTAGCCAAAATAGCATGGTACTGCTACCAAAGCAGACACATA 4782
                          i   i     ii   i i  ii        vi iv iiii     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_185469690_   4783 GACCAATAGAACAAAATAGAAAATTCAGAAATAAAACCACATATCTACAA 4832
                           i    i   i i   v  i i i          v   i i  i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_185469690_   4833 CCATCTGATCTTCAACAAACCTGACAAAAGCAATTAATGAAGAAAGGATT 4882
                         i  vi    i   i    ivv  v   i v  v i    ii     i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_185469690_   4883 CCCCATTTAATAAATGGTGCTGGGAGAACTGTTTAGCCATATGCAGAAAA 4932
                         vi iv  i  i              v     vv  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_185469690_   4933 TTGAAACTGGACCCTTTCCTTACACCTTATACAAAAATTAACTCAAGATG 4982
                         v    ii       i v   i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_185469690_   4983 GATTAAAGACTTAAATGTAAAATCCCAAACTATAAAAACCCTAGAAGAAA 5032
                            i ?    i         i v iv           vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_185469690_   5033 ATCTAGGC---AATGGCATTCAGGGCATAGGCATGGGCAAAGAATTTAT- 5078
                          iv    ?---   -- -   iv i v v  vv i     v iv  iv -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_185469690_   5079 GATGAAATAGCCAAAAGCAATTGCAACAAAATCAGAAATTGACAAATGGG 5128
                            ivi i -         vvv         vv i    v  i    v  
  L1M4_orf2#LINE/    592 GATATGACA-CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_185469690_   5129 ATCTAATTAAACTGAAGAGCT---GCATGGCAAATGGA-ACTATCATCAG 5174
                          ii v  i   v v  i i  --- iiivv    -   -       vv i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAA 689

  chr1_185469690_   5175 ATCAAACAGACAACATATAGAATGGGAGAACATTTTTGCAATTTATCCAT 5224
                          vii  v       vi i            v  v       v i  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_185469690_   5225 CCGACAAAGGTCTCATATCCAGAATCTACATGGAACTTAAGAAAATTTAA 5274
                          i  i  i  v  ii          v  i vi     iv-v v  i i  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAACTCAA 788

  chr1_185469690_   5275 -AAGAAAAATAAAAACAAACAATCCCATTAAAAAGTGGGCAAAATATATG 5323
                         -  v     ----i     i  i  v   ?    i        iv  v  
  L1M4_orf2#LINE/    789 TAATAAAAA----GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_185469690_   5324 AACAGACACTTCTC-AGAAAAGACAAACATGTGGCCAACAAACATATGAA 5372
                           i     i     - i i    i v   vi       i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_185469690_   5373 GAAA-GCTCAACATCACTGATGTT 5395
                         i i -           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (152 / 88)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.62 (34 / 21)  


2225 28.32 6.47 1.62  chr1_185489679_185491557      522  1386 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_185489679_    522 GGAAA-AGATTCCATGCTCATAGAGTGTAACAATCAATATTGTTACAATG 570
                              - v  i     i    i  v  v  v v i          vi   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_185489679_    571 GCCAT-CTGCCCAAAGCTATCTAAAGATTCAACAATATTCCTATCAAATT 619
                           v  -  v      viv     v         ivv  i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_185489679_    620 ACCAA-TGTCTTTCTTCACAGAATTTAAAAAAAT-ATTATAAAATTCATA 667
                         v   i-  i    i  -i     v  i v  iv -  iv           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_185489679_    668 TGGCACCCAAATATAGG-----CTGAATAGCCAGAGTCATTCTAAGCAGA 712
                            -----    ii i ----- v         i iiv  ii i iv ii
  L1M4_orf2#LINE/    151 TGG-----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_185489679_    713 AAGAATAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATGCTCTAA 762
                              i    i      vv     i v  ii i      viv i  vi  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_185489679_    763 GGCTACATTTACCAAGATAGTGTGGTACTGGCATACAAACAGACACATAG 812
                         i      v v i     i                 vii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_185489679_    813 ACCAAAGGAACAGAATAGAGTACCCAGAAGTAAAGCTTCACACT-GCAGT 861
                          i   v    i     v   vii      i    v ivi   i -iii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_185489679_    862 TATCTGATACTAAACAAAGTCAACAAAAATAAGCAATGGGGAAAAGACTC 911
                         i vi    vi vi    i viiv   i vi vv           ii ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_185489679_    912 CCTATTAAATAAATGGTGCAGTGATAGCTGGCTAGCCATATGCAGAAGAA 961
                         i  v  v  i         v v  i i    v  ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_185489679_    962 TGAGACTGGAACCCCCATCTTACAACACATATGTAAGTC--TTCAAACTA 1009
                            iii    -    i i  i   v  i   iiv  i i--i     v i
  L1M4_orf2#LINE/    446 TGAAGTTGGA-CCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_185489679_   1010 GA----AGAATTGAG---AAGA---AAACCTAGAAAATGTCATTTTGGA- 1048
                           ----   vi i i---    ---   v   v    i---- i  i  -
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC----TCTTAGAA 540

  chr1_185489679_   1049 -----CATAGG---------------CCTTGGG------AAAGAATTTAT 1072
                         -----      ---------------       ------  v iv  iv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_185489679_   1073 GATTAAGTCCTCAAAAGTAATTACAACAAAAACAAAAATTGGCATGTGGG 1122
                         iiv  v v vi      i vvvi        iv      v ii vi v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_185489679_   1123 ATCT----AAATACACTACAGATTTCCATACAGCAAAAGAAACTATCCAA 1168
                          ii ----   --- i  v i i  iii i vv    i  v      v i
  L1M4_orf2#LINE/    641 ACTTCATCAAA---ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_185489679_   1169 AGAGTAAACAGACAACTTACAGAATTGGAGAAAATATTCACAAACTATGC 1218
                          i   i  v       ii       v            ii    ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_185489679_   1219 ATCTGAGAAAGGTCTAATATTCAGAATCTTTGAGGTGTGTCAACAAATCA 1268
                               v  i  v  vi   i      v v i i viiviiv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_185489679_   1269 GCAAGCATAA-ACAAGTAACCCCATTAAAATGTGGACAAAAGACATGAAC 1317
                         ii  vv v  -    i      v   ?   vi   i    i  iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_185489679_   1318 AGACATTTCTCAAAAGATGACATACAAGCAGCCAACAA--ACATGAAAAC 1365
                                    v     v  i      iii     i  --         v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_185489679_   1366 ATTCTCCACATCACAAATCAT 1386
                           v   v      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 3.33 (70 / 21)  


2152 27.29 6.08 1.19  chr1_185530677_185533358     1354  2192 (490)    L1M4_orf2#LINE/L1       29   908 (0)  

  chr1_185530677_   1354 GAAGATCTGAATAA-ATGAAAATGTCAATTCTCCC-AAACTGATCTA--- 1398
                              -  v    v-i v  i   v    v     -   i       ---
  L1M4_orf2#LINE/     29 GAAGA-CTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chr1_185530677_   1399 ATTCCAACATATTTCCCATGAAATACCTAGCCTACTTTCTTTTCTAGAAA 1448
                             -   ii v i  i  v   vv  i   - i i  -    vi     
  L1M4_orf2#LINE/     78 ATTC-AACGCAATCCCTATCAAAATCCCAGC-TGCCTT-TTTTGCAGAAA 124

  chr1_185530677_   1449 CTTACTTGATGATACTAAAGTTTATAGGGGTAAGCAAAGAACCTACAACA 1498
                         i v  vv v    v     i  i   v  iv v    i i   i v  i 
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr1_185530677_   1499 GACAATACAATTTTTTAAAAGAAGAAGAGTGCTAGAGAACTTACATTTCT 1548
                          v   v     i  vv          v iv i i   i   i   i   i
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr1_185530677_   1549 GTATTGTACAATTTACTATAAACCCATAGCAATCAAGA--GTGTGGTATT 1596
                         vv   vi v  i      i   v i i  i        --        i 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_185530677_   1597 GATGTCAAGATG--------------TG--ATAGAATTGAG--TCCAGAA 1628
                          iii v i   i--------------  --           --       
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_185530677_   1629 ATAAATCTTAACATTTATGGTCAATTGAATTT-GACAAAGATAC-AGGAT 1676
                              i ivv                  v   -     i i i - i  i
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_185530677_   1677 AATTCAACAGATCGAGAATAAGTCTTTATAACAAGTAGTTTTTAGACAAC 1726
                         v      ii ivvi      -      vi     i i  vi vi      
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATA-GTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_185530677_   1727 TGAATATCTAAAAGCAAATAAATGAAATAGTAGTTTTAATTCAAACCATG 1776
                           i   ? i v v     vi      i v v viii  vi   v     i
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_185530677_   1777 CATGAAAAT-ATCTAAAAATCGATCATAGATTGATGTATAATAGTTAAAA 1825
                         i ii     - v  v     v     ?   iiv vi i   v  i     
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_185530677_   1826 CCATAAAATTTCTAAAAGAAAACATTAAG----ACTTTTTTTAAATTTAG 1871
                          i      i ii  i          - i ---- v i  iv i vi  - 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACAT-AGGNGTAAATCTTCGTGACCTT-G 571

  chr1_185530677_   1872 GGCTAGACAAAGATTTTTTAAATATAATACCAAGTGCATTATCTATTTAA 1921
                           i   i   v i   i   i    i i     iv   iv v v ivv  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_185530677_   1922 --AAAAACAGA-AAATTGGAGTTTATCAAA-TTAAAAGTGTTTTCCACTG 1967
                         --     i   -        v  i      -      ii-    vii  v
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTT 670

  chr1_185530677_   1968 CAAAAAAGATACCATTAAGAAAATGAAAGGGCAAATTGCAAAATAAGAAA 2017
                             i--  i  i  i      i     i i   viii  i   ii  i 
  L1M4_orf2#LINE/    671 CAAAG--GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_185530677_   2018 AATTAATTGCGAAT--TATACCAGATAAAGGATTTGTATCCAGAATTTAT 2065
                           v  v    i   --    i v     i   i             v   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_185530677_   2066 AAGGAAG-----------AAGAGCAGATAGGTAAA-ATCTCAAATAAAAT 2103
                           i   v-----------  v ii i v  ii   - v i   v ?   v
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_185530677_   2104 TTGAACACAA-ATTTGCAAAGACATTTCACTAAAGAAGGTATATTAGTGA 2152
                         v  ii  v i-     v v         v i       i    iv i  i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_185530677_   2153 TAAATAGTCATACGACAAGATGTACAACAATATTATTCAT 2192
                         iv    iv  i i  v      iv     vi ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (137 / 89)
Gap_init rate = 0.03 (27 / 880), avg. gap size = 2.26 (61 / 27)  


2696 25.48 2.04 4.62  chr1_185592385_185595059     1253  2182 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_185592385_   1253 GGAAGATATTCTGTGTTCATGGATTGAAAAAATTAATATTGTTAAAACGT 1302
                          i       i ii             i  i v             i i v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_185592385_   1303 CAATACTGCCCAAAGTGTTCCACAGATTCAAGGTAATCCCTATCCAAATT 1352
                                v      v  v  i          v i          v    i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_185592385_   1353 CCAAG-GACAGTTTTGTAGAAATAGAAAGACCAGCCCTAAAATTTGTGTA 1401
                            iv- v vv     i      v  v ii iiii         ii i i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_185592385_   1402 AAACCACAGCACATCCTGAA-AAACAATA-AATCTTGAGTAGTAAGAACA 1449
                         i  vii  iviv i  v   - iv   v -        iv iv       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_185592385_   1450 AAGCTGGAGGCCTCACACTTACCTGACTTCAAATTATACTACAAAGCTGT 1499
                            i      v         -  ii i      viv            ii
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_185592385_   1500 AGTTAT--AAACAGTATGATGACAGCATTACACACACACACACACACACA 1547
                            v  -- i     i  i ivii    ----------------------
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCAT---------------------- 279

  chr1_185592385_   1548 CACACACACACACACACACATTAATGGAACAGAATGGAGAGTCCAAAAAT 1597
                         --- viv i v   i i v  i       i     v         i    
  L1M4_orf2#LINE/    280 ---AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_185592385_   1598 AAATTCATG--TTTGTAGTCAACTGATTTTAAACAAGT-TGCCACAAAAA 1644
                            ii   i--   i i     i       vi     v-     vi vv 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_185592385_   1645 TACAATGAGAAAAGGGAAATTTCTTCAATAAATTGAGCTGAAAAAATTGA 1694
                          v     i i    iiv i i i     i    v v    ii v  i  i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_185592385_   1695 AGATTCACGTGCAGACAAATAA--TCAGACCCATATTTCATATTACAAAC 1742
                          v ?i   i    i vi   i -- ii     v  ii   i ii i v  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_185592385_   1743 AAAAATCAGCTCAAAATGGATTAGAGATTTAAACACA-GATCAGAAACTG 1791
                               i i            i ?   ii    iii -  v vi     i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_185592385_   1792 TAAAACTACTAGGAAAAAA-ATAG-AGTAAATGCACCATGACATTGGATG 1839
                                vi   i i    -    -?      - vi i    v    i v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTT 575

  chr1_185592385_   1840 AG-TAATTATTCTTTGGATATGACCCCAAAAGCCCATGCAACAAAAGTAA 1888
                           -i   vi  ii  i        v        v  v          v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_185592385_   1889 AAATAAACAAGTGGTATTACATCAAA--CAAATAAGCTTCTGCACAGTCA 1936
                              i i  i v v i v       --i   -- i   i  ii vviv 
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAA--AACTTTTGTGCTTCAA 673

  chr1_185592385_   1937 AGGAAACAATCATCAGAGCAAAGAGACAATCTACAGAATGAGAGAATATA 1986
                             v  v    vv i  ii  i      i i        i     v   
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_185592385_   1987 TTTGCAAACCAAACTTATAATAAGAGGTTAATA-CCACAAATGTATAAGG 2035
                                 i  v iv v i     i ii vi  -   -i   i     i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCA-GAATATATAAAG 772

  chr1_185592385_   2036 AATGCAAACAAATCAATACCAAGAAAACAGAAAACCTAATTAAAAATGAC 2085
                           iv vv    v      vi  i  i   i v    i    ?    ----
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA---- 818

  chr1_185592385_   2086 CTGAATAGATAGAGCAAATGACCTGAATAGATAGATCTTAAAAGAAGACA 2135
                         --------  i -     v  ii        i vv   iv        i 
  L1M4_orf2#LINE/    819 --------ATGG-GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_185592385_   2136 TACACATGGCCAAGAAGTATA--AAAAAATGCTTAACTTCACTAATAAT 2182
                             v        v   i i --    i     i   v   ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (149 / 84)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 2.95 (62 / 21)  


2889 26.10 1.76 1.98  chr1_185623699_185626243     1146  2053 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_185623699_   1146 GAAAAATATTGCATGTTCAAGGATGAGAATAATTAAGATTGTGAAAAAGA 1195
                             i    iv        v    vi   v v    v     v  i v i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_185623699_   1196 CAATACTACCCAAAGCAACTTCCAGATTTAATGCAGTCCTTTTCCAAACA 1245
                                v      vii ii v      i  i   i   i v  v   iv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_185623699_   1246 CCA-CTGACATTCTCCATAGAAATAGAAAAATAAATCCTAAAATTCATAA 1294
                            -   v -  i iiii      v  v  iivi               v
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_185623699_   1295 GGAACCACAAAAGATCCCAAATAGCCAAAGCAGTCCTGAGCAAAAGAAAA 1344
                             vii   ii  i  vi          i  i  i   --       i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAGA 199

  chr1_185623699_   1345 TCCG----GGAGGCCTCATACAACCTGACTTCAAAATTTACTACAAAGTT 1390
                         v vi----     v    i  vv  ii i       i           i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_185623699_   1391 ATAGTAACTGAAA-AGCATAGTATTGGTGTAAAAACAAATATATAAAGCA 1439
                          i     iii i -  ii i   i   ii   ii i i i     i v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_185623699_   1440 ATGGAACAGAATATAGAACCTACATATAAATGCACACATTTACTACCAAG 1489
                               i     vv   ii i v v     iv  i       ivii   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_185623699_   1490 TCGTCTTCCAAAAAGATGCCAAGAACATATAATGGGGAAATGACAGTATT 1539
                          vi i   v v  i i        v   vi          vi i   v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_185623699_   1540 TTTAATAAATGGTATTTGGAAAACTGGATAACAATATGCAGAAGAATGAA 1589
                           i  i       ii v   v         ? v i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_185623699_   1590 ACCAGACCCCTACCTCTCACCATACAAAAAAATCAAATCAAAATGGATTG 1639
                         iiii            v       i v      i  v           ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_185623699_   1640 AAGGCTTAAACCTAAGATCGGAAACTGGGGAATTATAATATGAAACGAAA 1689
                         ?  i i    iv     v vi     ivii  i v --  -   --    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT--TA-GAA--GAAA 544

  chr1_185623699_   1690 ACACTGGGG-AAATCCTCTAGGAGAC--TGGTCTAGGCAGAGATTTTTTG 1736
                            iv  ? -     i  --- v   --   vi      iv i   i  i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTC---GTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_185623699_   1737 --TGTAACATCTGAAAACACAGACAACCAAAGCAAAAATAAAT---TGGG 1781
                         -- i i   i -i   i    ii    v    v       i  --- v  
  L1M4_orf2#LINE/    592 GATATGACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_185623699_   1782 ATTACATGAAGCTAAAAAGCTTTGGAACAACAAAGGAAACAATCCAAAAA 1831
                          i v   v  iv v    i    v vi vv       v  v   v i   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_185623699_   1832 GTGAAGAGACAATTCACAAGATGGGAGAAAATATTTCTAAACTACTCGTT 1881
                              i      ii    ii                vi   ii ivii i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_185623699_   1882 TGTCAAGGAATTAATAACCAGAATAGAGAAGGAACTCAAACAACTCAATA 1931
                           vi    i i vi  v        v v  i      vv           
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_185623699_   1932 GCAAAATAATAATAATAATAATCCAATT-AAAAATGAGCAAAAGATCTAA 1980
                         ii    vi i  -----    i      -       i     i   i i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAA-----ATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_185623699_   1981 ACAGGCAGTCCTCAAAAGAAGACATACTAATGGCCAACAGCTATATGAGA 2030
                          i  i  v i   v        i    v         i ivi i    - 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-A 884

  chr1_185623699_   2031 AAAATGCTAAACAT-ACTAATCAT 2053
                           i     v     - ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (149 / 85)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 1.89 (34 / 18)  


2204 26.53 6.13 1.42  chr1_185655503_185658545     1703  2550 (493)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr1_185655503_   1703 ATGGATTAGAAGAATCAATATTATCAAAATGGCCATACTGCCCAAATCAA 1752
                                i     v i      i i  i     v     v       ii 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr1_185655503_   1753 -CTACAGATTCAACACTATTTCTATCAAACTATCAACATCTTTCTTCACA 1801
                         -             i v  ii        v vi  i vv i  i  ii  
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr1_185655503_   1802 GCATTAGAAAAAAAAGATTCTAAAAT----------------------CT 1829
                          v v v  v  ivv-   i       ---------------------- v
  L1M4_orf2#LINE/    121 GAAATTGACAAGCT-GATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_185655503_   1830 GAATAGCCAAAGCAATCCTAAACAAAAAGAACAAAGCCAGAGGCATCACA 1879
                                    i     i i  v  i          iii    vv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_185655503_   1880 CTATCTGACTTCCAAATATGCTATTAAGACACAGTAACCAAAACAGCTTG 1929
                           vi ii i   v   iv i   iv   vi       i   i    iv  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_185655503_   1930 GTACTGGTTAAAAGA---ACA-ATAGA---ATGAAATACAAAACTCAGAA 1972
                                ivv  i  ---   -     ---   i    --i  i v   i
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATA--GAATTGAGAG 317

  chr1_185655503_   1973 ATAATAAATAGAGCTGCATACTTACAATCATTTGATATTTGATAAGACTG 2022
                         viv v     i v iii i i   iii   v     v  i  i   iv  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_185655503_   2023 ACAAAAACAAGAAGTGAG-AAAGAACTCCCTATCGGATAAATGGTTCTGG 2071
                         v   i v  vvv i  i -      ivvi  v ivi i       v    
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_185655503_   2072 GATAACTGGCTAACCATATGCTAAAAATTGAAGCTGGATTTCTACCTTTC 2121
                           i      v  ?   i    v   i v     i    iii      iv 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_185655503_   2122 ACAATATACAAAAATTTACTGAAAATAGATCAAAGATTTAAATGTAAGAC 2171
                           v             v   v     i     ?   ii           v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_185655503_   2172 CTCAAACAATATAAATCTTGGAAAACAACCTAAGAAATATTCTTCTCAAC 2221
                           v    v   v  v    i   i v   v  i ?ivv v     vii  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_185655503_   2222 ATCAAACTTTACAAATTATTT-TTGGCTAAATCCTCAAAA--ACAATTGC 2268
                         v iiiii vvi   - vi   -  i v  viv vi     --    --  
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAA--GC 614

  chr1_185655503_   2269 AACCAAAACAAAAATAGGCAAGTGGGAACT------AATTAAAGAGCTTC 2312
                            v   iv        ii  i v   vi ------       i -   i
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTT 663

  chr1_185655503_   2313 TGTATAGCAAAATAAACTGTCATTAGAAA---AACAGAAAACCTACAAAA 2359
                            iivv    iv v   i   --     ---  v   v    i   i  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCA--AGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_185655503_   2360 TGGGAGAAGATATTTGCAAACTATGCATCTGACAAAAGCCTAATATCCAG 2409
                                 i           ii  ii      i  ii v  vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_185655503_   2410 AATCTATAAGTAACT--TAAAAA--AATAAACTAGCAAAAATAAATAACC 2455
                            v     iv    --  v  v--     --  i-   i i        
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAA--TAA-AAAGACAAATAACC 808

  chr1_185655503_   2456 CA-TTAAAAAATAGACAAAA-ACATGACT-GACGCTTCTCAAAATAAGAC 2502
                           -  ?      i i    i- iv   v -   ii     v   v    i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_185655503_   2503 ATACGAGCAGCCAACAA--ACATGAAAAAATGTTCAGCATCACTAATCAT 2550
                             i iii     i  --         i   i   i     ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (131 / 90)
Gap_init rate = 0.03 (24 / 888), avg. gap size = 2.67 (64 / 24)  


 825 25.55 5.29 0.44  chr1_185681631_185687838.rev     2278  2504 (3704)  C L1M4_orf2#LINE/L1   (318)   590   353  

C chr1_185681631_   2504 TTTTTGACGAAGTT-CTAAAGCTAATTTAATGAGGAAGAGACAATCTTTT 2456
                             i   i i v - i  ii i -  i    i    iii i i      
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCTTTT 401

C chr1_185681631_   2455 CAACATATGGTGCTGTAACAACTGTATATCCAGAGGCAAAATAATAAACT 2406
                              v         vi       v   ?   v v      v   i  v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

C chr1_185681631_   2405 TCTACCCATACCTTACCGCATACGTAAAAATCAACCCAAA-TGGACTAGA 2357
                          vv    v     i  vv    iii      i   i    -    ii ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

C chr1_185681631_   2356 GGCCTAA-TATGAAAGCTAAAACTATAAAGCCTCTAGAATAAA---CAGG 2311
                          i     - i i i               i iii     v   ---i   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

C chr1_185681631_   2310 C--AAAT----ATAACCTTGGAGTAAGCAAAGATTTCCT 2278
                         ?--    ----i i       iv  i    v i    i 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 2.44 (39 / 16)
Gap_init rate = 0.03 (7 / 238), avg. gap size = 1.86 (13 / 7)  

2749 26.97 2.11 1.66  chr1_185681631_185687838.rev     4825  5725 (483)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_185681631_   4825 AAAAACATTTCATCCTCATGGATAGAAAGAATCAATATCATGAAAATGGC 4874
                            i i  ii   vi        v i    v i     ii v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_185681631_   4875 CATACTGCCAAAAGTAATTTATAGATTCAATGCTATTCCCATGAAACTAC 4924
                         v     v  v   v i  i  i        i  v  i  i  v   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_185681631_   4925 CATTGACATTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTTATATG 4973
                           vivi v  i  ii     v v  v  i-  -  ii    v  i     
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATG 152

  chr1_185681631_   4974 -AAATAAAAGAAGAGCCCACA-CAGCCAAGACAATTCTAAGCAAAAGGAA 5021
                         -    iv   -- ii    v -i      i     ii i iv  i i   
  L1M4_orf2#LINE/    153 GAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_185681631_   5022 CAAAGATGGAGGCATCACGCTACCTGACTTCACACTATACTACAAGGCTA 5071
                              v      vv    i  v  ii i    v viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_185681631_   5072 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGCCATATAGACCAA 5121
                               i   i    ii         i iv ii i  v        i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_185681631_   5122 TGGAGCAGAACAGAGGCCTCAGAAGTAACACCACACATCTACAACCATCT 5171
                             ii    iv   ivii     i   vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_185681631_   5172 GATCTTCGACAAACATGACAAAAACAAACAAGGGGGACAGGATCTCCTAT 5221
                            i        ivi  v   i v  vv   v     v  i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_185681631_   5222 TCAGTAAATGGTGCTGGGAAAACTGGCTAGCTATTGGCAGAAAACTGAAA 5271
                            ii              v      v  ? i ivv   i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_185681631_   5272 CTGGACCCCTTCCTTAAACCTTGTACAAAAATTAACTCAAGATGGATTAA 5321
                         i         v   i v   v i                 i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_185681631_   5322 AGACTTAAATGTGAAACCCAAAATCATAAAAACCC-AGAGGAAAACCAAG 5370
                             i       i i v i    ii      vi i-   i      vv  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_185681631_   5371 GCA-ATACCATTCA-GGTCATAGGCACAGGCAAAGACTT------TATGA 5412
                          ?i- v i -   i- ii v i  i-i      v ii  ------     
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGA 598

  chr1_185681631_   5413 CAAAAATGCCAAAAGCAATCA--CAACAAAAGCCAAAATTAACAAATGGG 5460
                           ------         --  --         vv     vi i    v  
  L1M4_orf2#LINE/    599 CA------CCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_185681631_   5461 ATCTAATTTTACTTAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGT 5510
                          ii v  ivv v    i i   i  ii vv    i  v       vv iv
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_185681631_   5511 GTGTACAGGCAACCTACAGATTGGGAGAAAATTGTTGCAGTCTACCCATC 5560
                            v v  i     i     v           vv     ivii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_185681631_   5561 TGACAAAGATCTAATATTCAGAATTTACAAGGAACT-TAACATATTTACA 5609
                            i  i iv  vi   i      v  i  i     - v   - i i - 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCA-A 788

  chr1_185681631_   5610 AGATAAAA---CAAACAACCCCATC-AAAAATGAGCAAAGGATATGAACA 5655
                         vi      ---    i     v  i-       i         v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_185681631_   5656 GACACTTTTCAAAAGAAGACATTTACATGGCCAACAAACACATGAAAAAA 5705
                             i  i  v        i  vi v        i  i          i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_185681631_   5706 AGCTGAACACTGATCATCAG 5725
                         v   v    iii????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 1.79 (34 / 19)  


2376 29.25 2.45 1.67  chr1_185748931_185753488.rev     3169  4067 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_185748931_   3169 GAAAAACAGTCCATGCTCATGGAATAGAAGAATCAATATTGCTAAAATGG 3218
                             i i vi     i       v i     v i       i   i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_185748931_   3219 CCATATTGCCCAAA-------GCAA--CCAACGCTATTTCTGTCAAACTA 3259
                          v   i v      -------i  i--i      v  ii  i     v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_185748931_   3260 CCAAGATTA--TTTTTCACAGAATTACAACAAACT-ATTTTAAAAT---- 3302
                            i--i i--     ii     v -ii    i  -  ii      ----
  L1M4_orf2#LINE/    103 CCAG--CTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_185748931_   3303 ATGAAGTTGAAAAAGAGTCAGGATAGTCAAATTCATACTAAGCAATAAGA 3352
                            i iv  v  ii  vi   i    i    viv  vi i iv  v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_185748931_   3353 ACAAAGCCAGAGGCATCACATTATCTGACCTCAAAGTGTACTGAAAGGAT 3402
                               iii    vv     i vi ii ii     iiv    iv  i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_185748931_   3403 ATAGTAAACAAAAACACCATCATACTGGTACAAAAACAGATACATGGACC 3452
                          i     v   i -  vii vi      i i  ii i   i i  i  i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_185748931_   3453 AATGGAACACAATGGGAAACCCAGAAATAACGCTGTACACCTACAACCAT 3502
                                i v   v ii ii          vv ii    ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_185748931_   3503 AGAATCTTTGACAAAGCCAACAAAACCAATTAAAGGGGGAGAAACTTG-C 3551
                         vvi  i  i     i viiv   i    -  v  v     i i v v - 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTC 397

  chr1_185748931_   3552 TATTCAATAAATGATGTGTGGATAACTGAGTAGCCACGTGCAGAATAATG 3601
                          v     i     i  ivv   i     ii  ?    i    i  v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_185748931_   3602 AAACTAAATACCTACCTTTCACCATGTACAAAAATTAACTCAACATGGAT 3651
                           ii ii iv       iv      i                 v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_185748931_   3652 TAAGTAATCTTATGTAAATATAAGATCTCAAACTATAAAAAATCCTAGAA 3701
                         i ?i-i i  -----    i     v  v           v-  i     
  L1M4_orf2#LINE/    498 CAWA-GACCT-----AAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAA 540

  chr1_185748931_   3702 GAAAACCTAGAA-CACATCATTGTGGACATGGACCTTAGCAAATAATTTT 3750
                               v   i?-i v   v i   iv v   i--    vv   ii   i
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTC 588

  chr1_185748931_   3751 TT-GCTAAGTCCCCAGAAGCAATTGCAACAAAAACAAAAATGGACAAGGA 3799
                           - v  v v v   i     vvv         iv      i  i  ivv
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_185748931_   3800 AGACCTAATTAAACTAAAGAGCTTCTGCAAAGCAAAGGGAATTATCAGTA 3849
                         i   i v  i   v v  i i   i  iivvv      iv i     iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_185748931_   3850 CAGTAAACAGACAACCTAGAGAATTGGGGAAAA-ATTCTGTAAAATATGC 3898
                         v   i  v        i v     v  i     -   -  i   vi  ii
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT-TGCAAATCATAT 737

  chr1_185748931_   3899 ATCTGACACAATTCTAATATCCATAATCTATAAGGGACTTAAAGAAATCA 3948
                               i viivv  vi      v   v     i i   ivv v  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_185748931_   3949 ACAAGCAAAAACCAAATAACCAAATTAAAAAATGGGCAAAGGACATGAAC 3998
                          i  vv    iv         v    ?                iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_185748931_   3999 AGATGCTTCTAAAAAGAAGACGTACAAGCAGGTACTAA--ACATGAAAAA 4046
                            iii    vv        ii     iii vi v   --         i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_185748931_   4047 ATACTCTGCATCATTAATCAT 4067
                           i   vi     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (160 / 99)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 1.95 (37 / 19)  


2714 23.86 6.87 1.63  chr1_185755267_185758474     1857  2715 (493)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr1_185755267_   1857 AATATGTCCAATGTTCATAGACTGGCCAAGTTAATATTGTTAAGATGTCA 1906
                           v  i   v        i  i   vvi v                 v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_185755267_   1907 ATACTACTTAAAAAAAAGCTGCTGATTCAGTGAATTCTCT-TTAATATTC 1955
                              v ii   vvi -v  i v      ii v v  i  - i  v  i 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGA-TCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_185755267_   1956 CAATGACTTTTTTTTTCCAGAAGCAGAAAAACTTTCTCTAAAAATCACAT 2005
                           iivi i      v--     iiv  v  i  vvii      v   i  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTG--CAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_185755267_   2006 GGATTTTCACAGCACCTTAAATAGGCAAAACAGAACTGAAAAAGAAACAC 2055
                            vv v  vi v   ivi     v       ivvi          iv  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_185755267_   2056 AAAGCTGG-GAATTCTCACTCCCTGATTTCAAAATTTATCCCAAATCTAC 2104
                             i   - i i  v    i  ii         i   iiv    v    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_185755267_   2105 AGTAATTAAAATATT-TAGTGCTTCTATAAATATAGATATACAGATTAAT 2153
                               i  i i v - i  i  vvi    iv     i   i    i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_185755267_   2154 GGAAGAAAATAGAGAGCCCAGAAATAAACCCTCATATATACTGTAAAATT 2203
                             v i   v     i              vi i  v  iv  v  v v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_185755267_   2204 ATTTTTGACAAAGTTGACAAGACCATTCAATATGGAAAAAACAGTCTTCT 2253
                              i     i v  v              iv     i  i      i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_185755267_   2254 CA----------TT------------TAGTCATCAT---------TTAAG 2272
                           ----------i ------------  ?i  -   --------- v   
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCA-CATGCAAAAGAATGAAG 450

  chr1_185755267_   2273 TTAGACCCTTACA-AACATTATATACAAAAATTAGTGCAAAATGAATCAA 2321
                           i     i   v-v   ii              iiv       i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_185755267_   2322 ATATCTATATGTAAGATCTAAAACTACAAAATATGTAGAAGACCTCATAG 2371
                          v i   v        v         i    iviv       vvv     
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_185755267_   2372 GGAAAAATCATCATGATATTGGATTTTGCAGTGATTTATTGAATATGACA 2421
                          ?iv     v  i   iv    i  vv   i  i   v  ii        
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_185755267_   2422 TAAAATGCTCAGTTAACAAAAGAATAAACAGACAAGTTAGACTTTAT--- 2468
                         iv   v  v  ivi          v   i   i  i  i     i  ---
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_185755267_   2469 AATT-----TTTTAATTGTTCATTGAAAGACAATATAAAGAA--TAAAAA 2511
                             -----i   ---   v v ii  i    v   v     -- i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTT---TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_185755267_   2512 GACAACTTAC-GAAAGGGAGAATATATTTGTAAGTCATATATGTAATAAG 2560
                               ii  -   v       v       i  i        v i     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_185755267_   2561 AAA----TATTCAGAGTATGCAGAGAACTCCTA-AACTCAACAACAGCAG 2605
                         ii ----   i    i   ii i       i  -       i  i -- i
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA--AA 795

  chr1_185755267_   2606 TAAAACAAACAACCCGATTCAAAAATGAGCA--------GAATAAACATA 2647
                         -  i     i     i   ?       i   --------     i    v
  L1M4_orf2#LINE/    796 -AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_185755267_   2648 TCTCCAAAGAAGATATACAAATAACTAGTAAATAAGCACTTGAAAAGAAT 2697
                                               ii i ----        v        vv
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCA----ATAAGCACATGAAAAGATG 890

  chr1_185755267_   2698 TTCAACATCATTAATTTT 2715
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (118 / 83)
Gap_init rate = 0.02 (21 / 904), avg. gap size = 3.48 (73 / 21)  


3259 23.77 2.13 0.45  chr1_185813937_185816962.rev     1644  2535 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_185813937_   1644 GGAAAACT-TTTAATGTTCATGGATCAGAAGACTTATTGTTGTTAAGAAG 1692
                              iv - iiv            ii         v i         v 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_185813937_   1693 GCAGAACTTGTCAAATTTGTCTACAGATTCAAAATAATCAGTATGAAAGT 1742
                            iv   ivi      vi             vii    vv   v   i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_185813937_   1743 CGCAACTGGAATTATTGGAGAAATTGACAGTCTTTTTTAAAAATACTTAT 1792
                          v  i   vvv  v   v           iv  vv iiv     v v   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_185813937_   1793 GAAATCTCAAGGAACCCAGGATATCCAACACAATCTTGAAAGA----AAC 1838
                          i  viv     i      i   v    v            i ----   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_185813937_   1839 AAAGCTGGAGGACTCACATTTTCTAATTTAAAACCTGACCTGAAAGCTAA 1888
                             i             i  i i     v   v  v  ivv       v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_185813937_   1889 AACAATAAAGTAGGTGTGCTA-TAATATACGAATAGACATG-AGATTAAT 1936
                          ii   v   vvi     v  - iii   v i        i-    i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_185813937_   1937 GAAAAAGAACTAAAAGTTCCAAAACCGACCC-CACATTTATGATCACTTG 1985
                          i  v    i i i   i vi   ivi    -i         i   v   
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_185813937_   1986 GTTTTTGGCAAACGTGCCAATAAAATTCAATAGGGAAAAAATTATCCTGT 2035
                         i    i i   iv       v vv       i      i   vi  i v 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_185813937_   2036 CAA-AAATGTTTCTGGAAAAAGTGTATATCCACATACAAAGCAATTA-GT 2083
                            -     v v    i v  v  v   ?      i    iv   v -  
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_185813937_   2084 ACAGATAGCTACCTCAAATTACACACAAATATTAACTCAAGATGAAATAT 2133
                         -ii  ivv        v ii i i     v          i   i vi ?
  L1M4_orf2#LINE/    452 -TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_185813937_   2134 AGACCTACATGTTATAGTTAAAACTATAACATTATTAGAAGAAAACATAG 2183
                                v    v v  i           v i v                
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_185813937_   2184 AA-TATATTACCCTAACCTTGAATTTGGCAATATTTTGTTACATATGACA 2232
                         i?-  v  ivi v i      ii  v      iv   v   v        
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_185813937_   2233 GCAAAAGCACAAATGATAAAATAAAAAATCTTACATGTATTAGACCTCA- 2281
                         v           iii i    v       --- v  iv   i   i   -
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAAT---AGATAAATTGGACTTCAT 647

  chr1_185813937_   2282 --AAATTAAAATGTTTTGTGCTGCAAAGCATACCATCAAGAAA---AAAA 2326
                         --         vv         v     v i  i         ---    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_185813937_   2327 AAAAACTCAGTGAAAAGGAAAAAATACTTGCAAATAATATGTCTGATATA 2376
                         i v   i  vv   vi   i      i        v    i       vi
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_185813937_   2377 GGACTAGTGTCCAGAATATATACATAATTCCTAAAATTGAATAATAAATA 2426
                              v  i             v v  i  i  v  i v         v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_185813937_   2427 GAGAAATAACCCAATTAAACATTTAGCAAAGTATCCAAATAGATACTTCT 2476
                           v             ?  v v vi      v  iii      i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_185813937_   2477 TGAAAGAAAATATATG--TGGCTAATAAGCATATGAAAATATGCTCAATA 2524
                         iv      i     ii--    i        i       v        i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_185813937_   2525 TCATTGAAAAG 2535
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.10 (109 / 99)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 1.77 (23 / 13)  


 744 23.67 3.27 2.45  chr1_185827169_185829768      735   979 (1621)    L1M4_orf2#LINE/L1        4   250 (658)  

  chr1_185827169_    735 AGAAATATACCAAGTCTTCAT--ATTGGAAGAATTAATATTGTTAAAATG 782
                          i i    v   v  --    --         v             i   
  L1M4_orf2#LINE/      4 AAAGATATCCCATGT--TCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_185827169_    783 TTCATACTATGCAAAGTAGTATACTGAGCAAATGTAATCCCTATGAAAAT 832
                         viv     viv    v ii v   v  viv  i i         v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_185827169_    833 CCCAGTAACAATTTTTACAGAATATTTTTTAA--AATC-TCAATTTCATG 879
                              ivi vv     i     -   vviv i--i   - v  v     i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_185827169_    880 TGGAA-TACCAGAGGGCTTTGAAAAGCCATAGCAATCTTGAGAAAGAAAA 928
                              - i v  -  i iiv   v     v i         i      i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_185827169_    929 ACAAAGTTGGAGGCATCTCACTTCTTAATTTCAAG--TTATTTTATAAAT 976
                                      vv  v      ii        i--   i -- i   v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT--ACAAAG 247

  chr1_185827169_    977 CTA 979
                            
  L1M4_orf2#LINE/    248 CTA 250

Transitions / transversions = 1.00 (29 / 29)
Gap_init rate = 0.04 (9 / 247), avg. gap size = 1.56 (14 / 9)  

1400 22.37 1.86 14.51  chr1_185827169_185829768     1357  2107 (493)    L1M4_orf2#LINE/L1      253   908 (0)  

  chr1_185827169_   1357 GTGATTAAAAAAAAATTTATGTTACTGGCATAAAAACAGACATATA-ATC 1405
                           i  i  i v i---- i  v           ii i         -   
  L1M4_orf2#LINE/    253 GTAATCAAGACAG----TGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_185827169_   1406 TAATGGAACACAAGAGAGAGTTCAGAAATAAACCCAAGCCTATACAATCA 1455
                         -       i v  vv      i              vi v v  iii   
  L1M4_orf2#LINE/    299 -AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_185827169_   1456 ACCAATTTTTGTACAAGAGCACCAAGAATACACAATGGGAAGAGGATAGT 1505
                          iii     i -     i ii      vi iv       i i  i     
  L1M4_orf2#LINE/    348 ATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_185827169_   1506 CTCTCCATTAAATTTTGCTAAGAGAACTGGATATCTACATGCAAAACAAA 1555
                           i i  vi    vv    ii  v         ? i          v  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_185827169_   1556 AAATCTGGACCCTTATCTTATACCATATAAAAAAATCAACTCAAAATGAA 1605
                         i  vi       i  i  i i        v      i           i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_185827169_   1606 TAAAAACTCTAAATGTAAAGCCTGACATCA--ATACTCT-ACAATGAAAT 1652
                          v ? ivi          iiv  i v ii -- v     - v  vi   i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_185827169_   1653 ATATGGTGAGGCCTTACACTTAATGTTTTTATTCATTTTGTATATCTTAT 1702
                            -  ? ------------   --------------------     -i
  L1M4_orf2#LINE/    547 ATA-GGNG------------TAA--------------------ATCTT-C 562

  chr1_185827169_   1703 TTGAACAAAAAGTATATTTTTCCTTTGGTTGTCTGACACTTGACAATGGC 1752
                         v   -----------------    v    i-------------------
  L1M4_orf2#LINE/    563 GTGA-----------------CCTTGGGTTA------------------- 576

  chr1_185827169_   1753 ATTGGCAACGATTGCTTCAATATGACAC--AAAACAATCAGACAATCAAA 1800
                         ---     i i  v   vi         --   i  --  ii   iv   
  L1M4_orf2#LINE/    577 ---GGCAATGGTTTCTTAGATATGACACCAAAAGCA--CAAGCAACAAAA 621

  chr1_185827169_   1801 GGAAAAATAAAACTAAATATAATATCAAACCAAAAAACAAGTGAGAATAT 1850
                          i       i --     vvi iv   --i     -------------- 
  L1M4_orf2#LINE/    622 GAAAAAATAGA--TAAATTGGACTTCA--TCAAAA--------------T 653

  chr1_185827169_   1851 TAAATCCAAAAACTTATGCACAGCAAAAGAAAC----AGCAAAATGAAAA 1896
                             ------     v  ii vv    i  v  ---- iv   i      
  L1M4_orf2#LINE/    654 TAAA------AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_185827169_   1897 AGTCAGGATGTGTATTGGAAGAAAATATTTGCAAACCATGTATCTTGCAA 1946
                         - v  ivviiiiv v   i                i   i     vii  
  L1M4_orf2#LINE/    698 -GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_185827169_   1947 GGAGTTAATATCTAAAAATACATTAGGAACTCCCACAACTCAATAACACA 1996
                           iii vi    i i  -  i  v i      ii            i v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAA-TATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_185827169_   1997 CATGCACAAAAAAACTGATTTTAAAATTAGAAAACAACCTAAATTTACAG 2046
                         v - -     v  v ii   ?v     vi v   vi ii i   vv   v
  L1M4_orf2#LINE/    796 AA-G-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_185827169_   2047 TTTTTCAAAGAAGATATACAAATAGCCA----GTGTATAAAAATGTGTTC 2092
                           i i                  i    ---- iii  i    vi  i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_185827169_   2093 AATATCACTAATCAT 2107
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (106 / 58)
Gap_init rate = 0.04 (24 / 656), avg. gap size = 5.12 (123 / 24)  


2096 27.96 2.71 0.71  chr1_185853208_185854914.rev      516  1216 (491)    L1M4_orf2#LINE/L1      194   908 (0)  

  chr1_185853208_    516 AGAAAGATAAAATCTGGAGACATCACATTGTCTGACTTGAAACCATACTG 565
                             ii i   i -     ivv     i vi ii i  v   v v    i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_185853208_    566 CATGGCTATAGTAACTAAAATAGCATACGACTAGTACAAA-ATAGACACA 614
                           vi    i     ii  i i  ii ivv   i i i  i-       i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_185853208_    615 TAGATAAATAGAACAGAATAGAGAACCCAAAAATAAAGCCACATACCCAT 664
                              v   i   i     v    ii   i       v   i i iii  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_185853208_    665 AACCAACTGATCTGCGATAAAGTCAACAAAAACAAACAATGGGAAAAGGG 714
                         iii   i    i v   i  i viiv   i v  vv       i    ii
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_185853208_    715 CAACCTATTCAAAAAATGATGCTAGGAAAACTGGCTAGGCATATGCAGAA 764
                         i ii  v     v     i    i   v      v  ?v  i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_185853208_    765 AAATGAAAAGTGGACCCCTATATCACACCATACACAAAA------TTAAG 808
                         i      i-v          iv          i      ------ i  i
  L1M4_orf2#LINE/    443 GAATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_185853208_    809 ATGAATTAAATACTTAAATGTAAGATCTGAAACGACAGAAATCCTAAAAA 858
                            i  i ? v  i           v  i    v i i  v  i  i  i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_185853208_    859 AAA--------GAAACTCTTTTGGACACTGGCCTAGGCAAAGAATTTATG 900
                            -------- v  v    ivv   vi   vi       v iv  iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_185853208_    901 ---ATGACGACCCAGATTAAATGCAACAGAAACAAAAATAGACAAATGGG 947
                         ---     -   v i vi v v      i  iv         i    v  
  L1M4_orf2#LINE/    592 GATATGAC-ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_185853208_    948 ATTTAATCAAGCTAAAAGTCTTCTACACAACAAAATAAACTATCAACAGA 997
                          i  v     iv v   iv   i iii vv    iv v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_185853208_    998 CTAAAAAGACAAAATTACAGGATGGAAGAAAATATTCGCAAATTATGCCT 1047
                         v i         v-ii    i    i          i      i  iiv 
  L1M4_orf2#LINE/    691 GTGAAAAGACAAC-CCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_185853208_   1048 CTAACGAGGGACTAATATCCAGTATCTACAAGTTACTTGAACAACTCAAT 1097
                           i ii       vi       v  v  i  ivv   ivv          
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_185853208_   1098 AACAACAACAATAAAAAGCCCA-CTAAAAACTGAGCAAAAGACATGTGCA 1146
                           i  v  -i i   v i    -i ?    v  i     i  iv  vii 
  L1M4_orf2#LINE/    790 AATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_185853208_   1147 GACATTTCTCAAAAGAAGACATACAAGTGGCCAACAAACATATGAAAAAG 1196
                                   v        i      i       i  i  i       ii
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_185853208_   1197 TGCTTAACATCACTAGTCAT 1216
                             i       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (124 / 69)
Gap_init rate = 0.01 (10 / 715), avg. gap size = 2.40 (24 / 10)  


3045 27.39 0.88 0.99  chr1_185863316_185867748.rev     3034  3942 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_185863316_   3034 TGGAAAAACATTCCATGCTTATGGATAGGAAGAATCAACATTGTGAAAAT 3083
                               i i  i     i i      v      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_185863316_   3084 GGCCATACTGCCAAAAGTAATTTATAGATTCAACGCTATCTCCATCATGC 3133
                            v     v  v   v i  i  i           v   i i    viv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_185863316_   3134 TACCATTGACTTTCCTTACAGAATTGGAAAAAAAAAGAAAACACTTTAAA 3183
                          v   vivi i  ii  i     v v  v  ivvi -------iii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-------TCCTAAA 143

  chr1_185863316_   3184 TTTCATATGGAACCAAAACAGAGCCTGCATAGCCAAGACAGTCCTAAGCA 3233
                         v           viiv  vi  v  v v        i   i  i i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_185863316_   3234 AAAAGAACAAAGCTGGGGGCATCATGCAACCTGACTTCAAATTATATTAC 3283
                          i          i   i  vv   ii vv  ii i      viv  i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_185863316_   3284 AAGTCTACAGTAACCAAAACAGTATGGTACTAGCAGGAAAACAGATATAT 3333
                           iv         i   i     i       i   vi ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_185863316_   3334 AGACCAATGGAACAGAACAGGGGACTCAGAAATAACACCACACATCTACA 3383
                            i        i    iv i iiii         vv   i    i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_185863316_   3384 A-CAACCTGATCTTTGACAAACCTGACAAAAACAAGAAATAGGGAAATAA 3432
                         i-   i-    i  i     ivv  v   i v  vvv   i      v  
  L1M4_orf2#LINE/    344 GTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_185863316_   3433 TTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATACGTGGAA 3482
                          vvi  v  i  i        i     v      v  ?   i i iii  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_185863316_   3483 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGA 3532
                         iiv    ii    i    v   i     v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_185863316_   3533 TGGATTAAAGACTTAAACGTAAGAACTAAACCCATCAAACCCT-AGAAGA 3581
                              i ?    i    i      i     v i  v    i  -      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_185863316_   3582 AAACCTAGGCA-ATACCATTCAGGACATAGCAT-GGGCAAATACCTCATT 3629
                             v    ?i- v i -   iv   v v vi -i     vviii  v v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_185863316_   3630 ACTAAAACACCAAAAGCAACTGCAACAAAAGCCAAAATTGACAAATGGGA 3679
                         iv  vi            vvv          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_185863316_   3680 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAG 3729
                         ii v  i   v v  i i   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_185863316_   3730 TTAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 3779
                          v  v  i     i                 v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_185863316_   3780 GACAAAGAGCTAATATCCAGAATTTACAAAGAACTTGAACAAATTTACAA 3829
                           i  i ii  vi          v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_185863316_   3830 GAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAAGATATGAACAGAC 3875
                         v     i    ----   v  i?    i        i   v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_185863316_   3876 ACTTCTCAAAAGAAGACATTTATGCGGCCAACGGACACATGAAAAAAAGC 3925
                          i     v        i  vi vii      iiii          i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_185863316_   3926 TCATCATCACTGGTCAT 3942
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


2857 23.40 2.98 6.38  chr1_185902111_185904302      760  1699 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_185902111_    760 TAGAAAGACACCTCATGCTCAAGAATTGGAATAGTTAATATTTTTAAGAC 809
                          i      i i i    i   v i       v v        v      i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_185902111_    810 GTCAGTATTACCCAAAGGTGGTCTACAGATTTGATGCGATCACTATCAAA 859
                          v  i  i v      v-  i          ii i  i   v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_185902111_    860 ATCACAATGGCACTTTTTGCCAAAGCAGAAAAATATATTCTAAAATTCAT 909
                            v  iiv  vi       vi  iiv  v  iivv  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_185902111_    910 ATAGAATCTTAGGAAACCCCAAATAGCTAAAA-AATTCTCAAAAAAAAGA 958
                           i   vivi i ii    vi      i    -   ii v     i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_185902111_    959 -CA---TT-------TCACACTTACCAATTTCAAAACTTAATGAAAACCT 997
                         -  ---  -------        v                ----------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA---------- 239

  chr1_185902111_    998 TGGAACTTATTAAACAATGACAGAATCAGTGAATTTATGTTTTCTACAAA 1047
                         -------------------------------------------       
  L1M4_orf2#LINE/    240 -------------------------------------------CTACAAA 246

  chr1_185902111_   1048 GCTGTAATAATAAAAGTATTGTGGGATTGGCATAAAAACAGAGATAGCCA 1097
                            ii i    v  iii v     v i        ii i   v   vvv 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_185902111_   1098 CCCATCAAATAGAATAGTGAGCCCAGAAATAACCCTTCATATATATGGTC 1147
                         i v  vi        v v   i          v  ivi i  v       
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_185902111_   1148 AAATGATTTTTAATGAAAGAGTCAAAACCATTCAATGGAGGAAAAGAGAG 1197
                           v       ii ii ii v i   i            -     ii v  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAG 395

  chr1_185902111_   1198 TCTTTTTAATCAGTGGTGTTGGGGAAATTGGACATCCACATGCAAAAAAA 1247
                               i  iv i     i    iv  i    i ?            i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_185902111_   1248 TGAAATGGAATCCTTACCTTATGACACATACAAAAATTAACATAAG-TAG 1296
                             i v i i  i     i iiv  i              vi  i- i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_185902111_   1297 GTCAAAGACCTGAATGTAAGAGCTAAAACTTAAAAACCCCTGGAAGCAAA 1346
                         i   ?      i                  vv     i i i    v   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_185902111_   1347 CATAGGGGAAAATCTT---GACATTGGATTTGACAATAAAATATTGTATG 1393
                               ? v       ---   v    i  v i    iivv v  iv  i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_185902111_   1394 TGACACGGAAAATAGAGGTAA--AAAATAAAAATGGA-AAACTGGAAGGA 1440
                               vi   ii v i i  --   iv      i  -   i    vvv-
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT- 644

  chr1_185902111_   1441 TATCAACATTTTTAAAAG--TCTGTACAACATAAGACACAATTAC-AGAG 1487
                         i     v   ---    i-- i   i vv  v i     v  i v- i  
  L1M4_orf2#LINE/    645 CATCAAAATT---AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_185902111_   1488 TAAAAATAAAAGCTATGGAATGAAAGAAA-T-CTTGCTAAATCATATTTC 1535
                          i    v v  v i ii     ii     - -i    -         v  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC-AAATCATATATC 740

  chr1_185902111_   1536 CAATAAGGGGTTAATATTTAGAATATATAAAGAA---TCATAACTTAA-A 1581
                         ii       ii vi   ii               --- i i    i  - 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_185902111_   1582 ACAGAAAAACAAATAGCCTAATTTAAAAATGAGCAAAGAACTTGAATGAA 1631
                          i i   i       i  i    ?       i      i i      ii 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_185902111_   1632 CATATCTTCAAATAAGACATTCAAATGGCTAACAACCATGTGAAAAGATA 1681
                            v   i    v    i  v        i  i  v  ii         i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_185902111_   1682 TGCAACAGCACTAATCTT 1699
                         iv     v  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (140 / 76)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.40 (88 / 20)  


2686 20.88 2.20 0.47  chr1_185987919_185989547.rev      502  1138 (491)    L1M4_orf2#LINE/L1      261   908 (0)  

  chr1_185987919_    502 GACAGTGTGGTGCTGGCCCAAAAATAAACGTATGAGTTAATGGGATATAA 551
                                    i     vi  ii   i  i   iii i     i   v  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_185987919_    552 TGGAGTATCCAGCAATAATTTCATACATTTATGGTCAACTGATTTT-AAC 600
                          v   vi     v     vii                 i       -i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr1_185987919_    601 AAATGTGTCAAAAGTATTCAACATAAAAAGGATAGTCTTATCAAAAAATT 650
                           iv   i   i vi      iivii    i        v    v    v
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_185987919_    651 GTTTTGGGACAAGTAAATAGCCACATGCAAAA--------TTGAGCTCTT 692
                           vi        v ii   ?            --------   ii i i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_185987919_    693 ACTTCACATCATATAAATAAAGTAAAAATAAATAGTTCAAAGATCTAAAT 742
                           i     i      v v   v   vvvv    i v   ?   i      
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_185987919_    743 GGAAGAGGTAAAACTATAAACTTCATAAAAGAAAATATATGGGCAAATAT 792
                          v     v            vi  v  i       i   v ? i    v 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_185987919_    793 TCATGACCCTGGATTTCACAAAGTATTCTTTCCTATGA-ACCAAAAGCAA 841
                           i     i   i  vvi   v vv     vvv     -          v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_185987919_    842 AAACAACAAAAGATAAAAACAGATAAACTAGACCTCATCTAAATTAAACA 891
                           i          -     i       i i   i     v        v 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_185987919_    892 CATTTGTACCTCAAAGGATACCATCAAGAAGGTGAAAAGACAATCTACAG 941
                          v     i i        i  i        i            i i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_185987919_    942 AATGGGAGAACATATTTTCAAAGCATACATATGATA-GAGTCTT-TATTT 989
                                   v      v    v    i  v     - i v   -   ii
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_185987919_    990 AGAATATATAAA-AACTCTTACTACTT-GTAATAAAAAGACAAATAACCC 1037
                                     -         v   i-i                     
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_185987919_   1038 AATATTAAAGAAAGCCATAAGTTTATAAATAGACATTGCCCCAAGGAAAA 1087
                            - ?   i vi v  v i v  - i          v i    i   i 
  L1M4_orf2#LINE/    810 AAT-TWAAAAATGGGCAAAGGATT-TGAATAGACATTTCTCCAAAGAAGA 857

  chr1_185987919_   1088 TATCCAAAAGGCCAATGAGCTCATAAAGAGATGATTGACATCATTATTCA 1137
                            v    v       i   v   i  i     v ii      ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_185987919_   1138 T 1138
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.35 (74 / 55)
Gap_init rate = 0.02 (10 / 648), avg. gap size = 1.70 (17 / 10)  


2356 25.66 6.21 1.73  chr1_186017469_186020260     1431  2299 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186017469_   1431 TGGAAAGA------ATGGCCATGAATTTAAAGCATTAATGATGTTAAAGT 1474
                                 ------   vi    i   vi   vv     iv      ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186017469_   1475 GCTCATTTTACCCAGAGTTATCTATAAATTCAATGCA-TTCCTGTCAAAA 1523
                          viv  vi v    i v v     i i      i   - i   i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186017469_   1524 TTCCAA-TATAATTTTTCAAAGAAGAAA--AACAAA---ATT---AAACT 1564
                          i   i- iivv     ---- v     --i    i---  i---   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT----GCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_186017469_   1565 CATATTGAACTAGAAAAGACCTCAAACAGTCAAAGGAATCTTGAGAAA-- 1612
                              v   v iv  ii    ivi  i  i    iv        i   --
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_186017469_   1613 AGAGGAAGGCTGGAGACATCACATGCCTTGATTTCAAACTATATTACAAA 1662
                            iv  i i     ivv     ivi iii        viv  i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_186017469_   1663 GCTAAAGTGATCAAAAAAGTATGTCATTGGCCTCAAAATACATATATAGA 1712
                             v   i     i v   i  vi i    v v ii   v i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_186017469_   1713 CAAATGGAGTAGAAT-AAGTAGCCCAGAAATAAACTCATGCAAATACAGT 1761
                         iv      i      -i  -  i            i   i  vv  ii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_186017469_   1762 TAGCTAATCTTTGACAAGATCACCTAGAATACATAATGGA-AAAGGATAA 1810
                         i ii i  i  i      ivii  v   vi ivi     i-    i   i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_186017469_   1811 TCTCTTCAGTA----GTTCTGGAAAAAACTGAATATCTACCTG-AAAAGA 1855
                            i    ii ----  v    i v  -   i   ? i  v  -      
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGA 444

  chr1_186017469_   1856 ATAAAATAGG-CCTCTTTTTTACACTATACACACAAAAAAATTCAAAAGT 1904
                           i  i v  -  i  vii i    i   i   v   vv  i      vv
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_186017469_   1905 GATTAAAGACTTAAATGTAAGAACTGAAACCATAAAACACT-ACCA-AAA 1952
                            i ?    i           i  i    i       v  - vv -   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_186017469_   1953 ACATAGAA--AAA-------GA----GTGTT-GGCAATA-TTTTTTA-AT 1986
                               i?--   -------  ---- v   -      i-   i   -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_186017469_   1987 ATTACAGTCAAAGCACAGGCAATGGAGGCAAAATAATCAAGAAA---GAC 2033
                           v   viv        i    iii i -    -   vi v   ---   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAG-AAAA-AATAGATAAATTGGAC 642

  chr1_186017469_   2034 TATTGTACATCAAA-CTAAA---TTCTGTACAGCAGAGAAAACAGTCAAC 2079
                          ---- -       -i    ---  i   i vv  i  i v  vi    v
  L1M4_orf2#LINE/    643 T----T-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_186017469_   2080 AAAATGAAAGG-CAGCCTACAGAATATTAGGAAATGTTTGCAA-TCAATA 2127
                            i     i -  i  i       ivv  i    i       -   -  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TA 736

  chr1_186017469_   2128 TATCTAATAAGAGGTTAATAAACAAAATATATACAAAATATGTGTAAAAT 2177
                              i     i ii vi  vv  i        v i  iviv ii  v- 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-T 785

  chr1_186017469_   2178 CAATATCAAAAGAGCAAATAACCTGATTAAAAAATGGGCAAAGGATCT-A 2226
                              vi    iii         ii   ?                 i - 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_186017469_   2227 ATAGACATTTTTCCAACAAAGACTTACAAATGGCCAACCAGTATATAAAA 2276
                                   i     vi    iv             iv  i i  i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_186017469_   2277 AGATCCCAAACATCATTAATTAT 2299
                             v iv       ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (142 / 77)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 1.97 (69 / 35)  


3037 27.40 1.10 0.77  chr1_186026321_186032715.rev     5000  5904 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186026321_   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5049
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186026321_   5050 GGCCATATTGCTCAAGGTAATTTATAGATTCAATGCCATACCCATCAAGC 5099
                            v   i v i   iv i  i  i        i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186026321_   5100 TACCAATGATTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5147
                          v   iiviii  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_186026321_   5148 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5197
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_186026321_   5198 GAACAAAGCTGGAGGCATCACACTACCTGACTTTAAACTATACTACAAGG 5247
                                 i      vv       v  ii i  i   viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_186026321_   5248 CTACAGTAACCAAAACAGCATGGTACTTATACCAAAACATAGATATAGAT 5297
                                  i   i    ii       vii iv ii i v v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_186026321_   5298 CAATGGAACAAAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5345
                                 i i  i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_186026321_   5346 CATCTGATCACTGACAAACCTGAGAAAAACAAGCAATGGG-AAAGGATTC 5394
                           vi    ivii     ivv  vv  i v  vv       -    i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_186026321_   5395 CCTATTTAATAAACGGTGCTGGGAAAACTGGCTGGCCATATGTAGAAAGG 5444
                         i  v  i  i   i          v      v i?   i   i i  iii
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_186026321_   5445 TGAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGG 5494
                             ii    i    v   i    iv              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_186026321_   5495 ATTAAAGACTTACCTGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5544
                           i ?    i  vv   v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_186026321_   5545 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5593
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_186026321_   5594 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5643
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_186026321_   5644 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAATACCATCAGAGTGA 5693
                         v  i   v v  i i   i  ii vv    i  v v  i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_186026321_   5694 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5743
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_186026321_   5744 AAAGGGTTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5793
                           i  ii vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_186026321_   5794 ATAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 5843
                          v i     i     v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_186026321_   5844 TCTCAAAAGACATTTATGCA----GCCAAAAGACACATGAAAAAATGCTC 5889
                             v     - vv   i  ----     v ii          i      
  L1M4_orf2#LINE/    845 TCTCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_186026321_   5890 ATCATCACTGGCCAT 5904
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


1092 26.91 0.79 5.28  chr1_186054235_186056834      527   905 (1695)    L1M4_orf2#LINE/L1        3   364 (544)  

  chr1_186054235_    527 GAACAATATACCATGTCCACAGATTGGAAGAATTAATATTGTTAAAATAT 576
                            vi    v      i  ii          v             i  iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_186054235_    577 CCATACAACCCAAATCAATATACACATGAAGCAAAATACATATTGAATGA 626
                          v    vv       ii  v    v  vv i iv   -------------
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAAT------------- 89

  chr1_186054235_    627 TTTCCCTAT--AAATTCCAATGACATTTTTCACAGAAATAGAAAAATGC- 673
                         ---      --    i   iivi v     ii       v  v  --  -
  L1M4_orf2#LINE/     90 ---CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCT 134

  chr1_186054235_    674 AATCCTAAACTTTGTATGGAATCACAAAAGACCAGAAATAGTCAAAGTGA 723
                         i        v  ii       vii   ii    vii     i    iii 
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_186054235_    724 TCTTGGAAGTAAATTAAAAAAGTTTGAAAGCATCACATTTCCTGATATTA 773
                              i  ivi  v-  v      v  iii -     i    ii  v i 
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAG-AACAAAGTTGGAGGAC-TCACACTTCCCAATTTCA 232

  chr1_186054235_    774 AATTATATTACAAAGGTATAGTGTTTAAGACAGTATGATACTGGCATAAA 823
                           viv  i       v  i   iv i        i  i           i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_186054235_    824 AAAGGACACCTAAACCAATGCAATGAAATAGAAAGCCCAGAAGTAAACTC 873
                         i vi    iv  i i     v   ii   v  i  i      i     i 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_186054235_    874 AAGCACATACAGCGAACTAATTTCCAACAAGG 905
                          vi  iv  ii iv  i i    i i      
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGG 364

Transitions / transversions = 1.91 (67 / 35)
Gap_init rate = 0.02 (6 / 362), avg. gap size = 3.83 (23 / 6)  

1267 22.20 6.05 4.71  chr1_186054235_186056834     1303  1748 (852)    L1M4_orf2#LINE/L1      379   830 (78)  

  chr1_186054235_   1303 CAATGAGGAAAGAATAGTCTTTTCGATAAATGATGTTGAGTGAACTGAAT 1352
                              i                  i i     i  i  i vv     i  
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_186054235_   1353 ATCCACATGCAAAGAAATGAAACTGGACCCTTATCTTACACTAGACACAA 1402
                          ?           ii      ii       i  i  i    i v i    
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_186054235_   1403 AAATCAACTTAAAAAAGATTAAAAACCTAAACATAAAACCTGAAACCATG 1452
                             i    i    vi   i ? i       ii   i v  i    i  i
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_186054235_   1453 AAATTCCTACAAGTAGAC-TAGGGGAAAAGCTTCTTGATATTGCTGTT-G 1500
                            i  i  v   v i  -    ? v   v    v   iv   v-   - 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAG 577

  chr1_186054235_   1501 GCAATATTTTTTTTGTCTTATCACACCAAAAGCTCAGGTAACAAAAGCAA 1550
                              iv   i  v v--   v           v  i i        -  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGA--TATGACACCAAAAGCACAAGCAACAAAAG-AA 624

  chr1_186054235_   1551 AAAATAAAAATAAAAATAAA----ATAGAAAT---AAACT---GGGCCT- 1589
                               i --    v- ii ----  vi    ---     --- v  i -
  L1M4_orf2#LINE/    625 AAAATAGA--TAAAT-TGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_186054235_   1590 -----ATATCTAACTAGAAAGCTTCTTTGAAGCATGGACAATAATCAACA 1634
                         ----- i -   v v      ------    ------ vi i  i v   
  L1M4_orf2#LINE/    672 AAAGGACA-CTATCAAGAAAG------TGAA------AAGACAACCCACA 708

  chr1_186054235_   1635 AGAAC---AAAAAG-----GCAGCCCATATATCTGAAAAGGGGTGAATAT 1676
                         -   i--- i   i-----   ivi           v     iivvi   
  L1M4_orf2#LINE/    709 -GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_186054235_   1677 CCAAAATATAGAAGGAATTCACACAACTCTATAGCAAAAGGACAAATAAC 1726
                            i      v  i   i  vi       v   ii    i          
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_186054235_   1727 TCCATT-AAAAATGTGGAAAAAA 1748
                         i v   -       v v   ii 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.82 (62 / 34)
Gap_init rate = 0.04 (18 / 452), avg. gap size = 2.67 (48 / 18)  


1910 28.18 1.90 1.90  chr1_186094798_186096465      491  1175 (493)    L1M4_orf2#LINE/L1      224   908 (0)  

  chr1_186094798_    491 CTAACTTCAGA-CTTCAAACTATGCAAGACCACAGTAACCAAAATAGCAT 539
                          i  i    i -   ---    --   ii i       i   i i  ii 
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTT---ACTA--CAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_186094798_    540 GGTACTCATACAAAAACAGGCACATAGACCAATGGAAGAGAATAGAGAAC 589
                               vii i  ii i  i  i     i        v     v    ii
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_186094798_    590 TCAGAAATTAATCCGCACATCTACAACCATCTGATCTTCAACAAACCTGA 639
                         i       v  i  ii    i  iiii  vi    i   i    ivv  v
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_186094798_    640 CAAAGACAAGCAATGGGGAAAGGATTCTATATTTAATAAATGGTGCTGGG 689
                            iiv  vv            i  vv v v  i  i             
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_186094798_    690 AAAACTGGTTACCCACATGCCGAAAACTGAAATTGGATCCCTTCTTTACA 739
                          v      v  ?        vi  i v    i     i    v i i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_186094798_    740 CCATATGCAAAAAATTAAGTCAAGATGGATTAAAGACTTGACTGCAAAAC 789
                               i      -    v    i      i ?    i i v  i  i v
  L1M4_orf2#LINE/    469 CCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_186094798_    790 CCAAAATTATAAAAACCCTAGAAGAAAATCTAGAC---AATGC-CATACA 835
                          i    i       vi i          iv   i?---   vi- i ---
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT--- 564

  chr1_186094798_    836 GACATAAGCATGGACAAAGACTTTAT-GATGAAATCACCAAAAGCAATTG 884
                            v vi vv i i   v ii  iv -   ivi -           vvv 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-CACCAAAAGCACAAG 613

  chr1_186094798_    885 GAACAAAAGCAACAACTGACAAATGCGA-----TCTAAACTAAAGAGCTT 929
                         v        v  v  iv  i    vv  -----  v   i    i -   
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTT 662

  chr1_186094798_    930 CTGCACAGCGAAAGAGCCTATCATCAGAGTGAATAGACATCTTATGGAAT 979
                         i  ii vv i  i  vv      vv i      v     v ii ii    
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_186094798_    980 GGGACAGAATTTTTGCAATCTCTCCATCTGACAGTGGTCTAATATCCAGA 1029
                             v i   v       viiv vi      i iv  v  vi        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_186094798_   1030 ATCTACAAGGAACTTAAACACATTTACAAGCAAAAAACAAA--ACCCCAT 1077
                           v  i  i     ivv   vv iv i  vv    i     --    v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_186094798_   1078 CAAACAGTGGGCAAAGGATATGAACAGATGCTTCTCAAAAGAACACATTT 1127
                         i?  v i            v    i   iii     v      v i  vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_186094798_   1128 ATGCCACCAGCAAACATATATGAAACAAAGCTCAACATCACTGATCAT 1175
                          viivi   ii  i  i  --    vi v           ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACAT--GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (112 / 77)
Gap_init rate = 0.02 (13 / 685), avg. gap size = 2.00 (26 / 13)  


3055 26.40 1.54 1.65  chr1_186111674_186117941.rev     4869  5777 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186111674_   4869 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCATGCAAAT 4918
                              ii    i     i        v      v i     ii vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186111674_   4919 GACCATATTGACCAAGGTAATTTATAGATTCAATGCAATCCCCATCAAGC 4968
                          i v   i vv    iv i  i  i        i        i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186111674_   4969 TACCAA-TGACTTTTTT-CATATAATTGGAAAAAACT-ACTTTAAAGTTC 5015
                          v   i-  v       -  v -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_186111674_   5016 ATATGGAACCAAAAAAGAGCCCGCATGGCCAAGACAATCCTAAGCCAAAA 5065
                                 viiv  ii  v  v v  i     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_186111674_   5066 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5115
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_186111674_   5116 CTACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5165
                               i  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_186111674_   5166 CAATGGAACAGAACAGAGCTCTCAGAAATAATACCACACATCTACAACCA 5215
                                 i    iv   vvii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_186111674_   5216 TCTGCTCTTTGACAAACTTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5265
                         vi  v i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_186111674_   5266 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATTTGTAGAAAGCTG 5315
                          v  i  i              v      v  ?   iv  i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_186111674_   5316 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGAT 5365
                           ii    i    v   i     v              i    ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_186111674_   5366 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAACACC 5415
                         i ?    i       v   v       i      vi i        v  v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_186111674_   5416 TAGGCA-ATACCATTCAGGGCATAGGCATGTT---TAAGGACTTCATGAC 5461
                             ?i- v i -   iv i v v  ---   ---i  v ii   v iiv
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGG---GTTAGGCAATGGTTTCTTAGA 593

  chr1_186111674_   5462 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGTATC 5511
                           vi            vvi          vv     v  i    v v ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_186111674_   5512 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATG 5561
                          v  i   v v  i i   i  ii vv    i  v    i  vv i i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_186111674_   5562 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 5611
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_186111674_   5612 CAAACGGCCAATATCCAGAATCTACAAAGAACTTAAGGAAATTTACAA-- 5659
                         i  iv i ivi          v  i        i--------      --
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTC--------TTACAACT 785

  chr1_186111674_   5660 ----GATGAAAAT-CAAACAACCCCATCAAAAAGTCAGCAAAGGATATGA 5704
                         ----i  i    v-    i     v  i?    i vi         v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_186111674_   5705 ACAAACACTTTTCAAAAGAAGAGATTTATGCAGCCAACAGACACATGAAA 5754
                          i i   i  i  v        v  vi viii     i ii         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_186111674_   5755 AAATGCTCATCATCACTAATCAT 5777
                          i       v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  


2867 25.03 2.61 3.81  chr1_186152892_186156387.rev     2087  3005 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186152892_   2087 TGAAAAGATATTACATGCTCATGAATTAAAAAAATTAAT---GTTCAAAT 2133
                           i        iv    i     i   ii  i v     ---   v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186152892_   2134 GGCAACACTATCAAAATCAGTTTACAGATTCAGTGCAATCT-TATCAAAA 2182
                              i   vi v    iii i          ii      i-        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186152892_   2183 TATTCA--TGACATTCTTCACAGAAAGAGAAAAAA-AATCCCCAAATTTA 2229
                          -ii  --  v -  i  ii      vv  v  iv-i    iv     i 
  L1M4_orf2#LINE/    101 T-CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_186152892_   2230 TATGGAACCATAAGAAAGAAACCCCAAATAGCTAAAGTAATTCTGAACCA 2279
                                --  -- v   ii    vi      i   ii   ii    vv 
  L1M4_orf2#LINE/    149 TATGGAA--AT--GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_186152892_   2280 AAAGAACAAAGCTGGAGGCATCACACTATCTGACTTTAAAATTTACTATA 2329
                         i          i      vv       vi ii i  i    i      i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_186152892_   2330 AAGCTATAATAACCAAAGTATCATGGCATTGGACTGAAAACAGGCACATA 2379
                               i i   i   iii vii   i i   vv i ii i  i  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_186152892_   2380 GACCAATGGGGCAGAATAGAGAACCCAGATATATATCCATACATTTACAA 2429
                           i      iii     v    ii     v   v i           iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_186152892_   2430 CCCACTCATCTTTGACAAAGGCACCAAGAACA--------GGCAAG--TA 2469
                         i v i v  i  i     i  ii      v  --------  v   --  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_186152892_   2470 ---CTTTCAGTAAATGGTACTGGTATATATAGACTTTTGTATAACTTTAT 2516
                         ---i     ii       i    v i -----   --- v   ? ivi  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACA-----ACT---GGATAKCCACAT 436

  chr1_186152892_   2517 GCAAAAGAATAAAACTAGACACCTGTATCTCACCAACCA-ATAAATGAAA 2565
                                   i  ii i   v   -- i     --    -   v -i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCT--ACCTCAC--ACCATATACA-AAAA 481

  chr1_186152892_   2566 GTAA---AACATGGTTTAAAAACTGAAATGTAGGATCTGAAACTATAAAA 2612
                         v   ---  v    v i ? i  iv       i  v  i           
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_186152892_   2613 CTACTGGAGGAAAACACTGGGGGAAAACTCCAGGATATTGCTCTGGAAAA 2662
                           vi i  i       iv  ? v   v  i iv  iv   vvi i iv  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_186152892_   2663 AGATTTTTTGTGTGTGTTTAAGACCTGAAAACCCCAGGCAACCAAAGCAA 2712
                         v i   i  ivi i  ---- v   --    v v  i     v    v  
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATG----ACACC--AAAAGCACAAGCAACAAAAGAAA 625

  chr1_186152892_   2713 AAGTAGACAGCTGTGATTACATCAATCTAACAAAGCTTCTGCACAGCAAA 2762
                           i    i iv vv  i v      vv v -   i   i  ii vv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAA 674

  chr1_186152892_   2763 GGAAACAATTAGAGAAGTGAATAGACAACACACAGAGTAAGAGAAAATAT 2812
                            v  v  i iii       v       v      i ii          
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_186152892_   2813 TTGCAAACTATCTATCTGACAAGGAACTAATAACCAGAATATATAAGGAG 2862
                                ii  v       i    i   vi  v             i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_186152892_   2863 CTCAGACAACTCAATAGTTTTTTTTAAAAAAAGCAAATAATCTGATTTTA 2912
                            vv           i --------     ii       i ii   ?- 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAAT--------AAAAAGACAAATAACCCAATTW-A 815

  chr1_186152892_   2913 AAAATTGGCAAAAGATCTGAGCAGATATTTCTCAAAAGAAGACATACAAA 2962
                              v      i   i   ii   i       v        i       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_186152892_   2963 TGGCCCATACATATATGGAAAAATGTTCAACATCACTAATCAT 3005
                              v   vii i   i   i   i         ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (150 / 76)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.57 (59 / 23)  


3324 25.99 0.55 0.55  chr1_186169773_186176055.rev     4885  5792 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186169773_   4885 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4934
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186169773_   4935 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4984
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186169773_   4985 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTC 5031
                          v   i-       i  -i     -   -- v  i  - iii v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_186169773_   5032 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5081
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_186169773_   5082 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5131
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_186169773_   5132 CTACAGTAACCAAAACACCATGGTACTGGTACCAAAACAGAGATATAGAT 5181
                                  i   i   vii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_186169773_   5182 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAA 5229
                                 i    i--    i  --        vv   i i  i  iiiv
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_186169773_   5230 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5279
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_186169773_   5280 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5329
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_186169773_   5330 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5379
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_186169773_   5380 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5429
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_186169773_   5430 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5479
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_186169773_   5480 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5529
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_186169773_   5530 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5579
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_186169773_   5580 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5629
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_186169773_   5630 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5679
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_186169773_   5680 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5729
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_186169773_   5730 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5779
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_186169773_   5780 CATCACTGGCCAT 5792
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (136 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 453 29.05 2.03 0.00  chr1_186213805_186219609     4325  4472 (1333)    L1M4_orf2#LINE/L1        1   151 (757)  

  chr1_186213805_   4325 TGGAAAAACATTCAATGCTTATGAATAGGAAGAATCAATATAGTGAAAAT 4374
                               i i  i v   i i   i  v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186213805_   4375 GGCCATAGTGCCCAAAGTAATTTATAGATTCAATCCTATTCCCATTAAGC 4424
                            v   v v      v i  i  i        iv v  i  i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186213805_   4425 TACCA-TTGACATCTTCACAGAATTAGAAAAACTA--CTTAAAATATATA 4471
                          v   -i  v v i  ii     v v  v  i  i-- i      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_186213805_   4472 T 4472
                          
  L1M4_orf2#LINE/    151 T 151

Transitions / transversions = 1.26 (24 / 19)
Gap_init rate = 0.01 (2 / 151), avg. gap size = 1.50 (3 / 2)  

1955 27.53 4.52 2.26  chr1_186213805_186219609     4563  5314 (491)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr1_186213805_   4563 TAAAATACATATAAAATTG------GCCCATATT-GCCAAGACAATACTA 4605
                               v     ii  v  ------i    v v -     i     vi i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_186213805_   4606 AGCAAAAAGAACAAAGCTGGAAGCATCATGCTAACTGACCTCAAACTATA 4655
                          iv  i          i    i vv   ii  vv ii ii     viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_186213805_   4656 CTACAAGGCTACAGTAACCAAAATAGCATGGTACTGGCACTAAAACAGAC 4705
                               i          i   i i  ii           iv ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_186213805_   4706 ACCTGGACCAATGGAAAAGAATAGAGATCTCAAAAATAACACTGCACATC 4755
                          iv i  i        v     v    vii  i      vv iii    i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_186213805_   4756 TGCAATCCTCTGATTCTCCACAAACCTGAAAAAAAAAAAAAAGAACGAGC 4805
                          iiii  vvi     i  v    ivv  vv  ----------  v ivv 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAA----------GACCATTC 379

  chr1_186213805_   4806 AATGGGGAAAGGATCCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTA 4855
                                    i  vvi  v  i  i        i     v      v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_186213805_   4856 GCCATATGTAGAAAGTTGAAACTGGAGCCTTTCCTTACACCTTATACAGA 4905
                         ?   i   i i  iiv    ii    v  i v   i     v      i 
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_186213805_   4906 AATTAACTGAAGATGGATTAAAGACTTAAATGCAAAACTCCAAACTATAA 4955
                                 v  i      i ?    i      i  i viiv         
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_186213805_   4956 AAACCCTAGAAGAAAATCTAGG---AAATACCATCCAGGACATAGGCACT 5002
                           vi i          iv    ---    -- - i iv   v v  -ii 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGG-GTT 575

  chr1_186213805_   5003 --GCAAAGATTTCATG---ATGAAAACACAAGCAATGGCAACAGAAGCAA 5047
                         --    v i    v i---    v v  v     vvi      i   v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_186213805_   5048 AAATAGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAACAAAA 5097
                                i    v   ii v  i   v v  i i   i  ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_186213805_   5098 GA------------AGTGAACAGACAACCTACAGAATGAACAAAAAAT-T 5134
                           ------------      v        i        ii- i     - 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG-AGAAAATAT 724

  chr1_186213805_   5135 TTGCCCCCTATCCGTCTGACAAAGGTCTAATATCTAGGATCTATAAGAAA 5184
                             vvvii  vii     i  i  v  vi    i  i  v     ii  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_186213805_   5185 CT--TA-AACACATTTACAAGAAAAAAAGAAAC---ATCAAAAAGTGGGC 5228
                           --  -   v  v v i  i  i v  iv   ---  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_186213805_   5229 AAATGACATGAACAGACAACTTCTCAAAAGAAAACATTTATGCAGCCAAA 5278
                            v  iv    i     -i     v      i i  vi viii     v
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACA-TTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_186213805_   5279 AAACATATGAAAAAAAAGCTCATCATTGATCATTAG 5314
                           i  i       i v-     v   ii????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (123 / 81)
Gap_init rate = 0.02 (17 / 769), avg. gap size = 3.00 (51 / 17)  


2832 26.00 2.56 1.67  chr1_186247962_186250728.rev     1377  2276 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186247962_   1377 TGGAAATACATCTCATATTCATGAATCAGAATAATTAATATTCTTAAAAT 1426
                               v i   i   i      i  ii   v v        v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186247962_   1427 GTTAA-AATTCTTAAAGTG-TCTACAGACTCAATGCACTCCGTATTCAAA 1474
                          vi  - v i ii   v  -        i    i   v   v   -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-CAAA 99

  chr1_186247962_   1475 GACTCA-TAACAATCTTCACAGAAATAGAAAATATATTCATAAAATTTAT 1523
                         iv i  -ivi vv i  ii       v  v  vv iv  v       i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_186247962_   1524 ATGAAATCACAGAATACCCCAGATAGCCAACATAATCTTGAATAGAAAGA 1573
                            i  vii  iiiv    vii        v i         v ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_186247962_   1574 ACAAAGCTGGAGTGA-TCACATCATCTGACCTCAAAATATACTGCAAAGC 1622
                               i     -  -     iivi ii ii      iv    i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAG-GACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_186247962_   1623 TATAGTAGCCAAAACAGAATGGGACTGGCCTAAAAACAGACACA-GGAT- 1670
                           i    ii   i    vi   v      v   ii i     i -i   -
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_186247962_   1671 AATGGAACAGAATGGAAATCTTATATATAAATTCACACATTTAGAGCCAA 1720
                                i     v  i viii v v     ii  i       vi i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_186247962_   1721 CTAATTTTTGACAAAGATGCCAAGAACA--CAA--GTAAAAGAGAAGTCT 1766
                         i i     i     i i        v  --   -- vi     iv     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_186247962_   1767 C--CAATAAATTGTACAGGGAAAACTAGATATCCAAATGCAGATGAATGA 1814
                         i--   i    v  i v    v    i    ?   v     i v      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_186247962_   1815 AATTATACCCATATCTCACACTATATACTAAAATTAACTAAAAA--AATT 1862
                          i  iv    v  i       i      v          v    --i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_186247962_   1863 AAAGACTTAAATGTAAGACCTGAAACTATGAAACTAATAGAAGAAAACAG 1912
                          ?    i           v  i       i     vv            v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_186247962_   1913 TGGA--AAACCTTCAGGATATTAC-CTGGGCAGTCATTTTTTTGGATATA 1959
                         v  ?--   i    iv  iv  iv-i i    i vi   i  -i     i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chr1_186247962_   1960 CCCCAAAAAACACCAGCAATGAAAGCAAAAATATCCAAATGGGATTACAT 2009
                         v v v    i   v     ii    v       vvi    v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_186247962_   2010 CAAA--TAAAATGTTTCTGCACAGCAAAAGAAGCAATGAACAAAGTAAAG 2057
                             --     -ii  i  ii vv    i  vi v  v  v     i  i
  L1M4_orf2#LINE/    648 CAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_186247962_   2058 AGACAGCCCACAGAACCGGAGAAAATATTTGCAAACTATATATCGAATGA 2107
                              i         iv                  ii       vi  i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_186247962_   2108 GAGGTTAATATTCAAATTATATAAGAAACTCACATAACTCAGGAAGAAAA 2157
                          i ii vi   i  i v       ii     vi i      iv  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_186247962_   2158 ---CAAATAACCTGAATAAAATGTAGACATTTCTCCATTTAACAACT-GA 2203
                         ---         ii v ?   vi i i  -----------  vi i -  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCA-----------AAGGATTTGA 835

  chr1_186247962_   2204 GTGGAAGTTTCTCAAAAGACAACATACAAGTGGCCAACGAATATATGAAA 2253
                         i i  vi      v     vi i      i       ii ii i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_186247962_   2254 AATTACTCAACATCACTAGTCAT 2276
                          iv i          ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (146 / 84)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.90 (38 / 20)  

 448 28.91 8.59 3.52  chr1_186247962_186250728.rev     2512  2767 (0)  C L1M4_orf2#LINE/L1   (551)   357    89  

C chr1_186247962_   2767 TCCTAATCAAAATGCTTGCAGGATGTTTTCATGGAAAT--ACATGTATTG 2720
                            iv        v iv  v vv -    iiii     --   v i--  
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGC--TG 135

C chr1_186247962_   2719 A-ACTAAAATCTGTTTGAAAATGCCAGTTCACCTATACTGGATAAAATCT 2671
                          -v       iii v  i      v  vv-   i v v i vi    - v
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGG-ACCCAGAATAGCCAAAA-CA 183

C chr1_186247962_   2670 ATTTTGAAAAAAATAAGAACAA-TCTGGTTGACTTACACCACCTGGTTTT 2622
                           i        i --       -vi   vv    i    iv  iii   i
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGA--AGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

C chr1_186247962_   2621 AAGAACTAAGATGCAATTACAGTAATCAAGAAAGCATGCTGTTGGCATGA 2572
                           i vi  vv iiv ii              v  ii  v ii      i 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

C chr1_186247962_   2571 AAATAGATATAGAGA-AAATATAACAAAATGCTGA-----TAGAAATA-- 2530
                         ii     i   v   -v   iv  i i   --   -----i       --
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAAT--TGAGAGTCCAGAAATAAA 329

C chr1_186247962_   2529 ----------TATGCTTAGTTGATTTCC 2512
                         ----------    v i i       i 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTC 357

Transitions / transversions = 1.47 (44 / 30)
Gap_init rate = 0.04 (12 / 269), avg. gap size = 2.58 (31 / 12)  


1289 29.29 5.33 2.66  chr1_186345950_186348046      752  1427 (670)    L1M4_orf2#LINE/L1      114   807 (101)  

  chr1_186345950_    752 TTTTGCATATGTTTCCCAGCTGATCCTAAAATACATATGGAAATGAAAAT 801
                                v vi  vv v               v            v  iv
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_186345950_    802 AAACCAGAATAGTCAAAACAAT-TTGAGGAA-AAGAACAAACCTGGAGGA 849
                         i v         i         -    ii  -         vi       
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_186345950_    850 CTTAAACTAATAGATATCAAA---CACTGTTAATTTAGAGTAAGTCAGGC 896
                           i v   vvivi  v     ---i   iiv  vi  v     viv  i 
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_186345950_    897 AATATGTTATAAGCACA-GGATAGAAACCT-TATCAGTGGAATGAAATGG 944
                          i i  v  ivi   i -       v iv -v    i      ii   v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_186345950_    945 AGAGCCTGGAAAAAGATTCAGACATAGA-GATAACCTGATTTATGAGATA 993
                             i ii    v i ii  v    vv - i v vi      vi  v - 
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA-A 362

  chr1_186345950_    994 TGTAATGCTACAGCTCAT------AGAAAAAAACTTAACCTTGTCATTAA 1037
                         v --i   i -  vi   ------i i   i  --  ii   v   vi  
  L1M4_orf2#LINE/    363 GG--GTGCCA-AGACCATTCAATGGGGAAAGAA--TAGTCTTTTCAACAA 407

  chr1_186345950_   1038 ATTTTGCTG---TCTTTGACTATCAATAGGGAAAAATAGTGCA-TTGG-T 1082
                           vv     ---ivvi  iv  ? v i v v    i- i  v -    -i
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AATGAAGTTGGAC 456

  chr1_186345950_   1083 CCCTATCTTTCACCACAATTACAAAT-TTAACGCAGA-TGGATAGTAGTT 1130
                              i  iv     i --      v-     v  i -     vi?  vi
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATA--TACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_186345950_   1131 CTAAATGTCACCAGC-AAAGCTATAAATCTTGCAGATAAAAGCACAGGAG 1179
                                 v v-   -   i       v  ivi   vi   i  i   ? 
  L1M4_orf2#LINE/    505 CTAAATGTAAG-AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_186345950_   1180 ---ATCACATCAGCAACCTGGGAGGT--GGCAAACATTTTTGAAAAACAA 1224
                         ---   --- iv ii    v  --  --     vvi   i v i v ii 
  L1M4_orf2#LINE/    554 TAAATC---TTCGTGACCTTGG--GTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_186345950_   1225 CACAAAAAGCATTACCCACAGAAGAAAAAA-GTAT---CTGGGTTATGTT 1270
                            v       iv v v   i         -iv  ---i   ii vii i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_186345950_   1271 AAAATCAAACATTTTTTTA--TGAAGAAATACTGTCCAGAGAGCAATAGG 1318
                              i   v i    v i-- v  iii i   i  v   i  ii v i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_186345950_   1319 GCGGCACACAAAATAGTAGGAGATATTTACCATGTATATATACAATTTAG 1368
                         i ii v    i   i v  i i      i v vvi      vii  vvi 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_186345950_   1369 GACTCATATCCAGAATATATAGTAAGAATATATATAA---AATATAAAAA 1415
                             ii               --     iviv  i  ---    vv    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATA--AAGAACTCTTACAACTCAATAATAAAA 796

  chr1_186345950_   1416 AGAATAAATAAC 1427
                            -i       
  L1M4_orf2#LINE/    797 AGA-CAAATAAC 807

Transitions / transversions = 1.27 (109 / 86)
Gap_init rate = 0.04 (30 / 694), avg. gap size = 1.80 (54 / 30)  


3023 26.55 1.00 0.55  chr1_186387575_186389581.rev      613  1516 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186387575_    613 TAAAAACACATCCCATGCTCTTGGATGGGTAGAATCAATGTTGTGAAAAT 662
                          ii   v i        i  v     v  v   v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186387575_    663 GAGCATACTACCAAAAGCAATCTATAAATTCAATGCAATTCTCATCAAAA 712
                          ivv     v  v   vii     i i      i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186387575_    713 TACTACCATCATTCTTTAAAGAACTAGAAAAAGCAATTCTAAAATTCATA 762
                          v i v vv v  i   iv    v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_186387575_    763 TGTAAACAAAATGAGCCTACA-TAGCCAAAGCAAGACTAAGCAAAAAGAA 811
                           v   iiv  v ii  i v -        i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_186387575_    812 CAAATCTGGAGACACT-ACATTACCTGATTTCAAAGTATACTATAAGGCC 860
                             vi     i-   -   i v  ii        iiv     i  i  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_186387575_    861 ATCATCAAT-AAAACAGCATGGTACTGGTATGAAAATGG-CACATAGACC 908
                          -  vi   -  i    ii         i  i ii  i -  i     i 
  L1M4_orf2#LINE/    250 A-CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_186387575_    909 AATGGAACAGAATTGAGAACCCAGAAATAAACCCAAATACTTATAGCCAA 958
                                i          ii               v i i    i i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_186387575_    959 CTGATTTTCAACAAAGGAAACAAAAGCATAAAGTGAGGAAAGGACACTCA 1008
                         i        i    i  viv   i v   vv i  i      i i v  v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_186387575_   1009 ATTAAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAAGAAAATGA 1058
                         v  v                 i  i   vv ?       i  i i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_186387575_   1059 AGCTTCATCCTCATCTATCACCTTATACAAAAATCAGCTCAACATGGATC 1108
                           i vv i  ii i  vv    v           i i     v       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_186387575_   1109 AAGGACTTAAATCTAAAACCTGAAACAATAAAAATTCTAGAAGATAACTC 1158
                          ?i   i     v   i v  i    v      v ii       v   vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_186387575_   1159 TGGAAAAAATGTTTTAGACATTGGGTTAGACAAAGATTTCATGACCAAGA 1208
                         v  ?iv    v  ivv   v         i   v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_186387575_   1209 ATGCAAAATCAAATGCGACAAAAACAATGATAAATAGGTGGGACTTAATT 1258
                         vvv     v  v v  i      iv  vi   i   ii v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_186387575_   1259 AAA-TTAAAGAGTTTTTGCATGCT-AAAAGGA-ATAGTCAGTAGAGTAAA 1305
                            -     i -i     --    -v      - ivi   iv i   i  
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTG--TGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_186387575_   1306 CAGATAACCCACAGAGTGGGAGAAAATCTTCATAATGTATACTTCTGACA 1355
                         v   i          i           v  iii  vvi   iv     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_186387575_   1356 AAACATTAACATCCAGAATCTACAAGGAACTCTAGGAAATTAGCAAGAAA 1405
                          iiv i vii         v  i  i       viv  v i ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_186387575_   1406 AAAACAAACAATCCCATAAAAAAGTGGGTTAAGGATGTGAATAGACAGTT 1455
                           i     i  i  v  v?    i    iv      v          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_186387575_   1456 TTCAAAAGAAGATCTACAAATGGCCAAAAA--ACATGAAAAAATGCCCAA 1503
                         i  v         v             v  --         i    i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_186387575_   1504 CATCACTAATGAT 1516
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.17 (14 / 12)  


2445 27.75 1.52 2.72  chr1_186410074_186415030     3546  4464 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186410074_   3546 TGGAAAAACACTCGATGCTCATGGACAGGAAGAAATAATGTTGTTAAAAT 3595
                               i i ii v   i       iv      vv    i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186410074_   3596 ATTCATACTGCCTAAAGCAATTTACAAAACTGAAAACTATTTCTGTCAAA 3645
                         iviv     v  i   vii  i    i -i v  vi v  ii  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGA-TTCAACGCAATCCCTATCAAA 99

  chr1_186410074_   3646 CTACCAACAGCACTTTTTTTTTTACAGAATTAGAAAAAAACT-ATTCTAA 3694
                         v v   i v  -----i      i     v v  v  i--  -  i    
  L1M4_orf2#LINE/    100 ATCCCAGCTGC-----CTTTTTTGCAGAAATTGACAAG--CTGATCCTAA 142

  chr1_186410074_   3695 G-CTCATATGGAACAAACAAAT-ATTCTGAATAGCCAAAGCAATCCAATG 3742
                         i-i          - vi   iv- ii v           i     i--  
  L1M4_orf2#LINE/    143 AATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCT--TG 189

  chr1_186410074_   3743 AAAAAAAA--ACAAAGTCTGAGGTATCACATTACACTACTTCAAACTATA 3790
                              i  --       iv    vv     i v v v i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_186410074_   3791 CTACAAGGCTACAGTAACCAAAACAGCATGATACTGCTAGAAACGTAGAC 3840
                               i          i   i    ii  i     vi v  ivi     
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_186410074_   3841 ACATAGACGAATGGAACAGGTTAGAAACCTTATAAATAGTGTCACACACC 3890
                          i     iv       i  iv v  i viii v     ivvi  i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_186410074_   3891 TAGAATCATCTGATCTCCAACAAACTCTACAATAGCAAACAATGGGGAAA 3940
                           vii   vi    i i i    ivvivv   v v  vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_186410074_   3941 GAAATCCCTATTCAATGAATGATGCTGGGATAACTGGCTAGCCATATGCA 3990
                            vvvi  v     ii    i        i      v  ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_186410074_   3991 GATTATAGAATTTGGACTCT--CCTTTTACCATGTACAAAAATAAACTCA 4038
                         i vv vv   v      i i--   ivi     i         v      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_186410074_   4039 AGATAGATTGTCAATTGAAATGTAAAATGTCACACTATAAAGACCCTAGA 4088
                          i  i   ii?vi iiv        i vv v v        ivi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_186410074_   4089 TGAAAATCTAGGT-CATATCATTCTGGACATAGACCTGGACAAAGAATTT 4137
                         v     iv    ?-i v   -   vv   v v ivi i i   v iv  i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_186410074_   4138 ACAATGAAGACACCAAAAGCAATTTCAACAAAAACAAAAATAGATAAATG 4187
                         vi ivv v             vvvv        iv              v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_186410074_   4188 GGGTCTAATTAAACT--AAAGCGTTTCTGCTCTGCAAAGGAAACTATTAA 4235
                           iii v  i   v --   i v   v    i--       v     i  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAA 686

  chr1_186410074_   4236 CAGAGTAGATAGACAAACTAGAGAATGAGAGAAGATATTTGCAAACTATG 4285
                         v i   ii v      v i v      i     i           ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_186410074_   4286 CATCTGACAACAGTCTAATATCCAGAATTTATAAGGAACTTAAACAAATC 4335
                         i      i  vi v  vi          v     i     ivv    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_186410074_   4336 AACAAGCAAAAAACAAACAACCCCATT-AAAAGTGGTCAAACA---TGAA 4381
                           i  vv    i     i     v   -    i   v    vi---    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_186410074_   4382 CAGGCACTTCTCAAAGGAATACATACACATGGCGTACACATGGCCAACAA 4431
                         i  i  i     v  i   v i     ---------- -        i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACA----------A-ATGGCCAATAA 875

  chr1_186410074_   4432 CCGTAAGACAAAATGCTCAAAATCACAAATCAG 4464
                         v ii v  v  i        v    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (138 / 114)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.17 (39 / 18)  


 640 25.00 3.31 8.09  chr1_186427577_186430446.rev      246   517 (2353)    L1M4_orf2#LINE/L1      157   415 (493)  

  chr1_186427577_    246 TGCAAG--ACCCAGAATAGACAAAATA-TCCTGAGCAAAAAGAACTACCT 292
                               --           v     i -  i   iv  i      -----
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC----- 201

  chr1_186427577_    293 GATTTTAAGTCAG-GCACT-ATAATACTTGACTTTAAGTTGTACAACACA 340
                         - ----    ii - v   - i v v iii i  i  iviv   v   v 
  L1M4_orf2#LINE/    202 -A----AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_186427577_    341 TTTACAATAACCAAAATA---TGGCATTTACATAAAAACAGACACATAAA 387
                         vi    i   i   i i ---   i i vi     ii i     i   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_186427577_    388 CCAATGGAACAGAATAGAAAGTTAAAGTACAAATCCACACATTTACAGTG 437
                         i        i     v  i   iv iiv i   i   i       ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_186427577_    438 AATTCATTTTCTTTTTTTACAAAGATGCCAAGACCATACACTGGAGAAAA 487
                             v      v------    i i            v  v   i    i
  L1M4_orf2#LINE/    347 AATTGATTTTCG------ACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_186427577_    488 GAAAGTCTCCTAATCAGTAATAAATAG-GCT 517
                         i v     ii ------i  i    i -   
  L1M4_orf2#LINE/    391 AATAGTCTTTT------CAACAAATGGTGCT 415

Transitions / transversions = 2.40 (48 / 20)
Gap_init rate = 0.04 (10 / 259), avg. gap size = 3.10 (31 / 10)  

2563 28.77 1.42 2.08  chr1_186427577_186430446.rev     1472  2385 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186427577_   1472 TGAAAAAACATCCCATGCCTACGGATGGGAAGAATCAACATCATTAAAAT 1521
                           i   i i        iii i    v      v i  i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186427577_   1522 GGCTACACTGCTAAAAGCAATTTACAGATTCAACACTATTCCTGTCAAAC 1571
                            v i   v iv   vii  i            i v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186427577_   1572 TACCAATGACATTCTTCACAAAACTAGAAAAAGATCTG-TTTTAAAATTT 1620
                          v   iivi v  i  ii  i  v v  v  i---   - ii       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr1_186427577_   1621 ATATAGAACCAAAAAAGAGTGCAAATAGCCAAGGCAACCATAAGCCAAAA 1670
                             i   viiv  ii  vivvi         ii   i v i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_186427577_   1671 GAACAAAACTGAAGGTATCATGTTACCCAACTTCAAACTATGCTGCAG-G 1719
                                ii  i   vv   iii v     i      viv i  i  i- 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_186427577_   1720 CTAAAGTAG-CAAAATAGCATGGTACTGGTACAAAAACAGACACATAGAC 1768
                            v    i-   i i  ii         i i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_186427577_   1769 AAATGGAACAGAATAGAGAGCCCAGAAATAAGGCTGCACACCCATGACCA 1818
                         v       i     v     i          iv iii   iii   ii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_186427577_   1819 TCTGATCTTCAACAAGGCTGACAAAAGCAAGCAATGTGGAAAGAACTCCC 1868
                         vi    i   i      v  v   i v  vv     v        ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_186427577_   1869 TATTTTACAAATTCTTCTAGGATACCTGGCTAGCCATACGCAAAAGATTG 1918
                          v  iv      vv v  i   i v    v  ?   i i        v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_186427577_   1919 AAACTGGACCCATCCCTTACACCACATACAAAAATCAACTCAAGATGAAC 1968
                           ii       v v   i      i          i       i   i i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_186427577_   1969 -----ACTGAAGCATAAGACCCAATACTATAAAAACCCTGGAAGACAATC 2013
                         -----  iv  iii     v i  v         vi i i     v  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_186427577_   2014 TGGGCAATACTATTCTGGACATGGGAACTCACGACTTAA-GGATTCATAG 2062
                          i  ?ivv v v   vv   v v  i-- i - i --  -  v   v   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGG--TTA-GGC--AATGGTTTCTTAG 592

  chr1_186427577_   2063 GAATTTCATGACAAAGATACCAAAAGCAATCTCAACAAAAGTAAAAATTG 2112
                         --  ---      ------         vvvv         v      v 
  L1M4_orf2#LINE/    593 --AT---ATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_186427577_   2113 ACAAATGGGGTCTAAGTAAACCAAAGAGCTTCTGCACAACCAAAGAAATA 2162
                          i    v  iii v vi   viv  i i   i  ii vv v  i  v iv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_186427577_   2163 ATCAGCAGAGTAAACAGACAACCTACAAAACGGGAGAAAATATTTGCAAA 2212
                             iv i   i  v        i   i  i                   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_186427577_   2213 CTATGCATTTGACAAAGGTCTAATATCCAGCATCTATAAGAAACT--TAC 2260
                         ii  ii  i   i  i  v  vi       v  v     ii    --   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_186427577_   2261 AAATTTACAA-AAAAAAAAAAACAGCCCCATTAAAAAATTGGTAAAGAAC 2309
                           v iv i  -     i v   i i   v   ?      v  i    i i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_186427577_   2310 ATGAACAGATACTTTTCGAAAGAAGACATACATGCAGCCAATAAGTGCAG 2359
                         v    i   i i  i  v        i     viii         ii  v
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_186427577_   2360 GAGAA-ACGCTCAATAGTACTGATCAT 2385
                           i  - i      i vi ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (162 / 98)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.13 (32 / 15)  


3271 26.87 0.44 0.44  chr1_186458584_186461489     1506  2413 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186458584_   1506 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1555
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186458584_   1556 GGCCATACGGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1605
                            v    vv     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186458584_   1606 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1653
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_186458584_   1654 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 1703
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_186458584_   1704 AACAAAGCTGGAGGAATCATGCTACCTGACTTCAAACTATACTACAAGGC 1753
                                i       v   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_186458584_   1754 TACAGTAACCAAAACTGCATGGTACTGGTACCAAAACAGAGATATAGATC 1803
                                 i   i  v ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_186458584_   1804 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1851
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_186458584_   1852 ACCTGATCTTTGACAAACCTGAGAAAAACAAGGAATGGGGAAAGGATTCC 1901
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_186458584_   1902 CTATTTAATAAATGGTGCTGGGAAAGCTGGCTAGCCATATGTAGAAAGGT 1951
                           v  i  i              v i    v  ?   i   i i  iii 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_186458584_   1952 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2001
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_186458584_   2002 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2051
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_186458584_   2052 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2101
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_186458584_   2102 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 2151
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_186458584_   2152 TTAAACGAAAGAGCTTCAGCCCAGCAAAAGAAACTACCATCAGAGTGAAC 2201
                          i   vvv  i i   iv iv vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_186458584_   2202 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 2251
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_186458584_   2252 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2301
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_186458584_   2302 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 2351
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_186458584_   2352 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 2401
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_186458584_   2402 ATCACTGGCCAT 2413
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2693 25.76 3.28 4.15  chr1_186468742_186470879      742  1657 (481)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186468742_    742 TAGAGAGATATTCCATGTATATGTTTAGGAAGATTTAATCTTGCCAAGAT 791
                          i  i      i      vi   vv v      i     v   ii     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186468742_    792 GTCAGTTCTTCCAAAATTGATC----------ATG---------TCAAAA 822
                          v  i v  i  v         ---------- i ---------      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186468742_    823 CCCCA--TAT-TATTTTGTGAATATAGACAAACTGA-CTTAAAAGCTTTT 868
                         i    -- ii- v     iii v  v     i    - i     -i iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCAT 149

  chr1_186468742_    869 ATGAAAAGGCAAAAGACCCAGAATGGTCAAGAAAATATTGAAGGAAAAGA 918
                            i   v    ii          i i   i v   v     ii i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_186468742_    919 ACAAGTTTGAAGGACTGACATTATCCAACTTCAAGATTTGATATAAAGCT 968
                             iv   i      v   i vi    i     i i  iv  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_186468742_    969 AGAGTAATTAAGACCGTGTGGTAATGGTAAAATAATAAGCAAATCAATCA 1018
                          v      i     v        v   i v  vi   ii  v  vi    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_186468742_   1019 ATGCTACAGAAGAGAGAGCCAAGAAATACACCTACACAAATATATTCAAC 1068
                            vv i    vv     i v       v   i i   vv   iv    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_186468742_   1069 TGATTTTTGACACAGGAGCAAAGGCAGTTCAATGGGGAAAAAATAGCCTT 1118
                                i    vi  v  v   i vi             i     i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_186468742_   1119 CTCAAGAAATGGTTATACAACATCTGGACATCCACATGTCAAA-AATGAA 1167
                         i    v       vv ivi   v     i ?       iv   -      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_186468742_   1168 TCTAGATACAGATCCTATGCCTTTCACAAAAATTAACTCTAAATGAATCA 1217
                         vi i  iv vv i ii ii  v vi              v     i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_186468742_   1218 TCAATCTAGAAGCAAAACACAAAACTATACAGCTTCAAGATTATAACATA 1267
                         ?vi i   i v i  i vvi         v i  iiv   vv v      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_186468742_   1268 AAGGACAATCTAGGTGAACCTGGGTTTAACTAAGGTAGTATCAACCAACA 1317
                         ii? vv     vv    v i      ------   -------------  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTT------AGG-------------CA 580

  chr1_186468742_   1318 ATGACTTTTTAGAAACAGTAACAAAATCACA-GTACCAATGCGTGGAAGA 1366
                            ii  i     v iiii v     v    - i v   -------    
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA-------AAGA 623

  chr1_186468742_   1367 AAAACTTGTTAAATTGGATGTCATTAAAATTAGAAACTTCTGCTTTACAA 1416
                             v v v         iv    i       i      i  ivi v   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_186468742_   1417 AGGGCACTGTCATAAGAATGAAAAGACAAACCATATATTGAGAGAGAATA 1466
                            i    i   vi i i           v   i v v  i    i    
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_186468742_   1467 TTTGCATTTGCAAAGTGCAAATCTGTTAAAGGACTAGTATCTAAAATACA 1516
                               ------  viii v     v   i     v     i i    i 
  L1M4_orf2#LINE/    724 TTTGCA------AATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_186468742_   1517 CAAGGAACACTTTAAACTCAACCACAAGAGGACAGAAGACCCAATTTAAA 1566
                         i  i    v   vv       iv i  i i    i vi        ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_186468742_   1567 AAAGGGCGGGGGAGGAACTCTTAACAGACTCCTCACCAAAGAAGATAAAC 1616
                           v    iii   ----- i v  i    vii  v            v  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGA-----TTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_186468742_   1617 AAATGG-----AAACCTTTGAAAAGACACGACGCATTATAGCCATC 1657
                               -----  i viv        ii vvvi   i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (133 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.86 (68 / 14)  


1508 30.26 1.29 1.11  chr1_186494592_186496882.rev      526  1067 (1224)    L1M4_orf2#LINE/L1        1   543 (365)  

  chr1_186494592_    526 TGGAATAACATTCCATGCTTATGGATAGAAATCATCAATATTTTAAAAAT 575
                              vi i  i     i i      v i  vvv i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186494592_    576 GGCCATACTGCCCAAAGCAACTTACAGATTTCATGCTATTCCTATCAAAC 625
                            v     v      vii ii        iv i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186494592_    626 TACCAACATCATTTTTCAAAGAATTAGAAAAAACT-ATTCTAAAGT-CAA 673
                          v   i vv v     iiv    v v  v  i-  -  i     i -  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_186494592_    674 ATGGAAGCAAAACAGAACCTGAATAACCCAAGCGATCCTATGCAAAAAGA 723
                               iiiv  vi  v  v     i  v  i i   i iviv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_186494592_    724 ACAAAGCCAGAGACATCATATTACCCTACTTCAAACTATACTGTAAGGCT 773
                               iii   ivv   i i v   v i      viv    ii  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_186494592_    774 ACAGTAACCAACACAGCATAGTAGTGGTACAAAAACAGGCACATAGACCA 823
                                i   v    ii i   v   i i  ii i  i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_186494592_    824 ATGGAACAAGTAATAAATAAATAAATAAATAAAGCCACAAACCTACCACC 873
                               i i--   vi -i i vv v       v   i v ii  ivii 
  L1M4_orf2#LINE/    300 ATGGAATAG--AATTGA-GAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_186494592_    874 ATCTGATCTTTGACAAAGTCAATAAAAC-AGGCAATGAACAAAGCAC--T 920
                          vi    i  i     i viivi  i  - vv     iiv    v i-- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_186494592_    921 CCCAATTCAATAAATAGTGCTGGGATAACAGGCTAGCCATATGCAGAAGA 970
                          ii--     i    i         i   v  v  ?   i     i    
  L1M4_orf2#LINE/    397 CTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_186494592_    971 TTGAAACTGGACCCATTCCTTTTACCATATGCAGAAATCAACTCGA--TA 1018
                         v    ii       v v   ivi       i  i    i     i -- i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_186494592_   1019 GATTAAATATTTAAATATAAGACATAAAACTATGAGAACCCTAGAAGAA 1067
                            i ? v ii     i     vv         i i vi i        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

Transitions / transversions = 1.66 (101 / 61)
Gap_init rate = 0.02 (9 / 543), avg. gap size = 1.44 (13 / 9)  

 692 27.00 3.20 3.89  chr1_186494592_186496882.rev     1364  1800 (491)    L1M4_orf2#LINE/L1      475   908 (0)  

  chr1_186494592_   1364 ACAAGAGTTAGACTCTGTCTCAAAAAAAAAACAAAAAACAAAAC---AAA 1410
                             i i   -    -------    vii v  ? i v v   i--- i 
  L1M4_orf2#LINE/    475 ACAAAAATTA-ACTC-------AAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_186494592_   1411 ACAAAAA--A-AAAACC--TAAAAGAAAACCTAGGAAATAACATTC-TGA 1454
                         i v    -- -     i--  i        v    ?ivv  iv   -   
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_186494592_   1455 ACATAAGCATTGGCAAATATTCCATAACGAAGACTCCAAAAACAATTGAA 1504
                         v v ii i- v     vvi  i v  ivv v   v      i  v---  
  L1M4_orf2#LINE/    567 CCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC---AA 612

  chr1_186494592_   1505 ACAAATACAAGAAAAAA-AAACAAGTGAGACCTAATTAAACTAAAGAGCT 1553
                         i   -i v         - i i  i vi   i v  i   v v  i i  
  L1M4_orf2#LINE/    613 GCAA-CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_186494592_   1554 TCTGGACAGCAAAATAAATTGTCAAGAGAGTAAACAGAAAACCTACAGAA 1603
                          i  vi vv    iv v i i      i   i  v   v    i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_186494592_   1604 TTTAAAAATATGTTTGCAAACTATGCATCTGACAAAGGCCTAATGTCCAG 1653
                          vvi i  v  i        ii  ii      i  i  v  vi i     
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_186494592_   1654 G-TAC-TAAA--ATTACCTTAAACAAATCAAAAAGCAAAAATCAAACAAC 1699
                         i-  i-    -- i --    --   v    v  vv    iv    i   
  L1M4_orf2#LINE/    762 AATATATAAAGAACT--CTTA--CAACTCAATAATAAAAAGACAAATAAC 807

  chr1_186494592_   1700 CCACTTAAAAAAAGTACAAAGGACATGAACAGACACTTTTCAAAAGAAGG 1749
                            v  ?     v vi       iv    i     i  i  v       i
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_186494592_   1750 CATACATGCAGCCACTAAGCATATGACAAAATGCTCAACATCACTCATCA 1799
                         i     viii    v      i    v  i             ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_186494592_   1800 C 1800
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.30 (65 / 50)
Gap_init rate = 0.04 (16 / 434), avg. gap size = 1.94 (31 / 16)  


2587 23.56 6.10 2.58  chr1_186508327_186510735.rev     1095  1947 (462)    L1M4_orf2#LINE/L1        4   886 (22)  

  chr1_186508327_   1095 AAAGACATTT-GTGCTCATAGATGGAAAGACTTAATATTGTGAGCATGAC 1143
                              i  ii-i  i    i   v i               v iv   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_186508327_   1144 ---------CAAATGCATTCTACAGATTCAATGCAATTTCTATCAAA-TC 1183
                         ---------     vv  -            i     ii        -  
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGAT-CTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_186508327_   1184 CCAAGGATAATGTTTGCAGAAATAGAAACATTCTTCCTAAAGTTCATTTG 1233
                            ivviivv v           v  v vii vv       i     v  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_186508327_   1234 GATTCTTAAGGGACCCAGG-TAACCTTAACAATACTGAAAATAAATAACA 1282
                           vvivi           i-  i  vv      vi      vi  v    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_186508327_   1283 AAGTTGGAGTACTCTCACTTCATGATTTCAATACTTACTACAAAGTTGTT 1332
                                  v    v      vii       v             i ---
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT--- 249

  chr1_186508327_   1333 ATAGTAATCAAAACAGTGAATTACTGGCATAAAGAAAAACATATAGACCA 1382
                          i         i      viv           i  v i         i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_186508327_   1383 ATGAAGCTGAATAGAGAGCCCAGAAATAAAACCTCACATATATGGTCAAA 1432
                            i iiv    v     i           v  vi    v         v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_186508327_   1433 GGGTTTTCAACAAAAGTGACAAGAACATTCAATAAGGAAAATAGCAATCT 1482
                         v i     i    ii   v     v        ii     i- ii i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCT 398

  chr1_186508327_   1483 TCTCAG-AAATGG-------AAAATGATATAACCACATGCAAAATAA-GA 1523
                          i   i-      ------- v  iviv   ?            v  -  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_186508327_   1524 AATATGAGTCTTTTCCTTA-----TATACAGAAA---ACTCAAAATATTT 1565
                          i -  iii ii v   i -----      i   ---         ivv 
  L1M4_orf2#LINE/    449 AGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_186508327_   1566 TAAAG-TTTAAGCATAAAAGTTAAAAGTATAAAAATCTT----TAAAA-A 1609
                         i ?  -ii   iii   i  i     v       v    ----v    - 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_186508327_   1610 TAGGGAAAATTATTCATGTCATTCGATTTGGCAATAATTACTTCTT-GAA 1658
                             ?iv  v v   i  v v  v i  v      ii  ---    -  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT---TCTTAGAT 594

  chr1_186508327_   1659 AGAATATCAAAAGCACAGGTAATATAAGAAAAATTAGATATATTGGACTT 1708
                          vi i i          i i  i v        v      v         
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_186508327_   1709 GATCAACATT------TTTT-------AAAGGATACTAAAAACAGAGTGA 1745
                         v     v   ------    -------      i    vv  v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_186508327_   1746 AAAGGCAACACATGGAATGAGAGAACATATTTGCTAATCGTATATCTTAT 1795
                             i    v  ii     i     v        v    i       v  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_186508327_   1796 AAAGAGTTAATATTTAGAATATATAAAAAAAGCTCCTATAGGTTATCAGC 1845
                           i iii vi   ii            i  --   i  i iv ---  ii
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAA--CTCTTACAACT---CAAT 789

  chr1_186508327_   1846 AACACAAAAACCCAAACAACCTATTTTTCAAAAGGGCAAACAATTTTAGT 1895
                           i v   i  --   i    i v  ?vv   v       vi    v i 
  L1M4_orf2#LINE/    790 AATAAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_186508327_   1896 GATCAGTTCTCCAAAACCATAGAGTATATATATGTGGACA-TAA--ACAT 1942
                         iiv  v         ------  iv     i vi   v  -   --    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAA------GAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_186508327_   1943 GGAAA 1947
                          i   
  L1M4_orf2#LINE/    882 GAAAA 886

Transitions / transversions = 1.32 (112 / 85)
Gap_init rate = 0.03 (26 / 883), avg. gap size = 2.85 (74 / 26)  

 213 17.07 0.00 0.00  chr1_186508327_186510735.rev     2363  2403 (6)    L1M4_orf2#LINE/L1      854   894 (14)  

  chr1_186508327_   2363 AAAATACATAAATGTTCAATAAGCACATGAAAAGATATTCA 2403
                           i   i i     vi                    ii   
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 6.00 (6 / 1)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  


2831 28.45 0.47 0.47  chr1_186513556_186515511.rev      604  1457 (499)    L1M4_orf2#LINE/L1        1   854 (54)  

  chr1_186513556_    604 TAGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 653
                          i    i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186513556_    654 GGCCATACTGGCCCAAGTAATTTATGGATTCACTGCTATTCCCATCAAAC 703
                            v     vv  v  v i  i  ii      vi  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186513556_    704 TACCA-CTGACTTTCCTCACAGAATTAGAATAAACT-ACTTTAAATTTCA 751
                          v   -   v    ii -i     v v  -i  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chr1_186513556_    752 TATGGAAACAAAAAAGAGCCCATATAGTAAAGACAATCCTAAGCAAAAAG 801
                                 iiv  ii  v  viv    iv  i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_186513556_    802 AACAAAGCTGGAGGCATCACACCACCTGACTTCAAACTATACTACAAGGC 851
                                i      vv      iv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_186513556_    852 TACAGTAACCAAAACAGCATGATACTGGTATCAAAACAGGTATATAGCCC 901
                                 i   i    ii  i      i  v ii i  ii      vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_186513556_    902 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 951
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_186513556_    952 CTGATCTTTGACAAACCTGACAAAAATCAAGCAATGTAGAAAAGATTCCC 1001
                         i    i  i     ivv  v   i -i  vv     vi    ii  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAGTC 397

  chr1_186513556_   1002 TATTTAATAAATGGTGCTGCAAAAACTGGCTAGTCATAAGCAGAAAACTG 1051
                          v  i  i           vi v      v  ?i  i v   i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_186513556_   1052 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 1101
                           ii         v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_186513556_   1102 TAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTGGAAGAAAACC 1151
                         i ?    i           v       i      vi i i         v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_186513556_   1152 TAGGCA-ATATCATTCAGGACATAAGCATGGGTAAAGACTTCATGACTCA 1200
                             ?i- v   -   iv   v vi vv i  i  v ii   v iiv vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_186513556_   1201 AGCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1250
                         ii           vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_186513556_   1251 TTAAACTAAAGAGCTTCTGCATAGCAAAATAAACTACCATCATAGTGAAC 1300
                          i   v v  i i   i  iiivv    iv v    i  vv v      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_186513556_   1301 AGGTAACCTACAGAATAGAAGAAAATTTCTGCAATCTATCCATCTGGCAA 1350
                           ii    i       i i       v i     vii  vi     ii  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_186513556_   1351 AGGTCTAACATTCAGAATCTACAAGGAACTTAAACAAATTTACAATAAAA 1400
                         i  v  vii  i      v  i  i     ivv    v iv i       
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_186513556_   1401 AT-CAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 1449
                          v-    i     v  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_186513556_   1450 TTAAAAGA 1457
                          iv     
  L1M4_orf2#LINE/    847 TCCAAAGA 854

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (8 / 854), avg. gap size = 1.00 (8 / 8)  


2381 26.91 4.17 1.91  chr1_186526940_186531411     3092  3979 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186526940_   3092 TAGGAAAACATTCCATGCTCATGGATAGAAATCAAC--AATATTGTTGAA 3139
                          i i  i i  i     i        v i  --i  --         i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAA--GACTTAATATTGTTAAG 48

  chr1_186526940_   3140 AAAGCCATACTGCTCAAAGCAACTTACAGATTCAATGCTATTCCTATCAA 3189
                          vi  v     v i    vii ii           i  v  i        
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_186526940_   3190 ACTACCAACATTATTTTTCAAAGAATTAGAGAAAATGATTCTAAAG--CA 3237
                          v v   i vviv     iiv    v v  v  iv    i     i--  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_186526940_   3238 TATGGAACACCAAAAGAGCC-TAATAGCCAAAGCAATCATAAGCAAAAAG 3286
                                vvv   ii  v  -v          i     v i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_186526940_   3287 AACAAAGCCAGAGCCATTACACTACTCTAATTCAAACTATACCACAAGGC 3336
                                iii   vvv i     v i v v      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_186526940_   3337 TACCATAACCAAAAC-GCATGGTACTGCTATAAACACAGACATATAGACA 3385
                            vi   i   i  - ii        vi    iv i           iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_186526940_   3386 AATGAAACAGGTTAGAG-GACCAGAAATAATGTGTTACACCCATAGTCAT 3434
                             i  i  iv v   - v          vvivv    iii  i    v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_186526940_   3435 CTGTTTTCTGACACAGTAAAAAATAACAAG------CAATGGAGAAATAA 3478
                         i  v   ii    ------ iii iv    ------      i    v  
  L1M4_orf2#LINE/    349 TTGATTTTCGACA------AGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_186526940_   3479 --ATCCCTATATTAATAAATCATGCTGGAATAACTGGTCAGCCATATTCA 3526
                         --i  ii --- i  i    vi      i i      vi ?   i  v  
  L1M4_orf2#LINE/    393 TAGTCTTT---TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_186526940_   3527 GAAGATTGAAACTGGAACCCTTACACTCAC--CATGTG-AAATATTAACT 3573
                         i    v    ii    -   i   -     --   i i-   v       
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGA-CCCCTAC-CTCACACCATATACAAAAATTAACT 487

  chr1_186526940_   3574 CCAAGTGCATTTAAGTTTTCAATATAAGACATAAAACTATGAAAACCTTA 3623
                          v  i  v  iv?  vii v   i     vv         i   vi    
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_186526940_   3624 GCAAAAACCCAAGG---AAATAGCATTCTGGCTATAAATGTTGGCAAAGA 3670
                          v i   v vv   ---    -- v iv  i iv iii - v     v i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGT-TAGGCAATGG 584

  chr1_186526940_   3671 TTTCATGACAAAGACTTCAAAAGCAATTGCAATAAAAACAAAAATAGACA 3720
                             v iivv v   vi        vvv    i    iv         i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_186526940_   3721 CGTGGGACCTAATTAGA-CTAAAGAGTTTTGCATAGCAAAAGAAACTATC 3769
                         vi v    i v  i i -i    i v     iiivv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_186526940_   3770 AACAGAGTAAA----CAACATACATAAGAAGAGAAATTATTTGCAAACTA 3815
                           v i   i  ----    vi   v  vii      v          ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_186526940_   3816 TG-ATCTGACAAAGGTCTAATATCCAGAATCTATAAGGAAC------AAA 3858
                          i-      i  i  v  vi          v     i    ------  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_186526940_   3859 TCAATG-TGCAAAGCACAAACAACCTTATTAAAAAATGGGCAAAGGATAT 3907
                              i- iv    -     i    iv   ?                 v 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_186526940_   3908 AAATAGAGTATTCTCAAAAGAAGGCATGCACATGGCCACCAAGCACA--- 3954
                         i      vvv     v       ii  i  v       vi       ---
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_186526940_   3955 AAAAATGCTCAACATTACTAATTAG 3979
                            i           i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (134 / 102)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.25 (54 / 24)  


2244 26.72 4.18 2.16  chr1_186542643_186544355.rev      482  1222 (491)    L1M4_orf2#LINE/L1      153   908 (0)  

  chr1_186542643_    482 GAAATTCAGAAAATTTCTAAAATAGCCAAAGTAATCTTGAGCAAATAGAA 531
                              v  iiii i-- i i          ii        iv  iv    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_186542643_    532 CAAAGTTGGAGGCATCACACTATCTGAATTCAAAATATACTACAAAGCTG 581
                                     vv       vi ii v       iv            i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_186542643_    582 CAGTAACCAAAACAACATAGTACTTGCATAAAAACAGACACATAGACCAA 631
                               i   i   iii i     v      ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_186542643_    632 TGGAATAGAATATAGAGCCCAGAAATAAATTTGTATATTTACAGCCAATT 681
                                    vv    i           iiii  i     ii i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_186542643_    682 GATTTTTGATAAAAGAGACAAGGACGCACAATAGGAAAAAGAGACATCAT 731
                               i  i  ii v v    iv iiv    i  i   ii v -i  - 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-GTC-T 398

  chr1_186542643_    732 CTTCAATAAATGATATTTGCAAAACTGAGTATCAACATGCAGAAAAATGA 781
                         i     i     i ii v v v     ii  ? v       i  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_186542643_    782 -------CCCTTATCCCA-ACCAAGCATAAAAATCAAACTGAAATGGATT 823
                         -------   i  i i  -    vii i      i  viii        i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_186542643_    824 AAAGACTTCAATGTGTAACCTGAAACTCAACTCTAAAACTACTATAATAA 873
                          ?    i v     ivi v  i     -- ---       vi  v  v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACT--A---TAAAACTCTTAGAAGAA 543

  chr1_186542643_    874 AACACAAGAGAAAAGCTCCATGTCATTGGTCTGGGCGATGATTTTTTTTA 923
                             i i ? v   v  i i  v v    vi i   i   i   i  ---
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--- 590

  chr1_186542643_    924 GAAAATATTACCCCGAAAGCACAGTTAATACA-GTGAAAATAGACAAATG 972
                         -- i    v  v  i        ivi  i v - vi        i    v
  L1M4_orf2#LINE/    591 --AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_186542643_    973 AAATTACATGAAACTAAAAAGCTTCTACACAGCAAAATAAACAATTGACA 1022
                         ii i v   v   v v    i   i iii vv    iv v  v  ii v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_186542643_   1023 GAATGAAGAGACAAATGGAACAATGTGATAAAATATTTGCAAGCTATACA 1072
                         i i    i      viviv v    v  v             iii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_186542643_   1073 TCTAATGAGGA----GT------------TAA------CTTAAGCAATTC 1100
                            i  i   i----  ------------   ------    --   i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTC 786

  chr1_186542643_   1101 AATAGTAAGAAAACAAATAATATGATGAGAAAATGGGGAAAGGACCTGAA 1150
                             i   i  i        ivii  v?i        v      ii    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_186542643_   1151 AAGACATTTCTCAAAAGAAGAAATGCGACTGGCCAACTGGTATATAAAAA 1200
                         v           v        v  i i v       ivi i i  i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_186542643_   1201 TATGCTCGACATCATTAATCAT 1222
                         v      i      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (130 / 64)
Gap_init rate = 0.02 (13 / 756), avg. gap size = 3.62 (47 / 13)  


 913 26.86 17.75 3.95  chr1_186572332_186573982      500  1158 (493)    L1M4_orf2#LINE/L1      159   908 (0)  

  chr1_186572332_    500 CAAAACATTTAGAATAGCTAAAACAATTTTGTTTTTTTTAAAAAG----- 544
                            iiv iii        i        i   --------      -----
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTG--------AAAAAGAAGAA 200

  chr1_186572332_    545 -----------GACTTATACTACCTAATGTCAAGATTCATTATCAATGAA 583
                         -----------    i i   v  i   v    i i i i  iv  vvv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_186572332_    584 CAGTAATCAAGACAACATGGTGTTGACACAAAATCTGAAAAAATAGATTA 633
                                       iii    ii  i  i  ii-v ii v v      i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAGACATATAGATCA 299

  chr1_186572332_    634 ATGAAACACAA--GAGAATATTCAGAAATAGGTGTATATTTATATAGTCA 681
                            i  i v  --    i --i        iiivi   iv v   i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGT--CCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_186572332_    682 ATTAATTTTTGAAAAAGTCACTAAACCCATTCAAGGGAGAAAGGGATGAT 731
                            i     i  v  i vii i  iv        v  i     i-  ii 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGT 396

  chr1_186572332_    732 --TTTGAATCAAATTGCAATGCAGAAAATTTAAAAACACATAAAACACAT 779
                         --   v  -     v iiv  -i  v  i vi v ? --------     
  L1M4_orf2#LINE/    397 CTTTTCAA-CAAATGGTGCTG-GGACAACTGGATAKC--------CACAT 436

  chr1_186572332_    780 GTAAAGAAATGAACCTTGG--CACTAACTCATATTA------------AA 815
                          i   ii      v-    -- v   v    i ii ------------  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_186572332_    816 CTGAAGAGTTGTTTA--GACATAA--------GTTAA--CT-TAAAGCC- 851
                           v  i - v v i --   v   -------- i   --  -    i i-
  L1M4_orf2#LINE/    486 CTCAAAA-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_186572332_    852 -----------------------TCTATGCAGCTATGGAG-AGACAA-AG 876
                         -----------------------   vi iii iv   iv-  i   -i 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_186572332_    877 TTTTATCAATAT----CTATAAATCAGTAACTATAAAATAAGACAATG-- 920
                            iv vi    ---- i -   v  vv i v i    v  i -   i--
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCA-AAAGCACAAGCAACAAAAGAAAA-AATAGA 632

  chr1_186572332_    921 TGAATTGGATTTGATTAAAATTAAA----------CTTCTAA-------- 952
                          i       i  v  i         ----------    v  --------
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_186572332_    953 ---------TGAATAGATAGTTCACAGA-TGGCAGGAAATAGTTTTAATA 992
                         ---------    v   i iii      -   v  i     v  vi  vv
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_186572332_    993 CATCTATCTGA-AAACTACTAGTGTTCCAAATATATAAATAATTTTTATA 1041
                            v       -  ivv   v  i i vi          v  i i   i 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_186572332_   1042 ACTGAACAATATAATAAAAAACAACCCCATT--------GACATAAGATT 1083
                            v  i    v  vi v   i     v   -------- i  v i    
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_186572332_   1084 TGAAAAGATACT-CTCCAAAGAAAACATACAAATGCTCAAGACAAACACG 1132
                             v   i i -          i i         vi   v viv   i 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_186572332_   1133 AAAAGGTGATCAATATCATTAGTTTT 1158
                              i  v    i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (109 / 67)
Gap_init rate = 0.04 (31 / 750), avg. gap size = 4.61 (143 / 31)  


2559 27.55 3.14 1.46  chr1_186617596_186620403.rev     1425  2317 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186617596_   1425 TGGAAAATCATCCTATGCCCATGGATTGGATGAATCAATATTGTTAAAAT 1474
                               ivi    i   ii           v  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186617596_   1475 GACCATACTGCTCAAAGCAGTTTACAGATTCAGTGAAATATCTATCAAAT 1524
                          i v     v i    viii i          ii v   vi        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186617596_   1525 TACCAACATCATTTTTCACAGGATTAGAAAAACAAAATTTTAAAATTCTT 1574
                          v   i vv v     ii   i v v  v  i vi - ii        v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_186617596_   1575 ATAGAACCAAAAAAGAGCCAGGATAGCCAAACAAATTATAAGCAAGAAGA 1624
                           i   viiv  ii  v    i         vv   iv i iv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_186617596_   1625 AC---TCCAGAAGCATCACATTACCAGACTTCAAACTATACTACAAAGCT 1671
                           ---viii  i vv     i v  vi i      viv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_186617596_   1672 ACAGCAAACAAAAGAGCATGGTGC-AGTACAAAAATAAACATGTAGATCA 1720
                             i  v   i v  ii    i -i i i  ii   i    i       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_186617596_   1721 ATGGAACAGAATAAAGAACCCAGAAATAAGGGCACAAACCTACCACCAAC 1770
                               i     vi   ii          ivv  i v ii  ivii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_186617596_   1771 TGATCGTTGATGAAG---TCAATACAAATAAACAACAGGAAAAGGACACT 1817
                             iv i  ii i ---i   v  v v ---   ii  i    i i v 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAAGAATAGT 396

  chr1_186617596_   1818 CTCTATTCAATAAATGGTTCTTGGAAAATTGGTTAGTCACATTCAGAAGA 1867
                           i --    i       v  v   v  i   v  ?i     v  i    
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_186617596_   1868 ATAAAACTGGACCCTTATCTCTCAGCATATACAAA--TTAACTCAAGATG 1915
                           i  ii       i  i   v  v          --         i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_186617596_   1916 GGTTACAAACTTTAATGTAAGACCTGAAACTATAAAAATCCTAGAAGGAA 1965
                          i i ? i  i v         v  i           v  i      i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_186617596_   1966 ATCTAAAG---AATTTTCTTCTGGACATTAGTCTAAGCAAAGAATTAATA 2012
                          iv  ii?---   i   v ---   v  i vi  i    v iv  vv  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT---GACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_186617596_   2013 ACTACGACATCAAAAGCAAATGCCATAAAGACAGAGATAGACAAATGGGA 2062
                         iv  i    i        v v  v i   iiv i i     i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_186617596_   2063 CTTAAGTAA--CTAAAGAGCTTCCACACAACAAAAGAAACCA------GA 2104
                            v vi  --i    i -   iiiii vv    i  v  i ------i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_186617596_   2105 GTATACAGACAAAACTAATGGAATGGGAGAAAATATTTGCAAACTATATA 2154
                           iv v      -- iv ii                       ii     
  L1M4_orf2#LINE/    691 GTGAAAAGACAA--CCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_186617596_   2155 TCTGACAAAGGACTAATATCCAGGCTCTATAAA--ACACTTA-AACAAAG 2201
                              i  i     vi       iv v      --  v    -   vv i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_186617596_   2202 AAGTGAAAAAA--ATTAATCCCTTTAAAAAGTGAGCAAAGGATGTGAACA 2249
                         v i i    i -- v   i  vv  ?    i  i         v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_186617596_   2250 CACACTTCTCAAATAAAGGCATAGAAGCAGTCAACAA--ACATGAAAA-A 2296
                         v   i     v  vi   ii   v  iii i   i  --         - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_186617596_   2297 TGAGTTAACATCACTAATCAC 2317
                           v- i       ????????
  L1M4_orf2#LINE/    889 TGC-TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (150 / 92)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.16 (41 / 19)  


2468 23.56 4.45 5.86  chr1_186624734_186626647      507  1427 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186624734_    507 TGGAAAAACATTCCATGCACATGGAAAGGAAGACTCAACATTGCTAAAAT 556
                               i i  i     iv      vv        i  i    i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186624734_    557 GACCATACTGCACAAAGCAGTATACAGATTCAATGCTATTTCTATCAAAT 606
                          i v     v v    viii v           i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186624734_    607 TACCAATAACATTCTTTACAGAATTAGAAAACAACT-ACTTTAAATTTCA 655
                          v   iivi v  i   i     v v  v  --i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr1_186624734_    656 CATGGAAACAAACAAAAAAAGCCTA-AATAGCCAAGGCAATCTTAAGCAA 704
                         i       ii--   iii --  i -         ii       i iv  
  L1M4_orf2#LINE/    149 TATGGAAATG--CAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_186624734_    705 AAAAAACAAAGATGGAGGAATCACATTACCAGACTTCAAACCATACTACA 754
                         i  i       v       v     i v  vi i      v v       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_186624734_    755 AGTCTACAGTAATCAAAACAGCATGGTACAGGTACAAAAAGAGACACATA 804
                          iv             i    ii      v  i i  ii v     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_186624734_    805 GACAAATGGAA--GA--TGTGTGT------ACAAAC-------------A 831
                           iv       --  --  v v  ------ i    -------------i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_186624734_    832 TC---TGATCTTTGACAATGTCAACAAAAACAAGCAATGGGGAAATAAC- 877
                           ---    i  i     v viiv   i v  vv           v  i-
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_186624734_    878 -TCTTTATTCAATAAATGATGCTGGGATAACTGGCCAGCCATATGCAGAA 926
                         -     --    i     i        i      vi ?   i     i  
  L1M4_orf2#LINE/    395 GTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_186624734_    927 GATTGAAACTGGAACCTTTCCTTACACCATATACAAAAGTCAATGGAAGA 976
                           v    ii    v  i v   i               i i  ivv  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_186624734_    977 TAGATTAAAGACTTAAATGTAAAACCTAAAACTATACAAACCCT-GGAAG 1025
                          i   i ?    i         i v           -    i  -i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAG 541

  chr1_186624734_   1026 ATAATCTAGG---AAATACCATTCTGGACATCAACCCTGGCAAAGATTTC 1072
                          v  iv    ---    -- -   vv   v iiiviiv     v i    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_186624734_   1073 AT-GATGAAGACACCAAA-GCAAATGCAACGAAACAAATATT-GTCAAAT 1119
                         v -   - v         -   v v     i   v   v v - vi    
  L1M4_orf2#LINE/    589 TTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_186624734_   1120 TGGGCCTAATTAAACTAAAGAGCTTACGTACAGCAAAAGAAAAATAAGGA 1169
                            i i v  i   v v  i i   vi  i vv    i  v --------
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-------- 679

  chr1_186624734_   1170 AAAGGAAAGAAAAAAGGGAAAAAAAAAACTCTGTCAACAGAGTAAACAGA 1219
                         ------------------------------  i    v i   i  v   
  L1M4_orf2#LINE/    680 ------------------------------CTATCAAGAAAGTGAAAAGA 699

  chr1_186624734_   1220 CAACCTACAGAATGGGAGAAAGTATTTGTAACCTATGCCTCTGACAAAGG 1269
                              i               i      i  vii  iiv     i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_186624734_   1270 TCTATTATCCAGCATCTCCAATGAACATAAACAAATGTTCAAGCA-AAAA 1318
                         v  vv       v  v vi  v    vivv    ---i    vv -    
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAA---CTCAATAATAAAA 796

  chr1_186624734_   1319 AGA--AGCAACCCTATTAAAAAGTGGGCAAAGAACTTGAACAAACACTTT 1366
                            -- ii     v   ?    i         i i     i i   i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_186624734_   1367 TC-AAAGAAGAAATACATAAGGCCAACAAAGATATGAAAAAAAGCTCAAT 1415
                           -        v     v v      i  iv i       i v      i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_186624734_   1416 ACCACTAATCAT 1427
                          i  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (125 / 89)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.65 (95 / 26)  


2192 27.41 4.29 1.67  chr1_186628547_186630733.rev      863  1701 (486)    L1M4_orf2#LINE/L1       16   876 (32)  

  chr1_186628547_    863 TGTTTATTGATAACAAGAGTTAATATT-T---GAT--CAATTCTTTCTAA 906
                             i  v   viv    v        - ---   --    v  ii i  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_186628547_    907 -CTGATGTATCAATTCAACGCAATCCTAATAAAAATTCC-GCCAACTTAT 954
                         -i    v  ivi              iv  v     i  -  iiv   - 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT-T 114

  chr1_186628547_    955 TTTGTAGATGTTGAAAGACTGATTGATTCTAATGTTTATATGGAGAAGTA 1004
                             i   vi    v ii     i----    vi  i       i v i 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATC----CTAAAATTCATATGGAAATGCA 160

  chr1_186628547_   1005 CATGACCCAGAAAAGTCCATTCAATATTGAAGGAGAATAACAAAGCCA-A 1053
                         viv         v  i v vv    v     ii    v       iii- 
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_186628547_   1054 GGACTAACACTACCCTAATTCAAGACTTACTATAAAAC-ACAATAATTAA 1102
                              v     v   v v     i        i   i -   i    i  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr1_186628547_   1103 GACAGTGAGCTATTGGCAAAGGAATAAACAAATATATAAATGATACAGAG 1152
                                v v  i     v i i   i   v   v  v    iv i   i
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_186628547_   1153 TAAAATGTCTAGAAATATATGCACATA---------AATTTGATATCTTG 1193
                          vi iv   i       v iv  i i ---------    -   - i i 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT-GAT-TTTCG 358

  chr1_186628547_   1194 ACAAAAAATGGGAAAAC-----ACTGAAGACAAGATAATCTTATCAACAC 1238
                             iii-  vv  i  ----- v  ii  v ii   i    v      v
  L1M4_orf2#LINE/    359 ACAAGGG-TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_186628547_   1239 ATTTTGCTAG---AACTGGACATCTACATGAAAAAAAGTGAAGCTAGACA 1285
                           vv    i ---       i ? i     v    i i     i i   v
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_186628547_   1286 CAGATCTTAAGCCCTTCACAAATATTAACTTGAAATGCATCATAGGCCTA 1335
                          vv i  i vi  v vi     v       ii     v    ?  i    
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_186628547_   1336 TATGTAATCTCAAAAAATATAAAACACCTAGAAGATAGTACAGGAGAAAA 1385
                         v      vvv v    v        v i       v ii i   ? v   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_186628547_   1386 CCTACATGACTCTGGGTATGGCAATGACTT--TAGATATAACACCAAACA 1433
                         i  v i    ii     vv       ii  --       i        vi
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_186628547_   1434 AATTATCTATGAAAGAAGTTTTATTGATAACTTATACTTAAGGAAAATTA 1483
                         v iv v v ii      ivvv  --     v  iv    v vv       
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTCATCAAAATTA 655

  chr1_186628547_   1484 GAAACTTCTTCTCTATGAAAGACAATAACAAGATAATGAAAAGACAAGCC 1533
                         i      i viv  vii  i    v  v     v i           v  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_186628547_   1534 ACAGACTTGGGGAGAGGATTTGCAAAATACATATCTGATAAAAAAATGCT 1583
                              v v  i  i iv         vi i           iii v vv 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_186628547_   1584 TTCCAAAATATA----AAACTTTCTTAAAACTTAACAATAAGAAAATTAA 1629
                         v    i      ----i    --    v    i  i     i  i iv  
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACT--CTTACAACTCAATAATAAAAAGACAAA 803

  chr1_186628547_   1630 CAACCCCATT--AAAATAAGTCCAAAACCTTT-AAGAGACACTGTACTGA 1676
                         i     v   --     ii --    ivv   -  v     i viv ii 
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGG--CAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_186628547_   1677 AGAAGATACACACAGAGTGAACAAG 1701
                                 i   v vi iv  i   
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAG 876

Transitions / transversions = 1.16 (122 / 105)
Gap_init rate = 0.03 (22 / 861), avg. gap size = 2.27 (50 / 22)  


1239 27.40 6.32 4.48  chr1_186665651_186667376.rev      502  1260 (466)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_186665651_    502 ATTTTAAATTTTAAACAGAAATGCAAGAGACATAAATTATCCCAA-CAAT 550
                           ii    v  i v ii          i   vi i v  v  v  -    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_186665651_    551 TTTGAAAGGCAA---CAAAATTGGAGGACTTTCATTATCTGAATTCAAAT 597
                         i      iiv  ---    i          iv  i vi ii v      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_186665651_    598 TTCAGTCTAAAATAAATGTTATCAAGACATTGTGGTATTGGCATAAGGAG 647
                         i i v vi   iiv vv  v         v       i           v
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_186665651_    648 AGAGA----AATCAATGAAATAGAAT--AGCTTTCTATAATGGACCTATA 691
                            v ----i       i        --  vv i viv   ii   i   
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_186665651_    692 TTTATATGATCAAATAATTTTTGACAAAGCAACTTCATCCGTTCAATTCA 741
                         iv v    i    v i     i     i vvi ivviv  i      vvi
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_186665651_    742 GAATGAAGAGCATTTTCAAAAAATGGTAC-AAAAAAATTAGGTATCTGTA 790
                            v   v  iv       v       i -iii v  i i i  ? iii 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_186665651_    791 TGAAAAATGATGAGCCTTGAACCTT-CCTTTCACTATATACGAAATTTAT 839
                           v    vi    ivi v  v  i -   iv   i      i   v   v
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_186665651_    840 TTTGAGATGGATTACTGACCTAAACTTAAAATCAAACACTATATAGTT-T 888
                         i ii i      i ?v        iv   i v v  v      v ii - 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_186665651_    889 TAAAAGAAAATATGAGAAAACATATTTGTAATCTGGGATTAG-CAAAAGC 937
                           i       i  ii ?iv v  v  i  i i  v  i    -   vi i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_186665651_    938 TGTCATTA--CATTACCCAAAAAATCTAATCAT-------AAAAATATCT 978
                          -  -   --i  v  v v    iivi  v  v-------       ---
  L1M4_orf2#LINE/    586 T-TC-TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA--- 630

  chr1_186665651_    979 GATTAAAAGGATCTTA--AAAACTTAAATATTTATTTATGAACTACATAT 1026
                            v  vv   ii i --    -     v i  --  i  --  ------
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAA-TTAAAAACTT--TTGTG--CT------ 669

  chr1_186665651_   1027 ATATAATTCAAAATACATTA------AAATGAATA-ATAAT--ACAAATT 1067
                         -------     iv   i  ------  i    v - i  i--   i v 
  L1M4_orf2#LINE/    670 -------TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_186665651_   1068 TGTGGAGAAAATATTTGCAATACAAATATTTGGCAAAGTAGTTAAATAAA 1117
                         - -                 vv  v    i  ii  i v v  iv  vv 
  L1M4_orf2#LINE/    713 -G-GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_186665651_   1118 GAACATATAAACAACTCCTTA-AGCTCAATGATAGAGAAAAGTCA--TA- 1163
                            i       v     -   - i      i   ---     v  --  -
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTC-TTACAACTCAATAATA---AAAAGACAAATAA 806

  chr1_186665651_   1164 -CCAG---GAAAACTGGTAAAATATTCAAACAGAT-TTTATGCAAATAAC 1208
                         -   i---i    iv  i   iv   ii  i   i-   v v    v  v
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_186665651_   1209 TTGTAGGAATGACCAATAA-CAGATTATTTAAAAGAGTG----GCATCAT 1253
                         v i  vi    i       -  v  v ----     -  ----i     ?
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGA----AAAGA-TGCTCAACATCAZ 901

  chr1_186665651_   1254 TGAGTTA 1260
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.25 (114 / 91)
Gap_init rate = 0.04 (34 / 773), avg. gap size = 2.41 (82 / 34)  


2610 26.85 3.03 1.57  chr1_186675802_186681715.rev     4534  5423 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_186675802_   4534 AGATATTCCATTTTCATGCATGGGAAAAATCAGTATTTTTGTATTGTTTT 4583
                               i    v      v  v    i v i i    v  iviv  vivv
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_186675802_   4584 TACTACCCAAAGCAAATTCAAGATTGAACCCAATCTCTATCAAAATAACA 4633
                             v      vii vi vv     v   v     i          vv  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_186675802_   4634 ATAACATTCTTCACAGAAATAGAAAAAATAATCTAATCCTAAAGTTTATA 4683
                         iivi v  i  ii       v  v  i-----  i        i  i   
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAATTCATA 150

  chr1_186675802_   4684 TAGAACTAAAAAATACCCAAAATAGCTAAAGCCATCCTTAGCAAAATGAA 4733
                          i   v iv  iiv     i      i   i v   i v iv  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_186675802_   4734 CAAAAATGGAGGAATTACATTACCTGACTT-AAAATTATATTACAAAGCT 4782
                             iv       v i   i v  ii i  -    i -  i         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr1_186675802_   4783 ATAATAACCAAAACAGCATGGTACTAGCATACAAACAAACACATAGACCA 4832
                          i i   i   i    ii       i     vii i i   i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_186675802_   4833 ATGGAGAAAAATAGAAAATCCATAAATAAATAAATATATTATTAGTCAAT 4882
                              iv i   v  i i    v       ivv   i   vv i      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_186675802_   4883 CTTTTTTCAACAAAAGCACCAAGAACACACATTCGGGGAAGA-CAGTCTT 4931
                         ivv     i    ii ii      v  iv  v v   i    -i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_186675802_   4932 TTCAGTAAATGGTGCTGGGACAATTAGATATCCACATGCAGAAAAATGAA 4981
                             ii                 i i    ?         i  i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_186675802_   4982 ACTAGACCCCTATCTCTCACCGTATA--AAAATACAATCAAATTTGATTA 5029
                         ii i        i   v    i    --     vv v     v v   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_186675802_   5030 AAGACTTACATTTAATACCTGATACTGTGAAACTCCCATAATAAAACATT 5079
                         ?    i  v  v   v v  i v   i i      ii v  v       v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_186675802_   5080 GGGGAGACTCTCCAGGACATTGGTCTATTCAAGGATATCTTGAGTA--AC 5127
                           ? vi v   i iv   v    vi  vv   v i v    iii  --  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_186675802_   5128 AACTCAAAAGCATAGGCAACCACAGCAAAAATGGGCA---CGAGTCACAT 5174
                          --i        i i     v v  v      i ii ---i iiiiv   
  L1M4_orf2#LINE/    600 A--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_186675802_   5175 CAAGCAA--AGATACTTCTGCACAGCAAAGAAAAC-ATAATACAAAGTGA 5221
                            --  -- i v    i  ii vv     i v  -  v - v       
  L1M4_orf2#LINE/    648 CAA--AATTAAAAACTTTTGTGCTTCAAAGGACACTATCA-AGAAAGTGA 694

  chr1_186675802_   5222 AGACACAAC--ACAAAACGTGAGAAAATATTTTGTAAACTATCCATCTGA 5269
                          i v     --   i  i v            - i   ii  vi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGA 743

  chr1_186675802_   5270 GAAGGGATAAATATC-AGAATATATAAAGAGCTC--ACACTTTACAGTAG 5316
                         v      ivvi    -              i   --   vi --  i  i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--CAATAA 791

  chr1_186675802_   5317 AAAAGAAAAAAACAATCTGCTTTAATGATTGGCAAA--ATCTGAATAAAT 5364
                         v   i i v   i  i iiv  ?  vi  v      --  i      i i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_186675802_   5365 ATTTCTC-----AAGACACGCAAATGTCCAAGATGTATA---AAAAATGC 5406
                                -----    i ii      v    v v i i ---   i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_186675802_   5407 TCAACATTAGTAATCAG 5423
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.02 (20 / 903), avg. gap size = 2.05 (41 / 20)  


2552 26.29 5.86 1.61  chr1_186687300_186689428.rev      768  1638 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186687300_    768 TGAAGAAATATTCCATGTTCATGAA-----ATAATCAATAATGTTAAGGT 812
                           i i i    i           i ----- v v i    v       i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186687300_    813 ----AT-----CCAAAGCAAACTGCAAATGGAATCCAATCCCTATCAAAA 853
                         ----  -----     vii v  i  i  vv  iv               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186687300_    854 TACCAATGACATTCTTCACAGCAATAGAAATACAAAAAACAGTTG----T 899
                          v   iivi v  i  ii   v   v  ----   ------ i  ---- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA----CAA------GCTGATCCT 140

  chr1_186687300_    900 ACAGTATCTATGAAACCACAAAGGATCCAGAATAGCCAAAGCTATTCTGA 949
                          v i viv    i  vii   i   i              i v  ii   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_186687300_    950 GCAAAATGAACCTAACTAGAAGAATCACA-TTACCAATTTTCAAATTATA 998
                         iv  i v    vv ii i  i  v     -  v       iv   i -  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TA 239

  chr1_186687300_    999 CTACA--GCTATAGTTACCAAAACAGCATGGTACTGGCATAAAAACATAC 1046
                              --    i   v i   i    ii              ii i v  
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_186687300_   1047 ACACAGGCCAGTGGAACAGAATACACGATCCAAATATAAATCCATATATT 1096
                          i i  ii  i     i     vv vii    i v     i     i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_186687300_   1097 TACAGTAAGCTAATTTTCAAACGAGGTGCCAAGAACATACATTGGGGAAA 1146
                           ii  v ii i      i vvii          v   v  v        
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_186687300_   1147 GGACAGTCTTTTCAATAAATGCTGCTGGGGAAATAGGATATCGATATTTA 1196
                          i i           i     v       iv  iv     ? v i  vi 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_186687300_   1197 GAA-AATGAAACTAGAACCCTGTCTCTCACCATATTAAAAAAAGTCAAAT 1245
                         i  -      ii i  v    ii   v        -- v    i i  v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATAT--ACAAAAATTAACT 487

  chr1_186687300_   1246 -AAAATTGATTGAAGACTTAAATCTAAAACCTAAA-CTTTGAAACTACTA 1293
                         -     v   ii?    i     v   i v     -  v i     vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_186687300_   1294 AAA-AAAAT---GGGGAAGTTCTCCAGGACATTGGTCT--GCA--GATTT 1335
                         i  -    i---  ? v iv   i iv   v    vi --   -- i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_186687300_   1336 CTCAAGGGCTATACCAAAAGTGCAGGCAACTGAAGCAAAAATGG------ 1379
                           i iiviiv i        ii  i     vi   v      i ------
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_186687300_   1380 ------TCA-CACAA-----AGCTTCTGTA-TGCAAAAGAAACAATTAAC 1416
                         ------   -  v  ----- i   i   i- v    i  v  v  i  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_186687300_   1417 ATTTTGATGAGACAGCACATAGAATGAGAGAAAATGTTCATTAACTATCC 1466
                          vvv   vi     i v  i      i        i  iiiv  ii  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_186687300_   1467 ACCTTACAAGGTATTAATAACCAGAATATATAAGGAGCTCACACACCTCA 1516
                          i  v i    v i vi  v             i  i   vi   v    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_186687300_   1517 ATAAGAAAAAAATCTAATAATCTGAATTAAAAATGGGCAAAAGAACTGAA 1566
                             v     i - v     i ii v ?             i  vi    
  L1M4_orf2#LINE/    788 ATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_186687300_   1567 TAAACATTTCTCAAAAGAAGACATACAAATGGAAAACAGGAATATGAAAA 1616
                           i         v        i          vv  i i v i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_186687300_   1617 GATGCCCAACATTACTGACCAT 1638
                              i      i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (139 / 86)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.95 (65 / 22)  


2885 25.58 2.78 1.78  chr1_186710303_186714578     2885  3783 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186710303_   2885 TGGAAACACATCCCAGGTACATGGCTGGGTAGAATCAATATTGTGAAAAT 2934
                               v i      v  v     v v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186710303_   2935 TACCATACTTAACATACTGCCAAAAGCAATCTCCAAATTCAATGCAATTC 2984
                         vi v     i---------  v   vii    v  i      i     i 
  L1M4_orf2#LINE/     51 GGCAATACTC---------CCCAAATTGATCTACAGATTCAACGCAATCC 91

  chr1_186710303_   2985 CCATCAAAATACCACCATCATTATTCACATAATTAGAAAAAACAATTCTA 3034
                          i        v   v vv v  v  ii  v  v v  v  ivii  i   
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr1_186710303_   3035 AAATTCATATGGAACCAAAAAAAGCGCCAGCATAGCCAAAGCAAGATTAA 3084
                                       viiv  iiii -    v         i   vv  i 
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGA 190

  chr1_186710303_   3085 GCAA-AAGAACAAATCTGGAGGCATCACACTACCTGATTTCAAACTAAAC 3133
                         iv  -         vi      vv       v  ii        vivv  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_186710303_   3134 TATAAGGTCATAGTCA-CAAAACAGCATGGTACTGGTATAAAAATAGGCA 3182
                           i  i ii i   v -   i    ii         i    ii    i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_186710303_   3183 CATAAACCAGTGGAACAAAATAGAGAACCCAGAAATAAACCCAAATACTT 3232
                         i   i i  i     i i   v    ii               v i i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_186710303_   3233 ACAGACAGCTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAG 3282
                          ii v  ii    i  i     i vviv   i v   vv i         
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_186710303_   3283 GATACCCTCTTCAAAAAATGGTGCTGGGATAATTGGCTAGCTACATGTAA 3332
                         i   vi  i     v              i  i   v  ? i     i  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_186710303_   3333 GAGAATGAAACTGGATCCTCATCTCTCATT-TATACAAAAATCAACTCAA 3381
                         i        ii    i  ii i   v  ii-           i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_186710303_   3382 GATAGATTAAGGACTTAAATCTAAGAACTGAAACTATAAAAATTATAGAA 3431
                         i  i   i ?i   i     v     i  i           v iv     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_186710303_   3432 GATAACATTGGAAAAAACCTTCTAGACATTGGCTTAGGCAAGGATTTCAT 3481
                           v     v  ?iv   i    vv   v    v        v i    v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_186710303_   3482 GACCAAGAACTCAAATGCAAATGCAATAAAAACAAAGATAAATAGCTGGG 3531
                         iivi v  vvi    v   v v    i    iv   i   i   iv v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_186710303_   3532 ACCTAATTAAACTAAAGAGCTTTTGCACAGCAAAAGA-ACAGTCAGCAGA 3580
                           i v  i   v v  i i      ii vv    i  -  vi   ---- 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA----A 686

  chr1_186710303_   3581 GAAAATGGAAA----ACCCACAGAGTGGGAGAAAATCTTCACAATCTATA 3626
                             i  i   ----         i           v  ii   vii   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_186710303_   3627 CATCTGACAAAGGACTAATATCCAGAATCTACAGCAAACGCAAACAAATC 3676
                         i      i  i     vi          v  i ivi   v vv    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_186710303_   3677 AG----AAAAA-----ATATCTCA--TCAAAAATTTGGGTAG-GGACATG 3714
                          i----     -----   v i  -- ?      --   i i-   iv  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAAT--GGGCAAAGGATTTG 834

  chr1_186710303_   3715 AATACACAATGCT-----AAAAATATACAAATGGTCAAGAAACATATGAA 3759
                             v   v v  -----i  i            i   v  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_186710303_   3760 AAAATGCTCAACATCACTAATGAT 3783
                           i             ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (132 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.93 (41 / 14)  


1135 25.19 3.78 3.78  chr1_186732286_186734290.rev      534   930 (1075)    L1M4_orf2#LINE/L1      194   590 (318)  

  chr1_186732286_    534 AGAAGAAGAAATCTGA--GACATCTACTTTCCTATTTGAAAA--TATTTC 579
                                v   vi  i--   vivi    i  v    v    --  i v 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_186732286_    580 AAAGCTACAGTAATAAAAATGTACACAGTATGGTACTAGCATAAAGAAAT 629
                                       v  i ------    i       i      i  -- 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGA------CAGTGTGGTACTGGCATAAGGA--T 285

  chr1_186732286_    630 AGGCATA--GACCAATGAAACAGGGT-GAG---CCAGAATTATATCAGCA 673
                           i    --  i     i  i  ii -   ---      v  v i --  
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CA 333

  chr1_186732286_    674 TA-ATACACAGTCAACTAATCTTTTACAAGGGTACCAAGATTACACAATG 722
                           -  vi ii     i i  i  iv        i      ii iv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_186732286_    723 GGGAAAAAAATAATGTCTTCAATAAATGGTGTTGAAAAAGGTGAATAATT 772
                               i  -  i v i     i        i  ii v iv  i   ?ii
  L1M4_orf2#LINE/    384 GGGAAAGAA-TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_186732286_    773 ATGTG-GAAATAATGAAATTGAATTTTTATTTTAAA--ATATGCTTAAAA 819
                          ii  -i   v      i   i iiii  ii i v --    i --    
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC--AAAA 480

  chr1_186732286_    820 TATCAACTCAAAATGGATTAAAAACTTAAATCTAATACCTGAAACTATCA 869
                         -  i              i ? i  i     v   v v  i       v 
  L1M4_orf2#LINE/    481 -ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_186732286_    870 AACCACTATAATAAAAAACAGAGG-AAATGCTCCGTGACATTCGTCTGGA 918
                            ivi  v  v    v i  i? -    -  i      v  v vi i i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGG 578

  chr1_186732286_    919 CAAAGATTTTTT 930
                            v i   i  
  L1M4_orf2#LINE/    579 CAATGGTTTCTT 590

Transitions / transversions = 2.23 (67 / 30)
Gap_init rate = 0.04 (16 / 397), avg. gap size = 1.88 (30 / 16)  

 703 23.65 13.85 1.35  chr1_186732286_186734290.rev     1221  1516 (489)    L1M4_orf2#LINE/L1      576   908 (0)  

  chr1_186732286_   1221 AGCCAAT--TTTTAAAAATATGACCCCAAAAGCACAGGTAACAGAAGTAA 1268
                           v    --   ivv i       v           i i    i   v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_186732286_   1269 AAATGGACAAAT-GAA----AT--AAATAAAAAGTTTCTGCA-TACAAAA 1310
                             i  i    - i ----  --    v    ii  i  ii- v    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_186732286_   1311 GAAACAATAAACAGAATAAAAAGA-GACCTACGAAGTGGGAGAAAATATT 1359
                           v  v  v  v i i i      -i   i  ii i              
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_186732286_   1360 CGCAAGCCACTGTAGATCTAATAAGGAACTCCTA-CCA------------ 1396
                         i    ii  ---  v    i      i   iv  -   ------------
  L1M4_orf2#LINE/    726 TGCAAATCA---TATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_186732286_   1397 ---TCTCAAAA-TAAATAAAGAAAGAACAAGTAATCTGATTTAAAAATAA 1442
                         ---   i v  - v     vi   ii    i   i ii   ?      ii
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_186732286_   1443 GC-------TTCAGTAGAGATTTC------AAAGACATTCAAATGGCCAA 1479
                           -------  v i    v     ------i    i  v           
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_186732286_   1480 CAGGTGTATGAAAAAAATGTTCAACATTGCTCATACC 1516
                         i i iii       i -  i       ii????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.63 (50 / 19)
Gap_init rate = 0.04 (13 / 333), avg. gap size = 3.46 (45 / 13)  


2763 26.40 3.82 1.80  chr1_186757077_186759879.rev     1423  2312 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186757077_   1423 TGGAAAAATATTGCATACTTATGGATTGGAAGAATCTACATTGTTAAAAT 1472
                               i    iv   ii i             v iv i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186757077_   1473 GGCCATACTGCCCAAAGCAACGTACAGATTCGACACTATTTCTATCAAAC 1522
                            v     v      vii iv         i  i v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186757077_   1523 TACCAACAGTCATTTTTCACAGAATTAGAAAAAA-AATCTTCAAATTCAT 1571
                          v   i v i -     ii     v v  v  iv-i   i v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_186757077_   1572 ATGGAACCAAAAAGGTCCCA-AATATCCAAAGCAATCCTCAGAAAAAAGA 1620
                               viiv  i  v    -    v     i     i v i   i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_186757077_   1621 ACAAAGCCAGAGGCATAACATTACGCGACTTCAAA-----CTATGAGACT 1665
                               iii    vv v   i v v i i      -----   ii ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_186757077_   1666 ACAGTAACCAAAACAGCATGGTGCTGCTACAGAAACAGACATATAGATCA 1715
                                i   i    ii    i   vi i iii i              
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_186757077_   1716 GTGGGACAGAATAGAGAACCCAGAAATAAAGCTGCACATCTACAGCCATC 1765
                         i   i i     v    ii           v iii    i  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_186757077_   1766 TGCTCTTCAACAAAGCTGACAAAAACAAGCAATAGGGAAAAGACTCCCTT 1815
                           v i   i    i v  v   i v  vv    i      ii ivvi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_186757077_   1816 TTCAA-AAATGGGTGCTAGGATAGCTGGCTAGCCAAATGCAGAAGAGTAA 1864
                              -      -    i   i i    v  ?   v     i    i i 
  L1M4_orf2#LINE/    400 TTCAACAAATGG-TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_186757077_   1865 AACTGGTCCCCTGCCTTTTCACTGTGTACAAAAGTTAACTCAAGATGGAC 1914
                          ii   v     i   iv-   ii i       i         i     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_186757077_   1915 TAAAGATTTACATGTAATTACATGTAATATGTCAAATTATAAGAATCTTA 1964
                         i ?   ii  v      vvi ---   -------  i     i v     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGC---TAA-------AACTATAAAACTCTTA 537

  chr1_186757077_   1965 GAAGAAAATCTAGGAAACAACATTCTTGAGAAAGAACTTATG-AATAAGT 2013
                                 iv    ?ivv  iv   v   vvvv ii-   v -   iiv 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTT 586

  chr1_186757077_   2014 CCTCTAG---------CAATTGCA---ACAACAACA-AAAAAATTGGCAA 2050
                         i  -   ---------   vv   ---i      v -       v ii  
  L1M4_orf2#LINE/    587 TCT-TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_186757077_   2051 GTAAGACCTAATTAAACTAAAGAGTTTCTACAGAGCAAAAGAAACTATCA 2100
                         i vi   i v  i   v v  i ii  i iiivvv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_186757077_   2101 ACAGAGTAAACAGACTACCTACAGAATGGGAGAAAATATTTGCAAACTAT 2150
                          v i   i  v    v   i                          ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_186757077_   2151 TCTTCCAACAAAAGCCTGATATCTAGAATCTGTAAGAAAC---------- 2190
                         viv  ii i  ii v  vi    i     v i   ii   ----------
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_186757077_   2191 CAACAAGCAAAAAACAAACAACCTCATT--AAAATAGACAAAGGACATGA 2238
                            i  vv    i     i    iv   --     i i       iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_186757077_   2239 ACAGACACTTCTCAAAAGAAGACTTACAAGTGGGCAACAAACACATGAAA 2288
                          i     i     v        iv     i   v   i  i         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_186757077_   2289 AAAATGCTCAATATCACCATGAGG 2312
                          i -       i    ????????
  L1M4_orf2#LINE/    886 AGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (148 / 84)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.78 (50 / 18)  


2712 25.91 2.31 2.63  chr1_186887413_186890691.rev     1878  2788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186887413_   1878 TAAAAAAATACCCTGTGTTCATGAGTTGGAATACTTAATATTGTTAAAAT 1927
                          ii   i   i  ii        ii      v               i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186887413_   1928 GTCCATACTACCCAAAACAATCTATAGATTAAATCCAATTCTTATCAAAA 1977
                          v v     v      vii     i     v  iv    i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186887413_   1978 TATCAATAAGATTTTTCAAAAAAAATAGAAAAAAAAA--CTGAAATTTGA 2025
                          vi  iivivv     iiv i   v -  v  ivvi --  i     iiv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chr1_186887413_   2026 ACGATACTGCAAAAGCCTCTGAATAGCCAAAGCAATCCTGAGCAAATAGA 2075
                          i iv v     ii v i v           i     i   iv  iv   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_186887413_   2076 ACAAACCTGGAGACATCACACTATCTGACCTCAAAATACACTATAAAGCT 2125
                              vi     ivv       vi ii ii      ivi    i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_186887413_   2126 GTAGAAAAAAAAGAAAAACACAAAA-AACATGGCACTGGCATGGAAATAG 2174
                         ii  v  v------------   i - iii   i        iiii    
  L1M4_orf2#LINE/    250 ACAGTAAT------------CAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_186887413_   2175 AC--------CAATTGAATAGAAAAGAAAGTCCTGAAATAAATCCATGCA 2216
                           --------    v        vv  i     v        i    i  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_186887413_   2217 TTTACAGTGAACTACTTTTTGGCAAAGATGCCAGGAACATACAATGGAGA 2266
                             ii  v  i iv    i i   i i     i  v   v      i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_186887413_   2267 AAAGACAGTCTT--CAATAAATAGTGTTGGGAAAACTGAACATCTGTACA 2314
                           ii i      --   i    i   i     v     i i ? iii ii
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_186887413_   2315 GAAAAGAATAAAATTAGAAAATTTTGTCACGCCATATACATAAATCAAGT 2364
                         v        i  i  i  vvvi viv    i         v    i  v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_186887413_   2365 AAAAATAGATTAAATAATTAAATATAAGACCCAAA-TTATGAAACTAATA 2413
                         v     i   i ? v vi     i     v i   -i   i     vv  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_186887413_   2414 GGAGAAAACACAGA---AAATACCTCCATGATGTTGGTCTGGTCAATGGG 2460
                          i        i  i---    --  i i   iv    vi i v      v
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_186887413_   2461 TTTTTGCCTATGGCTTCAAAAGCACAGGCAACAAAAGCAAAAGTATACTA 2510
                           i  ivv    i vi          i          v    i  v iv 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_186887413_   2511 ATAGGATTACATAAAAATAAAAAAATATTCTGCACTTAAAGGAAACAAAT 2560
                           v   i v   v     v     v v  v   -i i      v  v - 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTA-T 683

  chr1_186887413_   2561 CATAGAA--TGAAGTGAAAACCAGTAGAATGGGAGAGAAACATTTGCCAA 2608
                           -    --    iv  v    vii           -   i      v  
  L1M4_orf2#LINE/    684 CA-AGAAAGTGAAAAGACAACCCACAGAATGGGAGA-AAATATTTGCAAA 731

  chr1_186887413_   2609 CTATACATCTGATAAGGAGGCAATAT--GGAAAATATAACAGTAACTCAA 2656
                         ii   i           iivivi   --i   v      -  -     vv
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAA-AG-AACTCTT 779

  chr1_186887413_   2657 ACAACTTAATAGCAATAAAACAAATTAGCCAATTTAAAATTGGGAAAAAG 2706
                               i    ii  v  i      v v      ?    v    v   --
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA-- 827

  chr1_186887413_   2707 GGACCTAAATGAACATTTCTCAAAAAAAGACTTATGAATGGCCAATAGGC 2756
                            ii i   ii         v   i    iv  ii           i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_186887413_   2757 ATATGAATTAAATGGTCAACATCACTGATCAT 2788
                          i     v- i   v         ????????
  L1M4_orf2#LINE/    878 ACATGAAA-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.37 (45 / 19)  


2743 24.07 3.06 3.72  chr1_186921832_186926197     2960  3873 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_186921832_   2960 TGTAAAGATATTTCATATGTATGGATTGGAATATTTAATGTTGTTAAAAT 3009
                           v        ii   i vi           v i     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_186921832_   3010 GACAATACTACT-AAAGCAATTTACGGATTCAGCACAATCCCCATCAAAA 3058
                          i       v i-   vii  i   i      i i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_186921832_   3059 ---CAGTGGCATTCTTCACAGAAATAGAAAAAAAAAATTATAAAAT--AT 3103
                         ---   iv  v  i  ii       v  v  ivvi - iv      --  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_186921832_   3104 GTGCAGGACAT-CAAAAGATACCCA-AATAACTAAAGTAATCATGAGCAA 3151
                         i  ---  v  -   ii  --    -    i i   ii    v   i-  
  L1M4_orf2#LINE/    150 ATG---GAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAA-AA 193

  chr1_186921832_   3152 AAAAGAACAAAGCTAGAATCATCACACCACCTGACTTCAAA-TTTACTAC 3200
                          i          i i  ivvv      iv  ii i      -i       
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_186921832_   3201 AAAGCTATCACAATCAAAACAGCATAGTACTGGGATAAAAGCAGACACAT 3250
                                ivii      i    ii i       v    iiii     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_186921832_   3251 AGACCAATGGAATAGAATAGAGAA-CCATATATATATCCACACATTTACA 3299
                            i              v    i-   v v   v i   i       ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_186921832_   3300 GCCAACTCAACTTTGACAAAGACTACA----CATACGTTGGGGAAAAGAA 3345
                          i   i v vi  i     i iivv  ----   v iv        ii v
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_186921832_   3346 AATCTTTTAAATAAATATTGCTGGAAAAAATGGATAATTTTATGCAGAAA 3395
                          i      v  i    iv      i v  v      ?iivi     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_186921832_   3396 AA---ATCTAGACCCCTATCTCTCACCATACACAAAAATCAAATAAAAAT 3442
                           --- vi i        i   v       i        i  v v     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_186921832_   3443 AAATTATAGACTTAAATCTAAAACTTAAAAATATAAAACT---AAAAACG 3489
                         ii  i ?    i     v   i vi     v         --- i  -- 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA--G 541

  chr1_186921832_   3490 AAATTATTTAGG---AAACACTACAGGACATTGGTCTGGGCAAAGATTTT 3536
                            vi  --   ---   i-  v iv   v    vi i     v i   i
  L1M4_orf2#LINE/    542 AAAACAT--AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_186921832_   3537 TTTGTTTGTAAAACCTCAACATTACAGACAACTAAAGCAAAAAATAGACA 3586
                           v ---i  vi  vi   v vi   ii    v    -          i 
  L1M4_orf2#LINE/    589 TTAG---ATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATA 634

  chr1_186921832_   3587 AATGGAATTATATCAAGCTAAAAAGCCTCTGTAC-----AGTAAACAATC 3631
                            v i i vi     iv v    i i i   i -----  v v  v   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_186921832_   3632 AGCAAAGTGAAGAGATAACCCACAGAATGGGAGAAAATATTTACAAACCA 3681
                          iv        i   i                          i    i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_186921832_   3682 TTCATCTGTCCAGGGATTAATAACCAGAATACATAAGGAGCTCAAACAAC 3731
                          vi     viv     i vi  v        i    i  i   vv     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_186921832_   3732 TAAATAACCAAAACAAAATACTAAAAACCAAAACTAATAACCCAATTAAA 3781
                          v     --------------      ----i  v            ?  
  L1M4_orf2#LINE/    785 TCAATAA--------------TAAAAA----GACAAATAACCCAATTWAA 816

  chr1_186921832_   3782 GACTGGGCAGAATATCTGAATACATATTTCTCATAAGAAGACATAAAGAT 3831
                         i v      i iv  i      v i       vv       i   v i  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_186921832_   3832 GGCAAACAGATATATGAAATAATGCTCAACATCACTAATTAT 3873
                            v  i iii i      vi             ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (137 / 80)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.70 (62 / 23)  


2586 24.52 3.42 0.30  chr1_187004645_187006311      502  1174 (493)    L1M4_orf2#LINE/L1      215   908 (0)  

  chr1_187004645_    502 TCACACTATATGACTTCAAAGCATACTACGAAGATATATTAACCCAAAC- 550
                                vivii i      i v      i   v  i v   i v i  -
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_187004645_    551 ---TGATACTGGTATAAGAACAGACACATAGACCAATGAAACAGAAGAGA 597
                         ---  i      i     i i     i     i     i  i    vv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_187004645_    598 GAGCTCAGAAATAAATCCATGTAGTTATAGCCAACTGATTTTTAACAAAG 647
                            ii          i    ii v    i i   i       ii    i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_187004645_    648 GTGCTAAGAACA--CACTG---AAAGGACAGTTTCTTCAAAAAATGGCAC 692
                             i    v  --  v  ---    i i   i i     v      ii 
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_187004645_    693 TGGGAAAAC--GATATTATCATGCAGATATATGAAATTAGATATTTATCT 740
                              v   --    ?ivv      i viv     i  i  ivii  i  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_187004645_    741 CCCACCATATGCAAAAAC-AACACAAAATGGATCAAAGATTTAAATTTAA 789
                          v        i      i-   v            ?   ii     v   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_187004645_    790 GACTTGAAACTA-----------GGAGAAAAAGCATAGGAAAAAAGCTCC 828
                           vi i      ----------- i      --      ?iv   v  i 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATCTTC 562

  chr1_187004645_    829 ATGTTACTGGTCTAGGTTAGGATGTTTTGGATAAAACCTCAAAAGCACAG 878
                         i  vivi   vi    iv v i v i  i    vi  vi          i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_187004645_    879 ACAATAAAGGCAAATATAGATAGATAAGATTACATGAAAGTAAAAAGCTT 928
                         i   i   i v   v       i  vi  i v   v   i v    i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_187004645_    929 CTGCACAGCAAAGGAAACTTCCGACAAAGTGAAGAGACAACCCACAGAAT 978
                         i  ii vv       v   vi i v        i                
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_187004645_    979 GGGAGAAAATATCTGCAAACCATCCACCTGGCAAAGGATTAATAACCGAA 1028
                                     i      i   vi i   ii  i   i vi  v  ii 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_187004645_   1029 ATATACAAGGAGCTCAAACAGCTCAACAGCAAAAAATCAAATAATCCAGT 1078
                              i  i  i   vv   i     i ii     iv       i   i 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_187004645_   1079 TAAAAACTGGGCAAAAAATTTGAAGAGACATTTCTCAAAAGAAGACATAC 1128
                          ?    v        ii       v           v        i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_187004645_   1129 AAATGGCCAATAGGCATCTGGAAAAATTCTCAACATTATTAATCAT 1174
                                     i   iv  i   i  v        i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (107 / 54)
Gap_init rate = 0.01 (7 / 694), avg. gap size = 3.57 (25 / 7)  


2164 27.45 7.36 1.29  chr1_187026495_187031679     3837  4692 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187026495_   3837 TGAAAAAACATTACATGCTCATAGATTGGAATAACTGATATTGTTAAAAT 3886
                           i   i i  iv    i    i        v vi i          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187026495_   3887 GAACATATT------ATCGAGCTAC----------CAAT----ATTA--- 3913
                          ivv   i ------  i  v    ----------    ----  i ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187026495_   3914 ---------TTTTTTTCACAGAATTATGA-AATCT-ATTCCAAAAGTCAT 3952
                         ---------ii     ii     v -   -  v  -  i i    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_187026495_   3953 ATGAGATTAAAAAATGAGCCTGAATAGCCAAAGCAACCCTGAGCACAAAG 4002
                            ii v iv  ii-  v  v           i   i i   iv vi   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_187026495_   4003 AACAAAGTCAGCGGCATCACGTTGCCAAACTT-AAAACTATACTACGAGG 4051
                                 ii v  vv    ii v  v  i  -      -      i i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_187026495_   4052 CCACAGTAACCAAAACAGCATAGTACTGACACAAAAACAGAC-------- 4093
                          i       i   i    ii i      i  i  ii i    --------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_187026495_   4094 TAATGGAACAGG-TTAGAAATCCAGAAATAAATCCACATACCTAGAGCCA 4142
                         i       i  i-  iii i            i   i i ii  vi i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_187026495_   4143 TCTGATCTTCAATGAACTCATTAAAACTAAGCAAAAGATAAAGGACACTC 4192
                         vi    i   i ii ivviiii  i  i vv   vi iv    i i v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_187026495_   4193 T----AATATATGGTGCTGGGACACCTGGCTAGCCATCTGCAGAAGAATG 4238
                          ----  i v              v    v  ?   iv    i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_187026495_   4239 AAACTGGACCCATACCATTCATCATAAAAAAAAAGC--CTCAACGTGGAT 4286
                           ii       v    viv  i    v v     vi--     vi     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_187026495_   4287 TAAAAATTAAAATATAAGATCTAAAACTATAAGAATCCTTGAAGAAAACT 4336
                         i ? i iiv    i     v            i v  i v         v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_187026495_   4337 TAGGAA-ATATCATTCTGGTCATTTTCCATGTTACAGAAT------TTAT 4379
                             ?i- v   -   --  v ii  --iv    viv   ------   -
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTC--GTGACCTT--GGGTTAGGCAATGGTTTCTTA- 591

  chr1_187026495_   4380 GACTATGTTCACAAAAGCAATTGAAACAAAAATAAAAACTGGCAAGTAGG 4429
                           -    vivv        vvv v       iv     iv ii  i v  
  L1M4_orf2#LINE/    592 GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_187026495_   4430 ACCT-ATTAAAACAAAATAGCTTCTGCACAGTAAAATAAACGATCAACAG 4478
                           i -  i    iv   - i   i  ii vvi   iv v  v     v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_187026495_   4479 AATAAATAAAAAAACTACAGAATGAGAGAAAATATTCAAGAACTATGCAT 4528
                          i i  v i v  v i        i           iivi  ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_187026495_   4529 GCGACAAAGGCCTAATAGCTAGAATCTATAAGGAACT--TA-AAC-CAAC 4574
                         vi  i  i  v  vi  v i     v     i     --  -   -   i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_187026495_   4575 AAGTAAAATACAAGTAACCCCATT-AAAAATGGGCAAAATACATGAACAG 4623
                           vv    v    i      v   -             iv iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_187026495_   4624 ACACCTCTTAAAAGAAGACATACAAGTGGCCAACAAATATATGAAAAAAT 4673
                            ii   iv        i      i       i  ii i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_187026495_   4674 GTTCCACATCACTAATCAT 4692
                          i  v      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (148 / 84)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.74 (74 / 27)  


2800 27.64 1.55 1.66  chr1_187071224_187073098.rev      494  1394 (481)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr1_187071224_    494 TATGCCAGATGCCCCTGGATTAAAATAATTGATATCGTTAAATTTAACAA 543
                            v   --  ii v      ii  v v  i    i     i------- 
  L1M4_orf2#LINE/      9 TATCCCA--TGTTCATGGATTGGAAGACTTAATATTGTTAAG-------A 49

  chr1_187071224_    544 TATCCATACTACTCAACATGATTTATAGATTCAATGCAATCCTTATCAAA 593
                          iv v     v i   vv    i  i        i       i       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_187071224_    594 ATTCTTAGA-ACATTTCTCAAGGGACTAGAAAAACTTAATCCTAAAATTA 642
                           i i-  v-i v   i iivi i v v  v  i  -i           v
  L1M4_orf2#LINE/    100 ATCCC-AGCTGCCTTTTTTGCAGAAATTGACAAGCT-GATCCTAAAATTC 147

  chr1_187071224_    643 ATATGGAACCATAAAAGACAC----TAGTCAAAAC--TATTGAGCAAAAA 686
                                 viii  ii   v ----   i      -- v    iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_187071224_    687 GAATACCCCTGTAGCCGTCACACTACCTGACTTCAAAATATACTGCAAAG 736
                            i vvvi  v  vvv       v  ii i       iv    i     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_187071224_    737 CTATAGTAATCAAAGCATCATGATAATGGCATAAAAACAGAAGCAGTGGC 786
                            i         ii  vii  i  v        ii i   vii vv ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_187071224_    787 CAATGGAAAGGCAATGAAAATCCAGAAAGAAACCTACAAATATACAGTCA 836
                                 vi v v   i i        v     i i v  v  ii    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_187071224_    837 ATTGATTTTTCACAAAGGTGCCAAGAACATATAATGGGGAAAGGACAGTG 886
                                  iv    i          v   vi           i i   v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_187071224_    887 TCTTCA-CTAATGATATTGGTAAAACTAGATATCCACATGCAGCAGAATA 935
                          i    - v    i ii   v v    i    ?         iv     i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_187071224_    936 AAATTAGAACCTTTTATCACACCATCTATGGGAATCAACTCAAAATGGAT 985
                           i  i  v  i viv         v  iiii   i              
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_187071224_    986 TAAAAACTTGTACATAACAATTGAAATTTTAAAACTACTAGAAGAAAACT 1035
                         i ? i  i iv ii   v ii i   i v       vi           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_187071224_   1036 TAGAGGAAAGCCTCCGCAACATTGATCTGGGCAATTACTTTTTGGAAATT 1085
                            i? v  ii  i  ii  v   ivi i      vii  i  i  v  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_187071224_   1086 ATGCCAAAA-CACAGGCAACAAATACAAAAATACATAAAGGGGATTGCAT 1134
                          ii      -    i        viv       v     vv   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_187071224_   1135 CAAA-CTAAATGTTTTTGCACAGCAAAGGAAAGAAGAAACAGAGTGAGTA 1183
                             -i    vii     ii vv       v vv vv  v i     iv 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_187071224_   1184 GTCTACCTACAAATTTGGATAAAATATTTGCAAACCAAAGATGTGATAAG 1233
                          v v   i   i v v   v              i  v v  v       
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_187071224_   1234 AGGCTAGTATTGAAAATATATAAGGAATTC----AATTCAATAGCAATTG 1279
                         i i  v    iv i         i   i  ----  i      ii  vvi
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_187071224_   1280 AACAAATAGTTCAATAATAATATGGGCAAATAACTTGAATAGACATTTCT 1329
                         i       iii    v?v  v         vi i                
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_187071224_   1330 CAAAGGAAGACAACCAGATGACCAACAGGTATTTGATAAAATGATCATGA 1379
                          v  i     i vv  i   i    i i i iv   v  i   v   ---
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA--- 894

  chr1_187071224_   1380 GACATTATTAATCAT 1394
                         -    i ????????
  L1M4_orf2#LINE/    895 -ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (12 / 900), avg. gap size = 2.42 (29 / 12)  


1980 26.58 1.58 1.74  chr1_187243188_187245474.rev      601  1232 (1055)    L1M4_orf2#LINE/L1        1   631 (277)  

  chr1_187243188_    601 TGGAAACACATCCCGTGTTCACGAATAGGTAGAATCAATATTGTGAAAAG 650
                               v i     i      i i  v  v   v i        v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187243188_    651 GACCACACTGCCAAAAGCCACGTACAAATTCAACGCAGTTCCCATCAAAA 700
                          i v i   v  v   viv iv    i          i i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187243188_    701 TATCACCATCATTCTTCACAGAACT--ACAAAAAGGAATCCTAAAATTCA 748
                          vi  v vv v  i  ii     v --    ivv --             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCA 148

  chr1_187243188_    749 TATGGAA-TGAAAAAAGAGCCCACA-TAGCTAAAGCAAGACTAAGTAAGA 796
                                -  v  i-- ii    v -    i   i   vvi i iv    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_187243188_    797 AAAACAAATCTGGAGGCATCACATTACCTGATTTCAAACTATACTATAAG 846
                          i      vi      vv     i v  ii        viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_187243188_    847 ACCATAGTCACCAAAACAGCATGGTACTGGCATAAAAATTGGCACATAGA 896
                         i i i   v i   i    ii              ii  v i  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_187243188_    897 CCAATGGAACAGAATACAGAACCCAGAAATAAACCCAAACTCTTACAGCC 946
                         i        i     vv   ii               v  vi   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_187243188_    947 AAT-GATCTTTGACAAAG---CAAACACAAACTTAAAGTGGGGAAAGGAC 992
                            -   i  i     i --- v  v  v --  v  -         i i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCA--TTCAA-TGGGGAAAGAAT 393

  chr1_187243188_    993 ACCCTATTAAACAAATGGTGCTAGGATAATTGGCAAGTCACATGTAGGAG 1042
                          vi  v  v             i   i  i   vv ?i      i ii  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_187243188_   1043 AATGAAACTGGATCTTCATCTCTCACCTTACATAAAAATCAACTCAAAAT 1092
                               ii    i iii i   v    v  i i      i          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_187243188_   1093 GAATCAATTCAAAA--TAAATTGCAGACCTGAAACTATAAAAATTCTAGA 1140
                          i    ?---- i --     vvv   v  i           v ii    
  L1M4_orf2#LINE/    494 GGATCAW----AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_187243188_   1141 AGATAACATTGGAAAAACCCTTCTAAACGTTGTCTTAGGCAAGGATTTCA 1190
                            v     v  ?iv  vi    vvi  v   vv        v i    v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_187243188_   1191 TGACCAAGAACCCCAAAGCAAATGCAATAAAAACAAAGACAG 1232
                          iivi v  vv  v      v v    i    iv   i i  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

Transitions / transversions = 1.29 (93 / 72)
Gap_init rate = 0.02 (11 / 631), avg. gap size = 1.91 (21 / 11)  

 837 25.00 2.46 0.35  chr1_187243188_187245474.rev     1513  1796 (491)    L1M4_orf2#LINE/L1      619   908 (0)  

  chr1_187243188_   1513 AAAAAAAAGATAAATAGCTGAGACTTAATTAAACTAAATAGC----ATGG 1558
                            i    i   i   iv vi     v  i   v v  v i ----i  v
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_187243188_   1559 --CAGAAGGA-ACAGTCATCAGAGTAAACAGACAACTCACAGAGTGGGAG 1605
                         --  -     -  vi   vv i   i  v       i      i      
  L1M4_orf2#LINE/    669 TTCA-AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_187243188_   1606 AAAATCTTCACAATCTATACAACTGACATAGGACTAATATGCAGAATCTA 1655
                              v  ii   vii   i v    i vi     vi   v      v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_187243188_   1656 CAATGAACTCAAACAAATTAGCAAGAAAAAAGCAAAAAATACCATTGAAA 1705
                         i  v      vv    v i ii  v     ii    v  iv v   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_187243188_   1706 AGTGGGCTAAAGATATGAATAGACAATTCTCAAAAGAAGATATATAAATA 1755
                          i     v  i   v          v     v            i    i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_187243188_   1756 GCCAAAAAACGTGTGTAAAAATGCTCAACACCACTAATGAT 1796
                              v  i iii  v   i          i  ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (38 / 32)
Gap_init rate = 0.01 (4 / 290), avg. gap size = 2.00 (8 / 4)  


 648 30.25 2.52 1.26  chr1_187270316_187272403.rev      885  1122 (966)    L1M4_orf2#LINE/L1        4   244 (664)  

  chr1_187270316_    885 AAAAATATTTTTTGCTCACGAATTAGAAGAATCAAAAGTGTTAAAAATTT 934
                            i    iiiv  i   i i   i     v i  v v      i - vv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-TGG 52

  chr1_187270316_    935 CCATACTACTCATAGCTATATACAAGTTCAATGCAATACCTATTAAAATC 984
                          v     v i  v viv  v    ii     i     v     i      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_187270316_    985 TGAGTGGCATTCTTCACAGGAATAGAAAAAATTATCCTAAAATTTGCACA 1034
                         iv  iv  v  i  ii   i   v  v  iv v           iii ii
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_187270316_   1035 AAACCACAAAAGACTCCAAATAGCCAATGTAATTCTGGGAAATAA----A 1080
                         i  vii   ii   i vi         vii   ii  ii   v  ---- 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_187270316_   1081 AAGTTGAAGGCATCATACTTCCTAATT--GAAAATTACGTTACA 1122
                               i   vv   i      i    --i   v    --    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACA 244

Transitions / transversions = 1.67 (45 / 27)
Gap_init rate = 0.02 (4 / 241), avg. gap size = 2.25 (9 / 4)  

1216 26.04 1.84 1.84  chr1_187270316_187272403.rev     1164  1597 (491)    L1M4_orf2#LINE/L1      475   908 (0)  

  chr1_187270316_   1164 ACAAAAATTAACTAAAAATAGA-CAAAAAACTAAACTTAAGACCTTCAAC 1212
                                      v     i  -  ? i v     iv     v  vv   
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_187270316_   1213 CATAAAAGTTCTAGAAGAGA-TATAGGAGAAAA-CTCCTTGACATTGGCC 1260
                         i      v ii       i -i     ? v   -  i v    v    vi
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_187270316_   1261 T---TAATGTTTGTTTATATATCACGTTGAAAGCTTAGGCTACAAAAGCA 1307
                          ---i    v  vi   v    v  iiii     vi i  v       v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_187270316_   1308 AACTATATCAAAGAAAG-GGACTATATCAAACTAAAGTATCTCTGCACAG 1356
                           ---- vi i v   v-     vi      v v  iv ii i  ii vv
  L1M4_orf2#LINE/    625 AA----AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_187270316_   1357 CACAGGAAACCATCAATAAAATGAAAAGGCAACCTATAAATTGGGA-ATG 1405
                           v    v  i     v   i       i     i i i v     - vi
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_187270316_   1406 ATATTTGTAAACCCTGTATCTGATAAGGGGTTAATAAGCCAAATTTATAA 1455
                                i   i v i             ii vi  vv vi   v     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_187270316_   1456 AGAACACATACAATTCAATAGTATACAAGGAAGTAACATAATTAAAAAAT 1505
                              v v     i      i  v v iiv  i    vi    ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_187270316_   1506 GGCCAAAAATCCTGAATAGACATTTTTAAAAAGAAGACAGAAACATGGCC 1555
                           v    iivii             i vv        i v v v      
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_187270316_   1556 AACATGTATATGAAAAGACAGAAACTCAACATCATTAAGTAT 1597
                           i v i i         ii----          ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATG----CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (58 / 52)
Gap_init rate = 0.02 (8 / 434), avg. gap size = 2.00 (16 / 8)  


2709 24.48 2.07 7.88  chr1_187328994_187333336.rev     2890  3853 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187328994_   2890 TGGAGAGGTATTCTATGTTCATGGATTGAAAGAATCAATATTGTTAAAAA 2939
                             i  i   i i              i    v i           i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr1_187328994_   2940 TGTCCATACCACCCAAGC-AATCTACAGATTCACTTTAATCCCTATCAGA 2988
                           v v    iv     ii-i             vivi           i 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_187328994_   2989 ATACCAATGACATTCTTCAATAAAGTAGAAAT-AACA--TTG----TAAA 3031
                           v   iivi v  i  i------ i      -i   --i  ----    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT------GCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_187328994_   3032 ATTTATGTGGAAGCATAAAAGACCCAGAATAACCAAAGTTATACTGGGCA 3081
                            i  i     iiii  ii           i     iiv  vi  iiv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_187328994_   3082 AAAGCAACAGAACTGGAGAAATCACATTATCTTACTTCAAATTACACTAC 3131
                          i iv    i ii     i v     i vi iv i      vivi     
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_187328994_   3132 GGAGCTATAGTAACCAATACAGCATGGTACTGGCATAAAAACAGACACAT 3181
                         ii     i     i   v    ii              ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_187328994_   3182 AGAGCAATGCAACAGGA--AACAATACCCAGAAACAAATCCATACATCTA 3229
                            v     v  i  i --i v i --       i   i        i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGT--CCAGAAATAAACCCATACATTTA 341

  chr1_187328994_   3230 CAGTGAACTCATTTTAGACAATGGTGTCAGGAATATACAATGGGAAAACG 3279
                         ii  v  i v     v     v    i  i  vi  v       i   vi
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_187328994_   3280 ACGATGTCTTCAATAAATGCCCCTGGAAAAAAATTGATATATATATGCAG 3329
                          iii v i     i     viv    i v  v- v    ?vi i     i
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAAC-TGGATAKCCACATGCAA 440

  chr1_187328994_   3330 AAGAATGAAACTAAATTCCTGTTTCTCACCATATCCAAAAGTCTAATT-A 3378
                                  ii ii ii   iii  v        v     i -   i - 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAACTCA 489

  chr1_187328994_   3379 AAATAGTTTAAAGACTTAA-TCTAAGATCTCAAACTATGAA---TGTGAA 3424
                             i v i ?    i   - v     v  v       i  ---iv ii 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_187328994_   3425 ATAAAACAT-TGAGTAAATTCTTCATTACATTGGAGTGGGCAAGGACTTC 3473
                          v       -v ?      -    i v  v    iv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_187328994_   3474 TTGAGTAATATCCCACATGCGCAGGCAGCCAAAGCAAAAATGGACAAATT 3523
                           iii  vv iv   v v  i  i   i v    v      i  i     
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_187328994_   3524 GAATCACATCAAG-TTAAAAAAGCTTCTACACAGCAAAGGATACAGTCAA 3572
                          i iiv      i-       --   i iii vv       i  vi    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_187328994_   3573 CGAAGTGAAGAGACAACCCACAGAATGGGAGTATTTCCAAACTACCCATA 3622
                         vi       i                     -------------------
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAG------------------- 717

  chr1_187328994_   3623 TGACAAGAGATTAATAACCAGAAGAGACAACCCACAGAATGGGAGTATTT 3672
                         ----------------------------------- i   ------    
  L1M4_orf2#LINE/    718 -----------------------------------AAAAT------ATTT 726

  chr1_187328994_   3673 CCAAACTACCCATATGACAAGAGATTAATAACCAGAATATATGAAGAACT 3722
                         v    ii ivi  v   i   i  i vi  v           i       
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_187328994_   3723 CAAACAACTCTATTAGAAAAAAATCTAATAATCTGATTTTTAAACTGGGC 3772
                          vv       v  v v     i - v     i ii   ?v-   v     
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWA-AAAATGGGC 824

  chr1_187328994_   3773 AAAATATCTGAATAGACACTTCTC---AAATGACATACAAATGACAAACA 3819
                            iv  i          i     --- i v  i         i v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_187328994_   3820 GGTATATGAAAAGGTGCTTATCATCGTTTATCAT 3853
                         i i i        i    i v    i????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (154 / 78)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.36 (96 / 22)  


2651 27.54 2.34 1.11  chr1_187422030_187426245.rev     2829  3725 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187422030_   2829 TGGAGAGATATTCCAATTTAATTAATATGAAGACCCAATATGGCCAAGAT 2878
                             i      i   vv  v  vi  vv      ii     v ii     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187422030_   2879 GTCAGTTCTTCCCAATATT-ATCTTTAGGCTCAATGCAATCCCAATGAAA 2927
                          v  i v  i     -   -    vi  ii    i        v  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA-ATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_187422030_   2928 ATCCATGACAATTA--TTTTGTGCATA--TCAACAAACTGATTCTTAATT 2973
                             ----  ii i--    v    v -- ii    i     i  v  v 
  L1M4_orf2#LINE/    100 ATCC----CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_187422030_   2974 TTATAGGAAGAGACAAAAGACCTTGAATAGCCAACACTCTATTGTT---G 3020
                          i   v i i vi   ii    iv          v  vv v   vv--- 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_187422030_   3021 AAGAACAAAGTTGAAGGATGAACACTACCTAACTTTAAGACTTACTATAA 3070
                                      i    ivv     v  i  i  i  i        i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_187422030_   3071 AGCTACAATAATTAAGACAGTGTGGTATTGGTAAAAGAGGAAACTAATAA 3120
                                i    i              i   i v   iiv i  vv   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_187422030_   3121 ATCAGTGTACTAGAATAAACATCCCAGGAATACATGCATACACATAGGGT 3170
                             i  v v      vi v vi    i    v iv      iv  v   
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_187422030_   3171 CAATCGATCTTTGAGAAAGCAACAAAGGAAATACAATGGAGAAAAGACAG 3220
                             i   i  i  v  i vvi v   ivv  v      i    ii i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_187422030_   3221 TATATTCAACAAATAGTGCTAGAACAACTGGAGATCCATATCTAAAATAA 3270
                          v v          i     i i         v ?   i  vi    ---
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA--- 442

  chr1_187422030_   3271 GCAATAAATCTAGATTCTATTCTTAAATCCTTCAAGAAAATCAG-TCATA 3319
                          -   i  vi i  ii ivvi  i v i v vi vi     i i-   v 
  L1M4_orf2#LINE/    443 G-AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_187422030_   3320 ACGGATCACAAACCAAAATGTAAAATGC-AAAGCTATAAAGCTCCTAAAA 3368
                          i      ? i   v        i -  -   i       i   i  i  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAA 540

  chr1_187422030_   3369 -ATAACAGAAGA--AAATCAAGTTGACCC-AGGTTTAGTGATATCTTTTT 3414
                         - v    v i ?--     vvvv     i-i    vi ii  ivi  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_187422030_   3415 AGATATGACAGCAAA-GAACAACCTATGAAAGAAACAATTGATAAGCTGG 3463
                                   v    - v    v v ii       v   v     ii   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_187422030_   3464 ACTTCAGTAACACTAGAAGTCTTTATTTTGTGAAAGATAATGGTAACAGA 3513
                               vi  v i  i  iii   i vi vii  i  i v ivi  v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_187422030_   3514 ATGAAAAGATAAGCCACACACTGGAAGAATATATTCACTAAGGGCATAGC 3563
                         i        i  v     v v   i    v     ii v  vvii   v 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_187422030_   3564 TGAGAAAGGACTGTTATCCAAAATATACCAAAAATACT--CAA---AACA 3608
                            v  i     vv      i      iv  i  iv  --   ---  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_187422030_   3609 ATAAGAAATCAAATAAGCCAATT-AAAAATGGGCCAAAGACCTTAACAAA 3657
                             i  iv       v      -          v  i  ii v  i i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_187422030_   3658 CACCTCATCAAAGAAGATATACAGAAGGCACGTAATCATATAAAAAGATG 3707
                           ii  vi               i v   vvi   v  i  i        
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_187422030_   3708 CTCCACATTATATATAAT 3725
                            v    i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (139 / 105)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.72 (31 / 18)  


3191 27.64 0.44 0.44  chr1_187431348_187435677.rev     2932  3839 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187431348_   2932 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2981
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187431348_   2982 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3031
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187431348_   3032 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3079
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_187431348_   3080 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3129
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_187431348_   3130 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3179
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_187431348_   3180 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3229
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_187431348_   3230 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATACCTACAACT 3277
                                i    i--    i  --        vv iii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_187431348_   3278 ATCTGATCCTTGACAAACCTGAGGAAAACAAGCAATGGGGAAAGGATTCC 3327
                          vi    ii i     ivv  vvi i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_187431348_   3328 CTATTTAATAAATGGTGCTGGGAAAACTGCCTAGCCATATGTAGAAAGCT 3377
                           v  i  i              v     vv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_187431348_   3378 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 3427
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_187431348_   3428 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3477
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_187431348_   3478 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 3527
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_187431348_   3528 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3577
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_187431348_   3578 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3627
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_187431348_   3628 ACGCAGCCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3677
                          vi  i  i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_187431348_   3678 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3727
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_187431348_   3728 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACGTGAACAGACACTTC 3777
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_187431348_   3778 TCAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTCATC 3827
                           v        i  vi viii     v  ii         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_187431348_   3828 ATCACTGGCCAT 3839
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1713 29.80 4.24 4.58  chr1_187522240_187526059     2432  3327 (493)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr1_187522240_   2432 TATTTATGGATCAGAATACCCAATGTTGTTAAGATATCAACTCTTACCAA 2481
                          i  i      ii   v  ii   i          iv   iv  iv    
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_187522240_   2482 -TT-ATACATATGTTCAACAAAATCTCTCTCTAAATCCCATCAAATTGTA 2529
                         -  -  vi i vi      iv    i  v  v        v ------ i
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC------TG 109

  chr1_187522240_   2530 CTTTTCTTGGTGTA---GACATACTGATTCTAAAGGTTATAAGACAAGTC 2576
                          i   i   vv v ---    vi     i     iv i   v iv  vv 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_187522240_   2577 AAAAAACCTAGAATAATCAATACTACTTCGCTTAAGAAGAACAAAGTTAG 2626
                           iii   i      ii   v  v ii i vvv               i 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_187522240_   2627 AAGACACACTCTACCCAATCTCAAGGCATACCACAAAGCTAAGGCAAACA 2676
                          i   v   v  v      i    ii v   i         vi i  v  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_187522240_   2677 AGACAGCATGGTTCTCGTGAAAAGATAGATACCTAAAGCATTAAGACAGG 2726
                               ii    v  v iiv  i      i iv  i v  v iii i  i
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_187522240_   2727 AAAAAATGTTGAGATACAGCCCCACAGAAATACAGTCACCTGA----CAA 2772
                          vvi iv  iv   v i iv    i v vv  ii    vi   ---- i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_187522240_   2773 AAAGGA----AAGGCATTTCAATAAAAGAAGACTGATCATTTCACCAAAT 2818
                         v    i----   i vv      iiiii    v ii  v     v     
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_187522240_   2819 GGCATTGGAATAATTGGGTGTCCTTATGCAAAACAAAACAGAGAAGCAAA 2868
                           iii   i i  i   i i?  vi        ---------   v---i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAA---------GAAT---G 447

  chr1_187522240_   2869 AAACTAGAAAAAGACCTTATACTTTTCACTAAAATTAACTCATAATAGAT 2918
                           ii i  vvvvv    i i  iv vi  v            v   i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_187522240_   2919 TGTCAGAT-TAAATGTAA-------AAC-ATAAAATT--TAAAAAAAAAT 2957
                         ii?-   i-         -------   -      i --  i  i    i
  L1M4_orf2#LINE/    498 CAW-AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_187522240_   2958 TGTAGAAGAAAATGTTGGTGATCTTAGATTTGT--ATGAGCTTTTAAGTA 3005
                         -i   i? v    v  v    i   i i  v v--   ivi i   ii  
  L1M4_orf2#LINE/    547 -ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_187522240_   3006 TATTTCTAGATGAATAACCCATGGCAGAAAAAACAAAGTGATAAACTAGA 3055
                          iviv i i v v i  v v iiiv        i ----      i i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATA----GATAAATTGGA 641

  chr1_187522240_   3056 TATTA-CTAAGTTAAAAACTACTGCTCATAACAGCATCTTAGTAGCAAAG 3104
                         iv i - v  i         vi  ---- i-------   -----     
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTG----TG-------CTT-----CAAAG 675

  chr1_187522240_   3105 GATACTGTTTAAAAAATTTAAAG------TACAGACTC--ATAAGCTTTT 3146
                           i   i iv i   i vv    ------i     v v-- v  iv v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_187522240_   3147 TTCAAAACGAATATCCCATAAAGGACTTGAATAAAAAATATACAAAAAAT 3196
                          v    v iv     iv    i       v  vv i      i   i  i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_187522240_   3197 ATTGTAAAACTCAACAATTAGAAAACAAGCAACCCAATTTAAAAATGGGC 3246
                         - iv  v       i   v i  i    ii         ?          
  L1M4_orf2#LINE/    776 -TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_187522240_   3247 AAAAGATCTAAATAGACA---CTTCAGCTTACATAAACAAATAGAAAATA 3293
                            i   i i        ---  i  ivvv v   v      i vv    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_187522240_   3294 AACATACAAAGTCATACTCAATGTCACTTGTCAT 3327
                          i  i ii  ivv  i     ii   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (157 / 106)
Gap_init rate = 0.03 (24 / 893), avg. gap size = 3.29 (79 / 24)  


2176 26.44 1.59 4.28  chr1_187546392_187548630      487  1303 (936)    L1M4_orf2#LINE/L1       33   827 (81)  

  chr1_187546392_    487 ACTTTATATTAATAAAATGGCCCTACTGCCCAAAGGTAGTTAGAGATTCA 536
                             v     iv   i     vv    v      vvv vi  v       
  L1M4_orf2#LINE/     33 ACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCA 82

  chr1_187546392_    537 ATGCTATTCCTATCAAACTACCAATAATATTTTTAACATAATCAGAAAAA 586
                          i  v  i         v v   iiviiv     vi  v  viv  v  i
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG 132

  chr1_187546392_    587 AC-ATTTTAAAATTCATTTGGAATTTAAAAAGAACACA-AATAGCCAAAG 634
                         vi-  ii          v     v -iv  i i  v  -          i
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAA 181

  chr1_187546392_    635 TAATCCTGAGCAAAAAGAGCAAAGCTAGAGGCATCACATTACCCGGCTT- 683
                         i    i   iv  i    i     i i    vv     i v   iii  -
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_187546392_    684 AAAACTATACTACAGGACCACAGTAACTAAAACAACGTGGTACTGGTACA 733
                               -       iii i       ii  i   ii          i i 
  L1M4_orf2#LINE/    232 AAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_187546392_    734 AAAACAGACTCATAGACCAATGGAACAGGTTAGAGAATGCAGAAATAAAG 783
                          ii i    vi     i        i  iv v    i v          v
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_187546392_    784 CCTCACACCTACAAACATCTGATCTTCAACAAAGCTAACAAAGCCAAGGA 833
                           vi   ii  iiiv  vi    i   i    i v iv   ii   vvv 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_187546392_    834 ATTTGGGAAATGATTCCCTGTTGAGTAAATGCTGCTGGAATAACTGACTA 883
                           v-      vi  vvi  v  v ii     v      i i     iv  
  L1M4_orf2#LINE/    381 ATG-GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_187546392_    884 GGCATATGCAGAAGATTGAAGCTGGACCCCTACCTTTCACCATTTACAAA 933
                         ?v  i     i    v     i             iv      v      
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_187546392_    934 AATCAACTCAAGATGGATTAAACACTTAAATGTAAAGCCTAAAACTATAA 983
                            i       i      i ? v  i         iiv            
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_187546392_    984 AAACTCT-GGATGATAACCTAGG---AAATACCATTCTGGATATCAGCCC 1029
                           -    -i  v  v   v    ---    -- -   vv  iv ii vii
  L1M4_orf2#LINE/    530 AA-CTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTT 575

  chr1_187546392_   1030 AGGCAAAGACTTCATGAGGAAGACTAC--AAAGCAATTGCAACAGAAACA 1077
                               v ii   v iiiv v   -  --      vvv      i  iv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGAC-ACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_187546392_   1078 AAAATTGAGTAGTGGGAACTAATTAAACTAAAGAGCTTCTGCACAGCGAA 1127
                              v  vv i v   vi v  i   v v  i i   i  ii vv ---
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC--- 671

  chr1_187546392_   1128 AACAAACAACAACAACAACAACAAAAGACTATCAACAGAGTAAACAGACA 1177
                         ---   vi   -----------------       v i   i  v     
  L1M4_orf2#LINE/    672 ---AAAGGACA-----------------CTATCAAGAAAGTGAAAAGACA 701

  chr1_187546392_   1178 ACCTACAGAATGGGAGAAGATACTTGCAAACTATGTATTCAAAAAAGG-- 1225
                            i              i   i       ii  i   iii v  i  --
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_187546392_   1226 TTGAATATTAAGAATCTATTAGGAACTC--AAAACAAATTAAAAAGCAAA 1273
                            --   iv     v   v i      -- v   vv v   v  --   
  L1M4_orf2#LINE/    752 TTG--TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA--AAA 797

  chr1_187546392_   1274 AACAAACAACACCATTAGAAAATGGGCAAA 1303
                         i     i   v v   ?i            
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAA 827

Transitions / transversions = 1.24 (118 / 95)
Gap_init rate = 0.02 (19 / 795), avg. gap size = 2.53 (48 / 19)  

 268 23.08 3.30 0.00  chr1_187546392_187548630     1656  1746 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_187546392_   1656 AAAAAGGGGAAATGAAATT-AACAGACACTTCTCAAAAGAAAACACA-GC 1703
                              v   v  v i v  -  i     i     v      i i i -iv
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_187546392_   1704 GTGGCCAACA-GCATACTAAAAAATGCTCAGTATCACTAGTCAG 1746
                         i       i -   i iv    i       ii    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.03 (3 / 94), avg. gap size = 1.00 (3 / 3)  


2504 27.15 2.32 2.10  chr1_187553166_187556831.rev     2270  3175 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187553166_   2270 TGAAAAAATATTCCATGCTCAAGGATTTTAAGAATCAATATTGTGAAAAT 2319
                           i   i    i     i   v     vv    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187553166_   2320 GACCATACTACCCAAAACAATTTACAGATTCAATGCTATCCCTATCAAAC 2369
                          i v     v      vii  i           i  v            v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187553166_   2370 TACCAATGACATTCTTCACAGAA-TTGGGATAAACT-ATTCTAAAACTCA 2417
                          v   iivi v  i  ii     -   -- i  i  -  i      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_187553166_   2418 TGTAGAGCCCAAAATAAG---CCTACA-TAGCTTAAGCAATCCTAAGCAA 2463
                          i i  ----  vii   ---  i v -    iv  i     i i iv  
  L1M4_orf2#LINE/    149 TATGGA----AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_187553166_   2464 AAAGAAGAAAGCCAGAGGCATCACATTACCTGACTTCAAACTATACTACA 2513
                         i     v    iii    vv     i v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_187553166_   2514 AGACCACAGTAACTAAAACAGT-TGGTATGCGTGTAAG-ACAGAAACAAA 2561
                          ii i       ii  i     -     ivv ii    - i   v i v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_187553166_   2562 GACCAAGAGAACAGAA--GAATATCCAGAA-TAAAGCCATGCACCTACAA 2608
                           i   vi   i    --  ivi       -    v    i  ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_187553166_   2609 CCATCTGATCTTCGACAAGTCCAACAAAAACAAGCAATGGGAAAAGGACC 2658
                         i  vi    i         vviiv   i v  vv       i    i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_187553166_   2659 CCCTATTGAATAAATGGTGCTGTGGA-AACTGGCTAGCCATATGCAAAAG 2707
                         vi  v  v  i           -   -      v  ?   i         
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCAAAAG 443

  chr1_187553166_   2708 ATTGAAGCTGGACCCCTACCTCTCCTCCTCCACAAA--TTAACTCAGAGT 2755
                          v     i              v vi v vi     --        i i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_187553166_   2756 GGATCAGA-ATTTAAATGTAGTACCTTATACCATAAAAATCCTGGAAGAC 2804
                               ? - ii        iv v  v v  i      v  i i     v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_187553166_   2805 AATCCAGGAAATACTTTTCTCAACATTGGCTTTAGCAAAAAGAATTTTAT 2854
                           ivi   ?ivv v i   vii  v    v  vi    vii----   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG----TTTCT 589

  chr1_187553166_   2855 TAAGT----CCCCAAAGGCAATTACAACAAAAATAAAAATTGACAAGTGG 2900
                           ii ---- v     i   vvvi        iv      v  i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_187553166_   2901 GAACTAATTCAA--CAAACGAGCTTCTGAACAGCATAAGAAACTATCAAC 2948
                           vi v  iv  --i   -- i   i  vi vv  v i  v        v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAA--AACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_187553166_   2949 AGAGTAGATAGACAACCTAAAGAATGGGAGAAGATATTTGCAAATAATAC 2998
                          i   ii v        i v            i            v   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_187553166_   2999 ATCAAACAAAGCCCTAATTTCTAGAATCTGTAGGTAAGTTAAACAAATCA 3048
                            vi i  i vv  vi v  i     v i  iiv  v ivv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_187553166_   3049 ACAAGCAAAAAAAGAAATAACCCCCCCAAAAGAAAATGCGCAAAGAACAT 3098
                          i  -i     i v         vvii?   ---    v      i iv 
  L1M4_orf2#LINE/    788 ATAA-TAAAAAGACAAATAACCCAATTWAAA---AATGGGCAAAGGATTT 833

  chr1_187553166_   3099 GAAAAGACACTTCTCAAAAGAAATCATACAAGTGACCAACACGCACATTG 3148
                            v     i     v      ivi      i  i    i v      --
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-- 881

  chr1_187553166_   3149 AAAAAAATGTTCAGCATCACTAATCAT 3175
                         i    i   i   i     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (140 / 102)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.90 (40 / 21)  


1915 26.59 4.41 6.67  chr1_187575840_187578968     1708  2636 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187575840_   1708 TGGAGAGAGATTTCATGTTCATAGACTGGAGAACTCAATAGTGTTAAAAT 1757
                             i   v  ii         i  i    ii   i    v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187575840_   1758 GTCAGTTCTTTCCAACTTGATTCATATATTCAAAACAATCA-TAGCAGCA 1806
                          v  i v  ii    v     ii i v      vi     v-  v  i- 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-A 99

  chr1_187575840_   1807 GTTCCAACAAGCTTTTTTGTA----TCAACAAATTAACTGGAAGGTTTAT 1852
                         i i   i viv        i ---- ii    ii i iivv  ii  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_187575840_   1853 ATGGAAACAAAAGAACACCCTAAAATTTTCTGCACAATACTGAAGAAGA- 1901
                                iiv   ii-    - i   vvi viv     vi    i    -
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGG-ACCC-AGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_187575840_   1902 GAA--AAGTAAGAGGACTGATA-TAACCAAATGCATGGTTTGGTTATAAT 1948
                            --    vi       v i - vv    v v  viii  i-i  i  -
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAA- 245

  chr1_187575840_   1949 TAAGCTATTATAATCTGTACACCATGTTATTGATATATTTATCAAAA-GG 1997
                         --     ivi     viv   vii  v  i  ii   ------ ii -i 
  L1M4_orf2#LINE/    246 --AGCTACAGTAATCAAGACAGTGTGGTACTGGCATA------AGGATAG 287

  chr1_187575840_   1998 TTATATAAATGAGTGGAAAAGAATAGAGAACCCAGAAATAGATCTACAAA 2047
                         vi     i  v i     v     v    ii         i i i i v 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_187575840_   2048 AATATAGTTAACTAATCATTGAAAAAAGAGCAAAGGCAGTTCAATGGATA 2097
                         vv   i  i  i i  iv i  v  ii v  v   i vi        ---
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG--- 384

  chr1_187575840_   2098 AAGTATAGTCTTTAGGATAAAGTATAGTCTTTAGGATAAAGTATAGTCTT 2147
                         ---------------------------------   --   v        
  L1M4_orf2#LINE/    385 ---------------------------------GGA--AAGAATAGTCTT 399

  chr1_187575840_   2148 TACAACAAATGGTACTAAAAAGATTGGATGTTCATATTAAAAAAAATGAA 2197
                          v           i  iii vi i     i?i  i  vv    i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_187575840_   2198 TGTAGGCACAAACCTTACACCTTTCACAAAAAGTAACTCAAAATAGTTCA 2247
                         vv i i v vv    i     v vi       v           i v   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_187575840_   2248 TATACCCAAATATAAAA--CAGCACTATAAAACTAGCAGAGGAAAACATA 2295
                         ? v   i    i   i --i iv           vvi   i         
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_187575840_   2296 GAAGAAAATTTATGTGACTCTGTGTTTG----TGGTGTGTTTTTAGATAT 2341
                          i? v    i vi     ii  v   v ----    ---  i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT---TTCTTAGATAT 596

  chr1_187575840_   2342 TAATACAACATCAAAAGAACAATCTATTAAA-----AATTGATGAACTGA 2386
                         ------i   i      v    v v iv   -----   v   i  i  i
  L1M4_orf2#LINE/    597 ------GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_187575840_   2387 ACTGTATTAAAAGTAAGTTCTTTGGTTCTGTAAAG-ACATAGTGAAGCGA 2435
                            vi  i    v   ivv    v  v  vi    -   ivi v   vi 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_187575840_   2436 ATCAAAAGAGAAGCCACAGACTAA-AGAAAATATTTGCTTAACATCTATC 2484
                         i v      v  v       v ii-             vv v   v    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_187575840_   2485 TGATAAGTGA-TTGTATCCA-AATTCACAGA-AATATTTAAATCTCAATA 2531
                                v  -         -   vi i i -  ivi   v v       
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_187575840_   2532 ATAA-----CG--TGATTCAATT-AAAAATGGGCAA--GATCTGAAAAGA 2571
                             ----- i-- i ii     -            --   i    v   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_187575840_   2572 -AT----CCACACCAAATTTATGTAAATGACAAACAAGCATGTAAGAAGA 2616
                         -  ----   v vv i  --  ii     i v  i     ii i i    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGAT--ATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_187575840_   2617 TATTCAGCATTATTTGTCAT 2636
                          ii   i   i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 3.32 (103 / 31)  


2345 25.59 0.47 0.47  chr1_187618632_187620266.rev      504  1144 (491)    L1M4_orf2#LINE/L1      268   908 (0)  

  chr1_187618632_    504 TGGTACTGGTACCAAAACAGAGATATAGACCAATGGAACAGAAC--AGAG 551
                                  i iv ii i   v       i        i    i--    
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_187618632_    552 CCCTAAGAAATGATGCCACATATCTACAACCATCTGATCTTTGACAAACC 601
                         i  --      i vv   i i  i  iiii  vi    i  i     ivv
  L1M4_orf2#LINE/    318 TCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_187618632_    602 TGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCT 651
                           v   i v  vvv           i  vvi  v  i  i          
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_187618632_    652 GGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGTTCCCTTCCTT 701
                             v      v  ?   i   i i  iiv    ii   vi    v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_187618632_    702 ACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTACATGTTAC 751
                              v              i    i      i ?    i  v    v v
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_187618632_    752 ACCTAAAACCATAAAAACCCCAGAAGAAAACCTAGGCA-ATATCATTCAG 800
                          v       i      vi ii          v    ?i- v   -   iv
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGT 564

  chr1_187618632_    801 GACATAGGCATGGGCAAGGACTTTATGTCTAAAACACCAAAAGCAATGGC 850
                            v v  vv i     v ii  iv ivv  vi            vvi  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_187618632_    851 AACAAAAGACAAAATTGATAAATGGGATCTAATTAAAATAAAGAGCTTCT 900
                                  v     v       v   ii v  i     v  i i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_187618632_    901 GCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGG 950
                          ii vv    i  v    i  vv i      v  i     i         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_187618632_    951 GAGAAAATTTTTGCAATCTACTCATCTGACAAAGGGCTAATATCCAGAAT 1000
                                 v       vii ivi      i  i  i  vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_187618632_   1001 CTACAATGAACTCAAACAAATCTACAAGAAAAAAACAAACAACCCCATCA 1050
                         v  i  v      vv    v  v i  v     i     i     v  i?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_187618632_   1051 ACAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAGGAAGACATTTAT 1100
                          v  i            v    i     i     v  i     i  vi v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_187618632_   1101 GCAGCCAAAAGACACATGAAAAAATGCTCATCATCACTGGCCAT 1144
                         iii     v ii          i       v     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (90 / 70)
Gap_init rate = 0.01 (4 / 641), avg. gap size = 1.50 (6 / 4)  


2720 25.68 1.97 2.73  chr1_187661479_187664427     1542  2456 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187661479_   1542 TAGATAAATCTCTCATGCTCATGGATTGGAATAATTGATATTATTTAAAT 1591
                          i  v i  v  i    i             v v  i     i  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187661479_   1592 GACCATACTGCCCAAAGAAATCTACAGATTAAATGCAATTCTTATGAAGT 1641
                          i v     v      vvi           v  i     i i   v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187661479_   1642 TACCAAC-ATCATTTTTACTGAATTATAAAAAGC-AATCTTAAAAATAAA 1689
                          v   i -ii v     i v   v - i v    -i   i     v v v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_187661479_   1690 ATGAAACCGAGAAAAAGAGCCTGAATAGCCAAAGCAATCCTATGCAAAAA 1739
                            i  vi v--  ii  v  v           i     i iviv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_187661479_   1740 GAATAAAGCTGGAGGCATCACATCACCTGACTTTAA--TTATACTACAAG 1787
                            i    i      vv     iiv  ii i  i  --i -        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr1_187661479_   1788 GCTATAGTAACCAAACCAGCATGGCACAAGCATAACAATAGACATATAGA 1837
                             i     i   iv   ii   i  vi      vi             
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_187661479_   1838 TGAATGGAACAGAATGGAGAGAATAGAGAACCCAGAAATCAAGTCATATA 1887
                          v       i     v     ---------i        v  vi    --
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAG---------TCCAGAAATAAACCCATA-- 335

  chr1_187661479_   1888 CATCCAC---CAACCAGTCTTCAACAAAGTCAACAAAAATATACAATGGA 1934
                            ii i---   iiii i   i    i viiv   i vi  v      i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_187661479_   1935 GAAAG--TA--CTTCCGATTCAACAAATGCTGCTGGGAAAATTGGACAGA 1980
                              --  --   ----           v        v  i    i ?v
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTT----TTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_187661479_   1981 CGTATTCAGAAGAAAAAATCTGGACCCTTATCTCTCACCATATAAAAATA 2030
                          ii  v  i     vi  vi       i  i   v         v   v 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_187661479_   2031 TTAACTCAAGATGGATTAAAGCCTTACACTTAAGACTTGAAACTACAAAA 2080
                                  i      i ?  v i  v iv     vi i      i    
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_187661479_   2081 AATCCTAGAAGAAACC-TAGGACAACCTCTTTAGGACATTGGCTGAAACA 2129
                         v-  i         v -    ?vv vv    iiv   v    v v ii  
  L1M4_orf2#LINE/    532 C-TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_187661479_   2130 AAGAATTAATGACTAAAACCCTAAAAGCAAATTCAATAAA-GCAACAATG 2178
                          v iv  vv iiv  vi  v i       v vv   i   - v  v   i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_187661479_   2179 GATAAGTGGGGCTTCATTAAACTAACAAGCTTATGCACAGCGAA--ATAC 2226
                              i v  i      i   v v v  i   v  ii vv i  -- i  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_187661479_   2227 -ATCAGCTGAGTAAATTGACAACTTACCACATGAAAGAACATATTTGCAA 2275
                         -    ivvi   i  vv      ii  viv   ii    v          
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_187661479_   2276 ACTATGCATCTATTATAACAGATGACTAATATTTAGAATCTACAAGGAAC 2325
                          ii  ii    i--    -- i-    vi   ii     v  i  i    
  L1M4_orf2#LINE/    731 ATCATATATCTG--ATAA--GG-GACTTGTATCCAGAATATATAAAGAAC 775

  chr1_187661479_   2326 TCAAACAACTCAAAAAGAAAATGACAAATAACCCTTTTAAAAAGTGGGCA 2375
                           vv         v  v    v            vv  ?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_187661479_   2376 AAGGACATGAATAGGTACTTCTCAAAAGAAGATATACAAGTAGCAAACAA 2425
                              iv       ii i     v               i i  v  i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_187661479_   2426 --ACATGAAAATATGCTCAGCATCACTACTAAT 2456
                         --         v       i     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (129 / 102)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.05 (43 / 21)  


 556 28.59 14.38 4.36  chr1_187690500_187692062.rev      455  1073 (490)    L1M4_orf2#LINE/L1      228   908 (0)  

  chr1_187690500_    455 TCTCAAAAC--AAAACAAAACAACAACAA--AAAA------AGCAATAAC 494
                          i       -- vv     i v   ii  --  i ------i i v ii 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_187690500_    495 AAAAAG-TGGATAGAAAGATCAATGAAACAAAGTAGGTGGGCCAGTAACA 543
                          v  i - i  i v v         i  i i i v ivi v    v  i 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_187690500_    544 GATCTAGACAGATATATTCAGTATAAGTTT-GACAAAGTAAATAGAATGA 592
                         i i i v   vv   iv   i - i v   -     i --------i  v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAAT-TGATTTTCGACAAGG--------GTGC 368

  chr1_187690500_    593 CAAGGC-ATTCTAAAAAGAAAATGAA-AGATTCCTCAACAAATAATATTG 640
                             i -    -  vii i   -   -  vi ii         ii ii  
  L1M4_orf2#LINE/    369 CAAGACCATTC-AATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_187690500_    641 A-ACATACTGGAGAAATGTATGATAAAGCACTAAAATAAATGCTTATCAC 689
                         i-   -      v ?viii   vv    v iv  iv ii iv i  i v 
  L1M4_orf2#LINE/    417 GGACA-ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_187690500_    690 AAATTATACATAAAAATGCATTTGAAATAAAACATA--CTTACACATATA 737
                          v ii   i i      vv i ii    ii v  ? -- i  - -  i  
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA-A-ATGTA 513

  chr1_187690500_    738 TAAGCTAAA-CAGTAAAGTTTCCGGAAAGAGACACAGGA-TAATATATTT 785
                         vi       - vi    ii iiii   ii i   i   ?-   -  v  i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTC 562

  chr1_187690500_    786 GTAGAACT-GAGACAG-CAAAAAATTCCTAA----GACACAATAAAGCAC 829
                           -  v  - i vi  -   viiv   i  i----     v -       
  L1M4_orf2#LINE/    563 GT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA-AAAGCAC 610

  chr1_187690500_    830 TAATCATAAAAAAAA-----GATAAAT-GGACTTTTTCAAATTATTAATA 873
                         v iiv i    i   -----       -      iv     --     --
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA--ATTAA-- 656

  chr1_187690500_    874 TAAGTTTATGTATGTTT--------------------GTG---------- 893
                         -  ii  v   -- i  --------------------   ----------
  L1M4_orf2#LINE/    657 -AAACTTTTGT--GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_187690500_    894 --------TGT------ATATTTACAC-TCAG-----TGAT---GCATCA 920
                         --------  v------      i  v-   v-----    --- v iiv
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_187690500_    921 GCATCTAGAGTATATAAAGGACTCCTACAAATAGATTTTAAAAAATAGAG 970
                          i   i   i         i    i     v vi  vv      ---  v
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA---GAC 800

  chr1_187690500_    971 AAGTA---CAAT--AAAAATGAGCAAGAGACTTGAACAGATATTTTTCAA 1015
                           i  ---    --       i    ii  i     i   i    i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_187690500_   1016 CAAAAGATTTAGGAATAGCCAATAATCATGTAGAAAGGTGCTGAGCATCG 1065
                         v i     v  vi   i        v  ii ii    i    v i    i
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_187690500_   1066 CTAGTCAG 1073
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.90 (114 / 60)
Gap_init rate = 0.06 (38 / 681), avg. gap size = 3.05 (116 / 38)  


2573 26.36 3.67 2.67  chr1_187731314_187733891     1187  2085 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187731314_   1187 TGGAAAAATATCTCATGCTCATGGATAGTAAGAATCAATGTTGTAAAAAT 1236
                               i     i    i        v v    v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187731314_   1237 GGCGA-AGGGGCAAAAGTAATTTATAGATTCAATGCTGTTCCCATCGA-- 1283
                            i - vvvv v   v i  i  i        i  vi i  i   i --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187731314_   1284 --CTACCTTTGACATTCTTCACAGAATTTGAAAAAAACT-ACTTTAAACT 1330
                         -- i v  ---i v  i  ii     v    v  i--  - iii    v 
  L1M4_orf2#LINE/    101 TCCCAGCT---GCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAAT 145

  chr1_187731314_   1331 TCATATGGAACCAAACAAAGGCCCTA---TAGCCAAGACAATCTTAAGCA 1377
                                   -- vi   i  v  i ---       i        i iv 
  L1M4_orf2#LINE/    146 TCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_187731314_   1378 AAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTAC 1427
                          i          i      vv       v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_187731314_   1428 AGGGCCATGGTAAACAAAACAGCATGTTACTGGTATCAAAACCGATATAT 1477
                          ii  i ii    v   i    ii  v      i  v ii iv  i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_187731314_   1478 AGACCAATGGGACATAACAGAGACGTCAGAAATTACACCACACATTTACA 1527
                            i      i i v  iv    vvi       v vv   i       ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_187731314_   1528 ACCATCTGATCTTTAACAAACCTGACAGAAACAAGCATTGGTGAAAGGAT 1577
                         ii  vi    i  ii    ivv  v  ii v  vv  v   v     i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_187731314_   1578 TCCCTATTTAACAAATGGTGCTGTGAGAACTGGCTAGACATATGCAGAAA 1627
                         vvi  v  i              v  v      v  ?v  i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_187731314_   1628 TCTGAAACTGGACTCCTTCCTTACACCTTATACAAAAATTAACTTAAGGT 1677
                         vv    ii     i   v   i     v                i  ii 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_187731314_   1678 AGATTAAACACTTAAATGTAAAACCCAAAACCATCAAAACCCT-AGAAGA 1726
                         i   i ? v  i         i v i     i  -     i  -      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGA 542

  chr1_187731314_   1727 AAACCTAGG--TAATATCATTCAGGACATAGGCATGGACAAAGATTTC-- 1772
                             v    --   -   -   iv   v v  vv i i   v i    --
  L1M4_orf2#LINE/    543 AAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_187731314_   1773 ----ATGACAAAAATGCCAAA-GCAATTGCAACAAAAGCCAAAATTGACA 1817
                         ----      ------     -   vvv          vv     v  i 
  L1M4_orf2#LINE/    591 AGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_187731314_   1818 A-TGGGATCTAATTAAAGTAAAGAGCTTCTTAACAGCAAAAGAAACTATC 1866
                          - v   ii v  i   i v  i i   i vvi vv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_187731314_   1867 ATCAGAGTGACAAGGCAACCTACTGCATTAGAGGAAACTTTTGTAATCTA 1916
                          vv i     v   i     i  v v  vi   i   iv    i  vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_187731314_   1917 CCCATCTGACAAAGGTCTAATATCCGGAATCTATGAGGAGCT--TA-AAT 1963
                         ivi      i  i  v  vi     i    v   i i  i  --  -  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_187731314_   1964 ACAA-AAGAAAAAAACAA----CCTCATCAAAAAGTGGGCAAAGGGTAAG 2008
                         v   -  v     i    ----  iv  i?    i          i vv 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_187731314_   2009 GACAGACACTTCTC-----AAGACATTTATGTGGCCAACAAACATACAAA 2053
                         i i     i     -----    i  vi vi       i  i  ------
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA------ 878

  chr1_187731314_   2054 AACAAAAAAAAAGGCTCATCATCACTGATCAT 2085
                         --  vi    i v     v     ????????
  L1M4_orf2#LINE/    879 --CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (134 / 100)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.59 (57 / 22)  

 663 23.13 0.00 0.00  chr1_187731314_187733891     2443  2576 (2)  C L1M4_orf2#LINE/L1   (380)   528   395  

C chr1_187731314_   2576 GCCTATTTAATAAATGGTGCTGGGAAAACTGGATAGCCATATGTAGAAAT 2527
                          i  v  i  i              v         ?   i   i i  iv
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chr1_187731314_   2526 CTGAAACTGGATCCCTTCCTTACACATTATACAAAAATTAATTCAAGATA 2477
                         v    ii    i    v   i    vv              i    i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chr1_187731314_   2476 GATTGAAGACTTAAATGTTAGACTTAAAACCACA 2443
                            ii?    i       v   vi      i i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

Transitions / transversions = 2.22 (20 / 9)
Gap_init rate = 0.00 (0 / 134), avg. gap size = 0.00 (0 / 0)  


3239 26.54 0.66 0.66  chr1_187740160_187742367      808  1715 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187740160_    808 TGGAAGAACATTCCATGCTCATGGGTCGGAAGAATCAATATCATGAAAAT 857
                              ii i  i     i      i i      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187740160_    858 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 907
                           iv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187740160_    908 TACCAATGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTAAAGTTCA 955
                          v   iivi i  i  ii    i-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_187740160_    956 TATGGAAGCAAAAAAGAGCCCTCATCGCCAAGTCAATCCTAAGCCAAAAG 1005
                                iiiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_187740160_   1006 AACAAAGCTGGAGGAATCACGCTACCTGACTTCAAACTATACTACAAGGC 1055
                                i       v    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_187740160_   1056 TACAGTAACTAAAACAGCATGGTACTGGTAACAAAACAGAGATATAGATC 1105
                                 ii  i    ii         i vv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_187740160_   1106 AATGGAACAGAAC--AGAGTCCTCAGAAATAATGCCGCATATCTACAACC 1153
                                i    i--       --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_187740160_   1154 ATCTGATCTTTGACAACC-TGACAAAAACAAGCAATGGGGAAAGGATTCC 1202
                          vi    i  i     vv-  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_187740160_   1203 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAACGCT 1252
                           v  i  i              v      v  ?   i   i i  viv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_187740160_   1253 AAAACTGGAACCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1302
                         i  ii    v    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_187740160_   1303 TTTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1352
                          i- ?    i  v    v   v       i      vi i          
  L1M4_orf2#LINE/    497 TC-AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_187740160_   1353 CCTAGGCA-ATACCATTCAGGATATAGACATGTGCAAGGACTTCATGTCT 1401
                          v    ?i- v i -   iv  iv v ivv iv    v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_187740160_   1402 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 1451
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_187740160_   1452 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 1501
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_187740160_   1502 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 1551
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_187740160_   1552 AAAGGGCTAATATCCAGAACCTACAATGAACTCAAACAAATTTACAAGAA 1601
                           i  i  vi         iv  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_187740160_   1602 AAAAGCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 1651
                            ii    i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_187740160_   1652 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 1701
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_187740160_   1702 TCATCACTGGCCAT 1715
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2818 28.30 0.77 0.77  chr1_187758328_187763608.rev     3885  4792 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187758328_   3885 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATGAATATCATTAAAAT 3934
                               i i  i     i        v      v v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187758328_   3935 GGCCATACTGCTCAAAGTAATATAAAGATTCAATGCTATCCCCATCAG-- 3982
                            v     v i    v i  v  v        i  v     i    i--
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187758328_   3983 TACTATTGACTTTCTTCACAGAATTAGAAGGAACT-ACTTTACATTTCAT 4031
                          v i vivi i  i  ii     v v  vi- i  - iii  v v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr1_187758328_   4032 GTGGAACAAAAAAAGAGTCCGAAGAGCCAAGACAATCGTAAGCAAAAGGA 4081
                         i     vviv  ii  vi v   v      i      v i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_187758328_   4082 ACAGAACTGGAGTCATCTCGGTACCTGACTTCAAACTGTACT-ACTGCAA 4130
                            i ii     vvv  v iv v  ii i      ----   -   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACTTACTACAA 245

  chr1_187758328_   4131 GGCTATAGTAACCAAAACAGCATGGTACTAGTACCAATCCAGATATATAG 4180
                         i    i     i   i    ii       i i iv ivvi   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_187758328_   4181 ACAAATGGAACAGAGCAGAGACCTCAGGAATAATGCCACACAACTACAAC 4230
                          iv       i   iiv    vii   i     vv   i   vi  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_187758328_   4231 CATCTGATCTTTGACAAACCTGACAAAAACAGGCAATGGGGAAAGGATTC 4280
                           vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_187758328_   4281 CCTATATAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAT 4330
                         i  v vi  i        i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_187758328_   4331 TGAAACTACACCCCTTCCTTACACCTTATACAAAAATTAACTCAACATGG 4380
                             ii iv      v   i     v                   v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_187758328_   4381 ATTAAAGACTTAAACATAATACCTAAAACCATAAAAACCCTAGAATAAAA 4430
                           i ?    i    ii   v v       i      vi i     v    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_187758328_   4431 CCTAGGCA-ATACCATTCAGGACATAGGCGTGGGCAAAGACTTCATGACT 4479
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_187758328_   4480 AAAACATTAAAAGCAATGGCAACAAAAGCCAACATTGACAAATGGGATCT 4529
                          vi   ii       vvi          vv  v  v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_187758328_   4530 AATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACTATCATCTGAGTGA 4579
                         v  i   v v    i   i  ii vv    i  v       vvvi     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_187758328_   4580 ACAGACACCCTACAGAATGGGAGGAAATTTCTA-AAATCTATTCATCTGA 4628
                          v     v  i            i    v i i-     -  vi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGA 743

  chr1_187758328_   4629 CAAGGGTCTAATATCCAAAATCTACAAAGAATTTAAACAAATTCATAAGA 4678
                         i     v  vi      i   v  i      i ivv    v iv    v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_187758328_   4679 AAAAAACAAACAACCCTGTCAAAAAGTGTGCCAAGTATATGATCAGACAA 4728
                             i     i     vi i?    i  v  v   v  v   vi     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_187758328_   4729 GTCTCAAAAGAAGACATTTATGCGACCAACAATCATATGAAAAAA-GCTC 4777
                         v    v        i  vi vii i    i  v  i       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_187758328_   4778 AACATGATTGGTCCT 4792
                              v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (139 / 114)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


1850 28.06 2.66 1.10  chr1_187793424_187795043      497  1134 (486)    L1M4_orf2#LINE/L1      261   908 (0)  

  chr1_187793424_    497 GAAAGGATAGTACTGGCACTAAAACAGACACATAGATCAATGGAACAGAA 546
                           v  vi i         iv ii i     i              i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_187793424_    547 TAGAGAACCCAGAAATAAAGCTGCCCACCTATAGCCA-TTAAGTCTTTGA 595
                          v    ii           v iiiv  ii   i i  -  i - i  i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA-TTTTCGA 359

  chr1_187793424_    596 CAAAGGCGACAAAATAAG-CAATGAGGAAATGATCCTCTATTGAATAAAT 644
                            i  i v   i iv v-     i     vi  vv   v  v  i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_187793424_    645 GGTGCTGGTGTAGCTGGCTAGCCACATGTAGAAGAATGAAACTGGATGCA 694
                                 vii i    v  ?       i i         ii    iv v
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_187793424_    695 TATCTTTCACAATATACAAAAACCAACTCAATGTGGATTAAAGATTTAAA 744
                           i  iv   v           ii       vi     i ?   ii    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_187793424_    745 TGTAAGACCTCAAACTGTTAGATTTCTAAAAGAAAGCCTAGAAA-ACACC 793
                                v  v     i v i i ii  i      i v   i?i- v i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_187793424_    794 ATTCTAGATATCGGCATTGGGAAAGAATTTAT--GACTAAGTCTTCTAAA 841
                         -   vv  iv i  -i  i  v  vii   v --  -  v v vi v   
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGA-TATGACACCAAAA 606

  chr1_187793424_    842 GCAATTGCAACAAAAACAAAAATTGACAGATAGAACCTAATTAAACTACA 891
                            vvv         iv      v  i i  v i  i v  i   v vv 
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_187793424_    892 GAAAATTTGCACAACAAAAGAAACTATCAACAGAGCAAACAGACAACCTA 941
                         i  vv    ii vv    i  v        v i  ii  v        i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_187793424_    942 CACAATGGGAGAAAATATTTACAAACTATGCATCTGACAGAAGTATAATA 991
                           v                 i    ii  ii      i iii vv vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_187793424_    992 TCCAAAATCTGTAG-GAACTTAAGCAATTTATCAGGCATAAAAA------ 1034
                             i   v i  i-     ivvi   i i vi ---       ------
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATA---ATAAAAAGACAAA 803

  chr1_187793424_   1035 TAACCCC-TTTAAAAATTGTCAAAAGAC----ATAGCCACTTATTCAAAG 1079
                               v-  ?      v v    i  i----    v  i  v i     
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_187793424_   1080 AAGACATACAAGCAGCCAACAAACATATAAAAAAGTGTTCCACATTACTA 1129
                             i      iii     i  i  i  i    ii  i  v    i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_187793424_   1130 TCACA 1134
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.61 (108 / 67)
Gap_init rate = 0.02 (13 / 648), avg. gap size = 1.85 (24 / 13)  


2663 25.43 4.90 1.37  chr1_187827908_187832785     3509  4385 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187827908_   3509 TGGAAAACCACTGCATGTTTATGGATTAGAAGAATCAATATCGTTAA-AT 3557
                               ivi iiv      i       i     v i     i     -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187827908_   3558 GGCCATACTGCCCAAAGCAATGTATAGATTCAATGGTATGTCTATTAAAC 3607
                            v     v      vii  v  i        i vv  vi    i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187827908_   3608 TACCAAC-GTTATTTTTCTAGGGAATTGGAAAACT-ATTCTAAAGTTCAT 3655
                          v   i - iiv     vi  i-     iv  i  -  i     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_187827908_   3656 TTGGAACCAAAAAAGTGCTCA-AATAGCCAAAGAAATTCTAAGCAAAAAG 3704
                         v     viiv  ii -i i  -          iv   ii i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_187827908_   3705 AACACACCTGGAGGCATCACACTATCC---------------TGTAAGGC 3739
                             v vi      vv       vi  --------------- ii  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_187827908_   3740 TACGGTAATCAAAACAAGATGGTGCTGGTACAAAAACAGACGCATAGACC 3789
                            i        i   ivi    i    i i  ii i    ii     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_187827908_   3790 AATGGAACAGAACACAGAATGCAGAAATAAGGCTGCCCACCTACAA-CAA 3838
                                i    ivv   i v         iv iiiv  ii  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_187827908_   3839 TTTGATCTTCAACAAGGTTGACAAAAACAAACAATAGAGAAAG--TAATC 3886
                           -   i   i      v  v   i v  vv    i i     --  i  
  L1M4_orf2#LINE/    349 TT-GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_187827908_   3887 CCTATTCAATAAATGGTGCTGGGATAACTGGCTAGTTGCATACAGAAGAA 3936
                         -- v     i              i      v  ?iii   i  i     
  L1M4_orf2#LINE/    398 --TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_187827908_   3937 TGAAACTGGACCACTACCTT-CACCATACACAAAAAATAACTCAAGATGG 3985
                             ii      v      i-       i       v        i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_187827908_   3986 AT-AAAGATTTAAAGGTAAGTCCTCAAACTATAAAAAAATTTAGATGAAA 4034
                           - ?   ii    v     vv  v           vv-i     v    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAA 544

  chr1_187827908_   4035 AACCA-----------CTTCTGGACATTGCACTTGGCAAATAATTTAT-- 4071
                          --  -----------    vv   v   vii v     - ii   v --
  L1M4_orf2#LINE/    545 A--CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA 591

  chr1_187827908_   4072 GAC-TGAGTTCTCAAAAGCAATTGCAATAAAACCAAAAATTGACAAATGG 4120
                           i-   --ivi        vvv    i    vv      v  i    v 
  L1M4_orf2#LINE/    592 GATATGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_187827908_   4121 GACCCAATTAAACTAAAGATCTCCTGCACAGCAAAAGAAAGTATCAACAG 4170
                            iiv  i   v v  i v  ii  ii vv    i  v v      v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_187827908_   4171 AGTAAACAGACAACCTACAGAATGGGAGAAAATATTTTGCAACT-ATGCA 4219
                            i  v        i                     -    v -  ii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATA 738

  chr1_187827908_   4220 TCCAATAAGGTTCTAATAGCTAAAATCTATAAAGAATTAC-ACAAATCAA 4268
                           ii      vv  vi  v i i   v         i vi-    v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_187827908_   4269 CAAGCATAAAAGAAGTAACTTTAT-AAAAAATGTGCAAAGGATATGAACA 4317
                         i  vv v  i v  i    iiv  -?       v         v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_187827908_   4318 GATACTTCTCAAAAGAAGGCATACAAGTGGCCCAGAA--ACATGCATAAA 4365
                           i i     v       ii      i     v v  --     v v i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_187827908_   4366 TGCTCATCATCACTAATCAT 4385
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (128 / 92)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.20 (55 / 25)  


2663 28.04 2.79 1.34  chr1_187913065_187915128.rev      679  1573 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187913065_    679 TGAAAAAACATTTCATGGTCACGGAGAGTAAAAATCAATATT---AAAAT 725
                           i   i i  ii    v   i   vv v  i v i      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187913065_    726 GGCCATACTTCCCAAAGCAATTCACAGAGTCAATGATACTCCTATCAAAC 775
                            v     i      vii  ii     v    i vv ii         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187913065_    776 TACCAATGACATTTTTAACAAAACTAGAAAAGGACT-ATTTTAAAATTCA 824
                          v   iivi v     vi  i  v v  v   --  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_187913065_    825 TATGGAACTA-AAAAGATCCTAAATAGCCAGGACACTTTTAAGTAAAAAG 873
                                v i-  ii  i  vi        ii   v i  i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_187913065_    874 AACAAAGCTGAAGTCATCACACTATCTGACTTCAAAATATACTACAAGGC 923
                                i  i  vvv       vi ii i       iv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_187913065_    924 TACAGTAACCAAAACAGCATGGTGCTGGTACAAAAACAGACACATAGATC 973
                                 i   i    ii    i    i i  ii i     i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_187913065_    974 AATAGGACAGAATAGAGAGCCCAGAAGTAAGGCCACACACGTACAATTAT 1023
                            i i i     v     i      i   iv   i   iv  iii i v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_187913065_   1024 CTGATCTTTGGCAAAGCTGACAAGA--AAGCAATGGGGAAAGGACTCCCT 1071
                         i    i  i i   i v  v     -- vv            i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_187913065_   1072 ATTCAATATATGGTACTGGGATAACTAGGTAGCCATATGGAGAGGCTTGA 1121
                         v     i v     i      i    i i  ?   i   v i i vv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_187913065_   1122 AACTGGACTTATTCCTTTCACCTTATACAAAGATCAATGCAAGAT----- 1166
                          ii     iiv v   iv    v        i  i  iv   i  -----
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_187913065_   1167 AAACACTTACATGTAAAACTCAAAGCTATAAAAATCCTGGAAGACAACGT 1216
                          ? v  i  v      i vii   i        v  i i     v   i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_187913065_   1217 AGGC---AATACCACTCTG-GACACAGGAACTGGCAAAGATTTCATGACA 1262
                            ?---   ----  ii -   viv  iviv     v i    v iivv
  L1M4_orf2#LINE/    549 AGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_187913065_   1263 AAGATGCCAAAAGCAATTTCAACAA--GCAAAAATTGACAAATGGGATCT 1310
                          v  ii         vvvv      -- v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_187913065_   1311 AATTAAATTTAAGAGCTTATGCGCAGCAAAAGAAATTATCAACAGAGTAA 1360
                         v  i   v    i i   v  i  vv    i  v i      v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_187913065_   1361 AAAGATAAGCTATCGAATGGGAGAAAATATTTTCAAACTATGCATGTGAC 1410
                              i  v i iv                  v    ii  ii  v   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_187913065_   1411 AAAGGTCTAATATCCAGCATTTATAAATAACT--TA-AA---GATATTTA 1454
                           i  v  vi       v  v      v    --  -  ---i   v v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_187913065_   1455 CAAGAAAAATTGTAGCAATACCATTAAAAAGCATGCAAAA-ACATGAACA 1503
                         v    v    ------  iv v   ?    iiiv     i- iv    i 
  L1M4_orf2#LINE/    795 AAAGACAAAT------AACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_187913065_   1504 GACACCATTCAAAAGAAGACATGCATGTGGCCATCAAGCATATGAAGAAA 1553
                             iivi  v        i  i  vi      vi     i     i i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_187913065_   1554 AACTCAATATCATTGACCAT 1573
                         vi     i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.47 (37 / 15)  


2663 29.10 2.81 0.79  chr1_187950925_187955161.rev     2857  3746 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_187950925_   2857 TGGAAAGATATTCTCT-TTCATGAATTGAAAGGATCGATATGGTTAAACT 2905
                                    i iv -      i    i   iv ii    v     iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_187950925_   2906 GTCCATAGTACCCAAATTGTTCTACAGAGTCAGTGTACTCCATATCAAAA 2955
                          v v   v v         v        v   ii i v   v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_187950925_   2956 TGTCAA-TGACATTTTCACAGAAATAGAAAAAAAAATTCTAAAATACATA 3004
                          vi  i-  v v    ii       v  v  ivvi  i       v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_187950925_   3005 TGAAAACACAATTGACCCAGAATAGCCAAAGCAATTTTGGGCCAAAAGAA 3054
                           i   ii   vv                 i    i   iivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_187950925_   3055 GAAAGCTGGAGGCATCACGTTACCTAACCTCAAATTATACTAGAAAGTTA 3104
                         v    i      vv    ii v  i  ii     viv     v    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_187950925_   3105 CAGTGACCAAAACAGCACGATACTGGCAATACAATGGACATACAGGCTAA 3154
                             i i   i    iii i        vv vi  i      i  iii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_187950925_   3155 TGAAACAGAATAGAGAACTTA--AATAAATCTGCACGCCTAAAATGCACT 3202
                           i  i     v    iiii --      i iii  iii  vii vv i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_187950925_   3203 AATTTTTGACAAAGGCGCCAAGAGCATACTTTGGGGAAAGAGCAGTCTCT 3252
                         i     i     i  i       v   v vv          ii     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_187950925_   3253 TCAGTAAATGATATTAGGAAAAGTGGATATCCATCTGCAGA-GAACGAAA 3301
                            ii     i ii i   v  v      ?   iv    i -   i   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_187950925_   3302 CTGGGTTTCTATCTCTCACCATACACAAAAATCAAATCAAAGTAGATTAA 3351
                         i   iiii   i   v       i        i  v     i i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_187950925_   3352 AGATTTAAATATAAGATTTGTAACTCTAAAAATTCTAGAAGAAAACATTG 3401
                            ii     i     vi iv    v     v ii             v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_187950925_   3402 GGGAACA-CTCCAGTACATTGGTCTGGGCAAAGAGTTTTTGTGTAAGATC 3450
                          ? v v -  i ivv  v    vi i     v iv  i  ivi  v  iv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_187950925_   3451 TCAAAAACACAGATAA----AGCAAAAATTGACCAATGTGATCACATCAA 3496
                         i     i    iii  ----  v      v  iv   vv  iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_187950925_   3497 GA--GAAAAT-------CTCCAAACAGAGAAACAATTAACAAAGCTGCAG 3537
                         i --i    i-------  i    ---i  v  v  i  v    -  v i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAA---GGACACTATCAAGAAAG-TGAAA 696

  chr1_187950925_   3538 ACGGAATCTACATAATGGGAGAAAATATTTGCAAACTGCTCGTCTGAAAA 3587
                          viv  i i   v                      iiiivii     v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_187950925_   3588 AGGATTAATAATCCGAATATATGAGAAACAA--ACAACTCAATAGCAGAA 3635
                         i   i vi  vi v        i ii   vv--           ii i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_187950925_   3636 AAA--AATAATTTGGTT-AAAAATGTCCCAGAAATCTAAACAAACATTTC 3682
                          i --     iiiii  -       vv v iii  i i  i i       
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_187950925_   3683 TCTCTCTAAAAAAAAATGCAAACTGCCAACAGGTATATAAAAA-ATTTTC 3731
                           --- v  i  i v  i    iv     i i i i  i    -  vi  
  L1M4_orf2#LINE/    847 TC---CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_187950925_   3732 AAAATTAGTAATCAT 3746
                           v  i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (165 / 91)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.13 (32 / 15)  


2451 22.51 8.00 4.23  chr1_188065915_188067953.rev      677  1551 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188065915_    677 TAGGAAGATATCCTGTCCTCATGGATTGGAAGAATTAACGTTGTTAACAT 726
                          i i         ii vi               v    ii       v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188065915_    727 GTCCAGTCTACCCAAATAAATATACAGATTCAACACAACTGCTTCCTACT 776
                          v v vv  v       vi  v            i   ---- i    ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAA----TCCCTATC 96

  chr1_188065915_    777 GCTAGGAGGAATCCCAATGACATTCTTCATAAAAGTAG-CAAAATGGTCC 825
                         i-------i       iivi v  i  iii i  i v -   iv  i   
  L1M4_orf2#LINE/     97 A-------AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr1_188065915_    826 TAAAATTCATATGGAAACATAAAAGACCCCC--TAG---AAACAATTCTT 870
                                          iii  ii     vv--   ---       i-- 
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC--T 187

  chr1_188065915_    871 TGGGAAAAAA--ATA---TTGGAGTCACT-ATACCTCCTGATTT-AAAAT 913
                           ii   i  -- i ---      v-   - i  i   ii    -    i
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAAC 236

  chr1_188065915_    914 TATATTA-AAAGCCTACAGTAATTAAAACAGTATGATGCTGGCTTAAA-A 961
                          -  i  -     -         i  i     i  i i     v   i- 
  L1M4_orf2#LINE/    237 T-TACTACAAAGC-TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_188065915_    962 CAGACAAATAATCCAGTAGAACACAATAGAGAGCCCAGTGATAACTCCAA 1011
                         i     v   ivi  i i   i v   v     i    vi    vi   v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_188065915_   1012 ACAC--ACAGTCAACTAATTTTTGACAAGACTGCCAAGACGGCACAATGA 1059
                            i-- ii     i i     i      iv         viiv     i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_188065915_   1060 GGAAAGAGTAGTCTCTTCAATAAATGATGTTGAGAAAATCATATTTTCAC 1109
                                i      i     i     i  i  i  v  iiiv  v?i   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_188065915_   1110 ATGGAAAAGAATAAAACTGGACACATATCTTATTCCATACACACACACAC 1159
                            v        i  ii     v v  i  ---------     -  i i
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCT---------CACAC-CATAT 474

  chr1_188065915_   1160 ACAGGAA--AACTCAAAATGGATGAAAGACCGAAATGTAAGA-CTAGAAA 1206
                            ii  --              v ?     v          -   -   
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAA 523

  chr1_188065915_   1207 CTATAAAACTTCTAGAAGAAAACATAGAAGAAAAGCT-------CTTGGG 1249
                                   ii               i? v   v  -------      
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_188065915_   1250 --AAG---TGATTTTTATATATATATGTTATCACTACAAATGCTCAGTCT 1294
                         -- i ---  i   i ---  v     -- -   --    v  v  iv v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCT---TAGATATG--A-CAC--CAAAAGCACAAGCA 615

  chr1_188065915_   1295 ACAGAAATAAAATTTTAAAAAG-GGACTACATCAAACTAAAAAACTTATG 1343
                            i  iv    v vv v   v-     v       v v        v  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_188065915_   1344 CACAGCAAAGAA----ATCAACAAAATGAAATGGCAGACTATAAACTGAG 1389
                         ii vv     i ----     v   i     v i  iv i i i v  i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_188065915_   1390 A-AAAACATTTGCA-----TATACCTGA---------------------- 1411
                          -    i       -----    i    ----------------------
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_188065915_   1412 ---AACAAAC-CATACAACTCAATAGTAGAAAAACACATAACTCAATTTT 1457
                         ---  vi   - v            i  i   i   v     i     ?-
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW- 814

  chr1_188065915_   1458 TAAAAATGAGCAAAAAACCTAAACAGACATTTCTCTAGTGAAGATATAAA 1507
                         -       i     ii ii i  i           i iv         v 
  L1M4_orf2#LINE/    815 -AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_188065915_   1508 CATCACCAACAGGTAAAGGAAAAGGTGTTCAAC-TCAATGTAGTC 1551
                         v  vi    i i i v v      i  i     -   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (125 / 68)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 2.97 (107 / 36)  


3043 27.39 1.56 0.45  chr1_188073839_188080226.rev     5000  5897 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188073839_   5000 TGGAAGAACCTTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5049
                              ii iv i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188073839_   5050 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5099
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_188073839_   5100 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5147
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_188073839_   5148 TATGGAACCAAAGAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAG 5197
                                viiv iii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_188073839_   5198 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTATAAGGC 5247
                                i      vv   ii  v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_188073839_   5248 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGGTAGACC 5297
                                 i   i    ii         i iv ii i   v vi    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_188073839_   5298 AATGGAACAGAACAGAGGCCTCAGAAATACCACCACACATCTACAACCAT 5347
                                i    iv   ivii        vvv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_188073839_   5348 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGATTTCCCT 5397
                         i    i  i     ivv  v   i v  vvv            v vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_188073839_   5398 ATTTAATAAATGGTGCCTGGA-AACTGGCTAGCCATATGTAGAAAGCTGA 5446
                         v  i  i         iv   -      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_188073839_   5447 AACTGCATCCCTTCCTTACACTTTATACAAAAATTAATTGAAGATGGATT 5496
                          ii  v i    v   i    iv              i v  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_188073839_   5497 AAAGACTTAAATGTTAGACCTAATACCATAAAAACCATAGAAGAAAACCT 5546
                          ?    i       v   v    v  i      vi v           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_188073839_   5547 AGGCAGTA--CCATTCAGGGCATAGGCATGGGCAAGGACTTCATGTCTAA 5594
                            ?-   --i -   iv i v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_188073839_   5595 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 5644
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_188073839_   5645 TTAAACTAAAGAACTTCTGCACAGCAAAAGAAAGTACCATCAGAGTGAAC 5694
                          i   v v  i     i  ii vv    i  v v  i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_188073839_   5695 AGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTACCCATCTGACAA 5744
                           i     i       i         v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_188073839_   5745 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATT-----TACAA 5789
                         i  i  vi          v  i        ivv    v i-----  v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_188073839_   5790 AGAAAAA-AA---AATCAAAAAGTGGGCAAAGGATATGAACAGACACTTT 5835
                            v   -  ---   i?    i            v    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_188073839_   5836 TCAAAAGAAGACATTTATGCAGCCAACAGACACCTGAAGAAATTCTCATC 5885
                           v        i  vi viii     i ii   v    i i  v    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_188073839_   5886 ATCACTGTTCAT 5897
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


2929 23.96 4.03 2.35  chr1_188089785_188094874     3705  4597 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188089785_   3705 TGGAAAAATATTCCATGCTCATGAATGATTAGAAGAATTAATATTGTTAA 3754
                               i    i     i     ---    i     v             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATG---GATTGGAAGACTTAATATTGTTAA 47

  chr1_188089785_   3755 -ATGCCCAAATTACCAGAAGCAATTTACAGAATCAGTGCCATCTCTTTCA 3803
                         -   v v v i v  vi  vii  i      v   ii  v   i  v   
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_188089785_   3804 AAATCCCAATGGCATTTTTTACTGTAATAGA---ACT-ATGCTAAAATTC 3849
                                 iiv  v      i v v   v  ---i  -  v         
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_188089785_   3850 ATTTGAAATTACAAAACACCCTGAATGGCTAAACCAATTTTGAGCAAAAG 3899
                           v  i  v i   iiv    v    i  i   v    i    iv  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_188089785_   3900 GAATAAAGTTAGAGGTATGATGTTCCTTGATTTCAAAATACATTGCAAAT 3949
                            i      i    vv v iii i iii         ivi i i    v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_188089785_   3950 CTAGAGTAATCAAAATAGTATGAGACTAATAAAAAAATTGACAC------ 3993
                            v         i i   i  iv   iii v  ii  v    i------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_188089785_   3994 CAGTGTAACAGAACAAAGACTC-AGAAGTAAACCCATGCTTATATGAGCA 4042
                           i  v  i    ivi   v  -    i         i v v    iv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_188089785_   4043 ATTCGTCTTC--CATGGGT--CAAGATTACACAATTTGGAAAGTATAGTC 4088
                            vi i   --  v    --     ii iv    vv      v      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_188089785_   4089 TCTTCAACAAATGGC-TTGGGCAAAACTGGATATCCATAAGCAAAAGAAT 4137
                          i            i-i    - v         ?   i v          
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGG-ACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_188089785_   4138 AAATTTGAACCTTTATCTCATACCATACAAAAAAAAAAATTCAAAAATGC 4187
                         i  v   i   ii  i    i      i v     vv  i      -  v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGG 495

  chr1_188089785_   4188 TTTGAAGAC--AAAGGTAAAATCTGAAGCCATAAAACTATTAGAAGAAAA 4235
                         v ii?    --   v    i v  i  i i        v           
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_188089785_   4236 CATAAAA--AAATTTTTTT---CTTGGATTTGGCAACAATTTCTTGCATC 4280
                             ii?--    i  iv ---     i  v     iii      iv  v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_188089785_   4281 TAATACCAAG-GCTCAGGCAACAACGACAAATACAGACAAGCTG-ACTTA 4328
                          i i     i-  v  i       viiv   v i   i  ii  -    -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT- 644

  chr1_188089785_   4329 CATTAAA-CTAAAAATTTTCCACATATCAAAGGAAACAATCAACAAAATA 4377
                            i   -i      i   i-iiiiv        v  v     v   i i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_188089785_   4378 CAAAGTCAGCC------ATAGGAGGAAAAATTTGCAAATTGTTTATCTGA 4421
                         v    v  i  ------  i    i   v          ii v       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_188089785_   4422 TAAGGGGTTAATATTAAAAATAT-TAAGGAACTCATATACAACTCAATAG 4470
                               ii vi   iv i     -   i      - -            -
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTC-T-TACAACTCAATA- 790

  chr1_188089785_   4471 AAAACAAAACCAAACCCCAGATAATCCAACTATTTAAA--TGGGCAAAGA 4518
                         --- i    -- i  --- i    i    ---  ?   --         i
  L1M4_orf2#LINE/    791 ---ATAAAA--AGAC---AAATAACCCAA---TTWAAAAATGGGCAAAGG 829

  chr1_188089785_   4519 ACCTGAATAAACATTTCTCCCAAGAGGATATACAAATGGCCAGCAGGTAT 4568
                          ii      i          v    i                ii i i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_188089785_   4569 ATAAATAGGTGCTTAACATCACTAATCAT 4597
                           i  v  i    i       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (136 / 74)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.04 (57 / 28)  


1898 28.00 7.71 0.83  chr1_188099279_188101399      792  1634 (487)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_188099279_    792 ATAACTAACATTTGTGAATTAGAATATTCAATACTAGTAAGCTGTCAATT 841
                            v iv ii  ii  i   i   v i i    i iv    v  v    v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_188099279_    842 CTTCTTAGCTTGCTCTATAGGTTCATGGCAATCCC----AAATATGCCAG 887
                           i ii iv   v    i  i    vv        ----   -  v    
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA-ATCCCAG 106

  chr1_188099279_    888 AAAGTTATTGTGTAGATATTAACAAATTCATTCTAAA-TTTATATAGAAA 936
                         vvivi v  v  i   v   i    ii v  i     -  i    i    
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_188099279_    937 ------GGTCAC-------CCAACACAATACTAAAGCAACAGAGCAGAGT 973
                         ------  v v -------    v     vi i  iv iv   i  i   
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_188099279_    974 TGGTAGACTAAC---TC---ATTTCAAGACTTACTACAAAGTTATAAGAA 1017
                            vi    v  ---  ---       i             i  i iv  
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_188099279_   1018 TCAAGACAGCACAATATTGAGGAAAGAATGAGGACACAGATCAATGGAGT 1067
                                  iiiii  i  iviv   i  iiiv i i           i 
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_188099279_   1068 AGGATAAAGAGAACAGACATAGACTCACGCAAATATAATCAAATGAACTG 1117
                           i  vi    vv    v   i  i  ii  vv   ii    v   vi v
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_188099279_   1118 TGACAAAGAT-CCACAGCCAATTCAATGGAGAAAGGATAGTGTATTCAAC 1166
                         i     i i -   -  v v         i     i     v v      
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_188099279_   1167 AAGTCATGCTGAAACAAATAGATGTCCATATCCAAAA-AATGAGGCAAGA 1215
                           i vi     ii    v i   i?   i  v     -     i ivi  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_188099279_   1216 CACACAGCATACACCTTCAT-CAGAAAATAACTCAAAATTGATCATAAAT 1264
                          v vi v vi     v -  -  i   v           v     ? i i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCAT-ATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_188099279_   1265 CTAAATGTAATGCAG--AAAAGCCTGAAACTTCTGGGAGAAAACATAGGA 1312
                                   - -  --    viv i     ii i i            ?
  L1M4_orf2#LINE/    505 CTAAATGTAA-G-AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_188099279_   1313 AAGAATGTATGTGA---TGA---AG--------TCCTT-GATATAACACC 1347
                         ivi   v vi    ---  i---  -------- i   -     i     
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_188099279_   1348 AATAGTACAACCCATGAAAGAAAAAAAATGACAATTTGTATTTTTTAAAA 1397
                           v  i    v v ii          v -  i  v   v i  iv v   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTCATCAAA 651

  chr1_188099279_   1398 ATTAAAAATTCTTCT-CTGTGAAACACAGAAATGAAAGAAT-AAAAGATA 1445
                                 i i  v -  vii  iv   vv vii i i i -      i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_188099279_   1446 AGCTATATA-TGTGGGAACATATTGGAAAAACAT-----TAATAAAGGTC 1489
                          v i i v -  v i   v     v v   v   ----- i    i  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_188099279_   1490 TTGTATGTAAAATATACAA-GAACATTTAAAAC-CATACAATAAGAA--- 1534
                               vi i      i  -    vi   v   -  - i     i  ---
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCA-ATAATAAAAAGAC 800

  chr1_188099279_   1535 --ATTACAAAATT--AAAATGG-CAAAAGATCAGAACAGACACCTCATTA 1579
                         --  v  vv    --       -    i   iv   i     ii  vii 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_188099279_   1580 AAGT---TACACATAAGGCAAATAAACATGTAACTATATGCTCACAATTA 1626
                            v---  i   v v   v     i  ii i vv v       vv  i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_188099279_   1627 TTTGTCAC 1634
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.35 (134 / 99)
Gap_init rate = 0.03 (31 / 901), avg. gap size = 2.32 (72 / 31)  


2620 28.83 1.90 0.45  chr1_188135332_188139974     3256  4150 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188135332_   3256 TGGAAA--CAGCTCATGCTCATGGATGGCTAGAATCAGCATTGTGAAAAT 3303
                               --i v i    i        v vv   v i ii     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188135332_   3304 GACCACACTGCCAAAAGGAATCTATAATTTTAATG-AATTCCCATCAAAA 3352
                          i v i   v  v   vvi     i iv  i  i -   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_188135332_   3353 TACCATCATCATTCTTCATAGAACTAAAAAATACAATCCTAAAATACACA 3402
                          v   v vv v  i  iii    v vi v  vvii          v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_188135332_   3403 TGGAACCA-AAAAGAGTCTGCATAGCCAAAGAAAGACTAAGCAAAAAGAA 3451
                              vii-  ii  vi v v         iv  vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_188135332_   3452 CAAATCTGGAGGCATCACGTTATTTAACTTCAAACAATACTACAAGGCTA 3501
                             vi      vv    ii viii  i      vvv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_188135332_   3502 TAGTTACCAAAACATCATGGCACTGATATAAAAGCAGGCACATAGACCAA 3551
                         i   v i   i   vii   i    ii    iiii  i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_188135332_   3552 TGGAACAAAATAGAAAACCTAGAAATAAAGCCAAATACTTAAAGCCAACT 3601
                              i i   v  i ii i         v   v i i   vi i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_188135332_   3602 GATCTTTAACAAGGCAAACAAAAACATAAAGTGGGGAAAAAA-------- 3643
                            i  ii      vviv   i v   vv i        i  --------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_188135332_   3644 -CAACAAATGGTGCTGGGATAACTGGCAAGTCACATGTAGAAGAATGAAA 3692
                         -                  i      vv ?i      i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_188135332_   3693 CTGGATCC-TCTCTCTCATCTCATACAAAAATCAACTCAAGATGGATCAA 3741
                         i    i  - vi   v  i vi          i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_188135332_   3742 AGACTTAAATCAAAGACCTGAAACCATAAAAATTCTAGAAGATAACATTA 3791
                             i     vv    v  i    i      v ii       v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_188135332_   3792 GAAAAACTGTTCTAGACATTGGCTTAGGCAAGGAGTTTATGACCAAGAAC 3841
                          ?iv  v v   vv   v    v        v iv  iv iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_188135332_   3842 CCAAAAGCAAATATAACAAAAACAAAGAAAAATAGATGGGACTTAATTAA 3891
                                  v vii       iv   i v i   i  v      v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_188135332_   3892 ACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTAAACGGGT 3941
                          v v    i   i  ii vv    i  v iv    iv i   i  vi ii
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_188135332_   3942 AGCCCACAGAGTGGGAAAAAAATCTTCACAAACTATGCTTCTTACAAATG 3991
                          i        i     i    - v  ii    ii  iiv   v i  iv 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGG 749

  chr1_188135332_   3992 GCTAATATTCAGAATCTACAAGGAAATCAAACAAATCAGCAAGAAAAA-- 4039
                         i  vi   i      v  i  i   v  vv    v   ii  v     --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_188135332_   4040 -AAATAATCCCTTCAAAAAGTGAGCTAAGGACATGAATAGACAATTCTCA 4088
                         -      i  vv i?    i  i  v     iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_188135332_   4089 AAAGAAGATACACAAATGGCCAACAAACATGTGAAAAAAAAATGCTAAAC 4138
                                   i            i  i  ii      i ---    v   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA---TGCTCAAC 896

  chr1_188135332_   4139 ATCAATAGCGAT 4150
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (147 / 107)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.62 (21 / 8)  


2984 27.08 2.58 0.56  chr1_188143829_188150176.rev     4968  5857 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188143829_   4968 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5017
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188143829_   5018 AGTCATACTGCCCAAGGTAATTTATAAATTTAATGCCATCCCTATCAAGC 5067
                         i iv     v     iv i  i  i i   i  i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_188143829_   5068 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5115
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_188143829_   5116 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5165
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_188143829_   5166 AGCAATGATGGAGGCATCACGCTACCTGACTTCAAACCATACTACAAGGC 5215
                          i   v v      vv    i  v  ii i      v v        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_188143829_   5216 TACAGTAACCAAAACAGCATGATACTGGTGCCAAAACAGAGATACAGACC 5265
                                 i   i    ii  i      iiiv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_188143829_   5266 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5313
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_188143829_   5314 ATCTGATCTTTGACAAACCTGAGAAAAACAATTAATGGGGAAAGGATTCC 5363
                          vi    i  i     ivv  vv  i v  v i           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_188143829_   5364 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA---- 5409
                           v  i  i              v      v  ?   i   i i  ----
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_188143829_   5410 --AG------------CTTACACCTTATACAAAAATTAATTCAAGGTGGA 5445
                         --  ------------  i     v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_188143829_   5446 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5495
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_188143829_   5496 CCAGGCA-ATACCATTCAGGACATAGGCATCGGCAAGGACTTCATGTCTA 5544
                         vi   ?i- v i -   iv   v v  vv v     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_188143829_   5545 AAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5594
                         vi            vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_188143829_   5595 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5644
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_188143829_   5645 CAGGCAACCTAGAGAATGGGAGAAAATTTTTGCGATCTACTCATCTGACA 5694
                         v  i     i v               v     i vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_188143829_   5695 AACGGCTAATATCCAGAATCTACAAAGAACTCAGACAAATTTACAAGAAA 5744
                          iv i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_188143829_   5745 AAAACAAACAACCCCATCAAAAAGTAGGTGACGTATATGAACAGACACTT 5794
                           i     i     v  i?    i i  ii v v  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_188143829_   5795 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5844
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_188143829_   5845 CATCACTGGCCAT 5857
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.11 (28 / 9)  


3090 28.07 0.66 1.10  chr1_188172760_188177081     2918  3829 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188172760_   2918 TGGAAAAACATTTCTTGCTTATGGATAGGAAGAATTAATATCATGAAAAT 2967
                               i i  ii v  i i      v      v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188172760_   2968 GGCCACGCTGCCTAAAGTAATTTATAGATGCAAAGCTATTCCCATCAAGC 3017
                            v ii  v  i   v i  i  i    v   v  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_188172760_   3018 TACCATTGACTTTCTTCATAGAATTAGAAAAAACGACTTTAAGTTTCATA 3067
                          v   vivi i  i  iii    v v  v  ivi  iii   iv      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_188172760_   3068 TGGAATCAAAAAGAGCCC-TCGTAGCCAAGACTATCCTAAGCAAAGAGAA 3116
                              viiv  i ii   -vvi       i  v   i i iv  ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_188172760_   3117 CAAAGCTGGAGGCATCATGCTACTTGACTTCAAACTATATTACAAGGTTA 3166
                              i      vv   ii  v iii i      viv  i     i i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_188172760_   3167 CAGTAACCAAAACAGCATGGTACTGGTACCAAAATAAATATATAGACCAA 3216
                               i   i    ii         i iv ii   i i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_188172760_   3217 CGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 3266
                         i    i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_188172760_   3267 GATCTTTGACAAACCTGACAAAAACAAGCAATGGCAAAAGGATTCCCTAT 3316
                            i  i     ivv  v   i v  vv      vi    i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_188172760_   3317 TTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACAGTCA 3366
                          i  i        i     v      v  ?   i     i  i vv vvi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_188172760_   3367 CTGGACCCCTCCCTTATACCTTATACAAAAATTAACTCCAGATGGATTAA 3416
                         i         v   i i   v                 v i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_188172760_   3417 AGGTTTAAATGTAAGACTTAAAACTATAAAAAAAAAACCCCTAGAAGAAA 3466
                           iii           vi             ------ i i         
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA------CTCTTAGAAGAAA 544

  chr1_188172760_   3467 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAC 3515
                           v    ?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_188172760_   3516 TGAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTAACAAATGGGATA 3565
                          ivi            vvv          vv     vi i    v   iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_188172760_   3566 TAATTAAACTAAAGAGTTTCTGTACAGCAAAAGAAACTATCATCAGAGTG 3615
                          v  i   v v  i ii  i   i vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_188172760_   3616 AACAGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTATCCATCTGA 3665
                           v  i     i                 i       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_188172760_   3666 CAAAGGGCTAATATCCTGAATCTGCAAAGAACTTATACAAATTTACAAGA 3715
                         i  i  i  vi     v    v ii        iv     v ---   v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATA 790

  chr1_188172760_   3716 A-AAAAAAACAAACAATCCCATCAAAAAGTGGGCAAAGGATGTGAACAGA 3764
                          -     i     i  i  v  i?    i            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_188172760_   3765 CACTTCTC---AAAAGACATTTATGTGGCCAACAAACATATGAAAAAAAG 3811
                           i     --- i    i  vi vi       i  i  i       i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_188172760_   3812 CTCATCGTTACTGGTCAT 3829
                             v i i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (154 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


2654 26.83 0.97 3.12  chr1_188281427_188286927.rev     4083  5010 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188281427_   4083 TGGAAAAGCATTCTATGCTCATGGATAGGAAGAATCAATATTATGAAAGT 4132
                               iii  i i   i        v      v i      i v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188281427_   4133 GGCCATATTGCCCAAAGCAATTTGTAGATTCAATATATAGTTTATTCCCA 4182
                            v   i v      vii  i ii        iii ------  i  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA------ATCCCTA 94

  chr1_188281427_   4183 TCAAACTACCATGGACATTCTTCACAGAATTAGAAAAAAACTG-TTTTAA 4231
                              v v   vvvi v  i  ii     v v  v  i--   - ii   
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAA 142

  chr1_188281427_   4232 AATTAATTTGAAACCAAAAAAGTGCCCGCATAGTCCAA-CATTCCAAAAC 4280
                             v  v  i  viiv  ii vv  v v    i v  -  v  ivi  v
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_188281427_   4281 AAAAAGAACAAAGCTGGGAGCATAATGCTACCCAACTTCAAACTATACTA 4330
                           i          i   ii vv v ii  v     i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_188281427_   4331 CATCACTACAGTAACCAAAAAAGCATAATACTGTTA-AAAGATCAGACAC 4379
                           vvi         i   i v  ii ii     vi -  i   -     i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACAT 291

  chr1_188281427_   4380 ATAGATCCATGGAACAGAATAGGGAACCCAGAAATAAGACCGCACACCTA 4429
                                v      i     v i  ii          iv  ii   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_188281427_   4430 CAACCATCTTATCTTCGACAAAGCTAGCAAAAACTAG-CAATGGGGAAAT 4478
                         iiii  vi v  i        i v -  v  i  i v-           v
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAG 390

  chr1_188281427_   4479 AATTCCCTATTTAATAAATGGTGCTGGGAGAATTGGATAGCCATATGCAG 4528
                            vvi  v  i  i              v  i      ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_188281427_   4529 AAAGTTGAAACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAA 4578
                           iiv    ii         v   i                 i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_188281427_   4579 GATGGATTAAAGACTTAAATGTAAAACTCAAAACTATAAAACCCTAGGAA 4628
                         i      i ?    i         i vii             i  v----
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT---- 536

  chr1_188281427_   4629 AAAAAAAAAAAAAAAAAAAAACGTAGGCA-ATACCATTCAGGACATAGGC 4677
                         ------------ i  i     i    ?i- v i -   iv   v v  v
  L1M4_orf2#LINE/    537 ------------AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

  chr1_188281427_   4678 ACAGGCAAAGATTTCATGACTA-GATGCCAAAAGCAATTGCAGCAAAAAC 4726
                         vi      v i    v iiv  -  ii         vvv   i     iv
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_188281427_   4727 AAAAATTGACAAATATAATATAATTAAA-TTAAAGAGCTTCTGCACAGCA 4775
                               v  i    vvi iv v  i   -     i -   i  ii vv  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCA 672

  chr1_188281427_   4776 AAAGAAACTATCAACAGAGTAAACAGACAACCTAAAGGAATGGGAGAAAA 4825
                           i  v        v i   i  v        i v  -            
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG-AATGGGAGAAAA 721

  chr1_188281427_   4826 ATTTTGCAATCTCTCTATCTGACAAAGGTCTAATATC-AGCATCTATAAG 4874
                         vv       viiv v       i  i  v  vi    -  v  v     i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_188281427_   4875 GAACTTAAACAAATTTACAAGAAAAA-ACACACAATCCCATTAAAAAGTG 4923
                              ivv    v iv i  v     -   v i  i  v   ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_188281427_   4924 GTAAAATGACATGAACAGACACTTCTCATAAGAAAGCATACCTGTAGCCA 4973
                          vv   v  iv    i     i     vv     iii    vvi i    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_188281427_   4974 ACAAACCCATGTAAAAAAGCTCAACATCACTGATCAT 5010
                          i  i v    v   i v           ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (140 / 105)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  


2702 24.45 2.32 6.64  chr1_188332138_188334949     1371  2319 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188332138_   1371 TAGAAATATATTCCATGTTTATGAATTGGATGAATCAGTATTGTTAAAAA 1420
                          i    v    i       i   i      v  v i i         i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188332138_   1421 GTCCATACTACCCAAAGCAATCTACAGATTCAGTGCAATCTCTATGAAAA 1470
                          v v     v      vii             ii      i    -----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT----- 95

  chr1_188332138_   1471 TATTAGGTTGGTGCAAAAAGAATTGCAGTCCTTGCCATTACCTTTAATAT 1520
                         -------------     ----------   iv  --- i     -----
  L1M4_orf2#LINE/     96 -------------CAAAA----------TCCCAGC---TGCCTTT----- 114

  chr1_188332138_   1521 CAATGCTACTCTTTATAGACATAGAAAAAC-AATCTTAAAATTTATATGG 1569
                         -----------   ii   v  v  v  i -i   i       i      
  L1M4_orf2#LINE/    115 -----------TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_188332138_   1570 AAACATGAAAGACCTAGAATAGCCAAAAGTATCCTGAGCAAAAGGAACAA 1619
                            iiii ii    i             vv   i   iv  i i      
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_188332138_   1620 AACTGGAGGAATTACATTAGCTGACTTCAGATTATACCACAGATCTAGAG 1669
                          ii       v i   i vv ii i    i viv   i   i v   v  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_188332138_   1670 GAACCAAAACAGCATGATATTGACATAAATGCAGACACATAGACTGATGG 1719
                         v  i   i    ii  i  i  i     ivii     i     iii    
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_188332138_   1720 AACATAATGGAACACATGAGTAGAGAACACAGAAACAA-CCCACACGTG- 1767
                           i v   v  ------    ------ -      i  -    i  i v-
  L1M4_orf2#LINE/    304 AATAGAATTGA------GAGT------C-CAGAAATAAACCCATACATTT 340

  chr1_188332138_   1768 ATCAGTGAACTCATTTTTGACAAACGTGCCAAAAACAT--AATTAGGTAA 1815
                           -i  v  i v     i     iv       i v   --   vi  -  
  L1M4_orf2#LINE/    341 AT-GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AA 388

  chr1_188332138_   1816 AAGACAGTCTTTTTAATCGATGGTGCAGGGAAAACTGGTTATCTGTATGC 1865
                          ii i        i  ivi       v    v      v  ? iii    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_188332138_   1866 AGAACAATGAAACTTGATCCCTATCTCTCACCTTATACAAAAATCAAATC 1915
                          i  v      ii v  i     i   v    v           i  v  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_188332138_   1916 AAAATGGATTAAAGACTTAAATCAAAGATCTCAAACTATGAAACTACTA- 1964
                                  i ?    i     vv    v  v       i     vi  -
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_188332138_   1965 AAGAAAACATTGGGGAAAACCTCCAGGACATTGGTCTGGGTAAAAATTTC 2014
                                   v  ? v   i  i iv   v    vi i  i  vii    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_188332138_   2015 TTGACTAATACCCCACAAGCTCAGGCAACCAAAGGAAAAATGGGTAAATG 2064
                           iiv  vv  v   v    v  i     v    i      i i     v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_188332138_   2065 GGATCACATTAAG-TTAACGAGCTCCTACACAGCAAAAGAAACAATCAGG 2113
                            iiv   i  i-    -i i  ii iii vv    i  v  v    i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_188332138_   2114 AAATTAAAGAGAACATTCACAAAATGGGAGAAAATATT-GCAAGCTACCT 2162
                            v i  i   vv ii    i                -    iii iv 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_188332138_   2163 TTCTGACAGTCAA----TAACTAGAACATATAAGAAGCTCAAACAACTCT 2208
                         v     i ivvi ----  v i    i      ii i   vv       v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_188332138_   2209 ATGGGAAAAAATCTAATAACCCAATCAGAAAA---GC------TTTTAAT 2249
                           iiv     iv v           i?i    ---  ------   v   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_188332138_   2250 TGACATTTCTCAAAAAAAGACATA-AATCGGAAAACAGTCATATGAAAAG 2298
                         v          v   i    i   -  vi  vv  i iv  i        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_188332138_   2299 ATGCTCATCCTCACTGATTAT 2319
                                v v   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (140 / 88)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.05 (85 / 21)  


2617 24.43 3.47 4.19  chr1_188436311_188438135.rev      502  1336 (489)    L1M4_orf2#LINE/L1       80   908 (0)  

  chr1_188436311_    502 TCTATGCATTCCCCATCAAAATTCTAACAGCAATTTT-ACAGAAATAGAA 550
                           v i   v    i        i i i v  vv    -i       v  v
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chr1_188436311_    551 AGGGCAATTCTAAAATTCATGTGGAAATATGCAAG--ATCCCAAATAGCC 598
                          i vii  i           i       --     -- i  vi       
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAAT--GCAAGGGACCCAGAATAGCC 177

  chr1_188436311_    599 AAAGCAATCTT---AAGCAAGAACAGGTCTGGAGGCAC-CACATTCCCTG 644
                            i       ---  iv       iivi      -  -    i i  ii
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCA 226

  chr1_188436311_    645 ATTTCAAATTATGTTACAACATTGTAGTATTCAAAACAGTATGGTAGTAG 694
                                 viv ii     vii ii    v    i     i     v i 
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr1_188436311_    695 TATAAAAGCAAATATATCAACCAACAGAACAGAATAGAGAGCCCGGAAAT 744
                         i    iiii i i    vi i   ii   i     v     i  i     
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_188436311_    745 A----CA----------GTCAACACATTCTTGACAATG-CACCAAGAATA 779
                          ----  ----------     ivv   i i     v -ii      vi 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_188436311_    780 CACGACTGGAAAAGAATAGTCTTTTCAA-AAATGGTGTTAGGAAAACTGA 828
                         iv i iv  i                  -        i i   v     i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_188436311_    829 ATAGCCCCAAGCAAAAGAATTAAATTGGACCCTTATTATATGTCATACAC 878
                            ?  v  v          v  i        i  iivi iii    i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_188436311_    879 AAAAATCGGCTCAAAA-GAATTAAAGAATTAT-TTTAAAACTTGAAACAA 926
                               iii       - i  i ?   vi  v- v   i vi i    v 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_188436311_    927 TAAAACTTCCAAAAGGCAATGTAGGAAGTAAG-CTCCTTGACAATGGCAT 975
                                iii i   iv  ii    ?-    i-  i v    vv   vv 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGN-GTAAATCTTCGTGACCTTGGGTT 575

  chr1_188436311_    976 TGGCAATGATTTTTTTTGGATATGAAACCAAAAGCATAGGCAACAAAAGC 1025
                         v       i   i  --i       v          i i          v
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTT--AGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_188436311_   1026 AGGAATAAACACATGGGACTACATTAAA-CTAAAAACAAACAAACTAACA 1074
                          ii    i i v  v     v   i   -i       -------------
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC------------- 660

  chr1_188436311_   1075 AACAAAAAATTCTCCATAGCAAAGAAAACAATCAACAAAATAAAAAGGCA 1124
                         ---------  i viiivv     i v  v     v   i i     i  
  L1M4_orf2#LINE/    661 ---------TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_188436311_   1125 ACTTATGGAATAGGAGAACATATTTGCAAACCATATATCTGATAAGGGGT 1174
                           ii ii    i      v           i                 ii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_188436311_   1175 TAATATCTAAAATGTATAAGAAACTCCTACAACTCAATAGTTAAGTATGC 1224
                          vi    i i   i     ii     i            i v  ------
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA------ 795

  chr1_188436311_   1225 AAATCAAATAAACCAATTAAAATTTGGGCGAAGAACCT-AATAGACATTT 1273
                           iv       v      ?   vv     i   i ii -           
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_188436311_   1274 CTCCAAAAAAAGACATATAAGTT-TCAATAGGTATATTAAACGTTGCTCA 1322
                                i  -  i   i  i v-i     i i i  v   v v      
  L1M4_orf2#LINE/    846 CTCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_188436311_   1323 AAATTTTAATCATT 1336
                          v  iv????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (135 / 65)
Gap_init rate = 0.03 (21 / 829), avg. gap size = 3.05 (64 / 21)  


2473 27.00 4.92 1.37  chr1_188476013_188480585     3212  4085 (488)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_188476013_   3212 AAACATATCCTGTGTTCATGTATTGGCAGAATTACTATTGCTAAAATATA 3261
                            v      ii        v     v   v   v     i   i  ivv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_188476013_   3262 TATACTATCCAAAGCAGTCTACAAATTTAATGCAGTCCCTATCAAAATAT 3311
                         v     vi     viii      i   i  i   i             vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_188476013_   3312 CAATAACATTCATCACAGAAAT--ACAAAGAAAATTCTAAAATTTGTATG 3359
                           iivi v  iv ii       --    - vvi  i        ii    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATG 152

  chr1_188476013_   3360 GAAACACAAAATACCTCAAGGAGTCAG--CAATCTTGAGCAAAAAGAGCA 3407
                             ii   iiv   ivi iv  i  i--         iv  i    i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_188476013_   3408 AAGGTGGAGATATCACACTACCTGACCTTAAAATATCCTACAAAGTTGTA 3457
                            v     ivv       v  ii ii i    iv v        i ii 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_188476013_   3458 AGTAACCAAATCAGCATGATACTGGCATAAAAA-AGACACACAGACAAAT 3506
                         -    i   iv   ii  i           ii -     i i   iv   
  L1M4_orf2#LINE/    253 -GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_188476013_   3507 AGAACAGAATGAAACATCAATAAATAAACCCAAGCATTTACATCCCACTG 3556
                         i   i     vi ivi  v v           vi      iivi v i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_188476013_   3557 ATTTTCAACAAAAGTGCCAATAACACACATTAGAGAAA-ACCAAGCTCTT 3605
                               i    ii       v v  iv  v i i    - vi iv  i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_188476013_   3606 CAATAAATGGTGTTGGAAAAACTAAATATCCACTTGCAGAAGAATGAAAT 3655
                            i        i   i v    ii   ?    v    i         i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_188476013_   3656 TAGATACATATCTTTCAACATATA-AAAAATCAACTCTAAATATATCAAA 3704
                          i  iv v  i  iv  v      -      i     v    iv    ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_188476013_   3705 GACCTAAATGTAAGA-TTGAAACTATAAAACT---ACCAGAAAACCTCAG 3750
                                        -i i             --- vv       v -  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AG 550

  chr1_188476013_   3751 GAAAAAAACTTCATGACCTTAGTCTGAGCAAGAATTTTTTTTTTTATGAC 3800
                          ?iv   v    i       i vi ii    vii   i  vvv -     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGAC 599

  chr1_188476013_   3801 ACCTCAAAAACATAGGAAACAAAAGCAAAAATAAGCAAAAATAGAC---- 3846
                            --    i  i i v        v       iii   v- i   ----
  L1M4_orf2#LINE/    600 ACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT-TGGACTTCA 646

  chr1_188476013_   3847 -CAAAA--AAAGA---------------GAAAATAACTAACAGAGTAAAA 3878
                         -     --   i --------------- i v iv ii  v i   i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_188476013_   3879 AT-TAAC--ATATGATAGAATATATTAATATTTACAAGCTATACATCTGA 3925
                          v-i   -- i vi  i i v - --       i   iii   i      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGA-A--AATATTTGCAAATCATATATCTGA 743

  chr1_188476013_   3926 TAAGGAGTTCATATCAAAAATATATAAGGGATTC----AACTCACTAACA 3971
                              iii ii    v i         i i i  ----      v   i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_188476013_   3972 AAAACAAATAAATAACCTGATTTTAAAATGGACCAAAGACCTAAGTAAGC 4021
                             --i i        ii   ?v       i v  i  ii i i  ii 
  L1M4_orf2#LINE/    794 AAAA--GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_188476013_   4022 ATTTCTCAAAAAGAGACATA---ATGGCCAAAAGGAGTATGAGAAAGTGC 4068
                                v   ii   i   ---        v i vii    i  ii   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_188476013_   4069 TTAAGAGCACTAGTTAT 4085
                          i  v v  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (155 / 77)
Gap_init rate = 0.03 (23 / 905), avg. gap size = 2.39 (55 / 23)  


3193 25.88 1.32 1.32  chr1_188532181_188534101.rev      522  1429 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188532181_    522 TGGAAGAACATTCCATGCTCATGGATAGGAAGATTCAATATCGTGAAAAT 571
                              ii i  i     i        v      i i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188532181_    572 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 621
                            v     v     iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_188532181_    622 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAACTGAAC------TTCA 664
                          v   iivi i  i  ii     -   -- v  i    v ------    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_188532181_    665 TATGGAATGAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCTAAAG 714
                                vviv  ii  v  v v  v     iv     i i ivvvi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_188532181_    715 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAA--CTACTACAAGCC 762
                                i      vv       v  ii i      --i        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_188532181_    763 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 812
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_188532181_    813 AATGGAACAGAAC--AGAGCCCTTAGAAATAATGCCACGTATCTACAACC 860
                                i    i--    i  --        vv   iii  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_188532181_    861 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 910
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_188532181_    911 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 960
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_188532181_    961 GAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGA 1010
                            ii    i    v   i     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_188532181_   1011 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1060
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_188532181_   1061 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTA 1109
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_188532181_   1110 AAACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTC 1159
                         vi            vvi     i    vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_188532181_   1160 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1209
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_188532181_   1210 CAGGCAACTTATAGAATGGGAGAAAATTTTTACAATCTACTCATCTGACA 1259
                         v  i    ii i               v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_188532181_   1260 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1309
                          i  i  vi          v  i  v      vv    v ---   v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAAT 792

  chr1_188532181_   1310 AAAAAAACAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACA 1359
                              i     i  ----   v  i? v  i     i      v    i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAA----CCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_188532181_   1360 GACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAA 1409
                             i     v        i  vi viii     v ii          i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_188532181_   1410 TGCTCATCATCACTGGCCAT 1429
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.40 (24 / 10)  


2274 26.46 2.04 2.04  chr1_188563148_188567301     2927  3663 (490)    L1M4_orf2#LINE/L1      172   908 (0)  

  chr1_188563148_   2927 ACAGCCAAACCATATCACTATCCTAAGCAAAAAAAAGCAAAATTGGAGGA 2976
                          i       v  -------   i i i-   i  i i    i        
  L1M4_orf2#LINE/    172 ATAGCCAAAACA-------ATCTTGAA-AAAGAAGAACAAAGTTGGAGGA 213

  chr1_188563148_   2977 ATCACGTTACCTGGCTTCAAATTATAATACAGAGCTGTAGTAACCAAAGC 3026
                         v    ii v  iiii      viv  v    i    ii     i   ii 
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_188563148_   3027 AGCATAGTACAGGCATAAAAACAGATACATAGATGAATGGAACAGAATAA 3076
                           ii i    v       ii i   i i      v       i     vi
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_188563148_   3077 AGGACCCAGAAACAAATCCACGCACCTACATTAAACACATTTTAGACAAA 3126
                           iii       i   i   ii  ii  iiv v  ivv     v     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_188563148_   3127 CGTGCCAAGAACATAGTC--TGAGAAAACGACAGACTCTTCAATAAATAA 3174
                         v         v   --  --  i i   vi i  v  i     i    ii
  L1M4_orf2#LINE/    364 GGTGCCAAGACCAT--TCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_188563148_   3175 T-CTGAGAAGCCTGGGTATCCACATACAGAAGCAGGAAACTAGACACCCT 3223
                          -   i  viv    i  ?      i  i   v v   ii i   -    
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC-CCCT 460

  chr1_188563148_   3224 ATCTCTCACCATATACAAAAATCAAATCAAAATGAATTAAAGATTTAAAT 3273
                          i   v                i  v        i  i ?   ii     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_188563148_   3274 CGAAGACCTCAAACTGTGAAACTACTACAAGAAAAAATTGCTG-ACA-CT 3321
                         vv    v  v     i i     vi  v       v  v v? - v -  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_188563148_   3322 TCAGGAAATTGGTCTGGGCAAAAATTTATTGAGCAATACCTCACGAGCAC 3371
                           iv  vv    vi i     vii   v  iiii vv  vi  vi     
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_188563148_   3372 AGGCAACCAAAACAAAAATAGACAAATGGGATCACATCGAGTTCAAAGGC 3421
                          i     v   iv         i    v   iiv    i iv i   ii 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_188563148_   3422 TACTGTACAGCAACGTATACAAT-AAGCAAAGTGAAGAGACAACCCACAG 3470
                          vi   i vv   v v i  v  -   -        i             
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAAAGACAACCCACAG 709

  chr1_188563148_   3471 ATTGAGATAAAATATTTTCAAACTACCTCTCTGAAAAGGGATTCATAACT 3520
                          v  i  v         v    ii iv v     v      i ii  v i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_188563148_   3521 AGAATATATAAGAAGCTCAAACAACTCCACAGAAAAAAAAACCTAATGAT 3570
                                    ii i   vv       v i iv     i -- v   i -
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CAAATAA- 806

  chr1_188563148_   3571 CCCATTTTTAAAATGGGCTAAAGATTTGAAT-GACATTTCTCAAAAGAAG 3619
                             v  ?v         v  i         -          v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_188563148_   3620 ACACGCAAATGGC--------ATATGAACAGGTGCTTGACATTGCTGATC 3661
                          i ii        -------- i     v  i    ii    ii??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_188563148_   3662 AT 3663
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.65 (119 / 72)
Gap_init rate = 0.02 (14 / 737), avg. gap size = 2.14 (30 / 14)  

 256 24.42 2.33 0.00  chr1_188563148_188567301     4068  4153 (0)  C L1M4_orf2#LINE/L1   (0)   908   821  

C chr1_188563148_   4153 GAGAAAGAGACATGAAAAGGCACAT-TCAAAAGAAGACATTCAAATGGCT 4105
                          i v  ii  iv    v  i  iv -  v        i  v        i
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

C chr1_188563148_   4104 AGCAAGCATATGAAAA-ATGTTCATCACTAATCACCAG 4068
                          ii     i       -   i   v  ii ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.02 (2 / 88), avg. gap size = 1.00 (2 / 2)  


1271 27.24 11.08 4.01  chr1_188572309_188575479     1832  2679 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188572309_   1832 TAAAGAGATATTTTTTCTTTCATGCTTGAAAAGACTCAATAAAACTAAAA 1881
                          ii i      iiiv v  -    vv vii      i    vvii   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTT-CATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_188572309_   1882 TATAAATTCTCCCCAAAATTGGTCTATAGATTCAGCTTAA--CTTA--AA 1927
                          ivv   v         -   i    i       i vi  -- i  --  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_188572309_   1928 AAATATTCCCAAAAGTACTTTTTA-AGAAATTGACAAGCTGATTTTAAA- 1975
                           ----     ivv ivi     i-                  ii    -
  L1M4_orf2#LINE/     99 AA----TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_188572309_   1976 TTTAGGCAAATATTTTAAGCATATAGAATAGCCAAAACAGTCTTTAAAAT 2025
                           i viiii v  viv i v ivi               i    v    v
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_188572309_   2026 GAA---CA--GTTAAGGAAC--ATATTTGTCTCCATTTCAAAGCTTAACA 2068
                            ---  --   iii i  -- i i  -- i v        i    vi 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTT--CCCAATTTCAAAACTTACTA 242

  chr1_188572309_   2069 TGAAGTTGCAGTCATTAAGAGAGTG--GTATT----CAAGAAAAAAAATA 2112
                         ii   i i    v  i    v    --   i ----i   i v i v   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_188572309_   2113 ACAGGTCTATGGGACAGGATATAGAGTGCAGAAATAGATCCA-------- 2154
                         -i  i  v    i i  i  vv     v        i i   --------
  L1M4_orf2#LINE/    293 -TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_188572309_   2155 -GGT-GATT---TTTTGA-AAAGCCATCAAGTCTATTTATTGGTGGATGT 2198
                         -   -i   ---   i  -  i viii    v i   i v   v i v -
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG- 390

  chr1_188572309_   2199 AAATTTTTTCTCTTTCTTTTTCAATAAATGGTGGTAATAAAATAGGACAA 2248
                         -   vv i ---------      i        v iiv v  iv   i ?
  L1M4_orf2#LINE/    391 -AATAGTCT---------TTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_188572309_   2249 ACACAT----AGGGGCAACAATT----CTTGACCTCACACCATGAACAGA 2290
                         v     ---- i iiii - i  ---- iiv            iv   i 
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGA-AGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_188572309_   2291 TATTAG-----AATAAATTATAGATATAAAT---AGA---AAAA-TGTAA 2328
                         v    i-----   ii  i ?   iv     ---   ---    - i   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_188572309_   2329 AACTTAT-GAAG----------TGTTTTTTTTTTTG-CTTTGAAATATGC 2366
                             iv -    ----------?  vvv i  iv  - i   iiv  v  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_188572309_   2367 AA-ATTTTCTTAGG---GAGAATAGAAAAATAGTAAACAAATGGAAGAAA 2412
                           -iv        i---  v vi i  iv i ivv      -i   -   
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA-AGAA-AAA 627

  chr1_188572309_   2413 ACACTTAAGTTTCACTTCACCAAC-TTAAACCCTTATGTTTGTCAAA--A 2459
                          i vv   i  vv      i   v-     vv   v   viv     -- 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_188572309_   2460 CATAA--AAGAAATTTTAAAAACCATC-AGAGACTTAGAGAAAACGCTTT 2506
                           iv --      v vv   i  v i - v   v vi       iii  v
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_188572309_   2507 TCTGTC-TATTATCTGACAACA-ACTTGTATCTAGAATACATAAATAATT 2554
                         ivvi  -   -      i  vi-         i      i     v  i 
  L1M4_orf2#LINE/    728 CAAATCATAT-ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_188572309_   2555 CCCACA---CA----TAAATA-----ACAACTTAGTAAAAAGTTGGACAA 2592
                          ii   ---  ----    v ----- i   ii i v?   iv   i   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_188572309_   2593 TAGACTTGAA--AATATTTTTAATAATATCACCAAAAAAGATATACAAAT 2640
                         vi  i     --i i    i ----------     i             
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCT----------CCAAAGAAGATATACAAAT 866

  chr1_188572309_   2641 TGCCAATAAGCACATGAAAATGTGCT-AACA--AACTATAGT 2679
                         v                   vi    -    -- ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (137 / 90)
Gap_init rate = 0.05 (48 / 908), avg. gap size = 2.67 (128 / 48)  


2241 28.32 4.78 1.28  chr1_188679896_188682534.rev     1295  2152 (487)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr1_188679896_   1295 ATGGATTAGAGAACT-AATATTGATAAAATGATCATATATCCCAAAGCAA 1343
                                i  ii   -       v   i   iiv   ivi      vii 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr1_188679896_   1344 TCTACAGATTCAATTCAAAATCCATTAAAATGCCAACATCATTTTTTACA 1393
                                      iv   vvi i  i     v   i vv v      i  
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr1_188679896_   1394 GAATTATAAAAAA--AATCCTAAAGTTCAT-TGGAACCAAAAAATACCCC 1440
                            v - i v  i--i        i     -     viiv  iiv    v
  L1M4_orf2#LINE/    121 GAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_188679896_   1441 ACATAGCCAAAGCAATTCTGAGCAAAAGGAACAAAGCTGGAGATATAACA 1490
                         iv         i    ii   iv  i i        i     ivv v   
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_188679896_   1491 CTACCTGACTTCAAAATATATTACAAGGCTATA--AAGAAAAGCAGTTTG 1538
                           v  ii i       iv  i     i    i --  vv  ii    v  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_188679896_   1539 GTATTGGTATAAAAACAGACATG--GAACAATTTAACAGACT--AGAGTT 1584
                            i   i    ii i      i--  v    vv  i   v --     i
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_188679896_   1585 AAATAAAAAAAC--ATGTATTTACAGCCAACTGATTTTTGACTGAGGCAT 1632
                         v i-   v    --  ii     ii i   i       i   vii  iii
  L1M4_orf2#LINE/    320 CAG-AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_188679896_   1633 AAAGAACATTCAGTGGG-AAAGA-TATTTTCTTCAACACATGGTTCTGGG 1680
                         v    v      i    -     -  v i i       v     v     
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_188679896_   1681 AAAACTGGATATTCACATGTAGAAGAAGGAAACAGCACCCTTATCTTTCA 1730
                          v         ?i      i i     v   iiv v    i  i  iv  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_188679896_   1731 CCATACACAAAAATCAACCAAAGATAAATTAAAGACTTAAA--------- 1771
                              i        i   iv  i  ii  i ?    i    ---------
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_188679896_   1772 ----ACTATAAAACTACAAGAGGAAGCCTACACAAATATTAATATTTCTG 1817
                         ----           viv   i   i---   i ii?i v   -i   vv
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAA---ACATAGGNGTAAAT-CTTCGT 564

  chr1_188679896_   1818 GATATTCATCTAGGCGAAGGTTTTATGGTTA--GTACCTAAAAAAATACA 1865
                           iv  vivi     i v     iv i v  --ii   ---    ii   
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC---AAAAGCACA 611

  chr1_188679896_   1866 AAAAACAACC--AAAAATAGACAAGTACATCTCTATTAAGCT--AAAATT 1911
                          iv     vv--         i  i vviv  ii  i  iv --    i 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_188679896_   1912 TTTCTGTATAACAAAGGAAAATGTCAATAGAGTAAAGAGAAAACCTGTTG 1961
                            v  iv --       v v i    v i   i  i   v    iiiv 
  L1M4_orf2#LINE/    662 TTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_188679896_   1962 AATTGGATAAAACATTTGCAAACTATTAATCTAATGAGAGACTAGTGCTC 2011
                            v   v    i         ii  vv    i  i  i    v  iii 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_188679896_   2012 GGAATATAAAAGGTAGTTAAAGAATCCAACAGGAAAAAAACAAATCAC-- 2059
                         i       v  i v v ivv v  ii   i iv     i      v  --
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_188679896_   2060 -ATTAAAAAGTGGACAAACAACATAAATAGACATTTCTCAAAAAAAGAAA 2108
                         -   ?    i   i    vi iv i              v   i    v 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_188679896_   2109 TACAAACAACCAACAGGTGTATTTAAAAAT-----ACATTATTTTTATT 2152
                               iii    i i iii  vv   i  -----    i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (150 / 89)
Gap_init rate = 0.02 (21 / 888), avg. gap size = 2.48 (52 / 21)  


2552 27.40 2.10 1.77  chr1_188725789_188730803.rev     3620  4524 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188725789_   3620 TGGAAAAACATTCCATGCTCATGGATAAAAAGAAGTAATATTGTTAGAAT 3669
                               i i  i     i        vii    vv           ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188725789_   3670 GGCTACAGTACCCAAAGCAATTTACAGATTTAATGCTATTTCCATCAAAC 3719
                            v i v v      vii  i        i  i  v  ii i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_188725789_   3720 TACCAATGACATTCTGCATAGAACTGGAAAAAAACT-ATTTTAAAGTTCA 3768
                          v   iivi v  i viii    v v  v  i--  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_188725789_   3769 TATGGAACCAAATAGGAGCCTGAACAGCCAAGGAAACCCTAAGCAAGAAG 3818
                                viiv vi   v  v   i      iiv  i i i iv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_188725789_   3819 AACAAAGCTG-AGGACATCATGCTACCTTACTTCAAACTATTGTACAGGA 3867
                                i  -     -   ii  v  iv i      viv vv    iii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_188725789_   3868 CATACAGTAACCAAAACAGCATGGTACTGGTAC-----TTG-CATGTAGA 3911
                          -        i   i    ii         i i----- v -   i    
  L1M4_orf2#LINE/    248 C-TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_188725789_   3912 ACAATAGAACAGAATAGAGTGGCAAGAAATAAGGCCACACACCTACAACC 3961
                         v    i   i     v   v v v        iv   i   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_188725789_   3962 ATTTGATCTTTTGACAAAGCTGAGAAAGAAAAAGTAACAGGAAAAGGACT 4011
                          v     -   i     i v  vv  -  vv vvi  ii  i    i iv
  L1M4_orf2#LINE/    347 AATTGAT-TTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATA 394

  chr1_188725789_   4012 CACTATTCAATAAATGGTGTTGGGATAATTGGCTAGCCATATGCAGAAGA 4061
                         vv  v     i        i     i  i   v  ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_188725789_   4062 TTGAAACTGGACCCATTTCTTACACAATATATAAAAATCAACTCAAAATA 4111
                         v    ii       v vi  i    v     i      i          i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_188725789_   4112 GATTA-AGACTTAAATGTAA-AGCCAAAATTTATAAAAATTTTTGGAGGC 4159
                            i -    i         -   i    i -      v i  v i  iv
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTTAGAAGAA 543

  chr1_188725789_   4160 AATCTAGGCA-ATACCATTCTGGACATATGAGCAGGTAGAGATGCAACAG 4208
                           iv    ?i- v i -   vv   v -  i i---   ----    ii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCT-TGGGT---TAG----GCAATGG 584

  chr1_188725789_   4209 GTAAATGAAAAAGATGCAAAAAGCAATTGTAACAAAAGCAAAAATTGAAA 4258
                         v vvv ii v v  ii v       vvv i        v      v  v 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_188725789_   4259 AATGGGATCTGATTAAACTAAAGAGATTCTCCATAGCAAAAGAATAAATC 4308
                            v   ii v  i   v v  i iv  i viiivv    i  vvvv   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_188725789_   4309 AATAGAGTAAACAGACAACCTACAGAATGGGAGAATATATTTGCAAACTA 4358
                           v i   i  v        i              v           ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_188725789_   4359 TACATCTGACAAAGGTCTAATAGC----ATATATAAGGAACTTAAACAAA 4404
                           i      i  i  v  vi  v ----        i     ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_188725789_   4405 TTTACAAGAAAAACAC---CCACCCA-TTAAAAAGTGGGCAAAGGACATA 4450
                          iv i  v     v  ---iv     -  ?    i           iv i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_188725789_   4451 AAAAGACACTTATCAAAAGAATACATACATGTGTCCAACAAACATATGAA 4500
                           v     i  v  v      v i     vi  v    i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_188725789_   4501 AAAAAGCTCAACATCACTGATCTT 4524
                           i v           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (138 / 107)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.75 (35 / 20)  


2504 27.02 3.36 1.57  chr1_188910405_188912547      787  1678 (465)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_188910405_    787 TGGAAACACACCCAATGCTAATGGATGGGAAAAATCAGTATTTTGAAAAT 836
                               v i i  v   i v      v    i v i i    v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188910405_    837 GACCACACTGCCAAAAGCAATCTACAGACTCAATACAATTCCCAACAAAA 886
                          i v i   v  v   vii         i    ii    i  i v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_188910405_    887 TACCATCATCATTCTTCACAGAACTAGAAAAAACAATTCTAAAATTCGTA 936
                          v   v vv v  i  ii     v v  v  ivii  i         i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_188910405_    937 TGGAACCAAAAAAGAGCCAGAATAACCAAAGCAAGACTAAGCAAAAAGAA 986
                              viiv  ii  v        i     i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_188910405_    987 CAAAGCTGAAGGCATCGCATTACCCAACTTCAAATTGTACTGAAAGGCTA 1036
                              i  i   vv  i  i v     i      viv    iv  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_188910405_   1037 TGGTTACCAACACAGCATGATACTGGTATAAAAATAAGCATGTGGACCAG 1086
                         ii  v i   v    ii  i      i    ii   ii   i i  i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_188910405_   1087 TGGAACAGAATAGAGAATCCATAATTAAAGCCGAATAC-TTAACAGACAA 1135
                              i     v    i    v  v    v  --    -  v ii v   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCC--ATACATTTATGGTCAA 348

  chr1_188910405_   1136 CTGAACTTCATCAAAGCATTCCAAAAC-ATAAATTGGTGAAAGGACACCC 1184
                         i   vi   iv   i -i v    i  -  vv v   v     i i vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_188910405_   1185 TATTCAATAAACAGTGCTGGAAAAACTGGCAAGCCACATGAAGAAAAATG 1234
                          v     i   ii       i v      vv ?       v i  i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_188910405_   1235 AAACTGGATTAATTTATCTCAC--CTTATACAAAAAGTACATGCAAGGTA 1282
                           ii    ii--ii  i     -- v          v  - iv   ii i
  L1M4_orf2#LINE/    448 AAGTTGGACC--CCTACCTCACACCATATACAAAAATTA-ACTCAAAATG 494

  chr1_188910405_   1283 GATCAAAGACTTAAATCTAAGACCCGAAGTCATAAA-TTTATAGAAGACA 1331
                              ?    i     v     v ii  iii     -i iv       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_188910405_   1332 GCATTGGAAAAACTCTTCTGGACATTGACTTAGGTAAAGATTTCAT-GAC 1380
                         i   v  ?iv  v     vv   v   iv     i  v i    v -  i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_188910405_   1381 -TGAGACCTACAGAGCAAATGCAACAAAAACAAAAATAAATAAATCTGAC 1429
                         -   v   - - i    v v         iv       i      iv   
  L1M4_orf2#LINE/    595 ATGACACC-A-AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_188910405_   1430 TTAATTAAACTAAAAAGCTTCTGCACAGCAAAAG-TAGTAATCAGCAGAG 1478
                           v  i   v v    i   i  ii vv    i -i v  -   iv i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAG 691

  chr1_188910405_   1479 TAAACAGACAACCCACAGTGTGGGAGAAAATATTTTCAAACTATGCAACC 1528
                          i  v             vi               v    ii  ii v i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_188910405_   1529 AACATAGTTTGTTTGTTGTATCCAGAATCTACACGGAACTCAAATAAATC 1578
                         i i vi --- vi --            v  i vi      vv i  v  
  L1M4_orf2#LINE/    742 GATAAGG---GACT--TGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_188910405_   1579 AGCAAGAAAGAAACAA-TA--CCA-TCAAAAAGTGGGCAAAGAACATGAA 1624
                          ii  v   i i    -  --   - i?    i         i iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_188910405_   1625 TAGACATTTCTC---AAAAGAT----------CCA-----CACATGAAAA 1656
                                     --- i     ----------   -----          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_188910405_   1657 AATTCTGAACGTTACTAATCAT 1678
                         i  v  v   i i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.00 (44 / 22)  


2152 27.13 5.24 1.18  chr1_188913199_188916668     1767  2529 (941)    L1M4_orf2#LINE/L1        1   794 (114)  

  chr1_188913199_   1767 TGGAGATGTATTTCATGTTTGTAGAT-AAAAGAC--AATATT---AAGG- 1809
                             i vi   ii      ii i   -ii     --      ---   i-
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188913199_   1810 GCCAGTTCTTCCCAACTTGGTTTGTATATTCAATTCAATCCCAAGTAAAA 1859
                          v  i v  i     v   i i ii v      iv       v vi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_188913199_   1860 TTCCAAAAAGTTATTTTG-------TGA-AAACTGATTATAAG-TTCATT 1900
                          i   ivvivi v     -------   -  i     iv   i-     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_188913199_   1901 TGGAAAAGAAAAAGACTTAGAATGGCCAACACAATATTGAAGAAGAAGAA 1950
                               v v  ii   ii     i     v     v     i        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_188913199_   1951 CGAAGTTGAAAGACTTAAACTACCGAACTTGAAGTCTTATTTTAAAAATG 2000
                          i      i i    i v   v  v  i  v  iv    i vi   iv i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_188913199_   2001 CAGTAATTAAGACAATCTGCTATGAGTGAAAGAATAGACA----AATCAG 2046
                                i      i v  v  ivi iiv   i       ----i    i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_188913199_   2047 TGGAACAAAAGAGAGAGCCTAGAATTATAACCACATATATATAGCCAACT 2096
                              i i  vv     i i    v  v v   i i  v   i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_188913199_   2097 GA-------CAAAGGTGTAAATCCAATCCAATTGAGAAATAATACTCATT 2139
                           -------   i    iv  vv v  i    v i    v    v  v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_188913199_   2140 TCAACAAATGATGATGAAACAATTGGACATCCATGTGCAAAAAAGTTAAT 2189
                                   i  v  ii    i    i ?   ii       i i v  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_188913199_   2190 GTAGAAACTAACCT-ACAGTTTTCATA---AAAAA--AATTCATAATTGA 2233
                         v i  vv iv    -   ----i    ---     --  i   v   v  
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACA----CCATATACAAAAATTAACTCAAAATGGA 496

  chr1_188913199_   2234 ACGCAGACCTAAATGTAAGTAAAATGCAAAACTATGAAACTCTTAGAAAA 2283
                         v i?               -- iv --        i            i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAG--AGCT--AAAACTATAAAACTCTTAGAAGA 542

  chr1_188913199_   2284 CAACAAAGA---AAATGTAAGTGACCATAGGTTTGGCTATAAGTTTTTAG 2330
                         v    v  i---    v vv      v i    v   v  iiv  i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_188913199_   2331 ATACAACACTAAAATCATAACCTATGAAAGTAAAACATGG-TAAGTCAGG 2379
                            ii    i    v  i  v v ii    -    v  i -   i ii i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGA 641

  chr1_188913199_   2380 CATTCTTAAAATGAAAATCTTCTGCTCTGTGAAAGACACTGGTAAGGGAC 2429
                          v iv i     v    v   i  iv  vii  i      ivi   ii v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_188913199_   2430 TGAAAAGACCAGTCA--GTCTTGGGGAAAATATTTGCACA-CACATATCT 2476
                                  v vi  -- vv v  i             v -  i      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_188913199_   2477 ATTAAAAAACTTATATACAGAATATACACAGAACCCTAAAAATTCAATAA 2526
                         iv   iii    i   v         i v     i  v v  i       
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_188913199_   2527 CAA 2529
                         i  
  L1M4_orf2#LINE/    792 TAA 794

Transitions / transversions = 1.38 (119 / 86)
Gap_init rate = 0.03 (20 / 794), avg. gap size = 2.45 (49 / 20)  

 549 19.69 0.00 0.00  chr1_188913199_188916668     2851  2977 (493)    L1M4_orf2#LINE/L1      782   908 (0)  

  chr1_188913199_   2851 AATTCAATAACAAGAAAACAAACAACATTATTAAAAATTGGGCTAAAGAC 2900
                           i       i  i  i     i   viv   ?    v     v  i  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_188913199_   2901 CAGAACAGACACTTCACCAAAGAAGATATGCAGATGTCAAATAAGCATAT 2950
                         iv   i     i   v             i  i   v v        i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_188913199_   2951 AAAAAGATGCTCAACCTCATTTGTCAC 2977
                         i              v   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (15 / 9)
Gap_init rate = 0.00 (0 / 127), avg. gap size = 0.00 (0 / 0)  


2817 24.57 3.83 1.36  chr1_188916786_188919298.rev      723  1532 (981)    L1M4_orf2#LINE/L1        1   830 (78)  

  chr1_188916786_    723 TGGAAAGATATTTTATGTACATGCATTAGAAGA----AT---GTTAAAAT 765
                                    iii    v    v   i     ----  ---     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_188916786_    766 GTCTGTA-TACCCAAAGCGATCCACAGATTCATTGCAATGCTTACCAAAA 814
                          v vi  - v      vi    i         vi     v i  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_188916786_    815 TTCCTA-TGCCATTCTTTAACAGAAGT--AAAAGA-AACCCTAAAATT-A 859
                          i  vi-    -  i   i-     i -- v   v-i i         - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_188916786_    860 TATGAAACCACACAAGACCCCAAAGAGCCACAGCAATCTTGAGAAAAGTT 909
                             i  vii  vii     vi  v     v i         -     vv
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAA 197

  chr1_188916786_    910 TAA--AAGCTTAAGGCATC-CTTTTTCCAATTTTTAACTATGTTACAAAA 956
                         v  --   i vi   vv  - vi  i       iv  viv ii      i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_188916786_    957 CTATCATAATTAAAGTGGTATGATACTGGCATAAAAATGAATACATAGGG 1006
                            ivi    i  iiii  i  i           ii  ii i i    iv
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_188916786_   1007 CAATGATACAGAATTAAGAGCCCGGAAATAAACCCATGTATATGTATAGT 1056
                              iv i      i    i  i             -- i  v   i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT--ACATTTATGGT 345

  chr1_188916786_   1057 CAACTGATTTTTGACAAAAATACCTAGAAGATACAATGG--AAAAATCAG 1104
                            i       i     iii i  v   vv  v      --   i vi  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_188916786_   1105 TTTCTTCAATAAATGGTGCTGTAAATAGTGGATATTCACATGGAAGTGAA 1154
                          i i     i           vi vv v      ?i      v  iv   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_188916786_   1155 TGGAGTTAGACCTTT--TTTACACTACATATAAAAACTAACTCAAAATGA 1202
                           i    i    ii --i i    i i   i     i            i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_188916786_   1203 ATTAAAGATGTAAACAT--GACCTAGAATTGTAAAACTTTTATAAGAAAG 1250
                           i ?   iv    ii --  v   i  i i       i   v      i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_188916786_   1251 CA--GGGAAAAACTTCCTTGACATTGGTTTTGGCAATGATTTTTTAGGTA 1298
                           --  ?iv   ii i v    v    v  v       i   i    i  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_188916786_   1299 TGACACCAAAAACACAGGCAA--AAAGACAAAAATAAATAAATAAGCAGC 1346
                                    i    i    --     -       i      vi ----
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGG---- 640

  chr1_188916786_   1347 ACTATATTAAA-CTAAAAACTTTCTGCACAGCAAAAGAAACAATCAAAA- 1394
                            vi  i   -i          -  ii vv    i  v  v     i -
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_188916786_   1395 --TGAAAAGATAGCCTATAGAATGGGAGAACATATTTGTAAACTATATAT 1442
                         --        i i  i i            v       i   ii      
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_188916786_   1443 CTGATAGGGAATTAACATCCATAATATACAAGAAATTCATATAACTCAAT 1492
                               i  i i vii     v      i  ii  i  v  i        
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_188916786_   1493 AGCAAAAA-ACAAGTAATCCAACCAAAAACTGGTTAAATGA 1532
                          ii     -    i   i    ii?    v   vi   v  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 2.15 (133 / 62)
Gap_init rate = 0.03 (24 / 830), avg. gap size = 1.75 (42 / 24)  

 298 22.22 4.17 0.00  chr1_188916786_188919298.rev     1951  2022 (491)    L1M4_orf2#LINE/L1      834   908 (0)  

  chr1_188916786_   1951 GAGTAGCTCTTTCCTCAAAAA---CATAAAAATAGCCAACAGGTATATGG 1997
                           i   viv    ii    i ---i   v    i     i i i i   i
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_188916786_   1998 AAAGGTGCTCAACATCACTGATTAT 2022
                             i            ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.33 (13 / 3)
Gap_init rate = 0.01 (1 / 75), avg. gap size = 3.00 (3 / 1)  


 444 28.66 0.64 0.64  chr1_188986987_188988845        1   157 (1702)    L1M4_orf2#LINE/L1      613   769 (139)  

  chr1_188986987_      1 GCAACAAAAGCAAAAATACACAAATGGAAATACATCAAACTAAAAAGCTT 50
                                   v       v i    v i v v       v v    i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_188986987_     51 CTGCATAGCAAAGGAAACAATCAACAGAATGAAGAGATGACATATAGAAC 100
                         i  iiivv       v  v     v i i    i   ii  vi i    i
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_188986987_    101 AGGTGAACATATTTGCAGACTATGCATTTGAGTCAGGG-TTAAGATCTCA 149
                         i  v   v         i ii  ii  i   - v    -i viv   ivi
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGA-TAAGGGACTTGTATCCAG 761

  chr1_188986987_    150 AATATATA 157
                                 
  L1M4_orf2#LINE/    762 AATATATA 769

Transitions / transversions = 1.37 (26 / 19)
Gap_init rate = 0.01 (2 / 157), avg. gap size = 1.00 (2 / 2)  

 441 23.26 2.91 12.21  chr1_188986987_188988845      320   491 (1368)  C L1M4_orf2#LINE/L1   (616)   292   137  

C chr1_188986987_    491 TCCTAAAATTTGTGTAAAATCACAAAAGATCTGTAATAGCCAAAGCAATC 442
                                   ii i ii  vii   ii  i iiv          i     
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

C chr1_188986987_    441 CTGAGCAAAAAGAGCAAAAATGAATCAATTTCGCTCGAAGATAAAGGCAT 392
                         i   iv  i    i    iv  --------------  i  i------- 
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTG--------------GAGGAC-------T 215

C chr1_188986987_    391 CAGAATACCTGACTTCAAAATGTATGACAAAGC-ATAGTAACTAAAACAG 343
                           v v v  ii i       iv  iv       - i     ii  i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

C chr1_188986987_    342 CGTGGTACTGGCATAA----AAACATA 320
                         i               ---- i     
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATA 292

Transitions / transversions = 3.44 (31 / 9)
Gap_init rate = 0.03 (4 / 156), avg. gap size = 6.50 (26 / 4)  

3478 20.73 4.47 1.26  chr1_188986987_188988845      494  1366 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_188986987_    494 ATATGCCCACGTTTATAGATCAGAAGAGATAAAATTGTTAAGATAGCAAT 543
                             -    i   i  i   ii     vv   v           i     
  L1M4_orf2#LINE/      8 ATAT-CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_188986987_    544 ATTTTTCAACTTAATCCACAGATTCAATGTAATCCCTATCGAAATCCCAG 593
                          i iii   v  i   i          i i          i         
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_188986987_    594 CTGGCTTTTT-AAGGAAATTGATAAGCTGATTGTAAATTTGATGTGGAAA 642
                            v      -ivi        i        iv    v  v  i      
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_188986987_    643 TTCAGGGGACTCAAAAAGGCCAGAACATTATTGAAAAAGAA---CCAAGT 689
                          v  i     i  i  vi    i    v v           --- v    
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_188986987_    690 TGGAACACTCATATGTCCTGATTTCAAAACTTACTACAAAACTACAGTAA 739
                             iv     i iv   ii                    i         
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_188986987_    740 TCAAGACACTGAGGTACTTGCATAAGGATAGATACAGCAATAAAAGGAAT 789
                                 v  v      v             i i vvi  v  v     
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_188986987_    790 AGGATTTATAGCCTAGAAATAAAATCAT---TGTAT--TCAGTTGATTTT 834
                           i   v v  i i         vi   --- v   --   i        
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_188986987_    835 CAACAAAAGTGCCAGGATAATATAATGGATAAAAAATAGCCATTT-AATA 883
                          i    ii      i  iv  vi     iv   i     i v   -  i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_188986987_    884 AATGGTGCTGAGACAACAGACTAGCCATAGGCAAAATAATATAATTGAAC 933
                                   i      v iv  ?   i v      v   iv i   i  
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_188986987_    934 TCCTAGCTTAAACCACACACATAAAAATGCCTCGTAATGGATCATAGAGC 983
                         i    v  i v    i i   -    v iv   iv         ?   v 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACA-AAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_188986987_    984 TAAATA----AACTAAAATTATGAAAACT-TTAGGAGAAAATACTATATA 1028
                              i---- i      i   -      -    i      i -----  
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA-----TA 549

  chr1_188986987_   1029 AGAGCAAATATTTGTGAC-TTGCACAAGACAGGGGTTTCTTATGCATGAC 1077
                         i ? i    v  i     -   viiv  i  iv         vii     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_188986987_   1078 ACCAAAA-CACAAGTGACAACA----AATTACA-AAATTGGACTTCAGCA 1121
                                -      ii    v ----  v  v -             v  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_188986987_   1122 AAATGTAAAACTTCTGTG--TCATAATGATTCAATCAAGAAGATG----- 1164
                             vv       i    --   -  v  iv v        ii  -----
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_188986987_   1165 ------TACAGAATGAGAAGTAATCTTTGCAGATTATCCATTTTATAATG 1208
                         ------i        i  iiv   v      i  i  vi  i v    v 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_188986987_   1209 GAATTTTATCCACAATATACAAAAACTTCTTATAACTAATTAATAAAATG 1258
                           v  v      v      i   i vi     i    v v        v 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_188986987_   1259 ATAAATAGCCTAATGTTTAAAA--GGACAAAGGATCTGAACATAAGTTTC 1306
                          i     i  i   -- ?    --  i        i    i v vi    
  L1M4_orf2#LINE/    799 ACAAATAACCCAAT--TWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_188986987_   1307 --CAAAGAAGATATACAAATTACCAAGAAGCATATGAAAAGATACACAGC 1354
                         --                  vi    v     i          i v  i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_188986987_   1355 ATCATTAGCCAT 1366
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (104 / 73)
Gap_init rate = 0.02 (21 / 901), avg. gap size = 2.38 (50 / 21)  


2726 22.35 10.58 2.62  chr1_189083453_189086565     1781  2621 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_189083453_   1781 TGGAAAGCCATTTCATGTTCATGGATTAGAAGACTTAATATTTGTAAAAA 1830
                                vi  ii              i              vv   i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_189083453_   1831 ATTTATACTATCTGAAGTAATCTACAGGTTCAATGAAATCTCTATCAAAA 1880
                         iviv     vi ii  v i        i     i v    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_189083453_   1881 TCCCAA-TGCCATTATTTTGCAGGAAT-AAAAAACAAATCATTAAATTCA 1928
                              i-    -  -        i   -i v  i vi   v v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_189083453_   1929 TATGGAATTCCAAAGGACCCTGAATAACCAAAACAATCTTGAGAAACAAA 1978
                                v v   i      v     i               i   v  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_189083453_   1979 AGAAAAGCTTGAGGCCTCATACTTCCTGATTTTAAAACATATTATAAAAC 2028
                          iv    i v    v    i      ii    i     v  i  i   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_189083453_   2029 TATAGTAATCAAAACAGTATGCTACTGATATAAAGACAGGTATATAGACC 2078
                           i         i     i  v     ii    i  i  ii       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_189083453_   2079 CACAAAACCAAATAGAGATACTAGAAATAAACTGATTCAT--ATGGTCGA 2126
                         v iii  ivi   v    vv i          iv  v   --      i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_189083453_   2127 ATGATCTCCAACAAAGGCGAAAAGGCTACACAAAAGCTATGATGGGGGAA 2176
                         v    i i i    i  i vv   i i iv   ---------     i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAA---------TGGGGAAA 389

  chr1_189083453_   2177 AAAAGGGGTGCGGCCTCTTTAACAAATTGTGTAGAGAAAACCAGATATCC 2226
                         i  -------ii i  i  i       v   iv i  v   ii    ?  
  L1M4_orf2#LINE/    390 GAA-------TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_189083453_   2227 ACATGCAAAAGAATGAAGTTGGACCCTAACCTCACACCATATACAAAAGT 2276
                                                   iv                    i 
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_189083453_   2277 GAACTCAAAATACATTAAAGACCTAAACACAAGACCTGAAATTATAAAAC 2326
                         v          iv  i ?         iii    v  i   i        
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_189083453_   2327 TCTAAAGAGAAAACGGAATAGATAAAAA-CTTCAAGACTTTGTATTTGGC 2375
                            v ii       ---    i?iv   -    iv   i   vi  v   
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAAC---ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_189083453_   2376 AAT---TTCTTGTATATG---------------GCAAGAAAAGCAAAAAT 2407
                            ---     iv     ---------------    v     v      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_189083453_   2408 A--CAAGTGGG--TATATCAAAA----AATCTTCTGCTCAGCAAAAGAAA 2449
                          --i  i v  -- vi       ----  v   i  iv vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_189083453_   2450 C----AACAGAGTGAAAAGGCAACTTTAAAAATGGAAGAAA--------- 2486
                          ----  v i         i    iivv i     i     ---------
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_189083453_   2487 ---------------------------------------------TTCCT 2491
                         ---------------------------------------------i  i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_189083453_   2492 ACAACTCAACAGCAACAGAAAAAAAAATCTAATTTAAAACTGGGCAAAGA 2541
                                  i ii  v ii v   v  i i    ?    v         i
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_189083453_   2542 ACAAAAATAGACATTTCTCCCAAAATAAAAATACAAAGGGCAAACAAGCA 2591
                          ivvi               v  i - i v       v   v  i     
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCA 878

  chr1_189083453_   2592 AATGAAAAGATGCTCAACCTCCCTTACATT 2621
                         v                 v  v????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (113 / 71)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 6.53 (111 / 17)  


1495 21.60 2.47 14.85  chr1_189091453_189093327      500  1388 (487)    L1M4_orf2#LINE/L1      130   908 (0)  

  chr1_189091453_    500 AAACT-ATTCTAGCATTCATATA-AAAT-CAAACAAGACCCCAAATAGCC 546
                           i  -  i   iv        i-    -   i--i     vi       
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAG--GGACCCAGAATAGCC 177

  chr1_189091453_    547 AAGGCAATTTTAAGTAAAAAGAATAAAGCCAGAGGCATCACATTATCTAA 596
                           ii    i  i iv  i     i    iii    vv     i vi i  
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_189091453_    597 CTTCAAACTATACTACAAGGGTACACTAACCACAGCAGCATGGCACCGGT 646
                         i      viv        i v    v   i  vii   ii   i  i  i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_189091453_    647 ACAAAAATAGA----TAGAC--ACGGAACAGAATACAGACCCCTGAAAAA 690
                          i  ii     ----    i-- i    i     vv   vi  -------
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC------- 320

  chr1_189091453_    691 AAAAAAAAAAGACACACAT--ACAACCAACTGATCTTTAACAAAGTTGAC 738
                         - i   v   vv  i    -- iiii   i    i  ii    i v  v 
  L1M4_orf2#LINE/    321 -AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_189091453_    739 AAAAATAAACAACACCATTTAACAAAGTTGACAAAAATAACACCATTCAA 788
                           i ----------     i  iiii --- -  i    ii- iv     
  L1M4_orf2#LINE/    370 AAGA----------CCATTCAATGGGG---A-AAGAATAGT-CTTTTCAA 404

  chr1_189091453_    789 CAAATGGTACTGGGA-AACTGGCTAACCGTATGAAGGAGAGTGAGTGAAA 837
                                 i      -      v  ?  ii   v ii   i   ---- i
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA----AG 450

  chr1_189091453_    838 CTGGACCCATAGCTCTCACCTCATACAAAAACGAACCCTAGACAGATTAA 887
                         i       v  v   v    vi         iv   i v i ii   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_189091453_    888 AGAATTAAATATAAGACCTCAAACTATAATGCCCT-AGAAGAAAATCTAG 936
                            vi     i     v  v         vi i  -         iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_189091453_    937 GGAATACTCTTCCAGATATTGGCCTAGGCAAATAATTT-------ATGAC 979
                          ?ivv v     vv  iv    vi       - ii   -------     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGAC 599

  chr1_189091453_    980 CAACTCCTCAAAAGCAAATGTAACAAAAACGAACAAAAAAATTGGAATCT 1029
                         --  ----        v v i       i------       v iv ---
  L1M4_orf2#LINE/    600 --AC----CAAAAGCACAAGCAACAAAAG------AAAAAATAGATA--- 634

  chr1_189091453_   1030 AATTAAGCAGGAACTTCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGG 1079
                             ------ i     ---v   -------  i ---------  v --
  L1M4_orf2#LINE/    635 AATT------GGACTTC---ATCA-------AAAT---------TAAA-- 657

  chr1_189091453_   1080 CACATGCCACCACGCCCAACTCATTTTTTTTCTTTTAGTAGAATATATTA 1129
                         -----------------    ----   v v   ----------------
  L1M4_orf2#LINE/    658 -----------------AACT----TTTGTGCTT---------------- 670

  chr1_189091453_   1130 CCAAAAGAAACAATCAACAGAGTAAACGGACAACCTACAGAATGGGAGAA 1179
                         -    i  v  v     v i   i  vi       i              
  L1M4_orf2#LINE/    671 -CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_189091453_   1180 AATATTTGCAAACTATGTATCTGACAAAGGACTAATGTCCAGAATTTATA 1229
                                     ii  i       i  i     vi i        v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_189091453_   1230 AAG--TTCTTAAAGAAGTTAACAAGAAAATAAAAGAAAACACAAATTATC 1277
                            --i     v -- v i  i  v    ----   -----     v i 
  L1M4_orf2#LINE/    770 AAGAACTCTTACA--ACTCAATAATAAAA----AGA-----CAAATAACC 808

  chr1_189091453_   1278 CCGTTTAAAATAATCCCATCAAAGGACATGAACAGTAACTTCTCAAAAGA 1327
                          vi  ?    --  v--iv       iv    i  vv i     v     
  L1M4_orf2#LINE/    809 CAATTWAAAA--ATG--GGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_189091453_   1328 AGGCATACAAGCAGCCAACAAACATACAAAAACACAAATGCAAATCAAAA 1377
                           ii      iii     i  i  i ii    ----i    ---    v 
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAA----GATGC---TCAACA 897

  chr1_189091453_   1378 CCACAATGAGA 1388
                         i  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.85 (122 / 66)
Gap_init rate = 0.05 (36 / 779), avg. gap size = 4.28 (154 / 36)  


2851 26.06 0.98 2.39  chr1_189127420_189134275     5443  6363 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_189127420_   5443 TGGGAAAACTTTTCATGATGATGTATCAAAAGAGCTAATATTGTTAAAAT 5492
                            i  i iv ii    v v   v  iii    vi            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_189127420_   5493 GACCATACTAAC-AAAGCAATCTACAGATTCAATTGAATCTCTATCTAAA 5541
                          i v     vv -   vii              ivv    i     v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_189127420_   5542 TACCAA-TGTCACTTCTCACAGCAATAGAAAAAGCAATCCTAAAATTGAT 5590
                          v   i-  i -i  i ii   v   v  v  ivii           v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_189127420_   5591 ACAGAATCAAAAAAGAACCCAAATAGCCAAAGAAATCTTGCACAAAGACA 5640
                          ii   viiv  ii  v  vi          iv       v v  ii v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_189127420_   5641 ACAAGGGTGGAGACATCATACTACCCAACTTCAAAATTTATTACAAGACT 5690
                             i v     ivv   i   v     i       i   i     ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_189127420_   5691 AGAACAACCAAAACAATATAGTAAAGGGAAAAAAAATGCACAAAAAAACA 5740
                          v ii  i   i   i i i   vv  -------------  v  ii i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGG-------------CATAAGGATA 286

  chr1_189127420_   5741 GACACAAAGACCAATGGAACAGGATAGAAAGCCCATCAAAAAACCCACAC 5790
                             i v   i        i  i  v  i  i   vv  v       i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_189127420_   5791 ACTTAATTACCAACTCATTTTCAAGAAAACTGCCAAGAACATACACTGAG 5840
                          i   - vii   i v      i v  iiv        v   v  v  i 
  L1M4_orf2#LINE/    337 ATTTA-TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_189127420_   5841 GAAAGAATATCCTCTTCAATAAATGATGTTGGAAAAACTGGATATT-ATA 5889
                                  vi  i     i     i  i   i v         ?i- i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_189127420_   5890 TGCAGAAGAATGGAACTAGACTTCTATATCTCACCATATACAAAAATCAA 5939
                             i       i ii i   ii   iv  v                i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_189127420_   5940 CTCAAAATGGATTAAAGACTTAAACATAAGACCTGGTATTATAAAACGAC 5989
                                     i ?    i    ii     v  iiv i        vvi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_189127420_   5990 TAGAAGAAAACATAGGTGATACA-CTACAGGACTTTGGTCTATGCAAAGA 6038
                                         ? -  v -  v iv   i    vi  v    v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_189127420_   6039 TTTTTATAGCTA--ACACTTCAAAAGCAAAGGCAACAAAAGCAAAAATAG 6086
                            i -   v  --    --        v i          v        
  L1M4_orf2#LINE/    585 TTTCT-TAGATATGACAC--CAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_189127420_   6087 ACAAATGGGACTATATTAAA-CTAAAAACTTTCTGCACAACAGAGCAAAC 6135
                          i    v     vi  i   -i          -  ii vv  i  v v  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACAC 680

  chr1_189127420_   6136 AATCAACAAAGTAAAGAGACGACTTGTTGAATGGGAGATGACATTTACAA 6185
                         v     v     i  i    i  iiiiv          vi i    i   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_189127420_   6186 AATATTCATCTGGAAAGGGACTAATATCCA-AATATACTTGAAATTCAAA 6234
                          vi  vi     iv        vi      -      ivvii  i  vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_189127420_   6235 CAATGCAAAGAAATAGAAACAAATAATCTTATT-AAAAAGAAGCAAAGGA 6283
                            iv   vi v v i i        i iv   -     vii        
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_189127420_   6284 CATGAACAGACATTTCTTAAAAGAAGACATACAAATGGCCTGCAGGTATT 6333
                         iv    i          iv        i            vii i i iv
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_189127420_   6334 TAAGATAAAACATTCACCATCACTAATCAT 6363
                          --  v  i iii   v     ????????
  L1M4_orf2#LINE/    881 T--GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.94 (31 / 16)  


2744 26.35 4.81 0.80  chr1_189167252_189169825.rev     1211  2083 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_189167252_   1211 TGAAAAGATATTCCATGTTCATGGATTGGAATAATCAACATTGTTAAAAT 1260
                           i        i                   v v i  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_189167252_   1261 GTTCATAGTACCCAAAGCAATCTACAGATTCAGTGCAATCCCTATCAAAA 1310
                          viv   v v      vii             ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_189167252_   1311 TACCAATGACATTCATCATAGAAATAGAAAAA--AATCATAAAATTTATA 1358
                          v   iivi v  iv iii      v  v  i--i   v       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_189167252_   1359 TGGAAACACAAAAGATCCAAAATAGCTACAGTCATCCTGAGCAAAAAGCA 1408
                               ii   ii  i   i      i v iiv   i   iv  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_189167252_   1409 CA---TTAC----CTC---CTGTTGTAAT--CAAATTATACTGCAGCATT 1446
                           ---  iv----   ---  - ivi   --    viv    i  ivii 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACT-TCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_189167252_   1447 ATAATAACCGAAGCAGCATAAT-TT---ATAAAAACAGACACGAAGTCTA 1492
                          i i   i i ii   ii ii -i ---    ii i     iiv  vii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_189167252_   1493 GTGGAAAAGAGTAGAGAATCCACAAATAAATCCAGACATCTACAGAGAAC 1542
                         i     v   i v    i    v       i   v    i  ii vv  -
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA- 348

  chr1_189167252_   1543 TCTT--TTTTTGATAAAGGTGCTAAGAACACACATCGGTGAAAGGATAGT 1590
                         --  --    i  i  i     i    v  iv  vi  v     i     
  L1M4_orf2#LINE/    349 --TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_189167252_   1591 CTCTTCAATAAGTGATGCTGGGAAAACTGGATATCCATATGCAGAGAAAA 1640
                           i     i  i  i        v         ?   i     i ii  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_189167252_   1641 AAAACTAGATCTCTATCTCTTGCTGTATATAAAAATCAAATCAAAATAGA 1690
                         i  ii i  i i   i   vii ii    i      i  v       i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_189167252_   1691 TTAAATATTTAAATCTAAGACCTTAAACTA-----------AAGGAAAAC 1729
                          i ? v ii     v     v  v      -----------i i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_189167252_   1730 ATTGGGGAAACTCTCAAAGACATTGATCTGGGTAAAGATTTCTTGAGTAA 1779
                           v  ? v  v   iviv   v   ivi i  i  v i      iii  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA- 595

  chr1_189167252_   1780 TGCC-TTAAAAGCACAGGAAACTAAAGCAAAAATGGACAA-TAGGA--TC 1825
                           v -ii         i v   v    v      i  i  - v   --  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_189167252_   1826 ATAACAATCTGAAAAGCCTCTGCACAGCAAAGGAAAG----AACAAAGTG 1871
                           v v   i--    i i i  ii vv       v v----  v      
  L1M4_orf2#LINE/    646 ATCAAAATT--AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_189167252_   1872 AAGACACAAACCACAGAATGGTAGAAAATATTTGCAAACTACCCATCAGA 1921
                           i v    v           v                ii ivi   v  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_189167252_   1922 CAAGAGA-TTAAAACCAAAATGTACAAGGAGTTCAAACAACTCAATAGAA 1970
                         i   i  -  iv v   i   i  i  i  ii  vv           iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_189167252_   1971 AAAGAACAACTAATCAAATTTTCAAATGGGCAAAAGATCTGAATAGACAT 2020
                            ii    v   i v    ?vv           i   i           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_189167252_   2021 TTCTCAAAAGAAGACATACAAATGAGCAGCA-GTATATAAAAA-ATGCTC 2068
                              v        i         iv  ii - i i  i    -      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_189167252_   2069 AACATCATTAATCAT 2083
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (147 / 79)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.45 (49 / 20)  


3257 26.43 0.66 0.66  chr1_189200872_189207149     4878  5785 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_189200872_   4878 TGGAATTACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              vv i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_189200872_   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_189200872_   4978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_189200872_   5026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_189200872_   5076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5125
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_189200872_   5126 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_189200872_   5176 AATGGAACAGAAC--AGAGCCCTCAGGAATAACGCCGCATACAT--ACAA 5221
                                i    i--    i  --  i     -i  -       -- iii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAA-ACC-CATACATTTATGG 344

  chr1_189200872_   5222 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5271
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_189200872_   5272 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5321
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_189200872_   5322 CTGAAACTGGATCCTTTCCTTACACCTTATACAAAAATCAATTCAAGTTG 5371
                         v    ii    i  i v   i     v           i  i    iv  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_189200872_   5372 GATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5421
                            i ?   ii    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_189200872_   5422 ACCTAGGCATTACAATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCC 5471
                           v    ?i v vvv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_189200872_   5472 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5521
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_189200872_   5522 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5571
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_189200872_   5572 ACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5621
                          v  i     i   iv            v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_189200872_   5622 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5671
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_189200872_   5672 AAAAACAAATAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5721
                            i           v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_189200872_   5722 TCTCAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTCA 5771
                             v        i  vi viii     v  ii         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_189200872_   5772 TCATCACTGGCCAT 5785
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


2626 26.57 0.53 0.53  chr1_189238053_189239797      504  1252 (493)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr1_189238053_    504 AAAAGAGCCCGCATAGCCAAGACAATCCTCGGCAAGAAGAACAAAGCTGG 553
                           ii  v  v v        i      i viiv             i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_189238053_    554 AGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCA 603
                            vv       v  ii i      viv        i          i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_189238053_    604 AAACAGCATGGTACCTGTACCAAAACAGATGTATAGACCAATGGAACAAA 653
                          i    ii      iv i iv ii i   ii      i        i i 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_189238053_    654 ACAAAGGCCTCAGAAATAACACCACACATCTACAACCACCTGATCTTTGA 703
                          ivi  ivii         vv   i    i  iiii  vi    i  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_189238053_    704 CAAACCTGACAAAAACGAGCAATGGGGAAAGGATTCTCTATTTAATAAAT 753
                            ivv  v   i v ivv            i  vv   v  i  i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_189238053_    754 GGTGTTGGAAAAACCGGCTAGCCATATGCAGAAAACTGAAACTGGGCCCA 803
                             i   i v   i  v  ?   i     i  i v    ii   i   v
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_189238053_    804 TTCCTTACACCTTATACAAAAATCAACTGAAGA--GATCAAAGACTTAAA 851
                          v   i     v           i    v  i --     ?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_189238053_    852 CGTAAGACCTAGTACCATAAAAATCCTAGAAGAAAACCTGGGCA-ATACC 900
                         i      v   iv  i      v  i           v i  ?i- v i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_189238053_    901 ATTCAGGACATAGGCATGGGCAAAGACTTCACATCTAAAACACCAAAATC 950
                         -   iv   v v  vv i     v ii   vi vv  vi         v 
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_189238053_    951 AATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAATTAAACTAAAGA 1000
                          vvi          vv     v  i    vi  ii v  i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_189238053_   1001 GTTTCTGCATATCAAAAGAAACTATCAGCAGAGTGAACAGGCAACCTACA 1050
                         ii  i  iiiv     i  v       iv i      v  i     i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_189238053_   1051 GATTGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAGGGCTAATATC 1100
                           v           v       vii ivi      i  i  i  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_189238053_   1101 CAGAATCTACAAAGAACTTAAACAAATTTACAAGAA-AAAAAAACAAACA 1149
                               v  i        ivv    v ---   v  -     i     i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACT---CAATAATAAAAAGACAAATA 805

  chr1_189238053_   1150 ACCCCATCAAAAAGTGGGTAAAGGATATGAACAGACACTTCTCAAAAGAA 1199
                             v  i?    i    i       v    i     i     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_189238053_   1200 GACATTTATGCAGCCAATAGACATATGAAAAAATGCTCATCATCACTGGT 1249
                           i  vi viii       ii  i       i       v     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_189238053_   1250 CAT 1252
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.50 (117 / 78)
Gap_init rate = 0.01 (5 / 749), avg. gap size = 1.60 (8 / 5)  


3331 26.62 0.44 0.55  chr1_189363997_189369673.rev     4278  5186 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_189363997_   4278 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCACTAAAAT 4327
                              ii i  i     i      i v      v i     iii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_189363997_   4328 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 4377
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_189363997_   4378 TTCCACTGGCTTTCTTCACAGAA-TTGGAAAAAAACTCCTTTAAATTTCA 4426
                          i   viv  i  i  ii     -   iv  ivviv    --   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chr1_189363997_   4427 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCCAAAAG 4476
                                viiv  ii  v  viv        i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_189363997_   4477 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTTTACTACAAGGC 4526
                                i      vv       v  ii i      vi         i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_189363997_   4527 CACAGTAATCAAAACAGCATAGTACTGGTACCAAAACAGAGATATAGAGC 4576
                         i           i    ii i       i iv ii i   v       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_189363997_   4577 AATGGAAGAGAACAGAGGCCTCATAAATAACACCATACATCTATAACCAT 4626
                                v    iv   ivii  v      vv        i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_189363997_   4627 CTGAGCTTTGACAAACCTTACAAAAACAAGCAATGGGGGAAGGATTCCCT 4676
                         i   vi  i     ivv vv   i v  vv        i   i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_189363997_   4677 ATTTAATAAATGGTGCTGGGAAAACTGGGTAGCCATACATAGAAAGCTGA 4726
                         v  i  i              v      i  ?   i iii i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_189363997_   4727 AACTGGATCCCTTGTTTACACCATATACAAAAATTAACTCAAGATGGATT 4776
                          ii    i    vvi i                         i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_189363997_   4777 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACCTTAGAAGAAAACCC 4826
                          ?    i           v       i      vi             vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_189363997_   4827 TGGCAATACCCTTCAGGACAT--AGTCATGGGCAAAGACTTCATGACTAA 4874
                         v  ?ivv vi    iv   v --i  i --     v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATAT 596

  chr1_189363997_   4875 AACACCAAAAGCAACGGCAACAAAAGTCAAAATAGACAAATGGGATCTAA 4924
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_189363997_   4925 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAGCAGAGTGAAC 4974
                          i   v v  i i   i  ii vv    i  v       iv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_189363997_   4975 AGTCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 5024
                           v     i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_189363997_   5025 AGGGGCTAATATCCAGAATCTACGAAGAACTTAAACAAATTTACAAGAAA 5074
                         -   i  vi          v  ii       ivv    v iv i  v   
  L1M4_orf2#LINE/    747 -GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_189363997_   5075 AA-ACAAACAACCCCACCTAAAAGTGGGCAAAGGATATGAACAGACACTT 5123
                           -     i     v ii?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_189363997_   5124 CTCAAAAGAAGACATTTATGCAGCTGACAGACATATTAAAAAATGCTCAT 5173
                            v        i  vi viii  ii i ii  i  v    i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_189363997_   5174 CATCACTGGTCAT 5186
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3279 23.05 4.93 0.80  chr1_189459051_189461698.rev     1286  2157 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_189459051_   1286 TGGAACACCATTCCATGTTCTTGGATAGGAAGACTTAATACCATCAACAT 1335
                              vivi  i        v     v             iii i  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_189459051_   1336 GTCAGTTCTCCCTAACTTTGATCCATAAATTCAGTTCACTTTAAATCATA 1385
                          v  i v     i  v  -    i i i     iiv  v iivv    v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATT-GATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_189459051_   1386 ATCCCAGC----------------------AAGTT-ATTCTAAAGTTTAT 1412
                                 ----------------------   i -  i     i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_189459051_   1413 TTAAAGAGGCAAAAGACCCAGAATAAC-AACACAATATTGAGGGAGAAGA 1461
                         v ii i v    ii           i -  v     v    iii      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_189459051_   1462 -CA---TTCAATAGTCTGACACTACCTGACTTCAAGATTTACTGTAAAGA 1507
                         -  ---  vi -i v  v     v  ii i     i i     ii    v
  L1M4_orf2#LINE/    200 ACAAAGTTGGA-GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_189459051_   1508 TACAATAATCAAGACAGTGTGATAGTGACAAAAGAATAGGCAAATAGATC 1557
                             i                i  v  i  v   i    i  v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_189459051_   1558 AATGCAACAGAATGGAGATCCCAGAAATAGACTTACGTAAATAAAGCCAA 1607
                             v  i     v    vi         i  ii iii vv  vi i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_189459051_   1608 CTGATCTTTGACACAGGAGCAAAGGCAATACAATGGAGCAAAGATAGTCT 1657
                         i    i  i    vi  v  v   i v  v      i v  ii       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_189459051_   1658 TTTCAACAAATGGTGCACAAATAACTGGACTGCCACAT-TAAACAAGTGA 1706
                                         vvii i       iv?      -i   vi i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_189459051_   1707 GTCTAGACACAGACCTTACAC-------AAACATGAAATCAAAATGGATT 1749
                         ivi i   v vv    i    -------   v  v  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_189459051_   1750 ACAGACCTAAATGTAAAATGC-AAAACTATAAA-CTCCTAGAAGACAATG 1797
                          ?              i -  -           -   i       v  ii
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_189459051_   1798 TAGGAGAAAATCTAGATGACCTTGGATATGGCGATGACTTCTTATTTACA 1847
                             ? v      vvi         i vv   i   ii      vv  ii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_189459051_   1848 ACACCAAAGACATGATCCATGAAAGAAAGAATTGATAAAGCTGAACTTCA 1897
                                 ii  ii v v ii       i   v      -i  i      
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA-TTGGACTTCA 646

  chr1_189459051_   1898 TTAAAATGAAAAATCACTTCTCTGT---GAAAGACAATATCAAGGGAATG 1944
                          i     v     ---   i v  i---i  i    v       ii i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA---CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_189459051_   1945 AAAAGACAAGCCACAGACTGGGAGAAAATATTTGCAAAACATATATCTGA 1994
                                  v       v                    v           
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_189459051_   1995 TAAAGGACTATTATCCAAAACACA--GAGAACCCTTAAAACTCAACAATA 2042
                            i     vv      i  i i --i     i    v       i    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_189459051_   2043 AGAAAACAAACAACCCAACTAACAAATGGTCCAAAGACCTTAACAGATAC 2092
                          i  i     i       i ? v      v v  i  ii v  i   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_189459051_   2093 CTCACCAAAGAAGATATACAGATGGCAAATAAGCATGTGAAAAGATGCTC 2142
                         i  v                i     v        ii             
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_189459051_   2143 CACATCATATGTCAA 2157
                         v      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (122 / 75)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.12 (50 / 16)  


3163 25.52 0.55 1.10  chr1_189479697_189483578.rev     2482  3394 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_189479697_   2482 TAGAAACATATCCCATGCTCATGGATGGATAGAATCAATCTTGTGAAAAT 2531
                          i    v          i        v iv   v i   v    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_189479697_   2532 GACTATACTGCCAAAAGCAATCTACAAATTCATTTTAATGCAATCCCCAT 2581
                          i v     v  v   vii       i     ----- i        i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCA-----ACGCAATCCCTAT 95

  chr1_189479697_   2582 CAAAATACCACCATCATTATTCACAGAATTAGAAAAAACAATCCTAAAAT 2631
                               v   v vv v  v  ii     v v  v  ivii          
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_189479697_   2632 CCCTATGGAACCAAAAAAGAGTCCACATAGCCAAAGCAAGACTAAGCAAA 2681
                         i v       viiv  ii  vi viv         i   vvi i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_189479697_   2682 AAGAACAAATCTGGAGCA-TCACACTACTGGATTTCAAACTATACTATAA 2730
                                  vi     v -       v ivi        viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_189479697_   2731 AGCCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAG 2780
                            i i   v i   i    ii         i    ii    i  i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_189479697_   2781 ACCAATGGAACAGAATAGAGAACCCAGAAATAAGCCCAAATACTTA-AGC 2829
                          i        i     v    ii          i    v i i   -i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_189479697_   2830 CAACTGATCTTTGACAAGGCAAACAAAAACATAAAGTGGGGAAAGGACAC 2879
                            i    i  i       vviv   i v   vv i         i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_189479697_   2880 CCTATTCAACAAATGGGGCTGGGATAATTGGCTAGCCACATGTAGGAGAA 2929
                         i  v            v       i  i   v  ?       i ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_189479697_   2930 TGAAACTGGATCCTCATCTCTCATCTTATACAAATCTTAACTCAAGATGG 2979
                             ii    i  ii i   v  i v        vv         i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_189479697_   2980 ATTAAGGACTTAAAGCTAAGACCTGAAACTATTAAAAATTCTAGAAGAAA 3029
                           i ?i   i    vv     v  i       -    v ii         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAA 544

  chr1_189479697_   3030 ACGTTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACC 3079
                           i v  ?iv  vi    vv   v    v        v i    v iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_189479697_   3080 AAGAACCCAAAAGCAAATACAATAAAAACAAAGATAAATAGCTGGGACTT 3129
                          v  vv         v vi   i    iv   i   i   iv v      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_189479697_   3130 AATTAAACTAAAGAGTTTTTGCACCGCACAAGGA-ACAGCCTGCAGAGTA 3178
                         v  i   v v  i ii     ii iv  -     -  vii viv i   i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGAAAGTG 693

  chr1_189479697_   3179 AACAGACAGCCCACAGAGTGGGAGAAAAT--CTGCACAATCTATACATCT 3226
                           v     i        i           --i    -    -   i    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCT 741

  chr1_189479697_   3227 GACAAAGGACTAATATTCAGAATCCCCAACAAACGCAAACAAATCAGTAA 3276
                           i  i     vi   i      vivi  vi   v vv    v   i   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_189479697_   3277 GGAAAAAAACAATCAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGA 3326
                         -v     i    vi  i  v  i?    i     v     iv        
  L1M4_orf2#LINE/    792 -TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_189479697_   3327 CAATTCTCAAAAGAAGACATACAAATGGCCAAGAAACATATGAAAAAATG 3376
                           v     v        i              v  i  i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_189479697_   3377 CGCAACAACTCTAATGAT 3394
                          v     v v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (128 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3026 26.95 1.56 0.45  chr1_189623564_189625501      548  1445 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_189623564_    548 TGAAAAAACATCCCATGCTCTTGGATTAGAAGAATCAATATCATTAAAAT 597
                           i   i i        i  v      i     v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_189623564_    598 GACCATACTACCCAAAGCAATCTACAGATTCAGTGCAATCTCTATCAAA- 646
                          i v     v      vii             ii      i        -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_189623564_    647 TCACCAA-TGTCATTTTTCACAGAATTAGAAAAAAAAATCCTAAAGTTCA 695
                           -   i-  i -     ii     v v  v  ivvi        i    
  L1M4_orf2#LINE/    101 TC-CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_189623564_    696 TATGGAACCAAAAAAGAACCTGGACAGCCAAAGCAATCCTAAGCAAAAAG 745
                                viiv  ii  v  v i i       i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_189623564_    746 AACAAATCTAGAGACATCGCATTACCTGACTTCAAATTATACTACAAGGC 795
                               vi i   ivv  i  i v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_189623564_    796 TCTAGTAACTGAAACAACATGGTACTAGTACAAAAACAGTCATAAAGGTC 845
                          vi     iii i   iii       i i i  ii i  v    v  i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_189623564_    846 AACGGAACATAACAGAGGACCCAAAAATAAAGCCACCTACCTACAAGCAA 895
                           i    i v  iv   iii   i       v   ivi ii  iiiv   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_189623564_    896 CTTATCCTCAACAAAGTCAACAAAAATA---AACAGGAAAAAGATACCCT 942
                         i v  ii  i    i viiv   i vi ---  ii  i   ii   vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_189623564_    943 ATTCAATAAATAATGCTGGGAAAATGGGTTAGTCATATGCAGGAGAATGA 992
                         v     i    ii        v  iv  v  ?i  i     ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_189623564_    993 AACTGGACCCCTATCTCTCACTATATATAAAAATTAACTGAAAATGGAGT 1042
                          ii          i   v   i     i           v        vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_189623564_   1043 AAAGACTTAAACATAAGACCTGAAACTATTAAAATCCCAGAAGAAAACCT 1092
                          ?    i    ii     v  i       v   v  ii          v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_189623564_   1093 AAGGAAAATTATTCTGGACATTGGCCTAGGCAAAGAATTTAT-GATGAAG 1141
                          i ?iv  v v   vv   v    vi       v iv  iv -   - v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr1_189623564_   1142 AAACCCAAAGCAAATGCAACAAAAACAAAAATAGACAAATGGGAC---AG 1188
                          v   v      v v         iv         i    v    --- v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_189623564_   1189 TTAAACTAAAAGCTTCCGCACAGCAAAAGAAACAATTAGCAGAGTAAACA 1238
                         iv   i     i   ii ii vv    i  v  v  i iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_189623564_   1239 AACAACCTACAGAATGGGAGAAAATATTTGTAAATTATGCATCTGACAAA 1288
                         i      i                      i    i  ii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_189623564_   1289 GGACTAATATCCAGAACTCACAAGGAGCTCAAATAATTTAGCAAGAAAAA 1338
                              vi         ivi i  i  i   vv i  i i ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_189623564_   1339 AACAAG---CCCA--TTAAAAATGAGACAAACAACACGAACAGACATTTC 1383
                         i    i---    -- ?       i -    vi ivi   i         
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGG-CAAAGGATTTGAATAGACATTTC 846

  chr1_189623564_   1384 TCAAAAGAAGAAATACAAGCTGCCAATAAACATATGAAAAAATGTTCAAC 1433
                           v        v      iiv        i  i       i   i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_189623564_   1434 ATCACTAATCAT 1445
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (158 / 80)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


1806 26.00 6.50 4.43  chr1_189700739_189702873      501  1223 (912)    L1M4_orf2#LINE/L1       70   807 (101)  

  chr1_189700739_    501 ATTTATAGCTTCATTGTAATTCCTATCAAAATACCAATGTCCTTATTCAC 550
                           i  i  v    vi i   i           v   iivv    v  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chr1_189700739_    551 GG---TTAGAAAAAACAATCCTAAAGTTCATTTCAAAA---AAGAG-CCC 593
                         i ---  -  v  ivii        i     v vi   ---   i -   
  L1M4_orf2#LINE/    120 AGAAATT-GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr1_189700739_    594 A-AATAGCCAAAGCACTCTTAAGCAAAAAGAACAAAGTTGGAGGCATCAT 642
                          -          i  v    i iv  i                 vv   i
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_189700739_    643 AGTACTTGACTTCAAATTATACTACAAGGCTGCAGTAACCAAAAAAAGCA 692
                          v v iii i      viv        i   i      i   i v - ii
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA-GTG 267

  chr1_189700739_    693 TGTTATTGATATAAAAATAGACACATAGATCAATACAACAGAATAGAGAA 742
                           v  i  ii    ii       i          iv  i     v    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_189700739_    743 CCCATAAATAAAGTCACATACCTACACACAACTGATCTTCAACAAAATCA 792
                         i   v       vi  i i ii  iivv   i    i   i    iivii
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_189700739_    793 ACAGAAAC-TTAAACTGAAGGAGGGATACCCTAATTCAATAAATAGTTCT 841
                         v  ii v -  v  -  ii i i i   vi  v-     i    i  v  
  L1M4_orf2#LINE/    368 CCAAGACCATTCAA-TGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCT 415

  chr1_189700739_    842 GAGAAAACTGGATAGCCATCTGCGAAACAATGAAACTAGATCCCTATCTC 891
                          i  v         ?   iv   i   v      ii i  i     i   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_189700739_    892 TCACTATATACAAAAATTAA-----GATGGAGTAAAGACTTAAATATATT 936
                         v   i               -----i     vi ?    i     i  vv
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_189700739_    937 ACCTGAAACTATAAAAATTCTAGAAGAAACCCTAG----AAAACTTC--- 979
                          v  i           v ii         v v   ----   v    ---
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_189700739_    980 -CTTTGGA-----CATTGG---CTTAGGTA---------------AATGT 1005
                         - i    i-----  v   ---     i  ---------------  - i
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA-GC 614

  chr1_189700739_   1006 AACAAAAACAAAAATAGACAAAAGGGACTTAATTAAACTAAAAAGCTGCT 1055
                                iv         i   vv      v  i   v v    i  vi 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_189700739_   1056 GCACAGCAAAAAAAAAAAAAAGAAAGAAAGAAAAAAGAAAATTATGAACA 1105
                          ii vv    -------------------------- i v i   v  v 
  L1M4_orf2#LINE/    665 GTGCTTCAAA--------------------------GGACACTATCAAGA 688

  chr1_189700739_   1106 GAGAGAACACGCAACCTATGGGATGTGAGAAAATATTTGTAAACGATACA 1155
                         i  v   v vi     i ii i   v             i   iv   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_189700739_   1156 GCCAACAAAGGACTAATATCCAGAAGCTACAGGGAACTCAAACAAG--AA 1203
                         v ii i  i     vi         vv  i ii      vv    v--  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_189700739_   1204 CAACAAAAAAAGCAAATAGC 1223
                         i  i     i -      i 
  L1M4_orf2#LINE/    789 TAATAAAAAGA-CAAATAAC 807

Transitions / transversions = 1.66 (116 / 70)
Gap_init rate = 0.03 (19 / 738), avg. gap size = 4.16 (79 / 19)  

 420 14.52 3.23 4.84  chr1_189700739_189702873     1519  1642 (493)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr1_189700739_   1519 AAAAAAAAAAAAGCAAATAAAATCTCCCCATTAAAAACTGGGCAAATAAT 1568
                           v  v     ii       -----   v   ?    v        vi  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAA-----CCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_189700739_   1569 ACGAACTGACATTT-TCCAAAGGAAGACATGCAAATGTCCAACAAGCATA 1617
                         vi   iv       -       -    i  i      v    i     i 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACA 880

  chr1_189700739_   1618 TGAAAAGATGC---ACATCACTAATCAT 1642
                                    ---      ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.03 (4 / 122), avg. gap size = 2.50 (10 / 4)  


3467 25.50 0.78 0.33  chr1_189736408_189741693     3896  4793 (493)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr1_189736408_   3896 GATATTCCATCCTCATGAACTGGAAGAATTAATATTGTTAAAATGACAAT 3945
                              i    vi     i i       v             i   i    
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_189736408_   3946 TCTACTGAAAGCAATGGACAGATTCAATGCACTCCCTATCAAAATACCAA 3995
                         v  v iv   vii  vv          i   v             v   i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_189736408_   3996 CGGCATTCTTCATAGAAACAGAAAAAGCAATCCCAAAATTTATACGGAA- 4044
                          v  v  i  iii     iv  v  ivii    i      i   i    -
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_189736408_   4045 CACAAAAGACCCGAGATGGCCAAAGCAATCCTGAGCAAAAAGAACTAAAC 4094
                         ii   ii     iii  i      i     i   iv  i      v  ii
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_189736408_   4095 TGGAAGAATCACATTATCTGACTTCAAAATAGACTACAAAGCTATAATAA 4144
                             i  v     i vi ii i       ivv            i i   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_189736408_   4145 CCAAATCAACAGGATTCTAGCATAAATACAGACACATAGACCAATGGAAC 4194
                         i   iv  iiiv i v  i      iv i     i     i        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_189736408_   4195 AGAATAGAGAATCCAGATATAACTCCATGCATTTACAGATAAATCATTTT 4244
                              v    i      v    vi    i      ii vi  v v     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_189736408_   4245 CAACAAAGGTGCCAAGAATATACAATAGAGAAAGGGTAGTTCCTCCAATA 4294
                          i    i          vi  v    i i     ii    iii i   i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_189736408_   4295 AATGGTTCTGGGAAAACTGGATAACCAT-TGCAGAAAAAAGAAACTAGAT 4343
                               v      v         ?   i-    i  i  v   ii i  i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_189736408_   4344 CCCAGTGTCCCACCGTACACAAAAATCAAATCAAAATGGATTAAAGACTT 4393
                            viiv  v    i  i        i  v           i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_189736408_   4394 AAATATAAGACTTGAAATTATGAAGCTACTATAAGAAAACATTGGGGAAA 4443
                             i     vi i   i   i  i  vi  v          v  ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_189736408_   4444 ATCTCCAGAACACTGGTCGGGGCAAAAATTTTTTAG-TAAGACCTCAAAA 4492
                             i ivi  vi   vivi     vii   i    -  v   vi     
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_189736408_   4493 AGCACAGACAACAAAAGCAAAAATAAATGAATAGGATTACATCAAACTAA 4542
                         -     ii         v       i  i   v   i v       v v 
  L1M4_orf2#LINE/    607 -GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_189736408_   4543 GAAGCTTCTGCATAACAAAGGAACCAATCAACAAAGTAAAGCGACAACCC 4592
                         i  i   i  iiivv       vv v     v     i  iv        
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_189736408_   4593 ACAGAATGGGAGAAAATATTTGCAAACTACCCATCTTATAAAGGATTAAC 4642
                                                   ii ivi    v    i   i vii
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_189736408_   4643 GACCAGGATATATAAGAAGCTCAAGCAACTCAACAG-GAGAAGATAAAAA 4691
                         iv    i        ii i   vvi        i i-i i    i   v 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_189736408_   4692 AAATCAGATTTAAAAATGGACAGAAGATCTGAATAGACATTTCTC---AA 4738
                          --i vi   ?        i  i i   i                --- i
  L1M4_orf2#LINE/    806 A--CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_189736408_   4739 AAGACATACAAATGGCCAACAGGTATATAAAAAAATACTCAACATCATTA 4788
                             i              i i i i  i    i  i          ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_189736408_   4789 ATCAT 4793
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.12 (153 / 72)
Gap_init rate = 0.01 (7 / 902), avg. gap size = 1.43 (10 / 7)  


3694 18.21 7.64 0.94  chr1_189896046_189898634.rev     1248  2098 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_189896046_   1248 TGGAAAGACATTT-GTATTCAGGGACTAGAAAA----ATATT---AAGAT 1289
                                 i  ii-i i    v   i i   i ----     ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_189896046_   1290 TTCTATACT----------ATC---AGATGCACAACACAATCCCTATCAA 1326
                         vv v     ----------   ---    v  --  i             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCA--ACGCAATCCCTATCAA 98

  chr1_189896046_   1327 AA-CTCAACA----TTTTTGCAGAAATAGAAAAACTCATCCTAAAAGTCA 1371
                           - i  i v----             v  v  i  v         v   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_189896046_   1372 CATGGAATCTCACGGGACCTCAAATACTTAGCCAAACTCATTGTGAAAAA 1421
                         i      viv  v      ivi    ----      viv  iv       
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATA----GCCAAAACAATCTTGAAAAA 194

  chr1_189896046_   1422 GAT---CAAAGTTGGAGGACTCAAACTTCCAGATTTCAAAACTTACTGCA 1468
                           v---                 v      vi               i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_189896046_   1469 AAGCAACAGTAAACAGAAGAG----------GCATAAAGACAGACATACA 1508
                             v       v  ii v  ----------      i  i       i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_189896046_   1509 GATTAATGGACTAGAAT-----ACCCAGAAATAACCTCACACGTATATGG 1553
                            i      v      -----ii          v i  i  i v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_189896046_   1554 TCAACTAATTTTTGACAAGGGTGTCCAGACCATTCAATAAGGAAAGGACA 1603
                             i i     i          i v            ii      i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_189896046_   1604 GCCTTTTCAACAAATGGTGCTGGGGAAACTGGATAGCCACACGCAAAAGG 1653
                          i                      iv         ?     i       i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_189896046_   1654 ACGAAGTTGGACCATTACTTTAAACTATATACAAAT-TTAACTCAAAAAG 1702
                          i           vi   i i v  i         v-           v 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_189896046_   1703 GATCAAAAGACTAAACTTAAGAGTGAAAACTATAAAACTCTTAGAAGAAA 1752
                              ? iiv     iv      iv                         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_189896046_   1753 ACAGAGGA--AAAGCTTCATGAAACTGAATTTAGCACTGATGTCTTGGAT 1800
                            v   ?--   v    i   vvi  ii  vi   v  i v    i   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_189896046_   1801 ATGAAACCAAAAGTACAGACAAC----GGAAAAAGAAACAAACTGGATTC 1846
                             v        i   ii    ---- i     v i i   i    i i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_189896046_   1847 CATCAAAATTTAAAACTTTTGTGC---AAAGGA---TATCAACACAGTGA 1890
                                   v             ---      ---      v v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_189896046_   1891 AAAGGCAACCTACAGGAAGGGAAAAAATATTTGCAAGTCACACAT---AT 1937
                             i     i    i v    i             i   i i  ---  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_189896046_   1938 AAGAAATTAATATCCAGACTATATAAAGAACTCCTGCAACTCAACAACAA 1987
                            ii i vi        v              i i        i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_189896046_   1988 CAAAACACAAACCAGCCAATTTAAATATGGGCAAAGGATTTGAATAGGTA 2037
                         --   v     iv v      ?   v                     ii 
  L1M4_orf2#LINE/    795 --AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_189896046_   2038 TTTCTCCAGAGA-----TACAGATGGCTAATAAGTGCATGAAAATACACC 2082
                                 i   -----    i     i      ii        v ii i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_189896046_   2083 AGACATCACTAATCGT 2098
                         vi      ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (95 / 56)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.65 (73 / 20)  


2877 24.06 5.25 1.94  chr1_189915813_189920434     3253  4129 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_189915813_   3253 GAAAAACATTTCATGTGCATGGATAGGAAGAATCAATATTGTTAAAGTGG 3302
                             i i  ii     v       v      v i           ii   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_189915813_   3303 CCATAACTGCCCAAAACAACTTACAGATTCACTGCTATTCCTAGCAAACT 3352
                          v   -  v      vii ii          vi  v  i    v    v 
  L1M4_orf2#LINE/     53 CAATA-CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_189915813_   3353 ACCAGATTTCATTTTTCTCAGAAATTCGAACAAACT-ATTCTAAAATCCA 3401
                         v    v vi -     iv        --i    i  -  i       i  
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr1_189915813_   3402 TATGGAACCAAAAAGGAGGCAGAATAGCCAAAGCA-TCCTAAGCAAAAAG 3450
                                viiv  i   vv             i  -  i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_189915813_   3451 ACCAAAGTTGGAGGCATCACACTACACAATTTCAAACTATACAACAAGAC 3500
                          v            vv       v v          viv   v    ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_189915813_   3501 TAGAGTAACCAAAAC--TGTAGTACTGGTACAAAAACAGGCACACAGACC 3548
                           v     i   i  --   i       i i  ii i  i  i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_189915813_   3549 AATGGAACAAGTTAGAGAATCCACAAATAAAGCTGCCCAGCAGCAACCAT 3598
                                i iiv v    i    v       v iiiv  viviiiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_189915813_   3599 CTGCTTTTTGACAAAGTCGACAGGAACAAGCAGTGGGGAAAG--TGCTCA 3646
                         i  v    i     i vi v  i  v  vv  i         -- iv  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chr1_189915813_   3647 TTATTCAG----TGATGCTGGGATAACTGGCTAGCCAAATGCAGAAGATT 3692
                           -    i----  i        i      v  ?   v     i    v 
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_189915813_   3693 GAAACCGAACCCCTTCCTTTCACCATATGCAAAAATCAACTCAAGATGGA 3742
                            iii i      v   iv        i       i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_189915813_   3743 TTAAAAGACTTAATTGTAGGACCTGAAACTATAAAAACCCTAGGAAAAAA 3792
                          i ? -   i   v    i  v  i           vi i   -  i   
  L1M4_orf2#LINE/    497 TCAWA-GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG-AAGAAA 544

  chr1_189915813_   3793 ACA---GGGCATGCCATTCTGGACATAGGCCTTGGTAAACATTT------ 3833
                            --- ? i vii -   vv   v v  vi v  i  vvi   ------
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_189915813_   3834 TATGACAAAGTCTTCAAAAGCAAATGCAGCAAAAACAAAAATAGACAAAT 3883
                                ------i        v v   i     iv         i    
  L1M4_orf2#LINE/    594 TATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_189915813_   3884 GGGAGCT-----AAACCAAAAAGCTTCTGCCCAGCAAAAGACATTGTCAA 3928
                         v   vi -----   ii     -   i  iv vv    i    i i    
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_189915813_   3929 CAGAGTAAACAGACAACATACAGAATGGGAGAGAATATTTGCAAGGTATG 3978
                         v i   i  v       vi             i           ivi  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_189915813_   3979 CATCTGACAAAGATCTAATACCCAGAATGTATAAGGA--CCTTA-AGC-- 4023
                         i      i  i iv  vi  i       i     i  --i    - i --
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_189915813_   4024 ----ATAAAA---CAAACAGTCC----------TGAGCAAAGGACACGAA 4056
                         ----      ---    i ii  ----------  i        ivi   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_189915813_   4057 CAGACACTTCTCAAAAGAAGATATACACATGGCCAACAAACATAGGAAAG 4106
                         i     i     v              v        i  i  i v    -
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA- 885

  chr1_189915813_   4107 AAATGTTTAACATCACTAATCAT 4129
                          i   i i       ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (130 / 78)
Gap_init rate = 0.03 (24 / 906), avg. gap size = 2.62 (63 / 24)  


1965 24.71 1.71 5.71  chr1_189925946_189927635.rev      500  1199 (491)    L1M4_orf2#LINE/L1      237   908 (0)  

  chr1_189925946_    500 TCACTATAAGGACACAGTCACCAAAACAGCATGGCACTGGTATAAA-ATA 548
                          i    i  i vi     v i   i    ii   i     i    i-   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_189925946_    549 GGCACAAGGACCAACGGAACAGAATAGAGAATCCAGAAATAAACCCAAAT 598
                          i  i vi  i   i    i     v    i                v i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_189925946_    599 ACTTACAGCCAACTGTAAGTATTTTGCCAACTGATCTTTGGCAAAACAAA 648
                          i   --------  ---------- i   i    i  i i   iivviv
  L1M4_orf2#LINE/    337 ATTTA--------TG----------GTCAATTGATTTTCGACAAGGGTGC 368

  chr1_189925946_    649 CAAAAACATAAAGTGGGGAAAGGACAACCTATTCAACATATGGTGCTGGG 698
                            i v   vv i         i i ii  v       v           
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_189925946_    699 ATAATTGGCAAGTCACATGTAGGAGAATGAAACTGGATC---ATCTCTCA 745
                          i  i   vv ?i      i ii        ii    i --- i   v  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_189925946_    746 CCTTATACAAAAATCAACTCAAGATGGGTCAAGGACTTAAGTCCTGAAAC 795
                           v           i       i    i   ?i   i   i --------
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT-------- 510

  chr1_189925946_    796 ACATCAAGGACAAAGACCTGAAACTAGAAAAATTCTAGAAGATAACACAG 845
                         --i --------    v  i      v    v ii       v    i  
  L1M4_orf2#LINE/    511 --GT--------AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_189925946_    846 GAAAAACCCTTCTAGACACCGGCTTAGGCAAGGATTTCATGACCACGA-A 894
                          ?iv  vi    vv   vii  v        v i    v iivi i  - 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_189925946_    895 CCAAAAAGCAGATGCAGTAAAAACAAATATAAATGGCTGAGACCTAATTA 944
                               -   v v   ii    iv   v   i  iiv vi   i v  i 
  L1M4_orf2#LINE/    601 CCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_189925946_    945 AACTAAAGAGCTTTTGCACGGCAAAAGGAACAGTCAGCAGAGTAAACAGT 994
                           v v  i i      ii vv    i iv  vi   iv i   i  v  v
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_189925946_    995 CAACTCACAGAGTGGGAGAAAA-ATCTTCATAATCTATACCTCTGACAAA 1043
                             i      i          -  i v  -    -   iv     i  i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGATAAG 747

  chr1_189925946_   1044 GGACTAATATCCAGAATCTACCTCAAACTC----AAATTAGCAAGAAAAA 1089
                              vi          v  ivvvi     ----  v i ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_189925946_   1090 AACAAACAATCCCATGAAAAAGTGGGCTAAGGGCAGGAAAAGACAATTCT 1139
                         i     i  i  v  v?    i     v    iivv   v     v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_189925946_   1140 CAAAGGAAGATAAACAAATGGCCAAGAA--ATATGAAAAAAATGCTCAAC 1187
                          v  i       v            v  -- i       i -        
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAAC 896

  chr1_189925946_   1188 ATCACTAATGAT 1199
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (104 / 65)
Gap_init rate = 0.02 (14 / 672), avg. gap size = 3.71 (52 / 14)  


1469 27.87 13.86 1.42  chr1_189928683_189930309      500  1134 (493)    L1M4_orf2#LINE/L1      195   908 (0)  

  chr1_189928683_    500 GAGGAACAAAGAGAGAGGACTCACACTACCTGATTTCAAGACTTACTATC 549
                           i        vvi             v  ii       i        iv
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_189928683_    550 AAGTTGCAATAATCCACACAATGTACTAACGATGTAAAGATAGA----TA 595
                            i i  i     v v   i   iv  vi iii   i      ----  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_189928683_    596 GATGAATGAAA-ATAATGGAGATTGCTTAAATGGGGCTATAC---TAT-- 639
                            v    i  - v   v    v v vv    iiiv i    ---   --
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_189928683_    640 ---------TTTCGACAAAGACATCAATGCAATTCAATTAAGAAACAAAT 680
                         ---------         i iiii   vi v       vii    v  vv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_189928683_    681 GCCTTAGCAATAAATGGTACTGGAACAATTGGATAAATATATGGGTGGAG 730
                          i   vv   i       i    i    i      ?vi i   v---- i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC----AA 440

  chr1_189928683_    731 AGGAATGACTGTCAG-CCATTACCTAACACCATACACAAACATTT-TTTA 778
                          i      v-  ii -  vi     v        i     v   v-i i 
  L1M4_orf2#LINE/    441 AAGAATGAA-GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_189928683_    779 AGGTAGATTGTACACACAAACTTAAAAGCTGAAACTGTAAGGCTTCTAGA 828
                          ii i   ii? v  vi   iv   i    i     i   ii  ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_189928683_    829 ATAAAGCATAATAGAATGTTTTTGTGACTTTGA-------AATAGTTTTT 871
                          v   i    iv? v vi i  i     i   i-------   i    i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_189928683_    872 TT--TTTGA-------AGGGTGAACCATAAAA--AGAAAT---------- 900
                          v-- v   -------  viii i v i    -- i    ----------
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_189928683_    901 -------------TTTAAAACTTCTGTTCATCAAAAGACACCATTAAGAA 937
                         -------------  v       i   v v     i     i  i     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_189928683_    938 AATAAAAAGGCCAGCCACATGCTGGGAGAAAATCTTTTCATTGCACATTT 987
                          i i     i v v     viv           v   v  vvv  i  v 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_189928683_    988 GTAACAGAAAATTTGTATCTAGAAT------------CCTGTGTGTCAGT 1025
                         v i i iiii i       i     ------------ i iiivv   i 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_189928683_   1026 ATTTTTAAAAA---------TCCTATT-AAAAATAAGCAAGAGAT----G 1061
                          v ---     ---------i  v   -      ii    ii   ----i
  L1M4_orf2#LINE/    790 AAT---AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_189928683_   1062 TTGACACTCCACAAAACAAGGTATACAAATGGCCAATCAGCGCATGAAAA 1111
                          v    i i v v   v   i                v   i        
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_189928683_   1112 AAATTCTCAGTATCATCAGTTGT 1134
                         i - v    ii    ????????
  L1M4_orf2#LINE/    887 GA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (108 / 66)
Gap_init rate = 0.03 (19 / 714), avg. gap size = 5.11 (97 / 19)  


1906 25.25 1.51 5.35  chr1_189965400_189969335.rev      920  1517 (2419)    L1M4_orf2#LINE/L1       15   589 (319)  

  chr1_189965400_    920 ATATTCATGGATTAGAAGACTCAACATAGTAAAGATGGTAGTTTTTCCCA 969
                           i          i       i  i  v  v       i i vi i    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr1_189965400_    970 AACTGATCTATAAGTTTAACATAATTTCTATCCAAATCTTGGCAAGGTAT 1019
                           i       i ii  i   ii   ii     v     iii  vivv v 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr1_189965400_   1020 TTTGGAAAATATAAAGAAGTTTATTTTAAAGTTTACATGGAAAGGCAAAG 1069
                             v i  -  vi v   i v  ii    i  i i       v    i 
  L1M4_orf2#LINE/    115 TTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_189965400_   1070 GAATTAGACTAGCTAATAGAATTTTTAAAAAGAA---TGAAATGGGAGAA 1116
                           vii   v    i  v v   i  v        ---ii  i v    i 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_189965400_   1117 AACATTCTACCCAATATTATATTTTACTACATAGCTACAGTAATCAAGAC 1166
                         vv  iv  v      v i v vi        v                  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_189965400_   1167 AGCATAGTATTGA---AAGGATAAATACATAAATCAATGGAACAGAATAG 1213
                           ii i   i  i---       i i i   i          i     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_189965400_   1214 AGAACCCAGAAACAGACCAACACATAGATGGATAGCTGATTTCTGACAAA 1263
                            ii       i i   v i    vv    vi ii      ii     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_189965400_   1264 GGTGCAAAGGAAGGATTGTGAGTAGAGGGAGGATTGTCTTTTCAACAAAT 1313
                              v   -- vv   v-- i i i ii  i  v               
  L1M4_orf2#LINE/    364 GGTGCCAAG--ACCATTC--AATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_189965400_   1314 GGTGCTAAAGCAACTGGACACCTACAGGCAAAAGCAAACAAACAAAA--- 1360
                               iiii        i ? i   v       ------  ii  i---
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAG------AATGAAGTTG 453

  chr1_189965400_   1361 AACCCCAAAAAACAATATAAGCCTCATATCTTATATAAAAATCAATTCAT 1410
                         i     -----------  --     i i v    i      i  i   v
  L1M4_orf2#LINE/    454 GACCCC-----------TA--CCTCACACCATATACAAAAATTAACTCAA 490

  chr1_189965400_   1411 AATGGAACATAGGTTTGAGTAAGTAAACCTAGACCATAAACCTATAAAAC 1460
                               v  ?  iii i i --    -----  v -    v         
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAAT--GTAA-----GAGC-TAAAACTATAAAAC 532

  chr1_189965400_   1461 TTTTTAAATAAAACATAGAAGAAAATCTTTGGGACCTATAACTAGGTAAA 1510
                          i  vi  v         i? v       i v     vviii    i  v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_189965400_   1511 GAGTTCT 1517
                          iv    
  L1M4_orf2#LINE/    583 GGTTTCT 589

Transitions / transversions = 1.90 (97 / 51)
Gap_init rate = 0.02 (12 / 575), avg. gap size = 3.42 (41 / 12)  

 648 26.56 1.04 1.04  chr1_189965400_189969335.rev     1828  2019 (1917)    L1M4_orf2#LINE/L1      586   777 (131)  

  chr1_189965400_   1828 TTCTTAGATGTGACACAAAAGGCACTATCTATAAAATTTTAAAAACAGAT 1877
                                  i      v   i    v v v i    --vv     i    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAA--GAAAAAATAGAT 633

  chr1_189965400_   1878 AAATTAGACTCCATCTCAACTAAA-GCCTTTACTCTATGAAAGACCCTGT 1926
                              i    i    vv  i    -i i   iiv  vii  i   v  i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_189965400_   1927 TAAGAGGATGAAAAGACAAGCTACAGGCCAAGAGAAAATATTTGCAAAAC 1976
                         i    iii           v i    iviii                 v 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_189965400_   1977 ACAAGTGCGACAAAGGACTTGTATCTTGAAGACACAA-GCACTC 2019
                          i vi vi  i  i           iv   v i i  - v    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.02 (3 / 192), avg. gap size = 1.33 (4 / 3)  

 310 22.40 1.60 4.00  chr1_189965400_189969335.rev     3322  3446 (490)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr1_189965400_   3322 AAAAAAAAAAAAAAAAAAAATCACATT--ACAGTGGGCAAAAAACATGAA 3369
                           v  v     i v   v  i vv   -- v i        ii iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_189965400_   3370 CAGACATTTCACCAAAGAGGATATATGTTATAGATAGCAAATTAATACCT 3419
                         i         v       i      i----- i  i  v   v ii  v 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATAC-----AAATGGCCAATAAGCACAT 881

  chr1_189965400_   3420 GAATATATGCTCAACATCTTTAGCTGT 3446
                            v v            v????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.87 (13 / 15)
Gap_init rate = 0.02 (2 / 122), avg. gap size = 3.50 (7 / 2)  


2927 25.47 1.98 2.31  chr1_189971510_189975791.rev     2881  3791 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_189971510_   2881 TGGAAACAAATCCCATGCTCATGGATGGGAAGAATCAATATTGTGAAAAT 2930
                               v v        i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_189971510_   2931 GACCATACTGCCAAAAGCAACCTATAAATTCGGCACAATCCCCATCAAAA 2980
                          i v     v  v   vii i   i i    ii i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_189971510_   2981 TACCACCATCATTCTTTACTGAATTGGGAAAAACAATTCTAAAATTCAAA 3030
                          v   v vv v  i   i v   v v iv  ivii  i          v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_189971510_   3031 TAGAAC--CAAAAAACAGCCTGCATAGCCAAAGCAAAACTAAGCAAAAAG 3078
                          i   v--   iii  --  v v         i   vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_189971510_   3079 AACAAATCTGGAGGTATCACACTACCTGATTTCAAACTATACTATATGGC 3128
                               vi      vv       v  ii        viv     i vi  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_189971510_   3129 CACAGTCACCAAAACAGCATAGTGCTGGTATAAA-ATAGGCACATAGACC 3177
                         i     v i   i    ii i  i    i    i-    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_189971510_   3178 AATGGAACAGAATAAAGAATCCAGAAATAAACCCAAATACTTACAGCCAA 3227
                                i     vi   i                v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_189971510_   3228 CTGATCTTTGAAAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCT 3277
                         i    i  i  v  i vviv   i v   vv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_189971510_   3278 ATTCAACAAATGGTGCTGG-ATAACTGGCAAGTCACATGTAGGAGAATGA 3326
                         v                  - i      vv ?i      i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_189971510_   3327 AACTGGATC---ATCTCTCACCTTACACAAAAATCAACTCAAGATGGGTC 3373
                          ii    i --- i   v    v  i        i       i    i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_189971510_   3374 AAGGACTTAAGTCCTGAAACACATCAAGGACTAAGACCTGAAACTAGAAA 3423
                          ?i   i   i ---------------- --     v  i      v   
  L1M4_orf2#LINE/    499 AWAGACCTAAAT----------------G--TAAGAGCTAAAACTATAAA 530

  chr1_189971510_   3424 AATTCTAGAAGATAACACAGGAAAAACCCTTCTAGACAATGGCTTAGGCA 3473
                          v ii       v    i   ?iv  vi    vv   vv   v       
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_189971510_   3474 AGGATTTCATGACCAAGAACCCAAAAGCAGATGCAATAAAAACAAAGATA 3523
                          v i    v iivi v  vv         v v    i    iv   i   
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_189971510_   3524 AATGGCTGGGACTTAATTAAACTAAAGAGCTTTTGCAAGGCAAAAGGAAC 3573
                         i  iiv v      v  i   v v  i i      iivvv    i iv  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_189971510_   3574 AGTCAGCAGAGTAAACAGTCAACCCACGGAGTGGGAGAAAA-ATCTTCAA 3622
                         vi   iv i   i  v  v        i  i          -  i v   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_189971510_   3623 ATCTATACCTCTGACAAAAGACTAATATCCAGAATCTAAAACAAACTC-- 3670
                            -   iv     i  ii    vi          v  v  vi     --
  L1M4_orf2#LINE/    731 ATC-ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_189971510_   3671 --AAATTAGCAAGAAAAA-----ACAATCTTATGAAAAAGTGGGCTAAGG 3713
                         --  v i ii  v     ----- i  i iv  v?    i     v    
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_189971510_   3714 ACATGAATAGACAATTCTCAACAGGAGATATACACATGACCAACAAGCAT 3763
                          iv          v     v v  i         v   i    i     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_189971510_   3764 ATGAAAA-ATGTTCAACATCACTGAATGA 3791
                                -   i         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (130 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.25 (39 / 12)  


2361 24.52 2.55 0.48  chr1_190028446_190033544.rev     3410  4037 (1062)    L1M4_orf2#LINE/L1        1   641 (267)  

  chr1_190028446_   3410 TGGAAAAATATATCATCTTCATGGATTTGAAGAATTAATATTATTAAAAT 3459
                               i    vi   v          v     v        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190028446_   3460 GTGCA-TACTACCCAAAGCAATCTAGAGATTCTATGCAGTCCCTAACAAA 3508
                          -   -    v      vii     v      v i   i      v    
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_190028446_   3509 ATATCA-TAACTTTCTTTACAGAAATAGGAAAAAAAA--CTAAAATCTGT 3555
                           vi  -ivi i  i   i       v iv  ivvi --       iii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_190028446_   3556 ATAAAACCACAAATGACCCCAAATAGCCAAAACAATCTTGAGCTAAAAGA 3605
                           ii  vii   iv     vi                    ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_190028446_   3606 ACACAG----AGTCATCACACCACCTGACTTCAAA-CATATTATAAAGCT 3650
                            v  ----  vvv      iv  ii i      - v  i  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_190028446_   3651 ATAGTAACCAA-ACAGCATGGTACTGGCATAAAAAGAGACACACAGACCA 3699
                          i     i   -    ii              ii v     i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_190028446_   3700 ACAGTACAGAATACAGCGCCTAGAAATAAGTCCACA-ATCTTATAGCCAA 3748
                          ii v i     vv  v i i        ii   i -  -    i i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-TTATGGTCAA 348

  chr1_190028446_   3749 CTGATTTTTGACAAAAGTGCCAAGAAAACAGAATGGGGAAGGGATTGGTT 3798
                         i       i     ii         vv ivv         i i  v vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_190028446_   3799 TTTAAATAAGTGGTCCTGGTAAAATTGAATATTCACATGCAAGAGAATGA 3848
                            v  i  i    v    v v  i  i   ?i         i       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_190028446_   3849 AATTACATCCCTCTGTCTCACCATATACAAAAATCAACTTAAAATGGATT 3898
                          i  iv i    viv  v                i    i         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_190028446_   3899 TAAGACTTAAGTGTAAGACCTGAAGCTAT-----TACTAGAAGAAAACAT 3943
                         v?    i   i       v  i  i    ----- vi             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_190028446_   3944 GGGGGAAAAGTTTCATGAAATTTGCCTTGGCAATGATTTTTTTATATATG 3993
                         i  ? v   vi   i   vv  v vi v       i   i  - v     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chr1_190028446_   3994 ATCTCAAAAGCACAGTAAACAAAAGCAAAAATAGACAAATAAGA 4037
                          ivi          ivv        v         i    vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

Transitions / transversions = 1.48 (90 / 61)
Gap_init rate = 0.02 (11 / 641), avg. gap size = 1.73 (19 / 11)  

 986 24.24 0.00 0.38  chr1_190028446_190033544.rev     4345  4608 (491)    L1M4_orf2#LINE/L1      646   908 (0)  

  chr1_190028446_   4345 ATCAAACTAAAAAAGCTTCTGCGCAGCAAAGGACTCAATTAACTGAATGA 4394
                               v v     -   i  i  vv        v v  i  vvi i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_190028446_   4395 AGAGACAACATACAGAATGGAAGAAAATATTGGCAAACTATCCATCTAAT 4444
                          i       vi         i          v     ii  vi    i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_190028446_   4445 AAGGGGATAATATTCAAAATAAATAAGGAACTCAAACAATTCAATAGCAA 4494
                              iv vi   i  i    v    i      vv    i      ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_190028446_   4495 GAAAACAAATAGCTGAATTTGAAAATGGGAAAAAGACCTGAAGAAACATT 4544
                         i  i       i iv    ?i        v   i  ii    v i     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_190028446_   4545 TCTCAAAAGAAGACACACAAACACTTAACAGGTATATGAGAAAATGCTCA 4594
                             v        i i     iivii  i i i i    i  i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_190028446_   4595 ACATTATTAATCAT 4608
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (42 / 21)
Gap_init rate = 0.00 (1 / 263), avg. gap size = 1.00 (1 / 1)  


 253 15.38 0.00 0.00  chr1_190185633_190187401      449   500 (1268)  C L1M4_orf2#LINE/L1   (0)   908   857  

C chr1_190185633_    500 ACATACAAATGACCAACAGGTAAATGAAAAGTTGCTCAACATTACTAATT 451
                          i         i    i i i v        v          i ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

C chr1_190185633_    450 AT 449
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.00 (0 / 0)  

2633 24.90 6.16 0.66  chr1_190185633_190187401      506  1268 (500)    L1M4_orf2#LINE/L1       56   860 (48)  

  chr1_190185633_    506 TGCTGCCCAAAGCAATCTACATATTCAGTGCAATCCCTGTCAGAATTCCA 555
                          i  v      vii       v     ii         i   i   i   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_190185633_    556 ATGGAATTTTTTACAGAAATATAAAAAAC-AATTCTAAAATTCATATGGA 604
                         iiv vv      i       - i v  i -i  i                
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_190185633_    605 ACCACAAAAGACCTGGAATAGGTAACACAATCTTGAGCAAGAA---CAAA 651
                          vii   ii    ii      vi  v          iv     ---    
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_190185633_    652 GCTATAGGCATCATACTTCCTGACTTCAAATTATATTACAAAACTGTAGT 701
                          i iv   vv   i      ii i      viv  i      i  ii   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_190185633_    702 AATCAAAACAATATGGTACCAGAGTAAAAACAGACACATAGACCAATGGG 751
                               i   i i      ii vi   ii i     i     i      i
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_190185633_    752 ACAGAATAGCGATCCCAGAAATAAACTCATGCATATATTGTCATCTAATC 801
                          i     v v  vi            i   i   v   v    vi i  i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_190185633_    802 TCTGACAAAGCCGGCAAGAATATGCCACAGGGAAAAGATAGTCTCTTCAA 851
                          ii     i vi v     vi  v v ii      ii       i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_190185633_    852 TAAATGGCATTGGTGA-AACTGGATATCCACGTGCCAAAAAA---AATCT 897
                         i      iii   -  -         ?    i   v   i  --- i iv
  L1M4_orf2#LINE/    405 CAAATGGTGCTGG-GACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_190185633_    898 GATTTC-ACC--ATAC---ATACAAAGA--AACTAACAATGGATTAAAGA 939
                           iii -   -- i  ---       i --    v v       i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_190185633_    940 CTTAAA------AACTGGAGCCATAAAACT--TAGAAGAAGACATAGGGG 981
                          i    ------ i  ii i i        --        i       ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_190185633_    982 AAAAACTCTATGACACTGATGTT-GGCATTGATATTTT-GATATGACACT 1029
                         v   v  iii    vi  i-   -    v  i v i  -          i
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_190185633_   1030 AAAAGTACAGGCAACAAAGGCAAAAA-AGA---GTGGGACTAAAT-GCAA 1074
                              i   i        i v     -   ---i v     vv  -iv  
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_190185633_   1075 CTAAAACATTGTG-GCATAGCAAAGGAAAC----AACAATATGAGAAGGC 1119
                         i     vv  v  -  v --       v  ----  v  vi   i   i 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_190185633_   1120 AGCCTATAGATTAGAAGAGAATATCTGCAAACTGTATAGCCAATAAGGGG 1169
                          i  i i   v i i   i     i      iii    v ii       i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_190185633_   1170 TTAATATCTAAAATACACATGGAACTTGTACAACTCAATAGCAAAA---- 1215
                         i vi    i i    i i vi     iv            ii    ----
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_190185633_   1216 ---TAACCAATTTAAAAAATGGGCAAAGAAC----ATAGATATTTTTCCC 1258
                         ---     v v  ?              i i----     i    i   v
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_190185633_   1259 AAGAAAATAT 1268
                              i    
  L1M4_orf2#LINE/    851 AAGAAGATAT 860

Transitions / transversions = 2.26 (129 / 57)
Gap_init rate = 0.03 (23 / 805), avg. gap size = 2.26 (52 / 23)  


3049 26.14 1.67 0.67  chr1_190209768_190214239.rev     3083  3981 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_190209768_   3083 TGGAAAAATCATTCCATCCTCATGGATAGGAAGAATCAATATCGTTAAAA 3132
                               i  -  i    vi        v      v i     i     i 
  L1M4_orf2#LINE/      1 TGGAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_190209768_   3133 TGGCCATACTGCCCCAAAGTAATCTATAGATTCAATGTTATTCCCACCAA 3182
                             v     -       v i     i        i iv  i  i i   
  L1M4_orf2#LINE/     50 TGGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_190209768_   3183 GTGACCAGTGACTTTCTTTGCTAAATTATAAAAAACT-ACTTTAAATTTC 3231
                         ivvv    ivi i  i     vi  v - i v  i  - iii    v   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTC 147

  chr1_190209768_   3232 ATATGGAAC--CAAAAAACAGCCTGTATAGCCAAGACAATCCTAAGCCAA 3279
                                 v--   iii  --  v v        i      i i ivv i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_190209768_   3280 AAGAACAAACCTGGCGGCATCATGCTACCTGACTTCAAAGTATACTACAA 3329
                                  vi   v  vv   ii  v  ii i      iiv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_190209768_   3330 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACTGATATATAG 3379
                         i          i   i    ii         i iv ii iv  i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_190209768_   3380 ACCAATGGAACAGAACTGAGACCTCAGAAATAACACCACACATCTACAAC 3429
                          i        i    i     vii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_190209768_   3430 CATCTGATCTTTGACAAACCTGACAAATACAAGCAATGGGGAAAGGATTC 3479
                           vi    i  i     ivv  v   ivv  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_190209768_   3480 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAAC 3529
                         i  v  i  i              v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_190209768_   3530 AGAAACTGGAACCCTTTCTTACACCTTATACAAAAATTAACTCAAGCTGG 3579
                         v   ii    v    vi  i     v                   iv   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_190209768_   3580 ATTAAAGCCTTAAATGTAAAGCCCAAAACCATAAAAACCCTAGAAGAAAA 3629
                           i ?  v i         iiv i     i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_190209768_   3630 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATAACT 3678
                          v    ?i- v i -   iv   v v  vv i     v ii   v  iv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_190209768_   3679 ACAACACCAAAAGCTATTGCAACAAAAGCCAAAATTGACAAATGTGATCT 3728
                          ii           vvvv          vv     v  i    vv  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_190209768_   3729 AATCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGA 3778
                         v      v v  i i   i  ii vv    i  v    i  vv i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_190209768_   3779 ACAGGCAACCTACAGAATGGGAGAAAATTTTTCCAAGCTACCCATCCGAC 3828
                          v  i     i                 v   v   iii ivi   i  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_190209768_   3829 AAAGGTATAATATCCAGAATCTACAAGGA--TCTTA-AATTTA-CAAGAA 3874
                           i  vv vi          v  i  i  --     -  i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_190209768_   3875 AAAAA-AACCAACACCATTAAAAAGTGGGCAAAGGATATGAACAGACATC 3923
                            i -  vi   v v   ?    i            v    i      i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_190209768_   3924 TCACCAAGGAAGACATTTATGTGGCCAAGAA--ACCTGAAAAAA-GCTCA 3970
                           v    i     i  vi vi       v  --  v      i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_190209768_   3971 ---TCACTGGTCAT 3981
                         ---   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (134 / 97)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.40 (21 / 15)  


3219 25.31 3.88 0.34  chr1_190318971_190321049      710  1586 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_190318971_    710 TGGAAATATATC------TCATGGATTGGAAAAATTAATATTGCTAAAAT 753
                               v     ------             i v         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190318971_    754 ATCTGTACAACCCAAGGCAATCTACAGATTCAATGCAATCCCTGTCAAAA 803
                         iv vi   vv     ivii              i         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_190318971_    804 TATCAATGACATTCTTCACAAAAATAGAAAAAA-AATCCTAAAACTTGTA 852
                          vi  iivi v  i  ii  i    v  v  iv-i         i ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_190318971_    853 TGAAACCGCAAAG-ATCTTGAATAGCCAAAGCCATCCTGAGCAAAAAGAA 901
                           i  vi    i - i iv           i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_190318971_    902 CAAAACTGGAAGCATCATACTATCTGACCTCAAAATATACTACAAAGCTA 951
                             ii    i vv   i   vi ii ii      iv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_190318971_    952 CAGTAACCACCATAGCATGGCAATGGCATAAAAATAGACACATAGACCAA 1001
                               i  vv i  ii   i v        ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_190318971_   1002 TAGAACAGAATGAAGAGTCCAGAAGTAAATCTACACATTTAGAGTCCACT 1051
                          i   i     vi           i    i i i       vi   v i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_190318971_   1052 GATTTTCCATAAAGGTGCCAAGAATACACACTGGAGAAAGGACAGTCTCA 1101
                                v i  i          vi iv  v   i     i i     iv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_190318971_   1102 TCAATAAATTGTGCTGGGAAAGCTTGATATCCACATGCAGACAAAC---- 1147
                             i    v         v i  v    ?         i vi  i----
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_190318971_   1148 -TAGACCTTGAACGTTCACCATATACAAAAATTAACTCAAAATGAATTAG 1196
                         - i    iiv v viv                            i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_190318971_   1197 AGACTTAAA-----GACCTGAAACTATAAAAACTACTAGAAGAAAACATA 1241
                             i    -----  v  i           -  vi              
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATA 549

  chr1_190318971_   1242 AGGGAAACACTTCATGACATTGGTCTAGGCAAAGATGTTCTGAATATGAT 1291
                         i ? v  vv    i    v    vi       v i v ii ii      i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_190318971_   1292 CTCAAAAGCATGGGCAACAAAAGCCAAAATGAACAAGTGGAATTATACCA 1341
                         vi        iii          vv     ii i  i v i i vi i  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_190318971_   1342 AACTAAAAAAGCT----GCTCAGCAAAGGAAACAATACATAGAGTGAAGA 1387
                           v v     vi ----   i--       v  v  vv v i      i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_190318971_   1388 GACAACTTACAGAATGCGA-AAAATGTTTGTAAACTATGTACTTGACAAA 1436
                               ii        v  -     i    i   ii  i  ii   i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_190318971_   1437 GAGTTAATGTCTAGAATATATAAGGAAC----ACAA-----TAGCAAACC 1477
                          iii vi i  i           i    ----    -----  ii   vv
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_190318971_   1478 --CAAATACTCTGATTAAAAAATGATCAAAAGACCTGAATAACCATATCT 1525
                         --      vi ii   ?       iv    i  ii      iv   v   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_190318971_   1526 CAAAAGAAGACACACAAATGTCCAGCAGGTATATGACAAAGTGCTCAATA 1575
                          v        i i       v   ii i i i    v  ii       i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_190318971_   1576 TCACTAATCAT 1586
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.99 (145 / 73)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.08 (37 / 12)  


2872 28.02 1.22 0.66  chr1_190340456_190346579.rev     4731  5633 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_190340456_   4731 TGGAAAAGCATTCCATGCTCATGGATAGAAAGAATCAATATCGTGAAAAT 4780
                               iii  i     i        v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190340456_   4781 AATCATACTGCCCAAAGTAATTTACAGATTCAATACTATTCCCATCAAGC 4830
                         iiiv     v      v i  i           ii v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_190340456_   4831 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTTAA 4879
                          v   vivi i  i  ii     v v  v  i-  - iii    i  i v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_190340456_   4880 AAGGAACCAAAAAAGGCCCATA-TAGCCAAGACAATCCTAAGCAAAAAGA 4928
                          v    viiv  ii i    v -       i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_190340456_   4929 ACAAAGCTGGAGGCATCATGCTACCTGACATCAAACTATACTACAAAGCT 4978
                               i      vv   ii  v  ii iv     viv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_190340456_   4979 ACAGTAATCAAAACAGCATG-CACTGTTACCAAAACAGATATATAGACCA 5027
                                    i    ii  -i    vi iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_190340456_   5028 ATGGAACAGAACAGAGGCCTCAGAAATAAAACCAT----TTACAACCATC 5073
                               i    iv   ivii          v    ----   iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_190340456_   5074 TGATCTTTGATAAACCTGACAAGAACAAGCAATGGGGAAAGGATTCCCTA 5123
                             i  i  i  ivv  v     v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_190340456_   5124 TTTAATAAATGGTGTTAGGAAAACGTGCCAGCAATACGCAGAAAACTGAA 5173
                           i  i        i i   v   vv vi ? v i i   i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_190340456_   5174 ACTGGACCCCTTCTTTACACTTCATACAAAAATTAACTCAAGATGGATTA 5223
                         ii         v i i    ivi                  i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_190340456_   5224 GATATTTAAATGTAAGACCTAAAAAACATAAAAACCCTAGAAGAAAACCT 5273
                         ? v ii           v      v-i      vi i           v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAAC-TATAAAACTCTTAGAAGAAAACAT 548

  chr1_190340456_   5274 AGGC---AATGCCATTCAGGACATAGGCATGGGCGAAGACTTCATGACTA 5320
                            ?---   -- -   iv   v v  vv i   i v ii   v iiv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_190340456_   5321 AAACACCAAAAGCAATTGCAACGAAAGCCAGAATTGACATATGGGATCTA 5370
                         vi            vvv     i    vv i   v  i v  v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_190340456_   5371 ATTAAACTAAAGAGCTTCTGCACAGCAAAGAA-ACTATCATCAGAGTGAA 5419
                           i   v v  i i   i  ii vv     i -       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_190340456_   5420 CAGGCAACCTACAGAGTGGGAGAAAAATTTTGCAATCTACCTATCTGACA 5469
                         v  i     i     i          vv       vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_190340456_   5470 AAGGTCTATTATCCAGAATCTAAAAGGAACTTAAACAAATTTACAAGAAA 5519
                          i  v  vv          v  v  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_190340456_   5520 AAAACAAACAACCCCATTAAAAAGTGGGTGAGGAATATTAATAGACACTT 5569
                           i     i     v   ?    i    ii i i  v v        i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_190340456_   5570 TTCAAAAGAAGACATTTATGTGGCCAACAAACATGAAAAAAAAAAGCTCA 5619
                         i  v        i  vi vi       i  i  i- vi    i v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCAC-ATGAAAAGATGCTCA 894

  chr1_190340456_   5620 TCATCATTGGTCAT 5633
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


3042 25.22 1.74 3.04  chr1_190347580_190351787.rev     2798  3717 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_190347580_   2798 TGGAAAGATATTCCGTGTTCATGGATTGGAAGAATCAATACTGTTAAAAT 2847
                                    i  i                  v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190347580_   2848 GTTCATATTACCCTCAAAGCAATCTACAGATTCAATGTAGTCCCCAT-AA 2896
                          viv   i --  i    vii              i i i    i  -  
  L1M4_orf2#LINE/     51 GGCAATACT--CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_190347580_   2897 AATACCAATGATATTCTTCACAGAAACAGAAAAAAAAAATCCTAAAATTT 2946
                            v   iiviiv  i  ii      iv  v  ivvi -          i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTC 147

  chr1_190347580_   2947 ATATGGAACCACGAAG-ACCAAGAATAGCCAAAACTATCCTGAGTAAAAA 2995
                                 vii i i -   v              v   i   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_190347580_   2996 GAACAAAATTAGAGGAATCACATTATCTGACTTCAAA--TTATTCTGCAA 3043
                                i  i     v     i vi ii i      --   --  i   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAA 245

  chr1_190347580_   3044 AGCTATAGGGACCAAAACAGCATGACACTGTCATAAATACAGATACATCA 3093
                              i  vi i   i    ii  ii    v     iv i   i i  vi
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_190347580_   3094 ATCAATGTAACAGAATAGAGAACCCAGAAATAAATTCGCATGCCTAGAGT 3143
                                v  i     v    ii           ii ii iiii  vi  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_190347580_   3144 GAACTCATTTT-GACAAAGGTGACAAGAATATACATTCAAGAAAGGACAG 3192
                         v  i v     -     i    v     vi  v  v vii     i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_190347580_   3193 TTTCTTCAGTAAATGGTGCTGGGAAAACTGGATATCCATTTGCAGAAGAA 3242
                          i i    ii              v         ?   iv    i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_190347580_   3243 TGATATTAGACCCCTATCTCTCACAATACACAACAATTAAATCAAG-TGG 3291
                            vi  i        i   v   v   i    v      v    i-   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_190347580_   3292 ATGAAATATTTAAATCTAAAACCTCAAGCTATAAAACTATTAAAAGAAAA 3341
                           v ? v ii     v   i v  v  i          v   i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_190347580_   3342 CACTGG-GTAAGCCCTCCAGAACACTGGACTGGACAAGGATCTCTTGAGT 3390
                           iv  -    ii i  -ivi  vi   ii i i   v i i    iii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_190347580_   3391 AATACCCTACAAGCACAGATGCTTGTAGATACCCTAAAACATCAAAGCAA 3440
                          vv  v i v       i--  ---------------    --    v  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA--GC---------------AACA--AAAGAAA 625

  chr1_190347580_   3441 AAATGAACAAATAGGATCATATTATG-TTAAGAACCTTCTGCACAGCAAA 3489
                             ii i    v   iivi  i vi-    i   i  -  ii vv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAA 674

  chr1_190347580_   3490 GGAAACAAT---GAAAGTGAAGAGATAACCCACAGAATATGAGAAAATAT 3536
                            v  v  ---         i   i            iv          
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_190347580_   3537 TTGTAAATTATCCATCTGACAAGAGATAAATAACCAGAATA----AAGAG 3582
                            i    i  vi      i   i  ivvi  v        ----    i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_190347580_   3583 TTCAAACAACTCTATAGGGAAAACAATCTAATAATATGATTTTAAGATGG 3632
                         i  vv       v   ivi    v -- v     ivii   ?v  i    
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGG 822

  chr1_190347580_   3633 GTAAAA-ATCCGAATATACATTTCTAAAAAGAAGGCATACACGTGGCAAA 3681
                          i   i-  ii     v        vv       ii     vi    v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_190347580_   3682 CAGGTATATAAAAAGATGTTCAGTATCACTTATTAT 3717
                         i i i i  i        i   ii    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (151 / 78)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.32 (44 / 19)  


3208 26.90 0.66 0.55  chr1_190418903_190425179.rev     4880  5786 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_190418903_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190418903_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCACCCCCATCAAGC 4979
                            v     v     iv i  i           i  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_190418903_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_190418903_   5028 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_190418903_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_190418903_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAT-TAGATC 5176
                                 i   i    ii         i iv ii i   v  -      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_190418903_   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5224
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_190418903_   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_190418903_   5275 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_190418903_   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_190418903_   5375 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_190418903_   5425 CTAGGCA-ATACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCA 5473
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_190418903_   5474 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5523
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_190418903_   5524 ATTAAACTAAAGAGCTTCTGCCCAGCAAAAGAAACTACCATCAGAGTGAA 5573
                           i   v v  i i   i  iv vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_190418903_   5574 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5623
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_190418903_   5624 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5673
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_190418903_   5674 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5723
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_190418903_   5724 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCAT 5773
                            v        i  vi viii     v  i        i i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_190418903_   5774 CATCACTGGCCAT 5786
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


 654 28.78 11.07 1.85  chr1_190458644_190462403     2022  2292 (1468)    L1M4_orf2#LINE/L1        1   296 (612)  

  chr1_190458644_   2022 TGGAGAAACACGCAATACTTGTGGATCTTAAGACTCGATATTATTGAAAT 2071
                             i i i iv v  ii ii     ivv      ii     i  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190458644_   2072 ATAAATGTTACCAAAATTGACTTATTGAATCAATGCAATCTCTAT----- 2116
                         ivv   ii v  v       ii  iv  v    i      i    -----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_190458644_   2117 ----AG--GCTTTAATTTTGTTGGCATGTACAAGTGAATTCTAAAATTTA 2160
                         ----  --  i  --     iv iv  vv     ivi  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_190458644_   2161 TGTGAGAATTGAAAGGACCTTAAGTAGTTGCTAAAGTAATTT------AG 2204
                          i  ii   vv  i     ivi i   --- i   ii   i ------  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAG---CCAAAACAATCTTGAAAAAG 195

  chr1_190458644_   2205 AAAAACA---TTAGA---TTTACACTACATAATTTTAAGACTTACTATAA 2248
                           i    ---  i  ---i i     v vi     i  i        i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_190458644_   2249 AGCTACAGTAATAAAGAC-------TTTTGCCACAAAGAGATATATATAA 2291
                                     v     ------- vi  v  i  i  v v i     i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_190458644_   2292 A 2292
                          
  L1M4_orf2#LINE/    296 A 296

Transitions / transversions = 2.12 (53 / 25)
Gap_init rate = 0.03 (8 / 296), avg. gap size = 4.38 (35 / 8)  

1216 26.75 10.29 1.44  chr1_190458644_190462403     2782  3267 (493)    L1M4_orf2#LINE/L1      380   908 (0)  

  chr1_190458644_   2782 AATAAAGGTAGGATTGTCTTTACTACAAATGGTGCGTGAACATCTGGAAA 2831
                            iii iv  i  v      v v           vv i   v     v 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_190458644_   2832 TC-------------------TTAAACCTCAAATACCACACATAATACAC 2862
                         ? -------------------  ii   i ---    v    iv   i  
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCC---TACCTCACACCATATAC 476

  chr1_190458644_   2863 AAAA------TC-----GAACCATAGGCCTTAGTATAAAAGCTAAA--TA 2899
                             ------  ----- i i  ?  i   v i i   i       --  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_190458644_   2900 TATAATTTTT----GAAAACATAGGCAT---TTTCCACAACCTTGGGACA 2942
                           v  i i  ----           ?i --- i i iii        vi 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_190458644_   2943 GGCAAACATTTTTTAGGCAAGACAGTAAAATCAAAACCAA-AGAGGAAAT 2991
                              vvi   i    ii v    vi    v  v  v   - i i    v
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_190458644_   2992 AATGGACAAATTGAACTTTATGAAAGTAAACAAACTCT-GCTCTTTGAAA 3040
                            i  i      i    i  v   i v  -     i - iv   ii  i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAG 675

  chr1_190458644_   3041 AGCATCTTTAAGAAAGTGAAAAGGTGAGCCACAGGCTGGGAGAAGATAAT 3090
                         ii  iiv i              iii v      iv        i   v 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_190458644_   3091 TGTAAATGATTTATGT-ATGAATTAGGATTTTTATCTAAAATGTGTTAAG 3139
                           i    v  v   v -  i i---   i  v    i i   i i v   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAG---GGACTTGTATCCAGAATATATAAAG 772

  chr1_190458644_   3140 TACTTCTGAAACTCATTAATAA---GACAAACAACTTAAAAACAAAGTAA 3186
                         v   ii iv      v      ---      i   ii  vv?v   i ii
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_190458644_   3187 GCAAAATATTTAAACA---ATTTC-CCAAAGACAACATACAAATGGCAAA 3232
                              iv    i  i ---     -       vi i           v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_190458644_   3233 CT-GTATATGCAAAGCTTCCAAACATCACAATTTTC 3267
                         iv- i i   v    v v iv       ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (79 / 47)
Gap_init rate = 0.03 (16 / 529), avg. gap size = 3.56 (57 / 16)  


2883 26.11 2.43 1.99  chr1_190522935_190526434     2111  3014 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_190522935_   2111 TGGAAA--CATCCCATACTCATTAATGGGTAGAATTAATATTGTGAAAAT 2158
                               --i       ii    vi  v  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190522935_   2159 GAACGTACTGCCAAGAGCAATGTGCAAATTCAATGCAATTCCCATCAAAA 2208
                          ivvi    v  v i vii  v i  i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_190522935_   2209 TACCACCATTATTATTCATGTAATAATGTAAAATGTAATATGTAAAAACA 2258
                          v   v -- iiiv  iv  i iv   - i v v i----  ------- 
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAAT-TGACAAGC----TG-------A 136

  chr1_190522935_   2259 TCCTAAAATTCATATGGAACCAAAAAAGAGTGCACATAGCCAAAGCAAGC 2308
                                            viiv  ii  vivviv         i   v 
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_190522935_   2309 TTCA----GCGAAACAACTCTGGAGACATCGCATTACATGACTTCA---- 2350
                           v ---- vii     vvi     ivv  i  i v vii i    ----
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_190522935_   2351 -TACCGCAAGGCCATAGTCACTAAAACAGCACAGTACTGGTATAAAAATA 2399
                         -   ii   i  i i   v ii  i    iiii       i    ii   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_190522935_   2400 GGCATATAGACCAAAGGAACAGAATATAGAACCCGGAAATAAAATCAAAT 2449
                          i        i   v    i     vv   ii  i        vi  v i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_190522935_   2450 ACTTACAGTCAACTTGATCTTCAACAA---TGCAAAGAAAAACATAAAGT 2496
                          i   ii     -     i   i    ---   v    v---   vv i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAA-TTGATTTTCGACAAGGGTGCCAAGAC---CATTCAAT 382

  chr1_190522935_   2497 GGGGAAAGGACACTCTATTCAACAAATGGTGCTGGGATAATTGGCTAGCC 2546
                                 i i v   v                    i  i   v  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_190522935_   2547 ACATGTAGAAGAATGAAACTGGATCCTCATCTCTCACCCTATATGAAAAT 2596
                              i i         ii    i  ii i   v    v    ii     
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_190522935_   2597 CAACTCAGGATGGATCAAAGACTTAAATATAACACCTGAAACCATAAAAA 2646
                         i      ii        ?    i     i   v v  i    i      v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_190522935_   2647 TTCTAGACCATAACATTGGAAAAACCCTTCTGGACACTGGCTTAGGCTAA 2696
                          ii    vv v     v  ?iv  vi    vv   vi   v      v v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_190522935_   2697 GACTTCAT-GATA--AC-CCAAAAACAAATACAACAAAAACAAAGATAAA 2742
                          ii   v -    --  -      i  v vi        iv   i   i 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_190522935_   2743 TAGATGGGACTTAATTAAA--CAAAAGCTTCTGCACAGCAAAAGAAACAA 2790
                           i  v      v  i   --i    i   i  ii vv    i  v  v 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_190522935_   2791 TCAGCAGAGTAAGCAGACAACCCATAGAGTGGGAGACAATCTTTGCAATC 2840
                            iv i   i iv          i   i       v   v       vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_190522935_   2841 TATTCATCTGACAAAGGACTAATATCCAGAATCTACAAGGAACTCAAGCA 2890
                         i  vi      i  i     vi          v  i  i      vvi  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_190522935_   2891 AATTAGCAAGGACAAAACAAAAAATCCCATCAAAAAGTGGGCTATGGACA 2940
                          v i ii  vi v  i     v  i  v  i?    i     v v   iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_190522935_   2941 TGAATAGACAATTTGCAAAAGAAGATATACAAATGGCCAACAA--ACATG 2988
                                   v  iv v                       i  --     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_190522935_   2989 AAAAAATGCTCCACATTACTAATTAT 3014
                             i      v    i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  


1175 28.04 2.65 0.26  chr1_190572257_190577549        8   385 (4908)  C L1M4_orf2#LINE/L1   (125)   783   397  

C chr1_190572257_    385 CTTTTTAATAAATGTTTCTGGGAAAGCTGGCTAGCCATATGCAGAAAATT 336
                              i  i     v v      v i    v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chr1_190572257_    335 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 286
                            ii         v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chr1_190572257_    285 ATAAAGAGTTAAATCTAAAACCCAAAACTATAAAAACCCTAGAAGAAGAG 236
                         vi ?   vi     v   i v i            vi i        i v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chr1_190572257_    235 CTAGGCA-ATACCGTTCAGGACATAGGCACAGGCAAATATTTCATAACAA 187
                         v    ?i- v i -   iv   v v  vvi      vvi    v  ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chr1_190572257_    186 AAATGTCAAAAGCAGTTGCAACAGAAGCAAAACTTGACAAATGGGATCTG 137
                         vi iii        vvv      i   v    v v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chr1_190572257_    136 ACTAAAG-----AGCTTCTGCACAGCAAAAGAAATTATCATCAGAGTGAA 92
                          ii   i----- i   i  ii vv    i  v i     vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chr1_190572257_     91 ----CAACGTACAGAATGGGATAAAATTTTTGCAATCTCTCCATCTGACA 46
                         ----    vi           v     v       viiv vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chr1_190572257_     45 AAGTTCTAATATCTAGAATCTACAAGGAACTTAAACAA 8
                          i vv  vi    i     v  i  i     ivv    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

Transitions / transversions = 1.02 (52 / 51)
Gap_init rate = 0.01 (4 / 387), avg. gap size = 2.75 (11 / 4)  

3002 26.35 3.15 0.90  chr1_190572257_190577549     3913  4800 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_190572257_   3913 TAGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 3962
                          i   ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190572257_   3963 GGCCATACTGCCCAAGGTAATTTGTAGATTCGGTGCTATCCCCATCAAGC 4012
                            v     v     iv i  i ii      iii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_190572257_   4013 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4060
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_190572257_   4061 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 4110
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_190572257_   4111 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCTATACTACAAGGC 4160
                                i      vv    i  v  ii i     iviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_190572257_   4161 TACAGTAACCAAAAAAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4210
                                 i   i v  ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_190572257_   4211 AACGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACGTCTACAACC 4258
                           i    i    i--    i  --        vv   i  i i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_190572257_   4259 ATCCGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAA-------- 4300
                          vii   i  i     ivv  v   i v  vvv         --------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_190572257_   4301 --------TAAATGGTGCTGGGAAAACAGGCTAGCCATATGTAGAAAGCT 4342
                         --------i              v   v  v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_190572257_   4343 GAAACTGGATCTTTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4392
                            ii    i ii v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_190572257_   4393 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4442
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_190572257_   4443 CTAGGCA-ATACCATTCAGGACACAGGCTTGGGCAAGGACTTCATGTCTA 4491
                         v    ?i- v i -   iv   viv  v  i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_190572257_   4492 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGGATCTA 4541
                         vi            vvi          vv     v  i   iv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_190572257_   4542 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAGCTGCCATCAGAGTGAA 4591
                           i   v v  i i   i  ii vv    i  vi  ii  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_190572257_   4592 CAGGCAACCTACAGAGCGGGAGAAAATTTTTGCAATCTCCT-TATCTGAC 4640
                         v  i     i     ii          v       -v  v -       i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGAT 744

  chr1_190572257_   4641 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAA----ATTTTAA 4686
                           i  i  vi          v  i         vv    ----  vv   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_190572257_   4687 AGAGAAAAACAACCCTATCAAAAAGTGGGTAAAGTATATGAACAGACACT 4736
                          i   v   i     v  i?    i    i    v  v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_190572257_   4737 TCTCAAAAGAAGACA--CTGATGCAGCCAACAGACACATGAAAAAATGCT 4784
                             v        i -- vi   --     i ii          i     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCT 892

  chr1_190572257_   4785 CATCATCACCGGTCAT 4800
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (140 / 90)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.77 (36 / 13)  


2815 26.67 2.72 0.79  chr1_190675432_190678078.rev     1268  2148 (499)    L1M4_orf2#LINE/L1        1   898 (10)  

  chr1_190675432_   1268 TGGAAAGTTATCCTGTGTTTATGGATTACAAGATTTAATATAGCCAAAAT 1317
                                v     ii    i       iv    i       v ii  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190675432_   1318 GACCATACTAGGCAAAGCAACCTATGGATTGAATGCAATGTCTCTGAAAA 1367
                          i v     vvv    vii i   ii    v  i     vi  v v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_190675432_   1368 TATCAG-TGTTAATCTTCAAGAAAAATAGAAAAATAAA--ATAAAATTTG 1414
                          vi   -  ii-- i  iviv i    v  v  iivi --v       ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_190675432_   1415 TATGGAACAACAAAAGACTCCAAATAGCCAAAGCAGTCTTTAGCAA-AAG 1463
                                vvi   ii   i vi          i  i    v iv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_190675432_   1464 AACAAAGTTGGAGGCATCACACTACCTGACTTCAAAATACACTAGAAACC 1513
                                       vv       v  ii i       ivi    v   v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_190675432_   1514 TATAGTAACCAAGACAGCATGATAGTGGTATAAAAATAGACACATGGACC 1563
                           i     i        ii  i  v   i    ii       i  i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_190675432_   1564 AATAAAACAGAATAGAGAAACAAAAAATAAATCCATATATTTACATCCAA 1613
                            ii  i     v    iv v i       i     i     iivi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_190675432_   1614 CTAATTTTTGACAAAGACACCAAGAACAAACATTGTGGAAAGAATATTAT 1663
                         i i     i     i iii      v  vv  v  v          v v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_190675432_   1664 CTTCAATAAATAATGTTGGAA-AACTGGATTTCCATGTGCAAAACAATGA 1712
                         i     i    ii  i   i -        v?   ii       v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_190675432_   1713 AAGTAGACCCCTATCTTTCACCACATACAAAA-TCAACGCAAAACAGATT 1761
                          iv i        i  iv     i        - i   v     ii   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_190675432_   1762 AAAGATTTAAATGTAAGA-CTGACACTTTGAAAATACGAGAAGAAAACAT 1810
                          ?   ii           -  i v   v i   v viv            
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_190675432_   1811 TGGGAAAAATGCTTCAGCACATTGGTCTGGGAAAAGATTTTATGAATAAG 1860
                         v  ?iv    -    ivv  v    vi i  v  v i   iv ii   v 
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_190675432_   1861 ACCTCAAAAGCACAGGCAACAAAGGCGAAAATTGACCAGTGGGATTACAT 1910
                           vi          i        i vi     v  iv i v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_190675432_   1911 GAAGGTAAAAAGCTTCTGCACAGCAAAGGAAAGAAACAACGATATAGTGT 1960
                         v  ii v    i   i  ii vv       v vv v   vi ---    v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA---AGTGA 694

  chr1_190675432_   1961 AGAGGCAGCAGACAGAAAGGGAGAAAATATTTA-AAAT-ATTCACTCAAC 2008
                          i  i  i vv      v              i-    -  vi iiii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_190675432_   2009 AAGGGATTAATATCCAGAATATATAAA---------CAATTCAATAGCAA 2049
                               i vi                 ---------   i      ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_190675432_   2050 AAAAAAAAAAGA------TTAAAACTGTACAAGTGATCTGAATAGACATT 2093
                            i v   vi ------ ?    v  vi   iv   i            
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_190675432_   2094 TTTGAAAAGAAGACATACAAATGGACAAGAAGTATTTGAAAAAAATGCTC 2143
                          i vv        i          v   v   i iv      i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chr1_190675432_   2144 AACAT 2148
                              
  L1M4_orf2#LINE/    894 AACAT 898

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.02 (14 / 898), avg. gap size = 2.21 (31 / 14)  


1346 23.41 18.96 3.69  chr1_190681927_190685946.rev     2754  3539 (481)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_190681927_   2754 GAGAGATATACCTTATTCATGGGTTGGAAAATTCAATATTAGTAAAATGT 2803
                           i      v  v i       i      i i i      iv   i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_190681927_   2804 CAAATTTTCCTTTATTAGTCTTT-GACTCAATGCAGTACCAACCCAAAAC 2852
                            vvi i  ivv   ii   vi-  i    i   i v  v i v   v 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_190681927_   2853 TCAGCAAA---TTTTA-AGAAATAAACTGACAAACTGATTCTAAAATTTA 2898
                         i    viv---    i-      ----      i     i        i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAAT----TGACAAGCTGATCCTAAAATTCA 148

  chr1_190681927_   2899 TGAGGAACTGCAAAGAACCTAGAATAGACAAAGAGCCAA----GAAAAAA 2944
                          iv    v     i i   i       v    i---   ----      i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAA---CAATCTTGAAAAAG 195

  chr1_190681927_   2945 CAAAACAA-------------------CTCAAG---AAAA---ATAACAA 2969
                         v i     ------------------- i   v---    --- iv    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_190681927_   2970 AA--ACAATATTTA-----GTGT-----TTGCATTCTGATAGACAAATTG 3007
                          i--   i  v i -----    ----- v    vvv        v  v 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_190681927_   3008 ATCAA-GAGACACAA---ACAG---AGAACTGA--TTAT---TTTATG-- 3043
                              - ii i v  --- v  ---    v i --ii  ---      --
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_190681927_   3044 ----TAGTTT------------CTAAGATAATTCATAAAATAAAGTACAA 3077
                         ---- ii   ------------ i    iv     vviiiv    v i i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_190681927_   3078 T-TTTTCAACAGATGGTTGGTGCTAGAACAACTGGATATCAATATGCAAC 3126
                          -         i     ----   i i           ? v i      v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGT----GCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_190681927_   3127 AGAAAAAAAGATAGAAATTCTGATCCATACTTTGCACCAAATACAAAAAT 3176
                             ------- -   i  v-  i  v   i ii     v          
  L1M4_orf2#LINE/    442 AGAA-------T-GAAGTTG-GACCCCTACCTCACACCATATACAAAAAT 482

  chr1_190681927_   3177 TAGTTGAAGATGAATTTTATGTCTAAATATAACA-CAAACACTCTAAGAT 3225
                           ii v  i   i  iv? vii      i   v - v  v   v   i i
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_190681927_   3226 TTCTAGAAGATAATATAGTGG-AAATATTCAT--TTTTGGAACAGGCAA- 3271
                          ii       v  i    v? -    v   i --ii    ivi      -
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_190681927_   3272 -GTTTACTTAGATATGACATCAAAA-TACAATCTTTAAAGGAACAAATTT 3319
                         -    -             i     -i    v vvi   i   v    vv
  L1M4_orf2#LINE/    583 GGTTT-CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_190681927_   3320 ATAAATTAGAGTTCATAAAAATGGAAACATTCTGCTCTTCAAAAGACAC- 3368
                                i  v     v     vi   vv  i  iv       i     -
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_190681927_   3369 ---AATAAATTAAAAAAACAA---GCAGAA-------------------- 3392
                         ---  v   v i    i    ---i     --------------------
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_190681927_   3393 ------------------GCTTGT--------TA---AGAGAACTCTAAA 3413
                         ------------------i     --------  --- i        v v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_190681927_   3414 TACTCAACAATTAAAAAA-AAA-AACCCAATGTGGGGGAAAACGGACAAA 3461
                         v      i   v    i -   -        v?i----    i  i    
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWA----AAAATGGGCAAA 827

  chr1_190681927_   3462 AGATTTAAACAGACA---CATCACAGAAGATATACAAGAGGCAAATAAAC 3508
                         i     i  i     --- vi  v             iv   v     i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_190681927_   3509 ACA----AAGATCCTCATTAGACATTAGAGAAATG 3539
                            ----     v    ----    i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCA----ACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (104 / 76)
Gap_init rate = 0.05 (41 / 906), avg. gap size = 4.34 (178 / 41)  


2428 25.49 3.69 5.21  chr1_190690518_190695771     3840  4761 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_190690518_   3840 TGGAAAGAAATCC-ATGCTCATGGACTGGAATAATTGTTATTGTTAAAAT 3888
                                 v    -   i       i     v v  iv         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190690518_   3889 GCCTGTACTACGCAAAGTGATCTACAGATTCAATGCACTCTCTATCTGAA 3938
                          v vi    v v    v                i   v  i     vi  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_190690518_   3939 TGCCAATGACATTCTTCACAGAAATAGAAAAAAAAAATCTTAAAATTCAT 3988
                          v   iivi v  i  ii       v  v  ivvi -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_190690518_   3989 ATAAAACCACAAAAGACCCTGAACAGCCTAAGCAATCCTGAGCAAAAAGA 4038
                           ii  vii   ii     v   i    v  i     i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_190690518_   4039 GCAAAGCGGGAATCATCACGCTACCTGACTTCAAAATCTACTATAAA-CT 4087
                         i     iv   ivvv    i  v  ii i       ii     i   -  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_190690518_   4088 ATAGTAGTCAGAACAGCATGATACTGGCATAAAAACAGACACATAGAACA 4137
                          i    i   ii    ii  i           ii i     i     v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_190690518_   4138 ATGGAAT-GAACAGAGAACAGAGAAATAAATCTGAACATACACAGCCAAC 4186
                                -   iv    iivv         i iiv    vi ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_190690518_   4187 CAGTTTTCAGCAAAGGCAACAAGAACATACCACAGGGAAAGGAGAGCATC 4236
                         iii     ii   i  iiv     v   v v ii       i v  --  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG--TC 397

  chr1_190690518_   4237 TTCCGTAAATGATGAAAGGAGAGCATCTTCAATAAACGATGTCAGAA-AA 4285
                           -------------------------     i   i i  iii i -  
  L1M4_orf2#LINE/    398 TT-------------------------TTCAACAAATGGTGCTGGGACAA 422

  chr1_190690518_   4286 CGAAATGTCCGTATGCAGAAGAATGAAACTACACCCC-ATCTCTTATCGC 4334
                          vii  i?  ii     i         ii iv     - i   vi i ii
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_190690518_   4335 ATACAAAGATCAACTCAAAATGGATTAAAGACGTAAATGCAACACCTGAA 4384
                                i  i              i ?    v      i  v v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_190690518_   4385 ACTTTGAAAATCCTTC----AACACATTGGTCTGGGTAAA-------GAC 4423
                            v -    ii   v----  v    v  ?----     -------   
  L1M4_orf2#LINE/    523 ACTAT-AAAACTCTTAGAAGAAAACATAGGN----GTAAATCTTCGTGAC 567

  chr1_190690518_   4424 TTCTTGGCTGAGACAACA-------AAACAAAAACAACAAAAACAAAAAC 4466
                         --     v v  i   ii------- i i vi -  v     i  v  i 
  L1M4_orf2#LINE/    568 --CTTGGGTTAGGCAATGGTTTCTTAGATATGA-CACCAAAAGCACAAGC 614

  chr1_190690518_   4467 AATGCAAAAAAGTAAA-AGACAAGTGGAATTATGTCAAG-CTAAAACCTT 4514
                           --     i iv   -   i  i v i i vii    i-i     v   
  L1M4_orf2#LINE/    615 AA--CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_190690518_   4515 CTGCACAGCAAAGGAAATAATCAACAAAGTGAAGAGAGACAACATCTACA 4564
                         i  ii vv       v iv     v        i   --    -- i   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA--CAAC--CCACA 708

  chr1_190690518_   4565 --ATGGGAGAAAATATCTGCAAACTATTCATCAGACAAAAGATTAATAAC 4612
                         --              i      ii  vi   v  i  ii  i vi  v 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_190690518_   4613 CAGAATATATAAGG--CCCT--CAATTCAATAG--AAAAAATAA-TAATT 4655
                                     i -- i  --   i      i--    i i  -   ii
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_190690518_   4656 TATCAGAAAAATGGATGAATGGTCTGAATATAATAGACATTTTTCAAAAG 4705
                         i viv?        iii  v i i      -----       i  v    
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATA-----GACATTTCTCCAAAG 853

  chr1_190690518_   4706 AAGACAATCACAGGGCTAATAAGAGGTATACAAAAATGCTCAATATCACT 4755
                             i vv  v v   i      vi-i  iv   i        i    ??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCA-CATGAAAAGATGCTCAACATCAZZ 902

  chr1_190690518_   4756 AATCAT 4761
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 2.04 (155 / 76)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.04 (82 / 27)  


3264 26.74 0.66 0.33  chr1_190716412_190721117.rev     3311  4215 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_190716412_   3311 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3360
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190716412_   3361 GGCCATACTGCCCAAGATAATTTATAGATTCATTGCCATCCCCATCAAGC 3410
                            v     v     iv i  i  i       vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_190716412_   3411 TACCAA-TGACTTTTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 3458
                          v   i-  v      ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_190716412_   3459 TGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 3508
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_190716412_   3509 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTCTACTACAAGACTA 3558
                              i      vv       v  ii i      vii        ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_190716412_   3559 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGATCAA 3608
                               i   i    ii         i iv ii i   v   i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_190716412_   3609 TGGAACAGAAC--AGGGCCCTCAGAAATAATGCCGCATATCTACAACCAT 3656
                              i    i--  i i  --        vv  ii i  i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_190716412_   3657 CTGATGTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 3706
                         i    v  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_190716412_   3707 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3756
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_190716412_   3757 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3806
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_190716412_   3807 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3856
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_190716412_   3857 AGGCA-ATACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAAA 3905
                            ?i- v i -   iv   v v  vvii     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_190716412_   3906 ACACCAAAAGAATG-GCAACAAAAGCCAAAATTGACAAATGGGTTCTAAT 3954
                                   v ii-          vv     v  i    v  vii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_190716412_   3955 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 4004
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_190716412_   4005 GGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCGTCTGACAAA 4054
                          i     i   i             v  ii   vii ivii     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_190716412_   4055 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 4104
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_190716412_   4105 AACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCT 4154
                         i     i     v  i?    i     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_190716412_   4155 CAAAAGAAGACATTTATGCAGCCAAAAAACGCATGAAAAAATGCTCATCA 4204
                          v        i  vi viii     v  i i        i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_190716412_   4205 TCACTGGCCAA 4215
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


2392 24.97 8.86 1.72  chr1_190839741_190842265     1222  2034 (491)    L1M4_orf2#LINE/L1        1   871 (37)  

  chr1_190839741_   1222 TGGAAAGACATCGTATAGTCATGGATTGAAAGAATTACTATTGTTAAAAT 1271
                                 i   vi  iv          i    v   v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190839741_   1272 TTCCATACTATACAAAGTGATTTGTAGATTCAATGTAGTCTTTATCAAAA 1321
                         vv v     viv    v    i ii        i i i  ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_190839741_   1322 TTCCCAA--GTCTTTGTTAACAGCAATAGAAAAA--AAACCTCAAAATGT 1367
                          -    i-- i    v  i-   v   v  v  i--i v   -     vi
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCT-AAAATTC 147

  chr1_190839741_   1368 ATATGGAACTATAAA--ATCCCAAGTAGCTAAAGTTACCTTAACCAAAAA 1415
                                 v ii  i-- i  vi i    i   iiv i   i vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_190839741_   1416 GAACAAAGTTCTAGGCATTATACATTACACAGATTTTAAAATACATTACA 1465
                                   vv   - i -i   i v v  -    i    ivi i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACT-CACACTTCCCA-ATTTCAAAACTTACTACA 244

  chr1_190839741_   1466 AAGCTATAGTAACCCAAACAGTGTGGTACTGTCATTAAAAAAAAAGGCAC 1515
                               i     i v i              v   ---  ii v  i  i
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT---AAGGATAGACAT 291

  chr1_190839741_   1516 ATCAACCAATGGATTAGAATAGAGAGCTGCAAAATAAATCTGCACACCTA 1565
                           vi i       v      v     iivvi       i iii   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_190839741_   1566 CAGTCAACTGACGTCTGACAAAGGTGCCAAGAACACACAATGGGGAAAAG 1615
                         ii     i   iv ii     i          v  iv           ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_190839741_   1616 ACATTTCTTTTCAGTAAATGGTGCTGAGA--------------------- 1644
                          i v -       ii           i  ---------------------
  L1M4_orf2#LINE/    392 ATAGT-CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_190839741_   1645 --------------ACCCCT---------------TAAAATTCAAATCAA 1665
                         --------------      ---------------i    v i  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_190839741_   1666 AATGGATTAAAAACTTAGATTTAAAACTTAATAATGTAAAACTACTAGAA 1715
                                i ? i  i  i  v   i vi   v v i       vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_190839741_   1716 GAAA-CATGAGAGAAAA-CTCC-TGACACATGT-CTGGGCAGTGATTTCT 1761
                             -   ii ? v   -  i -    - v  v-i i    i  i     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCT 589

  chr1_190839741_   1762 TGGGTATGACCCCAAAAGCACAGGCAACAAGAACAAAAATAGACAAATGG 1811
                          i i      v           i       i iv         i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_190839741_   1812 GATTGAATCAAAC---AAAACGGTTGCTCTACAGCAAAGGAAACAATTAA 1858
                           i vv      v---     vv   --- i vv       v  v  i  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTG---TGCTTCAAAGGACACTATCAA 686

  chr1_190839741_   1859 CAAAGT-AAAATATAACACACAGATTGGAAAAAAAT---TGCAAATCACA 1904
                         v     -    v i   v      v   i i     ---         i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_190839741_   1905 AATCAAATAAGAGGGTAACATTCAAAATACACTGGGAACTCAGTCTACTC 1954
                         v   vi     i iv vii  i  i    i ivii      vvv v    
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_190839741_   1955 AATAATAAGGAAACAA----CCCTCTTAAAAAATGGGCAAAGTCCCTGAG 2000
                                 ii i    ----   vv  ?              vvii   i
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_190839741_   2001 TGGACATTTCTTATAAGAAGACATACAAA-GGCCA 2034
                          i         ivv       i       -     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.53 (121 / 79)
Gap_init rate = 0.03 (24 / 871), avg. gap size = 3.58 (86 / 24)  


2071 25.33 2.06 9.78  chr1_190858056_190860259.rev      743  1713 (491)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr1_190858056_    743 CTGTGTTCATGGATTGAATGAC--AATATTGATCGGGTATCCACACTAAA 790
                          ii             i v   --       v vi i iv v i   vvv
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_190858056_    791 CAAAGTAATCTACAGATTTAAATTTATTGCCATCAAATTCCCAATGGCAT 840
                             v i           i  vviv  iv i      v     iiv  v 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_190858056_    841 TTTTTA---AAATATAAAAGC-AATT-TGAAATTCATATGGAACTACAAA 885
                              i---    vv v    -i  i- i              v i   i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr1_190858056_    886 AGATCCAAAACACCCACAGAAATCTTGAGACAGAGGAACAAAGCTGAAGG 935
                         i  i   i  i v   v iv        i v   i        i  i   
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr1_190858056_    936 TATCACACTTCCTGATTTCAAAATATATTATAGAGCTACAGTAAT-AAAA 984
                         vv          ii         iv  i  i i            -  i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_190858056_    985 CAGTATGGTACAAGCATAAAGACAAACATATAAACAAACAGAACAGAATG 1034
                             i      vi      i  i i       i iv  ii   i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_190858056_   1035 GAGAGCCCAGAAATAAACCCATATAT--ATGGACAAGTGACCTGTGACAC 1082
                              i                 i  --    v   v   ii vi    v
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_190858056_   1083 AGATGCCAAGAATACACAGTAGGGAATGGATACTCTCTTCAACAAATGGC 1132
                         i i        vi iv  i i     v i   v   i            -
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG- 411

  chr1_190858056_   1133 ATGAAGAATATCAGGTATCATGGAGTTTTCAGCCTTTTTGCGTGGGTTTT 1182
                         -  -------- v  -------  -----  i ---------   i v?-
  L1M4_orf2#LINE/    412 -TG--------CTGG-------GA-----CAAC---------TGGATAK- 430

  chr1_190858056_   1183 CCCTCATGTTCATGGATTTATCTACCTTTGGTCTTTGATGCTGGTGACCT 1232
                         -  v    ivv v i  -------------------  v i   --   i
  L1M4_orf2#LINE/    431 -CCACATGCAAAAGAAT-------------------GAAGTTGG--ACCC 458

  chr1_190858056_   1233 TCAGGTGGGGTTTTTGTGTGAATGTCCTTTTTGATGATGTTGATGTTATT 1282
                         ii --------ii i------ iii -------  -  iivi vi   vi
  L1M4_orf2#LINE/    459 CTA--------CCTC------ACACC-------AT-ATACAAAAATTAAC 486

  chr1_190858056_   1283 CCTTTCTGTTTGTTGGTTTTCAGGTTAAAGACTTAAACCTAAGACCTAAA 1332
                         ----  vivv  ---------- i i ?    i    iv     v     
  L1M4_orf2#LINE/    487 ----TCAAAATG----------GATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_190858056_   1333 AATCATAAAAGCCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATA 1381
                          v -      vi i           v    ?i- v i -   iv   v v
  L1M4_orf2#LINE/    523 ACT-ATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTT 570

  chr1_190858056_   1382 GGCACGGGCAAAGACTTTATGACTAAAACACCAAAAGCAATTGCAACAAA 1431
                           vvii     v ii  iv iiv  vi            vvv        
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_190858056_   1432 AGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAG 1481
                           vv     v  i    v   ii v  i   v v  i i   i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_190858056_   1482 CAAAAGAAATTATCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAA 1531
                             i  v i     vv i      v  i     i               
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_190858056_   1532 ATTTTTGCAATCTATTCATCTGACAAAGGGCTAATATCCAGAATCTAAAA 1581
                           v       vii  vi      i  i  i  vi          v  v  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_190858056_   1582 GGAACTTAAACAAATTTACAAGGAAAA---AAA------AATCAAAAAGT 1622
                         i     ivv    v iv i  vi    ---   ------   i?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_190858056_   1623 GGGTGAAGACTATGGAAAGACACTTTTCAAAAGAAGACATTTATGCAGCC 1672
                            ii   iv v  i v     i  i  v        i  vi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_190858056_   1673 AAAAAACATGAAAAAAAAAAAAGCTCATCATCACTGGTTAT 1713
                           v  i  i--- vi    i v     v     ????????
  L1M4_orf2#LINE/    871 AATAAGCAC---ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.03 (26 / 896), avg. gap size = 4.42 (115 / 26)  


2469 25.76 4.63 2.26  chr1_190870953_190873633.rev     1309  2193 (488)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_190870953_   1309 GAAAAACATCCCATGTTAATGGATTGGAAGTATAAACATCATTAAAGTGA 1358
                             i i          v            vv v  i  ii    ii  i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_190870953_   1359 CCACACTGCCAAAAGCAATATGCAGAGATCCAATGCAACTCCTATCAAAT 1408
                          v i   v  v   vii  v i    -- i   i    ii         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGA--TTCAACGCAATCCCTATCAAAA 100

  chr1_190870953_   1409 TACCAA-TGTCGTTTTCCACAGAATTAGAAAAA-TAATTCTAAAATTAAT 1456
                          v   i-  i -    iii     v v  v  i- i  i        v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_190870953_   1457 ATGGAACCAAAAATGAGCCGGAATAGACAAAGCAAACCTAAGCAAAGAGA 1506
                               viiv  iv  v  i      v    i   v i i i-     - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGA-A 197

  chr1_190870953_   1507 GAGCAAAGCTAGAGGTCTCATATTACCTAACTTCAAATTATACCACAAGG 1556
                           i     i i    v    i i v  i  i      viv   i    i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_190870953_   1557 CTATGGTAATCAAAATAACATGGGACTTGTACAAAAATAGAT-------- 1598
                            ii        i i iii   v   v i i  ii     i--------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_190870953_   1599 ----------GCACTGA----TCAGAAATGAAGCCACATGCCTACAACCA 1634
                         ---------- v i   ----i       i  v   i iiii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_190870953_   1635 ACAGATCTTTGATAAAGTTGACAAAAATGCACAATGGGAAAAGGACTCCC 1684
                          iv   i  i  i  i v  v   i viiiv       i    i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_190870953_   1685 CCTTCAATAAATGGTGCTGGACAAACTGGCTAATGATATGTCGAAGAAAG 1734
                         ii     i            ivv      v  ?iv i   ivi     v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_190870953_   1735 AAACTGGATCCCTA--TAAATCAGCATATACAAAAATTAACTCAAAATTG 1782
                           ii    i     -- v --  v                        v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCA--CACCATATACAAAAATTAACTCAAAATGG 495

  chr1_190870953_   1783 ATTAAAGACTTAAATGTAAGCCCCAAAACTATAAACATTCT-AGAAGAGA 1831
                           i ?    i          vv i           - i   -      i 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAA 544

  chr1_190870953_   1832 ACCTAG-TACAAACTCTTCCGGACATTGGCCTAGGCAAGTAACTTGT--G 1878
                           v   -?ii   -     vv   v    vi       - iii  v -- 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAG 592

  chr1_190870953_   1879 ACTAAGGCTTCAAAAGCAAATGCAACTGAAACAAAAAAAATAAACAAATG 1928
                          -  v i vi        v v     --   - i        i i    v
  L1M4_orf2#LINE/    593 A-TATGACACCAAAAGCACAAGCAAC--AAA-AGAAAAAATAGATAAATT 638

  chr1_190870953_   1929 AGACTTACTTTAA--CTAAAAACTTCTGCACAGCAAAAGAAATAACCAAC 1976
                         i     - v i  --i         i  ii vv    i  v iv i   v
  L1M4_orf2#LINE/    639 GGACTT-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_190870953_   1977 AGAGT-AAACGACAACCTACAGAATGGGAGAAGATATTTGCAAACTATGC 2025
                          i   -   v       i              i           ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_190870953_   2026 ATATGACAAAGGACCAATATC-AGAATCTACAG-GAACT-TAACAAC--A 2070
                           v   i  i    ivi    -     v  i i-     - v     -- 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_190870953_   2071 ACAACACACACACAAGA-AAATTACTACATTCAAAACTGGGCAAAGAACA 2119
                          i  i v -----    -    v  ivv   ?    v         i iv
  L1M4_orf2#LINE/    788 ATAATAAA-----AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_190870953_   2120 TGAACAGACAGTTCTCTAAAAAAGACATGCAAGTGGCCCACGAACATATG 2169
                             i     v     i   i    i  i   i     v ii i  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_190870953_   2170 AAAAAA--ATCAACACTACTAATTAC 2193
                             i --v      ii ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (146 / 78)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 2.10 (61 / 29)  


2144 27.68 2.35 1.57  chr1_190907933_190910063      500  1265 (866)    L1M4_orf2#LINE/L1       89   860 (48)  

  chr1_190907933_    500 TTCCCATCAGCATACCACCATCATTCTTCACAGAATTAGAAAAAAACACT 549
                          i  i    iv  v   v vv v  i  ii     v v  v  ivvv - 
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-T 137

  chr1_190907933_    550 TCTAAAATTCATACGGAA-T-CAA----CCC-TCATAGTCAAAGCAAGAC 592
                         i            i    - -   ----   -vv    i    i   vvi
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_190907933_    593 TAAGCCAAAAGAACAAATCTGAAAGCATCACATTACCTGATTTCAAACTA 642
                          i ivv i         vi  i i vv     i v  ii        viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_190907933_    643 TACTATAAGGCCACAGCAACCCAAACAGCATGGTAGTAGCATAAAAATAG 692
                              i  i  i    i  i v i    ii     v i      ii    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_190907933_    693 TCACAAAGACCAATGGAACAGAATAGATAACCCAGAAATAAACCCAAATA 742
                         v  i v   i        i     v  v ii               v i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_190907933_    743 CTTACAGCTGACTGATCTTTGACAACGTAAACAAAAATATAAAGTGGGTA 792
                         i   ii iii i    i  i     v vviv   i vi  vv i    v 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_190907933_    793 AATGAA-ACCCATTTCAACATATGATGCTGGGATAATTGGCTAGCCACAT 841
                           -   - vi v        v   i        i  i   v  ?      
  L1M4_orf2#LINE/    388 AA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_190907933_    842 GTAGGAGAATGAAACTCAATCCTTATCTCTCTCACCTTATAAAAATATCA 891
                          i ii        ii vi i  i  i   v --   v    v   v  i 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCAC--ACCATATACAAAAATTA 484

  chr1_190907933_    892 ACTCAAGATGGATTAAAGACTTAAACCTAAGACCTGAAGCTATAAATATT 941
                               i      i ?    i    iv     v  i  i       - i 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACT 533

  chr1_190907933_    942 CT--AAAGGTAATATTGGAAAAAACCCTTCTAGACATTGGCTTAGGTAAG 989
                           --i   iv  i  v  ?iv   i -   vv   v    v     i  v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chr1_190907933_    990 GATTTC------ATGACAAAAACCCAAAAGCAAATGTAATAAAAACAAAG 1033
                          i    ------      -----         v v i  i    iv   i
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACA-----CCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_190907933_   1034 ATAAATTGCTGGGACTTAAATACACGTAAGAGCTTTTGCACAGCAAAAGG 1083
                            i  viv v      v vi v vv   i i      ii vv    i i
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_190907933_   1084 AAC-AGTAAGTGGAGTAAACAGACAACCCAAAGAGTGGGA-AAAATCTTT 1131
                         v  - vi   -ii   i  v          v   i     -     v   
  L1M4_orf2#LINE/    678 CACTATCAAG-AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_190907933_   1132 ACAATCTATACACCTGATAAAGGACTAATATCCAGAATCTACAATGAACT 1181
                         i   vii   i i       i     vi          v  i  v     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_190907933_   1182 CAAACATATCAACAAGAAAAAAACAAACAATCCCATCAAAGAGTAAGCTA 1231
                          vv   vv    i  v     i     i  i  v  i?  i i ii  v 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_190907933_   1232 AGGACATCAATGGACAATTCTCAAAAGAAGATAT 1265
                             iv v   i    v     v           
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.29 (117 / 91)
Gap_init rate = 0.02 (16 / 772), avg. gap size = 1.88 (30 / 16)  

 323 11.67 0.00 0.00  chr1_190907933_190910063     1579  1638 (493)    L1M4_orf2#LINE/L1      849   908 (0)  

  chr1_190907933_   1579 CAAAAAAGATATGCAAATGGCCAACAAACATAGGAAAAAATGCTCAACAT 1628
                             i       i           i  i  i v     i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_190907933_   1629 CACTAATGAT 1638
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 6.00 (6 / 1)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.00 (0 / 0)  


 302 27.06 3.53 0.00  chr1_190920852_190924935     2844  2928 (1156)    L1M4_orf2#LINE/L1        1    88 (820)  

  chr1_190920852_   2844 TGGAAAGATAGTCCATGCTCAAGGGTTAGAAAAATTAAT---GTTCAAAT 2890
                                   vi     i   v  i  i   i v     ---   v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190920852_   2891 GACAATATCAACAAAAGCAATTTACAGATTTCATGCAA 2928
                          i     iivv v   vii  i        iv i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAA 88

Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 3.00 (3 / 1)  

2024 25.68 5.14 1.51  chr1_190920852_190924935     2930  3591 (493)    L1M4_orf2#LINE/L1      223   908 (0)  

  chr1_190920852_   2930 CCCAAT--CAAAATTTACTACCAAGCCATCATAACCAA------------ 2965
                               --     i       v    i ivi   i   ------------
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_190920852_   2966 -------AAAGA--GACATATAGACCAATGGAACAGAAAATAAAACCCAG 3006
                         -------  i  --          i        i    vvv i ii    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_190920852_   3007 ATATAAATTCACACATCTACAGGTAACTCATTTTCAACGAAGATACCAAG 3056
                          v     ii  i    i  ii vi  i v      i  i i i i     
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_190920852_   3057 AGCACACGATGGAGAAAGGATAGTCTTCTTAATAAATGGTAGCAGGAAAA 3106
                          v  iv i    i     i        i i  i       ivii   v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_190920852_   3107 CTGGATAACTGTCTACTGAAAAATAAAACTAAATCCTTATCTCTCACCAT 3156
                                ? iiiv i vi  i   i  ii ii i  i  i   v      
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_190920852_   3157 ACACGAAAATCAAATAAAAATGGATTAAGGATTTAAATCTAAGACCTGAA 3206
                          i  i     i  v v         i ?i  ii     v     v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_190920852_   3207 ACTATGAAACTGCTAGAGAAAAAAAAAACACCTGGGAAACATTCCAGGAC 3256
                              i     vi    ----- i      ivv ? v  vvi i iv   
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGA-----AGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_190920852_   3257 ACTGGTCTTGGCAAAGACTTTTTGAGTAAGACCTCAAAAGCACAGGCAAC 3306
                         vi   vi v     v ii  i  iii  v   vi          i     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_190920852_   3307 CAAAGCAAAAATAGGCAAATCCGACTAAATCAAG-CTAAAAATGCTTCTG 3355
                         v    v        ii    iv    vv     i-i      --   i  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA--CTTTTG 665

  chr1_190920852_   3356 TACAGCAAAGGAAACAACCGATAAAATAAAGAGACAATTCCCAGAAAGGG 3405
                          i vv       v  v i i v   i i  i      ii v     v   
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_190920852_   3406 AGAAAATATTTG-AAATCTATCCATCTGACAAG--ATTAATAACCATAAT 3452
                                     -     -  vi      i   -- i vi  v   v   
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATC-ATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_190920852_   3453 ATATAATAAGCTCAAACAATTCAATAGCAAAATAAGAAGAAGAATCCAA- 3501
                               vi i   vv    i      ii    --   vi  v  i    -
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAA--AGACAAATAACCCAAT 812

  chr1_190920852_   3502 -----AATGGGCAAAATAATTGAACAGACATTTCTC-AAAAAAGACATAA 3545
                         -----          iv v     i           -   i    i   v
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_190920852_   3546 AAATGGCCAACAGGTATATTACGAATTGCTCAACATCACTAATCAT 3591
                                   i i i i  v vi iv            ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (108 / 59)
Gap_init rate = 0.02 (12 / 686), avg. gap size = 3.67 (44 / 12)  


2451 22.78 4.88 1.48  chr1_190937238_190938901      496  1171 (492)    L1M4_orf2#LINE/L1      210   908 (0)  

  chr1_190937238_    496 AGAACATCACATTACCTGACTTCAAAGT---------AGCTGCAGTAATC 536
                           i  -     i v  ii i      ii---------    i        
  L1M4_orf2#LINE/    210 AGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_190937238_    537 AAAACAGCAAGGTATTGGCAATAGAAACAGACACATAGACTAATGGAAAA 586
                           i    iiv    i     -  iii i     i     ii       v 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATCAATGGAATA 307

  chr1_190937238_    587 GTATAGATAGCCCAGAAATAAATT-ATGTTATATATGGTGAGCTGATTTT 635
                          v  v  v  i           ii-  ii-  v      v ii       
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATAC-ATTTATGGTCAATTGATTTT 356

  chr1_190937238_    636 TGACA-----------------CAATGGGGAAAGGACAGTTTCTTCAATA 668
                         i    -----------------            i i   i i     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_190937238_    669 GATGATGGTGGGACAACTGGATAGCCACCTACAGAAGAATGAAATAATTA 718
                         i   i  v               ?    v i  i         i --- i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT---TG 453

  chr1_190937238_    719 GATCCTCATCTCATACCATATACAAAAATTAACAGAAAATCAATTAGAGA 768
                           i  ii i    i                   vv     vi  i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_190937238_    769 CTTAAATGTAAGACCTAAAATTA--AAACTCCTCAAACAGAAAGTAGAAG 816
                          i           v      i  --      i vi  v i  vi   i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_190937238_    817 AAAAGCTCTATGACATTGGTCTGGGCAATTATTTTTTAGATATGA-ACCG 865
                         v   v  iii    v    vi i      vi   i          -   -
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC- 602

  chr1_190937238_    866 AAAAGCACAGGTAACAAAGCCAAAAATAGACAAAT-GGATTACATTAAA- 913
                                  i i      ivv         i    -   i v   i   -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_190937238_    914 CTAAAAAGCTCTGAACA-AAAAAGAAACCATAAACACAATGAAGAGACAA 962
                         i      vi i  vi v-v   i  v  i  v  v v i    i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_190937238_    963 ACTATGGAATGGAAGGAAATCTATTTGCAAACCCTACAACTAATAAAGTA 1012
                         v i ii      i  i    --         i v  i v  i    i v 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAAT--ATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_190937238_   1013 TTCATATCCAAAATATATAAGAAATTCAAACAATTCAATAGTAAGAAAAC 1062
                         i ii      i         ii  i  vv    i      i   i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_190937238_   1063 AAATAACCCAATTGAAAAATGGGCAAAGGATCTGAACAGCAATTTCTCAA 1112
                                      ?                 i    i  vv       v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_190937238_   1113 AAGAAAACATGCCAAATGGCCAAAAGGTATAAGAAATAATGCTAAATATT 1162
                              i i  i -          v i i i v    vi     v  i  i
  L1M4_orf2#LINE/    851 AAGAAGATATAC-AAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_190937238_   1163 ATTAATCAT 1171
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.26 (104 / 46)
Gap_init rate = 0.02 (15 / 699), avg. gap size = 2.87 (43 / 15)  


 206 30.56 1.39 0.00  chr1_190948020_190952805     3022  3093 (1693)    L1M4_orf2#LINE/L1        1    73 (835)  

  chr1_190948020_   3022 TGGAAAGACATCCACTATTCATGGACAGGAAGAACAAATAT-ATTTAAAT 3070
                                 i    vv i        iv      viv     -i  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_190948020_   3071 GTTCACACTATCTATATTAGTCT 3093
                          viv i   vi i v   ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCT 73

Transitions / transversions = 1.20 (12 / 10)
Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1)  

2750 26.85 2.15 0.36  chr1_190948020_190952805     3456  4293 (493)    L1M4_orf2#LINE/L1       56   908 (0)  

  chr1_190948020_   3456 TACCACCCAATTCAGTTTATAGATTCAATGCAATTCCTATGAACATCTGA 3505
                            iv     v iii i  i        i     i     v  v   iv 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_190948020_   3506 -TTGCATTATTTACAAAAATAGAAAAGAAAATTCTAAAATTCATATGGAT 3554
                         -i   v  v   i  i    v  v   vvi  i                v
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_190948020_   3555 -CACAATGATTCC-GAATAGTTTAAGACA-TCTTGAGCAGGAAGAACAAA 3601
                         -ii   v ivi  -      ii-  i   -      iv i          
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCC-AAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_190948020_   3602 GCTGGAGGCATAACACCTCT-GATTTCAAAATATGTTTCACAGG-ACAGT 3649
                          i      vv v    i  i-i         iv ii v  v  v-     
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_190948020_   3650 AATCAAAAC-GTATGGTACTGGCATATAAACAGACATTTAATACTAATGG 3698
                               i  -  i             vii i      v  i- ii     
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG-ATCAATGG 303

  chr1_190948020_   3699 ATGAGAAAAGATAGAGCAGAAATAAATCCACACATTTTTAGTCAACTGAT 3748
                          vv    vv  v  vv          i   i      v i     i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_190948020_   3749 CTTTGACAACATTGTCAAGCACACAAAATGGGAAAAGGG-AGTCTCATCA 3797
                         i  i     viv  i    vv  ivv      i    ii-     iv   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_190948020_   3798 ATAAACAATGTTGTGAAAACTGGATATGCATATGCAGAAGAAGAAAATTG 3847
                          i   iii  i  v  v         ?v  i     i     vi  i   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_190948020_   3848 TATCTTTAATTTATAACATATACAAAAATAAACT--AAACTGACTACAGA 3895
                         v i ii  vi i i v             v    --   iv  ii ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_190948020_   3896 CTTAAATTTAAGACCTGCAACTATAAAACTATTAGGAGAAATCCTAAGGA 3945
                          i     v     v  iv            v    i     v v  -  ?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA-GGN 552

  chr1_190948020_   3946 ATAAG-CTTCTTGATATTCATCTTGGAATTAATTT-TTGGATATAATACC 3993
                         i   i-    v   iv  vivi v  v v ii   -  i     i i   
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_190948020_   3994 AAAAGCACAGATAATGAAAGAAAAAATAAGTGGGTTCG----CATCAAAC 4039
                                  iii  ii            ii iii  v ----       v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_190948020_   4040 TAAATAGCTTCTGCGCAACAGGGTAGGCAATCAACAGAGTGTAAAGACAA 4089
                          v  v i   i  i  vv  ii v vi v     v i    v        
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_190948020_   4090 CTCACAGAATGGAAGAAGGTATTTTTAATCCATCTATTTGATGAGAAGTT 4139
                          i          i    ii     vi  vi   v   i    i  iiii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_190948020_   4140 AATATCTAAATTATATAGGGAACTCATAAAAGTCAATAGAATAAAAGCAA 4189
                         vi    i i v      ii      v  v  v      iv v   ii   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_190948020_   4190 ATGACCCCAGTAGAAAATGGTTAAAAGACATACATAGACATTTCTCAAAA 4239
                           i    v v ?i       vi   i  iv iv             v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_190948020_   4240 GAAGATATACAAGTGGC--ACAGCTATGTGTAAAGATGCTCAACATCACT 4287
                                     i    -- i ivi ii  v                 ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_190948020_   4288 AATTAT 4293
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.46 (131 / 90)
Gap_init rate = 0.02 (16 / 853), avg. gap size = 1.31 (21 / 16)  


2527 25.67 3.51 2.78  chr1_190977514_190979331      500  1325 (493)    L1M4_orf2#LINE/L1       77   908 (0)  

  chr1_190977514_    500 GATTCAATGCTATTCCTATCAAACTACCAA-TGATGTTTTCATAGAATTA 548
                                i  v  i         v v   i-  viv    iii    v v
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

  chr1_190977514_    549 GAAGAAACT-ATTCTAAAATTCGTATGGAACCAAAAAAAAAAAAAAAAGC 597
                           v-  i  -  i         i       -------- viv  iii v 
  L1M4_orf2#LINE/    127 GAC-AAGCTGATCCTAAAATTCATATGGAA--------ATGCAAGGGACC 167

  chr1_190977514_    598 CTGAATAGCCAAAGCAATCGTATGCAAACAGTACAAAGCCAGAGGCATCA 647
                          v           i     v iviv  iv  v      iii    vv   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr1_190977514_    648 CACTACCCAACTTCAAGCTATACAACAAGGCTACAGTAATCAAAACAGCA 697
                             v     i     iviv   v    i              i    ii
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_190977514_    698 TAGTACTGGTACAAAAATAGACACATAGACAAATGGATCATGGTGGAGAG 747
                          i       i i  ii       i     iv      vi vii v     
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_190977514_    748 CCTAGAAATAAAGCCACACACCTACAACCATCTGATATTTGACAGAAA-- 795
                         i i         v   i   ii  iiii  vi    v  i    iiii--
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_190977514_    796 -CAAG------CAACAGGGAAAGGAATCG-CTAGTCAATAAATAGTGCTT 837
                         -    ------   ii       -   v -  vv    i    i     v
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_190977514_    838 GCATAACTTTCTAGCCATAAGCAAAAGATTGAAACTGGACCTTTTCCTTT 887
                          v i    vvv  ?   i v        v    ii      ii v   iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_190977514_    888 TATCATAAACTAAAATCAATTCGAAATGGATTAGAGATTTAAATGTAAAA 937
                         i i    v  v     i  i  i        i ?   ii         i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_190977514_    938 GCCAGAACTATAAAAACCT--GGAAATAAC-TAGG---AAATAC-CAT-- 978
                           i i          vi  -- i i v   -    ---    vi- i --
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_190977514_    979 TCTGGAAATAGGCACTGGGAAATATTTTGTTATAAA-GACTCCAAAAGCA 1027
                         i  v iiv      v   -------   v   v v -   v         
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGG-------TTTCTTAGATATGACACCAAAAGCA 609

  chr1_190977514_   1028 ATTGCAACAAAAACAAAAATTAACAAGTGGGACTTAATTAAACTGAAGAG 1077
                         vvv         iv      vi i  i v      v  i   v v  i i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_190977514_   1078 CTTCTGCACAGCAAAGGAAACTTTTAACAGAGTAAAGAGATGACCTATGA 1127
                            i  ii vv       v   v i  v i   i  i   ii   i iii
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_190977514_   1128 AATGGAAGAAAATATTTGCAAACTATGCATCTGACAAGGGCCTACTATCC 1177
                              i                ii  ii      i     v  vv     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_190977514_   1178 AGAATCCATAAAGAACTTAAACAATTTAACAATAAAAAAA-----AACC- 1221
                              vi          ivv    i i  i        i -----    -
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_190977514_   1222 -ATTAAAAAATGGGCAAAAAATGTGAATGGACACTTCTCAAGAGAAGACA 1270
                         -   ?             ii  v     i    i     v i      i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_190977514_   1271 TACACGTAGCCAGCACGCATGTAAAAAAAAAAAAATGTTCAATATCACTA 1320
                             vi i    ii v   ii i    i ------  i    i    ???
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGA------TGCTCAACATCAZZZ 903

  chr1_190977514_   1321 ATCAC 1325
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.68 (131 / 78)
Gap_init rate = 0.02 (18 / 832), avg. gap size = 2.89 (52 / 18)  


2570 26.91 1.59 5.40  chr1_191090774_191094819     2628  3571 (475)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_191090774_   2628 TGGAAATAATATCC-ATGCTCATGGATAGGAAGATTCTGCATCATTAAAG 2676
                               -i      -   i        v      i ivii  ii    ii
  L1M4_orf2#LINE/      1 TGGAAA-GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_191090774_   2677 TGGCCATACTACCCAAAGCAATTTATAGATTCAACATTATTCTTATCAAA 2726
                             v     v      vii  i  i         iiv  i i       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_191090774_   2727 CTACCAA-TGCTATTCTTCACAGACCTAGAAAAAATATTTTTAAAATTCA 2775
                         v v   i-   i-  i  ii    vv v  v  iv iv ii         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_191090774_   2776 CATGGAACCAAAAAAGAGGCTGAATAACCAAGGCAATTCTAAGCAAAAAC 2825
                         i      viiv  ii  vv v     i    ii    ii ----------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT---------- 188

  chr1_191090774_   2826 AAAAACAAGAAAAATAGAAAAAAACAGACAAACAAAAAACAAAACTGGAG 2875
                         ----------------      i ----------- i      ii     
  L1M4_orf2#LINE/    189 ----------------GAAAAAGA-----------AGAACAAAGTTGGAG 211

  chr1_191090774_   2876 GCATCACATTACCCAACTTCAAACTATACTATAGGGCTATTGTAACAAAA 2925
                          vv     i v     i      viv     i ii    iv    iv  i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_191090774_   2926 ACAGCATGGTACTGGCATAAAAGCTGACACATTGGCCAATGGAACAAAAC 2975
                             ii              iiiiv    i  v ii        i i  i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_191090774_   2976 GGAGAGCCCAGAAGTAAGGTTGCACACCTACAACCATCTGATCTTTGACA 3025
                         v     i      i   iviiii   ii  iiii  vi    i  i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_191090774_   3026 AAGCTGACAAAAAGAGAAAATGTGGAAAGAAATCCCTATTCAATAAATGG 3075
                          i v  v   i vv vvv    v        vvvi  v     i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_191090774_   3076 TGCCAAAATAACTGGACAGCCATATGCAGAAGATTGAAACTGGACTTCTT 3125
                            iiii i       i ?   i     i    v    ii     ii  v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_191090774_   3126 CCATATACCATATACAAAAATCAACTGAAAATGGATTAAAGACTTAAAAA 3175
                           vi i               i    v         i ?    i    vi
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_191090774_   3176 TAAAACCCCAAACTATAAAAACCCTGGAAGACAGCCTGGAAGGCAATACC 3225
                            i v iv           vi i i     v i v i i? vv   -- 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C 559

  chr1_191090774_   3226 ATTCTGGACATAAGAATGGACAAAGATTTCATGTTGAAGATG---CCAAA 3272
                         -   vv   v vi iv i i   v i    ---  ii v   ---     
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTC---TTAGATATGACACCAAA 605

  chr1_191090774_   3273 AGCATTTGCAACAAAAGCAAAAATAAACAAATGGGATCTAATTAAACTAA 3322
                             ivv          v       i i    v   ii v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_191090774_   3323 AGAGCTTCTGCACCAGAAAAGAAACTATTAAGAAAC-----AGACAACCT 3367
                          i i   i  ii ivv   i  v     i      v-----        i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_191090774_   3368 ACAGAATGGGAATAAATATTTGCAAACTATGCATCTGACAAAGGTTTAAT 3417
                                    iv             ii  ii      i  i  vi vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_191090774_   3418 ATACAGTGTCTATAAGAAACTGTAACAAATTTACAAGCAAAAAA-AAAT- 3465
                           v   vi v     ii    v v    v iv i  vv    i -    -
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_191090774_   3466 -CCCA--TTAAATATGGGCAAAGGACATGAACAGAGAGTTTTCCAAAGAA 3512
                         -    -- ?   v            iv    i   v v  i         
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_191090774_   3513 GACATACCTACAGTGAAGAAACATATGAAAAAAAAAAAAAACTCAACATC 3562
                           i    vv ii iv  v  i  i       i vi------         
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATG------CTCAACATC 899

  chr1_191090774_   3563 ACTGATTGT 3571
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.66 (156 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.40 (66 / 15)  


 629 20.36 20.36 5.82  chr1_191115387_191118801     1014  1288 (2126)    L1M4_orf2#LINE/L1      145   459 (449)  

  chr1_191115387_   1014 TTC-TATAGGAAAGCAATGAAC----AAT--TCAAAAC-----TGAAACT 1051
                            -   i i  v    v i  ----   --i      -----     --
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-- 192

  chr1_191115387_   1052 AAGATGACTTCATTTACAATTGCATCTAGAAGAATACAATAATTCGCAAT 1101
                             v  --------    ---- vi i  i  v -  -i v   v    
  L1M4_orf2#LINE/    193 AAGAAGA--------ACAA----AGTTGGAGGACT-CA-CACTTCCCAAT 228

  chr1_191115387_   1102 TTCAAAATTTAGTTTGAAGCTATAG-AATTAAGACATTATGGTACTAATA 1150
                                i   v vii      i  -   i      v i       iii 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_191115387_   1151 T----------------------------------------CACAAGTAA 1160
                          ----------------------------------------  v  i   
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_191115387_   1161 ACCCTTACATTCATGCTCAATTGATTTTTAACAAGTGTGACAAGACAATT 1210
                             v      i   v            ii     v   v      v   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_191115387_   1211 CAATGGAGAAA-AACAGTATTTTCCACACCTAGAGCTGGAACAACTAGAT 1259
                               i    -  i   v     v   vv i v     i      i   
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_191115387_   1260 ATCCAGAGACAAAGG--TGTAGGGAGACCCC 1288
                          ?   v vi    i --  v  vvi      
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCC 459

Transitions / transversions = 1.12 (29 / 26)
Gap_init rate = 0.04 (13 / 315), avg. gap size = 5.54 (72 / 13)  

 671 25.26 2.58 0.52  chr1_191115387_191118801     2146  2339 (1075)    L1M4_orf2#LINE/L1      435   632 (276)  

  chr1_191115387_   2146 ATACAGAGGAATGAAGTTGGACCCTTTCTTTACATCATACACAAATCTTA 2195
                           i  i i                i v i i   i    i     vv   
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_191115387_   2196 ATTGAAAAGGAATCATAGACCTAAATACATAAGCTAAAGTCTA---AGCT 2242
                          i v    v i    ?          ii vi       i-   --- i  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACT 533

  chr1_191115387_   2243 CTTTTAGGAAAATATAAGATTAAGTCATTGTGACTTTGATTTAGGCAAAT 2292
                            vv i     i   i ?v   i  v i     i   iv        vv
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_191115387_   2293 CCTTCTTACATATAACAGCAAAAAAAAAA--AAAAAAAAAAAAAACGGA 2339
                         vi      v    i   v     iv v  --  v    i      ii  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

Transitions / transversions = 1.47 (28 / 19)
Gap_init rate = 0.02 (3 / 198), avg. gap size = 2.00 (6 / 3)  

1035 19.62 8.30 0.38  chr1_191115387_191118801     2658  2922 (492)    L1M4_orf2#LINE/L1      623   908 (0)  

  chr1_191115387_   2658 AAAATATAGGTAAAGTGGCCTTCATTAGAATTAAATATGTTTGCAAGTCT 2707
                             v    i    v   v      i i       v iv    iivv  v
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_191115387_   2708 ATGGATGCCATGAAGAAAGTGGAGGGACAACCCACAGAATAGAAGAAAAC 2757
                          v   ii i  v         i ii               i i      i
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_191115387_   2758 ATTTGAAAATTATGTACCTGATAAAAAACTTATATCTA--ACATATAAAG 2805
                              v    i  i  i       iii    i    i -- i        
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_191115387_   2806 AACTGATACTGCTGAATAA--AAAATAC-------------TAAAAATGG 2840
                             vv   vi  v     --    v  -------------?        
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_191115387_   2841 GCAAAA-ATCT----AGACATTTTTTCCAAAGAAGGCATACAATTGGCCA 2885
                              i-  i ----        i -         ii      v      
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCT-CCAAAGAAGATATACAAATGGCCA 871

  chr1_191115387_   2886 ATAAGTACATGAAAACATGTTCACCATCATTAGCCAT 2922
                              i         v   i   v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.02 (6 / 286), avg. gap size = 3.83 (23 / 6)  


2660 28.19 2.68 1.12  chr1_191140404_191142534      745  1638 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_191140404_    745 TGGAAAAACATTCCATGCTTATGGATAGGAAGAATCAATATTGCAAAAAT 794
                               i i  i     i i      v      v i       iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_191140404_    795 GACCACACTGCCCAAAGCAATGCATAGATTCAATGCTATTTCTATAAGAC 844
                          i v i   v      vii  vi i        i  v  ii    v i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_191140404_    845 TACCATGGACATTCTTCACAGAACTAGATAATACT-ATTTTAAAATTCAT 893
                          v   vvvi v  i  ii     v v  i  -i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_191140404_    894 ATAAAACCAAACAAGAG-CCC-GAATATCCAAGGCAATGCTAAGCAAACA 941
                           ii  -- vi    i -   -     v    ii    vi i iv  iv 
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_191140404_    942 GAACAAAGCTGGAGGCATCATGCTTCTTGACTTCAAACTCTACTATATGG 991
                                 i      vv   ii    iii i      vii     i vi 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_191140404_    992 CTGCGGTAACCACAACAGCATGGTACTGGGACAGGAGCAGACACATTGAC 1041
                           i i    i  vi    ii         v i i iii     i  v  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_191140404_   1042 CAATGGAACAGAACAGGGATCCCAGAAATAAGGCTGCACACCTACAAGTA 1091
                                 i    iv i  vi          iv iii   ii  iiivi 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_191140404_   1092 TTTAGTCTTTGACAAATCTGACAAACACAAGCAATGGGGAAAGGATCCCC 1141
                         v  ii i  i     ivv  v   ivv  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_191140404_   1142 TATTCAACAAAGAGTGCTTGGATAACTGGCTAGTTATATGCAGAAGATTG 1191
                          v         vi     v   i      v  ?ii i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_191140404_   1192 AAATTAGAGCCCTTTCTTACACCATATACAAAAATTAACTCGAGATGGAT 1241
                           i  i  v    vi  i                       i i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_191140404_   1242 TAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCAGGAACACAACC 1291
                         i ?    i         i v i            vi ivi   v v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_191140404_   1292 TAGGC---AATATGACTCAGGACATAAGAATGGGCAAAGATTTCATGACA 1338
                             ?---   v ---  iv   v vi iv i     v i    v --- 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCT---TCGTGACCTTGGGTTAGGCAATGGTTTCTT---A 591

  chr1_191140404_   1339 AAGATG----CAAAAGCAATTGCAACAAAACAAAAGTT-GACAAATTGGA 1383
                         i v   ----        vvv         v    iv -  i        
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_191140404_   1384 TCT------AATTAAAGAGCTTCCACCCAGCAAAAGAAACTATCAACAGA 1427
                         ii ------       i -   iiiiv vv    i  v        v i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_191140404_   1428 CTGACT-GAAAACCTACAAAATGGG-GAAAATTTTTGCAAACTATGCATT 1475
                         v   vv-  v    i   i      -      v        ii  ii  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_191140404_   1476 TGACAAAGT-CTAATATCCAACATCTATAAGGAGCATACACAAAT---TT 1521
                            i  i v-  vi      iv  v     i  i vivi    v --- v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_191140404_   1522 ACAAAAAAGCCAACAATCCCATTCGAAAGTGGACAAAGTACATGAACAGA 1571
                          i     ii v  i  i  v   ?i   i   i     v iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_191140404_   1572 CACTTCTCAAAAAAAGATATACATGTGACCAACAATCATGAAAAAAAA-A 1620
                           i     v   i          vi  i    i  v  iivi    i -i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_191140404_   1621 CTCAACATCACTGATCAT 1638
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (153 / 95)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


2106 24.34 4.37 1.25  chr1_191144940_191147358.rev      692  1332 (1087)    L1M4_orf2#LINE/L1        2   662 (246)  

  chr1_191144940_    692 GGAAAAACAATCCTAGGTTCAT-------AATATTTGATATT--TA-TAT 731
                              i i -   i v      -------  v i  i     --  -v  
  L1M4_orf2#LINE/      2 GGAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_191144940_    732 GTTACCACATTTGAAATTTAATTAGAGATTCTATGTTAATC--TGTCAAA 779
                          vi vi  viiiv     v vi  v      v i i-    -- i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAAA 99

  chr1_191144940_    780 -TTCCATGTGCTTTTTTCCCCGAAATTGATAAATTGATCCTAATGTTCAT 828
                         - i   vv   i     iv v        i  ii         vi     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_191144940_    829 ACGCAATGAAAAAAGACACAGAATAGCCTAAACAGACTTGACAAAGAAGA 878
                          i v  vviv  ii   v          v     iv     v        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_191144940_    879 ACAAGAGTGGAGGATTCCATCATTTACTAATTTGAAAAC--ACTGTAAG- 925
                             iiv       i  - -  i  v i     v     --   ii  i-
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTC-A-CACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_191144940_    926 --ATAGTACCAATCAATACAGTGTAACACTTGTAAGATAATAGAAAAATT 973
                         -- i    ---     v       iii   v i vi vi     v v  v
  L1M4_orf2#LINE/    248 CTACAGTA---ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_191144940_    974 GGTCAATGGAATAAAATTAAAATTCCATAAATATGCCCTTATATTTGTGA 1023
                          i           i    i i v    v     vi   v  i    i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_191144940_   1024 TCAATTCGTTTTTGATAAGACTTCCTGGACAATTCAAAGGGGGAAAGAAT 1073
                               vi    i  i   iv v  vi   v      -v           
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAAT 393

  chr1_191144940_   1074 AGTATTTTCAACTATTGATGTTGATATAATTGGATATCCACAGGCAAAAG 1123
                            v        v v  i  i  iv i  i      ?     v       
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_191144940_   1124 AATGACGTCAGACCCCTTCCTAACACAATTAACAGACATTAACTCAAAAG 1173
                              v  ii       v   v    v  vv   i v            v
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_191144940_   1174 GAATCATAGACCTACATGTAAAAGACATAATTGTAAAAATCTTAGAAGAA 1223
                          i    ?       v      i  vi v  i i     v           
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_191144940_   1224 AATGTAAGATTAAATCAGTGAAATCTTCATTTTGGCAAAA---TCTTAGA 1270
                           ii  i ?v      vvi vi i   viv  v     vi---       
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_191144940_   1271 TAT-----CAAAAGCTCAATTTACCAAAGAAAA--TAAATAAATTGGACT 1313
                            -----       v   viv  v        --  i            
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_191144940_   1314 CCATTAAATTTAAAAACTT 1332
                         i   i   v          
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTT 662

Transitions / transversions = 1.07 (79 / 74)
Gap_init rate = 0.02 (16 / 661), avg. gap size = 2.25 (36 / 16)  

 976 16.72 7.17 2.39  chr1_191144940_191147358.rev     1636  1928 (491)    L1M4_orf2#LINE/L1      602   908 (0)  

  chr1_191144940_   1636 CAAAA--ACAAGCAAACAAAGAAACAAACA-ACAA---------CAACAA 1673
                              --        vv       -   i - i  ---------  v   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAA 650

  chr1_191144940_   1674 CA--AAAAACCCTTGAGCTTTAAAGAATG-TCTCAAGTAC---AAAAGA- 1716
                         v --      ii   v    i    i ii- v     v v---      -
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_191144940_   1717 AATCATGAATAAAATGGGAGAGTATATTTGAAAATCATATATCTGATGCA 1766
                           i v--- i i         iv       v                ivi
  L1M4_orf2#LINE/    701 AACCC---ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_191144940_   1767 GGAATTATCTCCAGAATAAACAAAGAACTCTTACAATTCAGT--CAAAAA 1814
                            v  i v         v i               i   i --i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_191144940_   1815 GACAAAGAACCCAACTGAAAAATAGCCAAAGGATTTGAATAAACATTTCT 1864
                               v       i ?      i v               i        
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_191144940_   1865 GCAAGGAACATATACAAATGAGCAATGAGCAGATGATAATATGCTTGACA 1914
                         v   i   v           iv    i    v    v  v     ---  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT---CA 894

  chr1_191144940_   1915 ACATCAGCCAACAT 1928
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (25 / 23)
Gap_init rate = 0.04 (11 / 307), avg. gap size = 2.55 (28 / 11)  


2658 23.86 5.46 4.24  chr1_191186452_191188435.rev      597  1493 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_191186452_    597 TGTAAAGATATCACATACTTCTGGATTGAAAGAATTAATGTTATTAAAAT 646
                           v         v   ii iv       i    v     i  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_191186452_    647 GTCTGTACTAC--AGATT---TTACAGATTCAATGCAATTCCTATCAAAA 691
                          v vi    v -- i   ---i           i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_191186452_    692 TTCTAATAGCATTTTTCACAGAAACAGA-AAAC-AATCCTAAAACTTATA 739
                          i i iiv  v     ii      iv  -  i -i         i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_191186452_    740 TGCAACCAGAAAAGATCACAAATAGTCAAAGAAA-CTT-AAGAACAAGAA 787
                           v  viiv  ii  i vvi     i    iv  -   -  i  v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_191186452_    788 CAAAGCTGAAGG-CATACATTACCTGATTTCAAATAATGTCACAAAGCTA 836
                              i  i   - vi   i v  ii        vvv iii         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_191186452_    837 TAGTAATCAAAACAGTGTGGTACTGGCATAAAAAAAGACACATGGAGCAA 886
                         i         i                    ii v     i  i  v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_191186452_    887 CAGAACACAATAAAGA-TCACAGAAACAAACCCATATATATATATATCCA 935
                         ii   i v   vi   -  -      i         i  v   iv-----
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGG----- 344

  chr1_191186452_    936 TTCAACTAATATTCAACAAAAGTGCCAAGAATACACAATGGTGAAAGAAC 985
                         -    i i  v   i    ii         vi iv      v       i
  L1M4_orf2#LINE/    345 -TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_191186452_    986 AGTGTCTTTGTTAAACGCCATTGGGATAACTGGATGTTCAGATGCCAAGT 1035
                            v i  iivi   i viii     i        i?i  v    v  iv
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_191186452_   1036 AACAAAATTGGGCCCTTATATTATATCATACACAAAAATCAA-------T 1078
                           ii  i    i   i  iv i i i    i        i  ------- 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_191186452_   1079 G---CATAGACTTCAATGTAAAACCTGAAACTGTAAAAATCC--AAAGAA 1123
                          ---  ?    i v       i v  i     i     v  i--i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_191186452_   1124 AACATACGTAAAAAGTTCTTTG-AATTTT---TTGGG----GG------- 1158
                               v ?iv   --    i -i ii  ---  i  ----  -------
  L1M4_orf2#LINE/    544 AACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_191186452_   1159 GGTATAACACCAAAAGCACAGGCAACTAAAGCAAAAATA--T---CTGTG 1203
                          i   i              i     v    v       -- ---i  - 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG-G 640

  chr1_191186452_   1204 ATTACATCAAACCAAAAAGTTTCCACACAGTAATGGAGAC----AACAAT 1249
                          i v       viv    ii  iiiii vvi  v   v  ----  v  -
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA- 689

  chr1_191186452_   1250 CAGT-AAAGGA-AACCTATGGAATGGGAGAAAATATTTGCAAATTATATA 1297
                         -   -   i  -    i ii                        i     
  L1M4_orf2#LINE/    690 -AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_191186452_   1298 TCCAATAAAAGCCTAATATCTAAAATATATAAGAAAGTTGTATGTGTATT 1347
                           ii    ii v  vi    i i         ii  v i---------- 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC----------T 778

  chr1_191186452_   1348 TATATACACACACAAAACTCAATAGCAAAATATAATAATAATGACCTGAT 1397
                           i ------------        ii    - -i i  --  i   ii  
  L1M4_orf2#LINE/    779 TACA------------ACTCAATAATAAAA-A-GACAA--ATAACCCAAT 812

  chr1_191186452_   1398 TTAAAAATGAGGAAAAGATCTGAAGAGACATTTTCCCAAAGAAGACATAC 1447
                          ?       i v   i   i    v        ii          i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_191186452_   1448 AAAAGTCTGACAGGCATATAAAATGGTACTCAACATCAGAGATCAT 1493
                            v v ii i i   i  i   v i i          ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.39 (148 / 62)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.90 (87 / 30)  


1434 27.01 8.96 3.61  chr1_191336022_191339129.rev     1759  2617 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_191336022_   1759 AAATAGACTCCAAGTATATGTATTGGAAGTCTCAGTATTGTACAGATGTC 1808
                            v v ii   v  vi   v        v  i i      vv     v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_191336022_   1809 AATTTTTCCCAG--TG-TC-ATTAATTCAATGCATATCCA-ACCAAAATT 1853
                            vi i    i--  -  - ivi      i   -    v- i      i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCA-ATCCCTATCAAAATC 102

  chr1_191336022_   1854 ATGAAAGCTAA----TTTGTAGAC-TTGAAATCCTGATTTAAAAATAAAT 1898
                         vi---    iv----    i   v-    v vv     iiv     vv  
  L1M4_orf2#LINE/    103 CC---AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_191336022_   1899 ACAGGAAGGTAA---AC---GAATAACAAACAAAATGTTAAAAAGGAAAA 1942
                          ii i  v i  ---  ---     i v  v v   v  i    i   i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_191336022_   1943 A-AA---TGTAGGACTAACACTACTTGACATCAAGATTTAATATAAA-CT 1987
                          -  ---  v      v     v iii iv    i i   v  i   -  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_191336022_   1988 ACAGTAATAAATTCAGCATAGTACAAACA---GAATA----------TCA 2024
                                 v  vv   ii i    vii  --- i   ----------   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_191336022_   2025 ATCAAACAGAATAGATAGATAAGAAATAGACCCATAAAAAATATG-TCAG 2073
                           vi  i     v  v  viv       i       v vv-    -   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGGTCAA 348

  chr1_191336022_   2074 CTGATTGCTGACAAAAGAGAAACGGTAATGCAAGGGAGAAATTCATAGTC 2123
                         i     vii     ii v vv v iiv  v   v  i    v-v      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTC 397

  chr1_191336022_   2124 TTTTTAATAAATGGAACTGGAGCATTTGTATGTATGTATGGTGTATATAC 2173
                             i  i      vi    ii  --------- i---   -----   ?
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACA---------AC---TGG-----ATAK 430

  chr1_191336022_   2174 ACACACACAAACACATATAGAAAATGA---CTTACTTCACACCG-----A 2215
                         v    ii    viv  ---   iv  i--- i   i       i----- 
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAAT---GAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_191336022_   2216 AAAAC-AACTCAAAATTGATCATAATTATAAATATAAAGGGTAAAATCAT 2264
                             i-          v     ? iviv     i   ii v     ii  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_191336022_   2265 AAAATTTCTTTAAAA------ATAGTAGACAAGTTATATGACCTTTGGTT 2308
                             i i--   i  ------    v? vv  vi vii       v    
  L1M4_orf2#LINE/    528 AAAACTC--TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_191336022_   2309 TGGTTATGCATTTCC-AGATTTAAAAACAGTAACATGATTCATAAGAGAA 2357
                         v  iv   -i    i-    v i v v  iv i  ii viv i  i    
  L1M4_orf2#LINE/    576 AGGCAATG-GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_191336022_   2358 AAATT-GATAATTTAGGTTTAATTAAAATGGAAAATTTTCTGCTCTGTGA 2406
                            v -     v  i ii  v  i     vi    i   -  iv  vii 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAA 673

  chr1_191336022_   2407 AAGACAATATCAATAAAATTAAAAAGTCAGTGAAAGATGAAGAGAAAACA 2456
                          i    v      v   i v    iiiv viv v   vvii       i 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_191336022_   2457 TTTGCAAAAC---TATC-AATGAAGGACTTG---CT----TATACCAAGA 2495
                                 v ---    -i  i i       --- i----    iv    
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_191336022_   2496 ACTCTTA-AATTGCAACAA-----AGA---ATAACATCATTAAAAAA-GA 2535
                                -  i -   i  -----   ---     viv   ?     - i
  L1M4_orf2#LINE/    774 ACTCTTACAACT-CAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_191336022_   2536 ACAAAAGAT--GAACAGACACCTCACCAAAAAAGATATACAGATGGAAAA 2583
                         i    i   --   i     ii  v     i          i    vv  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_191336022_   2584 CAAGCATATAAAAA--TGTTCAATATCATTTTCCTT 2617
                         i     i  i    --  i    i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (130 / 98)
Gap_init rate = 0.05 (42 / 905), avg. gap size = 2.57 (108 / 42)  


2520 26.51 2.64 2.75  chr1_191341428_191343465.rev      639  1547 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_191341428_    639 TGGAAAAATATTCCATGCTCATGGATAGAAATGA-TCAAAATT-TTAAAA 686
                               i    i     i        v i  -  - i  v   -    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAA-GACTTAATATTGTTAAGA 49

  chr1_191341428_    687 TGGCCATATTTCACAAAGAAAGTTACAGATTCAATGATATTCCTGTCAAA 736
                             v   i i v    vvi vi           i vv  i   i     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_191341428_    737 CTTAAAATGATATTCTTTAAAGAA-TTAGGAAGAAATCTTTTTTTTATGA 785
                         v ivv iiviiv  i   iv    -  iiv   ----  ---------  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CT---------GA 136

  chr1_191341428_    786 TTTTAAAATCCATATGGAAGTA-AAAGGAGCCTGAATAGCCAAAACAAAT 834
                          ii      i         i i-  i   v  v               vi
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_191341428_    835 GTAAGCTAAAAGAACAAAGCTGGAGGCATCACATTACTGGACCTTAAACT 884
                         v i ivv i          i      vv     i v ivi ii i   vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_191341428_    885 ATACTGCAAGGCTACAGTAACCAAAACATCATAGTACTGATACTTAAAAC 934
                         v    i   i          i   i   vii i      ii - v ii i
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGAT 285

  chr1_191341428_    935 AGACACACAAAACAATGAAATAGAATAGAGAACCCCAAAACAAAGTCACA 984
                              i i i v     i        v    ii  vi   i   vi  i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_191341428_    985 CACATACAATCATCTCATCTTTGACAAAATTCACAAAAATAAGCAATGGG 1034
                           iv  iii   vi v  i  i     iiv vv   i vi vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_191341428_   1035 GAAAGGACACCCTGTTCAATATATGGTACTGGGATAACTGGCTAGCCATA 1084
                              i i vi  v     i v     i      i      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_191341428_   1085 TGCAGAAGATTGAATCTGGACCCCTTCTTTATACCATATATAAAAATCAA 1134
                             i    v    vi         v i i i        i      i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_191341428_   1135 CTCAAGATGGCCTAAAGACTTGGATTTAA-ACCCAAAACCATAAAA-TCC 1182
                              i    vii ?    i ii  v   - v i     i      -  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_191341428_   1183 TGTAAGGCAACCTAGG---AAATACCATCCTGAACATTGGAACAGGCAAA 1229
                          iv   iv   v    ---    -- v  v   v -    ivi      v
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT--CTTCGTGACC-TTGGGTTAGGCAAT 582

  chr1_191341428_   1230 GATTACATGAGAAA-GATACCAAAAGAAATCA--CAGCAAAAGCATAAAA 1276
                          i  v - v   v -  i        v --  --  i      v -    
  L1M4_orf2#LINE/    583 GGTTTC-TTAGATATGACACCAAAAGCA--CAAGCAACAAAAGAA-AAAA 628

  chr1_191341428_   1277 TTGACAAATGGGA-----TCTAAACTACAG-CTTCTGCACAGCAAAAGAA 1320
                          v  i    v   -----  v   i  v i-   i  ii vv    i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_191341428_   1321 ACTATCAACAGAGTAAACAGAAAACCTTCAGAATTGGAGAAAATATATGT 1370
                                 v i   i  v   v    iv      v           v  i
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_191341428_   1371 AAACTATGCATCTGACAAAGGTCTAATATTTGGAATATATAAGGAACT-T 1419
                            ii  ii      i  i  v  vi   iii          i     - 
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_191341428_   1420 GAAAATATTTATAAGCAAAAAACAACT--CCT--TTACAAAGTGGGCAGA 1465
                         v v  i- iv    vv    i    v --  i--  ?v   i      i 
  L1M4_orf2#LINE/    779 TACAAC-TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_191341428_   1466 GGACACCAACAGAGCCTTTTCAAAAGAAGACAATATATGTGGTCAA-AAT 1514
                            iviv  i   vvi  i  v        i -  i vi   i   -  v
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATA-TACAAATGGCCAATAAG 876

  chr1_191341428_   1515 CATATGAAAAAAATGCTCAATATCAGTAATCAT 1547
                           i       i -       i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 1.81 (49 / 27)  


 446 22.22 2.96 2.22  chr1_191360054_191365587      365   499 (5035)  C L1M4_orf2#LINE/L1   (0)   908   773  

C chr1_191360054_    499 AATTTTTAACATTCAACAATAAGAAAGCAAA-AACT---TTAAAAAAAAT 454
                           i i   vv i    i     i  ii    -   i---  ?     ---
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA--- 819

C chr1_191360054_    453 TGGGCAGATGATCTGATCAGGTATGTCACCAAAGAAGATATACAGATGGC 404
                               i v   i   vi  ii  v  v                i     
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

C chr1_191360054_    403 AAATAAATCTATGACAATATGCTCAACTTGAGATGTCAT 365
                         v     iivi    v  v         v v ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (17 / 12)
Gap_init rate = 0.02 (3 / 136), avg. gap size = 2.33 (7 / 3)  

3103 26.93 0.99 0.77  chr1_191360054_191365587     4136  5041 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_191360054_   4136 TGGAAAGACATTTCATGCTCTTGGGTAGAAAGAATCAATATCGTGAAAAT 4185
                                 i  ii    i  v   i v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_191360054_   4186 GGACATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATAAAGC 4235
                           vv     v      v i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_191360054_   4236 TGCCA-TTGTCTTTCTTCACAGAATTAGAAAAATCTGCTTTTAAT-TTCA 4283
                          v   -i  i    i  -i     v v  v  i-   v ii   v-    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_191360054_   4284 TATGGAACCAAAAAGGAGCCTGCATAGCCAAGACAATCCTAAGCAAGAAG 4333
                                viiv  i   v  v v        i      i i iv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_191360054_   4334 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4383
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_191360054_   4384 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACATATATATATAGA 4433
                           i     i   i    ii         i i--  iv   v i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGA 296

  chr1_191360054_   4434 CCGATGGAAGAGAATGGAGGATTCAGAAATAATGTCACACATCTAGAACC 4483
                         i i      v     v   ii i         vvi  i    i  viii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_191360054_   4484 ATTTGATCTTTGACAAACCTGACAAAAACAAGCAATCGGGAAAGGATTAC 4533
                          v     i  i     ivv  v   i v  vv    v       i  vii
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_191360054_   4534 TTATTTAATAAATGCTATTGGGAAAATTGGCTAGCCATATGCAGAAAACA 4583
                         i v  i  i     v ii     v  i   v  ?   i     i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_191360054_   4584 GAAACTGGACCTCTTCCTTGCACTTTATACAAAAATTAACTCAAGATGGA 4633
                            ii      i  v   ii   iv                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_191360054_   4634 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 4682
                          i ?    i           v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_191360054_   4683 CCTAGGCA-ATACCAATTAG-AACATAGGCATGGACAAAGACTTCATGAC 4730
                          v    ?i- v i --  v -i  v v  vv i i   v ii   v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_191360054_   4731 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 4780
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_191360054_   4781 TAATTAAACTAAAGAGCATATGCACAGCAAAAGAAACTATCATCAGCATA 4830
                          v  i   v v  i i v v  ii vv    i  v       vv ivi i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_191360054_   4831 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGT 4880
                           v  i     i                 v       vii  vi     v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_191360054_   4881 CAAAGAGCTAATATCCAGAATCTACAGGGACCTTAAATAATTTTACAAGA 4930
                         i  i ii  vi          v  i ii  v  ivv i  i iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_191360054_   4931 AAAAAACAAA---CCCA-TCAAAAAGTGAGTGAAGGATATGAACAGATAC 4976
                             i     ---    - i?    i  i ii      v    i   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_191360054_   4977 TTCTCAAACGAAGACATTTATGTGGCCAATAATCATACGAAAAAAAGCTC 5026
                              v  v     i  vi vi          v  i i     i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_191360054_   5027 ATCATCACTGGTCAT 5041
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (139 / 101)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


2356 24.11 1.66 4.97  chr1_191367661_191369396      460  1243 (493)    L1M4_orf2#LINE/L1      151   908 (0)  

  chr1_191367661_    460 TGGAAACATTGTAAGAAGGAATTAAAGAAAGCATATATCCATCCTGAGCA 509
                               ---  i   --   vii i - v   -i v v v   i   -- 
  L1M4_orf2#LINE/    151 TGGAAA---TGCAAG--GGACCCAGA-ATAGC-CAAAACAATCTTGA--A 191

  chr1_191367661_    510 AAAAATAAAAAAAATTGGAGGAATCACATTACTTGACTTCAAATTATACT 559
                            i vi  v   i        v     i v iii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_191367661_    560 GCAAATCTGTAGTAACCAAACCAGCATGG-ATTTCCATAAAAAAAAACAC 608
                         i    v  ii     i   iv   ii   - i vv     ii v i   i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_191367661_    609 ACAGAGCAGTGAAACAGAATGGAGAGCCCAGAAATAAATCCACATACCTA 658
                          i   v  i  i  i     v     i           i   i i ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_191367661_    659 CAGTGAATC-ATTTTTGACAAAAGTACCAAGAGCATACATTGTAGAATAG 707
                         ii  v   i-     i     ii  i      v   v  v  vi   vii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_191367661_    708 ACAATCTCTTCAATAAATGGTGCTGAGAAAACTAGATATCTATATGCAGA 757
                          i i   i     i           i  v    i    ? i i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_191367661_    758 -GAACGAAACTAGATCCCTATCTCTTGCCATATACAAAAAT-----CAAA 801
                         -   i   ii i  i     i   vii              -----    
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_191367661_    802 ATTGATTAAAGACTTAAATGTAAGATCTCAAACTATGAAATGACTAAAAG 851
                           v   i ?    i           v  v       i   ivvi  i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_191367661_    852 AAAACATCGGGGAAAATTTCCAGGACATTGGACTTCTTGGGTCCAATGTC 901
                                v  ? v    i i iv   v    i----  i  --     --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGG----TTAGG--CAATG-- 583

  chr1_191367661_    902 CTGGAATTTCTGGCCAAATATTTCTTTTATCAGTACCCCACAATCACAGG 951
                         -----i     ---i i    ----------- -  v   v  v    i 
  L1M4_orf2#LINE/    584 -----GTTTCT---TAGATAT-----------G-ACACCAAAAGCACAAG 613

  chr1_191367661_    952 CAAACAAAGGAAAAATGGACAAATGGGA-TTAGTTCAAGTTAAAAAGCTT 1000
                            vv    i      i  i    v   -  vi iv  i       -   
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTT 662

  chr1_191367661_   1001 CTTCACACCAAAGAAAATGATCAACAAAGTGAAGAGACCATCTACACAAT 1050
                         i vii vi     i v iv     v        i    v i i   v   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_191367661_   1051 GGGAGAAAATAATTGCAAACTACCCAACTGACAAGAGATTAATAACCAGA 1100
                                    v       ii ivi v    i   i  i vi  v     
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_191367661_   1101 ATATATAAGGAA-TCAAACAACTTGACAGGAAACAATAAAATAATCTGAT 1149
                                 i   -  vv      ii i iv   v ivv      i ii  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_191367661_   1150 TTAAAAATGGACTAAAGATCTGAC--GATATTTTTCAAAAGAAGATATAC 1197
                          ?        i v  i   i   v--  i    i  v             
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_191367661_   1198 AAATGGACAAGAA-CATATGTGAAAAATGCTCAACATCATTAATCGT 1243
                               v   v  -  i   -i   i             ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (119 / 66)
Gap_init rate = 0.03 (21 / 758), avg. gap size = 2.48 (52 / 21)  


2601 25.65 4.72 2.59  chr1_191545922_191547902      600  1488 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_191545922_    600 TGGTAAGATATGTCATGCTCTTTGATTGGAAGAATTACTATTGTTAAAAT 649
                            v       vi    i  v v          v   v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_191545922_    650 ATCCATACTGCCCAAGGGGATCTACAGATTCAGTGCAATCCCTGTCAAGA 699
                         iv v     v     ivv              ii         i    i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_191545922_    700 TAACAA-TGAAATTCTTACAGAAACAGA------AATAC-AAAATGTATA 741
                          vv  i-  vvv  i  i      iv  ------i  v -     vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_191545922_    742 CAGAAACACAAAAAAACTCCAAATAACCAA-----TCCTGAACAAAAAGA 786
                         ii    ii   iii - i vi    i    -----  i    v  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_191545922_    787 AAAAAAGTGGAGGCATCACATTACCAGAATTCAAAATAAACCACAAAAAT 836
                          v   iv      vv     i v  vi v       ivv  i     iv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_191545922_    837 ATAGTAATCAAAAGAGTATAGTACTAGCATATAAACAGATACTTAGACCA 886
                          i         i v   i i     i     vii i   i iv    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_191545922_    887 ATGGAACAGAATAAAGAACCCAGACATAAATCCACACATTTACAGCCAAT 936
                               i     vi   ii     v     i   i       ii i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_191545922_    937 TCATTCTCAACAAAGGCACCAAAAACATATATTGGGGAAAAGATAGTTTC 986
                          v   i  i    i  ii    i v   vi v        ii     i i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_191545922_    987 TTTAATAAACGGTGCTAGGAAAGCTAAATATTCCATAAGCAGAAGAATGA 1036
                           i  i   i      i   v i  ii   ?-   i v   i        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAK-CCACATGCAAAAGAATGA 448

  chr1_191545922_   1037 AACTAGATCATTATCTCTCAC--TATACAAAAAG-----------GGATT 1073
                          ii i  i vi  i   v   --          v-----------    i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_191545922_   1074 AAAGACTGACATGTAAGTTTGAAACTTTGAAACTATGAGATTACTAGACA 1123
                          ?    iv v       ----- i  --i       i i i vi    vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAG-----AGCT--AAAACTATAAAACTCTTAGAAG 541

  chr1_191545922_   1124 AAAACA-AGGGGAAAATGCTCCAGGAAATCGGTATGGGTAAGGATATTTT 1172
                               -   ? v    -  i iv  vv i  vv i  i  v i -  i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGT-TTCT 589

  chr1_191545922_   1173 TGGGAAAGACCTCAAAAACACGGGCAACAAAAGTAAAAATAGACAAATAG 1222
                          i iv v   vi     i   ii          v         i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_191545922_   1223 AATTGTATCAAAGT--ACAACATTT---CTTAATGGCAAAGGAAAC---- 1263
                         i i vi      i -- v   v   ---   -----       v  ----
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTT-----CAAAGGACACTATC 684

  chr1_191545922_   1264 ---AGAGTGAAGAGTCTGTCCATTGAATGGGAGAAAATATTTGCAAACTA 1310
                         --- i      i  v vii   iv                       ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_191545922_   1311 CCCTTCTGACAAAAGATTAACAACCAGAATATATAAGGGACTTTAATAAC 1360
                         iviv     i  ii  i vii v             i i   i v i   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_191545922_   1361 TGAATAGCAAAAACAAACTGAACAACCTGATT-AAAAATGGGCAAAACAC 1409
                          v    ii     v v ---  i    ii   -             iv i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACA---AATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_191545922_   1410 CTGAATATTTATTTCTCAAATGAAGACATAAAAATGGCTCACCAATA--T 1457
                         i      vvi       v  v     i   v       ----     --i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC----CAATAAGC 877

  chr1_191545922_   1458 ATATACAATAAAGCTCAACCTCACTAATCAT 1488
                          i  iv  vi v       v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (139 / 86)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.10 (65 / 21)  


2301 23.83 1.98 6.91  chr1_191554104_191555927      522  1331 (493)    L1M4_orf2#LINE/L1      139   908 (0)  

  chr1_191554104_    522 CTAAAATTTGTGTGAAACCAAAAAAGACTCCAAAAAGCCAAAGTAGTTTT 571
                                 ii i  i  viiv  ii   i vi  v       ii i i  
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_191554104_    572 AAGCAAAAAGAACAAAACTGACAGCATTGCATAC---CTGACCTCAAAAT 618
                         i iv  i         ii  i-  v i -  i  --- ii ii      i
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGG-AGGACT-CACACTTCCCAATTTCAAAAC 236

  chr1_191554104_    619 ATGCAACAAAGCTATAGTAACCAAAACAGCAT---ATCGGCAAAATAAAT 665
                         v i v         i     i   i    ii --- ii    v  -ii  
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA-GGAT 285

  chr1_191554104_    666 AAATAAATAAATATTAAAAAATTAAAAAAAACAACCAGACACACACGCCA 715
                          i i v   i  ------------------------------------  
  L1M4_orf2#LINE/    286 AGACATATAGAT------------------------------------CA 299

  chr1_191554104_    716 ATGGAACAGAATAGAGAATGCAGAAATGAATCCATGCATTTACAGCCAGC 765
                               i     v    i v       i  i    i      ii i  ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_191554104_    766 TGATATTTGGCAAAAGTACCAAG-TAATACATTGGGGAAAAGACAGTCTC 814
                             v  i i   ii  i     -iv  v  v        ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_191554104_    815 TTTAATAAATGGTGCTAGGAAAACTGAATATCCATATGCAGAATAATGAA 864
                           i  i          i   v     i   ?   i     i  v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_191554104_    865 ACTAGATTACT--CTCTCCTCATATACAAAAATCAACTCAAAATGGAATC 912
                         ii i  iiv  --   v vi             i             -  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA-TC 498

  chr1_191554104_    913 A-ATACCTTAATGTAAGACCTGAAACTATGAAACCACTAGAAGAAAACAT 961
                          - v    v         v  i       i    ivi             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_191554104_    962 TAGAG-AAATGCTCAGGTAA--TTGGTCTGGGCAAAGATATTTTTGGTAA 1008
                         vi ? -    vi  --  i --    vi i     v i v i  v i  v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTC--GTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_191554104_   1009 GGCCTCAAAAGCACAGGTAGTAAAAGCAAAAATACACAAATCGGATTACA 1058
                          i vi          i i ii     v       v i    i   i v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_191554104_   1059 TCAAA-TTAAAGAGCTTATGTGCAGCAAAGGAAACAATCATCAGAGTGAA 1107
                              -     i -   v     vv       v  v    vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_191554104_   1108 AAGACAACTCACAGCATGGGAGAGAGTAATTGCAAACTATCCATTTGACA 1157
                                 i     v        i i  v       ii  vi  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_191554104_   1158 GGGAATTGATAACCAGACTACA--AGGGACTCAAAGAACTCAACAGCAGA 1205
                         i  i i vi  v     v  i -- i i    vv v       i ii i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_191554104_   1206 CCAATCACCACCAACAAAAATATCTGATTATAAAAATGGGCAAATTATCT 1255
                         --  --------i     v - i ii   ?-             vv  i 
  L1M4_orf2#LINE/    796 --AA--------GACAAATA-ACCCAATTW-AAAAATGGGCAAAGGATTT 833

  chr1_191554104_   1256 CAACATTTACTTCTCAAAAGAAGACATACAAGTGGCCACCAAGCAGATGA 1305
                         v  i vvi i     v        i      i      vi     v    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_191554104_   1306 AAAACATGTTTAACATCACTAATCAT 1331
                            i-   i i       ????????
  L1M4_orf2#LINE/    884 AAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (129 / 61)
Gap_init rate = 0.03 (21 / 770), avg. gap size = 3.43 (72 / 21)  


1577 20.50 16.50 7.33  chr1_191576032_191579041.rev     1374  1973 (1037)    L1M4_orf2#LINE/L1       10   664 (244)  

  chr1_191576032_   1374 ATCTCATATCCACGGCTTGGTAGACTTAATATTGTCAAGCTTGCAATACT 1423
                            i   i i  i  v    v              i   v v        
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_191576032_   1424 -------------TACAGATCTCATGCAATTACTAACAAAACCCGAGCT- 1459
                         -------------       iiv i     iv   v     i  v    -
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_191576032_   1460 ---------------------AGTTG---------TTT------------ 1467
                         ---------------------  i  ---------  i------------
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_191576032_   1468 -------------TAGCAAAAATAATTTTGAAAAA--ATTATGAAATTGA 1502
                         -------------    v    i   i        -- vv ii  i   i
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_191576032_   1503 AGAATTGACACTTTACAATGATAGAACTTGCTATAAAG------TAATCA 1546
                           i i v      iv    vvi i     i   i    ------      
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_191576032_   1547 AGATAGTTTGATAATTGTATAAGCATAGAAA-A-AGATACATGAAATGAA 1594
                            i   v  i  v v i     v     v - -    vv   i   ii 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_191576032_   1595 ATTGAAA-TCCAGAGATAAACTCA--CATTTATACTTA-CTGACTTTCAA 1640
                              i -      i      i  --       iv i -i   i    i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_191576032_   1641 CAAAGATATCAAGATAATTCAACAGGGAAAATCGTAGTCTTTTTAACAAG 1690
                            i i ii     iv      ii      i-vi         i     i
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAAA 408

  chr1_191576032_   1691 TGGTGCTGGGACAACTGGATGTCCACATGCAAAATAATG------GATCT 1734
                                             i?            v    ------  i i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_191576032_   1735 CTTTCTCACACCATATATAACA--TACATCAAAATAGATCCTAGACCTAA 1782
                           vi             i  v --  vv       i    v?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_191576032_   1783 ATGTGAAAGCTAAAACTATACCACTCATAGAATTATTATTAACTCATTAT 1832
                             i i             vv    v     ------------------
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAA------------------ 540

  chr1_191576032_   1833 TCTGAATAATATTGATTAATTTTTTAAACATAAGCA-ATATCTTGGTGAC 1881
                         ---   --------------------      i ?i- v     v     
  L1M4_orf2#LINE/    541 ---GAA--------------------AACATAGGNGTAAATCTTCGTGAC 567

  chr1_191576032_   1882 TTTAGGTTGGGCAAAACCTTCTTA-ACATGACAATAAAA-CATAAGTAA- 1928
                         i  i    i     vivi      - i      vi    -  i   i  -
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_191576032_   1929 ----AAAAAAGTGGGTAAGTTCTACTTTACCTAAAAGTAGAGAGCTTTT 1973
                         ----i     i i i   i  vv    i i -    v  i i -     
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATC-AAAATTAAAAA-CTTTT 664

Transitions / transversions = 1.86 (78 / 42)
Gap_init rate = 0.03 (22 / 655), avg. gap size = 6.50 (143 / 22)  

 773 19.26 7.38 3.28  chr1_191576032_191579041.rev     2280  2523 (487)    L1M4_orf2#LINE/L1      655   908 (0)  

  chr1_191576032_   2280 AAAAGCATTTTTTATAAAGCTTCAAATGATAGTATAAAGAAAGGGAAAAA 2329
                             i ---    i ---        v  i v   v       v     i
  L1M4_orf2#LINE/    655 AAAAAC---TTTTGT---GCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_191576032_   2330 AATGACTTACAGA-TGGGAGAAAATATTTGTAAATCTTTCATATTACAAG 2378
                          -ii  ii     -                i     v vi  v v i   
  L1M4_orf2#LINE/    699 A-CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_191576032_   2379 GGACTTGTATCTAAAATATATAAAAATCGTTCCCAAGTTAATAATAAAAA 2428
                                    i i          i v vi iv   v i           
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_191576032_   2429 ------TAACTCAATGTTTAAAATAGGCAA----------TAAATATATC 2462
                         ------    i    - ?v     i     ----------  i i  v  
  L1M4_orf2#LINE/    798 GACAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_191576032_   2463 TTCATAGAAGATATA-AAGTGGCAAATGAATACATGAAATTATGCTCAAC 2511
                          i  v          -  i    v   i ii        vv         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_191576032_   2512 CTTATTAACTAT 2523
                         v i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (27 / 19)
Gap_init rate = 0.03 (8 / 254), avg. gap size = 3.25 (26 / 8)  


2320 26.97 4.34 1.37  chr1_191643262_191646331     1703  2577 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_191643262_   1703 ATATTTTATATTCACAG-TAAGAAAATTAAACATTGTTAAG-TATCATTT 1750
                             iii  i    ii - vi   i i v  i         - iv  v v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_191643262_   1751 CTCTCCATCTGTTTTTCATGTATAGATTAAATATCATGTCAATTAAAATA 1800
                            i   vv ----- v  v  i     v  iiiv  vi v  i     v
  L1M4_orf2#LINE/     58 CTCCCCAAAT-----TGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_191643262_   1801 TCTGCTAGATATTGTGTGGATATCGACAAAATGCTGAT---AAATTTTAT 1847
                         i v   ivv v  v  ii  v  i     ---      ---   v  i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAA---GCTGATCCTAAAATTCAT 149

  chr1_191643262_   1848 TTGGA----CAAAAA--CTAGAATAGGCAACACAGTACTGAA------GA 1885
                         v    ----   iii-- i       v   v   i vi    ------  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_191643262_   1886 ACAA-GTTGAAGAACTGAAACTACCCTATTTCAAGACTTTCTATAAAGCT 1934
                             -    i  i   v v   v   v       i    v   i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_191643262_   1935 ACACTCATCAAGAGATAATGATATTGACTAAATAATAGAAACAAAAGATG 1984
                            v v       v vvi  i  i  i vv  vi     v i v -   v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA-GATC 298

  chr1_191643262_   1985 AATAAAACAGAATAGATATATCAGAAATGTACTCACGAATATAT--TCAA 2032
                            ii  i     v  v vvi       iv  i  iiv  v   --    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_191643262_   2033 CTGATCTTTGACAAAGAAGAAAAGAAAATTTAGTGGAGAAAGGACAGTCT 2082
                         i    i  i     i iv vv    vv   i i   i     i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_191643262_   2083 TTTCAACAAATGAAGATGGAGTAGCTAGAATTCTACATGGTGACAAGGTG 2132
                                     iv v   iii i  i  vv? i     -ii v iii  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAATG 447

  chr1_191643262_   2133 AATTTAGACAGAGA--TTACACTTTTCACAAAAATAAAATAAAAATAGAT 2180
                           v  i   vvvv -- i    iv vi        v  v v     i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_191643262_   2181 CATAGTCCTAAAATGTAA--------ACAGTGAAACTTTGAGAAGATAGC 2222
                           ?  v      -     --------  vi i     i v      v i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_191643262_   2223 ATGGATGAAAAATTAGGTGACCTTGGTTTTGTTAATGGGTT--TAGATA- 2269
                           i i? v   vi vv          v  v vi     v  --      -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_191643262_   2270 AATATGAAAAGCAAGATTCATGAAAGAAAAATTA-ATACGTCAAACTTCA 2318
                         i i iv       vi viv ii         v  -   vi iii      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_191643262_   2319 TTAAAATTAAAAAGTTCTGCTGTGTGAAAG-ACAGTATTAAGAGAATGAA 2367
                          i           v  i  -  iv v    -   v   i    i i    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_191643262_   2368 AAGACAAGCCACAGATTGGGAAGAAATGTTTGCAAAATACGTGTCTGATA 2417
                                v       v     ii    i        vi ii i       
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_191643262_   2418 AAAGACT---ATCCAAAATATACAAAGAAAACTTGAAAGTCAACAACAGA 2464
                          ii    ---     i      i      vv   iv  v    i  i i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_191643262_   2465 AAAACAATCCACCCAATTTAAAAATGAGCAAAAAATCTGAACAGACATCT 2514
                           i    viv        ?       i     ii  i    i      i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_191643262_   2515 CACCAAAGAAGATATAAAGATGGAATATAATCATATGAAAATATGCTCAT 2564
                          v              v i    vvv    v  i       v       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_191643262_   2565 CATCATATGTCAT 2577
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (125 / 107)
Gap_init rate = 0.02 (21 / 901), avg. gap size = 2.38 (50 / 21)  


 501 26.79 0.00 0.00  chr1_191649746_191654504     2471  2582 (2177)    L1M4_orf2#LINE/L1        3   114 (794)  

  chr1_191649746_   2471 GAAAAGCATCCCATATTCATAGAGTGGAAGAATTAACATCATTGAAATGA 2520
                             iii       i     i  v       v    i  ii  i i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_191649746_   2521 CCATATTGCTTAAAGCAATCTACAGATTCAACACAACCCCTATCAAATTC 2570
                          v   i v ii   vii               i   i          v  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_191649746_   2571 ACAGTCATTTTT 2582
                         v   iiiii   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTT 114

Transitions / transversions = 3.29 (23 / 7)
Gap_init rate = 0.00 (0 / 112), avg. gap size = 0.00 (0 / 0)  

 394 31.36 1.18 2.37  chr1_191649746_191654504     2894  3062 (1697)    L1M4_orf2#LINE/L1      109   275 (633)  

  chr1_191649746_   2894 GCCTATTTTTTACAGA--TTAAGAAAAAACAATCGTAAAGTTCACATGGA 2941
                             --     i    --  --  v  ivii   v    i    i     
  L1M4_orf2#LINE/    109 GCCT--TTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_191649746_   2942 ACCAAAAAATAATCTGAAGAGGCAAAGCAATTCTAACCAAAAAGAACAAA 2991
                          viiv  iiv vi v   v  v    i    ii i vv  i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_191649746_   2992 CCTGGAAACATCACATTGCCTGACTTCAAATTATACCAGAAGCCTAAAGT 3041
                         vi    iivv     i v  ii i      viv   i v  iv   v   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_191649746_   3042 AATGAAAACAGCACGGTATTG 3062
                            v  i    iii    i  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTG 275

Transitions / transversions = 1.41 (31 / 22)
Gap_init rate = 0.02 (3 / 167), avg. gap size = 2.00 (6 / 3)  

1851 25.04 3.88 1.62  chr1_191649746_191654504     3648  4266 (493)    L1M4_orf2#LINE/L1      276   908 (0)  

  chr1_191649746_   3648 GTACAAAAACAGAAACACAGAGCAATGGAATAGA-----GAACCCAGAAA 3692
                          i i  ii i   v i i   v            -----  ii       
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_191649746_   3693 TGAAGCCAAATACCTAAAACCAACTGATTTGTGACAAAGTTGATAAAAAT 3742
                          i  v   v i ii  viii   i      vi     i v  vi  i vi
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_191649746_   3743 AAACATTGGAGCAAAAACATCCTATTCAATAAATGGTACTGGGATAACTA 3792
                          vv  v   i v  i  i vi  v     i       i      i    i
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_191649746_   3793 GCTTGCCATATGCATAAGACTGAAACTAGACCTTTATCTGTGATCATACA 3842
                          v v?   i     v    v    ii i    ii  i  vvv i    i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_191649746_   3843 CAAAAATTAACTCAAGATGGGTTAAAAACTTAAATATAATATTTAAAACT 3892
                                        i    i i ? i  i     i   v vi       
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_191649746_   3893 ATAAAAATCC-AGAAATAATAAAACA-AGAAA-AACTCTTCATTGTGTTG 3939
                               v  i-    i----      -  i?i-  v     i viiv   
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAG----AAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_191649746_   3940 GCCTAGGCAAATAATTTAT--GATAAAGACCTCGAAAGCAAATGCAACAA 3987
                          vi       - ii   v --    v-   vi i      v v       
  L1M4_orf2#LINE/    572 GGTTAGGCAA-TGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAACAA 619

  chr1_191649746_   3988 AAACAAAAATAGACAAATGGGACCTAATTAAACTACAGAGTTTCTGTAAA 4037
                           iv         i    v    i v  i   v vv i ii  i   ivv
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_191649746_   4038 GCAAAAGAAATAATCAAGA--GTAAACATACAACCTACAGAATGGGAGGA 4085
                         v    i  v iv       --  i  v v      i            i 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_191649746_   4086 AATATTTGCAAATTATGCCCACAACAAAGGACTAATATCCAGAATCTACA 4135
                                      i  iivivii i  i     vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_191649746_   4136 AGGAACTC----AACTCAATAAGAAAAAAAAAAAATCTA--CCAAGTGAA 4179
                          i      ----          v     i v   ---  --    v ?  
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAA---TAACCCAATTWAA 816

  chr1_191649746_   4180 AAACTGGGCAAAAGAC------AGACATTTCTCAAAAGAAGAAATAGAAG 4223
                            -        i  i------           v        v   v  i
  L1M4_orf2#LINE/    817 AAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_191649746_   4224 TAAACAACAAACACATGAAAAAATGTTCAACATCACTAATCAT 4266
                          iiv   i  i          i   i         ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (93 / 58)
Gap_init rate = 0.02 (14 / 633), avg. gap size = 2.43 (34 / 14)  


1472 26.66 7.24 7.00  chr1_191678684_191680374.rev      372  1200 (491)    L1M4_orf2#LINE/L1       78   908 (0)  

  chr1_191678684_    372 ATTCAACATAGTAC---TGGAAGTCCTAGCCACAGCAATCATGCAAGAA- 417
                                ii i v --- vi  i   i   ii -- vv iv    ii  -
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGC--CTTTTTTGCAGAAAT 125

  chr1_191678684_    418 -AAAAAAATAATAATAAAAGACATATAAATAGAAAGTGAGGAAGTCAAAC 466
                         -i v  iv i  vv     vv     ii ---  v ii   i vi  i v
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGA---AATGCAAGGGACCCAGAA 172

  chr1_191678684_    467 TATCCCTGTTTGCAGACAATATAATTCTAGACTAGAA-AAC-----TGAA 510
                           ---------  ---   v i   ii ii vv    -   -----  i 
  L1M4_orf2#LINE/    173 TA---------GC---CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_191678684_    511 GGCATCACATTACTTGGCTTCAAACTACACTAAAAGGCTACAGTATACAG 560
                           vv     i v iiiii      vivi    v  i         --- v
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA---AT 257

  chr1_191678684_    561 TAAGAGAAACAGCATGGTACTTGCTTTTGTACAAAAACCAACACATAGGT 610
                         i    ----   ii       v  ------ i  ii ivi   i    i 
  L1M4_orf2#LINE/    258 CAAGA----CAGTGTGGTACTGGC------ATAAGGATAGACATATAGAT 297

  chr1_191678684_    611 GAATGGAATAAGATAGAGATCCCAGAAATAAAGCCACACACTTACAACTA 660
                         v         ii  v    vi           v   i   i   iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_191678684_    661 TCTAATCTTCAAGAAAGTAAAATAATAATAATAATAATAATAACAATGGA 710
                         vi i  i   i v  i ----------i ivi  v vi v --      i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG----------GTGCCAAGACCATT--CAATGGG 385

  chr1_191678684_    711 GAAAAGGTTCCCTATTTAATAAAAGGTGCTGGCATAACTGGTTAGCCATA 760
                             iii vvi  v  i  i   v        v i      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_191678684_    761 TGCACATATGCCTAAGATTGAAGTGGGGCCCCTTTCTTATACCATATACA 810
                             --- -----    v      v  i     vi  i i          
  L1M4_orf2#LINE/    436 TGCA---A-----AAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_191678684_    811 AACATCAAATCAAGATGGATTAAGTACTTAAATGTAAAACCTAAAACTAT 860
                           v  i  v    i      i ?iv  i         i v          
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_191678684_    861 AAAAACCTTGGAAAATAAAC-TAGG---AAATATGATTCTGGACATAGGC 906
                             vi   i   i -    -    ---    v ---  vv   v v  v
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGA-AAACATAGGNGTAAATCT---TCGTGACCTTGGG 573

  chr1_191678684_    907 TCTGGCAAAAATTTCATGACAAAGACATCAAAAGTA---ATTACAAAAAA 953
                          iv     vii    v iivv v    i      i ---iiv      i 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_191678684_    954 ACCCAAAATTGACAATTGGGACCTAAATAAA-TTAAACAGCTTCTACACA 1002
                          ---     v  i  v v    i v vi   -     - i   i iii v
  L1M4_orf2#LINE/    624 A---AAAATAGATAAATTGGACTTCATCAAAATTAAA-AACTTTTGTGCT 669

  chr1_191678684_   1003 GCAAAAGAAACTATCAATGGAGCAAACAGACAACCTACAGAAAAGGAGGA 1052
                         v    i  v        vii  ii  v        i      vi    i 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_191678684_   1053 AATATTTGAAAACTATGCATCTG---------------TCA-AATATCTA 1086
                                 v   ii  ii     ---------------i  -     v  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_191678684_   1087 A--------TA----TC-------------CAAACAACCACATTAAAAAG 1111
                          --------  ----  -------------    i    vv   ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_191678684_   1112 TAGGCAAAGGATATGAACAAACACTTTTCAAAAAAAGACAGACATGCAGC 1161
                          i          v    i i   i  i  v   i    i v   viii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_191678684_   1162 CAACAAGCATATTAAAAAGTGCTCAACATTACTAATCAT 1200
                            i     i  v    ii          i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (135 / 83)
Gap_init rate = 0.03 (28 / 831), avg. gap size = 4.21 (118 / 28)  


2626 26.17 4.89 1.59  chr1_191723545_191725597      682  1560 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_191723545_    682 TGGAAAGATATCTCATATTCACCAATTTGGAAGAA--AATATTGTTAAAG 729
                                     i   i    ivi   -      v--           ii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT-GGAAGACTTAATATTGTTAAGA 49

  chr1_191723545_    730 CGTGAATACTACCCAAAGCAATCTAAATATTCAATGCAACCCCTATCAGA 779
                         i vv      v      vii     v v      i    i        i 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_191723545_    780 GACCCAATGACATTTTTTAGAGAATTTGAAAAAACAATTACAACACTCAC 829
                         iv    iivi v      iv    v    v  ivii  ivi  v i   i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_191723545_    830 ATAAAACCACAAAAGACGGCAAATAAGCAAATCAATCTTGATAAAGAAGA 879
                           ii  vii   ii   vvvi    iv    v         v        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_191723545_    880 ACAAAGCTAGAGGCATCATATTTCCTGATTTCAAATTATACTGCAATTCT 929
                               i i    vv   i i    ii        viv    i   vv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_191723545_    930 A-AGCAATCAAAACAGTTTGGTACTAATATAAAGACAGATATACAGA-CA 977
                          -  i      i     v       iii    i  i   i   i   -  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_191723545_    978 A----ATAGAACACAGGGCCCAGAAATAAATCCATGCATATATGGCCAGC 1023
                          ----      ivv  i i           i    i   v     i  ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_191723545_   1024 TGATCTTTGAAATATACGCCAAGAATACACAATAGAGAAAAGATTGTCTC 1073
                             i  i  v vivii       vi iv    i i    ii  v    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_191723545_   1074 TTCAACAGAAGATGTTAG-AGAACTAGATATTCACATGCAAAAGGATAAA 1122
                                i v i  i i - v    i    ?i            i  i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_191723545_   1123 ATTGGAC----AC-TCATATCATACTACAAGTA--AACCCAATATGAATT 1165
                         i      ----  -   i i    -     iv --   i   v   i  i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATA-TACAAAAATTAACTCAAAATGGATC 498

  chr1_191723545_   1166 AAAGGCTTAAACATAAGATCTGAAA-TATAAAA-----------AAAT-- 1201
                          ?  i i    ii     v  i   -       -----------   i--
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_191723545_   1202 -GGGGAAAAGATTTATGACGTTTTTTT--GCAATGATT-ATTGGATACAA 1247
                         -  ? v   vv  ii    v  vvv  --      i  -v  i    ii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_191723545_   1248 CACCAAGAGCACAGTCAACAAAACCAAAAATAAACAAACAAAACTACTTC 1297
                               i      iv        vv       i i   ivii   v v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_191723545_   1298 AAATTTAAAAATTTCTGCGCAGCAGTGAAAACAAT---GAGTAGTGAAAA 1344
                            v       i  i  i  vv  iv i v  v  ---  i-        
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA-AGTGAAAA 697

  chr1_191723545_   1345 CACAGCCTATGGAATGGGCCAAAGTATTTGCAAACCAGATAGCTGATAAG 1394
                         v   i  i ii       vv   i          i  v   v        
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_191723545_   1395 AGGTTAATCTTCAAAACATATAAGCAACTCCTAAAACACAATAGTAACCC 1444
                         i ii vi v i  i  i      iv     i  v   v     i   ---
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA--- 794

  chr1_191723545_   1445 AACCAACCCAAATTAATAACTCAATTAAAAAAACAGTCAAAGGATCTGAA 1494
                         ----  --- i iv      i     ?     -ii v        i    
  L1M4_orf2#LINE/    795 ----AA---AGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chr1_191723545_   1495 AA-----TTTTCCAAGGAAGACACGCAAATAACCAAGAGGTATATAAGAA 1539
                         v -----  i     i     i ii     ii    v i i i  i i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_191723545_   1540 -ATGTTCAATGTTACTAATCAT 1560
                         -   i    ii i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (147 / 79)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.59 (57 / 22)  


2709 26.53 1.78 1.00  chr1_191732178_191736469.rev     2905  3801 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr1_191732178_   2905 AAGTACATTCCATGCTCATGATTTGTTGGAATCAATATAATAAAAATGAT 2954
                            - i  i     i     iv   vvi  v i     vi v  i   ii
  L1M4_orf2#LINE/      5 AAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_191732178_   2955 CATCATGCCCAAAACAATCTACAGATTCAATGCAATTGCTATCAGAATAC 3004
                         v  vv v      vii              i     iv      i   v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_191732178_   3005 CAACATCATTTTTCACAGTATTAGAGAAAAAAAATCCTAAAATTCATTTG 3054
                           i vv v     ii   v v v  v  ivvi -             v  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATATG 152

  chr1_191732178_   3055 GAATTTAAAAAGAGCATGAATAGCCAAAGTAATCCTAAGCAAAATGAACA 3104
                            v vv  ii  v vv           ii    i i iv  i v     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_191732178_   3105 AATCTGGAGGCATCACATTGCATAACTTTATTAC--ACTAGAAGGCTATA 3152
                           vi      vv     i v vi  i  i vv  --    v  i    i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_191732178_   3153 GTTACCAAAACAGCATCGTACTGGCATAAAAGTAGATACATAGAGCAATG 3202
                           v i   i    ii v            iii    i i     v     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_191732178_   3203 GAAAAGAATAGAGAACCCAGAAATAAATTCCAAATACAT--ACAATAAAG 3250
                            v     v    ii           ii ---      -- iii v  v
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCC---ATACATTTATGGTCAAT 349

  chr1_191732178_   3251 TGACCTTTGGCAAAGCATGC-AAAAGAATAAATTGGTGAAAGAACACTCT 3299
                            ii  i i   i -i   -  i vv  vv v   v       i v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_191732178_   3300 ATTCAATAAGTGATACTGGGAAAACTGGATAACCGCATGTAGAAGAATGA 3349
                         v     i  i  i i      v         ?  i    i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_191732178_   3350 AACTGGATCCCTAACTCTTACCATATACAAAAATTAACTCAAGATAGATT 3399
                          ii    i     v   vi                       i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_191732178_   3400 AAAGACTTAAATCTGAGACCTGAAACCATATAAATTCT-AGAAGAAAACC 3448
                          ?    i     v i   v  i    i   -   i   -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACA 547

  chr1_191732178_   3449 TAGGAAAAACTCTTC-TGTACCTTGGCCTACCAAATA-TTTAT--GACTA 3494
                             ?iv  v     -  -       vi  vvv   i-   v --  -  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGA-TA 595

  chr1_191732178_   3495 AGACCCCAAAAGCAAATGCAACAGAAACAAAAATAAATAAATGGGACCTA 3544
                         v   v         v v      i  iv       i      v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_191732178_   3545 ATTAAACTAAAAAGCTTCTGCACAGTGAAATAAATAATAAACAGAATAAA 3594
                           i   v v    i   i  ii vvii  iv v iv  v  v i i i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_191732178_   3595 CACACAACTCACAAAATGGGGGCAAGTATTTGCAAACTATGCATCTGGCA 3644
                         v v     i    i      i v  i          ii  ii     ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_191732178_   3645 AAGGACTAATGTCAAGAAAGTACCAGGACCTCAAACAAATTAGCAAGAAA 3694
                          i     vi i  v    vi  iv i  v   vv    v i ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_191732178_   3695 AA-----ATATTCCCATC-AAAACTGAGCAAATAACATGAGTAGACACTT 3738
                           -----   vi  v  i-    v  i     vi iv   i      i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_191732178_   3739 CTGAAATGAAGATATACAAAAAGCCAACAAATATATGAAAAAATACTCAA 3788
                           vv  v             vi     i  ii i       i  i     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_191732178_   3789 CAACACTAATCAA 3801
                           v  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (130 / 105)
Gap_init rate = 0.02 (16 / 904), avg. gap size = 1.56 (25 / 16)  


2304 29.78 3.28 0.79  chr1_191795253_191797310.rev      691  1573 (485)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_191795253_    691 AAAAATATCCCGTGCTCACGGATAGGAAAAATCAACATAATTAAAATGGT 740
                            i       i  i   i    v    i v i  i  vi    i    i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_191795253_    741 CATACTGTACAAAGTG-TTTATACATCCAATGCTGTTCCTATCAAACTAC 789
                         v     viv    v  - i  i v  i   i  vi i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_191795253_    790 CAA-TGACTTTTTAACAAGAACTAGAAAAAAAACT-ATTTTGAAATTCAT 837
                           i-  v      vi  ii  i i---- v  i  -  ii i        
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATTCAT 149

  chr1_191795253_    838 ATGGAACCAAAAAAGAGCCTGAAGAGCCAAGGGAGTCCTAAATAAATAGA 887
                               viiv  ii  v  v   v      iiv i  i i  v  iv   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_191795253_    888 ACAAAGCTGAAGCCATCGTGCTACCCTATTTCCAACTGTCCTACATGGCT 937
                               i  i  vvv  iii  v   v     v  viv v     vi   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_191795253_    938 GCAGTAACCAAAACATCATAGTACTGGTACAAAAACAGACACATAGTCCA 987
                         i      i   i   vii i       i i  ii i     i    vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_191795253_    988 ATGGAACATAATAGAAAACCCAAAAATAAGACCACACAGCTACAACTATC 1037
                               i v   v  i ii   i      iv   i   vi  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_191795253_   1038 TGATCTTCAACAGAGCTGATAAAAAACAAGCAATGAGGAAAGGGCTCCCT 1087
                             i   i   ii v  vi  i v-  vv     i      iiivvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCT 398

  chr1_191795253_   1088 ATTCAATAATTGGTGCTGAGATAACTGGCTAGCCATATGCAGAAGATTGA 1137
                         v     i  v        i  i      v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_191795253_   1138 AACTAGACCCCTTCCTTACACCATA-A-AAAAATCAACTCAA------TT 1179
                          ii i       v   i        - -      i       ------ i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_191795253_   1180 AAAAACTTAAATGTAAAACCACAAATTATAAAAATCCTAGAAGTCAACC- 1228
                          ? i  i         i v vv   i       v  i      vv   v-
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_191795253_   1229 -GAAGTAA-TATTATGGACACAGGAATGAGCAAATATTTCAT-GATGAAG 1275
                         - i?    - v  vvv   viv  iv ii    vvi    v -   - v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr1_191795253_   1276 ATGCCAGAAGCAATTCTGGCAAAAGCAAAATTTGACAAACGGGATCT--- 1322
                          ii   i     vvvviii      v    v v  i   iv   ii ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_191795253_   1323 ---AATTAAAGAGCTTCTACACGGCTAAAGAAACTATCAACAGATTAAAC 1369
                         ---       i -   i iii vv v  i  v        v i v i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_191795253_   1370 ACACAACC-ACAGAATGGGAGCAAACTTTTGCAAACTATGCATCTGACAA 1418
                          v      -            v   iv        ii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_191795253_   1419 AGGTCTAATATCTATCATTCATAAGGAACTTAAACAAAT---TTACAAGA 1465
                         i  v  vi    i vv  vi    i     ivv    v --- v i  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_191795253_   1466 TGACAA-CAACCTCATTAACAAGTGGGGAAAGGACGTGAACAGACACTTC 1514
                         v     -i    iv   ? v  i    v      iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_191795253_   1515 TTAGAAGAAAA-ATATGCAT--CCAACAATCATATGAAAAAAAGTTCAAT 1561
                          ivi     i -   iiv  --    i  v  i       i v i    i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_191795253_   1562 ATTGCTGATAGT 1573
                           ii????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (154 / 105)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 1.89 (36 / 19)  


3039 27.72 0.66 0.77  chr1_191808009_191812344     2935  3843 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_191808009_   2935 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATTAATATCGTGAAAAT 2984
                              ii i  i     i      i v      v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_191808009_   2985 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 3034
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_191808009_   3035 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3082
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_191808009_   3083 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTCAGCCAAAAG 3132
                                viiv  ii  v  viv  v     iv     i v ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_191808009_   3133 AACAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTATACTGCAATGC 3182
                                i i    vv   ii  v  ii i      viv    i   v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_191808009_   3183 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 3232
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_191808009_   3233 AAAGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACTTATCTACAACT 3280
                           v    i    i--    i  --        vv   ivi  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_191808009_   3281 ATCTGATCTTTGACAAACCTGACAAAAACGAGAAATGGGGAAAGGATTCC 3330
                          vi    i  i     ivv  v   i v ivvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_191808009_   3331 CTATTCAATAAATGGTGCTGGGAAAAACTGGCTAGCCATATACAGAAAGC 3380
                           v     i              v  -    v  ?   i  i  i  iiv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAA 445

  chr1_191808009_   3381 TGAGACTGGATCACTTCCTTACACATTATACAAAAATTAATTCAAGCTGG 3430
                            iii    i v  v   i    vv              i    iv   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_191808009_   3431 ATTAAATACTTACATGTTAGACCTAAAACCACAAAAATCCTAGAAGAAAA 3480
                           i ? v  i  v    v   v       i i    v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_191808009_   3481 CCTAGGCAGTA--CCATTCAGGATATAAGCATGGGCAAGGACTTCATGTC 3528
                          v    ?-   --i -   iv  iv vi vv i     v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_191808009_   3529 TAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTAACAAATGGGATC 3578
                           vi            vvi           v     vi i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_191808009_   3579 TAATTAAACTGAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 3628
                          v  i   v v  i ii  i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_191808009_   3629 AACAGGCAACCTACAGAGTGGGAGAAAACTTTTGCAATCTACTCATCTGA 3678
                           v  i     i     i          iv       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_191808009_   3679 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 3728
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_191808009_   3729 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 3778
                             i     i     v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_191808009_   3779 TTCTCAAAAGAAGACATTTATGCAGCCAAAGGACACATGAAAAAATGCTC 3828
                              v        i  vi viii     viii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_191808009_   3829 ATCATCACTGGCCAT 3843
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2387 29.90 1.42 1.97  chr1_191881431_191885119.rev     2286  3198 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_191881431_   2286 TAGAAAAACATTTCATGCTCATGGATTGGAATAATCAATGTCATTAAAAT 2335
                          i    i i  ii    i             v v i   i ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_191881431_   2336 GG--ACACATTCCTGAAGCAATTTACAGATTCAACAGTATTCCTATCAAA 2383
                           -- i  - i  ii  vii  i            ivv  i         
  L1M4_orf2#LINE/     51 GGCAATAC-TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_191881431_   2384 CTACCAATATTAC--TTTTCAAAGAATTAGAAAAATCTTTTCCAAACTTC 2431
                         v v   ii-- i --    iiv    v v  v  iiivv i i   v   
  L1M4_orf2#LINE/    100 ATCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_191881431_   2432 ATATAGAACCAAAAGGAGCTC-TAATAGCCAAAGCCATCCTAAACATGAA 2480
                             i   viiv    ii i -v          i v   i i  v v   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_191881431_   2481 GAATAGAACCAGAGGTGTCACATTACCCAAATTCAAACTACACTACAAGA 2530
                            i i iiii    vv     i v     v      vivi       ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_191881431_   2531 TGATATTTACCACAACAGCATGGTACTGCTATAAAAACAGATGCATACAC 2580
                         iv i v v i  vi    ii        vi    ii i   iii   v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_191881431_   2581 CAATGCAACAGGATAGAAAACCCAGAAATAAAGCTGCACATTTACAATCA 2630
                              v  i  i  v  i ii           v iii       iii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_191881431_   2631 TCTGATTTTTGACAAAGTTGGCAAAAGTAAGCAATGGGGAAAAGACTCCC 2680
                         vi       i     i v  v   i vi vv           ii ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_191881431_   2681 TGTTCAATAAATTGTGCCTGGGGTAACTAGCCAGCCATATGCAAGAAAAA 2730
                          v     i    v    -    ii    i vi ?   i      ----  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGC-TGGGACAACTGGATAKCCACATGCAA----AA 442

  chr1_191881431_   2731 AAAAAAAACTGGATTTCTACCTATCACCATTCATAAAA-TTAACTCAGGG 2779
                         i  vi  ii    iii      vv      vi i    -        iii
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_191881431_   2780 TGGATTAAAAAGACTTAAATGTAAGAACTCAAAGTATAAGAATCCAAGAA 2829
                              i ? --   i           i  v   v     i v  iv    
  L1M4_orf2#LINE/    493 TGGATCAWA--GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_191881431_   2830 -AAATCTTTGAGAAGATAACACTTCTTGATATAAGCTTTGATGAAGAATT 2878
                         -   v v --  i? -   vv    v   iv vi v  v iii v iv  
  L1M4_orf2#LINE/    541 GAAAACAT--AGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_191881431_   2879 TATAGCTGAGCCCTCAAA--CTGAACTGCAACAAAAATAAAAATTGACAA 2926
                         iv   v iv v vi    -- vv  --         iv      v  i  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAA 635

  chr1_191881431_   2927 GTGGGACCTAATTAAGCTAAAGAACTTCTGCACAGCAAGAGGAAA-TATT 2975
                         i v    i v  i  iv v  i     i  ii vv   -    v -   i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACTATC 684

  chr1_191881431_   2976 GG---AGTAAGCAGACAACTTTCAGAATGAGAGAAAATATTTACAAACTA 3022
                         ii---   i iv       iiv       i            i    ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_191881431_   3023 TGCATCCAAGAAAAGGCTAATATCCAGAATATATATGGAACTTAAACAAA 3072
                          ii   ii v  ii i  vi               vi     ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_191881431_   3073 AATTAACAAGCAAAAAATAAACAAACCCATTAAAATACAGCCAAAGGGCA 3122
                         -- i  i  vv    i i   i  v  v   ?   v ii v      iiv
  L1M4_orf2#LINE/    785 --TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_191881431_   3123 CGAACAGACCGTTCTCAAAAGAACACATACAAGCAGCCAGCAAACAAATG 3172
                         i   i    vv     v      v i      iii    ii  i  v   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_191881431_   3173 AAAAAATGCTCATCATCACTAATTAC 3198
                             i       v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (167 / 102)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.72 (31 / 18)  


2996 24.57 1.49 4.89  chr1_192021232_192025551.rev     2889  3828 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192021232_   2889 TGAAAAACTATTCCATGTTCATGGATGGGATCAATAAGTATTGTGAAAAT 2938
                           i   iv   i              v   vv v v i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192021232_   2939 GTCCATACTACCTAAAGCAATCTATAGATTCAATGCAATTCCTATCAAAA 2988
                          v v     v  i   vii     i        i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192021232_   2989 TACCAATGACATTCTTTGCAGAAATAGAAAAAA-AATTCTAAAATTTATA 3037
                          v   iivi v  i           v  v  iv-i  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_192021232_   3038 TGGAGCCACAAAGGATCTAGACTAGCCAAATCTGTACACACTGAAAATTT 3087
                             ivii   i   i i   v        -------   ------  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAA-------ACA------ATCT 187

  chr1_192021232_   3088 TTAAAAAACTTAGGAATCAGATTAAACTGACTTCAAATT-----ACTTCA 3132
                          v     i--- i   iv ii  ii v-    -  v i ----- i    
  L1M4_orf2#LINE/    188 TGAAAAAG---AAGAACAAAGTTGGAG-GACT-CACACTTCCCAATTTCA 232

  chr1_192021232_   3133 AATTGTACCACAGAGCTATAGTAACAAAAAGAGCATGGTACTGGTATCAA 3182
                           viv   i   i     i     iv  i v  ii         i  v i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_192021232_   3183 AGCAGACACATAGATCAATGGAACAGTATAGAGAACCCAGAAACAAATTC 3232
                         iii     i              i  v  v    ii       i   ii 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_192021232_   3233 ATACATCTATAGTAAACTCGTTTTCAGCAAAGATGCCAAGGCCATGCATT 3282
                               i   i  v  i vi     ii   i i       i    v  v 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_192021232_   3283 GGGGAAAGATCAATCTCTTTAATAAATGATTCTGGGAATACTGGATATCT 3332
                                  vi i   i  i  i     i v      vv        ? i
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_192021232_   3333 ACATGCAAAAGAATAAAATTGGACCTTTATCTCTCACCATATACAAAT-T 3381
                                       i  i       ii  i   v             v- 
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_192021232_   3382 CAAATAAAAATAGATTAAATACTTAAACCTAAGACCTCATACTATGAAAC 3431
                         i  v v     i   i ? v  i    iv     v  v v     i    
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_192021232_   3432 TACTACAAGAAAAGATTGGGGTAAATCTCCAGGACATTGATCTGGGCA-- 3479
                          vi  v       v  v  ?        i iv   v   ivi i    --
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_192021232_   3480 GATTTCTTGAGTAATATCCCACAAGCACAGGCAACCAAACTAA---TAGA 3526
                          i      iii  vv iv   v       i     v   vv  ---    
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_192021232_   3527 CAAAAGGTATCATATCAAG-TTAAAAAATCTTCTGCACAGTAAAAGAAAC 3575
                         i   vv v iivi     i-       --   i  ii vvi   i  v  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACAC 680

  chr1_192021232_   3576 AATCAACATAGTGAAGAGACAACCCACAGAATGGGAGAAAATATTTTCAA 3625
                         v     v v      i                              v   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_192021232_   3626 ACTATCCATATGACAAGGGATTAATAACCAGAATATGTAAGGAGCTGAAA 3675
                          ii  vi  v   i      i vi  v         i   i  i  vvv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_192021232_   3676 CTACCCTGTAGGAAGAAAACTAATAATTTAATTTTTAAATGGGCAAAAAA 3725
                          v  i vi  iv  i  i  v     iii    ?vv           ii 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_192021232_   3726 CCCTAATAATCTAATTTTAAAATGGGCAAAATAGATACTTCTC-ACAAAA 3774
                         ---------------   i  ----------    i i     - v i  
  L1M4_orf2#LINE/    831 ---------------TTTGAA----------TAGACATTTCTCCAAAGAA 855

  chr1_192021232_   3775 GACATATGAATGGCAAACAGGCATATATGAAAGGTTCTCAAAATTATTGC 3824
                           i   ii      v  i i   i  i-i    i v     v  i ????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATG-AAAAGATGCTCAACATCAZZZZ 904

  chr1_192021232_   3825 TCAT 3828
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.55 (138 / 89)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.75 (60 / 16)  


1418 29.13 7.38 2.82  chr1_192033018_192036544.rev     1782  2526 (1001)    L1M4_orf2#LINE/L1        1   779 (129)  

  chr1_192033018_   1782 TGGGAAGACATAC-ATGTTTGTGGATTGGAATATTTAA-ACTAGTAACAA 1829
                            i    i  v -     ii          v i    - i iv   -i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA-GA 49

  chr1_192033018_   1830 TGTCAATTCTCCCTAAACAGATCTATATTTTTAA-GCAATTCATATTAAA 1878
                           v    v     i   iv      i vv  i  -     i v   i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_192033018_   1879 ATGTCAACAATAC----TCTGTGGATATAAACAAGTTGCATCTACCTTTT 1924
                           vi  i -- i ---- i  ii  v  vi     i  vvi   vvv  i
  L1M4_orf2#LINE/    100 ATCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_192033018_   1925 ATATGAAAAACCAAAAAAATTAACATAGACAAAACAATTTTGAGAAAAAA 1974
                              i   vv   iii vii iv    v         i    i   i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_192033018_   1975 ---TAAATTTGGAAGAATTAGAGCATGTGAATTT-AAGAC--ACTATA-- 2016
                         ---i   v     i  v i v - v viv     -  i  --    i --
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACA-CTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_192033018_   2017 GCTCTAGTAAATTGGAGAATGTGGTGGTTGGCAGATAAATAAACACATGG 2066
                            vi     vivi  v i      i-i     v vii   i   i  i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTA-CTGGCATAAGGATAGACATATAG 295

  chr1_192033018_   2067 ATAAAAGAAACAGAATAAAGAAGCTAGAAATTGACCTACATGGTTACAGT 2116
                           v  v i  i     vi   iv i      vi   i i iiv   ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_192033018_   2117 CAACTGATTTTAGGCAAATATACAAAAGGCCCCTTAACAGAACAACTAGA 2166
                            i       v i   ivi i v  - i  vi i  ii iiv  vv v 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATA 394

  chr1_192033018_   2167 GATTTTTCAACAAATAGT---------ATTAGATATTTATA-GAAAAAAT 2206
                          vi            i  --------- i i    ?ii i - v    i-
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG- 443

  chr1_192033018_   2207 CAATGAAACTCAACCAA-ATTTCACATCTTATTCAAAGATTAACTCAAGA 2255
                         -      ii vi   vv- ii     i v   v    i          i 
  L1M4_orf2#LINE/    444 -AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_192033018_   2256 TGTAT--AAGACTTAAACGCAA-----AACACAACAAAACT-TTGGAAAA 2297
                           v  --?    i    i i  -----  v  v i      -  i   i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_192033018_   2298 AAA-ATAAGAGAACAATCTTTAGTATCTAGGACAAGGTGAAGTATTCTTA 2346
                            -   i ? v -      iivv i  v  iiv   ii v vv      
  L1M4_orf2#LINE/    543 AAACATAGGNGTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_192033018_   2347 CTCATGATACCAAAATTATAATCAATAATTTTTTTAA------ATG--TA 2388
                         vvi    i       vi i  v   i  -------  ------  i--  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAA-------AAGAAAAAATAGATA 634

  chr1_192033018_   2389 AACTG-ACTTCCTCAAAATTAAATGCTTTTTTACACTGCATAAAGAGCAC 2437
                           i  -     v           vi     v i -- v  --   ii   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGC--TTCA--AAGGACAC 680

  chr1_192033018_   2438 GTTTAAGTATATTAAGAAGACAAGACACAGTCTAGGATAAACTATTTGTA 2487
                         vv i   v - v i i       vv     vv i   v   v      i 
  L1M4_orf2#LINE/    681 TATCAAGAA-AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_192033018_   2488 GATCACATATTTGACA-----------TTCAAAGTATATTAAAAACTCTT 2526
                         i    i    i   i ----------- i  i i     v  i       
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

Transitions / transversions = 1.52 (129 / 85)
Gap_init rate = 0.04 (30 / 779), avg. gap size = 2.53 (76 / 30)  

 271 21.21 6.06 3.79  chr1_192033018_192036544.rev     2911  3042 (485)    L1M4_orf2#LINE/L1      774   908 (0)  

  chr1_192033018_   2911 ACTCTCTA-AAGTCAATAGTAAAAA-ATAATAATAATTCAATTAGAGAAT 2958
                              -  -  v      i      - i  --    ii     ?i i   
  L1M4_orf2#LINE/    774 ACTCT-TACAACTCAATAATAAAAAGACAA--ATAACCCAATTWAAAAAT 820

  chr1_192033018_   2959 GG-CAAAA----TAAACGTTGACATTTGGCTGAAGA-TATGTACAGATGG 3002
                           -    i---- i  -- v       vv ii    -v  i    i    
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAA--TAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_192033018_   3003 AAGATAAACACATAAAAATATGTTCATAATTACTACATTT 3042
                         vvi    i     i    v   i   vv  i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.06 (8 / 135), avg. gap size = 1.62 (13 / 8)  


3134 27.27 0.89 0.22  chr1_192061698_192065121     2030  2931 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192061698_   2030 TGGAAAAATATTCCATGGTCATGGATCGAAAGAATCAATATTTTTAAAAT 2079
                               i    i     v        i i    v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192061698_   2080 CTCCATAATACTGAAAGTAATCTACAGATTTAATGCAACCTTTATCAAAA 2129
                         vv v   v v iv   v i           i  i    i ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192061698_   2130 TACCAATGATATTCTTTACAGAAATAGAAAA--TAATTCTAAAATTTATA 2177
                          v   iiviiv  i   i       v  v  -- i  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_192061698_   2178 TGGACCCATTAAAGATTCATAATAGTCAAAGCCATCCTAAGCAAAAAGAA 2227
                             vviiiv ii  ii  v     i    i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_192061698_   2228 CAAAACTGGAGGAATCGCATTACCTGAATTCAAATTACACTACATAGGTA 2277
                             ii       v  i  i v  ii v      vivi      v  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_192061698_   2278 TAGTAACCAAAACAGTATAATACTGGCATAA-AACAGACACATAACCCAG 2326
                         i     i   i     i ii           -i i     i   ivi  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_192061698_   2327 TGGAACAGAATGGAGAATGCAGAAACAAATCCAGACACCTATAGTGAACT 2376
                              i     v    i v      i   i   v   ii   i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_192061698_   2377 TATTTTCAACAAGG-TGTCAAGAACATACATCACAGAAAATACAGTCTCT 2425
                         v      i      -  i     v   v  viivi    iv i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_192061698_   2426 TCAACAAATGGTGCTGGGGAAACTAGATATCCATATGCAGAAGAAGAAAA 2475
                                           iv    i    ?   i     i     vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_192061698_   2476 CTAGATGCCTATGCCTTGCCATTTA-AAAACTCAAATAAAAACGATTCAA 2524
                         i i  iv    ivi vii    v  -    v i  v v    i iv   ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_192061698_   2525 AT-CTTAAATCTAAGACCAAAAGCTATGAAACCATCACAAGAAATCCTTG 2573
                          v- i     v     v v   i    i    iv i v      v v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_192061698_   2574 GGGGAGATCTCCAGCATATAGGTCTGGGCCAAAATTTCTCAAACCAT-AC 2622
                          ? v i    i ivv iv v  vi i   v vii     i i -i  -  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGAC 599

  chr1_192061698_   2623 CCCAGAAGCACAGGCAAACAGAGCAAAAATGGACAAATAGGATCACATCA 2672
                         v   i       i    vv i  v      i  i    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_192061698_   2673 A-GTTAAAAAGCTTCTACACAGAAAGGGATAAAATCAACAAAGTGAAGAG 2721
                          -i       -   i iii vvv  i   i vv     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_192061698_   2722 ACAACCAACAGAATGGAAGAAAATATTTTCAAGCTACACATCTGACAAGG 2771
                               v         i           v   iii i i      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_192061698_   2772 GATTAATACCTGGAATACAAATGGAGCTCACACAACTCTATACGAAAAAA 2821
                           i vi  i ii     i v vi  i   vi       v   vv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_192061698_   2822 TCTAATAATCCAATTTAAACATGGATAAATGATTTGAATAGACATTTCTC 2871
                         v v     i      ?   v    ii   v                    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_192061698_   2872 AATGGAAGACATACAGTTGGCCAACAGGCTTATGAAAAAGTGCTTAACAT 2921
                         v vi     i     iv       i i  vi       ii    i     
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_192061698_   2922 CACTGATCAT 2931
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


1303 30.11 5.96 1.45  chr1_192082068_192083680      500  1120 (493)    L1M4_orf2#LINE/L1      260   908 (0)  

  chr1_192082068_    500 AGAAAGTGTGCTTTTGTCAAAGAGAAAAACATGAATATCAGTGAAACAGA 549
                            v      v vi  v  v ii  v i    iv v    i  i  i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_192082068_    550 TTAGATAACCCAAAAATAGGCCCCAT-CAAATATACCCAACTGATATTTC 598
                         v v  v ii   i     ii   -  -  vv   ivi   i    v  iv
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCC-ATACATTTATGGTCAATTGATTTTCG 358

  chr1_192082068_    599 ACAAAGAGGAAAAAGCAGTTCAATGGAAGAAGCAGAG-CTTTTCAGCAGG 647
                             i iv vv  ii vi        iii   v v  -       i  ii
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_192082068_    648 TAGAACTGGAGATT-TTGGACATCCATAGGCAAAGACACAAAAGTCACAC 696
                          i vi    -  iv-i    i ?   i v     iiv ii  -  iiv  
  L1M4_orf2#LINE/    409 TGGTGCTGG-GACAACTGGATAKCCACATGCAAAAGAATGAA-GTTGGAC 456

  chr1_192082068_    697 TTTTTACATTACATGAT---CAAAAATT-----------GATCATGGACT 732
                         iii -  v i   iv  ---        -----------     ?i   i
  L1M4_orf2#LINE/    457 CCCT-ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_192082068_    733 TGAATGTAAAATGTAAAACCTTAGAACTTTCAGCAAACAAAAACATGGGA 782
                          i       i vv      iv  i    i i  -  i--       i  ?
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAG-AAG--AAAACATAGGN 552

  chr1_192082068_    783 GAAAATCTTAGAGATCTATGGCTAGAAAGTGAGTTCTTAAATTTCATACT 832
                          v       v v  i  vv  i   iv i  iv      i  v v i  i
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_192082068_    833 AAAAATATCATTCATAAGAGGAAAATTTGATATAAT---ATTTCATCACA 879
                             ii iv viv i  i  i    v v    -   --- i       v 
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATA-AATTGGACTTCATCAAA 651

  chr1_192082068_    880 AT-GAAAACT---GTTCTGGGAAAGACCCTCTTAAGAGTATATAAAGAGT 925
                           -i      ---  v  vvi  i   v  v i    ivi iv     vv
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_192082068_    926 AGCTATAGATTGAAAGAAAATATTTGTAAACCACAAATCCAACAAAGGAT 975
                          v i i   v  ii            i   i  i v   ii i  i   i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_192082068_    976 GAGTATACACTTTTT-TAAA--ATTCTCAAAACTTAATAG---------A 1013
                         vv    v  vvv v -    -- i   i v    i    i--------- 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_192082068_   1014 AATAATCCAATTAAAATATGGACAAATGACATTGA-CAGACATTTCATTG 1062
                              i      ?   v    i    v  i-    -i         viii
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGACATTTCTCCA 850

  chr1_192082068_   1063 AAGAGAATATAGAGATGGCAAATATGCATATGAAAAGATGTTTTATATTA 1112
                             ii     v i     v    v   i           i iv i  i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_192082068_   1113 TTAACCAT 1120
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.47 (109 / 74)
Gap_init rate = 0.03 (20 / 649), avg. gap size = 2.30 (46 / 20)  


2426 27.85 4.27 0.39  chr1_192090483_192092928.rev      767  1538 (908)    L1M4_orf2#LINE/L1        1   802 (106)  

  chr1_192090483_    767 TGAGAAAATATCCTATGCTCAGGTATTGGAAGAATTAATGTTGTTTAAGT 816
                           ii  i      i   i   v v         v     i     v ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192090483_    817 GATCATACTACCCAAAGCAATCTACAGATTCACTGCAATCCCTGTCAAAA 866
                          iiv     v      vii             vi         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192090483_    867 TAC-AATGACACTCTTCACAGATGTAGGGAAGAAAAATCCTAAAATTTGT 915
                          v - iivi vi i  ii    vi v iv   vvi -          ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_192090483_    916 ATGAAACCAAAAAAGACCTGGAAGAGCCAAAGAAATTCCCGAGCAAAAAG 965
                            i  viiv  ii    ii   v       iv   - ii  iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAG 198

  chr1_192090483_    966 AACAAAGCTGGAAGTAAAACACTACCAGAC-----AACATACAACAAAGC 1010
                                i    i vvvv     v  vi i-----   v   v       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_192090483_   1011 TGTAGTAACTAAAACAGCATGGTAGTGGCATAAAAACAGACATATAGATT 1060
                          ii     ii  i    ii     v        ii i            i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_192090483_   1061 AATGAAACAGAGT---------AGAAATTAATCCACTTATCCACAGAAAA 1101
                             i  i   i ---------      v  i   ivi  ii ii vv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_192090483_   1102 CTGATTTTAG-CAAAGGTGTCAAGAACATCCATTAGGGAAAGAAGAATCT 1150
                         i       v -   i    i     v   i  v i         v i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_192090483_   1151 CTTCAATAAATGATACTGGGACAACTGGATGTTCATATGCAGAAAAATGA 1200
                         i     i     i i               i?i  i     i  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_192090483_   1201 AAGTAGACCCTCACCTCTCACTCAGTACAAAAGTCAACTCAAAGTAAATC 1250
                          iv i     ii     v   ivvi       i i        i ii   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_192090483_   1251 AAAGACCTAAATGTAATACCTGAAACTAGGAAACTACTAAAATAAAACAT 1300
                          ?              v v  i      vi     vi  i  v       
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_192090483_   1301 AGGA-TAAATATTTCAAAACAAAGGTCTGAGAATAAATTTTAAGAGTAAG 1349
                            ?-     v  ivvi v vvi   iv iv   iiv  i v   -  v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATG 597

  chr1_192090483_   1350 GCCTCAAAAACACAGGCCACAA--GAACAAGT-GA-------GATTACGT 1389
                         i vi     i    i  v    --   v  i -  -------  i v i 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_192090483_   1390 CAAGCTAAAAAGCTTCTACATAGTAAAGGAAAC----AGTAGAGTGAAAA 1435
                            iv v    i   i iiiivvi      v  ---- iv i        
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_192090483_   1436 AGCAACCTCCAGAATGGGAGAAAATATTTGCAAACTATCCATCTGACAGA 1485
                         ii     iv                         ii  vi      i ii
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_192090483_   1486 GGATTGATATTCAAAATATACAAGAAAGTCAAACATCTCAACAGCAAA-- 1533
                            i vi   i  i      i  ii  v  vv   v     i ii   --
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_192090483_   1534 GACAA 1538
                              
  L1M4_orf2#LINE/    798 GACAA 802

Transitions / transversions = 1.83 (137 / 75)
Gap_init rate = 0.02 (13 / 802), avg. gap size = 2.77 (36 / 13)  

 431 16.67 4.63 1.85  chr1_192090483_192092928.rev     1852  1959 (487)    L1M4_orf2#LINE/L1      798   908 (0)  

  chr1_192090483_   1852 GGCCAATAAATTAGATTTTAAAATGGGCAAATGATCTGAACAGACATTTC 1901
                          i v     vii -   ?v            v   i    i         
  L1M4_orf2#LINE/    798 GACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_192090483_   1902 TC-AAAGTAAGACACAGAAATGGCCAACAGATACATGAAAAAATGCT--- 1947
                           -    -    i i v          i iii         i     ---
  L1M4_orf2#LINE/    847 TCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_192090483_   1948 -ATCACTGATCAT 1959
                         -    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.04 (4 / 111), avg. gap size = 1.75 (7 / 4)  


3091 26.25 1.33 0.78  chr1_192145989_192150951     3568  4470 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192145989_   3568 TGGAAAGACATCCCATGCTTATGGATGGGTAGAATCAATATTGTGAAAAT 3617
                                 i        i i      v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192145989_   3618 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCTATCAAAA 3667
                          i v     v  v   vii       i      i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192145989_   3668 TACCA-CTGTCATTCTTCACAGAA-TTAAAAAAAAAATTCTAAAATTCAT 3715
                          v   -   i -  i  ii     -  i v  ivvi  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_192145989_   3716 ATGGAACTAGAAAAGAGCCCGCATAGCCAAAGAAAGACTAGGCAAAAAGA 3765
                               v iv  ii  v  v v         iv  vvi iiiv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_192145989_   3766 ACAAATCTGGAGGCAC-CACATTACCTGATTTCAAACTATATTATAAGGC 3814
                              vi      -  -    i v  ii        viv  i  i  i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_192145989_   3815 CATAGTCACCAAAACAGCATGGCACTGGTATAAAAATAGGCACATAGACC 3864
                         i i   v i   i    ii   i     i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_192145989_   3865 AAAGAAACAGAATAGAGAACCCAGCAATAAACCCAAATACTTATAGCCAC 3914
                           v i  i     v    ii    v          v i i    i i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_192145989_   3915 CTGATTTTCGACAAAGCAAACAAAATCATGAAGTGAGGAAGGA-CACCCT 3963
                         i             i vviv   i i   vv i  i    i  -i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_192145989_   3964 TCTCAACAATTGATCCTGAGATAATTGGCTAGCCACATGTAGGAGGATGA 4013
                          i       v  i v   i  i  i   v  ?       i ii  i    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_192145989_   4014 AACTGGATCCTCATGTCTCACAT--TAAACAAAAATCAACTCAAGATGGA 4061
                          ii    i  ii i--      i--  v        i       i     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTAC--CTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_192145989_   4062 TTAAGTACTTAAATCAAAGACATGAAACTATAAAAAATATAGAAGATGAC 4111
                          i ?iv  i     vv    vv i           vviv       vi  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_192145989_   4112 ATCAGAA-AAACCTTTGTAGACATTGGCTTAGGCAAGGATTTCACGACCA 4160
                           vi ?i-   i   i  -   v    v        v i    viiivi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_192145989_   4161 AGA-ACCAAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTAGGACTT 4209
                         v  -       -   v v    i    iv   i   i   iv v      
  L1M4_orf2#LINE/    596 TGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_192145989_   4210 TATTAAACTAAAAAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAA 4259
                         i  i   v v    i      iiivv    i iv  vi   iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_192145989_   4260 AAAGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTACACATCTGAC 4309
                                         i           v  ii   vii i i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_192145989_   4310 AAAAGACTAATATCCACAATCTACAATGAACTC----AAATAAACAAGGA 4355
                           ii    vi      v   v  i  v      ----  v v  i  v- 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-A 793

  chr1_192145989_   4356 AAAAAACAAACAGTCCCATCAAAAAGTGTGCTAAGAACATGAATAGACAA 4405
                             i     i ii  v  i?    i  v  v   i iv          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_192145989_   4406 TTCTCAAAACAGGATGTACAAATGACCAACAAATGTATTAAAAAATGCTC 4455
                              v   v i   i        i    i  iiii  v    i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_192145989_   4456 AACATCACTAATGAT 4470
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (147 / 86)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.36 (19 / 14)  


 227 32.18 0.00 0.00  chr1_192174739_192177716        3    89 (2889)    L1M4_orf2#LINE/L1      822   908 (0)  

  chr1_192174739_      3 GGCAATAAATATAAAAAGGCATTTCTTCTAAGTGGATATAGAGATAATGA 52
                              vii  v i  v  i       i v   vi      v i  iiiv 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_192174739_     53 ATAAATACATTAAAAAGCATTTAGCCTCATTAGCTTT 89
                             ii    v    iiiii i i v   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (19 / 9)
Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.00 (0 / 0)  

1631 27.26 1.87 4.43  chr1_192174739_192177716      924  1510 (1468)    L1M4_orf2#LINE/L1        1   572 (336)  

  chr1_192174739_    924 TAGAAAAACACCCCAGGTTCATGGATTGAAAGAATTAACATCATTAAAAT 973
                          i    i i i    v            i    v    i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192174739_    974 TACCATACTGCCCAAAGCAATCTCTGAGGATTCAACCCAATCTCTATCTA 1023
                         vi v     v      vii    vii--        v     i     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA--GATTCAACGCAATCCCTATCAA 98

  chr1_192174739_   1024 AAT----ACATCATTTTTCACAGAATTAGAAAAAAAAAAAAAATCTAAAG 1069
                            ----i vv v     ii     v v  v  ivvi v----i     i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT----CCTAAAA 144

  chr1_192174739_   1070 TTCATATGGAACTGAAAAAGAGCTGCAATAGCCAATGCCATTGTAAGCAA 1119
                                    v  v  ii  v iiv         vi v  iv i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_192174739_   1120 CAAGAACAAACCTGAAAGCATCACATTACCTGACCCCAAATTATACTACA 1169
                         v         vi  i i vv     i v  ii iii    viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_192174739_   1170 AGTCCA----AACTAAAACAGGATAGTACTGGTATACAAATAGATATCAA 1215
                          iv i ----  ii  i    vi i       i   vii     i  -- 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT--A 292

  chr1_192174739_   1216 TACCATTCAGTTCCATTCTTATCAATAGAACCAAATAGAGGACCCAGAAA 1265
                           ------- ----------      i   ivi   v   iii       
  L1M4_orf2#LINE/    293 TA-------G----------ATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_192174739_   1266 TAGAGCCACAGATCTATAGACATCTCATCTTTGAGAAAGTCAACAAAAAC 1315
                           i v   i v  i   i v  vi v  i  i  v  i viiv   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_192174739_   1316 ATACACTGGAGAAAGAACAACTTTTTCAAAAAATGGTGCAGAGAAAATTG 1365
                           v  v   i       i iii       v         v i  v  i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_192174739_   1366 GATTGTCATATGCAGAA-AATGAAGCTGGACCCCTATCACTCACCGTATA 1414
                            v?i  i     i  -       i          i v v    i    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_192174739_   1415 AAAACATCAACTCAAGATGCATCGAAGACTTAAATGTAAGACCTGAAAGT 1464
                         v   v  i       i   v   i?    i           v  i   v 
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_192174739_   1465 ATAAAAATCCTGGAAGAGAACCTAGAA--AAACTTTTCTGAACATTGG 1510
                               v  i i     i   v   i?--   ii  iv   v -    
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC-TTGG 572

Transitions / transversions = 1.45 (93 / 64)
Gap_init rate = 0.02 (10 / 572), avg. gap size = 3.70 (37 / 10)  

 786 26.53 2.33 2.92  chr1_192174739_192177716     2144  2486 (492)    L1M4_orf2#LINE/L1      568   908 (0)  

  chr1_192174739_   2144 CTCAGTCTAGGCAAATAATTCATGAATAAGACCTCCAAAGCACAAGCAA- 2192
                           ii vi       vviv   v ii   v   vi v             -
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_192174739_   2193 --AAAAAAAAATTAACAAATGGGACTT----AAAATATAAATA-TTCTAC 2235
                         --  i       vi i    v      ----     -    v -  i ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTTTGT 666

  chr1_192174739_   2236 ACAGAAATAAAAAATAATCAACAGAGTGAAGAGAAAACCTGCAGAATGGT 2285
                         i vvv  - ii v iv     v i      i   v    ii        v
  L1M4_orf2#LINE/    667 GCTTCAA-AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_192174739_   2286 AGAAAATGTATGCAAACTCTGAATCTGACAGGGGACTGATAATTGAGAGT 2335
                                i v      iiv iv      i i      vi  - iv   i 
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA-TCCAGAAT 764

  chr1_192174739_   2336 TTACAGGAAACTCAAACAAGCCACCAACAATAATACACAAAAAAACTCCA 2385
                         v  i iii     vv    vi  vi  i  v  v   ---  v   i v 
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACA---AATAACCCAA 811

  chr1_192174739_   2386 TTAAAAAGTGGGCAAAGGACCTGAATAGACATTTTAAAAAAGAAGACATA 2435
                           ?    i           ii             ivvv        i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_192174739_   2436 CACATGGTTAACAAGGATATAAAAAAGAAAACACTCAACATCCTAATAAT 2485
                           v    ii  i   v i  i    i---- ii         v???????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAG----ATGCTCAACATCAZZZZZZZ 907

  chr1_192174739_   2486 A 2486
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.31 (51 / 39)
Gap_init rate = 0.02 (8 / 341), avg. gap size = 2.25 (18 / 8)  


2552 27.65 5.07 0.46  chr1_192220083_192224952     3510  4377 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192220083_   3510 TGGAAAAACATCCCATGCTCATGGATTAGAAGAATAAATATTATTTAAAT 3559
                               i i        i         i     v v      i  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192220083_   3560 GTTCATACTGCCCAAAGAAATGTACGGATTTCATGCGAATCCTATCAAAT 3609
                          viv     v      vvi  v   i    iv i  i vi         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192220083_   3610 TACTACCATCATTTTTCACAGAATTAGAAAAAATGATTGTGAAGTTCG-A 3658
                          v i v vv v     ii     v v  v  iv    iv i  i   i- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_192220083_   3659 CCAAAA------AGACCCCAAATAACCACAACAATCCTAAGTAAAAAGAA 3702
                         ivi   ------i     vi    i   v       i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_192220083_   3703 CAAAGCTGGAGGCATCACATTACCCAACTTCAGACTATACTACAAAGCTA 3752
                              i      vv     i v     i    i viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_192220083_   3753 CTGTAAACAAAA--ATGT--TACTGGTGCAAAAATAGACATTCAGACCAA 3798
                          v    v   i --i   --      iii  ii        vi   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_192220083_   3799 TGGAACAAAATAAAGAACCCAGAAATAAGACCACACACTCA----CAACT 3844
                              i i   vi   ii          iv   i   i i ----   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_192220083_   3845 GATTATTGAAAAAGTTGATGGTAAA------CAATGGGGAAAAGACACTC 3888
                             v i  v  i ---i  vi  i------           ii i v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG---GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_192220083_   3889 TATTTAACAGATTCTGCTGAGAAAGCTGGCTAACTGTGTGCAGAATAAAG 3938
                          v  i    i  vv     i  v i    v  ? iiii    i  v  v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_192220083_   3939 AAACTGAGCCCCTACCTCTCACGTTATACAAAAAATAACTCATGACGAGT 3988
                           ii  ii          v   vv          v       vi i ii 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_192220083_   3989 TAAAGATTTAAATGCAAGACTTCAAACTACAACAATCCTATAAGAAAACT 4038
                         i ?   ii      i    vi v      i  v v  i  v        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_192220083_   4039 TAGGGAATACTTTTTTTTGACATTGCCCTATGCAGAGAATTTATAACTAA 4088
                             ?i-  vv i  iv    v   vvi  v   iv iv  iv  iv  v
  L1M4_orf2#LINE/    548 TAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_192220083_   4089 GTCCTCAATAGCAAATGCAACAAAAGCAAAAATTGACAATTGGGAACTAA 4138
                          v vi   v    v v          v      v  i  v v   vi v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_192220083_   4139 TTAAACTGGAGAGATTCTACACTGTAAAAGAAACCATCAACAGAGTAAAC 4188
                          i   v vi i iv  i iii  vi   i  v  i     v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_192220083_   4189 AGACAACGTACAGAATGGGAAAAAATATTCACAAACAGTGCACCCAACAA 4238
                                vi           i        ii    ivi ii i ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_192220083_   4239 AGGACTAGTATTCAGAATATATAAGGAACCTAAACAAATCAACAA----- 4283
                         i     v    i            i    iivv    v    i  -----
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_192220083_   4284 --GCAAA-AAC--------AAAATGGGCAAGGGACATGAA--GACACTTC 4320
                         --i    -   --------           i   iv    --    i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_192220083_   4321 TC-----AAGACATACAAGTAGGCAATAAACATACTAAATAATGCTCAAC 4365
                           -----    i      i i v      i  i iv   vi         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_192220083_   4366 ATCACTAATCAT 4377
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.69 (48 / 13)  


3233 26.10 1.10 1.10  chr1_192228611_192233169     3159  4066 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192228611_   3159 TGGAAAGATATTCCATGTTCATGGACTGGAAGAATCACTGTTGTTAAAAT 3208
                                    i             i       v i v i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192228611_   3209 GTTCACATTACCCAAATCAGTCTAGAGATTTAATGCAATTGCTGCCAAAA 3258
                          viv i i v       iii    v     i  i     iv  ii     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192228611_   3259 TACCAAAGACATTCTTCACAGACATAGAAAAAC-AATCCTAAAATTTGTA 3307
                          v   ivvi v  i  ii    v  v  v  i -i           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_192228611_   3308 TCAAACCACAAACGACCTATAACAGCCAAAGCAATCCTGAGCACAAAAGA 3357
                          vi  vii   iv    i v  i       i     i   iv - i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA-AGAAGA 199

  chr1_192228611_   3358 GCAAAGCTGGAGGCCTTACAATACCTGACTTCAA-----GTTACAAAGCA 3402
                         i     i      v  i   v v  ii i     -----ii        v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_192228611_   3403 ACAGTAACCAAAATAGCATGGTAGTGGCATAAAAACAGATACATAGACCA 3452
                                i   i i  ii     v        ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_192228611_   3453 ATGAAAAAGATTCAAGAATCCAGAAATAAATCAATGAATTTCCAGTCAAC 3502
                            i  v   v ii   i            i v  iv    vii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_192228611_   3503 TCATTTTTAACAAAGTAACCAAGAACATACATTAGAGAAAGGAAAATCTC 3552
                          v     ii    i vvi      v   v  v i i     i v i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_192228611_   3553 TTCAATAAATGTTGCTAGGA-AACTGGATATTCATATGCAGAAGAATGAA 3601
                              i     v    i   -         ?i  i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_192228611_   3602 AGTAAGTCCCTACCTCTTACCTTATACAAAAATCAAAACAAAATGGCTTA 3651
                         iv iiii         vi   v           i  vv        v i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_192228611_   3652 AACACTTCAATGGAAGACCTGAAAATATGAAACTACTGGAAAAAAACGTT 3701
                         ? v  i v    v    v  i   v   i     vi i   i     i v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_192228611_   3702 GAGGAAACACTCCAGGACATTGGGCTGGGCAAAGATTTCTTGAATAAGAC 3751
                          i? v  vv  i iv   v     i i     v i      ii   v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_192228611_   3752 CTCGAAAGCACAGATAATCACAGCAAAAATTGACAAA-AGGGTAACATCA 3800
                         vi i        iii  iv v  v      v  i   -v  iivv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_192228611_   3801 AGCTAAAAAACTTCTGCAGAGCAAAGGAAAAAGTCAACAAAGTTAAGAGC 3850
                          iv v        i  iivvv       v vvi    v     v  i  v
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_192228611_   3851 CCACGTACATAACAGGA--AAATATTTGCAAACTACCTATCTAGCAAGGG 3898
                          v  vi   v  ii   --             ii iv     iii     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_192228611_   3899 GTTAATAAACAAAATATCTAAGGATCTCTAACAACTCAATAGCAAAAAAA 3948
                         ii vi  vv  i     v   i  v    v           ii     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_192228611_   3949 AAAAAAACCAAATAATTCAATTTAAAAGATGGGCAAAAGTTCTGAATAGA 3998
                         --------       ii     ?    -         i v i        
  L1M4_orf2#LINE/    800 --------CAAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAGA 840

  chr1_192228611_   3999 CATTTCTCAAAAGAAGATATACAAATGGCCAACAGATATAGGATAAAATG 4048
                                 v                       i iii i v  v  i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_192228611_   4049 CTCAGCATCATTAATCTG 4066
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.50 (20 / 8)  


 206  9.76 0.00 0.00  chr1_192252180_192254533      453   493 (1861)  C L1M4_orf2#LINE/L1   (0)   908   868  

C chr1_192252180_    493 GCCAAAAAACACATGAAAAAATGCTCATCATCACTAGCCAT 453
                              v  i          i       v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (2 / 2)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  

3091 28.34 0.34 0.34  chr1_192252180_192254533      975  1856 (498)    L1M4_orf2#LINE/L1        1   882 (26)  

  chr1_192252180_    975 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1024
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192252180_   1025 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1074
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192252180_   1075 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 1123
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_192252180_   1124 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGTCAAAAGA 1173
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_192252180_   1174 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 1223
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_192252180_   1224 ACAGTAACCAAAACAGCATGGTACTGGTTCCAAAACAGAGATATAGATCA 1273
                                i   i    ii         iviv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_192252180_   1274 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATACCTACAACTA 1321
                               i    i--    i  --        vv iii i ii  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_192252180_   1322 TCTGATCTTTGACAAACCTGAGAAAAGTAAGCAATGGGGAAAGGATTCCC 1371
                         vi    i  i     ivv  vv  i vi vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_192252180_   1372 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 1421
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_192252180_   1422 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 1471
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_192252180_   1472 TAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTGGAAGAAAACC 1521
                         i ?   ii       v   v       i      vi i i         v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_192252180_   1522 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAA 1571
                             ?i v viv   iv   v v  vv i     v ii   v ivvi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_192252180_   1572 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1621
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_192252180_   1622 TCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1671
                         iv  v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_192252180_   1672 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 1721
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_192252180_   1722 GGGCTAATATCCAGAATCTACGATGAACTCAAACAAATTTACAAGAAAAA 1771
                           i  vi          v  ii v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_192252180_   1772 AACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCT 1821
                         i     i     v  i?    i    ii     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_192252180_   1822 CAAAAGAAGACATTTATGCAGCCAAAAAACACGTG 1856
                          v        i  vi viii     v  i   i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.00 (4 / 882), avg. gap size = 1.50 (6 / 4)  


3187 24.89 2.39 2.27  chr1_192272366_192274956     1220  2099 (492)    L1M4_orf2#LINE/L1        1   881 (27)  

  chr1_192272366_   1220 TGGAAATATATGCCTTGTTCATGAATTACAATAGTTAATATTATTTAAAC 1269
                               v    v  v        i   iv  v v        i  v i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192272366_   1270 ATCTATACTACCTAAAGCAATCTACAAAGTCAGCGCATTCCTTATCAAAA 1319
                         iv v     v  i   vii       i v   i    v   i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192272366_   1320 TACCAACGACATTCTTTACCAAAATAGAAAAAGTGACCCTAAAATTTCTG 1369
                          v   i vi v  i   i vi    v  v  iv   i         iv i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_192272366_   1370 TGGAAATGCAAAAGATCCTGAATAGCTAAACCAATCTTGAGCAAGAGAAG 1419
                                    ii  i  v       i   v         iv    ii i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_192272366_   1420 CAAAGCTGGA--ATTACCAGACTATCTGACTTCAAAATATGTCACAAAGC 1467
                              i    -- i --  v   vi ii i       iv iii       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACT--CACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_192272366_   1468 TATAGTAATTAAAACAGTATGATACTGGCATAAAAAAACAGACACATAGA 1517
                           i      i  i     i  i           ii --i     i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA--TAGACATATAGA 296

  chr1_192272366_   1518 CTGATAGAACAGAATAGAGAGCTCAGAAATAGATCCACAAACCTACAAGT 1567
                         iii  i   i     v     ii        i i   i v ii  ii-  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG-GT 345

  chr1_192272366_   1568 CAACTGATTTTCAATAAAAGTGACCAGAACACACATTGTAGAAGGGACAA 1617
                            i        i i  ii   v v   v  iv  v  vi   i i i i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_192272366_   1618 TCTCTTCAATAAATGGTGCTGGGTAAATTGGATATCCACATGCAGAAGAA 1667
                            i     i             vv  i      ?         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_192272366_   1668 TGATATCAGAACTCTACCTCTCATCACATACA----------CAAA-TGG 1706
                            vi ii  v i       v  i  i     ----------    -   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_192272366_   1707 ATTAAAGATTTAAATGTAAAACTTGAAACTATGAAACTACC-GAAGAAAA 1755
                           i ?   ii         i vi i       i     vii-        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_192272366_   1756 CACAGGAAAAAAAAAAACTTCATGACATTAGTCTGGGCAGTAATTTTTCC 1805
                           i   ?iv   v----    i    v  i vi i    i ii   i iv
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_192272366_   1806 AATGTGATCTCAAAAGTACAGGCAACAAAAGCAAAAATAGACAGATTGAA 1855
                         i  i   ivi      i   i          v         i i    i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_192272366_   1856 TTACATTAAACTCAAAG--CTCTGCATAGCAAAGGAAACAATCAGCAGAG 1903
                         i v   i   v i   i--i i  iiivv       v  v    iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_192272366_   1904 TAAAGAGACAACCTACAGAAATGGAAAACAAATCCTTAGAAGCTATATAT 1953
                          i  i        i      -   i i -    vi  iv  iii      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAA-TGGGAGA-AAATATTTGCAAATCATATAT 739

  chr1_192272366_   1954 TTAATA-----TTTTAGTATCTCAAATATATAAAGAACTAGGAACCACTC 1998
                         i i   -----i  --     ivi               vvv - v    
  L1M4_orf2#LINE/    740 CTGATAAGGGACTT--GTATCCAGAATATATAAAGAACTCTTA-CAACTC 786

  chr1_192272366_   1999 AATAGCAAAGAAAGAAAAAATAATAACCCAATTGGAAAATGGGCAAAGGA 2048
                             ii   --    v   ----          ?i               
  L1M4_orf2#LINE/    787 AATAATAAA--AAGACAAA----TAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_192272366_   2049 TCTGAGTAGATATTTCTCAAAAGAAGACATACAAATGACTAATGACTACA 2098
                          i   i    i       v        i         i i   i vi   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_192272366_   2099 T 2099
                          
  L1M4_orf2#LINE/    881 T 881

Transitions / transversions = 2.26 (149 / 66)
Gap_init rate = 0.02 (16 / 881), avg. gap size = 2.56 (41 / 16)  


2624 24.64 10.44 0.49  chr1_192287420_192291650     2915  3738 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_192287420_   2915 GAAAAATGTTCCATGTTAATGGGTTGGAAGAGTAAGTATTGTTAAAATGT 2964
                             i  i i       v    i        v v i         i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_192287420_   2965 CCATACTACCAAAAGCAATCTACAGAGTTAATGCAATTTCTATCAAAATA 3014
                          v     v  v   vii         v i  i     ii          v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_192287420_   3015 CCAA-------------------TGACA------TTCT-----TCACATA 3034
                            i-------------------     ------ i  -----   i  i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_192287420_   3035 -------AAGAGA----------------------TAAAAAAGA------ 3049
                         -------   i  ---------------------- i       ------
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_192287420_   3050 --------GGATTCACATTACCTGACTTCAAA--TTAAAATACAGAGCTG 3089
                         --------   i     i v  ii i      --   v--    i    i
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGCTA 250

  chr1_192287420_   3090 TAGCAACCAAAACAACATGGTCCTCGCTTAGAAACAGACACATGGGCCAA 3139
                         i  i  i   i   iii    v  v  v  iii i     i  i ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_192287420_   3140 TGGAACAGAATAGAGAACTCAGAAACAAATCCACACACCTACAGTGAACT 3189
                              i     v    iii      i   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_192287420_   3190 GATTTTCAACAAAGTTTCCAAGAACATACACTGGGGAAAAGACAGTCTCT 3239
                                i    i v v      v   v  v        ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_192287420_   3240 TCAATAAATTGTGCTGGGAAAACTGCATTTCCATATGCAGAATAACGAAA 3289
                             i    v         v     v  v?   i     i  v  i   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_192287420_   3290 CTAG-----TATATGGC--CATATACAAAAAA-AAATCAAAGTGGATTAA 3331
                         i i -----  iv vi --            v-  v     i     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_192287420_   3332 AGACTTAAATCTAATACCTGAAACTATTAAACTACTACAAAAAAGCACTG 3381
                             i     v   v v  i       v     vi  v  i   i  iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_192287420_   3382 GGG-AAATCTTCAGGACATTGGTCTGGGCCAAAATTTCTTGAGTAATACC 3430
                          ? -        iv   v    vi i   v vii      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_192287420_   3431 CCACAAACACAGGCAAACAAAGCAAAAATGGATAAATGAGATCACATCAA 3480
                            v  i    i    vv    v      i       vi  iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_192287420_   3481 G-TTAAAAAGCTTCTGCACAGCAAAGTAAACAATCAGTAAATTAAAAGGA 3529
                         i-       -   i  ii vv     v v  v    iv   v i   i  
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_192287420_   3530 CAGCTCACAGAAAGGGAGAAAATATTTGCAAACTACGCATCTGACAGGGG 3579
                           i i       v                   ii iii      i i   
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_192287420_   3580 ACTAATAACCAGAATATATAAGGAACTCAGACTCCTCTACAGAAAAAAAT 3629
                            vi  v             i      vv  vv   v i iv     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_192287420_   3630 CTAATAATCTGAAAAAAAAAATGGGCAACAGATCTGAATAGAGATTTCTA 3679
                          v     i i-  vv?            vi   i        v      v
  L1M4_orf2#LINE/    800 CAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_192287420_   3680 AAAAGGATACATACAAATGGC-AACAGGCATATGAAAAAGTGCTCAATAT 3728
                         v    i v i           -  i i   i       ii       i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_192287420_   3729 CACTGATCAT 3738
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.58 (122 / 77)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 5.62 (90 / 16)  


2667 26.52 4.38 2.36  chr1_192330373_192333777     2023  2912 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192330373_   2023 TAGAAAATTATTGTATGTTCA-GGGTTAATGAAAATT--ATATTGTTAAA 2069
                          i    iv   ivi       -  i  i--   i i --          i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTG--GAAGACTTAATATTGTTAAG 48

  chr1_192330373_   2070 ATATCTATACTCCCCAAAGTGGTCTACAGATTCAATGCATTTTGTATCAA 2119
                           iv v            v  i             i   v iiv      
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_192330373_   2120 AATCCC--CTGTTATTTTTCATAGAAATAGAAAAA-TAGTCCTAAAATTT 2166
                               --   ii-     iii      v  v  i- ii          i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_192330373_   2167 ATATGAAATTACAAAAAAATCTGAATAGCCAAAGTAATAATGAGCAAAAA 2216
                              i  v i   iii vi v           ii   vv   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_192330373_   2217 GAACAAAGCTGGAGACATCACACTACCTGATTTCAAACTATACTACAAA- 2265
                                 i     ivv       v  ii        viv         -
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_192330373_   2266 --ACAATAAT-AAAACAGCATGGTACTGACATAAAAACAGACATATTTAC 2312
                         --   i    -  i    ii        i     ii i        vv i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_192330373_   2313 GAATGAGACAGAATAGAGAGCCCAGAAACGAAACTATGTATGTATGTTTA 2362
                         v    ii i     v     i       ii  v i  ii  v    v i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_192330373_   2363 ACCGATTTTTTACAAAGTTGCCAAGAATACACAGCAGGGAAAGGAAAGTT 2412
                          ii      iv    i v        vi iv  iii       i v   i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_192330373_   2413 TTTTT--CA---------------------TATTCACATGAAAAAGAATG 2439
                             i--  ---------------------  ?i      v         
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_192330373_   2440 AAATTAAATGTTTTTCTTACACCATATATAAAAATCAATTCAAAATGGGT 2489
                           i  ii ivii vi  i          i      i  i         i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_192330373_   2490 TTAAGACTTAAATGTAAGACCTAAGACTGCAGTACTGCTATAAGAAAACA 2539
                         iv?    i           v    i   ii iv   vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_192330373_   2540 GGGGAAAAAA-CTACAAAATATTGATCTGGGCAATGACTTTTTTTTTTTT 2588
                         vi  ?iv   -  v ivi iv   ivi i       i------------ 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG------------T 585

  chr1_192330373_   2589 TTTTTTTTTTTGGCTCCCAAAATGTAGACAACAAAAGCAGAAATAG-CAA 2637
                           i  vvv v  i v  v   iiii ii         v i      -i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_192330373_   2638 ATGGGATTGCATCACT-TTAAGAATCTTCCGCACAACAAAGAAAGCAATT 2686
                           v   i v     vv-    i  -   ii ii vv     i vi v  i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chr1_192330373_   2687 AACAGAGTGACGAGCCAATCTAGAAATTGGGAGAAAATATTTGTAAGCCA 2736
                           v i     vi  v   i i v i v                i  ii  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_192330373_   2737 CACCTCCAATATGGGGTTAATATCCAAAATATATAAGGAACTCAAACAAA 2786
                         i iv  ii   v   ii vi      i         i      vv    -
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA- 783

  chr1_192330373_   2787 ATTTTATAGTAAGAAAACAAATAACCTAATTGTATAAAATAG-CAAGGGA 2835
                         -i iv   i   i  i          i    -? -     i -   i   
  L1M4_orf2#LINE/    784 -CTCAATAATAAAAAGACAAATAACCCAATT-WA-AAAATGGGCAAAGGA 830

  chr1_192330373_   2836 CCAGAACAGACATTTCTCAAACGATGACAGA--AATGGGCAAAAGATGTA 2883
                         iiv   i           v  v  v  i v --     v   v iiiii 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_192330373_   2884 AGAAAAAAATGCTCAACATCACTAATCAT 2912
                         v     i -            ????????
  L1M4_orf2#LINE/    881 TGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (152 / 80)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.86 (60 / 21)  


 290 20.00 8.00 11.00  chr1_192353769_192356144      493   692 (1684)    L1M4_orf2#LINE/L1      178   371 (537)  

  chr1_192353769_    493 AAAAAAAT--TGAGATAGGGTAACAA-GTTAGAAATCTTATAACACT--- 536
                             v   --   i v  iiv     -   i  iiv  i ---    ---
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA---CACTTCC 224

  chr1_192353769_    537 -AATTTTAAGAGGTATAATAATGTAGCTAAA--AGT---GACAATGTGTC 580
                         -     i  i vv  iv i  ---     v -- i ---    i    vi
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAA---AGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_192353769_    581 ATTGAAA-AAGGATATATGTATATACATACTTGTATAAATCAGTGGAATA 629
                          i  iv -       --- -----     ------  i    i       
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATA---G-----ACATA------TAGATCAATGGAATA 307

  chr1_192353769_    630 GAATAAAGAG--CAGCAAAATAGACATAGATATTTAAGGTCAATTGATTT 677
                             vi    --   --     i  vi v i     v             
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAG--AAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_192353769_    678 TC-ATAAAAATGCCAA 692
                           - i  iii      
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAA 371

Transitions / transversions = 1.86 (26 / 14)
Gap_init rate = 0.07 (14 / 194), avg. gap size = 2.71 (38 / 14)  

 555 27.84 5.57 5.36  chr1_192353769_192356144     1401  1885 (491)    L1M4_orf2#LINE/L1      423   908 (0)  

  chr1_192353769_   1401 CTGAGTAGCCACATG-AGAAAAACAAAATAAACTGAAACTTCATCCTCAA 1449
                            ii  ?       - i  i  ii  i ----  i v iii -     v
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGT----TGGACCCCTA-CCTCAC 467

  chr1_192353769_   1450 AGTTTACATAAAGTTTCATTCAAAGTAGAT-ATGAACTAAAATGTGAAAG 1498
                          viv  i i   iv  v i     i i   - ?ii  iv      i i  
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_192353769_   1499 ACACAAATATAAAATT-TTAGAAGAAAATCAAGGAATA--TTTTCATGAA 1545
                         vi v  v       i -           ivv   ?i  -- i   i   v
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_192353769_   1546 CTCGGTATAGGCAAGAGTATATTAGATG-GA-AGCAAAAGTTGTTACCAA 1593
                           i  vv       vi  v v      i-  - v      i-iiv v   
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC-ACAAGCAA 616

  chr1_192353769_   1594 CAAAAAATTAATTATAAAAATTGTTACTTC-------TTAAAACATTTTG 1636
                              i vv  v  v v      v-     -------      vv     
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGG-ACTTCATCAAAATTAAAAACTTTTG 665

  chr1_192353769_   1637 CTTTTCAAATGTTAGCACTAAACAAATAAAAGACAAAAGACAGCACTCAG 1686
                         ivi      v ---i     v-   i--    vv        i v v   
  L1M4_orf2#LINE/    666 TGCTTCAAAGG---ACACTAT-CAAG--AAAGTGAAAAGACAACCCACAG 709

  chr1_192353769_   1687 GCTGGGAGAAATTTATACACACACATACATACAT---ATATG---CATAT 1730
                         iv         ---   ivii  v  -    i  ---   v --- v i 
  L1M4_orf2#LINE/    710 AATGGGAGAAA---ATATTTGCAAAT-CATATATCTGATAAGGGACTTGT 755

  chr1_192353769_   1731 GACCCAAAATATTACGTACAGATATATAACAAACACAGAAATATTAGAAG 1780
                         - i   i     ---i  v   vv v v    - v  iv    -- i   
  L1M4_orf2#LINE/    756 -ATCCAGAATAT---ATAAAGAACTCTTACAA-CTCAATAATA--AAAAG 798

  chr1_192353769_   1781 ATCAG--ACTCTAATACAAATTATGTTTGAGATCTCAAGAGA---TCCTT 1825
                          iv i--  i v v ?v   v iv ivvii   i v  v   --- i  i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_192353769_   1826 CACA--AGTTATATAAATAGCTAATGTATACACATTTAAAGATGTTCAAC 1873
                           v --  v    i    i  i   -- vi     vv       i     
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAAT--AAGCACATGAAAAGATGCTCAAC 896

  chr1_192353769_   1874 ATAATTAGGCAA 1885
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.05 (67 / 64)
Gap_init rate = 0.05 (26 / 486), avg. gap size = 2.04 (53 / 26)  


3499 18.74 6.51 2.74  chr1_192391230_192394311     1725  2599 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192391230_   1725 TGGAAA-ACATTCCATGTTCATGGC-----AG---TAATATTGTTAAATT 1765
                               - i  i            v-----  ---            iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192391230_   1766 GACAATACTACCCAAAGTGATCTACAGATTCAATACAATACTTATAAAAT 1815
                          i       v      v                ii    v i   v   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr1_192391230_   1816 TAATTGAATCCTCATTTTGATGGCCTTTTCTTTTGGGAGAAATGGAAAAG 1865
                         -------    -  vi -----       i ---- v      v  v   
  L1M4_orf2#LINE/    100 -------ATCC-CAGCT-----GCCTTTTTT----GCAGAAATTGACAAG 132

  chr1_192391230_   1866 CCAATCCCCAAATTCATATGGAGTTGCAAGGGATTCAAAATAACCAAAAC 1915
                          ii    iv             iv         ii  i    i       
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr1_192391230_   1916 AATCTTAAAAA-----------------GGAC---CGTGTTCTAGATTTC 1945
                               i    -----------------    --- iiv i i -     
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTC 231

  chr1_192391230_   1946 TAAACTTACCACAAAGCTACAGTTAGTTACCAAGACTCTGTGGAACTGGC 1995
                         v        i             - i ---      vv     v      
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGT-AAT---CAAGACAGTGTGGTACTGGC 277

  chr1_192391230_   1996 ATAAGCATAGATAAATAGATCAATCAAACAGAATTAAGAATCCAGAAATA 2045
                              v     i v          vi  i      i   i          
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_192391230_   2046 AACACATATATTCATGGTCAATTCATTTGCAATAAGAGTGCCAAGATCAT 2095
                            v    i   i          v    v i i   i         i   
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_192391230_   2096 TGAGTGGGGTAAGAATAATTTCTTCAAGATACCGTCCTGGAATAATTGGT 2145
                          v i     v       i i i     v v iv  v    i i  i   v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_192391230_   2146 CATCCACATGCAAA-GAAGGAAATTAGACTCCTACCTCACATCATATACA 2194
                         i ?           -   v   i  i   i           i        
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_192391230_   2195 AAA-TTAACTCAAAGTAGAAAAACAACCCCAAATAT--GAGTTAAA-CAA 2240
                            -          i i  vv ?vi   i-    i --   i    - v 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCT-AAATGTAAGAGCTAAAACTA 526

  chr1_192391230_   2241 TTAAACTCTAAG--GAAAAAATAGAAGTAAATCTTTATGATCTTGGATTT 2288
                          v       v  --     v    i?         ii   i     i  v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_192391230_   2289 GGCAGTGGGTTCTTAGGTATGGCAGCAAAAACATGAACAA-------AAA 2331
                             i   v       i    i  v     i  ii i   -------   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_192391230_   2332 AATGGACAAATTGGATTTCATCAAAAGTAAAAACTTCTGTGCATGAAGGG 2381
                            i  i        i          v         i     v v  i  
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_192391230_   2382 ACATTAT-AAAAAAGT---AAGACAAACTATAAAATGGGAGAACATATAT 2427
                            i   -  i     ---       v i i i          v    v 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_192391230_   2428 GCAAAGCATATACCTAATACAGGTCTTATATTCAGAATATATAAAGAGCT 2477
                              v      i  i   vi  v   i   i               i  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_192391230_   2478 TCTATAACACAACT-TAAAAA--CAAAGGACCTAGTTTCAAAGTGGGCAA 2524
                         ii  i   v   iv-      --    vi   i i  ?v   i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_192391230_   2525 AATGCTTTACTGGAAATTTCTCCAATTAAGATAT-------GCCAAAAAG 2567
                          ivii  v v i  v          vv       -------     v   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_192391230_   2568 CACATAAAAAGATGAAAAACATAAGTCATTGG 2599
                              i        vvv     v ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (95 / 65)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.38 (81 / 24)  


1340 26.71 8.55 5.55  chr1_192446188_192448411.rev      871  1735 (489)    L1M4_orf2#LINE/L1       18   908 (0)  

  chr1_192446188_    871 TTTATTAATTTAAAAATTTATTATTGT--------CAGTTTTACTGAAAT 912
                           i  vi   vi  i i   v      --------  i vi v iv    
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr1_192446188_    913 TGACCAATAGGTTCAACAAAATTTC-ATGCAGAATATCAGCAAGAATTTT 961
                            i v i  i      iv   ii -  -  i   vi    vivvv    
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTAT-CAAAATCCCAGCTGCCTTTTT 116

  chr1_192446188_    962 ---ATATATT-ACGCAAAGCTAATATTAAACTTTATATGGAAATACAAAT 1007
                         --- v v   -  ---     i  vi    v  i          i   iv
  L1M4_orf2#LINE/    117 TGCAGAAATTGAC---AAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_192446188_   1008 GGTGAATAATAGTCAAAAGGATTTTGAAAAACAGATACAAAGTTGGATGA 1057
                          iivv v     i     vi  i        v iiv           v  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_192446188_   1058 TTTTAACTACCTGACATTAAGAC--AATATAAATCTACAGCAATCGAGAC 1105
                         i ivv   v  ii iv i  i  -- v  i   v      i    i    
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_192446188_   1106 AGTGTGTTATTGGCATAATGATAGATTGTGAACATAGTGGATCAATAGAA 1155
                               v  i        v      -------    - i       i   
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGA-------CATA-TAGATCAATGGAA 305

  chr1_192446188_   1156 -AG-------------GAAATAGATCTACATATCTGTGATTAATTGATAT 1191
                         -  -------------      i i i i i  i i  i i       v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_192446188_   1192 TTCACCATGTTGTTAAGATAAAGTATTCA----GCTAAATATGCTCTTTT 1237
                          iv  v v v  ii    i----i     ---- vv  iv  iv      
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGAC----CATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_192446188_   1238 CGGGCAAATAGTAATAAAACAGCTGAATATCCATTTGGGAATAAATAAAC 1287
                          ii-     i  iv iii   i   i   ?   iv  vi  vi   i  v
  L1M4_orf2#LINE/    402 CAA-CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_192446188_   1288 TTTG-CTCAT---TCACACTATATATAAAAATT---TCA--------CTT 1322
                           v - i v ---      i     i       ---   -------- v?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_192446188_   1323 AGACCTACATTTAAAAGTTAAAATTATACAAATTCT-AAAAGGAATGTTA 1371
                                v  v   i  i     i    -   i   - i   i  vvv  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATA 549

  chr1_192446188_   1372 GGAAAAAATCATTGTGACTTTGGTGTAG--AATAAGGTATTCCACTTGTG 1419
                           ?iv     v i     i    vv   --   --   v iii vv i  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT--GGTTTCTTAGATATG 597

  chr1_192446188_   1420 ACAC-AGACTCATAA--AACAAAA--ATAAATTGGTATTTT---TTTCTT 1461
                             - i vv  i  --       -- v    v i  vv  ---i   v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_192446188_   1462 TAAAAATGTTAACATCTGCTTTTCCA-GAATACCAAGAAGAAAATAAAAA 1510
                         i    v ivv   v i  ivi   v - i i  i vv      i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_192446188_   1511 TATAAGCCTCAGCTTTCAAAAATGCATTTACAATATTATCTATCTATCTA 1560
                         v i  v  v   vv vvi i  vii    i   -  i  v     i--- 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTG---A 743

  chr1_192446188_   1561 T------CTCATCTATCTA-AAT---TGAAGCAATGTTATAAAACTCAGC 1600
                          ------  -- v    i -   --- i   v v v   i  --    i-
  L1M4_orf2#LINE/    744 TAAGGGACT--TGTATCCAGAATATATAAAGAACTCTTACAA--CTCAA- 788

  chr1_192446188_   1601 GATGACTATTAATAAAACTTATTATTGAG-CAAA-AGTTCAATT-AAAAA 1647
                         ---------        ----------  -    - iii     -     
  L1M4_orf2#LINE/    789 ---------TAATAAAA----------AGACAAATAACCCAATTWAAAAA 819

  chr1_192446188_   1648 TGCTCAAAAG-TTTTAATAGAGCTTTCACAAAAGAAAGTATATGGATTGC 1696
                           vv    i -   v      vv    v v      ii    iii  v  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_192446188_   1697 TAAGAAGCACATAAAAATATGTTCCACATTTAGTGTGTG 1735
                         i  v        i    v   i  v    iv????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (126 / 102)
Gap_init rate = 0.04 (40 / 891), avg. gap size = 3.05 (122 / 40)  


2747 27.85 2.01 0.45  chr1_192543360_192545467.rev      724  1617 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192543360_    724 TGGAAACACATACCATGCTCATGGATGGGCAGAATCAATATGGAGAAAAT 773
                               v i  v     i        v  v   v i     v vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192543360_    774 GACCATATTACCAAAAGCATTCTA-AAATTTAATACAATTCCCATCAAAA 822
                          i v   i v  v   viiv    - i   i  ii    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192543360_    823 TACCACCAATACTCTTCACAGAACCAGAAAAAAAAAAATCCTAAAATTCA 872
                          v   v viivi i  ii     -- vvi v  ivvi             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr1_192543360_    873 TATGGAACCAAAATGAGCCCACA-TAGTGAAAGCAAGACTAAGAAAAAAA 921
                                viiv  v ii    v -   iv   i   vvi i -    i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAA 197

  chr1_192543360_    922 GAACAAATCTAAAGGCATTACATTAGCCAACTTCAAACCATGCTATTAGG 971
                                vi ii   vv i   i vv    i      v v i   iv i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_192543360_    972 CCATAGGCACCAAAACAGCACGGTAATGGTATAAAAATAGGCACATAGAC 1021
                          i i  vv i   i    iii    v   i    ii    i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_192543360_   1022 CAATGGAATAAAATAGAGAACTCAGAAATAAAGCCAAA----TACAGCCA 1067
                                   i   v    iii          v   v ----  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_192543360_   1068 ACTGATCTTCGATAAAGCAAACAAA--CATAAAGTGGGGAAAAGACATCC 1115
                          i    i     i  i vviv   i--   vv i        ii i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_192543360_   1116 TATTCAATAAACGGTGTTGGGATAATTGGCAAGCCACATGTAAAAGAATG 1165
                          v     i   i    i     i  i   vv ?       i         
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_192543360_   1166 AAAATGGATCCTCTTCTCTCACCTTATATAAAAATCAACTGAAGATGGAT 1215
                           iv    i  iivi   v    v    i      i    v  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_192543360_   1216 CAAAGACTTAAATATAAGACCTGAAACCGTAAAAGTTCTAGAAGATAACA 1265
                           ?    i     i     v  i    ii     v ii       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_192543360_   1266 TTAGAAAAACACTTCTAGACGTTGGCTTAGGTAAAGACTTCATGACCAAA 1315
                          vi ?iv  vv    vv   v    v     i  v ii   v iivi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_192543360_   1316 AAAACAAAAGCAAATGCAACAAAAACAAAGATAAATAGATAGAACTT--- 1362
                          v v        v v         iv   i   i   i  v i    ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_192543360_   1363 --AAACTGAAAAGTTCTGCACAGCAAAATAAATCAT-AAGCAGAGTAAAC 1409
                         --   i i    v  i  ii vv    iv v ii  -   - i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAA 696

  chr1_192543360_   1410 AGACAGCCCACAGAGTGGGAGAAAATCTTCACAATCTATACTTCTGACAA 1459
                              i        i           v  ii   vii   iv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_192543360_   1460 AGGACTAATAGCCAGGATATACAGGGAAC----GCAAATCAGCAAGGAAA 1505
                         i     vi  v    i     i ii    ----i   v   ii  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_192543360_   1506 GAACAAACAATCCCATCTAAACGTGGACAAAGGACATGAATAGACAATTC 1555
                         ii     i  i  v  i?   vi   i       iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_192543360_   1556 TCAAAAGAAGATATACAAATGGCCAACAAATATACGAAAAAATGCTCAAC 1605
                           v                       i  ii i i     i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_192543360_   1606 ATCACTAATGAT 1617
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (149 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.20 (22 / 10)  


1717 25.09 6.70 4.51  chr1_192622137_192623949      500  1320 (493)    L1M4_orf2#LINE/L1       70   908 (0)  

  chr1_192622137_    500 ATCTAAAGA----ACACATTTCCAGTCAAAGTACTAGTAGG--TGTTTAT 543
                              v   ----  i  v i  vi     i v i  iv v-- v   ii
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chr1_192622137_    544 AGATATTAACGAGCTGATTAGAAAATTTGTCTTGAAATGCAAAGAATTTA 593
                            v   i  i       ivv      ii v v         i i iii 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_192622137_    594 GAATAGACAAAACAATTTTGAAATAGATGAATAA-GTTGGAGACCTTACA 642
                               v         i      v   v   i  -       iv  i   
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_192622137_    643 TTACCTAAGTTCAAGGCTTAATTTAAAGCTGTGGATATTACTAGAGTGTG 692
                         i v  i  v     ii    v vi      iii vv  i vv v      
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_192622137_    693 GTATTACTGCAAAGACAGACAAATAGATCAATGCAATC------AGAGTC 736
                            i iviii  i  i     v           v   v------      
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_192622137_    737 CAGAAA---GCC---ACATATATA-CCAATGAGTGGCTTCCAACAATGAG 779
                               ---i  ---    v   i-i    ---  ii  i i    v iv
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAAT---TGATTTTCGACAAGGGT 366

  chr1_192622137_    780 AAAAGGAAAATGGGGTGGAGAAAGAACGGTACTTTCAAAACAAAACAACA 829
                         ivv i  vv  vvii   i       ii  vi      --    ------
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA--CAAA------ 408

  chr1_192622137_    830 ATTAT-TTGGAAAAACTGGATATCTATATGAGAAAAAGAAAAGAAAAGAA 878
                         - vi -i   i v         ? i i   v-------       v-   
  L1M4_orf2#LINE/    409 -TGGTGCTGGGACAACTGGATAKCCACATGC-------AAAAGAAT-GAA 449

  chr1_192622137_    879 A--AGAACTTTAGTTAACAGCTTATAGCATATAAAAATCAACTTGAAATA 926
                         i--i  v ii  vi v   v --   ---  i      i    ii    i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACC--ATA---TACAAAAATTAACTCAAAATG 494

  chr1_192622137_    927 TACCAGAGATATATTTGTAAAACCTAAAATTATTAAACTTCTAAAAAAAA 976
                         v i  ?   iv  vv     i v      i   v     -  v i  i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAA 543

  chr1_192622137_    977 AACATAAGAGAAAATCTT-GTGACATC---TTAGAAAAT--CCTTCTAGA 1020
                               i ? v       -     v i---    iv   --ii ii    
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_192622137_   1021 -ATGAAATGTCAAAA-TATT-TCCCCATAA----AAATTGATAAATTTGA 1063
                         -    v i--     -i iv-v vv  v  ----    v        v  
  L1M4_orf2#LINE/    594 TATGACAC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_192622137_   1064 CTTTATCAGAA-----GGCATATGTTCTTCAAAG-ACATTATTACTAAGA 1107
                            i    i  -----ii v v   v        -   i   i ---   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA---AGA 688

  chr1_192622137_   1108 GAATGAAAAGACAAACCACACA-TGGTTAGATTATATTCACAAAT-A-AT 1154
                         i i           v     v -   v-   vv     ii     - -  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGG-AGAAAATATTTGCAAATCATAT 737

  chr1_192622137_   1155 ATCTAATACATGTCTTGTATTCAGAATATATGAAGAACTCTCA-AATCCC 1203
                             i   viv v       i          i         i -  -- i
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CT 785

  chr1_192622137_   1204 CAACAATTAGATGTTAAATAAATCAATTTTAAAAATTGGGCAAAA-ATTT 1252
                            i   v i v vi      vi     ?-      -       i-    
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTW-AAAAAT-GGGCAAAGGATTT 833

  chr1_192622137_   1253 TAACAGACACTTACTTCAA--------TTTGGATAGCAGTTAAACACATA 1294
                         v  i     i  -  i   -------- viii  i  viv   i     i
  L1M4_orf2#LINE/    834 GAATAGACATTT-CTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_192622137_   1295 AAAATATGTTCAACATCATTAGTCAT 1320
                             v   i         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (117 / 85)
Gap_init rate = 0.05 (39 / 839), avg. gap size = 2.36 (92 / 39)  


3324 26.32 0.55 0.55  chr1_192626030_192630607.rev     3180  4087 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192626030_   3180 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3229
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192626030_   3230 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3279
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192626030_   3280 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 3326
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_192626030_   3327 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 3376
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_192626030_   3377 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 3426
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_192626030_   3427 TTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 3476
                         i        i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_192626030_   3477 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 3524
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_192626030_   3525 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 3574
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_192626030_   3575 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3624
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_192626030_   3625 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 3674
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_192626030_   3675 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3724
                           i ?   ii    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_192626030_   3725 CCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCA 3774
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_192626030_   3775 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3824
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_192626030_   3825 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3874
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_192626030_   3875 CAGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 3924
                         v  i     i   iv            v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_192626030_   3925 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 3974
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_192626030_   3975 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 4024
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_192626030_   4025 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCAT 4074
                            v        i  vi viii     v  i        i i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_192626030_   4075 CATCACTGGCCAT 4087
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3353 23.71 3.03 1.01  chr1_192676482_192680186.rev     2329  3218 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192676482_   2329 TGGAAAGATATTCCATGTTCATTTATTGGAAGAATCAGTATTGTTAAAAT 2378
                                    i          vv         v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192676482_   2379 GTCCATACTACCCTAAGTAATATATAGATTCAATGTAATCCCTATCAAAA 2428
                          v v     v   v  v i  v  i        i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192676482_   2429 CACCAATGGCATTCTTCACCAAAATAGAAAAA--AATCCTAAAATTTATA 2476
                         iv   iiv  v  i  ii vi    v  v  i--i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_192676482_   2477 TGGAACCACAAAAGACTCAGAATAAGCAAAGATATCCTAAGCAAAAGAAG 2526
                              vii   ii   i       iv    ivv   i i --        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chr1_192676482_   2527 AAGA---CTGGAGGAATCACATTACCTGACTTCAAA--TTATTCTACACA 2571
                           v ---i       v     i v  ii i      --   --     v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAA 246

  chr1_192676482_   2572 GTTGTAGTAACCAAAACAACATGGTACTGGCATAAAAACAGACACAGAGG 2621
                          i ii     i   i   iii              ii i     i v  i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_192676482_   2622 CCAATGTAATAGAATAGAGAACCCAGAAACAAATCCTCACACCTACAGTG 2671
                         i     v        v    ii       i   i  vi   ii  ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_192676482_   2672 AACTCATTTTCGATGAGGGTGCCAAGGACATGGATTGGGGAAAAGACAGT 2721
                           i v        ii           iv   vv v        ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_192676482_   2722 CTCTTTAACAAATGGTTCTGGTAAAACTGGATATCCATATGAAGAATAAT 2771
                           i  i          v    v v         ?   i   v i  v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_192676482_   2772 GAAACTAGACCCCTGTCTCTCACCATATACAAAATTCTAGTCAAAATGGA 2821
                            ii i       ii   v              v iv v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_192676482_   2822 ATAAAGGCTTAAGTCTAAGGCCTCAAACTATTAAAATACTGCAAGAAA-C 2870
                         vi ?  i i   i v    iv  v       v   v vi iv      - 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_192676482_   2871 -----------TCTCCAGGACATTGGTCTGGGCAAAAATTTCTTGAGTGA 2909
                         -----------   i iv   v    vi i     vii      iii - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr1_192676482_   2910 T-ACCCCACAAGCATAGGCAACTAACGCAAAAATAGACAAATGGGATCAC 2958
                          -  v   v     i i     v  v v         i    v   iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_192676482_   2959 ATCAAG-TTAAAAAGCTTCTGCACAGCCAAGGAAACAGTCAACAAAGTGA 3007
                              i-       -   i  ii vv v     v  vi    v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_192676482_   3008 AGCAATAACCCACAGAATGGGAGAAAATATTTGCAAACCACCCATCTGAC 3057
                          ivi i                               i  ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_192676482_   3058 AAAGGATTAATA-CCAGAACATACAAGGAGCTCAAACAACTCCCTAGGAA 3106
                           i   i vi  -      i   i  i  i   vv       vv  iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_192676482_   3107 AAAAAATCTAATAATCTGAATT--AAAATGGGCAAAATACTTAAATAGAC 3154
                            i -- v     i i-    --            iv i  i       
  L1M4_orf2#LINE/    795 AAAGA--CAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_192676482_   3155 ACTTTTCAAAAGAAGACATAC---TGGCAGACAGGCATATGAAAAGGTGC 3201
                          i  i  v        i    ---    vi i i   i        i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_192676482_   3202 TCAACGTTGCTGATCAC 3218
                              i ii????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (130 / 79)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.25 (36 / 16)  


2519 27.47 3.03 1.23  chr1_192736939_192738838.rev      542  1433 (467)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192736939_    542 TGGAAAGTCATCTCATGCTTATGAATTAGAAGAAGTAATGATGTTAAAAT 591
                                vi   i    i i   i   i     vv    iv      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192736939_    592 GACCATAAAACCCAAAGTGATCT------TCAATGTAATCCTTATCAAAA 635
                          i v   vvv      v      ------    i i     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192736939_    636 TACCA--TAACATTATT-CACAAATAGAAAAAG-AATTCTAAAATTTGTG 681
                          v   -- iv v  v  -  v    v  v  iv-i  i        ii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_192736939_    682 TGGAATTTTAAAAGACT--GAATATCTAAAGCAATACTGAGTGAAACAAA 729
                              v vi  ii   i--     v i   i    -  ---     --  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT---TGAAA--AA 194

  chr1_192736939_    730 CAAAAAAACAACTGGAAGCATCATACTACATGATTTCAAATTATAATACA 779
                         v  i  v v ii    i vv   i   v vii        viv  v    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_192736939_    780 AATCTAAAGTAATCAAAAAATTTTGGCATTA-TGTTGAAACAGACACATC 828
                           v   v         i v v v   i i i-ii viii i     i  v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_192736939_    829 AACCAATGGAACAGAGTAGAAAACTCAGAAATAAATTCCCATATTCACAA 878
                         i i        i   i v  i iii          ii vi i   i iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_192736939_    879 CCAACTGATTTTT-ACAGAGGCACCAAAAACATACATTGAAGAAAGA-CA 926
                         i   i       i-   ii  ii    i v   v  v  ii      -i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_192736939_    927 CTGACTTCAATAAATGTTGCTGGAAAAACTGGATATCCATATGCAGAAGA 976
                         v vvi     i     v      i v         ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_192736939_    977 ATGAATCTAGACCCCCTTCTCTCACCATATTTTTAAAAA--AGCTTAAAA 1024
                              vi i      ivi   v        vi--     -- i  i    
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATAC--AAAAATTAACTCAAAA 492

  chr1_192736939_   1025 TAGATTAAAAACTTAAATGTAAGAAACAAAACTGTCAGACTACTAAAAGA 1074
                          i   i ? i  i           ivi      i v i   vi  i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_192736939_   1075 AAACAT-GAAAAAAATGCTTCAAGACATTGGTCTAGGCGAAGATTTTATG 1123
                               - i?iv    -    iv   v    vi     i v i   iv i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_192736939_   1124 GGTAAGACTTCAAATGCACAGATAACAAAAGCAAAAACATATA--TGAGA 1171
                          i  v   vi    v     iii        v     i v   -- vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_192736939_   1172 CTATGTCAAA-CTAAACACATTTTTTCACAGTAAAGAAAACAATCAATAC 1220
                           vii     -i    v  --    vii vvi    i v  v     v v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAAC--TTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_192736939_   1221 AGTGAAGAGACAATCTGTTGAATGGGAGAAAATATTTGCAAACTATACAT 1270
                               i      i iiiv                       ii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_192736939_   1271 TGGACAAAATACTAATATTCTAGATAGACAAGGAACTCAAACAACTCAAC 1320
                         iv  i  iiv   vi   i vii   v i  i      vv         i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_192736939_   1321 AGCCAAAAG-CAAATAATCTGATTTTAAAATGGGCAAACGCTGTGAGTAG 1369
                          iiv     -       i ii   ?v            v v v   i   
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_192736939_   1370 ACATTTCTC-AAAAAAATCATACAAATGACCAA---GTAAATTTTAAAAT 1415
                                  -   i  ivi         i    --- i v  vvv  i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_192736939_   1416 -TTTAACATCACTAATCTT 1433
                         -i i       ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.73 (38 / 22)  


2106 27.38 15.46 0.38  chr1_192767960_192769882.rev      644  1432 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192767960_    644 TGGAGAGATACACTGTGTTCATAGATTATAAGATTCAATACTGTTTAGAT 693
                             i     iv ii       i    iv    i i    i    v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192767960_    694 GCCAAAGCTCC------TGAT----AG--TAAGTGTTGTGTTT------- 724
                          v   vi    ------    ----  -- v ii ivi vii -------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192767960_    725 -----GTTTTTGTTTTTG-AAAAATATGGCAAGCTGGTTCTAAAATTTAT 768
                         ----- i viiv      - i    -  i       i i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_192767960_    769 ATAGAGATGTAA-------------------------------------- 780
                           i  i   i  --------------------------------------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_192767960_    781 ----AATTGGAGGACTTATACTATGTGAATTCAACACTTATCATAAAGCT 826
                         ---- i          i i   vivii v     v     ii i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_192767960_    827 ATAGCAATCAAGGCAG----------------------ACAAATAGGTCA 854
                          i  i       i   ----------------------   v    i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_192767960_    855 ATGGAATAGAACAAAGAGTAGAGAAACCAATCCACACGTATATGATCAAC 904
                                    ivi     vv     iv  i   i  i v    i    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_192767960_    905 TGATTTATGGCAAAGTTACAAAGGCAATTTAGTGGAGAAAAGGTAGTCTT 954
                               vi i   i v i v   i v   i i   i    iii       
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_192767960_    955 TTCAACAAATGGAGCTGGAACAATTGCATATTCATATGCAAAAGTATTAC 1004
                                     v     i    i  v   ?i  i         v  v v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_192767960_   1005 TTTTGATCTATTACCAAGTACCAAGAGCAAAAATTAAATAAAAATGGATT 1054
                         v  v  i i-i    vvii    vivi          v v         i
  L1M4_orf2#LINE/    450 GTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_192767960_   1055 GTAGACCTAAATGCAAAACTTAAGGTTATAAAATCTCTAGACAAAAACAT 1104
                         i?           i  i vi   iii       iiii    vi       
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_192767960_   1105 AGGAGAAAATTTTTGTGGTTTTGAGTTAGCCAATGATTTCTTAGATGTGA 1154
                            ? v    i  i   iii   i     v     i          i   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_192767960_   1155 TAATATAACCATGATCTATAAGGTAACAAATTTACAAATTTGACTT-AT- 1202
                         i vi v  v  ii v v i  iiv  v    vv i     v     -  -
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_192767960_   1203 ----TTA---------GT-----------CAGTGTTAAGAGGATGGAAAG 1228
                         ----   ---------  -----------  v i i    iii  i    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_192767960_   1229 AGAGGCTGCAAACCAGGAAAAACTATGTGCAAATTACACATCTGCAAAGG 1278
                          v iv ii  i vii   i   v   v       i i i     vv    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_192767960_   1279 --CTTAAATGTAGAATATTTCACAAAAC-CTCAAAATCCCATAATAATGG 1325
                         --   iv  vi       v v - i   -  i v  ii v       vii
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAA-AGAACTCTTACAACTCAATAATAAAAA 797

  chr1_192767960_   1326 AACACACAATCCACTTTAAAG-TGTGCAAAATATTTGAGTAGACATTTT- 1373
                         i   v i  i   v  ?   i-  v     iv      i         i-
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_192767960_   1374 --AAGGAAGATAAACTGATGGCTAGCAAGAACGGGGAAAGATGCTCAATA 1421
                         --  i       v  vi     i ii   v  iv i            i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_192767960_   1422 TCAGTATTTAT 1432
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.86 (138 / 74)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 6.94 (125 / 18)  


1995 26.39 5.99 5.43  chr1_192817953_192819868      522  1423 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_192817953_    522 GGAAAAACATTCCATGCTCACGGATCAGAATA---AATATAGATAA-ATT 567
                              i i  i     i   i    ii   v ---     v v   -  v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_192817953_    568 GTTCTCATCCCTGAAATGCTCTGT-GATT------AGTTTCT--CAGGAC 608
                          ivv vv    ii  v  v   ii-    ------ i ii  --  ii i
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_192817953_    609 CCAACCTCCCATTGTATGTTCACAAAGGTCAA--AGCCAA----AAGATT 652
                           v v  v  v  -----  ii  i ii ii --   ii ----  i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTT-----TTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_192817953_    653 T---TGAAAAT---AGAG-CCCAGA-TAGCCAAAGCAATCCTAAACAAAA 694
                         i---  i    ---  i -      -        i     i i  v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_192817953_    695 AGAA----GCCAGAGGCATCACATCACCAGACTTCAAACTATACTACAAT 740
                             ---- iii    vv     iiv  vi i      viv        v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_192817953_    741 GCTGCAGTAACCAAGATAACATGGTGCTAGCACAAAAACAAACACATAGA 790
                            i      i     i iii    i  i   i  ii i i   i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_192817953_    791 CCAGTGAAACAGGGTGAAGAACACAAAAATAAAGCCGCATACCCACAGCC 840
                         i  i  i  i  ii vi   iiv  i       v  ii i iii ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_192817953_    841 ATCTGAGGTTTGACAAAGTTGACAAAA-------ATAGG-AAAGAACACC 882
                          vi   vv  i     i v  v   i -------  i  -      i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_192817953_    883 CTATTCAATAAATTGTGCTGGGAAAACTGGTTAACTGTTTGCAGAAGAAT 932
                           v     i    v         v      v  ? iiiv    i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_192817953_    933 GAAACTGGACCCCTATCTATCACCATATACAAAAAAATTAACTCAAGATG 982
                            ii          i  vv               --         i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAATG 494

  chr1_192817953_    983 CATTAAAGTCTTAAATGTAAGACCTCAAATTTTAAAAACTCCTAGAAGAA 1032
                         v  i ?  v i           v  v   i v     -   i        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chr1_192817953_   1033 AACCTAGGAAATACTCTTCTGGACATTGGCCTAGACAAATAAATTATGAC 1082
                            v    ?ivv v     vv   v    vi   i   --------  ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA--------TGGT 585

  chr1_192817953_   1083 TAAGTCCTCAAAAGCAAACACACACACACACACACACACACACACGCGCG 1132
                          ---  i ------- i i ii---    -  v vi    vi  ------
  L1M4_orf2#LINE/    586 T---TCTT-------AGATATG---ACAC-CAAAAGCACAAGCA------ 615

  chr1_192817953_   1133 CGCGCGCACACACACACACATAATTGACAAGTGGGACCTAATTAAA-CTA 1181
                         ---------   v - v v v   v  i  i v    i v  i   -i  
  L1M4_orf2#LINE/    616 ---------ACAAA-AGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_192817953_   1182 GAGATTTTTGCACAGCAAAAGAAACTATCAACAAAC-----AGACAACCT 1226
                         i i i     ii vv    i  v        v   v-----        i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_192817953_   1227 ACGGAATGAGAAAAAAATATTCACAACCTATGCATCCAACAAAGGACTAA 1276
                           i     i  i    -    ii   vii  ii   ii i  i     vi
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_192817953_   1277 TATCCAGAATTTATAAGGG--TCTTAAACAAATCAACAAGAAAAA-ACAA 1323
                                   v     i i--     --   v    i  v     -    
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAAAAGACAA 802

  chr1_192817953_   1324 CTG------TTAAAAAGCAAGCAAACAACACGAACAGAAATGCCTCAAAA 1367
                         v i------  ?    iiii     vi ivi   i   v  vi   v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_192817953_   1368 GAAGACATACAAGCAACCAACAAACATATGCAAAAATGCTCAACATCACG 1417
                              i      iiii    i  i  i   v   i             ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_192817953_   1418 AATCAT 1423
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 2.00 (156 / 78)
Gap_init rate = 0.03 (31 / 907), avg. gap size = 3.32 (103 / 31)  


2282 26.26 5.50 3.59  chr1_192854066_192856469.rev     1023  1913 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192854066_   1023 TGAAAAGATATACTGTATTCATAGAT-AGAAAA---AATATTGTCAAAAT 1068
                           i        v ii i     i   -i   i ---        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192854066_   1069 ATCCATATTACCCAAAGCGATCTACGTATTTAATACAATCTCTATCAAAA 1118
                         iv v   i v      vi       iv   i  ii     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192854066_   1119 TTTAAATTGCGTTTTTCACAGGAATAGAAAAATCAATTCTACAATTTATA 1168
                          iiv ii   v     ii   i   v  v  iiii  i   v    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_192854066_   1169 TGAAGCTACAAAAGCTCCAGAACAGCTGAAGCAATCTTAAGTGAGAGGAA 1218
                           i iv i   ii vi      i   ii  i       i ivi   i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_192854066_   1219 GAAACCTTGGGGGA-TCACATTTTCTGATTTCAAATTATATTGCAAAGC- 1266
                         v   v-    i   -     i  i ii        viv  i i      -
  L1M4_orf2#LINE/    201 CAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_192854066_   1267 --AGAAATTTAATTTAGT-TATTAATAACTTAA---TC--CTTATATTTC 1308
                         --  v   i-  vvi   - iv  v ii v   --- v-- v    vv  
  L1M4_orf2#LINE/    250 ACAGTAATC-AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_192854066_   1309 CAGTAGAATCAAAATAGTGCGATACTGGTGTAAAAACAAGCACATA---- 1354
                         - i i    - i   --  v  -----  vi i   i  i v    ----
  L1M4_orf2#LINE/    299 -AATGGAAT-AGAAT--TGAGA-----GTCCAGAAATAAACCCATACATT 339

  chr1_192854066_   1355 ---GACCAATGGAAG---GGCATAGAGGGCTCAGA--AATAAA--GGTAA 1394
                         --- ii    v  vv--- i  -  i v  iv   -- v v  --  v  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACA-AGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_192854066_   1395 ACGATAGTCTCTTTGATA---GG-GTTGGGAAAACTGGATATTCATATGC 1440
                          vi       i  ii i ---  - i     v         ?i  i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_192854066_   1441 AAAATA-TTAAATTGGATCATTATCTTACACTATACATAAAAATCAACTC 1489
                             v - v  i     i vi  i  i    i   i i      i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_192854066_   1490 AAAATATATTGAAGACTTACACATAATACTTGAAACCATAAAACTCTCAG 1539
                              iv  ii?    i  v ii   v vi i    i          i  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_192854066_   1540 AGAAAAACATTGATA-AAAGCTCTGCAACATTGTTCTAGGCAACAATTTT 1588
                          ii       v i?i-   v  ii ii  v   vvi       iii   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_192854066_   1589 TTGGATATGACACCAAAACTACAGGGAATAAAAGTAAAAATAAACAAGTG 1638
                           i               vi   i v  i     v       i i  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_192854066_   1639 GAACTGCATTAAA-TTAAAAATGTTCTGCACAGTAGAGAAAAC----AAC 1683
                          i   v   i   -       i-  i  ii vvi i  i v  ----  v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_192854066_   1684 AAA-TGAGAAGGCAAATCAGGGAATGGAAGAAAATATTTGCAAG-CATAT 1731
                            -   i   i   vi  vi      i               i-     
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_192854066_   1732 ATCTGACAAGGGGTTATTATAAAAAA---ATAAGGAATTTATACAATTCA 1778
                               i     ii vv   vv i  ---    i   i iv     i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_192854066_   1779 ATAGCAAAGCAAAGCAAAACAAAACAAAACCTAATT-AAAAGTAGGCAAA 1827
                            ii   -------  i     v---    i    -    i i      
  L1M4_orf2#LINE/    788 ATAATAAA-------AAGACAAAT---AACCCAATTWAAAAATGGGCAAA 827

  chr1_192854066_   1828 GGACTTGAATAACCTGAGTGAATATTTTTCCAAAGA---CATACCA-TGG 1873
                            i       i--------- i    i        ---i    v -   
  L1M4_orf2#LINE/    828 GGATTTGAATAG---------ACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_192854066_   1874 CAAATGGATATTTTAAAAGACGCTCAATATCACATATCAT 1913
                          v   iiii iv v      i      i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (157 / 74)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 2.38 (81 / 34)  


3079 23.20 2.15 4.62  chr1_192865661_192868352     1269  2199 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192865661_   1269 TAGAAAGGCATTTTATATTCATGTATTAGAAGAATTGATATTGTAAAAAT 1318
                          i     ii  iii  i      v   i     v  i       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192865661_   1319 GTCTATACAATACAAAGTGATCTACAGATTCAATGCAATCACTATCAAAA 1368
                          v v    vviv    v                i      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192865661_   1369 TTCCAG-TGTCATTTTTTACA-AAATAGAAAGAAACAG-TCTTTTAATGT 1415
                          i    -  i -      i  -    v  v -- i v -  i vv   vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACA--AGCTGATCCTAAAATTC 147

  chr1_192865661_   1416 GAATGGCACCACAAAAGACCCTGAATAGCAAAAACAATCTTGAACAAAAA 1465
                         iv    v vii   ii     v       v              v  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_192865661_   1466 GAACAAAACTGGCAGCATCATACT-CCTTGTTTCAAAGCACATTATAAAG 1514
                                ii   vi vv   i   -  ivi       i vi i  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_192865661_   1515 --AGATTAATTAAAACCTAATAGTACTGGGATAAA-ACAGACACATA-AC 1560
                         -- v v    i  i  vvvi i       v    i- i     i   - i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_192865661_   1561 CAATGAAAAAGGGTAGAAATCCCAGAAATAA-CCCACACATTCATGGTCA 1609
                              i  v  ii v  i vi          -    i     i       
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_192865661_   1610 ACTGATGTTTTACAAAGGTGCCAAGAACACATAATGGGGAACGGATGGTC 1659
                          i    v  iv    i          v  ivi         v i  i   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_192865661_   1660 TCCTCATTAAATG-TGTCGGAAAAACTGGATAACCACATGCAAAAGAGTG 1708
                          ii   vi     -  ii  i v         ?              i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_192865661_   1709 TAATTAGATCCTAATCTCACACCACATACAACATTAAACTCAAAATGGAT 1758
                         v i  i  i  iv i         i      v v v              
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_192865661_   1759 TAAATACTTAAAAGTGGAACCTGAAACCGTGAAACTACTAGAAGAGAACA 1808
                         i ? v  i    v  iii v  i    ii i     vi       i    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_192865661_   1809 TAGGGGAAAAGCTCCATGACATTGGTCTGAACAACAATTTTGTTTTTGTT 1858
                             ? v   v  i i    v    vi iii   iii   i---------
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC--------- 588

  chr1_192865661_   1859 TTGTTTTGTTTTTGGATATGACCATGAAAGTGCAGGCAAAACAAAAACAA 1908
                         -----------  i        ----------------- v     i  v
  L1M4_orf2#LINE/    589 -----------TTAGATATGAC-----------------ACCAAAAGCAC 610

  chr1_192865661_   1909 AAACAAACAAACAAAAAAACCCAGCTACATAGGATGGCATTAAACTAAAA 1958
                           i   -    vi      i--  v  v  v   ivv   i   v v   
  L1M4_orf2#LINE/    611 AAGCAA-CAAAAGAAAAAAT--AGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_192865661_   1959 ATCTTCTGCACAGCAAAGGAAAC----AATAAAGTGAAAAGACAACCCAT 2004
                          v   i  ii vv       v  ----  v                   i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_192865661_   2005 GGATTAGAAGAAAATATTTGCACACCATACATCTGATAAGGGGTCAGTAT 2054
                         i  v i i              v i    i            iiiv    
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_192865661_   2055 TCAAAATATATCAGAAACTC----AACTCAGTAGCAAGAAAACAAATAAG 2100
                         i  i       v ii     ----      i  ii  i  i        v
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_192865661_   2101 TTGACTTTAAAATGGGCAAAGGACCTGAACAGACATTTCTC-AAAGCAGA 2149
                         iii i ?v               ii    i           -    v   
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_192865661_   2150 CATACAAAAGGCCA-TGGGTACGTTAAAAAATGCTCAAAATCACTGATTA 2198
                         i       v     - ii i  i v    i        v    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_192865661_   2199 T 2199
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.62 (131 / 81)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.32 (63 / 19)  


3109 27.31 0.55 0.88  chr1_192888318_192894724.rev     5009  5916 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_192888318_   5009 AAAGAAAATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAATGG 5058
                              v - i     i      i v      v i     ii v  i    
  L1M4_orf2#LINE/      4 AAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_192888318_   5059 CCATATTGCCCCAGGTAATTTATAGATTCATTGCCATCCCCATGAATCTA 5108
                          v   i v   v iv i  i  i       vi  v     i  v  vv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_192888318_   5109 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 5156
                            iivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr1_192888318_   5157 TGGAACCAATAAAAGAG--CTTGCATTGCCAAGACAATCCTAAGCCAAAA 5204
                              ---  iv   i -- iv v  v     i      i i ivv i  
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_192888318_   5205 GAATAAAGCTGGAGGTATCATGCTACTTGACTTCAAACTATACTACAAGG 5254
                            i    i      vv   ii  v iii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_192888318_   5255 CTACAGTAACCAAAACAGCATGGTACTGGAACCAAAACAGAGACATAAAC 5304
                                  i   i    ii         v iv ii i   v i   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_192888318_   5305 CAATGGAACAGAACTGAGCCCTCAGAAATAATACCACACATCTACAACCA 5354
                                 i    i    vvii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_192888318_   5355 TCTGATCTTTGATAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5404
                         vi    i  i  i  ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_192888318_   5405 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5454
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_192888318_   5455 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTTAAGATGGAT 5504
                           ii    i    v   i     v              i i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_192888318_   5505 TAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5554
                         i ?   ii       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_192888318_   5555 TAGGCA-ATACCATTCAGGACATAGGTATGGGCAAGGACTTCATGACTAA 5603
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_192888318_   5604 AACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAA 5653
                         i            vvi      i   vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_192888318_   5654 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5703
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_192888318_   5704 AGGCAACCTACAGAAAGGGAGAAAATTTTTACAATCTACCCATCTGTCAA 5753
                           i     i      v          v   i   vii ivi     vi  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_192888318_   5754 AGGGCTGATATCCAGAATCCACAAATAACTTAAACAAATTTACAAGAAAA 5803
                         i  i  vi          vi i   v    ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_192888318_   5804 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5853
                          i -    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_192888318_   5854 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5903
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_192888318_   5904 CATCACTGGCCAT 5916
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (9 / 905), avg. gap size = 1.44 (13 / 9)  


3248 27.20 0.44 0.44  chr1_192920410_192926689.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_192920410_   4882 TGGAAGAGCATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              iiii  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_192920410_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192920410_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_192920410_   5030 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_192920410_   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_192920410_   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_192920410_   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5227
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_192920410_   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_192920410_   5278 CTATTTAATAAATGGTGATGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i        v     v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_192920410_   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_192920410_   5378 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_192920410_   5428 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_192920410_   5478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5527
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_192920410_   5528 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_192920410_   5578 AGGCAACCTACAACACGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5627
                           i     i   iv i          v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_192920410_   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_192920410_   5678 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_192920410_   5728 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5777
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_192920410_   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2740 24.00 2.80 5.27  chr1_192947215_192952170     3535  4463 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_192947215_   3535 GAATGATATTTCATATTCACAGATATTTCATGTTCACATATTGTTAAAAT 3584
                            v     ii   i    ii   - vvv vii i -          i  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGAT-TGGAAGACTTA-ATATTGTTAAGAT 50

  chr1_192947215_   3585 GCCCATACTATCCAAAACAATCTACAGATTCAATGTAATCCCTATCAAAA 3634
                          v v     vi     vii              i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_192947215_   3635 TACCAATGATATTCTTCACACAAATAAAAAAAAAAGC--ATTCTAAAATT 3682
                          v   iiviiv  i  ii  v    vi v  ----  --  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA----GCTGATCCTAAAATT 146

  chr1_192947215_   3683 TATATGGTACCACAAAG-ACCCAGTATAGCTA------CCCTGAGCAAAA 3725
                         i      v vii   i -      v     i ------i i   i-   i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAG 195

  chr1_192947215_   3726 AAGAACAAAACTGGCAGAATCACATTACCTGACTTCATATTATACTACGG 3775
                                  ii   vi  v     i v  ii i    v viv      ii
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_192947215_   3776 AGCTAAAGTAACTAAAGCAGCATGGTACTGGCATAAAAACACAGCATGAA 3825
                              v     ii  ii   ii              --------------
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA-------------- 281

  chr1_192947215_   3826 ACATGGTACTGGCATGGTACAGCATGGTACAGACACACAGACCAATGGAA 3875
                         -------------------------  - i     i i   i        
  L1M4_orf2#LINE/    282 -------------------------GG-ATAGACATATAGATCAATGGAA 305

  chr1_192947215_   3876 CAGATTAGAGAACCCAGAAACAAAACCAGATATCAACAGTGAATTCATTT 3925
                         i   v v    ii       i   v   v i  iv ii  v    v    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_192947215_   3926 TCCACAAAGGTGCCAAGAACATACATTGGGGAAAGGA-A----TTTCAAT 3970
                           v    i          v   v  v         i - ----      i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_192947215_   3971 AAATGATTCTAGGAAAACTGGATATCTATATGTGGAAGAATGAAGCTAGA 4020
                              i v  i   v         ? i i   iii          i i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_192947215_   4021 CCATTACCTCTCACCATTTACAAAAAT-AAATCAAAAT---TCA-AGAGT 4065
                           vi      v      v         -  v       ---   -   vi
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_192947215_   4066 TAAATTTAAGA-CTACTAACTATGAAAGTACTAAGAGAAAACATTGGGAA 4114
                              v     -   v-      i   v vi  ii         v  ?iv
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAA-AACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr1_192947215_   4115 AACTCTTCAGGACATTGGACTGGGTAATGATTTTTTA-ATA---CCCCAG 4160
                           v     iv   v    ii i  i    i   i   -   --- v   i
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_192947215_   4161 AAGCACAGACAACCAATGCAAAAATTGACAAATGGGATCACATCAAG-TT 4209
                                ii    v  v v      v  i    v   iiv      i-  
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_192947215_   4210 AAAAAGCTTATTCACAGCAAAGGAAACAAACAACAAAGTGAAGTTACAAC 4259
                              -   v vii vv       v  v v   v        ivv     
  L1M4_orf2#LINE/    655 AAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_192947215_   4260 CCACAATATGGGAGAAACTATCTGCAAACTGTGTATCTGACAAGTGATTA 4309
                              iv          v   i      iii i       i   v  i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_192947215_   4310 ATAACCAGAATGTGTAAGGAGCTCAAACAACTTTATGTGAAATAATCTAG 4359
                         i  v       i i   i  i   vv      iv  ivv   v iv v i
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_192947215_   4360 TA-TTCAATTTAAAAATGGGCAAAAGAGATGAATAAACATTGGTGAAAAG 4408
                           -ii     ?             i  vv      i     vv vv    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_192947215_   4409 AAGACATATCAATGAAAAACAGGTATATGTAAAGTTCCTCAATGTCACTG 4458
                             i   iv    ivv  i i i i   v    v v     ii   ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_192947215_   4459 ATCAT 4463
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.34 (126 / 94)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 3.57 (75 / 21)  


2703 24.18 0.62 8.74  chr1_192992525_192995400     1412  2383 (493)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr1_192992525_   1412 TGGTCATAAACTGGAAGAAACAATATTGTTAAAATATCCATACTATTCAA 1461
                           v    ii i       vvi           i  iv v     vii   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_192992525_   1462 AGTGATCTTCAGATTTACTGCAATCCTGATTGAAATATCAA-TGTCATTT 1510
                          v      v      i vi       iv  ii    vi  i-  i -   
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTT 114

  chr1_192992525_   1511 TTCACAGAATTTTGATAAAACAGTCCTAAAATTTGTATAGAATCACAAAA 1560
                           ii     v  -  i  iviii          ii   i   vii   ii
  L1M4_orf2#LINE/    115 TTTGCAGAAATT-GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_192992525_   1561 GACCTCAAACAGCCAAAGCAATCTTAAGAGAAAAAAACAAAACAAAACAA 1610
                             ivi  i       i       i -----------------------
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGA----------------------- 190

  chr1_192992525_   1611 AACAAAAGAAAAAACAAATCTGGAGACATCACAGTATCTGACTTCAAAAT 1660
                         ---       i  -    vi     ivv     v vi ii i       i
  L1M4_orf2#LINE/    191 ---AAAAGAAGAA-CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_192992525_   1661 CTATTACAAAGCTATAGTAATCTAGATAGAATGGTACTGGCATAAAAGCA 1710
                         i  i          i       v   i  vi              iiii 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_192992525_   1711 GACAGGAAGATTGACCAATAGAACAGGATAAAGAGCCCAGCAATAAACCC 1760
                             viv    ----    i   i  i  vi    i    v         
  L1M4_orf2#LINE/    287 GACATATAGAT----CAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_192992525_   1761 ATGAATTAATGGCCTATTGATTTTTTTAACAAAGGTGCCAGG-CCACACC 1809
                           iv   v    i v         i--i    i       i -   iv v
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTC--GACAAGGGTGCCAAGACCATTCA 380

  chr1_192992525_   1810 ATGGAGAAAAGATCATCTCTTCACTAAACTGTGCTGGGAAAACTGGATAT 1859
                             i    ii  vi   i    vi   iv         v         ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_192992525_   1860 CTGCAAGCAAAGGCATGAAATTGGACCT-TATCTCATGCTATATGCAAAA 1908
                          ii  v     i v     i       i-  i    ii i    i     
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_192992525_   1909 ATTTGGACCTTATCTCATGCTATATGCAAAAATCAACTCAAAGACTTAAA 1958
                            -------- v    ------------    vi -   ?    i    
  L1M4_orf2#LINE/    481 ATT--------AACTCA------------AAATGGA-TCAWAGACCTAAA 509

  chr1_192992525_   1959 TGTAAG-GCCAGAAATTGTCAAACTATTAGAAGAAAACATAAAGG-AAGT 2006
                               -  i -   i i v     v               ii? -  i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_192992525_   2007 ATTCCACAACATTGCTCTGGGCAATAATTTATTGTCTAGGAACCCAAAAG 2056
                         v   -iii  v   vvi i      ii   v  ivv  v  vv       
  L1M4_orf2#LINE/    559 CTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_192992525_   2057 CACAAGCAACAAGAACATAAACAAACAAATGGGATTATAACAAACTAAAA 2106
                                     i iv v   i i i    v   i vi v    v v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_192992525_   2107 GGCTTCTGCACAGTCAAAAAAAAAAAAAACAAAAAAACAAAAAACAAAAC 2156
                         ii   i  ii -- i----------------------    ii   --- 
  L1M4_orf2#LINE/    658 AACTTTTGTGC--TT----------------------CAAAGGACA---C 680

  chr1_192992525_   2157 AATTAATGGAACGAACAGACATCCTATAGATTAGGAGAAAATATTGGCAA 2206
                         v  i  vii ii   v     v  i i   v i            v    
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_192992525_   2207 ATAATACATTTGATAGGGGGCTCATATCCAAAATATATAAGGA-CTCAAA 2255
                           v   i  i     i   i  ii      i         i  -   vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_192992525_   2256 CAACTCAACAGCAATAAAACACATAACTGAGTCACAAAAAAGACAATGGA 2305
                                 i ii  v  i   v     iv i i?v    vi i   v   
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_192992525_   2306 CCTACAGAAACACCTCTCAAAAGAACATATATAACCGGCCAACACGTATA 2355
                         ii iv v i   ii    v      v     i  vi      i v i i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_192992525_   2356 GGAAAAGCTGATCAACATCACTGATCAT 2383
                         v      v  v         ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (149 / 82)
Gap_init rate = 0.02 (20 / 893), avg. gap size = 4.55 (91 / 20)  


2051 27.64 4.47 2.29  chr1_193087951_193090248.rev      936  1807 (491)    L1M4_orf2#LINE/L1       18   908 (0)  

  chr1_193087951_    936 TTCAAGGGTTAAAAGATTCAATATT-TTAACATGTTAATTATATCCAAAT 984
                             v  i  ii    i i      -    v   vi   vv vi      
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr1_193087951_    985 TAACCTACAGATTCAATACG-TTTCAACTGAAATTATAGCTGTCACTTT- 1032
                          i i            ii i- ii v iii    ivi     i vi   -
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr1_193087951_   1033 G-AAATATTAATAATCTTATTTTAAA--TAATATAAAAATGTAAAG---- 1075
                          - i v   i i  v  v  ii    -- v    ii     i  i ----
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr1_193087951_   1076 -ATAATAGTCATAACAACTATGAAAAAGAAGATTCATGTCAGAATATCCG 1124
                         - v     i  v     iiv            viv v  ii  iv ii i
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr1_193087951_   1125 TAGTACCTCTGTTGTGAAGCTTTACTGTAATACTAAAGTATTAAAGACAG 1174
                         i v v  - vi  vii  i   -   ii  vi   v    v v       
  L1M4_orf2#LINE/    218 CACTTCC-CAATTTCAAAACTT-ACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_193087951_   1175 CATGAAATTATCATAATGATAGACAAATAGATCAATGGAACAGAAT--AC 1222
                         ii  iv i iv     v        v              i     -- v
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_193087951_   1223 AACCCAGAAGTAGATC-A-ACTTGTAT---------ATTTTCATCAACGA 1261
                          ii      i  i i - -  v v   ---------      iv   v i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_193087951_   1262 TGCCAAGTTAATTACCTTGGAGAGGCAATAATCTT--CAACAGATAGTTC 1309
                                viv   - vv   i  iiv    i    --     i  i  v 
  L1M4_orf2#LINE/    366 TGCCAAGACCATT-CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_193087951_   1310 AGGATCAACTTTATATCCTTCTGGAAAA-AATGTATATCTTGAGCCTTAC 1358
                         v  iv     vv   ?  viv  v    -    v -i - v  v  i   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAA-GT-TGGACCCCTAC 462

  chr1_193087951_   1359 CTCACACCACACAGTGAATATTAACTTGAAATAAATTATACTCTTAAATG 1408
                                  i i -ii  v       ii    ii  i ? vv i      
  L1M4_orf2#LINE/    463 CTCACACCATATA-CAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_193087951_   1409 TAAAAAGTGAGACTACAACATATCTAAAATAAAACATAGAGGAATGTTTT 1458
                            i iv i i    i  v ivii  i  v         i? v vi i  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_193087951_   1459 CACAGACTTGAGT--AGCAAATATTTCTTAGCTGAGACACACGAAAACCA 1506
                          iiiiv    i  --i    vvi        v iv     - -    v  
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC-C-AAAAGCA 609

  chr1_193087951_   1507 CAAACCATAAGAGAAAAAAAAAAAAAAGAAAAATTGGCTTTCATCAAAAT 1556
                            i v i  ------  i      v   v       vi           
  L1M4_orf2#LINE/    610 CAAGCAACAA------AAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_193087951_   1557 TAAAC-CTTCCACTCTTCACTAGACAATTTCAAAGAA-TG----GCGAAC 1600
                             v-   iiiiv     vvi    v v    ii  -  ---- vv   
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_193087951_   1601 CC-CAGACTGGAATGAAAATATTCACAATGAATATATCTGATTAAAG-TT 1648
                           -    v   i -         ii   vvv           v ii -i 
  L1M4_orf2#LINE/    704 CCACAGAATGGGA-GAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_193087951_   1649 TGAATCCAAACGTATATAAAGAACTCCTACAATTCAATTTTAAGAGTCCA 1698
                           v     i -i              i     i     vv   i ivv  
  L1M4_orf2#LINE/    753 TGTATCCAGA-ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_193087951_   1699 AACAAACCAAT--AAAAATAGGTAGAAGAATCGAACGGATATTTTATACA 1746
                           i  v     --      i  i i i  v i   ii  i    i- v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC-TCCA 850

  chr1_193087951_   1747 CACACAAGGATATACCAATGACCATTAAGCATATGAAAAGATTGTCAATA 1796
                         v ---i i       v    i   v      i          vv    i 
  L1M4_orf2#LINE/    851 AA---GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_193087951_   1797 TCACTAATCAT 1807
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.04 (32 / 891), avg. gap size = 1.84 (59 / 32)  


3119 25.72 1.44 0.78  chr1_193253304_193257696     2999  3900 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_193253304_   2999 TGAAAAAATTTTCCATGTTCACAGGTTGGAAGAATCAATATTGTTAAAAT 3048
                           i   i  v i         ii i        v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_193253304_   3049 GTCCATACGACCCAAAGCAATCTACTTATTCAATGCCATCCCAATTAAAA 3098
                          v v    vv      vii      vv      i  v     v  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_193253304_   3099 TACCAATGACATTCTTCACAGAAATAAAAAAAT--ATA-TAAAATTTATA 3145
                          v   iivi v  i  ii       vi v  ii--  v-       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_193253304_   3146 TGGAATCACAAAACACCCAGA-TAGCAAAGGTTATCCTAAGCAAAAATAA 3194
                              vii   iiv       -    v  iiiv   i i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_193253304_   3195 CAAACCTGAAAGAATCACATGACCTGATT-CAAATTATACTGCAAAGCTG 3243
                             vi  i i  v     ivv  ii   -    viv    i       i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_193253304_   3244 TAGTAACCAAAACAGCATGGTAGGTACTGGCATAAAAACAGACACACAGA 3293
                         i     i   i    ii     ----         ii i     i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTA----CTGGCATAAGGATAGACATATAGA 296

  chr1_193253304_   3294 CCAATGGAAAACAATAAAGAACCCAAAAACAAATCCACATCCCTATGGTG 3343
                         i        v v   vi   ii   i   i   i   i ivii      v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_193253304_   3344 ATCTCATTTTTGACAAATGTGTCAAAACTATTCATTGGGGAAAGGACAGT 3393
                          vi v     i     iv   i   i  i     v         i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_193253304_   3394 CTCTTCTATAAATAGTGCTGGGAAAACTGGATATCCATATGCACAATATT 3443
                           i   v i    i         v         ?   i     v  v v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_193253304_   3444 GAAATTTGACCCCTATATCTCACCTTATACAAAAATCAAATCAAAATGAA 3493
                            i  v        iv  v    v           i  v        i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_193253304_   3494 TTAAAGACTTAAATCTAAGACCTCAAGCTGTGAAACTACTACAAGAAAAC 3543
                          i ?    i     v     v  v  i  i i     vi  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_193253304_   3544 ACTGGGGAAACTCTCCAGAACATTGATCTGGGCAAAAATTTCTTGAGTAA 3593
                          iv  ? v  v   i ivi  v   ivi i     vii      iii  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA- 595

  chr1_193253304_   3594 TAAC-CCACAAGCACAGGCAACCAA-GCAAAAAC-GACAAATAAGATCAC 3640
                          i  -   v       i     v  - v     i-  i    vi  iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_193253304_   3641 ATCAAG-TTAAAAACCTTCTGCTCTGCAAAAGAAGCAGTCAACAAAGTGA 3689
                              i-        i  -  iv  v    i  vi vi    v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_193253304_   3690 AGACACAACACACAGAATGGGAGAAAGTATTTCCAAAT-ACCCATTTCAC 3738
                          i v     v                i     v     - ivi  i v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_193253304_   3739 AAGAGATTAATAACCAAAATATA--AAGAGGTCAAACAACTCTATAGGAA 3786
                            i  i vi  v   i      --    iv  vv       v   iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_193253304_   3787 AACCATCTAATAATTCAATT-AAAATTGGGTGAAAGATTTGAATACACGT 3835
                           vv - v     ii     -    v    ii  i          v  i 
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_193253304_   3836 TTTTCAAAAGAAAACATACGAATGGCAAACAGGTATATGAGAAGGAACTC 3885
                           i  v      i i    i      v  i i i i    i   ivi   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_193253304_   3886 AACATCATTGATCAT 3900
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (139 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.33 (20 / 15)  


2564 24.20 8.62 1.65  chr1_193263759_193266491     1394  2240 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_193263759_   1394 GAAAAATATTGCATGTTCATGGAATATAATAATTAATATTGCTAAAATGT 1443
                             i    iv            v iv  v v         i   i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_193263759_   1444 CCACACTACCCAG--TGATCTACAGATTCATTGATATCCATATTAAAATT 1491
                          v i   v    i--               vi vv    v   i     i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_193263759_   1492 CTAATGACATTATTCACAGAAATGGAAAAATCAATTCCAAAATTTGAATG 1541
                          i iivi v  v  ii       v  v  iiii  i i      iiv   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_193263759_   1542 AAGCCACAAAAGACCACAAAA-AGTCAACTCAATCTTCAGCAAAAAGAAA 1590
                         i ivii   ii    -  i  -  i   vv       -- -        i
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTT--G-AAAAAGAAG 198

  chr1_193263759_   1591 AA--AAGTCAAAGGAACCACACTATCTGGCTTCAAA-TATACCACAAAGC 1637
                           --    iii    vi      vi iiii      -iv   i       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_193263759_   1638 TATAGTAATCAAAACAGCATAGTACTGGTATAAAAACAGATACAAAGATC 1687
                           i         i    ii i       i    ii i   i i v     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_193263759_   1688 AATGGAACAGAATAGACAGCCTAGAAATAAATAGATACTTTAAAAGTCAA 1737
                                i     v  v  i i         ivv    v  v vi     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_193263759_   1738 TTGATTTTCAGCAAAGAAGACAAGGACACACAATGGAGAAAGGACAATCT 1787
                                  ii   i iv v    iv  iv      i     i i i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_193263759_   1788 CTTCAATAAATGGTGTTGGGACAACT-----------TGCAGAACAGTGA 1826
                         i     i        i          -----------    i  v i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_193263759_   1827 A-TTGAATTCTTA----------TACACAAAATTCAACACAGA-TTAACT 1864
                          -   i ii i  ----------  i      v i   v  i - vi ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_193263759_   1865 AAAGACCTAAATACA-GACCTGAAACTGTAAAAGTAATAGATGAAAACAT 1913
                          ?          ii -  v  i     i     v vv    v        
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_193263759_   1914 AGGAGAAAAGCTCCATGGCCTTTGTTTGGGCAATAATTTTTTGGATATCA 1963
                            ? v   v  i i  i    v v  i      ii   i  i     v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_193263759_   1964 CCCCTTATGCATAGGCAACAAAACCAAAAAATAATCAAATAGGGTTACAT 2013
                          v  vv v   i i         v-        ivi    v  ii v   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCAT 647

  chr1_193263759_   2014 --------AAAAC-------ATCCCAGGAAAACAATCAACAGAGTGAAAG 2048
                         --------     -------v i v i i v  v     v i       -
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA- 696

  chr1_193263759_   2049 TAAAAGACAATCTACAGAATAGGAGAAAATATTTGCAAACCATATATCTG 2098
                         ----      i i       i                  i          
  L1M4_orf2#LINE/    697 ----AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_193263759_   2099 ATAAAGGATTAACATACAAAATAAATAGAAAAAAAA-----ACAAATCAA 2143
                             i   i vii  v  i    v   ----  i  -----    v    
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATA----AAGAACTCTTACAACTCAA 788

  chr1_193263759_   2144 TAGCAAAAAAAAAAAG----CAATTTACAAATGGG--------------- 2174
                           ii     i v   v----     ? v       ---------------
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_193263759_   2175 ----TTTCTCAAAGAAAAACATATAAATGGCCAATAGATATATGAAAAAA 2220
                         ----      v  ii  i i   i            iii i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_193263759_   2221 TCCTCAACATCACTAATCAT 2240
                          v          ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (130 / 72)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 4.35 (87 / 20)  


2935 24.51 2.98 1.43  chr1_193345544_193347291      485  1255 (493)    L1M4_orf2#LINE/L1      126   908 (0)  

  chr1_193345544_    485 TGACAAGC----CCAGAGTAATTCATATGGAAACACAAAAGTTCCCAAAT 530
                                 ----  vi --              ii   ii vi  vi   
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAA--AATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chr1_193345544_    531 AATCAAAACAATTTTGAATAGAAAAAATAAAGGTGGAGGCATCATACTCC 580
                          ii         i     v ii  i  i    v      vv   i   i 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr1_193345544_    581 TTGATTTCAAAATTTATTATAAAACTATTGTAATCAAAACAACATGGTGC 630
                         iii         i   i  i   i   iv        i   iii    i 
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_193345544_    631 TGGCATAGAAACAAACATATTTATCAACGAAACAAGATAGAAAGCCCAGA 680
                                iii i i      vv     i i  i ii  v  i  i     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_193345544_    681 AATAAACCCATGCATTTACGGCCAATTGATTTTCAATAAAGGTGCCAAGA 730
                                    i      i  i            i i  i          
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_193345544_    731 ACACACAATGAAGAAAGGACAGACTCATCAACAAATTGTATTGGGAAAAT 780
                         v  iv     ii     i i  v  iv         v  ii     v  i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_193345544_    781 TGGGTATCTGTATGCAGAAGGATTAAATTGGATCTTTATCTTACACTAGA 830
                            i  ? iii     i   i  v  i     i ii  i  i    i v 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_193345544_    831 TACAAAAATCAACTCAAAATGGATTAAAGAC--AAA-----------AAA 867
                                  i              i ?    --   -----------   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_193345544_    868 CTGTAAAATTACTAGAAGAAA---TGAGTTAAAATCTCCACAATATTGCA 914
                           i     i vi         --- ii ?vv      i iii iv   vi
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_193345544_    915 ATTTATTTTTATTTTTATTTTTTTAG---TGTCTCTGAAAGCACAGGCAA 961
                         --   -----ivivv iv   i    ---  v v ii        i    
  L1M4_orf2#LINE/    574 --TTA-----GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_193345544_    962 CAAAAGTGAAAATAGACAAATGGGATTTCATCAAACTAAAGAGCTTCTGT 1011
                               vi        i    v   i         v v  i i   i   
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_193345544_   1012 ACAGCTATGGAAACAAATAACAGAATGAAGAGAAAGCCTATGGAATGGGA 1061
                         i vv v v   v  v vi  v i i    i   v i  i ii        
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_193345544_   1062 GAAAACATTTGTAAACCATACACTTGATAAGGAGTTAATGTCCAAAATAT 1111
                              i     i   i    i ii        iii vi i    i     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_193345544_   1112 ATAAGGAACTCTAAACAACTCAATAGCAAGAAAACAAATAACATAATTTA 1161
                             i       v -          ii  i  i         vi    ? 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTA-CAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_193345544_   1162 AAAATGGGCAAAGGAACTGATCAGACATTTCTCAAAAGAAAACATACAAA 1211
                                        vi   vi           v      i i       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_193345544_   1212 TAACTAGCAGGTTCATGAAAAAAATACTCAACATCAATAACTAT 1255
                          ii i ii i iv        i - i          ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.70 (135 / 50)
Gap_init rate = 0.01 (10 / 783), avg. gap size = 3.40 (34 / 10)  


2569 24.13 6.96 1.80  chr1_193455114_193457119      672  1504 (502)    L1M4_orf2#LINE/L1        3   878 (30)  

  chr1_193455114_    672 GAAAAATAGCCCATGTTCAGGGACTGCAAGATTTAATATGGATAAAATGT 721
                             i   v          v   i  v    i       v v   i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_193455114_    722 TCATATTACACAAAAAGATGTAAGGATTCAATGCAGTCCCCATCAAAATT 771
                         iv   i v v    vv   v  vi       i   i    i        i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_193455114_    772 CTAA-TGTCATTTTTCACAGAAAAATGAAAAACAG-TTCAAAAATATGTA 819
                          i i-  i -     ii      v-   v  i v - i v     vii  
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATA 150

  chr1_193455114_    820 TG-AAATGACAAGAGATCCCGAA-GGTCAAAGTAATTTTGATTAAAAAGA 867
                           -     -    i  i  v   -i i    ii   i    vv  i    
  L1M4_orf2#LINE/    151 TGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_193455114_    868 ACAAAGCTGGAGGCATTACACTTCTAAATTTTGAA--TTATGATATAATG 915
                               i      vv i       iv     ii  --   i--  i  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAG 247

  chr1_193455114_    916 CTATTATAGGCACGATAGCATGACATTGGCATAAAACAAGACAC------ 959
                            ivi  iv  v  i  ii  ii i        iivv     i------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_193455114_    960 CAATAAAACAGAAT--AGAATTCA-----------ATATATTT----TCA 992
                             ii  i     --   i i  -----------   i    ----   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_193455114_    993 AT-----------AAAGATGACAAGA--ACTCACATAGGGAAAATAATAG 1029
                           -----------  i i  v     -- i   -  i      i-     
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAG-AATAG 395

  chr1_193455114_   1030 TCTCTTCAATACATCTTGCTGGGAAAATCGGATATTCACACATAGAAGAA 1079
                            i     i v  vv        v  ii     ?i    iii i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_193455114_   1080 TGTAATTGATCCACTGTTTCACACTACATA---AAACTA-CTCAGAATAT 1125
                           v i   iv  v  iii      i i   ---   i  -    i   iv
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_193455114_   1126 ATGTAAGACTGACATGTAA-AGCTTGAAACTATAAAACTGCTAGAGGAAA 1174
                           vv?    iv v      -    -i             vi    i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAA 544

  chr1_193455114_   1175 ATAAAAGAGAAAAAAATACATGACATTGGTCTGGGCTATGATTTCTTGGA 1224
                          i v i ? v   vvv - i    v    vi i   v   i      i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_193455114_   1225 T-TGGTTCCCCAAGCATAGGCAACAAAAGGAAAAATACACACATTGTATT 1273
                          -  iiv  vv     i i          i       v i v    v i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_193455114_   1274 ACATCAAACTAAAAAGCTTCTGCACAGCAAAGTAAACAATGCCCAGA--G 1321
                         v       v v    i   i  ii vv     --i   v ii v   -- 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAG--GACACTATCAAGAAAG 691

  chr1_193455114_   1322 TGAAGAGACAACTCAT-GAGTTGGA-AAAATATTTGCAAGCCATATATCT 1369
                             i       i  i-  i v   -             ii         
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_193455114_   1370 GATAAAGCGTTAATATTCAAAATATATAAGGAACTC----AACTCAATGG 1415
                              i vii vi   i  i         i      ----        --
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-- 789

  chr1_193455114_   1416 CTAATAAAAAGG-AATTAACC-AATTTAAAAATAGGCAATGTACCTGAAT 1463
                         --         i-  v     -    ?      i     v v ii     
  L1M4_orf2#LINE/    790 --AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_193455114_   1464 GGACATTTCTCAAAAGAAGACGTACCAATGGCCAACAAGTA 1504
                         i          v        ii   v         i   i 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

Transitions / transversions = 1.70 (124 / 73)
Gap_init rate = 0.04 (31 / 876), avg. gap size = 2.35 (73 / 31)  


2956 25.67 2.23 1.23  chr1_193459261_193462756.rev     2112  3007 (489)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_193459261_   2112 AAAGATATTTCATGATCATGGACTGGAAGGATCAATATTGTTATAATGTC 2161
                                 ii    v       i      iv i          vi   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_193459261_   2162 CATACTACCCAAGGCAATCTACAGATTCAA-GAAATCACTATGAAAATAC 2210
                         v     v     ivii              - v    v    v     v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_193459261_   2211 CAGGGACATTCTTCACAGTAATAGAGAAAAACAATCCTAAAATTTTTATG 2260
                            vvi v  i  ii   v   v  v  iv-ii           iv    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATG 152

  chr1_193459261_   2261 GTACCACAAAAGCTAAAGGTACCCAAAATAGCTAAAGCTATCCTAAGCAA 2310
                          ------   v  --    v     i      i   i v   i i iv  
  L1M4_orf2#LINE/    153 G------AAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_193459261_   2311 TAAAAACAAAACTGAAGGAATAACATTACCTGACTTCAAATTATACTACA 2360
                         v  i      ii  i    v v   i v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_193459261_   2361 GAGTTGTAGTAACTAAAACAGCATAGTACTGGCATAAAAACAGACATACA 2410
                         i  i ii     ii  i    ii i            ii i       i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_193459261_   2411 GTCTAATGGAACAGAATAGAGAACACAGAAACAAATTTACACATCTACAG 2460
                          vii       i     v    iiv      i   iii i    i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_193459261_   2461 TGAATGCATTTTTGACAAAGG------GAC-GTT----GTGGAAAAGACA 2499
                          v   vv     i     i  ------   -i  ---- v     ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_193459261_   2500 GTCTCTTCAATTAACGGTTCTAGGAAAACTGGATTTTCATATGCAGAAGA 2549
                             i     iv  i   v  i   v        v?i  i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_193459261_   2550 ATGAAACTAGACCTCTATGTTTCACCATATCCAAAAATCAAATCAAA-TG 2598
                              ii i    i   iv iv        v       i  v     -  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_193459261_   2599 GAT-AAAGACTTAAGTCTAAGACCTCAAACTATGAAACTTCTACCAGAAA 2647
                            - ?    i   i v     v  v       i     ii  vv     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_193459261_   2648 ACATTGGGGAAAATCTCAAGGACTTTGTTCTGGGCAAAAATTTCTTCAGC 2697
                             v  ? v      iviv   i   vvi i     vii      -  v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGA 593

  chr1_193459261_   2698 AATAAC-TCACAAGCACAGGCAAGCAAAGCAGAAATGGACAAATGAGATC 2746
                         v  i  -i  v       i    vv    v i    i  i    vi  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_193459261_   2747 ACATCAAG-TTAAAAATGTTCTGCACAGCAAAGGACACAATGAACAAAGT 2795
                         v      i-       i-  i  ii vv          v  v  v     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_193459261_   2796 GAAGAAATAAC--ACTGAGTGGGACAAAATATT-GCAAACTACCCATCTG 2842
                            i i i   --  v  i     v        -     ii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_193459261_   2843 ACAAGGGATTAATAACCAGAATAATTAAAGAGCTCAAACAACTCTATCAG 2892
                          i      i vi  v        vv      i   vv       v  v v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_193459261_   2893 AAATCATCTAATAATCAGATCAAAAAA-GGGCAAAAGATCTGAATATAGA 2941
                            vviv v     i vi  i?     -       i   i      v v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_193459261_   2942 TTTCTTAAAAGGATACATTCAAATGGAAAACAGACATGTGAAAAGATGAT 2991
                              iv    i v i  v       vv  i ii  ii          v 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_193459261_   2992 CAACATAACTGATCAT 3007
                               v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (131 / 95)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 1.94 (31 / 16)  


3102 28.52 0.22 0.22  chr1_193481840_193488242.rev     5005  5912 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_193481840_   5005 TGGAAGAACATTCCATGCTCATGGGTAGGAGGAATCAATATCATGAAAAT 5054
                              ii i  i     i      i v   i  v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_193481840_   5055 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5104
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_193481840_   5105 TACCAATGACTTTCTTCACCAAAGTGGAAAAAAGTACTTTAAAGTTCATA 5154
                          v   iivi i  i  ii vi  i v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_193481840_   5155 TGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGAA 5204
                              viiv  ii  v  v v  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_193481840_   5205 CAAAGCTGGAGGCATCACACTACGTGACTTCAAACTATACTACAAGGCTA 5254
                              i      vv       v vii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_193481840_   5255 CAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGAGATATAGATCAA 5304
                               i   i    ii        vi iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_193481840_   5305 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACTAT 5352
                              i    i--    i  --        vv iii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_193481840_   5353 CTGATCTTTGACAAACCTGAGAAAAACAAGTAATGGGGAAAGGATTCCCT 5402
                         i    i  i     ivv  vv  i v  vvi           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_193481840_   5403 ATTTAATAAATGTTGCTGGGAAAACAGGCTAGCCATATGTAGAAAGCTGA 5452
                         v  i  i     v        v   v  v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_193481840_   5453 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5502
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_193481840_   5503 AAAGACTTAAATGATAGACCTAACACCATAAAAACCCTAAAAGAAAACCT 5552
                          ?    i      vv   v    v  i      vi i  i        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_193481840_   5553 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5602
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_193481840_   5603 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5652
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_193481840_   5653 AAACTAAAGAGCTTCCGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5702
                            v v  i i   ii ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_193481840_   5703 GCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAG 5752
                         i     i   i             v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_193481840_   5753 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5802
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_193481840_   5803 ACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGATGCTTCTC 5852
                              i     v  i?    i           iv    i   iii     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_193481840_   5853 AAAAGAAGACATTTACGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5902
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_193481840_   5903 CACTGGCCAT 5912
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.41 (149 / 106)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


2582 24.02 6.70 2.08  chr1_193539796_193541802      673  1538 (469)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_193539796_    673 GAAAAATAGCCCATGTTCAGGGACTGCAAGATTTAATATGGGTAAAATGT 722
                             i   v          v   i  v    i       v v   i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_193539796_    723 TCATATTACACAAAAAGATGTAAGGATTCAATGCAGTCCCCATCAAAATT 772
                         iv   i v v    vv   v  vi       i   i    i        i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_193539796_    773 CTAA-TGTCATTTTTCACAGAAAAATGAAAAACAG-TTCAAAAATATGTA 820
                          i i-  i -     ii      v-   v  i v - i v     vii  
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATA 150

  chr1_193539796_    821 TG-AAATGACAAGAGATCCCGAA-GGTCAAAGTAATTTTGATTAAAAAGA 868
                           -     -    i  i  v   -i i    ii   i    vv  i    
  L1M4_orf2#LINE/    151 TGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_193539796_    869 ACAAAGCTGGAGGCATTACACTTCTAAATTTTGAA--TTATGATATAATG 916
                               i      vv i       iv     ii  --   i--  i  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAG 247

  chr1_193539796_    917 CTATTATAGGCAAGATAGCATGACATTGGCATAAAACAAGACAC------ 960
                            ivi  iv     i  ii  ii i        iivv     i------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_193539796_    961 CAATAAAACAGAAT--AGAATTCA-----------ATATATTT----TCA 993
                             ii  i     --   i i  -----------   i    ----   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_193539796_    994 AT-----------AAAGATGACAAGA--ACTCACATAGGGAAAATAATAG 1030
                           -----------  i i  v     -- i   -  i      i-     
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAG-AATAG 395

  chr1_193539796_   1031 TCTCTTCAATACATCTTGCTGGGAAAATCGGATATTCACACATAGAAGAA 1080
                            i     i v  vv        v  ii     ?i    iii i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_193539796_   1081 TGTAATTGATCCGCTGTTTCACACTACATA---AAACTA-CTCAGAATAT 1126
                           v i   iv  v  iii      i i   ---   i  -    i   iv
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_193539796_   1127 ATGTAAGACTGACATGTAA-AGCTTGAAACTATAAAACTGCTAGAGGAAA 1175
                           vv?    iv v      -    -i             vi    i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAA 544

  chr1_193539796_   1176 ATAAAAGAGAAAAAAATACATGACATTGGTCTGGGCTATGATTTCTTGGA 1225
                          i v i ? v   vvv - i    v    vi i   v   i      i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_193539796_   1226 T-TGGTTCCCCAAGCATAGGCAACAAAAGGAAAAATACACACATTGTATT 1274
                          -  iiv  vv     i i          i       v i v    v i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_193539796_   1275 ACATCAAACTAAAAAGCTTCTGCACAGCAAAGTAAACAATGCCCAGA--G 1322
                         v       v v    i   i  ii vv     --i   v ii v   -- 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAG--GACACTATCAAGAAAG 691

  chr1_193539796_   1323 TGAAGAGACAACTCAT-GAGTTGGA-AAAATATTTGCAAGCCATATATCT 1370
                             i       i  i-  i v   -             ii         
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_193539796_   1371 GATAAAGCGTTAATATTCAAAATATATAAGGAACTC----AACTCAATGG 1416
                              i vii vi   i  i         i      ----        --
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-- 789

  chr1_193539796_   1417 CTAATAAAAAGG-AATTAACC-AATTTAAAAATAGGCAATGTACCTGAAT 1464
                         --         i-  v     -    ?      i     v v ii     
  L1M4_orf2#LINE/    790 --AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_193539796_   1465 GGACATTTCTCAAAAGAAGACGTACCAATGGCCAACAAGTATTATTATCA 1514
                         i          v        ii   v         i   i i-  v -- 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC-ATGA--A 884

  chr1_193539796_   1515 ACAATACAAAAAATCATCAAGTGT 1538
                          vi  i vv  v    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (127 / 77)
Gap_init rate = 0.04 (33 / 906), avg. gap size = 2.30 (76 / 33)  


2838 26.17 2.46 1.23  chr1_193543945_193547432.rev     2106  2999 (489)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_193543945_   2106 AAAGATATTTCATGATCATGGACTGGAAGGATCAATATTGTTATAATGTC 2155
                                 ii    v       i      iv i          vi   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_193543945_   2156 CATACTACCCAAGGCAATCTACAGATTCAA-GAAATCACTATGAAAATAC 2204
                         v     v     ivii              - v    v    v     v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_193543945_   2205 CAGGGACATTCTTCACAGTAATAGAGAAAAACAATCCTAAAATTTTTATG 2254
                            vvi v  i  ii   v   v  v  iv-ii           iv    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATG 152

  chr1_193543945_   2255 GTACCACAAAAGCTAAAGGTACCAAAAATAGCTAAAGCTATCCTAAGCAA 2304
                          ------   v  --    v   v i      i   i v   i i iv  
  L1M4_orf2#LINE/    153 G------AAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_193543945_   2305 TAAAAACAAAACTGAAGGAATAACATTACCTGACTTCAAATTATACTACA 2354
                         v  i      ii  i    v v   i v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_193543945_   2355 GAGTTGTAGTAACTAAAACAGGATAGTACTGGCATAAAAACAGACATACA 2404
                         i  i ii     ii  i    vi i            ii i       i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_193543945_   2405 GTCTAATGGAACAGAATAGAAAACACAGAAACAAATTTACACATCTACAG 2454
                          vii       i     v  i iiv      i   iii i    i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_193543945_   2455 TGAATGCATTTTTGACAAAGG----AACGCTGT------GGAAAAGA--- 2491
                          v   vv     i     i  ----  vi ii ------  i     ---
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_193543945_   2492 GTCTCTGCAATTAACAGTTCTAGGAAAACTGGATTTTCATATGCAGAAGA 2541
                             i v   iv  ii  v  i   v        v?i  i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_193543945_   2542 ATGAAACTAGACCTCTATGTTTCACCATATCCAAAAATCAAATCAAA-TG 2590
                              ii i    i   iv iv        v       i  v     -  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_193543945_   2591 GAT-AAAGACTTAAGTCTAAGACCTCAAACTATGAAACTTCTACCAGAAA 2639
                            - ?    i   i v     v  v       i     ii  vv     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_193543945_   2640 ACATTGGGGAAAATCTCAAGGACTTTGTTCTGGGCAAAAATTTCTTCAGC 2689
                             v  ? v      iviv   i   vvi i     vii      -  v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGA 593

  chr1_193543945_   2690 AATAAC-TCACAAGCACAGGCAAGCAAAGCAGAAATGGACAAATGAGATC 2738
                         v  i  -i  v       i    vv    v i    i  i    vi  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_193543945_   2739 ACATCAAG-TTAAAAATGTTCTGCACAGCAAAGGACACAATGAACAAAGT 2787
                         v      i-       i-  i  ii vv          v  v  v     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_193543945_   2788 GAAGAAATAAC--ACTGAGTGGGACAAAATATT-GCAAACTACCCATCTG 2834
                            i i i   --  v  i     v        -     ii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_193543945_   2835 ACAAGGGATTAATAACCAGAATAATTAAAGAGCTCAAACAACTCTATCAG 2884
                          i      i vi  v        vv      i   vv       v  v v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_193543945_   2885 AAATCATCTAATAATCAGATCAAAAAA-GGGCAAAAGATCTGAATATAGA 2933
                            vviv v     i vi  i?     -       i   i      v v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_193543945_   2934 TTTCTTAAAAGGATACATTCAAATGGAAAACAGACATGTGAAAAGATGAT 2983
                              iv    i v i  v       vv  i ii  ii          v 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_193543945_   2984 CAACATAACTGATCAT 2999
                               v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (132 / 98)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 2.06 (33 / 16)  


2907 27.34 0.93 0.58  chr1_193581958_193583805      500  1355 (493)    L1M4_orf2#LINE/L1       50   908 (0)  

  chr1_193581958_    500 TGGCCATAATGCCCAAGGTAAATTATAGATTCAATGCCATCCCCATCAAG 549
                             v   v v     iv i vi  i        i  v     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_193581958_    550 CTACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCAC 599
                         v v   iivi i  i  ii     v v  v  iv v iii    i    i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_193581958_    600 ATGGAACCAAAAAAAATCCCGCATTTCCTAGTCAATCCTAAGACAAAAGA 649
                               viiv  iii i  v v  vv  v iv     i i i v i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_193581958_    650 ACAAAGCTGGAGGCATCACGCTACCTGACTTTAAACTATACTGCAATGCT 699
                               i      vv    i  v  ii i  i   viv    i   v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_193581958_    700 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACCA 749
                                i   i    ii         i iv ii i   v   i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_193581958_    750 ATGGAACAGAAC--AGAGTCCTCAGAAATAATACCACACATCTACAACTA 797
                               i    i--       --        vv   i    i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_193581958_    798 TCTGATCTTTGGCAAACCTGACAAAAACAAGAAATGGGGGAAGGATTCCC 847
                         vi    i  i i   ivv  v   i v  vvv       i   i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_193581958_    848 TATTTAATAAATGGTGCTTGGAAAACTGGCTAGCCATATGTAGAAAGCTG 897
                          v  i  i          v   v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_193581958_    898 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 947
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_193581958_    948 TAAAGACTTAAATGTTAGACCTAAAAACCATAAAAACCCTAGAAGAAAAC 997
                         i ?    i       v   v      - i      vi i           
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAAC 546

  chr1_193581958_    998 CTAGGCG-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1046
                         v    ? - v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_193581958_   1047 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGGCAAATGGGATCTA 1096
                         vi            vvi          vv     v ii    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_193581958_   1097 ATTAAACTAAAGAGCTTCTGCACTGCAAAAGAAACTA-CAATCAGATTGA 1145
                           i   v v  i i   i  ii  v    i  v    -   v- i v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGA 694

  chr1_193581958_   1146 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 1195
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_193581958_   1196 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAG 1245
                           i  i  vi          v  i         vv    v iv i  v i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_193581958_   1246 AAAAAC---TACCCCA-TCGAAAAGTGGGCAAAGGATATGAACAGACACT 1291
                            i  ---  v    - i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_193581958_   1292 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 1341
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_193581958_   1342 TCTTCACTAGCCGT 1355
                         v v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.01 (9 / 859), avg. gap size = 1.44 (13 / 9)  


2959 26.49 1.77 1.55  chr1_193637001_193642403.rev     4007  4912 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_193637001_   4007 TGGAAGAACATTTCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4056
                              ii i  ii    i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_193637001_   4057 GGCCATACTGCCCAAGGTGATTTATAGATTCAATGCCATTCCCATCAAGC 4106
                            v     v     iv    i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_193637001_   4107 TACCAA-TGTCTTTCTTCACAGAATTGGACAAAACT-ACTTTAAAGTTCA 4154
                          v   i-  i    i  -i     v v     i-  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_193637001_   4155 TATGGAACCAAAAAAGAGCCCTCATTACCAAAGCAATCCTAAGCAAAAAG 4204
                                viiv  ii  v  vvv  vi     i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_193637001_   4205 AACAAAGCTGGAAGCTTCACGCTACCTGACTTCAAA-----CTAT---GC 4246
                                i    i vi    i  v  ii i      -----   i---  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_193637001_   4247 TACAGTAACCAAAACAGCATGGTACAGCATGGTACCGGTACCAAAACAGA 4296
                                 i   i    ii      ----   i ----  -- ii i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTAC----TGGCA----TA--AGGATAGA 288

  chr1_193637001_   4297 GATATAGACCAATGGACCAGAACAGAGGCCTCAGAAATAACACCACACAT 4346
                         v       i       vi    iv   ivii         vv   i    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_193637001_   4347 CTACAACCATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGAGAA 4396
                         i  iiii  vi    i  i     ivv  vv  i v  vvv     i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_193637001_   4397 AGGATTTCCTATTTCTTAAATGGTGTTGGGAAAACTGGCTAGCCATATAT 4446
                           i  vvi  v  ivvi        i     v      v  ?   i  ii
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_193637001_   4447 AGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTC 4496
                          i  iiv    ii    i    v   i     v              i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_193637001_   4497 AAGATGGATTAAAGACTTAAATGTTAGACCCAAAACCATAAAAACCCAAA 4546
                           i      i ?    i       v   v i     i      vi iv i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_193637001_   4547 AAGAAAACCTAAGC-CATACCATTCAGGACATAGGCACGGGCAAGGACTT 4595
                                 v  i ?-i v i -   iv   v v  vvii     v ii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_193637001_   4596 CATCACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAAT 4645
                          v viv  vi            vvi          vv        i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_193637001_   4646 GGGATCTAATTACACTAAAGAACTTGTGCACAGCAAAAGAAACTACCATC 4695
                         v   ii v  i v v v  i     v  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_193637001_   4696 AGGGTGAACGGGCAACCTACAGAATGGGAGAAAATTTTTTGCAATCTACC 4745
                          ii     vi i     i                 v   -    vii iv
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATA 736

  chr1_193637001_   4746 CATCTGATAAACGGCTGATAGCCAGAATCTACAAAGAACT-TAACAAATT 4794
                         i         iv i  vi  v       v  i        - v    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_193637001_   4795 TAGAAGAAAAAAACAAA---CCCA-TCAAAAAGTGGGCAAAGGATAAGAA 4840
                         v v  v     i     ---    - i?    i            vv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_193637001_   4841 CAGACTCTTCTCAAAAGAAGATATTTATTCAGCCAACAGACACATGAAAA 4890
                         i    vi     v           vi vvii     i ii          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_193637001_   4891 AATGCTCATCATCACTGGTCAT 4912
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.00 (30 / 15)  


 656 33.12 2.27 0.65  chr1_193671815_193673970        2   309 (1847)    L1M4_orf2#LINE/L1       13   325 (583)  

  chr1_193671815_      2 CCATGTTCTTGGGCTAGAATACTCAACAGGATAAATAAATAAATTTTTCT 51
                                 v   ii i   v   i  i vvi v  v vivv   vi i i
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_193671815_     52 CAAATTGTACTATAGGCTTAACATAATTACTTATTAAAATTTCAAGAGAA 101
                                vv   i  ii i   ii   i- i   i     ii  ivv vv
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATC-CCTATCAAAATCCCAGCTGCC 111

  chr1_193671815_    102 TTCTTTGTAAATATAGATCATTTCATACTAAA-TTTATATTAAAATGCAC 150
                           i    i i v  v  iv vi v  v     -  i    vi       v
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_193671815_    151 AGGAGTTAGAATGGCTGAAACATTTTTTTAAAATAA---TAAAGTTGAAA 197
                         i   vii     i  ii     v i  vv    v  ---i       i i
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_193671815_    198 GGATCACACAAATCAAATTTGAGGCCTCAAAATATAGCTACCATATTAAA 247
                          iv      -vvi v     v iiv  i vv i v      vi  v v  
  L1M4_orf2#LINE/    212 GACTCACAC-TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr1_193671815_    248 AACAGTATAGTATTGATGGAGGGATAGACATA--AATCAATAGAACAGA- 294
                         i     i i   i  iiiv i           --i      i   i   -
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_193671815_    295 TACAGAATCCAGAAA 309
                          vv   i        
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAA 325

Transitions / transversions = 1.32 (58 / 44)
Gap_init rate = 0.02 (6 / 313), avg. gap size = 1.50 (9 / 6)  

 845 33.33 2.27 1.01  chr1_193671815_193673970      519   914 (1242)    L1M4_orf2#LINE/L1        1   401 (507)  

  chr1_193671815_    519 TAGAGAGCAATACCATGTTCTTGGGCTAGAATACTCAACAGGATAAATAA 568
                          i  i  vv  v        v   ii i   v   i  i vvi v  --i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA--G 48

  chr1_193671815_    569 ATA--AATTTTTCTCAAATTGTACTATAGGCTTAACATAATTACTTATTA 616
                           i--   vi i i       vv   i  ii i   ii   i- i   i 
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC-CCTATCA 97

  chr1_193671815_    617 AAATTTCAACAGAATTCTTTGTAAATATAGATCATTCCATACTAAA-TTT 665
                             ii  i v vv  i    i i v  v  iv viiv  v     -  i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_193671815_    666 ATATTAAAATGCACAGGAGTTAGAATGGCTGAAACATTTTTTTAAAATAA 715
                             vi       vi   vii     i  ii     v i  vv    v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_193671815_    716 ---TAAAGTTGAAAGGATCACAAAAATCAAATTTGAGGCCTCAAAATATA 762
                         ---i       i i iv     vvvvi   -   v iiv  i vv i v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAA-TTTCAAAACTTACTACAAA 246

  chr1_193671815_    763 GCTACCATATTAGAAACAATATAGTATTGATGGAGGGATAGACATA--AA 810
                              vi  v vi i   i i i   i  iiiv i           --i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_193671815_    811 TCAATAGAACAGA-TACAGAATCCAGAAATAGACCCACACAAATATGCTC 859
                              i   i   - vv   i          i     i   vv    v  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_193671815_    860 AAGTAACTTTTAACAAAGATGCACAAATAATTCAATACAGAAAAGATCCT 909
                           v i i   ii    i i   vv i iv       ivi    ii  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_193671815_    910 TTTTT 914
                         i    
  L1M4_orf2#LINE/    397 CTTTT 401

Transitions / transversions = 1.49 (79 / 53)
Gap_init rate = 0.02 (8 / 401), avg. gap size = 1.62 (13 / 8)  

1221 24.85 6.61 2.40  chr1_193671815_193673970     1165  1663 (493)    L1M4_orf2#LINE/L1      389   908 (0)  

  chr1_193671815_   1165 AGAAAAGTTTCTTTTCAACAAATTGTGTTGGGG--ACTAGCACTTTCTTA 1212
                             v   --             v   i    i--   i - iv?i vi 
  L1M4_orf2#LINE/    389 AGAATAGT--CTTTTCAACAAATGGTGCTGGGACAACTGG-ATAKCCACA 435

  chr1_193671815_   1213 -GCCAAAAAATTAATTTTGATTTA-ATCTCACATATTTTACAAAACCTAA 1260
                         -  v   i   v  v  v  iiiv- i      ivv v       vi   
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_193671815_   1261 CTCCAAATGGTTCCTATATCTAAATGCATAATGTAAAACAATCAAACTTG 1310
                            v      v  v? v i       i vi vv      v  v     iv
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_193671815_   1311 TAGAGGAA-------GAGAAAATCTTTGTGATCTGGGGTTTGATGGAATT 1353
                             i   ------- ? v       i    i  v     v -- v   v
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG--GCAATG 583

  chr1_193671815_   1354 GTT-CTTAAACAGGACACCTAAAGGATGACCCATAAAAGAGTGAAATA-A 1401
                            -    i i v      v    v ii v v i      i-i     - 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA-AAAATAGA 632

  chr1_193671815_   1402 TAA-TAATACTTTATCAACATTAAACACTTTT-TA-TCCATGAAAGACAT 1448
                            - viv    i     v      v      - i- i  --  i    -
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACA- 679

  chr1_193671815_   1449 TCTAT---GAGAGTGAAAAGATAAGCTACTTATTAGCAAAAAATATTTGC 1495
                         -    ---  i          i  v i  vv v i v i           
  L1M4_orf2#LINE/    680 -CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_193671815_   1496 AAATAACGTATCTGACAGAGGACTTATACATGGAATATATAAAGAATGCT 1545
                             v ii       i ii      i  ivii              iv  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_193671815_   1546 CTA-AACACAG--GTAAAA-------CAATCCAATCAATAAAGGTGCCAA 1585
                         -  -   v  i--i     -------i  i     i? v   v v  v  
  L1M4_orf2#LINE/    779 -TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_193671815_   1586 AGCCTTGAACAGA----TCTAACAAAAAAGATATTCAGATGGAAAATAAA 1631
                         i vi     i   ----   v-    i       v  i    vv     i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTC-CAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_193671815_   1632 CATGTGAAAAGTTATTCAATGTCATTAACCAT 1663
                           ii       v ii    ii   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.14 (64 / 56)
Gap_init rate = 0.04 (22 / 520), avg. gap size = 2.05 (45 / 22)  


3013 26.68 1.32 1.21  chr1_193687407_193693944.rev     5141  6047 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_193687407_   5141 TGGAAGAACTTTCCATGCTCATGGAGAGGAAGAATCAATATCGTGAAAAT 5190
                              ii iv i     i       vv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_193687407_   5191 GGCCATACTGCCCAAGGTAATTTATAGAGTCAATGCCATCCGCATCAAGT 5240
                            v     v     iv i  i  i   v    i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_193687407_   5241 TACCA-CTAACTTTCTTCACAGAATAGGACAAAACT-ACTTTAAAGTTCA 5288
                          v   -  iv    i  -i     vvv     i-  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_193687407_   5289 TATGGAATCAAAAAAGGGGCT--GCATTGCCAAGACAATCCTAAGCAAAA 5336
                                -- viv     i i-- v  v     i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_193687407_   5337 AGAACAAAGCTGGAGGCATCAGGCTACCTAACTTCAAACTATACTACAAG 5386
                                  i      vv   vi  v  i  i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_193687407_   5387 GCTATACTACAAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGA 5436
                             i ------    i   i    ii         i iv ii i   v 
  L1M4_orf2#LINE/    247 GCTACA------GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_193687407_   5437 TATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCT 5486
                               i        i    iv   ivii         vv   i    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_193687407_   5487 ACAACCATTTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAG 5536
                          iiii  v     i  i     ivv  vv  i v  vvv           
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_193687407_   5537 GATTCCCTATTTAATAAATGGTGCTGGGAAAACTGCCTGGCCATATGTAG 5586
                         i  vvi  v  i  i              v     vv i?   i   i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_193687407_   5587 AAAGCTGAAACTGGATCCCTTACTTACACCTTATACAAAAATTAATTCAA 5636
                           iiv    ii    i    vv  i     v              i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_193687407_   5637 GATGGATTAAAGACTTAAATGTTAGACCTAAAAACCATAAAAACCCTAGA 5686
                         i      i ?    i       v   v      - i      vi i    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGA 539

  chr1_193687407_   5687 AGAAAACCTAGGCCTTAGCATTCAGGACAAAGGCATGGGCAAGTACTTCA 5736
                                v    ?v v iiv   iv   vvv  vv i     vvii   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_193687407_   5737 TGACTAAAACACAAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGG 5786
                          iiv  vi    v       vvi          vv        i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_193687407_   5787 AATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG 5836
                         i ii v  i   v v  i i   i  ii vv    i  v    i  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_193687407_   5837 AGTGAACAGGCAACGTACAGAATGGGAGAAAATCTTTGCAATCTACCCAT 5886
                               v  i    vi                 v       vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_193687407_   5887 CTGATAAAGGGCTGATAGCCAGAATCTACAAAGAACTTAAACAAATCTAC 5936
                                i  i  vi  v       v  i        ivv    v  v i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_193687407_   5937 AAGAAAAA--------ACCCCATCAAAAAGTGGGCAAAGGATATGAACAG 5978
                           v     --------    v  i?    i            v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_193687407_   5979 ACACTTCTTAAAAGAAGACATTTATTCAGCCAACAGACACATGAAAAAAT 6028
                            i    iv        i  vi vvii     i ii          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_193687407_   6029 GCTGATCATCACTGGTCAT 6047
                            v v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (132 / 106)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.56 (23 / 9)  


1906 24.36 5.28 5.01  chr1_193726026_193727735.rev      481  1219 (491)    L1M4_orf2#LINE/L1      168   908 (0)  

  chr1_193726026_    481 CAAAACAG--AAAACAAAC----AAACAAAAAACAAAACAAAAGGCATCA 524
                           i  i  --       v ----   vi  i      iivii   vv   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr1_193726026_    525 CATTACCTGACTCCAAACCACACTATAAGGCTACATTAATCAAAACTGCA 574
                           i v  ii i i    v vi    i  i      v       i  v ii
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_193726026_    575 TGTCACTGGTACAAAGACAGACATATACACCAATGGAACAGAA---GGAT 621
                           vi     i i  i  i         v i        i    ---i  v
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_193726026_    622 CCCAGAAATGAAGCTGAAGCTGTACACCTACAAACCATTTGATCTTTGAA 671
                         i        i  - ----- ii    ii  iii-i  v     i  i  v
  L1M4_orf2#LINE/    318 TCCAGAAATAAA-C-----CCATACATTTATGG-TCAATTGATTTTCGAC 360

  chr1_193726026_    672 AAAGTTCACAAAAATAAACAATGGGGGAAAGGATGCCCTATTTAATAAAT 721
                           i v vv   i vi vv        -    i  ivi  v  i  i    
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAAT 409

  chr1_193726026_    722 GGTGCTGAGATACCTGGCTAGCTA--TGCAGAAGAATGAAACTAGACCCC 769
                                i  i v    v  ? i --    i         ii i      
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_193726026_    770 TAATCTTACCCTATATACAAAAATTAACTCAAGATGGAGTAAAGATTTAA 819
                           -i  i  v i                    i     vi ?   ii   
  L1M4_orf2#LINE/    460 TA-CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_193726026_    820 ATGTAAGACCTCAAACTATAAAAACCTTAGAAGAAAACCTAGG---AAAT 866
                                 v  v           vi             v    ---    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_193726026_    867 ACTATTTTG-GACATCAACCTTGGCAAATAATTTAT--GACTAAGTCCTC 913
                         ----i  i -   v iiivi v     - ii   v --  -  v v vi 
  L1M4_orf2#LINE/    559 ----CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA-TATGACACC 602

  chr1_193726026_    914 AAAAGCAATTGCAACAATACCAAAAATGGACAAGTGGGGCCTAGTTAAAC 963
                                vvv       v vv      i  i  i v  i i vi i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_193726026_    964 TGAAAAGCTTC----CTTCACAGCAAAACAGCAACAACAGCAAACAC-AT 1008
                          v    i   i----     v  -------------------i    -  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAG-------------------GACACTAT 683

  chr1_193726026_   1009 CAACAGGGTAAACAGACAACCTACAGAATGGAAGAAACTATTCACAAGCT 1058
                            v ii  i  v        i         i     v    ii   iii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_193726026_   1059 ATGCATGTGCCAAAG---TTTTAACATCAGAATCTGTAAGAAACTT---- 1101
                           ii  v  vi  i ---  v  v --      v i   ii    i----
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATC--CAGAATATATAAAGAACTCTTAC 781

  chr1_193726026_   1102 AATTCAACAA-------ACAAAGTAACCCCATTATAAAATGGGCAAAGGA 1144
                           i    i  -------     -      v   ?v               
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_193726026_   1145 CATGAACAGATACTTCTCAAAAGAATATACACAATCAGTCA-TAA--ACA 1191
                         iv    i   i i     v      v   i    vii i  -   --   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_193726026_   1192 TGAAAAAACTCCCAACATTACTAATCAT 1219
                               i iv i      i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (113 / 64)
Gap_init rate = 0.03 (25 / 741), avg. gap size = 3.04 (76 / 25)  


2726 28.56 1.78 0.89  chr1_193772025_193776646     3230  4129 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_193772025_   3230 TGGAAACACATCCCATGCTCATCGATGAGTGGAATCAATATTGTGAAAAT 3279
                               v i        i    v   vi vi  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_193772025_   3280 GACCATACTGCCAAAAGCAGTTTACAAATTCAATGCAATTCCTATCAAAA 3329
                          i v     v  v   viii i    i      i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_193772025_   3330 TACCATCATCATTCTTCACAGAACTAGAAAAAACAATACTAAAGTGTATA 3379
                          v   v vv v  i  ii     v v  v  ivii  v     i vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_193772025_   3380 TGAAACCAAAAAGAGAGCCCACACACCCAAAGCAAGACTAAGCAAAAAGA 3429
                           i  viiv  i -  v  viv i v     i   vvi i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_193772025_   3430 ACAAATCATTTGGAGGCATCATGTTACCTGACTTCACACTATACTATAAG 3479
                              v---       vv   iii v  ii i    v viv     i  i
  L1M4_orf2#LINE/    200 ACAAAG---TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_193772025_   3480 GCCATAGGCACCAAAACATCATGGTACTGGTATAAAAATAGGCACATAGA 3529
                           i i  vv i   i   vii         i    ii    i  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_193772025_   3530 CCAATGGAACAGAATGGAGAACCCAGAAATAAACCCAAATAGTTACAGCC 3579
                         i        i     v    ii               v i v   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_193772025_   3580 AACTGATCTTCAACAAGTCAAACAAAAACATAAAGTGGG-AAAGGACACC 3628
                           i    i   i     vvviv   i v   vv i    -    i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_193772025_   3629 CTATTCAACAAATGGTGCTGGGATAATTGTCAAGCCATATGTAGGAGAAT 3678
                           v                    i  i  vvv ?   i   i ii     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_193772025_   3679 GAAATTGGATACTCATCTCTCACCTTACACAAAAAAAATCAACTCAAGAT 3728
                            i     iv ii i   v    v  i       --- i       i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA---TTAACTCAAAAT 493

  chr1_193772025_   3729 GGATCAAGGACTTAAATCTAAGACATGAAACTATAAAAATTCTAGAAGAT 3778
                               ?i   i     v     vv i           v ii       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_193772025_   3779 AACATTGGAAAAACCCTTTTAGACATTGGCTTAGGCAAAGACTTCATGAC 3828
                              v  ?iv  vi   ivv   v    v        v ii   v iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_193772025_   3829 CAAGAACCCAAAAGCAAATGCAACAAAAACAAAGATTAATAGATGGGACT 3878
                         i v  vv         v v         iv   i  vi   i  v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_193772025_   3879 TAATTAAACTAAAGAGCTTCTGCATGGCAAAAGGAACAGTCAGCA----G 3924
                          v  i   v v  i i   i  iiivv    i iv  vi   iv ---- 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_193772025_   3925 AATAAACA-----------GGGAGAAAGTCTTCACAATCTATGCATTTGT 3963
                           v i   -----------        i v  ii   vii  ii  i  v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_193772025_   3964 CAAAGGACTAATGTCTAGAATCTACAAAGAACTTAAACAAATAAGCAATA 4013
                         i  i     vi i  i     v  i        ivv    v v ii    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_193772025_   4014 AAAAAAAAAAACAATCCCATCCAAAAGTAGTCTAAGGACATAAACAGACA 4063
                             i v   -i  i  v  i?    i i v v     iv i  i     
  L1M4_orf2#LINE/    794 AAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_193772025_   4064 ATTCTCAAAAGAAGATATACAAATGGCCAACAAATGTGTGAAAAAATGTT 4113
                         v     v                       i  iiiii      i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_193772025_   4114 CAACATCACTCATGAT 4129
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (147 / 106)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.43 (24 / 7)  


 874 25.68 16.12 1.64  chr1_193811049_193812629        1   366 (1215)    L1M4_orf2#LINE/L1      332   750 (158)  

  chr1_193811049_      1 CACACAT--ATGACCAACTGATTTATGACAAAGGTGCAAAGACATTTCAA 48
                           i    --   ii   i      vi     i     v     vv     
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_193811049_     49 TGTGGAAAGAATAGTTTTTTACAGCAAATAGTGTTGGAATAATTGGACAT 98
                           v            i    -  i     i   i   i i  i    i ?
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_193811049_     99 GTATATATAAAAAAAGTGAACATTGA---CCTAACCCTTACCTTAGAGGA 145
                         vi i  ii    i  -    -i   i---    v i vi   v  v vi 
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAA-TGAA-GTTGGACCCCTACCTCACACCATATACAA 478

  chr1_193811049_    146 GAACTAACACAAAATACATCATAGGTCAAAATTTAGAATGAAAAATTATA 195
                         i  i    v      iv    ?  ii v    v  ii vvv    i    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_193811049_    196 AAACTTTTAGA-------------GTA----------------------- 209
                              i     -------------   -----------------------
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_193811049_    210 ---------CTTTGATATGACGCTAAAAGCATAATCCATAAAAGAAGAAA 250
                         ---------   v        i i       i  v v i       -   
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA-AAA 627

  chr1_193811049_    251 AGTGATAA-CTGGATTCCAATAAAATGAACTACTTCTG--CTGAACAAAA 297
                          vv     -i    i i  vi     v  vv    i  --  v--    i
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAG 675

  chr1_193811049_    298 AGCCCTGTTACAAGAATAAAAAGACAAGCTGCAGATTGGGAGAAATTGTG 347
                         ii v  i i vi i i i         v ii    v         v i v
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_193811049_    348 TG-AAATCA-----CTAACAAAGAA 366
                           -      -----  i i  i i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGA 750

Transitions / transversions = 1.71 (58 / 34)
Gap_init rate = 0.03 (13 / 419), avg. gap size = 5.00 (65 / 13)  

1628 25.73 5.66 1.03  chr1_193811049_193812629      506  1088 (493)    L1M4_orf2#LINE/L1      299   908 (0)  

  chr1_193811049_    506 AATAGAAAAGGGTAGAGAACCCAAAAATAAAACCACATACCTAAAACCAC 555
                            i   v  ii v    ii   i       v   i i ii  viii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_193811049_    556 CTGATCTTTGACATAGTTGACAATAACAAACAATGGGGAAAGGATATGCT 605
                         i    i  i    vi v  v   v v  vv            i   vv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_193811049_    606 ATTCAATAAACGGT-------CAG-------------TGCAGAAGATTAA 635
                         v     i   i   -------  i-------------    i    v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_193811049_    636 AATTGGACGCTTTCCTTTCACCACATACAAAAAATTAATGCAAGATGGAT 685
                          i      v i v   iv     i         -    iv   i      
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGAT 497

  chr1_193811049_    686 TAAAGACTTAAATGTAAGACCCAAACCAATAAAAACCCTAGAAGAAAACC 735
                         i ?    i           v i   v v      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_193811049_    736 TAGG---AAATACTACTCCG-GATATCAGCCTTGGGAAAGAATTTATAAC 781
                             ---    ----  i  -  iv ii v-  i  v  vii   v v v
  L1M4_orf2#LINE/    548 TAGGNGTAAAT----CTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAG 592

  chr1_193811049_    782 AAA-GTCCCCAAAAGCAATTGCAACAAAAAACATAATTGACAAATGGGAC 830
                          v - v v         vvv         i v v   v  i    v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_193811049_    831 CTAATTAAACTAAAGAGATTCTGCACAGCAAAATAAACTATCAACAGAAT 880
                         i v  i   v v  i iv  i  ii vv    iv v        v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_193811049_    881 AAACAGACAACCTACAGAATGGGAGAAAATATTTGCAAACAATGTATCTA 930
                         i  v        i                          iv  i     i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_193811049_    931 ACAAAGGTCTAATATTCAGTATCTATAAGGAACTT----AATTCAAAAAA 976
                          i  i  v  vi   i   v  v     i     i----  i    v  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_193811049_    977 CAAAAAACAAATAACCCCACTAAAAAATGGGCAAAGGAC----ATACACA 1022
                         v    i           v i ?                i----   v   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_193811049_   1023 CCTCTCAAAGGAAGACACACATGCGGCCAAGAAATCTATGAAAAAATGCC 1072
                         ii    v  i     i i   vii      v  iivi       i    i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_193811049_   1073 CATCACCACTAAACAT 1088
                           v  i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (81 / 67)
Gap_init rate = 0.02 (10 / 610), avg. gap size = 3.90 (39 / 10)  


2190 23.17 15.59 1.93  chr1_193886042_193888263      599  1323 (899)    L1M4_orf2#LINE/L1        1   824 (84)  

  chr1_193886042_    599 TGAAGAGATATCCCATGTTCATGGAAAGAAAGACTCAA------------ 636
                           i i                    vv i      i  ------------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_193886042_    637 -------CTTCACAACATGATCTATACATTCAATGCAATCCCAATCAAAA 679
                         -------  i v   vv       i v      i        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_193886042_    680 TCCCAGAAAGTCATTTTGTGGATATCAACAAACTGATTCTAAAGTTAATA 729
                               vviviiv     ii  v  ii    i     i     i  v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_193886042_    730 TGGAAAGGCAAAAGATCCAGAAGAGCCAACACAACACTGAAGGAGAAAAA 779
                               v    ii  i      v      v    ivi    ii    i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_193886042_    780 TAAGGTTGGAGGGCTGACATTACTTGGCTTTAAATCTTACTATAAAGTTA 829
                         i  i        i  v   i v iiiii  i   v       i    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_193886042_    830 CAGTAATCAAGACAGTGTAGTATTGGCAAAAATAAAAAATAAAAAAAAAA 879
                                           i   i     ----   ii -  i v v v -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA----TAAGGA-TAGACATATA- 294

  chr1_193886042_    880 GATCAACAGAACAGAATACAGAGCCCAGAAACAGACCTACATAAATATGG 929
                               ii   i     vv    i       i i   i i i vv     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_193886042_    930 TCAACTAATCTTTCACAAAGAAGCAGAGCCAATACAATATAGTAAAGATA 979
                             i i  i  iv    i iv  vi  v v  v    ivi v  ii   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_193886042_    980 GTCTTTTTAAGAAATGGTCCTAGTACAAATGGATATCCACAGACAAAAAA 1029
                                i  v       v  i v    v      ?     vi     i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_193886042_   1030 AAAAAAAATACATCTAGACACAGACCTTACATCCTTTGCAAAAGTGAACT 1079
                          vi  i-------i i   v vv    i   i v v i     i v    
  L1M4_orf2#LINE/    445 ATGAAG-------TTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_193886042_   1080 CAAAATGAATCACAAA----AATGTA-GA--------------------- 1103
                                i    ? i ----      -  ---------------------
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_193886042_   1104 --------------------------TGACCTTAGGTTTGGCAATGACTT 1127
                         --------------------------       i    v       ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_193886042_   1128 C------------------GCACAATCCATGAAAGAAACAATGGATAAAT 1159
                          ------------------      v v ii       v   i       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_193886042_   1160 TGGACTTAATTAAAATT-----TTCCTCTG--TCACAGAA-ACTGTCAAG 1201
                                v  i      -----i ii v  --   v  i -   i     
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_193886042_   1202 ATGATGAAAAG-----TCACAGA-TGAAAGGAAATACTTGAAAAGAA-AT 1244
                          vii       -----i      -  ii  i     i   v   vv -  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_193886042_   1245 ATCTGATAAG-----TGTTATCCAAAATATACAAAGAACTCTCAAAACTC 1289
                                   -----   -     i      i          i v     
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_193886042_   1290 AACAATAAG----TAAGCAACTTGATTAAAAAATGGGC 1323
                           i     i----i  ii   iii   ?          
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

Transitions / transversions = 1.80 (106 / 59)
Gap_init rate = 0.02 (18 / 824), avg. gap size = 7.06 (127 / 18)  

 327 16.07 7.14 0.89  chr1_193886042_193888263     1618  1729 (493)    L1M4_orf2#LINE/L1      790   908 (0)  

  chr1_193886042_   1618 AACAAAAAAACAAAAAAACCAA--AAAAAATTGGGCCAAAGACT-GAACA 1664
                           i     i     v  v    --?      -    v  i  i -   i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAAT-GGGCAAAGGATTTGAATA 838

  chr1_193886042_   1665 GACACCACACCAAAGA---TATACAGATGGTAAATAA--ACATGAAAAGA 1709
                             iiv v       ---      i    iv     --           
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_193886042_   1710 TGCTCCACATTATATGCATC 1729
                              v    i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (10 / 7)
Gap_init rate = 0.04 (5 / 119), avg. gap size = 1.80 (9 / 5)  


2852 27.06 1.89 0.78  chr1_193941239_193946163.rev     3537  4434 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_193941239_   3537 TGGAAA-ACATTCCATGCTCATGGATGGGAAGAATCAATACTGTGAAAAT 3585
                               - i  i     i        v      v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_193941239_   3586 GGCCATACTGTCCAAAGCAATGCATAGATTCAATGCTATTCCCATCAAGC 3635
                            v     vi     vii  vi i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_193941239_   3636 TACC-GTTGACTTTGTT-CAGAGAATTAGAAAAAAAAA----AAAAACTA 3679
                          v  - i  v    v  -    -    -  v  ivvi ----    vii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATT-GACAAGCTGATCCTAAAATTCA 148

  chr1_193941239_   3680 CTTTAAAA-G-AAGAGCCCCT--ATAGCCAAGACAATCCTAAGCAAAAAG 3725
                         iv vi   - -   i v   v--        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_193941239_   3726 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGCC 3775
                                i      vv   ii  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_193941239_   3776 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 3825
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_193941239_   3826 AATGGAACAGGATAGAGGCCTCAGAAATAATGCCACACATCTACAACCAT 3875
                                i  i  v   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_193941239_   3876 CCGAACTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGAAT--TCC 3923
                         ii  vi  i     ivv  v   i v  vv               --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_193941239_   3924 TTATTTAATAAATGGTGTTGGAAAAACTCACTAGGCATATGCAGAAAACT 3973
                           -- i  i        i   i v    viv  ?v  i     i  i v 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_193941239_   3974 GCAACTGGTCCTCTTCCTTACACCTTGTACAAAAATTAACTCAAGATGGA 4023
                          v ii   v  i  v   i     v i                 i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_193941239_   4024 TTAAAGACTGAAATGCAAGACCTAAAACCATAAAAACCCTAGAGTAAAAC 4073
                          i ?    iv     i    v       i      vi i    iv     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_193941239_   4074 CTACAGAATA--CCATTCAGGACGTAGGCATGGGCAAAGACTTCATGACT 4121
                         v  -i ?i  --i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATA-GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_193941239_   4122 AAAACATCAAAAGCA-ATGCCAACAAAAGCCAAAATTGACAAATAAGATC 4170
                          vi   i        - v  -        vv     v  i    vi  ii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_193941239_   4171 CAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 4220
                         iv  i   v v  i i   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_193941239_   4221 AACAGGCAACCTACAGAATGGGAGAAAAGTTTTGCAATCTATCCATCTGA 4270
                           v  i     i                vv       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_193941239_   4271 CAAAGGGCTAATATCCAGAATCTACAAGGAGCTTAAACAAATTTACAAGA 4320
                         i  i  i  vi          v  i  i  i  ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_193941239_   4321 AAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGGCAC 4370
                             i     i     v  i?    i    ii      v    i  i  i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_193941239_   4371 TTCTCAAAAGAACACATTTATGAGGCCAACAAACATATGAGAAAA-GTTC 4419
                              v      v i  vi viv      i  i  i    i  i - i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_193941239_   4420 ATCATCAATGGTCAT 4434
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.41 (24 / 17)  


 616 30.50 9.95 4.51  chr1_193998803_194000537      500  1253 (482)    L1M4_orf2#LINE/L1      114   908 (0)  

  chr1_193998803_    500 TTTTGGACAAAATGAACAAGTTGATTCTAAAATTGA---GGAGAATAACA 546
                              v -i    vi     i    i        v ---   -   i-  
  L1M4_orf2#LINE/    114 TTTTGCA-GAAATTGACAAGCTGATCCTAAAATTCATATGGA-AATG-CA 160

  chr1_193998803_    547 AAGAAT--AAAACTGGCTAAAACACTCCTGAGGAAGAATAATGAC-TTGG 593
                          i i i-- i  - i  i      v  i   ii     v  ii v-    
  L1M4_orf2#LINE/    161 AGGGACCCAGAA-TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_193998803_    594 AGGGAATATGTCCTACCAGATAATATAGCAAGAATTATTATAATGCTATA 643
                            -- iviiiv  v  ---i   v --   i v   i  i  v    i 
  L1M4_orf2#LINE/    210 AGG--ACTCACACTTCC---CAATTT--CAAAACTTACTACAAAGCTACA 252

  chr1_193998803_    644 ACAATTTTAAAAGGATGACATTGGCTCAAGGGGTAAATATATAAAACAA- 692
                         ii   ivvi v  vi  ii i    vi    i-  i i     i v   -
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAAT 301

  chr1_193998803_    693 ------------AGACTC-AGAAACGG--CCATATATAAGTGGAAAATTA 727
                         ------------   v  -     iii--     i  vvi   vv    i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_193998803_    728 ---TAC-ATAAGAGAAATGGTATTGCCAT-CATTGGGAACAGAA------ 766
                         --- v - i   i ---  vi vvi    -  v    i v    ------
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGG---TGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_193998803_    767 ------CAAATGGCATTAAAATTTTTTTGCCCAATTATTTATTGATAT-T 809
                         ------       iii iii ----------   i ivv  ?iv i  -i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGA----------CAACTGGATAKCCACATGC 438

  chr1_193998803_    810 GAAAACATAGAGTTGATCTTCT-TCTCAT-TTATACATAAAAACTAATTC 857
                         i   iv  ii     iv ii  -i    i-ii   i i     i   i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_193998803_    858 CAAATAAATTAA----TTACATGGGAAAAGCAAAAACTTTATA-CT-TTA 901
                         v    ii  i ?----i  v   v-  i   v      v  v -  -   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTA 537

  chr1_193998803_    902 CAA--AAGCAAAAGAATA---TTTCATTACCTCAATGTAGG-AATACATT 945
                         v  --  i  v i ?i  ---i   i v    iiivv    -   i-i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTT 586

  chr1_193998803_    946 TATT---TAAGACA---AAAGTG---GTAATTATGAAAAAATTAAGGATA 986
                          v  ---  v    ---    ii--- i  iv vii     v  --    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATA 634

  chr1_193998803_    987 AATTCAATTACATTAAA-TTAA---CTATAATAGT-CAAAA-ATACTGT- 1029
                             vi i v   i   -    ---  v vi iv -    i- i   i -
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_193998803_   1030 AAGTAATGTAGAAAAAAAATCAACAAACTGGGAGAAGGAATTTGCATGGC 1079
                            v  -  ii   i v  i v   i v        iiv       viv 
  L1M4_orf2#LINE/    685 AAGAAA-GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_193998803_   1080 ATACAGTCAACAAGATAATGATGATCT-TAGTATGTAAAGCACTCCTTCA 1128
                            i viii i   iv v vi -   i-v i   i     v    i v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACA 782

  chr1_193998803_   1129 AATCAATGAGAAAGTGACAA-TGGACCAATTAATAAAATGGAAATGAGAC 1177
                          v     i v   iv     - iiv      ? -       iv vii  i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGAT 831

  chr1_193998803_   1178 ATGAAGAACTATTTCACAGAAGAGGAAGCACGAATGGTCAA-AA--ACAT 1224
                         v    v ivi     v vi    i  vii  i     i   -  --    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_193998803_   1225 AAGAAAATGCAGTCCATCTCACTAGTTAT 1253
                         i i  i    --  v iv   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGC--TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (143 / 83)
Gap_init rate = 0.06 (48 / 795), avg. gap size = 2.27 (109 / 48)  


 419 14.29 4.08 8.16  chr1_194016991_194019543      824   921 (1632)    L1M4_orf2#LINE/L1        8   101 (807)  

  chr1_194016991_    824 ATATCTCATGTTCATGGATCAGAAGAAATAATATTGTTAAAATGTCCGTA 873
                              i             ii     vv            i   -----i
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG-----G 52

  chr1_194016991_    874 CAATGTACACCTC----TGCACCTGCAGATTCAGTGCAATCTCTATCAAA 919
                             --  v  i ----  - i  i        ii      i        
  L1M4_orf2#LINE/     53 CAAT--ACTCCCCAAATTG-ATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_194016991_    920 AT 921
                           
  L1M4_orf2#LINE/    100 AT 101

Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.04 (4 / 94), avg. gap size = 3.00 (12 / 4)  

2942 24.12 1.82 1.56  chr1_194016991_194019543     1290  2060 (493)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_194016991_   1290 ATCTTAAAATTTGTGTGCAACCACAGAAGGCCCCAAATTACCCAAGCAAT 1339
                            i       ii i  v  vii  iii i   vi   vi  v  i    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_194016991_   1340 CTTGAGCAAAAATAACACGGTTGGATACATCACATGACCTGACTTCAAAA 1389
                              iv  i  v    vi      vivv     ivv  ii i       
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_194016991_   1390 TATACCAAAAGGCTAGAGTAACCAAAACAGCATGGTAAATGGAATAAAAA 1439
                         iv   i v  i    v     i   i    ii     v-   v    ii 
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC-TGGCATAAGGA 284

  chr1_194016991_   1440 TAGACACATAGACTAATGAACT-GAATAGAGGGCCCAGAAATAAATCCCT 1488
                               i     ii    i v -    v   i i           i  v 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_194016991_   1489 GCATCTACGGCCCACTAATTTTTGACAATGGTGCCAAGTATAGACAATGG 1538
                         i   i  i  i v i i     i     v         vvi vv      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_194016991_   1539 GGAAAGGACAGCCTTTTCAATAAATGGTACTGGGTAAACTGCATATGCAC 1588
                               i i  i        i       i     vv     v   ?v   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_194016991_   1589 ATGCAGAACAATGAAACTAGACTCCTATCTCTCACCATATACAAAAATCA 1638
                              i  v      ii i   i    i   v                i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_194016991_   1639 ACTCAAAATTGATTAAAGACTTAAACATAAGACCTGAAA---TGAAACTA 1685
                                  v   i ?    i    ii     v  i   --- i     v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_194016991_   1686 CTAACAGAAAACATAGGGGAAAAGCTCTGTGACATTGGCCTAGGTAAGGA 1735
                         i  iv            ? v   v  ii     v    vi    i  v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_194016991_   1736 TTTTTTTTTTTTGTAAAAAACCTCAAAAGTCTGAGCAACAAAAACAAATA 1785
                            i  vvv v  ------  vi      ivii          iv   v 
  L1M4_orf2#LINE/    585 TTTCTTAGATATG------ACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_194016991_   1786 TAGACAAATAGGATTACATCAAACTAAAAAGCTTCTGCATAGCAAAGGGA 1835
                             i    v   i v       v v    i   i  iiivv      iv
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_194016991_   1836 ACAATCAATAGAGCAAAGAGGCAACCTATAGAATGGGAGAAAATATTTGA 1885
                           v     v i  ii  i  i     i i                    v
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_194016991_   1886 AAACTCTACATCTAATAAGGGGTTAATATCCAAAATATATAAGAAACTC- 1934
                            iiv  i    i       ii vi      i         ii     -
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_194016991_   1935 ---AACACCAACAACAAAAGTA-----AACCCA-TCAAAAAATGAGCGAA 1975
                         ---   -i   i  i    iv -----      - i?       i  i  
  L1M4_orf2#LINE/    779 TACAAC-TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_194016991_   1976 AGACTTGAGTAGATATTTCTCAAAAGAAGATATACAAATGGCCAACAGAT 2025
                         i  i    i    i       v                       i iii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_194016991_   2026 AAATGAAAAAGAAGATGTTCAACATCAGAAATCAT 2060
                          v       ----    i         ????????
  L1M4_orf2#LINE/    878 ACATGAAAA----GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (117 / 65)
Gap_init rate = 0.01 (9 / 773), avg. gap size = 2.89 (26 / 9)  


2416 26.43 6.90 1.52  chr1_194095963_194098476     1167  2021 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_194095963_   1167 ATATTTCACGTTCACTGATTGAAATACTCAACGTTGCTAAAATGTTAATT 1216
                             ii  i     iv     i  v   i  ii   i   i   vi   v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_194095963_   1217 TTTGCAAATTTAATCTCTGCATTCAATGTAATCCAAATGAAAATATCAAT 1266
                         i iv v  v  i    viiv      i i     vv  v     vi  ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr1_194095963_   1267 AGGATTTTTTTTTGTAGAAATTGATAGGCTGATTCTAAAATTTGTATGGA 1316
                         v ---ii       i         i i      i        ii      
  L1M4_orf2#LINE/    108 TG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr1_194095963_   1317 AAGCCAAAGGAAATAAAACAATAAAAACCAATTTGGAAAAGATGAACAAA 1366
                           vv   i   vvi i  i iiv     v vi   i      v       
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_194095963_   1367 GTTGAAGGACTCACACTATCTGACTTCAAGATCTGTTATAGAAGC-ACAG 1415
                             i            vi ii i     i ii ii  i -    -    
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA-AAGCTACAG 253

  chr1_194095963_   1416 CAATCAAGATAATGTAGAGTTGGCA-AAGGATAGAAATA----------- 1453
                         i        i i   i vii     -         v   -----------
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_194095963_   1454 AACACAATAAAGAATGCAGAAATAGGCTCACACACTTATGATTAATTCAT 1503
                           i v   vi   i v        ii i  i   i     i i    v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_194095963_   1504 TTTAAACAAAGGTGTAAAG-CGAATCTCTGGAGAAAAGGAAGTCCTCTCA 1552
                            vi    i    iv   - v v  vv   i    iiiv    i i   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_194095963_   1553 ACAAACAAAGCTAGCACAA-TGCATGCAGCCATATTGCAGGGAAATGAAC 1601
                              iiiv   i v    -  v  -- ?   i  -   iiii      v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGAT--AKCCACAT-GCAAAAGAATGAAG 450

  chr1_194095963_   1602 TTCAACTCAAATTTTATACAATCAAATGCAAAAACTAACTCCA------T 1645
                           vi  i vv ii i i  v  ---  i      i      v ------ 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCAT---ATACAAAAATTAACTCAAAATGGAT 497

  chr1_194095963_   1646 TA-AAACTCAGATTTAA----------TATAAAACT--TCGAAGAGAACA 1682
                         i - i  ii i  v   ----------         -- v     i    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_194095963_   1683 CAGA---AAATATCTGGGATCTTGGGCTCAGCAAAGATTT-TTAAA-ATT 1727
                         i  i---    v ii v  i      i vi    v i   -   i -  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_194095963_   1728 ATACCTAAAAAAGTACAAATGATATAAGGGAATCT-GATAAATTGCACTT 1776
                          i   ---     i    iii i v   ii  vv -         v    
  L1M4_orf2#LINE/    598 ACACC---AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_194095963_   1777 CACCAAAATTAAAAGTTTCAGCTCTTTGAAAGACACT--TAAAAAAATAA 1824
                           i           ii  iv iv   ii  i      --i  i   i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_194095963_   1825 GAAGACAAACCACAGAATGTGA--AAATATT-GCAAAACATGTTTTTTCT 1871
                         i       v          v  --       -     v   i v i vv 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_194095963_   1872 TACATATTGATATTCAGAATATTTAAAGAGCTCTCAAAACTCAAGAATGT 1921
                         v viv i vi   i        v      i    i v       v   iv
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_194095963_   1922 AAA--CAAA----CCAGTTTAAAAATATACAAAAAATTTAAATAAATACT 1965
                            --    ----   i  ?      ivi    ii    i    i i i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_194095963_   1966 TCATCACATAAGATA--------GCAAATAAGCACATGAAAAGATACTCA 2007
                           vi  v v      --------  v                   i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_194095963_   2008 ATATCAATAACATG 2021
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (147 / 77)
Gap_init rate = 0.03 (25 / 901), avg. gap size = 2.88 (72 / 25)  


2842 25.65 1.52 2.83  chr1_194188936_194194222     3875  4794 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_194188936_   3875 TGGAAACACATCC-ATGCTCATGGATGCATAGAATAAATATTGTGAAAAC 3923
                               v i    -   i        vviv   v v        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_194188936_   3924 AAC--TACTGCCTAAAGCAATCTGCAGATTCAATACAATTCCTATCAAAA 3971
                         ii --    v  i   vii    i         ii    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_194188936_   3972 TACCACCATCTTTCTTCACAGAACTAGAAAAAC-AATCCTAAAATTCTTA 4020
                          v   v vv i  i  ii     v v  v  i -i            v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_194188936_   4021 TGGAACCATAAAAGAGCCCACATAACCAAAGTAATACTAAGCAAAAAGAA 4070
                              viii  ii  v  viv   i     ii   vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_194188936_   4071 CAAATCTGGTGGCATCACATTACACAAATTCAAATTATACTACAAGGCTA 4120
                             vi   v  vv     i v v   v      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_194188936_   4121 TTGTTACCAAAATGGCATGGTACTGGTATAAAAATGG-CATGTAGTCCAA 4169
                         iv  v i   i ii ii         i    ii  i -   i   vi   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_194188936_   4170 TGGAACAAAACAGAAAACCCAGAAATAAAGCCAGA----TACAGCCAACT 4215
                              i i  iv  i ii           v   v ----  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_194188936_   4216 GATCTTCAACAAAGCATACAAAAAC-AT-AAATCAGGGAAAGGACACCCT 4263
                            i   i    i -i i v  i  -  -v   -i       i i vi  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCT 398

  chr1_194188936_   4264 ATTCAATAAATGGTGCTGGGAAAACTGGCAAGCCATATGTAGAAGAATGA 4313
                         v     i              v      vv ?   i   i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_194188936_   4314 AACTAGATCTTCATCTCTCACCTTATA-AAAAATCAACTCAAATTGAATA 4362
                          ii i  i iii i   v    v    -      i        v  i  v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_194188936_   4363 AAAAACTGAAATCTAAAACCTGAAACCATAAAAATCCTAGAAGATAACGT 4412
                          ? i  iv    v   i v  i    i      v  i       v   i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_194188936_   4413 TGGAAAAACTCTTCTGGACATTGGCTTAGGCAAAGAATTCATGACTAAGA 4462
                         v  ?iv  v     vv   v    v        v iv   v iiv  v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_194188936_   4463 CCTCAAAAGCAAGTGCAACAAAACCAAAAATAAATAAATGGGACCTAACT 4512
                          vi        viv         vv       i      v    i v ii
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_194188936_   4513 AAACTGAAAGGCTTCTGCATAGCAAAAGAAATAATCAGCAGGGTAAACAG 4562
                            v v   ii   i  iiivv    i  v iv    iv ii  i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_194188936_   4563 ACAACCCACAGAGTGTGAGAAAATATTCACAAACTGTGTATCCAAGAAAG 4612
                                     i  v           ii    iii i    ii v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_194188936_   4613 GACTAATATCCAGAATCTACAAGGAACTCAAACCAATCAGCAAAATAAAT 4662
                             vi          v  i  i      vv  v v   ---------  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA---------AT 789

  chr1_194188936_   4663 AAATAAATAAAATAAAATAATAAAAATAATAATCCCATCAAAAAGTGGGC 4712
                           -    -  i i   -------------   i  v  i?    i     
  L1M4_orf2#LINE/    790 AA-TAAA-AAGACAAA-------------TAACCCAATTWAAAAATGGGC 824

  chr1_194188936_   4713 AGAGGGCATGAATAGACAATTCTCAAATGAAGATATACAAACAGCCAACA 4762
                          i   iiv          v     v  v             ii     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_194188936_   4763 A--ACATGAAAAAATGCTCAACATCACTAATTAT 4794
                          --         i             ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  


 231 21.05 0.00 0.00  chr1_194232528_194235441      446   502 (2412)  C L1M4_orf2#LINE/L1   (0)   908   852  

C chr1_194232528_    502 AGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCAC 453
                               i  vi viii     v  i        i i       v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

C chr1_194232528_    452 TGGCCAT 446
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.00 (0 / 0)  

3084 26.67 0.70 0.70  chr1_194232528_194235441     1551  2405 (509)    L1M4_orf2#LINE/L1        1   855 (53)  

  chr1_194232528_   1551 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1600
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_194232528_   1601 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1650
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_194232528_   1651 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1698
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_194232528_   1699 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1748
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_194232528_   1749 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1798
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_194232528_   1799 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1848
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_194232528_   1849 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1896
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_194232528_   1897 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1946
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_194232528_   1947 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1996
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_194232528_   1997 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 2046
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_194232528_   2047 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 2096
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_194232528_   2097 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 2146
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_194232528_   2147 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 2196
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_194232528_   2197 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2246
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_194232528_   2247 AGGCAACCTACAAAATGGGAGAAAATTTTCGCA--TCCTACTCATCTGAC 2294
                           i     i   i             v  i   --  v  i--      i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGAT 744

  chr1_194232528_   2295 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 2344
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_194232528_   2345 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 2394
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_194232528_   2395 TCTCAAAACAA 2405
                             v   v  
  L1M4_orf2#LINE/    845 TCTCCAAAGAA 855

Transitions / transversions = 1.49 (134 / 90)
Gap_init rate = 0.01 (7 / 855), avg. gap size = 1.71 (12 / 7)  


1849 22.96 1.89 5.19  chr1_194255276_194256903      500  1135 (493)    L1M4_orf2#LINE/L1      294   908 (0)  

  chr1_194255276_    500 AGACCAAGGGAACAGAATAGAGACACCTGAAATAAAGCTGCACACCTACA 549
                            i   v    i     v    vv  v        v iii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_194255276_    550 ACCAACTGATCTTTAACAAAATTGACAAAAATAAGTAATGGTGAAAGA-C 598
                         ii   i    i  ii    iiv  v   i vi vvi     v      -i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_194255276_    599 ACCCTTTTCAATATATG-TGCCAGGAAAACTGGCTAACCATATGCAGAAG 647
                          vi        i v   -   ii   v      v  ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_194255276_    648 AATGAAACTGGAGTCTTACATCTCAAGATATATTAAAAAAAATTAACTCA 697
                               ii    vi i   v  v  vv     i----             
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATAC----AAAAATTAACTCA 489

  chr1_194255276_    698 AGGTGAATTAAAGACTTAAATGTAAGACCTCAAACTAAAAACCTTTCTCC 747
                          ii  i  i ?    i           v  v      v   v  i ----
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT---- 535

  chr1_194255276_    748 CTAGAAGAAAACCTTTCTTCCTAGAAGAAAACCTAGGAAATACCTTTCCA 797
                         -           v --------  i? v   i  ------------  vv
  L1M4_orf2#LINE/    536 -TAGAAGAAAACAT--------AGGNGTAAATCT------------TCGT 564

  chr1_194255276_    798 GACACTTGC-CTAGGCAA--ATAACCTATGACTAAGTCTTCAAAAGTAAA 844
                            -    v-i       --i vv i  -  -  v v vi      i v 
  L1M4_orf2#LINE/    565 GAC-CTTGGGTTAGGCAATGGTTTCTTA-GA-TATGACACCAAAAGCACA 611

  chr1_194255276_    845 TGTAACAAAACCAAAAATTGA-AAATTGGGGCCCAATTAAACTAAAGAGC 893
                         v i       vv      v  -       ivii  - i   v v  i i 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCA-TCAAAATTAAAAAC 660

  chr1_194255276_    894 TTCTGCACAGCAAAAGAAACTATCAATGGAGTAAACAGACAACCTACAGA 943
                           i  ii vv    i  v        vii   i  v        i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_194255276_    944 ATGGGAGAAAATACTGGCAAACTATGCATCCAACAAAGGACTAATATCCA 993
                                      i v     ii  ii   ii i  i     vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_194255276_    994 GAATCTATAAGAAACT--TA-AAC-CAACAAGAAAAAAACAAGTAACTCC 1039
                             v     ii    --  -   -   i  v     i    i    i v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_194255276_   1040 ATTAAAAATTGGGCAAAGGACATGAACAGACACTGCTCAAAAGAAGATAT 1089
                            ?    v           iv    i     i v   v           
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_194255276_   1090 A--AGTGGCCAAGAAACATATGAAAGAATGCTCAACATCACTAATCAT 1135
                          -- i       v  i  i      ii             ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (84 / 58)
Gap_init rate = 0.03 (17 / 615), avg. gap size = 2.65 (45 / 17)  


2902 23.03 9.79 1.43  chr1_194267296_194270473     1848  2685 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_194267296_   1848 TAGAAAAATATTCCATGTTCATGTGTTCATGGATGGAAGAATTAGCATTG 1897
                          i    i    i           vi  -------      v   ii    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT-------GGAAGACTTAATATTG 43

  chr1_194267296_   1898 CTAAACTATCCATACTACCCAAAGGGATCTACAG-TTCAACGTAATTCCT 1946
                         i   iv iv v     v      vv         -       i   i   
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr1_194267296_   1947 ACCAAGGTTCCAATGATATTTTTCTCAGAAATATAAAAATCAATCCTAAA 1996
                          i   ii i   iiviiv     iv       vv v  iiii        
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_194267296_   1997 ATTCATATGGAACCACAAAAGACCTCAAATAGACAAAACAATCTTGAATA 2046
                                     vii   ii    ivi     v               v 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_194267296_   2047 AAAGGAGCAAAGCTGGAGACATCACATTATCTGATCTCAAAATATACTAT 2096
                          i i  i     i     ivv     i vi ii  i      iv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_194267296_   2097 GAAGCCATAATAACCAAAATGGCATGGTACTAGCATAAAAACAGATATAC 2146
                         i    i i i   i   i ii ii       i      ii i   i   i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_194267296_   2147 AGA-CATATGAAATAGAATAGAAAACCCAAAAATAAATCCATACATTTCC 2195
                            -  -   i        v  i ii   i       i          vi
  L1M4_orf2#LINE/    294 AGATCA-ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_194267296_   2196 CATCAACTGATCTTCAACTAAGGTGCTAAGAACACAAAATGGAGAA---- 2241
                         vi    i    i   i  v i     i    v  ivv     i   ----
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_194267296_   2242 --------------------------------GGACATCCATGTGCAGAA 2259
                         --------------------------------   i ?   ii    i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_194267296_   2260 GAATAAAATAGGGCACTTATCTCAGATTATATATAAAAATCAATTCAAAA 2309
                             i  i v  i v i  i    v ii     i      i  i      
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_194267296_   2310 TGGATT-TA----TAAACATAAGACCTGAAACCATAAAACTACAAGAAGA 2354
                              i-? ----    ii     v  i    i        viv      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_194267296_   2355 AAACACAGGGGAAAAGCTTCTCAACACTGGTCTGAGCAAAGATTTTTTGG 2404
                              i   ? v   v    vii  vi   vi ii    v i   i  i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_194267296_   2405 ATCATGACTTCAAAAGCACAGGCAACGAAAGCAAAAATAGACAAATATGA 2454
                           -     vi          i     i    v         i    vv  
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_194267296_   2455 TTACA------------------------CAAAGGAAAT----AACAGAG 2476
                         i v  ------------------------       v i----  v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_194267296_   2477 TGAAGAGACAATCTCTGCAATGGGAGAAAATATTTGTAAAT--TATATCT 2524
                             i      i iviiv                  i    --       
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_194267296_   2525 GATAAGGAATTGATATCCAAAATATATAAAGAACTCAAACAAAT---TAA 2571
                                i i vi      i                vv    v ---   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_194267296_   2572 TAAGAAAATAAATAACCCAATT-AAAAATGGGCAAAATATTTGGAAAAAA 2620
                            i  i i             -             iv     ---  v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG---AATA 838

  chr1_194267296_   2621 AACATTGATCATAAGAAGACATACAAATGGCCAACAG-----TGAAAAAA 2665
                         i     vv  vv       i              i i-----      i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_194267296_   2666 TGTTCAACATCACTAATCAT 2685
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (130 / 60)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 6.27 (94 / 15)  


1996 24.90 1.36 0.39  chr1_194324868_194330225        1   514 (4844)    L1M4_orf2#LINE/L1      145   663 (245)  

  chr1_194324868_      1 TTTCTATCGAGAAGCAAAAGACACAGAATAGTCAACACAATTCTGAAA-- 48
                           iv   v  i v    ii   v        i   v     ii     --
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_194324868_     49 ---GAACAAAGTTGGAGGACTGACACTATCTGAGTTCAAAACTTATTATA 95
                         ---                  v     vi ii v           i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_194324868_     96 AAGCTACAATATTCAAAACAGTGTAGCATTTATAAAAGAACATACAATTA 145
                                 i  v    i       i i i vii v   i i v   vv  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_194324868_    146 GATCAATGAAACAGAATAGAGAGCCCACAAATAGACCCACATAAATATAA 195
                                 i  i     v     i   v     i     i i vv   ii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_194324868_    196 TCAACTAATCTTTGACAAAGAAGCAAAGGCAATACAATGAATAAAAGACA 245
                             i i  i  i     i iv  v   i v  v     iiv   ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_194324868_    246 GTCTTATCAATAAATGGTGCTGGAAGAAGTGGACATCCACATGCCAAAAA 295
                              v    i            i v  v    i ?        -    i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-AAAAG 443

  chr1_194324868_    296 AATGAATCTAGATACAGTCCTCACACTTTTCATGAAAATTTACTCAAAAT 345
                               vi i  iv vvv        iv vi ii      v         
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_194324868_    346 GAATCACAGACCTAAATGTAAAATGC-AAAACTATAAAACTCCTAGAGGA 394
                          i    ?              i -  -               i    i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_194324868_    395 TAATACAGGAGAAAATCTACATGAACTAGGGCTTGGCAATGACTT-TTAG 443
                         v  i i   ? v      v i   v  v   i v       ii  -    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_194324868_    444 AGACAACACCAAAGTCATGAACCATGAAAAAATTAATTGATAAGCTGGAT 493
                          v ii        iv  ii i v ii   i  vv   v     ii    i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_194324868_    494 TTCATTAAAACTGGAAACTCT 514
                              i    i ii     i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTT 663

Transitions / transversions = 1.72 (79 / 46)
Gap_init rate = 0.01 (5 / 519), avg. gap size = 1.80 (9 / 5)  

3239 27.31 0.44 0.44  chr1_194324868_194330225     3958  4865 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_194324868_   3958 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCATGAAAAT 4007
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_194324868_   4008 GGCCATACTGCCCAAGGTATTTTATAGATTCAATGCCATCCCCATAAAGC 4057
                            v     v     iv iv i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_194324868_   4058 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4105
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_194324868_   4106 TATAGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4155
                            i   viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_194324868_   4156 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4205
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_194324868_   4206 TATAGTAACCAAAACAGTGTGGTACTGGTACCAAAACAGATATATAGATC 4255
                           i     i   i               i iv ii i   i         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_194324868_   4256 AACGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATAACTACAACT 4303
                           i    i    i--    i  --        vv  ii i vi  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_194324868_   4304 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAACGATTCC 4353
                          vi    i  i     ivv  v   i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_194324868_   4354 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4403
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_194324868_   4404 GAAACTGGATCCCCTCCTTACACCTTTTACAAAAATTAATTCAAGATGGA 4453
                            ii    i   iv   i     v v            i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_194324868_   4454 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4503
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_194324868_   4504 CTAGGTGTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4553
                         v    ?  v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_194324868_   4554 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4603
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_194324868_   4604 TTAAACTAAAGAGCTTCTGCACAGCAAAAAAAACTACCATCAGAGTGAAC 4653
                          i   v v  i i   i  ii vv    ii v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_194324868_   4654 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 4703
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_194324868_   4704 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4753
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_194324868_   4754 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 4803
                          i     i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_194324868_   4804 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 4853
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_194324868_   4854 ATCACTGGCCAT 4865
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2105 25.29 3.31 0.33  chr1_194349804_194351400      500  1104 (493)    L1M4_orf2#LINE/L1      286   908 (0)  

  chr1_194349804_    500 AGACACATGGACCAATGGAACAGAATAGAGAACCCAGAAATAAACCCAAA 549
                              i  i  i        i     v    ii               v 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_194349804_    550 TACTAACAGCCAACTGATCTTCGACAAAGCAAACAAAAACATAAAGCAGA 599
                         i i v ii i   i    i        i vviv   i v   vv iii i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_194349804_    600 GAAATGACACTCTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACA 649
                             vi i v                        i  i   v  ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_194349804_    650 TGTAGGAGAATGAAACTGGATCCTCATCTCTCAGCTTATACAAAAAGCAA 699
                           i ii        ii    i  ii i   v  v v          vi  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_194349804_    700 CTCAAGATTGATCAAGGACTTAAATCTAAGATCTGAAACTATAAAACTTC 749
                              i  v     ?i   i     v     v  i             ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_194349804_    750 TAGAATAAAACACTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGAT 799
                              v      iv  ?iv  vi    vv   v    v        v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_194349804_    800 CTCATGACCAAGAAACCAAAAGCAAATGCAATGAAAACAAAGATAAATAG 849
                         i  v iivi v  v          v v    ii   iv   i   i   i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_194349804_    850 TTGGGACTTAATTAAGCTAAAGAGCTTTTGCAGGGCAAAAGGTAC-AGTA 898
                         v v      v  i  iv v  i i      iivvv    i ii  - vi 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_194349804_    899 AGCAGAGTAAACAGACAACACATAGAATGGGAGAAAAT-CTCACAGTCTA 947
                           - i   i  v       v  i               -i ii  ivii 
  L1M4_orf2#LINE/    686 AG-AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_194349804_    948 TACATCTGAT-----------GTTCAGAATCTACAATAAATTCAAACAAA 986
                           i       -----------i i      v  i  vi  i  vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_194349804_    987 TCAGTAA-----AAATAAACAATCCCATTAAAAAGTGAGCTAAGGACATG 1031
                            i   ----- i i   i  i  v   ?    i  i  v     iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_194349804_   1032 AATAGACATTTCTCAAAAGAATATATTCAAATGGCCAACAA--ACATGAA 1079
                                       v      v    v           i  --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_194349804_   1080 AAAAAAGCTTAACATCACTAATGAA 1104
                           i -v   i       ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (90 / 59)
Gap_init rate = 0.01 (7 / 623), avg. gap size = 3.14 (22 / 7)  


2607 26.85 4.55 1.37  chr1_194397889_194402132     2873  3751 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_194397889_   2873 GGAAAAGCATTCCATCCTCATGAATAGGAAGAATCAATATCATGAAGATG 2922
                              iii  i    vi     i  v      v i     ii v      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_194397889_   2923 GCCATACTGTCCAAAGTAATTTATAGATTCAATGTTATTTCCATCAAACT 2972
                           v     vi     v i  i  i        i iv  ii i      v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_194397889_   2973 ACCA-TTAAATTCTTCATAGAATTAGAAAAAAACT-ATTTTAAATTTCAT 3020
                         v   -i ivv  i  iii    v v  v  i--  -  ii    v     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCAT 149

  chr1_194397889_   3021 ACGGAATCAAAGGAGACTCCATAGAGCCAAGTAAAAAGTAAAACCCTAAG 3070
                          i    viiv i i   i viv v      i-------- v  i i i i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAA--------ACAATCTTGAA 191

  chr1_194397889_   3071 TAAAAAGAACAAAGTTGGAGGCATCACGCTACCTGACTTCAGACTGTATT 3120
                         v  i                 vv    i  v  ii i    i viv  i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_194397889_   3121 ACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAACAT 3170
                             i          i   i    ii         i iv ii i i    
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_194397889_   3171 ATAGACCAATGGAACAGAAAAGAGACCTCAGAAATAACACCACACACCTA 3220
                              i        i    vv    vii         vv   i   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_194397889_   3221 CAACCATCTGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGGAAAGG 3270
                         iiii  vi    i  i i   ivv  v   i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_194397889_   3271 ATCTCCTATTCA------GGAGCTAGGAAAACTGGCTAGCCATATGCAGA 3314
                           vvi  v    ------  v   i   v      v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_194397889_   3315 AAACTGAAACTGGACCACTGCCTTACACCTTATACAAAAATTAACTCAAG 3364
                          i v    ii      v  i   i     v                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_194397889_   3365 ATGGATTAAAGATTTAAATGTAAAACCAAAAACCATAAAAACTCT-AGAA 3413
                               i ?   ii         i v v     i      -    -    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAA 540

  chr1_194397889_   3414 GAAAACCTAGGCA-ATATCATTCAGGACACAGACATGGGCAAAGACTTC- 3461
                               v    ?i- v   -   iv   viv ivv i     v ii   -
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_194397889_   3462 -----ATGACA---AAAACAACTTCAACAAAAGCCAAAATTGATAAATGA 3503
                         -----      ---   i  vvvv         vv     v       vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_194397889_   3504 GATGTAATTAAACTAACAGA------------AAAAGAAACTATCATCAG 3541
                           iv v  i   v v v i ------------   i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_194397889_   3542 AATGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCCACCTAT 3591
                          i    v  i     i                 v       vi  iv   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_194397889_   3592 CTGGCAAACGTCTAATATCCAGAATTTACAAGGAACTTAAACAAATTTAC 3641
                            ii  iv v  vi          v  i  i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_194397889_   3642 AAGAAAAA-----ACAACCCCATCAAAAAGTAGGCAAAGGATATCAACAG 3686
                           v     ----- i     v  i?    i i          v v  i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_194397889_   3687 ACACTACTCAAAAGAAGACATTTATGCAGCCAACAAAC----GAGAAAAA 3732
                            i v   v        i  vi viii     i  i ----  i  i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_194397889_   3733 GCTTAACATCACTGATCAC 3751
                            i       ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (135 / 97)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 3.71 (52 / 14)  


3327 26.76 0.44 0.44  chr1_194408002_194414282     4881  5788 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_194408002_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_194408002_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_194408002_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_194408002_   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_194408002_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_194408002_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_194408002_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_194408002_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_194408002_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_194408002_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_194408002_   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_194408002_   5427 CTAGGCATTACCATTCAGGACATAGGAGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  iv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_194408002_   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_194408002_   5527 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_194408002_   5577 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_194408002_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_194408002_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_194408002_   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_194408002_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1767 28.46 2.24 0.81  chr1_194493575_194499693.rev     4045  4536 (1583)    L1M4_orf2#LINE/L1        1   499 (409)  

  chr1_194493575_   4045 TAGAAAAACATTTTATGCTCATGGATAGGAAAAATCAATATCATTAAAAT 4094
                          i    i i  iii   i        v    i v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_194493575_   4095 GGCCATACTGTCCAAAGCAATTTACAGATTTAGTACTATTCCTATCAA-- 4142
                            v     vi     vii  i        i iii v  i        --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_194493575_   4143 ------TTACATTCTTCACAGAATTAGAAGAAAACAACTGTAAAATTCAT 4186
                         ------i i v  i  ii     v v - v  ivii iiv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr1_194493575_   4187 ATGGAA-TGCAAAAAGAGCTCA-AATAGCCAAGGCAATCCTAAGCAAAAA 4234
                               -     --i ii i  -         ii     i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAA--GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_194493575_   4235 GAATAAAGCTGAAGGCATCATGCTACCTGACTTCAAATTTATACTACAGG 4284
                            i    i  i   vv   ii  v  ii i      vi -       ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr1_194493575_   4285 GCTATAGTAACCAAAACAGCATGGTACTGCTACAAAAACAGACACATGGG 4334
                             i     i   i    ii        vi i  ii i     i  i i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_194493575_   4335 CCAATGGAACAGAATAGAGGGCCCAGAAATAAGGCTGCATACCAACAAAC 4384
                         i        i     v   i i          iv iii i iiv iiiv 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_194493575_   4385 ACGTGATCTTCAACAAAGCTGACAAAAACAAGCAATGGAAAAGGACT-CC 4433
                          vv    i   i    i v  v   i v  vv      ii  i  v -vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_194493575_   4434 CTATTAAATAATTGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGATC 4483
                           v  v  i  v           i      v  ?   i     i    vi
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_194493575_   4484 AAGACTGGACCCCTTCCTTACACCGTATACAAAAATCAACTTAAGATGGA 4533
                         i iii         v   i     i           i    i  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_194493575_   4534 TTA 4536
                          i 
  L1M4_orf2#LINE/    497 TCA 499

Transitions / transversions = 2.76 (102 / 37)
Gap_init rate = 0.01 (7 / 499), avg. gap size = 2.14 (15 / 7)  

 899 26.23 2.19 3.55  chr1_194493575_194499693.rev     4835  5200 (919)    L1M4_orf2#LINE/L1      489   849 (59)  

  chr1_194493575_   4835 AAGATGGGTTAAATACTTAAATATAAAATGTAAAACTATAAAAACCCTGG 4884
                           i    i i ? v  i     i   i vv             vi i i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_194493575_   4885 AAGATAACCTAGG---AAATACCATTCTGGACATAGGTACAGGGAAAGAT 4931
                             v   v    ---    -- v iv  iv v i   -i   v  v i 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGT-TAGGCAATGGT 585

  chr1_194493575_   4932 TTCAT-GATGAAGATGCTAAAAGCAATTGCAACAAAC-AGAAAATTGACA 4979
                            v -   - v  ii i       vvv        v- i     v  i 
  L1M4_orf2#LINE/    586 TTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_194493575_   4980 AATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAGAAGAAACTATC 5029
                            v   ii v  i   v v  i i   i  ii vv  i i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_194493575_   5030 AACAGAGTAAATAGACAACCTACAGAATGGGAGAAAGTATTTGCCAACTA 5079
                           v i   i  v        i               i       v  ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_194493575_   5080 TGCATCCAGCAAAGGTCTAATATCCAGAATCTATAAGGAACTTAAACATT 5129
                          ii   iiii  i  v  vi          v     i     i-----  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC-----TT 779

  chr1_194493575_   5130 ACAAGCAAAAAAAAAAAAAAAAAAAAAAAAACTCACT--AAAAGTGAGTA 5177
                             viv  v  v     i v   v  ---- i  v --    i  i i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAA----CCCAATTWAAAAATGGGCA 825

  chr1_194493575_   5178 AAGAACATGAACAGACACTT-TCC 5200
                            i iv    i     i  -   
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCC 849

Transitions / transversions = 1.38 (55 / 40)
Gap_init rate = 0.03 (10 / 361), avg. gap size = 2.10 (21 / 10)  

 334 20.27 0.00 0.00  chr1_194493575_194499693.rev     5555  5628 (491)    L1M4_orf2#LINE/L1      835   908 (0)  

  chr1_194493575_   5555 AACAGACACTTTTCAGAAGAAACCATATATGTGGCCAAGAAGCATATGAA 5604
                           i     i  i  vi     ivi   i vi       v     i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_194493575_   5605 AAAATGCTCAACATTACTAATTAT 5628
                           i           i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.00 (0 / 0)  


 245 22.00 0.00 0.00  chr1_194530043_194535822      352   401 (5379)    L1M4_orf2#LINE/L1        1    50 (858)  

  chr1_194530043_    352 TGGAAGAATGTTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 401
                              ii  i i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.00 (0 / 0)  

3282 26.65 0.44 0.44  chr1_194530043_194535822     4380  5287 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_194530043_   4380 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCATGAAAAT 4429
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_194530043_   4430 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4479
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_194530043_   4480 TACCAATGACTTTCTTCACAGAATTGGAAAAATCTAATT-TAAAGTTCCT 4528
                          v   iivi i  i  ii     v v  v  i-  i  i-    i   v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_194530043_   4529 ATGGAACCAAAAAAGAGCCCACATCGCCAAGTCTATCCTAAGCCAAAAGA 4578
                               viiv  ii  v  viv  v     iv v   i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_194530043_   4579 ACAAAGCTGGAGGCATCACACTGCCTGACTTCAAACTATACTACAAGGCT 4628
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_194530043_   4629 ACAGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGAGATATAGACAA 4678
                                i   i    ii     v   i iv ii i   v       iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_194530043_   4679 ATGGAACAAAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAGCTA 4726
                               i i  i--    i  --        vv  ii i  i  ii ii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_194530043_   4727 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 4776
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_194530043_   4777 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4826
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_194530043_   4827 AAACTGGATCCCTTCCTTACAACTTATACAAAAATTAATTCAAGATGGAT 4876
                           ii    i    v   i   v v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_194530043_   4877 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4926
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_194530043_   4927 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4975
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_194530043_   4976 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5025
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_194530043_   5026 TTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCACCAGAGTGAAC 5075
                          i   v v  i i   i  ii vv       v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_194530043_   5076 AGGCAACCCACAGAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5125
                           i                       v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_194530043_   5126 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5175
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_194530043_   5176 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5225
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_194530043_   5226 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5275
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_194530043_   5276 ATCACTGGCCAT 5287
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


 263 21.13 0.00 4.23  chr1_194575454_194580401.rev      318   388 (4559)    L1M4_orf2#LINE/L1      679   746 (162)  

  chr1_194575454_    318 ACTATCATCAGAGAGAACAAGCAACCTACAGAATGGGAGAAAAGTTTTGC 367
                                vv i  v   v ii     i                vv     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_194575454_    368 AATCTATCCATCTTTGGATAA 388
                           vii  vi    ---     
  L1M4_orf2#LINE/    729 AAATCATATATCT---GATAA 746

Transitions / transversions = 0.88 (7 / 8)
Gap_init rate = 0.01 (1 / 68), avg. gap size = 3.00 (3 / 1)  

2641 20.00 3.64 1.16  chr1_194575454_194580401.rev     3174  3778 (1169)    L1M4_orf2#LINE/L1       21   640 (268)  

  chr1_194575454_   3174 ATAAATCTAAAAATTTAATATTGTGCAGATGTAACTACTACCTAAAGTGA 3223
                           ii  ivi  i i          vv     vv v    v  i   v   
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr1_194575454_   3224 TCTACAGATTTAATGCAATCTTTGTCAATATCCTAATGACTTATTTTTTG 3273
                                   i  i      ii i    v    i iivi i --      
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT--TTTTTG 118

  chr1_194575454_   3274 CAGAAATAGAAAAACCCATTCTGAAATTCAAATGGAATCTCAAGTGACCC 3323
                                v  v  i iv  i  i       v      viv    v     
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr1_194575454_   3324 CAAATAGCCAAAACAATCTTGCAAAAAAAGAATAAAG----A------AT 3363
                         vi                   v    i     i    ---- ------ i
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_194575454_   3364 ATGTCCTGATTTCAAAACTTACTACAAAGCTACAGGAATCAAAACAGTG- 3412
                          iv   ii                           v      i      -
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_194575454_   3413 GG-----GCATAAAAACAGACATATAGACCAATGGAATAGAATAGACAGT 3457
                           -----      ii i           i              v  v   
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_194575454_   3458 TCCAAAACAA--TCATTGCATATATTGTCAAATGATTTTAGACAAGGGTG 3505
                         i vi   i  --i   -i   v   v     v       v          
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCAT-ACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_194575454_   3506 TCAAGACCATTCAATAGGGAAAAGACAGTCTTTTTAAAGAAGTGGGGCTG 3555
                         i              i      ii i        i  vi  -   v    
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA-TGGTGCTG 416

  chr1_194575454_   3556 GGAAAACTGGATATATCCACATCCAAAAGAATGAAGCTGGATCCTTATCT 3605
                            v         ?--      v             i    i  i  i  
  L1M4_orf2#LINE/    417 GGACAACTGGATAK--CCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_194575454_   3606 AACATCATATACAAAAATTAATTCAAACTGGATCCACCAGCTAA-TGTAA 3654
                         v   i                i     v      v?vv v    -     
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_194575454_   3655 GACCTAAAACTGGACAACTGTTAGAA---AACACAGGGCAAGAGTTTCAC 3701
                           v        iv v    v      ---    i   ?vv i vi   ii
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_194575454_   3702 AACATTGGATTTGGCAATTATTTCTTGGATATGACACCAAAGGCATAGGC 3751
                         i  v    i  v      vi      i              i   i i  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_194575454_   3752 AATAACAATAACAAAAAGACAAATTGG 3778
                           i  -  v  v   v   i       
  L1M4_orf2#LINE/    615 AACAA-AAGAAAAAATAGATAAATTGG 640

Transitions / transversions = 1.31 (67 / 51)
Gap_init rate = 0.02 (12 / 620), avg. gap size = 2.42 (29 / 12)  

1097 17.31 3.53 1.41  chr1_194575454_194580401.rev     4174  4456 (491)    L1M4_orf2#LINE/L1      620   908 (0)  

  chr1_194575454_   4174 AAGAAAAAAAA---AAATCGAACTTCATGGAAATGTAAAAA-TTTTGTGC 4219
                                  v ---    i i       vi    -      -        
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTTTGTGC 668

  chr1_194575454_   4220 ATCAATAGACAACTATCAACACAGTAAAAAGACAACC---AAAA--GGA- 4263
                         v    vi    -       v v   i           --- i  --   -
  L1M4_orf2#LINE/    669 TTCAAAGGACA-CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_194575454_   4264 AAAATATTTACAAATCATCTATTTCATAAGAAATTAATATCCAGAATATA 4313
                                  i        v   i v     ii i vi             
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_194575454_   4314 TAGAGAACTCCTAAAACTCAACAACCAAAAAACCCAAGCAATTTAATTCC 4363
                           i       i  v       i  iv    i  --  ii  iii    ?v
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGAC--AAATAACCCAATTWA 815

  chr1_194575454_   4364 AAAATGAGCAAAGAGCTTAAACAGACATTTCTCCAAACTAGACATATAAA 4413
                               i      iii  i  i               vv   i   i   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_194575454_   4414 TGGCCAATAAGTCCATGAAGAGATGCTCAACAACACAAATCAT 4456
                                    iv      i            v  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (32 / 16)
Gap_init rate = 0.03 (8 / 289), avg. gap size = 1.75 (14 / 8)  


1284 27.48 6.93 6.00  chr1_194586695_194589073.rev     1015  1880 (499)    L1M4_orf2#LINE/L1       19   892 (16)  

  chr1_194586695_   1015 TTATAGATAG--AGACTCAATATAATAGCAATATCAATGGTTCTTACACT 1062
                          i  i   v --     i     vi vivi  iv    iv i ii v i 
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chr1_194586695_   1063 GATCTCTATATTCAGTGTATTTCCCATCATGAAAA--CCAACAGGGATTT 1110
                              vi v     ii i v i  i    ---   --   i v vvv   
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCA---AAATCCCAGCTGCCTTTT 115

  chr1_194586695_   1111 TCACTGAACATGAAAAGCTGATTTTAAAATGAAATCATTCCAAGTGTAAT 1160
                          ii v   vv   v        ii      ----    -----i  v  -
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAAT----TCAT-----ATGGAA- 155

  chr1_194586695_   1161 CATTTTATATGGAAGAGA-----AATAGGCAGACTACTACAGAAGACTTT 1205
                         --------   v   i  -----     v  i -----   ---- ii  
  L1M4_orf2#LINE/    156 --------ATGCAAGGGACCCAGAATAGCCAAA-----ACA----ATCTT 188

  chr1_194586695_   1206 GAAAAGAAAGAACAAGATATGGGGTGGTACT-ACCCTGTTAGATTTCCAG 1254
                              ii        ii -   i -- -   -  v  viivi     v i
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGT-TGGAG--G-ACTCACACTTCCCAATTTCAAA 234

  chr1_194586695_   1255 ATATATTGTAAAAGTAATGCAATTAAGACAACATGG-ACTTGGATAAGTG 1303
                          iv  i ii   iv  vv i   i      iii   -   v v     --
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-- 282

  chr1_194586695_   1304 GTAGTAGACAAATAG-TCATTGGAACATAGCAT--ACATCTCATAAACAG 1350
                         --ii      v    -   v     --   v  -- v vii  v   i i
  L1M4_orf2#LINE/    283 --GATAGACATATAGATCAATGGAA--TAGAATTGAGAGTCCAGAAATAA 328

  chr1_194586695_   1351 ACACACAAATATATAGAAACTTGAT-----ATAA---TGC--AG--TAGT 1388
                           v  i v  v   i vv v     ----- i  ---   --  --i v 
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_194586695_   1389 GGCATTGAAGAAATATGTAGACTATTTAATCAATAGTCCTAGCTTATTTA 1438
                         --  v  ii    v -i   v  v  i  iv   i  v  i vvi vi i
  L1M4_orf2#LINE/    379 --CAATGGGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_194586695_   1439 GATAAGTATATTTTTAAAAAAA-GATGT-------CTATTTCACACTATA 1480
                             ?vi i  vi--    i  -  v  -------   ii      i   
  L1M4_orf2#LINE/    426 GATAKCCACATGC--AAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_194586695_   1481 TATAAAACCCAGCTTCTGCTGAATAAAATACTTCAAAGTGAAAAGTAAAA 1530
                           i    vii i  ivviv  i  v ? v  i v  v  i i iv     
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_194586695_   1531 CTTTAAATTTTCCAAGACAATACATGAGATTA---CTTTATGACTTTTGA 1577
                           v    vi iii ii v  v    ii ?v  ---   ii    i  - i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT-GG 572

  chr1_194586695_   1578 GTTAGGGGAATT-TTTTTCAAACAAGATATAAAAAGCACAAT--ACATAA 1624
                               v-   v-   i i i i v  i iv          v--   -  
  L1M4_orf2#LINE/    573 GTTAGGC-AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA-AA 620

  chr1_194586695_   1625 AGAAAATGATAGATAAATTTGACTAAAGTAAAATTAAA--CTTCTGTTCT 1672
                               -i           v    vv vi         --   i   v  
  L1M4_orf2#LINE/    621 AGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_194586695_   1673 TCAAAATACACCAT---AAAAGTAAAGAGGCAGGCCACAAACTGGGAGAA 1719
                              iv    i  ---i     i  i  i  iv     i v        
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_194586695_   1720 AATATTTGTAA--CATATAACTGACAAAAGATTATTGTCCAGAA-ATATA 1766
                                 i  --      v    i  ii  i vv i       -     
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_194586695_   1767 ATAAACTCATACAAACTGGTAAGAACAATACAAAT----TAAT---AAAA 1809
                          vi     v     viiii   v  v  v      ----i   ---    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_194586695_   1810 TGT-CAAAAGACATGAACAGTTATTTC----AAGAAAATAAAACATAAAT 1854
                           v-    i  iv    i  vi     ----     i   ---i i    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA---TACAAAT 866

  chr1_194586695_   1855 GTCTAATAAAAGTATGAAAAAATGCT 1880
                          v i     ivii       i     
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.05 (43 / 874), avg. gap size = 2.60 (112 / 43)  


3133 23.43 2.65 2.32  chr1_194757889_194760814.rev     1532  2436 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_194757889_   1532 TGAATAAATGAACCCCTTGTTCACGGGTCAGGAGAGTCAATATTGTTAAT 1581
                           i v i  -- i   v      i  i ii i   v i           v
  L1M4_orf2#LINE/      1 TGGAAAGAT--ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_194757889_   1582 ATGTCAACTTTTCCCAAATTGAGCTATAGATTTA-C-CAATCCCATTCAA 1629
                            v   ivi i          v   i     i - -       vv    
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_194757889_   1630 AATCCCAGCAAGCTTTATTTTTTTTAAAAATAAACAAGCTAATCATAATA 1679
                                  v-  i  ---    vi i    vi       i   v   v 
  L1M4_orf2#LINE/     99 AATCCCAGCT-GCCTT---TTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_194757889_   1680 TTCATATGTAAATACAAATTATCTGGAAAAGTCAAATCA-TTTAGAAAAA 1728
                                 v    i   ivv i ii   v  i    v  - i v      
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_194757889_   1729 TAAAAACAAAGTTAGAAGAGTAACAGTACCTGATT-CAACATTTATTATA 1777
                         v  i         i  i  v v   v v  ii   -   v i   i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_194757889_   1778 AAGCCAAAATAATCAAGACAGTGTGCTATTGGTGTAAAGGCAAATAAATA 1827
                             i v i                v  i   ii   i ii i i v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_194757889_   1828 CATCAATGGAACAAAACTGTGAATCTAGAAATAAATCCACACATATATGG 1877
                         v          i i  i  v  i  i         i   i    v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_194757889_   1878 TCAACTAATTTTCAAGAAAGGCACAAAGTCCATTCAGTGGGAAAAGGATA 1927
                             i i      i v  i  ii v   v       i    i    i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_194757889_   1928 GTCTTTTTTTAACAA-TGGTGCTGGAACAATTGGAGATATATATATATAT 1976
                                i--     -         i    i    ------  ?vi i  
  L1M4_orf2#LINE/    395 GTCTTTTC--AACAAATGGTGCTGGGACAACTGGA------TAKCCACAT 436

  chr1_194757889_   1977 GCAAAA--ATAAACTTCCATCCATGCCTTGCACTGCATATAAAATTTAAA 2024
                               --  i  v  vv i  v i   ii   iii   i    v    v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_194757889_   2025 AGAAAATGCATTATATACCTAAATGTAAATCCTAAAACTATACAAATTAT 2074
                         vv      v  i ? v            ivv           v  v iv 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_194757889_   2075 AGAAGATTATACATGAGACAATCTTTGTGACCTATGGTTAGGCAAATATT 2124
                               vv i i v ? vv      i       vv          vvi  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_194757889_   2125 TCTTAACTATGAACACCAGAAGCACAATCCATAAAAGAAAAAATTGATAA 2174
                              iv     -     i        v v i            v     
  L1M4_orf2#LINE/    587 TCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_194757889_   2175 ATTATACTTTAACACAATTGAAACCTTCTGCTATTTTAA--GACATTTTT 2222
                            iv    i v  v    i   v   i  - ii  i  --    i v i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATC 684

  chr1_194757889_   2223 AA---AGCCACA-GACTTTCAAAGCCACAAACCATGAAAAAATATTTTCA 2268
                           ---  iv v -   -----  v     i viiv  i         v  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGAC-----AACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_194757889_   2269 AAGTATGTATCTGACAAAAGACTTAAATTTAGAATATATAAAGAGCTCTC 2318
                           vi  i       i  ii     iv  ii              i    i
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_194757889_   2319 AATACTTAAAAGTGAGAAAACAGATACCCCAATTAAGAAACGAGCAAATG 2368
                          vv   i  v i i i  i   i   v       ? i   i i     v 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_194757889_   2369 ATTTAAACAGAG--TTC-ACAAAAAAGAT--------GGCAAATAAGCAC 2407
                             i  i   v--   -v    i     --------   v         
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_194757889_   2408 ATGAAAAGTTGCTCATCATCGTTAGTCAT 2436
                                 v      v    i????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (121 / 87)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.25 (45 / 20)  


2850 25.94 1.88 1.44  chr1_194838583_194842865.rev     2891  3792 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_194838583_   2891 GAAACACATCTCATGCTCATGAATGGGTGGAA-AC--AATATTGTGAAAA 2937
                             v i   i    i     i  ---     -  --        v  i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGAT---TGGAAGACTTAATATTGTTAAGA 49

  chr1_194838583_   2938 TGATCATACTGCCAAGAGCAATCTACAAATTCAATGCAATTCCCATCAAA 2987
                           iiv     v  v i vii       i      i     i  i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_194838583_   2988 ATAGTACCATCATTCTTCACACAACTAGACAAAA-AATCCTAAAATTCAT 3036
                           vvi v vv v  i  ii  v  v v     iv-i              
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_194838583_   3037 ATTGAACCAAAAAAGAGCCCACATAGCCAAAGCAAAAT-GAAGCAAAAAA 3085
                           v   viiv  ii  v  viv         i   vv -   --   i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--AAAGAA 197

  chr1_194838583_   3086 GAACAAATCTGGAGGCATCACACTACCTGACTTCAAACTATACTATAAAG 3135
                                vi      vv       v  ii i      viv     i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_194838583_   3136 CCATAGTCACCAAAACACCACGGTACTGGTATAAAAATAGACACATAGAC 3185
                          i i   v i   i   viii        i    ii       i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_194838583_   3186 CAACTGGACAGAATAGGGAACCCATAAATAAAGCCAGATACTTACAGCCT 3235
                            iv i i     v i  ii   v       v   v i i   ii i v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_194838583_   3236 ACTTATCTTCAACGAAGCAAACAAAAACATAAAGTGGGGAAAGAACACCC 3285
                          i v  i   i  i i vviv   i v   vv i           i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_194838583_   3286 TATTCAACAAATAGTGCTGGGATAATTGGCAAGCCACATGTAGA-GAATG 3334
                          v          i         i  i   vv ?       i i -     
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_194838583_   3335 AAACTAGATCCTCATCTCTCACCTTATACAAAAATCA-CTCAAGATGGAT 3383
                           ii i  i  ii i   v    v           i -     i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_194838583_   3384 CAAGGACTTAAATCTAAGGCCTGAAACCATAAAAATTCAAGAAGATAACT 3433
                           ?i   i     v    iv  i    i      v iiv      v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_194838583_   3434 TTGGAAAAAAGCCTTCTAGACATTGGCTTAGGCAAAGGCTT------TAT 3477
                          v  ?iv   -i    vv   v    v        v  i  ------   
  L1M4_orf2#LINE/    548 TAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_194838583_   3478 GACCAAGAACCCAAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGG 3527
                            -----   --       v v         iv   i   i   i  v 
  L1M4_orf2#LINE/    597 GAC-----ACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_194838583_   3528 GATTTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACAATCAGCAG 3577
                           i  v  i   v v    i   i  ii vv    i  v  v    iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_194838583_   3578 AGTAAAAAGACAATCCACAGAGTGGGAGAAAATCTTCACCGTCTATGCAT 3627
                            i         i       i           v  ii vivii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_194838583_   3628 CCCACAAATGACTAATATCCAGAATCTACAAGGAAATCAAACAAAT---T 3674
                          iv i  iv    vi          v  i  i   v  vv    v --- 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_194838583_   3675 AGCAAGAAGA-AACCAATCCCATCAAAAAGTGGGATAAGGACATGAAAAG 3723
                          ii  i    -  vi  i  v  i?    i    vv     iv    v  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_194838583_   3724 ATAGTTCTCAAAAGAAGATATACAAATGACCAACAAACATATGAAAAAAT 3773
                          i v     v                  i    i  i  i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_194838583_   3774 ATTCAACATCACTAATGAT 3792
                         ii         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (135 / 95)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 2.14 (30 / 14)  


2820 24.72 4.42 1.47  chr1_194914789_194920105     3943  4824 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_194914789_   3943 TGGAAATACATCCCATGCTCAGGGATTGAAAGAATCAATATTGTGAAAAT 3992
                               v i        i   v      i    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_194914789_   3993 GACCATACTGCCTAAAGCAATC--------CTATGAAATTCCTATGAAAA 4034
                          i v     v  i   vii   -------- v i v   i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_194914789_   4035 TACCAA-TATCATTTTCACAGAA-TTAGGAAAAAC-AATCCTCAAATTTA 4081
                          v   i- ii v    ii     -  --  v  i -i     v     i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr1_194914789_   4082 TATGGAAC--CAAAAAGCCCA-AATTGCTAAAACAATCCTAAGCAAAAAG 4128
                                v--   iiii    -   v  i         i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_194914789_   4129 CATAAGTCTGGAAGCATTACATTACCTGACTTCAAATCATACTACAAGGC 4178
                         v i  ivi    i vv i   i v  ii i      v v        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_194914789_   4179 TGTAGTAATCCAAACTGCATGGTACTGGTATAAAAGTAGATGCAAAGACT 4228
                          ii       v i  v ii         i    iii    iii v   ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_194914789_   4229 AATGGAACAGAATAGAGAACCTCTAAATAAAGACAGACACTTAAAACTAA 4278
                                i     v    ii ivv       vv  v   i   viiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_194914789_   4279 CTGATCTTCGACAAAGAATACAAAAACAT-AAATTGGGAAATAGACACCC 4327
                         i    i        i ivvv   i v   -v   v      v - i vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTC 397

  chr1_194914789_   4328 TATTTGATAAATGGCGCTGGGAAAATTGGATAGCCACATGTAGAAGAATG 4377
                          v  ii i      i       v  i      ?       i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_194914789_   4378 AAACTGGATCCCTTTCTCTCACTATATTACAAAAGTTAACTCAAAATGGA 4427
                           ii    i    vi   v   i    -      i               
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGA 496

  chr1_194914789_   4428 TTAAAGATTTAAATCCAAGACCTGAAACTATAAAAATTCTAGAAGAAAAC 4477
                          i ?   ii     vi    v  i           v ii           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_194914789_   4478 CTAAGAAAAACTCTTCTGGACATTGATCTAGGTAAAGAATTTAT-GATAA 4526
                         v  i ?iv  v     vv   v   ivi    i  v iv  iv -    v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_194914789_   4527 AGACTCCAAAAACAAATGCAACAAAACCAAAAATAAATAAATGGGACCAA 4576
                         -   v      i  v v         vv       i      v    ivv
  L1M4_orf2#LINE/    597 -GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_194914789_   4577 ATTAAA-TTAAAAAGCTTCTACACAGCAAAATAAATAATCATCA----GA 4621
                           i   -       -   i iii vv    iv v iv    vv ----  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_194914789_   4622 ATAGACAACCTGTAGAATGGGAGAAAATATTTGCAAATTATGAACCCAAC 4671
                          v        iii                         i  iv i ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_194914789_   4672 AAAGGACTGATATGCGGAATATACAAA---------TAAATCAGCAAGAA 4712
                           i     vi   v i       i   ---------i  v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_194914789_   4713 AAA-------AATCCAATTAAAAGATTGGCAAAAAAAAAAAGCATGAATA 4755
                            -------  i      ?   i  v      ii ------iv      
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA------TTTGAATA 838

  chr1_194914789_   4756 GACATTTCTCAAAAGAAGATATACAAGTGGCCAACAA--ATATGAAAAAA 4803
                                   v               i       i  -- i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_194914789_   4804 ATGCTCAACATCACTTATCAT 4824
                         -            ????????
  L1M4_orf2#LINE/    889 -TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (130 / 84)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.60 (52 / 20)  


3090 27.41 1.22 0.44  chr1_195010483_195016749.rev     4877  5777 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_195010483_   4877 TGGAAGAACATTCCATGCTCGTGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i  i   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_195010483_   4927 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATTCCCATCAAGC 4976
                            v     vi    iv i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_195010483_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_195010483_   5025 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCGAAAAG 5074
                                viiv  ii  v  v v  v     iv     i i ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_195010483_   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_195010483_   5125 TACAGTAACCAAAACAGCATGGTAGTGGTCCAAA-ACAGAGATATAGATC 5173
                                 i   i    ii     v   ivi  i- i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_195010483_   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACGTATCTA----C 5217
                                i    i--    i  --        vv   iii  i  ---- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_195010483_   5218 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5267
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_195010483_   5268 CTATTTAATAAATGGTGTTGGGGAAACTGACTAGCCGTATGTAGAAAGCT 5317
                           v  i  i        i    iv     iv  ?  ii   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_195010483_   5318 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5367
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_195010483_   5368 TTAAAGACTTAAACGTTAGACCTATAACCATAAAAACCCTAGAAGAAAAC 5417
                          i ?    i    i  v   v   v   i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_195010483_   5418 CTAGGCGTTACCATTCAGGACATACCAT-GGGCAAGGACTTCATGTCTAA 5466
                         v    ?  v viv   iv   v vvvi -i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_195010483_   5467 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5516
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_195010483_   5517 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5566
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_195010483_   5567 AGGCAGCCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5616
                           i  i  i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_195010483_   5617 AGG-CTAATATCCAGAATCTACAATGAACTCAAACAAATCTACAAGAAAA 5665
                         i  -  vi          v  i  v      vv    v  v i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_195010483_   5666 AAACAAACAACGCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5715
                          i     i   v v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_195010483_   5716 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5765
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_195010483_   5766 ATCGCTGGCCAT 5777
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2211 23.99 2.92 0.49  chr1_195135692_195137300.rev      502  1118 (491)    L1M4_orf2#LINE/L1      277   908 (0)  

  chr1_195135692_    502 CATAAAAATAGACACATAGAC--ATGAAGCAGAATAGAGAATCAGAAAAT 549
                              ii       i     i--   i ii     v    i  vii    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_195135692_    550 AAGCCAATACATTTA-GGCCAACTGATCTTCAACAAAGCCAGCAAGAGTG 598
                           i  v         -  i   i    i   i    i viiv     vii
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_195135692_    599 TTCATTGGGGAAAAAACCCCATCTTCAATAAATGGTTCTAGGAAAATTGG 648
                             v        i  ivviv i     i       v  i   v  i   
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_195135692_    649 ATAGCCATATGCAGAAGAATGAAACAGGTCCCCTATCCCTTACCATATAC 698
                            ?   i     i         iiv  v      i i vi         
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_195135692_    699 AAAAATCAACGCAAAATGGATTGAAGACTTAAACATAAGAGCCAAAAGTA 748
                               i   v          ii?    i    ii       i    v  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_195135692_    749 TTAAAATGCTAGAACAAAAGCTAGG--TAAACTCTCCAGGACTATGGTCT 796
                          v   v vi     v    vv    --    -   i iv   iv   vi 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTT 575

  chr1_195135692_    797 AGGCAAAGAATTTATTAC-TAAGACCTCAATAGCACAGGCAACAAAAACA 845
                               v i-   v   v-  v   vi   v      i         iv 
  L1M4_orf2#LINE/    576 AGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_195135692_    846 AAAATAGACAAATGAGATTATATTAAA-CTAGAAAGCTCTGTATGGCAAA 894
                                 i    vi  i vi  i   -i  i   vi i   iivv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_195135692_    895 GGAAAC----AACACAGTGAGGAGTCAATCTACTGAATAGAAGAAAATGT 940
                            v  ----  v v     ii  v   i i  v    i i       i 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_195135692_    941 CTGCAAACCAT----CTGACAAGGGACT---ATCAAGAATATACAAGGAA 983
                         i      i   ----    i        ---   v        i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_195135692_    984 TTCAAACTATTCAACAGGAAAAATACTTAAAATCCCATTAAAAAGTGGGC 1033
                         i  vv  v i    i iv     v  vv v  i  v   ?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_195135692_   1034 AAAAGATATGAGTAAACATTTCTCAAAAAAAAGACATACAAATGGCCAAC 1083
                            i   v   i  i         v   i  -  i              i
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAA-GATATACAAATGGCCAAT 873

  chr1_195135692_   1084 ATGTATATGAAAAAATGCTCAACACCACTAATCAT 1118
                          v i i       i          i  ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (89 / 56)
Gap_init rate = 0.02 (11 / 632), avg. gap size = 1.91 (21 / 11)  


2971 22.90 2.62 0.69  chr1_195202742_195207441.rev     2743  3467 (1233)    L1M4_orf2#LINE/L1        1   739 (169)  

  chr1_195202742_   2743 TGGAAAGATATCCCATGTTCTTGGATTGGAAGACTAAATATTGTTAAAAT 2792
                                             v              v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_195202742_   2793 ATCAATACTATTCAAACTGATCTACACAGT-AATGCTGTCTTATTCAAAA 2841
                         iv       vii    i         v v -  i  vi  iivv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_195202742_   2842 TTCCAG-TGTTTTTTTTCGTAGAAA---AC---CCCATCTTAAAATTCAT 2884
                          i    -  ii      - i     ---  --- iv   i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_195202742_   2885 ATGGAATCACAAAAGACCCCTGAATAGTCAAAACAATCTTGAGAAAGAAG 2934
                               vii   ii     v-      i              i       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_195202742_   2935 AATGAAGCTGGCAGACTAATACTTCCTGACT-CAAAACACATTACAAAGC 2983
                           ii   i   vi    v i      ii i -      vi i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_195202742_   2984 TACAGTAATCAAAGCAGTATGACACCAGCAAAAATGCAGACAT-TAGATT 3032
                                     ii    i  ii  ii   v  ivii      -     i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_195202742_   3033 AATGGAACTGAAT-ACAAGCCCAAAAACAAACTCACACATATACAATCAA 3081
                                iv    -ivi  i   i   i    i  i    v  iii    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_195202742_   3082 AAGATATTTTTGCAAGGAAGCCAAGATTACACAATGGAGAAAGGGCAGTC 3131
                         vv   -   ivi     iv       ii iv      i     iii    
  L1M4_orf2#LINE/    349 TTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_195202742_   3132 TCTTCAACAAATGGTGTTGGAGAAACTGGATATTCATATGCAAAACAATA 3181
                          i              i   iiv         ?i  i        v   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_195202742_   3182 CATTTGGACTCATACCACACAC---ACACAAAAAA-AACTCAAAAAAGGA 3227
                         v v      i v    v     --- i       v-         v-   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT-GGA 496

  chr1_195202742_   3228 TTAAAGACTTAAATGTAAGAGCTGCAACTATAAATCTCCTAAAAGAAAAC 3277
                          i ?    i              iv         v   i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_195202742_   3278 ATAGGAGAAAA-CTTCATAACATTGTTCTTGGTAAGAATTTCTTAGATAT 3326
                              ? v   -    i i  v   vvi v  i  vii            
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_195202742_   3327 GTCACTAGAAGTACAGACAACAACAAGAAGAAATAAACAAGTGGGACTAT 3376
                          v   i i   i   ii      -     i     i i  i v     vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAA-AAGAAAAAATAGATAAATTGGACTTC 645

  chr1_195202742_   3377 ATCAAACTAAAGAGCGTCTACAC---AAGGAAAACCATCAACAGAGAGAA 3423
                               v v  i i v i iii ---  i i v  i     v i  v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_195202742_   3424 AAGGCAACCTATGGAATGAGGGGAAACATTTGCAAACCATATGT 3467
                            i     i ii     i i i   i         i     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

Transitions / transversions = 2.26 (113 / 50)
Gap_init rate = 0.02 (16 / 739), avg. gap size = 1.50 (24 / 16)  

 722 21.59 2.84 0.00  chr1_195202742_195207441.rev     4034  4209 (491)    L1M4_orf2#LINE/L1      728   908 (0)  

  chr1_195202742_   4034 CACATCATATATCTGATAAGGGGTTAATATCCAAAATATATAAGGAATGC 4083
                           v                   ii vi      i         i   iv 
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_195202742_   4084 CTACAACTCAATAGCAGGAA---AAA-AAGCCAATTTAAAAATGCACAAA 4129
                         i            ii ii  ---   -  v      ?       vi    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_195202742_   4130 GGATTTAAATAGACATTTTTCTGA-GACTACATACAAATGATTACCAGGT 4178
                               i           i  ii -  vv i         iii vi i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_195202742_   4179 ATATGGAAAGAATTCCAACATCATAAAGTAT 4209
                          i   i     vvii        ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.70 (27 / 10)
Gap_init rate = 0.02 (3 / 181), avg. gap size = 1.67 (5 / 3)  


2851 27.85 0.91 0.11  chr1_195207511_195209351.rev      474  1349 (491)    L1M4_orf2#LINE/L1       26   908 (0)  

  chr1_195207511_    474 TTGGGAGCCCTGAC--TAATACAATGATGATACTGCAAAAAGCAATCTAC 521
                             i  v i i i-- iv  vi   iii     v vv   vii      
  L1M4_orf2#LINE/     26 TTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chr1_195207511_    522 AGATTCAATGCAATTCTCATCAAAATGCCATCATCATTTCTCACAAAACT 571
                                 i     i ii        v   v vv v   i ii  i  v 
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr1_195207511_    572 AGAAAAAACAATCCCAAAATTCATATGGAACCAAAAAAGAGCCCACATAG 621
                         v  v  ivii    i               viiv  ii  v  viv    
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr1_195207511_    622 CTAAAGCAAGACTAAGCAAAAAGAACAAACCTGGATATATCACATTACCT 671
                          i   i   vvi i iv  i         vi    vivv     i v  i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr1_195207511_    672 CACTTCAAGCTATATTACAAGGCTATAGTTAACAAAACATCATGGTGCTA 721
                         v i     iviv  i     i    i   v v   i   vii    i  i
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_195207511_    722 GCATAAAAATAAACACATAGACCAAATGGAACAGGATAGAGAAACCAGAA 771
                               ii   i   i     i   -     i  i  v    iv      
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAA-TGGAATAGAATTGAGAGTCCAGAA 324

  chr1_195207511_    772 ATAAAGCCAAATACTTATAGCCAACTGATCTTCAACAAAGCAAACAAAAA 821
                              v   v i i    i i   i    i   i    i vviv   i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_195207511_    822 CACAAAGTGGGGAAAGA-CACCCTAATCAACAAATGGTGCTGGGATAACT 870
                           ivv i          -i vi  vv                   i    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_195207511_    871 GGCAAGCCACATGTAGGAGAATGAAACTGGATCTTCATCTCTCACCTTAT 920
                           vv ?       i ii        ii    i iii i   v    v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_195207511_    921 ACAAAAATCAACTGAAGATGGATCAAAGACTTAAATTTAAGACCTGAAAC 970
                                 i    v  i        ?    i     v     v  i    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_195207511_    971 TGTAAAAATTCCAGAAGATAACATAAGAATAACTATTCTAGACATTGGCT 1020
                          i     v iii      v      i ?i   v v   vv   v    v 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_195207511_   1021 TAAGCAAGGAGTTTATGAACAAGA-ACCAAAAGCAAATGTGACAAATACA 1069
                           i    v iv  iv ii i v  -          v v ii     viv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_195207511_   1070 AAAATAAATAAATGGGATGTAATTAAC-CTAAAAGCTTCTGCACAATAGA 1118
                               i      v   iv v  i  v-i     i   i  ii vvi i 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_195207511_   1119 AGAAATTATCAGCAGAGTAAACAGACAACCCACAAAGTGGGAGAAAATAT 1168
                         i  v i     iv i   i  v            i i             
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_195207511_   1169 CTGCAAAGTATGCATCTAACAAAGGACTAATATCCAGAATCCACAAGGAA 1218
                         i      vi  ii    i i  i     vi          vi i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_195207511_   1219 TTCAAACAAATCAGCAAGAAAAAAAAAAAT--CCCA-TCAAAAAGTGGGC 1265
                         i  vv    v   ii  v     i v    --    - i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_195207511_   1266 AAAGGACGTAAATAAAAAATTCTCAAAAGAAGATATATAAATGGCCAACA 1315
                               iv i    i v v     v            i          i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_195207511_   1316 AACATATGCACAAATGATCAATGTCACTAATTAT 1349
                          i  i   v v i   v    ii   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (7 / 883), avg. gap size = 1.29 (9 / 7)  


2770 27.91 0.92 0.81  chr1_195266457_195269656.rev     1505  2371 (829)    L1M4_orf2#LINE/L1        1   868 (40)  

  chr1_195266457_   1505 TGGAAAAATAATCCATGCTCATAAATAGGAAGAAAAAA-ATCATTAAAAT 1553
                               i   vi     i    ii  v      vvv  -  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_195266457_   1554 GGCCATACTGACCAAAGCAATTTATAGATTCAATACTATTTCTGTCAAAC 1603
                            v     vv     vii  i  i        ii v  ii  i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_195266457_   1604 TACCAATGACATTCTTCACAGAACTAGAAAAATCTACTTTAAAATTCATA 1653
                          v   iivi v  i  ii     v v  v  iiiv iii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_195266457_   1654 CGGAATCAAAAAAGAGCCTGAATAGCCAAGGCAATCCTAAGCAAAAAGAA 1703
                         i    viiv  ii  v  v          ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_195266457_   1704 CAAAGCTGGAGGCATCACACTATCCAACTTCAATCTGTACTACAGGCCTA 1753
                              i      vv       vi    i     vviv       iiv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_195266457_   1754 CAGTAACCAAAACAGCATGGCACGAGTACCAAAATAGACACATTGGCCAA 1803
                               i   i    ii   i  vi i iv ii       i  v ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_195266457_   1804 TGGAACAGAATAGATAGCCCAGAAATAAGGCCATACACCTACAATCATCT 1853
                              i     v  v  i          iv       ii  iii   vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_195266457_   1854 GATCTTTAACAAAGCAGACAAAAACAAACAAAGAGGAAAAGGCTCCCTAT 1903
                            i  ii    i vv v   i v  vv   v i     iiiivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_195266457_   1904 CCAATAAATGGTGCTGGGATAACTAGACAGCCATATGCAGACGATTGAAA 1953
                         i   i              i    i  i ?   i     i v  v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_195266457_   1954 TTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGATTAA 2003
                                   v   i                 i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_195266457_   2004 ATACTTAAATGTAAAAATGTAAACTATAAAAAGGCCGGAAGAAAAC-TAA 2052
                          v  i         i iivv           vvviii         -  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_195266457_   2053 GCA-ATACCATTCTGGACATAGGAATGGGCAAAGATTTCAT-GATAAAGA 2100
                          ?i- v i -   vv   v v  iv i     v i    v -    v-  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-GA 598

  chr1_195266457_   2101 TGGCAAAAGCATT-GCAACAAAAGCAAAACTTGACAAATGGGATCTAATT 2149
                         iiv        iv-          v    v v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_195266457_   2150 AAACTAAAGAGCTTTTGCACAGCAAAAGAAATTATCAAGAGAGTAAATAA 2199
                            v v  i i      ii vv    i  v i        i   i  v i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_195266457_   2200 ATAACCTACAGAATGGGAGAAAAATTTTGCAAACTATGCAACCAACAAAA 2249
                          i    i                vv        ii  ii v ii i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_195266457_   2250 GCCTAATATCCAGCATCTATAATGAACTTAAACAATTTACGAGAAAAAAA 2299
                          v  vi       v  v     v     ivv    i i -- v  v    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA--ATAATAAAA 796

  chr1_195266457_   2300 AAAATCCAAATA--CCA-TTAAAAAGTGGGCAAAGGACATGAACTGACAC 2346
                          i ---      --   -  ?    i           iv    iv    i
  L1M4_orf2#LINE/    797 AGA---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_195266457_   2347 TTTTCAAAAGAAAACATACAGCTGG 2371
                           i  v      i i     iv   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGG 868

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (11 / 868), avg. gap size = 1.36 (15 / 11)  


1085 23.51 4.48 0.00  chr1_195278016_195281162.rev     1453  1720 (1427)    L1M4_orf2#LINE/L1       16   295 (613)  

  chr1_195278016_   1453 TGTTCATGGATGAGGAGACTCAATATT-TTGTAATGCAGATATGCTGCAA 1501
                                    vi i     i      -  ivi   vvi   iv iv   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_195278016_   1502 ATTAATATATAGATTCAATGTATTCCCAGTCAAAATTTCATCAAGCTTTT 1551
                            i  v  i        i i v    vi       ii  v viv     
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_195278016_   1552 ATGTACAAATTGATAAGCTGATTCTAAAATTTGC-TGGAAATTTAAGGGA 1600
                         v  i v       i        i        iii-       vi      
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_195278016_   1601 CCTAGAAAAGCCAAAGCAATTTTATAAAAGAAAAACAAAG----AGGATT 1646
                           i    v       i    i  iv       i       ----    i 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_195278016_   1647 AGCTCTACCTAACTTCGAGACT------AAGGTTAAAGTAATAAAGACAG 1690
                         vi v  v  i  i   i i   ------  i i  v      v       
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_195278016_   1691 TGTGGTATTGGTATTAAGATAGACAAATAG 1720
                                i   i  v i        v    
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 1.62 (39 / 24)
Gap_init rate = 0.01 (4 / 280), avg. gap size = 3.00 (12 / 4)  

1830 21.31 4.35 6.53  chr1_195278016_195281162.rev     2022  2664 (483)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr1_195278016_   2022 AAAAATAGACAAATAGATCAATGGACCAAACC--AGAGTCCAGAAACAGG 2069
                           ii       v             vi i vi--            i ii
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_195278016_   2070 CCCATACATATAGAGACAACTGATTTTTTGGCAACAGTGAAAAGGCAATT 2119
                                  v  vi v   i       i- i   vi   vv   i v   
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTC-GACAAGGGTGCCAAGACCATT 378

  chr1_195278016_   2120 CAGTGGAGAAAAGATAGTCTTTT-GACAAATGGTGCTAGAACAATTGGAT 2168
                           i   i    ii          -i            i i    i     
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_195278016_   2169 AATGGCATGCAAAATA-TAAACTTTGGTTCGCACCTCACATCATATACAA 2217
                          ?ivi         v - i  v  v iii vi        i         
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_195278016_   2218 AAATTAGCTAAAAATTGATCCTAGACCTAAATGCAAAACCAAAAGCATTA 2267
                               i  v     v    v?           i  i v v   i vv  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_195278016_   2268 ACACTTGTAAAACA---CATAGAAAT---TTTTTGTGACTTTGCATTAAA 2311
                          v   iv  i  v ---     i?i --- i  i     i   vi   ii
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_195278016_   2312 CAAAGATTTAATTGATATGAAACTGAAAGAATAATCCATTAAAAG----- 2356
                            v i   vv v       v  ii    v i  v v i-     -----
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-AAAAGAAAAA 627

  chr1_195278016_   2357 -TTAATAAATTGTATTTTATAAAAATTAAAA---TGTGTGACCTTTAAAA 2402
                         - vi        v i  i  v          --- v    --   i   i
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG--CTTCAAAG 675

  chr1_195278016_   2403 GTTACTGTTAAAAAA-TGCAAAGATAAATCACAGACTGGGAGAAAATATT 2451
                          vi   i i  i   -  v     i  vi      v              
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_195278016_   2452 TGCAAATAATATCTGTAATAAGGCAATTGTTACAGATATTATTTGTATTA 2501
                                v    v v i      -----------  i-----      i-
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGG-----------GAC-----TTGTATC- 758

  chr1_195278016_   2502 TTTGAGAGTTCTTCAGATAATATAAAGAACTCTCAAAACTTAAGAGTAAG 2551
                         -------------    vv              i v    i  v i   i
  L1M4_orf2#LINE/    759 -------------CAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_195278016_   2552 AAAA-AAAT---TCAATTGTTAAAATGGAAAAATTATTTGAAGAGACACA 2597
                           i -    ---i     -?v       iv   vv       v     iv
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_195278016_   2598 TCACAAAAGAA----TACAAGTGTATGGCCAAGAGGCACATGAACAGATG 2643
                           v v      ----     ----        v i         v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAA----ATGGCCAATAAGCACATGAAAAGATG 890

  chr1_195278016_   2644 CTCAAATGTATTAGTCATTGG 2664
                              ---i  i ????????
  L1M4_orf2#LINE/    891 CTCAA---CATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (74 / 59)
Gap_init rate = 0.03 (20 / 629), avg. gap size = 3.50 (70 / 20)  


3867 21.65 1.34 0.33  chr1_195285822_195290357.rev     3150  4045 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_195285822_   3150 AAAGCAAATCCCATGTTAACAGCTTGAACAACC--ATGTTGTTAAGATGC 3197
                             - v          v ii v   i vi  i--  i           v
  L1M4_orf2#LINE/      4 AAAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_195285822_   3198 CGATGCTACCCAGAGTGA-CTACAGATTCAATGCAACCCCTATTAAAACT 3246
                          i  i  v    i v   -            i    i      i    ii
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_195285822_   3247 GCAATGACATGTTTTGCAGAAATAGAAAAATCCATCTTAAAATTCATATG 3296
                         v  iivi v v            v  v  iiiv   i             
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_195285822_   3297 GAGTTTCAAGGTATGATGAGTAGCCAAAACAATCATGAAAAATAAGAACA 3346
                           iv v     v ivvv  i              v       v       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_195285822_   3347 AAACTGAAGGATTCACACTTTCTGATTTTAAAATTTACTGCAAATCTATA 3396
                           ii  i    i        i ii    i    i     i    v   i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_195285822_   3397 GCGATCAAAATAATGTGGAACTGGCATAGTGATAGACACAAAACCCAATG 3446
                          ii     i i i     v         iv        i v ivi     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_195285822_   3447 GAATAGAATAGATAATCCAGAAATAAAATCTCAGATATATGGTCAAATGG 3496
                                  v  v i            vi vi v  v         v  i
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_195285822_   3497 TTTTTGAGGAGG-TGCCAAGACCATCCAATGAGGAAATTACAGTCTTTTA 3545
                             i  vi   -            i     i     vv i        v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_195285822_   3546 AACAAATGACACTATGAAAATTGGATATCTACATGCAAAATAATAAAGTT 3595
                                 iii  iv  v  i      ? i          v   i     
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr1_195285822_   3596 CAGTTCTCATCTAACACCATATACAAAAATTAATTCAAAATGGATCCATT 3645
                         viiii ii i  v                    i            v?vv
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_195285822_   3646 ACC-AAATATAAGATCTAAAATGATAAAACTCTTAGAAGGAAACATAGGG 3694
                            -    i     v      iv                i         ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_195285822_   3695 CAAAAACTTCATGACACTGGATCTGGCAATAGTTTATTTGGTGTGATTCC 3744
                         vv   v    i    vi   i iv      i    v  v i i   iv  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_195285822_   3745 AACGG-ACAGGCAACAAAAGCAAAAAT-GATAAAGTATACTTTATGAAAA 3792
                           vi -   i          v      -      v iv    i  v    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_195285822_   3793 TTTAAAATTTTTATTCATCAAAAAACACTACCAACAGAGTTAAAGG-CAA 3841
                           v    i    i v v     ii      i   v i   v   i -   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_195285822_   3842 C----AGAATGCAAGAAAATATTTGCAAAATATATATCTGATAAGGAATT 3887
                          ----      vi                vi               i i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_195285822_   3888 AATATCCAGAATATAGAGAGAACCCCTTAAAAACTCAACAACAAAAACAC 3937
                         vi             v i     i i -- v       i  i     v  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTT--ACAACTCAATAATAAAAAGAC 800

  chr1_195285822_   3938 AAGCAACCCAATTCAAACATGGGCAGAGGACTTGAATAGACATTTCTCCA 3987
                           ii         ?   v       i    i                   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_195285822_   3988 AGGAATATATGCAAATCACTGGTAAACAAATAAAAAGATACTCAAGATCA 4037
                          i   v    i     vi iii   i  v  i       i     v    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_195285822_   4038 CTAATCAT 4045
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.47 (113 / 77)
Gap_init rate = 0.01 (10 / 905), avg. gap size = 1.50 (15 / 10)  


1693 26.73 4.51 9.33  chr1_195316653_195318706      608  1561 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_195316653_    608 TGGAAGTGTATACCATATTAATAGTTTGAAAGACAAGTAATAT-----AA 652
                              ivi   v    i  v  i v   i     --v      ----- i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC--TTAATATTGTTAAG 48

  chr1_195316653_    653 ATA--AATTATCTCTAAATTGCTGTA----TCTAATACAATCTCAATAAA 696
                           i--   vv  i i      v v  ---- ii  ii     i v  v  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_195316653_    697 AATCTCAGGAGA-TATTTTG-AGAACATTGCCAAGCTGTTTCCAAAATGT 744
                             i   vv v- v     -    -    v       v i i     vi
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTC 147

  chr1_195316653_    745 ATAAAGAAATGCAAAGGACCAAGATTAGCCAAGATGATGTTGAG------ 788
                            vi         i     v   v       i ii  v    i------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_195316653_    789 GAGCCATGCTGGGGGGCTTACATTTTTATATATCAATATATAAAAGCAAG 838
                           i v v i   i  i  i   i  iivv  v    v iv  ---- v v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA----CTAC 243

  chr1_195316653_    839 AAAGAGAGAGTAAAATCCTATAATAATCAGTAATTATGAGTATTAATAAA 888
                             -------------   i i      -------------------- 
  L1M4_orf2#LINE/    244 AAAG-------------CTACAGTAATCA--------------------A 260

  chr1_195316653_    889 GGTAAAGTAATTTTGAGTGTTGGTGTAAAAATAGA----TAAACTAA-AG 933
                          ii iv  i-------  ii   ii   ii     ----  i ii  -i 
  L1M4_orf2#LINE/    261 GACAGTGTG-------GTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_195316653_    934 AGCTGAAT--AGAATCCAGAAACAAACCTAAACATAAATTGTT--TTACA 979
                          iiv    --   i        i     i v    vv  v  i--  i--
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG-- 351

  chr1_195316653_    980 ATTTATGACAAAGATACCACTACAGTTCACCAGAGGAAGGGGTGTTTTTT 1029
                             vi     i i i   vv  vi    vii -    i ii i------
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATA------ 394

  chr1_195316653_   1030 TTTGTTGTTGTTGTTGTTTTTTCTTCAGTAAATGGTGCTGGGTCAGCTGG 1079
                         ---------------  i     --- ii             v  i    
  L1M4_orf2#LINE/    395 ---------------GTCTTTTC---AACAAATGGTGCTGGGACAACTGG 426

  chr1_195316653_   1080 ATAAACTATGTGGAAATACAT--ATCCCGACCCATACCTCAACATCACGG 1127
                            ?- i ii  v   viv  -- viiv     v       -  i  iiv
  L1M4_orf2#LINE/    427 ATAK-CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA-CACCATAT 474

  chr1_195316653_   1128 ACAGATATCAATTCCAGATGGATTGTATATCTGAATATGAATGCTCAAAT 1177
                            i v  i  i  v i      ii? v i  i   i i iv   v   i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_195316653_   1178 AATAAATGTTCAAAAAGAAATCATAGCAGAATATCTTCGTGAACTTCAGA 1227
                         v     vv iiv i      v     v? v v          v   vi v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_195316653_   1228 TGGCCAACAATTTTCTGTACAGGGTACAAAAATTACTCTTCTTAGAAGGA 1277
                          i v   iii   ii iv i v ii  v    vi  vvvivvi i   i 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_195316653_   1278 AAAATCTTAAAAAGGCAAATTAGACCACATTAAAATTGAGAACTTTTGAT 1327
                              -------  ii     i   iv   i      i i        vv
  L1M4_orf2#LINE/    625 AAAAT-------AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_195316653_   1328 CATGAAAAACCA-TATTAG--AGGTGAAAAGTCATGCCCACATG-TGGGA 1373
                          v v   iiv  -   i i-- i        v  -i      vi-     
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACA-ACCCACAGAATGGGA 716

  chr1_195316653_   1374 GAAAATAATTTGCAAGTC-------TGACAAAGT-CTTGTATTTAGAATA 1415
                                -       i  -------   i  i v-       ii      
  L1M4_orf2#LINE/    717 GAAAATA-TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_195316653_   1416 TATAAAGAATTTCTACAAATCAATTAGGAAAGGAGGGAAAACTCAAAAGA 1465
                                  i ii     v     v vi   i  vii v   i   vv? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr1_195316653_   1466 AAAGAAAATGGACAAAGGACTTTGACAGGCACTTCACAAAATAGGATATC 1515
                            ----    i       i  vi i  i  i   v v   v i     v
  L1M4_orf2#LINE/    816 AAA----ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_195316653_   1516 CAAATGGCCAATGGACTTGTGAAAAG-TATTCAACTTCATTCATAAT 1561
                                     iii vii       - ii     v   ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (152 / 99)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 4.00 (132 / 33)  


1211 27.27 9.09 1.05  chr1_195411601_195413164      500  1071 (493)    L1M4_orf2#LINE/L1      291   908 (0)  

  chr1_195411601_    500 TATA-ATCAATGCAACAAAATAGAAATCCCAGAAA---AC---------T 536
                             -       v  i i   v  i vi       ---  --------- 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_195411601_    537 ATGTTTTAT--ATTT--GAAAACAGCACAAAATGTTTTCAGTGGGGGAAA 582
                            v iv  --    --  v  vi ii v  ivviv    i     i  i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_195411601_    583 AATAGTCTTTTCAACTAATGATCCTGGTATCTCTG--TA-------GAAA 623
                                        v    i v    v ivv   --  ------- v  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_195411601_    624 AAAAATGAACATCAGCTCTCACCTCTCAACAAACACAAAAATTAATTCAA 673
                           i      vv vii i ii     v  v  v i           i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_195411601_    674 AATGGATTCCAGACCTAAATACTAAAGCTATAATTTAAAAAATTCT-AAT 722
                                iv?          iiv i     v  i - v    i   - iv
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTTAGA 539

  chr1_195411601_    723 CAAAGACATAGGAGAAAAT----GTG----TAGCTTTAGCAAAGATTTCC 764
                         vi  i       ? v    ----   ---- i v  vi    v i    i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_195411601_    765 TAG----GGCAC-AAAAGCA--AGAAACATAAAACTTTTTTGATGAATTG 807
                            ---- i   -       --  v    v  i vvvvv v   i     
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_195411601_    808 GAGTGCATAAAAATTGAATATTCCTGCTCTTTGGATGAGGCCACTAAGGA 857
                           v v   v      i  v i ii  iv   iii v  vi i ii   i 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_195411601_    858 AATAAAAAAGCAATAAATAGT-TTGTAAAAAAT-----CAAAATTAATTT 901
                          i i    ii   ivv i  v- v v i     -----    -- v  v 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA--TCATAT 737

  chr1_195411601_    902 TTTCAACAACAGAAGTTTTTCCAGAATATACAGAGAGCTCTTTCAGCTGC 951
                         v iii i  vi  vv v v           i i   i     v  i  - 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT-C 786

  chr1_195411601_    952 AA-AATAAG--GACTAAAACAGCTCAATT-GAAAATGGACAAACATTTTT 997
                           -     i--   --   i i i     -i       i    viv   v
  L1M4_orf2#LINE/    787 AATAATAAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_195411601_    998 AATATATACTTCACAAAAGAGGATACACAGGTGGTTAATAAGCACATTAA 1047
                             v i i   v v     i    i   ii   ii           v  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_195411601_   1048 ATGATGCTCAGCATCATTAGTTAA 1071
                          v        i     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (84 / 70)
Gap_init rate = 0.04 (22 / 618), avg. gap size = 2.64 (58 / 22)  


2108 21.96 1.64 10.78  chr1_195553146_195554874      502  1234 (495)    L1M4_orf2#LINE/L1      215   880 (28)  

  chr1_195553146_    502 TCACACTTCCTAATTTCAAAAGATTTCATAAAACTATTGCAATCAAAAAC 551
                                   i          vv vii i   i   iv i      i - 
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA-C 263

  chr1_195553146_    552 AGCATCGTACTGGCCTAAA-ACAGACACATCAACCAAAGAAACAA----G 596
                           ii v        v   i- i     i  vi i   v i  i i---- 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_195553146_    597 AAAGCCCAGTAATAAACCCAACTACTTATGGTCAACTGATTGTTGACAAA 646
                          i  i    v          vvi i          i     v i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_195553146_    647 GGTGCCAAGAACACACAATGGGGGAAAGACAACTACTTCAACAAATGGTG 696
                                   v  iv        i  ii i iiivi              
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_195553146_    697 TTGGGAAAACTGGATAGCCACTTGCAGAAGAATAAAATTGGACCCTTATC 746
                         i     v         ?    v    i      i  i        i  i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_195553146_    747 TTATACCACACACTCACATCAACCCAAAATGGATAAAGGACTTGAAATAT 796
                          i i    i i  vv v  i   i          v ?i   i -    i 
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT-AAATGT 512

  chr1_195553146_    797 AAGACCTGAAACTA--GAACTTTTAGAAGAAAACAGAGAGAAAAATCTCC 844
                             v  i      --i    i             v  i?iv      i 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_195553146_    845 ATAACATTGGTCTGAGCAACGACTTCTTGGCTATTACCCCAAAAGCAAAA 894
                         i i  v    vi ii    i ii     i v   v  v         v  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_195553146_    895 ACAACAAAAACAAAAATAGACAAGTGGGATGGCATTAAACT---AAGTTG 941
                         i        iv         i  i v   ivv   i   v ---  ii -
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT- 661

  chr1_195553146_    942 TTTCTGCAGAGCAAAGAAAACAATTATGAGAGTGAAGAGACACATAAGTG 991
                            v   vv--     i v  v  i v  i      i     --------
  L1M4_orf2#LINE/    662 TTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACA-------- 701

  chr1_195553146_    992 ATATATAGATATATAATAATGTGTGTGTGTGTATATATATATATATATAT 1041
                         --------------------------------------------------
  L1M4_orf2#LINE/    702 -------------------------------------------------- 701

  chr1_195553146_   1042 ATATTCTCATCCATGGACTGGAAGAGAGTATTTCCAAACTATATATCTGG 1091
                         -------- i   ii  v   i   i i     v    ii         i
  L1M4_orf2#LINE/    702 --------ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_195553146_   1092 TAACAGGTTAAGATCCATAACATGTAAGGCATTCCAATTTAAACAATTCA 1141
                            vi ii viv     v  i  i   i v i  ----   --   i   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTC----TTA--CAACTCA 787

  chr1_195553146_   1142 ATAGCAAGAAAAGAAAAA-AACCTAATT-AAAAATGGGTAAAGGATCTGA 1189
                            ii  --     v   -    i    -         i       i   
  L1M4_orf2#LINE/    788 ATAATAA--AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_195553146_   1190 ACAAACATTTACCAAAAGAAGATACACACATGGCCAACATTCACA 1234
                          i i      vi v          i   v        i vv    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

Transitions / transversions = 1.93 (104 / 54)
Gap_init rate = 0.02 (14 / 666), avg. gap size = 6.50 (91 / 14)  


2862 23.75 2.24 5.64  chr1_195655033_195657215      795  1733 (450)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_195655033_    795 GGAAATATACTTTCTATTCATGAATTGGAAGAATCAATATTGTTAAAATC 844
                              v   iiiiv i      i         v i           i  v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_195655033_    845 -CTATACTACCCAAAGTGAT----AGAGTCAATGAAATCCTTACCAAAAT 889
                         - v     v      v    ----   v    i v     i  i      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_195655033_    890 TCAATAACATTGTTCATTATTCACAGAAATTAAAAAAC-AATT-TAAAAT 937
                         i --i i --  -- v  v  ii        i v  i -i  i-      
  L1M4_orf2#LINE/    102 CC--CAGC--TG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_195655033_    938 TTGTATGAAACTGCCACAGACACAAAACTGAATTGTTAAAGTAATCTTGA 987
                          ii    i  v   v vi   v  -----    v ii   ii        
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCA-----GAATAGCCAAAACAATCTTGA 190

  chr1_195655033_    988 GCAAGAAGAACAA-GCTGGAGGTATCACACTTCCTTATTTCAAATTATAT 1036
                         iv           - i      vv          iv        viv  i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_195655033_   1037 TACAAAACTATCATAATCAAAACAGTATGGTACTG-CATAAAAACAGACA 1085
                               i   ivi       i     i        -     ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_195655033_   1086 CATAGAGCAATGGAACATAATAAAAATCCCAGAAATAAACCTACATATAT 1135
                         i     v        i v   vi i vi             i i i  v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_195655033_   1136 AGGGTCCACTAATTTTTGACAAGGGCACTAAGAGGACACAATGGGGAAAG 1185
                          v    v i i     i        ii i    vv iv            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_195655033_   1186 AATAGTCTGTTCAGTAAATAGTGTTGGAAAAA--ACATATCTTTTATGGA 1233
                                 v    ii    i   i   i v  --iv   ? ivi-   v 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC-ATGCA 439

  chr1_195655033_   1234 AAAGAATAAAACTGGATCCTTATATTACACTGTATGCAAATATTAATTCA 1283
                                i  ii    i  i  iv i    ii   i    v     i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_195655033_   1284 AAATGAATTGAAGACTTAAATGTAAGACCTGAAATCCTAAAACTTCTAGA 1333
                              i  ii?    i           v  i   iiv       ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_195655033_   1334 AGAAAACATAGG-GTAAACTCTCCCTGACATCAGTCTTGGCAATGATTTT 1382
                                     -     -   i v    v ii vi v       i   i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_195655033_   1383 TTTTTTTTTTGAAACAAAAAAAATGATTTTTTTTGTTTGTTTTTATAAAA 1432
                           ---------------- i v    i---------------------- 
  L1M4_orf2#LINE/    589 TT----------------AGATATGAC----------------------A 600

  chr1_195655033_   1433 ACAAAGGAATGGGCAACAAAAGCAAAAATAAACAA-TGAGACTATACCAA 1481
                         v    i v iii          v       i i  - vi    vi i   
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_195655033_   1482 ACTAATATGTTTCTGAACAACAAAGGAAACAAT-AAAAAAATGAAATGAC 1530
                          v v v vii  i  vi vv       v  v  -  i   i     v   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_195655033_   1531 AACCTATGGAATGGTAGAAAATATTTGCACACCATGTATCTGATAAGGGG 1580
                             i ii      v              v i   i             i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_195655033_   1581 TTAATATTCAAAATTTATAAGGGACTCACATAACTCAATAG--AAAATAT 1628
                         i vi   i  i   v     i i    vi i         i--    v i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_195655033_   1629 AAACAACCTGATTACAAAATTAGCAAACGACCTCAATAGATACTTTTCCA 1678
                            i    ii   ?v     vi     v  ii v      i i  i    
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_195655033_   1679 AAGATGCTCAACATCACTAATCATTAGGGAAATGCAAA-----TCAAAAC 1723
                             v v vv   -- v iii  v  i v v   v   -----    v i
  L1M4_orf2#LINE/    851 AAGAAGATATACA--AATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_195655033_   1724 CACAATGTGC 1733
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.65 (137 / 83)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 3.52 (74 / 21)  


2524 28.48 0.25 0.99  chr1_195661615_195666191.rev     2864  3674 (903)    L1M4_orf2#LINE/L1        1   805 (103)  

  chr1_195661615_   2864 TGGAAACACATCACATGTTCATGGATGGGTAGAATCAATATCGTGAAAAT 2913
                               v i   v             v  v   v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_195661615_   2914 GACCATACTTCCAAAAACAATCCACAAATTCCATGCAATCCCCATCAGAA 2963
                          i v     i  v   vii   i   i    v i        i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_195661615_   2964 TACCACCATCATTCTTCACATAATTAGTAAAAAC-AATTTTAAAATTCAT 3012
                          v   v vv v  i  ii  v  v v - v  i -i  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr1_195661615_   3013 ATGGAACCAAAAAAGAGCCCCCATAGCCAAAGCAAGACTAACCAAAAAGA 3062
                               viiv  ii  v  vvv         i   vvi i vv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_195661615_   3063 ACAAATCTGGAGGCATCACATTACCTGATTTCAAACTATACTATAAGGCC 3112
                              vi      vv     i v  ii        viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_195661615_   3113 ATAGTCACCAAAACAGCATGGCACTGGTATAAAAAATAGGCACATAGGCT 3162
                          i   v i   i    ii   i     i    ii -   i  i    iii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATC 298

  chr1_195661615_   3163 AATGGAACAGAATAGAGAACCCAGAAAAAAACTCAAAAACTTACAGCCAG 3212
                                i     v    ii       v    i  v v i   ii i  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_195661615_   3213 CTGACCTTTGACAAAACAAACAAAAACATTAAGTGGGTAAAGGACACCCT 3262
                         i   ii  i     iivviv   i v    v i    v    i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_195661615_   3263 TTCCAACACATGGTGCTGGAATAATTGGCTAGCCACATGTAGGAGAATGA 3312
                           i     v          i i  i   v  ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_195661615_   3313 AACTGGATTCTTATCTCTCACCTTATACAAAAATCAACTCAAGATAAATG 3362
                          ii    ii i  i   v    v           i       i  ii  v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_195661615_   3363 AAGGACTTAAACCTAAGACCTGAAACTATAAAAATTTTAAAAGATAATGT 3412
                          ?i   i    iv     v  i           v i   i    v  ii 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_195661615_   3413 TGGAAAAACTCTTCTAGACATTGGCTTAGGCAAGGAGTTCATGACCAAGA 3462
                         v  ?iv  v     vv   v    v        v iv   v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_195661615_   3463 ACCCAAAAGCAAATGCAATGAAAACAAAGATAAATAAATAGCTGGGACCT 3512
                         vv         v v    ii   iv   i   i      ---   -  i 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT---TGG-ACTT 644

  chr1_195661615_   3513 AATTAAACTAAAGAGTTTTTCCACGGCAAAAAGAACAGTCAGCAGAGTAA 3562
                         v  i   v v  i ii    vii vv    iiiv  vi   iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_195661615_   3563 ACAGACAACCCACAGAGCAGGAGAAGAATCTTCACAATCTATATATCTGA 3612
                          v              iii      -   v  ii   vii          
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCATATATCTGA 743

  chr1_195661615_   3613 CAAGG-ACTAATATCCAGAATCTACAACAAACTCAAACAAATAAGTTAAG 3661
                         i    -   vi          v  i  vi     vv    v v i -  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-AAT 792

  chr1_195661615_   3662 AAAAACTCAAACA 3674
                              vv    i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATA 805

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.01 (8 / 805), avg. gap size = 1.25 (10 / 8)  

 541 15.57 0.00 0.00  chr1_195661615_195666191.rev     3965  4086 (491)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr1_195661615_   3965 AAAAAAAAAAAATCAAACAATCCCATCAAAAAATGGGCTAAGGACATGAA 4014
                           v  v     iv    i  i  v  i?          v     iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_195661615_   4015 TAGACAATTCTCAAAAGAAGATACACAAATGGCCAACAAACATATGAAAA 4064
                               v     v          i            i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_195661615_   4065 AATGCTCAACATCACTAATGAT 4086
                         i             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (10 / 8)
Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.00 (0 / 0)  


2206 25.76 3.57 5.30  chr1_195747703_195752627     3509  4432 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_195747703_   3509 TGGAAA-ACATTCCATGCTCATCGAAAGGGAAAATCAAT--TGTTAAAAT 3555
                               - i  i     i    v  vv  i i v i   --      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_195747703_   3556 AGCCATACTGCCCAAAACAATTTATAGATTCAACACTATTGATATAAAAC 3605
                         i  v     v      vii  i  i         i v  ivv   v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_195747703_   3606 TACCAA-TGTCATTATTCACAGAATTATAGGAAACT-ATTCTGAAATTTG 3653
                          v   i-  i v  -  ii     v - iiv  i  -  i  i     ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chr1_195747703_   3654 TATGGAACTAAAAAAAAAATCCCA-AATAGCCAAAGTAATCCTTATCAAA 3702
                                v iv  iii ---    -          ii    -  ivv   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATC-TTGAAAAA 194

  chr1_195747703_   3703 AAAGAACAAACCCAGCAG---CATCATTCTCTGACTT-AAAACTATACTT 3748
                         i         viii vi ---  -  i ii ii i  -      -    v
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACT-TACTA 242

  chr1_195747703_   3749 TCAAGGATACAGTAACCAAAACAGCATGGTAGTGGTACAAAAATATACAC 3798
                         -   i v        i   i    ii     v   i i  ii   v   i
  L1M4_orf2#LINE/    243 -CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_195747703_   3799 ACAGACCA-CAGAACAGAATAGAAAACTCATTAATAATAAATAAAGCCGC 3847
                          i   i  -ii   i     v  i iii  v-------       v  ii
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAG-------AAATAAACCCAT 334

  chr1_195747703_   3848 GCACCTA----CAACCG-TT----ACAAAGGCTGACAAAAACAAGCAATG 3888
                         i  ii  ----   ii -  ----    i  -  v   i v  vv     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGG-TGCCAAGACCATTCAATG 383

  chr1_195747703_   3889 GAGAAAGGACTTCCTGTTCAATAAATGGTGCTTGGATAACTGGCTAGCCA 3938
                          i     i ivvi  v     i          v   i      v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_195747703_   3939 TATGCACAACAATGAAACTCTACCTTTACCTTTCACCGTATACCAAAATT 3988
                         i     v  v      ii vv   ii     iv    i     v      
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_195747703_   3989 AATGCAAGATGAAATAAAGATTTAAGTATAAGACCTCAAACTATAAAACC 4038
                           iv   i   i vi ?   ii   i i     v  v            i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_195747703_   4039 CCTAGAAGAAAACCTAGG---AAATACCCTTTTCAACATCAGCCTTGGCA 4085
                          i           v    ---    ---   ivii  v ii vi v    
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCA 580

  chr1_195747703_   4086 AAGGATTTTTGGCTAAGTCCCCAAAAGCAATTGCAACTAAGACAAAAATT 4135
                          v  v  i  i v  v v v         vvv     v  iiv      v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_195747703_   4136 GACAAGT-GAACATAATTAAA-TGAAATAGCTTCTCTACAGCAAAGAA-A 4182
                           i  i - i  v v  i   - v   - i   i v i vv     i - 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACA 679

  chr1_195747703_   4183 CCATCAACAGAGTAAACAGACAACCTACAGAATGGGGGAAAATTTAAAAA 4232
                          i     v i   i  v        i          i      -------
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT------- 722

  chr1_195747703_   4233 AAAAGAATGGGGGAAAATATCTACAAACTGTGCATCCAACAAAGGTCTAA 4282
                         ------------------  i i    iii ii   ii i  i  v  vi
  L1M4_orf2#LINE/    723 ------------------ATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_195747703_   4283 TATCCAGAATCTATAAGGAACTTAAACACATCAACAAGCAAAAAACGA-- 4330
                                   v     i     ivv   vv    i  vv    i  i --
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_195747703_   4331 --CCTGATTTTTAAAATGGG-AAAAGATCATGAACAGACACTTCTCAAAA 4377
                         --  ii   ?v-        -   i   i-    i     i     v   
  L1M4_orf2#LINE/    805 AACCCAATTWA-AAAATGGGCAAAGGATT-TGAATAGACATTTCTCCAAA 852

  chr1_195747703_   4378 AAAACACATACGAGTGGCCAACAA--ATAGGAAAAAATGCTCATGATCAT 4425
                         i  i- i    i i       i  -- i v     i       vv    ?
  L1M4_orf2#LINE/    853 GAAG-ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_195747703_   4426 CAGAGAA 4432
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.70 (148 / 87)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 2.48 (82 / 33)  


2955 23.20 0.63 3.53  chr1_195760731_195762515      500  1292 (493)    L1M4_orf2#LINE/L1      139   908 (0)  

  chr1_195760731_    500 CTAAAGTTGATATGGAGACAGAAAAGACCCAGAACAGCCAACACAATATT 549
                              i  v       i iiv  ii         i      v     v  
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr1_195760731_    550 GAAGGAGAAGAACAAAGTTGGAGGACTGACACTACCCAACTCCAACACTT 599
                            ii                      v     v     i i   v    
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_195760731_    600 ACTATAAAGCCATTATAATCAAAGCAGTGTGATATTGATGGAAAAATAGA 649
                             i     i ivi       ii       i  i  iiiv  ii     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_195760731_    650 CAAATAGATCAATGGAACAGAATAAAAAGCCCAGAAACAGACTCATATTT 699
                           v              i     vi i  i       i i  i    iv 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_195760731_    700 ATATAGTCAACTGACCTTCAACAAAGGAGCAAAAGCAACATAATGGAGAA 749
                         v   i     i   ii   i    i  v  v  ii v ivi     i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_195760731_    750 AAAATAATCTGTTCAACAAATGGTG-TCCAACAATTGGACATCTACACAG 798
                          i    i   v              - vvi    i    i ? i   iiv
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_195760731_    799 AAATGATTAAATCTAGACACAGACCTTACACCCTTCATAAAAATTAACTC 848
                            v  v i  vi i   v vv    i     v vi i            
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_195760731_    849 AAAGTGGATCATACACCTAAATGTAAAATTCAAAACTATGAAACTTTTAG 898
                            i       ? v            i vii        i     i    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_195760731_    899 AATATAACA--GGAGAAAATCTACATGATGTTGGGTATAGCAATGACTTT 946
                           v v    --  ? v      v i   iv      vvi      ii  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_195760731_    947 ACAGATATAATATCAAAAGCAGAATCCATGAAAGAAATAATTGATAAGTT 996
                         vi      i i i        v  v v ii       v   v     i  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_195760731_    997 GGACTCCACTGAAATTAAAATTTTCTGTTCTCCAGAAGACACTGTCAAGA 1046
                              i  iii         vi  i   v  i  i i      i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_195760731_   1047 GAATGAGAAGATTTCTTACAGTTTGGGAGAAAATATTTGCAAAAGACATA 1096
                         i i   i    ivv ii    vv                    vv i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_195760731_   1097 TCCAA-AAGAAACATTGACTTTTTTTTCCTAATAAAAGATGGTTATCTAA 1145
                           ii -   ii  -   --------------------------    i i
  L1M4_orf2#LINE/    739 TCTGATAAGGGAC-TTG--------------------------TATCCAG 761

  chr1_195760731_   1146 AATATACAAATAAATCTCAAAATGCAACAATCAAAA-ATGAACAGCTAGA 1194
                               i   v  v   i v  iv   i   v    - ii  i i ivi 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_195760731_   1195 TTAAAAAATGGGCAAAAAAACCTGAACAGACACCTCACCAAAGAAAATAT 1244
                           ?             ii -ii    i     ii  v        i    
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGA-TTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_195760731_   1245 ACACATGGAAAATAAGCATATGAAAAGATGCTCAACATCATATATCAT 1292
                            v    vv        i                     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (118 / 62)
Gap_init rate = 0.01 (7 / 770), avg. gap size = 4.71 (33 / 7)  


4581 17.20 1.53 2.08  chr1_195937842_195939830.rev      586  1498 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_195937842_    586 TGGAAAGGCATTTCATGGACTAAAAGTTTATGGACTGGAAGACTTAATAT 635
                                ii  ii    ---------  i     i               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATG---------TTCATGGATTGGAAGACTTAATAT 41

  chr1_195937842_    636 TTTTAAGATGATAATACTCCTTGAAGTAATGTATCAATTTAATACAATCT 685
                          v        ii        iii  v i  v  ivi   i  ii     i
  L1M4_orf2#LINE/     42 TGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chr1_195937842_    686 CTATCAAACTCTCAAGGATATTTTTTACAGAAAT--AAAAACTTATCCTA 733
                                 v  i  ivviiv      i       -- v  i  v      
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr1_195937842_    734 AAATTCACATACAATCTCAAAGGACCTCAAATAACCAAAACAATTTTGAA 783
                                i  iv  viv   i     ivi    i          i     
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_195937842_    784 AAAGAG---CAAAGTTGGAGGGGTCACACTTCCTGATTTTAAAAGTTTCT 830
                              i---            iv          ii    i    v  v  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_195937842_    831 ACAAAGCTACAGTAATCAAAATAGTGTGGTACTGGCATAAAGATAGAAAT 880
                                            i i                  i      v  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_195937842_    881 GTAGATAAGTGGAATAAAATACAGAACTCAGGAATAAACCTTGGCATATA 930
                         i     v i       i   vv   iii   i        ----    i 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC----CATACA 337

  chr1_195937842_    931 ---ATGTTGAATTAATTTTCAACAAGGGTGCCAAGACCATTCAATAGGGA 977
                         ---   v v    i      i                        i    
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_195937842_    978 AAATGGTAGTCTTTTCAACAGGTGGTACTGGGAAAACTAGATATCCACAT 1027
                           i-ii              ii    i      v    i    ?      
  L1M4_orf2#LINE/    388 AAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_195937842_   1028 GAAACAGAATGAAGTTAGATCCTTGCCTTACAGCATATA-AAAAAC-AGT 1075
                          v  v           i  i  i i   i   v      -     i- ii
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_195937842_   1076 TCAAA-TAGATCAAAGACCTAA-TATATGAGCTAAAACTGTAAACCTCTT 1123
                              - i     ?        - i  v           i    v     
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_195937842_   1124 ACAAGAAAATATAGGGGAAAATCTTTATGATATTGGATTTGGTGATGATT 1173
                          v       i     ? v       ii   iv    i  v  ii   i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_195937842_   1174 TTTTGGATGTAACACCAAAAGCACAGACAATTAAAGAAAAAATAGGTAAG 1223
                          i  i   i i              ii   iv             i   i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_195937842_   1224 TTGAGCTTCATCAAAATTAAAAACTTTTGTGCATGAAAGAACACTATCAA 1273
                            ii                           v v    i          
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_195937842_   1274 GGGAGTGAAAAGTCAACCCACAGAATGGGGGTAA-TATTTGCAAATCATA 1322
                          ii         v                i v  -               
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_195937842_   1323 TATCTGATAAGGGATTAATATCCAGAATGTATAAAGAATTCCTTA-AATT 1371
                                       i vi          i         i  -   -  i 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC-TTACAACT 785

  chr1_195937842_   1372 CAACAATTAAAACACAAACAAAAGACCCAATTTAAATATGGACAAAGAAT 1421
                            i   v    v     i  ----       ?   v    i     i  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAA----CCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_195937842_   1422 TCAAATAGACATTTCTCCAAAGAAGATATACAAATGACCAATAAGTAGGT 1471
                          ii                                 i        i vi 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_195937842_   1472 AAAACGATGCCCAATATCACTAGTCAT 1498
                         i   v     i   i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.48 (109 / 44)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.36 (33 / 14)  


2943 25.54 1.30 2.61  chr1_195954030_195958684.rev     3245  4164 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_195954030_   3245 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTAAAAAT 3294
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_195954030_   3295 GACCTTACTGCC-AAATGCAATCTACAAATTCAATGCAATTTCCATCAAA 3343
                          i vv    v  -    -ii       i      i     ii i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_195954030_   3344 ATGCCACCATTTTTCTTCACAGAACAAGAAAAAGC-AATCCTAAAATTCA 3392
                           v   v vvii  i  ii     - vvi v    -i             
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCA 148

  chr1_195954030_   3393 TATGGACCCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAATAAA-AAG 3441
                               vviiv  ii  v  viv         i   vvi i v   -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_195954030_   3442 AACAAATCTGGAGGCATCACATTACTCAACTTCAAACTATGCTGTAAGGC 3491
                               vi      vv     i v i   i      viv i  ii  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_195954030_   3492 TATCATCACCAAAACAGCATGGTATTGGTATAAAAATAGGCACATAGACC 3541
                           ivi v i   i    ii     i   i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_195954030_   3542 AATGGAACATAATAAAGAACCCAGAAATAAACCCAAATCCTTACAGCCAA 3591
                                i v   vi   ii               v ivi   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_195954030_   3592 CTGCTCTTCAACAAAGCAAACAAAAACATGAAGTGGGGAAAGAACACCCT 3641
                         i  v i   i    i vviv   i v   vv i           i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_195954030_   3642 ATTCAACAAGTGGTGCTGGGATAATCGGCAAGCCACAAGTAGGAGAATGA 3691
                         v        i           i  ii  vv ?     v i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_195954030_   3692 AATTGGATCCTCATCTCTCACCTTATAGAAAAATCAACCCAAGGTTGATG 3741
                          i     i  ii i   v    v    v      i   i   ii v   v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_195954030_   3742 AAGGACTTAAATCTCAGGCCTGAAACCATAAAAATTCTAGAAGATAACAT 3791
                          ?i   i     v v  iv  i    i      v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_195954030_   3792 TGGAA-AAACCTTTCTAGACATTGGCTTAGGCAAAGACTTTATGACCAAG 3840
                         v  ?i-   i   iv -   v    v        v ii  iv iivi v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_195954030_   3841 AACCCAAAAGCAAATGCAACAAAAACGAAAATAAATAGATGGGACTT-AT 3889
                          vv         v v         ivi      i   i  v      -  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_195954030_   3890 TAAA-CCAAAAGCTTCTGTACAGAAAAAGAAATAATCAGGA--GTTAACA 3936
                         i   -ii    i   i   i vvv   i  v iv    i  --  v  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_195954030_   3937 GACAACCCACAGAGTGGGAGAAAATCTTCACAGTCTATACATCTGAAAAA 3986
                                      i           v  ii  ivii   i      ----
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA---- 743

  chr1_195954030_   3987 GATTAAGTGTTTTCTATATTCTAATAACCAGAATCTACAAAGAACTC--- 4033
                         ---    v vi  v   ----------       v  i         ---
  L1M4_orf2#LINE/    744 ---TAAGGGACTTGTAT----------CCAGAATATATAAAGAACTCTTA 780

  chr1_195954030_   4034 -AAATCAGCAAGAAAAAACAAACAAACAATCCCATGCAACAGTGGGCTAA 4082
                         -  v   ii  v     i---     i  i  v  v?  v i     v  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAG---ACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_195954030_   4083 GTACATGAACAGACAACACTCAAAGGAAGATATACAAATGGCCAGCAAGC 4132
                          v iv    i     viv   v  i                   ii    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_195954030_   4133 ATATGGAAAATATGCTCAACATCACTAATTAT 4164
                          i   -    v             ????????
  L1M4_orf2#LINE/    878 ACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (134 / 97)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.40 (36 / 15)  


2697 28.72 1.79 0.56  chr1_196019929_196022426.rev     1115  2009 (489)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_196019929_   1115 GAAAAACATTCCATGCTCATGGATAAGAAAAATCAATATTGTTAAAATGG 1164
                             i i  i     i        vi   i v i           i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_196019929_   1165 CCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTTCTATGAATCTA 1214
                          v     v      vii  i           i  v  ii    v  vv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_196019929_   1215 CCATTGAGATTCTTCACAGAACCAGAAAAAAACTAATTTTAAAAAT-ATA 1263
                            vivivv  i  ii     -- vvi v  i  i  ii     v -   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_196019929_   1264 TGGAACCTTAAAAGAGCCGAAATAGTGAAGAAAATCCTAACAAA-AAGAA 1312
                              vivi  ii  v  ii     iv  i v    i i v   -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_196019929_   1313 CAAAGGTGGAGGCATCACACTACCTGACTTCAAACTATTCTACAGGACTA 1362
                              v      vv       v  ii i      viv v     iii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_196019929_   1363 CAATAACCAAAACAGCATGGT-CTGGTACAAAAACAGACATA--GATCAA 1409
                           i   i   i    ii    -    i i  ii i       --      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_196019929_   1410 TGGAACAGGTTAGATAACCTTGAAATAAGACCACATACCTACAACTATCT 1459
                              i  iv v  v ii iv       iv   i i ii  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_196019929_   1460 GATCTTTGACAAATCTAACAAAAACAAGCAATGGGGAAGTGATTCCCTTT 1509
                            i  i     ivv iv   i v  vv          ivi  vvi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_196019929_   1510 CCAATAAACAGTGGTAGGATAACTGGCTAGCCATAGGCAGAAGATTGAAA 1559
                         i   i   ii   v i   i      v  ?   i v   i    v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_196019929_   1560 CTGAACTACTTCCTTATACCATATACAAAAATTAACTCAAGATGGATTAA 1609
                         i  i  iv  v   i i                       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_196019929_   1610 AGACTTACAAGTAAAACCCAAAACTATAAAAACCCTGGTAGACAACCTAG 1659
                             i  v v    i v i            vi i i v   v   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_196019929_   1660 GCA-ATACCACTCAGGACATAGGCATGGGCAAAGATTTCATGACAAAGAT 1708
                          ?i- v i -i  iv   v v  vv i     v i    v iivv v  i
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_196019929_   1709 GCCAAAA--ACAATTGTGACAAAAGCAAAAATTGACAAATGGGATCTAAT 1756
                         i      --    -- ii       v      v  i    v   ii v  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_196019929_   1757 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATAAATAGAATAAATA 1806
                         i   v v  i i   i  ii vv    i  v     v  v i i i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_196019929_   1807 GACAATCTACAGAATGGGAGAAAATTGTTGCAAACTGTGCATCTGACAAA 1856
                              i i                 vv       iii ii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_196019929_   1857 AGTCCAATATCCAGCATCTATTAGGAACTTCAACAAATTTATAAGAAAAA 1906
                         i v ivi       v  v   v i     iiv    v iv    v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_196019929_   1907 ---AAAT--CCTCGCTAAAAAGTGGGCAAAGGGTATGAACA--CTTTTCA 1949
                         ---    --  ivii ?    i          i v    i -- v    v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_196019929_   1950 CAAAAAAAGACATACATGTGGCCAGCAATCATATGAAAAAA-GCGCAACA 1998
                          v   i    i     vi      ii  v  i       i -  v     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_196019929_   1999 TGACTGATCAT 2009
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (151 / 102)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 1.62 (21 / 13)  


3660 21.28 3.15 0.90  chr1_196023983_196029076     3714  4601 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196023983_   3714 TGGAAA-ATATCTGATGTTCATGGATTAAAAGACTTAAAGTTGTTAAAAT 3762
                               -     iv             ii         vi       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196023983_   3763 GTCTAAACTACCCAAAGTGATCTACAGATTCAATGCAATCCCTATCAAAG 3812
                          v v v   v      v                i               i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196023983_   3813 TGTCAA-TGCTATTTTTTGCCAAAA---AAAAACCCAAAATCTAAAATCC 3858
                          vi  i-   i-        vi   --- v  i i--i vi       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCT--GATCCTAAAATTC 147

  chr1_196023983_   3859 ATATGGAATCTCAAAGGGCCCCAAATATTAAAATCAATCTTCAGAAAGAA 3908
                                 viv   i  i   vi    viv   v       v i      
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_196023983_   3909 AAACAAAGCTGGAGGCCTCACACTTCCTGATTTCAAAATATCTTACAAAG 3958
                         i       i      v           ii         iv vi       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_196023983_   3959 CTACAGTAATCAAAATGGTATGGTACTGGCATAAAGACAGACATATAGAA 4008
                                      i ii  i              i  i           v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_196023983_   4009 CAATGAAACAGAATGAAGAATCCAAAAATAAATCCTCATATATATGGTCA 4058
                              i  i     vi   i    i       i  vi i  v        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_196023983_   4059 AATGATCTTTGACAAAGGTGCCAAGGGCTTCACAATGGGGAAAAGGATAG 4108
                          v    i  i     i         iv v i-           - i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAA-GAATAG 395

  chr1_196023983_   4109 TCTATTCAATACATACTTGTGGGAAAACTGTATATCCACATACAGAAAAA 4158
                            v     i v  iv vv     v     v   ?      i  i  i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_196023983_   4159 TAAAATTGGACACTTACCTTAAATCATACACAAAAGTCAACTCAAAATTG 4208
                          i  i      v i     i v i    i      i i          v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_196023983_   4209 ATTAAGGACCTAAAT-TAAGGCCTGAAATCATAAAATCCCTGGAAGAAAA 4257
                           i ?i         -    iv  i   ii      ii i i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_196023983_   4258 CATGGGGAAAAACTTCCTTGAAATTGACCTTGACAGTGATTTTTTGGATA 4307
                            i  ?iv   ii i v   vv   ivi v i  i  i   i  i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_196023983_   4308 CGACATCAACTGCTCAGGCAACAAAAGCAAAA-TAAACAAGTGGTACTAT 4356
                         i    i   vv  v  i          v    -  i i  i v v   vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_196023983_   4357 ATCAAA--CAAAAAA------GCTTCTACAGAACAAAATAACGAAA-TAA 4397
                               --i     v------     - v  i   vv  v v    - i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTC-AAAGGACACTATCAAGAAAGTGA 694

  chr1_196023983_   4398 AAAATTTACCTACAGGTTGGGAGAAAATATTTGCAAACCATATA------ 4441
                            iviv   i    iv                    i      ------
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_196023983_   4442 AAGGG--TTACTATTCAGAATATAGAAAGAATTCCTCTAACTCAACAACA 4489
                              --  i-   i         v      i  i vi       i  i 
  L1M4_orf2#LINE/    745 AAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_196023983_   4490 AGCAAACCAAACAATCCAATTCAAAA-TAGGCAAAAAGATTAAACAGACA 4538
                          iv i  -   i  i      ?    - i      iiiv  i  i     
  L1M4_orf2#LINE/    794 AAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_196023983_   4539 TTTTTTCAAAGA---TATATAAATGGCCAACAAGCACATGAAAAGATGTT 4585
                            i i      ---    i          i                 i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_196023983_   4586 CAACATCAGCAATCAG 4601
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (120 / 65)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.89 (36 / 19)  


2512 29.97 0.44 0.77  chr1_196038116_196043446     3934  4844 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196038116_   3934 TGGAAAAACATTCCATGCTCATGGATAAGAAAAACCAATATTGTTAAATT 3983
                               i i  i     i        vi   i vii           iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196038116_   3984 GGCCATACTGCCTAAAGCAATTTACAGATTCAATGCTATTCCTATTAATC 4033
                            v     v  i   vii  i           i  v  i     i  vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196038116_   4034 TACCATTGAGATTTTTCACAGAACTAGAAGAAACTAATT-TAAAAATCAT 4082
                          v   vivivv     ii     v v  v-  i  i  i-     v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr1_196038116_   4083 ATGGAACCAAAAAAGAGCCCAAATAGCCAAGGAAATAC-GAACTAAAAGA 4131
                               viiv  ii  v  vi         iiv   vi-   vv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_196038116_   4132 ACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAGGGCT 4181
                               i      vv     i v  ii i      viv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_196038116_   4182 GCAGTAACCAACAAAGCATGGTCCCGGCACAGAAACAGCTACATTGACCA 4231
                         i      i   v v  ii    v i    i iii i  vi i  v  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_196038116_   4232 ATGAAACAGGTTAGAGAACCCAGGAGTAAGACTGCACACACACCTACAAC 4281
                            i  i  iv v    ii    i i   -  i---  i   ii  iiii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAA-ACC---CATACATTTATGGT 345

  chr1_196038116_   4282 TATCTGATCTTTGACACACCTGACAAAAACAAGCAATGGGGAAAAGATTC 4331
                         i vi    i  i    vivv  v   i v  vv           ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_196038116_   4332 CCTATTCAATAAGCAGTGGTAGGATAACTGGCTAACCATAGGGAGAAGAT 4381
                         i  v     i  iii   v i   i      v  ?   i v v i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_196038116_   4382 TGAAACTGAACCCATTCCTTATACTATAAAAAAAAGTTAACTCAAGATGA 4431
                             ii  i    v v   i i  i   v v    i         i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_196038116_   4432 GTTAAAGACTTAAATATAAAACCCAAAACTATAAAAACCCTGGTATACAA 4481
                         i i ?    i     i   i v i            vi i i v v v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_196038116_   4482 CCTAGGCA-ATACCATTCAGGACATAGGCATAGGTAAACATTACATGACA 4530
                          v    ?i- v i -   iv   v v  vv    i  vvi  v v iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_196038116_   4531 AAGACACCAAAAGCAATTGCAACAAAAGCAAACCTTCAAAAATAGGATCT 4580
                          v             vvv          v   vv vv v    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_196038116_   4581 AATTAAA-CCAAGAGCTTCAGCACAGCAAAAGAAACTATAAACAGAATAA 4629
                         v  i   -ii  i i   iv ii vv    i  v     v  v i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_196038116_   4630 ACAGACAACCTACAGAATGGAAGGAAATTGTTGCAAATTATACATCAGAC 4679
                          v        i         i  i    vv        i   i   v  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_196038116_   4680 AAAAGTCTAATATCCAGCATCTATAAGGAACTTAAACAACTTTACAAGAA 4729
                           ii v  vi       v  v     i     ivv      iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_196038116_   4730 AAAAATCAAACAACCCCATTAAAATGTGAGCAAAGGATATGAACAGACAT 4779
                            i -    i     v   ?   vi  i         v    i      
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_196038116_   4780 GTTTCAAAAAAATACATACATGTGGTGAACAATCATAAGAAAAAAAGCTC 4829
                         v i  v   i  v i     vi   iv  i  v  i v     i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_196038116_   4830 AAGACCACTGGTCAT 4844
                           v i  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (151 / 118)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.22 (11 / 9)  


3117 23.19 5.24 0.82  chr1_196076271_196078122      502  1359 (493)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr1_196076271_    502 CTATGTTCATGAATCAGAAGACACAGTATCATTAACATACCAATTCTTCC 551
                          i         i  ii      vi i   ii    v  iv    v  i  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_196076271_    552 CAAAGTTATCTACAGATTCAATGTAAATTCAATCAAATTGCCAACAGGGT 601
                             v v              i i  vii v      v v   i --v i
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC--TGC 110

  chr1_196076271_    602 TTTTGTTTTGTAAATATCAGTGTGTTAATTCAAATATTTATATGAAAAGG 651
                         i   --    i i v  iiiiiv i i  i v  v   i     i   v 
  L1M4_orf2#LINE/    111 CTTT--TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr1_196076271_    652 CAAAGGAACAAGACTAGCCAAAACAATTTTGAAAAAGTA----AAAGTTG 697
                            i   v v   v             i         v ----       
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_196076271_    698 GAGGACTCACACTACCTAATTTCAAGTTTGATTATAAAGCT---GTGATA 744
                                      v  i        ivi v i  i      ---  i  v
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_196076271_    745 AAAACAGTATAGTACTGAAAT---------TTTATAGATCAATGAAATA- 784
                           i     i i      iv  ---------iv            i    -
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_196076271_    785 --T----AGTTCAGAAATAGACCTACACAAATATGATAAATTGATTATCA 828
                         -- ----   i        i   i i   vv    i v        v  i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_196076271_    829 ACAAAGGTGCAAAGGCAAGTCAATGAAGAAAGGATAGTCTTT-------A 871
                             i     v   i v v      ii     i         ------- 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_196076271_    872 T----------CAACTAGATATTTACATGTAAACAACAATGGACCTCATT 911
                          ----------     i    ?ii     i   -- v    i vi vivi
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAA--AGAATGAAGTTGGAC 456

  chr1_196076271_    912 CCATACCTTCTACCATACACAAGTATCAGTTCAAAAGGGATCATAGCTCT 961
                           v     ivi      i    iv  i ii      v      ?  vi  
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_196076271_    962 AAACTG-AAAATCAAAAACCATAAACTGGCTAGAAAAGAATATAGGGAAA 1010
                            -  -  i v v     i     vivvi     i i  i     ?iv 
  L1M4_orf2#LINE/    507 AAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_196076271_   1011 AATATTTGAGACCTTCAGTTAGGCAAAGCTTTGTTAGATATTACACTAAA 1060
                            v  i v      vi         v v   v        v    i   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_196076271_   1061 AGCACAAGCCATAAAGGAAAAAGCGG-TAAGTTGGACTTTATCAAAATGC 1109
                                  v i   i      iii -   i        i        vv
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_196076271_   1110 AAAACTTCTGTTCTTCAAAAGACACAATTAAGAAAACAAAAAGATAAGCC 1159
                                i   v       i     v  i      iii      i  v  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_196076271_   1160 ATAGGCTGATAGAAAATATTTGCAATTCATATATTTGATAATGGACTTGT 1209
                          i  iv  iv               v        i      v        
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_196076271_   1210 ACCCACAATATATAAATAACTCT-A-AACTCAATAATAAGAAAACAA-CA 1256
                          i   v          v      - -             i  i    -i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_196076271_   1257 TTTCAGTTTAAAAATAGGACAATGATTTGTATAGACAGTTCATAAAAAAA 1306
                         vii  i  ?      i  vv  v      v       v   viv   i  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_196076271_   1307 GATATATCAATGGAAAATAAGCCTATGAAAACATAATCAATCTCAATAGG 1356
                               iv     vv       vi       v  iv    iv   ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_196076271_   1357 TAT 1359
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.38 (113 / 82)
Gap_init rate = 0.02 (16 / 896), avg. gap size = 3.25 (52 / 16)  


3516 21.11 3.61 1.13  chr1_196081875_196084116.rev      866  1751 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196081875_    866 TAGAAAAATATTCCATATTTATAGATTAGAGGACTTAATAT-GTTAACAT 914
                          i    i    i    i  i  i    i  i          -     v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196081875_    915 GACAATATTACTCCCCATGATGGTCTACAGATTCAACACAATCTCTATAA 964
                          i     ---       viv  i              i     i    v 
  L1M4_orf2#LINE/     51 GGCAATA---CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_196081875_    965 AAATCTCAGCT----TTTTTGCCTAAGTGTAAAAACTAATTCTGAAATTC 1010
                              i     ----       vv  i vv v  i  i  i  i      
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_196081875_   1011 ATATAAAATTTCAAGGGACCCAGAATATCCAAAATAATATTGGAAAA--A 1058
                             ii  v v                v      i   v   i    -- 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_196081875_   1059 GAATAAAGTTATAGGAATCACACTTCATGATTTCAAAACAGTCTACAAAG 1108
                            i      iv    v         vii          vvv        
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_196081875_   1109 TTAAAATAATCAAGTCAGAGTGGTACTGGCCTAACAATAGATTTATCAAT 1158
                         i  v i        v   v           v   vi     iv   vi  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_196081875_   1159 CAATGGAACAGAATTTTGAATCCAGAAATAAATCCTTATCTATATGGTCA 1208
                                 i      vv  i            i  v  iv v        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_196081875_   1209 ATTGATTTTAAACAAAAATGTCAA-ATTATTTAATGGAGA--GATTTTTT 1255
                                  vi    iii  i   - ii   i     i  --  v vv i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_196081875_   1256 TTTTCAGTTAATTGTGCTGGAACTACTGAAAATCCATATGCAAAAGAATG 1305
                               iiv   v       i  v    i v ?   i             
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_196081875_   1306 AAGATGAACCCATTTTATACACCATACACAGCA-TTAACT-GAAATTAAT 1353
                            v  i    v viivi        i   iv -      -i    vi  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_196081875_   1354 CACAGACC--AACATTACAGCTAAAACTATAAACATTTTATAA------- 1394
                           ?     --  ii v v               vv i   v  -------
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_196081875_   1395 ----AGTAAGTCTTCATGACTTTTAGTTAAGTAATGACTTGTTAGATACA 1440
                         ----?    i     i    i  vi    i i    ii  v       ii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_196081875_   1441 ACACTGAAAGTACAACCAACCAAAGGGGAAAAAACCCAGGTAAATTGTTT 1490
                             ii    i    v    v    ---      i--  i       vvi
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAG---AAAAAAT--AGATAAATTGGAC 642

  chr1_196081875_   1491 TTTGTCAAA-CTAAAAACTTCTGCATCACAAAAAACACTGT-AAGAAAGT 1538
                           ii     -i         i  iiiiv    ii     i -        
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_196081875_   1539 AAAAAGGAAACCCTATAAAGTGAGAAAAAA-AT--GTAAATTACATATCT 1585
                         i     iv     - i i i  i  i    -  -- i    i i      
  L1M4_orf2#LINE/    693 GAAAAGACAACCC-ACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_196081875_   1586 AATAAGAGATTTGTATCCAGAATATATTTAGAATTCTTACAAATCAACAA 1635
                         i     i  i                 vv    i        v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_196081875_   1636 TAAAAAGACAAATA-CGCA-TTTAAAAGTACACAAAGGCTATGAATAAGT 1683
                                       - v  -  ?    i ivi      v v      iii
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_196081875_   1684 ATTTCTCTAAAGAAGATATACAAATTGGCAAAAAAACATCTGAAAAGATG 1733
                                i                 -   v  v  i  iv          
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAAT-GGCCAATAAGCACATGAAAAGATG 890

  chr1_196081875_   1734 TTCAACAACATTAGTCAT 1751
                         i      v  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (114 / 69)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.10 (42 / 20)  


2621 27.00 2.56 1.67  chr1_196116923_196119239      925  1824 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196116923_    925 TAAAAAAGCCTCCCATACTCATGAGTTAGA-GAATCAATATGATTAAAAT 973
                          ii   iiiv      ii     ii  i  -  v i     vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196116923_    974 GACCATTCTGACCAAAGTAATCTACAGGTTCAATGCAATCCCTTTCAAAT 1023
                          i v  v  vv     v i        i     i         v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196116923_   1024 TACCAAC-ACTATTTTT-CACCAAATAAGAAAAGAATCCTAAAATTTATA 1071
                          v   i -i iv     -  vv  v i v  ivvi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_196116923_   1072 TGGAACCAGAAAAGACCCCAAATCACTAAAGCAATTCTAAACAAAAAGAA 1121
                              viiv  ii     vi   vi i   i    ii i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_196116923_   1122 CAAATCTGGAGGAATTACACTGCCTGACTTCAAATTATACTACAAAGCTA 1171
                             vi       v i     v  ii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_196116923_   1172 TAATAACTAAAACAGCATGCTACTGGTACAAAAATACATACATAGATAAA 1221
                         i i   ii  i    ii  v      i i  ii   v i i      v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_196116923_   1222 AGGAACAGAATGAAGAATCAAGATGCAAAGCTACAAACCTACAGCCAAAT 1271
                         v    i     vi   i  v   vii   v i i v ii  ii i   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_196116923_   1272 GATCTTTGACAAGGTAGACAAAAATAAACAATGGGAAAAGGACATCTTTT 1321
                            i  i       vv v   i vi vv       i    i i vii   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_196116923_   1322 TCAATAAATGGTGCTGGGAAAATTGGCCAGCCATATGCAGAAGAATGAAA 1371
                             i              v  i   vi ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_196116923_   1372 ATGGACACTTATCTCTTACCATATATAAAAAATAA--------------- 1406
                         v     v i  i   vi        i     v   ---------------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_196116923_   1407 AGATTTAA-TATAAGACTTGAAGCTACATAAATTCT-AGAAGAAAACCTA 1454
                            ii   - i     vi i  i   i -   i   -          v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATA 549

  chr1_196116923_   1455 GAAAAAAATATTCTGGACATTGGCCTAGGCAAATAATTTATCATTAAGTG 1504
                          i?iv    v   vv   v    vi       - ii   v i ------ 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA------G 592

  chr1_196116923_   1505 ATATTTTCTCCAAAATGAAATGCAACTAAAACAAAAAATAGACAA-TGGG 1553
                             vv- v      vv v v     -    v          i  - v  
  L1M4_orf2#LINE/    593 ATATGA-CACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGG 640

  chr1_196116923_   1554 AATTAATTAAACTAAAAAGCTTCTGCACAGTAGAAAAAAAAA--AACAGA 1601
                          v  v  i   v v    i   i  ii vvi i ii v vv --  v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_196116923_   1602 ATAAACAGACCATCTACAGAAAGGGAGAAAATATTTGCAAATTATGCTTC 1651
                         i i  v    v i i      v                    i  iiv  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_196116923_   1652 TGGCAAAGGATTCATATTCAGAATCTACAAGGAACTCAAACAACTCAACA 1701
                           ii  i   i ii   i      v  i  i      vv         i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_196116923_   1702 AGAGAAAAAACATACAACCCCATTAAAAGTTGGGCAAAGGACATGAACAA 1751
                          v -    i   v i     v   ?   iv           iv    i i
  L1M4_orf2#LINE/    791 ATA-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_196116923_   1752 ACATTTCCCAAAAGAAGAAATGCAAGCAACCAGAAAATACATGAAAAAAA 1801
                                i v        v  i   iiii   iv  ii         i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA- 888

  chr1_196116923_   1802 TAAACCTTAACATCATTAATCAA 1824
                          i---  i       ????????
  L1M4_orf2#LINE/    889 TG---CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.38 (38 / 16)  


2164 28.31 2.12 5.83  chr1_196123860_196131574     1950  2892 (4823)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196123860_   1950 TGAAAAAACATTGCATGCTCATAGATTGGAAGACTCTATATTGCTAAAAT 1999
                           i   i i  iv    i    i            iv      i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196123860_   2000 GAACATATGGCCCAAAGCAGTTTACAGATCCAATGTCATCCCTTTCAAAT 2049
                          ivv   ivv      viii i       i   i iv      v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196123860_   2050 TACCAGCATCATTTTCAACAGAATTAGAAAAAACAAATTTAAAATTCATT 2099
                          v     vv v    ivi     v v  v  ivii vii          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_196123860_   2100 AGGAACCAAAAAAAAAAAAAAAAAAAAAAAGAAAAGCTCAAGTAGTC--A 2147
                         v    ----------- viv  iii vvv    v   iv  ii i  --i
  L1M4_orf2#LINE/    151 TGGAA-----------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_196123860_   2148 AACAACAATGAAAGAATAAAGCTAAAGGCATTATATTACCTGACTTGAAA 2197
                           v  -----i     i    i ii   vv i i i v  ii i  v   
  L1M4_orf2#LINE/    190 AAAAA-----GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_196123860_   2198 TTATACTACAAGGTTATAGTAAGCAAAACAGCATGATGCTGATATAAAAA 2247
                         viv        i i  i     v   i    ii  i i   ii    ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_196123860_   2248 CAGACACACTTTTCAGTGATACAGAGCAGAGAACCCAGACATAAAACCAC 2297
                         i     i ivvv   i  iv i   iiv    ii     v     v   i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_196123860_   2298 ATACCTAAAATTAAGTTTTCTTCAATAAAGTCAACAAAAATATATACACT 2347
                          i ii  vii i  v vv i   i i  i viiv   i vi  - -  v 
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT-T-CAAT 382

  chr1_196123860_   2348 GGGGAAAGGACAACCTATTCAGTAAATGGTGCTGGAAAAATTGTATTGCC 2397
                                 i i ii  v    ii            i v  i  v  v?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_196123860_   2398 ATGAGCAGAAGAAAGAAACTGGGCCCC-ATCTCTCCAGGCTAGCTGATGA 2446
                          iiv   i     v   ii   i    - i   -----------------
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTC----------------- 465

  chr1_196123860_   2447 AGTACCAAACTGTATACTGTATACAAAGACTAACTCAAGATGGATTGAAG 2496
                         ------------- i  ii        i i        i      ii?  
  L1M4_orf2#LINE/    466 -------------ACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_196123860_   2497 ACTTAAATGTATGATGTGACACTATATAAGTCTTAGAAAAAAAAACTGAG 2546
                           i        v  vv i v      v  v        i    v i--  
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT--AG 550

  chr1_196123860_   2547 GAAAAACTCTTCTAGACGAATTGGCCTAGGTAAATAATTT-------ATG 2589
                          ?iv  v     vv   v--    vi    i  - ii   -------   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACC--TTGGGTTAGGCAA-TGGTTTCTTAGATATG 597

  chr1_196123860_   2590 AC--CAATTTGTCAAATGCAACAAAAACACAAATAGACAAATGGAACTTA 2637
                           --   v--iv  v v         iv v       i    v i    v
  L1M4_orf2#LINE/    598 ACACCAAA--AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_196123860_   2638 GTTAAACTAAAAAGCTTCTGCAAAGCAAAATATATGATCAACATAGTAAA 2687
                         i i   v v    i   i  iivvv    iv i iv     v v   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_196123860_   2688 TAGACAACCTACAGAATGGGAAAAAATATTTGCAAGCCATGCATCCAATA 2737
                         v        i           i             ii   ii   ii   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_196123860_   2738 AAGGCCTACTATGCAGAATCTA-------CCCAAACAACTGGACAGGAAA 2780
                          i  v  vv   v      v  ------- i vv      vi i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_196123860_   2781 AA-ACAAACAACCCCATTAAAAAGTGGACATAGGACATGAACAGATATTT 2829
                           -     i     v   ?    i   i  v    iv    i   i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_196123860_   2830 TTCAAAAGAAGGCATACAAAAATCCAACAAGCATATGAAAACATGCTTGG 2879
                         i  v       ii       viv    i     i       v     iii
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_196123860_   2880 TATCACTAAAAAT 2892
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (158 / 105)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 5.00 (75 / 15)  

3132 21.16 3.73 4.39  chr1_196123860_196131574     6320  7231 (484)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_196123860_   6320 GAAAGAT--CTTGTGTTCATGGATTTGAAGAATTAATATTTTTTTAAATG 6367
                                -- iii            v     v        v  v- i   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGATG 51

  chr1_196123860_   6368 TCCATACCACCCCAAAT-GATATACAGATTCAATGCAATCCCTATCAAAA 6416
                         v v    i-        -   v           i                
  L1M4_orf2#LINE/     52 GCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196123860_   6417 TCCCAAATGGTATTTTTAACCAACATAGAGAAGACAATTCCAAAACTTGT 6466
                              iv  viv     i- vi v  v  v   vii  i i    i ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_196123860_   6467 ATGTAACCACAAAAGACCCCAAATATTCA------CCTTGAGAAAGAA-- 6508
                            v  vii   ii     vi    vi  ------i     i      --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_196123860_   6509 -CAAAGTTGGAGGCATCACACTTCCTAATTT-AAAATTATATTACAAAGC 6556
                         -            vv          i     -    i -  i        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr1_196123860_   6557 TATAGCAATCAAAACACTGT--TACTGGCATAATTATAGAAACATAGACC 6604
                           i  i      i   v   --           vv     v i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_196123860_   6605 AATAGAACTGAATTGAAAGGCTGGAAATAGACCTTAACATATA----CAA 6650
                            i   iv       i  v ii      i   ivv    v  ----   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_196123860_   6651 TCAATTTTCAACAAGGGCACCAAGAATACACAATGGAGAGAGAATAGCCT 6700
                          ii      i       ii      vi iv      i  i       i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_196123860_   6701 CTTCAACTAATGGTTCTGGAAAAACTGGATACCCACATGTAAAAAAATAA 6750
                         i      v      v    i v         ?       i    i   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_196123860_   6751 AATAAAATAAAACTCTACCCTTACACCATACACAAAAATCAACACAAAAT 6800
                          i ---- ii v i     - i        i        i   v      
  L1M4_orf2#LINE/    449 AGT----TGGACCCCTACC-TCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_196123860_   6801 TAATTAGTTAAAACAACACAAAATTAAATACTTAAATGTAATATCTGAAA 6850
                         --------------------ii  i ? v  i         v v  i   
  L1M4_orf2#LINE/    494 --------------------GGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_196123860_   6851 CGGTAAAACACCTAGTAAAGAACAT-GGGGAAAATCTTCTTGATATTGGC 6899
                          vi      v i   v i i     -  ? v        v   iv    v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_196123860_   6900 ATTGACAATAA---CTTGGATATAATAGCAAAAGC-TAAGCCAACAAAAT 6945
                         v v i    ii---   i     i i v       -i    -       v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC-AACAAAAG 622

  chr1_196123860_   6946 AAAATATATACAAGTGGAACTACATCAGACTTTAAAACTTCTGCACAGCA 6995
                             v   v i  i v i   v     i v  v       i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_196123860_   6996 AAGGA-ACTAATCAGTGAAATGAAAAGACAACCCATGGACTGAAAGAAAA 7044
                              -    -   ivi  i               ii  v  ii      
  L1M4_orf2#LINE/    673 AAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_196123860_   7045 TATTTGCAAACCATATAT--GATGAGGG-TTAACATTCAAAACATATAAG 7091
                                   i       --   i    -i vii  i  i  i      i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_196123860_   7092 TATCTCCTACAACGCAACAATAACAGCAATAAAGAAACCAATAATCCAAT 7141
                         v v   i      v   i     -------     -- v     i     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAA-------AAAGA--CAAATAACCCAAT 812

  chr1_196123860_   7142 TTAAAAATGGGCAA-GGACTTGAACAGATTTTTTTCCAAAGATGACATAC 7190
                          ?            -   i     i   iv   i        v  i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_196123860_   7191 AAATGGATAAGTGGTATCTGAAAAG-----CAACACTGGACAAATG 7231
                               vi  vvi i iv       -----     iii????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (117 / 72)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 2.85 (74 / 26)  


3371 24.83 1.10 0.88  chr1_196139017_196141653     1239  2144 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196139017_   1239 TGGAAAGATATTTCACTTTCATGGATTGGAAGAATCAATATTGTTAAAAT 1288
                                    ii  iv                v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196139017_   1289 GTCCATATTACTCAGAACAATCTACAGATTCAACACAATCCTTATCAAAG 1338
                          v v   i v i  i vii               i      i       i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196139017_   1339 TACCCA--TGACATTCTTCACATAAATAGAAAAAAAAATCCTGAAATTTA 1386
                          -    --  v -  i  ii  v    v  v  ivvi     i     i 
  L1M4_orf2#LINE/    101 T-CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_196139017_   1387 TATGGAAACACAAAAGACCCAGAATAGCCAAAGCCATCCTGAGCAAAAAG 1436
                                 ii   ii                 i v   i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_196139017_   1437 AACAAAACTGGAGGGATTACATTACCTGACTTCAAATTTTACTACAGAGC 1486
                               ii      iv i   i v  ii i      vi        i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_196139017_   1487 TAAAGTAAACAAAATAGCATGGCACTGGTATAAAAAGAGACACATTAACC 1536
                           v     v   i i  ii   i     i    ii v     i  vi i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_196139017_   1537 AGTGGAACAGAATAAACAATC-AGAAACAAATTTATATATCTAAAGTGAA 1585
                          i     i     vi v i  -     i   iii   i  i  vi  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_196139017_   1586 TTCATTTTTCATAAAGGTGCCAAGAACACACA-TAGGAAAAGAACTGTCT 1634
                           v     iv i  i          v  iv  - i  i      iv    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_196139017_   1635 CTTCAATAAAGGGTGCTGGGAAAACAGGATATACATATGCAGAAGAATGA 1684
                         i     i   v          v   v     ?v  i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_196139017_   1685 AAGTAGACCCGT--CTCTCACCATATACAAAAATCGAATCGAAATGGATT 1732
                          iv i     v --   v                ii v  i        i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_196139017_   1733 AAAAACTTAAATCTAAGACCTCAAACTATAAAGCCACTAAAAGAAAATGT 1782
                          ? i  i     v     v  v          i ivi  i       ii 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_196139017_   1783 TGGAGAAACTTTCCAGGACATTGGAGTAGGCAAATATTTCTTGAGCAATA 1832
                         v  ? v  v i i iv   v    iv       vvi      iiii vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_196139017_   1833 CCCCACAAGCACAGGAAACCAAAGCAAATGTGAACAAATGGGATCACATC 1882
                          v   v       i v   v    v   vi ii i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_196139017_   1883 TAG-TTAAAAAGCTTCTGAACAGCAAATGAAACCATCAACAAGGGAAAGA 1931
                         v i-       -   i  vi vv    v  v  i     v  i vi  i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_196139017_   1932 GACAACCCACAGGATGGGAGAAAATATTTGCAGACTCTCCATCTGACAAG 1981
                                     i                   i iiv vi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_196139017_   1982 GGATTAATAACTAGAATATGTAACAAGCTCAAACAACTCTATAGAAAAAA 2031
                            i vi  v i       i   vi i   vv       v   - v    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAAA 796

  chr1_196139017_   2032 AAATCTAAAAATAA---GATTTAAAAACAGGCAAAAGATCAGAATAGACA 2078
                          i i----      ---i   ?     ii      i   iv         
  L1M4_orf2#LINE/    797 AGAC----AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_196139017_   2079 TTTCTCAGAAGTAGACATATAAATGGCAAACAGATATGTGAAAAGTTTAT 2128
                               vi   v   i   i       v  i iii ii       v vv 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_196139017_   2129 CAGCATCATTGATCAT 2144
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (137 / 84)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


2831 28.54 0.44 0.77  chr1_196143200_196148986.rev     4386  5296 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196143200_   4386 TGGAAAAATATTCCATCCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4435
                               i    i    vi        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196143200_   4436 GGCAATACTGTCCAAAGTAATTTATAGATTCAATACTATTCCCATCAAAC 4485
                                  vi     v i  i  i        ii v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196143200_   4486 TACCATTGGCATTCTTCACAGTATTAGAAAAAACT-ATTTTAAATTTCAT 4534
                          v   viv  v  i  ii   v v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_196143200_   4535 ATGGAA-T-CAAAGAATACCCCATATAGCCAAGACAACCGTAAGCAAAAA 4582
                               - -   i i --   viv        i    i v i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_196143200_   4583 GAACAAAGCTGGAGGCATCATGTTACCTGGCTTCAAACTATACTACAAGG 4632
                                 i      vv   iii v  iiii      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_196143200_   4633 TTACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGGCATATAAGA 4682
                         i        i v i    ii         i iv ii i  i      -  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA-GA 296

  chr1_196143200_   4683 CCAATGGAGCAGAAGAGAGACCTCAGAAATAACACCATACATCTACAACC 4732
                         i       ii    vv    vii         vv        i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_196143200_   4733 GTCTACAACATTGACAATCCTGACAGAAACAAGCAATGTGGAAAGGATCT 4782
                         ivi i- viv i     vvv  v  ii v  vv     v      i  vv
  L1M4_orf2#LINE/    347 AATTG-ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_196143200_   4783 CCTATTCAGTAAATGGTGCTGGGAAAAGTGGCTAGCCATATGCAGAAAAC 4832
                         i  v    ii              v  v   v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_196143200_   4833 AGAAACTGGACCCCTTCCTTACACCTGATGCAAAAGTTAACGCAAGATGG 4882
                         v   ii         v   i     vv  i     i     v   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_196143200_   4883 ATTAAAGACTTAAATGTAAAGCCCAAAACCATAAAAACCCCAGAAGAAAA 4932
                           i ?    i         iiv i     i      vi ii         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_196143200_   4933 CCTAGGCA-ATACCATTCAGAAAACAGAGATGGGCAAAGACTTCATGACA 4981
                          v    ?i- v i -   ivi vviv i v i     v ii   v iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_196143200_   4982 AAAACGCCAAAAGCAATTGCAACAAAAGTCAAAATTTGCAAATGGGATCT 5031
                          vi  i         vvv          vv     vvii    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_196143200_   5032 AATTAAACTGAAAGAGCTTCTGCACAGCAAACAAAACTATCATCAGCGTG 5081
                         v  i   v v   i -   i  ii vv    vi v       vv iv   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_196143200_   5082 AATAGACAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGG 5131
                           v        i                 v       vii ivi     i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_196143200_   5132 CAAAGGTCTAATATCCATAATTTATAAAGAATTTAAACATGTTTACAAGA 5181
                         i  i  v  vi      v   v         i ivv   vv iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_196143200_   5182 AAAAAGCAAACAACACCATCAAAAAGTGGGCAAAGGACATGAGCAGACAC 5231
                             ii    i   v v  i?    i           iv   ii     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_196143200_   5232 TCCTTAAAAGAAGACATTTATGCAGCCAACAAACTTATGAAAAAAAGCTC 5281
                          i  iv        i  vi viii     i  i vi       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_196143200_   5282 AACATCACTGATCAG 5296
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (146 / 110)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.10 (11 / 10)  


2583 26.62 0.28 0.28  chr1_196170039_196171740.rev      502  1211 (491)    L1M4_orf2#LINE/L1      199   908 (0)  

  chr1_196170039_    502 AACAGTGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 551
                             iv i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_196170039_    552 TACAGTAACCAAAACAGCATGGTACTGGTGCCAAAACAGAGATATAGATC 601
                                 i   i    ii         iiiv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_196170039_    602 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 649
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_196170039_    650 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 699
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_196170039_    700 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 749
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_196170039_    750 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 799
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_196170039_    800 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 849
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_196170039_    850 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 899
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_196170039_    900 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 949
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_196170039_    950 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 999
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_196170039_   1000 AGGCAACCCACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 1049
                           i         iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_196170039_   1050 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1099
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_196170039_   1100 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 1149
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_196170039_   1150 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 1199
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_196170039_   1200 ATCACTGGCCAT 1211
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (109 / 76)
Gap_init rate = 0.00 (2 / 710), avg. gap size = 2.00 (4 / 2)  


3357 23.61 1.42 2.30  chr1_196195248_196204115     4887  5801 (3067)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_196195248_   4887 GAAAAGACATCCTATGGCCTTGGATCAGAAGAATTAATATAGTTAAAATG 4936
                          i     i    i   vi v     ii     v       v     i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_196195248_   4937 ACCATACTGCCCAAAGCAATCTACAGGTTCAATGCAATCTCTATCAAAAT 4986
                         i v     v      vii        i     i      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_196195248_   4987 ACCAAC-ATTATTTTCACAGAATTAGAAAAAACAATTCTAAAGTTTATAT 5035
                         v   i -iiiv    ii     v v  v  ivii  i     i  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_196195248_   5036 GGAACCAAAAAAGAGCCCAAACAGCCAAAGCAATCCTAAGCAAAAAGAAC 5085
                             viiv  ii  v  vi  i       i     i i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_196195248_   5086 AAAGTTGGAGGTATCACATTCCCTGACTTCAAATTATACTATAAGACTAC 5135
                                    vv     i i  ii i      viv     i  ii    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_196195248_   5136 AGTAACCAAAATAGCATGGTACTGGGATAGAAATAGACACATAGATCAGT 5185
                              i   i i  ii         v   iii       i        i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_196195248_   5186 GGAACAGAATAGAGATCCCAGAAATAAAGCCACATACTTACAGCCAACTG 5235
                             i     v    vi           v   i i i   ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_196195248_   5236 ATCTTTGACAAAGTCGATAATAACAAACAATGGGGAAAAGACACCCTTTT 5285
                           i  i     i vi vi  v v  vv           ii i vi     
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_196195248_   5286 CAATAAAGGCTGCTGGAAAAATTGGATGGCCATATGCAGAAGAATAAAAA 5335
                            i   v v      i v  i     i?   i     i      i  iv
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_196195248_   5336 TGGACCCCATATATTAC--TATATACAAAAATCAATTCAAGATGGGTTAA 5383
                                 -  iv i  --i            i  i    i    i i ?
  L1M4_orf2#LINE/    452 TGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_196195248_   5384 AGACTTGAATATAAGAACTGAAACTATAAAAATACTAGAAGAAAACCTAG 5433
                             i i   i     i  i           v vi           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_196195248_   5434 GA--AAATTATTCTAGACATTGGTTTAGGCCAAAAAAAAAATCTATCAC- 5480
                          ?--    i-   vv   v    v      ------  vii i v i v-
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGC------AATGGTTTCTTAGA 593

  chr1_196195248_   5481 TACGAACTCAAAAGCACAGGTAACAAAAACAAAAATAGACAAATGGGACT 5530
                           i  vvi          i i       iv         i    v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_196195248_   5531 TAACTAAACT--AAAAGTCTTCTGTTTGGCAAAAGAAATAATTAACAGAG 5578
                          v ii   v --    v i  v  i  --    i  v iv  i  v i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAG 691

  chr1_196195248_   5579 TGAACAGACAGCTTAAGGAATTGGAGAAAATACTTACAAATATTTCCGCT 5628
                             v     i ii vi    v          i  i     ----- i- 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT-----CA-T 735

  chr1_196195248_   5629 ATGCCTTCAAGAGGAGACTAATATCCAGAATTTACAAAAAACTCAAATAA 5678
                           ii  --i v i i    vi          v  i   i     vv i  
  L1M4_orf2#LINE/    736 ATATCT--GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_196195248_   5679 CTCAACAA-AAAAACCCTGAAATAATCCCATTAAAAAGTGGGCTCAGGAC 5727
                              i  -     vv --      i  v   ?    i     vv    i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_196195248_   5728 ATGAATAGACATTTTTCAAAAGAAGA----CAAATGGCCAATAAGCATAT 5773
                         v             i  v        ----                 i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_196195248_   5774 GAAAAGACTGCTCAATATTACTGATCAT 5801
                                -       i  i ????????
  L1M4_orf2#LINE/    882 GAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (138 / 74)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 2.12 (34 / 16)  

2990 24.92 3.95 1.58  chr1_196195248_196204115     7489  8375 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196195248_   7489 TGAAGAGATATTTCATGTTCATTGGCAAGAAGACTCAATACTGTTAAGAT 7538
                           i i      ii         v iivi       i    i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196195248_   7539 GTTGATTTTTTCCAACTTAATCTGTAGGTTCAGTAAAATCCTATTCAAGA 7588
                          vii  vi ii    v  i    ii  i    iiiv     ivv    i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196195248_   7589 TCCCA-CTG--------GTGGAAATTGATAAAATAATTATAAAATTTATA 7629
                              -   -------- ii        i  iv i  iv       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_196195248_   7630 TAGAAAGGCA-GATACCCAGAGGGGCCAAAATAATGCTGAA---GTAAAG 7675
                          i    v   - iv       ivi       i   vi    --- v i i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_196195248_   7676 TAAA-CTGAAGTGTTAACACTACCTGACTTCAAGACTTACTATAAAGCTA 7724
                         i   -i  i  vii v     v  ii i     i        i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_196195248_   7725 AAGTAACCAAGACACCATGGTATTGGCAAGAGAAGAAATAAATTTATCAA 7774
                         v     i       vii     i     vi  i v i i v  vv     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_196195248_   7775 TGGAACAGAATAGAGAGCCTAGAAATAGATGC---CATT-------AGCT 7814
                              i     v     i i       i iv ---    ------- ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_196195248_   7815 GATTTTGGGCATAAAAGCAAAAGAGT-TTTGATTGAGAAAGGATACTCTT 7863
                               v i  viiiv  v  -  vi-  ii  v i     i   v    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_196195248_   7864 TTCAACAACTCATGCTGGAACAATCGGACATCCACGTGCAAACACAAAAA 7913
                                 v vi      i    ii   i ?    i      ---- i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA----AGAA 445

  chr1_196195248_   7914 TAAATCTATACACAGACTTTCTATCTTTTAGAGCAATTAACTCAAAATAG 7963
                          i  vi iv  v vv  i ivi i v v  v iv              i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_196195248_   7964 ATTGTAGACCTAAATATAAAGAAC-AAAACTATAAA-CTTCTAGAGAATA 8011
                           ii?          i   -  i -           -  ii    ii v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAA-GAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_196195248_   8012 ACACAGGAGAAAATCTAAGTGACCTTTGATT------TGGTTT-TCAGAT 8054
                            i   ? v      vv        v i  ------      - i    
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_196195248_   8055 ACAACACCAATAGCACTATCCATGAAAGAAAAAATTGATAATTTGGTCTT 8104
                          ii       v     v v v ii           v     v    v   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_196195248_   8105 TATTAAAGTTAAAAACAACTGACCAGCTAAAGACACTCTTAAGAGAATGA 8154
                         i  i   i        vvi  vv vv v  i      v i    i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_196195248_   8155 AAAGACAAACCACAGAATGGGTGAAA-TATTTGCAAAGCATATATATTAT 8203
                                 v            v    -          v       v v  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_196195248_   8204 AAATAACTTGTATCCAAAATATACAAAAAAAAAAACCTCTTAAAATTCAA 8253
                           ivi           i      i   i  ------      v  i    
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAA------CTCTTACAACTCAA 788

  chr1_196195248_   8254 CAATTAAAAAAGCCAACAACCCAATTTAAGAAATGGACAAACAAACTAAA 8303
                         i   -     ii v  i         ?  -      i    vi vi i  
  L1M4_orf2#LINE/    789 TAAT-AAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAA 836

  chr1_196195248_   8304 CAGGCTCCTCACCAAAGAAGATGTACAGGTGCAAAATGTGCATAAGAAAA 8353
                         i  i vii  v           i    ii  vvv   iv   i v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_196195248_   8354 GATGCTCAACATCATATTCCTC 8375
                                       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (134 / 83)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.58 (49 / 19)  


2661 27.55 3.02 1.34  chr1_196239770_196244709     3552  4444 (496)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196239770_   3552 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATATCATTAAAAT 3601
                               i i  i     i               v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196239770_   3602 GGCCATACTGCTCAAAACAACCTATAGATTAAACACTATTATTATCAATC 3651
                            v     v i    vii i   i     v   i v  ivi      vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196239770_   3652 TATCAATATAATTTTTCATAGAGCTAGGAAAACCTATTCTAAAATTCATA 3701
                          vi  iivvvv     iii   iv v iv  i iv  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_196239770_   3702 TGGAATCAATA-AAGAGACC--AAATAGCCAAAGCAATCCTAAGCAAAAA 3748
                              ---  i-   i    --i          i     i i iv  i  
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_196239770_   3749 AAACCAAAGCCAGAGGAATCTCATTACCTTGACTACAAACTATATTACAA 3798
                         i   -    iii     v  v  i v  i-i i v    viv  i     
  L1M4_orf2#LINE/    198 GAAC-AAAGTTGGAGGACTCACACTTCCC-AATTTCAAAACTTACTACAA 245

  chr1_196239770_   3799 GACTACAGTAACCAAAAGAGCATGCTACTGGTACAAAAACAGATACCTAG 3848
                         ii         i   i v  ii  v      i i  ii i   i iv   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_196239770_   3849 ACCAATGGAAGAGAATAGAGAACCCAGAAATAAAGCCACACACCTACCGC 3898
                          i        v     v    ii           v   i   ii  iv i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_196239770_   3899 CATCTGATCTTTCACAAAGTTGACAAAAATAAGCAATGGGAAAAAGACTC 3948
                           vi    i  iv    i v  v   i vi vv       i   ii ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_196239770_   3949 CCTATTCAATAAATGGTGCTGTGATAGCTGGCTAGCCATATGCAGAAGAA 3998
                         i  v     i           v  i i    v  ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_196239770_   3999 TGAAAGTGGGCCCCTACATTTCACCATAAGCAAAAATTAACTTGAGATAG 4048
                             iv   i       v iv       vi            ii i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_196239770_   4049 ATTAAAGACTTAAGTGTAAAAG--AA-----------TCCTAGAAGAAAA 4085
                           i ?    i   i     i  --  -----------  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_196239770_   4086 CCTAGGAA-AAACCATTCTGGACATTGGCCTTGGG--AAAGAAAGAATTT 4132
                          v    ?i-   i -   -- ----  i       -- iiv  v iv  i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTC--G----TGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_196239770_   4133 TTAACTATGTCCTCGAAAGCAATTGCAACTAAAACAAAAACTGACAAGTG 4182
                            iv    v vi i      vvv     v   iv     iv  i  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_196239770_   4183 AGACCTAATTAAACTCAAGAGCTTCTACACAGCAAAAGAAACTATCAACA 4232
                         i   i v  i   v i  i i   i iii vv    i  v        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_196239770_   4233 GAGTAAACAGACAACCTACTAAATGGAAAAAAA-ATTAACAAACTATGAA 4281
                         i   i  v        i  vi     i i    -   vi    ii  iv 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_196239770_   4282 TCAAACAAAGATCTAACATCCAGAAGCCATTAGGAACT--TACA--TTAA 4327
                           vi i  i iv  vii        vvi  v i     --    -- i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_196239770_   4328 CAAGCAAAAAACAAACAATCC--CTCCAAAATGGGCAAAGGACATAAACA 4375
                         i  vv    i     i  i  --i ?v               iv i  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_196239770_   4376 GACACTTCCCAAAAGAAGAC-TACAAGAAGCCAACAAACATATGAATAAA 4424
                             i   i v        i-     ivi     i  i  i     v i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_196239770_   4425 TGCTCCACATCATCATTAAT 4444
                              v      ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (156 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.29 (39 / 17)  


3281 25.20 2.35 0.67  chr1_196256083_196258146      684  1576 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196256083_    684 TGGGAAGATACAACATGTTCATGGATTGCAAGAATCAATATTGTTAAAAT 733
                            i      ivv               v    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196256083_    734 GTCCATACTACCTAAGGCAATCTACAGATTTGATACAATCTCTATCAAAA 783
                          v v     v  i  ivii           ii ii     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196256083_    784 TACCAATGACATTCTTTACAGAAATAGAAAAG-TAATCCTAACATTTATA 832
                          v   iivi v  i   i       v  v   - i       v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_196256083_    833 TGGAACCACAGAAGACCCAGAACAGTCAAAGCTATTCTGAGCAAAAAGAA 882
                              vii  iii         i  i    i v  ii   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_196256083_    883 CAAAACTGGAGGAATCACATTATTTGACTTCAAATTATACTACTA--TTA 930
                             ii       v     i viiii i      viv      v --i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_196256083_    931 TAGTAACCCAAACAGCATGG------CATAAAAACAGACACATAGACCTA 974
                         i     i v i    ii   ------     ii i     i     i v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_196256083_    975 TGGAACAGAACAGAGAACCCAGAAACAAATCCACATATCTACAGTGAACT 1024
                              i    iv    ii       i   i   i i  i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_196256083_   1025 CATTATCGGCAAAGGTGCCAAGAACACACATTGGGGAAAAGACAATCTCT 1074
                         v   v   i   i          v  iv  v        ii i i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_196256083_   1075 TCAATAAATAGTGCTAGGAAAACTAGACATCCATACACAGAAGAACAAAA 1124
                             i    i     i   v    i  i ?   i ii  i     ii  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_196256083_   1125 CTAGACCCCTATCTCTTGCCATATACAAAAATCAA-TCAAAATGGATTAA 1173
                         i i        i   vii              i  -           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_196256083_   1174 AAACTCAAATCTAAGACCTCAAACTATGAAACTAATACAATAAAACATTG 1223
                          i  ii    v     v  v       i     vv  v  v       v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_196256083_   1224 GAAAAACTCTCCAAAACATTGGAGTGGGCAAAAATTTCTTGAGTAATAAT 1273
                          ?iv  v   i ivi  v    iv i     vii      iii  - i i
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGAC 599

  chr1_196256083_   1274 ACCCCATGAGCACAGACACCCAAAGCAAAA-TGGACAAATGGGA--TCAT 1320
                            -- vi      ii  v v    v    - i  i    v   --    
  L1M4_orf2#LINE/    600 ACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_196256083_   1321 ATAAAGTTAAAAAGCTCCTGCACAGCAAAGAAAACAATCAACAACATAAA 1370
                         -i   i       -  ii  ii vv     i v  v     v  vi i  
  L1M4_orf2#LINE/    648 -CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_196256083_   1371 GAGACAACTCAAAGAGTGGGAGAAAATATTTGCAAACTACTCATCTGAAA 1420
                         i       i  v   i                    ii ivi      v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_196256083_   1421 AGGGATTAATAACCAGAATATTCAAGTAGCTCAAATAACTCTTATAAT-- 1468
                              i vi  v         vi  iv i   vv i     v-     --
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-ATAATAA 794

  chr1_196256083_   1469 -----CTTATAATTCGATT-AAAAATGGGCAAAAGATCTGAATAGCCATT 1512
                         ----- vv    ii i   -             i   i       v    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_196256083_   1513 TCTCAAAAGAAGATATACAAATGACGAACAGGCTTATGAAAAGGTGCTCA 1562
                             v                  i v  i i  vi        i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_196256083_   1563 AGGCCAGGCACGGT 1576
                          vii  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (147 / 75)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.08 (27 / 13)  


 232 24.32 12.16 0.00  chr1_196265806_196267737      428   501 (1431)    L1M4_orf2#LINE/L1        1    83 (825)  

  chr1_196265806_    428 TAGAGAGACATACTATGTTCGTGGATTAATATATTCAATATTGTTAAAGT 477
                          i  i   i  v i      i      iiv v i i           ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196265806_    478 G-------TCCACAAGGT-ATCTATA-ATTCAA 501
                          -------   v   iv -     i -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA 83

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 3.00 (9 / 3)  

 808 31.33 12.97 2.20  chr1_196265806_196267737      625  1441 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_196265806_    625 AATGATTTATCATGTTCATAGATATAAATATACAATAT-ATTTAAATACC 673
                           v   v vi         i   vvi  v ivi     -i  v i  iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_196265806_    674 ACTTTTCTCAAAATTAACCTATAACTATAACGCAA---------AAATCC 714
                          v vi  i v     i i   i iv vi       ---------      
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_196265806_    715 CAACAGAGGTTATTTG---AAATTCTGCAAGTTAATTTTAAAATATACCT 761
                           i v vvv  -    ---     v-i    i i  ii      vi iv 
  L1M4_orf2#LINE/    104 CAGCTGCCTTT-TTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCATAT 151

  chr1_196265806_    762 GTAAGAACT-GGGATC---AATAGTCATAATATTTCTGGAGAAGAA---- 803
                          v  ivi v-    i ---     i  v  i v ii  i i     ----
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_196265806_    804 ATTGTTAGAGTATTAGCCCTTTCGGATACCAAACTTTATTATAAAACTAG 853
                          vv   i   v i vi v   i vi  vi    vi   i  i   i   v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_196265806_    854 AACAATTAAGATACAGCCATAATGACATATGGAT-GAT---CAAATCAAT 899
                          ii   i    i vv ivi  v  i    v    -  i---i i      
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_196265806_    900 AGAACAGA-TGAAAAACCCAGAAACA--TTTATGCCTGTGTATAA--AAT 944
                         i   i   - vi i ii       i --iii  i --i v   ii--   
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATAC--ATTTATGGTCAAT 349

  chr1_196265806_    945 TGCTCTCC--CAA---TGC-AA----ATTTG-TGAAGAAAGGGTAAACCA 983
                           v i i --   ---   -  ----   ii-  ii     ii  iv iv
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_196265806_    984 GTCAATAAATGGAATCAGTATAATTGGTT--CTGCTT--AAAA------A 1023
                         v    i      viiii v i  i   v -- ii v --    ------ 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_196265806_   1024 GTTAGATCTCAATGCCCTACCTTACACAAAGATAAATTCCAAAGGTATTA 1073
                            i  i i v ivi vi   v  i     i  v  i  v   v v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_196265806_   1074 AAGAACTAGATGTGAAAAGTAAAATT---------TTA-------ACATA 1107
                         ?   v   i    i i iv     i ---------   -------     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_196265806_   1108 AAATGAAGTCTTTTTGATCCTAGAGTAAGAAAGGAATTCTTTTAAA---A 1154
                         ii?vv  i    iv   i i i iv  i v  v iv     -- i ---i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--AGATATG 597

  chr1_196265806_   1155 ACACAAAGATTGTGATCCATAAA-GAA------GATTAATTTGACTGTAT 1197
                             v  i viiii v v i   -   ------   v    v    vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_196265806_   1198 TCAAATTTTAAAATGTCTGTTCATCAAATGACACCA--AACAAATTGAAG 1245
                         -    v  v    iv i   v v     v     i --  v   v    i
  L1M4_orf2#LINE/    648 -CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_196265806_   1246 AAATAAGCCATAATCATGA-AGAACATATTT-TAAATACATATA----AT 1289
                          i i  v   i i-v   i-    v      -i    -      ----  
  L1M4_orf2#LINE/    697 AGACAACCCACAG-AATGGGAGAAAATATTTGCAAAT-CATATATCTGAT 744

  chr1_196265806_   1290 AAGAAAATAACTTATATTCAGGACA-ACAAGAGAAAG---ACAACT---- 1331
                            ii ----   i   i   i i - i  -    vv---      ----
  L1M4_orf2#LINE/    745 AAGGGA----CTTGTATCCAGAATATATAA-AGAACTCTTACAACTCAAT 789

  chr1_196265806_   1332 --TAAAATGAT------CTCGTAGTAGGAAAATGAACAAAGTGTAGCAGT 1373
                         --     v  i------ i -- i v?i      ii     vi vvv i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCC--AATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_196265806_   1374 AGGCAATCCACAGGAGAAGAAA-GCAAATGGTATACAAGTTTA--AAAAG 1420
                           i  v i v vii      v -i       ivv i   ivi --     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_196265806_   1421 ATGCCCTCAAC--CAGTGACAAG 1441
                             --     --  ????????
  L1M4_orf2#LINE/    888 ATGC--TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (153 / 100)
Gap_init rate = 0.05 (46 / 905), avg. gap size = 2.70 (124 / 46)  


3146 25.11 1.43 1.86  chr1_196332838_196339545     5306  6217 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196332838_   5306 TGGGAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5355
                            i  i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196332838_   5356 GGCCATACTGCCCAAAGTAATTTTTAGATTCAATGCTATCCCCATCAAGC 5405
                            v     v      v i  i vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196332838_   5406 TACCA-CTGACTTTCTTTACAGAATTTTAAAAAGCT-ATATTAAATTTCA 5453
                          v   -   v    -   i     v  -i v     -  vi    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATT-GACAAGCTGATCCTAAAATTCA 148

  chr1_196332838_   5454 TATGGAACCATAGAAGAGCCAGA-TAGCCAAGGGAATCC-AAACCAAAAG 5501
                                viii iii  v     -       iiv    i-i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_196332838_   5502 AACAAACCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5551
                               vi      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_196332838_   5552 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGATATATAGACT 5601
                                 i   i    ii         i i  ii i   i       ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_196332838_   5602 AATGGAACAGAACAGAAGCCTGTGGAACAGTTGCAGATATAACACCACAC 5651
                                i    iv  i-----------   i-    v    vv   i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAG-----------AGTC-CAGAAATAAACCCATAC 336

  chr1_196332838_   5652 ATCTGCAACCATCTGATCTTTGACAAACGTGACACAAACAAGCAATGGGG 5701
                           i iiiii  vi    i  i     iv   v  vi v  vv        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_196332838_   5702 AAAGGATTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAT 5751
                             i  vvi  v  i  i        i     v      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_196332838_   5752 GCAGAAAACTGAATCTGGACCCCTTCCTTACACCTTATACAAAAATTAAC 5801
                            i  i v    vi         v   i     v               
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_196332838_   5802 TCAAGATGGTTTAAAGATTTAAACATAAGAACTAAAACCATGAAAACCCT 5851
                             i    v i ?   ii    ii     i       i  i   vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_196332838_   5852 AGAAGAAAATCTAGGCA-ATACCATTCAGAACATAGGCATGGGCAAGGAC 5900
                                  iv    ?i- v i -   ivi  v v  vv i     v ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_196332838_   5901 TTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAA 5950
                            v iiv  vi            vvi          vv i   v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_196332838_   5951 ATGGGGTCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCA 6000
                           v  iii v  i   v v  i i   i  ii vv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_196332838_   6001 TCAGAGTGAATAGGCAACCAACACAATGGGAGAAAATTTTTGCAATCTAT 6050
                         vv i      v  i     v   v             v       vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_196332838_   6051 CCATCTGACAAAGGGCTAATATCCAGAATCCACAA-GAA-TCTTAAGCAA 6098
                         vi      i  i  i  vi          vi i  -   -     --   
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAA 783

  chr1_196332838_   6099 ATTTACAATTAAAA---AAAAAACCCA-TCAAAAAGTGGGCAAAGGATAT 6144
                         v iv i   v    ---   v      - i?    i            v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_196332838_   6145 GAACAGACACTTTTCAAAAGAAGACATTTATGCTGCCAACAA--ACATGA 6192
                            i     i  i  v        i  vi viiv     i  --      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_196332838_   6193 AAAAATGCTCATCATGACTGGTCAT 6217
                            i       v   v ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (133 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


2783 24.56 2.43 2.10  chr1_196343120_196346212     1701  2604 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_196343120_   1701 GAAAATATAGTTCAT--TCATGGGGTTGGAGGACTTAATATTTCTAAGAT 1748
                          i   v   vii   --      i-     i           vi      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGA-TTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196343120_   1749 GTCAGTTCTTGCCAAATGGATTTATAGATTACACACAAACCAGATCTAAA 1798
                          v  i v  iv      v   i  i     vv  i   v  vv   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196343120_   1799 TCCCAGCAGACTTTTTAGCAGAAATTGAAAAACTGATTTCACAATTTTTA 1848
                                v v      v           v  i     iii v    iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_196343120_   1849 TGAAAATGCAAAGCACCTACAATAGCAAAAGCAATTTTGAAACAAAACAA 1898
                           i        i v   i v      v   i    i      -  i - i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGA-AG 198

  chr1_196343120_   1899 AACAATGTTGGAAGACTAACACTACCTGATTTCACAACTTAT---AAAGC 1945
                              v      i    v     v  ii      v      i---     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_196343120_   1946 TAT-TTAATTAAGACATTAAGACACTGTAGCATTCACAAGAGACACAGAC 1994
                           i-v    i      v iv ii    --    -- - i  v v   v i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTG--GCAT--A-AGGATAGACATAT 293

  chr1_196343120_   1995 AGATCCATGGAACAGGAT-AATAATACAGAAACAGACCCATATAT--GTG 2041
                              v      i  i  -i v i v      i i       i  --i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_196343120_   2042 GACAGCTGATTTTTTTATAAAGACATAAAGACAATTCAATAGAAAAAAGT 2091
                          v  ii       iv- i  i iiiiv     v       i ii   - v
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAA-GA 391

  chr1_196343120_   2092 ATGATTTGTTCAACAAATAGTACTGGAGCAATTGTATATCAA-ATGCAAA 2140
                           ii i v          i  i    ii   i  v   ? v -       
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_196343120_   2141 AAACAATTGAACTTCAATATCTATATCACACCATATTCTAAAATTCTGTC 2190
                          i --  -   v  vi ivi   iv           v v      vvv  
  L1M4_orf2#LINE/    442 AGA--AT-GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_196343120_   2191 AAAATGGATCATACACCTAAATGTGAAACTTAAAACTATAAA-CTTGTAA 2239
                                    ? v          i i vi            -  iv  i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_196343120_   2240 AATAAATCATAGAAGAAAATCTTCACAACTTTGAGTGAGACCAAGATTTC 2289
                           v   v     i? v        iii  i   i  v  i v v i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_196343120_   2290 TTAGATATAATACCAAAGGCATAATTAATTTTA-AAAACATACTGATGAA 2338
                                 i i      i   i  vi  ivvv -    v   --   i  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAA 636

  chr1_196343120_   2339 TTGGTCTTCAT-AAAATTTTAAACTCCTGCTCTTTAAAGGATACTGTTAA 2387
                             v      -      vv     ii  iv   i      i   i i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_196343120_   2388 GAGAATTAAAAGACAAGTCACATACTGAGAAAAAGAGATTTACAAGTCTT 2437
                           i i v         vi    v v  i  i   - v    i   i  v 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAA-ATATTTGCAAATCAT 735

  chr1_196343120_   2438 ATATCCAAAAAAAAGAATTTCTATCCAGAATATATAAATGAATTCTTAAA 2487
                              ii v  i-- i i  v                 -   i     v 
  L1M4_orf2#LINE/    736 ATATCTGATAAG--GGACTTGTATCCAGAATATATAAA-GAACTCTTACA 782

  chr1_196343120_   2488 AGTCAGTAATAACAAAA-AAGCAATT---TTTCTAAATGGGCAAAATATT 2533
                          v   i      v  i -  ii  ii---  ?vv           iv   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_196343120_   2534 TTAACATGCCTTTCATCAACAA---TATATGAATAGTAAATAATT-CAT- 2578
                          v  i vi v    vi   vi ---    ii   i iv     vi-   -
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_196343120_   2579 AAAAGCTGCTTAACTTTAATGTAATT 2604
                              v    i   v i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (125 / 93)
Gap_init rate = 0.03 (28 / 907), avg. gap size = 1.46 (41 / 28)  


3084 27.86 1.22 0.44  chr1_196347637_196354007     4978  5878 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196347637_   4978 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5027
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196347637_   5028 GGCCATGCTGCC-------ATTTATAGATTCAACGCCATTCCCATCAAGC 5070
                            v  i  v  -------  i  i           v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196347637_   5071 TACTAATGATTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5119
                          v i iiviii  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_196347637_   5120 TGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAGAA 5169
                              viiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_196347637_   5170 CGAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5219
                          i   i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_196347637_   5220 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATCTAGACCAA 5269
                               i   i    ii         i iv ii i   v  v    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_196347637_   5270 TGGAACAAAAC--AGAGCCCTCAGAAATAATACAACACATCTACAACCAT 5317
                              i i  i--    i  --        vv v i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_196347637_   5318 CTGATCTTTGACAAACCTGACAAAAACAAGAATTGGGGAAAGGATTCCCT 5367
                         i    i  i     ivv  v   i v  vvv v         i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_196347637_   5368 ATTTAATAAATGCTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5417
                         v  i  i     v        v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_196347637_   5418 AACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5467
                          ii    iv   v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_196347637_   5468 AAAGAATTAAATGTTAGACTTAAAACCATAAAAACCCTAGAAGAAAATCT 5517
                          ?   vi       v   vi      i      vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_196347637_   5518 AGACA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTGAA 5566
                           i?i- v i -   iv   v v  vv i     v ii   v iiv ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_196347637_   5567 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATGTAAT 5616
                                     vvi          vv     v  i    v   iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_196347637_   5617 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5666
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_196347637_   5667 GGCAATCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACAAA 5716
                          i   i i                 v   i   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_196347637_   5717 GGGCTAATATCCAGAATCTACAAAGAACTTCAACAAATTTACAAGAAAAA 5766
                           i  vi          v  i        iiv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_196347637_   5767 AATGAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5816
                         i i-   i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    798 GAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_196347637_   5817 TCAAAGGAAGACATTCATGCAGCCAACAGACACATGAAAAAACGCTCATC 5866
                           v  i     i  v  viii     i ii          i i     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_196347637_   5867 ATCACTGGCCAT 5878
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (151 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.14 (15 / 7)  


2954 25.40 0.75 3.01  chr1_196413129_196415972     1435  2363 (481)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196413129_   1435 TGGAAAAACATTCCATGCTCATGAATAAAAAGAATCAATATCATTAAAAT 1484
                               i i  i     i     i  vii    v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196413129_   1485 GGCCATACTGGCCAAAACAATTTATAGATTCAATGCTATTCCTATCAAAC 1534
                            v     vv     vii  i  i        i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196413129_   1535 TACCAATAACATCCTTCACCGAACTAGAAAAAAAACT-ATTTTAAAATTA 1583
                          v   iivi v ii  ii v   v v  v  i---  -  ii       v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr1_196413129_   1584 ATATGGAACCAAAAAAGAGCTCAAATAGCCAAGGCAATCCTAAGCAAAAA 1633
                                 viiv  ii  v ivi         ii     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_196413129_   1634 GAATAAAGCTGGAGGCATCATGCTACCCAACTTCAAACTATACTACAGGG 1683
                            i    i      vv   ii  v     i      viv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_196413129_   1684 CTACAGTAACCAAAACAGCATGATACTGGTTTTATAAAAAGAAAAAACAG 1733
                                  i   i    ii  i      i---    ii -------i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGC---ATAAGGA-------TAG 287

  chr1_196413129_   1734 ACACATAGACCAATGGAACAGGATAGAGAGTCCAGAAATAAGTCCACACA 1783
                            i     i        i  i  v                ii   i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_196413129_   1784 CCTACA---AATCTGTTTTTTGACAAAGTTGACAAAAACAAGCAATGGAG 1830
                         ii  ii---   -  v    i     i v  v   i v  vv      i 
  L1M4_orf2#LINE/    338 TTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_196413129_   1831 AAATGACTCTCTATTCAATAAATGGTGCTGGGGTAACTGG-CAACTGTAT 1879
                            vi ivv   v     i             ii      -i ? iii  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_196413129_   1880 GCAGAAGATTGAAATTGGACCCCTTCCTTACACCATATACAAAAATCTAC 1929
                            i    v    i          v   i                 iv  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_196413129_   1930 TCAACATGGATCAAAGACTTAAATATAAAACCCAAAAACAATAAAAGCCC 1979
                             v        ?    i     i   i v i    - v      vi i
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCT 535

  chr1_196413129_   1980 TGGAAGACAACCTAGGCA-ATACCATTCTGGACACAGGAATGGGCAAAGA 2028
                          i     v   v    ?i- v i -   vv   viv  iv i     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_196413129_   2029 TTTCATAACAAAGATGCCAAAAGCAATTGCAACAAAGGAAAAATT-GACA 2077
                             v  ivv v  ii         vvv        i      v -  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_196413129_   2078 AATTGTATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATC 2127
                              v ii v  i   v v  i i   i  ii vv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_196413129_   2128 AACAGAGTAAACAGACAACCTACAGAATGAAAGAAAATTTTTTCAAACTA 2177
                           v i   i  v        i        ii       v   v    ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_196413129_   2178 TACATCTAACAAAGGTCTAATATCCAGCATCTATAAGAAACTTAAACAAC 2227
                           i    i i  i  v  vi       v  v     ii    ivv     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_196413129_   2228 TCTACAAGAAAAACAAAACAAAACAAAACAAAACAAAACATAAAAATGTG 2277
                           ------  v  i    -- i     v---   vv  iv?       - 
  L1M4_orf2#LINE/    785 TC------AATAATAAAA--AGACAAAT---AACCCAATTWAAAAATG-G 822

  chr1_196413129_   2278 GTCAAGGACATGAACAGACACTTTTCAAAAGAAGACATACATGTGGCCAA 2327
                          iv     iv    i     i  i  v        i     vi       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_196413129_   2328 CCAGCATATGAAAGAAAGTGCAAGATCACTGATCAT 2363
                         iv    i      ii v iv   v    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (141 / 91)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.33 (35 / 15)  


3170 27.40 0.88 0.55  chr1_196581988_196588369.rev     4987  5891 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196581988_   4987 TGGAAGAACATTCCATGTTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5036
                              ii i  i            i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196581988_   5037 GGCCATACTGTCCAGGGTAATTTATAGATTCAATGCCGTCCCCATCAAGC 5086
                            v     vi   iiv i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196581988_   5087 TACCAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGGTCA 5134
                          v   iivi i  i  ii  -      -- v  i  - iii    iv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_196581988_   5135 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5184
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_196581988_   5185 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5234
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_196581988_   5235 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATCTAGACC 5284
                                 i   i    ii         i iv ii i   v  v    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_196581988_   5285 AATGGAACAAAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAGC 5332
                                i i  i--    i  --        vv   i    i  iiiv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_196581988_   5333 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGATTCC 5382
                          vi    i  i     ivv  v   i v  vv     i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_196581988_   5383 CTCTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5432
                           i  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_196581988_   5433 GAAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATAGA 5482
                            ii    i i  v   i     v              i    i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_196581988_   5483 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5532
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_196581988_   5533 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAGGGACTTCATGTCTA 5581
                         v    ?i- v i -   iv   v v  vv i    iv ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_196581988_   5582 AAACACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGTTCTA 5631
                         vi            vvi          vv   i v  i    v  vii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_196581988_   5632 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCGCCATCAGAGTGAA 5681
                           i   v v  i i   i  ii vv    i  v  iii  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_196581988_   5682 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5731
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_196581988_   5732 AAGGGCTAATATCCAGAATCTGCAGTGAACTC--A-AACTTACAAGAAAA 5778
                          i  i  vi          v ii iv      -- -    i vv iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_196581988_   5779 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5828
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_196581988_   5829 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5878
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_196581988_   5879 CATCACTGGCCAT 5891
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (151 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


3287 26.62 0.44 0.55  chr1_196885653_196892054     5001  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_196885653_   5001 TGGAAGAACATTCCATGCTCATGGGTAGGAAAAATCAATATTGTGAAAAT 5050
                              ii i  i     i      i v    i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_196885653_   5051 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5100
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_196885653_   5101 TACCAATGACTTTCTTCACAGAATTGGAAAATACT-ACTTTAAAGTTCAT 5149
                          v   iivi i  i  ii     v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_196885653_   5150 ATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGA 5199
                               viiv  ii  v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_196885653_   5200 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5249
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_196885653_   5250 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5299
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_196885653_   5300 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTAATATTA 5347
                               i    i--    i  --        vv   i i  i  vvi i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_196885653_   5348 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5397
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_196885653_   5398 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTTG 5447
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_196885653_   5448 AAACTGGATCCCTTCCTTACACCTTATACAAAAATAAATTCAAGATGGAT 5497
                           ii    i    v   i     v           v  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_196885653_   5498 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5547
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_196885653_   5548 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5596
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_196885653_   5597 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5646
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_196885653_   5647 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 5696
                          i   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_196885653_   5697 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5746
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_196885653_   5747 AGGGCTAATATCCAGCATCTACAATGAACTCAAACAAATTTATAAGAAAA 5796
                         i  i  vi       v  v  i  v      vv    v iv    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_196885653_   5797 AAAACAAACAACCTCATCAAAAAGTGGGCGAAGGATATGAACAGACGCTT 5846
                          i -    i    iv  i?    i     i      v    i    ii  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_196885653_   5847 TTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5896
                         i  v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_196885653_   5897 CATCACTGGCCAT 5909
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


 998 18.72 0.00 1.07  chr1_197385861_197387782      492   678 (1244)    L1M4_orf2#LINE/L1      268   452 (456)  

  chr1_197385861_    492 TAATAGTTGCACAAGCATAGACATATAGGTCAGAAAAATAGAATTGAAAG 541
                          ii  v v   i   v            i   ivii           i  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_197385861_    542 TCCAGAAGTAAACCCTTTCACTTATGGTCAATTGATTTTTAACAAGGGCG 591
                                i       v v  i                  ii       i 
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_197385861_    592 TCTAGCCAATTCAATGAGGGTAAAGAATAATCTTTTCAATAAATGTTGCT 641
                         i v  v v        i  --        i         i     v    
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGG--AAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_197385861_    642 GGGATGACTGGATATCCATGTATAAAAGAATTAAGTT 678
                             ii        ?   ii ii        v     
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

Transitions / transversions = 2.09 (23 / 11)
Gap_init rate = 0.01 (1 / 185), avg. gap size = 2.00 (2 / 1)  

1837 17.90 4.80 2.18  chr1_197385861_197387782      972  1429 (493)    L1M4_orf2#LINE/L1      439   908 (0)  

  chr1_197385861_    972 AAAAGAATTAAGTTTAACCCCAGCCTCACACT-TAC-CAAAAATTAAATC 1019
                                 v     vi     vi        i-  i-          v  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_197385861_   1020 AAA-TGGATCA--GACTCTAATCTCTAATGTCAGAGCTAAAGTTAGAAAA 1066
                            -       --   -    ------    v         ii  v    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGAC-CTAA------ATGTAAGAGCTAAAACTATAAAA 531

  chr1_197385861_   1067 TCTGTAGAAGAAAATACAGGCACAA-TTTTCATGACCTTGAGTCAGACAA 1115
                         iiiv          i i   ?ii  - i   i        i  i  i   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_197385861_   1116 AACCTTCTAAGATACAGCACCAAAAGCGTAAGAGACAAAAGAAAAAAATA 1165
                         vivi    v     iii          ii   vi             -  
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TA 630

  chr1_197385861_   1166 GATAAAGTAGACTTCATCAAG-TTAAAAACTTTTGTGCTGCAAGTGATAC 1214
                               v i           i-                 v   iv  i  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_197385861_   1215 TATCATGAAAAT-AAAAGACAATTCATAGAATGGAATAAATGATTTGTAA 1263
                              v    i -         ii  i       i v   vv     i  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_197385861_   1264 TTAATATATATCTGATAAGAGACTTGTAACCAGAATTTATAATGAAGTCT 1313
                         v --i              i        v       v     v   v   
  L1M4_orf2#LINE/    731 AT--CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_197385861_   1314 TAATACTT--TAAAAAAAAAACAAATT------TTTAAAA--GGACAGAG 1353
                           vv   i--   v     i      v------  ?    --  i  i  
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_197385861_   1354 GATCTGAATAGACCCTTTTCCATAGAAAATATGCAGATAACCAATA---- 1399
                            i         vi  i    v    i    i  i  ii      ----
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_197385861_   1400 CATGAAAAGATGCTTAACATCATTGGTAAT 1429
                                       i       ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (51 / 29)
Gap_init rate = 0.03 (15 / 470), avg. gap size = 2.13 (32 / 15)  


2045 22.45 11.62 2.35  chr1_197483587_197487662.rev     2451  3087 (989)    L1M4_orf2#LINE/L1        1   696 (212)  

  chr1_197483587_   2451 TGAGAAGAGAAACCATGTT--TTCACTGGAAGACACAA-ATTGTTAAACT 2497
                           ii    v vv       -- vv i        vi  -        iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_197483587_   2498 ATTAATTCTTCCCAAAATGGTCTATAGATTCAACACAATTCCAATCTAAA 2547
                         ivi   v  i      v  i    i         i    i  v   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_197483587_   2548 TCCTAGCAAGCTTTTTTTTTAATAGAAATTGACAAGTTGATTCTAAAATT 2597
                            i   v-  i      ---ii             i    i        
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_197483587_   2598 TATATGGAAATGCAAAGAACCTAGAATAACGAAAACAATTTTGATAAAAA 2647
                         i              i i   i      i v        i    v   i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_197483587_   2648 ACAACAAAGCCGGATGGCTTACACTAACAAGTTTCAAGACTTATTATGAA 2697
                          v       ii   v i  i     vv v i      i     i  ii  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_197483587_   2698 GCTACATTAGTCAAGACTGTGTGGCAC-AGCCTAA---CAGACATCTAAA 2743
                               v  i       v      i  -i  v   ---i      v  i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_197483587_   2744 TCAATGGAA-------GAGA------------------------------ 2756
                                  -------    ------------------------------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_197483587_   2757 -------------CACAGGTGTCGACGTCAGTCAATGAGGAGACAACAGT 2793
                         -------------  vi    i i vii  v      i   i v  i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_197483587_   2794 CTT--CAATAAATACTACTGGAACAACTAGATAATCTTGTTAAAAAAAAA 2841
                            --   i    iv i    i      i    ?i vii vv    i  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_197483587_   2842 GGGTAAAATGAACCTCGACC--ACACTATACAAAAAAACTGATCCAAAAT 2889
                          ---  iv  i   i v   --    i   i v     i i ii      
  L1M4_orf2#LINE/    447 G---AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_197483587_   2890 GAATCATAGTTCTAAATGAAAAAGCTAAAACTGTAAA-CTTCGAGAAGAA 2938
                          i    ?  vi       v  i          i    -  iiv       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_197483587_   2939 AACATAGGGGAAAAAAATCTTTACAACCATAATATAGGCAAGAAAAGATT 2988
                                 ? v   ---    iiii   v iivv       v---- i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAAT----GGTT 586

  chr1_197483587_   2989 TCTTAG----GACAT-AAAAGCACTAACTAAAAAAGAAAAAAATTG-TAA 3032
                               ----    i-        v i v v           - v -   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAA 635

  chr1_197483587_   3033 ACTGGTCTTCATCAAAATTTAAAATT------CCTTGAAAGACACCACGA 3076
                          i   v             v    i ------ i ii  i     i iv 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_197483587_   3077 AGAAAATGAAA 3087
                              i     
  L1M4_orf2#LINE/    686 AGAAAGTGAAA 696

Transitions / transversions = 1.75 (89 / 51)
Gap_init rate = 0.03 (19 / 696), avg. gap size = 4.68 (89 / 19)  

 642 21.00 13.24 2.28  chr1_197483587_197487662.rev     3373  3591 (485)    L1M4_orf2#LINE/L1      666   908 (0)  

  chr1_197483587_   3373 TGTCTCAAAAGA--------AGAAAA-GAAAAGAAAATGTGAACCACAGA 3413
                           ii     i  --------     i-       v  i-----       
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC-----CCACAGA 710

  chr1_197483587_   3414 TTAGGAGAAACTATCTGCAATGCATGTATTTGTCAAAGGACTTGTATTCA 3463
                         v i       v   i     vv   i   i  vi  i          i  
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_197483587_   3464 G----TATAAATAACTCCTACAG-----TAATAAGAAAATAAAAACCCCA 3504
                          ----      v     i    i-----      i  i i   v v    
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_197483587_   3505 ATAAGACACTGAGAAAAAGATTTGAACAGACATTTC---ATAAAAGATGT 3551
                           v?i v v  i v   i        i         --- v i     i 
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_197483587_   3552 ATGAATGACCAGTAAGCATACAAAAA--------ACATTAAATTCTAT 3591
                          ii    i   i      i ii    --------    i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (31 / 14)
Gap_init rate = 0.03 (7 / 243), avg. gap size = 4.86 (34 / 7)  


3217 22.80 5.64 0.71  chr1_197489238_197491300.rev      714  1564 (499)    L1M4_orf2#LINE/L1        1   893 (15)  

  chr1_197489238_    714 TGGAGAG----TCCATGTTCATGGATAAAAAGACTCAGTATCATCAAGAT 759
                             i  ----i              vii      i i   ii i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_197489238_    760 ACCGGTTTTTCCCAACTTGATCTACAGATTCAATGCAATCCCAGTAAAAA 809
                         iv ii vi i     v                 i        vi v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_197489238_    810 TTCCAGCAAGTTATTTTGTAGATATTGATGAATTGATC-TAAAGTTTACA 858
                          i     vivi v     i   v     ii ii     -    i  i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_197489238_    859 TGGAGAGGCAAAAGACCTAGAATAGC--AAATAATATTGAAGGAGAAGAA 906
                             i v    ii    i        --   i   v     ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_197489238_    907 TAAAGTTAGAGAACTGATGCTACCCACCTTCAAAGCTCACTACAGAGATT 956
                         i      i   i   v ii  v    vi      i  i      i  v v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_197489238_    957 CAGTAATCAACACAATGTGGTACTGGCA-AAAGA---ACAAATAGATCAC 1002
                                   v   i             -  i  ---   v        v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_197489238_   1003 CGGAACAGAATATAGAGCACACGAACAAA--------------GTCAACT 1038
                         i    i     vv    iv  vi  i   --------------     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_197489238_   1039 GATCTCTGACAAAGAAGCAAATAAGGCAATGCAGTGGAGAAAGA-CAGTC 1087
                            i ii     i iv  ---i   i v  v  i   i      -i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGC---CAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_197489238_   1088 TTTTTAACAAATGGTGCTAGAACAACCAGACATCCACATGAAAAAAAAAA 1137
                             i             i i     ii  i ?       v    i  vi
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_197489238_   1138 GACTCTAGACAG--ACTTTACAGCCTTCATAAAAATTAACTCAAAATGAA 1185
                         i v - i   vv--  i i   v v vi i                  i 
  L1M4_orf2#LINE/    448 AAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_197489238_   1186 TCACAGACCTAAATGTACAA--CAAAACTATAAAACTTCTAGAAGATAAC 1233
                            ?             vi --i              ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_197489238_   1234 AGAAGA--AAAACTAGATAATATTGGGCTTGGCAATGACTTCTTAGATAC 1281
                          v i ?--   v  vvi i iv     i v       ii          i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_197489238_   1282 AAAACCAAATGCACAATCCATGAAA-AAATAATTGATAAGCTGGACTTTA 1330
                         i v      v      v v ii   -   v   v     ii       i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_197489238_   1331 TTAAAAT-AAAAAATTTTGCACTGCGGAAGGG---TGTCAAGAGAATGAA 1376
                          i     -     v     ii  v i-    i--- i      i i    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGAAAGTGAA 695

  chr1_197489238_   1377 AAACATAAGCCACAGACTGGGAGAAAACAATTGCAAAAGACATCTCTGAT 1426
                           i- i  v       v          i v       vv i  v      
  L1M4_orf2#LINE/    696 AAG-ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_197489238_   1427 AAAGGACTGTTATCCAAAATATACAAAAAACTCTTAAAACTCA------- 1469
                           i     vv      i      i   i        v      -------
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_197489238_   1470 ---GA-AAACAACCCAATTAAAAAACAGGCCAACAACCTTAACAAACACC 1515
                         ---  -   i         ?     ii   v  vi ii v  i i   ii
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_197489238_   1516 TCACCAAAGAAGATATAAAGATGGCAAGTAAGCATATGAAAAGATGTTC 1564
                           v              v i     v i      i           i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.88 (124 / 66)
Gap_init rate = 0.02 (19 / 893), avg. gap size = 2.84 (54 / 19)  


3313 26.80 0.78 0.22  chr1_197497708_197502992.rev     3893  4795 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_197497708_   3893 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCGTGAAAAT 3942
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_197497708_   3943 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3992
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_197497708_   3993 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 4037
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_197497708_   4038 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 4087
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_197497708_   4088 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 4137
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_197497708_   4138 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 4187
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_197497708_   4188 TGGAACAGGAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACTAT 4235
                              i  i i--    i  --        vv  ii i ii  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_197497708_   4236 CTGATCTTTGACAAACCTGACAAAAACATGCAATGGGGAAAGGATTCCCT 4285
                         i    i  i     ivv  v   i v   v            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_197497708_   4286 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 4335
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_197497708_   4336 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 4385
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_197497708_   4386 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 4435
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_197497708_   4436 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 4485
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_197497708_   4486 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 4535
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_197497708_   4536 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 4585
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_197497708_   4586 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 4635
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_197497708_   4636 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 4685
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_197497708_   4686 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 4735
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_197497708_   4736 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 4785
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_197497708_   4786 CGCTGGCCAT 4795
                          i????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.25 (9 / 4)  


 298 25.00 14.13 0.00  chr1_197862370_197864254      500   591 (1294)    L1M4_orf2#LINE/L1      252   356 (552)  

  chr1_197862370_    500 AGTGATCAAGAGTGTGTGGTATTAGTGGAGGTATAGACATATAGAACA-- 547
                            i       vv        i i iiv i v             v  --
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_197862370_    548 -----------GAGAACCCAGGCATAGATCTAAACAAATATGCCCAATTG 586
                         -----------    ii    iv   i i i v   vv    vi      
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_197862370_    587 ATTTT 591
                              
  L1M4_orf2#LINE/    352 ATTTT 356

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.01 (1 / 105), avg. gap size = 13.00 (13 / 1)  

1956 20.56 7.14 3.14  chr1_197862370_197864254      819  1392 (493)    L1M4_orf2#LINE/L1      312   908 (0)  

  chr1_197862370_    819 TGGGATTCCAGGCATGAGCCACTGTGCCTCGCCTTATGCCCCATTGATTT 868
                           i  v     iv  i i  --ii i v ----     vi v        
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACC--CATACAT----TTATGGTCAATTGATTT 355

  chr1_197862370_    869 TTGACAAAAGTGTATAAG-CAATGAAGCGGAGGAAAGATAGCCTTT-CAA 916
                          i     ii   i-i   - v  vv ii  i i  ii    i    -   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_197862370_    917 TGAATGGTGCCGGAACAACTGGACATACATAGGGAAAAAAAAAAAA--AA 964
                         ii        i  i         i ?v  i v v    i  vi  i--ii
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_197862370_    965 ACCCTGACTGAAGTCTCATACCTTGTA-AAAAATATAACTCAAAAAGAAT 1013
                             iv  ------    i   v i  -      -          v i  
  L1M4_orf2#LINE/    455 ACCCCTAC------CTCACACCATATACAAAAAT-TAACTCAAAATGGAT 497

  chr1_197862370_   1014 CATAGACTTAAATGTAAAACTGAAAACTTTAAAAATACTTAGAAAAAAAT 1063
                           ?    i         i viv      v     v -       i    -
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAA- 545

  chr1_197862370_   1064 CATAAGAGAAAATTATTGGAATCTAGGGCTAGGCAAAGAGTTCTTA---- 1109
                             i ? v    iv i vi i  v   i       v iv      ----
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_197862370_   1110 --ACACCAAAAGCACAATCCACAAAAGAAAACAAATGGTTAA-TTGGACT 1156
                         --               v v           --   i v   -       
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAA--AATAGATAAATTGGACT 643

  chr1_197862370_   1157 TCATCAAAATTAAAAACTTTTGCTCTGTGAAAGACCCTGTTAAGA----- 1201
                                               iv  vii  i   v  i i    -----
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_197862370_   1202 ----GACGA------GAA----AGAAAATATTTGCACATGACATATCTAA 1237
                         ----   i ------   ----              v  v i      i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_197862370_   1238 TGAAGGACTGGTATGTAATATATATGAAGAACTTTTACAACTCAACAGTA 1287
                          i i     v    vi iv      i       i           i i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_197862370_   1288 AAAAAA-AAATA---CAATTAGAAAGTAGGCAAAAGAC----AGAGACAT 1329
                             i -     ---     ?i   i i      i  i---- v      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_197862370_   1330 TTCACTAAAGAGGATATACATATGGCAAATAAGTACATGAAAAGAT--TC 1377
                            v i     i        v     v      i            --  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_197862370_   1378 AACGTCACAGCCATT 1392
                            i   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (74 / 40)
Gap_init rate = 0.04 (21 / 597), avg. gap size = 2.81 (59 / 21)  


 251 21.31 3.28 3.28  chr1_197935144_197941547.rev      272   332 (6072)    L1M4_orf2#LINE/L1      302   362 (546)  

  chr1_197935144_    272 GGAGTAAGTAATAAAGAGTCTAAAAGTAGACCCACACAT--ACGGTCAGT 319
                            i  i--   vi      i i  i  i     i    -- i     i 
  L1M4_orf2#LINE/    302 GGAATAG--AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_197935144_    320 TGACTTTCAACAA 332
                            i    i    
  L1M4_orf2#LINE/    350 TGATTTTCGACAA 362

Transitions / transversions = 12.00 (12 / 1)
Gap_init rate = 0.03 (2 / 61), avg. gap size = 2.00 (4 / 2)  

3260 26.49 0.77 0.55  chr1_197935144_197941547.rev     5009  5914 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_197935144_   5009 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5058
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_197935144_   5059 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_197935144_   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_197935144_   5157 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5206
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_197935144_   5207 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5256
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_197935144_   5257 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5306
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_197935144_   5307 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCACATATCTACAACT 5354
                                i    i--    i  --    i   vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_197935144_   5355 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5404
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_197935144_   5405 CTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGTAGAAAGCT 5454
                           v  i  i           i  v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_197935144_   5455 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGA 5504
                            ii    i    v   i     v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_197935144_   5505 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 5553
                          i ?    i       v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_197935144_   5554 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5603
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_197935144_   5604 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5653
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_197935144_   5654 ATTAAACTAAAGAGCTTCTGCACAGCAAAGAA-ACTACCATCAGAGTGAA 5702
                           i   v v  i i   i  ii vv     i -    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_197935144_   5703 CAGGCAACCTACAAATTGGGAGAAAATTTTTGCAACCTACTCATC-AACA 5751
                         v  i     i   i v           v       vii ivi   -i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_197935144_   5752 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5801
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_197935144_   5802 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5851
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_197935144_   5852 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5901
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_197935144_   5902 CATCGCTGGCCAT 5914
                             i????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1728 30.00 7.53 1.53  chr1_197946270_197948675     1064  1913 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_197946270_   1064 ACATGCTATGTTCCAGGATAGGAAGA--TAATATTTCAAAGATGTTAAT- 1110
                          i  v i      vv    v      --       viv      vi   -
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_197946270_   1111 -----CGAGT----CTGTAGATTCAATGTA-TTTCAATAAAAATCCCAAT 1150
                         ----- i i ----  ii        i i - ii v  v         ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr1_197946270_   1151 GGGGTTTTTCATGCAAATTGACAAAGTGATTATAAAATTGATGTGAATGA 1200
                         v vv     iiiiv          iv    iv       v  i  i viv
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_197946270_   1201 GCCAAGAATCAAAAATAGTGAAGACATTGCTGAAGAAGGAAAAGGAGGG- 1249
                           v i i i v i     iv  i   v vi    i   i i  vi i v-
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_197946270_   1250 AGAAAATGTGCCCTATTAGAATTGAAGACTTATTATC--TCTATAGTAAT 1297
                         i  ii ivii v  viivi v  v  i     i  iv--v   i      
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_197946270_   1298 TAAAGCAGTGTGATATTGGTGTATCAATAGACACATAGA---ATAG--TA 1342
                         i  ii       i  i   ii  vvi       i     ---  i --  
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_197946270_   1343 GAA----------AACAATAGACCCACGCCTATTTGGAAACTTAATCCAT 1382
                            ---------- iv    i     ii v v v   vv v  i  iivi
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_197946270_   1383 GACACAGTGGTTATTACAGGTCAATAGTTTAAAGATAAACTGTTTAATAC 1432
                             vi vv ii vv  viv     i vvv  ii   iv  v  i  i v
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_197946270_   1433 GTTGTTCTGGGACGATTGGTTATCCA----------AGTGAAATTGAATC 1472
                         i v  v       i i   v  ?   ---------- i    i   i i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_197946270_   1473 CCTACCTTATACCATATACAAAAATGAATTCCAGATGTATTAGACGTTTA 1522
                                i i               v  i  v i   v  i ? viii  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_197946270_   1523 TACGTAGGTGGCAAAACTATAAA--TCTTAGAAGACGCTGTAGGAAAATA 1570
                         v i   i v vi           --          vivii    ?iv v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_197946270_   1571 TCTCTGTTCCTCTTAGGT-AGAGAAGGATTTCTTGAACAAGATTCCGAAA 1619
                            ii  vv -   i   -  iv  v i      ii i v  iv  i   
  L1M4_orf2#LINE/    558 TCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_197946270_   1620 GCA-AAGCCATAAAGGAAAAGAT-TATAAATTTGACTATATTAAAATTAG 1667
                            -    v i   i     i  -v       v    vi  i       i
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_197946270_   1668 ACATGTGTTTTCATCAAAAGACAATA--AGGAATGTCAAAGGATATGCCA 1715
                          v iv v v v v     i    v  -- i   v  v   i  i vv   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_197946270_   1716 CAGGGTAGAAGAAA-TATTTGCCA--CAGGAATATCTGTCAAATTA-TTG 1761
                            ii i i     -       v --  v--       vi  ivv -   
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCAT--ATATCTGATAAGGGACTTG 754

  chr1_197946270_   1762 TACATAATTAATATTCATGAGAAACCCTT-CAAATCAGTGAGAAAAAAA- 1809
                           ivi i--     --  i ii   i   -   v   i i v     i -
  L1M4_orf2#LINE/    755 TATCCAG--AATAT--ATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_197946270_   1810 -AAT--CTCAAGAAAAAAATTGGCAAAAAAT---AA-AGACATTTC---A 1849
                         -   -- i   vv?      v      ii  ---  -         --- 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_197946270_   1850 AACAAGAGATAATACCAGTATTGGCCCATAAACTTGTGAAAAGATACTTA 1899
                           v    v   ----  -- v     v    i vii         i  i 
  L1M4_orf2#LINE/    851 AAGAAGATATA----CA--AATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_197946270_   1900 GCATCATTTGTAAC 1913
                         i     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (144 / 107)
Gap_init rate = 0.03 (30 / 901), avg. gap size = 2.57 (77 / 30)  


4127 17.71 1.00 0.25  chr1_198141313_198143106      500  1301 (493)    L1M4_orf2#LINE/L1      101   908 (0)  

  chr1_198141313_    500 TCCCAACAACATCTTCTTTAAAAATAGAAAAATCCATCCTAAAATTTATG 549
                              i vi v i  i vi i    v  v  iiiv           i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_198141313_    550 TGGAACCTCAAAGGACCCTAAA-ACCCAAAACAATTGTGAAAAAGAACAG 598
                              viv   i      vi  - v          iv          v i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_198141313_    599 CAAAGCTGGAGGTCTCACAGTTTCTGATTTCAAAACTTAGCTACAAAGCT 648
                              i      v      v  i ii             -          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAAAGCT 249

  chr1_198141313_    649 ACAGTCTTCAAAACAGTGTGGTACTGGCATAAAGACAGACATATCAATCA 698
                              vv    i                    i  i        vi    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_198141313_    699 ATGGAATAGAATAGAGAGTCCAGAAACAAACCCTCGCATATATGGTCAAA 748
                                     v             i      vii   v         v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_198141313_    749 TGATTTTAGACAAGGGTGCCACAACCCTTCAGTGGGAAAAAGACAGTCAT 798
                                v             vi   v    i    i   ii i    v 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_198141313_    799 TTCAACAAATGGTGCTGGGGAAAGTGGATATCCACATGATAAAGAATGAA 848
                                            iv  v      ?       vv          
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_198141313_    849 GTTGGACCCTTACGTAACACCATATGCAAAAATTAACTCACAATGGACCA 898
                                  i   v v         i              v      i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_198141313_    899 AAGACCCAAATATAAGAGCTAAAAACTACAAAACACTTAGAAGAAAATGT 948
                         ?     i    i            -   i     v            ii 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACAT 548

  chr1_198141313_    949 AGG-GCAAAACTTTACGACATTGAATTTGGCAATGACTTCCTGGATATGA 997
                            - i   v   iii   v   ii  v       ii   i i       
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_198141313_    998 CACCAAAGGCAGAGGCATCAAAAGCAAAAATAGACAAATTGGACTTCATA 1047
                                i   v i   v      v         i              v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_198141313_   1048 AAAATTGAAAACTTTTATGCATTAAAACACACTACCAACAGAGTGAAAAG 1097
                               i         i   v i   iv      i   v i         
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_198141313_   1098 GCAACCTGCTGAATGGGACAGCATACTTGCAAATCATGTATCTGATAAGA 1147
                         i     ii v        v iv   i           i           i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_198141313_   1148 TATTAATATCCAGAACATATAGAGAACT---ACAACTCAACAACAAAA-- 1192
                         v i vi         i     i      ---         i  i    --
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_198141313_   1193 -CAACCAACCAGATTAAAAAATGGTCAAAGGACTTGAACAGGTATTTTTC 1241
                         -   vi    vi   ?        v       i     i  ii    i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_198141313_   1242 CAGAGAAAATATATGAATAGTCAATAAGCACATGAAAAGATGCTCAACTT 1291
                           i    i     ii   i i                           v 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_198141313_   1292 CACTAATTGA 1301
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.67 (87 / 52)
Gap_init rate = 0.01 (6 / 808), avg. gap size = 1.67 (10 / 6)  


4418 13.82 3.92 5.44  chr1_198497032_198499162.rev      730  1648 (483)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_198497032_    730 AAAGGCATGCC-TGTTCATGGATTGGAAGACTTAACATTGTTAAGA-GGC 777
                             ii  v  -                       i          -   
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_198497032_    778 AATACTCTCTAAATTGATATACAGATTCAATGCAATCCCTAGCAAAATTC 827
                                i i        v           i          v      i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_198497032_    828 AATCTG------------AGATTAACAAACGAATCCTGAAATTCACATGG 865
                         v v   ------------ i   i    i vi     i       i    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_198497032_    866 AAATGCAAAGGACACAGAGTAGCCAAAACAACCTTGAAAAAGAA---CAA 912
                                 i    v    i            i            ---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_198497032_    913 AGTTGGAGGACTCACACTTCCCAATTTCCAAACTTACTACAAAGCTACAG 962
                                                     v                     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_198497032_    963 TAATCAAAACAATGTGGTACTGGC-CAAGGATAGACATATAGAAGAATGG 1011
                                i   i            -i                 -------
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA------- 296

  chr1_198497032_   1012 AATAGAACTGAAAGTCTAGAAAGAAACTCATATAGAAGAATGGAATAGAA 1061
                         ---------------------------   ---------           
  L1M4_orf2#LINE/    297 ---------------------------TCA---------ATGGAATAGAA 310

  chr1_198497032_   1062 CTGAAAGTCTAGAATGAAACTCATATATGTATAGTCAATTGATTTCCTA- 1110
                         i   i    i    vv    i    i  v   i            i v -
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr1_198497032_   1111 --GAGTGCCAAGACAATTCAGTGGGGGAAAAAATAGTCTTTTCAGCAAAT 1158
                         -- i          v     i     -   i             i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAAT 409

  chr1_198497032_   1159 GATGCTGGAACAACTGGATATTCTCATGTAAAAGAATGAAGTTAGACTGC 1208
                          i      i           ?i v    i              i   i- 
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC-C 458

  chr1_198497032_   1209 CTACCTCATACCATGTACAAAAATTTACTAAAAATGGAACAAAGACCTAA 1258
                                 i     i          v   v        v  ?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_198497032_   1259 A-------ACTAAAA----AAAAAT-TTAGAAGGAATTCCAGGAGTAAGT 1296
                          -------i      ----    v -       i  vivi   ?    i 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_198497032_   1297 CTTCATGACCCTGGATTAGGCAATAATTTCTTAGATACAGCACCTAAAGC 1346
                             i     i   i         ii           iii    v     
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_198497032_   1347 ACAAGTAGCCAAAGGAAAAAACTAGATAAATGATGCCTCATGAAAATGGA 1396
                              i i -   i       -         vivi i    v     vi 
  L1M4_orf2#LINE/    609 ACAAGCAAC-AAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_198497032_   1397 AAACTTTTGTTCTTCAAAGAATATTTTCAAGAAAGCAAAACAGCAACCCA 1446
                                   v        i i i v         ii   vii       
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_198497032_   1447 TACAATGAGAGAAACTATTTTTCAAATCATGTGTCTGATAAGGGTCTAAT 1496
                         i v    i      v     v-        i i           v  vi 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTG-CAAATCATATATCTGATAAGGGACTTGT 755

  chr1_198497032_   1497 ATTCAGAAT-TATTAAAAAACTCTTAAAGCTCAACAACAAAA-GACAAAT 1544
                           i      -   -   i        v i     i  i    -       
  L1M4_orf2#LINE/    756 ATCCAGAATATAT-AAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_198497032_   1545 AACCTGATTTTAAAAGTGGGCCAAGGATTTGAATACACATTTCTCCATA- 1593
                             ii   ?-    i     v             v           v -
  L1M4_orf2#LINE/    805 AACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_198497032_   1594 AAGACATACAAATAGCAAATAAGCACATGAAAAGATGCTTGGTATTAGCC 1643
                             i        i  v                      iiii  i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_198497032_   1644 ATTAA 1648
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.24 (85 / 38)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 4.10 (86 / 21)  


3056 22.26 1.05 6.29  chr1_199631898_199636463.rev     2799  3656 (910)    L1M4_orf2#LINE/L1        1   813 (95)  

  chr1_199631898_   2799 TAAAAAGATATTCCATGTTCATGGATTGGGAGAATCAATATTGTTAAAAT 2848
                          ii        i                 i   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_199631898_   2849 GTCCATATTACCCAAAGCAATCTACAGATTCAATGCAATCTCTA---AAA 2895
                          v v   i v      vii              i      i   ---   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_199631898_   2896 TACCAGTAACATTCTTCACAGAAAC--ATAAAC-AATCCTCAAATGTATA 2942
                          v    ivi v  i  ii      i-- i  i -i     v    vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_199631898_   2943 TGAAAGCACAAAAGACCTAGAGTAGCCAAATCTATCCTGAGCAAAAAGAA 2992
                           i  iii   ii    i   i        v v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_199631898_   2993 TAAAATGGGACAAATCACATTACCTGACTTCAAATTATACTACAGAGCTA 3042
                         i   i v   vi v     i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_199631898_   3043 TAGTAACCAAAACAGCATGGTACTGTCATAAAAACACACAGAGAGAACAA 3092
                         i     i   i    ii        v     ii i v   v v   v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_199631898_   3093 TGGAACACAACAGAGAATCCAGAAACAAATCCGCATACCTATGATGAATT 3142
                              i v  iv    i        i   i  ii i ii    i v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_199631898_   3143 CATTTTCGACAAAGCTGCCAAAGAACATACACTGGGAAAA--AGAGTCTC 3190
                         v           i v      -  v   v  v    i   -- v     i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_199631898_   3191 TTCAATAAATGGTATTGGGGGAACTGGATATCCACATGCAAAAGAATGAA 3240
                              i       ii    iv         ?                   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_199631898_   3241 ACTAGACCCCTATCTCTCACCATATGCAAAAATCAAATCAACATGGATTA 3290
                         ii i        i   v        i       i  v    v      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_199631898_   3291 AAGACTTAAATCTAAGACCTCAAACTATGAAACCACTATAAGAAAACTTT 3340
                         ?    i     v     v  v       i    ivi  v        v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_199631898_   3341 GGGGAAAATCTCCAGGACATTGGTCTGGGCAAAAATTTCTTTATTTTTTT 3390
                           ? v      i iv   v    vi i     vii      ---------
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--------- 590

  chr1_199631898_   3391 TTTTAAAGATTCTTGTTTCCAGTGGGGTTGGAAAAAATTTCTTGAGTAAT 3440
                         ------    -----------------------------------i i i
  L1M4_orf2#LINE/    591 ------AGAT-----------------------------------ATGAC 599

  chr1_199631898_   3441 ACTGCATGAATACAAGAAACCAAAGCAAAAATGGGCAAATGGGATCCCAT 3490
                           --  vi ii     v   v    v      i ii    v   iii   
  L1M4_orf2#LINE/    600 AC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_199631898_   3491 CAAG-TTAACAAGATTCTGCACAGCAAAGGAAACCATCAATAAAGTGAAG 3539
                            i-    -  iv  i  ii vv       v  i     v        i
  L1M4_orf2#LINE/    648 CAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_199631898_   3540 AGACAATCCACAGAATGGGAGAAAATATTTTCAAATTACCCATCTGATAA 3589
                               i                       v     i ivi         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_199631898_   3590 GGGATGAATAACTAGAATATATAAGGGGCTCAAACAACTCTATAGAAAAA 3639
                             ivvi  v i           i ii   vv       v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_199631898_   3640 AATCTAATAATCTGATT 3656
                          iv v     i ii   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATT 813

Transitions / transversions = 1.69 (118 / 70)
Gap_init rate = 0.01 (10 / 813), avg. gap size = 6.30 (63 / 10)  

 340 21.31 4.10 1.64  chr1_199631898_199636463.rev     3956  4077 (489)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr1_199631898_   3956 CTCAA-AATAAATAAATAAATATTTAAAAAATAAAAGTTGGGCAAAATAT 4004
                              -      v i i     viiv  v-- ?   iv        iv  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAAT--TWAAAAATGGGCAAAGGAT 831

  chr1_199631898_   4005 TT----AGACATTTCTCAAAAAAAGACATAAAAATGGTAAACAGGCATAA 4050
                           ----           v   i    i   v      iv  i i   i v
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_199631898_   4051 GAAGAGGTGCTCAACATAATTAATCAG 4077
                            i  i          v ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (14 / 11)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 2.33 (7 / 3)  


2067 24.65 2.95 3.41  chr1_199672939_199675439.rev      597  1241 (1260)    L1M4_orf2#LINE/L1        1   642 (266)  

  chr1_199672939_    597 TGGAAACAT----TACATTCATGGATCTGAAAACTTAACATAATAAAGAT 642
                               v  ----i ii         iv   i      i  vi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_199672939_    643 CTCATT-CTCTTCTATACTGATGTATAGATTTAACACAGTTCCAATTGAA 691
                         vv  v -   ii v - i    v  i     i   i  i i  v  ii  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA-ATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_199672939_    692 ATCCCAGCAGAATTCTTTTGGAATTGAGATTAGACAAGCTAATCTCAA-- 739
                                 v vv  -     v ---  i   -        i   ii  --
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTT-TTTTGCA---GAAATT-GACAAGCTGATCCTAAAA 144

  chr1_199672939_    740 TCTATATAGAAAGGCAAAGAACC-AGAATAGTTAAAACAATGTTGGAAAA 788
                          ii    i    v    i i   -       ii        v   i    
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_199672939_    789 GAAGAATAAAGTTGGAGTAATCACACTATCTAATTTCAAGACCTACTATA 838
                               i          v v       vi i        i  i     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_199672939_    839 AAGCTACAGGAATCAAGACAGTATGGTATT--CATGAAGGGACAGACACA 886
                                  v            i     i --   i --   i     i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA--GGATAGACATA 292

  chr1_199672939_    887 TAGTTCAATATAACAGAACACAGAAATCATAAATAGACCCACAAAAATAT 936
                            v     iv  i    ivv   ivi  v     i     i v vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_199672939_    937 A-CCAACTGATTTTTGAGGAGAGTGCAAAAGCAGCTCAGTGGAGAAAGGA 985
                         i-i   i       i  vi  i    v  ii vii   i   i     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_199672939_    986 TAGTCTTTTCTACAAAAGAAGCTGGAACAAAAGAACATCTGTATACAAAA 1035
                                   v     v iv     i    vv i i ? iii  i     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_199672939_   1036 --ATAAA--CAAACCATAACCTAAACCTTATACTTCATGCAAAATAAAAT 1081
                         --  i  --iii   ----    --   i i  ivi  i     vvv  i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACC----CCTA--CCTCACACCATATACAAAAATTAAC 486

  chr1_199672939_   1082 TTAAAATAGATCATGGATAGAAATGTAAACCACAAAGCTATACAACTTTT 1131
                          i     i     ?i  ivv        ivvvi   i     v    i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_199672939_   1132 AGAAGAAAATATAGGATAAAATCTTTATAACTTGGGGTTAGGCAAAGTGT 1181
                                  i     ?vv       ii i  i v           v vv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_199672939_   1182 TCTCCGATGTGACACTTTAAATGTGCAGCATGCTGCATTTAAAGAA---- 1227
                            iv   i      i--   v ii  i---  vi  ---      ----
  L1M4_orf2#LINE/    587 TCTTAGATATGACACC--AAAAGCACAA---GCAACA---AAAGAAAAAA 628

  chr1_199672939_   1228 TTGATAGATTGGAC 1241
                          v    i       
  L1M4_orf2#LINE/    629 TAGATAAATTGGAC 642

Transitions / transversions = 1.74 (99 / 57)
Gap_init rate = 0.03 (19 / 642), avg. gap size = 2.16 (41 / 19)  

 642 20.38 4.46 0.64  chr1_199672939_199675439.rev     1439  1595 (906)    L1M4_orf2#LINE/L1      618   780 (128)  

  chr1_199672939_   1439 AAAAAAAAAATTTGATAAATTGGACTTCAACAAAACTGAAAACCTTCTCA 1488
                             i     v v                v     i i     i  ivii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_199672939_   1489 GTGCAAAAGACACT-TTAAGACAATGGAAAGACAAGCTACAGGCTGAAAT 1537
                         v v    i      - i    v i  i        v i    iv  ii v
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_199672939_   1538 AAAATATTTGCAA------TATCCAACAAGGAGTTTTGTATTCAGAATAT 1581
                                      ------    ii i    - vi      i        
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGG-GACTTGTATCCAGAATAT 766

  chr1_199672939_   1582 ATAAAGAACTCTCA 1595
                                     i 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTA 780

Transitions / transversions = 1.91 (21 / 11)
Gap_init rate = 0.02 (3 / 163), avg. gap size = 2.67 (8 / 3)  

 440 18.35 4.59 0.00  chr1_199672939_199675439.rev     1894  2002 (499)    L1M4_orf2#LINE/L1      769   882 (26)  

  chr1_199672939_   1894 AAAGAGCCCTCACAACTCAA--GTGGAA-GA-AAACAATCCAATT-AAAA 1938
                              i i  i         --i ii  -  -   i  i      -    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_199672939_   1939 CTGGGCAAAATACTTGAACAGACACTTCACCAAAGATGATATATAGATGG 1988
                         v        iv i     i     i   v       v      i i    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_199672939_   1989 CAAATAAGAACATG 2002
                          v      v     
  L1M4_orf2#LINE/    869 CCAATAAGCACATG 882

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.04 (4 / 114), avg. gap size = 1.25 (5 / 4)  


3809 17.58 1.92 0.14  chr1_199694963_199699032     2368  3095 (975)    L1M4_orf2#LINE/L1        1   741 (167)  

  chr1_199694963_   2368 TGGAAAGCCATCCTATGTTCATTGATTGGAACACTTAATATTGTTAAGAT 2417
                                vi    i        v        v                  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_199694963_   2418 GTTAATACTTTC-AAAGTCATCTACAGATTCAATGCAATACCCATCAAAA 2466
                          vi      ii -   v v              i     v  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_199694963_   2467 TCCCAATGATGTCTTTTGCAGAAATAGAAAAATCCTTCCTAAAATTCATA 2516
                              iiviiv i            v  v  iiivv              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_199694963_   2517 TGGAATTT------GCCTTGAGTAGGCAAAACAGTCTTGAAAAAGAAGAG 2560
                              v v------i  iv  i   v       i               i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_199694963_   2561 CAAAGTTGGAGGACTCACACTTCCTTATTTCAAAACTCACTACAAAGCTA 2610
                                                 iv           i            
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_199694963_   2611 CAGTAATCAAAAC-GTGTGGTATTGGCATAAAGGAAGACATATAGACTAA 2659
                                   i  -        i        i iv           ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_199694963_   2660 TGGAATGGAAAAGAAAGCCCAGAAATAAACTCTAACAT--ACAGTCAAAT 2707
                               i   vv  i  i            i vv    -- ii     v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_199694963_   2708 GATTTTTGATAAGGGAGCCAAGACCATTCAATGGGAAAAGGACAGTCTTT 2757
                               i  i     v                   i    i i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_199694963_   2758 TCAACAAATGGTGCTCTGAAAGCTGGATATGCACACAACATAAGAATGAA 2807
                                        vv  v i       ?v    ii-  v         
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAATGAA 449

  chr1_199694963_   2808 GTTGGATCCTTACCTTACATCACATACAAAAATTAAATTGATATGGATGA 2857
                               i  i     i   i  i             v ii v      v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_199694963_   2858 AAGAC--AAACTTGAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 2905
                         ?    --   iv i                                    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_199694963_   2906 GGCA-AAAGCTTCACAGTATTGGATTTGGCAATGAATTTTTGGATATGAC 2954
                           ?i-   v    iiiiiv    i  v       iv  i  i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_199694963_   2955 ACCAAGGGGACTGGCAACAAAAGAAAGAATAGACAATTTAGACTTTATGA 3004
                              ii v  vi             i      i  v  i     i  v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_199694963_   3005 AAATTAAAAGCTTTTGTGCATCAAAA-ACACTATCAACAGAGTAAAACGG 3053
                                  i         v     i-          v i   i   v i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_199694963_   3054 CAACCCACAAAGTTGGAAAAAATATTTGAAAATCCTACATCT 3095
                                  i i v   i          v     v  i    
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

Transitions / transversions = 1.60 (77 / 48)
Gap_init rate = 0.01 (8 / 741), avg. gap size = 1.88 (15 / 8)  

 942 12.83 0.00 3.21  chr1_199694963_199699032     3391  3577 (493)    L1M4_orf2#LINE/L1      728   908 (0)  

  chr1_199694963_   3391 CAAATCATGTATCTTATAAGGGATTAGTATCCAGTTTATATAGAGAACTC 3440
                                 i     v        i v        vv      i       
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_199694963_   3441 CAAACACTCAACAGCAGCAACAACAACAAAAAAACCTGATTCAAAAATGG 3490
                         iv vv      i ii iv  ----i     v  -  ii   ?        
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAA----GACAAATAA-CCCAATTWAAAAATGG 822

  chr1_199694963_   3491 GCAAAAGGAGTTGAATAGACATTTCTCCAAAGAAGATATATAAATGGCCA 3540
                              -   v                              i         
  L1M4_orf2#LINE/    823 GCAAA-GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_199694963_   3541 ATAAGCACATGAAAAGATGCTCAATATCACTGATCAT 3577
                                                 i    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.02 (3 / 181), avg. gap size = 2.00 (6 / 3)  


1378 28.39 5.05 4.57  chr1_199805453_199811218      492  1125 (4641)  C L1M4_orf2#LINE/L1   (0)   908   272  

C chr1_199805453_   1125 ACTGGTGCAAGGGTAGA------------TGGGAGACAAT--ATAGTCCA 1090
                              iii    i    ------------   i v v   -- v      
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

C chr1_199805453_   1089 GAAATG----CATATAT--ATAGTTACTTGATTTTCAACGAAGATATCAT 1046
                              i----    i  --  i  i v         i  i i i ii  -
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA- 370

C chr1_199805453_   1045 CG--CATTGCAGTGGGGAAACAATCATCTTTTCAATAAATCATATGATGT 998
                         v --    -  i        v   vi         i    vi iiviv v
  L1M4_orf2#LINE/    371 AGACCATT-CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

C chr1_199805453_    997 CGGTTGAACATCCATATGATGGGAAAAAGTAAATGTTTATTCCTCCACCT 948
                          iii  i i ?   i   v---i   i i i  -   vivi  - i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGC---AAAAGAATGAA-GTTGGACCC-CTACCT 464

C chr1_199805453_    947 CAAACCACATACAAAATTCAGTTCCAGGCATATGA-AGACATATGTGTGA 899
                           v    i        v i ii  v iiiiv  v -    v  vi   i 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

C chr1_199805453_    898 AACATAAAACAATAAAACTTCTGGGAGAAAACAGAAAAACAGTATCTGCG 849
                         i vv      v        ii i i        v ii?ii i-    v  
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCG 563

C chr1_199805453_    848 TGACCTTACAATGACCAAAGATTTAACAGGAATGA-----AAAGCATTAA 804
                                iviv iiv   v i   vvi  iv    -----      iv i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

C chr1_199805453_    803 CCCTAAAGTAAGAGACTGACAAACTAGACTTCATTTAAAT-AAAAATTTT 755
                          vvi   iv  i i iv  i   i i        iv    -     i   
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

C chr1_199805453_    754 CTGTTCACCAAAAGACATGCTTAAGAGAGTGAAAAAGCAAACCAGAGGA- 706
                         -   v vi    i    ivv i    i        ii   v   v  i -
  L1M4_orf2#LINE/    664 -TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

C chr1_199805453_    705 -GAAGAAGACATTTGTAGTTACACACACACACACACACACACACCACATT 657
                         - i    i i     i iv -----------------  i i i --- v
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAAT-----------------CATATATC---TG 742

C chr1_199805453_    656 ACAAAAGACTACCATTAAGAATATCTGAAGAACTTCTGCAA-TCAATGAG 608
                          i  ii    vvi  iv       v i       ii i   -     i v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

C chr1_199805453_    607 AAAATGACAAATGATCCAATAGAAAAATGGGCAAACTACTTGAACAGGAA 558
                             v       i i     v?             vv i     i  iv 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

C chr1_199805453_    557 TTTCACAAATGAAGAAATCTGAATGACCAGTAAACATCTGAAAAAATGTT 508
                             v v  v     v  vii    i   i   i  iv      i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

C chr1_199805453_    507 CAACTTCATTAGTCAT 492
                             v   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (113 / 64)
Gap_init rate = 0.03 (19 / 637), avg. gap size = 3.21 (61 / 19)  

 322 32.85 5.11 0.73  chr1_199805453_199811218     1158  1294 (4472)  C L1M4_orf2#LINE/L1   (765)   143     1  

C chr1_199805453_   1294 TAGAGAGATACACCAAATTCATGGGTTAAAAGACTCAATATGGTGAAGAT 1245
                          i  i     iv   vi       i  ii      i     v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_199805453_   1244 GTTAGTCCTTTCCCAAATT---CTA-GGAGTCTTTTTGTTTGTTGTTTG- 1200
                          vi i v  i-        ---   -i  v  vviviiv ivi i ivi-
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

C chr1_199805453_   1199 --CTTGGTTGGTTTTCTGGTAGAAATTGGCAAGCTGGTTCTAAA 1158
                         -- iii i  vi   i v i        i       i i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

Transitions / transversions = 2.00 (30 / 15)
Gap_init rate = 0.03 (4 / 143), avg. gap size = 2.00 (8 / 4)  

 280 21.92 0.00 1.37  chr1_199805453_199811218     3161  3233 (2533)  C L1M4_orf2#LINE/L1   (803)   105    34  

C chr1_199805453_   3233 CTTCAAATTATAAAGATGTCAATTCTCCCCTATATTAATCTGTAGTTTCA 3184
                            v v   i v      v    v      v -   i    ii  v    
  L1M4_orf2#LINE/     34 CTTAATATTGTTAAGATGGCAATACTCCCCAA-ATTGATCTACAGATTCA 82

C chr1_199805453_   3183 ATGCAATTTCAATCAAAATCTCA 3161
                          i     ii v         i  
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCA 105

Transitions / transversions = 1.00 (8 / 8)
Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1)  

2649 25.16 2.37 4.73  chr1_199805453_199811218     4344  5273 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_199805453_   4344 TGGGAAAACATCCCATGTCCGTAGACTGAAAGAGTCAATATCATTTAAAT 4393
                            i  i i         i i i  i  i    v i     ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_199805453_   4394 GTCCATACCACCCAAAGCAATCTACAGATTCAATGCTATTCCTGTCAAAT 4443
                          v v    iv      vii              i  v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_199805453_   4444 TACAAATTCTGTTTTTCACAGAATTAGAATAACCT-ATTCTAAAATTCAT 4492
                          v v ii viv     ii     v v  -i  v  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr1_199805453_   4493 ATGGAACCAAAAAGGAGCCTGAATAGCAAAAAAAAAAAAAAAAAAAAAAA 4542
                               viiv  i   v  v       v    v  ---------------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA--------------- 184

  chr1_199805453_   4543 AAAAAAAAAAATCCTGAGCAAAAGAAAAAAAAAGCCAAAGACATCA-ATT 4591
                         -----------  i   --       i  v    iiii  ivv   - i 
  L1M4_orf2#LINE/    185 -----------TCTTGA--AAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_199805453_   4592 ACCTAACTTCAAACTACACTACAAGGCTACAAGTAGCCAAAACAGCATGG 4641
                         v  i  i      vivi       i      -   ii   i    ii   
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACA-GTAATCAAGACAGTGTGG 270

  chr1_199805453_   4642 TACTAGTACAAAAATAGCCACGTACACCAATGGAACAGAATACAGAACCC 4691
                             i i i  ii    v  ii  v i        i     vv   ii  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_199805453_   4692 AGAAATAAATCTGCACAACCTACAACCAATTGATCTTTGACAAAGTCAGC 4741
                                  i iii   -ii  iiii        i  i     i viiv 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACA-TTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_199805453_   4742 AAAAAGAAGCAGTGGAGAAAGGACTCCCTATTCAATAAATGGTGCTGGGA 4791
                           i vv vv  i   i     i ivvi  v     i              
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_199805453_   4792 AAACTGGCTAACGATATGCAGAAGAATGAAACTGGATCCCTGTGTATCAC 4841
                         v      v  ? v i     i         ii    i    iiv vv   
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_199805453_   4842 CATATACAAAA-----CTCAAGATGGGTTAGATACTTAAATGTAAGACCT 4886
                                    -----     i    i i ? v  i           v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_199805453_   4887 CAAACTATAAATATCCTAGAAGAAAGCCTAGAAACAGTCCTTC-TGCACA 4935
                         v          vv  i         i v   i?ii ivi    -  -  v
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACC 568

  chr1_199805453_   4936 TCACCCTTGGCAAAGA--------ATATGACTACGTCCTCAAAAGCAATT 4977
                          iivvi v     v i--------       -  -----        vvv
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGAC-AC-----CAAAAGCACAA 612

  chr1_199805453_   4978 GCAACGAAACAAAAAACTGACAGGTGGGACACAATTAAACTTTAAAAAGC 5027
                              i   v      iv  i ii v    viv  i   v  --    i 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT--AAAAAC 660

  chr1_199805453_   5028 TTGTGCACAGCAAAAGAAACTATCAACAGAGAAAACAGACAATCTACAGA 5077
                           v  ii vv    i  v        v i  vi  v      i i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_199805453_   5078 ATGGGAGAAAACATTCACAAACTATGCATCTGACAAAGCACTGATATCCA 5127
                                    i   ii    ii  ii      i  i v   vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_199805453_   5128 GAATCTATAAGGAACTTAAACAAATCAACAAGAAAAAAAACCAAATAACC 5177
                             v     i     ivv    v    i  v     i --         
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CAAATAACC 808

  chr1_199805453_   5178 CCATTAAAAAGTGGGCAAAACAT--GAA----CACTTTTCAAAAGAAGAC 5221
                          v   ?    i        iv  --   ----  i  i  v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_199805453_   5222 ATACATGCAGCCAACAAGCATGTATGTCAACAATCTCAACATCACTGATC 5271
                              viii     i     i--   vv  v vv          ??????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCAC--ATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_199805453_   5272 AT 5273
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.56 (140 / 90)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.67 (66 / 18)  


1403 31.46 9.93 1.91  chr1_199909614_199911463      526  1361 (489)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_199909614_    526 AGATATACCATGTTTTTAGATAAGGAGACTTAATATCATACAGATGCCAA 575
                               v       iv i   vi i           ii vv     v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_199909614_    576 TTCTTCTCAA-----TCTATAGATTCAGTGCAATTATAATCAAAACCTGG 620
                          v  i i   -----    i       ii     iviv       i ivi
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_199909614_    621 ACAGAATTTTTAATGGAATTTGGCAATATAATTCTAACATATACATGGAA 670
                         i v vv     viii   v   i   vv i  i    v  vi i      
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_199909614_    671 AAGTAAGAG-CTAAGAACATCCAAGACATTTCTGAAACA-AAGAACACAG 718
                          v i   i - iv    i v    i   v ii     v -       v  
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_199909614_    719 TATAAAGATTTGCTGTAATAAATATCAGGATTTATTATAAGGCTTTAGTA 768
                          vvi i  i ii vv vviv   v   ii i   i  i  i   vi    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_199909614_    769 ATTAAGATAGTGAGTTATTGGGGCAGCAAAAGAAAAATACACCAATGGAA 818
                           i    i    v v  i   vii ivi v   v v   v i        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_199909614_    819 CAGAA---AGATTCC-----------CATGTGTGTACAGAAACATAATTT 854
                         i    ---   v   -----------   iii v  ii vv vv i    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_199909614_    855 GTTTCAGGGATGGTATTGTAGG----TTAGTATGAAAGGGATAGATTATT 900
                         vivv  i  i  vi ----  i---- i i iv i  i i    vi v  
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCA----AGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_199909614_    901 CAATAAATAGTGCTTGAATAACCAGTTATCCGTATAGAAAAAAA----AT 946
                            i    i     v i i   ii v  ?  ii  iv    i  ----i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_199909614_    947 TAGATACA-ACCTTACAGCATATTTAAATGGCAATT---TCAGTA-AGAC 991
                          i  iv v-    i   v     vi   ----    ---   iv -i  i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAA----AATTAACTCAAAATGGAT 497

  chr1_199909614_    992 TAAAGGCTTAAGTGGGAAA---AAAGCTACAAAACTTTTAGAAGATAATA 1038
                         i ?  i i   i  vi i ---   i   i      i        v  i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_199909614_   1039 TAGGA--AAATAGCTCTTGACTTCAGACTAGAGAAAAATTTCTCAA---- 1082
                             ?--    v-i  v    i ii ii   iv  vii     i i----
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_199909614_   1083 GATACAGAAAGTAAAAACCATAAAGAATAAGATTGGTAAATCTGACTACA 1132
                           i  vi    i v  i v i   ii v  i  v i     iv    v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_199909614_   1133 TTAAA------------------------GGCACC-TAAGGAGAATGAAA 1157
                          i   ------------------------ i   i- v i  i i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_199909614_   1158 AGCCAAGCCTCAACCCAGAAGA-----TTTAGCCAAACC-TGCAGTC--A 1199
                           v   v  v  ivvii i   -----   i--    i - ii -  -- 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTG--CAAATCATATA-TCTGA 743

  chr1_199909614_   1200 TGAGTGGATTTGTGTTCGGAGCATGGAAAGAACGCCTACATTTCAGTAAG 1249
                          i  -   i    i i i  ii  iv       v i    vi   i   v
  L1M4_orf2#LINE/    744 TAAG-GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_199909614_   1250 AAAGATATAAACAACCCAATAGAAAAATGA-CAAGAGACACATTG----G 1294
                            i v i   i        v?       i-   ii  i---   ---- 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT---TTGAATAG 839

  chr1_199909614_   1295 ACTATTCACAAAAGACAA-ACACATATTGCTTATAGGTATAGGAAAAGAT 1343
                           vv   v v     vi - i   v  v  iv   i i i v        
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_199909614_   1344 GCTGAA-ACTATAATGAGT 1361
                            v  - ii ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (161 / 98)
Gap_init rate = 0.03 (29 / 903), avg. gap size = 3.41 (99 / 29)  


 818 26.00 2.00 0.40  chr1_199942986_199946902      127   376 (3541)  C L1M4_orf2#LINE/L1   (0)   908   655  

C chr1_199942986_    376 AAGAGCTTCTGCACAGCGAAAGAAATTATCATCAGAGTGAA----CAACC 331
                           i i   i  ii vv i  i  v i     vv i      ----     
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

C chr1_199942986_    330 TACAGAATGGGAGAAAATTTTTGCATTCTATCTATCTGACAAAAGTCTAA 281
                         i                 v      vvii  v       i  ii v  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

C chr1_199942986_    280 TAGCCAGAGTCTACAAGGAACTTACACAAATTTACAAGAGAAAAA-ACCC 232
                           v     i v  i  i     ivi    v iv i  v i   i - vvi
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

C chr1_199942986_    231 AACCCCATTAAAAAGTGGGCAAAGGATATGAGCAGACACGTCTCAAAAGA 182
                              v   ?    i            v   ii     iv    v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

C chr1_199942986_    181 AGACATACATGGAGCCAACCAAACATATGAAAAAAAGTTCAACATCACTG 132
                            i     vivi     i-  i  i       i v i         ???
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAAT-AAGCACATGAAAAGATGCTCAACATCAZZZ 903

C chr1_199942986_    131 ATCAT 127
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.46 (38 / 26)
Gap_init rate = 0.01 (3 / 254), avg. gap size = 2.00 (6 / 3)  

1469 26.17 5.93 0.00  chr1_199942986_199946902     1988  2392 (1525)    L1M4_orf2#LINE/L1        1   429 (479)  

  chr1_199942986_   1988 TGCAGAGACATTCTATGTTAATAGGTAGGTATAATCAATATTGTTAAGAT 2037
                           v i   i  i i     v  i i v  v v v i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_199942986_   2038 GCCAATTCTTATCAGTTTGACCTATCAATTCAACACAATCCCAACCAAAA 2087
                          v    v  ivi  iv    i   ivi       i       v i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_199942986_   2088 TCCCAGCAATCAATATCATGGATATTGATAAACTGATTTCAAAGTTTATA 2137
                                vii vv v iiii  v     i  i     iii   i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_199942986_   2138 TGGAAACACAAGAGGCC---AATA------------TTGAAGAAGAAGAA 2172
                               ii    i i  ---    ------------     i        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_199942986_   2173 ---AATCAGAAGACTGACAATAC---AT---GACACTTATTTGGAAGATA 2213
                         --- i ii  i    v   v v ---  ---i v     i vvi   v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_199942986_   2214 TAGTAATCAAGACAGGGTGGTATTAATAAAAGAATAGTTGAATATATTAA 2263
                         i              v      i iii v   i    viiv   v  i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_199942986_   2264 TGTATCAGAATAGAGAGCCCAGAAATAAACCCACGCAAATATAGTCAACT 2313
                           v vi     v     i               ii  vv   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_199942986_   2314 GATCTTTGACAAAGGAGCAAAGGCAATTCAATGGAGAAAGGATAGGCTTT 2363
                            i  i     i  v  v   i v         i     i    v    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_199942986_   2364 CCAACAAATGGTGCCAAAACAATTGGACA 2392
                         i             iiii    i    i 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATA 429

Transitions / transversions = 1.79 (68 / 38)
Gap_init rate = 0.01 (5 / 429), avg. gap size = 4.80 (24 / 5)  

1424 26.06 5.93 0.64  chr1_199942986_199946902     2954  3425 (492)    L1M4_orf2#LINE/L1      412   908 (0)  

  chr1_199942986_   2954 TGCTGCACAGGCATCTAGAT-GCCA---AGAAAAAAAAAAAACCAAACAC 2999
                              ---i i  v  i   -?   ---iv    i  vi  iiiii  v 
  L1M4_orf2#LINE/    412 TGCTG---GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_199942986_   3000 AGATCTAGCATGTTTTATAAAAGTTAGCTCAATATGAATCATAAATCTAA 3049
                         vv i  vi  ivv v  i    i   i     v   i    ? i i    
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_199942986_   3050 ATGTCAAACACGAAACTATAAAACTTATAGAAGATAAGAGAGGAGAAAAT 3099
                             v i vvii             iv       v  v v   ? v    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_199942986_   3100 CTAGGTGACCTTGG---AG---ATGAGTTTTTAGATACAGCATCAAAAGC 3143
                           vv          ---  ---   iv  i       iii  i       
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_199942986_   3144 ACAATACATGGAAGAAAAAATGG-TAAGTTGGAATTTACTAAAATGAAAA 3192
                             vvv iii          i -   i     v  i ii     v    
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_199942986_   3193 ACTTCTGCTTTGTGAAAGACACTGTTAAGAGAAT---AAG-----CCACA 3234
                             i  ivi vii  i      i i    i i ---   -----     
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_199942986_   3235 GATTGGGAGGAAATATTTGTAAAACACATATCTAAAGAAGGATTTATGTT 3284
                           v      i         i   v  i      i vi i   i  i i i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr1_199942986_   3285 CAAAATATACAAAAAACTCTTA-AATGCA-CAATAAAAAAACA------C 3326
                           i      i   i        -  iv  -i        i   ------ 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_199942986_   3327 CAATT-AAAAATGGGCAAAAGATTTAAAGAAACACCTCACTAAAGGAGAT 3375
                              -             i     i  v i   ii  v i    i    
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_199942986_   3376 ATATGGATGACAAATAAATATACGAAAATATATTTAACATCCTATTGATA 3425
                            iii   i v     ii i i     v  ii i      v????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (82 / 38)
Gap_init rate = 0.02 (12 / 497), avg. gap size = 2.58 (31 / 12)  


2568 27.35 0.54 0.27  chr1_199958934_199960583.rev      425  1159 (491)    L1M4_orf2#LINE/L1      172   908 (0)  

  chr1_199958934_    425 ATCACCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACACT 474
                           vi    iv     i i ivv i          i      vv       
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_199958934_    475 ACCTGACTTCAAACTATACCACAAGGCTACAGTAACCAAAACAACATGAT 524
                         v  ii i      viv   i    i          i   i   iii  i 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_199958934_    525 ACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCT 572
                              i iv ii i   v                i    i--    i  -
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC- 320

  chr1_199958934_    573 CAGAAATAACGCTGCATATCTACAACTATCTAATCTTTGACAAACCTGAA 622
                         -        vv iii i  i  iiiii vi i  i  i     ivv  vv
  L1M4_orf2#LINE/    321 -AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_199958934_    623 AAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGA 672
                           i v  vv            i  vvi  v  i  i              
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_199958934_    673 AAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACAC 722
                         v      v  ?   i   i i  iiv    ii    i    v   i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_199958934_    723 CTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGATCT 772
                          v              i    i      i ?    i    i  v   v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_199958934_    773 AAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACAT 822
                              i      vi i           v    ?i v viv   iv   v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr1_199958934_    823 AGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAA 872
                         v  vv i     v ii   v ivv  vi            vvi       
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr1_199958934_    873 AAGCCAAAATTGACAAATGGGGTCTAATTAAACTAAAGAGCTTCTACACA 922
                            vv     v  i    v  iii v  i   v v  i i   i iii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_199958934_    923 GCAAAAGAAACTACTATGAGAGTGAACAGGCAACCTACAAAATGGGAGAA 972
                         v    i  v    ii v  i      v  i     i   i          
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_199958934_    973 AATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACA 1022
                            v  i    vii ivi      i  i  i  vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_199958934_   1023 ATGAACTCAAACAAATTTACAAGAAGAAAACAAACAACCCCATCAAAAAG 1072
                          v      vv    v iv i  v  i  i     i     v  i?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_199958934_   1073 TGGGTGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGC 1122
                             ii     iv    i     i     v        i  vi viii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_199958934_   1123 CAAAAA--ACATGAAAAAATGCTCACCATCACTGGCCAT 1159
                            v  --         i       v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (119 / 78)
Gap_init rate = 0.00 (3 / 737), avg. gap size = 2.00 (6 / 3)  


 778 28.38 0.90 0.90  chr1_200098473_200100298.rev       38   259 (1567)    L1M4_orf2#LINE/L1        1   222 (686)  

  chr1_200098473_     38 TGGAAAGATATTCTGTGCTCATGGATCAGAAGAATTAATATTGTTAAAAT 87
                                    i ii  i        ii     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_200098473_     88 GTCCCTATTATCCAAAGCAATATACAGACTTGACACAATTCTTATCAAAA 137
                          v vv  i vi     vii  v      i ii  i    i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_200098473_    138 TCCCAATGACATTCTTCATGGAAATAGAAAAAAAAAATTCCTACAATTCA 187
                              iivi v  i  iiii     v  v  ivvi --     v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chr1_200098473_    188 TACAGAACCACAAAAGACCCCAAATAGCCAAAACAATTCTAAGAAAGAAA 237
                           ii   vii   ii     vi               ii i i      i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_200098473_    238 TACAAA--TAGAAATCTTCCATTT 259
                         v     -- i  iiv  iv  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTT 222

Transitions / transversions = 2.32 (44 / 19)
Gap_init rate = 0.01 (2 / 222), avg. gap size = 2.00 (4 / 2)  

2149 17.06 0.12 19.91  chr1_200098473_200100298.rev      492  1335 (491)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr1_200098473_    492 AAAAATTACTATATATTTCAAAACCATAGTAAACAAAACAGTATGGTACT 541
                             v      -------    i i i     v   i     i       
  L1M4_orf2#LINE/    232 AAAACTTACTA-------CAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_200098473_    542 GACAGAAAAAAAGACATATAGGCCAACGGAACAGAAGAGACAGCCTAGAA 591
                          i  v  ii v          ii   i    i    vv  v  i i    
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_200098473_    592 ATAATTTCAAACATATATGGTCAACTCATTTTTGTCAAGGGCTCCAAGAG 641
                             vii  v    v         i v     i v      iv      v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_200098473_    642 GACAAAATGGGGCAAGGATGGTCTTCTCAATAAATGATGCCAGGAAAACT 691
                         v ivv       v   i  i     i    i     i   ii   v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_200098473_    692 GGATTTCCACATGCAAAAGAATGACACTAGACCCTTATCTGACACCATAC 741
                             v?                  vii i     i  i  v        i
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_200098473_    742 ACAAAAATCAACTCAAAATAGATTTTTTTAAAAAAACCTAAATGCAAGAT 791
                                 i          i   i------- ? i         i    v
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATC-------AWAGACCTAAATGTAAGAG 517

  chr1_200098473_    792 CTGAAACTATAAAACTCCTAGAAGAAAACATGGAGGAAAAGTTCCTGGAC 841
                           i              i             i i? v   ----------
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA---------- 557

  chr1_200098473_    842 AGTTGCCTTGGCAATGATTTTTTTCATTTTCTTTTTCCTTTTTGGTAGAG 891
                         -------------------------------- i   -------------
  L1M4_orf2#LINE/    558 --------------------------------TCTTC------------- 562

  chr1_200098473_    892 ACAGCATCTCCTTATGTTGCCCAGGCTGGTCTCGAACCTCTGGACTCAAG 941
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    563 -------------------------------------------------G 563

  chr1_200098473_    942 TGATCCTCCCACCTCACATCCCAAAGTGCTGGGATTATAAGTGTGAGCCA 991
                            i i ------------------------  i   -------------
  L1M4_orf2#LINE/    564 TGACCTT------------------------GGGTTA------------- 576

  chr1_200098473_    992 CCACATCCAACTGGCAATGATTTTTTGGAGATCGCAGCAAAAGCTCAGGC 1041
                         ------------       i   i  i  v  vi  v       v  i  
  L1M4_orf2#LINE/    577 ------------GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_200098473_   1042 TACAAAAGCAAAAATAAATAAATGGGGCTACATCAAA-TTAAAAAGATTC 1090
                         v       v       i      v  i  v       -       v-  i
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC-TTT 663

  chr1_200098473_   1091 TGCACAACAAAGGAAACAATCAACAAAACAAAATAGCAACTTATGGACTG 1140
                           ii vv       v  v     v   iii   vii    ii ii  v  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_200098473_   1141 GGAAAAAATTTTTGCAAACCATATATCCGATAAGGGGTTAATATCCAACA 1190
                            i     v        i        i        ii vi      iv 
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_200098473_   1191 TTTATAAAGTACACATACAAATCAATTATAGAAAAACAAATAAACTAATT 1240
                          v       v  v v     v     v   i   i        v i    
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_200098473_   1241 TTAAAATGGGCAAAGGACCTGAATAGACATTTCTCCGAAGAAGACATAAA 1290
                         ?v               ii                 i       i   v 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_200098473_   1291 AATGGCCAACAGATATATGAAAAGGTCCTTGACATCATTAATCAT 1335
                                  i iii i        i v  ii      ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (87 / 53)
Gap_init rate = 0.01 (8 / 677), avg. gap size = 21.12 (169 / 8)  


3342 26.07 0.55 0.66  chr1_200111784_200118665     5481  6389 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_200111784_   5481 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5530
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_200111784_   5531 GACTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5580
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_200111784_   5581 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTGTAAAGTTCAT 5629
                          v   iivi i  i  ii     v v  v  i-  - iiv    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_200111784_   5630 ATGGAACCAAAAAAGAGGCGGCATTGCCAAGACAATCCTCAGCCAAAAGA 5679
                               viiv  ii  vv i v  v     i      i v ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_200111784_   5680 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5729
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_200111784_   5730 ACGGTAACCAAAACAGCATGATACTGGTACCAAAATAGAGATATAGACCA 5779
                           i    i   i    ii  i      i iv ii     v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_200111784_   5780 ATGGAACAGAAT--AGAGCCCTCAGAAATAATACCACACATCTACAACCA 5827
                               i     --    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_200111784_   5828 TCTGATCTTTGACAAACCTGGCAAAAACAAGCAATGGGGAAAGGATTCCC 5877
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_200111784_   5878 CATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCTG 5927
                         iv  i  i              v      v  ?       i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_200111784_   5928 AAACTGGATCCCCTCCTTACACCTTATACAAAAATTAATTGAGGATGGAT 5977
                           ii    i   iv   i     v              i v ii      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_200111784_   5978 TAAAGACTTAAATGTCAGACCTAAACCCATAAAAACCCTAGAAGAAAACC 6027
                         i ?    i       v   v     v i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_200111784_   6028 TAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 6075
                             ?-   --i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_200111784_   6076 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 6125
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_200111784_   6126 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 6175
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_200111784_   6176 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCTATTTGACA 6225
                         v  i     i                 v       vii iv   i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_200111784_   6226 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 6275
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_200111784_   6276 AAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 6325
                           i -    i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_200111784_   6326 TCTCAGAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 6375
                             vi       i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_200111784_   6376 TCATCACTGGCCAT 6389
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2055 18.57 1.43 0.71  chr1_200671872_200674477      500   919 (1687)    L1M4_orf2#LINE/L1      242   664 (244)  

  chr1_200671872_    500 ACAAAACAACA-CAA--AAGATAGTGTGATATGGGCATGAGTACAGAAAT 546
                              i v   -i  --    i      i  iv     i  v i   v  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_200671872_    547 ATAAATCAATGAAATAGAATTGAGAGTCCCAAAATAAACCCATATATCTA 596
                            i       i                 vi             i  i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_200671872_    597 TCACCAACTGGTTTTTAATAAGAGTCCCAAAATTATTCATTAGGAATGAA 646
                          vii   i  i    ii i   i  v    i ii     v i  ---   
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG---GAA 388

  chr1_200671872_    647 AGAATATTTTCTTCAATAAATGGTATGGGAAAAGTTGAATAGCCACATGC 696
                               v i i     i       iiv  i v ii  i   ?        
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_200671872_    697 AAAA-AATGAATTTGAACCCCAACCTCACATCATATACAAAAATTAACTC 745
                             -      v   i     v        i                   
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_200671872_    746 AAAAAGGCTCATAGACTTAAATTTAAGAACTAAAACTATAAAACTCTTAG 795
                             v  v   ?    i     v     i                     
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_200671872_    796 AAGAAAACATATGTGTAAATATTCTTGACTTTGGATTAGACAATAGGTTT 845
                                    v ?      v   v    i    i    i    i v  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_200671872_    846 TTGGAGATGACACCAAAAGTACAAGAGACAAA-GAAAGAATAGATGAATT 894
                           i  v             i     vi     -    i       i    
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_200671872_    895 AAAATTCATCATA-CTAGAAACTTTT 919
                         ii v       v -i  i        
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTT 664

Transitions / transversions = 2.12 (51 / 24)
Gap_init rate = 0.01 (6 / 423), avg. gap size = 1.50 (9 / 6)  

 229 23.08 0.00 0.00  chr1_200671872_200674477     1219  1270 (1336)    L1M4_orf2#LINE/L1      649   700 (208)  

  chr1_200671872_   1219 AAAAAAAGAAACTTTTGTGTTTTGAAGAATACCATCAAGCAAGTGAAAAA 1268
                             vv i           i  ii   i i  i      v         i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_200671872_   1269 GC 1270
                         i 
  L1M4_orf2#LINE/    699 AC 700

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.00 (0 / 0)  

 512 17.89 0.81 1.63  chr1_200671872_200674477     1578  1700 (906)    L1M4_orf2#LINE/L1      685   806 (102)  

  chr1_200671872_   1578 AAGAAAGAGAAAAAAATAACTCCTGGAATGTGAGGAAGTATTTTCAAGTC 1627
                                v -    i i   i vii     v   i  i     v   i  
  L1M4_orf2#LINE/    685 AAGAAAGTG-AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_200671872_   1628 ATACATCAG-TAAGAGGAGTTATATCCAGAATATTTGAAAAACGCTTACA 1676
                            i   v -    -   v  i            v i  i   v      
  L1M4_orf2#LINE/    734 ATATATCTGATAAG-GGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_200671872_   1677 ACTCCATAATAAAAAGAGAAATAA 1700
                             v            v      
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAA 806

Transitions / transversions = 1.20 (12 / 10)
Gap_init rate = 0.02 (3 / 122), avg. gap size = 1.00 (3 / 3)  

 649 15.00 1.67 0.00  chr1_200671872_200674477     1994  2113 (493)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr1_200671872_   1994 AATAA--AAAAGACAAATAAGCCAATTTAAAAATGGTCAAAGGATTTGAA 2041
                              --             v      ?        v             
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_200671872_   2042 CAGACATTTTTTCAAAGGAGATACACAAATTGTTGATGGGCTCATGAAAA 2091
                         i        i i     i     i      v iii  ii  v        
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_200671872_   2092 GGTGCTCAATGTCACTCTGTGT 2113
                          i       ii   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 2.00 (2 / 1)  


 229 19.05 0.00 0.00  chr1_201095146_201096853        3    44 (1664)    L1M4_orf2#LINE/L1      123   164 (744)  

  chr1_201095146_      3 AATTAATAAGCTAGTCCTGAAATTCAAATAGAAATGCAAAGG 44
                             i i     ii    i       v  i         i  
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

Transitions / transversions = 7.00 (7 / 1)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.00 (0 / 0)  

2345 22.77 7.82 2.37  chr1_201095146_201096853      500  1215 (493)    L1M4_orf2#LINE/L1      154   908 (0)  

  chr1_201095146_    500 AAAAGCAAAGGGCCTGGAGTAACAAAAACCATTTTGAAAAAGAA---CAA 546
                            v    i  i  ii  i  i v     v  i           ---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_201095146_    547 AGT-------------------AATTTCAAGACTCACTATAAAGTTACAG 577
                            -------------------        i   i    i    i     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_201095146_    578 TAATCAAGGCAGTGTGGTATTTATGTAAGCACAGAGATACAGATCAATGA 627
                                 i          i viii    v i   v   i         i
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_201095146_    628 AACAGAATACAGGGTCCAGAAATAGATCCATCTAC--ATGGTCAACTGAA 675
                           i     vv  i           i i    vi i--        i   v
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_201095146_    676 ATTTGAAAAATATGTCAAAATTACTCAATGGAGAAAGGATAGTCTTTTCA 725
                         v  i  v  ivi  i   i ii i       i     i            
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_201095146_    726 ACAA---------------TTGAATATCCATGTGCAAAAATATGAAGCTT 760
                             ---------------i  i   ?   ii       iv      i v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_201095146_    761 AACCCTTGCCCTCATAACACATACAAAGGTTAACTCAGAGTGAATGACAA 810
                         i    i i  -   i v  i       ii        i i  i  v -? 
  L1M4_orf2#LINE/    454 GACCCCTACC-TCACACCATATACAAAAATTAACTCAAAATGGATCA-WA 501

  chr1_201095146_    811 GACTTAAATGTCAGAGCTAAAACTACAAAACTTCTAGAAGTAAACATAAA 860
                            i       v             i      ii      v       ii
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_201095146_    861 CAAAAATATTCATGACTTTG--TTAGGGAAAAACTTCTAAGACCTTTGG- 907
                         ?iv    v   i    i   --     v  viii    v   -- v  i-
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA--TATGAC 599

  chr1_201095146_    908 ---AAAAGCATGGACCATAGAAGAAAAAATTGATAAACTGAACTTCTGCA 954
                         ---       iiii v i i          v      i  i     vv  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_201095146_    955 AAATTAAAAAAATTCTGCTCCCCAAATTACATAATTTAAAAAATAAAAAG 1004
                                   v-  i  iv ii    vv   iv  iv i   i i     
  L1M4_orf2#LINE/    650 AAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_201095146_   1005 GCAAGCCACAGACTGGGAGAAA-TATTTGCAAA--ATATA-------AAG 1044
                         i   v       v         -          --     ------- i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_201095146_   1045 GACTTATATCTAGAATATGTTTTTAAAGACACACACACATACACAAATCC 1094
                              i    i       i ----     -  v vi   -  v   --iv
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATAT----AAAGA-ACTCTTACA-ACTCAA--TA 790

  chr1_201095146_   1095 ATATAAATACTAACAATTTGGCTTAAAAAAAAGGACAAAAGATTTGAACA 1144
                            v   v  v  i  iiiiii ?     v--  i    i        i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAAT--GGGCAAAGGATTTGAATA 838

  chr1_201095146_   1145 GACACTTGACTGAAGAAGGTATTTATCAATG-CAAATAAACATGTGGAAA 1193
                             i  vv ii      i   -- iv    - v     i  ii  i   
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAA 886

  chr1_201095146_   1194 GATGCTCCATATCATTAAACAC 1215
                                v i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.18 (109 / 50)
Gap_init rate = 0.03 (20 / 755), avg. gap size = 3.65 (73 / 20)  


3025 11.51 2.79 25.97  chr1_201439387_201442427.rev     1369  2550 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_201439387_   1369 TGGAAAGACATCCCATATTCATGGATTGGAATACTTAACATTGTCAACGT 1418
                                 i       i              v      i     i  vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_201439387_   1419 GATAATACTCCCCAAACTGATCTACAGATCCAGTGCAATCACTATCAAAA 1468
                          ii             i            i  ii      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_201439387_   1469 TCCCAGATTCCTTTTT--CATAAATTCACAAGCTGATTCCAAAATTCATA 1516
                               v v       --  v     v          i i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_201439387_   1517 TGGAAATAAAAGGGACCTAGAATACCTCAAACAATATTTAAAAAGAACAA 1566
                                iv        i      v iv       v  v        v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_201439387_   1567 CCAAGTTGGAGGACTCATACATCCCTATT-CAAAACCTATTATAAAGCTA 1615
                          v               i  v    v   -      i  i  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_201439387_   1616 CAATAATCAAGACAATGTGGTACTGGCATAAGGATCGACATGTAGATCAA 1665
                           i           i                    v     i        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_201439387_   1666 ATGAATAAAACTGAGATTTCAGAGATAAACCTTTAAATTTATGTTTAATT 1715
                         vv     i  i     v i    i       iv  v       v i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_201439387_   1716 GATTTTCAA-AAAAGTGTTAAGACAATTCAATGGGGGAAAGAGGTTTTTT 1764
                                i -  ii   ii     v           -     ivvv i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTT 399

  chr1_201439387_   1765 TTCCACCAAAATAG-----GGAAAACTAGATATCCATATGCAAAATAATA 1809
                            v  --    i -----   v    i    ?   i        v   i
  L1M4_orf2#LINE/    400 TTCAAC--AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_201439387_   1810 AAGTTAAACCTCTATCTCATATCATATACAAAAAT-AACTCAACATGAAT 1858
                              ii   i   i    i i             -       v   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_201439387_   1859 CACATACCCAAATATAAGAGCTAAAACTATAAATCAGGCCAGGCATGGTG 1908
                           ? v   i    i                   -----------------
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA----------------- 530

  chr1_201439387_   1909 GCTCATGCTTGTAATTCCAGCACTTCGGGAAGCCAAGGTGGGCAGATCAT 1958
                         --------------------------------------------------
  L1M4_orf2#LINE/    531 -------------------------------------------------- 530

  chr1_201439387_   1959 ATGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCATC 2008
                         --------------------------------------------------
  L1M4_orf2#LINE/    531 -------------------------------------------------- 530

  chr1_201439387_   2009 TCTACTAAAAATACAAAAATTAGCCAAGCATGGTGGCACACACCTGTAAT 2058
                         --------------------------------------------------
  L1M4_orf2#LINE/    531 -------------------------------------------------- 530

  chr1_201439387_   2059 CCCTACTTTGGAGGCTGAGGTATGAGAATCACTTAAACCCAGGAGGCAGA 2108
                         --------------------------------------------------
  L1M4_orf2#LINE/    531 -------------------------------------------------- 530

  chr1_201439387_   2109 GGTTGCAGTGAGCCAAGATCACACCGTTGCACTCCAGCCTGGGTGACAGA 2158
                         --------------------------------------------------
  L1M4_orf2#LINE/    531 -------------------------------------------------- 530

  chr1_201439387_   2159 GCAAGACTCTGTCTCTAAATAAATAAATAAAACTATAAATTTTCTAGAAA 2208
                         -----     -----------------  i  ---------------i  
  L1M4_orf2#LINE/    531 -----ACTCT-----------------TAGAA---------------GAA 543

  chr1_201439387_   2209 AAAATAGGAATATATCTTTGTGATCTTTGGTTATGCAATGGCTTCTTAGA 2258
                           v     ?i  v     i    i   v     v       i        
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_201439387_   2259 TATAACATCCAA--CATGAGCAACAGAAGAAAAA-TAGAAAAATTGGACT 2305
                            i   i v  --  ii       i        -    v          
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_201439387_   2306 TTATCCAATTTAAAAACTTTTGTGTGTCAAAGGAGACTATCAAGAAAGTG 2355
                          i   v  v               iv        v               
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_201439387_   2356 AAAAGACAATTTATAGAATG--AGAAAGTATT-GTAAATCATAT------ 2396
                                  iii i      --     i    - i         ------
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_201439387_   2397 ----------GTATCCAGAATATATAAGGAACTCTTACAATTAAATGATA 2436
                         ----------                 i            i v   i   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_201439387_   2437 AAAC-ACAAGTAACTAAATTTAAAGATTGGCAAAAAAGTTGAATGGACAT 2485
                            v-    i    iv    ?   i  v      ii v      i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_201439387_   2486 TTCTCCAAAGAGAATATACAAATGGCCAGTAAATACATGAAAAGATGTTC 2535
                                    ii               i   ii             i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_201439387_   2536 AGCTTCATTAGGCAT 2550
                          i v   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (84 / 48)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 21.25 (340 / 16)  


2451 26.89 5.54 2.94  chr1_201609638_201613690.rev     2678  3562 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_201609638_   2678 TGGAGAGGCCTACTTTGTTCATAAACTGGAATACTCCACACAGTAAAGAT 2727
                             i  iiv v iv       ii i     v   iv i iv  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_201609638_   2728 GCAAATTATCTCCATATATATATACTGGTTTAATGCAATCCTTATTAAAA 2777
                          vv   vv  i   v  vv  v   v i  i  i       i   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_201609638_   2778 TCCCAACAAAATTTTTAACAGCTA--GACAAATT-ATTTTAAAATTTATA 2824
                              i vivv     vi   vv --     ii -  ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_201609638_   2825 TGGAAATAAAAAGGAACAAGAATAGCTGAAACAAATTTGACAAAGAAGAA 2874
                                iv  i   v v        ii      vi    v         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_201609638_   2875 AAACATAGGAGGA-TCAGTCTACCCAATTTAAAGACTCATTATATAACTA 2923
                         v  vi v      -   vv  v        v  i   i i  i v i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_201609638_   2924 CAGTAACCAAACCTACATGGTATTGGTGAAGGAAGAGACACATAGATCAA 2973
                               i   iv viii     i   iiv i i v     i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_201609638_   2974 TGGAACATAATTAAAAAAAAAACCCA-AAATAGAAACACACAT--ATACT 3020
                              i v    i i i-----i   -     i vv  i    --  iv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAG-----TCCAGAAATAAACCCATACATTTATGGT 345

  chr1_201609638_   3021 TAACTGATTTTTGATAAAGATGCAAAAGCAAGTCAATGGAGAAAAGACAG 3070
                         i  i       i  i  i i   v  ii v v       i    ii i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_201609638_   3071 TCTTTTCGACAAATGATGCTGAAATAATTGGATATCCTTAGGCAAAAAGA 3120
                                i       i     ii i  i      ?  vi v      ---
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA--- 442

  chr1_201609638_   3121 AAGAAAGAAAGAAAGAAAAAAG--GAATCTTAACCTAAGTCCTTATACAA 3168
                         --------------   vi   -- i i iiv    v vv  v       
  L1M4_orf2#LINE/    443 --------------GAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_201609638_   3169 AGACAAACTCAAATTGGATGGCCAACTTAAACATAAAATGTAGAACTATA 3218
                          i iv        v     vi?vi  i    ii   i vv  i       
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_201609638_   3219 AAACTTGTACAATAAAA-ATAGGAGAAAATTGTTGCAATCTGGAGCTAGA 3267
                              iv  v  v    -     ? v    iv i ii i  v i i   i
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_201609638_   3268 CAAACAATTCTTAGATCTGACACCAAAAGTATAATTCATAGAAGGAACAA 3317
                            vviv         v            i i  viv i i   i  -  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA-AA 627

  chr1_201609638_   3318 TTTATGGATAAACTGAACTTCACTAAAATTAAG--CTTTTAT-CTGC--- 3361
                         ---  i      i  i      ii        i--     i -  v ---
  L1M4_orf2#LINE/    628 ---ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_201609638_   3362 ------------GAAAG----AAGATGAC-----GAGTGGGAGAAA---- 3386
                         ------------     ----    ii  -----  i         ----
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_201609638_   3387 -------CCACACATATGACGAAGAACTAGT-TCTAGAATATGTGAAGAA 3428
                         -------i  i i  v   ii i i   v  -  i       i i     
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_201609638_   3429 CTTTCAAAATTCAGCAGTAGAGGCACAAATAATCCAACTAGAACATGGGC 3478
                           i i v  i   ii i  i iiv        i    i ?i  v      
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_201609638_   3479 ACAAGACATAAAAAGACATTTCATCAGAGTAGAAATACAGACAACAAATA 3528
                          v i  iv i  v         vi  i  v   v     i iii v    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_201609638_   3529 CGCACATGAAAAGGCATTCAACATCATCAGCCAC 3562
                         v            iiii         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (148 / 86)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.17 (75 / 18)  


3280 26.51 0.44 0.99  chr1_202101733_202108144.rev     5009  5921 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_202101733_   5009 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5058
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_202101733_   5059 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_202101733_   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_202101733_   5157 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5206
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_202101733_   5207 AACAAAGCTGAAGGCATCACGCTACCCGACTTCAAACTATACTACAAGGC 5256
                                i  i   vv    i  v   i i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_202101733_   5257 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGATC 5306
                                 i   i    ii  i      i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_202101733_   5307 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5354
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_202101733_   5355 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5404
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_202101733_   5405 CCATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5454
                          iv  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_202101733_   5455 GAAACTGGATCCCTTCCTTACACATTATACAAAAATTAATTCAAGATGGA 5504
                            ii    i    v   i    vv              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_202101733_   5505 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5554
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_202101733_   5555 CTAGGCATTACCATTCAGAACATAGGCATGGGCAAGGACTTCATGTCTAA 5604
                         v    ?i v viv   ivi  v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_202101733_   5605 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5654
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_202101733_   5655 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCACAGCAAAAGAG 5704
                          i   v v  i i   i  ii vv    i  v    i  ----- i i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA-----AGAAAG 691

  chr1_202101733_   5705 TGAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCT 5754
                             v  i     i   i             v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_202101733_   5755 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 5804
                           i  i  i  vi          v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_202101733_   5805 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 5854
                         v     i     i     v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_202101733_   5855 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGC 5904
                          i     v        i  vi viii     v ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_202101733_   5905 TCATCATCACTGGCCAT 5921
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.17 (13 / 6)  


2192 24.36 0.42 6.52  chr1_202564519_202566216      500  1205 (493)    L1M4_orf2#LINE/L1      246   908 (0)  

  chr1_202564519_    500 AGCTATAGTTACCAATAAAGCATGGTACTGGTATTAAAATAGGCATGTGT 549
                              i   v i   v v  ii         i  v ii    i   i i-
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA- 294

  chr1_202564519_    550 TCTGTTCCAATGGAACAGAATAGAGAACCCAGAAACAAAGCCAAATATTT 599
                         --- v  -       i     v    ii       i   v   v i    
  L1M4_orf2#LINE/    295 ---GATC-AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_202564519_    600 ACAGCCAACTGATCTCTGACAAAGCAAACAAAAACATAAAGTGGGGAAAG 649
                          ii i   i    i ii     i vviv   i v   vv i         
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_202564519_    650 GACACCCTATTCCACAAATAGTGCAGGGATAATTGGCAAGCCACATGTAG 699
                         i i vi  v   v      i    v    i  i   vv ?       i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_202564519_    700 AAAAATGAAGCTGGATCCTCGTCTCTCACTTTATACAAAAATCAACTCAA 749
                           i       i    i  iiii   v   iv           i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_202564519_    750 AATGGGTCAAAGTCTTAACTCTAAGACCTGAAACCATAACAATTCT-AGA 798
                              i   ?  v i   v v     v  i    i    -  i   -   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGA 539

  chr1_202564519_    799 AAATAACATTGGAAAAACTCTTCTAGACATTGGTTTAGGCAAAAAGTTCA 848
                          i v     v  ?iv  v     vv   v    v        viiv   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_202564519_    849 TGACCAAGAACCCAAAAGCAAATGCAATAAAAAGGAAGATAAATAGATGG 898
                          iivi v  vv         v v    i    iii  i   i   i  v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_202564519_    899 GACCTAATTAAGCTGAAAAGCTTCTGCATAGCAAAAGAAATAATCAGCAG 948
                            i v  i  iv v    i   i  iiivv    i  v iv    iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_202564519_    949 AGCAAACAGACAACCCACAGGGTGGGAGAAAATATTTGCAAGCTATGTAT 998
                           ii  v             ii                   iii  i   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_202564519_    999 CTGACAATGGACTAATATCCAGAATCTACAAGGAATTCAAACAATTAGCA 1048
                             i  v     vi          v  i  i   i  ------   ---
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC------TTA--- 780

  chr1_202564519_   1049 AGAAAAAACACTTGTATTGTGTTTGTTCTGTAAATCAGCAAGAAAAAAAT 1098
                         ------------------------------i  v   ii  v     i -
  L1M4_orf2#LINE/    781 ------------------------------CAACTCAATAATAAAAAGA- 799

  chr1_202564519_   1099 CACATAATTTCATTAAAAAGTGGGTAAAGGACATGAACAGACAATTCAT- 1147
                           v    iiiv   ?    i    i      iv    i     v   vi-
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_202564519_   1148 -AAGAAGATATACAAGTGGCCAACAAACATATGAGAAAATGCTCAACATC 1196
                         -              i       i  i  i    i  i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_202564519_   1197 ACTAATTAT 1205
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.67 (105 / 63)
Gap_init rate = 0.01 (8 / 663), avg. gap size = 6.12 (49 / 8)  


2363 23.85 0.82 1.15  chr1_202577016_202578971.rev      495  1102 (854)    L1M4_orf2#LINE/L1      266   871 (37)  

  chr1_202577016_    495 TGAGGCACTGGTATAAAAACAGACACATAGACCAATGGAACAGAATAGAC 544
                           v  i     i    ii i     i     i        i     v  v
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_202577016_    545 AGTCCAGAAATAAATCCACACATTCACAGCTAACTGATTTTCAATAAAAG 594
                                       i   i     i ii ii  i        i i  ii 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_202577016_    595 CTTCAAGAACATACACTGGGGGAAAGATACCCTCTTCAATAAATGATGTT 644
                         ivi     v   v  v     i  ii   vi  i     i     i  i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_202577016_    645 GGGAAAATTGGATATCTGTATCCAGAAGAATGAAACTGGACCCTTTTCTC 694
                             v  i      ? iii  v  i         ii       i vi   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_202577016_    695 TCCCCATACACAAAAATCA-CTGAAGATGGATTAAAACTGTAAACATAAG 743
                         v v     i        i -  v  i      i ? iviv    ii    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_202577016_    744 ACCCGAAACTATAAAACTGCTAGGAAAAAACATAGAGA-AAATATTTTAA 792
                          v ii             vi   i i         i?i-    -i  iiv
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGT 564

  chr1_202577016_    793 GACAT-GAGTCTAGGCAAAGATTTTATGGCTAAGACCTCAAAAGCACA-G 840
                            v - i  -       v i   iv i v  v   vi          - 
  L1M4_orf2#LINE/    565 GACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_202577016_    841 AAACTATAACAAAAATAGACAAATGGGACTATATTGAACTAAAAAGCTTC 890
                         v   v v iv         i    v     vi  ii  v v    i   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_202577016_    891 TACACATCAAAGGAAACAATCAACAGAGTGAAGAGACAACTTACTGAATG 940
                          iii v        v  v     v i      i       ii  v     
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_202577016_    941 GGAGAAAATATTTGCAAACTATTCATCTGACAAGGGACTAATAGCCAGAA 990
                                           ii  vi      i        vi  v      
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_202577016_    991 TATACAG-GAATATCAAACAACTCAACAATAATAAAAAAACAAATAATCT 1039
                             i i-   i-  vv         ---         i        i i
  L1M4_orf2#LINE/    764 TATATAAAGAAC-TCTTACAACTCAA---TAATAAAAAGACAAATAACCC 809

  chr1_202577016_   1040 CATTTAAAAGTGGGCAAATGACATGAATACATATTTCTCAAAAGAAGACA 1089
                         v   ?    i        v  iv      v i       v        i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_202577016_   1090 TACAGACTGGGCA 1102
                             i -   v  
  L1M4_orf2#LINE/    860 TACAAA-TGGCCA 871

Transitions / transversions = 1.88 (92 / 49)
Gap_init rate = 0.02 (10 / 606), avg. gap size = 1.20 (12 / 10)  

 257 15.79 1.75 0.00  chr1_202577016_202578971.rev     1409  1465 (491)    L1M4_orf2#LINE/L1      851   908 (0)  

  chr1_202577016_   1409 AAAAAGAC-TACAAATGGACAGCAGGTATATGAAAAAATGCTCAACATCA 1457
                           i    i-         v  ii i i i       i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_202577016_   1458 CTAAGCAT 1465
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 8.00 (8 / 1)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1)  


2357 20.60 1.40 16.78  chr1_202581363_202585688.rev     2763  3835 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_202581363_   2763 TGGAAAAATATCCCATCCTCATGGAATGGAATAATTCATATAATTAAAAT 2812
                               i         vi       v     v v  v    vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_202581363_   2813 GACAATCCTAACCAATGCAATCTGCAGATTCAATCCAATCCCTATGAAAA 2862
                          i    v  vv    vvii    i         iv          v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_202581363_   2863 TACCAATGACATTTTTCAGAGAAATAGAAAAAAAAAATCCTAAAATTTGT 2912
                          v   iivi v     iiv      v  v  ivvi -          ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_202581363_   2913 GTGGAACCACAAAAGACTCCAAATGGCCAAAGCAACCCTGAGCAAAAAGA 2962
                         i     vii   ii   i vi   i      i   i i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_202581363_   2963 ACAATGCTAGAGATATCACAATACCAGACCTCAACATATACTACAGAGCT 3012
                             v i i   ivv     v v  vi ii    v iv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_202581363_   3013 ATAGTAACCAAAACA-CATGGTATTG-CATAAAAACAGACACATAGACCA 3060
                          i     i   i   -ii     i  -     ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_202581363_   3061 ATAGAACAGAGTAGAGAACCCAGAAATTAATCCACATATTTACAGCCAAC 3110
                           i   i   i v    ii        v  i   i i     ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_202581363_   3111 TGATTTTTGACAAAGATGTCAAGAACACTCATTGGGACACCTCTTCAATA 3160
                                i     i i  i     ----i    -----------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGA----CCATT----------------- 378

  chr1_202581363_   3161 AATGATGCTGGGGGCTGGGTCCAATGGCTCACATCTATAATTCCAGCACT 3210
                         ---------------------      -----------------------
  L1M4_orf2#LINE/    379 ---------------------CAATGG----------------------- 384

  chr1_202581363_   3211 TTGGGAGGCTGAGGTGACCTCTCACCTCTTCCCTTGCTTGAGCCTGGGAA 3260
                         ---------------------------------------------  i  
  L1M4_orf2#LINE/    385 ---------------------------------------------GGAAA 389

  chr1_202581363_   3261 GTCAAGGCTGCAGTGTGCTGTGACTGCACCACTGCTCTCCAGCCTGGGCA 3310
                          ------------------------------------------------ 
  L1M4_orf2#LINE/    390 G------------------------------------------------A 391

  chr1_202581363_   3311 ACAGAGTGAGATTCTGTCTCAAAAAAATAAACGTGATGCTAGGAAAACTG 3360
                          i  --------   - i    v   -------  i    i   v     
  L1M4_orf2#LINE/    392 ATAG--------TCT-TTTCAACAAA-------TGGTGCTGGGACAACTG 425

  chr1_202581363_   3361 GATACCAACATGCA---GAATGAAACTAGGCTCCCACCACTCACCCTATA 3407
                             ? v       ---       ii i i i  i   v v    v    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_202581363_   3408 CAAAAATTAACTGAAAATGGATCTAAGACCTAAATGTAAGACACACAACA 3457
                                     v          v?                vvi v   v
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_202581363_   3458 ATTAAACTACTGGAAGAAAACATAGGGGAAACACTTCAGGACATTGGTCT 3507
                           v     vi i              ? v  vv    iv   v    vi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_202581363_   3508 GGAAAAAGATTTTATGGATA--ATACCTTATAAGCACAGGCAACAAAAGC 3555
                         i iv  v i   iv i    -- i   -- v       i          v
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACC--AAAAGCACAAGCAACAAAAGA 623

  chr1_202581363_   3556 AAAAACAAGCAAATGGGATT--ACCAAACCAAAAAGCTTTTGCACAACAA 3603
                              i iii    v   i -- i    viv    i      ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_202581363_   3604 CAGAAACCATCAACAGAGGGAAAAAACAACTTACAGAATGGGTGAAAATA 3653
                         vi  v  i     v i  v     i     ii          v       
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_202581363_   3654 TTTTCAAACTACTTATCCAACAGGAAATTTATATCCAGAATATATAAAGA 3703
                            v    ii iv    ii i i ii i  i                   
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_202581363_   3704 ACTCAAACTTCTTAACAGTCAAAAAACAA----TCTGATTTAAAAATGGG 3749
                             vv  vv  i  i i v    i    ----i ii   ?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_202581363_   3750 CAAGTGACCTGAACAGACACTTCTCAAGAGAGGACATATAAATGGCCAAC 3799
                            iv  ii    i     i     v i   i  i   i          i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_202581363_   3800 AGGTATAATTTTAAAA--TGCTAAACATCACTAATCAT 3835
                          i i i --- v    --    v       ????????
  L1M4_orf2#LINE/    874 AAGCACA---TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (137 / 80)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 11.47 (195 / 17)  


3227 26.07 2.47 0.45  chr1_202599599_202606158     5178  6067 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_202599599_   5178 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCATTATTATGAAAAT 5227
                              ii i  i     i        v      v i v    i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_202599599_   5228 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 5277
                            v     v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_202599599_   5278 TACCA-CTGACTATCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5324
                          v   -   v  - i  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_202599599_   5325 ATATGGAGCCAAAAAAGGGCCTGCATAGCCAAAACAATCCTAAGCAAAAA 5374
                                iviiv  ii iv  v v               i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_202599599_   5375 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACCTCAAGG 5424
                                 i      vv   ii  v  ii i      viv   iv   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_202599599_   5425 CTGCAGTAACCAAAACTGCATGGTATTGGTACCAAAACAGATATATAGAC 5474
                           i      i   i  v ii     i   i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_202599599_   5475 CAATGGAACAGAACAGAGGCCTCAGAAACAACACCACACATCTACAACCA 5524
                                 i    iv   ivii      i  vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_202599599_   5525 TCTGATCTTTGACAAACCTGACAAAAGCAAGCACTGGG-AAAGGATTCTC 5573
                         vi    i  i     ivv  v   i v  vv  v    -    i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_202599599_   5574 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5623
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_202599599_   5624 AAACTGGATCCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGGGT 5673
                           ii    i    v   i     v  i                i    i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_202599599_   5674 TAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5723
                         i ?    i           v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_202599599_   5724 TAGGCA-ATACCATTCAGGATGTAGGCATGGACAAAGACTTCATGACTAA 5772
                             ?i- v i -   iv  iv v  vv i i   v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_202599599_   5773 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGATAAATGGGATCTAA 5822
                         i            vvi          vv             v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_202599599_   5823 TTAAA-CTAAGGGATTTTGCA-TGCAAAAGAAACTATCAGCAGAGCGAAC 5870
                          i   -i   iiiv     ii- v    i  v       iv i  i   v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_202599599_   5871 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 5920
                           i     i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_202599599_   5921 AGGTCTAATATCCAGAATCTACAAAGAACT---------------TAAAC 5955
                         i  v  vi          v  i        ---------------    v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_202599599_   5956 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 6005
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_202599599_   6006 TCAAAAGAAGACATTTATGCATCCAACAGACATATGAAAAAATGCTGCTC 6055
                           v        i  vi viiiv    i ii  i       i     vvv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_202599599_   6056 ATCAGTGGTCAT 6067
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (142 / 86)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.36 (26 / 11)  


1070 29.33 13.40 2.40  chr1_202762755_202764517      481  1271 (492)    L1M4_orf2#LINE/L1       31   908 (0)  

  chr1_202762755_    481 AGACCTGAATGAAATCATAAATATATCAATTATTTCCCAAATTAATCTCT 530
                             i -   ---  ii v  v  iv    - i i        i    vi
  L1M4_orf2#LINE/     31 AGACTT-AAT---ATTGTTAAGATGGCAAT-ACTCCCCAAATTGATCTAC 75

  chr1_202762755_    531 AAAGTCAATGC--CTCAAACCAGAAACTCAATAACAGAACTTTTTTG--G 576
                          i v    i  --ii vv i  i  v i  iivi ----        -- 
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGC----CTTTTTTGCAG 121

  chr1_202762755_    577 AACCCAATAAACTGATACCAAATTTCACCAT-----TTCAAA--ATTTTG 619
                           viii i  i     v i   v    i-  ----- v   i-- iiiv 
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCAT-ATGGAAATGCAAGGGACCCAG 170

  chr1_202762755_    620 AG------AAACA-TTTT-AAAAATAAGAACAAAG--GGAGG-CTTGTTT 658
                          i------     - i  -     v          --     -  iiivi
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr1_202762755_    659 TTACCAAGAATTAAGGCTCATTAGAAAGCTGTTGTACCTAAAATAGTGAA 708
                           v    vv- i  ii  i i  v      iiv   vii  i i    vi
  L1M4_orf2#LINE/    221 TTCCCAATT-TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_202762755_    709 ATATTGGGATAGGGATAGAAAAATAAATTAATAGAATAGGCCAGAGATTC 758
                         i  i   v   i       v v   i  i   i      iviv    v  
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_202762755_    759 CAGAAATAGCCTCATATA---------AA---ATTTGAAATAATG-TATT 795
                                 iv i    i ---------  ---    vvi i  v - iii
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_202762755_    796 ATACAGATGAT--AGTTGAGAAATGATGGACAATTCAATAAATGGAGT-- 841
                          ---   iv  -- i v i    vi  i v vv     i      v i--
  L1M4_orf2#LINE/    370 A---AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_202762755_    842 ----AATTGGCTTGCC-C-TGCTGGGGAAAAAATGAAGTTAGATTCTTAC 885
                         ----  i   v v?  - -   ----i   i         i  ii i   
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGC----AAAAGAATGAAGTTGGACCCCTAC 462

  chr1_202762755_    886 TCAACAC-ATAATAGAAAAATAAATTCCAGTTGGATTAAAGCTCTAAATA 934
                         iiv    -   -  v      v  i  v iv     i ?  vi      i
  L1M4_orf2#LINE/    463 CTCACACCATA-TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_202762755_    935 TGAAAAACAAAAGT-TAAATTTGTTAGAAGAACATACAGGGGGAAATATT 983
                          i i ivi    v -    vi v         v i i   ? v    v  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_202762755_    984 TCTATTCTCAAGGTACAGAAC----------ACAAGACACAAAAAGCCAA 1023
                         iv ivi  iii v  viv  i---------- i v     v      vv 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_202762755_   1024 AATAATAAAAGGAGGAATTGAT----TG-----CATCATAATTTAAATTT 1064
                          ii  i     i ii   v   ----  -----     v    v   vi 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_202762755_   1065 TCTGTGTAACAAAAGACCCCATCCA--AAGCAAAAAGATAGTG-ACAGA- 1110
                          i    ivv    i   v i   v --   ii      i iiv-     -
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_202762755_   1111 TTAGAGAAGATATTTTCAA--CATAT---------------------CAG 1137
                          vi     i      v   --     ---------------------   
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_202762755_   1138 AATATATACAGG--TCCTACAATTTGATAA------GAAAAACAATCTAA 1179
                                 v  i--  i     i ii    ------  v   i  i i  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_202762755_   1180 TAAAAAGTTGAGCAGAAGATATGAAT-GA---TTTACAGAAGAGAAAATC 1225
                          v?   iv  i   i i   v     -  ---  iv vi    ii v  v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_202762755_   1226 CAAACAACAAATAAATACAAGGAAAGATACTCAAAAT-ACTCAGTAA 1271
                             iii v     ii   v i      i     v  - ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (141 / 87)
Gap_init rate = 0.05 (40 / 878), avg. gap size = 3.12 (125 / 40)  


 275 21.74 2.17 9.78  chr1_203440964_203444891      500   591 (3337)    L1M4_orf2#LINE/L1       54   138 (770)  

  chr1_203440964_    500 AATGCTTCGTAAATGATGGTGAATACATATATAATATA--CTCTATCAAA 547
                            i  i vi    --  i v--    v  vi  iii -- i        
  L1M4_orf2#LINE/     54 AATACTCCCCAAAT--TGATC--TACAGATTCAACGCAATCCCTATCAAA 99

  chr1_203440964_    548 ATCTCAACTGGCATTTTTTTTTTGCAGAAATTAACGAATTGATC 591
                            i  i   v -----               i  i ii     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-----TTTTTTGCAGAAATTGACAAGCTGATC 138

Transitions / transversions = 3.00 (15 / 5)
Gap_init rate = 0.05 (4 / 85), avg. gap size = 2.75 (11 / 4)  

2076 13.90 1.34 1.34  chr1_203440964_203444891     1357  1730 (2198)    L1M4_orf2#LINE/L1      122   495 (413)  

  chr1_203440964_   1357 AAATTAACATCACATGATCTTAAA-TTCATATG-AAAT-TAAGGGAACCC 1403
                              i   -- vv     i    -        -    -i      -   
  L1M4_orf2#LINE/    122 AAATTGACA--AGCTGATCCTAAAATTCATATGGAAATGCAAGGGA-CCC 168

  chr1_203440964_   1404 AGAAGAGCCAAAATAATCTTGAAAAAGATAAACAACGTTGGAAGACTCAC 1453
                             v        i              vi     v      i       
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_203440964_   1454 ATTTCCCAGTTTCAAA-CTTATTACAAAGCTATGGTAATTAAGACAGGCT 1502
                          i      i       -    i          ii     i       vv 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_203440964_   1503 CATACTGGTAAAAGACTAGACATGCAGATCAATGAAATAGTGTTGAGAGC 1552
                         vi      i v   iv       ii         i     vi       i
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_203440964_   1553 CCAGAAATAAATCCTTACATTTATGGTCACTTGATTTTTCAACAAGGGTG 1602
                                    i  v              v        - i         
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTT-CGACAAGGGTG 367

  chr1_203440964_   1603 ACATTACTATTCAATGGGGAAAATAATAGTCTTTCCAACAAATGGTGTTG 1652
                         v  vv  i              i-          i            i  
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_203440964_   1653 GGACAATTGGATATCCATAAGTAAAAGAATGATGCTGGACCCCTAT-TCA 1701
                               i      ?   i v i          v i          i-   
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_203440964_   1702 CAACATATACAAAAATTGACTCAAAATGG 1730
                           v              i           
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGG 495

Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.02 (9 / 374), avg. gap size = 1.11 (10 / 9)  

 701 18.90 4.27 0.00  chr1_203440964_203444891     2032  2195 (1733)    L1M4_orf2#LINE/L1      513   683 (225)  

  chr1_203440964_   2032 AAAAGCCGAAG-TATAAAATTTATATAAGAAAGCA-----GTAATTATTT 2075
                           i   ii  i-       i iv  v      i  -----    v v  i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_203440964_   2076 ATGACCTTGGATTAAGCAAAGCTTTCTTAGATATGACACTAAGAGCAGAA 2125
                         i         i   i    v v                 i  i    v  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_203440964_   2126 GCAACATGAGAAAAAAAAGATAAATTGGAGTTCATGAAAATTTTAAACTG 2175
                               vi        v            v     v      vv     v
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_203440964_   2176 T-ATGCTTTAAAGGACACCAT 2195
                          -i     i         i  
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTAT 683

Transitions / transversions = 1.21 (17 / 14)
Gap_init rate = 0.02 (3 / 171), avg. gap size = 2.33 (7 / 3)  

 403 12.82 3.85 0.00  chr1_203440964_203444891     2502  2579 (1349)    L1M4_orf2#LINE/L1      672   752 (156)  

  chr1_203440964_   2502 AAAGGACACTATCAAGAAAGT-AAAAGACAATTGACAGAATGAAAGAACA 2550
                                              -         iiv        ii    v 
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_203440964_   2551 TATTTGCAAAT--TATATTAGATGAGGAACT 2579
                                    --     iv   i   i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACT 752

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.50 (3 / 2)  

 561 12.26 14.84 5.81  chr1_203440964_203444891     3281  3435 (493)    L1M4_orf2#LINE/L1      740   908 (0)  

  chr1_203440964_   3281 CTAATACAGGAACTTAGCCTACAGAAAATGTAAAGAACATTTAAAACTCA 3330
                           i   -   i    - iv v     v  i        vi   v      
  L1M4_orf2#LINE/    740 CTGATA-AGGGACTT-GTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_203440964_   3331 ATGATAAAAAGACAA----TCCA------------------GATT-GAAT 3357
                           i            ----i   ------------------    -    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_203440964_   3358 AGACGTCTCACCAAACAAACAAAAAGATGTATGAATGGCCAATAAGCACA 3407
                             i i  v     -------i     i  ii                 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAA-------GAAGATATACAAATGGCCAATAAGCACA 880

  chr1_203440964_   3408 TGAAAAGATGCTCAACATCATTAGTCAT 3435
                                             ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.04 (6 / 169), avg. gap size = 5.33 (32 / 6)  


2296 27.53 4.27 2.25  chr1_203746161_203748120.rev      580  1469 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_203746161_    580 TAGGAAAATA--CCATGTTTATGGATTAGAAGGCACAATGTTGTATAGAT 627
                          i i  i   --       i       i    i vi   i    vv    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_203746161_    628 ATCAATTCCTCCCAAATTCATACATCAATCAAATGCA-TTCTAATAAAAA 676
                         iv    v ii        v  vi ivi  iv  i   - i iv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_203746161_    677 TTTCAAAAGAATTTTG-GTGAAAATTGACAAGCTGATTTTAAAATTCATT 725
                          ii  ivv vv    v- iii                ii          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_203746161_    726 T--AAGTGCAAAGGAGC-AAAGTTGTCAATGTAATCTAAAGAGGCGGTGG 772
                          --  i     i   v - i i v i   vii     vi i --------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-------- 192

  chr1_203746161_    773 AGGAGGAATAGGA--GAAGGACCCACATTGCCAGATATTAAGGCTCATTA 820
                          i  i   i iii-- i     i    i v  vi  v i  ii  i i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_203746161_    821 TGAAGCTGTAGTAAAGAAGACATTGTGGTATTGGCGTAAG-ATAGCCAAA 869
                         ii     ii     vv      v       i    i    -    v  v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_203746161_    870 CAGACCAA-GGGCTAACAACTGTGACTCAAGAA-CAAACATCAAATATGC 917
                         i   i   -  iv  i-  i  v  v  v    -i    -i  v i  vi
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAG-AATTGAGAGTCCAGAAATAAAC-CCATACATTT 340

  chr1_203746161_    918 ATAGCTAATTGGCTTATGACAAAG-TGACACTACAGAGCAATGGGAGAAA 966
                           i ii     ii  vi     i -  v  vv  vivv       -    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAA 389

  chr1_203746161_    967 GGATGGTCTTTTTAATAAATTATACCAGATTAATTGTATGTCCATATGGA 1016
                          i  i       i  i    vi i ii ivi  i  v  i?   i   v 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_203746161_   1017 AAAAAATGAATCTTGGTCCTTTACCTTACACGATA-GCAG---TTA--T- 1059
                            i      v-    v  ii     i    v   -i  i---   -- -
  L1M4_orf2#LINE/    440 AAAGAATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_203746161_   1060 -GGGTGGATCATAGTTCTAGGTGTGAAAG-TAAAATTCTAAATATCTTAA 1107
                         -iii       ?  vi   ii   i i  -     i v    vv     i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_203746161_   1108 AAGAAAACATGGGC--AAA-------GATTTGGGGGTAGGCATAGATTTC 1148
                                   i  ?--   -------  ii v   v      vv i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_203746161_   1149 TTAAATGGGATAC-AAAACTCTAATCAA-AAAGGAAGCACTTGATATATT 1196
                            i  iv  i  -    vivi  v   -   i   iv v v    v   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_203746161_   1197 GTACTACATTAAAATTAGGAA--TTTATGTTTATAAAACACATAACTTTA 1244
                          v   v   i       ii  --   i  i  -i   iv   iv -- i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTT-CAAAGGACACTA--TCA 685

  chr1_203746161_   1245 TAAAAGTAAAAAAAGCCAGGCCATAGATCAGGAAAAAGATATTTGCAA-- 1292
                         vi     i    i --  iv   i   vii   i   -          --
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGA--CAACCCACAGAATGGGAGAAA-ATATTTGCAAAT 732

  chr1_203746161_   1293 TACATATCTCATAAAGGACTTTTGTCCAGAATATATTAAAAACTCCTACA 1342
                         i i      v    i      v i            v  i     i    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_203746161_   1343 ACTAAATTAGAACTAGGTAAATCATCCAATAGAAAAATGAGTAAATGACT 1392
                            v   v v  vv  ii    v i     v?       i i   v  i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_203746161_   1393 TGAACTAGA-ACTTCACAGAAAAGGAATATCTAAATGGTCAATAAACATA 1441
                             -    - i   v vi  i i  -   vi      i      i  i 
  L1M4_orf2#LINE/    833 TGAA-TAGACATTTCTCCAAAGAAGA-TATACAAATGGCCAATAAGCACA 880

  chr1_203746161_   1442 TGAAAAGTAATTCAACCTCACTAATCAC 1469
                                vvii     v   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (152 / 89)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 1.76 (58 / 33)  


3165 26.14 0.54 1.63  chr1_203757244_203763569     4916  5833 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_203757244_   4916 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4965
                              ii    i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_203757244_   4966 GACCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5015
                          i v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_203757244_   5016 TACCAATGATTTTCTTCACAGAA-TTGGAAAAAAAAAAACT-ACTTTAAA 5063
                          v   iiviii  i  ii     -   ------- v  i  - iii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-------ACAAGCTGATCCTAAA 143

  chr1_203757244_   5064 TTTCATATAGAACCAAAAAAGAGCCCGCATTGCCCAGACAATCCTAAGCC 5113
                         v       i   viiv  ii  v  v v  v   v i      i i ivv
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_203757244_   5114 AAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTAC 5163
                          i          i      vv    i  v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_203757244_   5164 AAGGCTACAGTAACCAAAACAGCATGGTACTGGTATCAAAAGAGATATAT 5213
                           i          i   i    ii         i  v ii v   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_203757244_   5214 AGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTA 5261
                            i        i    i--    i  --        vv   i    i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chr1_203757244_   5262 CAACCATATGACCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGG 5311
                         iiii  vv   ii  i     ivv  v   i v  vvv           i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_203757244_   5312 ATTCCCTATTTAATAAATGGTTCTGGGAAAACTAAACTGGCTAGCCATAT 5361
                           vvi  v  i  i       v      --- --      v  ?   i  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGA---C--AACTGGATAKCCACAT 436

  chr1_203757244_   5362 GTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTGATACAAAAATTAAT 5411
                          i i  iiv    ii    i    v   i     vv             i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_203757244_   5412 TCAAGATGGATTAAAGACTTAAATGGTAGAGCTAAAACCATAAAAACCCT 5461
                             i      i ?    i      vv           i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_203757244_   5462 AGAAGAAAACCAAGGCA-ATACCATTCAGGACATAGGCATAGACAAGGAC 5510
                                   vv   ?i- v i -   iv   v v  vv   i   v ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_203757244_   5511 TTCACGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAA 5560
                            viiiv  vi            vvi          vv        i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_203757244_   5561 AAGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCA 5610
                          vv   ii v  i   v v  i i   i  ii vv    i  v    i  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_203757244_   5611 TCAGAGTGAACAGACAACCTACAGAATGGAAGAAAATTTTTGCAATCTAC 5660
                         vv i      v        i         i       v       vii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_203757244_   5661 GCTTCTGACAAAGGGCTAATATCCAAAATCTACAAAGAACTAAAACAAAT 5710
                         iiv     i  i  i  vi      i   v  i        vvv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_203757244_   5711 TTACAAGAAAAAAGCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGA 5760
                         iv i  v     ii    i     v  i?    i            v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_203757244_   5761 ACAGATACTTCTCAAAAGAAGACATCTATGCAGCCAACAGACAGATGAAA 5810
                          i   i i     v        i  vi viii     i ii  v      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_203757244_   5811 AAATGCTCATCATCACTGGTCAT 5833
                          i       v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


3138 26.26 0.88 1.53  chr1_203767975_203774397     5017  5930 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_203767975_   5017 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAC 5066
                              ii i  i     i      i v      v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_203767975_   5067 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5116
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_203767975_   5117 TACCAATGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5164
                          v   iivi i  i   i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_203767975_   5165 TATGGAACCAAAAAAGAGCCTGCATTGACAAGTCAATCCTAAGCCAAAAG 5214
                                viiv  ii  v  v v  v v   iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_203767975_   5215 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5264
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_203767975_   5265 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 5314
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_203767975_   5315 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5362
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_203767975_   5363 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAACGATTCC 5412
                          vi    i  i     ivv  v   i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_203767975_   5413 CTATTTAATAAATGGTGCTGGGAAAACTAAACTGGCTAGCCATATGTAGA 5462
                           v  i  i              --- --      v  ?   i   i i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGA---C--AACTGGATAKCCACATGCAAA 441

  chr1_203767975_   5463 AAGCTGAAACTGGATCCCTTCCTCACACCTTATACAAAAATTAATTCAAG 5512
                          iiv    ii    i    v         v              i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_203767975_   5513 ATGTATTAAAGACTTAAATGTTAAAGATGAAAACAATAAAAACCCTAGAA 5562
                            v  i ?    i       v i  v -     v      vi i     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAA 540

  chr1_203767975_   5563 GAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCA 5611
                               v    ?i- v i -   iv   v v  vv i     v ii   -
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC- 588

  chr1_203767975_   5612 TGTTGAA---AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAA 5658
                         --  ii ---i            vvi          vv     v  i   
  L1M4_orf2#LINE/    589 --TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_203767975_   5659 TGGGATCTAATTAAACTAAAGAGCATCTGCACAGCAAAAGAAACTACCAT 5708
                          v   ii v  i   v v  i i v i  ii vv    i  v    i  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_203767975_   5709 CAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACT 5758
                         v i      v  i     i                 v       vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_203767975_   5759 CATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATT 5808
                         i      i  i  i  vi          v  i  v      vv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_203767975_   5809 TGCAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATCAA 5858
                         vii  v     i     i     v  i?    i     i      v v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_203767975_   5859 CAGACACTTCTCAAAAGAAGATATTTATGCAGCCAAAAGACACATGAAAA 5908
                         i     i     v           vi viii     v ii          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_203767975_   5909 AATGCTCACCATCATTGGCCAT 5930
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


3540 24.30 1.34 0.11  chr1_203813956_203816762.rev     1420  2316 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_203813956_   1420 TGGAAAGATATTCCATGTTTATGGATTAGAAGAATCAATATTGTTTAAAT 1469
                                    i       i       i     v i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_203813956_   1470 GTCTACACTACCCAAAGAAATTGACAAATTCAATGCAATCTCTATCAAAA 1519
                          v v i   v      vvi  iv   i      i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_203813956_   1520 TACCAATGACATTCTTAACAGAAATAGAAAAA--AATCCTAAAGTTTATA 1567
                          v   iivi v  i  vi       v  v  i--i        i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_203813956_   1568 TGGAACCACAAAAGAACCAGAAGAGCCAAAGCCATCCTGAGCAAAAAGAA 1617
                              vii   ii  v      v       i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_203813956_   1618 CAAAACAGCAGGCATCACATTACCTGACTTCAAATTATACTACAGAGCTA 1667
                             iiv v   vv     i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_203813956_   1668 TAGTAACCAAAACTGCATGGTGGTGGCATAAAAACAGACACATAGACCGA 1717
                         i     i   i  v ii    iv        ii i     i     i i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_203813956_   1718 TGGAATAGAATCGAGAACTAGGAAATAAATCTATACATCTACAGTGAACT 1767
                                    i    iiivi        i i      i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_203813956_   1768 CACTTTTAATAAAGGTGCCAAGAATATACATTAGGATAAAACCAGTCTT- 1816
                         v i   ii i  i          vi  v  v i  iv  i vi      -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_203813956_   1817 --AAAAAATGTTGCTGGG-CAACTCAATATCCACTTGCAGAAGAATGAAA 1863
                         --  v     v       -     vi   ?    v    i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_203813956_   1864 CTAGACCCCTGTCTCTCACCATATTAAAAAATCAAATCAAAATGGATTAA 1913
                         i i       ii   v        vv      i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_203813956_   1914 AAACTTAAATCTAAAACTTCAAACTATTAAACTACTAGAAGAAAACACTG 1963
                          i  i     v   i vi v       v     vi            iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_203813956_   1964 CA--AAAACTTCAGGACATTGGAGTGAGCAAAGATTTCTTGAGTAATACC 2011
                         v?--   v    iv   v    iv ii    v i      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_203813956_   2012 CCAGAAGCGCAGGCAACCAAAGCAAAA-TGGACAAATGGGATCACATTAC 2060
                            i    i  i     v    v    - i  i    v   iiv   i v
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_203813956_   2061 A-TTAAAAAGCTTTTGTACAGCAGAGAAGACAATCAACAAAGTGAAGAGA 2109
                          -       -       i vv  i  i v  v     v        i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_203813956_   2110 CAACCCACAGAATGGGAGAAAATATTTGCAAATTACCCATCCGACAAGGG 2159
                                                          i ivi   i  i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_203813956_   2160 ATTAATAAGCTGAATATATAAGGAGCTCAAACAACTCTATAGGAAAAAAT 2209
                          i vi  vv v          i  i   vv       v   iv     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_203813956_   2210 CAAATAATCTGAGTTAAAAA-GGGCAAAAGATCTGAATAGAGATTTCTTA 2258
                                i ii v ?     -       i   i        v      iv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_203813956_   2259 AAAGGAGACCTACAAATGGCAAACA-GTATATGAAAAAGTGCTTAATATC 2307
                             i   iv          v  i - i i       ii    i  i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_203813956_   2308 ATTATCAGA 2316
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.55 (130 / 84)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


3477 24.33 1.22 0.33  chr1_203834733_203838969.rev     2847  3746 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_203834733_   2847 TGGAAAGACATTCCATGTTTATGGATTAAAAGAATCAATATTGTTAAAAA 2896
                                 i  i       i       ii    v i           i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr1_203834733_   2897 TTTCCATACTACCCAAAGAAATCAACAGATTCAATGCAATCTCTATCAAA 2946
                          vv v     v      vvi   v          i      i        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_203834733_   2947 ATACCAACAACATTGGTCACAGAAATAGAAAAAATAATCCTAAAATTTAT 2996
                           v   i vi v  vv ii       v  v  iv i           i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_203834733_   2997 ATGGAACTACAAAAGACCCAGAAGAGCCAAAGCCACCCTGAGCAA-AAGA 3045
                               v i   ii         v       i v i i   iv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_203834733_   3046 ACAAAACAGCAGGCATCACATTACCTGACTTCAAATTATACTACAGAGCT 3095
                              iiv v   vv     i v  ii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_203834733_   3096 ATAGTAACCAAAACAGCATGGTGGTGGCATAAAAACAGACACA--GACCA 3143
                          i     i   i    ii    iv        ii i     i --  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_203834733_   3144 ATGGAATAGAATCAAGAACTAAGAAATAAATCTATACACCTACAGTGAAC 3193
                                     ii   iiiv         i i     ii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_203834733_   3194 TCACTT-CAATAAAAGTGCCAAGAATATACGTTAGAGAAAGAACAGTCTT 3242
                          v i  - i i  ii         vi  v iv i i       i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_203834733_   3243 ---AAAAAATGGTG-TGGGGCAACTGGATATCCACTTGCAGAAGAATGAA 3288
                         ---  v        -    i          ?    v    i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_203834733_   3289 ACTAGATCCCTATCTCTCACCATATTAAAAAATCAAATCAAAATGGATTA 3338
                         ii i  i     i   v        vv      i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_203834733_   3339 AATATTTAAATCAAAAACTTCAAACTATGAAACTACTAGAAGAAAACATT 3388
                         ? v ii     vv  i vi v       i     vi             v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_203834733_   3389 GCAAAAACTCTTCAGGACATTAGAGTGGGCAAAGATTTCTTGAGTAATAC 3438
                          v?iv  v     iv   v  i iv i     v i      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_203834733_   3439 CCCAGAAGCACAGGCAACCAAAGCAAAA-TGGACAAATGGGATCACATTA 3487
                         v   i       i     v    v    - i  i    v   iiv   i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_203834733_   3488 -GGTTAAAAAGCTTTTGCACAGCAAAGAAGGCAATCAACAAAGTGAAAAG 3536
                         -ii       -      ii vv     i vi v     v           
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_203834733_   3537 GTAGCCCACAGAATGGGAAAAAATGTTTGCAAACTACCCATCTGACAAGG 3586
                         ii i              i     i        ii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_203834733_   3587 AATTAATAAATAGAATATATAAGGAGCTCAAACAACTCTAGAAGGAAAAA 3636
                         i i vi  vvi           i  i   vv       v v  vi    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_203834733_   3637 ATCTAATAATTTGATT-AAAAATGGACAAAAGATCTGAATAGACATCTCT 3685
                          - v     iiii   -        i    i   i           i   
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_203834733_   3686 TAAAAGAAGATATACAAATGGCAAACAGGTATGTGAAAAGGCACTAAACA 3735
                         iv                    v  i i i ii       iii  v    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_203834733_   3736 TCATTGATCAG 3746
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.73 (137 / 79)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


2842 24.32 4.77 1.70  chr1_203902287_203906428.rev     2797  3676 (466)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_203902287_   2797 GGAAAGACATCCCATGCTCACGGACTGGAAGAGCTATTATTGTTAAAATG 2846
                                i        i   i   i       vi  v         i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_203902287_   2847 ACTACACTGCC-AAAGCAATCTAAAGATTCAGTACAACCCCTATCAAGAT 2895
                         i v i   v  -   vii     v       iii   i         i  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_203902287_   2896 ATCAA-TGCCATTTTTCACAGAAATAGAAAAAAAAAAGTCCTAAAATGAT 2944
                         vi  i-    -     ii       v  v  ivvi --         vvv
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chr1_203902287_   2945 TGTGGAAC--CAAAAGAGTCCAAAGAGCTAACACAACCC----GAGCAAA 2988
                          i     v--   ii  vi vi  v   i  v    i i----i iv  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_203902287_   2989 AACAAAGCTGGCAGCATCACGCTACCTGACTTCAAAA-----TATAAGGT 3033
                                i   vi vv    i  v  ii i       -----  i  i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_203902287_   3034 TATAGTAACCAAAAACAGCATGGTATTGGTATAAAAACAGGCACACAGAA 3083
                           i     i   i -   ii     i   i    ii i  i  i i   v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_203902287_   3084 TAATGGAACAGAATAGAGAACCCAGAAATAAATCCACATATTTATAGCTA 3133
                         i       i     v    ii           i   i i      i ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_203902287_   3134 ACTGATTTTTTTACAAAGGTGCCAAGAACATACATTGGAAAATGGATACC 3183
                          i       iv-    i          v   v  v   ii  v i   vi
  L1M4_orf2#LINE/    348 ATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_203902287_   3184 TTCTTCAATAAATAGTGCTGGGA-AA------------ATACAGAAGAAT 3220
                         i i     i    i         -  ------------  i  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_203902287_   3221 GAAACTGGACCTCTGCCCCTCACCATGTACAAAAATCAAATCGAGATG-A 3269
                            ii      i  i  i v      i         i  v  i i   - 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_203902287_   3270 TTAAAAACTTAAACATAAGATCCACAACTATAAAAATACTAGAAGAAAAC 3319
                          i ? i  i    ii     v i v          v vi           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_203902287_   3320 ATCAGGA--AGATGCTACAGGACATTAGTCTAGGCAAAGGTTTAATGGCT 3367
                           -   ?-- i  -  v iv   v  i vi       v     vv i v 
  L1M4_orf2#LINE/    547 AT-AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_203902287_   3368 AAAACCTCAAAAGCATAGACAATAAAAACAAAAATAGATAAATAGGACTA 3417
                          vi  vi        i ii   i    iv              v     v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_203902287_   3418 TATTAAACTAAAAAGCTTGTGTACAGCAAAGGAAACAATCAACAGAGTGA 3467
                         i  i   v v    i   v   i vv       v  v     v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_203902287_   3468 AGAGACAACCTGCTAAATGGAAGAAAATATCTATAAACTATTCATCTGTA 3517
                          i        ii vi     i         i ii   ii  vi     vv
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_203902287_   3518 AAGGTACTAATATCCAGAATATACAACGAACTC----AACTTACTAGCGA 3563
                             v   vi             i  v      ----    i v  iii 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_203902287_   3564 AAA-ACAAATAATCACACTAAAAAGTGGGCAAAAGACATGAACAGACATT 3612
                            -        i vv i ?    i        i  iv    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_203902287_   3613 TCTC---AGCAGGTATATGAAAAACTGCTCATCACTAATCATCATGGAAA 3659
                             ---  v  i    i---   iv  ----  v   v  -    i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATAC---AAATGGC----CAATAAGCA-CATGAAAA 886

  chr1_203902287_   3660 --TGC--AA-ATCAAGCTCCAC 3676
                         --   --  -    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (137 / 74)
Gap_init rate = 0.03 (24 / 907), avg. gap size = 2.38 (57 / 24)  


 288 18.64 0.00 0.00  chr1_203909559_203913775.rev     2498  2556 (1661)    L1M4_orf2#LINE/L1        1    59 (849)  

  chr1_203909559_   2498 TGGAAAAATATTCCATGCTCATGCATAGGAAGAATAAATATTTTTAAAAG 2547
                               i    i     i     v  v      v v      v    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_203909559_   2548 GGCCATACT 2556
                            v     
  L1M4_orf2#LINE/     51 GGCAATACT 59

Transitions / transversions = 0.57 (4 / 7)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  

2779 24.06 2.04 2.27  chr1_203909559_203913775.rev     2846  3726 (491)    L1M4_orf2#LINE/L1       30   908 (0)  

  chr1_203909559_   2846 AAAAATTAATACAAAATTTTTAAAAAGGGCCATACTGCCTAAAGCAATTT 2895
                           i v      -----  v    i -v   v     v  i   vii  i 
  L1M4_orf2#LINE/     30 AAGACTTAATA-----TTGTTAAGA-TGGCAATACTCCCCAAATTGATCT 73

  chr1_203909559_   2896 ATAGATCCAATGCTATTCCTATCAAACTACCAATGATATCTTT----CAG 2941
                          i    i   i  v  i         v v   -- v ii    ----   
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCA--GCTGCCTTTTTTGCAG 121

  chr1_203909559_   2942 AGAATTAAAAAATATACATTCTAAAATTCATATGGAATCAAAAAAGAACC 2991
                          -    i v  ii- i-  i                 viiv  ii  v  
  L1M4_orf2#LINE/    122 A-AATTGACAAGC-TG-ATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr1_203909559_   2992 CAAATAGCCAAAACAACCGTAAGTAAAAAGAACAAAGCTGGAAGCATCAC 3041
                         vi              i v i iv  i          i    i vv    
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_203909559_   3042 ACTACCTGATTTCAAACTATATTACAAGGCTACAGTAACCAAAACAGCAT 3091
                            v  ii        viv  i     i          i   i    ii 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_203909559_   3092 GGTACTGGTACAAAAATAGACACATAGACCAATGGAAGAGGTTAGAAAAC 3141
                                 i i  ii       i     i        v  iv v  i ii
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_203909559_   3142 CCAGATATAAAGCCACACCCCTACAACCATCTGATCTTCAATGAAGTCGA 3191
                              v     v   i  vii  iiii  vi    i   i ii i vi v
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_203909559_   3192 CAATAACAAGCAATGGGGAATGGATTCTCTATTCAATAAATG---CT--- 3235
                            v v  vv          v i  vv   v     i     ---  ---
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_203909559_   3236 ATAACTGGCTAGCCATATGCAGAAGATTGAAAATGGACCCCTACCTTTCA 3285
                          i      v  ?   i     i    v    iv             iv  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_203909559_   3286 CCATATACAAAAATCAACTCAATATGGATTAAAGAATTAAACTTAAAACC 3335
                                       i       v      i ?   vi    iv   i v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_203909559_   3336 TAAAAGTATAAAAACTCT-AGAAGAAAACCTAGG---AAATACCATTCTG 3381
                              v       -    -          v    ---    -- v iv  
  L1M4_orf2#LINE/    519 TAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTG 565

  chr1_203909559_   3382 ACATAGGTGTT-GGTAAATATTTCAT-GATGAGGTCTCCAAAAGCAATTG 3429
                           v v  -   -  i  vvi    v -   - v v v         vvv 
  L1M4_orf2#LINE/    566 ACCTTGG-GTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAG 613

  chr1_203909559_   3430 CAACAAAAACAAAAATTGACAAGTGGGACATAATTAAACTAAAGTGCTTC 3479
                                 iv      v  i  i v    v v  i   v v  ivi   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_203909559_   3480 TGCATGGCAAAAAAATATATATCAACAGAGAAAACAGACAACCTACAGAA 3529
                           iiivv    ii -i i-      v i  vi  v        i      
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGA-CAC-TATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_203909559_   3530 AAGGAGAAAATATTTGCAAACTATGCATCTAACAAAGTTCTAATATTCAA 3579
                         vi                  ii  ii    i i  i vv  vi   i  i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_203909559_   3580 AATCTCTAAGGAACTTAAACAAATCAACAAACAAAAATCAAACCAACCC- 3628
                            v v   i     ivv    v    i  vv    iv    i-     -
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT-AACCCA 810

  chr1_203909559_   3629 -TTAAAAAATGGGCAAAGGACATAAACAGACACTTCTCAAAAGAAGACAT 3677
                         -  ?                iv i  i     i     v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_203909559_   3678 ACATGAGGCCAACAAGCATATGAAAAAAATGCTCAACATCACTAATCAT 3726
                            viv      i     i       i -            ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (118 / 91)
Gap_init rate = 0.03 (22 / 879), avg. gap size = 1.73 (38 / 22)  


3023 25.33 1.54 2.30  chr1_204152064_204156104     2637  3548 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_204152064_   2637 AAAAACATTTCACGATTGTGGATAGGAAGAATCAATATCATGAAAATGGC 2686
                            i i  ii  i v ii     v      v i     ii v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_204152064_   2687 CATACTGCCCAAGGTAATTTATACAGTCAATGCTATCCCCATCAAATTAC 2736
                         v     v     iv i  i  i v v    i  v     i      v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_204152064_   2737 CAATGGCTTTCTTCACAGAA-TTACAAAAAAAAAAAAAAAAAAACT-ACT 2784
                           iiv  i  i  ii     -  i--------------- v  i  - ii
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTG---------------ACAAGCTGATC 138

  chr1_204152064_   2785 TTAAACTTCATATGGAAC--CAAAAAATAGCCCATA-TAGCCAAGACAAT 2831
                         i    v           v--   iii ---    v -       i     
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAAT 185

  chr1_204152064_   2832 CCTAAGCAAAAAGAACAAAGCTGGAGGCAC-CACGCTACATGACTTCAAA 2880
                          i i iv  i          i      -  -   i  v vii i      
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAA 234

  chr1_204152064_   2881 CTATACTATAAGGCTACAGTAAGCAAAACAGCATCGTACTGGTACCAAAA 2930
                         viv     i  i          v   i    ii v       i iv ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_204152064_   2931 CAGATATATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCAC 2980
                         i   i       i        i    iv   ivii         vv   i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_204152064_   2981 ACATCTACAACCATCTGATCTTTGATGAACCTGACAAAAACAAGCAATGG 3030
                             i  iiii  vi    i  i  ii ivv  v   i v  vv      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_204152064_   3031 GGAAAGGATTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCAG 3080
                               i  vvi  v  i  i        i     v      v  ?   v
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_204152064_   3081 ATGCAGAAAACTGAAGCTGGACCCCTTCCTTTACATCTTATACAAAAACT 3130
                              i  i v     i         v   i-   i v          i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTC-ACACCATATACAAAAATT 483

  chr1_204152064_   3131 AACTCAAGATGTATTAAAGACTTAAATGTAAGACCTAAAACTATAAAAAC 3180
                                i   v  i ?    i           v              vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_204152064_   3181 CCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAA 3229
                          i           v    ?i- v i -   iv   v v  vv i     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chr1_204152064_   3230 GACTTCATTACTAAAACACCAAAAGCAATGGTAACAAAAACCAAAATTGA 3279
                          ii   v viv  vi            vvi i       ivv     v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_204152064_   3280 CAAATGGGATCTAATGAAACTAAAGAGCTTCTGCACAGCAAGAGAAACTA 3329
                         i    v   ii v  v   v v  i i   i  ii vv   ii  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_204152064_   3330 TCATCAGAGTGAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAATC 3379
                            vv i      v        i                 v       vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_204152064_   3380 CATCCATATGACAAAGGACTAATATCCAGAATCTACAAGGAACTTAAACA 3429
                            vi  v   i  i     vi          v  i  i     ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_204152064_   3430 AATTTACAAGAAAAA-----ACAACCCTATCGAAAAGAGGGCAAAGGATA 3474
                          v iv i  v     ----- i     v  i?    iv           v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_204152064_   3475 TGAACAGACATTTCTCAAAAGAAGACATTTATGCAGCCAACAA--ACATG 3522
                             i           v        i  vi viii     i  --     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_204152064_   3523 AAAAAAAGCTCATCATCACTGGTCAT 3548
                             i v     v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 2.69 (35 / 13)  


3339 26.07 0.55 0.66  chr1_204291707_204297983     4876  5784 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_204291707_   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4925
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_204291707_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_204291707_   4976 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 5022
                          v   i-       i  -i     -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr1_204291707_   5023 CATATGGAACCAAAAAAGAGTCCATATAGCCAAGACAATCCTAAGCAAAA 5072
                                  viiv  ii  vi viv        i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_204291707_   5073 AGAACAAAGCTGGAGACATCAAGCTACCTGACTTCAAACTATACTACAAG 5122
                                  i     ivv   vi  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_204291707_   5123 GCTACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGA 5172
                                   i   i    ii        ii iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_204291707_   5173 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAA 5220
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_204291707_   5221 CTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5270
                         ii vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_204291707_   5271 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5320
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_204291707_   5321 CTGAAACTGGATCCCTTCCTCACACCTTATACAAAAATCAATTCAAGATG 5370
                         v    ii    i    v         v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_204291707_   5371 GATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5420
                            i ?    i    ii v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_204291707_   5421 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5470
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_204291707_   5471 AAAACACCAAAAGCAACGGCAACAAAAGACAAAATTGACAAATGGGATCT 5520
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_204291707_   5521 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5570
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_204291707_   5571 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5620
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_204291707_   5621 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5670
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_204291707_   5671 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACT 5720
                            i     i     v  i?    i    ii     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_204291707_   5721 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5770
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_204291707_   5771 TCATCACTGGCCAT 5784
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3127 26.55 1.11 0.66  chr1_204332391_204335883.rev     2099  3002 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_204332391_   2099 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGGGAAAAT 2148
                              ii i  i     i        v      v i       vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_204332391_   2149 GGCCATACTACCCAAGGTAATTTATAGATTCAATGCTATCCACATCAAGC 2198
                            v     v     iv i  i  i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_204332391_   2199 TACCA-CTGAATTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2245
                          v   -   vv   i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_204332391_   2246 ATATGGAACCAAAAAAGAGTCCATATAGCCAAGACAACCCTAAGCAAAAA 2295
                                 viiv  ii  vi viv        i    i i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_204332391_   2296 GAACAAAGCTGGAGACATCAAGCTACCTGACTTCAAACTATACTACAAGG 2345
                                 i     ivv   vi  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_204332391_   2346 CTACAGTGACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAT 2395
                                i i   i    ii         i iv ii i   i        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_204332391_   2396 CAATGGAACAGAATAGAGGCCTTAGAAATAACAACTCA--CATCTACAAC 2443
                                 i     v   iviii        --  i  --   i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAA--ACCCATACATTTATGGT 345

  chr1_204332391_   2444 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAGGGATTC 2493
                           vi    i  i     ivv  v   i v  vvv         i i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_204332391_   2494 CCTATTTAATAAACGGTGCTGGGAAAACTGACTAGCCGTATGTAGAAAGC 2543
                         i  v  i  i   i          v     iv  ?  ii   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_204332391_   2544 TGAAACTGGATCCCTTCCTCACACCTTATACAAAAATTAACTCAAGATGG 2593
                             ii    i    v         v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_204332391_   2594 ATTGAAGACTTAAATGTAAGACCTAACACCATAAAAACCCAACAAGAAAA 2643
                           ii?    i           v    v  i      vi iv v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_204332391_   2644 CCTAGGCA-ATACCATTCAGGACATAGGCACGGGCAAATACTTCATAACT 2692
                          v    ?i- v i -   iv   v v  vvii     vvii   v  iv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_204332391_   2693 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 2742
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_204332391_   2743 AATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 2792
                         v  v   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_204332391_   2793 ACAGGCAACGTACAGAATGGGAGAAAATCTTTGCAATCTGCCCATCTGAC 2842
                          v  i    vi                 v       viiiivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_204332391_   2843 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAATAAATTTACAAGAA 2892
                           i  i  vi          v  i        ivv i  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_204332391_   2893 AAAAACA--CCACC--ATCAAAAAGTGGGCAAAGGATATGAACAGACACT 2938
                            i   --iv   --  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_204332391_   2939 TCTCAAAAGAAGACATTTATACAGCCAACAGACATATGAAAAAATGCTCA 2988
                             v        i  vi v ii     i ii  i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_204332391_   2989 TCATCACTGGTCAT 3002
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3836 17.87 4.94 2.92  chr1_204342434_204344840.rev     1029  1918 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_204342434_   1029 TGGAAAGACA-CTTGTGTTTATGGATTGGAAAAATTTAGTATTTTTAAAC 1077
                                 i - iii    i           i -i   i    v    iv
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA-CTTAATATTGTTAAGA 49

  chr1_204342434_   1078 TGTCAATACTATACAAAGCAATCTTCAGATTTAGTGCAACCCCTATGAAA 1127
                           v       viv    vii    v      i ii    i      v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_204342434_   1128 ATCCTGATGATGGTATTTTTTGGTTTTTTTTTTCTGAAATAGAAAAATCC 1177
                             ii-- v  ------------ii      v v     v  v  iiiv
  L1M4_orf2#LINE/    100 ATCCCA--GCTG------------CCTTTTTTGCAGAAATTGACAAGCTG 135

  chr1_204342434_   1178 ATTCCAAAATACATATGAAATCTCAAGGGACCACAAATAGCCAAAACAAT 1227
                           i i     v      i  viv         vvi               
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_204342434_   1228 CCTAGAAACAAAGAGCAAAGTTGAGAAGGCTCACACTTTCTGATTCCAAA 1277
                          i ii   vi    i        -  i i         i ii   i    
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTG-GAGGACTCACACTTCCCAATTTCAAA 234

  chr1_204342434_   1278 ACT------------ATAATAATCAAAACAATG--GTAATGACAAAAAGG 1313
                            ------------ i i       i   i  --   v  i  v  i i
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_204342434_   1314 CAGACATACAGACCAATGGAATAGAACAGAGACCTCGGAAATAAACCCCT 1363
                         i       i   i             iv    vii i           v 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_204342434_   1364 GCATATATGGTCAAACGGTTTTCAACAAGCGTGACAAGGAACAGTCAAAT 1413
                         i   v         vi i     i     v   v    - v  v    - 
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG-ACCATTCAA-T 382

  chr1_204342434_   1414 GGGGAAAGGG-AGTCTCTTCTACAAATGGTGCTGGTAAAACTGGATATCC 1462
                                 ii-     i   v              v v         ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_204342434_   1463 ACATGCAAAAAAAGTGAAGCTGGACCCTTATC-------ATATACAAACA 1505
                                   i  -     i       i  i -------         v 
  L1M4_orf2#LINE/    433 ACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_204342434_   1506 CAAACTCAAAATAGATCAGAGACCTAAACATAAGAGGTAAAACTATAAAA 1555
                         iv          i     ?         ii      v             
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_204342434_   1556 CTCTCAGAAGAAAACAGAGG---AAATGCTTCTTGACATTTGATCTGGCT 1602
                             i           v   ---    -    v    v  v i iv   v
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCA 580

  chr1_204342434_   1603 ATGATTTATTGGATGTGACTCTAAAAGCCCAGGCAAGACAAGAAAAAA-- 1650
                            i   v  i   i    v i      v  i    v v         --
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_204342434_   1651 -----ATTATATTTCATCAA--TTAAAAGCAAATTTTGTGCATCAAATGA 1693
                         -----   iv i        --      i ---        v     v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAAC---TTTTGTGCTTCAAAGGA 677

  chr1_204342434_   1694 CACTATCAACAGAGTGAAAAGGCAACCCACAGAATGAGAGGAAATATTTG 1743
                                  v i         i              i   i         
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_204342434_   1744 TAAATCATATATTTGATAAGGAAGTAATATCCAGAACATATAAATAACTC 1793
                         i           i        i v vi         i       v     
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_204342434_   1794 TTAAAACTCAGTAA--------CAAATGTCAACCCAACTTGAAAATGGGC 1835
                            v      i   --------     ---       i ?i         
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAAT---AACCCAATTWAAAAATGGGC 824

  chr1_204342434_   1836 AAAAGACTTAAAAAGATGTTTCTCTAAAGAAGATATACAAATGACCAATA 1885
                            i  i  i  v   ii      i                  i      
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_204342434_   1886 AGCACATGAAAAGATTCTCAACA-CATTTCTAAT 1918
                                        v       -  ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (98 / 58)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.50 (70 / 20)  


3197 26.61 0.89 0.22  chr1_205001731_205006007.rev     2885  3786 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_205001731_   2885 TGGAAACACATCCCATGCTCATGGATGAGTAGAATCAATATTGTGAAAAT 2934
                               v i        i        vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_205001731_   2935 GACCATACTGCCAAAAGCAATCTACTAATTCAATCCAATCCCCATCAAAA 2984
                          i v     v  v   vii      vi      iv       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_205001731_   2985 TAGCA-CTATCATTCTTCACAGAGTTAGAAAAAACAATTCTAAAATTCAT 3033
                          vv  -  ii -  i  ii    iv v  v  ivii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_205001731_   3034 ATGGAACCAAAAAAGAGCCTGCATGGCTGAAGCAAGACTAAGCTAAAAGA 3083
                               viiv  ii  v  v v  i  ii  i   vvi i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_205001731_   3084 ACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGCC 3133
                              vi      vv       v  ii        viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_205001731_   3134 ATAGCCACCAAAACAGTGTGGTACTGGTATTAAAATAGGCACATAGACCA 3183
                          i  iv i   i               i  v ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_205001731_   3184 ATGGAATGGAATAGACAGCCCAGAAATAAACCCAAATACTTAAAGCCAAC 3233
                                i    v  v  i               v i i   vi i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_205001731_   3234 TGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCATT 3283
                             i   i    i vviv   i v   vv i         i i viv  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_205001731_   3284 TTCAACAAATGGTAATGGGATAATTGGCTAGCC-CATGTAGGAGAATGAA 3332
                                      iv     i  i   v  ?  -    i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_205001731_   3333 ACTGGATCCTCATCTCTCATCTTATACAAAAATCAACTCAAGATGGATTA 3382
                         ii    i  ii i   v  i v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_205001731_   3383 AGGACTTAAACCTAAGACCTGAAACTATAAAAATTCTATAAGATAACATT 3432
                         ?i   i    iv     v  i           v ii  v    v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_205001731_   3433 GGAAAAACCCCTTTTAGACATTGGCTTTGGCAAGGATTTCACGACCAAGA 3482
                           ?iv  vi i iv -   v    v  v     v i    viiivi v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_205001731_   3483 ACCCAAAAGCAAATGCAATAAAAACAATGATAAATAGCTGGGACCTAATT 3532
                         vv         v v    i    iv  vi   i   iv v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_205001731_   3533 AAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAG 3582
                            v v  i i      ii vv    i iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_205001731_   3583 ACAACCCACAGAGTGGGAGAAAATCTTCACAATCTCTACACCTGAGAAAG 3632
                                     i           v  ii   viiv  i i    v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_205001731_   3633 GACTAATATCCAAAATCTACAACAAACTCAAACAAATCAAGAAGAAAAAA 3682
                             vi      i   v  i  vi     vv    v    v  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_205001731_   3683 A-----AATCCCATCTAAAATTGGGCTAAGGACATGAATAGACAGTTC-C 3726
                          -----  i  v  i?    v     v     iv          v   - 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_205001731_   3727 CAAAGAAGATATACAAATGGCCCACAAACATATGAAAAAATACTCAACAT 3776
                                               v i  i  i       i  i        
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_205001731_   3777 CACTAATGAT 3786
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.34 (135 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3457 22.95 3.52 0.34  chr1_205180965_205185467     3131  4010 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_205180965_   3131 TGGAAAAATATTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 3180
                               i    i                     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_205180965_   3181 GTTCATACTACCCAAAGAAATATACAGATTCAATGCAATCCCTATCAAAA 3230
                          viv     v      vvi  v           i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_205180965_   3231 TACCAATGGCATTCTTCACAGAAATAAAAAAA---ATTATAAAATTTATA 3277
                          v   iiv  v  i  ii       vi v  i---  iv       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_205180965_   3278 TGGAACCACAAAAGACCCAGGATTTCCAAAGCTATTCTAAGCAAAAAGAA 3327
                              vii   ii       i  vv     i v  ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_205180965_   3328 TAAAACAAGAGGAATCACATTACCTGACTTCTAATTATACTACAGAGCTA 3377
                         i   iivi     v     i v  ii i   v  viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_205180965_   3378 TAGTAATCACAACAGCTTGGTACTGGCATAGAAACAGACCCATAGACAAA 3427
                         i        vi    iv             iii i    vi     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_205180965_   3428 TGGAACAGAATAGAGAACCCAGAAACAAATCCACACAGCTATACTGAACT 3477
                              i     v    ii       i   i   i   vi   iv v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_205180965_   3478 CATTTTTGACAAAGATGCCAATAATATAAACTGGGTAAA--AGAGTCTCT 3525
                         v     i     i i      v vi  vv v    v   -- v     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_205180965_   3526 TCAATAAATGGTGCTGGGAAAACTGGATATTCATATGCAGAAGAATGAAA 3575
                             i              v         ?i  i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_205180965_   3576 CTAGACCCCCATCTCTCACCATATACAAAAATCAAATAAAAATGGATTAG 3625
                         i i      i i   v                i  v v         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_205180965_   3626 AGACTAAAATCTAAGGCCTCAAACTATGAAACTACTACAAGAAAACATTG 3675
                             iv    v    iv  v       i     vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_205180965_   3676 GGGAAAATCTCTGGGACATTGATTTGGGCAAAAATTTCTCAACCAATACC 3725
                          ? v      ii v   v   iv  i     vii     i ivi vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_205180965_   3726 CCACAAGCACAAGCAACCAAAGCAAAAATAGACAAAAGGGGTCACATCAA 3775
                            v             v    v         i   vv  iiiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_205180965_   3776 G-TTAAAAAGCTTTTGCACAGCAAAAGATACAATCAACAAAGTGAAGAGA 3824
                         i-       -      ii vv    i  i  v     v        i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_205180965_   3825 TAATCCACAGAATGAGAGAAAATAT------ATTA--------ATAA--- 3857
                         i  i          i          ------  i --------    ---
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_205180965_   3858 --------CCAGAATATATAAAGAGCTCAAACAACTCTATAGGAAAAAAA 3899
                         --------                i   vv       v   iv     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_205180965_   3900 ACCTAAAAATTTTATCAAAAAATGAGCAGAATATTTGAATAGGCATTTCT 3949
                         -- v  v  iiiv  i?       i   i iv          i       
  L1M4_orf2#LINE/    800 --CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_205180965_   3950 GAAAAGAAGACACACAAATGGCAAACAGGCATATGAAAAGATGGTCACTA 3999
                         vv        i i         v  i i   i           v   vi 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_205180965_   4000 TCATTGGTCAT 4010
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.39 (115 / 83)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 4.25 (34 / 8)  


 713 32.81 6.65 4.85  chr1_205234267_205237109.rev     1466  2352 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_205234267_   1466 AGACATACCATATG-GTGAGATAAAAGGACTCAACAACAT-AAGACTATA 1513
                            i  v    i v-i  -   vii i    i  i vii -    --- i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATG-GATTGGAAGACTTAATATTGTTAAGA---TG 51

  chr1_205234267_   1514 TCAATTATTCCTGAGCTGAACTTTTATATTTAACATGATTCCAATACAAA 1563
                         v    vv i  ii ii   v  vi- v   i   iii  i  v  vv   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTAC-AGATTCAACGCAATCCCTATCAAAA 100

  chr1_205234267_   1564 TGTCAATAAGATTTGTTTCTGGAAGCATACAAGCTTATTCTGAAATTCAA 1613
                          vi  iiv- vi  v   vii   iivv       v  i  i       v
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_205234267_   1614 ATGGAGAAACAA-------AGAAAAG---GAACAAAATTTAAAAATATGT 1653
                              i vi   -------    v  ---i     vv  v     v ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA--- 196

  chr1_205234267_   1654 AAAATGGAGT--GAGAAATT-CATTATCAGATATTAAAA--TATCAT--- 1695
                          i  iii   --   i v i-  i vi vi  v i    --  ii i---
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_205234267_   1696 GCTGCAATAAT-AAAAT--TTTGGTTCTGGTACATGAATAAACTGGCAG- 1741
                            i  i    -  i i-- v    v    i i v i   i  vvii  -
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_205234267_   1742 CCAATGGGACAGAACTGAAAGTCTAGAAATAGGCCAAAAGACTTACG--- 1788
                         i      i i    i   i    i       ii  v v v i   i ---
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_205234267_   1789 ---TGACTTTAGTATA----TGATAAATTTTCATTTCATATTAGTGAGAA 1831
                         ---   i   v - i ----  vi  ivi--    iv  i----- i   
  L1M4_orf2#LINE/    347 AATTGATTTTCG-ACAAGGGTGCCAAGAC--CATTCAATG-----GGGAA 388

  chr1_205234267_   1832 AATATGGATTATTCAATAAATTTTGTTGGAA-AACTGGGTCACCATCTGG 1880
                          iv  i vi v     i    vv  i   i -      i v?   iv  v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_205234267_   1881 AAAAAAATTTAAGTTGAATTCATACTTTAAGTCTTATACCAGGATAAATT 1930
                             i   v-      i ii v   i i vii v     v ii  v  i 
  L1M4_orf2#LINE/    439 AAAAGAATG-AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_205234267_   1931 AAAACTGGATCAAAGAATTAGGGGTAAAAAGTGAAACCATAGAGTTACCA 1980
                         v   v       ?   vi  iiv    i iv i    i   i ii vii 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_205234267_   1981 GAGGAAACTAAGAGAACAAATT---ATAATCTCATAGTGTAGAAAGAAGG 2027
                           i    vi vii ?ii    i---i i i  -- i vv   iv - v  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCT--TGGGTTAGGCA-ATGG 584

  chr1_205234267_   2028 CCTTTTTAACCATTTCAC--AAATCTTGGAGT--TAAAAGAAAATATTAA 2073
                         i-  i   ivi  vv   --   v vii-  i--i         v  vi 
  L1M4_orf2#LINE/    585 T-TTCTTAGATATGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGA 632

  chr1_205234267_   2074 TACACCAAACTACAGTAAA-TTAGAAAACAT--ACACTTAAGGCAAAATA 2120
                           v iiii   v  vi   -   -     v --iii   ----    iv 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTT----CAAAGGA 677

  chr1_205234267_   2121 TAATCATTCAAAAGCTTGTGATAA----ACTC------TG--AAAAAATA 2158
                         i v -  iv i  i---    v  ----  i ------  -- i      
  L1M4_orf2#LINE/    678 CACT-ATCAAGAAA---GTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_205234267_   2159 CTTCTTTAAAAATCTTATCATGGACAGAAGACCAATTTCTGTAATATAAA 2208
                         ----   iv     v   vviv  i iii   ivi v  iiv      v 
  L1M4_orf2#LINE/    724 ----TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_205234267_   2209 AATAATTCACATAAGCCTTTAACAAAAAGACAAACATCCCTAAAGGAAA- 2257
                           v  i  vi i  vi vv   i           i v   -------  -
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC-------AAT 812

  chr1_205234267_   2258 -AAAAAAAGGATGAAAGACGTGAACATACAGTTCACAGAAAAATTTATAC 2306
                         -?     v  iii  i  iv    i v   v   v vi  i  vv     
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_205234267_   2307 AATTGGCTACTAATCATGTAAAAAGGTCCTTGACTTCATTCATGTT 2352
                           v    i v   v  ii i     i v  ii  v   ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (174 / 113)
Gap_init rate = 0.05 (42 / 903), avg. gap size = 2.43 (102 / 42)  


1942 24.55 6.44 4.53  chr1_205260042_205261872      500  1338 (493)    L1M4_orf2#LINE/L1       54   908 (0)  

  chr1_205260042_    500 AATTCTCTCCCAAATTAATTTATAGGTTCAATACAATCCCAATCAAAATG 549
                            v   -        i  i  i  i     ii       v        v
  L1M4_orf2#LINE/     54 AATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_205260042_    550 AACAGCAGGCTTTTTTTCCCTTACAAATTAAAAAAATAGTTTCTGTAAGT 599
                         v-    v v       v ---- v     i v  iv - v i  iv  v 
  L1M4_orf2#LINE/    103 C-CAGCTGCCTTTTTTGC----AGAAATTGACAAGCT-GATCCTAAAATT 146

  chr1_205260042_    600 TATATGAAAATGTAGTGGGACT--ACATTGGCAAATCAACTTTCTAAAAG 647
                         i     i     i i-     i--iv  v v    v   ii  vv     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_205260042_    648 AACTAAAACAGCTTTAAAAATAACAAGGAAAACCCA-ATTTAA-AATTTT 695
                           ---i    -------  i v----   ii  i  - i  vv-     i
  L1M4_orf2#LINE/    196 AA---GAACA-------AAGTT----GGAGGACTCACACTTCCCAATTTC 231

  chr1_205260042_    696 AATACTTATTGTAAAGCTAGAATAATTGATTCTGCATGGT-TTGG---AA 741
                           v     i ii       v i    ii vv v ii    -i   ---  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_205260042_    742 AAACAAGATATATTCAGCAATGAAACAGGATAGAAAATCAAGTAATGGAC 791
                         ii i -  i    vv v     i  i  i  v  i i  v  v   ii  
  L1M4_orf2#LINE/    282 GGATA-GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_205260042_    792 ACGCATATATGTGGTCAATCGATGTTCAACAAAACTGCCACGGCAATTCA 841
                         v ii i  v i        i   v   i    iiv     v i v     
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_205260042_    842 GTAGAGGAAAAGCAATCTCTTCAAGATACGTTGCTGGAACAATTGGAGAG 891
                         i i i i  i ii i   i     v v i v      i    i    v ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_205260042_    892 CCATCTACAAA----TGAACTTCAATCTTTATCT-ACCTCA---ACAAGA 933
                            iv i    ----    v  vi i ii  i  -  vi  ---    i 
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_205260042_    934 A---ACACAGAATAGATGAGAAAAC-AAATGTGGGAGCTAAAAATGTAAA 979
                          ---  v  i   i   v ? i v -      ii         v i    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_205260042_    980 TATTCT-AGAAGTAATCA---GGATAAAGTCTTAATGATCTTATGTTTAG 1025
                         - i   -     v  v  --- ?i    -    vi   i   iv   vi 
  L1M4_orf2#LINE/    531 -ACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGG 578

  chr1_205260042_   1026 CAAATATTTCTTAAGAAT--CA--AAAAACACAA------AAAGAAAATT 1065
                            vvi       iiv  --  --    i     ------        vv
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_205260042_   1066 TCAATAAATTGGAATTCATAAAAATGTTAAACATT-----GCTTTTGAAG 1110
                          vi          v     v     --    v i -----    ivi i 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAAT--TAAAAACTTTTGTGCTTCAAAGG 676

  chr1_205260042_   1111 GCACTGTTA-----GT----AG-----CCACAGTCTGGGAGAAAATAGTT 1146
                         i    i i -----  ----  -----      vv            v  
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_205260042_   1147 CCAAAATATGTATCTGAGAAATAACTTATATCGAGAAGGCATTAAGAACT 1196
                         v    vi  i       v  ivi    i    v    vii  v       
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_205260042_   1197 GTTACAACTCAAAAATTAGAAGACAAAAATATTTTAAATTTTAAAAATGG 1246
                         v           v   v i        --  viii  --  ?        
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAA--TAACCCAA--TTWAAAAATGG 822

  chr1_205260042_   1247 GGAAAG-ATTTGAATAGACACTTTTCAAAAAAAGATAATTCAAATGGCAA 1295
                          v    -             i  i  v   i      - v        v 
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA-TACAAATGGCCA 871

  chr1_205260042_   1296 ATGAGGTAAAAATGGCAAAAAAATGCTCAACGTCATTAATCAT 1338
                           i  v--- v   ---    i         i   ????????
  L1M4_orf2#LINE/    872 ATAAGC---ACATG---AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (116 / 86)
Gap_init rate = 0.04 (37 / 855), avg. gap size = 2.49 (92 / 37)  

 469 29.75 11.35 2.15  chr1_205260042_205261872     1357  1682 (149)    L1M4_orf2#LINE/L1      347   702 (206)  

  chr1_205260042_   1357 AAATGATTTTTAAAGAAAGGATGT---GGTAATTTAATTGAGAAATAAGA 1403
                           v       ii v--    i  i--- iiv   i   v i    v  v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGAC--AAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_205260042_   1404 ACTTTATCTACAAATAATTCTGGAACAACTGGTCCTTCCTAAGAAAACAC 1453
                         iii  v  v      ii v    i        viv?i vi v v   viv
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_205260042_   1454 AAGAATTTCAACCTTAGCCTCTCCTTGTAAACAAAAACTAATTCAAAATA 1503
                          v   v  vi   iivi    v viii  v       i   i       i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_205260042_   1504 AAGGATAGACCTAGAAGTAAAAG-TAAAATTTTAGAAATTCCAGAAGAAA 1552
                         i vv ?       i v    i  -     i v  i  v iii        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_205260042_   1553 ACTAATTAGAGAAAGAGTTTTGTGACAT---GTTA-----------CTCA 1588
                           --  vi ? v  - vi  i     v ---    -----------  i 
  L1M4_orf2#LINE/    545 AC--ATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_205260042_   1589 -----------AAAAGTATAA--AACA---TAAAAGTTGGATAAATTGTA 1622
                         -----------     i i  --    ---v    iv i         v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_205260042_   1623 ATTCATTAAAATAATTAACT---GCTCTTCCAAAGACACCATTAATAAAT 1669
                         v     i     v vv    --- iv    v  i     i  i  v   -
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA- 690

  chr1_205260042_   1670 GGTCAATAAACAA 1682
                         -  v  v i    
  L1M4_orf2#LINE/    691 -GTGAAAAGACAA 702

Transitions / transversions = 1.14 (50 / 44)
Gap_init rate = 0.03 (12 / 356), avg. gap size = 3.67 (44 / 12)  


 557 26.19 0.79 0.00  chr1_205263935_205270519     5002  5127 (1458)    L1M4_orf2#LINE/L1        1   127 (781)  

  chr1_205263935_   5002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5051
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_205263935_   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_205263935_   5102 TACCAATGACTTTCTTCACAGAA-TTG 5127
                          v   iivi i  i  ii     -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG 127

Transitions / transversions = 2.30 (23 / 10)
Gap_init rate = 0.01 (1 / 127), avg. gap size = 1.00 (1 / 1)  

 323 28.40 1.23 0.00  chr1_205263935_205270519     5129  5209 (1376)    L1M4_orf2#LINE/L1       46   127 (781)  

  chr1_205263935_   5129 AAAATGGCCGTACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCAT 5178
                           i     vi    v     iv i  i  i        i  v     i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_205263935_   5179 CAAGCTACCAATGACTTTCTTCACAGAA-TTG 5209
                            iv v   iivi i  i  ii     -   
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1)  

2831 26.19 1.02 3.17  chr1_205263935_205270519     5211  6092 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_205263935_   5211 AAAATGACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCAT 5260
                           i   i v     v     iv i  i  i        i  v     i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_205263935_   5261 CGAGCTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAA 5308
                          i iv v   iivi i  i  ii     -   -- v  i  - iii    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAA 143

  chr1_205263935_   5309 GTTCATATGGCACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCC 5358
                         i         v viiv  ii  v  v v  v     iv     i i ivv
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_205263935_   5359 AAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTAC 5408
                          i          i      vv       v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_205263935_   5409 AAGGCTACAGTGACCAAAACAGCATGGTATTGGTACCAAAACAACATGGT 5458
                           i        i i   i    ii     i   i ---------------
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA--------------- 278

  chr1_205263935_   5459 ATTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCT 5506
                         -----  -- ii i   v                i    i--    i  -
  L1M4_orf2#LINE/    279 -----TA--AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC- 320

  chr1_205263935_   5507 CAGAAATAACGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGAA 5556
                         -        vv  ii i  i  iiiii vi    i  i     ivv  vv
  L1M4_orf2#LINE/    321 -AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_205263935_   5557 AAAAATAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGA 5606
                           i vi vv            i  vvi  v  i  i              
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_205263935_   5607 AAACTGGCTAGCCATAGGTAGAAAGCTGAAACTGGATCCCTTCCTTACAC 5656
                         v      v  ?   i v i i  iiv    ii    i    v   i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_205263935_   5657 CTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCT 5706
                          v              i    i      i ?    i    i  v   v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_205263935_   5707 AAAACCATAAAAACTCT-AGAAGAAAACCTAGGCATTACCATTCAGGACA 5755
                              i      -    -          v    ?i v viv   iv   v
  L1M4_orf2#LINE/    520 AAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_205263935_   5756 CAGGCATGGGCAAGGACTTCATGTCTAAAATACCAAAAGCAATGGCAACA 5805
                         iv  vv i     v ii   v ivv  vi i          vvi      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_205263935_   5806 AAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCAC 5855
                             vv     v  i    v   ii v  i   v v  i i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_205263935_   5856 AGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGA 5905
                         vv    i  v    i  vv i      v  i     i   i         
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_205263935_   5906 ACTTTTTTTGCAACCTATTCATCTGACAAAGGGCTAATATCCAGAATCTA 5955
                          vv v   -    vii  vi      i  i  i  vi          v  
  L1M4_orf2#LINE/    719 AAATATTT-GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_205263935_   5956 CAATGAACTCAAACAAATTTACAAGAAAAAAACAA----CCCCATGAAAA 6001
                         i  v      vv    v iv i  v     i    ----   v  v?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_205263935_   6002 AGTGGGCAAAGGACATGAATAGACACTTCTCAAAAGAAGACATTTATGCA 6051
                          i           iv          i     v        i  vi viii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_205263935_   6052 GCCAAAAAACACATGAGAAAATGCTCACCATCACTGGCTAT 6092
                              v  i       i  i       v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.01 (11 / 863), avg. gap size = 3.36 (37 / 11)  


4280 16.40 5.70 0.12  chr1_205272867_205275236.rev     1020  1879 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_205272867_   1020 TAGAAATACATCATATGTTCATAGATTCGAAGTCTTAATATTGTAAAGAT 1069
                          i    v i   vi        i    v    v           v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_205272867_   1070 GGTGATATGCTCTAA-CTGATCTATAGATTCAATACAATTCCTATCAAAA 1118
                           ii   iv i i  -i       i        ii    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_205272867_   1119 TCATAGCTGTCTT----ATAGTACTTGACAATATATTTCTGAAATGTATA 1164
                           vi     i   ----ii  v v       vv iv i  i    vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_205272867_   1165 TGGAAAT-CAATGGACCAATAATAGTCAAAATAATCTTGAAAAATAAGAA 1213
                                -   v     v v     i     i            v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_205272867_   1214 TAAATTTGGAAGATTAACACTTCCCAATTTTATA-CTTACCACAAAGATA 1262
                         i   v     i  i v              i v -     i      v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_205272867_   1263 CAGTAATCAAGACAATGTTGTACTGGCATAAGGCTAGACATATAGATCAA 1312
                                       i   v              v                
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_205272867_   1313 TGGAATAGCAGTGATAGTCCAGAAACAAGGCCTTTACATTTATGATCAAT 1362
                                 v v   v          i  i-  iv          i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTCAAT 349

  chr1_205272867_   1363 TGATTTGTGACAA--------------TTCAATGGGAAAATAATAGTCTT 1398
                               vi     --------------         i   v         
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_205272867_   1399 TTTAAGAAGTGGTGTTGGAACAACTGGATATTCATATGCAAAA--AT--- 1443
                           i  v  i     i   i           ?i  i        --  ---
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_205272867_   1444 ----------------ACACCACACACAAAA-TTATCACATAATGGATTG 1476
                         ----------------      i i      -   v v  v       ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_205272867_   1477 TGGACTTAAATTTAGGGATTGAAAGTAGAAAACTCTTGGAAGAAAACATA 1526
                         ?i   i     v  i iii i   v  v         i            
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_205272867_   1527 GAAGTAAATCTTTGTGATCTTGGTTTAGGTAATGGTTTCTTAGATATGAC 1576
                          i?         i    i     v     i                    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_205272867_   1577 ACCAAAAGCAAAAGTAACAAACTAAAAAATTGATAAATTGGATTTTATCA 1626
                                   v   i      vv       v           i  i    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_205272867_   1627 AAATTGAATACTTTTATACTATAAACCATGTCATCAAGAAAGGGGAAAGA 1676
                              i  v      i i  vi   vv iiii          v i     
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_205272867_   1677 AACCCCAAAGAATTAGAGAAAGTATTTGCAAGTCATATATCTGTTAAGGG 1726
                         v v    v     vi      i         i           v      
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_205272867_   1727 AAT-GTATCCAGAATATATAAATAACTTTTAGTACTCAACAATAAAAAGA 1775
                          v -                  v    i   vv      i          
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_205272867_   1776 ----TAACCCAATTTAAAAATGGGCAAAGGATTTGAATAGACATTTCTC- 1820
                         ----          ?                                  -
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_205272867_   1821 AAAAAAGATTCACAAATGGCCAATAAGGACATAAAAATATGCTCAGCATC 1870
                            i     vi                v    i    v       i    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_205272867_   1871 ATTTGCCAT 1879
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.36 (79 / 58)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 4.17 (50 / 12)  


2315 25.95 4.57 3.45  chr1_205458565_205460690.rev      738  1635 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_205458565_    738 TGGCAAGACATACCATGTTCATGGGTTGGAAGATACAACATAGTAAAGAT 787
                            v    i  v            i        ivi  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_205458565_    788 GTCAATTTTCCCCAAACTTATATACAGGTTTAACATAATTCCTATCAAAA 837
                          v    vi        i v  v     i  i   ii   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_205458565_    838 TTCTGGAAGAATGCTTTATAGATATAGACAAGATTATTCTAAAATGTAAA 887
                          i ii vv vv vi   ii   v  v      v v  i       vi v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_205458565_    888 TGGAAGGATAAAAACAGACACAAAGAAA--AAAACAA-----AAAAAGAA 930
                              --  iv  i-i   v  i iv i--       -----        
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_205458565_    931 ACTAAAAAATTTTGTAAATGAAAACTAAGGCAAGAT-GAAACTGACTTCA 979
                         i--  v   v  v vii ivv v   vvv-   vv -i     v   v  
  L1M4_orf2#LINE/    198 G--AACAAAGTTGGAGGACTCACACTTCC-CAATTTCAAAACTTACTACA 244

  chr1_205458565_    980 G-GTTAAAGTAAGCAAGAGAGTATGA------CAGAGGTATAGGTGCATA 1022
                         i- i  v     v     v   i  i------  v i v    iiii   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_205458565_   1023 AATCAATGGAACAGAATAGAAAACTCCAAAATAGAC----AAATGTA--A 1066
                         i          i     v  i iii vi     i  ---- v  v  --i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_205458565_   1067 CCAACAAACTTTTGACAAAG-TGCAAAAGCAATTTAATGGTAGAAGA-TA 1114
                         i   ivi i   i     i -   v  ii v   i     vii    -  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_205458565_   1115 GTCCTTTCAACAAATAGTGCTGGGA-AATTGGATATACACA-----AAAA 1158
                            i           i         -  i      ?v    -----  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_205458565_   1159 ATGACCTTG-ACCTGAACCTCACACCTTTTACAAAAATTAGCTCAATAT- 1206
                             vv   -   ivv          v v           i     v  -
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_205458565_   1207 -ATCACAGACTTAAAAGTG-GTTATAAGACTATAAAACTTTCAGAAATAA 1254
                         -    ?    i    v  i- vvv   i           i i    iv  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_205458565_   1255 ATATAGGAGAAAATATTTGAGATCTAGAGCTAGGCAAAAATATTTTAGAC 1304
                          i     ? v    v  i v  i  v i i       vii v i     i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_205458565_   1305 TTAACACCAAAC-CACAGTTTACAAAAGAAAAAA-----AAACTATACTT 1348
                         v i        v-    iviv             -----   i iv    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_205458565_   1349 CTTCAAAATTACAAACTTTTACTCTGCAGAAGATACTTTTAAGAGGATGA 1398
                          v         v        iiv  v  i i  i   v i    iii   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_205458565_   1399 AAAGAGGAGGTATAGATGGGAAGAAAATATTTCCAAAGCATATAGCCATC 1448
                              vi vvi i   vv  i           v    v      v iivi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_205458565_   1449 AAAAGGCTAATACCTAGTATGTAGAAAATACTCTCAAAACTCAACAGTAA 1498
                           ii i  vi  i i  v  i  v   iv     i v       i i   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_205458565_   1499 AAAAAAAAAAAAAAAAAAAAAAAAAAAACCCAAATAATCCAGTTAGAAAA 1548
                            i -------------------------       i   i  ?i    
  L1M4_orf2#LINE/    795 AAAGA-------------------------CAAATAACCCAATTWAAAAA 819

  chr1_205458565_   1549 TGGGTAAAAGACATGAA--GACATTTCACTGAAAAGAATGTATGGATGGC 1596
                             i   i  iv    --        v ii  i ii  i  iii     
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_205458565_   1597 AAATAAGCACATAAAAAGATGTTCATTATCACTATGCAT 1635
                         v           i        i   vi    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (132 / 97)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.27 (72 / 22)  


3274 27.09 0.33 0.33  chr1_205552691_205559078     4988  5895 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_205552691_   4988 TGGAAGAGCATTCCATGCTCATGGATAGGAATAATCAATATCATGAAAAT 5037
                              iiii  i     i        v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_205552691_   5038 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5087
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_205552691_   5088 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5135
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_205552691_   5136 TATGGAACCAAAAGAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5185
                                viiv   i  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_205552691_   5186 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGGC 5235
                                i      vv   ii  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_205552691_   5236 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAAACC 5285
                                 i   i    ii         i iv ii i   v     i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_205552691_   5286 AATGGAACAGAACAGAGCTCTCAGAAATAATACCATACATCTACAACCAT 5335
                                i    iv   vvii         vv        i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_205552691_   5336 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5385
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_205552691_   5386 GTTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATACGTAGAAAGCTGA 5435
                         v  i  i        i     v      v  ?   i i i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_205552691_   5436 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5485
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_205552691_   5486 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5535
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_205552691_   5536 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5584
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_205552691_   5585 ACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGGGATCTAAT 5634
                                     vvi         ivv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_205552691_   5635 TAAACTAAAGAGCTTCTTAACAGCAAAGGAAACTACCATTAAAGTGAGCA 5684
                         i   v v  i i   i vvi vv       v    i  vv       iv 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_205552691_   5685 GGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACAAA 5734
                          i     i                 v   i   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_205552691_   5735 GGGCTAATATCCAGAATCTACAAAGAACTTAAACGAATTTACAGGAAAAA 5784
                           i  vi          v  i        ivv  i v iv i iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_205552691_   5785 GTCAAACAACCCCATCAAAAACTGGGCAAAGGAGATGAACAGACACTTCT 5834
                          v    i     v  i?    v           vv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_205552691_   5835 CAAAAGAAGACATTTATGCTGCCAACAGACACATGAAAAAATGCTCATCA 5884
                          v        i  vi viiv     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_205552691_   5885 TCACTGGCCAT 5895
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


2724 28.05 1.55 1.11  chr1_205613601_205619569     4575  5476 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_205613601_   4575 GAAGAACATCCCTGGCTCATGAATAGGAATAATCAATATTATTAAAATGG 4624
                            ii i     vv i     i  v    v v i      i    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_205613601_   4625 TCATACTGCCCAAAGCAATTTACAGACTTATTGCTATTCCTACCAAAACT 4674
                         iv     v      vii  i      i i vi  v  i    i     - 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-T 101

  chr1_205613601_   4675 ACCAACAACATTCGTCACAGAACTAGAAAAACTG-TTTTGAA-TTCATAT 4722
                         v   i vi v  iv ii     v v  v  i   - ii i  -       
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_205613601_   4723 GGAACCAAAAAAGAACCTGAATAGCCAAGGCAATCCTAAGCAAAAAGAAC 4772
                             viiv  ii  v  v          ii     i i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_205613601_   4773 AAAGCTGGAGGCATCACGCTACCCAACTTCAAACTATACTACAGAACCAT 4822
                             i      vv    i  v     i      viv       i i i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_205613601_   4823 AGTAACCAAATTAGCATCGTACTGGTATGAAAATAGACACATAGACCAAT 4872
                              i   ivi  ii v       i  i ii       i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_205613601_   4873 GGAACAGAATAGAGAACCCAGAAATAAGGC---ACACCTACAACTATCTA 4919
                             i     v    ii          iv ---   ii  iiiii vi i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_205613601_   4920 ATCTTCCACAAACCTAACTAAAACAAGCAATGGGGAAAGTATTCCCTGTA 4969
                           i   v    ivv iv v i v  vv            v  vvi  v v
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_205613601_   4970 CAATAAATGGTTCTGGGATAACTGGCTAGCTATATGCAGAATATTAAAAC 5019
                            i       v      i      v  ? i i     i  v v i  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_205613601_   5020 TAGACCCCTTTCTTACACCATATA-AAAGATCACCTCAAGATGGATTAAA 5068
                          i       vi  i          -   i  i v     i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_205613601_   5069 AACGTATAAGTGTAAAATCCAAAACTATAAAAACCCTGGAAGACAAAC-T 5117
                         i  v  -- i     i v i            vi i i     -    - 
  L1M4_orf2#LINE/    502 GACCTA--AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA-AAACAT 548

  chr1_205613601_   5118 AGGCA-ATACCACTCAGGACATAGGTAGAGGAAAATATTTCATGTTGAAG 5166
                            ?i- v i -i  iv   v v  vvv   v  vvi    ---  ii v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC---TTAGAT 594

  chr1_205613601_   5167 GTG---CCAATAGCAATTGCAACAGAAGCAAAAATTGACAAATAGAATCT 5213
                         i  ---    v    vvv      i   v      v  i    v i ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_205613601_   5214 AATTAAACTTAGGAGCTTCTACACAGTAAAATAAATTATCAACAGAATAA 5263
                         v  i   v   ii i   i iii vvi   iv v i      v i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_205613601_   5264 ACAGACAACCTACAGAGTGGGAGAAAGT-TTTGTAAACTATATATCCAAC 5312
                          v        i     i         i -    i   ii       ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_205613601_   5313 GAAGGTCTGATATCCAGCATCTCTAAGGAACTTACACAAATTTACAAGAA 5362
                         i i  v  vi       v  v v   i     ivi    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_205613601_   5363 AAAAACAAGCATCCCCATAAATAAAGTGGGCAAAAGACATGAACAGACAC 5412
                            i    ii v   v  v? -   i        i  iv    i     i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_205613601_   5413 TTCTCAAAAGAAGACATTCA--TGCACCAACAATCATATGAAAAAAAGCT 5460
                              v        i  v  --  -i    i  v  i       i v   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATG-GCCAATAAGCACATGAAAAGATGCT 892

  chr1_205613601_   5461 CAACATCAGTGATCAT 5476
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (152 / 97)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 1.50 (24 / 16)  


 396 29.25 8.84 7.14  chr1_205635625_205637744      622   915 (1205)    L1M4_orf2#LINE/L1        5   303 (605)  

  chr1_205635625_    622 AAGGCATACCATGTTTCTGAAATAGAAGCCTCAATATAGTGAATATGTCA 671
                            ii  v       iv  i v i    v  i     v  v  v   v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_205635625_    672 ATCCTCTCCA----GATCTACAAGTTCACTAAAATTTTCTATCAGAATTA 717
                           v   i   ----        ii    viiv   ii-      i   iv
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCC-CTATCAAAATCC 103

  chr1_205635625_    718 CAAGAGTTTTTATTTGTTCATGTTTTTTAAAATTTGACA---T--TTCTA 762
                           ivv ii   -    i----------- i  v      --- -- i   
  L1M4_orf2#LINE/    104 CAGCTGCCTTT-TTTGC-----------AGAAATTGACAAGCTGATCCTA 141

  chr1_205635625_    763 AAGTTTATACATAAAATG--ATTTATGTAAAAGAGC--AAATAAATTTTT 808
                           i  i   ii-i     -- vvv ivi i  v   --   i  -- i  
  L1M4_orf2#LINE/    142 AAATTCATATG-GAAATGCAAGGGACCCAGAATAGCCAAAACAA--TCTT 188

  chr1_205635625_    809 GGAAAAGAAAAATAAATGAGTGTTTG-----TCATAC----AGATATCAA 849
                          i       i  i   -----   v -----   i  ----vi  v    
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAA-----GTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_205635625_    850 AATACACTATAAACCTACAACTGT----ATGGCATGGTATTGACTCAGGA 895
                           ivi    i   v     iivi ---- ii ii     i  i vi i i
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_205635625_    896 ATAGATTCATAAGTAAGTAG 915
                              ivi   ii v i i 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGG 303

Transitions / transversions = 1.97 (57 / 29)
Gap_init rate = 0.05 (14 / 299), avg. gap size = 3.36 (47 / 14)  

 284 25.89 25.65 3.09  chr1_205635625_205637744     1207  1627 (493)    L1M4_orf2#LINE/L1      393   908 (0)  

  chr1_205635625_   1207 TAGACTAGTCAATAAATAGTGTTGAAAT-------TAGCTTTTTGGAAAA 1249
                            v  vv    i    i   i  ii i-------  ? iviv  v    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_205635625_   1250 -----AAGTCTGAACTC-----TCCCACTATGCACAAAAATAAAATCCAT 1289
                         -----    -  i  i -----  v   i  ii        v  v  v v
  L1M4_orf2#LINE/    443 GAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_205635625_   1290 TTAAATGCAAGCATCTAAATGTGAAAATGAAAACTATAAAAGTATCAGAA 1339
                         v ii  -  ?iv i        i i iiv            v v i    
  L1M4_orf2#LINE/    492 ATGGAT-CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_205635625_   1340 AAAA--------GTAGA------------------AGACA---------- 1353
                         i   --------   i ------------------  i  ----------
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_205635625_   1354 -----------CAGAAACATGA----------AAAAAATTAACAGATGTG 1382
                         -----------  i  i  ii ----------       vi i i  vv 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_205635625_   1383 ATTACATAAAGCTTTAAAGGTTCTATACT-CAAAAGAC--T-----GAAA 1424
                          i v   v  iv  v   iv  i i i  -    i   -- -----    
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_205635625_   1425 GTAATTATAAAACA--CCAGGAAAGACTGGGAGAAAATATTTGCAATGAT 1472
                           i -- -  i   --   v---   v                   --  
  L1M4_orf2#LINE/    691 GTGA--A-AAGACAACCCAC---AGAATGGGAGAAAATATTTGCAA--AT 732

  chr1_205635625_   1473 --TGTATGAAACAAAAGATTAATATCCAAAATATATAAATCACACCTACA 1520
                         -- i   vvi i  ii  i vi      i          vv  v i    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_205635625_   1521 AATTAATTTTAAAA---TATATAGACTAAATTTTTAAAAATACGAACAGG 1567
                          v i   vv     ---i v   iv i  ---  ?      iv v v   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAA---TTWAAAAATGGGCAAAGG 829

  chr1_205635625_   1568 A----AAT----------TCACAGAAGAAAT-CAAATAGCCAATGAAGAT 1602
                          ----   ----------i  v      v  -     i      i iv i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_205635625_   1603 -T---AAGTTGCTCAGCCTCACCAGGAAT 1627
                         - ---   v      i v   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (61 / 45)
Gap_init rate = 0.05 (25 / 516), avg. gap size = 4.84 (121 / 25)  


4088 18.05 2.84 3.50  chr1_205726933_205729550     1212  2125 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_205726933_   1212 TGGAAAAATAGGCCATGTTCACAGACTA-AAGACCTAATATTGTTAACAT 1260
                               i   vv         ii  i i-     i            v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_205726933_   1261 GGCAACATTCCCCTAACTGATCTACAGATTTAATGCAATCTCTACCATAA 1310
                              i i     v  i             i  i      i   i  v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_205726933_   1311 TTCCAGCTGGCTTTTTTGCAGAAATTGACAAATGGATTCTATGATT---- 1356
                          i       v                     iiv   i   vi   ----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_205726933_   1357 ------TGCAAGAGATCTAGAATAAGCAAAGCAATTTTGAAAACAAA--A 1398
                         ------      i  i i      iv    i    i       vi  -- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_205726933_   1399 CAAAGTTTGAGGTCTCATACTCCCTATTTCCAAAACCATTTAAAAAAAGA 1448
                                v    v    i   i  i v  i      ---   --------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC---TTA-------- 239

  chr1_205726933_   1449 ATTATAGAACAAAATAGAGCTATAATCATTAGGACAATGTGATACTGACA 1498
                         -i  -----    -----    i i v  i i    i    i     i  
  L1M4_orf2#LINE/    240 -CTA-----CAAA-----GCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_205726933_   1499 TAAGGAAAGACATGTAGATCAATGAAATAAAAGTGAGAGTTTTGAAATAA 1548
                               v      i          i    i  v       iiv       
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_205726933_   1549 AACCTCAAATTTATGGTAAACTAATATTATTTT-ACAAGGGTGCCAAGGC 1597
                          v  vi v         v  i i  ----   i-              i 
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGAT----TTTCGACAAGGGTGCCAAGAC 374

  chr1_205726933_   1598 AATTCAACGGAAAAAGAGCCATCTTTTCAACAAATGGTGCTGACACAAAT 1647
                         v      i  ii     iivi                     iv    v 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_205726933_   1648 GTTTATCTGTACGCAAAAGAATGAAGTAGGACCCCTACCTCACACCATAT 1697
                          vv  ? iii i               v                      
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_205726933_   1698 AC------TAAATTAAATTGGAGCAAACATCTAAATGTTAAAGTCAAAAT 1741
                           ------   v i   v    v  ? v i        v i  ii    i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_205726933_   1742 TCTAAAACTCTTAGAGGAAAACATAAACATAAACCTTTATGACTTTGGAT 1791
                          v             i         ii?i    i   ii    i    i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_205726933_   1792 TAAGAAAGCATTTCTTCAATATGACACCAAAAA-ACAAGCAACAATGACA 1840
                           i v  vvi      vi              i-           ---- 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA----A 620

  chr1_205726933_   1841 AAAACAGAAACAGACAAATTCAACTTTATCAAAATTTAAAATTTTTGCAT 1890
                          i  --i   i   i     vi    i         v    i     iii
  L1M4_orf2#LINE/    621 AGAA--AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_205726933_   1891 TTTAAAGTACACTATTAAAATAGTGAAAAGACAACCCATAGAATGAGAGA 1940
                           i    v       i  i v                 i      i    
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_205726933_   1941 AAATATTTACAAATCATATATCTGATAAAGGACTTCTTTGCAGACTGTAT 1990
                                 i                   i      v v v    v i   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_205726933_   1991 AACAAACTCTTACAACTCAACAATAAAAA-ATAAATGACCCAATTTTCAA 2039
                           vi                i        - i    i        ?vv  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_205726933_   2040 ATGGGGAAAGTATCTGAACAGACATTTCTCCAAAAA---TACACAGATGG 2086
                              v    v  i    i               i ---  i   i    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_205726933_   2087 ACAATAAGCA-ATAAAACTTTGCTCAACATTACTATTCAT 2125
                         v         -  i   vvv          i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (106 / 55)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.62 (58 / 16)  


2998 25.82 0.66 0.88  chr1_205739292_205744267     3574  4483 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_205739292_   3574 TGGAAGCACATCTCATGCTCATAAATGGGTAGAATCAATACTGTGAAAAT 3623
                              iv i   i    i    ii  v  v   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_205739292_   3624 GACCATACTACCAAAAGCAATATACAAATTTAATGTAATTTCCCTCAAAA 3673
                          i v     v  v   vii  v    i   i  i i   ii iv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_205739292_   3674 TACCA-CATCATTCTTCACAGAACAAGAGAAAACAATTCTAAAATTCATA 3722
                          v   - vv v  i  ii     vvv  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_205739292_   3723 TAGGACCAAAAAAGAGCCAGCATAGTTAAAACCAGACTAAACAAAAATAA 3772
                          i i viiv  ii  v    v    ii     v vvi i  v  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_205739292_   3773 AAAATATGGAGGCATGACAGTACCTGACTTTAAACCACACTATATATAAG 3822
                         v   vv      vv v   v v  ii i  i   v vi    i ---- i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA----AA 246

  chr1_205739292_   3823 GCCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGA 3872
                           i i   v i   i    ii         i    ii    i  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_205739292_   3873 CCAATGGAACAGAATAGAGAATCCAGAAATAAAGCCAAATACTTACAACC 3922
                         i        i     v    i            v   v i i   iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_205739292_   3923 AACTGATATTTGTGAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACC 3972
                           i    v  i vv  i vviv   i v   vv i         i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_205739292_   3973 CTATTCAACAAATGCTGCTGGGATAATTGGCAAGCCACATGTGAA-GAAT 4021
                           v           v        i  i   vv ?       ii  -    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_205739292_   4022 GAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGGTGGA 4071
                            ii    i  ii i   v    v           i       ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_205739292_   4072 TCAAAGACTTAAATCTAAGA-CTGAAACCATAAAAACTCT-AGAAGATAA 4119
                            ?    i     v     -  i    i      -    -      v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_205739292_   4120 CATCAGAA-AAATCCTACTAAACATTGGGTTAGGCAAAGACTTCATGGCC 4168
                            vi ?i-     i - vvi  v             v ii   v i vi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_205739292_   4169 AAGAACCCAAAAGCAATTGCAACAAAAACAAAGATAAATAGATGGAACTT 4218
                          v  vv         vvv         iv   i   i   i  v i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_205739292_   4219 AATTAAACTAAAAACCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTTA 4268
                         v  i   v v    v   i  ii vv    i  v iv    iv i   v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_205739292_   4269 ACAGACAACCCACAGAGTGGGAGAAAA-ATTTTCACAATCTATACATTCC 4317
                          v              i          -    v  -    -   i  iiv
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTG 742

  chr1_205739292_   4318 ACAAAGGACTAATATCCAGAATCTACAAAGAACTCAAACAAATCAGCAAG 4367
                          i  i     vi          v  i         vv    v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_205739292_   4368 AAAAAAACAAACAACCCTATCAAAAAGTGGGCCAAGGACATGAATAGACA 4417
                              i     i     v  i?    i     v     iv          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_205739292_   4418 ATTATCAAAAGAAGATATACTAATGGCCAAGAAGCACATGGAAAAATGCT 4467
                         v  v  v             v         v         i   i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_205739292_   4468 CAACACCACTAATGAT 4483
                              i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (128 / 103)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


2777 24.15 1.81 5.43  chr1_205835235_205838791.rev     2127  3066 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_205835235_   2127 GAAAAACATTATTCTATTCTCATGGAATAGAATAATCAATATTGTTAAAA 2176
                             i ---   i i  vi       v i   v v i           i 
  L1M4_orf2#LINE/      3 GAAAGA---TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_205835235_   2177 TGTCCATACTGCCCAAAGCAATCTACAGATTTAACACAATTTTTATCAAA 2226
                           v v     v      vii           i   i    iii       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_205835235_   2227 CTGCCAA-TGTCATTTTTTACAGAATCAGAAAAAACAATTC-AAAATTTG 2274
                         v v   i-  i -      i     viv  v  ivii  i -      ii
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_205835235_   2275 TATGAAACAAGAGAAGAACCT-GAACATCCAAAGCAATCCTAAGCAAAAA 2323
                             i  - v vi i i   i-   i v     i     i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_205835235_   2324 GAATAAAGATGGAGGCAC-CACATTACCCAACTTCAAACTATACTATAAG 2372
                            i    v      -  -    i v     i      viv     i  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_205835235_   2373 GCCACAGTAAACAAAGCAGCATGGTATTTGTTAAAAAAAAAAATAGACAC 2422
                           i       v   ii   ii     i v i----- v  ii       i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGC-----ATAAGGATAGACAT 291

  chr1_205835235_   2423 ATAGACCAATGGAACAAATTAGAGAACCCAGAAACAAAGCTGTATATATC 2472
                              i        i i v v    ii       i   v i--   i  i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC--ATACATT 339

  chr1_205835235_   2473 TACAACCAACTAGTCTTTGACAAAGTCAACAAAAATAAACTATGGGGAAA 2522
                           iiii   i ii i  i     i viiv   i vi vv v         
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_205835235_   2523 GGACAACCTATTTAATAAATGATGCTGGAAAAACTAGCTAGCTATATGCA 2572
                          i i ii  v  i  i     i      i v    i v  ? i i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_205835235_   2573 GAAGAATGAAACTGGACTTCTACCTCTCACCATATA-AAAAATTAGCTCA 2621
                         i         ii     ii       v         -        i    
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_205835235_   2622 ATATTACATTTGTAATGTAATCTTTAAATGTAAGTTTTACATTTAAAGAT 2671
                          ------------    -i   ---------------------- ?   i
  L1M4_orf2#LINE/    490 A------------AATG-GATC----------------------AWAGAC 504

  chr1_205835235_   2672 GTAAATGTAAGACTTCAATCTGTAAAAAATATTAGAACAAAACCTAGGAA 2721
                         v           vi v  v  i     v- v      v     v    ?i
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACATAGGNG 553

  chr1_205835235_   2722 ATACTCTTC-TGGCCT------AGGCAAAAATTTAT-AACTAAGACCTCA 2763
                         vv v     -  i   ------      vii   v - iv  v   vi  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_205835235_   2764 AAAGCAAATGCAACAAAAACAAAAATGTACAACTGGGACCTAATTAAAGT 2813
                               v v         iv      iv i  v v    i v  i   i 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_205835235_   2814 AAAGGACTTCTGCAGGGCAAAATAAATTATCAATAGAGTAAATGGACAAC 2863
                         v  ii    i  iivvv    iv v i      v i   i  vi      
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_205835235_   2864 CTACAGAATGGAAGACAATATTTGCAAACTATGCATTCCACAAAGGAATA 2913
                          i         i   v            ii  ii  iiv i  i   v v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_205835235_   2914 ATATTCAGAATCTATAAGGAACTT----AAATCAACAAGAAAAAAAATCA 2959
                         i   i      v     i     i----  v    i  v     i --  
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CA 801

  chr1_205835235_   2960 AATAACTCCATTAAAAAGTGGGCAAAGGACACTAACAGACAATTCTCAAA 3009
                               i v   ?    i           iviv  i     v     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_205835235_   3010 AGAAGACATACAAATGGCCAAGAAGCATATGAAAAAATGCTCAACATCAC 3059
                               i              v     i       i             ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_205835235_   3060 TAATCAT 3066
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.72 (141 / 82)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 3.40 (68 / 20)  


3220 24.35 3.38 1.01  chr1_206277186_206279557      993  1879 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_206277186_    993 TGGAAATATATCCCATGCTCATGGATTAGAATAATTAATGTTGTTAACAT 1042
                               v          i         i   v v     i       v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_206277186_   1043 GACCATAATACCAAGAGCAATCTATAGATTCAGTGCAATTCCTATCAAAA 1092
                          i v   v v  v i vii     i       ii     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_206277186_   1093 TACCAATGACATTTTTCATAGAAATAGAAAAAAAAAACCTAAAATTTGTA 1142
                          v   iivi v     iii      v  v  ivvi v         ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_206277186_   1143 -----------GGGAC--GAAATAGCCAAAGCAATCCTAAGCAAAAAGAA 1179
                         -----------     --ii          i     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_206277186_   1180 CAAAACTGCAAGTAATACATTACCTGACTTGAAAATATATTA-AAGGCTA 1228
                             ii  v i vvvi   i v  ii i  v    iv  i  -  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_206277186_   1229 TAGTAACCAAAACAGCATGGTATTGGTAGGAAAATAGACA---AAA-CAA 1274
                         i     i   i    ii     i   i vi ii       --- i -   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_206277186_   1275 TGGACAAGAATAGAGAACCCAGAAATAAACCGATGTATTCACAGCCAAGT 1324
                             vv     v    ii             v  ii   i ii i   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_206277186_   1325 GATTTTCAACAAAGGCACCAAGAACATGCATTGGGGAAAGGACAGTCTCT 1374
                                i    i  ii      v   v  v         i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_206277186_   1375 TCAATAAATGGTGCTGGAAAAACTGAATATTCATATGCAGAAGAATGAAA 1424
                             i            i v     i   ?i  i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_206277186_   1425 CTAGATCTCTATCTCTCACCATATACAAAAATTGATGCCCAACAGATTAA 1474
                         i i  i i   i   v                 i iv vv  ii   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_206277186_   1475 AGACTTAAATGTAAGACCTGAAACTATGAAACC---AGAAGAAAATGTAG 1521
                             i           v  i       i    i---         ii   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_206277186_   1522 GGAGAACATTCCATGACATTGGTCTAGGCAAATATTTTATGACTAAGACC 1571
                          ?iv  vvi i i    v    vi       vvi   iv iiv  v   v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_206277186_   1572 CCAAAAGCACAGGCAA---AAACAAAAATAGACAAAGAGGACTATATTAA 1618
                                    i    ---  iv         i   vv     vi  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_206277186_   1619 A-CTAAAAACCTTCA-GCATAGAAAAGGAAACAATCAACAGAGTGAAAAG 1666
                          -i       i  ii-  v v--      v  v     v i         
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTC--AAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_206277186_   1667 ACCACCTGTTTAACGGGAGAAAATATTTGCAAAATATTCATGCGACAAGG 1716
                           v   iiivv  i                   vi  vi  vi  i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_206277186_   1717 -ACTAATATCCAGAATATACAAGGTACTCAAATAACTCAATAGGAAAAAA 1765
                         -   vi             i  i v    vv i         iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_206277186_   1766 A--ACTATCTGATTTTAAAAATGGGCAAAAGACCTGAACAGACATCTCTC 1813
                          -- v  v iv v  ?             i  ii    i      i    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_206277186_   1814 AAAAAAAGACATAGAACATATAAATGGTTAACAAGTATATGAAAA-ATGC 1862
                         v   i    i   -------i      ii  i   i i       -    
  L1M4_orf2#LINE/    849 CAAAGAAGATATA-------CAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_206277186_   1863 TCAGCATCACTAATCAT 1879
                            i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (136 / 76)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.79 (39 / 14)  


3208 27.20 0.44 0.44  chr1_206475785_206482063.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_206475785_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_206475785_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_206475785_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_206475785_   5029 TATGGAACCCAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                vivv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_206475785_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTACAAACTATACTACAAGGC 5128
                                i      vv       v  ii i v    viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_206475785_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_206475785_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5226
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_206475785_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_206475785_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_206475785_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_206475785_   5377 TTAAAGATTTAAACGTTAGACATAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   vv      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_206475785_   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_206475785_   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_206475785_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_206475785_   5577 AGGCAACCTACAACATTGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   iv  v         v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_206475785_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_206475785_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGAACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i   i iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_206475785_   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_206475785_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3076 27.78 0.55 0.55  chr1_206531057_206541590.rev     4992  5898 (4636)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_206531057_   4992 GGAAGAACATTCCATGCTCATAGGTAGGAATAATCAATATTGTGAAAATG 5041
                             ii i  i     i    i i v    v v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_206531057_   5042 GCCAAATTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGCT 5091
                           v v i v     iv i  i  i        i  v   i i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_206531057_   5092 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 5139
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr1_206531057_   5140 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTATGCCAAAAGA 5189
                               viiv  ii  v  v v  v     iv     i ivivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_206531057_   5190 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5239
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_206531057_   5240 ACAGTAACCAAAACAGCATGGTACTGGTACCACAACAGAGATATAGACCA 5289
                                i   i    ii         i iv vi i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_206531057_   5290 ATGGAACAGAAC--AGAGCCCTGAGAAATAATGCCACATATCTACAACCA 5337
                               i    i--    i  --        vv   i i  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_206531057_   5338 CCCGATCTTTGACAAATCTGACAAAAACAAGAAATGGGTAAACGATTCCC 5387
                         vii   i  i     ivv  v   i v  vvv      v   vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_206531057_   5388 TATTTAATAAGTGGTGCTGGAAAAACTGGCTAGCCATATGTAGAAAGCTG 5437
                          v  i  i  i         i v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_206531057_   5438 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5487
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_206531057_   5488 TAAAGATGTAAATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAACC 5537
                         i ?   iv       v   v  i    i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_206531057_   5538 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5586
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_206531057_   5587 AACACCAAAAGCAATGGTAACAAAAGCCAAAATTGACAAATGGGATCTAA 5636
                         i            vvi i        vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_206531057_   5637 CTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5686
                         ii   v v    i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_206531057_   5687 AGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTACTCATCTGACAA 5736
                           i     i              v  v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_206531057_   5737 AGGGCTAATATCCAGATTCTACAATGAACTCAAACAAATTTACAAGGAAA 5786
                         i  i  vi        v v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_206531057_   5787 AAAAAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 5836
                          i v   i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_206531057_   5837 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5886
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_206531057_   5887 ATCACTGGCAAT 5898
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 1.43 (10 / 7)  

 323 19.35 1.61 0.00  chr1_206531057_206541590.rev     8814  8875 (1659)    L1M4_orf2#LINE/L1        1    63 (845)  

  chr1_206531057_   8814 TGGAAAAACATTCCATGCTCATGGATTGGA-GAGTAAGTATCATTAAAAT 8862
                               i i  i     i            -  v v i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_206531057_   8863 GGCCATACTGCCC 8875
                            v     v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCC 63

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1)  

2724 26.51 2.09 1.74  chr1_206531057_206541590.rev     9184 10043 (491)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_206531057_   9184 AAAAAAGCCATACTGCCCAAAGCAATCTGTAAATTCAATGCTATTCCTAC 9233
                           i vi  v     v      vii    ii i      i  v  i    i
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_206531057_   9234 CAAACTACCAA-TGTCATTCTTCACAGAATTAGAAAAAAACT-ATTCTAA 9281
                             v v   i-  i -  i  ii     v v  v  i--  -  i    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAA 142

  chr1_206531057_   9282 AATTCATATGGAACCAAAAAAGAGCCCAAATAGTGAAAGCCATCCTAAGC 9331
                                      viiv  ii  v  vi     iv   i v   i i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_206531057_   9332 AAAAAGAATAAAGCTGGATGCATCACATTACCTGACTTTAAA-CTAAATG 9380
                           i     i    i    v vv     i v  ii i  i   -  --- i
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT---TA 239

  chr1_206531057_   9381 GTATAAGGCTATAGTAACCAGAACAGCATGGTACTGATACAAAAACAGAC 9430
                         v  i  i    i     i  ii    ii        ii i  ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_206531057_   9431 ACATAGACCAAGAGGACAGAACAGACAACCCAGAAATAAAGGTACGTACC 9480
                          i     i   vi i i    iv  v ii           vvi iii ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_206531057_   9481 TATAGCCAACTGATCTCTGACAAAGTTAACAAAAACATACACTGGGGAAA 9530
                            i i   i    i ii     i v iv   i v   v  v        
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_206531057_   9531 GGACACCCTATTCA-TAAATGGAGCTGGAAAAACTGGATTACTATATGTG 9579
                          i i vi  v    -i      v     i v        v? i i   ii
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_206531057_   9580 ---GAATGAAACTGGACCCCTATCTCTCACTATACACAAAAATTAACTCA 9626
                         ---       ii          i   v   i   i               
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_206531057_   9627 AGATGGATTAAAGACTTAAATGTAAATTCTGAAGCTATAAAAATTCTAAA 9676
                          i      i ?    i         ivv  i  i        v ii  i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_206531057_   9677 AGAAAATATAGGAAAACCTCCTCTGGACATTGGGCTAGACAAAGAATTCA 9726
                               i     ?iv vv  i  vv   v     i   i   v iv   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_206531057_   9727 TGACTGAGACCCCCAAAGCAAATGCAACAAAAACAAAAATAGACAAATGG 9776
                          iiv iv   v  v      v v         iv         i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_206531057_   9777 GACTACATCAA--CTAAAAAGCTTCTGCACAGTAAAAGAAGTAATCAACA 9824
                             v      --i      -   i  ii vvi   i  viiv     v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_206531057_   9825 CAATGAGCAGCCAGCCTGCAGAATGGGAGAAAATATTTGCATATTTGCAA 9874
                         v i   iv  v  i  ii                       -------- 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA--------A 730

  chr1_206531057_   9875 ACTATGTATCTGACAAAGATCTAACATCCAGAATCTATAAGAAATAA--A 9922
                          ii  i       i  i iv  vii         v     ii  ivv-- 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_206531057_   9923 CAATTCAACAA---ACAGA-AAACAACCCCATTAAAAAGTGAGCAAAG-A 9967
                            i    i  --- v   -   i     v   ?    i  i      - 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_206531057_   9968 CATAAACAGACACTTCTCAAAAGAAGACATACAAGCAGCCAACAA--ACA 10015
                         iv i  i     i     v        i      iii     i  --   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_206531057_  10016 TGAAAAAATGGTCAATATCACTAATCAT 10043
                               i   v    i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (147 / 77)
Gap_init rate = 0.02 (16 / 863), avg. gap size = 2.06 (33 / 16)  


2321 26.93 2.01 0.43  chr1_206552093_206553782      500  1197 (493)    L1M4_orf2#LINE/L1      200   908 (0)  

  chr1_206552093_    500 ACAAAGTTGGAGGTATCACTTTACCTGACTTCAAATTATACTGCAAGGTG 549
                                      vv    vi v  ii i      viv    i   i iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_206552093_    550 TTAGTAACCAAAATAGCATGGTA------TAAAAATAGTCGCA--GATTA 591
                         vi     i   i i  ii     ------   ii    v ii --   i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_206552093_    592 GTAGAATAGAATAGAGAACCCAGAAATAAAGCCCCACACTTACAGCAAAC 641
                         i i         v    ii           v  vi   i   ii iv  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_206552093_    642 TGATCTTTGATAAAGTCAACAAAATTATACACTGGGGAAAGGACACCCTA 691
                             i  i  i  i viiv   i ii  v  v         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_206552093_    692 TTCAGTAAGTGGCGCTAGGAAAATTGGATTGCCATATGCA---GAATGAA 738
                             ii  i   i   i   v  i     v?   i     ---       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_206552093_    739 ACTGGACTCCTAACTCTCACCACATACAAAAAATAACTCAAGATGGATTA 788
                         ii     i    v   v     i         v        i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_206552093_    789 AAGCCTTAAATGTAAGTCCTGAAGCTGCAAAAAGTGTAGAAGAAAATCTA 838
                         ?  v i          vv  i  i  ii    vviv          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_206552093_    839 GGAAAAACTCCTCCAGACATTGGCCTAGACCAAGAATTCAT-GAC-TGAG 886
                           ?iv  v  i  vv   v    vi   i v v iv   v -  i-   v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_206552093_    887 ACCTTCAAAAGCAAATGCAACAAAAACAAAAGTAGACAAATGGGGCTATA 936
                            ---       v v         iv    i    i    v  i  vi 
  L1M4_orf2#LINE/    600 ACC---AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_206552093_    937 T-AAACTGAAAAGCTTCTGCACAGTAAAAGAAATAATCAACACAGTGAAC 985
                          -   v v    i   i  ii vvi   i  v iv     v v      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_206552093_    986 AGACAACCTGCAGAATGGGGGAAAATACTAGCCAACTTTGCATCTGATAA 1035
                                 ii         i       i v  v  iiv ii         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_206552093_   1036 AGGTCCAATGTCCAGAATCTACAAGGAATGCAAACAACTCAACCAAAATC 1085
                         i  v ivi i        v  i  i   iv vv         iv v  vv
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_206552093_   1086 CCTCAAATAACCCCATTAAAAAGTGAGCAACGGAAATGCACAGACATTTT 1135
                         vvv          v   ?    i  i    v   vv  v i        i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_206552093_   1136 GCAAAGGAAGACATACATATGGCCAAGAAGCATATGAAAAAATGCTCAAC 1185
                         v v  i     i     v        v     i       i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_206552093_   1186 ATCACTAATCAT 1197
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (103 / 81)
Gap_init rate = 0.01 (7 / 709), avg. gap size = 2.43 (17 / 7)  


2915 24.97 3.67 2.18  chr1_206559381_206561391      673  1545 (466)    L1M4_orf2#LINE/L1        1   886 (22)  

  chr1_206559381_    673 TGGAAAGCCATCCCGTGCTCATGGATTGGAAGAGTTAATATTATTAAAAT 722
                                vi     i  i               v        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_206559381_    723 GACCATATTACACAAAGTGGTCTACACATTCAGTGCAATCCCTGTCAGAA 772
                          i v   i v v    v  i      v     ii         i   i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_206559381_    773 TATCAA-TGTCATTTTTAACAGAAATAGAGAAAACAACTCTAGAATTTGT 821
                          vi  i-  i v     i-       v  v  ivii ii   i    ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_206559381_    822 ATAGAACTAAAAAAAATACCCCAAATAGTCAAAACAGTCCCGAGCAAAAA 871
                           i   v iv  iii --   vi     i       i  ii  iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_206559381_    872 GAATAAAGCTGGAAGCAGCATACTATCTGACTTCAAAA-----TACAAGG 916
                            i    i    i vvv  i   vi ii i       -----     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_206559381_    917 CTATAGTAA-CAGAACAGCATGATGTTGATATTAAAGCAGACACATAAAC 965
                            i     -  ii    ii  i ii  ii  v iiii     i   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_206559381_    966 CAATGGAATAGAACAAAGAACCCAGAAATAAATCTATGTATTTATATCCA 1015
                                      ivi   ii           i i  ii      ivi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_206559381_   1016 ACTCATTTT-GACAAAAGCCCCAAGAACATATTTTGTGGAAAGAACAGCC 1064
                          i v     -     ii iv      v   vivv  v        i  i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_206559381_   1065 TCTTCAATAAATGGTGTTGGGAAATCTGGATATTCATATGCAGAAAAATG 1114
                          i     i        i     v v       ?i  i     i  i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_206559381_   1115 AAACTGTACTCCT--CTCTCACCATATACAAAAATGAACTCAAGATTGAT 1162
                           ii  v  i   --   v                v       i  v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_206559381_   1163 TAAAGACTTAAAAGTAAGACCCGAAACTATAAAACTACTGAAAGAAAA-A 1211
                         i ?    i    v      v ii             vi ii       - 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_206559381_   1212 -AGGAG-AAATACTTCAGGACATTGGGTTAAGCAATA-TTTTATGGCTAA 1258
                         -   ? -    -    iv   v        i     i-   iv i v  v
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_206559381_   1259 GACCTCAAAAGCACAAGC--TAAAACCCCCCAAAATAGACAAATGGGACT 1306
                            vi             --i    vvv---        i    v     
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAA---AAAATAGATAAATTGGACT 643

  chr1_206559381_   1307 ATATTAAGCTAAAAAGCTTCTGCACAGCAAAGAAAAC----AACAGAGCA 1352
                         vi  i  iv v    i   i  ii vv     i v  ----  v i  ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_206559381_   1353 AAAAGACAACATGTTGAATGGGAGAAAATATAAAGTATTAGCAGGAACT- 1401
                                   viiiv                ------  -   --  ii-
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATAT------TT-GCA--AATCA 734

  chr1_206559381_   1402 --TATTTGACAAGGAACTTATTTGCAGAATTTACAA-GAA--------AC 1440
                         --   i   i    i    i v v      v  i  -   --------  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_206559381_   1441 TCAGTGGCAGAAAAGTAAATAATCCCATTAAAAAGTGGGCAAAGGAGATG 1490
                            i iii i   iii      i  v   ?    i           vv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_206559381_   1491 AATAGACATTTCTGAAAAGACAGTTTCATATCACTGATCATCAGGGAAAT 1540
                                      vv     -  v --   iv v  ii  vi i v v  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGA-AGAT--ATACAAATGGCCAATAAGCACAT 881

  chr1_206559381_   1541 GCAAA 1545
                          v   
  L1M4_orf2#LINE/    882 GAAAA 886

Transitions / transversions = 1.93 (141 / 73)
Gap_init rate = 0.03 (23 / 886), avg. gap size = 2.22 (51 / 23)  


 787 31.45 10.09 3.41  chr1_206563937_206565598.rev      502  1175 (487)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr1_206563937_    502 AGAATGAAAACTAAAG--GGAGGAA--ACTCTACCAGATACCAAGAATTA 547
                          i  v   i vi    --      v--  v  v  vi  vi   i v   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_206563937_    548 TTTTAAAAGTAGAATAATTAAAACTAGATGATATTGGCACAGGAATAGAT 597
                         i vi   iv  v i    i  i  vivi  i  i     i i i     i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_206563937_    598 A-ACAGACCAA--------------AAGGCCAGACACAGACACTTGCACA 632
                          - i   i   --------------i  v     v i i  v v i  iv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_206563937_    633 CATGGATTC---TGATGTATGACAAAGTTGGCTGCAGAGCAGTGGGTGAG 679
                         i    --  ---    v vi     i v  v --v   v  v vii  i 
  L1M4_orf2#LINE/    340 TATGG--TCAATTGATTTTCGACAAGGGTGCC--AAGACCATTCAATGGG 385

  chr1_206563937_    680 TGAGGGATCATGTTTTGAATGCATTGTGCTTGGAAAATCGAGGATAT--- 726
                         vi i i  vi v    v  iiv  v     v   v  ii --    ?---
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG--GATAKCCA 433

  chr1_206563937_    727 -AAGGGAAA-AATGAATTT------------------ACATACAAA--CC 754
                         - v vi   -      v  ------------------ i       --ii
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_206563937_    755 AATTCTAGATAGACTATAGATCTAAATGTGAAATGCTTTAGCCAATCAAT 804
                           i  v i  i  ii ?   i        i i -   vv i i - v  v
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTA-TAAAA 531

  chr1_206563937_    805 TTTGTAGAAAAAAATACAAATACTTTTCTTCATGATCCCA----AGGCAA 850
                         i iv     i    i i ii?iivvv     i   i iii----      
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_206563937_    851 GGGATTTCTTACTAAACAAGACATAAAAAGCATAAATCACACAAGAGAAT 900
                         v  -       ---i i v    iv       i  iiv   v    i  v
  L1M4_orf2#LINE/    582 TGG-TTTCTTA---GATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_206563937_    901 ACTGATAAATTTTATTACATTAAAATTTAAAATTTCTGATCATCAAAAGA 950
                          iv        vv i v   i      v    i  i  vv v     i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_206563937_    951 TAT---------AATGACTAGGCAAGCCCAATAATATATTATATGGAATA 991
                         i i--------- i   vv  i   -    ----i v ----    i v 
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAA-CCCA----CAGA----ATGGGAGA 718

  chr1_206563937_    992 ATGTATTTGCAACACATA-ATCAGGAGGAAAAGGCTCATATCTA-AATAC 1039
                          vi         vv    -   v i--v  ii i  ii    i -    i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGA--TAAGGGACTTGTATCCAGAATAT 766

  chr1_206563937_   1040 ATAAAAAATGTGTAAAAA-CATTTTTTTAAAGACAG----CACAGTAAAA 1084
                              i  iviv  v  v-  v vv vv       i---- v  i v?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_206563937_   1085 AAATGGGCAAAGT-CCTGATCAGGCTTATCATGAAGGATAAAACAAAAAT 1133
                                     v-ii   vi  i v v  viv  i  vi v i v    
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_206563937_   1134 GGCCAATAAATGTATGAAAAGGTGTTCAACTTTGTTATGTAT 1175
                                  iiii        i  i     v ii????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (118 / 90)
Gap_init rate = 0.04 (27 / 719), avg. gap size = 3.37 (91 / 27)  


3813 20.16 4.24 0.23  chr1_206590267_206592948.rev     1320  2192 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_206590267_   1320 TGAGAAGGCACACTATGTTGATGC-TTAGAAAACTTAAT---GTTAACAT 1365
                           ii   ii iv i     v   v-  i   i       ---     v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_206590267_   1366 GTCAATAATACCAAAAGTGATTTACAGATTTAATGCCACCTCCA-CAAAA 1414
                          v     v v  v   v    i        i  i  v i i i -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_206590267_   1415 TTCCAATGACATTTCTTGCAGAAATAGAAAAACC--TCCTAAAATTCATA 1462
                          i   iivi v   i          v  v  i i--              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_206590267_   1463 TGGAATCTCAAAGAGATCC-------------CAATTCTGAAAAAGAGAA 1499
                              viv   i -  i  -------------    ii         ii 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_206590267_   1500 ACATAGCTGGAGGACTCAAACTTCTTGATTTCAAAATGTACTATAAAGCT 1549
                            v  i           v     iii         iv     i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_206590267_   1550 ACAGTAATCAAAACACTGTTGTACTGGC-TAAAGACAAACATATAGACCA 1598
                                    i   v   v        -   i  i i         i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_206590267_   1599 ATGGAATGAAACAGAGAGTCCTGAAATAAAACCTTGCATATATGGTCAAA 1648
                                ii  iv        v        v  v i   v         v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_206590267_   1649 TGATTTTTGACAGGGG-ACCAAGACCACACAATGT----AGAAGAGCCTT 1693
                                i    i   -i         iv     v----    v  i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_206590267_   1694 TTTAACAAATGTT-CTGGGAAAACTGGATATCCAAATGTAAAAGAATGAA 1742
                           i        v -      v         ?   v   i           
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_206590267_   1743 AATGAACCCTTGCCGAATATCGTATATAAAAATTAACTCAAAATGGATCA 1792
                         iv  i    i i  vv i i i    i                       
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_206590267_   1793 CAT-CATAACGATAAGACTTAAAACTACGAAACTCTTAGAAGAAAACATA 1841
                         ? v- v   vvi     vi        ii                     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_206590267_   1842 GGGAAAAAGCCTCACAACATTGGATTTGGCA--GATTTCTTGGATATGAC 1889
                           ?iv   v i  iii  v    i  v    -- i      i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_206590267_   1890 ATCAAAGGCACAGAAAACAACA--AAAAATACAAAAAGTGGATTTCATGA 1937
                          i    i     iiv     v --       v v   v    i     v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_206590267_   1938 AAATTAAAACATTTTGTCTATCAAAAGATACTATCAATAGAGTAAAAAAT 1987
                                  vv      viv     i  i        v i   i    i-
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG- 698

  chr1_206590267_   1988 GCCATCC-CAAAATGGGAAAAAATATTTGCAAACCATATATCTGATAAGA 2036
                         i v i  -  i       i              i               i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_206590267_   2037 GATTAATATCCAAAATATATGGAGAATTCCTAAAACTCAACAACCAACCA 2086
                           i vi      i       ii    i  i  v       i  iv  vvi
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_206590267_   2087 ACAAACAATGCAATTCCAAAATGGGCAAAAGATTTG----GACATTTCTC 2132
                              i  iv     ?v            i      ----          
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_206590267_   2133 CAAAAAAGATATACAAATAGCCAATAAGCACATGAAATGATGTTCAGTGT 2182
                             i             i                  v    i   iii 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_206590267_   2183 CGCTAATAAT 2192
                          i????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.65 (107 / 65)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.44 (39 / 16)  


2536 26.22 3.41 3.18  chr1_206596414_206600683.rev     2891  3771 (499)    L1M4_orf2#LINE/L1        1   883 (25)  

  chr1_206596414_   2891 TGGAGAGACAACCCATGCTCAGGGATTGGAAGAACTGATACTATTAAAAT 2940
                             i   i v      i   v           vi i   i i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_206596414_   2941 GACCATACTACACAAAGTGTTCTATAGATTCAGTGTAATCCCCAACAAAA 2990
                          i v     v v    v  v    i       ii i      i v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_206596414_   2991 TAACAATATCGTTTTTCACGGAATTAGAAAAAACAATCCCCAAATTCAGA 3040
                          vv  iivv v     ii i   v v  v  ivii    iv       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_206596414_   3041 TAGAACCAACAAGAAGCCCA-AATAGCCAAAATAACCTTAAGCAA-AAGA 3088
                          i   vii-    iii    -           i  i   i iv  -    
  L1M4_orf2#LINE/    151 TGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_206596414_   3089 ACAAAGCTAGAAGCATTACATGACCTGACTTCAAATTATACTGTAAGGCT 3138
                               i i  i vv i   ivv  ii i      viv    ii  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_206596414_   3139 ATAATAACCAAAACAGCATGGTACTGGTACAAAAATAGACTTACAGATGA 3188
                          i i   i   i    ii         i i  ii      v  i    v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_206596414_   3189 ATGGAACAGAACAGAGAACCCAGAAATAA--------------------C 3218
                               i    iv    ii          --------------------i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_206596414_   3219 TGATCTTTAACAAAGTCAACCAAAAC-ATACACTGGGGAAATGACACACT 3267
                             i  ii    i vii-    i  -  v  v        vi i vv  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_206596414_   3268 ATTCCATAAATGGTGTTAGGAAAATTGGATTTCCATTCCTCTGCTATATG 3317
                         v   v i        i i   v  i     v?   i-----------   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC-----------ATG 437

  chr1_206596414_   3318 CAGAAGAATGACACTGGACCCCTATCCCTCATGACATAAAAAAATTATCT 3367
                           i        vii          i i v  iv i   v        v  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_206596414_   3368 CAAGATGGATTAAATACTTAAACACAAGTCTGGAAACTTTAAAAACTCT- 3416
                            i      i ? v  i    iii   vvivi     v     -    -
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTT 536

  chr1_206596414_   3417 AGAAGAAAATCTAGGAAAAACTCCTCTAGACATTGGCCTAGACAAAGAAT 3466
                                  iv    ?iv  v  i  vv   v    vi   i   v iv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_206596414_   3467 TCATGACTAAGACATCAAAAGCAAAAACAACAGAAACAAAAATAGACAAA 3516
                           v iiv  v    i        v  i     i  iv         i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_206596414_   3517 TGGGACTATAT--AAACTAAAAGGCAACT---GCACAGCAAAAAA-ACAA 3560
                          v     vi  --   i     ----   --- ii vv    ii -  v 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAA----ACTTTTGTGCTTCAAAGGACACTA 682

  chr1_206596414_   3561 TCAACACAGTCAACAGACAACTTGAAAAATGGGAGAAAATATTTCCAAAC 3610
                             v v   v  v       iiiv i                 v    i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_206596414_   3611 TATGCATCTGATAGACAAGTTATAATATCCAGAATCTACGAGGAATGCAA 3660
                         i  ii        iivi v  i  ---        v  ii i   iv vv
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTA---TCCAGAATATATAAAGAACTCTT 779

  chr1_206596414_   3661 ACAACTCAACCAAAACCCCTCAAATAACCCTATTAAAAAGTGGGCAAAGG 3710
                                  iv v  vvvvv          v   ?    i          
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_206596414_   3711 AAATGAATACACATTTTGCAAAAGAAGGTGTACATTTTGCAAATGGCCAA 3760
                          vv      v      iv v       i i    -------         
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACA-------AATGGCCAA 872

  chr1_206596414_   3761 CAAGCATATGA 3771
                         i     i    
  L1M4_orf2#LINE/    873 TAAGCACATGA 883

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.02 (15 / 883), avg. gap size = 3.87 (58 / 15)  


3452 18.50 3.08 9.76  chr1_206627718_206629730.rev      550  1522 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_206627718_    550 TGGACAAACATCTCATGTTCATGAATTAGAAGACTTAATATT---AAGAT 596
                             v i i   i          i   i              ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_206627718_    597 GGCAATATCCTCCAAAGTAATCTACAGATTCAACACAATCTCCATAAGGA 646
                                ii i     v i               i     i i  v ii 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_206627718_    647 TCTCAGACGAATTCTTTGTAAAAATTGTCAAGTTGATTCTAAAATCCATA 696
                           i   vi vv  i    i i      v    i    i       i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_206627718_    697 CGGAATTGCAAGGATAACCAGAATAGCTAAAACAATAAAGAAAAAGAAGA 746
                         i    v       i- v          i        vvv           
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_206627718_    747 ATACAGTAGGAAGACTCACACTTTATGATTTCAAG-CTTAGTA-AAAGCA 794
                          i v   v   i           ivii       i-    v  -     v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_206627718_    795 ACTGTAATCAAGAGAGTGTGGTACTGGCAAGAGGACAGACACGTAGATCA 844
                           v          v               vi    i     ii       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_206627718_    845 ATGACATATACTTGACAGTCCAGAAACAAAACCATATGTGTATGGTCAAC 894
                            iv   v v    v          i   v     ii v         i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_206627718_    895 TGAT-------AAGGGTGCCAAGGCCATTCAATGGGGAAAGAACAGTCTT 937
                             -------            i                   i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_206627718_    938 --CAACAAATGGTGCTAAG-----TGGTTATTCACATGCAAAAGAATGAA 980
                         --              ii -----   v  ?i                  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_206627718_    981 ATTAGACCCTTATCTTATACTATATATAGAAATTAACTCAAAAT----TA 1026
                         i  i     i  i  i i  i     i i               ----i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_206627718_   1027 AATACCTAAATATAAGAGCTTAAAGTATAAAACTCTTGGAAGAAAAT--- 1073
                         ? v        i        v   v            i        i---
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_206627718_   1074 -GAAAAATTTTTTATGACACTGGTTTTGGGAATTATTTCTTGGATACAAC 1122
                         - ?iv  v i  ii    vi   v  v  v   vi      i    ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_206627718_   1123 TAACAAAA-CACAGGCAACAAAAGGACCAAGAGATAAATTGAAATTCATC 1171
                         - v     -    i          i vv  v          i v      
  L1M4_orf2#LINE/    600 -ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_206627718_   1172 AAACACTTTTCATTGAGCACTGTATTAGTCCGTTCTCACGCTGCTAATAA 1221
                            -----------------------------------------------
  L1M4_orf2#LINE/    649 AAA----------------------------------------------- 651

  chr1_206627718_   1222 AGACATACCTACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAA 1271
                         --------------------------------------------- i   
  L1M4_orf2#LINE/    652 ---------------------------------------------ATTAA 656

  chr1_206627718_   1272 AAAGCTTCTGCACAGCAAAAGAAATTACCATCAGAGTGAACAGGCAACCT 1321
                            -   i  ii vv    i  v i  i  vv i      v  i     i
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_206627718_   1322 ACAGAATGGGAGAACATTTTTGCAACCTACTCATCTGACAACGGGCTAAC 1371
                                       v  v       vii ivi      i  v  i  vii
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_206627718_   1372 ATCCGGAATACA--ATGAACTCAAACAAATTTACAAGAAAAAAACAAACA 1419
                             i     i -- v      vv    v iv i  v     i     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_206627718_   1420 ACCCCATCAAAAAGTGAGCGAAGGATATGAACAGACACTTCTCAAAAGAA 1469
                             v  i?    i  i  i      v    i     i     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_206627718_   1470 GACATTTATGCAGCCAACAGATACATGAAAAAATGCTCATCATCACTGGC 1519
                           i  vi viii     i iii         i       v     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_206627718_   1520 CAT 1522
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.67 (110 / 66)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 8.93 (125 / 14)  


4177 13.99 1.74 8.99  chr1_206701568_206703764.rev      845  1823 (374)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_206701568_    845 TGAAAAGACATCTCATGCTAATGGACTGGAAGACTTAA-ATTGTTAAGAC 893
                           i     i   i    i v     i            -          i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_206701568_    894 AGTAATGTAGCCCAAAGTACGGATCAAACAGATTTGATGCGATCCCTATC 943
                         i i   iivv      v ---    v -      ii i  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATT---GATCTA-CAGATTCAACGCAATCCCTATC 96

  chr1_206701568_    944 AAAATTGCTATGGCCTTCTTTTTTTTTTTTTTTTTTGCAGAAACAAAGAA 993
                              iv viiv     ---------------           ivi v  
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTT---------------TTTTGCAGAAATTGACAA 131

  chr1_206701568_    994 GTCAATCCTAAAATTTAAGTGTCCTAAAATTCATATGTAAGTGCAAGGGA 1043
                          ------  i ----------                v  i         
  L1M4_orf2#LINE/    132 G------CTGA----------TCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_206701568_   1044 CCCAGAATAGCCAAGACAATCTTGAAAAACAATAACAAGGTTGGAGGACT 1093
                                       i              v  v     i           
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_206701568_   1094 CACACTTCCCAATTTTAAAACTGATTATAAAGCTTCAATAATCAAGAAAG 1143
                                        i      v i  i      v  i         v  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_206701568_   1144 TGTGGTACTGGCAGAAGGATAGACAAATAGATTAACGAACTATAATTGAC 1193
                                      v           v      i  i i v  v      v
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_206701568_   1194 AGTTCAGAAATAAAAACTTACATTTATGGGCAATTCATTTTCAACAAGGG 1243
                            i          vv v           v     v      i       
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_206701568_   1244 TGCCAACACAAATAAATGAAAAAAAGAT-TTTTTTTCAACAAAT--TGTT 1290
                               v  v v v    iii   ii  -v i            --  i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_206701568_   1291 GGGACAACTGGATATCCACATGTAAAAGAATTAATTTGGACCTCTCCCTC 1340
                                       ?       i        v  v       i  v    
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_206701568_   1341 ACACCGTATTAAAAAATCAACTCAAA-TGGATCATAGTCCTAAATTTAAG 1389
                              i   vv      i        -       ?  v       v    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_206701568_   1390 AGCTAAAACCATAAAACTACTAGAAGAAAACATAGTAGTAAATCTTTAT- 1438
                                  i        vi               v?         ii -
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_206701568_   1439 --CTTATATTAGGCAATGGTTTCATAGATAAGACACTAACAACACAAGCA 1486
                         --   ivi               v      v     i  v i        
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_206701568_   1487 ACAGAAGGAAAAAATCAATAAACTGAATTTC-TCAAAATTAAAAACCTT- 1534
                            i   -       vi     i  i i   -              i  -
  L1M4_orf2#LINE/    616 ACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_206701568_   1535 GTGCTTCATAGAACATCATCAAG----TAAAAAGAAAA---GCAGAATAG 1577
                                 v  i   ii      ---- i      v  ---i      i 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_206701568_   1578 GAGGAAATATTATCAAATCACTTATCTTATAAGGGACCGATTTCCTGAAT 1627
                            i       vv       iv     v         ivi v   v    
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_206701568_   1628 ATGTAAAGAACTCTTACAGCTCAAAAATAAAGAGACAAAGGCAAAGGATT 1677
                           i               i     v      i       -----------
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA----------- 803

  chr1_206701568_   1678 TTAATAGAAATTTATCCAAAGGCAAAATTTATCCAAATTTATCCAAAGGC 1727
                         -   ----------------------------  v    ? ---------
  L1M4_orf2#LINE/    804 -TAA----------------------------CCCAATTWA--------- 815

  chr1_206701568_   1728 AAAAAAATAGGCAAAGGATTTTAATAGAAATTTATCCAAAGAAGATACAC 1777
                         ---     i            v      v    v             i  
  L1M4_orf2#LINE/    816 ---AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_206701568_   1778 GAATGGTCAATAAGCACATGAAAAGATGCTCAACATCATTAGTCAT 1823
                         i     i                               ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (74 / 59)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 5.83 (105 / 18)  


2805 26.89 2.22 1.33  chr1_206984564_206990377.rev     2649  3548 (2266)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_206984564_   2649 TGGAAGAACATTCCATGCTCATGGATGGGAAGAATCAATATTGTGAAAAT 2698
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_206984564_   2699 GGCCATACTGCTCAAAGCAATTTATAGGTTCAATGCTATTCCTATCAAAC 2748
                            v     v i    vii  i  i  i     i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_206984564_   2749 TACCATTGACATTCTTCACAGAACTAGAAAAAAATTATTTTAAAATTCAT 2798
                          v   vivi v  i  ii     v v  v  iv- v  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_206984564_   2799 ATGGAAC--CAAAGAAGAGCCCATA-TATCCAAGGCAATCCTAAGCAAAA 2845
                               v--   i i ---    v -  v    ii     i i iv  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_206984564_   2846 AGAACAAAGCTGGAGGCATCATGCTACCCAACTTCAAATAAC--ACTAAA 2893
                                  i      vv   ii  v     i      --  --    v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACA 244

  chr1_206984564_   2894 GGGCTATAGTAACCAAAACAGCATGATACTGATACAGAAACCGACACATA 2943
                         ii    i     i   i    ii  i     ii i iii iv    i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_206984564_   2944 GACTGACAAAACAGAATAGAGAACCCAGAAATAAGGCCACACATGTACAA 2993
                           iii iii  i     v    ii          iv   i    v  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_206984564_   2994 CTATATGAACTTCAACACACCTGGCAAAAACAAGCAATGGGGAAATAATT 3043
                         ii vv   vi   i   vivv  v   i v  vv           v   v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_206984564_   3044 CCCTCCTCAATAAATGGTGCTGGG-TAACCGGCTAGCCACATGCAGAAGA 3092
                         vi  ii    i             -i   i  v  ?         i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_206984564_   3093 CTAAAACTGGACCCCTTCTTTATAGCACATACAAAAATTAACCCAAGATC 3142
                         v i  ii         v i i i v  i              i   i  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_206984564_   3143 GATTAAAGACATAAATGTAAAACCCAAAACTATAAAAATCCTGGAAGACA 3192
                            i ?    v         i v i            v  i i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_206984564_   3193 ATCTAGGCA-ATACCATTTGGGACACAGGCATGGACAAAGACTTCATGAC 3241
                          iv    ?i- v i -  i v   viv  vv i i   v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_206984564_   3242 GAAGAGGACAAAAGCAATTGCAACAAAAGCAAAATT-GACAAATGGGATC 3290
                         v v  viv        vvv          v    v -  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_206984564_   3291 T------AATTAAAGAGCTTCTGCACAGCAAAACAAACTATCAACAGAGT 3334
                          ------       i -   i  ii vv    iv v        v i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_206984564_   3335 AAACAGACAACCTACAAAATGGGAGAAAATTTTTGCAAACTATGCATCTG 3384
                         i  v        i   i             v        ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_206984564_   3385 ACAAAGGTCTAATGTCTAGCATCT-CAAAGAACT--TA-AATGTACAAGG 3430
                          i  i  v  vi i  i  v  v -i        --  -  ivi vv iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_206984564_   3431 AAAAAAATAAACAATCTCATTAAGTAATGGGCAAAGGACATAAACAGAC- 3479
                              i i   i  i iv   ? iv             iv i  i    -
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_206984564_   3480 TTTC-CAAAAGAAGACATACATGTGGCCAAGAATCATGTGGGGAAAAAAA 3528
                             - v        i     vi       v  v  ii  ----    i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG----AAAAGA 888

  chr1_206984564_   3529 AGCTCAGCATCACTGCTCAT 3548
                         v     i     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.78 (32 / 18)  

3197 24.08 5.18 0.58  chr1_206984564_206990377.rev     4456  5323 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_206984564_   4456 TGGAAAAACAACCCATGCTCATGGATTGAAAGA----ATATTGTTAAAAT 4501
                               i i v      i          i    ----          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_206984564_   4502 GACAATACTACTCAAAGCAATTGATAGATTTAATACAATTCCTATCAAAA 4551
                          i       v i    vii  iv i     i  ii    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_206984564_   4552 TACCAGTAACATTCTTCACAGAAATAGAAGAAAAAAACCTAAAAATTGTG 4601
                          v    ivi v  i  ii       v  vi ivvi v       v ii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_206984564_   4602 TGGAACCACAAAAGATCCTGACCAGCCAAAGCAATTCTGAGCAAAAAGTA 4651
                              vii   ii  i  v  vi       i    ii   iv  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_206984564_   4652 CAAAGCTGGAG---TCAGAACACTGCCAGACCTCAAAATATACTACAAAA 4698
                              i     ---   ---    v  vi ii      iv         i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCA---CACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_206984564_   4699 CTGTAGTAACCAAAACAGCATGGTACATGCATAGAAACAGGCATGTAGAT 4748
                           ii     i   i    ii      vv     iii i  i   i     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_206984564_   4749 CAATATAAAAGAATAGAGAATCCAGAAATTAATCCACATATCTACAGCCA 4798
                             iv  v     v    i         v  i   i i  i  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_206984564_   4799 ACTGATTTTTGACAAAGATGCCAAAAACACTCATTAAGGAAAGGACAATC 4848
                          i       i     i i      i v  i   v ii      i i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_206984564_   4849 TGTTCAACAAATGGTACTGAGAAAACTGGATACCCATATGCAGAAGAATG 4898
                          v             i   i  v         ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_206984564_   4899 GAACCAGACCCCCACCTCTCACC---------------CTCAAAATGGAT 4933
                         i iiii      i     v    ---------------            
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_206984564_   4934 CAAAGACCTATGTGTA-TACCTGAAGCAATAAAAATACTAGAAGAAAGCA 4982
                           ?       vi    -v v  i  i v      v vi         i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_206984564_   4983 TTAGGAG--AATCCGTCAGGACATTGG-TCAGGGAAAGGTTTTATAAATA 5029
                          -   ? --    i-  iv   v    - i   v  v     iv  i   
  L1M4_orf2#LINE/    548 T-AGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_206984564_   5030 AGACTTCTAAAGCACAGGCAACAAAAGCAAAAATAAACAAATGGGATAT- 5078
                         v   vi v        i          v       i i    v   iv -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_206984564_   5079 ATCAAACTAAAAAGCTTCTGCAAAGAAAAGGAAAC----AACAGAGTGAA 5124
                               v v    i   i  iivvvv      v  ----  v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_206984564_   5125 AAGACAACTTACAGAATAGGAGAAAATATTTGCAAACTACTTATCCAACA 5174
                                 ii       i                  ii iv    ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_206984564_   5175 GGTGATTAATATCCAGAATATACAAGGAACTCAGACATCTCAACAGCAAA 5224
                         i v  i vi             i  i      vv   v     i ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_206984564_   5225 C---TAAACAATCTGATTTAAAAATGGGCTAATGATCTGAACAGATATTT 5271
                         v---i   i  i ii   ?          v  v   i    i   i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_206984564_   5272 TCTCAAA--AGA------AATGGTCAATAAATATGTGAAAAG---CTCAA 5310
                         iii    --   ------     i      ii ii       ---     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_206984564_   5311 TATCACTAATCAT 5323
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (139 / 66)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.33 (50 / 15)  


3791 17.67 3.53 2.24  chr1_207174140_207176639.rev     1168  2016 (484)    L1M4_orf2#LINE/L1       28   887 (21)  

  chr1_207174140_   1168 GGAAGA----ATATTGTTAAAATAACAATACTACCCAAAGTGATCCACAG 1213
                               ----          i  ii       v      v     i    
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chr1_207174140_   1214 ATCCAGTATAATCCCTATCAAAATCCCAATGACATTCTTTGGAAAAATAG 1263
                           i  iiii                   iivi v  i    v i    v 
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chr1_207174140_   1264 AAAACCCCACCCTAAAATTCACCTGAGATCTCAAATGGCCCCAACTGGCC 1313
                          v  v iv i           iv  ii viv   iv i   vi v i   
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr1_207174140_   1314 AAAACAACCTTGAAAAAGCAGAACAAAGTTGCAGGACACAAACTTCCTGA 1363
                                i          v            v     v  v      ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_207174140_   1364 TTTTAACACTTA-----AAGCTACAATAATCAAAACTGTGTGGTACTGAC 1408
                            i  v     -----        i       i  v           i 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_207174140_   1409 ATAAAGATAAACATATAGACCAATGGAATAGAATAGAGAGACCAGAAATA 1458
                             i    i         i              v     v         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_207174140_   1459 AACCCTTATATACGGTTAAATAGTTTTCAACAAGGCCAAATGATCCTCAA 1508
                              v  i  ----   -- i  ------------   v    ii  i 
  L1M4_orf2#LINE/    328 AACCCATACAT----TTA--TGGT------------CAATTGATTTTCGA 359

  chr1_207174140_   1509 CAAGGGCAGAAAGAGCATTTAATGAGGAAAGAACAGTCTTTCCAACAAAT 1558
                               iivv    v    i    i        i       i        
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_207174140_   1559 GGTTCTGGAAAACCTGGATATACACATGCAAAAGAACGAAACTGGACCCT 1608
                            v    i v v       ?v              i   ii       i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_207174140_   1609 TAT-----ACCATACACAAAAATTAACTCAAAAGGGTTCAAGTATCTAAA 1653
                           i-----      i                  v  v   ?iv i     
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_207174140_   1654 AAGATGAACTAAAACTATAAAACTCTTAAAAGAAAACA--GGGGGAGACC 1701
                         viv v  i                    i         --  ? v i i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_207174140_   1702 TTCATGACATTGGATTTAGCAATGATTTCTTGGCTATGACACAAAAAGCA 1751
                            i    v    i  vi      i      i v        v       
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_207174140_   1752 CCATCAACAAAAGTAAAAAGAGATAAACTTGACCTTACCAAA-TTAA--- 1797
                          v v         v     v       i v   i i i    -    ---
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_207174140_   1798 CTTTTATTCATCAAATGATACTATTAACAGAGTAAAAAGACAACCCA-GG 1846
                              i v v     v  i     i  v i   i             -i 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_207174140_   1847 AATGGGAGAAAAGATCTGCAA-TCACATAT-TGATAAGAGCTTAATATCC 1894
                                     v  i     -   i    -       i vi vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_207174140_   1895 AGAATATATCAAGAACTCCTATAACACAACAACCAAAA---AAAT---CC 1938
                                  v        i  i   v   i  iv    ---    ---  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_207174140_   1939 AACTTTAAAAATGGACAAAGAATTTGAATAGACATTTATCCAAAGAAGAT 1988
                           -  ?        i     i                v            
  L1M4_orf2#LINE/    810 AA-TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_207174140_   1989 ATACAAATGGCCAGTAAGCACA-AAAAAG 2016
                                      i        -i     
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAG 887

Transitions / transversions = 1.47 (87 / 59)
Gap_init rate = 0.02 (16 / 860), avg. gap size = 3.06 (49 / 16)  


1556 26.64 13.38 3.28  chr1_207203844_207205645.rev      526  1317 (485)    L1M4_orf2#LINE/L1       37   908 (0)  

  chr1_207203844_    526 AATATTGTAGAGATGTCAATTCTTAACAAATTTATATACACATTCAATGT 575
                                 vi     v    v  ivv      v  v    v      i i
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chr1_207203844_    576 AATTCCAATCTAAAGCCAACCAAGTTAAATTTTTTTGTAGAAACTGACAA 625
                            i  v   v   v  ---  - i iv-i       i     i      
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCC---CA-GCTGC-CTTTTTTGCAGAAATTGACAA 131

  chr1_207203844_    626 GATGTTTCCGAAGT--A---AAAAATTTAAGTG--------TATCCAAGA 662
                          v  v i ii  i -- ---ii    vi   v --------  v    i 
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_207203844_    663 CAATTTTGAA------GAATGAAGATTAAGGAATTACATT---------- 696
                             i     ------   ii   v vi    v i   i ----------
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_207203844_    697 -----------CACAGCAACAAGATTTAAGATAGTGCAGTATTGGCCCAG 735
                         -----------  v   v   iv v i    i    ii   i    vi i
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_207203844_    736 ----------------CAA--------------GAGGC---AAACAGACC 752
                         ----------------   --------------   v ---   i i   
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_207203844_    753 ---------ATGGACATTTGATTTATGACAAAGGCTGT-AGTACACATCT 792
                         ---------    v  v       vi     i  -  i- iv  -   ii
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGG-TGCCAAGAC-CATTC 379

  chr1_207203844_    793 GTGGGGGATACAATGGTTTTTTCAATGAATGTTGCTGGGTCAATTAAATA 842
                         ivv     v v   i  i       ii    v       v   i ii   
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_207203844_    843 TCCAAACAGACCAAAAAA---AATTG-ATCCTTATCGCACATTATACACA 888
                         ?   --  vi v   i  --- i   - i  i  i v    ii   i   
  L1M4_orf2#LINE/    430 KCCA--CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_207203844_    889 AAA-TTAATACTAAACATATTGTAGATGTAAATAGGGAAATTAAAAAAGT 937
                            -    iv v   iiv  ii?   iv     iviii ii     vvi 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_207203844_    938 AAAGCTTCTACTAATAGAAGATAACATAG-AGCAATATCTTCATGAGCTT 986
                            i  ----  --       v       -? i  -      i   v   
  L1M4_orf2#LINE/    528 AAAACT----CT--TAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTT 570

  chr1_207203844_    987 GGGGTAAGCAAGTATTTCCTAATCAGAACATAGAAAGTACTAACAATGAA 1036
                            v  i    vvi    i  ivi vi   ivi    i  v i   ii  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_207203844_   1037 GGAACTCACTGATAAATAGGACTTGA---AAAGTAAAAACCTT-GTCCCT 1082
                         i   vvv iv       v      v ---   v       i  -  v i 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_207203844_   1083 CAGAAAACATCATTAAAAGAGTAAAAAATGGAAGCCACAGAGTGGGAGAA 1132
                           i ii   ii  i  i i   i    i-iv  v       i        
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAG-ACAACCCACAGAATGGGAGAA 719

  chr1_207203844_   1133 CATATTTACAA--CATATAAAACCAACAAAAAATTCTTACCCAGAATATA 1180
                         v      i   --      v-- ii i  iii i iv  i          
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATAT--CTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_207203844_   1181 TG-------CCTATAAATCGAGAAGAAAAAGCCAATCAACTCAATT--AT 1221
                          i------- i  i  v  i v  v      v   vi   i     -- -
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA- 816

  chr1_207203844_   1222 TTTTAAATGGCCAAAAGACTTCTAAAGACATTTC-ACAGAAAAGAGTATA 1270
                         ----      v    i  i  vv v         -v  i i    -    
  L1M4_orf2#LINE/    817 ----AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA-TATA 861

  chr1_207203844_   1271 CAGATGGCTAATAAACAT-TGCAAAGATACTTAAACTTTAGTCATCAA 1317
                           i     i     i  i-  v      i  i  - v i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (128 / 80)
Gap_init rate = 0.04 (35 / 872), avg. gap size = 3.77 (132 / 35)  


3049 25.97 1.78 1.22  chr1_207320866_207326861     4603  5503 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_207320866_   4603 GAAAAGCATTCCATACTTATGAATTGGAAGAATCAGCATCATTAAAATGT 4652
                             iii  i    ii i   i         v i ii  ii    i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG- 51

  chr1_207320866_   4653 GCA-TACTTCCCAAAGCAATGTACAGATTCAACACTATTCCTATCAAGTT 4701
                            -    i      vii  v            i v  i        iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_207320866_   4702 ACCAATGTCATTTTTTTCACAGAATTAGAAAAAAACT-ATTCTAAAATTC 4750
                         v   -- iiiii     ii     v v  v  i--  -  i         
  L1M4_orf2#LINE/    102 CCCA--GCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr1_207320866_   4751 ATATGGAAC--CAAAAAACAGCGCAAATAACCAAGGCAATCCTACACAAA 4798
                                 v--   iii  -- vvi    i    ii     i iv v  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_207320866_   4799 AAGAGTAAAGCTGGAGGCAATCACATTATCCAACTTCAAAGTACATTACG 4848
                             ii    i      - v     i vi    i      iivi i   i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_207320866_   4849 AGGTTACAGTAACAAAAACAGCATGGTACTGGTACAAAAACAGATGAATA 4898
                          i i        iv  i    ii         i i  ii i   iiv   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_207320866_   4899 CACCAATGGAACAGAATAGAAAGTTT-GAAATGAAGCCACACACCTAAAA 4947
                         v i        i     v  i   ii-     i  v   i   ii  vii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_207320866_   4948 CTAACTGGTCTTTGACAAAGCCAACAAAAATAAACAATAGGGAAAGAATA 4997
                         ii  i  i i  i     i viiv   i vi vv    i           
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_207320866_   4998 CCCTATTCAATAAATGATAC-GAGAAAATTGGCTAACTATATGCAGAAGA 5046
                         vi  v     i     i i - i  v  i   v  ? i i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_207320866_   5047 ATGAAACTGGACCCCTACCTCTCACCATATACAGAAATTAACACAAGATG 5096
                              ii              v           i        v   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_207320866_   5097 AATTAAAGACTTAAATGTAATACCTCAAACTATAAAAATCCTAGAAGAAA 5146
                         i  i ?    i         v v  v           v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_207320866_   5147 ACCTAGAAA-ACACCCTCCTAGATATTGACCTAGGCAAATAATTTAT--G 5193
                           v   i?i- v i i  v -  iv   ivi       - ii   v -- 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAA-TGGTTTCTTAG 592

  chr1_207320866_   5194 CTAAGTCCTCAAAAGCAAATGCAACAAAAATTAAAATTGACAATTGGGGT 5243
                         v  v v vi        v v         ivv     v  i  v v  ii
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_207320866_   5244 CTAATTAAA-TGAAAGAGCTTCTGCACAGCAAAAGAAACTATGAACAGAG 5292
                         i v  i   - v   i -   i  ii vv    i  v     v  v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_207320866_   5293 TAAACAGACAATCTACTGGATGGGAGAAAATATTTACAAACCATGCATCT 5342
                          i  v      i i  v i                i    i   ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_207320866_   5343 GATAAAGAACTAATATCCAGAATCTATGAGGAACTT----AAATCAACAA 5388
                              i i   vi          v   i i     i----  v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_207320866_   5389 GCAAAAACCAAATAACTTCATTAAAAAGTGGGCAAACGACATGAACAGAT 5438
                         vv    iv        iiv   ?    i        v  iv    i   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_207320866_   5439 GCTTCTCAAAGGAAGACATCCTAATGGCCAAGAA--ACATGAAAAAATGT 5486
                         ii     v  i     i  v v         v  --         i   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_207320866_   5487 TCAACATCACTATCATC 5503
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.99 (153 / 77)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 1.50 (27 / 18)  


3292 23.65 3.15 0.90  chr1_207439329_207443218     2510  3397 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_207439329_   2510 TAGAGAGGCAGTCCATGTTCATGGTTAGGAAGGCTCAATATTGTCAAGAT 2559
                          i  i  ii vi            v v     i  i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_207439329_   2560 GTCAGTTCCTCCCAAATTGATCTGTAGATTTAATACAATTCCAATGAAAA 2609
                          v  i v ii             ii     i  ii    i  v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_207439329_   2610 TTCCAAGTGAGTTATTCTGTGGACATCAACAAGCTGATTCTAAAGTTTAT 2659
                          i   iv  vv  -  i  ii  v  ii          i     i  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_207439329_   2660 ATGGAGAGGCAAAGGACCCAGAATAGCCAATATAACATTGAAGGAGAAGA 2709
                              i v    i                 v i  iv     ii      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_207439329_   2710 ACAAAACTAGAGGAGTGACACCATCCAGCTTCAAGACTTATTATTAAAAG 2759
                              ii i     v v    ivi   ii     i     i  i--    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC--AAAG 247

  chr1_207439329_   2760 CTACAGTAATCAA--CAATACAGTGTTGGTAAAAGAATAAACAAATAAAT 2807
                                      --  i iii  ii   i v   i   i   v   i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_207439329_   2808 CCATGCAACAGAATAGAAAGCCCAGAAATAGAC--ATACAAATATAGTTA 2855
                          v   v  i     v  i  i         i  --     vv   i  i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_207439329_   2856 ATTGATCTTTAATAAAGGAGTAAAAGCAA--CAATGGAGAAAAGATAGTC 2903
                               i  ii i  i  v iv  ii v --      i    ii      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_207439329_   2904 TTTTCAACAAATGTTGCTCTGAAGACTGGATATCCACATGCAAAAACATG 2953
                                      v    vv  vi        ?            iv   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_207439329_   2954 AATCTAGACACAGACCATACACC-TCTGACAAAAATTAACTCAAAATAGA 3002
                           vi i   v vv   vi     - v -                   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGA 496

  chr1_207439329_   3003 TTAAAGACTTACACATAAAA--TACAACCATACAACTTTCAGAAGAAAAC 3050
                          i ?    i  v ii   i --  v   i   v    i i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_207439329_   3051 A--GGAGAAAATCTAGATCATCTCGGGTTTGGTGATGACTGTTTAGTTGC 3098
                          --  ? v      vvi v i  i     v  ii   ii vi    v ii
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_207439329_   3099 CGCACCAAAGGCACAAG----AAAAGAAATAACGGATAAGGTGGACCTCA 3144
                         vi       i       ----        v  ii     iv     i   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_207439329_   3145 GTAAAATTAAAA--TTTTCTCCTCTGTCAAAG-ACACTGTCAAGAGAATG 3191
                         vi          --    v v  ---      -     i      i i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCT---TCAAAGGACACTATCAAGAAAGTG 693

  chr1_207439329_   3192 AGAAGGCAAGCCACAAAATGGGGGAAAAAATTC-CAAAAGACATGTTAGA 3240
                          i   i   v     i      i     v   i-    vv i  i iv  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_207439329_   3241 TAAAAGACT-GTTTCCCGCAATAAATAAAGAACTCT-AAAACTCAAAAAT 3288
                            ii    -  v   v -    v            - v       v   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAG-AATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_207439329_   3289 AAAAA--TAAA--ATCTGATTTTAAAATGGGCCA--TACTT-AATAGAGA 3331
                              --i   -- i ii   ?v         v --v i  -      v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_207439329_   3332 CCTTATGAAGGACAATAAACAGATGGTAAGTAAGCATATAAAAAGATATT 3381
                         ii iviv  i  vi   v   i    iv i      i  i       ii 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_207439329_   3382 CCACATCATATACCAT 3397
                          v      ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (132 / 74)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.71 (36 / 21)  


2841 28.21 1.00 0.55  chr1_207446364_207453039     5280  6183 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_207446364_   5280 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 5329
                              ii    i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_207446364_   5330 GGCCATACTGCCCAAAGTAATTCATAAATTCAATGCTATCCCCATCAAGC 5379
                            v     v      v i  ii i i      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_207446364_   5380 CACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5428
                         iv   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_207446364_   5429 ATGGAA-TGAAAAAAGAGCCCATA-TGCCCAAGACAATCCTCAGCAAAAA 5476
                               -  v  i-- ii    v - iv    i      i v iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_207446364_   5477 GAACAAAGCTGGAGGCATCAGGCTACCTGATGTCAAACTATACTACAAGG 5526
                                 i      vv   vi  v  ii  v     viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_207446364_   5527 CTACAGTAACCAAATCAGCTCGGTACTGGTACCAAAACAGATATACAGAC 5576
                                  i   iv   ivi        i iv ii i   i   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_207446364_   5577 CAGTGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5626
                           i     i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_207446364_   5627 TCTGATCATTGACACATCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5676
                         vi    iv i    vivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_207446364_   5677 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5726
                          v  i  i              v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_207446364_   5727 AAACTGGACCCCTTCCTTACACTTTATACAAAAATTAATTCCAGAAGGAT 5776
                           ii         v   i    iv              i  v i v    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_207446364_   5777 TAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5826
                         i ?    i           v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_207446364_   5827 TAGGCAATACTATTCAGGACATAGGCATGGGCAAACACTTCATGACTAAA 5876
                             ?ivv v v   iv   v v  vv i     vvii   v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_207446364_   5877 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5926
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_207446364_   5927 TAAACTAAAGAGCTTTTGCACAGCAAAAGGAACTATCATCAGAGTGAACT 5976
                         i   v v  i i      ii vv    i iv       vv i      vv
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_207446364_   5977 GGCACCCTACAGAATGGGAGAAAATGTCTGCAATCTATCCATCTGACAAA 6026
                          i  v  i                 i i     vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_207446364_   6027 CGGA-TAATACCCAGGATCTACAAGGAACTTAAACAAATTGACAAGAAAA 6075
                         -   - vi  i    i  v  i  i     ivv    v ii i  v    
  L1M4_orf2#LINE/    748 -GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_207446364_   6076 A---AAA-AACCCCATCAAAAAGTGGGTATAGCATATGA-CAGACACTTA 6120
                          ---   -     v  i?    i    i v  v  v   -i     i  v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_207446364_   6121 TAAAAGGAAGACATTTATGCAGGCAACAAACATATGAAAGAAAAGTTCAT 6170
                          vv  i     i  vi viii v   i  i  i      - i v i   v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATGCTCAA 895

  chr1_207446364_   6171 CATCAGTGGTCAC 6183
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (143 / 108)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3020 25.17 1.43 1.21  chr1_207488922_207493179     2860  3765 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_207488922_   2860 TGGAAACACAGCCCATGCTCATGGATGGGTAGAACCAATATCATGAAAAT 2909
                               v i v      i        v  v   vii     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_207488922_   2910 GACCACGCTGTCAAAAACAATCTACAAAGTCAATGCAATTCCCATCAAAA 2959
                          i v ii  vi v   vii       i v    i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_207488922_   2960 TACCACCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCTTA 3009
                          v   v vv v  i  ii     v v  v  ivii            v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_207488922_   3010 TGGAA-T-CAAGAGAGAGCCCACA-TAGCCAAAGCAAGACTAAGCAAAAA 3056
                              - -    i  ---    v -        i   vvi i iv  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_207488922_   3057 GAACAAATCTGGAGGCATCAGATTAATTACCTAACTGCAAACTATATTAT 3106
                                vi      vv   v i --- -  i  i v    viv  i  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACT---T-CCCAATTTCAAAACTTACTAC 243

  chr1_207488922_   3107 AAGGCCATCGTCACCAAAACAGCATAGTACTGGTATAAAAATAAGCACAT 3156
                           i  i iv  v i   i    ii i       i    ii   ii  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_207488922_   3157 AGACCAATGGAATAGAATAAGGAACCCAGAAATAAACCCAAATACTTACA 3206
                            i              vii  ii               v i i   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_207488922_   3207 GCCAACTGATTTTTGACATAGCAAACAAAAA--ATAAAGTGGGGAAAAGA 3254
                          i   i       i    -  vivi v  i --  vv i        ii 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACA-AGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_207488922_   3255 CA--CTGATTCAACAAATGGTGCTGGGATAACTGGCAAGCCACATGTAGA 3302
                         i --  v-                    i      vv ?       i i 
  L1M4_orf2#LINE/    393 TAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_207488922_   3303 AGAATAAAACAGAATCCTCATCTCTCACCTTATACAAAAATCAACTCAAG 3352
                              i  iiv i i  ii i   v    v           i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_207488922_   3353 ATGGATTAAAGACTTAAATCTAAGACCCAAAACCATAAAGAGTCT-AGAA 3401
                               i ?    i     v     v i     i     - v   -    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAA 540

  chr1_207488922_   3402 GATAACATTGGAAAAAACCCTTCTAGACATTGACTTAGGCAAAGACTTCA 3451
                           v     v  ?iv   i -   vv   v   iv        v ii   v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_207488922_   3452 TGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGGTGG 3501
                          iivi v  vv         v v    i    iv   i   i   ii v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_207488922_   3502 GACTTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAAGCAGCAG 3551
                              v  i   v v    i   i  ii vv    i  v iv v  iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_207488922_   3552 AGTTAATAGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACAT 3601
                            v  v              i           v  ii   vii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_207488922_   3602 CTGACAGAGGACTAATATCCAGAATCAACAAAGAACTC----AAATCAGC 3647
                             i ii     vi          vv i         ----  v   ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_207488922_   3648 AAGAAAAA-ACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAG 3696
                           v     -     i  i  v  i?    i     v     iv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_207488922_   3697 ACAATTCTCAAAAGAAAATATACAAATGGCCAACAAGCATATGGAAAAAT 3746
                            v     v      i                i     i   i   i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_207488922_   3747 GCTAAACATTACTAATTAT 3765
                            v     i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (133 / 91)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.60 (24 / 15)  


2096 24.18 3.45 2.63  chr1_207494988_207496931      512  1119 (825)    L1M4_orf2#LINE/L1      215   827 (81)  

  chr1_207494988_    512 TCACACTATCTGACTTCAAAATTTACTACAAAGCTATAGTAACCAAAACA 561
                                vi ii i       i              i     i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_207494988_    562 GCATAGTACTGGCATTAAGACAGACACATAGACCAATGGA-TAGAATAAA 610
                          ii i          v i  i     i     i       -      vi 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_207494988_    611 GAACCCACAAATAAACCCATGTATTTACACCCAATTTATTTTCAAAAAAG 660
                           ii   v            ii     iivi     v      i v  i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_207494988_    661 GTCCCAAGGACATACATTGGGGAAAGGACAGTATCTTCAATAAATGATGT 710
                           v     iv   v  v         i i   v i     i     i  i
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_207494988_    711 TGGGGAAACTGGATATCCATATACAGAAGGATGAAACTAGACTCCTATCT 760
                             iv         ?   i  i  i   i     ii i   i    i  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_207494988_    761 CTCACTATATGCAAAAATCAACACGAAATGGATTAAAGACTTACATCTAA 810
                          v   i    i       i   v i        i ?    i  v  v   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_207494988_    811 GA-CTAGAAATTATGAAATTACTGTAAGAAAACATAGGGA-AAATGCTTC 858
                           -   -   i   i   i vi iv             ?i-    -    
  L1M4_orf2#LINE/    515 GAGCTA-AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTC 562

  chr1_207494988_    859 AGGACATTAGTCTGGGAAAAGATTTTATGGGTA--ACTCCTCAAAAGTAC 906
                         iv   v  i vi i  v  v i   iv i i  --  v  --     i  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC--AAAAGCAC 610

  chr1_207494988_    907 AGGTAGCAAAAGCCAGAATAGACAAATGGGATTATATAAAACTGCAAAGC 956
                          i i i      vv i      i    v   i vi  v   v vv   i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_207494988_    957 TTCTGTAAAGCAAAGGAAACAATCCATAGAGTGAAGAGACAACCTAAAGA 1006
                           i   ivvv       v  v   v v i      i        i v   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_207494988_   1007 ATGG--------ATTTGTAAACTCTCCATCCAACAAGGATGAATATCCTT 1048
                             --------     i   iiv vi   ii i    --  -----   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG--GA-----CTT 753

  chr1_207494988_   1049 AAGTAATATCTAGAATATACAAGGAACTCA-ACAGCAAAACATTTAAAA- 1096
                         i-----    i        i  i      v-   i vv  i v v    -
  L1M4_orf2#LINE/    754 G-----TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_207494988_   1097 -----TAATCTGATT-AAGAATTGGCAGA 1119
                         -----   i ii   -  i   v    i 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAA 827

Transitions / transversions = 1.88 (94 / 50)
Gap_init rate = 0.02 (14 / 613), avg. gap size = 2.64 (37 / 14)  


3140 27.88 0.77 0.33  chr1_207515893_207517698.rev      412  1315 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_207515893_    412 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATCAATATCGTGAAAAT 461
                              ii i  i     i       iv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_207515893_    462 GGCCATACTGCCCAAGATAATTTACAGATTCAATGCCATCCCCATCAAGC 511
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_207515893_    512 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 559
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_207515893_    560 TATGGAACCAAAAAAGAGTCCACATAGCCAAGACAATCCTAAGCCAAAAG 609
                                viiv  ii  vi viv        i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_207515893_    610 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAAGGC 659
                                i      vv    i  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_207515893_    660 TACAGTAGTGAAAACAGCATGCTTCTGGTACCAAAGCAGATATACAGACT 709
                                i v  i    ii  v v    i iv iiii   i   i   ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_207515893_    710 AATAGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTATAACCAT 759
                            i   i    iv   ivii         vv   i    i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_207515893_    760 CTGATCTTTGACATACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 809
                         i    i  i    vivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_207515893_    810 GTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 859
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_207515893_    860 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAAGTCAAGATGGATT 909
                          ii    i    v   i     v              v    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_207515893_    910 AAAGTCTTAAATGTGAGACCTAAAACCGTAAAAACCCTAGAAGAAAACCT 959
                          ?  v i       i   v       ii     vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_207515893_    960 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAGTAAA 1008
                            ?i- v i -   iv   v v  vv i     v ii   v iii  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_207515893_   1009 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTCACAAATGGGATCTAAT 1058
                                     vvi          vv     vv i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_207515893_   1059 TAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGGACA 1108
                         i  iv v  i i   i  ii vv    i  v    i  vv i    i v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_207515893_   1109 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 1158
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_207515893_   1159 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAA---AGTTACAAGAA 1205
                           i  vi          v  i        ivv    --- i v i  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_207515893_   1206 AA-AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 1254
                         i -   i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_207515893_   1255 GAAAAGAAGACATTTGTGCAGCCAACGGACACATGAAAAAATGGTCATCA 1304
                         vv        i  viiviii     iiii          i   v   v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_207515893_   1305 TCACTGGTCAT 1315
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.64 (154 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2604 25.58 0.82 0.96  chr1_207536531_207538249      496  1226 (493)    L1M4_orf2#LINE/L1      179   908 (0)  

  chr1_207536531_    496 AGATAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGAC 545
                          i i    i i ivv i          i      vv       v  ii i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_207536531_    546 TTCAAACTATGCTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTA 595
                               viv i      i          i   i    ii         i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_207536531_    596 CCAAAACAGAGATGTAGACCAATGGAACAGAACAGAGCCTTCAGGAATAA 645
                         iv ii i   v  i    i        i    iv   vv i   i     
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_207536531_    646 TACCACACATCTACAACCATCTGATCTTTGACAAACCTGACAAAAAAGAA 695
                         vv   i    i  iiii  vi    i  i     ivv  v   ----  v
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA----GAC 374

  chr1_207536531_    696 GA---AATGGGGAAAGGATTCCCTATTTAATAAATGGTGATGGGGAAACT 742
                         v ---           i  vvi  v  i  i        v    iv    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_207536531_    743 GGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTAT 792
                           v  ?   i   i i  iiv    ii    i    v   i     v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_207536531_    793 ACAACAATTAATTGAAGATGGATTAAAGACTTATATGTTAGACCTAAAGC 842
                             v      i v  i      i ?    i  v    v   v     i 
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_207536531_    843 CATAAAAACTCT-AGAAGAAAACCTAGGCA-ACACCATTCAGGACATGGG 890
                         i      -    -          v    ?i- v i -   iv   v v  
  L1M4_orf2#LINE/    525 TATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGG 572

  chr1_207536531_    891 CATAGGCAAGGACTTCACATCTAAAACACCAAAAGCAATGGCAACAAAAG 940
                         vv       v ii   vi vv  vi            vvi          
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_207536531_    941 CCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA 990
                         vv     v  i    v   ii v  i   v v  i i   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_207536531_    991 AAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAAT 1040
                           i  v    i  vv i      v  i     i                 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_207536531_   1041 TTTTGCAGTCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAAAG 1090
                         v      ivii ivi      i  i  i  vi          v  i    
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_207536531_   1091 AACTCAAACAAACTTA-CAAGAAAAAAACAAACAACCCCATCAAAAAGTA 1139
                              vv    -  i -i  v     i     i     v  i?    i i
  L1M4_orf2#LINE/    773 AACTCTTACAA-CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_207536531_   1140 GGCGAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCA 1189
                            i      v    i     i     v        i  vi viii    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_207536531_   1190 ATACACACATGAAAAAATGCTCATCATCACTGGCTAT 1226
                            vi          i       v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (107 / 76)
Gap_init rate = 0.01 (8 / 730), avg. gap size = 1.62 (13 / 8)  


3024 28.16 0.88 0.99  chr1_207544258_207550668.rev     5012  5920 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_207544258_   5012 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAATATCACGAAAAT 5061
                              ii i  i     i    i i v      v i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_207544258_   5062 GGCCATACTGCCCAAAGTAATTTATAGATTGAATGCCATTCCCATCAAGC 5111
                            v     v      v i  i  i     v  i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_207544258_   5112 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5159
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_207544258_   5160 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCGATGCTAAGCCAAAAG 5209
                                viiv  ii  v  v v  v     iv i  vi i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_207544258_   5210 AACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTACACTACAAGGC 5259
                                i     ivv    i  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_207544258_   5260 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACT 5309
                                 i   i    ii         i iv ii i   v       ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_207544258_   5310 GATGCAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATGTCTGCAACT 5357
                         i   v  i    i--    i  --        vv iii ii i iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_207544258_   5358 ATCTGATCTTTGACAAACCTGACAAAAAAGAAGA---AATGGGGAAAGGA 5404
                          vi    i  i     ivv  v   ----  vv ---           i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAA----GACCATTCAATGGGGAAAGAA 392

  chr1_207544258_   5405 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 5454
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_207544258_   5455 AGCTGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGA 5504
                         iiv    ii    i    v   i     v  i           i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_207544258_   5505 TGGATTAAAGACTTATATGTTAGACCTAAAACCATAAGAACCCTAGAAGA 5554
                              i ?    i  v    v   v       i    i vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_207544258_   5555 AAACCTAGGCA-ATACCATTCAGAACATAGGCGTGGGCAAGGACTTCATG 5603
                             v    ?i- v i -   ivi  v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_207544258_   5604 ACTAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGA 5653
                         iv  vi            vvi           v     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_207544258_   5654 TTTAATTAAATTTAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5703
                         i  v  i   v    i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_207544258_   5704 TGAACAGGCAACCTACAGAATGGGAGAACATTTCTGCAATCTACTCATCT 5753
                             v  i     i              v  v i     vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_207544258_   5754 GACAAATGGCTAATATGCAGAATCTACAGTGAACTCAAACAAATTTACAA 5803
                           i  iv i  vi   v      v  i iv      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_207544258_   5804 GAAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGAC 5853
                         v     i     i     v  i?    i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_207544258_   5854 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACGGGAAAAAATGC 5903
                          i     v        i  vi viii     v  i   iv     i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_207544258_   5904 TCATCATCACTGGCCAT 5920
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (156 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


3183 27.09 0.55 0.55  chr1_207561154_207563662     1109  2016 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_207561154_   1109 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 1158
                              ii i  i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_207561154_   1159 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1208
                           iv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_207561154_   1209 TAACAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTTGA 1256
                          vv  iivi i  i  ii  -      -- v  i  - iii    i  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_207561154_   1257 TATGGAACAAAAAAAGAGCCTACATTGCCAAGTCAATCCTAAGGCAAAAG 1306
                                vviv  ii  v  viv  v     iv     i i iiv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_207561154_   1307 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1356
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_207561154_   1357 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1406
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_207561154_   1407 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACAAATCTACAACC 1454
                                i    i--    i  --        vv   i v  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_207561154_   1455 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 1504
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_207561154_   1505 CTATTTAATCAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1554
                           v  i  iv             v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_207561154_   1555 GAAACTGGATCCCTTCCTTATACCTTATATGAACATTAATTCAAGATGGA 1604
                            ii    i    v   i i   v    ii  v     i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_207561154_   1605 TTAAAGACTTATATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1654
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_207561154_   1655 CCAGGCA-ATACCATTCAGGACGTAGGCATGGGCAAGGACTTCATGTATA 1703
                         vi   ?i- v i -   iv   v v  vv i     v ii   v iv   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_207561154_   1704 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATGTA 1753
                         vi            vvi           v     v  i    v   iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_207561154_   1754 ATCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1803
                               v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_207561154_   1804 CAGGCAACCTACAGAGTGGGAGAACATTTTTGCAATCTACTCATCTGACA 1853
                         v  i     i     i        v  v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_207561154_   1854 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1903
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_207561154_   1904 AAAACAAACAACCCCATCAAAAAGTGAACAAAGGATATGAACAGACACTT 1953
                           i     i     v  i?    i  ii        v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_207561154_   1954 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 2003
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_207561154_   2004 CATCACTGGCCAT 2016
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3493 25.06 1.01 0.67  chr1_207580913_207584972     2678  3567 (493)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr1_207580913_   2678 TATTCATGGATTAGGAGAATTAATATTATTACAATGTGCAAT--TACCCA 2725
                          i          i i   v        i   vi   -     -- v    
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATG-GCAATACTCCCCA 64

  chr1_207580913_   2726 AAGCAATCTACAGATTCAATGCAATCCCTATTAAAATACCAATGACAATC 2775
                           vii              i           i     v   iivi vv i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr1_207580913_   2776 TTCACAGAAATAGAAAAAATTAATCCTAAAATTTATATGGAATCACAGAA 2825
                           ii       v  v  -ii i           i        vii  iii
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr1_207580913_   2826 GACCCAGAATAGCAAAAACTATCCTGAGCAAAAAGAACAAAACTAGAGGA 2875
                                      v     v   i   iv  i         ii i     
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_207580913_   2876 ATCACATTACCTGACTTCAAATTATACTACAGAGTTATAGTAACCAAAAC 2925
                         v     i v  ii i      viv       i  i  i     i   i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr1_207580913_   2926 AACAGGGTAGTTGCATAAAAACAGACACATAGACCAATGGAACAGAACAG 2975
                          iiiv    v v      ii i     i     i        i    iv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_207580913_   2976 AGAACCCAGAAATAAATCCATGTATCTACAATGAACTCATTTTCAACAAA 3025
                            ii           i    ii  i  iii v  i v      i    i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_207580913_   3026 GGCGCCAAGAATATACATTGAGAATAGGACAGTCTCTTCAACAAATGGTG 3075
                           i       vi  v  v  i i v  i i     i              
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_207580913_   3076 CTGGGAAAACTGGATATCCATATGCAGAAGAATGAAATTAGACCCCTATC 3125
                               v         ?   i     i         i  i        i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_207580913_   3126 TCTTCTCATATTCAAAAATCAAATCAAA-TGGATTAAAAATTTAAATCCA 3174
                           vivi     v       i  v     -     i ? i ii     vi 
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_207580913_   3175 AGACTTCAAACTATAGAATCGATAAAATAAAACTTCGGGGAAACTCTCCA 3224
                            vi v        i  iivv  i  v     v v  ? v  v   i i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_207580913_   3225 GGATGTTGGACTGGGCAAAGATTTTTAAGGTA-AACCTCAAAAGTACAGG 3273
                         v  iv    ii i     v i   i v  i  -i  vi      i   i 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_207580913_   3274 CAACCAAGGCAAAAATAGCCAAATAGGATTATATCAAGCTGAAAAGCTTC 3323
                             v  i v        vi    v   i vi     iv v    i   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_207580913_   3324 TGCACAGCAAAGTAAACAATCAACAGAATGAAGAGACAACCTACAGAATG 3373
                           ii vv     v v  v     v i i    i        i        
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_207580913_   3374 GGAGAAAATACCTGCAAACTATTCATCTGACAAGGGATTAATATCTAGAA 3423
                                   ii      ii  vi      i      i vi    i    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_207580913_   3424 TATACAAGGAATTC----AACTCAACAGCAAAAAT-TGAATAATGTGATT 3468
                             i  i   i  ----       i ii     v-ii     ivii   
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_207580913_   3469 TAAAAATGAGGAAGTAATCTGAATAGCTATTTATCAAAGGAATACATACA 3518
                         ?       i v  ivi  i       vi    v  v  i   v i     
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_207580913_   3519 AATAAATGGCTAACAGGGATATGAAAAAATGCTCATCATTACTAATCAT 3567
                            ----   i  i i v i       i       v   i ????????
  L1M4_orf2#LINE/    864 AAT----GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (146 / 73)
Gap_init rate = 0.01 (8 / 893), avg. gap size = 1.88 (15 / 8)  


2021 22.29 4.76 12.77  chr1_207588957_207593233     2801  3787 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_207588957_   2801 TGGAGAGACATACCATGTTCCTAAATTAGAAGACAAAACATACTGAAGAT 2850
                             i   i  v        v ii   i      vv  i  vv v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_207588957_   2851 ATCCATTCGCTCCAAATCGTTATACAAGTTTAGCACAATTTCTATCAAAA 2900
                         iv v  v v i      i v v    ii  i i i    ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_207588957_   2901 TGCTGGCAAGAGTTTTTGTAGATGTGCACAAGATTACTTTAAAATTTATA 2950
                          v ii  vivvv      i   vi vv     v v iii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_207588957_   2951 TGAAAGT-CAAAGAAACAAAAATAGCTAAAACAATCTTGAATAACAAAAA 2999
                           i  i -   i i v v i      i              v  v  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_207588957_   3000 TAAAGTGGTTCAAACTCATCAAATTATATACATTAAACATAACTGGGTTT 3049
                         i     -------------------------------------   i---
  L1M4_orf2#LINE/    201 CAAAGT-------------------------------------TGGA--- 210

  chr1_207588957_   3050 TTAGTTTTGGTTTTGGGTTAATATATCAATTATACTTCAATAAAGCTGTT 3099
                         ---------------  ---------- v i i     ------------
  L1M4_orf2#LINE/    211 ---------------GG----------ACTCACACTTC------------ 223

  chr1_207588957_   3100 TTTAAAAAGAAAGTAGGAGGAATCAGTCTAACCAATCACAAGACTTGATA 3149
                         -------------------------------     iv   i    iv  
  L1M4_orf2#LINE/    224 -------------------------------CCAATTTCAAAACTTACTA 242

  chr1_207588957_   3150 TATAGC-ACAGTAATGAAGACTATGTGGTATTGGAA-AAAGA-----ATA 3192
                         i v   -        v     vi       i   v -  i  -----   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_207588957_   3193 TAGATTCATAGAACAGAATAGAGATTCCAGAAATAGACCCATACAAATAT 3242
                              iv  i   i     v    v          i         vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_207588957_   3243 ACTCAACTAATTTTTCACAATGGTGCAAACGCAATTTG-TGCAGGAAAGA 3291
                         iv    i i     iv    v     v  vi v   ii-  -i       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGA 391

  chr1_207588957_   3292 -CAGCCTTTTTAACAAACGGCATGGGAACAAGTGGACATCAATAAGCCAG 3340
                         -i  i     i      i  iiiv  i    v    i ? v i v  v i
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_207588957_   3341 AAAAGGAACCAGGACCTAAGTCTCGCATCTTATTTAAAAATTAACTCAAA 3390
                          i  v   viv     ivvii   i  i v   vi               
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_207588957_   3391 ATGGATTGTGGACTTAAATATAAAACATAAAACTAAAAAAGTTTTTTTTA 3440
                               ii?i   i     i   i vv        v    ----i i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA----CTCTTA 537

  chr1_207588957_   3441 GAAAAAAA---AAGA--AAATCTTCAGAATCTAGGGCTAGGCAAACTG-- 3483
                            i    --- i ?--        ivi i  v   i       --  --
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA--TGGT 585

  chr1_207588957_   3484 TTCTTAGATTTGACACCAAAAGCATAATCCATAAATGGGAAAACTGACAA 3533
                                  v              i  v v i   v ii    iv  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_207588957_   3534 GATGGACTTCATCAAAATTTAAAAC-----------AAAAGACTGTGTTG 3572
                         iv                 v     -----------   i   vv i ii
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_207588957_   3573 AGGA--TGAAATGAAAATCTAT-GACTGAAAGGAA-TATCTGCAAAGCAA 3618
                           i --     v  v  i i i-  v  ii  i  -   i      v  v
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_207588957_   3619 ACGTCAAATAAAGAAATAGTATCTAGAATATATAATCTATAATATATAAC 3668
                          ii  vi    i i v v     i           ---------- v   
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAA----------AGAAC 775

  chr1_207588957_   3669 -CTCAAAACTCAACTATAAAAA-----ATG-------TAAAAGCTGAGTA 3705
                         -  i v       iv       -----  i------- ?   iv  i i 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_207588957_   3706 AAAGGTATAAACAGACATTTACCCAAA-AGGAGATACAGATAACCAATAA 3754
                           i i v i  i        vi     - i  v     i  ii       
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_207588957_   3755 GCACATGAAAAAAATGTTCAAC-TCATTAGCCAT 3787
                                    i -  i     -   ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (130 / 86)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 6.41 (173 / 27)  


3415 24.39 1.67 0.67  chr1_207619928_207624957     3640  4537 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_207619928_   3640 GGAAAAGTATTCCATGCCCATGAGTTAGAAGAATCAATATTATTACAATA 3689
                              ii   i     ii    ii  i     v i      i   vi  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_207619928_   3690 TCCA-ACTACCCAAAGCAATCTACAAATTCAATGCAATCCCTATTAAAAT 3738
                         v v -   v      vii       i      i           i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_207619928_   3739 ACTAATGGCATGCTTCACAGAAATACAAAAATTAATCCTAAAATTTATAT 3788
                         v i iiv  v vi  ii       vv v  ii i           i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_207619928_   3789 GGAGCAACAGAAGACCCAGAATAGCCAAAGCTATTCTGAGCAAAAAGAAC 3838
                            ivvi  iii                 i v  ii   iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_207619928_   3839 AGAACTGGAAGAATCACATTATCTGACTTCAAATTATACTACAAAGCTGT 3888
                          i ii    i  v     i vi ii i      viv            ii
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_207619928_   3889 AATAACCAAAATAGCACGGTACTCACATAAAAACAGACACATAGACCAAT 3938
                          i   i   i i  iii      vi     ii i     i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_207619928_   3939 AGAATAGAATGGAGAGCCCGGAAATAAATCCATACTTCTAGAGTGAACTC 3988
                         i         v     i  i        i      v i  vi  v  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_207619928_   3989 ATTTTTGACAAAGGTATGAAAAACATACATTGGGGAAAGAACAGTCTCTT 4038
                              i     i   iiv  i v   v  v           i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_207619928_   4039 CAACAAATGGTGCCAGGAAAACTGGATTATCCATATGAAGAAGGATGAAA 4088
                                      ii   v        - ?   i   v i   i     i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCAAAAGAATGAAG 450

  chr1_207619928_   4089 TTAGACCCCTATCTTGCACCCAACACAAAAATCAAATCAAAATGGATTAA 4138
                           i        i  ii    vv i        i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_207619928_   4139 AAACTTAAATCTAATACCTAA--CTATGAAACCACTAAAAGAAA-CATTG 4185
                          i  i     v   v v    --    i    ivi  i      -   v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_207619928_   4186 GGGAAACTCTCCAATACATTGGACTGGGCAAAGATTTCTTGAGTA--ATA 4233
                          ? v  v   i ivv  v    ii i     v i      iii  -- i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_207619928_   4234 CCACACAAGTACAGGCAACCAAAGCAAAAATGGACAAATAGCATCATATC 4283
                            - -   i   i     v    v      i  i    v v iivi   
  L1M4_orf2#LINE/    601 CCA-A-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_207619928_   4284 AA-GTTAAAAATCTTCTGCATGGCAAAGGAAACAATCAACAAAG-----A 4327
                           -i       -   i  iiivv       v  v     v    ----- 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_207619928_   4328 AACAATCTACAGAATAGGAGAAAATATTTGCAAACTATCCCTCTGACAAG 4377
                         i    i i       i                  ii  viv     i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_207619928_   4378 GGATTAATAACCATAGTAATATATGGAACTCAAACAACTCTATAAGTTAA 4427
                            i vi  v   v i  -    vi      vv       v    - v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATA-TATAAAGAACTCTTACAACTCAATAA-TAAA 795

  chr1_207619928_   4428 AAG-CTAATAATCTCATTTAAAA-TGGACAAAAGATCTAAATAGATATTT 4475
                            - v     i iv   ?    -   i    i   i i      i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_207619928_   4476 CTCAAAAGACGACATACAAATGGCAAAGAGGTATGTGAAA-GATGCTAAA 4524
                            v     v  i           v  v i i ii     -      v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_207619928_   4525 CATCACTGATCAG 4537
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (141 / 74)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 1.40 (21 / 15)  


 856 18.75 0.62 0.62  chr1_207881373_207883365      152   311 (1682)    L1M4_orf2#LINE/L1       16   175 (733)  

  chr1_207881373_    152 TGTTCATGGATTGGAAGA-TTGATATTGTTAAAATGGCATTTCTCCTCAA 200
                                           -  i          i      v v    i   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_207881373_    201 ACTGATTTATAGATTCAATCTAATTCTTATAAAAATCCTAGCAGGCTTAT 250
                          i    i  i        ivi   i i   v       i   v v   - 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT-T 114

  chr1_207881373_    251 TTTGCACAGACTGGCAAACTGATTTTGAAATTTATATGGTAATGCAAAGG 300
                               v i i  i   i     ii i     i      v       i  
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_207881373_    301 ACCTAGAACAG 311
                            i    i  
  L1M4_orf2#LINE/    165 ACCCAGAATAG 175

Transitions / transversions = 2.75 (22 / 8)
Gap_init rate = 0.01 (2 / 160), avg. gap size = 1.00 (2 / 2)  

1072 25.15 10.78 3.29  chr1_207881373_207883365      496   829 (1164)    L1M4_orf2#LINE/L1      165   523 (385)  

  chr1_207881373_    496 ACTTAAAATAGACAAAACAATTTTGAA---GAAGAACAAAATTGGGTGAT 542
                           ii i     v         i     ---          i    iv  i
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_207881373_    543 TGGCACTAACTGATTTCCATATTTGTTATAAAGATGCAATAATCAAGAT- 591
                          vi    vv ii     v v i  ii  i    v i  i         i-
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_207881373_    592 -TGTAATATTGGTGTAATGATGGACATATAGATCAATGGAACAAAAT--A 638
                         -   ii  i   ii   v   i                   i i   -- 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_207881373_    639 GAGTCCAGAAATAGACTCATCCATATGTGATCAACTAATTTTCAATGAAA 688
                                      i  i   v   v i  i    i i      i ii ii
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_207881373_    689 GTGTCAGTGTAATTCAATGGCAGAAG------------------TGATA- 719
                            i  iviiv         vii   ------------------  i i-
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_207881373_    720 ----------GAATATCTGCATGCAAAAAAAAAAACCTCCAATAAACCTT 759
                         ---------- i   ? ii         i  ----------- i  vi v
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAA-----------TGAAGTTG 453

  chr1_207881373_    760 GATCCTTCCCTCACATCATGCATAAAAATAAACATGAGATGGAACACAGA 809
                           i  i v       i   ii i      v   vii i     v  ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_207881373_    810 CCTAAATATAAGAACAAAAA 829
                                i     i v    
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAA 523

Transitions / transversions = 2.90 (61 / 21)
Gap_init rate = 0.02 (6 / 359), avg. gap size = 7.83 (47 / 6)  

 903 20.83 6.73 4.81  chr1_207881373_207883365     1189  1500 (493)    L1M4_orf2#LINE/L1      591   908 (0)  

  chr1_207881373_   1189 AAATATATCACTGAA-GCATGATCCATAATAGAAAAAATTGATAAATTAT 1237
                          i    iv   ii  -   ii v v i  v         v        iv
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_207881373_   1238 ATTTCATCAAAATTAAAAATGTTCCT-TTTCAAAAGACAC----AAGAAA 1282
                          i                 iv  iv -i      i     ----      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_207881373_   1283 ATGAAAAGGTTAGCCATCGGTCAGGAGAAAATATTTGCCAAACATATGTC 1332
                         i       iiv v   iv ivii               v  v     i  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_207881373_   1333 TGATCAAAGATTTGTATCCAGAATATATAACAAACTCTTCCAATTCAA-- 1380
                             v ii  i                   vi       v   i    --
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_207881373_   1381 ATATAAGCGCTCTTTCAAATCAATAATAGAACAAAAAGAGCGGGGTGGTG 1430
                            v  ---------- i iv     ivv  iv?   i -i   ----ii
  L1M4_orf2#LINE/    791 ATAAAA----------AGACAAATAACCCAATTWAAAAA-TGGG----CA 825

  chr1_207881373_   1431 GAAGATTTGGATAGACATTTG-CCGAAGAAGATATGCAAATGG-----AA 1474
                         i i      i          v-  i          i       -----  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_207881373_   1475 A------AAAAGATGATCA-CATCATTAGTCAT 1500
                         i------        v   -     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (40 / 24)
Gap_init rate = 0.03 (11 / 318), avg. gap size = 3.27 (36 / 11)  

 262 18.18 5.19 1.30  chr1_207881373_207883365     1917  1993 (0)  C L1M4_orf2#LINE/L1   (361)   547   468  

C chr1_207881373_   1993 ACCATGCATAAAAATTAACC--AGATGGAGCATAAGATCTAAATATAAGA 1946
                              ii i          i-- i     v  ? -  i      i     
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWA-GACCTAAATGTAAGA 516

C chr1_207881373_   1945 AC-AAAACTATAAATTTCT-AGAAAAATACA 1917
                         i -           vi   -    i  v   
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACA 547

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.05 (4 / 80), avg. gap size = 1.25 (5 / 4)  


1329 25.88 8.33 8.99  chr1_207947439_207950448     1606  2517 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_207947439_   1606 GAAAGAAGACCCATAGTGTTCATGGATTGGAAAATTCAGTATAGTTAAAA 1655
                               viv     ---               i i i i   v     i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCAT---GTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_207947439_   1656 TGTCAGTTCTCCCTAAATAGATCCATGAATTTGA-----TTACAGTCAAA 1700
                           v  i v     i    v    i iii   ii ----- iv vi     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_207947439_   1701 GTCCAAGCAAGATTTTT-GTAGGCATAGGTTACTTGATTGTAAAGTTGAT 1749
                         i   v   vivv     - i  iv  v iiv vi    iv    i  v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_207947439_   1750 AAGGAAAGGTAAAGGAACTAAATTAGC-AAAAGAGTTTTTAGAACGAAGA 1798
                          v     v i  i   v i i v    -    v i i  v i  v     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_207947439_   1799 GCAGAGCTGAAGGATTCACATGACCTGATTTTAAAACCTAAAATTCTTTT 1848
                         i  i  i  i    i     ivv  ii    i     i  -----  ---
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-----CT--- 241

  chr1_207947439_   1849 TTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTCGCT-CTGTCCCCCAGG 1897
                         ------------------------ iii  -----  - v  vvi v  i
  L1M4_orf2#LINE/    242 ------------------------ACAAAG-----CTACAGTAATCAAGA 262

  chr1_207947439_   1898 CTGGAGTGCAGT---GGCA---GGAT-----CTTGGCTCACTGCAAGCTC 1936
                          ---    ii  ---    ---    -----iv i v   v  v  ---i
  L1M4_orf2#LINE/    263 C---AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA---T 306

  chr1_207947439_   1937 CGCCTTCTGGGTTCACA-------CCATTC--TCCTGCCTCAGCCTCCTG 1977
                         v vv  vv i  i  v -------    v -- iv  v-   ii----  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG-TCAAT----TG 351

  chr1_207947439_   1978 AGTAGCTGGGACTACAGGCACCTGCCA---CCATGCC-TGCCTAATTTTT 2023
                          v vv ---   - vi  ----     ---    v v-  vvv  vvvv 
  L1M4_orf2#LINE/    352 ATTTTC---GAC-AAGGG----TGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_207947439_   2024 TGTATTTTTAGTAGAGACGGGGTT----TCACTGTGTTAGCCA------- 2062
                         v  v    i -- v i i  v i ----iv    - v  ?   -------
  L1M4_orf2#LINE/    394 AGTCTTTTCA--ACAAATGGTGCTGGGACAACTG-GATAKCCACATGCAA 440

  chr1_207947439_   2063 --GGATGGTCTCCATCTCCTGACCTCGTG--ATCTGCCCGCCTCGGCCTC 2108
                         -- i   ivv iviv i   -     iii--  v i vvivv iii i--
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACT-- 487

  chr1_207947439_   2109 CCAAAGTGCTGGGATTACAGGCATGAGC-CACGGCGCCCAGCCTAAAACC 2157
                         -    i  ----   i ?  i v i ii-i v ------   -      i
  L1M4_orf2#LINE/    488 -CAAAATG----GATCAWAGACCTAAATGTAAG------AGC-TAAAACT 525

  chr1_207947439_   2158 -TAAAATTCTT-TAGGAAAACATAGAAGAAAATGTTTGTGACATTGGGTT 2205
                         -     i    -v i          i? v    v  i     v       
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_207947439_   2206 AGGCAAAGAATTATTAGGTA--ACAACAAAAGCA---GTATCTATGAAGA 2250
                               v iv  v    i  --   v        --- i v v --    
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA--AAGA 623

  chr1_207947439_   2251 AAAA---GATCAATTGAATTTCATCAAAA--AATA--TTTTGCTATATAA 2293
                             ---   v     i i          --  v --     ivv vi  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_207947439_   2294 AGGGTACCGTAAAGAGAATGAAA-GACAAACCATGT--TAGGAGAAAATA 2340
                            ii  ii v    i i     -     v   iiv-- i          
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_207947439_   2341 TTTGCAAATCACATACTTGACCAAAGGCTTTTATATCCAGAATATATAAA 2390
                                    i   ii   i--    vvi  i                 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGAT--AAGGGACTTGTATCCAGAATATATAAA 771

  chr1_207947439_   2391 GAATTTCCAAAACC---TAACAAGAAACCAAATAACCCAATTAAAAAAAT 2437
                            i iii v   i---   i  i  iv              ?     - 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-T 820

  chr1_207947439_   2438 AGGCAAAAAGTT-----GGACACTTCGCCAGTGA---TATACAGCTAGCA 2479
                         i      iii  -----i    i   v   iv  ---      iv i  v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_207947439_   2480 AATAAGCACGTGAAAATACGTTCAACATCATTAATCAT 2517
                                  i      v i i         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (131 / 101)
Gap_init rate = 0.05 (48 / 906), avg. gap size = 3.29 (158 / 48)  


3036 27.33 0.77 1.10  chr1_207962576_207970648.rev     4968  5878 (2195)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_207962576_   4968 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5017
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_207962576_   5018 GGCCACACTGCCCAAGGTAATTTATAGATCCAATGCCGTCCCTATCAAGC 5067
                            v i   v     iv i  i  i    i   i  vi          iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_207962576_   5068 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5115
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_207962576_   5116 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5165
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_207962576_   5166 AACAAAGCTGGAAGCATCATGCTACCTGACTTCAAACTATAGTGCAAGGC 5215
                                i    i vv   ii  v  ii i      viv  v i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_207962576_   5216 TTACAGTAACCAAAACAGCATGGTACATGTAGCAAAACAGAGATATAGAC 5265
                          -       i   i    ii      vv i vv ii i   v       i
  L1M4_orf2#LINE/    249 T-ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_207962576_   5266 CAATGGAACAGAA--AAGAGCCCTCAGAAATAATACCACACATCTACAAC 5313
                                 i    --i    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_207962576_   5314 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGATTC 5363
                           vi    i  i     ivv  v   i v  vv     i      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_207962576_   5364 CCTATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCATATGTAGAAAGC 5413
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_207962576_   5414 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5463
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_207962576_   5464 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5513
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_207962576_   5514 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5562
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_207962576_   5563 AAAACACCAAAAGCAATGGAAACAAAAGCCAAAACTGACAAATGGGATCT 5612
                          vi            vvi v        vv    iv  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_207962576_   5613 AATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5662
                         v  i   v v  i ii  i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_207962576_   5663 ACAGGCAACCTACAGAATGGGAGAAAATTTTTATAATCTACCCATCTGAC 5712
                          v  i     i                 v   ii  vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_207962576_   5713 AAAGGGCTAATATCCAGAATCTACAAAGAACT--TAACCAAATTTACAAG 5760
                           i  i  vi          v  i        --  --   v iv i  v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAAT 792

  chr1_207962576_   5761 AAAAAAATCAAACAACCCCATCAAAAAGTGAGTGAAGGATATGAACAGAC 5810
                              i -    i     v  i?    i  i ii      v    i    
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_207962576_   5811 ACTTTGCAAAAGAAGACATTTATGGAGCCAACAGACACATGAAAAAATGC 5860
                          i  iv v        i  vi vivi     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_207962576_   5861 TCATCCATCATTGGCCAT 5878
                            -v     ????????
  L1M4_orf2#LINE/    892 TCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  

3600 23.52 2.13 0.56  chr1_207962576_207970648.rev     6690  7582 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_207962576_   6690 GAAAAAATAGTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAATA 6739
                          i   i   vi                     v i           i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_207962576_   6740 TCCATACTCTCTAAAGCAGTCTACAGATTTAATGCAATCCCTATGAAAAT 6789
                         v v      i i   viii          i  i           v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_207962576_   6790 ACCAAAT--------TGGAAAAA-----AAG----TCCTAAAATTTATAC 6822
                         v   iv --------  v i   -----   ----          i   i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_207962576_   6823 AGAACAAGAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAAAGAAA 6872
                         i   vviv  ii                 i v   i   iv  i     v
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_207962576_   6873 AAAACTGGAGGAATCACATTACTTGACTTCAAATTATACTACAAAGCTAC 6922
                            ii       v     i v iii i      viv              
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_207962576_   6923 AGTAACCCAAACAGCATGGTACTGGCATAAAAACAGACACACAGACCAAT 6972
                              i v i    ii              ii i     i i   i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_207962576_   6973 GGAACAGAATAGAGAACCCAGAAACAAACACGTACATCTACAGTGAACTC 7022
                             i     v    ii       i    v i     i  ii  v  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_207962576_   7023 ATTTTTGACAAAGGTACCAAAAGGATATATTGGGGAAAAGACATTCTCTT 7072
                              i     i   i    i vv  vi v        ii i v   i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_207962576_   7073 CAATAAATGGTGCTGGGAAAATTGGATATCCATATGTAGAAGAATGAAAC 7122
                            i              v  i      ?   i   i i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_207962576_   7123 TAGACCTCCATCTCTTGCCAGATACAAAAATCAAATCAAAATGTATTAAA 7172
                          i    i i i   vii   v          i  v        v  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_207962576_   7173 GACTTAAATTTATGACCAAAAACTATAAAACTACTACAAGAAAACATTAG 7222
                            i     v  v  v v              vi  v          -  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AG 550

  chr1_207962576_   7223 GAGAAACTCTCTAGGACATTGGACTGGTCAACGATTTCTTGAGTAATACC 7272
                          ? v  v   iiiv   v    ii i v   i i      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_207962576_   7273 CTACGAGCACAGGCAACTGAAACACAAATGTACAAATGGGA--TCATATG 7320
                          i vi      i     vi  iv v    iv i    v   --    -ii
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT-CA 649

  chr1_207962576_   7321 AAGTTAAAAAGCTTCTGCACTGCAAAGGAAACAATTAACAAAATGAAGAG 7370
                           i       -   i  ii  v       v  v  i  v   i    i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_207962576_   7371 ACAACCCACAGAATGGGAGAAAATTCCTTCAAACTATCCTTCTGACAAGG 7420
                                                 vii v    ii  viv     i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_207962576_   7421 GATTGATAACCCTTGAATATAAAACAAGCTCAAACAACTCTATAGGAAAA 7470
                           i vi  v  v--       v  vi i   vv       v   iv    
  L1M4_orf2#LINE/    749 GACTTGTATCCA--GAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_207962576_   7471 AATCTAATAATCCTATTTTTAAATGGGCAAAAGGTCTGAATAGACATTTC 7520
                          iv v     i  v   ?vv           i i i              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_207962576_   7521 CCAAAAGAAGACACACAAATGGCAAACAGGCATATGAAAAGGTGCTCAAC 7570
                         i v        i i         v  i i   i        i        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_207962576_   7571 ATCACTGATTAT 7582
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (128 / 78)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 3.00 (24 / 8)  


3287 21.02 4.65 4.42  chr1_207970817_207973360     1156  2059 (485)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_207970817_   1156 GAGAGATACTCCATGTTCATGTATATTG------TTAAGTATATTGTTAA 1199
                           i     ii           v  --  ------    ---         
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGAT--TGGAAGACTTAA---TATTGTTAA 47

  chr1_207970817_   1200 GATAGCAATTTTATCCTAATTAATCTATAGATTCAATGCCCTCCCTACTA 1249
                            i     vi vi  v    i     i        i  vv      ii 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_207970817_   1250 AAATCACATCAGGCTT----AAAAAAAAATAAATTGACAGGCTGATTCTA 1295
                              v  v v v   ----iv i   ------      i      i   
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAA------TTGACAAGCTGATCCTA 141

  chr1_207970817_   1296 AAATGTATATGGAA-TTCAAAAGTCTTAAAATAGTCAATGCAATTTGGAA 1344
                             vi        - v   ii v ii i     i   vi    i v   
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_207970817_   1345 AAAGAA---CAAAGATTAAGGACTTACACTACCCAGTTTTAAAACTTAT- 1390
                               ---     v vi      i     v    i   i        i-
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_207970817_   1391 --GAAGCAACAGTAATCACAGCAATGTGCTGTTGGCTTAAGGATAGATA- 1437
                         --i    v          vii  i    v ii    v          i -
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_207970817_   1438 ACAGACTAACGAAACAGAATTGGAAGTCCAGGATAAAACCCTTACATTTA 1487
                          i   ii  i i  i       ii       i vv      v        
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_207970817_   1488 TGGTCAGTTGACTTTTGACAAAAGCGTCAAGATAATTCAATGGGGGAAAT 1537
                               i    i   i     ii i i     iv           -   v
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAG 390

  chr1_207970817_   1538 GATAATTTTTTCAACAGATGGTGCTGGGACAATTATACATCCATATGCAA 1587
                         i   i i         i               i iv i ?   i      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_207970817_   1588 AAAAA---ATTTG-----TTATCTCATGCCATGTGCAAAATTTAACTCTA 1629
                           i  --- v   -----i  i    ii    i i     v       v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_207970817_   1630 AATGGATCATAGACTTACATATAAGAGCTAAA----TAAAGTTTCTAGAA 1675
                                  ?    i  v  i           ----    ii ii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_207970817_   1676 AGTGGCA-AGGAGAAAATTTTTGTGACTTTGGGTTAGACAGGTATTTCTT 1724
                         iivii  -   ? v    i  i     i         i  ivvi      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_207970817_   1725 GGATATGACAACAAAAACATGATCCACAAGAGAACGGAATTAATAGATTG 1774
                         i         v     i  ii v v    i    -ii   vi   i    
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAA-AAAATAGATAAATTG 639

  chr1_207970817_   1775 AACTTCATCAAAATAGAAAAAATTCTGCTCTTCAAAAGGCACCATTAAGT 1824
                         i             -v     v  i  iv       i i   i  i   -
  L1M4_orf2#LINE/    640 GACTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAG- 687

  chr1_207970817_   1825 GGAATTAAAAGACAAGTCATAGACTGGGA-AAAATATTTGCAAATCTTAT 1873
                         ii i v         vi  i   v     -                v   
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_207970817_   1874 ATGTAATAGAGGACTTTTATCT-GAATATATAAAGAACTCTTATAATTTG 1922
                           v i   ii      v    i-                    i  i ii
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_207970817_   1923 ATAGTAAGA-------TAATCCAGTTTTTTAAATGGGATAAAAAACATTT 1965
                            i   i -------   i   i  ?vv-       -i   ii --   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAA-AAATGGG-CAAAGGA--TTT 833

  chr1_207970817_   1966 AAAAATTAG-TATTTATTATGTTTTAACTAAAGAACAGTTTTCTTTATAC 2014
                         i  ---   -i    v ---------- i      v --------     
  L1M4_orf2#LINE/    834 GAA---TAGACATTTCT----------CCAAAGAAGA--------TATAC 862

  chr1_207970817_   2015 AA-TGGCTTATATATACATGAAAAGATGCTTCATAGCATTAGCCTT 2059
                           -    iv   vii               iv i v  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (128 / 58)
Gap_init rate = 0.03 (28 / 906), avg. gap size = 2.93 (82 / 28)  


4318 16.98 2.57 1.23  chr1_208005444_208007642      812  1706 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_208005444_    812 GAAAAGCCACCCCATGTTCATGGATTGGAAGACTTAATACTGTTAAGATG 861
                          i    vi i                             i          
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_208005444_    862 TCAGTACTACCCAAAGTACTCTACAGATTCAATACAATCTTTATTGAAAT 911
                         v  i    v      v iv             ii     ii   ii    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_208005444_    912 TCCAATGACATTTTTTTGCAGAAATGTGGAAATCC-ATGCTAAAATTCAC 960
                         i   iivi -i              -  iv  v i-  v          i
  L1M4_orf2#LINE/    102 CCCAGCTGC-CTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr1_208005444_    961 ATGGAATAT-CAAGAGACCGCAAATTGCCAAAACAATCCTGGAAAAGAAT 1009
                               -  -    i    vvi   v            i  i       v
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_208005444_   1010 AATAAAGTTAGCAAGACTCAC--TTTTTGATTTCAAAACTTATTACAAAG 1057
                           i      i - i       --  iiii             i       
  L1M4_orf2#LINE/    199 AACAAAGTTGG-AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_208005444_   1058 CTACAGTAATCAAAACAGTATAGTGCTGGTGTAAA-ATAC-TATATAGCC 1105
                                      i     i i  i    ii   i-   v-i      vi
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_208005444_   1106 CAATGGAATAGAATAGAGAGTCCTGAAACAAACACATA----TATGGTCA 1151
                                       v        v    i    v    ----        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_208005444_   1152 AGTAATTTTCAACAAGGGTGCCAAGATCACTCAGTGGGGAAAGGGCAGTC 1201
                          v i      i               i  i   i         iii    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_208005444_   1202 TTTTCAACAAATAGTGCTGAGAAAACTGGATATCCACATGCAAAAGAATG 1251
                                     i      i  v         ?                 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_208005444_   1252 AAGTTAGACCCTTACACAACACCATACACAAAAATTAACT---AATGGAT 1298
                              i     i   viv        i             ---       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_208005444_   1299 CAAAGACCTAAACATAAGAGATTAGACTATGCAATTCTTAGAAGAAAACA 1348
                           ?         ii      v v i     iv  i               
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_208005444_   1349 TAGGGGGAAATCTTCATGACATTGGATTTGGCAATGAATTCTTGAATATG 1398
                             ? v        i    v    i  v       iv     ii     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_208005444_   1399 ACCCCAAAAGCACAGGCTACAATTGTGAAAAACAAACAAATCGAACTTCA 1448
                           v           i  v    vv -i     i i i    i i      
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCA 646

  chr1_208005444_   1449 --AAATTTAAA--CTTTTGTGCATTAAAGAACACTATCAACAG-GTAAAA 1493
                         --   v     --         v i    i          v i-  i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_208005444_   1494 ATGTAACCCACAGAATAAGGAGAAAATATTTGTAAGTCACATATCCTCAA 1543
                          vii            i-              i  i   i     - v v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATG-GGAGAAAATATTTGCAAATCATATATC-TGAT 744

  chr1_208005444_   1544 AAGGGATAAATATCCAGAATATAGCATAAAGAACTCCTAACATTCAACAA 1593
                               ivvi             ---          i  vv i    i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATA---TAAAGAACTCTTACAACTCAATAA 791

  chr1_208005444_   1594 CAAAAA--CAAAAAACCCAAATTTAAAAATTGTCTAAAGACTTCGATAGA 1641
                         i     --    v       -  ?      v v v  i  i  vi     
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_208005444_   1642 CATTTTTACAAAAAAGACATACAGTTGACCAATAAGCTCATGAAAAGATG 1691
                              i v    i    i     iv  i         v            
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_208005444_   1692 C---ACATCACTAATAAT 1706
                          ---      ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (97 / 51)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 1.62 (34 / 21)  


3212 26.57 0.77 0.66  chr1_208015702_208020999     3899  4805 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_208015702_   3899 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3948
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_208015702_   3949 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3998
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_208015702_   3999 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4046
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_208015702_   4047 TATGGAACCAAAAAAGGGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 4096
                                viiv  ii iv  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_208015702_   4097 AACAAAGCTGGAGGCAC-CACACTACCTGACTTCAAACTATACTACAAGG 4145
                                i      -  -      v  ii i      viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_208015702_   4146 -TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 4194
                         -  i     i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_208015702_   4195 CAATGGAACAGACC--AGAGCCCTCAGAAATAATACCACACATCTACAGC 4242
                                 i   vi--    i  --        vv   i    i  ii i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_208015702_   4243 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 4292
                           vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_208015702_   4293 CCTATTTAATAAATAGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 4342
                         i  v  i  i    i         v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_208015702_   4343 TGAAACTGGATCCCTTCCTTACACCTTATACAAACATTAATTCAAGATGG 4392
                             ii    i    v   i     v        v     i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_208015702_   4393 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4442
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_208015702_   4443 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 4491
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_208015702_   4492 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4541
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_208015702_   4542 AATTAAACTAAAGAGCTTATGCACAGCAAAAGGAACTACCATCAGAGTGA 4591
                         v  i   v v  i i   v  ii vv    i iv    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_208015702_   4592 ACAGGCAACCTACAGAATGGTAGAAAATTTTTGCAATCTACTCTTCTGAC 4641
                          v  i     i         v       v       vii iviv     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_208015702_   4642 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 4691
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_208015702_   4692 AAAAACAAACAATCCCATCAAAAAGTGGGCGAAGGAGATGCACAGACACT 4741
                            i     i  i  v  i?    i     i     vv  v i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_208015702_   4742 TCTCAAATGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 4791
                             v  v     i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_208015702_   4792 TCATCACTGGCCAT 4805
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2074 21.49 6.96 10.43  chr1_208366286_208370725     2728  3532 (908)    L1M4_orf2#LINE/L1        1   777 (131)  

  chr1_208366286_   2728 TGAAGAGACATACTATGGTTATGGATTAAAAGACTCAACATAGCAAAAAT 2777
                           i i   i  v i   v i       ii      i  i  v iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_208366286_   2778 GTCTATTCACCCACAACTTGATCTACAAATGTAACTCGAAGCCAGTCAAA 2827
                          v v  v v   -   v          i  vi   v i vv  vi     
  L1M4_orf2#LINE/     51 GGCAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_208366286_   2828 A------CTGCATTAAAAATTTTTGCACA------TAAGTGAATTTTAAA 2865
                          ------    v  ------       v ------i   ivi  ii    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTT------TTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_208366286_   2866 ATGTATATAGAAAAGTCAGCAAACTAGACTAGCCAAAATAACTTTGAAAA 2915
                           vi    i    v iv  vi v i   v         i  ii       
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_208366286_   2916 AAAA--ATAAAGTTGGAAGAATCGCACTACCCAGTTTTAAAACTTACCAT 2963
                          i  -- i         i  v  i    v    i   i         i i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_208366286_   2964 AAAACTACAATAATTAAGATGGTGTGGCATTGGTGAAGGGACAGACACAT 3013
                            i     i    i    ii      i i   iiv i   i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_208366286_   3014 AAATCAACAGAACAGAAAAGAGGATCCTGAAATAGAC---TACGTAAGTA 3060
                          i     ii   i    vv   ii   v      i  ---   i --v  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT--TTA 341

  chr1_208366286_   3061 TGGTCAAATGATCTTTGACAAAGATGTAAAGTCACC--TGAATGGAAAAA 3108
                                v    i  i     i i  iv   --   -- v     ii   
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAG--ACCATTCAATGGGGAAA 389

  chr1_208366286_   3109 GAATAGTCTTTTCAACAAATAATGTTG---CAA----------------A 3139
                                             ii  i  ---   ---------------- 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_208366286_   3140 AAAAATGTGAACCTTGACCCAAACCTCATACCTGATAGAATGATTAATTC 3189
                            i -i    vi v     vv      i   vv   v  vi     i  
  L1M4_orf2#LINE/    440 AAAGA-ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_208366286_   3190 AAAATGGATCACAGAGATGTATGTAAAATGC-AGAACTATAAAACTCCTA 3238
                                    ?   vv iv      i -  - i             i  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTA 537

  chr1_208366286_   3239 GAAGAAAACACAGGAGAAAATCTCCATAACCTGAGTTTGGGCAAAGTACT 3288
                                   i   ? v      i i i    vi v  i     v vvi 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_208366286_   3289 CTTAGACATGACATGAAAAACACAAGCCATAAAAGAAAATAACATCAATG 3338
                               i      iv    i       v i         -----------
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA----------- 626

  chr1_208366286_   3339 AACTGGGGAGTCTCTCTCAACCTATTCTGGCTTGGGGGCTGCCCAATTTT 3388
                         --------------------------------------------------
  L1M4_orf2#LINE/    627 -------------------------------------------------- 626

  chr1_208366286_   3389 TTTAAAAAAATCAATAAATTAGACTTTATCAAAATGTAAACATTTTAATG 3438
                         --------   vi       i     i        -    v i   vi  
  L1M4_orf2#LINE/    627 --------AATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTTTGTG 667

  chr1_208366286_   3439 AGG-AAAAGACACTGTTAAGAGAATAAAA---------------TGAGAG 3472
                         vvv-   i      i i    i i i   ---------------  i   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_208366286_   3473 AAAATAATATGCAA-TCACATATCCAACAAAGGGTTTATATCCCAAGTAT 3521
                               v -     -   i     ii i  i  ii  i     vi i   
  L1M4_orf2#LINE/    718 AAAATATT-TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_208366286_   3522 ATAGAAAACTC 3532
                            i i     
  L1M4_orf2#LINE/    767 ATAAAGAACTC 777

Transitions / transversions = 1.85 (111 / 60)
Gap_init rate = 0.03 (20 / 777), avg. gap size = 7.00 (140 / 20)  

 412 19.76 4.19 4.79  chr1_208366286_208370725     3781  3947 (493)    L1M4_orf2#LINE/L1      743   908 (0)  

  chr1_208366286_   3781 ACAAGGGCGAAACTCCGTCTCAAAAAAAAAAAAAAAACCTCTCAAAACTC 3830
                          i     ----   i-  v  v i  v v v   i   -   i v     
  L1M4_orf2#LINE/    743 ATAAGGG----ACTT-GTATCCAGAATATATAAAGAAC-TCTTACAACTC 786

  chr1_208366286_   3831 AGCATTAAGAGAACAAACTACCCAATTAAAAAAATTAAG-AAAAGACTTG 3879
                          ii v   i ii     iv        ?     -- ii -   i  i   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTG 834

  chr1_208366286_   3880 ----GACACTTCACCAAAGA-GA-ACACAGATGGCAAATAACTATATGAA 3923
                         ----    i   v       -  - i   i     v     vi i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_208366286_   3924 AAGATGTTCAACATCATTAGCCAC 3947
                               i         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (21 / 11)
Gap_init rate = 0.05 (8 / 166), avg. gap size = 1.88 (15 / 8)  


1628 14.24 2.37 1.36  chr1_208410584_208413335.rev      781  1075 (1677)    L1M4_orf2#LINE/L1       23   320 (588)  

  chr1_208410584_    781 GAATGAAAAGACTTAATATTGTTAAGATGGCAATACTCCCCAGG--GCAC 828
                          i  vii                                   ii-- vv 
  L1M4_orf2#LINE/     23 GGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATC 72

  chr1_208410584_    829 TATAGATATAACACAATCCTTATCATAATTCCATCTGGCCTCT--ACAGA 876
                           i    vi   i      i     v   i   v   v i i --i    
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chr1_208410584_    877 AATCAACAAGCTGATCCTAAAATTAATATGGTAATTCAAGGGACCCAGAA 926
                            ii                   v      v   v              
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr1_208410584_    927 TAGCTAAA-CAATCTTGAAGAAGAAGAATAAATTTGGAGGACTCACACAT 975
                             i   -          i        i   v               v 
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr1_208410584_    976 CCTGATTT-AAAACTTACTATGAAGCTACAGTAATCAAAACAGTATGGTA 1024
                           ii    -           ii                i     i     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_208410584_   1025 CTGGCATAAGGAGAGACAGTCATACAGATTAACGGA-TAGAAGTGAGAGA 1073
                                     v     ----  i    i  i   -     v      v
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACA----TATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_208410584_   1074 CC 1075
                           
  L1M4_orf2#LINE/    319 CC 320

Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.02 (6 / 298), avg. gap size = 1.83 (11 / 6)  

1691 16.30 10.50 1.10  chr1_208410584_208413335.rev     1382  1743 (1009)    L1M4_orf2#LINE/L1      304   699 (209)  

  chr1_208410584_   1382 AAAAGAAGTGAGAGACCAGAAATAAGCCCTCACATCTATGGTCAATGAAT 1431
                           v    v      v          i   vi    i          vi  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_208410584_   1432 TTT-GACAAGGGTTTTAAGACCATCCAATGGAGAAAAGGTAGTCTTTTTA 1480
                            -         vii        i      i    iii         i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_208410584_   1481 ACAAGTGGTACTGGGAAAACTAAATACCCATATGCAAAAGAATAAAGTTG 1530
                             i    i      v    ii   ?   i            i      
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_208410584_   1531 GATACCTCCCAACCTTGTACCATATATAAAAATTTATTCAAAATG----- 1575
                           iv   ----    iii        i       v i        -----
  L1M4_orf2#LINE/    454 GACCCCT----ACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_208410584_   1576 ------------TAGGA-CTAAAACT-TAAAG-TCTTAGAAAAAG---TA 1607
                         ------------  i  -        -    i-        i  i---  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_208410584_   1608 GGTATAAATCTTTGTGATCTTGAATTAAGCAATGGCTTCCTAGATATGAC 1657
                           ?i        i    i    ii   i       i   i          
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_208410584_   1658 ACCAAAAGCACAAACAACAACA-ACAAAATA--TAAATTGGACATCATTA 1704
                                      i      v - v      --          v    i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_208410584_   1705 AAATTAG----TTTTGTGCTTTA-------CCCCCAAAAAGGTGAAAAGA 1743
                               i----          i ------- ivi   i  i         
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

Transitions / transversions = 3.38 (44 / 13)
Gap_init rate = 0.03 (11 / 396), avg. gap size = 3.82 (42 / 11)  

 715 15.29 10.00 0.00  chr1_208410584_208413335.rev     2089  2258 (494)    L1M4_orf2#LINE/L1      685   871 (37)  

  chr1_208410584_   2089 AACAACGTGAAAAGAAAATCTGCAGAATGGGAGAAAATATTTGCCA--TA 2136
                           v  v         v  i ii                      v --i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_208410584_   2137 TATACCTGATAAAGAAGTCGCATTTAGAATATATAA-GA--TATTACAAC 2183
                             i       i i v i i  ii           -  -- v       
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_208410584_   2184 TCAACAATAAAAAGA----TAATCCAATTAAAA------CAAAGCATCTC 2223
                             i          ----   i      ?   ------     v  i v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_208410584_   2224 AATAGAGATTTCTCCAAATAAAATATACAA--GGCCA 2258
                               v           v  i        --     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.03 (6 / 187), avg. gap size = 2.83 (17 / 6)  


3064 24.89 1.76 1.76  chr1_208441898_208444150.rev      855  1762 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_208441898_    855 TGGAAAAATATTTCATGCTCATGGATAGAAAGTATCAATATTTATAAAAT 904
                               i    ii    i        v i   vv i      vv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_208441898_    905 GGCCATACTGCCAAAAGCAATTTACAGAGTCAATGCTATTCCTATCAAAC 954
                            v     v  v   vii  i      v    i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_208441898_    955 TACCAATAACATTCTTCAGAGAACTAGAAAAAACT-ATTTTAAAACTCAT 1003
                          v   iivi v  i  iiv    v v  v  i-  -  ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_208441898_   1004 ATGGAACCAAAAAAGAGCCTGAATAGCCAAGACAATTCAAAGCAAAAAGA 1053
                               viiv  ii  v  v          i     iivi iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_208441898_   1054 ACAAGGCTGAAGGCATCAGGTTACCCAACTTCAAACTATACTACAAGGCT 1103
                             i i  i   vv   vii v     i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_208441898_   1104 ACAGTAACCAAAACAGCATGGTACCACTACAAAAACAGACACATAGATCA 1153
                                i   i    ii      iivi i  ii i     i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_208441898_   1154 ATGGAACAGAATAGAG-GCCTAGAAATAAAGCTACACACTTAAAACCAAC 1202
                               i     v   - i i         v i i   i   viii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_208441898_   1203 TGATTTTCCACAAAGTTGACAAAAACAAGCAGTGGGGAGAAGACTTTCTA 1252
                                 v    i v  v   i v  vv  i      i ii ivv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_208441898_   1253 GTCAATAAATGGTGCTGGGATAATTG-ATAGCTATATGCAGAACACTGAA 1301
                         v    i              i  i  -   ? i i     i  v v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_208441898_   1302 GCCGGACCTCTTACTTTCGCTATATACAAAAATCAACTCAAGATGTATTA 1351
                          ii     i  vv  iv i i            i       i   v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_208441898_   1352 AAGACTTAAGTGAACAACCTAAAACTACAAAA-TCT-GGATGATAATCTA 1399
                         ?    i   i  v vi v         i    -   -i  v  v  iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_208441898_   1400 GGAAATAACACTGTG-GACATGGGACCTGGCAAAGATTTCAT-GATGAAG 1447
                           ?i-   vv  vi -   v v  iiiv     v i    v -   - v 
  L1M4_orf2#LINE/    550 GGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr1_208441898_   1448 ACACCAAAAGCAATAGCAACAAAAGCAAAAATTGACAAATGGGACCTAAT 1497
                                     vv           v      v  i    v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_208441898_   1498 TAAA-TTAAAGAACTTCTGCACAGCAAAAGAAACTATCAACAGAATAAAC 1546
                         i   -     -     i  ii vv    i  v        v i i i  v
  L1M4_orf2#LINE/    648 CAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_208441898_   1547 AGACAACCTACAGAATGGGAGAAAATATGTGCCTCCCATAGAGAAAACTA 1596
                                 i                   v   ------------   ii 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGC------------AAATCA 734

  chr1_208441898_   1597 TGCCTCTGACAAAGGTCTAATGTCCAGAATCTATAAGTAACT--TA-AAT 1643
                          iiv     i  i  v  vi i        v     iv    --  -  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_208441898_   1644 TTA-TAAGCAAAAAACAA----CCTCATTAAAAAGTGGGTAAAGGACATG 1688
                          i -   vv    i    ----  iv   ?    i    i      iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_208441898_   1689 AACAGAAAGTTTTCAAAAGAAGACATACACACGGCCAACAAGCATATGAA 1738
                           i   v v  i  v        i     v i      i     i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_208441898_   1739 AAAATGGTCAACATCACTAACTAT 1762
                           i   v         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (130 / 92)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.88 (32 / 17)  


3183 26.88 1.00 0.55  chr1_208515388_208517698.rev      917  1820 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_208515388_    917 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 966
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_208515388_    967 GGCCATACTACCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1016
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_208515388_   1017 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1064
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_208515388_   1065 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAACCAAAAG 1114
                                viiv  ii  v  viv  vi    iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_208515388_   1115 AACAAAGCCGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1164
                                ii     vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_208515388_   1165 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGATC 1214
                                 i   i    ii         i iv ii i   v  i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_208515388_   1215 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 1262
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_208515388_   1263 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 1312
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_208515388_   1313 CTATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCATATGTAGAAAGCT 1362
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_208515388_   1363 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1412
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_208515388_   1413 TTAAAGACTTACATGTTTGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1462
                          i ?    i  v    vv  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_208515388_   1463 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1511
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_208515388_   1512 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTCACAAATGGGGTCTA 1561
                         vi            vvi          vv     vv i    v  iii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_208515388_   1562 ATTAAACTAAAGAGCTTCTGCACAGCAAAACAAACTACCATCAGAGTGAA 1611
                           i   v v  i i   i  ii vv    iv v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_208515388_   1612 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 1661
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_208515388_   1662 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 1711
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_208515388_   1712 AAAACAA----CCCCATCAAAAAGTGAGCGAAGGACATGAACAGACACTT 1757
                           i    ----   v  i?    i  i  i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_208515388_   1758 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 1807
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_208515388_   1808 CATCACTAGCCAT 1820
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3023 24.83 3.85 1.02  chr1_208521548_208527429     4524  5405 (477)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_208521548_   4524 GGAAAAACATTCCATGCTCATGAATAGGAGAAATCAATATTGTTAAAATG 4573
                              i i  i     i     i  v   ii v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_208521548_   4574 GCCATACTGCCCAAAGCAACGTATAGATTCAATGCTATTCCTATCAAACT 4623
                           v     v      vii iv  i        i  v  i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_208521548_   4624 GCCAACGACATTCTTCGCAGAATTAGAAGAAACT-ATTTTAAAATTCATA 4672
                         v   i vi v  i  i      v v  v-  i  -  ii           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCATA 150

  chr1_208521548_   4673 TGGAACCAAAAAGAGCCCA-AACAGCCAAGGCAATCCTAAGCAAAAAGAG 4721
                              viiv  i ii    -  i      ii     i i iv  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_208521548_   4722 CAAAGCTGGAGGCATCAGGCTACCCAACTTCAAACTATACTACAAGTCTA 4771
                              i      vv   vi  v     i      viv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_208521548_   4772 CAGTAACCTAAACAGCATGGTACTGGTATACAAAAAGACACACAGACCAA 4821
                               i v i    ii         i   vii v     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_208521548_   4822 TGGAATAGAATAGAGAGCCCAGAAACAAGGCCACACACTCCTACAACCAT 4871
                                    v     i       i  iv   i   i --  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAA 348

  chr1_208521548_   4872 CTGATCTTTGACAAAGCTGACAAAAACAAGCAATAGGGAAAGGATTTCCT 4921
                         i    i  i     i v  v   i v  vv    i       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_208521548_   4922 GTTCAATAGATGGTGCTGGGATAACCG-AT-GTCATATGCAGAAGATGGA 4969
                         v     i i            i   i -  -?i  i     i    vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_208521548_   4970 AACTGGACCCCTTCCTTACACCACAGACAAAAATCAACTCAAGATGGATT 5019
                          ii         v   i      i v        i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_208521548_   5020 AAAGACTTAAATGTAAAACCCAAAATGATAGAACCCT-GGAAGACAAC-- 5066
                          ?    i         i v i    iv   i   i  -i     v   --
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_208521548_   5067 ----------CTTCAGGAC--TAGGCATGGGCAAGGATTTCATGACAAAG 5104
                         ----------    iv   -- i  i- i     v i    v iivv v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chr1_208521548_   5105 ATGCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTAAT 5154
                          ii         vvv          v      v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_208521548_   5155 -AAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCCACAGATTAAAC 5203
                         -    i    i -   i  ii vv    i  v      v v i v i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_208521548_   5204 AAACAACCTACAGAATGGGAGAAAAT-TTTTCTAACTATGCATCTGACAA 5252
                          i      i                 -   v v  ii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_208521548_   5253 AGTTCTAATATCAAGCATCTATAAGGAACTTGAATTATTTA-CAAGAAAA 5301
                         i vv  vi    v  v  v     i     ivv iv i i -i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_208521548_   5302 AAACAAG---CCCA-TTAAAAAGTGGGCAAAGGACATGAA----CACTTT 5343
                          i    i---    -  ?    i           iv    ----  i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_208521548_   5344 TC----AAAGACATACACATGGCCAACAAGCACATAAAAAAAAAAAAACT 5389
                           ----i    i     v        i        i    i vi----  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG----CT 892

  chr1_208521548_   5390 CAACATCGCTGATCAT 5405
                                i????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (136 / 80)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 2.26 (43 / 19)  


 601 20.28 2.80 2.10  chr1_208559509_208561149      126   268 (1373)    L1M4_orf2#LINE/L1       37   180 (728)  

  chr1_208559509_    126 AATACTATTAAGATGTCAATTCGTCCCAAATTGATCTTTAGATGTAAAG- 174
                             i i        v    v vi             vi    vi  v -
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chr1_208559509_    175 A---CCAACAAAAATCCCAGCAGCCTTTTTTTTCATAGAAATTTACAAAC 221
                          ---  v iv           v         ---ii       v    i 
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTT---GCAGAAATTGACAAGC 133

  chr1_208559509_    222 TGATTCTAAATTTTACATGGAAAGGCAGTAGACCTAGAACAGCCAAA 268
                             i     v  i i       v   ivi    i    i       
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.02 (3 / 144), avg. gap size = 2.33 (7 / 3)  

2106 21.57 13.87 1.54  chr1_208559509_208561149      500  1148 (493)    L1M4_orf2#LINE/L1      180   908 (0)  

  chr1_208559509_    500 AACAATTTCGAAAAAGAAATACAAAGGTAGGGGACTCACACTATCTGATT 549
                               i i         iv      v i i           vi ii   
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_208559509_    550 CCAAGAGTTGCCATAAAACGATGGTAATCAAGACAGTGTATTATTTGCAC 599
                         i   i v  i i i   i v ii                iv  i v   i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_208559509_    600 A--------------GACCAATAGAACAGAAT--AGAATTTGGAAATAAA 633
                          --------------  i    i   i     --   i iii        
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_208559509_    634 TCCATACAGATATTGTCAACTGATTTTCAACAAAGATGCTAAAGTAATTC 683
                         i       vv   v     i        i    i i   i  iiiv    
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_208559509_    684 AATGGGGAAAGAAAAGTTTTCCCCACAAAATGGTGCC---ACAACTGGCT 730
                                      v   i  ii v     -      i---        v 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAA-TGGTGCTGGGACAACTGGAT 428

  chr1_208559509_    731 ATCCA-------AAGCAC----CTTGATGCCTACCTTGTACCATACACAA 769
                          ?   -------   v i----i v  iv       iii      i    
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_208559509_    770 AAGTCAACTCAAAATGGATCACACAGGGCTATATATAAAA-CTTAAACTA 818
                           i i                ? -- iv   v  i   i -  v      
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWA--GACCTAAATGTAAGAGCTAAAACTA 526

  chr1_208559509_    819 TAAAACTTTTAGGAGAAAAC------------TTTTGTGATTTTGGATTA 856
                                i    i       ------------i  i    ii    i   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_208559509_    857 GGCA--GACTTCTTAGATA---------AAATACAACCTATAAAAGAAAA 895
                             -- ii          ---------  ii    v v i         
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_208559509_    896 AAACATTAATAAACTAGATAGATTTTATCAAAACTTAAAACTTCT---TT 942
                           --- vi     i i  i----  i       i v       i ---i 
  L1M4_orf2#LINE/    627 AA---TAGATAAATTGGAC----TTCATCAAAATTAAAAACTTTTGTGCT 669

  chr1_208559509_    943 TTAAAAGACA-------GATACT--AAAGATA-----CATATTGAGAGGG 978
                          i   i    -------  v v --     i -----  v v  i   ii
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_208559509_    979 AATATTTGTAAAACATACATCTGATAAAGGATTAATATCAAGAATATATA 1028
                                 i   v    i         i   i vi    v          
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_208559509_   1029 AATAAC-----------AATAACAAAAAGACAAAAAAACCTAATAAAAAA 1067
                           v   -----------     i           v  v  v v ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_208559509_   1068 AGAATAAAATATTAGAATAGGCACTTCACTGAAGA-----TACAGATGAC 1112
                         v iii   iv   v      i  i   v ii    -----    i   i 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_208559509_   1113 AAATAAGCCTGT---AAGATGCTCAACATCATTAGCCAT 1148
                         v       vii ---                ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.26 (95 / 42)
Gap_init rate = 0.03 (20 / 729), avg. gap size = 5.00 (100 / 20)  


2634 25.96 6.49 1.27  chr1_208584738_208586692.rev      602  1464 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_208584738_    602 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATATCATTAAAAT 651
                               i i  i     i               v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_208584738_    652 GGCCAAACTGCCCAAAGCAATCTACAGAGT----GCTATTACTATCAAAC 697
                            v v   v      vii         v ----  v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_208584738_    698 TATCAACATCATTTTTCACAGAATTAGAAAAAAAAAACTCTTCTAAAATT 747
                          vi  i vv v     ii     v v  v  ivvi ---- i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA----TCCTAAAATT 146

  chr1_208584738_    748 CATATGGAACCAAAAAAGAGCGTAAATAGCCAAACCAATCCTAAGCAA-A 796
                                  viiv  ii  v vvi          v     i i iv  - 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_208584738_    797 CTAACAAAACTGAAGGCATCACATTACCCAATTTCAAACTATTT--TGTA 844
                         vv      ii  i   vv     i v            -- i  -- ii 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACA 244

  chr1_208584738_    845 AGGCCACAGTAACCAAAACAGCATGGTACTGGTACACACACAGTCACATA 894
                          i  i       i   i    ii         i i viv i  v  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_208584738_    895 GA-CAGCAGAATAGA-----GAACCCAGAGATAAAGCTGCACACCTGCAG 938
                           -  iii       -----  ii     i     v iii   ii iii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_208584738_    939 CCATCTGATCTTCAACAAAGTCGATAAAAATAAGCAATGGGAAAAGGACT 988
                         i  vi    i   i    i vi vi  i vi vv       i    i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_208584738_    989 CCCTATGCAATAAATGGTACAGGGATAGCTGGCTAGCCCTATGCAGAAGA 1038
                         vi  v v   i       i v    i i    v  ?  vi     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_208584738_   1039 ATGAAACTGGACCCCTACCTTTCACCATATACAAAAATTAA-----GGTG 1083
                              ii             iv                   -----ii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_208584738_   1084 GATTAAATATTCAAATGTAAGACCTCAAACTCTAAGAATCCTAGAAGAAA 1133
                            i ? v iii          v  v     v   i v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_208584738_   1134 ATCAGCATTGGGAAAGA-ATTTGTGAC----------------------T 1160
                          ----   v  ?iv i -v  i     ---------------------- 
  L1M4_orf2#LINE/    545 A----CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_208584738_   1161 AAAT----CCTCAAAAGCAATTGCAACAAAACCAAAAATGGACAAGTGGG 1206
                          i  ---- vi        vvv         vv      i  i  i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_208584738_   1207 ACCTAATTAAGCAGAAGAGCATCTGCACAGCAAAAGAAACTATCAACAGA 1256
                           i v  i  ivvv  i i v i  ii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_208584738_   1257 GTAAA----CAGCCTACAGAATGGGAGAAAATATTTGCAAACTATGCATG 1302
                           i  ----  i  i                          ii  ii  v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_208584738_   1303 TGACAAAGGTGTAATATCTAGAGTCTATAAGGAACTT----AATTCAACA 1348
                            i  i  vv vi    i   i v     i     i----  i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_208584738_   1349 AGCAAAAACCAAATAACCCTATTAAAAAGTGGGCAAAGGACATGAAAAAG 1398
                          vv    iv          v   ?    i           iv    v ii
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_208584738_   1399 CATT-CTCAAAAGAAGACATACAAGCAGTCAACAA--ACATGAAAAAAAT 1445
                             -   v        i      iii i   i  --         i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-T 889

  chr1_208584738_   1446 GCTCAGCTTCAGTAATCAT 1464
                              i v   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (135 / 85)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.94 (67 / 17)  


4035 17.38 5.98 1.50  chr1_208646635_208648497.rev      504  1372 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_208646635_    504 TAGAAAGACATCCAA-GTTCATGGACCAGAAGATTTAACATTATTACGAT 552
                          i      i    v -         iii     i    i   i   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_208646635_    553 GTCAATACTTCCATAACTGATCTACACAGTCACTGCAATTCCTATCAAAA 602
                          v       i  vv  i         v v   vi     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_208646635_    603 TCCTAGCTGGCTATTTTGCAAACAATGACAAGCTGAAACTAAAATTTGTA 652
                            i     v  v       i v v           vv        ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_208646635_    653 TAAAA------GAGACCCAGAACAGTCGAGACAATCTTGAAATAAAAGAA 696
                          ii  ------ i         i  i i i            v i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_208646635_    697 GAAAACAGAAGTAG-----------GATTTCAAAACCTACTACAAAGCTA 735
                         v   iiv i  v v-----------i          i             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_208646635_    736 CAGTAATGAAGACAATGCAGAACCATAATAAGGACAGATACATAGATCAA 785
                                v      i  ii v  iivv       i   i i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_208646635_    786 TGGAAT-----TGAGAAGTCAGAAATAAACCCTCACATTTATGGTCAATT 830
                               -----     ivi             vi                
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_208646635_    831 GATTTTTGGCAGATTTTTACCAAGGGTGCCATGACGATTCAATGGGCTAA 880
                               i i  -----------         v   v          v-  
  L1M4_orf2#LINE/    351 GATTTTCGACA-----------AGGGTGCCAAGACCATTCAATGGGG-AA 388

  chr1_208646635_    881 AGAATAGTCTCTTTAACAAGTGATGGTGAGAAAGTTAAATATCCATATGT 930
                                   i  i     i  i  v  i  v ii ii   ?   i   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_208646635_    931 AAAA-AAT----TTGAATGCCTAACTCACACCATAACACAAAAATAAACT 975
                             -   ----   i iv    v           -i        v    
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATA-TACAAAAATTAACT 487

  chr1_208646635_    976 CAAAACGAATCACAGGCCTAAA--------CTAAAA------AACT---A 1008
                              i i    ?  i      --------      ------    --- 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_208646635_   1009 GAAGAAAGCATTGGAGTAAATCCTTGTTACCTCAGAAGAGGCAATAGTTT 1058
                                i   v  ?       i i  v    ii ivv       i    
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_208646635_   1059 CTTTGATTTAACATCAAAAGCATAAGTGACAAAGGAAAAAACAGATAAAC 1108
                            v   v i   i        i   ii     i       i       i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_208646635_   1109 TGAACTTCATCAAAATTATAAAGTTACATGTGTCAAGAGACACCATCAAG 1158
                           i               v   v  vii  iv    ii     i      
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_208646635_   1159 AAAGTAAAAACACAACCCACAGAAT------AAATCATTGCAAATCAT-T 1201
                              i    v              ------    vv           - 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_208646635_   1202 ACATGATAAGGGACTTATGTCCAGAATATATAAAGAATGCTTACAACTCA 1251
                          iv             i i                  iv           
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_208646635_   1252 ACAATAAAAAGACAAATAACCCAATTAGAATATGGGCAGAAGATCTGCAT 1301
                          i                        ?i  v       i i   i  v  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_208646635_   1302 AGACATTTCACCAAGGAAAATATATAAATGGCCAATAAGCACATGAAAAG 1351
                                  v    i   i     i                         
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_208646635_   1352 ATGTTCAGCATCACTGGCCAT 1372
                            i   i     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (96 / 51)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.64 (65 / 14)  


1874 22.94 17.46 3.03  chr1_208840599_208843010.rev      499  1191 (1221)    L1M4_orf2#LINE/L1       28   820 (88)  

  chr1_208840599_    499 GGAAA--TTAATATTGTTAAAATGTTCATCCAAAGCAATATATAGATTTA 546
                             i--             i   ----------      i------- v
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATG----------GCAATAC-------TC 60

  chr1_208840599_    547 TCCAAAGCAATATATAGATTTAACCCAGTCCCTATCAAAATTCCAGTGGC 596
                         i     vii  v  i     i   v  i             i    iv  
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr1_208840599_    597 ATTCTTTACAGAAATAGAAAAAACAAT---AAAATTCATTTGCAACCACA 643
                         v  i   i       v  v  ivii  ---         v  v  vii  
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr1_208840599_    644 AAAATTCCCAAATAGCCAAAGCAATACTGAAAAACGA----AAAGTTAGA 689
                          iiivi  vi          i    vi       vi ----      i  
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_208840599_    690 GGTATCATACTTCCTGATTTAAAAGTATATTACAAAGCTATAGTAATCAA 739
                           vv   i      ii    v   iiv  i          i         
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr1_208840599_    740 AACAGAATAGTTCTGGCATAAAAACAGACACATAAACCAGTGGAACAGAA 789
                         i    vi i  v         ii i     i   i i  i     i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_208840599_    790 TAGAGAGCCCAGAGATAAATTCAACCGTATATG----------------- 822
                          v     i     i     ii  vv i v    -----------------
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr1_208840599_    823 -------------------------------ATAGTCTCTTCAATAAA-G 840
                         -------------------------------       i     i   - 
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_208840599_    841 ATGCTAGGAAAACCATACATCCACATG-AAAACAATGAAATTGGACCTTT 889
                         i    i   v   iiv i ?       -    v      i       ii 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_208840599_    890 AT-----ACCATACACTAAAATCATCTTAAAAT----CA----------- 919
                          i-----      i  v     i v  i     ----  -----------
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_208840599_    920 ----------------------------------ACATAGGGA-AAATGC 934
                         ----------------------------------       ?i-    - 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-C 559

  chr1_208840599_    935 TCCTTGACATTGGCCTTGGCAATGATTTTTGTTTTTATATTATATCAAAA 984
                          i v    v    vi v       i   i --- vv    v i i     
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCT---TAGATATGACACCAAAA 606

  chr1_208840599_    985 ----AGGGTACAAAAGCAAAAA-AACTAAATGGGACA-CATCAAACCAAA 1028
                         ---- i vv       v     - iv     v    v-       viv  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_208840599_   1029 AAGCTTCTGCATGGCAAAGGGAACAATCAACAAAATGAAAAGGTAACCTA 1078
                           i   i  iiivv      iv  v     v   i       ii    i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_208840599_   1079 TGGAATGGAAAAAAA-ATTTGCAAACCACATATCTGGTAAGGGGTTAGTA 1127
                         ii      i i    -         i  i       i      ii v   
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_208840599_   1128 TCCAAAATTTATAAAGGACTCTTACAACTCAATAGCAGAAAAATAAATAA 1177
                             i   v       i                 ii i   i i      
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_208840599_   1178 CCTAAAAAAAAAAT 1191
                           i  vv?      
  L1M4_orf2#LINE/    807 CCCAATTWAAAAAT 820

Transitions / transversions = 1.84 (101 / 55)
Gap_init rate = 0.02 (18 / 793), avg. gap size = 7.89 (142 / 18)  

 354 19.78 5.49 0.00  chr1_208840599_208843010.rev     1488  1578 (834)    L1M4_orf2#LINE/L1      784   879 (29)  

  chr1_208840599_   1488 CTCAAAAACAAATAAATAAATAA---AAT--AAAAATGGACAAAAGACCT 1532
                              v  i   v i i      ---   --        i    i  ii 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_208840599_   1533 GAACAGACATTTCTCTAAAGAAGACATAAAAATGGTCAACAGGTGC 1578
                            i           i        i   v      i   i i ii 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

Transitions / transversions = 5.00 (15 / 3)
Gap_init rate = 0.02 (2 / 96), avg. gap size = 2.50 (5 / 2)  


3053 17.85 9.49 0.71  chr1_208864578_208866278.rev      505  1210 (491)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_208864578_    505 AAAACTTAACTTTGCAATTATAAATAACCCAATAACAGCCGAAACAATCC 554
                             i i -- v  v  v ii  ivi     i-  i    i        i
  L1M4_orf2#LINE/    141 AAAATTCA--TATGGAAATGCAAGGGACCCAG-AATAGCCAAAACAATCT 187

  chr1_208864578_    555 TGAAAAAGAAAAACAAAGTAGGAAGATTCACACTATCCCATTTCAAAACT 604
                                   i        v   i  i       vi  v           
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_208864578_    605 TACTATATAAAACA-AGTAATCAAGACAGTGTGGTACTGACACAAGAACA 653
                              i -  ivi -                        i  i   i i 
  L1M4_orf2#LINE/    238 TACTACA-AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_208864578_    654 GACATACAGATCAATGGGATAGAATTGAGAATCCAGAAATAAAACCATG- 702
                               i          i            i            v    i-
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_208864578_    703 -----TG-----CTAATTTTCAACAAAAGGGCCAAGACCATCTAACGGGG 742
                         -----  -----i i      i    ii v           ii  i    
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_208864578_    743 AAAGAA--GTATTTTCAACAAGTGGTGTGGAGATAAATGTGATAACTACA 790
                               --  v          i     iv i  i  v  -    ? i   
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG-GATAKCCACA 435

  chr1_208864578_    791 CACAAAATAATGAATTTGAATCCTTAAGTCATACCCTATATAAAAATTAA 840
                         ii     v      v   i i  i  vv   i   v    i         
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_208864578_    841 CTAAAAATGG-CCAAAGACCTAAATGTAAAGGTTAAAATTACAAAATTCT 889
                           v       -i  ?              ii i     i  i    i   
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_208864578_    890 TAGAAGAAAACACAG-AGTAAATCTTCATAGCCTCATATCTGGGAAAGGA 938
                                     i  -?          i ii   iivi iv  v  v  v
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_208864578_    939 TCCTTAGAAATGACTCCAAAAGCACAAGTAACAA--GAAAAAAGAGA--A 984
                          i      v     v             i     --       v   -- 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_208864578_    985 TTTAGACTTACTCAAAATTTAAAACATTTGCGCTTCAAAGGATACCACCA 1034
                         v  i     vv        v     v    i           i  i i  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_208864578_   1035 AGAAAGTGAAAAGACA---------------------------------- 1050
                                         ----------------------------------
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_208864578_   1051 --------CAAGGGGCTTATATCAAGGACATATAAAGAATTCTTACAACT 1092
                         --------i     i   i    v  i i          i          
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_208864578_   1093 CGATAA---AAAGACAAATAAC--AATTCAAAAGTGGGCAAAGGATCTAA 1137
                          i    ---             --    ?    i            i i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_208864578_   1138 AGAGTCATTTCTCCAAGGAACATATACAAATGGCCAATAAGCATGTTCAA 1187
                          v  v           i   v                      ii vv  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_208864578_   1188 AGACACTTGACATCATTAGTAAT 1210
                            ii  ii      ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (84 / 38)
Gap_init rate = 0.02 (15 / 768), avg. gap size = 4.80 (72 / 15)  


3656 23.10 2.01 0.67  chr1_208930579_208936000     4034  4929 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_208930579_   4034 TGGAAAAATATCCTATGGTTCATGGATTGGAAGAACTAGCAT------AA 4077
                               i      i  -                 vi  ii  ------i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_208930579_   4078 TGTCCACACTACCCAAAGCAATCTACAGATTGAATGCAATTCCTAT-AAA 4126
                           v v i   v      vii           v  i     i     -   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_208930579_   4127 ATACCAATGACATTCTTTACAGAAGTAGAAAAAA-AATCCTAAATTTTGT 4175
                           v   iivi v  i   i     i v  v  iv-i        v  ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_208930579_   4176 ATGGAACTACAAAAAACCCCAGATAGCCAAACCAATCCTGGGCAAAAAGA 4225
                               v i   iii    vii         v     i  iiv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_208930579_   4226 ACAAAGCTGAAGGCATCACACTACCTGACTTCAAAATATACTACAAAGTT 4275
                               i  i   vv       v  ii i       iv          i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_208930579_   4276 ATAGTAAACAAAGCAGCATGGTATTGGCATAAAAACAGACACATAGACCA 4325
                          i     v   ii   ii     i        ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_208930579_   4326 ATGGAACAGAACAGAGAATCTAGAAATAAATCCATGTATATGCAACGAAC 4375
                               i    iv    i  i         i    ii  v iiiiiv  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_208930579_   4376 TCATTTTTGACAAAGGCACCAAGAAAATACAATTGGGAAAGGATAATCTC 4425
                          v     i     i  ii      vv  v    v       i   i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_208930579_   4426 TTCAATAAATGGTGCTGGGAAAATTGGATATCCATATGCAGAAGAATGAA 4475
                              i              v  i      ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_208930579_   4476 ACTAGACCCCTATCTCTTACTATATAGAAAAATCCACTCAAAAT------ 4519
                         ii i        i   vi  i     v      iv         ------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_208930579_   4520 -AGACTCAAATCTAAGACTTGAAATTATGAAACT---AGAAGAAAACACT 4565
                         -    ii    v     vi i   i   i     ---           iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_208930579_   4566 GGGATAATGCTTTAGGACACTGGTCTGGACAAAGATCTTTTTGGTAAGAC 4615
                           ?i   vv   iiv   vi   vi i i   v i i i  v i  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_208930579_   4616 CTCAAAAAGCAGAGTCAACAAAGGCGAAAACAGAAAAATGGGATTACATT 4665
                         vi     -   v iv       i vi    i   v    v   i v   i
  L1M4_orf2#LINE/    600 ACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_208930579_   4666 AAGCTAAAAAGCTTCTGTACAGCAAAGGAAACAATCAACAAAGTTAAGAG 4715
                           iv v    i   i   i vv       v  v     v     v  i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_208930579_   4716 ACAACCTACAGAATGAGAGAAATTATTTGCAAACTATGCATCCAACAAGG 4765
                               i        i      v          ii  ii   ii i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_208930579_   4766 GATTAGTAACCAGAATATATAAGGAACTCAAACAACTCAATAGCAAAAAA 4815
                           i v   v             i      vv           ii     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_208930579_   4816 AGCCAAATAATTCAATTTTAAAATGGGCAAGAGATCTGAATAGAGATTTA 4865
                          --       ii     ?v           ii   i        v    v
  L1M4_orf2#LINE/    799 A--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_208930579_   4866 TCCCAAAAGATGATATTCAAATGGCCAAAAGGCATATGAAAATATGCTCA 4915
                            --     v     v           v i   i       v       
  L1M4_orf2#LINE/    847 TCC--AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_208930579_   4916 ACAACACTAATCAA 4929
                            v  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (131 / 73)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  


3266 26.57 0.66 0.55  chr1_208951703_208958085     4984  5890 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_208951703_   4984 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAACAT 5033
                              ii i  i     i        v      v i     ii v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_208951703_   5034 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5083
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_208951703_   5084 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5131
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_208951703_   5132 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5181
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_208951703_   5182 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAAGC 5231
                                i      vv    i  v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_208951703_   5232 AACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5281
                         v       i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_208951703_   5282 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCGCACATCTACAACT 5329
                                i    i--    i  --        vv  ii    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_208951703_   5330 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5379
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_208951703_   5380 CTATTTAACAAACGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5429
                           v  i      i i        v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_208951703_   5430 GAAACTGGATCCCTTCCTTACACTGTATACAAAAATTAATTCAAGATGGA 5479
                            ii    i    v   i    ii              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_208951703_   5480 TTAAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5529
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_208951703_   5530 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5578
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_208951703_   5579 AAACACCAAAAGCAATAGCAACAAAAGCCAAAATTGACAAATGGGGCCTA 5628
                         vi            vv           vv     v  i    v  i i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_208951703_   5629 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTTAA 5678
                           i   v v  i i   i  ii vv    i  v    i  vv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_208951703_   5679 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5728
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_208951703_   5729 AAGGGCTAATATCCAGAATCTACAAAGAACTCCAACACATTTACAAGAAA 5778
                          i  i  vi          v  i         iv   vv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_208951703_   5779 AAAA-AAACAACCCCATCAACAAGTGAGTGAAGGATATGAATGGATACTT 5827
                           i -   i     v  i? v  i  i ii      v     i  i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_208951703_   5828 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5877
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_208951703_   5878 CATCACTGGCCAT 5890
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3154 27.21 1.00 0.55  chr1_209219263_209225675     5017  5920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_209219263_   5017 TGGAAGAACATTCCATGCTCATCAGTAGGAAGAATCAATATCATGAAAAT 5066
                              ii i  i     i    vii v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_209219263_   5067 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5116
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_209219263_   5117 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5164
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_209219263_   5165 TATGGAACCAAAAAAAAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5214
                                viiv  iii v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_209219263_   5215 AACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTATACTACAAGGC 5264
                                i     ivv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_209219263_   5265 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5314
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_209219263_   5315 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACC 5362
                                i    i--    i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_209219263_   5363 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAACGGGGAAACGATTCC 5412
                          vi    i  i     ivv  v   i v  vvv  i       vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_209219263_   5413 CTATTTAACAAATGATGCTGGCAAAACTGGCTAGCCATATATAGAAAGCT 5462
                           v  i        i      v v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_209219263_   5463 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 5512
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_209219263_   5513 TTAAAGACTTAAATGTTAGACCTAAAACCGTAAAAACCCTAGAAGAAAAC 5562
                          i ?    i       v   v       ii     vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_209219263_   5563 CTAGGCA-ATACCATTCAGGACATAGGCGTGGGCAAAGACTTCATGTCTA 5611
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_209219263_   5612 AAACACCAAAAGCAATAGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5661
                         vi            vv           vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_209219263_   5662 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5711
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_209219263_   5712 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5761
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_209219263_   5762 AAGGGCGAATATCCAGAATCTACAACGAACTCACACAAATTTACAAGAAA 5811
                          i  i vvi          v  i  v      vi    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_209219263_   5812 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAATAGACACTT 5857
                           i    ----   v  i?    i    ii      v          i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_209219263_   5858 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5907
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_209219263_   5908 CATCACTGGCCAT 5920
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


1492 25.00 3.86 2.95  chr1_209275843_209280271.rev     2420  2859 (1570)    L1M4_orf2#LINE/L1        2   445 (463)  

  chr1_209275843_   2420 GAAGAGACACAACATGTCCATGGAT-GGAAGACTCAAT-CTG-------G 2460
                          i i   i ivv     i       -        i   -i  ------- 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_209275843_   2461 CCAATTCGCTCCAGATTTATACACATATTTAATGTAATTTCTATCAAAAT 2510
                         v    v v i   i   v  vi   v   i  i i   ii          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_209275843_   2511 CCCAGTAAGTAAGTAAAATCCCAAAATACATATACACAAGATTATTTTAA 2560
                              ivivivvv ---- iv  i  -----  vv     v v  ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTT----TTGCAGAA-----ATTGACAAGCTGATCCTAA 142

  chr1_209275843_   2561 AATGTATATGGAAAGGCAAAGGAATTAGAATAGCTAAACCAATCTTGAAA 2610
                            vi         v    i   vii        i   v           
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_209275843_   2611 AAGAAGAA---AGTAGAGAGACTCAGTCTATCCAATTTCAAGACTTATTA 2657
                                 ---   v iii      vv  vi          i     i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_209275843_   2658 TATAGCTATAGTGA---AGACTGTGGGATATTGGCAGAGAGGTAGACACA 2704
                         i v     i   i ---    v   v i  i     v ii i      i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_209275843_   2705 CAGATCAA--GACCACACAGAATAGAGAACCCAGAAGTAGACTCACACAA 2752
                         i       --  ---- i     v    ii      i  i  i  i   v
  L1M4_orf2#LINE/    293 TAGATCAATGGA----ATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_209275843_   2753 ATATGGCCAGCTGAGTTCTGTCAATGGTGCAAAAGCAATTCAAGGAGGAA 2802
                         v     i  ii   v  ii v   v     v  ii v      v i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_209275843_   2803 AGATAAGTCTTTTCAACAAATGGTACTGGAACAATTGAGCATCCATGGGT 2852
                            vv                   i    i    i  iii ?   iiv i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_209275843_   2853 AAAAGAA 2859
                                
  L1M4_orf2#LINE/    439 AAAAGAA 445

Transitions / transversions = 1.60 (67 / 42)
Gap_init rate = 0.02 (9 / 444), avg. gap size = 3.33 (30 / 9)  

1049 24.48 4.18 2.39  chr1_209275843_209280271.rev     3163  3497 (932)    L1M4_orf2#LINE/L1      439   779 (129)  

  chr1_209275843_   3163 AAAAAAAAAAAGTAAGGAACATCCACCTAAGTCTCACGCTTTATGGAAAA 3212
                             i  vi    v-   ----  -    --i     i iv   iv    
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTT-GGA----CC-CCTA--CCTCACACCATATACAAAA 480

  chr1_209275843_   3213 ATTAAC-----ATGGGTCACACACTTAAATATCAAATATATAACTG--AA 3255
                               -----    i   ? v  i     i v i vv  v    i--  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_209275843_   3256 GCATTTAGAA--AAAC-TAGGAGAAAATCTTCAGGATCTAGGGCTAAGCA 3302
                         i vi      --    -    ? v        iv  i  v   i  i   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_209275843_   3303 AAGAGTTCTTAAACTTGACACCAAAAGCATCATT--CATTTTTAAAAATG 3350
                          v iv      i iv              iv vi--  vvvvv      i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_209275843_   3351 GATAAATTGGA-TTCGTTAAAATTAAAGA-TTTTGCCTTTTGAAAGATGT 3398
                                    -   i i         i -     ivi  ii  i  iii
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_209275843_   3399 TGTTAAAAGGATGAAAAGACAAGCTATAAAGTGGGAGAAAATATTTGCAA 3448
                          i i  i iii           v i i i i                   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_209275843_   3449 ACCGTGTATCTGACAAAAGATTAGTATCTTGAATATATAAATAACTCTT 3497
                          i i i       i  ii  i v     iv           v       
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

Transitions / transversions = 1.86 (52 / 28)
Gap_init rate = 0.03 (11 / 341), avg. gap size = 2.00 (22 / 11)  

 320 26.76 2.82 2.82  chr1_209275843_209280271.rev     3797  3938 (491)    L1M4_orf2#LINE/L1      767   908 (0)  

  chr1_209275843_   3797 ACAAAAAAGCCTCTCAGAACTCTGAACTGCAAAACAGCAAGCAACATAAT 3846
                          i   i  --    i v     --  ivii    vii   ii   vi   
  L1M4_orf2#LINE/    767 ATAAAGAA--CTCTTACAACTC--AATAATAAAAAGACAAATAACCCAAT 812

  chr1_209275843_   3847 TATAAAATGCACAAAAGAC----ATAAACATTTCATGAAACGGCATATAT 3892
                          ?v      vi    i  i----   i       viv   viiv     i
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_209275843_   3893 GGATGACAAATAAACACCTGAAAAGATGTTCAACATTAATAGTCAA 3938
                         ii   i v     i   v          i       i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (25 / 12)
Gap_init rate = 0.02 (3 / 142), avg. gap size = 2.67 (8 / 3)  


3063 26.27 2.59 0.23  chr1_209324650_209330069     4041  4927 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_209324650_   4041 TGGAAAACACATCCCATGTTCATGGATGGGTAGAATCAATATTGTGAAAA 4090
                               i- i                 v  v   v i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_209324650_   4091 TGACCATACTGCCAGACGCAATCTACAAATTCAACGCAATTCCCATCAAG 4140
                           i v     v  vi vvii       i            i  i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_209324650_   4141 ATACCACCATAATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCAT 4190
                           v   v vvvv  i  ii     v v  v  ivii              
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_209324650_   4191 ATGAAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGGAAAAAGA 4240
                            i  viiv  ii  v  viv         i   vvi i ii  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_209324650_   4241 ACAAATCTGGAGGCTTTACATTATCTGACTTCAAACTATACTGTTAGGCC 4290
                              vi      vi i   i vi ii i      viv    iiv i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_209324650_   4291 ACAGTCACCAAAACAACATGGTACTGGTATAAAAATAGGCACACAGATCA 4340
                              v i   i   iii         i    ii    i  i i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_209324650_   4341 ATGGAACAGAACAGAGAACTCAGAAATAAAGCCAAATACTTACAGTCAAC 4390
                               i    iv    iii          v   v i i   ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_209324650_   4391 TGATCTTTGACAAAACAAACAAAAACATAAAGTGGGGAAAGGACA-TCCT 4439
                             i  i     iivviv   i v   vv i         i i -  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_209324650_   4440 ---------------------AATTGGCAAGCCACATGTAGAAGAATGAA 4468
                         ---------------------  i   vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_209324650_   4469 ACTGGATCCTCATCTCTCACCTTATACAAAAATCGACTCAAGATCGATCA 4518
                         ii    i  ii i   v    v           ii      i  v     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_209324650_   4519 AAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACATC 4568
                         ?    i     v     v  i    i      v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_209324650_   4569 AGACAAACTCTTCTAAACATTGGCTTAGGCAAAGAATTCATGACTAACAC 4618
                         i ?vv  v     vvi  v    v        v iv   v iiv  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_209324650_   4619 CCCCAAAGCAAATGCAACAAAGACAAAAATAAATAAATGGGACCTAATTA 4668
                         v  v      v v        iiv       i      v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_209324650_   4669 AACTAAAAAGCTTCCGTAGAGCAAAAGAAATAATCAGCAGAGTAAACAGA 4718
                           v v    i   ii  ivvv    i  v iv    iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_209324650_   4719 CAACCCACAGAGTGGGAGAAAATATTCACAAATTATGTATCTGACAAAGG 4768
                                    i              ii     i  i       i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_209324650_   4769 ACTAATATCCAGAATCTACAAGAAACTCAAACAAATCAGCAAGAAAAAAA 4818
                            vi          v  i  ii     vv    v   ii  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_209324650_   4819 CAAATAGTCCCATCAAAAAGTGGGCAAAGGACATGGATAGACAATTCTC- 4867
                               ii  v  i?    i           iv  i       v     -
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_209324650_   4868 AAATAAGATGTACAAACAGCCAACAAACATATGAAAAAAATGCTTAACAT 4917
                            v     i      ii     i  i  i       i -    i     
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACAT 898

  chr1_209324650_   4918 CACTAATCAT 4927
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 5.00 (25 / 5)  


 396 31.43 0.71 0.00  chr1_209331503_209335678     2472  2611 (1565)    L1M4_orf2#LINE/L1        1   141 (767)  

  chr1_209331503_   2472 TAGAAAGACATCCCTTGTGCACAAATCAGAAGAATTAACATTAT-AAAAT 2520
                          i      i     v   v  iii  ii     v    i   i -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_209331503_   2521 AACCATAATACCCAAAGCAATCTACGAATACAATGTAATTCCTACCAAAA 2570
                         ii v   v v      vii      ii  v   i i   i    i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_209331503_   2571 TACCAATAACATTCCTCACAGAAATAGAGAAAGCAATCCTA 2611
                          v   iivi v  ii ii       v  v  ivii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

Transitions / transversions = 2.14 (30 / 14)
Gap_init rate = 0.01 (1 / 141), avg. gap size = 1.00 (1 / 1)  

2495 26.70 3.47 0.27  chr1_209331503_209335678     2937  3685 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_209331503_   2937 ACCCTAAAATTAGTACAAAACCACAAGAGTCC--GAATAGCCAAAGCAAT 2984
                          i         vi  iii  vii    i v  --           i    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_209331503_   2985 ACTGAACCAAAATAATAAAGCTGGAAACATCATACTACCTCACTTCAAAA 3034
                         vi    vv i  v  i    i    iivv   i   v  iv i       
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_209331503_   3035 TATACTACAAAGCTACAGTAACCAAAATAACATGATATTGGTATTTAAAA 3084
                         iv                   i   i i iii  i  i   i  vvii v
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_209331503_   3085 AGACATG--GACCAGTGGAACAGAAC--AGA-TGCATGGAAAT----CTA 3125
                               i--  i  i     i    i--   - v  --     ---- i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCA--GAAATAAACCCA 333

  chr1_209331503_   3126 GGTATTTATAGCCA-CTGATTTTCAACAAAAGCACCAAGAACACACAATG 3174
                         vii      i i  -i        i    ii ii      v  iv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_209331503_   3175 GGGAAAGGACACCCTCTTCAATAAATGGTGCTGGGAAAATTGGATATCCA 3224
                                i i vi  i     i              v  i      ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_209331503_   3225 TATGCACAAGAATAAAACTAGACTCCTATCTTTCATCATAGA--AAAATC 3272
                         i     v      i  ii i   i    i  iv  i    v --     i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_209331503_   3273 AGCTCAAGACGGATTAATGACTTAAACATAATACCCAAAACTATAAAACT 3322
                          i     i i    i ?v   i    ii   v v i              
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_209331503_   3323 ACTATAGGGAAACATAGGAAAAACACTCTAGGACATC----CAGGCAAAG 3368
                         vi  v i i         ?iv  vv  iiiv   v i----i      v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_209331503_   3369 ATTTTACGGCTAGGACCTCAAAAGCACAGGGAACAAAA------ACAGAC 3412
                         i   ivii v  v   vi          i v       ------ i   i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_209331503_   3413 AAATGGGATTACATCAAACTAAAAAGTTTCTGCACAGCAAAGGAAACAAT 3462
                             v   i v       v v    ii  i  ii vv       v  v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_209331503_   3463 CAACAGAGTAATGAGACA-CCTGTTGAATGGGAGAAACTATATGCAAACT 3511
                            v i   i vi     -  iiiv            v   v      ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_209331503_   3512 ATTCATCCAATGGGGGACTAGTATCCAATATACACAAGAAGCTCAAATAA 3561
                           vi   ii  ii      v       iv   i i  ii i   vv i  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_209331503_   3562 CTCAACAGCAAAGAAAAAAA-AATCCTGTTAAAAAGAAGGTAAAGGATCT 3610
                              i ii   i i v   -  i  vi  ?    ivi  i       i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_209331503_   3611 GAATAGACATTTCTCAAAAGAAGACATGCAAATAGCCAAAAGATATATGA 3660
                                        v        i  i     i     v iii i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_209331503_   3661 AAAGATGCTCAACATAACTAAACAT 3685
                                        v ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (132 / 64)
Gap_init rate = 0.02 (12 / 773), avg. gap size = 2.33 (28 / 12)  


4164 17.07 3.58 1.61  chr1_209602899_209604734.rev      487  1353 (483)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr1_209602899_    487 ATTGAGAGA---AA-GTCATTAAGATGGCAATACTCCCCAAATTGA-ATA 531
                             ii   ---  -i ii                           -v  
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr1_209602899_    532 CAAATTCAGTGCAATCCCTATTAAAATTTCAACTTTTTTTTTTAACAGAA 581
                           i     ii           i     ii  i  vii      i-     
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG-CAGAA 123

  chr1_209602899_    582 AGGAACAAGTTGATCTTAAAATTCATATGGAAATGCAAAGGACTCTGAAT 631
                          vvi     i     i                      i    i v    
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chr1_209602899_    632 AGC-AAAACAATGTTAATAAAGA---------TTGGAGAATTCACATGTC 671
                            -        v  i v     ---------      i i     iv  
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr1_209602899_    672 CTGATTTCAAAACTCACTACAAATCTACAGTAATCAAGGCAGTGTGATAC 721
                          ii           i        v              i       i   
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_209602899_    722 TGGTATAAAGGTAACTGTATAGAT-AATGGCATAGAGTTGTGAGTTCAGA 770
                            i    i i  ivii       -     v     i   v    i    
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_209602899_    771 CATATATCCATATGTTTACAGTCAAGCGATTTTCAACAAAAA-GCAATCA 819
                         v   v i     ii    ii     vi       i    iii-  ---  
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC---CA 370

  chr1_209602899_    820 ATAGGAAGGAGAGATGGGGAGAGCAGAGAAATAGTCTT--CAACAAATGG 867
                          v vv vvv ---       i  ------         --          
  L1M4_orf2#LINE/    371 AGACCATTCA---ATGGGGAAAG------AATAGTCTTTTCAACAAATGG 411

  chr1_209602899_    868 TGCTGGGAAAACTAGATATTCACATGTAAAATAATGAATTTAGACCCCT- 916
                                 v    i    ?i      i    v      v  i       -
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_209602899_    917 CCTAACACCACATACTAAAATTAACTCAAAATAGACTAAAGATGGAAATG 966
                            v      i    v                i  ii ?   ivv     
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_209602899_    967 TAAGAGGTAAAAGCATAAAGCTCTTAGAAGGAAACATAAGTGTGTATCTT 1016
                               v     vi     i          i       i ?  iv     
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_209602899_   1017 CATGGCCTTGTAACAGGAAATGGTTT----GCTATGACACCAAAAAGCAC 1062
                          i  i     vivi   v        ---- v             -    
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA-GCAC 610

  chr1_209602899_   1063 AAGCAGGCAAAGTAAAAATAGATAAGATGGAATTCATCAAAATTAAAAGC 1112
                              ivv    v            iv    v                i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_209602899_   1113 TTTTGTGTGTCAAAGAACACTATCAA---AGTGAAAAGAGAATCTACAGA 1159
                                iv      i          ---          v  i i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_209602899_   1160 ATGGGAGAAAATATATGCAAATCATGTATCTGACTAGAGTCTAGTATCCA 1209
                                       v          i       iv  i v  v       
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_209602899_   1210 GAATATATAAAGAACTCTTTCAACCCAACAATAGAAGGATAAATAACTCA 1259
                                            v    i   i    i  i  i       i  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_209602899_   1260 ATTTTAAAATAGGCAAATGATCTGAA--AATGTTTCTCCAAAGAATCCAT 1307
                            ?v     i      v   i    --i ii             vvi  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_209602899_   1308 ACCCATGGCCAATAAGCACATGAAAAGATGT--AGCATTAGTCATCAG 1353
                           vv                          i-- i   i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (91 / 53)
Gap_init rate = 0.02 (18 / 884), avg. gap size = 2.50 (45 / 18)  


 472 18.48 2.17 0.00  chr1_209669122_209671800.rev      949  1040 (1639)    L1M4_orf2#LINE/L1       10   103 (805)  

  chr1_209669122_    949 ATTTCATTTTCATGGATTGCAAGA--TAATATTGTTAAAATGACAATTTT 996
                           ii   v           v    --            i   i    vi 
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_209669122_    997 CCCCAAACTGAACTACAGATTCAATACAATTCTAATCAGAATTC 1040
                                i   v            ii    i iv    i   i 
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 2.00 (2 / 1)  

2598 21.46 8.87 1.06  chr1_209669122_209671800.rev     1434  2188 (491)    L1M4_orf2#LINE/L1       95   908 (0)  

  chr1_209669122_   1434 TTAAAATTCTATGAGAATTTTTTGTTCACATGGATAAGCTGCCACTAAAA 1483
                          i     i i vvv vv       ivv v  v  i      viv      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_209669122_   1484 ATTTTTATGGAAGTTCAAAGAACTCAAAATTGCCATAACAATTTTGAAAA 1533
                         -  iv       i v   i i  i  i   v    v      i       
  L1M4_orf2#LINE/    145 -TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_209669122_   1534 AG-----TAAAGTAGGCAAACTTACACTAGCTGACTTCAATACTTA--A- 1575
                           -----i     v  vii   i     vv ii i     v     -- -
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_209669122_   1576 AAAGCTACAGTAATCAAGACAGTATGGTTCTAGGATAAG-ACAGGCACGT 1624
                                                i    v  i v     - i  i  ii 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_209669122_   1625 AGATTAATAGAACT--ATCAACAGTCCAGAAATAAGCCATTATAATTACA 1672
                             i   i   iv--  ii v             i  vv  i v   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_209669122_   1673 GTCAATTTACTTTCAGCAAGAGTCCCAAGGTGATTCAATGAGGA-----T 1717
                                v i    ii    i  v     iiv        i   ----- 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_209669122_   1718 AGTCTTTTCAACAAATGATGCTCAGAATATTAGATATACACACACCAGAA 1767
                                          i    vi  vv i i    ?v    ii v i i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_209669122_   1768 GATGAATTTAGACCGTTCCTTCACACCGTATATAAAA-TGAACTAAAAAT 1816
                         i     v  i    vi v i       i    i    - v    v     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_209669122_   1817 GAATCACAGACCT----GTAACA--T-------TAAAACTTCTAAAAGTA 1853
                          i    ?      ----    v -- -------       ii  i   v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_209669122_   1854 AACAGAAGA--AAATCTTCATGATCTTGGGATACTCGAAAAGTTCCTGGG 1901
                             v i ?--        i   i      v  vv i viiv   i i i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_209669122_   1902 TATGACA-----GGCATAACCCAAAAAAGAAAAAATATATATAAATTATA 1946
                                -----i   i  v v v             v   --    iv 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA--AATTGGA 641

  chr1_209669122_   1947 CATCATATCAAAGCTAAAAGCTTTTGAGCTTCAAATGACACCACTAAGAA 1996
                          v    --    ii     i      v        v     i ii     
  L1M4_orf2#LINE/    642 CTTCAT--CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_209669122_   1997 AACTAAAAGGC----TACAGACTGGGGAGAAAATATTTACAAATCACTTA 2042
                          iiv     i ----i     v    -           i       iv  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGG-AGAAAATATTTGCAAATCATATA 738

  chr1_209669122_   2043 TCTGATAAG--ACTGTTTATACAGAATATATTCAGAACTCTTACAACTCA 2090
                                  --   - v   v          vv                 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACT-TGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_209669122_   2091 ATGATAA------------CCCAATCAAAAAAATGGGTA---GATTTTAA 2125
                           i    ------------      i?     -    i ---     v  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chr1_209669122_   2126 TGGACATTTCACCAAAGA---TATATGAA-----AA-AAGCAGAGGAAAA 2166
                          i        v       ---    ii  -----  -     v v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_209669122_   2167 CATGCTCAACATCATTAGCCAT 2188
                         v             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (90 / 68)
Gap_init rate = 0.03 (25 / 814), avg. gap size = 3.00 (75 / 25)  


3121 26.77 1.11 0.66  chr1_209674551_209679228.rev     3284  4187 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_209674551_   3284 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCCATATCGTGAAAAT 3333
                              ii    i     i      i v      v iv    i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_209674551_   3334 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCACCAAGC 3383
                            v     v     iv i  i           i  v     i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_209674551_   3384 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3431
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_209674551_   3432 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 3481
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_209674551_   3482 AACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGGC 3531
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_209674551_   3532 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAATAGAGATATAGATC 3581
                                 i   i    ii         i iv ii     v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_209674551_   3582 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 3629
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_209674551_   3630 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAAGGATTCC 3679
                          vi    i  i     ivv  vv  i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_209674551_   3680 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3729
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_209674551_   3730 GAAACTGGATCCCTTCCTTACACCTCATACAGAAATCAATTCAAGATGGA 3779
                            ii    i    v   i     vi     i    i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_209674551_   3780 TTAAAGACTTAAACGTTAGACCTAAAACCATCAAAACCCT-AGAAGAAAA 3828
                          i ?    i    i  v   v       i  -     i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chr1_209674551_   3829 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3878
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_209674551_   3879 AAACACCAAAAGCA-ATGTCAACAAAAGCCAAAATTGACAAATGGGATCT 3927
                         vi            - v -         vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_209674551_   3928 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3977
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_209674551_   3978 ACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 4027
                          v  i     i   iv            v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_209674551_   4028 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 4077
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_209674551_   4078 AAAAACAA----CCCCATCAAAAAGTGGGCGAAGGACAAGAACAGACACT 4123
                            i    ----   v  i?    i     i     ivv   i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_209674551_   4124 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 4173
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_209674551_   4174 CCATCACTGGCCAT 4187
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2794 25.73 3.24 1.68  chr1_209700350_209704610.rev     2883  3776 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_209700350_   2883 TAGAAAAGCATTCCATGCTCATGGAT-AAAAGAGTCAGTATTATTAAAAT 2931
                          i    iii  i     i        -ii    v i i    i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_209700350_   2932 TACCATACTCCCCAAAGCTATTTACAGATTCAATGCTATTCCTATCAAAC 2981
                         vi v            viv  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_209700350_   2982 TATTAATGACATTTTTTCACAGAATAAGAAAAAA-AATTCTAAAATTCAT 3030
                          vii iivi v      -i     vvv  v  iv-i  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_209700350_   3031 TTGGAATAAGAAAAGAGCCTGAATAGCCAAAGCAATCATAAGCAAAAAGA 3080
                         v     vviv  ii  v  v           i     v i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_209700350_   3081 ACAAACCTGGAGGCATCACACTACCCAACTTCAAA-TATACTACAAGGCT 3129
                              vi      vv       v     i      -iv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_209700350_   3130 ATAGTAACAAAAACAGCATGGTACTGGTACAAAAACAGACACACAGACCA 3179
                          i     iv  i    ii         i i  ii i     i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_209700350_   3180 ATGAAACCCTTCTTTA---TT-----TCTAGGTTATGGAACCCAGAACAC 3221
                            i  --------  ---  -----  i  iv-  i-      v -  i
  L1M4_orf2#LINE/    300 ATGGAA--------TAGAATTGAGAGTCCAGAA-ATA-AACCCATA-CAT 338

  chr1_209700350_   3222 CTATAACTATCTGATCTTTGACAAAGCCAACAATAGCAAGCAATGGGGAA 3271
                         i   iiii vi    i  i     i viiv   v v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_209700350_   3272 AGGATGGCCTATTCAAAAAATGGTGCTGGGATAACTGGCTA-CCATATGC 3320
                           i  i i  v     v              i      v  -   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_209700350_   3321 AAAAGATTGGAAATGGACTCCTACTTTTTACCATATATAAAAATCAACTA 3370
                               v  i iv     i     i ivi        i      i    v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_209700350_   3371 AAGATGGATTAAAGACTTAAAAGTAAAACCTAAGACTATAAAGACCCTAA 3420
                           i      i ?    i    v    i v    i        ivi i  i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_209700350_   3421 AAGAAAACCTAGG---AAATACCATTCCACACATCAGCCCAGGCAAAGAC 3467
                                 v    ---    -- -   vvv  v ii vii      v ii
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_209700350_   3468 TTCATGACAAAGACTCCAAAAAAATTTGCAACAAAA----ACACTGACAA 3513
                            v iivv v   v      iv ivv         ---- v iv  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_209700350_   3514 -CTGGGCCTAATTAAACTAAAGAGTTTCTGCATAGCAAAACAAACTATCA 3562
                         -i   i i v  i   v v  i ii  i  iiivv    iv v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_209700350_   3563 ACAGAATAAACAGACAACCCATAGAACAGGATAAAATATTTGCAAACTAT 3612
                          v i i i  v          i    ii   v              ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_209700350_   3613 GTATCTGACAAAGGTCTAATATTCAGAATCTATAAGGAACTC----AAAT 3658
                         i       i  i  v  vi   i      v     i      ----  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_209700350_   3659 CAACAAGTAAAAAACAA----CCCCATTAAAAAATGGGCAG-GGACATGA 3703
                            i  vv    i    ----   v   ?           i-   iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_209700350_   3704 ACAGGCACTTCTCAAAAGAAGACATACTAGCAGCCAACAAACATATGAAA 3753
                          i  i  i     v        i    v iii     i  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_209700350_   3754 ACATGCTCAATATAACTAATCAG 3776
                          v        i  v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (141 / 87)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.32 (44 / 19)  


3516 24.25 1.11 0.55  chr1_209708188_209712401.rev     2820  3722 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_209708188_   2820 TGGAAAAATATTCCATGTTCATGGATTGGTAGAATCAATATTGTTAAAAT 2869
                               i    i                 v   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_209708188_   2870 GTCCATATGACCCACAGCAATCTACAGATCCAATGGAATCCTGATCAAAA 2919
                          v v   ivv    v vii          i   i v     iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_209708188_   2920 TATCAATGACGTTCTTCACAGAAATAGAAAAAC-AACACTAAAATTTATA 2968
                          vi  iivi v  i  ii       v  v  i -i iv        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_209708188_   2969 TGGAACCACAAAAGATCCAGAATAGCCAAAGTGATCCTAAGCAAAAAGAA 3018
                              vii   ii  i              iii   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_209708188_   3019 GAAAACTGGAGGAATCACATAACCTGACTTCAAATTATGCTACAGAGCCA 3068
                         v   ii       v     ivv  ii i      viv i     i   i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_209708188_   3069 TTGTAACCAAAACAGCAAGCTACCAGCATCAAAACAGACACATAGATGAG 3118
                         iv    i   i    iiv v   ii    v ii i     i      v i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_209708188_   3119 TGGAACAGAATAGAGAACTCAGAAAGAAATCCACACACCTACAGTGAACT 3168
                              i     v    iii      v   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_209708188_   3169 CATTTTCGACAAAGGTGCCAAGAACATACACTGAAGAAAAGACAGTTTCT 3218
                         v           i          v   v  v  ii    ii i   i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_209708188_   3219 TCAATAAATGGTACTGGGAAAACTGAATACCCATATGCAGAAGAATGAAA 3268
                             i       i      v     i   ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_209708188_   3269 TTACACCCCTATCTCTTGCCATACACAAAAATCAAATCAAAATGGATTAA 3318
                           iv       i   vii     i        i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_209708188_   3319 AGACTTAAAGTCTAAGAACTCAAACTATAAAACCACTACAACAAAACATT 3368
                             i    - v     i  v            ivi  v  v       v
  L1M4_orf2#LINE/    501 AGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_209708188_   3369 GGGGAAAATCTCCAGGATATTGGTTTGGGAAAAGATTTTTTGAGTTAT-A 3417
                           ? v      i iv  iv    v  i  v  v i   i  -  v   - 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chr1_209708188_   3418 CCCCACAAGCACCAGCAATCAAAGCAAAAAATGGACAAATGGCATCACAT 3467
                          v   v      v     iv    -       i  i    v v iiv   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCAT 647

  chr1_209708188_   3468 CAAG-TTAAAAAGCTTCTGCACAGCAAATGATACAATCAAAAAAGTGAAG 3516
                            i-       -   i  ii vv    v  i  v     i        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_209708188_   3517 AGACAGCCCATAGAATGGGAGGAAATATTTACAAACTACCCATCTCACAA 3566
                              i    i          i        i    ii ivi    v i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_209708188_   3567 GGGATTAATA----GAATATATAAGATGCTCAAACAACTCTATAGGGAAA 3612
                             i vi  ----          iivi   vv       v   ivi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_209708188_   3613 AAATCTAATAATCCAATCAAAAAACGGGCATAAGATATGAACAGACATTT 3662
                          i - v     i     i?     i     v i   v    i        
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_209708188_   3663 CTC---AAAAGACATACACATGGCAAACAAACATAAGAAAAGGTGCTCAA 3709
                            --- i    i     v     v  i  i  i v      i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_209708188_   3710 CATCACTGATCAT 3722
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (137 / 78)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2766 25.81 3.94 1.85  chr1_209760141_209763091     1597  2460 (491)    L1M4_orf2#LINE/L1        1   882 (26)  

  chr1_209760141_   1597 TGGGAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTTAAAAT 1646
                            i  i i  i     i        v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_209760141_   1647 GGCCATACTGCCCAAAGCAGTTTATAGAT--AATGCTATTTCTATTAAAC 1694
                            v     v      viii i  i    --  i  v  ii    i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_209760141_   1695 TACCATTGAGATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 1743
                          v   vivivv  i  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_209760141_   1744 ATGGAACCAAAAAGGAACCTGAATAGCTAAGGTAATCCTAAGCAAAAAGA 1793
                               viiv  i   v  v       i  iii    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_209760141_   1794 ACAAAGCTGTAGGCATCATGCTACATGACTTCAAAGTATACTACAAGGCT 1843
                               i  v   vv   ii  v vii i      iiv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_209760141_   1844 ACAGTAACCAAAACAGCATGATACTGGCATAAAAACAGATACATAGACCA 1893
                                i   i    ii  i           ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_209760141_   1894 ATGGAACAGAATAGAGAACCCAGAAATAAGACTGCATACCCACAACTATC 1943
                               i     v    ii          iv iii i iii iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_209760141_   1944 TGATCTTTGACAGACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 1993
                             i  i    iivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_209760141_   1994 TTCAGTAAATGGTGCTGGGATAACTGGCTAGCCACATGCAGAAGACAGAA 2043
                             ii              i      v  ?         i    vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_209760141_   2044 ACTAGACTCCTTCCTTACACCATTTTCAAAAATTAACTCAAGATGAATTA 2093
                         ii i   i   v   i       v v               i   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_209760141_   2094 AAGACTAAAATGTAAAATACAAAACTATAAAAACCCTT-GAAGACAACCT 2142
                         ?    iv        i vvi            - i   -     v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr1_209760141_   2143 AGG--TAATACCATTAAGGACATAGGCACTGGCAATGATTTTATGTCAAA 2190
                            --   - i -  viv   v v  vviv       i   i--- i i 
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC---TTAGA 593

  chr1_209760141_   2191 GATG---CCAAAAGCAATGGCAA--AAAACAAAAATTGACAAATGGGATC 2235
                         v   ---         vvi    --   iv      v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_209760141_   2236 T-ATTTAAACTAAAGAGCAAACTTTAAACTGCACAGCAAAAGAAACTATC 2284
                          -  iv   i    -----      ----  ii vv    i  v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAA-----AACTTT----TGTGCTTCAAAGGACACTATC 684

  chr1_209760141_   2285 AA-------------CAA---ACAGAATGGGAGAAAAT-TTTGGAAACTA 2317
                           -------------   ---                 -    v   ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_209760141_   2318 TGCATCCAACGAAGGTCTAATATCCAGCATCTATAAGGAACT--TA-AAT 2364
                          ii   ii ii i  v  vi       v  v     i     --  -  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_209760141_   2365 TTA-CAAGAAGAAAA-AAACAGCCCCATTGAAAAGTGGGCAAAGGACATG 2412
                          i -i  v  i  i -   i i   v   ?    i           iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_209760141_   2413 AACAGACACTTTTTAAAAGAAGACATACATGCAGCCAACAATCTTATG 2460
                           i     i  i iv        i     viii     i  v vi   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

Transitions / transversions = 1.82 (142 / 78)
Gap_init rate = 0.02 (21 / 882), avg. gap size = 2.38 (50 / 21)  


2660 24.81 5.12 1.28  chr1_209774070_209781508      490  1271 (6168)  C L1M4_orf2#LINE/L1   (0)   908    97  

C chr1_209774070_   1271 AAAATTTTAAATGATTGTCTAGTGGTTATCAACGAACTGATTCTAAACTT 1222
                              iii iv  vi v i v ii vv  ii  i i     i     v  
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

C chr1_209774070_   1221 TATGTAGAAATGCAAAAGACCCAGAATAGCTAACACAATACTGAA----- 1177
                         i  i i         ii             i  v     vi    -----
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

C chr1_209774070_   1176 -GAACAAAGCTGGAGGACTGATACTACCTGACTCCAAGGCTTCCTATAAA 1128
                         -        i         v i   v  ii i i   ii   v   i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

C chr1_209774070_   1127 GCCACAGTAATCAAGACAGTGTGGTATTGGCTAAAGAATAGACAAACCAA 1078
                           i                       i    vv   i       v ivi 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chr1_209774070_   1077 TCAATGCAACAGAACAGAGAGCCCAGAAGGAGACCCACATAAATATACTC 1028
                               v  i    iv     i      iv i     i i vv   iv  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

C chr1_209774070_   1027 AACTCGCTTTTGACAGAAGAGCAAAGGGAATACAATGGAGCAAAGA---G 981
                           i vii   i    iii v  v   ivv  v      i -     --- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAG 395

C chr1_209774070_    980 CCCTTTCAA-AAATGGTGCTAG---------ACAGCCACATGCAAAAATG 941
                         i i      -          i --------- i ?            ivi
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

C chr1_209774070_    940 TGAATCTAGAACAG-ACCTTACACCCTTAACAAAAATTAAC--AAAATGG 894
                             vi i  v vv-    i     v vv            --       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

C chr1_209774070_    893 ATCATAGACCTAAATGTAAAATATAAAATTATTAAAATCCTGGAAGATAA 844
                             ?              i vv     i   v   v  i i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

C chr1_209774070_    843 CACAGGAGAAAACCTAGATAACTCTGAATATGGTGATGACTTTTCTGAGA 794
                           i   ? v   i  vvi i  ii  ii vv  ii   ii  i iv  v 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chr1_209774070_    793 TAATATCAAAGGCAGAACCCACTCGTATGAAAGAAACAATTGATAAGATA 744
                          i i i    i   v  v v  ------i       v   v     iv i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAAC------AAAAGAAAAAATAGATAAATTG 639

C chr1_209774070_    743 GACTTTGTTAAAATTAAAAACTT--ATGCTCCATGAAAAACAATGTCAAG 696
                              ii i              --i    i  --  ii   v i     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAG 687

C chr1_209774070_    695 AGAATGAGAAAACAAGCCACTGCCAGAGAGAAAATATTTATAAATGATAC 646
                          i i   i  i    v    v vvv i            ii    v   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

C chr1_209774070_    645 ATCTGATAATGGACCATTAGCCAAAACATACAAAGAACTCTTAATAATTT 596
                                  v    ivv  v   i  i   i            -i  i i
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTC 786

C chr1_209774070_    595 -----TAAAAA---------CCTGATTAAAAAATGGGCCAAAGACT--AA 562
                         -----      ---------  ii   ?          v  i  i --  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

C chr1_209774070_    561 CAGACACCTCACCAAACAAGATATACAGATGGCAAATAAGCATATAAAAA 512
                         i     ii  v     v          i     v        i  i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

C chr1_209774070_    511 GATACTCAACATTGCATGTCAT 490
                            i        ii????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (121 / 69)
Gap_init rate = 0.02 (14 / 812), avg. gap size = 3.57 (50 / 14)  

3057 27.15 2.12 0.67  chr1_209774070_209781508     6052  6946 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_209774070_   6052 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 6101
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_209774070_   6102 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCATCAAGC 6151
                            v     v     iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_209774070_   6152 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6199
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_209774070_   6200 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 6249
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_209774070_   6250 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6299
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_209774070_   6300 TACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 6349
                             i   i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_209774070_   6350 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 6397
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_209774070_   6398 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAAGGATTCC 6447
                          vi    i  i     ivv  vv  i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_209774070_   6448 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6497
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_209774070_   6498 GAAACTGGATCCCTTCCTTACACCTTATAAAAAAATTAAATT----TGGA 6543
                            ii    i    v   i     v    v         v i----    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_209774070_   6544 TTGAAGACTTAAATGTTAGACCTAAAACTGTAAAAGCCCTAGAAGAAAAC 6593
                          ii?    i       v   v        i     vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_209774070_   6594 CTAGGCA-ATACCATTCAGGACAT------AGACATAGGACTTCATGTCT 6636
                         v    ?i- v i -   iv   v ------  i  - v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAGAT 594

  chr1_209774070_   6637 AAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGTATCT 6686
                          vi            vvi          vv i   v  i    v v ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_209774070_   6687 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 6736
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_209774070_   6737 ACAGCCAACCTACAGAATGGGAGAAAATTTCTGCAATCTACTTATCTGAC 6786
                          v  v     i                 v i     vii iv       i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_209774070_   6787 AAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAA 6836
                           i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_209774070_   6837 AAATG----TAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACACT 6882
                            vi----      v  i? v  i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_209774070_   6883 TTTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 6932
                          i  v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_209774070_   6933 TCATCACTGGCCAT 6946
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.27 (25 / 11)  


3105 26.83 1.44 0.78  chr1_210193612_210199263     4258  5159 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_210193612_   4258 TGGAAGAACGTTCCATGCTTATGGATAGGAAGAATCAATATTGTGAAAAT 4307
                              ii ii i     i i      v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_210193612_   4308 GGCCATACTGCCCAAGGTAATTCATAGATTCAGTGCCATCCCTATCAAGC 4357
                            v     v     iv i  ii i       ii  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_210193612_   4358 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4405
                          vi  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_210193612_   4406 TATGGAACCAAAAAAGAGCCCTCATTGCCAAGAGAAACCTAAGCAAAAAG 4455
                                viiv  ii  v  vvv  v     i v  v i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_210193612_   4456 AACAAAGCTGGAGGCATCATGCT----GACTTCAAACTATACTACAAGGC 4501
                                i      vv   ii  ----i i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_210193612_   4502 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGTATATATAGAC 4551
                                 i   i    ii         i iv ii i  - i       i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG-ACATATAGAT 297

  chr1_210193612_   4552 CAATGGATCAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAAC 4599
                                vi    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_210193612_   4600 TCTCTGATCTTTGACAATC-TGACAAAAACAAGAAATGGGGAAAGGATTC 4648
                         ivvi    i  i     vv-  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_210193612_   4649 CCTATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGTAGAAAGC 4698
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_210193612_   4699 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 4748
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_210193612_   4749 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4798
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_210193612_   4799 CCTAGGCA-ATACCACTCAGGACATAGGCATGGGCAAGAACTTCATGACT 4847
                          v    ?i- v i -i  iv   v v  vv i     viii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_210193612_   4848 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4897
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_210193612_   4898 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGC 4947
                         v  i   v v  i i   i  ii vv    i  v    i  vv i    v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_210193612_   4948 ACAGGCAACCTACAGAATGGGAGAAAAATTTTTGCAATCTACTCATCTGA 4997
                          v  i     i                - v       vii ivi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGA 743

  chr1_210193612_   4998 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAATAAATTTAGAAGA 5047
                         i  i  i  vi          v  i        ivv i  v iv v  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_210193612_   5048 AAAA---AAACAACCCCATCAAAAAATGGGCAAAGGATATGAACAGGCAC 5094
                             ---   i     v  i?                 v    i  i  i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_210193612_   5095 TTCTCAAAAGAAGACATTTATGCAGTCAACAGACACATGAAAGAATGCTC 5144
                              v        i  vi viii i   i ii         ii      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_210193612_   5145 ATCATCACTGGCCAT 5159
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


2450 25.47 7.98 1.41  chr1_210199394_210203383.rev     2648  3499 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_210199394_   2648 TGGAGAGACA--AAATATCCATGGCATAGAAGACTCAGCATACTAAAGAT 2695
                             i   i --vv  i i     vv i       i ii  vv v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_210199394_   2696 ATTGGCTTTCCCTAAATTGAGATATAGATTTAAT-CAAGTACCAACCAAA 2744
                         iviiiivi    i       vv  i     i  i-   viv i v v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_210199394_   2745 TTCCAGCATGCCTTTTTTGCAGAAATTGGTAGGCAGATTCTAAAACACAC 2794
                          i     -                    ii i  v   i      iv  i
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_210199394_   2795 ACAGAAATGAAAAGGACCCAGAATGGGCAAAGCAA-CTTGGGAAA--AGA 2841
                          ii      v  i           i v    i   -    ii   --   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_210199394_   2842 ATAAAGTTGAAGAAATCTAACTACATGATATCAATACTTACTATAAAGTT 2891
                          i       i  i v  vv   v vii  v    v        i    i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_210199394_   2892 ACAGTATTCAAAACA-CATGGTATTGGTA-AAGGATTAGACAAATAGATC 2939
                               v    i   -ii     i   i -      -     v       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGATC 298

  chr1_210199394_   2940 AATGGAACATAATAAAGA--CCAAAAACAGGCCCATACAAATTTAC--CC 2985
                                i v   vi   --   i   i ii        --    i--i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA--TTTATGGTC 346

  chr1_210199394_   2986 ATCTAATATGTGACAAAAGTGCAAAAGCAACTTAATAAAGTAAAAATAGT 3035
                          vi i  v vi     ii    v  ii v i i   iii v  i      
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_210199394_   3036 ATTTCCAACAAATGGTTTTAAACCAATTAGTCACTTATATGCAAAAAAAA 3085
                         v   i           vi iiiv   i i vi ?ii i        i  -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA- 445

  chr1_210199394_   3086 CCCAAAACAAATCTTGTCCTATACCTCAAACCTTATATAAAATGTAACTA 3135
                         -------ii  vi v v  iv       v   v    i    vv     v
  L1M4_orf2#LINE/    446 -------TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_210199394_   3136 AAAGTGAATCATAGATTTAAAT-------TTAAAA-TGTATAACTTTTAG 3177
                            i  i    ?   ii     -------i     - i  v    i    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_210199394_   3178 AAGAAGACATAGGAGAAAATCTTCACGACCT-GAATTATGTGAAGACCTC 3226
                              i       ? v        ii     - ii   v ii v iii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_210199394_   3227 CTAGACATGAAAACTAAAGGATAATCCATAAAAGAAAAACT-GAAAGATT 3275
                         i    i    v v v    v i  v v i          v -  v i   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_210199394_   3276 AGAGTTTATCAAAATTTAGAACTTTTGCTCT-----------------GA 3308
                         i  v  i         v i        iv  -----------------  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_210199394_   3309 GAATGAAATGACAAACTACAGACTGGGAGAAAATATTTGCAAATCACA-A 3357
                         i i     v     v i     v                       i - 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_210199394_   3358 TTCAA------AC--------AAAACATTTAAAGAATTTTCAAAACTCAA 3393
                          iii ------  -------- i  i  v       i i i v       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_210199394_   3394 CAATAAGAAAAGAAACAATCCAGCTAAAAATTCGGCAAAA-ATTTGAATA 3442
                         i     i  i v   i  i   ii ?    v v      i-         
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_210199394_   3443 TA----TCATCAAAAAAGATACCTATAGGGCAAATAA---------AAGA 3479
                         v ----  vi    i      ivi v v   v     ---------    
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_210199394_   3480 TGCTTAACATCATTACCTAT 3499
                             i       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (135 / 78)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.48 (80 / 23)  


3094 27.68 1.23 0.22  chr1_210268538_210275207.rev     5284  6179 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_210268538_   5284 AAAAAAATTCCATGCTCATGGATAGAAAGAATCAATATCCTGAAAATTGC 5333
                            i v  i     i        v i    v i     iv v  i  v  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_210268538_   5334 CATACTGCCCAAAGTAATTTAGAAATTCAATGCCATTCCTATCAAGCTAC 5383
                         v     v      v i  i  v i      i  v  i        iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_210268538_   5384 CATTGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAATTTTATATGG 5432
                           vivi i  i  ii     v v  v  i  - iii    v  i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_210268538_   5433 AACCAAAAAAGAGCCAGTATAGCCAAGGCAATGCTAAGCAAAAAGAGCAA 5482
                           viiv  ii  v    v        ii    vi i iv  i    i   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_210268538_   5483 ACTTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGACTACAG 5532
                          v       vv   ii  v  ii i      viv        ii      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_210268538_   5533 TAACCAAAACAGCATGGTACTGGCACCAAAACAGATATATAGACTAATGG 5582
                            i   i    ii           iv ii i   i       ii     
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_210268538_   5583 AGCAGAACAGAGACCTCAGAAATAATGCCACACATCTACAACCATCTGAT 5632
                          ii    iv    vii         vv   i    i  iiii  vi    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_210268538_   5633 CTTTGACAAATCTGACAAAAACAAGTAATGGGGAAAGGATTCCCTATTTA 5682
                         i  i     ivv  v   i v  vvi           i  vvi  v  i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr1_210268538_   5683 ATAAATGGTGTTGAGAAAACTGGCTAGCCATATGCAGAAAACTGAAACTA 5732
                          i        i  i  v      v  ?   i     i  i v    ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_210268538_   5733 GACCCGTTTCTTACACCTTATACAAAAATTAACTCAAGATGGATTAAAGA 5782
                              v vi  i     v                   i      i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_210268538_   5783 TTTAAATGTAAGACATAAAACGATAAAAACCCTAGATGAAAACCTAGGCA 5832
                         ii           vv      v      vi i    v      v    ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_210268538_   5833 -ATACCATTCAGGACATAGCAT-GGGCAAAGACTTCATGACTAAAACACC 5880
                         - v i -   iv   v v vi -i     v ii   v iiv  vi     
  L1M4_orf2#LINE/    554 TAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_210268538_   5881 AAAAGCAATTGCAGCAAAAGTCAAAATTGACAAATGAGATCT------AA 5924
                                vvv   i      vv     v  i    vi  ii ------  
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_210268538_   5925 TTAAAGAGCTTCTGTACAGCAATAGAAACTATCATCTGAGTGAACAGGCA 5974
                              i -   i   i vv   vi  v       vvvi      v  i  
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_210268538_   5975 ACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGCC 6024
                            i                 v       vii  vi      i  i  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_210268538_   6025 TAATATCTAGAATCTACAAGGAATTTAAATAAATTTACAAGAAAAAAA-- 6072
                          vi    i     v  i  i   i ivv i  v iv i  v     i --
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_210268538_   6073 AACAACCCCATCAAAAAGTGGGTGAAGGGTGTGAACAGACACTTTTCAAA 6122
                           i     v  i?    i    ii    i v    i     i  i  v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_210268538_   6123 AGAAGACATTTATGCGGCCAATAAACATATGAAAAAAAGCTCATCATCAC 6172
                               i  vi vii         i  i       i v     v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_210268538_   6173 TGTTCAT 6179
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (7 / 905), avg. gap size = 1.86 (13 / 7)  


2794 26.47 2.21 1.66  chr1_210654615_210660054     4045  4947 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_210654615_   4045 TGGAAAAACATTTAAAGCTCACGGATAGGAAGAATAAATATTGTTAAAAT 4094
                               i i  iiv v i   i    v      v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_210654615_   4095 GGCCATACTATCCAAAGCAATTTACAGATTCAATGCTACTCTTATCAAAC 4144
                            v     vi     vii  i           i  v ii i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_210654615_   4145 TACCAATGACATTTTTCACAGAATTAGAAAAAATTGCTCC-AAAATTCAT 4193
                          v   iivi v     ii     v v  v  i-i  v   -         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_210654615_   4194 ATAGAAA--CAAAAAACAGTCTGAATAGCCAAACCAATCCTAGGCAAAAA 4241
                           i    --   iii  --i v           v     i iiiv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_210654615_   4242 GAACAAGACCAGAGGCATCACACTACCTAACTTCAAACTGTATTACAAGA 4291
                               iiiii    vv       v  i  i      viv  i     ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_210654615_   4292 TTACAGTAACCAAAACAGCATTGTACTGGTACAAAAATAGACACAAAGAC 4341
                         i        i   i    ii v       i i  ii       i v   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_210654615_   4342 CCATGGAATAGGTTAGAGAACACATAAATAAAGC--TACACCTACAACCA 4389
                          v         iv v    iiv  v       v --    ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_210654615_   4390 CCTGATCTTTGAAAAAGCTGAAAAAACAAG-CAATGGAGAAAGGGCTCCC 4438
                         vi    i  i  v  i v  vv  i  v v-      i     iiivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_210654615_   4439 TATTCAATAAATAGCGCTGAAATATCTGGCTAGTCATATGCAGAAAATTG 4488
                          v     i    i i    ii i v    v  ?i  i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_210654615_   4489 AAACTGGACTCTT---TCAT--CATATACAAACATCAACTCACAATGGAT 4533
                           ii     i i ---   i--          v  i      v       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_210654615_   4534 TAAAGACTTAAATATACAACCTAAAACTATAAAAACCCTAGAAGAAAAAC 4583
                         i ?    i     i  vi v              vi i          - 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-C 546

  chr1_210654615_   4584 CTAGA---AAA----CATCATTCTGGATGTAGGCCCTGGCAAATATTTTA 4626
                         v   i---   ---- i v iii   i -     vv   i-----  i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGT-----TTCTT 590

  chr1_210654615_   4627 AGAGAAAGACTGCAAAAGCAATTGTAGCAAAAACAAAAATTGACACCCGG 4676
                            v v-   vv        vvv i i     iv      v  i vviv 
  L1M4_orf2#LINE/    591 AGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_210654615_   4677 GACATAATTAAACTAAAGTGCTTTTGCACAACAAAAGAAATTATCAATAG 4726
                            v v  i   v v  ivi      ii vv    i  v i      v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_210654615_   4727 AGCAAACAGACAACCTAGAGAATGGAAGAAAATATTCACAAACTATGCAT 4776
                           ii  v        i v       i          ii    ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_210654615_   4777 CCAACAAAGGTCTAATATCCAGAATCTATAAGGAACTTGAGCAAATTAAC 4826
                          ii i  i  v  vi          v     i     ivvi   v i  i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_210654615_   4827 AAGCAAAAAACAAACAACCCCATTTTAAAAAAGGGGCAAAGGAGATGAAA 4876
                           vv    i     i     v   ?--     v          vv    -
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAA- 836

  chr1_210654615_   4877 ATAGAC--TTCTCAAAAGAAGACATACACATGGCCAACAAGCATATGAAA 4924
                         -     --     v        i     v        i     i      
  L1M4_orf2#LINE/    837 -TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_210654615_   4925 AAATGTTCAACATCACTAATTAT 4947
                          i   i         ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.06 (35 / 17)  


 924 26.36 3.49 1.55  chr1_210695647_210697552.rev      491   748 (1158)    L1M4_orf2#LINE/L1      244   506 (402)  

  chr1_210695647_    491 AAAATTATCTCAATCAAGACTGTGTGATATTGGCAGAGGGACAGGAACAT 540
                            ii  ivvi         v     i  i     v i   i  iv i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_210695647_    541 AGATAAATGGAACAAAATAGACAACACAAAAATAGGGCTACACAGC-ACA 589
                             v       i i   v  v iiv  i     iiv i i   vi- ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_210695647_    590 ACCAATTAATTTTTGACAGAAGTGCAAAAGCAATTCAGTAAGGAAGGA-T 638
                         ii     i     i    iii    v  ii v     i ii    i  - 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_210695647_    639 AGCCTTCTCAACAAATGGTTCTGGAGCAACTGGGCAGCCACAGGCAAAAA 688
                           i   i            v    ii       ii ?     v      i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_210695647_    689 AATGAA------CCAACCTAAGCTTCACTCCTTATACAAAAATCAACTTA 732
                               ------  --    -- i    v  v           i    i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACC--CCTA--CCTCACACCATATACAAAAATTAACTCA 489

  chr1_210695647_    733 CA-TGGGTCATAGATTT 748
                         v -   i   ?   ii 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCT 506

Transitions / transversions = 2.67 (48 / 18)
Gap_init rate = 0.02 (6 / 263), avg. gap size = 2.17 (13 / 6)  

 799 23.78 14.86 3.24  chr1_210695647_210697552.rev     1047  1416 (490)    L1M4_orf2#LINE/L1      496   908 (0)  

  chr1_210695647_   1047 ATCATAGATTTTAATGTTAATG-TAAAACCATAAAACTTCTAGAAGAAAA 1095
                             ?   ii v     v iv -      i        ii          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_210695647_   1096 TATAGGAGAGAGTCTTTGAGACCCAGAACTTGGTAAAGAATTCTTAGATA 1145
                         i     ? vi i    i v    iv iii v  i  v iv          
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_210695647_   1146 TGACATCAAA-GCATGATTCAAAAAAAGAAAAACATTGATAAATTGAA-- 1192
                              i    -   ii v-   v          -  v         i --
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAG-CAACAAAAGAAAAA-ATAGATAAATTGGACT 643

  chr1_210695647_   1193 ----------TAAAAA----------TCAAA------------------- 1203
                         ----------      ----------     -------------------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_210695647_   1204 ----------CTACGGATGGGGAGAAAGCATTTAAAAATTGCATGTTTGA 1243
                         ---------- i  i  vv        ii    iv    iii  i i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_210695647_   1244 -AATTTAATCGTATGTAGACTATATGGAGAACTCTCAAAAC-CAAGTTTT 1291
                         -  vvv v i    vi   v     ii        i v   -   -----
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA----- 788

  chr1_210695647_   1292 TTTTTAAAAAAGCAAATAAACAGTTCAATTATAAAATAGACAAAAAGCAT 1341
                         - vv      ii       v ----     ?v     i i    iiiiv 
  L1M4_orf2#LINE/    789 -TAATAAAAAGACAAATAACC----CAATTWAAAAATGGGCAAAGGATTT 833

  chr1_210695647_   1342 GAAGAAACCTTTCACCAAAGAATATATACAGATGACAAATGAGAACATGA 1391
                            v i  v    v        v       i   i v   i  v      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_210695647_   1392 AAAGATTTCCACCATCTCTAGCCAT 1416
                               vii  v    v????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (49 / 36)
Gap_init rate = 0.03 (11 / 413), avg. gap size = 6.09 (67 / 11)  


1955 16.04 2.17 26.32  chr1_210971143_210973457.rev      628  1824 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_210971143_    628 TGGAAAGATACCCCATCTTCGTGGATTGGAAGAATCAATATTGTTAAAAT 677
                                   i     v   i            v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_210971143_    678 G----T-CTGCCAAAAGTAATCTACAAATT-AATGCAATCCCTATCAAAA 721
                          ---- -  v  v   v i       i   -  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_210971143_    722 TTCCAACATCATTCTTCATGGAAATAGA-AAAC-AATCCTAAAATTCATT 769
                          i   i vv v  i  iiii     v  -  i -i              v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_210971143_    770 TGGAGTCACCAAAGACCCCAAATAGCCCAAGTAATTTTGAGCAA-AAGAA 818
                             ivii v ii     vi       v  ii   i    iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_210971143_    819 CTAAGCAGGAGATAC-CACACTACCTTATTTCAAACTGTATATCAAAGCT 867
                          v   iv    i-  -      v  iv        viv  ivv       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_210971143_    868 ATAGTAATTAAAACAATATGGGACTAGCAAAAAAATAGGCACAATGACCA 917
                          i      i  i   i i   v   i   v  ii    i  i vv  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_210971143_    918 ATGGAAAAGAATAGAACACCCAGAAGTAAATCACACACATCTAAAACCAA 967
                               v     v  ivii      i    i -  i    i  viii   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACC-CATACATTTATGGTCAA 348

  chr1_210971143_    968 TAGATTTTTCAACAGAGGGGCCAAGAACA--CACTGGTGAAAGGGCAGTA 1015
                          v      - i   ii  v       v  --  v   v     iii   v
  L1M4_orf2#LINE/    349 TTGATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_210971143_   1016 TATTCAGCAATTGGTGCTGGGAAAACTGGCCATCTACATGCAGAGGACTG 1065
                          v    i   v           v      vi ? i       i i  v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_210971143_   1066 AATTTGGATCCTTATCTCACCCTTTGTACAAAAGTAAATTCAAAATGTAT 1115
                           v     i  i  i     v iv i       i v  i        v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_210971143_   1116 TAAAGACTTAAATGTGGCCAGGCGCGGTGGCTCACGCCCATAATCTCAGC 1165
                         i ?    i       -----------------------------------
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGT----------------------------------- 512

  chr1_210971143_   1166 ACTTTGGGAGGCCTAGGCGGCCGGATCACAAGGTCAAAAGGTGGAGACCA 1215
                         -----------------------------------  i  ----------
  L1M4_orf2#LINE/    513 -----------------------------------AAGAG---------- 517

  chr1_210971143_   1216 TCCTGGACAATATGGTGAAACCCCATCTCTACTAAAACTACAAAAATTAT 1265
                         -------------------------------         i    -----
  L1M4_orf2#LINE/    518 -------------------------------CTAAAACTATAAAA----- 531

  chr1_210971143_   1266 CTGGGCTTGGTGGCACACACCTCTAGTCCCAGCTACTCAGGAGGCTGAGG 1315
                         --------------------    --------------------------
  L1M4_orf2#LINE/    532 --------------------CTCT-------------------------- 535

  chr1_210971143_   1316 CAGGAGAATCGCTTGAACCCCTGGTGGAGGTTGCAGTGAGCCGAGATTGT 1365
                         --------------------------------------------------
  L1M4_orf2#LINE/    536 -------------------------------------------------- 535

  chr1_210971143_   1366 GCCACTGCACTCCAGCCTGGCCACAAAGCAAGACTTTGTCTCAAAAAAAA 1415
                         --------------------------------------------------
  L1M4_orf2#LINE/    536 -------------------------------------------------- 535

  chr1_210971143_   1416 AAAAAGAAAAAAAAAAGACTTAAATGTAAGACCTGAAAGTATAAAACACT 1465
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    536 -------------------------------------------------T 536

  chr1_210971143_   1466 AGAAGAAAACATGGGGGAAAAGCTACATGACATTGGTCTGGGCAGCGATT 1515
                                     i  ? v   v  v i    v    vi i    ii i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_210971143_   1516 TCTTGCATATGACCCCAAAAACATAGGCAACAAAAGTAAAAATAAATAAA 1565
                             iv       v      i  i i          v       i     
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_210971143_   1566 TGAGATTGTATCAAACTAAAAAGCTTCTGTGCAACAAAGGAAACAAC--A 1613
                          vi  i vi      v v    i   i     vv       v  v i-- 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_210971143_   1614 GATA-TAAAGAGACAACCCACACATTGAAAGAAAATATTTGCAAATTATA 1662
                           v - i  i            v v  ii                 i   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_210971143_   1663 CATCAGATAAGGGGCT------CAAAATATATAAGGAACTCAAACTACTC 1706
                         i   v        i  ------  i         i      vv  v    
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_210971143_   1707 AACAAGAAAA---CAAATAGCCCTATTAAAAAAATGGTCAAGGGACCTGA 1753
                           i  v    ---      i   v   ?     -   v   i   ii   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGA 835

  chr1_210971143_   1754 ATAGACATTTCTCAAAAGAA-ATATACAGAAGGCCAACAGACATATGAAA 1802
                                      v      -       i v      i ii  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_210971143_   1803 A-ATGCCCAGCATCACTAATCAT 1824
                          -    i  i     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (113 / 75)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 15.50 (341 / 22)  


2758 25.09 5.47 1.94  chr1_211158295_211160377      714  1590 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_211158295_    714 TGGAAGAGATGTATGCTGTCTGTG--TCAGAAGGCACAATATTCTTAAG- 760
                              -    i vivv   iii  -- ii    i vi      v     -
  L1M4_orf2#LINE/      1 TGGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_211158295_    761 --------TTCTCCAAACTGATCCGTAGATTCAAAGTAATCCCTGTCAAA 802
                         --------i  i     i     iii        v i       i     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_211158295_    803 ATCCCAGGAGGCTTTT--GGGAAAATTAATATTCTCATTTTATTCTGAAT 850
                                vv v     -- vii     i i vv  v  ii  ----i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA----AAAT 145

  chr1_211158295_    851 TTTTATGAAAA-GTAAGGGCTCTAGAATAGACAATACAATTTTGAAAAGG 899
                          iv    i   - i     vi i       v   v     i       i 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_211158295_    900 ATCATCA---TTGGAAGACTTACATTACCCAATTTCTTGACTTATCATTA 946
                          vv v  ---     i    i   i v         vvi     ii iv 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_211158295_    947 AGCTACAGTGATGAATACAGTGTGATACAGATGTAAAGATATGACATATA 996
                                  i  v  v        i   v iii   i    -        
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATA 294

  chr1_211158295_    997 GATCAGTGGAACAGAATACAAAGGC-AAAAGTAGATCTATATTTATATGG 1045
                              i     i     vv i  v - i  i  i i i   iv v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_211158295_   1046 TCAATTAATTTTCAACAAAGACGCTAAGGTAATTCAGTGGGGAAAGGATA 1095
                               i      i    i ii  i   iiv     i         i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_211158295_   1096 ATTTTTGTAACAAATGGTGTCAGAACAACTAGATCTCTGTATGGGAAAAT 1145
                         i i   vi           iii i      i   v? iii   v-    v
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-AAAAG 443

  chr1_211158295_   1146 ATATAAACTTTAACTTTTATGTCACACCATACAGAAAAATTTACCCAAA- 1194
                          -  i  v  vi  iii  iv          i v       v  i    -
  L1M4_orf2#LINE/    444 A-ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_211158295_   1195 TAGATTATAGAGTTAAATGTGAAAGTTCAAATTATAAAACATCCAGGAGA 1244
                          i   i ?   vi       i i  i v   i        viii  i   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_211158295_   1245 TAATATGAGAGAAAGTCTTTCTAAACTAGGTAAAAGTGAAG-ATTTATTT 1293
                         v  i  ii ? v  i    iv i v  v  -----  v i - v vi   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGG-----GTTAGGCAATGGTTT 587

  chr1_211158295_   1294 CTTAGATAAGACACACAAAAAGCATGA-CA-CGAGAGAAAAG-TGAATCA 1340
                                 v     -     -   ii -  - i i      i- ii  v 
  L1M4_orf2#LINE/    588 CTTAGATATGACAC-CAAAA-GCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_211158295_   1341 -TTAGAGTCCATCAAAGTTTAG----TTTGCGTTTTATGAAAGACATCAC 1385
                         -  i  v i       i  v i----    i i  i --  i    ii i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTAT 683

  chr1_211158295_   1386 TGAGAAATTGAAAAGACAAGCAATAGACTGCGAGAAAATTTTTGTAAAAC 1435
                         ii     v           v v i   v  v        v    i   v 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_211158295_   1436 ATGTATGTGATATAGGCCTTGTATCCAGA-TATATGA-GAAATC------ 1477
                           i   v     vi  v            -     i -   v  ------
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_211158295_   1478 -------ATAGAA-GATAA-CAACTCAGTAAAAATATAGG-AAAAGATTT 1517
                         -------   i  -  i  -i   i  i v?   v  i  -   i     
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_211158295_   1518 TAA--GACACTTTACAAAAGAAAATCTATAAACAGCCAATAAGCACATCA 1565
                         v  --    i  iv v      i  v  i   ii              v 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_211158295_   1566 GAAGATGTTCAACATCATTGGTCAT 1590
                         i      i         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (141 / 75)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.24 (65 / 29)  


1692 27.05 4.32 3.88  chr1_211270830_211273171.rev      691  1385 (957)    L1M4_orf2#LINE/L1        5   702 (206)  

  chr1_211270830_    691 AAGATATACTATATTCACAGACTAGATGATCCAACATAGTAAAGA----- 735
                                v i  i    ii  i i  v  iii  i  v  v    -----
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_211270830_    736 -----CCCCAA-CTGATATACTGGCTTAAAGCAATTCCCACCAAAATTCC 779
                         -----      -i    v   v ii i  v     i  i i      i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_211270830_    780 AGCAAGATTTTT-GTAGACAT--AAAAGATACTATTCTAAAATTTAGATG 826
                            vivv     - i   v  -- v   v i--  i        i v   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCATATG 152

  chr1_211270830_    827 GAAAGAAAAAGGAAGTAGAATAGCTAAAACAATTTTGTAAAGAATTGATA 876
                             viv  i   vvi        i        i   v   ii vvi i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_211270830_    877 AAATAGGAGGAATCAGTCTGCATGATGATTTCAACACTTA-TA-AAAGTT 924
                           i v      v   vv  v vii  ---     v     -  -    i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAAT---TTCAAAACTTACTACAAAGCT 249

  chr1_211270830_    925 G------TCAAAACTGTGTGGTGGTATTGGTGGAGGGATAGACACATAGA 968
                         i------    i  v       --- i   iiv i         i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGT---ACTGGCATAAGGATAGACATATAGA 296

  chr1_211270830_    969 TTAATGGAACATAATAAAGAACCCCAAAATAGACCTATACAAATATGTCC 1018
                          i       i v   vi   ii  vi     i   i     vv    vi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_211270830_   1019 AACTGATTTTTGACAAATGTGC-AATATCAATTTAATGAAGGAAAG--T- 1064
                           i       i     iv    -  v i  -  i    i-      -- -
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGG-GGAAAGAATA 394

  chr1_211270830_   1065 GCCATTTCAACAAATGGTGCTGGAGTAATTGAACGTTCATACACACACCA 1114
                          i v                   iii  i  i ii?i  i ii  -----
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA----- 439

  chr1_211270830_   1115 TAAAGAAAAAAC---AACCTCAAACTAAGTCTCACACCTTATACAAAAAG 1161
                         -      vi  v---i   i ----  --i        v          v
  L1M4_orf2#LINE/    440 -AAAGAATGAAGTTGGACCCC----TA--CCTCACACCATATACAAAAAT 482

  chr1_211270830_   1162 TTACTCAAAATTGTTGTAACAGACTTATATGCGGAAGGTAAAACTGTAAA 1211
                          v         v --i v ?    i  v   iiii  v       i    
  L1M4_orf2#LINE/    483 TAACTCAAAATGG--ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_211270830_   1212 CTTTTAAGAAAAAAATCATGGGACAAAAAGCTTCAGAATCTAGAGCTAAC 1261
                         vi i v    i    -   i  ?-iv   v    ivi i  v i i  iv
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAA-CATAGGN-GTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_211270830_   1262 CAAAGAGTTCTTAAACCTGACCCAAAAAGCTTAATCTATTAAATTTAAAA 1311
                            v iv      i iv    v v      vi  v v iv   vv-    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAA 627

  chr1_211270830_   1312 ATTGATCA-TTGGATTTCATCAACACTAAAAATGTTTCCTCTACAAAAGT 1360
                           v   v -     i        v i      iv   viv  v    i v
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_211270830_   1361 TTTTGTTAAAAGCATGAAAAGACAA 1385
                         ivi i i  i ivi           
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAA 702

Transitions / transversions = 1.43 (109 / 76)
Gap_init rate = 0.03 (24 / 698), avg. gap size = 2.38 (57 / 24)  

 673 23.44 0.00 2.60  chr1_211270830_211273171.rev     1654  1845 (497)    L1M4_orf2#LINE/L1      694   880 (28)  

  chr1_211270830_   1654 AAAAGACAAGCTGCAAAGTGAGAGAAAACATTTGCAAATCACATATCCAA 1703
                                  v ii  i i  i       i            i     ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_211270830_   1704 CAAATAACTTCTATGTAAAAAATATGTATATAACTCTCAAAACTCATCAG 1753
                         i  ivi    v   vi i  --   i  v v      i v      vi i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAA--TATATAAAGAACTCTTACAACTCAATAA 791

  chr1_211270830_   1754 TTAAAAAAAAGCAAACAATACAATTAGAATATGAGCAAAAGACGTGAAGT 1803
                          ---     ii    i  iv     ?i  v   i     i  iv    vv
  L1M4_orf2#LINE/    792 T---AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_211270830_   1804 GACATTTCACCAAAAAAGCTATACAGATGGCAAATAAGCACA 1845
                                 v     i   v      i     v          
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

Transitions / transversions = 1.75 (28 / 16)
Gap_init rate = 0.01 (2 / 187), avg. gap size = 2.50 (5 / 2)  


3160 26.85 0.88 0.55  chr1_211283682_211289791.rev     4715  5619 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_211283682_   4715 TGGAAAAACATTCCATGCTCATGGACAGGAAGAATCAATATTGTCAAAAT 4764
                               i i  i     i       iv      v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_211283682_   4765 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4814
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_211283682_   4815 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTTA 4862
                          v   vivi i  i  ii     -   -- v  i  - iii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_211283682_   4863 TATAGAACCAAAAAAAGAGCCC-GAATAGCCAAGACAATCCTAAGCAAAA 4911
                            i   -- viv  i ii   -          i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_211283682_   4912 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTTAAACTATACTACAAG 4961
                                  i      vv    i  v  ii i  i   viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_211283682_   4962 GCTACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGATACACAGA 5011
                                   iv  i    ii         i iv ii i   i i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_211283682_   5012 CCAGTGGAACAGAACAGAGGCCTCAGAAGTAATGCCACACATCTACAACC 5061
                         i  i     i    iv   ivii     i   vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_211283682_   5062 ATCTGATCT-CTACAAACCTGACAAAAACAAGCAAGGGGGAAAGGATTCC 5110
                          vi    i - v    ivv  v   i v  vv   v        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_211283682_   5111 CTATTTTATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5160
                           v  iv i        i     v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_211283682_   5161 ACAACTGGATCCCTTTCTTACACCTTATACAAAAATTAACTCAAGATGAA 5210
                         iv ii    i    vi  i     v                   i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_211283682_   5211 TTAAAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5260
                          i ?    i    i      v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_211283682_   5261 CTAAGGA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5309
                         v  i ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_211283682_   5310 AAACACAAAAAGAAATGGCAACAAAAGCCAAAATAGATGAATGGGATCTA 5359
                         vi    v     v vvi          vv         i   v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_211283682_   5360 ATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTATCAGCAGAGTGAA 5409
                           i   v v  i i   i  ii vv       v       iv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_211283682_   5410 AAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTAACCATCTGAAA 5459
                            i     i                 v       vii vvi      v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_211283682_   5460 AAGGGCTAATATCCAAAATCTACAAAGAACTTAAACGAATTTACAAGAAA 5509
                          i  i  vi      i   v  i        ivv  i v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_211283682_   5510 AAAA--AACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5557
                           i --  i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_211283682_   5558 CTCAAAAGATGACATTTATGCAGCCAACAAACATATGAAAAAA-GCTCAT 5606
                            v     v  i  vi viii     i  i  i       i -     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_211283682_   5607 CATCACTGGTCAT 5619
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (148 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2776 26.24 4.05 1.39  chr1_211355919_211359252.rev     2001  2865 (469)    L1M4_orf2#LINE/L1        1   888 (20)  

  chr1_211355919_   2001 TGGAAAAACATTCCATGCTCACATGTTGGAAGAATCAATATTGTTAAAAT 2050
                               i i  i     i   iivi        v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_211355919_   2051 TACCATAGTGCCCAAAACAATCTACAGATTCAATGCAATTTCTATAAAAT 2100
                         vi v   v v      vii              i     ii    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_211355919_   2101 TGCCAA-TGTCTTTTTTCACAGAACTCACAAAAAC-AATTCTAAAAGTCA 2148
                          v   i-  i       -i     v ii- v  i -i  i      v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG-ACAAGCTGATCCTAAAATTCA 148

  chr1_211355919_   2149 TATGAAACCAAAAAAGAGCCCAAATAGCCCAAGCAATCCTAAGCACAAAG 2198
                             i  viiv  ii  v  vi       v  i     i i iv vi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_211355919_   2199 TACAAAGCTAGAAGCATCCCATTACCCAACTTCAAACTATACTATAAGTC 2248
                         v      i i  i vv  v  i v     i      viv     i  iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_211355919_   2249 TATAGTAACCAAAACATCATGGTACTGGTACAAAAATAGACACATAGATC 2298
                           i     i   i   vii         i i  ii       i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_211355919_   2299 AGTGGAACTAAATAGAGAATACACAAATAAAGCTACATACCTACAACCAA 2348
                          i     ivi   v    i v  v       v i i i ii  iiii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_211355919_   2349 CTGATCTTTAACAAAGTCAATAAAAATAGACAATGAGGAAAGGACTCCCT 2398
                         i    i  ii    i viivi  i vi vv     i      i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_211355919_   2399 ATCCAATAAATTGGGCAGGGAAAACTGGCTAGCCATAT------------ 2436
                         v i   i    v v  v    v      v  ?   i  ------------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_211355919_   2437 --------------CTCTCACCATAT-CAAAAGTTAACTCTAGATAGATT 2471
                         --------------   v        -     i       v i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_211355919_   2472 AAAGACCTAAATGTAACATCTGAAACTACAGAAATCTTAGAAGAAAACTT 2521
                          ?              v v  i      i i  v              v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_211355919_   2522 AGGGAAAACTCTTCTGGACATTGGCCTAGGCAAATAATTT-TTGACTGAG 2570
                            ?iv  v     vv   v    vi       - ii   -  iiv iv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATG 597

  chr1_211355919_   2571 ACCTCAAAAGCAAATGCAACAAAACCGAAAATAGACAAATGGGACTTAAT 2620
                           vi        v v         vvi        i    v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_211355919_   2621 TAAA--TGAAAGTGCTCCTGCACAGCGAAGAA-ACAATCAACAGAGTAAA 2667
                         i   -- i   i--  ii  ii vv i   i -  v     v i   i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_211355919_   2668 TGGACAACCTACAGTATGGGAGAAAATATTTGCAAGTTATGCATCTGGCA 2717
                         vi       i    v                    i i  ii     ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_211355919_   2718 GAGGTCTAATATCCAGAATCTATAAGGAACTAGAATAAATCAACAAGATA 2767
                         ii  v  vi          v     i     vvv i  v    i  v v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_211355919_   2768 AAAACAAGTAACTCCATTAAAAAGTGGGCAAAGGATATGAACAGACACTT 2817
                           i    i    i v   ?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_211355919_   2818 CTCAAAAGAAGACACACA--CTGCTAATTCAAGCAGTGGAGATAAAAAGA 2865
                            v        i i   --iv  i   --     v-----  i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAAT--AAGCAC-----ATGAAAAGA 888

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.02 (14 / 888), avg. gap size = 3.36 (47 / 14)  

 212 21.43 0.00 1.79  chr1_211355919_211359252.rev     2867  2922 (412)    L1M4_orf2#LINE/L1      854   908 (0)  

  chr1_211355919_   2867 AAGACACACAAGTGGTCAACAAATGCATGAAAAACATGCTAAATGTCACT 2916
                             i i    i   i   i  iii        i-     v  ii   ??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAG-ATGCTCAACATCAZZ 902

  chr1_211355919_   2917 AACGGT 2922
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 11.00 (11 / 1)
Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1)  


1550 25.78 14.34 4.94  chr1_211386502_211388587.rev      772  1601 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_211386502_    772 TGAAAAGATACCTCATGTTCATAAATCGAAGGACTCAACACTCTTT---T 818
                           i       i i         ii  i i i    i  i i v  v--- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_211386502_    819 GTCCATTTGACCCAAGTTGATCT-C---TTTAATACGTTCTCAAACAAA- 863
                          v v  vivv     i       - ---  i  ii iv  i v v    -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_211386502_    864 TCCCAGCAGACTGCTTATGAAGAAATTGACAAGCTGA------------- 900
                                v v  vi  -  v                 -------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_211386502_    901 --------------------------------------------GGAAGA 906
                         --------------------------------------------i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_211386502_    907 ACAAAATTAAAGGATGTATACTACTTCATT-CAAAACTAACCATAAAGT- 954
                              i  ii    ivi i   v iiv   -       v  i i    i-
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_211386502_    955 --AATA-TTATGACAGTGTGCTATTGCTACATAGATAGACAAATCAATCA 1001
                         -- i  - i v         v  i  vi i vi        v  vi    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_211386502_   1002 GTGTAACAGAATAGAGATTCCAGAAATAGATCTGCACAAT-ATAGGCAGG 1050
                         i  v  i     v    v          i i iii   v -  i v  iv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_211386502_   1051 TGGTTTTCCCCAAAGATGCCAAGGTAATTCATCAGGGGAAACAA-AGTCT 1099
                           i     vv   i i       iiv     vi-       v  -     
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCT 398

  chr1_211386502_   1100 TTTGTACAAGTGGTAGTGAAAAAACTAGA-ATCCAAATGAACAAAAATAA 1148
                            vv    i    iv  ii v    i  - ?   v   --     i-- 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG--CAAAAG--A 444

  chr1_211386502_   1149 ATAAACCTCAACTGCTACCTCATCCCAT-T-CAAAAATTAATTTGAAATG 1196
                           i  vi vi  iv        iv    - -          i ii     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_211386502_   1197 GATCATAGGCCTAAACTTAAAAACTAGAGCTATAACACTCT--------- 1237
                              ?  i      iv   i i   i i      v     ---------
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_211386502_   1238 ACA-----GTAGAT---------------------GAAGATTGCTTAGGT 1261
                            -----   i  ---------------------i v i  v     i 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_211386502_   1262 ----CAC-AAAAGTAATAGCCATAGAAGTGGAAATTGATAACTTAGATTC 1306
                         ----   -     i vv   v i i   vii    v     v  i  i i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_211386502_   1307 CATCAAAATTAAAACCTGCTGCTCATTAAAAC-CACTACTTACAAAACTA 1355
                                       v  vi  iv v i   iv-     iiv v   iiv 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_211386502_   1356 ATAGGTAAACCACAGACTAGGAAAAATATATATTGGTTAAAAATC-TGTT 1404
                          v  ii  v       v i   i   ---     v i---     - i v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAA---ATATTTGC---AAATCATATA 738

  chr1_211386502_   1405 TTTAAAAATCTGGCATCCTTTATATAGA-TACACAAAGAATTCCTACAAA 1453
                          i i v  ---  v - i v   vi   -  i i      i  i     v
  L1M4_orf2#LINE/    739 TCTGATAA---GGGA-CTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_211386502_   1454 TCAACAGGGGAAAAAAATGAATAATCTAATTTTTAAAATGAACAAATATA 1503
                             i iv--     i ii     i i    ?v-      ii    vi- 
  L1M4_orf2#LINE/    785 TCAATAAT--AAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGG-A 830

  chr1_211386502_   1504 TTCAAACAAACTTGTCTCACACACACACACACACACACACACACAAGATT 1553
                           ii  i i  v v    ---------------------  v v     v
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTC---------------------CAAAGAAGATA 859

  chr1_211386502_   1554 TACAAGTAACCAATACAAA-ATAAAAAGATGCTCATTATTATTCAAAGG 1601
                              i ii      viv -  i            vi  i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (128 / 83)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 4.71 (160 / 34)  


3133 27.24 1.11 0.55  chr1_211440184_211442321.rev      745  1647 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_211440184_    745 TGGAAGAACATTCCATGTTCATGGAGAGTAAGAATCAATATGGTGAAAAT 794
                              ii i  i             vv v    v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_211440184_    795 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 844
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_211440184_    845 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 892
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_211440184_    893 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCA-AAG 941
                                viiv  ii  v  v v  v     iv     i i ivv -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_211440184_    942 AACAAAGCTGGAGGCATCATGCTGCCTGACTTCAAACTATACTAGAAGGC 991
                                i      vv   ii  v  ii i      viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_211440184_    992 TACAGTAACCAAAACAGCATGGTACAGGTACCAAAACAGAGATATAGACC 1041
                                 i   i    ii      v  i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_211440184_   1042 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1089
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_211440184_   1090 ACCTGATCTTTGACAAACCTGACAAAAACAAGCAAGGCGGAAAGGATTCC 1139
                          vi    i  i     ivv  v   i v  vv   v v      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_211440184_   1140 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1189
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_211440184_   1190 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGA 1239
                            ii    i    v   i     v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_211440184_   1240 TTAAAGACTTAAATGTTAGACCTAAAACCGTAAAAACCCTAGAAGAAAAC 1289
                          i ?    i       v   v       ii     vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_211440184_   1290 CTAGGCA-ATACCGTTCAGGACATAGGCATGGGCAAGGACTTCATGTCTG 1338
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_211440184_   1339 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTTACAAATGGGATCTA 1388
                         vi            vvi          vv     vv i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_211440184_   1389 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGTAACTACCATCAGAGTGAA 1438
                           i   v i  i i   i  ii vv    i vv    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_211440184_   1439 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 1488
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_211440184_   1489 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 1538
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_211440184_   1539 AAAACAA----CCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTT 1584
                           i    ----   v  i? v  i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_211440184_   1585 CTCAAAAGAAGACATTTATGCAGCCAAAAGACATATGAAAAAATGCTCAT 1634
                            v        i  vi viii     v ii  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_211440184_   1635 CATCACTGGCCGT 1647
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


1962 24.86 5.31 0.57  chr1_211591393_211594067.rev      958  1484 (1191)    L1M4_orf2#LINE/L1        2   553 (355)  

  chr1_211591393_    958 GGAAAGATATTTCATGTTCATGGCTACGAAGACTCTATATAGTCAAGATG 1007
                                   ii           v vv       iv    v  i      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_211591393_   1008 TCAGTCCTTCACAGCTTCTTAATCTGCAGATTCAATGCCATCCTGACCAA 1057
                         v  i v  i v  iv  ---i    i         i  v    iv i   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATT---GATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_211591393_   1058 AATCCCAGTGGCT------------ATCGACAAACTGATGCTTAAGTTTA 1095
                                 iv  i------------  i     i     v  v  i  i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_211591393_   1096 TATGGTGATGCAAAAGACCTAGAATAGCCAACATAATATTGCAGGTAAA- 1144
                              vi      ii    i           v i   v   v iivi  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_211591393_   1145 ---AAAGTCAGAGGACTGATAATCCCTGACTTCAAGACTTACTATAAAGC 1191
                         ---     ii       v i v i  ii i     i        i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_211591393_   1192 TACAGTAATTAAGACAATGTGG-A--GA---AAGAATAGACAAATCAATC 1235
                                  i      i     - -- i---   i       v  vi   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_211591393_   1236 AATGGAACAGAAAAGAAAGCCCAGAAACAGACCCATATAGATATGGTCAA 1285
                                i    vv  i  i       i i       i vv         
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_211591393_   1286 CAGTTCTTCGACGATGAAGCAAAGGAAATACAATGGAGAAAAAAAGGTCT 1335
                         iv v i      i v iv  v   ivv  v      i    i  vi    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_211591393_   1336 TTTCAACAAATGATGCTGG-ACAACTGAGTATCCACATGTAAAAAAATGA 1384
                                     i      -       ii  ?       i    i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_211591393_   1385 ATCGAGATGCAGATCTTACATCCTTCATAAAA-----CCCAAAAGAAATC 1429
                          vivi  iv vv i  i   i v vi i    ----- i     vii   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_211591393_   1430 ACAGAACCGAATGTAAAACACAGAACTATAAAACTTGTAAAAGATAACAC 1479
                          ?   v ii       i vvi i            iv  i    v    i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_211591393_   1480 AAGAG 1484
                          i ? 
  L1M4_orf2#LINE/    549 AGGNG 553

Transitions / transversions = 1.61 (79 / 49)
Gap_init rate = 0.01 (8 / 552), avg. gap size = 3.88 (31 / 8)  

1349 21.57 2.04 1.46  chr1_211591393_211594067.rev     1842  2184 (491)    L1M4_orf2#LINE/L1      564   908 (0)  

  chr1_211591393_   1842 TGGCTGTGGCTTTGGTGATGACTTTTTAGATACAACACCAAAGGCACAAT 1891
                           i iv   v  v  ii   ii  i       ii        i      v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_211591393_   1892 CCATAATAGAAAGTATGTATAAACAATAAAGTTTATTAAA-TTAAAA--T 1938
                          v i  v     iv  iv     i-- ii v  i  i   -      -- 
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAAT--TGGACTTCATCAAAATTAAAAACT 661

  chr1_211591393_   1939 TTTCTGCTTGGCAAAAGAGACTATCAAGAAAAGGGAAAGACAAGCCACAA 1988
                            v     --    i  v            iv i        v     i
  L1M4_orf2#LINE/    662 TTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_211591393_   1989 GCTGGGAGAAAATATTTGCAATGGAAATACCTGATAAAGGACT-GTATTC 2037
                         iv                   vvv v   i       i     -    - 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT-C 758

  chr1_211591393_   2038 CAAAATA---AAAGAACTCTTAAAACTCAGCAATGAGAAAACAAACAACC 2084
                           i    ---            v      ii   i i  i     i    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr1_211591393_   2085 CAATTAAAAAACGGGTCAAAGACCGTAACAGACACCTCATCAGAGAAGAT 2134
                              ?     i   iv  i  iivv  i     ii  vi  i       
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_211591393_   2135 ACACAAATGACAAATAAGCGTATGAAAAGATGCTTCACATTACATGTCAT 2184
                          i       i v       ii             iv    i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (48 / 25)
Gap_init rate = 0.02 (7 / 345), avg. gap size = 1.71 (12 / 7)  


2673 27.38 1.91 1.91  chr1_211610491_211612553.rev      682  1572 (491)    L1M4_orf2#LINE/L1       18   908 (0)  

  chr1_211610491_    682 TTCATGGGTTAGAAGACTCAACATAGCAAAAATCTCAATTCTCCCCATGT 731
                                i  i       i  i  v iv  i  vv    v       vi 
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr1_211610491_    732 TGATCTATAGGTTTAATACAACTCTTATCAAAATCTCACCAAGGTTTTTT 781
                                i  i  i  ii   ii i          i  v vivv      
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr1_211610491_    782 ATAGACATAGATAAGCTTATTATAAAATTTATGGAGGAAGGCACAGGCTC 831
                         ii   v  v  i     v  iv       i  ivi i  v   vi  vi 
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr1_211610491_    832 TAGGATAACTGAAACAATCTTGACAAATAAGAATAAAGTGGTAGGAATCA 881
                         i  i   i ii            v   v     i     v v    v   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr1_211610491_    882 CTCTACCTGATATGAAGACCTGTTATAATGCTATAGTAATTAAGGTAAGG 931
                          v  v  ii  v v  i  i ii  i  v    i      i   ii iv 
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_211610491_    932 TGATATTGATGGAAGGATAAACACATAGATTCTGAGAACATAATAGAGAA 981
                           i  i  iiiv       i   i      ivvvi   i v   v    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_211610491_    982 CCCACAACTAAATCCACACAA--ATAGCCCCAACTAATTTTTCACAAAGA 1029
                         i   v  v    i   i   v--  i i --  i i     iv    i i
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTC--AATTGATTTTCGACAAGGG 365

  chr1_211610491_   1030 TGTAAAAGCAACTTCATGGAGAAGGAA-AGACTTT-CATCAAATGGTAAG 1077
                           iv  ii v i iv    i   i   -  v    -  v        ivv
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_211610491_   1078 GAAGCAAGTGGACTTTCATTGGCTAAAAAAATAAATAAATAAATAACCTA 1127
                          iii   v    iv?i  ivv  -    i   i  -------i ---- i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGC-AAAAGAATGAA-------GT----TG 453

  chr1_211610491_   1128 AATCTAAACCTCATATTTTATTCAAAAATTCACTCAAAATGAATTATGTG 1177
                         i i ivv      i iiv   v        v          i  i ?ivi
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_211610491_   1178 CCTCACTGTAACATGTAGAGGTGTAAAACTTTTAGA-GAAAA-ATAAGAG 1225
                            v v     v vv  i iv i       i     -     -   i ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_211610491_   1226 AAAAGCTCTAAGACCTAGAGCCATGAAAAGGGTTATTTGACTTGACACAA 1275
                         v   v  iiiv     v i ii v v  v  v  v  v  iv      v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_211610491_   1276 AAAGCACAATCTATAAAAGAAAAGAATTAATAAATCGGACCTCATCAAAA 1325
                                  v v i         -   vi      i    i         
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAA 652

  chr1_211610491_   1326 TTATCAACTTTTGTTCAGTGAAAGAAC-CTGTTAAGAGAATAAAAAGACA 1374
                            vv         v -v v    i  -  i i    i i i        
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_211610491_   1375 AGCCACAGACTGGAAGGAAATATTTGTAAACCATATATCTGACAGTGGAC 1424
                          v       v   i  i         i   i           i iv    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_211610491_   1425 TAGTATCTATAATATATAAAGATCTCTCAAAAC--AGTG-TAAACA---A 1468
                          v     i v            v    i v   -- i i-    v --- 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_211610491_   1469 AAT--CTTGAT-AGAAAATGAGCAAAAGACAGGAAAAACACATTTCACTG 1515
                            -- iii  -?i      i     i  ivv   v i-       v ii
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG-ACATTTCTCCA 850

  chr1_211610491_   1516 AAGTGGATGTA-AGATGGCAAGTAAGCACATGAAAATATGTTTAACTTCA 1564
                            vi   i  - i     v i              v   i i   v   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_211610491_   1565 TTCAGCCA 1572
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.02 (19 / 891), avg. gap size = 1.79 (34 / 19)  


2487 25.48 1.49 0.60  chr1_211671210_211673633.rev     1263  1933 (491)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr1_211671210_   1263 AAAATCTAGAACAAAACAAAAATAAATGTCGAAACCATGTGATGCTGTCA 1312
                             ii  vv     i v v i   ---  i i  vi    i i   v  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAA---TCAAGACAGTGTGGTACTGGCA 278

  chr1_211671210_   1313 TAAACACAGGCATATGGACCAATGGAACAGAATCAAGAATCCAGAAATAA 1362
                            iv i  i     i  i        i     ii   i           
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_211671210_   1363 AGCTATGCATATATAATCAAATGATCTTCAACAAGGGTGTCAAGATTGCA 1412
                          v i  i   v   ii    v    i   i         i     iiiiv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_211671210_   1413 TAATGAGGAAAGGATAGTCTTTTCAATAAATAGTTTTGAGAAAATTTGAT 1462
                         i    i      i             i    i  vi  i  v  i v   
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_211671210_   1463 ATACACACCAAAAAGAGGGAAACTGGACCCTTAGCTTACACTATACATAA 1512
                          ?v    ivv      iv   ii       i  v  i    i   i i  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_211671210_   1513 AAATCAACTCAAGAGGGGTTAAAGACTTAAACATAAGACCTAAAATTATA 1562
                             i       i v  i i ?    i    ii     v      i    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_211671210_   1563 AAACTACTAGAAGAAAACACAGTGAAAGCTCTTCAAGACATTGATCGAGG 1612
                              vi            i  v?iv iv     iv   v   iviv   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_211671210_   1613 CAAAAATGTTATGGCTAAGACCTCAAAAGCACAGGCAACAAAAACAAAAA 1662
                            vii v iv i v  v   vi          i         iv     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_211671210_   1663 TAGACAAATGGGACTATATTAAACTAAAAAGCTTCTGCACAGCAAAAGAA 1712
                             i    v     vi  i   v v    i   i  ii vv    i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_211671210_   1713 ATAATCAACAAAGTGAAGAAGCAACCTGTTGAATAAGAGAAAATATTTAC 1762
                          iv     v        i ii     iiiv    ii            i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_211671210_   1763 AAACTATTCATCCAACAAGGGACTCATATCCAGAAGGTGCAAGAAACTC- 1811
                            ii  vi   ii i        ii         vi ii  ii     -
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_211671210_   1812 ---AACCCAACAA-----ACACTAAATAATCCCATTAAAAAATATGCAAA 1853
                         ---   i   i  ----- v  -      i  v   ?      iv     
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_211671210_   1854 AGACATAAATAGACATTTCTCAAAAGAAGACATACAAATGGCCAGCAGGT 1903
                         i  iv i              v        i             ii i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr1_211671210_   1904 ATACAAAAA-ATGCTCAACATCACTACTCAT 1933
                          i ii    -             ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (114 / 53)
Gap_init rate = 0.01 (5 / 677), avg. gap size = 2.80 (14 / 5)  


2669 26.03 1.38 5.29  chr1_211738328_211743315.rev     3553  4497 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_211738328_   3553 TAGAGAAATATTCCATATTCATGGATTGAAAGAATCAATATTTTTAAAAG 3602
                          i  i i    i    i           i    v i      v    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_211738328_   3603 TACCATACTGTCCAAAGCAATCTATAGACTCAACGCTATTTCTATTAAGC 3652
                         vi v     vi     vii     i   i       v  ii    i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_211738328_   3653 TACCAATATCGTTTTTCGCAAAGCTAGAAAAAGCTCTTCC-AAAATTCAT 3701
                          v   iivv v     i   i iv v  v  -   vv   -         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_211738328_   3702 ATAGAATCAAAAAGGAGCCTGAACAGTCAAAGTAATCCTAAAAAAAAA-- 3749
                           i   viiv  i   v  v   i  i    ii    i i     i  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_211738328_   3750 ---AAGCTGGAGACATCACATTACTCGACTTCAAACAAC--ACTACAAGG 3794
                         ---   i     ivv     i v i i i      --  --       i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAG 247

  chr1_211738328_   3795 GTAGAGTAACCGAAACAGCATGGTACTGCTACAAAAAAAAAAAATATATA 3844
                         v  v     i i i    ii        vi i  ii -------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA------------- 284

  chr1_211738328_   3845 TATATATATATACACATATATATATAGGCCAGTGGAGCAGAATAGAGAAC 3894
                         ----------------  v i      ii  i    ii     v    ii
  L1M4_orf2#LINE/    285 ----------------TAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_211738328_   3895 CCAGAAATAAACC-ACACACCTACAGTCATGTGATGTTTGACAAAGTCAA 3943
                                      - i   ii  ii    vv    v  i     i viiv
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_211738328_   3944 TAAAA--ATTAGTAGTGAGGAAAGGATTCCCTATTCAATAAATGGTGCTG 3991
                         i  i --   --i i  i      i  vvi  v     i           
  L1M4_orf2#LINE/    369 CAAGACCATT--CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_211738328_   3992 GGATAGCTAGCTAGC-ATATAAAGAAGGATGAAACTGGACCCCTAACTTT 4040
                            i i  i v  ? - i  iv i   i     ii          v  iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_211738328_   4041 CACCATATACAAAAATTAACTCAAGATGGATTAAATATTTAAATGTAAGA 4090
                                                 i      i ? v ii           
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_211738328_   4091 CCTCAAACTATAAGAATCCTAGAAGAAAATTTAGGAAACACTATTCTGGA 4140
                         v  v         i v  i          iv    ?ivv v v   vv  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_211738328_   4141 CATCAGCCTTGGGAAAGAATTTGTGACTATGTCCTCAAAAGCAATTTCAA 4190
                          v ii vi v  v  v iv  iv iiv    v vi        vvvv   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_211738328_   4191 CTAAAACAAAAATTGACAAATAGGACCTAATTAAACTAAAGTGCTTCTGC 4240
                          v   iv      v  i    v    i v  i   v v  ivi   i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_211738328_   4241 ACAGCAAAAGAAACTATCAACAGAGTAAACAGACAACCTATAGAATTGGA 4290
                         i vv    i  v        v i   i  v        i i     v   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_211738328_   4291 TAAAATAAGTATAACCTATGCATCTGACAAAGGTCTAACATCCAGAATCT 4340
                         v      vv ii  vii  ii      i  i  v  vii         v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_211738328_   4341 -TAAAGGAATTTAAACAAATCAACAAGCAAAAAACAACACAATTAAAAAG 4389
                         -     -  i ivv    v    i  vv    i    - i  ii------
  L1M4_orf2#LINE/    767 ATAAAG-AACTCTTACAACTCAATAATAAAAAGACAA-ATAACC------ 808

  chr1_211738328_   4390 TGGGCAAAGCACTAAAAAGTGGGCAAAAGACATGAATAGACACTTCTCAA 4439
                         ----   ----i ?    i        i  iv          i     v 
  L1M4_orf2#LINE/    809 ----CAA----TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr1_211738328_   4440 AAGAAGACATTCATGTGGCCAAGAAACATATGAAAAAAAACTCAACATCA 4489
                                i  v  vi       v  i  i       i vi          
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_211738328_   4490 GTGATCAT 4497
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.20 (63 / 15)  


3039 25.12 0.62 1.24  chr1_211944103_211948731     2861  3668 (961)    L1M4_orf2#LINE/L1        1   803 (105)  

  chr1_211944103_   2861 TGGAAAAATATTTCATGTTCGTGGATTGGAAGAATTAATATTGTTAAAAC 2910
                               i    ii       i            v             i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_211944103_   2911 GTCCATACTAGGCAAAGCAATCTATAGATTAAATGCAATCCCTATCAAAA 2960
                          v v     vvv    vii     i     v  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_211944103_   2961 TGCCAATGGCATTCTTCACAGAAATAGAAAAAC-AATCCAAAAGTTTATA 3009
                          v   iiv  v  i  ii       v  v  i -i    v   i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_211944103_   3010 TGGAACCATAAAATACCCAGAATAGCCAAAGCTATCCTAAGAAAAAAGAA 3059
                              viii  iiv                i v   i i i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_211944103_   3060 CAAAGCTGGAGAAGGCACATTATCTGACTTCAAATTATACCACAGAGCTA 3109
                              i     i vv    i vi ii i      viv   i   i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_211944103_   3110 TAATAGCCAAAACAGCATGGTGTTGGCATGAAAACAGACACATAGACCAA 3159
                         i i  ii   i    ii    ii      i ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_211944103_   3160 TAGAACAGAATAGAGAAACCAGAAACAAATCCACACACCTACAGAGAATT 3209
                          i   i     v    iv       i   i   i   ii  ii vv    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_211944103_   3210 CATTTTTGACAAAGGTACCTAGAACATACACTGTGGAAAAGACAGTCTCT 3259
                         v     i     i   i  v   v   v  v  v     ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_211944103_   3260 TCAATAAATGGTGCTGGGAAAATGAGATATCCATATACAGAAGAATATAA 3309
                             i              v  ivi    ?   i  i  i      iv i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_211944103_   3310 CTAGACCCCTAACTCTCATCATATACAAAAATCAAATCAAAATGGATTAA 3359
                         i i        v   v  i             i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_211944103_   3360 AGATTTAAATATAAGGCCTCAAACTACGAAACTACTACAAGAAGATATTG 3409
                            ii     i    iv  v      ii     vi  v     i i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_211944103_   3410 GGGAAAAATTTCCAGGATATTGTTCTGGGCAAAAATTTCTTGAGAAAT-A 3458
                          ? v   - i i iv  iv   vvi i     vii      -   v  - 
  L1M4_orf2#LINE/    551 GNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chr1_211944103_   3459 CCCCATAAGCACAGGCAACTAAAGCAAAAAAATGGATAAATGAGATTGCA 3508
                          v   v       i     v    --       i       vi  i v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAG--AAAAAATAGATAAATTGGACTTCA 646

  chr1_211944103_   3509 TCAAGTTTAAAAGCTTCTGCACAGCAAAGCATACAATCAACAAAGTGAAG 3558
                             iv      i   i  ii vv     v i  v     v        i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_211944103_   3559 AGACAATCCACAGAATGAAAGAAAATACCTGCAAACTACCCATCTGTATT 3608
                               i          ii        ii      ii ivi     -  v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG-ATA 745

  chr1_211944103_   3609 AG---CCTGTTTTCATGCTGATGATAAAGACATACTCAAGACTGGGTAAT 3655
                           --- i   v i  viv -  -       - iv  i vi   vii    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAAT-AT-ATAAAGA-ACTCTTACAACTCAATAAT 792

  chr1_211944103_   3656 TTATAAAGAAAAA 3668
                         -- v     v   
  L1M4_orf2#LINE/    793 --AAAAAGACAAA 803

Transitions / transversions = 1.82 (129 / 71)
Gap_init rate = 0.01 (11 / 803), avg. gap size = 1.36 (15 / 11)  

 708 20.11 1.09 2.72  chr1_211944103_211948731     3953  4136 (493)    L1M4_orf2#LINE/L1      728   908 (0)  

  chr1_211944103_   3953 CAAACCTTATTACCATCTGACAAAGGATTAATAATCAGAATATATAAGGA 4002
                             i v   ----      i  i   i vi  vi            i  
  L1M4_orf2#LINE/    728 CAAATCATAT----ATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_211944103_   4003 GCTCAAACAATTCTATAGGAAAAAAATTCAATAATCTGATC-ACAAATGG 4051
                         i   vv    i  v   iv     i i-v     i ii  i- v      
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGG 822

  chr1_211944103_   4052 GCAAAAGATTTGAACAGGTATTTCTC-AAAGAAGACATACAAATGGCAAA 4100
                              i        i  ii       -        i           v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_211944103_   4101 CAGACATATGAAAATGTGCTCAACATCACTGATCAT 4136
                         i ii  i       vi            ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.36 (26 / 11)
Gap_init rate = 0.02 (4 / 181), avg. gap size = 1.75 (7 / 4)  


 960 28.10 9.15 3.49  chr1_211989140_211995845.rev       35   493 (6213)    L1M4_orf2#LINE/L1        1   485 (423)  

  chr1_211989140_     35 TGAAATAATATATTGCATTCATGAAT--AAAG--------TTGTTAAATA 74
                           i  vi    viiiii      i  --i   --------       i- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-A 49

  chr1_211989140_     75 TTACAATATATAATTTGTTGCTATATTTATCTATAGATACAATGCAATCC 124
                          vi     i-------- iv i v   v     i    v   i       
  L1M4_orf2#LINE/     50 TGGCAATAC--------TCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chr1_211989140_    125 CAGTGAAAATTACAGTCGTTGTTTTAGAGGAAATATA-AAGCTGAT--TA 171
                          vi v     iv   ii iiv    v vi     vv -        --  
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr1_211989140_    172 AAATTTATATCAAAAGGCAAATAATTGAGAATAGGCAAAGTAACTTTGAA 221
                              i    vi   v    ivi iiv       v    ii  ii     
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_211989140_    222 ------GAACAAAGTTAGAAGACTTAAATTACTAGATTTCTGGTCTCATT 265
                         ------          i  i    i v i v ivi     viiv  i i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_211989140_    266 -TAAATATATAATTATCAAGT--GTATAGTACTGGCATAAGGATAGACAA 312
                         -i   vv  i i v      v--  i i                     v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_211989140_    313 ATAAGTCAATGGAACAGAAT-GTGTAATTCAGCAACAGATCCACACATAT 361
                            ii         i     - v - i i   v  i i i   i    v 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTT 340

  chr1_211989140_    362 TTGGTCACCTAATT----ATAA---T-CCAAATATTACCA--CAACAG-- 399
                         v      vi i   ---- i  --- -    i----    --   ii --
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAG----ACCATTCAATGGGG 386

  chr1_211989140_    400 -----ATGGCCTTGTCTATAA-TAGTGCTAGAACAACAGGCTATTCCTAT 443
                         -----  i i   v  v i  - i     i i     v  v  ?i vi  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_211989140_    444 TGTGAAATGAAGAACATTG-ATCTTTACTTCATATCAGCCATAAAAATGA 492
                         - ii   -   vi vi   - i ii   i   i i  vvi i      v 
  L1M4_orf2#LINE/    437 -GCAAAA-GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_211989140_    493 A 493
                          
  L1M4_orf2#LINE/    485 A 485

Transitions / transversions = 1.84 (83 / 45)
Gap_init rate = 0.04 (21 / 485), avg. gap size = 2.76 (58 / 21)  

3011 27.28 0.78 0.67  chr1_211989140_211995845.rev     5318  6215 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr1_211989140_   5318 ATTCCATGCTCATGGATAGGAAGAATCAATGTTGTGAAAATGGCCATAAT 5367
                           i     i        v      v i   i    v  i     v   v 
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_211989140_   5368 ACCCAATGTAATTTATAGATTCAATGCTATTCCCATCAAGCTACCA-CTG 5416
                         v     vv i  i  i        i  v  i  i     iv v   -   
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_211989140_   5417 AATTTCTTCACAGAATTAGAAAAAACGACTTTAAATTTCATATGGAACCA 5466
                         vv   i  -i     v v  v  ivi  iii    v           vii
  L1M4_orf2#LINE/    110 CCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr1_211989140_   5467 AAAAAATAGCCTGCATAGCCAAGACAATCCTAATCGAAAAGGACAAAGCT 5516
                         v  iii- v  v v        i      i i vvi i   i      i 
  L1M4_orf2#LINE/    159 CAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_211989140_   5517 GGAAGCATCACACTACCTGACTTCAAACTACGCTACAAGGCTACAGTAGC 5566
                            i vv       v  ii i      vivii      i         ii
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_211989140_   5567 CAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAATGCAACA 5616
                            i    ii         i iv ii i   i       i     v  i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_211989140_   5617 GAACCGAGGCCTTGGAAATAACACCACACATCTACAA-CAATCTGATCTT 5665
                            ii   iviiii       vv   i    i  iii-    -    i  
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT-TGATTTT 356

  chr1_211989140_   5666 TGACAAACCTGACATAAATGAG-CAATCGGAAATG--TTCCCTATTTAAT 5712
                         i     ivv  v  - i iv v-    v  i  v -- vvi  v  i  i
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr1_211989140_   5713 AAATGTTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAACTGGA 5762
                              v  i     v      v  ?   i     i  i v    ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr1_211989140_   5763 CCCCTTCCTTACACCTAATACAAAAATTAACTCAAGGTGGATTAAAGACT 5812
                              v   i     vv                  ii     i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr1_211989140_   5813 TAAATGTAATACCTAAAACCATAAATATCCTAGAAGAAAACCTAGGCA-A 5861
                                  v v       i     vv  i           v    ?i- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr1_211989140_   5862 TACCATTCA-GGTTATAGGCATGGGCAAAGACTTCATGTCTAAAACACCA 5910
                         v i -   i- iiiv i  i- i     v ii   v ivv  vi      
  L1M4_orf2#LINE/    556 AATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_211989140_   5911 AAAGGAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAATGAAACT 5960
                             v vvi          vv        i    v   ii v  v   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_211989140_   5961 AAAGAGGTTCTGCACAGCAAAAGAAACTATCATCAGGGTGAACAGGCAAC 6010
                         v  i iv  i  ii vv    i  v       vv ii     v  i    
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_211989140_   6011 CTACAGAATGGGAGAAAAGTTTTGCAATCTATCTATCTGACAAAGGGCTA 6060
                          i                vv       vii  v       i  i  i  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_211989140_   6061 ACATCCAGAATCTACAAAGAACTTAAACCAATTTACAGGAAAAAAGCAAA 6110
                         ii         v  i        ivv  v v iv i iv     ii    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_211989140_   6111 CAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAG 6160
                         i     v  i?    i            v    i     i     v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_211989140_   6161 ATGACATTTAAGGAGCCAACAAACATATGAGAAAATGCTCATCATCACTG 6210
                          v  i  vi  ivi     i  i  i    i  i       v     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_211989140_   6211 GTCAT 6215
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (12 / 899), avg. gap size = 1.08 (13 / 12)  


2506 25.38 8.70 2.00  chr1_211997261_212001659.rev     3058  3908 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_211997261_   3058 TGCAAAGACACTATTTGCTCACGGATCAGAATAATTAATATTGTTAAAAT 3107
                           v     i iiviv  i   i    ii   v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_211997261_   3108 GACCATATCACTCAAGGCAATCTGCAGATTCAGTGCAATCCCTATCAAAA 3157
                          i v   iiv i   ivii    i        ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_211997261_   3158 TACCAAGAACACTTTTCATAGAAAT--AAAAAT--ATCCCCAAATTTGTA 3203
                          v   ivvi vi    iii      -- v  ii--    iv     ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_211997261_   3204 TGGAACCA-AATAGAGCCAGAATAGCCAAAGCAGTCCTGAGCAAAACATA 3252
                              vii-  vi  v              i  i  i   i---------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--------- 191

  chr1_211997261_   3253 AACAAACAAAAACCCAAAATTTAAGGCATTACACTACTTGACTTTAA--T 3300
                         ---   v  i   --   i  vi   vv i     v iii i  i  --i
  L1M4_orf2#LINE/    192 ---AAAGAAGAAC--AAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_211997261_   3301 CTAATACAAATATATAGTA-CCAAGAACAGCATCATACTGTCATAAAAAT 3349
                         i  v      vv  i    -i     -   ii vi     v     ii  
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGAT 285

  chr1_211997261_   3350 AGACACATACACCAACGGAAAAGAATAAAGAACCCAGAAATAAATCCATA 3399
                              i   v i   i    v     vi   ii           i     
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_211997261_   3400 TACTTACAACCAACC-ATTTTTGACAAAGACGTGAAGAAAATACATTGAG 3448
                         i i   iiii   ii-     i     i ii iv    vv  v  v  i 
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_211997261_   3449 GAAA--------------------------------------TATCCACA 3460
                             --------------------------------------  ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_211997261_   3461 TGCAGAAGAAGGAAACTCTACCCCTAACTCTTACCATATAAAAAAATT-- 3508
                             i     v   ii vv       v   vi        v       --
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_211997261_   3509 --CAAAATGGACCAAAGACTTAAATATAAGATCCAAAACTATAAAACTAC 3556
                         --         i  ?    i     i     v i              vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_211997261_   3557 TAGAAGAAAATATAGGG--AAATGCTTAAGGACATTGGTCTAGGCAAAGG 3604
                                   i     ?--    -   viv   v    vi       v  
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_211997261_   3605 TTTTTATAGCTAAAATTTTGAAGACACAGGCAATAA--TAAAAAATAGAC 3652
                            i -   v  vi iviii  ii    i    i  --v          i
  L1M4_orf2#LINE/    585 TTTCT-TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_211997261_   3653 AAACATGACTACATTAAACTGAAAAGCTTCTGTACAGTCAAGTAAAC--- 3699
                            ivv    v   i   v v    i   i   i vviv   v v  ---
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_211997261_   3700 -AATAGAGTGTAGGAACAACTTGCAGAATGGGAGAAAATATTTGCAAGCT 3748
                         -  v i    v iii     iii                        iii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_211997261_   3749 ATTCATCTG------------TATTTAGAATAGACAAGGAATTCAAACAA 3786
                           vi     ------------   ii      v i  i   i  vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_211997261_   3787 GTCAACAACAAAA---TAAATAAATCCATTAAAAAGTGAGTAAAGGATAT 3833
                         v    i  i    ---i      vi v   ?    i  i i       v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_211997261_   3834 GAATAGCCATTTCTTAGAAGAAGACGTACAAATGGCCAACGGGTATATGA 3883
                               v       ivi       ii             iii i i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_211997261_   3884 AAAAATGCTCAACATCACTCATCAT 3908
                            i             ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (138 / 74)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 5.06 (91 / 18)  


 563 29.32 13.66 3.85  chr1_212031878_212033633      459  1263 (493)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr1_212031878_    459 ACTGGAGAAATT--TATTATTA------TAATTCTCCAAAAACAAGTCC- 499
                          i    ii v  --    i   ------i   v    vv   ivii  i-
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr1_212031878_    500 TAAATTTAGTATCATCCAAATCCAAATTCCAACAGGATTTCT----GAAG 545
                         i i   i iiiiv    vv   v    i   i v vv   i ----   i
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr1_212031878_    546 GTGTTTGACAGGCTTATTCAAAAATTCATGTAGGAGGTCTTCA------C 589
                         ----      i   v  i v         i i i i--- v  ------ 
  L1M4_orf2#LINE/    125 ----TTGACAAGCTGATCCTAAAATTCATATGGAAA---TGCAAGGGACC 167

  chr1_212031878_    590 CATAAGAATA--TAAAAGGCATTTTTAAAAAGAAGAACAAAGACAAGGGA 637
                           ---     --i    vi-  i  v                viiii   
  L1M4_orf2#LINE/    168 CA---GAATAGCCAAAACA-ATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr1_212031878_    638 TTATCAAAAT-----ATATCTAAACATAGTAACAACATA-AGAAATCAAA 681
                         i --  v v -----  v  v    v  v  vv  vv  -  v      i
  L1M4_orf2#LINE/    214 CT--CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_212031878_    682 ATTGGCTAGTATTAAAACAAGAATAGA---ATAGGATATCAATAAATCGG 728
                          iv vv i   i iiv i   i     ---    ---      ii vii 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAG---ATCAATGGAATAG 308

  chr1_212031878_    729 AATACAGACTTCAGAAACAGACTAACATA-ATTCA-----AACTACTTTT 772
                            vv   v i      i i  i--    -   i -----  i iv    
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCAATTGATTTT 356

  chr1_212031878_    773 CAA-------GCTA---C-------TGAGGAGATGATATGGTATTCAAAA 805
                          i -------  i --- -------  i   i vi   vvv v     v 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_212031878_    806 AATTGGGTTGGGGTAATTGAATGTTAACTTTGATAATAAAAAGTGAAGT- 854
                            v v i    ii  i  i  i?iv  ----  ivv   i i      -
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCAC----ATGCAAAAGAATGAAGTT 452

  chr1_212031878_    855 ----CCCTACCTCACAGAA-ATAATAAAAACAAGTTTTAAATTGA----A 895
                         ----            vv -   -i     iv ii iv    v  ---- 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATA-CAAAAATTAACTCAAAATGGATCAWA 501

  chr1_212031878_    896 GATACAAATATAA-AGC-----------AATGTTTA-AGGTAATTATGAA 932
                           ivi    i   -   -----------  ivi   - i v  vi  - i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AG 550

  chr1_212031878_    933 AAATACATCTACA--AACATGGAATAAATGA-GGTCATCTTCAACAAGAT 979
                         i?i  v    v i-- v v   iv  iiii -   i-    vi i v  i
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAGATATGAC 599

  chr1_212031878_    980 ACAAAAAATA-AAATATTAAAAGAA--------TAA-TTTGCCTACATAA 1019
                           v    ii -  ii vi       --------   -  v v  v   v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_212031878_   1020 AAATTATAACCTATTTATGTT--AAAAGATGCCATTAATAGATTATTAAA 1067
                               v  v  -   i  i --   i  ii i  i  v i v ivv  i
  L1M4_orf2#LINE/    650 AAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_212031878_   1068 CCCAACAATAAAA-AGGAGAAATATATTTG-AAAT-GTATAT--AATAAG 1112
                         v v v v i i  -i       -       -    -i     --i     
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAA-ATATTTGCAAATCATATATCTGATAAG 747

  chr1_212031878_   1113 CAAAAAGTTAGTATACAGTATGTGAAAATAACTCCTACAAATTAATATTT 1162
                         ---ii v  -    v   v  i iv   v     i     v i    v v
  L1M4_orf2#LINE/    748 ---GGACTT-GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_212031878_   1163 TAAAGAC-------CCA---CAAAAATGGG-ACAGAATGTAAACACACAA 1201
                         v      -------   ---?         - v  i  v i  i v   v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_212031878_   1202 TTC-CAAGAGAGAAGACCTAAATAACCAGTAAGCA--TGAGAAGATATGC 1248
                            - v i   ii v ivi    ii   i      --   i     iiv 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_212031878_   1249 AGCCTCATTGGTTAG 1263
                          i v   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (134 / 99)
Gap_init rate = 0.06 (50 / 884), avg. gap size = 2.82 (141 / 50)  


2423 25.83 8.65 1.07  chr1_212074613_212076896      950  1793 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_212074613_    950 TGGAAAGCCATCTCATGCTCATGGATCAGAAAA---AATATTGTTAAAAT 996
                                vi   i    i        ii   i ---           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_212074613_    997 GACCACACGACTCAAAGCAACCAATATATTCAAGGAAATTGGTATATAAA 1046
                          i v i  vv i    vii i v i v      v v   ivv   -i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-CAAA 99

  chr1_212074613_   1047 AAATCAGTGACATTGTTCGTAGAAAATTTTTAAA--GA-CCTAAAATT-A 1092
                          vvi   ivi v  v  i i     -  vvi  i--  -         - 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCA 148

  chr1_212074613_   1093 T-------CACAAAAGATGCCAAATAGCCAAAGCAATCCTAAGCAAAAAG 1135
                          -------ii   ii  iv vi          i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_212074613_   1136 AACAAAGCTCATGGCATCAGACTATCTGACTTCAAAATATGCTACAAAGC 1185
                                i viv  vv   v   vi ii i       iv i         
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_212074613_   1186 TATAAAAACCAAAACAATATGGTATTGGTATAAAAATAGACACATAAATT 1235
                           i iv  i   i   i i     i   i    ii       i   i  i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_212074613_   1236 AATGGTACAGAATACAGAAACCAGAAATAAATCCATGTATTTACAACTAA 1285
                              v i     vv   iv           i    ii     iiiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_212074613_   1286 TTGGTGTTTGACAAAAGTACCAAGAACATACATTGGGGAAAGGTTACTCT 1335
                            i v  i     ii  i      v   v  v         iv  v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_212074613_   1336 CTTCAACAAATGATAAGAGGAAAACTAAATA------------------- 1366
                         i           i ivvi   v    ii   -------------------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_212074613_   1367 -------------------------TACAAAAACCAACTCTCAATGGATT 1391
                         -------------------------        ii     vv       i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_212074613_   1392 AAAGACTTAAATGTAAGGGCCAAAACTATAAAACTACAAGAATGAAA--T 1439
                          ?    i          i  i              viv    vi   -- 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_212074613_   1440 AGGGG-AAATGCTACAGGACATTAT-CTAGGCAAAGATTTTATGACTACC 1487
                            ? -    -  v iv   v  iv-i       v i   iv iiv  iv
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_212074613_   1488 ACTTCATAGGCACAAG-AACCAAA-AAAAAATTGACAAATGAGACTCTA- 1534
                           vi  v i       -   v   -       v  i    vi    ii -
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_212074613_   1535 CTTAACTAAATATCTT----CTTCAAAGCAAAGGAAACAATCAACAGAGT 1580
                          vv  i    v ii  ----        -----  v  v     v i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAG-----GACACTATCAAGAAAGT 692

  chr1_212074613_   1581 GAAGAGACAACCTGCAGGACGGGAAAAATATATTTGTAAATGATTCATCT 1630
                            i        ii   i i    i   -       i    v  vi    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAA-ATATTTGCAAATCATATATCT 741

  chr1_212074613_   1631 GACAAGGGGCTGATATGCAAAATACACAAGGACATCAAACAACTCAATAG 1680
                           i     i  vi   v  i    i i  i  vv  vv           i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_212074613_   1681 TAATAATA---ATAATGCCTTTAAAAAGTGGGCAAAGGATGTGAATAGGC 1727
                            v  v ---    iv vv  ?    i            v       i 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_212074613_   1728 AGTTCTCAAAAGAAGACATACAAATGGTCAACTGGTATATAAAAA-ATTC 1776
                          v     v        i          i   ivi i i  i    -  v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_212074613_   1777 TCAACATTGCTAATCAT 1793
                                ii????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (131 / 84)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.10 (82 / 20)  


3134 27.18 0.99 0.66  chr1_212093440_212099859     5023  5927 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_212093440_   5023 TGGAAGAACATTCCATGCTGATGGATAGGAAGAATCAATATCATGAAAAT 5072
                              ii i  i     i v      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_212093440_   5073 GGCAATACTGCCCAAGGTAAT-TATAGACACAATGCCATCCCCATCAAGC 5121
                                  v     iv i  -  i   iv   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_212093440_   5122 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTTATA 5170
                          v   iivi i  i  ii     v v  v  i  - iii    i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_212093440_   5171 TGGAACCAAAAAAGAGCCCGTATTGCCAAGACAATCCTAAGCCAAAAGAA 5220
                              viiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_212093440_   5221 CAAAGCCGGAGG---CATTACTCCCTGACGTCAAACTGTACCTCAAGGCT 5267
                              ii     ---  i-   i  ii iv     viv   iv   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_212093440_   5268 ACAGTAACCAAAACAGCATGGTACTGGTGCCAAAACAGAGATGTAGATCA 5317
                                i   i    ii         iiiv ii i   v  i       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_212093440_   5318 ATGGAACAGAAC--AGAGCCCTCAGAAATAACACCATACATCTACAACCA 5365
                               i    i--    i  --        vv        i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_212093440_   5366 TCTGATCTTTGGCGAACCTGACAAAAATAAGAAATGGGGAAAGGATTCCC 5415
                         vi    i  i i i ivv  v   i vi vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_212093440_   5416 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5465
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_212093440_   5466 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5515
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_212093440_   5516 TAAAGACTTAAATGTTAGACCTAAAACAATAAAAACCCTAGAAGAAAACC 5565
                         i ?    i       v   v       v      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_212093440_   5566 TAGGCAGTA--CCATTCAGGACATAGGCACGGGAAAGGACTTCATGACTA 5613
                             ?-   --i -   iv   v v  vvii  v  v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_212093440_   5614 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5663
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_212093440_   5664 ATTCAACTCAAGAGCTTCTGCATGGCAGAAGAAACTACCATCAGAGTGAA 5713
                           iv  v i  i i   i  iiivv  i i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_212093440_   5714 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCCACCCATCTGACA 5763
                         v  i     i                 v       vi  ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_212093440_   5764 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5813
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_212093440_   5814 AAAATCAAACAACCCCATCAAAAAGTGGATGAAGGATATGAACAGACACT 5863
                           i -    i     v  i?    i   iii      v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_212093440_   5864 TCTCAAAAGAAGACATTTATCCAGCCAACAGACACATGAAAAAATGCTCA 5913
                             v        i  vi vvii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_212093440_   5914 TCATCACTGGCCAT 5927
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


 560 29.03 1.21 5.24  chr1_212110500_212117154.rev     3143  3390 (3265)    L1M4_orf2#LINE/L1        1   238 (670)  

  chr1_212110500_   3143 TGGAAATACTTTCTACGTGCATGGATTACAAGAATTAATATCATTGAAAT 3192
                               v iv i i i  v        iv    v       ii  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_212110500_   3193 CACCATACTGCATTAAGCAATCTACAAATTCAGTGCAATCTCTATCAAAA 3242
                         vi v     v viv  vii       i     ii      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_212110500_   3243 TACCAATGACATTTTTCACAAAAATAGAAAAAAACT-ATCCTAAATATTG 3291
                          v   iivi v     ii  i    v  v  i--  -        vv ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_212110500_   3292 TATAAAACCAAAATAGAACCGAAATAGCTTTATTTAAGTAATCTTAAGTA 3341
                            ii  viiv  vi  v  ii      i-- ---  ii      i i- 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCC--A---AAACAATCTTGAA-A 192

  chr1_212110500_   3342 AAGAGGGCAGGGCCAGGTGTGGTGG-CTCACGCTTGT-AATCCCAGCACT 3389
                             ----  ii v i  -   v  -     i   vi-   ii  iv   
  L1M4_orf2#LINE/    193 AAGA----AGAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_212110500_   3390 T 3390
                          
  L1M4_orf2#LINE/    238 T 238

Transitions / transversions = 1.77 (46 / 26)
Gap_init rate = 0.04 (9 / 238), avg. gap size = 1.78 (16 / 9)  

2401 24.28 3.96 2.59  chr1_212110500_212117154.rev     3626  4358 (2297)    L1M4_orf2#LINE/L1      166   908 (0)  

  chr1_212110500_   3626 CTCAAAA-AG--AAAAAAATT----AAAAGGAGGGCAAAGCTGGAAGCAT 3668
                          i  i  -  --    v   i----     i  ii     i    i vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_212110500_   3669 CACACCACCTGACTTAAAAATATATTACAAGGCTATAGAAACCAAAAAAG 3718
                              iv  ii i  v    iv  i     i    i  v  i   i v  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_212110500_   3719 CATGGTATTGGTATAAAAACAGACACATTGACCAATGGATAGAGAATAGA 3768
                         ii     i   i    ii i     i  v  i       ------     
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA------ATAGA 309

  chr1_212110500_   3769 GAATCCAGAATAGAGAATCCAGAAATAAACCCATATATTTATAGGCAGCT 3818
                         ---------  v    i                  i      i v  ii 
  L1M4_orf2#LINE/    310 ---------ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_212110500_   3819 GATTTTTGACAAAGGCACCAAGAATATACATTGGGGGTAAAAAGTCAACC 3868
                               i     i  ii      vi  v  v     --   i i - ii 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAAGAAT-AGTC 397

  chr1_212110500_   3869 TCTTCAATAAAAGGTGCTGGAAAAATTGGATATC----TGCA------TA 3908
                          i     i   v        i v  i      ? ----    ------ i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_212110500_   3909 AACCTAGACCCCTAACTCTCACCATATATAAAAATAAACTTATTATGGAT 3958
                           vi i        v   v         i      v    i vv      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_212110500_   3959 TAAAGACTTAAACATAAGACCTGAAACTATAAAATTACTAACAGAAAACA 4008
                         i ?    i    ii     v  i           i vi  iv        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_212110500_   4009 TAGGGAAAACACTTCAGGATGTTGGCCTTGGCAAAGATATTATGGCTAAA 4058
                             ?iv  vv    iv  iv    vi v     v i v iv i v  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_212110500_   4059 ATCTCAAAAGCA---ACAACAAAA----AAATTGATAAATACGACTATAT 4101
                          ivi        ---i        ----    v       vv    vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_212110500_   4102 TAAACTGAAAAGTTTCTG-----CAAATGAAACAATCAGCAGAATGAAGA 4146
                         i   v v    ii  i  -----    v  v  v    iv i i    i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_212110500_   4147 GACAACATGTTGAGTTGGAGAAAATATTTGCAAACTATTCATCCACCAAA 4196
                               viiiv  i v                  ii  vi   iivi  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_212110500_   4197 GGACGGATATCCAGAATACACAAGGAACTCAAACAACTCAACAGTAAAAG 4246
                             vvi           i i  i      vv         i i     i
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_212110500_   4247 TAACAAATAATCCCATTAAAAAGTGGGCAAAGGACATGGATAGACAGTTT 4296
                         -i        i  v   ?    i           iv  i       v  i
  L1M4_orf2#LINE/    798 -GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_212110500_   4297 TCAAAAGAAGACATACAAATGTCCAACAGGTTTATGAAAAAATGCTAAAT 4346
                           v        i         v    i i ivi       i     v  i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_212110500_   4347 TTCACTAATCAT 4358
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (109 / 65)
Gap_init rate = 0.02 (13 / 743), avg. gap size = 3.69 (48 / 13)  

2128 25.92 5.59 2.38  chr1_212110500_212117154.rev     5327  6167 (488)    L1M4_orf2#LINE/L1       41   908 (0)  

  chr1_212110500_   5327 TTCTCAATATATTAATTCTCCTGAAATTGATGTGTAGATTCAATGCAATC 5376
                           v i  v  ivi   v    iv        v ii        i      
  L1M4_orf2#LINE/     41 TTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chr1_212110500_   5377 TGAAAAAAAATCCTAGCACACTTCTTCATATATATAGATAAGCTGATTCT 5426
                         ivv vv       i   vvv   i  iii v v  v  i        i  
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr1_212110500_   5427 AACATTAATGTGGATATGCAAAAGTTCTAGAAAAGCCAAAAAAATACTTC 5476
                           v   v  i    v      ii vi i    v        v   -   v
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTG 189

  chr1_212110500_   5477 AAAAAGATAAAACAAAGTAGG-GGACTAACACTACCTCATTTCAAGACTT 5525
                                - i        v  -     v     v  iv       i    
  L1M4_orf2#LINE/    190 AAAAAGA-AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_212110500_   5526 AGTTTTTAAAAATGTGAACATAAAAAT-GTGTGATATTCTTGTGAAGATA 5574
                          --i vi   iv iiiivv  v  i i-     i  i vvii i i    
  L1M4_orf2#LINE/    239 A--CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_212110500_   5575 GACCAT-TCAACCAATGGGACAGAA----GAGTCCAGAAATAGACCCATA 5619
                            -  - vi i      i i    ----             i       
  L1M4_orf2#LINE/    287 GAC-ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_212110500_   5620 GATTTTTACAAAGGTGCAAGTTG--------CAAGG-TGCCAGGTGCAAG 5660
                         v    v -----   -   -   --------     -     i vv  --
  L1M4_orf2#LINE/    336 CATTTAT-----GGT-CAA-TTGATTTTCGACAAGGGTGCCAAGACCA-- 376

  chr1_212110500_   5661 TTTTAAGTAGAAAAAAGGTCATTTTTTAAAACTAATTATGCTAAAACAGT 5710
                         -  i  - i ii   iii vi i    v  - v   vi    iii   ii
  L1M4_orf2#LINE/    377 -TTCAA-TGGGGAAAGAATAGTCTTTTCAA-CAAATGGTGCTGGGACAAC 423

  chr1_212110500_   5711 TTGATATTTATACATAACAAAAAT-AGCTTTAATC--TATTT-GCACTA- 5755
                          v    ?ii i iii  -  i   - iv  vi i --  ii -i   i -
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAA-AAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_212110500_   5756 --ACAAAAATTA-TTCAAAATTGACCATAGACCTAAATGTAAT--CTAAA 5800
                         --          -i       v  i  ?              v--     
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_212110500_   5801 AATGTAAAATTTTTTGAAGAGAACATAACAGGAAAATTTTGTGACCTTCA 5850
                          v i     i i  v     i      iv? v   vi  i        vi
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_212110500_   5851 TGTAGGCCAAGCTTTTTTTAATA---CACCATAA-----------AAAAG 5886
                         vv     v v v   i  vi   ---     v  -----------     
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_212110500_   5887 AAG---TTGATAAATTGGCCTTAATCAAAATTAAAAACATCTGAATTTTG 5933
                           i--- v          v   v               v i  vii  ii
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_212110500_   5934 AAATCAACTTTTAAGAGAAAGAAAAGGCTAGCTACCAATCGAAAGAACAC 5983
                           ivvv   v i    i iv      i v v i  vi vi ii    v i
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_212110500_   5984 ATT-GCAAATCACATAGCAGA-AACGGACTTGTATTCAGAATGTATAAAG 6031
                            -        i   v v  -  v          i      i       
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_212110500_   6032 AACCCCTG-AAGTCAATAATAAAACAACAAAACAAAAAAATT-AAACATG 6079
                            i i i-  v            vi     -i  vvv    -   v   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAA-TAACCCAATTWAAAAATG 821

  chr1_212110500_   6080 GACAAAAGATGTGAATGGACACTTCAATGAAGAAAGTATATCGAAGGCAA 6129
                          i    i   v     i    i   vvii     ii    ivi v   v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_212110500_   6130 AGTAAGCACATGTAAAGATGCTCAACACTGTTAATTGC 6167
                          -          v              iii????????
  L1M4_orf2#LINE/    872 A-TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (123 / 92)
Gap_init rate = 0.04 (32 / 868), avg. gap size = 2.09 (67 / 32)  


3155 26.30 1.33 0.55  chr1_212259812_212265947.rev     4745  5645 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_212259812_   4745 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATCAATATCCTGAAAAT 4794
                               i    i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_212259812_   4795 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTACCCC-ATCAAGC 4843
                            v     v      v i  i  i        i  v i   -     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_212259812_   4844 TACCA-TTGACTTTCTT-CATGAAATTAGTAAAAATTACTTTAAATTTCA 4891
                          v   -i  v    i  -  -      iii  iv- v iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTGACAAGC-TGATCCTAAAATTCA 148

  chr1_212259812_   4892 TATGGAACCAAAAAAGAGCCCATATAACCAAGACAATCTTAAGCAAAAAG 4941
                                viiv  ii  v  viv   i    i        i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_212259812_   4942 AACAAAGCTGGAGGCATCATGCTACCTAACTTCAAACTATACTACAAGGC 4991
                                i      vv   ii  v  i  i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_212259812_   4992 TACAGTAACCAAAACAGCATAGCACTGGTACCAAAACAGATATATAGACC 5041
                                 i   i    ii i i     i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_212259812_   5042 AATGAAACAGAACAGAGGCCTCAGAAGTAACAACATACATCTACAACCAT 5091
                             i  i    iv   ivii     i   vvv       i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_212259812_   5092 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5141
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_212259812_   5142 ATTTAATAAACAGTGTTGGGAAAACTGGCTACCTATATGCAGAAAACTGA 5191
                         v  i  i   ii   i     v      v  ? i i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_212259812_   5192 AACTGGACCCCTTTCTTAGACCTTATACAAAAATTAA-----GATGGATT 5236
                          ii         vi  i v   v              -----i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_212259812_   5237 AAAGATTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5286
                          ?   ii    ii     v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_212259812_   5287 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGAC--CTTATGACTA 5333
                            ?i- v i -   iv   v v  vv i     v ii--    -  -  
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GA-TA 595

  chr1_212259812_   5334 AAACACCAAAAGCAATGGCAACAAAAGCTAATATTGACAAATGGGATCTG 5383
                         vi            vvi          vv  v  v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_212259812_   5384 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5433
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_212259812_   5434 AAGGCAATCTACAGAATGGGAGAAAATTTTTGCAACCTATCCATCTGACA 5483
                            i   i i                 v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_212259812_   5484 AAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAA 5533
                          i  i  vi          v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_212259812_   5534 AAAACAAATAACCTCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5583
                           i          iv  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_212259812_   5584 TTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAGCCTCA- 5632
                         i  v        i  vi viii     i  i  i       i vv    -
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_212259812_   5633 TATCACTGGTAAT 5645
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


4088 18.90 2.80 1.23  chr1_212362054_212364763     1324  2217 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_212362054_   1324 TGGAAGAACATCCCATGTTTATGGACTGGGAGCCTTAATGTTGTTAAGGT 1373
                              ii i          i     i   i  v      i        i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_212362054_   1374 GCCAGTACTGCTCAAGT-GATCTACAGAATCAATTCAATCCCTATCAAAA 1422
                          v  i    v i   i -          v    iv               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_212362054_   1423 TCCCAA-TGC--TTTTTGCAGAAGCAGAAGAAGCC-ATTATAAAATTCAC 1468
                              i-   --           iiv  v-    i-  iv         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr1_212362054_   1469 ATGGAATCTCAAAAAACTGCAAATAGTCAAAACAACATTGAAAAAGAA-- 1516
                               viv   iii  ivvi     i        iv           --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_212362054_   1517 -CAAAGTTGGAGATCTCCCACTTTCTGATTTCAAAACTTACTACAAAGTT 1565
                         -           iv   v     i ii                     i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_212362054_   1566 ACAGTAATCAAAA--GTGTGTTACTGGTACAAAGACAGACACATAGACCA 1613
                                    i --     v      i i  i  i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_212362054_   1614 ATGGGATAGAACAGAGATCCTAAAAATGAACCCTTGCATATATGGGCAAA 1663
                             i      iv    vi i i    i     v i   v     v   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_212362054_   1664 TGATTTTCAACAAAAGTGCCAAGACCATTTAATGAGGAAAGGACCTTTTT 1713
                                 i    ii              i    i      i -- vv i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA--TAGTC 397

  chr1_212362054_   1714 TTTTTTTTAAAGAATGTTGGAAAAGTTGAATATCCACATGCCAAAGAATG 1763
                             ivvi   vii  i   i v ii  i   ?        v        
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_212362054_   1764 ATATTGAACCCTTACTTTATACCATATACCAAAACTAACTCAAAATGGAT 1813
                          vi   i    i   i i i         v    i               
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_212362054_   1814 CAAAGATCTAGATGTAAAAGCTAAAACT-TACAATTCTTAGACGAAAGCA 1862
                           ?   i   i      i          -  v  i       v    i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_212362054_   1863 AAGGGG-AAAT-TTCATGACATTGGGTCTGCCAATGATTTCTTGGCTATG 1910
                         v   ? -    -   i    v      iv v     i      i v    
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_212362054_   1911 ACACTGAAAGCAGAAGCAATAAG-GAAAAAA--GATGAATTGGA-TTCAT 1956
                             ii      v      i  i-       --   i       -     
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_212362054_   1957 CATAATTAATATTAATAACTTTTTGGCATCAAAGAACACTGTCAACAAAG 2006
                           v      ----  --      vv  v      i     i    v    
  L1M4_orf2#LINE/    648 CAAAATTAA----AA--ACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_212362054_   2007 TGAAAAGGCAACTCAT-------GAGAAAATATATTAAAATTATATATCT 2049
                                i    i  i-------          v vv    i        
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_212362054_   2050 GATAAGGAAGTAGTATCCAGAATGTATAAAGAACTTCTATAACTCAAAAA 2099
                                i v v           i           ii  i       v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_212362054_   2100 CATGAA-ACAAAGACCTTATTTTTTAAATGGGCAAATAACTTTAATAGAC 2148
                         i vi  -     v v ii v  ?vv           vi i  v       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_212362054_   2149 ACTTTTTTCCAAAGAAGACATACAAATAGCCAATAAACACATGAAAATAT 2198
                          --   i           i        i        i          v  
  L1M4_orf2#LINE/    842 A--TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_212362054_   2199 ACTCAATATTAGTAATAAG 2217
                         i     i  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (106 / 59)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.89 (36 / 19)  


2322 26.96 4.10 1.76  chr1_212392952_212396176     1872  2724 (501)    L1M4_orf2#LINE/L1       16   888 (20)  

  chr1_212392952_   1872 TGTTCTTGAATCAGAACATTTGATATTGTTAAGATGTCAATTCTCTACCA 1921
                              v  i  ii   v i  i              v    v   iv v 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_212392952_   1922 ATTGATCCACAAATTCAATGCAGTTCTAATCAAAATCACA--TG----TT 1965
                                i   i      i   i i iv         v  --  ----  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_212392952_   1966 TTGTAGATATCAATGACCTGTTTCTGAAATTTATATGGACAGGCAAAGTA 2015
                            i   v  ii ii v   v i  i     i       v v    i v 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_212392952_   2016 GTGAGAAAGGCCAAAATGATTTTTATAAAGGT---CAAAGTTGGAGGACT 2062
                         viv    vi       ii  i  v v    iv---               
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_212392952_   2063 CATACAATGTGATTTGACAGCTTACTATAGAGCTGTAGTAATCAAGATTG 2112
                           i  vvivii    v v i       i i    ii           iv 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_212392952_   2113 TGCGATATTGGTATA--GATATACATATTGATAAATTGAACATAAAAGAG 2160
                           i i  i   i   --    v      v   v   v   i v  vv   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_212392952_   2161 AGTCCAAAAATGG-CCTACAAAACGTGTTTA-----AATTGATTTTTGAC 2204
                               i    ii-  i i v -----    -----          i   
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACA-----TTTATGGTCAATTGATTTTCGAC 360

  chr1_212392952_   2205 AAAAAT-CTAAAAATATTCAATAAAGAAAAGATAATCTTTCCAA-AAATT 2252
                           iii - i  i vi       iii    ii   i     i   -    v
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_212392952_   2253 TTGTTGATACTATTAAATACTTACATGCCAAAAAAAATTAACCTTGACTC 2302
                         v  i  iv  v i ii   ?ii      --    i   v  vi v   i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGC--AAAAGAATGAAGTTGGACCC 458

  chr1_212392952_   2303 ATGCCTCAG--TGTATACAAAAATTAACACAAAACCAATCATAGACATAA 2350
                         v i     v--ii               v     ivi    ?    v   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_212392952_   2351 ATTCAACATGTAAACATACAAATGTTCTAG--GAAATAGACAAGAGAAAG 2398
                           vi  v vv    vv  i   vv ii   --    - v i i ? v  i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA-ACATAGGNGTAAA 557

  chr1_212392952_   2399 TCTCTGTGACCTTAACTCAGGCAAAAAGTTCTTAGATAAAATACCAGATG 2448
                            ii        iiv i      viiv          vi i    i v 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_212392952_   2449 CACAAACTGTCAAGGAAAAAGTA-ACAAATCTAACTCTCTTGGAAAGTTA 2497
                              i viiv  i      i  - i    ivi   -  v vi   v v 
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACT-TCATCAAAATTAA 656

  chr1_212392952_   2498 AAACTCTTTCTCTTAAAAACACACAAATAAGATAATTGAAAA--CAAATC 2545
                              i  viv   v   iv    v vi    -  v      --   vi 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGA-AAGTGAAAAGACAACCC 705

  chr1_212392952_   2546 ATAAGGTAGAGAAGAAATATCTGTAAATCACATATGTGACAAAA-ACTCA 2594
                          i iii i -  ii      i  i      i    v   i  ii-   ii
  L1M4_orf2#LINE/    706 ACAGAATGG-GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_212392952_   2595 AATCCAAAATATATTTAAAAAATTTTCAAAACTCAAAAAATAAGAAAACA 2644
                         v     i       --   i  i i i v       v  -   i  i   
  L1M4_orf2#LINE/    755 TATCCAGAATATAT--AAAGAACTCTTACAACTCAATAA-TAAAAAGACA 801

  chr1_212392952_   2645 AAGAATCTAATTAAGAAATTTGCAAAAGATTTGGAGATACCATTTC-CCA 2693
                           v  i i    ? i    vv     i      i v v  -     -   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC-ATTTCTCCA 850

  chr1_212392952_   2694 GAG----TAAACAAATG-CCAA--AGTGCATGCAAAAA 2724
                         i  ----  v       -    --  ii    v   i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.57 (138 / 88)
Gap_init rate = 0.03 (26 / 873), avg. gap size = 1.92 (50 / 26)  


2970 27.27 1.25 0.80  chr1_212402258_212404174      537  1416 (501)    L1M4_orf2#LINE/L1        1   884 (24)  

  chr1_212402258_    537 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATAAATATCATGAAAAT 586
                               i i  i     i        v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_212402258_    587 GGCCATATTGCTCAAAGTAATTAATAGATTCAATGATATTCCCATTAAAC 636
                            v   i v i    v i  iv i        i vv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_212402258_    637 TACCAATGACATTCTTCACA-AAATTAGAAAAAACT-ACTTTAAAGTTCA 684
                          v   iivi v  i  ii  -     i-- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_212402258_    685 TATGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCATAAGCAAAAAG 734
                                viiv  ii  v  v v        i      v i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_212402258_    735 AACAAAGGTGGAGGCATCACACTACCTGACTTTAGGCTATACTACAAGGC 784
                                v      vv       v  ii i  i iiviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_212402258_    785 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATGGACC 834
                                 i   i    ii         i i  ii i     i  i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_212402258_    835 AATGGAACGGAATAGAGATCTCAGAAATAAGACTGCACATTTACCACTAT 884
                                ii    v    vii         iv iii       iviii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_212402258_    885 CTGATCTTCGACAAACCTGACAAAAACAAGCAGTGGGGAAAGGATTCCCT 934
                         i    i        ivv  v   i v  vv  i         i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_212402258_    935 ATTTAATAAATGGTACTGGAAAAACTGGCTAGCCATATGCAGAAAATTGA 984
                         v  i  i       i    i v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_212402258_    985 AACTGGATCCCTTCCTTACATCTTATACAAAAAGTAACTCAAGATGGATT 1034
                          ii    i    v   i   i v          v        i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_212402258_   1035 AAAGACTTAAATGTAAAACCCAAAACTATAAAAATCCTAGAAGAAAACCC 1084
                          ?    i         i v i            v  i           vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_212402258_   1085 AGGCA-ATACCATTCAGGACATAGGCACAGGCAAACATTTCATGACAAAA 1133
                            ?i- v i -   iv   v v  vvi      vvi    v iivv vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_212402258_   1134 ACATCAAAA--ACAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTA 1181
                            i     --    --          v      v  i    v   ii v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_212402258_   1182 ATTAAACTAAAGAGCTTCTGCATAGCAACAGAAACTATCCTCAGAGTGAA 1231
                           i   v v  i i   i  iiivv   vi  v      vvv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_212402258_   1232 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACA 1281
                         v  i     i                 v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_212402258_   1282 AAGGTTTAATATCTAGAATCTATAAGAAACTTAAACAAATTTGCAAGAAA 1331
                          i  vi vi    i     v     ii    ivv    v ivii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_212402258_   1332 AA-----ACAACCCCATCAAAAAAAATGGGCAAAGGACATGAACAGACAC 1376
                           ----- i     v  i?     --           iv    i     i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATAGACAT 843

  chr1_212402258_   1377 GTCTCCAAAGAAGA-ATTTATGCGGCCAACAAACATATAAA 1416
                         v             -  vi vii      i  i  i  i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (10 / 884), avg. gap size = 1.80 (18 / 10)  


2653 24.84 0.84 6.05  chr1_212415638_212418696     1609  2566 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_212415638_   1609 TGAAAACAAATCCCATATACATGGATGGGTAGAATCAATATTGTGAAAAT 1658
                           i   v v       i v       v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_212415638_   1659 GATCATACTGCCAAAAGCAATCTGCAAATTCAATGCAATTCCCATCAAAT 1708
                          iiv     v  v   vii    i  i      i     i  i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr1_212415638_   1709 TACCATCAACACAATTCCCATCAATGCAATTCCCATCAAAATACCACCAT 1758
                         ----   ----------   -----  -------------- i  -----
  L1M4_orf2#LINE/    100 ----ATC----------CCA-----GC--------------TGCC----- 111

  chr1_212415638_   1759 CATTCTTCACAGAACTTGAAAAA--AATCCTAAAATTCATATGTAATCAA 1806
                         --  i  ii     v    v  i--i                 v  viiv
  L1M4_orf2#LINE/    112 --TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_212415638_   1807 AAAAGAACTCACATAGCCAAAGCAAGACTATGCTAAA--AGGACAAATCT 1854
                           ii  v iviv         i   v-  -  vv   --  i     vi 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGAAGAACAAAGTT 207

  chr1_212415638_   1855 GGAGGTAACACATCACCTGACCTCAAACTATACTAAAAGGCCATAGTCAC 1904
                              vvv    iiv  ii ii     viv     v  i  i i   v i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_212415638_   1905 AAAAACAGTATGGTACTGGTATAAAAATAGGCATATAGACCAATGAAACA 1954
                         v  i     i         i    ii    i        i     i  i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_212415638_   1955 AAATAGAGAACTCAGAAATAAAGCCAAATATTTACAGCCAACTGATCTTT 2004
                         i   v    iii          v   v i     ii i   i    i  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_212415638_   2005 GACAAAAGAAACAAAAACATAAAGTGGGTAAAGGACAACCTATTCAACAA 2054
                              ii viv   i v   vv i    v    i i ii  v        
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_212415638_   2055 ATGGTGCTGGCATAATTTGCAAGCCACATGTAGAAGAATGAAACTAGATC 2104
                                   v i  i v vv ?       i i         ii i  i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_212415638_   2105 CTCATCTCTCACCTTGTACAAAAATCAACTCAAGATGGAACAAAGACTTA 2154
                          ii i   v    v i         i       i     v  ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_212415638_   2155 AATCTAAAACCTGAAACCACAAAAATTCTAGAAGATAACATTGGAA-AAA 2203
                            v   i v  i    i i    v ii       v     v  ?i-   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_212415638_   2204 TCCTTCTAGACATTAGTTTAGGCAAAGACTTTGT-GACAAAGAACCTAAA 2252
                           -   vv   v  i v        v ii  iv -  i viiv   -   
  L1M4_orf2#LINE/    558 TC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC-AAA 605

  chr1_212415638_   2253 AGCAAATGCAACAAAAAGAAAGATAAATAGTTGGAACTTAATTAAACTAA 2302
                             v v         ii   i   i   iv v i    v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_212415638_   2303 AAAGCTTCTGCACAGCAAAAGAAATAACCAGCAGAGTAAATAGACAACCC 2352
                            i   i  ii vv    i  v iv i  iv i   i  v         
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_212415638_   2353 ACAGAGTGGGAGACAGT-CTTAAAAATCTTTACTTCTGACAAAGGACTAA 2401
                              i       v i -i  iv     v - iv     i  i     vi
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCAT-ATATCTGATAAGGGACTTG 754

  chr1_212415638_   2402 TATCCAGAATCTACAAGCAACTCAAACAAATTAGCAAGAAAAATACAAAC 2451
                                   v  i  iv     vv    v i ii  v     v     i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr1_212415638_   2452 AATCAAGTCAAAAAGTGGGCTAAAGACATTAATAGACAATTCTCAAAAGA 2501
                           i v i i?    i     v  i  iv v        v     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_212415638_   2502 AGAATGGCCAAGAAACGTGCAAATGGCCAAAAAACATATGAAAA-ATACT 2550
                            ------------ii i           v  i  i       -  i  
  L1M4_orf2#LINE/    855 AGA------------TATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_212415638_   2551 CAACATCACTAATGAT 2566
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.88 (66 / 17)  


2763 26.30 4.18 1.69  chr1_212536328_212539231.rev     1528  2413 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_212536328_   1528 TGGAAAAATGTTCCATGCTCATGAAGTGGAAGAATCAATAATCACTAAAA 1577
                               i  i i     i     i v       v i    - iii   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA-TTGTTAAGA 49

  chr1_212536328_   1578 TGGCCATAGTGCCCAAAGCAATTTACAGATTCAATGCTATTTCTATCAAA 1627
                             v   v v      vii  i           i  v  ii        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_212536328_   1628 CTACCAATATCATTTTTCACAGAATTAGGAAAAAGCT-ATTCTAAAATTC 1676
                         v v   iivv v     ii     v v -- v     -  i         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_212536328_   1677 ATATGGAACCCAAAAAGAGCCCAAAAAGAGCCAAAGCAATTCTACACAAA 1726
                                 vivv  ii  -    i  -v       i    ii iv v  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAA-TAGCCAAAACAATCTTGAAAAAG 195

  chr1_212536328_   1727 AAGAACAAAGCTGGAGGCATCACATTACTCAACTTCAAACTATACTATAA 1776
                                   i      vv     i v i   i      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_212536328_   1777 GGCTACAGTAACCAAAACAACATGATACTGGTACAAAAACAGACACATAG 1826
                         i          i   i   iii  i      i i  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_212536328_   1827 ACCAATGGAACAGAAAAGAGAATCTAGAAATACAGCTGTGCACCTACAGC 1876
                          i        i    vv    i  i       v v ii i  ii  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_212536328_   1877 TATCTGATCTTTTACAAAGTCAACAAAAATAATCAATGGAGAAAGGACTG 1926
                         i vi    i  iv    i viiv   i vi v       i     i iv 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_212536328_   1927 CCTATTTTAA-AAATGGTGCTGGGGTAGCTTGCTAGCCTTATGCAGCAAA 1975
                         i  -   i  -             ii i  v v  ?  vi     iv i 
  L1M4_orf2#LINE/    396 TCT-TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_212536328_   1976 ------CCAGACCCCTACTTTTCATCATATACAAAAACTAGCTCAAGATG 2019
                         ------iii         i iv  i            i  i     i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_212536328_   2020 GATTAAAGATTTAAATATAAGATCTCATATTATAAGAATCCTAGAGGAAA 2069
                            i ?   ii     i     v  v v i     i v  i    i    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_212536328_   2070 ACTTAGGAA-ACACCATTCTGGATGTTGTCCTTGGG--AAAGAA------ 2110
                           v    ?i- v i -   -----  - v       -- iiv  ------
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTC-----GT-GACCTTGGGTTAGGCAATGGTTT 587

  chr1_212536328_   2111 CTTATGACCAAGTCCTCAAAAGCAATTGCAACAAAA------ATTGACAA 2154
                             -  i- v v vi        vvv         ------  v  i  
  L1M4_orf2#LINE/    588 CTTA-GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_212536328_   2155 GATAAACCTAATTAAACTAAAGAGCTTCAGCACAGCAAAATAAACTATCA 2204
                         iv ii  i v  i   v v  i i   iv ii vv    iv v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_212536328_   2205 ACAGAGTAAACAGACAAATTACAGAGTGGGAGAAAATATTCACAAACCAT 2254
                          v i   i  v      vii     i              ii    i   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_212536328_   2255 CCATTTGACAAAGGTCAAATATCCAGAATCTATAAGAAACTT----AAAT 2300
                         vi  i   i  i  v vvi          v     ii    i----  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_212536328_   2301 CAACAAGTAAAAAACAAATAACCTCATTAAAAAGTGGGTAAAAGACATGA 2350
                            i  vv    i          iv   ?    i    i   i  iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_212536328_   2351 ACAGACACTTCTCAAAAGAAGGCAGACAAACAGCTAACAAACA------- 2393
                          i     i     v       ii v     ii  i  i  i  -------
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_212536328_   2394 ---TGCTCAACATCACTAATCAT 2413
                         ---            ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (148 / 81)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.74 (52 / 19)  


2028 26.69 2.14 0.16  chr1_212665714_212667308      496  1102 (493)    L1M4_orf2#LINE/L1      290   908 (0)  

  chr1_212665714_    496 ACATAGACCAATGGAACAGAACAGAGCCTTCAGAAATAATGCCACATATG 545
                          i     i        i    iv   vv i         vv   i i  v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_212665714_    546 TACAACCATCTGATCTTTGACAAACCTGACGAAAATAAGAAATGGGGAAA 595
                           iiii  vi    i  i     ivv  v i i vi vvv          
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_212665714_    596 GGATTCACTATTAAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTA 645
                          i  vvv  v  v  i              v      v  ?   i   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_212665714_    646 GAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCA 695
                         i  iiv    ii    i    v   i     v              i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_212665714_    696 AGATGGATTAAAGACTTAAATGTTAGACCTAAAAGCATAAAAACCCTAGA 745
                          i      i ?    i       v   v      vi      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_212665714_    746 AGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTC 794
                                v    ?i- v i -   iv   v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_212665714_    795 ATGTCTAAAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATG 844
                         v ivv  vi    v       vvi          vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_212665714_    845 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCA 894
                            ii v  i   v v  i i   i  ii vv    i  v    i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_212665714_    895 GAGTGAACAGGCAACCTACAGAATGGGAGAAATTTTTTGCAATCTACTCA 944
                         i      v  i     i               v v       vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_212665714_    945 TCTGACAAAGGGCTAATATCCAGAAT---CAAACAAAT-TTACAAG---- 986
                              i  i  i  vi          ---i   v  v -      v----
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_212665714_    987 ----AAAGAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACA 1032
                         ----   i i     i     v  i?    i     i      v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_212665714_   1033 CATACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAA 1082
                         v i i     v        i  vi viii     i ii          i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_212665714_   1083 TGCTCTTCATCACTGGCCAT 1102
                              vv     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (86 / 72)
Gap_init rate = 0.01 (5 / 619), avg. gap size = 2.80 (14 / 5)  

 897 27.30 10.17 2.73  chr1_212665714_212667308     1167  1569 (26)  C L1M4_orf2#LINE/L1   (249)   659   227  

C chr1_212665714_   1569 ATTTCAAGATTTAAAATAAAGCCATAATAATTAAGACTTCATAGTATTTG 1520
                                i i   vv i     i i i    i     vvii i   i v 
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

C chr1_212665714_   1519 TAC---------------------TGGCA---AATTAA----TCAGAAAT 1498
                         i i---------------------   v ---    i ----i       
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

C chr1_212665714_   1497 AGACTCAGACTTCCAATGTCAATTAAAATTTGATAGAGGT---AAGGCAG 1451
                          i  i  v  v ii vv       i vv  i  i ii   ---   i vi
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

C chr1_212665714_   1450 TTCAATGGGGCGAGTACAATCTTTTCAACAAATAGTACTGT-ATAG-TGT 1403
                                   vi  v i i              i  i   v- i i-  v
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

C chr1_212665714_   1402 ATAGGAGTCAAA-AAAAAACAATAAAGCTTGACCCCTATCTCACATCATG 1354
                            ?---i  v -iv    v   i   i v        i      i   i
  L1M4_orf2#LINE/    427 ATAK---CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

C chr1_212665714_   1353 CATACAATTTAATTTGAGATGGGTTCATAGACCTAATAAATAAAAGCTGA 1304
                         i i v  v    i ii i    i -  ?        - vi   i    i 
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGAT-CAWAGACCTAA-ATGTAAGAGCTAA 521

C chr1_212665714_   1303 AATTATAAAGCTTCTAGAAGATAA-ATGAGAAAATATCTTGATCATCTTG 1255
                           i      i  ii       v  -  ii ?iv v     vi v i    
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

C chr1_212665714_   1254 GTGTT-GGTAAAGATTTCTCAGACAAGGTACAAACAAAGCGCTAACCAT- 1207
                          -   -  i  v i     i   i v ii  v  --    i v i v i-
  L1M4_orf2#LINE/    572 G-GTTAGGCAATGGTTTCTTAGATATGACACCAA--AAGCACAAGCAACA 618

C chr1_212665714_   1206 ---TAAAAAATGG-TAAATTCAACTTCATCTAAAATATTAAGAA 1167
                         ---v       i -      vi        -     --   i  
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATC-AAAAT--TAAAAA 659

Transitions / transversions = 1.97 (71 / 36)
Gap_init rate = 0.04 (18 / 433), avg. gap size = 2.89 (52 / 18)  


 633 29.26 0.53 0.53  chr1_212824015_212827498     1841  2028 (1456)    L1M4_orf2#LINE/L1        1   188 (720)  

  chr1_212824015_   1841 TGGAAAGGCATCCCATGATCATGGATTAGAGGAACTAATATTATAAAAAT 1890
                                ii        v         i  i  vi       i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_212824015_   1891 GACTGTATTATCAAAAGCAATCTACAGATTCAATATGATTCCTATCAAAA 1940
                          i vi  i vi v   vii              iiii  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_212824015_   1941 TACTAATGATATTCTTCACAGAAATAGAAGAAAAAATTCTTTAAATTCCC 1990
                          v i iiviiv  i  ii       v  vi ivvi  i - v      vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC-TAAAATTCAT 149

  chr1_212824015_   1991 ATGGAACCATAAAG-ACCCAGAATAGACAAAGCAATTTT 2028
                               viii  i -           v    i    i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

Transitions / transversions = 2.06 (37 / 18)
Gap_init rate = 0.01 (2 / 188), avg. gap size = 1.00 (2 / 2)  

2007 24.74 11.56 2.52  chr1_212824015_212827498     2319  2993 (491)    L1M4_orf2#LINE/L1      173   908 (0)  

  chr1_212824015_   2319 TAGACAAATCAATCTTGAGACAAAGTCACCTGTTCAAAAAGAGCAAGACT 2368
                            v    v         i ---------------  i    i   iii 
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAA---------------AAGAAGAACAAAGTT 207

  chr1_212824015_   2369 G-AGGATATCATACTACTTAACTGCAAAATTTACTACAAAGCTATA---- 2413
                          -    i-   i   v ii  i v     i              i ----
  L1M4_orf2#LINE/    208 GGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_212824015_   2414 ------CAGCATGATACTGTCGTAAA-ACAGACACAGAAACCAATGGAAC 2456
                         ------   ii  i     v i   i- i     i v i i        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_212824015_   2457 AGAATAGAGAACCCAGAAATAAATCCACCTATTTACTGCCAACGGGTTTT 2506
                              v    ii           i   ivi     iv i   iv i    
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_212824015_   2507 CAACAAAGTCACCAAAAACAAAGAGTGGGAAAAGGACATCCTCTTCAATA 2556
                          i    i vii    i v  vvv i    i    i i vi  i     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_212824015_   2557 AATGGTGCTGGGGAAACTGGCTATCCATGTGCAAATGAATGAAAATAGAC 2606
                                     iv      v  ?   ii      v       iv i   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_212824015_   2607 CCCCGTCTCTCACCATATACAAAAATCCACTCAAAATGGACTAAACTCTT 2656
                            iii   v                iv            ii ? vv i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_212824015_   2657 CAACGTAAGACCCAAAACTATGAAAATACTAGAAGTAAACCTAGGAG-AC 2705
                         v  i      v i        i   v vi      v    v    ? - v
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_212824015_   2706 GTGCTTCAGGACATTGGTCTGGGCAA-------------ATG-------- 2734
                         i -    iv   v    vi i     -------------   --------
  L1M4_orf2#LINE/    557 AT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_212824015_   2735 ---------------------------------GAATTACATCAAACTAA 2751
                         --------------------------------- i i v       v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_212824015_   2752 AATGCCCTTTCGCAGCAAAAGAAACTACCAACAAAGTGGAGAGACGACCT 2801
                           vi ii  vi  vv    i  v    i   v      i i    i   i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr1_212824015_   2802 ACAGAATGGAA--AAATACTTGCAAGGTATTCATCCAAGAAATGTTTAAT 2849
                                  i --     i      ivi  vi   ii v  iv vi vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr1_212824015_   2850 ACCTAGAATATATAAGAAAATC----AACTCAATGGCCC-----CAAATA 2890
                          i i           ii  v  ----        iiivv-----      
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_212824015_   2891 ATCCAATTAAAACAGGTGCAAATGGTCTGGACAGACATTTCTCAAAAGAA 2940
                          i      ?   v v v     v i i  i i           v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_212824015_   2941 GACATACAAATAGCCAACAAGTACACGAAAAAATGCTCAACATTGCTAAT 2990
                           i        i     i   i   i     i           ii?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_212824015_   2991 CAT 2993
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.86 (106 / 57)
Gap_init rate = 0.02 (12 / 736), avg. gap size = 7.92 (95 / 12)  


3820 19.56 3.72 4.48  chr1_212843195_212845830.rev     1231  2145 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_212843195_   1231 TAGAATGACACCCAATGCTCATGTATCAGAAGACTTAATATTATTAAATT 1280
                          i   v  i i  v   i     v  ii              i    iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_212843195_   1281 AACAACACTCTCCAA-TTGATCTACAGATTTAGTGTAATCTTTGTTAAAT 1329
                         ii   i    i    -              i ii i    ii i i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_212843195_   1330 GCCCACCTTACTTCTTTGCAGACATTGACCATATGATCCTAAAGTTTGTA 1379
                         v    v  vv   i        v      v vv          i  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_212843195_   1380 TG-AAATTCATGGGACTCAAAAATGTCCAAGATAACCTTATAAAAAAAGA 1428
                           -    v  v     i  i  - iv    i i  i   iv    i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAA-TAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_212843195_   1429 -----GTTGGAAAACTCACCCTTCCCAATTTCAAAATTTACTA------- 1466
                         -----      ii      v                i      -------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_212843195_   1467 ----TAATCAAGACAGCATGGTACTGGGATAAAGATAGACATAGAGACAT 1512
                         ----            ii         v    i          v   ---
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA--- 296

  chr1_212843195_   1513 ATTCACTGAAATAGAATTGAGAATTTACAAATAAGCCCTCATATTTATAG 1562
                         --   v  i             i ii v      i   vi i      i 
  L1M4_orf2#LINE/    297 --TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_212843195_   1563 TCAATTGATTTTTGACAACAGTGCCAAGACAGTTCAGTGGAGAAAGTGTA 1612
                                     i     vi          vi    i   i     vi  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_212843195_   1613 GTCGTTTTAACAAATGGTCCTGGGACAATTGTGTTTTTATATGCAAAAGA 1662
                            v   i          v         i  vi v?ii i          
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_212843195_   1663 ATGAACTTGGACTCCTACCCCACCTCACATATAAACAAATTAATTCAAAT 1712
                              v      i      i   vi  i   i   --      i     v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAA--AATTAACTCAAAA 492

  chr1_212843195_   1713 TAAA-CAAAATATTGAATATAAAAGCTAAAATTATAAAATCTTGAGAAGA 1761
                          ii -  ? ivvi i   i   i        i       iii v      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_212843195_   1762 AAATGTAGATGCAAATCTTCATGTCCTCGGATTAGCCAGTGGCTTTTTAG 1811
                            ii   i? i        i  v   i  i    v  i   i  i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_212843195_   1812 ATATGACACCAAACGCCTAAGAAACAGAAGATAAAATGTGTAAGTTGGAC 1861
                                      v  vi   v    i    v     ivi   i      
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_212843195_   1862 TTCATTAGAATTAA---------TATTTCAAAGCACACCAACAAGAAAGT 1902
                              i i      --------- ii       v    i v         
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_212843195_   1903 GAAATAAACAACCCAAAGAATTAGTTGCAAAGTATATAATAAATCTGTAA 1952
                             - i        v     ------------------------- ---
  L1M4_orf2#LINE/    693 GAAA-AGACAACCCACAGAAT-------------------------G--- 713

  chr1_212843195_   1953 TAATGAAGAAAATATTTGCACAGCATATATCTGATAAGAAGCTTGT--CT 2000
                         ---- i              v v               iii     -- i
  L1M4_orf2#LINE/    714 ----GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_212843195_   2001 AGTATATATGAAGAACTTG---AAGTGAATAATCAAAAGACAAATAACTC 2047
                           v      i       iv---  v v      v              i 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_212843195_   2048 AATTTTAAAATGCGCAAATAATCTGAATAGATATTTCTCTAAGGAAGATA 2097
                             ?v      v     vi  i        i       i  i       
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_212843195_   2098 TA-AAATTACCAGCAAGCACATAAAAAGATTTTTGACATTAGTCATCAG 2145
                           -    vi   ii        i       vi ii    i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (117 / 58)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 5.00 (75 / 15)  


1670 28.27 9.38 2.38  chr1_212920994_212923886     1559  2400 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_212920994_   1559 ATATATTACATTTATGGGCTGGA-TACTTGATATTGTTCAGATGCCCATT 1607
                             vii ii  i    ii    -v    i        v     v v  v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_212920994_   1608 CTCCT-AAAT------ACAAAT--GA-GTAATTT------AAATCTCAAC 1641
                             i-    ------   i  --i - i   ii------     i  i 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr1_212920994_   1642 AGAATTTTTTATGAAAATTGAAAAACTGTTTCTAAAATTCATAT----AT 1687
                         v vv      iiii       v  i   v i             ----  
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_212920994_   1688 -------------AATAGCCAAGGCAATCTT--AAAAGAAAAA--AAGTT 1720
                         -------------         ii       --       i  --     
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_212920994_   1721 GGAGAACT---ACT---AGATATGAAGACATG-TATGAAGTTACAGTAAT 1763
                             i   ---   ---vi  v v  i  v i-  ii   i         
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_212920994_   1764 TAAAACTAAATATTTTGGCCCAAGTATA--GACAGACAGACAGATCACTG 1811
                         i  i  -- i i ---  iv vi i   --  i     v i      v  
  L1M4_orf2#LINE/    258 CAAGAC--AGTGT---GGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_212920994_   1812 GGGCAGAATAGAAAGTTCAGAAAGAAACCCATCTTCACATATACAGAGAC 1861
                          iii     v  i   i      v        ----    v  ii vv v
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCAT----ACATTTATGGTCAA 348

  chr1_212920994_   1862 CTGATTCACGACAACGTTACCA---CTGCAGAATGGTAGAAACATTGATT 1908
                         i     iv      v v i   --- iiivv     -i    v v ii i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTC 397

  chr1_212920994_   1909 TGTTTCAAGAGGCAA--GGTTTTCTAGGTTAATTACACATTCAGGTGGGA 1956
                          -      ----   --   v--  i  vi  i iv i ?i  vi  vi 
  L1M4_orf2#LINE/    398 T-TTTCAA----CAAATGGTG--CTGGGACAACTGGATAKCCACATGCAA 440

  chr1_212920994_   1957 CAAAAAT----TTTGACCCCTACCTTATATAACCTCAAAAAATCTATTCC 2002
                         -  i   ----  v           i i iv iv vv      iv i  v
  L1M4_orf2#LINE/    441 -AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_212920994_   2003 AGATAGAACATAGACCAAAATTTGAAAAGTAAAATAATAAAGCTTCCTGA 2052
                          i  i  v  ?     v    v i i iv     iv     i  iiiv  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_212920994_   2053 ATAAACTGTAGGAGGATATCTTCGTGATATCAGGGTTTGCAAAAATAGTC 2102
                          v   vii    ? v v          iv ii  v vv    vii vvii
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_212920994_   2103 TAAACAGAACACAAAAAGTATTAAGTA-TAAAACAA----TGACTAAATT 2147
                           i i vi    v     i i-   i -i    v  ---- iiv      
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCAC-AAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_212920994_   2148 AGACT-CATTAAAATTAAGAAGATCTGCTTATCGACAAATACCATCAAGA 2196
                         i    -   i        i  vv i  iviv  i vii i  i       
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_212920994_   2197 GAATGTGACTGTAAGCCTTAGCCCAGAAGACCATATTTGCTA-TCATGTA 2245
                         i i  vi vvii  v  vi  vvii i   vv        v -    i  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_212920994_   2246 TTTGTCAAAGAACTCATATTCAAAATATG-GAAGACCTCCTATAAATTAT 2294
                          i  vi  i i   ii   i  i     i-i    v   i  i  v i v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_212920994_   2295 TAAGAAAAATACAAACTGTCCAATT-AAAACTTGGCAAA----------A 2333
                            v     v     ivii      -    v v      ---------- 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_212920994_   2334 GGC--TTC-CCAAAAAAGCATATTCATTTGGCAAATAAGCACATGAAAAG 2380
                          i --   -     i   -    v  vv    v                 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_212920994_   2381 AT-CTCAGTATCACTAATGAT 2400
                           -    ii    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.04 (37 / 901), avg. gap size = 2.68 (99 / 37)  


2401 27.54 4.80 1.71  chr1_212970357_212972355      632  1506 (493)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr1_212970357_    632 GACATTCCATGCTCATGAATAGGAAGGACCAATATCGTTAAAATGGCCAT 681
                           i  i     i     i  v     ivii     i     i     v  
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_212970357_    682 ATTGCCCAAAGCAATTTACAGATTCAGTGCTATTTCTATCAAACAAACAA 731
                          i v      vii  i          ii  v  ii        vvvv  i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_212970357_    732 CGACATTCTTGGAATAACTAGAAAAA--AACTTTTTAAATTCATATAAAA 779
                          vi v  i  v v v  v v  v  i--i - ii v          ii  
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATATGGAA 155

  chr1_212970357_    780 CCAAAAATGAGCCCAAATAGACAGAG-AATCCTACACAAAAATAACAAAG 828
                         viiv  iv  v  vi     v  i i-    i iv v  i  v       
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_212970357_    829 GTGGAGGCATTGCATTACTTGACTGCAAACTATACTACAGGGCTACAGTA 878
                         v      vv ii  i v iii i v    viv       ii         
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_212970357_    879 AGCAAAACAGCATGAATCTGGTACAAAAACAGACACATAGACCGAAGAAA 928
                          v   i    ii  ivv    i i  ii i     i     i i v i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_212970357_    929 AAGAATAGAGAGCCCAGAAATAAGGCCATCACACCTACCACCATCTGATC 978
                         v     v     i          iv    -   ii  ivii  vi    i
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGGTCAATTGATT 354

  chr1_212970357_    979 TTTGAGAAAGCTGACAAAAACAAGCAATGGGGAAAGGACTCCCTATTCAA 1028
                           i  v  i v  v   i v  vv            i ivvi  v     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_212970357_   1029 TAAATG---TTGGGATAACTGGCTAGCCATATGCAGAAGATTGAAACTGG 1075
                         i     ---i     i      v  ?   i     i    v    ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_212970357_   1076 ACCCCTTCCTTATACCATATATAAAAATCAACTCAAGTTGGAATAAAGAC 1125
                               v   i i        i      i       iv    vi ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_212970357_   1126 TTAAACGTAAAACCCAAAACTA-AAAGCC--TGAAAGACAATCTAGGCAA 1172
                         i    i    i v i       -   i i-- ii    v  iv    ?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG- 553

  chr1_212970357_   1173 TAGCATTCTGGACATAGGAAATAGGAACAGGCAAAGATTTCACGACAGAG 1222
                           i-  ii --- i --  vv v  ivi      v i    vi---   v
  L1M4_orf2#LINE/    554 TAA-ATCTT---CGT--GACCTTGGGTTAGGCAATGGTTTCTT---AGAT 594

  chr1_212970357_   1223 ATG---CCAAAAGCA---ATGACAAATGG-------GATCAAATT----- 1254
                            ---         ---iii     v i-------   -     -----
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT-AAATTGGACT 643

  chr1_212970357_   1255 ------AAATTAAAGAGCTTCTGCACAGCAAAACGA-ACTATCAACAGAG 1297
                         ------        i -   i  ii vv    i-  -        v i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAG-GACACTATCAAGAAAG 691

  chr1_212970357_   1298 TGAACAGATAACCTATAGAGTGAGAGAAAAGTTTTGCAAACTATACATCT 1347
                             v   i    i i   i  i       vv        ii   i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_212970357_   1348 GGCAAAGGTCTGATAGCTGGCCTCTATAACAAACTTCAACAAATCTACAA 1397
                          ii  i  v  vi  v ii vv v     vi    iiv    v  v i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_212970357_   1398 GAAAAAAACAA----CCCTATTAAAAAGTGGGCAAAGGACATAAATAGAC 1443
                         v     i    ----   v   ?    i           iv i       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_212970357_   1444 CCTTTTCAAAAGAAGACATACATGTGGCCAACAAGCATATGAT----CGC 1489
                         vi  i  v        i     vi       i     i    v----i  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_212970357_   1490 TGATCATCAGAGCAATG 1506
                          v v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.02 (22 / 902), avg. gap size = 2.59 (57 / 22)  


3182 26.98 0.66 0.66  chr1_213046883_213056782     4818  5725 (4175)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_213046883_   4818 TGGAAGAACATTCCAAGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4867
                              ii i  i   v i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_213046883_   4868 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4917
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_213046883_   4918 TACCAATGACTTTCTTCACAGAA-TTGAAAAAAACT-ACTTTAAAGTTCA 4965
                          v   iivi i  i  ii     -    v  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_213046883_   4966 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCACTCCTAATCCAAAAG 5015
                                viiv  ii  v  v v  v     iv  v  i i vvv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_213046883_   5016 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5065
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_213046883_   5066 TACAGTAACCAAAACACCATGGTACTGGTACCAAAACAGAGATATAGATC 5115
                                 i   i   vii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_213046883_   5116 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5163
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_213046883_   5164 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGA--GT 5211
                          vi    i  i     ivv  vv  i v  vv            i --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_213046883_   5212 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5261
                          -- v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_213046883_   5262 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5311
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_213046883_   5312 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5361
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_213046883_   5362 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5411
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_213046883_   5412 AAAACACCAAAAGCAATGGCAACAGAAGACAAAATTGACAAATGGGATCT 5461
                          vi            vvi      i    v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_213046883_   5462 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5511
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_213046883_   5512 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5561
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_213046883_   5562 AAAGGGCTAATATCCAGAATCTACAAGGAAGTCAAACAAATTTACAAGAA 5611
                           i  i  vi          v  i  i   v  vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_213046883_   5612 AAAAACAAGCAGCCCCATCAAAAAGTGGGAGAAGGAGATGAACAGACACT 5661
                            i    ii i   v  i?    i    vi     vv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_213046883_   5662 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5711
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_213046883_   5712 TCATCACTGGGCAT 5725
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  

 618 29.59 9.86 6.96  chr1_213046883_213056782     8251  8767 (1133)    L1M4_orf2#LINE/L1       14   545 (363)  

  chr1_213046883_   8251 CATGCTCATTAATAGGAAGTCTCAATGTAACACAGATGTAAAT---CTAC 8297
                             i    vi  v     v  i   i viivv     vv   --- iv 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr1_213046883_   8298 ACATTGATCTATAGAATCAATGCTATCTTAATTAAAATATTAACAGGTGT 8347
                          v         i   v    i  v   iiv  i     vii i ------
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC------ 107

  chr1_213046883_   8348 GTGTCTGTGTGTGTGTGTGTGTAATTGATAAGATGATTCTATATTTTCTA 8397
                         -  i  v v -----  ii- v      i   v    i   v v  iv  
  L1M4_orf2#LINE/    108 -TGCCTTTTT-----TGCA-GAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_213046883_   8398 TAGAAATGCTAA-----------AGCCAAGATA--CTTAGGGGAAAGACA 8434
                          i       v i-----------      i i --   ----    i v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT----GAAAAAGA 196

  chr1_213046883_   8435 ACAGTAAAGT-GCA--ACT-GCTCTGTCAGATATCAAGCCTTAT----AA 8476
                          v ii     - v --   -i v  vi vi  v    iv    i----  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_213046883_   8477 G-TATTTTAGGAAGTAGTTAAGAATGTGTAGCATTGATACAAAGAT---- 8521
                          -  i-------    i i    vv    i i i  ii i  i   ----
  L1M4_orf2#LINE/    247 GCTAC-------AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_213046883_   8522 -TGTTGAACGAATAGAACAGAAAAGGAGAG-CCAGAAAAAGACCCATATA 8569
                         - i v  v -   i   i    v-v     -       v i       i 
  L1M4_orf2#LINE/    290 ATATAGATC-AATGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACA 337

  chr1_213046883_   8570 TTGCAAAGGCAAC--ACTTTCAA-------GC--------TTCA---GAG 8599
                           -i vi v   i-- i    i -------  --------    --- i 
  L1M4_orf2#LINE/    338 TT-TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_213046883_   8600 AAAGGTCAGTCTTTTCAACAAAGGGTGTTTTAGACAACTGGATGTCTGTA 8649
                             ivi               v    i v-i           i? iii 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTG-GGACAACTGGATAKCCACA 435

  chr1_213046883_   8650 TAGAAAAACAAAGAGATATAATACTTAACCTCCATTGTATATCACACGCA 8699
                          i------    -   -  i vii vi   i i iivi i i  i ii  
  L1M4_orf2#LINE/    436 TG------CAAA-AGA-ATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_213046883_   8700 AGAGTGAATTTCAGCTCATTTGAATTTTTAAAAGAGAAAAGTAAAACAAT 8749
                          i i v  i iv iv viv ii? vvii    v vi i iv      v  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_213046883_   8750 GAAACCTTTAGAAAATAA 8767
                         i    ii      i v  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAA 545

Transitions / transversions = 1.65 (94 / 57)
Gap_init rate = 0.05 (26 / 532), avg. gap size = 3.35 (87 / 26)  

 493 30.12 9.94 1.55  chr1_213046883_213056782     9086  9407 (493)    L1M4_orf2#LINE/L1      560   908 (0)  

  chr1_213046883_   9086 TTTTTAACCTCAAAGAAGGGAAGTATTTCTCAAACA-GA-ATTAAA-GCA 9132
                           iv i    iiiivv   v  vvi     i i i -  - ii   -   
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_213046883_   9133 CAAACTACAGAGAAAATGACTGATAACCTGGATCATGTTAAAATTAAGAA 9182
                            i v   i ii   vi iv     vi    iivii i        i  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_213046883_   9183 CTT-----CATTAAAAGAGACCATTAAGAGAGTAAAAATTCAAG--ACAG 9225
                            ----- v i   i  v  i  i    i   i    vv   v--    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_213046883_   9226 --TTACAGAAGTTATTT-----TCTTATAACTG------GA-TCATACCC 9261
                         -- viv    iv     -----  v    v   ------  - ii  i  
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_213046883_   9262 AGAATAAATTAAAAACATCTACAAATCAATAA-----GTACAGACCACCA 9306
                               v  v  i   vii     v       -----iv   i iv   v
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_213046883_   9307 GAAATTTGAAA--GGGCAATTATTTACTTAAACAGAAACTTC-ATAAAAA 9353
                         --    ?i   --      vvi--- i  i  i   v i   -vi   i 
  L1M4_orf2#LINE/    810 --AATTWAAAAATGGGCAAAGG---ATTTGAATAGACATTTCTCCAAAGA 854

  chr1_213046883_   9354 AGATATCCAAATGGCTAATACATGTATAAAAGAGTGTTCAATATTATTAG 9403
                               v        i    viiii  i   iii  i    i  i ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_213046883_   9404 TCCT 9407
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.82 (62 / 34)
Gap_init rate = 0.04 (14 / 349), avg. gap size = 2.64 (37 / 14)  


2839 25.23 4.64 2.15  chr1_213430060_213433944.rev     2516  3399 (486)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_213430060_   2516 GAGACATACACTATGTTCATGAATCAGAAGATTCAACAAAGTAAAGATGT 2565
                           i v   iv i         i  ii     i i  i vv  v      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_213430060_   2566 TGGTTCTACCCAATTTGATCAATAGATTTAATGAAATTTCTATAAAATTC 2615
                         iii v  v     v      v i     i  i v   ii    v   v  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_213430060_   2616 CTAGGCGGATGTTCTTGTGGACATAGACAAACTGATTCTAAAGTTTTTAT 2665
                          i  - v viv  i   ii  v  v     i     i     i  iv   
  L1M4_orf2#LINE/    103 CCAG-CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_213430060_   2666 GGAAAGGCAAAGGAGCTAGCATAACTGAACTGATTTTGAAAAAGAA---T 2712
                              v    i   v i  v   i ii  vii  i           ---i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_213430060_   2713 AAACTTAAAGGAATCATACTTTCTGATTTTAAGACTTACTATATAGCTAC 2762
                            v  ii    v   i    i ii    i  i        i v      
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_213430060_   2763 ACTAATCAAGACCATGTGGTATTG----AA--ATAGACA-AT-TACCAAT 2804
                          v          vi       i  ----  --       -  -v i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_213430060_   2805 AGACCTCAAC-AAGAATCCAGAAATAAACTCACATAAATATGACCAATTA 2853
                         i  vivv  i-i   i             i  i i vv    ii     i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_213430060_   2854 TTTTTTGACAATGGTACAAAAGCAATT--------------TTGTCCTTT 2889
                         v    i     v   i v  ii v   -------------- v   i   
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_213430060_   2890 CAGCAAATGATGTTGGAAAAACTGAACATCAACAGG---GGGAA-AAAGT 2935
                           i      i  i   i v     i i ? v   v ---ii   -i    
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_213430060_   2936 TAAACCTTCACCTAAACCTCACATCTTATACAAAAATTAACTCAAAACTT 2985
                          ii   ----    --       i v                     ---
  L1M4_orf2#LINE/    452 TGGACC----CCTA--CCTCACACCATATACAAAAATTAACTCAAAA--- 492

  chr1_213430060_   2986 AAAAGTGAA-CAAAAATCTAGATGTAAAACATAAAACTATAAAACGTTTA 3034
                         -----  i -  ? i i   i      i vv              vi   
  L1M4_orf2#LINE/    493 -----TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_213430060_   3035 GAAGACAACATAAGAGAAAACTATCATTATCTAGGGTTAGGCAAAAAGTT 3084
                              v      i ? v   iiv  i v i  v           viiv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_213430060_   3085 CTTAAACATGGCACTAAAAATATAATCCATAAAACAAAAAATTGATAAAT 3134
                             i i   i   i    ii i  v v i    v       v       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_213430060_   3135 TGGTCTCCAACAAAATTTAAAATGTTTGCACTCT------CACTATTAAG 3178
                            v  i  v       v    iv    ii  ii------      i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_213430060_   3179 AAAATGAGAGGACAATTCTCTTGCTGAGAGGAAATATTTGCAAAGCACAT 3228
                            i   i i     ii v vviv  i   i             v  i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_213430060_   3229 AGCCGACAAAGCTCTCATAACAAGAGTAAATAAGGAATT--TACAAGACT 3276
                          v i  i  i vv  ii  v v   i  v    i   i --     --  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CT 785

  chr1_213430060_   3277 GAGTAGTAAGAAAACTAACAACCTAATTTTAAAATGTGCAAAAGACTTGA 3326
                         v i  i   i  i  v  i    i    ?v      v     i  i    
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_213430060_   3327 ACAGACATTTTAAGAAAGGAAATATATGAAATG--CATATAAACACATGA 3374
                          i        ivvv    i i     i-     --  -    i       
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATAC-AAATGGCCA-ATAAGCACATGA 883

  chr1_213430060_   3375 AAGGACGTTCAATGCCATTAGTTAT 3399
                           i  i i    iii  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (140 / 79)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 3.00 (60 / 20)  


2477 20.15 2.79 9.71  chr1_213517036_213518841.rev      492  1315 (491)    L1M4_orf2#LINE/L1      142   908 (0)  

  chr1_213517036_    492 AAATTCCATAATATGGAACCACAAAAGACTTCAAATAGCCAGAGAAATAC 541
                               ----        vii   ii   iivi        i iv   vi
  L1M4_orf2#LINE/    142 AAATTC----ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_213517036_    542 T--AAAAG--GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAAATA 587
                          --     --        i      vv       v  ii i       iv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_213517036_    588 TACTACAAAGCGATAGTGATCAAAACAGCATGGTACTGGTATAAAAACTG 637
                                    v i   i     i    ii         i    ii iv 
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_213517036_    638 ACACATAGACCGATGGAACAGAGTAGATAACTCAGAAATAAATCCACATA 687
                            i     i i      i   i v  v iii          i   i i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_213517036_    688 TTTATAGGCAATTGATTTCCCACAAAGGTGCCAATAACATTCATTGAGGT 737
                              i v          i v    i        v v      v  i  -
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG- 386

  chr1_213517036_    738 GTTGTTAGAGAAAGAAAGAGTTTAGGATGTTTCTGAAGTTCTGGGGCTGT 787
                         ----------      -v   i ------    -----------------
  L1M4_orf2#LINE/    387 ----------AAAGAA-TAGTCT------TTTC----------------- 402

  chr1_213517036_    788 GCAACCACAAGATGTAAACTACTGGAGAAGGATAGATGGTGTTGGGGAAA 837
                         ----------------   -------------- i      i    iv  
  L1M4_orf2#LINE/    403 ----------------AAC--------------AAATGGTGCTGGGACAA 422

  chr1_213517036_    838 GTGGATATCTATATGCAGAAGATTGAAACTGTATCCCTATCCCTCGCCAC 887
                         v      ? i i     i    v    ii  v i     i i v i   i
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_213517036_    888 ATACAAAAATAAACTTAAAATGGATTAAAGACTTAACTGGAAGACCTGAA 937
                                   v    i         i ?    i   v  v    v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_213517036_    938 ACTATAAA-CTACTAGAAAAAAACATACAGGAAACTCTTCAGGACATTGG 986
                                 -  vi     i        vi? v  v     iv   v    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_213517036_    987 TCTAGGAAAAGATTTTGTATGTAAGACTGTAAAAACACAGACAGCAACC- 1035
                         vi    v  v i   iv  vi  v   vvi    i    ii  i   vv-
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_213517036_   1036 AAAAAGTAGATA--TTAAACT-----GAAG----AAACTTCTGCACAGCA 1074
                              i      --  ii   -----i  i----      i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_213517036_   1075 AAGGAAACAATTTATGAAGTCAAAAGACAACCTGTA-AATGGGAGAAAAT 1123
                              v  v  iv vi    v           iii -             
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_213517036_   1124 ATTTGCAAACTGACACAGACTAGCTGTGACAAGGGACCAATATCCAGAAT 1173
                                  i---  i ---  v   -- i       ivi          
  L1M4_orf2#LINE/    723 ATTTGCAAAT---CATA---TATCTG--ATAAGGGACTTGTATCCAGAAT 764

  chr1_213517036_   1174 ACACAAGAAAC----ACAACAGCAAAAACAAAGCAAAACAAATAATTCAA 1219
                          i i  ii   ----     -v   v  i   --  i        ii   
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAAC-TCAATAATAAA--AAGACAAATAACCCAA 811

  chr1_213517036_   1220 TT-AGAAATGGGCAAAGGATCTCAATAGAGATTTCTTAAAAGAAGATGTA 1268
                           - i               i v      v      iv         i  
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_213517036_   1269 CAAATAGCCAATAAGTATTTGAAAAAATGTTCAACATCACTAGTCAT 1315
                              i         i iv      i   i         ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (105 / 58)
Gap_init rate = 0.03 (21 / 767), avg. gap size = 4.90 (103 / 21)  


3106 23.91 4.69 1.37  chr1_213529235_213531217.rev      619  1492 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_213529235_    619 AGATATTCCATGTTCATGGATAGGAAGACTCAATATTGCCAA-ATGTCAG 667
                               i              v        i       ii  -   v  i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_213529235_    668 CTCTTGCCAACTTGACCTATAGATTCAATGCAATTCCAATCAAAATTTCA 717
                         iv  iv    v    i   i        i     i  v        ii  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_213529235_    718 GCAAGTTAGTCTGTGGATATCAACCCATGGATTCTTAAATTTATAGAGAC 767
                           vivi vv i  ii  v  ii  vviiv   i  v     i   vi  -
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA- 154

  chr1_213529235_    768 AAAAAAAAAAAAAGACCCATACTAGTCAACACAAGAATGAAAGAGAATAA 817
                         ----  viv  ii      v v   i   v    vvv     i    v  
  L1M4_orf2#LINE/    155 ----AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_213529235_    818 TA---TGAGAGAACTGATACT-------------ACTT----TAAAGCTA 847
                         i --- vi   i   v i   -------------    ----i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_213529235_    848 CAGTAATCAAGACAGTGTGGTATTGGCAAAATAATAGGCAAGTAGATTAA 897
                                               i     v  vi    i  vi     i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_213529235_    898 TGTAACAGAATAGAGAGCTCAAAACTAGACCACATAAAC--ACAGTCAGT 945
                           v  i     v     ii  i  v  i   -    v i-- ii    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACC-CATACATTTATGGTCAAT 349

  chr1_213529235_    946 TAATCTTTGACAATGGAGCTGGGGAAATACAATGGGGAAAAAATAGCCTT 995
                          i  i  i     v  v  iii ivv  v           i     i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_213529235_    996 TTCAACAAATGGTGCTTGAACAACTGGATATCCACATGCAAAAATAAAAG 1045
                                         v i           ?            ------ 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA------G 443

  chr1_213529235_   1046 AATGAATCTAGACATAGATCTTACATTCTTCACAAAAATTAACTCAAAAT 1095
                               vi i   vivv i  i   iiv vi                   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_213529235_   1096 GTGTCATATACCTAAATGTAAAATGTAAAACCATAAAACTTTTAGAAGAG 1145
                          vi   ? v            i vv      i        i        i
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_213529235_   1146 AACATATGAGAAAATGTAAATGACTTTGGGTATGCCAATGACTCTTTAGA 1195
                               v ? v    v vvi    i      vv v     ii ii     
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_213529235_   1196 TACAGCACCAAAGGTACAATTCATGAAA-------TAAATAA-TTG-ATT 1236
                           iii       i i    viv ii   -------  i    -   - i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_213529235_   1237 TCATTAAACTTAAAAATTTCTTCCCTGTGAAAGACACTGTCAAGGGAATG 1286
                             i   v       i  i viv  vii  i      i     ii i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_213529235_   1287 AGAAAACAAGCCAAAGACTGGGAGAAAACATTTATAAA--AGACATCTTA 1334
                          i  i    v   v   v          i    ii   -- v i    v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_213529235_   1335 TAAAGGATTGTTATCCAAAATATACAAAGAACTCTTAAAACTCAACAATA 1384
                            i   i vv      i      i            v       i    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_213529235_   1385 AGAAATCAAATAACCCAATTAAAAAATAAGCAAAAGACCAGAGCAGAAAA 1434
                          i  iv              ?      ii     i  iiv  ii   v v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_213529235_   1435 CTTACAAAAGAAGAAATACAAATAGCAAATAAG---AT----AGACAATC 1477
                         i iv v        v        i  v      ---  ----   iiv  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_213529235_   1478 AACATCATATGATGT 1492
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (124 / 81)
Gap_init rate = 0.02 (14 / 903), avg. gap size = 3.79 (53 / 14)  


3101 25.83 0.66 2.54  chr1_213707825_213712103     2881  3786 (493)    L1M4_orf2#LINE/L1       20   908 (0)  

  chr1_213707825_   2881 CATGGATACAAAGACACAATATTGTCAGTATGTCAGTTTTTCCCAACTTG 2930
                                vvi     vi        i iv   v  i vi i     v   
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chr1_213707825_   2931 ATCTATAGATTTATTGTAATCCCAGTAAGTTTTCTCAATAAAATCCCAGT 2980
                              i     i vi i      --  -------    ---        i
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCC--TA-------TCAA---AATCCCAGC 107

  chr1_213707825_   2981 AAGTTATTCTGTAGATATTGACAAACTGATTCTGAAGTTTATATGGAAG- 3029
                         vivi v  i  i   v        i     i  i  i  i        i-
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr1_213707825_   3030 GCGAAAGACCCAGAATGGCCAACTCAATATTGAAGAAGAAGAACAAAGTC 3079
                           i ii          i     vv    v     i              i
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr1_213707825_   3080 AGAGGGCTGACATTAGTCAAATTTGAGACTTACTATAAAGCTACAGTAAT 3129
                         i    i  v   i vvi   v  ii i        i              
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr1_213707825_   3130 CAAGACAATGTGGCATTAGTGAAAGAACAGACAAATAAATCAGTGGAACA 3179
                                i     i i i iiv   i i     v   i    i     i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_213707825_   3180 GAACGGAGAGCCAAGAAATAGGCTTACACAAATGGAGTCAAGTCATCTTT 3229
                            iv     i v       ii ii i   vv ivi     v v  i  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_213707825_   3230 GAAAAAGGAGC-AAGGCAGTAGAATGAAGCAAAGATAGTATTTTCAACAA 3278
                           v  i  v  -   i vi vv    ii v  ii     v          
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_213707825_   3279 ATGATGCTAGAACAACTAGATATTCACGTGCAAAAAAAAAAAAAAAAGAA 3328
                            i    i i      i    ?i   i       i  v--------   
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT--------GAA 449

  chr1_213707825_   3329 TCTAGACACAGATTTCACACCCTTCACAGAAATTACCACAAAATAGATCA 3378
                         vi i   v vv ii       v vi   i      v v      i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_213707825_   3379 TAGATCTAAATG-AAAATCACAAAACTCTGAAACTCCTAAAAGATAACAC 3427
                         ?   i       -  i v -i      v i      i  i    v    i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_213707825_   3428 AGGAGAAAACCTAGATGACATTTCATATGGTGGTGACTTTTCAGATACAG 3477
                            ? v   i  vvi    v  vvi vv  iii  ii  i i     iii
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_213707825_   3478 CCCCAAAGGCAGGATCCATGAGAGAAACAATTAATAAGCTGGACCTCATT 3527
                          v     i   vi v v ii i     v   vi    ii     i    i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_213707825_   3528 AAAATTAAAAACTTCTGCTCTGTGAAA-ACAATATAAAGTGAAAGAGAAA 3576
                                       i  iv  vii  i-   v   v   --    v    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG--AAAGTGAAA 696

  chr1_213707825_   3577 A-ACAGCC-ACAGAATGGAAGAAAATATTTTCAAAAGACACATATGATGA 3624
                          -   i  -         i           v    vv i i  v    i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_213707825_   3625 AAGACTGTTATCAAAAATATACAAAGAATTCTTAAAACTCAAGAGTAAGA 3674
                         ii    vv    v i      i      i     v       v i   i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_213707825_   3675 AAATGAGCAACCCAATTCAAAAGTGAGAAAAAGACCAGAACAGACACCTC 3724
                          i ii ii         ?    i  i v   i  iiv   i     ii  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_213707825_   3725 ATCAAAGAAGATGTACAGGTGATATGTAAGCATATGAAAAGATGGTCCAC 3774
                         vi          i    ii  iivvi      i           v  v  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_213707825_   3775 CTCATATGTCAT 3786
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (147 / 83)
Gap_init rate = 0.01 (12 / 889), avg. gap size = 2.42 (29 / 12)  


1979 26.30 9.66 2.03  chr1_213761486_213763426.rev      664  1450 (491)    L1M4_orf2#LINE/L1       62   908 (0)  

  chr1_213761486_    664 CCAAATTGATCTATGGAATAAACACAATACCAATCAAAATCTCATGGACT 713
                                      ii  v v   i    v  v         i  vvvi i
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr1_213761486_    714 TTTTTTGGTAGAA-TTGACAAGTTGATTCTAAAAGTTATATAAAAATTCA 762
                                -i    -        i    i      v i    ii    v  
  L1M4_orf2#LINE/    112 TTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr1_213761486_    763 AAGGACTTGGAATGGCTAAAAACGTCTTGAGAAAGAA---CAAATTTGGA 809
                          i    iii    i  i    vvi      i      ---    v     
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_213761486_    810 AGGTTCACTCTACCTGATTTCAAAACTTACTACAATGCAACAGTAATCAG 859
                         i ii    v  v  ii                   v  v          i
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr1_213761486_    860 GATAGTGTAGTATTAATGTAACTAAAGACAAATAGGTAATTGGAACATAA 909
                           i     i   i iiii   vv v     v    i v v     i v  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr1_213761486_    910 T--AGAGCCCAAAAATATACCCAGACATATCTTATCAACTGATTTTCCAC 957
                          --    i   i     v     v    v v vi    i        v  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr1_213761486_    958 AAATGTGTTAAGGCTATTCAATATGGACAGGACAATT------------- 994
                           iv   ii   i i       iv   v  i i i i-------------
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_213761486_    995 GTGCTAAAGCAACCGGAAAA--ATGTG-AGAAAAATAAA--TGAACCCCA 1039
                              iiii    i   v ?-- ii  - i  i   i  --  i     v
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_213761486_   1040 ACATCA-ACCCTTAAAATATACACAGACATTACTTTGAGATGGACTGTAC 1088
                           v   -   --------   i   i v    vi ii i     iii? v
  L1M4_orf2#LINE/    461 ACCTCACACC--------ATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_213761486_   1089 ACCTAAAATTAAAATCTGTAATTATAAAAATTCTAGAAGAAAATA---GA 1135
                                vv   i v  iv  i       v ii          i --- ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_213761486_   1136 ATAAAGTT--GTGACGTTGGAATAGGCAAATATTTCTCA---ATGAGAAC 1180
                         i    vi --     v    iv       vvi     i ---    v v 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_213761486_   1181 AAAAATGTACTAATTATTTTAAAAGTCA---TAG------TGTTCTTCAT 1221
                             -- i  v iiv i---     vv ---   ------  vv      
  L1M4_orf2#LINE/    603 AAAA--GCACAAGCAAC---AAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_213761486_   1222 CAAAATTAAAAAGTCT---GCTAATCAGCAGACA-TATTAGGTAAATGAA 1267
                                     v i ---   --   ivi    -   i i v  i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_213761486_   1268 AAAGCAAGCCTTAGATTGGAAGAA--TACTTGCATTACACACATGTGACA 1315
                           ii   v  vi   v   i    --  i     vvv  i i  v   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_213761486_   1316 AAAGATTTAAAGCTAGAA---------GAC------------------AA 1338
                          ii  i  iv v i    ---------i  ------------------  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_213761486_   1339 AAGACAAGTA-TCCAATAAAAATATATGCCAAAATATGGAACAGACACTT 1387
                                i  -i     v?   v  iv  v  iivv v   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_213761486_   1388 TGCAAAAAAAGTTACATGAATGGTCAAAAAATACATTAAAAGTTGATCAA 1437
                         iv v   i   v  i ii     i   v  ii    v     v  v    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_213761486_   1438 AGTCATAAGTTAT 1450
                         vi   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (120 / 83)
Gap_init rate = 0.03 (24 / 847), avg. gap size = 3.83 (92 / 24)  


3032 23.86 3.46 3.12  chr1_213846754_213848672.rev      532  1428 (491)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr1_213846754_    532 TATACTTTGTTCATGGGTTGGAAGAATTAACATTGTCAAAATGACCATAC 581
                            v iv         i        v    i     i  i   i v    
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr1_213846754_    582 TACACAAAGCAATCTACAGGTTCAA---------------AATACCAGTG 616
                          v v    vii        i     ---------------   v    iv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr1_213846754_    617 ACATTCTTCACAAAAATAGAAAAA--AATCCTAAAATTCCTATGGAACCA 664
                         i v  i  ii  i    v  v  i--i            v       vii
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr1_213846754_    665 CAAAGGACCCCAAATAGCCAAAGCATTATTGAGCAAAAAGAG-AAAGCTA 713
                            i      vi          i  v v    iv  i    i-    i i
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_213846754_    714 GAGGCATCACACTACCTGACTTCAAAATTTACTACAAAGCTATAA-AATC 762
                             vv       v  ii i       i              i i-    
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_213846754_    763 CAAAATAACATGGTACTTGTATAAAAATATATACATAGACCAATAGAGCA 812
                         -  i i iii       v i    ii   v i i     i    i  ii 
  L1M4_orf2#LINE/    259 -AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr1_213846754_    813 GAATAGAGAACTCATAAACAAATCCACATATTTACAGCCAACTGTTTTTC 862
                             v    iii  v   i   i   i i     ii i   i  v     
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_213846754_    863 TACAAAGGTGCCAAGAACATATATTGAGGCAAGAACACCCTGTTTAATAA 912
                         v    i          v   vi v  i  v     i vi  v  i  i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_213846754_    913 ATGGTGCTGAAGAAACTAAATATACATAAGCAGAAGAGTGAAACTAGCCC 962
                                  iiiv    ii   ?v  i v   i    i    ii i v  
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_213846754_    963 CCCATCTCTTACCATAGACAAAAATCAACTCAAAATGAATTAAAGACTTA 1012
                           i i   vi      v        i           i  i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_213846754_   1013 AATGTAAGACTCAAAACAATAAAATTACTAGAAGGAA-----GGG--AAA 1055
                                  vii     v      i vi      i  -----  ?--   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_213846754_   1056 TGCTTCAGGACATTAGTCTGGGCAAAGAGTTTATGAG-TAAGACTTTAAA 1104
                          -    iv   v  i vi i     v -    v v  -  v   vii   
  L1M4_orf2#LINE/    558 T-CTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTAGATATGACACCAAA 605

  chr1_213846754_   1105 AGCATAGGCACCAAAAGCAAAAATAGATAAATGGGA--TCATACCAAACT 1152
                             i i   v      v              v   --    - v   i 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT-CAAAATT 654

  chr1_213846754_   1153 AAGAAGCTTCTGTACGGCAAAGGA-ATAATCTTCAGAGTGAAGAGAAAAC 1201
                           i  -   i   i vv       - iv   vvv i      i   v   
  L1M4_orf2#LINE/    655 AAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_213846754_   1202 CTGCAGAATAGGAGAAAATATTTTCAAGCTATTTATCCAACAAGGAATTA 1251
                          ii      i             v   iii  v    ii i    i i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_213846754_   1252 ATATGAAGGATATACAAGAAACTCAAACAACTCAACAGCAAAAGACAAAA 1301
                         i   vv  i     i  ii     vv         i ii    -------
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA------- 796

  chr1_213846754_   1302 CAGAGAACAAAACAAA-AATCAAATAATTTGATGAAAAATGGACAAAGTG 1350
                         --------- i     -  i v   ------- ?        i     vi
  L1M4_orf2#LINE/    797 ---------AGACAAATAACCCAAT-------TWAAAAATGGGCAAAGGA 830

  chr1_213846754_   1351 TCTGAATAGACATTTCTCAGAAGAAGACATACGAATGACCAACAGGTATA 1400
                          i                vi       i    i    i    i i i i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_213846754_   1401 TTTAAAAATGCTCAATATCATTAATGAT 1428
                          vv   i        i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (137 / 73)
Gap_init rate = 0.02 (17 / 900), avg. gap size = 3.47 (59 / 17)  


3131 26.94 1.11 0.44  chr1_213940597_213947339     5349  6250 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_213940597_   5349 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5398
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_213940597_   5399 GGCCACATTGCCCAAAGTAATTTATAGATTCAACGCTATCCCCATCAAGC 5448
                            v i i v      v i  i  i           v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_213940597_   5449 TACCATTGACTTTCTTCACA-AAATTAGAAAAAACT-ACTTTAAATTTCA 5496
                          v   vivi i  i  ii  -     i-- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_213940597_   5497 TATGGAAGCAAAAAAGAGCCCATATATCCAAGACAATCCTAAACAAAAGG 5546
                                iiiv  ii  v  viv   v    i      i i  v  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_213940597_   5547 AGCAAAGCTGGAGGCATCATGCCACCTGACTTCAAACTATACTACAAGGT 5596
                          i     i      vv   ii iv  ii i      viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_213940597_   5597 CATAGTAACCAAAACTGCATGGTACTGGTACCAAAACAGATATAAAGACC 5646
                         i i     i   i  v ii         i iv ii i   i   v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_213940597_   5647 AATGGAACAGAACAGA-AGCCTCAGAAATAATGCCACACACCTACAACCA 5695
                                i    iv  -  i -         vv   i   ii  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chr1_213940597_   5696 TTTGATCTTTGACAAGCCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5745
                         v     i  i      vv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_213940597_   5746 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5795
                          v  i  i        i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_213940597_   5796 AAACTGGACCCCCTCCTTACACCTTATATAAAAATGAACTCAAGATGGAT 5845
                           ii        iv   i     v    i      v       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_213940597_   5846 TAAGG--TTAAACGTAAGACCTGAAACCATAAAAACCCTAGAAGAAAACC 5893
                         i ?i --i    i      v  i    i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_213940597_   5894 TAGGCA-ATACCATTCAGGACAAAGGCATGGGCAAAGACTTCATGTCTAA 5942
                             ?i- v i -   iv   vvv  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_213940597_   5943 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5992
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_213940597_   5993 TTAAACTAAAGTGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 6042
                          i   v v  ivi   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_213940597_   6043 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 6092
                           i     i   i             v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_213940597_   6093 AGGGCTAATATCCAAAATCTACAGGGAACTTAAACAAATTTACAAGAAAA 6142
                         i  i  vi      i   v  i ii     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_213940597_   6143 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 6188
                          i    ----   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_213940597_   6189 TCAAAAGAAGACAGTTATGCGGCCAACAAACATATGAAAAAATGCTCATC 6238
                           v        i vvi vii      i  i  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_213940597_   6239 ATCACCAGTCAC 6250
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3268 27.09 0.44 0.44  chr1_214252478_214258760.rev     4885  5792 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_214252478_   4885 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4934
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_214252478_   4935 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4984
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_214252478_   4985 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5032
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_214252478_   5033 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5082
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_214252478_   5083 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5132
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_214252478_   5133 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5182
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_214252478_   5183 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5230
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_214252478_   5231 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5280
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_214252478_   5281 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5330
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_214252478_   5331 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5380
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_214252478_   5381 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5430
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_214252478_   5431 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5480
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_214252478_   5481 AACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTAA 5530
                         i            vvi   i      vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_214252478_   5531 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5580
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_214252478_   5581 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5630
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_214252478_   5631 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5680
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_214252478_   5681 AAACATACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5730
                          i   v i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_214252478_   5731 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5780
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_214252478_   5781 ATCACTGGCCAT 5792
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2307 26.41 6.72 1.22  chr1_214260698_214262503.rev      502  1319 (487)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_214260698_    502 AAAATGAATCAATTCTTCCCAAATTGGTCTACAGATTTAATTAAATTCCT 551
                           i   i--    v  i         i          i  ivv   i   
  L1M4_orf2#LINE/     46 AAGATGG--CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr1_214260698_    552 AACAAAATTCCAGCCAAGTGTTTTGTAGACATATATAACCTTATTCTAAA 601
                          v      i     iivv v     i   v  vv i  v  v  i     
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_214260698_    602 ATATATATGGAAAAGCAAAAGGCTGAGAATAAATGAAAACAACCTTGAAA 651
                           vi         v    ii i iv      ivi-       i       
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCC-AAAACAATCTTGAAA 192

  chr1_214260698_    652 AAAAA---TAGAGTGAAAGGAATCCCCCTGCCCAACGTTAAGGTTTATTA 698
                           i  ---i i   vii    v  v v  v     iv i  iii   i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_214260698_    699 TATAGTTACAGTAGATAAGATAGTGTGTT-TTGTCAGTGGGATAGACACA 747
                         i v  i       ivi    i      v -i  v  vvi         i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_214260698_    748 TAGACAAAAAGGACAGAAGGGAAAGTCCAAAAATAGACCCACATAATGAT 797
                             iv  vi i i    vv  i      i     i     i i v v  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_214260698_    798 ACCTACCTTGTTTTTGACAAGG-TGCAAAAGCAATTCAATGAAGGAAAGA 846
                         ivii vi vi    i       -   v  ii v        ii i  ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_214260698_    847 TAGCCTCTTCAAAGAATGGTGCTAGAACAATTAGATATCCA--------- 887
                            i  i     vi         i i    i i    ?   ---------
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_214260698_    888 --------TTG----------TCACA-----------AATGAACTAAAAA 908
                         --------   ----------     -----------   v    v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_214260698_    909 TGAATCACAAAC--AAATGTAGAATGGACGACAATAAAACTTTTAGAAAA 956
                           i    ? i  --       ii vvv vi  v        i      i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_214260698_    957 AAA---AGGAGAAAATCTTTGGGATCTAGGGACAGACAAAGCCATCTTAG 1003
                            ---   ? v       i v  i  v   vi  i   v viv      
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_214260698_   1004 ACTA-GACTCCAAAATAATGATTCATAGAAGGAAATATTCAAAAACTGGA 1052
                          -  -   v      vv ii viv i i   i   v  vv v   i    
  L1M4_orf2#LINE/    593 A-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_214260698_   1053 TGCCGTTAAAATTAAAAAGTTATGTTCTGTGAAAAGATCATACTAAGAGA 1102
                         ivi i i           v  v   v  - v   i  ivv  ii    i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAA 690

  chr1_214260698_   1103 ATGAAAAGACAAGCTACACATTGAAAGAAAATATTTTCAAACCACATATT 1152
                         i           v i   v v  ii           v    i  i    i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_214260698_   1153 TGACAAAA-ATATGTATCCAGAATACATTTTTAAAAACTCCCAAAATCTC 1201
                            i  ii- iv             i  v---  i     ii v  -   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATA---AAGAACTCTTACAA-CTC 786

  chr1_214260698_   1202 AACCATAAAAATA----TAATCTAATTAGAAAATGGGCAAAACACATGAA 1247
                           iv       v ----   i i    ?i            iv iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_214260698_   1248 AAGACAGTTCTC-AAAAAAGTATATGCAAATGGCAAATAAACACATGAAA 1296
                         v     v     -   i   -    i        v     i         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_214260698_   1297 AGGTATTAAACTTTCTTAGTCAT 1319
                           i ii v   v iv????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (125 / 87)
Gap_init rate = 0.02 (19 / 863), avg. gap size = 3.42 (65 / 19)  


1677 26.57 5.41 2.54  chr1_214266392_214269804.rev     1740  2330 (1083)    L1M4_orf2#LINE/L1       27   634 (274)  

  chr1_214266392_   1740 TAGAAGAAATCAATATTGTTAAAATGGCCACACTGCCCAAAGCAATTTAC 1789
                          i     v- i           i     v i   v      vii  i   
  L1M4_orf2#LINE/     27 TGGAAGAC-TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chr1_214266392_   1790 AGGCTCAATGCTATTCCTATCAAA---CTATGTATGAAATTCTTCACAGA 1836
                           ii    i  v  i         --- i vv iiv---  i  ii    
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC---TTTTTTGCAGA 122

  chr1_214266392_   1837 ATTAGAAAAAAACTA---CTACAATTCCTATGGAG--GCAAAAAA---AG 1878
                          v v  v  i--  i---   v     v      i--    iii ---  
  L1M4_orf2#LINE/    123 AATTGACAAG--CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr1_214266392_   1879 AGCTCAGTCAAGGCAATTCTAAATAAAAAGAACAAAGCTAGCAGCATCAT 1928
                          ii--  i   ii    ii i  v  i          i i vi vv   i
  L1M4_orf2#LINE/    171 AAT--AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_214266392_   1929 GTTACTCAAATTCAAACTATACTACAAGACTACAGAAACCAAAACAGCAT 1978
                         ii v i   v      viv        ii      v  i   i    ii 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr1_214266392_   1979 GGTAGTGCTACAAAAACAGACACATATGCCAATGGAACTGAATAGAGAGT 2028
                             v  vi i  ii i     i   vii        iv    v      
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_214266392_   2029 CCAGAAATAACGCTGCACACCTACAACCA--------TCAACAAAAA-G- 2068
                                   vv iii   ii  iiii  --------  i    iii- -
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_214266392_   2069 -AAG------CAATGGGGAAAGGATTCCCTGTTCAATAAATGGTGCTGGA 2111
                         -   ------            i  vvi  v     i            i
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_214266392_   2112 ATAACTGGCTATCCATTTGCAGAAGATTGAAACTGAACCTCTTCCTTACA 2161
                          i      v  ?   iv    i    v    ii  i   i  v   i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_214266392_   2162 CCATACATAAAAATCAACTCAAGATGGATTAAAGACTTAAATGTAAAACC 2211
                              i i      i       i      i ?    i         i v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_214266392_   2212 TAAAACTATAAAAACCCTGGAAGATAACCTAGGA-CATACCATTCTGGA- 2259
                                      vi i i     v   v    ?-i v i -   vv  -
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGAC 567

  chr1_214266392_   2260 --TAAGATGCTGGCAAAGTTTTCATGAAGAAGACAACAAAACCATTTGCA 2307
                         -- ii v i--     v v    v ii v v    v     v  ivv   
  L1M4_orf2#LINE/    568 CTTGGGTTA--GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_214266392_   2308 ACAAAAATTAAAAATCACAAATA 2330
                               i--     -- i i   
  L1M4_orf2#LINE/    616 ACAAAAG--AAAAA--ATAGATA 634

Transitions / transversions = 1.91 (101 / 53)
Gap_init rate = 0.03 (18 / 608), avg. gap size = 2.61 (47 / 18)  

 954 24.20 0.64 2.55  chr1_214266392_214269804.rev     2609  2922 (491)    L1M4_orf2#LINE/L1      601   908 (0)  

  chr1_214266392_   2609 CCAAAAAAAAAAAAAAAAAAAAAAAAAAAAGACAACTAGAATCTAATTGA 2658
                               iv v  iv  v    i      v   i  v v i ii v  ii 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_214266392_   2659 GATAAAGAGCTTCTGCACAGCAAAATTTAAAAAGAACTGTGAACACAGTA 2708
                         i  v  i i   i  ii -------  i   iiiv   i v  v v   i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGC-------TTCAAAGGACACTATCAAGAAAGTG 693

  chr1_214266392_   2709 AAGAGACAACCTACAGAATAGGAGGAAATATTTGCA--TCTATGCATCTG 2756
                           i        i       i    i           --  -  ii     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTG 742

  chr1_214266392_   2757 ACAAAGTTCTAATATCCAGAATTTATAAGGAACTTAAACAAATCAACAAG 2806
                          i  i vv  vi          v     i     ivv    v    i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_214266392_   2807 GAAAAAACAAACAATCCCAATGAAAAGTGGGCAAAGGACATGAACAGACA 2856
                         i    i     i  i  v v ?    i           iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_214266392_   2857 CTTATCAAAAGAAGATATTCATGTGGCCAACATGAATATGAAAAAATGCT 2906
                         i  v  v           v  vi       i v v i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_214266392_   2907 CAACATCACTAATTGT 2922
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (45 / 30)
Gap_init rate = 0.01 (3 / 308), avg. gap size = 3.33 (10 / 3)  


 600 20.00 1.43 1.43  chr1_214364128_214367036     1204  1343 (1566)    L1M4_orf2#LINE/L1        1   140 (768)  

  chr1_214364128_   1204 TGGAAAGGTATTCTGTGTTCATGGACTGGAAAAATTTAATATTGTTAAAA 1253
                                i   i ii          i     i -i             i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA-CTTAATATTGTTAAGA 49

  chr1_214364128_   1254 TGTCCATA-TAAACAAAGTGATCAACTGAGTCAATACAATCCCTATCAAA 1302
                           v v   - vvv    v     v  v  v    ii              
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_214364128_   1303 ATCCCAA-TGTCATTTTTCACAGAAATAGAAAAAATAATCCT 1343
                               i-  i -     ii       v  v  iv i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 1.33 (16 / 12)
Gap_init rate = 0.03 (4 / 140), avg. gap size = 1.00 (4 / 4)  

3208 22.66 2.86 0.13  chr1_214364128_214367036     1649  2416 (493)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr1_214364128_   1649 AGAAAAGAAAAAAC-AATCCTAAAATTCCT---GAACCACAAAAGACCCT 1694
                              vvi v  i -i            v ---   vii   ii     v
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_214364128_   1695 GAACAGCCAAAGCAATCTTGAGCAAAAAGACTAAAGATGGAAGCATCACA 1744
                            i       i         iv  i    vi    v    i vv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_214364128_   1745 CTATCTGATTTCAAATTATATTACAAAGTCATAGTAATCAATACAACATG 1794
                           vi ii        viv  i       ii i         v   iii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_214364128_   1795 GTCCTAGCATAAAAAATAGACACATCAAACAATGGAATAGGATACAGAAC 1844
                           v  i      ii -      i  vi v           i  vv   ii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr1_214364128_   1845 CCAGAAATAAATGCACACATTTGTGCTCAATTGATCTTTGACAAAGGTCC 1894
                                    iv  i      i  v         i  i     i   v 
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr1_214364128_   1895 CAAATACACACAGTGGGGACAGGATGGTCTCTTCAACAAATAGTGATGAG 1944
                            ivv  iv  i      v  i  i    i          i   v  i 
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr1_214364128_   1945 AAAACTGTATATCCAC-TGCAGAAGAATGAAAGTGGATCCTTATCTCACA 1993
                          v     v   ?    -    i         iv    i  i  i      
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr1_214364128_   1994 CCATATGCAAATATCAACTAAAACTAGAT--------------TAAGACC 2029
                               i    v  i    v   v i   --------------     v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_214364128_   2030 TGAAACTGTAAAACTACTAGAAGGAAATATAGGAAAAAAGCTTCTTGACA 2079
                          i     i       vi      i   i     ?iv   v    v    v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_214364128_   2080 TTGGTCTAAGCAATTATTTTTTGGATATGACCCCAAAAGTATAGGCAACA 2129
                             vi  i     vi   i  i        v       i i i      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_214364128_   2130 AAAGCAAAAATAGACAAATAGAATTGCATCAAA-CCAAAAAGCTTTGCAC 2178
                             v         i    v i i v       -ii     vi    ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_214364128_   2179 AGCAAAGGAAATGATCAACAGCGTAAAGAGACAAACTATGGAATAGGAAA 2228
                         vv       v iv     v iv  i  i      v i ii    i   i 
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_214364128_   2229 AAAAATTTGCCAACCATACATTTGATAGAG--TTAATATCTGAAATATAT 2276
                            v      v  i    i  i     ii --i vi    iii       
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_214364128_   2277 AAGGAACTCATACAACTCAATAGCAAGAAAACAAATAACCTCTTTTAAAA 2326
                           i      v            ii  i  i          ivv  ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_214364128_   2327 ATGGGCAAAAGACTGGAATAGACATTTCTCAAAAGAAGACATGCAAATGG 2376
                                  i  i v               v        i  i       
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_214364128_   2377 CCAACAAGTATATGAGAAGATGCTCAACATCACTAATCAT 2416
                             i   i i    i                ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (109 / 62)
Gap_init rate = 0.01 (7 / 789), avg. gap size = 3.29 (23 / 7)  


 471 22.88 5.08 0.00  chr1_214388473_214391091      547   664 (1955)    L1M4_orf2#LINE/L1        1   124 (784)  

  chr1_214388473_    547 TGGAAAGGTATCCTATGTTTATGCAAAGGAAGAATTAATATTGTTAAAAT 596
                                i     i     i   v vv      v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_214388473_    597 GTCCATACTACCCAAAGCAATATACACATTTAAGACAATTTCTATTAAAA 646
                          v v     v      vii  v    v   i  vi    ii    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_214388473_    647 TTATAA-TGCCT-----GCAGAGA 664
                          ivi i-     -----     i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA 124

Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.02 (2 / 124), avg. gap size = 3.00 (6 / 2)  

2750 22.39 2.52 3.27  chr1_214388473_214391091     1332  2126 (493)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr1_214388473_   1332 AGAAA---ACAAA--AATCCTAAAATTTGTATGGAACCACAAAAGAAACC 1376
                              ---    i--i           ii       vii   ii  v-  
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC-CC 168

  chr1_214388473_   1377 TGAATATTCAAGGCAGTAT----GAATAAAAACAATGTTAGAGACATCAT 1422
                         v     vi   ii  i v ----i  v  i     v   i   ivv   i
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_214388473_   1423 ACTTTCTGATTT-AAAGTTATATTACAAAACTACAATAATCAAAACAGTA 1471
                             i ii    -   ii -  i      i     i       i     i
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_214388473_   1472 TGGTACTAGCATAAAAACAGAAACATAGACCAACAGAACAGAATAGAGAA 1521
                                i      ii i   v i     i   ii   i     v    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_214388473_   1522 CCCAGAAATAAATTGAAACATATGTGGTCAACTAATTTTTGACAAGGGCA 1571
                         i           iiv v    v i       i i     i        ii
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_214388473_   1572 CCAAGAGGACACTGTGGGGAACTGATAGTCTCTTTGACAAATGATGCAAG 1621
                               vv iv vi       vvi       i  ii       i   vi 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_214388473_   1622 GA-AACTGGATTTCCAAATGCAAAAGAATGAAATTGGATGC-TATTTTTT 1669
                           -        v?   v               i     iv -  ii ivi
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_214388473_   1670 ACCATACATAAAAACCAACTTAAAATGGATCAAAGACCTAAATGTAACAT 1719
                               i i     ii    i           ?              v v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_214388473_   1720 CTGAATTTATACAAATCCTAGAAGAGGATATAGG--TAGAACTTCTTTGA 1767
                           i  vi    v  v  i       ii i     --  i v    v -  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT-GA 566

  chr1_214388473_   1768 TATTGACATTGGAAATGATTTTTTGAATATCACACCAAAAAAAAAAGGCT 1817
                         iv   ivv v  v    i   i  ii    v         iv v   - v
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG-CA 615

  chr1_214388473_   1818 ACCAAAACAAAAATAAATAAAATGGGACTAAAAAGCTTCAAACTAAACTA 1867
                           v   iv       i     v   i---------     ----------
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGA---------CTTCA---------- 646

  chr1_214388473_   1868 AATCTAAACTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAACATG 1917
                         --  v   i      -   i  ii vv       v  v     v  vi  
  L1M4_orf2#LINE/    647 --TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_214388473_   1918 AAAAGGCAACCTACAAACTGGG-GAAAAAAATTGCAAACCACTCATCTGA 1966
                              i     i   i v    -     v v       i  ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_214388473_   1967 TAAGGGTCA-ATATTCAGATTTTATAAAGAACATTTACAACTCAACAGCA 2015
                               v v-i   i    v v          vi           i ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_214388473_   2016 AGAA---AAATAAGCCAATTAAAAAGTGGGCAAAGAATATGAACAGACAT 2062
                          i  ---      v      ?    i         i  v    i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_214388473_   2063 TTCTCTAAAGAAGATATAAAAATG-TCAACAGGTACATTAAAAGATGCTC 2111
                              i            v     -i   i i i    v           
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_214388473_   2112 AGTATTACTAATCAT 2126
                          ii  i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (111 / 64)
Gap_init rate = 0.02 (18 / 789), avg. gap size = 2.56 (46 / 18)  


1376 27.74 1.22 0.73  chr1_214528908_214534286.rev     2331  2741 (2638)    L1M4_orf2#LINE/L1        5   417 (491)  

  chr1_214528908_   2331 AAAACATTTCATGCTTATAGAT-AGAAAAATCAATATCATTAAAATGGCC 2379
                           i i  ii    i i  i   -i   i v i     ii    i     v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_214528908_   2380 ATACTACCCAAAGCAATCTACAGATTCAAGGATATTCCTATAAAACTACT 2429
                              v      vii              v vv  i     v   v v i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_214528908_   2430 AATGACATTCTTTACAGAATTAGAAAAAACT-ACTCTAAACTTCATGTGG 2478
                          iivi v  i   i     v v  v  i-  - ii     v     i   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGG 153

  chr1_214528908_   2479 AAC--CAAATAATGCCCA-AATAGCCAAGACAATCCTAACAAAAAAGAAC 2525
                           v--   ivi --    -         i      i i v   i      
  L1M4_orf2#LINE/    154 AAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_214528908_   2526 AAAACTGGATACATCATATTACCCAACTTCAAACTATACTACAGGGCTAC 2575
                            ii    vivv   i i v     i      viv       ii     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_214528908_   2576 AGTAACCAAAGCAGCATGATACTGATATAAAAGCAAACATGTAGACCAAT 2625
                              i   ii   ii  i     ii    iiii i    i    i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_214528908_   2626 GGAACAGAAGAGAGAGCCCTAAAATAATGCCACACACCTACAACCCTCTG 2675
                             i    vv     i  vi      vv   i   ii  iiii vvi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_214528908_   2676 ATCTTCGACAAAGTTGACAAAAACAAGCAATGGGGAAAGGACTTCCTATT 2725
                           i        i v  v   i v  vv            i ivvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_214528908_   2726 CAATAAATGGTGCTGG 2741
                            i            
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGG 417

Transitions / transversions = 1.85 (74 / 40)
Gap_init rate = 0.01 (6 / 413), avg. gap size = 1.33 (8 / 6)  

1439 23.39 4.59 2.06  chr1_214528908_214534286.rev     4445  4880 (499)    L1M4_orf2#LINE/L1      414   860 (48)  

  chr1_214528908_   4445 CTGGAATAACTGGCTAGCCATTTGCAGAGGATTGAAACTGGACCCCTTCC 4494
                             i i      v  ?   iv    i i  v    ii         v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_214528908_   4495 TTGCACCATA--CAAAAATCAACTCAAAATGGATGAAAAACTTAAATGTA 4542
                          ii       --       i              v ? i  i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_214528908_   4543 AAACCCAAAA-TATAAAAACTCT-GGAAGATAACTTAGG---AAATACCA 4587
                          i v i    -       -    -i     v   v    ---    -- v
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAAT--CT 560

  chr1_214528908_   4588 TTCTGTATATAGGACCTGGCAAAGATTTCAT-GATGAAGATGCCAAAAGT 4636
                          iv  - iv v  iiiv     v i    v -   - v  ii       i
  L1M4_orf2#LINE/    561 TCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGC 608

  chr1_214528908_   4637 AATCA--CAACAAAAACAAAAATTGACAAATGGGACTTCGTTAGACTAAA 4684
                          --  --        iv      v  i    v       i i i v v  
  L1M4_orf2#LINE/    609 A--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr1_214528908_   4685 GAGCTTCTGCATAGCAAAATAAACTGTCAACAGAGTAAGCAGACAACCTA 4734
                         i i   i  iiivv    iv v   i    v i   i iv        i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_214528908_   4735 CAGAATGGGAGAAAATGTTTGTGAACTATGCATCTGACAAAGGTCTAATA 4784
                                         i    ii  ii  ii      i  i  v  vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_214528908_   4785 TCTAGAATCTTTAAGAAACT--TA-AATTTACAAGAATAAAA-------C 4824
                           i     v v   ii    --  -  i --   v       -------i
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACT--CAATAATAAAAAGACAAAT 804

  chr1_214528908_   4825 AACTCCATTAAAAAGTGGACAAAGGACATGAACAGACACTTTTCAAAAGA 4874
                            i v   ?    i   i       iv    i     i  i  v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr1_214528908_   4875 AGACAT 4880
                            i  
  L1M4_orf2#LINE/    855 AGATAT 860

Transitions / transversions = 1.83 (64 / 35)
Gap_init rate = 0.03 (15 / 447), avg. gap size = 1.93 (29 / 15)  


3219 27.10 0.88 0.44  chr1_214571216_214577489.rev     4880  5783 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_214571216_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_214571216_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_214571216_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_214571216_   5028 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_214571216_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_214571216_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_214571216_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACTCCACATACCTACAACT 5225
                                i    i--    i  --        vi   i i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_214571216_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_214571216_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_214571216_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_214571216_   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_214571216_   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_214571216_   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_214571216_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_214571216_   5576 AGGCAACCTACAACATCGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv  v         v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_214571216_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_214571216_   5676 AAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5721
                          i    ----   v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_214571216_   5722 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGGAGAAATGCTCATC 5771
                           v        i  vi viii     v  i      i i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_214571216_   5772 ATCACTGGCCAT 5783
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


 313 28.57 4.20 5.88  chr1_214598270_214601147     1154  1272 (1606)    L1M4_orf2#LINE/L1        1   117 (791)  

  chr1_214598270_   1154 TGGAAAAGC-TTTTAGGTTCATAGATCAGAAGAC--AACA--GTTCAGAT 1198
                               iii- iii v      i   ii      --  i --   v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_214598270_   1199 GGTAATATTCCACAAACTGATACCTAGGTTTAACAAAAACTTTACCATTT 1248
                           i    i   v    i    vivi  i  i   iv  v ii  i  ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA--- 97

  chr1_214598270_   1249 ACCGGTATCTCAGCTGATTTCTTT 1272
                         ----iv   i      vi  i   
  L1M4_orf2#LINE/     98 ----AAATCCCAGCTGCCTTTTTT 117

Transitions / transversions = 2.78 (25 / 9)
Gap_init rate = 0.03 (4 / 117), avg. gap size = 3.00 (12 / 4)  

3507 18.59 3.59 3.59  chr1_214598270_214601147     1580  2386 (492)    L1M4_orf2#LINE/L1      102   908 (0)  

  chr1_214598270_   1580 CCCAGCTGATTTCTTTGTAGATATTAACAATTTAATACTAAAATTCACAT 1629
                                 vi  i    i   v   i    vi i  v          i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_214598270_   1630 GTAATTGCAAGGGGACAAAAATAGCAAAAACAATCCTGAAGAA----AAT 1675
                          v  v        iv v i      v         i    i  ----  i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_214598270_   1676 AAGGTTGGAGAATTCA--------GATTTCAAAACTTACTACAAAGTGAC 1717
                           i       i i   --------i                     iv  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_214598270_   1718 AGTACTCAAAACAGTGTGGCACTGGCACAGGAATGAACATATAGATCCAT 1767
                             v    i         i       i i i  ii           v  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_214598270_   1768 GGAATGGAACTGAGACTCCAGAAATAAACTGATACATCTATGATCAATTG 1817
                              i   i     v             iv      i    i       
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_214598270_   1818 ATTTTCAATAAGGGTGCTAACACCATTCAATAGGAAAAGAATAGTTTTGT 1867
                               i i        i  v          i  i          i  --
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-- 399

  chr1_214598270_   1868 GGGTTTTTTTTTTAACAAATGGAACAGATATAAC--AATAGTCACATGTA 1915
                         ----------  i         vi v iv i   --i   ?i      i 
  L1M4_orf2#LINE/    400 ----------TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_214598270_   1916 AAAAGATAAAGTTGGATCCCTACTTCATGTAGTGTATAGAAATTAACTCA 1965
                            ii  i        i      i   iiivi i  i i           
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_214598270_   1966 AAATGGTTCAAAGACCTAGATGAAAGAATTAAAACTTTACAGTTTTTAGA 2015
                               v   ?       i   v    ii       v  v ii i     
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_214598270_   2016 AAAAAATATAGGTCTAAATCTTCATAATCTTGGATTTGGCAAATTG--TT 2063
                          i    i     ?v         i i i     i  v     --  --  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA--TGGTTT 587

  chr1_214598270_   2064 CTCAGAGATGGAAGAAAAAGCATGAGCAAAAAAGGAAAAAAAGAAAAAAA 2113
                           i   v   iv vv       ii     v   i       ---------
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA--------- 628

  chr1_214598270_   2114 TAGATGAATTGAATGTCATTGATATTAAAAATTGTTGTTCTTCAAAGAAC 2163
                              i     i iv    ii v        i v    v        i  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_214598270_   2164 ACCATCAAGAA-GTAGAAAAGACAACCAACAGAACGGGAGAATATATTTG 2212
                           i        -  -            v      i       v       
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGT-GAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_214598270_   2213 CAAATTATGTGCCCAA-AAGTGGCCTGGTATATAGAATATATAG----CT 2257
                              i  i ii ii -   -  v  v    vi          i----  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAG-GGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_214598270_   2258 TTTATAACTCAATCATGTAAA-----ACAACTCAATTTTTAAAATGGACA 2302
                         i   i        v  iv   ----- i   i     ?v-       i  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCA 825

  chr1_214598270_   2303 AAAGATCTGAATAGACATTTCTCCA--GACAATAGGGTACAAATGGTCAA 2350
                           i   i                  --  vi   ---         i   
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATA---TACAAATGGCCAA 872

  chr1_214598270_   2351 TGAACCCATGAAAAGATGGTCAACATCCTTAGTTAT 2386
                          i i v            v        v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (100 / 46)
Gap_init rate = 0.02 (16 / 807), avg. gap size = 3.62 (58 / 16)  


4374 16.47 6.54 0.47  chr1_214618243_214619986.rev      400  1255 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_214618243_    400 TGGACTAATATTCTATGTTTCTG-ATTGAAAGACTTAAAATTGTTACTAT 448
                             vvi    i i     iv  -    i         v       vv  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_214618243_    449 TGCAAACAATACTCCCCAAATTGATTTACAGATTCAATGCAATACCTGTC 498
                         v    ----                i           i     v   i  
  L1M4_orf2#LINE/     51 GGCAA----TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_214618243_    499 AAAAT----------TTT--------------------------AAAATT 512
                              ----------   --------------------------      
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_214618243_    513 ----------TGCAGGAGTCCCAGAGTAGCCAAAATGATCTTGAAATGGA 552
                         ----------    i i v      i         ii         vi  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_214618243_    553 AGAACAAAGTTGGAGGATTCTCACTTCCTGATTTTAAA-CTTA-TGTAAA 600
                                          i  v       ii    i   -    - ii   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_214618243_    601 GCTACAGTGATAAAGACAGCGTGATATTTGCAAAAGAATAGACACGTAGA 650
                                 i  v       i   i  i v   v   i       ii    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_214618243_    651 TCAATGGAATAAAAGCAAAAGTCCAGAAATTAACCCATAGATCTATGGTT 700
                                    i  vii i           v        v  i      i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_214618243_    701 ATCTGGTTTTCAACAAGGATGCCACGATCACTCAATGGTGAAAGCATAGT 750
                          vi  i     i      i     v  i  i       v     v     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_214618243_    751 CTT--CACCAAATGATGCTGGGACAACTGGATATTCATTTGCAAAAGAAT 798
                            --  v      i                  ?i  iv           
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_214618243_    799 AAACTTGAATCCCTACTTTCTATCATGTGTAAAAATTAACTCTAAATGCA 848
                         i  v   i i      i ivi i   i ii            v     v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_214618243_    849 TCAAAAACTTAAATGTAAG--CTAAAGGTATAAAACTCC--GAAGAAAAC 894
                            ? i  i          --     iv          i--         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_214618243_    895 ATGAGTATAAATCTTCATGACCTTGGAATAGACAATGGTTTCTTAGATAT 944
                           ii ?i         i         iv   i                  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_214618243_    945 GACACCAAAAGCACAAGCAACCAAAGAAAAAGTATATATATTGGACTTCC 994
                                              v         i  v   v          v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_214618243_    995 TCAAAATTGAAAATGATTATGCATCAAAAGACAATACCAAGAAAGTGAAA 1044
                                 i    ivv  i   v     i    v  i             
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_214618243_   1045 CAACAACCCACAGAATGGGAAAAAATATGTGTAAATCATATACCTAATAA 1094
                         vi                  i       v  i          i  i    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_214618243_   1095 AGTTCTGGTATTCAGAATATATAAAGATTTCTTACAACTCAACAACAAAA 1144
                         i vv  v    i               vi             i  i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_214618243_   1145 AGACAAACAGGC-AACTGAAAAATGGACAACAGATTTAAACAGATATTTC 1193
                                i iv -  i ?        i   vi     i  i   i     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_214618243_   1194 TCCAAAGAAGATACACAAATGGCCAACAAGCACATGAAAAGGTGCTTAAC 1243
                                      i            i              i    i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_214618243_   1244 ATTGTTAGTCAT 1255
                           ii????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (92 / 45)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 5.45 (60 / 11)  


1732 25.78 12.27 1.40  chr1_214697643_214699923      613  1256 (1025)    L1M4_orf2#LINE/L1        1   714 (194)  

  chr1_214697643_    613 TGGAAAGACTTCCTAGGTTCAAGAATTAGAAGACTCAATAATGTGAAGCC 662
                                 iv   i v     v i   i       i    v   v   vi
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_214697643_    663 ATTAATTCTCCCTCAATTGATCTATAGAG--ATCTCAATCATT--CAAAA 708
                         ivi   v     iv          i   v-- v v     vi --     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_214697643_    709 TCTAAGTTGGATGTA--GTAAAAATCAACAAGCTGGTTCAAAAATTTATG 756
                           iv  i  vv v v-- i i    ii        i i v      i  -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT- 149

  chr1_214697643_    757 ATGAAAATGCACAGGACCTAAAATAGTCATGGTAATTTTGAAACAAAATA 806
                            i       vi     i i     i  viii   i      v i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_214697643_    807 -----GTTGGAGGACTTATATACTACTCTGATTTCAAAACAAAATATAAA 851
                         -----           i i --  v i -i          vv v  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACA--CTTCCC-AATTTCAAAACTTACTACAAA 246

  chr1_214697643_    852 GCTGCAGTAATCAAGGCAGTG-GGTATTCATGTAAGAAT----------- 889
                            i           i     -    i viii    i  -----------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_214697643_    890 -CAATGGGATAGAA---AAAG-----------ATCCACACATATATGGGT 924
                         -      i      --- i  ----------- i   i    v     vi
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_214697643_    925 GATTGGTATATGACAGGAGTACCAAGGTACTTCAATGAGAAAGGGATAGT 974
                         i    i v vi    i i  i     iivv       i i  i i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_214697643_    975 CTTTTCAACAAATGGCGCTGT-----CT----ATCGATATGAAAAAAATT 1015
                                        i    v-----  ---- ? v i   v    i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_214697643_   1016 GACATCC-ATCTTTACTTCACACCATAGAC------TGA---------GG 1049
                           vi iv- i ii   i          v  ------ i --------- i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_214697643_   1050 TCACATACCTAAACATAGAAGTCAAAATGATAAAACATCCAGAAGAAAAC 1099
                            ? v       ii  ii  ii    iv       viii          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_214697643_   1100 ATAAGAGAAAACACTTTTTAGCCTTGTAGTAGTCGTCCAGATTTTTAGGA 1149
                            i ? v   i-   iv ii     viv   v ivi-- i   i vi  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAAT--GGTTTCTTAGA 593

  chr1_214697643_   1150 TACAA----AAAAGCAAAAGCCATAAAAGAAAAA---GATAATATATGTA 1192
                           ii ----       v    v i          ---     -  -  v 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA-AT-TGGA 641

  chr1_214697643_   1193 CTTCATCAAAATGTAAAACTTATGCTTTTCAAAT-ACACCATTA------ 1235
                                     vv       v  ivi      v-    i  i ------
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_214697643_   1236 CAAAAAAACAAC--GAAAAATGG 1256
                         ii    i     --iv i     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGG 714

Transitions / transversions = 1.72 (103 / 60)
Gap_init rate = 0.04 (25 / 714), avg. gap size = 3.52 (88 / 25)  

 519 22.54 3.47 2.89  chr1_214697643_214699923     1616  1788 (493)    L1M4_orf2#LINE/L1      735   908 (0)  

  chr1_214697643_   1616 TACAGCTGAGAAATTACTAATATCCAGAATTTGTAAAGAACTCTTACAAC 1665
                           i v    v  ivv   vi          v i                 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_214697643_   1666 -CAATAATAAGAAGATAAA--ATCTAGTTTTTAAAAATGAACACAAAGCT 1712
                         -         i    i   -- i i i  --?       ii  v iiii 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATT--WAAAAATGGGCAAAGGATT 832

  chr1_214697643_   1713 TCAACAGA---TTCTTCACAAAAGATTATATGCGAATTGCCAACTATCAA 1759
                          v  i   ---    i  v i     ---  i i   v     iv v  v
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGAT---ATACAAATGGCCAATAAGCAC 879

  chr1_214697643_   1760 ATAAAAAGATTCTCAATATTATTAGTCTT 1788
                           i       v     i  i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (24 / 14)
Gap_init rate = 0.03 (5 / 174), avg. gap size = 2.20 (11 / 5)  


2858 25.80 4.68 1.03  chr1_214703074_214707307     2866  3741 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_214703074_   2866 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAACATTGTGAAAAT 2915
                               v i        i        v  v   v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_214703074_   2916 GACCATACTGCCAAAAGCAATCAACAAATTCCATGCAACTCCCATCAAAA 2965
                          i v     v  v   vii   v   i    v i    ii  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_214703074_   2966 TACTA-CTATTATTCTTCACAGAATTAGAAAAAAAACAATCCTAAAATAC 3014
                          v i -  iii-  i  ii     v v  v  iv--ii          v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTC 147

  chr1_214703074_   3015 ATATGGGACAAAAAAAGAGGCC--ATACAGTCAAAGCAA----GACTAAG 3058
                               i -- viv   i i  --iv i  i    i   ----  vv   
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_214703074_   3059 CAAAAAACAAATCTGGAGGCATCACATTACCCGACTTCAAA-----CTAT 3103
                         --  i      vi      vv     i v   i i      -----   i
  L1M4_orf2#LINE/    196 --AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_214703074_   3104 AAGGCTATAGTCACCAAAACAGCATGGTACTGGTATAAAAAGAGGCACAT 3153
                           i    i   v i   i    ii         i    ii v  i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_214703074_   3154 AGATCAGTGAAACAGAATTGAGAACCCAGAAATAAAGTCAAATACTTACA 3203
                               i  i  i          ii           vi  v i i   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_214703074_   3204 GCTAACTGATCTTCAACAAAGCAAACAAAAACATAAAGTGAAGAAAGGAT 3253
                          ii  i    i   i    i vviv   i v   vv i  ii     i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_214703074_   3254 A-TCTTATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGAA 3302
                          -    -                    i  i   vv ?       i i  
  L1M4_orf2#LINE/    394 AGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_214703074_   3303 GAATGAAACTGGATCCTCATCTCTCATCTTATTCACAGATCAACTCAAGA 3352
                                ii    i  ii i   v  i v   v  v i  i       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_214703074_   3353 TGGATCAAAGACTTAAACCTAAGACCTGAAATCACAAAAATTCTGGAAGG 3402
                                ?    i    iv     v  i   ii i    v ii i    i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_214703074_   3403 TAACATTGGAA-AAACCATTCTAGACATTTGCCTAGGCAAAGACTTC--- 3448
                         v     v  ?i-   i -   vv   v  v vi       v ii   ---
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_214703074_   3449 ---ATGAC--CAAGAACCCGA-------------AAACAAGTAGATGGGA 3480
                         ---     --   i i v i -------------   i ii  i  v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_214703074_   3481 CTTAATTAAACTAAAAAGCTTCTGCACAGCAAAGGAAATAATCAGCAGAG 3530
                            v  i   v v    i   i  ii vv       v iv    iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_214703074_   3531 TAAACAGA-AACCCATAGAGTGGGAGAAAATCTCCGTAAACTATGCATCC 3579
                          i  v   -      i   i           v ii i   ii  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_214703074_   3580 AACAAAAGACCAACATCCAGAATCCACAAGGAACTC----AGATCAACAA 3625
                         i i  ii   ivii         vi i  i      ---- iv    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_214703074_   3626 GAAAAAAACAAACAATTCCATCAAAAAGTGGGCTAAGGACATGAATAGAC 3675
                         v     i     i  ii v  i?    i     v     iv         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_214703074_   3676 AATTCTCAAAAGAAGATACACAAATGGCCAATAAACATATGAAAA-ATGC 3724
                          v     v          i               i  i       -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_214703074_   3725 TCAACATTACTAATGAT 3741
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (148 / 74)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.78 (50 / 18)  


 541 29.41 11.07 0.69  chr1_214709611_214712780     1480  1768 (1402)    L1M4_orf2#LINE/L1        1   319 (589)  

  chr1_214709611_   1480 TGATAGGATGTATCATGCTTATTGCTTAAAAGAGT-AATATTGTAAAGAT 1528
                           iv i   i vi    i i  v v  ii    v -        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_214709611_   1529 GTAAATTCTCCTTTCAAAT-ACTTCATAGAA-AAATCTAACTCCAGTGAA 1576
                          vv   v    i--     -iv ii i   v-v  ivi  ii  vi v  
  L1M4_orf2#LINE/     51 GGCAATACTCCC--CAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_214709611_   1577 AA-ACCA------TATTTTGTGGAAAT-GA-AAGA-AATTT---AATTAA 1613
                           -v   ------ v     ii     -  -   v-i  ii---    v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_214709611_   1614 CAAGAAAACACAAAGGATCAATATCAGCCATGACAACTTTGAA---GAAG 1660
                         i v i   ii   i   i v v vi     vi    ii     ---    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_214709611_   1661 AACAAGATTAGAGAACTAAAACCACC--------AGACTTAC---AAATC 1699
                              ii  i   i   v v  iv  -------- i      ---   v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_214709611_   1700 TACAGTAATTAAGACAGTGTGCTATCAGTGCCAGAACAGATGAACTGAGC 1749
                                  i           v  iii iiiv  i i   iiv iv  v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_214709611_   1750 AATGGAACAGAAT--AGAGTC 1768
                                i     --      
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC 319

Transitions / transversions = 1.58 (52 / 33)
Gap_init rate = 0.04 (14 / 319), avg. gap size = 2.43 (34 / 14)  

 932 26.39 7.30 3.22  chr1_214709611_214712780     2212  2677 (493)    L1M4_orf2#LINE/L1      424   908 (0)  

  chr1_214709611_   2212 TAGGTATCAGCATGGGAAAAAAATAATAATTCTTGACTGTCACCTCACAC 2261
                          i i  ? vi    v-    i   i - i  v--   ivii         
  L1M4_orf2#LINE/    424 TGGATAKCCACATGC-AAAAGAATGA-AGTTG--GACCCCTACCTCACAC 469

  chr1_214709611_   2262 AAAACACAAAAATCAACTTCAGATCTATTT----CCTAAATGTAAGAAGT 2307
                         v v i        i    iv i  vv  iv----             iv 
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_214709611_   2308 AAAACAATAAATTTTTTAAAATTTAATATAGAA--AAGTGTCTGTAGGCT 2355
                              v     vi i   i  vvv  i    i?--  i v ii  - i i
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACC 568

  chr1_214709611_   2356 GTGAGGATGAGCAATGATTTCTTAAATAGGATAGAAAAAGCA---ATAAT 2402
                         v  -  v ii      i       i   v  i vv       ---ii  -
  L1M4_orf2#LINE/    569 TTG-GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA- 616

  chr1_214709611_   2403 TCTAAAGAAGAAAATGGACGAATTAGACCTTATTGACTTTAAGAACTTCT 2452
                         - v      -     i  ii    i   i i  ii vv    i     i 
  L1M4_orf2#LINE/    617 -CAAAAGAA-AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_214709611_   2453 ATTCATCAA--GACACTCTTAAGCTAGTGAATGAGA-AAGCCACAGAATG 2499
                         i v v    --      v i   vv      -i   -  v          
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAA-AAGACAACCCACAGAATG 713

  chr1_214709611_   2500 AGAGA-------TGCATATCATACGTATATCCAACAAATAATGGAAATCC 2542
                         i    -------    v      ----    ii i  ivi ivviv    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATA----TATCTGATAAGGGACTTGTATCC 759

  chr1_214709611_   2543 AGACTATA-AATGAACCCCCAGAAATCATTAATAAAAATAAAGATA-TCC 2590
                            v    -  v    i ii v  v   v         v v i   -i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_214709611_   2591 AAT---------AGCAAAAAATTTAAACAAGGCATTTC---AAAGAGTAT 2628
                            ---------i     ii    i  i - i      ---     iv  
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATA-GACATTTCTCCAAAGAAGAT 858

  chr1_214709611_   2629 ATTCAT-TACCCAATAAAGAAATGAAAAGGCATTCAATATCATGCACCAG 2677
                           v  v- iv       iv v        iiii    i    ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (72 / 49)
Gap_init rate = 0.04 (21 / 485), avg. gap size = 2.33 (49 / 21)  


2818 20.92 5.58 8.69  chr1_214838199_214840226.rev      608  1539 (489)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr1_214838199_    608 AGATATACAATGTTCCTGGGTCAGAAGACTTAAAATTATTAAGATGTTAA 657
                               v v      v   i ii          v   i        vi  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_214838199_    658 TTCTTCCCAAATTGACCTACAGATTCAATGCAATCCCTATAAAAATTCCA 707
                          v  i          i            i           v     i   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_214838199_    708 GCAGACTTCTTTGTAGAAGTTAGTAAGTTTATCCTAAAATTTATATGGAA 757
                           v v   i    i    i  iii   i v           i        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_214838199_    758 TTTCAAATGATCTAGAATAGCAAAGAAACAACTTTGAAAAAGAAGAAAAA 807
                         v v   iv  i i        v  --     ii              v  
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAA--AACAATCTTGAAAAAGAAGAACAA 203

  chr1_214838199_    808 ATTTGAAGGCCTAACACTACCTGATTTCAAGACTTATGATAA-GCGTGTG 856
                          v   i   v  v     v  ii       i     iv i  -  - iii
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC-TACA 252

  chr1_214838199_    857 GTTATTAAAACAGTGTAGTATTAA-ATCAAGGTAGACAAATAGAACAATT 905
                           v  i  i       i   i ii-  v i i      v     v    v
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_214838199_    906 AAACAGAATAGGGCATAAAGAAAAGACATCTATCTATCTATCTATCTATC 955
                         i  i     v i vi vv     vi --------------------- i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAA---------------------ACC 331

  chr1_214838199_    956 TATCTATCTATCTGTCTATCTATGAAAAACTGATTGTTGACAAAGGCATA 1005
                         i  vi  i   v-   -----------  i     v i     i  iiiv
  L1M4_orf2#LINE/    332 CATACATTTATG-GTC-----------AATTGATTTTCGACAAGGGTGCC 369

  chr1_214838199_   1006 AAGTCAATACAATGGAGAAAAGATAGTATTTTCAACAAATGTTCTTGGAA 1055
                            v v  v      i    ii     v             v vi   i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_214838199_   1056 CAATTGGATATTCATATACCAAAAAAAGAAAAGAGAAAAAAATTGGATAT 1105
                            i      ?i  i  i -----------  i    vi  i     ---
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGC-----------AAAAGAATGAAGTTGGA--- 455

  chr1_214838199_   1106 CTATATACAAAAACCTGTACTTCAATTTATACCTCACACCATACATAAAA 1155
                         ------------------- ii ------              i i    
  L1M4_orf2#LINE/    456 -------------------CCCC------TACCTCACACCATATACAAAA 480

  chr1_214838199_   1156 ATTGACTCAAAACGGA--ATAGCCCTGAAGACAAAACACGC---AACTAT 1200
                            i        i   -- ?  v   i  vii  i ---  ---      
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA---GCTAAAACTAT 527

  chr1_214838199_   1201 AAAGCTTCTATACGAAG-CACTGGAGAAAACCATTGTGCCCTTGGGTTAG 1249
                            i  ii  v v   i-  iv  ? v   i v i   v           
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_214838199_   1250 GCAAAGATTTCCTAGGTACAAC--CACAAGCATGATCTATAAAGGGACAA 1297
                             v i    i   i  ii  --  v     ii v v i   i i v  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_214838199_   1298 CTTGTTAAATTGAACTTTATCAAAATTTAGAACCTGC-TACCTGAAAGAC 1346
                         v v v       i    i         v i   i vi- i i v    i-
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG- 676

  chr1_214838199_   1347 AAAGTATAAAGAA--TGAAAAGACAGGCCACAGGCGGGGAGAAAATATTT 1394
                          v v   v     --          iv      ivv              
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_214838199_   1395 GCAAAGCATACATCTGATAAAAGA-TTGTGTCTAGAATGCATAAAGAATT 1443
                              v    i         ii  -    i  i     ii        i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_214838199_   1444 CTC-CAATTCAGTA----------------TTCA---------------- 1460
                           i-   i   i  ----------------ii  ----------------
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_214838199_   1461 ----CTTGAATATTGACACTTCACCAAAGAAGATATACCAATGGCAGATA 1506
                         ----i       --    i   v               v      vi   
  L1M4_orf2#LINE/    827 AGGATTTGAATA--GACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_214838199_   1507 A-CACATGAAAAGATGTTCAACATTGTAAGTCAC 1539
                          -              i       ii????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (122 / 70)
Gap_init rate = 0.03 (24 / 903), avg. gap size = 5.54 (133 / 24)  


3099 26.40 0.88 0.99  chr1_215189785_215195543.rev     4360  5268 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_215189785_   4360 TGGAAAAACATTCCATTCTCATGGATAGGAAGAATGATTATGGTGAAAAC 4409
                               i i  i    vi        v      v v v   v  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_215189785_   4410 GGTCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 4459
                           iv     v      v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_215189785_   4460 TACCATTGATATTCTTCACAGAATTAGAAAAAATTACTTTAAATTTTATA 4509
                          v   viviiv  i  ii     v v  v  iv v iii    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_215189785_   4510 TGGAA-T-CAAAGAAGACCCCGTGTAGCTGAGACAATCCTAAGCAAAAAG 4557
                              - -   i --     v vi    ii i      i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_215189785_   4558 AATAAAACTGGAGGCATCATGCTACCTGACTTCAAACTATACTATAAGGC 4607
                           i   ii      vv   ii  v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_215189785_   4608 TCCAGTAACCAAAACAGTATGGTACT--CATACCAAAACAGACATATAGA 4655
                          v      i   i     i       --    -- ii i           
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATATAGA 296

  chr1_215189785_   4656 CTAATGGACCAGAACAGAGACTTCAGAAATAACACCACACATCTATAACC 4705
                         ii      vi    iv    v i         vv   i    i   iii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_215189785_   4706 ATCTGATCTTTGACAAACCTGACAAAAACTAGCAATGGGGAAAGGATCTC 4755
                          vi    i  i     ivv  v   i v vvv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_215189785_   4756 CTATTCAGTAAATGGTGCTGGGAAAACTGACTAGCCATATGCAGAAAACT 4805
                           v    ii              v     iv  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_215189785_   4806 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 4855
                            ii         v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_215189785_   4856 TTAAAGACTTAAATTTAAAACCCAAAACCATAAAAACTCT-AGAGGAAAA 4904
                          i ?    i     v   i v i     i      -    -   i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_215189785_   4905 CCTAGGCA-ATACCATTCAGGACATAGGCCTGGGCAAAGACTTCATGACA 4953
                          v    ?i- v i -   iv   v v  vi i     v ii   v iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_215189785_   4954 AAAACACCAAAAGTAATTGCGACAAAAGCTAAAATTGACAAATGGGATCT 5003
                          vi          i vvv  i       vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_215189785_   5004 AATTGAACTAAAGAGCTTCTGCACGGCAAAAGAAACTACCATCAGAGTGA 5053
                         v  ii  v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_215189785_   5054 ACAGGCAACCTACAGAATGGGAGAAAAT-TTTTCACTATCTACCTATCTG 5102
                          v  i     i                 -   v  v-   - iv      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATC-ATATATCTG 742

  chr1_215189785_   5103 ACAGAGGTCTAATACCCAGAAATTACAAAGAACTTAAACAAATTTACGAG 5152
                          i ii  v  vi  i      vv  i        ivv    -i i vv i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAA 791

  chr1_215189785_   5153 AAAAAAAACAAACAACCCCATCGAAAAGTGGGTGAAGGATATGAACAGAC 5202
                         v     i     i     v  i?    i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_215189785_   5203 ACTTCTCAAAAGAAGACGT-TACATGGTCAACAAACATAGGAAAAGAAGT 5251
                          i     v        ii -i v    i   i  i  i v       v i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_215189785_   5252 TCAACATCACTGATCAT 5268
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.21 (17 / 14)  


3057 24.50 3.01 1.89  chr1_215209484_215215554.rev     4683  5580 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_215209484_   4683 TGGAAAAACATTCCATGGTCATGGATACGAAGAATTAATATTGTGAAAAT 4732
                               i i  i     v        vv     v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_215209484_   4733 AGCTATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 4782
                         i  v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_215209484_   4783 TATCATTGACTTCCTTCACAGAATTAGAAAAAAAACT-ACTTTAAATTGC 4831
                          vi  vivi i ii  ii     v v  v  i---  - iii    v v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr1_215209484_   4832 ATATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCATAATCAAAAA 4881
                                 viiv  ii  v  viv        i      v i vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_215209484_   4882 GAACAAAGCTGGAGGCATCACGCTACCTGATTTCAAACTATACTACAAGG 4931
                                 i      vv    i  v  ii        viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_215209484_   4932 CTACAGTAACCAATATAGCATGGTACTGGTACCAAAACAGATATATAGAC 4981
                                  i   v i  ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_215209484_   4982 CAAGGGAACAGAAC--AGAGGCCTCCA-AAATAACACCACACATCTACAA 5028
                            v    i    i--    ---    -      vv   i    i  iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAG---TCCAGAAATAAACCCATACATTTATGG 344

  chr1_215209484_   5029 CCATCTGATCTTTGACAAACCTAACAAAAACAAGCAATGGGGAAAGGATT 5078
                         i  vi    i  i     ivv iv   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_215209484_   5079 CCCTATTTAATAAATGATGTTGGGAAAACTGGCTAGCCATATGCAGAAAA 5128
                         vi  v  i  i     i  i     v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_215209484_   5129 CTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGATG 5178
                         v    ii         v   i     v           i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_215209484_   5179 GATTAAAGATTTAAATGTAAGACCTAAAACCATAAAAACCATAGAAGAAA 5228
                            i ?   ii           v       i      vi v         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_215209484_   5229 ACCTAGGCA-ATACCATTCA-GACCATAGGCATGGGCAATGAATTC---- 5272
                           v    ?i- v i -   i-    v i  i- i       iv   ----
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAG 592

  chr1_215209484_   5273 --ATGACA--AAAATGCAAAAAATAATTGCAACAAAAGTCAAAAAT-GAC 5317
                         --      --    -   v  -------          -v      -  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAA-GCACAA-------GCAACAAAAG-AAAAAATAGAT 633

  chr1_215209484_   5318 AAATGGGATCTAAGTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTAT 5367
                             v   ii v vi   v v  i i   i  ii vv       v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_215209484_   5368 CATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCT 5417
                           vv i      v  i     i                 v       vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_215209484_   5418 CTCCATCTGACAAAGGA-----ATC-------TACAAGGAGCTTAAACAA 5455
                         v vi      i  i   -----   -------  i  i  i  ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_215209484_   5456 ATTTACAAGAAAGAAGCAAACAACCCCATCAAAAAGTGGGCAAAGGATAT 5505
                         v iv i  v   i ii    i     v  i?    i            v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_215209484_   5506 GAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGA 5555
                            i     i     v        i  vi viii     i  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_215209484_   5556 AAAAAAGCTCATCATCACTGGTCAT 5580
                            i v     v     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (129 / 87)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.59 (44 / 17)  


2749 23.14 8.50 1.53  chr1_215351825_215353663.rev      502  1348 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_215351825_    502 GACAGATATACCTTGTTCAAAGGTTAGAAAACATAATATTGTTAAAATGA 551
                           v      v  v      vi i  i   i  v            i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_215351825_    552 CAACTCTCCTCAAAATGGTCT-TAGATTCAATG------------AAATC 588
                            iv    i    v  i   -i        i ------------     
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_215351825_    589 CCAGTTGAAACTTTTTTTGTAGAAAT--GCACTCT--TTC-AAAATTCAT 633
                             i  --- i       i      --i  vv  -- i -         
  L1M4_orf2#LINE/    103 CCAGCTG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_215351825_    634 AT----------------TATAATAGCCAAAACAGTGTTTTTAAAAGA-- 665
                           ----------------i v             i -i  vv      --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAG 198

  chr1_215351825_    666 ------GTTGAAAGACTAATCTTACCTGATTGTAAGATTTATTATGAATA 709
                         ------    i i    v ivi v  ii   vi  i i   i  i---- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC----A 244

  chr1_215351825_    710 AAGCTACAGTAATAAAGACAGTGTGATACAGGTAAAATAACAGAGAATTA 759
                                      v           i   v  i v  vi i   v vv  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_215351825_    760 GATCAGTGACACAAAAT--AGATTCTAGAAATAGGCCCACACATGTATAT 807
                              i  iv i i   --   v  i       ii    i    - -   
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-T-TAT 342

  chr1_215351825_    808 AGACAAGAGATTTTTGACAAAGGGGCAAAGGTGATTCAGTGAAGAACATA 857
                         i v   vv      i     i  v  v   iiv     i  ii   viv 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_215351825_    858 TAGTCTTTTCAAAAAACAAGGCTAGGTCGATTGGATACACACAGACAAAA 907
                                     v   iiiv   i  v i i      ?v    vi     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_215351825_    908 AAATTGAACTCCAGTCCACACCAAACACCGTTCACAAAAATTAACTCAAA 957
                         i   -   v iviii  vi   vv     i vi                 
  L1M4_orf2#LINE/    443 GAAT-GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_215351825_    958 AGGGATAAGAGATCTAAATGTAAT-GCATAAAATTATAAAACTCT-AGAT 1005
                          v    v ?   i          v-  -     i           -   v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAA 540

  chr1_215351825_   1006 AAAAACATAGGAAAAGCTCTTTGTGATATTGGATTAGGCA--GATTTCTT 1053
                         i          ?iv iv    i    iv    i       -- i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_215351825_   1054 AGATATGACA----ATGTACAATTCATAAAACACAA------TAAATTAG 1093
                                   ---- v i    viv i    v v  ------      i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_215351825_   1094 ACTTCACCAAAATTTAAGACTTCTGCTCTTTAAAAGACACTATTAAAAGA 1143
                               i       v  i    i  iv   i   i        i  i i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_215351825_   1144 ATCAAGAGACTAGCCACAGAC----AGAAATTATTTGCA-----TAT--- 1181
                         i v  i    v v       v----     v        -----   ---
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_215351825_   1182 -GATAAAGGACTTATTCCTAAAATATGTGAAGAATGTTCAAAACTCAATA 1230
                         -     i      i vi i i     i i     ivi i v         
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_215351825_   1231 ATAAGAAAATTAAAGGCTCAATCTTTTAAATGGGCAAACAATTTGAACAG 1280
                             i  i iv  vii i    - ?vv           vi       i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_215351825_   1281 ACATGTCCCAAAAGAGGATATATGGATGTTAAATAAGCACTTGAAA-TAT 1329
                             v  i v     i      iii   viv         v     -v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_215351825_   1330 GCTCAACATTACTAGTCAT 1348
                                  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (115 / 77)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 3.40 (85 / 25)  


2877 24.38 4.03 2.68  chr1_215360190_215364681.rev     3108  4001 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_215360190_   3108 GAAAAATATTCCATGCTTATGGATAGGAAGA----ATATGGTTAAAATGA 3153
                             i    i     i i      v      ----    v     i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_215360190_   3154 CCATACTGCCCAAAGCAAT--ACAGATTCAGTGCTATTCCTATCAAACTA 3201
                          v     v      vii  --         ii  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_215360190_   3202 CCAA-TGTCATTGTTCATACAACTAGAAAAAAGCT-ATTTTAAAATTCAC 3249
                            i-  i -  v  iii v  v v  v  --   -  ii         i
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCAT 149

  chr1_215360190_   3250 ATGGAATTAAACAACAAAAAAGGCCT-GAATAGCCAAAGTAAACCTAAGG 3298
                               ------- iiv  ii i  i-           ii  v i i ii
  L1M4_orf2#LINE/    150 ATGGAA-------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_215360190_   3299 AAAAAGAATA-----------------CTACCCAACTTCAAACTATACTA 3331
                           i     i -----------------  v     i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_215360190_   3332 CAAGGCTACTTTGTATACGAAAACAGCATGGCACTGTTACAAAAACAGAT 3381
                            i     v--   - iv  i    ii   i    vi i  ii i   i
  L1M4_orf2#LINE/    243 CAAAGCTACA--GTA-ATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_215360190_   3382 GCATAGACCAATGGAACAGAATAGAGAGCCCAGAAATAAAGCCACACACC 3431
                         ii     i        i     v     i           v   i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_215360190_   3432 TATAACCATTTGATCTTCAACAAAGTCAATAGTAACAAG------CAATG 3475
                            iii  v     i   i    i ------  iv    ------     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGG------GTGCCAAGACCATTCAATG 383

  chr1_215360190_   3476 GGGAAAGGACTCCCTCTTCAATTAATGGTGCTAGAATAACTGGTTAGCCG 3525
                                i ivvi  i     iv         i i i      v  ?  i
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_215360190_   3526 TATGCAGAAGATTGAAACTGGACCCCTTCCTTTCACCATATCCAAAAATC 3575
                         i     i    v    ii         v   iv        v       i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_215360190_   3576 AACTCAAGATGGATGAAAGACTTAAACATAAAACCTAAAACTATAAAAAC 3625
                                i      v ?    i    ii   i v              vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_215360190_   3626 CCTAGAAGAAAACCTATGAA-ATATCACTGTGGACATAGGCCTTCACAAA 3674
                          i           v  v ?i- v   vii   -  v v  vi vvi   v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAAT 582

  chr1_215360190_   3675 GATATCAT-GATGAAGATTTCAAAAGCAATTGCAAACAAAAATAAAAATG 3723
                          i v  v -   - v  ivi        vvv    -     iv      i
  L1M4_orf2#LINE/    583 GGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAA-CAAAAGAAAAAATA 630

  chr1_215360190_   3724 TATAACTGGGCCGTAATTAAACTAAAGCACTTCTG--CTTAGCAAAGGAG 3771
                         v    v v  v v v  i   v v  iv    i  --   --       v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGAC 678

  chr1_215360190_   3772 ACCATCAACAGAGTAAACAGACAATCTAAAGAATGACAGAAAATATTTGT 3821
                           i     v i   i  v      i i v      iv            i
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_215360190_   3822 GAACTATGCATCCAACAAAGGTCTAATATCCAGATTCTATGAGGAACTTA 3871
                         i  ii  ii   ii i  i  v  vi        v v   i i     iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_215360190_   3872 TACAAATCAACAAGCGAAAAACAAACAACCCCATTAAAAAGTGAACAAAG 3921
                              v    i  vvi   i     i     v   ?    i  ii     
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_215360190_   3922 GACATGAACAGACACTTTTCAAAAGAAGACATACATGCAGCCAATAAGCA 3971
                           iv    i     i  i  v        i     viii           
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_215360190_   3972 TATGAAAAAATGCTCAACATCACTAATCAT 4001
                         i       i             ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (134 / 80)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 3.00 (60 / 20)  


2943 26.35 6.44 0.12  chr1_215391537_215393541      659  1512 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_215391537_    659 TAGAAAGACATTTCGTGTTCATAGATCAGAAAAATTAAGATTATTAAAAT 708
                          i      i  ii i       i   ii   i v    v   i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_215391537_    709 GTCAATATTTCTCAAAGCAATCTTCAG--TCAATGTAATTCCTATCAAAA 756
                          v     i i i    vii    v   --    i i   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_215391537_    757 TCCAAATGACATTTTTTACAGAAGT----AAAACAATCCTGAAATTCATT 802
                            v iivi v      i     i ----  ivii     i        v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_215391537_    803 TGGAAACACAAAATGAACCTGGACAAGGAAAGCAAT-TTGGAAAAAAAGA 851
                               ii   ii-  v  v i i ivv   i    -   i    i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_215391537_    852 ATAAAACTGGAGG---CATATTCCCTGATTTCAAAACACATTACAAAGCT 898
                          i   ii      ---  i i i  ii          vi i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_215391537_    899 ATAGCAGGCACAAGAGTATGGTAGTGGAATAAAAATATACACAGAGATCA 948
                          i  i iv  vi v   i     v   v    ii   v   i v      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_215391537_    949 ATGGAACAAAAT----AGCTCCAAGATAAATCCATGAATATATGGTTGGC 994
                               i i   ----  ii vi i     i    iv  v      iiii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_215391537_    995 TGATCCTCAATAAGGGTGCCAAAAATATATAATGGTGAAAAGATGGTATC 1044
                             ii  i i           i vi  vi     v    ii  i  v i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_215391537_   1045 CTCAATAAGTGATGT------------------ACATGCAAAATAATGAA 1076
                         i    i  i  i  i------------------          v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_215391537_   1077 -TTAAAAAT-TATCTTATTCCATATACAAAAGTCAATGCAAAATAAATTT 1124
                         -  ii vvi-  i  i iv            i i  iv      ii  iv
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_215391537_   1125 AAAACTTACATGTAAAACCTGAAGTAATAATACTCTTAGAAGAAAATATA 1174
                         ? i  i  v      i v  i  iiv    v               i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_215391537_   1175 GGGGAAAAGCGTCCAGACTTTAACCTAGTCAATGTTTCCTTGGCCACAAG 1224
                           ? v   v v  vv   i  iivi   v     v  i   i vi ii v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_215391537_   1225 CCCAGAAGCACATGCAACAAAACAAAAAATATACAAGTGGGATTACTTCA 1274
                         v   i       v         v        v i  i v   i v v   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_215391537_   1275 AA-TTAAAAATCTTT------TAAACGACA---------AAATGTAAAGT 1308
                           -       ii   ------i   v    ---------  i  v    v
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_215391537_   1309 CAATATATGCAAAGGGAGAGAATATCTGCAGACCATATATCTGATAAAGG 1358
                            ivi iiv  v      i     i    i i              i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_215391537_   1359 ATTAATATCCAAAATATATAA----CTCCTATAACTCAATAGCAAAATGT 1404
                          i vi      i         ----   i  i         ii    v v
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_215391537_   1405 CAAATAACCTGATTTGAAA-CAGCCAAGGGGGCTGAATAGACATTTCTCC 1453
                                  ii   ?i   -ii v   i  ivi                 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_215391537_   1454 AAAGAAGACATACAGATGACCAACAGGTATATGAAAAAGTGCTCACCGTC 1503
                                 i     i   i    i i i i       ii      v i  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_215391537_   1504 ACTAATCAT 1512
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.26 (154 / 68)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.00 (56 / 14)  


3554 19.45 5.12 2.05  chr1_215591156_215593772     1248  2126 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_215591156_   1248 GAAGGACATCACATGTTCATGGATTTGAAGACAAAATATTATTAAGATGG 1297
                            i  i   v              v      vv      i         
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_215591156_   1298 TGATACTTCTCAAATTAATCTACAGACTCAATGCAATCCCTATCAAAATT 1347
                         ii     i i      i         i    i                 i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_215591156_   1348 CCATCTGTATTATTCACTGAAATGGAAAAGTTGATCCTAA--TCCATATG 1395
                            v   iv  v  ii v     v  v   i         -- i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_215591156_   1396 GAACTGCAAGAGTCCCAAAAATAGCCAAAATA-TCTTGGGGAAAGATAGA 1444
                            v      i v    i  -         i -     ii-     vii 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAA-TAGCCAAAACAATCTTGAA-AAAGAAGAA 200

  chr1_215591156_   1445 CATATCTTATCTTTATGACGGTATCACACT-----AT--CA--------T 1479
                           v ----i -----  iv  vv       -----  --  -------- 
  L1M4_orf2#LINE/    201 CAAA----GT-----TGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_215591156_   1480 ACAAAGCTACAGTAATTAAGACAGTGTGATACTGACATAAAGATAGACAT 1529
                                         i           i     i     i         
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_215591156_   1530 ATCACTTAATGGAATGGAACTCAAAGTCTGTAAATAAACC--------TG 1571
                           viv i        i   i v i    iiv         -------- i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_215591156_   1572 TG--CAATTTAGTTTTGACAATGGCACTAAGGTCATTTAATCAAAAGAGA 1619
                           --     v v   i     v  ii i   ii    i   viii i   
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_215591156_   1620 ATA--TTTTTCAACAAATTGTTTGGGGACAACTGAATATCCAGATGAAAA 1667
                            --i            v  viv          i   ?   v   v   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_215591156_   1668 CAAATGAATTTGGGCACATACCTCACAATGTATACAAAAA---ACTTCAT 1714
                         vi      v    i v v         vii          ---   iv v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_215591156_   1715 ATAAATCAGAGTCTTAAGACTATTAACTAAAACTGTACAACTCTTAGGAG 1764
                           ii    ?  v i   ivv  vv i        i  v         i  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_215591156_   1765 AAAACAATGAGGAAAATATTCATAGCATTGGATTTGGCAATGATTTCATA 1814
                               vv i? v    v   i ii v    i  v       i    v  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_215591156_   1815 GGCATAACACCAATAGCACAGCCAACAAAATAAAATATAGATAAATTGGG 1864
                          ii  i       v      iv        v    v             i
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_215591156_   1865 CTTCA----AATACAAAACTTTTGTTCTTCAAATGACACTATTAAGAAAG 1910
                              ----   vv           v       v        i       
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_215591156_   1911 TACAAA---AACCCACAAAGTGG-ATAACATATTTGTAAATCATATGTCT 1956
                          iv   ---        i i   - v  v       i         i   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_215591156_   1957 GATAAGGGATTAATATCCAGAATATATAAAGAACTCTATATAACTCAACA 2006
                                  i vi                        -  i       i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAACTCAATA 790

  chr1_215591156_   2007 ATTAAAAAAAAAACCCAAATAATCCAGTTTAAAA-TGGGCAAAGGATCTG 2055
                           ----     i  --      i   i  ?    -            i  
  L1M4_orf2#LINE/    791 AT----AAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_215591156_   2056 AACAAATATTTCTCTAAACA---TGTAAAAATGATAAATAACCATGTAAA 2102
                           i i i       i   v --- i  v     iiv     v  ii i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_215591156_   2103 ATGATGATCAACATAATTATTCAT 2126
                          v    v       v ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (98 / 69)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 3.00 (63 / 21)  


3099 25.11 3.39 0.68  chr1_215618380_215621228     1473  2356 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_215618380_   1473 TGAAAAGATATCCCAGGTTCATGGAATAAAAAATTTAATGTTTTTAAATT 1522
                           i            v         v ii  i i     i  v    iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_215618380_   1523 GTCCATTGTAGCCAAAGTGATCTACAGACTCAATGCAACTACCATAAAAA 1572
                          v v  vv vv     v           i    i    iiv i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_215618380_   1573 TCCCAATAGTACTTTTTGCAGAAATAGGAAAAAAAATTATAAAATTTATA 1622
                              iiv ivi             v iv  ivvi  iv       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_215618380_   1623 TGAAACCACAAAAAA---AGAA-AACCCAGATAG-CT--------AAAAA 1659
                           i  vii   iii ---    - i  v i i i-  --------  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_215618380_   1660 CAC----------CTCACACTTTCTGACTTCAAAACATATTACAGAGGTA 1699
                           v----------         i ii i        v  i    i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_215618380_   1700 GAGTAATCATAATAGGATGGTACTGGCATAAAGACAAGTCTATAGA-CAA 1748
                         v        vi i  vi              i  i iiiv      -   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_215618380_   1749 CAGAGGAAAATAGAGAGTACAGAAATAAACCTTTACATAGTGGGTCAAAT 1798
                         ii  iv i   v      v            iv     vvvv      v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_215618380_   1799 GATCTTTGATAAGGGCACCAAGACCA--CAGATGGGAAAATGATAGTCTG 1846
                            i  i  i     ii         --  -     i   vi       v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAGAATAGTCTT 399

  chr1_215618380_   1847 TTTTACAAATGAATTTAGGAAACCTGGATGCCCACATGCAAACAAATGAA 1896
                           iv       ivvi i   v v      i?           vi      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_215618380_   1897 ACTGGACTCATCTTTCACAT--TACACAAAAATCAACTCAAAATGTATTA 1944
                         ii     i v vii     i--  i        i           v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_215618380_   1945 AATCCTTAAGTGTAATACCTAAAACTATAAAACTCAGAGAAAACAACATA 1994
                         ? vv i   i     v v                 vv    i v      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_215618380_   1995 GAAGGAAAGCTTCATAACATTGATCTTAGCAATGATTTCCTGGATATAAC 2044
                          i? v   v    i i  v   ivi vi      i    i i     i  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_215618380_   2045 ACTAAAAGCAGAGGCAACAAAAGCAAAAACACACAAGCCGGATTAAATCA 2094
                           i       v i          v     i v i  iii   i vv    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_215618380_   2095 AACTAAAAAGCTTGTGTAAAGCAAAGGAAACAATCAC-AGAGTGAAAAGG 2143
                           v v    i   v   ivvv       v  v    v- i         i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_215618380_   2144 GAACATATAGAATGGGAGAAAATATCTGTAGACCACATATCTGATAAGGG 2193
                         v   vi i                 i  i i i  i              
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_215618380_   2194 GTTAATATCCAGT-CATGTGAGGAACTCCTACAACTAAATAATAAGAAAA 2242
                         ii vi       v-i  i i i      i       v        i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_215618380_   2243 AAAATGAAATATTTGATTTTTAAAATAAACAAAGAACTTAAATAGACCTT 2292
                         v    i vvi v  ? -----     iii     i i  i       v  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWA-----AAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_215618380_   2293 TCTCCAAGGAAGACATACAAGTAGTCAATATGTACATGAAAAGACTCTCA 2342
                                i     i      i i i     v i           iv    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_215618380_   2343 ATATCACTAATATT 2356
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (131 / 87)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.00 (36 / 12)  


2389 25.03 4.80 4.13  chr1_215622462_215626272     2424  3318 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_215622462_   2424 ATATGCCATATTTGTTGATTGGAAAACATGATATTGTTGAGATGTCTCTC 2473
                             v    i  ii v        i  v i        i     v ----
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC---- 53

  chr1_215622462_   2474 CAAATTCTCTCCTCAAATTCATCTCCTCAAATTGGTCAATGAACTTATTC 2523
                         --   v   i  --     v    v -- i   ---   i v ---  i 
  L1M4_orf2#LINE/     54 --AATACTCCCC--AAATTGATCTAC--AGATT---CAACGCA---ATCC 91

  chr1_215622462_   2524 ATTAAAATTGGCAATCACAAAATTCTAACAAGCTTATTTGTTGAAAGTGA 2573
                         v -----------    --    i i i viv   v    iv    v   
  L1M4_orf2#LINE/     92 CT-----------ATCA--AAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chr1_215622462_   2574 CAAGCTGATGTTAAT-TTTATGTGGAAATGCAAAAGACTTAGAATAATTG 2622
                                  vi   v-  i  i           ii   ii      iiii
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr1_215622462_   2623 AAACAATTTTGAAAAAGGAGAACAAATCTGGAGGAGTTACGCTATCTTAT 2672
                                i         i        vi       v i  i  vi iv  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr1_215622462_   2673 TTCAGA-CTT----TAAAGCTATAGCTATCAAGATACTG-GTTATCGGTA 2716
                             i -   ----i       i  iv       i v  - v  ii  i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr1_215622462_   2717 TGAACAAAGATATACAGATCAATGGGCCAGAATACAGAAAAGAGATATAG 2766
                          i iv v   i   i          ivi     vv   ivvv   v   i
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_215622462_   2767 ACACATACAAATATGG-CAATTAATTT-CAACTAAGGTGTCAAGGCAATT 2814
                           v      vv     -     i    - i  v i    i    i v   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_215622462_   2815 CAAAAGGGAAAAGATAGTCTTTTCAATGAATGTTTC-AGGACAATTGAGG 2863
                            vi      ii             ii    v v -i      i  -- 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG--G 426

  chr1_215622462_   2864 ATATTCGTATGCAAGAAAATAAA--TAAACCTCCCTTACCTAATACTATA 2911
                            ?i ii      i i   i  -- ii   i ---     v i  i   
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCC---TACCTCACACCATA 473

  chr1_215622462_   2912 TATAAAA-TTAATTTCAAATGCATGCTAGATCTAAATAGAACAGCTAAAA 2960
                           i    -    i iv     v  vv?   i      iv  v        
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_215622462_   2961 TTTTTAAACTTTCAGAATAAAACAGAA----AATTCCTC-TGAGCTGGGA 3005
                         i v v     i i    v      v i----  v  i  -   v  v  i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_215622462_   3006 GTAGAAAA-GATTTCTCAGATAGGA-ATGAAAAGCACAAATCGTACAA-- 3051
                         v   iv  - i     i     v  - iv          iivii v  --
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_215622462_   3052 -----T-GATAAATTGAACTTCATCAAAATGTTTATAAATTGTTGT---T 3092
                         ----- -         i             ---  v   i v    --- 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAAT---TAAAAACTTTTGTGCTT 670

  chr1_215622462_   3093 TAGGGAATACTGTTTTAAAAATGAAAGTGTAAGTTACATACTAAGAGGTA 3142
                         i ii i i   i ivvi   i     ivii  vii   v v ii   iv 
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_215622462_   3143 GTATGTTCATGACATA-ATATGATAAAGGAGGTATATATTAAATATATAA 3191
                         i   v v  viv    -  v      i   vv i   vivi         
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_215622462_   3192 AGAACTCTCACAACTCTGCAATAAAAAATT------TGCAATTTAAAAA- 3234
                                 i       vii        ivi------iv     ?     -
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_215622462_   3235 GGGAGAAATAT----ATGGACATATTACCAAAGAAGACAAACAAATAGCA 3280
                            vi  iv  ----  i     v iv          i v      i  v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_215622462_   3281 AATAAGCACACAAAAAAATACTTAATATCAGTAATGTT 3318
                                   ii    i  i  i  i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (134 / 87)
Gap_init rate = 0.03 (30 / 901), avg. gap size = 2.67 (80 / 30)  


3402 24.58 1.67 0.67  chr1_215652074_215656165     2701  3599 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_215652074_   2701 TGAAAAGATACTCTATGCTCATGGATTGGAAGAATCAATATTGTTAAAAT 2750
                           i       ii i   i               v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_215652074_   2751 GTCTGCACTATTCAAAGTAATCTACAGATTCAGTGCAATCATTATTAAAA 2800
                          v vii   vii    v i             ii      vi   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_215652074_   2801 TACCAA-TACAATCTTCACATTAATAGAAAAAAATCATTCCAAAATTCAT 2849
                          v   i- i vv i  ii  vv   v  v  iv- v  i i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_215652074_   2850 GTGAAATCACAAAAGACCCAGAATAGCCAAAGTCATTCTGAGCAAAAAGA 2899
                         i  i  vii   ii                 iiv  ii   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_215652074_   2900 ACAAAATGAGAGGAAGCACATTCTCTGATTTTGAA--TTATTCTATAGAG 2947
                              i vi     vv    i ii ii    ii  --   --   i i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAG 247

  chr1_215652074_   2948 CTATAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACACATAGAC 2997
                            i     i   i    ii              ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_215652074_   2998 CAAAGAAACAGAATAGATAAATCAGAAACAAATCCATACAGCTATGTTGA 3047
                            v i  i     v  v ivi      i   i       vi    v v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_215652074_   3048 ATTTATTTTTGACAAAGGCGCCAAGAACATACAGTGGAGAAAGA-CAATC 3096
                            v     i     i  i       v   v  i   i      -i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_215652074_   3097 TCTTAAATAAATTGTGCTAGGAAAACTAGACGTCTATAGGCAGAAGAATG 3146
                          i  v  i    v     i   v    i  ii? i i v   i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_215652074_   3147 AAGCTAGAACCCTATTTTTCATCATCTACAAAAATCAAATCAAAATGTAT 3196
                            i i  v     ii iv  i   v         i  v        v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_215652074_   3197 TAAAGAGCTAAATCTAAGACCTAAGACTATTAAACTATCAAAAGAAAACA 3246
                         i ?   v      v     v    i     v     v i i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_215652074_   3247 TTGGGAAAACTCCACAGGACATTGGTCTGGGCAAAGGTTTCTTGAATA-- 3294
                          v  ?iv  v  iv iv   v    vi i     v        ii   --
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_215652074_   3295 ACACCTCAAAAACAGAGATAACCATAGCAAAAATGGGCAAATGGGATCAC 3344
                              --    i  v iii   v v  v      i ii    v   iiv 
  L1M4_orf2#LINE/    598 ACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_215652074_   3345 ATCAAG-TTAAAAAGCGTCTGCACAGAAAAAAA-ATT--TAACAAAGTGA 3390
                              i-       - v i  ii vvv   ii - i --i  v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_215652074_   3391 AGAGACAACCCACAGAATGGGAGAAAA-ATTTTCAAACTATCCATCTGTC 3439
                          i                         -    v    ii  vi     vi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_215652074_   3440 AAGGAATTTATAACCAGAATATATAAGGAGCTCAAACAATTGGA----AA 3485
                             i i  i  v             i  i   vv    i vi ----  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_215652074_   3486 AAAATCTAATAATCCAATTTAAAAATGGGCAAAATGTCCAAATAGTCATT 3535
                            iv v     i      ?             ivi iii     v    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_215652074_   3536 TCTCAAAAGAAGACATATAAATGGCAAATAGGTATGTGAAAAGATGCTCA 3585
                             v        i   i       v    i i ii              
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_215652074_   3586 ACATCACTGATCAT 3599
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (140 / 77)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


4262 19.61 1.09 2.18  chr1_215697524_215701104     2171  3088 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_215697524_   2171 TAAAAACACATTCCATATTCATGGATCAAAAGACTTAGTATTATTAAAAT 2220
                          ii   v i  i    i         iii        i    i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_215697524_   2221 GCCAATACTACCCAAAGTGATTTATTGATTCAATGTAATCCCTGTCAACA 2270
                          v       v      v    i  iv       i i       i    v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_215697524_   2271 TTCCAATAATATTTTTTGCATAAATAGAAAAATCCATTTTGAAACTTATA 2320
                          i   iiviiv         v    v  v  iiiv  ii i   i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_215697524_   2321 TGAAATCTCAAGAGATCCTAAATAGACAAAACAATCTTGAAAAAGAAAAA 2370
                           i  viv    i  i  vi     v                     i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_215697524_   2371 CAGAGTTAAAGGATTCACACTTTTTGATTTCAACACTTACTACAAAGCTA 2420
                           i    ii    i        iiii       v                
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_215697524_   2421 CAGTAATCAAAACAGTGTGGTACTGGCATAAGGACAGACATGTAATTGAA 2470
                                   i                       i      i  iv v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_215697524_   2471 TGGAATAAA-----GAGCACAGAAATAAACCTTCACATATATGGCCAAAT 2515
                                i -----   iv            ivi    v     i   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_215697524_   2516 GATTTTTGACAAGGGTGGCAAGAACTTTTAATGGGAAAAGGACAGTCTCT 2565
                               i          v     v v  i      i    i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_215697524_   2566 TCAACAAATAGTTATGAGAAAACTGGGTAAACACATGCCAAAGAAGGAAG 2615
                                  i  vv  i  v      i  ?v       v      v    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_215697524_   2616 CTGGGCCCTTATCTAATACCACATACAAAAATTAACCCAAAATGGATCAA 2665
                         i   i   i  i  v i    i              i            ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_215697524_   2666 AATTCTAAGTGTAAGACTCAAAACTATAAAACTTTTAGAGGAAAACCTAG 2715
                          ivi    i       vii              i     i      v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_215697524_   2716 GGCAAAATCTTTACAACAATGAATTAGGCAATGACTTCTTGGATATGACA 2765
                          ?vv       iiii  vv  ii          ii     i         
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_215697524_   2766 CCAAAGTTACAGTCAACAAAAGAAAAAATGGACAAATTGGATTTCATGAA 2815
                              ivi   iv                i  i        i     v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_215697524_   2816 AATTTTTAAAA---TTTGTGCAACAAAAGACAATATCAACAAAGTAAAAA 2862
                             ---    ---       vv    i    v      v     i    
  L1M4_orf2#LINE/    651 AATT---AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_215697524_   2863 GGCAACCCACAGAATGGAAGAAAATATTTATGA-TCAAATATCTTATAAA 2911
                          i               i           iii -   v      v    i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_215697524_   2912 AAATTAATGTTTGGAATGTATAGAGAATTCCTAAAACTCAACAGCAAAAA 2961
                         ii i vi i iii    i    i    i  i  v       i ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_215697524_   2962 AAAACAACGACAACAACAAAAAAAAACTTGATTGAAAAATGAGTAAAGGA 3011
                         --------     --------- v   iii   ?       i i      
  L1M4_orf2#LINE/    798 --------GACAA---------ATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_215697524_   3012 CTTGAATAGACATTTCTTCAAA-AAGATGTACAAATGGCCAATAAGCATA 3060
                         i                i    -     i                   i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_215697524_   3061 TGAAAAAATCCTCAACATCAGTAATCAT 3088
                               i  v          ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.32 (123 / 53)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 4.29 (30 / 7)  


 250 10.14 5.80 2.90  chr1_215757743_215760115      430   498 (1875)  C L1M4_orf2#LINE/L1   (0)   908   838  

C chr1_215757743_    498 AGACATTTCTCAAAAGAA--TACACTTATGCAGCCAAAAA--ACATGAAA 453
                                    v      --  i  vv   --     v  --        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAA 885

C chr1_215757743_    452 AAAAGCTCAACATCACTTATCAT 430
                          i v           ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.40 (2 / 5)
Gap_init rate = 0.04 (3 / 71), avg. gap size = 2.00 (6 / 3)  

2705 27.73 2.34 1.22  chr1_215757743_215760115      991  1888 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_215757743_    991 TGGAGAAACATTCTATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 1040
                             i i i  i i   i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_215757743_   1041 GGCCATACTACCCGAAGTAATTTATAGATTCAATGCTATGCCCATTAAAC 1090
                            v     v   i  v i  i  i        i  v  v  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_215757743_   1091 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAAATT--- 1136
                          v   vivi v  i  ii     v v  v  i-  - iii       ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_215757743_   1137 --GGAACCAAAAAAGAGCCCATATAGCCAAGATAGTCCTAAGCAAAAAGG 1184
                         --    viiv  ii  v  viv        i i i  i i iv  i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_215757743_   1185 ACAAAGGTGGAGGCATCATGCTACCCAACTTCAAACTATACTACAAGGCT 1234
                               v      vv   ii  v     i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_215757743_   1235 ACAGTAACCAA-ACAGCATGGCACTGGTACAAAAACAGACACATAGACCA 1283
                                i   -    ii   i     i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_215757743_   1284 ATGGAACAGAATAGAGATCTCAGAAATAAGACCTCACATCTACAACCATC 1333
                               i     v    vii         iv  vi    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_215757743_   1334 TGATCTTCAACAAATCTGACAAAAACAAACAGTGGGGAAAGGATTCCCTA 1383
                             i   i    ivv  v   i v  vv  i         i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_215757743_   1384 TTTAATAAATGGTGCTGAGTAAACTGGCTAGCCATATGCAGAAAATTGAA 1433
                           i  i           i vv      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_215757743_   1434 ACTGGACCCCTTACTTACACCTTATACAAAAACTAACTCAAGATGGATTA 1483
                         ii         vv  i     v          i        i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_215757743_   1484 AAGACTGAAATGTAAAACCAAAAATTATAAAAACCCTAGAAGTAAATCTA 1533
                         ?    iv        i v v    i       vi i      v   iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_215757743_   1534 GGCA-ATACCATTCACAACATAGACATGGGCAAAGATTTTAT-GATGAAA 1581
                           ?i- v i -   iii  v v ivv i     v i   iv -   - vi
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr1_215757743_   1582 ATTTCAAAAGCAATAGCAACAAAAGCAGAAGTTGACAGATGGTATCTAAT 1631
                          ivi        vv           v i  i v  i i  v v ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_215757743_   1632 --AAACTAAAGCACTTCTGCACAGCAAAAGAAGCTGTCATCAGAGTGAAC 1679
                         --   i    i-    i  ii vv    i  vi  i   vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_215757743_   1680 AGACAGCCTACAGAATGGGAGAAAATTTTTGCGATCTATCCATCTGACCA 1729
                              i  i                 v     i vii  vi      iv 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_215757743_   1730 AGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 1779
                         i  v  vi          v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_215757743_   1780 AGA-AAA---CCCCATTAAAAGGTGGGCAAAGTACATGAACAGATGCTTC 1825
                            -   ---   v   ?   ii         v iv    i   iii   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_215757743_   1826 TC-AAAGCAGAAACAAATCTTAAATGAAGTTAA-ACACACATATAAAAA- 1872
                           -    v   v i -----i     -- ii  - vi     iv   i -
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATA-----CAAATG--GCCAATAAGCACATGAAAAGAT 889

  chr1_215757743_   1873 ---CAGTAGCAGGAGAGGT 1888
                         ---  ii v  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.88 (32 / 17)  


 304 31.95 13.02 0.59  chr1_215811033_215817242.rev      271   439 (5771)    L1M4_orf2#LINE/L1        8   197 (711)  

  chr1_215811033_    271 ATATACCATATTTATAAAAAATAAAAGTTATTATAAT---AATGTCAATT 317
                             v    i  i  ii vviv  i v   v   vi ---i   v    v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr1_215811033_    318 CTCCCCAAATTCATCCATAATTTTAATACAATTTCAATCAAAATGTCAAT 367
                                    v   i i iv  i  ii    ii v        vi  ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr1_215811033_    368 ATACCT-------------------GCTGATTCCAATATTTATATAGAAA 398
                         - i   -------------------      i i  v   i    i    
  L1M4_orf2#LINE/    108 -TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_215811033_    399 TTTAAAGAGCCTATAAAAGTCAAGGCTTTCTTTAGGAAGAA 439
                          vi  i ii  i v  v  i   ii vv    v ii     
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

Transitions / transversions = 1.70 (34 / 20)
Gap_init rate = 0.02 (3 / 190), avg. gap size = 7.67 (23 / 3)  

2599 27.30 4.78 1.48  chr1_215811033_215817242.rev     3580  4458 (1752)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_215811033_   3580 TGGAAAAACAGCTCATGCTCATGGATAGGAAAAATCAATATCACTAAAAT 3629
                               i i v i    i        v    i v i     iii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_215811033_   3630 GACTATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCTATCAAAC 3679
                          i v     v      vii  i  i        i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_215811033_   3680 TATCAGCTACATTCTTTACAGAACTAGAAAAAGCT-ATTTTAATATTCAT 3728
                          vi     i v  i   i     v v  v  -   -  ii   v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_215811033_   3729 ATGGAACCAAAAAGGAGCCTGAATAGACAACACAATCCTAAGCCAAAAGA 3778
                               viiv  i   v  v      v   v      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_215811033_   3779 ACAAAGCTGGAGGCATCACATTATGCAACTTCCAACTATACTACAAGGCT 3828
                               i      vv     i viv   i   v  viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_215811033_   3829 ACAGTAATCAAAACACTATGGTACTGATACAAAAAGAGGCACACAGGCCA 3878
                                    i   v i        ii i  ii v  i  i i  ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_215811033_   3879 ATGAAACAGAATAGAGAGCCCCGAAATAAGGCTGCACATTTACAACCATC 3928
                            i  i     v     i  v       iv iii       iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_215811033_   3929 TGATCTTTGACAAAGCTGACAAAAAAAAATCAGTGGGGAAAAGACTCCCT 3978
                             i  i     i v  v   i vv v-   i        ii ivvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGTCT 398

  chr1_215811033_   3979 ATTTAATAAATGATGCTAGGATAACTGGCTAGCCATATGCAGAAGATTGA 4028
                         v  i  i     i    i   i      v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_215811033_   4029 AGCTGGACCCTTTCCTTATGCCACATGCAAAA-TCAACTCAAGATGGATC 4077
                           i       i v   i ii   i  i     - i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_215811033_   4078 AAAGACTTAAATGTAAAACCCCAAATTATAAAAACCCTAGAAGACAACCT 4127
                          ?    i         i v iv   i       vi i       v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_215811033_   4128 AGGC---AAT-------ACATAGGAACAGGCAAATATTTAATGACAAAAA 4167
                            ?---   -------  v v  ivi      vvi   vv iivv vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_215811033_   4168 CACCAAAAGCAATTGCAATGAAAACAAAAATTGACAAATGGGAACTAATT 4217
                                    vvv    ii   iv      v  i    v   vi v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_215811033_   4218 AAACTGAAGAGCTTCCACACAGCAAAAAACA--AACAGAAAAACAAACCA 4265
                            v v  i i   iiiii vv    ii   -- v  ii   i-------
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG------- 691

  chr1_215811033_   4266 TCCATAAACAGAAAACCTACAGAATGGGAGAACAAATT-GCAAACTATGC 4314
                         ---- i  v   v    i              v v   -     ii  ii
  L1M4_orf2#LINE/    692 ----TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_215811033_   4315 ACCTGACAAAGGTCTAACACCCAGCATTTATAAGGAACTTAAACAAATTT 4364
                          i    i  i  v  vii i    v  v     i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_215811033_   4365 ATGA------GAAAAACAACCCCATTAAAAAGTGGGCAAAGGACATAAAC 4408
                           i ------  v   i     v   ?    i           iv i  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_215811033_   4409 AG--------CCA---------TGCA----GCCAACAAGCATGTGAAAAA 4437
                           --------   --------- i  ----     i     ii      i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_215811033_   4438 AAATTCACTATCTCTGATCAT 4458
                          vii   vi   v????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.23 (55 / 13)  

 964 30.76 9.73 3.29  chr1_215811033_215817242.rev     5027  5725 (485)    L1M4_orf2#LINE/L1      165   908 (0)  

  chr1_215811033_   5027 ACCTAAAATAAAAGTTAAAATAA------AAATGAAATACAATGCC--AA 5068
                            i i    --- ii    i  ------   v   iv    v ii-- i
  L1M4_orf2#LINE/    165 ACCCAGAATA---GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_215811033_   5069 GACTTATGC--CACAAGGCCTCAAGACTTATTATAAAATGATACTAATTA 5116
                             i ii -- v   --ii    i     i  i   iiv i v    i 
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAA--TTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr1_215811033_   5117 ATGCTTTGAGCCATCGCTTCAAGAATAGGC--------CAAAAGAACAGA 5158
                          vi vv  v vi ii vivi   i    i --------   vi   i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr1_215811033_   5159 ---GGGAAT--AGAAACAAACACAGATAT--GTGGTCACAAGATTA-CAA 5200
                         --- i  i --     i    v  v i  --i      vvv    v- i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr1_215811033_   5201 CAAGGGTAACAGGGCAGTGTGGTAGGGAAAGGGTAATCATTTCAGTAAAT 5250
                                iv  i i vi viii i       ii  i  v     ii    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr1_215811033_   5251 GGTTCTATGTAAGTTGAATATCCATACAGAAAAAAGTGAATCTTGATTCC 5300
                            v  iv vv ii  i   ?   i iiv    i i    vi v  ii  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr1_215811033_   5301 T-TCT-ATACCATATACAAAAATCAAATTATA-TAGAATATAGATCTAAA 5347
                          -i  - i               i  v i v - i  vi ?   i     
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_215811033_   5348 -----GAG-TAA---TATACTTAAGCTTTTA----AACACAGAAGAATAA 5384
                         -----   -   ---    ---  i  i   ----  v   v i ?i   
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATA---AAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_215811033_   5385 --CTTTGTGACTTTGGTGTAGACAAAAATATTTCCTTA-ACACCACTGGT 5431
                         --   i     i    vv   i   --- iv  i    - i ------- 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAA---TGGTTTCTTAGATA-------T 596

  chr1_215811033_   5432 GCTACTCAAAAGATGCTAAACA-TAAACAAGAAAATTAATAAATTGGCTT 5480
                          vi  -      -ii -  i  -i   vi i     vi         vi 
  L1M4_orf2#LINE/    597 GACAC-CAAAAG-CAC-AAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_215811033_   5481 AAATTAACATTAGTAGTTTCT-TAATTTATCAAGACACCACAAAGAGAGT 5529
                         vv  i  v    iv ii  i - iv  i -v i     i iv    i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGAAAGT 692

  chr1_215811033_   5530 GAAAAAGCAA-----AGAATGGGAGACTATATGTCACCAGTC---TGTGC 5571
                              ii   -----           vv    - ii v i  --- i vi
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATAT-TTGCAAATCATATATCT 741

  chr1_215811033_   5572 AACAATAAACTCAGATT-ATGATCTTTAAA--ATTCTTACAATTAAACAA 5618
                         i i  vii   iiv  i- vi  v v    -- i        i v  i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_215811033_   5619 ACAAAAAGCAAATGG---------GAAATGGACAAAAGATATGAGCAGAC 5659
                         vv    ii     ii---------i      i    i   v   ii    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_215811033_   5660 ACTTTAGAAAAGTAAATATCCCAATGTCTA-TCAACACGCAAATAAGTGT 5708
                          i  ivvv    v i    v v    v i - v i   iii  v ii  i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_215811033_   5709 TCAGTTTCACTAGTTAT 5725
                            iiv   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (139 / 73)
Gap_init rate = 0.05 (35 / 744), avg. gap size = 2.60 (91 / 35)  


 450 23.73 2.54 1.69  chr1_215936851_215938958      508   625 (1483)    L1M4_orf2#LINE/L1      112   230 (678)  

  chr1_215936851_    508 TTTTTTACAGATAC--ATAAACATTTATCCTAAAATTCATGTGGAA-TCT 554
                               i    v i-- i  i -- v              i     - vi
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCATATGGAAATGC 159

  chr1_215936851_    555 AAAGCATCCCAAATAACCACAGCAATCTTGAAAAAGAAAAACCAAATTGG 604
                           i v i  vi    i   v i                i   v  i    
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_215936851_    605 AGTTTTTATGCTTCCTGATTT 625
                           vvi i ii     ii    
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTT 230

Transitions / transversions = 2.11 (19 / 9)
Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.67 (5 / 3)  

2586 20.43 5.47 5.18  chr1_215936851_215938958      923  1617 (491)    L1M4_orf2#LINE/L1      212   908 (0)  

  chr1_215936851_    923 GGCCTATGCTTCCTGATTTTCTAACTTACTACAAACCTACATTAATCAAA 972
                          i ii ii     ii    ivv             v     v       i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_215936851_    973 ATAGTGTGGTACTGGTAAAATATGTCATGTTATGTATATTTTATCACGTA 1022
                          i             i -------------------------------  
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCA-------------------------------TA 280

  chr1_215936851_   1023 AAGATGGACATATAGACCAGTGAAATAAAGCAGAGAGTCCAGAAATA--- 1069
                          i   i          i  i  i    i iiv               ---
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_215936851_   1070 ---------TATGTTCAAATGATTTTTGAGAAGGATGCTAAGACCACTTA 1110
                         ---------    v    v       i  v    i   i       i i 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_215936851_   1111 ATGGGGAAAAAAATGGCAGTTTCTTCAACAAATGGTGTTTAAA-AACTAT 1159
                                  i  ----i   i i              i vii -    iv
  L1M4_orf2#LINE/    381 ATGGGGAAAGAA----TAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_215936851_   1160 ATATCCACTTGCAAAAGAATAAAGTTGAACCTTTATCTTACATCATACAC 1209
                            ?    v           i      i   ii  i  i   i    i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_215936851_   1210 AAAAATTAACTCAAAATGGATTAAAGAC--AAATATAAAAGCAAAAATTA 1257
                                              i ?    --    i   i   v    i  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_215936851_   1258 TAAAACCCTTAGAAGAAAATATTGGGAGGAAATTTT-ATGACAT-ACCTT 1305
                               i            i  -i  ? v    i  -i    v -ivv  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_215936851_   1306 AG-CAGTGATTTCTTGAATATGACACCAAAAACAACGGAAACAAAA---- 1350
                           -  i  i      ii              i  vvi v       ----
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_215936851_   1351 AAATTGGCAA-TTGAATTAC-T----GTTGAAAACTTTTGTGCATTGAAA 1394
                             v ii  -   i i v - ----i  i             v ii  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_215936851_   1395 GATACTATCAACAGAGTGAAAAGACAAGTCATGGAATAGCACAAAAT--- 1441
                           i        v i             vi  ii    i v v     ---
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_215936851_   1442 TG-------TATGTTTGAGTAGAGGTTGGCATCCATAATATGTAAAGAAC 1484
                           -------   i i   vv  i ii v i     v     i        
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_215936851_   1485 CCCTAAAACCCAACAAGAAAACAACTAACAACCTGATTTAAAAATGGGCA 1534
                         i i  v   i   i  v    vi  v  i    ii   ?           
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr1_215936851_   1535 AAGGGTAAGGATATATATTTCTCTAAAAAATACATGCAAATTGTCAATAA 1584
                             i vv i   v i       i   i  v i  i     v i      
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_215936851_   1585 GCACATAAAAAGGTGCTTAACATTGCTAATCAT 1617
                               i     i    i     ii????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.54 (99 / 39)
Gap_init rate = 0.02 (15 / 697), avg. gap size = 4.93 (74 / 15)  


1593 26.46 8.99 2.47  chr1_216013009_216015362.rev      702  1268 (1086)    L1M4_orf2#LINE/L1        1   604 (304)  

  chr1_216013009_    702 TAGAAAAATATGCCATATTTATGGATTAGGA-ATTCAGTTTTGTTAAGAT 750
                          i    i    v    i  i       i i - i i i v          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216013009_    751 CTCAAGTTTACCCTAACTGAACTGTAGATTCAATGCAATCCTGATCAAA- 799
                         vv   vvi v   v  i   v  ii        i       iv      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216013009_    800 TACCAATAAATTTTTCTTTGTGGAAATTGACAAGCTTTTTCTAAAGTGTA 849
                          v   iivivi    --   ii              vv i     i vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT--TTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_216013009_    850 TATGGAAATATAAAAGTCGTAGAATTGCCAAGACAATTTTGAAAAAAAA- 898
                                  ii  ii v vi     v     i     i        i  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_216013009_    899 ---AAAGATGAAATGGC-AACACTTAATAAGATTTTAAGATTCACAGTAA 944
                         ---    v  i i- i -v      vvi  --   i  i i i  vii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAG-GACTCACACTTCCCAA--TTTCAAAACTTACTACAA 245

  chr1_216013009_    945 AA--ACAGTAATTAAGGGAGTGTGGTATTGGTGCACGGCTAGACAAGTAG 992
                          i--        i   iv         i   iii v  v      vi   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_216013009_    993 GTAAATTGAATAGTATAGAGAGTCCAGAAAAAGGCCCACACATATATAGT 1042
                         i v   v      v  v             v ii    i    v   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_216013009_   1043 CAGTTGATTTTCAGCAACACTGGTACTGCAATTTAGTGGAGAAAG--TGG 1090
                           i         ii   viv  vi vvi v   i i   i     -- i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_216013009_   1091 CCTTTTCAATCAAAGTGATGCT---------------------------- 1112
                         i        -    -  i    ----------------------------
  L1M4_orf2#LINE/    396 TCTTTTCAA-CAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_216013009_   1113 -----AGT--GACACCTGTCTCACATCATACACAAAAATTAATGTGCAAT 1155
                         -----   --   v   ii      i    i           iviiv   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_216013009_   1156 GGCTTGTAAATCTAAATATAAAACATTTTTTTAAA----TAAAGGCTTTA 1201
                           v ii? i i      i   i v------i    ----    ivii   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAG------CTAAAACTATAAAACTCTTA 537

  chr1_216013009_   1202 GATGAAATTATAGAAGAGTATCTTCATGAATTTGGGGGTAAGCAAATATT 1251
                           v    vi    i? viv      i   vi     v-  i    vvi  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTT 586

  chr1_216013009_   1252 TCTTAAATA-GGCACTAA 1268
                              i   - i   i  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAA 604

Transitions / transversions = 1.74 (94 / 54)
Gap_init rate = 0.03 (17 / 604), avg. gap size = 3.82 (65 / 17)  

 602 26.72 4.20 1.53  chr1_216013009_216015362.rev     1602  1863 (491)    L1M4_orf2#LINE/L1      640   908 (0)  

  chr1_216013009_   1602 GGCTTCCTTATATTTAAACAATTCTATTAATGTAAAAATACCATTAAGAA 1651
                          i    v i v v     v v  i i vvv vv  ii i  i  i     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_216013009_   1652 A----AAAGGCAAGCCACAGCATGCAAGAAGACAGTTATAATACATACGT 1697
                          ----    i   v      v   vi    i i v  ii  vv    ii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_216013009_   1698 CTAA-AAACTACTTCTGTCCAGAATATACA--GAATCTTCTACAAATCAA 1744
                           i -  ivv    v i           i --   -  ii     v    
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAA 788

  chr1_216013009_   1745 TGAGAAAATG-CATATAACTCAATTTTAAAATGCATAAAAAACTCCTGAG 1793
                          i v    v -  v     i     ?v      vii   ii i --   i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT--TGAA 836

  chr1_216013009_   1794 CAAAAATTTTATAAAAGAGGATATCCAAAGGGCCA-TA--CACATAGAAA 1840
                         i i v    iviv     i     v    v     -  --     -    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-GAAA 885

  chr1_216013009_   1841 AAAGGTTCAACATCATTACTCTT 1863
                          i v i         ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (38 / 31)
Gap_init rate = 0.03 (9 / 269), avg. gap size = 1.67 (15 / 9)  


3059 24.15 4.81 2.70  chr1_216145217_216147291.rev      724  1576 (499)    L1M4_orf2#LINE/L1        1   871 (37)  

  chr1_216145217_    724 TGAAAAGACATCCCATGTTCATGAATTG---------------TTAAAAT 758
                           i     i              i    ---------------    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216145217_    759 GACCATACGACTCAAAGAGATGTATATATTCAATGCAATCCCTATCAAAA 808
                          i v    vv i    vv   v  i v      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216145217_    809 TACCAATTACGTTCTTCACAGAAATAGAAAAAGCAATTGTAAAATTTGTA 858
                          v   ii i v  i  ii       v  v  ivii  iv       ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_216145217_    859 TGGAGCTACAAAACACCCTGAGTAGCCAAAGCAATCCTGAGCAAAAAGAA 908
                             iv i   iiv    v  i        i     i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_216145217_    909 CAAAACCGAAGGCATTACACT-ACTAACTTCAGAATATACTATAAAGCTA 957
                             iii i   vv i     -v i  i    i  iv     i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_216145217_    958 TAGTAATCAAGACCGCAAGATATTGGTATAAAAACAGACACATAGACCAA 1007
                         i            v iiv i  i   i    ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_216145217_   1008 CGGAACAGAATAGAGACATCAGAAATAAATCCATGTATTTATAGCCAACC 1057
                         i    i     v    vvi          i    ii      i i   ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_216145217_   1058 AAGTTTTGACAAAGGTGCCACAAACACATACTGGGGGAAAGGACAACCTC 1107
                         i v   i     i       vi v  ivi v     -    i i ii  i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTT 399

  chr1_216145217_   1108 TGCAGTAAATGGTGCTGAGAAAATTGGATATCCATATGCAGAAAAATAAA 1157
                          v  ii           i  v  i      ?   i     i  i   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_216145217_   1158 ACTAGATGCCTATCTCCCACCATATATAAAAATCAACTCAAAATGGATTA 1207
                         ii i  iv    i   v         i      i              i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_216145217_   1208 AATATTTAAACATAAGATCTGAAGCTATAAAACTACTAGAAGAAAACA-- 1255
                         ? v ii    ii     v  i  i          vi            --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_216145217_   1256 GGGG-AAATGCTCTAGGCCATTGGTATAGGCAAAGATTTTATGGGTAAGA 1304
                           ? -    vi  vv i  v v   -       v i   iv i i  v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGA 598

  chr1_216145217_   1305 CTTCAAAAGCATAGATAACAAGTG----------------GGATTATATC 1338
                          vi        i iii     iv ----------------   i vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_216145217_   1339 AGACTAAAAAGCTTCTG-----CACAGTAAACAATCAACAGAGTAAAGAG 1383
                          i v v    i   i  -----  v  v v  v     v i   i  i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_216145217_   1384 ACAACCTGTAGAATGGGAGGAAATATTTGCAAACTATTAATATTGCAAAC 1433
                               iii          i             ii  --    ------ 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT--ATAT------C 740

  chr1_216145217_   1434 TATTAATCCAACATGGAATCAGTATCCAGAATGCACAAGGAACTCA-ACA 1482
                          iv   --------  i iiv           ii i  i      v-   
  L1M4_orf2#LINE/    741 TGATAA--------GGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_216145217_   1483 GCAAAATAAATAAATAAATAAATAAATAATCTGATTAAAAAATGGGCAAA 1532
                         i ---- v     -    v i i      i ii   ?             
  L1M4_orf2#LINE/    783 AC----TCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_216145217_   1533 GGATCTGAATAGATATTTCACAAAAGAAGACACACAAATGGCTA 1576
                             i        i     v v        i i         i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 2.21 (139 / 63)
Gap_init rate = 0.02 (14 / 871), avg. gap size = 4.57 (64 / 14)  


2474 25.27 8.02 1.94  chr1_216174933_216177916     1661  2483 (501)    L1M4_orf2#LINE/L1        1   873 (35)  

  chr1_216174933_   1661 TGAAGAAACTTCACCATCTTCATAGATTGAAAAACTCAATACAACAAAGA 1710
                           i i i iv  -    v     i     i  i   i    iviiv    
  L1M4_orf2#LINE/      1 TGGAAAGATATC-CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_216174933_   1711 TGTCAATTTTTTCCAAATTGATGTTTAGGTTTAATGCAATTCCTAT---- 1756
                           v    vi ii          v vi  i  i  i     i     ----
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_216174933_   1757 ATTGCAA-TA--TTTGTTACAGATGTAAACAA----------AAGTTTAT 1793
                           iv  i- i--   v  i    vi vi    ----------  i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_216174933_   1794 AGGAAAAGGCAAAGGAAATAGAGTAGCTAAAACAATTTTGAAAGAGAAGA 1843
                          v i   v    i   vvi   i    i        i      i      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_216174933_   1844 ATAAATTGGGAAAAATAAGTCCACCCAATTTCAAAATTTACTGTGTAGCT 1893
                          i   v v   ii v v vv iv             i     iiiv    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_216174933_   1894 ACAGTAATCAAGACAGTGTCACACGGGCAAAGAGATAGACACACGAATCA 1943
                                            vii  v    v ii        i iii    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_216174933_   1944 ATGGAACAGAATAGAGAACCCAGTAATAAACCCATGCGAATATACCCAAC 1993
                               i     v    ii    v           i ivv   ivi   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_216174933_   1994 TGATTTTTGACAAAAGTACAAAAGCGATTTAATAAAAGAAGAATAATCTT 2043
                                i     ii  i v  ii v   i   iiiii       i    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_216174933_   2044 TTCAACAAATGGTACCGGAGTAATTGGATATCAGTAGCCAAAAACCTCAA 2093
                                      i i  iii  i      ? vii vv     ivv v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_216174933_   2094 --------CCTAAGTTTTACAT-ATCATACAAAAATTAACTCAAAATGGA 2134
                         --------    --ii i   i-  -                        
  L1M4_orf2#LINE/    450 GTTGGACCCCTA--CCTCACACCAT-ATACAAAAATTAACTCAAAATGGA 496

  chr1_216174933_   2135 CCATGGACTCAAA-GTAAAATGTCAAACTATAAAGCCTTGTTTTTAAA-- 2181
                         i  ?i   ii   -    i vv v          i ----- i   i --
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-----TCTTAGAAG 541

  chr1_216174933_   2182 ------TAGGAGAAAATCTTCAGGATCCAGGGCTAGGCA--GAGTTGTTA 2223
                         ------    ? v        iv  i iv   i      -- iv  v   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_216174933_   2224 GGTTTGACACTGAAAGTGCAATCTATAAAAGAAAAAGTTAATAAATTTGA 2273
                          i v      ii    ii   v v i          i vi       v  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_216174933_   2274 CTTGATCAAA-TTAAAAACTTTTGGTCTATCAAAG---ACTGTTAAAAAG 2319
                            v      -             vv  -      ---   i i  i  i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAA 690

  chr1_216174933_   2320 ATGAAAG------TCGCAAGCTGGTAGAAAATATTTGTAGACCACATATC 2363
                         i     i------i i  iiv   v            i i i  i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_216174933_   2364 TGAGTA--------GTATTTTGAATATATTATTAAACTCTCAAAACTTAA 2405
                            -  --------    iiv        v v-i      i v    i  
  L1M4_orf2#LINE/    741 TGA-TAAGGGACTTGTATCCAGAATATATAAA-GAACTCTTACAACTCAA 788

  chr1_216174933_   2406 CAGCTAAAATATTTTTAAA--ATCTAATTAGAAAATGG-CATAAGAC--A 2450
                         i iiv    v i----   -- i i    ?i       -  v i  i--i
  L1M4_orf2#LINE/    789 TAATAAAAAGAC----AAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_216174933_   2451 AAAAGACA-----CCAAAGAGGATGTACGA-TGGCAAAT 2483
                           v     -----       i   i   i -    v   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

Transitions / transversions = 2.04 (137 / 67)
Gap_init rate = 0.03 (26 / 873), avg. gap size = 3.15 (82 / 26)  


3780 24.37 0.44 0.33  chr1_216204555_216208782     2829  3735 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216204555_   2829 TGGAAAGGTATTTTATGTTCATGGATTAGAATAATCAATAGTGTTAAGAT 2878
                                i   iii             i   v v i    v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216204555_   2879 GTCCATACTATCTGAAGCAATCTACAGATTCAATCCAATTCCTATCGAAA 2928
                          v v     vi ii  vii              iv    i      i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216204555_   2929 TACCAATGACTTTCTTCACAGAAATAGAAAAAATATTTCTAAA-TTTATA 2977
                          v   iivi i  i  ii       v  v  iv iv i     -  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_216204555_   2978 TGGAACCACAAAAGATCCAGAATAGTCAAAACTATCCTGAGCAAAAGGAA 3027
                              vii   ii  i         i      v   i   iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_216204555_   3028 CAAAACTGGAGGGATCACATCACCTGACTTCAAATTATGCTACAAAGCTT 3077
                             ii      iv     iiv  ii i      viv i          v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_216204555_   3078 TAGTAACCAAAACAGCTTCGTATTGGCCTAAAAACAGACACATAGATCAG 3127
                         i     i   i    iv v   i    v   ii i     i        i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_216204555_   3128 TGAAACAGAATAAAGAACCTAGAGATAAATCCATGCATCTTCAGTGAACT 3177
                           i  i     vi   ii i   i     i    i   i vii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_216204555_   3178 CATTTTTGACAAAGATGCCAAGAACATACATTGGGGAAAGGACCGTCTCT 3227
                         v     i     i i        v   v  v         i iv    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_216204555_   3228 TCAATAAATGATGCTGGGAAAACTGCATATCCACGTGCAGAGGAATGAAA 3277
                             i     i        v     v   ?    i    i i       i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_216204555_   3278 CTAGATCCCTATCTCTCACCGTATACAAAAATGAAACAAAAGTGGATTAA 3327
                         i i  i     i   v    i           v  viv   i     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_216204555_   3328 AGACTTAAATCTAAGACCTCAAA-TATGAAATTACTAAATGAAAACATTG 3376
                             i     v     v  v   -   i   i vi  i v        v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_216204555_   3377 AGGAAACTCTCCAGGACGTTGGACTGGGCAAAGATTTCTTAAGTAATACC 3426
                         i? v  v   i iv   v    ii i     v i       ii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_216204555_   3427 CTACAAGCACAGGCAACTAAAGCAAAAACGGACAAAT-GGATCACAT-AA 3474
                          i v       i     v    v     ii  i    -   iiv   -  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_216204555_   3475 AGTTAAAAAGCTTCTGCATAGCAAAGGAAACAATCAACAAAGTAAAGAGA 3524
                          i       -   i  iiivv       v  v     v     i  i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_216204555_   3525 AAACCTGCAGAATGGGAGAAAATATTCGCAAATTACCCATCTAACAAGGG 3574
                         v    ii                   i      i ivi    i i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_216204555_   3575 ATTAATAACTAGAATATATAAAATGCTCAAACAACTCTATAGGAAAAAAA 3624
                          i vi  v i            ivi   vv       v   iv     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_216204555_   3625 ATCTAATAATTTGCTTTAAAAATGGGCAAAATATCTGAATAGACATTTCT 3674
                         -- v     iiiiv  ?             iv  i               
  L1M4_orf2#LINE/    800 --CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_216204555_   3675 CAAAAGAAGACATACAAATGGCAAACAAGCATATGAAAAGGTGCTCAACA 3724
                          v        i           v  i     i        i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_216204555_   3725 TCATTAATCAT 3735
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.86 (141 / 76)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


3457 21.86 4.19 1.36  chr1_216315547_216317703      783  1665 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216315547_    783 TGGTAACATATAATATGTCCATGGGTTGGAAGACTCAATATTCTTAAGAT 832
                            v  v    vvi    i     i          i      v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216315547_    833 ATCAATTCTCCCCAG-----TCTGTAGATTCAGTGCAATCCAAATCAAAA 877
                         iv    v       i-----   ii       ii       vv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216315547_    878 TCCAAGCAGGCTCTTTTTGTAGGAACTGACAATCTGACTCTAAAATTTAT 927
                            v   v v  -      i  i  i      v    ii        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_216315547_    928 CTGGAAACGCAAGG-ACCTAGAATAGCCAGAACAGCTTTGAAAAGGAA-- 974
                         v      i      -   i          i    iii       i   --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_216315547_    975 -TAAAGTTGGAGGACTAACACTATCTGATTTCAAGCCTCAT--CAGAGCT 1021
                         -i              v     vi ii       iv  i i--  i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_216315547_   1022 AAGGTGATCAAGACAGTATGGTATTGACTTCA--ACAGAAATAGGCATCA 1069
                          vi  i           i     i  i v v -- i   v   viv    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_216315547_   1070 ATGGAACACGTACAAT-----GTCCATACATGCCTCACATACATATA--- 1111
                               ----  v   -----     v v  ivvi -       v  ---
  L1M4_orf2#LINE/    300 ATGGAA----TAGAATTGAGAGTCCAGAAATAAACC-CATACATTTATGG 344

  chr1_216315547_   1112 -CAGCTGATTTT-GGCAAAAATGCAAAAACAATTCAGTGGACAAAGAATA 1159
                         -  ii       - i   iii   v  i  v     i   iv        
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_216315547_   1160 TTATTTTCAACAAGTGGTGCTGGAACACTTGGGTGTTTACAAGCAAAAAA 1209
                         v v          i         i   vi   i i?ii   v      i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_216315547_   1210 AATAAACTTTGATCCGTATCTTGCAACATATACAAAAGT-AACTCAAA-T 1257
                          - i  v  v  i  v  i  ii  v           i -        - 
  L1M4_orf2#LINE/    445 A-TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_216315547_   1258 GAATCATAGACTGAAATGTTAACCCTAAAACTACAAAACATGTAGAAAAA 1307
                          i    ?    iv      v ivv         i     viv     i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_216315547_   1308 AGCATGGAAGAAAATCTTTTTGACCTCAGGTTAGGCAAAAATTTCTTAAA 1357
                          i   i i? v       iv      ii          vii       i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_216315547_   1358 TACAACACCAAAAGCACAATCCATGAAAGAAAAAGTAAGTGATAATTAGA 1407
                           ii               v v ii         i  ---     v v i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA---GATAAATTGG 640

  chr1_216315547_   1408 ATTTTATCAAAATTTAAAACTTCTGCTTTTTAAAAGACATTAGTTAGAGA 1457
                          i  i         v       i  ivi  i   i    i  viv   i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_216315547_   1458 ATGAATAAACAAGCCATAG--TCGTAGAGAAATATTTGCAAATCATATGC 1505
                         i    v i    v   i  -- v v   -                   ii
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGA-AAATATTTGCAAATCATATAT 739

  chr1_216315547_   1506 CTGATAAAGTACTTGTATCCACAATATATAAAGAACTCTTA-------AT 1548
                                i v           v                   -------  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_216315547_   1549 AGGAAGAAAGCAAACA-CCCACATTTTTTAATGGACAAACTATTTGAACA 1597
                          iv  i  ii    i -    -   ?vvv     i    vv       i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_216315547_   1598 GACACTTCACCAATAAAGGAATATAGATGCCAAATAAGTACATGAA--GA 1645
                             i   v    vi   iv   i i   v v      i       --  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_216315547_   1646 TGCTCAGCATCGTTAGTCAT 1665
                               i    i????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (115 / 74)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.33 (49 / 21)  


3294 26.70 0.44 0.66  chr1_216327102_216331374     2871  3780 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216327102_   2871 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2920
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216327102_   2921 GACCATACTGCCAAAAGCAATCTACAAATTCAGCACAATCCTCATTTGAA 2970
                          i v     v  v   vii       i     i i      ii  ivi  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216327102_   2971 TACCAGCCACCATCATTCCTTACAGAATTAGAAAAAACCATTCTAAAATT 3020
                          v     ii  ----  ii  i     v v  v  iviv  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_216327102_   3021 CATATGGAACCAACAAAGAGCCT-GCACAGCCAAAGCAAGACTAAGCAAA 3069
                                  vi-i   i ii  i- v i       i   vvi i iv  i
  L1M4_orf2#LINE/    147 CATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_216327102_   3070 AAGGACAAATCTGGAAACATCACACTACCTGATTTCAAACTACACTATGA 3119
                            i     vi    iivv       v  ii        vivi    ii 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_216327102_   3120 GGCCATAGTCACCAAAACAGCATGGTACTGGTGTAAAAATAGGCACATAG 3169
                         i  i i   v i   i    ii         ii   ii    i  i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_216327102_   3170 ACCAATGGAACAGAATAGAGAATCCAGAAATAAACCCAAATACTTACAGC 3219
                          i        i     v    i                v i i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_216327102_   3220 CAACTGATCTTCGACAAAGCAAACAAAAATATAAAGTGGGGAAAGGATAC 3269
                            i    i        i vviv   i vi  vv i         i   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_216327102_   3270 CCTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATATAGGAGAA 3319
                         i                       i  i   v  ?      ii ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_216327102_   3320 TAAAACTGTATCTTCATCTCTAACCTTATACAAAAATCCACTCAAGATGA 3369
                          i  ii  v i iii i   vv   v           iv      i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_216327102_   3370 ATTAAAGACTTAAAC-TGAGACCTGAAACGAGAAAAATTCTAGAGGATAA 3418
                           i ?    i    i- i   v  i    v v    v ii    i  v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_216327102_   3419 CATTGGAA-AAACCCTTGTAGACATTGGCTTAGGCAAGGATTTCCCCACC 3467
                            v  ?i-   i i i  -   v    v        v i    iivivi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_216327102_   3468 AAGAACCCAAAAACAAATGCAATAAAAACAAAGATAAATAGCTGGGACCT 3517
                          v  vv      i  v v    i    iv   i   i   iv v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_216327102_   3518 AATCAAACTAAAGAGCTTTTTCATGGCAAAAGGAACAGTCAGCAGAGTAA 3567
                         v      v v  i i     viiivv    i iv  vi   iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_216327102_   3568 ACAGACAACTCACAGAGTGGGAGAAAATCTTCACAATCTGTACATCTGAC 3617
                          v       i      i           v  ii   viii  i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_216327102_   3618 AAAGGACTAATATCCAGAATCTACAATGAACTCAAATAAATCAGTAAGAA 3667
                           i     vi          v  i  v      vv i  v   i   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_216327102_   3668 AAAAACAAACAATCCCATCAAAAAGTGGGCTAAGGACATAAACAGACAAT 3717
                            i     i  i  v  i?    i     v     iv i  i     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_216327102_   3718 TCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAA-ATGTTCA 3766
                             v                       i  i  i       -   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_216327102_   3767 GCATCACTAATGAT 3780
                         i     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (153 / 86)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3183 26.16 0.43 2.27  chr1_216400568_216406995     5011  5935 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216400568_   5011 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCATGAAAAT 5060
                              ii i  i     i      i v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216400568_   5061 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5110
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216400568_   5111 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5158
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_216400568_   5159 TATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 5208
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_216400568_   5209 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5258
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_216400568_   5259 TACAGTAACCAAAACAGCACGATACTGGTACCAAAACAGAGATATAGATC 5308
                                 i   i    iii i      i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_216400568_   5309 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5356
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_216400568_   5357 ATCTGATTTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5406
                          vi       i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_216400568_   5407 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5456
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_216400568_   5457 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTATTTCAAGATGGG 5506
                            ii    i    v   i     v             vi    i    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_216400568_   5507 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5556
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_216400568_   5557 CATTCAGGACATAGGCATTACCATTCAGGACATAGGCATGGGCAAGGGCT 5606
                         ----------     ?i v viv   iv   v v  vv i     v  i 
  L1M4_orf2#LINE/    547 ----------ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_216400568_   5607 TCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAA 5656
                           v ivv  vi            vvi          vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_216400568_   5657 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAT 5706
                          v   ii v  i   v v  i i   i  ii vv    i  v    i  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_216400568_   5707 CAGATTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACT 5756
                         v i v    v  i     i   i             v  i    vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_216400568_   5757 CATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATT 5806
                         i      i  i  i  vi          v  i  v      vv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_216400568_   5807 TACAAGAAAAAATCAAACAACTCCATCAAAAAGTGGGCAAAGGACATGAA 5856
                         v i  v     iv    i   i v  i?    i           iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_216400568_   5857 TGGACACTTCTCAAAAGAAGGCATTTTACATTTATGCAGCCAAAAAACAC 5906
                          i    i     v       ii  ---   v--   --     v  i   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATAT---ACAA--ATG--GCCAATAAGCAC 879

  chr1_216400568_   5907 ATGAAAAAATGCTTACCATCACTGGCCAT 5935
                                i     i v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.78 (25 / 9)  


2672 26.08 4.21 0.80  chr1_216410200_216414432     2863  3740 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216410200_   2863 TGGAAACACATACCACATTCATGGATGGGTAGAATCAGTATTGTGAAAAT 2912
                               v i  v   ii         v  v   v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216410200_   2913 GACTATACTGCCTAAAGCGATCTGCAGATTCAGTGCAATTCCCATCAAAA 2962
                          i v     v  i   vi     i        ii     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216410200_   2963 TACCATCATCATTCTTCACAGAACTAGAAAAAA-AATCATAAAATTCCTA 3011
                          v   v vv v  i  ii     v v  v  iv-i   v        v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_216410200_   3012 TGGAACAAAAAGTAAGAG-CCTACA-TAGCCAAAGCAAGACTAAGCAAAA 3059
                              ---- v i   i -  i v -        i   vvi i iv  i 
  L1M4_orf2#LINE/    151 TGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_216410200_   3060 AGCACAAATCTGGGGGCATCACATTATCCCACTTCAAACTATACTACAAG 3109
                           v     vi   i  vv     i vi  v i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_216410200_   3110 G-----GTA-TTAAAA---------------ATAAGAATG------TAGA 3132
                          -----   - i  i ---------------     i  i------    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_216410200_   3133 CTAATGGAACAGAATAGAAAACCCAGAAATAAAGCCAAATACGTACAACC 3182
                         ii       i     v  i ii           v   v i iv  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_216410200_   3183 AACTGATCTTCAACAAAGCAAACAAAAGCATATAGTGGGGAAAGAACATC 3232
                           i    i   i    i vviv   i v   vi i           i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_216410200_   3233 CTATACAACAAATGGTACTGGGATAATTGGCAAGCCACATGTAAAAGAAT 3282
                           v v           i      i  i   vv ?       i        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_216410200_   3283 AAAACTGTATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGA 3332
                         i  ii  v i  ii i   v    v           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_216410200_   3333 TCAAAAACTTAAATCTAAAACCTGAAACCATAAAAATTCTGGAAGGTAAT 3382
                            ? i  i     v   i v  i    i      v ii i    iv  i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_216410200_   3383 ACCAGAAAAACTCTT-GTAGACACTGGCTTAGGCAAAGAATTTAT-GATC 3430
                          ivi ?iv  v    -  -   vi   v        v iv  iv -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr1_216410200_   3431 AAGA-ACCAGACAGCAAATGCAACAAAA--ACAAATAAATAGATGGGACC 3477
                          v  -    i -    v v         -- v     i   i  v    i
  L1M4_orf2#LINE/    595 ATGACACCAAA-AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_216410200_   3478 TAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTA 3527
                          v  i   v v    i   i  ii vv    i  v iv    iv i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_216410200_   3528 AACAGACAACCCACAGACTGGGAGAAAATATTAACAAACTATGCACCCGA 3577
                           v              v              vi    ii  ii i i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_216410200_   3578 CAAAGGACTAATGTCTATAACCTATAAGGAACTCAAACAAATCAGCATTA 3627
                         i  i     vi i  i v  iv     i      vv    v   ii v  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_216410200_   3628 AAAAAATAA-TAATCTTATCAAAAAGTGGGCAAATGACATGAATAGACGA 3676
                             i i  -   i iv  i?    i        v  iv         iv
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_216410200_   3677 TTCTCAAAAGAAGATATACAAGTGGACAGTAAA-ATAAGAAAAAATGCTC 3725
                              v               i   v  i   i- i v     i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_216410200_   3726 ACCATCACCAATTAT 3740
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (132 / 93)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.59 (44 / 17)  


3167 26.99 0.88 0.44  chr1_216415896_216420990.rev     3701  4604 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216415896_   3701 TGGAAGAATGTTCCATGCTCTTGGATAGGAAGAATCCATATTGTGCAAAT 3750
                              ii  i i     i  v     v      v iv       vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216415896_   3751 GGCCATACTGCCCAAAGTTATTTATAGATTCAATGCTATCCCCATCAAGC 3800
                            v     v      v v  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216415896_   3801 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3848
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_216415896_   3849 TATGGAACCAAAAAAAAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 3898
                                viiv  iii v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_216415896_   3899 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3948
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_216415896_   3949 TACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3998
                            i    i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_216415896_   3999 AATGGAACAGAACAGAGGCCTCAGAAATAATGTCACACATCTACAACCAT 4048
                                i    iv   ivii         vvi  i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_216415896_   4049 CTGATCTTTGACAAAACTGACAAAAACAAGAAATGGGGAAAGGATATCCT 4098
                         i    i  i     iiv  v   i v  vvv           i   vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_216415896_   4099 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGCTGA 4148
                         v  i  i              v      v  ?   i  ii i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_216415896_   4149 AATTGGATCCCTTCCTTACACCTTATACAAAAATTAACTGAAGATGGATT 4198
                          i     i    v   i     v                v  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_216415896_   4199 AAAGACTTAAATGTTAGGCCTAAAACCATAAAAACCCTGGAAGAAAATCT 4248
                          ?    i       v  iv       i      vi i i        iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_216415896_   4249 AGGCA-ATACCATTCAGGACATAGGCATGGCCAAGGACTTCATGACTAAA 4297
                            ?i- v i -   iv   v v  vv i v   v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_216415896_   4298 ACACCAAAAGCGATAA-CAACAAAAGCCAAAATACACAAATGGGATCTAA 4346
                                    - i  -         vv      v i    v   ii v 
  L1M4_orf2#LINE/    598 ACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_216415896_   4347 TTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACTATCATCAGAGTGAAC 4396
                          i   v v  i i   i vii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_216415896_   4397 AGGCAACCTACAGAATATGAGAAAATTTTTGCAACCTACCCGTCTGACAA 4446
                           i     i       iv        v       vii ivii     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_216415896_   4447 GGGGCTAATATTCAGAATCTACAAATAACTCAAACAAATTTACAAGAAAG 4496
                            i  vi   i      v  i   v     vv    v iv i  v   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_216415896_   4497 AAACAAA---CCCA-TCATAACATGCGCAAAGGATATGAACAGACACTTC 4542
                          i     ---    - i?v  v   v         v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_216415896_   4543 TCAAAAGAATACATTTACATAGCCAACAGACACGTGAAAAAATGCTCATC 4592
                           v      v i  vi v  i     i ii   i      i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_216415896_   4593 ATCACTGGTCAT 4604
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3225 27.34 0.33 0.22  chr1_216424808_216431078     4872  5778 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216424808_   4872 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4921
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216424808_   4922 GGCCATACTGCCCAAGGTAATTTACCGATTCAATGCCATCCCCATCAAGC 4971
                            v     v     iv i  i   v       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216424808_   4972 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5020
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_216424808_   5021 TGGAACCAAAACAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5070
                              viiv  vi  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_216424808_   5071 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5120
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_216424808_   5121 CAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGATCAA 5170
                               i   i    iii        i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_216424808_   5171 TTGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5218
                          v   i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_216424808_   5219 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5268
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_216424808_   5269 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5318
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_216424808_   5319 AACTGGATCCCTTCCTTACACCTTATAGAAAAATCAATTCAAGATGGATT 5368
                          ii    i    v   i     v    v      i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_216424808_   5369 AAAGACTTAAACGTTACACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5418
                          ?    i    i  v v v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_216424808_   5419 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATATCTAAAA 5468
                            ?i v viv   iv   v v  vv i     v ii   v  vv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_216424808_   5469 CACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5518
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_216424808_   5519 AAACTAAAGAGCTTCCACACAGCAAAAGAAACTACCATCAGAGTGAACAG 5568
                            v v  i i   iiiii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_216424808_   5569 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5618
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_216424808_   5619 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5668
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_216424808_   5669 ACAAACAACCCCATCCAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5718
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_216424808_   5719 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5768
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_216424808_   5769 CACTGGCCAT 5778
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.67 (5 / 3)  


3186 25.86 1.78 1.00  chr1_216448574_216456504     4360  5260 (2671)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216448574_   4360 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4409
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216448574_   4410 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4459
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216448574_   4460 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 4507
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_216448574_   4508 TATGGAACCAAAAAGAGCCC-GCATTGCCAAGACAATCCTAAGCCAAAAG 4556
                                viiv  i ii   - v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_216448574_   4557 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG- 4605
                                i      vv   ii  v  ii i      viv        i -
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_216448574_   4606 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAAC 4655
                                 i   i    ii         i iv ii i   v       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_216448574_   4656 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACC 4703
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_216448574_   4704 ATCTGATCTTTGACAAACCTGACTAAAACAAGCAATGGGGAAAGGAT--T 4751
                          vi    i  i     ivv  v v i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_216448574_   4752 CCATATTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 4801
                          iv - i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    397 CTTT-TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_216448574_   4802 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 4851
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_216448574_   4852 ATTAAAGACTTAAATGTTAGACCTAAACCCATAAAAACCCTAGAGGAAAA 4901
                           i ?    i       v   v     v i      vi i    i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_216448574_   4902 CCTAGGCA-ATACCATTCAGGACATGGGCATGGGCAAGGACTTCATGTCT 4950
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_216448574_   4951 AAAACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGGAATGT 5000
                          vi            vvi         ivv     v  i    v i iv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_216448574_   5001 AATCAAACTAAAGAGCTTCTGCACAGCAGAAGAAACCACTATCAG---AG 5047
                         v      v v  i i   i  ii vv  i i  ---        i---  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGA---CACTATCAAGAAAG 691

  chr1_216448574_   5048 TGAACAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCG 5097
                             v  i  i  i                 v       vii ivi   v
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_216448574_   5098 GACAAAGGGTTAATATCCAGAATCTACAAAGAACTC----AAATTTACAA 5143
                           i  i  ii vi          v  i         ----  v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_216448574_   5144 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGAC 5193
                         v     i     i     v  i?    i     i      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_216448574_   5194 ACTTCTCAAAAGAAGACATTTAGGCAGCCAAAACACACACGAAAAAATGC 5243
                          i     v        i  vi iiii     v vi    i     i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_216448574_   5244 TCATCATCACTGGCCAT 5260
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (142 / 87)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.79 (25 / 14)  

1974 15.46 3.03 26.72  chr1_216448574_216456504     6249  7438 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216448574_   6249 TGGAAAAACATGCCTAGTTCATGGACTGGAA-ACTTAAGATTGTTAAAAT 6297
                               i i  v  vv         i     -      v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216448574_   6298 GGTCATACTATCCAAAGTGACCTACAGATTCAATGCAATCCCTATCAAAA 6347
                           iv     vi     v   i            i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216448574_   6348 TGCCAGTGGCATTTT-----GAAATAGAAACAAC-AATCCTAA--CTCAT 6389
                          v    iv  v    -----     v  v - i -i       --i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr1_216448574_   6390 ATGGAACCACAAAGGACTCCAGA-TAGCCAAAACAATCTTGAAAAAGAG- 6437
                               vii   i    -     -                        i-
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_216448574_   6438 --CAAAGCTGGAAGCATCGTGGTTTTTA-TTTCAAAAATATATTATAAAG 6484
                         --     i    i vv  iiiv  iii -        v -  i  i    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_216448574_   6485 CTACGGTAATTTAAAAAGTATGATAGTGGCATAAACACAGGAACATAGGC 6534
                             i     iv i v   i  i  v        iv i  iv i    ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_216448574_   6535 CAATGAAACAGAATACAGAGCCTAGAAATAAACACAGAGCCTAGAAATAA 6584
                              i  i     -------------- i -----   i i        
  L1M4_orf2#LINE/    298 CAATGGAATAGAAT--------------TGA-----GAGTCCAGAAATAA 328

  chr1_216448574_   6585 ATCCATTCATTTGTGATCAATTGACCATGCCAAGAATACACAATGGGGAA 6634
                          i    v     i  i        --------------------------
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGA-------------------------- 352

  chr1_216448574_   6635 AGAATAGTATCTTCAACAAACGGTTTCGGGGCCAGGCACAGTGGTTCACA 6684
                         --------- i   i    i-   ------    ----------------
  L1M4_orf2#LINE/    353 ---------TTTTCGACAAG-GGT------GCCA---------------- 370

  chr1_216448574_   6685 CCTGTATTCCCAGGACTTTGGGAGGCTGAGGCTGATGGATCACTTGAGCC 6734
                         ----------------------------------------------  v 
  L1M4_orf2#LINE/    371 ----------------------------------------------AGAC 374

  chr1_216448574_   6735 CAAGAGTTCAAGACCAGCCTGGGCAACATGGCGAGACCCTGTCTCTACAA 6784
                           ----     --------    ---------------------------
  L1M4_orf2#LINE/    375 CA----TTCAA--------TGGG--------------------------- 385

  chr1_216448574_   6785 AAAATGCAAAAGTTAGCCAAATGTGGTGGCACACGCCTGTGATCCAAGCT 6834
                         -------i    -------   ----------------------------
  L1M4_orf2#LINE/    386 -------GAAAG-------AAT---------------------------- 393

  chr1_216448574_   6835 ACTCAGGAGGCTGAGATAGGAGGACTGGCTTGAGCCTGGGAAGTAAAGGC 6884
                         --------------------------------------------------
  L1M4_orf2#LINE/    394 -------------------------------------------------- 393

  chr1_216448574_   6885 TGCACTGAGCCATGTTTGCACCACCGCACTTCAGTCTGGGTGATAGAGCA 6934
                         --------------------------------     -------------
  L1M4_orf2#LINE/    394 --------------------------------AGTCT------------- 398

  chr1_216448574_   6935 AGAGCCTGTCTCAAATAAATAAACGGTGTTGGGAAAACCAAATATCCACA 6984
                         -------- i    -----i   i    i     v   iii   ?     
  L1M4_orf2#LINE/    399 --------TTTCAA-----CAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_216448574_   6985 TGCAAAAGAATAAAATTGGAACCTTAATTTACACCATACACAAGAATCAA 7034
                                    i  i     v  i  vi i        i    i   i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_216448574_   7035 TTCAAAGTAGATTAAAAAATTAAATGTAATATCTAAAAGAGTAAAACCCC 7084
                         i     i i   i ? i vi         v v      vvi      i i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_216448574_   7085 TATAAGAAAATATAGGGGAAAACCT-CATGGCAGTGGTCTTGGCAATAAT 7133
                           v       i     ? v   i  - i  i vv   vi v      ii 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_216448574_   7134 TTCTTGGATGTGACATTAAAAGTACACACAACAAAAGCAAAAATAGACAA 7183
                              i   i     ii     i   vi         v         i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_216448574_   7184 GATGAGTTACATCGAACTAAAAAGTTTCTGCACAGCAAAGGGGAC-ATTA 7232
                         iv  iii v    i  v v    ii  i  ii vv      iv  -  i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_216448574_   7233 ACAGAGTGAAA-TACAATCTACAGAATGGGAGAAAATATTTGCAAGCCAT 7281
                          v i       -v    i i                         ii   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_216448574_   7282 ATATCTGATGAGGGGTTAATATTCAAAATATATAAGGAACTCCTTCAATT 7331
                                  i    ii vi   i  i         i      i v   i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_216448574_   7332 C--TAGCAAAAAGAAAAAAAAACGCTCAATTTAAAAATGA---------- 7369
                          --  ii       v   v  --- i     ?       i----------
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAA---CCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_216448574_   7370 -------ACATTTCTCAAAAAAAGACATACAAATGGCCAATACTTATATG 7412
                         -------         v   i    i                vvi i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_216448574_   7413 AAAGGATACGCAACATCACTAATCAT 7438
                            i   i v        ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (123 / 57)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 12.21 (354 / 29)  


2807 25.55 1.64 2.51  chr1_216816482_216822237     4348  5263 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216816482_   4348 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4397
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216816482_   4398 GGTCATACTGCCCAAAGTAATTTATGGATTCAATGCTATTCCCATTAAAC 4447
                           iv     v      v i  i  ii       i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216816482_   4448 TACCA-CTGACATTCTTCACAGAATTAGAAAAAAAAATTATTTTAAAATT 4496
                          v   -   v -  i  ii     v v  v  iv--- v  ii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC---TGATCCTAAAATT 146

  chr1_216816482_   4497 CATATGGAACCAAATAAGAG-CCCA-AATAGCCAAGACAATTCTAAGCAA 4544
                                  -- vii   i -    -         i     ii i iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_216816482_   4545 AAAGAACATAGCTGGAGGCATCACACTACCTTATTTCAAACTATACTGCA 4594
                         i       v  i      vv       v  iv        viv    i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_216816482_   4595 A-GCTATAGTAACCAAAACAGTATGGTACTGGTAGAAGAACAGACACATA 4643
                          -    i     i   i     i         i v   i i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_216816482_   4644 CACCAATGGAACAGAACAGAGAACTCAGAAATAAGGCCCTTAC--CTACA 4691
                         v i        i    iv    iii         i-   v   --i  ii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATG 343

  chr1_216816482_   4692 ATCATGTGATCTTTGACAAATTTGACAAAAACAAGTAATGGGGGAAGGAC 4741
                         i   vv    i  i     ivv  v   i v  vvi       i   i -
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA- 392

  chr1_216816482_   4742 TCCTTATTTAATAAATTTAATAAATTTAATAAATGGGACTACTGCCTAGC 4791
                         --------  i vvv  i  i    --ii iv-      v    vv  ? 
  L1M4_orf2#LINE/    393 --------TAGTCTTTTCAACAAAT--GGTGC-TGGGACAACTGGATAKC 431

  chr1_216816482_   4792 CATATGCAGATCATCGAAACTGGACCCCTTCCTTACAACATATACAAAAT 4841
                           i     i vv vi   ii         v   i   v           v
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_216816482_   4842 TTAACCCAAGATGGATTAAAGACTTAAAGGTAAAACCCAAAACTATAAAA 4891
                              i   i      i ?    i    v    i v i            
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_216816482_   4892 ACCCTAGAAGAAAATCTAGCAATA--CCATTCAGGACATAGGCATGGGCA 4939
                         vi i          iv   v?i  --i -   iv   v v  vv i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chr1_216816482_   4940 AAGATTTCAT-GATGAAAATGCCAAAAGCAATTGCAACAAAAGCAAAAAT 4988
                          v i    v -   - vi ii         vvv          v      
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_216816482_   4989 TGACAAATGTGATCTAATTAAACAAAAGAGCTTCTGCACAGCAAAAGAAA 5038
                         v  i    vv  ii v  i   vvv  i i   i  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_216816482_   5039 CTATTGTCAGAGTGAACTGATAATCTACAG-----GAGAAAATTTTTGCA 5083
                             iivv i      vv  i  i i    -----        v      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_216816482_   5084 ATCTATCCATCTGACAAAAGTCTAATTATCCAGAGTCTACAAGGAACTTA 5133
                          vii  vi      i  ii v  vi -       i v  i  i     iv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGT-ATCCAGAATATATAAAGAACTCT 778

  chr1_216816482_   5134 AACAAATTTACAAGAAAAA-ACAAGCAACCACATTATAAACTGGGCAAAG 5182
                         v    v iv i  v     -    ii    vv   ?v   v         
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_216816482_   5183 GATATGAACAGACACTTCTCAAAAGAAGACATACATGCAGCCAAAAAACA 5232
                            v    i     i     v        i     viii     v  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_216816482_   5233 TATTGAAAAAAAGCTCAATATCACTAATCAT 5263
                         i  -     i v      i    ????????
  L1M4_orf2#LINE/    879 CAT-GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (130 / 100)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.90 (38 / 20)  


3328 20.60 2.32 0.55  chr1_216824286_216826009.rev      501  1233 (491)    L1M4_orf2#LINE/L1      163   908 (0)  

  chr1_216824286_    501 GGACCCCAAACAGCTAAAACAATTTTGGAAAAGAAGAAACAAGTTAGAAG 550
                               vi  i   i        i   i          vv     i  i 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr1_216824286_    551 ATTCACACTTTCTGATTTCAAAGCATATTGCAAAGCTGTAATAACCCAAA 600
                          i        i ii        i v  i i       ii i   i v i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr1_216824286_    601 CTGTATGATACTGGCATAAAGACAAACA----AACCAATGGAATGGAATA 646
                          v  i  i           i  i i   ----i i         i    v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr1_216824286_    647 GATAGCTGATAAGTAAACCCTCACATACATGGTCAAGATGATCTTCAGCA 696
                           v  iiv v  i       vi    vi        v-    i   ii  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT-TGATTTTCGACA 361

  chr1_216824286_    697 AGTGTGCCAAGAGCATTCTTTGGGGGAAAAGACAGCTTCTTGAATATATG 746
                           v         v     vv     i  i - i  ii i  v  i v   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACAAATG 410

  chr1_216824286_    747 ATGTTAGAGGAAATGGCTATCCATATGCAAAAGAATGAAATTGAATCCTT 796
                         i  i i iiv  v   v  ?   i               i   i i  i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr1_216824286_    797 ATCTTATACCATATACAAAAATTAA------ATAGATTAAAGACCTAAAT 840
                          i  i i                  ------  i   i ?          
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr1_216824286_    841 GCAGCACCTAACACTGTAAAACT-TTAGAATAAAACATAGGAGAAAAGCT 889
                          i iv v    v   i       -      v          ? v   v  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_216824286_    890 TCATGACATTGGACT-TGCA-TGCTTT--TGGATATGACACCAAAAGCAT 935
                           i    v    ii -v   -  v   -- i                  i
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_216824286_    936 AGGCAGCAGAAGCAAAAGTGGACAAATGGGGCTACACTAAGCTTAAAAAC 985
                          i   i  i   v    i i  i    v  i  v  ii  iv        
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr1_216824286_    986 TTT-GTGCATCAAAGGACACAATCAACAGTGTGAAAAGGCAGTTTTCAAA 1034
                            -    v           v     v iv        i  iiiiv  i 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr1_216824286_   1035 ATGGGAGAAAATATTTGCAAATCATGTATCTGATATGGGATTAATATCCA 1084
                                                  i         v    i vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr1_216824286_   1085 GAATATATAAAGAATTCCTGCAACTCAATAACAACAACAAAAAATCAACC 1134
                                       i  i i           i  v  -i v    -    
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAA-GACAAAT-AACC 808

  chr1_216824286_   1135 CTATTTAAAA-TGAGCAAAGGACTTAAGTAGACATTTCTTCAAGGATGAT 1183
                          v   ?    -  i        i  i i           i   i  v   
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_216824286_   1184 ATACAGATGACCAAAAAGAACATGAAAAGATGCTTAACATCACTAATCAT 1233
                              i   i    v   v               i       ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (99 / 48)
Gap_init rate = 0.02 (12 / 746), avg. gap size = 1.75 (21 / 12)  


2949 24.60 3.95 1.47  chr1_216960069_216965366.rev     3922  4807 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_216960069_   3922 TGGAAAAACATTCTATGATCGTGGATTGGAAGGATCAACATCATTAAAAT 3971
                               i i  i i   v  i           iv i  i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_216960069_   3972 GGCCATACTGCCCAAAGCATTCTACAGATTTAATGCTATTCCTATCAAGA 4021
                            v     v      viiv          i  i  v  i        i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_216960069_   4022 TACCAA-TGTCATTTTTCACAGAATTAGAAAAA-TCATTCTAAAATTCAC 4069
                          v   i-  i -     ii     v v  v  i- v  i          i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_216960069_   4070 TTGGAACCAAAAAAAGAGCCCA-AATAGCCAATACAATCCTTGCAAAAG- 4117
                         v     -- viv  i ii    -         v      -   v     -
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAAGA 196

  chr1_216960069_   4118 -GAACAAAGCCAGAGGGACT-GCATTACCTAACTTCAAACTATACTATAA 4165
                         -        iii    -   -i  i v  i  i      viv     i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_216960069_   4166 GGCTACAGTAATCAA-ACAGCATGCTGCTGGTACAAAAAAAGATACATAG 4214
                         i              -    ii  v i    i i  ii v   i i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_216960069_   4215 ACCAGTGGAACAGAACAGAGAACCCAGGAATAAAGCTGCACACCTACAGC 4264
                          i  i     i    iv    ii    i      v iii   ii  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_216960069_   4265 CATTTGATCTTTGACAAGGTTGACAAAAATAAGCAATGGGGAAAAGAATC 4314
                           v     i  i       v  v   i vi vv           -    v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATA 394

  chr1_216960069_   4315 -CCTATTCAATAAATAGTGTGGGTATAGCTGGTTAGCCAAAGGCAGAAGA 4363
                         -i  v     i    i   iv  v i i    v  ?   v v   i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_216960069_   4364 ATGAAACTGGACCCCTACCTTTCCCCATATATAAACATTTATTCAAGATG 4413
                              ii             iv v       i   v   v i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_216960069_   4414 GATTAAAGATTTAAAGGTAAGCCCTCAAACTATAAGAATCCTGGAATTAA 4463
                            i ?   ii    v     vv  v         i v  i i   v-  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG-AA 543

  chr1_216960069_   4464 AATCTAGG---AAATACCACTGTGGACATCAGCCTTGGGAAATAATTTAT 4510
                           iv    ---    -- vii   -  v ii v-  i  v   ii   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT--CTTCGTG-ACCTTGGG-TTAGGCAATGGTTTCT 589

  chr1_216960069_   4511 --GACTAAGTCCTCAAAAGCAATTGCAACAAAAATAAAAATTACCAAGTA 4558
                         --  -  v v vi        vvv         iv      vivi  i v
  L1M4_orf2#LINE/    590 TAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_216960069_   4559 GTACTT------AATTAAAGAGGTTCTGCACACCAAAAGAAACTATCTAC 4602
                          v    ------       i v-  i  ii vi    i  v      v v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_216960069_   4603 AGAGTAAACAGACAACATATAGAATGGGAGAAAATATTTGCAAACTATAC 4652
                          i   i  v       vi i                        ii   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_216960069_   4653 ATCCAACAAAGGTCTAATATCCAAAATCTATAAGGAACTT----AATTCA 4698
                            ii i  i  v  vi      i   v     i     i----  i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_216960069_   4699 ACAAGCAAAAAGCAAATAAATCCATTAAAAAGTGGGCAAAAGATTT---- 4744
                          i  vv    ii       vi v   ?    i        i     ----
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_216960069_   4745 --------CTCACAAGAAGACAGACAAATGATCAATAAATATATTAAAAA 4786
                         --------   vv       i v       ii      ii i  v    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_216960069_   4787 ATGCTCAACATCACTAATTAT 4807
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (133 / 82)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.09 (48 / 23)  


2947 27.83 2.36 0.45  chr1_217096565_217102344.rev     1889  2779 (3001)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217096565_   1889 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1938
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_217096565_   1939 GGCCATACTGCCCAAGGTAATTTATAGAGTCAATGCCATCCCCATCAAGC 1988
                            v     v     iv i  i  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_217096565_   1989 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2036
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_217096565_   2037 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 2086
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_217096565_   2087 AACAAAGCTGGAGG-------CTACCTGACTTCAAACTATACTACAAGGC 2129
                                i      -------  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_217096565_   2130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAATAGAGATATAGATC 2179
                                 i   i    ii         i iv ii     v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_217096565_   2180 AATGCAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 2227
                             v  i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_217096565_   2228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_217096565_   2278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_217096565_   2328 GAAACTGGATCCCTTCCTTACACCTTATACTAAAATGAATTCAAGATGGA 2377
                            ii    i    v   i     v     v     v  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_217096565_   2378 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2427
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_217096565_   2428 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_217096565_   2478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACAGGATCTAA 2527
                         i            vvi          vv     v  i   iv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_217096565_   2528 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAAC 2577
                          i   v v  i i   i  ii vv    i  v    i  vv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_217096565_   2578 AGGTAACCTACA----------AAATTTTCACAACCTACTCATCTGACAA 2617
                           ii    i   ----------    v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_217096565_   2618 AAGGCTAATATCCAGAATCTTCAATGAACTCAAACAAATTTACAAGAAAA 2667
                         ii i  vi          v vi  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_217096565_   2668 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 2717
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_217096565_   2718 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 2767
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_217096565_   2768 ATCACTGACCAT 2779
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.57 (25 / 7)  

2732 22.34 10.22 0.27  chr1_217096565_217102344.rev     4556  5289 (491)    L1M4_orf2#LINE/L1      102   908 (0)  

  chr1_217096565_   4556 CCTAATGGCATTTTTTACAGAAACAAAAAAA--AAGTATAAAATTCATAT 4603
                           i iiv  v      i      ivi v  i--i viv            
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_217096565_   4604 GGAACCACAAAGGACCCTGAATGGCCTAAACAATCTTCAGAAAGAA---C 4650
                             vii   i      v    i   v          v i      --- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_217096565_   4651 AAAGTTAGAAGCCTCACACTTACTGGCTTCAAAACATATTACAAAGCTAT 4700
                               i  i v         v iiii        v  i          i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_217096565_   4701 GGTAATCAAAATAGTATAGTAATAGCTTAAAGACAGAGATATACACTAA- 4749
                         i        i i   i i   v i  v   i  i   v     v ii  -
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_217096565_   4750 -GAACAGAATAGAGAGCTCAGAAATGAACCCATGCATACACAGTCAAATG 4798
                         -   i     v     ii       i       i   vi ii     v  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_217096565_   4799 ATTTTCAACATGGATGCCAAAA--ATTCACAATGGGTAAAGGACAGTCTT 4846
                               i   v  i      i --     --     v    i i      
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAGAATAGTCTT 399

  chr1_217096565_   4847 TTCAACAAATGGTGCTGGGAAAA-TGGATATATATATGCAAAAGAATGAC 4895
                                             v  -      ?vi i              v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_217096565_   4896 ACTGGACCCTCATTTTATATCATACACAAAAACTATCTCAAAAGGGATTA 4945
                         ii       ii ii i i i    i       i  v       v    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_217096565_   4946 AAGATTTAAATTTAAGA-CTTGAATTATAAAATCCCTAGAAGAAAACATA 4994
                         ?   ii     v     -  vi  i       ii i              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_217096565_   4995 GGAGAAGAGCTTCATGATATTGGTCTTGACAAAGATTTCTTGTATATGAT 5044
                           ? v i v    i   iv    vi v i   v i      iv      i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_217096565_   5045 ATCAAAAGCACAGCCAACAAAAGCAAAAATAGACAATCAGGACTAAATCA 5094
                          i          iv         v         i  viv     vv    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_217096565_   5095 AACTAAAAAGCTTCTGCACATCAAAGAAAAC----AACAGAGTGAAAAAG 5140
                           v v    i   i  ii v      i v  ----  v i        ii
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_217096565_   5141 CACACTACAGTATGAGCAAAACTATATGCAAA------------------ 5172
                           vv i    v   i vi   v   v      ------------------
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_217096565_   5173 -CTTG-ATT---------------------------------TAAAAA-- 5185
                         -    -  i---------------------------------      --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_217096565_   5186 -----AACTTGATTTTTAAATGTGCAAAGGAGTTGAATAGACATTTCTCT 5230
                         -----   iii   ?vv     v        v                 i
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_217096565_   5231 AAAGAAGACATACAAATGGCCAGCAGGTACATAAAAAGACGGTGAACATC 5280
                                 i             ii i i    i      i v v      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_217096565_   5281 ACAAATCAT 5289
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.71 (101 / 59)
Gap_init rate = 0.01 (12 / 807), avg. gap size = 6.42 (77 / 12)  


3228 27.18 0.66 0.33  chr1_217167512_217173927.rev     5021  5925 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217167512_   5021 TGGAAGAATATTCCATGCTCACGGATAGGAAGAATCAATATTGTGAAAAT 5070
                              ii    i     i   i    v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_217167512_   5071 GGCTATGCTACCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5120
                            v  i  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_217167512_   5121 TACCAATAACTTTCTTCACAGAATTTGAAAAAACT-ACTTTAAAATTCAT 5169
                          v   iivi i  i  ii     v    v  i-  - iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_217167512_   5170 ATGGAACCAAAAAAGAGCCTGCATTGTGAAGACAATCCTAAGCAAAAAGA 5219
                               viiv  ii  v  v v  v iv  i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_217167512_   5220 ACAAACCTGGAGGCATCATGCTACCTGATTTCAGACTATACTACAAGGCT 5269
                              vi      vv   ii  v  ii      i viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_217167512_   5270 ACAGTAACTGAAAGAGCATGGTACTGGTACCAAAACAGAAATACAGACCA 5319
                                iii i v  ii         i iv ii i   v   i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_217167512_   5320 ATGGAACAGAACAGAGGCCTCAGAAATAATGCCGCACATCTACAACCATC 5369
                               i    iv   ivii         vv  ii    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_217167512_   5370 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 5419
                             i  i     ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_217167512_   5420 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 5469
                           i  i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_217167512_   5470 ACTGGATCCCTTCCTTACACCTTACACAAAAATTGA----AGATGGATTA 5515
                         ii    i    v   i     v  i         i ---- i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_217167512_   5516 AAGACTTAAATGCTAGACCTAAAACCATAAAAGCCCTAGAAGAAAATCTA 5565
                         ?    i      iv   v       i      vi i          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_217167512_   5566 GGCA-ATACCATTAAGGACATAGGCATGGGCAAGGACTTCATGACTAAAA 5614
                           ?i- v i -  viv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_217167512_   5615 CACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATTAGGATCTAAT 5664
                                    vvi          vv        i     -   ii v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT-GGACTTCAT 647

  chr1_217167512_   5665 TAAACTAAAAAGCTTCTGCACGGCAAAAGAAACTACCATCAGAGTGAACA 5714
                         i   v v    i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_217167512_   5715 GGCAACCTACAGAATGGGAGAAAAGTTTTGCAATCTACCCATCTGACAAA 5764
                          i     i                vv       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_217167512_   5765 GGGCTAATATCCAGAACCTACAAAGAACTCACAGAAATTTACAAGAAAAA 5814
                           i  vi         iv  i         vi v  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_217167512_   5815 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5864
                         i     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_217167512_   5865 CAAAACAAGACATCTATGCAGCCAACAGACACATGAAAAAATGCTCAACA 5914
                          v   v    i  vi viii     i ii          i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_217167512_   5915 TCACTGGTAAT 5925
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2945 26.92 1.67 0.67  chr1_217203816_217209547     4341  5239 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217203816_   4341 TGGAAAAACATTCCACGTTCATGGATAGGAAGAATCAATATTGTCAAAAT 4390
                               i i  i   i          v      v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_217203816_   4391 GACCATACTGCC-AAAGCAACTTATAAATTCAATGCTATTCCCATTAAAC 4439
                          i v     v  -   vii ii  i i      i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_217203816_   4440 CACCATTGACATTCTTCACAGAATTAGAAAAAAACT-ATTTTAAAATTCA 4488
                         iv   vivi v  i  ii     v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr1_217203816_   4489 TATGGAACCAAAAAAGGGCTCGTATAGCCAAGATAATCCT---AAGCAAA 4535
                                viiv  ii iv iv v        i i    i ---  iv  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_217203816_   4536 AACAAAGCCAGAGGCATCACGCTATCTGACAT-AAAACTGTACTACAAGG 4584
                                iii    vv    i  vi ii iv -      -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr1_217203816_   4585 CTACAGTAACCAAAACAGCATGGTATTGGTACAAAAACAGGCATGTAGAC 4634
                                  i   i    ii     i   i i  ii i  i   i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_217203816_   4635 CAATGGAACAGAATAGAGAACTCAGAAATAAAACT-TGCATCTACAACCA 4683
                                 i     v    iii          v i- i   i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_217203816_   4684 TCTCATCTTCAACAAACTTTACAAAAACAAGCAATGGGGAAAGGAATCCC 4733
                         vi v  i   i    ivv vv   i v  vv            -   vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGT 396

  chr1_217203816_   4734 TATTTTAACAAATTGTGCTGGGAGAACTAGCTAGCCATATGCAGAAAATT 4783
                         iv   i       v         v    i v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_217203816_   4784 GAAACTGGACCCTTTCCTTATACCTTATACAAAAATTAACTCAAGATGGA 4833
                            ii       i v   i i   v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_217203816_   4834 GTAAAGACTTAAATGTAAAATCCAAAACTATAAAATCCCTAGAAGAAAAT 4883
                         vi ?    i         i v i            ii i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_217203816_   4884 CTAGGCA-ATACCACTCAGGACACAGGCATGGGCAAAGATTGTAT-GATG 4931
                         v    ?i- v i -i  iv   viv  vv i     v i  viv -   i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_217203816_   4932 AAATCGCCAAAAGGAATTGCAACAAAAGCAAAAATTGACAAATGGGATCT 4981
                         vi - i       v vvv          v      v  i    v   ii 
  L1M4_orf2#LINE/    596 TGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_217203816_   4982 AATTAAACTAAAGACCTTCTGCATAGCAAAATAAACTGTCATCAGAGTGA 5031
                         v  i   v v  i v   i  iiivv    iv v   i   vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_217203816_   5032 ACAGACAGTCTACAGAATGGAAGAAAATTTTTGCAATCTATCCATCTGAC 5081
                          v     ii i         i       v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_217203816_   5082 AAAGGTCTAACATCCAGAATCTACAAGGAACTTAAGCAAATTTACAAGAA 5131
                           i  v  vii         v  i  i     ivvi   v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_217203816_   5132 AAA----AAGAACCCCATTAAAAAGTGGGCAAAGGACATAAACAGACATT 5177
                            ----  v     v   ?    i           iv i  i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_217203816_   5178 TCTCAAAAGAAGACATACACATGGCCAACAA--ACAAGAAAAAAAGGTCA 5225
                             v        i     v        i  --   v     i v v   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_217203816_   5226 ACATCACTAATCAT 5239
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


3594 24.75 0.66 0.33  chr1_217409208_217413832.rev     3230  4134 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217409208_   3230 TGGAAAGACATTCCA-GTTTATGGGTTGGAAGAATTAGTATTGTTAAAAT 3278
                                 i  i   -   i    i        v   i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_217409208_   3279 GACTATTCTACTCAAAGCAATTTACCGATTCAATGCAATCCCTATCAAAA 3328
                          i v  v  v i    vii  i   v       i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_217409208_   3329 TACCAATGACGTTTTTCACAAAAATAGAAAAAAGAATCCTAAAATTTATA 3378
                          v   iivi v     ii  i    v  v  ivvi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_217409208_   3379 TGGACCCACAGAAGACCCCCAATACCCAAAGCAATCCTGAGTGAAAAAAA 3428
                             vvii  iii     vv    v     i     i   ivi i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_217409208_   3429 GAAAGCTGGAAGCATCACACTACCTGATTTCAAAATATGCTACAAAGCTA 3478
                         v    i    i vv       v  ii         iv i           
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_217409208_   3479 TAGTAAGTAAATCATCATGGTATTGGCATAAAAACAGATATGTAGACCAA 3528
                         i     vi  iv  vii     i        ii i   i  i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_217409208_   3529 TGGAACACAATAAAGAACCTAGATATAAATTCATGCATTTATGGCCAACT 3578
                              i v   vi   ii i   v     ii   i         i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_217409208_   3579 CATTTTCAACAAAGTTGCCCAGAACATGCAATGAGGCAAGGACAATTTCT 3628
                         v      i    i v    v   v   v     i  v   i i i i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_217409208_   3629 TCAATATATGGTTCTGGGAAAACTGAATAACCATATGTAGAAGAAAAAAA 3678
                             i v     v      v     i   ?   i   i i     vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_217409208_   3679 CTAGAGCCCTATCTCTCCTCATATACAAAACTCAAA-CAAAATGCATTAA 3727
                         i i  v     i   v vi           v i  v-       v  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_217409208_   3728 AGATTTAAATCTAAGACTTGAAACTATAAAACTACTCAAAGAAAATATTG 3777
                            ii     v     vi i             vi vi       i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_217409208_   3778 GGG-AAATGCCCAATGGCATTGGCCTGGGCAAAGATTACTTGTGTAAGAC 3826
                          ? -    vii i-  i v    vi i     v i  v   ivi  v   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_217409208_   3827 CTCAAAAGCACAGGCAACTAAAACAAAAATCAACAAATAGGATT--ATCA 3874
                         vi          i     v   iv      vi i    v   i --    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_217409208_   3875 AGCTAAAAGGCTTCTGCACAGCAAAGGAAATAATCAACAAAGTGAAGACA 3924
                          iv v   ii   i  ii vv       v iv     v        i v 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_217409208_   3925 TAACCCATAGAATGGGAGAAAATATTTGCAAACTATCCATCTGACAAGGG 3974
                         i      i                        ii  vi      i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_217409208_   3975 A-TTGAATAGCCAGAATATATAAAGACCTCAAACAACACAGTAGCAAAAA 4023
                          -   --  v                v   vv     v  i  ii     
  L1M4_orf2#LINE/    750 ACTTG--TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_217409208_   4024 AACAAATAATCCAATTTTTAAATGGGTAAAAGACCTAAACACAAATATCT 4073
                         i        i      ?vv       i   i  ii i  i v v  v   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_217409208_   4074 CAAAAGAAAACATACAAATGGCTAACAGGTATATGAAAAAATGCTTAACA 4123
                          v      i i           i  i i i i       i     i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_217409208_   4124 TCACTAATTAT 4134
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.65 (137 / 83)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


2865 22.78 9.95 1.08  chr1_217417876_217420944.rev     1745  2578 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217417876_   1745 TGGAAAGATATTCCATGTTCATGGATTCGAAGAATTGATACTATTAAAAT 1794
                                    i               v     v  i   i i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_217417876_   1795 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCAGTCCCTACCAAAA 1844
                          v v     v      vii              i   i      i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_217417876_   1845 TACCAA-------------GGAAATT------CT-----------TCACA 1864
                          v   i-------------i      ------  -----------   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_217417876_   1865 --GAAAT-----------AGAA-----AAAACAA------------AGAA 1884
                         --     -----------    -----       ------------    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_217417876_   1885 CAAAACTAATGGAATCAGTGCAC---CTAATTTCCAATTATACTACAGAG 1931
                             ii iiv   v   ---   --- i      v  viv       i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCA---CACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_217417876_   1932 CTATAATAACCAATGCAGCCTGGTATTGGCATAGAAACAGACACATAGAT 1981
                            i i   i   vi   iv     i       iii i     i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_217417876_   1982 CAATGGAACACAATAAAGAACCCAGAAACAAATCTACAAACCTACAGTGA 2031
                                 i v   vi   ii       i   i i i v ii  ii  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_217417876_   2032 ACTTATTTTCAAAAAAGGTGCCAAGAGCACACAGTGAGAAAAAGACAATC 2081
                          i v      i v  i          v  iv  i  i i   ii i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_217417876_   2082 TCTTCAATAAATGGTGCTGCAAAAACTGGATATCCATATGCAGAAGAATA 2131
                          i     i           vi v         ?   i     i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_217417876_   2132 AAACTAGACCCCTCGCTCTCACCATAGACACAAATCAAATCAAAATGGAT 2181
                           ii i       vv   v       v   v    i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_217417876_   2182 TAAAGACTTCAATCTAAGACCTCACACTATGAAACTACTACAAGAAAACA 2231
                         i ?    i v   v     v  v v     i     vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_217417876_   2232 TTGAGGAAGCTCTCCAGGACATTGGTCTGGGCAAGAATTTCTTTGA-GTA 2280
                          v i? v iv   i iv   v    vi i     vii      v  -i i
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_217417876_   2281 ATACCCACAATCACAGGCAACCAAAGCCAAAATGGACAAATGGTATCACA 2330
                          i   v -  v    i     v    vv     i  i    v v iiv  
  L1M4_orf2#LINE/    598 ACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_217417876_   2331 TCAAG-TTAAAAAGCTTCTGCACAACAAAGGAAATGATCAACAAAGTGAA 2379
                             i-       -   i  ii vv       v iv     v        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_217417876_   2380 GAGACAACCCACAGAATGGAAGAAAATATTTGCAAACTACCCATCTGACA 2429
                         i                  i                ii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_217417876_   2430 AGGGATCAATAACCAGAATACACAAGGAGCTCAGACAACTCTACAGAAAA 2479
                              iivi  v        i i  i  i   vv       v i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_217417876_   2480 AAAAAATCTAATAATCTGATTTAAAAATGGGCA----------------- 2512
                           i v ---     i ii   ?           -----------------
  L1M4_orf2#LINE/    796 AAGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_217417876_   2513 TTTC-CCAAATGAAGACATACAAATGGCAAGCAGGCATATACAAGGGTGC 2561
                             -     -     i           v ii i   i  iv  i i   
  L1M4_orf2#LINE/    843 TTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_217417876_   2562 TTAACATCATTGGTCAT 2578
                          i       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (118 / 68)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 5.41 (92 / 17)  


2744 26.92 0.26 0.26  chr1_217556934_217558700      506  1274 (493)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr1_217556934_    506 TAAAGTTCATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTA 555
                             i           viiv  ii  v  v v  vi    iv     i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_217556934_    556 AGCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATA 605
                          ivv i          i      vv       v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_217556934_    606 CTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAG 655
                               i          i   i    ii         i iv ii i   v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_217556934_    656 ATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATA 703
                                         i    i--    i  --        vv  ii i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACA 337

  chr1_217556934_    704 TCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGA 753
                          i  iiiii vi    i  i     ivv  vv  i v  vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_217556934_    754 AAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATG 803
                            i  vvi  v  i  i              v      v  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_217556934_    804 TAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATT 853
                         i i  iiv    ii    i    v   i     v           i  i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_217556934_    854 CAAGATGGATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTA 903
                            i      i ?   ii    i  v   v       i      vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_217556934_    904 GAAGAAAACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTT 953
                                  v    ?i v viv   iv   v v  vv i     v ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_217556934_    954 CATGTCCAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAT 1003
                          v ivvi vi            vvi          vv     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_217556934_   1004 GGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATC 1053
                         v   ii v  i   v v  i i   i  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_217556934_   1054 AGAGTGAACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTC 1103
                          i      v  i     i   iv            v  i    vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_217556934_   1104 ATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTT 1153
                               i  i  i  vi          v  i  v      vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_217556934_   1154 ACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAAC 1203
                          i  v     i     i     v  i?    i     i     iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_217556934_   1204 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAA 1253
                              i     v        i  vi viii     v  i          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_217556934_   1254 ATGCTCATCATCACTGGCCAT 1274
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (118 / 85)
Gap_init rate = 0.00 (2 / 769), avg. gap size = 2.00 (4 / 2)  


2898 27.75 2.36 0.34  chr1_217608937_217615036     4718  5607 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217608937_   4718 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCTTGAAAAT 4767
                               i i  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_217608937_   4768 GGCCACACTGCCCAAAGCAATTTATAGATTCAATGCTATCCCCATCAAGC 4817
                            v i   v      vii  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_217608937_   4818 TACCATTGACTTTCTTTACAGAATTAGAAAAAACT-ACTTTAAATTTCTT 4866
                          v   vivi i  i   i     v v  v  i-  - iii    v   v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_217608937_   4867 TTGGAACCAAAAAAGAGCACATATATGCAAGAAAATCCTAAGCAAAAAGA 4916
                         v     viiv  ii  v vviv   vv   i v    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_217608937_   4917 ATAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGAT 4966
                          i    i      vv   ii  v  ii i      viv        i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_217608937_   4967 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAATAAATATATAAACCA 5016
                                i   i    ii         i iv ii   i i     i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_217608937_   5017 ATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAGCCCTC 5066
                               i    iv   ivii         vv   i    i  ii i vvi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_217608937_   5067 TCATCTTTGACAAACCTGACAAAAACCAG-CAATGGGGAAACGATTCCCT 5115
                          v  i  i     ivv  v   i -   v-           vi  vvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAGTCT 398

  chr1_217608937_   5116 ATTTAATAAGTGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5165
                         v  i  i  i     i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_217608937_   5166 AACTGGACACCTTCCTTACATCTTATACAAAAATTAACTCAAGATGGATT 5215
                          ii     v   v   i   i v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_217608937_   5216 AAAGACTTAAATGTAAAACCTAAAACCATAAAAACTTTAGAAGAAAACCT 5265
                          ?    i         i v       i      vii            v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_217608937_   5266 AGGCAATACCCTTCAGGACATAGGCATGAGCAAAGACATCACGACTAAAA 5315
                            ?ivv vi    iv   v v  vv ii    v iiv  viiiv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_217608937_   5316 CACCAAAAGCAATGACAACAAAAGCCAAAATTGATAGATAGGGTCT---- 5361
                                    vvii         vv     v    i  v  iii ----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_217608937_   5362 --AATTAAAGAGCTTCTGCACAGCAGAAGAGACTATCATCAGAGTGAACA 5409
                         --       i -   i  ii vv  i i  v       vv i      v 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_217608937_   5410 GGCAACCTACAGAATCGGAGACAATTTTGGCAATCTATCCATCTGACAAA 5459
                          i     i       v     v   v  v    vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_217608937_   5460 GGGCTAATATCCAGAATTTATAAGGAACTTAAACAA---ACTTACAAAAA 5506
                           i  vi          v     i     ivv    --- v v i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_217608937_   5507 AA----------AATCAAAAAGTAGGCAAAAGATATGAACAGACAGTTCT 5546
                         i ----------   i?    i i      i   v    i     v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_217608937_   5547 CAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAATCTCATCA 5596
                          v        i  vi vi       i  i  i       i vv    v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_217608937_   5597 TCACTGGTCAT 5607
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.34 (139 / 104)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.00 (24 / 8)  


 903 23.24 6.49 4.59  chr1_217687959_217690851      135   504 (2388)  C L1M4_orf2#LINE/L1   (0)   908   532  

C chr1_217687959_    504 CTTCTAGAAGATAACAGAGGAAGAATGCTAGATAACCATGGGTTTGGACA 455
                           ii       v    v   ?iv  vv  vvi i   v      v  -  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG-CA 580

C chr1_217687959_    454 ------CCTTG--TATAACACTGAAAGCATACTCCATGAAAGAAAAACAT 413
                         ------i   i--   i    ii      i vv v ii         -  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-AT 629

C chr1_217687959_    412 -GATACATTGGACTTTGTTAAAATCAAAA-CTTTTGCCCTACAAAATATA 365
                         -    v         ii i     i    -      iv  v    iv i 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

C chr1_217687959_    364 CCGTAAAGAGAATGAAA-GACATGCCAAAAACTTGAAGAAATTATTTGCA 316
                          ii v    i i     -    vv   v i v v i     v        
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

C chr1_217687959_    315 ACACACATATCTGATAAAGGACTTGTGTTTAAAATATACAAAAAAAACTC 266
                          vv  i           i        i ii i      i   i  --   
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA--CTC 777

C chr1_217687959_    265 TTAAAACT-AACAA--AAAAGA-AAA-AACTTTACTTAAAAATAAGCAAA 221
                            v    -  i  --      -   -   iiv i ?      ii     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

C chr1_217687959_    220 AGACCTGA-----TATATCACCACAGAAGATATACA---GACTTTAAAAA 179
                         i  ii   -----i  v  v   v            --- i i-------
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC------- 870

C chr1_217687959_    178 AAAAAGTATACCGAAAGAAAAAAATGCGCAACATCGTTTGTCAT 135
                           v   i i i------i    i    v       i????????
  L1M4_orf2#LINE/    871 AATAAGCACAT------GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (52 / 32)
Gap_init rate = 0.04 (16 / 377), avg. gap size = 2.56 (41 / 16)  

2379 24.52 2.03 9.66  chr1_217687959_217690851     1418  2400 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217687959_   1418 TGGAAGAATACCC-------ATGGATTGGAAGAGTCAATATTGTTAAAAA 1460
                              ii   i  -------             v i           i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr1_217687959_   1461 TGGCCATGATGCCCAAAGCAATCTATAGATTCAGTGCTATTCCTATCAAA 1510
                             v  iv v      vii     i       ii  v  i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_217687959_   1511 CTACCAA-TGTCATTTTTCATAGAAATAGAAAAAAACT-ATTCTAAAATT 1558
                         v v   i-  i -     iii      v  v  i--  -  i        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT 146

  chr1_217687959_   1559 CACATGGAACCAGAAAAGAGCCTGACTACCCAAAGTAGTCCTAGGCAAAA 1608
                           i      viiv  ii  v  v  v  v     ii i  i ii------
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------ 190

  chr1_217687959_   1609 ACAAAACAAAAGAAAACAAAACAAAACTGAAACAAACAAACAAAAAAACA 1658
                         -------       i ----     ii  i i------------------
  L1M4_orf2#LINE/    191 -------AAAAGAAGA----ACAAAGTTGGAG------------------ 211

  chr1_217687959_   1659 AAGCCGAGACATTACATTACCTAACTTCAAACTATACTACAAGGCTACAG 1708
                         -------   - i   i v  i  i      viv        i       
  L1M4_orf2#LINE/    212 -------GAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_217687959_   1709 TAACCAAAACAATAATGGTACTGGTACAAAAATAGATACATATACCACAT 1758
                            i   i   i i-         i i  ii     ---------  i  
  L1M4_orf2#LINE/    254 TAATCAAGACAGTG-TGGTACTGGCATAAGGATAGA---------CATAT 293

  chr1_217687959_   1759 AAATCAATGGAAAAGAATAGAGAGCCCAGAAATACAAATGCGCATCTACA 1808
                          i          v     v     i         v vviiii   i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_217687959_   1809 ATTATCTGATCTTCAACAAAGTCTACAAAAATAAGCAGTGGGGAGAGGAC 1858
                         i i vi    i   i    i vivv   i vi vv  i      i  i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_217687959_   1859 TGTCTATTTGATCAATGGTAATGTGATAGCTGACTATCCATATGCAGAAG 1908
                         v    v  ii iv      iv  v  i i   iv  ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_217687959_   1909 AATGAAGCTGGACCTCTACCTTTCACCATATACAAAAGTAAATTCAAAAT 1958
                                i      i      iv              i v  i       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_217687959_   1959 AGATTAAAGATTTAACTGGAAGACTTCAAATTATAAAATGTTCTAGAAGA 2008
                         i   i ?   ii   v  v    vi v   i       i- ii       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGA 542

  chr1_217687959_   2009 AAACCTAGG---AAATGTCATTCTGGACATCAACCTCTGCAA-AGTATTT 2054
                             v    ---    -- -   vv   v iiivi vv    -i  v i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_217687959_   2055 -----ATGACTAACTCCTCAAAAGCAATTGCAACAAAATTAAAAATTAAT 2099
                         -----     --  ----        vvv         vv      vi  
  L1M4_orf2#LINE/    590 TAGATATGAC--AC----CAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_217687959_   2100 AAATAGTGCCTAATTAAACTAAGGAGCTTCTGCACAGCAAAAGAAACTAT 2149
                             v vi i v  i   v v ii i   i  ii vv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_217687959_   2150 GAGTAGAGTAAACAGACAACT-AGAGAACAGGA-AAAATATTTATAAGCT 2197
                         v iv i   i  v       i- v    ii   -         ii  iii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_217687959_   2198 ATGCATCCAACAAAGGTCTAATATTAAGAATCTATAAGGAACTTAAACAG 2247
                           ii   ii i  i  v  vi   iv     v     i     ivv   i
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_217687959_   2248 TTGAACAAGCAAAAAACAAACAATTTCATTAAGAAGCAGGCAAAGGATAG 2297
                         i v  i  vv    i     i  iiiv   ? i  iii          vv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_217687959_   2298 GAAAGTCAAGTCTCAGGATATAAAACTTCTACAGACACTTCTCAAAAGAA 2347
                            ----------------------------i     i     v      
  L1M4_orf2#LINE/    834 GAA----------------------------TAGACATTTCTCCAAAGAA 855

  chr1_217687959_   2348 GACATCCAAGTGGCCAAAAAACATATGAAAAAACACTCAACATCACTAAT 2397
                           i  v   i       v  i  i       i ii          ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_217687959_   2398 CAT 2400
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.83 (154 / 84)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 5.00 (115 / 23)  


 486 34.09 0.57 0.00  chr1_217757012_217760058.rev      232   407 (2640)  C L1M4_orf2#LINE/L1   (731)   177     1  

C chr1_217757012_    407 TGGAAA-ACATTTCATGCTCATGGGTAGGAAGAATCAATAGTATTAAAAT 359
                               - i  ii    i      i v      v i    v i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_217757012_    358 GGTCATACTGCCCAAATCAATGTATAGATTCAACACTATGCCTACTAAAC 309
                           iv     v       ii  v  i         i v  v    ii   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_217757012_    308 TATCATTGATAGTCTTCATAGAACTAGAAAAAACTATCTGGGGACTCATA 259
                          vi  viviivv i  iii    v v  v  iviv   iviii i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr1_217757012_    258 TGGAACCAAAAAAAAGCCCAAATAGCC 232
                              viiv  iii v  vi       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCC 177

Transitions / transversions = 1.50 (36 / 24)
Gap_init rate = 0.01 (1 / 177), avg. gap size = 1.00 (1 / 1)  

 491 17.65 0.00 0.00  chr1_217757012_217760058.rev      796   880 (2167)    L1M4_orf2#LINE/L1        5    89 (819)  

  chr1_217757012_    796 AAAACATCCCATGCTCATGAATCAGAAGACCTAACATGGTTAAGATGGCA 845
                           i i        i     i  ii      i   i  v            
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_217757012_    846 ATACTCACCAAAATAATCTATAGATTCAGTGCAAT 880
                               v     v i     i       ii     
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.00 (0 / 0)  

4256 16.52 2.57 0.49  chr1_217757012_217760058.rev     1744  2560 (487)    L1M4_orf2#LINE/L1       75   908 (0)  

  chr1_217757012_   1744 CAGATCCCACAATACAATACCTTTCAAAATCCT-GTTGATTTCTTTATAC 1792
                              i ---  ii    v   v         i- i  vi  i   ii v
  L1M4_orf2#LINE/     75 CAGATTC---AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAG 121

  chr1_217757012_   1793 AAATT----AGCTGATTCTAAAATTCATATGAAATTTCATGGGACCAAGT 1838
                              ----       i              i  v v  v      v  v
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr1_217757012_   1839 ATACCCAAAACAATCCTGGAAAAGAATAATAAAGTAGGAGGGCTCAGAGG 1888
                            v           i  i       v  i     v     i    v vv
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_217757012_   1889 TCCCTATTTTAA----TACTACAAAACAATAGTAAT-AAGAGAGTGTGCT 1933
                             v    i  ----         i v i      -    v      v 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_217757012_   1934 ACTGGCACAAGTATAGGCATATAAATCAATCAAATAGAATTGAGAATTCA 1983
                                i   v    i      i      vi             i i  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_217757012_   1984 GAAATAAGCCTATACATCTGCAGTTAACTGATT----ACAAGGGTGTCAA 2029
                                i  i      i iii  i  i     ----         i   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_217757012_   2030 GACCATTTGATGGAGAGATGATAGCCTTT-CAATAAATGATTCTGAGAAA 2078
                                ii    i  i vi    i    -   i     i v   i  v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_217757012_   2079 ACTGAATAGCCACATGCAAAAGAATGAAACTGAACCCCTATATCACACTG 2128
                             i   ?                   ii  i       iv      ii
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_217757012_   2129 CATA-AAAACTTAACTCAAAATGGATCA-AAACCTAAATATAAGGGCAAA 2176
                         i   -    v                  - i        i    i  v  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr1_217757012_   2177 AATTACAGAACTCTTAGAAGCAAATATAGGAGTAAACCTTCATGATCTGG 2226
                           i  i i            v   i     ?     i    i   i  v 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_217757012_   2227 GATCTGGCAAAGGATTCTAAGATATGACACCAAAAGCATGAGCAACAAAA 2276
                          i iv     v  v    v                   ii          
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_217757012_   2277 GAAAAAAATAGATAAGTTAGACTTCATCAAAATTCAAAACTTTTGTGCTT 2326
                                -       i  i               v               
  L1M4_orf2#LINE/    622 GAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_217757012_   2327 CAAAAGACACCATTAAGAAAGTGAAAAGACAACTCACAAAATGAGAGAAA 2376
                             i     i  i                   i    i    i      
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_217757012_   2377 ATATTTGCATATCACATATCTGATAAGGAACTTCTATCTAAAATATATAA 2426
                                  v    i             i    v    i i         
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_217757012_   2427 AAGACTCTAACAACTCAATAATATGAAGACAA----TCCAATTAAAAAAT 2472
                          ii     v              vi       ----i      ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_217757012_   2473 GGGTAAAGAATCTGAATAGATATTTTCCCAAAGAAGAGATACAAATGACC 2522
                            i    i  i        i    ii          v         i  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_217757012_   2523 AATACACACATGAAAAAATGTTCAACGTGACTAGGTAT 2560
                             vi          i   i     i v ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.22 (91 / 41)
Gap_init rate = 0.01 (11 / 834), avg. gap size = 2.27 (25 / 11)  


2158 20.28 4.91 12.21  chr1_217814671_217817021      939  1855 (496)    L1M4_orf2#LINE/L1       47   896 (12)  

  chr1_217814671_    939 AGATGATAGTTCACCCCCAATTAGTACAATAAAATCAATGCAATCCCTAT 988
                              ii i v v    v    ii - v i i v    i           
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGAT-CTACAGATTCAACGCAATCCCTAT 95

  chr1_217814671_    989 CAAAATATCAGCAGGCATTTTTGTACAAATTGATAACATTTTTCTAAAAT 1038
                               vi    v v v      i v       i  vv vv i       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_217814671_   1039 TTACATAAAAATGCAAAGGATATGGAG-AGCCAAAAGAACTTTTGAAAAA 1087
                          i i  ii        i   ivii  i-        v  - i        
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAA 194

  chr1_217814671_   1088 GAA---CAAAGTTGGAGGATT---ACTTTACCTGATTTCAAAATTTACTA 1131
                            ---             i ---    --  ii         i      
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTT--CCCAATTTCAAAACTTACTA 242

  chr1_217814671_   1132 TAACATAAAAGTAGAAAACACAATGTGGTGAAATATAAAACTATTGTAAA 1181
                         i  viiv v    ivv  v   i      ----------   i-- i v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGT----------ACTG--GCATA 280

  chr1_217814671_   1182 AGAATATACACTTCAATAGATAAATGGCACAGAATCGAGAGTTTAGAAA- 1230
                           i   v   i----      v     v i     i      ii     -
  L1M4_orf2#LINE/    281 AGGATAGACAT----ATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_217814671_   1231 ----CCAAACATTTCGTTAAAGGATGAGTGATTTTCAACAAATATGGCAA 1276
                         ----   v      ----- v  vii v        i    ivi  v   
  L1M4_orf2#LINE/    327 AAACCCATACATTT-----ATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_217814671_   1277 GACAAT-CAATGGGGATAGAATAGTGTCTTCAACAA-TGGTGCTGGAACA 1324
                            v  -         v        v i        -         i   
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr1_217814671_   1325 ATTGTATGCTCATGTGAAAAAAAAACTGAACTTAGAGCTATACCTCACAC 1374
                          i  v  i?i  ii  v    i  --    v  i  v iv          
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAA--TGAAGTTGGACCCCTACCTCACAC 469

  chr1_217814671_   1375 CATACATAACAGTTGAATCAAAATGCAATCAAAATACTGTATTTGCATTT 1424
                             i i  v i  i v        -i    ? -----------------
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATG-GATCAWA----------------- 501

  chr1_217814671_   1425 TATTGACCAAACTGCAAAAGTTTGGTCAATAAAATAAAACTATACAAATT 1474
                         ----    ------------------------------------------
  L1M4_orf2#LINE/    502 ----GACC------------------------------------------ 505

  chr1_217814671_   1475 CTTGAAGAAAATAAATGCAAAAAATAAAACTATACAAATTCTT-GAAGAA 1523
                         -----------      i  i iv          -   i    -      
  L1M4_orf2#LINE/    506 -----------TAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAA 543

  chr1_217814671_   1524 AATGATTGAAAAAAGTCTTTGTGATCTTGAGT-AGATGAAAAGTTCCTAA 1572
                           i-  v i?iv  i    i    i    i  -  ii-  vi   i  v 
  L1M4_orf2#LINE/    544 AAC-ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTA 591

  chr1_217814671_   1573 TGA-ATGACCCCAAAAACATGGTGCA-TAAAA----AAACAGACAAATTG 1616
                         -  -     v      i  iii-   -i    ----   i   i      
  L1M4_orf2#LINE/    592 -GATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_217814671_   1617 AACCTTATCAAAATGTAAAATGTTTGTGTTACAAAAAATATCACTAAGCC 1666
                         i  i i        vv    iv      i v    ii i ii ii   vv
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_217814671_   1667 AATGGAAAAACAAGTTCTTCATA--GGGAGAAAACATTTGCCAGTCATAT 1714
                          i  i   i    --i iv  v --         i      v i      
  L1M4_orf2#LINE/    690 AGTGAAAAGACAA--CCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_217814671_   1715 TTTTGATAAAGAACTTGTATCTAGACTATATAAAGAGTT-TTATA-CTCA 1762
                         v i      i i         i   v          ii -   i -    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_217814671_   1763 A------------AAATAA---AATTTAAA--TGAGCAAAAGATTTGAGT 1795
                          ------------      ---    ?   --  i     i       i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_217814671_   1796 AGACACTTTACTAAAGAGAATATTCAAATTGCCAATCATGGTGCATAAAA 1845
                              i  iv i     ii    v     v      v -- ii   i   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA--GCACATGAAA 885

  chr1_217814671_   1846 TAGAT--TTAAC 1855
                         -    -- i   
  L1M4_orf2#LINE/    886 -AGATGCTCAAC 896

Transitions / transversions = 1.89 (119 / 63)
Gap_init rate = 0.04 (37 / 850), avg. gap size = 4.24 (157 / 37)  


3088 27.24 1.22 0.66  chr1_217819442_217825851.rev     5016  5918 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217819442_   5016 TGGAAGAACATTCCATGCTCATCGATAGGAAGAATCAATATCATGAAAAT 5065
                              ii i  i     i    v   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_217819442_   5066 GGCCATACTACCCAAGGTAATTTATATAGATTCAGTGCCATCCCCATGAA 5115
                            v     v     iv i  i  i --      ii  v     i  v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA--GATTCAACGCAATCCCTATCAA 98

  chr1_217819442_   5116 GCTATCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTC 5164
                         iv vi  iivi i  i  ii     v v  v  i-  - iii    i   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr1_217819442_   5165 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAA 5214
                                 viiv  ii  v  v v  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_217819442_   5215 GAGCAAAGCTGGAGGCATCACACTACCTGACT--A-----TACTATAAGG 5257
                           i     i      vv       v  ii i -- -----     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_217819442_   5258 CTACAGTAATCAAAACAGCATGGTACTGCTACCAAAACAGATATATAGAC 5307
                                      i    ii        vi iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_217819442_   5308 CAATGGAACAGAAC--AGAGCCCTCAGAAATACTACCACACATCTACAAC 5355
                                 i    i--    i  --       vvv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_217819442_   5356 CATCTGATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTT 5405
                           vi    i        ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_217819442_   5406 CCTATTTAATAAATGGTGCAGGGAAAACTGGCTAGCCATATGTAGAAAGC 5455
                         i  v  i  i         v    v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_217819442_   5456 TGAAACTGGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5505
                             ii    i  i v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_217819442_   5506 ATTAAAGACTTACATGTTAGACCTAAAACTGTAAAAACCCTAGAGGAAAA 5555
                           i ?    i  v    v   v        i     vi i    i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_217819442_   5556 CCTAGGCA-ATACCATTCAGAACATAGGCATGGGCAGGGACTTTATGACT 5604
                          v    ?i- v i -   ivi  v v  vv i    iv ii  iv iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_217819442_   5605 AAAACACCAAAAGGAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5654
                          vi          v vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_217819442_   5655 AATTAAACTAAAGAGCTTCTAAACAACAAAAGAAACTACCATCAGATTGA 5704
                         v  i   v v  i i   i ivi vv    i  v    i  vv i v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_217819442_   5705 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5754
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_217819442_   5755 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5804
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_217819442_   5805 AAAATCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5854
                            iv    i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_217819442_   5855 TCTCAAAAGAAGATATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5904
                             v           vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_217819442_   5905 TCATCACTGCCCAT 5918
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


2731 26.52 1.30 2.61  chr1_217842455_217844532.rev      668  1587 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217842455_    668 TGAAGAAACATTCTATACTCATGGATTAGAAGACTCAATTTCATTAAGAA 717
                           i i i i  i i  ii         i       i   v ii      v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_217842455_    718 GGTCATATTGCCCAAAGCAATTTTCAGATTCAACCTGATTCCTATCAAAC 767
                           iv   i v      vii  i v          vii  i         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr1_217842455_    768 TATAATACCAA-TGTCATTTTTCACAGAA-TTAAAAAAAATACGCTAAAA 815
                         ----  v   i-  i -     ii     -  i v  ivvv iv      
  L1M4_orf2#LINE/    100 ----ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_217842455_    816 TTTATATGGAACCAAAAAGGAGCCCGAATAGCCAAAGCAAACCTAAGCAA 865
                           i        viiv  i   v  v           i   v i i --  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AA 192

  chr1_217842455_    866 AAAAACAACAACAACAACAAAAAAAAGCAAACCCATCACATTACCAGTCT 915
                           i  v     ------- ivvii i ---  i  -   -  v   i i 
  L1M4_orf2#LINE/    193 AAGAAGAACAA-------AGTTGGAGG---ACTCA-CAC-TTCCCAATTT 230

  chr1_217842455_    916 TCAAACTATACTACAAGGCTACAGTAACCAAAATAGTATGGTATTGGTAC 965
                         iv     -        i          i   i i   i     i   i i
  L1M4_orf2#LINE/    231 CAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_217842455_    966 AAAAAGAGACACATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAA 1015
                           ii v     i     i        i     v    ii           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_217842455_   1016 GCCACACACCTACAACCATGTGATCTTCAACGAAGTAGAGAAAAATAAGC 1065
                         v   i   ii  iiii  vv    i   i  i i vv vv  i vi vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_217842455_   1066 AATGGGGAAAAGACTCCCTATTCAATAAATGGTGCTGATATAGCTAGTGA 1115
                                   ii ivvi  v     i           iv i i  i vv 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_217842455_   1116 GCCACATGCAGAAGAATGAAACTGGATGCCTAACTTTCGCCATGTACAAA 1165
                         ?         i         ii    iv    v  iv i    i      
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_217842455_   1166 AATTAACTCAAGATGAATTAAAGATTTTAATGTAAGACCTCAAACTATAA 1215
                                    i   i  i ?   ii v         v  v         
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_217842455_   1216 GAATTCTAGACGAAAACTTAAAAA-ACACCATTCTGGACATGGGACTTAC 1264
                         i v ii    v      v  ii?i- v i v iv  iv v    --   v
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAG 577

  chr1_217842455_   1265 GAAAGAATTTAT--GACTAAGTTTTCAAAAGCAATTGCAACAAAACCCAA 1312
                          v  vii   v --  -  v vivi        vvv         vvv  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_217842455_   1313 AATTGACAAAGAAGACCTAATTAAACTAAGGGCCTTCTGTACAGCAAAAG 1362
                            v  i   vvi   i v  i   v v iiiv   i   i vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_217842455_   1363 AAACTGTCAACAGAGTAAACAGACAACATACAGAATGAGAGAAAATATTT 1412
                          v   i    v i   i  v       vi        i            
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_217842455_   1413 GCAAACTACGCATCCAACAAAGGTTTAATATCCATAATTTATAAATAAC- 1461
                              ii iii   ii i  i  vi vi      v   v      v   -
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_217842455_   1462 ---ATAAC--AACAAGCAAAAAACAAATAATCCCATT-AAAAATGGTCAA 1505
                         --- i   --  i  vv    i        i  v   -        v   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_217842455_   1506 AAGACAAGAACAGACACTTCTCAAAAGAAGACATATAAGTGGCCAACAAA 1555
                          i  ivv   i     i     v        i   i  i       i  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_217842455_   1556 CATATGAAAAAATGCTGCACATCACTAATCAT 1587
                           i       i     vv      ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


3224 27.20 0.55 0.55  chr1_217945049_217951436.rev     4990  5897 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217945049_   4990 TGGAAGAACATTCCATGCTAATGGGTAGGAAAAATCAATATCATGAAAAT 5039
                              ii i  i     i v    i v    i v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_217945049_   5040 GGCCGTACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5089
                            vi    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_217945049_   5090 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 5137
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_217945049_   5138 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5187
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_217945049_   5188 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5237
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_217945049_   5238 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5287
                           i     i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_217945049_   5288 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5335
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_217945049_   5336 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5385
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_217945049_   5386 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTT 5435
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_217945049_   5436 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5485
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_217945049_   5486 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGACAAC 5535
                          i ?   ii       v   v       i      vi i       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_217945049_   5536 CTAGGCA-ATACCATTCAGGACATAGGCATAGGCAAGGACTTCATGTCTA 5584
                         v    ?i- v i -   iv   v v  vv       v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_217945049_   5585 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5634
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_217945049_   5635 ATTAAACTAAAGAGTTTCTATATAGCAAAAGAAACTACCATTAGAGTGAA 5684
                           i   v v  i ii  i i iivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_217945049_   5685 CAGGCAACCTACACAATGGGAGAAAATTTTTGCAGTCTACTCATCTGACA 5734
                         v  i     i   v             v      ivii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_217945049_   5735 AAGGGCTAATATCCAGAATCTACAAACAACTCAAACAAATTTACAAGAAA 5784
                          i  i  vi          v  i   v     vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_217945049_   5785 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5834
                           i     i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_217945049_   5835 CTCAAAAGAAGATATTTATGCAGCCAACAGACACATGAAAAACTGCTCAT 5884
                            v           vi viii     i ii          iv      v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_217945049_   5885 CATCACTGGCCAT 5897
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3250 24.23 3.75 0.46  chr1_217960937_217965218     2911  3789 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_217960937_   2911 TAAAAAAAAATTGCATGTTCATGGATTGAAAGAATCAATATTGCTAAAAT 2960
                          ii   i v  iv               i    v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_217960937_   2961 GCCCATACTACCCAAAGCAATCTGCAGATTCAATGCAATCTCTATCAAAA 3010
                          v v     v      vii    i         i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_217960937_   3011 TACCAATGACATTCTACACAGAAATAGAAAAAGCAATCCTAAAATATATA 3060
                          v   iivi v  i vii       v  v  ivii          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_217960937_   3061 TGGAA-----------CCAC--TAAGCAAAAT---------------GAA 3082
                              -----------   v--  iv     i---------------   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_217960937_   3083 CAAAAGTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGACCTA 3132
                             iv       v     i v  ii i      viv       i v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_217960937_   3133 TAGTAACCAAAGCAACATGGTACTGGCATAGAAACAGACACATAGATCAG 3182
                         i     i   ii  iii             iii i     i        i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_217960937_   3183 TGGAACAGAATAGAGAACCCAGAAACAAATCCACACACCTACAGTGAACT 3232
                              i     v    ii       i   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_217960937_   3233 CATTTTCAACAATGGTGCCAAGAACATACCCTGGAGAAAAGACAGTCTTT 3282
                         v      i    v          v   v vv   i    ii i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_217960937_   3283 TCAATAAATAGTAATGGAAAAACTGGATATCCATATGCAAAAGAATGAAA 3332
                             i    i  iv   i v         ?   i               i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_217960937_   3333 CTAGACCTCTATCTCTCACCATATA-AAAAATCACAC-CAAAATGAATTA 3380
                         i i    i   i   v         -      i -  -       i  i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTA-ACTCAAAATGGATCA 499

  chr1_217960937_   3381 AAGAC--AAATCTAAGACATCAAATCATAAAACTACTACAAGAAA-CAGT 3427
                         ?    --    v     vv v   ii        vi  v      -  --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-- 547

  chr1_217960937_   3428 CAGAGGAAAATCTCTAGGACATTGGCCTGGGCAAAGATTTCTTCACCAAT 3477
                         i  i? v      iiiv   v    vi i     v i      vivi vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_217960937_   3478 ACCCCACAAGCACAAGCAACCAAAGCAAAAATGGACAAATAAGATGACAT 3527
                           v   v             v    v      i  i    vi  ivv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_217960937_   3528 TAAGTTTAAAAAGCTTCTGCACAGCAAATAATATGATCAAGAAAGTGAAG 3577
                         i  iv       -   i  ii vv    vi i iv              i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_217960937_   3578 AGACAACCCATAGAATGGGAGAAAATATTTGCAAACTACCCATCTGACAA 3627
                                   i                        ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_217960937_   3628 GAGATTAATAATCAGACTATATAAGGAGCTCAAATAACTCCACAAGAAAA 3677
                          i  i vi  vi    v       i  i   vv i     v i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_217960937_   3678 AGTATAATAAGCCGATCAAAAAATAAACAGATGATTTGAATAGAGATTTC 3727
                           vvv     v  i  i?      iii  i v            v     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_217960937_   3728 TCAAAAGAAGACACACAAGTGGCAAACAGACATACGAAAATGTGCTCAAT 3777
                           v        i i    i    v  i ii  i i     vi       i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_217960937_   3778 GTCATTGATCAT 3789
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (131 / 78)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.70 (37 / 10)  


1061 25.65 1.12 0.74  chr1_218014248_218016473.rev      502   770 (1456)    L1M4_orf2#LINE/L1      272   541 (367)  

  chr1_218014248_    502 ATTGGTATAAAAGCAGACACACAGACCAATGGAACAGAAGAGGGAACCCA 551
                          i   i    iiii     i i   i        i    vv i  ii   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_218014248_    552 GAAATAAATTCGTCGAATTTCAGCCAATTGATTTT-GACAAAGGTGTCAG 600
                                 ii i vv v  vii i           -     i    i  i
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_218014248_    601 GAACATACAACTGAGAAAAGACAT-GT-TCATCAATATGTAGTGCTGGGG 648
                           v   v   -  i i     -  -  - iv    i vi i        i
  L1M4_orf2#LINE/    372 GACCATTCAA-TGGGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_218014248_    649 AAACTGGATATTCATATGCAGAAGAATAAAACTAGACCCCTATTTCTTAC 698
                         v         ?i  i     i      i  ii i        ii  vi  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_218014248_    699 CATATACAAAAATCAAATCAAAATGAATCAATGACTTAAACATAACACCT 748
                                      i  v        i    ?v   i    ii   v v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_218014248_    749 GAAGTTATAAAGCTACTAGAGG 770
                         i  ii      i  vi    i 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAG 541

Transitions / transversions = 2.94 (50 / 17)
Gap_init rate = 0.02 (5 / 270), avg. gap size = 1.00 (5 / 5)  

1217 24.21 2.37 2.11  chr1_218014248_218016473.rev     1356  1735 (491)    L1M4_orf2#LINE/L1      528   908 (0)  

  chr1_218014248_   1356 AAAGCTACTAGAAGAAAACATAGGAGAAACATTTCAGGAATTTGGTCTAG 1405
                            i  vi                ? v  vvi   iv  vi    vi   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_218014248_   1406 GCAATGATTTTATAGCTAAGTCTTAC--ATAACATAGGCGACGAAAACAA 1453
                               i   iv   v  v v --  -- v i  i i  i  i   iv  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGAC--ACCAAAAGCACAAGCAACAAAAGAAA 625

  chr1_218014248_   1454 AAATACACAAATAGGACTATATTAAACTAAGAAGCTTCTGCACATCAAAG 1503
                              v i    v     vi  i   v v i  i   i  ii v      
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_218014248_   1504 GAAATAATCAAGA--GTGAAGAGATAACCTGTAGAATGGGAGATAATATT 1551
                           v iv       --     i   i    iii           v      
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_218014248_   1552 TGTAAACTACTCATTCAATCAGAAACTAATATCCAGAGTATACAAGGAAC 1601
                           i   ii ivi  iii  v  ii   vi        i    i  i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_218014248_   1602 CC----AACTCACCAGAAAATAATAATCACAA-TAATCTCATTAAAAAGT 1646
                         i ----      ---- v     v  v-    -   i iv   ?    i 
  L1M4_orf2#LINE/    776 TCTTACAACTCA----ATAATAAAAAG-ACAAATAACCCAATTWAAAAAT 820

  chr1_218014248_   1647 GGGCAAATAATCTGAATAGGCATTTTTCAAAAGAACACATAAAAAATGAC 1696
                                vi  i       i     i  v      v i   v   -  i 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGC 869

  chr1_218014248_   1697 CAACAAGCATATTAAAAAATGCTCAATATCACTGACATC 1735
                            i     i  v    i        i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (56 / 34)
Gap_init rate = 0.02 (8 / 381), avg. gap size = 2.12 (17 / 8)  


2953 26.35 1.65 1.98  chr1_218067258_218071936     3280  4186 (493)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr1_218067258_   3280 AAAATATTCCATACTCACGAATTTGAAGAATCAATATTGTTAAAATGGCC 3329
                           i    i    ii   i i   v     v i           i     v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_218067258_   3330 ATACTGCCCAAAGCAATCTACAGATTTAGCACTATGTCTATCAAACTACC 3379
                              v      vii           i i i v  vi        v v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_218067258_   3380 AA-TGTCATTTTCACA-AAATTAGAAAAAAAACT-ATTCTAAAATTCAAA 3426
                          i-  i v    ii  -     i---- v  i  -  i          v 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATTCATA 150

  chr1_218067258_   3427 TGGAACCAAAATAGAGCCTGAATAGCTAAAGCAACCCTATGAAAAGAGAA 3476
                              viiv  vi  v  v       i   i   i i ivi   ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_218067258_   3477 CAAAGCTGGAGGCATCACATTACCTGACTTCAAGCCATACTATAAGGCTG 3526
                              i      vv     i v  ii i     iv v     i  i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_218067258_   3527 TAGTAACCAAAACAGCATGGTAATGGTACCAAAGGA--GACAGGTAGACC 3574
                         i     i   i    ii     v   i i--     --    vi    i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGATC 298

  chr1_218067258_   3575 AATGGAACAGAATAGAGAACCCAGAGGTAAAGCCTCACATCTACAG-CAA 3623
                                i     v    ii     ii    v  vi    i  ii -   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_218067258_   3624 TCTGATCTTTGACAAAGTTGACAAAGGTAAGCACTGGGGAAAGGACTCCC 3673
                          -    i  i     i v  v   iivi vv  v         i ivvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_218067258_   3674 CATTCAATAAATTGTCCCGGGTTAGCTGGCTAGCCATATGAAGAAGAATG 3723
                         iv     i    v  v i   vi i    v  ?   i   v i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_218067258_   3724 AAACTGGACCCCTACCTTTTACCATATGCAAAAATTAAC-CAAGTTAAAG 3772
                           ii             ivi       i           -   iv ii v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_218067258_   3773 TAAAGATTTAAACATAAAATGTCAAACTATAGGAATACTAGAAGAAAACC 3822
                         i ?   ii    ii   i vv v        ii v vi           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_218067258_   3823 TAGGAAATACCTAGGAAACACTCTGGACATAGGGCTTTGGAAAGAATTTA 3872
                             ?-------- v   ivi  vv   v v   -  v  v  vii   v
  L1M4_orf2#LINE/    548 TAGGN--------GTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTC 588

  chr1_218067258_   3873 T--GACTAGGTTCTCAAAAACAGTTGCAACAATAACAAAAATTGAACAGT 3920
                          --  -  v vivi     i  vvv       v iv      v  vv i 
  L1M4_orf2#LINE/    589 TTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_218067258_   3921 GAGACCT------AATTAAAGAGCTTCTGCACAACAAAAGAAACTATCAA 3964
                         vi   i ------       i -   i  ii vv    i  v        
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_218067258_   3965 CAGAGTAAACAGACAACCTACAGAGTGGGAGAAAACCTCTACAAACTGTG 4014
                         v i   i  v        i     i          iv i i    iii i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_218067258_   4015 CATCTGACAAAGGTTTAATACCCAGAATCTGTAAGGAACTTTAACAATTC 4064
                         i      i  i  vi vi  i       v i   i     i v    i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_218067258_   4065 AACAAGCAAAACACAAATTACTCTATTAAAAAGTGGGCAAAGGACACGAA 4114
                           i  vv    v      v  i v   ?    i           ivi   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_218067258_   4115 CAGACACTTCTCAAAAGAAGGCATACAAGTGGACAACAAACACATGAAAA 4164
                         i     i     v       ii      i   v   i  i          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_218067258_   4165 AATGTTCCACATCACTAATCAT 4186
                         i   i  v      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.02 (15 / 904), avg. gap size = 2.20 (33 / 15)  


3522 17.64 10.01 1.79  chr1_218219758_218224300.rev     3221  4059 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_218219758_   3221 TGGAAAGACATTTCATATTTATGGATTGGGAAACTTAGTATTGTTAATAT 3270
                                 i  ii   i  i         i i     i         v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_218219758_   3271 AGTAAAACTTCCCAAAGTGAGCTATAGATTTA-TGAAATCCTTATCAAAA 3319
                         i i  v   i      v   v   i     i -i v     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_218219758_   3320 TCCCAGCTGAAC---TCTTATAGAAATCAATAATCTGATCCTAAAATTTA 3366
                                  -- --- i  ii      ii i  v              i 
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_218219758_   3367 TAACAAAATTTAAAAAAAAAACAGAAAAGCTGAAACAATCTTAAAAAAGA 3416
                           vvi    vi  iii vv--     v   ii          i       
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACC--CAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_218219758_   3417 A---CAAAGTTGGAGGATTCACACTTCCTGGTTTCAAAATTTACTACAAA 3463
                          ---             i          iii        i          
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_218219758_   3464 ACAGCAGGAATCAAGAGAGT------------------------------ 3483
                         i vi   v        v   ------------------------------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_218219758_   3484 ---ATGAAATTGAATTGAAAGTTTAGAAACAAATCCTCACGTTTATGGTC 3530
                         ---   i   v       i   ii     i   i  vi  i         
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_218219758_   3531 A-TTGATTTTTGACAAGGAGGGCAAGACAATTAAATGGAGGGAAATAATG 3579
                          -        i       iv v      v   v     --     v   i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG--GGAAAGAATA 394

  chr1_218219758_   3580 GTCTTTTCAACATATGGTGCTGGGACAACTGTGTATCCACAGGCAAAAAA 3629
                                     v                  vi  ?     v      i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_218219758_   3630 AAAAAA--------------------------AAAAA--AA---AAAAAA 3648
                          vi  i--------------------------     --  ---    vi
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_218219758_   3649 GATTCAAAACCTAAATATAAGAGCTAAAACTACAAAATTCTTAGAAGAAA 3698
                            iv? i        i               i    i            
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_218219758_   3699 ATCCAATC-TAAA--------ACCTTGAGTTTGGCCATGTTTCCTTGCAT 3739
                          ivi iv?-    --------      i   v   v   v  i   iv  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_218219758_   3740 ATGACACCAAAAGCTCAAGCAACAACAATAACAACAACAACAAAATAAAT 3789
                                       v          -------  v  v  vv i      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAA-------AAGAAAAAATAGATAAAT 637

  chr1_218219758_   3790 TGGACTCTGTCAAAATTAAAAACTGT-GTGTTTCAAAGGACAGTAATAAG 3838
                               iii               v -   i           v  vi   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_218219758_   3839 AAAGTGAAAAGACAACTCACAGAATGAGAGAGAATGTTTGTAAATCATAT 3888
                                         i         i    i   i    i         
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_218219758_   3889 ATATGAAAAAGAACTGGTATTCAGAATATGTAAACAACTCTTGCAACTCA 3938
                           v   v  i i   v    i        i    v       i       
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_218219758_   3939 ATAATAAAAAGATAAATAACTCAATAAAAAATTGAGCAA-TTATTTGAGT 3987
                                     i       i    v?    v  i    -vv      i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_218219758_   3988 AGAGATTTCTCCCCAAAAGACATACAAATGGCCAGCA-GCACATGAAAAG 4036
                            v        vv i    i             ii -            
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_218219758_   4037 ATCCTCAATTTATTAGTCACTAG 4059
                           v     i--  i ????????
  L1M4_orf2#LINE/    888 ATGCTCAAC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (90 / 54)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 5.50 (99 / 18)  


1049 25.00 3.42 2.40  chr1_218454004_218456753     1049  1340 (1410)    L1M4_orf2#LINE/L1        1   295 (613)  

  chr1_218454004_   1049 TGGAAAAATATTCCATGCTCATGGATTGGAAGAATCAGTATCATTAA-AT 1097
                               i    i     i               v i i   ii    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_218454004_   1098 GGCTATACTGTCTAAAGCAATCTACAGATTCAATGCTATTCCTGTCAAAC 1147
                            v     vi i   vii              i  v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_218454004_   1148 TACCAATGGCATTTTCCACAGAATTAGAAAAAAAAAAAACT-ATTCTAAA 1196
                          v   iiv  v    iii     v v  v  i-------  -  i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-------CTGATCCTAAA 143

  chr1_218454004_   1197 ATTCATATGGAACCGAAAAAGAGCCCAAATAGCCAAAGCAATCCT---AT 1243
                                     vi v  ii  v  vi          i     i --- v
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_218454004_   1244 ACAAACACAAAGCCGGAGGCATCACATTATCTGATTTCAA--C---CTAT 1288
                          v  iv      ii     vv     i vi ii       -- ---   i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_218454004_   1289 AAGACTATAATAACCCAAACAGCATGGTACTGGTACAAAAACAAACTTAT 1338
                           ii   i i   i v i    ii         i i  ii i i  v   
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_218454004_   1339 AG 1340
                           
  L1M4_orf2#LINE/    294 AG 295

Transitions / transversions = 2.04 (49 / 24)
Gap_init rate = 0.02 (6 / 295), avg. gap size = 2.83 (17 / 6)  

1682 26.70 5.97 2.65  chr1_218454004_218456753     1655  2257 (493)    L1M4_orf2#LINE/L1      286   908 (0)  

  chr1_218454004_   1655 AAACACATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAAGTTGCA 1704
                          i   i     i        i     v    ii           viiii 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_218454004_   1705 TACCTGCAGCACACCTTTGCCTGATCTTTGATGACATCAGCAAAAATAAG 1754
                         i ii iii ------- iivi    i  i  ii viviiv   i vi vv
  L1M4_orf2#LINE/    336 CATTTATGG-------TCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_218454004_   1755 CAATGAGGAAAGGACTCCCCTATTCAATAAATGGTTCTATGACAGCTGGC 1804
                              i      i - vvi  v     i       v  iv    i    v
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAA-TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_218454004_   1805 TAGCCATAGGCAGAAGAATAAAACTCGACCCCTACCTTTCATCATATATA 1854
                           ?   i v   i      i  ii v           iv  i      i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_218454004_   1855 AAAATTAACTCCAGATGGATTAAAGACTTAAATATAAGACCTCAAACTAT 1904
                                    v i      i ?    i     i     v  v       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_218454004_   1905 AAGCATCCTAGAAGAAAACCTAGAAA-ACACCATTCTGGGCATTAATCTT 1953
                           ivv  i           v   i?i- v i -   --- --- i i   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC---G---TGACCTT 570

  chr1_218454004_   1954 GGG--AAATAATG----TATGGCTAAGTCCTCAAAAGCAATTGTAGCAAA 1997
                            -- iii    ----iv i v  v v vi        vvv i i    
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_218454004_   1998 AACAAAAATTGACAACTGAGAACTAATTACA-TTAAGGAGATTCTGCACA 2046
                          iv      v  i  v vi  vi v  i v -    ii v-  i  ii v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCT 669

  chr1_218454004_   2047 GCAAAAGGAAGTAACAG---AGTAAACAGACAACCTACGGAATGGGAGAA 2093
                         v    i iv v  v  i---   i  v        i  i           
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_218454004_   2094 AGTATTCACAAACTATGCATCCAACAAAGACCTAATATTCAGAATCTATA 2143
                          i    ii    ii  ii   ii i  i iv  vi   i      v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_218454004_   2144 AAGAAC-----------------AAAAAAA-AAA-------ATTTAAAAG 2168
                               -----------------     i -   -------   ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_218454004_   2169 TGGGCAAAAGACATGAACAGACATTTTTCAAAAGAAAACACACAAGTGGC 2218
                                 i  iv    i        i  v      i i i    i    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_218454004_   2219 CAAGAAGCATATGAAAACATGTTCAACATCACTTACCAG 2257
                            v     i       v   i         ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (103 / 54)
Gap_init rate = 0.02 (14 / 623), avg. gap size = 3.71 (52 / 14)  


2681 25.41 4.64 4.42  chr1_218492327_218496948     3225  4129 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_218492327_   3225 GGAAAGGTATTCCACGGTTACGGAT-GGAA------ATATCTGT------ 3261
                               i   i   i v i i    -    ------    -   ------
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-TGTTAAGAT 50

  chr1_218492327_   3262 GCCA------CCCAAAGCAACCTACAGAATCAATGCAATTCCTGTCAAAA 3305
                          v  ------      vii i       v    i     i   i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_218492327_   3306 TACCAATGACATTCTCCACAGAAACAGAAAA--TAATCCTGAAATTTATA 3353
                          v   iivi v  i iii      iv  v  -- i     i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_218492327_   3354 TAAAACCATAACAGACCCAAAAAAAGCCAAAGCCATTCTGAGCATAAATA 3403
                          ii  viii  vi      i  v -      i v  ii   ---------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATA-GCCAAAACAATCTTGA--------- 190

  chr1_218492327_   3404 AATAAATAAATAAATAAATAAATAAATAAATAAATAAATACTGGAGAAAT 3453
                         -----------------------   vi  -i  i   -ii     i v 
  L1M4_orf2#LINE/    191 -----------------------AAAAGAA-GAACAAA-GTTGGAGGACT 215

  chr1_218492327_   3454 CACATTACCTGGCTTTAAATTATACTACAGAGCTATACTAACCAAAACAG 3503
                             i v  iiii  i   viv       i     i v   i   i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_218492327_   3504 CATGGTACTGGCATAAAAACAGATACATAGAACACTGGAACAGAATAGAG 3553
                         ii              ii i   i i     v  v     i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_218492327_   3554 AACCCAGAAACAAATCCACATACCCACAGTGAACTCATTTTTGACAAAGG 3603
                          ii       i   i   i i iii ii  v  i v     i     i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_218492327_   3604 TGTCAAGAACATACACTGGGAAAAAA---GCCTCTTTAATAAATGGTGTT 3650
                           i     v   v  v    i   i --- i  i  i  i        i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_218492327_   3651 GGGAAAACTGGATATCTGTATGCAGAAAAATGAAACTAGATTCCTATCTC 3700
                             v         ? iii     i  i      ii i  ii    i   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_218492327_   3701 TTGTCATATACAAAAATCAAATCAAAATGAATTAAATACTTAGATCTAAG 3750
                         viii             i  v        i  i ? v  i  i  v    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_218492327_   3751 ATCTAGAACTATAAAACTACTAAAAGAAAACTTAGGGA-AATTCTCCAGG 3799
                          v   i            vi  i        v    ?i-  v   i iv 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_218492327_   3800 ATATTAGTCTGGGCAAAGATTTCTTGAGTAATACCCCACAAGCACAGGCA 3849
                          iv  i vi i     v i      iii  vv  v   v       i   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_218492327_   3850 GACAAA-GCAAAAACGGACAAAT-GGA-TTGACCACAAGTTAAAAAGCTT 3896
                         -     - v     ii  i    -   -  v i  -  i       -   
  L1M4_orf2#LINE/    616 -ACAAAAGAAAAAATAGATAAATTGGACTTCATCA-AAATTAAAAA-CTT 662

  chr1_218492327_   3897 CTTCACAGCAAAGGAAAACAATTAATAAAGTGAAGAGACAACATACAAAA 3946
                         i vii vv       v - v  i  v        i       vi   i  
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACA-CTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_218492327_   3947 TAGGAGAAAATATTTGCAAGCTATCCATCTGACAAAAGACTAATAACTAG 3996
                          i                 iii  vi      i  ii    vi  v i  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_218492327_   3997 TGTATATGAGGAGCTTAAACAACTCAATAGGAAAA------------CAT 4034
                         vi     i i  i  ivv           iv    ------------  v
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_218492327_   4035 TTTTTAAATGGGCAAAATATCTGAATGGATATCTCTTAAAAGAAGACATA 4084
                           ?vv           iv  i     i  i  i   iv        i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_218492327_   4085 --AATGTCAAACAGTTATATAAAGGTGTGCTCAACATTATTGATCAC 4129
                         --    v v  i ivi i  i  iivi          i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.28 (157 / 69)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 3.90 (82 / 21)  


3018 27.61 0.77 0.88  chr1_218515699_218519376     2277  3185 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_218515699_   2277 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAATATCATGAAAAT 2326
                               i i  i    vi        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_218515699_   2327 GGCCATACTGCCCAAGGTAATTTATAGGATTAATGCCATCCCCATCAAGC 2376
                            v     v     iv i  i  i  iv i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_218515699_   2377 TACCAACGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2424
                          v   i vi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_218515699_   2425 TATGGAACCAAAAAAGAGCCCACATTGCCAAGATAATCCTAAGCAAAAAG 2474
                                viiv  ii  v  viv  v     i i    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_218515699_   2475 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2524
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_218515699_   2525 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGAGATAGACC 2574
                                 i   i    ii       v i iv ii i   v v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_218515699_   2575 AATGGAACAGAA--GAGAGGCCTCGGAAATAACACTACACATCTACCACC 2622
                                i    --     v  --i       vv i i    i  ivii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_218515699_   2623 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGAGGAAAGGATTCC 2672
                          vi    i  i     ivv  v   i v  vvv    i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_218515699_   2673 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2722
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_218515699_   2723 GAAACTGGATCTCTTCCCTACACCTTATACAAAAATTAATTAAAGATGGA 2772
                            ii    i i  v  ii     v              i v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_218515699_   2773 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2822
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_218515699_   2823 CTAGACAATACCAATC---AGGACACAGACATGGGCAAGGACTTCATGAC 2869
                         v   i?i-  --    ---iv   viv ivv i     v ii   v iiv
  L1M4_orf2#LINE/    547 ATAGGNG-TA--AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_218515699_   2870 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGAATC 2919
                           vi            vvi          vv        i    v i ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_218515699_   2920 TAATTGAACTAAAGAGCTTCTGCACAGCGAAAGAAACTACCATCAGAGTG 2969
                          v  ii  v v  i i   i  ii vv i  i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_218515699_   2970 AACAGGAAACCTACAGAATGGGAGAAAAATTTTGCAATCTACCCATCTGA 3019
                           v  iv    i                vv       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_218515699_   3020 CAAAGGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTTACCAG 3069
                         i  i  i  vi          v  i   v    ivv    -i iv iv v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAAT 792

  chr1_218515699_   3070 AAAAAAAAAAACAACCCCATCAGAAAGTGGGCAAAGGATATGAGCAGACA 3119
                              i v   i     v  i?i   i            v   ii     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_218515699_   3120 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCT 3169
                         i     v        i  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_218515699_   3170 CATCATCACTGGTCAT 3185
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3326 24.25 0.43 2.59  chr1_218701113_218705396     2864  3791 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_218701113_   2864 TGAAAAGATATTTCATATTCATGGGTTGGAACAATTAATACTGTTAAAAT 2913
                           i        ii   i       i      v v      i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_218701113_   2914 GTTCATACTACCCAAAGCAATCTACATATTCAACACAATCCATATCAAAA 2963
                          viv     v      vii       v       i      v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_218701113_   2964 TGCCAATGACATTCTTCAAAGAAATAGAAGAAACAATCAAAAAATGTATA 3013
                          v   iivi v  i  iiv      v  vi ivii   vv     vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_218701113_   3014 TGGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAAATAA 3063
                              vii   ii                 i v   i   --    iv i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chr1_218701113_   3064 AACAAAACTGGAGGAATCACAATACCTGACTTCAAATTATACTACAGAGC 3113
                               ii       v     v v  ii i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_218701113_   3114 TATAATAACCAAAACAGCATGGTAACTGGCACAAGAACAGACACATGGAC 3163
                           i i   i   i    ii     -      i   i i     i  i  i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTA-CTGGCATAAGGATAGACATATAGAT 297

  chr1_218701113_   3164 CAAGGGAACAAAATAAAGAACCCAGAAATAAATCCATACATCTACAGCAA 3213
                            v    i i   vi   ii           i        i  ii iv 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_218701113_   3214 ACTTATTTTCAACAAAGGTGACAAGAACACACATTGGGAAAAGGATAGTC 3263
                          i v      i    i    v     v  iv  v    i    i      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_218701113_   3264 TCTTCAATATACGGTGCTGAGAAAACTGGATATACACATGCA---GAATA 3310
                          i     i v i       i  v         ?v        ---    i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_218701113_   3311 AAACTAGACCCCCATCTCTCATCACATTCCAAAATCAAATCAAAATGGAG 3360
                           ii i      i i   v  i  i  v v     i  v          v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_218701113_   3361 TAAAAACTTAACTATATCACTTCAAAGTATAAAACTACTAAAAGAAAACA 3410
                         i ? i  i   v i  vv vi v   v         vi  i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_218701113_   3411 TTACAGAAACTTTCCAGGACATTGGACTGGCCAAAGATTTATTGAATAAT 3460
                          viv? v  v i i iv   v    ii i v   v i   v  ii   vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_218701113_   3461 ATCCCGCAAGCACAAGCAGCCAAAGCAAAAATGGACAAACAGCATCACAT 3510
                          iv  iv           i v    v      i  i   iv v iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_218701113_   3511 CAAG-TTAAAAATCATCTGCACCTCAAAGGAAACAATCAACAAAGTTGAT 3559
                            i-       - v i  ii i        v  v     v     ----
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT---- 692

  chr1_218701113_   3560 TGACAACAACAAAGTTGAAAAGACAACCCACAGAATGAGAAAAAATATTT 3609
                         ----------------                     i  i         
  L1M4_orf2#LINE/    693 ----------------GAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_218701113_   3610 ACAAACAATTTATCTGACAAGAGATTAATAACTAGAGTATATAAGGAATT 3659
                         i    iv  v       i   i  i vi  v i   i       i   i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_218701113_   3660 CAAACAGCTCTATAGGAAAAAATGTAATAATCCAATTTAAAAATGGGAAA 3709
                          vv   i   v   iv     ivvv     i      ?         v  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_218701113_   3710 AATATCTGCATAGACATTTCTCAAAAGAAGACATACAAATGGAAAATAGG 3759
                          iv  i  v             v        i          vv    i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_218701113_   3760 TATATGAAAAGGTGTTCAATATCATTGATCAG 3791
                         i i        i  i    i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 4.67 (28 / 6)  


3202 26.18 0.66 0.77  chr1_218706739_218713324     5185  6093 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_218706739_   5185 TGGAAGAACATTCCAGGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5234
                              ii i  i   v i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_218706739_   5235 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5284
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_218706739_   5285 TACCAA-TGACTTTCTT-CAAAGAATTGGAAAAAAACTGCTT-TAAAGTT 5331
                          v   i-  v    i  -  i -     --- v  i   v i-    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAGCTGATCCTAAAATT 146

  chr1_218706739_   5332 CATATGGAACCAAAAAAGAGCCCATATTGCCAAGACAATCCTAAGCAAAA 5381
                                  viiv  ii  v  viv  v     i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_218706739_   5382 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTGTACTACAAG 5431
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_218706739_   5432 TCTACAGTAACCAAAACAGCATGGTACTGATATTAAAACAGATATATAGA 5481
                         v         i   i    ii        ii  v ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_218706739_   5482 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAGCC 5531
                         i        i    iv   ivii         vv   i    i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_218706739_   5532 ATCTGATCTTTGAAGAACCTAACAAAAACAAGCAATGGGGAAAGGATTTC 5581
                          vi    i  i  vi ivv iv   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_218706739_   5582 CTATTTAACAATTGGTGTTGACAAAACTGGCTAGCCATATGCAGAAAACT 5631
                           v  i     v     i  iv v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_218706739_   5632 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAAATGGT 5681
                            ii         v   i     v                        v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_218706739_   5682 TTAAAGATTTAAACATAAGACCTAAAACCATAAAAACCCTGGAAGAAAAC 5731
                          i ?   ii    ii     v       i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_218706739_   5732 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5780
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_218706739_   5781 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGAATCTA 5830
                         vi            vvi          vv        i    v i ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_218706739_   5831 ATTAAACTAAAGAGCTTCTGCACAGCAAAAG-CAGCTATGACCAGAGTGA 5879
                           i   v v  i i   i  ii vv    i -  -    v vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGAAAGTGA 694

  chr1_218706739_   5880 ACAGGCAACCTACAGAATGGGAGAAAAGTTTTGCAATCTATCCATCTGAC 5929
                          v  i     i                vv       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_218706739_   5930 AAAGGGCTAATATCCAGAATATACAAGGAACTTAAACAAATTTACAAGAA 5979
                           i  i  vi             i  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_218706739_   5980 AAAAAACAAATAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGAAAC 6029
                            i -          v  i?    i    ii      v    i   v i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_218706739_   6030 TTTTCAAAAAAAGACATTTAGTCAGCCAACAAACATATAAAAAAA-GCTC 6078
                           i  v   i    i  vi ivii     i  i  i  i    i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_218706739_   6079 ATCATCACTGGTCAT 6093
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.18 (13 / 11)  


2714 27.57 2.21 1.66  chr1_218739608_218742347     1345  2247 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_218739608_   1345 TGCAAAAGCATTCTATGCTTATGGATTGGAAGAATCAATATTGTTAAAAT 1394
                           v   iii  i i   i i             v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_218739608_   1395 GGCAATACTGCCCAAAGCGATCCACAGATTCATCGC--TTTCTAACAAAC 1442
                                  v      vi    i         v   -- ii   v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_218739608_   1443 TATGAA-TGTCATTTTTCACAGAA-TTGGGAAAAAAAGCT-ATTCTAAAA 1489
                          viv i-  i -     ii     -   ----- v     -  i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTG-----ACAAGCTGATCCTAAAA 144

  chr1_218739608_   1490 TTTATATAGAGCCAAAAAAGAACCAAAACAGTCAAGGGAATTCTAGCAAA 1539
                           i    i  iviiv  ii  v   i  i  i   iiv   ii iiv   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_218739608_   1540 --AGAACAAAGCTGGGGGCATCATA-TTACTGACTTCAAAATATACT-CA 1585
                         --         i   i  vv   i -  v ii i       iv    -  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_218739608_   1586 AAGACAACAGTAAGCAAAACAACATGGTGCTGGTACAAAAATAGACCCAT 1635
                            - v       v   i   iii    i    i i  ii      vi  
  L1M4_orf2#LINE/    245 AAG-CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_218739608_   1636 AGAGCAAAGGAACAAAAT-AAGAACCCAGAAATAAAGTCGCACACCTACA 1684
                            v   v    i i   -i   ii           vi ii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_218739608_   1685 ACCATTTGATCTTCAACAAAGTCGACAAAAATAAGCAATAGAGGAAGGAC 1734
                         ii  v     i   i    i vi v   i vi vv    i i i   i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_218739608_   1735 TCCCTGTTCAACAAATAGTGCTGGGATAGCCGGTGAGCCATATGCAGAAG 1784
                         vvi  v          i         i i i  vv ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_218739608_   1785 AATGAAACTGGACCCCTACCTGTCCTCATGTATAAAAATTATCTCAAGAC 1834
                               ii             vv vi   i  i        v     i i
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_218739608_   1835 AGATTAAATATTTAAATGTAAGACCCCAAACTATACCAATCCTGGAGAAA 1884
                         i   i ? v ii           v iv        vv v  i i  ii  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_218739608_   1885 AATCT-GGGGAACCCCTTTCTGGATATCAACCTTGGG---GAAAA--ATT 1928
                           iv -  ? v vvi   iv  -------        --- iv  --i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTG-------ACCTTGGGTTAGGCAATGGTT 586

  chr1_218739608_   1929 TGT--GACTAAGTCCTCAAAAGCAATTACAACAAAAACAAAAATTGACAA 1976
                          v --  -  v v vi        vvvi        iv      v  i  
  L1M4_orf2#LINE/    587 TCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_218739608_   1977 GTAGAACCTAATTGAACTAAAGAGCTTCTACACGACAAAAGAAACTATCA 2026
                         i v i  i v  ii  v v  i i   i iii vv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_218739608_   2027 ACAGAGTAAACAGACAATCTACAAAATGGGAGAAAATATTTGCAAACTAT 2076
                          v i   i  v      i i   i                      ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_218739608_   2077 GCACCTGACAAATGTCTAATATTCACAATCTATAAGGAAATTAAACAATT 2126
                         ii i    i  iv v  vi   i  v   v     i   v ivv    i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_218739608_   2127 GAATGAGGAATA-ACAAACAGCCCCATTTTAAAATGGGCAAAAGACATGA 2175
                         v   i vi  v -     i i   v   ?v            i  iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_218739608_   2176 GCATACACTTCTCAAAAGGAGACATTCAAGAACCCAA-AAAAAAGTGAAA 2224
                         ii v   i     v    i   i  v   iviv    -  iv vi     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_218739608_   2225 AAATGCTCAACATCACAAATTAT 2247
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (154 / 91)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.84 (35 / 19)  


2421 28.70 5.21 0.12  chr1_218767973_218769948.rev      622  1485 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_218767973_    622 TGAAAAAACATCCCATGATTATGAATTGAAAGAATCAATGTCATTAAAAT 671
                           i   i i        v i   i    i    v i   i ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_218767973_    672 GACCCTGCTGCCCAAAGCAGTCTATAGATTCAACCCAGTTCCTATCAAAT 721
                          i vv i  v      viii    i         v  i i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_218767973_    722 TAACAACATCATTTTCAACAGAA-TTAGGAAAAAAATCCTAAAGTTTATA 770
                          vv  i vv v    ivi     -  iiv  ivvi        i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_218767973_    771 TTGAAAAAAATGAAGTGCA-AATAATCAAAGCACTACTAAGCAAAAAGAA 819
                          v    viv v iiiiv  -    ii    i  v vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_218767973_    820 CAAATCTGTAGGCATCACATTACCTGGATTCAAATTGTACCACAAGGCTA 869
                             vi  v   vv     i v  iiiv      viv   i    i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_218767973_    870 TAATAACTAAAACAGCATAGCACTGGTAGAAAAGTAGACATATAGATTAA 919
                         i i   ii  i    ii i i     i v  iii             i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_218767973_    920 TGGAACAGAATACAGAACCCAGAAGTAAAGCCACATGACTACAATCAACC 969
                              i     vv   ii      i    v   i iivi  iii    ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_218767973_    970 AATCTGCAACTAAATTGACAAAAATAAACATCTAGAAAAGGACACTGTAT 1019
                         i  i v i  v iiv  v   i vi vv  vivi i    i i v v v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_218767973_   1020 TTAATAAATGGTGCTGGAAAAATTGGCAGACCATATGCAGAAGAGTGAAA 1069
                          i  i            i v  i   vvi?   i     i    i    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_218767973_   1070 CTGGATCCCCTGGCTCCCACCGTATACAAAAATTAACTCAAGGTGGATTA 1119
                         i    -     iv   v    i                   ii     i 
  L1M4_orf2#LINE/    451 TTGGA-CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_218767973_   1120 AAGACTTAAAGGTAAGACCTGAAACTATACAAATCCTAG--GAAAA---- 1163
                         ?    i    v      v  i        v  v  i   --     ----
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_218767973_   1164 -GC-----TTTTCTGGACATTGGCATAGGCAAAGAATT------TATGGC 1201
                         - ?----- i   vv   v    vv       v iv  ------    i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_218767973_   1202 A--AAGACCCCCAA-AACAAAATGAGAAATAGACAAA------------- 1235
                          --  i v v v i-       vi i       i   -------------
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_218767973_   1236 ------AAAGCTCT-GCACAGCAAAATAAATAATCAACAGAGTAAACAGA 1278
                         ------   i  i - ii vv    iv v iv     v i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_218767973_   1279 CAACCTAAAGAATGGGAGAAAATATTTGCAAAGTATGCTTCCAACAAAGG 1328
                              i v                        vi  iiv  ii i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_218767973_   1329 ACTAATATCCACCATCTACAAGAAACTCAAACAACTCAACAA-AAAACAA 1377
                            vi      vv  v  i  ii     vv         i  -    vi 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_218767973_   1378 CAAACAGCCCTATTATAGGCCGGGCAAATGACATGAACAGACATTTCTCA 1427
                             i i   v   ?v iivi       v  iv    i           v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_218767973_   1428 GAAGAAGAAATACAAGAAGCCAACAAACCTATGAAAA-ATGCTCAACATC 1476
                         i       v      ivi     i  i vi       -            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_218767973_   1477 ACTAATCAT 1485
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.54 (46 / 13)  


2336 18.51 0.98 20.20  chr1_218819879_218822415      921  2044 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_218819879_    921 TGGTGAGATACATCATGTTCATGAGCCAGAAGACTCAATACTGTTAAAAT 970
                            vi     ivi          iiiii       i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_218819879_    971 GTCATTTCTCCCAAAATTGACCTAGAAAATCAACACAACTCCAAAAGCAA 1020
                          v  v v     v       i   v i v     i   ii  v ------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA------ 94

  chr1_218819879_   1021 AGACCAGTCAAAATCCCCAAATTCCTTTTTTTGTGGAAATTGAAAAACTG 1070
                         -------          -- ii v i       ii        v  i   
  L1M4_orf2#LINE/     95 -------TCAAAATCCC--AGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chr1_218819879_   1071 ATTCTAAAATTCATATGGAAATATGAAGGATCTAGAATAGCAAAAGCAAC 1120
                           i                   iii i   i i        v   i   i
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_218819879_   1121 TTTGAAAATAAAGAACATAGTTGGAAGACTAACACAACCCACTTTCAAAA 1170
                         i       vi       v       i    v    ---------------
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC--------------- 220

  chr1_218819879_   1171 TGTATTATAACACTATAGCAGGAGTTAGCAAATTAAGACCTGCAGACCAA 1220
                         --------------------------------------------------
  L1M4_orf2#LINE/    221 -------------------------------------------------- 220

  chr1_218819879_   1221 ATTCAGCCCATGACCTGTTTTTTACAGTCCCCAAGCTAAGAATGGTTTTT 1270
                         --------------------------- i     ----------------
  L1M4_orf2#LINE/    221 ---------------------------TTCCCAA---------------- 227

  chr1_218819879_   1271 ATATTTTTAAATGGTTGTTAAAAGAAACACACACTACAGAGGACGTATAT 1320
                         ----   i   ---------------------------------------
  L1M4_orf2#LINE/    228 ----TTTCAAA--------------------------------------- 234

  chr1_218819879_   1321 GCCTCACAAAGCCTAAAATATTTACTATCTGACCCATTATGGAAAAAGTT 1370
                         ------------------- i      -----------------------
  L1M4_orf2#LINE/    235 -------------------ACTTACTA----------------------- 242

  chr1_218819879_   1371 TGCTCACCCTCAAGCTACAGTAACCAAGACAATGTAGTATTATCATATAG 1420
                         ----  -----            i       i   i   i iv    vi 
  L1M4_orf2#LINE/    243 ----CA-----AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_218819879_   1421 ACACAAAAATAGATCAGTGGAGCAGAAGACAGAACCCAAAAATAGACCCA 1470
                          i v v v        i    ii    vvv   ii   i     i     
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_218819879_   1471 CTCATATATGGACCACTGATTTTTTTACAAAGGTGCAAAGGCAATTCAGT 1520
                         iv   v     v v i       iv-    i     v   i v     i 
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAAT 382

  chr1_218819879_   1521 GGACAAATTATAGTCTTACTATCAAATGGTGCTGAAAGAATTGGATATCC 1570
                           iv   vv        vii v            ii v  i      ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_218819879_   1571 ATGTGCATAAAAAGTAAACTTTGGTCTATGTTAAACTTTGAATAATATAC 1620
                          ii    -   i i i  v  v ii iv -----  i iiv iv      
  L1M4_orf2#LINE/    433 ACATGCA-AAAGAATGAAGTTGGACCCCT-----ACCTCACACCATATAC 476

  chr1_218819879_   1621 AAAAATTAACTCAAAATGTATCATA-ATCTAAATGTAAAGCCTAAAATTA 1669
                                           v    ? - i          iiv      i  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_218819879_   1670 TATAACTTCTAGAAGAAAACGTAAAAGAAAATCTTTGTGACCTTGGATTT 1719
                           v    ii           i  ii? v       i          i  v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr1_218819879_   1720 GTCAAAGATAACCCTTAGCTATGACACTAAA-GCAAGATCCATGAAGAAA 1768
                          v   v i --ii     v        i   -   vi v v ii  - i 
  L1M4_orf2#LINE/    577 GGCAATGGT--TTCTTAGATATGACACCAAAAGCACAAGCAACAAA-AGA 623

  chr1_218819879_   1769 AAAAATTGACAAATTGAACTTTAACTAAATTTAAAATGTCTGTTCT-CAA 1817
                               v  i      i    i v v     v    iv i   v  -   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_218819879_   1818 AAATCACTGTTAAAAGATT-AAAATACAAGACAAATACTAGAAGAAAA-A 1865
                          iiv    i i  i i v -    v    vv  v v v i i      - 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_218819879_   1866 TTTGCAAATCATGTATCTGATAAAGAATTTGCATGTAGAATACACAAAGA 1915
                                     i          i i i   i  vi      i i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_218819879_   1916 ACCCTCAAAACTCAATAATCAAAAC-CTAATA---TATTTTAAACA--GG 1959
                           i  i v           v    v- v    ---i v  ?   v --  
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_218819879_   1960 CAAAATATTTGAACAGACATTTCACTAAAGAAGATATAAACACAGCAAAT 2009
                             iv       i         v i            v v ii  v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_218819879_   2010 AAGCACATGAAATGAGGGTCAACATCATTAGTCAT 2044
                                     v  v v         ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (123 / 81)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 11.90 (238 / 20)  


2964 24.58 2.67 1.67  chr1_218989502_218991417      525  1423 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_218989502_    525 TGGAAATACATCCCATGCTCATGGATTGAAAGAATCAACATTGTGAAAAC 574
                               v i        i          i    v i  i     v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_218989502_    575 AACCATACTGCCCAAAGCAATCCACAAATTCAATGCAATTTCTATCAAAA 624
                         ii v     v      vii   i   i      i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_218989502_    625 TACCAACATCATTTGTCTCATAATTAGAAAAAACAATCCTAAAATTCATA 674
                          v   i vv v   v iv  v  v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_218989502_    675 TGGAACCAAAAAGGAGCTCAAATAGCTAAAATAATAGTAAGCAAAAAGAA 724
                              viiv  i   v ivi      i    i   vv i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_218989502_    725 CAAATCTGGAGG---CATATTATCTGACTTTAAA--TTATTATACAAGGT 769
                             vi      ---  i i vi ii i  i   --   i  --   i i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA--CAAAGC 248

  chr1_218989502_    770 TATATATAA-----ACGGCATGGTGCTGGTATAAAATTAGATACATAGAC 814
                           i -i   -----  i ii    i    i    iiv    i i     i
  L1M4_orf2#LINE/    249 TACA-GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_218989502_    815 CAATGGAACAGAATAGAGAATGCAGAAATAAAGCTGAAAAATTACAACCA 864
                                 i     v    i v          v iiv v v   iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_218989502_    865 ACTGATCTTCAACACATCATACGAAAAC-AT-CAATTGGGGAAAGGATAC 912
                          i    i   i   - vvi i v  i  -  -    -        i   v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACA-AGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAG 395

  chr1_218989502_    913 CCTATTCAATTAATGATGCTGGGGAAACTGGATAGCCACATGTAGAAGAA 962
                         i  v     iv    i       iv         ?       i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_218989502_    963 TAAAACTGGATCTCTATCTC-TACCATATTAAAAAAATCACCTCAAGATG 1011
                          i  ii    i i   i   -i       - v      i v     i   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATG 494

  chr1_218989502_   1012 GATCAAAGTCTTAAATCTAAGACCTGAAACAGTAAAAATTTCTAGAAGAA 1061
                              ?  v i     v     v  i    vi     v i -        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAA 543

  chr1_218989502_   1062 AACCTAAGAAAAATTCTTCTGGACATTGGTCTAGGCAAAGAATTTATGAC 1111
                            v  i ?iv  v     vv   v    vi       v iv  iv iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_218989502_   1112 TAAGGCCCTAAAAGCAAGTGCAACAAAA------ATAAATAAATGAGACC 1155
                           v i v i       viv         ------   i      vi   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_218989502_   1156 CAATTAAACTAAAAAAAGCTACTGCACAGCAAAAGAAACAATCAGAGTAA 1205
                         iv  i   v v     --  vi  ii vv    i  v  v    -  v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCA-AGAAA 690

  chr1_218989502_   1206 GTG----GACAACCCACAGAATGTGAGAAAATATTTGCAGGCTATGCATC 1251
                            ----                v               iiii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_218989502_   1252 CGACAAAGGACGAATATCCATAATCTACAAGGAACTCAAACAAATCAGCA 1301
                         i  i  i    vvi      v   v  i  i      vv    v   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_218989502_   1302 A-GAAAACACAAATAATCCCATCCAAAAAAAACGGACAAATGACATGAAT 1350
                          -i    v        i  v  i---?     i  i    v  iv     
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATT---WAAAAATGGGCAAAGGATTTGAAT 837

  chr1_218989502_   1351 AGACATTTCACAAAAGGAGATATACAAATGGCCAATAAACATATGAAAAA 1400
                                  v v    i                     i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_218989502_   1401 AAATGCTCAACATCACGAATCAT 1423
                          --            ????????
  L1M4_orf2#LINE/    888 A--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (131 / 86)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.05 (39 / 19)  


1829 24.01 6.65 9.32  chr1_219128713_219130762      625  1557 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_219128713_    625 TGGAGAGACATGCCATGTTTACACTTTGGAAACCTCAATACAGTTGAGAT 674
                             i   i  v       i iivv      iv  i    iv   i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_219128713_    675 GTCAATTCTCTC-AAACTGATCTATAGATTCAA---AATCTC-AGCAAGA 719
                          v    v   i -   i       i        ---    i - v   i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_219128713_    720 CC----------TTTTTGTAGCAACAGGTAAGTTGATTATACAATATACA 759
                         i ----------      i  v  iv ii   i    iv  v   vi i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_219128713_    760 TGGAAAGTTAAAGAACCTAGAAAAGCCAAAAGCAATTTTGAAAAAGAA-- 807
                               vvi  i i   i    v        -    i           --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGA 199

  chr1_219128713_    808 -CAAATTTGTATGACTTTCATGATATGATTCCAAGACTTGCTACAAAGCT 856
                         -    v   v v    iv  ivvivii   i   i    i          
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_219128713_    857 ACAGTAACCATATTAAGGCCACA-TGAGATATTACTACACACCCACTAGA 905
                                ----- i   ---   -  v i  i i--i  i ------  i
  L1M4_orf2#LINE/    250 ACAGTAA-----TCAAG---ACAGTGTGGTACTG--GCATA------AGG 283

  chr1_219128713_    906 ATGGCAATAACTCACATTTAGAAGACCTACAATATGAAGTATTGGCAAGG 955
                           i ---------    v    ----- -    -- i i  ---------
  L1M4_orf2#LINE/    284 ATAG---------ACATATAGA-----T-CAAT--GGAATA--------- 307

  chr1_219128713_    956 ATGTGGAGAAACTGAATTTTCATCTATTGAGGTGGAAATATACATCACTA 1005
                         --------i  i   ivv i  ------------      ----------
  L1M4_orf2#LINE/    308 --------GAATTGAGAGTCCA------------GAAATA---------- 327

  chr1_219128713_   1006 GAACACAACAGACTTCATATACAGCCTACTGGTTTTCAACAAAGTT-CCA 1054
                         -   v  ------ v   v  ii i v i  i     i    i v -   
  L1M4_orf2#LINE/    328 -AACCCA------TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_219128713_   1055 AATGTACTAAATGGAGAAAGGAGAGTCTT--CAATA--TAATGCTGGAAC 1100
                          ivvi i v     i     i v      --   i -- ii      i  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_219128713_   1101 AAC--------CACATGGGAAAAAATGAACCTTGACCTTTGCCACACACT 1142
                            --------      vi   i      vi v    ii i  v     i
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_219128713_   1143 ACCCACAAAAAAATAGCTAAAAATCTACCAT-GACCTAAACATAA----- 1186
                          ivi       v-  i  v     vv i  ?-        ii   -----
  L1M4_orf2#LINE/    471 ATATACAAAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr1_219128713_   1187 --AACTATACAACACATCTAGAAAAAAAAAAAAAAAAGAACTCTTCATTA 1234
                         --       v   ---   vii  i    v v ii?iv  v     i v 
  L1M4_orf2#LINE/    520 AAAACTATAAAAC---TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_219128713_   1235 TCTTGAGATAGGCAAATATTTCTTAGACA-------AAAAGCACTAACCA 1277
                         i    i v       vvi         i -------        v i v 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_219128713_   1278 TAAAAGAAAAAAAAATGTACAAACTGAAC---ATCAAAACTAGAAGTTTC 1324
                         i           v i--- i   i  i  ---       i  i  ii  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAG---ATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_219128713_   1325 TACTCTTTGAAAGATACTATTAAGGAAACCAAAAGGCAAGGCACAGTCAG 1374
                          iiv   ii  i  i     i   i  iiv     i   vv     vvv 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_219128713_   1375 AGAGAAAATATTCATAATTAATATTCTTCACAAAGGACTTATATCCAGAT 1424
                         i           iii  v v    vii v i  i      i        v
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_219128713_   1425 TATATAAAAATTTC---CAAATCAGTAA---GAAGACAATTGATCCC-CC 1467
                                 i vi  ---   v   i   ---i       v i i  v-ii
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_219128713_   1468 CAAAAATAGACTAAGTAGTTG----GACACATGACAAAAGAAGATACA-G 1512
                         ?      i i v   v v   ----    iv vv v          i -i
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_219128713_   1513 GATGGCCAATAGACATACTAAAAGATGCTCAACATCACTAGTCAT 1557
                         i          ii  i iv                  ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (139 / 82)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 4.26 (149 / 35)  


 754 16.67 17.22 0.56  chr1_219131955_219135751     1518  1697 (2099)    L1M4_orf2#LINE/L1        1   210 (698)  

  chr1_219131955_   1518 TGAAAAGACACTCTGTGTTCA---GTTGAAAGACTTACTATTGT------ 1558
                           i     i ii ii      ---i   i        v      ------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_219131955_   1559 ------------CAAATTGATCTACAGATACA-TGTAATTCCTATCAAAA 1595
                         ------------                 v  -i i   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_219131955_   1596 ACTCGGCC----TTTTTGCATAAGTTGACAGGCTGATTCTATAATTCATA 1641
                         v i i  i----        v  i      i      i   v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_219131955_   1642 CGAAAATGCAAGGGACCAAAGAAGAAC--AAAGAATCTTTAAAAAGGA-- 1687
                         i i              v -   v i --   v      v      i --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_219131955_   1688 -CAAAGTTGGA 1697
                         -          
  L1M4_orf2#LINE/    200 ACAAAGTTGGA 210

Transitions / transversions = 2.33 (21 / 9)
Gap_init rate = 0.03 (7 / 210), avg. gap size = 4.57 (32 / 7)  

 606 17.60 2.40 1.60  chr1_219131955_219135751     2015  2139 (1657)    L1M4_orf2#LINE/L1      232   357 (551)  

  chr1_219131955_   2015 AAAAAGTACTACAAAGCTGTAGTAATCAAGACTGTGTGATATGGGCAGAA 2064
                             vv            ii            v     i  iv    v  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_219131955_   2065 AGAGAGACACATGTAGATCAATGGAA---GATTTAGAGTCCAGAAGTAAA 2111
                         i  v     i  --            ---i   v           i    
  L1M4_orf2#LINE/    282 GGATAGACATAT--AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_219131955_   2112 CCTCTACATTTATAGGTAACTAATTTTC 2139
                           iv         i vi  i i      
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTC 357

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.02 (2 / 126), avg. gap size = 2.50 (5 / 2)  

1680 15.29 8.53 0.88  chr1_219131955_219135751     2441  2780 (1016)    L1M4_orf2#LINE/L1      344   709 (199)  

  chr1_219131955_   2441 GCTAACTAATTTTCAGTAAGGGTGCCAAGACAATTCAGTGGGAAAATAAT 2490
                          ii  i i      iii              v     i    i   v   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_219131955_   2491 AGACTTTTCAATAAATG---CT---ACAACTGGATATCCACATACAAAAT 2534
                           v        i     ---  ---           ?      i     v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_219131955_   2535 AATAAAGTTGGGCCCCTACCT-ACTTCATA----AAAATTAACTCAAA-- 2577
                            i       i         -  vi    ----              --
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_219131955_   2578 --------GGCCAAAATATAAGAGCTAAAACTTTAAAACTCTCAGAAGAA 2619
                         -------- i  v    i              v         i       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_219131955_   2620 -------GTGAAAATCTTTGCGACCTTGCAGTAGGCAACAGCTTCTTAGA 2662
                         ------- ? v       i i       viv       ii i        
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_219131955_   2663 TGTGATACCAAAACCACAAGCAACAAAAGAAGAAACAGTTAAATTAAACC 2712
                          i   i       v                 i   i  v      ii  i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_219131955_   2713 TCATCAAA-TGAAACACTTTTATGCTTCAAAGGACACCATCAAGATAGTG 2761
                                 - v   v      i               i       v    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_219131955_   2762 AAAAGAAGGCCAGGCACAG 2780
                               vii  ---     
  L1M4_orf2#LINE/    694 AAAAGACAACC---CACAG 709

Transitions / transversions = 2.12 (34 / 16)
Gap_init rate = 0.02 (8 / 366), avg. gap size = 4.00 (32 / 8)  

 871 15.32 2.55 7.23  chr1_219131955_219135751     3070  3304 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_219131955_   3070 AATAAAATAAAAAGATAGTGAAAACACACAGAAAAGGTGAAAATATTTCC 3119
                           v   i i      i ------  v       vi  v          v 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACA------ACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_219131955_   3120 AAGTCATGAATCTGATATATCTGATAAGAGAATTCTGTCTAGAACA-ACT 3168
                           i    ---------            i  v  v i  i    i - iv
  L1M4_orf2#LINE/    729 AAATCAT---------ATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr1_219131955_   3169 AAGTACTCTTACAAAACTCAATAATCTAAAAGCAGGTAA-----TTAAAA 3213
                            v          --         vv   ii  ii   -----  ?   
  L1M4_orf2#LINE/    770 AAGAACTCTTACAA--CTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_219131955_   3214 TATGAGCAAAAGATCTGAATGAAAATTTCTCCAAAAATGATATACAAATG 3263
                         v   i     i   i     ii v           i v            
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_219131955_   3264 GCCCATAAGCACATGAAAAGATGCTCAACATCATTAACACC 3304
                            v                             ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (20 / 15)
Gap_init rate = 0.02 (5 / 224), avg. gap size = 4.60 (23 / 5)  


2224 22.26 6.18 2.78  chr1_219163806_219172475.rev     6655  7301 (1369)    L1M4_orf2#LINE/L1        1   669 (239)  

  chr1_219163806_   6655 TGGAAAGCTATGCCATCTTCACAGACTAGAAGACTTAA-ATGTGTAATGA 6703
                                v   v    v    ii  i i          -  -   v v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-TGTTAAGA 49

  chr1_219163806_   6704 TGTCCATTTTCCCCTAATTACTTGATGGATTTAATACAAGCCCAATCAAA 6753
                           v v  vi     v    iv iv ii    i  ii   v   v      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_219163806_   6754 ATTC-AGCAGGCTTCTTTGTAGAAATTGACAAGCTAATTTTAAGATTTAC 6802
                           i -   v v   i    i               i  ii   i   i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_219163806_   6803 ATGGAAAT-CATATAATAAGGACAGAGAATAGCCAAAATA-TCTTTGAAA 6850
                                 -  ------ i    vv             i -    vi   
  L1M4_orf2#LINE/    150 ATGGAAATGCA------AGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_219163806_   6851 AGAACAACAAAGTTGGAGGAGTTACATTGCC---TTTACCAAGATTTATT 6897
                             v               v i   i v  ---   --   i i   i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT--CAAAACTTACT 241

  chr1_219163806_   6898 ATTAAGTTATATTAATTAGAACAATGTGGTATTGTTGTAAACACAGACAT 6947
                          iv   i  i v    i ii   i       i  vii   iv i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_219163806_   6948 ACAGGTCAATAGAACAGAATTGAGGGTGTAAAAATTGACCCACACATATA 6997
                          i  i     i   i         i  vi i    vi     i    v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_219163806_   6998 TAGACAACTGATTTTCAACAAACATGGCAAGAGAATTCAACTGGAGAAAG 7047
                          i v   i        i    ivi  v     vv      -   i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAG 390

  chr1_219163806_   7048 G-TAATCTTTATAATAAATGGTGCTGAAACAATTGCATAGCCATA-ACTA 7095
                         i-  i     vi  i           ii    i  v   ?   i -i v 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_219163806_   7096 AAAAATAAATAAATAACTTCAATCCTTGCCACATATGATATA-AAAAATT 7144
                           i   i  v-------  vi i  i i  v  i iv     -       
  L1M4_orf2#LINE/    441 AAGAATGAAG-------TTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_219163806_   7145 AACTCAAAATAGATCATAGACCTAAATGTCAGAACTAAAGGTATAAAACT 7194
                                   i     ?            v   i     iv         
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_219163806_   7195 TCTAGAATAAAACATAGGC--AAA-------GATTTTAA-------AAT- 7227
                         ii     v          ?--   -------  ii  ii-------   -
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_219163806_   7228 -------ACATACAA----AAAAGCACAATCTCTAAAAGAAGTAAATTAA 7266
                         ------- v   ii ----          v vvi       i-    vi 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGA 632

  chr1_219163806_   7267 TCTATTGGGCTTAAT-AAAACTAAACACTTTTG-GCT 7301
                          vv     i   v  -    i    v       -   
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

Transitions / transversions = 1.71 (89 / 52)
Gap_init rate = 0.03 (21 / 669), avg. gap size = 2.76 (58 / 21)  

 496 28.19 0.00 0.67  chr1_219163806_219172475.rev     7600  7748 (922)    L1M4_orf2#LINE/L1      655   802 (106)  

  chr1_219163806_   7600 AAAAACTTTTGCTGTCTCTACATTCACTGTTATGAAAATGGAAAGGTAAG 7649
                                    -  ii  v vivv    i i v    i  i    ii  v
  L1M4_orf2#LINE/    655 AAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_219163806_   7650 CCATAGACTAGGAGAAAGTATTTGCAAAACATCTACTCAAAAAAAGAATG 7699
                            i   v i       i          v   v  iiii v  ii  v v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_219163806_   7700 GTATTTACAGCATATAAATAATTCTTACAACTTATCAATAAGAAAACAA 7748
                             ii v ii       v  i          i vi     i  i    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.01 (1 / 148), avg. gap size = 1.00 (1 / 1)  

 473 18.10 0.86 1.72  chr1_219163806_219172475.rev     8064  8179 (491)    L1M4_orf2#LINE/L1      794   908 (0)  

  chr1_219163806_   8064 AAAAGA-GAACAATCCAATTGGGGAAAATTGGCAAAAGATTTGAACAGAC 8112
                               -i  i  i      ?i--     v      i        i    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWA--AAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_219163806_   8113 ATTTCGCCAAAGTAGATCTGCATATGGCAAACATATACATGAAAAGACAC 8162
                              v      v    v i  v     v  i vii           ii 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_219163806_   8163 TCAAAATCATTAGCCAT 8179
                             v    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (12 / 8)
Gap_init rate = 0.02 (2 / 115), avg. gap size = 1.50 (3 / 2)  


2318 22.96 16.45 0.64  chr1_219199239_219203213     2701  3484 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_219199239_   2701 TGGAGAGATAGACCTTGTTTATGAGTCAGAAGACT--ATATTGTTAAG-- 2746
                             i     vv  v    i   ii ii       --           --
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_219199239_   2747 -------CTCCCCAATTTGATCACTTGCA---TTAACATAGCCCCAATTA 2786
                         -------        v      --- i  --- i   ii ii   v  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATC---TACAGATTCAACGCAATCCCTATCA 97

  chr1_219199239_   2787 AAATCTCAGAAGGATTTTTTTTTAAA--TGACAAGCTGATTCTACAATTC 2834
                              i   vv vv      vivi  --            i   v     
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_219199239_   2835 ATATGGAAAATGCAGAGGACCTAGAATAGCCCAAGCA-TCATG------- 2876
                                  -    ii     i         v  i  -  v  -------
  L1M4_orf2#LINE/    148 ATATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_219199239_   2877 ----------------------------TAATTTCAAGACTTACTATAAA 2898
                         ----------------------------i        i        i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_219199239_   2899 GCTCTAGTAAGTAAGACAG-----------CAGATGAATAGAC------- 2930
                            vi     vi       -----------  v v i      -------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_219199239_   2931 -CATTGGAACAAAATAGAAAATCTGGAAATA------TACATGTATGA-C 2972
                         -  v     i i   v  i i  ii      ------     v    i- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_219199239_   2973 AGTGGACTTCTGACAAAGGTGGAAAGACAATTAAATGTACAAAGGAAAGT 3022
                          i v  i  ii     i    vv     v   v    viv    i v   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_219199239_   3023 CTTTTCAACAAATGGTACCAAAACTATTAGATATTTATATGCAAAAAA-- 3070
                                         i iiii  v i i    ?ii i        i --
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_219199239_   3071 ----TTG-ATCCATACCTCACATGATGTACATAAATTAACTCAAAGCAGA 3115
                         ----   - i  v         iv  i    v             iii  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_219199239_   3116 TAATAGACTTAAATGTAAACCCTAAAACCATAAAACTTCTAG--GAAAAA 3163
                          v ?    i         ivv       i        ii   --     v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_219199239_   3164 TTAAGAGAAAAATTTTGTTGAACTTGGATT-GGCAAAGATTTCTTACAGT 3212
                         v  i ? v   vi  i  -  v     i  -     v i       v vv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_219199239_   3213 TGACATCAAAAGTATGATTCATAAAGGAGAAATTTGATTATTTGGATTTA 3262
                              i      i ii viv i   i  i   v v   v v     i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_219199239_   3263 ATCAAAAT-AAAAACATCT---CTTCAAAACACACTGTTA------T--- 3299
                                 -      v i ---       iv     i i ------ ---
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_219199239_   3300 ---ACAAACTACAGACTGGGAAAGAGTCACTGCAAAGCATCTATCTGATA 3346
                         ---    v i     v     i i i vvi      v   v         
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_219199239_   3347 AAATATTTGTATTCAGAATACATAAAGAACTCTCAAAATTCATC--TAAA 3394
                          iiv i      i       i            i v  i   vi--    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_219199239_   3395 AAAATG--TAATGCA------------GTAAA--ATT-------ACACTT 3421
                           i ii--   iv  ------------ i   --   -------   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_219199239_   3422 TACCAAGGAAGATATACCAATTGCAAGTAAGCACATTTAAAAATGTTCAC 3471
                         iv    i          v   v  v i         vv   i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_219199239_   3472 CATAATTATCAGG 3484
                            v ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (105 / 72)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 5.15 (134 / 26)  


 749 28.29 11.22 4.55  chr1_219204047_219205640.rev      496  1110 (484)    L1M4_orf2#LINE/L1      253   908 (0)  

  chr1_219204047_    496 GTAAT---AACAGTATGGTACTGGCCCAAGGATG--CAGACCGACCA-CG 539
                              ---i     i          vi      i--  v iv  i  -i 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_219204047_    540 GGGCAGAATAAAAAATCCAGAAATAGACCCAACTGCACT---GG--AA-- 582
                          iii     vi i i          i     -- i  i ---  --  --
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAATT 350

  chr1_219204047_    583 -ATTTGCGATACAG----CAAGGCAGCT----GGTTAA----CAGACTTT 619
                         -    v   i vi ----    i vii ----  vv  ----i  v    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_219204047_    620 TTAATAAGTGGTATTAC-ATATCTAGATAACAATATGGAAAATGATAAAA 668
                          i  i  i    ii iv- i v  i    ? v i   v    vi  i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_219204047_    669 CTGGATCTTTTTCTCAT----TGTTCATAAATT----CCAAGTTAATCAG 710
                         i    i ii vi    i---- i v  v     ---- v  i vi    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_219204047_    711 AAACCTGAATGTAAAAAATGAAAAC----AAACA---AGTTGAAAAAAT- 752
                          i    i       i iv -     ----    v---  vv     v  -
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_219204047_    753 TGAGTGACTGTCTCTATGTATTATGTGAGTGGGCAAGACCTTCCTAATTA 802
                         v ?  i --i   iii  - iiv  - iv i     vivi   i  iv  
  L1M4_orf2#LINE/    550 GGNGTAA--ATCTTCGTG-ACCTTG-GGTTAGGCAATGGTTTCTTAGATA 595

  chr1_219204047_    803 TG-TATCAAAATCCAAAAGCAACAAAGGAAAATATTCGTAAATTTGATTA 851
                           -i i     v - v          i     v  vvi      v  i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_219204047_    852 CTGGAAAACCAAAAAAACTTGCCC-------AACCCCATCCAAAAAAATT 894
                          vvv    ii     vvi   iv -------i  v i   --  i   v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC--AAGAAAGT 692

  chr1_219204047_    895 GCAAAATAATCAAACTTTGGCAATGGTAACCTAAGAAAAAATATTTGTAA 944
                          -    v --   v ivii -     --------  i          i  
  L1M4_orf2#LINE/    693 G-AAAAGA--CAACCCACAG-AATGG--------GAGAAAATATTTGCAA 730

  chr1_219204047_    945 --CATAT-T---ATGAAGGATTAATATTCCTAAAATATAAAGTGCT-TTA 987
                         --     - ---  i i   i vi   i vv  v        vi  -   
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_219204047_    988 CAA-------ATAAGAAGATAGCCGCTAGCAAACCTATAGAAAAATGGGC 1030
                            -------    i    i ------ ii  v  v  v?          
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACA------AATAACCCAATTWAAAAATGGGC 824

  chr1_219204047_   1031 TGAGGTAATGAACAGA----TCCCAGGAAAAGAAATGCAAATAATTTAAA 1076
                         vi   vvv    i   ----  i vii i    v  i     iiiiv v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_219204047_   1077 AACATATGGAAACATGCTCTGCCTCACTCATGAT 1110
                          i  i   i   v      vi v   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (102 / 68)
Gap_init rate = 0.05 (35 / 656), avg. gap size = 2.77 (97 / 35)  


 489 23.50 12.39 5.56  chr1_219339038_219340972       74   307 (1628)  C L1M4_orf2#LINE/L1   (299)   609   360  

C chr1_219339038_    307 CAAAAGTGCTATTTGA--AGTCAATGGGAAAACAATGGTTTATTTTATAT 260
                            ii    i v--  -- v        i   v   i  i v  iv i v
  L1M4_orf2#LINE/    360 CAAGGGTGCCAA--GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

C chr1_219339038_    259 -TGGT--TAGGACACAACTGG----CC---TGGAGGAAAATAAAGTTAGA 220
                         -    -- i     --     ----  ---  v ii i   i     i  
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACA--ACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

C chr1_219339038_    219 CCCCTGTTTCACACCATATACAAAAATCAATTTCCAAAAAAACTTA-AAA 171
                              iii                   i  i --     viiv i - i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACT--CAAAATGGATCAWAGA 503

C chr1_219339038_    170 TCTGTATGTAAA--CAAAAACTATAGAACAGTTTTAAGAGAATACAT--- 126
                         i  iv      i-- v         i   -- i   ii    v    ---
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAAC--TCTTAGAAGAAAACATAGG 551

C chr1_219339038_    125 -GTA--------TAAGCTTGGGTTTGAAAAGAACTTTTTAACCAAGATA- 86
                         -   -------- i v        v iv  viii  i   -----    -
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-----GATAT 596

C chr1_219339038_     85 GAC-CTAGAGGCA 74
                            - i i i   
  L1M4_orf2#LINE/    597 GACACCAAAAGCA 609

Transitions / transversions = 2.44 (39 / 16)
Gap_init rate = 0.06 (16 / 250), avg. gap size = 2.62 (42 / 16)  

 390 23.71 13.55 7.17  chr1_219339038_219340972      937  1438 (497)    L1M4_orf2#LINE/L1      360   893 (15)  

  chr1_219339038_    937 CAAAAGTGCTATTTCAAGTTAATGGGAAAACTATGGTTTATTTTAA--AT 984
                            ii    i vvv v v i      i   vv  i  i -   i  -- v
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT-TTTCAACAAA 408

  chr1_219339038_    985 TGGTTATGACACAACTGG----CC---TAGAGAAGAATAAAATTGGGATC 1027
                             vv  iv        ----  --- iv i      i  i    - i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG-ACC 457

  chr1_219339038_   1028 CCTGCTTCACACCATATACAAAAATAAATTTCCAGAA--AAACTTAAACT 1075
                            i i                   v  i --  i  --i v v? i  -
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACT--CAAAATGGATCAWAGAC- 504

  chr1_219339038_   1076 CTATATGTAAA--CAAAAACTATAGAACAATTTTAAAAGAA--TATATGT 1121
                            v      i-- v         i   -- i   i     --i   v ?
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAAC--TCTTAGAAGAAAACATAGGN 552

  chr1_219339038_   1122 GTAAG----------CTAGGGTTTGGAGAGAGAAACCTTTTTAATCAAGA 1161
                             i----------  v     v  vi vi ----i  i   ivi v  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGG----TTTCTTAGATATGA 598

  chr1_219339038_   1162 CA---AGAGCCTAGAGGCAATAAAATATAAAATAAATATATTCGATGATA 1208
                           --- i   -- v i    i    v v      i   v   v  ivvi 
  L1M4_orf2#LINE/    599 CACCAAAAGC--ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_219339038_   1209 T-AAAATATAAAA--TGTTATATGGCAAAATAAA-----AACAAAATCAC 1250
                          -     -     -- v  i iivv    iv v -----  v   i v v
  L1M4_orf2#LINE/    647 TCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_219339038_   1251 AAGACAA---AAAGATTGATAAAAAGTATGTGCCACAAAAATAACTCACA 1297
                                --- v   v  iv i   i   v   -----    ----  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGC-----AAAT----CATA 736

  chr1_219339038_   1298 CAT---AAAATGAATATGCATATCTGTCAGAAGGTTCCTATAAATTGACT 1344
                         i  --- v  v i iv  --    ---     vi ----     v-i   
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTG--TATC---CAGAATAT----ATAAAG-AACT 776

  chr1_219339038_   1345 AT--CAACAGAATACAGAAATAGAGACAAATAA----ATATAAAAA--GT 1386
                         v --    vv    - v   --i          ----  v?     -- v
  L1M4_orf2#LINE/    777 CTTACAACTCAATA-ATAAA--AAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_219339038_   1387 CAA----TTT--ATAGA---------AGAGAA---ATGCAAATGGTCAAT 1418
                            ----   --     --------- i    ---  i       i    
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_219339038_   1419 AAACCAATGAAAATATTTTC 1438
                           i vv       v  vi  
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.00 (58 / 58)
Gap_init rate = 0.07 (36 / 534), avg. gap size = 2.89 (104 / 36)  


3167 27.42 0.55 0.55  chr1_219431778_219437178.rev     4003  4910 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_219431778_   4003 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4052
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_219431778_   4053 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCACCCCCATCAAGC 4102
                            v     v     iv i  i  i       ii  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_219431778_   4103 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4150
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_219431778_   4151 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 4200
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_219431778_   4201 AACAAAGCTGGAGGCATCATGCTACCGGACTTCAAACTATACTACAAGGC 4250
                                i      vv   ii  v  vi i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_219431778_   4251 TACAGTAACCAAAATAGTATGGTACTGGTCCCAAAACAGAGATATAGACC 4300
                                 i   i i   i         iviv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_219431778_   4301 AATGGAACAGAAC--AGAGCCCTTAGAAATAATGCCGCGTATCTACAACT 4348
                                i    i--    i  --        vv  iiii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_219431778_   4349 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 4398
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_219431778_   4399 CTATTTAATAAATAGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4448
                           v  i  i    i         v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_219431778_   4449 GAAACTGGATCCCTTCCTTACACTTTACACAAAAATTAATTCAAGATGCA 4498
                            ii    i    v   i    iv  i           i    i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_219431778_   4499 TTAAAGACTTACATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4548
                          i ?    i  v        v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_219431778_   4549 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4597
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_219431778_   4598 AAACACCAAAAGCAATGGCAACAAAATCCAAAATTGACAAATGGCATCTA 4647
                         vi            vvi         vvv     v  i    v v ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_219431778_   4648 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 4697
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_219431778_   4698 CAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACTCATCGGACA 4747
                         v  i     i i               v       vii ivi   v  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_219431778_   4748 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4797
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_219431778_   4798 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 4847
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_219431778_   4848 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 4897
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_219431778_   4898 CATCACTGGCCAT 4910
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1348 24.70 3.33 3.56  chr1_219456841_219459048      500   920 (1288)    L1M4_orf2#LINE/L1      283   702 (206)  

  chr1_219456841_    500 GATTGATAAACAGATCAATGGAACAGAATAAAGAGTCCTGAAA--GACTC 547
                            v  i v i            i     vi       v    --i  i 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_219456841_    548 ACACATACATGGCCGGCTGATTTTTCAGCAAAGGTGCCAAGGTAATTCAA 597
                          i    vi    i iii       - ii   i         iiv      
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTT-CGACAAGGGTGCCAAGACCATTCAA 381

  chr1_219456841_    598 TGGAGAAGGATCAGTCTTTTCCACATATGATG---GGTTAACTGGATCTC 644
                            i   i  vi         v   v   i  ---  vi        v? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_219456841_    645 TTGCAGGTGGAGAGGGA--AAACTTGATCTCTATCCCACAGCAAATATAA 692
                         ---  vi  v i i i --  ii v  i i   i i    v  v   i  
  L1M4_orf2#LINE/    432 ---CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_219456841_    693 AAATTTTCTAAAAGTAGATTATAGACCTAAATGCTGTAA-ACCTAAGGCT 741
                              vv  v   i i   i ?           ---   - v    ii  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATG---TAAGAGCTAAAACT 525

  chr1_219456841_    742 ATGAAACTTTTAGAAGAAAACATAGAG---AATCTTTGTGACCTTAGGAA 788
                           i     i                i?---      i        i  vv
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_219456841_    789 AGGCACAAAGATTTCTCAAGATTTTTTA--AAAAGCCTATTCA-TAAGAT 835
                              -- v i     i -   v vvi --      vi vv  -i  i v
  L1M4_orf2#LINE/    576 AGGCA--ATGGTTTCTTA-GATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_219456841_    836 TTTTTAAAGTGTTGATAAATTGGACTTTATCGTAATTACAAATTTCTGCT 885
                         -----   ivi v              i   iv     v   i  i  iv
  L1M4_orf2#LINE/    623 -----AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_219456841_    886 CTTCAAAAGATACCATTTAAAAAATGAAAAAGCGA 920
                                i  i  i  iv i   i      ii i 
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

Transitions / transversions = 1.81 (65 / 36)
Gap_init rate = 0.03 (13 / 420), avg. gap size = 2.23 (29 / 13)  

 708 18.36 10.63 2.42  chr1_219456841_219459048     1509  1715 (493)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_219456841_   1509 AAAAAGGTAAAAAGAAAAAGCAAGGTACAAAGTAGGAGAAAATATTTGTA 1558
                           i  i  i      -----   vvi   i i i              i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGA-----CAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_219456841_   1559 ATACA-ATGTGTGACAAAGGGCTTGTATCTAGAATGTTAAAAGAACTCTT 1607
                          vv  -  i v   i  i  i        i     i vv           
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_219456841_   1608 ACA--T------------GGCAAACAACTT--TTAAGAGGTGAGCAAAG- 1640
                            -- ------------ i    i   ii--  ? i ii  i      -
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_219456841_   1641 ATTTGAAAAGACAC----ACAAAGAAGATATACAGATGGCCAATAAGCAC 1686
                                v     i----v               i               
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_219456841_   1687 ATGGAAAGATGAGCATCATCATTAGTCAT 1715
                            i       vv  v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (25 / 12)
Gap_init rate = 0.03 (7 / 224), avg. gap size = 3.86 (27 / 7)  


3296 25.94 0.77 0.55  chr1_219712274_219718510     4839  5744 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_219712274_   4839 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAAACAATATCGTGAAAAT 4888
                              ii    i     i      i v      vvi     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_219712274_   4889 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCTATCAAGC 4938
                            v     v     iv i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_219712274_   4939 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTC 4985
                          v   i-       i  -i     -   -- v  i  - iii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_219712274_   4986 CTATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5035
                         v       viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_219712274_   5036 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAATTATACTACAAGG 5085
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_219712274_   5086 CTACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGAT 5135
                                  i   i    ii        ii iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_219712274_   5136 CAATGCAACAGAAC--AGAGCCCTCAGAAATAACGCCATA--TCTACAAT 5181
                              v  i    i--    i  --        vv     -- i  iii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_219712274_   5182 TGTCTGATCTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAAGGATTC 5231
                         iivi    i  i     ivv  vv  i v  vv   i        i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_219712274_   5232 CCTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGC 5281
                         i  v  i  i              v  i   v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_219712274_   5282 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5331
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_219712274_   5332 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5381
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_219712274_   5382 CCTAGGCATTACCGTTCAGGACATAGGCATGGTCAAGGACTTCATGTCTA 5431
                          v    ?i v viv   iv   v v  vv i v   v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_219712274_   5432 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5481
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_219712274_   5482 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5531
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_219712274_   5532 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5581
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_219712274_   5582 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5631
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_219712274_   5632 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5681
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_219712274_   5682 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5731
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_219712274_   5732 CATCACTTGCCGT 5744
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (133 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


1811 25.63 5.38 1.43  chr1_219730417_219732897      500  1057 (1424)    L1M4_orf2#LINE/L1      244   823 (85)  

  chr1_219730417_    500 AAAACATAAAATAATCAAGATTGTTTTGGTCTTGGTGGAGGGAGAGTCAT 549
                            i -  v i         iv  v -   vi   iiv i   v  v   
  L1M4_orf2#LINE/    244 AAAGC-TACAGTAATCAAGACAGTGT-GGTACTGGCATAAGGATAGACAT 291

  chr1_219730417_    550 ACAGA--------ACAGAACAGAGAAGCCAAAAATAGACCCACACAAATG 591
                          i   -------- i    iv    iv   i     i     i   vv i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_219730417_    592 TGA-CAACTGATTTGCAGCAAAGGTTCAAAAGTAATTCAGTGGAGGAAAG 640
                           i-   i      v ii   i   v v  iiiv     i   i i  ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_219730417_    641 ACAGCCTTT-CAACAAATGGTGCTGGAGCTATTGGACATCCATAGGCAAA 689
                          i  i    -                ii v i    i ?   i v     
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_219730417_    690 ATACATGCACTTCAACC--TAATTCTCATACCTCATACAAAAATTAACAT 737
                          v -   v v  vi   --  --i    i   vi              vi
  L1M4_orf2#LINE/    442 AGA-ATGAAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTC 488

  chr1_219730417_    738 AAAATGGATCACAGACTTAAATGTAA-------AATTATAAAAC----AG 776
                                    ?    i         -------  i        ----  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_219730417_    777 AAAAAAAAACATAGAGA-AAATCTTTGGGCTCTAGGGCTAGTCAAGCAGT 825
                           i    --     i?i-       i v vi  v   i   v   -ii  
  L1M4_orf2#LINE/    539 AAGAAAA--CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGT 585

  chr1_219730417_    826 T----AGACCTAACATGAAAAGCATGATCCATAAAAGGAAAAACTGATAA 871
                          ----   iv i   iv       ii v v i     i     iv     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_219730417_    872 ATTGGATTTCATCAAGACTGGAAACTTTTGCTCTATGAAAGAC-CCATTA 920
                               i        i i ii         iv  vii  i   - i  i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_219730417_    921 AGATCATAAAAAGACAAGCTAGAGAGTAAGAGAAAATAGTTGCAAACCAC 970
                            vvi i         v i v   i ii         v       i  i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_219730417_    971 ACGTCCAACAAAAGGCTAGCATCTAGAATATATAAAGAACTCTCAAAACT 1020
                          ii  ii i  ii i  v i   i                   i v    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_219730417_   1021 TAACAATAAAAAG-CGAACGATTCAATTAGAACGTGGG 1057
                         i  i         - i  ii ii     ?i  vi    
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

Transitions / transversions = 2.31 (97 / 42)
Gap_init rate = 0.03 (16 / 580), avg. gap size = 2.38 (38 / 16)  


3294 24.47 2.56 1.56  chr1_219780738_219784992.rev     2874  3772 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_219780738_   2874 TGGAGAGATAGTCCATATTCATGGATAGGAAGACTCAATATTGTCCAGAT 2923
                             i     vi    i         v        i        iv    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_219780738_   2924 GTTCGTTCTTCCCAACTTGCTCTATAGATTCAATGTAGTCTTAATCAAAA 2973
                          vivi v  i     v   v    i        i i i  iiv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_219780738_   2974 TTCCAGCAAGTTATTTTTTG---ATATTATTAAACTAATTCTAAAGTTTA 3020
                          i     v- ii-       --- v   ivi  i  i  i     i  i 
  L1M4_orf2#LINE/    101 TCCCAGCT-GCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_219780738_   3021 TATGGGGAAGCAAAAAACTGAGAATAGCCAACACAATATTGAA---GGAG 3067
                              ii v    iii  iv           v     v     --- i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_219780738_   3068 AACAAAGTGGGAGGACTGACATTGCCTGACCTCAAGACTTATCATAATGC 3117
                                 v        v   i v  ii ii    i     ii i  v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_219780738_   3118 TACAGTAATCAAGACAGCATGGTATTAGTGAAATAATTGACAAATAGATC 3167
                                          ii     i i iiv  vi  v    v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_219780738_   3168 AATGGAACACAATAGAGAGCCTAGAAATAGACTTACGTAAATATAGTCAA 3217
                                i v   v     i i       i  ii iii vv   i     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_219780738_   3218 CTGATATTTGGCACAGGAT-CAAAGGCAATATAATGGAACAAAGACAGAC 3266
                         i    v  i i  -   i - v   i v  vi     iiv  ii i  v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACA-AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_219780738_   3267 TTTTCAACAAATAATGCTGGAACTATTGGGCATCCACATACAAAAACAAA 3316
                                     ii      i  v i   ii ?      i     i----
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG---- 443

  chr1_219780738_   3317 AAAAAAAAAAGCTAGACACAGACCTTACACTCT-TCCATAAAATTAACTC 3365
                         ----  vi   i i   v vv    i    iv - v  -           
  L1M4_orf2#LINE/    444 ----AATGAAGTTGGACCCCTACCTCACACCATATACA-AAAATTAACTC 488

  chr1_219780738_   3366 AAAATAGATCGTATACCTAAATGTAAAATGC-AAAACTGTGAAACTCTTA 3414
                              i    i? v            i -  -      i i         
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTA 537

  chr1_219780738_   3415 GAGTATAACATGGAAGAAAATCCAGATGACCT-GTGTATGGCGATGTCTT 3463
                           iv v     i i? v     ivvi      - v  vv   i   vi  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_219780738_   3464 TTTAGATA---CACCAGTGGCATGATGCA-TGAAGGAAATAATTGATAAG 3509
                         i       ---     ivi   ii -   -ii  i    v   v     i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAA 636

  chr1_219780738_   3510 TTGGACTTCATTAAAATTAACAACTTCTGTTCTGCAAAAGACAATGTTAA 3559
                                    i        v     i   v  v    i    v i i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_219780738_   3560 CAGAATGAGAAGACAAGCCACACACTTGTAGAAAATATTTGCAAAAGGCA 3609
                         v i i   i       v     v v v v                vvii 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_219780738_   3610 CATCTGATAAAGGACTGTTATCCAAAATATTCAAAGAACTATTAAAAGTC 3659
                         i         i     vv      i     vi        v   v  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_219780738_   3660 TACAACAAGAACACAAACAACCTGATTTTAAAATGTTCCAAAGACCTTAA 3709
                         v i  i  i  v     i    ii   ?v      vv v  i  ii v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_219780738_   3710 CA---------CCATCAAAGATATACAGATGGCAAACAAGCATATGAAAA 3750
                         i ---------   vvi          i     v  i     i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_219780738_   3751 GATGCTTCAAGTCATATGTCAT 3772
                               iv vi   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (132 / 84)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.31 (37 / 16)  


3041 26.95 1.78 0.67  chr1_219822710_219829113     5014  5911 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_219822710_   5014 TGGAAGAACATTCTATGCTCATGGGTAGGAACAATCAATATTGTGAAAAT 5063
                              ii i  i i   i      i v    v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_219822710_   5064 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5113
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_219822710_   5114 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5161
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_219822710_   5162 TATAGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5211
                            i   viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_219822710_   5212 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5261
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_219822710_   5262 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5311
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_219822710_   5312 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTGCAACC 5359
                                i    i--    i  --        vv   i    i iiiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_219822710_   5360 ATCTGATCTTTGACAAACCTGACAAAAACTAGCAATGGGGAAAGCATTCT 5409
                          vi    i  i     ivv  v   i v vvv            v  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_219822710_   5410 GTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA---- 5455
                         v v  i                 v      v  ?   i   i i  ----
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_219822710_   5456 --AGCT----TCCTTCCTTACACCTTATATGAAAATTAAATTCAAGATGG 5499
                         --  i ----i   v   i     v    ii        -i    i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA-CTCAAAATGG 495

  chr1_219822710_   5500 ATTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCGTAGAAGAAAA 5549
                           i ?    i     i v   v       i      vi v          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_219822710_   5550 CCTAGGCA-ATACCATTCAGGACATAGGCAAGGGCAAGGACTTCATGTCT 5598
                          v    ?i- v i -   iv   v v  vvvi     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_219822710_   5599 AAAACACCAAAAGCAATGGTAACAACAGTCAAAATTGACAAATGGGATCT 5648
                          vi            vvi i     v  vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_219822710_   5649 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5698
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_219822710_   5699 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5748
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_219822710_   5749 AAAGGGCTAATATCTAGAATCTACAAATAAATGAAACAAATTTACAAGAA 5798
                           i  i  vi    i     v  i   v  v vvv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_219822710_   5799 AAAAACAAACAACCTCATC-AAAAATGGGTGAAGGATATGAACAGATACT 5847
                            i     i    iv  i-         ii      v    i   i i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_219822710_   5848 TCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTCA 5897
                             v        i  vi viii     i ii  i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_219822710_   5898 TCATCACTGGCCAT 5911
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


3261 26.76 0.55 0.55  chr1_219911909_219918308.rev     5002  5909 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_219911909_   5002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5051
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_219911909_   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_219911909_   5102 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_219911909_   5150 TATGAAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5199
                             i  viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_219911909_   5200 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5249
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_219911909_   5250 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGATC 5299
                                 i   i    iii        i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_219911909_   5300 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCGTATCTACAACT 5347
                                i    i--    i  --        vv iiiii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_219911909_   5348 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5397
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_219911909_   5398 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5447
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_219911909_   5448 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5497
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_219911909_   5498 TTAAAGACTTAAATGTTAGACCTAAAACCATCAAAACCCT-AGAAGAAAA 5546
                          i ?    i       v   v       i  -     i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chr1_219911909_   5547 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5596
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_219911909_   5597 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5646
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_219911909_   5647 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5696
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_219911909_   5697 CAGGCAACCCACAAAATGGGAGAAAATTTCCACAACCTACTCATCTGACA 5746
                         v  i         i             v iii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_219911909_   5747 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5796
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_219911909_   5797 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5846
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_219911909_   5847 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5896
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_219911909_   5897 CATCACTGGCCAT 5909
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3196 27.32 0.88 0.44  chr1_219940909_219947178.rev     4876  5779 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_219940909_   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4925
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_219940909_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_219940909_   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_219940909_   5024 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_219940909_   5074 AACAAAGCTGGAGGCATCACACTACCTGACTTCGAACTATACTACAAGGC 5123
                                i      vv       v  ii i   i  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_219940909_   5124 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5173
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_219940909_   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCTTACCTACAACT 5221
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_219940909_   5222 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5271
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_219940909_   5272 CTTTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5321
                              i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_219940909_   5322 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5371
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_219940909_   5372 CTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5421
                         ii ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_219940909_   5422 CTAGGCATTACCATTCAGGACACAGGCGTGGGCAAGGACTTCATGTCCAA 5471
                         v    ?i v viv   iv   viv  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_219940909_   5472 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5521
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_219940909_   5522 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5571
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_219940909_   5572 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5621
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_219940909_   5622 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5671
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_219940909_   5672 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5717
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_219940909_   5718 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5767
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_219940909_   5768 ATCACTGGCCAT 5779
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3206 26.68 0.66 0.55  chr1_219991613_219997892     4881  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_219991613_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4930
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_219991613_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_219991613_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_219991613_   5029 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_219991613_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_219991613_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_219991613_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_219991613_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_219991613_   5277 CTATTTAATAAATAGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i    i         v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_219991613_   5327 GAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGA 5376
                            ii    i    v   i    iv              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_219991613_   5377 TTAAAGACTTAAACGTTAGACCTAAAACCATCAAAACCCT-AGAAGAAAA 5425
                          i ?    i    i  v   v       i  -     i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chr1_219991613_   5426 CCTAGGCATTACCATTCAGGACACAGGCATGGGCAAAAACTTCAT-GCTA 5474
                          v    ?i v viv   iv   viv  vv i     viii   v - v  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_219991613_   5475 AAACACCAAAAGCAATGGCAAAAAAAGCCAAAATTGACAAATGGGATCTA 5524
                         vi            vvi    v     vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_219991613_   5525 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5574
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_219991613_   5575 CAGGCAACCCACAAAATGGGAGAAAATTTTTGCAACTTACTCATCTGACA 5624
                         v  i         i             v       v i ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_219991613_   5625 AAGGGCTAATATCAAGAATCTACAATGAACTCCAAAAAATTTACAAGAAA 5674
                          i  i  vi    v     v  i  v      iv v  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_219991613_   5675 AAAACAAACAACCCCATCAAAAAGCGGGCAAAGGACATGAACAGACACTT 5724
                           i     i     v  i?    ii          iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_219991613_   5725 CTCAGAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5774
                            vi       i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_219991613_   5775 CATCACTGGCCAT 5787
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1534 28.07 9.66 3.66  chr1_220003581_220005313.rev      490  1255 (478)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr1_220003581_    490 AATATCTTAGCAGATTTATTTGGGGGGAATTTACATACTGATCCTAGAAG 539
                           v   ii   v vi  -   v vi i    v   vi         i  v
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_220003581_    540 TCATATGGAAACTAAAAGGATCTAGACTAGCTAAGGTAAATCTTAGAGAA 589
                                    ivv  i   i i   v    i  iii  -    ii i  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAA 194

  chr1_220003581_    590 AAAGAGCAAAGCTGGAATATTTATACT----AGT-----AGCT-AC--CA 627
                         i    i     i    iv i i i   ---- i ----- i  -  --  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_220003581_    628 AAATTTC-----TTA------TGTGGTAGTGGCA--AAGATAGCCAAATA 664
                           ii v ----- i ------       v     -- i     v  v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_220003581_    665 GACCAAAGGAACAGAATAGAGAATTAGGAGATAGGCCTACACATATGTAG 714
                           i   v    i     v    i ivi  i   ii  i i    v i i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_220003581_    715 TCACCTGATCTGAGTCAAGGGTGCCACTGCAATTCTATGGGGGCAAGGGC 764
                            vi    i vv v           vvi v    v      i-   iii
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAAT 393

  chr1_220003581_    765 TGTCTTTTACATAAGTGGTGCTGGGTCAATTAGATATCCACATCCAAAAA 814
                         v       vv i  i          v   i i    ?      v     i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_220003581_    815 AAAAAAAGAAAAAGAAAAAGAACCTTGACCCGTTACC---TCCAAAAGT- 860
                           v----------   ivv i   iiv   ivvi   --- v     i -
  L1M4_orf2#LINE/    444 AAT----------GAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_220003581_    861 AATTTCAGGCATATTGTAGATATAAATACAAATGGTAAAAACAATACAGT 910
                           i iv iiiiv  ii?   iv     ii  iv v     - v   v ii
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAAC 532

  chr1_220003581_    911 CTCTAGAAGAACAACATAGA---ATATTTTCATAATCTTGGGGTAGACAA 957
                         iii        -       i--- v  i   i i i      v   i   
  L1M4_orf2#LINE/    533 TCTTAGAAGAA-AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_220003581_    958 -----------ACAGGACAAAAAATGCAGCAGCCACAAAA-AGAAGATTG 995
                         ----------- i v    vv   v   vv   v      - i  i  v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_220003581_    996 AT-----GG-------------TAGGAACTTGTATTCTCCAAAACATACC 1027
                           -----  -------------  ii     v i v  i    iv i  i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_220003581_   1028 ATTAGCAGAGTGAAAATGCAAGTCATAGCCTGGGAGATGGTATTCACTGA 1077
                           i iv i        vi   vi  i  vv       vii    ii vi 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_220003581_   1078 ATAGATACCTAA----GAACTCACATACAGAATAGTTAAAGAAACTCT-A 1122
                         vi v   i  i ---- i   iii  v       vv       -    - 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTA 780

  chr1_220003581_   1123 TAAATCAA-AATACAAAG-TAGATAATTCAACTTAACTTCATAAAAGGGT 1170
                         i  v    -    v    -i i    ii   i ?  -------   --- 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAA-------AAA---T 820

  chr1_220003581_   1171 AGGCAAAAGACTTGAACAGGTACTTCATAACACAGGATATCCAA-TGGTC 1219
                         i      i  i     i  ii i   viv v v i     v   -   i 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_220003581_   1220 AGTA-GCATATGGAAATGGAT--TCGACA-CAAGTACTCA 1255
                          i  -   i   i   --   --  i   -  ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAA--GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (133 / 79)
Gap_init rate = 0.04 (32 / 812), avg. gap size = 3.19 (102 / 32)  


3352 26.27 0.44 0.22  chr1_220062545_220064709      767  1672 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_220062545_    767 TGGAAATATATCCCGTGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 816
                               v       i  i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_220062545_    817 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 866
                          i v     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_220062545_    867 TACCACCATTG--TTCTTCACAGAATTAGAAAATACAATTCTAAAATTCA 914
                          v   v --  --  i  ii     v v  v  vvii  i          
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_220062545_    915 CATAGAACCAAAAAAGATCCTGCTTAGCCAAAGCAAGACTAAGCAAAAAG 964
                         i  i   viiv  ii  i  v vv        i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_220062545_    965 AACAAATCTGGAGGTATCACACTACCTGTTTTCAAACTATCTTATAAGGC 1014
                               vi      vv       v  iiv       viv vi  i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_220062545_   1015 CATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGTGCGTAGACC 1064
                         i i   v i   i    ii         i    ii    iiiii    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_220062545_   1065 AATGGAACAGAATAGAGAATCCAGAAATAAACCCAAATACTTATAGCCAA 1114
                                i     v    i                v i i    i i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_220062545_   1115 CTGATCTTTGACAAAGCAAACAAAAACACAAAGTGGGGAAAGGACACCCT 1164
                         i    i  i     i vviv   i v  ivv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_220062545_   1165 TTTCAACAAATGGGGCTGGCATAATTGGCTAGCCACGTGTAGGAGACTGA 1214
                                      v     v i  i   v  ?    i  i ii   v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_220062545_   1215 AACTGGATCCTCATATCTCACCTTACACAAAAATCAACTCAAAATGGATT 1264
                          ii    i  ii iv  v    v  i        i              i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_220062545_   1265 AAGGACTTAAGCCCAAGACCTGAAACTATAAAAATTCTAGAAGATAACAT 1314
                          ?i   i   iivi    v  i           v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_220062545_   1315 TGGAA-AACCCTTCCAGACATTGACTTAGGCAAGGATTTCATGACCAAGA 1363
                         v  ?i-  vi    vv   v   iv        v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_220062545_   1364 ACTCAAAAGCAAATGCAATAAAAACAAAGATAAACAGCTGGGACCTAATT 1413
                         vvi        v v    i    iv   i   i i iv v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_220062545_   1414 AAACTAAAGAGCTTTTGCAAGGCAAAAGGAACAGTCAGCAGAGTAAATAG 1463
                            v v  i i      iivvv    i iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_220062545_   1464 ACAACCCACAGAGTGGGAGAAAATCTTTATAATCTATACATCTGACAAAG 1513
                                     i           v   ii  vii   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_220062545_   1514 GAATAATATCCAGAATCTACAACGAACTCAAATAAATCAGTAAGAAAAAA 1563
                           v vi          v  i  v      vv i  v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_220062545_   1564 ACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTATC 1613
                              i  i  v  i?    i     v     iv          v  v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_220062545_   1614 AAAAGAAGATATACAAATGGCCAACAAACATATGAAAA-ATGCTCAACAT 1662
                         v                       i  i  i       -           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_220062545_   1663 CACTAATGAT 1672
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


 729 17.67 9.77 2.33  chr1_220359530_220366547.rev      287   501 (6517)    L1M4_orf2#LINE/L1      465   695 (213)  

  chr1_220359530_    287 CATACCAGACATACACAAAATAATTAAAAATGGATCATGGACCTAAAATT 336
                           i    --i     v   v   i v           ?i        -- 
  L1M4_orf2#LINE/    465 CACACCA--TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA--T 510

  chr1_220359530_    337 GTAA----------TATAAAAGTGCTAGAAGCAAACATGGGAGAAAAT-- 374
                             ----------       v vi      v      i  ? v    --
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr1_220359530_    375 --GAAACCTTGGGTTAAGCAA-GATTTCTTAG----GATGCAAAAAGCAC 417
                         -- vi           i    - i        ----  ii v        
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr1_220359530_    418 AA-CACATAAAAGAAAAAAATGATAAATTTAACTTCATCAAAATTAGAAT 466
                           -  - i           vv        vi               i  v
  L1M4_orf2#LINE/    611 AAGCA-ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_220359530_    467 GTTTCCT-CTTTGAATGACACTCTTAAGAAAATGAA 501
                         v   iv -   ii  v      v i      i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

Transitions / transversions = 1.12 (19 / 17)
Gap_init rate = 0.04 (9 / 231), avg. gap size = 2.89 (26 / 9)  

3175 26.84 0.44 0.66  chr1_220359530_220366547.rev     5619  6527 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_220359530_   5619 GAAAAAAAATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAATG 5668
                          i   i v  i     i        v      v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_220359530_   5669 GCCATACTACCCAAAGTAATTTATAGATTCAATGCTGTTCCCATCAAGCC 5718
                           v     v      v i  i  i        i  vi i  i     ivi
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_220359530_   5719 ACCATTGACTTTCTTCACAGAATTAGAAAAGAAACT-ACTTTAAATTTCA 5767
                         v   vivi i  i  ii     v v  v   ---  - iii    v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCA 148

  chr1_220359530_   5768 TATGGAACAAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAG 5817
                                vviv  ii  v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_220359530_   5818 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5867
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_220359530_   5868 TACAGTAACCAAAACAGTACGGTACTAGTACCAAAACAGATATATGGACT 5917
                                 i   i     ii      i i iv ii i   i    i  ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_220359530_   5918 AACGGAACAGAACCAAGACCCCAGAAATAACACCACACATCTATAACCAT 5967
                           i    i    iii   vi          vv   i    i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_220359530_   5968 CTGCTGTTTGATAAACCTAACAAAAACAAGCAATGGGGAAAAGATTCGCT 6017
                         i  v v  i  i  ivv iv   i v  vv           ii  vvv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_220359530_   6018 ATTTCATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACAGA 6067
                         v  iv i              v      v  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_220359530_   6068 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 6117
                          ii         v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_220359530_   6118 AAAGACTTAAATGTAAAACCTGAAACCATAAAAAACTCT-AGAAGAAAAC 6166
                          ?    i         i v  i    i      --    -          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA--CTCTTAGAAGAAAAC 546

  chr1_220359530_   6167 CTAGGCA-ATACCATTCAGGACATAGGCACGGGCAAAGACTTCATGACTA 6215
                         v    ?i- v i -   iv   v v  vvii     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_220359530_   6216 AAACACCAAAAGCAATCGCAACAAAAGCCAAAATTGACAAATGGGATCTA 6265
                         vi            vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_220359530_   6266 ATTGAACTAAAGAGCCTCTGGACAGCAAAAGAAACTATCATCAGAGTGAA 6315
                           ii  v v  i i i i  vi vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_220359530_   6316 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 6365
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_220359530_   6366 AAGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAA 6415
                          i  v  vi          v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_220359530_   6416 AAAACAAA-AACTGCATTGAAAAGTGGGTGAAGAATATGAACAGACACTT 6464
                           i     -   ivv   ?    i    ii   i  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_220359530_   6465 CTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCAT 6514
                            v        i  vi viii     i  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_220359530_   6515 CATCACTGATCAT 6527
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 1.43 (10 / 7)  


2332 26.81 1.04 0.30  chr1_220518572_220520250.rev      504  1178 (501)    L1M4_orf2#LINE/L1      215   894 (14)  

  chr1_220518572_    504 TCATACTACCTGACTTCAGACTATATTACAAGGCTACAGTAACCAAAACA 553
                            i   v  ii i    i viv  i     i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_220518572_    554 GCATGATACTGGTACCAAAACAGATATATAGACCAATGGAACAGAACAGA 603
                          ii  i      i iv ii i   i       i        i    iv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_220518572_    604 GGCCTCAGAAATAACGCCACACATCTACAACCATCTGATCTTTCACAAAC 653
                          ivii         vv   i    i  iiii  vi    i  iv    iv
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_220518572_    654 CTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGT 703
                         v  vv  i v  vv            i  vvi  v  i  i        i
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_220518572_    704 TGGGAAAACTGGCTAGCCATATGCAAAAAACTGAAACTGGACCACTTCCT 753
                              v      v  ?   i        i v    ii      v  v   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_220518572_    754 TACACCTTTATACAAAAATTAACTCAAGATGGATTAAAGACTTAAACATA 803
                         i     v -                  i      i ?    i    ii  
  L1M4_orf2#LINE/    465 CACACCAT-ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_220518572_    804 AGACCTAAAACCATAAAAACCCTACAAGAAAAGCTAGGCA-ATACCATTC 852
                            v       i      vi i  v       vv    ?i- v i -   
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC 562

  chr1_220518572_    853 AGGACATAGGCATGGGCAAAGACTTGATGTCTAAAACACCAAAAGCAATG 902
                         iv   v v  vv i     v ii  vv ivv  vi            vvi
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_220518572_    903 GCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTT 952
                                   vv     v  i    v   ii v  i   v v  i i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_220518572_    953 CTGCATAGCAAAAGAAACTATCATCAGAGCGAAGAGGCAACCTACAGAAT 1002
                         i  iiivv    i  v       vv i  i   i  i     i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_220518572_   1003 GGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAACATCCAGA 1052
                                   v       vii  vi      i  i  i  vii       
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_220518572_   1053 ATCTACAAAGAACTTAAACAAATTTACAAGAAAAAAACAA----CCCCAT 1098
                           v  i        ivv    v iv i  v     i    ----   v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_220518572_   1099 CAAAAAGTGGGTAAAGGATATGAACAGACACTTCTCAAAAGAAGAAATTT 1148
                         i?    i    i       v    i     i     v        v  vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_220518572_   1149 ATGCAGCCAACAA--ACATGAAAAAAAGCTCA 1178
                          viii     i  --         i v     
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.39 (103 / 74)
Gap_init rate = 0.01 (5 / 680), avg. gap size = 1.80 (9 / 5)  


 520 27.85 0.00 0.63  chr1_220596983_220598892      351   508 (1402)  C L1M4_orf2#LINE/L1   (644)   264   108 *

C chr1_220596983_    508 TGTCATTTTTCACAGAATTAGAAAAAGCAACCCTAAAATTCATATGGAAT 459
                           i -     ii     v v  v  ivii i                  v
  L1M4_orf2#LINE/    108 TGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

C chr1_220596983_    458 CAAAAAAGAGCCTGAAAAGCCAAAGCAATCCTAAGCAAAAAGAACAAATC 409
                         iiv  ii  v  v   v       i     i i iv  i         vi
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

C chr1_220596983_    408 TGGAGGCATCACATTATCTGACTTCAAATCATACTACAAGCCTATAGCAA 359
                               vv     i vi ii i      v v        iv   i  i  
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

C chr1_220596983_    358 CCAAAACA 351
                         i   i   
  L1M4_orf2#LINE/    257 TCAAGACA 264

Transitions / transversions = 1.59 (27 / 17)
Gap_init rate = 0.01 (1 / 157), avg. gap size = 1.00 (1 / 1)  

1499 26.09 8.41 0.88  chr1_220596983_220598892      500  1070 (840)    L1M4_orf2#LINE/L1      259   872 (36)  

  chr1_220596983_    500 AAAATGACATAGTACTGGTATAAAAGTAGAAACACAGACCAATGGAACAA 549
                           i iiiii i       i    iii    v i i   i        i i
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_220596983_    550 AACAGAGAACCCAGAAATAAAGCCAAATGCCTACAACCAACAGATCTTCA 599
                           iv    ii           v   v iiii  iiii   iv   i   i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_220596983_    600 ACAAAGCAGACAAAAACACACACTAGAGAAAGGACACCCTATTCAATACA 649
                             i vv v   i v  iv  v i i     i i vi  v     i v 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_220596983_    650 TGGTGCTGGGATAAATGGATAGCCGCATGCCAAAGAATGAAACTGGATCC 699
                                    i  v      ?  i     v          ii    i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_220596983_    700 GTATCTCTCCCCACATACAAAAATTAACTCAAAATAGATTAAAGAAGTAA 749
                         v  i   v v   i                     i   i ?   vv   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_220596983_    750 ATGTAAGACCCGAAACCATTAAAATTCT-AGAAGAAAACATAGGAAAAAT 798
                                 v ii    i  -    i   -               ?iv  v
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_220596983_    799 TCTTCTGGACATTGGCCTAAGCAAATAATTTAT--GACTAAGAAAACAAA 846
                              vv   v    vi  i    - ii   v --  -  v  v v    
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA-TATGACACCAAA 605

  chr1_220596983_    847 AGCAAAAGCAAGAAAACCAAAAATAAATACATGAGACTTAATTAAACTAA 896
                             v      v    vv       i   v  vi     v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr1_220596983_    897 AAAAGTGTCTGCCCAACAAAAGAAATAATTAACAAAGTAAA----TAACC 942
                             v - i  iv vv    i  v iv  i  v     i  ----i    
  L1M4_orf2#LINE/    656 AAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_220596983_    943 TACA------------------------------TCTGACAAAGGACTAA 962
                         i   ------------------------------     i  i     vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_220596983_    963 TATCAAGAATCCACAAAGAATTCAAAAAACATCAA----GAAAA------ 1002
                             v     vi i      i  vv v   -    ----i    ------
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAAC-TCAATAATAAAAAGACAAA 803

  chr1_220596983_   1003 -AATCCCATTAAAAAGCAGGCAAACGACACGAACAGACATTTTTCAAAAT 1051
                         -  i  v   ?    iii      v  ivi   i        i  v   v
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_220596983_   1052 AAGACACGCAAATGGCCAA 1070
                             i ii           
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAA 872

Transitions / transversions = 1.46 (86 / 59)
Gap_init rate = 0.02 (11 / 614), avg. gap size = 4.82 (53 / 11)  

 213 14.29 8.93 0.00  chr1_220596983_220598892     1362  1417 (493)    L1M4_orf2#LINE/L1      848   908 (0)  

  chr1_220596983_   1362 CCAAACAA-----ACAAATGGCCAAGAAACATATGAAAAAATGTACAGCA 1406
                              v  -----            v  i  i       i   iv  i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_220596983_   1407 TCACTACTCAT 1417
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.02 (1 / 61), avg. gap size = 5.00 (5 / 1)  


3557 16.57 5.99 8.58  chr1_220624665_220627275      892  1742 (869)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr1_220624665_    892 TGGAAAGGCATTCTGTGTTCATGGATTTGAAGACTTCATATTGTTAAGAT 941
                                ii  i ii            v        v             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_220624665_    942 GACGGTACTCCCCAGATGAATCTACACATTCAGTGTGATAGGGGTTGACA 991
                          i ii         i  vi       v     ii ---------------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACG--------------- 85

  chr1_220624665_    992 ATAAGGTACAATATGTTTTGTTTGTTTCTTGACTTTTTTTTTTGTAACCC 1041
                         --------    ------------------------------------  
  L1M4_orf2#LINE/     86 --------CAAT------------------------------------CC 91

  chr1_220624665_   1042 CTGTCAAAAATTCAGCTGTCTTTTTTTTTTTCCCCAAAACTTGATACACT 1091
                           i      vii      i       v-------  i  v    i vi  
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTG-------CAGAAATTGACAAGCT 134

  chr1_220624665_   1092 GATCCTAAAATTCCTGTGGAAATACAAGAGTCTGACAATAACCAAAGCAA 1141
                                      v i       i    i v iv v    i     i   
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_220624665_   1142 TTTTGAAAAAGGAGAGCAGTATTGGAAGACTCACACTTCCCACTTTCAAA 1191
                          i         i   i  ivi     i               v       
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_220624665_   1192 ACTTAGTACAGAGCTATAGTAATCAAAACAGTATGGCACTGGCATAAGGA 1241
                              v    i     i         i     i   i             
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_220624665_   1242 TAGACCTGTAGATCAAAGAAGCAAAAGCAAAAGTCTGGATAATAAACCT- 1290
                              v i        v i ii i  vii i    ii  -        i-
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA-AATAAACCCA 333

  chr1_220624665_   1291 TATATTTTTAATCAGTTGATTTT-AACAAGGATGTCAAGATAATTCAATG 1339
                           i    v ii   i        -i      i  i     iv        
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_220624665_   1340 CAGTAAGAATAGTATTTTCAACAAATGATGCTGGGACAACTAGTTATCT- 1388
                         vi v         v             i             i v  ? i-
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_220624665_   1389 --TGAAAATGAATGAAGTTGGACCTCTTCCTCATACTGTATATAAAAGTT 1436
                         --  v   v               i  v     i  ii    i    i  
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_220624665_   1437 AACTCAAAAGGGATCATAGACCTAAGTGTAAATGTCAGCACTATACTATA 1486
                                  v      ?        i     iv ii ----- v      
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-----AAACTATA 528

  chr1_220624665_   1487 TAACCCTTAGAAGAAAACATAGTAGTAAGTCTTCATGAACTTGGATTAGG 1536
                         v   i                 v?    i     i   v     i     
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_220624665_   1537 CAGTG--------------ACACCAAAAGCACAAGTAGCAAAAGAAAAAA 1572
                           i  --------------                i i            
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_220624665_   1573 TTAAGCAAATTGGACTT----AAAATGTAAAACTTTTGTGGCTCAAAAGA 1618
                          - iii           ----     vv            vi     i  
  L1M4_orf2#LINE/    629 T-AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr1_220624665_   1619 CACCGTTAAGAAAATGAAAAGACACCCCACAAAATGGGAGAAAACCTGCG 1668
                            ii i      i          v      i            iv vi 
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_220624665_   1669 TAAATCAT------------------GTATCCAGATTATATGAGGAACTC 1700
                         i       ------------------         v     i i      
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_220624665_   1701 TTACAACTCAACAATAAAA----------CCTATTTTAAAAGTGGGTAGA 1740
                                    i       ----------  i v  ?    i    i i 
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_220624665_   1741 GG 1742
                           
  L1M4_orf2#LINE/    828 GG 829

Transitions / transversions = 2.34 (96 / 41)
Gap_init rate = 0.02 (13 / 829), avg. gap size = 9.54 (124 / 13)  

 524  8.33 5.21 0.00  chr1_220624665_220627275     2023  2118 (493)    L1M4_orf2#LINE/L1      808   908 (0)  

  chr1_220624665_   2023 CCAA---AAAAAAGGACAAAGGATTTGAATAGACACTTCTCCAAAGAAGA 2069
                             ---     v  i                   i              
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_220624665_   2070 TA-AGTAATAGCCAACAAGCACATGAAAGG-TGCTCAACATCATTAGTCG 2117
                           - vv   i     i            i -            ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_220624665_   2118 T 2118
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.03 (3 / 101), avg. gap size = 1.67 (5 / 3)  


1294 23.53 3.07 3.07  chr1_220747880_220751046.rev      502   892 (2275)    L1M4_orf2#LINE/L1      262   652 (256)  

  chr1_220747880_    502 ACGGCATGGTAATTGGCATAGAGCTGAGACAGATAAATAAAAGGAACAGA 551
                           i ii    - i       ii v -     v   i  v  v    i   
  L1M4_orf2#LINE/    262 ACAGTGTGGT-ACTGGCATAAGGAT-AGACATATAGATCAATGGAATAGA 309

  chr1_220747880_    552 A-AAAAAATCCAGAAATATTCCTATGCATATCTAGATAGTTGATGTATTT 600
                          -vi i i          vv  i  i   v v i vi i     v - iv
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT-TCG 358

  chr1_220747880_    601 A-AAAAGCACAAAGGCAATGCAGTGGAGAATGTATAGTCTTTTCAACAA- 648
                          -  ii ii v   i v  v  i   i   v v                -
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_220747880_    649 TGGTACTGGAGCAACTGAATATCCATATGCAAAAAGA-AAAATTGAACCT 697
                             i    ii      i   ?   i        ii -i  i   i   -
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC- 457

  chr1_220747880_    698 TAATTCATACCTTTTACCACATACAAAAAATAACTCAAAATGAATCAAAG 747
                         ----- v     ivi    i         v            i    ?  
  L1M4_orf2#LINE/    458 -----CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr1_220747880_    748 ACC---AT-TGAAAAC-AACATTATAAAACTCTTGGAAGAAAACACTGGA 792
                            ---  - i i i -  v i            i          iv  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_220747880_    793 G-AAATTTTTTTCTACCTTGAATTAAGCAAAGATTTCCTA--TATGATAT 839
                          -    i  iv v-      ii   i    v i    i  --     i i
  L1M4_orf2#LINE/    553 GTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_220747880_    840 TAAAAGCGTAAACCATAAAAGAGCAAATAGATAAACTGAACTGCTCTTCA 889
                         i      ii  i v i      iv           i  i   --  v   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT--TCATCA 649

  chr1_220747880_    890 AAA 892
                            
  L1M4_orf2#LINE/    650 AAA 652

Transitions / transversions = 2.18 (61 / 28)
Gap_init rate = 0.04 (15 / 391), avg. gap size = 1.60 (24 / 15)  

 360 16.18 0.00 0.00  chr1_220747880_220751046.rev     1034  1101 (2066)    L1M4_orf2#LINE/L1      685   752 (156)  

  chr1_220747880_   1034 AAGAGAATATAAAGATAAACCACAGACTAGGAGAAAATATTTGCAAAGCA 1083
                             i i iv     i  v       v i                  v  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_220747880_   1084 TATATCTGATAAAGGATT 1101
                                     i   i 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACT 752

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.00 (0 / 0)  

 353 19.10 5.62 0.00  chr1_220747880_220751046.rev     2588  2676 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_220747880_   2588 AAAAATGGCCAAAAGATTTGTACAGTTACTTCACCATAGGAGGTGTACAA 2637
                                 v    i      v i  vi i   v   v  i  i i     
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_220747880_   2638 ATGGC----AAACTCATGAAAA-ATGCTTCACACCATTAGTCAC 2676
                              ----  i v        -     iv   i  ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (10 / 7)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 2.50 (5 / 2)  


2043 24.94 4.67 5.41  chr1_220939144_220941488.rev      639  1452 (893)    L1M4_orf2#LINE/L1        1   808 (100)  

  chr1_220939144_    639 TAGAGAAACATGCCATATTCCTAGACACAAAGATTCAATGTTATAAAGAT 688
                          i  i i i  v    i   v i  ivvi    i i   i  i v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_220939144_    689 GTCTGTTCTCCCCAAATTGACCCAAATATTTAATGCAGTTCCAATCAAAA 738
                          v vi v             i i v v   i  i   i i  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_220939144_    739 TTTGACAAATTG----TTTTGTGGAAATTGA-----TGAGTCTATACTTT 779
                          i--- v ii  ----     ii        -----   vi   v v  i
  L1M4_orf2#LINE/    101 TC---CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_220939144_    780 ATATG-AAATGCAAAGGGCCCAGAATAGCCAAGACAATACTGACAAAAAA 828
                              -        i  i              i     vi   -------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------- 190

  chr1_220939144_    829 AAAAAAAAAAAACAAAGTTGAAATAATTATACTACCAAATGGCAAA-CTT 877
                         --    i  i          i iv v i i   v  v   vv    -   
  L1M4_orf2#LINE/    191 --AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_220939144_    878 ACTATAAAATTACAGCAGCAAGTAAGTCAGTATGGTATCAGCACAAACTT 927
                             i   ii     i --- vi   v    i     iii   i  i---
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTA---ATCAAGACAGTGTGGTACTGGCATAAG--- 282

  chr1_220939144_    928 TTGCCAGTTAAGACATAAAGAT--ATGTGAATACAGCAATTGAGCAGAGA 975
                         ------ v  -      v    --   -     -- -       ----- 
  L1M4_orf2#LINE/    283 ------GATA-GACATATAGATCAATG-GAATA--G-AATTGAG-----A 316

  chr1_220939144_    976 GTTTAGAAACATACCCACACATATACAGTGCTCTAATTTATAACAACACC 1025
                           ii     i v     i    v  ii  vvvi i    vii    vivi
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr1_220939144_   1026 ACTGCAAGAT-----AGGGGGGAAAGGAT--TTTCTTTACCCTGTGGTG- 1067
                         i --     i----- iv        i  -- i i  i v vvi     -
  L1M4_orf2#LINE/    367 GC--CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_220939144_   1068 TGGGTCAACTGGACATTCACATGGAAAAACAATGAACTGTGG-CCCCTAC 1116
                             v        i ?i      v    i-      v -   -       
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAG-AATGAAGT-TGGACCCCTAC 462

  chr1_220939144_   1117 CTCACACCAGTCAGAAAACTAAACTACAGAATGG-TTGTAGACATAAACA 1165
                                  vvi v    v v    -  i     - ii?    v    ii
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACT-CAAAATGGATCAWAGACCTAAATG 511

  chr1_220939144_   1166 TGAAAGGCAAAACGTTGAAACTTCCAGAGGATATAACACAGAAGAATATA 1215
                          i i  vi     vv i     iii   i  - -    i  i? v v  v
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGA-A-AACATAGGNGTAAATC 559

  chr1_220939144_   1216 TTTATGCCCTTGAGGACGAGAAATGACTTCTAAAGTAAAACACAAAAAGC 1265
                           ii  v     -  viii v    ii    v ii  vi    v      
  L1M4_orf2#LINE/    560 TTCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_220939144_   1266 ACAAACCATAAAG---AGAACTGATGAACTGGATTTCAT------TAAGA 1306
                             i v i   i--- i  iv   i  i    i     ------   i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_220939144_   1307 ACTTCTGTTCATCAA--GACAACATTAAGAGAGC-AAAAGCAAACCACAC 1353
                             i   v v    --    vi  i    i  i-     vv    -   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC-CAC 707

  chr1_220939144_   1354 AGA--GGGAAAATAAATTTGCAGTACATACATCCAACAAAGGACTCACAT 1401
                            --    i  v v       ivv    i   ii i  i     iii  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_220939144_   1402 CCAGAATATACACAGAATTCC-ACACATCAATAATAGAAAGGCAACACAA 1450
                                   i v    i  i-   vv         i    i   - i  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA-ATAA 806

  chr1_220939144_   1451 TC 1452
                         i 
  L1M4_orf2#LINE/    807 CC 808

Transitions / transversions = 1.74 (127 / 73)
Gap_init rate = 0.04 (34 / 808), avg. gap size = 2.41 (82 / 34)  


1342 20.19 0.95 3.47  chr1_220957198_220959704.rev      478   794 (1713)    L1M4_orf2#LINE/L1      183   491 (417)  

  chr1_220957198_    478 AATCTTTAAAAAAAAGAAGAATACAGCTGGAAGACTTATGCTACCTGACT 527
                               ---i           i v  i    i    i ii  v  ii i 
  L1M4_orf2#LINE/    183 AATCTT---GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_220957198_    528 TCAAGATTTATTTAAAAGCTACAGGAATCAAAACAGTGTGGT-TTGGTAT 576
                             i i   i vv          v      i          -i   i  
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_220957198_    577 AAATAAGGAAA-ATAGATAAATGGAACAGAATATGGAAATC-AGAAATAG 624
                           iv vi  v -      v       i     -  ii i  -       i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAAT-TGAGAGTCCAGAAATAA 328

  chr1_220957198_    625 ATCCATACATAAATGGAGAACTAATTTTTTACAAAGGTGCCAAGGCAATC 674
                          i        vv    vv  i i     iv    i         i v  i
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_220957198_    675 CAATGGAGAAAGGATAGTTTTTTCAAGAAATAGTTCTGGAACAATTGGAT 724
                               i     i     i       v    i  v    i    i     
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_220957198_    725 ATCCACATGCAAAAAAGAAAGAAATGAACTTTGATCCATAACTCACACCA 774
                          ?            i -------     v  v  i  v  v         
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGA-------ATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_220957198_    775 TACATAAAAATTAGCTTAAA 794
                           i i        i  i   
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAA 491

Transitions / transversions = 2.00 (42 / 21)
Gap_init rate = 0.02 (6 / 309), avg. gap size = 2.33 (14 / 6)  

 835 21.94 6.75 0.00  chr1_220957198_220959704.rev      944  1180 (1327)    L1M4_orf2#LINE/L1      454   706 (202)  

  chr1_220957198_    944 GACCCC-ATCTCAAA------AAAAAAATCAATTCAAAATAGAGCATTGA 986
                               - i    v ------ v      i  i       i  v  ?v  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_220957198_    987 CCTAAATGAATAACCTAAAACTATAAAACTTCTAGAAGAAAACACTGGAG 1036
                                 v vi v                ii            iv  ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_220957198_   1037 AAAAATTTTGTGGCCTTGGG----GCAAAGATTGCTTAGACATGACACCA 1082
                         v   vi  i   i       ----    v i  v      i         
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_220957198_   1083 AGAGCATAACCCATAAAA-AATAAATA--TAAAGTGAACTCCATCAAAAT 1129
                          i    i  v v i    -  v     --    v  i   i         
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_220957198_   1130 TTAAAGGTTAAGCTCTTCAAAAGATACTCCGAAAAGAATGAA--GACAAT 1177
                          v   iv  vv iv       i  i   viv  i i i    --     i
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr1_220957198_   1178 CCA 1180
                            
  L1M4_orf2#LINE/    704 CCA 706

Transitions / transversions = 1.17 (27 / 23)
Gap_init rate = 0.02 (6 / 253), avg. gap size = 2.67 (16 / 6)  

 284 20.55 4.11 2.74  chr1_220957198_220959704.rev     1489  1561 (946)    L1M4_orf2#LINE/L1      685   758 (150)  

  chr1_220957198_   1489 AAAAAAATGAG--GACAATTCATAAGCTGGGAGAAAA-ATCATCACAAAG 1535
                           i   i   i--     ii  i iiv          -  -- ii    v
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT--TTGCAAAT 732

  chr1_220957198_   1536 CACATATCTGATAAAAGACTTGTATC 1561
                           i           ii          
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATC 758

Transitions / transversions = 6.50 (13 / 2)
Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.67 (5 / 3)  

 214 24.70 6.02 7.23  chr1_220957198_220959704.rev     1851  2016 (491)    L1M4_orf2#LINE/L1      745   908 (0)  

  chr1_220957198_   1851 AAAAGACTTGTATTCA-----TGCTAATAACTCCAAAAATT----AATAA 1891
                           ii         i  ----- iiv  v     iv v  i ----     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_220957198_   1892 CGAGA-AAACAACACAATTTTTTAAATGGCCAAAGGATTTTTAACAAAAC 1940
                         vi   -   i   v     ?vv-      v          --i vv i  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTT--GAATAGAC 841

  chr1_220957198_   1941 ATTTTAACAAAAGACTGACCATCCCAAGAGTCAGCAAGGATATGAAGAAA 1990
                             ivv    ii --  i-  v v  vi i  ii   v i     i --
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAA--GAT-ATACAAATGGCCAATAAGCACATGAAAA-- 886

  chr1_220957198_   1991 CCGGACTCTCACACATCATTGGGAAT 2016
                         ---  iv    -      ????????
  L1M4_orf2#LINE/    887 ---GATGCTCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (22 / 18)
Gap_init rate = 0.05 (9 / 164), avg. gap size = 2.44 (22 / 9)  


1510 27.63 5.25 3.39  chr1_220960780_220963641.rev      883  1472 (1390)    L1M4_orf2#LINE/L1        6   606 (302)  

  chr1_220960780_    883 AGAAATACTGTGTTTATGACTTAGAAAACTCAACACTA--AAAACATCAA 930
                            v  v ii    i   iv  i   i   i  i i i--  i iiv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_220960780_    931 TTTTTCCCAAATTGATTTACA---------TAATTCCTATCCAAATTCCA 971
                          vi i           i    ---------i   i      v    i   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_220960780_    972 GCAAGGCTTCTTATAGATATAAATAA-CTTATTCTAAAATTTATATGGAA 1020
                           vivvi  i  ii   v  vi i  -  v  i        i        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_220960780_   1021 AGGTAAAGGACCTAAAATAGTTACGACAATTTTGAAAAAGAAGAAT---G 1067
                          v i  i     i i     ii vi     i              i--- 
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_220960780_   1068 TTGTAAGAAGAATCATTCTACCCAATGTTAAGGCTTACTAAATAACTTCA 1117
                            ---  i  v   iv  v      v i  ii       v v i  v  
  L1M4_orf2#LINE/    206 TTG---GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_220960780_   1118 GTAATCAAGACAGTAGAGTACTGGTGGAAGAATAAATATGTAGATCAATG 1167
                                       ivi       iiv   i   i i  i          
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_220960780_   1168 AAATATAATAGAGGA---AACAATAGAATCACAAAAGAATGTACAACTGA 1214
                         i    v   v   ii--- iv    i vi  i v vvv   vv   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_220960780_   1215 TTTTTTTAAAGAAAAAAGGTACAAACATGATTTAATAGAGGAAGGACGGC 1264
                             i------i v  i   i v  v iv   i   i i i   i ii i
  L1M4_orf2#LINE/    353 TTTTC------GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_220960780_   1265 CCTTTCAACAATTGGTGAAGAAAAAAAAAAAGTCTG--TAGGC-CAAGAA 1311
                          i         v     vv ii v  -------   --  ?v -  v v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAA-------CTGGATAKCCACATGCA 439

  chr1_220960780_   1312 AAAAAAAGAAG--AG-------CCTCATACCTTTTACAAAAATTAACTTA 1352
                            i  v    --i -------     i   v v              i 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_220960780_   1353 AAATGAATCATTGATTTAAACATACCATGTAAAACTATGAAACTTTTGGA 1402
                              i    ?v  ii    ii  vv vv         i     i  ---
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT--- 536

  chr1_220960780_   1403 AAAAAAAAAAACAGGAGGAAATCTTCAAAACCTACGGCTGGGAGAACAGT 1452
                          i  i    v i   ? v        ivi    vv  i i  v-  ii  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC-AATGGT 585

  chr1_220960780_   1453 A-CTTCAACTTGATATCAAAA 1472
                         v-   vi iv   i i     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAA 606

Transitions / transversions = 1.62 (99 / 61)
Gap_init rate = 0.02 (15 / 601), avg. gap size = 3.40 (51 / 15)  

 276 27.85 0.00 0.00  chr1_220960780_220963641.rev     1794  1872 (990)    L1M4_orf2#LINE/L1      621   699 (209)  

  chr1_220960780_   1794 AGGAAAACTTGATAAATTGGACCTCTTAAGAATTAGAAAATTTTGCTCTG 1843
                           i    v v            i  v v i     i   v     iv  v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_220960780_   1844 TGAAAGCTCCTGTTAAGAGAATGAAAAGA 1872
                         ii  i viv  i i    i i        
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGA 699

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.00 (0 / 0)  

 665 24.64 7.58 0.47  chr1_220960780_220963641.rev     2161  2371 (491)    L1M4_orf2#LINE/L1      683   908 (0)  

  chr1_220960780_   2161 TCAAGAGAATGAAAAGATAAATTACAGACTGGGAGAAAATATTTGCAAGC 2210
                               i i        i  vii     v                   ii
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_220960780_   2211 CAAATATCCAACAAAGGATTTAGTATCTAGAATATA--AAGAATTTCCAA 2258
                           v     ii i  i   i  -     i        --     i iii v
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTT-GTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_220960780_   2259 AACTCAACAGTAGAAAAGCAAACAATATAATTAGCAAGTGTACTAA---- 2304
                                i i  i   ii    i  ivi    ?iv  i  vi v  ----
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_220960780_   2305 ------AAACATTTCACTGAGGAGTAGATACA---GGT-AACAAGCTAAT 2344
                         ------ i       v ii i  iv v     ---  i-  i    vv  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_220960780_   2345 AAAAAGATGTTCAACCTCAGTGATTAG 2371
                         i        i     v   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.64 (37 / 14)
Gap_init rate = 0.02 (5 / 226), avg. gap size = 3.40 (17 / 5)  


 498 22.12 0.88 0.88  chr1_221307583_221310193      548   660 (1951)    L1M4_orf2#LINE/L1        1   113 (795)  

  chr1_221307583_    548 TGGAAAGACATGCTGTGCTAATGGATTGGAAGACTTAATAATGTTAAAAT 597
                                 i  v ii  i v                    v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221307583_    598 GTCCCTACTATGCAAAAGCAATCTACAGATTCAATGCAACCCCTAT-AAA 646
                          v vv    viv    -vii              i    i      -   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_221307583_    647 ATTCTAATGGCATT 660
                           i i iiv  v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTT 113

Transitions / transversions = 1.27 (14 / 11)
Gap_init rate = 0.02 (2 / 113), avg. gap size = 1.00 (2 / 2)  

3368 20.24 5.16 0.14  chr1_221307583_221310193     1383  2118 (493)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_221307583_   1383 ATCCTAAAATTTGTATGGAACAT-CAAGGGACCCTGAATAGTCAAAACAA 1431
                                    ii       -  -          v      i        
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_221307583_   1432 TTTTGAAAAAGGA---CAAAGTTTGAGGCTTCACATTCTCTGGCTTTAAA 1478
                          i         i ---       v    vi     i ii iiii  i   
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_221307583_   1479 ACACAGTACAAAGCAAAAATAATTAAGATGATGTGGTAGTGGTATTAAGA 1528
                           vi v        v v i    i    iii       v   i  v i  
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_221307583_   1529 TAGA--TATAGATGAATGAAACAGAATAGAGAATCCAGAAATAAACCCTT 1576
                             --       v    i  i     v    i               v 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_221307583_   1577 GCATATA-GGTCAAATGATTTTTGACAAGAGCAGCAAAACTACACAATTG 1625
                         i   v  -      v       i      i iiv   i  i iv    v 
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_221307583_   1626 GAAAAAGACAGTCTCTTCAACAAATGGTACTGGGAAAACCGAATATCCAC 1675
                          i   ii i     i             i      v   i i   ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_221307583_   1676 ATACAAAAGAATGAAGTTGGATCCTTACTTTATATCATGTACACAAATTA 1725
                           i                  i  i   i i i i   i    v      
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_221307583_   1726 ACTCAAAATGGATTAAAAACCTAAATCTAAGGCCCAAAACTATTAAACTT 1775
                                      i ? i        v    iv i        v     i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_221307583_   1776 CTAGGAGAAGACATAGGGG-AAATCTTCAGGGCATTGGATTTGGCAAT-- 1822
                         i   i    i       ? -        iv i v    i  v      --
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_221307583_   1823 -TTCTTTGAGATGACACCAAAAGCACAGACCACAGAACAAAAAATACACA 1871
                         -     v  v                 ii v   i  v        v i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_221307583_   1872 AATAGGACTATATCAAGCTTAAAAACTCCTGCACATCAAAAGAAAC---- 1917
                            v     vi     iv         ii  ii v     i  v  ----
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_221307583_   1918 -----AGTGACAAGGCAACCTATGGAATGGGAAAGAATAACTGCGCATCA 1962
                         -----     v   i     i ii        i i    vi   iv    
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_221307583_   1963 TATATCTGATA-----------TCTAGGATATATAGGGAACTT---CAAC 1998
                                    -----------  i  i       ii     i---    
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_221307583_   1999 TCAACAA----AAACCAAACAAGCTGATTAAGAAATGGGCAAAGGATTTG 2044
                             i  ----  iv    i  v ii   ? i                  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_221307583_   2045 TATAGATAGTTCTTTAAAGAAAGTATCTGAATGGCCAATAAGTACATGCA 2094
                         v     i v    ii      ii   vii             i     v 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_221307583_   2095 AAGATGTTCAGTATCACTAATTAT 2118
                               i   ii    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.30 (101 / 44)
Gap_init rate = 0.01 (11 / 773), avg. gap size = 3.55 (39 / 11)  


2952 25.65 3.63 0.57  chr1_221426143_221433386      492  1372 (5872)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_221426143_   1372 TAAAAAAGCATCCCATGCTCATGGATAGGAAGAATTAATATCATTTAAAT 1323
                          ii   iii        i        v      v       ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_221426143_   1322 GACCGTATTGCCAAAAGCAATTTACAGATTCAATGCAATTCCTATCAAAA 1273
                          i vi  i v  v   vii  i           i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_221426143_   1272 TACCAATATCATTCTTCACAGAATTAGAAAAA--AATCCCCCAAATTCAT 1225
                          v   iivv v  i  ii     v v  v  i--i    iv-        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA-AAATTCAT 149

C chr1_221426143_   1224 ATGGAATAAAAAAAGAGCCTGAATAGCCAAAGAAATCCTGAACAAAAAGA 1175
                               vviv  ii  v  v           iv    i    v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

C chr1_221426143_   1174 ACAAAGTTGGAGGCATCACAATACCTGACTTCAAAATATACTACAAAGCT 1125
                                      vv     v v  ii i       iv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

C chr1_221426143_   1124 ATAATAACCCAAACTGCATGGCAATGGTATAAAAACAGACACACAGACCA 1075
                          i i   i v i  v ii   i v   i    ii i     i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

C chr1_221426143_   1074 ATTGTACCAAATAAAGAACCAAGAATTAAAGCCACATATTTATAGCCAAC 1025
                           v v ivi   vi   ii v    v    v   i i      i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

C chr1_221426143_   1024 TGACTTACAACAAAACTGACAAGAACCTACATTGGAGAAAGCATACCCTT 975
                            i  v i    iiv  v     v v v  v   i     v   vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

C chr1_221426143_    974 TTCAATAAATGATGCCTGGAAAACTGGACAGCCACATGCAGAAGAATGAA 925
                              i     i   iv   v       i ?         i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chr1_221426143_    924 ACTGGACCACTATCTCTCACCATATACAAAAATCATCTCAAAATGGATTA 875
                         ii      v   i   v                i v            i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chr1_221426143_    874 AAGACTTAAACATAAGATCCAAAACTA------------GGGAAAAC--- 840
                         ?    i    ii     v i       ------------ii      ---
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

C chr1_221426143_    839 --------TCTCCTGGACATTAGGCTAGGCAAATAATTTGT--GACTAAG 800
                         --------   i vv   v  i  i       - ii   v --  -  v 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA-TATG 597

C chr1_221426143_    799 ACCTCAAAAGCACAGGCAATAAAAATAAAAATAGACAAATCGGACTT--- 753
                           vi          i    i    iv         i    i      ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

C chr1_221426143_    752 --AAACTAGAAAGTTTCTGCACAGCAAAACAAATAATCAACAGAGTGAAA 705
                         --   i  i   v   -  ii vv    iv v iv     v i       
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chr1_221426143_    704 AAACAGCCTGTTCAATAGGAGAAAAAAATTGCAAACTATTCATTTGACAG 655
                          i   i  iiivv   i        v v       ii  vi  i   i i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chr1_221426143_    654 GGAACCAAGATCCATAATATACAAGGAACTGAAACAACTCAACAGGAAAA 605
                           i  iviv     v      i  i     vvv         i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chr1_221426143_    604 GCACAAACAATCCCATTAAAAAGTATGCAAAGGACAAGCATAGACATTTC 555
                         iv     i  i  v   ?    i iv        ivv v           
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chr1_221426143_    554 TTAAAAGAAGACATGTAACCAGCCAATAGGTATTTGAAAAAAATGCTCAC 505
                          iv        i  ii  vii       i i iv      i -      v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

C chr1_221426143_    504 CACCACCAGAAAA 492
                           i  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.70 (37 / 10)  

3320 26.06 1.56 0.45  chr1_221426143_221433386     5856  6753 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221426143_   5856 TGAAATATATATTCCATGCTCATGGATCAGAAGAATTAATATTATTAAAA 5905
                           i  - v    i     i        ii     v        i    i 
  L1M4_orf2#LINE/      1 TGGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_221426143_   5906 TGACAATACTACCCAAAGCAATTTACATATTCAGTGCAGTCCCTAGCTAA 5955
                           i       v      vii  i    v     ii   i      v v  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_221426143_   5956 ATACCAATGACATCCTGCACAGAAATAGAAAAAACACTTCTAAAATTTGT 6005
                           v   iivi v ii vii       v  v  iviiv i        ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_221426143_   6006 ATGGAACCACAAAAGATTCTGAATAGCCAAAGCCCTCCTGAGCAAAAAGA 6055
                               vii   ii  ii v           i vv  i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_221426143_   6056 ACAAAGCTAGAGACATCACACTACCAGACTTTAAAATGTACTCCCAAACT 6105
                               i i   ivv       v  vi i  i    iv    v v  i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_221426143_   6106 ATAGTAACCAAAACAGTATGATACTGGCATAAAAACAGATCCATAGACCA 6155
                          i     i   i     i  i           ii i   ivi     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_221426143_   6156 ATGGAACAGAAGAGAGAACCCCGGTATAAATTCACACATTTACAACCAAC 6205
                               i    vv    ii  v iv     ii  i       iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_221426143_   6206 TGATCTTTGACAAAGTCACCAAGAACATTCAGTGGGGAAAGGCAGGTCTT 6255
                             i  i     i vii      v      i         ivvi     
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_221426143_   6256 TTCAATACATGGTGTTAGGAAAGCTGGATAACTCTATGCAGAATAATAAA 6305
                              i v      i i   v i       ? ivi     i  v   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_221426143_   6306 ACTGGACCCCTATCTCTCACCATACACAAAAATGAAATCAAAATGGATTA 6355
                         ii          i   v       i        v  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_221426143_   6356 AAGACCTGAATCTAAGAACTGAAACTATGAAACTACTAAAAGAAAATGTT 6405
                         ?      i   v     i  i       i     vi  i       ii v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_221426143_   6406 GGGA-AAAT------GATCCAGGTATTTGGCAAAGATTTATTTTGTGTAA 6448
                           ?i-    ------  i iv  -i  v     v i   --i  ivi  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTT--CTTAGATAT 596

  chr1_221426143_   6449 GACTTCAAAAGCACTGACAACCAAAGCAAAAAGAGATTA-TTGGATTACA 6497
                            vi         vii    v    v     v    v -     i v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_221426143_   6498 TCAAG-CCATAAGCTTCCACACAGCAAAAGAAACAATCAACAGAGTGAAT 6546
                             i-ii v  i   iiiii vv    i  v  v     v i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_221426143_   6547 AGACAATCTACAGAAAGGGAGAACGTATTTGCAACCTAAGCATATGACAA 6596
                               i i      v       vi         vii vii  v   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_221426143_   6597 GGGATTAATAACCAGAATATATAAGGAGCTCAAATAACTCAATAGCGAAA 6646
                             i vi  v             i  i   vv i         iii   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_221426143_   6647 AAACAAA-AG---GATT-AAAAATAGACAAAAGATATGAACAGACATTTC 6691
                          i     - i---i   -      i i    i   v    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_221426143_   6692 TCAAAAGAAGTCATACAAATGGCCAAAAGGCATATGAAAACGTGTTTGAC 6741
                           v       vi              v i   i       vi  i ii  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_221426143_   6742 ATTGCTAATAAT 6753
                           ii????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (152 / 79)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


3093 26.79 1.90 0.56  chr1_221435207_221441555.rev     4963  5858 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221435207_   4963 TGGAAGAACATTCCATGCTCATGGGTAGAAAGAATCAATATCGTGAAAAT 5012
                              ii i  i     i      i v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221435207_   5013 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5062
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221435207_   5063 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5110
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_221435207_   5111 TATGGAACCAAAAAAGAGCCCGCATTGTTAAGTCAATGCTAAGCCA-AAG 5159
                                viiv  ii  v  v v  v ii  iv    vi i ivv -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_221435207_   5160 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5209
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_221435207_   5210 TACAGTAACCAAAACAGCATGCTACTGGTACCAAAACAGAGATATAGACC 5259
                                 i   i    ii  v      i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_221435207_   5260 AATGGAACAAAAC--AGAGCCCTCAGCAATAATGCCACATATCTACAACC 5307
                                i i  i--    i  --  v     vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_221435207_   5308 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5357
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_221435207_   5358 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5407
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_221435207_   5408 GAAACTGGATCCCTTCCTTACACCTGGTATAAAAATTAATTCAAGATGGA 5457
                            ii    i    v   i     vvi  i         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_221435207_   5458 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTGGAAGAAAAC 5507
                          i ?    i       v   v       i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_221435207_   5508 CTAGGCA-ATACCATTCAGGACATAGGGCT---TCATG---TCT-AAA-- 5547
                         v    ?i- v i -   iv   v v   i ---iv   ---   - i --
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_221435207_   5548 --ACACCAAAAGTGATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5595
                         --          iivvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_221435207_   5596 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTCAA 5645
                           i   v v  i i   i  ii vv    i  v    i  vv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_221435207_   5646 CAGGCAACCTACAGAATGAGAGAAAATTTTTGCAATCTACTCATCTGACA 5695
                         v  i     i        i        v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_221435207_   5696 AAGGGCTAATATCCAGAATCTACAATGAAGTCAAACAAATTTACAAGAAA 5745
                          i  i  vi          v  i  v   v  vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_221435207_   5746 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5795
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_221435207_   5796 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5845
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_221435207_   5846 CATCACTGGCCAT 5858
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


2938 22.40 1.22 8.76  chr1_221477296_221479816     1047  2028 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221477296_   1047 TGGAAACACATCCCATGCTCATGGATGAGTAGAATCAATATTGTGAAAAT 1096
                               v i        i        vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221477296_   1097 GACCATACTGCCAAAAGCAATCTACAAATTCAACCCAATCCCCACCAAAA 1146
                          i v     v  v   vii       i       v       i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221477296_   1147 TACCATCATAATTCTTCACAGAG-TTAGGAAAAAC-AATTCTAAAATTCA 1194
                          v   v vvvv  i  ii    i-  --  v  i -i  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr1_221477296_   1195 TATGGAACCAAAAAAGAGTCTGCATAGCCAAAGCAAGACTAAGCAAAAAG 1244
                                viiv  ii  vi v v         i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_221477296_   1245 AACAAATCTGGAGGCATCACACTGCCTGATTTCAAACTATATCACAAGGC 1294
                               vi      vv       v  ii        viv  ii    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_221477296_   1295 CATAGTCTCCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACC 1344
                         i i   vvi   i    ii         i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_221477296_   1345 AATGAAACAGAAGAGAGAACCCAGAAATAAACCTGAATACTTACAGTCAA 1394
                             i  i    vv    ii             iiv i i   ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_221477296_   1395 CTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGAAAGGACTC-CCT 1443
                         i    i  i     i vviv   i v   vv i    i  i  v v-i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_221477296_   1444 TTTTAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGA 1493
                            i                 i  i   v  ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_221477296_   1494 AACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTGAAGATGGATT 1543
                          ii    i  ii i   v    v           i    v  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_221477296_   1544 AAGGACTTAAACCTAATACCTGAAACTATAAAAATTCCAGAAGATAACAT 1593
                          ?i   i    iv   v v  i           v iii      v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_221477296_   1594 TGGAA-AAACCTTTCTAGACACTGGCTTAGGCAAGGATTTC------ATG 1636
                         v  ?i-   i   iv -   vi   v        v i    ------   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_221477296_   1637 AC--CAAAAACGCAAAAACAATTGCAATAAAAACAAAGATAAATAGGGGG 1684
                           --     i i   --------    i    iv   i   i   iivv 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA--------GCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_221477296_   1685 GACTTAATTAAACTAAAGAGCTCTTGCACTGCAAAAGGAATAGTCAGCAG 1734
                              v  i   v v  i i  i   ii  v    i iv ivi   iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_221477296_   1735 AGTAAACAGACAATCCACAGAGTGGGAGAAAATCTTTACAATCTATACAT 1784
                            i  v      i       i           v   i   vii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_221477296_   1785 CTGAGAAAGGACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGT 1834
                             v  i     vi          v  i  v      vv    v   i 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_221477296_   1835 AAGAAAAAACAATCCCATCAAAAGTGGGCTGACAAAGGACTAATATCCAG 1884
                           v     ----------------------      ----   -------
  L1M4_orf2#LINE/    790 AATAAAAA----------------------GACAAA----TAA------- 806

  chr1_221477296_   1885 AATCTACAATGAATTCCAACAAATCAGTAAGAGAAAAAACAATCCCATAA 1934
                         ---------------  ----------------------    ---- ? 
  L1M4_orf2#LINE/    807 ---------------CC----------------------CAAT----TWA 815

  chr1_221477296_   1935 AAAAGTGGGCTAAGGACATAAATAGAAAATTCTCAAAATAAGATATACAA 1984
                             -     v     iv i      v v     v   v           
  L1M4_orf2#LINE/    816 AAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_221477296_   1985 ATGGCTAACAAACACATGAAAAAATGCTCAACATCACTAATGAT 2028
                              i  i  i          i             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (131 / 85)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 6.53 (98 / 15)  


3065 26.81 1.36 0.45  chr1_221502803_221509350.rev     5161  6044 (504)    L1M4_orf2#LINE/L1        1   892 (16)  

  chr1_221502803_   5161 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATAATGTGAAAAT 5210
                               i i  i     i        v      v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221502803_   5211 GGTCATACTTCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 5260
                           iv     i      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221502803_   5261 TACCA-TTGACTTTCTT-CACGTAATTAGAAAAAACT-ACTTTAAATTTA 5307
                          v   -i  v    i  -  - v    i-- v  i  - iii    v  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_221502803_   5308 ATATGGAACCAAAAAAGAGCCTTTATAGCCAAGACAATCCTAAGCAAAAA 5357
                                 viiv  ii  v  vvv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_221502803_   5358 GAACAAAGCTGGAGGCATTATGCTACCTGACTTCAAACTATATTACAAGG 5407
                                 i      vv i ii  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_221502803_   5408 CTGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5457
                           i      i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_221502803_   5458 CAATGGAACAGAACAGAGGCCTCAGAAGTAACATCACACATCTACAACCA 5507
                                 i    iv   ivii     i   vvi  i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_221502803_   5508 TCTGATCTTTGAAAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5557
                         vi    i  i  v  ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_221502803_   5558 TATTTAACTAAAAGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5607
                          v  i   v  vi   i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_221502803_   5608 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATAGAT 5657
                           ii         v   i     v                   i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_221502803_   5658 TAAAGGCTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5707
                         i ?  i i           v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_221502803_   5708 TAGG--TAATAC--CAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 5753
                             --   vv -- iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_221502803_   5754 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5803
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_221502803_   5804 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5853
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_221502803_   5854 TGCAACCTACAGAATGGGAGAAAATTTTTACAATCTATCCATCTGACAAA 5903
                         vi     i                 v   i   vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_221502803_   5904 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACGAGAAAAA 5953
                           i  vi          v  i        ivv    v iv ii v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_221502803_   5954 -----ACAACCCCATTAAAAAGTGGGCAAAGGATATGAACAAACACTTTT 5998
                         ----- i     v   ?    i            v    i i   i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_221502803_   5999 CAAAAGAAGACATTCATGTGGCCAAAAAAGGATATGAACAGACACT 6044
                          v        i  v  vi       v  - v i     v   ii  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAA-GCACATGAAAAGATGCT 892

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.01 (9 / 892), avg. gap size = 1.78 (16 / 9)  

 251 17.91 0.00 4.48  chr1_221502803_221509350.rev     6045  6111 (437)    L1M4_orf2#LINE/L1      845   908 (0)  

  chr1_221502803_   6045 TTTCAAAAGAAGACATTCATGTGGCCAACAAACATATGAAAAAAAACAGC 6094
                          i  v        i  v  vi       i  i  i       i ---v  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA---TGC 891

  chr1_221502803_   6095 TCATCATCACTGGTCAT 6111
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (7 / 5)
Gap_init rate = 0.02 (1 / 64), avg. gap size = 3.00 (3 / 1)  


2697 24.97 5.25 1.71  chr1_221512215_221517449     3870  4746 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221512215_   3870 TGGAAAAACATTCCATGCTGATGAATAGGAAAAATCAATATTGTTAAAAT 3919
                               i i  i     i v   i  v    i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221512215_   3920 GGCCATACTGCCCAAAGCAGTTTACAGACTTGATGCTATTCCTGTCAAAT 3969
                            v     v      viii i      i ii i  v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221512215_   3970 TACCAACATCATTTTTCACAATTCAAAA--AAAAAACT-ATTCTAAAATT 4016
                          v   i vv v     ii  i----   --i v  i  -  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG----AAATTGACAAGCTGATCCTAAAATT 146

  chr1_221512215_   4017 TGTGTTGAAC--CAAAGAACCT-GAATTGCCAAAGCAATCCAAAGCAAAA 4063
                         ii i v   v--   i i   i-    v      i     ivi iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_221512215_   4064 AGAGCAAAGCTGGAGGCATCACATTACCCGACTTCAAA--CTA-TACAAG 4110
                            i     i      vv     i v   i i      --i  -     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_221512215_   4111 ACTACAGTAACCAA-ACAGCATGGTAAGGGTACAAAAACAGATACATAGA 4159
                         i         i   -    ii     vv  i i  ii i   i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_221512215_   4160 CCAATGGAACAAAGTAGAGAACTCAGAAATAAAGCCACACAGTCTA---- 4205
                         i        i i i v    iii          v   i   - i  ----
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA-TTTATGGT 345

  chr1_221512215_   4206 CAAT--------GACAA----------------CAATGGAGAAAGAACTC 4231
                             --------     ----------------      i       ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_221512215_   4232 CCTTTTCAATAAATGCTTCTGGGATAACTGGCTAGCCATATTCAGAAGAT 4281
                         i        i     v v      i      v  ?   i  v  i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_221512215_   4282 TGAAACTGGATCCCTTCCTGTCACTATATACAAAAATTAACTCAAGATGG 4331
                             ii    i    v   vv   i                    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_221512215_   4332 ATTAAAGACTTAAATGTAAGACCTAAAACAGTACAAACCCT-AGAAGAAA 4380
                           i ?    i           v       vi  -    i  -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAA 544

  chr1_221512215_   4381 ACCTAGG---AAATACCATTCTGGACATCAACCTTGACAAAGAATTTATG 4427
                           v    ---    -- -   vv   v iiivi v i   v i-   v v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGG-TTTCTT 590

  chr1_221512215_   4428 ACCTA-GTCCCCAAATGCAATTGCAGCAAAA-ACAAAATTGATAAGTGGG 4475
                          vv  - v v     v   vvv   i     - v     v     i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_221512215_   4476 ACCTAATGAAACTAAAGGGCTTCTGCATGGCAAGCAAAATTATCAACAGA 4525
                           i v  v   v v  iii   i  iiivv   ivi v i      v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_221512215_   4526 GTAAACAGACAACTTACAGAATGAGAGAAAATATTCACAATCTGTGCATC 4575
                           i  v       ii        i           ii   viii ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_221512215_   4576 TGACAAAGTTCTAACATCCAGAGTCTATAAGG--CTCTTTAACACCCCAA 4623
                            i  i vv  vii       i v     i --     --   v i   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT--ACAACTCAA 788

  chr1_221512215_   4624 CAAACAAAAAACCAAATAACTCCACTAAAAAATGGGCAAAGGATATGAAC 4673
                         i  -i     iv        i v i ?                 v    i
  L1M4_orf2#LINE/    789 TAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_221512215_   4674 AAATACTTCTCAAAAGAAGACATACATGTAGCCAACAAATATATTAAAAA 4723
                          i i i     v        i     vi i     i  ii i  v    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_221512215_   4724 TATGACCACCAATCATTAGAGAA 4746
                         -   vi  v  -   ????????
  L1M4_orf2#LINE/    888 -ATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.67 (135 / 81)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.44 (61 / 25)  


 287 22.76 4.07 3.25  chr1_221519838_221523532.rev      377   499 (3196)  C L1M4_orf2#LINE/L1   (0)   908   785  

C chr1_221519838_    499 TCAAT--TAAAAAAAATCCCAAACAAGTTAATTTTAAAATGGGTGAAAGA 452
                              --      i ----    i  vii    ?v        ii  i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGA----CAAATAACCCAATTWAAAAATGGGCAAAGGA 830

C chr1_221519838_    451 TCTAAGCAGACATTTCATCAAAGAAGA-A-ACAGATTGCAAATAAATGTT 404
                          i i ii         vi         - -   i  v  v     iiiiv
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

C chr1_221519838_    403 TTAAA-GATGCTATAAATCATTAGACAT 377
                          v   -      vv v    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.04 (5 / 124), avg. gap size = 1.80 (9 / 5)  

3678 14.71 1.38 11.75  chr1_221519838_221523532.rev     2192  3204 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221519838_   2192 TGGAAAGACAGACCATGTTCATGGACTGGAAGACT--ATACTATTAGAAT 2239
                                 i vv             i         --   i i   ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221519838_   2240 GAAAATACTCCTCATATTTATCTCCAGTTTTAATGCTGCCTCTATCAAAA 2289
                          iv        i  v   v    v   v  i  i  vii i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221519838_   2290 TTCTAGCTGAATATTT-GCAGAAATTGTCAAGCTGATTCTAAAATTCATA 2338
                          i i     vv v   -          v         i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_221519838_   2339 TGAAAATGCAAGGGACCCACAATAGCCAAAACAATGTTGAAAAAGAAGAG 2388
                           i                v               v             i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_221519838_   2389 CAATGTTAGAAAATTCCCAATTCCTAATTTCAAAACTTACTACAAAGCTA 2438
                            v   i  ii i  v  v    i                         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_221519838_   2439 TAGTAATCAAGACAGTATGGTACTGGCATAAGGACAGACATGGAG--CAA 2486
                         i               i                 i      iv  --   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_221519838_   2487 TGAAATGAAATTGAGGGTCTGAAAATAAACCCACACATTTTTGGTCAGCT 2536
                           i   ii       i   iii           i      v      ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_221519838_   2537 GATTGTCAACGAGGGTGCCAAGACAATTCAATAGAGAAAGAAATAGTGTT 2586
                             v  i  i             v       i i       -    ---
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGT--- 396

  chr1_221519838_   2587 ATTCTTTTCAACAAATAGTACTGGGACAACTGGATATTCGTATACAAAAG 2636
                         ---             i  i                ?i ii  i      
  L1M4_orf2#LINE/    397 ---CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_221519838_   2637 AAGAAATTTGGACCC-TATCTCATACCATCTACAAAAATTAACTCAAAAT 2685
                           vi  v        -  i    i     v                    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_221519838_   2686 GCATCAAAG-CCTAAATGCAAGAGCTAAAGTTATAAGA-TCTTAGATAAA 2733
                          v    ?  -        i          ii     i -       vi  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_221519838_   2734 AACA--AGAGTAAATCTTCAAGACTTTGGATTAGGCAATGATTTCTTAGA 2781
                             --i ?          iv   i    i          i         
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_221519838_   2782 TA---CACTTAAAGCACAATCAATCAAATACAAGTTAAATTAAATAAAAA 2828
                           ---   iv         v   -    ----  --   --     i --
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAA-CAAA----AG--AAA--AAATAGA-- 632

  chr1_221519838_   2829 TAAAATTAAAAATTAAATAAAAATTAGAAATTAAAAACTTTTTTACTCCA 2878
                             -  ii vv i -------- i -               v i  i  
  L1M4_orf2#LINE/    633 TAAA-TTGGACTTCA--------TCA-AAATTAAAAACTTTTGTGCTTCA 672

  chr1_221519838_   2879 AAGGATACTATTAAAAAAA-GAAAAGAAGACCCACAGAATCTAATAAATA 2927
                              i     i  i   i-       vi           ------iiv 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT------GGGA 716

  chr1_221519838_   2928 AAGAACTCTTAGAACTCAGCAATCAAAAGACAAATAACTTAGTTGGGCAT 2977
                         i i  ivi  i-----  --     v -------  v  -----------
  L1M4_orf2#LINE/    717 GAAAATATTTG-----CA--AATCATA-------TATCT----------- 741

  chr1_221519838_   2978 GATAGCATGAACCTGTAGTCCCAGCTATGTGGGAGGCTGAGGTGAGAGTA 3027
                             -- v i  i    -   -----------------------   i  
  L1M4_orf2#LINE/    742 GATA--AGGGACTTGTA-TCC-----------------------AGAATA 765

  chr1_221519838_   3028 TCGCTTGAGCCCAGGAGTTCAAGACAAGTCTGAGAAACACAAGACCCCAT 3077
                          -------------- -- v    -- v   ------i    --------
  L1M4_orf2#LINE/    766 T--------------A--TAAAGA--ACTCT------TACAA-------- 783

  chr1_221519838_   3078 CTAAATTAATTAATTAATTAACTAACACAATTTAAAAATGAACAAAGAGT 3127
                           v   -   v  vvi i-  v    v     ?       ii     ii 
  L1M4_orf2#LINE/    784 CTCAAT-AATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_221519838_   3128 TTGAATAGATATTTCCTCAAAGAACATATATAAATGGCCAAAAAGCACAT 3177
                                  i     ii       v     i          v        
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_221519838_   3178 GCAAAGATGTTCAATATCATTAGTCAT 3204
                          v       i    i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (96 / 49)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 3.91 (133 / 34)  


3105 26.91 1.22 0.66  chr1_221550224_221556593.rev     4977  5879 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221550224_   4977 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGCAAAT 5026
                              ii i  i     i      i v      v i     i  vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221550224_   5027 GGGCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5076
                           vv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221550224_   5077 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5124
                          v   ivvi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_221550224_   5125 CTATGGAACCAAAAAAGGGCCCGCATTGACAAGTCAATCCTAAGTCAAAA 5174
                         v       viiv  ii iv  v v  v v   iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_221550224_   5175 GAACAAAGCTGGACACATCACGCTACCTGACTTCAAACTATACTACAAGG 5224
                                 i    vivv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_221550224_   5225 CTACAGTAACCGAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5274
                                  i i i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_221550224_   5275 CAACGGAACAGAAC--AGAGCCCTCAGAAATAATTCCACATATCTACAAC 5322
                            i    i    i--    i  --        vi   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_221550224_   5323 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGTATTC 5372
                           vi    i  i     ivv  v   i v  vvv           v  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_221550224_   5373 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5422
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_221550224_   5423 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5472
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_221550224_   5473 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAGAACCCTAGAAGAAAA 5522
                           i ?    i       v   v       i    i vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_221550224_   5523 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATATCT 5571
                          v    ?i- v i -   iv   v v  vv i     v ii   v  vv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_221550224_   5572 AAAACACCAAAAGCGATGGCAACAGAAGCCAAAATTGACAAATGGGATCT 5621
                          vi           ivvi      i   vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_221550224_   5622 AATTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTACCATCAGAGTGA 5671
                         v  i   v v  i i      ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_221550224_   5672 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5721
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_221550224_   5722 AAAGGGCTAATATCAAGAATCTACAATGAACTCAAACAAATTTACAAGCA 5771
                           i  i  vi    v     v  i  v      vv    v iv i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_221550224_   5772 AAAAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 5817
                            i    ----   v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_221550224_   5818 TCTCAAAAGAAGACATTTATGCAGCCAA-AAG-ACATGAAAAAATGCTCA 5865
                             v        i  vi viii     -   -         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_221550224_   5866 TCATCACTGGCCTT 5879
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


2682 26.72 3.38 1.01  chr1_221561655_221568018.rev     4987  5873 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221561655_   4987 TGGAGAAACATTCCATGCTCATGGATAGGAAGAATCAGTATTGTGAAAAT 5036
                             i i i  i     i        v      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221561655_   5037 GGCTATACTGCCCAAAACAATTT-TAGATTCAATGCTATTTCCATTAAAC 5085
                            v     v      vii  i -i        i  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221561655_   5086 TACCATTGACATTCTTCACAGAACTAGAGAAAACT-ATTTAAAGATTCAA 5134
                          v   vivi v  i  ii     v v  v  i-  -  iiv  i     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_221561655_   5135 GTGAAACCAGAAAAAGAACCCA-AATAGCCAAGACAATCC--AATCAAAG 5181
                         i  i  -- viv  i i     -         i      i--  --    
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--AAAG 195

  chr1_221561655_   5182 A-GAACAAAGCTGGAGGCATCACACTACCCATCTTCATACTACACTACAG 5230
                          -        i      vv       v    vi    v vivi      i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_221561655_   5231 GGCTACACTAACCAAAACAGCAAGGTACTGGTACAAGAAAAGGCACATAG 5280
                         i      v   i   i    iiv        i i   i v  i  i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_221561655_   5281 ACCAAGGGAACAGAACAGAAAGCCCAGAAATAGGACCACACACCTACAAC 5330
                          i   v    i    iv  i  i         iiv   i   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_221561655_   5331 TATCAGATCTTCAACAAACCTGACAAAGACAAGCAATGGGGAAAGGAATC 5380
                         i viv   i   i    ivv  v   iiv  vv            -   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATA 394

  chr1_221561655_   5381 -CCTATTCAATAAATGATGCTGGGATAACTGGCTAGCCATATGCTGAAGA 5429
                         -i  v     i     i        i      v  ?   i    vi    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_221561655_   5430 TTGAAATTGAACCCCTTCCTTATACCATATACAAAAATTTTCTCAAGATG 5479
                         v    i   i      v   i i                vv     i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_221561655_   5480 AATTAAAGACTTAAATGTAAAACCCCAAACTATAAAAGCCCTGGAAGATG 5529
                         i  i ?    i         i v iv           vi i i     vi
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_221561655_   5530 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTCAT-GA 5577
                           v    ?i- v i -   iv   v v  vv i     v i    v -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_221561655_   5578 TGAAGATGCCAAAAGCAATTGCAATAAAAGCAAAAATTGACAAATGGAAT 5627
                          - v  ii         vvv    i     v      v  i    v i i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_221561655_   5628 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAGACTATCAACAGAGT 5677
                         i v  i   v v  i i   i  ii vv    i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_221561655_   5678 AAA----CAGCCCAGAGAATGGGAGAAAATTTTTGCAAACTAGTCATCTA 5723
                         i  ----  i    v               v        ii vvi    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_221561655_   5724 ACAGAGATCTAATATCCAGCATCTATAAGGAATGTAAACAAATTTACAAG 5773
                          i ii iv  vi       v  v     i   ivivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_221561655_   5774 AAAAAT-CAAACAACTCAATAAAAAAGTGGGTAAAGGACATCAACAGTCA 5822
                              v-    i   i    v?    i    i      iv v  i  v  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_221561655_   5823 CT------------ACATGCA----GCCGACAATCACATGAAAAAAAAGC 5856
                         i ------------ i  i  ----   i i  v          i v-  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GC 891

  chr1_221561655_   5857 TCAACATCACTGATCAT 5873
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.05 (39 / 19)  


3105 21.99 4.26 1.89  chr1_221582659_221589866     2037  2882 (4326)    L1M4_orf2#LINE/L1        3   868 (40)  

  chr1_221582659_   2037 GGAAGATACATTGTGTTCATCCATTGAAAGACCTAATA-----AAGATGT 2081
                          i      iviii       vv    i     i     -----      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_221582659_   2082 CAAATA-TCACCAAATGGATCTCTAGATTCAACACAATCCTAATCAGAAT 2130
                            -  -  v      v     vi         i      iv    i   
  L1M4_orf2#LINE/     53 CAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_221582659_   2131 CCTAGCAGACTACTT-GTAGAAATTGACAAGCTGATTCTACAATTCTTGT 2179
                           i   v v  vi  - i                  i   v     v i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_221582659_   2180 GGAAATGTAAAAGTCCTAGAATAGTGTAAACAATTTTACAAAAGAAGAAC 2229
                                i  ii v  i       ivv       i  iv           
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_221582659_   2230 AAAGTTGGAGCATTAAAACTACCTA--TTCAGAGGCTCATTATAAGGCCA 2277
                                   v i v v   v  i --    i i-  i i  i  i  i 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAA-CTTACTACAAAGCTA 250

  chr1_221582659_   2278 CAGTTATCAAAACAGTATTTT-TTGGTTTAAAGATAGACA---------- 2316
                             v     i     i vv -i   iv   i        ----------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_221582659_   2317 -AGAA-AGA---GAGAGTACAGAAATAGACCCACATACGTATGGACAACT 2361
                         -i   -   ---      v        i     i i iv     v   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_221582659_   2362 GATTTTCAACAAATATGCAAAGATAATTCA---GAGAAAAAACAGCCAAT 2408
                                i    ivi   v    iv     --- i    i  i  i ---
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC--- 397

  chr1_221582659_   2409 TTTTAAAGAAATTGTGCTAGCATAATTGAACAATCATATGCAAAACAAAC 2458
                             v  v    v     i v i  i  i i ?i  i        -i  i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAAT 446

  chr1_221582659_   2459 AAAAAACTCTTAAGCCAC-ATCTTACAACATACACAAACATTTAACACAT 2507
                         i  i-----  iii  v - i  i   v    i     v   -   v  -
  L1M4_orf2#LINE/    447 GAAG-----TTGGACCCCTACCTCACACCATATACAAAAATT-AACTCA- 489

  chr1_221582659_   2508 AAAAGGATTATGGACCTAAATGCAAAACCTAAAACTATAAAACTTTGAGA 2557
                            v    i ?i          i  i v                i v   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_221582659_   2558 A-AAAACATAAGAG-ATATTTTTGTGACCTTGCTTTAGGCA--GATTTCT 2603
                          -        i ? - v  i  i         vv       -- i     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_221582659_   2604 TCAATATGGCACCAAAAGCACTATCCATAGAAGGAAAATT-TATGTATTA 2652
                          vi     i            v v v i i   i    v -v  iv   i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_221582659_   2653 GATTTCATCAAAATTAAAAA--TTCGTGCTCCTATAAAGACACTTTTAAG 2700
                           i                 --  i     i - -  i      v i   
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTC-A-AAGGACACTATCAAG 687

  chr1_221582659_   2701 TGAATACAAATATAAACCAGAGACTGGGAGAAAATATTTGTAAAGCATAC 2750
                         vi i iv   v i  v   v   v                i   v    i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_221582659_   2751 ATCTGATAAAGGACTTGTATCCAGAATATATAAAGAACTCTCAAAATTCA 2800
                                  i                               i v  i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_221582659_   2801 TTGATAAGAAAACAAAACAATCCTGTAAAGAGATGGGCAAAATATTAAAA 2850
                         v i    i  i     -i  i  vi v? i i         iv   vi  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_221582659_   2851 TAGAGACTTTACCAAAGTGGATATATGAATGG 2882
                             v i  iv      vi      ii     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGG 868

Transitions / transversions = 1.64 (113 / 69)
Gap_init rate = 0.03 (25 / 866), avg. gap size = 2.08 (52 / 25)  

2697 26.24 1.27 5.40  chr1_221582659_221589866     5774  6718 (490)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_221582659_   5774 GAAAACCATTCCATGCTCATGGATAGGAAGAATCAATATTACTAAAACAG 5823
                             ivi  i     i        v      v i      ii   i ii 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_221582659_   5824 CCATACTGCCCAAAGCGTTTTACAGATTCAGTGCTGTTCTTATCATGCTA 5873
                          v     v      vi v i          ii  vi i i     viv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_221582659_   5874 CCAATGACATTCTTCACAGAATTAGAAAAA-TG-TTTTAAAATTCATATG 5921
                            iivi v  i  ii     v v  v  i-  - ii             
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_221582659_   5922 GAACCAAAAAAGAGCCCAAATAGCCAAGTCAATACTAAGCAA-AAGAACA 5970
                            viiv  ii  v  vi         iv    vi i iv  -       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_221582659_   5971 AAGCTGGAGGCATTACATCACCTAACTTCAAACTATACTTCAAGGCTACA 6020
                            i      vv i   iiv  i  i      viv    v   i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_221582659_   6021 GTAACCAAAACAGCATGGTACTGGTACAAAAGCAGACACATAGAACAGTG 6070
                             i   i    ii         i i  iiii     i     v  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_221582659_   6071 GAACAGAATAGAGAGCCCAGAAATAAAGCCGCATACCTACGACCATCTGA 6120
                            i     v     i           v  ii i ii  i ii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_221582659_   6121 TCTTTGACAAAGTTGACAAAAACAAGGCATAGGGGAAGAATTTTATATTC 6170
                          i  i     i v  v   i v  vvvv  i   i      vv v v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr1_221582659_   6171 TATGGAATAA--CTGGAATAACTGGCTAGCCATATGCAGAAGATTGAAAC 6218
                         v ii-   ii--    i i      v  ?   i     i    v    ii
  L1M4_orf2#LINE/    403 AACA-AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_221582659_   6219 TGGAACCCTTCCTTTCAACATATACAAAAATCAACTAAGCATGGATTAAA 6268
                             v    v   iv  v             i    v iv      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_221582659_   6269 GACTTAACTGTAAAACCTAAACCTGTAAAAACCCTGGAAAATAACCTAGG 6318
                            i   v     i v     v  i     vi i i   i v   v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_221582659_   6319 ---AAATAC-CAT--TCTAGGGGCCAAGGCAAAGATTTCATAACAAAGTC 6362
                         ---    vi- i --i  v   vi--      v i    v  ivv v v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTT--AGGCAATGGTTTCTTAGATATGAC 599

  chr1_221582659_   6363 ACCAAAAGCAATTGTAATGTAAACAAAAATTGACAAATGGGACCTAATTA 6412
                                   vvv i  iiv  iv      v  i    v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_221582659_   6413 AACTAGAAAGCTTCTGCACAGCAAAAAAAAAAAAAAAAAAAAAACAACAA 6462
                           v vi   i   i  ii vv    ii ----------------------
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGA---------------------- 677

  chr1_221582659_   6463 AACAAACAAACAAAAAAACGCTATCAACAGAGTAAACAGACAACCTATAG 6512
                         ------------------ i       v i   i  v        i i  
  L1M4_orf2#LINE/    678 ------------------CACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_221582659_   6513 CATGGGAGAAAATTTTTGCAAACTATGCGTCTGATGAAGGTATAATATCC 6562
                         v            v        ii  iii      i i  vv vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_221582659_   6563 AGAATCTATAAGGAACTTAAACACATTTACAGG-CAAAAAAAAAAAAAAA 6611
                              v     i     i--------     iv-   v  v     i v 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTC--------TTACAACTCAATAATAAAAAGACA 801

  chr1_221582659_   6612 AACAACCCCATTAAAAAGTGGGTAAAGGACACAAACAGACACTTTTCAAA 6661
                           i     v   ?    i    i      ivii  i     i  i  v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_221582659_   6662 AGAAGACATACACATGGCCAACAAGCATATGAAAAATTTCTCATCACTAA 6711
                               i     v        i     i       iv v    v  ii ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_221582659_   6712 TCATGAG 6718
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 5.25 (63 / 12)  


3060 26.82 1.32 1.10  chr1_221596579_221602311.rev     4337  5242 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221596579_   4337 TGGAAGAACATTCCATGCTCATGGGTAGAAAGAATCAATATCGTGAAAAT 4386
                              ii i  i     i      i v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221596579_   4387 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4436
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221596579_   4437 TACCAATGACTTTCTTCACAGAA-TTGGAAACAA-CT-ACTTTAAAGTTC 4483
                          v   iivi i  i  ii     -   ---    -  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_221596579_   4484 ATATGGAACCAAAAAAGAGCCCGCATTGTCAAGTCAATGCTAAGCCAAAA 4533
                                 viiv  ii  v  v v  v i   iv    vi i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_221596579_   4534 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 4583
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_221596579_   4584 CTATAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGAT 4633
                            i     i   i    ii        ii iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_221596579_   4634 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGTCCCATA--TCTACA 4679
                                 i    i--    i  --        v--      -- i  ii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAA--CCCATACATTTATG 343

  chr1_221596579_   4680 ACCATCTGATCTTTGAGAAACCTGATAAAAACAAGCAATGTGGAAAGTAT 4729
                         ii  vi    i  i  v  ivv  vi  i v  vv     v      v  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_221596579_   4730 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 4779
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_221596579_   4780 GCTGAAACTGGATCTGTTCCTTACACCTCATACAAAAATTAATTCAAGAT 4829
                         iv    ii    i iv v   i     vi             i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_221596579_   4830 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 4879
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_221596579_   4880 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGCCAAGGACTTCATGT 4928
                            v    ?i- v i -   iv   v v  vv i v   v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_221596579_   4929 CTAAAACAACAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 4978
                         v  vi   v        vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_221596579_   4979 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATACCATCAG---A 5025
                         i v  i   v v  i i   i  ii vv    i  --i  i    i--- 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA--CACTATCAAGAAA 690

  chr1_221596579_   5026 GTGAACAGGCAACCTACAGGATGGCAGAAAATTTTTGCAATCTACTCATC 5075
                              v  i     i    i    v       v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_221596579_   5076 TAACAAAGGGCTAATATCCAGAATCTACAATGAACTCAGTCAGATTTACA 5125
                          i i  i  i  vi          v  i  v      vvv  iv iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_221596579_   5126 AGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGA 5175
                          v     i     i     v  i?    i     i      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_221596579_   5176 CACTTCTCAAAAGAAGACATTTATGCAGCCAA-ATACACATGAAAAAATG 5224
                           i     v        i  vi viii     - vi          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_221596579_   5225 CTCATCATCACTGGCCAT 5242
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


3132 26.67 0.45 2.26  chr1_221602411_221606587.rev     2788  3672 (505)    L1M4_orf2#LINE/L1        1   869 (39)  

  chr1_221602411_   2788 TGGAAAGATATTCCATATTACATGAATTGCAAGAATCAATATTGTTAAAA 2837
                                    i    i  -    i    v    v i           i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTT-CATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr1_221602411_   2838 TGTCCCCACTACTCAAAGCAATGTACAGAGTCAATGCAGTCCCTATCAGA 2887
                           v vvi   v i    vii  v      v    i   i         i 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_221602411_   2888 GTACCAATGACATTCTTCACAGAAATAGAAAAACT-ATCCTAAAATTTAT 2936
                         i v   iivi v  i  ii       v  v  i  -           i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_221602411_   2937 ACTGAGCCACAAAAGACCCAGAATATCCAAAGCTATTCTGGGCAAAAAGA 2986
                          iv  ivii   ii           v     i v  ii  iiv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_221602411_   2987 ACAAAGCTGGAAGAATCACATTACCTGACTTTAAACTGTATCACAGAACT 3036
                               i    i  v     i v  ii i  i   viv  ii   i i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_221602411_   3037 ACAGCAACCAAAATAGCAAACTAGTCACATAAAAACAGACACATAGACCA 3086
                             i  i   i i  iiviv  v vi     ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_221602411_   3087 GTGGAACAGAAT-GAGAAATCCAGAAACGAATCCGTACATCTACAGTGAA 3135
                         i     i     -    i-        ii  i  i     i  ii  v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAG-TCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_221602411_   3136 CTCATTTTTGACCAAGGTGCCAAGAACATACATTGGAAAAAGGGCAGGTT 3185
                         i v     i   v i          v   v  v   ii    iii  vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_221602411_   3186 CCTCAACAAATGATGCAGGAAAAATTGGATATCTATATGCAGAAGAATAA 3235
                         ii          i   v  i v  i      ? i i     i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_221602411_   3236 AACTAGACTCCTATCTTTCGCCATATACAAAAATCAAATTAAAATGGATT 3285
                          ii i   i    i  iv i              i  v i         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_221602411_   3286 TCACACTTAAATCTGAGACCTCAAACTATTAAACTACTAAAAGAAAACGC 3335
                         v? v  i     v i   v  v       v     vi  i        ii
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_221602411_   3336 TGTGGAAATTCTCTATTTTATTAGACTGGGCAAAGATTTCTTGAGTAGTA 3385
                         v v? v  v   iii vviv  i ii i     v i      iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_221602411_   3386 CCTTATGAGCACAGACAACCACAGGAAAAATGGACAAATGGGATCATATC 3435
                          vii vi      ii    v v  i      i  i    v   iivi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_221602411_   3436 AAG-TTAAAAAGCTTTTGCACAACAAAGGA-ATCAACAAAATAATGAAGA 3483
                           i-       -      ii vv       - ii v   i v i    i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_221602411_   3484 GACAACCCACAGAATGGGAGAAAATACTTTTAAACTATCCATCTGACAAG 3533
                                                   i  vi   ii  vi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_221602411_   3534 GGATTAATAACTATTAATAGAATATACATGGAGTTCAAACAGCTCTATAG 3583
                            i vi  v i ------       i vi  ii  vv   i   v   i
  L1M4_orf2#LINE/    748 GGACTTGTATCCA------GAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_221602411_   3584 GAAAAAATGCAATAAAAATTTAATAATCTGATTTTAAAATGGGCAAAAGA 3633
                         v     i---- i   -------   i ii   ?v            i  
  L1M4_orf2#LINE/    792 TAAAAAG----ACAAA-------TAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_221602411_   3634 TCTGAATAGACATTTCTCAAAAGAAGACATACAAATGGC 3672
                          i                v        i           
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

Transitions / transversions = 2.05 (156 / 76)
Gap_init rate = 0.01 (10 / 869), avg. gap size = 2.40 (24 / 10)  


2924 27.31 0.99 0.99  chr1_221626912_221631041.rev     2732  3639 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221626912_   2732 TGGAGAAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATAAAAAC 2781
                             i i i  i     i        v      v i i   ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221626912_   2782 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATTAAAC 2831
                            v     v      v i  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221626912_   2832 TACCA-CTGACATTCTCCATAGAATTAGAAAAACT-ACTTTAAAATTCAT 2879
                          v   -   v -  i iiii    v v  v  i  - iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_221626912_   2880 ATGGAACCAAAAAAGAGCCCAAATAGCCAAGTCAATACTAAGCAAAAAGA 2929
                               viiv  ii  v  vi         iv    vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_221626912_   2930 ACGAATCTGGAGGCATCACACTACTTGACTTCAAACTATACTACAAGGCT 2979
                           i  vi      vv       v iii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_221626912_   2980 ACAGTGACCAAAACAGCATGGTGCTGGTACAAAAACAGACACATAGACCA 3029
                              i i   i    ii    i    i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_221626912_   3030 ATGTAACAGAACAGAGAACCCAGAAATAGAACCTCACACCTACAGCCATT 3079
                            v  i    iv    ii         i v  vi   ii  ii i  v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_221626912_   3080 TGATTTTCCACAAACATGATCAAAACAAG-CAACGGGGAAAGGATTTCCT 3128
                                 v    ivi  -i   i  v v-   i        i  vvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_221626912_   3129 ATTTAAGAAATGGTGCTGGGAGAA-TGGCTAGCCATATCTAGAAAAGTGA 3177
                         v  i  v              v  -   v  ?   i  vi i  i i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_221626912_   3178 AAGTGGAACCCTTCCTTACACCATATACGAAAATTAACTCAAGATGGAAT 3227
                          iv    v    v   i           i             i     vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_221626912_   3228 AAAGGCTTAAATCTAAAAACCAAAACTATAAAAACCCTAGAAGAAAATCT 3277
                          ?  i i     v   i i i            vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_221626912_   3278 AGGCA-ATACCAGTCAGGATATAGGCATGGGCAAAGACTTCATGAAAAAA 3326
                            ?i- v i -v  iv  iv v  vv i     v ii   v ii v vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_221626912_   3327 ATTCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGAGATCTAAC 3376
                          iv         vvv          v      v  i    vi  ii v i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_221626912_   3377 TGAACTAAAGAGCTTCTGCACAGCACAGCAAAAGAAACTATCATCAGAGT 3426
                         ii  v v  i i   i  ii vv  -----  i  v       vv i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCA-----AAGGACACTATCAAGAAAGT 692

  chr1_221626912_   3427 GAACAAACAACCTACAGAATGGGAGAAAATTTTTGCAATCTCTCCATCTG 3476
                            v i      i                 v       viiv vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_221626912_   3477 ACAAAGGGCTAATACCCAGAATTTACAAGGAACT--TA-AACACATTTAC 3523
                          i  i  i  vi  i       v  i  i     --  -   v  v v i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_221626912_   3524 AAGA-GAAAAAAAACTCCATTAAAAAGTGGGCAAAGGACATGAACAGATA 3572
                           i -  v   v   i v   ?    i           iv    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_221626912_   3573 CTTCTCAAAAAAAAGACATACATGCGCCCAACAAACATTTGAAAAAAACC 3622
                         i     v   i  -  i     vii v    i  i  iv      i vv 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_221626912_   3623 TCAACATTACTAATTGT 3639
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (149 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.38 (18 / 13)  


1017 28.33 12.26 4.17  chr1_221648087_221649977      563  1402 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221648087_    563 TGAAATAATATACCACATTAATAAAATCATAACATCTTAAAGGACTTAAC 612
                           i  vi    v   ii  v  ii -----------  ii i       i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGA-----------TTGGAAGACTTAAT 39

  chr1_221648087_    613 ATCATAATGATTTAAATACTCTAAACATTAATTTACGAATGGAAATGCAA 662
                           ii v v   vvv       ivv v   i  i   ii  vv  -i    
  L1M4_orf2#LINE/     40 ATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAA 88

  chr1_221648087_    663 TCTCAGTAAAATATTAAAAGGATATTTAGTTTGTTAATTTGCTTATTTTT 712
                           i -------   i    --- -iii  i vvi vv     vv vv  -
  L1M4_orf2#LINE/     89 TCCC-------TATCAAAA---T-CCCAGCTGCCTTTTTTGCAGAAATT- 126

  chr1_221648087_    713 GGGCAAGCTGGTCCTAAAGTTCACATGGAAA---AATGAGTC-----TAG 754
                         - i       i       i    i       ---  v iii -----   
  L1M4_orf2#LINE/    127 -GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr1_221648087_    755 CTAGAAAAATATTAAAAAGCAAGAGTAA---TGAAGGGGAGATATCCCTT 801
                          i i  v   v  i    iv    ii  ---  i   ivvv i iii ii
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr1_221648087_    802 TATGTATTAAGACATATAACAAAGCTTCAATAATTAAAACACTGTGGTAC 851
                         v  - - i  i  v  iv        v  i    i  i   v        
  L1M4_orf2#LINE/    226 AAT-T-TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr1_221648087_    852 TGGCTCATGAGTAGAAAAGCAAACCATTGGAACAGTAT--AGA------A 893
                             vi v ii    v vii i i  v     i  v  --   ------ 
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_221648087_    894 AATAGAACTATATGCTT-TGGGCA-TTTATT----------ATATCAAAA 931
                             i v i   iii  -   v  -  v   ----------i ii   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_221648087_    932 --ATCCA-TGGGGAA-GAATAGACTTTTTAATGAATGCTTTTGGGAAAAC 977
                         --  i  -       -      v     i  ii    v vi     v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_221648087_    978 TAAACAGCCATCAGGATAAAGA-TCAAGTTGCAACCATTGTC-CACATCA 1025
                          ii i ?   -  v vv     - v      -i   vi ii -    i  
  L1M4_orf2#LINE/    424 TGGATAKCCA-CATGCAAAAGAATGAAGTTG-GACCCCTACCTCACACCA 471

  chr1_221648087_   1026 TTTACTAGGATAAACTCTAAAAGGATAAAATAATTTAAATGTAA-----A 1070
                          v   v ii  v     v   v    v ? -i ii         ----- 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWA-GACCTAAATGTAAGAGCTA 520

  chr1_221648087_   1071 AAATT-TAAATGTACTT-GAAGAAA-CATA--TGT---CCTTTTT--TCT 1110
                            i -    vv -   -       -    --?  ---i   iv --i  
  L1M4_orf2#LINE/    521 AAACTATAAAACT-CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr1_221648087_   1111 TGGAGTACGGAA-GATCTTTAAAACTAAGACTCTAAATCTAGAAGCCACA 1159
                            iv  v v  - i i i v i -  v   v i   vvi v    v   
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACA 618

  chr1_221648087_   1160 AAAAAAAAGATTTATAAAT-GG------TCAAAAATACA---TTTTTTG- 1198
                            i    i  vv      -  ------      v  v ---    v  -
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_221648087_   1199 --------------------AAGTCAAAAGACAATTGATAAACTAGGGAA 1228
                         --------------------    v         iiv i i v -    i
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT-GGGAG 717

  chr1_221648087_   1229 AAAAT---TGTAACTCATATTACACATAG----CTTATCCTCTTAATATA 1271
                              ---  i  v      vv vv   i----   i vii vv      
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_221648087_   1272 TAAAGATTTTCTAGACATT---TGGGGAAAAAATCAACAG--------GA 1310
                               vi ii  v - i --- iivi    i iv  i i--------i 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACA-ACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_221648087_   1311 AAATGGGCAAAGGACATCAACAGATAGTTCTTGGAAAAAGAAATATGAAA 1360
                                       iv v  i   i v    ivi  i    v   ii  v
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_221648087_   1361 GTGCCT-TAAATATATGAAAATACACTCAACCCCACACGTAAT 1402
                          -   v-   ii i       v ii      vi  ????????
  L1M4_orf2#LINE/    867 G-GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.05 (46 / 908), avg. gap size = 3.00 (138 / 46)  


3247 22.81 2.68 5.46  chr1_221655696_221658849.rev     1730  2663 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221655696_   1730 TGGAAAGCTATTCCATGTTCATGGATTCCAAGAATCAATATTGTTAAAAT 1779
                                v   i               vv    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221655696_   1780 GTTCATATTACCCAAAACAATCTACAGATTCAATGCAGTCC-TATCAAAA 1828
                          viv   i v      vii              i   i   -        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221655696_   1829 TACCAATGACATTCTTCACAGAAATAGAAAAAACAATTCTAAAATTTACA 1878
                          v   iivi v  i  ii       v  v  ivii  i        i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_221655696_   1879 TGGTATCACAAACAACCCAGAATAGCCAAAGCTATCCTGAACAAAAAGAA 1928
                            v vii   ivi                i v   i    v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_221655696_   1929 CAAA-CTGGAGGAATCACATTACCTGACTTCAAATTATACCTCAGAGCTA 1977
                             -i       v     i v  ii i      viv   iv  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_221655696_   1978 TAGCAACCCAAATAGAATGGTCTTGGCAGAGAAATAGACACACAGACCAA 2027
                         i  i  i v i i  vi    vi     v iii       i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_221655696_   2028 TGGAAAAGACCAGAAAATAGACACACAGACCAATATCCATACAGACGAAC 2077
                              ------------    -------------  i-------------
  L1M4_orf2#LINE/    301 TGGAA------------TAGA-------------ATT------------- 312

  chr1_221655696_   2078 GGAACAAAACAGAAAACCCAGAAACAAATACACACACCTGTGGTGAACTT 2127
                         -----------  i ii       i   iv  i   ii i    v  i v
  L1M4_orf2#LINE/    313 -----------GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_221655696_   2128 ATTTTCAACAAAGGTGTCAGGAACGTAC--------------------TT 2157
                               i    i    i  i  v i v --------------------  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_221655696_   2158 CAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAAAC 2207
                            i              v         ?   i     i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_221655696_   2208 TAGACCCCTATCTCTTGTCATACATAAAAATCAAATAAAAATGGATTAAA 2257
                          i        i   viii    i i      i  v v         i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_221655696_   2258 GGCTTAAATCTAAGACCTCAAATTATGAAACTATTAACAAGAAAACATTG 2307
                          i i     v     v  v   i   i     v   i-          v 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG-AAGAAAACATAG 550

  chr1_221655696_   2308 GGGAAAATGTCTAGGACATTGGTCTGGGCAAAAATTTCTTGAGTAATACC 2357
                          ? v    v iiiv   v    vi i     vii      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_221655696_   2358 CCACAAGCACAGGCAACCAAAGCAAAAATGGGTAAATGGAATCGCAT-GA 2406
                            v       i     v    v      i i     v i iiv   -i 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_221655696_   2407 AGTTAAAAAGCTTCTGCACAGCAAAGGATGCAATCAACAAAGTGAAGAGA 2456
                          i       -   i  ii vv       ii v     v        i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_221655696_   2457 CAACCCACAGAATGGGAGAAAATATTTACAAACTACCCATCTGACATGGA 2506
                                                    i    ii ivi      i v  i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_221655696_   2507 ATTAGTAACCAGAATATATAAGGAGCTCAAACAATTCTATAGGAGCAAAT 2556
                          i v   v             i  i   vv    i  v   iv iv  iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_221655696_   2557 CTAATAATCCAAT-AAAAAGTGGACAAAAGATTTGAATAGACATTCCTCA 2605
                          v     i     -?    i   i    i                i   v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_221655696_   2606 AAAGAAGACTTAGAAATGGCAAATGGGTA-ATGAAAAGGTGCTCAAAATT 2654
                                 iv  v       v   ii i -        i       v  i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_221655696_   2655 ATTGATCAT 2663
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.75 (133 / 76)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 6.91 (76 / 11)  


3057 27.57 1.11 0.55  chr1_221662126_221668458     4938  5840 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221662126_   4938 TGGAAGAACATTCCATGCTCATGGGCAGAAAGAATCAATATCGTGCAAAT 4987
                              ii i  i     i      iiv i    v i     i  vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221662126_   4988 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCTTCAAGC 5037
                            v     v     iv i  i  i        i  v    iiv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221662126_   5038 TACCAGTGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAATTCATA 5082
                          v    ivi i  i  ii     v v  v  i--- --            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_221662126_   5083 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5132
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_221662126_   5133 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5182
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_221662126_   5183 CCATAACCAAAGCAGCATGGTACTGGTACCAAAACCAAGATATAGACCAA 5232
                          vi   i   ii   ii         i iv ii ivi v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_221662126_   5233 TGGAACAGAAC--AGAGCCCTCAGAAATGATGCCACATATGTCCAACTAT 5280
                              i    i--    i  --      i vv   i i  v viiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_221662126_   5281 TGGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT--TCC 5328
                          v   i  i     ivv  v   i v  vvv           i  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_221662126_   5329 TTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5378
                           -- i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_221662126_   5379 GAAACTGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5428
                            ii  i i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_221662126_   5429 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5478
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_221662126_   5479 CTAGGCA-ATACCATTCAGGACATAGGCATGGCCAAGGACTTCATGTCTA 5527
                         v    ?i- v i -   iv   v v  vv i v   v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_221662126_   5528 AAACAACAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5577
                         vi   v        vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_221662126_   5578 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTCAA 5627
                           i   v v  i i   i  ii vv    i  v    i  vv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_221662126_   5628 CAGGCAACCTACAGAATGGGGGAAAATTTTTGCAATCTACTCATCTGACA 5677
                         v  i     i          i      v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_221662126_   5678 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATCTACAAGAAA 5727
                          i  i  vi          v  i         vv    v  v i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_221662126_   5728 AGAACAAACAGCCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5777
                          ii     i i   v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_221662126_   5778 CTCAAAAGAAGACATTTTTGCAGCCAAAAGACACATGAGAAAATGCTCAT 5827
                            v        i  vivviii     v ii       i  i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_221662126_   5828 CATCACTGGCCAT 5840
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


2512 25.69 6.88 2.75  chr1_221687527_221689861      971  1842 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221687527_    971 TGGAAAAACATTCCATGGTCATGGATTGGAAGATTCGATACTGTTAAAAT 1020
                               i i  i     v               i ii   i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221687527_   1021 GGCCATACTGCGCAAAGCAAT-TACAGACTTAATGCTATTCCTATCAAC- 1068
                            v     v v    vii  -      i i  i  v  i        v-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221687527_   1069 TACCAGTGACATTTTTCACAGAATTAGAAAAAACT-ATTATAAAATTCTT 1117
                          v    ivi v     ii     v v  v  i-  -  iv        v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_221687527_   1118 A-GGAAA--CAA-------AAAAGAGCC----------TGAA-------- 1139
                          -     --   ------- i  v    ----------    --------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_221687527_   1140 -TGAAGCTGAAGGCATCATGTTACCCAATTTCAAACTATACTACAAGGCT 1188
                         -ii   i  i   vv   iii v            viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_221687527_   1189 ACAGTAACCAAAACAACATGATACTTATACAAATGCAGACACATAGACAA 1238
                                i   i   iii  i    vii i  ivii     i     iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_221687527_   1239 GTAGAGCAGAAT----AGCCCAGAAATAATACTGCACACTTACAACCATC 1284
                         i i  ii     ----  i          vv iii   i   iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_221687527_   1285 TGATCTTTGACAAAGTTGACAAAAAGTTGCCAAAGTTTGAAAAAATAAGC 1334
                             i  i     i v  v   i -----   ----  ----------- 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGA-----CCA----TT-----------C 379

  chr1_221687527_   1335 AGTGGCAAAAGGACTTCCTGTTCAATACATGATGTTGGGATACCTGGCTA 1384
                          i   vi    i ivvi  v     i v   i  i     i v    v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr1_221687527_   1385 GATGTATGCAGAAGATTGAAACTGGACCCCTTCCTTTCACGATATACAAA 1434
                         ?viii     i    v    ii         v   iv   v         
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr1_221687527_   1435 AATCAACTCAAGATAGATTAATGATTTACATGTAAAACTTGAAACTATA- 1483
                            i       i  i   i ?v  ii  v      i vi i        -
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr1_221687527_   1484 --------GAAGAAACC-TAGGA--AAATCATTCTGTATATGTGCCTGGG 1522
                         --------       v -    ?--     v iv  - iv vv vi i  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGG 578

  chr1_221687527_   1523 CAAAGATTTCAT-GATGAAGACACCAAAAGCAATTGCAATGAAACAAAAA 1571
                            v i    v -   - v             vvv    ii   v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr1_221687527_   1572 TT-GATAATTGGGACCT------AATTAAAGAGCTGCTGCACAGAAAAAA 1614
                         v -     v v    i ------       i -  vi  ii vvv   ii
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGG 676

  chr1_221687527_   1615 AGGCTATCAACAGAATAAGCAGATAACCTATAGAATTGGAGAAAATATTT 1664
                          vi       v i i i iv   i    i i     v             
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_221687527_   1665 GCAAACTGTGTATCCGATAAAAATCTAATATCTGGAATCCATAAGAAACT 1714
                              iii i    i     iiiv  vi    ii    vi    ii    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_221687527_   1715 TAAACAAATTGGCAAGAAAAAAACA--T--CCCCACTAAAAAGTGGGCAA 1760
                         ivv    v iiii  v     i   -- --   v i ?    i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_221687527_   1761 AGGATATGAACAGACACTTCTCCAAAGAAGATATACATTGAGCCAATAAC 1810
                              v    i     i                    vvvi        v
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_221687527_   1811 CATATGAAAAAATACTCATCATCACTAATTAT 1842
                           i       i  i    v     ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (137 / 83)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.50 (84 / 24)  


3079 24.57 1.07 4.06  chr1_221690702_221695302.rev     3175  4110 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221690702_   3175 TGGAAACACATTCCATGCTCATGGATGGGTAGAATCAATATTGTAAAAAT 3224
                               v i  i     i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221690702_   3225 GACCATACTGCCAAAAAAGCAATCTACAAATTCAACACAATTTCCGTCAA 3274
                          i v     v  v   vv --       i       i    ii ii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_221690702_   3275 AATACCA-CTATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTT 3323
                            v   -  ii -  i  ii     v v  v  ivii           i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_221690702_   3324 ATATGGAACCAAAAAAGAGCCCATATAGCCAAAGCAAGACTAAGCAAAAA 3373
                                 viiv  ii  v  viv         i   vvi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_221690702_   3374 TAACAAATTTGGAGGCAC-CATATTACTTGATTTCAGGCTATACTATAAG 3422
                         v      v       -  -  i i v iii      iiviv     i  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_221690702_   3423 GCCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGA 3472
                           i i   v i   i    ii         i    ii    i  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_221690702_   3473 CCAATGGAAAAATATAGAGAATCCAGAAATAAAGCCAAATACTTACAGTC 3522
                         i        v iv  v    i            v   v i i   ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_221690702_   3523 AACTGATATTTGACAAAGCAAATAGAAACATAAAATGGGGAAAGGACACC 3572
                           i    v  i     i vvivi ii v   vv           i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_221690702_   3573 CTACTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATATAGGAGAAT 3622
                           vi                   i  i   vv ?      ii ii     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_221690702_   3623 GAAACTGGATCCTCATCTCTCACCTTATATAAAAATCAACTCAAGATGAA 3672
                            ii    i  ii i   v    v    i      i       i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_221690702_   3673 TCAAGGGCTTAAATCTAAGACCTGAAACCATAAAAATTCTACAAAATATC 3722
                            ?i i i     v     v  i    i      v ii  v  i v v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_221690702_   3723 ATTGAAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAA 3772
                           v i?iv  vi    vv   v    v        v i    v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_221690702_   3773 GAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGCTGGGACTT-- 3820
                           vv         v v         iv   i   i   iv v      --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_221690702_   3821 ----AATTAAAGAGTTTTGCACAGCAAAAGGTACAGTCAGCAGAGTAAAC 3866
                         ----       i v     ii vv    i ii  vi   iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_221690702_   3867 AGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATTTGATGA 3916
                                       i           v  ii   vii   i  i    i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_221690702_   3917 AGGACTAATATCCAGAATCTACAACAAACTCAAGTGAATTAGCAAGAAAA 3966
                         i     vi          v  i  vi     -------   -   -----
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTC-------TTA-CAA----- 783

  chr1_221690702_   3967 AAACTAAACAATACCATCAAATTAGCAAGAAAAAAAACAACCAATCCCAT 4016
                         ---  v  i    ------------------    i    vi  i  v  
  L1M4_orf2#LINE/    784 ---CTCAATAATA------------------AAAAGACAAATAACCCAAT 812

  chr1_221690702_   4017 CAATAAGTGGGCTAAAGATATGAATAGACAATTCTCAAAAGAAGATATAC 4066
                         i? v  i     v  i   v          v     v             
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_221690702_   4067 AAATGGCCAACAA--ACATGAAAAAATGCTCAACATCACTAATTAT 4110
                                   i  --         i             ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 4.36 (48 / 11)  


3111 27.20 0.77 0.77  chr1_221706594_221716498      492  1399 (8506)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_221706594_   1399 TGGAAGAACATCTCATGCTCATGGAAAGGAAGAATCAACATTGTGAAAAT 1350
                              ii i   i    i       vv      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_221706594_   1349 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCTTCAAGC 1300
                            v     v     iv i  i  i        i  v    iiv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_221706594_   1299 TACCAATCACTTTCTTCACAGAATTGGATAAAACTACTTC-AAAGTTCAT 1251
                          v   iiii i  i  ii     v v  i  i-  iv i -   i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

C chr1_221706594_   1250 ATGGAACCAAAAAAGAGCCCCCATTGCCAAGTCAATCCT----AAGCCAA 1205
                               viiv  ii  v  vvv  v     iv     i ----   --  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG--AA 197

C chr1_221706594_   1204 GAACAAAGCTGGAGGCATCATGCTTTCTGACTTCAAACTGTACTACAAGG 1155
                                 i      vv   ii   i ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chr1_221706594_   1154 CTACAGTAACCAAAACAGCATGGTACGGGTACCAAAACAGAGATATAGAC 1105
                                  i   i    ii      v  i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chr1_221706594_   1104 CAATGGAACAGAATAGAGCCCCCAGAAATAATACCACACATCTACAACCA 1055
                                 i     v   vvi          vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

C chr1_221706594_   1054 TCTGATCTTTGACAAACCTGACAAAAACAGGAAATGGGGAAAGGATTCCC 1005
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chr1_221706594_   1004 TATTTAATAAATGGTGCTGGGAAAACTCGCTAGCCATATGTAGAAAGTTG 955
                          v  i  i              v    v v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chr1_221706594_    954 AAACTGGATCACTTCCTTACATCTTATACATAAATTAATTCAAGATGGAT 905
                           ii    i v  v   i   i v      v       i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

C chr1_221706594_    904 CAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAAT 856
                           ?    i       v   v       i      -    -         i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

C chr1_221706594_    855 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 807
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chr1_221706594_    806 AAACACCAAAAGTAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 757
                         vi          i vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chr1_221706594_    756 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 707
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chr1_221706594_    706 AATGCAACCTACAGAATGGGAAACAATTTTTACAATCTACCCTTCTGACA 657
                           vi     i           i v   v   i   vii iviv     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chr1_221706594_    656 AAGGGCTGATATCCAGAATCTACAAAGAAGTTAAACGAATTTACAAGAAA 607
                          i  i  vi          v  i      v ivv  i v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chr1_221706594_    606 AAAAATCAAACAGCCCCGTCAAAAAGTGGGCAAACGATATGAACAGACAC 557
                           i --    i i   vi i?    i        v   v    i     i
  L1M4_orf2#LINE/    796 AAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

C chr1_221706594_    556 TTCTCAAAAGAAGAAATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 507
                              v        v  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

C chr1_221706594_    506 ATCATCATTGGCCAT 492
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  

2903 26.44 1.44 1.00  chr1_221706594_221716498     8509  9412 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221706594_   8509 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 8558
                               i    i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221706594_   8559 GGCCATACTGCCCAAAATAATTTATAGATTCAATGCTATTCCCATCAAGC 8608
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221706594_   8609 TAC-AATTGATTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTC 8656
                          v - ii  vi   i  -i     v v  v  i--  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr1_221706594_   8657 ACATGAAACCAAAAATGAGCCTGTATAGCCAAGAGAGTCCTAAGCAAAAA 8706
                          i   i  viiv  iv  v  v v        i v i  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_221706594_   8707 GAGCAAAGCTGGAGGCATCACACTGCCTTACTTCAAACTGTACTACAAGG 8756
                           i     i      vv       v  iv i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_221706594_   8757 CTTACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGATATATAGA 8806
                           -       iv  i    ii         i iv ii i   i       
  L1M4_orf2#LINE/    248 CT-ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_221706594_   8807 CCAATGGGACAGAACAGA-AGCCTCAGAAATAACACCACACATCTACAAC 8855
                         i      i i    iv  -  i -         vv   i    i  iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chr1_221706594_   8856 CAGCTGATCTTCGAGAAACTTGACAAAAACAAGCAATGGGGAAAGGATTC 8905
                           ii    i     v  ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_221706594_   8906 TCTATTTAATAAATGATGTTGGGAAAACTGGCTACACATATGCAGAAAAC 8955
                            v  i  i     i  i     v      v  ?v  i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_221706594_   8956 TGAAACTGGACCCATACCTTACACCTTATACAAAAATTAACTCAAGATGG 9005
                             ii       v     i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_221706594_   9006 ATTAAAAACTTAAACGTCAGACCTAAAAAACATAAAAAACCCT-AGAAGA 9054
                           i ? i  i    i  v   v      -- -  v     i  -      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAA--C-TATAAAACTCTTAGAAGA 542

  chr1_221706594_   9055 AAACCTAAGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCACA 9103
                             v  i ?i- v i -   iv   v v  vv i     v ii   vi 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_221706594_   9104 ACTAAGACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGTA 9153
                         iv  v             vvi          vv     v  i    v v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_221706594_   9154 TCTAATTAAACCAAAGACCTTCTGCACAGCAAAAGAAACTATCATCAGAG 9203
                         ii v  i   viv  i v   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_221706594_   9204 TCAACAGGCAACCTACAGATTGGGAGAAAACATTTGCAATCTGTGCCTCT 9253
                          v  v  i     i     v          i        viii iiv   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_221706594_   9254 GACAAAGGGCTAATATCCAGAATCCACAAGGAACTTAAACAAATTTACAA 9303
                           i  i  i  vi          vi i  i     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_221706594_   9304 GAAAAAGA-AAA----CCA-TCAAAAAGCAGGTAAAGGATATGAACAGAC 9347
                         v       -   ----   - i?    iii  i       v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_221706594_   9348 ACTTTTGAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAAGC 9395
                          i  i vv        i  vi viii     i  --         i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_221706594_   9396 TCATCTTCACTGGTCAT 9412
                            v v   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.38 (22 / 16)  


 441 23.96 1.04 11.98  chr1_221727496_221733663.rev     2409  2600 (3568)    L1M4_orf2#LINE/L1        1   171 (737)  

  chr1_221727496_   2409 TGGAAAAACCTTCTATGCTGATAGATAAGAAGAATCAATATTGTGAAAAT 2458
                               i iv i i   i v  i   vi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221727496_   2459 GACCATGCTGCCCAAAGCAATTTATAGAT-CAATGCTATTCCTATTAAAC 2507
                          i v  i  v      vii  i  i    -   i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221727496_   2508 TACCATTGACATTCTTCACAGGTATAGGGTTCAATTTGACAAGAAGAGCT 2557
                          v   vivi v  i  ii   -----------  v        -----  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG-----------AAATTGACAAG-----CT 134

  chr1_221727496_   2558 AACTATCCTAAA-TATATGTGCACCCAATACAGGAGCACCCAGA 2600
                         i ---       - vi  i  v ---   i  i i -       
  L1M4_orf2#LINE/    135 GA---TCCTAAAATTCATATGGA---AATGCAAGGG-ACCCAGA 171

Transitions / transversions = 1.71 (29 / 17)
Gap_init rate = 0.04 (7 / 171), avg. gap size = 3.57 (25 / 7)  

 741 28.23 0.00 0.00  chr1_221727496_221733663.rev     4534  4742 (1426)    L1M4_orf2#LINE/L1        1   209 (699)  

  chr1_221727496_   4534 TGGAACAACATTCTATGCTCATGGATAAGAAGAATCAATATTGTGAAAAG 4583
                              vi i  i i   i        vi     v i        v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221727496_   4584 GACCATACTGCCCAAAGCAATTTAGAGATTCAATGCTATTCCTATTAAAC 4633
                          i v     v      vii  i  v        i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221727496_   4634 TACCATCGACATTCTTCACAGAACTAGAAAAAAATACTTTAAAATTCATA 4683
                          v   v vi v  i  ii     v v  v  ivvv iii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_221727496_   4684 TGGAACCAAAAAAGAGCCTGAATAGCCAAACCAATCCTATGAAAAAAGAA 4733
                              viiv  ii  v  v           v     i ivi   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_221727496_   4734 CAAAGCTGG 4742
                              i   
  L1M4_orf2#LINE/    201 CAAAGTTGG 209

Transitions / transversions = 1.19 (32 / 27)
Gap_init rate = 0.00 (0 / 209), avg. gap size = 0.00 (0 / 0)  

2275 24.96 4.16 1.04  chr1_221727496_221733663.rev     5005  5677 (491)    L1M4_orf2#LINE/L1      215   908 (0)  

  chr1_221727496_   5005 TCACACTGCCCAACTTCAAACTATACTACAAGGCTACAGTAACCAAAACA 5054
                                v     i      viv        i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_221727496_   5055 ACAAGGTACTGGCACAAAAACAGACACAGAGACCAATGGAATGGAATAGA 5104
                         iiiv          i  ii i     i v   i         i    v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_221727496_   5105 GAACTCAGAAATAAGATTGTACATCTACAACCATCTGATCTTTGACAAAT 5154
                           iii         iviii     i  iiii  vi    i  i     iv
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_221727496_   5155 GTGACAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGC 5204
                            v   i v  vv            i  vvi  v  i  i         
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_221727496_   5205 TGGGAGAATTGGCTAGCCATATGCAGAAAACTGAAACTGGACCCCTTCCT 5254
                              v  i   v  ?   i     i  i v    ii         v   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_221727496_   5255 TACACGTTATACAAAAATTAACTCAAGATAGATTAAAGACTTAAATGTAA 5304
                         i    vv                   i  i   i ?    i         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_221727496_   5305 AACCAAAAACTATAAAAACCCTAGAAGAAAATCTAGGCAAATACCATTCA 5354
                         i v v            vi i          iv    ?iv v i -   i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCG 563

  chr1_221727496_   5355 GAATATAGGCACGGGCAAAAATTT------TATGACAAAAATTTGAAACG 5398
                         vi iv v  vvii     vii   ------       vv  ----  i i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA----AAGCA 609

  chr1_221727496_   5399 CAATTGCAACTAAAGCAAAAATTGACAAATGGGATCTAATCAAACTAAAG 5448
                            --     v    v      v  i    v   ii v      v v  i
  L1M4_orf2#LINE/    610 CAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_221727496_   5449 AGCATCTGCACAGCAAAATAAGCTATCATTAGAGTGAACAGACAACCTAC 5498
                          i v i  ii vv    iv vi      vv i      v        i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_221727496_   5499 AGAATGGGAGAAAATTTTTGCAGTCTATCCATCTGACAAAGGTCTAATAT 5548
                                        v      ivii  vi      i  i  v  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_221727496_   5549 CCAGAGTCTACAAGGAAGT--TA-GGCTGATT--TAGGAGAAAAAAAAAC 5593
                              i v  i  i   v --  -ii  v v --  ii ii v   v   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_221727496_   5594 ---ATTAAAAAATGGGCAAAAGACATGAACAGATACTTCTTAAAAG---- 5636
                         ---   ?             i  iv    i   i i    iv    ----
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_221727496_   5637 --------TGGCCAACAA--ACATGAAAGAAAGCTCAACATCACTGATCA 5676
                         --------       i  --        ii v           ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_221727496_   5677 T 5677
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.52 (99 / 65)
Gap_init rate = 0.01 (10 / 694), avg. gap size = 3.50 (35 / 10)  


2746 25.22 2.12 1.00  chr1_221756078_221757877.rev      501  1301 (499)    L1M4_orf2#LINE/L1       48   857 (51)  

  chr1_221756078_    501 GATGACCATACTGCCCAAGC-AATCTACAGATTTAATGCAATTCTTATAA 549
                             i v     v     ii-i           i  i     i i   v 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_221756078_    550 AAAATATCAA-TGTCATTTTTCACAGGG-TTAAAAAA---ATACTAAAAT 594
                            - vi  i-  i -     ii   ii-  i v  i---  v       
  L1M4_orf2#LINE/     98 AAA-TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_221756078_    595 TTATACGGAA-T-CAAAGACAGACT--GAAGAGCCAAAGCAATCCTAAGC 640
                          i   i    - -   i ---   i--   v       i     i i iv
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGG---GACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_221756078_    641 AAAAAGAACAAACTTAGAGGCATCACATTACCCAACTTCAGATTATAATA 690
                           i         v  i    vv     i v     i    i viv  v  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_221756078_    691 CAAGGCTATAGTAATCAAAACAGGATGGTACTGGTATAAAAGTAGACACA 740
                            i    i         i    vi         i    iii      i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_221756078_    741 TAGATCAAAGGAACAAAACAGAGAACCCAGAAATAAAGCCAAATACTTAC 790
                                 v    i i  iv    ii           v   v i i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_221756078_    791 AACCAACTGATCTTCGACAAATCAGACAAAAACATACACTGGGGAAATA- 839
                         iii   i    i        ivvv v   i v   v  v        v -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_221756078_    840 CACTCTATTCAA-AAATGGTGCTGGGAAAATTGGATAGCCACATCATATA 888
                         i v   v     -              v  i      ?      ---ii 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT---GCA 439

  chr1_221756078_    889 GAAGAATGAAACTGGATTCTTATCTCTTACTGTGTGCAAAAATGATCTCA 938
                         i         ii    ii i  i   vi  ii i i       v v    
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_221756078_    939 AGATGGATTAAAGACTTAAATGTAAGACCTGAAACCATAAGAATTCTAGA 988
                          i      i ?    i           v  i    i    i v ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_221756078_    989 AAAAAACCTAAGAAAAACTCTTCTGGACATTGGCCTAGGCAAAGAATTTA 1038
                          i     v  i ?iv  v     vv   v    vi       v iv  iv
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_221756078_   1039 TGATTAAGACACCAAAGGCAAATGCAACAAAAACTGAAATAAATAAATGG 1088
                          iiv  v         i   v v         ivvi     i      v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_221756078_   1089 AACCTAATTAAACTAAGAAGCTTCTGCACAGCAAAAGAAATAATAAACAG 1138
                         i  i v  i   v v i  i   i  ii vv    i  v iv  v  v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_221756078_   1139 AGTACACAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCAT 1188
                            iv v        i                          ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_221756078_   1189 CTGACAAAGGACTAATATCCAGAATCTACAAGAAACTCAAACAAATTAGC 1238
                             i  i     vi          v  i  ii     vv    v i ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_221756078_   1239 AAGAAAAA---AAA-AACCCA-TTAAAAGGCAGGCAAATGACATGAACAG 1283
                           v     ---   -      -  ?   iiii      v  iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_221756078_   1284 CCACTTCTCAAAAGAAGA 1301
                         v  i     v        
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGA 857

Transitions / transversions = 1.68 (124 / 74)
Gap_init rate = 0.02 (16 / 810), avg. gap size = 1.56 (25 / 16)  


 414 22.12 0.00 0.00  chr1_221785763_221787920.rev      394   497 (1661)  C L1M4_orf2#LINE/L1   (0)   908   805  

C chr1_221785763_    497 AACCCCATAAAAAAGTGGGCAAAAGACATGAACAGACACTTTTCAAAAGA 448
                              v  v?    i        i  iv    i     i  i  v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

C chr1_221785763_    447 AGACATACATGTAGCCAACAATTATATGTTAAAAAGCTCAACATCACTGA 398
                            i     vi i     i  vi i   vv  i v           ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

C chr1_221785763_    397 TAGT 394
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.00 (0 / 104), avg. gap size = 0.00 (0 / 0)  

3251 22.82 1.51 3.77  chr1_221785763_221787920.rev      739  1667 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_221785763_    739 TGGAAAGACATCCCATGTTCATGAATCAAAAAAACTAATATTGTTAAGAT 788
                                 i              i  iii  i vi               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_221785763_    789 GACCATACTACCTAAAGCAATCTATAGATTTGTTGCAATCTCTG-AAAAA 837
                          i v     v  i   vii     i     iivi      i  i-v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_221785763_    838 TGCTAATGATATTCTTCACAGAAATAGAAAAA--AATTCCTAAAATTCAA 885
                          v i iiviiv  i  ii       v  v  i--i  -           v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chr1_221785763_    886 ATAGAACCACAAAATATCTCAAAAATCCAAAGCAATTCTGAGCAAAAAGA 935
                           i   vii   iiv i ivi  v v     i    ii   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_221785763_    936 ACAAAATTGGAGGCATCACACTACCAGACTTCAAAATACATTACAAAGCT 985
                              i       vv       v  vi i       ivi i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_221785763_    986 ATAGTAACCAAAACAGCATGGTATGGGAACAAAAACAGACACATAGACCA 1035
                          i     i   i    ii     iv  v i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_221785763_   1036 ATGGAATAGAATAGAGTACCCAGAAATTAATCCATGTATCAATGGCCAAC 1085
                                     v   vii        v  i    ii  iv    i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_221785763_   1086 TCATTTTTGACAAATGCACTGAGAACATACAATGGAAAAAAGTCAGTCTT 1135
                          v     i     iv ii ii   v   v      ii   iivi      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_221785763_   1136 --CAATAAATGGTGCTGGGAAAGTTGAATATCCATATATAGAAGAATGAA 1183
                         --   i              v ii  i   ?   i  ii i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_221785763_   1184 AATAGACCCCCACCTCTCACCCCATCCAAGAATCAACTCAAAATTAATTA 1233
                         iv i      i     v    vi  v   i   i          vi  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_221785763_   1234 AAGAGCTAAATGTAAGACCTGAAACTATAAAACTACTGGAAGAAAACATA 1283
                         ?   v            v  i             vi i            
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_221785763_   1284 AGGG-AAATGCTTCAGGACATTGGTCTTGGAAAAGAATTTATAAATAAGA 1332
                         i ? -    -    iv   v    vi v  v  v iv  iv  i   v  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_221785763_   1333 CCTCAAAAGCACAGGCAACAAAAGCAAATATAAACAAATGGAATTATATC 1382
                          vi          i          v   v   i i    v i i vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_221785763_   1383 AAA-CTAAAAAGCATGGTAAATTTCCTTCTGTACAGCAAAGGAAACAAT- 1430
                            -i      --------------   i   i vv       v  v  -
  L1M4_orf2#LINE/    649 AAAATTAAAAA--------------CTTTTGTGCTTCAAAGGACACTATC 684

  chr1_221785763_   1431 -AGAA--TGAAAAGACAAACTACAGAATAGGAGAAAATATTTGCAAATGA 1477
                         -    --           v i       i                   v 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_221785763_   1478 TTCATCCAATAGAGGATTCATATCTAGAATATACAAGGAACTCAAACTTA 1527
                          vi   ii   ii   i ii    i        i  i      ----   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC----TTA 780

  chr1_221785763_   1528 ACAGCAAAAACAAAAAATAAAGAACGAAAAACAAAACAAAACCTGATTAA 1577
                         -  i -----iv  v      ------  i     v---    ii   ? 
  L1M4_orf2#LINE/    781 -CAAC-----TCAATAATAAA------AAGACAAAT---AACCCAATTWA 815

  chr1_221785763_   1578 AAAATGGGCAAATGATGTGAACAGATATTTCTCAAAAGAAGACATACAAA 1627
                                     v   v    i   i       v        i       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr1_221785763_   1628 TGGCCAAAAAA---ATGAATAAATGCTCAATATCACTAATTAC 1667
                                v  i---     v i        i    ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (136 / 72)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.06 (49 / 16)  


3213 26.77 1.00 0.66  chr1_221805136_221811747.rev     5218  6121 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_221805136_   5218 GGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCAGGAAAATG 5267
                              i i  i     i        v      v i     iivv  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_221805136_   5268 GCCATACTGCTCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGTT 5317
                           v     v i    v i  i  i        i  v  i  i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_221805136_   5318 ACCA-TTGACTTTTTTTCACAGAATTAGAAAAAACT-ACTCTAAATTTCA 5365
                         v   -i  v       --i     v v  v  i-  - ii     v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT--GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_221805136_   5366 TATGGAAC--CAAAAAACAGCCTGTATATCCAAGACAATCCTAAGCAAAA 5413
                                v--   iii  --  v v   v    i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_221805136_   5414 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAAGTATACTACAAG 5463
                                  i      vv    i  v  ii i      iiv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_221805136_   5464 GCTACAGTAACCAAAACAGCATGCTACTGGTACTAAAACAGATATATAGA 5513
                                   i   i    ii  v      i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_221805136_   5514 CCAATGGAACAGAACAGAGGCCTCAGAAATAACCCTACACATCTACAACC 5563
                         i        i    iv   ivii         v  i i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_221805136_   5564 ATCTGATCTTTGACAAACTGGACACAACCAG-CAATGGGGAAAGGATTCC 5612
                          vi    i  i     ivvv v  vi    v-            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_221805136_   5613 CTATTTAATA----GTGTTGGGAAAATTGGCTAGCTATATGCAGAAAACT 5658
                           v  i  i ----   i     v  i   v  ? i i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_221805136_   5659 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGGTGGA 5708
                            ii         v   i     v                   ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_221805136_   5709 TTAAAGATTTAAATGTAAGACCCCAAACCATAAAAACCCTAGAAGAAAAC 5758
                          i ?   ii           v iv    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_221805136_   5759 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5808
                         v    ?i v viv   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_221805136_   5809 AACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5858
                         i            vvv          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_221805136_   5859 TTAAACTAAAGAGCTTCCGCACAGCAAAAGAAACTATCATCAGAGTGAAC 5908
                          i   v v  i i   ii ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_221805136_   5909 AGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTATCTGTTTGACAA 5958
                           i  i  i                 v       vii  v i i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_221805136_   5959 AGAGCTAATATCCAGAATCTGGAAGGAACTTAAAGAAATTTACAAGAAAA 6008
                         i ii  vi          v iv  i     ivv v  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_221805136_   6009 AAACAAACGACCTCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTT 6058
                          i     ii   iv  i?    i            v    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_221805136_   6059 TCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAAGCTTAT 6108
                           v        i  vi vi       i  i  i       i v-   i v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAA 895

  chr1_221805136_   6109 CATTACTGGTCAT 6121
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 1.67 (15 / 9)  


 979 29.61 12.01 3.28  chr1_221866045_221867873      515  1338 (491)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr1_221866045_    515 CCATGTTC-TTTATGGGAAGGCTTCCCATATCAT--AACTATCAATTCTT 561
                                 - vv  v     i   v--    ii -- iv iv    v  i
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTA--ATATTGTTAAGATGGCAATACTC 60

  chr1_221866045_    562 CCAAAATTAATAATCAGATATAATGCAGTTCCAATTAAAATCCTA----- 606
                           v     i  vvv     vi  i   i i  v  i       i -----
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr1_221866045_    607 -----TTAGAGAAGTTT-CAGAATTAAT---AAAATTCATATGGAAGAAC 647
                         -----  iv    i  v-  - ii i  ---               ivi 
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATATGGAAATGC 159

  chr1_221866045_    648 AGATGCTGAAGAATAAGCTAGGA--ATGT--ACAAAAAAGAAAAATCCTG 693
                          iiv vivv      -  i ii --  v -- v   i     v  vvi  
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATA-GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_221866045_    694 AAAGGGTCCTCCTTCACCAGATATCAAAACATGGTAAAAATCCACTATAC 743
                         i i iv  viv    -   -  v       v iv  v   v i  vi  v
  L1M4_orf2#LINE/    209 GAGGACTCACACTTC-CCA-ATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_221866045_    744 TAAAATCAATATTGT-TTGGCAGAGAAGTAGACA-ATAAATCGGTGGGAC 791
                          v  iv  i i v  -i     v iiii      -   i   ii   i i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_221866045_    792 ATAGTTGAGGGTGCAAAAAT----CTAAGTTTTTATGAGATT--TTAATA 835
                          v i     i  v  i    ---- i viiv      i-- i--  i  v
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG--TCAATTGATT 354

  chr1_221866045_    836 TTTGACACAGGT---AATAT--TTCAACTGAGGAAAAAG--GGATTTTCA 878
                           i    vi   ---  v i--     -  i     i i-- vv      
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCA 403

  chr1_221866045_    879 AAAAGTAAATGATACTGGCACAACTGGCCATCCAGCTGGAAGAAAAGTAC 928
                          ----i     i i    v        vi ?   vv  v  i i  vv -
  L1M4_orf2#LINE/    404 A----CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA- 448

  chr1_221866045_    929 TAGTT---CCTTTATCTTATATCCTATATAAAAATAAATTCCCGAATGGA 975
                         -    ---  ii  i  i i i v    i      v  i  v-i      
  L1M4_orf2#LINE/    449 -AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA-AAATGGA 496

  chr1_221866045_    976 ATA-AAATTTAAATGTA-----TAACAATACAAATAACC---AAAATAAA 1016
                         vi - i ii        -----   v v  i   --  i--- i  v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA--ACTCTTAGAAGAAA 544

  chr1_221866045_   1017 TC-TAGGAGATTACATGTACA--ATCTTGGAGTTGGGAACAA--GT---- 1057
                         v -    ? --  v  v v i-- i     -   i  --   --  ----
  L1M4_orf2#LINE/    545 ACATAGGNG--TAAATCTTCGTGACCTTGG-GTTAGG--CAATGGTTTCT 589

  chr1_221866045_   1058 --AACCCGA-ATTGAAAACCCAGAACCATAAAAGAAAAGATAGGCATATT 1104
                         --i ivi  - iii   i v  - i v i         i    ii v   
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_221866045_   1105 TGATTACA--------AAAAACTTTTATATGGTAAATGG---TGGCAAAA 1143
                         v  i v  --------          i iivvi   v i--- iv   i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_221866045_   1144 TAAAGTCAATGGACAAATGCCAGATTTAGGATAA------TGCAAATGA- 1186
                         --    v  vi     vivv    v -i   v  ------       v -
  L1M4_orf2#LINE/    689 --AAGTGAAAAGACAACCCACAGAAT-GGGAGAAAATATTTGCAAATCAT 735

  chr1_221866045_   1187 ----CTGACAGAGAGTTAATATCTGTGACATACAAAGAGCTCTTATCTAT 1232
                         ----    i ii iii vi    iivi i   i     i      ivvv 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_221866045_   1233 TAACAAGAAAAAGACCAACAAGCCAAAGGAAAAACAGGC---GG---TGT 1276
                         i  i  v        v  i  v    vv?     ii   ---  ---  v
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_221866045_   1277 ATAGA-----------GGATTGTACTTAAATGACCAACGGACATAAGAAA 1315
                              -----------i  vvi  ivi     i    iiii  i v    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_221866045_   1316 AGATGCTCAAAATAACCAGTACT 1338
                                   v  v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (140 / 101)
Gap_init rate = 0.05 (47 / 896), avg. gap size = 2.68 (126 / 47)  


 876 15.44 2.01 0.00  chr1_221949539_221953121      500   648 (2935)    L1M4_orf2#LINE/L1      144   295 (613)  

  chr1_221949539_    500 ATTCATGTAGATGTTCAAGGGACGCAGGATAGCCAGAACAATCCTGAAAA 549
                               i i  vi v        v   i       i       i      
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_221949539_    550 AGAA---CGAAGTTGGAGGACTCACACTTTCTGATTTCAAACCTTACTGC 596
                             --- i                    i ii        v      i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_221949539_    597 AAAGCTGCAGTAATCAAGACTGTGTGATCCTAGCATTAGAATAGAGATAT 646
                               i             v     i v  i    v  i     v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_221949539_    647 AG 648
                           
  L1M4_orf2#LINE/    294 AG 295

Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.01 (1 / 152), avg. gap size = 3.00 (3 / 1)  

1107 18.91 8.82 1.26  chr1_221949539_221953121      942  1179 (2404)    L1M4_orf2#LINE/L1      280   535 (373)  

  chr1_221949539_    942 AAGAATAGAGATATATAGATAAATGGAATGGAATTGAGAGTTCAGAAGCA 991
                            i     --i        v        i           i     ii 
  L1M4_orf2#LINE/    280 AAGGATAGA--CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_221949539_    992 CATTCTCACATTTACAGCCAATTAATTCTTGACAAGGATGCCAAGAC--- 1038
                         v ii vi       ii i     i   i i       i         ---
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_221949539_   1039 --AAT----------------TTTCAATAAATGGGGCTGGGACAACTTAG 1070
                         --   ----------------      i      v            -i 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT-GG 426

  chr1_221949539_   1071 ACATCCACGCATAAAAGAATGAAGTTAGAACACTGCCTCACCTCATACAC 1120
                          i ?    iiii              i  v v  i      vi    i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_221949539_   1121 AAAAATTAACTTAAAATGGATCAAAGACTTAAATATAAGAAGTAAAATTA 1170
                                    i           ?    i     i     iv     i  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_221949539_   1171 TACACTTCT 1179
                           v vi   
  L1M4_orf2#LINE/    527 TAAAACTCT 535

Transitions / transversions = 3.30 (33 / 10)
Gap_init rate = 0.02 (4 / 256), avg. gap size = 6.00 (24 / 4)  

1258 16.93 2.76 0.79  chr1_221949539_221953121     2422  2675 (908)    L1M4_orf2#LINE/L1      547   805 (103)  

  chr1_221949539_   2422 ATAGACGTAAATTTT---GACATCAAGGTAGGCAATGGTTTTTAAAACAT 2468
                             i?      i  ---   v iii v             i v i i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_221949539_   2469 GACACCAAAAGTACAAGCAACCAAAGGAAAAACATGGATAAATTGGGCTT 2518
                                    i         -   i      -  i          i   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAAC-AAAAGAAAAA-ATAGATAAATTGGACTT 644

  chr1_221949539_   2519 CGTTCAAATTAAAAACTTTGGTGTTTTAAAAGACACTATTAAGCCAGTGA 2568
                          i iv              v   i  i   i        i   vv     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_221949539_   2569 AAAAACAACCCACAGAATGG-AGAAAAGTTTTGTAAATCATACGCCT--- 2614
                            i                -      vv    i        iii  ---
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_221949539_   2615 AAGAGACTTGTCTCTAGCATATATGAAGAACTCTCACAAACCAATAATAA 2664
                            i       v  i  v      i         i    vi         
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_221949539_   2665 AAATATAAATA 2675
                            v i     
  L1M4_orf2#LINE/    795 AAAGACAAATA 805

Transitions / transversions = 2.23 (29 / 13)
Gap_init rate = 0.02 (5 / 259), avg. gap size = 1.80 (9 / 5)  

 574 16.39 1.64 1.64  chr1_221949539_221953121     2970  3091 (492)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr1_221949539_   2970 AATAATAAAAATAAATAAATATTCTAATTTAAAA-CGGGCAAGGGATCTG 3018
                                    --i i     vi i    ?    -i      i    i  
  L1M4_orf2#LINE/    787 AATAATAAAAA--GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_221949539_   3019 AATAGACGTTTCT-TAAGGAAGATACACAAATGGTCAATGAGTACATGAA 3067
                                i     -i  i       i        i    i  i       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_221949539_   3068 AAGCTGCTGAACACCGTTAGCCAT 3091
                            v    v    i i????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 5.33 (16 / 3)
Gap_init rate = 0.02 (3 / 122), avg. gap size = 1.33 (4 / 3)  


1397 29.57 9.86 2.33  chr1_222050395_222052153.rev      502  1272 (487)    L1M4_orf2#LINE/L1       58   886 (22)  

  chr1_222050395_    502 CTCCTCAGATTGATATGTTAGCTTTCATGCAACC----TCAAAGTCCCCA 547
                             i  i      v ii-  v  iv i    i ----     i    vi
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTAC-AGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_222050395_    548 AAATTTCTTTGGTAGAAACTGATAATCAGAATGTAAAACT-AGCTGCACA 596
                         vviii i   v i     i   i  v v  viv     i - vv  v v 
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_222050395_    597 --CAAAGGACTGAGAAGAGCCAAAGCAATTTTGAAGAATGA-AACA---- 639
                         --   i    iv    v       i    i     i  vi -    ----
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_222050395_    640 -GGAAGAC--ACACT--CTAATGGTCATCTAGATTTCGTATAAAGCTACA 684
                         -   i   --     -- i   v-   --- i i  vv  i         
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATT-TCA---AAACTTACTACAAAGCTACA 252

  chr1_222050395_    685 ACAGTTAAGACATTGTAGAGTTGGCAAAA----AGGCATATTGATC--TG 728
                         ii i i      v   i vii     v  ----  i     v    --  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_222050395_    729 ---TAGG--TGA--------AAATAGAGCC------TTATAGACACTTGA 759
                         ---   i--   --------     i v  ------    i v  v    
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_222050395_    760 TTT---AT----GTGCTGCAGGCAAACC--TGC----AGCACAGT----- 791
                            --- i----    ii-  i v vi --  v----  v i   -----
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_222050395_    792 -----GATAGTGCTGGATCATTTGGACAGCCATATTGAAACAAATAGCAA 836
                         -----i  i       iv  vi    i ?   i  vv   vi   i--  
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG--AA 449

  chr1_222050395_    837 ACTTGATCCCTACCTCACACCATAGGCACAGATCAATTCCAGTTGGATTG 886
                         ii v  i                 vi  v i  i  i  v iv     ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_222050395_    887 GGGATAGAAATATGAAAGGTAAAATAATAAAGCTTCTACAAGATAATATG 936
                         ?i  ivv    i i i  v     iv     i  ii  v    v  i  i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_222050395_    937 GGACAATATTTTCATGACCTTGTGATTGAGAAACA-TTTGTTAAACAGGG 985
                           ?vv v  i   i        - i  ii v  ii-   v   i i v i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_222050395_    986 CACTAAA-GCAGTAACTATAAAGGAAAAGATTGCTAATTTGAACAGAATC 1034
                            i   -   vv i v i   i     i  v v   v   i  vvv   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_222050395_   1035 AAAGTGAAGAACTTACATCCATCAA--GACACCGTTAAGA--GTGAAAAG 1080
                            i v  i     vii v v    --     ii i    --        
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_222050395_   1081 GCGATTCATAGAATGGCATAAGATATATGCA--TCACAGATAACCAACAA 1128
                         i i ii  i       v v  i    v    --   i v  -- ii i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT--CTGATAA 746

  chr1_222050395_   1129 TGATATCATATCTAGAATATATAAAGGGCT--TAGAAATCAAAGAAGAAA 1176
                         v ivv ii    i             ii  --  v  v    -v  v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA-TAATAAA 795

  chr1_222050395_   1177 AAAGTTGACAACTCAGGAGAAAAATGGACAAGAGACTTAATTCAAGCAGA 1226
                           iiivi i   i  ivv?        i   ii  i  i v -----   
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT-----AGA 840

  chr1_222050395_   1227 TATT-CACAAAAAGAGACATCTAGATACCTAATAAAAATCAGGGAAA 1272
                         i   - v v   ii   i  vi i  iv i     iv -  v i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA-CATGAAAA 886

Transitions / transversions = 1.55 (136 / 88)
Gap_init rate = 0.04 (35 / 829), avg. gap size = 2.69 (94 / 35)  


3377 21.33 2.78 3.67  chr1_222754034_222757472     2039  2938 (501)    L1M4_orf2#LINE/L1        4   895 (13)  

  chr1_222754034_   2039 AGAGATATTTCATGTTCATGGATAAGAAGACACAACACTGTCAAGATACC 2088
                          i      ii             vi      vi  i i   i     iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_222754034_   2089 AGTTCTTCTCAACTTGATCTATAAATTCAATTCAATACAAGTCAAAATCC 2138
                          i v  i i   v        i i      iv    v vvi         
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_222754034_   2139 CAGCGAGTTGTTTTATGGATATTGACAAAATGATTCTAAAGTCTATATTG 2188
                             vivi v    iii  v        iv    i     i ii    v 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_222754034_   2189 AAAGGCAAAAGACCTACTATAGCCAACACAATATTGAAGTAGAAGAACAA 2238
                            v    ii    i vv        v     v     iv          
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_222754034_   2239 AGTTGAAGGACTGACACTATTCAACTTCAAAACATACTATAAACCTACAG 2288
                              i      v     vii   i        v     i   v      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_222754034_   2289 TAATCAAGACAGTGTGGTAGTGGCA-AAGAATAAA-ATAAAATAGATCAA 2336
                                            v     -   i   i -   ---        
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA---TAGATCAA 300

  chr1_222754034_   2337 TGGAACAGAATAGAGAGCCCAGAAATAAATCCACATA------GTCAATT 2380
                              i     v     i           i   i i ------       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_222754034_   2381 -ATCTTCAACAAATGGGCAAAGGCAGTTGCGCAACAAATGGGCAACAGTG 2429
                         -  i   i    iv v  v   i vi  ------   -    v  -----
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATT------CAA-TGGGGAA----- 388

  chr1_222754034_   2430 GAGAAAAGTCAAGTCTTCAACAAATGGTGCTGCAACAACTGGACATCCAC 2479
                         -    v    --- i                 vi         i ?    
  L1M4_orf2#LINE/    389 -AGAATAGTC---TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_222754034_   2480 AAACAAACAACAAAAAAATGAATCTAGACAAAAACCTTACACCTTTCACA 2529
                          vi    ------- i      vi i   vvvv    i     v vi   
  L1M4_orf2#LINE/    435 ATGCAAA-------AGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_222754034_   2530 AAGG------------GAATCACAAACATAGATGTAAAATCCAAAACTAT 2567
                           ii------------ i    ? i  v  i      i v i        
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr1_222754034_   2568 AAAACTCCTAGAAAGTAACACAGGAAAAAAAATCTAGATGACTTTGGTTT 2617
                                i     iiv    i   ?iv   --   vvi    i    v  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTT 575

  chr1_222754034_   2618 TGTGACAACCAACT-TTAGATATGACATCAAGGGCATGATCCATGTAAGA 2666
                         v --i   ivivi -            i   ii   ii v v iiv    
  L1M4_orf2#LINE/    576 AG--GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_222754034_   2667 ATGAAAT-GATGAGCTGAACTTCATTAAAATTAAAAACTTCTGTTTGGTT 2715
                          -i    -   i ii  i       i              i   -- v  
  L1M4_orf2#LINE/    624 A-AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT--GCTT 670

  chr1_222754034_   2716 --AAAGACATTGTAAAGAGAATGAAAAGACAAGCCACAGACTGGGAGAAA 2763
                         --  i    i i v    i i           v       v         
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_222754034_   2764 ATATTTGTAAAATATACATCCGATAAGGAACTGCTTTCCAAAATATACAA 2813
                                i   vi   i   i       i   vv v    i      i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_222754034_   2814 AGAACTCTTAAAACCCAACAATAAGAAAACAAACAATTGGATTAAAAAAT 2863
                                   v   i   i     i  i     i  iivi   ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_222754034_   2864 GAGCCAAAGACCTTAACAGACACCTCACCAAAGAAGATATACAGATGGCA 2913
                          i  v  i  ii v  i     ii  v                i     v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_222754034_   2914 GATAAGCATATGAAAAGATGGTCAA 2938
                         i       i           v    
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.69 (118 / 70)
Gap_init rate = 0.02 (18 / 892), avg. gap size = 3.22 (58 / 18)  


3400 24.25 1.45 0.67  chr1_222980377_222982957.rev     1192  2090 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_222980377_   1192 GAAAGAGATTCCATGATCATGAAGTGGAAGAATTAATATTGTTAA-ATGT 1240
                               v  i     v     i v       v             -   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_222980377_   1241 CAATAC---CCAAAGTGATCTACAGATTCAATGCAATCCCAATCAAAATA 1287
                               ---     v                i        v        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_222980377_   1288 CCAA-TGCTATTCTTCATGGAAATAGAAAAAACAATTCCAAAATAAGCAC 1336
                            i-   i-  i  iiii     v  v  ivii  i i     vvii i
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_222980377_   1337 AGAAACACAAATACCCCCTAATAGCCTGAGCAATCCTGAGCAAAAAGAAC 1386
                         i    ii   iviv   vv       vi i     i   iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_222980377_   1387 AAAGCTGGCGGCATCATATTGCCTGACCTCAAAATATGCTACAAAGATAT 1436
                             i   v  vv   i i v  ii ii      iv i        v  i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_222980377_   1437 AGTAACAAAAACAGCCTAATCCCGGCATAAAAACAGACATGAATGGA--- 1483
                              iv  i    iv ii v i       ii i      --  i  ---
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT--ATAGATCA 299

  chr1_222980377_   1484 ATAGAATAGAATAGAGAAAATAGAAATAAATCCATGCATTTACAGCCAAC 1533
                           i         v    ivvi         i    i      ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_222980377_   1534 TCATTTTTGACAAAAGCATCAAGAATATACATTAAGGAAATAACAGTCTC 1583
                          v     i     ii iii     vi  v  v ii     v  i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_222980377_   1584 TTTAATAAATGGTGCTGGGAAAACTGAATATCCATATGCAGAATAATAAA 1633
                           i  i              v     i   ?   i     i  v   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_222980377_   1634 ACTAAACCCCTATCTCTCACCATATACAAAAATCAAATCAAAATCGATTA 1683
                         ii ii       i   v                i  v       v   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_222980377_   1684 AAGACGTAAATTTAAGACCTGAAGCTATAAAACTACTAGAAGAAAACTTT 1733
                         ?    v     v     v  i  i          vi           v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_222980377_   1734 GGGGAAACACTTCAGGACACTGGTCTGGGCAAAGATATTTTGGGTAAGAC 1783
                           ? v  vv    iv   vi   vi i     v i v i  i i  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_222980377_   1784 TTCAAAAAGCACAGGCAAGGAAAGCAAAAATAGACAAATGAGATGATATC 1833
                         vi     -     i    vi    v         i    vi  ivvi   
  L1M4_orf2#LINE/    600 ACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_222980377_   1834 AAACTAAAAAGCTTCTGCACAGCAAGGGAAACAATCAACAAAGTGAAGAG 1883
                            v v    i   i  ii vv   i   v  v     v        i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_222980377_   1884 ACAAACTACAGAATGGGAGAAAATATTTGCAAACTATCCATCCAACAAGA 1933
                             v i                          ii  vi   ii i   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_222980377_   1934 GATTAATAACCAGAAAATATAAGGAACTCAAACAACTTAACAGCAAAAAA 1983
                           i vi  v      v      i      vv      i  i ii     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_222980377_   1984 CCACAAATAATCTGATTTTTAAATGTGCAAAAGATCTGAATAGACATTTC 2033
                         --        i ii   ?vv     v     i   i              
  L1M4_orf2#LINE/    799 --ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_222980377_   2034 TT----GAA-ACATACAAATGAACCACAAGTACATGAAAGAATGCTCAAC 2078
                          i----   - i         iv v i   i        ii         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_222980377_   2079 ATCACTAATGAT 2090
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (133 / 81)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.90 (19 / 10)  


3210 27.64 0.44 0.44  chr1_222993935_222995681.rev      349  1256 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_222993935_    349 TGGAAGAACATTCTATGCTCATGGATAGGAAGAATCAACATCGTGAAAAT 398
                              ii i  i i   i        v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_222993935_    399 GGCCATACTGCCCAAGGTAATTTATAGATTCACTGCTATCCCCATCAAGC 448
                            v     v     iv i  i  i       vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_222993935_    449 TACCAATGACTTTCTTCACAGAACTAGAAAAAACT-ACTTTAAAGTTCAT 497
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_222993935_    498 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGA 547
                               viiv  ii  v  v v  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_222993935_    548 AGAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGTCT 597
                          v    i      vv   ii  v  ii i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_222993935_    598 ACAGTAACCAAAACAGCATGGTACTGGTACCAACACAGAGATATAGACCA 647
                                i   i    ii         i iv iv i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_222993935_    648 ATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCA 695
                               i    i--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_222993935_    696 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 745
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_222993935_    746 TATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATGTAGAAAGCTG 795
                          v  i  i              i      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_222993935_    796 AAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGGAT 845
                           ii    i    v   i     v i            i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_222993935_    846 TAAAGACTTAAATGTTAGACCTTAAACCATAAAAACCGTAGAAGAAAACC 895
                         i ?    i       v   v  v    i      vi v           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_222993935_    896 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAGGGACTTCATGACTAA 944
                             ?i- v i -   iv   v v  vv i    iv ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_222993935_    945 AACACCGAAAGCAATGGCAGCAAAAGCCAAAATAGACAAATGGGATCTAA 994
                         i     i      vvi   i      vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_222993935_    995 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTGAAC 1044
                          i   v v  i i   i  ii vv    i  v   ii  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_222993935_   1045 CGGCAACCTACGGAATGGGAGAAAATTTTTGCAAGCTACCCATCTGACAA 1094
                         v i     i  i              v       iii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_222993935_   1095 AGGGCTAATATCCAGAATCTACAAAGAACTTAAATAAATTTACAAGAAAA 1144
                         i  i  vi          v  i        ivv i  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_222993935_   1145 AATCAAACAACCTCATCAAAAAGTGGGCAAAGGACATGAACAGACACTCC 1194
                          iv    i    iv  i?    i           iv    i     i i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_222993935_   1195 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 1244
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_222993935_   1245 ATCACTGGCCAT 1256
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (151 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


1408 26.90 12.78 2.21  chr1_223543154_223545181      722  1535 (493)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr1_223543154_    722 TATACCATGTTCATAGAT-GGAATACCCAGTATCATGAAAGATGTCAATT 770
                            v          i   -    v  ii i   ii v  -    v    v
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA-GATGGCAATA 57

  chr1_223543154_    771 CTCCTCAAATAGATCTATACATT-AATGCAATTCCAATCAAAAGCCCCA- 818
                             i     v      i v   -  i     i  v       -i    -
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCCAG 106

  chr1_223543154_    819 ----------TGTGAAATTTGACAAGCTGACCTTAAAAGTAATATGAAAA 858
                         ----------  iii  v            i i     v v     i   
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_223543154_    859 ACTAAAAGGTCAAGAA----------------GAAAAGGAAGAAGGTATG 892
                         vvi  ii ii v    ----------------     i      viv - 
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA-G 205

  chr1_223543154_    893 TGGGATGGCTCAC-CATACCAGGTATCAGGAATTATTTTAGAGTGAAAGT 941
                          v   v i     - v v   iv -   ii v   i vi i  iv v   
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATT-TCAAAACTTACTACAAAGCTACAGT 254

  chr1_223543154_    942 AATTGTAATTAAGACAAT-T--TACTGCCAATGCAGGAAAAACCAAAAGA 988
                            i------      i - --     v  - i-    v i  vv v   
  L1M4_orf2#LINE/    255 AATC------AAGACAGTGTGGTACTGGCA-TA-AGGATAGACATATAGA 296

  chr1_223543154_    989 ACAATGGAAAAGAATTGAGAGTATCCA--AACAGATCCATGCATATAAAG 1036
                         v        v            --   --  i i i    i   v  vi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGT--CCAGAAATAAACCCATACATTTATGG 344

  chr1_223543154_   1037 -CA---GA-----AATA-----GCCATTACAAATCGATGGGGGGA-AATA 1071
                         -  ---  -----i i -----    vv  v v  i      ii -    
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_223543154_   1072 -------TAGCA---------GGGTCACTTG----TTCACATGGGAAAAA 1101
                         -------i i  ---------   v  vi  ----?i      vi   i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_223543154_   1102 --GACATTAGAAGCCCATTTCCCATTATACATAACAATATATATCAGT-T 1148
                         --  vi  i  vv  i ii  v  ii   i i  v   -  vv   iv- 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAACTCAAAAT 493

  chr1_223543154_   1149 TGATTAAGGTCCTAAACAAGTAAAAGCAAAATTTA-AAAACTTTTAGAAG 1197
                         v   i ?i v      i--    i   v   vi  -      i       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAAT--GTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_223543154_   1198 AAAATATAGAAGAAAATCTTTATAATCTCTGCATAGAGAACTGTTT--TA 1245
                             i    i? v       ii i i  iv vv   iv  iv    --  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_223543154_   1246 AAAA-GACATAAAAAGCAGAAGTCATAAAGAAAAAGACTGATAAATCTGA 1294
                         i v -    iv       v   iv i   ii    i iv       iv  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_223543154_   1295 CTATTTTAAAATCAAAA-CTTTTGCAAGACAAAAAGACACCACAAATAAA 1343
                           viv i     i    -      iivvv    i-     i iv  v   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAA 690

  chr1_223543154_   1344 ATTTTAAAATAAGCCACAGACTGGGAGAAAATATTTGCAATGCATATAGC 1393
                         i vvv  i i  v       v                   vv      v 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_223543154_   1394 TAGCAAAGAATTAGTATCTAGAGTATATAATGAAC----ACAA---AA-A 1435
                          iii  i i i v     i   i       v    ----    ---  - 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_223543154_   1436 GCTATAAGAAAAATGATTCAATAGAACAA----CAAAGGACACAAACAGG 1481
                         iiv v    v    i ii    v?  v  ----       ivii  i  i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_223543154_   1482 CAAATCATCAA--------------TGGTCAATAAACATACAAAAAGATG 1517
                           vv  vi   --------------   i      i  i ii        
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_223543154_   1518 CTGAATAACACTAGAAAA 1535
                           v  i v  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (122 / 93)
Gap_init rate = 0.04 (38 / 900), avg. gap size = 3.21 (122 / 38)  


2593 21.31 11.93 1.14  chr1_223580499_223582661.rev      551  1254 (909)    L1M4_orf2#LINE/L1        1   780 (128)  

  chr1_223580499_    551 TGGAGAGATAAACTATGTTAATGGATTGGAAGACTCAATATTGTTGGGAT 600
                             i     vv i     v               i         ii   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_223580499_    601 AGCAATTCTCCCCAAATTGATCTATAGGTTTTGGGACATCCCTATCAAAA 650
                         i     v                 i  i  iviv vv             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_223580499_    651 TTCTGGTAGGCTTTTT-GTTGGAATTCACAAGCTTACCCTTAAACTTATA 699
                          i ii iv v      - iv i    v       v i   v   i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_223580499_    700 GAGGAATAGAAAAGACCAAGAATAGTTCAGATA-TTTTGAGTAAAGTTAG 748
                         vi i   iv  ii    v       iiv i i - i    i-    v-  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGA-AG 198

  chr1_223580499_    749 AA----GTCGGAGGATTAACACTATGTAATTTTAATACTTGCTATAAAAA 794
                           ----  i      i v     vivi     i  v    i   i   iv
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_223580499_    795 TGCAGTAATCAAAAACATGTAGTACTGGCATAA----------------- 827
                          i          i vvi   i            -----------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_223580499_    828 --TGAAAC-GAA----GAGTCCAAAAATAAGTTCTTACATTTATGGTCAG 870
                         --  i  i-   ----       i      iii v              i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_223580499_    871 TTGATTTTCTGCATAAGTGCCAAGGCAATTCAATGGAAAAAGGATAATCT 920
                                  vi  vii        i v         ii    i   i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_223580499_    921 TTTCAT---ATAGTACTGGAACAATTGGATATCCATATGTGAGAAAAAAT 967
                              v---  i  i    i    i      ?   i   ii --  i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA--AAGAAT 446

  chr1_223580499_    968 GAACTTGGATCCTTACCTCATACCTTATACAAAAATTAACTCAAAGTGGA 1017
                            v     i  i       i   v                    i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_223580499_   1018 TCACAATCTGAAATATAAAAGGTAAG-----------------------C 1044
                            ? iv iv    i   i  v   i----------------------- 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_223580499_   1045 ATAGGAGAAAGTCTTTGTGATTCAGGGTTAAA-AATG---TCA-AGATAA 1089
                              ? v  i    i    iiiv      ii-    ---  v-     -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA- 595

  chr1_223580499_   1090 TGACATTAAAAGCACAGTGCA-TGAGAGAAGAGTAAT-GATAAATTGAGC 1137
                              ii         i-   -ii i    i --   -         ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAA-GCAACAAAAGAAAA--AATAGATAAATTGGAC 642

  chr1_223580499_   1138 ---ATCAAAATTTAAAA--------------AGAACATTA---AGAAAAT 1167
                         ---         v    --------------  i   i  ---     i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_223580499_   1168 GAAAAGACG-TGCACAGATGGGGAGGAAATATTTCCAAATCATTTATCTG 1216
                                 i-iv      vv     i        v        v      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_223580499_   1217 AAAAAAGACTTGTATTCATAATATGTAAAGAACTCTTA 1254
                          v  ii         i  v     i             
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

Transitions / transversions = 2.13 (100 / 47)
Gap_init rate = 0.03 (23 / 780), avg. gap size = 4.00 (92 / 23)  

 364 26.96 0.00 0.00  chr1_223580499_223582661.rev     1558  1672 (491)    L1M4_orf2#LINE/L1      794   908 (0)  

  chr1_223580499_   1558 AAAATATAAACAACTCAGTGTTTTAATGGGTAACAAAGCCGAATAGACAT 1607
                             v i   i   i  i v?vvv      i  vii vii          
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_223580499_   1608 TTCATGAAAGATGATACATGAATAACAAATAAGCACATGAAAAGATGATC 1657
                            viv     v    i ii   ii v                    v  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_223580499_   1658 GTCATTAGGAGAATG 1672
                         iv   i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (17 / 13)
Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.00 (0 / 0)  


3379 15.17 2.86 13.40  chr1_223600129_223602344.rev      711  1725 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_223600129_    711 TGGAAAGACATCTCATGTTTATGAATAGTGGGATTTAATATTGTTAAGAT 760
                                 i   i      i   i  v vii  i                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_223600129_    761 GCAGTACTACTACCTAAAGTTATGTACAGCTTCAATTCAGTCCCTATCAA 810
                          -- i v    v  i   v v  v     v     iv  i          
  L1M4_orf2#LINE/     51 G--GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_223600129_    811 AATTCAAA--GTCTTTTTTGCAGAAAT-AAAAAGCTGATCCTCAAATTCA 857
                            i v i-- i               -i v           v       
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_223600129_    858 TATGGAATTGCAAAGGACCTGGA-CAGCCAAAACAATCATAAAAAA--AG 904
                                v     i     ii  -i             v i     --  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_223600129_    905 GACAAAGTTGGAGGAGTCATACTTC--------AGAACTTACTACAAAGT 946
                         i              v   i     -------- i              i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_223600129_    947 TACAGTAATCAAAACAATGTGGTACTGTCATAAGGATAGACATACAGACC 996
                                     i   i          v                i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_223600129_    997 AATAAAATATAATTAAGAATACAGAAATAAATGCATGTATCTATGGTCAA 1046
                            ii    v    i   i v          iv   ii  i         
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_223600129_   1047 TTAATTTTTGACAAATGTACTAAGTCCATTCAATGGGGAAAGAATAGT-- 1094
                           i     i     iv  i i   v                       --
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_223600129_   1095 -TTCTACAGATGTT-TTGGGACAACTGAATATTAACCTACAAAAGAATGA 1142
                         -   v   i   v -i           i   ?iv  v i           
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_223600129_   1143 AATTGGTCACCTGCATCACACCAGTTATACAAA--TTAACTCAAATTGGA 1190
                          i    v v   i v        --        --          v    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCA--TATACAAAAATTAACTCAAAATGGA 496

  chr1_223600129_   1191 TCAGCAACTGAAATCTTACAGCTACAACTATAAAACTCAAGAGACCTTGG 1240
                            ?vi  iv    v v v     v             ------------
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC------------ 534

  chr1_223600129_   1241 ATTTGATAATGGATTCTTAGAAATAATACTGAAAGAAGAATTAACACCAA 1290
                         ----------------      --------    ---------   i---
  L1M4_orf2#LINE/    535 ----------------TTAGAA--------GAAA---------ACAT--- 548

  chr1_223600129_   1291 TCCTTCTCAAACTCTTTTTAAAATAGAAGAGGAGGAAACACTTCCTAACT 1340
                         -----------------------------   ? v   i-    v i  i
  L1M4_orf2#LINE/    549 -----------------------------AGGNGTAAAT-CTTCGTGACC 568

  chr1_223600129_   1341 GATTCTGTGAAGC--TGGCATTACCCTGAATACCAGAGCCAGACAAAAAA 1388
                         --  vv  v i  --   i-  -- i ii   i--------    vv   
  L1M4_orf2#LINE/    569 --TTGGGTTAGGCAATGGT-TT--CTTAGATAT--------GACACCAAA 605

  chr1_223600129_   1389 ATCACAAAATTACAGACCAACGTTTCTTATTAATATAGATGCATAAATAA 1438
                          v     i---------    -----------------------   - i
  L1M4_orf2#LINE/    606 AGCACAAG---------CAAC-----------------------AAA-AG 622

  chr1_223600129_   1439 CAAAAAAAGTATAAATTGGGCTTTATCAAAATTAAAACTTAATGTGTATG 1488
                         v     v  -         i   i             vi ---- v i  
  L1M4_orf2#LINE/    623 AAAAAATAG-ATAAATTGGACTTCATCAAAATTAAAAACT----TTTGTG 667

  chr1_223600129_   1489 GTATCAAAGGACATTATTAAGAAAGTAAAAAGACAGCTTAAGGGATGCAA 1538
                         v -          i   i        i        i ii vi i   vi 
  L1M4_orf2#LINE/    668 CT-TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_223600129_   1539 GAAAATATTTGCAAATCATATATGTGATAACAATTTAATATCCAGATTAT 1588
                                                v      viivi vi        v   
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_223600129_   1589 ATGAAGAACT---ACAGCTCAACAACAGAAAGACAA----CTCAATCAAA 1631
                           i       ---   i     i  i i        ---- i    i?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_223600129_   1632 AAATGGGCAAAAGACTTGAATAGACATTTCTCCAGAGAAGATATATATAA 1681
                                    i  i                   i          i -- 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA--A 864

  chr1_223600129_   1682 ATGGTCAATAAGCAAATTAAAAAATGCTCAACATTACTAATCAC 1725
                             i         v  v    i           i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (93 / 57)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 5.69 (165 / 29)  


 225 19.35 3.23 4.84  chr1_223677890_223679677.rev      394   455 (1333)    L1M4_orf2#LINE/L1       22    82 (826)  

  chr1_223677890_    394 TAGATTTGAAATGCTTTAAGCATTA--AAGATGTCAGTTCTTCCCAAATT 441
                          i    v   -- vi    -i   i--      v  i v  i        
  L1M4_orf2#LINE/     22 TGGATTGGAA--GACTTAA-TATTGTTAAGATGGCAATACTCCCCAAATT 68

  chr1_223677890_    442 GATCTACAGACTTA 455
                                   i i 
  L1M4_orf2#LINE/     69 GATCTACAGATTCA 82

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.67 (5 / 3)  

2169 24.97 7.03 1.76  chr1_223677890_223679677.rev      502  1298 (490)    L1M4_orf2#LINE/L1       70   908 (0)  

  chr1_223677890_    502 ATCTATAGGTTTATTGCAGTCTCT--CAAAATCCTAGCAAGATTCCTTT- 548
                              i  i  i vi   i  i  --        i   ---- v     -
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC----TGCCTTTT 115

  chr1_223677890_    549 ----AGATAGAGACAAGCTTATTTTAAATTTTATATGGAAAGGCAATAGA 594
                         ----   v vv        v  ii    v  i         v    vi  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_223677890_    595 ACTGGAGTAGTTAAA-CAGATTTTGAAAAAGGAGAATAAAGTGGAAAGAA 643
                         v ii  i   ii   -  -  i         i    i     v i i  v
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACA-ATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_223677890_    644 TCACTCTACCAGATATTAAGCCATGCTATATTGCCACCTTAAGCAGGACC 693
                             v  v  vi  v i  iv v i   i vv  i  vv   v  i   v
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_223677890_    694 ATGAGATAATTGCG-ATGTAATAAACACACAGATCATTGGACGACATTAG 742
                         i  v i  v v  i- v -i   i   i i      v    vv v v v 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAG-GATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_223677890_    743 CAAGCCCAGATGTAGGCTAACAGAGGTATTTTCAACTGATTTT-GAGAAA 791
                         vi  i     vi  ii iv i v vv   vv    i       -  v  i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_223677890_    792 GGTGCAAAAGC-------------AAAAATAATCTTG--AACAAATGGTG 826
                              v  ii -------------  i    i    v--           
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_223677890_    827 CTCAAATAA---GAGA-CCAAAAAAAAAACCCCAAAT-AACTT---CCCC 868
                           vii i  ---  v -   v viv    ----i   -  v  ---    
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAA----GAATGAAGTTGGACCCC 459

  chr1_223677890_    869 AAAGCTCTCATAA-ATACAAAAATTAATTCAAAATGGGTCATGGATTTAA 917
                         v v-   v  iv -             i         i   ?i  ii   
  L1M4_orf2#LINE/    460 TAC-CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_223677890_    918 ATGTACAACATAAAACTATAAAACTGTTGGAAGAAAATATTGGAGAACAT 967
                              vi vv               v  i        i  v  ? v v  
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_223677890_    968 TTTCTGGATCTAGGGCTTGGTAAGGAGTTTTTAGATATGACA--AAAAA- 1014
                         i   vv  i  v   i v  i  v iv  i            --    i-
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_223677890_   1015 --AATCAATAAAA------ATGAATAAATGGGACTTCATTAAAATTAAAA 1056
                         --  v   i    ------  ii      v         i          
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_223677890_   1057 --TTATGTGCTCAATGAAAGACCCTGGTAAGACTATAAAAAGACAAGCTA 1104
                         --  v      iv --  i   v  ivi    vvi i         v i 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCA--AAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_223677890_   1105 CAAAGTGGGAGAAAATAGTTGTCAAC---ATACCTTACAAAGGTTTTATA 1151
                           i i            v   iv  i---   i  v i  i  vi  i  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_223677890_   1152 TCTAGACTATATAAAGAACTCTCAAAATACAAT--TAAAAAGCCCAAGCA 1199
                           i   v               i v  iv    --       v -  ii 
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC-AAATA 805

  chr1_223677890_   1200 ATCTAATTACAAAATAGGGAAAAGAC---AATAGACATTTCACCCAAGAG 1246
                          i i    ?v     i  v   i  i---            v  v    i
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_223677890_   1247 GAGATAGAGATGGCAAGTAAGCACATGAAAAGATGTTCAATAT-ACTGAT 1295
                           v   v i     v i                  i    i  - ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_223677890_   1296 ATT 1298
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.13 (104 / 92)
Gap_init rate = 0.03 (27 / 839), avg. gap size = 2.59 (70 / 27)  


4585 16.55 3.29 0.45  chr1_223722715_223724627.rev      541  1422 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_223722715_    541 GAAAAGACATTGCATATTCATGGATTTGAAGAC--AATATTTTTAAGATG 588
                          i     i  iv   i          v      --      v        
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_223722715_    589 GCAGTATTACCCAAATTGATCTACAGATACAGTGCAATCCCTATAAAAAT 638
                            i  i v                   v  ii           v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_223722715_    639 TCAAGGTACCTTTCTGGTAGAAATGGACAAGCTGATTTTAAAATTTATGT 688
                         i v  v i     i v i      v           ii       i  i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_223722715_    689 AGAAATTTGAGAGTTCCAGAATAGCCAAAACAATTTTGAAAAAGAG---C 735
                         i     vii  i vi                   i          i--- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_223722715_    736 AAAGTTGGAGGACTCACACTTCCTGATTTCAAAACTTACTACAAAGCAAT 785
                                                ii                      v i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_223722715_    786 GGTAATCAAGGTTGTGTGGTACTGGCATAAGGCTC-ATATATAAATCAAG 834
                         i         iiv                   v v- i     i     v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_223722715_    835 AGAAAAGAATTGAAAGTCCATAAATAAATTTTTACATTTATGGACTATTG 884
                         i   v        i      v       iiiv           v v    
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_223722715_    885 GTTTTTGACAAGGGTGCTGAAACCA----AGGAGGTAA-AACAGTTTTTT 929
                         i    i           ii i    ---- v i  v  -  i   i    
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_223722715_    930 TTCCAACA----GTG-TGGGGCAACTGGATATCCACATGTGAAAGAATGA 974
                         ---     ----   -    i          ?       ii         
  L1M4_orf2#LINE/    402 ---CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_223722715_    975 AGTTGGACTC-TACTTCATACCATATTCAAAAATTAACTCAATATAGATC 1023
                                 i -   i   i       v               v  i    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_223722715_   1024 ATAGACATAAATGTAACAGATAAAACTATGAAACTCTTAGAAGGAAACAT 1073
                          ?    v         v  v         i             i      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_223722715_   1074 AGGTGTAAATTTTTGTGACCTTGGCTTAGGCAATGGTT-CTTAAATATGA 1122
                            ?      i  i          v             -    i      
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_223722715_   1123 CAC-GAAATCTCAGGCATCAAA-GAAAAAACAAA-AAATAAGATTTCATC 1169
                            -i   v v  i   v    -       i i -    vi  i      
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_223722715_   1170 AGAGTTTAAAACTTTTGTGCCTCCAAAAAACACCATCAGGGAAGGAAAAA 1219
                          i i  v             i  -   ii    i    i i   vi    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTC-AAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_223722715_   1220 GACAACTCACAGGGTGGGAGAAAATATTTGCAAATCATGTATCTGATGAG 1269
                               i     ii                        i        i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_223722715_   1270 GGCCCAGTGTCTGTGTTA---AAAGAACTCT-GCAACTCAGCAATAAAAG 1315
                           v iv  i  iiviv  ---          -i       ii       i
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_223722715_   1316 CACAA----CCTAATTTAAAAATTGATGAGTGATTTGGATAGCTGTTTCT 1361
                         v    ----  i    ?      v iii iv      i    vii     
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_223722715_   1362 CCAAAGAAGTTATACATATGGACAATATGTACATGAAAAGATGCTCAACA 1411
                                  v      v    v     v i                    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_223722715_   1412 TCACTGGTCAT 1422
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.96 (94 / 48)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 1.94 (33 / 17)  


1993 24.48 12.18 3.44  chr1_223733540_223736040     1188  2000 (501)    L1M4_orf2#LINE/L1        3   886 (22)  

  chr1_223733540_   1188 GAGAAATATC---TGCTTCAGAGACTAACAGACTCAACATTATTAAGATA 1234
                           i i     ---  -    vi  i iiv     i  i   i       i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATG-TTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_223733540_   1235 TTGGTCCTCCCAAAATTTATCTATGTACTCAGTGCATACTCAATTACA-- 1282
                         viii v     v     v     iiv i   ii   vv i v  i v --
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_223733540_   1283 -TCAGTAGGCTTTT--ATAAAAATTGATATATTGATTCTAAAAT------ 1323
                         -i   iv v     --ii i       i vii    i       ------
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_223733540_   1324 ------GCAAAAGTCTTCGAATAATTAAAACAATCTTGAAAAAGAA---C 1364
                         ------    ii v iiv     iii                    --- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_223733540_   1365 AAAGT---AGGACTCCATACACTCAGAGTTCATTACACAATCTCAACA-T 1410
                              ---       ---     ----- i ------    i    v - 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTC---ACACT-----TCC------CAATTTCAAAACT 237

  chr1_223733540_   1411 TAGTATAAAGCTATAGGAATCAAGAC--TGTGGTATTAGCATAAAGGCAG 1458
                           v  i       i  v         --       i i      i ii  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr1_223733540_   1459 ACA-ATGAGATAAAGAGAATAGA-----GAGGACAGCAATAGAGC---AC 1499
                            -  -    v  vi       -----   vv   v    i v ---  
  L1M4_orf2#LINE/    288 ACATAT-AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_223733540_   1500 AT----GGTC------TTTTT-ACTAAGGTGCTAAAATGACTTAATAAAG 1538
                           ----    ------    i-  v i     i  i iv i i   iii 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_223733540_   1539 GGAAAACAGCCTTTTCAACAAATGGTGCTGAAACAACTGGCTA--CAAAT 1586
                         ii i  i  i                    ii        v  --  v  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_223733540_   1587 ACAAAAAAAAAAA--TGAATCTCAATGCCGATATCACAT-CAGACATGAA 1633
                         i     i  vi  --  i i i v ivi - i i  i  -  i v  v  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTC-ACACCATATACAAAAATTAA 485

  chr1_223733540_   1634 TTTGAGATGGATCACCAATCTAAATATAGTAGCTAAAAATAGAAGGCTTT 1683
                         i ii i        ?vi i      i  iv        v  v  ii  i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_223733540_   1684 TAGAAAAAAAAAACATAGAT----ATCTTTGTGATCT-GAGTATAAACAA 1728
                              i    ---     i?----     i    i  - i  -  ii   
  L1M4_orf2#LINE/    536 TAGAAGAAAA---CATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAA 581

  chr1_223733540_   1729 GGATTTCTTAGA----ACACAGAAAATACTAACTGTAATAGAAAACAATT 1774
                         v i         ----    vi   ii  v i vii  v      -   v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATA 630

  chr1_223733540_   1775 GATAAAATTATACCT--TCAAAATTGAAAACTTCTG--CTCTAAACGATA 1820
                               -  iv  i --        i       i  --  ii   v  i 
  L1M4_orf2#LINE/    631 GATAAA-TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_223733540_   1821 ATTTTTTTAAAAAATGAA----CAAACCACACAGTCTGAGAAAATATTGC 1866
                         --i v iv i   i    ----   v     v i vv           vv
  L1M4_orf2#LINE/    680 --CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr1_223733540_   1867 TAAA----ACATCTGACAA------------------------AGAACTC 1888
                         i   ---- i      i  ------------------------       
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr1_223733540_   1889 CTACAGCTCAACAATAAAAATACAAACATTTCAATTTCTAAAGACTGAGC 1938
                         i    i     i        v     i vii     ?--   i -  i  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTW--AAAAA-TGGGC 824

  chr1_223733540_   1939 AAAAAATTTGAACATATACCTCACAAAGGAAGATATAAAAATGGTTAATA 1988
                            ii       i v i ii  v v  i         v      ii    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_223733540_   1989 GGCACACAAAAA 2000
                         i     ii    
  L1M4_orf2#LINE/    875 AGCACATGAAAA 886

Transitions / transversions = 2.27 (136 / 60)
Gap_init rate = 0.04 (38 / 884), avg. gap size = 3.34 (127 / 38)  


3401 23.15 1.96 3.26  chr1_223742163_223744645     1071  1990 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_223742163_   1071 TGAAAAAATATTCAATGTACATGGGTTAGAAGAATCAATACTGTTAAAAT 1120
                           i   i    i v    v     i  i     v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_223742163_   1121 ATCCATATTGCCCAAAGCAATCTACAGATTCAATGCAATCCCTGTCAAAG 1170
                         iv v   i v      vii              i         i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_223742163_   1171 TATTAATGACATTCTTTCACAGAAATAGAAAAAATAATCCTAAAATTTAT 1220
                          vii iivi v  i   -i       v  v  iv i           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_223742163_   1221 ATGGAATTACAAAAGACCCAGAATAGCCAAAGCTATCCCAAGCAAAAAGA 1270
                               v i   ii                 i v   iii iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_223742163_   1271 ACAAAACTGGAAGAATCATATTACCTGACTTCAAATGATACTACAGAGCT 1320
                              ii    i  v   i i v  ii i      vvv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_223742163_   1321 ACAGTAACCAAACTAGCATGGTACTGACATAAAAACAGACACATAGATTA 1370
                                i   ivi  ii        i     ii i     i      i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_223742163_   1371 ATGAAACAGAATAAAGAACCCAGAAGGAAATCCACATACATACAGGGAAC 1420
                            i  i     vi   ii      iv   i   i i iv  ii vv  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_223742163_   1421 TAATTTTCAACAACGGTGCCAAGAATGTT----AGGGAAAAGACAGTCTC 1466
                          i      i    v          vii  ----i      ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_223742163_   1467 TTCAATAAATGGTGCTGGGAAAACTGGATAACCATATGCAGAAGAAGGAA 1516
                              i              v         ?   i     i     v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_223742163_   1517 ATTTGATCCCTATCTCTCACCTTACATAAAAAACAAATCAAAATGGATTA 1566
                         i  v  i     i   v    v  i i     vi  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_223742163_   1567 AAGATTTAAGTCTAATACCTCAAAGTATAAAACTACTAAAAGAAAACATT 1616
                         ?   ii   i v   v v  v   v         vi  i          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_223742163_   1617 GGTGAAAATCTCCAGGACACTGGTCTGCACAAAAATTTCTTA-------- 1658
                           ? v      i iv   vi   vi ivi   vii       --------
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_223742163_   1659 -----AAACACAGCCAACCAAAGCAAAAATGGACAAATAAGATGACA-CG 1702
                         -----  i    iv    v    v      i  i    vi  ivv  - i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_223742163_   1703 AAATTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACCCACAGTGAAG 1752
                                   -   i  ii vv       v  v     ------------
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA------------ 686

  chr1_223742163_   1753 AGACAGAATCAAACCACAGTGAAGAGACAACCCACAGAATGGGAGGAAAT 1802
                         -----   ---------      i                     i    
  L1M4_orf2#LINE/    687 -----GAA---------AGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_223742163_   1803 ATTTGCAAACTACTCATCTGACAAGGGATTAATAACCAGAATATACAAGG 1852
                                  ii ivi      i      i vi  v          i  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_223742163_   1853 AATTCAAACAACTCTATAGGAAACAATCTGATAATCCAATTTTTAAAATG 1902
                           i  vv       v   iv   v iv vi    i      ?v-      
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATG 821

  chr1_223742163_   1903 GGCTAAAGATTTGAATAGACCTTTCTATAAAAAAGACATACGAATGGCAA 1952
                            v  i             v     vi   i    i    i      v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_223742163_   1953 ACAGGCATATGAAAAAAGTGGTCAACATCACTGATCAT 1990
                          i i   i       i -  v         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (134 / 75)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 5.33 (48 / 9)  


2464 15.83 3.96 0.21  chr1_223870640_223872583.rev      502   981 (963)    L1M4_orf2#LINE/L1      268   765 (143)  

  chr1_223870640_    502 TAGTAGTGGCAGAAGAATAGGCATATAGCTTAATGTAA-AAAATGGAGGG 550
                          i   v     v   i    i       v i    v  - i   v   i 
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_223870640_    551 TCCACATAC---CTCATG--TTTATGGTCAGTTGATTTT--GCAAGGG-G 592
                             v v i--- i   i--          i        --i      - 
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_223870640_    593 ATAAAACAATTTAATGGGGAAAGAATACTCTTTTCAACAAATAGTGCTGA 642
                         vi  i  v   i               v              i      i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_223870640_    643 GATAATT-------CACAGGCACAGGAATGAAATTGGACCCCTATGTCAA 685
                           i  i -------    v   v i       i           iv   v
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_223870640_    686 ACCATTCACAAAAATTAACTCAAAATCAATCATAGACCTAAACGTAAGAG 735
                              vi                   vi    ?         i       
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_223870640_    736 CTAACAGTTTACAACTCTTAGAAGAATGCATAGTGGTAAATCTTTATGAC 785
                             v v v  v              vi     v?         ii    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_223870640_    786 CTTGGGTAAGGCAATGCTTTCTCACATATGACACTAAA-GCAAAAATGTC 834
                                v        v     i v         i   -   v  iiiv 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_223870640_    835 AGGAAAAAAAAATAGATAAATTGAACT-CATTAAAATTAAAAACTTTTGT 883
                          i-  i                 i   -   i                  
  L1M4_orf2#LINE/    618 AA-AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_223870640_    884 GCTTCAAAGGACAA-ATCAAGACAGTGAAAAGACAACCCACAGAATGGGA 932
                                      v-       v                           
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_223870640_    933 GAAAATTTTTGCAAATCAACTATCCAATAAGAAACTTGTATTCAAAATA 981
                               v           vv    ii     ii        i  i    
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

Transitions / transversions = 1.31 (42 / 32)
Gap_init rate = 0.02 (10 / 498), avg. gap size = 2.00 (20 / 10)  

 781 15.23 1.32 0.00  chr1_223870640_223872583.rev     1303  1453 (491)    L1M4_orf2#LINE/L1      756   908 (0)  

  chr1_223870640_   1303 ACCCAAAATATAGGAAGAACTCTTACAACTCAACAATAAAAAAACCTGTA 1352
                          i   i      vi                   i        i  vvi  
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr1_223870640_   1353 ACTCAATTTGAAAATGGGCAAAGGATTC--ACAGACATTTCTCTAAACAA 1400
                           i     ?i                 i-- i           i   v  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr1_223870640_   1401 AATGTGCAAATGGCCAATAAGCATATGAAAAGATGCTAAAAATTATAAGT 1450
                         i  i i                 i             v  v  i ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr1_223870640_   1451 CAT 1453
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.67 (16 / 6)
Gap_init rate = 0.01 (1 / 153), avg. gap size = 2.00 (2 / 1)  


 268 28.99 0.00 0.00  chr1_223875673_223879703     2909  2977 (1054)    L1M4_orf2#LINE/L1        1    69 (839)  

  chr1_223875673_   2909 TGGAGAGATAGTCCGCATTAACGGAGAGGAAGACTCAATGTTGTCAAGAT 2958
                             i     vi  iii  v i   vv        i   i    i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_223875673_   2959 GTCAGTTTTTCCTAACTTG 2977
                          v  i vi i  i  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG 69

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.00 (0 / 0)  

1857 21.93 4.99 1.60  chr1_223875673_223879703     2978  3538 (493)    L1M4_orf2#LINE/L1      329   908 (0)  

  chr1_223875673_   2978 ATCTATAAATTCAATG--CAATCCTAATTTGTCATTGACAAAGTAGCAAA 3025
                          i i   v   i -  --    -- i    ---- i     i vv  v  
  L1M4_orf2#LINE/    329 ACCCATACATTTA-TGGTCAAT--TGATTT----TCGACAAGGGTGCCAA 371

  chr1_223875673_   3026 GGCAATGCAATGGAAAAAAAAATAATGTTTTCAACAAATGGTGCTGGAAT 3075
                          i v  v      ii   i  -  i v                    i i
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAA-TAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_223875673_   3076 AACTGGACATCGACAGGCAAAAAAATGTATTTAGACAAAGACCTTACACC 3125
                                i ? v   v      i    v v  i   vvvv    i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_223875673_   3126 CTACACAAAAATTAACTCAAAA------ACGGATCTAAATATAAAACACA 3169
                         v  i                  ------ ?i  i      i   i vvi 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_223875673_   3170 AAACTATAAATTTCT-AGAAGATAACATATGAGAAAATCTG-ATGACTTT 3217
                                   vi   -      v      v ? v      v-i    i  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_223875673_   3218 GGGTTTGGAAATGACTTTTTAGATAAAATATCAAAGGCATAATCCATGAA 3267
                              v  v    ii  i       vi i i    i   i  v v ii  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_223875673_   3268 AGAAAGAACCAATAAGCTGGACTTCACTAATATTAAAAA-TTTTG----- 3311
                              i  ivi    ii         ii  v        -     -----
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_223875673_   3312 --AAACATACTGTCAAGAGAAGGAAAAGCTAAGCCACAGATGGGGAGAAA 3359
                         --  iv i   i      i iv      vi  v       vv        
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_223875673_   3360 ACATTTGCAAAATAAGTATCTGATAAAAGGCT-GTAATCCAAAATATAAA 3408
                          i         vi vi          ii i  -   -    i      v 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTA-TCCAGAATATATA 769

  chr1_223875673_   3409 AATAACTCTTAAAAAGCAACAATAAAAAAA-AAA-----CAATTTAAAAC 3452
                           v        v  vv   i        i -   -----     ?    v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr1_223875673_   3453 TGGGCCAAAGATCTTAACAAACACCCCACAAAAGAAGATACAGAGACGGC 3502
                              v  i   i v  i i   iii v v          i v i i   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_223875673_   3503 AAATAAGCACATGAAAA--T-CTCAGCATCATACCTCAT 3538
                         v                -- -    i     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (69 / 50)
Gap_init rate = 0.03 (16 / 580), avg. gap size = 2.31 (37 / 16)  


1294 28.91 0.00 0.00  chr1_223896844_223901766     3184  3567 (1356)    L1M4_orf2#LINE/L1        4   387 (521)  

  chr1_223896844_   3184 AAACACATCCCATGCTCATGGATGGGTATAATCCATATTGTGAAAGTGAC 3233
                            v i        i        v  v v v iv       v  ii  i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_223896844_   3234 CATATTGCCAAAAGCAGTCTACAAATTCAACACAATCCCTATCAAAATAC 3283
                         v   i v  v   viii      i       i                v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_223896844_   3284 CACCATCATTCTTCATAGAATTAGAAAAAACAACTCTAAAATTCATATGG 3333
                           v vv v  i  iii    v v  v  ivii ii               
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_223896844_   3334 AACCAAAAAAGAACCTGCATAGCCAAAGCAAGACTAAACAAAAAGAACAA 3383
                           viiv  ii  v  v v         i   vvi i  v  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_223896844_   3384 ATCTAGAGGCATCATACTACCTGATTTCAAACTATACTGTAAGGCCATAA 3433
                          vi i    vv   i   v  ii        viv    ii  i  i i i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_223896844_   3434 TCACCAAAACAGCATGCTACTGGTATAAAAATAGGCACACAGATCAATGG 3483
                          v i   i    ii  v      i    ii    i  i i          
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr1_223896844_   3484 AACAGAATAGAGAATCCAGAAATAAACCCAAATACCTACAGCCAACTGAT 3533
                           i     v    i                v i ii  ii i   i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr1_223896844_   3534 CTTTGACAAAGCAAACAAAAACATAAAGTGAGGA 3567
                         i  i     i vviv   i v   vv i  i   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

Transitions / transversions = 1.52 (67 / 44)
Gap_init rate = 0.00 (0 / 384), avg. gap size = 0.00 (0 / 0)  

1997 25.10 0.77 0.00  chr1_223896844_223901766     3913  4430 (493)    L1M4_orf2#LINE/L1      387   908 (0)  

  chr1_223896844_   3913 AAAGGACACCCTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACAT 3962
                             i i vi                       i  i   v  ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_223896844_   3963 GTAGGAGAATGAAACTGGATCCTCATCTCTCAGCTTATACAAAAATCAAC 4012
                          i ii        ii    i  ii i   v  v v           i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_223896844_   4013 TCAAGATGGATTAAGGACTTAAATCTAAGACCTGAAACTATAAAAATTCT 4062
                             i      i ?i   i     v     v  i           v ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_223896844_   4063 AGAAGATAACATTGGAAAAACCCTTCTAGATATTGGTTTAGGCAAGGACT 4112
                               v     v  ?iv  vi    vv  iv    v        v ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_223896844_   4113 TGATGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGC 4162
                          vv iivi v  vv         v v    i    iv   i   i   iv
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_223896844_   4163 TGAGACCTAATTAAACTAAAGAGGTTTTGTATGGCAAAAGGAACAGCCAG 4212
                          vi   i v  i   v v  i iv      iivv    i iv  vii  i
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_223896844_   4213 CAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTGTA 4262
                         v i   i  v              i           v  ii   viii  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_223896844_   4263 CATCTGACAAAGGACTAATATCCAGAATCTACAATGAACTCAATGAAATC 4312
                         i      i  i     vi          v  i  v      vvvv  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_223896844_   4313 AGCAAGAAAAA----AATAATCCCATGAAAAAGTGGGCTAAGGACATGAA 4358
                          ii  v     ----     i  v  v?    i     v     iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_223896844_   4359 TAGATAATTCTCAAAAGAAGATATATAAATGGCCAACAAACATATGAAAA 4408
                             i v     v            i          i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_223896844_   4409 AATGCTCAACATCACTAATGAT 4430
                         i             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (71 / 55)
Gap_init rate = 0.00 (1 / 522), avg. gap size = 4.00 (4 / 1)  


2945 26.62 2.24 0.67  chr1_223967533_223974212     5294  6187 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_223967533_   5294 TAGAAAAACATTCCACGCTCATGGATAGGAAGAATAAATATCATGAAAAT 5343
                          i    i i  i   i i        v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_223967533_   5344 TGCTATACTGCCCCAAGTAATTTATGGATTCAATGTTATCCCCATCAAGA 5393
                         v  v     v   v  v i  i  ii       i iv     i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_223967533_   5394 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5442
                          v   vivi v  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_223967533_   5443 ATGGAACCAAAAAGAGCCCATG-TAGCCAAGACAATCCTAGGCAAAAAGA 5491
                               viiv  i ii    vi-       i      i iiiv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_223967533_   5492 TTGAAGCTGGAGGCATCATGCTACCTGACTTCAAACAATACTACAAGGCT 5541
                         vii   i      vv   ii  v  ii i      vvv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_223967533_   5542 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5591
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_223967533_   5592 AAGGAACAGAACAGAGACCTCAGAAATAATGCCACACATCTACAATCATC 5641
                          v    i    iv    vii         vv   i    i  iii   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_223967533_   5642 TGATCTTTGACAAACCTGACAAAAACCAG-CAATGGGGAAAAGATTCCCT 5690
                             i  i     ivv  v   i -   v-           ii  vvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAGTCT 398

  chr1_223967533_   5691 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5740
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_223967533_   5741 AACTGGATCCCTTTCTTACACCTTATACAAAACTTAACTCAAGGTGGATT 5790
                          ii    i    vi  i     v         v         ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_223967533_   5791 AAAGACCTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5840
                          ?         ii     v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_223967533_   5841 GGGCA-ATACCATTC---AGCATAGGCATGGGCAAAGACTTCAT-GATAA 5885
                         i  ?i- v i -   --- v v i  i- i     v ii   v -    v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT 596

  chr1_223967533_   5886 AACACCAAAAGCAATGGCAAAAAAAAGCCAAAATTGACAAATGGGATCTG 5935
                         i            vvi    v    - vv     v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTC 645

  chr1_223967533_   5936 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGAGAA 5985
                           i   v v  i i   i  ii vv    i  v       vv i  v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_223967533_   5986 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACA 6035
                         v  i     i                 v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_223967533_   6036 AAGGGCTAACATCCAGAATCTACAAA-AACTTAAACAAATTTACAAGAAA 6084
                          i  i  vii         v  i   -    ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_223967533_   6085 AA-----AT--CCCCATCAAAAAGTGGGCAAAGGAT----ATGGACACTT 6123
                           -----  --   v  i?    i            ----  i    i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_223967533_   6124 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAAAATCTCA 6173
                            v        i  vi viii     i ii          i vi-    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG-CTCA 894

  chr1_223967533_   6174 TCATCACTGGCCAT 6187
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.62 (26 / 16)  


3009 23.67 7.81 0.36  chr1_223976775_223979723     1612  2456 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_223976775_   1612 TGAAAAGACACTATGTGTTTATGGATTGGAAGACAAAACCTTGTCAAGAT 1661
                           i     i iivii    i              vv  iv    i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_223976775_   1662 GTCATTGTTATCTATAGTCATCTACAGATTCAATGAAATTCCTTTAAAAA 1711
                          v  v ii vi i v v v              i v   i   v v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_223976775_   1712 TCCCAACA------TTTGCAAAAGTAGAAAAACCTATTCTAAAATTCAGA 1755
                              i v------      i  i v  v  i iv  i          v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_223976775_   1756 CGAAATCTCAAAAAAACCCAAGAGT--CCCAATCTATATTAAAATA---- 1799
                         i i  viv   iii -    -  i --  v  v v  v  i   v ----
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCA-GAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_223976775_   1800 AATGAAGTTAGAGGATTAACGCCTCGTGGTTTTGAA-CTTACTACAATGC 1848
                           ii     i     i v  i i  viii   ii  -          v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_223976775_   1849 TTCAGTACCCAAAA-AATGTTGTACCAGCATAGAGACAGACATAAAGACC 1897
                          v     vi   i - i   v    ii     ii  i       v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_223976775_   1898 AAGGCAATA---TTG------------------------------GTCA- 1913
                           v v    ---   ------------------------------    -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_223976775_   1914 -TAATTTTCAACAAGGGAGCCAAAACTATTCAATGAG-AAAGGACAGTAT 1961
                         - i      i       v     i  i        i -    i i   v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_223976775_   1962 TTTT--TAAATAGTGCTAGAAAAACTGGATATTTACATGGAAAAGAATGA 2009
                            i--i    i     i i v         ?ii     v          
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_223976775_   2010 TGTTGAACCCTTACTTTACACCATGTACAAAA--CAATTAAAAATGGATC 2057
                         v    i    i   i i       i       --i  i v          
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_223976775_   2058 AAACATCTAATTGTAAGAGCTAAAACTATAAAACCCTTAGAAGAAAGCAT 2107
                          ? v i    v                       i           i   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_223976775_   2108 AGGGAAAAAGTTTCATAACATAGAATCTGGCAACAATTTCTTGGATATGA 2157
                            ?iv   vi   i i  v v ii iv     iii      i       
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_223976775_   2158 CAGTGAAAGTGCAGGCAACAACA-ACAAAATACATAAAAATAACTTTATT 2206
                           vii    ii  i       v - v      v     vvvi    i  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_223976775_   2207 AAAGTTAAGACCTTTTGTGTGTCTGAAGATACAATCAATAGATTGAAAAT 2256
                            i    i v        iv  vi i  i  v     v i v      v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_223976775_   2257 ACAATTCACAGAGGGGGAGAAAATATCCACACATTATATATCTGATAAGT 2306
                             ii      iv            iii  v  i              v
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_223976775_   2307 AATTAATATCCAGGCTATATAAAGACCTCA-GCAAC--AACAACAA---- 2349
                         i i vi       iv          v   v-i    --  i  i  ----
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_223976775_   2350 -CAAA--ATCAAATTTAAAAATGAGCAAAGGTTTTAAAATACACATTTCT 2396
                         -    -- i v    ?       i       v   i  -  v        
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA-TAGACATTTCT 847

  chr1_223976775_   2397 TTAAAGAAGATATACAAATGACCAGTAAGCACA-GGTGAGGTGCTCAGCA 2445
                         ii                  i   i        - ivi  i      i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_223976775_   2446 TCAATTATCAT 2456
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.72 (124 / 72)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.45 (69 / 20)  


3072 25.06 2.13 0.56  chr1_224021178_224026452.rev     3891  4784 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_224021178_   3891 TGAAAACACATCCCATGCTCATGGATGGGTAGAATTAATGTTGTGAAAAT 3940
                           i   v i        i        v  v   v     i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_224021178_   3941 GACCATACTGCCAAAGGCAATCTACAAATTCAACGCAATCCCCATCTGAA 3990
                          i v     v  v  ivii       i               i   vi  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_224021178_   3991 GACCACCATCATTCTTCACAGAATTACAAAAAC-AATTCTAAAATTCATA 4039
                         vv   v vv v  i  ii     v vv v  i -i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_224021178_   4040 TGGAACCAAAAGAGAGCC-TCATAGCCAAAGCAAGACTAAGCAAAAAGAA 4088
                              viiv   i  v  -vv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_224021178_   4089 CAAACCTATAGGCATCACACTACCTGATTTCAAACTGTACTATAAGGCCG 4138
                             vi iv   vv       v  ii        viv     i  i  ii
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_224021178_   4139 TAGTTACCAGAACAGCATGGTACTGGTATAGAAATAGGCACATAGACCAA 4188
                         i   v i  ii    ii         i   iii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_224021178_   4189 TGGAACAGAATAGAGAACCCAGAAATTAACCCAAA----TACAGCCAAAT 4234
                              i     v    ii        v      v ----  ii i   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_224021178_   4235 GATCTTCGACAAAGCAAACGAAAACATAAAGTGGGGAAAGGACACCATTT 4284
                            i        i vviv i i v   vv i         i i viv   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_224021178_   4285 TCAACACATGGTGTTGGGATAATTGGCAAACCTCATGTAGGAGAATGAAA 4334
                               v      i     i  i   vv ?  v    i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_224021178_   4335 CTGGATCCTGATCTGTCACCTTATACAAAAATCTATTCAAGATGGATTAA 4384
                         i    i  iv i  vv    v           iv i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_224021178_   4385 GGACTTAAACCTAAGTCCTGAAACTCTAAAAATTCTAGAAGATAACACTG 4434
                         i   i    iv    vv  i     v     v ii       v    iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_224021178_   4435 GA-TAAACCCTTCTAGACATTGGCATAGGCAAGGGTTTTAT-GAC-CAAC 4481
                          ?-    i -   vv   v    vv       v     iv -  i-ii  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_224021178_   4482 AACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTAAT 4531
                          --         v v    i    iv   i   i   iv v    i v  
  L1M4_orf2#LINE/    600 A--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_224021178_   4532 TAAA-CTAAGAGCTTTTGCATGGCAAAGGGAACAGTCAGCAGAGTAAATA 4580
                         i   -i   i i      iiivv      iv  vi   iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_224021178_   4581 GACAACCCACAGAGTGGGAGAAAA-ATCTTCATAATCTATACATCTGACA 4629
                                      i          -  i v  -    -   i      i 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGATA 745

  chr1_224021178_   4630 GATGACTAATATCCAGAATCTACAACGAACTCAAACAAATCAGTAAGAAA 4679
                         iiv    vi          v  i  v      vv    v   i   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_224021178_   4680 AA---AAA-AACC--ATCAAAAAATGGGCTAAAGACATGAATAGACAGTT 4723
                           ---   -    --  i?          v  i  iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_224021178_   4724 CTCAAAAGAAGTTATACAAATGGCCAACAA--ACATGAAGAAATGCTCAA 4771
                            v       v               i  --       i i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_224021178_   4772 CATCACTAATGAT 4784
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (123 / 97)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.50 (24 / 16)  


3189 27.12 0.33 0.22  chr1_224044238_224050205     4569  5475 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_224044238_   4569 TGGAGAAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 4618
                             i i i  i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_224044238_   4619 GGCCATACTACCCAAAGTAATTTAAAGATTCAACGCTATCCCCATCAAAC 4668
                            v     v      v i  i  v           v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_224044238_   4669 TACCATTGACTTTCTTCACAGAATTGGAAAACACT-ACTTTAGGCTTCAT 4717
                          v   vivi i  i  ii     v v  v  -i  - iii  iiv     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_224044238_   4718 ATGGAACCAAAAAAGGGCCTGCATAGCCAAGACAATACTAAGCAAAAAGA 4767
                               viiv  ii iv  v v        i     vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_224044238_   4768 ACAAAGCTGGAAGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 4817
                               i    i vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_224044238_   4818 ACAGTAACCAAAACAGCATGGAACTGGCACTAAAACAAATATATAGACCA 4867
                                i   i    ii   v       iv ii i i i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_224044238_   4868 ATGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACAACCATA 4917
                               i    iv   ivii         vv   i    i  iiii  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_224044238_   4918 TAATCTTTGACAAACCTGACACAAACAAGCAATGGGGAAAGGATTCTCTA 4967
                          i  i  i     ivv  v  vi v  vv            i  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_224044238_   4968 TTTAATAAATGGTGTTGGGAAAACTGACTAGCTATACGCAGAAAACTGAA 5017
                           i  i        i     v     iv  ? i i i   i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_224044238_   5018 ACTGGACTCCTTCCCTACACCTTATACAAAACTTAACTCAAGATGGAATA 5067
                         ii     i   v  ii     v         v         i     vi 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_224044238_   5068 -AGACTTAATCGTAAGACCTAAAATGATAAAAATCCTAGAAGAAAACCCA 5116
                         -    i   vi      v      iv      v  i           vi 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_224044238_   5117 GGCA-ATACCATTCAGGACATAGGCATGGGCAAATACTTCATGTCTAAAA 5165
                           ?i- v i -   iv   v v  vv i     vvii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_224044238_   5166 CACCAAAAGCAATAGCAACAAAAGCCAAAATAGACAAATGGGATCTAATT 5215
                                    vv           vv        i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_224044238_   5216 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCGTCAGAGTGAACAG 5265
                            v v  i i   i  ii vv    i  v  i i ivv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_224044238_   5266 GCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAG 5315
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_224044238_   5316 GGCTAATATCCAGAATCTACAATGAACTCAAACACATTTACAAGAAAAAA 5365
                          i  vi          v  i  v      vv   vv iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_224044238_   5366 ACAAATAACCCCATCAAAAAGTGGGCAAAGGATGTGAATAGACACTTCTC 5415
                                    v  i?    i            v          i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_224044238_   5416 AAAAGAAGACATTTATGCAGCCAAAAAACGCATGAAAAAATGCTCATCAT 5465
                         v        i  vi viii     v  i i        i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_224044238_   5466 CACTGGCCAT 5475
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


2184 22.96 3.37 10.82  chr1_224068360_224073827.rev     4000  4979 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_224068360_   4000 GGAAAAACATTCCATGCTTA-AGATAGAAAAAAAATCAGTATTGTAAAAA 4048
                              i i  i     i i -i   v i  i v-- i i      v  i 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGAC--TTAATATTGTTAAGA 49

  chr1_224068360_   4049 TGGCCATACTGCCCAAAAACAATTTATAGATTCAATGCTATTTCTATTAA 4098
                             v     v      v-ii  i  i        i  v  ii    i  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_224068360_   4099 ACTACCAATGAGATGC----TTCACAGAACTAGAGAAAACT-ATTTTAAA 4143
                          v v   ---- v   ----  ii     v v  v  i-  -  ii    
  L1M4_orf2#LINE/     99 AATCCCA----GCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAA 143

  chr1_224068360_   4144 ATTCATATAGACCAAA---AAAATAGCCTGAATAGCCAAGGCAATCCCTT 4190
                                 i  ---  ---  iiv v  v          ii     --  
  L1M4_orf2#LINE/    144 ATTCATATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATC--TT 188

  chr1_224068360_   4191 GCAAAA--AGAACAAAGCTGGAGGCATCATGCTACCCAACTTCAAACTAT 4238
                          v    --         i      vv   ii  v     i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_224068360_   4239 ACTACAGGGCTACAATAACCAAAACAGCATGGTATTGG------AACAAA 4282
                               ii      i   i   i    ii     i   ------i i i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_224068360_   4283 CACATATACCAATGGAATAGAACAGAAAACCTAGAAATAAGGCTGCACAC 4332
                           i   v i             iv  i ii i        ------  v 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA------ACCC 332

  chr1_224068360_   4333 CTACAACTATA--CAACTATTTGATCTTCGACAAACCTGATAAAAATAAG 4380
                         v    vi   i--   ----     i        ----------------
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAA----TTGATTTTCGACAA---------------- 362

  chr1_224068360_   4381 CAATGGGTGCCACTGCACTCCAGTCTGGGCAACAGAGTGAGACTATATCA 4430
                         ----        ---------------------------    i  -   
  L1M4_orf2#LINE/    363 ----GGGTGCCA---------------------------AGACCAT-TCA 380

  chr1_224068360_   4431 CAACAACAACAACAACAAAAAACCCCATAAGCAATGGGGAAAAGATTCCC 4480
                         ---------------------------------         ii  vvi 
  L1M4_orf2#LINE/    381 ---------------------------------ATGGGGAAAGAATAGTC 397

  chr1_224068360_   4481 TATTTAATAAATGTTACTGGGATAACTGGCTAGCCGTTTGCAGAAGATTG 4530
                          v  i  i     v i      i      v  ?  iiv    i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_224068360_   4531 AAATTGGACCCCTTCCTTACATCATGCACAAAAATTAACTTAAGATGGAT 4580
                           i          v   i   i   ii             i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_224068360_   4581 AGAACACTTACATGTAAAACCCAAAACTATAAAAACCCCAGAAGACAACC 4630
                         vi? v  i  v      i v i            vi ii      v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_224068360_   4631 TAGGCAGTA--TCATTCAGGACATAAAAATGGGCCAAGAATTCATGACAA 4678
                             ?-   --  -   iv   v viiiv i   v v iv   v iivv 
  L1M4_orf2#LINE/    548 TAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_224068360_   4679 AGGCGCCAAAAGCAATTTCAACAAAAGCAAAATTGG-CAAATGGGATTTG 4727
                         v i i         vvvv         v    v i -i    v   i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_224068360_   4728 ATTAAACTAAAGAGCTTCTACCCAGAAAAGAAAAATATCAACAGAG-GAA 4776
                           i   v v  i i   i iiv vvv    i v v      v i  -   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_224068360_   4777 CAGACAACCTACAGAATGGGAGAAAACTGTTGCAAACTACGCACCTGGCA 4826
                         v        i                ivv       ii iii i   ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_224068360_   4827 AAGGTCTAATATCCAGCATCTATAAGGAACT--TAAAA---AA-AACCAA 4870
                          i  v  vi       v  v     i     --  v  ---  -  iv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_224068360_   4871 AACACAA----CTCCATTAAAAAGTGGGCAAAGGAAATGAACAGACGCTT 4916
                           v    ---- i v   ?    i           vv    i    ii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_224068360_   4917 TTCAAAAGAAAACATCCATGCAACCAAAAATCATATTTCAAAATGCTCAA 4966
                         i  v      i i  v  viiii    v  v  i  vvv  i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_224068360_   4967 CATAACTGATCAT 4979
                            v ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (129 / 92)
Gap_init rate = 0.03 (28 / 907), avg. gap size = 4.96 (139 / 28)  


2070 28.21 7.98 0.95  chr1_224094480_224097087.rev     1280  2119 (489)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr1_224094480_   1280 ATTCCAAGGTCATGCATTTAAAAAAATCAGTATTATTAAAATGGTCATAC 1329
                           i   v v     v   -ii  i v i i    i    i    iv    
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATT-GGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr1_224094480_   1330 TGCCCGAAGCAATTTACAGATTCAATGCTATTCCTAACAAACTAGCAATG 1379
                          v   i  vii  i           i  v  i    v    v vv  iiv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr1_224094480_   1380 ACATTCTTCACAGAACTT------TT--TTTTAAAA-------------- 1407
                         i v  i  ii     v  ------i -- ii     --------------
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr1_224094480_   1408 -AAG--ACT--GAATAGCCATGAAAATCCAAAGCAAAAATAACAATGCTG 1452
                         -   --  i--         vi v    ivi iv  i  v     v i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr1_224094480_   1453 GAAGTATCACACTACCTGACTTCAAACTATACTACAGGGCTACAGTAACC 1502
                           i vv       v  ii i      viv       ii          i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_224094480_   1503 AAAGTGGCATGGTACTGATACAAAAACAGAAACATAGA-CACATGAAACA 1551
                           iiii ii        ii i  ii i   v i     -  -   i  i 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA-ATGGAATA 307

  chr1_224094480_   1552 GCATAGAGAGCCCAGACA----CCCACA--------ACCATCTGATCTTT 1589
                          v  v     i     v ----    i --------ii  vi    i  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr1_224094480_   1590 GACAAAGCTTAAAAAAACATGCAATGAATAAAGAA----CTTCCAATTTA 1635
                              i v vvv  i v   v     iiv      ----   ----  i 
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT----TTCA 403

  chr1_224094480_   1636 ATAAATGATGCTGGGAGAACTGGCTAGCCATATGCAGAAGATTGAAACGG 1685
                          i     i        v      v  ?   i     i    v    iiv 
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_224094480_   1686 GACCCCTTCTTTAAACCATACACAAAA-----CTCAAGATGAATCAAAGA 1730
                                v i i v      i      -----     i   i    ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_224094480_   1731 CTAAAATGTAAAATCCATAACTA---AACCCT-GGTATACAACCTAG--- 1773
                          iv        i v i v     ---   i  -i v v v   v   ---
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_224094480_   1774 TACCATCCT-G-GACATACAGACAGGCAAAGATTTCATGACGAAGATGCC 1821
                           v-   i - -   v vvi vi      v i    v iivv v  ii  
  L1M4_orf2#LINE/    554 TAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_224094480_   1822 AAAAGCAATTGCACTGAAAGGAAAAACTGGCAAATGGGGTCTAATTAAAC 1871
                                vvv   vii    i     iv ii    v  iii v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_224094480_   1872 TAAAGAGCTTCTGTACAGCAAAAGATACTACTGACAGAGTAAACAGACAA 1921
                          v  i i   i   i vv    i  i    iii v i   i  v      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_224094480_   1922 CATACAGAATGGGAGAGAATTTCTGCAAACTATGTATCTGACAAACGTCT 1971
                          vi             i   v i      ii  i       i  iv v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_224094480_   1972 CATATTCAACATCTATATGGAACTTAAACAAATCTAAAAGAAAAAAACAA 2021
                         ii   i  iv  v    vi     ivv    v  v v  v     i    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_224094480_   2022 ----CTCCATTAAAAAGTGGGCAAAGGAC---AAGA-ACACTTTTCAAAA 2063
                         ---- i v   ?    i           i---  v -   i  i  v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_224094480_   2064 AAAAGATATACATGCAGCCAACAATCATTTTTAAAAA-GCTCAACATAAC 2112
                         i  -        viii     i  v  iv vv   i -         v ?
  L1M4_orf2#LINE/    853 GAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_224094480_   2113 TGATTAG 2119
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.03 (24 / 899), avg. gap size = 3.12 (75 / 24)  


2296 26.03 5.96 1.83  chr1_224143720_224145934.rev      870  1741 (474)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_224143720_    870 TGTAAAGATACCCAATGTTTATGAATTAGAAGACTAATTATTGTAAAG-T 918
                           v       i  v     i   i   i       v v      v   - 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_224143720_    919 GTCA-TATTATCCAAAGCAATCAATAGATTCAATAAACTTCCTATCAAAA 967
                          v  -  i vi     vii   v i        iiv v i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_224143720_    968 TTCCAATGGCCATTTTTAAAATAATGGAATAAA---ATTTTAAAATTTAT 1014
                          i   iiv   v     iv iv   v  -i  i---  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr1_224143720_   1015 ATAGCATTACAAGACATT--GAATAG-----------TTGAGAAATAAGA 1051
                           i v v i    iv ii--      -----------    i   v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_224143720_   1052 ACAAAGCTGGGGGCATCACACTTTCTGATTT-AAAGCTCTATTTGAAAAC 1100
                               i   i  vv        i ii    -   i  -  i vv   i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr1_224143720_   1101 TATGGTAAT-AAGA----GTAGGA-TGGAACAAA-ATAGATACAAAAA-- 1141
                           ii     -    ----  i v -   v i  i-     i i v i --
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_224143720_   1142 AAGGGAACAAAATAGAGAGCTCAGAAATAAACCCATGCATATAAGTTCAA 1191
                           v    i i   v     ii               i   v  v v    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_224143720_   1192 TGAATCTTTAACAAGGGCGTCAAGAATACACAATGCACAAAAGATAGTTG 1241
                          vi  i  ii       i i     vi iv     viv   ii     iv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_224143720_   1242 CTTCAGTAATTGATGCTGGGCAAAAAGAATATCTACATGCAAG----TGA 1287
                         i    ii  v  i       vv  vv i   ? i        i----   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_224143720_   1288 AATTAGACAATTTTTTCTTACATGACAT-CAAGAAATTAACTCAAAAT-- 1334
                          i  i   --iii vi  i   iv i  -   -               --
  L1M4_orf2#LINE/    449 AGTTGGAC--CCCTACCTCACACCATATACAA-AAATTAACTCAAAATGG 495

  chr1_224143720_   1335 ---AAAGACTTAAATGTCAG-GCAGAAATCCTTAAAAATCTTAGAAGAAA 1380
                         --- ?    i       v  -  vi   - iv     v            
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAA 544

  chr1_224143720_   1381 ATATATTTTAAAAACTACTTGATAT--GGTTGTGGTAATGATTTTTTGAA 1428
                          i   vv?vv   v  v v   iv --    i-  i    i   i  ii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGA 593

  chr1_224143720_   1429 TATGACATCAAAAGTACAGGCAACAAAAGCAAATATTAACAAGTTGGACT 1478
                                i      i   i          v   v  vi i  i       
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_224143720_   1479 GCATGAAACTAAAAAGCATCTGCACAGCAAGAAAAAC----AATAAAAT- 1523
                         v   v   v v    i v i  ii vv   iii v  ----  v   i -
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_224143720_   1524 --AAGAAAACCTGAAGGATGGGAGAAAATATTTGCAATCCATATATCAAA 1571
                         --    v    iiv  i                    vi        vi 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_224143720_   1572 TAAAAGGTAGATATCAACAATATATGAGGAACTCAGAAATCAAAAGGAAC 1621
                            ii iivvi    v v       i i      ----- i v  ---- 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTC-----TTACAA----C 784

  chr1_224143720_   1622 ACAATAATAATGATAATAATAATAAAATTGAAAAACAGGCAAAAGACCC- 1670
                         v         vi v vv     ivv    ?     ii      i  iii-
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_224143720_   1671 AATAGATATTTTTCCAATGAAGACATACAAATG-CCAACAGATATATCAG 1719
                               i    i     v     i         -    i iii i  v i
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_224143720_   1720 AGG--GCTGACTATCACCAATCAT 1741
                          i --   v vi    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (134 / 89)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.34 (68 / 29)  


2866 25.41 1.64 2.62  chr1_224193832_224199964     4724  5640 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_224193832_   4724 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4773
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_224193832_   4774 AGCCATAGTGCCCAAAGTAATTTATAAATTCAGTGTTATCCCCATTAAGC 4823
                         i  v   v v      v i  i  i i     ii iv     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_224193832_   4824 TATCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 4872
                          vi  vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_224193832_   4873 ATGAAACCAAGAAAGAG-CCCATA-TAGCCAAGACAAAGGTCCTAAGCAA 4920
                            i  -- v v   i -    v -       i    ---  i i iv  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAA---TCTTGAAAAA 194

  chr1_224193832_   4921 AAAGAACAAACCCGGAGGCATCACACGACCTGACTTCAAACTATACCACA 4970
                         i         vii     vv      vv  ii i      viv   i   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_224193832_   4971 AGGCTACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGATATATA 5020
                          i          i   i     i         i iv ii i   i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_224193832_   5021 GACCAATGGAACAGAAC--ACAGTCCTCAGAAATAACACCACACATCTAC 5068
                           i        i    i-- v     --        vv   i    i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chr1_224193832_   5069 AA-CAATCTGATCTTTCACAAACCTGACAAAAACAAGCAATGAGGAAAGG 5117
                         ii-    -    i  iv    ivv  v   i v  vv     i      i
  L1M4_orf2#LINE/    343 GGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_224193832_   5118 ATTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCATA 5167
                           vvi  v  i  i        i     v      v  ?   i     v 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_224193832_   5168 AAACTGAAACTGGACCCTTA----A-ACCTTATACCAAAATTAACTCAAG 5212
                          i v    ii       i  ---- -   v     v             i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_224193832_   5213 ATGGATAAAAGATTTAAATGTAAGACCTAAAACCGTAAAATCCCTAGAAG 5262
                               v ?   ii           v       ii     ii i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_224193832_   5263 AAAAGCTAGGGA-ATACCATTCAGGACATAGGCATGAGCGAAGACTTCAT 5311
                             vv    ?i- v i -   iv   v v  vv ii  i v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_224193832_   5312 GACTAAAACACCAAAAACAATGGCAACAAA-GCCCAAATTGACAAATGGG 5360
                         iiv  vi         i  vvi        - vvv    v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_224193832_   5361 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTATCAGA 5410
                          ii v  i   v v  i i   i  ii vv    i  v     i vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_224193832_   5411 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTCCAATCTATCCATC 5460
                              v  i     i                 v   v   vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_224193832_   5461 TGACAAAGGGCTAATATCCAGAACTTA-AAACAAAT-TTACAAGAACTTA 5508
                            i  i  i  vi         iv  -   v  v -      ---  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA---CTCA 787

  chr1_224193832_   5509 AAAGAAATTTACAAGGAAAAAAACAAAAAACCCCATCAAAATGTGGGTAA 5558
                          v ---  --------     i     v     v  i?   vi    i  
  L1M4_orf2#LINE/    788 ATA---AT--------AAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_224193832_   5559 AGGATATGAACAGACACTTTTCAAAAGAAGATATTTGTGTGGCCAACAAA 5608
                              v    i     i  i  v           viivi       i  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_224193832_   5609 CATATGAAAAAAAGATCATCATCATTGGTCGT 5640
                           i       i v v   v     ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (133 / 96)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.95 (39 / 20)  


2787 19.67 1.95 2.10  chr1_224482195_224487007     3656  4321 (492)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr1_224482195_   3656 AAAGCTACAGTTATCAAAACAGTATGGTACAGGCATAAAGACAAACATAT 3705
                                    v     i     i      v       i  i i      
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_224482195_   3706 AGAACAATGAAACAGAATAGAGAGCCCATAAATAAACTCTCATGTACACA 3755
                            v     i  i     v     i   v        i vi ii vi ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_224482195_   3756 GCCAAATGATCTCCAACAAGACTGTCAAATCCATACACTAGAGAAACAAT 3805
                          i   v    i i i     iv  i   iv    v  v i i    v   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_224482195_   3806 GCACTCTTCGATAAATGGTGTTGGGAAAAATGGAGATGCACATGCAAAAG 3855
                         ivv  i   i i        i     v  v    v ?v            
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_224482195_   3856 AATGAAGTTGGACTCTAAGTTTACACCATAAACAAAAATTAACTCAAAAT 3905
                                      i iv vi i        v                   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_224482195_   3906 GGATTAGAGACCTAAACTTAAGACCTGAATCTATAAAATT-TCAGAAGAA 3954
                             i ?         iv     v  i  v        i - i       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_224482195_   3955 AATGTAGA---AAATTT----GACATTGGATTTTGCAATGGTTTCTTGAA 3997
                           ii   i---    i ----   v    i  vv             ii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_224482195_   3998 TATGACACCAAAAACACAGGCAACAAAGGCAAAAATAGACAAATGGGACT 4047
                                      i    i        i v         i    v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_224482195_   4048 AGATCAGACTTTAAAACTTCTGCACAGCAAAGGAGACAATCAACAGAG-- 4095
                         vv    i v  v       i  ii vv       v  v     v i  --
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_224482195_   4096 --AAGACAACTTACAACATGAAGAATGGGAGAGAATACTTGTAACACATA 4143
                         --        ii   -------          i    i   i  vv    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACA-------GAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_224482195_   4144 TATTTTGATAAAG-ATTAATATCAACAATATATCTAAAAACTCTTACAAC 4192
                            i -     i - i vi    v v       v-  i            
  L1M4_orf2#LINE/    737 TATCT-GATAAGGGACTTGTATCCAGAATATATA-AAGAACTCTTACAAC 784

  chr1_224482195_   4193 TCTTCAACAACAAGCACAACCAAATAACTTGACTAAAAAATGGGCAAAGG 4242
                           ---  i  i  -- v iv        iii i ?               
  L1M4_orf2#LINE/    785 TC---AATAATAA--AAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_224482195_   4243 ACTTGAATAGATGATTCTCAAAAGAAGACATACAAATGGCCAATAGGCAC 4292
                          i         iiv     v        i                i    
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_224482195_   4293 ATGGAAATATGCTCAACATCCTAATCATA 4321
                            i   v            v????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (77 / 51)
Gap_init rate = 0.02 (10 / 665), avg. gap size = 2.70 (27 / 10)  


3979 19.12 4.09 3.76  chr1_224518355_224521396.rev     1647  2551 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_224518355_   1647 TGGAAAGAC--CCTGAGCTCCTGAATTAAATAACTTAATATTGTTAAGGA 1694
                                 i--  iiv i  v  i   ii vi                iv
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_224518355_   1695 GGCAATGCTTCCCAAGGCAACCTACAGAATCAGTGAAATCCCCATGAAAA 1744
                               i  i     ivii i       v   ii v      i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_224518355_   1745 TCCCAGCAGCATTTTTTTTTGCACAAATGGAAAAACTGCTCCTAAAATTT 1794
                                v  ---i         v    v  v  i   v          i
  L1M4_orf2#LINE/    101 TCCCAGCTGC---CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_224518355_   1795 ACATATATTTGAAAGGGACCCCAAATAGCCAAAACAATCTTTTTTCCTGT 1844
                          i  iv vv  v         vi                  ---------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--------- 188

  chr1_224518355_   1845 CCCCCCCAAACAATCTGGAAAAGAAAGAACAAAGCTGGAAAACTTACTCT 1894
                         -----------------     ii          i    ii   i  v  
  L1M4_orf2#LINE/    189 -----------------GAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_224518355_   1895 TCCCAGTTTCAAAACATACCACAAAGCTACAACAATCAAAATAATGTGGT 1944
                              i         v   i           ii      i i i      
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_224518355_   1945 ATTGGTGACAGGACAGACATACAGACCAATAGACTGGAATTGAGAGTCCA 1994
                          i   iivv    i       i   i    i  v i              
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr1_224518355_   1995 GAAATAAACCTATACATCTATGACCAATTGATTTTCAACAAGGGTGCCAA 2044
                                   i      i    ii            i             
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr1_224518355_   2045 GACCATTTGATGGGAAAAAGAACAGTTTTTTCCATAGAAGGTACTGGAAT 2094
                                ii     i   -   i   i     v i i v   i    i i
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_224518355_   2095 AACTGAATTTCCATATGCAAAAAAATGTGGTTAGATTCCTACCTCATACC 2144
                              i  v?   i        i    vi   i  ii         i   
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_224518355_   2145 ATATAAAAAGATGAGCTCAAAATAGATTAAATACTTCAAAGTAAAAGATA 2194
                              v   i  v i        i   i ? v  i v  v    i  v  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr1_224518355_   2195 AA-CTATTAGGTTTTTTGAAGAAAACATAGATGTGAATCTTTGTGACCTT 2243
                           -    v iii i  v             i?  i      i        
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_224518355_   2244 ATGTTAGCTAATTCTTGCTTCAGTATGACATC------------------ 2275
                         iv     vi   vv  v   vii       i ------------------
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_224518355_   2276 --------TATATAAACTGGATTTCACCAAAATTAAAAAATTTTGTGTAT 2317
                         --------  v     i    i    i            v       iv 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_224518355_   2318 CAAAGGACACTCTCACAAAAATGAAAAAA--ACCTACACGATGAGAGAGA 2365
                                    v   vi   i      i --   i   vi   i    - 
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA-A 719

  chr1_224518355_   2366 AATATTCACCAATCATACATCTGAT---GCACATCCAGTATCCAGAATAT 2412
                               ii v       i       --- v  v ---             
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTT---GTATCCAGAATAT 766

  chr1_224518355_   2413 ATAAAGAACACTCACAACTCAACAACAAAAAGACAAAGAATCCAATTTAA 2462
                                  v  i         i  i           v  i      ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_224518355_   2463 AAATGGGCAAAGGACTTGACTAAACATTTC---AAAGAAGGTCTACAAAT 2509
                                       i    v  i       ---       i v       
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_224518355_   2510 GGCCCCAAAGCCCATGAAATGGTGCTTGGCATCATCGGTCAT 2551
                             vvv    v       v i    iii     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (110 / 59)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 6.45 (71 / 11)  


4458 17.31 3.51 0.79  chr1_224526865_224529501.rev     1263  2146 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_224526865_   1263 TAGGAAGATATCCTATGTTCATGGACCAGAAGACATAATATTAGTAGAA- 1311
                          i i         i           iii      v       iv  ii -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_224526865_   1312 --CAATATTTCCCAAACCGATCTACACATTCAACACAATTTCTA--AAAA 1357
                         --     i i      ii        v       i    ii   --    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_224526865_   1358 TCTAAGCT---TTTTTTGCAGAAATTGATGAGCTAATCCTAAAACTCACA 1404
                           iv    ---                 ii    i         i   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_224526865_   1405 TGGAACTGTAATTGTCTCCAAATAGCCAAAATAACCTTGAAAAGAAAGA- 1453
                              v  i  vv v i vi           i  i        ii    -
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_224526865_   1454 CGA-GCAGGAGGACTCACATGTTCTAATTTCAAAAC--ACTACAAAACTA 1500
                          i - iv            iv i i           --        i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_224526865_   1501 CAATAATCAAAACAGTGTGGCACTGGCATAAAGACAGACATATGGAACAA 1550
                           i       i         i          i  i        i  v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_224526865_   1551 TGGAATAGAATAAAGAGCACAGAGATAAATTCATACATCTAGGGCTAACT 1600
                                    vi    iv    i     ii       i  v  ii  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_224526865_   1601 GATTTGCAGTAAAGTTGCCAAGACTATTCAAAGGGGAAAGAACAGTCTG- 1649
                              v iii  i v         i      v          i     v-
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_224526865_   1650 -CAACAGATTGTGCTGGAATAACTGGATTTCCACATGCAAAAGAATGTGA 1698
                         -     i  v       i i        v?                 vii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_224526865_   1699 TTGGATCCCTGCCTCACATCGTCGATGAAAATTAA--------------- 1733
                              i    i       i i vv ii        ---------------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_224526865_   1734 AGACCGAGATGTAAGCACTAAAACGCTAAAACTCTTATTTAAAAAAAACC 1783
                              v i       vi       vv           ---i  i     -
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA---GAAGAAAAC- 546

  chr1_224526865_   1784 TAATGAAGAGTAGATCTTTGTGAGCTTGGGTTAGGCAATTGTCTCTTAGA 1833
                         --  - i ?   i     i    v               v  i       
  L1M4_orf2#LINE/    547 --AT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_224526865_   1834 TATGGCATCAAAAGC-CAAGGAACCAAATAAAAAACTGATAACTTGGAAT 1882
                             i  i       -    v   v   v      iv     v     v 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_224526865_   1883 TCGTCAAAATTAAAATCTTGCATGTATCAAAGGACACCATCAAGCAAGTG 1932
                           i            v   vii  iv           i      v     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_224526865_   1933 AAAAGACAACCCACAGAATGGGGGAAAATATTTGCAAGTCATGTATTGGA 1982
                                               i              i    i   iv  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_224526865_   1983 TAAGGGACTTGTAAGCAGACTATATAAAGCACTCTTACAACTCAACGACA 2032
                                      vv    v         v               ii i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_224526865_   2033 AAAAGACAAATAACCCAATTAAAATGTGGGTGGAAGAATGGAATA-ACAT 2081
                                             ?   vi    iii i  v v     -    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_224526865_   2082 TACTCCAAGGAAGAGAGGCAAATGGCCAATGAGCACATGAAAAGATGCTC 2131
                          v      i     v vi            i                   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_224526865_   2132 AACATCCTTAGATAT 2146
                               v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (98 / 52)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.92 (38 / 13)  


 882 22.22 5.85 7.31  chr1_224681780_224683817.rev      160   501 (1537)    L1M4_orf2#LINE/L1      166   502 (406)  

  chr1_224681780_    160 CCCAG--CAGCTAAAACCATCTTGAAAGAAAAGGA---AGTGGGAGGAAT 204
                              --i   i     v         i i   i ---   v      v 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_224681780_    205 TGCTGTACCTGCTGGTGAGTCTT----CCTACCGTACATGGCCACAGAAA 250
                         ii ---  i v i---- i i i---- i   --    vi  i    v  
  L1M4_orf2#LINE/    216 CAC---ACTTCCC----AATTTCAAAACTTAC--TACAAAGCTACAGTAA 256

  chr1_224681780_    251 -CAGGGCAGTGTGGCATCCACTGAGGGACAGACACACATATCAATGGAAC 299
                         -  i i        i iivi vv i   i     i i v          i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_224681780_    300 AGAATAGAGAGCCCAGAAA-AAGCCCCCTCAAATATG--CAAGACTGATT 346
                              v     i       -  i   viv  vv    --   --i     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA--TTGATT 354

  chr1_224681780_    347 CCTTTCTATAAAGGTGC--AGCTCCAATTCAGTGGAGAAGGG-CAGCCCT 393
                         ---   v i  i     --  vi --     i   i   i i-i  i i 
  L1M4_orf2#LINE/    355 ---TTCGACAAGGGTGCCAAGACC--ATTCAATGGGGAAAGAATAGTCTT 399

  chr1_224681780_    394 TTCAGCAAATGGTGCCAGAGCAACTAGATACCCACA---AAAGGGAAAAA 440
                             i          ii ii     i    ?     ---   i i vi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_224681780_    441 GT-GAACCTCAGCCTAAACCTTGCTGCACCTTATACAAAAATTACCTCCA 489
                           - i   ----    --   ii ---   v             v   v 
  L1M4_orf2#LINE/    450 GTTGGACC----CCTA--CCTCAC---ACCATATACAAAAATTAACTCAA 490

  chr1_224681780_    490 AATGGATCATGG 501
                                  ?i 
  L1M4_orf2#LINE/    491 AATGGATCAWAG 502

Transitions / transversions = 2.52 (53 / 21)
Gap_init rate = 0.06 (19 / 337), avg. gap size = 2.37 (45 / 19)  

3408 23.36 4.65 1.70  chr1_224681780_224683817.rev      666  1547 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_224681780_    666 TGGGAAGATATTCCCTGATGATGGATTGGAAGAATTAATATTGTTAAAAT 715
                            i       i  v  v v             v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_224681780_    716 GACAGTACTAGCCAAAACAATTTACAGATTTGATGCAATCCCTATCAAAA 765
                          i  i    vv     vii  i        ii i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_224681780_    766 TACCAATGACATTCTGCACAGAAATAGAAAAAA-AATCTTAAAATTTACA 814
                          v   iivi v  i vii       v  v  iv-i   i       i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_224681780_    815 TAGAACCACAAAAGACCCAGCTAAAGACCGAGGATAGCCAAAGCTATCCT 864
                          i   vii   ii       ------------i         i v   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAG------------AATAGCCAAAACAATCTT 188

  chr1_224681780_    865 GAGAAAAAAGAACAAAACTGGAGGCATCACATTACCAGACTTCAAACTAT 914
                           i   i         ii      vv     i v  vi i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_224681780_    915 ACTACAGAGTTATAATAACCAAAACAGCATGGTACTGGCATAAAAATAGA 964
                               i  i  i i   i   i    ii              ii     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_224681780_    965 CACATAGGCCAATTGAAACAGAATAGAAAACCCAGATAGAAATCCAACCG 1014
                           i    ii    - i  i     v  i ii     v v   i   vv i
  L1M4_orf2#LINE/    289 CATATAGATCAAT-GGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_224681780_   1015 TTTACAACCAACTCATCTTTGACAAAGGTGCCAAGAACATACACTGGGGA 1064
                             iiii   i v  i  i     i          v   v  v      
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_224681780_   1065 AAAGACAGTCTCTTCAATAAA--------------CTGGATATCCATATG 1100
                           ii i     i     i   --------------       ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_224681780_   1101 CAGAAGAATGAAACTAGACCCCTATCTCTCACCATATACAAAAATCAACT 1150
                           i         ii i        i   v                i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_224681780_   1151 CGAAATGGATTAAAGACTTAAATGTAAGAACTGAAATTATGAAACTGCTA 1200
                          i        i ?    i           i  i   i   i     vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_224681780_   1201 GAAGAAAACATTGGAGAAACTCTGCAGGACATCGGTGTGGGCAAATGCTT 1250
                                    v  ? v  v   v iv   v i  vv i     vv i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_224681780_   1251 CCTGTGTAAGATCTCAAAAGCACAGGCAACGAAAGCAAACA-AGA----- 1294
                          i ivi  v  ivi          i     i    v   v -   -----
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_224681780_   1295 -------------AGCTAAAAAGCTTCTGCACAGCGAAGGAAAC------ 1325
                         ------------- ii      -   i  ii vv i     v  ------
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_224681780_   1326 -AAAATGGAGAGACAACCCACAGAATGGGAGAAAATATTTACAAACTACC 1374
                         -   i  i i                              i    ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_224681780_   1375 CATCAGACAAGGGAGTAATAATCAGAATATATAAGAAGCTCAAACAACTC 1424
                         i   v  i      v vi  vi            ii i   vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_224681780_   1425 AACAGGAAAAAAATATAGTAATCTGATTTAAAAATGGGCAAAAGATCCAA 1474
                           i iv     i i - i   i ii   ?             i   iii 
  L1M4_orf2#LINE/    787 AATAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_224681780_   1475 ATAGACATTCTTCAAAAGAAGACATACAAATGACCAATAGGTATACAGAA 1524
                                  ii  v        i         i      i i i iii  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_224681780_   1525 AAATATTCAACATCACTGATCAT 1547
                          i  ii         ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.37 (142 / 60)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 6.22 (56 / 9)  


 352 33.33 1.96 0.00  chr1_224747263_224751169     2040  2192 (1715)    L1M4_orf2#LINE/L1      191   346 (562)  

  chr1_224747263_   2040 AAAAGAAAATCAAAGTATGAACATT-ACTCTACCAGATGTCAAAAATTAT 2088
                                i v      vv  iv i -  v  v  vi  v      v   i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_224747263_   2089 CATAAAGTTACAGTAATTAAGACAATG-GATTTCAATGAATGGTTAGATA 2137
                         i i    i         i      i  - i viiiiiiv v  v    i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_224747263_   2138 T-CAGAACAAAGAAATGGAATAGTGAGCTCAGGAACAGTTCTATGCATCA 2186
                          -i   v   v i   i    v v   ii   i  i ivi i  i   iv
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_224747263_   2187 GTGATC 2192
                         i  i  
  L1M4_orf2#LINE/    341 ATGGTC 346

Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.02 (3 / 156), avg. gap size = 1.00 (3 / 3)  

 483 31.79 7.88 2.72  chr1_224747263_224751169     2584  2951 (956)    L1M4_orf2#LINE/L1      388   774 (134)  

  chr1_224747263_   2584 AAGGATAGTGTTTTCA-TAACTAGTGTGTGGACCATTT--TAAACATATG 2630
                            i     v      -i  v i   ivv    v i v--  ?v  i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_224747263_   2631 GGAAGAATTAAAGCATATTGG-----TAATTCATAGCATGCGCGAGAGTC 2675
                         vi  ii v i   ----    -----  vi   i v   iii i i i i
  L1M4_orf2#LINE/    438 CAAAAGAATGAAG----TTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_224747263_   2676 AGCTCCTGGTGGGTTAGAGACCTCAGGGTAAAAGGTAAAACAATAAA-CC 2724
                          i   vvii   i i ?      v iv    i  v      v     - i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_224747263_   2725 CCAAGATGGTAAGCATAGGC-TA--TCTACAGAATTTAGGGTAAGGAAGT 2771
                          iv   v i-  i      ?-  --   v ivi ii v    v   v i 
  L1M4_orf2#LINE/    534 CTTAGAAGA-AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_224747263_   2772 G----TTTAAATAGAACAC-AAATGCCCTAACCACAATGGACAAGATTGA 2816
                          ----i   i   vi    -   v  v v i v    vi  v  i  v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_224747263_   2817 TATATTTGAGTACATTAAAACTAAAAGGTCTGATTCATCAGAAGGTGCCA 2866
                           v   v  v v   i    i     iv i vi v v   i i iii i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_224747263_   2867 T-AAGAGA-TGAAAACCCAAGTCACACAGGTAGG-GAAGATA----CAAA 2909
                          -    i -      vv   vi    v i- i  -   i   ----    
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAA-TGGGAGAAAATATTTGCAAA 731

  chr1_224747263_   2910 GTGCATAATTG-T----GACCTCTCTAACATTAAAATATATGAAGAA 2951
                         viii   vi  - ----   i v v ----ii i       i     
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTAT----CCAGAATATATAAAGAA 774

Transitions / transversions = 1.38 (66 / 48)
Gap_init rate = 0.05 (18 / 387), avg. gap size = 2.17 (39 / 18)  


2660 26.67 4.54 1.70  chr1_224819127_224821245      746  1626 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_224819127_    746 GAGAGACATACCATGTTCATGGATTGGAA--CTCAACATAGCTAAGATG- 792
                           i   i  v                   --  i  i  v i       -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_224819127_    793 ---------CCAAATTGATATGTAGGTTTAATGCAGTTCCTATAAAAATC 833
                         ---------          v ii  i  i  i   i i     v      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_224819127_    834 CCAACAAGATTTTTTTATATACACAGATGAGCTTGTTCTAAAATGTATAT 883
                            i v- vi      ii v v iv  ii    vi i       vi    
  L1M4_orf2#LINE/    103 CCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_224819127_    884 GGGAAGGCACAGAACTTAAAATAGCTAAAAACCATTTTGAAAAACAAGAA 933
                           i  v   vi i  ii i      i    - v  i        v     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAA 200

  chr1_224819127_    934 TAAAATGGGAAGGAC-CATTCTACTTAATGTTAAGATTTACTATTTAGCT 982
                         i   i v   -    -  iv  v ii   v i  i i      ivv    
  L1M4_orf2#LINE/    201 CAAAGTTGGA-GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_224819127_    983 TAAGTATTAAAGACAGTGTGGAATTTGTAGAGGGATTGACACATAAATCA 1032
                         vv    v v            v i v i v i    v    i   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_224819127_   1033 GTGGGACAAAATGGAGAATACAGATTTAGACTCATACAAATATGTCCAAG 1082
                         i   i i i   v    i v    vv  i  i      vv    vi   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_224819127_   1083 TGATTTTTGACAAAAGTGCAAAAGCAATTAAATGGAGGAAGGATAGAATT 1132
                                i     ii    v  ii v   v     i i   i    vv  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_224819127_   1133 T-CAACAAATTTGGTGCTGGAGAAATTTGGACATGCATAGGCAAAA-AAT 1180
                          -        --        -  v vi    i ?v  i v      -   
  L1M4_orf2#LINE/    400 TTCAACAAAT--GGTGCTGG-GACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_224819127_   1181 GACCCTTAACCTAAACTTCACACCTTATATGAAAATTAACTCAAAATCAA 1230
                           vvi vi   ivv  i       v    ii                vi 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_224819127_   1231 TTGCATCCTTAAAT---------------ATAAAACTTTTAGGGGAAAAA 1265
                          ii? vv i     ---------------        i    ii     v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_224819127_   1266 AATGGCAGAGAATCTTTAGGATCTTAGGCTATGAAAAGACTTCTTAGACT 1315
                          - i v? vi      iiv  i   i  i  v v  v ii        iv
  L1M4_orf2#LINE/    547 A-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_224819127_   1316 TGACAGTTAAAGCACCATCCATAAAAGGAAAAACTGGTAAACTGGATCTC 1365
                              viv       v v v i     i     iv i    i    ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_224819127_   1366 ACCAAAATTGAAAACTTTTGCTCTGAGAAAAACCCTGCTGTGTAGAGGAT 1415
                          i       i          iv  vvi  ii  ---i  i vv   iii 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC---ACTATCAAGAAAGT 692

  chr1_224819127_   1416 GAAATG-----TTACAGATTGGAAGAACATGTTCACAAATTATGTATCTT 1460
                             v -----ii     v   i    v  i  ii     i  i     v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_224819127_   1461 GTAAGGGACTTTTATCTAAATAAATACAAAGAATGCTCAAAATTAAGCAG 1510
                         i          v    i i - v   i      iv  i v  i v ii i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGA-ATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_224819127_   1511 TAAAGAATTTTAAA-AATCCAGTTGTAACATGGGCAAAAGACT---ATCC 1556
                             i ivi--   -  i   i  ?v  v         i  i ---  --
  L1M4_orf2#LINE/    792 TAAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT-- 837

  chr1_224819127_   1557 AGTCATTTCATGGGAGAGGATATGCAGAAGGTAAATTAGCATATGAAA-G 1605
                           v      vivii   i     i  i v  iv   v    i      - 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_224819127_   1606 ATGTTCAACATCATTAGCCAT 1626
                            i         ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (139 / 92)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 2.75 (55 / 20)  


3206 27.25 0.44 0.66  chr1_225015377_225021771.rev     4995  5904 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_225015377_   4995 TGGAAGAATATTCCATGCTCATGAGTAGGAAGAATCAATATCATGAAAAT 5044
                              ii    i     i     ii v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_225015377_   5045 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5094
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_225015377_   5095 TACCAATGACTTTCTTCACAGAA-TCGGAAAAAACTA---CTTAAGTTCA 5140
                          v   iivi i  i  ii     - i -- v  i  i---  v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_225015377_   5141 TATGGAACCACAAAAGAGCCCGCATTGCCAAGTCAATACTAAGCCAAAAG 5190
                                vii   ii  v  v v  v     iv    vi i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_225015377_   5191 AACAAAGCTGGAGGCATCATTCTACCTGACTTCAAACTACACTACAAGGC 5240
                                i      vv   iv  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_225015377_   5241 TACAGTAACCAAAACAGCATGGTACTGGTCCCAAAACAGAGATATAGACC 5290
                                 i   i    ii         iviv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_225015377_   5291 AATGGAACAGAATAGAGACCTCAGAAATAATGCCACATATCTACAACTAT 5340
                                i     v    vii         vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_225015377_   5341 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGAAAAGGATTCCCT 5390
                         i    i  i     ivv  v   i v  vvv      i    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_225015377_   5391 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5440
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_225015377_   5441 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5490
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_225015377_   5491 AAAGACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAACCT 5540
                          ?    i       v   v       i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_225015377_   5541 AGGCGATACTATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5590
                            ? vv v v   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_225015377_   5591 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5640
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_225015377_   5641 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAACAG 5690
                            v v  i i   i  ii vv    i  v    i  vv i i    v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_225015377_   5691 GCAACCATTCTGTAGAATAGGAGAAAATTTTTGCAATCTACTCATCTGAC 5740
                         i     ----iii     i         v       vii ivi      i
  L1M4_orf2#LINE/    699 ACAACC----CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_225015377_   5741 AAAGGGCTAATATCCAGAATCTACAATTAACTCAAACAAATTTACAAGAA 5790
                           i  i  vi          v  i  vv     vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_225015377_   5791 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGAGGCT 5840
                            i     i     v  i?    i            v    i   vii 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_225015377_   5841 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5890
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_225015377_   5891 TCATCACTGGCCAT 5904
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.50 (10 / 4)  


2982 26.97 1.44 0.67  chr1_225098791_225105073     4890  5790 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_225098791_   4890 TGGAAGAACATTCCATGCTCATGGATAGGAAGCATCAATATCATGAAAAT 4939
                              ii i  i     i        v     vv i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_225098791_   4940 GGCCGTACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4989
                            vi    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_225098791_   4990 TACCAA-TGA---TTTAACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5033
                          v   i-  v---   vi     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_225098791_   5034 T--GGAACCAAAAAAGAGCCCTCATTGCCAAGACAATCTTAAGCAAAAAG 5081
                          --    viiv  ii  v  vvv  v     i        i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_225098791_   5082 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5131
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_225098791_   5132 TACAGTAACCAA-ACAGCATGGTACTGGTCCCAAAACAGAGATATAGACC 5180
                                 i   -    ii         iviv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_225098791_   5181 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACACCTACAACC 5228
                                i    i--    i  --        vv   i   ii  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_225098791_   5229 ATCTGATCTTTGACAAACCTGGCAAAAACAATAACTGGGAAAAGGATTCC 5278
                          vi    i  i     ivv  v   i v  v v v    i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_225098791_   5279 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5328
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_225098791_   5329 GAAACTGGATCACTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5378
                            ii    i v  v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_225098791_   5379 TTCAAGACTTAAACATTAGGCCTAAAACCATAAAAACCCTAGAAGAAAAC 5428
                          iv?    i    ii v  iv       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_225098791_   5429 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACGTCATGACTG 5477
                         v    ?i- v i -   iv   v v  vv i     v iiv  v iiv i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_225098791_   5478 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGGTCTA 5527
                         vi            vvi          vv     v  i    v  iii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_225098791_   5528 AATAAA-TTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGA 5576
                          vi   -     i -   i  ii vv v  i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_225098791_   5577 ACAGGTAATCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5626
                          v  ii  i i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_225098791_   5627 AAAGGACTAATATCCAGAATCTACAGAGAACTTAAACAAATTTACAAGAA 5676
                           i     vi          v  i i      ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_225098791_   5677 AAAAACAAACAAACCCATCAAAAAGTGGACAAAGTATATGAACAGACACT 5726
                            i     i  v  v  i?    i   i     v  v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_225098791_   5727 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5776
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_225098791_   5777 TCATCACTGGTCAT 5790
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


 843 28.48 11.92 3.53  chr1_225116102_225118687.rev      727  1179 (1407)    L1M4_orf2#LINE/L1       63   553 (355)  

  chr1_225116102_    727 CAAATTTATCTATAGATTCAATGCAATCTCAAACAAAATCCCAATAGCTT 776
                               v     i        i      i v v          iiv  i 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_225116102_    777 TTGTGTCTGTGTGTGGAAATTTAAAAGTCAATC-TAAAATT--TGTGGAA 823
                           v -------  ii      v v   iii   -       -- i     
  L1M4_orf2#LINE/    113 TTTT-------TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_225116102_    824 ATA-AA-----CAAAAGTAGCTACAAAAATGTAGAAGAAGGAGGAGATAG 867
                           i-  ----- v i i    i v  v   v v   i   i  i v v  
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_225116102_    868 TTCAAGGACTAACACTACT-------AAAATTTAT-------CTA----- 898
                           vi      v     v i-------    i   i-------   -----
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_225116102_    899 --------------GTATAAATACAAGGATATAAA-ATAAACTGATGGGA 933
                         --------------   iviii i       v v -   i iii    i 
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr1_225116102_    934 AAAAATAGAGATTCCATAAACAGACCCATGCTCCTATGCACACTTGATCT 983
                         v i   v    v    v   i i      i vii    vv  v     i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr1_225116102_    984 GTGATAGGAGACACTGC-AGAACCCT------GAGGAAGAATGATCTTTT 1026
                         vi  i i i ----   - ii   v ------ i i      ii      
  L1M4_orf2#LINE/    356 TCGACAAGGG----TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_225116102_   1027 CAAGAAACAGTGCTGCTTCAATTTCATATCAATAAGGAGGAAAATGAAAC 1076
                            v   ii      vvv   i vv   ? v i v v ii i      ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_225116102_   1077 TTGAACCCTACTTAA-ATCACATGCAAGCATATCAATCCTTG---TGAAC 1122
                          v  v      i v - i  i  i   -- v  i  --  ii---  i i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAA--AAATTAA--CTCAAAATGGAT 497

  chr1_225116102_   1123 TGCAGATCTAAGTTTGAAAAGTAAAACAATAAAGGTTCTTAGAATATAAT 1172
                         ii?   i    i v i i iv      v     i-i        v v  i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr1_225116102_   1173 ATAGGAG 1179
                              ? 
  L1M4_orf2#LINE/    547 ATAGGNG 553

Transitions / transversions = 1.62 (78 / 48)
Gap_init rate = 0.03 (17 / 491), avg. gap size = 4.12 (70 / 17)  

 346 23.53 28.99 0.42  chr1_225116102_225118687.rev     1858  2095 (491)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr1_225116102_   1858 AAAGGTACTAAACA-CTAAGGAAAAGATGTGTATATTAGACTAAATTAAA 1906
                            i i  -  i  - v  i     i  ivi  v   i    vv  i   
  L1M4_orf2#LINE/    603 AAAAGCAC-AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_225116102_   1907 ATCAGGAACCT--------CAAACGATTGCATTAAGAGAACTAAATGACA 1948
                           i ii   i --------    v  ivvi  i    i iiv   v    
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_225116102_   1949 A------------GAGAATGTGTTTGCAG--TATATATTTGACAAAGGA- 1983
                          ------------     vi i      i--i      i   i  i   -
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_225116102_   1984 --------AGA---------------------CTTAATAA-GAAAAGACA 2003
                         --------   ---------------------  i     -i        
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_225116102_   2004 AATAG--------AAAAATGGCCAA--GAT----ATATA-ACTTCACAAA 2038
                             i--------        v   --   ----   v - i   v v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_225116102_   2039 AGAGGATATTCAAATGGCCAATGCATGCATGAAAAGGAACTCAATATCAA 2088
                            i     v            iviii         ivi     i    ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_225116102_   2089 TTGTTAT 2095
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.11 (38 / 18)
Gap_init rate = 0.04 (12 / 306), avg. gap size = 5.83 (70 / 12)  


3280 26.98 0.44 0.44  chr1_225149393_225155053     4261  5168 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_225149393_   4261 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4310
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_225149393_   4311 GGCCATACTGCCCAAGGTAATTTACAGATTCAGTGCCATCCCCATCAAGC 4360
                            v     v     iv i  i          ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_225149393_   4361 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4408
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_225149393_   4409 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4458
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_225149393_   4459 AACAAAGCTGGAGGCGTCACACTACTTGACTTCAAACTATACTACAAGGC 4508
                                i      vv       v iii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_225149393_   4509 TACAATAACCAAAAAAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4558
                             i   i   i v  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_225149393_   4559 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 4606
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_225149393_   4607 ATCTGATCTGTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 4656
                          vi    i vi     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_225149393_   4657 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4706
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_225149393_   4707 GAAACTGGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATGGG 4756
                            ii    i  i v   i     v              i    i    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_225149393_   4757 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4806
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_225149393_   4807 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4856
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_225149393_   4857 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4906
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_225149393_   4907 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4956
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_225149393_   4957 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5006
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_225149393_   5007 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5056
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_225149393_   5057 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5106
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_225149393_   5107 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5156
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_225149393_   5157 ATCACTGGCCAT 5168
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2033 27.88 7.76 1.76  chr1_225408935_225411832.rev     1562  2411 (487)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr1_225408935_   1562 ATATACCATATTCATGGATTCAAAAAAACTAAATATT-TGGAGGTATTGA 1610
                             v    i          --ii  i   v      - vi  i ivii 
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATT--GGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_225408935_   1611 TTGTTTCCTAAAG-GGTCTATATTGATTTAATGAAATTCTGATCAATATC 1659
                          -ii i  i   v- i    i --    i  i v   i iv     v   
  L1M4_orf2#LINE/     56 T-ACTCCCCAAATTGATCTACA--GATTCAACGCAATCCCTATCAAAATC 102

  chr1_225408935_   1660 CCAGCAGAATTTGTGGTGGAAACCGACAAGCTGATGCTATAATTTATATA 1709
                              v vv   v v ii    ii           v   v    i    i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_225408935_   1710 TAGCCACATGTAAAAGGCTAAAAATCGCTAAGACAAACTTAAAGAAGAAG 1759
                         v i----   i  ii i iv i   v  i  i    v   i  i      
  L1M4_orf2#LINE/    153 GAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_225408935_   1760 AAAATAGTTGTGGGACATGCACTACTAGACATAAAGACTCAT---AAATC 1806
                           v v     vi    vii    v ivi iv v  i   i i---   v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_225408935_   1807 GATAGTAGTTAAGACAGTGCAGGACTG-CAGCAAGAATATATGGGTAGAC 1855
                         v i    i i         ii v    -  -i   i   v iivi    i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGAT 297

  chr1_225408935_   1856 CCATGGTACAGAAT--AGAGTCCAGCAATAGGCCCA--CATTATATGGAT 1901
                          v    v i     --         v    ii    --    -     vi
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGGTC 346

  chr1_225408935_   1902 ATGTGATTTATGACAAAGGTAGCACATAAAAT--AATGGAGAAAGGAT-- 1947
                          vv      vi     i   iv  - v vv  --     i     i  --
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAG 395

  chr1_225408935_   1948 TTTTTTAAAAAACAAATGATGCTGGGTTGATTAGATATCCAAA---AAAC 1994
                          i    v  ---      i       vii i i    ?   v ---   v
  L1M4_orf2#LINE/    396 TCTTTTCAA---CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_225408935_   1995 GAATAATCTTG-ACGTTTATC-------ATATACCAAAAGCAATTTCAGG 2036
                             i vv   -  vii  i -------      v    vi  i iv ii
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_225408935_   2037 TGGACCACAGATCAAAATGTGAAAGATAAAATAATAAGGCTCATAGAGCA 2086
                             i  ?   i v      i i  v     iv    ii   v    iv 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_225408935_   2087 TAACATTGGAGACTGTCTTTGTGACTTTGAGGTAG-------------AG 2123
                         v     v  ? vvvi    i     i   i v   -------------  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_225408935_   2124 A----ACACAAAAAGCAGTAGCCATAAAGGGAAAGATTGATAAACTGGAC 2169
                          ----    v       vv   v i   i i   i  v      i     
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_225408935_   2170 TATATTAAAATTTATAACTTCTGTTCATCAAAGTATACCATTAAAAGAAT 2219
                          vi  i      v v     i   v v      v i  i  i  i i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_225408935_   2220 GAAAAGA-------------------AGATATCTGCAA--CATGTAACAA 2248
                                ------------------- i    i     --   i  v vi
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_225408935_   2249 A-AAGG--TTCATAAGAAGAATAAATAAAAGACTCCTACTGATCAATATG 2295
                          -    --i ii  vvv      v     ii    i   viv      vv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_225408935_   2296 AAAAGGACAGACAACCCAGTAGAAAAATTGGCCAAAGACCTGAATAGGCA 2345
                             i    i i      i v?      v   v  i  ii       i  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_225408935_   2346 CTTAACACATGAGAACCTCTAAATAGCTAATAAACATATGAAAAGGTGCT 2395
                         i  vv vv v  ii iv vi    i  i     i  i        i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_225408935_   2396 AAACCTTATCAAACAT 2411
                         v   v i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.03 (25 / 901), avg. gap size = 3.24 (81 / 25)  


4383 17.13 2.21 1.88  chr1_225435785_225437812      631  1535 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_225435785_    631 TAGAAAGATTTCCCAAGGCCATGGATAGGAAGAC--AATATTATTGAGAT 678
                          i       v     v vi       v       --      i  i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_225435785_    679 GACAATTCTCTCCAAACTGATCTATAGATCTAACACAATCTTTACCAAAA 728
                          i    v   i     i       i    ii   i     ii  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_225435785_    729 TTCTAACCAGCTCTTTTTCAGAAATTATTAACAAGCTGATCCTAAAATTC 778
                          i i i iiv  i    v        i---                    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_225435785_    779 ATGTGAAAATGCTAGGGACCCAGAATAGCCAAAACAATCTAGGAAAAGAA 828
                           i  i      v                           v i       
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_225435785_    829 ---CAAACTTGAAGTTTTCACACTTCCTGATTTTCAAACTTATTATAAAG 875
                         ---    v   i  vvi          ii    iv       i  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_225435785_    876 CTATAGTAATCA-GACCATATGGTACTGACATAAGGA-AAACATA--GAT 921
                            i        -   vi i        i        - i     --   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_225435785_    922 CAATGAAATGTAATCGAGTGTCCAGAAATAAACCCTT-TATTTATGGTCA 970
                              i   iv   i   v                v -i           
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_225435785_    971 ATTGATTTTTCAGAAGGGTGCCAAGACAACTGAATGGGGGAAAAATAGAC 1020
                                  iv v              v i v       i  i     v 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_225435785_   1021 TCTTGAACAAACAGTGGTGGACACAAATAAACAGTGATGTCCACAAATAA 1070
                          i  v      ii   v   i-    v i------   i?     vii  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGG-ACAACTG------GATAKCCACATGCAA 440

  chr1_225435785_   1071 AAAAGTAAAGTTGGACCCTCTACCTCACGCCATACACAGAAATTAACTCA 1120
                           i i i           -         i     i   i           
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_225435785_   1121 GAATAG-TCACAGACATAAAGGTAAGAGCTAACGTCATGAAACCCTTTGG 1169
                         i   i -   ?    v    v           viii  i    i   v i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_225435785_   1170 AAAAAAAACAG-----AATCTGTACGATCTTGATTTAGGCAATGGTTTGT 1214
                          i    v i  -----     viii  i    iv              v 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_225435785_   1215 TACATATAGCACCAAAAGCACAAACAACAAAAGAAAAAAATAGATAAATT 1264
                           v    ii              i               -          
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATT 638

  chr1_225435785_   1265 GAACTCTGTCAAAGTTAAAA-TTTTTGTGCTGCAAACAATACTATCAAGA 1313
                          i   iii     i      -i         v    vi i          
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_225435785_   1314 AAGAGGAAAAAAATAACCCACAGAATAGAGGGAACTATTAGCAAATTCAC 1363
                            v --    i i            i ii i  v    v      -  i
  L1M4_orf2#LINE/    689 AAGTG--AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT-CAT 735

  chr1_225435785_   1364 GTAT--AGCAAGGGATTTATATCCAGAGTATATAAAAGAATTCTTACAAC 1411
                         i   --iii      i  i        i        -   i         
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAA-GAACTCTTACAAC 784

  chr1_225435785_   1412 TCAATAATAAAAAGACAAGTAATCCAATT-AAAAATGGGCAAAGGATTTG 1460
                                           i   i      -                    
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_225435785_   1461 AGTAAACATGTCTCCAAAGAAGACATATGAATGACAAATAAGAACTTGAA 1510
                          i  i    v             i   ii    i v      v  v    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_225435785_   1511 AAAAATGCTCATCATCATTAATCAT 1535
                           i -      v     ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (108 / 45)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.85 (37 / 20)  


2784 28.13 1.33 0.78  chr1_225492518_225494957     1045  1947 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_225492518_   1045 TGGAAACACATCTCACACTCATGGATGGGTAAAATCAATATGGTGCAAAT 1094
                               v i   i  iii        v  v i v i     v  vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_225492518_   1095 GACCTTATTGCCAAAAGCAATCTACAAGTTCAGTGCAACTCTCATCAAAA 1144
                          i vv  i v  v   vii       ii    ii    ii ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_225492518_   1145 TACCATCATTG--TTCTTCACAGAACTAGAAAAAAAAATCCTAAAATTCA 1192
                          v   v --  --  i  ii     v v  v  ivvi             
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_225492518_   1193 TGTGAAACCAAAAAAAGAGTCCATA-TAGCCCAAACAAGACTAAGCAAAA 1241
                          i  i  -- viv  i iii   v -     v      vvi i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_225492518_   1242 AGAACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAAG 1291
                                 vi      vv     i v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_225492518_   1292 ACTTTAGTCACCAAAACAGCATGGTACTGGCATTAAAATAGGCACATAGA 1341
                         i  vi   v i   i    ii            v ii    i  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_225492518_   1342 CCAATGAAACAGAACAGAGAACCCAGAAATAAAGCCAAATACTTACAAGT 1391
                         i     i  i    iv    ii           v   v i i   iiivi
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_225492518_   1392 AGCTGATCTTTCACAAAGCGAACAAAAATGTAAAGTGGGGAAAGGACATC 1441
                          ii    i  iv    i vviv   i vii vv i         i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_225492518_   1442 CTGTTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATATAGGAGAAT 1491
                           v                    i  i   vv ?      ii ii     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_225492518_   1492 AAGGTGAGATCCTCGTCTCTCACCTTACACAAAAATCAACTCAAGATGGA 1541
                         i i  vi  i  iiii   v    v  i        i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_225492518_   1542 TCAAAGACTCAAATCTAAGAACTGAAACCAAAAATATTCT-AGAAGATAA 1590
                            ?    ii    v     i  i    i v   - i   -      v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chr1_225492518_   1591 CATCAGA--AAACCCGTTCTAGACTTTGGCTTAGGCAAAGATTTCATGAC 1638
                            vi ?--   i --   vv   i    v        v i    v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_225492518_   1639 CAAGAACCCCAAAGGAAATGCAACAAAAACAAAGATAAATAGGTGGGACT 1688
                         i v  vv  v    v v v         iv   i   i   ii v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_225492518_   1689 TAATTAAACTAAAAAGAGTCTGCACAGCAAAAGAAATAACCAGCAGATTA 1738
                          v  i   v v    ivv i  ii vv    i  v iv i  iv i v i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_225492518_   1739 AATAGACAACCCACAGAGTGGAAGAAAATCTTTGCAAACTATGTATCCAA 1788
                           v              i   i       v        ii  i    ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_225492518_   1789 CAAAGAACGAATATCCAGAATCTACAAGAAATTCAAACAAACCGGCAAGA 1838
                         i  i i  vvi          v  i  ii  i  vv    vi iii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_225492518_   1839 AAAAAA-AAAT--CCCA---TCAAAATGGGCTAAGTACATGAATGGACAA 1882
                             i -    --    ---?v         v   v iv     i    v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_225492518_   1883 TTCTCAAAAGAAGATATACAAATGGCCGACAAACACATGAAAAAAGGTTC 1932
                              v                     i i  i          i v i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_225492518_   1933 AACATCAATAATTAT 1947
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (151 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


2950 25.37 8.25 0.25  chr1_225522914_225526114.rev     1900  2711 (490)    L1M4_orf2#LINE/L1       32   908 (0)  

  chr1_225522914_   1900 GACTCAATATTATCAAGATGTCAGTTCTTTCCAATTAGGTCTATGTATTC 1949
                             i      i i      v  i v  ii    v v i    iiv    
  L1M4_orf2#LINE/     32 GACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTC 81

  chr1_225522914_   1950 AATGTAATCTCAACCCAAATTACAGAAAGTTATTTTGTGGATATTGAAAA 1999
                           i i    i v i v    iv   vvivi v     ii  v     v  
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

  chr1_225522914_   2000 ACTGATTCCAAAGTTTATATGAAGAGGCAGAAGACC-------------- 2035
                         i     i i   i  i     i i v   iii    --------------
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_225522914_   2036 ------TGAA-------------GTTGGAGGACTGAC------------- 2053
                         ------    -------------           v  -------------
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_225522914_   2054 ---------TATAAGGCCACAATAATCACGACAGTGTGGCATTGGCACAG 2094
                         ---------  i  i  i   i      v          i i     i i
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_225522914_   2095 AAATGAAC-T---GATCAATGGAACAGAAAAAAGAGCCCAGAAATAGACC 2140
                         ii  ii  - ---           i    vvi    i         i   
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_225522914_   2141 CACACAAATATAATCAACTGACCTTTGACAAAGGAGCAAAGGAAATTCAA 2190
                           i   vv   ii    i   ii  i     i  v  v   ivv      
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_225522914_   2191 CGGAGAAAGGATAGTCTTTTCAACACATGGTGCTGGAACAACTGGATATT 2240
                         i  i     i               v          i           ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_225522914_   2241 CACATGCAAATCAGTGAATCTAGACACGCATCTTTCACCTTTCACAAAAA 2290
                                   vv i    vi i   v vi i  iv    v vi       
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_225522914_   2291 CTAACTCAAAATGAATCATAGACCTAAATGTAAATCAG--AAAACCATAA 2338
                         i            i    ?              i--  --     i    
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAG--AGCTAAAACTATAA 529

  chr1_225522914_   2339 AACTCCTATAAGATGACACAGGAGAAAATGTAGGTGACTTTGGGTTTGGC 2388
                              i  v    vi   i   ? v    v vv     i       v   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_225522914_   2389 AATCACTTTTTAGACACAACAGCAAAAGTACCATTCATAGCACAGAACAT 2438
                            vii  i     i ii   v      i  v viv i iv v i  v  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_225522914_   2439 TGGTAGGTTGGATTTTACTAAAATTAAACATTTCAGCTCTGTGAGAGACA 2488
                         v i  ii     i  i ii         v i  iv iv  vii ii    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_225522914_   2489 CTGTGAAAAAAAT-AAGACACAATTCACAAGATGGGGAAAAATATTTGCA 2537
                           i v  i   i -  i v    ii    ii     ii            
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_225522914_   2538 AAACACAAAGCTGATAATGGTCTGGTATCCAAAATAGACACAGAACTCCT 2587
                           v  i v v       v  v  v       i    v i v       i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr1_225522914_   2588 AAAACTCAACAATAAAAAAGTGAACAAC-----TTAAGAATGGGCAAAAG 2632
                          v       i        iiii  i   ----- ?  i          i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_225522914_   2633 ACTCAAACAGACACCTCACCAAAGAAGGTGTATGGATGGCAAATAAACAT 2682
                          i ii  i     ii  v         i i  iii     v     i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_225522914_   2683 ATGAAAAGATGCTCCACATCGTCTGTCAT 2711
                                       v     i????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (134 / 68)
Gap_init rate = 0.01 (9 / 877), avg. gap size = 7.67 (69 / 9)  


1787 26.98 0.20 0.40  chr1_225795819_225799232.rev        1   504 (2910)    L1M4_orf2#LINE/L1      295   797 (111)  

  chr1_225795819_      1 GACCAATGGAACAGAATAGAGAACCCAGAAATAATCCCAAATATTTACAG 50
                           i        i     v    ii          v    v i     ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_225795819_     51 CCAACTGATTTTCAACAAAGCAAACAAAAACACAAAGTGGGGAAAGGACA 100
                         i   i        i    i vviv   i v  ivv i         i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_225795819_    101 CCCTTTTCAACAAATGGTGCTGGGATAATTAGTTAGCCACATGTAGGAGA 150
                         vi                       i  i i v  ?       i ii   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_225795819_    151 ATGAAATTGGATCCTCATCTCTCACCTTACACAAAAATCAACTCAAAATG 200
                              i     i  ii i   v    v  i        i           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_225795819_    201 GATTAAGGACTTAAACGTAAGACCTGAAACTGTAAAAATTCTAGAAGATA 250
                            i ?i   i    i      v  i     i     v ii       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_225795819_    251 ACATTGGAAAAACCCTTCTAAACATTGGCTTAGGCAAGGGTTTCATGACC 300
                             v  ?iv  vi    vvi  v    v        v      v iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_225795819_    301 AAGAACTTCAAAGTGAATGCAATAAAAACAAAGCTAAATAGTTGGAACCT 350
                          v  vviiv    iiv v    i    iv   iv  i   iv v i  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_225795819_    351 AATTAAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAA 400
                         v  i   v v  i i      ii vv    i iv  vi   iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_225795819_    401 ACAGACAACCCACAGAGTAGGAGAAAA-ATCTTCACAATCTATACATCTG 449
                          v              i i        -  i v  -    -   i     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTG 742

  chr1_225795819_    450 ACACAGGACTAACATCCAGAATCTACAATGAACTCAAAGAAATCAGTGAG 499
                          i vi     vii         v  i  v      vv v  v   i i v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_225795819_    500 AAAAA 504
                              
  L1M4_orf2#LINE/    793 AAAAA 797

Transitions / transversions = 1.42 (78 / 55)
Gap_init rate = 0.01 (3 / 503), avg. gap size = 1.00 (3 / 3)  

4491 17.43 1.31 2.40  chr1_225795819_225799232.rev     2006  2923 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_225795819_   2006 TGGAAAGACATCTCATATTAATGGATTGGAAGACTTAATAAGACACTATT 2055
                                 i   i   i  v                    ----------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA---------- 40

  chr1_225795819_   2056 AATAAGACTTAATAAGATGCTATTACTACCCAAAATGACCTACAGATTCA 2105
                         --------  iv       vi v    v      v   i           
  L1M4_orf2#LINE/     41 --------TTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCA 82

  chr1_225795819_   2106 ATACAATCTCTATCAAAATCCTAGCAGTTTTTTTTGCAGAAATGGAAAAA 2155
                          ii     i            i   v ii              v  v  i
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG 132

  chr1_225795819_   2156 CTCATCTTAAAATGCATATGGAATTGTAAGGGACCTTGAATAGCTAAAAC 2205
                           v   i      v         v  i        iv       i     
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr1_225795819_   2206 AATCT-GGAAAAGAAGAACAATGTTGGAAGACTCACACTTCCTGATTTCA 2254
                              - i             v      i             ii      
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_225795819_   2255 AAACATATTGCAAAGCTATAGTAGTCAAAACAGTATGGTATGGGCAAAAA 2304
                             v  i i        i    i    i     i     iv    v  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_225795819_   2305 GTCAGACATATAGACCAATGGAATAGA-----GAGTCCAGTAATCAGCCC 2349
                          vi           i            -----        v   v i   
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_225795819_   2350 TCAGATATATGGTCAAATGATTTTTGACAAGGGTGCCAAGACCATTCAAT 2399
                         vi v  v         v       i                         
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_225795819_   2400 GGGAAAAGTAAAGTCTTTTCAACAAATAATGCTAGGAAAATTGGATATTC 2449
                            i    v v                ii    i   v  i      ?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_225795819_   2450 ACACATAAAAGAATGAAGCTGGACCCTTACCTAACACCATAAACAAAAAT 2499
                            iii            i       i     v        v        
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr1_225795819_   2500 TAACTCAAAATGGGTCAAAGACCTAAATGTAGGACCTAAACCTTTAAAAC 2549
                                      i   ?             i  v     v  v      
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_225795819_   2550 TCTTAGAAGAAAATGTTGGGCAAAAGCTATATAATATTGGGTTTGGCAGT 2599
                                      ii v  ?vv   v  vii i iv       v    i 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_225795819_   2600 GATTTCTTGGCTATAACACTGAAGGCACAGGCAAAAACATAAGAAATAGA 2649
                          i      i v   i    ii  i     i    v  v v  i       
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr1_225795819_   2650 CAAATTGAGCCTTACAAAAAATTTTTAAAA---TTTGTTCATCAAAAGAA 2696
                         i      ii i i iv    ----      ---     v v     i  v
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAA----TTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_225795819_   2697 GCTATCAGTAGAATAACAGGA-AATCTACAGAATGGGAGAAAATATTTGC 2745
                         i      iv i i i v i  -  i i                       
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_225795819_   2746 AAATCATATACTTGAAAAGGGATTAGTATTCA-AATGCACCAAGAACTCT 2794
                                   ii   v      i v    i  -   ii iv         
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_225795819_   2795 TAAAATTCGATGACAGAAAGACAAAGAATTGAATTCAAAAATAGGCAAAT 2844
                           v  i  i  i i i         v  iiv    ?      i      v
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_225795819_   2845 AACATGAATAGACATTT-TGCAAAGAAGATATACAAAAGACCAAGAAGCC 2893
                         i iv             - v                 v i    v    v
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_225795819_   2894 CATGAAAAGATGCTCAACATCACTAACGTT 2923
                                               ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (95 / 61)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 4.25 (34 / 8)  


1644 23.97 5.90 9.62  chr1_225941966_225943685.rev      450  1229 (491)    L1M4_orf2#LINE/L1      158   908 (0)  

  chr1_225941966_    450 GTAGGTGACTTAAAAGCTTATTTAAATAAACTTTTTACAACAAGGACATC 499
                          i i v   ii i  ---  vii   vv  ii  vv v  v   i   --
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAA---TAGCCAAAACAATCTTGAAAAAGAAGAACA-- 202

  chr1_225941966_    500 CTAAAGTTAGAGGAATCATCCTCTTTGATTTTGAGATATAACTATAAACC 549
                         ---     i     v   iv  iiiii    ii i iv  -   i   v 
  L1M4_orf2#LINE/    203 ---AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAAAGC 248

  chr1_225941966_    550 TATAGAAATCAAGATATTGTGGTATTGGCAAAGAGAGCTACACACATAGG 599
                           i  v        i v       i     v ii  --  v   i    i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA--TAGACATATAGA 296

  chr1_225941966_    600 TCAGTGTAACAGAATAGAGAATACAGTTATAGATCCACATA---AAGGCA 646
                            i  v  i     v    i v   vv   i i   i i --- v  i-
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT- 345

  chr1_225941966_    647 CCCATTTGGTCTTTGATGAAGGTGCAAAAGCAATTCA-----GAAAGGAT 691
                         --  v   i i  i  ii i     v  ii v     -----     i  
  L1M4_orf2#LINE/    346 --CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_225941966_    692 GGTTTTTGACGATGATTTTTCTCTGTATCAATGCATAGTGTAGGAACATT 741
                         i  i   --------------------    iiv  i   iv  i   vi
  L1M4_orf2#LINE/    394 AGTCTTT--------------------TCAACAAATGGTGCTGGGACAAC 423

  chr1_225941966_    742 TGTAATTTTAAAATTACAAATGACCAATTTGTATTGTATTGTATTGAATT 791
                           -i  v?iv v  -i    v  --------------  vivi   i --
  L1M4_orf2#LINE/    424 TG-GATAKCCACAT-GCAAAAGA--------------ATGAAGTTGGA-- 455

  chr1_225941966_    792 TTCCCTTAAACCTCATACCTTGTTACAAAGATTAATTTGAAATGGGTCAT 841
                         --   i  --     i   v i -     i     i ii      i   ?
  L1M4_orf2#LINE/    456 --CCCCTA--CCTCACACCATAT-ACAAAAATTAACTCAAAATGGATCAW 500

  chr1_225941966_    842 AGATCTAAATGTAA-------AACAGTAAAACTTTTAGAAGAAAACAGAA 884
                            i          -------   vi       i             v i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_225941966_    885 GA--AAATCATCATGACCTGAGATTAGACA--GAGTTCTTGGAAAT--CA 928
                          ?--     v  i      vi i    i  -- iv     i  v  --  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_225941966_    929 CCAAAAGCATGATCCATAAAAGAAAAGTTTGATAAAATTAATAATAAAAT 978
                                  ii v v i         iv v      -  ii-- ivvv  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA-TTGG--ACTTCAT 647

  chr1_225941966_    979 TAAAATAAAATAAAAATTTAAAGCGTTGCTTTGCCAAAGACA------AG 1022
                         i     ----      i  ------   ivi v v  i    ------  
  L1M4_orf2#LINE/    648 CAAAAT----TAAAAACTT------TTGTGCTTCAAAGGACACTATCAAG 687

  chr1_225941966_   1023 AAAATGAAGAGACAAGTTACAGAGTAAGAAGAA---TTTGCAAATCATGT 1069
                            i    i      vii     i ii  ii  ---            i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_225941966_   1070 ATCCAGCAAAGGACTTGTATCCAGAATAT--------TTTTTAAAATTC- 1110
                            iiii  i                   --------i i   v  i  -
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_225941966_   1111 -TAAACTTGATAAGA-AAACAATGCAGTTTAAAAACAGGGGCTA-GGACT 1157
                         -   --- i v    -   i  iv  i  ?     i--    v -   i 
  L1M4_orf2#LINE/    788 ATAA---TAAAAAGACAAATAACCCAATTWAAAAAT--GGGCAAAGGATT 832

  chr1_225941966_   1158 TGAACAGACACTT----AGTGAGGATATAAGGATGGCACATAAGCACATG 1203
                             i     i  ---- iv  i      vii     vv           
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_225941966_   1204 AAGAGATGTTCAGCATCATTAGCCAT 1229
                           i     i   i     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (123 / 60)
Gap_init rate = 0.04 (31 / 751), avg. gap size = 3.90 (121 / 31)  


3411 17.65 3.14 11.66  chr1_226122660_226124983.rev      848  1833 (491)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr1_226122660_    848 GACATCC-ATACTCATGGATTGGAAGACATTGTATTGTTTAGATTACAGT 896
                           i    -  ii                v vi       v    vi  i 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_226122660_    897 AACACTCAAAGCTATCTACAGATTCAATGAAACCCCTAT-AAAGTCCTAA 945
                          viv i    viv              i v  i      -   i   i i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_226122660_    946 CTGTTTTTTTTTCAGAAATAGAAAAAC-------------CATATAGAAT 982
                            ii      v       v  v  i -------------     i   v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_226122660_    983 TTCAAAGTACCCTAAACAGCCAA-----TCTTGAGAAAGAAAAACAGAGC 1027
                          v   i v    vi  i      -----      i      i    i  i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_226122660_   1028 TAAAGATCTCATACTTCTTGATTTCAATATATATTACAAAGCTATAGTAA 1077
                          ii  iv    i     iii       v iv  i          i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_226122660_   1078 TCAAAACAGTATCGTACCGGCAAAAAGACAG---TATACA-CACTACAAT 1123
                             i     i v    i    v  i  i  ---    v -  v iv   
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_226122660_   1124 AGAATAGAGAGCCCAGAAATAAGCCCTCATGTTTGTGGTCAAATGGTCTT 1173
                              v     i          i   vi ii   i       v  i i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_226122660_   1174 TGACAAGGGCGTCAAACATACACAATAGGGAAAGGATAGTCTCTTCAACA 1223
                         i        i i   ivvi iv    i       i       i       
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_226122660_   1224 AATGATGTTGGGAAAACCACACATCCACATGCAAAAGAATAAA-TTGTAC 1272
                             i  i     v   iiv i ?                i  -   v  
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr1_226122660_   1273 CC--ATCTCACAGCATATTAAAAAATTAACTCAAAATGGATCAAAGACCT 1320
                           -- i      v     vv                       ?      
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr1_226122660_   1321 AAATTTA-GACCTAAAACTATAAAACTCTTTGAAGAAAACA-GGGCACCA 1368
                             v  -  v                   v          -i  ?iiv 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr1_226122660_   1369 GCC--CATGACATTGGATTTGGCAATGACTTCTCGGACCTGATACCAAAA 1416
                         ii -- i    v    i  v       ii    ii  iv   i       
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr1_226122660_   1417 GCACAGGTAATAAAAAAAAAAAAATAGGTAAATTGAGCTTCATCAAAATT 1466
                              i i  i    i      --   i       ii             
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAA--TAGATAAATTGGACTTCATCAAAATT 654

  chr1_226122660_   1467 AAGAACTTTTGTGCATCAAAATACACCATCAAAAGATAATTTATACCATC 1516
                           i           v     iv    i     i i -----------i v
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA-----------GTG 693

  chr1_226122660_   1517 AAAAGAGAAGTAATATATCTTATATTACTTATACTAATAAATTACTAATT 1566
                               --------------------------------------------
  L1M4_orf2#LINE/    694 AAAAGA-------------------------------------------- 699

  chr1_226122660_   1567 ATATATTATTAGTAATATATTTTGATGCACTTACCTTTTGTGCATCAAAA 1616
                         --------------------------------------------------
  L1M4_orf2#LINE/    700 -------------------------------------------------- 699

  chr1_226122660_   1617 CATACCATCAACACATAGAATGGGAGAAAGTATTTACAAATCATTTATCT 1666
                         --------    v  i             i     i        v     
  L1M4_orf2#LINE/    700 --------CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_226122660_   1667 AATAAGAGGTTAATGTCCAGGATATACAAAGAACTCTGATAACTCAATAA 1716
                         i     i ii vi i     i     i          v i          
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_226122660_   1717 CAATAACATAAACAAACAAATTTAAAAATGGGCAAAGGACTTGAATAGAC 1766
                         i  v  v i   i  v v    ?                i          
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_226122660_   1767 ATGTCTCCAAAAAAGATAGACAAATGGCCAACAAGAACATGAAAAGAGGC 1816
                           v        i      v            i   v           v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_226122660_   1817 TCAGTGTCACTAATCAT 1833
                            iii   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (112 / 58)
Gap_init rate = 0.02 (14 / 902), avg. gap size = 10.43 (146 / 14)  


2845 25.31 2.80 1.12  chr1_226184736_226190377.rev     4259  5151 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_226184736_   4259 TGGAAAAACATTCTATGCTCATGGATACCAAGAATCAATATTGTTAAAAT 4308
                               i i  i i   i        vvv    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226184736_   4309 GGCCATACTGACAAAAGCAATTCACAGATTCAA-GCTATTCCTATCAAAC 4357
                            v     vv v   vii  ii          -  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226184736_   4358 TACCAATGACATTCTTCATAGAATTAGAAAAAGT-ATT-TAACATTCCTA 4405
                          v   iivi v  i  iii    v v  v  iv -  i-   v    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_226184736_   4406 TGGAACCATAAAAGAGCCCAAATAGACAAAGCAATCCTAAGCAAAAAGAA 4455
                              viii  ii  v  vi     v    i     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_226184736_   4456 CAAAGCTGGGGCA-TCACATTACCTGACTTCAAACTATACTACAAAGGCT 4504
                              i   i v -     i v  ii i      viv          -  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG-CT 249

  chr1_226184736_   4505 ACAGTAACAAAAACAG-ATGATACTGGTACAAAAACAGACACA--GACCA 4551
                                iv  i    -i  i      i i  ii i     i --  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_226184736_   4552 ACGGAACAGAATGGAGAGCTCAGAAATAAACT-GTACACCTACAACGACC 4600
                          i    i     v     ii           i-i    ii  iiiiv vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_226184736_   4601 AGATCTTTAATAAGTCAATG--AAAACAAG-CAATGGGGAAAAGACTTCC 4647
                         v   i  ii i   --ii  --  i  v v-           ii ivvi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAG--GGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_226184736_   4648 TATTCAATAAATGGTGCTGGAATAACTGGCTAGCCATATGCAGAAGATTC 4697
                          v     i            i i      v  ?   i     i    v v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_226184736_   4698 AAACTGGGCACCTTATTTACACCATATACAAAAGTCAACTCAAGATAAAT 4747
                           ii   i v   vvi i               i i       i  ii  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_226184736_   4748 TAAAGACTTAAATGTAAAACCTAAAACTATAGAAACCCTAAAAGATAACC 4797
                         i ?    i         i v           i  vi i  i    v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_226184736_   4798 TAGG---AAATACCATC-TGGCCATAGGCCCTGGGAAA-GATTTCA-GGA 4841
                             ---    -- v  -  i  v i  i-- i  v  - i    v-i  
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--CTTCGTGACCTTGGGT--TAGGCAATGGTTTCTTAGA 593

  chr1_226184736_   4842 TGAAGACACCAAA--CACAATTGCAACAAAAATAAAAATTGACAGATAGG 4889
                          - v         --     --         iv      v  i i  v  
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_226184736_   4890 ACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGA 4939
                           i v  i   v v  i i   i  ii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_226184736_   4940 GTAAACAGAAAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATC 4989
                           i  v   v    i                          ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_226184736_   4990 CAACAAAGGTCTAATATCCAGAAGCTACAAGGAACT--TA-AACT-AACA 5035
                         ii i  i  v  vi         vv  i  i     --  -    -  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_226184736_   5036 AGTAAAAAACAAGCAACCCCATTAAAAAGTGGGCAAAAGACATGAACAGG 5085
                          vv    i    ii     v   ?    i        i  iv    i  i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_226184736_   5086 CACTTTTCAAAAGAA-ACATGCACACAGCCAACAAGAATATGAAAA-ATG 5133
                           i  i  v      - i  i  v ii     i   v i       -   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_226184736_   5134 TTCAATATCACTAATCGT 5151
                         i    i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (146 / 77)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 1.40 (35 / 25)  


3238 21.13 11.92 0.37  chr1_226205383_226209280.rev      859  1672 (2226)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_226205383_    859 TGGAAA--CATTCAATGTTCATGGATTGAACGAC--AATATTA------- 897
                               --i  i v              i v   --      i-------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226205383_    898 ----------CCCAAAACAATCTACAGATTAAATGCAATCCCTATCAAAA 937
                         ----------      vii           v  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226205383_    938 TTCCAATAGCTTTTTTGGCAGAAACAGAAAAATCCATCCTAAAACTCATG 987
                          i   iiv  i     v       iv  v  iiiv         i    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_226205383_    988 TGGAATCCTAAGGGACCCCAAATAGCCAAAGTA-TGTTGAAAAAGAAGAG 1036
                              vivi         vi          ii - v             i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_226205383_   1037 CAGAGTTGGAAGTTTCACACTTCCTAATTTCAAGACTCA----------- 1075
                           i       i vi          i        i   i -----------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_226205383_   1076 ------------------------------------------TAGAACAA 1083
                         ------------------------------------------    v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_226205383_   1084 TGGAATGAAACAGAGATCCCAGAAATAAATCCTTGCATACATAGTCAAAT 1133
                               ii  iv    vi           i  v i   vi  i     v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_226205383_   1134 AATCTATGAC-----TGC---------TTAATGGGGAAAGGACAGCCTTT 1169
                         i  i vi   -----   --------- i           i i  i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_226205383_   1170 TCAACAAGTGGTATTGGAA-AACTGAATATTCATGTGCAAATGAATGAAG 1218
                                i    ii   i -     i   ?i  ii      v        
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_226205383_   1219 TCGTACTCATACTT-ATACTATATACAAAAATTAACATGAAATGAACCAA 1267
                          i v  i v   i - i  i                vii     i i  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_226205383_   1268 AGGTCTAAACTCAAGGACTAAAACTATAAAACCCTTAGAAGAAAACATAG 1317
                           ii     ivi   ii               i                 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_226205383_   1318 GGGAAAAGCTTTATGACATTGGCTTTGGCAAAGATTTTTTTTGGTTATGA 1367
                          ? v   v   ii    v    v  v     v i   i  --i v     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--AGATATGA 598

  chr1_226205383_   1368 TACTGAAAGCAGAGTCAACAGAAGAAAAAGTAGACAAATTGCACTACATC 1417
                         i  ii      v iv     i        i    i      v   v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_226205383_   1418 AAAATTAAAATTTTTTTATACATCAAAAGACAC----AAAGTAGTGAAAA 1463
                                   vi    -i i v     i     ----  iiv        
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_226205383_   1464 AGCAATCCAATAAATGAAACAAAATATTTTCAAATTATATATTTCATAAG 1513
                         ii   i   vvi    ii v         v     i      i v     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_226205383_   1514 GAGTAAATATCCAGAATATATAAAGAACTCTTACAACTCAACAACAAAAG 1563
                          iiivvi                                  i  i    i
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_226205383_   1564 AACAAACAGCCCGATTTTTAAATGGTCAAAGGACTTGAACAGACATTTCC 1613
                         i     i i   i   ?vv      v       i     i         i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_226205383_   1614 TCAAAGAAAATATGCAAATAACCAATAAACACATGAA--GATGCCCAATG 1661
                         i       i    i     ii       i        --     i   ii
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_226205383_   1662 CCACTAATCAT 1672
                         i  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.36 (118 / 50)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 7.69 (100 / 13)  

2872 24.04 4.85 2.37  chr1_226205383_226209280.rev     2547  3432 (466)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_226205383_   2547 TGGAGAGATTTCTTGTGTTCATAGATTGGAGGAATCAATGTAGTAAAGAC 2596
                             i    v  iii       i       i  v i   i v  v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226205383_   2597 ATCAGTTCTCCTCA----GATACATAGATTTGTCAAAATTCCTTTTAAAA 2642
                         iv  i v    i  ----   vi i     iiv iv   i   v i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226205383_   2643 TTTCTGCAAGATTTTTTGTAAATATAGATAA-CTGTGTTCTAAACTTTAT 2691
                          ii v  vivv       i i v  v  i  -   -i i     v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chr1_226205383_   2692 A-AGAAAGGCAAACAAACTTGGAGAGCTAACCCAATTTTGCAAAAGAAGA 2740
                          -i    v    ivi v iv i v   i  vv    i   v         
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_226205383_   2741 ATAGAGGCGAAGGAATCAGCCTACCCAATTTCCACACCT-CTA----GTT 2785
                          i i  vi i    v   vv  v         v v  i -   ---- i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_226205383_   2786 ACAGTAACCAAGACTGTGTGGTATTGGCAGAAGGGTAGACTTACAGATCA 2835
                                i      v        i     v    i     v  i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_226205383_   2836 ACAGAGCAGAACAGAGAACCCAGAAATAGACCTGTACAAATATGCCCAAT 2885
                          ii  ii    iv    ii         i   ii    vv    vi    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_226205383_   2886 -GATTTT-GACAAAGGTGCAAACGCAATTCAGCGAGGAAAGA-TAGCCTT 2932
                         -      -     i     v  vi v     ii i       -   i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_226205383_   2933 TTCAGCAAATGGTGCTGGAGCATATGGACATCCATAATTAAAAACATGAA 2982
                             i             ii  vv    i ?   i vvi    iv     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_226205383_   2983 CCTCCATCTCAATCTCATATCTTATACAAAG-TTAACTCAAAATAAATCA 3031
                         vi vv i i v i    i i v        i-            ii    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_226205383_   3032 CAGACTTCAAT------------AC-ATAAAACTTTTAGAAAAA----TA 3064
                         ?    i v   ------------  -        i      i  ----  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_226205383_   3065 GGAGAAAACTTTTAGGATCTAGGGCTAGGCAAAGTGTTCTTACATTTGAC 3114
                           ? v   ii  iiv  i  v   i       v vv      v  v    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_226205383_   3115 ACCAAAAGCATGATCCATAAAAGGAAAAATTGATCAATTGGGCTTGATCA 3164
                                   ii v v i     i      v   v      i   v    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_226205383_   3165 AAACAAAAAACTTCTGCTCTATCAAAG-ACCCTGTCAAGAGGGTGAAAAG 3213
                            iv        i  iv  -      -  v  i      ii        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_226205383_   3214 ACAAGCCATAGGCTGGGAAAGAAAAATTTGCAAACCACACATCTGATGAA 3263
                             v   i  iv     i -   v         i  i i       i i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGA-AAATATTTGCAAATCATATATCTGATAAG 747

  chr1_226205383_   3264 TAACTAGAGTCTAGAACATATTTTTTTAAA---CTCTCA-AACTCAATAG 3309
                         vi   v vi  i    i    ------   ---    i -         i
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATAT------AAAGAACTCTTACAACTCAATAA 791

  chr1_226205383_   3310 TGAAAAAACAAATGA----ATAAGAAAATGGGCCAAAGGAAAAAAAAAGC 3355
                          i    i      i ----  v?i         -      vvvi  ----
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGC-AAAGGATTTGAA---- 836

  chr1_226205383_   3356 TAGAAATATTTCACCAAAGAGGATGGATAGGTGGCAAATAAGCATCTATG 3405
                             --i     v       i   iv i ii    v        i--   
  L1M4_orf2#LINE/    837 TAGA--CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC--ATG 882

  chr1_226205383_   3406 GCAA-ATGCAAATTAA-ATCACAGTGTAC 3432
                         iv  -    --- i  -    ????????
  L1M4_orf2#LINE/    883 AAAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (126 / 83)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.37 (64 / 27)  


2501 22.92 10.03 1.17  chr1_226346138_226347902      505  1272 (493)    L1M4_orf2#LINE/L1       73   908 (0)  

  chr1_226346138_    505 TACCAATATCAAAGCAAATCCAATGAAAATCCTAGCAGAAGTTTTTTCTT 554
                            vi  -    v    vi  v  v       i   v -----ii  i  
  L1M4_orf2#LINE/     73 TACAGAT-TCAACGCAATCCCTATCAAAATCCCAGCTG-----CCTTTTT 116

  chr1_226346138_    555 TGGTAGAAATTAACAAGATGATTATAAAATATATTTGGAA-TACAGAAG- 602
                           -i       i     v    iv      vi  v     - i  iii -
  L1M4_orf2#LINE/    117 TG-CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_226346138_    603 -------------------TTTTGAAAAAGAA---CAAAGTTAGGGGACC 630
                         ------------------- i           ---       i i    i
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_226346138_    631 CTCATATCT-GATTTCAATTTTTACTATGAAGCTATAGTAATCAAGAGAG 679
                          v  iv  i-i       vvi      ii      i           v  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_226346138_    680 TGTGATTTTGGAATAAAGATAGACATATCGGTCAACGTAAATGAACAGGG 729
                             i vi   v    i           v i    i v  vv   iv i 
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr1_226346138_    730 TGTCTAGAAATAGATCCATACATATATAGTCCATTGAATTTTGACAAGG- 778
                         v   i       i i        v   i   v     v   i       -
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr1_226346138_    779 CATCAGGGTAATTAAATGGAAAAACA-T-GTCTTTTTGACA-----TACT 821
                         iii  i iiv   v     ii   v - -       ii   ----- i  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr1_226346138_    822 -------TT--------------AAAAAAATGAA------CATTTACCTC 844
                         -------i --------------    i      ------ vii      
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr1_226346138_    845 ACAACATATACAAAAATTAATTCAAAAT----CATAGACTTAAATGGAAA 890
                            v                i       ----  ?    i      v  i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_226346138_    891 AGCTAAAGCTATAAAATTTCTAGAAGAAAATATAGGA--AAACAATTATG 938
                                i        i ii          i     ?--   ivv ii  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_226346138_    939 ACATTGGGTTAGGCAACATATTTTTAGATAAAACACTAAGAGCATGAACC 988
                           v             iivv  i       vi    i  i    ii i v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_226346138_    989 ATAAAAAAGAAAATTGGTAAATTAGACTTCA---AAATGTTAAAATGTTT 1035
                          i    i i     v i      i       ---    - v    iv   
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTTT 664

  chr1_226346138_   1036 GCTCTTTAAAAGGCATGGTTAAGAAAATGAAAAGATAAGCCATAGACTGG 1085
                          iv   i   i i  ivi i      i        i  v   i   v   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_226346138_   1086 GAGGAAATATTTGCATAATGCATATCTGATAAAGGACT-GTATTCAAAAT 1134
                            i           v viii           i     -    i  i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_226346138_   1135 AAATAAACAACTC----AATTCAATTATAAGAAAGCAATT---CCATTTA 1177
                          v     v     ----  i     v    i  ii   v ---   v  ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_226346138_   1178 AAAAAAAAGGCAAAAAATGTGAATAGATATTTTACCAGAGAAGAAATATG 1227
                              vi-      ii  v        i    iv   i      v   ii
  L1M4_orf2#LINE/    815 AAAAATG-GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr1_226346138_   1228 TGTAACCAATTTGCATATGAAAAGATGCTCATCATTATACCTCGC 1272
                         vi ii     vv   i               v   i ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (112 / 61)
Gap_init rate = 0.03 (22 / 836), avg. gap size = 3.91 (86 / 22)  


2311 20.74 18.18 1.92  chr1_226376412_226379601     1917  2697 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_226376412_   1917 TAGAGAGACATACC---TTTGTGGGTTGGAAGAATTAAT-TT--TAAGAT 1960
                          i  i   i  v  ---  ii   i        v     -  --      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226376412_   1961 GTCAATTTTCCTCAAATAGATGTATGTACTTAATGCAATCTCTATAAAAA 2010
                          v    vi   i     v   v  iiv i i  i      i    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226376412_   2011 T------------------AGAAATTGACAAGCTGATTCTAAAATTTATA 2042
                          ------------------                  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_226376412_   2043 TGGAAATGCCAAGTACCTGAAGTAGCAAAAATAATTTTGAAAAAGAA--- 2089
                                  v i v   iii i    v    i   i           ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_226376412_   2090 CAAA-----------------------TTT-------------------- 2096
                             -----------------------   --------------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_226376412_   2097 ------------------GGTATTGGCGTAAAGATAGA----TAGATCAA 2124
                         ------------------    i    i   i      ----        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_226376412_   2125 TGGAATAGAAT----AGTC-AGAAA--AATTCACACAC--GTGAAAAACT 2165
                                    ----    -     --  ii  i   i--i  ivv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_226376412_   2166 GATTTTTAATCAAAAT---AGAATCGTAATTCAGTAGAGAAAGCATAGTC 2212
                               ii iv iii --- ii i ---     i i i     v      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACC---ATTCAATGGGGAAAGAATAGTC 397

  chr1_226376412_   2213 TTAGGAACTAAATAGTGTCAGAACAGTTACTG----------TGCAAAAA 2252
                           vvv   -    i   iii i   ---    ----------       i
  L1M4_orf2#LINE/    398 TTTTCAAC-AAATGGTGCTGGGACA---ACTGGATAKCCACATGCAAAAG 443

  chr1_226376412_   2253 AACCCTCAA-TTCAA----TATTTCATACTATATATAAAAATTAA----- 2292
                           --- v  -  vi ----  ii   i  i     i         -----
  L1M4_orf2#LINE/    444 AA---TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_226376412_   2293 -ATGGTTCACAAATCTAAATGAAAAACCTACAACTATAACAATTCT-GGA 2340
                         -    v   ? i i       v  i v   v        -  i   -i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGA 539

  chr1_226376412_   2341 AGACAATGGAGAAGAAAATTTTTGTTACCTTAGGTTAGGTAAAGGTATTT 2390
                            v  iiv  i? v    i  i  v     i       i  v   v i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_226376412_   2391 TAGATATGACATCAAAAACA-AAGTGTATATGAGAACAAATTGATAAACT 2439
                                    i     i  -   ii- i vi    v    v      i 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCA-ACAAAAGAAAAAATAGATAAATT 638

  chr1_226376412_   2440 AAAC--CATCAAAATTAAAAACGTTTTCTTTTCCAAAGACATTGTTAAGA 2487
                         ii  --                v   vivi   v  i    i i i    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_226376412_   2488 GA-----AAGATAAGTCACAGATTGGAAGAAAATATTTGCCAATCATATA 2532
                         i -----    i  vi      v   i             v         
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_226376412_   2533 TGTGATAAAGGACTAGTATCCGGAATATATTGAGAACTCTCTA-AACTTA 2581
                          v      i     v      i        vi        -  -    i 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAACTCA 787

  chr1_226376412_   2582 ATAGTAAGAAAACAAACAACTTAAGTCTTAAAAGTGGGCGAAAGATTTGA 2631
                            i   i  i     i   ii  --i ?    i     i  i       
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAA--TTWAAAAATGGGCAAAGGATTTGA 835

  chr1_226376412_   2632 ATAGGAACTTCACCAAAGAAGACACATGTGTAGCAAA-------ATGCAA 2674
                             iv i   v          i i iivi i  v  -------   v  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_226376412_   2675 AGATGCTCAACATCATTAGTTAT 2697
                                        ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (111 / 48)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 5.06 (157 / 31)  


3162 23.31 1.96 3.05  chr1_226397371_226401666.rev     2888  3805 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_226397371_   2888 TGGAAACATATCCCATACTCATGGATGGGTAGAATCAATATTGTGAAAAT 2937
                               v         ii        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226397371_   2938 CACCATGCTGCC-AAAGCAATCTACAAATTCAACGTCATCCCCATCAAAA 2986
                         vi v  i  v  -   vii       i        iv     i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226397371_   2987 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTACAATTCATA 3036
                          v   v vv v  i  ii     v v  v  ivii  i   v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_226397371_   3037 TGTAACCAAAAAAGTGCCCACA-TAGCCAAAGCAAGGCTAAGCAAAAAGA 3085
                           v  viiv  ii -i    v -        i   vvi i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_226397371_   3086 ACAAATCTGGAGGCATCACACTACCTGATTTCAAAATGTACTATAAGGCC 3135
                              vi      vv       v  ii         iv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_226397371_   3136 ATAGTCACCAAAACAGCTTGGTACCAGTATAAAAAATAGGCACATAGACC 3185
                          i   v i   i    iv      ii i    ii -   i  i     i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATC 298

  chr1_226397371_   3186 AATGGAACAGAATAGAGAACCCAGAAATAAGCCCAAATACTTACAGCCAA 3235
                                i     v    ii          i    v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_226397371_   3236 CTGATCTTTGACAAGG----CAAACACAAACAAAAAGTGGGGAAAGGACA 3281
                         i    i  i       ----   ivv  vv   ----         i i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAA----TGGGGAAAGAATA 394

  chr1_226397371_   3282 CCCTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGA 3331
                         vi                       i  i   v  ?       i ii   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_226397371_   3332 ATGAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATG 3381
                              ii    i  ii i   v    v           i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_226397371_   3382 GATTAAGGACTTAAATCTAAGACCCAAAACTATAAAAATTCTAGAAAATA 3431
                            i ?i   i     v     v i            v ii     i v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_226397371_   3432 ACATTGGAA-AAACCTTTCTAGACATTGGCTTAGGCAAGGATTTCATGAC 3480
                             v  ?i-   i   iv -   v    v        v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_226397371_   3481 CAAG-CACCTAAAAGCAAATGCAAAGCTAAAAACAAATGCAAAGCTAAAA 3529
                         i v -    -       ----   -  ----      --- i ---    
  L1M4_orf2#LINE/    594 TATGACACC-AAAAGCA----CAA-GC----AACAAA---AGA---AAAA 627

  chr1_226397371_   3530 ACGAAGATAAATAGTTGGACTTAATTAAACTAAAGAGCTTTTGCATGGCA 3579
                          i--        ---       v  i   v v  i i      iiivv  
  L1M4_orf2#LINE/    628 AT--AGATAAAT---TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_226397371_   3580 AAAGGAACAGTCAGCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAAT 3629
                           i iv  vi   iv i   i  v              i           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_226397371_   3630 CTTCACAATCTATACCTCTGACAAAGGACTAATATCCAGAATCTACAACA 3679
                         v  ii   vii   iv     i  i     vi          v  i  vi
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_226397371_   3680 AACCCAAACAAATCAGTAAGAAAAAAGCA----------TCAAAAAGTAG 3719
                            i vv    v   i   v     ii  ---------- i?    i i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_226397371_   3720 GCTAAGGACATGAAAAGACAATTCTCAAAAGAATATATACGAATGGCCAA 3769
                           v     iv    v     v     v      v      i         
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_226397371_   3770 CAAACATATGAAAAAACGCTCAACATCACTAATGAT 3805
                         i  i  i       i i           ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (129 / 81)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.56 (46 / 18)  


2992 24.43 1.41 4.76  chr1_226420035_226422824     1365  2289 (501)    L1M4_orf2#LINE/L1        1   894 (14)  

  chr1_226420035_   1365 TGGAGAGATATTCTATGTGTGTGGATAAGAAGACTCAATATTATCAAGAT 1414
                             i      i i    vii     vi       i      i i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226420035_   1415 ATCAGTTCTTCTCAATTTGATCTATAGATTCAATGCAATCCTAGTCAAAA 1464
                         iv  i v  i i   v        i        i       ivi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226420035_   1465 ATCTAAGGAAATTGC----TTTGTGAGTATGAACAAACTGATTCTAAAGT 1510
                         -  iv  ----i   ----    iiiiv  vi    i     i     i 
  L1M4_orf2#LINE/    101 -TCCCAG----CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr1_226420035_   1511 TTATATGGAGAGGCAAAAGACCAGGAAAAGCCAACACAATATTGAAGGAG 1560
                          i       i v    ii    vi   v      v     v     ii  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_226420035_   1561 AAGAATAAAATCAGAAAACTGACACAGCCTGACTTTTATTACTACTGCTA 1610
                              i   i ii  ii   v    vv  ii -   i vv   -------
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAA-TTTCAAAACT------- 237

  chr1_226420035_   1611 CTTCTACTAATTCTAATTCTACTATAATCAAGACAGTGTGTTATTGGCAA 1660
                         ----     ----i  vv    vi                v  i     v
  L1M4_orf2#LINE/    238 ----TACTA----CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_226420035_   1661 AAGAATTGACCCAAAAAACATCAGTGGGATAGAATACAGATGCCAAAACT 1710
                            i  v   --- v v v    i   i       vv   vv   i  v 
  L1M4_orf2#LINE/    280 AAGGATAGAC---ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_226420035_   1711 AAACTCACACCAATCTA--GTCAACTGATTTTTGACAAATAAGCAAAGGC 1758
                             i  i  --  i  --     i       i     iviv  v   i 
  L1M4_orf2#LINE/    327 AAACCCATAC--ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_226420035_   1759 AACACAATGGAGAAAGGCCAGTTTTTTCATCAAATATTCCTGGAACAATT 1808
                         v iv      i     ivi   i      v     iv v    i    i 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_226420035_   1809 TGACATCCATATGCAAAAAAAAAAAAAAAATGAAACTAGACACAGATCTT 1858
                         v  i ?   i        i  ---------    ii i   v vv i  i
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAA---------TGAAGTTGGACCCCTACCTC 465

  chr1_226420035_   1859 TTGCCCTTCACAAAAATTAACTCAAAATGGATCATAGACCTAAATGTAAA 1908
                         vii  v vi                         ?              i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_226420035_   1909 ATGTAAAATTATAAAAATCCTAGAAGATAACATAGAAGACCATCTAGGGG 1958
                          vv     i       v  i       v       i? vvv    vv v 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr1_226420035_   1959 ACCTTAGTTTTGGTGAAGACTTTCTAGATACAACATCAAAAGTTCAATCC 2008
                              i v  v  ii v ii  ii      ii   i      iv   v v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_226420035_   2009 ATGACAAAAATAATTGA--AGTTAGATTTCATTAAAATTAAAAACTACTG 2056
                          ii v i   v   v  -- i  i  i     i             vi  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_226420035_   2057 CTCAACGAAAGACACTGTTAAAAAAAT---AAGACAAACCAGACA--GGG 2101
                         iv vv i  i      i i  i   i ---       v   v v --   
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_226420035_   2102 AGAAAATTCTTGCAAAACACACATGTAATAAAGGACTAGTATGCAAAATA 2151
                                vi       v  i i  v i    i     v    v  i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_226420035_   2152 TACAAAAAAAATTCTTAAAACTCATCAATAAGAAAACAAACAACCCAATT 2201
                           i   i  --i     v      vi     i  i     i         
  L1M4_orf2#LINE/    766 TATAAAGAA--CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_226420035_   2202 TTTTAAATGGGCAAAAAATCTGAACACACACCTCACTGAAGAAGATGTAT 2251
                         ?vv-           ii  i    i v   ii  v ii        i  i
  L1M4_orf2#LINE/    814 WAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_226420035_   2252 GCATGTCCTGGGCAAATAAGCATATGAAAAAATACTCA 2289
                         iv   v  ------        i       i  i    
  L1M4_orf2#LINE/    863 AAATGGCC------AATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.52 (134 / 88)
Gap_init rate = 0.02 (16 / 894), avg. gap size = 3.56 (57 / 16)  


1567 25.74 2.22 5.56  chr1_226621534_226626268.rev     3029  3568 (1167)    L1M4_orf2#LINE/L1        1   522 (386)  

  chr1_226621534_   3029 TGAAAAAATATTTGACATTCATGGGGAGTAAGAC--AATATGGTCAAAAT 3076
                           i   i    iiv ii       ivv v     --     v  i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226621534_   3077 GTCAGTTAATCTCAACTTGATCTATAGATTCAATGCAATTAGAGCCAAAA 3126
                          v  i vvvi i   v        i        i     ivvvii     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226621534_   3127 TCCCAGCAAGTTGTTTTGTGGATATTAACAAACTGATTCTAAAATTTACA 3176
                                vivi v     ii  v   i    i     i        i --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA-- 148

  chr1_226621534_   3177 AATTTATATGGAACAGCAAAAGATCTGGAATAGCTAAAACTACCTTGAAA 3226
                         ------       vv    ii  i ii       i     v i       
  L1M4_orf2#LINE/    149 ------TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_226621534_   3227 --GAA-AACAAAGGTG----ACTAACACTACTCGGCTTCAAGACTT--TA 3267
                         --   -       v  ----   v     v i iii     i    --  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_226621534_   3268 CATGAAGTCATGGTAATCAAGGCAGTGTGGTAGTGGCAAAATAACAGAAA 3317
                           --   ii ii         i          v     v  vi i   v 
  L1M4_orf2#LINE/    243 CA--AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_226621534_   3318 AATAGACCAATGGAAGCAAATAAAGAGCTCCAATATAGAACCATACGAAT 3367
                         v     i        vvi   vi    ii vi v   i v      ivv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_226621534_   3368 ATTGCCAACTGATCTCTGACAAAGGAGCAAAGGCAATAAAGCGGAGAGAA 3417
                           v i   i    i ii     i  v  v   i v  vv ii  i  i i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_226621534_   3418 GAGAGTCTCTTCAGCAAATGTTTCTGGAAGACCTGGACACTCACATGCCA 3467
                         i v     i    i      v v    i v v     i ?i       --
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-- 438

  chr1_226621534_   3468 AAAAAAAAAAAAAAAAAAAAAAAAAGAACCTAGACACAGCTCTTACACTT 3517
                         -----------------    i  v   vi i   v vvvi  i    iv
  L1M4_orf2#LINE/    439 -----------------AAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_226621534_   3518 TTCACAAAA-TTAACTCCAAATGAATCACAGACCTAAATGTAAAACACCA 3566
                          vi      -       v     i    ?              i -i i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTA 520

  chr1_226621534_   3567 AA 3568
                           
  L1M4_orf2#LINE/    521 AA 522

Transitions / transversions = 1.45 (81 / 56)
Gap_init rate = 0.02 (10 / 522), avg. gap size = 4.20 (42 / 10)  

1274 22.31 5.11 0.81  chr1_226621534_226626268.rev     3873  4244 (491)    L1M4_orf2#LINE/L1      521   908 (0)  

  chr1_226621534_   3873 AAAGTATAAAACTCATAGAAGATAACATAGAAGAAAATCTAGGTGACCTT 3922
                            v          v       v       i? v      vv        
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_226621534_   3923 TTTGTCATGGTGAAGACTTTTTAGAGAAAACACCAAAGGCGTGA-CAATG 3971
                         -vv  i -  ii v ii  i     v vi        i  iii -   ii
  L1M4_orf2#LINE/    571 -GGGTTA-GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_226621534_   3972 AAGGAAATAATTGATAAGCCAGATTTTAATCAA--TTAAAATCTTCT--- 4016
                           i    v   v     iiii  i  i -    --      v   i ---
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCA-TCAAAATTAAAAACTTTTGTG 667

  chr1_226621534_   4017 ------AGGACACTATCAAGACAATGAGAAGACAGGCCACAGACTAGGAG 4060
                         ------               v i   i      iv       v i    
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_226621534_   4061 AAA-CATTTACAAAACCCATATCTGATAAAGGACGATTATCCTAAATGTA 4109
                            -i    i    v vi           i    vvv     vi   i  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_226621534_   4110 TACAGA-CTCTTAAAACTCAACAATAAGAAAATGAACCACTGGATT-AAA 4157
                           v   -      v       i     i  i ii  iv  ivi   -   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr1_226621534_   4158 AATGCGCAAAAG----GAGTGAACACCTCAGAAAAGAAAATATACAGATG 4203
                             v     i ----  i ii   ii  vvv      i       i   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr1_226621534_   4204 GCAAATAAGCCTATGAAAAGATGCTCAACATCATATGTCAT 4244
                           v       vi                     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (49 / 33)
Gap_init rate = 0.03 (10 / 388), avg. gap size = 2.20 (22 / 10)  


3419 23.83 2.34 1.22  chr1_226887027_226888973      557  1454 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_226887027_    557 TGGAAGTGTGTCTCATCTTCATGGATGGAAAGAATTAATATTGCTAAAGT 606
                              ivi i  i   v         v i    v         i   ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226887027_    607 GCCCAT-TTACCCAAAGCAATATACATATTTCATGCAATCTCTATCAAAA 655
                          v v  -i v      vii  v    v   iv i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226887027_    656 TTCCAATTGCATTCTTCACAGAAATAAAACACAC-AATCCTAAGATTCAT 704
                          i   ii   v  i  ii       vi -  vi -i       i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr1_226887027_    705 ATAAAACCACAAAAAACCCCGAATAGCCAAAGCAATACTGAGAAAGAAAA 754
                           ii  vii   iii    v           i    vi   i      i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_226887027_    755 ACAAAGTTGGAGACATCACACTTTCTGATTT-AAAATTACAGTATATTAC 803
                                     ivv        i ii    -    i ------  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT------TACTAC 243

  chr1_226887027_    804 AAAGCTATAGTAATCAAAACAGTATGGTACTGGCATAA--ACAGAAACAT 851
                                i         i     i              -- i   v i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_226887027_    852 AGTCCAATGGAACAGAATAGAAAGCCCAGGAATAAATCCAAACATACGTG 901
                           vi        i     v  i  i    i      i   v    vii  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_226887027_    902 GTCCACTAATTTTTGACA--GACACCAAAGGACA--CCATAGGGAACAGA 947
                            v i i     i    -- iii    - iv  -- v  i     vii 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAA 392

  chr1_226887027_    948 TAGTCCCTTCAATAAATAGTACTGGGAAAACTGGATTTCCACAAGCAAAA 997
                              ii     i    i  i      v        v?     v      
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_226887027_    998 GAATGAAATTGGAACCTTATTTTATACCATACACAAATATCAACTCAAAA 1047
                                i     v  i  ii i i      i     v  i         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_226887027_   1048 TGGAAAAAAGTCCTAAATGTAAGACCTGAAATCATGAAAGTTATACAGGG 1097
                             vv ?  v             v  i   ii  i   v iv  v i i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_226887027_   1098 AAATATAG--------CTCCGTGACATTGGCCTTGGCAATAATTTTTGGG 1139
                            i    --------  i      v    vi v      ii   i vi 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_226887027_   1140 GTATCACACCAAAAGCTTAGGCTAAAACAGCTAATATAAATAA----GGC 1185
                         i   v           vi i  v v  v  vv  v   i    ---- i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_226887027_   1186 TACATCAAACTAAAAAGCTTCTGCACAGAAAAGGAAATAATCAACAAAAT 1235
                          v       v v    i   i  ii vvv      v iv     v   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_226887027_   1236 TCAAAGGCAACCGATAGATTGGTAAAAAATAATTGCAAACCACATATCTA 1285
                         vv    i     v i   v   v i      v       i  i      i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_226887027_   1286 ATAAAGGGTTAATAACCAAAATTTATTTAAAAAACTCTTACAACTCAGTA 1335
                             i  ii vi  v   i   v   --   i               i  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATAT--AAAGAACTCTTACAACTCAATA 790

  chr1_226887027_   1336 GTAGGAAAACAAAAAAGCCCAATTAAAAAATGGGCAAAGGCCCTAAACAG 1385
                         i  ii  i     v  -       ?               vii i  i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_226887027_   1386 ACATTTCTCTAAAAAAGACACAAAAGTAGCCAACAGGTGTATGAAAAGGT 1435
                                  i   i    i i v  i i     i i iii        i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_226887027_   1436 ACACCACATCACTAATCAT 1454
                         i v v      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (136 / 75)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.46 (32 / 13)  


2955 22.92 1.36 2.86  chr1_226903147_226905460      612  1344 (970)    L1M4_orf2#LINE/L1        1   722 (186)  

  chr1_226903147_    612 TGAAGAGAGATTTCATGTACATGTGTAGGAAGACTCAATATTGTCAAGAT 661
                           i i   v  ii     v    vi v        i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226903147_    662 GTCAGTTCTTCCTAACTTGATCTATAGATTCAATGTAATCCCAATCAAAA 711
                          v  i v  i  i  v        i        i i      v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226903147_    712 TCTCAGCAATTTAGTTGGTGGATGTAGACAACAAACTGATTCTGAAGTTT 761
                           i    viii vv  v ii  vi v     ---i     i  i  i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA---GCTGATCCTAAAATTC 147

  chr1_226903147_    762 ATATGGAAAGGCAAAAGATCCATGTCAGCTAACACGATATTGAGGAAGAA 811
                                  v    ii  i   vivi   i  v  i  v    ii     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_226903147_    812 GAACAAAGTCAGAGGATAGATACTCCCTGGCTTCCAGACTTACTATAAAG 861
                                  ii     ivv i   i  iiii   v i        i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_226903147_    862 CTACAGCAATCAAGACAGTGTGGTATTGGCAAAAGAATAGACAAACAGAT 911
                               i                  i     v   i       v i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_226903147_    912 CAATGAAACAGATTTAGCAGTGGAACAGACTACAGAGCTCAGAAATAGAC 961
                              i  i   v  i-----------------    ii        i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTG-----------------AGAGTCCAGAAATAAAC 330

  chr1_226903147_    962 CCACACACATATAGTCAACAAATTTT-GACAAAGGAGCAAAGGCAGTGCA 1010
                            i   iv   i     ivi     -     i  v  v   i vi v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_226903147_   1011 GTGGAGAAAGGCTAGTCTTTTCATCTAATGGTGCTGGAACGACTGGACCT 1060
                         i   i     iv           v v           i  i      iv?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_226903147_   1061 CTACTTGCAAATCAATGAATCTAGACATAGGCCTTACACGCTTCATAAAA 1110
                          i  v      vv      vi i   vivvi   i    vv vi i    
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_226903147_   1111 ATTAACTAAAAATGGATCATAGATCCAAATGTAA-AGCACAAAATTATAA 1159
                                v           ?   i i        -   -i    i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAA 529

  chr1_226903147_   1160 AGCTTCTAGAAGATAACATAGGAGAAAATGTAGTTGGTTTTGCGTTTAGC 1209
                          i  ii       v        ? v    v vvv  iii   v   vi  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_226903147_   1210 AATGGCTTTTTAGA----ACA--AAAAGCACAATCAATAAAAGAAAAAAA 1253
                              i  i     ----   --          v   i           v
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr1_226903147_   1254 TGATAAGTTGTGCTTCATTAAA-TTAAAAACTCTTGTGCTGCAAAAGACA 1302
                         v     i   vi      i   -         i       v    i    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr1_226903147_   1303 CTATCAAGCAAATGAAA-GACAGGCTACAGACTTAAAAAAAAT 1344
                                 v  i     -    iv i     v vii i     
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

Transitions / transversions = 1.62 (102 / 63)
Gap_init rate = 0.01 (9 / 722), avg. gap size = 3.44 (31 / 9)  

 376 23.20 12.37 0.52  chr1_226903147_226905460     1628  1821 (493)    L1M4_orf2#LINE/L1      692   908 (0)  

  chr1_226903147_   1628 TGAAAAAACAA---ACA-AACAACAAAAAACCCT--CA---CTTATATCT 1668
                               i    ---   -  iiiv i    ivi --  --- v       
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_226903147_   1669 AA-AACAAA-TAATATCCAGAATATACAAA---CTCT----ACT-----A 1704
                         i -  vii - vi             i   ---    ----   ----- 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_226903147_   1705 TAAGAAAACAATAAACTCAATTTTAAAAATAAGTGAAAGATCTGCAGAGA 1754
                            i  i    vv   i     ?-      ii ii  i   i  v v   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_226903147_   1755 CGCTTCATCAGAGAAGATATATTGATGGCAAACATGCACATCAAA-GATT 1803
                          ii   vi  i          ivi     v  i v      v   -   v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_226903147_   1804 ATCAACATCATATGTCAC 1821
                         v         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (28 / 16)
Gap_init rate = 0.05 (11 / 217), avg. gap size = 2.27 (25 / 11)  


3007 26.47 0.65 1.74  chr1_226913365_226920038.rev     5266  6183 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_226913365_   5266 TGGAAAAACATTACATGCTCATGGATAGGAAGAATCAATATTTGGAAAAT 5315
                               i i  iv    i        v      v i      vvv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226913365_   5316 GGCCACACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5365
                            v i   v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226913365_   5366 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 5413
                          v   -   v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr1_226913365_   5414 TATGTAACCAAGAAAGAG-CCCATA-TAGCCAAGATAATCCTAAGCAAAA 5461
                             v  -- v v   i -    v -       i i    i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_226913365_   5462 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 5511
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_226913365_   5512 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGA 5561
                                   i   i    ii         i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_226913365_   5562 CTAATGGAACACAACAGAGGCCTCAGAAATAATGCCACACATCTGTCAAA 5611
                         ii       i v  iv   ivii         vv   i    i i ----
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT---- 342

  chr1_226913365_   5612 GATCAACCATCTGATCTTTGACAAACCTGACAAAAACTAGCAACAGGGAA 5661
                          i    i----    i  i     ivv  v   i v vvv   ii     
  L1M4_orf2#LINE/    343 GGTCAAT----TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_226913365_   5662 AGGATTCCCTATTTAGTAAATGGTGTTGAGAAAACTGGCTATCCATATGC 5711
                           i  vvi  v  i ii        i  i  v      v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_226913365_   5712 AGAAAACTGAAACTGGATCCTCTTCCTTACACCTTATACAAAAACTAACT 5761
                          i  i v    ii    i  -  v   i     v          i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACT 487

  chr1_226913365_   5762 CAAGGTGGATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACTCT- 5810
                            ii     i ?    i           v       i      -    -
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTT 536

  chr1_226913365_   5811 AGAAGAAAACCTAGGCAATACCCTTCAGGACACAGGCATGGGCAAAGACT 5860
                                   v    ?ivv vi    iv   viv  vv i     v ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_226913365_   5861 TCATGACTAAAACACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAA 5910
                           v iiv  vi    i       vvi          vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_226913365_   5911 T-GGAATCTATTTAAACTAAAGAGCTTCTTCACAGCAAAAGAAAATATCA 5959
                          -   v ii  iv   i    i -   i vii vv    i  v v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_226913365_   5960 TCAGAGTGAACAGGCAACCTACAGAATAGGAGACAATTTTTGCAATCTAT 6009
                         vv i      v  i     i       i     v   v       vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_226913365_   6010 CCATCTGACAGAGGGCTAATATTCAGAATCTACAAGGAACCTAAACAAAT 6059
                         vi      i ii  i  vi   i      v  i  i    iivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_226913365_   6060 TTACAAGAAAAAAATCAAACAACCCCATCAAAAAGTGGGTGAAGGACATG 6109
                         iv i  v     i -    i     v  i?    i    ii     iv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_226913365_   6110 AACTGACACTTCTCCAAAGAAGACATTTATGTGACCAACAAACATCTTTT 6159
                           iv    i              i  vi vi  i    i  i  iv vvv
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_226913365_   6160 AAAAAGCTCATCATCACTGTTCAT 6183
                           i v     v     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.47 (22 / 15)  


2179 27.89 6.35 3.40  chr1_226934998_226936969      598  1479 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_226934998_    598 TGTAGAGATATACTATGTTTATGAATTAGAAGGCTCAATATT-TTAAAAT 646
                           v i      v i     i   i   i    i  i      -    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226934998_    647 GTTTATTCATTCTAAATTGATCTACAGTTTCAAC--------TATCAA-- 686
                          viv  v vii i              v      --------      --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226934998_    687 TTCCAGC-ACCTTTTTTGTTGAAACAGAAAATTTAATTCTGAAATTTTAA 735
                          i     -i         iv    iv  v  vi i  i  i     ivv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_226934998_    736 TGAAGATTCAGAGGCTCTAGAAATGCCAAAACTATCTCGACAAAGAAAAG 785
                           i i  v  ii  vi i    vv        v    i  v      i i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_226934998_    786 T---GTCAAAGAACTTACACTGCACGATTTCAAGGTTTCCTCTAAAGC-A 831
                         i---  iii  i   i     v v i       iii  v  vi     - 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_226934998_    832 CAGTAACCAAGACAGCATGGCATTGTT-TAAGGATAAACACCCAGGTCAA 880
                               i        ii   i i  vi-        i   ivi  i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_226934998_    881 TGACAGAGTCTAGAAATAGAGTCTAGCAAACCGAGTCTAGAAATAGACCT 930
                           i-----------      i iv  -------    i       i   i
  L1M4_orf2#LINE/    301 TGG-----------AATAGAATTGAG-------AGTCCAGAAATAAACCC 332

  chr1_226934998_    931 ATACTTTTATAGTCAACTGGTTTTTCACAAGGGCACCAAAGAAATTCAAT 980
                             v     i     i  i    iv       ii    iivv       
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_226934998_    981 GGTGAAAGGAAACTGGAACTACCTCAACCCCTGTCTTTAGCACCAC---A 1027
                           v     i v v ----  -ii     vvv  vivi i v  v  --- 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGT----CT-TTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_226934998_   1028 CACACACACACACAGACACACA--CAGACACACACAGACACACAC-ACAC 1074
                         i ?v    ii  v iiv iiv --ii   v vi  --- v     - i i
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC---CTCACACCATAT 474

  chr1_226934998_   1075 ACACAATTTGGCT-------GACCCAAAGCCTGTATGAAAAAGCCAGAAC 1117
                            v  v  ii  -------  i v? ii   iv   v  i   i i   
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_226934998_   1118 TAAAAAGCTTCTAGAATAATATATGAGAG--ATTCTTTGCAAATTTGAGT 1165
                           v   i  ii     v  v i  ii ? -- v    i ii vi   i  
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_226934998_   1166 TAATCAGAGATGCATGAGACAAGACACAGAAAGGACTAACCATAAAAGAA 1215
                           iv  iv i viv v   i v     vi    v  v i v i       
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_226934998_   1216 AAACAACTGGTAAATTGGACTTCACTACAATTAAAA-CTTCTGCCTATTC 1264
                            -- iv i              ii v        -   i  ivi-   
  L1M4_orf2#LINE/    625 AAA--ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC-TTC 671

  chr1_226934998_   1265 AAAT-ATGCCATTAAGAAAATGAATAGACAAACCACA-AACAGGGAAAAC 1312
                            v- ii i  i      i    v      v     -  ii  ii   v
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_226934998_   1313 TATTTGTAAAGCACATACCTGAAAAAAATGTTTATATTCAGGATATGT-- 1360
                               i   v  i   i    v  iii-ii  i   i   i    i --
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGG-ACTTGTATCCAGAATATATAA 770

  chr1_226934998_   1361 --------TAT-------TAATAAAATAATAAAT---TCAATTTTAAAAT 1392
                         --------  i-------        vi i    ---i     ?v     
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_226934998_   1393 GAACAAAAGACTTAAGTAGGTACTTCACAAAAGAACATGTACAAATGAAC 1442
                          ii    i  i  i i   ii i   v v      v  i        iv 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_226934998_   1443 AACAAACACGTGACAATATGCTCA-CATTATTAGTCAT 1479
                           i  i   i   v  v       -   i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (158 / 84)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.19 (86 / 27)  


2728 24.29 0.61 8.33  chr1_226963917_226970155.rev     4765  5748 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_226963917_   4765 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAA 4814
                               i i  i     i        v      v i        v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_226963917_   4815 GGCCATAGTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAATC 4864
                            v   v v      v i  i  i        i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_226963917_   4865 TACCATTGATTTTCTTCACAGAA-TTGGGAAAAAAACT-ATTTTAAAGTT 4912
                          v   viviii  i  ii     -   ---- v  i  -  ii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr1_226963917_   4913 CATATGGAAC--CAAAAAACAGCCCATATAGCCAAGACAATCCTAAGCAA 4960
                                  v--   iii  --  viv        i      i i iv  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_226963917_   4961 AAAGGACGAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATAGTATA 5010
                         i   i  i   i      vv    i  v  ii i      viv  v  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_226963917_   5011 TAG-TATAGACTTCAAACCGAAACAGCATGGTACTGGTACCAAAACAGAT 5059
                         v  -  i  --- --  i i i    ii         i iv ii i   i
  L1M4_orf2#LINE/    245 AAGCTACAG---T--AATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_226963917_   5060 ATACACCAAAACAGACCAATGGAATAGAACAGAGGCCTCAGAAATAACAC 5109
                            i --------  i             iv   ivii         vv 
  L1M4_orf2#LINE/    290 ATATA--------GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_226963917_   5110 CACACATCTACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAA 5159
                           i    i  iiii  vi    i  i     ivv  v   i v  vv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_226963917_   5160 TCGGTAAAGAATTCTTTATTTAATAAAACTGACAAAAACAAGCAACCGGT 5209
                          v  v       --------------------------------------
  L1M4_orf2#LINE/    382 TGGGGAAAGAAT-------------------------------------- 393

  chr1_226963917_   5210 AAAGAATTCTTTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATTT 5259
                         --  ---     -- i  i        i     v      v  ?   iv 
  L1M4_orf2#LINE/    394 --AG---TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_226963917_   5260 GCAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATAAAAAAATTAAC 5309
                            i  iiv    ii    i    v   i     v    v          
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_226963917_   5310 TCAAAATGAAATAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCT 5359
                                 i vi ?    i           v       i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_226963917_   5360 AGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGTAAAGAC 5408
                                   v    ?i- v i -   iv   v v  vv i  i  v ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_226963917_   5409 TTCATGACTAAAACACCAAAGACTTCATGACTAAAAAAGCAATGGCAACA 5458
                            v iiv  vi        ii ---------------i   --      
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGC---------------ACAA--GCAACA 618

  chr1_226963917_   5459 AAAGCCAAAATTGACAAATGGGATCTAATTTAACTAAAGAGCTTCTGAAC 5508
                             vv     v  i    v   ii v  iv  v v  i i   i  vi 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr1_226963917_   5509 AGCAAAAGAAACTATCACCAGAGTGAACAGGCAACCTACAGAATGGGAGA 5558
                         vv    i  v       vv i      v  i     i             
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr1_226963917_   5559 AAATTTTTGCAATCTATTCACCTGACAAAGGGCTAATAACCAGAATCTAC 5608
                             v       vii  vi i    i  i  i  vi  v       v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_226963917_   5609 AAAGAACTTAAACGAATTTACAAGAAAAAAACAAACAACCCCGTCAAAAA 5658
                                 ivv  i v iv i  v     i     i     vi i?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_226963917_   5659 GTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAG 5708
                         i            v    i     i     v        i  vi viii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_226963917_   5709 CCGAGAAACATATGAAAAAAAGCTCATCATCACTGGTCAT 5748
                           i v  i  i       i v     v     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 5.50 (88 / 16)  


4080 17.45 3.69 2.13  chr1_227253234_227256619.rev     2002  2895 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_227253234_   2002 TGGAAAGACATCCTATGTTAATG-ATTGAAAGAC--------ATTAAGAT 2042
                                 i    i     v   -    i     --------i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_227253234_   2043 ATCAATATTTCCCAAAGTGATCTACAGATTCAATGCAATCC-TATTAAAA 2091
                         iv     i i      v                i       -   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_227253234_   2092 TCT-AGGTGCTGTTTTTTTGCAGAGCTAGAAAAGCTTACCCTAAAGTTTA 2140
                           i-  v   i--           iv v  v     v i      i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_227253234_   2141 TATGAAATCTCCAAGAATTCCATATAAAACAATAAAGTCAAAACAACCCT 2190
                             i  -v v    iivi   v -------   -- i        i i 
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGA-------ATA--GCCAAAACAATCTT 188

  chr1_227253234_   2191 GAAAATGAAGAACAAAGTTGGAGGACTCATACTTCCTGATTTCAAAACTT 2240
                              v                       i      ii            
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_227253234_   2241 ACTATAAAGTTACAGTAATCAAAACAGTGTAGAACTGGCATGAAGACTGA 2290
                             i    i            i       i v        i i  iv  
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_227253234_   2291 ACTATAGACCAGCGGAATGGAATAAAGAGCCCAGAAAAAAAAAAAAACCT 2340
                         vv      i  ii     i    vi    i       v   v-----  v
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC-----CCA 333

  chr1_227253234_   2341 CACGTATATCGTCATTTGATTTT-GAT--GACTACCAAAACCATTCACTG 2387
                         i  i v   v    v        -  i-- iv i    i        v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_227253234_   2388 GGGGAAAAGACAGTCTTTTCAACAAATAGTACTGGGATAATTGGATTATT 2437
                            i  i - i                i  i      i  i     - ?i
  L1M4_orf2#LINE/    384 GGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT-AKC 431

  chr1_227253234_   2438 CACATGCAAAAGAATGAAATTGGATCCTTACTGAACACCGTATACAAAAA 2487
                                           i     i  i   ivv     i          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_227253234_   2488 TGAACTCAAAATGGATCAAAGGCCTAAATTTAATGACTAAAACTATAAAA 2537
                          v                ?  i       v   vii              
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_227253234_   2538 CTCCTAGACAAAAACATAGGAGAAAATCTTCATGACACTGGTTTTAGCAA 2587
                            i    vi          ? v        i    vi   v  vi    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_227253234_   2588 TGGTTTTTTGGTTATAACTCCAAAACCATAGGCAATAAAAGAAAAAA--- 2634
                               i  i v   i  v      v  i i    i           ---
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_227253234_   2635 ATAGAT-GAACTTCATCAAAATTAAAAAATTT-GTGCAACAAAAGAAACT 2682
                            i  - i                   v   -    vv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_227253234_   2683 ATTAAGAGAATAAAAAGACAATCCATGGAATG--AGAATAGAGTTGTAAA 2730
                           i    i i i         i   ii     --    v v v   i   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_227253234_   2731 TCATATATCTGCTAAAGGATCACTATTCAGAATATA---GGAACT---AC 2774
                                    v   i   iivv   i         ---i     ---  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_227253234_   2775 AATTCAACAATAAAAA-ACAAG----CCAATTCCAAAATGGGCAAAAGAC 2819
                           i    i        -    i----      ?v            i  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_227253234_   2820 TTGAGTAGACATTTCTCTAAAGAAAACATACAAATGCACAATAAGTGCAT 2869
                             i            i      i i         vv       ii   
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_227253234_   2870 GAAAAG-TGCTTAACATTATTTGTCAT 2895
                               -    i     i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (100 / 52)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.36 (52 / 22)  


1042 31.40 11.71 2.05  chr1_227369460_227371698.rev      943  1770 (469)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_227369460_    943 TGGTGAGAAATACTATGTTCATGGATTGGAAG-TTCAGTAACATTAGTAG 991
                            vi   v  v i                  -i i i  vii   iv v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_227369460_    992 GCCATTTATCTGCAAATTAAT-TATATATTTAATAAAATGCCATTCAAAA 1040
                          v  v vv  iv      i  -  i v   i  iiv   v  vv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_227369460_   1041 TCCCAAGT---TTTTTTGAGGCACTTGTTAAGC--------AAAT--GTA 1077
                              iv ---       vi v v   vi    --------    --i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_227369460_   1078 TTGAAGAACAAAGGACCAAGAGTAATCAAGATACTCCCAAAGAAGAGGAT 1127
                          v   ivi   i     v   i  ii   i i v  iii  i    i  v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_227369460_   1128 GCTCAGGCTTGAAGGGGAAGCTTCTCAT-CTTACCAGGTAGCAAAACTTA 1176
                         ---  iiv   i   i-------    i-   v   iv -v         
  L1M4_orf2#LINE/    201 ---CAAAGTTGGAGGA-------CTCACACTTCCCAATT-TCAAAACTTA 239

  chr1_227369460_   1177 ATATAA--------TAATGAA--CAGAATGGTATTGCTGCAGGGATAGAC 1216
                         v  i  --------    v  --   vi     i  viii i        
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_227369460_   1217 AAGTGGACTAA-GGAAGAGAATAGATAACTTAGA--TAAA---------- 1253
                          vi i  ii  -    v     v  v iiii   --    ----------
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_227369460_   1254 --TGG------GA--------AAGGTGTGTTAGAGATCAG--AGTGGGA- 1284
                         --   ------  --------    -   ii -   i  v-- i    i-
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGG-GTGCCA-AGACCATTCAATGGGGA 387

  chr1_227369460_   1285 ---------CTGGTTAAGATGTGGGAGTGGGCCAATTAAGTTATTTTATG 1325
                         ---------  vv i  v vi   viv    v   i iii v?iivi   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_227369460_   1326 GATAA-AATAAAATTG-ATATTTG--TGATGGCATA---GTAATCTAATT 1368
                         v v  -   i  i   - ivii i-- v iiv    ---iv  vi   i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_227369460_   1369 CCAAATGGATGAAAATCTGAAGTATGAATGGCAAAATATTTTAAACT-TT 1417
                          v        v ? iv iv  i i i iv vi    i- v v     -  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC-TATAAAACTCTT 536

  chr1_227369460_   1418 AGGAGGAAATATAAATGAAGATGTTTATGACTTTGGGGTAGACAAGGATT 1467
                           i  i   i   ii? v i  v  ii    i     v   i   v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_227369460_   1468 TC----ATAAGAAGCAC--AAAGCATAGATCTGAAACAAAAAGGTTGATA 1511
                           ----   v  --   --      i iiivvv   vi    ii v    
  L1M4_orf2#LINE/    587 TCTTAGATATGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_227369460_   1512 AATTGGACTACCTTGAACCTAAGAACTTCCGTTCAACAAATGACACCATA 1561
                                  v v ii  vi   i     ii  v vv    v     i  v
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_227369460_   1562 AGGAAAG---AAAAATAAGCC-CAAATTGGATAAAGATACTTGGAAATTT 1607
                          i     ---   i i  v  -  i v   ivi  i   i   v    iv
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_227369460_   1608 AATAACTGACCAAGAATTACTGTCCA-AATTTATGAAGTATCACTACAAA 1656
                         v   v    iv i i i vv i    -   v   i   v iivi     v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_227369460_   1657 TTAAAAAATAAGAGACAA-----CCAATAGAAAAGTGTGCAAAAGACATG 1701
                          i  v  vv  i      -----     v?    i  v     i  iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_227369460_   1702 AACAAGTAATTTTACCACAGGGAAAACATGAATGAC-AA-----ACATGA 1745
                           i iii v  i -   v  iii v i ii    i -  -----      
  L1M4_orf2#LINE/    835 AATAGACATTTCT-CCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_227369460_   1746 AGAGATACTTTAGTTCATAAATTAA 1770
                          i    i  iv vv   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (149 / 107)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 3.17 (114 / 36)  


 233 19.54 12.64 0.00  chr1_227406719_227408363      223   309 (1336)  C L1M4_orf2#LINE/L1   (0)   908   811  

C chr1_227406719_    309 ACTTAAAAATGAGCAAAGGATATAAGT-GA---TTTACAAAAGTGGAGAT 264
                          i ?       i         v i i -  ---  iv v    vi  v  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

C chr1_227406719_    263 ACAAATGGCCAATAAAC-CA---AAAG---TTTAACTTTATTAGTGGT 223
                                        i -  ---    ---i i   v i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.05 (5 / 98), avg. gap size = 2.20 (11 / 5)  

 253 16.28 0.00 0.00  chr1_227406719_227408363      361   403 (1242)  C L1M4_orf2#LINE/L1   (466)   442   400  

C chr1_227406719_    403 TTTAACAAGTGGTGCTGGGACAACTGGCTAACCATTTGGAAAA 361
                           i     i                  v  ?   iv  v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

Transitions / transversions = 1.00 (3 / 3)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.00 (0 / 0)  

2594 24.04 1.68 0.15  chr1_227406719_227408363      500  1152 (493)    L1M4_orf2#LINE/L1      246   908 (0)  

  chr1_227406719_    500 AGCTATAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACACACAG 549
                              i     i   i    ii              ii i     i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_227406719_    550 ACTAATGGAACAAAATAGAGAACCCAGAAACAAATCTACACGCCTACAGT 599
                          ii       i i   v    ii       i   i i i  iii  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_227406719_    600 GAACTCATTTTTGACAAAGGTGCCAAGAATACACACTGGGGAAGG--CAG 647
                         v  i v     i     i          vi iv  v       i --i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_227406719_    648 TCTTTTCAATAAATGGTGCTGGGAAAACTGAATATCCATATGCAAAAGAA 697
                                  i              v     i   ?   i           
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_227406719_    698 TGAAACTAGACTCCTATCCCTCACCATATACAAAA-TGAAATCTAAATGG 746
                             ii i   i    i i v              - v  v  v      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_227406719_    747 ATTAAAGACTTAAATCCAAGAACTCAAACTATGAAACTACTACAAGAAAA 796
                           i ?    i     vi    i  v       i     vi  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_227406719_    797 CGTTGGGGAAGCTCTCCATGATATTCATCTGGGCAAAGATCTCTTGAGTA 846
                          i v  ? v iv   i i   iv  vivi i     v i i    iii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_227406719_    847 --ACACCCACAAACACAGGCAACCAAAGCAAACAAGGACAAATGGGATCA 894
                         --     v -  i    i     v    v   v vi  i    v   iiv
  L1M4_orf2#LINE/    596 TGACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_227406719_    895 TGTCAAGTTGAAAAGCTTCCCCACAGCAAAAGATACAAGCAACAAAGTGA 944
                         ii    iv v    i   iivii vv    i  i  v v   v       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_227406719_    945 AGAGACAACCCACAGAATCAGATAAAATATTTGCAAACTACCCCTCTGAC 994
                          i                vi  v              ii iviv     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_227406719_    995 AAGCGATTAGTAACCAGAATATATAAGGAGCACAAACAACTGTATTGGAA 1044
                            v  i v   v             i  i v vv      vv  viv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_227406719_   1045 AAAATCTAATAATCCAACCAAAAAATGGGGAAAG-ATTTGAATAGACATT 1093
                            iv v     i    ii?         v    -               
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_227406719_   1094 TCTT-----AAGACATACAAAAGGCCAACAGGCATATGAAAAGGTGGTCA 1138
                            i-----    i       v      i i   i        i  v   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_227406719_   1139 ACATCATTGATCAT 1152
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (97 / 56)
Gap_init rate = 0.01 (6 / 663), avg. gap size = 2.00 (12 / 6)  


 479 19.63 6.54 0.93  chr1_227578849_227581788.rev     1269  1375 (1565)    L1M4_orf2#LINE/L1        1   113 (795)  

  chr1_227578849_   1269 TGGAAAAATAG-----GTCCATGACTTGGAAGAC--AATATTGTTAAGAT 1311
                               i   v-----  i    iv         --              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_227578849_   1312 GTCAGTATTTCTCAAAGTGATCTACAGATTAAATAATAATCCCTATCATG 1361
                          v  i  i i i    v             v  ii-i           vi
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACG-CAATCCCTATCAAA 99

  chr1_227578849_   1362 ATTCCAGTGGCATT 1375
                           i    iv  v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTT 113

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.03 (3 / 113), avg. gap size = 2.67 (8 / 3)  

3626 19.29 2.40 1.13  chr1_227578849_227581788.rev     1657  2449 (491)    L1M4_orf2#LINE/L1      106   908 (0)  

  chr1_227578849_   1657 GTTGTTTTTGTTGCAGACATAATAAAATTCATCCTAAAATTAATATGGAA 1706
                          i  ii   v       v  vivv  ii v           v        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr1_227578849_   1707 ACTCAAGGGACTCCAAATAGCCAAAACAATCTTGAAAAAGAA---CAAAG 1753
                          iv        i vi                           ---     
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr1_227578849_   1754 TTGAAGGTCTTAAATTTTCTAATTTCAAAATTTACCACA------CAGTA 1797
                            i   v  i v i  i i          i    i   ------     
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr1_227578849_   1798 ATCGAAATAGTGTAGCACTTGCATAAAGATCAACTTATAGA-CAACTAAA 1846
                            i i i     i i   v      i   vi  v      -   - ii 
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA-TGGA 304

  chr1_227578849_   1847 ATAGACCAGGGAGCTCAGAAACAAACCCTCACATAGATGGTCAGATGATT 1896
                              viv i   ii      i      vi    vv       iv     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_227578849_   1897 TTCAACAGAGGTGCCAAGACCATTCAAAGGGGGAATGGACTGTCTTCTCA 1946
                            i   ii                  v    i  - i iv     i   
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTCA 403

  chr1_227578849_   1947 ACAAATGGTGCTGAGAAAACTGAATGTCCACATGCAAAAGAATGAAGTTG 1996
                                      i  v     i  i?                       
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_227578849_   1997 GATCCTTACTCTACCACATATACAAAAATTAACTCAAAATTGGATTAAAG 2046
                           i  i   iii  vv                        -    i ?  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT-GGATCAWAG 502

  chr1_227578849_   2047 GCCTAAACATAACACCTAAAACTATAAAACTCCTAGAAAAAAACATAGGG 2096
                         i      ii   v v                 i     i          ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr1_227578849_   2097 GAACAGCTTCATGACATTGGATTTAGCAATGATTTCTTGACTATGACACC 2146
                          v v v    i    v    i  vi      i      iiv         
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr1_227578849_   2147 AAAAGTATAAGCAACAAAAGAAAAAAATAGAAAAAATGGACTATACTAAA 2196
                              i i                  -    v   v      vi ii   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAA 651

  chr1_227578849_   2197 ATGTACAACTTCTATGCATCAAAGGACACAATCAACAGAATGAAAAGGCA 2246
                           vv v     i i   v           v     v i i       i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_227578849_   2247 ATCAATGGCATGGGAGACGATACTTACAAATCATATATCTGACAAAGGGT 2296
                          i v ii v        vi   i  i                i  i  ii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_227578849_   2297 TAATATCTGGAATATATAAAGAATTCCTACAACCCAACAA--AAAATACC 2344
                          vi    ii              i  i      i   i  --    v  v
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_227578849_   2345 AG--ACTCACTT-AAAAATGCACAATAGACTTGAATAGACATTTCTTCAA 2391
                          i--  i  v  -       vi   vi  i                i   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_227578849_   2392 AGAAAATATACAAATGAGCAATA----CAGAAATTTTTAAAATGCTCAAT 2437
                             i           iv     ----  vi  -----  i        i
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAA-----AAGATGCTCAAC 896

  chr1_227578849_   2438 ATCAATAATCAT 2449
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (97 / 53)
Gap_init rate = 0.01 (12 / 803), avg. gap size = 2.33 (28 / 12)  


3715 22.27 2.56 1.45  chr1_227585257_227587606      960  1857 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_227585257_    960 TGGAAAGATATCCCATGTTCATGGATTGGAAGAATTAATGTCATTATAAT 1009
                                                          v     i ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_227585257_   1010 G--------TCCCAAAGTGATCTACAGATTCAATACAATTCTTATCAAAA 1051
                          --------i      v                ii    i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_227585257_   1052 TGCCA------TTTTTCACAGAAATAGAAAAA--AATTCTAAAATTCATG 1093
                          v   ------     ii       v  v  i--i  i           i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_227585257_   1094 TGGAATCACAAATGATCCCAAATAGCCAAAGAAAGCAATCTTTATCAAAA 1143
                              vii   iv  i  vi          i----       v vv  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAA----CAATCTTGAAAAAGA 196

  chr1_227585257_   1144 AGAACAAAGCTGGAGGCATCACACTATCTGCTCTCAAAATCTACTGCAAT 1193
                                  i      vv       vi iiv i      ii    i   v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_227585257_   1194 GATATAGTATCCAAAAAAAGAATGGTACTAGTACAAATACAGACATGTAG 1243
                          v  i    vi   i v - vi       i i i  iv i      i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACA-GTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_227585257_   1244 ACCAAAGGAATAGA-----GGACCCAGAAATAAATCTATGCGTTTACAGT 1288
                          i   v        ----- iii           i i  i i    ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_227585257_   1289 CAACTGATCTTTGAGAAAGGTACCAAGAACACACAATGGAGAAAGGACAG 1338
                            i    i  i  v  i   i      v  iv      i     i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_227585257_   1339 TGCTTTCAATAAATAGTGTTGGGAAAACCTGATATCCACATGCAGAGGAA 1388
                          vi      i    i   i     v   iv    ?         i i   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_227585257_   1389 TAAAACTAGACTCTTATCTCACCCCATATACAAAAATCAACTCAAAATGG 1438
                          i  ii i   i i  i     v              i            
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_227585257_   1439 AATAAAGACTTAAATATAAGACTTGAAACTGTAAAACTACTAGAAGAAAA 1488
                          vi ?    i     i     vi i     i       vi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_227585257_   1489 TATTGGGA-AAAGCTTCTTATCATTGGCCTGGGCAAATATTTTTCTGGAT 1537
                         i  v  ?i-   v    v iv v    vi i     - iv   ii i   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT 594

  chr1_227585257_   1538 ATGACCCCAAAAGCACAGGCAAGAAAAGCAAACATAGACAAATGGGACTG 1587
                              v           i    v     v   v     i    v     v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_227585257_   1588 CATTAAACTAAAAAACTTCAGCATAGCAAAGGAAATAATCAACAGAGTGA 1637
                            i   v v        iv iiivv       v iv     v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_227585257_   1638 AGAGACAGCCTACAGAATGAGAGAAAATATTTGTGAACCACATATTTGAT 1687
                          i     i  i        i             ii  i  i    i    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_227585257_   1688 GAAGGGTTAATATCCAAAATATATAAGGAACTCAAACAACTCAATAGCAA 1737
                         i i  ii vi      i         i      vv           ----
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA---- 790

  chr1_227585257_   1738 AATATAATAATAATAATAACCTCATT-GTAAATGGGCAAATGATCTGAAT 1786
                         -   v  vi i  --      iv   -iv           v   i     
  L1M4_orf2#LINE/    791 -ATAAAAAGACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_227585257_   1787 AGACTTCTGTCAAAAGAAAACATATATATGGCCAACAAGTATATGAAAAA 1836
                             v i v  v      i i   i v        i   i i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_227585257_   1837 ATGCCAAACATTACAATCATC 1857
                             iv     i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (130 / 67)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.27 (36 / 11)  


 654 24.80 1.97 8.66  chr1_227844047_227845965.rev      498   751 (1168)    L1M4_orf2#LINE/L1      284   520 (388)  

  chr1_227844047_    498 ATAGA--TGTAGAGCAATGGTACAGGGTGAAGAGTTCAGAAATAGACC-- 543
                              -- i    v      v i  ii vi     i        i   --
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_227844047_    544 TACACTAACAATATCAATTGATTTTTTTTTTTTAATAAAGATACTAAGGA 593
                             i v iii --           i-------i i  i i i i   iv
  L1M4_orf2#LINE/    334 TACATTTATGGT--CAATTGATTTTC-------GACAAGGGTGCCAAGAC 374

  chr1_227844047_    594 AATTCAGTACTGGCTAGGTTTTTGTTCTTTTTTTTTTCTTCTGTAAATGG 643
                         v     i iv-  vv  iv ---iv      --------- vii      
  L1M4_orf2#LINE/    375 CATTCAATGG-GGAAAGAAT---AGTCTTTT---------CAACAAATGG 411

  chr1_227844047_    644 TTTTGGAATACATGGCTATCTATGTGGAAAA-AATAAACCTTGACCCTTA 692
                          vi   i i vv   v  ? i ii  v    -   i  vi v     i  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_227844047_    693 TGTCCCACCATTTATAAAAATTAATTCAAAATGGATCACTGACCTAAATG 742
                         iv  v      v  i         i             ?v          
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_227844047_    743 TAAGACCTA 751
                              v   
  L1M4_orf2#LINE/    512 TAAGAGCTA 520

Transitions / transversions = 1.54 (37 / 24)
Gap_init rate = 0.03 (8 / 237), avg. gap size = 3.38 (27 / 8)  

1189 22.92 5.47 0.78  chr1_227844047_227845965.rev     1045  1428 (491)    L1M4_orf2#LINE/L1      507   908 (0)  

  chr1_227844047_   1045 AAAAGTAAGACCTAAATCCATAAAACT-TTAAAAGAAAACATCAGAGAAA 1093
                            v      v     v i        -   i          -  i?iv 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AGGNGTA 555

  chr1_227844047_   1094 AATCCTTGTGACCTCAAGATAAGCAAATATTTTTTAG----GACATAAAA 1139
                             i i       iii v  i    vvi   i    ----    iv   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr1_227844047_   1140 AAGATGAGCCATAAAAGAAAAACACTGATAAATTAGACCATGTCAACATT 1189
                          iv ii   v i          - iv        i   ivii    v   
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAATT 654

  chr1_227844047_   1190 AAAACGTTTTGCTTATCCAAAGATACCATTAAGAAAATGAAAAGACAAAC 1239
                             vv     iviv  v  i  i  i  i      i           - 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA-C 703

  chr1_227844047_   1240 CCTTT---TGAGAGAAAATATTTACAAG-CATAT-TC-AACAGAAGACTT 1283
                           viv---  i            i   i-     -  -i i iii     
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr1_227844047_   1284 GTATC-AGAATGTCTAAAGAA----TGTA--TTAATAAGAAGAAGAGAAA 1326
                              -     i v       ---- ii -- i     v  i    v   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_227844047_   1327 CAACCCAAAAGAAAAATAGGCAGAAAAATTGAACAGCTTTTTCACAAAAG 1376
                         i       vv?      i    i ii v     i  viv    v v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_227844047_   1377 AAGATACAGGAATGGCCAA---GTGCATGAAAAGATTCTCAACATCATTG 1423
                               i vi         --- ii           v          ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr1_227844047_   1424 GTTAC 1428
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.69 (54 / 32)
Gap_init rate = 0.03 (13 / 402), avg. gap size = 1.85 (24 / 13)  


3045 24.83 2.57 1.01  chr1_227890716_227894984     2883  3776 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_227890716_   2883 TGGAAACACATCTCATACTCATAGATGGGTAGAATTAATATTGTCAAAAT 2932
                               v i   i   ii    i   v  v   v          i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_227890716_   2933 GACCATACTGCCAAAAGCAATCTATAGATTCATTGCAATTCCCATTAAAA 2982
                          i v     v  v   vii     i       vi     i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_227890716_   2983 TAC-AATTACCATTCTTCACAAAACTAGAAAAA--AATCCTAAAATTTAT 3029
                          v - ii i  -  i  ii  i  v v  v  i--i           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_227890716_   3030 ATGGAACAAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGA 3079
                               vviv  ii  v  v v         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_227890716_   3080 AAAAATCTGGAGGCATCACACTACCCAACTTCAAACTACACTACAAGCCT 3129
                          v   vi      vv       v     i      vivi       iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_227890716_   3130 ATAGTTACCAAAACAGCATGGTACTGGTATAAAAACAGGCACATAGA-CA 3178
                          i   v i   i    ii         i    ii i  i  i     -  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_227890716_   3179 ATTGGAACAGAATAGAGAAACCAGAAATAAAGCCAAATACTTACAGCCAA 3228
                           -    i     v    iv           v   v i i   ii i   
  L1M4_orf2#LINE/    300 AT-GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_227890716_   3229 CTGTTCTTTGACAAAG----CAAA------CAA-AAAGAAAGGACACCCT 3267
                         i  v i  i     i ----   i------   -iii     i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_227890716_   3268 CTTCAACAAATGGTGCTGGGATAATTGGCAAGCCCTATGTAGAA-AATGA 3316
                         i                    i  i   vv ?  vi   i i  -     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_227890716_   3317 AACTGGATCCTCTTCTCTCACCTTATACAAAAATCAACTCAAGATGGATC 3366
                          ii    i  iivi   v    v           i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_227890716_   3367 AAAGACTTAAATCTTTTATGGCCTGAAACCATAAAAAAAATCT-AGAAGA 3415
                          ?    i     v --- v iv  i    i      v---   -      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGT---AAGAGCTAAAACTATAAAAC---TCTTAGAAGA 542

  chr1_227890716_   3416 TAACATTGGAAGAACTCTTCTAGACATTGGCTTAGGCAAAGAGTTCATGA 3465
                         v     v  ?iv  v     vv   v    v        v iv   v ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_227890716_   3466 CCAGGAACCCAAAAGCAAATGCAACAA--GGATAAATAGATG----GGAC 3509
                         vi v  vv         v v       -- i v        i----    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_227890716_   3510 TTAATTAAACTAAAAAGCTTCTGTACAGCAAAAGAAATAATCAGCAGATT 3559
                           v  i   v v    i   i   i vv    i  v iv    iv i v 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_227890716_   3560 AAACAGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCCG 3609
                         i  v              i           v  ii   vii   i   i 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_227890716_   3610 ACAAAGAACTAATATCCAGAATCTGCAAGGAACTCAAACAAATCAGCAAG 3659
                          i  i i   vi          v ii  i      vv    v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_227890716_   3660 AATAAAACAAAACAATCCAATAAAGAAGTGGGCTACGGACAAGAATAGAC 3709
                           v  i     -i  i     v? i  i     v v   ivv        
  L1M4_orf2#LINE/    793 AAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_227890716_   3710 AATTCTCAAAAGAAGATATACAAATGGTCAATAAACATATGAAAAAATGC 3759
                          v     v                   i      i  i       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_227890716_   3760 TCAACATCACTAATTAT 3776
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (127 / 91)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.13 (32 / 15)  


1393 21.69 0.34 0.34  chr1_227897004_227902430     3380  3674 (1753)    L1M4_orf2#LINE/L1        5   299 (609)  

  chr1_227897004_   3380 AAGATATTCTATGTTCATGAATTGGAAGAATTAATTTTGTGAAAATGTCC 3429
                                i i         i         v     v    v  i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr1_227897004_   3430 ATACTACCCAAAGTGATCTACAGATTCAATGCAATCTCTGTCAAAATTCC 3479
                              v      v                i      i  i       i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr1_227897004_   3480 AA-TGTCATTCTTCACAGAAATAGAAAAAATATTCCTAAAATGCATATGT 3528
                          i-  i -  i  ii       v  v  iv iv         v      v
  L1M4_orf2#LINE/    105 AGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_227897004_   3529 ACTCACAAAAGACTCTGAATAGTCAAAGCAATCTTGACCAAAAAGAACAA 3578
                          vvii   ii   i v      i    i         vv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_227897004_   3579 AGCTGAAGGCATCACACTACTGGATTTCAAAATATATTACAAAGCTATAG 3628
                           i  i   vv       v ivi         iv  i          i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_227897004_   3629 TAATCAAAACAGCATGGTACTGGTATGAAAACAGACACATATGTCA 3674
                                i    ii         i  i ii i     i   vi   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

Transitions / transversions = 1.67 (40 / 24)
Gap_init rate = 0.01 (2 / 295), avg. gap size = 1.00 (2 / 2)  

1072 22.75 2.15 0.86  chr1_227897004_227902430     3992  4224 (1203)    L1M4_orf2#LINE/L1      289   524 (384)  

  chr1_227897004_   3992 CACATTGACTGATGGAATAGAATACGGAGCTTAGAAATAAACCCACACAT 4041
                           i  v  iii            vvi   iii             i    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_227897004_   4042 CTATGTTCAACTGATTTTTTTGACAAAGGTGCTAAGAACACACAATAGGG 4091
                         i    v    i       --i     i     i    v  iv    i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTT--CGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_227897004_   4092 GAAAGACAGTCTTTTCAATAAATGGTGTTGAGAAAACTGGATATCCACAT 4141
                         i  ii i           i        i  i  v         ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_227897004_   4142 ATAGAAGAATGAATATGTACCTTTATC-----CTTTATACAAGAACCAAC 4186
                         ii i         vv  v   ii  i ----- iv       i  ii   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr1_227897004_   4187 TCAAAATGGATTAAAGACTTAAAAATAAGAGGTAGGAC 4224
                                    i ?    i    vi      v  ii  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

Transitions / transversions = 2.92 (38 / 13)
Gap_init rate = 0.01 (2 / 236), avg. gap size = 3.50 (7 / 2)  

1116 25.12 4.23 2.35  chr1_227897004_227902430     4510  4935 (492)    L1M4_orf2#LINE/L1      475   908 (0)  

  chr1_227897004_   4510 ACAAAA--CAAAACAAAACAAAACAAAAGACTTAGAAAACATGAGGCCTG 4557
                               --i  vv     iii v  ? -   i  ---  ii i  iv  i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWA-GACCTA---AATGTAAGAGCTA 520

  chr1_227897004_   4558 AAACCATAAAACTACTAGAAGAAAACATAGAGGAAACGCTTCATGACATT 4607
                             i        vi               i? v  vv    i    v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_227897004_   4608 GGTCTGGAAAGAGGGATCTTGCGTATGACCCTACAAACACAGGCAACAAA 4657
                           vi i iv iv  vv    ivi      v i v  i    i        
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_227897004_   4658 A-------TAGACAAGTGGGATTGC-TTACAACTAAAAAGTCTCTGCACA 4699
                          -------    i  i v   i v - i v  i      v i -  ii v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCT 669

  chr1_227897004_   4700 GCAAAGAAAACGATTTAGA--GTAAAGAGAGAATTCACAGATTGGGAGAA 4747
                         v     i v  v  iv   --  i  i   v  ii      v        
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr1_227897004_   4748 AACTATTTTCAAATAATACATCAGATAAAGGTCTAATATGCAAAATATAC 4797
                           -     v     v   i   v     i  v  vi   v  i      i
  L1M4_orf2#LINE/    720 AA-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr1_227897004_   4798 AAGAAAC----ATAAGTTACTCAGTAACGAAAA-ACAAATAATGCAATTA 4842
                           ii   ---- i  ----    i   ii    -        iv     ?
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAA----CTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_227897004_   4843 ACACATGGGCAAAT-AGTTGAATATACATTCCTCAACAGAAGACACACCT 4891
                          v v         v- v       v     i   v v      i i  vv
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_227897004_   4892 ATGGCCAACAGATATATCAAAAAATGCTCAACATCTCTTATCAC 4935
                                 i iii i  v    i            v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (58 / 46)
Gap_init rate = 0.03 (12 / 434), avg. gap size = 2.33 (28 / 12)  


2040 24.20 3.66 2.39  chr1_228080082_228081725.rev      526  1153 (491)    L1M4_orf2#LINE/L1      273   908 (0)  

  chr1_228080082_    526 CTGGTATAAAAATAGACACATAGATCAATGAAACAGAATAAAAAACCCAG 575
                             i    ii       i           i  i     vi i ii    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr1_228080082_    576 AAATAAAGCCACATATTTACAACCAACTGATCTTTGACAACATTGACAAG 625
                                v   i i     iiii   i    i  i     viv  v    
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr1_228080082_    626 AACATACACTGGGCAAAGGACACCCCTTTCAATAAATGATACTGGGGAAA 675
                          v   v  v    v    i i vi i      i     i i     iv  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr1_228080082_    676 TTGGATGGCCATATGCAGAAGAATGAAACTGGACCCCTATACCTCATCAT 725
                         i     i?   i     i         ii          ivi v  i   
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr1_228080082_    726 ATACAAAACTAAATTCAACTAAAGATGAATTAAAGTCTTATAAATAAGAC 775
                                 ----   -    v  i   i  i ?  v i  v vi     v
  L1M4_orf2#LINE/    473 ATACAAAA----ATT-AACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_228080082_    776 CCAAAACTATAAACATACTAGAAGAAAACTGAGGGAAAACTCTTCTGAAC 825
                          i           vv vi           vv   ?iv  v     vvi  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr1_228080082_    826 ATTGGTCTATGCAAAGAATTCATGACTAAGACCTCAAAAGCACAGGCAAC 875
                         v    vi  v    v iv   v iiv  v   vi          i     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr1_228080082_    876 AACAACAACAACAAAAAAGCATAGGGAAATGGTACTTAGTTAAACTAAAA 925
                           -------  v      ---   iv    v v    vi i   v v   
  L1M4_orf2#LINE/    618 AA-------AAGAAAAAA---TAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_228080082_    926 AGCTTCTGCAGAGCAAAGGAAATAATCAACAGACTTAAGAGACAACCTGC 975
                          i   i  iivvv       v iv     v i v v  i        ii 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_228080082_    976 AGAATGTGAGAAAATATTTGCAAACTATGCATCCAACAA--------TAT 1017
                               v                 ii  ii   ii i  --------   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_228080082_   1018 CCAGAATATGCAAGGAACCCAAACAATTCAACAACAACAACA-AAATAAT 1066
                                  ii  i    i vv    i    i  i  v  v -      i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_228080082_   1067 TCCATTAAAAAGTGTGAAAAGGACATGAATAGACATTTTTCAAAAGAAGA 1116
                         i v   ?    i  v v      iv             i  v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_228080082_   1117 CATACAAATGG--------------AAAACATGTTCAACATTACTACTAA 1152
                         i          --------------    v   i       i ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr1_228080082_   1153 T 1153
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.39 (86 / 62)
Gap_init rate = 0.01 (7 / 636), avg. gap size = 5.43 (38 / 7)  


3236 26.16 0.99 0.77  chr1_228088792_228095200.rev     5013  5918 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_228088792_   5013 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5062
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_228088792_   5063 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5112
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_228088792_   5113 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5160
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_228088792_   5161 TATGGAACCAAAAAAGAGCCTGCATTGCCAAAACAATCCTAAGCAAGAAG 5210
                                viiv  ii  v  v v  v            i i iv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_228088792_   5211 AACAAAGCTGGAGGCAACACACT-----ACTTCAAACTATACTACAAGGC 5255
                                i      vvv      ----- i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_228088792_   5256 TACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGAGATAGACC 5305
                                 i   i    ii    i    i iv ii i   v v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_228088792_   5306 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 5353
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_228088792_   5354 ATCTGATCTTTGACAAAGCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5403
                          vi    i  i     i v  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_228088792_   5404 CTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGTAGAAAGCT 5453
                           v  i  i           i  v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_228088792_   5454 GAAACTGGATCCCCTCCTTACACCTTATACAAAAATTAATTCAAGATGAA 5503
                            ii    i   iv   i     v              i    i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_228088792_   5504 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5553
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_228088792_   5554 CTAGGCAATACCTTTCAGGACATAGGCATGGGCAAGGACTTAATAACTGA 5603
                         v    ?ivv vii   iv   v v  vv i     v ii  vv  iv iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_228088792_   5604 AACACCAAAAGCAATGGCAACACAAGCCAAAATAGACAAATGGGATCTAA 5653
                         i            vvi      v   vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_228088792_   5654 TTAAACTAAAGAGCTTCTGCACAGCAACAGAAACTACCATCAGAGTGAAC 5703
                          i   v v  i i   i  ii vv   vi  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_228088792_   5704 AGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 5753
                           i     i i               v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_228088792_   5754 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATGTACAAGAAAA 5803
                         i  i  vi          v  i        ivv    v ---   v  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATA 793

  chr1_228088792_   5804 AACAAATAAACAAGCCCATCAAAAAGTGGGCAAAGGATATGAACAGAAAC 5853
                           v i i   i  v  v  i?    i            v    i   v i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_228088792_   5854 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 5903
                              v        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_228088792_   5904 ATCATCACTGGTCAT 5918
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


2203 25.50 7.02 1.53  chr1_228188693_228191816.rev     1454  2108 (1016)    L1M4_orf2#LINE/L1        1   691 (217)  

  chr1_228188693_   1454 TGAAAAGACAGCCCATACTGATGGATTGTAAGAATTAATATTGTTAAAAT 1503
                           i     i v     ii v        v    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_228188693_   1504 AACAGT----------------------------GCAATCTCTATCAAAA 1525
                         ii  i ----------------------------      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_228188693_   1526 TACCAATGACATTTCTCACAGAAACAGAAAAAAAAATCCTAAAGTTTGTA 1575
                          v   iivi v   i ii      iv  v  ivvi        i  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_228188693_   1576 TGGAACTACAAAAGACCCCAAATAACCAAAGTAATCATAAGCGAAAAGAA 1625
                              v i   ii     vi    i     ii    v i ivi i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_228188693_   1626 CAACACTGGAGGTATCACACTACCAGACCTCAAAATATACTACAAAGCTG 1675
                            vii      vv       v  vi ii      iv            i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_228188693_   1676 TAGTAACCAAAACAACATGGTACTGGCATAAAATTAGATACACGGACCGA 1725
                         i     i   i   iii              iiv    i i ii  i i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_228188693_   1726 TGGAACAGTATTGAGAATCCAGAAATTAATCCACATATATACTGTCAACT 1775
                              i  v       i         v  i   i i  v  iv     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_228188693_   1776 GATTTTTGGATTTTTGACAAAGGTTCCAAACACTAATCG--GGGAAAAGA 1823
                               i --------    i   v    i-  i v  i--   i     
  L1M4_orf2#LINE/    351 GATTTTCG--------ACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGA 391

  chr1_228188693_   1824 A-GGTCTCTTCAATAAATGGTGTTGGGAAAACTGTATATCCATATGCAGA 1872
                          -i    i     i        i     v     v   ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_228188693_   1873 AGGATGAAAGTAGACCCCTGTCTCTCACCTTATATGAAAATCTAGTCTAA 1922
                           i     iv i       ii   v    v    ii     iv v  v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_228188693_   1923 GTCAATCAAAGACCTAAATGTAAGACCAAAAATGATAAAATTATGAGAAG 1972
                         i vi    ?                v v    iv      i v v     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_228188693_   1973 AAAACAGAGGA---------CATGAGCCTGGGA-AAACA----TTTTATG 2008
                               v   ?--------- i   v i    v- ii  ----   iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_228188693_   2009 AATAAGATTTTAAAAGCACAGACAACAATAGCAAAACTAAACAAGTGAGA 2058
                         i   v  ivii         ii      v  v    v  i i  i vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_228188693_   2059 TTTTATCAAA-TTAAAAATCTTCTGCACAGCAAAGAAAACAATCAACAAG 2107
                         i  i      -       -   i  ii vv     i v  v     v  i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_228188693_   2108 G 2108
                          
  L1M4_orf2#LINE/    691 G 691

Transitions / transversions = 1.88 (107 / 57)
Gap_init rate = 0.01 (10 / 691), avg. gap size = 5.60 (56 / 10)  

 882 20.54 3.12 0.45  chr1_228188693_228191816.rev     2410  2633 (491)    L1M4_orf2#LINE/L1      679   908 (0)  

  chr1_228188693_   2410 ACAATCAACAGAGTGAAAAGACAACCTACAGAATGGGAGAAAATGTTTGC 2459
                           v     v i               i                 i     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_228188693_   2460 AAACTACCCATCCAACAGGGGATTACTATCCAGAATATACAAGGAACTGA 2509
                            ii ivi   ii i i    i vv             i  i     vv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_228188693_   2510 ATCATCTCAACAAAAGAAATACAA----TCTAATTTAAAAATGGGCAAAT 2555
                         vv  v     i  v i   v    ----i i    ?             v
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_228188693_   2556 AATCCGAACAGACATTTCTCAAAAGAAGGCATAAAAATGGCCAAAAATGT 2605
                         i  ii   i           v       ii   v          v  - i
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA-GC 877

  chr1_228188693_   2606 ATTTTTAA---TGCTCAACATCACTGATCAT 2633
                          iv vv  ---            ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (26 / 19)
Gap_init rate = 0.01 (3 / 230), avg. gap size = 2.67 (8 / 3)  


1875 25.04 11.99 1.05  chr1_228258182_228259808.rev      470  1136 (491)    L1M4_orf2#LINE/L1      169   908 (0)  

  chr1_228258182_    470 AGGATGACCAAAGCAATCCTTAAAAAG-----------TG-AG------- 500
                           i  ii     i     i v      -----------  -  -------
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr1_228258182_    501 ---TCTTGGTTTCAAGACTAATGCTAAAGCCACTATAAATCAAGGTAATA 547
                         ---  iiii      i   v ivvi     i  vi   -     ii i i
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA-TCAAGACAGTG 267

  chr1_228258182_    548 TGGCATTGA-ATATACATAGACAAACAGATCGATGGAATAGAATAAACAG 596
                            i i  i-   viv       v i     i            vi v  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_228258182_    597 TCCAGGAGTGGATTAACACATATACAGCCAA-----------CCAAAGTG 635
                              i i ii iiv i    v  ii i   ----------- v ii   
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_228258182_    636 CCAAAGCAAGTCAATGAGGAAAAGAAAGTATTTTCAATAAATGGTGCTGG 685
                             ii v v      i     ii v   v       i            
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_228258182_    686 AACAACTAGCTATCTACATGGAAAAAATATTAACCTTGATTCATACCTCA 735
                         i      i v  ? i     v    i -  v  vi v  ii v       
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGA-ATGAAGTTGGACCCCTACCTCA 466

  chr1_228258182_    736 AACCACA--CAAAAATTTAATTAAAGGTGGATCACAGGCCTACATGTAAA 783
                         v    i --        -  i v  ii       ?  i    v      i
  L1M4_orf2#LINE/    467 CACCATATACAAAAATT-AACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr1_228258182_    784 AGTTAAAACTATAAAGCTTCTACAAAAAAA-----AAATGAATATTTGAT 828
                           i            i  ii  v  i    -----i?i i   v  i --
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG-- 563

  chr1_228258182_    829 TGACTTTGGAGTAGGCAAGAACTTC--AGATAAGATACAGAAAACACTAT 876
                             i    iv       viii   --     v  i  vi   i   v v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_228258182_    877 TTTAAAAAG--------GATAAAT-GGGCTTTATCAAAATTAAAAACTTC 917
                         ivvv     --------       -  i   i                 i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_228258182_    918 T---CATCAAAAGACACAACTAAAAAA-TGAGACGACAAGTCACAGACTT 963
                          --- v     i     v ii  i   -   i v     vi      v v
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr1_228258182_    964 GGAGAAAATCATTGCA--TTATGTTTAACTGACAAGGAATT--------G 1003
                                  vv     -- i  i v --    i    i i -------- 
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATAT--CTGATAAGGGACTTGTATCCAG 761

  chr1_228258182_   1004 AATAC------------TACAACTTGACAATTAAAACACAAATGGTGCCA 1041
                             i------------       ii i   v    v      iiiv v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_228258182_   1042 TTGAAAAATGGTCAAATGACTT-AACAGGCATTT-TACAAAGTAGACGCA 1089
                           ?        v    v  i  -  i  i     - v     v   iii 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_228258182_   1090 CAAATGGCTAATAAGCATATGAAAAAACATTTGACATCATTAATCAT 1136
                                 i        i       i iii ii      ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (109 / 54)
Gap_init rate = 0.03 (22 / 740), avg. gap size = 3.95 (87 / 22)  


3051 27.16 1.22 0.55  chr1_228349907_228355716.rev     4418  5319 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_228349907_   4418 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGCGAAAAT 4467
                              ii i  i     i        v      v i     i iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_228349907_   4468 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCGCATCAAGC 4517
                            v     v     iv i  i  i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_228349907_   4518 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTGCAT 4566
                          v   iivi i  i  ii     v v  v  i-  - iii    i v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_228349907_   4567 ATGGAACCAAAAAGGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAGA 4616
                               viiv  i   v  viv  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_228349907_   4617 ACAAAGCTGGAGGCAACACACTACTTGACTTCAAATGATACTACAAGGCT 4666
                               i      vvv      v iii i      vvv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_228349907_   4667 ACAGTAA------CAGCATGGTACTGATATCAAAACAGAGATATAGACCA 4710
                                ------   ii        ii  v ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_228349907_   4711 ATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCA 4758
                               i    i--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr1_228349907_   4759 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACGATTCCC 4808
                         vi    i  i     ivv  v   i v  vvv          vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_228349907_   4809 TATTTAATAAATGGTGCTGGAAAAACTGGCTAGCCATATGTAGAAAGCTG 4858
                          v  i  i            i v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_228349907_   4859 AAACTGGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATGAAT 4908
                           ii    i  i v   i     v              i    i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_228349907_   4909 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4958
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_228349907_   4959 TAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGACTAA 5007
                             ?i- v i -   iv   viv  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_228349907_   5008 AACACCAAAAGCAACGGCAACAAAAGCCAAAGTTGACAAATGGGATCTAA 5057
                         i            vvi          vv   i v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_228349907_   5058 TTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGAAC 5107
                          i   v v  i i   i iii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_228349907_   5108 AGGCAACGTACAGAATGGGAGAAAA-GTTTAAAAATCTACCCATCTGACA 5156
                           i    vi                -i   iv     - ivi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATA 745

  chr1_228349907_   5157 AAAGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5206
                          ii i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_228349907_   5207 AAGTCAAACAACCCCATCAAAAAGTGAGCAAAGGATATGAACAGACACTT 5256
                            v    i     v  i?    i  i         v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_228349907_   5257 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGTTCAT 5306
                            v        i  vi viii     i ii          i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_228349907_   5307 CATCACTGACCAT 5319
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


1695 28.05 3.30 0.83  chr1_228443526_228445117      494  1099 (493)    L1M4_orf2#LINE/L1      288   908 (0)  

  chr1_228443526_    494 ACATAT-TATAAATA-AATTGAGATGAAACCCTAAAAATAGGTCCATAAA 541
                               -v  v   i-   v  iv   i vi i i     iii     v 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_228443526_    542 AATATGCTCAAATGATTTTTGGCGAAGGTATAAAAGTAATTCAGTGAAGG 591
                         vv    v    v       i i i i   iiv  iiiv     i  ii i
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_228443526_    592 AACAATAGAATTTTTAACAAATGGAGCTGGAGCTATTGAACATTCATAGG 641
                           v     vv    i         v     ii v i  i i ?i  i v 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_228443526_    642 GAAAAAGATGAACTCAAAC---TAAGTCTCATACTTCATGCAAAAATTAA 688
                         v    ii     v iii  ---  --i    i  ivi  i          
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAA 485

  chr1_228443526_    689 CTTAAAATGGATCAAGGACCTAATTGTAAAATATAAAACTATAAAACTTT 738
                           i           ?i       v     i vv               i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_228443526_    739 TAGGAAAAAAAA-AGGAGTCAGTCTTTGAGACCTAAGGCAAGGCAAAGAT 787
                            i i    v -   ?  v i    i v     vi  iv      v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_228443526_    788 TTCCAAGACTCGACATTAGAAGCACAATCAAGTAAAAGGAAACATTGATA 837
                            iv   ivi    ii i        v   -i     i   v  v    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAA-CAAAAGAAAAAATAGATA 634

  chr1_228443526_    838 AACTGAACCTCTTTGAAGT-AAAACCTTTTGCTCTGTAAAGATTCATGTG 886
                           i  i  i  v ii  i -    v      iv  vi    ivivv i v
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_228443526_    887 AAGAAGATGAAAAGACAAACTAGTGACTGGGAGACA-TGTTTGTAACCAT 935
                              ii           v i vv  v       v - i    i  --  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA--AT 732

  chr1_228443526_    936 -ATATATCTGACAAAGTATTAGTATGTACAATGTACAAAG---TCTCAAA 981
                         -          i  i v i v    vi v   i  i    ---   i v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_228443526_    982 ACCCAACACTAAAAA-----ATA--TTGAGTAGAAAAGAAGCAAAAGACA 1024
                           i   i v      -----   --iii v ?i    vii     i  iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_228443526_   1025 TAAA-ATACACCTCACTGAAGAGGCTATATGGATGGCAAAGAAGCACGTG 1073
                          i  - v   ii  v ii    i v    iii     v  v      i  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_228443526_   1074 AAAAGATAGTCAACATCATTAGAAAT 1099
                                iv         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (103 / 63)
Gap_init rate = 0.02 (14 / 621), avg. gap size = 1.79 (25 / 14)  


2969 27.92 0.66 0.66  chr1_228520530_228525095     3168  4073 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_228520530_   3168 GAAGAACATTCCATGCACATGGATAGGAAGAATCAATATCATGAAAATGG 3217
                            ii i  i     iv       v      v i     ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_228520530_   3218 CCATATTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGCTA 3267
                          v   i v     iv i  i  i       ii  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_228520530_   3268 CCAATGACTCTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCATAT 3316
                            iivi ii i  ii     v v  v  i-  - iii    i       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr1_228520530_   3317 GGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAGAAC 3366
                             viiv  ii  v  viv  v     i      i i ivv i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_228520530_   3367 AAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTAC 3416
                             i      vv   ii  v  ii i      viv        i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_228520530_   3417 AGTAACCAAAACAGTGTGGTACTGGTACCAAAACAGAGACATAGACCAAA 3466
                              i   i               i iv ii i   v i     i   v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_228520530_   3467 GGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCATC 3514
                             i    i--    i  --        vv   i    i  iiii  vi
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_228520530_   3515 TGATCTT-GACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 3563
                             i  -     ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_228520530_   3564 TTTAATAAATGATGCTGGGAAAACTGGCTAGCCATACGTAGAAAGCTAAA 3613
                           i  i     i        v      v  ?   i i i i  iiv i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_228520530_   3614 ACTGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA 3663
                         ii  i i    v   i     v              i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_228520530_   3664 AAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 3713
                         ?    i       v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_228520530_   3714 GGCA-ATACCATTTAGGACATAGGCATGGGCAAGGACTTCATGACTAAAA 3762
                           ?i- v i -  iiv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_228520530_   3763 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 3812
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_228520530_   3813 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 3862
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_228520530_   3863 GCAATCTACAGAATGGGAGAAAAGTTTTA-AAATCTACCCATCTGACAAA 3911
                         i   i i                vv   i-     - ivi      i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAG 747

  chr1_228520530_   3912 GGGCTAATATCCAGAATCCACAAAGAACTTAAACAAATTTACAAGAAAAA 3961
                           i  vi          vi i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_228520530_   3962 AATCAAACAACCCCGTCAAAAAGTGCGTGAAGGATAGGAACAGAAACTTC 4011
                         i -    i     vi i?    i  v ii      vv   i   v i   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_228520530_   4012 TCAAAAGAAGACATTTATGCAACCAACAGATACATGAAAAAATGCTCATC 4061
                           v        i  vi viiii    i iii         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_228520530_   4062 ATCACTGGCCAT 4073
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (153 / 96)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.20 (12 / 10)  


3765 20.23 5.20 0.23  chr1_228558762_228560945.rev      829  1693 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_228558762_    829 TGAAAATAT-TCCTATGATCATGGA-----AGAC--AATATTTTTAGGAC 870
                           i   v  -   i   v       -----    --      v   i  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_228558762_    871 ATCAGTACTACCCAAAGCAATCTATAGAGTGAGTGTAATCCCTATCAAAA 920
                         iv  i    v      vii     i   v v ii i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_228558762_    921 TTAGAACTTCTCTTTTTTGCAGAAATGGAAAAGCTGAGCCTCAAATCCAT 970
                          ivv i  v -               v  v       v   v    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_228558762_    971 ATGGAATTTCAAGG--CTTGGAATAGCCAAAAAAATTTTGAAAAAGAA-- 1016
                               v v     -- iii            v   i           --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_228558762_   1017 -CAAAGCTGAAGGATTTATATTTCCTAATTATACAACTTTCTATAAAGCT 1065
                         -     i  i    i i i i    i    vi v     v   i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_228558762_   1066 ACAGTAATCAAAA--GTGTGGTATGGACATAATGATAAACATATAGACAA 1113
                                    i --        iv i     v    i         iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_228558762_   1114 AATGAATATAATTGAGAGCCCCAAAATA--TTCATTTATCTATGGCCAAT 1161
                          vv     v         i  vi     --ii   vi  i     i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_228558762_   1162 TGATTTTCAACAAGGATGCCAAAACCATTCAATGGGGAAAAGGTTGTTTC 1211
                                 i      i      i                 iii v  i i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_228558762_   1212 TTCAACAAATGGTGCTTAGACCATCA------CACATGTGAAAGAATGAA 1255
                                         vi   v iii------      ii          
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_228558762_   1256 CTTGAACTTCT---TCACACCATGTGCAAATCTTAACTCAAAATGAGTCA 1302
                         v   i  ii  ---         i i    vv             ii   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_228558762_   1303 ATGATCTAAATATAAGAGCTAAAATCACAAAAATCTTAGAAGACAACATA 1352
                         ?v  i      i            ii i    v          v      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_228558762_   1353 GGGTTAAGTCTTTGTAACCTTCGATTTGGCAATCGATTCTTAAGTATAAT 1402
                           ?v   i    i  i     v i  v      v v      ii   i i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_228558762_   1403 ACCCAAAGCACAAGCTACAAAGG------TG------TTGGACTTTATAA 1440
                            v           v     i ------ i------        i  v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_228558762_   1441 AAAT-AAACAATTGTGTGCATATGTGGGCATAATCAAGAAAGTACAAAGA 1489
                             -   v v  v     v vviv  i  iv           iv     
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_228558762_   1490 CATCGTACAGAATGGGAGAAAATATTTGCAAATTACAGATCTCATA-TGA 1538
                           v vi                           i i v    v   -v i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_228558762_   1539 ATTCAATATTGAGAGTGTATAAAGAACTCT-ACAACTCAAGAGCAAAAAG 1587
                          i ii-   iv   i i             -         v ii      
  L1M4_orf2#LINE/    750 ACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_228558762_   1588 A-AAA---CCCCATTGAAAAATAGGCAATGGATTTAAATACACATTTTTC 1633
                          -   ---   v   ?      i     v      i    v      i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_228558762_   1634 TCAAGAAGACGTACAAATGGCCCATAAGTACAGTAAAAAATACTCAACCT 1683
                         iv       ii           v     i   vv    i  i      v 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_228558762_   1684 CATTAGTCAT 1693
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.46 (102 / 70)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.61 (47 / 18)  


 214 21.95 0.00 0.00  chr1_229489514_229494067     2951  2991 (1563)    L1M4_orf2#LINE/L1        1    41 (867)  

  chr1_229489514_   2951 TGGGAAAACATTCCTTGCTCATGGATTGGAAGAATCAACAT 2991
                            i  i i  i  v  i               v i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT 41

Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  

2713 25.91 2.58 1.41  chr1_229489514_229494067     3209  4061 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_229489514_   3209 AAAATGACCATACTGCCCAAAGCAGTCTATAGACTCTA-----TTCCCAT 3253
                           i   i v     v      viii    i   i  v ----- i  i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_229489514_   3254 CAAACTACCAA-TGTCATTTTTCACAGAGCTAGAAAAAAACT-ATTCTAA 3301
                             v v   i-  i -     ii    iv v  v  i--  -  i    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAA 142

  chr1_229489514_   3302 AATCCATACTGAATAAAAAAAAAAAGCCCA-AGTAGCAAAAGCAATCCTA 3350
                            i    -  i --  viv  iiii    - i    v   i     i i
  L1M4_orf2#LINE/    143 AATTCATA-TGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_229489514_   3351 AACAAAAGGAACAAATCCAGAGGCATCA-ATTACCCAACTTCAAACTATA 3399
                           v  i i       viii    vv   - i v     i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_229489514_   3400 CTCTAAGCCTATAGTAACCAAAACAGCATGGTAGTGGTACAAAAACAGAC 3449
                           vi  iv   i     i   i    ii     v   i i  ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_229489514_   3450 ACATAGACCAATGGAACAGAATAGCAAACCCGGAAATAAAAAGTCACACA 3499
                          i     i        i     v vi ii  i        v--i  i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC--CCATACA 337

  chr1_229489514_   3500 CCTATAGCCATCTGATCTTTGACAAAGTCAACAAAAATAAGCAATGGGGA 3549
                         ii   i i  vi    i  i     i viiv   i vi vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_229489514_   3550 AAGGGCTCCCTATTCAATAAATGGTGCTGGGATAGCTGGCTAGCCATGTG 3599
                            iiivvi  v     i              i i    v  ?   ii  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_229489514_   3600 CAGAAGAATGAAACAGGACCCCTACCTTTCACCATATACAAAAATTAACC 3649
                           i         iiv            iv                    i
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_229489514_   3650 CAAGATTGATTAAAGATTTAAATGTAAGACCTCAAACTATAG-------- 3691
                            i  v   i ?   ii           v  v        i--------
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_229489514_   3692 GAGGAAAACCTAGAAA-ACATTATTCTGGACATGGGCCTTAGGAAAGAAT 3740
                           i      v   i?i- v  iv iv  iv v    --     v  vii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGT 585

  chr1_229489514_   3741 TTAT--GACTAAGTCTTCAAAAGCAATTGCAA-AAAAACAAAAATGGGCA 3787
                           v --  -  v v vi        vvv    -    iv      i ii 
  L1M4_orf2#LINE/    586 TTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_229489514_   3788 AATGAGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATC 3837
                            vi   i v  i   v v  i i   i  ii vv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_229489514_   3838 AATAGAAT-AAAAGACAACCTACAGAATGGGAGATAATATTCCCAAACTA 3886
                           v i i -           i             v      iv    ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_229489514_   3887 TGTAACTGACAAAGGTCTAATATCCAGAATGTATAAGGGAATTAAACAAT 3936
                          i  v    i  i  v  vi          i     i i v ivv    i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_229489514_   3937 CAAACAAGCAAAAAATAAATAACCCCATTAAAAAATGGGTAAAAGATATG 3986
                         iv  i  vv    i i         v   ?         i   i   v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_229489514_   3987 AAGAGATACTTCTCAAAAGAAGACATACAAGTGGCCAACTAACACATGAA 4036
                           v   i i     v        i      i       iv i        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_229489514_   4037 AAAAATGCTCAACATCACTAATCAT 4061
                           i -            ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (137 / 80)
Gap_init rate = 0.02 (18 / 863), avg. gap size = 1.89 (34 / 18)  


1443 23.88 3.73 5.41  chr1_229557775_229563337     3447  3982 (1581)    L1M4_orf2#LINE/L1       19   545 (363)  

  chr1_229557775_   3447 TTACAGATTGGAAGAC--AACATAGAAAAGATGTCAATTCTCTCTAAACT 3494
                          i ii           --  i  v vv      v    v   i i   i 
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chr1_229557775_   3495 GATATAGAAGCTTA---CAATTCCTATTAAAATCTCAGCAAGTATGT-TT 3540
                            v  v iii i ---    i     i      i    -----  i-  
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-----TGCCTT 113

  chr1_229557775_   3541 TTTTACAGATGCAAT--AAAAATTAA-CCTAAAATTTATA-GGAAATGCA 3586
                             i    ---   -- v  ii i -         i   -         
  L1M4_orf2#LINE/    114 TTTTGCAGA---AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr1_229557775_   3587 AAGTTAACTAGAATAGC-AAAACAATTTTGGGAAAAAA---TAAAGTGGG 3632
                          i v- v i        -        i   ii   i  ---i     v  
  L1M4_orf2#LINE/    161 AGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr1_229557775_   3633 AAGAATC-CATCTACCCAATTTCAACTCTTTCAGTACAA--CTAAAGTAA 3679
                          i  v  -  -  v           vv   v --     --   v     
  L1M4_orf2#LINE/    210 AGGACTCACA-CTTCCCAATTTCAAAACTTAC--TACAAAGCTACAGTAA 256

  chr1_229557775_   3680 TCAAGACTTCTTGGTATTGGTGAAGGGATAAACAGATGGGTCAATAGAAT 3729
                                vviv     i   iiv i     i   v  i i     i    
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_229557775_   3730 AAAATATAGCACTCAGAAATATACTCACACAAACATGAGCAACTGATTTT 3779
                          i   vv  viii        v  i  i   vvi   iv   i       
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_229557775_   3780 -GACCAAGGTGCAAAAGCAATTCGAGGAAGGAAAGACAGTCATTTCAACA 3828
                         -   v i     v  ii v    i v ii i  ii i    v        
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_229557775_   3829 AATGGTGCTGGAATAATTAGATATAAATAGGCAAAAAAATTAAAAACAAA 3878
                                    i i  i i    ?vv i v      i   --------i 
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT--------GA 448

  chr1_229557775_   3879 AGCAAAACAAATAACCCTTTACCTAAGTCTCGTA-ATTCATATTAGCTCA 3927
                           ivii  ------    --    v -ivi i  - ivv v    i    
  L1M4_orf2#LINE/    449 AGTTGGAC------CCCT--ACCTCA-CACCATATACAAAAATTAACTCA 489

  chr1_229557775_   3928 ATAAAGATCACAGACTTAAGTATAAAA-CGAAAAGTATAAAACTTTTAGG 3976
                          v vi     ?    i   i i   i - v    v         i    i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_229557775_   3977 AAAAAA 3982
                          i    
  L1M4_orf2#LINE/    540 AGAAAA 545

Transitions / transversions = 1.68 (79 / 47)
Gap_init rate = 0.04 (22 / 527), avg. gap size = 2.23 (49 / 22)  

 793 26.96 0.87 0.43  chr1_229557775_229563337     4360  4589 (974)    L1M4_orf2#LINE/L1      539   769 (139)  

  chr1_229557775_   4360 AACAAAAAACAGGAGAAAATCTTGG-GGTCTAGAACCAGGCAAAGAGTTT 4408
                           v    v i   ? v       v - ii  v iiii      v -    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTT 587

  chr1_229557775_   4409 TTTGCACTTCACAC-AAAATTATGATCAATAAAAGAAATTATTGATAAAT 4457
                         i  iv iv v    -    vi ii v   i        vv  v       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_229557775_   4458 TAGACTTCACTAAAATTAAAACTTTTTGTACTACGAAAGACCCTATTAAG 4507
                          i       ii          vi      i  v i  i   v    i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_229557775_   4508 AGAAGGAAAAAACAAGCTACAGAGTGGGAGAAAGTATTTGCAGATGACAT 4557
                          i iv     i    v i     i         i        i  v i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_229557775_   4558 ATCCAACAAGGGAATCAAATCTAGAGTACACA 4589
                            ii i      v iiv   i   i  i i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATA 769

Transitions / transversions = 1.77 (39 / 22)
Gap_init rate = 0.01 (3 / 231), avg. gap size = 1.00 (3 / 3)  

 349 23.18 4.64 1.99  chr1_229557775_229563337     4920  5070 (493)    L1M4_orf2#LINE/L1      754   908 (0)  

  chr1_229557775_   4920 GTAT--AGAGTATATAAAGAATTCTCAAAATTAAACAGTAAAAACCCAAA 4967
                             --   i           i   i v  i v  i i      vv    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr1_229557775_   4968 CAATCCAATCTAGACCATA--CAAAAACTGTATGAA--GCCAGTTTACCA 5013
                         i  i     i? i v-  i--    ii--i v    -- v  v  iv   
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAA-ATGGGCAAAGG--ATTTGAATAGACATTTCTCCA 850

  chr1_229557775_   5014 AAGAATATATACAAATGGAGACTAAGCACCTAAACA-ATATTCCACATCA 5062
                              v            vv v       v i  v -  ii  v      
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr1_229557775_   5063 CTAACCTT 5070
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.12 (18 / 16)
Gap_init rate = 0.04 (6 / 155), avg. gap size = 1.67 (10 / 6)  


2134 24.94 6.12 7.14  chr1_229607585_229609592      626  1507 (501)    L1M4_orf2#LINE/L1        1   873 (35)  

  chr1_229607585_    626 TGGGGAGATATACTGCATTCCTGGATTTGAAGATTCAGTATTGTTAATAA 675
                            ii      v iiii   v      v     i i i         v v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_229607585_    676 GTCAATTCTCACAAAACTGATTGATAAATTCAATGAAATTGTAATGAAAA 725
                          v    v   v v   i    iv i i      i v   iviv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_229607585_    726 TTCTAGCAGAATTTTTTTTAGAAACGAACATGCTAATTTAAAAATGTACA 775
                          i i   v vv      vi     ivi   v   i  iiv     vi i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_229607585_    776 TGGAAATGCAATAGACCCTAGAATAGCTAAAACGACTTTGAAAAATAA-- 823
                                    vi     -        i     i ii        v  --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCC-AGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_229607585_    824 --AAAGTTGGAGGACATACAATACCTGGTTTCAAGGTTTATTACAAAGC- 870
                         --             vi   v v  iii      iii   i        -
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_229607585_    871 ACAGTAACTATGGTATTGATGGTATTGGTGCAA--ATACACATCTAGATC 918
                                ii v ii v  -     i   iii  --   v    v      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTG-TGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_229607585_    919 AATGGAAAAGAATAAAGTGTCCAGAAATAGGCCACAACAGATATATGACC 968
                                v     vi  v           ii  -  -i v  v    ii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACC-CA-TACATTTATGGTC 346

  chr1_229607585_    969 AATTGATTTTCGACAAAAGTGCAATGGTGAAATGACAAATCCCCTAAATG 1018
                                         ii    -------------   iv  vi v    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGC-------------CAAGACCATTCAATG 383

  chr1_229607585_   1019 AAGAAAAGGATAATCTTTTCTATGAAAGGTGCTGGAACAATGGAATAGCC 1068
                         ii    - i   i       v ii  v        i    iv i   ?  
  L1M4_orf2#LINE/    384 GGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_229607585_   1069 AACTATAAAAATAAATAAATAAATAAATAAATTAAATTAAACAATAACAA 1118
                          vv ii    i------------------   v  i  ii  --------
  L1M4_orf2#LINE/    433 ACATGCAAAAG------------------AATGAAGTTGGAC-------- 456

  chr1_229607585_   1119 AAACATCTTGATACTTTGCTGCACATACAGTAATTAACTCAACAT----C 1164
                         -----i i ---  i ii vv  i     iv           v  ---- 
  L1M4_orf2#LINE/    457 -----CCCT---ACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_229607585_   1165 ATGAACCTAA---------C--AAACCATCAAACTGCTCAAAGCAACCAT 1203
                          ?ii      --------- --    i  v     vi vi   v  v   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_229607585_   1204 AAGAGGAAATCTTAATGATCCTGGATTTGGCAAAGATTTCTTAAATGGAG 1253
                          i ? v       vi   i i   i  v     v i       i  ivii
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_229607585_   1254 CACTAAAAGTTGGAACTATAAAAGAAAAAATTAAATAAATTGGACATCAC 1303
                            i     ivvi i v i            - i           v   i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAATTGGACTTCAT 647

  chr1_229607585_   1304 AAAAATGTAAAACTTTTGCTCTTCGAAAGACACTTACAA--------AAA 1345
                         v     vv          iv    i  i      vv   --------   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_229607585_   1346 GGCAAGCCAAAGACTAGGGAAAAAA-------AAATTAC-TA-CTCATAA 1386
                          i   v   v   v -    i    -------    i i-  -  v    
  L1M4_orf2#LINE/    698 GACAACCCACAGAAT-GGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_229607585_   1387 A--ACCCACATTCA------ACAAAGGACATTTAC--CT-----ATAAAC 1421
                         i--  iiii  i  ------ i    i  vi    --  -----     v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_229607585_   1422 AAACAACACCCTCCTACATCCCCAGCTGCACATGATAAAAAGTTCTGAAC 1471
                          i    --------- i v   v vi?iv v   ivv   i v i    i
  L1M4_orf2#LINE/    797 AGACAA---------ATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_229607585_   1472 AGACGCTTCACTGAAGGAGATATACAGATGGCAAAT 1507
                             ii   v ii   i         i     v   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

Transitions / transversions = 1.54 (131 / 85)
Gap_init rate = 0.03 (26 / 873), avg. gap size = 4.50 (117 / 26)  


2213 24.46 12.35 3.48  chr1_229636618_229639596     1656  2489 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_229636618_   1656 TGGAACAATATACCATGTTCATGGATCAAAAAGTT--ACA--GTTAAGAT 1701
                              vi    v              iii  iii -- i --        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_229636618_   1702 GTCAGTTCTCCCCAAATTGATCTACAAATTCATCATAATCCCAACGAAAA 1751
                          v  i v                   i     v ii      v iv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_229636618_   1752 TTTTTGCAAA--TTTTGGTAGGAATTGTCAAACACAGTGTAAAACTTACT 1799
                          iiiv  viv--    v i  i     v   i vv viv     i i --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA-- 148

  chr1_229636618_   1800 TTTGAAGAAATAT----GACCTTTAATAGCAAAAACAATTTTGAAAAAGA 1845
                          v  --     ii----    ivv      v        i          
  L1M4_orf2#LINE/    149 TATG--GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_229636618_   1846 AGAATAAAATTGGGAGAC--ACACTATCTGATTTCAAAGCATATTATATA 1893
                             i   i    ii   --     vi ii        i v  i  i v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_229636618_   1894 GCTGCAGTAATAAAAACAATGTAATACTAACATAAAGAAAGGCATGCAGA 1943
                            i       v  i   i   ii    ii     i  v  i   ii   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_229636618_   1944 ACAATGAAATG--ATTAA-----------------------TTT------ 1962
                         v     i   i--   i -----------------------   ------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_229636618_   1963 --TTGGTTCTAAAC----GTTCCATGATAATTCAACGGAGAAAGGTTAGT 2006
                         --   i  i vi  ----  v   v  iv      i  i     iv    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_229636618_   2007 GTTTTCAACAAATGGTACTAG----------------------------T 2028
                         v               i  i ---------------------------- 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_229636618_   2029 AAATCTCAACCTTCACCTCATGTCATACACAAAAATCATCTCAAAAGAGA 2078
                         i  vi vi   iii      iii    i        i v       vi  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_229636618_   2079 TTTCAAATCTAAATATAAGTATATTCAAATCAAATCTAAATATAATACAA 2128
                          iv? i i      i    -------------- v     --------- 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAG--------------AGCTAAA---------A 523

  chr1_229636618_   2129 CTATAAAACTTGTAGTACAAAA-ATA----------TTTGTGACTTAGGG 2167
                                   iv   v v    -   ----------  i     i v   
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_229636618_   2168 TTAAGTAAATGTTTTCTAGGTAAGACATAAAAAAAAC---CCATAAAATA 2214
                            i i  vv    ii   i  v    iv    iv  --- v i    v 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_229636618_   2215 AATATTAGATAAATTGGACTTCATTGTAACTAAAAACTTCTGCTTTTCAA 2264
                           v v                   iiv  i         i  ivi     
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr1_229636618_   2265 AATATACTGTTAAAAAAATGAGAAGACAAGCCACAGCCTGAAAAAAAAAA 2314
                          iv i   i i  i   i   i       v      vv  ii i    v 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_229636618_   2315 TGTGTGTAGCATATATCTGTTAAAGGACTTGTATCTAGATTATGTAAAGA 2364
                          v  iiv v          v   i           i   v   i      
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_229636618_   2365 ACTCTTATGTCTCAATAATATGGCATACATATAATTT--TT---AAATGG 2409
                                iiv          -iiv v   v    iii--  ---      
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATA-AAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_229636618_   2410 ACAAAAGAC--AAGCAAATTTTTCATCAATGAAGTTATACAAATGTG--- 2454
                         i    i  i--i ii i iv    vi   v    v          - ---
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG-GCCA 871

  chr1_229636618_   2455 --AAACATACAGAAAGATGTTCAACACTATTCATTAT 2489
                         --  i  i iii       i      ii ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (132 / 71)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 5.74 (132 / 23)  


2089 26.76 8.22 1.64  chr1_229863004_229865395.rev     1050  1901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_229863004_   1050 TGGAAAGA-GTTGGATTTTCATGGACTGAAAGACTCAACATCTTTACTGA 1098
                                 -i ivv  v        i  i      i  i  iv   v-  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA-GA 49

  chr1_229863004_   1099 TGTCTGTTCTCCCCAAATTGTTATACATATTTAATTAAATTTTTATCAAA 1148
                           v vi v            v v    v   i  ivv   iii       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_229863004_   1149 A-CTCAATAAGATTTTTTGTAGATAGAGACAAGATTATTCCAAAATTTAC 1197
                          - i  iivivv       i   v vv      v v  i i      i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_229863004_   1198 ATGAAAA-GCAAAAGGATTT-GAATAGT-AAAACAATTTTGAAAAATAAT 1244
                            i   -    i-   iii-      i-        i        v  v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_229863004_   1245 AACA---TTGGAGGAATCAGTCTACCCAATTTCAAGATTTATTATGTATC 1291
                             ---        v   vv  v           i i   i  iiv v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_229863004_   1292 TGCAGTAATTAAGAC--TGTGATATTAA-AGGAGGATAGACACATAAATG 1338
                          i       i     --    i  i ii- vi          i   i  v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_229863004_   1339 AATGGAACAGAATAGAGAATTCAGAAACAGACCAGCACAAATATTCCCAA 1388
                                i     v    i i      i i   vii   vv   vvi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_229863004_   1389 ATGAATTTTTGCCAAAGG---CA--------CAAAGGG------------ 1415
                         v   -    i v   i  ---  --------   v   ------------
  L1M4_orf2#LINE/    349 TTGA-TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_229863004_   1416 ----CAA------GTGC----ACA--TTCACAGTCAAAAAGAAAAAAAAA 1449
                         ----   ------    ----   -- vv i ?i  v viv    i  vi
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_229863004_   1450 AAA--GAACCCTGATCAAAGTCTCATAGCTAATAAAAAAAGTAACTGAAC 1497
                           i-- i    iv i ------   i v vv   v     v     v  v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACC------TCACACCATATACAAAAATTAACTCAAA 491

  chr1_229863004_   1498 ATGGATCATAGACTTAAATGTCAAATGTAAAACT-TAAAA-----GGAAA 1541
                                 ?    i       v i vv       -     -----i   i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_229863004_   1542 AAAAT----GAGAAAGTATTC-TGGCTCTAGAGCTAGGCCAAAGTA-CTT 1585
                             i---- ? v  i v   -  i -  v i i     v vi  v-   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTT 590

  chr1_229863004_   1586 AGGCTGAACACCAAACACATGATTCATAAAAAGAAAAATTGATGAATTGG 1635
                           iivvi        vi  ii viv i    ii      v   i      
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_229863004_   1636 ACTTCATCAAAATTTAGAACTTTTGCTTTGTGTAAAACCTTGAGAAGAGG 1685
                                       v i        ivi viiv ii  vi ivv    ii
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_229863004_   1686 ATAAAAATACAAACTACAGACTAGGA-AAGATATTTTCAATCCATATATC 1734
                         i i    v    v i     v i   -  i      v   vi        
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_229863004_   1735 TAATGAAAGACTAGTATCTTCACTTTGTAAAGAACCCTCCTAACTTAATG 1784
                          i  i ii    v     ivv v v i        i  ivi    i   i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_229863004_   1785 GTGAAAAAA-AAAT----CAGTTTAGAAAATAGACAAAAGACATGAAGAG 1829
                         i i    i -    ----  i  ? -     i i    i  iv    v  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAG 839

  chr1_229863004_   1830 ATGTTTCACTGAAGGGGACATACAGATGACAAATAAATCCATGAAAAGAT 1879
                          ii    v ii   ii  i     i   i v     iiv           
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_229863004_   1880 GATGAACAACATCAGCCAGTAT 1901
                          v ---        ????????
  L1M4_orf2#LINE/    890 GCT---CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (131 / 93)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.80 (84 / 30)  


1784 28.14 8.89 1.34  chr1_229980767_229982580      497  1317 (497)    L1M4_orf2#LINE/L1       14   896 (12)  

  chr1_229980767_    497 CAT-TTCACAAATTAGAAGACTCAATAATATTAAGGTACAAATATTTCAT 545
                            -    iii   i       i    v i     i ivv    i i vi
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr1_229980767_    546 GAATTAATTTATAAATTTGACACTA-CTCAATCAAAAACTCAGCACGCCT 594
                         i    i  i  i i   ii  i v - i v       v i    -i    
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCT 112

  chr1_229980767_    595 TTTG-GTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAATCACAAA 643
                            v- i                  i        i        vii   i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr1_229980767_    644 AAAATTGAGACTAGGCAAAACAATCTTAAAAACAAAAAGTATCATTAAAA 693
                         ii vii-   v   v            i    vi  i ii vvi  ii i
  L1M4_orf2#LINE/    163 GGACCC-AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_229980767_    694 GAC----ATT----AATTT-A----TTACTATAAGGACATAGACATCAAG 730
                            ---- i ----     - ----      i  i vi i  vv      
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_229980767_    731 ACTTTATAATACTGG--TAAAAATAGATAAATTGATCATTTGAAAAGATT 778
                           vv i ii      --   ii     i v  v     v v   v   v 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_229980767_    779 TACAGAGCCCAGAAGTACATACATATGTATATATAGT-GGTTG-TTTTCA 826
                          i-    i      i  v iv    i--  v   i  -ii   -     i
  L1M4_orf2#LINE/    312 TG-AGAGTCCAGAAATAAACCCATAC--ATTTATGGTCAATTGATTTTCG 358

  chr1_229980767_    827 ACCAAGGTTCC-----CAATCAAT------------------TCAA---- 849
                           v i   v  -----  v     ------------------    ----
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_229980767_    850 TTGTGCTATATCAACTGGATATTCATAGGGCAAAAGAATGAG-------C 892
                          v     iviv          ?i  i v -           i------- 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAATGAAGTTGGACC 457

  chr1_229980767_    893 CCTACCTCATTC--TACACAGAAAG------AGAA---ATCATAGTTCTA 931
                                  iv --  i   i   v------ i  ---    ?  vi   
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_229980767_    932 CACATAAAAGCTAGAATCATAAAGCTTCTAGAAGGAAACATAGAA--AAA 979
                         v ii   i     i  ii     i  ii      i        i?--   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_229980767_    980 TATT-GTGAGCTTAAAGTACACAAAAAACTCTTAG----GACACAAATAA 1024
                          v  -    v   iiiv  vi   viivi      ----     v  v i
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_229980767_   1025 CACTAATCTCAAAA-AAATTCTACTTTATTTCTACTTCATGATAAAACAA 1073
                            v iivv     -   vvv  vv v v  vv       v -   vi  
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA-AAATTAA 656

  chr1_229980767_   1074 GGACTTATACTCTTTTTAAAACACTGTTAAGAAAGTTGAAAGGCAAATTA 1123
                         ii    v iiv   ivv ii     i i        vi    i   vii 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_229980767_   1124 GAGAGTAGAATAAAATATTCTTAATACAAATATCTAACAAAGGACTCATA 1173
                         v   i i i v        ivi  vv  v      i i  i     ii  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_229980767_   1174 TGGAGAACATATAAGTGACTCATACACCTCAATAATAAAAAAGGCAAACA 1223
                          vv    i      ivi    v    v              - i    i 
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA-GACAAATA 805

  chr1_229980767_   1224 ACCAATATTTTAAAAATAAGCAGAAAACTTGATCAGGCAATTTAAAAAGG 1273
                            --i v  ?      ii   i ii i    vi  i  v  ivvv  i 
  L1M4_orf2#LINE/    806 ACC--CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr1_229980767_   1274 ATGATATAAAAATATCTAATAAGCATAGGAAAATATGTTCTAAC 1317
                          v      v    iv i        i v     v   i  -   
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC-AAC 896

Transitions / transversions = 1.52 (137 / 90)
Gap_init rate = 0.03 (30 / 883), avg. gap size = 2.80 (84 / 30)  


4435 16.46 3.04 0.68  chr1_230194231_230196129.rev      522  1408 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_230194231_    522 TGGAAATACATCCCATGTTCATGGATGAGAGGAC--AATATTATTAAGAT 569
                               v i                 vi  i   --      i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230194231_    570 GGCAATACTCCTCACATTTATCTACAAATTTTATGCAAGTATTATTTTTT 619
                                    i  v   v       i   iv i    vivi   i----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC---- 96

  chr1_230194231_    620 AAAAACTCAGCTGCCTTTTTGGAAGAAATTGACAAGCTAATCCTAAAATT 669
                             v i             v v               i           
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_230194231_    670 CATATAGAAATTCAATAAATTCATAAAAATCAAAACTATATTTTAAAAGA 719
                              i     v   vii ii  v  v ii      v  v  vv      
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_230194231_    720 AGAACAAAGTTGAAGGACTCATACTTACTTATTTCAAAACTTCCTACAAA 769
                                     i        i    v iv            v       
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_230194231_    770 GCCACAGTAAACAAGACTTTGTGGTA-TAGCATAAGGACAGACATATATA 818
                           i       v      vv       - i         i         v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_230194231_    819 TCAATGGAATAGAATTGACAGTTCAGGAATAAACCCCTACACTTATGGTT 868
                                           v   i   i         v    i       i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_230194231_    869 GATTGATTTTTGACAACAGTGCCAAGACAATTCAATGGAGGGAAGAATAA 918
                         i         i     vi          v         -  i       i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAG 395

  chr1_230194231_    919 TCTTCTAAACAAATG-TGCTGAGACAAGTGAATATCCACATGTAAAAGAA 967
                             i v        -     i     v  i   ?       i       
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_230194231_    968 TGAAGGTGGACCCTTTCCTCACACTATGAACAAAAATTAACTCAAAATGG 1017
                              v       i v        i  iv                     
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_230194231_   1018 ATTACAGACATAAATGTTAGTGTCTAAAACTATAAAACTCTTAGGAGAAA 1067
                           i ?    v       v  v -                     i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAG-CTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_230194231_   1068 -TGTAAGAGCGAATCTTCACAAACTTGGGTTAGGCAAAAGC-------AC 1109
                         -ii  i ? ii       iii v              vi i------- i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_230194231_   1110 AAGAAACCAAATGCAGAAGTAACAGAAGAAAAGATAGATAAACTGAACTT 1159
                          v  v      v   v   i    i       i         i  i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_230194231_   1160 TATAAAAATTAAAAACGTTTGTGCGGCAAATAAT--TACTAAGAAAGTGA 1207
                         i  v            v       vv    vi i--  ii          
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_230194231_   1208 AA-GACAACCTACAGAATGAGAGAAAATATTTACAAACTATATATCTTGT 1256
                           -       i        i            i    ii        vi 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_230194231_   1257 AAG--ACTTGTAACCAGAATATGTAAAAA---CTTACA---CAATAATGA 1298
                            --       v         i    i ---      ---       i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_230194231_   1299 AAA---AAATAACCCAATCTAAAGATGGATAAAGGATCCCAACAGACATT 1345
                            ---            i?   i    ii       iiv  i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_230194231_   1346 TCTCCAAAGATGATATACAAATTGTCAATGAGTACACAAGAA-ATTCCCA 1394
                                   v           v i    i  i   ii i  -  v i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_230194231_   1395 ACATCATTAATCGT 1408
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (88 / 54)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


3198 27.80 0.33 0.55  chr1_230206902_230213271.rev     4970  5879 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_230206902_   4970 TGGAAGAGCATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5019
                              iiii  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230206902_   5020 GGCCATACTGCCTAAGGTAATTTGTAGATTTAATGCCATCCCCATCAAGC 5069
                            v     v  i  iv i  i ii     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_230206902_   5070 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5117
                          v   iivi i  i  iii    -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr1_230206902_   5118 ATGTGGAACCAAAAACGAGCCCGCATTGCCAAGTTAATCCTAGGCCAAAA 5167
                           i     viiv  iv  v  v v  v     ivi    i iiivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_230206902_   5168 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5217
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_230206902_   5218 CTACAGTAACCAAAACAGCTTGGTACTGGTACCAAAACAGAGATATAGAT 5267
                                  i   i    iv         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_230206902_   5268 AAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5317
                         v       i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_230206902_   5318 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5367
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_230206902_   5368 CTATTTAATAAATGGTGCCAGGAAAACTGGCTAGCCATATGTAGAAAGCT 5417
                         i -  i  i         ii   v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_230206902_   5418 GAAACTGCATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5467
                            ii  v i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_230206902_   5468 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5517
                          i ?    i           v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_230206902_   5518 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5566
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_230206902_   5567 AAATACCAAAAGCAATGGCAACAGAAGCCAAAATAGGCAAATGGGATCTA 5616
                         vi i          vvi      i   vv       ii    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_230206902_   5617 ATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTAACACCAGAGTGAA 5666
                           i   viv  i i   i  ii vv    i  v    v  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_230206902_   5667 CAGGCAACCTACAGAATGAAAGAAAATGTTTGCAATCTACCCATCTGACA 5716
                         v  i     i        ii       i       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_230206902_   5717 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAGCAAATTTACAAGAAA 5766
                          i  i  vi          v  i        ivvi   v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_230206902_   5767 AAAACAAACAATACCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5816
                           i     i  iv v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_230206902_   5817 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5866
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_230206902_   5867 CATCACTGGCCAT 5879
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (155 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


1639 23.00 1.00 8.40  chr1_230221265_230223458.rev      485   984 (1210)    L1M4_orf2#LINE/L1       50   512 (396)  

  chr1_230221265_    485 TGTCAACACTTCCTCAC---ATCTACAGATTCAATGCAATTCTTATTAAA 531
                           v   i   i  iv v---              i     i i   i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_230221265_    532 ACGCCAACATCATGTGTCACAGAATTAGAAAAACCAATCC-GAATTTCAT 580
                          iv   i vv v v v ii     v v  v  i ii    -i  v     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_230221265_    581 GTGAAAGCAAAAAAACAAACAAACAAACAACAACAACAAAAAAAAACAAG 630
                         i  i  -------------- vi   ivi  -------------------
  L1M4_orf2#LINE/    150 ATGGAA--------------ATGCAAGGGAC------------------- 166

  chr1_230221265_    631 AGCCTGAATAGCCAAAACAATCCTAAGCAAAAAGAACAAAGCTGGAGGCA 680
                         --  v                 i i iv  i          i      vv
  L1M4_orf2#LINE/    167 --CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_230221265_    681 TCATATTACCTGACTTTAAATTATACTACAAAGCTACAGTAACCAAAACA 730
                            i i v  ii i  i   viv                   i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_230221265_    731 GCATGGTACTGATGTAAAAATAGACACATGGATCAATAAAACAGAATAGA 780
                          ii        iii   ii       i  i       ii  i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_230221265_    781 GAGCCCAGAAATAAAGCCTAAAGCCACATACCTACAGACAACTGATCTTT 830
                            i           -  ------  i i ii  ii v   i    i  i
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAA-CC------CATACATTTATGGTCAATTGATTTTC 357

  chr1_230221265_    831 GAAAAGTAGGCAAAAAC-ATACACTGGAGAAAGGACACCCTATTTAATAA 879
                           v   viv  v  i  -  v  v   i     i i vi  v  i  i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr1_230221265_    880 GTGGTCCTGAGAAAACTGGATGGCCATATGCAGTAGAATGAAACTGGACC 929
                         i    v   i  v        i?   i     iv        ii      
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_230221265_    930 TCTATCTCTCACCATATACAAAAATTAACTCAAGATAGATTAAAGACTTA 979
                         i   i   v                        i  i   i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_230221265_    980 AATGT 984
                              
  L1M4_orf2#LINE/    508 AATGT 512

Transitions / transversions = 2.14 (77 / 36)
Gap_init rate = 0.02 (7 / 463), avg. gap size = 6.71 (47 / 7)  

1256 23.49 2.24 3.13  chr1_230221265_230223458.rev     1259  1705 (489)    L1M4_orf2#LINE/L1      466   908 (0)  

  chr1_230221265_   1259 ACTCCATCT-TAAAAA--AAC--AAAACAAAGCAAAAAAACTTAAATGTA 1303
                           v    v -i     --   --    iii v  ? i -- i        
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGA--CCTAAATGTA 513

  chr1_230221265_   1304 AGAGTAAAAACAATAAAAATTCTAGAATAAAACCTAGGAAAATAAAACCT 1353
                             iv     v      v ii     v     v    ?i--    v i 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG--TAAATCTT 561

  chr1_230221265_   1354 AGGAAAAACATTGGCCTAGGCAAAGAATTTATCACTAAGACCTAAAAACT 1403
                         v vi --- v    vi       v i-   ----  v   iv i v v v
  L1M4_orf2#LINE/    562 CGTGA---CCTTGGGTTAGGCAATGG-TTT----CTTAGATATGACACCA 603

  chr1_230221265_   1404 AAAAAACAAATTCAACAAAAACAAAAATAGACAAATGGGACTTAATGAAA 1453
                            iv    i--        iv         i    v      v  v   
  L1M4_orf2#LINE/    604 AAAGCACAAG--CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr1_230221265_   1454 CTAAAGAGCTTCTGTACAGCAAAGGA----AGTAACAGAGTAAACAGATA 1499
                         v v  i i   i   i vv       ---- vi  v i   i  v   i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_230221265_   1500 ACCTATGGCATGGGAGAAAATATATGTAAATGATGTATCTGGCAAAGGAC 1549
                            i ii v              v  i    v  i      ii  i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_230221265_   1550 TAATATCCAGAATCTATAAGAAACTCAAATAATTCAACAACAAAAA-ACA 1598
                          vi          v     ii     vv i  i    i  i     -   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_230221265_   1599 AATAATCCCATTAAAAAGTGAGCAAAAGATGTGAACAGACACTTCTTAAG 1648
                              i  v   ?    i  i     i   v    i     i    iv i
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_230221265_   1649 AGAAGACATATAAATGACCAACAAATATATGAAAAAATGCTCAACATTGC 1698
                               i   i     i    i  ii i       i           ii?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_230221265_   1699 TAATCAT 1705
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.49 (61 / 41)
Gap_init rate = 0.02 (11 / 443), avg. gap size = 2.18 (24 / 11)  


3023 26.65 2.91 1.23  chr1_230245055_230248594     2156  3048 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_230245055_   2156 TGGAGAGCTATTCCATGTACACAGAAAAGAAGACTCAATATTGCCAAAAT 2205
                             i  v   i      v  ii  vvi       i       ii  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230245055_   2206 GTCACTTTTTCCCAACTTGATCTATAGATTTAATGCAATCCCAATCAAAA 2255
                          v  v vi i     v        i     i  i        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_230245055_   2256 TCTCAGAAAATTCGTTTGTGGATATGAATAAAATGATTTTGAAGTTTATA 2305
                           i   vvivi iv    ii  v  vi i  iv    ii i  i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_230245055_   2306 TGGAAAGGCAAAAGATTCAGAATAGACAACACAATATTGGAGGAGACAAT 2355
                               v    ii  ii        v   v     v   i ii   vi v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_230245055_   2356 CAAAGTTGGAAGACTGACATTACTAAATTTCCAGGCTTACTGTAAAGCTG 2405
                                   i    v   i v iv      v ii      ii      i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_230245055_   2406 TGATCATCAAGACCATACA-TGTTAGCAAAAGAATGCACAGACAGATCAA 2454
                         iii v        vi iii- ii i   v   i  iv   v i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_230245055_   2455 TGGAGCCCGATAGTGAGCCCAGAAATAGGCCCATGCAAAAATATCTAACT 2504
                             iivvi  v v   i         ii     i  vvv  ivii  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_230245055_   2505 TATCTTTGACAGAGGAGCATAGGAAATTCAATGGAAAAA-ATTAGTCATT 2553
                         v  i  i    ii  v  vv  ivv         ii   - v     v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_230245055_   2554 TCAACAAATGGTGCTGGAATAATTGGACTTTCACATGCAAAACCAAAAAA 2603
                                          i i  i    iv?i           ------i 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA------GA 444

  chr1_230245055_   2604 AAAAAATCATCAAGACACAGACCTTATACCTTTCACAAAAATTAACTGAA 2653
                          vi  i ii----   v vv    i i   v vi             v  
  L1M4_orf2#LINE/    445 ATGAAGTTG----GACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_230245055_   2654 A--------------TAAATGTAAAATCCAAACCCAAAAATCTCCTAGAA 2689
                          --------------         i v i   v i v   v   i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_230245055_   2690 GATAAAATAGGAGAAAATAG--GTGTCCTTGGGTTTGGCAACAACTTCTT 2737
                           v  v     ? v    vv--   v         v     iiii     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_230245055_   2738 AGA----ACACCAAAGACAAAATCCATGAAAGAAA---CAG-TAAGTTGG 2779
                            ----        ii  v  v v ii       ---i  -   i    
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_230245055_   2780 AAATTATTAAAATTTAAAACTTCTGCACTGTGAAAGACATTGTTAAGAAT 2829
                          vv i  i      v       i  ii  vii  i    i i i     v
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_230245055_   2830 ATGAAAAGACACACGATAGACTGAGAGAGAATATTTGCAAAACACATATC 2879
                         i          vv v i   v  i    i            v  i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_230245055_   2880 TGATAAAGGACATCTCTCTAAAATATGCAAAGGACTTTTAACACTCAACA 2929
                               i    v v v  i i     ii    i   i   vv      i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_230245055_   2930 ATAAGGAAAGAAACAATCCAATTTAAAAAACAGGTAAAATATCTGAACAG 2979
                             ii i v   i  i      ?     -ii  i   iv  i    i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAG 839

  chr1_230245055_   2980 TCACCTCACCAAAGAAGATATATAGATGGCAAATAAGTATATGAAAAGAT 3029
                         v  ii  v              i i     v      i i          
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_230245055_   3030 ATTCAACATCTTATGTCAT 3048
                         ii        v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (145 / 90)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.70 (37 / 10)  


3137 20.81 9.81 1.20  chr1_230262936_230264939.rev      683  1518 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_230262936_    683 TGGAAAGATTTATGGTGCTTATGGATTGGAAGACTTATGTTTGTTAAGGT 732
                                  v vivi  i i                 vvv        i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230262936_    733 GTCCATAGTACCCAAAGTGATTTACAGGTTTAATATATTCCCAA-CAAAA 781
                          v v   v v      v    i     i  i  iii v    v -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_230262936_    782 TCTCAGTGGCATTTTTCTACAGAAATAGA-------ATCCTAAAATTCAT 824
                           i   iv  v     - i       v  -------              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_230262936_    825 ACTGAATCACAAAGGACCACAAATAGCCAGAACAGTCTCGAGAAGTAAGA 874
                          iv   vii   i     vvi        i    i   i  i  iv    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_230262936_    875 ACAAAGCCTGGAGG--TAACAGGCTTCC---------------------- 900
                               i-      -- v   --     ----------------------
  L1M4_orf2#LINE/    200 ACAAAGT-TGGAGGACTCACA--CTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_230262936_    901 --TACAATAATTAAAATAAATTGGTATTTGCATAAAGACAGACATATAAA 948
                         --    i    i  i i ivv     i v      i  i         i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_230262936_    949 TCAACGGAAGAGAATAGAGAGCCCAGAAA------CTTACCTTT---GTC 989
                             i    v     v     i       ------ v   v   ---   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_230262936_    990 AACTTACCTTTGAGAAGGATGCCAAGGATAGACAATGGGGAAAGGAAAGT 1039
                           i v ii  i  v    i       ivi vv            i v   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_230262936_   1040 CTCTTCAACAAATGGTATTTGAA-AACTGGATAGCCACATGCAGAAGAAT 1088
                           i             ii v i -         ?         i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_230262936_   1089 GAAATTTAA-----ACTT-ACACTTTATACTCAAA---ACCCAAAATAGA 1129
                            i  vi -----  i -    iv     vv   ---  i      i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_230262936_   1130 TTAAAGACTTAAATATAAGACCTAAAACTA--AAACTTCTAGAAGAAAAC 1177
                          i ?    i     i     v         --     ii           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_230262936_   1178 ATAAAGG-AAAGCTTCAT--CC-----------AATGACTTCTTGGATAT 1213
                            ii? -   v    i --  -----------    ii     i     
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_230262936_   1214 GATACCAAAAGCACAGGCAATGAAAGCAAAAATAGACATTTAGGACTAGA 1263
                           i            i    ii    v         i vv v     vv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_230262936_   1264 TCAAA-CTAAAAA-----GTGCCTGCATAGCAAAAGAAACAACTGATGGA 1307
                              -i      -----    i ------    i  v  v iii vii 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTT------CAAAGGACACTATCAAGAAA 690

  chr1_230262936_   1308 GTGAAAAAGCAAACTACAGAACAGGAGAAAATATTTGCAAACCATATATT 1357
                                ii   v i      ii                  i       i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_230262936_   1358 TGATAAACAGTTAATATTCAAAATATATAAGACATTCCTTCAACTCAATG 1407
                               iviii vi   i  i         iiv i  i v         i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_230262936_   1408 GCAAAAGAATGAATTATCCAATTAAAAAATGGGCAAAAGACTTGA-TAGA 1456
                         ii    ii ii   v i      ?             i  i    -    
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_230262936_   1457 CATTTCTCCAAAGAA----TACAAATGACCAAGAGGTTCATGAAAAGATG 1502
                                        ----        i    v i iv            
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_230262936_   1503 CTCAGC--CAGGCACACT 1518
                             i --  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (111 / 59)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 4.00 (92 / 23)  


2999 27.04 0.88 0.66  chr1_230266407_230270622     2818  3723 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_230266407_   2818 TGGGAAAACATTTCATGCTCATCGATAGGAATAATCAATATTGTGAAAAT 2867
                            i  i i  ii    i    v   v    v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230266407_   2868 GGCCATACTGCCCAAAGTAATTTATAAATTCATTGCTATCCCCATCAAGC 2917
                            v     v      v i  i  i i     vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_230266407_   2918 TACCA-TTGACTTTCTT-CACAGATTTGGAAAAAACT-ACTTTAAATTTC 2964
                          v   -i  v    i  -  v i   ---i v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chr1_230266407_   2965 ATATGGAATCAAAAAAAGG-CCCACA-TAGCCAAGACAATACTAAGCAAA 3012
                                 -- viv  i  -    v -       i     vi i iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_230266407_   3013 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTGCAA 3062
                                   i      vv   ii  v  ii i      viv    i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_230266407_   3063 GGCTACAGTAACCAAAACAGTAAGGTACTGGTACCAAAACAGATATATAG 3112
                         i          i   i     iv        i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_230266407_   3113 ACCAATGGAACACAACACAGACCTCAGAAATAACACCACATGTCTACAAC 3162
                          i        i v  ivv   vii         vv   i ii i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_230266407_   3163 CTTCTGAGCTTTGACAAACCTGACGAAAACAAGCATTGGGGAAAAGATTC 3212
                          vvi   vi  i     ivv  v i i v  vv  v        ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_230266407_   3213 CCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAGGCGGAAAAC 3262
                         i  v  i  i        i     v      v  ?   i v  ii  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_230266407_   3263 TGAAACTGGACCCCTTCCTTAAACCTTACACAAAGATTAACTCAAGATGG 3312
                             ii         v   i v   v  i     i          i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_230266407_   3313 ATTAAAGATTTAAATGTTAGACCTAAAACTATAAAAACCTGAGAAGAAAA 3362
                           i ?   ii       v   v              vi  v         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_230266407_   3363 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACCTCATGACT 3411
                          v    ?i- v i -   iv   v v  vv i     v iii  v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_230266407_   3412 AAAACACCAAAATCAATGGCAACAAAAGCCAAAATAGACAAATGGGAACT 3461
                          vi         v  vvi          vv        i    v   vi 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_230266407_   3462 AATTAAACTAAAGAGCTTCTGCACAGCAACAGAAACTATCATCCAAGTGA 3511
                         v  i   v v  i i   i  ii vv   vi  v       vvv      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_230266407_   3512 ACAGGCAACTTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 3561
                          v  i    ii                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_230266407_   3562 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 3611
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_230266407_   3612 AAA-ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAGCAGACACT 3660
                            -     i     v  i?    i            v   ii     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_230266407_   3661 CCTCAAAAGAAGACATTTATACAGCCCACAAACATATGAAAAAA-ACTCA 3709
                         i   v        i  vi v ii   v i  i  i       i -i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_230266407_   3710 TCATCACTGGCCAT 3723
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (137 / 104)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3412 21.57 2.16 4.21  chr1_230344423_230346881.rev     1042  1968 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_230344423_   1042 TAGAGAGATATTTTATGTTCATGGATGGAAAAATTTAATATTGTTAAGAT 1091
                          i  i      iii            v i  i i                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230344423_   1092 GTCAGTTCTTCCCAACTTCATCTATAGATTCAAAGTAATTCCAATCAGAA 1141
                          v  i v  i     v  v     i        v i   i  v    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_230344423_   1142 TCCCAGGAGGTTATTTTGTGAATATC-ACAAACTGATTCTCAAGTTTATA 1190
                               vv vi v     iii v  i-    i     i  v  i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_230344423_   1191 TGAAAAGGCAAAAGACCCATAATAGCCAACACAATATTAAAGGAGAAGAA 1240
                           i   v    ii      v         v     v  i  ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_230344423_   1241 CAAAGTCTGAGGACTGATATTGCCCAACTTCAAGACTTACTATA--GTTA 1288
                               iv       v i i v     i     i        i -- i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_230344423_   1289 CAGTAATCAAGACAGTGTGGTATTGGTGAAAGAGCAGACAAATAGATTAA 1338
                                               i   iiv   iii     v      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_230344423_   1339 TGGAACAGAATAGAGAGGCCA-AGATAGACCCACACAT--AGAGTCAAGT 1385
                              i     v     v   - i   i     i    -- vi     v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_230344423_   1386 GATCTTTGACAAAGGAGCAAAAGAAATCTAATGGAGAAAAGATCACCTTT 1435
                            i  i     i  v  v  iivv  ii     i    ii  vii    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_230344423_   1436 TCAACAAATGGTGCTAGAACAACTAGACATCCAATCACAAAAAAAAAAAA 1485
                                        i i      i  i ?   --  iiv    i  v--
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCA--CATGCAAAAGAAT-- 446

  chr1_230344423_   1486 GAAAGAAAGAGAGAAAAAAAGAAAAGAAGCTGGATACATAGATACAGACC 1535
                         -------------------------    i    iv v  --------  
  L1M4_orf2#LINE/    447 -------------------------GAAGTTGGACCCCTA--------CC 463

  chr1_230344423_   1536 TTACACCTTTCACAAAAATTAACTCAAAATAGATCATAGACCTAAATATA 1585
                          i     v vi                   i     ?          i  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_230344423_   1586 AAATGC-AAAACTATAAAACTCTTAGAAGATAAAA-AGGAGAAAACCTAG 1633
                          i -  -                       v  v -   ? v   i  vv
  L1M4_orf2#LINE/    514 AGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_230344423_   1634 GTGACCTTGGGTTTGTAAATGACATTTTAGATACAACATCAAAGGCATGA 1683
                                      v vv    iiv i       ii   i    i   ii 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_230344423_   1684 TCCATGAAAGTAAAAATTGGTA--TTGGACTTCGTTAAGATTAATAACTT 1731
                         v v ii    v      v i  --         i i  i     v     
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_230344423_   1732 CTGCTCTACAAAAGACACTGTTAAAACAATGGGAAGAAAAGCTACAGACC 1781
                         i  iv  v    i      i i  i v i  ii    v  v i     vi
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_230344423_   1782 AATAGAAAATATGT-CAAATCATATACATGATTAAGAACT-GTAATAAAA 1829
                         iiv         v -           iv    v i i   -   viv i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_230344423_   1830 A---ATAA-GAATAATTAGAACTCAACAATAAGAA----AATGATCCCAA 1871
                          ---    -   ivv   v       i     i  ----   i -     
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA-CCCAA 811

  chr1_230344423_   1872 TTAAAAAATTGGCAAAACAGCTGAACAAACATATCAATAGAGATGATATA 1921
                           ?      v      iv vi    i i    v  vvi i   v      
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_230344423_   1922 CAGATGGTAAATCAGCACATGAAAAGATGCTCCACATCATACATCAT 1968
                           i    iv   v                   v      ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (120 / 76)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.47 (59 / 17)  


3019 26.51 0.99 1.53  chr1_230364374_230369988.rev     4212  5124 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_230364374_   4212 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4261
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230364374_   4262 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATACCCATCAAGC 4311
                            v     v     iv i  i  i        i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_230364374_   4312 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4359
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_230364374_   4360 TATGGAACCAAAAAAGAGCCCACATTGTCAAGACAATTCTAAGCCAAAAG 4409
                                viiv  ii  v  viv  v i   i     ii i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_230364374_   4410 AACAAACCTGGAGGCATCACGCTACCTGACTTTAAACTATACTACAAGGC 4459
                               vi      vv    i  v  ii i  i   viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_230364374_   4460 TACAGTAACCAAAACAGCATGGTATTGGTACCAAAACGCGGATATAGACC 4509
                                 i   i    ii     i   i iv ii iiviv       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_230364374_   4510 AATGGTACATAAT--AGAGCCCTCAGAAATAATACCACACATCTACAACC 4557
                              v i v   --    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_230364374_   4558 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACGATTCC 4607
                          vi    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_230364374_   4608 CGATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4657
                          vv  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_230364374_   4658 GAAACTGGATCACTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4707
                            ii    i v  v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_230364374_   4708 TTAAAGACATAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 4756
                          i ?    v       v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr1_230364374_   4757 CCTAGGCA-ATACCATTCATGACAT-GGGTATGGGCAAGGACTTCATGAC 4804
                          v    ?i- v i -   i    v -    - i     v ii   v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGA 593

  chr1_230364374_   4805 TAAAACACCAAAGGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 4854
                           vi        i   vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_230364374_   4855 TAATTAAACTAAAGAGTTGCTGCACAGCAAAAGAAACTACCATCAGAGTG 4904
                          v  i   v v  i ii vi  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_230364374_   4905 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 4954
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_230364374_   4955 CAAAGGGCTAATATCCAGAATCTACAAAGGACTTAAACAAATTTACAAGA 5004
                         i  i  i  vi          v  i    i   ivv    v ---   v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATA 790

  chr1_230364374_   5005 AAAAAAAAAAAAAAAAAAGGCC--ATCAAAAAGTGGGCAAAAGATATGAA 5052
                          v     i v   v  ----  --  i?    i        i   v    
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAA----CCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_230364374_   5053 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAA 5102
                         i     i     v        i  vi viii     v ii          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_230364374_   5103 AATGCTCATCATCACTGGCCAT 5124
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


 888 23.94 0.94 0.47  chr1_230452729_230459041     4592  4804 (1509)    L1M4_orf2#LINE/L1        1   214 (694)  

  chr1_230452729_   4592 TGGAAAGGTATTCTGCATTCATGGATAAGAAGAATTAATATTGTTAAAAT 4641
                                i   i iiii         vi     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230452729_   4642 ATCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCTTATCAAAA 4691
                         iv v     v      vii              i       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_230452729_   4692 TTTCAGTAACACTTTTCACAGAAATAGAAAAAC-AATCCTAAAATTAATA 4740
                          ii   ivi vi    ii       v  v  i -i           v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_230452729_   4741 TAGAATCACAAAAAATCCTGGA-AGTCAAGATAATCTTGAACAAAAAGAA 4789
                          i   vii   iii i  v i -  i   i i         v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_230452729_   4790 CAAAGCTTGAATGGC 4804
                              -   i v i 
  L1M4_orf2#LINE/    201 CAAAG-TTGGAGGAC 214

Transitions / transversions = 2.40 (36 / 15)
Gap_init rate = 0.01 (3 / 214), avg. gap size = 1.00 (3 / 3)  

2955 21.24 2.53 1.41  chr1_230452729_230459041     5110  5820 (493)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr1_230452729_   5110 AAAAAATGCAAGAACAAAACTGGAAGCATCACACTACTTGATTTCTAACT 5159
                              i---         ii    i vv       v iii     v  vi
  L1M4_orf2#LINE/    190 AAAAAG---AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr1_230452729_   5160 ATCTTATAAAGCTATAGATATTAGAACAGTGTGATACTGGCATAAAAATA 5209
                         v vi  i       i  vv  i ii        i           ii   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_230452729_   5210 GACACATGGACTTATGGAACAGAATAGAGAGCTCAGAAATGAACCTATGC 5259
                             i  i  iiv      i     v     ii       i    i  i 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_230452729_   5260 ATTTTCAGTCAATTGATTTTCAACAAAGGTGCCAAGAACACACTATGGGG 5309
                             vii              i    i          v  iv v      
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_230452729_   5310 GAAAGGTCAGTCTCTTCAATAAAGGGTGTTGGGAAAACTGGATATCTACA 5359
                         -    ivi     i     i   v    i     v         ? i   
  L1M4_orf2#LINE/    387 -AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_230452729_   5360 TGCAGAAGAATGAAATTGGACCCTCATCTCACACCTTATACAAAAATAAA 5409
                             i         i        ii i        v           v  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_230452729_   5410 CTCAAAATGGATTAAAGATTTAAACATAAGACCTGAAACTGTAAAACTAT 5459
                                     i ?   ii    ii     v  i     i       v 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_230452729_   5460 AAGAAGAAGACATAGGGG-AAAGCTACATTGCTCTGGG-----CAATGAT 5503
                         v       i       ? -   v  v i vi ii    -----     i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_230452729_   5504 GTTTTGAATTTGACTCCAAATGCTCCAGTACCAAAAGCAAAAATAAATAA 5553
                         v i  ii  v    v     v  v v  i v      v       i    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_230452729_   5554 ACGGGATTACAACAAA-CTAAAAATTTTCTGCACCGCAAAGGAAAC---- 5598
                          iv   i v  v    -i      i   -  ii iv       v  ----
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATC 684

  chr1_230452729_   5599 AATAAAGTGAGGACACAGTCTACAGATTGGGAGAAAATATTTATAAGCCA 5648
                           v       ii v   ii i     v               ii  ii  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_230452729_   5649 TACATCTGATAAGGGGTGAATATCCAAATTATATAAGGAACCCAAAAGAA 5698
                           i            iivvi      i v       i    i vv v-  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC-AA 783

  chr1_230452729_   5699 CTCAATAGCAAGAAAACAAATAA----ATT-AGAAATGGACAAAGAACTT 5743
                                ii  i  i        ----   - i      i     i i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_230452729_   5744 GAATAGACATTTCTCCAAAAAAGACATACAAATGCCCAA-GAG-ATATGT 5791
                                            i    i         v    -i  - i   -
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG- 882

  chr1_230452729_   5792 TTTAAAAAATGTTCCACATCACTAATCAT 5820
                         ---    i   i  v      ????????
  L1M4_orf2#LINE/    883 ---AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (98 / 50)
Gap_init rate = 0.02 (13 / 719), avg. gap size = 2.15 (28 / 13)  


3250 26.54 0.55 0.55  chr1_230492370_230495681.rev     1914  2821 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_230492370_   1914 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 1963
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230492370_   1964 GGTCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCAATCAAGC 2013
                           iv     v     iv i  i           i  v     v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_230492370_   2014 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2061
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_230492370_   2062 TATGGAACCAAAAAAAGAGCCCGCAAT-GCCAAGACAATCCTAAGCCAAA 2110
                                -- viv  i ii   iv   -     i      i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_230492370_   2111 AGAACAAACCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACCAG 2160
                                 vi      vv    i  v  ii i      viv      v i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_230492370_   2161 GCTACAGTAACCAAAACAACATGGCACTAGTACCAAAACAGAGATATAGA 2210
                                   i   i   iii   i   i i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_230492370_   2211 CCAATGGAAGAGAACAGAGCCTTCAGAAATAATACCACACATCTACAACC 2260
                         i        v    iv   vv i         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_230492370_   2261 ATGTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATTCC 2310
                          vv    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_230492370_   2311 CGATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2360
                          vv  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_230492370_   2361 GAAACTGGATTCCTTCCTTACACCTTATCCAAAAATTAATTCAAGATGGG 2410
                            ii    ii   v   i     v   v          i    i    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_230492370_   2411 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTATAAGAAAAC 2460
                          i ?    i       v   v       i      vi i  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_230492370_   2461 CTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGATTTCATGACTA 2509
                         v    ?i- v   -   iv   v v  vv i     v i    v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_230492370_   2510 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGATCTA 2559
                         vi            vvi          vv     v       v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_230492370_   2560 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 2609
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_230492370_   2610 CAGGCAACTTACAGAATGGGA-AAAATTTTTGCAATCTACTCATCTGACA 2658
                         v  i    ii           -     v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_230492370_   2659 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTATAGGAAA 2708
                          i  i  vi          v  i        ivv    v iv   iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_230492370_   2709 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 2758
                           iv    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_230492370_   2759 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 2808
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_230492370_   2809 CATCACTGGTCAT 2821
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


2639 18.34 13.32 3.12  chr1_230520916_230522643      500  1235 (493)    L1M4_orf2#LINE/L1       98   908 (0)  

  chr1_230520916_    500 AAATTTCAACTGCCTCTTTTCCAGAAAAAAATCAA-AAGC-GGTTCTAAA 547
                             ii  i      i    v      ---- ii -    - i i     
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAA----TTGACAAGCTGATCCTAAA 143

  chr1_230520916_    548 -TTCATATAGAAAAACAAGGGACACTGAAAAGCCTAAATAATCTTGAGAA 596
                         -       i    vi        v v   v    v   i        i  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_230520916_    597 AGAA---CAAAGTTGGAAGACTTGCACTTTCCAATTTCAAAAGGTACTAC 643
                             ---          i    ii     i            vv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_230520916_    644 AAAGCAACTGTAATCAAGACAGTGTGCTGCTGGTACAGGGATAGACATAT 693
                              v  v                 v i    i i i            
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_230520916_    694 AGTTCAAGGGAATAGAATGACATAGTTCAGAAAGAAACCCATATATAAAT 743
                           v    v          vi- v   i      v         i  vv  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTG-AGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_230520916_    744 AATCAGTTGATTTTCAACAAGGGTACCAAGACTATTCAATGGGGAAG--- 790
                         ii   i         i        i       i             i---
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_230520916_    791 TAACCTTGTCAACAAATGGTGCTGGGACA--TGAGT--CTATTTTTTTTA 836
                           ii   v                     --  ii -- i i------- 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC-------A 435

  chr1_230520916_    837 TACG---GTGTGAGATTAGGGGTCTAACTT-CATTAT---------TT-- 871
                          i i--- vi   ii  i ivvi   v  i-  ii  ---------  --
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_230520916_    872 -------TGAA-----GACCTAAATGTCAGAGCTAAAACAGTAAAGCTCT 909
                         -------  i -----           v           vi    i    
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_230520916_    910 TAGAAGAAAACATAGGAGTAAATATTCATGATTTTAGATTAGGCATCAAT 959
                                         ?      v   i   ii  i i       viii 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_230520916_    960 TTCTTAAATATCAAACAAAAAGCACAAGCCACTAAAGAAAAA-CAGATAC 1008
                               i    v v  v            v  v         -i     v
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_230520916_   1009 TTTGGACTTCA--------------------------------------- 1019
                         v          ---------------------------------------
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_230520916_   1020 ---GAGTAAAAAGACAACCTACAGAAAGGCACAACGAT-TTTGCAAATTA 1065
                         ---i   i           i      v  v v  -i  -         i 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCA 734

  chr1_230520916_   1066 TATATTT--TGAG---TTTAGCATTCAGAATATACAATGAAAAAGTCAAC 1110
                              i -- i  ---i  - i  i         i  --- i  v  v--
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTT-GTATCCAGAATATATAA---AGAACTCT-- 778

  chr1_230520916_   1111 AATAAAACTCAACAATAAAAAAGTCATGAA------TGAAAAATGGGCAA 1154
                         --  v       i        iiiv vv  ------ ?            
  L1M4_orf2#LINE/    779 --TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_230520916_   1155 AGGATTTAAGTAAGCATTTATCTCAAGAAGATACACAAATGATCAATAAT 1204
                                i i  ii     v  iv         i       ii      v
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_230520916_   1205 CACCAATGAAA---TGTCTAACATCATTCATTAT 1235
                            --      ---  iii       ????????
  L1M4_orf2#LINE/    877 CAC--ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (87 / 46)
Gap_init rate = 0.03 (27 / 811), avg. gap size = 4.48 (121 / 27)  


 334 18.92 2.70 0.00  chr1_230571302_230573252      361   434 (1517)    L1M4_orf2#LINE/L1      833   908 (0)  

  chr1_230571302_    361 TAAATAGGCACTTTACAATAGAGGATATGCAGATGGCCAATA--CACATG 408
                          i     i  i  iv v v   i     i  i          --      
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_230571302_    409 AGAAGGTGCTCGACCTCATTGATCAT 434
                          i   i     i  v   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (10 / 4)
Gap_init rate = 0.01 (1 / 76), avg. gap size = 2.00 (2 / 1)  

2421 25.39 10.57 0.24  chr1_230571302_230573252      637  1459 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_230571302_    637 TGAAAAGATACACCATGTTTATGGTTTGGAAGACTCAACATT--TA-GAT 683
                           i       iv       i    v          i  i   --  -   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230571302_    684 GTCACT--TCCCCAACATTGATCCATAAAGTCAATGAAATCTCAGTCAAA 731
                          v  v --       -       i i i v    i v    i vi     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA-ATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_230571302_    732 ATCCTGGAGGGCTTTTTAG--GAGATTGACAAACAGATTCTGAATTGAAT 779
                             ii vv v      v --  i        i v   i  i  v vv  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_230571302_    780 GTGGAAATACAAAAGAACTCAGACTAGCCAA------------------G 811
                         i       i   ii  - i    v       ------------------ 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_230571302_    812 AACAAAGTTAGATAACT-ACATTACCAGATTCCAAAA---ATTATAAATT 857
                                  i  vi   -   i v  vi   i     --- i  i   vi
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_230571302_    858 TACGCTAATTAGGACAGTGTAGTATTGGTGTTAGGATAGACAAATAGAT- 906
                            iv    i i        i   i   ii v          v      -
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_230571302_    907 AATAGAAAAGAATACAGCATTCATAAAAACATCCACACCTGCAC--TCAC 954
                            i   v     vv  vi i  v   v v i   i  v vi i--   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_230571302_    955 TTGATTTTTGACAAAGGCACCAATACAATGCAATACGGAAAGAAT-GTTT 1003
                                 i     i  ii    v  v  v    iv         -  i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_230571302_   1004 TTTTAATTAATGATGCTGAAACAAATGAATATCCATATGGGGGGGAACTA 1053
                            i  iv    i     ii    v  i   ?   i   viiii   iv 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_230571302_   1054 ACCTTGACCTACACCTGAC--CATAAACAAAAATTAATTCTAAATGATTC 1101
                          vi v    ivi    v  --    v           i  v     iv  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_230571302_   1102 ACAGACCTAAACATAAAAGCTAATACTATAAAACCTCCAGAGGAAAACAT 1151
                          ?         ii   i      v          iiii   i        
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_230571302_   1152 AAGAAAATATCTT--TAATCTT-----------------CCTA----TGA 1178
                          i ?iv v     -- i i   ----------------- i  ----   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_230571302_   1179 ----AAGGACACAAACAGTGTAAGAAAG--TAG-TAAGTTGG-TGTCATC 1220
                         ----  iii     i  iiiv      i--   -   i    -iv     
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_230571302_   1221 AAATATAAAAACT---------CGAAG-ACACCATTTAGAAAC------- 1253
                            vv        --------- i   -    i  iv     v-------
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_230571302_   1254 ACAAGCCATAAACTGCAAGAAAATATTTACAATGTATACATCTGATGAAG 1303
                             v   i i v  vi           i   vvi   i       i i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_230571302_   1304 GACTT--ACCCAGAACACATAATTAATTCCTTCAAATTAACAATAGGAAT 1351
                              -- i      i i    vv  i  i v   v i  i    ii  v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_230571302_   1352 TCAAACAAGTTGATTTTAAAATGGACCAAACAACCAAACAGGTATTTTAC 1401
                         v    i  viii   ?v       i v  iv viii  i  ii    iv 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_230571302_   1402 AAAATAAGTTATCCAAATGGCCAATAAGCATATGAAAATTTGTTCAACA- 1450
                         v   v   v   v                 i       vv  i      -
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_230571302_   1451 -ATTGTTGCT 1459
                         - ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.56 (125 / 80)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.56 (89 / 25)  


 548 19.64 0.00 0.89  chr1_230640822_230642882      490   601 (1460)    L1M4_orf2#LINE/L1      166   276 (632)  

  chr1_230640822_    490 CCCTGAATAGCCAAAGATATCTTGAGCAAAAAGAACAAAGCTGGAGGTAT 539
                            v           ivv       iv  i          i      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_230640822_    540 CACACTACCTAATTTCAAAATATATTATAAAGCTATTGTAATCAAAACAG 589
                               v  i          iv  i  i       iv        i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr1_230640822_    590 CATGGCAGCTGG 601
                         ii   i -    
  L1M4_orf2#LINE/    266 TGTGGTA-CTGG 276

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.01 (1 / 111), avg. gap size = 1.00 (1 / 1)  

2847 20.84 0.93 1.24  chr1_230640822_230642882      927  1569 (492)    L1M4_orf2#LINE/L1      268   908 (0)  

  chr1_230640822_    927 TGGCACTGGCATGACGACAGACACATCAACCAGTGGAACAGGATATAAAG 976
                            i        i v  i     i  vi i  i     i  i  vv i  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_230640822_    977 CCCAGAAGTAAACCCAAGTATTTATGGGCAATTTATTTTCAATAACAGTG 1026
                         i      i        vii        v     v      i i  vi   
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_230640822_   1027 CCAAGAAGACACAATGGGGAAAGAGCAGTCTCTTCAATAAATGGTGCTGG 1076
                               vv iv             ii     i     i            
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_230640822_   1077 GAAAACTGTATGTTCATTCACATGCAGAAGAATGAAATTGGACC-TTATC 1125
                           v     v  ---- ?i        i         i       -i  i 
  L1M4_orf2#LINE/    418 GACAACTGGAT----AKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_230640822_   1126 TCAGACATTATATACAAAAAAATCAACTCAAAGTAGATTAAAGAC--AAA 1173
                            --  ii           -- i        i i   i ?    --   
  L1M4_orf2#LINE/    464 TCA--CACCATATACAAAAA--TTAACTCAAAATGGATCAWAGACCTAAA 509

  chr1_230640822_   1174 TGTAAGACCTGCAATTGTAAAGCTCCTAGAAGAAAACATAGGAGAAAGAC 1223
                                v  iv  i i    i   i                ? v  iv 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr1_230640822_   1224 TTTGTGACATTGGTCTGGGCAATGATTTTTTGG-T-TGACTCCAAAAGCA 1271
                           i     v    vi i       i   i  i - -    v         
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr1_230640822_   1272 TAGGCAACAAAAGCAAAAACAGTCATATGGGATTACATCAACATAAAAAG 1321
                         i i          v     i  vi v  v   i v      v  v    i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_230640822_   1322 TTTCTGCACAGCCAAGGAAATGACTAACAGAATGAAGAAACAATCCACAG 1371
                         i  i  ii vv v     v iv ii  v i i    i i    i      
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr1_230640822_   1372 ATTGGAAGAAAATATTTGCAAACCATACATCTGATAAGGGGCTAATATAC 1421
                          v   i                i    i            i  vi   v 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr1_230640822_   1422 AAAA-AAATAAGTAACTCAAACAACTCAATAGCAAGAAAACAAATAATCC 1470
                          i  - v    iv     vv           ii  i  i        i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_230640822_   1471 AATTAAAAAACGGGCAAAGGACCTGAACAGGCATTTGTCAAAAGAAGAGA 1520
                             ?     i          ii    i  i     v  v        v 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_230640822_   1521 TACAAATGGTCAACAGGTATATGAAAAAATGCTCAACATCTCTATCAGG 1569
                                  i   i i i i       i            v????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (86 / 44)
Gap_init rate = 0.01 (8 / 641), avg. gap size = 1.75 (14 / 8)  

1006 13.66 2.73 0.00  chr1_230640822_230642882     1879  2061 (0)  C L1M4_orf2#LINE/L1   (0)   908   721  

C chr1_230640822_   2061 ATATTTGCAAATTATATATCTAATAAGAAATTAGCATCTAGAATATGTGA 2012
                                     i        i     ii i v i   i       i i 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

C chr1_230640822_   2011 AGAACTCTTATAACTCAAAAATAAAAAGACAA----CCCAATTAAAAAAT 1966
                                   i       v             ----       ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

C chr1_230640822_   1965 GGGCAAAGAATCTGAAGAAGTATTTCCCCAAAGAAGATATACCAA-GGCC 1917
                                 i  i    v iii     i               v  -    
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

C chr1_230640822_   1916 AACAAACACATGAAAAGATGCTTAACGTCATTAGCCAT 1879
                           i  i                i   i   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 5.00 (20 / 4)
Gap_init rate = 0.01 (2 / 188), avg. gap size = 2.50 (5 / 2)  


4213 19.67 1.78 0.89  chr1_230781340_230783455      725  1624 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_230781340_    725 TAGAAAGATGTCCAATGTTTATGCTTAGGAAGACTTAATATTGTTAAGAT 774
                          i       i   v     i   vv v                       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230781340_    775 GTCAGCATTATGCAATGCAATCTACAGATTCAATTGAATCCCTAGTAAAA 824
                          v  ii i viv   vvii              ivv        vi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_230781340_    825 TGTCAACAGCCTTTTCTGTAGCAGTGGAAAAGCTGATCCTCAAATTCACA 874
                          vi  i v       i  i  v i v  v           v       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_230781340_    875 TTGGACTACAAGAGGCCCA-AATAGCCAAAACAATCTTGAAAAACAAGAA 923
                          v i v i    i i    -                        v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_230781340_    924 CAAAGTAAAAGGATTCACAATTTCAGATTTCAAAGTTTAATACAAAGCTA 973
                               vii    i     v  i vi        ii   v          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_230781340_    974 TAGTAATCAAAACAGTGTGGTACTGGCATACAGATAAACAGATAAACCAA 1023
                         i         i                   vi    i   v   i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_230781340_   1024 TGGAATACAATTGAGAG-CCAGAAATAAGCCTATACAACTATGGTTGATT 1072
                                v         -          i  i     vi      ii   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_230781340_   1073 AATTTTTGGCAAGGGTGCCAAGCCCACTCAATGGCAAAAAAGCAGTCTCT 1122
                         i     i i             v   i       vi   i ii     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_230781340_   1123 CAGACAAATTGTATTAGGACAACTGGATTTTCATATGCATTAAGGAAGGC 1172
                         ivi      v  ii i            v?i  i     --  i   v v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA--AAAGAATGA 448

  chr1_230781340_   1173 AGTTCAAACCCTACCTTATGCCATATAAAAAATTTAATTCAAAACAGCTC 1222
                             vi v        i ii       v    v    i      ii v  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_230781340_   1223 AAGAGAAAACCCTACACATGTGAACAAAAACCTTAAAACTCTTAGAAGAA 1272
                          ?-   ----    v ii iv  i v     iv                 
  L1M4_orf2#LINE/    499 AW-AGA----CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_230781340_   1273 A-----GAAGTAAATCTTCATGACCTTGGATTTGGCAATGGAATCTCAGA 1317
                          ----- i?          i         i  v        vv   i   
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_230781340_   1318 T--GATGTCAATAACATGAGCAACAAAAGAAAAAATAGATAAGTTGGATT 1365
                          --  iii   v i  ii                        i     i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_230781340_   1366 TTATCAAAATTTAAAACATTTGTGCATCAAAAGATATGATCAAGAAAATA 1415
                          i         v     v       v     i  i iv         i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_230781340_   1416 AAAATACATCCTAGAGAATGGGGGAAA-TATTTTCAAATCATATATTTGG 1464
                             v   v  i v        i    -     v            i  i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_230781340_   1465 TAAGAGCTTAGTATCCAGAATATGTAAAGAGCTCTTAAAACTCAACAACA 1514
                             i vi v             i      i      v       i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_230781340_   1515 TAAAGACAAA-----CAATTCAAAAATGAGCAAAGAACTTGAATAGACAT 1559
                         v         -----     ?       i      i i            
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_230781340_   1560 TT-TCTAATGAAGAGGTATAAATGGTAAATAAGCATAGGAGGAGAGGGCT 1608
                           -  i  v     vi  i      iv        i v  ii   v -  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG-CT 892

  chr1_230781340_   1609 CAACATCCTCAGTCAT 1624
                                v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (106 / 67)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.18 (24 / 11)  


3119 21.83 7.75 1.29  chr1_230829346_230831173      491  1342 (486)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_230829346_    491 GGGACGACTATACTGTGTTCATGGATTAGAAGACTCGCTATTGTTAAGAT 540
                           i v  -   v ii            i       iiv            
  L1M4_orf2#LINE/      2 GGAAAGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_230829346_    541 ATGGTTAAATTCTCTCCAATTTGATCTATAGGTTCAATACAACCCCAATC 590
                         --  i--   v   i    v        i  i     ii   i   v   
  L1M4_orf2#LINE/     51 --GGC--AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_230829346_    591 AAAATCTCAATAAGCTTTTTTGTAGATATTGACAAGCTGATTCTAAAATT 640
                               i  iiviv        i   v              i        
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_230829346_    641 TATATGGAAAAGTGAAGGAACTAAAATAGTCAAT----TCT--AAAAGGA 684
                         i         v ii i   v i i     i   v----   --    i  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_230829346_    685 AGAACAAAGTTGGAGGATTCACATTACTTGATTTCAAGACATATTTGGAA 734
                                          i     i v iii       i  v  i vvi  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_230829346_    735 GGTACAGTAATCAACACAGTATGGTATGGGCAAAACGAAAGA--TATAGT 782
                          v            v     i     iv    v  v  v   --     v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_230829346_    783 TTAATGGAACA--AT--AGAG-----------ACCCATATA---ATAGTC 814
                          i       i --  --    -----------       i ---  i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_230829346_    815 AACTGTGTTTGGACAGAAGTACAAAGGCATTTCAACAGAGAAAGGATAAT 864
                           i  vv   v    iii  i v   i vv     ii i     i   i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_230829346_    865 CTTTTCAACAAATAGTGCTAGAAAAATTGGATATCCAAACACACCAAAAA 914
                                      i     i i v  i      ?   --  ii v   i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA--CATGCAAAAGA 444

  chr1_230829346_    915 ATAAACTTTAACATC---CTTACGCTTGGTACAAAAATTAACTCAAAATG 961
                           i  v  vi  vi ---  i  i ivvi                     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_230829346_    962 GATCATAGAGCTAAATGTAAAATGTAAAACTATAAAACTT---GAAGAAA 1008
                              ?   v          i vv               i---       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_230829346_   1009 ATATGAAGAAGT---TCTGCATGATCTTGTGTCTGGAAATGAATTTTCAG 1055
                          i  --  i?  ---   v i   i    v  iv  v    iv  i i  
  L1M4_orf2#LINE/    545 ACAT--AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_230829346_   1056 ATAAAGCATCAAAAGCACAATCCATACAAGTAAAA---GCTAAATTGGAC 1102
                            vii  i           v v i v   v    --- v          
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_230829346_   1103 TTTATCAAAATTAAAAACTTTTGCTCTGCGAAAGATACTCTTAAAATAAT 1152
                           i                    iv  v i  i  i   v i  i v i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_230829346_   1153 GAA--GGTAAATTACAGACTGAGAGACAATGTTTGCAAATCATATATTTT 1200
                            -- ii  vii     v  i    v   i                i v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_230829346_   1201 ATGAGGAACTTGCATCCAGAATA---AA-----TCTTGTAATTCTCAA-A 1241
                           i   i     i          ---  -----    ii  --     - 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CTCAATA 790

  chr1_230829346_   1242 ATAAGAA---AAACAATCCAGTTTAAAAA-----ATAAGATTTTG-TACA 1282
                             i  ---   i  i   i  ?     ----- v i     vi-  v 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_230829346_   1283 TACTTCTT---AGAAGGTATAC---T--CTGAAAAATATATCAAAAGATG 1324
                         i i    i---     i     --- -- ii v  ii i  v        
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_230829346_   1325 CTCCATGTTACGAAACAT 1342
                            v ii i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (118 / 64)
Gap_init rate = 0.03 (27 / 907), avg. gap size = 2.85 (77 / 27)  


2906 21.36 1.19 11.37  chr1_231094304_231096906     1100  2110 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_231094304_   1100 TGGAAAGAGATCCCATATTCATGGACAGAAAGAATTAATATTGTTAAAAT 1149
                                 v       i        iv i    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_231094304_   1150 GTTCATAGTACACAAAGCAGTATGAAGATTCAAAGCCATCCTTGTCAATA 1199
                          viv   v v v    viii v iv        v  v    i i    v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_231094304_   1200 TTCCAATTACATTTTTTACAGAACTAGAGAAATCAGTTCTAAAATCTGTA 1249
                          i   ii i v      i     v v  v  iiiii i       iii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_231094304_   1250 TGGAATCACAGAAGACCCC-AATAGCCAAAGT--TATTAAGAAAGAAAAA 1296
                              vii  iii     v-          ii-- v  i i      i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_231094304_   1297 CAAAGTTGAAGTCATCATACTTGGTGATTTTTAAATTTTACTACAAATCT 1346
                                 i  vvv   i    vvii    iv   i  -        v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT-ACTACAAAGCT 249

  chr1_231094304_   1347 ATAGTAATCAAAACAGTATGGTATTGACATAAAAACAGACACATGAACCA 1396
                          i         i     i     i  i     ii i     i  ii i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_231094304_   1397 ACAGAACAGAATAGACAGTCCAGAAATAAACCCAAACATATACAATCAAC 1446
                          ii   i     v  v                  v    v  iii    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_231094304_   1447 TAATTTTTGACAAGAGCACCAAGAAGGTACAATGGAGAAAT--CAGTCTC 1494
                          i     i      i ii      vvi v      i    v--i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_231094304_   1495 TTTAGTAAATCGTGTTGGGAATGCAAGATATCCACATGAAAATGAATGAA 1544
                           i ii    v   i     vvi vi    ?       v   v       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_231094304_   1545 GTTAGACCT-TATCTTACAACAGACACAAAAATCAACTTAAAATAGATTA 1593
                            i    i-  i  i   v  v i        i    i     i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_231094304_   1594 -AGATGTAAGT-TAAGACCTGAAACCATGAAACTCCTAGAAGAAAACA-- 1639
                         -   iv   i -     v  i    i  i      i            --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_231094304_   1640 GGGGGAAAGCTCCTTGGCATTGGCCTTGGCAATGACTTTTTTTTAAATAT 1689
                           ? v   v  i v  i v    vi v       i---   i   i    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG---TTTCTTAGATAT 596

  chr1_231094304_   1690 TACATCAAAACCTCAGGCAACAAAAGCAAAAATAAATAAGTGGGACTATA 1739
                         v   i     v v  i          v       i    i v     vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_231094304_   1740 TCAAA-TTAAAAATTTTCCACACAGCAAGGAAAACAATCAACAAAATGAA 1788
                              -       i   i-iii vv   i i v  v     v   i    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_231094304_   1789 AAGAATAGAGCCTATGGATTGTGAGAGAATATTTGTGTACCATATATTAG 1838
                             v--- i  i ii  v  v    i        ---------------
  L1M4_orf2#LINE/    696 AAGAC---AACCCACAGAATGGGAGAAAATATTTG--------------- 727

  chr1_231094304_   1839 TAATTGCTGTTTTTGCCATTACTTTTAATGGCATTAATGGCAGTTTCTGC 1888
                         --------------------------------------------------
  L1M4_orf2#LINE/    728 -------------------------------------------------- 727

  chr1_231094304_   1889 CATTACTTTTAATGGCAAAAGCCACAATTCCTTTTGCACCAACATGATAT 1938
                         ---------------    ---------  -------------  -    
  L1M4_orf2#LINE/    728 ---------------CAAA---------TC-------------AT-ATAT 739

  chr1_231094304_   1939 TTGATACAGGGTTAATATACAAAATATATAG-GAACTCACACAACTCAAA 1987
                         i     vi  ii vi   v  i        i-      vi         -
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA- 788

  chr1_231094304_   1988 AGCAACAACAAGAACAGATAACCCAGTTAAAACATGGGCAAAGCACCTGA 2037
                         --i  i  v    -  i        i  ?   v          v ii   
  L1M4_orf2#LINE/    789 --TAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_231094304_   2038 ACAGACATTTCTCCAACGAAGACATAAAAATGGCCAGCAGGTGTATGAAA 2087
                          i              v     i   v         ii i iii      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_231094304_   2088 AGGTGCTCAGCATCACTAATTAT 2110
                           i      i     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (138 / 75)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 6.68 (127 / 19)  


2696 25.60 3.05 4.14  chr1_231239601_231242075     1065  1982 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_231239601_   1065 TGAAGAAGCATTACAAATTCATGAATCAGAAGACTCAACA--GTAAAGAT 1112
                           i i iii  iv  vi      i  ii       i  i --  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_231239601_   1113 GTCAATTCTCCCCATCTTGATATATGGGT-CAATATAACTGCAAACAAAA 1161
                          v    v       vv     v  ii i -   iii  iiv v v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_231239601_   1162 TCCCAGCAATATTATT-GCATAGATCTAGACAAGATTATCCTAAA-TGTA 1209
                                viiv  v  -   v i  i--      v v        - vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr1_231239601_   1210 TATAAAATGGCAGAGAAACTAGAATAGCTAAAACAATTTTGAAAAAGAAA 1259
                            ii  vv   ii i v i        i        i           i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_231239601_   1260 AATGAAATGGGATAGATT-AGTCTACCTAATGTCAAGATTTACTGTATAG 1308
                           ii  i v   -i  i - vv  v  i   v    i i     ii v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGA-GGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_231239601_   1309 CTACAGTGATCAAGGCTACATGCTATTAGTGAAGGGATAGATACACAGAC 1358
                                i      i viii  v  i i iiv i       i i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_231239601_   1359 CAGTGGAA----GTTAA-----TAGAAATAGGCCCACGCAAAATTT---- 1395
                           i     ----i  i -----i       ii    ii  ---   ----
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA---TTTATGG 344

  chr1_231239601_   1396 CCAACTGACTTTAGATAAGGGTACAAAGGCAATTCAATGGAGGAAAGATA 1445
                         i   i   i   v  i      i v   i v         i i  ii   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_231239601_   1446 CCCTTTTCAACAAATGGTATGGAAGCAA-TCGATATTCATAAGCAAAAAA 1494
                         vi                iiv iii   - v    ?i  i v      i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_231239601_   1495 TAAATAAA--TAAACCTCAATCTAGTCTCACGCTTCATGCAGAAATTAAC 1542
                         ---  i  -- ii   i ----  -i     i ivi  i  i        
  L1M4_orf2#LINE/    445 ---ATGAAGTTGGACCCC----TA-CCTCACACCATATACAAAAATTAAC 486

  chr1_231239601_   1543 TCCAAATTGATCATGGATTTATATGTAAAACATAAAACGATAAAACTTAT 1592
                           v    v     ?i  ii  v      i vv      v        iv 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr1_231239601_   1593 AGAGAAAAA---AAGAGAAAATATTTGAAAGCTAGGGCCAGGCAAGGAAT 1639
                            ii    --- i ? v    v  i vi v  v   ii      v iv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_231239601_   1640 TCTTAGACTTGATGCCAAAAGCATGAGCCATAAGAGGAAAAATGGTTAAA 1689
                                iv   ii         ii   v i  i  i      i v    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_231239601_   1690 TTAGACTTCATCAAAGTTAAACA--TTTGCTCTATGAAAGACCCTGTTAA 1737
                           i            i     v --    iv  vii  i   v  i i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_231239601_   1738 GAGGATGAAAAGTCAAGCTACAGACTGGGAGAAAATATTTGCAAACTGCC 1787
                           iii       v   v i     v                    iiiiv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_231239601_   1788 TATCTGACAAAGGACTAGTATGTAGAATATAGAAAGAACTCTCAAAACTC 1837
                                i  i     v    vi        v          i v     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_231239601_   1838 CACAGTAAAAAAAATAAAAAATAAATAAATAAGAATTTTTAAATTTGAAA 1887
                         ---------  v        i--- i      ------iiv    ?--  
  L1M4_orf2#LINE/    787 ---------AATAATAAAAAG---ACAAATAA------CCCAATTW--AA 816

  chr1_231239601_   1888 AAATGAG-AAAAGACATGAAGAGATATTTAACTGAAGAGGAAAATATACA 1936
                              i -   i  iv    v   i    vv ii    --- i       
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA---AGATATACA 863

  chr1_231239601_   1937 GGTGGCAAATAAGCATATGAAGAGGTAATTTAAAATCATTAGCCAT 1982
                         ii    v        i     i  i i-i i  v    ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATG-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (156 / 75)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.64 (66 / 25)  


3292 26.54 0.55 0.55  chr1_231871422_231877616.rev     4797  5704 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_231871422_   4797 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATTAATATCGTGAAAAT 4846
                              ii i  i     i      i v      v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_231871422_   4847 GGCCATACTGCCTAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4896
                            v     v  i  iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_231871422_   4897 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4944
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_231871422_   4945 TATAGAACCAAAAAAGAGCCCGCATCGCCATGTCAATCCTAAGCCAAAAG 4994
                            i   viiv  ii  v  v v  v    viv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_231871422_   4995 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5044
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_231871422_   5045 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5094
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_231871422_   5095 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5142
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_231871422_   5143 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5192
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_231871422_   5193 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5242
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_231871422_   5243 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5292
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_231871422_   5293 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5342
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_231871422_   5343 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCCAGGACTTCATGTCTA 5391
                         v    ?i- v i -   iv   v v  vv i   v v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_231871422_   5392 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5441
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_231871422_   5442 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5491
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_231871422_   5492 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5541
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_231871422_   5542 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5591
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_231871422_   5592 AAAACAAACAGCCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5641
                           i     i i   v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_231871422_   5642 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5691
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_231871422_   5692 CATCACTGGCCAT 5704
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 421 14.47 0.00 2.63  chr1_231951165_231954253      907   982 (2107)    L1M4_orf2#LINE/L1       20    93 (815)  

  chr1_231951165_    907 CATGGATGTTCAAAGACTTAATACTGTTAACACGGCAATACTCCCCAGGT 956
                                -- vi           i      v i              ii 
  L1M4_orf2#LINE/     20 CATGGAT--TGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr1_231951165_    957 TGATCCACAGATAGAATGCAATCCCT 982
                              i      vv  i         
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCT 93

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.01 (1 / 74), avg. gap size = 2.00 (2 / 1)  

 799 10.90 3.21 7.69  chr1_231951165_231954253     1601  1756 (1333)    L1M4_orf2#LINE/L1       83   231 (677)  

  chr1_231951165_   1601 ATGCAATCCCT-TAAAACATTCCAGCTAGGTTTTCTTTTTTTTTTTTGCA 1649
                          i         - v   -  i      i-----------ii         
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAA-ATCCCAGCTG-----------CCTTTTTTGCA 120

  chr1_231951165_   1650 CAAATTAACAAGCTGATCATAAAATTCATATGGAAGTGCAAGAGACCCAG 1699
                         v     i           v                i      i       
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr1_231951165_   1700 AATAGCCAAT-CAAGCTTGAAAAAGAA---CAAGGTTGGAGGATTCACAT 1745
                                  v-   v            ---   i         i     i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr1_231951165_   1746 TTCCTAATTTC 1756
                             i      
  L1M4_orf2#LINE/    221 TTCCCAATTTC 231

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.03 (5 / 149), avg. gap size = 3.40 (17 / 5)  

2420 13.86 22.66 0.94  chr1_231951165_231954253     2055  2588 (501)    L1M4_orf2#LINE/L1      220   869 (39)  

  chr1_231951165_   2055 CCTCCCAATTTCAAATCTTACTAAAAAGCTACA-TAATCAAGACAGTGTA 2103
                          i             v       v         -               i
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_231951165_   2104 GTACTGGT-TAAAGACGCAGACACATAGATCAATGGAATAGAATTGAGAG 2152
                                i-   i  i--     i                          
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGAT--AGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_231951165_   2153 TCCTCAAGTAAATCCTTACATCTACAGTCA-CTGATTTTCAACAA----- 2196
                            vv  i    i  v     i  ii    -i        i    -----
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_231951165_   2197 -------------ATGGG--------------------------TGCTGG 2207
                         -------------     --------------------------      
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_231951165_   2208 GACAACTGGATATCCACATGCAAAAGAATGAAGTTAAACCTCTATTTCAT 2257
                                     ?                      ii   i   ii   i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_231951165_   2258 GCCATATATGAAAATGAAC-----ATGGATCCAAGACCTACGTATAAGTG 2302
                         i       ii     v   -----       v?       vi i    v 
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr1_231951165_   2303 CTAAAACTATAAAACTCTTGGAACTGTAAAACAAAGGCACAAATCTTTGT 2352
                                            i   -- -      v   ?ii       i  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAA--G-AAAACATAGGNGTAAATCTTCGT 564

  chr1_231951165_   2353 GACCTCACATTAGACAATAGTTCCTTACATATGACAGCAAAAACAT--GT 2400
                              iivi    i    i   i    v        v     i  i-- i
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr1_231951165_   2401 GACAAAA---------------TTGGACTTCATCAAAATTTACAACTTTT 2435
                         i      ---------------                  v v       
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr1_231951165_   2436 GTGTGTTAAAGGGCACCAT------------------------------- 2454
                            iv i     i   i  -------------------------------
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_231951165_   2455 ----------TTGCAAAGCATGTATCTGATAAGGGACTTGTATCCAGCAT 2494
                         ----------       v   i                         v  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr1_231951165_   2495 ATATAAAGAACTCTTACAATTCAACAATAACAA----AATAAT----TTT 2536
                                            i    i     v  ----     i----  ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_231951165_   2537 ATAAATGGGCAAAGGATCTGAATAGATATTTCTCTAAAGA---TATACAA 2583
                          v               i        i       i     ---       
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_231951165_   2584 ATGAC 2588
                            i 
  L1M4_orf2#LINE/    865 ATGGC 869

Transitions / transversions = 2.50 (50 / 20)
Gap_init rate = 0.02 (15 / 650), avg. gap size = 8.40 (126 / 15)  

 381  3.33 0.00 1.67  chr1_231951165_231954253     2976  3035 (54)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_231951165_   2976 AAGGAAGATATACAAATGGCCAATAAGCACATGAAGAAAATGCTCAACAT 3025
                           i                                -  i           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGATGCTCAACAT 898

  chr1_231951165_   3026 CATTAGTTAT 3035
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.00 (2 / 0)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1)  


 607 22.22 0.00 0.00  chr1_232049774_232052711.rev      569   685 (2253)    L1M4_orf2#LINE/L1        1   117 (791)  

  chr1_232049774_    569 TGGAGAGATAGTCCATGTTCATGGATAAGAAGACTCAATATAGTTAAAAT 618
                             i     vi              vi       i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_232049774_    619 AGCAGTTTTTCCCAACTTGATCTGTAGATTCAATGTGATCCCAATCAGAA 668
                         i   i vi i     v       ii        i ii     v    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_232049774_    669 TCCCAGCAAATTTTCTT 685
                                vivi   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT 117

Transitions / transversions = 2.25 (18 / 8)
Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.00 (0 / 0)  

2724 23.92 1.64 0.45  chr1_232049774_232052711.rev     1009  1677 (1261)    L1M4_orf2#LINE/L1       96   772 (136)  

  chr1_232049774_   1009 CAAAATCCCAGCAAATCTTATCTTGTGGATATTGACAAAATGATTTTAAA 1058
                                     vi-i   - i   ii  v        iv    ii    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTG-CCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_232049774_   1059 GTTTATATGGAAAGCCAAAAGACCCAGAATAGCCAATAAAATACTGAAGG 1108
                         i  i         vv   ii                v v   vi    ii
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_232049774_   1109 AGAAGAACAAAGTTGGAGAACCGACACTACCTGACTGAAAGACTTACTAT 1158
                                           i  iv     v  ii i vv  i        i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_232049774_   1159 AAAACTACAGTAATTAAGACAATGTGGTATTGGTGAAAGAGTAGACGTGT 1208
                            i          i      i       i   iiv   ii     i i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_232049774_   1209 AGGTCAGTGGAACAGAATAGAGAGCCCCAAAATAGACCCATGTAAATATA 1258
                           i   i     i     v     i  vi     i      ii vv   i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_232049774_   1259 GCCAGCTGATCTTTGACAAAGGTGCAAAGCCAATACCATGAAGCAAAGAT 1308
                          i  ii    i  i     i     v   v v  v v   ii v  ii  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_232049774_   1309 AGTCTTTTCAACAAATACTGTAAGAACAACTGAACATCCACATGCAGAA- 1357
                                         iv  ivi i       i i ?         i  -
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_232049774_   1358 AATGAATCTAGACACAGACCTTTTACATTTTATAAAAATTAACTCAAAAT 1407
                               vi i   v vv    ivi  vv v  i                 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_232049774_   1408 AAATTATAGACATAAATATAAAAGAGTACACTACAGAACTTCTAGAAGAT 1457
                         ii  i ?    v     i   i  vvv v    i i    ii       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_232049774_   1458 GACATAGG---AAATCTAAGTGACCTTGGGTTTGGCAAAGAGTTTTTAGA 1504
                         i       ---      vv             v     v iv  i     
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_232049774_   1505 TACAACAGCAAAAGCACAATCCATCAAAGAAAAAAGTAGACAAGCTAGAT 1554
                           ii   v           v v iv          -    i  ii i  i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGAC 642

  chr1_232049774_   1555 TACAGTAAAATTTAAGACTTCAGTG----AAAAG-CACTGTTAAGGGAAT 1599
                          v  vi      v  i    iv   ----   i -    i i   ii i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_232049774_   1600 GAACA--CAAGCCACACGCTGGGAGAAAATATTTGTCAAACACATGCCTG 1647
                            v --   v     viv                iv  v  i  ii   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_232049774_   1648 ATAAAAGACTTGTATCCAAAATATATAAAG 1677
                             ii            i           
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAG 772

Transitions / transversions = 1.72 (100 / 58)
Gap_init rate = 0.01 (8 / 677), avg. gap size = 1.75 (14 / 8)  

 346 21.28 0.00 0.00  chr1_232049774_232052711.rev     2354  2447 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_232049774_   2354 AGAAAAGGGCAAAATTTCTGATCAGACACATCACAAAAGATGACATACAA 2403
                          i   v       ivv i   vi     iv  v v     v  i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_232049774_   2404 ATGGAAAATAAGCGTATGAAAACATGTTCAACATCATGTCACTA 2447
                             vv       ii       v   i         ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.82 (9 / 11)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3353 24.64 1.44 1.10  chr1_232335579_232340627     3652  4556 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_232335579_   3652 TGGAAACATATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3701
                               v          i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_232335579_   3702 GACTATACTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAAA 3751
                          i v     v  v   vii       i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_232335579_   3752 TACCA-CTATCATTCTTCACAGAATTAGAAAAAAAAATC-TAAAATTCAT 3799
                          v   -  ii -  i  ii     v v  v  ivvi   -          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_232335579_   3800 ATGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGTGAAAAGA 3849
                               viiv  ii  v  v v         i   vvi i ivi i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_232335579_   3850 ACAAATCTGGAGGCATCACATTACCTGATTTCAAACTATACTATAAGGCC 3899
                              vi      vv     i v  ii        viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_232335579_   3900 ATAGTCACCAAAATAGTGTGGTACTGGTATAAAAATAGGCACATAGACCA 3949
                          i   v i   i i             i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_232335579_   3950 ATGGAACACAATAGAGAACCCAGAAATAAACCCAAATACCTACAGCCAAC 3999
                               i v   v    ii               v i ii  ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_232335579_   4000 TGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACATTCTT 4049
                             i  i     i vviv   i v   vv i         i i v    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_232335579_   4050 TTCAACAAATCATGCTGGAATAATCAGCTAGCCGCATGTAGGAGAATGAA 4099
                                   vi      i i  iii v  ?  i    i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_232335579_   4100 ACTGGATCCTCATCTCTCACCTTATACAAAAAATCAACTACACATGTACT 4149
                         ii    i  ii i   v    v          - i    vv v   v ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATC 498

  chr1_232335579_   4150 AAGGACTTAAACTTAAGACCTGAAACTATAAAAATTCTAGAAGATAACAT 4199
                          ?i   i    iv     v  i           v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_232335579_   4200 TGGAA-AAACCTTTCTAGACATTGGCTTAGGCAAGGATTTC------ATG 4242
                         v  ?i-   i   iv -   v    v        v i    ------   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_232335579_   4243 ACAGAGAACCCAAAAGTAAATGCAATAACAACAAAGATAAATAGCTGGGA 4292
                            ------       i v v    i  v iv   i   i   iv v   
  L1M4_orf2#LINE/    598 ACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_232335579_   4293 CCTAATTAAACTAAAGAGCTTTTGCATGGCAAAAGTAACAGTCAGCAGAG 4342
                          i v  i   v v  i i      iiivv    i vv  vi   iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_232335579_   4343 TAAACAAACAACCCACAGAATTGGGAGAAAATCTTCACAATCTATACATC 4392
                          i  v i              -          v  ii   vii   i   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAAT-GGGAGAAAATATTTGCAAATCATATATC 740

  chr1_232335579_   4393 TGACAAAGGACTAATATCCAGAATCTACAACAAACTCAAACAAATCAGTA 4442
                            i  i     vi          v  i  vi     vv    v   i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_232335579_   4443 GGAAAAAAACAA----TCCCATCAAAAAGTGGGCTAAGGACATGAATAGA 4488
                         iv     i    ----i  v  i?    i     v     iv        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_232335579_   4489 CAGTTCTCAAAAGAAGATATATAAATGGCCAACAAACATATGAAAAAATG 4538
                           v     v            i          i  i  i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_232335579_   4539 CTCAACATCACTAATGAT 4556
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (132 / 87)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.30 (23 / 10)  


3087 27.03 1.33 0.33  chr1_232451957_232457332     3985  4883 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_232451957_   3985 TGGAAACACATCCCATGGTCCTAGATGGGTAGAATCAATATTGTGAAAAT 4034
                               v i        v  v i   v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_232451957_   4035 GACCACACTACCAAAAGCAATTTATAAATTCAATGCAATCCCCATCAAAA 4084
                          i v i   v  v   vii  i  i i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_232451957_   4085 TACCA-CCGTCATTCTTCACAGAATTAGAAAAAACAATCCTAAAATTCAT 4133
                          v   - i i -  i  ii     v v  v  ivii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_232451957_   4134 ATGGAACCAAAAAAGAGCCCACATAGCCAAG-CAAGACTAAGCAAAAAGA 4182
                               viiv  ii  v  viv        i-   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_232451957_   4183 ACAAATCTGGAGGCATCACACTACCCGATTTCAAA-----TTACATGTCC 4227
                              vi      vv       v   i        -----i    viv i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_232451957_   4228 GTAGTCACCAAAACAGCATGGTGCTGGTATGAAAATAGGCACATAGACCA 4277
                         ii   v i   i    ii    i    i  i ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_232451957_   4278 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAAC 4327
                               i     v    ii               v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_232451957_   4328 TGATCTTCAAAAAAGCAAACAAAATCATAAAGTGGGGAAAGGACACCCTT 4377
                             i   i v  i vviv   i i   vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_232451957_   4378 TTCAACAACTGGTGCTGGGATAATTGTGTAGCCACCTGTAGGCAAATGAA 4427
                                 v           i  i  vi  ?    v  i iivi      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_232451957_   4428 ACTGGATCCTCATCTCTCAGCTTACACAAAAATCTACTCAAGATGGACTA 4477
                         ii    i  ii i   v  v v  i        iv      i     ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_232451957_   4478 AGGACTTAAATCTAAGACCTGAAACCTTACAAATTCT-AGAAGATAACAT 4526
                         ?i   i     v     v  i    iv  -   i   -      v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACAT 548

  chr1_232451957_   4527 TGAAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGA 4576
                         v i?iv  vi    vv   v    v        v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_232451957_   4577 ACCCAAAAGCAAATGCAATAGAAACAAAGATAAATAGCTGGGACTTAATT 4626
                         vv         v v    i i  iv   i   i   iv v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_232451957_   4627 AAA-CTAAAGAGCTTTGCACGGCAAAAGGAACAGTCAGCAGAGTAAACAG 4675
                            -i    i vi    ii vv    i iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_232451957_   4676 ACAATCCACAGAGTGGGAGAAAATCTTCACAGTCTAGACATCTGACAAAG 4725
                             i       i           v  ii  ivii v i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_232451957_   4726 GACCAATATCCAGAATCTACAATGAACTCAAACAATATCAGCAAGAAATA 4775
                            ivi          v  i  v      vv    i-   ii  v   v 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAATAATAAAAA 797

  chr1_232451957_   4776 AACAAACAATCCCATCAAAAAGTGGGCTAAGGAC---AATAGACAATTCT 4822
                         i     i  i  v  i?    i     v     i---        v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_232451957_   4823 CAGAAGAAGATATACAAATAGCCAAAAAACTTATGAAAAAATACTCAACA 4872
                          vi                i     v  i vi       i  i       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_232451957_   4873 TCACTAATGAT 4883
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3356 21.65 3.61 1.24  chr1_232675942_232682633.rev     5315  6201 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_232675942_   5315 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5364
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_232675942_   5365 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATCCCCATCAAGC 5414
                            v     v      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_232675942_   5415 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTC 5461
                          v   -   v    i  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_232675942_   5462 ATATGGAACCAAAGAAGGG-CCCACA-TAGCCGAGACAATCCTAAGCAAA 5509
                                 -- viv     -    v -     i i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_232675942_   5510 AAGAACAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATGCTACAA 5559
                                   i      vv   ii  v  ii        viv i      
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_232675942_   5560 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAG 5609
                         i          i   i    ii         i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_232675942_   5610 ACCAATGGAACAGAACAGA-AGCCTCAGAAATAATACCACACATGTACAA 5658
                          i        i    iv  -  i -         vv   i    v  iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGG 344

  chr1_232675942_   5659 CCATCTGATCTTTGACAAACCTGACACAAACAAGCAATGGGGAAAGATT- 5707
                         i  vi    i  i     ivv  v  vi v  vv             v -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_232675942_   5708 -TCCTATTTAATAAATGGTGTTGGGAAAACTGGGTAGCCATATGCAGAAA 5756
                         -  i -  i  i        i     v      i  ?   i     i  i
  L1M4_orf2#LINE/    395 GTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_232675942_   5757 ACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAGTTAACTCAAGAT 5806
                          v    ii         v   i     v         i         i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_232675942_   5807 GGATTAAAGACTTAAACGTAAGACCTAAAACCATAAAAATCCTAGAAGAA 5856
                             i ?    i    i      v       i      v  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_232675942_   5857 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATTC 5905
                            v    ?i- v i -   iv   v v  vv i     v ii   -  v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTA 591

  chr1_232675942_   5906 --TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5953
                         --  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_232675942_   5954 TCTAATTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGA 6002
                         ii v  i   -     i -   i  ii vv    i  v       vv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_232675942_   6003 GTAAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATC 6052
                           i  v  i     i                 v       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_232675942_   6053 TGACAAAGGGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTA-CA 6098
                            i  i  i  vi          v  i        --  -  i i -i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_232675942_   6099 GGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGA 6144
                         iv     i    ----   v  i?    i            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_232675942_   6145 TACTTCTCAAAAGAAG---TGCA----GCCAATAA--ACATGAAAAATAT 6185
                         i i     v       --- i  ----        --         i-  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG-AT 889

  chr1_232675942_   6186 GCTCA---TCACTGGTCAT 6201
                              ---   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (115 / 73)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 1.59 (43 / 27)  


 424 24.30 0.00 1.87  chr1_232685979_232691329.rev     3373  3479 (1872)    L1M4_orf2#LINE/L1        1   105 (803)  

  chr1_232685979_   3373 TGGAAACACATCCCCCATGCTCACAGATGGGTAGAATCAATATTATGAAA 3422
                               v i     --   i   ii   v  v   v i      i v  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCC--ATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_232685979_   3423 GTGACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAA 3472
                         i  i v     v  v   vii       i      i     i  i     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_232685979_   3473 GATACCA 3479
                         i  v   
  L1M4_orf2#LINE/     99 AATCCCA 105

Transitions / transversions = 1.60 (16 / 10)
Gap_init rate = 0.01 (1 / 105), avg. gap size = 2.00 (2 / 1)  

 594 28.98 1.70 0.00  chr1_232685979_232691329.rev     3789  3964 (1387)    L1M4_orf2#LINE/L1      112   290 (618)  

  chr1_232685979_   3789 TTCTTCACAGAAATAGAAAAA---ATTCTAAAATTCGTATGGAACCAAAA 3835
                           i  ii       v  v  i---  i         i       viiv  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr1_232685979_   3836 AAGATCGTGCATAGCCAAAGCAAGACTAAGCAAAAAGAACAAATCTGGAG 3885
                         ii  i vv v         i   vvi i iv  i         vi     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr1_232685979_   3886 GTATCACATTACCCAGCTTCCAACTATATTACAAGGCTATAGTTACCAAA 3935
                          vv     i v    ii   v  viv  i     i    i   v i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr1_232685979_   3936 ACAGCATAGTACTCGTATAAGAATAGGCA 3964
                             ii i     v i     i    i  
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACA 290

Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.01 (1 / 179), avg. gap size = 3.00 (3 / 1)  

1989 25.62 0.99 0.66  chr1_232685979_232691329.rev     4252  4860 (491)    L1M4_orf2#LINE/L1      298   908 (0)  

  chr1_232685979_   4252 CAATGGAACAGAATAGAGAACCCAGAAATAAGGCCAAATATGTACAGACA 4301
                                 i     v    ii          iv   v i  v  ii v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_232685979_   4302 ACTGATCTTCAACAACACAAATAAAAACATAAAGTGGGGAAAGGACACCC 4351
                          i    i   i    vivvivi  i v   vv i         i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_232685979_   4352 TGTTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGAACAATG 4401
                          v                    i  i   vv ?       i i  v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_232685979_   4402 AAGCTGGATCCTCATCTCTCACCGTATACAAAAATCAACTCAAGATGGAT 4451
                            i    i  ii i   v    i           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_232685979_   4452 CAAAGACTTAAATCTAAGACCTGAAACCAGAAAAATTCTAGAAGATAA-A 4500
                           ?    i     v     v  i    i v    v ii       v  - 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_232685979_   4501 TCAGAAAAACTCTTCTAGACATTGTCTTAGGCAAAGAGATCATGACCAAG 4550
                          vi ?iv  v     vv   v   vv        v ivv  v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_232685979_   4551 AATCCAAAAGCAAATAAAACAAAAACTAAGATAAATACATGGGACCTAAT 4600
                          vv         v viv       ivv  i   i   v  v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_232685979_   4601 TAAA--CAAAAAGTCTTCTGTACAGCAAAGGAAATAATCAGCAGAGTAAA 4648
                         i   --i     --   i   i vv       v iv    iv i   i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_232685979_   4649 CAGACAAGTCATAGAGTAGGAGAAAATATTCACAGACTATGCATCCAGCA 4698
                         v      vi  i   i i            ii  i ii  ii   iiii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_232685979_   4699 ATGGACTAATATCCAAAATCT-TCAAGAACTCAAACATATCAGCAAGAAA 4747
                          v     vi      i   v - v        vv   vv   ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_232685979_   4748 AAAAAACAACTAATCCCATCCAAAAGTGGGCTAAGGACATGAATAGACAA 4797
                           i --   v   i  v  i?    i     v     iv          v
  L1M4_orf2#LINE/    796 AAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_232685979_   4798 TTCTCAAAAGAAGATATCCATATGGCCAACAA--ACATGAAAAAATCCTC 4845
                              v           v  v        i  --         i  v   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_232685979_   4846 AACATCACTAATTCT 4860
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (80 / 72)
Gap_init rate = 0.01 (6 / 611), avg. gap size = 1.67 (10 / 6)  


3313 23.19 1.63 3.25  chr1_232928445_232930362.rev      506  1428 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_232928445_    506 TGGAGAGATATTCCATGATCATAAATAGGAGGGCTCAATGTTGTCAAGGT 555
                             i      i     v    ii  v   i i  i   i    i   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_232928445_    556 ATCAGTTCTTCC-AAATTGATCTATAGATTAAATGCAATCCCAATCATAA 604
                         iv  i v  i  -           i     v  i        v    v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_232928445_    605 TCCCAGCAAGTTATTTTGTGAATGTCAACAAACTGATTCTAAAATTTACA 654
                                vivi v     iii vi ii    i     i        i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_232928445_    655 TGGAGGGACAAAAAGACCCAGAATAGCCAACACAACAGTGAAGGAAAAGA 704
                             iivi   ii-                v    ivv    ii i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_232928445_    705 ACAAAGTTGAAAGACTGATACTACCCAACTTTAAGACTTACTGGAAAGCT 754
                                  i i    v i   v     i  i  i       iv      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_232928445_    755 ACAGTAATCAAAACAGTGTGGTATTGGCA-AACAAGAGACAAATAAAAGC 803
                                    i           i     -  vi v     --  -----
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA--TA----- 292

  chr1_232928445_    804 AAAATAGATGAATGAAACAGAATACAGAACCCAGAAATAGGACCACATAA 853
                         ----     v    i  i     vv   ii         iiv   i i v
  L1M4_orf2#LINE/    293 ----TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_232928445_    854 ATATAGTCTATTGATTTTTAACAAAGGAGCAAAGGCAATATAATAGTGGA 903
                         v   i   v         ii    i  v  v   i v  vi   i -   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGA 387

  chr1_232928445_    904 AAGA-TAGTTTTTTCAACAAATGGTACTGGAATAACAAAAAAAAATTAGT 952
                             -    i               i    i i   vii ------  ?i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA------TAKC 431

  chr1_232928445_    953 CTAGACACACACCTTAAGCTCTCACAAAATTTAAACTCT---TTAAACTC 999
                          ---   ii  v---   v---- ii  i  vi v i  --- i v  iv
  L1M4_orf2#LINE/    432 C---ACATGCAA---AAGA----ATGAAGTTGGACCCCTACCTCACACCA 471

  chr1_232928445_   1000 T-CACAAAAATTAACTCAAAATGGGTCACAGACCTAGAAGTAAATAG--A 1046
                          -i                     i   ?       i v    i-  -- 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG-AGCTA 520

  chr1_232928445_   1047 AAATTATAAAATTTTTAGAAGATAGCATAGGAGACAATCTAGTTAACCTT 1096
                            i       i i        v i      ? vv     vvv i     
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr1_232928445_   1097 GGGCATGACAATGACTTTTTAGATATAGTACCAAAGGCACAATCCAAGAA 1146
                            ivv i     ii  i        iii      i      v v vi  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr1_232928445_   1147 AGAAATAATTGATAAACTGGACTTCATTAAAATTAAAGCTTTCTACTCTG 1196
                              v   v      i          i         ivi  i iiv  v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_232928445_   1197 TGAAAGACACTGTCAAAAGAATGAAAAGAAAAGACACAGACTGGAAGAAA 1246
                         ii  i      i    i i i        v  vv      v   i     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr1_232928445_   1247 ATATTTGCAAGGGACATATCAGATAAAGGACTGTTATCTGAAATATATAA 1296
                                   ivv i     v     i     vv    iii         
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr1_232928445_   1297 A-ACCTCTTTAAACTCAACAATAAGAA--CA--TAACCTGATTTTAAAAT 1341
                          - v     vv       i     i  --  --     ii   ?v     
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_232928445_   1342 GAGCCAAAGCCCTTAACAAACACCTCATCACAGAAGATACACAAATGGCA 1391
                          i  v  i vii v  i i   ii  vi  v        i         v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_232928445_   1392 AATAAGC-TATAAAATGATGCTCTACATCGTATATCAT 1428
                                -i  i   v       v     i????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (134 / 76)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.37 (45 / 19)  


2605 25.07 2.85 0.68  chr1_233309741_233312901.rev     1364  2101 (1059)    L1M4_orf2#LINE/L1        1   754 (154)  

  chr1_233309741_   1364 TGAAAACATATTTCAAGTTTATGAAGAGGAAGAC--AATATTGTTAAGAT 1411
                           i   v    ii  v   i   i vv       --              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_233309741_   1412 ATCATTTCTCACCC---TTGATCTATA--TTCAACAGAATCCCAATGAAA 1456
                         iv  v v   -   ---        i --      iv      v  v   
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_233309741_   1457 ATCCCAGCAGT-TACTTTGTGAATATCAACGAACTGATTCTAAAGTTTAT 1505
                                 v i- vi    iii v  ii  i i     i     i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_233309741_   1506 ATGGCGAGACAAAAGACCCAGAACAGCCAACACAATAATGAGAGAAAAAA 1555
                             vi vi   ii         i      v     vv   i i i  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_233309741_   1556 CAAAAGTTGAAGGACTGAC-CTACCCAACTCCAAGACTTACTAAAAAGCT 1604
                         vv       i      v  -  v     i i   i        v      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_233309741_   1605 AAAGCAATCAAGACAATGTGGAATTGGTGTAAGAAGAGACAAATAGATTA 1654
                          v  i          i     v i   ii    i v     v      i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_233309741_   1655 ATGAAACAGAAT--AGAGTCCAGAAATAGAACCACACAAATACATTCAAC 1702
                            i  i     --              i v   i   vv  iiv    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_233309741_   1703 TAATCTTTGACAGAAACAC--AGGCAATCCAATGGAGAACAGATATTCTT 1750
                          i  i  i    iiiiii --  i v  i      i   vii   v    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_233309741_   1751 TCCAATAAATGGTGCTGGAACAACTGGGCATCTGCATTTGAAAAAGTTAA 1800
                          i   i            i        ii ? ii   vii   i i v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_233309741_   1801 TTTAGACAG--ACATTACATCTTTCACAAAAACTAACTCAAAATGGAACA 1848
                         v  i   vv--  v i   i v vi       i              v  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_233309741_   1849 CAGACCTATATATAAATTGC-AAAACGATTAAAATTTT-GTAAATAACAC 1896
                         ?       v  i   iv-  -     v  v   v i  - v i v    i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_233309741_   1897 AGAAA-AAATTTAGATGATCGTGGGTTTGGCAATGAGTTTTTAGGTAAAA 1945
                           i?i-    i vvi   i v      v       iv  i    i  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_233309741_   1946 CAACAAAGGCAGGGTCCATGAAAGAAAAAAAACTGGTAACTAGAACTTCA 1995
                           v    i   viiv v ii          v -- i   v v i      
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTCA 646

  chr1_233309741_   1996 CTAAGATTTAAAACT---GTTCAGCAAAAGACAGTATTAAGTACATGAGA 2042
                         ii  i   v      ---  v vv    i    v   i   v vi   i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_233309741_   2043 AGACAAACCACAGGCTGGGAGAAAATATTTGCAAAACACATTATCTGATA 2092
                               v      iv                    v  i  -        
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATA 745

  chr1_233309741_   2093 AAGGATTTG 2101
                          i   i   
  L1M4_orf2#LINE/    746 AGGGACTTG 754

Transitions / transversions = 1.49 (109 / 73)
Gap_init rate = 0.02 (16 / 754), avg. gap size = 1.62 (26 / 16)  

 553 21.79 7.05 0.64  chr1_233309741_233312901.rev     2514  2669 (491)    L1M4_orf2#LINE/L1      743   908 (0)  

  chr1_233309741_   2514 ATGACAGACTTGCATCCAAAATATACAAAGAATTCTTAAAATTCAACAAC 2563
                           i vi      i     i      i      i     v  i    i  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_233309741_   2564 AAA-----------CGCAATTTTAAAAACTGTCTAAAGAGCTGACCAGCC 2602
                            ----------- v   -  ?     iv v v  i  vi   vi  v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_233309741_   2603 TCCTCACCAAAGAAGATATACAGATAGCAAGTAAGCATATGAAAAGATGC 2652
                         vii  v                i  i  v i      i            
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_233309741_   2653 TCAAAATTATCATGTTT 2669
                             v  i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (20 / 13)
Gap_init rate = 0.01 (2 / 166), avg. gap size = 6.00 (12 / 2)  


2940 25.75 2.18 2.41  chr1_233461835_233463704      500  1369 (501)    L1M4_orf2#LINE/L1        1   868 (40)  

  chr1_233461835_    500 TGGAGAGATATTCTGTGTTCATAGATTGGAAGACTCAATATTGTGAAGAT 549
                             i      i ii       i            i        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_233461835_    550 GTCAGTCCTTCCCAGCTTCATCTATAGATTCCTTGCAATCCTAATCAAAA 599
                          v  i v  i    iv  v     i      vvi       iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_233461835_    600 TTCTACAAGTTG----TTTTGTGGATAACACCAAACTGATCATAAAATGT 645
                          i i --- i  ----     ii  v viiv   i      v      vi
  L1M4_orf2#LINE/    101 TCCCA---GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_233461835_    646 ATACAGAAG-GCAGAACACCAATAATAAC-AACACAATCCTAAAAAAGAA 693
                            ii   i-   iiiv   v v    i -  v      i i        
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_233461835_    694 GA-CAAAGTTAGAGGGCTGACACTATCTGACTTCAAGGCTTATTACAAAA 742
                           -       i    i  v     vi ii i     ii    i      i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_233461835_    743 CTACAGTAATTGGGGCAGTGTGCTA-TGGTGAAAGAATAGACAAGTAGAT 791
                                   iii i       v  -   iiv   i       vi     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_233461835_    792 CAATGGAACAGAAAAGAGAGCTCAGAAATAGACCCACACAA--ACAGTCC 839
                                 i    vv     ii        i     i   v-- ii   v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_233461835_    840 ACTAATCTTTAACAAACGAGCAGAGGTAGTTCAATGCAGAAGGGACAGTC 889
                          i i  i  ii    iv v  vi  iivi       vi   i i i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_233461835_    890 TTTTCAACAGATGGTGCTGGAACAACTGCACATCCACAGGCAAAACAAAA 939
                                  i          i       v i ?     v      -----
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA----- 442

  chr1_233461835_    940 GCAAAAACAAAACTAAACGCAGACCTTACAACTTTTGCACAAATCAGCTG 989
                         ----i  ii  ii ii  v vv    i   v v v i  v    i i  v
  L1M4_orf2#LINE/    443 ----GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_233461835_    990 AGAAT--ATCATATGTAGACCTATATGCAAAATGTAAAACAAAAAAAGTT 1037
                          i   --    ? ----      v   i  i vv      v v    v i
  L1M4_orf2#LINE/    489 AAAATGGATCAWA----GACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_233461835_   1038 TGAGAAGAAGAAAACATAAGAGAAAATCT-AGTGACTCTGGGTTTGGCAG 1086
                          v       ---      i ? v      -v     ii      v    i
  L1M4_orf2#LINE/    535 TTAGAAGAA---AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_233461835_   1087 TGACTTTTGAGGTA---CACCAAAAATGTGATCCGTGAAAGAAAAAAATT 1133
                           ii  i v  i  ---        iiiii v viii          - v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TA 630

  chr1_233461835_   1134 GGTAAGTTGGACTTAGTTAAAATTAAAAACTTCCTCTCTGAAAAAGATGC 1183
                          i   i        vi i              iiviv  vv   i  ii 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_233461835_   1184 TATTAAGAGGATGGAAAGGCAAGCTACAGACTGAGAGATTGTATTTGCCA 1233
                            i    iii  i    i   v i     v  i    vvi       v 
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_233461835_   1234 AACACATATCTGATAAATGACTGGTATCCAAAATGTACCAAACAACGCTT 1283
                          v  i           iv    v       i   i  i-   v   v   
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATAT-AAAGAACTCTT 779

  chr1_233461835_   1284 AAAACTGAATTTTAAGAAAACAACTTAACTAA---AAAAATCAGCAAAAC 1330
                          v    v   vv   i  i    v v v i  ---      vi     iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_233461835_   1331 ATCTGAACAGACACCTCATAAAAGAAGAGATAAAGATGG 1369
                           i    i     ii  viv        v   v i    
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

Transitions / transversions = 1.66 (138 / 83)
Gap_init rate = 0.02 (16 / 868), avg. gap size = 2.50 (40 / 16)  


3303 26.87 0.44 0.44  chr1_233509058_233515335.rev     4880  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_233509058_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4929
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_233509058_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_233509058_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_233509058_   5028 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_233509058_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_233509058_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_233509058_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_233509058_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_233509058_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_233509058_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_233509058_   5376 TTAAAGATTTAAATGTTAGACCTAAATCCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii       v   v     v i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_233509058_   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_233509058_   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_233509058_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_233509058_   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_233509058_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_233509058_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_233509058_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_233509058_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1751 28.50 5.65 2.95  chr1_233549949_233552682.rev      962  1740 (994)    L1M4_orf2#LINE/L1        3   802 (106)  

  chr1_233549949_    962 GAAAGATATACCATGTTCATAGATTGGGAGTCTTAATATCGAAAAGATGT 1011
                                  v          i      i  v        i vv      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_233549949_   1012 TAATTCTTCTCAAACGGGTCTACAGATTTGATGCTATTTCATTAAAAATT 1061
                         i   v  i i    iv i          ii i  v  ii vv v     i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_233549949_   1062 CCAGCAGCTCATCTTGTGGAGATTTATAAGCTAATTCTAAAATTTAAACT 1111
                              v  iiv i   ii  i   v i     i  i        i v iv
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_233549949_   1112 GAAATGAAAGGAGCCAAGAATAGCAAAGATAATTTTGAAGACTTAGAGCA 1161
                               v    ii  v        v  i i   i     i vvv   i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_233549949_   1162 AAGTTAGAAGATGAACACCAACATATAACAAAAC--AGCAGAAATCTGGA 1209
                              i  i  ivv    ivv vv  vv      -- vi v   v  iv 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_233549949_   1210 GTTAATTTAAA-AGTTATAAATTTGGAACAAGAAAAGACAAATAGACCAA 1258
                           -   iv i -   -i iivvi   v i   i v     v     i   
  L1M4_orf2#LINE/    253 GT-AATCAAGACAGT-GTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_233549949_   1259 TGAAATAAAA--GAGAGTCAAGTAATAGATATCCCTGC--TTACAGCCAC 1304
                           i    i  --       v  v    i i--  v i --   ii i  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAAC--CCATACATTTATGGTCAA 348

  chr1_233549949_   1305 CTGACTTACTACCCAGGTACCACTGCAATGCAGTGATGAAAAGGTAGCCT 1354
                         i   i  v v  vvi   i   vvi v  v  i  iv    iii   i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_233549949_   1355 TTTAAATAACTAGTCCTGGATCAATTGGACATCCATAGGT----GGAGGG 1400
                            v  i  v i  v    iv   i    i ?   i v i---- i v i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_233549949_   1401 ACT--GATCTCTACCTCAAACTATAAACAAAATATCAATTCTAA---GAG 1445
                          v --  i i        v  i   v      -  i  i  v  ---  v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATGGAT 497

  chr1_233549949_   1446 CACAGACCTAAATATCAGCCTTAAAATAGTAAAGGCTGTAGAAGATAACA 1495
                           ?          i v  vvi     ivi    iviiv       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_233549949_   1496 TGGGAGAACAGC-------CTTTGGGT-AGGCAAAGA------AGATACA 1531
                          i  ? v v v ------- i      -      v i------     ii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_233549949_   1532 AAAAAAAAACCACAAACCATGATTTAAAAAAACT-GATAATCTGGACTTC 1580
                          v vv    v     i v ii v-- i     v -     vi        
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAA--AGAAAAAATAGATAAATTGGACTTC 645

  chr1_233549949_   1581 ATTAAAGTGAAAAACT---GCTCTTC----GACACTAACAACATCAGTAA 1623
                           i   i v       --- iv    ----       ------   ----
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA------TCA---- 685

  chr1_233549949_   1624 CAGAGGGGGGAAAAGCAA------GAGTGTTGGAAAAGATATTTGCAATA 1667
                         -   ii v i   ii   ------  i  --   i  i          vv
  L1M4_orf2#LINE/    686 -AGAAAGTGAAAAGACAACCCACAGAATG--GGAGAAAATATTTGCAAAT 732

  chr1_233549949_   1668 GACGTATCTAACAAAAGATTCCTATTCACATCATATAAAATACTCCCCAA 1717
                         v ii     i i  ii  i iv   i  v vi       iv    ii- v
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT-AC 781

  chr1_233549949_   1718 AAGTTAATGTTTAAAAAAGACAA 1740
                           v i   iv --          
  L1M4_orf2#LINE/    782 AACTCAATAAT--AAAAAGACAA 802

Transitions / transversions = 1.28 (123 / 96)
Gap_init rate = 0.03 (24 / 800), avg. gap size = 2.79 (67 / 24)  

 251 24.80 0.80 6.40  chr1_233549949_233552682.rev     2119  2243 (491)    L1M4_orf2#LINE/L1      791   908 (0)  

  chr1_233549949_   2119 ATAGATAGATAGAACAACCGTATTTTTAAAACAGGCTAAAG-CCTGAATA 2167
                            i v   i -  i    -i v  ?v    ii   v  i -ii      
  L1M4_orf2#LINE/    791 ATAAAAAGACA-AATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_233549949_   2168 GGTATTTCACAAAAGAATACAGTATATCCAAATGGACATTAAAGATACAA 2217
                          ii     v v      ---- -    v       v  v   iv i ii 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAA----G-ATATACAAATGGCCAATAAGCACATGA 883

  chr1_233549949_   2218 AGCAGGTGTTCCCCATCATGAGTTGT 2243
                          i-  i  i  vv     ????????
  L1M4_orf2#LINE/    884 AA-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (18 / 12)
Gap_init rate = 0.05 (6 / 118), avg. gap size = 1.50 (9 / 6)  


2223 25.87 6.68 2.85  chr1_233555437_233557596.rev      507  1314 (846)    L1M4_orf2#LINE/L1       16   854 (54)  

  chr1_233555437_    507 TGTTCACGCATTGGAAGACAAAATAATA--AAGATGCCAATTCAACCCAA 554
                               i v          vv    v i--      v    v vv     
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_233555437_    555 ATTGATACACAAGTTTTGCTACAATTCTTATCGAAACCCCGGTGAAATTT 604
                               vi   ii  ivi -i    i i    i   i   i ivivv   
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAAC-GCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr1_233555437_    605 TTTGTAGATATAGACAAGAATATTTTAACATTTATATAGAAAGACAAAGG 654
                             i   v  v      vvv  ii   v   i    i    vi   i  
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr1_233555437_    655 A-----AATGGT-AAAACAATTTTGAAAAAGAGGAATTAAATGAGAGAAA 698
                          -----   i i-        i          i   iv  i vi   i v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_233555437_    699 ACACGCTACCTGA---CA--------TATATAGCTACAGTAATCAACACT 737
                         v   i  v  ii ---  --------  i v               v  v
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_233555437_    738 GTATGGTATTGGTGGACAGCTAGACACATAGACGAATGAAGCGGAATACA 787
                           i     i   iiv vi v      i     iv    i iii    vv 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_233555437_    788 GAACACAGAAATAGCCCTGCACAAGTATGAACAAATAATTTT-------- 829
                           iiv        iv  iii   vv    iv   v i     --------
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_233555437_    830 GTACAAAAGCAATTCAATGGAGGAATGGTAATCTTTTCAACAAATGCTGC 879
                           i v  ii v         i i  vii  i               v   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_233555437_    880 TGGAATAATTGGAGA----CAGG-AAAAAAATA-----GAATCTCTACCT 919
                            i i  i    v ----  v -    i   i----- i i i      
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_233555437_    920 GAGTCTCATACCTTATTCAAAAATTAACTCAAAATCAGATCATCGA---- 965
                         ------  i   v   v                  -i     ?v  ----
  L1M4_orf2#LINE/    465 ------CACACCATATACAAAAATTAACTCAAAAT-GGATCAWAGACCTA 507

  chr1_233555437_    966 --TGAGAAACATAAAACTATAAAACATTTAGAAGAAAACATAAGAGAAAA 1013
                         --  vi i vv              vi               i ? v   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_233555437_   1014 TATTCAAGACCAAGAGCTTGGCAAAGAGTTCTTAGGCATGGGGCAAAAAA 1063
                          v   iv    vv i i v     v iv       ii   ivi v    -
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA- 606

  chr1_233555437_   1064 AAGCACAATCCATAAAAGAAAAATACCAATAAATTTTACTTCATCAAAAT 1113
                         --      v v i          - ivi       vv             
  L1M4_orf2#LINE/    607 --GCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAAT 653

  chr1_233555437_   1114 TAAAAACTTCTGTTTTTTTGAAAG---ACTGTTGAGAGGGAGAAAATGAT 1160
                                  i   vi  i--    ---   i ii   ii v     -  i
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTC--AAAGGACACTATCAAGAAAGTGAAAA-GAC 700

  chr1_233555437_   1161 GAGCTACAAACCAGGAGAAAACATTTGCAAACCATATATCTGACAAAAGA 1210
                         i v i   i vii        i         i           i  ii  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr1_233555437_   1211 CCCATATCTAAAATTGATAAAGAATTTTCGAAATTCAGCATTTTTTATAA 1260
                          iii    i i   vv        i i iiv  i   ii v ---- v  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT----AAAA 796

  chr1_233555437_   1261 AG--------TCCATTTAGAAGATAGGCAAACGACATGAAAAGACATTCG 1302
                           --------i   v  ?i  i  i      v  iv    v       --
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT-- 844

  chr1_233555437_   1303 ACTTTTAAAAGA 1314
                         -- i iv     
  L1M4_orf2#LINE/    845 --TCTCCAAAGA 854

Transitions / transversions = 1.51 (124 / 82)
Gap_init rate = 0.03 (21 / 839), avg. gap size = 3.67 (77 / 21)  

 233 15.79 3.51 0.00  chr1_233555437_233557596.rev     1613  1669 (491)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_233555437_   1613 AAAGAA-AGACACGGGTGGCAAATAAGCACATGAAA-GATGTTTAACATT 1660
                               - v i  iii    v               -    i i     i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_233555437_   1661 ACTAACCAT 1669
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2)  


3277 26.43 0.77 0.77  chr1_233567753_233570382     1230  2137 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_233567753_   1230 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1279
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_233567753_   1280 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAG- 1328
                            v     v     iv i  i           i  v     i     i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_233567753_   1329 --CTAGCAATGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGT 1374
                         -- i   --       i  -i     -   -- v  i  - iii    i 
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAAT 145

  chr1_233567753_   1375 TCACATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAA 1424
                            i      viiv  ii  v  v v  v     iv     i i ivv i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_233567753_   1425 AAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAA 1474
                                   i      vv       v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_233567753_   1475 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 1524
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_233567753_   1525 ATCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACA 1572
                                   i    i--    i  --        vv  ii i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr1_233567753_   1573 ACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT 1622
                         iii vi    i  i     ivv  vv  i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_233567753_   1623 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAA 1672
                         vvi  v  i  i              v      v  ?i  i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_233567753_   1673 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGAT 1722
                         iv    ii    i    v   i     v           i  i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_233567753_   1723 GGATTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAA 1772
                             i ?   ii    i  v i v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_233567753_   1773 AACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTC 1822
                            v    ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_233567753_   1823 CAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATC 1872
                         i vi            vvi           v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_233567753_   1873 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 1922
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_233567753_   1923 AACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGA 1972
                           v  i     i   iv            v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_233567753_   1973 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 2022
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_233567753_   2023 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAC 2072
                             i     i     v  i?    i     i     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_233567753_   2073 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACGTGAAGAAATGCTC 2122
                              v        i  vi viii     v  i   i    i i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_233567753_   2123 ATCATCACTGGCCAT 2137
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2192 27.21 4.84 1.28  chr1_234015107_234017141.rev      457  1158 (877)    L1M4_orf2#LINE/L1      105   831 (77)  

  chr1_234015107_    457 AGCTG--TTTTTGGGTGAGATTAACATTTAAATTGCTACACTTTGAGTTC 504
                              --     v vv  i   i   ---- ii  v --- i vi i   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACA----AGCTGAT---CCTAAAATTC 147

  chr1_234015107_    505 ACATGGAATCAAAAAAGAGTCCGAATAGCCAAGGCAATCCTAAGCAAAAT 554
                          i      viiv  ii  vi v          ii     i i iv  i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_234015107_    555 GAACAAATCCAGAGGCATCACATTGCCTGA--------CTTATATATAAG 596
                                viii    vv     i v  ii --------    i-  i  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC-TACAAA 246

  chr1_234015107_    597 GATATAGTAACTATAACAGCATGGTAATGGTACAAAATTAGACACATAGA 646
                          v  i     ii vi    ii     v   i i  iiv      i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_234015107_    647 TCAATGGAATGGAATACAGAACCCAAAAATAAAGCCACATACCTACAACC 696
                                   i    vv   ii   i       v   i i ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_234015107_    697 AACTGATCTTTGACAAAGTTAACAAAAATAAACACTGGAGAAATGACAAC 746
                           i    i  i     i v iv   i vi vv  v   i    vi i ii
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_234015107_    747 CTCTTCAATAAATGGTGCTGGAAAAAATGGCTAGCCATATGCGGAAGAAT 796
                           i     i            i v  v   v  ?   i    ii      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_234015107_    797 GAAATTGCACCTCTATCTCTCACCATGTACAAAAATTAACTCAAGATGGA 846
                            i   v   i   i   v      i                 i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_234015107_    847 TTAAAGATATAAATGTAAGA-----------------CCTAGAAGAAAAC 879
                          i ?   iv           ----------------- i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_234015107_    880 CTAGAAAAAACTCTTCTGGACATTGGCCTAGGTAG-AGTTTAT--GATAA 926
                         v   i?iv  v     vv   v    vi    i i-i    v --    v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_234015107_    927 AGATCCCAGAAGCAAATGCATCAAAAACAAAAATAGACAAATGGGACTTA 976
                         -  iv   i     v v   v     iv         i    v      v
  L1M4_orf2#LINE/    597 -GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_234015107_    977 ATCAAACTAAAAAGCATCTGCACAGCAAA--ATA--ATCTACAGAGTAAA 1022
                               v v    i v i  ii vv    -- i --   v v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_234015107_   1023 TAGACAACCTACAGAATGGGAGAAAGTATCTTCAAATTATGCCCCCAATG 1072
                         v        i               i   i v     i  iivi ii  i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_234015107_   1073 AAGGACTAATATCCAGAATCCACACAGAACTTAAACAACTCAACAGGAAA 1122
                          i     vi          vi i v      ivv         i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_234015107_   1123 AAAACAAACAACTGTATTAAAAACCGGCCAAAGGGT 1158
                           i     i   ivv   ?    vi  v      i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.63 (116 / 71)
Gap_init rate = 0.02 (11 / 727), avg. gap size = 3.91 (43 / 11)  

 203 25.22 2.61 0.87  chr1_234015107_234017141.rev     1437  1551 (484)    L1M4_orf2#LINE/L1      792   908 (0)  

  chr1_234015107_   1437 TGAAAAAAAAAAGAA---AAGAAAAGAAAGAAAAAAGGACATAAATAGAC 1483
                          i    i v   v  ---  vv?  i  v iiv      iv i       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_234015107_   1484 ATTTCTCAAAAGAGGAAATACAAGCAGCCAAATAAACACATTAAAAAATG 1533
                                v     i  v      iii     -   i     v    i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGATG 890

  chr1_234015107_   1534 ATCTGAATTACCAATCAT 1551
                         v  viv  i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (15 / 13)
Gap_init rate = 0.02 (2 / 117), avg. gap size = 2.00 (4 / 2)  


3119 26.48 0.77 1.42  chr1_234092300_234096677     2972  3885 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_234092300_   2972 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3021
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_234092300_   3022 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3071
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_234092300_   3072 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3119
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_234092300_   3120 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 3169
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_234092300_   3170 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3219
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_234092300_   3220 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 3269
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_234092300_   3270 AATGGAACAGAAC--AGAGCCCTCAGAAACAACACCACACATCTACAACC 3317
                                i    i--    i  --     i  vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_234092300_   3318 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACGATTCC 3367
                          vi    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_234092300_   3368 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3417
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_234092300_   3418 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTCATCCAAGGTGGA 3467
                            ii    i    v   i     v            v ii   ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_234092300_   3468 TTAAAGACTTAAATGTTCGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3517
                          i ?    i       vv  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_234092300_   3518 CTAGGCA-ATACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCTA 3566
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_234092300_   3567 AAACACCAAAAGCAATGGCAACAAAAACTAAAATTGACAAATGGGATCTA 3616
                         vi            vvi         ivv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_234092300_   3617 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTCAA 3666
                           i   v v  i i   i  ii vv    i  v    i  vv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_234092300_   3667 CAGGAAACCTACAGAATGGGAGAAAATTTTTGCATTTTTGCAATCTTCTC 3716
                         v  iv    i                 v      -------    v v -
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCA-------AATCATAT- 737

  chr1_234092300_   3717 ATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTT 3766
                               i  i  i  vi          v  i         vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_234092300_   3767 ACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGACAAAGGATATGAAC 3816
                          i  v     i     i     v  i?    i   i        v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr1_234092300_   3817 AGACACTTCTCAAAAGAAGTCATTTATGCAGCCAACAGACAC--GAAAAA 3864
                              i     v       vi  vi viii     i ii   --     i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_234092300_   3865 ATGCTCATCATCAATGGCCAT 3885
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


3083 27.23 0.88 0.77  chr1_234309056_234315767     5313  6219 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_234309056_   5313 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5362
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_234309056_   5363 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5412
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_234309056_   5413 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 5460
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_234309056_   5461 TGTGGAACCAAAAAAGAGCCCGCATAGCCCAGACAATCCTAAGCAGAAAG 5510
                          i     viiv  ii  v  v v      v i      i i iv ii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_234309056_   5511 AACAAAGCTGGAGGCATCACACTACCTGACTTCAGACTATACTACAAGGC 5560
                                i      vv       v  ii i    i viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_234309056_   5561 TACAGTAACAAAAAGAGTATGGTATTGGTATGAAAACAGATATATAGACC 5610
                                 iv  i v   i     i   i  i ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_234309056_   5611 AATGGAACAAAACAGAGGCCTCAGAAATAACACCACACATCTACAACTAT 5660
                                i i  iv   ivii         vv   i    i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_234309056_   5661 CTGATCTTTGACAAACCTGACAAAAAGAAGCACTGGGGAAAAGATTCCCT 5710
                         i    i  i     ivv  v   i vv vv  v        ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_234309056_   5711 ATTTAATAAATTGTGTTGAGAAAACTGGCTAGCCATATGCAGAAAGCTGA 5760
                         v  i  i    v   i  i  v      v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_234309056_   5761 AACTGGATCCCTTCATTACACCTTATACAAAAATTGACTCAAGATCGATT 5810
                          ii    i    v v i     v            i      i  v   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_234309056_   5811 AAAGACTTAAACATAAGACCTAAAACCATGAAAACTCC-AGAAAAAAACC 5859
                          ?    i    ii     v       i  -       i-    i     v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chr1_234309056_   5860 TAGGCAAATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5909
                             ?iv v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_234309056_   5910 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTAA 5959
                         i            vvi          vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_234309056_   5960 TTAAACTAAAGAGCTTCTG--CCTAGCAAAAGAAACTATCATCAGAGTGA 6007
                          i   v v  i i   i  -- i --    i  v       vv i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGA 694

  chr1_234309056_   6008 ACAGGCAACCTACAGAATGGGAGAAAATTTTTTGCTGTCTATCCATCTGA 6057
                          v  i     i                 v   -  vivii  vi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGA 743

  chr1_234309056_   6058 TATACAGCTAATATCCAGAATCTACAAAGAACTTAAACAACTTCATAAGA 6107
                           vivii  vi          v  i        ivv      iv    v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_234309056_   6108 ATAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 6157
                          v  i     i     v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_234309056_   6158 TTCTCAAAAGACGACATTTATGCAGCCAACAAACATATGAAAAATAGGTC 6207
                              v     v  i  vi viii     i  i  i       ivv v  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_234309056_   6208 A---TCACTGGTCAT 6219
                          ---   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


 723 26.21 1.21 5.24  chr1_234328712_234334720     4364  4611 (1398)    L1M4_orf2#LINE/L1        1   238 (670)  

  chr1_234328712_   4364 TAGTAAAACATCCCATGTTCATGGATAGGAAGAATCAATATTGCTAAAAT 4413
                          i v  i i                 v      v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_234328712_   4414 GACCATACTGCCCAAAGCAATTTATAGATTCAATGCTAGTCCTATTAAAC 4463
                          i v     v      vii  i  i        i  v vi     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_234328712_   4464 TACCAATGATATTCTTCACAGAACTAGAAAAAAATATTTTAAAATTCATA 4513
                          v   iiviiv  i  ii     v v  v  ivvv  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_234328712_   4514 TGGAATAAAATAAAAGAG-CTCA-AATAGCCAAGGTAATCCTAAGCAAAA 4561
                              ----  iv   i - i  -         iii    i i ---   
  L1M4_orf2#LINE/    151 TGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAA 193

  chr1_234328712_   4562 AGAAAAAAAGAGGCCGGGTGCGGTGGCTCACACCTGT-AATTCCAGCACT 4610
                             i  v i  viv i ------ i       i vi-    i  iv   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAG------GACTCACACTTCCCAATTTCAAAACT 237

  chr1_234328712_   4611 T 4611
                          
  L1M4_orf2#LINE/    238 T 238

Transitions / transversions = 1.71 (41 / 24)
Gap_init rate = 0.03 (6 / 238), avg. gap size = 2.67 (16 / 6)  

2355 25.31 2.64 1.81  chr1_234328712_234334720     4798  5516 (493)    L1M4_orf2#LINE/L1      184   908 (0)  

  chr1_234328712_   4798 ATCTCAAAAAAGAAAAAAAAAAAAGCTGGTGGCATCATGCTACCCAACTT 4847
                             ii        i  v   --- i   v  vv   ii  v     i  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAA---GTTGGAGGACTCACACTTCCCAATTT 230

  chr1_234328712_   4848 CTAA--CTA-TACAAATAGGGCTACAGTAACCAA--CAGCATGGTACACT 4892
                          v  --i  -      ----          i   --   ii      -- 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAA----GCTACAGTAATCAAGACAGTGTGGTAC--T 274

  chr1_234328712_   4893 GGTACAAAAATAGACACGTACACCAATGGAACAGAGTAAAGAACCCAGAA 4942
                           i i  ii       ii  v i        i   i vi   ii      
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_234328712_   4943 ATAAGGCCGTACACTTATAGCTATCTGATCTTCGACAAACCTGACAAAAA 4992
                             iv  i    i    i ii vi    i        ivv  v   i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_234328712_   4993 CAAGCAACAGGGGAAGGATTCCCTATTCAATAAATGGTTCTAGGATAACT 5042
                           vv   ii   i   i  vvi  v     i       v  i   i    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_234328712_   5043 GGCTAGCCATATGCAGAAGATTGAAACTAGACCCCT----TACACCACAT 5088
                           v  ?   i     i    v    ii i       ----i      i  
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_234328712_   5089 ACAAAAATTAACTCAAGGTAGATTAAAGATTTAAATGTAAAACCTAAAAC 5138
                                         ii i   i ?   ii         i v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_234328712_   5139 TAGAGAAACCCTGGAAGGCAACTTAGGC---AATGCCATTCTGGACATAG 5185
                           v i  vi i i    iv   v    ?---   -- -   vv   v v 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTG 571

  chr1_234328712_   5186 GAATGAACAAAGATTTCATGACAAAGACACTAAAAGCAATGGCAGCAAAA 5235
                          iv iii   v i    v iivv v     i       vvi   i     
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_234328712_   5236 GCAAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGC 5285
                          v      v  i    v   ii v  i   v v  i i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_234328712_   5286 AAAGGAAATTATCAGTAGAGTGAAGAGACAACCTACAGAATGGGAGAAAA 5335
                               v i     iv i      i        i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_234328712_   5336 ATTTTGCAAACTATGCATCTGTAAAAGGTCTAATATCCAGCATTCTATAA 5385
                         vv        ii  ii     vv  i  v  vi       v  -v     
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT-ATATAA 770

  chr1_234328712_   5386 AGAGCT--TGCATTT--ACAAGAGGAAAACAAACAACCCCATTAAAAAGT 5431
                            i  -- i  vi -- i  v ii  i     i     v   ?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr1_234328712_   5432 GGGCAAGGGACACGAA--AACACTTTTCAAAAAAAGACATACATGTAGCC 5479
                               i   ivi   --i   i  i  v   i    i     vi i   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr1_234328712_   5480 AACAAGAATATGAGAAAA-GCTCAATATCACTGATTTA 5516
                           i   v i    i  i -      i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (114 / 64)
Gap_init rate = 0.02 (15 / 725), avg. gap size = 2.13 (32 / 15)  


3165 16.96 1.79 5.61  chr1_234412035_234413797.rev      489  1272 (491)    L1M4_orf2#LINE/L1      155   908 (0)  

  chr1_234412035_    489 AATACA--GAACCT-TAATAGCCAGAA-AATATTGAATAAGAAAAAAAAA 534
                            i  -- i   i-v        i  -   v     v     i  v   
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr1_234412035_    535 AGTGTGAGGAATCACATCTTTTGATCTCGAATCTTACTACAAAGATACAG 584
                         iv  -     v     ii iiii  i  i  v            v     
  L1M4_orf2#LINE/    205 GTTG-GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_234412035_    585 TAATCAAGACCTTACTGGTACTGGCATGAAGATAGACATATAGATCTATG 634
                                   vv i-            i i                v   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTG-TGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_234412035_    635 GATTAAAATAGAAATGCCAGAAATAAATCCTCACATTTATGGTCAATTGA 684
                           v  i   v  i vv           i  vi                  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr1_234412035_    685 TTTTTGACAAGGCTGCCAAGACAATTCAGGGGGAACAAGAACAGTTGTTT 734
                             i       v         v     iv   i -     i   iv   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATAGTCTTTT 401

  chr1_234412035_    735 AAACAAATGATACTGGAATAACTAGATATCCCCATGAAAAAGAAAAAAGT 784
                         v        i i    i i    i    ?  v    v       vi    
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_234412035_    785 TGGACTCCTATGTCACACCATATACAAAAATTAACTAAAAAATGTGT--- 831
                              i    iv                        v    -  vi ---
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGATCAW 500

  chr1_234412035_    832 AGACCCAAATGTAAGAGCTAAAACTATAAAAACCCTTAGAAGAAAACAT- 880
                              i                         - i               -
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATA 549

  chr1_234412035_    881 -GGATACATCTTCATAACTGTGGATCAGCCAATGGTATCTTAGCTCTGAC 929
                         - ?i  v      i i  iv   i i  v       v      v v    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_234412035_    930 ACTGAAAGCACAAGTACAAGCCATAATCAAGCAACAGAAAAAGAAGGTAA 979
                           ii          -------------   -   v       iv  i   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAG-------------CAA-CAAAAGAAAAAATAGATAA 635

  chr1_234412035_    980 ACTAAATATCATCAAAAGTTTTTAAACTTTTTAGCTTCAAATACCATCAC 1029
                          i ii iv         --  vv        vv        vi-- -   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAA--TTAAAAACTTTTGTGCTTCAAAGG--A-CAC 680

  chr1_234412035_   1030 CATCAAGAAAGTGAAAAGACAACCTACAGAATGGGAGAAAATATTTGCAA 1079
                         i                       i                         
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_234412035_   1080 AACATATACCAGAAAAGTGAATTATATGTACAATACATCCAAAGATAAAA 1129
                          v      i v  v   v  v  i   vi v    i  --     -----
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATAT--AAAGA----- 773

  chr1_234412035_   1130 AAAACAAACCCACACACTTACAATTCGACCTTAAAAA----AGTGGCACA 1175
                         -------------  v       i  i ivv      ---- i ii v  
  L1M4_orf2#LINE/    774 -------------ACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr1_234412035_   1176 ATTTTAAAATGGACAAAAGACTGGAATAGTCATTTCTCCAAAGAAAACAT 1225
                            ?v       i    i  i v      v               i i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr1_234412035_   1226 ACAAATGACAAATA-GCATATGAAAAGATGCTTGATATCATTGGTCAT 1272
                                i v    -   i             ii i    ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (74 / 56)
Gap_init rate = 0.03 (19 / 754), avg. gap size = 3.05 (58 / 19)  


3757 22.12 2.12 0.67  chr1_234519929_234521983      668  1562 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_234519929_    668 TGGAAAGATACCTTGTGTTCATGAATTGGAAGAATTAATATTGTTAAAAT 717
                                   i iii        i         v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_234519929_    718 TGTCCATACTATCTGAAACAATCCACAGATTGAATACAATCCTTATGAAA 767
                         v - v     vi ii  vii   i       v  ii      i   v   
  L1M4_orf2#LINE/     51 GG-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_234519929_    768 ATTCCAATGACATTTTTCACA-AAATGGTAAAAAATGATTCTACG-TTCT 815
                           i   iivi v     ii  -    v - v  iv    i   vi-   v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCA 148

  chr1_234519929_    816 TATGGAACCACAAAGAACGCTGAATAGCCAAAAGCAACCACGAGTGAAAA 865
                                vii   i i  v v            -   i vi  ivi i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAA 197

  chr1_234519929_    866 GAACAAATCTGGAGGCATTACATTACTTGACTTCAAAATATATTACAAAG 915
                                vi      vv i   i v iii i       iv  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_234519929_    916 CCACAGTAATCAAAGCAGCATAATACCAGCACAAAAACAGATATAAAGGC 965
                          i           ii   ii ii   ii   i  ii i   i   v  ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_234519929_    966 CAATGGAACAGAATAGAGAGCCCAGAAATAAATCCATGCATTTACAGTCA 1015
                                 i     v     i           i    i      ii    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_234519929_   1016 ACTGATCTTCAACAATGGTGTCAAGCATATACAATGGCAAAAGGATAGTC 1065
                          i    i   i    v    i    vvi  v      vi    i      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_234519929_   1066 TCTTCAATAAATGGTGTTGGGA-AACTGGATATCATCA-ATGCAAAAAAG 1113
                          i     i        i     -         ? --  -        i i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKC--CACATGCAAAAGAA 445

  chr1_234519929_   1114 TGAAACTGGACCTCTATCTTACACCATTTACAAAAATTAACTAAAAATGG 1163
                             ii      i   i  i       v              v       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_234519929_   1164 AATAAAGACTTAAATGTAAGATCAGAAATCGTAAAACTCTTAGAAGAAAA 1213
                          vi ?    i           v vi   iii                   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_234519929_   1214 CGTAGGGGAAAATCTT---GACATTGATCTTGGCAATGATTTTTTA---- 1256
                          i    ? v       ---   v   ivi v       i   i   ----
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_234519929_   1257 TGACACCAAAAGCACAGGCAACAAA-GCAAAAATAAACAAATAGGACAAC 1305
                                         i        - v       i i    v    vv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_234519929_   1306 ATCAAACTAAAAATCTTCTGTGTAGCAAAGGAAACGATCAAGAAAATGAA 1355
                               v v    v   i    ivv       v  v         i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_234519929_   1356 AAAGCAACCTACAGAATGGGAAAAAAATAACTGCAAAT---ATATCTGAT 1402
                           ii     i           i    -  vi       ---         
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGAT 744

  chr1_234519929_   1403 AAGGTGTTACTATCTAAAATATGTGAGGAACACATACAATTCAATAGCAT 1452
                             vii vv    i i     i i i    v v     i      ii v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_234519929_   1453 CAAAACAAATAATCTGGTT-AAAAATATACAAAAGACCTAAATAAACATT 1501
                         v  i        i iii  -      ivi    i  ii i    i     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_234519929_   1502 TTTCCAAAGA---TACACAAATGGCTAATAGGTACATGAAAGGGTACTCA 1548
                          i        ---  i         i    i i        i i i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_234519929_   1549 TGATCACTAATTAT 1562
                         vv    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (133 / 62)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


3085 28.22 0.55 0.44  chr1_234526704_234533106.rev     5006  5912 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_234526704_   5006 TGGAAGAACGTTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5055
                              ii ii i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_234526704_   5056 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5105
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_234526704_   5106 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5153
                          v i iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_234526704_   5154 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5203
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_234526704_   5204 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACCTCAAGGC 5253
                                i      vv   ii  v  ii i      viv   iv   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_234526704_   5254 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5303
                                 i   i i  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_234526704_   5304 AATGGAACAAAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 5351
                                i i  i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_234526704_   5352 ATCTGATCCTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5401
                          vi    ii i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_234526704_   5402 CTATTTAATAAATGGTGCTGGGAAAACTTGCTAGCCATATGTAGAAAGTT 5451
                           v  i  i              v    v v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_234526704_   5452 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCGAGATGTA 5501
                            ii    i    v   i     v              i  i i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_234526704_   5502 TTAAAGACTTAAACGTTAGACTTAAAACCATAAAAACCCTAGAAGAAAAC 5551
                          i ?    i    i  v   vi      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_234526704_   5552 CTAGGCATTACCATTCAAGACACAGGCATGGGAAAAGACTTCATGTCTAA 5601
                         v    ?i v viv   iv   viv  vv i  v  v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_234526704_   5602 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5651
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_234526704_   5652 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAGC 5701
                          i   v v  i i   i  ii vv    i  v    i  vv i     iv
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_234526704_   5702 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCCACTCATCTGACAA 5751
                           i     i   i             v  i    vi  ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_234526704_   5752 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5801
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_234526704_   5802 AAACAAACAACCCCAT-GAAAAATGGGTGAAGGACATGAACAGACACTTC 5850
                          i     i     v  -?         ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_234526704_   5851 TCAAAAGAAGACATTTATGCAGTCAAAAGACACATGAAAAAATGCTCATC 5900
                           v        i  vi viii i   v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_234526704_   5901 ATCACTGGCCAT 5912
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (154 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3500 20.05 4.53 1.07  chr1_234566311_234568576.rev      938  1775 (491)    L1M4_orf2#LINE/L1       42   908 (0)  

  chr1_234566311_    938 TGTGAATATGACCTAGTACAGTTGTCAAATTCATCTACAGACTCAAAGCA 987
                            v  v   i -- i   -- ivi      v         i    v   
  L1M4_orf2#LINE/     42 TGTTAAGATGGC--AATAC--TCCCCAAATTGATCTACAGATTCAACGCA 87

  chr1_234566311_    988 ATTGCTATCAAAATTCCAGTTGCCTTTTCTTTGTAGACATAGACATGCTA 1037
                           iv          i    i        --   i   v  v    v   i
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTT--TTGCAGAAATTGACAAGCTG 135

  chr1_234566311_   1038 ATCCCAAAATTCACATGAAATTAAATGGGAATCAGAAAAGCCAAA----- 1082
                             i        i   i  v iv v    vi     v       -----
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_234566311_   1083 ---------GAAGAATGATGTTGGAGGGCTTGTACTTCCTGAGTTCAAAG 1123
                         ---------      ii v        i  iii      ii v      i
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_234566311_   1124 TTTACTACAAAAATACAGTAAGCAGAACAGGGTGGTAATGACATAAGAAT 1173
                         i          iv        v  ii    v      v  i      i  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr1_234566311_   1174 GTACATATAAAACAATGGA-TAGAATTAAGAG-CCAGAAATAAGCTTTCC 1221
                         iv       i v       -       i    -          i iiviv
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr1_234566311_   1222 CATTTATGGGCAATTGATTCTCAACAGAGTTGGCTGGACAATTCACTGAA 1271
                                  v         i  i   ii v  v vi   v     v  ii
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr1_234566311_   1272 GAAAGAATAGTCTTTCCAACAAGTGATACTTGGACAA------ATCCACA 1315
                                        i      i  i i  v      ------ ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_234566311_   1316 T---AAACAACGAATTTGGATCTCTATCTCACACTACATCACAAAA-TTA 1361
                          ---   v  i   v     i i   i       i i  -      -   
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTA 484

  chr1_234566311_   1362 ACAAAAAGTAAATCACA--CCCAAGCATATGAAATATACCTAC------- 1402
                           vv   i ii    ? --  i  iii  v  iv  v v   i-------
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_234566311_   1403 -CAGAAGAAAAAATTGGAGTAAACCATCATGATGATGGGGTGGGAAATGG 1451
                         -i         v  v  ?     i v  i   ivv    v i  v     
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_234566311_   1452 CTTCTGAGATAAGACATCAAAATAAAAAGAAGTAAAAGGGGAAAAAAAGA 1501
                         i    v     v    i     vv v   v ii     i--     v   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA--AAAAATAGA 632

  chr1_234566311_   1502 TAAATTGGGCATTATAAAAATTAAAAACTTTTGTGCTCCAAAGGACACTA 1551
                                 i v i  v                     i            
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_234566311_   1552 TCAAGAAAGTAAAAAGACAAAGTACAGAATGGGAGAAAATATTTGCAAAG 1601
                                   i         vvi                          v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_234566311_   1602 CATATATCTGATTAGGTATATGTAGCTAGAATATACAAAGAACCTTTACA 1651
                                     v   v iv    v i        i       ii     
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_234566311_   1652 ATTCAGTAATAAATATATA--TAACCCAATATTAAAATAAGCAAAATATT 1699
                          i   i       v v i --         v?v     ii     iv   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_234566311_   1700 TGAATAGACATTTTTCCAAAGAAGATAAACAAATGGCCAGTAAAGACACT 1749
                                      i             v           i   iv   iv
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_234566311_   1750 AAAAGATGCTGAACATCATTAAATAT 1775
                                   v       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (93 / 71)
Gap_init rate = 0.02 (14 / 867), avg. gap size = 3.36 (47 / 14)  


3003 24.80 3.95 1.58  chr1_234647963_234652072.rev     2733  3619 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_234647963_   2733 TGGATGAAAACTCCATGTTCATGGATTGGATGAATCAATATTGTTAAAAT 2782
                             vii v ii                  v  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_234647963_   2783 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATTCCTATAAAAA 2832
                          v v     v      vii              i     i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_234647963_   2833 T---AATGATATTCTTCACAGAGGTAGATACAAC-AATTCTAAAATTTAT 2878
                          --- iiviiv  i  ii    ii v  i - i -i  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr1_234647963_   2879 GTGGAACCACAAAAGATCCAGAATAGCCAAAGCCATCCTGAGCAATAAGA 2928
                         i     vii   ii  i              i v   i   iv  v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_234647963_   2929 ACAAAATTAGAGAAATGACATAACCTGACTCCAAATTATACTACACAGCT 2978
                              i  i   i v v   ivv  ii i i    viv       v    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_234647963_   2979 ACAGTAACCAAAACAGCATGGTACTGACATAAAAACAGACACATAAACCA 3028
                                i   i    ii        i     ii i     i   i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_234647963_   3029 AGGGAATAGAATGGAAAACCCAGAAACAAATCCATACACCTATGGTAAAC 3078
                          v          v  i ii       i   i       ii      v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_234647963_   3079 TCATTTTTGACA--GGTGCCAAGAACATACATTGGAGAAAGGACAGTTTC 3126
                          v     i    --          v   v  v   i     i i   i i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_234647963_   3127 TTCAGTAAATGGTTTTGGGAATACAGGGTATACAGGGTATCCATGTGCAG 3176
                             ii       vi     ---  ------  v  i  ?   ii    i
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGA---CA------ACTGGATAKCCACATGCAA 440

  chr1_234647963_   3177 AACAATGAAACTGGACCCCTATCTCTCGCCATATATGAAAATCAAATAAA 3226
                           v      ii          i   v i       ii     i  v v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_234647963_   3227 AATGTTTAAAAGACTTAAATCTAAGACCTCAAGCTATGAAACTACTACAA 3276
                             vv v ?    i     v     v  v  i    i     vi  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_234647963_   3277 GAAAACAATAAGGA-AACTCTCCAGGATACTGATCTAAACAAAAAATTTT 3325
                                -  i ?i-  v   i iv  ivi  ivi  ii   vii-   i
  L1M4_orf2#LINE/    541 GAAAACA-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTC 588

  chr1_234647963_   3326 TGAGTCATAGC-CCACAAGCACAGGCAACCAAAGGAAAGATGGACAAATA 3374
                          v  vi  ii -   v       i     v    i   i  i  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_234647963_   3375 GGATGACATCCAG-TTAAAAAGCTTCTACACAGTGAAGGAAACAATCAAC 3423
                            ivv    v i-       -   i iii vvii     v  v     v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_234647963_   3424 GAAGTGAGGACACAATTCACAGAATGGGAGAAAGTGTTT-CAACT-ACCC 3471
                         i      ii v    ii                i i   -   v - ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_234647963_   3472 ATCTGACAAGG-------ATTAATAACATGAAAAGAAGCTCAAACAACTC 3514
                               i    -------  iv v  i  iv      -   vv       
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTC 786

  chr1_234647963_   3515 TATAGGAAAAA--CTAGTAATCCAATC-AAAAACGGGCAAAATATTTGAA 3561
                         v   iv     -- v i   i     i-     i       iv       
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_234647963_   3562 TAG---T-----------AGACATCCAAATGGCAAACAGGCATGTGAAAA 3597
                            --- -----------   i  v        v  i i   ii      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_234647963_   3598 TGTACTCAACATCATTGATCAT 3619
                         vi i          ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (140 / 77)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.45 (49 / 20)  


3741 21.31 3.16 0.90  chr1_234831577_234835337.rev     2384  3270 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_234831577_   2384 GAAAAAACACTCTATGTTCATG-ATTGAAAGATTTAACATTGTTAAGATG 2432
                          i   i i ii i         -    i    i    i            
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_234831577_   2433 TCAATATTACC-AAAGCAACTTACAGATTCAATGCAATTCCTATCCAGAT 2481
                         v     i v  -   vii ii           i     i      v i  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_234831577_   2482 CCCA--TAAATTTTGGGGGGAACCAGAAAAACACATTCTAAAATTCATAT 2529
                             -- ivv    vv vi   viv  v  i vv  i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_234831577_   2530 GGCATCCCAAAGGACTCCAAACAGCCAAAACAATCTCAAAAGAAGAAGAA 2579
                           v viv   i    i vi  i              ii   -        
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGAAGAA 200

  chr1_234831577_   2580 AACAGTTGGAGGACTCACA-TTCCTGATTTCAAAGCT----ACAAAGCTA 2624
                         v v                -    ii        i  ----         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_234831577_   2625 GGGTAGTAAAAAGAGTGTGGTACTAGCATGAAGACAGACATATAGACCAA 2674
                         vi   i v  i v           i    i i  i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_234831577_   2675 TGGAATGGAATAGAATAGAGATCCCAGAAATAAACTATTGCATATACAGT 2724
                               -----     v    vi            ivv i   v  ii  
  L1M4_orf2#LINE/    301 TGGAAT-----AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_234831577_   2725 CAAATGATCTTTGACAAGTGTGCCAAGACTAATCAATGGGGAGAGGACAG 2774
                            v    i  i      v          i v          i  i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_234831577_   2775 TCTCTTCAATAA-TTGTTCTGGGAAAACTGGATATTTGCATGCAGAGGAA 2823
                            i     i  - v  v      v         ?iii      i i   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_234831577_   2824 TAAAGTTGAGCCCTTAC-----ACCACATACAAAAACTAACTCAAAATGG 2868
                          i      ii   i   -----    i         i             
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_234831577_   2869 ATCAAAGGCCTAAGTGTAAGATTTTAAACTGTAAGACTCTTAGAAGAAAG 2918
                             ?  i     i       vi v     i   i              i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_234831577_   2919 CATAGGAC--AATACTTCACAATACTGCATTTGGTGATGATTTATTGGAT 2966
                               ?v--   -    iii ivi  vi  v  ii   i   v  i   
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_234831577_   2967 GTG-TATCAAAGGCACAGGCAACAACAAAAA-------TAAATTGGATTT 3008
                         i  -i i    i     i       v i   -------         i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_234831577_   3009 TATAAAATTTCTAATATATTGTAC--AAAAAAATAAGTATCAATAGAGTA 3056
                         i  v   v  vv  vv v    i --v   ii i v-      v i   i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC-TATCAAGAAAGTG 693

  chr1_234831577_   3057 AAAAGGTAACCTACAGACTGGAAGAAAATATTTGCAAATAATATATCTGA 3106
                              ii    i     v   i                 v          
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_234831577_   3107 TAAAGGATTAATATTCACAACATATAGACAATTTCTAAAACTAAAAAA-A 3155
                            i   i vi   i  v  i     i v  i ii  v    v  v  - 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_234831577_   3156 AATACAAAAACACCTTGATTCAAGCATTGGCAAAGGATTTGAATGTACAT 3205
                           v v v   i v iii   ?  iv  v                iv    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_234831577_   3206 TTCTTCAAAGAAGATATATAAATGGTCAATAAGCACATGAAAAGATGCTT 3255
                             i             i      i                       i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_234831577_   3256 AGCATCACTAATCAT 3270
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (118 / 67)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 2.25 (36 / 16)  


2565 25.92 3.91 2.46  chr1_234842069_234845240.rev     1787  2681 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_234842069_   1787 TGGAAAACT-TTCCATGCTCTTGAG--GGAGGA-TCAATATTGTTGAAAT 1832
                               iv - i     i  v  ii--   i  - i         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_234842069_   1833 GGCCATACTGCCGAGAGCAATTTATAGATTTAATAGTATTCCTATCAAAC 1882
                            v     v  v i vii  i  i     i  iivv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_234842069_   1883 TACCAATGACATTTTTCACAGAATTAGAAAAAACT-ATTCTAAAATTTAT 1931
                          v   iivi v     ii     v v  v  i-  -  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_234842069_   1932 ATGGAACCAACTAAGAG-CCCA-AATAGTCAAAGAAATCCTAAGCAAAAA 1979
                               -- vvi   i -    -     i    iv    i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_234842069_   1980 GAACAATGCCAGAAGCATCACACTACCCATATTCAAACTATTCTATAAGC 2029
                               v iii  i vv       v    vv      viv v   i  iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_234842069_   2030 CTACAGTAACCAAAATAGCATGGTACTATTACAAAAACAGACATATAGAC 2079
                                  i   i i  ii       ivi i  ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_234842069_   2080 CAATGGAACAGGTTAAAGAACCCAGAAATATAGCTACATCCCTACAACCA 2129
                                 i  iv vi   ii         v v i i ivii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_234842069_   2130 TCTGATCTCTGACAAAGTCAACAATAACAAGCAATGGGGAAAGGAT--TC 2177
                         vi    i ii     i viiv   v v  vv            i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_234842069_   2178 GTTGTTCAATAAATGGTGCTGGGATAACTGGGAAGCCATATGCAGCCGAT 2227
                         -  -     i              i      iv ?   i     ivv  v
  L1M4_orf2#LINE/    398 -TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_234842069_   2228 TGAAACCAGACTCCTTCCTTTCATCATATACAAAAATCAACTAGAGATGG 2277
                             iiii   i   v   iv  i             i    vi i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_234842069_   2278 ATTAAAGACTTAAATCAAAAACCTAAAATTATAGAAGCCCTAGAAGAAAA 2327
                           i ?    i     vv  i v      i    i  vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_234842069_   2328 CCTAA---CAACTATCATTCTGGATATAGGCCTCAGCAAAGATTT----A 2370
                          v  i---i  --   -   vv  iv v  vi vi    v i   ----i
  L1M4_orf2#LINE/    546 CATAGGNGTAA--ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_234842069_   2371 ATGATGAAGTCTTCAAAAGCAATTGCAACTAAAACAAAAATAGACAAATG 2420
                           -    --- vi        vvv     v   iv         i    v
  L1M4_orf2#LINE/    593 AT-ATGA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_234842069_   2421 GGAC---AT---AATTAAACCAGCCAGCTTCTGCACAGCAAAAGAAACTA 2464
                             ---  ---       ------ i   i  ii vv    i  v    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAA------AACTTTTGTGCTTCAAAGGACACTA 682

  chr1_234842069_   2465 TCAA-AGAGTAAACAGAAAACTTATAGAATGAGAGAAAATATTTGCAAAC 2513
                             - i   i  v   v   ii i      i                 i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_234842069_   2514 TTTGCATCCAACAAAGGTTTAACGTTCAGAATATATAAGAAACT-TAACA 2562
                         iv ii   ii i  i  vi viii i            ii    - v   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_234842069_   2563 AG-CAA-AAT-------CAGACAACCT--CTGAAAAAATATGAGCAAAGG 2601
                          v-   -   -------  i i    i--i ?     ---  i       
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA---TGGGCAAAGG 829

  chr1_234842069_   2602 ACTTGAATAGACACTTCTACAAAGAAGACATACACATGGTCAAAAAAACA 2651
                          i           i    v         i     v    i   v  i-  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CA 878

  chr1_234842069_   2652 AATTTAAAAATGCTCAGCATCACTAATCAT 2681
                         v  vv   i       i     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (145 / 84)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.04 (57 / 28)  


3086 27.32 0.88 0.44  chr1_234916309_234920602.rev     2900  3803 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_234916309_   2900 TGGAAACACATCCCATGCTCATAGATGGGTGGAATCAATATTGTGAAAAT 2949
                               v i        i    i   v  vi  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_234916309_   2950 GACCATACTGCCAAAAGCAGTATATAAGTTCAGTGCAATCCCCATCAAAA 2999
                          i v     v  v   viii v  i ii    ii        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_234916309_   3000 TAC-AGCCATCATTTTTCACAGAATTAGAAAAAAAAATTGTTAAATTCAT 3048
                          v -   iii -     ii     v v  v  ivvi  iv v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_234916309_   3049 ATGAAACCAAAAAAAAAAACCCCAAATAGCCAAGGCAATACTAAGCAAAA 3098
                            i  --- viv  iii    vi         ii    vi i iv  i 
  L1M4_orf2#LINE/    150 ATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_234916309_   3099 AGAA---ATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAG 3145
                             --- vi      vv       v  ii        viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_234916309_   3146 GCCTTTGTCACCAAAACAGCATGGTATTGGTATAAAAATAGGCATATAGA 3195
                           iviv  v i   i    ii     i   i    ii    i        
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_234916309_   3196 CCAATGGAGCAGAATAGAGAACATAGAAATAAAGCCAAATACTTACAGCC 3245
                         i       ii     v    iivi         v   v i i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_234916309_   3246 AAGTGATCTTTGACAAAGCAAACAAAAACATGAAGTGGGGAAAGGACACC 3295
                           v    i  i     i vviv   i v   vv i         i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_234916309_   3296 CTATTCAACAAATGGTGCTGGGATAATTGGCAAGACAC-TGTAGGAGAAT 3344
                           v                    i  i   vv ?v   -  i ii     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_234916309_   3345 GAAACTGGATCCCCATCTCTAACCTTATACAAAAATCAACTCAAGATGGA 3394
                            ii    i   i i   vv   v           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_234916309_   3395 TTAAGGACTTAAACCTAAGACCTAAAACTGTAAAAGTTCTAGAAGATAAC 3444
                          i ?i   i    iv     v        i     v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_234916309_   3445 ATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGACTTCATGACCAA 3494
                           v  ?iv  vi    vv   v    v        v ii   v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_234916309_   3495 GAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGTTGGGACTTAA 3544
                           vv         v v    i    iv   i   i   iv v      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_234916309_   3545 TTAAACTAAAGAGCTTTTGCACAGCAAAAAGAACAGTCAGCAGAGGAAAC 3594
                          i   v v  i i      ii vv    iiiv  vi   iv i  vi  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_234916309_   3595 AGAT---CTACAGAGTGGGAGAAAATCTTCACAATCTGTACGTCTGACAA 3641
                            i--- i     i           v  ii   viii  ii     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_234916309_   3642 ATGACTAATATCCAGAATCTACAATGAACTTAAACAAATCAGTAAGAAAA 3691
                         iv    vi          v  i  v     ivv    v   i   v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_234916309_   3692 AAACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTC 3741
                          i     i  i  v  i?    i     v     iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_234916309_   3742 TCAAAAGAAGATATACAAATGGCCAACAAACATATGGAAAAATAATCAAC 3791
                           v                       i  i  i   i   i  iv     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_234916309_   3792 ATCACTAATGAT 3803
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


1463 29.32 6.44 0.17  chr1_234932792_234934364.rev      493  1082 (491)    L1M4_orf2#LINE/L1      282   908 (0)  

  chr1_234932792_    493 GGA-AAATGCATAAATAAATATACTAAAATAGAGAGATCAGAA-TAGATT 540
                            - i iii   i  v   iv v  i   v     vi     -  i ii
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_234932792_    541 CACATAAATATAATTAACTGCTCTTTGACAAATGAGGAAAGGTAAGTCAT 590
                           i i vv   ii i  i  v i  i     iv v vv   iiv v   v
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_234932792_    591 TGGGTAA----TAGTCTTTTCAATAATTGGTGCAGAAACAGTTGAATATC 636
                             v  ----            i  v      v ii   ii  i   ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_234932792_    637 AATATG-AAAAGAA--AATCTAGACGTAGACTTTACACCTTTCA-AAAAA 682
                         v i   -       --  vi i   vivv  i i     v vi -     
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_234932792_    683 TGAGCTTAGAGTTGATCATAGACCTAAAAGTAAAATGC-AAAACTACAAT 731
                          v i  i i i v     ?         v    i -  -       i  v
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAA 530

  chr1_234932792_    732 ATTTGCAGATGAAAATCTAGGAG--AAT----GTGACCATGGATTTGGTG 775
                          i ivi   v     iv    ? --   ----      v   i  v  ii
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_234932792_    776 GTGAGTTTTTAGATGTAACCTCAAATGCATAATTTATGAAACAAAAAGTT 825
                         i  iv  i      i i  vi    v   i  viv ii   v     i v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_234932792_    826 GATAAATTAGGCTATATTAAAAGTAAATACATCTGCTCTGCTACACACAG 875
                                 i i  vi  i    v    v  v i  iv  v v viv   v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_234932792_    876 TGTTAAGAGAATAAAATCATAAGCTAGATATGGGGAGAGAGTATTTGCAA 925
                          i i    i i i   vv i  v i v v vv      i i         
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_234932792_    926 AACACATACCTGATAAAGAACTTGCATTTGGAATATACGAAGAAACTTTA 975
                          v  i   i       i i     i  iii       ii     vii   
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_234932792_    976 AAACTCAACAAGAAAA---CAAACAACCGAAATTTAAAATGGCCAAA--A 1020
                         v       i  v    ---    i    v  v ?v       v    -- 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_234932792_   1021 TATAAACACACACGTCACCAAAGACG---TGCAGATGGC----------- 1056
                          v i  i v   iv  v       v --- i  i     -----------
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_234932792_   1057 --AAAGGATACCTAACATCATTTGTTAT 1082
                         --   i   i ii       ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (98 / 71)
Gap_init rate = 0.02 (14 / 627), avg. gap size = 2.79 (39 / 14)  


 281 28.67 2.10 6.99  chr1_234993207_234995979      500   642 (2131)    L1M4_orf2#LINE/L1       47   182 (726)  

  chr1_234993207_    500 AGATGTCAATAGTCTCCAAATCAATTTATAAATTCTATGCATTTCCAATC 549
                              v     v  i      ii  i  i i    v i   v i  v   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr1_234993207_    550 AATATACCAACAAAGTTTTTTTTTTCTTCTGTGGAAAATGAT--GGTATT 597
                           v  v   i ---- vii      ----- ii    v   i-- v iv 
  L1M4_orf2#LINE/     97 AAAATCCCAGC----TGCCTTTTTT-----GCAGAAATTGACAAGCTGAT 137

  chr1_234993207_    598 TCTACCATTTACATAGAAGAAAGAAAGGATA-AAAATAGCTAAGAC 642
                         i   vv   i i  i   - viv  i   iv- i      i  i  
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAAC 182

Transitions / transversions = 1.56 (25 / 16)
Gap_init rate = 0.04 (5 / 136), avg. gap size = 2.60 (13 / 5)  

 408 35.51 6.12 2.45  chr1_234993207_234995979      924  1413 (1360)    L1M4_orf2#LINE/L1      179   686 (222)  

  chr1_234993207_    924 AGACAATTTTTAAGAAGGATAA-AAAGTGACAGGACTT----TTCCAACA 968
                          i     i  v  i   i v  -     viv      i----    --  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC--CA 226

  chr1_234993207_    969 AGTTACAGAGAGTTATCTTAAACCCATAGCAATTAATATATTGTGATATT 1018
                          v  -  i - v   iivi   v i i  i   i  v i v    i  i 
  L1M4_orf2#LINE/    227 ATTT-CAAA-ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr1_234993207_   1019 GATATAGTCATTTACAAATAGAGTAAAGGAAAAGAGTAGCACGTCCA--A 1066
                          ii   ivv  vv   v     vi  v    v   i v viv     -- 
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_234993207_   1067 ATG--CTTACTCACATGAGGCAAATTGATGTTTGACTGAGGTAGTAATGC 1114
                           i-- ii iv  iv iv  iv       v  i   vii   ivi  vi 
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_234993207_   1115 -ATGTCAA-AGGGAAAGGA-AGGATGGTCAAGGAATCACACAGAGTTAGT 1161
                         -  -    -i       i -  vv vv    vi   viii v i vi ii
  L1M4_orf2#LINE/    375 CAT-TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_234993207_   1162 TAGA---CCATATGGCAACAAATATAATTATATTCTTACTGTATACCAAA 1208
                          i  ---   i   vv  vi   iv i  iv ii i   ivi i    v 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_234993207_   1209 TACCAAAAT-AATTCCAGGAAGAT-AAAGATATTAAACATGTAA---CTG 1253
                            v     -  i  v iivi   - ?   i-i    --     ---  i
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGAC-CTAAA--TGTAAGAGCTA 520

  chr1_234993207_   1254 AATTTTTACAATTTCAAAAAGAA----TGGGGGAGGATTTCTATATAACA 1299
                           vi v  v  i iiv i     ---- i  ? vii  --  vii i  v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTGACC 568

  chr1_234993207_   1300 TCAG---AGACTAATTGATTTATTAAATAAAATGCAAAAAGCACAAAAAG 1346
                          ii ---  i -   - i   v   i   vi ii v          iv i
  L1M4_orf2#LINE/    569 TTGGGTTAGGC-AAT-GGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_234993207_   1347 TCCAGGACATAATTCACG--TTATATCATATTAAAATGGGAAATTTTTGT 1394
                         ivv i  v v   vv ii--  iv iivi  i     vii   i      
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_234993207_   1395 TTATCAAAAG-TACCATAAA 1413
                         viv     i -i  i  v  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAA 686

Transitions / transversions = 1.46 (102 / 70)
Gap_init rate = 0.05 (24 / 508), avg. gap size = 1.75 (42 / 24)  

 230 23.65 8.37 2.46  chr1_234993207_234995979     2078  2280 (493)    L1M4_orf2#LINE/L1      694   908 (0)  

  chr1_234993207_   2078 AAAAGAAAAA--AAAGAA--AAAGAAAATATTTGCAA--CATATGTGACT 2121
                               v  v-- v    --ii               --     i --  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT--CT 741

  chr1_234993207_   2122 GACAAAGGCTTGGTAACCAGAAAGTCTACACAACCTTTAAAA-TCAAAAA 2170
                           i  i  vi v   v      vi v  v v   ii   v  -    v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_234993207_   2171 GAAAAGAGCCAAA-AATGTAACTAAAAAATAAGCAAAAGAGATGAACCAA 2219
                         v    -  v    -  ivi  i ?      ii     i  vv    i- i
  L1M4_orf2#LINE/    792 TAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT-AG 839

  chr1_234993207_   2220 ACAT-----CAAAGAAGAGGAAGAAATGAC----AAACCTATGATAAAGA 2260
                             -----         viv v     i ----  i vi    -     
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGA 888

  chr1_234993207_   2261 ATTTCAAAACCAGAAATCAG 2280
                         vvi    v i  ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.96 (23 / 24)
Gap_init rate = 0.05 (11 / 215), avg. gap size = 2.00 (22 / 11)  


2833 27.18 1.39 0.46  chr1_235119967_235121819.rev      502  1362 (491)    L1M4_orf2#LINE/L1       40   908 (0)  

  chr1_235119967_    502 ATTGTGAAAATGACCATACTGCCAAAAGCAATCTGCAAATTCAATGTAAT 551
                              v  i   i v     v  v   vii    i  i      i i   
  L1M4_orf2#LINE/     40 ATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

  chr1_235119967_    552 TCCTATCAAAATACCACCATCGTTCTTCACAGAACCAGAAAAAACAATCC 601
                         i           v   v vv v  i  ii     viv  v  ivii    
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr1_235119967_    602 TAAAATTCATATGGAACCAAAAAGGAGCCCACATAGCCAACACAAGACTC 651
                                         viiv  i   v  viv        v    vvi v
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_235119967_    652 AGTAAAAAGAACTAATCTGGGGACCTCACATTACCTGACTT-AAAACTAT 700
                          iv  i      v  vi   i iv      i v  ii i  -      - 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-T 238

  chr1_235119967_    701 ACTACAAGGCCATAGTCATCAAAACACCATGGTACTGGTATGAAAATAGG 750
                                i  i i   v     i   vii         i  i ii    i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_235119967_    751 CACATAGACCAGTAAAACAGGATAGAGAACCCAGAAATAAAGCCGAATTC 800
                           i     i  i ii  i  i  v    ii           v  iv ivi
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_235119967_    801 TCACAGCCAACTGACCTTCAACAAAGCAAACCAAAAC-ATAAAGGGGGGA 849
                          i ii i   i   ii   i    i -ivi    i  -  vv iv     
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGA 387

  chr1_235119967_    850 AAGGACACCCTATTCAACAAATGGTGCTGGACTACTTGGCTAGCCACATG 899
                            i i vi  v                  ivi vi   v  ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_235119967_    900 TAGAAGAATGAAATTGGATCATCATCTCTCAGCTTATACAAAAATAAACT 949
                         i i         i     i vii i   v  v v           v    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_235119967_    950 CAAGATGAATCAAAGACTTAAATCTAAGACCTGAAACCATAAAGATTCTA 999
                            i   i    ?    i     v     v  i    i     iv ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_235119967_   1000 GAAGATAACATTGGA--AAATCCCTTCTAGACATTGGCTTCGGCAAAAAC 1047
                              v     v  ?--     --   vv   v    v  v     viii
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_235119967_   1048 TTCATGACCGAGAACCCAAAAGCAAATGCAACACAAAGATAAATAGATG- 1096
                            v iiviiv  vv         v v      v  ii v        i-
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_235119967_   1097 ---GGACTTAATTAAACTAAAAAGCTTCTGTACAGCAGAAGAAA-TAGCA 1142
                         ---      v  i   v v    i   i   i vv  i i  v -  v  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_235119967_   1143 G---AGTTAGCAAACAACCCACAGAGTGGTAGAAAATATTCACAATCTAT 1189
                         i---   v iv i            i   v          ii   vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_235119967_   1190 ATATCCAACAAAGGACTAATACCAAGAATCCACAAGGAACTCAAACAAAT 1239
                              ii i  i     vi  i v     vi i  i      vv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_235119967_   1240 CAGCAAGAAAAAAACAAACAATTCCATCAAAAAGTGGACTAAGGACATAA 1289
                           ii  v     i     i  ii v  i?    i   i v     iv i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_235119967_   1290 ATAGACAATTCTCAAAAGAAGGCATACAAATGGCCAACAAGCATATGGAA 1339
                                v     v       ii              i     i   i  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_235119967_   1340 AAATGCTCAGTATCACTAATTAT 1362
                          i       ii    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.01 (9 / 869), avg. gap size = 1.78 (16 / 9)  


1598 27.15 2.50 2.96  chr1_235127473_235129080      500  1140 (468)    L1M4_orf2#LINE/L1      271   908 (0)  

  chr1_235127473_    500 TATTGGCAAAAGTTTAGACACATAGATCAATGGAACAAAACAGAAAGCCT 549
                           i     v   vv      i              i i  iv  i  i i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_235127473_    550 AGAGATAAACCCAAACAAGCATAATCAATTTATTTCTGACAAAGATTTAA 599
                            i         v   vvi  ii      v    ii     i i viv 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_235127473_    600 AAGAAATTTAATATAGAAAAGA-AATCTTT-CAACGAATGGTTCTTGAAC 647
                          iivv   i   ivi    ii - i     -    i      v  v i  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_235127473_    648 AACTGGACATCTATATGCAAAAAAATGAAACTCAACACATATTTTATGCC 697
                                i ? i i        i      ii vi  v v  ii i ii  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr1_235127473_    698 TTATACAATAACGAACAGAAAATGGATCATAGGCCTACATGAAAAACACA 747
                         v       v  iv   vv           ?  i    v   v  i -i v
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCT 519

  chr1_235127473_    748 AAAACTATAAAACTTATTTGA-GAAAACAGAAG---AAACGTTATTCA-- 791
                                       i-  v  -       v i ---   --- v   i--
  L1M4_orf2#LINE/    520 AAAACTATAAAACTC-TTAGAAGAAAACATAGGNGTAAA---TCTTCGTG 565

  chr1_235127473_    792 ACAATGAGTTTGGTGATGACTTTTTCAATACAAAACCAAATACATCATTC 841
                           vv  i   v  ii   ii  i  vi   ii v      vi  iv viv
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr1_235127473_    842 GTAAATGAATA--TTAATAAATTTGACTTTAGAAAAATTAAAAACTATTA 889
                         ii   v   v -- vi       v     i vv             v  i
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr1_235127473_    890 CTTTGCGAAAGAGACTGTTAAGACAAAAAAAGGACG--TTAAAGGTTAGG 937
                         ivi v i  i  v   i i    v ivi   i   i--ii v  iv i  
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr1_235127473_    938 AGAAA-TCCTTGCAAACCACATATCTGATGAAGGACTTGTATTGGGAATA 986
                              - vi       i  i         i i          ivi     
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_235127473_    987 CATTTAAAGAAACCATTTAAAACTCAAAATTAAGAAAATGAACAGCCCAA 1036
                         i  --      -- vi   v       v v   i  i ii  i i     
  L1M4_orf2#LINE/    766 TAT--AAAGAA--CTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_235127473_   1037 TT-AAAAATAGACAAAATAAATT--AACAGACACCTCATTAAAGAAGACA 1083
                           -      i i    i--i   --  i     ii  vii        i 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAG--GATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr1_235127473_   1084 TATTTAGGGAAAATAAGCATATGAGCATATTAACATATGATCTACATCAT 1133
                           i-------    iiv  -  i    i  v  v v   v  v      ?
  L1M4_orf2#LINE/    860 TAC-------AAATGGCCA-ATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_235127473_   1134 AGAGCTT 1140
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.65 (107 / 65)
Gap_init rate = 0.03 (18 / 638), avg. gap size = 1.94 (35 / 18)  

 364 28.40 9.47 1.18  chr1_235127473_235129080     1147  1315 (293)  C L1M4_orf2#LINE/L1   (427)   481   299  

C chr1_235127473_   1315 AATGGAACAAAACAGAAAGCCCA--AACAAGC----------ATCATCAG 1278
                                i i  iv  i  i   --  i  i ----------  vi   i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

C chr1_235127473_   1277 TTGATGTTTGACAAAGATTTAAAAGAAATGTAATGGAAAAAAGA-AATCT 1229
                              v  i     i i viv  iivv  vi     ii   ii - i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

C chr1_235127473_   1228 TTTCAACAAATGTTTCTTGAACAATTG-ATATCTATATGCAAAA-AGTGA 1181
                                     v v  v i    i  -   ? i i        - i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

C chr1_235127473_   1180 ACCTCAACACATATACCTTATATAATA-ACAAAAA 1147
                          vi vi  v v  --   i i iv   -       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTA--CCTCACACCATATACAAAAA 481

Transitions / transversions = 1.94 (31 / 16)
Gap_init rate = 0.04 (7 / 183), avg. gap size = 2.57 (18 / 7)  


2672 27.68 2.68 1.34  chr1_235169781_235176469     5315  6210 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_235169781_   5315 TAGAAGAACATTTTATGCTTCTGGATAGAAAGAATCAATATGACTAAAAT 5364
                          i   ii i  iii   i iv     v i    v i     vii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_235169781_   5365 GACCACACTCCACAAACCAATTTACAGATTCAATGCTATTCTTATCAAAC 5414
                          i v i     v    iii  i           i  v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_235169781_   5415 TACCAATGACATGTTTCATAGAACTAGAAAAAAAATCT-ATGCTAAAATT 5463
                          v   iivi v v   iii    v v  v  i----  -  v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chr1_235169781_   5464 CATATGGTACCATATAAGC-ACCCA-AATATCCAAGACAATCATAAGCAA 5511
                                v --  ii   v-     -    v    i      v i iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_235169781_   5512 AAAGAAAAAAAGCTGGAGGAACCACATTGCCCAACTTCAAACTGTGCTGC 5561
                         i     v   - i       vi    i v     i      viv i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_235169781_   5562 AAGGCTACGGTATCCAAAACAGCATGGTACTGGTACAAAAACAGACACAT 5611
                           i     i   vi   i    ii         i i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_235169781_   5612 AGAGCAATGGAACAGGGTAGAGAGTCCAGAAATAGAGCCTCAGACCTACA 5661
                            v        i  ii v               i v  vi v ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_235169781_   5662 ACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAAAAAGAC 5711
                         ii  vi    i  i     ivv  v   i v  vv       i   ii i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_235169781_   5712 TGCCTGTTCAATAAATGCAG-TGGGATAACTGTCTAGCTATATGCAGAAG 5760
                         v i  v     i     vv -     i     vv  ? i i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_235169781_   5761 ATTCAAACTGGAGCCTTTCCTTTCACCATACCCCAAAAACAACTCAAGAT 5810
                          v v  ii    v  i v   iv       iv v    vi       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_235169781_   5811 GGATTAAAGACCTAAATGTAAAACCCAAAGCTATAAAAATCCTGAAAAGT 5860
                             i ?              i v i   i        v  i ii  iiv
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_235169781_   5861 AACCTAGGA-TATACCATTTTTGACATAGAAACTT--GCAAAGATTTTGT 5907
                            v    ?-  v i -  iv    v v ii--  --    v i   iv 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGG--TTAGGCAATGGTTTCTT 590

  chr1_235169781_   5908 GACAAAGATGCCAAAAGCAATTGCAACAGAAGCAAAACTTGACAAATGGG 5957
                         iivv v  ii         vvv      i   v    v v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_235169781_   5958 ACCTCATTAGAG-----AGCTTCTGCACAGCAAAAGAAACTATCAACAGA 6002
                           i    i i i----- i   i  ii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_235169781_   6003 GTAAAATAGCAACCAAAATAATGGGAGAAAATACTTACAAACTATATATC 6052
                           i   vii     v v v              i  i    ii       
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_235169781_   6053 CTACAAGGGTCTAATATCCAGCATCTACAAGGCACT--TA-AAC------ 6093
                         iv i     v  vi       v  v  i  i v   --  -   ------
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_235169781_   6094 ATACAAGAAAAAAAAAC---ATTAAAAAGTGGGCCGAGGACATGAACAGA 6140
                            v  ii v   v   ---   ?    i     vi    iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_235169781_   6141 CATTTTTCAGAAGAAGACAGACATGCGGACAATAAGCACATTAAAAAAAC 6190
                              i  vi       i v   vii  v            v    i --
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-- 888

  chr1_235169781_   6191 CACTCAATATCGCTGATTAT 6210
                         ii     i   i????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


2561 24.58 9.62 1.78  chr1_235182907_235185200      966  1807 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_235182907_    966 TGGAAAAATACTCCATGTTCATGTTTTGGAAGACTTAATATTGTTAAC-T 1014
                               i   ii           vv                      v- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_235182907_   1015 GTTCATACAACCCAGAACAATCTGCAGATTCAATACAGTTCCTACCAAAA 1064
                          viv    vv    i vii    i         ii  i i    i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_235182907_   1065 TACCAA-TGTTATTTTTACAGAAATAAAAAAATAAAATTTTAAAATTCAT 1113
                          v   i-  iiv     i       vi v  iivi - ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_235182907_   1114 ATGATGAAA--AAAAGGACCCTGAATAGACAAAACAATATTGAGAAAGAA 1161
                            --    --v  i      v      v         v    i      
  L1M4_orf2#LINE/    150 ATG--GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_235182907_   1162 AAATATGCCTGGAGGTATCACACTTTGTTATTTAAAAATATATTACAAAG 1211
                         i  i vivi      vv        iviv    v    iv  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_235182907_   1212 CTACAGTAATTAAAACAG---GATAC--------AGACAGATATATAGAC 1250
                                   i  i    --- i   --------i  i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_235182907_   1251 CAATGGGATACAATAAAGAGCCTAGAAATAAATGCGCACATATAGGGTCA 1300
                               i   v   vi    i i         iv ii    v  v     
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_235182907_   1301 ACTCATGTTCAGCAAGAGTGCCAAAAATACACAATGGGGGCAGGATAGTT 1350
                          i v  v   ii    i       i vi iv        iv  i     i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_235182907_   1351 TCTTCAACAAATGGTATCGGAAAAAACTGAATATTCACCTTCGAAAGAAT 1400
                          i             iii  i v  -   i   ?i   v v i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAAT 446

  chr1_235182907_   1401 CAGGT---ACTCTTACCTTCTGCTACACACAATAAACAATACAAAATAGA 1447
                         v i  ---  i i     ivii i i i    v  vi  iv      i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_235182907_   1448 CTAAAGACTTAAATACAAGGCCTGAAACTATGAAATTCCTAGAAAAAA-- 1495
                         ii ?    i     ii   iv  i       i   i  i     i   --
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_235182907_   1496 -TGGGGGAAAATCTTCATGACATTGGTCTTGATAATAATTTTATAGAAAT 1544
                         - i  ? v        i    v    vi v ii   ii   iv    v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_235182907_   1545 AATATAGCTTTCATAGACAAGCTAAGGCAACATAAGCCAAGACAGACAAA 1594
                         i i i------  --- -    vv i      v   vv  i i   i   
  L1M4_orf2#LINE/    597 GACAC------CA---A-AAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_235182907_   1595 TGGCAGTACATCA-----------------GTCTAAAA-------ATC-- 1618
                          v v v v     ----------------- ii v   -------   --
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_235182907_   1619 -----TG-----------CACAGG-------------TCTGCAAACCACA 1639
                         -----  -----------     i------------- i      i  i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_235182907_   1640 TATTTAGGAAGGGGTTAATTTCCA-AATGTATAAGAAACTCCTATAACTC 1688
                            i iiv     ii vi v    -   i     ii     i  i     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_235182907_   1689 AATATCTACAAA---AAACAACCCAGTT-AAAAATGGACTAAGTAGTTTA 1734
                             -v  v   ---   i      i  -        i v   v v  v 
  L1M4_orf2#LINE/    787 AATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_235182907_   1735 ATAGACATTTCTTCAAAGAAAACCTACAAATGGCAAACAGGTACAAGAAA 1784
                                     i       i iv          v  i i i   v    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_235182907_   1785 AGATGCTCATGTTCACTAACCCT 1807
                                  vvv   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (129 / 75)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.36 (96 / 22)  


1830 26.23 10.35 1.56  chr1_235194731_235196577.rev      530  1360 (487)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr1_235194731_    530 AAGATA---CATAGTCATGTATTCAAAGGCT-AATCCTTGTTAA-----T 570
                               ---   iv     v   vi   i  -   v-       -----i
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATA-TTGTTAAGATGGC 53

  chr1_235194731_    571 TATGCTCTCCAATTTCATC-A-AGATTCTGTGCAACCCAAATGAAAACTC 618
                         v  i   i    v  v   - -      vii    i  vv  v    ii 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_235194731_    619 CATCATGC--TTTTTGTAGATATTGACAA-CTATATTTTAAAATTTGTAT 665
                           v -   --      i   v        -  i-  ii       ii   
  L1M4_orf2#LINE/    104 CAGC-TGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCATAT 151

  chr1_235194731_    666 GAAAAAGTAAGTGAACTAGAAAAGCTAAA-TAAT-TTGAAAATGGAAAAA 713
                          i   v i   v  v i    v   i   -i   -       -i   i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA-AGAAGAA 200

  chr1_235194731_    714 TGAAGATGGAGGATTCTCCTATCTTCATTTCAAGACTTAACATAAAGCTA 763
                         ii   v       i  v viv  iiv       i     vi i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_235194731_    764 CAGTAATCAAGAAGGCATAGTACTGGTGGAAAGATAGATATATAGAT-AA 812
                                     vi ii i       iiv  i      i        -  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_235194731_    813 T---ATA--------AGGCTAGAAATAGATCTGAGGAAATACAGTCTACT 851
                          ---   --------  v i       i i iiviv vv  ii   v i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_235194731_    852 GATTTTTTACAAAGACGCAAAGATAACTAAACAG--AATGGACAAGCTTT 899
                               iv    i ii  v    iv i v  ii --  v i i iv    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_235194731_    900 TGAACAA-CAGTACTAGAAAAA---AAAATCCA--TG-----GTATA--- 935
                          v     -ii  i  i i v  ---i v ?   --  ----- v  i---
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_235194731_    936 ---------TATTTTACACAAAAAATGAAAAT---CTGAAAATGGATCAT 973
                         ---------  ii i    v v v ii     ---  v           ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_235194731_    974 AGATGAAATTGTGAAATATAAAA-TATAAAACTTCTGAAAGAGAA----- 1017
                            ivv  v   i i vv     -         ii ii    i  -----
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_235194731_   1018 -----AATCTACATGACTTTGGATGTAGCAACAAGGTTT--TAATTATGA 1060
                         -----     v i    i    i vvi    i--     --  iv     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAAT--GGTTTCTTAGATATGA 598

  chr1_235194731_   1061 CATCAATA-TACCATCCATGAAAGAAACAAAAATTGATAAATAGGATTT- 1108
                           i   v -i  v v v ii       ---    v       v   i  -
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAA---AAATAGATAAATTGGACTTC 645

  chr1_235194731_   1109 ATAAACAATGACATCTTCTGCCTTGCAAAAGAC--TGTTAAGAGAATAAG 1156
                           v  v v i v v   i  ivi v    i   -- i i    i i i i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_235194731_   1157 TGCACAATCAACAGATATGG-AGAAA-TATCTTCAAAT--TATACCTGAT 1202
                         viv    i v     -    -     -   i v     --    i     
  L1M4_orf2#LINE/    696 AAGACAACCCACAGA-ATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_235194731_   1203 AAAAGCCTTATATCTGGATTGCATAAAGAATTCTTAAATCTGAACAATAA 1252
                           ii v   i    ii  v ii        i     v v  v  i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_235194731_   1253 AACAAAAACAAGCAACCCAAT--AAAAATAGGCAAAAGAT------AGAT 1294
                           --- i    ii        --      i      i   ------   i
  L1M4_orf2#LINE/    795 AA---AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_235194731_   1295 ACTTCATAAGAGAAGATATGCAGATT-CCAATACGTTTATAAAATGATTC 1343
                          i   viv i         i  i  v-      v ivi  i   v   v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_235194731_   1344 CCAACTTTATTAGGCAT 1360
                         i    v i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (132 / 84)
Gap_init rate = 0.04 (39 / 904), avg. gap size = 2.54 (99 / 39)  


1957 24.08 4.08 4.59  chr1_235262900_235264672.rev      502  1286 (487)    L1M4_orf2#LINE/L1      128   908 (0)  

  chr1_235262900_    502 ACAAGGTGATTCCAAAATTTATATGCAAACGCAATGGACCTAGAATAGCA 551
                              v    i i      i     v   i    v     i        v
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr1_235262900_    552 AAAATAATTTTGAAATAAAACTAAATATACAATTAATAGATAATATACTT 601
                             i   i      -  i -- i - i v i  iivi  iv-i i    
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAA-AAGA--AGA-ACAAAGTTGGAGGACT-CACACTT 222

  chr1_235262900_    602 ---AATTATATA-CTTACTACAAAGGTACAATAATCAAAATAATGTATTT 647
                         ---    vi v -            v    i       i i i   iv v
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr1_235262900_    648 TCAGGA-AAGGGTAGATATTAATATATAGATCAATGGAAAGGAAT--AGA 694
                         iii v -    i    i  ------              vi    --   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACAT------ATAGATCAATGGAATAGAATTGAGA 316

  chr1_235262900_    695 GTCCAGATGTAAACCTCACATATATATGGTTTGGTCCATTCATTGTT-AC 743
                                vi      -  i i  v      ----- v   v   v i-  
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACC-CATACATTTATGGT-----CAATTGATTTTCGAC 360

  chr1_235262900_    744 AAAG-TGACAAAGTGAATAAATTGGGTAAAGAGAGTCTTTTTAACCATTG 792
                           i -  v   iiiv v v   v   v  ii v        i   v v  
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr1_235262900_    793 GTGCCAGACTATTTGGAAGTTCAAATGCAAAATAAATAATAATGATAATA 842
                             ii ivi vi    vi?i  v        v  -------   -----
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-------TGA----- 448

  chr1_235262900_    843 ATTTTGACTATTACTACACAT-ATCATATAAAAAT-AATTTGAAATGAAT 890
                          v  v   ivi   iv    i-  -   i      -  i ii     i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCAT-ATACAAAAATTAACTCAAAATGGAT 497

  chr1_235262900_    891 TA-AAACCTAAATGCAAGAGCTAAAACTGTAA--TTCTTACAGAAGGAAA 937
                         i - i         i             i   --i     --    i   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA--GAAGAAAA 545

  chr1_235262900_    938 TGTAGAAGAGTATCTGTGTGATCTTGGCATTAGCAAATAGATCCTCTTA- 986
                         ii   i? viv    vi    i     -i    vv   i v --     -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTT--TCTTAG 592

  chr1_235262900_    987 ATAT-ATA--AAAATTCCAAATAATAAAAGAAAAAAT-GATAAATTTGAC 1032
                             - i --    viv   ii  i            -        v   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_235262900_   1033 TTTATCAAAATCAAAATCTTCTGTTCTTACAAA--ATGTTGTTAAGAAAA 1080
                           i        i    v   i   v   -    -- iii i i      i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTT-CAAAGGACACTATCAAGAAAG 691

  chr1_235262900_   1081 TGAACAGCTAAGCCCCATATTTGAAGTCAATATTTGTGAAATATATATTT 1130
                             v  vi  v  v  v v v i  vv        ii  vi      i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_235262900_   1131 TATAACATATTTGTATCTGAAATATGTAAAGAACCCTTACTACTCAATAA 1180
                         v    viv i       iii     i        i     v         
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_235262900_   1181 TAAAA-GACAAG----CCAATTTTTA--TGAG----ATATTTGGCCAGAT 1219
                              -     i----      ?vv --  i ----iv     ivi   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_235262900_   1220 AGTTTATCAAATCAGAAATGCAAATTGGCAATAAGCATAGGAAAATATTC 1269
                          v  ivi    vv   v  i     v v         i v     v  v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_235262900_   1270 TTAACCTTATTAGCCAT 1286
                          i   v i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (109 / 77)
Gap_init rate = 0.04 (33 / 781), avg. gap size = 2.06 (68 / 33)  


 657 24.51 3.43 1.47  chr1_235291975_235294362      677   880 (1508)    L1M4_orf2#LINE/L1        2   209 (699)  

  chr1_235291975_    677 GGAAGTATACTCCAT--TCATGCATTTGGAAAGTCAACATTATTAAGATG 724
                             iv   ii    --     v   v i i v i  i   i        
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_235291975_    725 TGGATTATTGTCCAAACTGAACTATAGATTCAATGCAATAACAATCAAAT 774
                         - v v  i vi     i   v   i        i     vv v      v
  L1M4_orf2#LINE/     52 -GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_235291975_    775 TCCCAGATTGC--TTTGGGTAGAAATAAACAAACTCATTTTAAAATTAAT 822
                               -i   --   vv i      vi    i  v  ii       v  
  L1M4_orf2#LINE/    101 TCCCAG-CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_235291975_    823 GTAAAAATGCAAGAGACCTAAAATAGAGAAAAACAAATCTGAAAAAGTAA 872
                         i ii         i    i i     vv    -   vii        v i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAG 198

  chr1_235291975_    873 AA---AATTGG 880
                           --- i    
  L1M4_orf2#LINE/    199 AACAAAGTTGG 209

Transitions / transversions = 1.38 (29 / 21)
Gap_init rate = 0.03 (6 / 208), avg. gap size = 1.67 (10 / 6)  

1324 23.90 6.59 7.83  chr1_235291975_235294362     1171  1898 (490)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr1_235291975_   1171 AAAAAAAAGAA-AAAGTAAAAAATGTAGA--TCATCACCAGTTGACTTTG 1217
                              i     -     ------  v  i--   -   ivviii i  ii
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGT------TGGAGGACTCA-CACTTCCCAATTTCA 232

  chr1_235291975_   1218 ATACTTACATTAAAGTTATCATAATCAAGCAAGTAAGTTACATGAGCTTT 1267
                          v      vvi    i  ivi        vv   iv v   -------- 
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC--------T 274

  chr1_235291975_   1268 AATGTAAGTATTAAAATCATAAAAATAAATAGATAAGTGGTACAGAATAT 1317
                         iiii    v  ----------- i i v      v i   v i     - 
  L1M4_orf2#LINE/    275 GGCATAAGGAT-----------AGACATATAGATCAATGGAATAGAAT-T 312

  chr1_235291975_   1318 GAGAATTCAGAAATAGAGCCATTCAAGCAT--TC---TAGTATTTGACAG 1362
                             i i        i v    v  vvi  --  --- ii v  i    i
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr1_235291975_   1363 AGGTTTCAGGAA-ATTAAATGGAGACAGGATAATGTTTTCAAGAAATTGT 1411
                         i   vi  i  v-   v     i  v  i   i v       v    v  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr1_235291975_   1412 GTTGTAACTATTGGATATACATATACCACATACATATACCACACAAAAAA 1461
                          i  vi  v i      ?-------      i  ----------   i  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAK-------CCACATGCA----------AAAGAA 445

  chr1_235291975_   1462 TAATATTTTTTGGCTCCTGCCTTTAACCATATATAAAAATTACC-----A 1506
                          i vi  v--- i i   i   ivv        i        v ----- 
  L1M4_orf2#LINE/    446 TGAAGTTG---GACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_235291975_   1507 TGAAT---AGACCTAAATGTAGTTGATGAAACTATAAACTTCTCAAAGAA 1553
                           i  ---             ivv v i          vi   i i ii 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_235291975_   1554 AAACATAAAAGGAAATCTTAGTGACTTTGGAATTTGGCAA-GATTTATTA 1602
                                ii? v       v     i    i-  v     - i   v   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTA 591

  chr1_235291975_   1603 AATAAGGCTTAAACATCACACACTACAAAAGGAATATAATCAGTAAAACG 1652
                         i   v i viv  v v    vi v       i  - -   vii    vi 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAA-A-AATAGATAAATTG 639

  chr1_235291975_   1653 CCTTTC-TCAAAATAAAAAAGTTATAT---TTAGAGTACAGTAATAAGAA 1698
                         vvi   -       v     v  v i --- i i  v   v  vi     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_235291975_   1699 A------AGGCAATGCACAAAATGGGAGAAAATATGTAAAAAT-ATAAAT 1741
                          ------  i   iv    i               v iv    -   v  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_235291975_   1742 CTGACAAAGGGCCTTTCTCTAGAATATATGAAGAACATCTTATATAACTC 1791
                             i  i  i i v v  i         i      -     i --    
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAAC-TCTTACA--ACTC 786

  chr1_235291975_   1792 AAGAATAGAAAGAT---TAACC-AATATTAAAAATTAATAAA-------- 1829
                           v    i     i---     -   - ?      viii   --------
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGA 835

  chr1_235291975_   1830 ATAA------CTCAGAAAAATGAGACATACAG-TGGCAAATAAGTACATA 1872
                            i------   vi  i  ---  i     i-    v      i    i
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAA---GATATACAAATGGCCAATAAGCACATG 882

  chr1_235291975_   1873 AAAATATCCTTAACAAAATTAATTAC 1898
                             v  v  i    vv ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (98 / 73)
Gap_init rate = 0.04 (32 / 719), avg. gap size = 3.28 (105 / 32)  


2065 26.47 3.15 2.49  chr1_235310489_235312216      475  1237 (491)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_235310489_    475 AAGACTCATATAATTTAAAAATTTGGCAAAAGACCCAAAATAGCCAATAC 524
                           i i      ii-----    ---    ii      i         v  
  L1M4_orf2#LINE/    141 AAAATTCATATGG-----AAAT---GCAAGGGACCCAGAATAGCCAAAAC 182

  chr1_235310489_    525 TGCCTTGAAGGAGAAAAACAAAGTTAGAAGAATAACA-TTCCTGACTTCA 573
                         vii      ii    i         i  i  v v   -    ii i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr1_235310489_    574 AGACTTACTATTA-GCTACAGTAATTAAGACAGTATGGTACTGGTGGAAA 622
                          i        iv -           i        i         iiv  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_235310489_    623 AAAACGGCAAATAGATCAACCGATATGGAATAGACACTCCAGAAATAGAT 672
                         i v - i  v         iv  -  i    v  v v          i i
  L1M4_orf2#LINE/    283 GATA-GACATATAGATCAATGGA-ATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_235310489_    673 CCA--CATCAATATTGCAACTGATCTTTGACAAAGTAGCAAAGGCAATAC 720
                            --   iv  iv -   i    i  i     i vv  v   i v  v 
  L1M4_orf2#LINE/    331 CCATACATTTATGGT-CAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_235310489_    721 AATGGAAAAAATATAGACTTTTTCAAGAAATTATGCCAGGACAGCTAGAT 770
                              ii   iv    v     -   v    vi   ii     i  i   
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_235310489_    771 ATCTATAGGGAAAAAAAAAAAAAAGAATGTAGACCTTA-ATCTTTCACAA 819
                          ? i i v v    i  vi  ivv i ivivv    i - i v vi    
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr1_235310489_    820 AAATTGATGCAAAATGGATCGTAGACC-AAATGTAAAATACAAAACAAAA 868
                              i iv           i?     -        i vvi     v v 
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr1_235310489_    869 AAACTCTTTAAA--ATATATAGGAGGAAATTTAGAAGACCTTAGGTATGG 916
                                 vi  -- v i     ? v    i vviv      i   vv  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr1_235310489_    917 TAATGACTTCTGAGATACAACACCAAAAGCATGATTCAT----GAAATAA 962
                         i    ii    v     ii            ii viv i----    v  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_235310489_    963 TTGATAAACTAGAAGACTTCATTATAATAAAAAATTTCTGCTCTAAGAAA 1012
                          v      i i  ---      i v   v     i  i  iv  vvi  i
  L1M4_orf2#LINE/    629 TAGATAAATTGGA---CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_235310489_   1013 GACACTGTCAAGAGAATGAGAAGACAAGCCACAGATCAGAAGAAAATATT 1062
                               i      i i   i       v       vii i          
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_235310489_   1063 TCAAAAGCATAT--CAAATAAAGTACTGTTATTTAAAATACACAAT---T 1107
                          vv   v     -- vi    i v   vv   ii i    i i  v---i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr1_235310489_   1108 TTTTAAAAATGTGCAACAAGAAAACAAATGAAGAAAACAATGAAAAAGGG 1157
                          i   v  v vvii  i  i  i      ----  vv    v?    iv 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAAT----AACCCAATTWAAAAATG 821

  chr1_235310489_   1158 AGCAACAAATCTGAA----CGCCTCATCAAAGA---TATACAGATGATAA 1200
                         i    vii  i    ---- iii  vi      ---      i   iiv 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_235310489_   1201 ATAGGCATATGAAAAGATCCTCAACATTGTCATTAAG 1237
                            i   i          v        ii????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (120 / 78)
Gap_init rate = 0.02 (19 / 768), avg. gap size = 2.26 (43 / 19)  


2815 26.64 2.00 1.22  chr1_235362465_235365551.rev     1695  2595 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_235362465_   1695 TGGAAACACATTTCTTGCTCATGGATAGGAAGAATCAATATTATGAAAAT 1744
                               v i  ii v  i        v      v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_235362465_   1745 GACCATGCTTCTCAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 1794
                          i v  i  i i    vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_235362465_   1795 TACCAGCACTATTTTTCATAGAATTAGA-AAATCAATCCGAAAATTTATA 1843
                          v     vviv     iii    v v  -  iiii    v      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_235362465_   1844 TAGAATTTAAAAAGAGCCCAAATAATATATGCAATCCTAAGCAACAAGAA 1893
                          i   v vv  ii  v  vi    iivv vi     i i iv  v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_235362465_   1894 CAAATCTGGAGGCATCACATTAACCAAATTTGAATTATACTATAAGGCTA 1943
                             vi      vv     i vv    v  ii  viv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_235362465_   1944 CAGTTATGAAAATAACATGGTATTTGTATGAAAGTAGGCACATAGACCAA 1993
                             v  v  i i iii     i v i  i iii   i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_235362465_   1994 TGGAAGAGAACAGGTAACCCAGAAATCAAGCCAAATACTTAACGACCAGC 2043
                              v    iv iv ii        v  v   v i i   -i ii  ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAAT 349

  chr1_235362465_   2044 TGATCTTTGACAAAGCATACAAAAAC-ATACATTGGGGAAATGAC-GCCT 2091
                             i  i     i -i i v  i  -  v  v        vi i- i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_235362465_   2092 TATTTAATAAATAGTGCCGGGAAAAGTGGCTAGCCACATGCAGAAGAATG 2141
                          -  i  i    i    i    v  v   v  ?         i       
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_235362465_   2142 AAACTGGATCCCTATCTCTCATGTTATATTCAAATAAACTCAAGATAGAT 2191
                           ii    i     i   v  ivv    ivv    v       i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_235362465_   2192 CCAAAACTTAAGTATAAGACCTGAAACCATAACAATTCT-AGAAGATAAT 2240
                          v? i  i   i i     v  i    i    -  i   -      v  i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAAC 546

  chr1_235362465_   2241 CT---TGTAAAAACTCTTCTAGAGATTGGCCTAGAAAAAGAATTCATAAC 2287
                         v ---?     ---     vv  vv    vi   iv  v iv   v  iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_235362465_   2288 CAAAACCCCAAAAACA-ATGTGACAAAAACAAAAGTAAATAAATGGGACC 2336
                         i vi  v      i  - v ii      iv    i  i      v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_235362465_   2337 TACCTAATTAAACTAAAAA-----GCACAGCAAAAGAAATTATCAC---A 2378
                          - v v --   i      ----- ii vv    i  v i     v--- 
  L1M4_orf2#LINE/    644 T-CATCA--AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_235362465_   2379 GTAAAAAGACAACCCACAGAGTTGGAGAAAATATTCGTGAATTATGAATC 2428
                           i                 i v            i ii   i  iv   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_235362465_   2429 CGTAAAAGGACTAGTATCCAGAATTTGCAAGGAACTCAGACAAGCCTGTA 2478
                         i vv  i     v           v ii  i      vv    vi vi  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_235362465_   2479 AGAAAGAAAACAAATAACCCCATCAAAAAGTGGGCAAATGACATAAGTAG 2528
                          v   -  i           v  i?    i        v  iv i i   
  L1M4_orf2#LINE/    791 ATAAA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_235362465_   2529 ACCTTTCTCAAAAGAAGATATACAAGTGGCCAAAAA--AGATGAAAAAAT 2576
                           v      v               i       v  -- v       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_235362465_   2577 ACTCAACATCACTAATCAT 2595
                         i          ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.71 (29 / 17)  


1563 27.12 10.51 3.58  chr1_235406599_235408513      615  1451 (464)    L1M4_orf2#LINE/L1        1   895 (13)  

  chr1_235406599_    615 TAGAGATATATAGCATGCTTCTAGTTTGGAAAA--------TGTTAGGAT 656
                          i  i v    vv    i iv i v      i --------     i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_235406599_    657 ATCATTTGTCCCTCTATTTATGTATGGATTCGATGCAATTCCAATCAAAA 706
                         iv  v vv    ivv   v  v  ii     i i     i  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_235406599_    707 TCCCAGTAGTATTTTTT----AAAT-GATAAATTGGCCTTAAA--TAATA 749
                               iv iv      ----    -  i  ii  ii i    -- v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_235406599_    750 TGTACGGATATAAAGGACATAAAATAGCCAAAACAATTTTGCAACAGTAA 799
                           v --i  ii  i    vi i               i   v  v  v i
  L1M4_orf2#LINE/    151 TGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_235406599_    800 AACAAGTTTAGAAACATTAGCCTTATACTACCTTATATCAGAATTTA--A 847
                              iv  i  i------ v  i i   v  iv  v   i  i   -- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAG------GACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_235406599_    848 CAAA-CTACAGTAATAAAGGCAG-------CT------AGGTT-----TC 878
                             -          v   i   -------  ------   v ----- v
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_235406599_    879 TAATATCAATGGATTAGAAT---AAATCTAAAATGTGAACC-AGACATAC 924
                           i-         v      ---i i  i i  -i i    - v    vi
  L1M4_orf2#LINE/    293 TAG-ATCAATGGAATAGAATTGAGAGTCCAGAA-ATAAACCCATACATTT 340

  chr1_235406599_    925 ATGGATGATTGATTTTTAACAAAGGTGTCATCAGAGTAACTCAATGGAGA 974
                             vii         ii    i    i  --   vi -i       i  
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCA--AGACCA-TTCAATGGGGA 387

  chr1_235406599_    975 AACAAAAGCTTTCCCAACAAATTGTGCCAGAACAACTGGATATC-ATTTG 1023
                           v  v  ii  ii        v    ii i           ? - iv  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_235406599_   1024 GGAGGAAACAAGTGAAGTACTATTTTTTCCTTCACGTCATACCAAAAAAA 1073
                         v----   vi i      vvv ------  iii  v   i    v v v 
  L1M4_orf2#LINE/    438 C----AAAAGAATGAAGTTGGA------CCCCTACCTCACACCATATACA 477

  chr1_235406599_   1074 AAAAAAAACTAAACTAAAAGTAGATCTTAAAACTAAACCTAAAATATATA 1123
                             ----- v    v   i i    v? i v     iv   i vv  v 
  L1M4_orf2#LINE/    478 AAAA-----TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_235406599_   1124 TCAATAAAGCAATTAGATGGAAATATAGGGG-ATATTTTTA-AAATTTGA 1171
                         v v     i vv     v i   i     ? - v  i  ii-i vi   i
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_235406599_   1172 GATGGGTAGAGACATCTTAGTTG-GACACTAAAAG-----G-AACAGAA- 1213
                          v i  i iv iiv      v i-     i     ----- -    i  -
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_235406599_   1214 -----ATA-ATAAATTACACTTTATCAATAATAATAACTTTT------CA 1251
                         -----   -       iv    i     v v   v       ------  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr1_235406599_   1252 AGAG-------CAA-AATGTAAACAGGCATGCTACAGAA-AGGAGAAGAT 1292
                          ii -------   -  v  i  v  i  vv i      -i      i  
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_235406599_   1293 ATTT-CAATACGTACATCTGACAAAGGACTGGAATTCAGAATATACAATG 1341
                             -   vv i  i      i  i     v v  i         i  v 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_235406599_   1342 ---TCT-ACCCCTTAATA-TAG-----CAGA-AACTCCATTTAGAG--GG 1378
                         ---   -  vv  i    -  i-----  i -   i v   ? i i--  
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_235406599_   1379 GCAAGAGATATAACCGGGCACCTCCTCGCAAAAGATTTGTGACACGAT-A 1427
                             ii   v i vii i  ii  ii iv i     v iii - i ii- 
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA-ATGGCCA 871

  chr1_235406599_   1428 ATGAGCCACATGGATGAAT-CTCAA 1451
                           i   -     i vii  -     
  L1M4_orf2#LINE/    872 ATAAGC-ACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.05 (43 / 895), avg. gap size = 2.74 (118 / 43)  


3271 26.16 0.66 0.44  chr1_235562795_235567014     2822  3727 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_235562795_   2822 TGGAAAGGTATTCAATGTTCACGAATTGGAAGAAGCAAAAATTGTTAAAA 2871
                                i   i v       i i         vvi  v -       i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA-TTGTTAAGA 49

  chr1_235562795_   2872 TGCTCATACTAGCCAAAGCAACCCACAAGTTCAATGCAATCCGTATCAAA 2921
                           viv     vv     vii i i   ii     i       v       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_235562795_   2922 ATACCAATGACATTCTTCACAGAAATAGAAAAAA-AATTCTAAAATTTAT 2970
                           v   iivi v  i  ii       v  v  iv-i  i        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_235562795_   2971 ATAGAATTACAACAAGACTTGGAATAGTAAAAACTATTCTGAACAAAAAG 3020
                           i   v i   -ii   iii      iv     v  ii    v  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_235562795_   3021 AGCAAAACTGGAGGAACCACACTACCAGACTTCAAATTATACTACAGAGC 3070
                          i    ii       vi      v  vi i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_235562795_   3071 TATAATAATTAAAACAGCATGGTACTGGCATATAAATAGACACACTGACC 3120
                           i i    i  i    ii             vii       i iv  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_235562795_   3121 AATGAAACAGAATATAAAACCGAAAAGCAAATTCACACACCCACTGTGAA 3170
                             i  i     vv i ii v i  ii   ii  i   iii iv  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_235562795_   3171 CTCATTTGCAACAAGAGTGCCAATAACATACCCTGGGGAAAAGACATTCT 3220
                         i v    v i     i       v v   v vv        ii i v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_235562795_   3221 CTTCAATAAATGGTGCTGGGAAAACTGGATATCGATATGCAGAAGAAAGA 3270
                         i     i              v         ? v i     i     v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_235562795_   3271 AATTAGATCCCTATCTCTC-CCTTGTACAAAAATTAAATCCAAATGGGTT 3319
                          i  i  i     i   v -  v i            v  v      i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_235562795_   3320 AAAGACTTAAGCCTAGGACCTCAAACTATGAAACTGCTACAAGAAAACAT 3369
                          ?    i   iiv  i  v  v       i     vi  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_235562795_   3370 TGAGGAATCTCTCCACAACATTGATCTGGGCAAAATTTTCTTGAGTAATA 3419
                         v i? v vv   i iii  v   ivi i     viv      iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_235562795_   3420 TCCCACAAGCAAAGGCAACCAAAGCAAAAATGGACAAAGAAGATCACATC 3469
                         iv   v     v i     v    v      i  i   vvi  iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_235562795_   3470 CAG-TTAACAAGCTTCTGCAGAGCAAAGGAAATAATCAACAAAGTGAAGA 3518
                         v i-    -  i   i  iivvv       v iv     v        i 
  L1M4_orf2#LINE/    649 AAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_235562795_   3519 GACAACCCACCAAATGGGAGAAAATATTTGAAAACTATCTGTCTGACAAG 3568
                                   vi                  v   ii  v i     i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_235562795_   3569 GAACTAATAACCAGAATATTTAAGAAGCTCAAACAACTCTATAGGAAAAA 3618
                          i   vi  v         v   ii i   vv       v   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_235562795_   3619 AAGCTATTAATTCAATTTAAAAATGGGCAA--GATTTGAATGGATATT-C 3665
                         i - v v   ii     ?            --         i  i   - 
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_235562795_   3666 TCAAAAGAAAACACACAAATGGCAAACAGGCATATGAAAAAGTGCTCAAC 3715
                           v      i i i         v  i i   i       ii        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_235562795_   3716 ATCACTGATCAT 3727
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


2806 28.12 1.56 0.22  chr1_235568803_235573017.rev     2829  3724 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_235568803_   2829 TGGAAACACATCTGATGCTCATAGATGGGTAGAATCAATACTGTGAAAAT 2878
                               v i   iv   i    i   v  v   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_235568803_   2879 AAGCATACTGCCAAAAGCAGTCTACAAATTCCATGCAATTCTCATCAAGA 2928
                         iivv     v  v   viii      i    v i     i ii     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_235568803_   2929 TACCACCATCATTCTTCACAGAACTAGAAAAAAAAATCCTAAAACTCATA 2978
                          v   v vv v  i  ii     v v  v  ivvi         i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_235568803_   2979 TAGAACCAAAAAAGAGCCCACACAGCCAAAACAAGACTAAGCACAAAGAA 3028
                          i   viiv  ii  v  viv i           vvi i iv vi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_235568803_   3029 CAAATCTGGAAGCATCACATTACCTGATTTCAAACTATGCTATAAGGCCA 3078
                             vi    i vv     i v  ii        viv i   i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_235568803_   3079 TAGTCACCAAAACAACATGGTACTAGTATAAAAATAGCCACATAGACCAA 3128
                         i   v i   i   iii       i i    ii    v  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_235568803_   3129 TGAAACAGAATAGATAACCCAGAAATAAAGTCAAATACTTATAGCCAACT 3178
                           i  i     v  v ii           vi  v i i    i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_235568803_   3179 GATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGGCACCCTAT 3228
                            i   i    i vviv   i v   vv i         iii vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_235568803_   3229 TCAACAAATGGTGCTGAGATAATTGGCAA---ACAAGTAGGAGAATGAAA 3275
                                         i  i  i   vv ---   v i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_235568803_   3276 CTGGATCCTCATCTCTCACCTTATATAAAAATCAACTCAAGATGGATCAA 3325
                         i    i  ii i   v    v    i      i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_235568803_   3326 AGACTTAAATCTAAGACATGAAGCTATAAAAATTCTAGAAGATAACATCA 3375
                             i     v     vv i  i        v ii       v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_235568803_   3376 GAA-AAATCCTTCTAGTCATTGGCTTAGGCAAGGATTTCAT-GATGAAGA 3423
                          ?i-     i iv iii -    v        v i    v -   - v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGAT-ATGA 598

  chr1_235568803_   3424 ACCCAAAAGCAAGTGCAATAAAAACAAATATAAATAGCTGGAACTTAATT 3473
                         vv         viv    i    iv   v   i   iv v i    v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_235568803_   3474 AAACTAAAGAGTTTCTACACAGCAAAAGAAAC----AGCAGAGTAAACAG 3519
                            v v  i ii  i iii vv    i  v  ---- iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_235568803_   3520 ACAACCCACAGAGTGGGATAAAATCTTCACAATCTATACATCTGACAAAC 3569
                                     i     v     v  ii   vii   i      i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_235568803_   3570 GACTGATATCCAGAATCTACAACGTACTCAAACAAATTAGCAAGAAAAA- 3618
                             vi          v  i  v v    vv    v i ii  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_235568803_   3619 ---AATATCCCA-TCAAAAAGTGGGCTAAGGACATGAATAGACAATAAGC 3664
                         ---    v    - i?    i     v     iv          v vvv 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_235568803_   3665 AAAAGAGGATATACAAATGGCCAACAAACATATGAAAAAATGCTTAGCAT 3714
                         v     i                 i  i  i       i     i i   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_235568803_   3715 CACTAAAGAT 3724
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (146 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


1213 23.69 7.65 12.47  chr1_235662758_235664752      549  1502 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_235662758_    549 TGAAAAGACATATCTTATTTGTTGATAAGAAGAATTAATATTGTTAAAAT 598
                           i     i  vi v i  ii v   vi     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_235662758_    599 AAATAACAATTCTTATTTTGATCTACAGAGATGGTGCAAGAATAATTACT 648
                         ii-i  i v i ii vv            ----- v   vi-i   iv  
  L1M4_orf2#LINE/     51 GG-CAATACTCCCCAAATTGATCTACAGA-----TTCAACG-CAATCCCT 93

  chr1_235662758_    649 ATAAGAA---CGG--GCATTTTTAG-AGCAGTTGACAAGCTATTTCTGAA 692
                           v i  --- i --  v     v -  v i          iv i  i  
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_235662758_    693 ATTCATCTGGAAATGCAAAGGACCTGGAAAAGGCAAAACAA-CTT----A 737
                               v           i     ii   v  v        -   ---- 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_235662758_    738 AGAATTATTTTAAAGCTGAAG---TCACCAAGACAGTGTGCTATGGGTTT 784
                             vv i---    i  i  ---    ----  -- - v i ---i   
  L1M4_orf2#LINE/    194 AGAAGAAC---AAAGTTGGAGGACTCAC----AC--T-TCCCA---ATTT 230

  chr1_235662758_    785 CAAGATAGACAAATAAATTAATGGGTTAGAAAAAAAGCC-TAGAAATATA 833
                            -----------  v   v --------- v     i-i  v   vv 
  L1M4_orf2#LINE/    231 CAA-----------AACTTACT---------ACAAAGCTACAGTAATCAA 260

  chr1_235662758_    834 TATATATATATATATGTATGTATATGTATATAGACATTGAATATATATAA 883
                         v i ---------i   i-   ivv i   vi  i --  ---i     i
  L1M4_orf2#LINE/    261 GACA---------GTGTG-GTACTGGCATAAGGATA--GA---CATATAG 295

  chr1_235662758_    884 ATATATATTCAATATATAAAAAATATAGGATATATATAATATATATAGAT 933
                           -------    iv - v i   vv  ii vi v -    v ivi ---
  L1M4_orf2#LINE/    296 AT-------CAATGGA-ATAGAATTGAGAGTCCAGA-AATAAACCCA--- 333

  chr1_235662758_    934 GTGTGTGTGTGTGTGTGTATATATAGAGAGAGAGAGAGAGAGAGAGCCAA 983
                         --------------- ii  v   i --------------------i   
  L1M4_orf2#LINE/    334 ---------------TACATTTATGG--------------------TCAA 348

  chr1_235662758_    984 TTCATTTTTTGACAAAGCTTATAGGAA-ATTGAGTGGAGAAAAGAGAGCA 1032
                           v     i-     i v vvi i  v-   v i   i    ii v  iv
  L1M4_orf2#LINE/    349 TTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_235662758_   1033 TTTTCAACAAA-GGTAGTGGAACATTTAGACATCCATTTA-AACTTCAAT 1080
                                    -   iv   i   vi i  i ?   iv i-  ----  v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA----AAG 443

  chr1_235662758_   1081 AATAACTTCAATAACTTCAATCCTTATCTCACATCATATA-AAAAATTAA 1129
                            i -------- v  vi i  i  i      i      -         
  L1M4_orf2#LINE/    444 AATGA--------AGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr1_235662758_   1130 AT-----TGGCTCATAGACCTAAATGGAAAA-CTAAAACTATTAAATTTC 1173
                         v -----   v   ?           v  i -          v   i ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_235662758_   1174 TGGGAGAAAATCGAGGA-TAAAGTCTTTGTAACTTTGGGTT--------- 1213
                          i i      ivv   ?-    -    i  i  i       ---------
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_235662758_   1214 -----------TGACATTAAAAGCACAAATGATAAAAGTAAAATTTGGCA 1252
                         -----------     ii          iii i     v    v v ii 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_235662758_   1253 AACTTGACTTT-TCAAA-TTAAGAAATTCTTCT-CTCCAAAGGAT--TAT 1297
                           i v     i-     -    -   i i  v -  i       i--   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_235662758_   1298 ---------AAAAAGATAAGTCATGGGTTGGGAACAGACATTTGCACATT 1338
                         ---------i      i  vi  ii iv     iv i i       v  i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_235662758_   1339 ACCTACTTGATAAAGTACTTGAGTCTAGAATATATAAAGAGCTTTCAAAA 1388
                          iv  ii      i v     vi  i              i  i i v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_235662758_   1389 TTCAACAATAAGAAAACAAA----CCAATACAAAGGGTGGGGCTAGAATT 1434
                         i    i     i  i     ----     -i?  iii    vvv  i   
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGATT 832

  chr1_235662758_   1435 TGAATAGCCGTGTC-ACAAA--------ATAGATGATAAATTAGAACGTT 1475
                                v i v  -v    -------- i i   iiv   v  v  i -
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT- 881

  chr1_235662758_   1476 AAAAAGGTCTTTAACATCACTAGTCAT 1502
                         i     i vi i       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (138 / 84)
Gap_init rate = 0.05 (49 / 908), avg. gap size = 3.92 (192 / 49)  


 204 26.37 15.38 2.20  chr1_235726189_235727841      374   464 (1189)    L1M4_orf2#LINE/L1       16   118 (790)  

  chr1_235726189_    374 TATTCATGG-CCAAAGGATTTAATAATTTTAACATGACGAATGTTCC--- 419
                          i       -iiii i  i      v v    v   i -   ii   ---
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC-AATACTCCCCA 64

  chr1_235726189_    420 ---------ATAGATTCTACATAA-CTCAATCAAAATCTTAGTAGGCATT 459
                         --------- i      v  ii  - i v         ii  i-v  v  
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCTT 113

  chr1_235726189_    460 TTTTG 464
                              
  L1M4_orf2#LINE/    114 TTTTG 118

Transitions / transversions = 2.43 (17 / 7)
Gap_init rate = 0.05 (5 / 103), avg. gap size = 3.20 (16 / 5)  

1861 24.60 4.60 2.88  chr1_235726189_235727841      466  1160 (493)    L1M4_orf2#LINE/L1      202   908 (0)  

  chr1_235726189_    466 AAAATTTAAGAAGCTCA---TTCTAAAATTCATGTGGACTTACAATAATC 512
                            i  vi  i -    ---   iv  v    ---ii      v i  vv
  L1M4_orf2#LINE/    202 AAAGTTGGAGGA-CTCACACTTCCCAATTTCA---AAACTTACTACAAAG 247

  chr1_235726189_    513 CTATATTA-CCAAGACAATGTGGCATTTGTAT--TGAAAGA------GAT 553
                            i v  -i       i     i i v i  --v  v   ------   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_235726189_    554 TAATAAAGTA--------AGTCCAGAAATGAACCC-CACATATATA-TCA 593
                         i   ii i  --------           i     -i    v   i-   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_235726189_    594 AT-AATTTTTTGGACAAGGGT-CAAAGGCAACTCAGTGGAGGAAAAACAA 641
                           -i     i--         - v   i v i   i   i i  i  i i
  L1M4_orf2#LINE/    348 ATTGATTTTC--GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_235726189_    642 TGTTTTCAGGTAATGTTGCTGGAAATCTTGGATCCATACATACACACACA 691
                          v      ivv    v      i vvvi     ------ ?v    ii  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGAT------AKCCACATGCA 439

  chr1_235726189_    692 CACACAATTTAATAACTTCAATTTATACCGAGCAACATACACAAAAAA-A 740
                         v - v   v----  v  vi iiiv    vvi  v    i       v- 
  L1M4_orf2#LINE/    440 AA-AGAATG----AAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_235726189_    741 ACTCAAAATAGATCACAAAGCTAAGTATAAAACCTAAAATTACAAAACTT 790
                                  i     ? i v    i i   i v      i  i      i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_235726189_    791 CTAAAAGAAAACA--AGTAAAAATCTACATAATCTTGGGTTATGCAAAGA 838
                         i  i         --i ?iv      v i i i         v    v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_235726189_    839 ATTCTTAGATATAACACCAAAACTACAAACTATAAAAGTACAAATTGATA 888
                         v           i         vi    i v i     v v    v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_235726189_    889 AACTGGATGAAATCAAAATTAAACAAATTTGCTCTTTGAATGATACTGCT 938
                           i    ivvv            v vv    iv   ii  v  i   iii
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_235726189_    939 AAGGAAATAAAAAGCAAAGTCACAGATAGTGAGAACATTTCTGTAATTCA 988
                            i  i i     vv  vi      vv v     v  v i  i  v   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_235726189_    989 TATATCTGATAAGGAACTTTTGTATCCAGAACATATAAAGAAGTCCTAAA 1038
                                       i    --          i          v  i  v 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTT--GTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_235726189_   1039 ATTCAGAAGGAAGAAAACAACT---CAAATTTTTAAATGGTCAAAATATT 1085
                          i   iv iv  i  i    v --- v    ?vv      v    iv   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_235726189_   1086 TGAACAGATACATTATCCAA-GAAG-TATAATCATGGCAACTAAGCACAT 1133
                             i   i i-  v     -    -    vvv     v v         
  L1M4_orf2#LINE/    833 TGAATAGACAT-TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_235726189_   1134 GAAAAGATGCTTATCATTATTTGTCAG 1160
                                    i v   i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (90 / 77)
Gap_init rate = 0.03 (22 / 707), avg. gap size = 2.36 (52 / 22)  


2474 24.53 1.73 4.27  chr1_235819382_235822398     1239  1988 (1029)    L1M4_orf2#LINE/L1        1   731 (177)  

  chr1_235819382_   1239 TAGATACATATTCCATGATCATTGAT--AAGGACCTGATATTGTCAAGAT 1286
                          i  v v    i     v    v   --i i   i i       i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_235819382_   1287 GTCAGTTCTTTCAAACTTGATGTATACATTCAGCACAATCCCAATCAGCA 1336
                          v  i v  ii v  v     v  i v     i i       v    iv 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_235819382_   1337 TCCCAGCAAGTTATCTTGTGGATATCAACAAACTGATGCTAAAGTTTATA 1386
                                vivi v i   ii  v  ii    i     v     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_235819382_   1387 TAAAGAGGCAAAAGACCCAACATAGCCAACTCAATATTGAA---GGGAAA 1433
                          ii i v    ii      iv        vv    v     --- iii  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_235819382_   1434 CAAAGTTGAAGAACTGACATTACTTGACTTCAAGACTTGCTG-ATAGCTA 1482
                                 i  i   v   i v iii i     i    i  i- v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_235819382_   1483 CAGTAATCAAGGTAGTGTGTTACTGGCAAAAGAACAGACAAAGAGATCAA 1532
                                    ii      v        v   i i     v v       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_235819382_   1533 AAGAATAGAATAAAGAACCCAGAAATAAGCCCACATAAATACATTCAATG 1582
                         vi         vi   ii          i    i i vv  iiv     v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_235819382_   1583 GATATTTGACAAAAG-ACTAAAAGCAATACAATGGAACAAAGATAATCTT 1631
                            v  i     ii -i i  i v  v -      iiv  ii   i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAGTCTT 399

  chr1_235819382_   1632 TTCAACAAATGGTGCTCAAACAACTGGACACTTAAATGCAAAAAAAAAAA 1681
                                         vii         i ?ii v        -------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA------- 442

  chr1_235819382_   1682 AAAAAAAGAAAGAAAAAAAAGAATCTGGACACAGATCTTACACCCTTTAC 1731
                         -------   v   i---------i     v vv i  i     v v   
  L1M4_orf2#LINE/    443 -------GAATGAAG---------TTGGACCCCTACCTCACACCATATAC 476

  chr1_235819382_   1732 AAACATTACCTCCAAATGAATCACAAACCAAATTACAAAATGC-AAAATT 1780
                            v    v   v     i    ? i   v  v ii  i -  -    i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACT 525

  chr1_235819382_   1781 ATAAAACTTCTAAAAGATAACATAGGAGAAAACCTAAGTGACCTTGAGTA 1830
                                 ii  i    v        ? v   i  vv         i  -
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT- 574

  chr1_235819382_   1831 TGGG--ATGGCATTTTAGATACAACACTGAAGGTACAATCTAGAAAAAAA 1878
                          i  --    iv i       ii    ii  i i    v ----  v   
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC----AACAAA 620

  chr1_235819382_   1879 ATAAAGAATTGATAAGCTGAACTTTATTAAAATTAAAATTTTCTGCACTG 1928
                          v   i   v     ii  i    i  i          vi  i  ii  v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr1_235819382_   1929 TGAACGACACTGTCAAGAGAAAAAGAAGACAAAACCGACTGAA---AAGA 1975
                         ii  v      i      i ivi i       --  v  v   ---i   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAA--CCCACAGAATGGGAGA 718

  chr1_235819382_   1976 AAATATTTGCAAA 1988
                                      
  L1M4_orf2#LINE/    719 AAATATTTGCAAA 731

Transitions / transversions = 1.70 (114 / 67)
Gap_init rate = 0.02 (14 / 731), avg. gap size = 3.21 (45 / 14)  

 632 24.00 0.57 0.57  chr1_235819382_235822398     2353  2527 (490)    L1M4_orf2#LINE/L1      734   908 (0)  

  chr1_235819382_   2353 ACACATCAGATAAAGAACTGTTATCCAAAATATACAAGGAACTCTTAAAA 2402
                          i i   v     i i   vv      i      i  i         v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_235819382_   2403 TTCAACAATATAAAAAACAA-CAATCCAATTTAAAAATGGGCAGAAGACC 2451
                         i    i    -    i    -i  i      ?           i i  ii
  L1M4_orf2#LINE/    784 CTCAATAATA-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr1_235819382_   2452 TAAACAGACATCTCATCAAAGGAGATCTACTGAAGGAAAGTAAGCATATG 2501
                          i  i      i  vi     i    v   vi v  vv i      i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr1_235819382_   2502 GAAATATACTTAATAGTATATGTCAT 2527
                         i   v  i  i  i vi ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.42 (29 / 12)
Gap_init rate = 0.01 (2 / 175), avg. gap size = 1.00 (2 / 2)  


2273 24.92 1.29 0.64  chr1_235889060_235890680.rev      501  1122 (499)    L1M4_orf2#LINE/L1      261   886 (22)  

  chr1_235889060_    501 GACTGCATGGTACTGGCATAAAAACACACACACACAGACCAATGGAATGG 550
                            v ii              ii i v   i i --  i         i 
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATA--GATCAATGGAATAG 308

  chr1_235889060_    551 AATAAAGAGCCCAAAAATAAATCTTTGTATTTACGGTCAACTGATCTTCA 600
                            vi    i   i       i iv ii     i      i    i   i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_235889060_    601 ACAAAGATGCCAAAAACACACAATGAAGAAAGGATA--CTCTTCAACAAA 648
                             i i      i v  iv     ii     i   --  i         
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_235889060_    649 CGCACTTGGGAGAACTGGATATCCACATGCAGAAGAATGAAATTGGATCT 698
                         i vvvi     v         ?         i         i     i i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr1_235889060_    699 -TATCTCACACCAAATACAAAAATCATATCAAATTGGATTAAAGACTTAA 747
                         -  i         v          i vv     v     i ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr1_235889060_    748 ATTTAAGGCCCAAAACTCTGAAACCACCATAAGAACACACTGGA--AAAT 795
                           v    iv i      v i    ivii v     v   iv  ?--    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr1_235889060_    796 GTTTAGAACATTAGTCTCGGCAAAGAACTTTTGGGTAAGATCTCAAAATC 845
                         v  iivi  v  i vi v     v ivi i  i i  v  ivi     v 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr1_235889060_    846 ACAGGCAACAAAAGCAAAAATAGACAAATGGAATTATATCAAGA--GAAA 893
                            i          v         i    v i i vi     i --i   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_235889060_    894 ACGTTTCTGCATGGCAAAGGAAAAAATAAACAAAGTGAAGAGGCGACCTA 943
                           v   v   v --       v vv  v  v        i  i i   i 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr1_235889060_    944 AACTATGGGAGAAAATATTTGCAAACTATCCATCTGACAAGGGATTAATA 993
                         v vv                     ii  vi      i      i vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr1_235889060_    994 ACCAGAACATATAAGGAAGTCA-AAAACTCAATAGCAAAAAAGAAAATAA 1042
                         v      i      i   v  v- v         ii     iiv      
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_235889060_   1043 TCTGATTAAAAAATAGGCAAAAGATGTGAACAGAGATTTCTCAAAATAAA 1092
                         i ii   ?      i      i   v    i   v       v   v  i
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_235889060_   1093 ACTTACAAATGGCCAACAGCTATATAAAAA 1122
                          iv             i ivi i  i    
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.60 (93 / 58)
Gap_init rate = 0.01 (7 / 626), avg. gap size = 1.71 (12 / 7)  


2968 25.00 1.97 2.41  chr1_235989599_235994167     3165  4076 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_235989599_   3165 TGGAAACACATTCCATGCTTATGGATGGCTGGAA---TCAATATTGTGAA 3211
                               v i  i     i i      ---     --- i        v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT---TGGAAGACTTAATATTGTTAA 47

  chr1_235989599_   3212 AGCAACCATACTGCCAAAAGCAGTCTACAAGTTCAATGCAATCCCCATCA 3261
                         iiiii v     v  v   viii      ii     i        i    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_235989599_   3262 AAATACCACCATCATTCTTCACAGAATTAGAAAAAAAAATTCTAAAAATA 3311
                             v   v vv v  i  ii     v v  v  ivvi  i      v v
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_235989599_   3312 ATATGAAACAAAACAAAACAAAAGGCCT-GCATAGCCAAAGCAATACTAA 3360
                              i  ------- vi   ii i  i- v         i    vi i 
  L1M4_orf2#LINE/    148 ATATGGAA-------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_235989599_   3361 GCAAAAAGAACAAATCTGGAGACATCACACTACCTGATTTCCAACTATAC 3410
                         iv  i         vi     ivv       v  ii     v  viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_235989599_   3411 TATAAGGCCATAGTCAACAAAACAGCATCGTACTGGTATAAAAATAGGCA 3460
                           i  i  i i   v v   i    ii v       i    ii    i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_235989599_   3461 CATAGACCAAAGGAACAGAATAGAGAACCCAGAAATGAACCCAAACACTT 3510
                         i     i   v    i     v    ii        i      v   i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_235989599_   3511 ACAGCCAACTGATCTTTGACAAAGCAAACAAAAAC-TTAAATTGGGGGAA 3559
                          ii i   i    i  i     i vviv   i v -  v   --      
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT--GGGGAA 388

  chr1_235989599_   3560 AGGACACCCTTTTCAACAAATGCTGCTGGGATAATTGGCTAGCCACATGT 3609
                           i i vi              v        i  i   v  ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr1_235989599_   3610 AGGAGAATGAAACTGGATCCTCATCTCTGGCCTTATA-AAAAATCAACTC 3658
                          ii        ii    i  ii i   vvi  v    -      i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_235989599_   3659 AAAATGGATTAAGTACTTAAATCTAATACCTGAAACTATAAAAGTTCTAG 3708
                                  i ?iv  i     v   v v  i           v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_235989599_   3709 AAGATAACATTAGAA-AAATCCTTCTAGACATTGGCTTAGGCAAGGATTT 3757
                             v     vi ?i-     -   vv   v    v        v i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_235989599_   3758 TATGGCCAAGAACCCAAAAGCAAATTCAATAAAAACAAAAA---ATATTT 3804
                         iv i vi v  vv         v vv   i    iv     ---   vv 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_235989599_   3805 GGGACTT-----AAACTAAAGAGCTTTTGCACAGCAAAAG-CTTTGTCAG 3848
                         v      -----   i    i -      ii vv    i - vi i   i
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_235989599_   3849 CAGAGTAAACAGACAATCCACAGTGTGGGAGAAAATCTTTGTAATCTATA 3898
                         v i   i  v      i      vi           v    i  vii   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_235989599_   3899 CATCTGACAAAGGACTAATATCCAGAATCTACAACAAACTCAAACAAATC 3948
                         i      i  i     vi          v  i  vi     vv    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_235989599_   3949 AGTAAGAGAAAAACAAAAAAACAAACAATCCCATAAAAAAGGGGGCTGAG 3998
                          i   --------i     i     i  i  v  v?    iv    vi  
  L1M4_orf2#LINE/    787 AATAA--------TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_235989599_   3999 GACATGCATAGGCAATTCTCAAAACAAGATATACAGATGACCAACAA--A 4046
                           iv  v    i  v     v   v          i   i    i  -- 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_235989599_   4047 CATGAAAAAATACTCAACATCACTAAGATC 4076
                                 i  i          ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (131 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  


3085 24.92 1.87 1.76  chr1_236002243_236004545.rev      924  1830 (473)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_236002243_    924 TGGAGAGACATTCCATGGTCCTAGATAGGAAGACTCAATATTGTGAAGAT 973
                             i   i  i     v  v i   v        i        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_236002243_    974 GTCAGTTCTTCTCAACTTGGTCTATTGATTCAATGCAATGCCAATCAGAA 1023
                          v  i v  i i   v   i    iv       i     v  v    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_236002243_   1024 TCCCAGCAAGATATTTTATA-ATACTGGCAAACTTGATTCTATAATTTAT 1072
                                vivv v    ii - v i  i   i  -   i   v    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT-GATCCTAAAATTCAT 149

  chr1_236002243_   1073 ACAGAGAGGCAAAAGACCCAGAATAGCCGACTGGATGTTGAA---GAAGA 1119
                          ii  i v    ii              i vvvi  v     ---     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_236002243_   1120 ACAAACCTGGAGGACTGGCATTACCCAACTTCAAAGCTTACTGTAAAACT 1169
                              vi         vi  i v     i      i      ii   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_236002243_   1170 ACTCTAATCAAGACAGAGCGGTGTTGGTGAAAAACTAGATAAATTGATCA 1219
                           vv            v i   ii   iiv  iiv    i v  v     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_236002243_   1220 AAAGAACAGAAAAAAGAGCCCTAAAAGAAGCACTGAATA-ACTAAGTATA 1268
                          vi   i    vvi    i  vi   v  i v ---   - i ---   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCC---ATACATT---TATG 343

  chr1_236002243_   1269 G-CAACTGATCTTTGACAAAGGAACAAATGCAATACTATGGAACAAAGAT 1317
                          -   i    i  i     i  vi v  vi v  v v    iiv  ii  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_236002243_   1318 A-TCGCTTCAACAAATGGTGCTGGGACAACCAGACATCCACATGCAAAAA 1366
                          -  vi                        ii  i ?            i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_236002243_   1367 AGAAAAAAAAATCTAGACACAGATCTTAAAACATTTATAAAATTTTATCC 1416
                          ---- vi  i - i   v vv i  i v v   v  i    v  v ii 
  L1M4_orf2#LINE/    444 A----ATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr1_236002243_   1417 AAAATGGATCATAGATCTAACTATAAAATATAAAACTATGTAACTCCTAA 1466
                                    ?   i    v i   i vv         iv     i  i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_236002243_   1467 AAGATAACAACGGAGAAACTCTAGATGACCTTGGATATGGCAATTGCTTT 1516
                             v    vv  ? v  v   vvi         i vv      v i  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_236002243_   1517 TTAGATAAAACACCAAAGACGTGATCCATAAAAGAAATAATTGACAAGTT 1566
                                vi        ii iii v v i        v   v  i  i  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_236002243_   1567 GAACTTCATTAAAATTAAAAGCTTCTG--CTTTGTTGAAGATATTGTCAA 1614
                          i       i          i   i  --   ii--i i  i i i    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAA 686

  chr1_236002243_   1615 GAGAAAGAGAATACAAGCCACAGACTGGGAGAAAATATTTGCAAAACATG 1664
                           i iv  i  v    v       v                    v   i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_236002243_   1665 TATCGGATAAAGGTATATTCATCCAAAATATACAGATAACACTTAAAATT 1714
                             v     i  - iv vi     i      i i v   v    v  i 
  L1M4_orf2#LINE/    737 TATCTGATAAGGG-ACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_236002243_   1715 CAACTATAAGAAAATAAATAACCCAATTAAAACATGGGCCAAATCCTTGA 1764
                            iv    i  i i             ?   v      v  ivvi    
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_236002243_   1765 CTG---ATTGCTCACCAAGAAGACACACAGATGGCAAGTAAGC-C-TGTA 1809
                         v i---   v   - v       i i   i     v i     - -  v 
  L1M4_orf2#LINE/    836 ATAGACATTTCTC-CAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_236002243_   1810 AACATA---AACATCATATGTCAC 1830
                           v  i---       ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (127 / 95)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.83 (33 / 18)  


3292 26.65 0.55 0.55  chr1_236113091_236115207.rev      719  1626 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_236113091_    719 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCGTGAAAAT 768
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_236113091_    769 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 818
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_236113091_    819 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 866
                          v   iivi i  i  ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_236113091_    867 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 916
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_236113091_    917 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 966
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_236113091_    967 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1016
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_236113091_   1017 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1064
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_236113091_   1065 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1114
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_236113091_   1115 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1164
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_236113091_   1165 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1214
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_236113091_   1215 TTAAAGATTTAAACGTTAGACCTAAAACCATAAATACCCT-AGAAGAAAA 1263
                          i ?   ii    i  v   v       i     -  i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chr1_236113091_   1264 CCTAGGCATTACCACTCAGGACATAGGTGTGGGCAAGGACTTCATGTCCA 1313
                          v    ?i v vivi  iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_236113091_   1314 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1363
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_236113091_   1364 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1413
                           i   v i  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_236113091_   1414 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 1463
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_236113091_   1464 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1513
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_236113091_   1514 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 1563
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_236113091_   1564 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCAT 1613
                            v        i  vi viii     v  i        i i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_236113091_   1614 CATCACTGGCCAT 1626
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3196 27.64 0.44 0.44  chr1_236127355_236133750.rev     4998  5905 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_236127355_   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTAAAAAT 5047
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_236127355_   5048 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCTATCAAGC 5097
                            v     vi    iv i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_236127355_   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_236127355_   5146 TATGGAACCAAAATAGAGCCTACATCACCAAGTCAATCCTAAGCCAAAAG 5195
                                viiv  vi  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_236127355_   5196 AACAAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv   i   v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_236127355_   5246 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5295
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_236127355_   5296 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5343
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_236127355_   5344 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5393
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_236127355_   5394 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5443
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_236127355_   5444 GAAACTGGATCCCTTCCTTATACCTTATATGAAAATTAATTCAAGATGGA 5493
                            ii    i    v   i i   v    ii        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_236127355_   5494 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5543
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_236127355_   5544 CTAGGCATTACCATTCAGGACATAGACATGGGCAAGGACTTCATGTCTAA 5593
                         v    ?i v viv   iv   v v ivv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_236127355_   5594 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5643
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_236127355_   5644 TTAAACTAACGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5693
                          i   v v vi i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_236127355_   5694 CAGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5743
                         vii     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_236127355_   5744 AGGGCTAATATCCAGAATCTACAGTGAACTCAAACCAATTTACAAGAAAA 5793
                         i  i  vi          v  i iv      vv  v v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_236127355_   5794 AACCAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5843
                          iv    i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_236127355_   5844 TCAAAAGAAGACATTCATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5893
                           v        i  v  viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_236127355_   5894 ATCACTGGCCAT 5905
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (147 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2955 25.62 4.29 1.81  chr1_236269219_236273054.rev     2461  3346 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_236269219_   2461 TGGAGAGATGTTTCATGCTCATGGATAGGAAGACTCCATATTGTCCAGAT 2510
                             i    i ii    i        v        iv       iv    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_236269219_   2511 GTCAGTTACTCCTCAT-TTGATTTCTAGATTCAATACAATCCCAATCAAA 2559
                          v  i -     i  v-     i vi        ii       v      
  L1M4_orf2#LINE/     51 GGCAAT-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_236269219_   2560 ATCCCAGAAAGTTATTTTGTGTATATGGGCAAAATGATTTTAAAGTTTAC 2609
                                vvivi v     iiv v  v i   iv    ii    i  i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_236269219_   2610 ATGGAGAGGCAAAAGATCCAGAATAATCAATACAATATT---AAAGGACA 2656
                              i v    ii  i        ii   v     v  ---    i v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_236269219_   2657 ACAAAGTCAGAGGCCTGATACCATCTTACTTCAAGACCTGTTA-AAAG-- 2703
                                ii    v  v i  ivi iv i     i  i ii  -    --
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_236269219_   2704 ---ATAATCAAGACAGTGTTCTATTGGTGAAAGGACAGACA----GATTA 2746
                         ---i               vv  i   iiv     i     ----   i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_236269219_   2747 ATAAAACAAAATAGAGAGCCCAGAAATAGGCCCACATGAATATAGTGAAC 2796
                           ii  i i   v     i         ii    i iivv   i  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_236269219_   2797 CGATCTTTCACAATGGTGCAAAGGCAATACAACAGACTACAGATAG-CTT 2845
                         i   i  iv    v     v   i v  v   ii ivv vii    -   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_236269219_   2846 TTCCACAA------CTGGAACGACTCGACATCTATACACACACACACACA 2889
                            v    ------    i  i   v  i ? --------------    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKC--------------CACA 435

  chr1_236269219_   2890 CACACACAAATAAATGTAGACACAGACCTTACACCCTTCACAAAACATTA 2939
                         ii  v vi   i  vv i   v vv    i     v vi      -    
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTA 484

  chr1_236269219_   2940 ACTCAAAATGAATCACATATCTAAATGTAAAATATAAAATTATAAAACTT 2989
                                   i    ? v i          i vv     i         i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_236269219_   2990 CTAGAACGTAACGAAGGAGAAAATCTAGGTGGCCTTGGGTTTGGTGATGA 3039
                         i     viv   iv   ? v      vv   i         v  ii   i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_236269219_   3040 CTTTTTTGATACAACACCAAAGTAACCATTCATGAAAGAAATAATTGATA 3089
                         i  i  v    ii        ivv  v viv ii       v   v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_236269219_   3090 AGCGGGACTTCATTAAAAT----GTCTTCTCTGT---GAGAGACACTGTC 3132
                          iiv         i     ----iv   i v  i---i ii      i  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_236269219_   3133 ATGAGAATGAGAAGAAAAGTCACAGACTGGAAGAAAATATTTGCAAAACA 3182
                          v  i i   i    v  vi      v   i                v  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_236269219_   3183 CATA-------AAGAACTGTTCTCCAAAATATACAAAGAATGCTTACAAC 3225
                         i   ------- i i   vv v    i      i      iv        
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_236269219_   3226 TCAACAATAAGAAAACCAACCACCTGATTAAAAAATGGTCAAAG--CCTG 3273
                             i     i  i  v  iv   ii   ?        v     --ii  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_236269219_   3274 AACAGACTCTTCACCAAAGAGGATATACAGTTGGCAAAGAAACATAGGAA 3323
                           i    vi   v       i        iv    v  v  i  i v   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_236269219_   3324 AACATGCTCAACAT-ATTTTCTTA 3346
                           v           - ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (134 / 89)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.60 (54 / 15)  


2927 24.07 1.59 5.51  chr1_236737657_236741636.rev     2547  3489 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_236737657_   2547 GAATAGACATTCCATGCTCATGGACAGGAAGAATAAATATTGTTGAAGTG 2596
                            -   i  i     i       iv      v v         i ii  
  L1M4_orf2#LINE/      3 GAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_236737657_   2597 ACCCTACTCCCCAAAACAATCTCCAGATCCAGTGCAATCCTTATCAAAA- 2645
                         i vv           vii    v     i  ii       i        -
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_236737657_   2646 --CAATGACATTTTTCACAGAAATACAAAAGC-AACCGTAAAATTCTTAT 2692
                         --  iivi v     ii       vv v    -i i v        v   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_236737657_   2693 GGA---GCCAAAAACAAACCTGAATAGACAAAGCAATCCGGAGCAAAACG 2739
                            ---  v iii  ---  v      v    i     iv  --    - 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGA--AAAA-G 195

  chr1_236737657_   2740 AATAAACAAACAAAGCTGGAGGTATCACACTGCCTGACCTCAAAATATAT 2789
                           -----i       i      vv       v  ii ii      iv  i
  L1M4_orf2#LINE/    196 AA-----GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_236737657_   2790 TACAAGGTTATAGTAATCAAAACTGTATGGTATTGATATAAAAACAAACA 2839
                              i i  i         i  v  i     i  ii    ii i i   
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_236737657_   2840 CATAGACCAATGGAAAAGAATAGAGAACCCAGATATAAATCCACATATTT 2889
                         i     i        v     v    ii     v     i   i i    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr1_236737657_   2890 ACAGGCAACTGATTTTCAACAAAGACACCAAGAACATACATGAGGGAAAA 2939
                          ii v   i        i    i iii      v   v  vvi      i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr1_236737657_   2940 GACACCCTCTTCAATAAATTGTGCTGGAAAAATTGGATATCTATATGCAG 2989
                         i i vi  i     i    v       i v  i      ? i i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr1_236737657_   2990 AACAATGAAACTTGACCCTTATCTCTCACCATATACAAAA-TCAGTGCAA 3038
                           v      ii v     i  i   v              - i iiv   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_236737657_   3039 GACGGATTAACAACTTAAAGGCAAGACTCGAAACTATAAATCTACTAGAA 3088
                         i i    i ?vi  i    v i    viii          v  vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_236737657_   3089 GTAAACAGAGGGA-AAATACTTCAGGAAATTGGTCTAGGCAAAGATTTTA 3137
                          v     v   ?i-    -    iv  vv    vi       v i   iv
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_236737657_   3138 TGGCTAAGACCTCAAAAGCACAGACAACTAAAACAAAAATAGACAAATGG 3187
                          i v  v   vi          ii    v   iv         i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr1_236737657_   3188 GACTATTTTGAGCTAAAAAGCTTCTGGACAGCAAAAAA-ACAATCAACAG 3236
                             viv ii iv v    i   i  vi vv    ii -  v     v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_236737657_   3237 AGT--AAAGACATTGCCTGTTTAATGGGAGAAAATATTTGTAAACTATTC 3284
                            --       --i  iiivv                  i   ii  vi
  L1M4_orf2#LINE/    690 AGTGAAAAGACA--ACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_236737657_   3285 ATTCAACATGGGACTAATATCCA---TATATGAGGAACTCAAACAACTCA 3331
                           iii i v      vi      ---     i i      vv        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_236737657_   3332 ACAGTACATAAAAAAATGAATAAGTAAGTAAATAAATAAATAAATAATTC 3381
                          i ----       i ii     vi---i  v ?  -    iiii  ---
  L1M4_orf2#LINE/    788 ATA----ATAAAAAGACAAATAACC---CAATTWAA-AAATGGGCAA--- 826

  chr1_236737657_   3382 ATCTCCTTTGCCCACTTTTTAAGGAGGATATGAGTAGACATTTCTCAAAA 3431
                         ------------------------     v   i            v   
  L1M4_orf2#LINE/    827 ------------------------AGGATTTGAATAGACATTTCTCCAAA 852

  chr1_236737657_   3432 GACAACATACGAATGGCCAACAGGTATATGAAAAAAACTGCTCAACATCA 3481
                           vi i    i         i i i i       i --            
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAACATCA 900

  chr1_236737657_   3482 CTAACCAT 3489
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.86 (145 / 78)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 3.35 (67 / 20)  


3408 21.68 3.43 2.99  chr1_236757639_236760084.rev     1052  1955 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_236757639_   1052 TGGAAAGATATGCTGTGTTTATGGATTGGAAGACTCAATATTGTTAAAAT 1101
                                    v ii    i               i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_236757639_   1102 GGCCATACTACCTAAAGCAATCTACAGATTCAATGTAATCCCAATCAAAA 1151
                            v     v  i   vii              i i      v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_236757639_   1152 TTCCAG-TGTCATTCTTCACAGAAATAGAAAAAATAATCCTAAAATTTAT 1200
                          i    -  i -  i  ii       v  v  iv i           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_236757639_   1201 TTGAAACCACAAAAAAAACCAAATAGCCAAAGTAATCTTGATCAAAAAGG 1250
                         v  i  vii   iii vv vi          ii        vv  i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_236757639_   1251 ACAAAACCAGAGAAATCACACAACCAGATTTGAAAATATATTACAAAGCT 1300
                              iiii   i v      vv  vi    v    iv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_236757639_   1301 ATAGTAATCAAAACAGTATGGTGGTGGCATAAAAATAGACACATCGTCCA 1350
                          i         i     i    iv        ii       i  v vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_236757639_   1351 GTGGAATAGAATGGAGTGTCCAGAAATAAACCCAGCTAACTACAGTCAAT 1400
                         i           v   v                 vvi vi  ii      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_236757639_   1401 TGATTTGCAACAAAGGTGTCAAGAACACAGAATGGGGAAAGGACAGCCTA 1450
                               v i    i    i     v  ivv           i i  i  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_236757639_   1451 TTTAATAAAAGGTGTTATTAAAACTGTACATCTATATATACACAAAAATG 1500
                           i  i   v    i ivv v     v i ? i i  i--  v  i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG--CAAAAGAATG 447

  chr1_236757639_   1501 AAAATAGATCCTTATTTCATCCTTCATAAAAGAATAAACTCAAAAGGAAT 1550
                           iv i  i  i  ii   iv ivi   v  i   v         v i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_236757639_   1551 TAAAGACTTAAA-------------ACTATAAAACTACTCGAAGAAAACA 1587
                         i ?    i    -------------           vi v          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_236757639_   1588 CAGGGGTTAGGAAAGGTTCCATGACATTGG-TCAGGGCAATTATTTCTCG 1636
                         i   ?  -----  ivi i i    v    - i   -    vi     ii
  L1M4_orf2#LINE/    548 TAGGNGT-----AAATCTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTA 591

  chr1_236757639_   1637 GATATGAC-CCAAAAGCACAGGCAATGAAAGTAGAAAATAGACAAATGGG 1685
                                 -           i    ii    - i        i    v  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGG 640

  chr1_236757639_   1686 ATGGCATCAAA-TCAAAATGCTTCTGCACA-CAAACAAAAC----AATAG 1729
                          ivv       - i    -i   i  ii v-    vi v  ----  v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_236757639_   1730 AGTGCAGAGACAACC-ACAAATTGGGAGAAAATATTTGCAAATCATGCA- 1777
                             v i        -   i v                        ii -
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_236757639_   1778 CTGAATAGGGGCTAATATCTAATATATTTATATGTCTAAATATATAACAA 1827
                             vv    i  vi    i i----------------         vi 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAG----------------AATATATAAAGA 773

  chr1_236757639_   1828 ACT------ACTCAATAACAGAAAGGCAAATAACCCTATT-GAAAATGGG 1870
                            ------         i i    i          v   -i        
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_236757639_   1871 CAAAGGATCTGAACAGACATTTCTCAGAAGAAGACATACAAATGGCCAAC 1920
                                 i    i           vi       i              i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr1_236757639_   1921 TGATAAATGAAAAAATGCTCTACATCACTAATCAG 1955
                         viii v       i      v      ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (124 / 69)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.22 (58 / 18)  


 974 31.59 4.89 4.01  chr1_236856063_236858240.rev      539  1111 (1067)    L1M4_orf2#LINE/L1       13   590 (318)  

  chr1_236856063_    539 CCATGTTCATAGATAGAAAGCCTTGATATCATAAAGATGTCAGTTCTACC 588
                                   i   v i   v   i    ii v      v  i v  v  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr1_236856063_    589 CAGTCTGATCTATAGCCT--GTGTAATTG-TGTCAGAATCCTAATAGTTT 635
                           ivi       i  vi --ii i   iv- i   i     i iiv ii 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr1_236856063_    636 TGTTTTGGTGGAACTTAACAACTTAATTCTTAAATT-ATATAGCAGAATA 684
                          -     -ii   v  i    vi i  i  v     -    i v ivii 
  L1M4_orf2#LINE/    113 T-TTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr1_236856063_    685 AACTACCAAGAGGAGGCATAA--ATCT----AAAGAAG------GT---A 719
                          ivv   v   iv  v  v  --    ----       ------  --- 
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr1_236856063_    720 GGAATCTAGCCTTTTCACATTTCAAGACTTATTAGAAGTCTACAGTAAAT 769
                            v  - vv   ii  -       i     i  v  iv         vi
  L1M4_orf2#LINE/    211 GGACTC-ACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr1_236856063_    770 AGAATAGTAACAGGTTTTGTTATAAGGATAAATAATGGAAATAGGCTAAT 819
                          ii i   iv--   vi  vi         i i - ----    iii   
  L1M4_orf2#LINE/    259 AAGACAGTGT--GGTACTGGCATAAGGATAGACA-T----ATAGATCAAT 301

  chr1_236856063_    820 GGAATAGTATAGAGAAAACCCAAGAA-AGCCTCATACATATATGGAAAGT 868
                                v  v    i--i   ii  - iv i       v     vv i 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAG--TCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_236856063_    869 TCCTACATGATAGAAATGGTACAG--CAT--ATTAGAGAGAAAACGGCTT 914
                          vv vivi  i iiii  vi -  --   -- v i i  i i  ii ii 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_236856063_    915 ATTCCTTACATGGCACTAA-ACAACTAAAACAGCATTATCCATATGACGT 963
                         v   vvi v    ii  ii-      ii -------  ?   i   vviv
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGA-------TAKCCACATGCAAA 441

  chr1_236856063_    964 AAAATTAAATGTGATTCCTATTGCAGATCATAGATAAAAATGAATTTCAA 1013
                          i   v  i vv  ii    iiv  v i    v i      v  i iv  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_236856063_   1014 ATAGACTGAAGGATTAAATGTGAAAGC-AAAACTATAAAATTTTCTTGG- 1061
                           i  iii?  ivi       i i   -            i --   i -
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT--CTTAGA 539

  chr1_236856063_   1062 -GAAAATAAAGGACATTATCTTTACCAACTTAGAGAAGGGAAGGATTTCT 1110
                         -     i v   ?vvvv     iiiv v   i ivv   v  v i     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_236856063_   1111 T 1111
                          
  L1M4_orf2#LINE/    590 T 590

Transitions / transversions = 1.58 (109 / 69)
Gap_init rate = 0.04 (24 / 578), avg. gap size = 2.12 (51 / 24)  

 352 29.63 4.71 3.37  chr1_236856063_236858240.rev     1415  1711 (467)    L1M4_orf2#LINE/L1      583   883 (25)  

  chr1_236856063_   1415 GATTTCTTAAATAAGGCAAAAAAATTAT--GCACCATCAAGAAAAAGGTT 1462
                          i       i   v i  vv    vi i--   v  --  ii    ii v
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACA--AAAGAAAAAATA 630

  chr1_236856063_   1463 GATAGATATCACTACATAGAAATAAAGAACTTTTAAAAT-CAATAGTCAG 1511
                             i  vvv   v   vi    v  i       iviv -   vi v  v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_236856063_   1512 CAAAAGAAAAATGAAAAGACAAGCTCCAAAGTGGGAGCAGGGCTTGGGAA 1561
                         i vv ii   i           v iv  i i      v iivv  v v  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_236856063_   1562 A--ATTTATCTGACCAC--ATTTTAATGTCCTCAATATATAAAGATGTCC 1607
                          --  v       iv v-- i  --i i   vv            vv  i
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTT--GTATCCAGAATATATAAAGAACTCT 778

  chr1_236856063_   1608 TAATAACTCAATAAGTAAAAGACAAGT----CA-TTAAAAAACAGCCAAA 1652
                           -i          vv         i ----  -  ?     ii v    
  L1M4_orf2#LINE/    779 TA-CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr1_236856063_   1653 AGACTCACAATGG-CATTACAGAGAAAAGGAAACAACTATAAATGTGTGA 1701
                         i  i ii-   i -    v vvv--    i i i --  i     vvii 
  L1M4_orf2#LINE/    828 GGATTTG-AATAGACATTTCTCC--AAAGAAGATA--TACAAATGGCCAA 872

  chr1_236856063_   1702 -AAACACATGA 1711
                         -  i       
  L1M4_orf2#LINE/    873 TAAGCACATGA 883

Transitions / transversions = 1.07 (45 / 42)
Gap_init rate = 0.05 (14 / 301), avg. gap size = 1.71 (24 / 14)  


2541 27.29 3.93 1.07  chr1_236868763_236873344     3251  4089 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr1_236868763_   3251 AAAATGACCATACTGTTCAAAGCAATCTACAAAATTGCAGAAGTGCAATT 3300
                           i   i v     vii    vii       i v i----- ii     i
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTC-----AACGCAATC 90

  chr1_236868763_   3301 CCTATCAAATTACCGACATCATTTTTCACAGAAA-----AAAC-AATCCT 3344
                                  v v  ii vv v     ii      -----  i -i     
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr1_236868763_   3345 AAAATTCATATGGAGCCAAAACTGAGCCTGAATAACCAAG-TAATCTTAA 3393
                                       iviiv  vv  v  v     i    i-i      i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_236868763_   3394 ATAAAAAGAAAAAAAA-ACAGGCATCACGTTTTGTAGCTTCAAATTGTAC 3442
                          v  i     v   iv-iv   vv    ii  ivi ii      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_236868763_   3443 CACAAGACTATAGTAACCCAAACTGCATGGTACTGGTACAAAATTAGGCA 3492
                         i    ii   i     i v i  v ii         i i  iiv   i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_236868763_   3493 CAATAGATCAGTAGAACAGAATAGAGCACCAAGAAACAAAGCCACATATG 3542
                         i -       i i   i     v   vii v     i   v   i i  v
  L1M4_orf2#LINE/    291 TA-TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_236868763_   3543 TACAACCAACCAATCTTAAACAAAGCTGACAGAAATAAACAATGAGTAAA 3592
                           iiii   iii  i  vi    i v  v  ii vi vv     i v   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_236868763_   3593 GGACACTGTATTCAATAAATGGTGCTAGGACAATTGGATAGCCATATGTA 3642
                          i i v v v     i          i      i      ?   i   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_236868763_   3643 AAACAATGGAACTGGACCCCAGTCTCTCACCATATACAAAATTTTACTCA 3692
                            v    i ii        vii   v              v  v     
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_236868763_   3693 AAATGGGCTAAAGACTTAAATGTAATACCTGAAACTGTAAAAATGCTAGA 3742
                               iii ?    i         v v  i     i     v vi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_236868763_   3743 AGAAAACCTAGGAAAAATTCTTCTGGACATTGGCCTAGGCAAAGAATTTA 3792
                                v    ?iv  v     vv   v    vi       v i-   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTC 588

  chr1_236868763_   3793 TGACAAA-GACCTCAAAAGCAAATGCAACAGAATAAAAAATAGATAAATG 3841
                          v v v -   vi        v v      i  v               v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_236868763_   3842 GGACTTAGTTAAA--TGAAAACGCTTCTGCACAGCAGAAGAGATAATTGA 3889
                               vi i   -- i     --  i  ii vv  i i  v iv  ii 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAAC--TTTTGTGCTTCAAAGGACACTATCAA 686

  chr1_236868763_   3890 CAGAGTAAACAGACAACCTATAGAATGGGATAAAATACTTGCAAATTATG 3939
                         v i   i  v        i i         v      i        i  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr1_236868763_   3940 CTCCTGAAAAAGAATTAGTATCAAGAATCCACAAGGAACTCAAACAACTC 3989
                         ivi    v  i i i v     v     vi i  i      vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr1_236868763_   3990 AACAAGAAGAAGACAA----TCCCATTAAAAAGT------------TGA- 4022
                           i  v  i       ----i  v   ?    i ------------   -
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr1_236868763_   4023 ----CATTTCTT-AAAGAAGACATATAAGTAGTCAACAAATTTATGAGAA 4067
                         ----       i-        i   i  i i i   i  iivi    i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_236868763_   4068 ACTGCTGAACATTATTAGTCAT 4089
                         iv    v     i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (137 / 88)
Gap_init rate = 0.02 (14 / 863), avg. gap size = 3.00 (42 / 14)  


 687 25.32 19.31 0.43  chr1_237235394_237237918      866  1098 (1427)    L1M4_orf2#LINE/L1        1   277 (631)  

  chr1_237235394_    866 TGGAAAGATACCGTGTGTTCATGGATTAGAAGAATTAATATTGTGAAAAT 915
                                   i vii            i     v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_237235394_    916 ATACATGCTCCTAAAGAT-ATCTACAGGTTCAATTCAATCCCTATCAAAA 964
                         ivvv  i    iv  iv -        i     iv               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_237235394_    965 TTCCAATGATTTTTTTTCACAGAAATAGAAAAAGCAATCTTAAA------ 1008
                          i   iiviii      -i       v  v  ivii   i    ------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_237235394_   1009 -----------------------------------TCTTGAGCAAAAAGA 1023
                         -----------------------------------      iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_237235394_   1024 ACAAAGCTGGAAGTAATACACTACCTGCTCTCAAAACCTACTAC-CAGAT 1072
                               i    i vvvi     v  iiv i       i      -v  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_237235394_   1073 ATAATACTCAAAATAGCATGGT--TGGC 1098
                          i i  v    i i  ii    --    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGC 277

Transitions / transversions = 1.68 (37 / 22)
Gap_init rate = 0.02 (5 / 277), avg. gap size = 9.20 (46 / 5)  

2514 24.77 1.56 0.31  chr1_237235394_237237918     1398  2039 (486)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr1_237235394_   1398 AAAAAAGCATGGCTCTGGCATGAAAACAGATGCATGGACCAATAGAGCA- 1446
                           i v  ii   iv       i ii i   iii  i  i    i  ii -
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr1_237235394_   1447 -ATAGAGAGCTCAGACATAAATCCATGCCTTTATGGTCAATTGATCTTTG 1495
                         -  v     ii    v     i    i v                i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr1_237235394_   1496 ACAAAGATGCCAAGAACGAACAATGGGGGAAGAAAAGTCTCTTCAACGTA 1545
                             i i        v ivv        i     v     i      iv 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr1_237235394_   1546 TGGTGTTGGGGAAAACCAGAAATCCATATGCAGAAGAATGAGATCAGATC 1595
                              i    - v   ii  v ?   i     i        ii ii  i 
  L1M4_orf2#LINE/    409 TGGTGCTGGG-ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr1_237235394_   1596 TTTATCTCACACCATTTACAAAAACTAACTCAAAACAGATTAAAGACTTA 1645
                         ii  i          v        i          ii   i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr1_237235394_   1646 AATGTAAGACCTGAAA--GTAAAACTACCA-AAGAAAACTTAGGCGAAAA 1692
                                  v  i   --i       vii -        v    ? v   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr1_237235394_   1693 GTTCCATTACATTGGTCTGGGCAATAATTTTTAAAATATGACCTCAAAAA 1742
                         vi i i v  v    vi i      ii   i v i       vi     i
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr1_237235394_   1743 CACAAGCAACAAAAGTAAAAATAGACAAGTGGAATTACATATAAGTAAAA 1792
                                        v         i  i v i i v   vv  i v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr1_237235394_   1793 AACATCTGGACAGCCAAGGAAACAATCAACAGAGTGAAAAGACAACCTGT 1842
                            v i  vi vv v     v  v     v i               iii
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr1_237235394_   1843 GAAATGGGAGAAAATATTTGCAAA--ACACACCTGGTAAGAGGTTAATAT 1890
                         ii                      -- i i i   i    i ii vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr1_237235394_   1891 CCAAAATATGTAAGGAGCTC--AAAACTGCTCAATAAGAAAACAAGTGAT 1938
                            i     i   i  i   -- v    vvvi     i  i    i i i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr1_237235394_   1939 CCATTTAAAAATTGGATGAAGGACCTGAATAAATATTTCTCAAAATAAGA 1988
                            v  ?    v   iii     ii      i i       v   v    
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr1_237235394_   1989 CATACAATTAACCAATGAGTATGTGAAAA-ATGCTCATTATTCATCATCA 2037
                         i      v ii     i  i ii      -       vi  -  ??????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT-CAZZZZZZ 906

  chr1_237235394_   2038 GG 2039
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.23 (107 / 48)
Gap_init rate = 0.01 (8 / 650), avg. gap size = 1.50 (12 / 8)  


3067 27.13 1.11 0.55  chr1_237384880_237387937.rev     1665  2567 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_237384880_   1665 TGGAATAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 1714
                              vi i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_237384880_   1715 GGCCATAGTGCCCAAGGTAATTTATAGATGCAATGCTATCCCCATCAAGC 1764
                            v   v v     iv i  i  i    v   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_237384880_   1765 TGCCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 1813
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_237384880_   1814 ATGGAACCAAAAAAGAGCCCACATTGCCAAAACAATCCTAAGCCAAAAGA 1863
                               viiv  ii  v  viv  v            i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_237384880_   1864 ACAAAGCTGGAGGCATCACGCTAACCTGACTTCAAACTATACTACAAGGC 1913
                               i      vv    i  v-  ii i      viv        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAAGC 248

  chr1_237384880_   1914 TGCAGTAACCAA-ACCGCATGGTACTGGTACCAAAACAGAGATATAGACC 1962
                          i      i   -  v ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_237384880_   1963 AGTGGAACAGAACGGAGCCCTCAGAAATAATACCACACATCTACAACCAT 2012
                          i     i    iv   vvii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_237384880_   2013 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 2062
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_237384880_   2063 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCTGA 2112
                         v  i  i              v      v  ?   i v i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_237384880_   2113 AACTGGATCCCTTCCTTACACCTTATACAAAAATTATTTCAAGATGGATT 2162
                          ii    i    v   i     v             vi    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_237384880_   2163 AAAGACTTAAATGTTAGACCTAAAACCATACAAACCCT-AAAAGTAATCC 2211
                          ?    i       v   v       i   -    i  - i   v  v v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACA 547

  chr1_237384880_   2212 TGGGCA-ATACCATTCAGGACATAGGCGTGGGCGAGGACTTCATGTCTAA 2260
                          i  ?i- v i -   iv   v v  vv i   i v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_237384880_   2261 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 2310
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_237384880_   2311 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2360
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_237384880_   2361 AGGCAACCTACAGAATGGGAGAAAATGTTTACAATCTACCCATCTGACAA 2410
                           i     i                 i   i   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_237384880_   2411 AGGGCTAATATCCAGAATCTATGAAGAACTTAAACAAACTTA-CAAGAAA 2459
                         i  i  vi          v   i       ivv    -  i -i  v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAA 795

  chr1_237384880_   2460 AAATCAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 2505
                           iv   ----   v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_237384880_   2506 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAAT-CTCAT 2554
                            v        i  vi viii     v ii          i  -    v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_237384880_   2555 CATCACTGGCCAT 2567
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


2888 24.80 4.91 1.14  chr1_237410178_237412473      929  1803 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_237410178_    929 TGGAAAGACATACCAAATATGTGGATAAGAAGACTCAATATTATTAAGAT 978
                                 i  v   vi vii     vi       i      i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_237410178_    979 GTGAGTTCTTTCCAACTTGACCTGTGAATTCAATGCAATCTCCATATAAA 1028
                          vv i v  ii    v    i  iiii      i      i i  vv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_237410178_   1029 TCCTAGCATAC----TTTGAGGATATTGACAAACCGATTCCAAAGTTGAA 1074
                            i   - i ----    vi  v        i i   i i   i  v v
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_237410178_   1075 GTGGAAA-GCAAAAGACCCAAATTACACAACACAATACTGAA---GGAAT 1120
                         i      -    ii      i v  vv   v     vi    --- i iv
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_237410178_   1121 GCAATGACAGAGAGTTGACACTACCAAACTTCAAAACTTACTATAAACCT 1170
                         i   v vii   iii v     v  v  i              i   v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_237410178_   1171 ATAGTAATCGAGGCAGTGTGGTATTGGCAAAAGAAGAAAAAAAATAAATC 1220
                          i       i  i          i     v   i v i v v -  i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGATC 298

  chr1_237410178_   1221 AAGGAAAAAGAATAGAGATTTCAGGAAGAGACTTA--------------- 1255
                           v i  v     v    v i   i  v i  ii ---------------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_237410178_   1256 ---------GACAAGGTAGAAAAGGTAATCGAATGGAGAGAAGATCCTAT 1296
                         ---------       vv vv   iiv  iv     i  i ii  vv v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_237410178_   1297 TTTCAAAAAATGGTGCTGGAACAACTAGACCTCTACATGCAAAAAAAATA 1346
                               v            i      i  iv? i          i  vv 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_237410178_   1347 AATATAGACTCCAGATTTTAC-TAATTTCACAAAAATTAACTTAAAATAA 1395
                          i - i   i  -v ii i  -iv  v -             i     ii
  L1M4_orf2#LINE/    449 AGT-TGGACCCC-TACCTCACACCATAT-ACAAAAATTAACTCAAAATGG 495

  chr1_237410178_   1396 ATTATACAACTAAAAATAAACTGTAAAACTATAAAACCTTTAGAATATAA 1445
                           i ? v v     vi   ivvv              ii      v v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_237410178_   1446 CATAGGAGAAAATCTAGGTGACCTTGAGTTTGGCAATGACTTTTTAGACA 1495
                               ? v      vv         i   v       ii  i     i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_237410178_   1496 CAACATCAAAAGCACAATCTATGA--GAAAAAATTG-TAAGTTGGAATTT 1542
                         ii   i           v v ii --        v -   i     v  i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_237410178_   1543 ATTAAAATTTAAAACTTTGATTCTTTTAAATACACCATTAAGACACTGAA 1592
                           i      v        vi v   iv  iv    i  i    v v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_237410178_   1593 A-GACAAACTACAGACTGGGGGAAAATCTTTGCAAA--ACGTATCTGATA 1639
                          -     v i     v    i      v        -- ii         
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_237410178_   1640 AAGCACTGGTATCCACAATATACAAGGAACTCTTACAATTCAACAATAAG 1689
                          i v   v       v      i  i            i    i     i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_237410178_   1690 AAAACAA----CACAATTAAAAAATCGGCAAAATATAATATCTGAACAGA 1735
                           i    ---- v     ?      v      iv  -----i    i   
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-----TTGAATAGA 840

  chr1_237410178_   1736 AAACTCAACAAAGAAGACGAACACTTGGCAAATATGCATGTGAAGAGGTG 1785
                         v vi  vv         iiv   vv    v    v   ii    i  i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_237410178_   1786 CTCAATATCATATGTTAT 1803
                              i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (121 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.31 (53 / 16)  


2254 25.00 7.37 2.76  chr1_237482305_237486669.rev     3007  3874 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_237482305_   3007 TGGAGAGACATACTTCAAATCCATGAA---GAA----TAACCTTGTATAA 3049
                             i   i  v --  vi i    i ---   ----   iv    -   
  L1M4_orf2#LINE/      1 TGGAAAGATATCC--CATGTTCATGGATTGGAAGACTTAATATTGT-TAA 47

  chr1_237482305_   3050 AA-GCCAGTTCTCCCCAAATTGATACACAAGTTTAATGAAATTCCTTTCA 3098
                         i - v  i v              vi   ii  i  i v   i   v   
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_237482305_   3099 AAACCCCAGCAAGATTTTTTTGTAGATATAGA---GATAATTCTAAGATT 3145
                            i      v- vi       i   v  v  --- v i  i    i   
  L1M4_orf2#LINE/     98 AAATCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr1_237482305_   3146 TATAGGTAAA-GCAAATGAAGTAGAACAGGTAAAACAATTTTGAAA--GA 3192
                         i   v v   -    iv  vvi    i  vi        i      --  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_237482305_   3193 AAAATAATGTGGGAGGAATTTATTTTATGTTTATATTATATATTCAAGAC 3242
                          i  i  v  v      ------i i iii  vi--i -  -     i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGA------CTCACACTTCC--CA-AT-TTCAAAAC 236

  chr1_237482305_   3243 --ATTATATAACTGTGGTAAACAGAACTGTGTGGTGTTGGTAGAAGGATA 3290
                         -- i  i v i  iii    v  ii  v       ii   i v       
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr1_237482305_   3291 GACATGTAGATCAATAAAACAGAATAGAGAATCCAGAAATAGATCCACAC 3340
                              i         ii  i     v    i          i i   i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_237482305_   3341 AAATAGACACAATGGATTTTTGACAAACATGGAAAAGCAATTCAACTGAG 3390
                          vv  vivv    v      i     ivi  vv  ii v      -  i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGG 385

  chr1_237482305_   3391 GAAAGA-TAGCTTTGTCAAGAAATGGTGCTAGAGCTATTGGACATTCACG 3439
                               -   ii  v    v          i ii v i    i ?i   i
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_237482305_   3440 GGCAAAA--AGGAAGTT---CCACCTAAGTCTCACAACTTATACAAACAC 3484
                         v      -- v      ---  -    --i      v v        v i
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACC-CCTA--CCTCACACCATATACAAAAAT 482

  chr1_237482305_   3485 TAATACAAAATGGA----------AAAT--------TAAAACAAAAAAAA 3516
                            iv         ----------    --------      v v    v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr1_237482305_   3517 T-TTAG--GAAAATAGTAGGAG-AAATTATTGGATATCTTGGTCTAGGCA 3562
                          -    --     i -    ? -    iv i vi- i     vi      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACA-TAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCA 580

  chr1_237482305_   3563 AAGAGTTCTTAGATTTAATACTA------TAATCTATAAAA-----AGTT 3601
                          v iv         v i i  i ------i  v v i    ----- i v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_237482305_   3602 GATAAATTGGACCTCATCCAAATTAAAAACTTTTTTTTTTTCTGAAAAAG 3651
                                     i     v               v vi  i----   i 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC----AAAGG 676

  chr1_237482305_   3652 ACCTTGTGAAGAGGGTGGAACAACAAGGTACAGAGTAAAAGAAATTATCT 3701
                           vi i v    ii   i  vi    vvi     i iii     v   i 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr1_237482305_   3702 GTAAACCACATATCCAAGAGAGGACTAGTATGTAGAATATAAAAAGAACT 3751
                          i   i  i     ii v ii     v    vi        v        
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr1_237482305_   3752 G--AAAAAACAATAGCAAAAA---AAAT----TAATTAGAAAATGGTCAA 3792
                         v-- v  vv     ii     ---    ----i    ?i       v   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr1_237482305_   3793 AAGACATGAAGAGACGTTTCACAGAAAAGGATGTACCTACACCAAAAAAG 3842
                          i  iv    v    i    v vi  i i   i   vv iiv v  v   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr1_237482305_   3843 CATATGAAAACATGTTCAATACCATTAGCCAC 3874
                           i       v   i    i i  ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (128 / 86)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 2.67 (88 / 33)  


 802 28.53 2.22 3.60  chr1_237678118_237681727.rev     1919  2279 (1331)    L1M4_orf2#LINE/L1        1   356 (552)  

  chr1_237678118_   1919 TGGACATAAATGCAATTTTTACTGATTGGAAAACTCGACATAGTAAAG-T 1967
                             v v v  v v  v  i iv        i   ii i  v  v   - 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_237678118_   1968 CTCAGTTCTTCACAAACTGACATACAGATTTAACATAATTCTTATCAAAA 2017
                         vv  i v  i v    i   iv        i   ii   i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_237678118_   2018 TATGAGCAAAATTTTT-ATAAATATTGA---GATTATTTTAAAATTCATA 2063
                          viv   vivv     -ii i v     --- v v  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_237678118_   2064 TGAAAATTCAAAGGAACTAAAATAGCTAAAACAATTTTGAAAA-GAAAAA 2112
                           i    v   i   v i i      i        i       -   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_237678118_   2113 TAATGTGATAAAAATAAATCTGCCTCATTTCAAGACTTACTATGTCACTA 2162
                         i  v  viv ii v v vv  v  iv       i        iivvi   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_237678118_   2163 TAGTA-TCAAGATTATCAGTGGAACAGACACATAAATCCACTAGCAATCA 2211
                         i    -      ivi --    v  v i  i vii  vv  -----  --
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGT--GTGGTACTGGCATAAGGATAGAC-----AT-- 291

  chr1_237678118_   2212 GAATAGAT-AGTTTGGAACACAATAGATGGTGTGGAAGTATACCCATACA 2260
                         --      - i --    i v   v  vi  vii   i  v         
  L1M4_orf2#LINE/    292 --ATAGATCAAT--GGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr1_237678118_   2261 GATAGGACCAGTTGATTTT 2279
                         vv  v ii  i        
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTT 356

Transitions / transversions = 1.10 (54 / 49)
Gap_init rate = 0.03 (10 / 356), avg. gap size = 2.10 (21 / 10)  

1616 24.56 3.71 3.53  chr1_237678118_237681727.rev     2555  3120 (490)    L1M4_orf2#LINE/L1      342   908 (0)  

  chr1_237678118_   2555 TGACCAATTGATTTTTTGGACAAAGATTCAAAAGCAATTCAATGAAGGAA 2604
                           ii           i--     i i v v  ii v        ii i  
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTC--GACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_237678118_   2605 ACATCACCTTT-CAACAAATGATACTAGAGCGATTAAATGTCCATAGACT 2653
                         iv  vii    -         i i  i ii i i ii  i?   i vi v
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_237678118_   2654 AAA--ATAAA--TGAACCTCAAGTCTCACACCTTGTACAAACTTTAAATA 2699
                            --  i  --  i   i v -i        v i      -----   -
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTA-CCTCACACCATATACAAA-----AAT- 482

  chr1_237678118_   2700 TATTAACTCAAAATGGAGCATGGACTTAAATGTAAAATGTAAAACTTTAT 2749
                         ---              v  ?i   i         i vv       --  
  L1M4_orf2#LINE/    483 ---TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT--AT 527

  chr1_237678118_   2750 AAAAAGTGTA-AAGAAAA---AGCAAAAAATATTCAGAATCTAGTCCTAG 2795
                             vviv  -       ---  v?iv    v   ivi i  v vvi   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr1_237678118_   2796 GCAAATAGCT-CTAAGACTTGATACCGAAAGCATGATTTATAAAAGAAAA 2844
                             - i i -  v   iv   i   i      ii viv i         
  L1M4_orf2#LINE/    578 GCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_237678118_   2845 AGTGAATAAATTGGACTTTATCAAAATTAAAACCTTTTGCCCTGTGAAAG 2894
                          i ii             i             v      iv  vii  i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr1_237678118_   2895 ACTTTGTTAAGTAAGGATGAAAAGCCAAGCTAGAGACCGGAAGAAAATAA 2944
                           vi i i   v   --       v   v i v   vi  i        v
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAG--TGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_237678118_   2945 TGGTAAACCCCATATCTAACAAAGGACTAGTATCTAGAATATAGACTATA 2994
                          v i   i vi      i i  i     v     i        ---  v 
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA---TAAA 771

  chr1_237678118_   2995 GAACTTCTA--ACACAACAGTAAGAATGCAAA-----CAATTAGACCAAG 3037
                              ii  --  v   i i   i  vi    -----     ?i vv v 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_237678118_   3038 GGCAAAG-ATATAAATAAACATTTTACCAAAGT---TATACAGATAGCAA 3083
                                -  v i    i      iv      v---      i  i  v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_237678118_   3084 ATAAGCACATAAAAAGATGTCCAACACCTAGGGAAAT 3120
                                   i        ii     i v????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (85 / 50)
Gap_init rate = 0.03 (18 / 567), avg. gap size = 2.28 (41 / 18)  


3221 26.97 1.11 0.33  chr1_237914573_237921226.rev     5263  6163 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_237914573_   5263 TGGAAATACATTCCATGCTTATGGAAAGGAAGAATCAATATCCTGAAAAT 5312
                               v i  i     i i     vv      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_237914573_   5313 GGCCATACTGTTCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5362
                            v     vii    v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_237914573_   5363 TACTA-TTGACTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAC 5410
                          v i -i  v   i  ii     v v  v  i-  - iii    v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_237914573_   5411 ACGGAACCAAAAAAGAGCCTGTATAGCCAAGACAGTCCTAAGCAAAAAGA 5460
                          i    viiv  ii  v  v v        i   i  i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_237914573_   5461 ATAAAGCTGGAGGCATCACACTACTTGACTTCAAACTCTACTACAAGGCT 5510
                          i    i      vv       v iii i      vii        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_237914573_   5511 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5560
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_237914573_   5561 ATGGAATAGAACAGAGGCCTCAGAAATAATGCCACACATCTACGACCATC 5610
                                    iv   ivii         vv   i    i  i ii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_237914573_   5611 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGTTTCCCTA 5660
                             i  i     ivv  v   i v  vv            iv vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_237914573_   5661 TTTAATAAATGGTGCTGGGAAGACTGGCTAGCCATATGCAGACAACTGAA 5710
                           i  i              vi     v  ?   i     i vi v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_237914573_   5711 ACTGGATCCCTTCGTTACACCTTATACAAAAATTAACTCAAGATGGATTA 5760
                         ii    i    v v i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_237914573_   5761 AAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5810
                         ?    i           v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_237914573_   5811 GGCA-ATACCATTCAGGACATAGGTCCTGGCAAAGACTTCATGACTAATT 5859
                           ?i- v i -   iv   v v  viiv     v ii   v iiv  vvv
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_237914573_   5860 CACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATTGTATCTAATT 5909
                                    vvi         ivv     v  i      v ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_237914573_   5910 AAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 5959
                           iv v  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_237914573_   5960 GCAACCTACAGAATGGGAGAAGATTTTTGCAATCTATCCATCTGACAAAG 6009
                         i     i              i  v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_237914573_   6010 GGCTAATATGCAGAATCTACAAGAAACTTAAACAAATTTACAAGAAGAA- 6058
                          i  vi   v      v  i  ii    ivv    v iv i  v  i  -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_237914573_   6059 ------AACCCCGTCAAAAAGTGGGTGAAGGATATGAACAGACACTTCTC 6102
                         ------     vi i?    i    ii      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_237914573_   6103 TAAAGAAGATATTTATGTGGCCAAGAAACATATGAAAAAAAAGCTCATCA 6152
                         i           vi vi       v  i  i       i v-     v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACA 897

  chr1_237914573_   6153 TCACTGGTCAT 6163
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2917 15.30 8.53 2.25  chr1_238132345_238133921      470  1090 (487)    L1M4_orf2#LINE/L1      249   908 (0)  

  chr1_238132345_    470 TACAGCAGTGCAAGAACAGCCTAATACACAGCATAAGGACAAACATGTAG 519
                              i i -     -   iv ii   -ii         i i    i   
  L1M4_orf2#LINE/    249 TACAGTAAT-CAAGA-CAGTGTGGTAC-TGGCATAAGGATAGACATATAG 295

  chr1_238132345_    520 ACCAATGGAATAGAATAGAGAGCCAAGATATAAACTCTTACATATATGGT 569
                          i              v     i v   v      i v     v      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_238132345_    570 CCATTGATTTTTGACAAGGATGCCAAGGCCATTCAATGGGGAAAGGAGGA 619
                          v         i       i       i                 i ---
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA--- 392

  chr1_238132345_    620 AAGGACAGTCTTTTCAACAAATGATGCTGGGAAAACTGCATATCCATGTG 669
                         -----i                 i        v     v   ?   ii  
  L1M4_orf2#LINE/    393 -----TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_238132345_    670 CAAATGAATGAAGTTGGAGCCTTACATTATATCATATATAAAAATTAACT 719
                             v             v  i   v i i i      i           
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_238132345_    720 CAAAATTGATTGGAGACCTATATGTAAAAGCTAAAACTATAAAACTTTTA 769
                               v   ii?       v      i                  i   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_238132345_    770 GAAGAAAAC---------------------------------------TT 780
                                  ---------------------------------------  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_238132345_    781 CTTGGGTATGACACCAAAAGCACAGGCAACAGGAGAAAAA-TAGCTAAAT 829
                            i i                  i      ii       -   v     
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_238132345_    830 TGGACTTTATCAAAATTAAAAACTGTTATGCATCAAAGGGCACTATCAAA 879
                                i                v  i   v       i         i
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_238132345_    880 AGAGTGAAAAGACAGCACAGCAAATGGGAGAAA-TACTTGCAAGTCATAT 928
                          i            i v  vvi           -  i      i      
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_238132345_    929 ATCTGATAAGG------CATC---AATATTATAAAGACCCCCTACAACTC 969
                                    ------i   ---     -       v i i        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATAT-ATAAAGAACTCTTACAACTC 786

  chr1_238132345_    970 AACAACAAAAAACTCCACACAACCCAATTCAGAAATAGGCAAAGGATCTG 1019
                           i  i     iv--  v i         ? i    i          i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_238132345_   1020 AGTAGACATTACTCCAAAAA---TATACTAATGGCCTAAAAGCACATGGA 1066
                          i        v       i ---     v       v v         i 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_238132345_   1067 AGGAAACTTACTGTGATTAGTCAT 1090
                          i  vi  i vii v ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (62 / 30)
Gap_init rate = 0.02 (12 / 660), avg. gap size = 5.58 (67 / 12)  


 734 23.40 4.17 6.73  chr1_238292810_238295880      122   433 (2638)    L1M4_orf2#LINE/L1      605   908 (0)  

  chr1_238292810_    122 AAGCACTGAGTA-CAAAAGAAAAGATAGGTAAATTGAATTATATTACAGT 170
                               -i  i -          i    i       i i vi  i v i 
  L1M4_orf2#LINE/    605 AAGCAC-AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr1_238292810_    171 TTAAAATTCCTGTTTACCAAAGAGAGACTATTAAGAAAGAAAAAAGGCAA 220
                          v    i ii   vivi     -  v     i       vi     i   
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_238292810_    221 GCTGTAGAATGGCAGAGA---TTTTCA--TTACCTGTAACTAAGAAAGGA 265
                         v iii       v   i ---   v  -- i -- i  v  i v  i   
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCA--TATATCTGATAAGGGA 750

  chr1_238292810_    266 CTTATATCTAAAATATATAAAGAACTCCAACAAATCAATAAGAAAAAT-C 314
                            i    i i                iv    v       v     v- 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr1_238292810_    315 AAGGCAATCCAGT---AGGATAGGCAAAAAAAAAAAAAAAAAACCATGAA 361
                           i-i  i   i --- ii  i      ii -------------iv    
  L1M4_orf2#LINE/    801 AAA-TAACCCAATTWAAAAATGGGCAAAGGA-------------TTTGAA 836

  chr1_238292810_    362 CTAACA---CTTCAGAGAAGAGGTTATGCAAATAGTCAATACATATATTA 408
                         ivi   ---  i  i      ---   i     i i     vii i  v 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGA---TATACAAATGGCCAATAAGCACATGA 883

  chr1_238292810_    409 AAAAATGCTCAACTTTCTTAATAGT 433
                            i         v iv????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.32 (51 / 22)
Gap_init rate = 0.04 (12 / 304), avg. gap size = 2.83 (34 / 12)  

2497 23.58 3.14 1.10  chr1_238292810_238295880      705  1340 (1731)    L1M4_orf2#LINE/L1        2   650 (258)  

  chr1_238292810_    705 GGAGAAATATTCCATGTTCATGGGTAAGAAGATTCAATATCATCAAGATG 754
                            i i    i            i vi     i i     ii i      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_238292810_    755 TCAGTTTTTCCCAACTTGATCTAAAAATTCAATGCAATCCCAACCAAAAC 804
                         v  i vi i     v        v i      i        v i     i
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_238292810_    805 CCCAGAAAATTACTTTGGGGATATTGAGGAACTGATTCTAAAGCTAATAT 854
                              vvivi vi    vi  v     vi i     i     ii v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_238292810_    855 GGAGAAGCAAAAGACACAGAATAGCAAACACAATGTTGAAGAAGAAGAAT 904
                            i v    ii   v         v  v     v     i        i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_238292810_    905 AAAGTTGGGGGACTGATA----------TCAAGACTTAGTATAAAGCTAT 944
                                 i     v i ----------    i     v  i       i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_238292810_    945 CGTGATCAAGACAGTGTGGTACTGGCA-----ACAGACATAAGAAATAGA 989
                         v  i                       ----- i       -----    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-----TAGA 296

  chr1_238292810_    990 TCAATGGGACAGAATAGAGAGCCCAGCACCAGACCCACATAAATACAGTC 1039
                                i i     v     i    v vi i     i i vv  ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_238292810_   1040 AACTGATCTTTGACAAAGGAGCAAAGATAACACAATGGAGAAAAAGATA- 1088
                           i    i  i     i  v  v    iv iv      i    i -   -
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAG 395

  chr1_238292810_   1089 -CACTTCCACACATGCTGCTGGAACAACTGGACATCCACGTGCAAAA-AA 1136
                         - vi   v   v   v      i         i ?    i       -  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_238292810_   1137 TGAATTCAGAAGCA-ACCTTACATCCTTCCCAAAAATTAGCTCAAAATGG 1185
                             v ii  vv v-    i   i v viv         i          
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_238292810_   1186 ATTATAAGCCTAAATGTATGATGTAAAACTGTAAAACTCCTAGAAGGTAA 1235
                           i ? ii          v  vv       i        i      iv  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_238292810_   1236 CATAGGAG-AAATTTTAAATTTCCTTCAATTTGGTAATGATGTTTTAGAT 1284
                               ? -    i  vi- vv    vii  v  i    i v i      
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_238292810_   1285 ACAACACCAAAGACACAATCTATGAAATAAGGAATTGATAAAGTTCACCT 1334
                          ii        ii     v v ii   v  ii   v      v vv  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_238292810_   1335 CATAAA 1340
                            v  
  L1M4_orf2#LINE/    645 CATCAA 650

Transitions / transversions = 1.45 (87 / 60)
Gap_init rate = 0.01 (9 / 649), avg. gap size = 3.00 (27 / 9)  

 614 24.03 0.00 0.00  chr1_238292810_238295880     1664  1817 (1254)    L1M4_orf2#LINE/L1      633   786 (122)  

  chr1_238292810_   1664 TAAACTGCACTTCATTAAGATTAAAATTATCTGCTCTGTAAGAGACACTG 1713
                             i  v       i  i       viv i  iv  vi  ii      i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_238292810_   1714 TCAAGAGAATGAAAAGACAAGACAAAGACTGGGAGAAAATGTTTGCAAAA 1763
                               i i           vv  v   v           i        v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_238292810_   1764 GACACATCTGATAAAGAACTGTTATCTAATATATAAGAAGAACTATTAAA 1813
                         v i i         i i   vv    i iv     vi       v   v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_238292810_   1814 ACTC 1817
                             
  L1M4_orf2#LINE/    783 ACTC 786

Transitions / transversions = 1.18 (20 / 17)
Gap_init rate = 0.00 (0 / 154), avg. gap size = 0.00 (0 / 0)  

 577 19.69 0.00 0.00  chr1_238292810_238295880     2453  2579 (492)    L1M4_orf2#LINE/L1      782   908 (0)  

  chr1_238292810_   2453 AACCCAACAGTAAGAACACAAACAACTCAATTTTAAAATGAGCCAAAGAC 2502
                            i   i i   i  v     i   i     ?v      i  v  i  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr1_238292810_   2503 TTTAACAGACATCTCATCAAGGAAGATATACAGTTGGCAAACAAGCATAT 2552
                           v  i      i  vi   i           iv    v  i     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_238292810_   2553 GAAAAGATGCTCAACATCCTATGTCAT 2579
                                           v????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.00 (0 / 127), avg. gap size = 0.00 (0 / 0)  


1166 25.13 2.65 4.76  chr1_238528902_238531191.rev      481   858 (1432)    L1M4_orf2#LINE/L1      221   590 (318)  

  chr1_238528902_    481 TTCCTAAATTAAAAA--------AAGGGCACAGTAATCAAGACAGTGTGG 522
                             i  v  v    --------  i vi                     
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr1_238528902_    523 TATTTGTGAAGAAACAGACAAAAACATCAATGAAACAGAATAGAGAGCTC 572
                           i v iiv iii i     v v v       i  i     v     ii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr1_238528902_    573 AGAAATAGATCCACATAAATAAAGTTAACTAATCTTTAACAAAGGAGCAA 622
                                i i   i i vv  vi  i  i i  i  ii    i  v  v 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr1_238528902_    623 AGGCAGTACAGTGGAGAACAGATTGTCTTTTCAACAAATGAAGCTGGAAC 672
                           i vi v  i   i   vii  v                iv     i  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr1_238528902_    673 AA-TGAACACCCACATGCAAAAGAAAAAAAAAAGAAAACAAAAGAATCTA 721
                           -  i i ?               v-----------------   vi i
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAAT-----------------GAAGTTG 453

  chr1_238528902_    722 GACACAGACCT-ACATTCTTTATAAAACTTAACTCAAAATGAATAATAGG 770
                            v vv    -   iiv v  i    v             i  v ?  i
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr1_238528902_    771 CCTAATTGTAAAATGTAAAACCACAAAAATCCTAGAAGATAATATAGGAG 820
                              v     i vv      i i    v  i       v  i     ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr1_238528902_    821 AAAATCTAGATGGCCTTGGTGTTTGGTAACGACTTTTT 858
                         v      vvi  i      -   v  i  i ii  i  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.49 (55 / 37)
Gap_init rate = 0.01 (5 / 370), avg. gap size = 5.60 (28 / 5)  

 676 26.67 3.56 1.78  chr1_238528902_238531191.rev     1160  1384 (906)    L1M4_orf2#LINE/L1      577   805 (103)  

  chr1_238528902_   1160 GGTAACGACTTTTTAGACACAATACCAAAATCACAATTCATGAAAGAA-- 1207
                           i  i ii  i     i ii i       v     viv ii      --
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr1_238528902_   1208 --CTGATAAGCTATACTTTATTATTAAATCAAAA--TTTT-TGCTTTGTG 1252
                         --iv     ii iv    i  i --    i    --    -     --ii
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCA--AAATTAAAAACTTTTGTGCTT--CA 672

  chr1_238528902_   1253 ACAGACACTGTCAAGAGAATGAAAAGACAAGTCATAGACTAG-AGAAAAT 1301
                          vi      i      i i           vi  i   v i -       
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr1_238528902_   1302 ATTTGCAAAAGACACATCTGGTAAAAGAATGTCATTCAAAGTATACAAAA 1351
                                  vv i i     i   ii  v vvi  i  i i    i   i
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr1_238528902_   1352 AACCCTTAAAACTCAACAATAAGAAATCAGACA 1384
                            i    v       i     i  iv  i i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATA 805

Transitions / transversions = 3.00 (45 / 15)
Gap_init rate = 0.03 (6 / 229), avg. gap size = 2.00 (12 / 6)  

 358 22.58 1.08 0.00  chr1_238528902_238531191.rev     1707  1799 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr1_238528902_   1707 AGAAACGTGCAGAAGACCTTAATAAACACCTCACCAAAGAAGATATACAG 1756
                          i   i v   i i  ii v    i   ii  v                i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_238528902_   1757 GTAGCAAA-AAGCATCTGAAAAGATACTCCATATCATATGTCAT 1799
                         i i  v  -     iv         i   v i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


3251 27.09 0.44 0.44  chr1_238535156_238541428.rev     4875  5782 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_238535156_   4875 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4924
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_238535156_   4925 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCGTCAAGC 4974
                            v     v     iv i  i           i  v     ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_238535156_   4975 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5022
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_238535156_   5023 TATGGAACCAAAAAAGAGCCCGCATCGCGAAGTCAATCCTAAGCCAAAAG 5072
                                viiv  ii  v  v v  v  v  iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_238535156_   5073 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5122
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_238535156_   5123 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5172
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_238535156_   5173 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGTCGCATACCTACAACT 5220
                                i    i--    i  --        vvi ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_238535156_   5221 ATCTGATATTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5270
                          vi    v  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_238535156_   5271 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5320
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_238535156_   5321 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5370
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_238535156_   5371 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5420
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_238535156_   5421 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5470
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_238535156_   5471 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5520
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_238535156_   5521 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5570
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_238535156_   5571 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5620
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_238535156_   5621 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5670
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_238535156_   5671 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5720
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_238535156_   5721 TCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5770
                           v           vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_238535156_   5771 AGCACTGGCCAT 5782
                          v  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2791 23.83 7.63 1.06  chr1_238554885_238558598.rev     2372  3223 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_238554885_   2372 TGAAAAGACATCGTGTGTTTATGGACTGGAAGACAAAACCTTGCCAAGAT 2421
                           i     i   vii    i     i        vv  iv   ii     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_238554885_   2422 GCCATTGTTATCTATAGTCATCTACGGATTCAAT------------AAAA 2459
                          v  v ii vi i v v v      i       i------------    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_238554885_   2460 TCCCAA------TATTTGCAAAAATAGAAAAACCTATTCTAAAATACAGA 2503
                              i------ v      i    v  v  i iv  i       v  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_238554885_   2504 TGAAATCTCAAAAAAACCCAAGTAGCCAAGTCAATCTTTACAATGAA--- 2550
                           i  viv   iii v  vi i       iv       v v  v   ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_238554885_   2551 CA--GTTAGAGGACTAAGACCTCCTGGTTTCAAA-CTCACTGCAATGCTT 2597
                           --   i       v v  i   iii       -  i   i   v   v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_238554885_   2598 TAGTACCCAAAACAGTATCATACCAGCATAGAGACAGACATAAAGCCCAA 2647
                         i    vi   i     i vi   ii     ii  i       v  vi   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_238554885_   2648 TGCAACACGAA--------CCAAAAA-------ATA------TGTTCA-- 2674
                           v  i -   --------   i   -------   ------  v   --
  L1M4_orf2#LINE/    301 TGGAATA-GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_238554885_   2675 TGATTTTCAACAAGGGAGTCAACACTATTCACGGGGGGAAGGATAGTATT 2724
                                 i       v i   v  i     vv    i   i     v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_238554885_   2725 TTT--TAAATGGTGTTAGAAAAAAAAATAGATATTTACATGGAAAAGAAT 2772
                           i--i        i i i v  v--- i    ?ii     v        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAAC---TGGATAKCCACATGCAAAAGAAT 446

  chr1_238554885_   2773 GAAGTTGGAGCCTTACTTTACACCATATAAAAAACTTTATTCAAAATGGA 2822
                                  v  i   i i          v    v  v i          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_238554885_   2823 CCAAACATCTAATTGTAAGAGCTAAAACTATAAAACCCTTAGAAGAAAAT 2872
                         i  ? v i    v                       i            i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_238554885_   2873 TTAGGGAAAAAT-TTCAAAACATAGAATCTGGCAATAATTTCTTGGATAT 2921
                         v    ?iv    -   ivi  v v ii iv      ii      i     
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_238554885_   2922 GAC--TGAAAGCACAGACAATGACAAACAACAAAAATACATAAAAAGAAC 2969
                            --ii        ii   ---    vi -       v     vv i  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAA---CAAAAGA-AAAAATAGATAAATTGGAC 642

  chr1_238554885_   2970 TTCA---AAGTTAAAAACTTTTAAGTATCTGAGGATACAATCAATAGATT 3016
                             ---  i            iv iv  vi    i  v     v i v 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_238554885_   3017 GAAAATACAATTCACAGAGGGGGAGAAAATATCCACACATTATATATCTG 3066
                              v    ii      iv            iii  v  i         
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_238554885_   3067 ATAAATAATTAATATCCAGGCTATATAAAGACCTCA-GCAAC--AACAAC 3113
                             ivi i vi       iv          v   v-i    --  i  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_238554885_   3114 AAAA-------TAATCAAATTTAAACATAAGCAAAGCTTTTAAAATACAC 3156
                             -------   i v    ?   v  ii      vv   i  -  v  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA-TAGAC 841

  chr1_238554885_   3157 ATTCCTTTACAGAAGATATACACATGACCAGTAAGCCCAGGATAAGGTGC 3206
                            i  ii v            v   i   i     v  v  v   i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_238554885_   3207 TCAGAATCACTAATCAT 3223
                            iv    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (116 / 83)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.52 (74 / 21)  


3088 26.28 1.78 0.67  chr1_238641951_238648612.rev     5274  6171 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_238641951_   5274 TGGAAAAACATCCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5323
                               i i        i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_238641951_   5324 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAA-- 5371
                            v     v      v i  i  i        i  v     i     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_238641951_   5372 TCT----TGACTTTCTT-CACCAAATTGGAAAAAACT-ACTTTAAACTTC 5415
                           i----  v    i  -  v-      -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG-AAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_238641951_   5416 ATATGGAACCAAAAAAGAGCCCACATAGCCAAGATAACCCTAAGCAAAAA 5465
                                 viiv  ii  v  viv        i i  i i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_238641951_   5466 GAATAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGG 5515
                            i    i      vv   vi  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_238641951_   5516 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5565
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_238641951_   5566 CAATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATCTACAACCC 5615
                                 i    iv   ivii         vv   i    i  iiii v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_238641951_   5616 TCTGATCTGTGACAAACCTGACACAAACAAGCAATGGGGAAAGGATTCCC 5665
                         vi    i vi     ivv  v  vi v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_238641951_   5666 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATGTAGAAAAC 5715
                          v  i  i              v      v  ?   i  -- i i  i v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT--GCAAAAGAA 445

  chr1_238641951_   5716 TGAAACTGGACCCCTTCCTTACACCTTATACAAATATTAACTCCAGATGG 5765
                             ii         v   i     v        v        v i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_238641951_   5766 ATTAAAGAGTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5815
                           i ?   vi    ii     v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_238641951_   5816 CCTAGGCG-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCT 5864
                          v    ? - v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_238641951_   5865 AAAACACCAAAAGCAATGGAAACAAAAGCCAAAATTGACAAATGGGATCT 5914
                          vi            vvi v        vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_238641951_   5915 AATTAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5964
                         v  i   v v  i i  ii  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_238641951_   5965 ACAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 6014
                          v  i  i  i                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_238641951_   6015 AAAGGGCTAATATCCAGAATCTACAAAGAATTTCCACAAATTTACAAGAA 6064
                           i  i  vi          v  i      i iii    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_238641951_   6065 AAAAA-----AACC--ATCAAAAAGTAGACAAAGGATATGAACAGACACT 6107
                            i -----    --  i?    i i i        v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_238641951_   6108 TCTCAAAAGAATACATCTATGCAGACAACAAACATATGAATAAATGCTCA 6157
                             v      v i  vi viii v   i  i  i     v i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_238641951_   6158 TCATCACTGGTCAT 6171
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (136 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


1542 32.16 8.86 0.97  chr1_238749776_238751572      500  1323 (474)    L1M4_orf2#LINE/L1       20   908 (0)  

  chr1_238749776_    500 CATGAAGTAAAAGATTCAATATTGTCCA--TGTCAATTTTCACCAAGTTT 547
                             i v ii    i i        iv --  v    vi  v    i  v
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chr1_238749776_    548 ATCTACAGAGTCAGTGTAATTCTAAT-ACAATTTCAGTAG----TTTTA- 591
                                  v   ii i   i iv  - v   ii   iv ----    i-
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chr1_238749776_    592 ------TGATAAGACGGTTCTAAAATTTGTTTCAAAACCTGAAGGTCCAA 635
                         ------   i   vi i i        ii v vi   ivii i  v  v 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr1_238749776_    636 GAATAACTAAGGCAGTTCTAAAAGTGAAAAACAAAGATGAAAGTTCCAC- 684
                              i i  ii  i ii i   iv   i       v  i i vii   -
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr1_238749776_    685 -----CATCTGTAACACATATTATAAAGGCAAGGTAA-----ACAGTATG 724
                         -----  vi vi  v  v  i  i    vi vi    -----     i  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr1_238749776_    725 GCATTGGTCCTGGGATAAACAAGTAGACTGAGAAAATACGGTAAAGAATT 774
                          i i   ivivi     i   vi    iii vii    vii vi   i i
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr1_238749776_    775 CAAAGACAGAACTA-AAAT--ACAGTCACCTAATTTTTAACAATGATGCC 821
                           i i i i v i - v  -- ii    vi i     ii    v i    
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_238749776_    822 TCGAACATGCAGTGAAGAAAC-----TTTTTTAAACGAACGACCCT---- 862
                         vv  v   v  i  ii    v----- i    v   i  i iiv  ----
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr1_238749776_    863 -----------CCGTAAGTATAAAAATGAACCTTTACTGCTACTTCATAC 901
                         -----------  ii v i v  i      vi vv  iv    i   i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr1_238749776_    902 CATAAGCAGAAATAAAGTCCAAACTTAACACAGACTTAAATCTGAACAGC 951
                             vi  i    v  v  v   ivv v  ?    i     v -  v   
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGC 518

  chr1_238749776_    952 -AAAATAATATAGTATCTAGAACACAACAAACAAGAAAATCTCCATGACC 1000
                         -    iv   v iivii     v v    v vi? v      i i     
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr1_238749776_   1001 TTGTGATGATAAATAGTTTGT-ATACAGGATGCAGTAAGCATCAACAATA 1049
                            v v iivv   i    v - v i v  ii viv     iv i   i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr1_238749776_   1050 AGGGAGTAATTA-ATAAATCAGATTTCATTAAAACTAAGAATTTCCATTT 1098
                          ii  iv  v  -      ii  i     i    i   i  i  ----  
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT----TT 664

  chr1_238749776_   1099 ATGT----AAACACATCCTTGGAAGAGTGAAAAGATAAGCCTCA-AATGG 1143
                         i  i----  iv   iiv iiii i          i  v  v  -     
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr1_238749776_   1144 ATGAAGATATATG-AAATACATATATCCAACAAAGGATTCAAATCTAGCC 1192
                         iv   i    v  -    -        ii i  i   i iiv   i  vv
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAAT-CATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr1_238749776_   1193 TA-ATAA--------------TCAATAGGAATGGGCCAATTAAAACAACA 1227
                           -    --------------      iv  vii v   v   vv   iv
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr1_238749776_   1228 ATAACACTGGGCAAAATACTTGCAGAGGCACCTTCTCCAA-GAGAATATG 1276
                         ?-  v v        iv i   v v  i  i-        -  ii    i
  L1M4_orf2#LINE/    814 W-AAAAATGGGCAAAGGATTTGAATAGACAT-TTCTCCAAAGAAGATATA 861

  chr1_238749776_   1277 GAAATGGTCAATAAGCATATGAGAAGATGCTCAATATAATTTGCCAT 1323
                         v      i         i    i           i  v ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (162 / 100)
Gap_init rate = 0.03 (24 / 889), avg. gap size = 3.38 (81 / 24)  


 367 24.17 4.58 9.58  chr1_238841639_238843481.rev      268   507 (1336)    L1M4_orf2#LINE/L1      612   839 (69)  

  chr1_238841639_    268 AGTTATAAAAAATAAAATAGGAATAAATTTAA--TCAAGGAGGTGAAAGA 315
                           iv i    i v       --       vi --   vvi ii v   i 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAG--ATAAATTGGACTTCATCAAAATTAAAAA 659

  chr1_238841639_    316 CTTTTACACCAAAAAGTATAAAACATTAATGAAAAAAATTGAAGACACAA 365
                              iii ivv    -----i   i  - v  i   i -   i v    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAG-----GACACTA-TCAAGAAAGT-GAAAAGACAA 702

  chr1_238841639_    366 ATATATGGAAATAATTCTGGCTGGAATAATTAATATT-GCAAGCCATGTA 414
                         vi-i ii   -----------   i v  --      -    ii   i  
  L1M4_orf2#LINE/    703 CC-CACAGAA-----------TGGGAGAA--AATATTTGCAAATCATATA 738

  chr1_238841639_    415 TCTGATAGAGAATTAGTATTCAAAATACCTAAGGAACTC----AACTC-- 458
                                ii i i v    i  i    iv   i      ----     --
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_238841639_    459 TA-TAGAAAGA-AAACAATCTGATTAAGAAATATGCAAAGGACCTGAATA 506
                           -  i     -   i  i ii   ? i    iv        ii      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_238841639_    507 G 507
                          
  L1M4_orf2#LINE/    839 G 839

Transitions / transversions = 2.80 (42 / 15)
Gap_init rate = 0.06 (13 / 228), avg. gap size = 2.62 (34 / 13)  

2668 27.34 4.02 0.95  chr1_238841639_238843481.rev      508  1352 (491)    L1M4_orf2#LINE/L1       38   908 (0)  

  chr1_238841639_    508 ATATTGT-AAGA--ATTACACTATGCAAAGAAATTTACAGATTTATTGCA 554
                                -    --iiv i   viv    vvi  i        i vi   
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chr1_238841639_    555 ATTCTTATCAAAATCCCAA-TGTCATTTTTCAAAGATATAGAGAACACAG 603
                           i i             i-  i -     iiv   v  v  v  vviii
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA 136

  chr1_238841639_    604 TCCTAAAATTCATATGGAACCATAAAAAACTCTTAATGGCCAAGGCAATC 653
                                            viii  iii  i vv   i     ii     
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr1_238841639_    654 ATTAGCAAAAGGAGCAAAGCCAGAGGCATCACACTACCTGATTTCAATCT 703
                         v v iv  i i  i     iii    vv       v  ii       v--
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-- 234

  chr1_238841639_    704 GTACTGTACTACAAAACAGTAGTAATTAAAGCAACATAGTACTGGCAAAA 753
                         --   -         i vii      i  ii  iii i         v  
  L1M4_orf2#LINE/    235 --ACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_238841639_    754 AAGTAGACACATTGACCAATGGAACAGAAGAGAGAGCACAGAAATTAAAC 803
                         iii      i  v  i        i    vv     iv       v  v 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_238841639_    804 CACACATCTGTGGTCAATTGATTTTTGACAAAGGTGCTAAGAATATACAA 853
                           i    i i               i     i     i    vi  v   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr1_238841639_    854 TGGAAAAAGAGCACTGTCTTCAATAAATGGTATTGGGAAAACTGGATATT 903
                            ii     ii v v i     i       ii     v         ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr1_238841639_    904 CATATGCAAAAGAAATACACTGTA----TAC---ACACTGTATACAAAAA 946
                           i           vv vii  v ----   ---    ii          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_238841639_    947 TCAACTCAAAATGGGTTAAAGA----AACATAAAACCTGAAAGCGTGAAA 992
                          i            i i ?   ----  ii   i v  i   vii i   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_238841639_    993 CTACTA-----AAACA--GGGGAAGAGCTACATGACATTGGCCTGGATGA 1035
                           vi  -----     --  ? v i v  v i    v    vi i iii 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_238841639_   1036 TAACATTTTTACATTTCACCTCGAAAGCACAGGCAACAAAGGCAAAAATA 1085
                          iii-  i   v  v v  vi i        i        i v       
  L1M4_orf2#LINE/    582 TGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_238841639_   1086 AACACATGGGATTACATTCAAATAAAAAGCTTATTTAAAACAAAGGA--- 1132
                         i i v  v   i v   iv    v    i   v v ivvv       ---
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_238841639_   1133 -ATTAGCAGAGTGAAGACACAACCTAGGGATTAGGAGAAAATACTTGCAA 1181
                         -  i iv i      i v      i vi  v i          i      
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr1_238841639_   1182 ACCATATACCTGATAGAAAACTAATATCCAAACTATACAAGAAACTC--- 1228
                          i      i      iiii   vi      i v    i  ii     ---
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_238841639_   1229 -AACTCTATGGGAAGAAAAACTAGTAATCTGATTAAGAAATAAGTAAAGG 1277
                         -     v  iiv  -   i  v i   i ii   ? i    ii i     
  L1M4_orf2#LINE/    781 CAACTCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr1_238841639_   1278 GCTTTCGCAGATATTTCTTTAAAGA---CATACAAATGGGTAACAGATAC 1324
                         ii  vvii   i      ii     ---i          vi  i iii  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr1_238841639_   1325 ATAAAAA-ATGTTCAGTATCACTAACCAT 1352
                           i    -   i   ii    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (153 / 74)
Gap_init rate = 0.02 (17 / 871), avg. gap size = 2.47 (42 / 17)  


 653 25.56 1.11 0.00  chr1_238968033_238976315      885  1064 (7219)    L1M4_orf2#LINE/L1       38   219 (689)  

  chr1_238968033_    885 ATATTGTTAAGATTTTAATTCTCCCAATATTGATGTATAGATTTAATGTT 934
                                      vvi   v     v v      v  i     i  i iv
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chr1_238968033_    935 ATCCTAATAAAAATCCCAAGAGACTTTT-GGTAGAAATTAACATGCTGAT 983
                             iv  v         ivv v     -v i       i   v      
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chr1_238968033_    984 GCTAAAATATATAT-AAAATGAAAATGACCTAGAATAGCCAAAATAACTT 1032
                         v       vi    -i     v  iv    i             i  ii 
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_238968033_   1033 TGAGGATGAGGACCATAGATAGAAAGCTTACA 1064
                            ii v  i  v  v  v i  iii  i   
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

Transitions / transversions = 1.09 (24 / 22)
Gap_init rate = 0.01 (2 / 182), avg. gap size = 1.00 (2 / 2)  

2346 25.04 4.24 0.85  chr1_238968033_238976315     1370  2076 (6207)    L1M4_orf2#LINE/L1      178   908 (0)  

  chr1_238968033_   1370 AAAACAA-----AAAAAAAGGAAAAAAG----AAAGCTTACATAATTTGA 1410
                                -----     i i   v    ---- iii  i   ivviiii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_238968033_   1411 CTTCAAGACATACTTTCAAACTGCAGTAATTAAGATAATGTGGTACTGGC 1460
                         i     i  v    viv  i  i       i    i i            
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr1_238968033_   1461 ATAAGGATGG-CATATAGATTAACTGGACAGAGTAGTGAATCCAGGAATA 1509
                                 i -         i  iv i i   i v v  i     i    
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_238968033_   1510 GATCAATACAACTATGGCCAATTGACTTTTTATAATAATGCCAAGAAAAT 1559
                         i i v     vi     i       i   iv i  vii        vv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_238968033_   1560 CCAATTGGTGTAGGGGTAGCCCTTTCAAAAAATGGTGCTAGAATAAATGG 1609
                         i    v  - v i ii   i i      v          i i i  v   
  L1M4_orf2#LINE/    378 TCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_238968033_   1610 ATAGCAACATGAAGAAAAGAAATAAACTTTAAACCCTATCTCACATCACA 1659
                            ? v     v --      - i  v  vi v     i      i  i 
  L1M4_orf2#LINE/    427 ATAKCCACATGCA--AAAGAA-TGAAGTTGGACCCCTACCTCACACCATA 473

  chr1_238968033_   1660 TACAAGAATTAA-----AATGAATTACAGACTTCAATCGAAGAGCTAAAA 1704
                              i      -----    i  i ?    i v   vv           
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr1_238968033_   1705 TTCTGAAACCTCTAGAAGAAAACATTGAAGGA-------GCAACTTTGGG 1747
                         i v i    iii             v i? v ------- ii  i     
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr1_238968033_   1748 GTAGGCAAAAGTTTCTTAAAGAGGATATAAACAACAATAACCATTAAAAA 1797
                         v       vi        i v v  i iv  v i  -i  v  vi    i
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA-CAAGCAACAAAAG 622

  chr1_238968033_   1798 AAAGAAAT-GATAAATCAGATGTCATCAAAATGGAAAACTTGTGCTCTGC 1846
                            -    -       ii  iv          vi       v  iv  v 
  L1M4_orf2#LINE/    623 AAA-AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_238968033_   1847 AAAAGACACCATTAAAAA--TAAATACGCAAACTACAGAGCTGGAGAAAA 1894
                            i     i  i  i  -- i  v vi   v i     iiv        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_238968033_   1895 TATTTGCAATATATATAGCTGACAAGAGTTTTATATCTA-AATGTAGAAA 1943
                                  vvi     v    i   i vi  i    i -   i  v   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_238968033_   1944 GATCTCTTAATATT-AATAATAAGAC--CAAGTAACCCA-TTAAAATTCA 1989
                           v      vv i -        i v--   i       -  ?   vvii
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_238968033_   1990 TGCAAAAGATCTGAACAGGCACTTCACAAAAGTAGATATGTGAATGATCA 2039
                         v     i   i    i  i  i   v v    v      iii    ii  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_238968033_   2040 ATAACCATATAAAAAGATGCTCAACTTCATTAGTCAT 2076
                             v  i  i              v   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (109 / 64)
Gap_init rate = 0.02 (16 / 731), avg. gap size = 2.25 (36 / 16)  

3186 27.69 0.66 0.11  chr1_238968033_238976315     6888  7790 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_238968033_   6888 TGGAAGAACATTCCATGCTCATGGGCAAGAAGAATCAATATCGTGAAAAT 6937
                              ii i  i     i      iivi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_238968033_   6938 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 6987
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_238968033_   6988 TACCAATGACTTTCTGCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 7037
                          v   iivi i  i vii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_238968033_   7038 TGGAACCAAAAAAGAGCTCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 7087
                              viiv  ii  v iv v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_238968033_   7088 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 7137
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_238968033_   7138 CAGTAAGCAAAACAGCATGGTCCTGGTACCAAAACAGAGATATAGACCAA 7187
                               v   i    ii    v    i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_238968033_   7188 TAGAACAGAACAGAGACCTCAGAAATAATGACACATATCTACAACTATCT 7237
                          i   i    iv    vii         vvv  i i  i  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_238968033_   7238 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 7287
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_238968033_   7288 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 7337
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_238968033_   7338 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 7387
                         i    i    v   i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_238968033_   7388 AGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 7437
                             i       v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_238968033_   7438 GCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCGAAAAC 7486
                          ?i- v i -   iv   v v  vv i     v ii   v ivvv vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_238968033_   7487 ACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATTA 7536
                                   vvi           v     v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr1_238968033_   7537 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGG 7586
                           v v  i i   i  ii vv    i  v    i  vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_238968033_   7587 AAACCTACAGAATGGGAGAAAATGTTTGCAATCTACTCATCTGACAAAGG 7636
                         v    i                 i       vii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_238968033_   7637 GCTAATATCCAGAATCTACAA-GAACTCAAACAAATTTACAAGAAAAAAA 7685
                         i  vi          v  i  -      vv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_238968033_   7686 CAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCA 7731
                            ----   v  i?    i     i      v    i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_238968033_   7732 AAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCATC 7781
                                 i  vi viii     v ii          i       v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_238968033_   7782 ACTGGCCAT 7790
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.75 (7 / 4)  


1498 28.42 6.07 7.92  chr1_239004897_239006755.rev      447  1368 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_239004897_    447 AAATATGTCAAATACTTAGGAAT----AAATTTAATAAAAGCTGGTAAGA 492
                            v  i  vv  ii i v i  ---- i i      ----i  v     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATA----TTGTTAAGA 49

  chr1_239004897_    493 CTTCTTTTTAATTCTCCCCTAAATTGACCTATAGAGTAGATCCATTTCCA 542
                         ----- vvi   v      -       i   i   v vi iv  v i  v
  L1M4_orf2#LINE/     50 -----TGGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCT 93

  chr1_239004897_    543 ATTAAAATGTCAACAAGTTTGTGTGTGTGTGTATTGAAAAA-TGATTCTA 591
                           i     vi  i vivi  v v  ii- vi-     v  i-    i   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCA-GAA-ATTGACAAGCTGATCCTA 141

  chr1_239004897_    592 AAATTTATATGGCAATGCAAAGGGCCAACAATAGCCAAGACAATCTTTAA 641
                              i      v       i  i  v v         i        v  
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_239004897_    642 AAAGAAGAACAAAG----------CCTGCTTCCAGGCATCTAAACTTATT 681
                                       ---------- vii     viiiv  v       i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_239004897_    682 CTAAAGCTAGATTAATTAAAGCAGTGTGGTATTGGTGCAAGGATAAACAA 731
                         vi       v v    i  ii          i   iii       i   v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_239004897_    732 ATGGATCAACTGA-CAAACTAGACAGTGCAGAAACAGACCTGTGCAG--A 778
                           i      iv  -i i v v  v   v      i i   ii i  v-- 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_239004897_    779 TAGATACTTGATTTATGACAAAAGTG-----ACTCTGTAATGCAGTGGGA 823
                          i vi v       vi     ii   -----  iv vi    ----    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG----GGGA 387

  chr1_239004897_    824 AAGAGATAATCTTTTCAAAAAAGGGTGCTGGGTCAGTTGCATATCCACAT 873
                             -   i         v   v         v  ii  v   ?      
  L1M4_orf2#LINE/    388 AAGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_239004897_    874 -TAAAATACGTATTCATTTG------TGTTTTA----ATATG----AATC 908
                         -i    v ---  vv v   ------ iii i ----    i----   i
  L1M4_orf2#LINE/    437 GCAAAAGA---ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_239004897_    909 AGTTTAATATGAGTTGTAAACCTAAATTGGAAAGTGAAA----TGAGGCT 954
                          ii i  v   ii ii? i        vvi i  iv   ---- i ii  
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_239004897_    955 TCTAGAACAAA-TGTAATAAAAAAATTCTTCATCAACTTGACTAAGGAAA 1003
                         ii     v   -ii  iv?iv   --     i v v    iv v   v  
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAA 581

  chr1_239004897_   1004 -AATTTT---GAAGCAGTTTTAATAATCCCAATTTATTAGAT------TA 1043
                         -ii   i---  viiiiivii  -  v v   viv iv i v------  
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAA-AAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_239004897_   1044 G-TAAACTGGACTATATTAGAAGTAAGTGCTTTTGTGTAT-AAAATATTT 1091
                          -    i      vi  i i  v   ivi        iv -   iv ivi
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr1_239004897_   1092 GATTAATAGCATGAGA-GACAAGTCACAAAGTAGAAGAATATGTATATAT 1140
                         v  i  v ivi   i -     vi    i i i i    v  i v ii -
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA- 729

  chr1_239004897_   1141 ATATATATATATATATATATATAATTTAACTTTAGAAGAATATATTTTTA 1190
                         ----------------------   i-------------      -----
  L1M4_orf2#LINE/    730 ----------------------AATC-------------ATATAT----- 739

  chr1_239004897_   1191 GCACACACTCTGACAAAGAGTTTTAATCCAGGATATGTAAAGAGCACCTA 1240
                         ---------    i  i iii  vv      i    i      i v i  
  L1M4_orf2#LINE/    740 ---------CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr1_239004897_   1241 CAAATCAATAAGAAAAATGTAGACAGCCCAACAGAAAAGTGAGGAAGACA 1290
                            v       v     vii i i i     iv?    i  i v  iiv 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_239004897_   1291 CTTGAACAGGAACTTCACAAAAGAGGATAATCAAATGGGCAGTAAATGCA 1340
                         i     i  iv i   v v     i    vv       v  i   iii  
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_239004897_   1341 TGAAAAGGTGCTTGATGTCATTAGTTAT 1368
                                i    ii ii   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (160 / 98)
Gap_init rate = 0.03 (31 / 905), avg. gap size = 4.16 (129 / 31)  


1002 31.53 13.01 1.96  chr1_239071937_239074019.rev      778  1592 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr1_239071937_    778 AGAGATGGATCATCTTCCTGAATTA-AAGACTGAGTATTTTAAAGATGTC 826
                          i    ivvi   v   v  i   i-      v i    v v      v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_239071937_    827 AGTTATCCACAA-CTGATCTATAAATTCAACAAAATCCCAATTACTA-CC 874
                          i vv   v   -i       i i       iv      v  i vv -  
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_239071937_    875 CAA-TAAGTTTCTTGTTATATCTTGGTCAGTCAGTTTGAAAGTGTA-GTG 922
                           i- ivv   i   i- v vv   iiv  iiii iiv   i vi -i  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGC-AGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_239071937_    923 TTAAATAC--GGAGCGAAGAATAGTCAAAACACACATGAA---GAACAAC 967
                         v-    i --  ii vv       i       vv v    ---   v   
  L1M4_orf2#LINE/    153 G-AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_239071937_    968 AGTATGAGAGAATTG-----TCCTA---TCAGA--TAGCAACTAAGTTG- 1006
                          ivi vi   i i v-----   i ---   i -- vi v  v   i i-
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_239071937_   1007 ---------GCCAAT-CGCTATTGTTGTAGAGATAGGCAAATAAAATAAC 1046
                         --------- v  i -i v  i  vii  ii     i  v   i vi  i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_239071937_   1047 AGAACAGAGTAGAAAGCTCAAGGACAAGTTCACTTATAGTATATTGACAC 1096
                         i   i   i v  i  ii  iii i  iii  --  i v -   v v  v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATT-TATGGTCAA 348

  chr1_239071937_   1097 TTGATTTAGGACAAATGTGGCATCAGAGAGCAGTT----GGGAGAAAATA 1142
                                vv     iv   v  ----   v  v i----    i i    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGAAAGAATA 394

  chr1_239071937_   1143 AATCCCCTTAATAAATGGTGCCAGAACAATAAAATGTTTATATA------ 1186
                         i-  iii i  i         ii i    ivii  i?ii i  i------
  L1M4_orf2#LINE/    395 G-TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_239071937_   1187 ----------GACCTCTACTTCAC-CC-----TAAAATTCAATTC----- 1215
                         ----------    i    i    -  -----i    v i  i  -----
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_239071937_   1216 ----CA--GATCTAAATGTGAAAAGC-AAGACAATAAAAATTTTAGAGAA 1258
                         ----  --  i        -  i   -  i  v      v i     ii 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_239071937_   1259 TAATAGATGAGCATATCTTTAGAATCTCATAATAAGC--TAATTTT---- 1302
                         v  i v v ? i v     iivi i  iiviv  i  -- ii   i----
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_239071937_   1303 -----------AAAGTACTAATCATAAAGGAAAAACAC---TTAATTGAA 1338
                         -----------    i  v iiv i   i      - i--- v     i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGA 641

  chr1_239071937_   1339 -TACATTAAAATCAAGCATTTCCATTAATAAAAAGTCA---TCAAGAGAG 1384
                         - v   i     i  iv i  iii vvv v   i v  ---      i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_239071937_   1385 ATAAAAGGTAAGCCCCCTGAACGTAAGAAA-TATTTGCAGCCCGCTTACC 1433
                         vv     ii  -   v v   i vi     -        ivi iiv  i 
  L1M4_orf2#LINE/    692 TGAAAAGACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_239071937_   1434 CAACCAAGGGGCTAGTATTGTTAACACA--AAGGACT---AGAAATCAAT 1478
                         ii i-     i  v    ivvv  i i --   i   --- v  v     
  L1M4_orf2#LINE/    741 TGAT-AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_239071937_   1479 AA-GAAAAGTCAGACATCCCA-TTAGAAAACTAGACAAAAGATTTGAATA 1526
                           -i     v  i i v    -  ?i    - i i    i          
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATA 838

  chr1_239071937_   1527 CGA-ACTTTAGAAAAGAAGATACTCAAATGGCTAGCAACCGTAT---AAG 1572
                         -  - i  ivvv          iv        i ii  v ii  ---   
  L1M4_orf2#LINE/    839 -GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_239071937_   1573 ATG-TCAATCTCACTCCTACC 1592
                            -    iv   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (160 / 94)
Gap_init rate = 0.05 (44 / 905), avg. gap size = 2.77 (122 / 44)  


3026 25.33 2.57 1.34  chr1_239075491_239082167     5289  6184 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_239075491_   5289 GGAAAAACATTCCATGCTCATGGATAGAAAGA----ACATTGTGAAAATG 5334
                              i i  i     i        v i    ---- i     v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_239075491_   5335 GCCATACTGCCTAAAGTAATTTATAGATTCAATGCTATCCCCGTTGAGAT 5384
                           v     v  i   v i  i  i        i  v     ii ii i  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_239075491_   5385 ---AACTTTGACTTTCTTCACAGAATTAGAGAAAACT-ACTTTAAATTTC 5430
                         --- i  ---i i  i  ii     v v  v  i-  - iii    v   
  L1M4_orf2#LINE/    102 CCCAGCT---GCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr1_239075491_   5431 ATATGGAACCAAAAAAGAGACT--GCATAGCCAAGACAATCCTAAGCAAA 5478
                                 -- viv   i   i-- v        i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_239075491_   5479 AAGAACAAAGCTGGAGGTATCATGCCACCTGACTTCAAACTATACTACAA 5528
                                   i      vv   ii iv  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_239075491_   5529 GGCTACAATAACGAAAACAGCATGGTACTTGTACCAAAACAGATATATAG 5578
                         i      i   iv  i    ii       v i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_239075491_   5579 AACAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAC 5628
                          v        i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_239075491_   5629 CATCTGATCTTTGACAAACATGACAAAAACAAACAAGCAATGGGGAAAGG 5678
                           vi    i  i     ivi  v   i - ---  vv            i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGA-C---CATTCAATGGGGAAAGA 391

  chr1_239075491_   5679 ATTCCCTATTTAATAAATGGTGTTGGGAAAACTAGCTAGCCATATGCAGA 5728
                           vvi  v  i  i        i     v    i v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_239075491_   5729 AAACTGAAACTGGACCCTTTCCTTACACCTTATACAAAAATTAACTCAAA 5778
                          i v    ii       i v   i     v                    
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_239075491_   5779 ATGTATTAAAGACTTAAATGTAAGACCAAAAACCATAAAAACCCTAGAAG 5828
                            v  i ?    i           v v     i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_239075491_   5829 ACAACCTAGGCA-ATACCATTCAGGACATAGGCATTGGCAAAGGCTTCAC 5877
                          v   v    ?i- v i -   iv   v v  vv v     v  i   vi
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_239075491_   5878 AACTAATACACCAAAAGCAAGGGCAACAAAAGCCAAAATTGACAAATGAG 5927
                          iv  vv            vii          vv     v  i    vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_239075491_   5928 ATCCAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGA 5977
                          iiiv  i   v v  i i   i  ii vv    i  v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_239075491_   5978 GTTAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCCATCTATCCATC 6027
                           v  v  i     i                 v     v vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_239075491_   6028 TGACAAAGGGCTAATATCCAGAATCTAGAAAGAACT--TA-AATTTA-CA 6073
                            i  i  i  vi          v  v        --  -  i i -i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_239075491_   6074 AGAAAAAAAGCAAA---CTCTATCAAAATGTGGGCAAAGGATATGAACAG 6120
                          v     i -    --- i v  i?   vi            v    i  
  L1M4_orf2#LINE/    791 ATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_239075491_   6121 ACACTTCTCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAT 6168
                            i     v        i  vi viii     i  --         i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_239075491_   6169 GCTCA---TCACTGGTCGT 6184
                              ---   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (136 / 87)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 1.94 (35 / 18)  


3200 26.77 1.00 0.55  chr1_239103800_239107856     2661  3564 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_239103800_   2661 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATCTCGTGAAAAT 2710
                              ii i  i     i        v      v i   v i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_239103800_   2711 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2760
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_239103800_   2761 TACCAATGACTTTCTGCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2808
                          v   iivi i  i vii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_239103800_   2809 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 2858
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_239103800_   2859 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGAC 2908
                                i      vv       v  ii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_239103800_   2909 TACAGTAACCAAAACAGCATGGTACTAATACCAAAACAGAGATATAGACC 2958
                                 i   i    ii       iii iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_239103800_   2959 AATGGAACAGAAC--AGAGCCCTCGGAAATAATACCACACATCTACAACC 3006
                                i    i--    i  --i       vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_239103800_   3007 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 3056
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_239103800_   3057 CTATTTAATAAATGGTGCTGGGAAAACTGACTAGTCATATGTAGAAAGCT 3106
                           v  i  i              v     iv  ?i  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_239103800_   3107 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCGAGATGGA 3156
                            ii    i    v   i     v              i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_239103800_   3157 TTAAAGACTTAAATGTTTGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3206
                          i ?    i       vv  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_239103800_   3207 CTAGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTA 3255
                         v    ?i- v i -   iv   v v  vv i i   v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_239103800_   3256 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 3305
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_239103800_   3306 ATTAAACTAAAGAGCTTCTGCACAGCAAGAGAAACTACCATCAGAGTGAA 3355
                           i   v v  i i   i  ii vv   ii  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_239103800_   3356 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCCATCTATCCATCTGACA 3405
                         v  i     i                 v     v vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_239103800_   3406 AAGGGCTAATATCCAGAATCTACAAAGAACGCAAACAAATTTACAAGAAA 3455
                          i  i  vi          v  i       v vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_239103800_   3456 AAAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 3501
                           i    ----   v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_239103800_   3502 CTCAAAAGAAGACATTTATGCAACCAACAAACACATGAAAAAATGCTCTT 3551
                            v        i  vi viiii    i  i          i      vv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_239103800_   3552 CATCACTGGCCAT 3564
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


 730 28.77 3.99 4.27  chr1_239108655_239110547.rev      502   852 (1041)    L1M4_orf2#LINE/L1      279   628 (280)  

  chr1_239108655_    502 TAAGAACAGATATACAGACCAGTGGATCAGA-TTAGAAGACCAAGAAAAA 550
                             i i   i   i   i  i    vi   -  iii  v   -    v 
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA-GAAATA 327

  chr1_239108655_    551 GACTCTCATGTATAAAGTCAATTGATTTCAGACAAAGCTCTCAAAGTAAT 600
                         i  i vi ii v  vi            iv     i v vi   iiiv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_239108655_    601 TCAATTGGGAATGGAT------TTCAAACAACAGTGCTGGAAAAA-TGGA 643
                              v     v i  ------     vv  ii       i v  -    
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_239108655_    644 TTATACATATTTCAGGAAATATGAGAGAGAACCTCAACCCTTTTATCATA 693
                          - ?v  i  v-  ii i -    iivv i   i v   ------   i 
  L1M4_orf2#LINE/    428 T-AKCCACATG-CAAAAGA-ATGAAGTTGGACCCCTACC------TCACA 468

  chr1_239108655_    694 CCAAATAGAAAAATTAA------ACAGATTGCAGACCTACTTGTTTAAGC 737
                            v   v         ------ ii   ii?       vv   vvi   
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr1_239108655_    738 TAACACTATAAAACATCTATCAGGAAACAAGGGAAAACATGAAATCTTTG 787
                            v          vii  vv  i     vi  ?i---- -       i 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNG----T-AAATCTTCG 563

  chr1_239108655_    788 TTACTTTAGGTTAGGTAAAGTTTTCCAAGAGAGGTCACAAAAATTCTGTA 837
                          v  i  i       i  v v    iv   v v v   v    viviivi
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_239108655_    838 CCATAAAAGAAAAAA 852
                          v i           
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAA 628

Transitions / transversions = 1.28 (55 / 43)
Gap_init rate = 0.03 (11 / 350), avg. gap size = 2.64 (29 / 11)  

 682 21.62 18.15 0.00  chr1_239108655_239110547.rev     1144  1402 (491)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr1_239108655_   1144 AAAAAAACAAAAAACAAAAAAAAA----GATGTATTGAACTTCGT-AAAT 1188
                             iv    iv       i    ----   iv    i     i -   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_239108655_   1189 TTAAAAACTCTTCCTCTTCAAAAAACATTGTTAAGAAAATGAAAAGACAG 1238
                                  i  viv       ii   i i i      i          i
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr1_239108655_   1239 GCTCCAGAA-GGGTGAAAATATTCTCAATGCATATACCTGACAA------ 1281
                         v iv     -   v         iv   vv      i    i  ------
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr1_239108655_   1282 ----------------------CCCTTATAGGTCAATAATAATAATTTGA 1309
                         ---------------------- i    i iv          v  vvii 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr1_239108655_   1310 ATAATCCAATT--AAAATGGGCACAATATCTCAATAGAGACTT-TCCAGA 1356
                             i      --          v iv  i v      v i  -    i 
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr1_239108655_   1357 AAAAA-----AAA-----AAAAGGCACATGAAGAGATGCTCAGCACCATT 1396
                         i  i -----   -----  v i         i         i  i  ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr1_239108655_   1397 AATCAA 1402
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.67 (35 / 21)
Gap_init rate = 0.03 (8 / 306), avg. gap size = 5.88 (47 / 8)  


 890 27.52 9.06 0.34  chr1_239170194_239173822     1456  1753 (1876)    L1M4_orf2#LINE/L1        1   324 (584)  

  chr1_239170194_   1456 TGGAGTGACATATCATGTTCATGGATGAGAA------------------T 1487
                             iv  i  vi             vi   ------------------ 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_239170194_   1488 GCCAAATCTTCCAGAATTTATGTATAAATTCAATGTAATCCCAATTATAA 1537
                          v   vv  i  vi    v  v  i i      i i      v  i v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_239170194_   1538 TCTCAGCTGGCTGTTTTTGTAGCAACTCACAAGCTGCTTCTAAAATGTAT 1587
                           i      v  -      i  v  i v        v i       vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_239170194_   1588 GTGGCTATGCAAATAACCTAAAATAAGCAAAACAATTTGGGGAATTAAAA 1637
                         i   vv      ivi   i i    iv         i v ii  vv  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_239170194_   1638 A-AAAATTGGAGGATTT-TACTATCTGATTTGAAGATTTATTATAAA-TG 1684
                          -   i        i i-i   vi ii    v  i i   i  i   -iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_239170194_   1685 ACAGTAATTAAAACAGGTTAGTAATGATATAACAATAGA------AATCA 1728
                                 i  i    vv i   v  ii    vi     ------i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_239170194_   1729 ATGCAATAGGAGAAAGATTCCAAAA 1753
                            v     i vvi   v    i  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAA 324

Transitions / transversions = 1.41 (48 / 34)
Gap_init rate = 0.02 (6 / 324), avg. gap size = 4.67 (28 / 6)  

 380 27.36 4.56 9.42  chr1_239170194_239173822     2284  2612 (1017)    L1M4_orf2#LINE/L1      386   698 (210)  

  chr1_239170194_   2284 GAAAGAATAGGATTTTCCAGAAATTGGACTGGAATAATTGGACATTTGTA 2333
                                   vv     v v    v vi    i i  i    i ?iiii 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr1_239170194_   2334 TGCAAAAATACAGTAAATCTTTGCCCCATAACTCACACGATAAACATAAA 2383
                                i--- i i  v-  v v   v  v       v   v   v   
  L1M4_orf2#LINE/    436 TGCAAAAG---AATGAAG-TTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_239170194_   2384 TTTACTTTTACATAAATTTACCTTACATAAATATAAATGTTGAGGATAAA 2433
                           v   ----  -    vv i ---- ? i iv       viii v    
  L1M4_orf2#LINE/    482 TTAACT----CA-AAATGGATC----AWAGACCTAAATGTAAGAGCTAAA 522

  chr1_239170194_   2434 ATTACAAAACTTCTAGAAGAGAA---------AAATCTT---GACCATGA 2471
                          i  i      ii       i  ---------       ---    v  i
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr1_239170194_   2472 TTTTGGCAAGAATGCTTTTCTATAAGGGTTTTTTAATACAGAAAAAAATT 2521
                         v  v     ---  v   ii  v ------- v i i  vi   iv ---
  L1M4_orf2#LINE/    573 GTTAGGCAA---TGGTTTCTTAGA-------TATGACACCAAAAGCA--- 609

  chr1_239170194_   2522 CCCTGCATATAATCTAATCTAATCTATAT---TTGGATTTCATCAAAATA 2568
                         - vv   - i  vvv  ---  vv  v  ---     i           v
  L1M4_orf2#LINE/    610 -CAAGCA-ACAAAAGAA---AAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_239170194_   2569 AAATGCTTCTTCTCCTTAAAAATTATTATTTAAATAATGAAAGG 2612
                            vi   i viv i i   iivi i   iv i v i     i 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

Transitions / transversions = 1.05 (45 / 43)
Gap_init rate = 0.04 (13 / 313), avg. gap size = 3.54 (46 / 13)  

 785 16.67 7.14 0.48  chr1_239170194_239173822     2927  3136 (493)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr1_239170194_   2927 AAGAAAA-GAAAGGGCAAGC-ACAGGCTGG-AGAAAATATTTGCAATACA 2973
                               i-    i i   v -    iv   -               vv  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_239170194_   2974 TATGTCTGACAAAG-ATTTGTATC-AGGATGATATAAAGAAGTTCTACAA 3021
                            i     i  i - i       -  i  -          v ii     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAAT-ATATAAAGAACTCTTACAA 783

  chr1_239170194_   3022 CTCAATAGTAAGATTATC--TAACCAAA---AGAAATGGAAAAAAAATT- 3065
                                i   i vv iv--     v  --- i      iv   ii   -
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_239170194_   3066 GAA----CACTTTACCAAAGAACATATACAAATGGCCAACAAGTACATGA 3111
                            ----  i  iv        v                i   i      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_239170194_   3112 AAAGATGCTCAACATTAACACTCAT 3136
                                        i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (23 / 12)
Gap_init rate = 0.04 (10 / 224), avg. gap size = 1.60 (16 / 10)  


2721 25.58 6.13 1.04  chr1_239193613_239196043     1075  1938 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_239193613_   1075 TGGAAAAGTTTTCCATGCTCGTAGATAGGAAAA----------------T 1108
                               ii v i     i  i i   v    i ---------------- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_239193613_   1109 GGTCATACTGCCCAAAGTAATTTACAGATTCAATGCTATTCCCATCAAAC 1158
                           iv     v      v i  i           i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_239193613_   1159 TACCATTGACGTTCTTCACAGAATTAGAAAAATCTACTTTAAAATTCATA 1208
                          v   vivi v  i  ii     v v  v  iiiv iii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_239193613_   1209 TGGAACCAAAAAAGGGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGAA 1258
                              viiv  ii iv  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_239193613_   1259 CAAAGCTGGAGCA-TCACACTACCCAACTTCAAA---CACTACAAGGCTA 1304
                              i     v -       v     i      ---i       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_239193613_   1305 CAGCAACCAAAACGGCATGGTACTGGTACCAAAACAGACA-------CAA 1347
                            i  i   i  i ii         i iv ii i     -------   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_239193613_   1348 TGGAGCAGAATAGAGA-TCT---------CTCA--CATCGATAACCATCT 1385
                             ii     v    -  i--------- i  --   iv  iii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_239193613_   1386 GATCTTTGACAAACCTTACAAAAACAG-CAATGAGGAAAGGCATTCCCTA 1434
                            i  i     ivv vv   i v  v-     i      i-  vvi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTT 399

  chr1_239193613_   1435 TTTAATAAGTGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAATTGGA 1484
                           i  i  i           v      v  ?   i     i  i v  i 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_239193613_   1485 ACTGGATCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGGAATA 1534
                         ii    i    v   i i   v                   i     vi 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_239193613_   1535 AAGACTTAAATGTAACACCCAAAACTATAAAAAGAGAGAGAAGAAAATCT 1584
                         ?    i         v v i            vvvv-v         iv 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAACAT 548

  chr1_239193613_   1585 AGGCAATACTATTCAGGACATAAGCACAGGCCAATA-TTTCATAATTAAA 1633
                            ?ivv v v   iv   v vi vvi    -   i-    v  iv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTAGATATG 597

  chr1_239193613_   1634 ACATCAAAAGGAATTGCAACAAAAGCAAAATTTGACAAATGGGACCTAAT 1683
                            i      v vvv          v    v v  i    v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_239193613_   1684 TAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCACCAGAGTGAAGA 1733
                         i   v v  i i   i  ii vv    i  v       vv i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_239193613_   1734 GACAACCTACAGAATGGGAGAAAATGTTTGCAATCTACCCATCTGATACA 1783
                                i                 i       vii ivi        vi
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_239193613_   1784 GGTCTAATATCCAGAATCTACAAGGAACT--TA---------AATGTACA 1822
                           v  vi          v  i  i     --  ---------   i- v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA-AAA 796

  chr1_239193613_   1823 AGAAAAAAAACTCA-TTCAAAAGTGGACAAAGGACATGAGCAGACACTTC 1871
                            v   v   i  -  ?    i   i       iv   ii     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_239193613_   1872 TCAAAAGAAGACATTCATGTGGCCAACAAACATATGAAAAAAAAAAAAGC 1921
                           v        i  v  vi       i  i  i       i v-----  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-----GC 891

  chr1_239193613_   1922 TCAACATCACTGATTAT 1938
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (125 / 92)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.65 (62 / 17)  


4058 17.43 2.63 3.07  chr1_239218312_239221096.rev     1383  2294 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_239218312_   1383 TGGAAAGACATCTCATGTTTATGGATTGAAAGACTTAATATTATGAAAAA 1432
                                 i   i      i        i             i v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr1_239218312_   1433 TGGAAA-GTTCCTCAAATTGAAATATAGATTGAACATAATTCCTATCAAA 1481
                            v  -ii   i        vv  i     v   ii   i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_239218312_   1482 ATCTTAGCTGTCTTTTTTTTTTTTTTGCAGAAATTGACAAGCTGATCCTA 1531
                            ii     i       --------                        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT--------GCAGAAATTGACAAGCTGATCCTA 141

  chr1_239218312_   1532 AAAATCACATGAAAATGTAAAGAATCCAGCAATCTCTTGGAAAAGAAGCC 1581
                            v   i   i     i  i i i    -   -------------    
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAG-AAT-------------AGCC 177

  chr1_239218312_   1582 AAAACAATATTGGAGAAGAAAAACAAAGTTGGAAAACTCACACTTCCTGA 1631
                                 v   i i     i            ii            ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr1_239218312_   1632 TATCATAACGTAATACAAAGCTACAGTAATTAAGGCTATTTGATTATCTG 1681
                          v   v   v  v                 i   i vi v  i - -   
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT-A-CTG 275

  chr1_239218312_   1682 GTATAAAGATAGACATATAGATCAATGCAGTAGAATTTAGAATTCAGGAA 1731
                          i    i                    v i       v   i i   i  
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_239218312_   1732 TAAACCTATTTATCTATGGATAATTAATTATCAACAAACACACCAAGACA 1781
                               i  vi  i     vi    i   v  i    iviii       v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_239218312_   1782 ATT----GGGGAAGCAATAGTTTTTTCAACAAATGGTGTTGGGGCAATTG 1827
                            ----      iv      i                i    i   i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_239218312_   1828 GATCACCACATTTAAA-GAATGAG--TGTAT---TA----ACACCATATA 1867
                            v?      vi   -      i--  v i---  ----          
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_239218312_   1868 -GAAAGCTGACTTATATCAGATCAAAAAC-TAAATATAAGAGCTAAAACT 1915
                         -i   ii i   i v vii     ? i  -     i              
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_239218312_   1916 ATAAAAACATTAGAAGAAAAAA-ATGTGTAAATATTTGTGACCTTGGATT 1964
                               viv           v - v ?      v  i          i  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_239218312_   1965 GGGCAACAGTTTCTTGAATATGACATGAATTGTACAAGCAAACAGAGAAA 2014
                         i     ii       ii        iv  vv i        -  i ii  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA-CAAAAGAA 624

  chr1_239218312_   2015 AAAATAGTTAAATTGAAC---ATCAAAATTAAGTACTTTTTGTACTTCCA 2061
                                v       i  ---           iv      -  i    v 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT-GTGCTTCAA 673

  chr1_239218312_   2062 AAGATACTATTGAGAAATTGAAAAGATTTTCTACAGAATGGGAGAAAATA 2111
                          i  i     ii     v        ivvi i                  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_239218312_   2112 TTTGAAAATCATATATCTGACAGGAGTTTAGTATACAGTTTATATAAA-A 2160
                             v               i i i vi v    v   vv        - 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_239218312_   2161 ACTCTTACAACTCA-TAGATAAAAAGACAAAGAACCCAATTAAAGTATGG 2209
                                       -  -             v         ?  iv    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr1_239218312_   2210 GCAAAGGATTTGAATAGATATTTCTCCAACGAAGGCATAAAAATAGCTGA 2259
                                           i          v    ii   v    i  ii 
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr1_239218312_   2260 TTAGCACATAAAAA-ATGTTCGATATCATTAGTCAT 2294
                          v       i    -   i  i i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (104 / 51)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.36 (52 / 22)  


1731 26.73 8.86 1.80  chr1_239221799_239223476      464  1185 (493)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_239221799_    464 ATTCTAAAGCATATATTGAAAGGTTAAGGGAACTAAAATAGCTAAGACAA 513
                           i     iivi    v    v i-      v i i      i  i    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGC-AAGGGACCCAGAATAGCCAAAACAA 184

  chr1_239221799_    514 TTTTGAAAAACAAGAAGAAAGT--GAGAATAAATAGTGTACCCAATTTCA 561
                          i        v     v     --   i ivv i v - -          
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT-T-CCCAATTTCA 232

  chr1_239221799_    562 AGTCTTATTAGATAGCTACATTAATTCAGG--GTGTGGCGTTGGCAGAGG 609
                          iv    i  v v       v    iv  i--      iii     v i 
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr1_239221799_    610 AATGGACACTTGTGTCAATGGAACTAAATACAAAACCCAGAAATAAAGTC 659
                         i  i    iv ivi         ivi   vv i ii           vi 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr1_239221799_    660 -----TTT-----CAATGGA---------AGGG----AAGAC-------- 678
                         -----   -----    v  ---------    ----     --------
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr1_239221799_    679 -----------AACCTTTTCAACAAACAGTGCTGGAGCATATGGACATTC 717
                         ----------- ii            ii       ii  vv    i ?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_239221799_    718 ATAAGTAAAGAAAATGAACCTTAATCTAAACATCACAACTCATACAAAAA 767
                          i v i   - i      vi vi i ivv  v     v vi         
  L1M4_orf2#LINE/    433 ACATGCAAA-AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr1_239221799_    768 GTAACTCAAAATAGATGATGGAC-----TGTAAAATGTAAAACTCTAAGA 812
                         v           i   v ?i   -----     i vv       v   i 
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr1_239221799_    813 CTTTTAGAAAAAATTCTATATGAGAAAGTATTCAGGATGTAAGGCTAGGC 862
                           i      i   --vi   v ? v  i v   iv  iv vi  i     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAA--ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr1_239221799_    863 AAGGCATTCTTAGACTTGATATCAAAGAGCATGACCCCAAAAAAGAAAAA 912
                           v vv        iv   i i    -    ii v --  v   ii    
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAA-AGCACAAGC--AACAAAAGAAAA 626

  chr1_239221799_    913 AATTGATAAATTATACTCCAGCAAAA-------CTTTTG--CTACACTAA 953
                            v        iv   i  v     -------      --  v  --  
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AA 674

  chr1_239221799_    954 AGATCTTGTTAAAAAGATAAAAAAGACAACT-ACACAAGGGAAGAAAACA 1002
                         i  ivi i i  i  ii i    -      i-   v  v  i      i 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAA-GACAACCCACAGAATGGGAGAAAATA 723

  chr1_239221799_   1003 TTTCCAAATCACGTATCCAACAAAGGACTAATGTTGAGAATATCAAAAGA 1052
                            v       ii    ii i  i     vi i iv       vv     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr1_239221799_   1053 ACTGTCA-AACT-GCTAGTAAAAACACAGACAATCCTAACAGGAAATGAG 1100
                            v i -    -iv  i      v   i i  i  v vi?ii     i 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_239221799_   1101 CAAAAGACATGAACAGACATTTTGCTGA-TAAGACTAAACAGATGGTAAA 1149
                             i  iv    i        iv ii -v    -  v   i    iv  
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGA-TATACAAATGGCCAA 872

  chr1_239221799_   1150 TAAACATATAACAACACATTTAACATCAGTAACCAT 1185
                            i  i  i v  v iii i       ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (115 / 74)
Gap_init rate = 0.03 (24 / 773), avg. gap size = 3.21 (77 / 24)  


3672 24.39 1.11 0.44  chr1_239254492_239258510     2625  3526 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_239254492_   2625 TAGAAAGATCCCTTATGTTCATGGATTGAAACA-TTAATATTGTTACAAT 2673
                          i       vi ii              i  v -            vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_239254492_   2674 GTCCATACTCACCAAAGCAATCTACAGATTCAGTGAAATCC-TATTGAAA 2722
                          v v      v     vii             ii v     -   ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_239254492_   2723 TATTGATGAGATTCTTCACAGAAATAGGAAAAACAATTCTAAAATCAACG 2772
                          viiiiivivv  i  ii       v iv  ivii  i       iv ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_239254492_   2773 TGGAACCACAAAAGATCCCAAATAGTCAAAGCAATCTTGAGCGAAAAGAA 2822
                              vii   ii  i  vi     i    i         ivi i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_239254492_   2823 CAAAGCTGGAAACATTACACTACCTGACTTCAAAATATACCGCGAACCTA 2872
                              i    iivv i     v  ii i       iv   ii i  v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_239254492_   2873 GAGTAACCAAAGCAGCATTGTACTGGCTGAAAAACAGACACATAGACCAA 2922
                         v     i   ii   ii v        vv  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_239254492_   2923 TGGAACAGAATAGAGAGCCCAAAAATAAATCCATGCACTGACGGTCAGTT 2972
                              i     v     i   i       i    i  i v i     i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_239254492_   2973 GATTTTCAACAAAGGTGCCAGGAACA--CAATGGGAAAAGAACAGTCTCT 3020
                                i    i       i  v  --       i      i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_239254492_   3021 TCAATAAATGGTGTTGGGACAACTAAATATCTATATACAGAAG---GAAA 3067
                             i        i          ii   ? i i  i  i   ---   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_239254492_   3068 TTAGACCCTTATCTCACAACATATACAGATATCAACTCAAAATGGATTAA 3117
                           i     i  i      v        i v  i              i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_239254492_   3118 AGACTTAAATACAAGA-CTGAA-TTATGAAACTACTAGAAGAAAACATAC 3165
                             i     ii    -  i  -i   i     vi              v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_239254492_   3166 GAGAATAGCTCCATGATATTGGTCTGGACGGTGATTTTTAAAATATAACC 3215
                          ? v v v  i i   iv    vi i i ii  i   i v i    i  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_239254492_   3216 CCAAAAGACTGGGCAACAAAAGCAAAAATAGATAAATGAGATAACATCAA 3265
                                vviii          v              vi  ivv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_239254492_   3266 ATTTAAAAGGTTCCCTATACAGCAAAGGA-ATTAATCAATAGATTGAAGA 3314
                          v      iv  i-- i i vv       - i  -    v i v    i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTT--TGTGCTTCAAAGGACACTA-TCAAGAAAGTGAAAA 697

  chr1_239254492_   3315 AACAACCTACAGAATGGGAGAATATATTTTCAAACCATACATCTGATGAA 3364
                         i      i              v      v    i    i       i i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_239254492_   3365 GGGTTAGTATCCAAAATTTACAAGGAACTCAAACAACTTAATAGCAATAA 3414
                           ii v       i   v  i  i      vv      i    ii  v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_239254492_   3415 AACAAATAACCCAATTAAAAATTGGGCAGATAACCTGAGTACACATTTCT 3464
                         i               ?    v      i vi ii   i  v        
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_239254492_   3465 CAAAATAAGACATGCAAATACCCAATGAACGTATGGAAAAAATGCTCAAC 3514
                          v   v    i  i     iv     i i ii   -    i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTCAAC 896

  chr1_239254492_   3515 ATCACTAATCAT 3526
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.22 (149 / 67)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


3080 27.16 0.89 0.22  chr1_239338758_239342482.rev     2333  3234 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_239338758_   2333 TGGAAACACATCCCATGCTCATGGATGGGTAAAATCAATATTGTGAAAAT 2382
                               v i        i        v  v i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_239338758_   2383 GACCATACTGTCAAAAGCAATCTATAAATTCAATGCAATCCCCATCAAAA 2432
                          i v     vi v   vii     i i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_239338758_   2433 TACCA-CCATTATTCTTACAGAATTAGAAAAAACAATCCTAAAATTCATA 2481
                          v   - iiiiv  i  i     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_239338758_   2482 TGGAACCA-AAAAAACAGCCTGCACACCCAAAGCAAACCTAAGCAA-AAG 2529
                              vii-  iii  --  v v i v     i   v i i iv  -   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_239338758_   2530 AACAAATCTGGAGGCATCACATTACCTGATTTCAAACTATACTATAAGGC 2579
                               vi      vv     i v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_239338758_   2580 CATAGCCGCCCAAACAGTATGGTACCAGTATAAAAATAGGCACATAGACC 2629
                         i i  ivii v i     i      ii i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_239338758_   2630 AATGGAAAAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAA 2679
                                v     v    ii               v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_239338758_   2680 ATGATCTTTAACAAAGCAAACAAAAACATAAGGTGAGGAAAGGACACTGT 2729
                         v    i  ii    i vviv   i v   vvii  i      i i v v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_239338758_   2730 TTTCAACAAATGGTGCTGGGATAATTGGCTAGACACATGTAGGAGAAGGA 2779
                                              i  i   v  ?v      i ii    v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_239338758_   2780 AACTGTAACCTCATCTCTCACCTTATACAAAAATTAACTCAAGATGGATT 2829
                          ii  v v  ii i   v    v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_239338758_   2830 AAGGACTTAAATATCAGACCTGAAACTATAAAAATTCTAGAAGACAACAT 2879
                          ?i   i     i v   v  i           v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_239338758_   2880 TGGAA-AAACCCTCTAGGCATTGGCTTAGGGAAGGATTTCATGACCAAGA 2928
                         v  ?i-   i i  vv i v    v     v  v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_239338758_   2929 ACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACATAATT 2978
                         vv         v v    i    iv   i   i   iv v    v v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_239338758_   2979 AAGCTAAAAAGCTTTTTCACAGCAAAAGGAACAGTCAGCAGAATAAACAG 3028
                           iv v    i     vii vv    i iv  vi   iv i i i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_239338758_   3029 ACAACACGCAGAGTGGGAGAAAATCTTCACAATCTACACATCAGACAAAG 3078
                              v i    i           v  ii   vii i i   v  i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_239338758_   3079 GACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGCAAGAAAAAA 3128
                             vi          v  i  v      vv    v   ii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_239338758_   3129 ACGA----CCCCATCAGAAAGTGGGCTAAGTACATGAATAGACAATTTTC 3174
                           i ----   v  i?i   i     v   v iv          v  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_239338758_   3175 AAAAGAAGGTAAACGAATGGCCAACAAACATATGAAAAAATACTCAACAT 3224
                         v       i  v  i         i  i  i       i  i        
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_239338758_   3225 CACTAATGAT 3234
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3030 24.54 3.54 0.91  chr1_239385735_239387935.rev      835  1710 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr1_239385735_    835 ATCCCATGCTCATGGGTTGGAAGAATCAATATTGTTAAAATGTCCATACT 884
                                 i      i        v i           i   v v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr1_239385735_    885 GCCGAAAGCAATCTACAGATTCAATGCTATTTCTACTAAATTAGCAACAC 934
                         v  v   vii              i  v  ii   ii   v vv  i vv
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr1_239385735_    935 CATTTTTTACAGAATTAGAAAAAAAACT-ATTCTAAAATTCATATGGAAT 983
                          v      i     v v  v  i---  -  i                 v
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCATATGGAAA 156

  chr1_239385735_    984 CAGAAAAGAGCCA-AATAGCCAAAGCAATCGTGAGCAAAAAGAATAAAGC 1032
                         iiv  ii  v   -          i     v   iv  i     i    i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_239385735_   1033 TGGAGGCATCACATTATCCAACTTCAAACTGTACTGCAAGGCTACAGTTA 1082
                               vv     i vi    i      viv    i   i        v 
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_239385735_   1083 CCAAGACATCGTGATACTGGTACAAAAACAGACACATAGACTAACAGAAC 1132
                         i       vi   i      i i  ii i     i     ii  ii   i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_239385735_   1133 AGA-----GACCCCTGAAACAAAGCCACACATCTACAAGCAGTTAATCTT 1177
                            -----  vi  v    i   v   i    i  iiiv  i  i  i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_239385735_   1178 CCTCA-GAGT-CCACAAACATAAACAATGGGCAAAGGACACCCTATT--- 1222
                          vv  - i  -   vi v   v--       v    i i vi  v  ---
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATT--CAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_239385735_   1223 -AAATAGTGCTGGGAAAACTGGCTAACCATATGCAGAATAATGAAATTGG 1271
                         -    i         v      v  ?   i     i  v      i    
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr1_239385735_   1272 ACCCCTGCCTC---TCATATACAAAATTAAACTCAAGATGGATTAAAGAC 1318
                               i    ---i           v v       i      i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr1_239385735_   1319 TTGAATGTAAGACCTCAAACTATAACAATTCT-AAAAGAAAACCTAGGAA 1367
                         i i         v  v         -  i   - i        v    ?i
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACATAGGNG 553

  chr1_239385735_   1368 ATACTCTTCTAGACATTGGCCTAGGCAAAGAATTTATGACTAAGTCCTCA 1417
                         vv v     vv   v    vi       v iv  iv iiv  v v vi  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr1_239385735_   1418 AAAGCAAATGCAA--AAAGACAAAAATTGACAATTGAGATATAATTAAA- 1464
                               v v    --     -      v  i  v vi  iv v  i   -
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAA 652

  chr1_239385735_   1465 CCAAGGATATTTTGCACAGCAAAAGAAACTATCAACAGAGTAAACAGACA 1514
                         ii  ii i-     ii vv    i  v        v i   i  v     
  L1M4_orf2#LINE/    653 TTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr1_239385735_   1515 ACCTACAGAATGGGAGAAAATGTTCACAAACTATACATCTGACAAATCAC 1564
                            i                 i  ii    ii   i      i  ivv  
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr1_239385735_   1565 TAATATTCAGAATCTATAAAGAACT--TA-AATCCAA--------AGAAT 1603
                          vi   i      v           --  -  ii   --------   vv
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr1_239385735_   1604 AATAACTTCATTAAAAAGTGGGTGAAGGACATAAGCAGACACTTCTCAAA 1653
                               iiv   ?    i    ii     iv i ii     i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_239385735_   1654 AGAAGACACACAAGCCGCCAGCAAACACATGAGAAAATGGTCACTATCAC 1703
                               i i    iiv    ii  i       i  i   v   vi    ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_239385735_   1704 TGATCAT 1710
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.45 (125 / 86)
Gap_init rate = 0.02 (18 / 899), avg. gap size = 2.17 (39 / 18)  


3038 15.98 11.39 0.32  chr1_239448581_239451567.rev     1362  1993 (994)    L1M4_orf2#LINE/L1        3   704 (204)  

  chr1_239448581_   1362 GAAAGAGATTCCATATCCATAGACTGGAA-------TATTGTTAAGATGG 1404
                               v  i    i i   i  i     -------              
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_239448581_   1405 AAGTCCTCTTCAAATTGATCTACAGATTTAACACAATCCC---------- 1444
                         v i v   ii                  i   i       ----------
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_239448581_   1445 --AGCTAGCTTCTTTGTAGAAATTGACATACTGAGTCTAAATTTCA---- 1488
                         --    iv   i    i           vi    vi     v    ----
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr1_239448581_   1489 GAACTGCAAGGGACTCAGAATAGCTAAAATAATCTTGAAAAAGAA---TA 1535
                            v          i         i    i               ---i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr1_239448581_   1536 AAGTAGGAAAACTCACACTTCT-GATTTCAAA-CTTATTATAAACTAATG 1583
                             v   ii           i-i        -    i  i   viv ii
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr1_239448581_   1584 GTAATCAAGAGAGT-----ACTGCCATAA------------------ATG 1610
                                   v   -----    v     ------------------   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr1_239448581_   1611 -AGTAGAATTGAGAGACCAGAAATTAAACCAATGCATCTATAGGTAATTG 1659
                         - i            v        -     v  i   i   i vi     
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAAT-AAACCCATACATTTATGGTCAATTG 351

  chr1_239448581_   1660 ATTTTCAACAAGGGTGCCAAGACCATTCAATAAGGAAAGA-TG--CTT-- 1704
                               i                        ii       - i--   --
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_239448581_   1705 ------ATGGTGCTAGGGCAATTGGCTATCCACATGCAAAACAATGAAGT 1748
                         ------        i  i   i   v  ?            v        
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_239448581_   1749 TGGACCCTCGCCTCACACTAGGTACAAACATTAATTCAAAATGGATCAAA 1798
                                iii        i vi      v     i             ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_239448581_   1799 GACCTAGATGTAAGAGCTAAAATTATACAACTCTTAGAAAAGAACATAGA 1848
                               i               i    v           i i       i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_239448581_   1849 AGTAAATCTTCAAGACCTTCAATTTGGCAATGGCC----AAATA-GAG-- 1891
                         ?          iv      vii  v        ii---- i   -  v--
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_239448581_   1892 CAAAAGCACAAACAATCATATAAGAAAATA--TCAATTGGGTTTCATTAA 1939
                                    i   -  v vi i      -- v      ii     i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAA-CAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_239448581_   1940 TATTAAAAACTTTCATACTCCAAAGGACACTATCAAGAAATTGAAAAGAC 1989
                         v            ii i  i                    v         
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_239448581_   1990 ATCC 1993
                          v  
  L1M4_orf2#LINE/    701 AACC 704

Transitions / transversions = 2.16 (67 / 31)
Gap_init rate = 0.03 (18 / 702), avg. gap size = 4.11 (74 / 18)  

 933 18.26 2.49 3.73  chr1_239448581_239451567.rev     2256  2496 (491)    L1M4_orf2#LINE/L1      671   908 (0)  

  chr1_239448581_   2256 CAAAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAAGACAACCCACGGTA 2305
                              ---   v i   ------  i   ivi              i v 
  L1M4_orf2#LINE/    671 CAAAG---GACACTATC------AAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_239448581_   2306 TGGGAGCCAATTTTTGAAAGTCATATGTCTGATAAGGGAGTTGTATCTAG 2355
                               vv   v    v  i      i            v       i  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr1_239448581_   2356 CACATATAAAAACCTCATACCACTCAAGAATAAAAAGAGAACCAACTCAA 2405
                         v i       i v   v   v      v          v  vi   i   
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr1_239448581_   2406 TTAAATAATGGGCAGAG-ACATGAATAGACGTTTCTCTG--TTATTTATA 2452
                           ?  v        i  - iv         i      ii--vv vv    
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_239448581_   2453 CAAATGGCCAGTA-GCACAT--AAAGATGCTTGATACCATTAGTCAT 2496
                                   i  -      --         ii i i  ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.05 (22 / 21)
Gap_init rate = 0.03 (6 / 238), avg. gap size = 2.50 (15 / 6)  


 847 25.62 21.32 1.59  chr1_239786535_239789095.rev      697  1137 (1424)    L1M4_orf2#LINE/L1        1   528 (380)  

  chr1_239786535_    697 TGGACTGATATGCAGTTTACAAGGATTAGA-----TAATATCAT-AAAAT 740
                             vv     v vi v v  v     i  -----      ii -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_239786535_    741 GTTGAT---TCTCAAAT-GACCTATAATTTATAATTTAAAGCCATCTCAA 786
                          vii  ---i i     -  i   i i------   i  v  v   i v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAG------ATTCAACGCAATCCCTA 94

  chr1_239786535_    787 TCAAAATCCCAAATGACTTTT----GGAACTTCACAA-----TTCTGAAC 827
                                    iv  v     ----i   v  v    ----- i  i  v
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_239786535_    828 TGTATTTGGAAATGCTAAAG----------GCCAAAG-------GATAAA 860
                          vi  v         v ii ----------      i-------  v   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_239786535_    861 GAA---CAATGTTGGAAGACTTGGTCTGCCAGATTTCAG----------- 896
                            ---   v      i    iivv  v  vi      i-----------
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_239786535_    897 --GCTATAACAATCAAGACAGTATAGTATTAGCA---------------- 928
                         --    i ii            i i   i i   ----------------
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_239786535_    929 ---CAATTAACTAAAAC--ACAGTCCAGTAATAGACCCAAATATATATGG 973
                         ---    vi v  i  i-- v       v    i     v i  v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_239786535_    974 ACAACTTATTTAGGAGAAAGGTACTA---TCAT--AAAGGCAAAGGACTA 1018
                         v   i v    vv  v  i   i i ---i   --  v  vi  i  v  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_239786535_   1019 -CCTTTCCAAGAAATGGTGCTTGGA----TGTATAAACACATAGGAAAAG 1063
                         -i    i   v          v   ----  v   ?v     - v     
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-GCAAAAG 443

  chr1_239786535_   1064 AACAAA---------CTA--TGACCCCATATACAAAAATAAATTCCAGGT 1102
                           ii  ---------   -- v  v              v  i  v ii 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_239786535_   1103 AGGTTGTAGATCTAAATGCAAAAAGTAAAACCATA 1137
                         i i ii?   i       i  i iv      i   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

Transitions / transversions = 1.27 (62 / 49)
Gap_init rate = 0.04 (20 / 528), avg. gap size = 5.05 (101 / 20)  

 600 23.66 12.10 5.65  chr1_239786535_239789095.rev     1702  2073 (488)    L1M4_orf2#LINE/L1      513   908 (0)  

  chr1_239786535_   1702 AAAAG-TGAAACTATAA--TTTCTAGAAGACTATGTAGAAG--AATTAGC 1746
                           i  - i         --i ii       vv ii   i? --   --- 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---C 559

  chr1_239786535_   1747 TTCATGA--TTGTAGTTGGAAAAAAACTTTTTTAAA-AGGACATAAAAAA 1793
                            i   --   -i   i iv  vii-   i   i - v    iv    i
  L1M4_orf2#LINE/    560 TTCGTGACCTTG-GGTTAGGCAATGG-TTTCTTAGATATGACACCAAAAG 607

  chr1_239786535_   1794 CAACTACATAATTAAGGAAAA------CAAACTGAAGTTCTAGCCATCAA 1837
                           --i vii  iv  i     ------i   i  i v   -----     
  L1M4_orf2#LINE/    608 CA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC-----ATCAA 650

  chr1_239786535_   1838 AGC---AAGC------------AAGCAAACTATCAAGAGAGTTACAAGCG 1872
                          ii---  i ------------   v v          i   v v   vv
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_239786535_   1873 AAGCCACAGAGTGGGAATATATATTTATAA--TATGTATACTGACAAAGG 1920
                           v       i     iv v      ii  --i  i   -    i  i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT-CTGATAAGGG 749

  chr1_239786535_   1921 GCTTGCATTCAGAATATATAAAGAACTC------CCCAA--ATAAATATG 1962
                         i    i  i                   ------ i   --     - --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-A-- 796

  chr1_239786535_   1963 TCAGATACATACCTTAATAAAAATAATAAG--AAGGATATCTGAATAGGC 2010
                         --   i v   v ii   v?   -   ii --      --i       i 
  L1M4_orf2#LINE/    797 --AGACAAATAACCCAATTWAAA-AATGGGCAAAGGAT--TTGAATAGAC 841

  chr1_239786535_   2011 GGCTCACAGAAGAGG-CAT-CAAATGGACAATAAATGTATGAAACAATAC 2058
                         ivi  v vi    i -i  -       v      iiii      vi  i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_239786535_   2059 TCAA--TCACACTAGTA 2073
                             --   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (60 / 26)
Gap_init rate = 0.06 (25 / 396), avg. gap size = 2.64 (66 / 25)  


2520 26.87 3.01 1.78  chr1_240070883_240075979     3708  4604 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_240070883_   3708 TGAAAAAACGTTCCATGCTCAGGGACTGGAAGAATCAATATCAGTAAAAT 3757
                           i   i ii i     i   v   i       v i     iiv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_240070883_   3758 AGCCATATTTCCCTGCCCAAAGCAATCTACAGATTCAAGGCTATACCTAC 3807
                         i  v   -----  v      vii              v  v  v    i
  L1M4_orf2#LINE/     51 GGCAATA-----CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr1_240070883_   3808 CAAACTACCAACATCATTTTTCACAGAACTGGAAAAAAAAAACTACAAAA 3857
                             v v   i vv v     ii     v v  v  ivvi v i-i    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC-TAAAA 144

  chr1_240070883_   3858 TTAACAAGAAACCAAAAAAGAGCCAGAATAGCCAAAGCAATCCTAATCAA 3907
                           v i v i  viiv  ii  v              i     i i vv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_240070883_   3908 AAAGAAGAAAGCTAGAGGTATCAAATTACCTGCCTTCGAACCATACTATA 3957
                         i     v    i i    vv   v i v  iivi   i  v v     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_240070883_   3958 AAGCTACAGCAACCAAAACAGCATGGTACTG-TAAAAAAACAGACACAAA 4006
                                  i  i   i    ii        -i v  ii i     i v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_240070883_   4007 GGCCAATGGAACATAATAGAGAGCCCAGAAATAAAGCCAGCCACCTACAA 4056
                          ii        i v   v     i           v   vv  ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_240070883_   4057 T-AATCTAATCTTTGGCAAGGCTGACAAAAATAAGCAATGGGGAAAGGAC 4105
                          -   - i  i  i i     v  v   i vi vv            i i
  L1M4_orf2#LINE/    345 TCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_240070883_   4106 --TCCTTATTCAATATATGGTGCTTCGACAGCTGGTGAGCCATACGCAGA 4153
                         --  i  --    i v        vv    i    vv ?   i i   i 
  L1M4_orf2#LINE/    394 AGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_240070883_   4154 GGAATGAAACTGGACCCCTATCTTTTACCATATACAAAAATTAACTCAAT 4203
                         i       ii          i  ivi                       v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_240070883_   4204 ATTGGTTAAAGATTTAAACGTAAAACCTCAAACTATAAGAATCCTAGAAG 4253
                           v i i ?   ii    i    i v  v         i v  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_240070883_   4254 AAAATCTAAGAA-ACACCATTCTTGACATTGGCACTGGAAAAAATT---- 4298
                             iv  i ?i- v i -   v    v    vviv  v  vii  ----
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_240070883_   4299 --ATATGACTAAGTCCTCGATAGCAATTG-AACAAAACCAAAAATCGACA 4345
                         --       -- ----i i v    vvv -       vv      v  i 
  L1M4_orf2#LINE/    591 AGATATGAC--A----CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_240070883_   4346 AGTGAGACCTAATTACACTAAAGAGAATCTGTACAGCAAAAGAAACTATC 4395
                          i vi   i v  i v v v  i ivv i   i vv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_240070883_   4396 AACAGGGTAAA-------CCTACAGAATGGGATAAAATATTCATAAAC-- 4436
                           v ii  i  -------  i           v        iii   i--
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_240070883_   4437 --TATCTGACAAAGGTCTAATATCCAAAGTGTATAAGAAAGTTAAACAAT 4484
                         --       i  i  v  vi      i i i     ii  v ivv    i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_240070883_   4485 TGAACAAGCTAAACACAAGTAACCCAAT-AAAAAATGAGCAAATGACATG 4533
                          v  i  vvv   v    i         -?       i     v  iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_240070883_   4534 AACAGACATTTCTCAAAAGAAGACATACAAGCAGCCACCAA--ATATGAA 4581
                           i           v        i      iii    vi  -- i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_240070883_   4582 AA-ATGCTGCACATCACTAATCTT 4604
                           -     vv      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (135 / 102)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.39 (43 / 18)  


1870 22.01 3.14 2.10  chr1_240077392_240079282      500   976 (915)    L1M4_orf2#LINE/L1      296   777 (131)  

  chr1_240077392_    500 ATCAATGGAAGAGAATCAAAAG-CCAAAAATAAATCCATGCCTATATGGT 548
                                   v     ii i  -   i       i    i v v      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_240077392_    549 CAACAAACATTTGACAAGGGTACTGAAAATACATAAGGGAGAAAGAACAA 598
                            ivi iv  i         i ii i vi ivi  v  i       i i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_240077392_    599 TCTCTTCAATAAATAGTGCTAGGAAAACTGGATATACACATGCAAAAGAA 648
                            i     i    i     i   v         ?v              
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_240077392_    649 TGTAAT-GGAGTCTTATCTTTCATCATATCAAAAAACCAACTCAAAATGG 697
                           v i -   vi i  i  iv  i     vv     ii            
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_240077392_    698 ATTAAAAACTTAAACGTAAGACCTGAAACTATAAAACTCCTAGAAGAAAA 747
                           i ? i  i    i      v  i              i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_240077392_    748 CATACCAAAAAAACCTCCTTGATATTGGTCTTGGCAAGTATTTCTTGGAT 797
                             v-i?iv   i  i v   iv    vi v     vvi      i   
  L1M4_orf2#LINE/    546 CATAG-GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_240077392_    798 ATGACACCAAAAGCACAAGCAACAAAGGCAGAGATAAATAGGTGGGACTA 847
                                                   i v i i   i   ii v     v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_240077392_    848 CTAT-----TTAT---CTCTT-TGCTTATGTGAAGCAAAGAAAACAATCA 888
                          -  -----   v---  i  -     --------     i v  v    
  L1M4_orf2#LINE/    645 C-ATCAAAATTAAAAACTTTTGTGCTT--------CAAAGGACACTATCA 685

  chr1_240077392_    889 ACAGAGTCAAAA----ACCTATGGAATGGGAGAAAATACTTGCAAATAAT 934
                          v i   v    ----   i ii               i        v  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_240077392_    935 ATATCTGATAAGAGGTCAATATCCCAAATATATACAAAACTC 976
                                     i iiivi     vi        v i     
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

Transitions / transversions = 1.83 (66 / 36)
Gap_init rate = 0.02 (9 / 482), avg. gap size = 2.78 (25 / 9)  

 413 21.43 3.57 0.00  chr1_240077392_240079282     1288  1399 (492)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr1_240077392_   1288 AAAAAGAAAAAAAATCTGATCAAAAAATAGGGAAAGGACCTGAATATAC- 1336
                                v   v  i ii  i?      i  v      ii      v  -
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_240077392_   1337 --TTTTCAAAGAAAATATACACGTGGCCAGCAGATACATGAAAAGGTGCT 1384
                         -- i i       i       vi      ii iii          i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_240077392_   1385 CAAGAT-AGATCACTA 1399
                            v  - ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.83 (17 / 6)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 2.00 (4 / 2)  


1158 23.70 11.85 0.87  chr1_240081856_240086312     1770  2115 (2342)    L1M4_orf2#LINE/L1       16   399 (509)  

  chr1_240081856_   1770 TGTCCATGGATTAGAAGACTCAATATT------------------CTTAA 1801
                            i        i       i      ------------------ ii  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr1_240081856_   1802 ATAGATTTATGGATTAAATGCAATCATAATCAAAGTTACAGCAGACTTTT 1851
                           v   i  ii    v  i      viv      i iv    v v     
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr1_240081856_   1852 TTGTAAAAATTGACATGATAAT----AAATTTATATGAAAATGCAGAGGA 1897
                            i i         v v i  ----     i     i       ii   
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr1_240081856_   1898 CACAGAAGAGTCAAAACAATTCTGAAAAA--AGAACAAAGTT-------- 1937
                          v     v  i         ii       --           --------
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr1_240081856_   1938 ----TTTCTCTATTTCAAAATATACTCCCAAAGCAACAATTATCAAGTTA 1983
                         ----i   i v         iv    -v      v   i v      vi 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACT-ACAAAGCTACAGTAATCAAGACA 264

  chr1_240081856_   1984 GCGTGGTACTGATGTAAAGAGAAACTCAAAGATCAATTAAACAGAATAAG 2033
                          i         iii   i  v i  vi v        vi  i     -v 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT-TG 313

  chr1_240081856_   2034 ACAGTGCAGAAACAGACCCATA--TGTGTGACAAACTGATTTTCAACAGA 2081
                          v   v      i i       -- v i  iiv  i        i   ii
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_240081856_   2082 GGTACCCAAGTCACACAATCAGAGACAG---GGTCTT 2115
                            i  v iii  iv    -i i  v  ---i     
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTT 399

Transitions / transversions = 1.83 (53 / 29)
Gap_init rate = 0.02 (9 / 384), avg. gap size = 4.89 (44 / 9)  

 459 26.38 3.07 2.45  chr1_240081856_240086312     2367  2529 (1928)    L1M4_orf2#LINE/L1      387   550 (358)  

  chr1_240081856_   2367 AAAGGACAGCCCTTTCAATGAAAGATAGTGAAAGAACAAGATGTCTGTAG 2416
                             i i  i i      ii  v i iv  ii v   vi   i? iii v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_240081856_   2417 GGGGAAAAAAATGAACCTCAACTCTTAGCTCACAGCATACATAAAAATTA 2466
                          v--    i      vi vi  i i  v      v    i i        
  L1M4_orf2#LINE/    437 GC--AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_240081856_   2467 A-----AATGGATCACAGACCTATACATGTAATAGGTACAACTTAAAAAG 2511
                          -----         ?       - -      v  v  v    vv    v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTA-A-ATGTAAGAGCTAAAACTATAAAAC 532

  chr1_240081856_   2512 TTTTAGAAGAAAATACAG 2529
                          i           i i  
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAG 550

Transitions / transversions = 1.56 (25 / 16)
Gap_init rate = 0.02 (4 / 164), avg. gap size = 2.25 (9 / 4)  

 901 27.59 4.89 0.86  chr1_240081856_240086312     3644  3991 (466)    L1M4_orf2#LINE/L1      547   908 (0)  

  chr1_240081856_   3644 ATAGGAG-AAAGATGTGTGACCTGGGGT-ACACAAACATTTCTTGGACAG 3691
                              ? -   vv vi       v    - vi   vvi      i  i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_240081856_   3692 TACACAAAAAAAGTGAAAACCATAAAAGGCAAGAATTGATAAATAAGAC- 3740
                         v    v    -- iiv  i v i     i-  i   v       vi   -
  L1M4_orf2#LINE/    597 GACACCAAAA--GCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACT 643

  chr1_240081856_   3741 --ATCAAAATTAAAAACGTCTGTTCCTCAAAAGACATCACTGAGAAAATG 3788
                         --               v i   v i     i    ii iii     i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_240081856_   3789 AAAAGGCAAGCTACAGTCTGGAAGAAACCATTTGTAATACAAATATTTGG 3838
                              i   v i    vv   i     vi     i  vv  v    i  i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_240081856_   3839 CAAACTATTTGTAACCAGAACATCCAAAGAACTCCTATAATTCAGTAA-- 3886
                         i  ivv i     v      i  vi         i  i  i   i   --
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_240081856_   3887 -GAAGATGAACAACCGAAT-----AATAGGTGAAATATTTGAATAGACAG 3930
                         -i    ii  i    v   -----   i  ii  iv             v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_240081856_   3931 GTCACAAAAG--TATATGCAA-TGGCAAA-AAGTCTGAGTGAAGACATTT 3976
                         v  v v    --v    i   -    v  -   iviiv vi    iii i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_240081856_   3977 CCTATCATTAGTCAT 3991
                         vvi    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (55 / 40)
Gap_init rate = 0.03 (10 / 362), avg. gap size = 2.00 (20 / 10)  


2988 21.67 7.07 1.85  chr1_240146225_240148207      628  1490 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_240146225_    628 TGGAAAGACATCCCATGTTCATGCACTGAAAGGTTTAATATTGTTAAGAT 677
                                 i              v i  i   ii                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_240146225_    678 GTCAACAC--CACAAAGTAAGCTACAGATTCAATGCAATCCTTTTCAAAA 725
                          v   i  -- v    v i v            i       i v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_240146225_    726 TCCTA-CAGCATTTTT-GCGGAAACAGAAAAAAAAAATCCTAAAATTCGT 773
                            i - v  v     -  i    iv  v  ivvi -           i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr1_240146225_    774 ATGGAAACCATAAAGAATCCCAAACAGCTGAAACAATCTTGAGAAAGCAA 823
                                i-ii  i i i  vi  i   ii            i    v i
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_240146225_    824 AA---AGCTGAGGGCTTCATACCTCCTGACTTCAAAATGCATTCTAAAGC 870
                           ---  i  ii  vi   i  i   ii i       ivi i vi     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_240146225_    871 TTCAGTAATTAAAACAGATTGGTACTGGCATAA----AGACATATAGACT 916
                          v       i  i    vv              ----           ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_240146225_    917 AATGGAACAGAACAGAGAGCCCAGGTAATAAAACCATATATATATACAGT 966
                                i    iv     i    i-      v     i  v   i--  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGA-AATAAACCCATACATTTATG--GT 345

  chr1_240146225_    967 CAAATGATCTTTGACAAGGGCGTCACAACTAACACAATGTGGAAA---TA 1013
                            v    i  i        i i  vi  i vi-     v     ---  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATA 394

  chr1_240146225_   1014 -T----------AATGCTGCTGAGAAAACTGGGTATCAACATGCAAAAGA 1052
                         - ----------    v     i  v      i  ? v            
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_240146225_   1053 ACAAAAGTGGAGCCTTATTTTACACCACACACAAAA-CCAACTCAAAATG 1101
                          ii  iv    v  i  ii i      i i      -ii           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_240146225_   1102 GATCAAAGAA-TAAATATAAGACATGAAACTACAAA-CTCCTAGGAAAAA 1149
                              ?   v-     i     vv i      i   -   i   i i   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_240146225_   1150 ACCACAGGAGAAAAGCTTCATAAT-TTGGTCTTTAGA-AATGATTTCTT- 1196
                           - i   ? v   v    i i i-    v--    i-    i      -
  L1M4_orf2#LINE/    545 AC-ATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTTA 591

  chr1_240146225_   1197 GATGCTGACA---AAAGCA---GTAA------------TAGATGAGTAGA 1228
                            i-     ---      --- i  ------------     i i v i
  L1M4_orf2#LINE/    592 GATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_240146225_   1229 AGTATATCAAAATAAAAAGCTTCTGCACAGCAAACAACAGAA-CAAAACA 1277
                          v vi        v    i   i  ii vv    vi   vv -   i v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_240146225_   1278 G--AAAA------CTACAGAATGAGAGAATATATTTCCAAACCATATGTC 1319
                          --    ------ i        i     v      v    i     i  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_240146225_   1320 TGATAAGGGCTTAATATTCAAAATGTATAGGGAACTCCTATAACTCAGTA 1369
                                  vi vi   i  i   i    ii      i  i      i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_240146225_   1370 GCGAAAACAAAAA-ACAGA-AACACAAGTAAAAACTTGGCAAAAGACTTG 1417
                         ------ i     -   i -   v   v ?    v v      i  i   
  L1M4_orf2#LINE/    791 ------ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_240146225_   1418 AATAGACATTTCTTCAAAGTAGACATACAAATGATACACAGGTATTTGAA 1467
                                      i     v   i         iivv i i i iv    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_240146225_   1468 AA-ATGCTTAGCATTACAAATTAT 1490
                           -     i i   i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (123 / 60)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 2.41 (77 / 32)  


2694 15.68 4.35 5.90  chr1_240258388_240260006.rev      485  1128 (491)    L1M4_orf2#LINE/L1      275   908 (0)  

  chr1_240258388_    485 GACATAGAGGAGAGA-A-GTAGATCAATGGAATATAATTGAGAATCCGGA 532
                          i    -    v   - -i               v        i   i  
  L1M4_orf2#LINE/    275 GGCATA-AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_240258388_    533 ATTTAAACCATACATATATGGCTAATTGGTATTCAACAAGGATGGCAAGG 582
                          v v  v        v     ii     i v   i      i  v    i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_240258388_    583 CGATTCAGTGTGGAA-GAATAGTCTT--CAAGAAATGATGATGGGACAAC 629
                          v     i  v    -          --   v     i  v         
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_240258388_    630 CCGATTTCCACATATAAAAGAATGAATTTGGACTCCTTACCTCACACCAT 679
                         iv   v?      ii           v      i   -            
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT-ACCTCACACCAT 472

  chr1_240258388_    680 GTGTAAAAATTAATGCAATGTGTATTAAACACCTAAATTATAAGAACTAA 729
                         i ii         iv   vi  v  i ? v        -i     i    
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT-GTAAGAGCTAA 521

  chr1_240258388_    730 AACT--------CTTAGAAGAAAACATAGGGGTGAATCTTTGTAATTTTG 771
                             --------                  ?  i      i  i ii   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr1_240258388_    772 GATTGGGCAATGGTTTATTACATTTGACACCAAAAGCACAAGCAGTCAAT 821
                          i  i           v   v  v                    iiv  v
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr1_240258388_    822 GAAAAAG-----AAAGTATACTTCATCAAAATAAAAAACTTGTATG--TC 864
                               i-----   v iv             v        v i  --  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_240258388_    865 AAAGGCCGCTGTCAAGAAAGTGAGAAGGTCTTCAGGAAACAACAATTTTT 914
                              v i  i            i   --------------    iii--
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAG--------------ACAACCC-- 705

  chr1_240258388_    915 AAGAAAGTGAAAAGAATAGAGTATGGGAGAAAATATTTGTAAATCATGAA 964
                         --------------- i   --                 i       iv 
  L1M4_orf2#LINE/    706 ---------------ACAGA--ATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_240258388_    965 TCTGATAAGGGCCTAGTATCCAGAATATATTAAAAATTCTTATATCTCAA 1014
                                    v  v               v  i  i     i v     
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_240258388_   1015 CAATGAAAAGACAA----CCCAATTAAGAAATCTGAATAGACAATATGAA 1060
                         i   i         ----       ? i    -- iii i vi  v    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAAT--GGGCAAAGGATTTGAA 836

  chr1_240258388_   1061 TAT---TTTCTCCAAAGAAGATAATCAAATGGCCAATAA-TACATGAAAA 1106
                           v---                 vv              -i         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_240258388_   1107 GATGCTCAACGTCATTAGCCAT 1128
                                   i   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (58 / 39)
Gap_init rate = 0.03 (17 / 634), avg. gap size = 3.88 (66 / 17)  


3257 26.65 0.55 0.55  chr1_240295891_240302277     4987  5894 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_240295891_   4987 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5036
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_240295891_   5037 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5086
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_240295891_   5087 TACCAATGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTACA 5134
                          v   iivi i  i   i     -   -- v  i  - iii    i v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_240295891_   5135 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5184
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_240295891_   5185 AAAAAAGCTGGAGGCATCATACTACCTGTCTTCAAATTATACTACAAGGC 5234
                           v    i      vv   i   v  iivi      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_240295891_   5235 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 5284
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_240295891_   5285 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACGTCTACAACC 5332
                                i    i--    i  --        vv   i  i i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_240295891_   5333 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5382
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_240295891_   5383 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAACCATATGTAGAAAGCT 5432
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_240295891_   5433 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 5482
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_240295891_   5483 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5532
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_240295891_   5533 CTGGGCA-ATACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTA 5581
                         v i  ?i- v i -   iv   v v  vvii     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_240295891_   5582 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTAACAAATGGGATCTA 5631
                         vi            vvi          vv     vi i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_240295891_   5632 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5681
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_240295891_   5682 CAGCCAACCTACAGAATGGCAGAAAATTTTTGCAATCTACTCATCTGACA 5731
                         v  v     i         v       v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_240295891_   5732 AAGGGTTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5781
                          i  ii vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_240295891_   5782 AAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACACTT 5831
                           i     i     v  i? v  i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_240295891_   5832 CTCAAAAGAAGACATTTATGCAGCCAAGAGACACATGAAAAAATGCTCAT 5881
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_240295891_   5882 CATCACTGGCCAT 5894
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2826 27.24 1.88 1.33  chr1_240308490_240314508     4624  5526 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_240308490_   4624 TGGAAAAACATCCCATGCTCATGGATAAGAAGAATCAATATCGTGAAAAT 4673
                               i i        i        vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_240308490_   4674 GGTCATACTGCCTAAAATAATTTATAGATTCAATACTATTCCCATTGAAC 4723
                           iv     v  i   v i  i  i        ii v  i  i  ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_240308490_   4724 TACCATTGACTTTCCTCACATAATAAGAAAAAACT-ACTTTAAAATTCAT 4772
                          v   vivi i  ii ii  v  - vvi v  i  - iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_240308490_   4773 ATGGAACCAAAAAAGAGCCTGAATAGCCAAGACAAATCCTAAGCAAAAAG 4822
                               viiv  ii  v  v          i    -  i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAG 198

  chr1_240308490_   4823 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACATGGC 4872
                                i      vv       v  ii i      viv       vi  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_240308490_   4873 TACAGAAACCATAACAGCATGGTACTGGTACCAAAACAGACACATAGACC 4922
                              v  i  vi    ii         i iv ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_240308490_   4923 AACGGAATAAAATAGAAATCTCAGATATAAGACCACAGGTCTATAACCAT 4972
                           i      i   v  i vii    v    iv   i vi i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_240308490_   4973 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5022
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_240308490_   5023 ATTTAACAAATGGTGCTAGGAGAACTGGCTAGCCATATGCAGAAAATTGA 5072
                         v  i             i   v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_240308490_   5073 AACTGGGCCCCTTCCTTACATCATATACAAAAATTAACTCAATACAGATT 5122
                          ii   i     v   i   i                     v ii   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_240308490_   5123 TAAAGACTTAAACATAAAACCCAAAACTATAAAAACTCT-AGAAGAAAAT 5171
                         - ?    i    ii   i v i            -    -         i
  L1M4_orf2#LINE/    499 -AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr1_240308490_   5172 CTAGGC--AATTCCATTCAGGACACAGGCATGGGCAA--ACTTTTCATGA 5217
                         v    ?--  v  --   iv   viv  vv i     --ii  i i -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GA 593

  chr1_240308490_   5218 TGAAAACATCAAAACCAATTGCAACAAAAGCAAAAATTGACGACTGGGAT 5267
                          - vi   i     v  vvv          v      v  ii v v   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_240308490_   5268 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 5317
                         i v  i   v v  i i   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_240308490_   5318 GAACAGACAATGTACAG----GGAGAAAATTTTTGCAATCTATCCATCTG 5363
                            v      ivi    ----         v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_240308490_   5364 ACAAAGGGCTAATATTCAGAATCTACAAAGACCTTAAACAAATTTTCAA- 5412
                          i  i  i  vi   i      v  i     v  ivv    ---i    -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA---CTCAAT 789

  chr1_240308490_   5413 GACAAAAAAA------ACTTCATTCGAAAGTGGGCAAAGAACATAAACAG 5456
                         i i     i ------  iiv   ?i   i         i iv i  i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_240308490_   5457 ACACTTTTCAAAAGAAGGCATACATGCAGCCAACAAACATGAAAAAAAAA 5506
                            i  i  v       ii     viii     i  i  i- vi    i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC-ATGAAAAGA 888

  chr1_240308490_   5507 AGCTCAATATCACTGATCAT 5526
                         v      i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (152 / 90)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.81 (29 / 16)  


2058 20.92 18.90 3.17  chr1_240891462_240893123      477  1169 (493)    L1M4_orf2#LINE/L1      107   908 (0)  

  chr1_240891462_    477 CTGCCATTTTT-------CTGAT--GCCAGCCCCAAAATTTATATC-AAA 516
                              v     -------i   i--  iiii  i      i    v-   
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_240891462_    517 CGCAAAAGACCCAGAATAGCAAAATCAATCTTGAAAA----GAACAAAGC 562
                         i    ii             v   v            ----        i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr1_240891462_    563 TGGAGGGCTTGTACTCCTGAATTTCAAAACATGCTATAAAGCCACAGTA- 611
                               i  iii   i iv           v i   i     i      -
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr1_240891462_    612 TCAAAACACTGTGGTGCTGGTATAAGAACAGA------------------ 643
                             i   v      i    i     i i   ------------------
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr1_240891462_    644 -------------------------------------------------- 643
                         --------------------------------------------------
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr1_240891462_    644 ------GGG-GCAAAGGCATTTCAATGGGAAAAGAATAGTATTTTCAACT 686
                         ------   -  v   i vv         i          v        v
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr1_240891462_    687 AACGGTGCGAGGACAAGTAAATATCTACACACAAGGAGATACACTTAAGG 736
                           i     vi      v ii   ? i   ii   iiii  iv v  i- i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG-GA 455

  chr1_240891462_    737 CTTTTACCTCGCATCACATG--AAAATTAACTCAACATGGATCACAGATG 784
                          iii      i  i  i  i--             v        ?   i-
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC- 504

  chr1_240891462_    785 ATTTTGTGAAATGGTCTTTCACACGTGAAAGTTTAAACTATACATTTTTT 834
                         ---i ---     ------------ i i  i v        v vi i  
  L1M4_orf2#LINE/    505 ---CT---AAATG------------TAAGAGCTAAAACTATAAAACTCTT 536

  chr1_240891462_    835 ----TAAAACATCAAATGAAACTTTTAATGACCTTGGATT-GGCA--GAT 877
                         ----v       - ii? v  v i  vi         i  -    -- i 
  L1M4_orf2#LINE/    537 AGAAGAAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr1_240891462_    878 TCCTTAAATGTGACACCAAAA--ACAACCTAGGTAAGGAAAAACTGATAA 925
                          i    i  i           --    v v viv   i     iv     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr1_240891462_    926 GTTGGATTTGACCAAAATTTAAAACTTTTGCACTTCAAAAAACATCACCA 975
                         i     i  v i       v          ii       ii   ii i  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_240891462_    976 AGACAATGAAATGGCAAGCCACAGACTAGAAAAAAA-ATTTGCAAAT--T 1022
                            v i     v i   v       v i i i    -          -- 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_240891462_   1023 ATGTCTAATACAGAATCTGTATCCAGAATGTATAATGACTTCTTATA--- 1069
                           i   i   vi i ii            i     v  vi     i ---
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr1_240891462_   1070 ---TAATTAAAA--CAA-----CCAATTTAAAAATGGGCAAAATATCTGA 1109
                         ---    v    --   -----      ?             iv  i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_240891462_   1110 ATAAACAT--CACCAAGGA---TATATAAATAG---------ACATAAAA 1145
                            i    -- v    i  ---    i    i ---------    i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_240891462_   1146 AAATGCTCAAACATCATTAGTCAT 1169
                          i        -     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 2.44 (100 / 41)
Gap_init rate = 0.03 (26 / 802), avg. gap size = 5.88 (153 / 26)  


3280 14.42 6.18 4.53  chr1_240958542_240960269      500  1227 (501)    L1M4_orf2#LINE/L1      142   881 (27)  

  chr1_240958542_    500 AAATTGTAAATGGAAATTCAAGAGTACCAGAATAGACAAAACAGTCTTGA 549
                              -i v        v    i vv         v       i      
  L1M4_orf2#LINE/    142 AAATT-CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_240958542_    550 AACAGAA----AAAGTGGAAGGACTCACAGTTCTTGACGTTTATACAATT 595
                           v    ----     v i          v   i-----------     
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCC-----------CAATT 229

  chr1_240958542_    596 GGTCATTTGAATACTAAGCTTACTACAAAGCTGCAGTAATTGAGACACTT 645
                         --   ----------  i              i       ii     v v
  L1M4_orf2#LINE/    230 --TCA----------AAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr1_240958542_    646 TGGTACTGACATA-GGATAGGAATATACATCAATGAGATAGAATTGAGAG 694
                                 i    -      iv     v       ii             
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr1_240958542_    695 TTCAGAAATAAAACCTCATATTTACAGTCAGTTGATTTTTGATAATGATA 744
                          i          v  vi i     ii    i        i  i  v i i
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr1_240958542_    745 CCAAGAGAATTGAATGGAAAAAGAAC----------------GGTACTGA 778
                               vv   v     ii      i----------------   i   i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr1_240958542_    779 AACAACTAGATACCTACATG-AAAAAAATGAATGTGGACCCC-ACCTCAG 826
                         i      i    ? i     -    i      vv        -      v
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr1_240958542_    827 ACCACACCCAAAATTATAACTCTGAATGGATCAAAGACCTAAATGTAAGA 876
                             i iv     v -      vi         ?                
  L1M4_orf2#LINE/    468 ACCATATACAAAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_240958542_    877 GCTAAAACTGTAAAACATATAGAAGAAAACATAAGGGAAAATC--CGTGA 924
                                  i      viv              i ? v     --     
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_240958542_    925 CCTTGGATTAGGTGATGGTTGCT---------CAC---AAGCACAAGCAA 962
                               i     ii      v  ---------   ---            
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_240958542_    963 CAAAAGAAAAAATAGATAAATTGGACATCATCAAAATTAAAGTCTTTTGT 1012
                                                   v              iv       
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_240958542_   1013 GCTTCTAAGGACATCATCAAGAAAGTGAA--GACAATTCACAGGATGGGA 1060
                              v       ii              --     ii     i      
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_240958542_   1061 GAGAAAT-TTTGTGATTCATGTATCTTATTATGGACTTGTTTTTAGA-TA 1108
                           -    -    ii v    i     v  v v        v ii   -  
  L1M4_orf2#LINE/    717 GA-AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr1_240958542_   1109 TATAAAGAACTACTATTGATATAATTTGGTAATAAAAATACAA----CCC 1154
                                    -  -----  i  i iii         v    ----   
  L1M4_orf2#LINE/    766 TATAAAGAACT-CT-----TACAACTCAATAATAAAAAGACAAATAACCC 809

  chr1_240958542_   1155 AGTTTTTTAAATGGGCAAAGGATCTGAATTGTCATTTCTCCAAAGAAGAT 1204
                          i  ?vv-               i     v v                  
  L1M4_orf2#LINE/    810 AATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr1_240958542_   1205 ATCCAAATGGCCAATAAGCACAT 1227
                           v                    
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 1.40 (59 / 42)
Gap_init rate = 0.03 (21 / 740), avg. gap size = 3.71 (78 / 21)  


1881 16.12 0.87 28.83  chr1_241018260_241023221.rev     3213  4471 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_241018260_   3213 GGAAA-ACATTCCATGTTCATGGATTGGAAGATTCAATATTGTTAAAATG 3261
                              - i  i                     i i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_241018260_   3262 TCTGCACTACCCAAAGCAATCTACAGGTTCAATGCAATCCTTATCAAAAT 3311
                         v vii   v      vii        i     i       i         
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_241018260_   3312 ACCAAAGACATTCTTTACAGAAATAGGAAAAAAAAATCCTAAAATTTTTA 3361
                         v   ivvi v  i   i       -v  v  ivvi           iv  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATA 150

  chr1_241018260_   3362 CAGAACCCACCAAAGACCCAGAATAGCCAAAGCTATCCTAAACAAAATGA 3411
                         ii   vi-i v ii                 i v   i i  v  i v  
  L1M4_orf2#LINE/    151 TGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_241018260_   3412 ACAAAACTGGATGAATCACATTACCTGACTTCAAATTATACCACAGAGCT 3461
                              ii    v  v     i v  ii i      viv   i   i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_241018260_   3462 ACAGTAACCAAAACAGCATGGTACTGGCATAGAAACAGACACATAGACCA 3511
                                i   i    ii             iii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_241018260_   3512 ATGGAAGAGAACAGAGAACCCAGAGACAAATCAATACATCTACAGTGAAC 3561
                               v    iv    ii     i i   i v      i  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_241018260_   3562 TCATTTTTGAGAAAGGTAGTAAGCACATATATTGGGGAAAGGACAGTCTC 3611
                          v     i  v  i   ivi   vv   vi v         i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_241018260_   3612 TTCAAGAAATGGTGCTGGGGGCTGGGCGCAGTGGTTCACACCTGTAATCC 3661
                              v             -------------------------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGG------------------------------- 418

  chr1_241018260_   3662 CAGCAATTTGGGAGGCTGAGCTGGTGGGGACTGCCTGAGGTCAGGAGTTC 3711
                         --------------------------------------------------
  L1M4_orf2#LINE/    419 -------------------------------------------------- 418

  chr1_241018260_   3712 AAGACCAGCCTGGCCAACATGGGGAAACCCCATCTCTACTGAAAAATACA 3761
                         --------------------------------------------------
  L1M4_orf2#LINE/    419 -------------------------------------------------- 418

  chr1_241018260_   3762 AAAGTTACACGGGCGTGGTGGGCACACACTTGTAATCCCAGCTACTCGGA 3811
                         --------------------------------------------------
  L1M4_orf2#LINE/    419 -------------------------------------------------- 418

  chr1_241018260_   3812 GGCTGAGGCAGGAGAATTGCTTGAACATGGGAGGTGGAGGTTGCAGTGAG 3861
                         --------------------------------------------------
  L1M4_orf2#LINE/    419 -------------------------------------------------- 418

  chr1_241018260_   3862 CCAAGATCATGCCATTGCACTTCAGCCTGGGTGACAAGAGTGAAACTCTT 3911
                         --------------------------------------------------
  L1M4_orf2#LINE/    419 -------------------------------------------------- 418

  chr1_241018260_   3912 GTCTCAAAAACAAAAATGGTGCTGGGAAAACTATATATCAGTATGCAGAA 3961
                         ---------    --------    ---------   ? vii     i  
  L1M4_orf2#LINE/    419 ---------ACAA--------CTGG---------ATAKCCACATGCAAAA 442

  chr1_241018260_   3962 GAATGAAACTAGACCCCTATCTCTTGCCATATACAAAAA---AC---AAG 4005
                                ii i        i   vii             ---  ---  i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_241018260_   4006 TGAATTAAAGACTTAAGTCTAAAACCTCAAACTATAAAACTACTAAAAGA 4055
                           i  i ?    i   i v   i v  v             vi  i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_241018260_   4056 AAACATTTAGGA--AACTCTCCAGAACATTGGAGTGGGCAAAGATTTCTT 4103
                               --   ?--  v   i ivi  v    iv i     v i      
  L1M4_orf2#LINE/    543 AAACAT--AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_241018260_   4104 GAGCAATATCCCATAAGCACAGGCAACCAAAGCAAAAATGGACAAGTAGA 4153
                         iiii vv iv   v       i     v    v      i  i  i v i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_241018260_   4154 ATCACATCAAG-TTAAAAAGCTTCTACAAAGTGAGACTCAAAAAATAAAA 4202
                          iiv      i-       -   i -----   -----------------
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTT-----GTG----------------- 667

  chr1_241018260_   4203 ATAAAAAATAAAATAAAAAGCTTCCGCACAGCAAAGGAAACAATCAAAAA 4252
                         --------------------    --------      v  v     i  
  L1M4_orf2#LINE/    668 --------------------CTTC--------AAAGGACACTATCAAGAA 689

  chr1_241018260_   4253 ATTGAAGAGACAATCCACAGAATGGGGGAAAATATTTGCAAACTATCCAT 4302
                          v    i      i            i               ii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_241018260_   4303 CTGACAAGGGATTAATAACCAGAATATATAAAGAGCTCAAACAACACTAT 4352
                             i      i vi  v                i   vv     v v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_241018260_   4353 AGGAAAAAAATATAATAATCCAAAT-AAAAATGGGCAAAAGATCTAAATA 4401
                          iv     i i -     i    v -             i   i i    
  L1M4_orf2#LINE/    790 AATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_241018260_   4402 GACATTTCTTAGGTGAAGACATAAAAATGGTAAATAGGTATATGAAAAGG 4451
                                  iviiv     i   v      iv    i i i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_241018260_   4452 TGCTCAACATCACTGATCAT 4471
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (130 / 70)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 22.00 (374 / 17)  


3116 25.78 2.13 0.45  chr1_241052359_241058587.rev     4847  5738 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_241052359_   4847 GGAAAAACATTCCAGGCTCATGGATAGGAAGAATCAGTATTGTGAAAATG 4896
                              i i  i   v i        v      v i i      v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_241052359_   4897 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAGACT 4946
                           v     v      v i  i  i        i  v     i    i v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_241052359_   4947 AC-ATTAACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCATA 4994
                         v - vivi i  i  ii     v v  v  i-  - iii    v      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr1_241052359_   4995 TGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAACAAAAAGAA 5044
                              viiv  ii  v  v v        i      i i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_241052359_   5045 CAAAGCTAGAGGTATCACGCTACCTGACTT-GAAACTATACTACAAGGCT 5093
                              i i    vv    i  v  ii i  -i     -        i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr1_241052359_   5094 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5143
                                i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_241052359_   5144 ATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAA-CAAT 5192
                               i    iv   ivii         vv   i    i  iii-    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_241052359_   5193 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5242
                         -    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_241052359_   5243 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAGCTGA 5292
                         v  i  i        i     v      v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_241052359_   5293 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAA-----GATGGATT 5337
                          ii    i    v   i     v              -----i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_241052359_   5338 AGAGACTTAAACTTAAGACCTAACACCACAAAAACCCTAAAAGAAAACCT 5387
                          ?    i    iv     v    v  i i    vi i  i        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_241052359_   5388 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATT-CATGACTAAA 5435
                            ?i- v i -   iv   v v  vv i     v i  - v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_241052359_   5436 ACACCAAAAGCAACGGCAACAATAGCCAAAATCGACAAATGGGATCTAAT 5485
                                     vvi       v  vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_241052359_   5486 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAAA 5535
                         i   v v  i i   i  ii vv    i  v       vv i        
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_241052359_   5536 GGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTATCCATCTGACAAA 5585
                          i     i                 v      ivii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_241052359_   5586 GGGCTAATATCCAGAATCTACAAA-AACCTGAACAAATTTACAAGAAAAA 5634
                           i  vi          v  i   -   iivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_241052359_   5635 -----ATAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 5679
                         -----       v  i?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_241052359_   5680 CAAAAGAAGACATTTATGCAGCCAACAA--ACATGGAAAAAAGCTCATCA 5727
                          v        i  vi viii     i  --     i   i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_241052359_   5728 TCACTGGTCAT 5738
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (135 / 91)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 1.64 (23 / 14)  


4400 15.99 4.81 0.72  chr1_241163928_241167239.rev     1982  2813 (499)    L1M4_orf2#LINE/L1        1   866 (42)  

  chr1_241163928_   1982 TGGAAAGACATTCCACGCTTGTGAACTGGAAGATTTAATACTGTTAGGAT 2031
                                 i  i   i i ii  i i       i      i     i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_241163928_   2032 GGTAATACTCTCCCAAGTTGACCTGAAGATTCACTGCCATTCTTGTCAAA 2081
                           i       -     i    i  iv       vi  v  i i i     
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_241163928_   2082 ATCTCAGCTGCCATTTTTTGCAGAAATTGACAAATTTA----AAAATTCA 2127
                            i        -                    ii v ----        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_241163928_   2128 TATGGAAATTCAAGAGACCTAGAATAGCTAAAACAATCTTGAAAAAG--- 2174
                                  v    i    i        i                  ---
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_241163928_   2175 -------TTATAGGACTCAGACTTCCTGATTTCAACATTTAGCACAGAGC 2217
                         -------  iv        v      ii       v i   vi   i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_241163928_   2218 TACAGTAATCAAGACAGTGTATTACTGGCATAAAGATAGACATACAGATC 2267
                                             iv           i          i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_241163928_   2268 AATGAAACAGAATTCAGAGTTCAGAAATAAGCCCCTATAATGATGGCCAA 2317
                             i  i      v     i         i   v  i v v    i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_241163928_   2318 CTGATCTTTAACAAAGGTGCCAAGACAATTCAGTGGGAAAAGAAGAGTCT 2367
                         i    i  ii    i           v     i    i      v     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_241163928_   2368 TTTCAACAAATAGAACTGAGACAACTGGAAATCCACATGCAAATGAATGA 2417
                                    i vi   i          v ?           v      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_241163928_   2418 AGCTGGTCTTCTACCTCATGCCATATATAAAAATTAATTTAA--TGGATC 2465
                           i   v ii        ii       i         i i  --      
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_241163928_   2466 AAAGACCTAAATGCAAGAGCTTAAATTATAAA-CTCTTGGAAGAGAA--- 2511
                          ?           i       v   i      -     i     i  ---
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_241163928_   2512 ----GCATATCTTCATGATCTTGGATTACGCAATGGCTTCATAGATATGA 2557
                         ---- i v      i   i     i   v       i   v         
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_241163928_   2558 CACCAAAAGCAAAAGCAACAAAAGAAAAAAATTGATGAA---------AG 2598
                                    v                  - v   i  --------- v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCAT 647

  chr1_241163928_   2599 CAGAATTTAAAACTTTAGTGCTTTGAAGAACACTATCAAGAAAGTGAAAA 2648
                           i    v        v      ii   i                     
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_241163928_   2649 GGGAAACCACAGCCTGGGAGAAAATTTTGGCAAGTCATATACC-GACAAG 2697
                          iv  v      vv           v  v    i       i -  i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_241163928_   2698 GGACTTATATGTAGAATACATATAAGAACTCTTAGAACTCAACGA----- 2742
                               i   vi      i   -           v       ii -----
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATA-AAGAACTCTTACAACTCAATAATAAAA 796

  chr1_241163928_   2743 -GACACATAACCCTACTAAAAAATGGGCAAAGGATCTAAAAAAAAGTATT 2791
                         -    v       v i ?                 i i  v i --i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA--CATT 844

  chr1_241163928_   2792 TCTTCTAAGAAGATACGCAAAT 2813
                            i v         ii     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAAT 866

Transitions / transversions = 2.17 (89 / 41)
Gap_init rate = 0.02 (13 / 866), avg. gap size = 3.54 (46 / 13)  


 780 29.06 8.62 2.96  chr1_241204343_241206900.rev      502   907 (1651)    L1M4_orf2#LINE/L1      125   553 (355)  

  chr1_241204343_    502 TTGAAAAGCTGATTCTAAA-TTTATATGGAAGAGTAAAAGGCCAAAAAAT 550
                             v        i     -  i        iv i  ii i  v i  - 
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA-T 173

  chr1_241204343_    551 AGCACGTAATAACTCCTGAATAAG---------GTAGGAGAACTTGCTCT 591
                            - iv  i  -  i    v   ---------  v    i   ii v  
  L1M4_orf2#LINE/    174 AGC-CAAAACAA-TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr1_241204343_    592 ACCACATAGTAAAACTTAT---AAACCTTCAGTAATTAAGATAGTGTGTC 638
                         v  vv  vvi        i---   v  v       i    i      vi
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr1_241204343_    639 ATTGGTCT--GGAGAGAGTATTTAAATAGACTGA-TGGACCTACAGAGTC 685
                          i   iv --   v   -i  v  i  vi iv  - i  vi i-      
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGA-CATATAGATCAATGGAATAGAATTG-AGAGTC 319

  chr1_241204343_    686 CAGAAACAGAGTCAAATATATATGGAAACTTGACTAATGG-AAAAGT--- 731
                               i i vi  v i  v     vv v    i vvi i-  ii  ---
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr1_241204343_    732 AGGA--ATTGTAGAACAGTGGCTAAAGGACAGACTATCCAGTGTATTGCG 779
                          i  --   ------  i   vv    i i  v  v i  iiiv  v i 
  L1M4_orf2#LINE/    370 AAGACCATT------CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_241204343_    780 TTAGGACAAATAGTTATTCATACG--AAAAAATTACATTGGCTCCCTACT 827
                         i i      v i v  ?i  i i --   i   v vi    vi      i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_241204343_    828 TCACACACACACACACAA-TCAATTGTGGTTGAATTAAAGACC--AATGC 874
                               -  i i   v  - i  i vviiv  i  i ?     --    i
  L1M4_orf2#LINE/    464 TCACAC-CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr1_241204343_    875 AAAAG--------ACAAAATACTTAGAAAAAAATATAGGAG 907
                           i  -------- i    iv       i    i     ? 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

Transitions / transversions = 1.56 (70 / 45)
Gap_init rate = 0.04 (19 / 429), avg. gap size = 2.47 (47 / 19)  

 437 28.06 7.14 2.04  chr1_241204343_241206900.rev     1476  1671 (887)    L1M4_orf2#LINE/L1      624   829 (79)  

  chr1_241204343_   1476 AAAACTATTGATATTTTCGACTGCATTAAAAT---GGGCTTCTGTTTCTC 1522
                             v  --    vv  v    v   i     ---iii   i   vii  
  L1M4_orf2#LINE/    624 AAAAATA--GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr1_241204343_   1523 AAAACACCTTAT--AGACAGTGAACAGACAAGTTTCAAACCGGGAGAAAA 1570
                            iv  vi   --   v      v      viiv  i vi         
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr1_241204343_   1571 TATTTGCAACT-ACAGAACTG-TCAAAGATTAGTAGTCAAGATATGTGAA 1618
                                  v - i v v   - v ii  i v   vi  ii    i i  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_241204343_   1619 GAGACCCTGCAA-------ATAAGAAGTAATAAATAATCCAGTAGAAAAA 1661
                           ivi i i   -------    i   -- i      i   i v?     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAG--ACAAATAACCCAATTWAAAAA 819

  chr1_241204343_   1662 GGGACAAAAG 1671
                         v  i    i 
  L1M4_orf2#LINE/    820 TGGGCAAAGG 829

Transitions / transversions = 1.45 (32 / 22)
Gap_init rate = 0.03 (7 / 206), avg. gap size = 2.57 (18 / 7)  


3180  9.89 1.98 27.95  chr1_241523933_241526133      496  1708 (493)    L1M4_orf2#LINE/L1       11   908 (0)  

  chr1_241523933_    496 TCATATGTATATAGATTGGAAGAGTTAATATTGTTATGATTGCAATACTC 545
                           vi    vi  i          v            v   v         
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chr1_241523933_    546 CCCAAATTGATTAACAGATTCATTGCAATCTCTATCAAAATCCTGGTTGC 595
                                    iv         vi      i            ii i   
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr1_241523933_    596 CTTTTTTTTTTTTTAAACAAATTGACA-GTTAATTCTAAAATTCATATAG 644
                                vi------- v         - i i  i             i 
  L1M4_orf2#LINE/    111 CTTTTTTGC-------AGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_241523933_    645 AAATGTAAGGGACCTAGAATAGCCAAAACAATCTTGAAAAAGGATAACAA 694
                              i        i                           i v     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_241523933_    695 AGTTGGA---CTCCCATTTCCCGATCTCAAAATTTACTGAAAAGCTACAG 741
                                ---   v  i     i  i      i     iv          
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr1_241523933_    742 TAATTAAGAC--TGTGATACTGGCATGATGATGTAAGGCTAGACACATGC 789
                             i     --    i         --------    v      i  iv
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCAT--------AAGGATAGACATATAG 295

  chr1_241523933_    790 ATCAGTGGAATAGAATTGAG--TCTGGAAATAAACCCTTACACTTATGGT 837
                             i               --  ii           v    i       
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_241523933_    838 CAATTGATCTTCAATAAAGGCGGCAAGACAATTCGATAGAAAAAAGAATA 887
                                 i   i i  i  i v      v    i  i ii   -     
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATA 394

  chr1_241523933_    888 GTCTTTACAACACATGATGCTAGGATGACTGAATATCCACATGCAAATGA 937
                               v     v   i    i   ii    i   ?           v  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_241523933_    938 ATGAAGTTGGACCC-TACCACACACCATATATGAAAATTAACTCAAAATG 986
                                       -    v           ii                 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_241523933_    987 GATAAAAGGGCTGGGCACAGTGGCTCACGCCTGTAATTCCAGCACTTTGG 1036
                            -----------------------------------------------
  L1M4_orf2#LINE/    495 GAT----------------------------------------------- 497

  chr1_241523933_   1037 GAGGCCAAGGCAGGCAGATCACCTGAGGTCAGGAGTTCAAGACCAGCCTG 1086
                         -----  ?-------------------------------     ------
  L1M4_orf2#LINE/    498 -----CAW-------------------------------AGACC------ 505

  chr1_241523933_   1087 GCCAACGTGGTGAAACCCCATTTCTACTAAACATACAAAAATTAGCTGGG 1136
                         ---------------------------    -------------------
  L1M4_orf2#LINE/    506 ---------------------------TAAA------------------- 509

  chr1_241523933_   1137 CACGGTGGTACACACCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGA 1186
                         ----------------     -----------------------------
  L1M4_orf2#LINE/    510 ----------------TGTAA----------------------------- 514

  chr1_241523933_   1187 GAATCGCTGGAACCTGGAAGGCGGGGGTTGCAGTGAGCCGAGATCACACC 1236
                         --------------------------------------------------
  L1M4_orf2#LINE/    515 -------------------------------------------------- 514

  chr1_241523933_   1237 ACTGCACTCCAGTCTGGGCAACAGAGCGAGACTCTGTCTCAAAAAAAAAA 1286
                         --------------------------------------------------
  L1M4_orf2#LINE/    515 -------------------------------------------------- 514

  chr1_241523933_   1287 AAAAAGAAGAAGAAGAAGAAGATAAAAGATCTCAATAAAGAGCTAAAATC 1336
                         ---------------------------------------         ii
  L1M4_orf2#LINE/    515 ---------------------------------------GAGCTAAAACT 525

  chr1_241523933_   1337 GTAAGACCCTTAGAAGAAAACATTGATGTGAATGTTTGTGACTTTGGATT 1386
                         i   i  i               v i?  i   v  i     i    i  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_241523933_   1387 AGGCAGTGGTTTCTTAGCTATGATACCTAAA--ACAAGCAACCCAAGACA 1434
                              i           v     i   v   --         vv    - 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-A 624

  chr1_241523933_   1435 AAAATAGATAAATTGAATTTCACCAAAATTAAAAACTTT-GTGCTTCAAA 1483
                                        i i    i                -          
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_241523933_   1484 GGACACTGTCAGGAAGATAAAGAGACAAGCCACAGAGTGGGAGAAAATAT 1533
                                i   i   ii i  i      v       i             
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_241523933_   1534 TTGCAAATCATATATCTGATAAGGGGTCTAGTACCTGTAATATATAAAAA 1583
                                                  i-  v   i iiv          i 
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGA-CTTGTATCCAGAATATATAAAGA 773

  chr1_241523933_   1584 ACTG--ACAAC-----AATAAAAAGACAA----CCCAATTAAAATGTGGA 1622
                            v--     -----             ----       ?   vi   i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr1_241523933_   1623 CAAAGTATTTGAATAGACATTTCTCCAAGGAAGATTATTTAA-TGGCCAA 1671
                              v                      i      -  vi  -       
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT-ATACAAATGGCCAA 872

  chr1_241523933_   1672 AACATCACATGAAAATATGCTAAGCATCATTAGTCAT 1708
                         v - v          v     v i     ????????
  L1M4_orf2#LINE/    873 TA-AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (78 / 38)
Gap_init rate = 0.03 (23 / 898), avg. gap size = 15.78 (363 / 23)  


2483 23.26 4.38 1.21  chr1_241566311_241567944      495  1156 (478)    L1M4_orf2#LINE/L1      226   908 (0)  

  chr1_241566311_    495 AATTACAAATTATGTTACAAAGCAAAAGTAATCAAAACAGTGTGGTACTG 544
                             v    viv ii        v v         i              
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_241566311_    545 GCACAAAAACAGTCATATAGACTATTGGAACAGAATAGAAAGCCTATAAA 594
                            i  ii i  v        ii v     i     v  i  i i v   
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_241566311_    595 TGAAGCCATGCATAAATGGCCAGCTAATCCTCAGCAAGAGTGCCAAGAAT 644
                          i  v    i   vv    i  ii i  ii  ii    i         vi
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr1_241566311_    645 ACACGATAGGGAAAGGATAGTGTCTTCAATGAATGATGATGGGAAAACTG 694
                          iv i  i       i     v i     ii    i  v     v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr1_241566311_    695 T-TATTTACATGGAGAAGAATGAAATTGGATCCGTATCTCACACCATACA 743
                         v-  ?ii     v i         i     i  v  i           i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr1_241566311_    744 CAGAAATCAACTCAAGCTGGATTAAAGATTTAAATGTGAGACTTGGAGCC 793
                           i    i       iv     i ?   ii       i   vi ii i i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_241566311_    794 ATAAAACT---AGAAGAAAACATAGGGA-AAATGCTCTTTGACATTGGTC 839
                                 ---               ?i-    -  iiv    v    vi
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGT 574

  chr1_241566311_    840 TGGGCAATGATTTTTTGGATATGATACTAAGAGCACAGGCAACAAAAGCA 889
                          i       i   i  i       i  i  i      i          v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_241566311_    890 AAAATAAACAAGTGGCACTACATCAAA-CTAAAAAGTTTC-TGCATGCAA 937
                               i i  i v v   v       -i      v   i-   - v   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC-TTCAA 673

  chr1_241566311_    938 AAGAAAC----AAGGAG---------CAACCTATGGAATGGGAGAAAATG 974
                          i  v  ----   i i---------     i ii              i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr1_241566311_    975 TT-GCAAACCATACATTTGACAAGGGATTAATATTCCAATACATATAAGG 1023
                           -     i    i  i   i      i vi   -   iv i      i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTAT-CCAGAATATATAAAG 772

  chr1_241566311_   1024 AACTCAGACAACTCAATTGCAAAAACAAAAACGACCTAATTAAAAAAAAC 1073
                              vv          vii     v v   ii   i    ?     ---
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA--- 819

  chr1_241566311_   1074 GGAAAAAAGGACCTGA-----CATTTTTTCAAAGGTGATGTACAAATGTC 1118
                         v iiv      ii   -----     i i     iv   i        v 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr1_241566311_   1119 CAACAGGTATATGAACATCATTGTTCA---TCAAGGAAATG 1156
                            i i i i     v --iv  i   ---   ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAA--GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (105 / 45)
Gap_init rate = 0.02 (15 / 683), avg. gap size = 2.47 (37 / 15)  


 465 34.10 4.05 3.18  chr1_241739516_241743585.rev     2455  2800 (1270)    L1M4_orf2#LINE/L1      286   634 (274)  

  chr1_241739516_   2455 AGATTTATAAACTCAATTAAATGGTGTGGAATTTAGTTCAGAGATAGATA 2504
                            iv    i -     vi   i vi v  i---   i    i   --- 
  L1M4_orf2#LINE/    286 AGACATATAGA-TCAATGGAATAGAATTGAG---AGTCCAGAAATA---A 328

  chr1_241739516_   2505 ACACAAACA-----GGAGAACTTGGTATGC--CAGAGGAAGCATCACAAA 2547
                           v  v   -----  vv  -   i v v --  ii  viv  vv  v v
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAA-TTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_241739516_   2548 TCCATGAGGATATGATAGACCATTCAATAAACAGTGCAGAAACAACTGGC 2597
                           v   i   v vi    v iv     i   ii    v ii        v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_241739516_   2598 TACTTCTATGCCAAA-AATGATAAATGAGATTCATATCTTTTACCAGTCA 2646
                           ?iivi    v   -     -- i vi  ii v  i  ivi    vvi 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGA--AGTTGGACCCCTACCTCACACCATATA 475

  chr1_241739516_   2647 CAAAAATAACCTCCAGTTAGGTTACAGTCTTAAATACAAAAAGGAATGTG 2696
                                v v   v iv i i i ?  v i     ii  i ivv  viiv
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr1_241739516_   2697 TTAAAATTATTAGAGAAAGATATAAGGAGCTACCTTTATGAA--TGGGGT 2744
                         v     i v     ii  i i   i ?ivvv i   ii   v--    v 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr1_241739516_   2745 AGGCAAGGATTTTTTTG-CATGATATTAAAATTATAAAGCGTTGAAA--- 2790
                               v i   i  v -i    i ii    vi i  -  ivii   ---
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA-GCAACAAAAGAA 624

  chr1_241739516_   2791 AAGACAGATA 2800
                           i i     
  L1M4_orf2#LINE/    625 AAAATAGATA 634

Transitions / transversions = 1.30 (65 / 50)
Gap_init rate = 0.03 (12 / 349), avg. gap size = 2.08 (25 / 12)  

 255 24.71 4.71 5.88  chr1_241739516_241743585.rev     3410  3579 (491)    L1M4_orf2#LINE/L1      741   908 (0)  

  chr1_241739516_   3410 TAACAAAAGATTTACATTCA-AATATCCTAA-AATTCAATTACAAT--AA 3455
                          i i  ii  i  ii  i  -     viv  -  i  --      i--  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCAA 788

  chr1_241739516_   3456 TGGACACAAATAAGACAA-TA---CAATGAGAAAAAACACGGGCAAAGAA 3501
                          i--- i   -       -  ---    v?i    ----i        i 
  L1M4_orf2#LINE/    789 TA---ATAAA-AAGACAAATAACCCAATTWAAAAA----TGGGCAAAGGA 830

  chr1_241739516_   3502 AATGAATAGGCAATTCTTAAAAGAGAAAACTCCCATGGTCAATAAAACTA 3551
                         vv       i  v    iv     ii v iv vv    i      ivvi 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_241739516_   3552 TGAAAAGATGTTCCATCTCAAAACAAGA 3579
                                   i  v iv   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (26 / 15)
Gap_init rate = 0.05 (9 / 168), avg. gap size = 2.00 (18 / 9)  


 515 30.21 9.64 5.21  chr1_241754083_241756051      469   852 (1116)    L1M4_orf2#LINE/L1      190   590 (318)  

  chr1_241754083_    469 AAAAAAAAAAAAAAAGTTGAGAAATACGGA------------GAGACTTA 506
                              i  i  v       iiii iv iv ------------i i     
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_241754083_    507 TTATGAAGCAATAAATAGTTATGACACGATGTTATTAACACTGGGAGAAA 556
                         i  ii    v i i-  i i v    vvi  v  i ii  ivi   v i 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAG-TAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_241754083_    557 CAAATAGACCGATGGAACAAAATAGATAG-CTAGAAATAGACTTCTACGT 605
                           v     i i      i i   v  v  - i       i  iiv   i 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_241754083_    606 --AAGGAAACTTGGTTATGCAGATAAACATTGTGGACAAG---------T 644
                         -- v  vv v   i  - v -  i  ivi ---- v    --------- 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATT-TTC-GACAAGGGT----GCCAAGACCATTCAAT 382

  chr1_241754083_    645 GGGAGAAGGAAGGATTATTCAATAAATAGTGCTGAGACAACTTAAAAATC 694
                            ii   i vi vi v     i    i      i       vi v ?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr1_241754083_    695 ATATTTTCAAGAGGTTGCAATGAAGGT---------CCTCACATATCCTA 735
                          i  v--   i  -----       v ---------       ---- i 
  L1M4_orf2#LINE/    433 ACATG--CAAAAG-----AATGAAGTTGGACCCCTACCTCACA----CCA 471

  chr1_241754083_    736 TATACAAAAAATTAGTTTGAAGTAGACCAAATACATCAATGTGAAAAGC- 784
                                   -   ii ii  i i  i  ? v  v v     -  i   -
  L1M4_orf2#LINE/    472 TATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCT 519

  chr1_241754083_    785 -AAATTCTAAACAGTTTAGGGAAGAATATAGGAAGATATTTTCATGAG-- 831
                         -   i v    vvvi    iii i  i     ?iv v  i   i   v--
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr1_241754083_    832 TGGTGTAGAGAATGACTTTTT 852
                            vv   iv    ii  i  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.76 (72 / 41)
Gap_init rate = 0.04 (16 / 401), avg. gap size = 3.56 (57 / 16)  

 669 26.23 8.52 0.66  chr1_241754083_241756051     1172  1476 (492)    L1M4_orf2#LINE/L1      580   908 (0)  

  chr1_241754083_   1172 AATGACTTTTTAAAGCATAA-GCAAAAAGCATAAACCATGAATTAATGAT 1220
                             ii  i   i -i  i -i v       i  i v ii  vv  vi v
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr1_241754083_   1221 T-GCTAAATTTGACTGTATTAAA-CAAAGAATATCAGTTTATCAAAAGAC 1268
                          - v      v    vi  i   -iv  i  iv iv  viv     i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr1_241754083_   1269 ACCAT----AAAGT-AAAAGA-GATCCACAAACTTAGAGAAGTTATTTGC 1312
                           i  ----     -      -i i     i v vi     iv       
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_241754083_   1313 AATATATATAACTGAAAAAGGATTTGTATTTAGAGTATGTAAAGAACTAT 1362
                           vvi     v    v  i   i      ii   i   i         v 
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_241754083_   1363 TA------AATAAGAAAAAGATA-----CTCAAA-AGAAAATGGGCAAAG 1400
                           ------     v       i ----- i   v-?i             
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_241754083_   1401 GACTTGAACAGGGATTTT---AGAGAAAATAGG--AATAGTTAATAAACC 1445
                           i     i  iv    i--- i    i   vi--   i ii     i v
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_241754083_   1446 TATGAAAAGGTACCTAATCATCAGAATTTAG 1476
                         i        i i ii  -     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (52 / 27)
Gap_init rate = 0.04 (13 / 329), avg. gap size = 2.15 (28 / 13)  


 204 13.95 0.00 6.98  chr1_241759362_241761256.rev      424   466 (1429)    L1M4_orf2#LINE/L1        1    40 (868)  

  chr1_241759362_    424 TGAAAAGTCAACATCCTATGTACATGGATTACAAGACTTAATA 466
                           i    --- i    i    v        iv           
  L1M4_orf2#LINE/      1 TGGAAAG---ATATCCCATGTTCATGGATTGGAAGACTTAATA 40

Transitions / transversions = 2.00 (4 / 2)
Gap_init rate = 0.03 (1 / 40), avg. gap size = 3.00 (3 / 1)  

3458 22.61 2.90 1.78  chr1_241759362_241761256.rev      507  1404 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_241759362_    507 TGAAAATTCAACATCCTATGTACATGGATTACAAGACTTAATATTGTTAA 556
                           i   ---i i    i    v        iv                  
  L1M4_orf2#LINE/      1 TGGAAA---GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chr1_241759362_    557 AATGTCCATAGTACCTGAAGTGAGTCATAGATTTAATGAAATTCCTAGCA 606
                         i   v v   v v  ii  v   vii i     i  i v   i    v  
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_241759362_    607 AATTCCCAATGGCATTTTTTGAAGAATAGAAAAAAACAG-TCCTAAAATT 655
                           v     iiv  v       v    - vvi v  i v -          
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATT 146

  chr1_241759362_    656 CACATGGAACCAACCACAAAGGACCCTGAATAGCCAAAACAATCTGAAGA 705
                           i      --- i-i   i      v                  vi i 
  L1M4_orf2#LINE/    147 CATATGGAA---AT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_241759362_    706 AAAAAGAACAAAGCTAGAATTTTCACACTTTCTGATCTCGAAACATCTTA 755
                           i          i i  ivvi        i ii  i  i    v vi  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_241759362_    756 CAAAGCTACTGTAATCAAAACAGTATGACATTGGCATAAAGACAGACACA 805
                                  v        i     i  ii i        i  i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_241759362_    806 CAGACCAGTGGAGCAGAATAGAGAGATCAGAAGTAAACCCACATATACAC 855
                         i   i  i    ii     v     vi     i        i i  vi i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_241759362_    856 AGAGAAATGATCTTCAGCAAGGGTGCCAAGACAACACAGTGGGGAAAGGA 905
                         i vv  v    i   ii               v iv  i         i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_241759362_    906 TTGTCTC----ACAAAGTGGTGCTAGGAAAACTAGATACCCACATGCAAA 951
                          v    i----     -       i   v    i    ?           
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_241759362_    952 AGAA-GCA-TTGGATCCTTATCTTACGC-ATACATAAACCTCAACTCAAA 998
                             - v -     i  i  i  i  i -   i i   vv i        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_241759362_    999 ATGGATTAAAGGACTTAAATGTA-GACCTGAAACTACAAACCTCCTAGAA 1047
                               i ?  -  i        -  v  i      i   v   i     
  L1M4_orf2#LINE/    492 ATGGATCAWAG-ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_241759362_   1048 GAAAACATAGGGGGAAAGTTTCAAAACATTGGTCTTGGCAATGATTTCTT 1097
                                    ? v   vi   ivi  v    vi v       i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_241759362_   1098 GGATATG---CCAA------------CAAAAGCAAAAATAGACAAGTGAG 1132
                         i      ---    ------------      v         i  i vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_241759362_   1133 ATTATATCAAACGAAAAACCTTCTGAATAGCAAAGGAAAGCATCAACAGA 1182
                          i vi      vvv    v   i  viivv       v vi     v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_241759362_   1183 GTGAAAAGGTAACCTGTGCAGTGGGAGAAAATACATGCAAACCATCTATC 1232
                                 ii    iiiiv i            iv      i   v    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_241759362_   1233 TGAAAAGAGATTGATATCTAAAATATACAAGGAATTCCTACAACTCAATA 1282
                            v   i  i vi    i i      i  i   i  i            
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_241759362_   1283 GCAAAAG--CAAATAAACCAATTTTTAAAATACATAAAGGAAAGGACCTA 1330
                         ii    i--       v      ?--    ---  ii- v      ii i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTW--AAAA---ATGG-GCAAAGGATTTG 834

  chr1_241759362_   1331 AATAGACCTTTCTGTAAGGAAAACATACAAATGACAAGCAGGTATATGAA 1380
                                v     vi  i   i i         i v ii i i i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_241759362_   1381 AAGATGCTCAATATCACAAATGTC 1404
                                    i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (130 / 69)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.33 (42 / 18)  


3047 27.13 1.00 0.44  chr1_242082766_242087935.rev     3777  4679 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242082766_   3777 TGGAAAAACATTCTATGCTTATGGAAAGGAAGAAACAATATCGTGAATAT 3826
                               i i  i i   i i     vv      vvi     i  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242082766_   3827 GGCCACACTGCCCAAAATAATTTATAGATTCAATGCTATTCCCACCAAGC 3876
                            v i   v      v i  i  i        i  v  i  i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_242082766_   3877 TACCATTGACTTTCTTCATAGAATTAGAAAAAACT-ACTTTAAATTTCAT 3925
                          v   vivi i  i  iii    v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr1_242082766_   3926 TTGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 3975
                         v     viiv  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_242082766_   3976 ACAAAGCTGGAGGCATCACGCTACCTGACCTCAAATTATACTACAAGGCT 4025
                               i      vv    i  v  ii ii     viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_242082766_   4026 ACACTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACAA 4075
                            v   i   i    ii         i iv ii i   v       iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_242082766_   4076 ATGTAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAT-AAT 4124
                            v  i    iv   ivii         vv   i    i  iii -   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_242082766_   4125 CTGGTCTTTGACAAACCTGACAAAACAAG-CAATGGGGAAAGGATTCCCT 4173
                         -  i i  i     ivv  v   i  v v-            i  vvi  
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_242082766_   4174 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 4223
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_242082766_   4224 AACCGGACCCCTTCCTTATACCTTATACAAAAAGTAACTCAAGTTGGATT 4273
                          iii        v   i i   v          v        iv     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_242082766_   4274 AAAGACTTAAATGTAAGACCTAAAACCATAAAACACCCTAGACAAAAATC 4323
                          ?    i           v       i       -i i    vi    iv
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACA 547

  chr1_242082766_   4324 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAA 4372
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_242082766_   4373 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4422
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_242082766_   4423 TTAAA-CTAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 4471
                          i   -i   i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_242082766_   4472 AGGCAACCTACAGAATGGAAGAAAATTTTTGCAATCTATTCATCTGACAT 4521
                           i     i         i       v       vii  vi      i v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_242082766_   4522 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 4571
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_242082766_   4572 AAACAAA---CCCA-TCAAAAAGCGGGAGAAGGATATGAACAGACACTTC 4617
                          i     ---    - i?    ii   vi      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_242082766_   4618 TCAAAAGAAAACATTTATGTGGCCAACAAACATATGAAAAAAAGCTCATC 4667
                           v      i i  vi vi       i  i  i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_242082766_   4668 ATCACTGGTCAT 4679
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.18 (13 / 11)  


3029 22.37 5.21 6.62  chr1_242113358_242115207.rev      439  1359 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242113358_    439 TAGAGAGAGATACTGTGCTCCTGGGTCAGAACACTCAATACTGTGAAGAG 488
                          i  i   v  v ii  i  v   i ii   v   i    i   v    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242113358_    489 GTCAATCATCTCCAAGTTG--CTATAGCTTCAATGCAATCCCAATCAGAA 536
                          v    vv  i    i   --   i  v     i        v    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_242113358_    537 TCCTGGTAGACTTCTTTGATAGAAATTTTTTCTACGTAATCCATTTAGA- 585
                            ii iv v   i    -i       --------------------  -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATT--------------------GAC 129

  chr1_242113358_    586 AAGC-GACTCTAAAATTTGTATGGAAATGCCAAATACACTGAATAGCCAA 634
                             -  ii        ii           v iiv  v v          
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr1_242113358_    635 AACAACTTTAAAAAATAAGAACAAAGTTGGAAGGTTAACATTACCTAATT 684
                              ii  i     v               i ii v   i v  i    
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr1_242113358_    685 TCAAGACCTATTATACATCCACCATAATCAAAACAGTGTGGTATTGGTGT 734
                             i  i  i  i v v i  vi       i           i   ii 
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr1_242113358_    735 AAAGATAGACAAATAGATCAATGGAACAGAAC--AGAGTCTAGAAATAGT 782
                           i        v              i    i--      i       iv
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr1_242113358_    783 TGCACATAAATATGGCCAACTAATCCTTGACAAAGGTA--------ATTT 824
                         iv  i i vv     i   i i  ii i     i   i--------   i
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr1_242113358_    825 AGTAGAGAAATAATAGCTTTTTACAACAAATGATACTGGAAATTTTGGAT 874
                          i i i    v     ii    -         i i    i vvvi     
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGAT 428

  chr1_242113358_    875 ACTATATTCATACACACACACAAAAAAACACCTAACCTCCCTCAACCTGA 924
                          ?i-----------    ii     i  -------------------   
  L1M4_orf2#LINE/    429 AKC-----------CACATGCAAAAGAA-------------------TGA 448

  chr1_242113358_    925 AAAAAACTACTTGAGTCCATACATTGCAAAATATACAAAAATTAACTAAA 974
                          i--------   iii  v   v ii  vv                 v  
  L1M4_orf2#LINE/    449 AG--------TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr1_242113358_    975 AATTGATCAAAGACCTAAATTTGAAGCCTAAAATTACAAAACTTCTAGAG 1024
                            v     ?          v i iiv      i  i      ii    i
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_242113358_   1025 GAGG-CATAAGAAGAAACCTTTTTGGCCTTGGGTTAGGCAAAGATTTCTT 1073
                           ii-    i ?iv   i   iv  i               v i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_242113358_   1074 AGATGTGACAGCAAAAACATGATTCATAAAAGAA----CATATAAATTGG 1119
                             i     v     i  ii viv i       ----i v         
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_242113358_   1120 ACTTCATAAAAA--AACAAGTATTTGTTTTTCAAAAGATGCTGTTGAGAA 1167
                                v    --  v  v -     vi      i  ii  i ii    
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_242113358_   1168 --TGAAGAGAGAAGCCACAGACTGAGAGAAAATATTTGCAAATACTATAT 1215
                         --    i   v  v       v  i                  vv     
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_242113358_   1216 CTTATAAAGGATTTGCATCCAGAATATATTAAAAACTTTCA--------- 1256
                           v    i   i   i             v  i    i i ---------
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr1_242113358_   1257 -------AAACAATT-------TTTAAAA--GGACAGAAGATTTGAAGGG 1290
                         ------- i    v -------  ?    --  i  i i        vi 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr1_242113358_   1291 ACATTTCACCAAAGAAGAGGTATGGATGCCGAATGGGCGTGTAGAAGGAT 1340
                                v          vi  iii   v v   ii  iii ii  i   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_242113358_   1341 GCTTGGCATCATTGGTCAT 1359
                            iii     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (138 / 64)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 5.74 (109 / 19)  


2591 25.48 5.60 1.55  chr1_242115339_242117171.rev      504  1343 (490)    L1M4_orf2#LINE/L1       35   908 (0)  

  chr1_242115339_    504 TTAACATTGTTAAAATGACCATCCTACTCAAAGCAATCTACAGACTCAAT 553
                             i        i   i v  v  v i    vii         i    i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr1_242115339_    554 GCAGTCTCTGTCGAAATATCCA--TGACATTCTT-CATGGAATT------ 594
                            i  i  i  i    -i   --  v v  i  -  - i    ------
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAAT-CCCAGCTGCCTTTTTTGCA-GAAATTGACAAG 132

  chr1_242115339_    595 -------TAAA---CACACAGAGA---AAA--ACCTTGCACA--CAAAGC 627
                         -------    ---  i ii  i ---  i--   iv v i --    i 
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr1_242115339_    628 AATACTGGAAAACAAAGAAACAAGCTGGAGGCATCACACTAGCTGACTTC 677
                            -  v     vi     vv   i      vv       vv ii i   
  L1M4_orf2#LINE/    183 AAT-CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_242115339_    678 AAAATACACTACTAGGAAGCTACTGTAACATAAAACAGGCTGGTATTGAC 727
                             ivi     ---i       v    i-i  i    vv     i  i 
  L1M4_orf2#LINE/    232 AAAACTTACTAC---AAAGCTACAGTAAT-CAAGACAGTGTGGTACTGGC 277

  chr1_242115339_    728 GTAAAAA--GACACATAGACCAATGGGACACAATAGAGAACCTACAGATA 775
                         i   ii --    i     i      i i v   v    ii i v i   
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_242115339_    776 AATCTATCTATTTACAGCCAACTCATTTTTGACAAAGGCACCAAGAACAT 825
                           i i  vi     ii i   i v     i     i  ii      v   
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr1_242115339_    826 GCATTGGGGAAAGGACATCCCCTTTAATAAATGGTGCTGGGAAAACTAGA 875
                         v  v         i i vi ii  i  i              v    i  
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr1_242115339_    876 TATCCATAAGCAGAAGGGTGAAACTAGACCGCTATCTCTTACCATATATA 925
                           ?   i v   i   ii    ii i    v   i   vi        i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr1_242115339_    926 AAAATCCACTCAAAATTTATTAAAGGCTTAAATATTAAGACCAAAAACAA 975
                              iv         vv  i ?  i i     i -    v v     v 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTA 526

  chr1_242115339_    976 TAA--CTCTACCAGATGAAAACATAGGGG-AAATGCTTTGGGACATTGGT 1022
                            --    --i   v           ? -    -   i v   v    v
  L1M4_orf2#LINE/    527 TAAAACTCT--TAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGG 573

  chr1_242115339_   1023 CCAGGCAAAGATTTTATGGCTAAGACTTTGAAAGCACAAGTAAGAAAACC 1072
                         ii      v i   iv i v  v   viii          i  v    vv
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr1_242115339_   1073 AAAATTAGAAAGATTGGAGTATGTTAAA-CTAAAAACGTTCTGCACAGCT 1121
                             v    v i      v vii i   -i       -  i  ii vv v
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCA 672

  chr1_242115339_   1122 AAGGAAACAATCAACAGAGCAAAGAGACAACCTGCAGAATGGAAAAAAAA 1171
                              v  v     v i  ii  i        ii        i i    -
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA- 721

  chr1_242115339_   1172 TATTTGCAAGCTGTTCATTCAACAAGGAATTAATATCCAGG--------- 1212
                                  iiii vi  iii i    i i vi       i---------
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr1_242115339_   1213 GAACTC--AAAAC--AGCAA--AAAACCCAAACAAACCCATTAAAAATTG 1256
                               -- v   -- ii  --    vv    i  v  v   ?    v  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr1_242115339_   1257 GGCAAAGGATCTGAATAGACATTTCTCAAAAGAAGTCATACACATGGCAA 1306
                                   i                v       vi     v     v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr1_242115339_   1307 CCAGGTATGTGAAAAAATGTTCAATGTCCCTAATCAT 1343
                         vi i i ii      i   i    ii  v????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (135 / 75)
Gap_init rate = 0.03 (25 / 874), avg. gap size = 2.40 (60 / 25)  


2842 26.15 2.58 0.67  chr1_242117279_242119836     1175  2065 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242117279_   1175 TGGAAAAACATCTCATCCTCATGGATAGGAAGAATCAATATCGTGAAAAT 1224
                               i i   i   vi        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242117279_   1225 GGCCATACTGCCAAAAT-AATTTATAGATCCAGTGCTATTCCCATCAAAC 1273
                            v     v  v    -i  i  i    i  ii  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_242117279_   1274 TAC--ACTGACAGTCTTCACAGAATTAGAAAAAGCT-ACTTTAAATTTCA 1320
                          v --i   v -v i  ii     v v  v  -   - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr1_242117279_   1321 TATGAAACCAAAAAAGAGCCCATATAGCAAAGACAATCCTAATCAAAAAG 1370
                             i  viiv  ii  v  viv     v  i      i i vv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_242117279_   1371 AACAAAGCTGGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 1420
                                i   ii i -    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_242117279_   1421 CTACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGACATATAGAC 1470
                                  i   i   iii         i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_242117279_   1471 CAATGGAACAGAACAGAGACCTCAGAAATAACACTACACATCTACAA-CA 1519
                                 i    iv    vii         vv i i    i  iii-  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_242117279_   1520 ATCTGATCTTCGACAAACCTGACAAAAACAAGCAATGGAGAAAGAACTCC 1569
                           -    i        ivv  v   i v  vv      i       ivvi
  L1M4_orf2#LINE/    348 AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_242117279_   1570 CTATTTAATAAATGGTACTGGGAAAA---GCTAGCCGTATGCAGAAAACT 1616
                           v  i  i       i      v  --- v  ?  ii     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_242117279_   1617 AAAACTGGACCCCTTCCTTACACCTTATAAAAAAATTAACTCAAGATGGA 1666
                         i  ii         v   i     v    v              i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_242117279_   1667 TTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAAC 1716
                          i ?    i         i v i     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_242117279_   1717 CTAGGCACTACCAGCCAGGACATAGGCAGAGGCAAAGACTTCATGAAGAA 1766
                         v    ?iiv vivvi iv   v v  vvv      v ii   v ii v v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_242117279_   1767 AACACCAAAAGCAATTGCCAACAAAAGCCACAATTGACAAATGGGATCTA 1816
                         i            vvv  -        vv v   v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_242117279_   1817 ATTAAG-TTAAAGAGCTCCTGCACAGCAAAAGAAACTAGCATCAGAGTGA 1865
                           i  i-     i -  ii  ii vv    i  v    v  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_242117279_   1866 ACAGACAACCTACAAAACGGGAGAAAGTTTTTGCAATCTATCCATCTGAC 1915
                          v        i   i  i        i v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_242117279_   1916 AAGGGTCTAATATCCAGAATCTACAAGGAAC--------CTAAAT--TTA 1955
                              v  vi          v  i  i    --------  v   -- v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_242117279_   1956 CAAGAAAAACAAAC--ATCAAAAAGTGGGCAAAGGATATGGAGAGACACT 2003
                         v    v   i  v --  i?    i            v  i v     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_242117279_   2004 TCTCAAAAGAAGACATTTATGTGGCCAACAA--ACATGAAAGAAAGCTCA 2051
                             v        i  vi vi       i  --        ii v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_242117279_   2052 ACATCACTGATCAT 2065
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (132 / 97)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.81 (29 / 16)  


3114 23.79 3.82 1.91  chr1_242126108_242130390.rev     2902  3792 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242126108_   2902 TGGAAAAATATCCCATGCTCA--AA---GAAGAATTAATATTATTAAAAT 2946
                               i          i   --i ---     v        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242126108_   2947 GTCTATACTACCCAAAGCAATCTACAGATTCACTGCAATCCCTATCAAAA 2996
                          v v     v      vii             vi                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_242126108_   2997 TACTCA--TGACATTCTTCACAGAAATAGAAAAAAGAAATCTTAAAATTC 3044
                          - i  --  v -  i  ii       v  v  ivvi -  i        
  L1M4_orf2#LINE/    101 T-CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTC 147

  chr1_242126108_   3045 TTATAGAATCACAAAAAACCCGTAGTAGATAAATCAATACTGACCAAAAA 3094
                         v   i   vii   iii    iv i   vi   v    vi   vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_242126108_   3095 TAACCAGGCTGGAAACATCATACTATCTGATTTCAAATTATACTACAA-G 3143
                         v   v i i    iivv   i   vi ii        viv        - 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_242126108_   3144 CTATAGTAAGCAA-AGAGTATACCACTGGCATAAAAACAGACACATAGAA 3192
                            i     v   - v   i ivi          ii i     i     -
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA- 296

  chr1_242126108_   3193 GACCAATGGAATACAATAGAAAACCCAGAAATAAATCTATGCACTTACAG 3242
                         --i          v   v  i ii           i i  i  i   ii 
  L1M4_orf2#LINE/    297 --TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_242126108_   3243 CCAACTCATTTTTGACAAAGGCACCAATAACATACATTGGGGAAAAGACA 3292
                         i   i v     i     i  ii    v v   v  v        ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_242126108_   3293 ATCTCTTTAATAAATGGTGCTGGGAAAACTGGATATTCATATGCAGAAGA 3342
                         i   i  i  i              v         ?i  i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_242126108_   3343 ATGAAACTAGAGCTTCATTTTTTATCACATTATGAAAATCAACTCAAAAT 3392
                              ii i  v iii ii ivi i  i  - ii     i          
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAAT 493

  chr1_242126108_   3393 GGA-------CTTAAATTTAA-ACCTGAAACTATGAAACTGCTGGGAGAA 3434
                            ------- i     v   - v  i       i     vi i i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_242126108_   3435 AACACTGGGG-AGATACTACAGGACATTGG------CGAATA-TTTTTGG 3476
                             iv  ? - i  -  v iv   v    ------ -   i-   i vi
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTA 591

  chr1_242126108_   3477 GGTAAGACCTCAAAAACATAGGCAATAAAAGCAAAAATAGACAAGTGGGA 3526
                          i  v   vi     i  i i    i     v         i  i v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_242126108_   3527 TTACATCAAGCTAAAAAGCTTCTACACAGAACAGGAAAC----AACAAAG 3572
                         i v      iv v    i   i iii vvv v    v  ----  v    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_242126108_   3573 TGAAAAGATAACCTACATATGGAATGGGAGAAAATATTTGCAAAT----T 3618
                                 i    i   ----                        ---- 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACA----GAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_242126108_   3619 ATTTGACAAGGGATTAATAACCAGAATATATGAGGAATTCAAACAACTCA 3668
                           i   i      i vi  v           i i   i  vv        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_242126108_   3669 ATGGGCCAAAACCCCCCAGATAATCCAATTTAAAA-TGAGCAAAAGACCT 3717
                           iivvv   iv ---- i    i      ?    -  i     i  ii 
  L1M4_orf2#LINE/    788 ATAATAAAAAGAC----AAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr1_242126108_   3718 GAATAGACATTTATCAGAAGAAGACACACAAGTGGCCAAGAGGTATGTGA 3767
                                     v  vi       i i    i       v i i ii   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_242126108_   3768 AAAGATGTTCAACATCACTAATCAT 3792
                                i         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (138 / 71)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.32 (51 / 22)  


2058 24.40 13.46 4.33  chr1_242213152_242223542     5085  5916 (4475)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242213152_   5085 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 5134
                               i i  i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242213152_   5135 GACCATACTGCCCAAAGTAATTTACAGATTCAGTGCTATTCCCATTAAAC 5184
                          i v     v      v i  i          ii  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_242213152_   5185 TACCA-CTGATATTCTTCACAGAATTAGA-AAACT-ATGTTAACATTCAT 5231
                          v   -   vi-  i  ii     v v  -  i  -  vi   v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_242213152_   5232 ATGGAACTAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCGAAAAGA 5281
                               v iv  ii  v  v v        i      i i ivi i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_242213152_   5282 ACAAAGCTGGAGGCATCACACTACCCAACTTCAAACTATACTACAAGGCT 5331
                               i      vv       v     i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_242213152_   5332 ACAGTAATCAAAACAGCATGGTACTAGTA-AAAAACAGACACATAGACCA 5380
                                    i    ii       i i -  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_242213152_   5381 ATGAAACAGAATAGAGAATTCAGAAATAAGACCGTTCACCTACAACCATC 5430
                            i  i     v    i i         iv  i v  ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_242213152_   5431 TGATCTTTGATAA----------ACC------------------------ 5446
                             i  i  i  ----------   ------------------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr1_242213152_   5447 ----------------------------------------------TGA- 5449
                         ----------------------------------------------   -
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_242213152_   5450 --------------------------CAAAAATTAACTCAAGATGTATTA 5473
                         --------------------------               i   v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_242213152_   5474 AAGACTTAAATGTAAAACCTCAAACAATAAAAACCCTAGAAGAGTATCTA 5523
                         ?    i         i v  v    v      vi i       iv iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_242213152_   5524 GGCA-ATACCATTCAGGACATAGGCACAGGCAAAGATTTCATGACAAAAA 5572
                           ?i- v i -   iv   v v  vvi      v i    v iivv vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_242213152_   5573 CACCAAAAGCAATTGCAACAGAAGCAAAAATTGACAAATAGGACCTAATT 5622
                                    vvv      i   v      v  i    v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_242213152_   5623 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 5672
                            v v  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_242213152_   5673 ACAACTTACAGAAAGGGAGAAAATTTTTGCAATCTAGCCATCTGACAAAG 5722
                              ii      v          v       vii vvi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_242213152_   5723 GTCTACAAGGAATTTAAGAGTCTAAAAGGTCTTAAACAAGTCTTAAAAGT 5772
                          v  -------- v  ----  i i  ----------------  -----
  L1M4_orf2#LINE/    749 GACT--------TGTA----TCCAGAA----------------TA----- 765

  chr1_242213152_   5773 CTACAAGGAACTTAAACAAATTTACAAGAAAAAACCAAAAAACCCCTTTA 5822
                         -  i  i     ivv    v iv i  v     iv    v     vv  ?
  L1M4_orf2#LINE/    766 -TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_242213152_   5823 AAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTCAT 5872
                             i            v    i     i     v        i  v  v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_242213152_   5873 GCAGCCAACAAACATATGAAAAAAAGCTCAGCGTCAGTGATCAT 5916
                         iii     i  i  i       i v     i i   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (117 / 83)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 10.57 (148 / 14)  

3399 24.67 1.44 1.00  chr1_242213152_242223542     8995  9898 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242213152_   8995 TGTAAAGATATTCCATATTCATGGATTGGAATAATCAATATTGTTAAAAT 9044
                           v        i    i              v v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242213152_   9045 GTCCATACTACTCAAGACAATCTGCAGATTTAACACAATCCCTATTCAAA 9094
                          v v     v i   ivii    i      i   i          -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-CAAA 99

  chr1_242213152_   9095 ATACCAATGACATTCTTCACAGAAATAGAAGAAATAATACTAAAATTTAT 9144
                           v   iivi v  i  ii       v  vi iv i  v        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_242213152_   9145 AAGGAACTACAGAAGACCTAGAATTGCCAAAGCTATCCTAAGCAAAAATA 9194
                          v    v i  iii    i     v      i v   i i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_242213152_   9195 ACAAAACTGGAGGAATCACATTAACCTGACTTCAAATTACACTACAGAGC 9244
                              ii       v     i v-  ii i      vivi      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAAGC 248

  chr1_242213152_   9245 TATAGTAACCAA-ATAGCACAGCACTGGCATAAAAACAGACACATAGAGC 9293
                           i     i   - i  iiii i          ii i     i     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_242213152_   9294 AGTAGAAAAGAATAGAAAATATAGAAATAAACCCATATATTTGTAGTGAA 9343
                          i i   v     v  i i vi               i    i i  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_242213152_   9344 CTCATTTT-GACAAAGGTGCCAAGAGCACATATTGGGGAAAGGACAGTCT 9392
                         i v     -     i          v  ivi v         i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_242213152_   9393 CTTCAATAAACGGTGCTGGGAAAACTGGATATCTGTATGCAGAAGAATGA 9442
                         i     i   i          v         ? iii     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_242213152_   9443 AACTAGACCTCTTTCTCTTGCCATTTACAAAAATCAAATCAAATCAAAAT 9492
                          ii i    i  vi   vii    v         i  -- ---       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAA--C---TCAAAAT 493

  chr1_242213152_   9493 GGATTAAACACTTAAACCTCAGACCTCAAACTATGAA-CTTCCACAAGAA 9541
                             i ? v  i    iv v   v  v       i  -  iii v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_242213152_   9542 AACATTGGGGAAACTCTCCAGGACATTGGACTGGACAAAGATTTCTTGAG 9591
                              v  ? v  v   i iv   v    ii i i   v i      iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_242213152_   9592 GAACACTCTACCAGCATAAGCAACCAAAGCAAAAATGGACAAATTGGAGG 9641
                         v vv  v i vv    i       v    v      i  i        vv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_242213152_   9642 GCATCAAG-TTAGAAGCGTTTGCACAGAAAAAGAAATAATCAACTAAGTG 9690
                         v      i-   i  i v    ii vvv   i  v iv     vv     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_242213152_   9691 AAGAGACTA---------TGGGAGAAAATATTTGCAAACGATCCATCTGA 9731
                           i    v ---------                    iv  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_242213152_   9732 CGAAGGAATAATAACCAGAATATATAAGAAGCTCAAACAACTCTATAGGA 9781
                         ii i   v vi  v             ii i   vv       v   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_242213152_   9782 ACAAAATTTAATAATCCAAGTAAAAAATGGGCAAAAAGATCTGAATAGAC 9831
                          v  i iv-     i    v ?             i-   i         
  L1M4_orf2#LINE/    794 AAAAGACA-AATAACCCAATTWAAAAATGGGCAAAG-GATTTGAATAGAC 841

  chr1_242213152_   9832 TTTTCTCAAAGGAAGACATACAAATGGCAAACAGGTAAATGAAAAGGCAC 9881
                         v      v  i     i           v  i i i v        iii 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_242213152_   9882 TCAACATTACTGATCTT 9898
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (134 / 85)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


3240 26.32 0.66 0.66  chr1_242305383_242311651     4869  5776 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242305383_   4869 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4918
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242305383_   4919 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATGAAGC 4968
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_242305383_   4969 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 5015
                          v   i-       i  -i     -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr1_242305383_   5016 CATATGGAACCAAAAAAGAGCCTGCATCTCCAAGTCAATCCTAAGCCAAA 5065
                                  viiv  ii  v  v v  vv    iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_242305383_   5066 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 5115
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_242305383_   5116 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5165
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_242305383_   5166 TCAATGGAACAGAAC--AGAGTCCTCAGAAATAACGCCACATATCTACAA 5213
                                  i    i--       --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr1_242305383_   5214 CTATCTGATCTTTGACAAACCTGACAAAAGAAG-CAATGGGGAAAGGATT 5262
                         ii vi    i  i     ivv  v   i vv v-            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_242305383_   5263 CCCTATTTAATAAATGGTGCTGCGAAAACTGGCTAGCCATATGTAGAAAG 5312
                         vi  v  i  i           v  v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_242305383_   5313 CTGAAACTGGATCCCTTTCTTACACCTTATAGAAAAATCAATTCAAGATT 5362
                         v    ii    i    vi  i     v    v      i  i    i  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_242305383_   5363 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5412
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr1_242305383_   5413 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5462
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_242305383_   5463 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5512
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_242305383_   5513 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5562
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_242305383_   5563 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5612
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_242305383_   5613 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5662
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_242305383_   5663 AAAAACAAACAACACCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5712
                            i     i   v v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_242305383_   5713 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAACATGCTCA 5762
                             v        i  vi viii     v ii          v       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_242305383_   5763 TCATCACTGGCCAT 5776
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (135 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


2093 26.49 11.18 0.85  chr1_242396541_242403719     3116  3938 (3241)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242396541_   3116 TGGAAAGATAGCCCATGT----GGATTGGAAGA----ATACTGCTAAAAT 3157
                                   v       ----           ----   i  i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242396541_   3158 GACCGTTCTATCCAAAGCAATCTACATTTTCAATGTAATCCATATCAAAA 3207
                          i vi v  vi     vii       vv     i i     v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_242396541_   3208 TATCAATGACACTCTGCACATGAAAAGAAAAAGGCAATCCGGAAATTCAT 3257
                          vi  iivi vi i vii  -    vvi v   vii    vi        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_242396541_   3258 ATGGAA---CAA------CA--------AAAGCAATCCTGGACAAAACGA 3290
                               ---   ------  --------   i     i  i v  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_242396541_   3291 ACAAAGCTGGAGGCATCACGTTACCTGACTTGAAAATGCTCTATAAAATT 3340
                               i      vv    ii v  ii i  v    iviv   i   ii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_242396541_   3341 ACAAAAAGCAAAGTAAGCATGGTACTAGCATAAAAATGGACATATGGACC 3390
                            iv  v   iii - ii       i      ii  i       i  i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACA-GTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_242396541_   3391 AATGGAACACA--TGAAAGAACGTAGAAACAAATCCACACATTTA--GTC 3436
                                i v --   i  vv --     i   i   i       --   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_242396541_   3437 AATGGAGTTTCAAGAAAGTCATCAAGAAAATACATTGAGAAAGGAA---- 3482
                            v  v    i v  i viii     vv  v  v  i i  i   ----
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_242396541_   3483 ----------AAT-------------CTAGATAGCCCATATGCAAAAGAA 3509
                         ----------   -------------  i    ?  - i           
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC-ACATGCAAAAGAA 445

  chr1_242396541_   3510 TAAAACTAGACCCCTATCTCTCCCCATATACAAAAGTCATATCAAAACAG 3559
                          i  ii i        i   v v            i i vv      ii 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_242396541_   3560 CTTAAATATTTGAATATAAGACCTAAAACCATGAAACTACTATAAGAAAA 3609
                         v i ? v ii i   i     v       i  i     vi  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_242396541_   3610 CATTGG-GTAAACACTTCA-GACATTGAGCTGGGCAACTACTTATTGAGC 3657
                            v  -     i-    i-   v   i i i     ivii  v  iiii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_242396541_   3658 AAGACCTCAAAAGCACAGGCAACCAAAGCAAATATAGAAACATGAGATCA 3707
                          v   vi          i     v    v   v     v v  vi  iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_242396541_   3708 AATCAAGCTAGAAAGCTTCTGCACAGCAAAGAAAATAATCAA-----TGA 3752
                         v     iv vi   i   i  ii vv     i v iv     -----   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_242396541_   3753 AGAAACAACCTATAGAATTGAAAAAAAAATTTGCAAAGTATTCATTGGAC 3802
                          i i      i i     v i i    v         vi  vi  iv  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_242396541_   3803 AAGAGATTAATAATCACAATATATAG-GAACTC--A-AACTCAATAGCAA 3848
                            i  i vi  vi  v        i-      -- -         ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_242396541_   3849 AAA-----ACAACCCAATT-AAGAACAGGCAAAATATGCTGAAT------ 3886
                            ----- i         -  i  ii      iv  -i     ------
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGACAT 843

  chr1_242396541_   3887 -TC------------ATAGAAATGGCCAACAGATATATAAAAAAATGTTC 3923
                         -  ------------   v          i iii i  i    i   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_242396541_   3924 AATAACATTAATGGT 3938
                           i v  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (138 / 78)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.96 (99 / 25)  

1845 25.19 2.99 0.93  chr1_242396541_242403719     5173  5708 (1471)    L1M4_orf2#LINE/L1        1   547 (361)  

  chr1_242396541_   5173 TGGAAAGGCATACCATGCTCATTAATTGGAAGAATTAATATTGTTAA-AT 5221
                                ii  v     i    vi         v             -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242396541_   5222 GATGATACTATCCAAAGCAATCTACAGATTCAATGCAATCCCTATTAAAA 5271
                          iii     vi     vii              i           i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_242396541_   5272 TACCAACGATATTCTTCA-AGAAATAGAACTAA--TGATCCTAAAATTAA 5318
                          v   i viiv  i  ii-      v  --i  --             v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCA 148

  chr1_242396541_   5319 CATGAAAACACAAAAGACCCCAAATAGCCAAGGCAATACCGAGCAAAAAG 5368
                         i   i   ii   ii     vi         ii    vii  iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_242396541_   5369 AACAAAGCTGGAGGTATCACACTACCTAACTTCAAAATATCCCACAAAGT 5418
                                i      vv       v  i  i       iv v i      i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_242396541_   5419 TATACTAACAAAAAAAACATGGAATTGGTATAAAAACAGACATATAGACC 5468
                           i v   iv  i v iii   v i   i    ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_242396541_   5469 AATGGAACAGAACAGAAAACGCACAATTAAATACACATTATTTATAGGCA 5518
                                i    iv  i iiv  v  v    iv  i i-      i v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC-ATTTATGGTCA 347

  chr1_242396541_   5519 ACTGATTGTCAACAAAGGCACCAAGAACACACAGTGGGGAAAGGACA-CC 5567
                          i     v  i    i  ii      v  iv  i         i i -i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_242396541_   5568 TCTTCAATTATTTGTCATCAGAAAAGTGGATATCCACGTGCAGAAGAATG 5617
                          i     iv v v  vv vi  v  v      ?    i    i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_242396541_   5618 AAACTAAACCCTTATCTGTCACCACACAGAAAAATCAAC-CAAAATTAAT 5666
                           ii ii    i  i  vv     i i v      i   -      vi  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_242396541_   5667 TA---ACT--ACTGT--GAGCCTGGAAACTATAATACT---AAAAGAAAA 5706
                         i ---  i-- v   --    i--i         v   --- i       
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCT--AAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_242396541_   5707 CA 5708
                           
  L1M4_orf2#LINE/    546 CA 547

Transitions / transversions = 1.98 (89 / 45)
Gap_init rate = 0.02 (12 / 547), avg. gap size = 1.75 (21 / 12)  

1187 22.31 4.36 3.08  chr1_242396541_242403719     6297  6686 (493)    L1M4_orf2#LINE/L1      514   908 (0)  

  chr1_242396541_   6297 AGAACTTAAACTATAA----TTTAAAAAAAAAAAAAGAAAACATAGGGGA 6342
                            i  v         ----i   i  ---------           ? v
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAA---------GAAAACATAGGNGT 554

  chr1_242396541_   6343 AACACTTCAGAACATTGGTCTAGGCAAAGATTTTATGGCTAAGACCACAA 6392
                           vv    ivi  v    vi       v i   iv i v  v   vv   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr1_242396541_   6393 AAGCACAAGCAACAAAAACAAAAATAGATAAATGAGACTGTATTAAACCA 6442
                                          iv              vi    vi  i   viv
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr1_242396541_   6443 AAATGCTTCTGCAGAGCAAAGGAAACACTCAACAGAGTGAAGAGACAACT 6492
                            vi   i  iivvv       v  vv    v i      i       i
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr1_242396541_   6493 -ATAAAATGGCAGAAAATATTTGCAAATTATGCATTCAAAAAGGAACTAA 6541
                         - i i     v                 i  ii  iii v    i   vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr1_242396541_   6542 TATCCAGAATATACAAGGAACTCAAACAACTCAACAGCAAAAATATCACA 6591
                                      i  i      vv         i ii     v ---  
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA---CA 801

  chr1_242396541_   6592 AATATTCCAATTCAAAAGAGGGCAAAGGATCTAAATAGATATTTATCTAA 6641
                             vi      ?    iv           i i      i    v  i  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_242396541_   6642 C--ACATATAGAAAAGGCCAATAA----------AAATGCTTATCAGCAA 6679
                         v-- v     v   v         ---------- i     i v  v  ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_242396541_   6680 CCATCAG 6686
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.07 (44 / 41)
Gap_init rate = 0.02 (6 / 395), avg. gap size = 4.83 (29 / 6)  


2982 25.47 2.68 1.23  chr1_242431393_242435233     2454  3348 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242431393_   2454 TGGAAAAATATTCCATGCTCATAGATAGGAGAAATCTT--TATTATGAAA 2501
                               i    i     i    i   v   ii --   --    i v  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA--CTTAATATTGTTAAG 48

  chr1_242431393_   2502 ATAGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATTAA 2551
                           i  v     v      v i  i  i        i  v  i  i  i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_242431393_   2552 ACTACCATTGACATTATTCACAGAATTAGAAAAAACT-ATTTTAAAATCC 2600
                          v v   vivi v  v  ii     v v  v  i-  -  ii      i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr1_242431393_   2601 ATATGGAACCAAAAGAGAGCCTGTAGAGCCAAGACAATCCTAAGCAAAAA 2650
                                 viiv   i  v  v v v      i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_242431393_   2651 GAACAAAGCCGGAGGCATCATGCTACCAAACTT-AAAACTACACTACAAG 2699
                                 ii     vv   ii  v  v  i  -      -i       i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr1_242431393_   2700 GCTACTGTAACTAAAACAGCATGGTACTGGTACAAAAACAGACATATAGA 2749
                              v    ii  i    ii         i i  ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_242431393_   2750 CTAATGGAACAGAATAGAGAACTCAGAAATAAGACTGCACATCTACCACC 2799
                         ii       i     v    iii         iv iii    i  ivii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_242431393_   2800 ATCTGATCTTCGATAAACCTGACAAAAGCA----ATGGAGAAAGGAT--T 2843
                          vi    i     i  ivv  v   i v  ----    i     i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_242431393_   2844 CCTTATTTAAAAAATGGTACTGGGGGAACTGGCTAGCCATATGCAGAAAA 2893
                          i  -- i  v       i     iv      v  ?   i     i  i 
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_242431393_   2894 CTGAAACTGGACCCCTTCCTTACACATTATACAAAAATTAACTCAAGATG 2943
                         v    ii         v   i    vv                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_242431393_   2944 GATTAAAGACATAAATATAAAACATAAAACTATAAAAAACTCC-AGAAAA 2992
                            i ?    v     i   i vv             --   i-    i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA--CTCTTAGAAGA 542

  chr1_242431393_   2993 AAATCTCGGCA-ATACCATTCAGGACATAGGCATAGGCAAAGATTTCATG 3041
                            iv v  ?i- v i -   iv   v v  vv       v i    v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_242431393_   3042 AAGAAAACATCAAAAGCAATTGCAACAAAAGCAAAAATGGACACATGGGA 3091
                         i v vi   i        vvv          v      i  i v  v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_242431393_   3092 TCT------AATTAAAGAGCTTTCGCACAGCAAAAGAAACTGTCATCAGA 3135
                         ii ------       i -    i ii vv    i  v   i   vv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_242431393_   3136 GCAAA----CAGCCTACAGAATGGAAGAAAATGTTTGCAATCTATCCATC 3181
                          ii  ----  i  i         i       i       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_242431393_   3182 TAACAATGGTCTAATGTCCAGAGTCTACAAGGAACTTAAACAAATTTACA 3231
                          i i  v  v  vi i      i v  i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr1_242431393_   3232 AGAAGAAAACAAACAGCCCCATTAAAAAAATGGGCAAAGGACATGAACAG 3281
                          v  i  i     i i   v   ?     -           iv    i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAG 839

  chr1_242431393_   3282 ACACTTCTCAAAAGAAGACATTTATGCTGCCAACAA--ACATGAAAAAAA 3329
                            i     v        i  vi viiv     i  --         i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr1_242431393_   3330 GCTCAACATCACTGATCAG 3348
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.94 (35 / 18)  


2461 26.51 9.55 0.75  chr1_242517064_242519597      878  1673 (861)    L1M4_orf2#LINE/L1        6   871 (37)  

  chr1_242517064_    878 AGATGTCCCATGCTTATAAATTGGAAGAATTAATATTGTTAAGATGACCA 927
                             i       i i  ii         v                 i v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr1_242517064_    928 TGCTACCCAAAGCAATCTACAGATGTAATGTAATACCTGTCAAAATACCA 977
                          i  v      vii          vi  i i   v   i       v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr1_242517064_    978 AACCACATGTTTCACAGAAATATTTTTTTAA----ATCCTAAAATTTGTA 1023
                         i- ii v v   ii       ---- vvi  ----           ii  
  L1M4_orf2#LINE/    106 G-CTGCCTTTTTTGCAGAAAT----TGACAAGCTGATCCTAAAATTCATA 150

  chr1_242517064_   1024 TGGAAACACAAAAGACCATGAATAGCCAAAGCAATAATGAGCAAAAATAA 1073
                               ii   ii    vv           i    vv   iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_242517064_   1074 CAAAACAGGAAGTATCACACTACCTGACTTCAAAATATGCTACAAAGCTA 1123
                             iiv   i vv       v  ii i       iv i           
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_242517064_   1124 TAGGAACCAAAACCATATGGTACTGGTATAAAAACAAACACACAAACCAT 1173
                         i  v  i   i  vi i         i    ii i i   i i i i  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_242517064_   1174 TAGCATAGAATAGAGAACCTAGAGATAAATTCACATATTTACAGCCAACC 1223
                          i v       v    ii i   i     ii  i i     ii i   ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_242517064_   1224 AATTGT--A-AAATGTGTCAAGAAAACAGACTGAGGAAAAGACACCCTGT 1270
                         i   v -- -  iv   i     vv ivv v  i     ii i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_242517064_   1271 TCAATAAATGGTGTTGGGAAGATTCCATATCCAAA-GCAGAAGAGTGAAA 1319
                             i        i     vi i vv   ?   v -   i    i    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_242517064_   1320 GGAGACCATTATC----ACTGTATACAAAAGTAAACTCAAAATGAATTAA 1365
                         vvi    vi  i ----  ii         i v           i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_242517064_   1366 AGATTTGAACATAGGACCCAAAACTATAAAACTACTAGAAGAAAACA--- 1412
                            ii i  ii  i  v i              vi            ---
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_242517064_   1413 --------CTTCAGGACATTGGTCTAGGCAAATATTTTATGGCTAAGACC 1454
                         --------    iv   v    vi       vvi   iv i v  v   v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr1_242517064_   1455 TCAAAAGTACAGCCAACAAAA------ATAGACAAATGGCACTATATTAA 1498
                         i      i   iv        ------     i    v v   vi  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr1_242517064_   1499 ACTAAAAGGTTTCTGTACAGCAAAGAAAACAATCAAGAGACTGAAGAGAC 1548
                          v v   iii  i   i vv     i v  v       i v    i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr1_242517064_   1549 AATCTGTAGCAAT------AAATATTTGCAAATTACATGTTCAGCAAGGA 1592
                           i iii  -   ------              i i  i iiiii    i
  L1M4_orf2#LINE/    701 AACCCACAG-AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr1_242517064_   1593 ATTAATATCCAAAATATA-------------------------------- 1610
                          i vi      i      --------------------------------
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr1_242517064_   1611 ------ATCCAGTTAAAAAGTGGGCAAATGATATGAATAGAAATGTCTCA 1654
                         ------ i   i  ?    i        v   v        v  v    v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr1_242517064_   1655 AAAGAAAATATGCA---GGCCA 1673
                               i    i  ---     
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.89 (136 / 72)
Gap_init rate = 0.02 (13 / 866), avg. gap size = 6.31 (82 / 13)  

 303 15.25 0.00 0.00  chr1_242517064_242519597     1983  2041 (493)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr1_242517064_   1983 AAAGAAAATATGCAAATGGCCAGCAAATATATGAAAAAATGTTCAACATC 2032
                               i    i          ii  ii i       i   i        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr1_242517064_   2033 ACTAATCAC 2041
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.00 (9 / 0)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


1934 21.26 6.09 13.00  chr1_242542053_242544012      510  1478 (482)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr1_242542053_    510 GACATACCATGTTCACG---------ATTCAATATT---AAGATGTCAAA 547
                           i  v         i --------- i i      ---      v   v
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr1_242542053_    548 TCTCCCCTAAGTGATCTACA--TTTCACACCATTTCAATCAAAAT---AG 592
                         v      v  v         --  iv  i v  ii v        ---  
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr1_242542053_    593 CAGGCTTTTT--AAAAAGCTAACAAGCTGATTAAAAAATGTTTATGAAAA 640
                          v v      --v i  ii i          ivv     viv    i   
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr1_242542053_    641 GGCAAGTGA----AAATAGCCAAATCAATTTTAAAGAGAGAAAAAAAAAA 686
                         v     v  ----i          v    i  i  i -    i  v   -
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA-AGAAGAACAAA- 204

  chr1_242542053_    687 GTTAGAGGGCATACACTACCTGATTTCAAGATTTACTAAAAAGCTATACT 736
                            i    i vi     v  ii       i i      v       i v 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr1_242542053_    737 AATCAGAATGGTGTGGTACTG----AAGAA-----------------AGG 765
                              ii ii           ----   i -----------------i i
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr1_242542053_    766 ATAGAATAGTGAGTCCAGAAACAGGCCTACACAAACATGGGCAATTGATC 815
                                v v           i ii  i i   vvi    v        i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr1_242542053_    816 TCCAACAAAGATGAAAAGGCAATTTAATGGAGAAAGGAAAGTCTCTTCAA 865
                          i i    i i  vv   i v   i     i     i v     i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr1_242542053_    866 AAAAATGATGCAGGAACAACTGTATATTTGTGTG---GAGAATCAAGA-A 911
                         v   -  i   v  i       v   ?iiiii  ---i     v   v-i
  L1M4_orf2#LINE/    405 CAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr1_242542053_    912 AACCCTTATGCCATAACATATTCAAAAGTTAATTAAAAATGGATTATAGT 961
                         i    i  ivi  i v     v     i    i v         i ?  -
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG- 502

  chr1_242542053_    962 TGGGCATGGTGGCAAATGCCTGTATTCCTGCTACTCGAGAGGCTGAGACA 1011
                         ---i v ------     -------------  ----    -  i i  -
  L1M4_orf2#LINE/    503 ---ACCT------AAATG-------------TA----AGAG-CTAAAAC- 524

  chr1_242542053_   1012 AGAGGATCGCTTTAGCCTGGGAGTTGGAATCCAGCCTGCATAATGTAGTG 1061
                         --------------------------------------i    -------
  L1M4_orf2#LINE/    525 --------------------------------------TATAA------- 529

  chr1_242542053_   1062 AGACCCGATCTCTATGGAAAAAAAAAAAAGATTATAAATTGAAATGTAAA 1111
                         ------- v    - i   i    --------i   ii?------     
  L1M4_orf2#LINE/    530 -------AACTCT-TAGAAGAAAA--------CATAGGN------GTAAA 557

  chr1_242542053_   1112 TGCTAAAACAGAAAACTCCTAGAAAATATTTGTGACTTTCCCTAAGAAAA 1161
                          -----------------  --------- i     i  vvv v  iv  
  L1M4_orf2#LINE/    558 T-----------------CT---------TCGTGACCTTGGGTTAGGCAA 581

  chr1_242542053_   1162 TA-TTTCTTAAATAAAAGAAGAAAA-CACAAACTATAAAAGTAAAAATTG 1209
                          i-       i   vi v vv    -     i v i     v      v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_242542053_   1210 ATCAAATGAACTTTATTAAAATTAAAAACTTCGGCTCTTCAAAAGATGCC 1259
                           v  v  i    i  i              iv iv       i  ii i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_242542053_   1260 ATTAAGAAAACAAAAAGACAAGTCACAAGTAAGGAGATAATATTTGCAA- 1308
                           i      iii         vi    iivvi     v           -
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_242542053_   1309 -TGCATATCTGACCCAGGACTTGTATCCATGTCATATAAAGAACTCTTAC 1357
                         -iii        ivvi             vivi                 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_242542053_   1358 AACTCAACAACATGAAAACAA----CCCAA--AATAATATAGGCAAAAGA 1401
                                i  i vi  i    ----     --? v  -  i      i  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGGA 830

  chr1_242542053_   1402 TT-GAACAAATACTTCTCAAAAGAAAAGATACAAATGGCAAAAAAGCACT 1450
                           -   i i i i     v      i v           v  v      v
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_242542053_   1451 TAAAAAGATAAGCAGTAGCATTAACTAA 1478
                          i       ivv  ii v  ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (124 / 78)
Gap_init rate = 0.04 (32 / 902), avg. gap size = 5.78 (185 / 32)  


1987 22.82 4.12 3.96  chr1_242581244_242582866      500  1130 (493)    L1M4_orf2#LINE/L1      277   908 (0)  

  chr1_242581244_    500 CATAAAAACTGGCAAATAGGCCAGTGGAATAGAACAGAGAATCCAAAAAC 549
                              ii iv i  v    ii  i          iv    i    i   i
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr1_242581244_    550 AAATCTGCACATTTACGGTCAACCCATTTTTGACAAAGGCACCAAGAACA 599
                            i iii       i      iiv     i     i  ii      v  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr1_242581244_    600 TACATTGGGGTAAGGACACCCTCATCAATAAACGGTGCTGAGAAAACTGG 649
                          v  v     v   i i vi  iv    i   i       i  v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr1_242581244_    650 ATATCCATATATAGAAGAATGCAAGTAGACCCC-ACCTCTCACCACATAC 698
                            ?   i  ii i       v iv i      -     v     i    
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr1_242581244_    699 AAAAATCCAATCAAAATGGATCAAGGAC--AAATGTACAACCCAAAGCTA 746
                               iv v             ?i   --       vi v i   i   
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr1_242581244_    747 TGAAGCTACTAGAAGAAAACATTGGAG-AAATGCTTCAGGGTATTGGCCC 795
                          i  i  vi             v  ? -    -    iv iiv    vii
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTT 575

  chr1_242581244_    796 -GGCAAAGATGTCTTTTGAGAAGACCACAAAAGCACAGGTAACAAAACCA 844
                         -     v i v    v-  v v   vv          i i       vv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTA-GATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr1_242581244_    845 AAAATAGACAAATGAGATTATATCAAGCTAAAAAGCTTTTGCATAGCAAA 894
                                 i    vi  i vi     iv v    i      iiivv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_242581244_    895 CAAAACAATCAACAGAGTAAAGAGACA-------GAATGGGAGAAGATAT 937
                         vi v  v     v i   i  i     -------           i    
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_242581244_    938 TTGCAAACTCTCCATCTGACAAGTGATTAATAATGAGACTATATAAGGAA 987
                                iiv vi      i   v  i vi  viv   v       i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_242581244_    988 CTC----AACTCAATAGCAAAAAAACCACCAAAAGCAGGAAAAAAA---A 1030
                            ----         ii     i  --------------   v  --- 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGAC--------------AAATAACCCA 810

  chr1_242581244_   1031 AACAAAAAATGGGCAAATTAACTGAATAAACTGAATAGACATTTTTC--- 1077
                          vi?             ------ i  ---i             i  ---
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAA------GGAT---TTGAATAGACATTTCTCCAA 851

  chr1_242581244_   1078 AGAAGA----CAAATGCCCAACACATATATGAAAAAATTCTCAACATCAT 1123
                               ----      v    i vii i       i  v          ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr1_242581244_   1124 TAATCAT 1130
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.59 (86 / 54)
Gap_init rate = 0.02 (14 / 632), avg. gap size = 3.64 (51 / 14)  


4089 18.87 3.28 0.68  chr1_242759911_242763832.rev     2547  3431 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242759911_   2547 TGGAAACATATCCCATGTTTGTGAACTGGAAGATTTAATATTGTTAAGAT 2596
                               v            ii  i i       i                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242759911_   2597 GTCATTACCTACCCAAAGGCCTCTACAGATTCAATGCGTTCCCTATCAAA 2646
                          v  v   - v      vvvv             i  iv           
  L1M4_orf2#LINE/     51 GGCAATAC-TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_242759911_   2647 ATCGCAATGATGT-TTTTTTGCAGAAAAGGAAAAAAAAATC-TAAAATTT 2694
                            v  -- v  i-             vv  v  ivvi   -       i
  L1M4_orf2#LINE/    100 ATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_242759911_   2695 ATATGGAATCTTGAGGGACTCCAAATAGCTAAAGTTATCTTGAAAAATAA 2744
                                 vivii      i vi      i   iiv           v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_242759911_   2745 ---CATAGCTGGATGACTCA-ATGTGCTGATTTCAAAATTTGCTAAGAAG 2790
                         ---  v  i    v      - iv v ii         i  i   vi   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_242759911_   2791 CTACTGTGACCAAAACAGTGTGTTACTGGCATAAAGACAGACATATAGAC 2840
                             v  i i   i        v           i  i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_242759911_   2841 CAATGGAATCAACGGGAAAGTCCAGAAGTAAAACCTCACCTATATGGTCA 2890
                                  vi vvv  i         i    v  vi  v v        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_242759911_   2891 AATGATTTTCGATGGGGGTGCCAAGACCCTTCAATGGAGAAAGCACAGTC 2940
                          v          iii             v        i     v i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_242759911_   2941 AATTCAACAAATGGTGCCAGGACAACTGGGTATCCATATGCAAAAGAATG 2990
                         vv               ii          i  ?   i             
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_242759911_   2991 AAGTTGGACCTTTATCTAAGTTTGTATACAAAAATCAACTCAAAATGGAT 3040
                                   ii  i  v vviii           i              
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_242759911_   3041 CAAAGACCTAAATGTAAGACCCCAAACTATAAAACTCCTAGAA---AACA 3087
                           ?                v iv              i     ---    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_242759911_   3088 TAGGGCAGAAGCTTCATGACATTGGATTTGTCAGTGGTATCTTGGGAATG 3137
                             ?vvi  v    i    v    i  v v  i    v    i iv   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_242759911_   3138 ACACCAAAGGAACAGGCAGCTAAAGAAAAAAAATAAACAAATTGTTCTTT 3187
                                 i v   i   i v          --  i i      vv   i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAAATTGGACTTC 645

  chr1_242759911_   3188 ATGAAAATTTAAAAAATTTGGTGCATCAAAAGACAGTATCAACA--GTTA 3235
                           v      -     v   v    v     i    v      v --  v 
  L1M4_orf2#LINE/    646 ATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_242759911_   3236 AAAGGTAACCCAGAGTATGGGAGAAGATATTTGCAAACCTTATATCTGAT 3285
                             ii      v  v         i           i v          
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_242759911_   3286 AATGGATCAATATC-AAAATATATAA------TTAAGAACTCAACAATAG 3328
                           v   iivi    - i         ------i v v       i    i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_242759911_   3329 AAAAGCAA----CATGATTTTAAAATGGGCAAAGGACTTAAGTAGACATT 3374
                            ii   ---- vii   ?v               i  i i        
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_242759911_   3375 TTTCCAAAGAAGATAC-------GCCAATAAGCACATGAAAAGATGCTTA 3417
                          i             i-------                         i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr1_242759911_   3418 GCATCACTAATCAT 3431
                         i     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (89 / 74)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.50 (35 / 14)  


3069 25.50 1.67 0.56  chr1_242846783_242851050     2878  3775 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_242846783_   2878 TGGAAACATGTCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2927
                               v  i       i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242846783_   2928 GGCCATATTGCCAAAAGCAATCTACAAATTCAATACAATTCCCATCTAAA 2977
                            v   i v  v   vii       i      ii    i  i   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_242846783_   2978 CACCA-CTATCATTCTTCACAAAACTAGAAAAAAAAAATCCTAAAATTCA 3026
                         iv   -  ii -  i  ii  i  v v  v  ivvi -            
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCA 148

  chr1_242846783_   3027 TACGGAACCAAAAAAGAGACC--ACATAGCCAAAGCAAGACTAAGCAAAA 3074
                           i    -- viv   i    --iv         i   vvi i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_242846783_   3075 AGAACAAATCTGGAGGCATCACATTATCCAACTCCAAACTATACTACAAG 3124
                                 vi      vv     i vi    i i    viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_242846783_   3125 GCCACAGTCACCAAAACAGCATAGTACTGTTATAAAAATAGGCA------ 3168
                           i     v i   i    ii i      vi    ii    i  ------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_242846783_   3169 -CAATGAAACAGAATAGACAACCCAGAAACAAACCCAAATACTGACAGCT 3217
                         -     i  i     v  v ii       i       v i i v ii ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_242846783_   3218 AACTGATCTTCAACAAAGCAAACAAAAACATAAAGTAGGGAAAGGACACC 3267
                           i    i   i    i vviv   i v   vv i i       i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_242846783_   3268 CTATTCAACAAATAGTGCTGGGACAATTGGCAAGCCACCTATAGAAGAAT 3317
                           v          i            i   vv ?    v ii i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_242846783_   3318 GAAACTGGATCCTCATCTCTCACCTTACACAAAAATCAACTCAAGATGAA 3367
                            ii    i  ii i   v    v  i        i       i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_242846783_   3368 TCAAAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAAC 3417
                            ?    i     v     v  i    i      v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_242846783_   3418 ATCGGAA-AAACCTTTCTAGACATTGGCTTAGGCAAAGACTTCATAACAA 3466
                           v  ?i-   i   iv -   v    v        v ii   v  ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_242846783_   3467 AGAACCCAAAAGCAAACGCAACAAAAGCAAACATAAATAGATGGGACTTA 3516
                         v  vv         v v          v   v   i   i  v      v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_242846783_   3517 ATTAAACCAAAAAGTTTCTGCACAGCAAAAGAAATAATCAGCAGAGTTAA 3566
                           i   viv    ii  i  ii vv    i  v iv    iv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_242846783_   3567 CAGACAAACCACAGAGTGGGAGAAAATCTTCACAATCTATACATCCGACA 3616
                         v      v       i           v  ii   vii   i   i  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_242846783_   3617 AAGGACTCATATCCAGAATCTACAAAGAACTCAAACAAATCAGCAAGAAC 3666
                          i     ii          v  i         vv    v   ii  v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_242846783_   3667 AAAACAGTT---CCA-TCAAAAAGTGGGCTAAAGACATGGACAGACAATT 3712
                           i   iv ---   - i?    i     v  i  iv  i i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_242846783_   3713 CTCAAAAGAAGATATACAAATGGCCAACAAGCATATGGAAAAATGCTCAA 3762
                            v                       i     i   i   i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_242846783_   3763 CATCACTAATTAT 3775
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (134 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


 301 23.33 0.00 0.00  chr1_242921799_242924400      871   930 (1672)    L1M4_orf2#LINE/L1        1    60 (848)  

  chr1_242921799_    871 TGGAAAAACATTCCATGCTCATGAATTAGAAGAATCAATATCACTAAAAT 920
                               i i  i     i     i   i     v i     iii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_242921799_    921 GGCCACACTC 930
                            v i    
  L1M4_orf2#LINE/     51 GGCAATACTC 60

Transitions / transversions = 6.00 (12 / 2)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.00 (0 / 0)  

2375 24.18 3.50 5.88  chr1_242921799_242924400     1225  2109 (493)    L1M4_orf2#LINE/L1       45   908 (0)  

  chr1_242921799_   1225 TAAAATAGCCATACTGCCCAAAGCAATCTACAGATTCAACGCTATGCCTA 1274
                            i  i  v     v      vii                 v  v    
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr1_242921799_   1275 TCAAACTACCAACATCATTTTTCACAGAATTAGAAAAAATTATTCTAAAA 1324
                              v v   i vv v     ii     v v  v  iv v  i      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_242921799_   1325 T----ATAGAACTCAAAAAGAGCCCAAAGGATTGCCCAAGCGATTCTAAG 1370
                          ----  i   v vv  ii  -    i --  v   v  i i  ii i i
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGA-CCCAGA--ATAGCCAAAACAATCTTGAA 191

  chr1_242921799_   1371 CAAAAGGAACAAAGCCAGAGGCATCACATTACCCAACTTCAAAGTATACT 1420
                         v  i i        iii    vv     i v     i      iiv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_242921799_   1421 ATAAGGCCAAACAGTAACCAAAACAGCATAGAACTGGTACAAAACCAAAC 1470
                          i  i  i --      i   i    ii i v     i i  iivi i  
  L1M4_orf2#LINE/    242 ACAAAGCTA--CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_242921799_   1471 ACATAGACCAATGGAGTACA---GAGAACCCAGAAATAAAGCTGCACACC 1517
                          i     i       i  v ---    ii           v iii   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_242921799_   1518 CACAGGCATCTGATCTTTAACAAAGTCACCAAAAATAAGCAATGGGGAAA 1567
                         i ii v  vi    i  ii    i vii    i vi vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_242921799_   1568 GGACCCTCTAGTCAATAAATGGTGCTGGGATA---GGCTACCTATATGCA 1614
                          i ivv   vv    i              i ---  v  ? i i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_242921799_   1615 GAAGAATACAACTGGACCTCTACCTTTCATCATGTACAGAAATTAAGTCA 1664
                         i      iv ii      i      iv  i   i    i       v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_242921799_   1665 AGATGGAT--AAGATTTAAATATAAGACCACATTCTACAAGAATCCTAGA 1712
                          i      --?   ii     i     v vv vv   i  i v  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr1_242921799_   1713 AGAAAACCAT---------TCTTCTAAAGGA--TTGGTTTAGGAAACACC 1751
                                -  ---------     ---iv  --    v     v  ----
  L1M4_orf2#LINE/    540 AGAAAAC-ATAGGNGTAAATCTTC---GTGACCTTGGGTTAGGCAA---- 581

  chr1_242921799_   1752 ATTCTGGACATCAGCTTTAGAAAAGAATGTGTGACTAAGTCCTCAAAAGC 1801
                         ----   vi-  ----     -------- i    -- ----i       
  L1M4_orf2#LINE/    582 ----TGGTT-TC----TTAGA--------TATGAC--A----CCAAAAGC 608

  chr1_242921799_   1802 AATTGCAACAAAAACAAAAATTGACAAGTGGAACCTAATTAAAATAAAGA 1851
                          vvv         iv      v  i  i v i  i v  i     v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr1_242921799_   1852 GCATCTGCACAGCAAAAGAAATTATCAACAGAGTAAACAGACAACATATA 1901
                         i v i  ii vv    i  v i      v i   i  v       vi i 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr1_242921799_   1902 GAATGGGAGAAAATATTCACAAACTGTGAATTTGTC-TATTTGTCATCCG 1950
                                          ii    -----------  -   -----   i 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAA-----------TCATAT-----ATCTG 742

  chr1_242921799_   1951 ACAAAGGTCTAATATCCAAAATCTATAATGAACTT----AATTCAACAAG 1996
                          i  i  v  vi      i   v     v     i----  i    i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_242921799_   1997 CAAAAAACAAATGACCCCAATACAAAATGGGCAAAT-ATATGAATAGACA 2045
                         v    i      i    v v ?v            v-  v          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_242921799_   2046 CTTCTCAAATGAAGACACACAAGCGGCAGACAA--ACATGAAAAAATGTT 2093
                         i     v  v     i i    ii   vi i  --         i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_242921799_   2094 CCACATCACTAATCAT 2109
                          v      ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (128 / 83)
Gap_init rate = 0.03 (23 / 864), avg. gap size = 3.61 (83 / 23)  


2314 19.62 5.90 1.56  chr1_243042091_243044942      962  1537 (1315)    L1M4_orf2#LINE/L1        1   601 (307)  

  chr1_243042091_    962 TGGAAAGACATTTCATGTTCGTGGATTGGAAGATTTAATATTGAATACTG 1011
                                 i  ii       i            i         -------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTG------- 43

  chr1_243042091_   1012 TTAAGATGCCACTACCACCCAAAGCAATCTCCAGATTCAACGCAATCCCT 1061
                                 v  v   iv      vii    v                   
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr1_243042091_   1062 AGGAAAATCCTAAC-GCATTTT--GGAGAAACAGAAAAATCCAGCCTAAA 1108
                          vv       i i -  v    -- v     iv  v  iiiv v      
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr1_243042091_   1109 ATCCATATAGAATCTCGAGGAAACTCAAATAGCCTAAACAATCATTAAAA 1158
                           i     i   viv i   i v ivi       v        v v    
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_243042091_   1159 AGAA---TAAATTTGGATGAATCAGCC--CCTGATTTCAAAACTTAC--C 1201
                             ---i   v     v  v   vv --  ii              -- 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_243042091_   1202 AAGGTAACAGTAG-CAACACAGTGTTGTCTTGGCCTAAGGACAAATATTT 1250
                           i iv      i-   v       v  vi    v      i i i  v 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_243042091_   1251 AGATCAATAGAATACAAT--AGAGCCCAGAAATAAACGCGTACACATATG 1298
                                 i     v   --    i            v i    iv    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_243042091_   1299 GTCAAATCATTTCTGACACCAACGCCAAAGCCATTTAATGGCAGTAAAGA 1348
                              v v    ii    vviii     ii     i     -- v     
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG--GGAAAGA 391

  chr1_243042091_   1349 ACAGTCTTTCCA-CAAACGGTGCTGGGAAAACTAGAT---------CAAA 1388
                          i       i  -    i          v    i   ---------    
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_243042091_   1389 -GAATGAAGCTGGAC----AC-TGAAACCATAAGCAAAATTTA-CTGAAA 1431
                         -        i     ----  - v v      vi     v   -  v   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr1_243042091_   1432 ATGGATCAAAGACCTAAAC--AAGAGCCAAAACTATAAAACTCTTAGAAG 1479
                                 ?         i--      i                      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_243042091_   1480 AAAACACAAGG--AAACCTTCACAACACTGGATTTGGCAATGATCTATTA 1527
                               i i ?--   i    iii  vi   i  v       i i v   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_243042091_   1528 GCTACGACAC 1537
                          v  i     
  L1M4_orf2#LINE/    592 GATATGACAC 601

Transitions / transversions = 1.27 (62 / 49)
Gap_init rate = 0.03 (17 / 601), avg. gap size = 2.53 (43 / 17)  

1399 14.95 4.98 0.33  chr1_243042091_243044942     2061  2361 (491)    L1M4_orf2#LINE/L1      594   908 (0)  

  chr1_243042091_   2061 TATGATACCAAAGGCACAGGCAACAAAAGAGAAAAAAAGACAAAGTTGAC 2110
                              i      i     i           -     v   i   v v   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGAC 642

  chr1_243042091_   2111 TTCATCAAAATGAAAAACTTTGG-GCATCAAAGGACACAATTAACAGGGT 2159
                                    v         v -  v           v  i  v ii  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_243042091_   2160 TAAAAGGCAACCCATAGAATGGGAGAAAATATTTGTAAATCATGTAT--G 2207
                         v     i       i                    i       i   -- 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_243042091_   2208 ATAAGAGATTAATATCCAGAATATATAAAGAACTCTTAAAACTCAGCAAC 2257
                              i  i vi                          v      ii  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_243042091_   2258 AAACA---AAATAACCCA--TTAAAAATGGGCAAATGTCTTGAACAGACA 2302
                            v ---          -- ?             v vi     i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_243042091_   2303 TTTCTT---AAAAGATATACA----GTCAGTACGTACATAAAAATATATT 2345
                              i--- i          ---- i  i  v i    i    v  ii 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr1_243042091_   2346 CAACATGACTAATTAT 2361
                               v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (27 / 17)
Gap_init rate = 0.02 (7 / 315), avg. gap size = 2.29 (16 / 7)  


2330 18.44 21.90 5.63  chr1_243161502_243165107     2333  3113 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_243161502_   2333 TGGAAAGCTAACCCATGTTTATGCACAGAAAGAC--AGTATTGTTAAGAT 2380
                                v  v        i   v iv i     -- i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_243161502_   2381 GTCAGTACCATCCAA--TG---TACAGGTTCAATGTGATCCCTATCAAAA 2425
                          v  i   ivi    --  ---     i     i ii             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_243161502_   2426 TTCCAACAGCCTCTTAGCGCAAGAATGGAAAAGTCAGTTTTCAAATTTAT 2475
                          i   i v    i  -vi   ii   v  v   iiii ii v     i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_243161502_   2476 ATGGCACTACAAGAGGACCCCGA-TAGCCAAAACCACCTTGAAAAAG--- 2521
                             v v i    -      v  -          v i          ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_243161502_   2522 -------TTGGGGGACTCACACTTCCCAATTTCAAAACTTTCTGTAGAGA 2564
                         -------    i                            v  ii i  v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_243161502_   2565 TACATTAGCCAAATCAGTGTGGTACTGCTATAAGGATAGACATATAGACC 2614
                             v  ii   iv             vi                   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_243161502_   2615 AGTGGAATAGAAGTGACACTCCAGAAATAAACCCACACGTCTTTGGCCAG 2664
                          i          v   v v                i  i i v   i  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_243161502_   2665 TTTATTTTT--------TG--------------TGGG------------- 2679
                           v     i--------  --------------    -------------
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_243161502_   2680 ----------------TATGACAA-------------------------- 2687
                         ---------------- iv     --------------------------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_243161502_   2688 -GT-------CT----------------------------------GATC 2695
                         -  -------  ----------------------------------    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_243161502_   2696 AACGACCTAAATACAAG--CTAAATCCATAAAACTCT--GAAGGAAACAT 2741
                          ?v         ii   --     v i          --    i      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_243161502_   2742 AAAAATGAATCTCCATAAATGTGGATTTGGCAATGTATTCTTAGCTATGA 2791
                          ii?i i     i i i viv   i  v       vv       v     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_243161502_   2792 CACCAAAAGCATGAATAATAATACA-----CAGGTAAATTACATGTCATC 2836
                                    ii ii  i  v v -----i  i      iv iv     
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_243161502_   2837 AGGGTT------TTTTAACGGTGCATTAAAGAACATTGTCAAGAAAATGA 2880
                          iii  ------    ----    v i    i   i i        i   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTT----GTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_243161502_   2881 AAAGATGACCCAAAGAATGGGAGGGAGTACTTGCAAATTACATA-ATAAT 2929
                              ii     v          ii i  i        i i   -v i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_243161502_   2930 AAGGGTTATGAAGAACTTACTCAACAAAAAGGTAAACATATACAGAGTCA 2979
                              ---------    i-------------------   v    i --
  L1M4_orf2#LINE/    745 AAGGG---------ACTTG-------------------TATCCAGAAT-- 764

  chr1_243161502_   2980 TGAAGAGTATATGAAGAGCTTC-----CTCAACAA---AAAGACAAACAA 3021
                         --------    i    i  ii-----     i  ---         i  
  L1M4_orf2#LINE/    765 --------ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr1_243161502_   3022 ----AT-----AATGGGCAAAGGACTTAAATACAGATTTATTCCAAGAAG 3062
                         ----  -----             i  i    v v    v i v      
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr1_243161502_   3063 ATACACAAATGGCCAATAA-CACATGACAAGATGCTCAACGTCATTGGTC 3111
                            i               -       v            i   ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr1_243161502_   3112 AT 3113
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.02 (95 / 47)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 7.96 (215 / 27)  


3000 27.86 0.55 0.55  chr1_243204119_243209442     3924  4831 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_243204119_   3924 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAA 3973
                              ii i  i     i      i v      v i     i  v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_243204119_   3974 TGCCATACTGCCCAAGGTAATTTACCGATTCAATGCTATCCCCATCAAGC 4023
                         v  v     v     iv i  i   v       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_243204119_   4024 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4071
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_243204119_   4072 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCCATCCTAAGCCAAAAG 4121
                                viiv  ii  v  v v  v     iv v   i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_243204119_   4122 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTAGAAAGC 4171
                                i      vv   ii  v  ii i      viv     v     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_243204119_   4172 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4221
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_243204119_   4222 AACGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 4269
                           i    i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_243204119_   4270 ATCTGATCTTTGACAAACCTGAAAAAAAGAAGAAATGGGGAAACGATTCC 4319
                          vi    i  i     ivv  vv  i vv vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_243204119_   4320 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCT 4369
                           v  i  i              v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_243204119_   4370 GAAACTGGATCCCTTCCTTACACCTTAAACAAAAATTAATTCACGATGGA 4419
                            ii    i    v   i     v  v           i   vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_243204119_   4420 TTAAAGACTTAAATGTTAGACCTAAAGCCATAAAAACCCTAGAAGAAAAC 4469
                          i ?    i       v   v     i i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_243204119_   4470 CTAGGCA-ATACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCA 4518
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_243204119_   4519 AAACACGAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 4568
                         vi    v       vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_243204119_   4569 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4618
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_243204119_   4619 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 4668
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_243204119_   4669 AAGGGCTAATAACCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4718
                          i  i  vi  v       v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_243204119_   4719 AAAACAAACAACCCTATCAAAAAGTGGGCGAAGGACATGAACAGACACAT 4768
                           i     i     v  i?    i     i     iv    i     iv 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_243204119_   4769 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 4818
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_243204119_   4819 CATCACTGGCCAT 4831
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (143 / 106)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 591 27.34 0.72 0.00  chr1_243323255_243326105      903  1041 (1810)    L1M4_orf2#LINE/L1        1   140 (768)  

  chr1_243323255_    903 TGAAAAAACATCCTATGTTCGTGGATCAGAAGACTTAAGGTCATTTGGAA 952
                           i   i i    i      i     ii          vi ii  vi  v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_243323255_    953 GGCAGTATTCACCAAACTAACATACAGATCCAGTGCAATCCCTAGGAGAA 1002
                             i  i  v     i i iv       i  ii          vv i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_243323255_   1003 -CCCACCTGACTTCTTTGTAGAAAATGCTGAGCTAATTTT 1041
                         -    v   v   i    i     v  vii    i  ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 2.45 (27 / 11)
Gap_init rate = 0.01 (1 / 140), avg. gap size = 1.00 (1 / 1)  

1783 11.84 6.67 28.76  chr1_243323255_243326105     1354  2358 (493)    L1M4_orf2#LINE/L1      126   908 (0)  

  chr1_243323255_   1354 TGATGAGCTGCTTCTAAAATTCATATGGAT-TGCAAAGGACCCATAGTAG 1402
                            ii     v i                v-     i       v i   
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr1_243323255_   1403 CTAAAACAATCTTGAAAATGAAGAAAAAAGT---AGAATTCACACTTCCT 1449
                          i                v      v     ---  i i          i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr1_243323255_   1450 GATTTCACAACTTAATACAAACCAACAGTAATGAAGGCAGTGTGGTATTG 1499
                         i      v      v      v v        v   i          i  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr1_243323255_   1500 ACA--AGGACAGACATACAAATTAAT-----AGAATTGAG--TCCAAAAA 1540
                         i  --    i       i i  i   -----         --    i   
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr1_243323255_   1541 TAAACCCTGACATCTATGGTCAGCTGATTTTTCAACAAGGCTGCTAGAAC 1590
                                vv    i        ii       - i      v   i ii  
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTT-CGACAAGGGTGCCAAGAC 374

  chr1_243323255_   1591 CATCCAATGGGGAAAAGAAGAGCCTTTTTAAGAAATGATACTGGGAGAAT 1640
                            i           -   v  i     i  v     i i      v  i
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_243323255_   1641 GGGATAGCTATGTGAGAAAGAATGAAATTGGCTGGATGCAGTGGCTCACG 1690
                         v     ? i ii  vi          i    -------------------
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGG------------------- 454

  chr1_243323255_   1691 CCTGTAATCTCAACTCTTTGGGAGCCTGAGGTAGGGGGATAGCTTGAGGC 1740
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chr1_243323255_   1741 CAGGAGTTTGAGACCAGCCTGGCAACATAGTGAGACCCTATCTCGATTAA 1790
                         ------------   ---------------------    i   ------
  L1M4_orf2#LINE/    455 ------------ACC---------------------CCTACCTC------ 465

  chr1_243323255_   1791 AAAAAGAAAAAAAAGTTGGGCATAGTGGCACATACCTATAGCCCTGGCTA 1840
                         --------------------------------------------------
  L1M4_orf2#LINE/    466 -------------------------------------------------- 465

  chr1_243323255_   1841 TTTTGGAGGCTGAAGTACGGGGAGTACCTGAGCCCAGGAGTTTGAGGTTA 1890
                         --------------------------------------------------
  L1M4_orf2#LINE/    466 -------------------------------------------------- 465

  chr1_243323255_   1891 CAGCGAGCTTTGATCACACCACTGCCCCCCAGCCTGGGTGACACAGTGAG 1940
                         ---------------      i------------------ i   -----
  L1M4_orf2#LINE/    466 ---------------ACACCAT------------------ATACA----- 477

  chr1_243323255_   1941 GCTCTGTCTCTTAAAAAAAAAAAAAATGAACTCTTACTATATACAAAATT 1990
                         ----------------------     v     -----------     -
  L1M4_orf2#LINE/    478 ----------------------AAAATTAACTC-----------AAAAT- 493

  chr1_243323255_   1991 ATCTTGAATTAAAAGCCTAAACGTAAGAGCTAAAACTATAAAAGCCTTAG 2040
                         ----- i  i ? ii      i                     vi     
  L1M4_orf2#LINE/    494 -----GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr1_243323255_   2041 GAGAA----CAGGAGTAAATCTGCATGGCCTTGGATTGGACAAGGGATTC 2086
                         i    ----i   ?        v i  i      i  i i   v  v   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr1_243323255_   2087 TTAGATATGACATCTAAAGCA-AAGCAA-----GAAAA----------TT 2120
                                     i v      -      -----     ----------  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_243323255_   2121 G-------CCAACATTTAAAATGTTTCTGCTTCAAAGAACACTG---AGA 2160
                          -------i   v   v    iv   v          i     i---   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_243323255_   2161 ATGTGAAAAATACAGTCCACAGAATGGGAGGAAA-ATTTGCAAATCATGT 2209
                          v       i-   ii              i   -             i 
  L1M4_orf2#LINE/    689 AAGTGAAAAG-ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_243323255_   2210 ATCTGATAAGG-ATTCATATTCATAATCTATAAAGA--TC----AGCTCA 2252
                                    - i ii   i  v   v        --  ---- i    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_243323255_   2253 ATAATAAAGA------TGACCCAGTTTAAAAAATGAGCAAAGAATCTGAA 2296
                                 i ------ i     i  ?     -  i      i  i    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chr1_243323255_   2297 TTGATACTTCTCCAG-GAAGATACACAAATACCC------C---TAAAAA 2336
                          v  i i       i-       i      iv  ------ --- i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_243323255_   2337 GATGCTTGATATCATTAGTCAC 2358
                               ii i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.48 (82 / 33)
Gap_init rate = 0.04 (30 / 783), avg. gap size = 11.87 (356 / 30)  


 734 30.16 1.19 1.19  chr1_243572465_243574458      495   746 (1248)    L1M4_orf2#LINE/L1      134   385 (523)  

  chr1_243572465_    495 TGGTATTAAAATTTATATGGAACCAAAAAAAGAGCCCA-AATAGCCAAGA 543
                           i vi       i        -- viv  i ii    -         i 
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAA 181

  chr1_243572465_    544 CAATCCTAAGCAAAAAGAGCAAAGCTAGAGGCCTCGTGGAACCTGACTTC 593
                              i i iv  i    i     i i    v   iiivvv  ii i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr1_243572465_    594 AAACTATACGACAGGGCTACAGTAACCAAAACAGCATGGTACTAGTACAA 643
                            viv   v   ii          i   i    ii       i i i  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr1_243572465_    644 GAACAGACACATAGACAAATGGAACA-AATAGAAGGCCCAGAAATAAGAT 692
                          i i     i     iv       i -   v  ii i          ivi
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr1_243572465_    693 CACATGCCTACAACTATCTGATCTTCCACAAACCTGACAAAAATCA-GCA 741
                           i iiii  iiiii vi    i   v    ivv  v   i -i  -v  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA-CCATTCA 380

  chr1_243572465_    742 ATGGG 746
                              
  L1M4_orf2#LINE/    381 ATGGG 385

Transitions / transversions = 2.80 (56 / 20)
Gap_init rate = 0.02 (5 / 252), avg. gap size = 1.20 (6 / 5)  

1294 25.86 2.52 3.66  chr1_243572465_243574458     1051  1487 (507)    L1M4_orf2#LINE/L1      414   845 (63)  

  chr1_243572465_   1051 CTGGAATAGCTGTCTAGCCATATGCAGAAAATTGAAACCGGACCCCTTCC 1100
                             i i i   vv  ?   i     i  i v    iii        v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_243572465_   1101 TTACACCATATACAAAAATTAACTCAAGGTAGATTAAAGACTTAAATGTA 1150
                          i                         ii i   i ?    i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_243572465_   1151 AAAACCAAAACTATAAAAATCCTGGAAGACAACCTAGGCA-ATACCATTC 1199
                          i i i            v  i i     v   v    ?i- v i -   
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC 562

  chr1_243572465_   1200 AGGACATAGGCACGGGCTAAGATTTCAC-GATAAAGATGCCAAAAGCAAT 1248
                         iv   v v  vvii   v v i    vi-    v-  ii         vv
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCACA 611

  chr1_243572465_   1249 TGCAACAGAAGCAAATATCGACAAATGGTATCTAATTAAACTAAAGAGCT 1298
                         v      i   v   v  v  i    v v ii v  i   v v  i i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_243572465_   1299 TCTGCACAGTGAAAGAAACTATTAACA---------GACAACCTACAGAA 1339
                          i  ii vvii  i  v     i  v ---------       i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_243572465_   1340 TGGGAGAAAATTTTTGCAAACTATGCATCTGACAAAGATCTAAGGAATAA 1389
                                    v        ii  ii      --------     -----
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGA--------TAAGG----- 748

  chr1_243572465_   1390 AGAATTTTAGCAAATGTAAATAAGGAATTTAAGCAAATTTACAAGAAAAA 1439
                         -  v  v  v v ivi  v    i   i ivvi   v iv i  v     
  L1M4_orf2#LINE/    749 -GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_243572465_   1440 AACAAACAACCCTATTAAAAAGTTGGCAAAGGACATGAACAGACACTT 1487
                         i     i     v   ?    i v         iv    i     i  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

Transitions / transversions = 1.32 (62 / 47)
Gap_init rate = 0.02 (7 / 432), avg. gap size = 3.86 (27 / 7)  


 493 27.71 1.81 1.81  chr1_243620762_243627712     5090  5255 (1696)    L1M4_orf2#LINE/L1        1   166 (742)  

  chr1_243620762_   5090 TGGAAAAA-ATTCCATCTTCATGGATAGGAATAATCAGTATCACAAAAAT 5138
                               i -  i    v         v    v v i i   iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_243620762_   5139 GGCCACACTGCCCAAAGTAATTTACAGATTCAGTGCTATTCCCATCAAAC 5188
                            v i   v      v i  i          ii  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_243620762_   5189 TACCATTGACATTCTTCACAGAA-TTAGCAAAAACT-ATTTAAAATTTCA 5236
                          v   vivi v  i  ii     -  ii   --i  -  iiv   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr1_243620762_   5237 TGTGAAATTGGCCAGGCAC 5255
                          i  i  v  - v   v  
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGAC 166

Transitions / transversions = 1.42 (27 / 19)
Gap_init rate = 0.03 (5 / 166), avg. gap size = 1.20 (6 / 5)  

1639 21.39 1.41 18.02  chr1_243620762_243627712     5538  6458 (493)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_243620762_   5538 AAAATT-ATATGGAG-T-CAAAGAAGACCCAATATACCCAAGACAATCCT 5584
                               -       i- -   i --      iv   v    i      i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTT 188

  chr1_243620762_   5585 AAGCAAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTAT 5634
                         i iv  i          i      vv   ii  v  ii i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr1_243620762_   5635 ACTACAAGGCTACAGCAGCCAAAATAGCATGCTACTGGTACCAAAACAGA 5684
                                i       i ii   i i  ii  v      i iv ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr1_243620762_   5685 TATATAGACCAACGGAGCAGAACAGAGACCTCAGAAATACCACCACACAT 5734
                         i       i   i   ii    iv    vii        vvv   i    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr1_243620762_   5735 CTAAAACCATCTGATCCTCGACAAACCTGACAAAAACAAGCAATGAAGAA 5784
                         i  viii  vi    ii       ivv  v   i v  vv     ii   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_243620762_   5785 AGGATC-TCTGATTCAGTAAATGGTGCTAGGAAAACTAGCCAGCCATATG 5833
                           i  v-   v-    ii          i   v    i vi ?   i   
  L1M4_orf2#LINE/    389 AGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_243620762_   5834 CAGAAAATGGAAACTGGACTGCTTCCTTATACCA-------AAATTAACT 5876
                           i  i vv   ii     iv  v   i i    -------         
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_243620762_   5877 CAAGATGGGTTGAAGATTTAAATGTAAAATCCAAAACCATAAAAACCCTA 5926
                            i    i ii?   ii         i v i     i      vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr1_243620762_   5927 GGAGAAAACCTAGGGAGGCCAGGTGCAGTGGCTCGTGCCTGTAATCCCAG 5976
                          i       v    ?-------------------  i-----    ----
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGN-------------------GTA-----AATC---- 559

  chr1_243620762_   5977 CAGTTTGGGAGGCCAAGGTGGGTGGATCATGAGGTTAGGCATTCGAGATC 6026
                         ---  i v  --  --------------- vi         ---------
  L1M4_orf2#LINE/    560 ---TTCGTGA--CC---------------TTGGGTTAGGCA--------- 580

  chr1_243620762_   6027 AGCCTGGCCAACATAGCGAAACCCTGTCTCTACTAAAAATACAAAAAAAA 6076
                         ------------  i ---------- i   -------------------
  L1M4_orf2#LINE/    581 ------------ATGG----------TTTCT------------------- 589

  chr1_243620762_   6077 AAAAAAAAAAAAAAAGAAAGAAAACCTAGGGAATATCACTCAGGACATAG 6126
                         --------------------------   ---    -------    i--
  L1M4_orf2#LINE/    590 --------------------------TAG---ATAT-------GACAC-- 601

  chr1_243620762_   6127 GCGTGGGCAACTTCATGGCAAAAATGCCGACAGCAATTGCAACAAAAGCA 6176
                         ------------------     i------  -   --          v 
  L1M4_orf2#LINE/    602 ------------------CAAAAG------CA-CAA--GCAACAAAAGAA 624

  chr1_243620762_   6177 AAAACTGACAAATTGGATCTAATTAAACTAAAGAGCTTATGCACAGCAAA 6226
                             iv  i        ii v  i   v v  i i   v  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr1_243620762_   6227 AGAAACTGTCCTCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTT 6276
                         i  v   i  vvv i      v  i     i   i             v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr1_243620762_   6277 CTGGAATCTATCCATCTGACAAAGGTCTAATATCCAGAATTTACAAGGAA 6326
                         i  v  vii  vi      i  i  v  vi          v  i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr1_243620762_   6327 CTTAAATATATTTACAAGAAAAA-ACAAAAAACTCA-TCAAAAAGTGGGC 6374
                           ivv i vv iv i  v     -     v   i  - i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr1_243620762_   6375 AAGGGATATGAATAGACACTTCTCAAAAGAAGACATTTATGCATCTAACA 6424
                           i    v          i     v        i  vi viiiv i  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr1_243620762_   6425 AACACATGAACAAAAGCTCAACATCACTGATCAT 6458
                          i        v i v           ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (123 / 70)
Gap_init rate = 0.03 (23 / 768), avg. gap size = 7.78 (179 / 23)  


1163 25.00 5.88 1.18  chr1_243650818_243655651     3158  3497 (1336)    L1M4_orf2#LINE/L1        1   356 (552)  

  chr1_243650818_   3158 TGGAAAAACATTCCATGCTCATTGATAGGAAGAATTAATATTGCTAAAAT 3207
                               i i  i     i    v   v      v         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_243650818_   3208 GGTCCAA--CTACCCAAAGCAATTTA--GATTCAATGCTATTCCTATCAA 3253
                           --   --  v      vii  i  --       i  v  i        
  L1M4_orf2#LINE/     51 GG--CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_243650818_   3254 ACTACCAATTACATTGTTCACCAAATTAGATAAAACT-ATTTTAAAATTC 3302
                          v v   ii i v  v  ii vi  v v  i  i-  -  ii        
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr1_243650818_   3303 ATGTGGAACCAATAAAGATCCCACATAGCCAAG-CAA----------GAA 3341
                           i     viivv ii  i  viv        i-   ----------   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_243650818_   3342 GAACAAAGTTTGGAGGCATCATATTAACCAACTTCAAACTATACTACAAA 3391
                                   -     vv   i i vv    i      viv         
  L1M4_orf2#LINE/    198 GAACAAAGTT-GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_243650818_   3392 GCTACTGTAACCAAAACAGCATGGTAATGGTATAAAAACAGACA----GA 3437
                              v    i   i    ii     v   i    ii i     ----  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_243650818_   3438 CTGATGGAGCAGAATGGAAAGCCCAGAAATAATGCCACACACCTACGACC 3487
                         iii     ii     v  i  i          vv   i   ii  i ii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_243650818_   3488 ATCTGATTTT 3497
                          vi       
  L1M4_orf2#LINE/    347 AATTGATTTT 356

Transitions / transversions = 1.83 (55 / 30)
Gap_init rate = 0.03 (9 / 356), avg. gap size = 2.67 (24 / 9)  

1415 24.95 5.61 3.07  chr1_243650818_243655651     3786  4338 (495)    L1M4_orf2#LINE/L1      342   908 (0)  

  chr1_243650818_   3786 TGGCCAACCATCTGATTTTTGACAAAATCAACAAAAACAAATAATGAGGA 3835
                            i   i----       i     iiviiv   i v  vvi    i   
  L1M4_orf2#LINE/    342 TGGTCAAT----TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr1_243650818_   3836 AAGGACTTCCTATTCGATAAATGGTGCTAGGATTACTGGCTAGCCACATG 3885
                            i ivvi  v   i i          i   iv     v  ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr1_243650818_   3886 CAGAAGATTGAAACTGGACCCCTTCCTTACACCATATACAAATATAAACT 3935
                           i    v    ii         v   i              v  v    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr1_243650818_   3936 TTAGATGCATTAAAGACTTAAATGTAAAAATTTAAAGATAAAAAAACCCT 3985
                         iv i   v  i ?    i         i ii -   iv  v    vi i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTT 536

  chr1_243650818_   3986 GGAAGATAACCTAGG---AAATACCATTCTGGACATAGGACCTGGCAAGT 4032
                         i     v   v    ---    -- -   vv   v v  iiiv     vv
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATG 583

  chr1_243650818_   4033 ATTTCAT-GATGAAGATGCCCAAAGCGACT-GCCACAAAAGAAAAAGTTG 4080
                         i    v -   - v  ii  v     -  v-  v            i v 
  L1M4_orf2#LINE/    584 GTTTCTTAGAT-ATGACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAG 631

  chr1_243650818_   4081 ACAAATGGGACATAATTAAACTAAAGAACTTCTTCACAGCAAAACAAACT 4130
                          i    v    v v  i   v v  i     i vii vv    iv v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_243650818_   4131 AACGGGA--TTAAACAGAGAACCTACAAAGTGAGAGAAAATATCTGCAAA 4178
                          v ii  --v i  v   v    i   i i  i          i      
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_243650818_   4179 CTATGCATCTAACAAGGGTCTAATATCCAGAATCTGTAAGAAACTTAAAT 4228
                         ii  ii    i i     v  vi          v i   ii    ivv i
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_243650818_   4229 AAATTAACAAGCAAAGAGGAAACAAGAATGAAACA-TTAAAAAGTGGGCA 4277
                           v i  i  -i   i  ---    --  i vv  -  ?    i      
  L1M4_orf2#LINE/    782 AACTCAATAA-TAAAAAG---ACAA--ATAACCCAATTWAAAAATGGGCA 825

  chr1_243650818_   4278 AAGGACATGAA----CACTTTTC---AAAAGATATACAAA---------- 4310
                              iv    ----  i  i  --- i            ----------
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr1_243650818_   4311 ---CATGAGAAAAATG---AACATTATCACTCAT 4338
                         ---     -   i   ---     i ????????
  L1M4_orf2#LINE/    876 GCACATGA-AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (78 / 57)
Gap_init rate = 0.03 (19 / 567), avg. gap size = 2.53 (48 / 19)  


 430 17.22 13.91 5.30  chr1_243684397_243686055      204   354 (1305)    L1M4_orf2#LINE/L1       46   209 (699)  

  chr1_243684397_    204 AAGGTATCAGTAC----CAACAGTGATGTACAAATTCAACGTAATCTCTA 249
                            i iv  i   ----   - v    v    i        i    i   
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAA-ATTGATCTACAGATTCAACGCAATCCCTA 94

  chr1_243684397_    250 TCTAAATCCCAATGGTACTTTTTTTGCAGAAATATTTTCCAA----ATCC 295
                           v        -- v i i              --- vv   ----    
  L1M4_orf2#LINE/     95 TCAAAATCCCA--GCTGCCTTTTTTGCAGAAAT---TGACAAGCTGATCC 139

  chr1_243684397_    296 TAAAATTTGTTTAGAAA----------CTATGACTAGCCAAATACCATTT 335
                                ii v i    ---------- i -  v        -  v  i 
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCA-GAATAGCCAAA-ACAATCT 187

  chr1_243684397_    336 C--AAAAGAAGAA-AAGGATGG 354
                         i--          -  i v   
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGG 209

Transitions / transversions = 1.36 (15 / 11)
Gap_init rate = 0.06 (10 / 164), avg. gap size = 2.90 (29 / 10)  

1589 27.27 8.80 1.88  chr1_243684397_243686055      474  1166 (493)    L1M4_orf2#LINE/L1      168   908 (0)  

  chr1_243684397_    474 CAAAACAACAACAACAACAACTATAAAATAAAAAGAATAAGA--AGAGGC 521
                           i  i i --   -     iiv i   -  i     i  ii--i    v
  L1M4_orf2#LINE/    168 CAGAATAGC--CAA-AACAATCTTGAAA-AAGAAGAACAAAGTTGGAGGA 213

  chr1_243684397_    522 TTTACACTTCCTGGTTTCAAACATATTAC-ACAAAGCTATA--AA--AAG 566
                         i i        iii       - i-    -         i --  --   
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAA-AC-TTACTACAAAGCTACAGTAATCAAG 261

  chr1_243684397_    567 ACAA------------ATATGAATAAAGA----GAT-AATGAAACAAGA- 598
                            i------------   v i   i v ----   -    i  i ii -
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr1_243684397_    599 -GAGAACCTAGATATAAACCCTTTTGGATACAATCAAATGATCTTCCACA 647
                         -    ii i   v        v viivv  iii    v    i   v   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr1_243684397_    648 AGGTTGCCATGGCCACACAACAGGGAGAGA-----CTCTTCGACAAACCA 692
                            v     v i   iv   ii    i   -----  i   i     ivi
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr1_243684397_    693 TGTTGAAA--ACGGAGTACCTACATG-AAAAAAATTAAGTTGGACCCTTC 739
                           i  ii --  v ii  ? i     -    i   v           i v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr1_243684397_    740 CTTTGCATTATATGCAAACAATATTTTAAAA-GGATTCAATGCTTAAACA 788
                          i ii  ii    i    v v  vi i    -    iv? vi i    ii
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr1_243684397_    789 TAAAAA-TATAAC---AAAACTCTCAGGAGAAAATATAGAGA-AGATC-- 831
                            i i-  v   ---        i  i      i    i?i- i   --
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr1_243684397_    832 -ATGACATTGGTCTTTGCACCGTTTTCTTGGATATGATGTCAAATGCATA 880
                         -i    v    vi vv   vi v      i       iii    v   i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr1_243684397_    881 AGCAACAAAGAACAAAA-----AAACTGAACTACATCAAACTTCAGAATT 925
                                  ii v    -----   i  i   v       v  v i  i 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr1_243684397_    926 TCTGAACATTAAAGGAACCAATTAGTGGAATGAAAATGTCACCTTAGA-A 974
                          i  vi v i      vv v  i ivii i      - v  v ii v - 
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GACAACCCACAGA 710

  chr1_243684397_    975 ATGGGTGAAAATATTGACCTATTAGATATTTGATA--GGAGTTAACGTA- 1021
                              v         vi vv  i v    i     --   v  ---   -
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT---GTAT 757

  chr1_243684397_   1022 -CAGAATGTAT------CTCTCCTAAAACTCAGCCCCCCAAAAATAA-TA 1063
                         -      i   ------    --  v      iivvivv   i i  -  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCT--TACAACTCAATAATAAAAAGACAAATA 805

  chr1_243684397_   1064 ATTTGATTTAAAAACAGACAAAGGATT-GAACTGACTTTTCTTTAAAAGA 1112
                          iiii   ?     ii i         -   iv   v     ii   -  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA-GA 854

  chr1_243684397_   1113 TAATACTCAAATGGCCAACAGGCACTTGAAAGAAAGCTGAAAATTACTAA 1162
                         vi   iv           i i    v     ii v   v  v  i ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr1_243684397_   1163 TTTG 1166
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.94 (122 / 63)
Gap_init rate = 0.04 (32 / 741), avg. gap size = 2.31 (74 / 32)  


1787 26.22 6.83 3.07  chr1_243722636_243724266      449  1165 (466)    L1M4_orf2#LINE/L1      165   908 (0)  

  chr1_243722636_    449 ACCCACAAAAATTAAAACAAA---AAGAAAGAAAAAGAAAA--AGAAAAG 493
                              v  v iii       v---i i      i  v   i--i  ii v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr1_243722636_    494 T-A--------AAT---GAAATAGATTACAAGGCAAAAGTAA-CAACAAT 530
                          - --------   ---i   ivv i     i  v v     -   -i i
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA-GAC 263

  chr1_243722636_    531 AGCATGGT--TGAGTTTAAAAGAGACACATAGTCCAGTGGAACAGAGTAT 578
                           ii    --  ivv v ii v     i    vi  i     i   i vv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr1_243722636_    579 AGAACAGAGAAATAAATCCATGTATTTACAGCCAACTGGTTTTCCACAAA 628
                            iivv         i    ii     ii i   i  i     v    i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr1_243722636_    629 GGCTCCAAGAACATACACTGGGTGTTGGACATTATTTTCAATGAATGGTG 678
                           iv      v   v  v    vivv i i v v       ii       
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr1_243722636_    679 CTGGGAAAACTGGATATCTACATGCAAAAGTATGAAACTGGACCCCTATT 728
                               v         ? i           v     ii          ii
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_243722636_    729 TCTCACCATATACAAAAATAAACTGAAGATGAATTATGAACTTATACATA 778
                           v                v    v  i   i  i ?ii  i  v ii  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_243722636_    779 AGACCTGAAACTATAAAACTATTAGATAAAAACACACAGAAAACACTTCA 828
                            v  i             v     vi      i vi?iv  vv    i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr1_243722636_    829 GAAC-----ATTAGGCAAATATTTTATGGCTAAGACATCAAAAACACACA 873
                         vi  -----i        vvi   iv i v  v    i     i    vi
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_243722636_    874 CAATGAAAATGAAAACAAAAACAAAAGCAGACAAATGGGAAAATATTATT 923
                            ------------     iv    ii   i    v   ---iv i  i
  L1M4_orf2#LINE/    614 CAA------------CAAAAGAAAAAATAGATAAATTGGA---CTTCATC 648

  chr1_243722636_    924 AAATAAAAAAACTTCTACATGGCAAAGGAAACAATCAATGGAGCAAAGAA 973
                            vvv        i iiiivv       v  v     vii  ii  i i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_243722636_    974 ACAACTTGTTGAATGGAAGAAAATATTTGCAAACTATTCATCTGATAAAG 1023
                              iiiiv      i                ii  vi         i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_243722636_   1024 AACTAACATCCAAAATATA---------CTCA------AATAGTAAAAAG 1058
                         i   vii     i      ---------  i ------    i       
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_243722636_   1059 -CAA-TCAC---ATTAAAAAGTGTGCAAAGGACATACATAGACATTTCTC 1103
                         -   - v  ---   ?    i  v        iv iv             
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_243722636_   1104 AAAAGAAGAAATGCAAATGGCTAACAGGTTTTTTTTTTTTAA----TGCT 1149
                         v        v  i        i  i i iviv v------  ----    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATG------AAAAGATGCT 892

  chr1_243722636_   1150 CAACATTACCAGTCAC 1165
                               i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (113 / 71)
Gap_init rate = 0.02 (18 / 744), avg. gap size = 3.94 (71 / 18)  


3280 25.67 0.56 1.00  chr1_243737922_243742210.rev     2895  3790 (499)    L1M4_orf2#LINE/L1        1   892 (16)  

  chr1_243737922_   2895 TGGAAAGATATTTCATGTTCATGTATTGGAAGAAACAATACTGTTAAAAT 2944
                                    ii          v         vvi    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_243737922_   2945 GTTTATACTACCCAAAGCAATCTACAAATAAAATGCAATCCCTGTCAAAA 2994
                          viv     v      vii       i  vv  i         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_243737922_   2995 TACCAATGAAATGCTATACAGAAATAGAAAAAACAATCCTGAAACTTATA 3044
                          v   iivivv vi v i       v  v  ivii     i   i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_243737922_   3045 TGAAACCACAAAAGATCCGGAATAGCCAAAAGTATCCTGAACGAGAAGAA 3094
                           i  vii   ii  i  i            vv   i    vi       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_243737922_   3095 CAAAACTGGAGGAACCACGTTACCTGACTTCATGTTACACTACAGAGCTG 3144
                             ii       vi   ii v  ii i    vivivi      i    i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_243737922_   3145 TAATAACCAAAAACAGCGTGGCACTGGCATAAAGGTAGACACATAGACCA 3194
                         i i   i   i -   i    i          i i      i     i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_243737922_   3195 ATAGAACAGAATAGAGAACTCAGAAATAATTCCACATACCTACAGTAAAC 3244
                           i   i     v    iii         vi   i i ii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_243737922_   3245 TCATTTTCAACAAACATGCCAAGAATACATATACACTGGGGGAAAAGACT 3294
                          v      i    ivi        --- -i  v  v     --     v 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGA---C-CATTCAATGGGG--AAAGAAT 393

  chr1_243737922_   3295 -GTCTCTTCATTAAATGGTGCTGAGAAAACTGGATATCCATATGCAGAAG 3343
                         -    i    vi           i  v         ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_243737922_   3344 AATGGAACTAGACCCCTCTCCTTCACCATATATAAAAATAAAATGAAAAT 3393
                             i ii i       vi iiv         i      v  v v     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_243737922_   3394 GGACTAAAGACTTAAATCTAAGACATTAAACCGTGAAACAACTACCAGAA 3443
                            ii ?    i     v     vv v    ii i    vvi  vv    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_243737922_   3444 AATACTGGAGAAAATCTCCAGGACATTGATCTGGGCAAAAATGTTTTGAG 3493
                           i iv  ? v      i iv   v   ivi i     vii v i  iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_243737922_   3494 CAATACCCCACTAGCACAGGTAACCAAAGCAAAAATAGACAAATGAGATC 3543
                         i vv  v   vv      i i   v    v         i    vi  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_243737922_   3544 ACATCAA-GTTAAAAAGTTTCTGCACAGCAAA---TACAATCAACAAAGT 3589
                         v      -i       v   -  ii vv    ---i  v     v     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_243737922_   3590 TAAGAGACAACCCACAGAATAGGAAAAAATATTTGCAAACCACCTATCTG 3639
                         v  i                i   i              i  iv      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_243737922_   3640 ACAAGGAGTTAGTAACCGTAATCTATAAGGAGCTCAAACAACTCTATACA 3689
                          i    iii v   v  iv   v     i  i   vv       v   - 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-A 791

  chr1_243737922_   3690 AAAAAAAACTAATAATTTGATCAAAAGATGGGCAAAAGAGTTGAATAACC 3739
                         v     i  v     iiii  i?   i         i  v       iv 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_243737922_   3740 ATTTCTCAAAAGAAGACATACAAATGGAAAATAAGCATATGAAAAGGTGC 3789
                                v        i          vv        i        i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_243737922_   3790 T 3790
                          
  L1M4_orf2#LINE/    892 T 892

Transitions / transversions = 1.60 (139 / 87)
Gap_init rate = 0.01 (9 / 892), avg. gap size = 1.56 (14 / 9)  


2932 26.64 1.67 0.96  chr1_243751575_243755556.rev     2166  3002 (980)    L1M4_orf2#LINE/L1        1   843 (65)  

  chr1_243751575_   2166 TGGAAAAATAGTCCATGTTCATGGATTAGAAGAATTAATGTTGTTAAAAT 2215
                               i   vi               i     v     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_243751575_   2216 GTCCATGCGACCCAAAGCAATCTACAGATTCAATACAATCTCTATCAAAA 2265
                          v v  i vv      vii              ii     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_243751575_   2266 AACCAATGACATTCTTCAGAGAAATAGATAAATCAATCATAAAACTTACA 2315
                         vv   iivi v  i  iiv      v  i  iiii   v     i i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_243751575_   2316 TAGAACAATTAAAGACCCAGGATAGCCAAAGTTATCCTAAAAAAAAAGAA 2365
                          i   vviiv ii       i         iiv   i i     i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_243751575_   2366 CAAAACTGGAGGGATCACATTAACTGACTTCAAATTATACTAAAGAGCTG 2415
                             ii      iv     i vv ii i      viv     v i    i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_243751575_   2416 TAATAACCAGAACAGCATGGTACTGGCATAAAAACAGACACATAGACCAG 2465
                         i i   i  ii    ii              ii i     i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_243751575_   2466 TGGAACAGAATAGAGAACTCAGAAATGAATCCACACACCTGCAGTGAACT 2515
                              i     v    iii       i  i   i   ii iii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_243751575_   2516 CATTTTTAACAAAGGTGCCAGGAACATACACTGGAGAAA--AGAGTCTCT 2563
                         v     ii    i       i  v   v  v   i    -- v     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_243751575_   2564 TCAATCAATGGTCCTGGGAAAAACTGCATATTCATATGCAGAAGAATTAA 2613
                             iv      v      v  -   v   ?i  i     i      v  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_243751575_   2614 ACTAGAGCC-TATCTCTTGCCATGTA--AAAATCAAATCAAAATGGATTG 2660
                         ii i  v  -  i   vii    i  --     i  v           ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_243751575_   2661 AAGACTTAAATCTAAGACCTTAAACTAAGAAACTGCTATAAGAAAACATT 2710
                         ?    i     v     v  v      vi     vi  v          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_243751575_   2711 GGGG--AACTTGCAGGACATTGGTCTGGGCAAAAATACTTTTGA-GTAAT 2757
                           ? --  ii v iv   v    vi i     vii vii  v  -i i i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr1_243751575_   2758 ATCCACAAACACAGGCAACCAAAACAAAAATGGACAAGTTGTATCACATC 2807
                          -   v  i    i     v   iv      i  i  i   v iiv    
  L1M4_orf2#LINE/    600 A-CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_243751575_   2808 AAG-TTAAAAGGCGTCTGCACAGTAATGAAAACAATCAACAAAGTGAATA 2856
                           i-      i- v i  ii vvi  v i v  v     v        v 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr1_243751575_   2857 GACGAATCACAGGATGGGAGAAAATATTTGCAACCTACCCATAAGACAAG 2906
                            i vi     i                    vii ivi  vv  i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_243751575_   2907 GGGTTAATAACCAGCATATATAAGGAACTCAAATAACTC-----TAAAGG 2951
                           ii vi  v    v        i      vv i     -----    ii
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_243751575_   2952 GAAAAATGCAAAATCTGATTTAAAAAATGGGCAAAGTATTTGAATAGCCA 3001
                           v    ----  i ii   ?     -         v          v  
  L1M4_orf2#LINE/    798 GACAAAT----AACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chr1_243751575_   3002 T 3002
                          
  L1M4_orf2#LINE/    843 T 843

Transitions / transversions = 1.77 (140 / 79)
Gap_init rate = 0.01 (12 / 843), avg. gap size = 1.83 (22 / 12)  

 321 19.12 0.00 0.00  chr1_243751575_243755556.rev     3424  3491 (491)    L1M4_orf2#LINE/L1      841   908 (0)  

  chr1_243751575_   3424 CATTTCTTAAAGGAAGACAGACAAATGGCCAACAGGTATATAAAAACGTG 3473
                                iv  i     i v            i i i i  i    vi  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_243751575_   3474 GTCAACATCATTGATCAT 3491
                         v         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.00 (0 / 0)  


 596 17.15 9.71 20.39  chr1_243902239_243904222.rev      502   810 (1174)    L1M4_orf2#LINE/L1      278   553 (355)  

  chr1_243902239_    502 ATAAAAACAGACCCATAGACCAGTGGAA--------------CAGAAATA 537
                             ii i    vi     i  i     --------------        
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr1_243902239_    538 AACTCAAGTATATGCAGTCAACTAATTCTTTGACAAGGTCACCAAGAAGA 587
                            i  vii  v iii     i i   -  i       vii      vv 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATT-TTCGACAAGGGTGCCAAGACCA 376

  chr1_243902239_    588 CACAATGGAGAAAGGACAATCTCTTCAATAAA-GATGTTGGCTATAGAAG 636
                         iv      i     i i i   i     i   - i  i   ---------
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG--------- 417

  chr1_243902239_    637 TGTGAAAAAAAAATCAAGAAAAATATAAGATTTTGAAAAATTAAGCTTTT 686
                         ----------------------------  i-------------------
  L1M4_orf2#LINE/    418 ----------------------------GAC------------------- 420

  chr1_243902239_    687 GGTGAAACTGGATTTCCACACGCAAAAGAATAAAACTTGG---------- 726
                         -----        v?     i          i  i-    ----------
  L1M4_orf2#LINE/    421 -----AACTGGATAKCCACATGCAAAAGAATGAAG-TTGGACCCCTACCT 464

  chr1_243902239_    727 CACAC-----ACAAAAACCAACTCAAAATGGATTAAAGATCTAAACATAA 771
                              -----       ii              i ?   i     ii   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_243902239_    772 GATCTAAAACTGTAAAACTCCTAGAAGAAAATAGAGAAG 810
                           v        i        i          i v  i? 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

Transitions / transversions = 4.00 (40 / 10)
Gap_init rate = 0.03 (8 / 276), avg. gap size = 11.62 (93 / 8)  

1106 25.91 2.85 0.26  chr1_243902239_243904222.rev     1108  1493 (491)    L1M4_orf2#LINE/L1      513   908 (0)  

  chr1_243902239_   1108 AAAAACTAAA--TATAAAA-----AATAGAAAACAGAGGAGAAAA-CTTC 1149
                           i i     --       ----- iv        v   ? v   -    
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr1_243902239_   1150 TTGATATTAGCCTTGGCATGGATATTTTTAATGTCTCAACAAAAGCA-AA 1198
                         v   iv  i vi v    vv i v i  vi  i vv  v        -  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_243902239_   1199 GGAACAAAAGTAAAGATAAATAAGTGGGAATACATCAAAGTAAAAAGCTC 1248
                          v        v   i   i    i v   v v       i v    i  i
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr1_243902239_   1249 CTGTATAGCAAAAGAAACAATCAACAGAGTGAAAAGGTAGCCAACAAATT 1298
                         i   iivv    i  v  v     v i         ii i  v   i v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr1_243902239_   1299 GGAAGAAAATAGTTTTAAGCCATATATCAGATAAGTAGTTAATATGCAAA 1348
                           i        v  vi  ii        v      viii vi   v  i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr1_243902239_   1349 ATATGTAAGGAATTCACACAACTCAA-AGCATAAA-ACAAATAATCTGAT 1396
                             i   i   i  vi         - ii v   -        i ii  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr1_243902239_   1397 TTTTAAAATGAAGAAAGGAACTGAATAGACATTTCTCTAAAAAAGAAACA 1446
                          ?v-      iiv      vi                i   i    v i 
  L1M4_orf2#LINE/    813 TWA-AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr1_243902239_   1447 AAAATGGTCAACATGTATACAAAAAAGTGCTCAACATCACTAATCAT 1493
                         v      i   i v i i ii    ii            ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (57 / 41)
Gap_init rate = 0.02 (7 / 396), avg. gap size = 1.71 (12 / 7)  


2539 26.09 2.02 5.32  chr1_243963860_243965893      606  1544 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_243963860_    606 TGGAACAACATTCCATGCTCATTGGTAGGAAGAATTAAAACTGCTAAAAT 655
                              vi i  i     i    v i v      v    v i  i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_243963860_    656 GACCACACTGTCCAAAGTAAGTTATAGATTTAATGCTAATCTTATCAAGC 705
                          i v i   vi     v i vi  i     i  i  v vi i      iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_243963860_    706 CACCAATGACATTCTTCACTGAATTAGAAGAAACT-ATTTTAAAATTCAT 754
                         iv   iivi v  i  ii v   v v  v-  i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr1_243963860_    755 ATGAAATCAAAAAAGAGCTTGAATAGCAAAGGTAATCCTAAACAAAAAGA 804
                            i  viiv  ii  v iv       v  iii    i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_243963860_    805 ACAAAGCCATAGG---CA------------TCACAACTATATTGTAAGGC 839
                               iiiv   ---  ------------   v    -  i ii  i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr1_243963860_    840 TACAATCATCAAAACAGCATGGTACTGGTTCAAAAACAGATACAAGAAAC 889
                             i v     i    ii         ivi  ii i   i i -v i i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGAT 297

  chr1_243963860_    890 CAAAGGAACAAAATAGAGAGCCCAGAAATAACATTGCAAACCTACAACCA 939
                            v    i i   v     i          vviiii v ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_243963860_    940 TCTGATCTTTGACAATGCTGACAAAAACAAGCAATGGGGAAACGATTCCC 989
                         vi    i  i     v v  v   i v  vv           vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_243963860_    990 TATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGATTG 1039
                          v     i              i      v  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_243963860_   1040 AAACTGGACCCCTTCCTTACACCATATACAAAAATGAACTCAAGATGGAT 1089
                           ii         v   i                 v       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_243963860_   1090 TAAAGATTTAAATGTAAAACCTAAAACTATAAAATCCCTGGAAGATAACC 1139
                         i ?   ii         i v              ii i i     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_243963860_   1140 CAGA---AAATACCATTCTGGACATAAACCCTGGCAAAAATTTCATGACA 1186
                         i  i---    -- -   vv   v viiviiv     vii    v iivv
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_243963860_   1187 AAGATGCCAAAAGACACCAAACAATTATTGCTCTTTTTGCAATAAGAGCA 1236
                          v  ii       -   -  i   ---------------   -    i- 
  L1M4_orf2#LINE/    595 ATGACACCAAAAG-CAC-AAGCAA---------------CAA-AAGAA-A 625

  chr1_243963860_   1237 AAATTGACAAATGAGATCTAATTAAATGTAAGAGCTTCTGTATAGCAAAA 1286
                             v  i    vi  ii v  i   vv   i i   i   iivv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr1_243963860_   1287 GACTCTATAAACAGAGTAAACAGACAGCCTACAGAATGTGAGAAAATATT 1336
                            v    v  v i   i  v     i  i        v           
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr1_243963860_   1337 TGCAAACTATGTATATGACAAAAGGTCTAATATGAAGAATCCATAAGGAC 1386
                               ii  i   v   i  i-  v  vi   vv     vi    i  v
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAG-GGACTTGTATCCAGAATATATAAAGAA 774

  chr1_243963860_   1387 CTTAAACAAAGTTACAAGCAAAAAAAAACAAACAAACCCAAAAAACAAAG 1436
                           i--------      viv  v  v  ------------   i     -
  L1M4_orf2#LINE/    775 CTC--------TTACAACTCAATAATAA------------AAAGACAAA- 803

  chr1_243963860_   1437 AACAACCCCATTAAAAAGTGGGCAAAAGACATGAACAGACACTTTTCAAA 1486
                         --i     v   ?    i        i  iv    i     i  i  v  
  L1M4_orf2#LINE/    804 --TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr1_243963860_   1487 AGAAGACATACATGTGACCATTCAGCATATGAAAAAGTGCTCAACATACA 1536
                               i     vi  i   v v    i       ii          -  
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT-CA 900

  chr1_243963860_   1537 TGGGGCAC 1544
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.63 (69 / 19)  


2321 28.81 4.12 0.24  chr1_243997109_244004964.rev      514  1339 (6517)    L1M4_orf2#LINE/L1        1   858 (50)  

  chr1_243997109_    514 TGGAAACACATCCCATGCTCATGGATGGGTACAATTAATATTATGAAAAT 563
                               v i        i        v  v v v        i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_243997109_    564 GACCATACTGCCAAAAGCAGTCTACAAGTTCAATGCAATTCCCATCAAAA 613
                          i v     v  v   viii      ii     i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_243997109_    614 TACCACCATCACTCTTCCCAGAACTAGAGAAAACAATCCTAAAATTTACA 663
                          v   v vv vi i  iv     v v  v  ivii           i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_243997109_    664 TGGAAGCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 713
                              iiiv  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_243997109_    714 CAAATCTGGAGG---CATTGTTACCCAACTTCAAACTATACTATAAGGCA 760
                             vi      ---  ivv  -     i      viv     i  i  v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_243997109_    761 GTAGTCACCAAAACAGCATGATACTGGTATAAAAAATCGGGACATTGACC 810
                         ii   v i   i    ii  i      i    ii - v iv i  v  i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATC 298

  chr1_243997109_    811 AATGGAACAGAATAAAGAAACCGTAATTAAAGCTAAA----TACAGTCAA 856
                                i     vi   iv  iv  v    v i v ----  ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_243997109_    857 TTGATCTTCGACAAAGCAAACAAAAC-ATAAAGTGGG-AAAGGACACCCT 904
                              i        i vviv   i  -  vv i    -    i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_243997109_    905 GTTCAACAAATAGTGCTGGAATAATTGGCAAGCCACATGTA---GAATGA 951
                         v          i       i i  i   vv ?       i ---      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_243997109_    952 AACTGGATCCTCCTCTCTCGCTTTATACAAAAATAAACTCAAGATGGATC 1001
                          ii    i  iivi   v i iv           v       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_243997109_   1002 AAAGACTTAAATCTAAGACCTGAAGCCATAAAGATTCTACAAGATAACAT 1051
                          ?    i     v     v  i  i i     iv ii  v    v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_243997109_   1052 TGGAAAAACCCTTCTAGATACTGGCTTAGGCAAAGACTTCATGACCAAGA 1101
                         v  ?iv  vi    vv  ivi   v        v ii   v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_243997109_   1102 ACCTAAAAGCAAATGGAACAAAAACAAAGATAAATAGATAGCACTTAAGT 1151
                         vv i       v v v       iv   i   i   i  v v    v vi
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_243997109_   1152 AAACTAAAAAGCTTCTGCACAGCAAAAGAAA-TAGCAG---AGTTAACAG 1197
                            v v    i   i  ii vv    i  v -  v  i---   v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_243997109_   1198 ACAACTGACAGAGTAGGAGAAAATCTTCACAATCTATACATCCAAAAAAG 1247
                              iv     i i         v  ii   vii   i   ii v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_243997109_   1248 GACTAATATCTAAAATCTACAAAGAACTC----AAATCAGTGC----GAG 1289
                             vi    i i   v  i         ----  v   i iv----i  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_243997109_   1290 AGAAA----------AAAAAGTGGGCTAAAGACACGAATAGACAATTCTT 1329
                          v   ----------?    i     v  i  ivi         v    i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_243997109_   1330 AAAAGAAGAT 1339
                         v         
  L1M4_orf2#LINE/    849 CAAAGAAGAT 858

Transitions / transversions = 1.27 (131 / 103)
Gap_init rate = 0.01 (12 / 858), avg. gap size = 3.00 (36 / 12)  

3037 25.17 2.23 1.11  chr1_243997109_244004964.rev     6468  7365 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_243997109_   6468 TGGAGAAACATCCCATGCTCATGGATAGGAAGAATTAAT-TCGTGAAGAT 6516
                             i i i        i        v      v     - i  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_243997109_   6517 GGCCATACTGCCCAAAGTAATTTATAAAAGAATTCAATGCTATTCCCATT 6566
                            v     v      v i  i  i i ----     i  v  i  i  i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGA----TTCAACGCAATCCCTATC 96

  chr1_243997109_   6567 AAACTAC-AACTGACATTCTTCACATAATTAGAAGAAACT-ATTTTAAAA 6614
                            v v - i   v -  i  ii  v  v v  v-  i  -  ii     
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCC-TTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAA 144

  chr1_243997109_   6615 TTCAGATGGAACCAAAAAAAGAGCCCA-AATCGCCAAGATGTTTCTAAGC 6663
                             v      -- viv  i ii    -   v     i iiv ii i iv
  L1M4_orf2#LINE/    145 TTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr1_243997109_   6664 AAAAAGAACAAAGCTGGAGGTATCACACTACCCAACTTCAAACTATATTA 6713
                           i          i      vv       v     i      viv  i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr1_243997109_   6714 TAAGGTTACAGTAACCAAAATAGCATGATACCGGTACCAAAACAGACACA 6763
                         i  i i        i   i i  ii  i   i  i iv ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr1_243997109_   6764 TAGACCAATGGAACAGAAT--------CAGAAATAAGACCATACACATAC 6805
                             i        i     --------         iv       iv  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr1_243997109_   6806 CACCATCTGTTCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGAA 6855
                         vii  vi  v i  i     ivv  v   i v  vv              
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_243997109_   6856 T-TCCTTCTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGCAGAA 6904
                          -vi   i i  i              v      v  ?         i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_243997109_   6905 AACTGAAAT-GGACACCTTCCTTACACTTTAAACAAAAATTAACTCAAGA 6953
                         i v    i -    v   v   i    iv  v                i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_243997109_   6954 TGGATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCTTAGAAGA 7003
                              i ?    i    ii     v       i      vi         
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_243997109_   7004 AGATCCAGGCGGTACCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 7053
                          i ivi   ? vv viv   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_243997109_   7054 CTAAAACACTAAAAGCAATGGCCAAAAAAAGCCAAAATTGACAAATGGGA 7103
                         v  vi    i       vvi  -  v     vv     v  i    v   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_243997109_   7104 TCTAATTAAACTTAAGAGTTTCTGCACAGCAAAAGAAACTATCATCAGAG 7153
                         ii v  i   v    i ii  i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_243997109_   7154 TGAACAGGCAACCTACAGAATGGCAGAAAATTTTTGCAA-TC---CATCT 7199
                             v  i     i         v       v       -  ---i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_243997109_   7200 GACAAAGGTCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAA 7249
                           i  i  v  vi          v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_243997109_   7250 GAAAAAAACAGA-AACCCA-TCAAAAAGTAGGCAAAGGATATAAATAGAC 7297
                         v     i   i -      - i?    i i          v i       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_243997109_   7298 ACTTCTCAAAAAGAAGACATTTATGTGGCCATCAAACATATGAAAAAAAG 7347
                          i     v   -     i  vi vi      vi  i  i       i v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_243997109_   7348 CTCATCATCACTGGTCAT 7365
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (129 / 93)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.76 (30 / 17)  


 735 28.37 0.96 0.00  chr1_244056771_244063479.rev      300   507 (6202)    L1M4_orf2#LINE/L1        1   210 (698)  

  chr1_244056771_    300 TGGAAAAATATTCCATGTTCAAGGATAGGAAGAAGCAATATCATAAAAAT 349
                               i    i         v    v      vvi     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244056771_    350 GGAAATACTGCCCAAAGTAATTTATAGATTCAATGCTATTTCCATCAAGC 399
                           v      v      v i  i  i        i  v  ii i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244056771_    400 TCCC--CGACTTTCTTCGCAGAACTAGAAAAAACTACTTTAAATTCCATA 447
                             -- vi i  i  i      v v  v  iviv iii    v i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_244056771_    448 TGGAACCAAAAAAGAGCCTGTTTAGCCAAGACAATCCTAAGCAAAAAGAA 497
                              viiv  ii  v  v vv       i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_244056771_    498 CAAAGCTGAA 507
                              i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGA 210

Transitions / transversions = 1.46 (35 / 24)
Gap_init rate = 0.00 (1 / 210), avg. gap size = 2.00 (2 / 1)  

3109 26.35 1.10 0.99  chr1_244056771_244063479.rev     5312  6218 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244056771_   5312 TGGAAAAACACTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5361
                               i i ii     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244056771_   5362 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 5411
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244056771_   5412 TACCA-TTGTCTTTCTT-CACATAATTAGAAAAAAAGCT--TCTTTAAAT 5457
                          v   -i  i    i  -  v -    i---- v     --  i v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG----ACAAGCTGATCCTAAAAT 145

  chr1_244056771_   5458 TTCATATGGAAACAAAAAAGTGCCCATA-TAGCCAAGACAATCCTAAGCA 5506
                          -          iiv  ii -i    v -       i      i i iv 
  L1M4_orf2#LINE/    146 T-CATATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_244056771_   5507 AAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTAC 5556
                          i          i      vv    i  v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_244056771_   5557 AAGGCTACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGATATAT 5606
                           i          i   i    ii        vi iv ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_244056771_   5607 AGACCAATGGAACAGAACAGAGGCCTCAGAAATGACACCACACAGCTACA 5656
                            i        i    iv   ivii       i vv   i   vi  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_244056771_   5657 ACCATCTGATCTTTGACAAACCTGAGAAAAGCAAGCAATGGGGAAATGAT 5706
                         ii  vi    i  i     ivv  vv  i v  vv           vi  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_244056771_   5707 TCACTATTTAATAAATGATGTTAGGAAAACTGGCTAGCCATATGCAGAAA 5756
                         vvv  v  i  i     i  i i   v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr1_244056771_   5757 ACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGTT 5806
                          v    ii         v   i     v                   iv 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr1_244056771_   5807 GGATTAAAGATTTAAATGTAGGACCTAAAACCATAAAAACCCTAGAAGAA 5856
                             i ?   ii        i  v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr1_244056771_   5857 AACTTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCTTGA 5905
                            v i  ?i- v i -   iv   v v  vv i     v ii     ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_244056771_   5906 CTAAAACACCAAAAGCAATTGCAACAGAAGCCAAAATTGACAAATGGGAT 5955
                         v  vi            vvv      i   vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_244056771_   5956 CAAATTAAACTAAAGGGCTTCTGCATGGCAAAAGGAACTATCATCAGAGT 6005
                         ivv  i   v v  iii   i  iiivv    i iv       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_244056771_   6006 GAACAGGCAATCTACAGAATGGGAGAAAAATTTTGCAATCTATCCATCTG 6055
                            v  i   i i                vv       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_244056771_   6056 ACAAAGAGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAG 6105
                          i  i ii  vi          v  i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_244056771_   6106 AAAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACA 6151
                              i    ----   v  i?    i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_244056771_   6152 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACATAAGAAAAAAAAGC 6201
                         i     v        i  vi viii     v  i  i v     i v-  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GC 891

  chr1_244056771_   6202 TAATCATCACCAGTCAT 6218
                          v v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


1911 28.69 1.99 3.41  chr1_244084121_244085810      494  1197 (493)    L1M4_orf2#LINE/L1      215   908 (0)  

  chr1_244084121_    494 TCATATTACCTAACTTCAAACTATACTATAAGGCTACAGTAACCAAAATG 543
                            i i v  i  i      viv     i  i          i   i ii
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_244084121_    544 GCATGGTACTGGTACATAAACAGACACATAGGCCAGTGGGACAGAATAGA 593
                          ii         i i vii i     i    ii  i   i i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_244084121_    594 GAACCTAGAAATAAATTCACGAACCTGCAACTATCTGATCTTCAACAAAA 643
                           ii i         ii  iiv ii iiiiii vi    i   i    ii
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_244084121_    644 TCAATAAAAATAAGCAGTGGGAAAAGGACTCCCTAGTCAATAAATGGTGC 693
                         viivi  i vi vv  i    i    i ivvi  vv    i         
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr1_244084121_    694 TGGTATAACTGGCTAACCACATGCAGAAGAAGGAAACTGTACCCCTACGT 743
                            v i      v  ?         i     v   ii  v        v 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr1_244084121_    744 TTCACCACATACAAAAATTAAATCAA----GATTAAAGACTTAAATGTAA 789
                         iv     i             v    ----   i ?    i         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr1_244084121_    790 G--TTCAAACTATAGAAATCCTAGAAAAAACCCTAAAGA-ACACCATTCT 836
                          --i v        i  v  i     i   v v  ii?i- v i v iv 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr1_244084121_    837 GTACATCAGTCTTGGCAAAGAATTTATCACTAAGTTCCCAAGAGCAATTG 886
                          -  v ii vi v     v iv  iv viv  v viv    i    vvv 
  L1M4_orf2#LINE/    565 G-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr1_244084121_    887 CAACAAAACAAAACATTTACAAGCTGAACCTAACTATACTAAAGAGCTTC 936
                                 v    v  vv i  ii  i  i v ii v v v  i i   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr1_244084121_    937 TGAACAGCAAAAAAAAAAAAAAAAAAAAAAAATTACCAACAGGGTGAACA 986
                           vi vv    ii v ----------------i  i   v ii     v 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACA----------------CTATCAAGAAAGTGAAAA 697

  chr1_244084121_    987 GACAATCTACAGAGTGAGAGAAAATATTCACAAACTGTGCATTTGACAAA 1036
                              i i     i  i           ii    iii ii  i   i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr1_244084121_   1037 GGTCTTATATCCAGAATCTACAAGGAACTT----AAATCAACAAGCAAAC 1082
                           v   i          v  i  i     i----  v    i  vv   v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_244084121_   1083 CACCCCCCCAAAAAAATCCAATT-AGAAATGGGCAAAGGACATGAACAGA 1131
                         v  -------   v  i      - i              iv    i   
  L1M4_orf2#LINE/    798 GAC-------AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr1_244084121_   1132 CATGTCTCAAAAGAAGACATATGAGCAGCCAATAA--ACATGAAAATGTG 1179
                            v    v        i   ii iii        --         vi  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr1_244084121_   1180 GTCAACATTACTAATTAT 1197
                         v       i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (128 / 71)
Gap_init rate = 0.01 (9 / 694), avg. gap size = 4.22 (38 / 9)  


3334 25.06 1.67 0.56  chr1_244096967_244101338     2982  3879 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244096967_   2982 TGGAAAAATATTTCATGTTCATGGATTGGAAGAATCGATATTGTTAAAAT 3031
                               i    ii                    v ii          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244096967_   3032 GTTCTTACTACTCAGAGGAATCTACAGATTCAAAGCAATCCCTATGAAAA 3081
                          vivv    v i  i vvi              v           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244096967_   3082 TACCAATGACATTCTTCACAGAAATAGAAAAAA-AATTATAAAACTTATA 3130
                          v   iivi v  i  ii       v  v  iv-i  iv     i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_244096967_   3131 TGGACCCACAAAAGACCCAGAATAACCAAAGCTATATTAAGCACAAAGAA 3180
                             vvii   ii           i     i v  v  i iv vi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_244096967_   3181 TAAAACTGGAGGAATCATATTACCTGACTTCAAATTATACTATAGTGCTA 3230
                         i   ii       v   i i v  ii i      viv     i iv    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_244096967_   3231 TAGTAACCAAAACAGCATGGTACTGGCACAAAAACTGACACAAAAATCAG 3280
                         i     i   i    ii           i  ii iv    i v i    i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_244096967_   3281 TGGAACAGAATAGAGAACACAGAAACAAATTCACACATGTACAGTGAACT 3330
                              i     v    iiv      i   ii  i    v  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_244096967_   3331 CATTTTCAACAAAGATGCCAAGAACATTCACTGGAAAAAGA-CAATCTCT 3379
                         v      i    i i        v      v   ii     -i i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_244096967_   3380 TCAATAAATGGCCCTGGGAAAACTGGATATCTACATTCAGAA-AATGAAA 3428
                             i      iv      v         ? i    v  i  -      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_244096967_   3429 CTAGACCCCCATCTCTCATCATATACAAAAATCAAATCATAAT----CA- 3473
                         i i      i i   v  i             i  v   v   ----  -
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_244096967_   3474 AGACTTAAATTTAAGACGTCAAACTATAAAACTACTACAAGAAAACATTG 3523
                             i     v     vv v             vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_244096967_   3524 AGGAAAATCTGTAGGACATTTG-TTGGGCAAAGATTTCTCTAGCAGTAAC 3572
                         i? v      viiv   v  v -  i     v i     -   vvi i  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT-TAGATATGAC 599

  chr1_244096967_   3573 ATCCCACAAGCGCAGGCAACCAAAGCAAATGTGGACAAATGGGA--TCAC 3620
                          --   v    i  i     v    v   vi i  i    v   --   i
  L1M4_orf2#LINE/    600 A--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr1_244096967_   3621 AGAAAGTCAAAATGCTTCTGCACAGCAAAGGATGCAATCAACAAACTAAA 3670
                         vi   v v    --   i  ii vv       ii v     v   v i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_244096967_   3671 GAGACAACCCACAGAATGGGAGAAAATATTTGCAAACTACCCA-CTGACA 3719
                         i                                   ii ivi -    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_244096967_   3720 AAGGGTTAATAATCAGAATACATAAGAAGCTCAAACACCTCTATAGGGAA 3769
                          i  ii vi  vi       i    ii i   vv   v   v   ivi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_244096967_   3770 AAATTTAATAATCTGATCAAAAGATGGGCAAAAGATTTCAATAGATATTT 3819
                           iviv     i ii  i?   i         i     v      i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_244096967_   3820 CTCAGAAGAAGACATACAAATGGCAGACAGGTATATGAAAAGGTGTTCA- 3868
                            vi       i           vi i i i i        i  i   -
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_244096967_   3869 --TCAGAGAAATG 3879
                         --   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (139 / 83)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


2802 27.13 1.20 1.86  chr1_244119297_244125148.rev     4448  5361 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244119297_   4448 TGGAAAAACATTCCATGCTCATGGATAGGAAAAATCAAGATCATGAAAAT 4497
                               i i  i     i        v    i v i  v  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244119297_   4498 GGCCATACTGCCCAAAGTAATTTATAGATCCAATGCTATCCCCATCAAGC 4547
                            v     v      v i  i  i    i   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244119297_   4548 TGCCA-CTGACTTTCTTCACAGAA-TTGGAAAAAAAAAAAAACT-ACCTT 4594
                          v   -   v    i  -i     -   --------- v  i  - i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---------ACAAGCTGATCCT 140

  chr1_244119297_   4595 AAATTTCATATGGAACCAAAAAAGAACCCACATAGCCAAGACAATCCTAT 4644
                            v           viiv  ii  v  viv        i      i iv
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_244119297_   4645 GCAAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATAC 4694
                         iv  i          i      vv   ii  v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr1_244119297_   4695 TACAAGGCTACAGTAACCAAAACAGCATGGCACTGCTACCAAAACAGGTA 4744
                              i          i   i    ii   i    vi iv ii i  ii 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr1_244119297_   4745 TACAGACCAATGGAACAAAAC--AGAGCCCTCAGAAATAACACCACACAT 4792
                           i   i        i i  i--    i  --        vv   i    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACAT 338

  chr1_244119297_   4793 CAACAACTACCCGATCTTTGACAAACCTGACAAGAACAAGCAATGGGGAA 4842
                         iv iiiii vii   i  i     ivv  v     v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr1_244119297_   4843 AGGAT--TCCATATTTAATAAATGGTGTTGGGACAAATGACTAGATATAA 4890
                           i  --  -- v  i  i        i        v  iv  ?vi i v
  L1M4_orf2#LINE/    389 AGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_244119297_   4891 GCAGAAAGCTGAAACTGGATTCCTTCCTTACACCTTATACAAAAAAATAA 4940
                            i  iiv    ii    ii   v   i     v          v-   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAA 485

  chr1_244119297_   4941 CTCTAGATGGATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCC 4990
                            v i      i ?    i    ii     v       i      vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr1_244119297_   4991 TAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGA 5039
                                    v    ?i- v i -   iv   v v  vv i     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr1_244119297_   5040 CTTCATGACTAATACACCAAAAGCAATGACAACAAAAGCCAAAATTGACA 5089
                         i   v iiv  vv            vvii         vv     v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr1_244119297_   5090 AATGGGATCTAATTAAACTAAAGAGTTTCTGCACAGCAAATGAAACTATC 5139
                            v   ii v  i   v v  i ii  i  ii vv    v  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr1_244119297_   5140 GTCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAACTTTTGCAATCTA 5189
                         ivv i      v  i     i                iv       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_244119297_   5190 TCCATCTGACCAAGGGCAAATATCTCAAATCTACAAAGAACTTAAACAAA 5239
                          vi      iv i  i vvi    ivi   v  i        ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_244119297_   5240 TTTACAAGAAAAA---AAACAACCCCATCAAAAAGTGCACCAAGGATATG 5286
                          iv i  v     ---   i     v  i?    i  vi v      v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_244119297_   5287 AACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAA 5336
                           i     i     v        i  vi viii     i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_244119297_   5337 AAAAAAGCTCATCATCACTGGTCAT 5361
                           i v-     v     ????????
  L1M4_orf2#LINE/    885 AAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  


2384 24.63 4.60 1.76  chr1_244145619_244148125.rev      656  1394 (1113)    L1M4_orf2#LINE/L1        1   760 (148)  

  chr1_244145619_    656 TGGAGACATATTCCACATTCATGCATTAAAAGGCCTGATATTGTCAAGAT 705
                             i v    i   ii      v   ii   i i i       i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244145619_    706 GTTGGTTCTTCC-AACTTGATCTATAGATTCAATGTAATCCCACTCAAAA 754
                          viii v  i  -  v        i        i i      vv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244145619_    755 TCCCAGCAAGTGACTTTGTATTT------ATTAAGAAACTTTTCCTAATA 798
                                ---  v    ---   ------   i v  i  vv      v 
  L1M4_orf2#LINE/    101 TCCCAGC---TGCCTTT---TTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr1_244145619_    799 GCTAAAGGAAGAAACAAAAGACCCAGAACAGCTAGAGCAACAGTGAAAGA 848
                         vii v v i i vi   ii         i   i i i   ivv     i 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_244145619_    849 GAATAACAAAGTTGGAGGACTTATACTACCTGAATTTGACATTTATTATA 898
                            v                 i i   v  ii v  ii v i   i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_244145619_    899 AAACTACAGTGATGAAGACAGTGTGGTATTGCTA-----ATAGACAAACA 943
                           i       i  v              i  vi -----       v i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_244145619_    944 GATTAACAGGAGAGGCT--AGAGCCCAGAAATAGTCCCACGTACAT--AT 989
                            i  ii i v  iv --    i         iv    --     --  
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTAT 342

  chr1_244145619_    990 AGTCAACAGATATTTGACAAAGAAGCAAAGGCAGTAAAACAGAGCAATAA 1039
                         i     iv   v  i     i iv  v   i vi vv  ii i v  v  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr1_244145619_   1040 TAGTCTT--CAACAAATGGTGCTCAAACAACTGCATATCCACGTGCAAAA 1087
                                --              vii       v   ?    i       
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_244145619_   1088 -AATAAA--TAGACATAAACCTTAAGTCCTTCACAAAAAGTAACTTAAAA 1134
                         -   i  -- i   vivv    i vii v vi       v     i    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_244145619_   1135 TGAATCACAGACTTAAATATAAAATGC-AAAACTATAAAACCCT---AAG 1180
                           i    ?    i     i   i -  -             i  ---   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAG 541

  chr1_244145619_   1181 ATGACATAGGGGAAAACCTAGATGATGTTGGGCATGGCGATAACTTTTTT 1230
                          vi       ? v   i  vvi   iv     ivv   i  ii-   i  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTT 590

  chr1_244145619_   1231 AGATAAAACAC-AAAAGCCACAATTCATAAAATAAATCATTGA-AAATTC 1278
                              vi    -      -    viv i    v   vv  v  -     -
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATT- 638

  chr1_244145619_   1279 AAACTTTATC----TTAAAGAAATCTGCTCTGTGAAACACAATGTCAAGA 1324
                         ii    i   ----     i vv i  iv  vii  iv   v i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_244145619_   1325 GGATGAGAAGACAAACCACACACTGGAAGAAAATATTTGACAAA-AATAC 1373
                         iii   i       v     v v   i            -    -v   i
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG-CAAATCATAT 737

  chr1_244145619_   1374 ATCTGATAAAGAACTT--ATCCA 1394
                                  i i    --     
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCA 760

Transitions / transversions = 1.56 (109 / 70)
Gap_init rate = 0.03 (23 / 760), avg. gap size = 2.04 (47 / 23)  

 564 20.86 0.72 0.00  chr1_244145619_244148125.rev     1879  2017 (490)    L1M4_orf2#LINE/L1      769   908 (0)  

  chr1_244145619_   1879 AAAGAACCCTTAAAACTCAACAATAAGAAAACTAACAACATAATT-AAAA 1927
                                i    v       i     i  i  v  i   vi    -    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr1_244145619_   1928 ATGGGCCAAGTACCTTAAGTGACACCTCACCAAGGAAGAAATATAGATGG 1977
                               v   v ii v  vv    ii  v    i     v   i i    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr1_244145619_   1978 CAAATAAGCATATGAGAAGATGCTCCATATCGTATGTTGT 2017
                          v        i    i         v i   i????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (17 / 12)
Gap_init rate = 0.01 (1 / 140), avg. gap size = 1.00 (1 / 1)  


2313 25.79 1.65 1.35  chr1_244173061_244182295      492  1158 (8077)  C L1M4_orf2#LINE/L1   (0)   908   240  

C chr1_244173061_   1158 CTACAAAGCTATAGTCATCCAAACAACAACTTACTGACATAAAAACAAAC 1109
                                    i   v   v i   iiivvv     i     ii i i  
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

C chr1_244173061_   1108 A----GATCAATGGGGCAGAATAGAGAGCCCAGCAATAAATACATGTATT 1063
                          ----         iii     v     i    v      iv   ii   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

C chr1_244173061_   1062 TATAGCCAATTGATTTTTGACAAATATGTCAACAACACACAATGGGGAAA 1013
                            i i           i     ivi  i   v v  iv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

C chr1_244173061_   1012 GGGCGGTCTCTTCAATAAATGTTGCTGAGAAAACTAGATATCCATATGCA 963
                          iiii    i     i     v     i  v    i    ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

C chr1_244173061_    962 AAAGAATCAAGTTAGAGCCTTATCTTACACTGTAAGCAAAAATTAATTCA 913
                                v     i  v  i  i  i    ii  vi          i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

C chr1_244173061_    912 AAATAGATTATACTCACAAAGGTAAAAGTTAAAACAGTAAAAGTACAAAA 863
                             i   i ? vv vi   v    i  i      vi     v viv i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

C chr1_244173061_    862 AGAAAACATAAGAGAAAAGTGCCATGAAATTGGTCTTGGCAATGACTTTC 813
                                   i ? v   vivi i   vv    vi v       i-    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTC 588

C chr1_244173061_    812 TTGGATTTGATCCTAAAATTGCAAACAACAAAAACAAAAATA----AATG 767
                           i   v   iv i    vii   i        iv       ----   v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

C chr1_244173061_    766 TGATTGCATCAAGCTACAAAGCTTGTAAACAGCAGAGGAAACAATCAGCA 717
                         v  i v      iv vv   i   v ivi vv  i    v  v    iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

C chr1_244173061_    716 --GTGAAGAGACAACCTATGAAATGGAAAAAACTATTTGAAAATCATACA 669
                         --     i        i iii     i i   v      v        i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

C chr1_244173061_    668 TTTGATAAGAGG-TTAAAGCCAAAAATATCTAAGTAACTCAAATAATTCT 620
                          i       i i-  iv v   i  -   v   iv     vv i  i  v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAA-TATATAAAGAACTCTTACAACTCA 787

C chr1_244173061_    619 ATAGTGAAAAAGAAAAAAACAAATAACTCAGTTAAAAAATGGTCCAAGGA 570
                            i -------     i         i  i  ?        v v     
  L1M4_orf2#LINE/    788 ATAAT-------AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

C chr1_244173061_    569 TCTGAATAGATATCACTCAAAAGAAGTCATGCATATGGCCAATTGATATA 520
                          i        i  iv   v       vi  i  v         viii i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

C chr1_244173061_    519 TGAGAAACTGTTCAACATTATTAAGCAT 492
                            i  iv  i       i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (102 / 66)
Gap_init rate = 0.01 (7 / 669), avg. gap size = 2.86 (20 / 7)  

3340 26.54 0.44 0.44  chr1_244173061_244182295     7835  8742 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244173061_   7835 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 7884
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244173061_   7885 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGT 7934
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244173061_   7935 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 7982
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_244173061_   7983 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 8032
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_244173061_   8033 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 8082
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_244173061_   8083 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 8132
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_244173061_   8133 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 8180
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_244173061_   8181 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 8230
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_244173061_   8231 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 8280
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_244173061_   8281 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 8330
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_244173061_   8331 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 8380
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_244173061_   8381 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 8430
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_244173061_   8431 AACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGGGATCTAA 8480
                         i            vvi         ivv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_244173061_   8481 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 8530
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_244173061_   8531 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 8580
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_244173061_   8581 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 8630
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_244173061_   8631 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 8680
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_244173061_   8681 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 8730
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_244173061_   8731 ATCACTGGCCAT 8742
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2216 22.58 6.91 2.00  chr1_244243774_244245412      497  1147 (492)    L1M4_orf2#LINE/L1      226   908 (0)  

  chr1_244243774_    497 AATTTTAAAATGCAATAAAAAGATACAGTAATCAAAAATGGCATGGTACT 546
                              i    ivi v  v    v            i -ii ii       
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACT 274

  chr1_244243774_    547 GGCATAAAAATAGACACATAGA-------AATA-AATTGA---------- 578
                                ii       i     -------    -      ----------
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr1_244243774_    579 ---------TACATTCATGGTCAATTGATCTTTGACAAAGGTGGTAGGGA 619
                         ---------      i             i  i     i    vi i iv
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr1_244243774_    620 CACACAATATGGAATGGACCATCTCTTCAATAAGTGGTTTTAGAACAACT 669
                           iv    iv    v i ivi   i     i  i    vi i i      
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr1_244243774_    670 GAATATCCATATGGAGATGAATGGAATTGGACCCTTATCTGACACCATAT 719
                          i   ?   i   v i v     i i        i  i  v         
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr1_244243774_    720 ACAAAAATCAACACAAAATATATTAAACACATAAACAGAAGACCAGAAAC 769
                                 i   v      iv  i ? v  v    iiv    v vi    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr1_244243774_    770 TATAAAACTAATAGAAGAAAGCACAGGGGGAAAGCTCTATGACATTGG-- 817
                                  vv         i  i   ? v   v  iii    v    --
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr1_244243774_    818 TATGCATGATAATCTTTTAGATATGACTCC-----CACAATTGACAAAAC 862
                           v   --  ii i i           v  -----     vii      v
  L1M4_orf2#LINE/    575 TAGGCA--ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr1_244243774_    863 TAAAATTA-ACAAGCGCTAGTAAATT------AAACTAAAAGTCTTT-TA 904
                         v    v  - i  ----- v ii i ------   i     iii   - i
  L1M4_orf2#LINE/    623 AAAAAATAGATAA-----ATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr1_244243774_    905 CAGCAAAGGTAACAACCAACAGAATGAAGAGATGACCTACAAAATGGGAG 954
                          vv      vv  v i   v i i    i   ii   i   i        
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr1_244243774_    955 AAAATATTTGCAAATCATACATCTGATAAGGAGTTAATATTCAAAGTATA 1004
                                            i           iii vi   i  i i    
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr1_244243774_   1005 TAAGGAGTTCAAATAACTCAGTAGCAAAAAACTGCCAAATAACACAATTT 1054
                            i  ii  vv i      i  ii     --- v        v     ?
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAA---GACAAATAACCCAATTW 814

  chr1_244243774_   1055 TTAAAAA-GAGCAAAGTACTTGAATAGACATTTCTCACAAGAAGACATTC 1103
                         --     - i      v i                 vv       i  v 
  L1M4_orf2#LINE/    815 --AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr1_244243774_   1104 AAATTGCCAACAG--ATATGAAAAAATGCTCAAAATCGTTATTCAT 1147
                             v     i i-- i       i        v   i????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (93 / 50)
Gap_init rate = 0.02 (15 / 683), avg. gap size = 3.87 (58 / 15)  


1026 27.68 11.61 1.79  chr1_244254120_244255671.rev      502  1061 (491)    L1M4_orf2#LINE/L1      294   908 (0)  

  chr1_244254120_    502 AGATCAATGAAACAGCATAGAGCATCCAGAAAGAGGCTGATACATTTATG 551
                                  i  i  v  v   vi        v ii iv           
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_244254120_    552 ATCAAAATATTGTCAAGAAAGACATCAAAGCTATT-----GGAAAA---- 592
                         i    vvv   v  i v  i iiii   ii i   -----  i   ----
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr1_244254120_    593 --TCTCTTCAAAATATTATGTTGGAAAAACTGTATATCCATATTGGAAAA 640
                         --   i     v v  vi  i   i v     v   ?   i  - v    
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-GCAAAA 442

  chr1_244254120_    641 AAACTA--TTA-ACTACTACCTCATACTGTACACAT---TTAATTTGAGA 684
                         i  iv --  i-  iv        i  ii  i   v---    i ii i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr1_244254120_    685 GAAATCATAGAGTTGAGCATAAAATGTAAAATTCTAAGGTT-TTAGAAGA 733
                         vii    ?   vi i iii   i vv     i v   iii -        
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr1_244254120_    734 AAGCA---------------GTG-----GGGT-ACGCAAAAACTTCTTTT 762
                           i  ---------------   -----    - v    viii     --
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-- 590

  chr1_244254120_    763 AAA---GACACAGAAAGCACTAATCTTAACCAAAATGATAAAATTGACA- 808
                          i ---     vi       -  v --   -    -  v     v  i -
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCAC-AAGC--AAC-AAAA-GAAAAAATAGATAA 635

  chr1_244254120_    809 ---GGAT---------ATTAAATATATATGCATATCAATAGACG-TATTG 845
                         ---   i---------      v iv v  iiiv    vi   i-   i-
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC- 684

  chr1_244254120_    846 AAGAAAACAAAAAGGCAAGCCAC----TGTGGGAAAGTATTAACACA-CG 890
                               iii     i   v    ----  v i    i    vi  v - i
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr1_244254120_    891 TGTATTTAATCATGGATTTGTGTTCTAAATGTATATTGAACTCCTGCAAT 940
                          i   i i  v v   i    i i vi   i    vv      i i   i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr1_244254120_    941 ACAATAGTAAT--GACAAAGAATCAAGTTAAAACACGAAAAAACAGACTT 988
                         v     i   v--      v  i v i  ?   v i iiv   -i  i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA-GGATTT 833

  chr1_244254120_    989 GAA-AGACACTTAACACAACATAATATACAAATGTCCAATAAGCA-ATGA 1036
                            -     i  vv vv  v vi           v          -    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr1_244254120_   1037 AATAAAGCTTAATATCATCTGTAAT 1061
                           vi v   i  i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (93 / 59)
Gap_init rate = 0.04 (26 / 615), avg. gap size = 2.88 (75 / 26)  


3208 27.21 0.88 0.44  chr1_244377916_244384181.rev     4872  5775 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244377916_   4872 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4921
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244377916_   4922 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4971
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244377916_   4972 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5019
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_244377916_   5020 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5069
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_244377916_   5070 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5119
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_244377916_   5120 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5169
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_244377916_   5170 AACGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCTTACCTACAACT 5217
                           i    i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_244377916_   5218 ATCTGATCTTTGACAAACCTGAGAAAAACAAGGAATGGGGAAAGGATTCC 5267
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_244377916_   5268 CTTTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5317
                              i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_244377916_   5318 GAAACTGGATCCTTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5367
                            ii    i  i v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_244377916_   5368 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5417
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_244377916_   5418 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5467
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_244377916_   5468 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5517
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_244377916_   5518 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5567
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_244377916_   5568 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5617
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_244377916_   5618 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5667
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_244377916_   5668 AAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5713
                          i    ----   v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_244377916_   5714 TCAAAAGAAAACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5763
                           v      i i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_244377916_   5764 ATCACTGGCCAT 5775
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2617 28.34 1.76 1.65  chr1_244401585_244403531      551  1457 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244401585_    551 TGGAAAAACATTCCATGCTTCTACATAGGAAGAATTAATATTGTTAAAAT 600
                               i i  i     i iv iv  v      v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244401585_    601 GCCCATACTGTACAAAGCAATTTACAGATTCAATGCTATTTCTACCAAAG 650
                          v v     viv    vii  i           i  v  ii   i    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244401585_    651 TACCAA-TGTCATTTTTCACAGAATTAGAAAAAACTAATCTAATGACCAA 699
                          v   i-  i -     ii     v v  v  i-  i   iv -----  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTA-----AA 143

  chr1_244401585_    700 ACTAAC-TGAAAGGTCAAAACTAACC--GAATGGCCATATCAATCTCAAG 746
                          i v i-  i  ivv   ii--i   --    i    v v      ii i
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAA 191

  chr1_244401585_    747 CCAAAAGAAAAGAGTTGGAGGAATCACACTCTCAGATTTCAAACTGTACT 796
                         vv i     v i          v       ii vi        viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr1_244401585_    797 ACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACTT 846
                             i          i   i    ii         i i  ii i    v 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr1_244401585_    847 ATAGACCAATGGGACAGCTTAGAAAACCCTGACACAAAGCTGCACACCTA 896
                              i      i i  vv v  i ii  v  v i   v iii   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr1_244401585_    897 TAACCAACTGATCT--GACAAAGTCGACAATAACAAGCAATGGGGAAAGG 944
                          iii   i    i --     i vi v   v v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr1_244401585_    945 ATTTTCTGTTCAATACA-GACTTCAGGATAACTGGCTAGCCATATGCAGA 993
                           vv   v     i v - iiviii   i      v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_244401585_    994 GGATTGAAACTGGATGTCTTTATTTCAC--CATGTACAAAAATCAACTCA 1041
                         i  v    ii    i-- ii  ii    --   i         i      
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGAC--CCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_244401585_   1042 AGATGGATTAAAGACTTAAATGTAAAACTTAAAGATAAAAAAACTCT-AG 1090
                          i      i ?    i         i vi    - iv v        -  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAA-ACTATAAAACTCTTAG 538

  chr1_244401585_   1091 AAGAATACCTACGGAAATACCATTCTGGACATAGGCCTTGGCAAAGGTTT 1140
                              v  v  v ?iv v i -   vv   v v  vi v     v     
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr1_244401585_   1141 CGCAAGGAAGACTCCAAAAGCAATTGCAACAAAAATAAATATTGGCAAGT 1190
                          vi iiv v   v         vvv         iv   v  v ii  i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr1_244401585_   1191 GGGACCTAATTTAA-CTAAAGGCCTTCTAACAGCAAAAGAAACTATAAAC 1239
                         v    i v  iv  -i    ii i  ivvi vv    i  v     v  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr1_244401585_   1240 AGAATAAACAGACAATGTAGAGAATGGGAAAAAAT--TTGCAAACCATGT 1287
                          i i i  v      ivi v         i     --       i   i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_244401585_   1288 GTCCAACGAAGGTTTAATATCCAGAATCTATAAGGAACTTAAACAAATCA 1337
                         i  ii ii i  vi vi          v     i     ivv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr1_244401585_   1338 ACAAGCCAAAAAAAGGAAT--TCCA-TTAAAAAATAGGCAAAGGGCAGGA 1384
                          i  --i     i vi   --i   -  ?      i        iivv  
  L1M4_orf2#LINE/    788 ATAA--TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr1_244401585_   1385 ACAGACACTTCTCAAAACAAGACATATGTGTGGTCTACAAGCATATGGAA 1434
                          i     i     v   v    i   iivi   i v i     i   i  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_244401585_   1435 AAATGCTTATCACTAATTATTAG 1457
                          i     i v  ii ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (154 / 99)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.63 (31 / 19)  


3104 26.83 1.44 0.78  chr1_244444543_244450930.rev     4996  5897 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244444543_   4996 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5045
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244444543_   5046 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244444543_   5096 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_244444543_   5144 TATGGAACCAAAAGAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5193
                                viiv   i  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_244444543_   5194 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5243
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_244444543_   5244 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5293
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_244444543_   5294 AATGGAACAGAA--GAGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5341
                                i    --     i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_244444543_   5342 CTCTGATCTTTGACAATCCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5391
                         vvi    i  i     vvv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_244444543_   5392 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5441
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_244444543_   5442 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5491
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_244444543_   5492 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5541
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_244444543_   5542 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5591
                         v    ?i v viv   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_244444543_   5592 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5641
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_244444543_   5642 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5691
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_244444543_   5692 AGGCAACCTACACAATGGGAGAAAATTTTTGCAATCTACTCATCTGAAAA 5741
                           i     i   v             v       vii ivi      v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_244444543_   5742 AGGGCTAATAATATACAGAATCTACAATGAACTCAAACAAATTCACAAGA 5791
                         i  i  -- i-   v      v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    747 GGGACT--TG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_244444543_   5792 AAAAAACAA----TCCCATCAAAAAGCAGGCGAAGAATATGAACGGACAC 5837
                             i    ----i  v  i?    iii   i   i  v    ii    i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_244444543_   5838 TTCTCAAAAGAAGACATTTATGCAGCCAA-AAGAA----AAAAAATGCTC 5882
                              v        i  vi viii     -   v ----    i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_244444543_   5883 ATCATCACTGGCCAT 5897
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


 252 28.40 0.00 2.47  chr1_244542552_244547422.rev      437   517 (4354)    L1M4_orf2#LINE/L1        1    79 (829)  

  chr1_244542552_    437 TGGAAATGCATCCTATATATTTATCAATTGGAAGGGTTAATACTGTTAAG 486
                               vii    i  i -- i  vi        iv      i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGT--TCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr1_244542552_    487 ATGTCAACAACAGCCAAAGTCACCCATTGAT 517
                            v   i vivv     v v i i iv   
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGAT 79

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.01 (1 / 79), avg. gap size = 2.00 (2 / 1)  

2606 27.45 2.92 0.90  chr1_244542552_244547422.rev     3492  4380 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_244542552_   3492 GGAAAAACATTCCATACTCATGGATAGGAAGAATCAATATTGTGAAAATG 3541
                              i i  i    ii        v      v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_244542552_   3542 GCCATACCGCCCAAAGCAATTTATAGATACAATGCTATTCCAAT--AAAT 3589
                           v    iv      vii  i  i    v   i  v  i  v  --    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_244542552_   3590 ACCATTGATATTCTTCACAGAATTAGAAAAAAAGAACT-ATTTTAAAAT- 3637
                         v   viviiv  i  ii     v v  v  i-----  -  ii      -
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAATT 146

  chr1_244542552_   3638 CATATGGAACCAAAAAAGAGCTTGCATAGCCAAA---------------- 3671
                                  viiv  ii  v iv v         ----------------
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_244542552_   3672 -GAACAAAGCTGGAGGCATCAGGCTACCCGACTGCAAACTATACTACAAA 3720
                         -        i      vv   vi  v   i i v    viv         
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_244542552_   3721 GCTACAGTAA-CATAAAC-TTATGGTACTGGTACAAAAACAAGCACATAG 3768
                                   -  - i  -v i         i i  ii i ii  i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCA-AGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_244542552_   3769 ACCAATGGAACAGAATAGAAAACTCAGAAATAAAACTGCACATCTACAAC 3818
                          i        i     v  i iii          v iii    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_244542552_   3819 CATCTGATCTTCAACAAACTGGAAAAAAACAAGCAACGGGGAAAAGATTC 3868
                           vi    i   i    ivvv vv  i v  vv   i       ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_244542552_   3869 CCTATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAAT 3918
                         i  v  i  i              v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_244542552_   3919 AGAAACTGGATTCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGG 3968
                         v   ii    ii   v   i     v  i                i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_244542552_   3969 ATTAAAGACTGAAATGTAAAACCCAAAACTATAAAAGCCCTAGAAGAAAA 4018
                           i ?    iv        i v i            vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_244542552_   4019 TCTAGGCA-ATATCATTCAGGAAGTAGGCATGGGAAAGGATTTTATGACA 4067
                         iv    ?i- v   -   iv  vv v  vv i  v  v i   iv iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_244542552_   4068 AAGACTCCAAAAGCAATTGCAACAATAGCAAAAATTGACAAATGGGATCT 4117
                          v   v         vvv       v  v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_244542552_   4118 AACTAAACTAAAGAGCTTCTACACAGCAACCAAAACTATCACCAGAATGA 4167
                         v ii   v v  i i   i iii vv   vvi v       vv i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_244542552_   4168 ACAGATAACCTACAGAATGGGAGAAAATTATTGCAATCTATCCATCTGAC 4217
                          v   i    i                 vv      vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_244542552_   4218 AAAGATCTAAT-TCCAGAATCTACAAAGAACTTAAGCAAATTTACAAGAA 4266
                           i iv  vi -        v  i        ivvi   v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_244542552_   4267 AAGAACAAACAACCCCATT-AAAATTGCGCAAAGGACATGAAAAGACATT 4315
                           ii     i     v   -    v  v        iv    v       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_244542552_   4316 TCTCAAAAAAAAGACATAGGTATGGCCAACAAACATATTTTAAAAAGCAC 4365
                             v   i  -  i   viv        i  i  i  vvv  i v  v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_244542552_   4366 AACATCACTGATCAT 4380
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (131 / 110)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 2.62 (34 / 13)  


3214 26.74 0.77 0.44  chr1_244556356_244562730     4978  5882 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244556356_   4978 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5027
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244556356_   5028 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5077
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244556356_   5078 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5125
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_244556356_   5126 TATGGAACCAGAAAAGAGCCCACATTGCCAACTCAATCCTAAGCCAAAAG 5175
                                viiv  ii  v  viv  v     vv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_244556356_   5176 AACAAAGCTAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5225
                                i i    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_244556356_   5226 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGATC 5275
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_244556356_   5276 AATGGAACAGAAC--AGAGTCCTCAGAAATAACGCTGCATATCTATGGCT 5323
                                i    i--       --        vv iii i  i     ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_244556356_   5324 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5373
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_244556356_   5374 CTATTTAATAAATGGTGCTGGGAAAACCC-ATAGCCATATGTAGAAAGCT 5422
                           v  i  i              v   iv-   ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_244556356_   5423 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5472
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_244556356_   5473 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5522
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_244556356_   5523 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5572
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_244556356_   5573 AACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTAA 5622
                         i            vvi   i      vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_244556356_   5623 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5672
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_244556356_   5673 AGGCAACCTACAAAATGGGATAAAATTTTTGCAACCTACACATCTGACAA 5722
                           i     i   i       v     v       vii i i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_244556356_   5723 AGGGCTAATATCCAGAACCTACAA-GACCTCAAACAAATTTACAAGAAAA 5771
                         i  i  vi         iv  i  -  v   vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_244556356_   5772 AAA-AAACAACCCCATCAAAAAGTGGGCAAAGCACATGAACAGACATTTC 5820
                          i -   i     v  i?    i         v iv    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_244556356_   5821 TCAAAAGAAGACGTTTATGCAGCTAAAAAACACATGAAAAAATGCTCACC 5870
                           v        ii vi viii  i  v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_244556356_   5871 ATCACTGGCCAT 5882
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2720 28.15 1.20 1.75  chr1_244579880_244582151.rev      868  1780 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244579880_    868 TAGAAAAACTTTCCATGTTCATGGATAGGAAGAATCAATATTCTTAAAAT 917
                          i    i iv i              v      v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244579880_    918 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTAGGTCAA 967
                            v     v      vii  i           i  v  i    --    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA--TCAA 98

  chr1_244579880_    968 ACTATCAATGACATTCCTCACAGGATTAGAGAAAACAATTTTAAAATTCA 1017
                          v vi  iivi v  ii ii   i v v  v  ivii  ii         
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_244579880_   1018 TATGGAATAAAAATAAATAAATAAAACCCA-AATAGCCAAGACAATCCTA 1066
                                ---------  iv viii     -         i      i i
  L1M4_orf2#LINE/    149 TATGGAA---------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr1_244579880_   1067 AGCCAAAAGAACAAAGCTGGAGACATCGCATTACTTGACTTCAAACTATA 1116
                          ivv i          i     ivv  i  i v iii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr1_244579880_   1117 CTACAAGGCTACAATAATCAAAACAGCATGTTAATGGTACAATGACAGAT 1166
                               i      i       i    ii  v  v   i i  v  i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr1_244579880_   1167 GCATAGACCAACGGAACAGAATGGAGAGCCCAGAAATAATGCCGTACACC 1216
                         ii     i   i    i     v     i          vv  i    ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr1_244579880_   1217 GAGAGCCATCTGATTTTCAACGAAGCCAACAAAAATAATCAATGGGGAAA 1266
                         v vi i  vi        i  i i viiv   i vi v            
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr1_244579880_   1267 TGACTTCCTGTTCAATAAATGGTGCTGGGATAACTAGCTAGTCAAATGCA 1316
                         vi ivvi  v     i              i    i v  ?i  v     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr1_244579880_   1317 GAAGATTGTAACTGGAACCCT-TTTTACATCACATACACAAATCAACTTC 1365
                         i    v  v ii    v    -ii i   i  i     v    i    iv
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr1_244579880_   1366 AGATGGATTAAAGACTTCAACATAAAACCTAAA-CTCTAAGTACTCT--G 1412
                          i      i ?    i v  ii   i v     -  v   i-     -- 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAG 538

  chr1_244579880_   1413 AAAAATAACTTAGGAA-ATGTCATTCTGGACATAGGACCTGGCAAAGATT 1461
                           i  -   v    ?i- vi  -   vv   v v  iiiv     v i  
  L1M4_orf2#LINE/    539 AAGAA-AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr1_244579880_   1462 TTACAATGAAGATACTAAAATTGATTTTAACAAAAACATAAATTAACAAG 1511
                          ivi ivv v  i  i    viivvvvi       iv v    vi i  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr1_244579880_   1512 TGGAACCTAATTAAA-TTAAAGAGCTCTTGCATAGCAAAATAAACTATCA 1560
                          v i  i v  i   -     i -  i   iiivv    iv v       
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chr1_244579880_   1561 AAAGAATAAACAGACAAACTACAGAATGGGATAAAATATTTGCAAAT-AT 1609
                          i i i i  v      v i           v               -  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr1_244579880_   1610 ACATGCAACAAAAGTTTACTATCCAAAATCTATAAAGAAATTTAAACAAA 1659
                          i  vii i  ii vi vv      i   v         v i -v    v
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAAC 784

  chr1_244579880_   1660 TCAA--GCAGAAA-ACAAACAGCTCCATTAAAAAGTGGGCAAAGAATATT 1706
                             --ii i   -     i i i v   ?    i         i  v v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr1_244579880_   1707 AGTAGACTCTTTTCAAAAGATGACATCCATGTTGCCAATAAGCATATGAA 1756
                          i     vi  i  v     v  i  v  vi v           i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr1_244579880_   1757 AAAGTACTCAACATTACTAATCAT 1780
                           ii i        i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (155 / 98)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.69 (27 / 16)  


2494 26.95 1.52 1.28  chr1_244612702_244614550.rev      502  1358 (491)    L1M4_orf2#LINE/L1       50   908 (0)  

  chr1_244612702_    502 TGACCATACTGCCAAAGGCAATCTACAAATTCAATACAATTCCCATCAAA 551
                           i v     v  v  ivii       i      ii    i  i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_244612702_    552 ATGCCACCATCATTCTTCACAAAACTAGAAAAAAAG-TCATAAAATTCAT 600
                           v   v vv v  i  ii  i  v v  v  ivv -  v          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_244612702_    601 ATGGAATCAAAATGGAGCCTTCATAACCAAAGCAA-----AACTAAAAAA 645
                               viiv  v   v  vvv   i     i   -----  --   i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--AAAGAA 197

  chr1_244612702_    646 TAACAAATCTGGAAATATCACATTGCCCAACTTCAGACTGTGCTATAAAG 695
                         v      vi    iivv     i v     i    i viv i   i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_244612702_    696 CCATAATCATGAAAGCAG---GGTAGTGGTATAAAAATCGGCACATAGAC 742
                          i i i v  v  ii   ---    v   i    ii  v i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_244612702_    743 TAATGGAACAGAATAGAGAACCCAGAAATAATGCCAAACGTTTACAGCTA 792
                         i       i     v    ii          vv   v  i    ii ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_244612702_    793 ACTGGCTTTCCACACAGCAAACAAAAACATAAACTGGAGAAAGGACAACC 842
                          i  ii    v   vi vviv   i v   vv v   i     i i ii 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_244612702_    843 TATTCAACAAATGGTGCTGGAATAATTGGCAAGCCACATGTAGGAGAATG 892
                          v                  i i  i   vv ?       i ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_244612702_    893 AAACTGAATCCTCATCTCTCACCTTATACAAAAATAAACTCAAGGTGGAT 942
                           ii  i i  ii i   v    v           v       ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_244612702_    943 CAAAGCCTTACATCTAAAACCTGAAACCATAAAGATTCTACAAGATAACA 992
                           ?  v i  v  v   i v  i    i     iv ii  v    v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_244612702_    993 TTGGCAACACCCTTCTAGACATTGGCTTAGGCAAAGACTTCATGACCAAG 1042
                          v  ?ivv vi    vv   v    v        v ii   v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr1_244612702_   1043 AACCCAAAAGAAAATGCAAAAAAAAAAATGGGATAAA-AAATAAGACTAA 1091
                          vv       v v v    v    i   --ii   i -    vi    vv
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAA--AAATAGATAAATTGGACTTC 645

  chr1_244612702_   1092 ATTAAACTAAAAAACTTCTGCACAGCAAAAGAAATAATCAACAGAGTTAA 1141
                           i   v v        i  ii vv    i  v iv     v i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_244612702_   1142 GAGACAAACCAGAGAATGGGAGAAAA-ATCTTCACAGTCTATGCATCTGA 1190
                         i      v   v              -  i v  - i  -  ii      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGA 743

  chr1_244612702_   1191 CAATCGAATAATATCCAGAATCTAAAAAGAACTCAAACAAATCAGCAAGA 1240
                         i  vv  v vi          v  v         vv    v   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_244612702_   1241 AGAAAATAAACAATCCCATCAAACTGGGATTGGGCTAAGGGACTTGAATA 1290
                          i  i i   i  i  v  i?  ----i v     -  i   i       
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAA----AAATGGGC-AAAGGATTTGAATA 838

  chr1_244612702_   1291 GACAATTCTC--AACAGGATATACAAATGGCCAATAAGCATATGAAAAAA 1338
                             v     --  v i                       i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_244612702_   1339 TGCTGAACATCACTAATTAT 1358
                             v       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.14 (121 / 106)
Gap_init rate = 0.01 (12 / 859), avg. gap size = 2.00 (24 / 12)  


2373 29.35 2.34 1.00  chr1_244618001_244623900     4512  5407 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244618001_   4512 TGGAAAAACATTCCATTCTTATGGATAGGAAGAATCAATATCATGTAAAT 4561
                               i i  i    vi i      v      v i     ii vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244618001_   4562 GGCCATACTGCCCAAAGTAATTTATAGATTTAATGTTACTCCCT-TCAAA 4610
                            v     v      v i  i  i     i  i i- v     -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAAA 99

  chr1_244618001_   4611 CTAC--ATTGACATTCTTCACAGAATTAGAAAATACT--TCTTTAAATTT 4656
                         v v --ii  v -  i  ii     v v  v  -i  --  i v     i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTC 147

  chr1_244618001_   4657 TACATGGAATCAAAAAAGAGCCTGTATAGCTAAGAAAATCCTAAACAAAA 4706
                         - i      viiv  ii  v  v v     i  i v    i i  v  i 
  L1M4_orf2#LINE/    148 -ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr1_244618001_   4707 AGAACAAC-CTAGAGGCATCATGCTACTTGACTTCAAACTACACTACAAG 4755
                                v-i i    vv   ii  v iii i      vivi       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr1_244618001_   4756 GCTACGGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGACATATAGG 4805
                              i    i   i    ii    i    i iv ii i          i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr1_244618001_   4806 CCAATAGAACAAAAGAGAAAATTCAGAAATAACACCGTATATCTACAGTC 4855
                         i    i   i i  vv  i i i         vv  i  i  i  ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_244618001_   4856 ATCTAATTTTTGACAAATCTGACAAAAATAAGCAATGGGGAAATTATTCC 4905
                          vi i     i     ivv  v   i vi vv           vv  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_244618001_   4906 CTTTTTAATAAATATTGCTGGGAAAACAGGCTAACCATATGCAGAAAACT 4955
                              i  i    iv        v   v  v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_244618001_   4956 GAAACTAGATCCCCCTCCTTACACATTATACAAAAATTAA-----GATAG 5000
                            ii i  -    iv   i    vv              -----i  i 
  L1M4_orf2#LINE/    447 GAAGTTGGA-CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_244618001_   5001 ATTGAAGACTTAAATATAAAACCCAAAAACATAAAATCACTAGAAGAAAA 5050
                           ii?    i     i   i v i    vi      iivi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_244618001_   5051 CATAAGCA-ATACCATTCAGGACAT--AGTCATGGGAAAACACTTCATCA 5097
                             i ?i- v i -   iv   v --i  i --  v  vvii   - i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTC-TTA 591

  chr1_244618001_   5098 CAAA-AACACCAAAAGCAATTGCAACAAACCCAAAATT-GACAAATCGGA 5145
                         v v -i            vvv        vvv    v -  i    i   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_244618001_   5146 TCTAATTAAACTGAAGAGCTTCTGCACAGCCAAATAAACTAGCATCAGAG 5195
                         ii v  i   v v  i i   i  ii vv v  iv v    v  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr1_244618001_   5196 TGAAGAGGCAACCTACAGAATGGGAGAAAA-ATTTGCAGTCTACCCATCT 5244
                             i  i     i                -       ivii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr1_244618001_   5245 CTCACAGTTCTAATATCCAGAATCTATAAGGAA----TATAAATGTACAA 5290
                         vvi vi vv  vi          v     i   ----  i  v vv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr1_244618001_   5291 GTCAAAACCAAACAACTTCATCAAAAAGTGGGCAAAGCATATGAACAGAC 5340
                         vvv   iv    i   iiv  i?    i         v  v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr1_244618001_   5341 ACTTCTCAAAAGAAGACATTTATGCAGGCAACAAACATATGAAAAAGAGC 5390
                          i     v        i  vi viii v   i  i  i       iiv  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr1_244618001_   5391 TCATCATCAGTGATTAT 5407
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (152 / 107)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.58 (30 / 19)  


2679 28.35 1.90 0.56  chr1_244635904_244641324.rev     4037  4932 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244635904_   4037 TGGAAACACATCTCATGCCCAGGGATGGTGGAA---TCAGTAGTGTGAAA 4083
                               v i   i    ii  v    --     --- i i  v   v  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT--TGGAAGACTTAATATTGTTAAG 48

  chr1_244635904_   4084 ATGACAATACTTCCAAAAGCAATCTATAAATTCCATGAAATTCCCATCAA 4133
                            i       i  v   vii     i i    v i v   i  i     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr1_244635904_   4134 AATGCCACCATCAATCTTCACAGAACTAGAAGAAACAATCCTGAAATGAA 4183
                            v   v vv vv i  ii     v v  vi ivii     i    vv 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr1_244635904_   4184 TATAGAGCCAAAAAAGAGCCTGCATAGCCAAAGCAACACTAAGCAA-AAG 4232
                            i  iviiv  ii  v  v v         i   ivi i iv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_244635904_   4233 AACAAATCTGGAGACATCATAATAACTGACTTCAGACTATACTATAAAGC 4282
                               vi     ivv   i v vv ii i    i viv     i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_244635904_   4283 CATAGTCATCAAAACAACATGGTGCTGGTATAAAAATAAGCACATAGATC 4332
                         i i   v     i   iii    i    i    ii   ii  i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_244635904_   4333 AATGAAACTCAATAGAGAACCCAGAAATAAAGTCAAA----TACAGCCAA 4378
                             i  ivv   v    ii           vi  v ----  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_244635904_   4379 CTGTTCTTCAACAAGGCAAACCAAAAC-ATAAAGTGGGGAAAGGACAAGG 4427
                         i  v i   i      -ivi    i  -  vv i         i i ivv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_244635904_   4428 TATTCAACAAATGGTGCTGGAATAATTGAAAAGCCACATGTAGGAGAATG 4477
                          v                  i i  i  i v ?       i ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_244635904_   4478 AAAGTGGATCCTCATCTCTCACCATATACAAAAATCAACTCAAGATGGAT 4527
                           iv    i  ii i   v                i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_244635904_   4528 TAAGGACTTACACCTAAGGCCTGATGCCATAAATATTATAGAAGATTACA 4577
                         i ?i   i  v iv    iv  i vi i     vv iv       vv   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_244635904_   4578 TCGGAA-ACACCCTCGTAGACATTGGCTTAGGAAAAGACTTCATGACCAA 4626
                          v  ?i- v i i    -   v    v     v  v ii   v iivi v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_244635904_   4627 GAACCCAAAAGCAAATGTGACAAAAACAAAAATAATTAGATGTGACTTAA 4676
                           vv         v v ii      iv       iv  i  vv     v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_244635904_   4677 TTAAACTAAAAAGCTTCAGCACAGCAAAAGATATAATCAGGAGAGTTACA 4726
                          i   v v    i   iv ii vv    i  i iv    i  i   v v 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_244635904_   4727 -GACAACACACAGAGTGGGAGAAAATCTTCACAGTCTATTCATTTGATGA 4775
                         -      v      i           v  ii  ivii  vi  i    i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_244635904_   4776 AGGAATAATTTCCAGAATCTACAAAGAACTCCAACAAATCAGCAAGAAAA 4825
                         i   v vi v        v  i         iv    v   ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_244635904_   4826 A---AAAT--TCCA-TCAAATAGTGGGCTAAGGGACATGAATAGACCATT 4869
                          ---    --i   - i?  v i     -  i   iv         vv  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGC-AAAGGATTTGAATAGACATTT 845

  chr1_244635904_   4870 CTCAAAAGAAGATATACAAATGGCCAACAAGCATATGGAAAAATGCTGGA 4919
                            v                       i     i   i   i     vi 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_244635904_   4920 CATAACTAATTAT 4932
                            v ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (146 / 104)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


3231 27.20 0.44 0.44  chr1_244656154_244660662.rev     3111  4018 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244656154_   3111 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3160
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244656154_   3161 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3210
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244656154_   3211 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3258
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr1_244656154_   3259 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCCATCCTAAGCCAAAAG 3308
                                viiv  ii  v  v v  v     iv v   i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_244656154_   3309 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3358
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_244656154_   3359 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACATAGATATAGATC 3408
                                 i   i    ii         i iv ii i v v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_244656154_   3409 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 3456
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr1_244656154_   3457 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3506
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_244656154_   3507 CTATTTAATAAATGGTGCTGGGAAAACTGGCAAGCCATATGTAGAAAGCT 3556
                           v  i  i              v      vv ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_244656154_   3557 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 3606
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_244656154_   3607 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3656
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_244656154_   3657 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 3706
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_244656154_   3707 AACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAA 3756
                         i            vvi      i   vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_244656154_   3757 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3806
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr1_244656154_   3807 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3856
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr1_244656154_   3857 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3906
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr1_244656154_   3907 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 3956
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr1_244656154_   3957 TCAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTCATC 4006
                           v        i  vi viii     v  ii         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr1_244656154_   4007 ATCACTGGCCAT 4018
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2713 27.77 0.54 2.06  chr1_244670755_244675059.rev     2893  3814 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244670755_   2893 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATAGTGG-AAAAT 2941
                               v i        i        v  v   v i    v  v-  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244670755_   2942 GACCATACTGCCAAAAGCAATCTACAAATTCCATGAGATTCCCATCAAAA 2991
                          i v     v  v   vii       i    v i vi  i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244670755_   2992 TGCCACCATCATTGTTCAGAGAACTAGAAGAAACATTTCTAAAATTCATA 3041
                          v   v vv v  v  iiv    v v  vi iviiv i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_244670755_   3042 TAGAACCAAAAAAAAAGCCTACA-TAGCCAAAGCAAGACTAAGCAAAAAG 3090
                          i   viiv  iii --  i v -        i   vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_244670755_   3091 TGCAAATCTGAAGGCATCACATGACCCAATTTCAGACTATATTCTAAAGC 3140
                         vi    vi  i   vv     ivv          i viv  i vi     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_244670755_   3141 CACAGTCACTAA-ACGGCATGGTACTGGTATAAAAATAGGCACATAGACC 3189
                         i     v ii  -  i ii         i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_244670755_   3190 AATGGAACAGAAGAGAGAACCCAGAAATAAACCAAAATATTTGCATCCAA 3239
                                i    vv    ii             v v i    iiivi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_244670755_   3240 CTGGTCTTCAACAAAGCAAACAAAAACATAAAGTAGGGAAAGGACAACCT 3289
                         i  i i   i    i vviv   i v   vv i i       i i ii  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_244670755_   3290 ATTCAACAGATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAGAATGA 3339
                         v       i            i  i   vv ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_244670755_   3340 AACTGGATCCTCATCTCTCACCTTATA-AAAAATCAACTCAGGATGGATC 3388
                          ii    i  ii i   v    v    -      i      ii       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_244670755_   3389 AAAGACTTACATCTAAGACCTGAAACCATAAAGATTCTAGAAGATAAAAT 3438
                          ?    i  v  v     v  i    i     iv ii       v  v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_244670755_   3439 CAGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCATGACCAAGA 3488
                         vi ?iv  vi    vv   v    v        v ii   v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_244670755_   3489 ACCCAATAGCAAATGCAA-AAAAGAAACAAACAAACAAAACAAAGATAAA 3537
                         vv    v    v v    -        ----------   i --      
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAA----------AAATA--GATAAA 636

  chr1_244670755_   3538 CAGAGAGGACTTAATTAAGCTAAAAAGCTTCTGCACAGCAAAAGAAATAA 3587
                         iv ----     v  i  iv v    i   i  ii vv    i  v iv 
  L1M4_orf2#LINE/    637 TTG----GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr1_244670755_   3588 TCCTCAGGGTTAACAGACAACCCATCGGGTGGAAGAAAATCTTCACAATC 3637
                           vvv ii  v  v          iv ii   i       v  ii   vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr1_244670755_   3638 TATACAGCTGACAAAAGAATAATATCCAGAATCTACAAAGAACTCAAACA 3687
                         i   i v    i  ii  v vi          v  i         vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr1_244670755_   3688 AATCAGCAAGAAGAAAACAAACAATCCCATCAAAAAGTGGTCTAAGGGAC 3737
                          v   ii  v  i  i     i  i  v  i?    i   v -  i   i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC-AAAGGAT 831

  chr1_244670755_   3738 ATAAACAGACAATTTTCACAAGAAGATATACAAATGGCCAACAAGCATAT 3787
                         v i  i     v  i  vv                      i     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr1_244670755_   3788 GGAAAAATGCTCAACATCACTAATTAT 3814
                          i   i             ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (144 / 108)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.40 (24 / 10)  


2583 29.80 0.99 0.77  chr1_244678339_244684203     4467  5372 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244678339_   4467 TGGAAAAACATTTCATCCTTGTGGATAGGAAGAATCTATATCATAAAAAT 4516
                               i i  ii   vi ii     v      v iv    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244678339_   4517 GGCCATATCGAGCAAAGAAATTTATAGATTCAATGCTAATCCC-ATCAAA 4565
                            v   iivvv    vvi  i  i        i  -      -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAAA 99

  chr1_244678339_   4566 CTACCATTGACATTCTTCACAGAATTAGAAAAAAACTTCTTTTAAT-TTC 4614
                         v v   vivi v  i  ii     v v  v  i--  vv ii   v-   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr1_244678339_   4615 ATATGGAACCAAAAAAGAGCCTGTATAGTCAAGACAATCTTAAGCAAGAA 4664
                                 viiv  ii  v  v v    i   i        i iv     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_244678339_   4665 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACAATATTGCAAGG 4714
                                 i      vv   ii  v  ii i      vvv  i i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_244678339_   4715 CTACCGTAACCAAAACAGCATGGTAGTGGTGCCAAAACAGATATATAGAC 4764
                             v    i   i    ii     v   iiiv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_244678339_   4765 CAATGGAACAGAACAGTGGCCTCAGAAATAGCACCACACATCTACAACCA 4814
                                 i    iv v ivii        ivv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr1_244678339_   4815 TCTAATCTTTGACAAACCTGACAAAAAAAG-CAATGGGGAAATTATTCCC 4863
                         vi i  i  i     ivv  v   i vv v-           vv  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr1_244678339_   4864 TTTTTAATAAATGGTGCTGGGAGAGCTGGCTAGCCATAAGCAGAAAACAG 4913
                             i  i              v i    v  ?   i v   i  i vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_244678339_   4914 AAACTAGACCCCTTCCTTACACCTTATATAAAAATTAACTCAAGATGGAT 4963
                           ii i       v   i     v    i              i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_244678339_   4964 TAAAGACTTAAATGTAAAACTCAAAACCATGAAAACCCTGGAAAAAAACC 5013
                         i ?    i         i vii     i  i   vi i i   i     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_244678339_   5014 TAGGCA-ATACCATTCAGGACATAGGTATAGGCAAAGACTTCATGACAAA 5062
                             ?i- v i -   iv   v v  vv       v ii   - v v v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATA 595

  chr1_244678339_   5063 AAACACCAAGAGCAATTGCAGCAAAAGCCAAAATTGACAAATGAGATCTA 5112
                         vi       i    vvv   i      vv     v  i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_244678339_   5113 ATTAAACTGAAGTGCTTCTGCACAGCAAAAGAAACTAGCATCAGAGTGAA 5162
                           i   v v  ivi   i  ii vv    i  v    v  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_244678339_   5163 CAGGCAACCTATGGAATGGGAACAAATTTTCACAATCTATCCATCTGACA 5212
                         v  i     i ii        iv    v  ii   vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_244678339_   5213 AAGGTCTAACATCCAGAATCTACAAGGAAC----ATAACCAAATTTACAA 5258
                          i  v  vii         v  i  i    ---- i   iv   v- i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAA 794

  chr1_244678339_   5259 GAAAA-AAACAACCTCATCAAAAAATGGGAGAAGTGTATGAACAGACACT 5307
                         i  i -   i    iv  i?         vi   vi v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_244678339_   5308 TCTCAAAAAAAGACATTTATGCATCCAACTAACATATGATAAAAAAGCTC 5357
                             v   i    i  vi viiiv    iv i  i    -   i v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTC 893

  chr1_244678339_   5358 ATCATCACTTATCAT 5372
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (154 / 112)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


2946 27.21 0.55 1.31  chr1_244693875_244698189.rev     2910  3824 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244693875_   2910 TGGAAATACATCCCATACTCATGGATGGGTAGAAACAATATTGTAAAAAT 2959
                               v i       ii        v  v   vvi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244693875_   2960 GACCATGCTGCCAAAAGCAATTTACAAATTCAATGCAATTCCCACTAAAA 3009
                          i v  i  v  v   vii  i    i      i     i  i ii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244693875_   3010 TATCACCATCCTTCTTAACAGAACTAGAAAGAACAATCCTAAAATTCATA 3059
                          vi  v vv    i  vi     v v  v iivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_244693875_   3060 TGGAA-TAAAAAAGTCCT-GCATAGCCATAGCAAGAATAAGCAAAAAGAA 3107
                              - iv  ii v  i- v       v i   vvv i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_244693875_   3108 CAAATCTGGAGGCACCACA-TACCCAACTTCAAATTATACTATAAAGCCA 3156
                             vi      vvi    - v     i      viv     i     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_244693875_   3157 TAGTCACCAAAACAGCATGGTACTGG-ATAAAAATAGAGACATAGACAGA 3205
                         i   v i   i    ii         -    ii     v i     ivi 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_244693875_   3206 CAAAACAGAATAGAGAACCCAGAAATAAACCAAAATACTTACAGCCATCT 3255
                         iii  i     v    ii             v v i i   ii i  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_244693875_   3256 GATCTTCAACAACACAAACAAAAACATGAAGTGGGGGAAAGAACACCATA 3305
                            i   i    vivviv   i v   vv i     -      i viv v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTT 399

  chr1_244693875_   3306 TTCAACAAATGGTGCTGGGCTAACTGACAGGCCACATGTAGAAGAATGAA 3355
                                            vi     ivvi?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr1_244693875_   3356 ACTGGATCCTCATCGCTCACCTTATACAAAAATCAACTCAAGATGGATAA 3405
                         ii    i  ii i v v    v           i       i      v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr1_244693875_   3406 AAACCTTAAATCTAAGTACTGAAAACATAAAGATTCCAGAAGATAACATC 3455
                         ? iv i     v    vi  i   vi     iv iii      v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr1_244693875_   3456 AGAG-AAATCCTTGTAGACATTGGCTTAGGCAAGGGTTTCATGAGCAAGA 3504
                         i ? -     i i  -   v    v        v      v iiii v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_244693875_   3505 ACCCAAAAACTAATGCAATAAAAACAAAGATAAATAGCTGGGAACTAATT 3554
                         vv      i vv v    i    iv   i   i   iv v   vi v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_244693875_   3555 AAACTAAAGACCTTTTGCACTGCAAAAGGAACGGTCAGCAGAGTAAATAG 3604
                            v v  i v      ii  v    i iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_244693875_   3605 ACAACCCATAGAGTGGGAGAAAATCTTCACAATTTATACATCTGAGAAGG 3654
                                 i   i           v  ii   v i   i      v    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_244693875_   3655 GATTAATTTCCAGAATCTACAAAGAACTCAAACAAATCAGCAAGAAGAAA 3704
                           i vi v        v  i         vv    v   ii  v  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_244693875_   3705 ACAAATGATCCCATCAAAAAGTGGGCCTAGGACATGAATAGACAATTCTC 3754
                               i i  v  i?    i     vv    iv          v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_244693875_   3755 AAAAGGAGATATATAAATATATATAAATAGCCAACAAGCATCTAGAAAAA 3804
                         v    i       i    ----------i     i     iv ii   i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAAT----------GGCCAATAAGCACATGAAAAGA 888

  chr1_244693875_   3805 TGCTTGACATCACTAATTAT 3824
                             ii      ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


 478 29.27 0.00 0.00  chr1_244712739_244717418.rev     2980  3102 (1578)    L1M4_orf2#LINE/L1        1   123 (785)  

  chr1_244712739_   2980 TGGAAAAACATTCCATGCTTATGAATAGGAAGAATCAATATAGTTTAAAT 3029
                               i i  i     i i   i  v      v i     v   v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244712739_   3030 GGTCATACTGCTCAAAGTAATTTACAGATTTAATGCTATTCCTATTAAAC 3079
                           iv     v i    v i  i        i  i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244712739_   3080 TACTGATGACATTCTTCACAGAA 3102
                          v iiiivi v  i  ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA 123

Transitions / transversions = 2.00 (24 / 12)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.00 (0 / 0)  

1896 27.74 2.71 2.97  chr1_244712739_244717418.rev     3415  4189 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr1_244712739_   3415 ATTCTAAAATTTATATGGAAC--CAAAAAGCTCA-AATAGCAATAGTAAC 3461
                           i        i        v--   iiii i  -      v v ii  i
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr1_244712739_   3462 CTTAAGCAAAATGAGAAAATCTGGAGGTATCACATCACCTGATTTTAAAC 3511
                            i iv  i v  iv   vi      vv     iiv  ii    i   v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr1_244712739_   3512 TATACTACAAGGCTACAGTAACCAAAATAGCATAATAACTGCTACCAAAA 3561
                         iv        i          i   i i  ii ii  -   vi i-----
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA-CTGGCAT----- 279

  chr1_244712739_   3562 AAAAAAAAAAAAAGACGTATAGATCAATGGAACAGTATATAGAGCCCAGA 3611
                         ------  ii v    i               i  v  vv    i     
  L1M4_orf2#LINE/    280 ------AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr1_244712739_   3612 AATAAAGT--TGCACCTACAACCATCTGATCTTCAAAAAAGTCAACAGAA 3659
                               vi-- i  ii  iiii  vi    i   i v  i viiv  ii 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr1_244712739_   3660 ACAAGCAATCAGGAAAGGACACCCTATTCAATAAGTGGTGCTGGCATAGC 3709
                         v  vv    vi      i i vi  v     i  i         v i i 
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr1_244712739_   3710 TGGCTAGCCATATGCAGAAGACTGATACTGGACCCTT--TTTGCACCATT 3757
                            v  ?   i     i    v   vii       i --i ii      -
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT- 472

  chr1_244712739_   3758 ATACACAAATAAACTCAAGGCGGATTAAAGACTTAAATGTAGAACCTAAA 3807
                              v    v       iii    i ?    i        ii v     
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr1_244712739_   3808 ATGATTAGTACTCT--GAAAAATATCCTAGG---AAATACCATTTTG-GA 3851
                          iv  v i-     --   i  v - v    ---    ----i  i -  
  L1M4_orf2#LINE/    523 ACTATAAA-ACTCTTAGAAGAAAA-CATAGGNGTAAAT----CTTCGTGA 566

  chr1_244712739_   3852 CAGAAGCCCTGGCAAATATTTCCTGAGGAACATACCAAAAGCAATTGTA- 3900
                          vvvi viiv     vvi    i iiiv vv i          vvv i -
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_244712739_   3901 CATAATCAAAAATTGACAAATGGGACTCCATTAAACTAAAGACCTTCTGG 3950
                           v  vv      v  i    v     i   i   v v  i v   i  v
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_244712739_   3951 ACAGCAAAAGAAACTATTAACGGAGTTAATAGACAAACTACAGAAAGGAA 4000
                         i vv    i  v     i  vii   v  v      v i      v  i 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_244712739_   4001 GAAAACATTTGAAAACTATGCATTCAACAAAGT-CTAATATACAGTATTT 4049
                              i     v   ii  ii  iii i  i v-  vi   v   v  v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_244712739_   4050 ATAA-GTATTATAACAAACAAAT--TAACAAGCAAAAAACAACTCCATT- 4095
                             - v i v v    viv   --   v   -- v   i   i v   -
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAG--ACAAATAACCCAATTW 814

  chr1_244712739_   4096 AAAAGTTGGCAAAGGATAAAAATAGACATTTTACGAAAGAAGACATA--A 4143
                             i v          vvi           iv v        i   -- 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_244712739_   4144 GTGTTGCCAACAAGCATATGAAAACATGCTCAACATCAATAATCAT 4189
                         i  --     i     i       v             ????????
  L1M4_orf2#LINE/    865 ATG--GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (124 / 89)
Gap_init rate = 0.03 (21 / 773), avg. gap size = 2.10 (44 / 21)  


2759 26.84 2.56 1.45  chr1_244723603_244725904.rev      914  1811 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244723603_    914 TGGAAAAATATTCCATGCTAATGGATGGGAAGAATCAATATCATGAAAAT 963
                               i    i     i v      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244723603_    964 GGCTATACTGCTCAA--TGTATGCCC---TTTAATGCTATTCCCATCAAA 1008
                            v     v i   --  -  viv ---  i  i  v  i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG-ATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr1_244723603_   1009 CTACCATGGACGTTTTTCACAGAATTAGATAAACT-ACTTTAAAAGTCCT 1057
                         v v   vvvi v     ii     v v  i  i  - iii     v  v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_244723603_   1058 ATGGAACCAAAAAGAAGCCCATGTAGCCAAGTCAATCCTAAGCAAAAAGA 1107
                               viiv  i i v  vivi       iv     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_244723603_   1108 ACAAAGCTGGAGGCATCACACTACTCGACGTCAAACTTTACTACAAGGCT 1157
                               i      vv       v i i iv     vi         i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_244723603_   1158 ACAGCAATCAAAACAGCATGGTACTCGTACCAAAACAGACACATAGACCA 1207
                             i      i    ii       v i iv ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr1_244723603_   1208 ACAGAACAGAATAGAGATCTCAGAAATAAGACCTGACATCTACAACCATC 1257
                          ii   i     v    vii         iv  vv    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr1_244723603_   1258 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGA--GTCCC 1305
                             i  i     ivv  v   i v  vv            i --   --
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-- 397

  chr1_244723603_   1306 TATTTAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 1355
                          v  i ii              v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_244723603_   1356 AAACTGGACCTTTATCTTACACCTTATACAAAAATAAGCTCAAGATGGAT 1405
                           ii      ii  i  i     v           v i     i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_244723603_   1406 TAAAGACTTAAATGTAAAATTCCAAACCATAAAAACCCTAGAAGAAAATC 1455
                         i ?    i         i viiv    i      vi i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr1_244723603_   1456 TAGGC---AATACGATTCAGGAAATAGGCATGGGCAAAGGTTTTATC-AT 1501
                             ?---   - --   iv  vv v  vv i     v     iv v-  
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-C--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr1_244723603_   1502 AAAATCACCTAAAGCAATTGCAATAAGAGCTAAAATTGAAAAATAGAGTC 1551
                          vi -    v      vvv    i  i  vv     v  v    v iiii
  L1M4_orf2#LINE/    595 ATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_244723603_   1552 TAATTAAACTAAAGGGCTTCTGCACAGCAAAATAAACTATCATCAGAGCA 1601
                          v  i   v v  iii   i  ii vv    iv v       vv i  ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_244723603_   1602 AACAGGCAACCTATAGAATGGGAGAAAA-ATTTTGGAATCTACCCATATG 1650
                           v  i     i i              -    vvi    - ivi  v  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTG 742

  chr1_244723603_   1651 ATAAAGGTCTAATATCCAGGATTTACAAGGAACT--TACATTT--ATAAG 1696
                             i  v  vi       i  v  i  i     --    vi --    v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_244723603_   1697 AAAAA-----ACAACCCCATCGAAAAGTAGGCAAAGGACATGAACAGACA 1741
                              ----- i     v  i?    i i         iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_244723603_   1742 CTTCTC-AAAGAAGACATATATGTGCCCAACATACCTATTAAAAAAAAAA 1790
                         i     -        i   i vi  v    i vi vi  -----i    i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-----GAAAAG 887

  chr1_244723603_   1791 AGGCTCAACATCACTGATCAT 1811
                          v           ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (137 / 100)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.00 (36 / 18)  


1530 24.84 3.34 1.88  chr1_244741705_244747968        1   479 (5785)  C L1M4_orf2#LINE/L1   (38)   870   385  

C chr1_244741705_    479 GAAAACAAGCAATCTATTCAACTAGTGGTGATGAGA-AACAGTATATCCA 431
                          i   v  -i i   v      v i     v  i  -   v v   ?   
  L1M4_orf2#LINE/    385 GGAAAGAA-TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

C chr1_244741705_    430 TATGCAAAACAGTGAAGTCAGGCTTTTATCTTACACCATGTA--AAGATT 383
                         i        v i      ii i iii  i  i       i  --  i   
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

C chr1_244741705_    382 AATTCAAG-TAGATAAAAAACTTTAATATAAGAACCAAAATGACGAAACT 334
                           i    i- i   v ? i  i v   i     i i    iv ii     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

C chr1_244741705_    333 CTTAGAAGAAAACAAAGGGAAAAATC---ATGACATTGTATTTGGCAATA 287
                                       v   ?iv     ---i    v   vi  v      i
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

C chr1_244741705_    286 ATTTTTTGTATGTAAAAACCAGAAGTATAGGCATTAAAAGAGGAAAACAA 237
                         i   i  iv  i i v -   i   i i i   vi      i-    i i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACA-CCAAAAGCACAAGCAACAAAAGAA-AAAATAG 631

C chr1_244741705_    236 ATAAAATTTATTTCATCAAAATTAACA--TTTTGCACATCAAAGGACACT 189
                              v vv i              v --     ii v            
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

C chr1_244741705_    188 TTCAGAAAAGTAAAAAGGCAGCTCTCTCATGATGGGA-AAAATAGTTGCA 140
                         v   ii     i     i  i i v -- vi      -      v     
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCAC--AGAATGGGAGAAAATATTTGCA 729

C chr1_244741705_    139 AAGTACATAGCTGATAAGAAA-TTAAATCTACAATATATTTTTAAAA--- 94
                           vi i   v        ii -  iv   i v       ----   i---
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATAT----AAAGAAC 775

C chr1_244741705_     93 -CTTACAATGAAATAACAACAAAATAGACAACCCAACTGAAAAATAGGCA 45
                         -       ivv     i  v  i i i i       i ?      i    
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

C chr1_244741705_     44 AAGAGCTTGAATAGGCATTTCTT-AAAAAAGATAAGCATGTGACC 1
                            iii        i       i-   i      vi  vi  i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

Transitions / transversions = 2.19 (79 / 36)
Gap_init rate = 0.03 (14 / 486), avg. gap size = 1.79 (25 / 14)  

3381 25.88 0.55 0.55  chr1_244741705_244747968     4864  5771 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244741705_   4864 TGGAAGAACATTCCATGCTCATGGGTAGGAAGACTCAATATCATGAAAAT 4913
                              ii i  i     i      i v        i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244741705_   4914 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4963
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244741705_   4964 TACCAA-TGCCTTTCTTCACAGAATTGGAAAAAACGACTTTAAAGTTCAT 5012
                          v   i-       i  -i     v v  v  ivi  iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr1_244741705_   5013 ATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTGAACCAAAAGA 5062
                               viiv  ii  v  viv  vi    iv     i    vv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_244741705_   5063 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTATAAGGCT 5112
                               i      vv       v  ii i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_244741705_   5113 GCAGTAACCAAAACAGCATGGTACTGGTACCTAA--ACAGAGATATAGAT 5160
                         i      i   i    ii         i --   -- i   v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATAGAT 297

  chr1_244741705_   5161 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5208
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_244741705_   5209 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5258
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_244741705_   5259 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5308
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_244741705_   5309 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATAAATTCAAGATGG 5358
                             ii    i    v   i     v           v  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_244741705_   5359 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5408
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_244741705_   5409 CATAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTA 5458
                               ?i v viv   iv   v v  vv i i   v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_244741705_   5459 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5508
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_244741705_   5509 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5558
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr1_244741705_   5559 CAGGCAACCTATAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5608
                         v  i     i i i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr1_244741705_   5609 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5658
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr1_244741705_   5659 AAGACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5708
                                 i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr1_244741705_   5709 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5758
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_244741705_   5759 CATCACTGGCCAT 5771
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


1057 29.20 4.14 3.22  chr1_244748241_244751207     1271  1705 (1262)    L1M4_orf2#LINE/L1        1   439 (469)  

  chr1_244748241_   1271 TGAAAAAAAATTCCATGCTCATGAATAGTAAGAATCAAAATAATTAAAAT 1320
                           i   i v  i     i     i  v v    v i  v  vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244748241_   1321 TACCATATTGCCCAAAGCAATTTACAGAGTCAGTGCTACC---ATTGACA 1367
                         vi v   i v      vii  i      v   ii  v i ---  ii v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244748241_   1368 TTCTTCACAG--GACT-------AAAAA--AACAAAACTAACTATTTTAA 1406
                          i ----   -- v  ------- i   --i    i-  i --- ii   
  L1M4_orf2#LINE/    101 TCC----CAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGA---TCCTAA 142

  chr1_244748241_   1407 AAATTATATGGAACCCAAATAGAAG---CTCAAAA-GGCCAAGGCAATCC 1452
                           v i        -----  iv   --- i  i  -i     ii     i
  L1M4_orf2#LINE/    143 AATTCATATGGAA-----ATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr1_244748241_   1453 TAAGAAAAAAGAAAAAAGCTGGAGGCATCACGCGATCTAACTTCAAACTA 1502
                          i i   i     v    i      vv    i vvi i  i      viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr1_244748241_   1503 TGGTACTGGGCTACAGTAACCAAAACAGCATAGATCCTGGTACAAAAACA 1552
                          iv   vii          i   i    ii i - v    i i  ii i 
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGG-TACTGGCATAAGGATA 286

  chr1_244748241_   1553 GAGGCATAGACCAATGGAACAGAATAGAGAACCCACAAATAAGACTATAC 1602
                           vii     i        i     v    ii   v      iv i    
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr1_244748241_   1603 ACCTACAATCATCTGATCTTTGAAAAACCTGACAAAAACAAGCAATGGGA 1652
                          ii  iii   vi    i  i  v  ivv  v   i v  vv       i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr1_244748241_   1653 AAAATATTCCCTATTTAATAATTGGTGCTGGGAGAACTGGCTAGAGATAT 1702
                            iv  vvi  v  i  i  v           v      v  ?vv i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr1_244748241_   1703 GCA 1705
                            
  L1M4_orf2#LINE/    437 GCA 439

Transitions / transversions = 1.68 (79 / 47)
Gap_init rate = 0.03 (11 / 439), avg. gap size = 2.91 (32 / 11)  

1981 29.69 1.56 1.56  chr1_244748241_244751207     1707  2474 (493)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr1_244748241_   1707 AAAACTCAAATAAAACCAAAAAAGAGCCCATATACTCAAGACAATCCTAA 1756
                             i   v  ii  viiv  ii  v  viv   vi   i      i i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr1_244748241_   1757 GCAAAAAGAGCAAAGCTGGAGGTATCATTATCATGCTACCTGACTTCAAA 1806
                         iv  i    i     i      ---- i --  ii  v  ii i      
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGG----ACT--CACACTTCCCAATTTCAAA 234

  chr1_244748241_   1807 CTACATTGCATGGTTACAGTAACCAAAAGAGCATGGTAGTGGTACAAAAA 1856
                         vivi i i  vi i        i   i v  ii     v   i i  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_244748241_   1857 CAGACACATAGAACAATGGAACAGAACAGACAACCCAGAAATTAGACCAG 1906
                         i     i     v        i    iv  v ii        v iv   v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_244748241_   1907 AC-CCTACAACTATCTGCTCTTTGACAAACCTGACAAAAACAAACAATGA 1955
                           -ii  iiiii vi  v i  i     ivv  v   i v  vv     i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_244748241_   1956 GTAAAGGATTCCCTATTCAATAAATAGTGCTGGGATAACTGGCTAGCTAT 2005
                          v    i  vvi  v     i    i         i      v  ? i i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr1_244748241_   2006 ATGCAGAAGATTAAAACTGGACCCATTTCTTACACCATATATAAAAATTA 2055
                              i    v i  ii       v vi  i          i        
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr1_244748241_   2056 ATGCAAGATGGATCAAAGACTTAAATGTAAAACCCAAAA-----ACACCC 2100
                          iv   i        ?    i         i v i    ----- v  i 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr1_244748241_   2101 T-GGAAAACAACCTAGG--TAATACCATTCAGGACATAGGAATGAGCAAA 2147
                          -i   i v   v    --   - i -   iv   v v  iv ii    v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chr1_244748241_   2148 TATTTCAT-GATGAAGATGCGAAAAGTATTTGCAACAAAAGCAAAAATTG 2196
                         vi    v -   - v  ii v     i ivv          v      v 
  L1M4_orf2#LINE/    583 GGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_244748241_   2197 ACAAATGGAACCTAATTGAACTAACGAGCATCTGCACAGCAAAATAAACT 2246
                          i    v i  i v  ii  v v vi i v i  ii vv    iv v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_244748241_   2247 CTCAGCAGAATAAACACACAACCTACGAAATGGGAGAACATTTCTGCAAA 2296
                         v   iv i i i  v v      i  ii          v  v i      
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_244748241_   2297 CTATGCATCTGACAAAGGTCTAATATCCAGCATCTATAAAGAACTGAAAA 2346
                         ii  ii      i  i  v  vi       v  v           vvv -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA- 780

  chr1_244748241_   2347 CAAATTTACAAGAAAACAACAAATAACCCCAT--AAAAATGTAGGCAAAG 2394
                            v iv i  v    vi           v  --       --       
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG--GGCAAAG 828

  chr1_244748241_   2395 GGCAAGAACAGATGCTTTTCAAAAGAAGACGTACATGCAGCTGACAATCA 2444
                          iivv   i   iii  i  v        ii    viii  ii i  v  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_244748241_   2445 TATTTAATAAAGCTCAGCATCACTGATCAT 2474
                         i  vv  vi v     i     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (135 / 91)
Gap_init rate = 0.02 (13 / 768), avg. gap size = 1.85 (24 / 13)  


2753 25.88 2.20 2.20  chr1_244770198_244774658.rev     3063  3970 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244770198_   3063 TGGAAAAACTTTCCATGTTCATGGATAGGAAAAAATCAATATTGTTAAAA 3112
                               i iv i              v    i v- i           i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chr1_244770198_   3113 TGGCCCTACTGCCCAAAGCAATTTACAGATTCAATAGTATTCCTAGGTCA 3162
                             vv    v      vii  i           iivv  i    --   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA--TCA 97

  chr1_244770198_   3163 AACTACCAATGACATTCCTCACATAATTAGAGAAAACAATTTTAAAATTC 3212
                           v v   iivi v  ii ii  v  v v  v  ivii  ii        
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr1_244770198_   3213 ATATGGAA-T-CAAAAAACAACCCAAATAGCCAAAGCAATCCTAAGCCAA 3260
                                 - -   iii  --  vi          i     i i ivv i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr1_244770198_   3261 AAGAACAAAGCTGGAGGCATTGCACTACCTGACTTCAAACTATACTACAA 3310
                                   i      vv ii    v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_244770198_   3311 GGCTACAATAATCAAAACAGCATGTTACTGGTACAACAACAGACACATAG 3360
                         i      i       i    ii  v      i i  vi i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_244770198_   3361 ACCAATGGAACAGAATGGAGAGCCCAGAAATAATGCCGTACACCTACAGC 3410
                          i        i     v     i          vv  i    ii  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_244770198_   3411 CATGTGATTTTCACCAAAGTCTACCAAGATAAT-CAATAGAGAAATGACT 3459
                           vv        iv   i v- i      iv  -    i i    vi iv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr1_244770198_   3460 TCCTGTTCAAAAAATGGTGCTGGGATAACTGTCTAGTCAAATGCAGAAGA 3509
                         vi  v     v              i     vv  ?i  v     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_244770198_   3510 TTGTAACTGGAACCCTTCCTCAAATCACATACAAAAGTCAACTTTAGATG 3559
                         v  v ii    v    v     v i  i        i i    iv i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_244770198_   3560 GACTAAAGACTTAAATGTAAAACATAAAACTATAAATACTCT--GAAAAC 3607
                           ii ?    i         i vv            -     --   i v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAA 543

  chr1_244770198_   3608 TAATTTAGG---AAATGCCATTCTGGATATAGGACCTGGCAAAGATTTTA 3654
                         -  iv    ---    -- -   vv  iv v  iiiv     v i   iv
  L1M4_orf2#LINE/    544 -AACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr1_244770198_   3655 CAACGAAGATGCCAAAATTGATTGCAACAAAAAAAAACCATAAATTAACA 3704
                         i ivv v  ii      viivvv         i    -----   vi i 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA-----AATAGATA 634

  chr1_244770198_   3705 AGTGGAACCTAATTAAA-TTAAAGAGCCCTTGCAGCAAAAAAGAAATTAT 3753
                          i v i  i v  i   -     i - ii   iivivv   i  v i   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chr1_244770198_   3754 TAA--AGGAGAAAACACAAACTACAGAATGGGATAAAATATTTGCAAAT- 3800
                         i  -- i v     v    v i           v               -
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_244770198_   3801 ATGCATGCAACAAA--ATTTACTATCCAGAATCTACAAGAAATTT----A 3844
                           ii  vii i  i-- i  i-          v  i  ii  i i---- 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACA 782

  chr1_244770198_   3845 A-TCAAATTAACAGAAA-ACAAACAACTCCAATAAAAAGTGGGCAAAGGA 3892
                          -    --   i i   -     i   i v v ?    i           
  L1M4_orf2#LINE/    783 ACTCAA--TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_244770198_   3893 CATGAATAGACCCTTTTCAAAAGATGACATTCATGTTGCCAATAAGCATA 3942
                         iv         vi  i  v     v  i  v  vi v           i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_244770198_   3943 TGGAAAAGTGCTCAACATCACTAATCGT 3970
                           i   ii            ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (142 / 90)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.67 (40 / 24)  


2429 25.53 3.36 4.37  chr1_244798207_244800153.rev      557  1449 (498)    L1M4_orf2#LINE/L1        4   887 (21)  

  chr1_244798207_    557 AAAAATATTCCTTGTTGATGGATTTGAAGAATCAATACTGTTAAAATGTC 606
                            i    i  v    v       v     v i    i      i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr1_244798207_    607 CATGCTACCCAAAGCAATTTACAGATTCAAACTCATCTCTATCAAAATAC 656
                         v  i  v      vii  i           vviv   i          v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr1_244798207_    657 CAATAACATTCTTCAAAAAAATAAAAAA----ATTCTAAAGTGCATATGG 702
                           iivi v  i  iiv i    vi v  ----  i     i v       
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr1_244798207_    703 AATCCTAAAAGACCTAGAATACCTAAAGCAATTTTGAGCAAAAAGAAAAA 752
                           vivi  ii    i      v i   i    i    iv  i     v  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr1_244798207_    753 AACTGAAGGAATCATAGTGCCTGAGTT-AAAATTATACTAAGGAACAATA 801
                          ii  i    v   i v v  ii v  -    i -     vii i v i 
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACA 252

  chr1_244798207_    802 GTAACCAAAACAACATGATACTGATGTTAAAAACAAACACATAGACTAAT 851
                             i   i   iii  i     iii -  ii i i   i     ii   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATCAAT 301

  chr1_244798207_    852 GGAATGGAA--GAGATTACCAAGAAACGAATCCATACAG----GG--AAC 893
                              i   --    v -   -    ii  i       v----  --  i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGT-CCA-GAAATAAACCCATACATTTATGGTCAAT 349

  chr1_244798207_    894 TCATTTTTGACAAAGATGCCAAGAACATATATTGGG--AATATTCAGTCT 941
                          v     i     i i        v   vi v    --  v v -     
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT-AGTCT 398

  chr1_244798207_    942 GTTCTATGAAATGGTGCTGGGAAAACTGAATATCCTTATGAAGAAAAATG 991
                         v   v i-              v     i   ?  vi   v i  i    
  L1M4_orf2#LINE/    399 TTTCAAC-AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr1_244798207_    992 AAACTAGACAACTATTTCTTGGCTTATACAAAAAT------AAAATTGTT 1035
                           ii i   vv   ii  viiv v           ------     v v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr1_244798207_   1036 TTAAATACTTTAATCTACAACCTCAAACTATGAAACTACTAACAGAAAAC 1085
                         i- ? v  i v   v  vi v  v       i     vi  iv       
  L1M4_orf2#LINE/    498 C-AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_244798207_   1086 ATTCAGG---AAATGCTCCAGGACATTGGACTAGGCAAAGATTTCTTGAG 1132
                           --   ---    -  i iv   v    ii       v i      iii
  L1M4_orf2#LINE/    547 AT--AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_244798207_   1133 CAATTCACTGCAGGAACAGGCAATCAAAGCAAAGGTGGACAAAT-GGA-- 1179
                         i vvv   iiv i v   i    iv    v   ii i  i    -   --
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_244798207_   1180 --ATCAAATTAAGTTAAAAAGCATCTGCAGAACAAAGAAAACAATCAACA 1227
                         --      ----i       - v i  iivvv     i v  v     v 
  L1M4_orf2#LINE/    644 TCATCAAA----ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_244798207_   1228 AAGTAAAGAGACAATCCACATGCCTGGGAGAAAATATTTTAAAACCACCC 1277
                             i  i      i     - vv               vv   i  ivi
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACA-GAATGGGAGAAAATATTTGCAAATCATAT 737

  chr1_244798207_   1278 ATCTAACAAGAAATTAGTACTCAGAATATATAAGGGGCTCAAACAACTCT 1327
                             i i   ii i v   ii            i ii   vv       -
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC- 786

  chr1_244798207_   1328 AATTGTCTAATAATTATTAGACAATTAGAAAAAGTCTAACAATTCATTTT 1377
                         --------      --------------      v v  i  ii  v  ?
  L1M4_orf2#LINE/    787 --------AATAAT--------------AAAAAGACAAATAACCCAATTW 814

  chr1_244798207_   1378 TAAAATGGGCAAAAGATTGGAATAGGC-TTTCTCCAAAGAAGACACACAA 1426
                         v            i    v      i -               i i    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_244798207_   1427 ATGGCAAACTGGTGTATGAAAAG 1449
                              v  ivi iii        
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAG 887

Transitions / transversions = 1.53 (136 / 89)
Gap_init rate = 0.03 (25 / 884), avg. gap size = 2.76 (69 / 25)  


2668 28.82 1.22 0.55  chr1_244800501_244807260.rev     5368  6269 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244800501_   5368 TGGAAAAACATTCCATCCTTATGGATAGGAAGAATCAATATCATGAAAAT 5417
                               i i  i    vi i      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244800501_   5418 GGCCATACTTCCCAGAGTAATTTATAGATTTAATGCTATTCCCTTCAAAC 5467
                            v     i    i v i  i  i     i  i  v  i  iv     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244800501_   5468 TACCATTGACATTGTTCACAGTATTAGAAAATATTTCCTTACATTTTATA 5517
                          v   vivi v  v  ii   v v v  v  vv vvi i  v v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_244800501_   5518 TGGAACCAAAAAGTAGCCCATATAGCCAAGACAATTCTAAACAAAAAGAA 5567
                              viiv  i v v  viv        i     ii i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_244800501_   5568 CAAAGCTGAAGGCATTATGCTACCTGAATTCAAACTATACTACAAGGCTA 5617
                              i  i   vv i ii  v  ii v      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_244800501_   5618 CAGTAACCAAAACAGTATGGTGCTAATAACAAAACAGACATATAAACCAA 5667
                               i   i     i    i  iii vv ii i         i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_244800501_   5668 TGGAACAGAACAGAGACCTCAAAAATAACACCATATATCTACAGCCATCT 5717
                              i    iv    vii  i      vv     i  i  ii i  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_244800501_   5718 AATTTTTGACAAATCTGACAAAAACAATCAATAGGGAAATTATTCCCTTT 5767
                         i     i     ivv  v   i v  v     i      vv  vvi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_244800501_   5768 CTAATAAATATTGCTGGGAAAACTGGCTAGCCATGTGCAGAAAACTGAAA 5817
                         ii  i    iv        v      v  ?   ii    i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_244800501_   5818 GTAGACCCCCACCTTACACCTTATACAAAAACTAACACAAGATGGATTAA 5867
                         v i      i    i     v          i    v   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_244800501_   5868 AGACTTAAATATAAAACCCAAAACCATAAATTTACTCGAAGAAAACCTAA 5917
                             i     i   i v i     i     vi vi v         v  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_244800501_   5918 GCA-ATACCATTTAGGACACACAGATGGGCAAAGACTTCT-AGACAAAAA 5965
                          ?i- v i -  iiv   vivvi v i     v ii    -   i vi -
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA- 598

  chr1_244800501_   5966 CACCAAAAGCAATTGCAACAAACCCAAAATTTGACAAATGGGATCTAATT 6015
                                    vvv        vvv    v v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_244800501_   6016 AAACTGAAGAGCTTCTGCACAACAAAATAAACTAGCATCAGAGTGAACAA 6065
                            v v  i i   i  ii vv    iv v    v  vv i      v i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_244800501_   6066 GCAACCTACAGAATGGGAGAAAA-ATTTGTAA-TCAACCCATCTGACAAA 6113
                         i     i                -     i  -   -ivi      i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGATAAG 747

  chr1_244800501_   6114 GGTCTAATATCCAGAATCTACAAGGAACT--TA-AATTTAA-AAGACAAA 6159
                           v  vi          v  i  i     --  -  i i  -  v v   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr1_244800501_   6160 AACAAACAACTTCATCAAAAAGTGGGTAAAGGATATGAACAAACACTTCT 6209
                         i     i   iiv  i?    i    i       v    i i   i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_244800501_   6210 CAAAAGAAAACATTTATGCATG--CAA-AAAAATATGTAAAAAAGCTTAT 6256
                          v      i i  -- iiv   --   -  iv i   v   i v   i v
  L1M4_orf2#LINE/    848 CCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr1_244800501_   6257 TATCACTGATTAT 6269
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (149 / 107)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.23 (16 / 13)  


2636 27.86 0.43 2.38  chr1_244808032_244812506     3057  3982 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244808032_   3057 TGGAAACACCTCCCTTGCACATGGGTGGGTAGAATCAATAGTGTGAAAAT 3106
                               v iv    v  iv     i v  v   v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244808032_   3107 GACCATACTGCCAAAGGCAATCTACAAATTCAATACAATTCCCATCAAAT 3156
                          i v     v  v  ivii       i      ii    i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244808032_   3157 TGCCACCATCATTCTTCACAAAACTAGAAGAAACAATCCTAAAATTCATA 3206
                          v   v vv v  i  ii  i  v v  vi ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_244808032_   3207 TGGAATCAAAATGGAGCCTGCACAGCCAAAGCAAAACTAAGCAAAAAGAA 3256
                              viiv  v   v  v v i       i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_244808032_   3257 CAAATCTGGAAATATCACATTACCCAACTTCAGATTGTACTATAAAGTCA 3306
                             vi    iivv     i v     i    i viv     i    ii 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_244808032_   3307 TTATCATGAAAACAGCATGGTACTGGTATAAAAATAGGCACATGGACAAA 3356
                         ivi v  v  i    ii         i    ii    i  i  i  iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_244808032_   3357 CCAAATAGAATAGAGAACCCAGAAATAATGTCAAATATTTACAGCAAACT 3406
                         ivi        v    ii          vvi  v i     ii iv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_244808032_   3407 GGTTTTCCACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACAACCTAT 3456
                          i     v    i vviv   i v   vv i         i i ii  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr1_244808032_   3457 TCAACAAATGCTGCTGGGATAATTGGCGCGCCACATGTAGGATAATGAAA 3506
                                   v        i  i   vvv?       i ii v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr1_244808032_   3507 CGGAATCCTCATCTCTCACCTTATACAAAAATAAATTCAAGGCCAATCAA 3556
                         iv i i  ii i   v    v           v  i    iiivi    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr1_244808032_   3557 AGACTTACGTCTAAAACCTGAAACCATAAAGATTCTAGAAGATAACATCG 3606
                             i  vi v   i v  i    i     iv ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr1_244808032_   3607 GGAACACCCTTCTAGATATTGGCTTAGGCAAAGACTTCAT-GATCGAGAA 3655
                          ?ivv vi    vv  iv    v        v ii   v -   -- vi 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGA 598

  chr1_244808032_   3656 C-CCAAAAGAAAATGCAAAAAAAAAAAAAAAAAAGAGGTGCGGGGATAAA 3704
                          -       v v v    v    i      v ------------      
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATA------------GATAAA 636

  chr1_244808032_   3705 AGATAAGACTAAATTAAACTAAAAAACTTCTGCAAAGCAAAAGAAATAAT 3754
                         --- vi    vv  i   v v        i  iivvv    i  v iv  
  L1M4_orf2#LINE/    637 ---TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr1_244808032_   3755 CAACAGAGTTAACAGACAACCCAGAGAGTGGGAGAAAATCTTCTCAATCT 3804
                            v i   v  v          v   i           v  iv   vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr1_244808032_   3805 ATACATCTGGCAATGGAATAATATCCAGAATCTACAAAGAACTCAAACAA 3854
                            i     ii  v   v vi          v  i         vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr1_244808032_   3855 ATTAGCAAGAAGAAAACAAACAATCCCATCAAACTGGGATTGGGCTAAGG 3904
                         v i ii  v  i  i     i  i  v  i?  ----i v     -  i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAA----AAATGGGC-AAAG 828

  chr1_244808032_   3905 GACTTGAATAGACAGTTCTC--AAGGAGATATACAAACGGCCAAAAAGCA 3952
                           i           v     --   i           i      v     
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_244808032_   3953 TAAGGAAAAATGCTGAACATCACTAATTAT 3982
                         i v i   i     v       ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (136 / 118)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.25 (26 / 8)  


2755 26.49 1.84 3.78  chr1_244830931_244832901.rev      555  1479 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr1_244830931_    555 GAAAACATATTTCTTGTTGATAGATTTGAATAATCAATATTGTTAAAATG 604
                          i   v    ii v    v  i    v   v v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr1_244830931_    605 TCTACACTACACAAAGCAATCTACAGATTCAATATTACCCCTATCAAAAT 654
                         v v i   v v    vii              iiiv i            
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_244830931_    655 ---AACAACATTCTTCACAAAAATTTTAAAA--AATGCTAAAATGTACAT 699
                         --- i vi v  i  ii  i     vvv  i--i  v       vi i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_244830931_    700 GGAATCTTAAAAGACCCAGAATACCCAAAGCAATCCTGAGCAAATAGAAC 749
                             vivi  ii           v     i     i   iv  iv     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_244830931_    750 AAAACTCAAGGAATCACATTGCCTGACTT-AAAATTATACTAAGGAGCTA 798
                            ii vi    v     i v  ii i  -    i -     vii     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTA 250

  chr1_244830931_    799 TAGTAACCAACACAGCATGATACTGACATAAAAAAAAACACATAGACTAA 848
                         i     i   v    ii  i     i     ii v i   i     ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_244830931_    849 TAGAACAGGAGAGAGAACCAGGAAACAAACACACAGACTAATGAGTGGAA 898
                          i   i  i vv    ii vi    i    v  i v i v   -  ----
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG-GT---- 345

  chr1_244830931_    899 GAGAGAAACAAGAAACAAATCCATACAGGAAGTTCATTTTTCATAAAGAT 948
                         ---------------   --------------  v     iv i  i i 
  L1M4_orf2#LINE/    346 ---------------CAA--------------TTGATTTTCGACAAGGGT 366

  chr1_244830931_    949 GCCAAGAACATACATAGGGGAAAAGACAGTCTCCTCAATAAATGGTGCCA 998
                                v   v  vv       ii i     ii    i         ii
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr1_244830931_    999 GGAAAACTGTATGTTCTTATGCAGAAGAATGAAACCAGACACCTATTTCT 1048
                            v     v  i?i vi     i         iiii   v    ii  v
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr1_244830931_   1049 TGGCTTATAAAAAAAT-----CAAAATGATTTAAAGACTT-----TAAGA 1088
                         iiv v    v      -----       iv i ?    i -----     
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr1_244830931_   1089 CCTCAAATTATGAAACTACTAACAGAAAACATTGGGGAAACTCTCCAGGA 1138
                         v  v   i   i     vi  iv         v  ? v  v   i iv  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr1_244830931_   1139 CATTGGACTGGGCAAAGATTTCTTGAGCAATTCACTGCAGGCACAGGCAG 1188
                          v    ii i     v i      iiii vvv   iiv i     i   i
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr1_244830931_   1189 TCAAAGCAAAGGTGCACAAATGGGATCAAATTAAGATAAAAAGCATTTGC 1238
                         iv    v   ii iv i    v   iivv  i  i  v    i v    i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr1_244830931_   1239 AGAACAAAGGAAACAATCAAGAAAGTAAAGAGACAATCCACAGAATGAGA 1288
                         ivvv       v  v           i  i      i          i  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr1_244830931_   1289 GAAAATATTTTAAAACTATTCATCTGACAAGGGATTAGTAACCAGAATTT 1338
                                   vv   ii  vi      i      i v   v       v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr1_244830931_   1339 ATAAGGGGCTCAAACAACTCTATAGGAAAAAGTCTAATAATCCAATTTAA 1388
                             i ii   vv       v   iv      v v     i      ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr1_244830931_   1389 AAATGGGAAAAAGTTCTGAAAAAAT-TTTCTACAAAGAAGACATACAAAT 1437
                                v   i v i    v i i-     v         i        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr1_244830931_   1438 GGCAAAATGGTGTATGAAAAGTTGCTCAACATCATCAATTAT 1479
                            v  vvi iii        v            ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 5.20 (52 / 10)  


3021 24.65 6.05 0.70  chr1_244853061_244855200      788  1647 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_244853061_    788 GAGAACTATCCCATATTCATGGATTGGAAGAATTAATAT-GTTAAATTTT 836
                           i iv        i                v       -     iv vv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_244853061_    837 TCATATTACCCAAAGGGGTCTATACATTTAATGACATTCTTGTCACA-TT 885
                         iv   i v      vv i    i v   i  i vv  i i i   v - i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_244853061_    886 TCAA-TGTCATTTTTCACAGAACTGGAGAAAAAAAT-----GATTTATAT 929
                         i  i-  i -     ii     v v  v  ivvi  -----i   i    
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_244853061_    930 G---------------------------AACAGT----------AAGAAC 942
                          ---------------------------    i ----------      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr1_244853061_    943 AAAAGGGGAGCA-TCACACTACTTTTTTTCTAAATATATTACAAAGCTAT 991
                            ivv    v -       v iivv    v   iv  i          i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr1_244853061_    992 GACACTCAAAACAGCATGGTACACGCATTACAAAAGGCACATTGACCAGT 1041
                         iii v    i    ii      vv    v vi v  i  i  v  i  i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr1_244853061_   1042 GGAACAGGATTTAGAGCCGAGAAATAAACCCACACATTTATAGTCAATTG 1091
                             i  i   v    i v             i        i        
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr1_244853061_   1092 ATTTTTGACAAATGTGCCAAAAACACACC-TGAGGAAAGGACTGTTCCTT 1140
                              i     iv       i v  iv v-  i      i iv  iii  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr1_244853061_   1141 CAACAAATGATACTGGAAAAATTAGATATCCACATGCAAAAGAACAAAAT 1190
                                  i i    i v  i i    ?               ii  i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr1_244853061_   1191 TGAACCCTTTTCTCACACCATATACAAAAATCAATTCAAAATGAATTA-- 1238
                           i    i vi                    i  i        i  i --
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr1_244853061_   1239 AACTTGGATATAAGACCCGAAACTGTAAAGCTACTAGAAGAAAATATAGG 1288
                         i  i ii  i     v ii     i    i  vi          i     
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr1_244853061_   1289 GA-AAAGCTCTGTGACATTGGTTTGGGCAATGTTTTTCTGGATATAAACT 1337
                         ?i-   v  ii     v    v  i       v   ii i     i vvi
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr1_244853061_   1338 CAAACTCCCATGGAACAAAAGCACAAATAAACAAATCAGATT--ATGCAA 1385
                             vv v  v v        v v     i i    ii  i --  -   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT-CAA 650

  chr1_244853061_   1386 AACTAAAAAGGTTCTGCACAGTAAAGGAAACAATCAATAGAGTGAAGGGA 1435
                           i      v-  i  ii vvi      v  v     v i      ii  
  L1M4_orf2#LINE/    651 AATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr1_244853061_   1436 CAACCCACAGAATTAGATAAAGTATTTGTAAACTATATTATCTGATAAGG 1485
                                      vi  v   i      i   ii    -           
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGG 748

  chr1_244853061_   1486 GATTAATAGAAAAAATATATCAGGAACTCAGAAACCTCAATAGTAAGAAA 1535
                           i vi  vvv i       v i      vv v v       i   i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_244853061_   1536 ATAAATAACACAATTTAAAAATGGGCATAAGACCTGAATAGACATTTCTG 1585
                          i       v     ?           v i  ii               v
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_244853061_   1586 GAAAGAAGACAGACAGATGGCCAACAGGTATATGAAAAATAATGCTTATT 1635
                         v        i v   i        i i i i       i--     i vi
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG--ATGCTCAAC 896

  chr1_244853061_   1636 ATCACTAGTCAT 1647
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (129 / 80)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 3.62 (58 / 16)  


3327 24.09 1.66 1.33  chr1_244859135_244861756.rev     1227  2131 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244859135_   1227 TGGAAAGATATTCCATGTTCATGAATGGGAAAAATAAATATTCTTAAAAT 1276
                                    i           i  v    i v v      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244859135_   1277 GTCCATACTATCTAAAGCAGTATACAGATTCAATGCAGTCCCTATCAATA 1326
                          v v     vi i   viii v           i   i          v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244859135_   1327 TACCAATGACATTTTTTACAGAAATGGAAAAAACAATCCTAAAATTTATA 1376
                          v   iivi v      i       v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_244859135_   1377 --GCAACCCATAAAAGACCCTGAATAGACAAAACTATCTTTAGCAAAAAC 1424
                         -- v  iv  -- ii     v      v      v     v iv  i  v
  L1M4_orf2#LINE/    151 TGGAAATGCA--AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr1_244859135_   1425 CACAA--CTAGAGGAATCACATTAATTGACTTCAAATTATACTACAGAGC 1472
                         v    --i i     v     i vviii i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr1_244859135_   1473 TATA-TAAACAAAATAGCAGGATACTGGCACAAAAACAGACACACAGACC 1521
                           i -   v   i i  iiv i        i  ii i     i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_244859135_   1522 AATGGAACAGCATAAAGA-CCCAAAAAGGAAATCCACACACCTACAGTTA 1570
                                i  v  vi   -i   i   v-   i   i   ii  ii  i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAAT-AAACCCATACATTTATGGTCA 347

  chr1_244859135_   1571 ACTCATTTGCAATCAAAGATGCCAAGTACATACATTGGGGAAAAGACAGT 1620
                          i v    v i -   i i       vv   v  v        ii i   
  L1M4_orf2#LINE/    348 ATTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr1_244859135_   1621 CTCTTCTATAAATG-TGCTGGGAAAACTGGATATTCACATGCAGAAGAAT 1669
                           i   v i     -        v         ?i        i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr1_244859135_   1670 GAAACTACACCCCTATCTCTTGCCATATACAAAAATCAAATCAAAATGGA 1719
                            ii iv       i   vii              i  v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr1_244859135_   1720 TTAAAGAGTTAAATCTAATACCTCAAATTATGAAAGTACTACAAGAAAAC 1769
                          i ?   vi     v   v v  v   i   i   v vi  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr1_244859135_   1770 ATTGGGAAAAGTCTCCAGGACATTGGTCTGGGCAAAGATTTCTTAAGTAA 1819
                           v  ?iv  i   i iv   v    vi i     v i       ii  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr1_244859135_   1820 TACCCTACAAGCACAGACAACAGA-GCAAAAATGGACAAATGGGATCCCA 1868
                         v  v i v       ii     i - v      i  i    v   iii  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr1_244859135_   1869 TCAAG-TTAAAAAGCTTCTGCACAGCAAAGGAAACTTATCAATCAATGAA 1917
                             i-       -   i  ii vv       v   -----     vi  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT-----ATCAAGAAA 690

  chr1_244859135_   1918 ATGAATAGACAATCCACAGAATGGGAGAAAATATTTGCAAACTACCCATC 1967
                         i    v      i                            ii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_244859135_   1968 TGACAAGGGATTAATAACCAGAGTATATAAGGAGCTCAAACAACTGTC-- 2015
                            i      i vi  v     i       i  i   vv      -- --
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--CAA 788

  chr1_244859135_   2016 ---TAGAAAT-CTAGTAATGTAATTATAAAATGGGCAAAAGATCTGAATG 2061
                         ---  i   v- v i   ivi    ?v            i   i     i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_244859135_   2062 CACATTTCTCCAAAGAAGACATACGAATTGCAAACACGCATAGAAAAGGG 2111
                         v                  i    i   v  v  i v   i vi   i i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_244859135_   2112 TGCTCAACATCATTGATTAT 2131
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (129 / 85)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.80 (27 / 15)  


2614 25.09 4.09 1.25  chr1_244950748_244954061     1941  2821 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_244950748_   1941 GAAACACATCCCATGCTCGTGGGTAGGTAGAATCAATAATTG--AAAATG 1988
                             v i        i  i   i v  v   v i    -   --  i   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA-TTGTTAAGATG 51

  chr1_244950748_   1989 ACCATATTGCC-AAAGCAATGGACAAATTCAATGCACTTCCCATCAATAC 2037
                         i v   i v  -   vii  vv   i      i   v i  i     v i
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_244950748_   2038 ACCACCATCATTCTTCACAGAA--CAACAA-----TCCTAAAATTCATAT 2080
                         v   v vv v  i  ii     --ii    -----               
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr1_244950748_   2081 GGAAC--CAAAAAGCCCACA-TAGCCAAAGCAAGACTAGGAAAAAAAGAA 2127
                             v--   iiii    v -        i   v-  v i    i     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAA 200

  chr1_244950748_   2128 CGAAACCAGAGGCATCACATTACTCGACTTCAAACTATACTATAAGGCCA 2177
                          i  iiii    vv     i v i i i      viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_244950748_   2178 TAGTCACCAAAATAGCTTGGTACTGGCATAAAAATCAGTATATAGACCAA 2227
                         i   v i   i i  iv              ii  viii       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_244950748_   2228 TGGAACAGTATAGAGAACCCAGAAATAAAACCAAATACT-ATAGCCAACT 2276
                              i  v  v    ii           v   v i i -  i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr1_244950748_   2277 GATCTTCAACAAAGCAAACAAAAACATAAAAGTGGGGGAAAGGACACCCT 2326
                            i   i    i vviv   i v   vv  -     -    i i vi  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGG-AAAGAATAGTCT 398

  chr1_244950748_   2327 ATTCAACAAATGGTGCTGAGAAAATTGGCAAGCCACATGTAAA-GAATGA 2375
                         v                 i  v  i   vv ?       i   -      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_244950748_   2376 AACTGGAACCTCATCTGTAACCTTATAGAAAAAACAACTCAAGATAGATC 2425
                          ii    v  ii i  vvv   v    v     vi       i  i    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_244950748_   2426 A--GACTTAAACCTAAGACCTGAAATTATTAAAATTCT-AGAAGATAACA 2472
                          --   i    iv     v  i   i   -    i   -      v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chr1_244950748_   2473 TCAGAA-AATGTTATCTT-GTAGACATTGGCTTAGGCAAAGACTTCATGA 2520
                          vi ?i-  ----     -  -   v    v        v ii   v ii
  L1M4_orf2#LINE/    548 TAGGNGTAA----ATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_244950748_   2521 CCAAGAACCCAAAAGCAAATGCAATAAAAACAAAAATAAATGA----GAC 2566
                         vi v  vv         v v    i    iv       i  i ----   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_244950748_   2567 TTAATTAAACTAAAAGGCTTGTGCACAGCAAAAGACATAATCATCAGAGT 2616
                           v  i   v v   ii   v  ii vv    i    iv    vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_244950748_   2617 AAACAGACAACCCATGGAGTGGGAGAAAATCTT--CAGTCTCTACATCCA 2664
                         i  v          ii  i           v  --  iviiv  i   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_244950748_   2665 ACAAAGGACTAATATCTAGAATCTACAAGAAACTC----AAATCAGCAAG 2710
                          i  i     vi    i     v  i  ii     ----  v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_244950748_   2711 AACAAAACAAA--GCC--ATTAAAAAGTGGGCTAAGGACACAAATAGACA 2756
                           v  i     --i  --   ?    i     v     ivii        
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr1_244950748_   2757 ATTCTCAAGAGAAAATATACAAATGGCCAACAA--ACATGAAAAAAATGC 2804
                         v     v i    i                i  --         i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chr1_244950748_   2805 TCAACATCACTAATTAT 2821
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (131 / 87)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 1.81 (47 / 26)  


2586 27.97 2.42 2.42  chr1_244956750_244958953.rev      808  1715 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244956750_    808 TGAAAACATATTCCAGATTCATGAACCAAAAGAATCAATATTGTTAAAAT 857
                           i   v    i   vi      i iiii    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244956750_    858 ATCCATAGTACTCAAAGCAATCTGTAGATTCAATGTTATCCTTATCAAAA 907
                         iv v   v v i    vii    ii        i iv    i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244956750_    908 TACCAATGACATTTCTTACAGATATAGAAGACACT-ATCCTAACATTTGT 956
                          v   iivi v   i  i    v  v  vi -i  -       v   ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_244956750_    957 ATGAAAGCACAAAACACCCAGAAGAGCCAAAATTATTCTAAGCAAAACCA 1006
                            i  iii   iiv        v        iv  ii i --    ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAA--- 194

  chr1_244956750_   1007 CCAACCAACCAACCCACCAAAACTGGAGGAATCCCATTGCCTGACTTCAA 1056
                         ------i vv   -----   ii       v  v  i v  ii i     
  L1M4_orf2#LINE/    195 ------GAAGAAC-----AAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_244956750_   1057 ATTATACTACAACAGAGCTACCATAACCAAAACAGCATGGTTCTGGCATA 1106
                          viv        ---      vi   i   i    ii    v        
  L1M4_orf2#LINE/    234 AACTTACTACAA---AGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr1_244956750_   1107 AACACAGATACATAGACCAATAAAACCGAAT-----ACTCAGAAACAAAT 1151
                          iv i   i i     i    ii  iv    -----iii      i   i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr1_244956750_   1152 CCACATACCTACAGTGAACTCATTTTCTACAAAGGTGCAAGGAACATACA 1201
                            i i ii  ii  v  i v      v    i     v i  v   v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr1_244956750_   1202 CCAGGGAAAAGATCGTCTCTTCAATAAGCTGTACTGGGAAAAGTGGATAT 1251
                         vii      ii  v    i     i  iiv  i      v  v      ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr1_244956750_   1252 CTATATGAAGAAAAATGAAACTAGTCCCGT--CTCTCGCCATATACAAAG 1299
                          i i   v i  i      ii i v   v --   v i           i
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr1_244956750_   1300 ATATAGTCAAAATGGACTAAAGACTT-----TAAGAACTCAAACTATGAA 1344
                           vv v          ii ?    i -----     i  v       i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr1_244956750_   1345 ACTACCAGAAGAAAACGTTGGAGAAAATCTCCAGGATATTTGTCTGGGCA 1394
                            vii          i v  ? v      i iv  iv  v vi i    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr1_244956750_   1395 AATATTTCTTGAGTAATACTCCATAA-CACAGGCAACCAAAGCAAACATG 1443
                          vvi      iii  vv  v   v  -    i     v    v   v  i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr1_244956750_   1444 GACAAAGGAGAGCACATTATG-TTAAAAAGCTTCTGCACAGTGAAGGAAA 1492
                           i   vvi  viv   i vi-       -   i  ii vvii     v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA 679

  chr1_244956750_   1493 TAAATCAA-----CGAAGAGACATCCCACAAAATGGAAGAAAATGTTTTC 1537
                         iv -    -----i   i     v      i     i       i   v 
  L1M4_orf2#LINE/    680 CTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr1_244956750_   1538 AAACTACACACCTGACAAGGAATTAATAACCACAATACATAGGGAGCTCA 1587
                            ii i i i    i    i i vi  v   v    i   ii  i   v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr1_244956750_   1588 AATAAATCTATAGGAAAAAATCTAATAATCTGATTTATATATTGATAAAA 1637
                         v i  v  v   iv     iv v     i ii   ? v v  v ii   i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr1_244956750_   1638 GATT-GAATAGACATTTCTCAAAAGACAACATACAAATCAAAAACAGGCA 1686
                             -               v     vi i        vivv  i i   
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr1_244956750_   1687 CATAAAAAG-TGCTCAACATTGATCAGAGA 1715
                            i     -          ii????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (156 / 94)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.75 (44 / 16)  


2347 24.15 11.35 1.69  chr1_244964785_244967237.rev     1135  1962 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244964785_   1135 TGGGAAGATATCTCATGTTAATGGGTTAGAATAACTAATATTCTTTAAAT 1184
                            i        i      v    i  i   v vi       v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244964785_   1185 GTCCATATTACTCCAGAAAATG-TCT---GATTCAGTATAACCCCAACTA 1230
                          v v   i - i   --  v  -   ---      iiii  i   v ii 
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCA--AATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_244964785_   1231 AAATCCACAG--GCATTTTTTACATAAATAGAATAAAACCATTCTAGAAA 1278
                               -   --  v      i  v    v  -i  iviv  i   -   
  L1M4_orf2#LINE/     98 AAATCC-CAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTA-AAA 144

  chr1_244964785_   1279 TTT-TGTG--AATGCACAAAAATATCAAATAGCCAAAGCAATATTGATAA 1325
                           i- i  --      - iii ivivi          i    v    v  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr1_244964785_   1326 A-AAGAACAAAGCTGGAGGCTTCAGACT--CCGATTTCAAA-----CTAT 1367
                          -          i      vi   v   --  i        -----   i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr1_244964785_   1368 A---TTACA--AAT---------------------------------TAT 1379
                          ---i    --   ---------------------------------   
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr1_244964785_   1380 AGA---------------------------AATAAAGCCATGCTTATATG 1402
                            ---------------------------      v    i v v    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr1_244964785_   1403 GTCAATTAGTCTTTGATGAGGGTGCCAAAA--ATGCAGCATGAAGAAAGG 1450
                                ii i  i  ii          i --  v  --   ii     i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAGA 391

  chr1_244964785_   1451 ATAGTCTGTTCAATAAATGGCATTGGGAAAACCAGATACATACATGCAGA 1500
                                v     i      iii     v   ii    ?vi       i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr1_244964785_   1501 GGAACGAAATTGGACTCTTATCCTACACTATTCCCCCAAAACCAAATCTA 1550
                         i   i   i      i i  i ii    i  -viv v    ii  v  v 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCAT-ATACAAAAATTAACTCAA 490

  chr1_244964785_   1551 AATGGATCGAAGACTTAAATGGAAGACCTGGACTTGTAAAAGTCCTAGAT 1600
                                 i?    i      v    v  ii vi i     v  i    v
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr1_244964785_   1601 GATGACATAGGGAAACAGCTCTTTGACATTGATCTTGGCCGTGATATTTT 1650
                           vi       ?iv v v  iiv    v   ivi v   vi  i v i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr1_244964785_   1651 TGATATGACACAAAAATTA-AGGCAACAAAAGCAAAA-TAAGCAAGTAGG 1698
                         v          v    vi - i          v    -  iii  i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr1_244964785_   1699 ACTGCATCAACATGCAAAAACTTTTGCACAGAAAAGGAAAC----AATAA 1744
                            v      v  -i           ii vvv      v  ----  v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr1_244964785_   1745 AATGAAAAGGTAATCTCTGCAATGGGAGAACATATCTGCAAACCATATTT 1794
                          i       ii  i iviiv          v    i      i     v 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr1_244964785_   1795 TGGATAAGGAGTTAGCATCCAAAATATA-AAAGAAA-CTGACAAAATCAT 1842
                         iv       iii v i     i      -      v-  v    v-   v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAA 788

  chr1_244964785_   1843 TAGCAAATAT-CAAATTACCCAACTTAAAAATGG-TAAAGACAGTGTGAA 1890
                           ii   v v-     v      i ?        -i    i--i v    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG--ATTTGAA 836

  chr1_244964785_   1891 TAGGCATTTTTCCAAAGAGGCAATACAAATAGCCAACAGGTGAATGAAAA 1940
                            i     i        i vv        i     i i iiv       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_244964785_   1941 GATGTTCAACATCACTAATCAT 1962
                             i         ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (120 / 76)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 3.48 (108 / 31)  


2344 28.40 3.48 1.57  chr1_244982745_244984980      853  1743 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_244982745_    853 TGGAAAGATTCCCCATGTTCGTGGATTAGAAGAATTGATATCATTAAAAT 902
                                  vi         i      i     v  i    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_244982745_    903 GTCCAT-CTACCAAAAGAGAGCTACAGAATTAAGGCAATCACTATCCGAA 951
                          v v  -  v  v   vv  v       v i  v      v     vi  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_244982745_    952 TACAAAAGATATTCTT--CAGAGATAGAAAAAAACAATCCTAAAGTTCAT 999
                          v v ivviiv  i  --    i  v  v  iv-ii        i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_244982745_   1000 ATGGAAGCAAAAAAGACTCCAAATAGCCAATGCAATTCTGAGCAAAATGA 1049
                               iiiv  ii   i vi         vi    ii   iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_244982745_   1050 ATGAATATGTAGGCATCATACTACCCGAT---A-----TACTACAA-GCT 1090
                          ii  vv  v   vv   i   v   i  --- -----        -   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_244982745_   1091 ATTAAACATCAAAAGAGAATGGTACTGGCATAAAAGCAGACACACA---- 1136
                          i- ivv     i v  vi              iiii     i i ----
  L1M4_orf2#LINE/    250 AC-AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_244982745_   1137 AACAGAAGAGAACCCCTGAGAGTCCAGATATAAATTCACTCATTTATAGT 1186
                           ii   v    i---            v     ii  iv       i  
  L1M4_orf2#LINE/    299 AATGGAATAGAAT---TGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_244982745_   1187 CAACTGATGTTTGACCAAGTTGAAAAGAACATACACCAAGAAAAGCACTA 1236
                            i    v  i   v i v  vv    v   v  viii i    v ivi
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_244982745_   1237 CTTCCTCAATAAATGGTGATGCAAAAAATGCATATCCAAATACA---GAA 1283
                         ii ii    i        v  vi v  v  v   ?   v  i  ---   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_244982745_   1284 TGAAACTAGACACTTATTTCAC----TATTTTAAA-----CTCAAATTGG 1324
                             ii i   v i  ii    ----   viv   -----      v   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_244982745_   1325 ATTAAAGACTTTAATATCAGATCTTAAACTGTAAAACTTCTGGTAGAAAA 1374
                           i ?    i v   i v   v  v     i       ii i v      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_244982745_   1375 CACAGGCAGAATGCATCATCACTACATTGATCTGGGCAAGAATTTTTAAA 1424
                           i   ?iv  ---   v  iiv  v   ivi i     vii   i v i
  L1M4_orf2#LINE/    546 CATAGGNGTAA---ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_244982745_   1425 GTAGAACCTCAAAATCACAGGGAA-AAATTAAAAAATTAAAAAATGAGAT 1473
                         i  vi  vi     v    i v  -   vv       vi v    vi  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_244982745_   1474 TACATCATACTGAAAGGTTCTT-CACAATAACGAAAACAATTCACAGAGT 1522
                          v     v v v   iii i  -ii vvi  v i v  v  iv v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_244982745_   1523 GAATAGATAACATAC-GAGTGGGAGAAAAGATTTGCCAACAATGCATTTG 1571
                            v   i   vi  -  i          v      v  iv  ii  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_244982745_   1572 ACAAGGGGTTCATATCCAGAATATATAAAGAACTCAAGTAACTGAGTACC 1621
                          i     ii ii                       vvii    v i  vi
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_244982745_   1622 AAAATTATCCCACAAATAATTTGATTTAAAAAATGGGCAAAAGACATCAA 1671
                             -- v---        iiii   ?     -        i  iv v  
  L1M4_orf2#LINE/    793 AAAA--AG---ACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chr1_244982745_   1672 AAAACATATTTCAAAAGAAGACATACAAATGGCTAGCACGTATATGACAA 1721
                         v i    v i  v        i           i ii v i i    v  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr1_244982745_   1722 AGTGCTCAACATCACTAATCAT 1743
                         ii            ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (141 / 108)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.37 (45 / 19)  


1800 26.29 1.59 0.60  chr1_245003707_245009108.rev        1   502 (4900)    L1M4_orf2#LINE/L1      215   721 (187)  

  chr1_245003707_      1 TCACACTACCTGACTTCGAACTATACTACAAGGCTACAGTAACCAAAACA 50
                                v  ii i   i  viv        i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr1_245003707_     51 GCATGGTAGTGGTACCAAAACAGATATATAGACCAATGGAACAGAACAGA 100
                          ii     v   i iv ii i   i       i        i    iv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr1_245003707_    101 GGCCTCGGAAATAACACCGCACATCTACAACCATCTGATCTTTGACAAAA 150
                          ivii i       vv  ii    i  iiii  vi    i  i     ii
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr1_245003707_    151 CTGACAAAAACAAGCAATGGGAAAAAAAATTCCCTGTTTAATAAATGGTG 200
                         v  v   i v  vv       i   i  - vvi  v  i  i        
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTTTTCAACAAATGGTG 413

  chr1_245003707_    201 CTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAACTGGACTTCTTCC 250
                               v      v  ?   i     i  i v    ii     ii  v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr1_245003707_    251 TTACATCTTATA-AAAAATTAACTCAAGATAGATTAAAGACTTAAATGTT 299
                          i   i v    -              i  i   i ?    i       v
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr1_245003707_    300 AGACCTAAAACAATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTC 348
                            v       v      vi i           v    ?i- v i -   
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC 562

  chr1_245003707_    349 AGGACATAGACGTGGGTAAAGACTTCATGACTAAAACACCAAAAGCAATG 398
                         iv   v v ivv i  i  v ii   v iiv  vi            vvi
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr1_245003707_    399 GCAACAAAAGCCAAAGTTGACAAATGGGATCT------AATTAAAGAGCT 442
                                   vv   i v  i    v   ii ------       i -  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CT 661

  chr1_245003707_    443 TCTGTGCAGCAAAGGAAACTATCATCATAGTGAACAGGCAAGCTATAGAA 492
                          i     vv       v       vv v      v  i   v i i    
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr1_245003707_    493 TGGGAGAAAA 502
                                   
  L1M4_orf2#LINE/    712 TGGGAGAAAA 721

Transitions / transversions = 1.48 (77 / 52)
Gap_init rate = 0.01 (6 / 507), avg. gap size = 1.83 (11 / 6)  

3082 26.36 1.78 0.78  chr1_245003707_245009108.rev     4013  4911 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_245003707_   4013 TGGAAGAACATTCTATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4062
                              ii i  i i   i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_245003707_   4063 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4112
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_245003707_   4113 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4159
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_245003707_   4160 ATATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAA 4209
                                 viiv  ii  v  viv  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_245003707_   4210 GAACAAACCTCGAGGCATCACACTACCTGAATTCAAACTATACTACAAGG 4259
                                vi v    vv       v  ii v      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_245003707_   4260 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGAT 4309
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_245003707_   4310 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 4357
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_245003707_   4358 TATCTGATCTTTGACAAACCTGAGAAAAGCA----ATGGGGAAAGGATTC 4403
                         i vi    i  i     ivv  vv  i v  ----          i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_245003707_   4404 CCTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCAATATGTAGAAAGC 4453
                         i  v  i  i              v  i   v  ? v i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_245003707_   4454 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 4503
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_245003707_   4504 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAA 4553
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_245003707_   4554 CCTAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 4601
                          v    ?-   --i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_245003707_   4602 TAAAACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATC 4651
                           vi            vvi   i      vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_245003707_   4652 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTG 4701
                          v  i   v v  i i   i  ii vv    i  v    i  vv i v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_245003707_   4702 AACAGGCAACCTACAAAATGGGAGGAAATTTTCGCAACCTACTCATCTGA 4751
                           v  i     i   i        i    v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_245003707_   4752 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 4801
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_245003707_   4802 AAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 4847
                             i    ----   v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_245003707_   4848 TTCTCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAA-ATGCTC 4896
                              v           vi viii     v  i          -      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_245003707_   4897 ATCATCACCGGCCAT 4911
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


 683 23.94 0.70 0.00  chr1_245015592_245023039        1   142 (7306)    L1M4_orf2#LINE/L1      279   421 (487)  

  chr1_245015592_      1 TAAAAACAGACACATGGGCCAATAGAACAGAATGGAGAACCTAGAAATAG 50
                            ii i     i  i ii    i   i     v    ii i       i
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr1_245015592_     51 ATTCATGTATTTACAGCCAACTGATTTTTGACAAAGGTGCCAAGAACATA 100
                          ii   ii     ii i   i       i     i          v   v
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr1_245015592_    101 CACTGGGGAAAGGAGAGTTTCTTCAATAAATG-TCCTGGAACA 142
                           v         i v   i i     i     - v    i   
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

Transitions / transversions = 4.67 (28 / 6)
Gap_init rate = 0.01 (1 / 143), avg. gap size = 1.00 (1 / 1)  

2934 27.40 2.01 0.45  chr1_245015592_245023039      492  1385 (6063)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr1_245015592_   1385 TGGAAGAACATTCCATGCTCATGGATAGGAAGAAGAAATACCATGAAAAT 1336
                              ii i  i     i        v      vvv    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr1_245015592_   1335 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1286
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr1_245015592_   1285 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 1241
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr1_245015592_   1240 TGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 1191
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chr1_245015592_   1190 CAAAGCTGGAGGCATCATGCTACCTAACTTTAAACTATACTACAAGGCTA 1141
                              i      vv   ii  v  i  i  i   viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chr1_245015592_   1140 CAGTAACCAAAATAGCATGGCACTGGTACCAAAACAGAGAGATAGACCAA 1091
                               i   i i  ii   i     i iv ii i   v v     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

C chr1_245015592_   1090 TGGAACAGAAC--AGAACCCTCCGAAATAATACCACACATCTTCAACTAT 1043
                              i    i--   ii  --v       vv   i    i viiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

C chr1_245015592_   1042 CTGATCTTTGACAAACCTGACAAAACAAG-AAATAGGGAAAGGATTCCCT 994
                         i    i  i     ivv  v   i  v v-v   i       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

C chr1_245015592_    993 ATTTAACAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCTGA 944
                         v  i                 v     iv  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

C chr1_245015592_    943 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 894
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

C chr1_245015592_    893 AAAGACGTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 844
                          ?    v       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

C chr1_245015592_    843 AGGC--AATTCCATTCAGGACATAGGCATGGATAAGGACTTCATGTCTAA 796
                            ?--  v  --   iv   v v  vv i ii  v ii   v ivv  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chr1_245015592_    795 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 746
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chr1_245015592_    745 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGTAC 696
                          i   v v  i i   i  ii vv    i  v    i  vv i    v v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chr1_245015592_    695 AGGCAACCTAGAGAATGGGAGAAAATTTTTGCAGTCTACTCATCTGACAA 646
                           i     i v               v      ivii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chr1_245015592_    645 AGGGATAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 596
                         i  iv vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chr1_245015592_    595 A---AAA-AACCCA-TCAAAAAGTGGGCGAAAGATATGAACAGACACTTC 551
                          ---   -      - i?    i     i  i   v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chr1_245015592_    550 TC---AAAAGATATTTATGCAGCCCACAGCCACATGAAAAAATGCTCATT 504
                           --- i       vi viii   v i iv          i       vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chr1_245015592_    503 ATCACTGGCCAT 492
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (140 / 101)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  

3082 26.36 1.78 0.78  chr1_245015592_245023039     6057  6955 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_245015592_   6057 TGGAAGAACATTCTATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 6106
                              ii i  i i   i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_245015592_   6107 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 6156
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_245015592_   6157 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 6203
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr1_245015592_   6204 ATATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAA 6253
                                 viiv  ii  v  viv  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr1_245015592_   6254 GAACAAACCTCGAGGCATCACACTACCTGAATTCAAACTATACTACAAGG 6303
                                vi v    vv       v  ii v      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr1_245015592_   6304 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGAT 6353
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr1_245015592_   6354 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 6401
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr1_245015592_   6402 TATCTGATCTTTGACAAACCTGAGAAAAGCA----ATGGGGAAAGGATTC 6447
                         i vi    i  i     ivv  vv  i v  ----          i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_245015592_   6448 CCTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCAATATGTAGAAAGC 6497
                         i  v  i  i              v  i   v  ? v i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_245015592_   6498 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 6547
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_245015592_   6548 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAA 6597
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_245015592_   6598 CCTAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 6645
                          v    ?-   --i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr1_245015592_   6646 TAAAACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATC 6695
                           vi            vvi   i      vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr1_245015592_   6696 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTG 6745
                          v  i   v v  i i   i  ii vv    i  v    i  vv i v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr1_245015592_   6746 AACAGGCAACCTACAAAATGGGAGGAAATTTTCGCAACCTACTCATCTGA 6795
                           v  i     i   i        i    v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr1_245015592_   6796 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 6845
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr1_245015592_   6846 AAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 6891
                             i    ----   v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr1_245015592_   6892 TTCTCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAA-ATGCTC 6940
                              v           vi viii     v  i          -      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr1_245015592_   6941 ATCATCACCGGCCAT 6955
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


2367 28.06 3.59 1.68  chr1_245041787_245044022.rev      855  1745 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_245041787_    855 TGGAAAGATTCCCCATGTTCGTGGATTAGAAGAATTGATATCATTAAAAT 904
                                  vi         i      i     v  i    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_245041787_    905 GTCCAT-CTACCAAAAGAGAGCTACAGAATTAAAGCAATCACTATCCGAA 953
                          v v  -  v  v   vv  v       v i  v      v     vi  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_245041787_    954 TACAAAAGATATTCTT--CAGAGATAGAAAAAAACAATCCTAAAGTTCAT 1001
                          v v ivviiv  i  --    i  v  v  iv-ii        i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr1_245041787_   1002 ATGGAAGCAAAAAAGACTCCAAATAGCCAATGCAATTCTGAGCAAAATGA 1051
                               iiiv  ii   i vi         vi    ii   iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr1_245041787_   1052 ATGAATATGTAGGCATCATACTACCCGAT---A-----TACTACAA-GCT 1092
                          ii  vv  v   vv   i   v   i  --- -----        -   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr1_245041787_   1093 ATTAAACATCAAAAGAGAATGGTACTGGCATAAAAGCAGACACACA---- 1138
                          i- ivv     i v  vi              iiii     i i ----
  L1M4_orf2#LINE/    250 AC-AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr1_245041787_   1139 AACAGAAGAGAACCCCTGAGAGCCCAGATATAAATTCACTCATTTATAGT 1188
                           ii   v    i---      i     v     ii  iv       i  
  L1M4_orf2#LINE/    299 AATGGAATAGAAT---TGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_245041787_   1189 CAACTGATGTTTGACCAAGTTGAAAAGAACATACACCAAGAAAAGCACTA 1238
                            i    v  i   v i v  vv    v   v  viii i    v ivi
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr1_245041787_   1239 CTTCCTCAATAAATGGTGATGCAAAAAATGCATATCCAAATACA---GAA 1285
                         ii ii    i        v  vi v  v  v   ?   v  i  ---   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_245041787_   1286 TGAAACTAGACACTTATTTCAC----TATTTTAAA-----CTCAAATTGG 1326
                             ii i   v i  ii    ----   viv   -----      v   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_245041787_   1327 ATTAAAGACTTTAATATCAGATCTTAAACTGTAAAACTTCTGGTAGAAAA 1376
                           i ?    i v   i v   v  v     i       ii i v      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_245041787_   1377 CACAGGCAGAATGCATCATCACTACATTGATCTGGGCAAGAATTTTTAAA 1426
                           i   ?iv  ---   v  iiv  v   ivi i     vii   i v i
  L1M4_orf2#LINE/    546 CATAGGNGTAA---ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr1_245041787_   1427 GTAGAACCTCAAAATCACAGGGAA-AAAATAAAAAATTAAAAAATGAGAT 1475
                         i  vi  vi     v    i v  -    v       vi v    vi  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr1_245041787_   1476 TACATCATA-CTGAAAGGTTCTGCACAATAACGAAAACAATTCACAGAGT 1524
                          v     v -i i   iv  i  ii vvi  v i v  v  iv v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr1_245041787_   1525 GAATAGATAACATAC-GAGTGGGAGAAAAGATTTGCCAACAATGCATTTG 1573
                            v   i   vi  -  i          v      v  iv  ii  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr1_245041787_   1574 ACAAGGGGTTCATATCCAGAATATATAAAGAACTCAAGTAACTGAGTACC 1623
                          i     ii ii                       vvii    v i  vi
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr1_245041787_   1624 AAAATTATCTCACAAATAATTTGATTTTAAAAATGGGCAAAAGACATCGA 1673
                             -- v---        iiii   ?-             i  i- i  
  L1M4_orf2#LINE/    793 AAAA--AG---ACAAATAACCCAATTW-AAAAATGGGCAAAGGAT-TTGA 835

  chr1_245041787_   1674 A-AAACATATTTCAAAAGAAGACATACAAATGGCTAGCACGTATATGACA 1722
                          - i    v i  v        i           i ii v i i    v 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr1_245041787_   1723 AAGTGCTCAACATCACTAATCAT 1745
                          ii            ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (143 / 103)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.24 (47 / 21)  


2286 24.79 11.37 1.57  chr1_245059548_245062003     1137  1963 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_245059548_   1137 TGGGAGGATATCTCATGTTAATGGGTTAGAATAACTAATATTCTTTAAAT 1186
                            i i      i      v    i  i   v vi       v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_245059548_   1187 GTCCATATTACTCCAGAAAATG-TCT---GATTCAGTATAACCCCAACTA 1232
                          v v   i - i   --  v  -   ---      iiii  i   v ii 
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCA--AATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr1_245059548_   1233 AAATTCCACAGGCATTTTTTACATAAATAGAATAAAACAACTCTAGAAAT 1282
                             i   vvv  v      i  v    v  -i  ivii ii   -    
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTA-AAAT 145

  chr1_245059548_   1283 TT-TGTG--AATGCACAAAAATATCAAATAGCCAAAGCAATATTGATAAA 1329
                          i- i  --      - iii ivivi          i    v    v   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr1_245059548_   1330 -AAGAACAAAGCTGGAGG-CTTG-ACT--CCGATTTCAAA-----CTATA 1369
                         -          i      -  ii-   --  i        -----   i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr1_245059548_   1370 ---TTACA--AAT---------------------------------TATA 1381
                         ---i    --   ---------------------------------    
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr1_245059548_   1382 GA---------------------------AATAAAGCCATGCTTATATGG 1404
                           ---------------------------      v    i v v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr1_245059548_   1405 TCAATTAGTCTTTGATGAGGGTGCCAAAA--ATGCAGCATGAAGAAAGGA 1452
                               ii i  i  ii          i --  v  --   ii     i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAGAA 392

  chr1_245059548_   1453 TAGTCTGTTCAATAAATGGCATTGGGAAAACCAGATACATACATGCAGAG 1502
                               v     i      iii     v   ii    ?vi       i i
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr1_245059548_   1503 GAACGAAATTGGACTCTTATCCTACACTATTCCCCCAAAACCAAATCTAA 1552
                            i   i      i i  i ii    i  -viv v    ii  v  v  
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCAT-ATACAAAAATTAACTCAAA 491

  chr1_245059548_   1553 ATGGATCGAAGACTTAAATGGAAGACCTGGACTTGTAAAAGTCCTAGATG 1602
                                i?    i      v    v  ii vi i     v  i    v 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr1_245059548_   1603 ATGACATAGGGAAACAGCTCTTTGACATTGATCTTGGCCGTGATATTTTT 1652
                          vi       ?iv v v  iiv    v   ivi v   vi  i v i  v
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr1_245059548_   1653 GATATGACACAAAAATTA-AGGCAACAAAAGCAAAA-TAAGCAAGTAGGA 1700
                                   v    vi - i          v    -  iii  i v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr1_245059548_   1701 CTGCATCAACATGCAAAAACTTTTGCACAGAAAAGGAAAC----AATAAA 1746
                           v      v  -i           ii vvv      v  ----  v   
  L1M4_orf2#LINE/    642 CTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr1_245059548_   1747 ATGAAAAGGTAATCTCTGCAATGGGAGAACATATCTGCAAACCATATTTT 1796
                         i       ii  i iviiv          v    i      i     v i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr1_245059548_   1797 GGATAAGGAGTTAGCATCCAAAATATA-AAAGAAA-CTGACAAAATCATT 1844
                         v       iii v i     i      -      v-  v    v-   v 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAAT 789

  chr1_245059548_   1845 AGCAAATAT-CAAATTACCCAACTTAAAAATGG-TAAAGACAGTGTGAAT 1892
                          ii   v v-     v      i ?        -i    i--i v     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG--ATTTGAAT 837

  chr1_245059548_   1893 AGGCATTTTTCCAAAGAGGCAATACAAATAGCCAACAGGTGAATGAAAAG 1942
                           i     i        i vv        i     i i iiv        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr1_245059548_   1943 ATGTTCAACATCACTAATCAT 1963
                            i         ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (125 / 76)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 3.45 (107 / 31)  


2624 28.13 1.98 2.20  chr1_245067753_245070104      952  1861 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr1_245067753_    952 TGAAAAGATATTCCAGGTTCATGAACCAAAAGAATCAATATTGTTAAAAT 1001
                           i        i   v       i iiii    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_245067753_   1002 ATCCATAGTACTCAAAGCAATCTATAGATTCAATGTTATCCTTATCAAAA 1051
                         iv v   v v i    vii     i        i iv    i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_245067753_   1052 TACCAATGACATTTCTTACAGATATAGAAGACACT-ATCCTATCATTTGT 1100
                          v   iivi v   i  i    v  v  vi -i  -      vv   ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr1_245067753_   1101 ATGAAGGCACAAAACACCCAGAGGAGCCAAAATTATTCTAAGCAAAACCG 1150
                            i iiii   iiv       iv        iv  ii i --    ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAA--- 194

  chr1_245067753_   1151 CCAACCAACCAACCCACCAAAACTGGAGGAATCCCATTGCCTGACTTCAA 1200
                         ------i vv   -----   ii       v  v  i v  ii i     
  L1M4_orf2#LINE/    195 ------GAAGAAC-----AAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr1_245067753_   1201 ATTATACTACAGAGCTACCATAACCAAAACAGCATGGTGCTGGCATAAAT 1250
                          viv       i      vi   i   i    ii    i         iv
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr1_245067753_   1251 GCAGATACATAGACCAATGAAACAGAATAGAGAACTCAGAAACAAATCCA 1300
                         ii   i i     i     i  i     v    iii      i   i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr1_245067753_   1301 CACACCTACAGTGAACTCATTTTCTACAAAGGTGCAAGGAACATACACCA 1350
                         i   ii  ii  v  i v      v    i     v i  v   v  vii
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr1_245067753_   1351 GGGAAAAGATCATCTCTTCAATAAGCAGCACTGGGAAAAGTGGATATCTA 1400
                               ii  vi   i     i  iii ii      v  v      ? i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_245067753_   1401 TATGAAGAAAAATGAAACTAGTCCCGT--CTCTCGCCATATACAAAGATA 1448
                         i   v i  i      ii i v   v --   v i           i  v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_245067753_   1449 TAGTCAAAATGGACTAAAGACTT-----TAAGACCTCAAACTATGAAACT 1493
                         v v          ii ?    i -----     v  v       i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_245067753_   1494 ACCAGAAGAAAACATTGGAGAAAATCTCCAGGATATTTGTCTGGGCAAAT 1543
                         vii            v  ? v      i iv  iv  v vi i     vv
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr1_245067753_   1544 ATTTCTTGAGTAATACTCCATAA-CACAGACAACCAAAGCAAACATGGAC 1592
                         i      iii  vv  v   v  -    ii    v    v   v  i  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr1_245067753_   1593 AAATGAGAGCACATTTTG-TTAAAAAGCTTCTGCACAGTGAAGGAAATAA 1641
                             vi  viv   ivvi-       -   i  ii vvii     v iv 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA 682

  chr1_245067753_   1642 ATCAACAAAG-----AGACATCCCACAAAATGGAAGAAAATGTTTTCAAA 1686
                         -    v    -----     v      i     i       i   v    
  L1M4_orf2#LINE/    683 -TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr1_245067753_   1687 CTACCCACCTGACAAGGAATTAATAACCGCAATACATAGGGAGCTCAAAC 1736
                         ii ivi i    i    i i vi  v  iv    i   ii  i   vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr1_245067753_   1737 AAATCTATAGGAAAAA-ATATAATAATCTGATTTATATACTGATAAAAGA 1785
                           v  v   iv     - i -     i ii   ? v v iv ii   i  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr1_245067753_   1786 TT-GAATACACATTTCTCAAAAGACAACATACAAATCAAAAACAGGCACA 1834
                           -     v         v     vi i        vivv  i i     
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr1_245067753_   1835 TAAAAAG-TGCTCAACATTGATCAGAGA 1861
                          i     -          ii????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (158 / 94)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.38 (38 / 16)  


2636 25.25 3.37 1.68  chr1_245072771_245076088.rev     1937  2827 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_245072771_   1937 GAAACACATCCCATGCTTATGGGTGAGTAGAATCAATAATTG--AAAATG 1984
                             v i        i i    i vi v   v i    -   --  i   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA-TTGTTAAGATG 51

  chr1_245072771_   1985 ACCATATTGCC-AAAGCAATGGACAAATTCAATGCACTTCCCATCAAAAC 2033
                         i v   i v  -   vii  vv   i      i   v i  i       i
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr1_245072771_   2034 ACCACCATCATTCTTCACAGAAA--AACAATCCTAAACAATCCTAAAATT 2081
                         v   v vv v  i  ii      --i    v i-----i           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT-----GATCCTAAAATT 146

  chr1_245072771_   2082 CATATGGAAC--CAAAAAGCCCACA-TAGCCAAAGCAAGACTAGGAAAAG 2128
                                  v--   iiii    v -        i   v-  v i     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAG 195

  chr1_245072771_   2129 A-GAACGAAACCAGAGGCATCACATTACTCGACTTCAAACTATACTATAA 2177
                          -    i  iiii    vv     i v i i i      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr1_245072771_   2178 GGCCATAGTCACCAAAATAGCTTGGTACTGGCATAAAAATCAGTATATAG 2227
                         i  i i   v i   i i  iv              ii  viii      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr1_245072771_   2228 ACCAATGGAACAGTATAGAGAACCCAGAAATAAAACCAAATACT-ACAGC 2276
                          i        i  v  v    ii           v   v i i - ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr1_245072771_   2277 CAACTGATCTTCAACAAAGCAAACAAAAACATAAAAGTGGGGAAAGGACA 2326
                            i    i   i    i vviv   i v   vv  -         i i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATA 394

  chr1_245072771_   2327 CCCTATTCAACAAATGGTGCTGAGAAAATTGGCAAGCCACATGTAAA-GA 2375
                         vi  v                 i  v  i   vv ?       i   -  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr1_245072771_   2376 ATGAAACTGGAACCTCATCTCTAACCTTATAGAAAAAACAACTCAGGATA 2425
                              ii    v  ii i   vv   v    v     vi      ii  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr1_245072771_   2426 GATCAAAGACTTAAACCTAAGACCTGAAATTATTAAAAATCT-GGAAAAT 2474
                              ?    i    iv     v  i   i   -    v   -i   i v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAA 543

  chr1_245072771_   2475 AACGTCAGAAAATGTTAA-CTT-GTAGACATTGGCTTAGGCAAAGACTTC 2522
                            i ---- ii?  v  -   -  -   v    v        v ii   
  L1M4_orf2#LINE/    544 AACAT----AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTC 588

  chr1_245072771_   2523 ATGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAAATA----AATG 2568
                         v iivi v  vv         v v    i    iv       ----   v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr1_245072771_   2569 GGACTTAATTAAACTAAAAAGCTTGTGCACAGCAAAAGACATAATCATCA 2618
                               v  i   v v    i   v  ii vv    i    iv    vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr1_245072771_   2619 GAGTAAACAGACAACCCATGGAGTGGGAGAAAATCTT--CAGTCTCTACA 2666
                         i   i  v          ii  i           v  --  iviiv  i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr1_245072771_   2667 TCCAACAAAGGACTAATATCTAGAATCTACAAGAAACTC----AAATCAG 2712
                           ii i  i     vi    i     v  i  ii     ----  v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr1_245072771_   2713 CAAGAACAAAACAAA--GCC--ATTAAAAAGTGGGCTAAGGACACAAATA 2758
                         i  v  v  i     --i  --   ?    i     v     ivii    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr1_245072771_   2759 GACAATTCTCAAGAGAAAATATACAAATGGCCAACAA--ACATGAAAAAA 2806
                             v     v i    i                i  --         i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr1_245072771_   2807 ATGCTCAACATCACTAATTAT 2827
                         -            ????????
  L1M4_orf2#LINE/    889 -TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 1.80 (45 / 25)  


1745 27.44 7.20 1.50  chr1_245094850_245096458.rev      453  1119 (490)    L1M4_orf2#LINE/L1      204   908 (0)  

  chr1_245094850_    453 AGGTGGAGCATATTGCACTTCCTCCCATTTTGGGACC-ACATCAAGATTA 501
                           v     v i- ii       -- v    iiii  i-  vv   iii  
  L1M4_orf2#LINE/    204 AGTTGGAGGAC-TCACACTTCC--CAATTTCAAAACTTACTACAAAGCTA 250

  chr1_245094850_    502 TACAGTAACCAA-ACAGCATGGCACTTGTCCA-AAAAACAGACACATAGA 549
                         --      i   -    ii   i   v --  -  ii i     i     
  L1M4_orf2#LINE/    251 --CAGTAATCAAGACAGTGTGGTACTGG--CATAAGGATAGACATATAGA 296

  chr1_245094850_    550 GCAACAGAATAGA-----GAACTCGGAAGCAAGGCCACAAACCAACAACC 594
                         v   ii       -----  iii i   ii  iv   i v iiv iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr1_245094850_    595 ATCTGATCTTTGACAAAGCT--TAAAACATAAGCAATGGGGAGAGGACTC 642
                          vi    i  i     i v --i  i  -i vv         i  i ivv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAG 395

  chr1_245094850_    643 CCTATTTAATAAATGGTACTGGGAAAACTGGCTACTCATATGCAAAAGAT 692
                         i  v  i  i       i      v      v  ?i  i          v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr1_245094850_    693 TAGAACTGGACCACTTCCTCACACCATTTACAAAAATCAACTCAAGATGA 742
                          ii ii      v  v           v         i       i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr1_245094850_    743 ATTAAAGACTTAAATGCAAAATCCAAACCTCTAGAAACCCCAGAAGACAA 792
                           i ?    i      i  i v i   v  v  i  vi ii      v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr1_245094850_    793 CCCAGGCAATACCTTTCAGCATATAAGAATGGGCAAAGATTTCAT-GATG 841
                          vi   ?ivv vii   ivv iv vi iv i     v i    v -   -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr1_245094850_    842 AAGATGCCAAAAGCA---------------AAAACTGACAAAT-GGA--- 872
                          v  ii         ---------------    iv  i    -   ---
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr1_245094850_    873 -ATCTAACTAAGGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAATAA 921
                         -   v  v v ii i   i  ii vv    i  v        v i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_245094850_    922 ACAGACAACTTACAGAATGGGAGAAAATATTTACAAACTATGCATCTGAC 971
                          v       ii                     i    ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_245094850_    972 AAAGGTCTAATGTCCAGTATCTATAGGAAACT--TA-AATTTA-CAAGAA 1017
                           i  v  vi i     v  v    iii    --  -  i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_245094850_   1018 AAA------------AATTAAAAAGTAGGCAAAGGACATGTACAGACACT 1055
                            ------------    ?    i i         iv  v i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_245094850_   1056 TTTCAAAAGAAGATATTCTTGTGGCCAAGAAGCATATGAGAAAAAT-CTC 1104
                          i  v           v vvi       v     i    -   i  -   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTC 893

  chr1_245094850_   1105 AACATCTGTGATCAT 1119
                               v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (117 / 62)
Gap_init rate = 0.03 (21 / 705), avg. gap size = 2.76 (58 / 21)  


2971 25.86 3.34 0.72  chr1_245206871_245211072     2863  3701 (501)    L1M4_orf2#LINE/L1        1   861 (47)  

  chr1_245206871_   2863 TGAAAAGGGATTCTACACTCCTAAATTGGAAGAATTGATATTGTTAAAAT 2912
                           i    iv  i i iii  v ii         v  i          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr1_245206871_   2913 GTCTACGCTACCCAAAACAACCTACAGATTGAA--------------AAA 2948
                          v v ii  v      vii i         v  --------------   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr1_245206871_   2949 TACAAATGGCATTCCACACAGAAATAGAAAACACAATCTTAAAATTTGTA 2998
                          v v iiv  v  iivii       v  v  vvii   i       ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr1_245206871_   2999 TGAAACCACAAAAGATCTTGAATAGCCAAAGCAATACTGAGTAAAAAGAA 3048
                           i  vii   ii  i iv           i    vi   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_245206871_   3049 CAAAGTTGTAGCA-TCACACCACCTGACTTGGAAATATACTATAAAGCTG 3097
                                 v  v -      iv  ii i  vi   iv     i      i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_245206871_   3098 TAGTAACCAAAACAACATGGTACTTGTATAAAAATGGATACATAAAGGTC 3147
                         i     i   i   iii       v i    ii  i  --    v  i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA--CATATAGATC 298

  chr1_245206871_   3148 AATGAAACAGAATGGAAAATCCAGAAATAAATCTATGCATTTATAGCCAA 3197
                             i  i     v  i i            i i  i       i i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr1_245206871_   3198 CTTATTTTTAAGAAAGGTGCCAAGAATATACATTGGGGAACGGACAGCCT 3247
                         i v     ii v  i          vi  v  v       v i i  i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_245206871_   3248 CTTCAATAAGCAGTGCTGGGAAAACTGAATATCTCTATAAAGAAGAATGA 3297
                         i     i  iii         v     i   ? ivi  iv i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_245206871_   3298 AATGAGACCCCTACTTCTTACCATATACAAAAATTAACTCAAAATGGACT 3347
                          i vi         i  vi                             ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_245206871_   3348 AAAGACTTAAAAGCAAGACCCAAAACTA--------CTAGAAAAAAAATA 3389
                          ?    i    v i    v i       --------i     i    --v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA--C 546

  chr1_245206871_   3390 ATAGGGG-AAATAGATGACAACATTGGCCTAGGCAATGATTTTATCAGTA 3438
                              ? -    vvvi -ii  v    vi         i   iv vii  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr1_245206871_   3439 AGACTTCAAAAGCACAAGCAACAAAAGCAAAAATAGACAAAT-AGCCTGT 3487
                         v   vi                     v         i    -i v  vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr1_245206871_   3488 ATCAAA-CTAAAAACTTTCTGCACAGCAAAGAACATAATCAATAGAGTGA 3536
                               -i          -  ii vv     i   iv     v i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr1_245206871_   3537 AGAGACAATCTGTAGAATGGAAGAAAATATTTGCAAACCACTCATTCTAC 3586
                          i      i iii       i                i  ivi  iiv i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr1_245206871_   3587 AGGGGACTAATATTCAGAATATAAAAGGAATTCAAATAAC--AACAACAA 3634
                          i      vi   i         v  i   i  vv i   --  i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr1_245206871_   3635 TAATAATAATAATCTGATTTAAAAGTGGTCAAAGGATCTGAATAAACATT 3684
                         v  v vv     i ii   ?    i   v        i      i     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr1_245206871_   3685 TCTCAGAAGGAGAAATA 3701
                             vi   i   v   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATA 861

Transitions / transversions = 1.96 (141 / 72)
Gap_init rate = 0.01 (11 / 861), avg. gap size = 3.09 (34 / 11)  


3285 26.82 0.44 0.44  chr1_245214174_245218461.rev     2892  3797 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_245214174_   2892 GAAGAACATTCCTTGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGG 2941
                            ii i  i  v  i      i v      v i     i  v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_245214174_   2942 CCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 2991
                          v     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_245214174_   2992 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 3039
                            iivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr1_245214174_   3040 TGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAGAA 3089
                              viiv  ii  v  viv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_245214174_   3090 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 3139
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_245214174_   3140 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGATCAA 3189
                               i   i    ii         i iv ii i   v v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_245214174_   3190 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACTAT 3237
                              i    i--    i  --        vv iii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_245214174_   3238 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 3287
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_245214174_   3288 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3337
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_245214174_   3338 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3387
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_245214174_   3388 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3437
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_245214174_   3438 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGATTTCATGTCTAAAA 3487
                            ?i v viv   iv   v v  vv i     v i    v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_245214174_   3488 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGTGATCTAATC 3537
                                    vvi          vv     v  i    vv  ii v   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_245214174_   3538 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 3587
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_245214174_   3588 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAA 3637
                         i     i   i             v  i    vii ivi      i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_245214174_   3638 GGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAAAA 3687
                          i  vi          v  i  v      iv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_245214174_   3688 ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 3737
                              i     v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr1_245214174_   3738 AAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCAT 3787
                         v        i  vi viii     v ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr1_245214174_   3788 CACTGGCCAT 3797
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (5 / 906), avg. gap size = 1.60 (8 / 5)  


3183 27.23 0.44 0.55  chr1_245267462_245271493     2633  3539 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr1_245267462_   2633 GAAGAACATTCCTTGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGG 2682
                            ii i  i  v  i      i v      v i     i  v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr1_245267462_   2683 CCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 2732
                          v     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr1_245267462_   2733 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 2780
                            iivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr1_245267462_   2781 TGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAGAA 2830
                              viiv  ii  v  viv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr1_245267462_   2831 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 2880
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr1_245267462_   2881 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGATCAA 2930
                               i   i    ii         i iv ii i   v v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr1_245267462_   2931 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACTAT 2978
                              i    i--    i  --        vv iii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr1_245267462_   2979 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 3028
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr1_245267462_   3029 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3078
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr1_245267462_   3079 AATTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3128
                          i     i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr1_245267462_   3129 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3178
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr1_245267462_   3179 AGGCATTACCATTCAGGACATAAGCATGGGCAAGGACTTCATGTCTAAAA 3228
                            ?i v viv   iv   v vi vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr1_245267462_   3229 CAGCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGGATCTAATT 3278
                           v        vvi          vv     v  i   iv   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr1_245267462_   3279 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGCATGAACAG 3328
                            v v  i i   i  ii vv    i  v    i  vv ivi    v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr1_245267462_   3329 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 3378
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr1_245267462_   3379 GGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAAAA 3428
                          i  vi          v  i  v      iv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr1_245267462_   3429 AACAAACAACCCCATCAAAAAGTGGGAAAAGGATATGAACAGACACTTCT 3478
                          -    i     v  i?    i    v       v    i     i    
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr1_245267462_   3479 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 3528
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr1_245267462_   3529 TCACTGGCCAT 3539
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (6 / 906), avg. gap size = 1.50 (9 / 6)  


2524 25.21 5.30 2.94  chr1_245301292_245305252.rev     2624  3472 (489)    L1M4_orf2#LINE/L1       40   908 (0)  

  chr1_245301292_   2624 ATTTTTAAAATGG-AATACAGATTTTCCC----TGGCTTTT---TTCAAT 2665
                            v    i    -     ----- i   ----  iii vi---     i
  L1M4_orf2#LINE/     40 ATTGTTAAGATGGCAATAC-----TCCCCAAATTGATCTACAGATTCAAC 84

  chr1_245301292_   2666 GCAGTCCCAATCAAAATCCCAGAAGG--TTATTGTAGATAGCAACAAACT 2713
                            i    v             vv v--  v   i   v vii    i  
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr1_245301292_   2714 AATTCTAAACTTTATATGAGAAGGCAGAAGATCTAGAGTAGCCAACACAA 2763
                         i  i     v  i     ii  v   iii  i i   i       v    
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr1_245301292_   2764 TATTAAAGAAGAAGAACAAATTTGGAGGAACGACACTACCCAATTTCAAA 2813
                          v  i  i            v        viv     v            
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr1_245301292_   2814 TCTTATTATACAGCTATAGTAATCAAGACAGCATATTATCAAT-TGAAGA 2862
                         v    i  i v     i              ii iv  iiiii- i i  
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr1_245301292_   2863 TAGTCACACAGATCAGTGAAACAGAATATAGAGAAGAGAAATAGATCCAC 2912
                            v  i i      i  i  i     vv    vvv       i i   i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr1_245301292_   2913 ATAAATATAGTCAACTGAACTTTGATGACAGGGCAAAGACAATTTAATGG 2962
                          i vv   i     i   vi  i  ii vi v  v     v   i     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr1_245301292_   2963 AGAGAAGATAGCCGCCTTCAGTAAAAAGTGCTGGATAAATTGAACAACTG 3012
                         i  i ii    i -ii    ii   vi       ivv  i  i i ? ii
  L1M4_orf2#LINE/    385 GGAAAGAATAGTC-TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr1_245301292_   3013 TATGCAAAAAAATGAACCTAGACAGAGACATTACACTTTATACAAAAGTT 3062
                         i        i      vi i   vvvv  v i    iv         i  
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr1_245301292_   3063 AGCTGAAAATAGA-CATACACATAAA-AT----GCCAAA-CTATAAAGCT 3105
                          i  v     i  -  ? v  v    -i ----  i   -       i  
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr1_245301292_   3106 ACTT-GAAAAAAA-ATAGGAGAAAATCTGCATGACTTTGGGTTTGATGAT 3153
                         -   -   i    -     ? v      v i    i       v iii  
  L1M4_orf2#LINE/    534 -CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr1_245301292_   3154 GTGTTTTTCA---ATG---------GCACTATCCATGGAATAAAAAATTA 3191
                          -    i i ---   ---------    v v v iii  v       vi
  L1M4_orf2#LINE/    583 G-GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr1_245301292_   3192 ACAAGTTGGACTT-GCTAAAATTGAAAACCTCTGATCTGCTAAAGACATG 3240
                          i  i        -iii      i     i i  vv  v v  i    iv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr1_245301292_   3241 GTTCAAAGGAAG--GAAAGATAAACCACAAATTGTGAGAAAA-ATTTGAA 3287
                         i i--   i   --i     i  v     i v  v       -     v 
  L1M4_orf2#LINE/    682 ATC--AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr1_245301292_   3288 CAATAGACATCTGATAATATCAAAATATACAAAGAACTTGTATTTAAAAT 3337
                         v vi v i         ---------------i i        ii i   
  L1M4_orf2#LINE/    730 AATCATATATCTGATAA---------------GGGACTTGTATCCAGAAT 764

  chr1_245301292_   3338 GTACAGAGAGTTCTTACAGCTCAACAA------GA-AAACAACCCAGTTC 3380
                         i  i i   ii       i     i  ------  -   i      i  ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr1_245301292_   3381 AAAAGTGGGCAAAAGATTTGAACAGACAC--CTTAAAAAAAGATATACAG 3428
                             i        i        i     i--  iv   i          i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr1_245301292_   3429 ATGGAAAATAAAAATATGAAACGGTGCTCAACATGATATGTCAG 3472
                             vv     iv i      v i          v ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (138 / 72)
Gap_init rate = 0.03 (25 / 869), avg. gap size = 2.80 (70 / 25)  


2783 26.73 2.12 1.00  chr2_80069_89140     7685  8582 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_80069_8914   7685 TGGATAAACATTTCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 7734
                             v i i  ii    i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_80069_8914   7735 GGCCATACTGCCAGAGGTAATTTATAGATTCAATGCTATCCCCATTAAGC 7784
                            v     v  vi iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_80069_8914   7785 TACCA-CTGACTTTCTT-CAAATAATTAGAAAAAAAAAACCTTTAAATTT 7832
                          v   -   v    i  -  i -    -  v  ivvi v   --   v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATT-GACAAGCTGATCCT--AAAATT 146

  chr2_80069_8914   7833 CCTATGGAACCAAAAAAGAGTCCCCA---TAGCCAAAACAATCCTAAGCA 7879
                          v       viiv  ii  ---    ---              i i iv 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_80069_8914   7880 AAAAGAACAAAGCTGGAGGCATCATGTTACCTGACTTCGAACTATACTAC 7929
                          i          i      vv   iii v  ii i   i  viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_80069_8914   7930 AAGGCTATGGTAACCAAAACAGCATGGTACTAGTACCAAAAGAGATATAT 7979
                           i    ii    i   i    ii       i i iv ii v   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_80069_8914   7980 AGACCAATGGAACAGAACAGAGGCCTCAGAAATAACAGCACACATCTACA 8029
                            i        i    iv   ivii         vvv  i    i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_80069_8914   8030 ACCATCTGATCTTTGACAAACCTGACAAAAACAAATAATGAGGAAATGAT 8079
                         ii  vi    i  i     ivv  v   i v  vvi    i     vi  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_80069_8914   8080 CCCCTATTTAATAAATGGTATAGGGAAAACTGGCTAGCCATATGCAGAAA 8129
                         vvi  v  i  i       iiv    v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_80069_8914   8130 ACTGAAACTGGAGCTCTTCCTTACACCTTCTACAAAAATTAACTCAAGAT 8179
                          v    ii    v i  v   i     v v                 i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_80069_8914   8180 GGTTTAAAAACTTAAAAGTAAGACCTAAAACCATAAAAACCCTAAAAGAA 8229
                           v i ? i  i    v      v       i      vi i  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_80069_8914   8230 AACCTAGGCA-ATACCATTCAGGACAT-GGGCATGGCAAAAGACTTCATG 8277
                            v    ?i- v i -   iv   v -   ivv     vi -i   v i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG-TTTCTTA 591

  chr2_80069_8914   8278 ACTAAAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGA 8327
                         iv  vi    v       vvi          vv     v  i    vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_80069_8914   8328 CCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAG 8377
                          i v  i   v v  i i   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_80069_8914   8378 TGAACAGGCAACCTACAGAAGGGGAGAAAATTTTTGCAA-TC---TATCC 8423
                             v  i     i      v          v       -  ---    i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_80069_8914   8424 GACAAAGGGCTACTATCCAGAACCTACAAAGAACT--TA-AATTTACAAG 8470
                           i  i  i  vv         iv  i        --  -  i i vv i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_80069_8914   8471 AAAAAAAACAAACAACACCATCAAAAAGTGTGCAAAGGATATGAACAGAC 8520
                         v     i     i   v v  i?    i  v         v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_80069_8914   8521 ACTTCTCAAAAGAAGACATTTATGCAACCAACAA--ACATAAAAAG---C 8565
                          i     v        i  vi viiii    i  --    i     --- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_80069_8914   8566 TCATCATTTCTGATCAC 8582
                            v   iv????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.65 (28 / 17)  


1845 25.75 5.52 2.34  chr2_157398_158983      489  1086 (500)    L1M4_orf2#LINE/L1      277   893 (15)  

  chr2_157398_158    489 CAGAAGACACATACACACACATCAGTGGAACACAACAGAGAGCCCAGAAA 538
                           v   i- i v   i i v    i     i v  iv     i       
  L1M4_orf2#LINE/    277 CATAAGG-ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_157398_158    539 CAGACTGAAA----TACAGCCGACTAATCTCTGACAAAGGAGCAAAAGCA 584
                         i i  iv v ----  ii i i i i  i ii     i  v  v  ii v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_157398_158    585 ATTCAATGGAGAAAGGAGAGTCTTTTTAACAAATGGTGCCGGAACAAGTG 634
                                  i     i v        i            i  i    v  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_157398_158    635 GGCATCCATATGCAAAAAAGAAAAAAAAAAAGAATCTAAAAACAGACCTT 684
                          ii ?   i        i ---------- v   vi ii vv vv    i
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGA----------ATGAAGTTGGACCCCTACCTC 465

  chr2_157398_158    685 ATACTTCTTACAAAAATTAATGCAAAGTAGATATTAGACCAATATATAAA 734
                          i  iviv            iv    i i   vv?     v v  i   i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_157398_158    735 ATGTAAAATTTTCAAACTTCTAGAAGATAACATAAGGAAAAAATCTAGTT 784
                          vv     i v v     ii       v      -  ?iv      vvv 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATA-GGNGTAAATCTTCGT 564

  chr2_157398_158    785 AACTTTGGATTTGG---TGACTTTTTAAAGATACAACACCAAAAGCATGA 831
                         i  i    i  v  ---  ii  i   --    ii            ii 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTA--GATATGACACCAAAAGCACAA 612

  chr2_157398_158    832 TCCACGAAGACAAAAATTGGTAAGCTGAATTTCATTAACATGAAAAACTT 881
                         v v  i  iiv      v i   ii  i i     i  v  v        
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_157398_158    882 TTGTTTTGCAAAAGATACCATTAAGAGAATAAAAAGACAAATCCCAAACT 931
                             vi v    i  i  i  i    i i i         vi v  i v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_157398_158    932 GTGAGAAAATATTTGCAAA--ATATATCTAA----GGATTCGTATCTGAA 975
                          v                 --        i ----   i i     iii 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_157398_158    976 ATATGCAAAGAACTGTTAAAACTCAACAAGAGGAAAACAAACAACCCAAT 1025
                             ii        v   v       i  v ii  i     i        
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_157398_158   1026 T-AAAAATGGGCAAAAG--CTGAACAGA-----------------TATGC 1055
                          -             i --i    i   -----------------   i 
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_157398_158   1056 AGATGGAAACTAACTATATGAAAAGATGCTC 1086
                          i    vv v   vi i              
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.80 (97 / 54)
Gap_init rate = 0.02 (11 / 617), avg. gap size = 4.27 (47 / 11)  


 918 24.61 0.78 0.78  chr2_321615_325738     2054  2309 (1815)    L1M4_orf2#LINE/L1       13   268 (640)  

  chr2_321615_325   2054 CTATTTTCATTAATTTAGACATTCAATCTTGTTAAGAATTCAGATA-TCC 2102
                          i  v     vi   vii v i i   v         vvv  -   -   
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA-ATACTCC 61

  chr2_321615_325   2103 ACAAATAGATTTTTAGATTCAATGCAACCCCAATCAAAATCTCAACAGTA 2152
                         v     v   i vi        i    i   v         i  i v iv
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_321615_325   2153 TGCTTTTGAAAAAAATTACAAGCTAAATCTAAAATTTATGTGGAA-TGCA 2201
                          -i     v i   v v       i vi        i  i     -    
  L1M4_orf2#LINE/    112 T-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_321615_325   2202 AAGGACTCAGAATAACCCAAATACTTCTGATAAGGAAGAACAAAACAGCA 2251
                          i    i       i  v   i v ii   v  i          iiv v 
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_321615_325   2252 GGACACAATCTACCTAATTTCAATACTTACTATAGAACTCCAGCAATAAA 2301
                             v  vv  v  i        v        i i i  v   i   v  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_321615_325   2302 GACAGTGT 2309
                                 
  L1M4_orf2#LINE/    261 GACAGTGT 268

Transitions / transversions = 1.10 (33 / 30)
Gap_init rate = 0.02 (4 / 256), avg. gap size = 1.00 (4 / 4)  

 913 30.26 7.61 2.43  chr2_321615_325738     3026  3643 (481)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr2_321615_325   3026 AAGACAGTGTGATATTAGTACACACATGGACCAT-TCCATCAATGAAACA 3074
                                    i  i i i i viv  i   -  - vv       i  i 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGAC-ATATAGATCAATGGAATA 307

  chr2_321615_325   3075 -AGCAGA-AGCACTGAA-TAGACACCCACATGGGAGGTAAATTTAATTCT 3121
                         - iiv  -  iv v   -  i  v vi    vviv   v    v v  ii
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_321615_325   3122 GACAAAAGTTCTAGAGAA-GTTAAATGGAGAAAGGAATATTTTCTTT--T 3168
                              ii  v i -   v-i  v     i     -    v i i  i--i
  L1M4_orf2#LINE/    358 GACAAGGGTGCCA-AGACCATTCAATGGGGAAAG-AATAGTCTTTTCAAC 405

  chr2_321615_325   3169 AGACGGTGCTGGAGTAACTGAAAGAAAACGTGGAGAAAAAGCAACCTGTA 3218
                          i i        iii     i vi?vv  i  v i  i  vv  vi  v 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_321615_325   3219 TCCCTACTTCTCACTACACATGTAAATTA--------TGGTTCATAGATT 3260
                         i      i  v   i i i iiv      --------   v   ?   i-
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC- 504

  chr2_321615_325   3261 AATACAAAATATAAG--CTATCACTATTAAGCTTCTAAAAGAAAACATAG 3308
                         ---- v    i    --   vv     v  i  ii  i            
  L1M4_orf2#LINE/    505 ----CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_321615_325   3309 GAGAATATTCTGGCAACCTTGGAGTAGGCAAAAGATTCTTACAGA-GA-A 3356
                          ? v v  ii v ii       iv       vi v      v v -  - 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_321615_325   3357 CGAAATG---AGGCATTTACCTAAGGAACAAATTGAAAAATTAAGCTGTA 3403
                          v   v --- i   ---  v-  i   v    v  v     iii  vi 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCA---ACA-AAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_321615_325   3404 TCAAAGTTAAAAATTCTTCTATTT-AAAACAGATCATTAAGACAACACAA 3452
                              i       i i  v ii  -   iv v ii  i    v iiiv  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_321615_325   3453 AAGCAAA--ACAGGCTTAGAGAAAATATTCATAATACACATATCATG-CA 3499
                          ii   v--    iv vi           iii  vv  i     -  -i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC-TGATA 745

  chr2_321615_325   3500 AAACATTTCTGTAAAGAACATATAGAG--CTCCAACAAA-CAAAAATAAA 3546
                          iiv i  v i vv    i     i  --   iv    v-   v      
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_321615_325   3547 TAAATACAAATGACTCAAT----------------GACTTATACATATAT 3580
                         --  v      i  i    ----------------  i  iv i v i  
  L1M4_orf2#LINE/    796 --AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_321615_325   3581 TCCACTAAAGAATATATTTG--TGTTCAATAAAAACATTAAAATATCAAA 3628
                          i v i      v    vii--  vi      iv    v    v  vvvv
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_321615_325   3629 AATATTAGATATGAG 3643
                           i  i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (104 / 80)
Gap_init rate = 0.04 (26 / 650), avg. gap size = 2.38 (62 / 26)  


3364 16.61 9.20 7.30  chr2_334672_337312.rev     1266  2156 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_334672_337   1266 TGGGAAGATATCCCATGTTTATGAACTGCA---CTTAATATTGTTAGTAT 1312
                            i               i   i i  v ---             iv  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_334672_337   1313 GAGAATATTCACCAAAGTGATCTACAGATTCAATGCAATTCCTGTCAAAA 1362
                          iv    i  v     v                i     i   i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_334672_337   1363 TTCTAATTGTCTTTTTTGCAGAAATGGAAAAGGTGATTCTCAAATTCATC 1412
                          i i ii  i               v  v   v    i  v        v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_334672_337   1413 TGGAAATGCAAAGAGTCCCAAATACCTAAAACGACCTTGAAAATGAAAAA 1462
                                    i iii  vi    v i     i i        v   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_334672_337   1463 CAAAGTAGGAAGACTCACACTTCCCAATTTCAAAACTTTCACCCTAAGGT 1512
                               v   i                           ------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT------------ 238

  chr2_334672_337   1513 CAAGAACAAGATAGAAGAACACTGCGGATGAGAATGTCATATGAGGCAGT 1562
                         --------------------   i -------  -------------  i
  L1M4_orf2#LINE/    239 --------------------ACTAC-------AA-------------AGC 248

  chr2_334672_337   1563 CACTGTGGAAAGTAATCAAAACGGTGTCATCCTGGCATAGGGATAGACGT 1612
                         i  -------         i  i    vi v        i        i 
  L1M4_orf2#LINE/    249 TAC-------AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_334672_337   1613 G--GACCAATGGAATAGAATTGC-AGTCCAGAAATAAGCCCAAACATCTA 1659
                         i--  i                v-             i    v    i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_334672_337   1660 TGGCCAAATGATTTTTCACAAGGGTACCAAGAC---TGAATGGGGAAAGA 1706
                            i   v       iv        i       --- v            
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_334672_337   1707 AGA--CTCTTCAAT------------------------------------ 1718
                          v --  i     i------------------------------------
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_334672_337   1719 ---------------CCCTACCTAACA---TACACAAAAAGTTAACTCAA 1750
                         ---------------        v   ---  i       -         
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAA 490

  chr2_334672_337   1751 GGTTAATCAATGACCTAACTAT--GAGCTAAAACCAAAAAACTCTTAGAA 1798
                         ii vi    ?v       v i --          i v             
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_334672_337   1799 GAAAGCACAGG--TAAACCTTC-TGATGTTAGATTTGGCAATGAAGTCTT 1845
                             i  i   --    i    -   iv  i i  v       ivv    
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_334672_337   1846 AGATTTGGCATGAAAAGAACAGGCAAGAAAAGAAAAAAACAGATACATTT 1895
                             v  i  iv     v   i    v           -i     v   v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTG 639

  chr2_334672_337   1896 GACTTCATAAAAATTGAAAACTTTTGAACATCAAAGAACATTATCAAGAA 1945
                                 v      i          vi v      i   i         
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_334672_337   1946 TATGAAAAGGCAATCTACGGAATGGGTGAAAACACTTGCAAAATTATATA 1995
                         vi       i   i i  i       v     i i       - i     
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATA 738

  chr2_334672_337   1996 TGTCATAAAGGTTTCATATTTAGAGCAATTTTAAAGAACTCTTACAACTT 2045
                          v v    i  vi ii   ii   ii -- v                  i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATA--TATAAAGAACTCTTACAACTC 786

  chr2_334672_337   2046 AACAACAAAAAAGGCAAAAAAT--ATTTTAAAAATGAGCAAAGGA----- 2088
                           i  i     - i    v  i-- v  ?       i        -----
  L1M4_orf2#LINE/    787 AATAATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_334672_337   2089 -----CATTTCTTCACATAAAATATACAAACGGTCAACAAGCACATGAAA 2133
                         -----       i  v v  i         i  i   i            
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_334672_337   2134 AGATGTTCCCTGTCACTGGTCAT 2156
                              i  vvii   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (94 / 52)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 7.00 (147 / 21)  


2488 22.69 2.05 10.49  chr2_368314_370745      646  1522 (910)    L1M4_orf2#LINE/L1        1   803 (105)  

  chr2_368314_370    646 TGGAATGATATCCATTGTTAATGAACTGGAAGAATTAATATTGTTAAAAT 695
                              v       vv    v   i i       v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_368314_370    696 GTCCATACTACCCAAAGCAATCTACAGATTCAATGTAATTCCTTTCAAAC 745
                          v v     v      vii              i i   i   v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_368314_370    746 TACCAACGGTGTTCTTCACAGAAATAAAAAAAAAGTAATTTTAAAATTCA 795
                          v   i v iv  i  ii       vi v  iv-- i  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chr2_368314_370    796 TATGAAATCATGAAAGATACT--GAAGAGCCCAAGGCATCTTGAGCAAGA 843
                             i  --   v   iv  i--   v    v  ivv       iv    
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_368314_370    844 ATAAAACAACAAACAACAATAAAAACAGCCACAGAAAGCTGGGTGCGTCA 893
                          ---------i     --------------------  i   iv vv   
  L1M4_orf2#LINE/    197 A---------GAACAA--------------------AGTTGGAGGACTCA 217

  chr2_368314_370    894 CACTACCTGACTTCAAAGTATACCACAAAGCTGTAGTAACCAAAATAGCA 943
                             v  ii i      iiv   i        ii     i   i i  ii
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_368314_370    944 TGGTATTGGCGTAAAAACAGACTCACAGACCAACAGGACAGAATAGAGAG 993
                              i    i   ii i    vi i   i   ii i i     v     
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_368314_370    994 CCTCGAAAAAAACACGTGCGTCTGCAGCCAACTGATTTTTCACAAAGGCA 1043
                         i iv    v    v i i i i iii i   i       iv    i  ii
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_368314_370   1044 TCAAGAACACACAGTGGGGAAAGAATAATCTCTTCAATAAATGGTGTTGG 1093
                         i     v  iv  i             i   i     i        i   
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_368314_370   1094 GAAAGGCAAATATCCACATGAAAAAGAACAAAATTGGACCTCT-TCTTAC 1142
                           v iviii   ?       v       ii  i       i  -i  i  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_368314_370   1143 ATCATACACAAAA-TCAGCTCAAAATGGATTAACAACATAAACATAGGAC 1191
                          i    i      - i i            i ?vi  v    ii  i  v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_368314_370   1192 CTTAAATGGCAACACTACTT-GAAGAAAACAGAGAGAAAAAACTTCTTGA 1240
                           v   ivii  v   -   -          v  i?iv   v    v   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_368314_370   1241 CGTTGGTGTGGGTAATG---------ATATGATACTAAAAGCACAAGGCA 1281
                          v    vv i  i    ---------      i  i           -  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG-CA 615

  chr2_368314_370   1282 ACAAAAGCGAACATGGACAAATGGGATTGCACCAAACCAAAACACTTCTG 1331
                                vi  v  i  i    v   i v  i    viv   v    i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_368314_370   1332 CCCACACAAAGGAAATGACCAACAGAGTGGGATTGCACCAAACCAAAACA 1381
                         ---------------------------------   --------------
  L1M4_orf2#LINE/    666 ---------------------------------TGC-------------- 668

  chr2_368314_370   1382 CTTCGGCCCACACAAAGGAAATGATCAACAGAGTGAAGAGACGATCTACA 1431
                         -   ---------      v iv     v i      i    i i i   
  L1M4_orf2#LINE/    669 -TTC---------AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_368314_370   1432 GAATGGGAGAAAATAATTGCAAACCATACATCTTATATGCAGTTAATATC 1481
                                        v       i    i    v   v viii vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_368314_370   1482 CAAACTATGTAAAGAACTC----AAGTCAATCACAAGAAAACAAA 1522
                           i v   i          ----  v     v i  i  i     
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

Transitions / transversions = 1.76 (125 / 71)
Gap_init rate = 0.02 (15 / 803), avg. gap size = 7.33 (110 / 15)  

 485 17.50 1.67 2.50  chr2_368314_370745     1821  1940 (492)    L1M4_orf2#LINE/L1      790   908 (0)  

  chr2_368314_370   1821 AAGAAAAAGACCCAAGGAGACCCAATTTAAAAATGAGCGAAGAACCTGAA 1870
                           v        --  iv -        ?       i  i   i ii    
  L1M4_orf2#LINE/    790 AATAAAAAGAC--AAATA-ACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_368314_370   1871 -AGATATTTCTCAAGAGAGG-CATACAAATGGCCAATACATATATGAAAA 1918
                         -   i       v i   i -i                vii i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_368314_370   1919 AATGTTCAATATCATGATCATC 1940
                         i   i    i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.00 (16 / 4)
Gap_init rate = 0.03 (4 / 119), avg. gap size = 1.25 (5 / 4)  


3177 24.32 2.30 3.50  chr2_401320_403236.rev      513  1425 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_401320_403    513 GATACTCCATGTTCAAGCATCAGAAAA-TAAATATTGTCAAAATAGCATC 561
                             ii         v v  ii   i - v        i  i  i   vi
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_401320_403    562 ACTATCCAACATGATCTACATGTTAAATATAATCTCTGTCAAAATTTCAA 611
                            vi    vv         vi  v  iii    i  i       ii  i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_401320_403    612 TGGCATTTTCAG-AGAACTTAAAAAAAAATCT-ATTCTAAAATTTGTATG 659
                         iv  v    iv -    v  i v  i----  -  i        ii    
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATTCATATG 152

  chr2_401320_403    660 GAATCACAAAAGATCCCAAATAGCTAAATCAATGTTGAGGAAAATGAACA 709
                            vii   ii  i  vi      i   v    v    ii  i v     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_401320_403    710 AAGCTGGAGGTGTCACACTTTCTGATTTCAAATTATATTGCAAAGCTATG 759
                            i      vv        i ii        viv  i i        ii
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_401320_403    760 GTAATCAAGACAGTATGGTTAGTACCACACAGACCAGTGGAAACAGATGC 809
                                       i    ---------  v i --i iiii i   iii
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGT---------ACTGGC--ATAAGGATAGACAT 291

  chr2_401320_403    810 ATGGACCAATGGAACATAAC-AAAAGTCCAGAAATAAATCCATGCATTTA 858
                           i  i        i v  i-i i              i    i      
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_401320_403    859 TAGTCAACTAATCATTAGCAAAGAGACCAAGAATACACAATGGGCAAAGG 908
                          i     i i  iv iii   i ivi      vi iv       v    i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_401320_403    909 AGAGTCTCTTCAATAGATGGTGTTGGGAAAACGTAACATCAACACTTAAA 958
                          v     i     i i      i     v   vvi i ? v   ivi   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_401320_403    959 AAAA--AATTAAGATTCTTAGCTTACAC---ATACAAA--TCAGCTCAAA 1001
                          i  --  v vi  ii i  v  i    ---       -- i i      
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_401320_403   1002 ATAGATTAGAGATTTAAACATGAGAACTGAAACCACAAAACTCTTTAAAA 1051
                           i   i ?   ii    ii i   i  i    i i         vi  i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_401320_403   1052 AAATCACATGGGGAAAAGATCCATGACATTGGTCTTGGCAATGATTT-TT 1100
                            v  i -  ? v   vv i i    v    vi v       i   -  
  L1M4_orf2#LINE/    542 AAAACATA-GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_401320_403   1101 GGATGTGACACTAGAAGCACAGGCAAGGAAAGCAAAAATAGAGAAATGGG 1150
                         i   i      i i       i    vi    v         v    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_401320_403   1151 ATTGCATCAAACTAAAAAAGCTTCTGTGT-----AGGAAACAATTGACAG 1195
                          i v       v v     -   i    i-----    v  v  ii v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_401320_403   1196 AGTGGAAA--CAACCTGAGACAAAATGAGGGGAAACATTTGCAAATCCTA 1243
                             i   --     i---   i    i i i   i           v  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCC---ACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_401320_403   1244 TATCACATAAGGGGCTAATGTCCAAAATACATAGGGAACTCATACAAGTC 1293
                             vv       i  vi i    i    i   ii      v     v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_401320_403   1294 AAGAGCCAAAAAAAAAAAAAAAAAGCAAATAACCCAATTTAAAAATG--C 1341
                           ----i  v     i --------              ?       -- 
  L1M4_orf2#LINE/    787 AA----TAATAAAAAGA--------CAAATAACCCAATTWAAAAATGGGC 824

  chr2_401320_403   1342 AAAGGATCTGAATAGACATTTTTCCAAAGAGGACATACAAATGACCTAGA 1391
                                i             i        i  i         i  v v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_401320_403   1392 GGTCTATGAGGAGGTGCTCAGCATCACTAATTGT 1425
                         i ivi    ii  i      i     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (151 / 67)
Gap_init rate = 0.02 (19 / 902), avg. gap size = 2.79 (53 / 19)  


 704 26.56 0.00 0.00  chr2_525707_527867      486   677 (1484)    L1M4_orf2#LINE/L1      174   365 (543)  

  chr2_525707_527    486 AGACAAAATCCCCTCCAAAAAGTAAAACAAAGTTGGAATCGTCACACTTC 535
                           v     ivvi  iv      v i            ivvv         
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr2_525707_527    536 CTGATTTAAAATCATATTACAAACTTATAATAAACAAAACAGCATGGCAC 585
                          ii    v   v v  i      vi  i i   v   i    ii   i  
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr2_525707_527    586 TGGCATAAAAACAGAAACATAGACCAAGGGAGCAGAACTCAGTGACCAGA 635
                                 ii i   v i     i   v   ii    i v  v v     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_525707_527    636 AATAAATTCAAACATATATGATCAACCAATTTATGACAAGGG 677
                               ii  v    v    i    iii    vi        
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

Transitions / transversions = 1.43 (30 / 21)
Gap_init rate = 0.00 (0 / 192), avg. gap size = 0.00 (0 / 0)  

1824 23.23 2.18 3.27  chr2_525707_527867     1119  1669 (492)    L1M4_orf2#LINE/L1      364   908 (0)  

  chr2_525707_527   1119 GGCTCCAAGAGGGCACAATGGG-AAAGA---GTCTCTTCAATAAACGGTG 1164
                           iv      vviiv       -     ---    i     i   i    
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_525707_527   1165 CTGGGGAAACTGGATTTCCACATGAAACAGAATAAAATTGAATGCATATT 1214
                              iv        v?       v  v     i  i   i iv v  ii
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_525707_527   1215 TCACACCATATACAAAAGTTAATTCAAAATGAATGGAAGACCTAAATGGA 1264
                                          i    i        i  vi?           v 
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_525707_527   1265 AGACCTGAAACCATAA--CTTCTAGTATAGAAAGGAGAAGAAAAAAATTT 1312
                            v  i    i    --  ii   - -     iv v i ?iv   vi  
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAG-A-AGAAAACATAGGNGTAAATCTT 561

  chr2_525707_527   1313 CTTGGCATTGGCCTTGGCAATATATTTTCTTAAATATTATATCAAACACT 1362
                          v  i v    vi v      iv--       i    v i i    vi v
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGG--TTTCTTAGATATGACACCAAAAGCA 609

  chr2_525707_527   1363 TATACTATAAAACCAAAAATAAATAAATAACACTACATTGAA-TCAAAAA 1411
                         i vi v i    vv       i      viv   v   ii  - i     
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_525707_527   1412 GCTTCTGTACAGCAAAGGAAACAATCAATAAAATTTAAAGTCACCTTA-- 1459
                         -   i   i vv       v  v     v   i vv    v  v ii --
  L1M4_orf2#LINE/    660 -CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_525707_527   1460 ---TGGAAAAAAATAATTGCAAACCATGTACCTGATAAGGGGTTACTATT 1506
                         ---   i i      v       i   i  i          ii vv   i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_525707_527   1507 CAAAATTTATAAAGAACTCCTACAACTCAATAGCAGGAAAACAACAACAA 1556
                           i   v            i            ii ii  i    -- i  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA--ATAA 806

  chr2_525707_527   1557 TTTGTCACAAAACAACTCAAAAAATGGGTGAAGAACCTGAACAGACAATT 1606
                         ----- v   ------ i?         ii   i ii    i     v  
  L1M4_orf2#LINE/    807 -----CCCAA------TTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_525707_527   1607 TTCCAAAGAAGACATAAAAATGGCCTTGAGGTACATGAAAAGGTGCTCAA 1656
                         i           i   v        vvv i i          i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_525707_527   1657 CATCATGAATCAT 1669
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (73 / 51)
Gap_init rate = 0.02 (12 / 545), avg. gap size = 2.50 (30 / 12)  


2607 25.49 3.83 4.49  chr2_529352_531328      572  1485 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_529352_531    572 TGGAAAAACATACCATGCTCATGGATAGCAAGAATTAATATTGTTAAAAT 621
                               i i  v     i        v v    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_529352_531    622 GGCCACACTGCCCAAAGTGATTTACAGGTTTAATGCTACTCCTATCAAAC 671
                            v i   v      v    i     i  i  i  v ii         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_529352_531    672 TACTAATGACATTTTTCAAAGAATTGGAAAAAAGAATTCTAAAGTTCATG 721
                          v i iivi v     iiv    v v  v  ivvi  i     i     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_529352_531    722 TGGAATAAAAAAAAAAGCCCA-AATAGCCAAAGCAGTCCTAAGCAAAAAG 770
                              -- viv  iiii    -          i  i  i i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_529352_531    771 AGCAAAGCCAATGGCATCACGTTACCTGACT-CTAAACTATACTACAAGG 819
                          i     iiiiv  vv    ii v  ii i - v     -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_529352_531    820 CTACAGTAACCAAAACAGCATAGTG-------------AGACACATAGAC 856
                                  i   i    ii i  i-------------     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_529352_531    857 CAATGGAACAGGTTTGAAAACCCAGAAATAAAGCTGCACACCTACAACTA 906
                                 i  iv    i ii           v iii   ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_529352_531    907 TCTGATATTTAACAAAATTCAAAAAAAAAAAGAAAGAAAGAAAAGAAAAG 956
                         vi    v  ii    iiv ------------------------------ 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGT------------------------------G 367

  chr2_529352_531    957 AAAAGAAATACAAGCAAGGGGGAAATAAC--TCTTTATTCAATAAATGGT 1004
                         vv    v---  vv   v       v  i--     --    i       
  L1M4_orf2#LINE/    368 CCAAGAC---CATTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGT 412

  chr2_529352_531   1005 GCTGGGATAACCAGCTAGCCATATGCCGAAAATTGAAACTGGACCTCTTC 1054
                                i   ii v  ?   i    vi  i v    ii      i  v 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_529352_531   1055 CTTTCACCATATACAAAAATCAACTCCAGATTGATTAAAGAATTAAATAT 1104
                           iv                i     v i  v   i ?   vi     i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_529352_531   1105 AAAATCTAAAACTATAAAAACCCTGGAAGAAAACCTAGA---AAATACCA 1151
                           i v              vi i i         v   i---    -- -
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C- 559

  chr2_529352_531   1152 TTCTGGACGTAAGCCTTGGCAACGATTTCATGACAAAGTCACCAAAAGCA 1201
                            vv   v vi vi v     i i    v iivv v v           
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_529352_531   1202 ATTGCAACAATACCAAAAATAGACAAATGAGACCTAATTAAACT--AGAA 1249
                         vvv       v vv         i    vi   i v  i   v -- i  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_529352_531   1250 CTTCTGCACAGCAGAAGAAACTATCAACAGAGTTAACAGACAACCTGTGG 1299
                            i  ii vv  i i  v        v i   v  v        iiii 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_529352_531   1300 AATGGGAGAAAATGTTTGCAAAGTATGCATCTGACAATGGTCTAATACCT 1349
                                      i        vi  ii      i  v  v  vi  i i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_529352_531   1350 AGCATCTATAA-GAA--------ACTTAATAAGCAAAAAACAA----CCC 1386
                           v  v     -   --------   i     vv    i    ----   
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_529352_531   1387 CTTTAATAAATAGACAAAAGACATGAACACACACTTCTAAAAAGAAGACA 1436
                         vv  ? v    i i    i  iv    i v   i    vv        i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_529352_531   1437 TAAACATGGCCAACAAACATATGAAAAAATGTTCGACATCAATAATAAT 1485
                           v v        i  i  i       i   i  i      ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.75 (76 / 16)  


 504 32.13 9.55 5.70  chr2_726388_728194.rev      462  1320 (487)    L1M4_orf2#LINE/L1       17   908 (0)  

  chr2_726388_728    462 GTTGATAGATATGAATATTTAACAGCATGAA-ATTTCATTTCTCCATAA- 509
                            v  i   vv   v i    i vii v  -  vv  v v    vi  -
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chr2_726388_728    510 -TGATATATAAAAACAAC--AAT-----TCAAGAACTCCAAAAGGATTGA 551
                         -    v  i i vv    --   -----    -  ii   ivv vv  vv
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAA-AATCCCAGCTGCCTTTT 115

  chr2_726388_728    552 TAATGGAACTAGATAAATTGATTCTACGATTTGTATGTGAGA-GTAAAGG 600
                          viii   v v  i  ii    i   vi   ii    -  i - i  i  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG-GAAATGCAAGGG 164

  chr2_726388_728    601 ATCAAAACCTGCCCCGGCGTATCTC-----AGAAGAACAAGGTTAGGAAA 645
                          i v i viv   vvii i-    i-----          i   i iii 
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACA-ATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_726388_728    646 CT---ACTTTGC-----CAGG------TATCAAGTAATAGAAATCACTAT 681
                           ---    iv -----  ii------  iv   iv i  v     vv i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_726388_728    682 TGCCTAGTCAC-AGCACGAGGGGAAACAAACAGATTAGAGAACACAGAAT 730
                         v iv i  -  -i   ii   iv i   v i    i iv i - i     
  L1M4_orf2#LINE/    264 AGTGTGGT-ACTGGCATAAGGATAGACATATAGATCAATGGA-ATAGAAT 311

  chr2_726388_728    731 --AGAACACTAGGAATTGAGCATCTCATACATT------CAA-------- 764
                         --   ii- i  i   vi ---- i        ------   --------
  L1M4_orf2#LINE/    312 TGAGAGT-CCAGAAATAAA----CCCATACATTTATGGTCAATTGATTTT 356

  chr2_726388_728    765 --ACAATGTAGCGCAGACATATTATTGTATATCAGTGAGTGAAAGAG--G 810
                         --    v vv  vv    ----i   ------  i  i -      i-- 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGAC----CATT------CAATGGG-GAAAGAATAG 395

  chr2_726388_728    811 TTCCTGCAGTGAACAGTGCTGGAACGCCTGGTTATCAATAT-TGAAAAAA 859
                          iii v  iii  ii       i  iv    v  ? v i  -ii   i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_726388_728    860 TTAACTTGGATTCCTACATCTTATC-T-TGCATTTATTTATTCCACAT-- 905
                          v  v     ii     v  vi i - - i  vvv   v i  v v  --
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_726388_728    906 ATAATAGGCATTTTAATTTGAAAG--GAAACC-TAAAATATCTGCAAGAA 952
                           v ?  -- ii v   v i i  --i    i-     ivii iv     
  L1M4_orf2#LINE/    496 ATCAWAG--ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_726388_728    953 AGTATGAAAATA--TCTTTATGAGCTGAGGATAGAAACATA-TTTCTTCA 999
                          ii  iii?i  --    ii   v  vi  v   iv -  i-      vi
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAG 592

  chr2_726388_728   1000 A-ATAA----AAAAGCATGAGTCATGCATTAAGAGCTTGCTGACTTAG-- 1042
                          -  i ----       ii  iv iiv vv  i iv v v i v  i --
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_726388_728   1043 CACATTAAAAATAGAAAATTCTATTAATCAGAAAACACCATTA-GAA--- 1088
                         iv   i    v  i   v  i i vvv   i ii    i  i -   ---
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_726388_728   1089 GAAATATTTGAGCTGCAGA-TTGAAGAAGATAAGTGCATGACATATAACT 1137
                             - vvii v ii    - v i    i   vv    viv      v  
  L1M4_orf2#LINE/    693 GAAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_726388_728   1138 GACAAAGCATTACTGTTGAGAATATAAAAATAATTACTGGGAGTTAATCT 1187
                           i  i v i vv i iv        v   v  i vi ivi v i   --
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-- 789

  chr2_726388_728   1188 GGAATAGAAACACAGCACTGTGTGTGTACACCCATATACACACAAATATA 1237
                         --    i   v   i----------i  -     --- iv? v    ivi
  L1M4_orf2#LINE/    790 --AATAAAAAGACAA----------ATA-ACCCA---ATTWAAAAATGGG 823

  chr2_726388_728   1238 CAGACATGCATGTGCATA--CATTCCAGATACAAGGAA-----ACAGA-G 1279
                           i --- v  v  v   --    i --- v   i   -----   i - 
  L1M4_orf2#LINE/    824 CAAA---GGATTTGAATAGACATTTC---TCCAAAGAAGATATACAAATG 867

  chr2_726388_728   1280 GCCAATAAGTGTTTGAAAAGATGTTCAATGACATTGCAACC 1320
                                  iiiv          i    iiv  ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (160 / 112)
Gap_init rate = 0.06 (50 / 892), avg. gap size = 2.62 (131 / 50)  


2653 25.84 1.48 0.81  chr2_734364_736128.rev      531  1273 (492)    L1M4_orf2#LINE/L1      161   908 (0)  

  chr2_734364_736    531 AGAGACC--ATATAGCCAAGACAATCCTAAGCAAAAAGAACAAAGCTGGA 578
                           i    --iv        i      i i iv  i          i    
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_734364_736    579 GGCATCATGCTACCAGACTTCAAACTATACTACAAGGCTACAGTAACCAA 628
                           vv   ii  v  vi i      viv        i          i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_734364_736    629 AACAGCATGGTACTGGTACCAAAACAGATATATAGACCAATGGAATAGAA 678
                         i    ii         i iv ii i   i       i             
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_734364_736    679 CAGAGGCCTCAGAAATAACACCACACATCTACAGCCATCTGATCTTTGAT 728
                         iv   ivii         vv   i    i  ii i  vi    i  i  i
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_734364_736    729 AAACCTGACAAAAACAAGCAATGGAGAAAGGATCCCCTATTTAATAAATG 778
                           ivv  v   i v  vv      i     i  vvi  v  i  i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_734364_736    779 GTGTTGGGAAAACTGGCTAGCCATATGTGGAAAACTGAAACTGGACCCCT 828
                            i     v      v  ?   i   iii  i v    ii         
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_734364_736    829 TCCTTACACCTTATACAAAAATTAACTCAAGGTGGATTAAAGATTTAAGC 878
                         v   i     v                   ii     i ?   ii   ii
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_734364_736    879 CTAAGACCTAAAACCATAAAAACCTTAGAAGAAAACCTAGGC---AATAC 925
                         v     v       i      vi             v    ?---   --
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-- 558

  chr2_734364_736    926 CACTTAG-GACA--GAGTCATGGACAAAGACTTCATGACTACAACACCAA 972
                         --   v -   v-- i  i -- i   v ii   v iiv  ii       
  L1M4_orf2#LINE/    559 --CTTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_734364_736    973 AAGCAATTGCAATAAAAGCCAAAATTGACCAATGGGATCTAATTAAACTA 1022
                              vvv    i     vv     v  iv   v   ii v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_734364_736   1023 AAGAGCTTCTGCACAGCAAAAGAAACTATCATCACAGTGAACAGGTAACC 1072
                           i i   i  ii vv    i  v       vv v      v  ii    
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_734364_736   1073 TACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCCAA 1122
                         i                 v       vii  vi      i  i  i ivi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_734364_736   1123 TATCCAGAACCTACAAGGAACTTAAACAAATTTACAAGAAAAAATCAAAC 1172
                                  iv  i  i     ivv    v iv i  v     iv    i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_734364_736   1173 AACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTTTCAAAAGA 1222
                              v  i?    i            v    i     i  i  v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_734364_736   1223 AGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCA---TCACTGG 1269
                            i  vi viii     i  i  i       i v     ---   ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_734364_736   1270 TCAT 1273
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.61 (116 / 72)
Gap_init rate = 0.01 (7 / 748), avg. gap size = 2.43 (17 / 7)  


3260 26.22 0.88 0.44  chr2_789052_795323     4877  5780 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_789052_795   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_789052_795   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_789052_795   4977 TACCAA-TGCCTTACTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5023
                          v   i-      -i  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_789052_795   5024 ACATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5073
                          i      viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_789052_795   5074 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5123
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_789052_795   5124 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5173
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_789052_795   5174 CAATGGAACAGAAC--AGAGCCTCAGAAATAACGCCGCATATCTACAACT 5221
                                 i    i--    i -         vv  ii i  i  iiiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTC 346

  chr2_789052_795   5222 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5271
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_789052_795   5272 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAGCT 5321
                           v  i  i              v      v  ?   i   iii  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_789052_795   5322 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5371
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_789052_795   5372 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5421
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_789052_795   5422 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAA 5471
                         v    ?i v viv   iv   v v  vvii     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_789052_795   5472 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5521
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_789052_795   5522 TTAAACAAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAATGAAC 5571
                          i   vvv  i i   i   i vv    i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_789052_795   5572 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCAACTCATCTGACAA 5621
                           i     i   i             v       viv ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_789052_795   5622 AGGGCTAATATCCAGAATCTACAATGAACTTAAACAAATTTACAAGAAAA 5671
                         i  i  vi          v  i  v     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_789052_795   5672 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5721
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_789052_795   5722 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA-- 5769
                           v        i  vi viii     v  i          i       --
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_789052_795   5770 -TCACTGGCCAT 5780
                         -   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


2295 24.00 2.07 6.62  chr2_929389_931105.rev      501  1225 (492)    L1M4_orf2#LINE/L1      217   908 (0)  

  chr2_929389_931    501 ACACCACTTGACTTCAAAATATACCACAAAGCTATAGTAACTAAAACAGC 550
                             iv iii i       iv   i         i     ii  i    i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_929389_931    551 ATGGTATTGGTATAAAAACAAACATGCAGACCAAAGAAACAGAATAGAAA 600
                         i     i   i    ii i i    ii   i   v i  i     v  i 
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_929389_931    601 GCCCAGAAATAAATCCACACATCTACAATCAAGTAATTTTTGACAAAGAC 650
                          i           i   i    i  iii    v i     i     i ii
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_929389_931    651 ACCAAGAACACACAGTGGGGAAAGGACCACCTTT---ATAAATGGTGCTG 697
                         i      v  iv  i         i ivii    --- i           
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_929389_931    698 AGGAAACTGGATAGCCACATGCAAAAGAATAAAACTGGACCCTTATCTGT 747
                         i iv         ?                i  ii       i  i  vv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_929389_931    748 CACCACTTA---AAATCAACTCGAAATGGATTAAATACTTGAATGTGAGA 794
                              iv  ---    i     i        i ? v  i i     i   
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_929389_931    795 CGCCCAAACTATGAAACTACCAGATTAAATATTTGAATGTGAGACCCCCA 844
                         ---------------i   ------------------------------ 
  L1M4_orf2#LINE/    517 ---------------GCTA------------------------------A 521

  chr2_929389_931    845 AACTATGAAACTACTAGAAGAAAACATAGG-GTGAACACCTCATGACCTT 893
                               i     vi                -  i  i- i  i       
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTT 570

  chr2_929389_931    894 GGACTGAGCAAGGACTTTTTGGATTAGTCCTCAAAAGCATAATCAACAAA 943
                           ii ii    v ii  i  i   vv v vi        i  v       
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_929389_931    944 AACAGAAATAGACAAATGATATTCCA--AAAACTATGAAGCTTTTGCACA 991
                          iv i       i    viv i i  --    i  -i  i      ii v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCT 669

  chr2_929389_931    992 GCAAAAGAAACAATCAACAGAGTGAAGGAAAGACTGACTGAATGGAAGAA 1041
                         v    i  v  v     v i      iii vi  iv  v      i    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_929389_931   1042 AATATGTGCAAATTCTACATCTGGCAAAGGTCTATTATCCAGGATATATA 1091
                              v       iv  i     ii  i  v  vv       i       
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_929389_931   1092 AGGAACTC--A-AAC--AATAGCAAAAATCTAAGTATTCTGATTAAAAAA 1136
                          i      -- -   --    ii     vvi  i  vi ii   ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_929389_931   1137 CAAGACAAAAACTTT-ATTAGATATGTCTCAAGAGAAGACATACAATTGG 1185
                         iii -    iiv   - v    i  v    v i      i      v   
  L1M4_orf2#LINE/    820 TGGG-CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_929389_931   1186 CCAACGGGTATATAAAAATGTGGTCAGCATCAGTATCACT 1225
                             iii i i  i    vi  v   i     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.72 (125 / 46)
Gap_init rate = 0.02 (13 / 692), avg. gap size = 4.85 (63 / 13)  


2536 26.67 2.47 1.53  chr2_953845_956050.rev      856  1706 (500)    L1M4_orf2#LINE/L1        3   861 (47)  

  chr2_953845_956    856 GAAAAACATTCCATGCTCATGGATAAGAAGAATCAATAGTGTTAAAATG- 904
                             i i  i     i        vi     v i    v      i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_953845_956    905 ---TACTGTCCAAAGTAATTTACAGATTCAATGCTATTTCTTTCAAACAA 951
                         ---    vi     v i  i           i  v  ii  v     vvv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_953845_956    952 CCAAGGACATTCTTCACAGAATTAGAAAAAAAACT-ATTATAAAATTCAT 1000
                            ivvi v  i  ii     v v  v  i---  -  iv          
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCAT 149

  chr2_953845_956   1001 ATGGCACAAA---AAAAGAGCTTGAATAGCCAAAGCAATCCTCAGCAAAA 1047
                             ---   ---  ii  v iv           i     i v iv  i 
  L1M4_orf2#LINE/    150 ATGG---AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_953845_956   1048 GGAACAAAGCTGGAGG-CACAACATTACCCAACTTCAAACTATACTACAA 1096
                         i        i      - v  -  i v     i      viv        
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_953845_956   1097 AGCTACAGTGGCCAAAACAGCATGGTACAGGTACAAAAACAAACACA--G 1144
                                  iii   i    ii      v  i i  ii i i   i -- 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_953845_956   1145 GCCAATGGAACCGAGTAGCAAGCCCAGAAATAAAGCCACACACCTGAAAT 1194
                         ii        iv  i v vi  i           v   i   ii ivii 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_953845_956   1195 CATCTAATCTTTGACAAAGGCAACATAAACCAT-CAGTGTGGGAAGGACC 1243
                           vi i  i  i     i  iiv  - i     -  i  v  i   i iv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATA 394

  chr2_953845_956   1244 CTCCAATTCAATAAATGGAGCTGGTGATAACTGACTTGCCATATGGAGAA 1293
                         v  iv-     i      v     -  i     iv v?   i   v i  
  L1M4_orf2#LINE/    395 GTCTT-TTCAACAAATGGTGCTGG-GACAACTGGATAKCCACATGCAAAA 442

  chr2_953845_956   1294 GATTGAAACTGGACCCCT-CCTTTCACCATATACTAAAATCAACTCGAAA 1342
                           v    ii         -   iv          v     i     i   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_953845_956   1343 TGCATTAAAGACTTAGATGTAAAACCTAAAACTATAAAAACTCT-AGAAG 1391
                           v  i ?    i  i      i v              -    -     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAG 541

  chr2_953845_956   1392 GAAAACCGAGACA-----CTCTG-GACATAGGGAGTGGCAAAGACTTCGT 1435
                         -     vv  i?i-----  ii -   v v   vvv     v ii   v 
  L1M4_orf2#LINE/    542 -AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_953845_956   1436 AACAAAGACTCCAAAAGCAATTGGAACAAAACCAAACATTGACAAATAGG 1485
                          ivv v   v         vvv v       vv   v  v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_953845_956   1486 ACCTAATTAAACTAAAGAGTTTCTGCATAGCAAAATAAACTTATCAATAG 1535
                           i v  i   v v  i ii  i  iiivv    iv v   -     v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGAA 689

  chr2_953845_956   1536 AGTAAAAAGACAACCTACAGGATGAAAGGAAATATTTGAAAACTATGTAT 1585
                            i           i    i   ii  i         v   ii  i   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_953845_956   1586 CTAGCAAAGATCTAATA-CCACAATCCATAAGTAACTTCAACAGATCAAT 1634
                           iii  i iv  vi  -   v   vi    iv    iiv   iv     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_953845_956   1635 AAGCAAAAAAGAAATAATCCCATTAAAAAATGGTTAAAGGACATGAACAG 1684
                           vv    i v      i  v   ?        vi      iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_953845_956   1685 ACACTTCCAAAAAGAAGACATA 1706
                            i   ivv        i   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATA 861

Transitions / transversions = 1.42 (131 / 92)
Gap_init rate = 0.02 (20 / 859), avg. gap size = 1.70 (34 / 20)  


3080 18.98 4.37 7.57  chr2_978959_981963.rev     1576  2513 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_978959_981   1576 TAGAAAGACAGTCCATGTTCATGGATTGAAGGCAATACAGTTAAAATTTA 1625
                          i      i vi                i ------------- i i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGA-------------AGACTTA 37

  chr2_978959_981   1626 ATAAATTCTTAATATTATGAAATGG--ATAATTCTCAAATTGATCTACAG 1673
                            --  v    --------i    --   v i i               
  L1M4_orf2#LINE/     38 ATA--TTGTTAA--------GATGGCAATACTCCCCAAATTGATCTACAG 77

  chr2_978959_981   1674 ATTCAATACAATGTCTATCAAAATCCCAGCTGATTTATTTGCAGAAATTG 1723
                               ii    vi                  vi  v             
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chr2_978959_981   1724 ACAAGCTAATTCTAAAATTT-TATGGATGTTCCAGGAACCCAGGACTGTC 1772
                                i  i        i-      vi v v   i      i iv i 
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_978959_981   1773 AGAAACAATCCTAACAAAGAAGAACAAAGTTGGAGG-TTCACATTTCCTA 1821
                          -        i i v                     -i     i    i 
  L1M4_orf2#LINE/    178 A-AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_978959_981   1822 ATTTCAAAACTTACTACCAAGGAACAATAATCAAGGCAGTACAGTGCTGG 1871
                                          v   vv   i        i    iii  i    
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_978959_981   1872 CATAAGCATGAAAATATTAACATAGCTTTATAAAAATAGAGATATAGATC 1921
                               ----------------------------i     v         
  L1M4_orf2#LINE/    277 CATAAG----------------------------GATAGACATATAGATC 298

  chr2_978959_981   1922 AATGGAATGGGAATGAGTATCCAGAAATAAACCCTCACATGTATTATATA 1971
                                 i i v    vi               vi    v   vi -i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT-CA 347

  chr2_978959_981   1972 ATTTGATTTTCAACAGGATTTCCAGGACAATTCAAAGGAGAGAAGAAAAG 2021
                            -       i   i iv v   i   v      v  i  -     v  
  L1M4_orf2#LINE/    348 ATT-GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATAG 395

  chr2_978959_981   2022 ACTTTTGAAAATATGATGCTGGGCTCTCTGGATATCCACAATTTAAAAAA 2071
                         v     v  v v   i       vivv       ?     vviv   i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_978959_981   2072 TAAATACGTTTATATTTGTTCTTCACACAATCACAAAAATACAAAAATAT 2121
                          i  ---   vi- iiiv v i      v  -------          vv
  L1M4_orf2#LINE/    446 TGAA---GTTGG-ACCCCTACCTCACACCAT-------ATACAAAAATTA 484

  chr2_978959_981   2122 ACTCAGAATAGACCCTTTACCTAATAGTAAGAAAGAAAATTATAAAAGTC 2171
                              i   i  i v?vv      vv      ivv    i       v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_978959_981   2172 C-AAAGGAAAACATAGGAGTGTATCTTTATAATCTTGGGTCAGACAATTG 2220
                         i- i i           ?  iv     ii i i       i  i    v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_978959_981   2221 TTTGCTAGGTAAAATAAGAAAAAAACTA-TAGCAAAAGTAAAAATAGATC 2269
                            vi   i  vi i vv    iv  v -i i      v          v
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_978959_981   2270 AACTGAACTTCATCAAAATATAAAACTTTACATGA--CAAAGGATACTTT 2317
                           i  i             vv        -ii  v--       i   v 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTAT 683

  chr2_978959_981   2318 GAAGAAAATGAAAAGGTAATCCACAAAATGAGAGTAAATATTTGTAAATC 2367
                         v      i       ii  i     i    i   v         i     
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_978959_981   2368 CTATATCT--------ACATGTATCCAGAACATA-AAATTATTTTTAAAA 2408
                         v       --------  v           i   -   vv i i   v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_978959_981   2409 CACTCA-CAACCGAAAAAGATAAATAATCCAATT-AAAAATGG------- 2449
                          --   -i  i--       i      i      -        -------
  L1M4_orf2#LINE/    784 C--TCAATAAT--AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_978959_981   2450 --------AAACATT-------AGAAAATATACAAATGGCAAATAATTAC 2484
                         -------- i     -------    i             v     vi  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_978959_981   2485 ATGTGAAGATACTTAACATTATTAATCAT 2513
                            vi     i  i     i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (102 / 73)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 4.31 (112 / 26)  


2491 27.47 3.59 1.79  chr2_983782_988694     3534  4425 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_983782_988   3534 TGGAAAAACCTCCCTGGCTCATGGATTGAAAAAAATCAATATTATTAAAA 3583
                               i iv    vv i          i  i v- i      i    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chr2_983782_988   3584 TAACCATACTACCCAAAGCAATCTAGAGATTCAGTGCAATTCTCACCAAA 3633
                          ii v     v      vii     v       ii     i ii i    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_983782_988   3634 ATATTAATATCATTTTTTA-AAAGATTAGAAAAAAAGTCCTAAAATCCAT 3682
                           vii iivv v      i- i i   iiv  ivvii         i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_983782_988   3683 GTGGAACTAAAAAAGAGGCTGAATAGCCAAG-CAGTTCTAAGTAAAAAGA 3731
                         i     v iv  ii  vv v          i-  i ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_983782_988   3732 ACAAAGCTGGAGGTATCACATTACCTGACTTCAAATTATACTACAAGGCT 3781
                               i      vv     i v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_983782_988   3782 ATATTAACCAAAAGAGCATGGTCCTGATATAAAAATAGACATGTAGATCA 3831
                          i v   i   i v  ii    v   ii    ii        i       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_983782_988   3832 A-GGAACAGAATAGAGAACCCAGACATAAAGCCACATACATACAGGCAAC 3880
                          -    i     v    ii     v     v   i i iv  ii v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_983782_988   3881 TGATCTTTTACAAAGTTGATGAAAACACACACTAATGTAAGGATACCCTA 3930
                             i  iv    i v  vii i v  iv  v iiv v   i   vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_983782_988   3931 TCCAA-AAATGGTGCTGGGAAAATTGGATAGCCATATGCAGAAGAATTCA 3979
                          i   -              v  i      ?   i     i      vv 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_983782_988   3980 GCTGGATCCATAGCTCTCACCATATACGAAAGTTAACTCAAAATAAGTTA 4029
                          i    i  v  v   v          i   i            iii i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_983782_988   4030 AAAATTTAAATATAACACCTGAAACTATAAAAAAACCAGAAGAAAATCTA 4079
                         ? i ii     i   v v  i           vvvii         iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_983782_988   4080 GGA--AAATCTCTTCTGGACATTGCCATGATCA---AATAATTTATTAC- 4123
                           ?--      --  vv   v   ---- i i ---   ii   v   v-
  L1M4_orf2#LINE/    550 GGNGTAAATCT--TCGTGACCTTG----GGTTAGGCAATGGTTTCTTAGA 593

  chr2_983782_988   4124 TAAGACCTCAAAAGCAAATGGAA---AACATCCCAAAAATAGACAAATTG 4170
                           v   vi        v v v  ---  v ----         i      
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGA----AAAAATAGATAAATTG 639

  chr2_983782_988   4171 AACT-----AAAAT-----GCTTCTGCACAGTGAAAGACAAAATTGACAT 4210
                         i   -----     -----i   i  ii vvii  i    vv  ii v v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_983782_988   4211 AGTGAACAGACAACTTATAGAATGGGGGAAAATATTTGCAAAC--TGCAT 4258
                               v       ii i        i               i-- ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_983782_988   4259 TTAGTGAGTAACTAATATCCAGAATCTACAAGGAATGCAAAAAACTCAAT 4308
                         i ii i  vi   vi          v  i  i   iv vv v        
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_983782_988   4309 AACAAAAGCAACCACTTAA---AAGTAGGCAAAAGTAGGCAAAAGACATG 4355
                           i    -- iv  vv   ---  v ?---    i i      i  iv  
  L1M4_orf2#LINE/    790 AATAAAA--AGACAAATAACCCAATTW---AAAAATGGGCAAAGGATTTG 834

  chr2_983782_988   4356 AACATATATTTTTC---AAAAGACAAACAAATGGTTA-CAAGCATTTGAA 4401
                           i v i    i  --- i    i v        ii -i     iv    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_983782_988   4402 TTAATGCTGAACGACACTGATCAT 4425
                         vvi     v   iv  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.40 (48 / 20)  


2664 25.16 1.70 5.63  chr2_1028308_1033663.rev     3923  4864 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_1028308_10   3923 AAAAAGATTCCACACTCATGGATAAGAAGGATCAATACTGTTAAAATGTC 3972
                            i v  i   iii        vi    iv i    i      i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_1028308_10   3973 CATACTGCCCAAAGCAATTTACAGATTCAGTGTTATTCCCATCAAACTAC 4022
                         v     v      vii  i          ii iv  i  i      v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_1028308_10   4023 CAA-TA--TTTTTCACAGAATTAGAAAAACCAATTATAAAATTCATA-GG 4068
                           i- i--     ii     v v  v  i ii  iv           -  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_1028308_10   4069 AAACCAAATATAGCCTAAATAGCCAAATCAATTGTAAGCAAAAAGAACAA 4118
                            ivv  viv v  vi          v    iv i iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_1028308_10   4119 ACCTGGGGGCATCACATGACCTGACTTCTAACTATACTACAAGGTTATAG 4168
                          vi   i  vv     ivv  ii i   v  viv        i i  i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_1028308_10   4169 TAACTAAAATAGCATAGTACTGTTACAAAAACAGACACACAGACCAATGG 4218
                            ii  i i  ii i      vi i  ii i     i i   i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_1028308_10   4219 GACAAATTAGAGAACCCAAAAATAAAGCCACCTACCTATAAGCATCTGAT 4268
                         i i i v v    ii   i       v   ivi ii   iiv  vi    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_1028308_10   4269 CTTCAACAAAGTCAACAGTAACAAGCAATGGGTAAAGAACTTCCTATTCA 4318
                         i   i    i viiv  iv v  vv       v      ivvi  v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_1028308_10   4319 GTAAATCGTGCTGGGATAACTGGCTAGCCATATGCAGAAGATTGAAACTG 4368
                         ii    v         i      v  ?   i     i    v    ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_1028308_10   4369 GACCTCTTCCTTTTACCACATACAAAAATCAACTTAAGATGGATTAAAGA 4418
                             i  v   ivi    i          i    i  i      i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_1028308_10   4419 CTTAAATGTAAAA---AAAACTATAAAAATCCTAGAAGAAA-CTTGGAAA 4464
                          i         i ---            v  i         - v i i?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_1028308_10   4465 TAC-TATTCTGGACATAGGGCCTAGCAAAGACTTCATTACAAA-AACTCC 4512
                           v- v   vv   v v   iivi    v ii   -   v v -i  v  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGACACC 602

  chr2_1028308_10   4513 AAATGCAATTGCAACAGAAACAAAAGTTGACAAATGGTACCTAATTAAG- 4561
                            v   vvv      i  iv    i v  i    v v  i v  i  i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_1028308_10   4562 CTAAAGA-----GTGTCTTCAGGGCAAAAGAAACTATCAACAGAGTAAAC 4606
                         i    i -----   -     -----  i  v        v i   i  v
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTG-CTTCA-----AAGGACACTATCAAGAAAGTGAAA 696

  chr2_1028308_10   4607 AGACAACCTACAGGATGGGATAAAATATTTGCAAACTATGCATCTGATAA 4656
                                 i    i      v              ii  ii         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_1028308_10   4657 GGGTATAATATCCAGAATCCATAGGAAACTTAAACAAATCTAACAAAAGA 4706
                            vv vi          --   -------    v  v   v    ----
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAAT--ATA-------TAAAGAACTCTTACAA---- 783

  chr2_1028308_10   4707 AACAAACAACCCCATTATAGGAAACTTCAACAAATCTAACAAAAGAAACA 4756
                         -------------------------i    ------   i    - i   
  L1M4_orf2#LINE/    784 -------------------------CTCAA------TAATAAAA-AGACA 801

  chr2_1028308_10   4757 AACAACCCCATTTTAAAAATGGGCAAAGGACATGAACAGGCACTTCTCAA 4806
                           i     v   ?-                iv    i  i  i     v 
  L1M4_orf2#LINE/    802 AATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_1028308_10   4807 AAAAAGACGTATATGTGGCCAACAAGCATATGAAACAATGGGCAACATCA 4856
                           i    ii  i vi       i     i      vi   vv        
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_1028308_10   4857 CTAATCAT 4864
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.02 (18 / 905), avg. gap size = 3.83 (69 / 18)  


2783 26.23 1.07 3.85  chr2_1181516_1186990     4050  4983 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_1181516_11   4050 TGGAAAGACATCTCATACTCATGGATCAAAAGAATTAATATAGTAAAAAT 4099
                                 i   i   ii        iii    v       v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_1181516_11   4100 GACCATATTTCCTAAAGCATTTAACAGATTTAATGCAATCCCTATAAAAA 4149
                          i v   i i  i   viiv iv       i  i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_1181516_11   4150 TACCAATAAAATTCTTTACAGAAATAGAAGATATAATTTTATTAATTTGT 4199
                          v   iivivv  i   i       v  vi vv i  ii  v-    ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA-AATTCAT 149

  chr2_1181516_11   4200 ATGGAACCACAAGAGAGCATGAATAGCCAAAGCAATCTTAAGCAAAAAGA 4249
                               vii    i  v vv           i       i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_1181516_11   4250 ACAGAACTTAAGCAAAAAGGGC--AGAAT----GACTTTGAAATACACTA 4293
                            i ii -------ii   i -- v v ----i i  ii   ivi    
  L1M4_orf2#LINE/    200 ACAAAGTT-------GGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_1181516_11   4294 CAGAGCTATAGTAATGAAAAAAGCATGGTACTGGTATAAAAACAGACACA 4343
                           i     i      v  i v  ii         i    ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_1181516_11   4344 GAGACCAATAAAATATAACAGAAAACATAGAAATAAATACACATATTGGC 4393
                         v   i    ii    v  iv  i iivi         iv  i i   vii
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_1181516_11   4394 AGCCAACTAATTTTTGACAAAGATACCAAGAACATACATTGGTGAAAGGA 4443
                         i i   i i     i     i i i      v   v  v   v     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_1181516_11   4444 TACTCTCTTCAATACATGGTTCTGGGAAAGCTGGATATTCATCTGCAGAA 4493
                           v   i     i v     v      v i       ?i  iv    i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_1181516_11   4494 AAATGAAACTGGACCCCTATTTCTCACCATATTAAAAAATCAACTCAAAG 4543
                         i      ii          ii  v        vv      i        i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_1181516_11   4544 TGGATTAAAAGCTTAAACGTGAGATCCAAAATTATAAAACTACTAGAAGT 4593
                              i ? ii i    i  i   v i    i         vi      v
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_1181516_11   4594 AAACATAGTAGAAACACTTCAGGACGCTGGTTTAGGAAAAGATTTTATGA 4643
                                 v? v  vv    iv   vi   v     v  v i   iv ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_1181516_11   4644 CTGAGACCTCAAAAGCACTGACAACAAAAACTTTTTTAAAATAAACAAAT 4693
                         v iv   vi         vii        ivv-----      i i    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAA-----AAAATAGATAAAT 637

  chr2_1181516_11   4694 GGAACTGTATTAAACTAAAAAGCTTCTGCACAACAAAGGA-ATAATCAAC 4742
                         v i   vi  i   v v    i   i  ii vv       - iv     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_1181516_11   4743 AGAGTGAAGCAACAATATATGTAATGAGA-AAAATATTTGCAAACTATTC 4791
                          i      ivi    ivi iiv    i  -              ii  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_1181516_11   4792 ATTCGACAAGAGACTAATATCCAGAATATACAAGGGACTCA-ACAGCAAA 4840
                           ii  i   i    vi             i  i i    v-   i vv 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_1181516_11   4841 AACAATAAGAAAAACAAACTAATCCTATT-AATACTGGGCAAAGTATCTG 4889
                          -i     -   i     -   i  v   -  v v         v  i  
  L1M4_orf2#LINE/    788 A-TAATAA-AAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_1181516_11   4890 AATAGAAAATTCTCAAAAGAAGACATATGGCCTATAGGCCAACAAATGGC 4939
                               v v     v        i   ---------------        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATA---------------CAAATGGC 869

  chr2_1181516_11   4940 CAACGAACAGATATATGAAAAAAATGCTTAGCATTACTAATCAT 4983
                            ii i  ----i       i -    i i   i ????????
  L1M4_orf2#LINE/    870 CAATAAGCA----CATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (155 / 87)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.07 (46 / 15)  


3835 20.68 3.16 0.68  chr2_1273385_1277052.rev     2292  3176 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_1273385_12   2292 GAAAAGACATCTTGTGCTCATGGATTGTTAGACTTAATGATGTTCGGATG 2341
                          i     i   iii  i          vv         iv    vi    
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_1273385_12   2342 TCCATACCACTCAAAGCTATCTGCAAATTCAATGCAGTCATTATCAAAAT 2391
                         v v    iv i    viv    i  i      i   i  vi         
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_1273385_12   2392 CCCAAAGACCTTTTTC-CAGAAATAGAAAAATCCATCTTAAAATTCCTAT 2440
                             ivvi       i-       v  v  iiiv   i        v   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_1273385_12   2441 GGAA-TGTCAAGGACCTTGAATAGCCAAAACAATCTTAAAAA-------C 2482
                             -  iv i     iv                   i    ------- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_1273385_12   2483 AA-GTTGGAGATTTCACAATCCCTGATTTCAAAACTTACTGCAAAGCTAC 2531
                           -       ivi     v i  ii               i         
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_1273385_12   2532 ATTAATCAAAACAATGTTGCACTGGCATAAAGAAAGACATA--GATCAAT 2579
                          v       i   i   v i          i  v       --       
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_1273385_12   2580 GGAACAGAACAGAGAG-CGATGAAAGAAACCCTCACATAGGTGCTCAGAT 2628
                             i    iv     - v -    v      vi    vvi  v   iv 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATGGTCAATT 350

  chr2_1273385_12   2629 AATTCCTAACAAAGTTGTCAAGACCATTCAATGGAGAAAGGCCAGTCTTT 2678
                         i   iiii    i v  i                i     ivi       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_1273385_12   2679 TCAATAAATGGTGCTGGGAAAACTGGATATCCATTTGCAAAA--ATGAAG 2726
                             i              v         ?   iv       --      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_1273385_12   2727 TGGAACCCTTATCTTACATCATATCCCAAAATTAAATCAAAACAGACCAA 2776
                          v i    i  i  i   i     v v        v      ii  i  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_1273385_12   2777 AACTCTAAATGTCACAGCTAAAATTGTAAAATTCTTGTGATTAAAA-ATA 2825
                          ivi        v v        i i     i    i-  vv    -   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA-GAAGAAAACATA 549

  chr2_1273385_12   2826 GGGGGAATACTGCATGACACTGGACTTGGCAATGATTTCTTGGATATGAC 2875
                           ? v  vv  v i    vi   ii v       i      i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_1273385_12   2876 ACCAAAAACACAGGCAACCAAA---AAAATAGACAAACAGAATAATACCA 2922
                                i    i     v   ---        i   iv i ivvi i  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_1273385_12   2923 AAATTAAAA-CTTTTGTGTATCAGAGGACACCACCAA-AGAGTGGAAATC 2970
                                  -        iv   i       i i   - i    i   vv
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_1273385_12   2971 CAACCCAGAGAATGTGAAAG----TTTGTAAATCATATATCTATTAAGGG 3016
                                v      v  i i----    i             iv      
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_1273385_12   3017 GTTGATGTCTAGAATACATAA-GAACTCCTACAACTGAACCAGAAGAAAA 3065
                         ii vi i  i      i    -      i       v  i---  v    
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT---AATAAAA 796

  chr2_1273385_12   3066 CAAGCAAACAACCCAATTAAAAGACGGGCAAAAGACCTGAATAGACATTA 3115
                         - ii    i         ?   i i       i  ii            v
  L1M4_orf2#LINE/    797 -AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_1273385_12   3116 CTCCAA-GAAGATATATCAATGACCCATCAGCACGTGGAAAGATGC-CAA 3163
                               -         iv    i  v  v     i  i        -   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_1273385_12   3164 CATCACCAGTGAT 3176
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (112 / 67)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 1.79 (34 / 19)  


3298 22.93 3.31 3.20  chr2_1318495_1321803.rev      686  1592 (1717)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_1318495_13    686 TGGAAAGGCATCCCATATTTATGGGTTGGAAGGCATAATGTTATTAAGGT 735
                                ii       i  i    i       i v    i  i     i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_1318495_13    736 GTTAATATTGCCAAAAGTGAACCTCAGATTCAATACATTCTCCATTCAAA 785
                          vi    i v  v   v   v iv         ii  v  i i  iv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_1318495_13    786 TCCCAAAGACATTTTTTT---AAATAGA------------AAAATGCCTC 820
                              ivvi v      v---    v  ------------     v v v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_1318495_13    821 TGTAATCTTAAAGGATCCTGACTAGCCAAAACAATCTTGAAAACAAATAA 870
                           v  vivi  i   i  v  v                     vi  -i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GA 199

  chr2_1318495_13    871 ACAAAGTCTGAAGTCTCATGGTTCCTGATTTTAAAGCTGATGGCAAAGCC 920
                                iv  i v    iiv    ii    i   i  v ivi      i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_1318495_13    921 ACAGTTATCAAAACACTGT---ACTGGTATAAAGAGAGACATACAGATGA 967
                              v     i   v   ---     i    i  v       i    v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_1318495_13    968 ATGGAATACACCAGAGAGCACAGAAGTAAAACCTGGCCTATGTGGTGCCA 1017
                                 v viv     iv     i    v  vvi v v i    - v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT-CAA 348

  chr2_1318495_13   1018 TGTAAGTCTGTGATTCAATCAGAAATGTC-----CGTGCAATGGGGAATG 1062
                          - i v ------   i -  iiii  i ----- i v          v 
  L1M4_orf2#LINE/    349 T-TGATT------TTCGA-CAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_1318495_13   1063 AGCAGTTTTTTAATCAACTGGTGCTGGGAAAATTAGATATCCGGTTGCAA 1112
                          ii   i    v v   v           v  i i    ?  ivv     
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_1318495_13   1113 AACAATGAATTTAGGCTCTTACCTTATACCATATATAAAAATTAACCCCA 1162
                           v      v  i i i i     i i        i          i v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_1318495_13   1163 AATGAATCAAGGACCTAAACATAAGAATTAAAACTTTAAAAAGTTTAGAA 1212
                             i    ?i        ii     ii       v     vvi      
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_1318495_13   1213 GAAAACATAGGG--AAACACTTATGACATTGGGTTTGGCAACAATTTCTT 1260
                                    ?--   ivi ii    v       v     iii      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_1318495_13   1261 GGATATGACACAAACAGCAAAGGCAATCAAAGAAAGCATAGATAAATTAA 1310
                         i          v  v    v i    iv       iv           i-
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG- 639

  chr2_1318495_13   1311 AAGAGATAATTAGATTGCACCAACATTAATAACTTTTGTGCATCAAAGGA 1360
                         ------------  i v  i   v     v           v        
  L1M4_orf2#LINE/    640 ------------GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_1318495_13   1361 CACTGTAAACAAAGAATAAAGAGAAAACTCCCAGAATGAGAGAAGACATC 1410
                             i v  v    -- i  i   v   i v       i     i i  i
  L1M4_orf2#LINE/    678 CACTATCAAGAAAG--TGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_1318495_13   1411 CGCAAATCACACATTTGATAAGGAGCTAATATCTAGAATATTTAA-GAAC 1459
                         i        i i  i        ii  vi    i       v   -    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_1318495_13   1460 TCTTATAAATCAGCAACAACAACAACAAAAGACAACTTGATAAGAAAATG 1509
                              i  v   ii  i  v  -i     ---i   iii  v?i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAA-GACAAA---TAACCCAATTWAAAAATG 821

  chr2_1318495_13   1510 GGCAAAAAATCTGAATA----TTTATTTAGGGAAGATATAGAAGTGTCCA 1555
                               ii  i      ----   v ii ii         v  i  v   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_1318495_13   1556 ATAAGCACATGAAAAGATGTTCAACATCAATAATCAT 1592
                                            i         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (123 / 81)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.69 (59 / 16)  

2993 27.27 1.56 0.24  chr2_1318495_1321803.rev     1982  2817 (492)    L1M4_orf2#LINE/L1       62   908 (0)  

  chr2_1318495_13   1982 CCAAAGCAATTTATAGATTCAATGCAATCCCTATCAAAATTCCAATGACA 2031
                              vii  i  i        i                 i   iivi v
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_1318495_13   2032 TGTTTGACTGAAACAGAAAAAA-AATTCTAAAATTCATATTGAACTGCAA 2080
                          v   vi v    iv  v  iv-i  i             v   v     
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_1318495_13   2081 AAGACCTTGACTAGCAAAAGCATTATTGGGTAAATAGAACAAAGCTAGGG 2130
                         ii    iv  v    v   i  v v   iiv  iv         i i i 
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_1318495_13   2131 GCACT-GCACTACCCAACTTCAAAATATACTACAAAGCTGTAACAACCAA 2179
                          -   -i    v     i       iv            ii ii  i   
  L1M4_orf2#LINE/    212 G-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_1318495_13   2180 AACAGCATGGTACTAGTGCTAAAACAGAAATATAGA-CAA--AAACAGAA 2226
                         i    ii       i iiiv ii i   v       -   --i  i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_1318495_13   2227 TTGAGACCCCAAAGATAAATCCACGCTTTTACCATCAGTTGCTCCTTTAC 2276
                               vi   i i     i   ii v    ivi   i   v ii iv  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_1318495_13   2277 AAGGGTGGCAAGAACACACAACGGGGAAAAGATAGTCTCTTCAATAAATG 2326
                                v     v  iv   i       ii       i     i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_1318495_13   2327 ATGTGGGGAAAACTGGATATTCACATTCAGAAGAATGAAATCAGATATTT 2376
                         i  iv    v         ?i     v  i         i ii  ivii 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_1318495_13   2377 ATTTCACACCATATA-AAAAATCAACTCAAAATGGATTAAAGATTTAAAT 2425
                          ii            -      i              i ?   ii     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_1318495_13   2426 GTAAGACCAAAAACTATAAAACCACTAGGATAAAACATAGGACAAAATAT 2475
                               v v             ivi   i v          ?vv    v 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_1318495_13   2476 TTTTGGCATTGGTCTGGGCAATGATGTTTTGGATATGATTCCAAAGGCAT 2525
                          iv  i v    vi i       i v i  i       iv     i   i
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_1318495_13   2526 AAGCGATGAAAGCAAA--CAGACAAATTAAAGTCCATTGAACTAAACAGT 2573
                             i ii    v   --i   i     ii v i   ii  v v  v ii
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_1318495_13   2574 GTCCGCACAGCAATAAAAATAATAAACAAAATGAAGTGACTACCTAAAGA 2623
                         v ii ii vv   vii v iv  v  v   i    iv   v   i v   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_1318495_13   2624 ATGG-AGGAAATATTTACAAGCCATGCATTTGATAAGGGGTTAATATCCA 2672
                             -  i        i   ii   ii  i         ii vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_1318495_13   2673 AAATATATAAGGAAGTCAAAGCACTCAAAAGCAAGAAAACAA----CCTG 2718
                         i         i   v  vv vv      v ii  i  i    ----  ii
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_1318495_13   2719 ATTTTAAAATGGGCGGAAAACTTGGACAGGCATTTCCCAAAAGAAGACAG 2768
                            ?v         ii ii i   i i  i      i v        i v
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_1318495_13   2769 ACAGATGGCCAGCAAGTCTATGAAACAAATGTTCAGTGTCACTAAGCAC 2817
                            i       ii   ivi      - i   i   iii   ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAA-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (151 / 73)
Gap_init rate = 0.01 (10 / 847), avg. gap size = 1.50 (15 / 10)  


3428 23.42 3.10 0.23  chr2_1338222_1340693.rev     1110  1980 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_1338222_13   1110 CCACGTTAATGAATTGTAAGTCTTAATATTGTTAAAATGTGTATACTACC 1159
                            i   v   i    v   v              i   vvv     v  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_1338222_13   1160 CAAAGTGATCTATAGATTCAATGCAACATCCATCAAAATCTCAA-TGGCA 1208
                             v       i        i    ivi i         i  i-  v v
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_1338222_13   1209 TTTTTACAGACATAGAAAAA---ATCCTAAAATTTATATGAAACCACAAA 1255
                              i    v  v  v  i---           i     i  vii   i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_1338222_13   1256 AAATCCTGAATAGCTAGGGCAATGTTGAGAAAGAA---CAAAGTTGGAGG 1302
                         ii i  v       i iii    v    i      ---            
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_1338222_13   1303 CATCTCACTTCCTTACTCTAAAACATATTACAAAGCCACAGTAATCAA-- 1350
                         vv  v       iv i ii     v  i        i           --
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_1338222_13   1351 TGGTATGGTACT-----AAAGACA--CATATAAACCAATGGAACAGAATA 1393
                         ii  i       -----  i  i --      i i        i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_1338222_13   1394 GAGAGCCCAGAAATATACTTATACCTACATTGTCAGGTGATCTTCCACAA 1443
                              i         v  ii    v vi  v    iv    i   v    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_1338222_13   1444 AGG-GCTAACGCTATACAGTGGGGAAAGGTCAGTCTCT-CAATAAATAGT 1491
                         i  -  i  vi i  v  i         ivi     i -   i    i  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_1338222_13   1492 GCTGTGAAAACTGGATATTCAGAAGCAAATGAATAAAATTGGACCTTTAT 1541
                             v  v         ?i  v v     v    i  i       ii  i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_1338222_13   1542 CTTACACCATACAGAAAAATCAACTCAAAATAGATTAACGACTTAAACAT 1591
                           i        i v      i          i   i ?v   i    ii 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_1338222_13   1592 AAGACCTGAAACTATAAAATTTCTAGAAGAAAACAGTGGA--AAAGATTC 1639
                             v  i           i ii            vv  ?--   vv   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_1338222_13   1640 ATCACATTGATCTTGGCACTGATTTTCACAGATATGACACCATAACCACA 1689
                         i v  v   ivi v    v  i   - vi             v  v    
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTT-CTTAGATATGACACCAAAAGCACA 611

  chr2_1338222_13   1690 GGCAACAAAAGCAAAAGTAGACATTTGGGTCCACGTCAAC-TGAAAAGCT 1738
                         i          v    i    i vv v  v iv i    v- v    i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_1338222_13   1739 TCTGCACAACAGAAGAAACAATCAGAAGAGTGTAAATGCAACCTATGGTA 1788
                          i  ii vv  i i  v  v    ii i    v   vi     i ii v 
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_1338222_13   1789 CAGGAGAAAATACCTACAAACCATAT--CTAATCAGGGGTTAATGTCCAA 1836
                         ii          ii i    i     --  i  v    ii vi i    i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_1338222_13   1837 AATGTATAAATAACTCCTACAACTCAATAGTAAAAA-ACAAAAAACCTGA 1885
                            i      v     i            i      -     v    ii 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_1338222_13   1886 TTTTCAAAATACGCAAGGGACTTGAATAGACATTTCTCTAAAGATGACAT 1935
                           ?-v     iv    i   i                 i     v  i  
  L1M4_orf2#LINE/    812 TTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_1338222_13   1936 TCAAGTGGCCAGCAA--ACATGAAAAGGCATTCA-CATCACCAAGCAT 1980
                         v   i      ii  --          iiii   -     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (125 / 75)
Gap_init rate = 0.02 (16 / 896), avg. gap size = 1.81 (29 / 16)  


2968 27.24 2.13 0.34  chr2_1365756_1372128.rev     4990  5881 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_1365756_13   4990 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATGGTGAAAAT 5039
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_1365756_13   5040 GACCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATGAAGC 5089
                          i v     v     iv i  i  i       ii  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_1365756_13   5090 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTACAGTTCATA 5134
                          v   iivi i  i  ii     v v  v  i--- --   v i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_1365756_13   5135 TGGAACCAAAAAAGAGCCTGCATTGCCAGGTCAATCCTAAGCCA-AAGAA 5183
                              viiv  ii  v  v v  v    iiv     i i ivv -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_1365756_13   5184 CATAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5233
                           v  i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_1365756_13   5234 CAGTAACCAAAACAGCATGGTACTGGTACCAA-ACAGAGATATAGACCAA 5282
                               i   i    ii         i iv i- i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_1365756_13   5283 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACTAT 5330
                              i    i--    i  --        vv   i    i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_1365756_13   5331 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGTATTCCCT 5380
                         i    i  i     ivv  v   i v  vvv           v  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_1365756_13   5381 ATTTAACAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5430
                         v  i      i          v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_1365756_13   5431 AACTGGATCCTTTCCTTACACATTATACAAAAGTTAATTCAAGATGGATT 5480
                          ii    i  i v   i    vv         i    i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_1365756_13   5481 AAAGACTTAAATGTTAGACCTAGAAG---AAAACC--TAGAAGAAAACCT 5525
                          ?    i       v   v   i  v---     i--           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_1365756_13   5526 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACGTCATGGCTAAA 5574
                            ?i- v i -   iv   v v  vv i     v iiv  v i v  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_1365756_13   5575 ACACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5624
                                  i  vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_1365756_13   5625 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5674
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_1365756_13   5675 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5724
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_1365756_13   5725 GGGCTGATACCCAGAATCTACAAAGAACTCAAACAAATTTGCAAGAAAAA 5774
                           i  vi  i       v  i         vv    v ivii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_1365756_13   5775 AACAA----CCCCATCAACAAGTGGGCAAAGCATATGAACAGACACTTCT 5820
                         i    ----   v  i? v  i         v  v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_1365756_13   5821 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAACTGCTCATCA 5870
                          v        i  vi viii     i ii          iv      v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_1365756_13   5871 TCACTGGCCAT 5881
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.34 (137 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


3115 25.92 1.01 0.78  chr2_1446933_1451500.rev     3185  4079 (489)    L1M4_orf2#LINE/L1       12   908 (0)  

  chr2_1446933_14   3185 CCCATGCACATGGATGGGTAGAGTCAATATTGTGAAAACAACCATACTGC 3234
                               iv       v  v   v i        v  i iii v     v 
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chr2_1446933_14   3235 TGAAAGCAATCTACAAATTCAACACAATTCCCATCAAAATACCA-CCATC 3283
                         iv   vii       i       i    i  i        v   - iii 
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_1446933_14   3284 ATTCTT-CATCAAATTAGAAAACAAAATCCTAAAATTCGTATGGAACCAA 3332
                         v  i  -  v-     iiv  i vi -           i       viiv
  L1M4_orf2#LINE/    112 TTTTTTGCAG-AAATTGACAAGCTGA-TCCTAAAATTCATATGGAAATGC 159

  chr2_1446933_14   3333 AAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAGAAAGAACAAATCTGG 3382
                           ii  v  v v         i   vvi i iv ii         vi   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_1446933_14   3383 AGGCATCACATTACCTGATTTCAAACTATACTATAAGGCCATAGTCACCA 3432
                            vv     i v  ii        viv     i  i  i i   v i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_1446933_14   3433 AAACAGCATAGTACTGGTACAAAAATAAGCACATAGACCAATGGAATAGA 3482
                          i    ii i       i i  ii   ii  i     i            
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_1446933_14   3483 ATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAATTGATCTTCGA 3532
                           v    ii               v i i   ii i        i     
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_1446933_14   3533 CAA---TGCAAACAAAAACATAAAGTGGGCAAAGGACACCCTATTCAACA 3579
                            ---   ---   i v   vv i    v    i i vi  v       
  L1M4_orf2#LINE/    360 CAAGGGTGC---CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_1446933_14   3580 AATGATGCTGCGATAATTGGCAAGCCATGTGTAGGAGAATGAAACTAGAT 3629
                             i     v  i  i   vv ?   ii  i ii        ii i  i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_1446933_14   3630 CCTCATCTCTCACCTTATACAAAAAC-AACTCAAGATGGATCAAGGACTT 3678
                           ii i   v    v          i-       i        ?i   i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_1446933_14   3679 AAGTCTAAGACCTGAAACCATAAAAACTCT-AGAAGATAACATTGGAAAA 3727
                           i v     v  i    i      -    -      v     v  ?iv 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTA 555

  chr2_1446933_14   3728 ATTCTTCTTGCTATTGGCTCAGGCAAGGATTTAATGACCAAGAACAC-AA 3776
                          v     v  viv    v i      v i   vv iivi v  -   -  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-CACCAA 604

  chr2_1446933_14   3777 AAGCAAATTCAATAAAAAGAAAGATAAATAGTTGGGACTTAATTAAACTA 3826
                              v vv   i    ii   i   i   iv v      v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_1446933_14   3827 AAGAGCTTTTGCACAGCAAAAGGAACAGTCAGTAGAGTAAACAGACAACT 3876
                           i i      ii vv    i iv  vi   iv i   i  v       i
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_1446933_14   3877 CACAGAGTGGGAGAAAATCTTCACAATCCACACATCTGACAAAGGATTAA 3926
                               i           v  ii   vi  i i      i  i   i vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_1446933_14   3927 TATCCAGAATCTACAACAAACTCAAACAAATCAGTAAGAAAAAC-CAAAC 3975
                                   v  i  vi     vv    v   i   v     v-    i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_1446933_14   3976 AATCCCATCAAAAAGTGGGCTAAGGACATGAATAGAGAATTCTCAAAAGA 4025
                           i  v  i?    i     v     iv        v v     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_1446933_14   4026 AGATACACACATGGCCAACAAACATATGAAAAAATGCTCATCACTAATGA 4075
                              i   v        i  i  i       i       v  ii ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_1446933_14   4076 TCAG 4079
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.56 (139 / 89)
Gap_init rate = 0.01 (12 / 897), avg. gap size = 1.33 (16 / 12)  


2801 26.53 2.90 1.67  chr2_1588972_1590975      616  1512 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_1588972_15    616 TGGAAAAACATCCCATGCTCATGGATTGGAAGAATCAATATCATTGAAAT 665
                               i i        i               v i     ii  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_1588972_15    666 GGCCATACTGTCCAAAGCAATTTATAGATTAAGTGCAATTCCTCTCAAAC 715
                            v     vi     vii  i  i     v ii     i   v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_1588972_15    716 TACCAATGACATTATTTTCACAGAATTAGAAAAAGCT-ATTCTAAAATTC 764
                          v   iivi v  --   ii     v v  v  -   -  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT--TTTTGCAGAAATTGACAA-GCTGATCCTAAAATTC 147

  chr2_1588972_15    765 ACATGGAACCAAAAAAGAGCCCGAATAGCCAAAGCAATCTTAAGCAAAAA 814
                          i      viiv  ii  v  v           i       i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_1588972_15    815 GAAGAAAGCCAGAGACCTCACATTACCGAACTTCACACTGTACTACAAAA 864
                            v    iii   iv      i v  v  i    v viv         i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_1588972_15    865 CCACAGCAACCAAAACTGCATGGTATAGGTAGAAAAA-AGACACATAGAC 913
                          i    i  i   i  v ii     iv  i v  ii -     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_1588972_15    914 CAATGAAACACAAAAGATAACCCACAAATAAAGCCACGCATCC-----CA 958
                              i  i v  vv  v ii   v       v   ii   ii-----  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_1588972_15    959 -----TCTTCAACAAAGCTGACAAAAACAACAAATGGAGAAAAGGC--CC 1001
                         ----- i   i    i v  v   i v  viv     i    iiii--i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_1588972_15   1002 TTAATTCAATAAATAGTGCTGGAATAACTGGCCAGCCATACGCAGAAGAT 1051
                           --     i    i       i i      vi ?   i i   i    v
  L1M4_orf2#LINE/    398 TT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_1588972_15   1052 TGAAACTGGATCCTTCCCTTTCACCATATTCAAAAATCAACTCAAGATGG 1101
                             ii    i  i v   iv        v       i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_1588972_15   1102 ATTTCAAAGACTTCAGCGTAAGGCCTCAAACTATAAAAATCCTAGAAGAA 1151
                           --  ?    i v ii     iv  v           v  i        
  L1M4_orf2#LINE/    496 AT--CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_1588972_15   1152 AACCTAGG---AAATGCTCTTC----TCTATATGAGTCTTGGCAAAAGAC 1194
                            v    ---    ---    ----i  ---  i  - v     vi vi
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT---CTTCGTGACCT---TGGGT-TAGGCAATGGTT 586

  chr2_1588972_15   1195 TTATGGCTAAGTCCTCAAAAGCAATTCCTACAAAA-ACAAAATTGACAGA 1243
                          iv i v  v v vi        vvvv v      - v     v  i i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_1588972_15   1244 TGAGACCTAATGAAGCTAAAGAGCTTCTATACAGCTAGAAAAACTATCAA 1293
                          vi   i v  v  iv v  i i   i i i vv v iii v        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_1588972_15   1294 CAGAGTAAACAGACAACCTGCAGAATGGGAGAAGATACTCACAAACTATG 1343
                         v i   i  v        ii             i   i ii    ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_1588972_15   1344 CATCCAACAGAGGTCTAATATCCAGTATCTATAAGGAGCTT----AAATC 1389
                         i   ii i ii  v  vi       v  v     i  i  i----  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_1588972_15   1390 CACAAGCAAAAGACAAATAACCCCCATTAAAAAGTGGGCAAAGGACATGA 1439
                         v i  vv                v-   ?    i           iv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_1588972_15   1440 ATGGACGCTTCTCAGAAGAAGAAATACAAGCAGCCAACACATATATGAAA 1489
                           i   ii     vi       v      iii     i vii i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_1588972_15   1490 AAATGCTCAGCATCACTAATCAT 1512
                          i       i     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (147 / 88)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.41 (41 / 17)  


3323 25.74 0.66 0.77  chr2_1733536_1739896     4961  5869 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_1733536_17   4961 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5010
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_1733536_17   5011 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5060
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_1733536_17   5061 TACCAATGACTTTCTTTGCAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5108
                          v   iivi i  i         -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_1733536_17   5109 TATGGAATCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5158
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_1733536_17   5159 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5208
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_1733536_17   5209 TACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5258
                               v i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_1733536_17   5259 AATGGAACAGAAT--AGAGCCCTCAGAAATAATACCACACATCTGTAAGC 5306
                                i     --    i  --        vv   i    i i iiv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_1733536_17   5307 ATCTAATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5356
                          vi i  i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_1733536_17   5357 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5406
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_1733536_17   5407 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5456
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_1733536_17   5457 TTAAAGACTTAAATGTTAGACATAAAACCATAAAAACCCTAGAAGAAAAC 5506
                          i ?    i       v   vv      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_1733536_17   5507 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5555
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_1733536_17   5556 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5605
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_1733536_17   5606 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5655
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_1733536_17   5656 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTCCT-CATCTGAC 5704
                         v  i     i   i             v  i    v-  v -i      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGAT 744

  chr2_1733536_17   5705 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAAGAAATTTACAAGAA 5754
                           i  i  vi          v  i        ivv v  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_1733536_17   5755 AAAAATCAAACAACCTCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5804
                            i -    i    iv  i?    i            v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_1733536_17   5805 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 5854
                              v        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_1733536_17   5855 CTCATCACTGGTCAT 5869
                         vv     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (136 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2997 23.43 2.27 4.21  chr2_1982005_1986354      493  1418 (2932)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_1982005_19   1418 TGAAAAGATATTTCATGTTCAT---TAGGAAGAATTAGTATTGTTAAAAT 1372
                           i        ii         --- v      v   i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_1982005_19   1371 GTCCATACTACCCAAAGTAATATACAGATTTAACACAATCCCTATTAAAA 1322
                          v v     v      v i  v        i   i          i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_1982005_19   1321 TCTTCAATAGCAACAATAGCAATTTTCACAGAAATTGGGAAAAT-ATCCT 1273
                           i----------  iiv  vv    ii         iv  iv -     
  L1M4_orf2#LINE/    101 TCC----------CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

C chr2_1982005_19   1272 AAAATGTTTGTAGAACCACAAAAAACTCCAAGAAGCCAGGAAAAAAAGAA 1223
                              viv i i   vii   iii  i vi iv     ------------
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA------------ 178

C chr2_1982005_19   1222 AAAAAAAACCACTGAGAAGGAAAAACAAAGTTGGAGGAATCATACTTCTT 1173
                         --   v  i -i   i  i   i               v   i     ii
  L1M4_orf2#LINE/    179 --AAACAATC-TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

C chr2_1982005_19   1172 GATTT-AAAATTATATTACAAAGCTATAGATATTAAAGCAGTATGATACT 1124
                         i    -    i -  i          i  vv  i  ii    i  i    
  L1M4_orf2#LINE/    226 AATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

C chr2_1982005_19   1123 GGCATAAAAACAGAACCATAGACCCGTGGAACAGAACAAAGAGCCCCCAA 1074
                                ii i   vvi     i vi     i    ivi    i  vv  
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

C chr2_1982005_19   1073 ATAAATTGAAACAAATATGCGCAACTAATTTTTGACAAGGTCACCAAGAG 1024
                              iiv v   vv    vv   i i     i       vii      v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

C chr2_1982005_19   1023 GACACAATGGGGAAAGGACAGTCCCTTCAATAAACCGTGCTGGGAAAACT 974
                         v iv            i i    ii     i   iv         v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

C chr2_1982005_19    973 GAATTTTCACATGGAAGATAATAAAATTGGATCCTTGTCTTATACATTA- 925
                          i  v?i      v  i v   i  i     i  i ii  i i  vv  -
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

C chr2_1982005_19    924 AAAAAAATAATAATAACTCAAAATGGATGCAAGCCCTAAATGTAAAACCT 875
                          v      -----               vv?  v           i v  
  L1M4_orf2#LINE/    475 ACAAAAAT-----TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

C chr2_1982005_19    874 GAAACCATAAAACTCCAAGAAGAAAATGTTGGGAAAAATCTCCTTGACCT 825
                         i    i         iv         ii v  ?iv      i v      
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

C chr2_1982005_19    824 TGG-TCACAGCAACACTTTTTAAAATGTTAC-CCAAAAGCTTAAATGACA 777
                            - i -i    iiv   i v i  i v  -        vi  iii   
  L1M4_orf2#LINE/    570 TGGGTTA-GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

C chr2_1982005_19    776 AAACAAAAA-TAAATAAAT-GGACTACA-CAAAACCATAAAGCTTCTGCA 730
                            v     -  i      -     v  -     ii -   i   i  ii
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA-AAAACTTTTGTG 667

C chr2_1982005_19    729 CAGCCAAAGAAACAATATCACAA---TGAAAAAGCAGCCTATAGAGTGGA 683
                          -vi     i -  v     vi ---      ii  i  i i   i   i
  L1M4_orf2#LINE/    668 C-TTCAAAGGA-CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

C chr2_1982005_19    682 AAAAAAAAGTTTGCAAATCACAT--CTGATAAGGGGTTAATATCCAAAAT 635
                          i    v -           i  --          ii vi      i   
  L1M4_orf2#LINE/    716 AGAAAATA-TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

C chr2_1982005_19    634 GTATAAATAACTCTTACAAATCAACAGTAAAAATAAGGCAAATAATCC-- 587
                         i      v           v    i i      --- i       i  --
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAA---GACAAATAACCCAA 811

C chr2_1982005_19    586 TC---AAATGAGCGAAGGCCGTAAACAGACATTTTTCAAAACAACAAATA 540
                          i---     i  i    viv i  i        i  v   v  v v   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

C chr2_1982005_19    539 AAAATGTCCAACAGGCAAATGAGAAGGTGTTCAGCATCACTCCTCAA 493
                         v     v    i i   v    i   i  i   i     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (139 / 75)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.50 (60 / 24)  

 902 18.42 4.47 17.63  chr2_1982005_1986354     2792  3171 (1179)    L1M4_orf2#LINE/L1      197   526 (382)  

  chr2_1982005_19   2792 AGAACAAAGTAGGAGGGCAAACACTTCCCGACTTCAAAACTCACTACAAA 2841
                                   v     i vv         i i         i        
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_1982005_19   2842 GCAACAGCAATCAAGACAGAGTGGTGCCA-CATATGGACAGACATGATGC 2890
                           v    i           v     i ii-    v   i      -  --
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT-AT-- 293

  chr2_1982005_19   2891 AGCTCAGCGGAACAGAACCCATA--CCAAGAAGTAACTCACGCGTCTACT 2938
                           v   ii    i    iiv v --   ii  vv   i  ii i i  iv
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_1982005_19   2939 GTCAACAGACTCTTCACAGGGGTGCCGGGGCTAGTCAAAGGGGAGAGAAT 2988
                              iv  i i iv   i       ii i i v    v     i     
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_1982005_19   2989 CATCTTTTTAAC--------------CAACCGGATATCCCCATGCAAACA 3024
                         vi      i   --------------    i     ?  v        - 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-A 442

  chr2_1982005_19   3025 GGGGTACTCATTTCTGAGTACTTCAGCCCAGTGAGATGGAGTTGGTGGCA 3074
                          i---------------------------------   i      -----
  L1M4_orf2#LINE/    443 GA---------------------------------ATGAAGTTGG----- 454

  chr2_1982005_19   3075 GCCTGCCTCCAGCATGTCCCTATCTCACACTGTGTACAATAATAAACTCA 3124
                         ---------------ii     i       ii i     v   v      
  L1M4_orf2#LINE/    455 ---------------ACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_1982005_19   3125 AAATGGATCCAAGACCCAAACTTGGATCCATATAAGAACTAAAAGTA 3171
                                  v?     i   ---------- i     i      v  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAA----------TGTAAGAGCTAAAACTA 526

Transitions / transversions = 2.09 (46 / 22)
Gap_init rate = 0.03 (9 / 330), avg. gap size = 9.33 (84 / 9)  

1272 19.40 4.37 2.73  chr2_1982005_1986354     3493  3858 (492)    L1M4_orf2#LINE/L1      537   908 (0)  

  chr2_1982005_19   3493 AGAAAAAAAAA-AACTGTAA--CTATACAACTCTCAGATTTGGCAACATA 3539
                             i    v - iv?    --  viiii  -  ii i  v     iivv
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGT 585

  chr2_1982005_19   3540 TTCTTAAATATGACAACAAAAGCATGAGCAAT----TAAAAAGTAGATAA 3585
                               i        v        ii     i----v     i       
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_1982005_19   3586 ATTGAACGCTATCAAAATTTTAAAAAACAGACTTTTGTGTTGCAAAT-AC 3634
                             i  vii         ---      ----       i v    v-  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATT---AAAAAC----TTTTGTGCTTCAAAGGAC 678

  chr2_1982005_19   3635 ACCACCACAAAAGTGAAAAAAACAATCTACAGAAGGGGAGAAGGTATTTA 3684
                           i i  vi          i -   i i      v       ii     i
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGA-CAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_1982005_19   3685 AAAATCATATAT-TGATAAGGGATTTCTATCCAGAATATATAAATAATTA 3733
                         v           -          i  v                 v  i v
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_1982005_19   3734 TTATAAATCAATAATAGAATGACAA----CCCAGTTAACAACTGG-CAAA 3778
                            i  v         i  v     ----    i  ? v  v   -    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_1982005_19   3779 GGATCTGAACAGATATTTCTCCAAAGAAAATCTGCAAAAAACCC-TAAAC 3827
                             i    i   i              i  v i    vii  v-   i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_1982005_19   3828 ACACAAAAAGACTG-TCAATATCATTAGTCAT 3858
                            ii      -  -    i    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (45 / 24)
Gap_init rate = 0.04 (14 / 372), avg. gap size = 1.86 (26 / 14)  


3200 20.47 6.45 2.11  chr2_2025452_2027249      501  1306 (492)    L1M4_orf2#LINE/L1       68   908 (0)  

  chr2_2025452_20    501 TGATCTACAAATTCAGTGCAATCCCTCTCAAAATCTTAAGGTCATTTTTT 550
                                  i     ii         v        ii -- iiiii    
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA--GCTGCCTTTT 115

  chr2_2025452_20    551 TTTCAAAAATAAATATATTG----CAAGATTCGTA----AATGTTAAGAG 592
                           v  i    vi i vii  ----i  i    i  ----    i-   i 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC-AAGGG 164

  chr2_2025452_20    593 ATCCCCAAATAGCCAAAACTATATTGAAAAAGAA---CATAGTTAGAAAT 639
                          -   vi            v  v           ---  v    i  iiv
  L1M4_orf2#LINE/    165 A-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_2025452_20    640 TTCATACTTTCTGATTTGAAAACTTACAACAAAGCTACTGTAATCAAAAT 689
                         i   i    i ii    v         v          v        i i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_2025452_20    690 AGTGTGGTACTGGCATAAAGACAGAGAAACAGACCAGTAGAACAGAATAG 739
                                           i  i   v v i   i  i i   i     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_2025452_20    740 AGAACCCAGAAATAAATTCTTGCATATACGGTCAAATGATTTTTGACAAG 789
                            ii           ii v i   v  i      v       i      
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_2025452_20    790 GGTGCCATAACCATTTATTGGAGCAAGGACAGTCTTTTCAACACACAGAG 839
                                vi      i v   i v   i i             v ii v 
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_2025452_20    840 T------------ATACCCACATGCAAAAGAATAAAGTTATAACATTACC 877
                         i------------   ?                i     iv v vi    
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_2025452_20    878 TTAAACCTGTAAAAAGAAAAATTAACTCCAAATGGGTTAGCAACTTAAAC 927
                          i v   --- v v v            v      i i ?vi  i    i
  L1M4_orf2#LINE/    464 TCACACC---ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_2025452_20    928 ACAGAGGCTAAAGCTATAAAACTCTTAGAAGAAAA--TAGGAAGGATCAG 975
                         ii iii      i                      --    ?ivi -- v
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA--AT 558

  chr2_2025452_20    976 CTTCCTGACATTGGATTTGGCAATGATTGATTGGATATGATACCCAAAGT 1025
                             v    v    i  v       i  vv  i       i   v    i
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_2025452_20   1026 ATAGGTTA------AAAAAATGTCTAAATTGGGCAACATCAAAACTTAAA 1069
                          i i iv ------       ivv        i vv        -     
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA-TTAAA 657

  chr2_2025452_20   1070 ACAACGAAATGTTTGTGTGTCAAGGGACACTACCAACAAAGTGAAAGG-C 1118
                          ------- iv      iv    i        i   v         i - 
  L1M4_orf2#LINE/    658 A-------ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_2025452_20   1119 AACCCATGAAACAGCAGAAGATATTTGCAAATCATATATATGATAAGGAG 1168
                               iii  ii v    i                   v        ii
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_2025452_20   1169 CTAATATCTATAATATATAA-GAATTCCTACAACTCAA--------AAAC 1209
                           vi    i v         -   i  i          -------- i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_2025452_20   1210 AAATAACT-GATTAA------GGCAAAGGACTT----AGACATTTCTCCA 1248
                                i-i   ? ------         i  ----             
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_2025452_20   1249 AAGAAGACATGCAAATGTCCCATAAACACATGGAAAGATGCTTAACACCA 1298
                                i  i      v  v    i      i         i    i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_2025452_20   1299 CTAATAAT 1306
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.98 (107 / 54)
Gap_init rate = 0.02 (19 / 841), avg. gap size = 3.63 (69 / 19)  


 571 22.02 13.10 0.60  chr2_2052335_2055153     1092  1259 (1560)    L1M4_orf2#LINE/L1        1   189 (719)  

  chr2_2052335_20   1092 TGGAAAGA-----CATGTTCACAGATCAGAATATTTAACATTATTAAGGT 1136
                                 -----        ii   ii   v i    i   i     i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_2052335_20   1137 AGCAATACTTCTCAAATTGATCTACAGATCCAA----ATTC-TA------ 1175
                         i        i i                 i   ----  i -  ------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_2052335_20   1176 ----AGTAGTATTTTTCAATGAAATTGCTAAGTTGATTTAAAAATTTTCA 1221
                         ----  iv iv     iivv       vi   i    iiv      ivi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_2052335_20   1222 TGACAATG-AAAGGACCCAGTATAAG-AAAACAAATCTTG 1259
                           iv    -  i        v   iv-       -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTG 189

Transitions / transversions = 2.36 (26 / 11)
Gap_init rate = 0.04 (7 / 189), avg. gap size = 3.29 (23 / 7)  

2711 19.61 2.11 5.92  chr2_2052335_2055153     1568  2327 (492)    L1M4_orf2#LINE/L1      178   908 (0)  

  chr2_2052335_20   1568 AAAATAAATCTTGAATAAAAAAAATAGGTTT--AGGAATTAGTCTTCTGG 1615
                             i  -       v  i  i  i iiv  --    v i vv    ivi
  L1M4_orf2#LINE/    178 AAAACAA-TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_2052335_20   1616 ATTTTAAAAATCTACTACAAATAAACAAGTAAGTGAATAAATAAATAAAC 1665
                             i    v -         ----------- i-----------  ---
  L1M4_orf2#LINE/    227 ATTTCAAAACT-TACTACAAA-----------GC-----------TA--- 250

  chr2_2052335_20   1666 AACAAACAGTAACTGAGAGAGGATGGTACCAGCATAAGGATAGA--TACT 1713
                         ------      iii   v  vi      ii             --  iv
  L1M4_orf2#LINE/    251 ------CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_2052335_20   1714 GATCAATGAAATAGAATGGGGAATCTAAAAATAAACC-ATCTCACTTATT 1762
                                 i        v i  i  i i         -  v-  i    v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATG 343

  chr2_2052335_20   1763 GTCAACTGATTTTTGACAAGGGTTTCAGAACAATTTAATGGGGGAA--AT 1810
                              i       i         vi  ii  v   i       i  --  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_2052335_20   1811 CAAGTCTTTTTAATGAATGGTGTTGGAACAACTGGGTATCCACATACAAA 1860
                         --        i  ii       i   i        i  ?      i    
  L1M4_orf2#LINE/    394 --AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_2052335_20   1861 TGAATAAAGTTGGACAGGTA--TCACACCATATACAAACATGGACGCAAA 1908
                         v    i         vvv  --                v  vi  v    
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_2052335_20   1909 ATGTATCAAAGGCCTAAATGTAGAAGTTAAAACTATATAACTCCTAGAAG 1958
                            v    ?  i          ii  i          v     i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_2052335_20   1959 AAAACCTATTAGTAAGTCTTTGTGTCCTTGGGTTAGGTGACGGCATCTTA 2008
                              v  vv?    i    i   v            ii i  iv     
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_2052335_20   2009 AATACACCACCAAAAACACAAGGGATAAGAGAAAAAAAAAGCAAACGCAT 2058
                         i   iiv        i      vi i  i        v i--------  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG--------AT 633

  chr2_2052335_20   2059 AAGTTTAGCTTAATCAAAACTAAAAAGTT--GATCTGACAAAGGCCACCA 2106
                           i  vii   v       i      v  -- vv  v-      v   i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT-CAAAGGACACTA 682

  chr2_2052335_20   2107 TCATGAAAATGGAAAAACAACAAAAAGAACAAGAATAAATATTTACAAAT 2156
                            v    i  i   i     vv v    iii  iv        i     
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_2052335_20   2157 TACATATATTACTTGGGACTTGTATGCATAATATGCAAATAATCCTTACA 2206
                         i i    v v ivv           v  v     ii   v  ii      
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_2052335_20   2207 AAGCAATAA-GAAAAGACAA-TA---CAATTTAATAATGTACAAATGATT 2251
                          vv      -i         -  ---     ?  v    vi    v    
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_2052335_20   2252 TGAATAGACATTTTCCCAAAGAAAATCTACAAATGGACAATAATCTCATG 2301
                                      ii        i  v         v      v v    
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_2052335_20   2302 AAAAGATGCTGAACATCATTTGTCAG 2327
                                   v       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (84 / 61)
Gap_init rate = 0.02 (18 / 731), avg. gap size = 3.39 (61 / 18)  


2669 26.22 0.41 0.41  chr2_2067010_2068739.rev      499  1238 (492)    L1M4_orf2#LINE/L1      169   908 (0)  

  chr2_2067010_20    499 AGCATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAAGCATCAC 548
                           v  v     iv     i i ivv i          i    i vv    
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_2067010_20    549 GCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGTAT 598
                         i  v  ii i      viv        i          i   i     i 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_2067010_20    599 GGTACTAGTACTGAAATAGAGATATAGACCAATGGAACAGAAC--AGAGC 646
                               i i iviii     v       i        i    i--    i
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_2067010_20    647 CCTCAGAAGTAATACCACACATCTACAACTATCTGATCTTTGACAAACCT 696
                           --    i   vv   i    i  iiiii vi    i  i     ivv 
  L1M4_orf2#LINE/    319 CC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_2067010_20    697 GACAAAAACAAGAAATTGGGAAAGGACTCCCTATTTAACAAATGGTGCTG 746
                          v   i v  vvv   v       i ivvi  v  i              
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_2067010_20    747 GGAAAACTGGCTAGCCATATGTAGAAAGCTGTAACTGGATCCCTTCCTTA 796
                            v      v  ?   i   i i  iiv  v ii    i    v   i 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_2067010_20    797 CACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGA 846
                             v              i    i      i ?    i       v   
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_2067010_20    847 CCTAAAACCATAAAAACCCTAGATGAAAACCTAGGCA-ATACCATTCAGG 895
                         v       i      vi i    v      v    ?i- v i -   iv 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTG 565

  chr2_2067010_20    896 ACATAGGCATGGGCAAGGACTTCACGTCTAAAACACCGAAAGCAATGGCA 945
                           v v  vv i     v ii   viivv  vi     i      vvi   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_2067010_20    946 ACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTG 995
                                vv     v  i    v   ii v  i   v v  i i   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_2067010_20    996 CACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGG 1045
                         ii vv    i  v    i  vv i      v  i     i          
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_2067010_20   1046 AGAAAATTTTTGCAATCTACTCATCTGACAAGGGGCTAATATTCAGAATC 1095
                                v       vii ivi      i     i  vi   i      v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_2067010_20   1096 TACAAAGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAA 1145
                           i         vv    v iv i  v     i     i     v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_2067010_20   1146 CAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATG 1195
                         v  i            v    i     i     v        i  vi vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_2067010_20   1196 CAGCCAAAAGACACATGAAAAAATGCTCATCATCACTGGCCAT 1238
                         ii     v ii          i       v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (109 / 81)
Gap_init rate = 0.01 (4 / 740), avg. gap size = 1.50 (6 / 4)  


2675 24.08 9.25 1.54  chr2_2183611_2185747.rev      803  1645 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_2183611_21    803 TGGAAAGGTATTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAC 852
                                i   i                     v i           i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_2183611_21    853 GTCCATACTACCCAAAGAAATCTACAGATTTAATGCAATTCCTATCAAGA 902
                          v v     v      vvi           i  i     i        i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_2183611_21    903 TACCAATGGCATTTTTCACATAAATAGAAAAAAT-ATCCTAAAATTAATA 951
                          v   iiv  v     ii  v    v  v  iv -           v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_2183611_21    952 TGTAACCACAAAAGACCTAGAATAGCCTAAAT--TTTGTGAAGCAAAAAG 999
                           v  vii   ii    i         v   i-- i -    i-  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT-TGAAA-AAGAAG 198

  chr2_2183611_21   1000 AACAAAACTGGAGGAATCACATTACCTGACTTCAGAGTATACTACAGAAC 1049
                               ii       v     i v  ii i    i iiv       i i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_2183611_21   1050 TATACAG-AATCAAAACAGCATGGAACTGGCATAAAAACAGACACATGGA 1098
                           --   -      i    ii   v          ii i     i  i  
  L1M4_orf2#LINE/    249 TA--CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_2183611_21   1099 TGCATGGAACAGAATAAAGAATCCAGAAGCAAATCCTTATACCTACAGTG 1148
                          vv      i     vi   i       ii   i  v  i ii  ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_2183611_21   1149 AACTCATTTTTGACAAAGGAGCCAAGGATAGACACTGGGAAAAGA-CAGT 1197
                           i v     i     i  v      ivi vv  v    i     -i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_2183611_21   1198 CTCTTCAACAAATGGTGCTGGGAAAACTGGA----------CAAA----- 1232
                           i                    v       ----------    -----
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_2183611_21   1233 ----CTTGACCCTTATCTCTTGCTTTATACAAAAATCAAATTAAAGTGAA 1278
                         ----i v     i  i   vii iv           i  v i   i  i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_2183611_21   1279 TTAAAAACTTAAATTTAAACATCTCAAACTATGAAATAGCTACAAGAAAG 1328
                          i ? i  i     v   i- v  v       i   ivvi  v      i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAG-AGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_2183611_21   1329 CATTGGGG-AAATGCTCTAGGATATTGGTCTGGGCAA-AGTTTCTTGAGT 1376
                            v  ? -    -  iiiv  iv    vi i     -i       iii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_2183611_21   1377 AATACCCCATAAGCACAGGCAACCAAAGCAGAAATCGACAAATGGGATCA 1426
                          vv  v   v       i     v    v i    v  i    v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_2183611_21   1427 TATCAAG-TTAAAAAAGCCTCTGCGCAGCAAAGGA--------------- 1460
                         i     i-       -- i i  i  vv       ---------------
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_2183611_21   1461 -AAAAGTCAACC--------------------------------TATCTG 1477
                         -     v     --------------------------------      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_2183611_21   1478 ACAAGGGATCAATAATCAGACTATAGAAGGAGATCAGACAAATCTATAGA 1527
                          i      iivi  vi    v    v  i  iv  vv    v  v   iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_2183611_21   1528 AAATAATCTAAAATG--TCAATT-AAAAATGGACAAAAGATCTGAATGGA 1574
                            v iv --    i--i     -        i    i   i     i  
  L1M4_orf2#LINE/    793 AAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_2183611_21   1575 CGTCTCTCAAAAGAAGAAGACACACAAATGGCAAGCAGGATTATGAAAAT 1624
                          i i    v        ---i i         v ii i vvi       v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGA---TATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_2183611_21   1625 GTGTTCAACATCACTGAACAT 1645
                         i  i         ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (125 / 76)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.33 (91 / 21)  


2708 26.45 1.77 1.42  chr2_2328328_2332000     2335  3181 (492)    L1M4_orf2#LINE/L1       59   908 (0)  

  chr2_2328328_23   2335 TCCACAAAT----CTACAGATTCAATGCAATCTTTATCAATCAAAATATC 2380
                            v     ----            i      ii      ----   vi 
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA----AATCCC 104

  chr2_2328328_23   2381 AACAAAATTTTTCACATAA-TTAGAGAAAAACT-ATTCTAAAATTCATAT 2428
                          i vivv     ii  v  -  ---  v  i  -  i             
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTCATAT 151

  chr2_2328328_23   2429 GAAACCAAAAAAGAGCCTGAATAGCCAAAGCAATCCTAAGCAAAAAGATC 2478
                          i  viiv  ii  v  v           i     i i iv  i    v 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_2328328_23   2479 AAAGTTGGAAGCATCACATTACTTGACTTCAAATTATATTA-AAAGTTAT 2527
                                  i vv     i v iii i      viv  i  -    i  i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_2328328_23   2528 AGTAAATAAAACAGCATAGTACTGGTATAAAAATAGACATATATGTGAAT 2577
                              vi  i    ii i       i    ii           vi v   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_2328328_23   2578 GAAACAAGATAGAGAACCCAGAAATAAAGCCACATATCTACAATCAACTG 2627
                          i  i ii  v    ii           v   i i  i  iii    i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_2328328_23   2628 ATCTTTGACAAAGTTGACAAGAACATGCAATGGAGAAAGAACATTCTT-- 2675
                           i  i     i v  v     v   v      i       i v    --
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_2328328_23   2676 CAATAAATGGTGCTGGGAAAATTGGATTGCTATATGCAGAACAATAAAAC 2725
                            i              v  i     v? i i     i  v   i  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_2328328_23   2726 TGGATT--TATCTCTCACCATATACAAAAATAACCCCAAGATGGATTAAA 2773
                             ii--  i   v                v v i   i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_2328328_23   2774 GCTTTAAATATAGGACCTGAATCTATGGAAATACCAGAAGAAAATCTATG 2823
                          vii     i  i  v  i  v    ii  v vii         iv  v 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_2328328_23   2824 GAAAACTTTTCTGAACATTGGTCTAGGTGAAGAATTCATGACAAAGACCT 2873
                         ?iv  v i   vvi  v    vi    ii v iv   v iivv v   vi
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_2328328_23   2874 CAAAAGCACAAGCAAAAACAACAACCAAAAAAAGACAAATAGGACTTGAT 2923
                                        ---   -  vv     v   i    v      v  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAA---CAA-AAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_2328328_23   2924 TATACTAAAAAGCTTCTGCACAACAAAAGAAATAATCAACAGAGTGAACA 2973
                         i v v v    i   i  ii vv    i  v iv     v i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_2328328_23   2974 GACAGTCTGCAAAGTAGGAGAAAATATTTGCAAACTATGCATCCAATAGG 3023
                             ii ii  i i i                  ii  ii   ii   i 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_2328328_23   3024 AAA---GTAATCCAGAATTTAAAGTGAAATAAAACAACTAAACAA-AACT 3069
                         ii ---   -        v  v iv   v vvv      v  i  -  vv
  L1M4_orf2#LINE/    748 GGACTTGTA-TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_2328328_23   3070 CTCCAAATAATCCCATTAAAAAGAGAGCAAAGGACACGAATAGATGTTTT 3119
                         vvv       i  v   ?    iv i        ivi       ii   i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_2328328_23   3120 TCAAAAGAAGACACACGAGTGGCCAAGAAGCATATGAAACAATGTTCAAC 3169
                           v        i i  i i       v     i      vi   i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_2328328_23   3170 ATCACTTATCAT 3181
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (133 / 87)
Gap_init rate = 0.02 (13 / 850), avg. gap size = 2.08 (27 / 13)  


2816 19.72 6.90 2.90  chr2_2388108_2391188     1300  2024 (1057)    L1M4_orf2#LINE/L1        4   757 (151)  

  chr2_2388108_23   1300 AAAAATATATCAT-TTGAACTTAGATATGAAGATTTAATATTATTGAGTT 1348
                            i    vi   -  v --- i   vv     i        i  i  v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCA---TGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_2388108_23   1349 G---ATATTTCCCAAATTGATGTACCGATTCAGCACAATATTTGTCATGA 1395
                          ---   i i           v   v      i i    vii i   vi 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_2388108_23   1396 TCCCAGCTATTATTTTTGCAGAAATTGACAAG---A--CAAAAATTAATA 1440
                                 iiiv                    --- -- v      v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_2388108_23   1441 TGGAA-TTTAAGGGATCCAGAATATTCAAAACCATCTTAAAACAGAAGAA 1489
                              - vi      i        vi      v     i   v       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_2388108_23   1490 CAAAGCTGAAGGACTCAGGCTTCCCAATGTCAAAGCTTCCTACACAGCTG 1539
                              i  i        vi         v     i   v     v    i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_2388108_23   1540 CAGTAATCAGAAAAGCATGGCACTGGCAGTCAGCACTGGTGAAAGGAGAG 1589
                                  ii v  ii   i       ----------- --     v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA-----------T--AAGGATAG 287

  chr2_2388108_23   1590 ACACACAGATTAATAGAATCCAACTGAGCGCCCAGAAGTAAATCCTCACG 1639
                            i i    i   i    vv  i    v i      i    i  vi  i
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_2388108_23   1640 TTTATTGTCAATTCATTTTTGAAAACAGTGCCAAAACAATGAAATAGGGG 1689
                              v       v     i  v  vi       i  v  vv   -    
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGG 386

  chr2_2388108_23   1690 AGGGAACAGTCTTCTCAACCATTGATGCTGGAATAATTGGATATTCAC-- 1737
                          ii   i      i     v v  i      i i  i      ?i   --
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_2388108_23   1738 --------------------CTCAACCT------ATATATAAAAATTAAC 1761
                         -------------------- i v    ------     i          
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_2388108_23   1762 TAAAAGTGTATCGAAGACCTGACTATAAGAGCTACAACTACAAAACTCTT 1811
                          v   i  v   i?      i v i         v     i         
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_2388108_23   1812 AGAAGAAAACC--AGTGCATTTCTTCGTGATCTTGAAATAGACTATATAG 1859
                                   v--i ? i vv         i    iiv   i - -  i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC-A-ATGG 584

  chr2_2388108_23   1860 TTTCTTAGATATCACACTAAAA--ACAAACAAGAAAAAGAAAGAAAATGA 1907
                                     v    i    --    i   v    -    i  v -  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA-GAAAAAATA-GA 632

  chr2_2388108_23   1908 TAAAACAGACTTCTTCAATATTAAAAATTTGTGTGCTTTGAAGAAT-CCA 1956
                             vii      v    v        i  v       ii   i i- i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_2388108_23   1957 TTAAGAAAAT-AAGAGATAACC-ACAGAATGGAAGAAAATATTAGGAAAT 2004
                          i      i -  i   i    -         i          v v    
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_2388108_23   2005 CATATCTT-----AGGGACTAATAT 2024
                              v i-----       vi   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTAT 757

Transitions / transversions = 1.55 (85 / 55)
Gap_init rate = 0.03 (21 / 754), avg. gap size = 3.38 (71 / 21)  

 475 12.50 2.50 0.83  chr2_2388108_2391188     2470  2589 (492)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr2_2388108_23   2470 AGTAATAGAAAGA-AAATAACACAATT-AAAAATGGGAAAATATATATGA 2517
                          i     i     -       v     -         v   -iv  v   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA-GGATTTGA 835

  chr2_2388108_23   2518 ATAAACAT-GCTCCAAATAAGATATTCAAATAGCCAAGAAACACAAGAAA 2566
                            i    -v       v       v     i     v  i    v    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_2388108_23   2567 AGATGCTCAACATCATTAGTTAT 2589
                                        ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.67 (6 / 9)
Gap_init rate = 0.03 (4 / 122), avg. gap size = 1.00 (4 / 4)  


1243 26.76 11.85 6.22  chr2_2400475_2403193     1414  2265 (454)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr2_2400475_24   1414 TATATCATATT-ATAGGGTTGCAAGA-TCATTATTGTAAATAAGTCAAT- 1460
                            vi   i  -  -  i   v    - i v      v  v v v    -
  L1M4_orf2#LINE/      9 TATCCCATGTTCAT-GGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_2400475_24   1461 -CCCCCAAAATGTATCTATTAATTCAATACTATCTC-ACC-----CCCTG 1503
                         -i       v  -     ivi      ii v   i - i -----   v 
  L1M4_orf2#LINE/     58 CTCCCCAAATTG-ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_2400475_24   1504 CTGGATTTGTGTTTGTGTGAGTGAGTTTTTTACTGTGCATATCCACAAGT 1553
                            vv   ---    i-------  ------------- v  iv     i
  L1M4_orf2#LINE/    107 CTGCCTTT---TTTGC-------AG-------------AAATTGACAAGC 133

  chr2_2400475_24   1554 TGATTCCAAACTGGATATGGCCATGCGAATTGCTAAGAAGAGCTAAGATA 1603
                             i i   v vv      vv    i ivvi iv    v   i  i i 
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr2_2400475_24   1604 ATATTGAA------TAACAAAGCTGGAGGACTTACAATGTCACATATTGG 1647
                           v     ------v       i         i   v vi vv  v iii
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_2400475_24   1648 GAC---CTATAAAGGTAATAGAAATCATTACAGTGTGCT-TTGGCAAACA 1693
                         i  ---   i    v  -i  v     vv        v -i     v - 
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTA-CAGTAATCAAGACAGTGTGGTACTGGCATA-A 281

  chr2_2400475_24   1694 AGATGAACGTTTCA--CAGTGGAACGTGAAAT---GTATCCAGAAATAGA 1738
                         i   ii  i v vi--  i     -- ii   --- vi          i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAA--TAGAATTGAGAGTCCAGAAATAAA 329

  chr2_2400475_24   1739 CCCATACACATACATGAACCCGAGTAAT----GACAGAGAT--CA----T 1778
                                 iv  --  i--i i v i  ----    ii i --  ----i
  L1M4_orf2#LINE/    330 CCCATACATTTA--TGG--TCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_2400475_24   1779 ACTTACTAGGGG-------GCCTTTTCAGTAAGTGGTGCTGGGCTCCCTG 1821
                          i i v i   i------- i       ii  i          vivv   
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_2400475_24   1822 GATTTTC-TATACACAA-AACCAGTTTGCATCCTTACTTTTTAAACTATT 1869
                            v?i -i  i  v  -  iv iv   v i  i   i i-- v  i  v
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC--ACACCATA 473

  chr2_2400475_24   1870 TACAAAAATTAACTTCAGATATAGTGCAGGTCTACATGTGACAGG-GAAG 1918
                                       iv i  iv vii?  ii   v    i v  v-i  i
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_2400475_24   1919 CCATAAAGAT-TTAGAAGAA--CATA--------TCTTCAAAGACATTGA 1957
                          i     iv -         --    --------     iv-   v   i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACCTTGG 572

  chr2_2400475_24   1958 AGTTTTTACT--TTTTTTGCATAT--CCTTAAAA---TAGGCAA------ 1994
                         iv vvvi v --   i  iv    -- vii    ---i i    ------
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_2400475_24   1995 ---AAAT-GATAG--TGAACAATACTAACATTAAAAACTTTGAT-CATCA 2037
                         ---    -    i--  i  vvi ii  v            vi - v   
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_2400475_24   2038 AAAGATACTACTAAAAGAAAGTGAAGAAGCAACTT-CAGAAAAGCAGGAA 2086
                           i  i    ii  --         i ii    ii-     vi v  i  
  L1M4_orf2#LINE/    673 AAGGACACTATCAA--GAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_2400475_24   2087 ATATTGCCACAT-ATATTTCCTACAAAGGGTATGTATTCGGTACATATAA 2135
                              vv  v  -    v  iv i  i  iiv     i i v i      
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_2400475_24   2136 AGAAATTCTACA------TA-----------------CCAATAAAAAAAT 2162
                             v ii    ------  -----------------     v?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_2400475_24   2163 GAGTAAAATATTTGAACAGACACTTTACACAAGAGGATATACAAAAAGGG 2212
                          i i   iv       i     i  iv vv    i          --v  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA--TGG 868

  chr2_2400475_24   2213 CCAATAAATCCTTCTAAATGAAGAAAACAGAGTGTTTAACTTTCAAACTG 2262
                                iiv ------     i i ------  i i   v -  ?????
  L1M4_orf2#LINE/    869 CCAATAAGCAC------ATGAAAAGA------TGCTCAACAT-CAZZZZZ 905

  chr2_2400475_24   2263 ACA 2265
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.45 (133 / 92)
Gap_init rate = 0.05 (48 / 900), avg. gap size = 3.21 (154 / 48)  


2856 17.55 2.28 13.98  chr2_2427903_2429767      443  1365 (500)    L1M4_orf2#LINE/L1       82   896 (12)  

  chr2_2427903_24    443 AGCACAAAACTTACCAGAATTGCAG-TGTACTTTTTGGCAGAAACCAACG 491
                          i i   vv i  i  i   iv   -  i-      v       iii  i
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGC-CTTTTTTGCAGAAATTGACA 130

  chr2_2427903_24    492 AGTTGATTATAACATTTACAAGAAATTCCAAGGAACCTAGAATGGCCAAA 541
                           i    iv   v   i i v i  v v     i   i     i      
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr2_2427903_24    542 ATATTTTTGAAAAACAGGAACAAAGT---AGAATGTACAGTTCATGGTTT 588
                          i v i        v i         ---  i ivi   v   viii   
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr2_2427903_24    589 GAAAACTTATTACAAAGTAACAGTGATGAAGACAGCGGGCCACTG-TAGA 637
                         v        i       iv     i  v       i v vi    -i v 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_2427903_24    638 AGGACAG-CAGTGTAGATCAATGGAATCAAATTGAGAACCCAGAAATAAA 686
                             i  -  - i              vi        ii           
  L1M4_orf2#LINE/    281 AGGATAGACA-TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_2427903_24    687 CCTATG--TCTATGGCCAACTGAACTTCAACAAGTGTGCCAAGACCATTC 734
                           i  i-- i     i   i   vi   i     v               
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_2427903_24    735 GATTGGGAAAGAATAGTCCTTTCAACAACTGAGGCTGGGACAACTGGACA 784
                         i  v              i         v  iv               i 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_2427903_24    785 GCCACATGCAAAAGAATGAGACTGGACACTTAACTTACACCATAAACAAA 834
                         ?                  iii     v i  v  i        v     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_2427903_24    835 AATTAACTCAGTATGGATCAGAGGTCTAAATGCAA----TAA---TATAA 877
                                   iv        ?  ii       i  ----   ---     
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_2427903_24    878 AATTATTAGGCAAAAACATAGGAATAAATCTCTGTAAC--TGTATTTGGC 925
                           i v    ivi          ?i       ii  i  --  vi  v   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_2427903_24    926 AAATAATTCTTACATATGACATTAAAATCACAA---ACAAAAGAAAATAT 972
                           vviv      v        ii    v     ---           v  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_2427903_24    973 AGATACATTGGACTTTATCAAAATTAAAATCCACACTTTAAAGAATGCCA 1022
                              v         i             -----     -----------
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAA-----ACTTT----------- 663

  chr2_2427903_24   1023 TTAAGAAAGAGACTGCACATGTACCCTAAAACTTAAAGTATAATAATAAG 1072
                         -------------------   i i------- i    ----------- 
  L1M4_orf2#LINE/    664 -------------------TGTGCT-------TCAAAG-----------G 676

  chr2_2427903_24   1073 AAAATAATTTTACAATATTACAATATTTTCATAACATTTAAAATATATTT 1122
                          -----------  v   i ------------------------------
  L1M4_orf2#LINE/    677 A-----------CACTATCA------------------------------ 685

  chr2_2427903_24   1123 TATTCCTCCAAGTAAAAAAAAAAAAAAAAAAAAAGAAAGAGAAAAGACAA 1172
                         ---------------------------------      v          
  L1M4_orf2#LINE/    686 ---------------------------------AGAAAGTGAAAAGACAA 702

  chr2_2427903_24   1173 TCCACAGGATGAGAGAAAGCTTTTACTGATCATATATTAGATAAGGCACA 1222
                         i      i   i      iiv   i vi         iv       v  v
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_2427903_24   1223 GGTATG-AGAATATATAAAGAATACTTGCAACTCAATAATAAGAAGATAA 1271
                         v    v-               iv   i              i    i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_2427903_24   1272 ATAACCCAGCTAAAAAGTTGACAGAAGATTATAATATACATTTCTGCCAA 1321
                                 ii ?    i v i  i i    vv    v        v v  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_2427903_24   1322 GAAGGTATATAAGTGGCCAATATACACATGTAAAGATGTTGAAC 1365
                             i    i  i         vi      v       i v   
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

Transitions / transversions = 1.63 (98 / 60)
Gap_init rate = 0.02 (18 / 815), avg. gap size = 8.33 (150 / 18)  


1426 29.81 5.11 2.04  chr2_2450159_2453470.rev     1631  2217 (1095)    L1M4_orf2#LINE/L1       24   628 (280)  

  chr2_2450159_24   1631 GATTGTAAGACTCAATATAGCTAAGATGAAAATATTCCCTGAATTGATCT 1680
                              v      i     v i       iv    i    ii         
  L1M4_orf2#LINE/     24 GATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCT 73

  chr2_2450159_24   1681 GGAAATTTAATGTAATACCCACTAAAATCTATGAAAGTAC---TTCCGTA 1727
                         iv i   i  i i   v  i ii      iv--- iv i ---  ii i 
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCC---AGCTGCCTTTTTTGCA 120

  chr2_2450159_24   1728 AAAATTTATAAGTTCATTCTGCAAT--GTACAGGAATGCAAAATGCCTAG 1775
                         i     v i   i v  i  iv   --i  ii i       iivi  i  
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr2_2450159_24   1776 AATAGTCAAAACAGC--TGTAAATGAC---CAAAGGTCAGAGACCTGCAC 1820
                              i       ii--  v   v  v---     v viii   iii   
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_2450159_24   1821 T----GATTTTAAGATTTCTCTA-AAAGTTTCA-TATTTTAGACAAAA-G 1863
                          ----i    i  i i  v-   -    i v  -  v iv     ivi- 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTA-CTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_2450159_24   1864 AAATTAGCACAAGGATAGACGTATACCTCAATAAGAGAGAATTGAGAGCC 1913
                         iv i i   i          i    vv     iii v           i 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_2450159_24   1914 CAGAAATGAATCAA---ATTTATGAGCTCAATTGATTTTTGAAAAATGTA 1960
                                i  i v ---       i--            i  v  iv  i
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGG--TCAATTGATTTTCGACAAGGGTG 367

  chr2_2450159_24   1961 CTTAGGTTATTTTCA--GAGAAAAGAATTGCCTTTTTAATAAATAGTGCT 2008
                          iv  iii   --  -- i i       v i     i  i    i     
  L1M4_orf2#LINE/    368 CCAAGACCATT--CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_2450159_24   2009 AAAATATCTAGATGTCTGTATGAAAATAAAAAGAACCTTGACCCATTCCT 2058
                         iii i v  i   i? iii   v   - i  v   vi v     v v   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAA-AGAATGAAGTTGGACCCCTACCT 464

  chr2_2450159_24   2059 CACATGGCAGATGAAAAT-GACTTCAAATGGACCAAAGGTCTAAACTTTA 2107
                             ivii v ii     -i   iv       i  ?  ii     iv v 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_2450159_24   2108 TAACTACAACTCTGAA--TATTATA-GAAAATATATACAAAAAGTTTTGT 2154
                         v i   v    v i  -- v   v -     i   vi?iv   vi  i  
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_2450159_24   2155 AATCTGGACATAGA----GGTTTCCTAAGTAGGAAACAAAAAATACAAGA 2200
                         i i  v ivv   i----      i  ii  v  v  v    ii     -
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG- 613

  chr2_2450159_24   2201 CTTAAGAAAAAAAAAAA 2217
                         --i  v    i      
  L1M4_orf2#LINE/    614 --CAACAAAAGAAAAAA 628

Transitions / transversions = 2.02 (115 / 57)
Gap_init rate = 0.03 (20 / 605), avg. gap size = 2.10 (42 / 20)  

 625 19.60 7.97 6.31  chr2_2450159_2453470.rev     2520  2820 (492)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr2_2450159_24   2520 AGAAGAAGAAG-AAGAAAAGAGAAAGGAAA-AAA--GG--TTGAT--AAA 2561
                          i   v v   -  v      i   iv i -   --  --  v  --   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_2450159_24   2562 TTAGACAACT------CTTCAAGAGACATCATGAAGAAA-TAAAAAGGTA 2604
                            i -    ------      ii    ii  v      - i     ii 
  L1M4_orf2#LINE/    653 TTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_2450159_24   2605 AACCACACTCTACAGGAAT---ATATAATTTTTTCAATACATAAATCTGA 2651
                          v     --------    --- v v   v   v   vv    v      
  L1M4_orf2#LINE/    702 ACCCACA--------GAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_2450159_24   2652 CAAAGGG-TTGCATGCATAATATATAAATA---CTTGCCAAACTTAAGTA 2697
                         i  i  i-   i  v  v          v ---   i --    i  -  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC--AACTCAA-TA 790

  chr2_2450159_24   2698 ACAAGAAGACAGACAATTACAA--AAAAGATGGGAGGGGACATAAGATTT 2745
                          i  i      i i  ii-   --?   i     ------  v i     
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACC-CAATTWAAAAATGGG------CAAAGGATTT 833

  chr2_2450159_24   2746 GAACGGATATTTCACAAACAAAGATATACAAATGGCCAATCAGCACATGA 2795
                            ii  i     v v  vi                    v         
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_2450159_24   2796 AAAGCCTTTTAATATCATTGACCAA 2820
                             vivi i  i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (34 / 24)
Gap_init rate = 0.06 (17 / 306), avg. gap size = 2.53 (43 / 17)  


1401 29.38 9.24 1.90  chr2_2460342_2463338.rev     1663  2506 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_2460342_24   1663 GAGATATATATTATGCTTATAGCTTAAAAATAATTACTAT-ATTAA--TT 1709
                           i v    vii   i i  i v  ii  i- v   v   -i    -- v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGATG 51

  chr2_2460342_24   1710 TCAATTTTTCCCCCAA--CAATCTGTACATATGATGCAATTACAATTAAA 1757
                         v    vi --      --ii    ii v  vii i     iv v  i   
  L1M4_orf2#LINE/     52 GCAATACT--CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_2460342_24   1758 ATTCTAGCAGGCTTTTT-ACAGACTGTTGAAAAATTGTTCCTAAAATTCC 1806
                           i i   v v      -i    v-i    v  ii  v           v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCA 148

  chr2_2460342_24   1807 TGTGGCAATGCAA----------ATGGTCAAGGCAATCTTGAAGAACAAG 1846
                          i   v       ----------  i i   ii          i  v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_2460342_24   1847 AATAGAGCTAAGTTACTGAAGCTACCAGATATTCAGATCTGA-TCTAAAG 1895
                           i i  i iiivv   v vi  v  vi  -    i v  v - vi    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAAT-TTCAAAACTTACTACAAAG 247

  chr2_2460342_24   1896 CTGCAGTAATTAAGACAGAAGAGT-----CA----GATAGAGAAACAGAC 1936
                           i       i       vivi  -----  ----      v v i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_2460342_24   1937 CAATAGAACAGAAC--AGAGTGTAGAA-TCATCCCACACACAAA-ATTCA 1982
                             i   i    i--     vi    - v v    i   ivv -iv   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_2460342_24   1983 CCTGGCTGATGAGAACTGTGGTGCTGCAGA-------ATGTGGACAGGCA 2025
                         vi  ii vvi  v  -- -     ii-   -------   v   v  -- 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAA--G-GGTGCCA-AGACCATTCAATGGGGAAAG--A 391

  chr2_2460342_24   2026 GGAGTCGTTTTAATAAATTGGGCTGAGTAAACAGGA-----AAAAGCAGA 2070
                         iv    v   i  i    v v    i vv   v   ----- v v   i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_2460342_24   2071 AAATTCATCTTA-ACCTTCACTTCAC-CAATTCACAGAAACAAACC--AG 2116
                          i v v vv  i-   iii  i    - v  vi   i   iv   i-- i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_2460342_24   2117 ATGCGCTGCACATCTAAATGTAAAAAATGAAACAGTAAAACTTTTAGAAT 2166
                            viiii? v i          i iv i    vi       i      v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_2460342_24   2167 A---CATAGA--TCATTCCT-ATG-TTTTGGAGTAAGGAAACATTTCTTA 2209
                          ---     i-- v v  i -i  -ii    iv  i v  vvi       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_2460342_24   2210 AATAGGACA----AAGC-TATG-AACAAAATA-----TTAATACATTTGA 2248
                         i   v    ----    -i v -       v ----- vi   v   v  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_2460342_24   2249 CTATAATAAGATTAAGTACTTCTGTTTATCAATGGGCATTA---AAAGAG 2295
                           vi vi  i     iv    i   viv    v  i  i  --- i i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_2460342_24   2296 TGAAAAGACAAACCATAGAGTT-----AAATGTTTGCAATGCATCCATCC 2340
                                    v   i   i v-----    i       vv   vi   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_2460342_24   2341 AACAAAAGATTCACA--CAGAGATATATAAAGAACTTGAATGAATCAATA 2388
                         i i  ii  i iii --    -              ivv ii v      
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGA-ATATATAAAGAACTCTTACAACTCAATA 790

  chr2_2460342_24   2389 AGAAAAAAAGCAAAGAAAAATCAAT-AAAAAATAGGGAAGCAAGTTAAAT 2437
                          v     i -    v  v--i    -?      i  v  ivi v  i   
  L1M4_orf2#LINE/    791 ATAAAAAGA-CAAATAAC--CCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_2460342_24   2438 AGCTATTTC---ATAAAAGCATGTGAAGATGGCCAATAAATATGTTCAAA 2484
                           vi     --- v i   -  i iv i           ii ii vv   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_2460342_24   2485 GATGTTGAACTTCCCTTGTCAC 2506
                             i v   v  v????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (140 / 106)
Gap_init rate = 0.05 (41 / 906), avg. gap size = 2.29 (94 / 41)  


2960 26.90 2.34 1.23  chr2_2567631_2572290     3273  4168 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_2567631_25   3273 GAAAGATATTTTATATTCACAGATTGGAAGAATAAATATTGTTAAAATGT 3322
                                  iii  i    ii          v v           i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_2567631_25   3323 CCTTACTACTCAAGC-AATCTACAGATTGAATGCAATCCCTATCAAAATA 3371
                          vv    v i   ii-i           v  i                 v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_2567631_25   3372 GCAATGACATTCTTCACAGAAATAAGAAAAATAATTCTAAAATTCGTGTG 3421
                         v  iivi v  i  ii       viiv  iv i  i         i i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_2567631_25   3422 GAACCACAAAAGACCTAGCATAGCTGAAGTCAACCTGAACAAAAAGAACA 3471
                            vii   ii    i  v     ii  iiv v i    v  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_2567631_25   3472 AAACTGGAGGAATCACATTATCTGACTT-AAAATTATGCTACAGAGCTAT 3520
                           ii       v     i vi ii i  -    i - i     i     i
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTAC 251

  chr2_2567631_25   3521 AGGAACAAAAACAGCATGGTACTGGCATAAAAACAGACTGATAAACCAAT 3570
                           v  iv  i    ii              ii i    vv   i i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_2567631_25   3571 GGAAAAGAATAGAAAACCAAGAAAAAAATCCACACATTTACAGCAAACTC 3620
                             v     v  i ii v     v   i   i       ii iv  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_2567631_25   3621 ATTTTCAACAAAGTTGGGGAGAACATACAATGGG-AAAGA-CAGTCTCTT 3668
                               i    i v  vvi   v   v       -     -i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_2567631_25   3669 CTTTTTTAAATAAATAATACTGGGAAAACTGAATATCCATATGCAGAAGA 3718
                          -------  i    ii i      v     i   ?   i     i    
  L1M4_orf2#LINE/    402 C-------AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_2567631_25   3719 ATGAAATGCCATCTCTATGTCTCACTTTATACAAAATGCAATTCAAAATG 3768
                              i vvv i i   iv  v   iv         vvi  i        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_2567631_25   3769 GATTAAATATTTAAATCTAAGACTTCAAAATATGAAACTCCTACAAGAAA 3818
                            i ? v ii     v     vi v   v   i      i  v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_2567631_25   3819 ACATTGGGAACACTCTCCAGGACATTAATCTTTGCAAAAGTTTCTTGAGT 3868
                             v  ?ivv v   i iv   v  iivi vv    vi       iii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_2567631_25   3869 AATACCCCATGAGCACAGGCAACCAAAGCAAAAATGGACAAATGGAATAA 3918
                          vv  v   vi      i     v    v      i  i    v i ivv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_2567631_25   3919 TATTGAGTTGAAAAGCTTCCTTTCCCAAAAAAGCG---TCAACCAATACT 3965
                         i  ii iv v    i   iiv v iiv   iii i---    --i v v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA--GAAAGT 692

  chr2_2567631_25   3966 GAAGAGACAACCTACCAAATGAAAGAAAATATGTGCAAACTACTCATCTG 4015
                            i        i  vi    ii         v      ii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_2567631_25   4016 GCAAGGGCTTAATAACCAGAATATATAAAGAGCTCAAACAACTCTATAGG 4065
                         ii     vi vi  v                i   vv       v   iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_2567631_25   4066 AAAAA-ATATAATAATCCGATTTAAAAATGGGCAAAAGATTTGAATAGAC 4114
                              - i -     i  i   ?             i             
  L1M4_orf2#LINE/    793 AAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_2567631_25   4115 ATTTC-CCAAA------------ATGGTAAACAGGCATATGCAAAGGTAT 4151
                              -     ------------    iv  i i   i   v    i ii
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_2567631_25   4152 TTGACATCAATGATCAT 4168
                          ii      ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (148 / 89)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 2.67 (32 / 12)  


3217 26.67 1.44 0.67  chr2_2583612_2586727     1725  2624 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_2583612_25   1725 GGAAAGATGTCTTGTGTTCTTGGATTGGGAAAATTAATAATGTTAAGATG 1774
                                 i  iii     v        i i v      v          
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_2583612_25   1775 CCTACAGTACTCAAAGCAATCTGTAGGTTCCATGCAATCCTTAGCAAAAT 1824
                         v v i v v i    vii    ii  i   v i       i  v      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_2583612_25   1825 CTCAA-TGACAATTTTATAGAACTAGAAAAA--AATTCCTAGCATTCACA 1871
                          i  i-  v vv    ii    v v  v  i--i  -    iv     i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCATA 150

  chr2_2583612_25   1872 TGGAATCACAAAAGACCTCTAATCACCAAAACATTCT-GAGCAAAAAGAA 1920
                              vii   ii    ivv   vi        v   -  iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_2583612_25   1921 CAAAGCTGGAAGCATTATGCTACCTGATCTCAAAACCTACTCCAAGGCTG 1970
                              i    i vv i ii  v  ii  i       i    v   i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_2583612_25   1971 TAATAATTAAAAGAATATGATATTGGCACAAAAACAGACACATCAACCAA 2020
                         i i    i  i v i i  i  i     i  ii i     i  vi i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_2583612_25   2021 TGGAACAGAATAGAGAGCCCATAAATAAATCTGTGCATTTATGGTCAAAT 2070
                              i     v     i   v       i ii i             v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_2583612_25   2071 AATATTTGACAAAGGTGACCAGAACC-CCCACTGGGGAAAGGACACTCTC 2119
                         i  v  i     i    -   ii   -ii  v         i i v   i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_2583612_25   2120 TTCAATAAATGATGTTAGGAAAACTAGACACCCATAGGCAGAAGAATGAA 2169
                              i     i  i i   v    i  i ?   i v   i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_2583612_25   2170 ACTGGACTCCGATTTCACCTTATAGACAAAAATTAATTCTAAATGGATTA 2219
                         ii     i  v ii    vii   v           i  v        i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_2583612_25   2220 AAGACTAAACTCTAAGACCAAAAACTGAAAAACTACTAGAAAAAAAAAAT 2269
                         ?    iv  v v     v v      iv      vi     i    v vv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_2583612_25   2270 AGAGAAAAGCTTTCTGGCATTGGTCTGGGTAAAGATCTTTTGAGTTTGAT 2319
                         i ? v   v   iv  i v    vi i  i  v i i i  iii v   i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_2583612_25   2320 CCCAAAAGCAGAGACAACAAAAGCAAAAATAGACAAATATG---TTTATA 2366
                         v         v ii         v         i    -  ---  i  -
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT-TGGACTTCAT- 647

  chr2_2583612_25   2367 TTAAATTAAAAGCTTCTGCACAGCAAAGGAAAC----AACAGAGTGAAGA 2412
                         iv         i   i  ii vv       v  ----  v i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_2583612_25   2413 GACAGCCTGGAGAATGGAAGAAAATATTTGTGGAACCATACCTCTGATAA 2462
                             i  iiv       i            ii-  i    iv        
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCA-AATCATATATCTGATAA 746

  chr2_2583612_25   2463 ACAGTTAATATTTAAAATACACAAGAAACTCAAAAAAACTCCATACTAAG 2512
                         iviii vi   ii i    i i  ii     vv v  -   v   v   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAA 795

  chr2_2583612_25   2513 GAAACAACAAACCTGATTAAAAAATGGGCAAAGAACCTGAAAAGACATTT 2562
                         i i    vv    ii   ?              i ii    v        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_2583612_25   2563 CTCAAAATAAGGC-TACAAATGGCCAACAGGTGTATGAGAAAATGCTCAA 2611
                            v   v   ii-             i i iii    i  i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_2583612_25   2612 CATTACTAATCAT 2624
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (156 / 80)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 1.46 (19 / 13)  


1564 28.27 10.48 3.65  chr2_2598874_2600722.rev      509  1357 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_2598874_26    509 GGAGAAATACACCATGTTCTTTGACTTGAAGACTCAATGTTATAATAGTG 558
                            i i   iv        v v  i v       i   i  i v vii  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_2598874_26    559 TCAGT--TCCCCGTCAATTTGTCAATGGATTCAATGCAATTCTCATCAAA 606
                         v  i --     i--    vi  v ii       i     i ii      
  L1M4_orf2#LINE/     52 GCAATACTCCCCA--AATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_2598874_26    607 ACCTCAACAA--TTTTTTGTGGAAACCAACAACCTGATACTTAAATATCT 654
                          i i  i vi--       ii    iii    v     v  v    viv 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_2598874_26    655 ATGGAAATGCCAAGGGTAATAAATAGCTGAAACAAT-TTCAAAAAGAAAA 703
                                   v i  iivvvi      ii       -  v        i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_2598874_26    704 AAACATTTGG-TGACTTA--------GATTTCAGGACTTATTATAAAGCT 744
                          v v v    -v    i --------i      ii     i  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_2598874_26    745 ACAGTAATATAAACAGTGTGATAGTGACAGACGCATATAAAAATAAATTT 794
                                 vv i        i  v  i  v v v   v v v   i  iv
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_2598874_26    795 -TGAAAAAGCAGTATAGAGAGTCCAGAGACAAACTGACATAGT-ATGATC 842
                         -  i  ---i  v  v           i i    iv i i v -   i  
  L1M4_orf2#LINE/    300 ATGGAA---TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_2598874_26    843 AACGAATTCACAGCAAAATTACCA---TTCTTCTGCATGGGTAAA--ATG 887
                           ivi   iv ii   iiv i   ---iiv   --v     v   --  i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTC--AATGGGGAAAGAATA 394

  chr2_2598874_26    888 GGCTTT-AAAAAAATTGGACCAGATCAATTGAACATTTATATGGAAA--- 933
                          v    -v  v    v vi ii iv   i  i i ?ii i   v   ---
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_2598874_26    934 -TGAAGTTAACCTTGATTCCCATTTCATAGCATACACAAGAAAATCCATT 982
                         -       i-----  ii  i ii   i v    i    --    iv i 
  L1M4_orf2#LINE/    445 ATGAAGTTG-----GACCCCTACCTCACACCATATACAA--AAATTAACT 487

  chr2_2598874_26    983 TCAAATGGGCCATAAACTTAAAAGTAAATCATAAAGCACCGAAACTTCTA 1032
                         iv      ii  ? i  i    v    ivvv    i vvii     ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_2598874_26   1033 CTAGA---CACAGTGGAAAAAGATCTTTATGAAGTTGTAGTATTAGA-AA 1078
                         vv   ---  i  v? v   ---    ii   vv   -i  --   i-  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAA---TCTTCGTGACCTTG-GGT--TAGGCAA 581

  chr2_2598874_26   1079 TAGTC-CTTAAACA---------AAGC-CAAGCAACATTAACTTTAAAGC 1117
                          i  i-    i i ---------    -         --------    -
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA--------AAAG- 622

  chr2_2598874_26   1118 TAACAAA-----AAAT---ATTTTACTAAGTGTAAGAAATTCTGCTCATC 1159
                         -  v   -----    --- i  i ii  ivv   i  v  i  iv v  
  L1M4_orf2#LINE/    623 -AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_2598874_26   1160 AAAACATACCATTAGGAGAGTTAAAATGCAAGCCACAGAGTAGGATAAGG 1209
                            iv i  i  i i  i   v    vi   v       i i   v  ii
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_2598874_26   1210 T-TTTACGATACATATATCCACTCACAAAC-------CAGAATATTTAAA 1251
                          -   i i vv        iiv v vii  -------        v    
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_2598874_26   1252 TAACTTTTACAAT-----------------AATAAC-------------G 1271
                         v    i      i-----------------      ------------- 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_2598874_26   1272 GGTAAATG-CTTGATAAGTCACTTCACAGAAGATGGTATCCAA-TGGCCT 1319
                           i   v -i    vv  v  i   v vi    v i   v   -     v
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_2598874_26   1320 ATAAACTTATAAAGTGTATGCTCAGCATCATTACTCGC 1357
                             i vi  i  iv -       i     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.04 (35 / 907), avg. gap size = 3.43 (120 / 35)  


2696 23.76 6.11 3.39  chr2_2792264_2796704     3066  3949 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_2792264_27   3066 TGGAAA-AT-TTCTGTGTTTGTG-ATTAGAAAACTTAATATTGTCAAAAT 3112
                               -  - i ii    ii  -   i   i            i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_2792264_27   3113 TTCCATACTACTGAAAGTGATTTACAGAGTTAATGCAATCCCTATCAAAA 3162
                         vv v     v iv   v    i      v i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_2792264_27   3163 TCCCAATAGCATTTTTTTCAAAAATAGA------------AAAA------ 3194
                              iiv  v      v  i    v  ------------    ------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_2792264_27   3195 --AAAACACAA----------ACAGTAAAAACGATCTTGATAAAGAA--- 3229
                         --i   ii   ---------- i  iv     i       v      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_2792264_27   3230 CAAAGT-AGAAGACATCATACTTCCTGGTTTTAGAATCTACTACAAAGCT 3278
                               -i  i   -   i      iii   i i  ii            
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_2792264_27   3279 ACACTAATCACAACAGTATGGTGTTGACATAAAAACAGACATATGCAGA- 3327
                            v      vi     i    ii  i     ii i        --   -
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT--AGAT 297

  chr2_2792264_27   3328 -AATCAAACTGGATAGAGAGCTTAGAAATAAATGTGCACATATATGGTCA 3376
                         -   vi  iv i  v     iii         iviii    v        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_2792264_27   3377 ACAGACCTTTGACAAGAGTACCAAGAGCATACAATGGGAAAAGGTCAGTC 3426
                          iv  ii  i      i  i      v   v       i    ivi    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_2792264_27   3427 TCTTCAACAAATGGTCTTGGAAAAAAATGAGTATCTACGTGCAAATAAAC 3476
                          i             vi   i v  v-  ii  ? i  i      vi  i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAAC-TGGATAKCCACATGCAAAAGAAT 446

  chr2_2792264_27   3477 AAAATTAGACCCTTATCTTACACCATACACAGAAGTAAACTCAAAATGGT 3526
                         i  i  i     i  i  i        i   i  i v            v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_2792264_27   3527 TTAAATACTTAAATGTGAGACCTAAAACTGTAAAACTCCATTTGTTTAA- 3575
                          i ? v  i       i   v        i        --  v vvv  -
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC--TTAGAAGAAA 544

  chr2_2792264_27   3576 -CATA--TGTAAATGTTTTCAAGGAGAAAACTTAGGGAAAGGCTTCATGA 3622
                         -    --?      --i   iv ------  i v   vv    -------
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--CTTCGTG------ACCTTGGGTTAGGC------- 579

  chr2_2792264_27   3623 CAATGGT--CTTAAATAT--TATTAAATGGATA--TAACACAACTAAAAA 3666
                         -      --    i    --i ii   v v i --i    v  --i    
  L1M4_orf2#LINE/    580 -AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA--GAAAA 626

  chr2_2792264_27   3667 GATAAATACATGGGACAGCTTCAAA-TTAAAAAGCTTCTGCACAACAAAA 3715
                         i   i   v  v    vv v     -       -   i  ii vv    i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAG 675

  chr2_2792264_27   3716 TAAATCACCAATAGAGTGAAAAGTCAGCTTATGAAAAGGGAGAATATGTT 3765
                         v v ii i   v i         v  i ii iii  v       v  i  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_2792264_27   3766 TGCAAACCATGCATTTGGTAATAGGTTATTCTCAAAAATATTTATGTAAC 3815
                               i   ii  i  i   vi ii vv v  v i     v  viv   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_2792264_27   3816 TCCTACAATTCAATAATTTTTTAAAT---CTAATAACCTGATATAAAAAT 3862
                           i     i        -----   v--- v       ii  v?      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAAT-----AAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_2792264_27   3863 TGGCTAAGGGTATAAATAGACATATCTCTAA-TAAGATATGCAAACAACC 3911
                         v   v    i v i         v    i  -v       i    iii  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_2792264_27   3912 AACAAGTATATGAAAAAGTGCTCAACATCACTAATGAT 3949
                           i   i i       ii            ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (134 / 72)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.11 (84 / 27)  


 305 29.66 14.41 0.00  chr2_2898128_2902784.rev     2954  3071 (1586)    L1M4_orf2#LINE/L1       15   149 (759)  

  chr2_2898128_29   2954 ATATTAATGTACAAAACGACTAAACGTTGTTAAAATGTCAGT-TTCCCCA 3002
                           i  v   v ivii v    v  ii       i   v  i -i      
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_2898128_29   3003 GCATGGTCCATGGATTCGATGCAATCCCAATCA-------------CTTT 3039
                         ivv  i  i ii     i i        v    -------------    
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr2_2898128_29   3040 GTTG---AAATCAACAAATTGGTTTTAAATTTTAT 3071
                         v   ---    ii    ii  i ii    v  i  
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

Transitions / transversions = 2.18 (24 / 11)
Gap_init rate = 0.02 (3 / 135), avg. gap size = 5.67 (17 / 3)  

2208 23.98 4.95 4.06  chr2_2898128_2902784.rev     3378  4165 (492)    L1M4_orf2#LINE/L1      114   908 (0)  

  chr2_2898128_29   3378 TTTTA-AAAACTTGCC---CTGGTTTTAAAATTTGTATGGAAAGGCAAAA 3423
                             i- i  v   v ---   i ii       ii        v    ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_2898128_29   3424 GATCCAGAATAGCCAATACAATATT---AAAGAAGTATAAAGGTAGAAGA 3470
                           i             v     v  ---       v i    v i  i  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_2898128_29   3471 CTGACACTACCTGACTTTAAA-CTTACTATGAAGCGA-AGCAATTCAGAG 3518
                           v     v  ii i  i   -       ii    v -  i   iv   v
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_2898128_29   3519 CATGCGGTGTTG-CAAATGAATGGACAAATATATCAATGGAACAGAACAG 3567
                         vi  i   ii  -  v v i  i    v   v          i    iv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_2898128_29   3568 ACAGCCCAGAAAGAGACCCACACACATATAG--AGT-------CAACAAA 3608
                          v  i       v i     i   iv   i -- i ------- i    i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_2898128_29   3609 GCAGAAAAGGCAATTCAATGGTGAAATTACAGTTTTGTCAACAAATGGTG 3658
                          vv vv   i v         v    vv i   i  v             
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_2898128_29   3659 CTGGAAAAA-TGGACATCTTCATGCAAGAAAACAAACAAAAACAAATAAA 3707
                             i v  -    i ? iv       i i  ii  ---------i ---
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAA---------GT--- 451

  chr2_2898128_29   3708 TGAATCTAGACAGAGAACTTGTAGCCCT-CACAACAATTAAGTCATGAGG 3756
                           i i ivv  ------  iii -  v -i    v      v   vi v 
  L1M4_orf2#LINE/    452 TGGACCCCTAC------CTCACA-CCATATACAAAAATTAACTCAAAATG 494

  chr2_2898128_29   3757 GATCACAGACCTACATGTAAAATGC-AAAACTAAAATAATTTCTAGAAAA 3805
                              ?       v      i -  -       v  -  i ii     i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGA-GCTAAAACTATAA-AACTCTTAGAAGA 542

  chr2_2898128_29   3806 TAAAATAGAAGAAAATTTAGGTGAAATTAGGTTTGATGATGAGTT-TTAG 3854
                         v  v    i? v    i vv    vv  i    v iii   iv  -    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_2898128_29   3855 ATATAATACCTAAAGCATCATCCATTAAAGAAAAACT-GATG--TTAGAC 3901
                             i i   v      iv v v iv         v -   i--  i   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_2898128_29   3902 TTTGTGAAAATTAAAA-CTTCTG--CTCCATGAAAGACATTGTTAAGAGA 3948
                           ii v          -   i  --  i  --  i    i i i    i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAAA 690

  chr2_2898128_29   3949 ATGAAAAGACGAGCCACAGACCAGGAGACAATATTTGCAAAAGTCATATT 3998
                         i         i v       vii     v            --      v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA--TCATATA 738

  chr2_2898128_29   3999 TCTAAT--GTCTTTTTGGACTTACATTCAAAATATACAAAAAACCCCC-- 4044
                            i  -- -------      ii  i  i      i   i   i ii--
  L1M4_orf2#LINE/    739 TCTGATAAG-------GGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_2898128_29   4045 --CTCAGCAATAAGAAAACAAACAACCTAATTAAAAATTTGGCAAAAAAT 4092
                         --    ii     i  i     i    i    ?    v v      ii  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_2898128_29   4093 CTGAACACGCACCTGATCAAAGA---TTTACAGATGGCAAATATGCATAT 4139
                         i    i vi  ii vvi      --- v    i     v    v   i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_2898128_29   4140 GAAA-GATAATAAACATCATATGCCAT 4165
                             -   iv v       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (114 / 71)
Gap_init rate = 0.04 (29 / 795), avg. gap size = 2.45 (71 / 29)  


1610 28.40 10.86 2.86  chr2_2931698_2933561      535  1372 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_2931698_29    535 AGAAATAACCTATTAAGTTTATGAATTA-AAGACTTAATGTT-TTAA-AT 581
                          i i   v  i  ---   i   i   i-          i  -    -  
  L1M4_orf2#LINE/      4 AAAGATATCCCAT---GTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_2931698_29    582 G-TATTACTCCCCCCAATCAATATATAGATTCAATGCAATCTTGATCGGA 630
                          -i v        v-   ii  v  i        i      iiv   ii 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCA-AATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_2931698_29    631 ATTCCAACACAGTGATGTGTGTGTGTTTGTGTGTGCAAATTAACAAATTT 680
                           i   i -------------  iv   v -  iiv     i    ii v
  L1M4_orf2#LINE/    100 ATCCCAGC-------------TGCCTTTTT-TGCAGAAATTGACAAGCTG 135

  chr2_2931698_29    681 ATTCT-----TTGTA--GAAGTGCAAATGTCAAAGAATAGCAAAGACAA- 722
                           i  ----- ii  --   i     iv v vv        v  i    -
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_2931698_29    723 ------GGAGAGGGACAGAGTTGGAGACTTTACAATTCCTGATTTCAAGT 766
                         ------ii   i i   i        ivi i   v    ii       iv
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_2931698_29    767 CT-ATTACAGAGATACAATAATTAATCTAATGTAATATTAGTGCAAGGAT 815
                           - i    i  v    i    i  vvi i   ii  i i iii      
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_2931698_29    816 ACACAAATTGACCAAAGGAACAAAATAG-GAATCTGTAAACAGATTCACA 864
                          v   v  v  i   v    i i   v -  i  iiv   i i ii  i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_2931698_29    865 CATATGTACTCACCTGATTTACCACAAAAGTGACACTATGATATGATGGG 914
                            v i iv   vi      v v    ii   v  vv iv  vii     
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_2931698_29    915 AAAATAATAATTTTCTTAA---ATTATGATCAATCTATTATATATTCACA 961
                         i   v    i i  i i  ---  vi  v viiv v i iv   ?i    
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_2931698_29    962 TAGGAAAATAATGAATCTTGATCCCTATCTCATACCATGTG--GAAACTG 1009
                          - v    v      vi v  i     i    i     i i--i   i i
  L1M4_orf2#LINE/    436 T-GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_2931698_29   1010 GCATTTCCATATTGATTGTAGACCTAAATGTGAAAAGTAAAACAATACAG 1059
                         i ---  v v  v   ii?            i i iv      v   v i
  L1M4_orf2#LINE/    485 AC---TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_2931698_29   1060 CATCTAGAA-----TATAG-----AATACTTTAT--CTTT--------CA 1089
                          vii     -----i    -----   -   ii -- i  --------  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCA 580

  chr2_2931698_29   1090 -TG------TAGAAAGGACATTAAA--CTTAAGT--CAAAGTA-----TT 1123
                         -  ------    v v    ii   -- vi   i--    iv ----- v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_2931698_29   1124 GATTAATTATACCTCATGAAAATTAACAAGTCT-GTCAGTCCTAGGACAA 1172
                            v    iv  i    v        v  v i -  vvv  vv      v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_2931698_29   1173 TGTTAGGAAG---------CAAGCTATAC--TGAGA-AAAATCTTCATAG 1210
                          i i i   i---------   v i i v--  i  -     v  iii i
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_2931698_29   1211 TACAAATATCACGA-AAAGGACCTGCATCCATAATACATAAAGAACTCAT 1259
                         vv  v     -i  -  i    i  i     v    i           v 
  L1M4_orf2#LINE/    731 ATCATATATC-TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_2931698_29   1260 ACAAATTAATA-CAAAAGGACAGAAAGTCCAAT-AAATCATGGGCAAAAG 1307
                             v i    -i    i    i v ii     -?  vv         i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_2931698_29   1308 TCCTGAACAGGC---TCTTCACA----------AAATGTTCAATAAG-AT 1343
                         vii    i  i ---   i  v ----------     vi       - i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_2931698_29   1344 ATGGAAAGCTGCCCAGTATTATTAGCTAT 1372
                            i    v   i  ii  i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (149 / 86)
Gap_init rate = 0.04 (38 / 905), avg. gap size = 3.03 (115 / 38)  


3068 25.87 1.79 0.78  chr2_2950548_2956770      978  1870 (4353)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_2950548_29    978 GACATTTCATGTTCATAAATTGGAAGAATTAGTATCATTAAAATGTCCAC 1027
                           i  ii         ii         v   i   ii    i   v v i
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_2950548_29   1028 ACTACCCACAGCAATATAGAAATTCAATGCAATTCCTAGAAATATTGCAA 1077
                            v    v vii  v  v i      i     i    vv  v  iv  i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_2950548_29   1078 TGACATTTTTCACAGAAATAGAAAAACATATCTTAAA-TTTATATGGAAC 1126
                         ivi v     ii       v  v  i vv   i    -  i        v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_2950548_29   1127 TACAAAA-ACCCTGAGTAGTCAAAACAGACTTGAGAAAGAAAAACAAA-T 1174
                          i   ii-    v  i   i       iv     i      i      - 
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_2950548_29   1175 TAGAGGCATCACACTTCCAGATTTCAAATTATATTACAAAGCTACAGTAA 1224
                          i    vv          vi        viv  i                
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_2950548_29   1225 TCAAAACAGTTTGGTAGTGGCATAAAAGCAAATATATAGACCAATGGATC 1274
                             i     v     v        iiii i i       i       vi
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_2950548_29   1275 AGAATAAATAGCCCAGAAATAAACCCACACATATATTAGTAGTGTATATC 1324
                              vi v  i               i    v   vivi i vv  - i
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT-TT 355

  chr2_2950548_29   1325 TTGACAAGGCCACCAAGAAAACAGAATGGTGAAACGATAGTCTCTTCAAT 1374
                          i       vii      vv ivv     v    vi       i     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_2950548_29   1375 AAATGATGGTGAGAAAGTTGACTATCCATATGCAGAAAAAAAAAAAACTG 1424
                              i  v  i  v ii  iv  ?   i     --   i  vi  ii  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCA--AAAGAATGAAGTTG 453

  chr2_2950548_29   1425 GGTCCTTATCTTACACTATTTACAAAAATCAACTTATAATTGATTAAAGA 1474
                          ii  i  i  i    i  v         i    i v   v   i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_2950548_29   1475 CCTAAACCTAAGACTTGGAATTATAAACCTACTAGAAGAAAACATGGAGA 1524
                               iv     vi ii  i      v  vi             i - ?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG-GN 552

  chr2_2950548_29   1525 AGAAAACTCCTTGATACCGGCTTTGGCAATTTTTTTTTA-ATATCACACC 1573
                         iv   v  i v   ivii  v  v      vv   i   -    v     
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_2950548_29   1574 AAAAGCTCAGGCAACAAAATAAAAAAAA---AAGTGGAACTACATCAAA- 1619
                               v  i         v      v ---  i v i   v       -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_2950548_29   1620 TTAAAAAGCTTCTGTAGAGCAAATGAAACAAACAACAAAATAAGAAAGTA 1669
                                -   i   ivvv    v  v  v v   v   i i i  iii 
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_2950548_29   1670 GCCAACATAGTGAGAGAAAATATTTGTGAACCCTGTACTAGACAAGGGGT 1719
                         i  v   v i  i             ii  i v i  iiv  i     ii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_2950548_29   1720 TAATATTCCAAATATGTAAGGAACTCACACTACTCAACAGCAAAACATCA 1769
                          vi   i vi     i   i      vi  v      i ii    viv  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_2950548_29   1770 AATAGCTCAATTTTTAAATGGGAAAATAACCTCAATAAACATTTCTCCAA 1819
                             i i     ?vv       v   vi ii v    i            
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_2950548_29   1820 GAAAGTCATATAAAAATGGCCAAT--------GAAAAAGTGCTCAGCATC 1861
                         ii   --     v           --------     ii      i    
  L1M4_orf2#LINE/    852 AGAAG--ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_2950548_29   1862 ACTAATCAT 1870
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.47 (135 / 92)
Gap_init rate = 0.01 (12 / 902), avg. gap size = 1.92 (23 / 12)  

1734 23.94 1.42 7.98  chr2_2950548_2956770     4480  5043 (1180)    L1M4_orf2#LINE/L1        1   527 (381)  

  chr2_2950548_29   4480 TGGTAAAACTTCTCATGCTCATGGATTGGAAGAATCAATACTGTTAAAAT 4529
                            v  i iv  i    i               v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_2950548_29   4530 GACTGTACTGCCCAAAACAATTTACAAATTCAATGCACTCCCTATCAAAT 4579
                          i vi    v      vii  i    i      i   v           v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_2950548_29   4580 TACCAATATCATTTTTCACAGAATTAGAAAAGACAATCCTAAAATTCATA 4629
                          v   iivv v     ii     v v  v   vii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_2950548_29   4630 TGGAATCAAAATAAAGAGTGCACA-TAACCAAAGTAATCTTAAGCCAAAA 4678
                              --- vii  i iiiv  v -  i     ii      i ivv i  
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_2950548_29   4679 -AACAAAACTGAAAGCATCACATTATCTGACTTCAGATTATATTATTAGG 4727
                         -      ii  i i vv     i vi ii i    i -- i-   i  --
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--AC-TTACTA-- 242

  chr2_2950548_29   4728 GTGGTGCAAAAGTAGCTGCGGTTTTTGCCATTACTTTCAAGGCTATAGTA 4777
                         -------------------------------------   i    i    
  L1M4_orf2#LINE/    243 -------------------------------------CAAAGCTACAGTA 255

  chr2_2950548_29   4778 ACCAAAACAGCATGGTACTGGTATAAAAATAGACACATAGATCAATGGAA 4827
                          i   i    ii         i    ii       i              
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_2950548_29   4828 CACAACAGAGAATCCAGAAATAAAGCCACATACCTA----CAACCAACTC 4873
                         i v  iv    i            v   i i ii  ----   iii i i
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_2950548_29   4874 T-GACAAAG-TCACAAAAATATACACTGAGGAAATGACACTCTATTCAAT 4921
                          -     i - vv   i vi  v  v  i     vi i v   v     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_2950548_29   4922 AAATGGTACAGAGAAAATTAGATAGCCATATGCAGAAGAATGAAACTGGA 4971
                                i v i  v  i i    ?   i     i         ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_2950548_29   4972 CCCATGCCTCTCATTATATACAAAAGTTAACTCAGGATGGATTAAAAACA 5021
                            v i    v  ii          i        ii      i ? i  v
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_2950548_29   5022 TAAACGTAAGGCCTGAAACTAT 5043
                             i     iv  i       
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTAT 527

Transitions / transversions = 2.24 (92 / 41)
Gap_init rate = 0.02 (9 / 527), avg. gap size = 5.89 (53 / 9)  

 998 23.90 1.10 0.37  chr2_2950548_2956770     5460  5731 (492)    L1M4_orf2#LINE/L1      635   908 (0)  

  chr2_2950548_29   5460 AATGGGATCTAATTAAACTAAAGATCTTCTGCACAGCAAAAGAAACTACC 5509
                            v   ii v  i   v v  i v   i  ii vv    i  v    i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_2950548_29   5510 ATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTA 5559
                          vv i      v  i     i                 v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_2950548_29   5560 TTCATTTGACAAAGGCCTAACATCCAGAGTCTACAAAGAACTCAAACAAA 5609
                          vi  i   i  i  v  vii       i v  i         vv    -
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA- 783

  chr2_2950548_29   5610 CTT-ATAAGAAAAA--CAAACAACCCCATCAAAAAGTGGGCGAAGGATAT 5656
                           i-    v     --    i     v  i?    i     i      v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_2950548_29   5657 GAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGA 5706
                            i     i     v        i  vi viii     i ii       
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_2950548_29   5707 AAAAATGCTCATCATCACTGGCCAT 5731
                            i       v     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (38 / 26)
Gap_init rate = 0.01 (3 / 274), avg. gap size = 1.33 (4 / 3)  

 285 29.69 6.25 4.17  chr2_2950548_2956770     6032  6223 (0)    L1M4_orf2#LINE/L1      485   680 (228)  

  chr2_2950548_29   6032 ATTCACAATAG--CAAAGACTT--------GGCCTGAAACTATTTTTAAA 6071
                          i   v   i --  ?    i -------- iv  i       ------ 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT------A 528

  chr2_2950548_29   6072 AAAATACTAGAAGAAACCTTAGGA--AAATCTTTTCTGCACATTGGTCTA 6119
                            v vi         v v    ?--       iv-  -  v    vi  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG-TG-ACCTTGGGTTA 576

  chr2_2950548_29   6120 GCCAAAGAATTTATGACCAAGCCCTCAATAGCAAATGCAATAAAAACGAA 6169
                          v   v iv  iv iivi v v vi   v    v v    i    ivi  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_2950548_29   6170 GATAAACAAATGAGACTTAATTAAACTAAAAAGCTTCTGCACAGCAAAAG 6219
                         i   i i    vi     v  i   v v    i   i  ii vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_2950548_29   6220 AAAC 6223
                          v  
  L1M4_orf2#LINE/    677 ACAC 680

Transitions / transversions = 0.96 (27 / 28)
Gap_init rate = 0.03 (6 / 196), avg. gap size = 3.33 (20 / 6)  


2732 27.60 1.19 0.36  chr2_2962276_2964095.rev      492  1328 (492)    L1M4_orf2#LINE/L1       65   908 (0)  

  chr2_2962276_29    492 AATTAAACCATAGATTCAGTGCTATTTCTATGAAACTACCATTGATATTC 541
                             i v i i       ii  v  ii    v   v v   viviiv  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr2_2962276_29    542 TTCACAGAACTAGAGAAAACT-ATTTAAAAATTTATATAGAACCGAAAAG 590
                           ii     v v  v  i-  -  iiv      i    i   vi v  i 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_2962276_29    591 GAGCCAAAATAACCAAAGCAATCCTACACAA-AAGAACAAAGCTAGAGAC 639
                           v   i    i     i     i iv v  -          i i   iv
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_2962276_29    640 ATCACACTACCCAACTTCAAACTATACTACAAGACTACAGTAGCCAAAAC 689
                         v       v     i      viv        ii        ii   i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_2962276_29    690 AGCATGGTACTAGTACAAAAGTAGACACATAGATGAATGGAACAGAATAG 739
                           ii       i i i  iii      i      v       i     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_2962276_29    740 AGAACCCAGAAATAAGATTGCACATCTACAACTATTTGATCTTTGACAAA 789
                            ii          iviiii    i  iiiii v     i  i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_2962276_29    790 CCTGACAAACACAAGCAATGAGGAAAGGACTCTCTATTCAATAAATGGTG 839
                         vv  v   ivv  vv     i      i ivv   v     i        
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_2962276_29    840 TTGAGATAACTGGCTAGCCATATGCAGAAAATTGAAACTGGACCCCTTCC 889
                         i  i  i      v  ?   i     i  i v    ii         v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_2962276_29    890 TTATGCCATATACAAAAATT--CTCAAGATGGATTAAAGACTTAAATGTA 937
                          i ii               --     i      i ?    i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_2962276_29    938 AAACCCAAAACTATAAAAAGCCTGGAAGACAACCTAGGCA-ATACCATTC 986
                          i v i            vv i i     v   v    ?i- v i -   
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC 562

  chr2_2962276_29    987 AGGACATAGGCATGGGAAAAGATTTCATGACGAAGATGCCAAAAGCAATT 1036
                         iv   v v  vv i  v  v i    v iivv v  ii         vvv
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_2962276_29   1037 TCAACGAAAGCAAAAGTTGACAAATGGGATCTAATTAAACTAAAGAGCTT 1086
                         v    i    v    i v  i    v   ii v  i   v v  i i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_2962276_29   1087 CTGCATAGCAAAAGAAACTATCAACAGAATAAATAGACAACCTACAGAGT 1136
                         i  iiivv    i  v        v i i i  v        i     i 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_2962276_29   1137 GGGAGAAAATGTTTTCAAACTATGCTTCTGACAAAGGTCTAATATCTAAC 1186
                                   i   v    ii  iiv     i  i  v  vi    i iv
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_2962276_29   1187 ATCTATAAGAAACATAAAAGAAATTTACAAGAAAAAAACAAA--ACC--A 1232
                           v     ii   - vvv v  v iv i  v     i     --   -- 
  L1M4_orf2#LINE/    763 ATATATAAAGAAC-TCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_2962276_29   1233 TTAAAAAGTGGGCAAAGAACATGAACAGACACTTCTCAAAAGAAGACACA 1282
                           ?    i         i iv    i     i     v        i i 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_2962276_29   1283 CACTTGGCCAAAAATCATACGAAGAAA-GCTCAACATCACTAATTAT 1328
                           vv       v  v  i i   i i -           ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (137 / 90)
Gap_init rate = 0.01 (10 / 844), avg. gap size = 1.30 (13 / 10)  


2926 20.81 0.91 10.76  chr2_2986976_2992167     3716  4700 (492)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr2_2986976_29   3716 ATTAATTGAAAGAATTAAT-----TAAAATTACCCTACTACCCAAAACAA 3760
                           vi    i    v     -----   i  vi vv    v      vii 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr2_2986976_29   3761 TCTACATATTCAATGCAATTCTTATTAAAATACAAATAACATTCTTCACA 3810
                               v      i     i i   i     v v iivi v  i  ii  
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr2_2986976_29   3811 GAAATAGAAAAAA-AACTTTAAAATTTGTATGGAACCACAAAAGATCATC 3859
                              v  v  iv-i iii       ii       vii   ii  i -- 
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC--C 168

  chr2_2986976_29   3860 ATACATAGGCAAAGCAATACTGAGCA-GAAAAAAAAAACTGGAGAAATTA 3908
                          v -    v    i    vi   iv -   i  v   ii     i v i 
  L1M4_orf2#LINE/    169 AGA-ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_2986976_29   3909 TACTCCCTAACTTCAAAATATACTACAAAGCTATACTAATTAAAACAGTA 3958
                         i   i  i  i       iv             i v    i  i     i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_2986976_29   3959 TGGTACTGACATAAAAGTAGACACATAGATGAATGAAACAGAATAGAGAA 4008
                                 i     iii      i      v    i  i     v    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_2986976_29   4009 TCCAGAAATAAATTTATATATTTACAGCCAACTGATCTGCAACAAAGGTG 4058
                                     iii   i     ii i   i    i v i    i    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_2986976_29   4059 CCAAGAACATACAATGGGGAAAGAATTCCCTTTTCAATAAATTGTTCTGG 4108
                               v   v               vvi        i    v  v    
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_2986976_29   4109 GAAAACTGGATAGCCATTTGAAGATGAGAAAAACTAGACCCCTATCTCTC 4158
                           v         ?   iv  v i v  ivi  ii i        i   v 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_2986976_29   4159 ACTATATAGAAAAATGAACTCAAAATGGATTAAAGCTTTAGATGTAAGTC 4208
                           i     v      v              i ?  vii  i       vv
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_2986976_29   4209 CCAAAACTATTAAATACT-AGAAGTAAACGTAGAAG-AAATGCTTCAGGA 4256
                          i        v   iv  -     v    i   i? -    -    iv  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGA 566

  chr2_2986976_29   4257 CATTGGTCTAGGCAAAGGTTTTATGGGTAAGACTTCAAAAGCACAGGCAA 4306
                          v    vi       v     iv i i  v   vi          i    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_2986976_29   4307 CAAAAATAAAAAATATTAGGTTGGTGCAAAAGTAAGTGCAGTTTTTGCCA 4356
                              i-        ---------------ii   i -------------
  L1M4_orf2#LINE/    617 CAAAAG-AAAAAATA---------------GATAAAT------------- 637

  chr2_2986976_29   4357 TTTAAAAGCAAATGGCAAAAGTAAACTAAATGCCAAGAATTGCAATTACT 4406
                         ------------   --------------------------------   
  L1M4_orf2#LINE/    638 ------------TGG--------------------------------ACT 643

  chr2_2986976_29   4407 TTTGCACCAACCTAATAGATAAATGGGACTGTGTTAAAAACTTCTGCACA 4456
                          ---  i   -----------   ----------         i  ii v
  L1M4_orf2#LINE/    644 T---CATCAA-----------AAT----------TAAAAACTTTTGTGCT 669

  chr2_2986976_29   4457 GCAAAGGAAACAATCAACAGAGTGAAGAGATAACTAACAGAATGGAGGAA 4506
                         v       v  v     v i      i   i   iv         ii   
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_2986976_29   4507 AGTGTTTGCAAACTATTCATCTGAGAAGGGACTAATTTCCAGAATATGCA 4556
                          i i        ii  vi      v        vi v          ii 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_2986976_29   4557 AATAACTCAAGCAACTCAATAGCAAAAAAAAAAAACTAATAATTTGATTT 4606
                           v     vvi          ----- v     i  v     iiii   ?
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATA-----ATAAAAAGACAAATAACCCAATTW 814

  chr2_2986976_29   4607 TTAAATGGGCAAAGAATCTGAATAAATATTTCTCAAAAAAAGACATACAA 4656
                         vv            i  i      i i       v   i    i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_2986976_29   4657 ATGGCCAACAACTATATGAAAAAATGCTCAACATCACTAATCAT 4700
                                 i  vi i       i             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (128 / 73)
Gap_init rate = 0.02 (16 / 888), avg. gap size = 7.19 (115 / 16)  


1854 27.14 2.58 1.94  chr2_3129884_3131494.rev      501  1119 (492)    L1M4_orf2#LINE/L1      286   908 (0)  

  chr2_3129884_31    501 AGACATTATA---CAATGGAACAGAACAGAGAACCCGAAACTAGATCTAC 547
                               -   ---        i    iv    ii  ii  v  i i i i
  L1M4_orf2#LINE/    286 AGACAT-ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_3129884_31    548 ACCGATACACTCAACTGCTTTCTCACAAAAGTACAAAAGCGATTCAGTGG 597
                           vvv  iiv    i  v   iiv    ii  i v  ii v     i   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_3129884_31    598 AGGGAAGACAGCATGTGCCATGAACGGTG-TGGAGCAACAGGACGTCCAT 646
                         i ii ii i  iv v v v ii  i    -   ii    v   ii?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_3129884_31    647 AGGCAAAA-----AAGATGAACCCCAATATAAGCCCCACACCTCATACAA 691
                          v      -----   v  i     ----  --  i      vi      
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCC----TA--CCTCACACCATATACAA 478

  chr2_3129884_31    692 AAACTATCTCAAAATAGATCATGGGCTTCAATGTAAAATGTAAACTTACA 741
                            i  v        i     ?i i i v       i vv    vi  i 
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_3129884_31    742 AAACTTTTAGAA-AAAATGGAAGAA-AAATCTTCAGGATCTAAGGCTAGG 789
                              i      -    iiv i ?i-        iv  i  vi  i    
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_3129884_31    790 CAA--ATCATTCTTTGATATTCTAACATCAAA-GTACAATCTATAAGAGC 836
                            --i --     v     ---i   i    - i    v v i  i  v
  L1M4_orf2#LINE/    579 CAATGGT--TTCTTAGATAT---GACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_3129884_31    837 AATAACTGATCAATGGAACTTCACCAAAATTAAAACCTTTTGCTCTGCAG 886
                           v  iv   v   v i      i           v      iv  v  i
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_3129884_31    887 AAGACCCCGTGAAGAAAATGCAAAGACAAGCTACAGGATGGGAGGAAGCA 936
                          i   v ii v      i  v        v i    i       i  ii 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_3129884_31    937 TCTGTCAGCCACAAATCCAGCAAAGGAGA-GTGTCGGGAATATAGAAAGA 985
                          i  iv ii  i v   iiii  i   vv-  i  vi       v     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_3129884_31    986 ACTCTCCGAACTTAACAGGAAAATAACAAACTGCCCAAGTAGCAAATGGG 1035
                              ivv    i  i iv    vi     ivi     v ?iv       
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_3129884_31   1036 CAAAA-ACATGAAGAGACATTTCACTAAAGAGGATATACAGTCGGCAAAT 1084
                             i- iv    v         v i     i        ivi   v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_3129884_31   1085 AAGCACATGAAAAGATGTTCAACGCCATTAGCCAT 1119
                                          i     ii  ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (105 / 59)
Gap_init rate = 0.02 (14 / 623), avg. gap size = 2.00 (28 / 14)  


3143 24.94 4.27 2.36  chr2_3158403_3163029.rev     3246  4135 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_3158403_31   3246 GAAAAAATATC---TGTTCGTGGATCAAAAGAATTAATATT-TCAAAATG 3291
                          i   i     ---     i     iii    v        - i  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_3158403_31   3292 TCCATACTACCCAATGCAATCTACAGATTCAGTGCAATCTCTATCAAAAT 3341
                         v v     v     vvii             ii      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_3158403_31   3342 TCCAAAGGCACTTTTCAGAGAAATGGAAAAAAAAATCCTAAAATTCATGT 3391
                         i   ivv  vi    iiv      v  v  ivvi              i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_3158403_31   3392 AAAACCATAAAAGGTCATGTATAGCCAAAGCAGCCTTAAGCAAGAAAAAC 3441
                         ii  viii  ii ii vv v         i  ii   i iv     i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_3158403_31   3442 AAAGCTGAAGGCATCACACTTCCTGATTTCAAATTATATTACAGATAGAT 3491
                             i  i   vv          ii        viv  i    i vvv i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_3158403_31   3492 GGTAATCAAACCAGTATACTTGCTCAAACAAGCACTGGCATAAAAACAGA 3541
                         i        iv    i i------------- i          ii i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTG-------------GTACTGGCATAAGGATAGA 288

  chr2_3158403_31   3542 CACATAGA-CAATAGAGCAGAGAAGAAAGCACAGAAATAAGCCCATGAGT 3590
                           i     -    i  ii   ivv  i  iv         i     i---
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA--- 335

  chr2_3158403_31   3591 GCATATACAGTCAACTAACCTTCAACAAAGGCAC---------------- 3624
                         -   v  ii     i i ii   i    i  ii ----------------
  L1M4_orf2#LINE/    336 -CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_3158403_31   3625 --AAAGAAT-------TCA-CAA-TGCTATTGGGAAAACTGAATATTCAC 3663
                         --       -------   -   -  v ii     v     i   ?i   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_3158403_31   3664 ATGCAAAAAAACAAAACTGAATCCTTGTCTTATACCATACATAAAAATCA 3713
                                 i  ii  ii  i i  i ii  i i      i i      i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_3158403_31   3714 GCTCAAAATAGA----AGACTTAAATGTAATACCTGAAATCACAGAACTC 3759
                         i        i  ----    i         v v  i   ii i i     
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_3158403_31   3760 CTAAAAGAAAATGTAAGGGAAAAGTTCCTTGACATTGGTCTTGGCAATGA 3809
                         i  i       ii  i ? v   vi i v    v    vi v       i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_3158403_31   3810 TTTTTTGGGATATGACCCCAAAAGCACATGCAACAAAAGCAAAAATAAAT 3859
                            i  i -       v           v          v       i  
  L1M4_orf2#LINE/    585 TTTCTTAG-ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_3158403_31   3860 AAGTGGTACTAACCTATCCAACTAACAAGTTTCTGCATAGCAAAGAAAGC 3909
                           i v v   ---ii   v  v v v  ii  i  iiivv     i vi 
  L1M4_orf2#LINE/    634 AAATTGGACT---TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_3158403_31   3910 AATCAACAAAACAGAAAGGTA-CCTATGGAATGGAAGACAGTATTTGCAA 3958
                         v     v   iiii    ii -  i ii      i   v i         
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_3158403_31   3959 ACCATATATCTGATAAGAGGTTAATATCCAAAATATGTAAGGAATTCATA 4008
                          i               i ii vi      i     i   i   i  v  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_3158403_31   4009 CAACTCAATAGCCGAAAAACAAATAACCCAATTTAAAAATGGGCAAAGAA 4058
                                   iivi   i               ?              i 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_3158403_31   4059 TCTGAATAGATATTTTTCTAA-GAAGACATACAAATGTCCAACAGGTTTA 4107
                          i        i    i  i  -     i         v    i i ivi 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_3158403_31   4108 TGGAAAGGTGGTCAACATCATCAATTAT 4135
                           i    i  v         ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.53 (157 / 62)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 4.21 (59 / 14)  


2909 22.27 7.89 2.55  chr2_3226195_3229230.rev     1684  2545 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_3226195_32   1684 TGGAAAGATGTTCCGTGCTCCTAGATTGAAAGAATTAATATTGTTAAAAT 1733
                                  i i  i  i  v i     i    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_3226195_32   1734 GACAGTACTATCCAAAGCAATTTACAGATTCAATTCAATCCCTATTAAAA 1783
                          i  i    vi     vii  i           iv          i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_3226195_32   1784 TACCAATGATATTCTTCTCAGAAATATTTTTAAAAAG-------TAAAAT 1826
                          v   iiviiv  i  iv       ----- i v   -------      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-----TGACAAGCTGATCCTAAAAT 145

  chr2_3226195_32   1827 TTAAATGAAA--------GACCCTGAATAACCAAAGCAA----------- 1857
                          i v   i  --------     v     i     i   -----------
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_3226195_32   1858 AAAAACAAAGCTGAAGGCATCACACTACCTGACTTCAAAATGTACTATGA 1907
                           i       i  i   vv       v  ii i       iv     ii 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_3226195_32   1908 AGCTATA-TAAGCAAATCAGAATGGTTATGGCATAAAAACAGACA----- 1951
                              i -   v   iv   vi    vv        ii i     -----
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_3226195_32   1952 ---------ACACAATAGAGAACCCAGATATAAATCAACACATTTACAGC 1992
                         --------- i v   v    ii     v     i v i       ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_3226195_32   1993 CAACTCATTCTCAATAAAGGCACCAAGAACACGCAATGGGGAA----CAG 2038
                            i v   i  i i  i  ii      v  iv          ----i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_3226195_32   2039 TCTCTTCAGTAAATGGTGCTGGGGAAACTAGATAACTGCATGCCGAAGAA 2088
                            i    ii             iv    i    ? ii     vi     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_3226195_32   2089 TGAAACTAGACTCCTATCTCTCACCTTATGCAAAA-TGAAATCAAAATGG 2137
                             ii i   i    i   v    v   i     - v  v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_3226195_32   2138 ATGAAAAACTTAAATCTAAGACCTAAAACTATGAACATTCT-AGAAGAAA 2186
                           v ? i  i     v     v          i  - i   -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAA 544

  chr2_3226195_32   2187 ACCTTGGGG-AAATGCTCTAGGACATTGGTCTTGGCAAATATTTGTGTG- 2234
                           v v  ? -    -  iiiv   v    vi v     vvi   v vv -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_3226195_32   2235 TAAGACCTCAAAAGCACAGGCAACAACAGGAAAAACAGACAAATGGGATT 2284
                           v   vi          i       v  i     i   i    v   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_3226195_32   2285 ACATCAAGCTAAAAGGCTGCTGT----CAAAGGAAAT----AACAAAGTG 2326
                         v      iv v   ii  vi   ----       v i----  v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_3226195_32   2327 GAGTGACAACCCATAGAGTTGGAAAAAAATATATTTGCAAACTATCCATC 2376
                         i iv         i   i v   i    ---          ii  vi   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAA---TATTTGCAAATCATATATC 740

  chr2_3226195_32   2377 TAAGAAGGGATTAATAACAAGAATATATAAGGACAACTCAATAGCTAACA 2426
                          i v      i vi  v v           i  --    ------ v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGA--ACTC------TTACA 782

  chr2_3226195_32   2427 ACTCAGTAGCAAAAA---AAATAA-----TTTATAAATGGGCAAAAGTTC 2468
                              i  ii     ---      -----  ? v           i v i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_3226195_32   2469 TGAATAGATATTTCTCAAAAGAAGGCATACAAATGGGCAACAGGTATATT 2518
                                 i       v       ii          v   i i i i  v
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_3226195_32   2519 TTTTAAA---TGCTCAACATCTCTAATCAT 2545
                         ----   ---           v????????
  L1M4_orf2#LINE/    883 ----AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (116 / 72)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.09 (90 / 22)  


3223 26.37 0.66 0.88  chr2_3335575_3341854.rev     4879  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_3335575_33   4879 TGGAAGAACATTCCATGCTCCTGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i  v   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_3335575_33   4929 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_3335575_33   4979 TACCAATGACTTTCTTCACGGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii i   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_3335575_33   5027 TATGGAACCAAAAAAGAGCCCGCATCGCCACGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v    viv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_3335575_33   5077 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_3335575_33   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_3335575_33   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_3335575_33   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_3335575_33   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?i  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_3335575_33   5325 GAAACTGGATCCCTTCCTCACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v         v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_3335575_33   5375 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_3335575_33   5425 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_3335575_33   5475 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5524
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_3335575_33   5525 TTAAA-CTAAAGAGCCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5573
                          i   -i    i --   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_3335575_33   5574 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTCCT-CATCTGA 5622
                          v  i     i   i             v  i    v-  v -i      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGA 743

  chr2_3335575_33   5623 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAAACAAATTTACAAG 5672
                         i  i  i  vi          v  i  v      vv -   v iv i  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAAT 792

  chr2_3335575_33   5673 AAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATAAACAGACA 5722
                              i     i     v  i?    i     i     iv i  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_3335575_33   5723 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 5772
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_3335575_33   5773 CACCATCACTGGCCAT 5788
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2945 28.00 1.90 0.22  chr2_3348743_3355546.rev     3359  4251 (2553)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_3348743_33   3359 TGGAAAAACATTCCATTCTCATGGACAGGAAGAATCAATATCGTGAAAAT 3408
                               i i  i    vi       iv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_3348743_33   3409 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCCTTCTCATCAAAC 3458
                            v     v      v i  i  i        i  vv i ii      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_3348743_33   3459 TAACATTGACATTCTTCACAGAATTAGAAAAAACTATTTTAAGTTTCATA 3508
                          vv  vivi v  i  ii     v v  v  iviv  ii   iv      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_3348743_33   3509 TGAAATTGAAGAAAACTCTGCATAGCCAAGATAATCCTAGGCAAAAAGAA 3558
                           i  v  v iiii  i v v        i i    i iiiv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_3348743_33   3559 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 3608
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_3348743_33   3609 CAGTAACCAAAACAGTGTGGTACTGGTACCAAAACAGACATATAGACCAA 3658
                               i   i               i iv ii i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_3348743_33   3659 TGGAGCAGAACAGAGACCTCAGAAATAACACCACATGTCTACAACCATCT 3708
                             ii    iv    vii         vv   i ii i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_3348743_33   3709 GATCTTCAACAAACCCAACAAAAACAAGCAATGGGGAAAGGATCTCCTGT 3758
                            i   i    ivviiv   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_3348743_33   3759 TCAGCAAATGGTGGTAGGAAAACTGGCTAGCCATATGCAGAAAACTGAAA 3808
                            i         v i   v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_3348743_33   3809 CTGGACCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGGATTAA 3858
                         i         v   i i   v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_3348743_33   3859 AGACTTAAATGTAAAACCCAAA-CCATAAAAACCCTAGAAGAAAACCTAG 3907
                             i         i v i   - i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_3348743_33   3908 G--TAATACCATTCAGGACACAGGCATGGGCAAAGACTTCATGACTAAAA 3955
                          --   - i -   iv   viv  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    551 GNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_3348743_33   3956 CACCAAAAGCAATTGAAACAAAAGCCAAAATTGACAAATGAGGTCTAATT 4005
                                    vvv v        vv     v  i    vi iii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_3348743_33   4006 AGAA----GAGTTTCTGCACAGCAAAAGAAATACTCATCAGAGTGCACAG 4051
                          i  ----i ii  i  ii vv    i  v ivv   vv i    v v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_3348743_33   4052 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAG 4101
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_3348743_33   4102 GTCTAATATCCAGAATTTACAAGGA-CTTAAACAAATTTACAAGAAAAAA 4150
                          v  vi          v  i  i  -  ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_3348743_33   4151 ACAA----CCCCATCAAAAAGTGG-TAAAAGATATGAGCAGACACTTTTC 4195
                             ----   v  i?    i   -i   i   v   ii     i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_3348743_33   4196 GAAAGA---CATTTATGTGGCTAACAAATACATGAAAAAA-GTTCAACAT 4241
                         v     ---i  vi vi    i  i  ii         i - i       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_3348743_33   4242 CGCTGATCAT 4251
                          i????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  

2143 24.97 5.49 2.19  chr2_3348743_3355546.rev     5204  5932 (872)    L1M4_orf2#LINE/L1        1   753 (155)  

  chr2_3348743_33   5204 TAGAGAGATAGAACATGTTCATGGTATTTTA-TACCCAATATCATTAGCA 5252
                          i  i     vvv           -   vv -v  ii     ii   iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGG-ATTGGAAGACTTAATATTGTTAAGA 49

  chr2_3348743_33   5253 TGTAGATTCTCCCTGAATTGATCTATAGAT-CAATGGAATCCCAATCAA- 5300
                           vvi  v     ii          i    -   i v      v     -
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_3348743_33   5301 -TACTAGCAGGATTGCT-ACAGAAATTGACAAGTCACATCTAACGCTGAC 5348
                         - v i   v vv  vi -i              iiivvi    ----i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA----AAT 145

  chr2_3348743_33   5349 TTATTTGTAAAAGCAAAAGATCTGAAATAGCTCAAAACAATGTTGAAAAG 5398
                          i  v  v   v    ii  i iii      -         v       i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGC-CAAAACAATCTTGAAAAA 194

  chr2_3348743_33   5399 GAAGAATAAAATTGGAGG-TTCACATAACCTGATTTCAAAACT------- 5440
                               i   i       -i     ivv  ii           -------
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_3348743_33   5441 -----GCAGTAATCAAGAAAGCTTCATATTGGTGAAAGGAAAAACACATA 5485
                         -----i            v  iv vi  i   iiv     v i   i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_3348743_33   5486 GATCAATGGGATAAACAT--AGAGTCCAGAAACAAACCAACACAAATATG 5533
                                  i   i -  --            i     v i   vv    
  L1M4_orf2#LINE/    295 GATCAATGGAATAGA-ATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_3348743_33   5534 GTTAGCTGGTTAT--A-AAAAATGC-AAGTAAC--TTTAAAGCAGAAAGT 5577
                           i ii  i  v -- -  iii   -   --  --  i  v vi     v
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAG--ACCATTCAATGGGGAAAGA 391

  chr2_3348743_33   5578 GTAGTTCTTTTCAACAGAAGGTACAAGAACAATCAGAAATTCATATGCAA 5627
                         i    -          i v   i vi i    iii  v ?i  i      
  L1M4_orf2#LINE/    392 ATAGT-CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_3348743_33   5628 AATTTAAAAAAAAATCCTCATTCCTACACTGCACTACCTATAAAAATTAA 5677
                           ----i  vi  i ivv- ii     viii   i iv  i         
  L1M4_orf2#LINE/    441 AA----GAATGAAGTTGG-ACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_3348743_33   5678 CTCAAAATGGGTCCTGGACATAAATGTAAAACATAAAACCA---AACTTC 5724
                                   i  v?i   v         i vv      i ---    ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_3348743_33   5725 CAAAATAAAACAGTAGA---AAATCTTTGAGACTTTGGGTTAGGCATAGA 5771
                         i i  v      -   i---       i v   i            vv i
  L1M4_orf2#LINE/    536 TAGAAGAAAACA-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_3348743_33   5772 AATTTTAGAAAGGACACAAAAGGCACAATCCGTGAGAGAAAAGATTGATA 5821
                         vv i     v v     v   i      v viii i      i  v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_3348743_33   5822 AATTGGACTTCA---AAATTAAAAGCTTCTGCTCTTCAAAT-ACAATGTT 5867
                                     ---         i   i  iv       v-   v i i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_3348743_33   5868 AAGAGAATGAGAAGACAAGCCACATACTGGCAAAAAACATTTGCAAA--- 5914
                             i i   i       v     v v   v i    i         ---
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_3348743_33   5915 -ACATCTGACAAGTAATTT 5932
                         - i      i   vi i  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTT 753

Transitions / transversions = 1.61 (111 / 69)
Gap_init rate = 0.03 (25 / 753), avg. gap size = 2.24 (56 / 25)  

 322 20.21 2.13 3.19  chr2_3348743_3355546.rev     6219  6312 (492)    L1M4_orf2#LINE/L1      816   908 (0)  

  chr2_3348743_33   6219 AAAATGG--AAACAATCCATTAAACAAACAGGTCCCCAAAGATGAAATGT 6266
                                --   vi  ---  i  i i   vv  i       v  v  ii
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGAT---TTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_3348743_33   6267 GAATGGCAAATAAGCGTATGAAAAGATGCGCAATGTCATTAGTTAT 6312
                         i      v       ii            v   ii   ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.02 (2 / 93), avg. gap size = 2.50 (5 / 2)  


2915 25.08 2.40 3.38  chr2_3533025_3536753.rev      641  1557 (2172)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_3533025_35    641 TGGAAAAACATTCCATGCTCATGGAGAGGAAGACTTAAAATTGTGAAAAT 690
                               i i  i     i       vv           v     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_3533025_35    691 GGCTACACTGCCCAAAGTAATTTATAGATTCAATAATATTCCCATTAAAC 740
                            v i   v      v i  i  i        iivv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_3533025_35    741 TATCATTGACATTGTTCACAGAA-TTAGGAAAAACT-ATGTTAAAATTCA 788
                          vi  vivi v  v  ii     -  --  v  i  -  vi         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr2_3533025_35    789 TATGGAACCAAAAAAGAGCCTGAATAGCCAAGACAATCCTAAGCAAAAAA 838
                                viiv  ii  v  v          i      i ----------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT---------- 188

  chr2_3533025_35    839 ACAAAAACAAAGAAACAACAAAAAAAAACAAAGCTGGAGGCGTCACGCTA 888
                         -----------    -----  i  i       i      vv    i  v
  L1M4_orf2#LINE/    189 -----------GAAA-----AAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr2_3533025_35    889 CCCAACTTCAGACTATACTACAAGGCTACAGTAACCAAAATAGCATGGTG 938
                              i    i viv        i          i   i i  ii    i
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_3533025_35    939 CTGGCACAAAAACAGACACATAGACCAATGGAACAGAATAGAGAACTCAG 988
                               i  ii i     i     i        i     v    iii   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_3533025_35    989 AAATAAAACCAAACACCTACAACCGTCTGATCTTTGACAAACCTGACAAA 1038
                                v   v   ii  iiii ivi    i  i     ivv  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_3533025_35   1039 AACAAGCAATGGGGAAAGGATCTCCTATTTAGTAAATGGTGCTGAGAGAG 1088
                          v  vv            i  vvi  v  i ii           i  v i
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_3533025_35   1089 CTGGCTAGCCAAATGCAGAAAATTGAAACTAGACCCCTGCCTTACATGTT 1138
                             v  ?   v     i  i v    ii i       i   i   ivv 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_3533025_35   1139 ATACAAAAAATAACTCAATATAGATTAAAGACTTAAATGTAAAACCCAAC 1188
                                  v        v  i   i ?    i         i v i  v
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_3533025_35   1189 ACTATAAAAACCCTAGAAGAAAATCTAGGCA-ATACCACTCAGGACACAG 1237
                                  vi i          iv    ?i- v i -i  iv   viv 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chr2_3533025_35   1238 GTATAGGCAAATATTTCAC-GATGAAACACCAAAAGCAATTGCAACAAAA 1286
                          vv       vvi    vi-   ivi            vvv         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_3533025_35   1287 ACAAAAACTGACCAACTGGATCTAATTAAACTAAAAAGCTTCTGCACAAC 1336
                         iv     iv  iv  i    ii v  i   v v    i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_3533025_35   1337 AAAAGAAACTTTCATCAAAGTGAACAGACAACCCACAGAATGGGAGAAAA 1386
                            i  v   v   vv        v                         
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_3533025_35   1387 TTTTTGCAATCTATCCATCTGACAAAGGTCTAATATCCAGAGTTGACAAG 1436
                          v       vii  vi      i  i  v  vi        i vv i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_3533025_35   1437 GAACTTAAACAAATTTATAAGAAAAA------------------AAAACA 1468
                              ivv    v iv    v     ------------------    ii
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_3533025_35   1469 AACAAAGGATATGAACAGACACTTCTCAAATGAAGACATTCATGGGGCCA 1518
                         ii        v    i     i     v  v     i  v  viv     
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_3533025_35   1519 ACAAATATATGAAAAAAAAAGCTCAACATCATTGATTAT 1557
                          i  ii i       i v--           ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (131 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 5.30 (53 / 10)  

2840 26.95 3.62 0.91  chr2_3533025_3536753.rev     2355  3237 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_3533025_35   2355 GGGGAGATATTCAGTATCCATGCATCAGAAAATTCAATATTGTTAAGGTA 2404
                           ii      i vi i i    v  ii   i i i            i i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_3533025_35   2405 TTAATTCTATCCAACTTGACTTATGGACTCAACATGATTCCAGTCAAAAT 2454
                         vi   v  vi    v    ii  ii  i     iii  i  vi       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_3533025_35   2455 CTCAGAAAGTTATTTTGTAGAAATCAACAAGTTGATTTTAAAGTTTATAT 2504
                          i   vvivi v     i      ii     i    ii    i  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_3533025_35   2505 GAAAAGAT--GAGACCTAGAACAAACAATACAAT---AAAATAGAAAAAA 2549
                          i   vii-- i    i    i iv   v     ---i   v    i  v
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_3533025_35   2550 AAAAGTTGAAATACTTAACACT-ACCAATTTCAAGATTTGTTGTAAAGCT 2598
                            -    i iv   i -    -v          i i  ii ii      
  L1M4_orf2#LINE/    202 AAA-GTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_3533025_35   2599 ACAGTAATCAATACCACATGATACT--CATGAAAGAAAAGACAAATAGAT 2646
                                    v  viii  i    --   --   i v     v      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGAT 297

  chr2_3533025_35   2647 CAATAGGGAACAGAATAGAGGGCCCAGAAATAGACCCACATAAATATAGT 2696
                             --    i     v   i i         i     i i vv   i  
  L1M4_orf2#LINE/    298 CAAT--GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_3533025_35   2697 TAGCTGATACTTGACAAAGGAGCAAAGGCAATTCAGTGAAGAAAGGGTAG 2746
                         i ii    vi i     i  v  v   i v     i  ii     ii   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_3533025_35   2747 TCTTTTCAACACATGGTGCTTTAACATTTGGATGTCCATATCCCAAAAAA 2796
                                    v        vvi   vi     i?   i  v v   i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_3533025_35   2797 AGAACCTATATGCAGACATTACACCTTTCACAAACATTAACTGAAAATGA 2846
                         v   vi iv iv vv  v i     v vi     v       v      i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_3533025_35   2847 ATCATACGCCTAAATGAAAAATACAACACTAAAAAACTCTTAAAGGGAAA 2896
                             ? vi        v  i vvi  v    v          i i i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_3533025_35   2897 C------------CTTTGTTTCCTTGGATTTTGTGATAAATTTTCAGCTA 2934
                          ------------   i  vv      i  vv ii  iiv  i i  v  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_3533025_35   2935 CAACACTAGAAGCA---GTTTCGTGAAAGAAAGCATT--TAGGTTGGACT 2979
                         ii    i i     --- ivv i--       iv  v--  ii       
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACA--AAAGAAAAAATAGATAAATTGGACT 643

  chr2_3533025_35   2980 -AATTAAAATTTAAAGATTCTGCTCTATAAAATATACTATTAAGTGATTG 3028
                         -v  i      v   iv  i  iv  vi   iv i     i   vi v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_3533025_35   3029 ATAACACAAGCCTCAAACCTGGAGAAAATATATGAAAACCACATATCTAA 3078
                          v  v    v  v  i viv           v  v   i  i      i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_3533025_35   3079 TTACAGATTTGTATCCAGAATATATAAAGAACTTTTACA-TTCAATAACA 3127
                          v vi  i                         i     -i       i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_3533025_35   3128 AGAAAACAA----CCCAAGGAAAAAGCAGACAAAATATCTGAACAGATAC 3173
                          i  i    ----     vv?    iii i    iv  i    i   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_3533025_35   3174 CTCACCAGAGACAATATACAAATGGCAAATAAGCATAT-AAAAGGTTCTC 3222
                         i  v   i   vi             v        i  -     i v   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_3533025_35   3223 AATATCACTTGCATT 3237
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (148 / 87)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 2.50 (40 / 16)  


2366 28.48 3.25 1.79  chr2_3572626_3574785.rev      777  1668 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_3572626_35    777 AAAAACATCCTATGCTCACGGATTGGAAAAATCAATATCATTAAAATCAC 826
                            i i    i   i   i         i v i     ii    i  vi 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_3572626_35    827 CATACTGTCCAAAGCAATTTACAGATTCAATGCTATTCCTATTAAACTAC 876
                         v     vi     vii  i           i  v  i     i   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_3572626_35    877 CAACATCATTCTTCACAGAATTCAAGAAAAACT---TTTAAAATTCATAT 923
                           i vv v  i  ii     v i--  v  i  ---ii            
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCATAT 151

  chr2_3572626_35    924 GGAACCCAAAAAAGAG-CCCA-AATAGACAAAGCAATCCTAAGCAAAGAG 971
                             --- viv   i -    -     v    i     i i iv  ii  
  L1M4_orf2#LINE/    152 GGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_3572626_35    972 AACAAAGCTGGATA--TTGCACTACCTGACTTCAAATTATACTATAAGTC 1019
                                i    vi-- ii    v  ii i      viv     i  iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_3572626_35   1020 TACA-------AAACACTGTGGTACTGGTACAAAAACAAACACATAGACC 1062
                             ------- i   v           i i  ii i i   i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_3572626_35   1063 AATGGAACAGAATAGAAAACTCAGAAATAAAACCACATGCCTACAA-CAA 1111
                                i     v  i iii          v   i iiii  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_3572626_35   1112 TCTGATATCTTCCACAAGGTCGAGAAAAATAAGCAATGGGGAAAGGACTT 1161
                          -    --i   v      vi vv  i vi vv            i ivv
  L1M4_orf2#LINE/    349 T-TGAT--TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_3572626_35   1162 CCTATTCAATAAACGGTGTTCAGATAACTGGTTAGCCATATGCAGACGAA 1211
                         i  v     i   i    i vi  i      v  ?   i     i v   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_3572626_35   1212 TGAAACTAGACCCGTATCTTTTACCATATACA----------TGAAATGG 1251
                             ii i     v  i  ivi          ----------ii      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_3572626_35   1252 ATTAAAGATTTAAATTGAATACCTCAAACTATAAAAATCTGAGAAGAAAA 1301
                           i ?   ii     vv  v v  v           v   v         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_3572626_35   1302 CTTAGG---AAATGTCCTTCTTGACATCAGCCTTGGCAAAGAATTTATGA 1348
                          v    ---    ---    v    v ii vi v     v iv  iv ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_3572626_35   1349 CCAAGTCCCCAAAAGAAATTGCAATAAAAACAAAAATTGACAAGTGGGAC 1398
                         vi v v v       v vvv    i    iv      v  i  i v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_3572626_35   1399 CTACTTAAACCAAAGGACTTCTGCACAGCAACAGAAACCGTCAATAAAAT 1448
                         i vv i   viv  ii    i  ii vv   vi  v  ii    v   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_3572626_35   1449 AAACAGACAATCTATGAAATAGGAGAAAATATTCACAAACTATGCACC-A 1497
                         i  v      i i iii   i            ii    ii  ii i -i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_3572626_35   1498 ACAAAAATCTAATATATAGAATCTATAAAAAAAAAAAGTAAACAAATCAA 1547
                          i  iiiv  vi   vi     v      i  v----vivv    v    
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAAC----TCTTACAACTCAA 788

  chr2_3572626_35   1548 CCAGCGAAAAACAAATAACCCCATTAAAATGTAGACAAAGGACATGAACA 1597
                         iv vvi   i           v   ?   vi i i       iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_3572626_35   1598 GACACTTCTCAAAACAAGACCCACAAGCTGCCAACAAACAAATGAAAAAA 1647
                             i     v   v    ivi    iiv     i  i  v       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_3572626_35   1648 ATGCTCATCATCACCAACCAG 1668
                         -      v     ????????
  L1M4_orf2#LINE/    889 -TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (154 / 97)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 2.81 (45 / 16)  

 405 30.75 13.32 4.36  chr2_3572626_3574785.rev     1747  2159 (1)    L1M4_orf2#LINE/L1      112   561 (347)  

  chr2_3572626_35   1747 TTTTTTATGGAACTTGGCAAATCAATTTTAAAGGTGAGA-ACAAACATCA 1795
                               iii   v   i   iiii  ii    iv v v -iv   iiiv 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_3572626_35   1796 GATGTTCAAGAATAGTTCTGAAA--ATTCTGAATAAGAACAACGAGGACA 1843
                          i- vi v       -- ii   --  ii    v     v   i i vii
  L1M4_orf2#LINE/    162 GG-GACCCAGAATAG--CCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_3572626_35   1844 AGAGGCTTGCGCT--CCAGTTGCTAAGATTCATTATAAAGCGATA----T 1887
                         iii i  ii i  --   i  v -  i i i i  i     v i ---- 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTC-AAAACTTACTACAAAGCTACAGTAAT 257

  chr2_3572626_35   1888 CAACTGATAGGGCGGCATTAGCATTGGGATAGACACACATATCTTTAGTA 1937
                            --  i  v i  i i i    vi         i i v   vv i v 
  L1M4_orf2#LINE/    258 CAA--GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_3572626_35   1938 CAAAA-----GGTCT-----TAGACTCACTCGT--GCGGTCTTGGAATAT 1975
                         i i  -----i   i-----  i  i  iv i --ii    ----   - 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC----AAT-T 350

  chr2_3572626_35   1976 GAT----GGAAAAGGTACTA---CAAATCAGTAGGGAAA---CAGTGTT- 2014
                            ---- iv  i   i i --- v v   i i      ---i   v  -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_3572626_35   2015 ----CACGTAGT-C----ACTACT-------CACAGGTAAAAACAATGAT 2048
                         ----  vi i  - ----  v   -------    v i    i-     -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AATGA- 448

  chr2_3572626_35   2049 AAAATTAAGTACCAACCTCACATTATACAGTGAAATAATCTCCTAATGGC 2098
                         -- i  iiiiv  v        ii   i vvi    v v   vv     v
  L1M4_orf2#LINE/    449 --AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_3572626_35   2099 TGAATAAACC---ATATATGAA--AAAATGCT-TAAAA-TATTAGAAGAA 2141
                          v ?- i   ---  i  v  i--    --  -     - v         
  L1M4_orf2#LINE/    497 TCAW-AGACCTAAATGTAAGAGCTAAAA--CTATAAAACTCTTAGAAGAA 543

  chr2_3572626_35   2142 AATATTGGTGAATATTTT 2159
                           i  v  ? v v  i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTT 561

Transitions / transversions = 1.98 (83 / 42)
Gap_init rate = 0.06 (28 / 450), avg. gap size = 2.61 (73 / 28)  


1365 22.44 27.63 3.42  chr2_3685676_3690456.rev     3559  4289 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_3685676_36   3559 TGGAGACACATTCCATGTACATGGATTAGAAGATTCAAAATTGTTAAAAT 3608
                             i v i  i      v        i     i i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_3685676_36   3609 GACAATTCTGTCCTAAGTGAACTATATGTCCAGTAAAAAAAGAAAAAGAA 3658
                          i    v  vi  v  v   v   i vi i  iiiv  vv----------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC---------- 90

  chr2_3685676_36   3659 CAAAAGAAAA--CAAA--GAATCTGTTGTATAAATTGGCAAGCTAGTCTT 3704
                          vv vv    -- v i-- vv i v   i v      i      ii  i 
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_3685676_36   3705 AAAATGGATATGAAAATACAAAGAACCTAGATTTGCCAGAACAATTTTGA 3754
                              vv     i    i   i i   i   v v    i      i    
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_3685676_36   3755 AAAATAA--ATGA----GGAAAACTTACATT----AATGTATTTAATAAA 3794
                             v  -- ii ----   ii   i   i ----   ---  i  -  v
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT---TTCAA-AAC 236

  chr2_3685676_36   3795 TTACTATAAAGATATACTA-------TATTCTA-TATTGGCATAAGAATA 3836
                               i    v  i v  -------i v v i-  i         i   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_3685676_36   3837 GACAAATAGATCAATGAAACTGAACAGAAAGTCCAATAACAAAACCCTTA 3886
                             v           i  iv   iv  i      iv  i   -   v  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATA 335

  chr2_3685676_36   3887 TATTTATGGTTAATAGATTTTCAACCAAAGTGCCAAAGCAATTTGATGAA 3936
                         i         i   v       i  v ii       ii v   ii   ii
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_3685676_36   3937 AAAAGGATAGTCTTTTCAATAAGCAGTAATGGTGCTGGGATAATGGGATA 3986
                         i    i             i  ------            i  iv     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAA------ATGGTGCTGGGACAACTGGATA 429

  chr2_3685676_36   3987 TCCAAATGTAAA----------------------------TATAT----- 4003
                         ?   v   i   ----------------------------i    -----
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_3685676_36   4004 -------------------------------------------------- 4003
                         --------------------------------------------------
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_3685676_36   4004 --------GAAGA------------------------------------- 4008
                         --------     -------------------------------------
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_3685676_36   4009 -----TTTCTTAGCTATGACATCAAAAGTACAAGCCATTAAA---ATAAT 4050
                         -----        v       i      i      v iv   --- v   
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_3685676_36   4051 CGATAAATTGGATTTTATCAATATTTAAAA-TTTGGCTCTTCATAAGATG 4099
                         v           i  i     v   v    -   v iv     v i  ii
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_3685676_36   4100 CAAATTTAAAAA--TTAAAAGGCATGCCACAGACTAAGAGACAATATTCT 4147
                          v -- i  i  -- v     i  vv       v ii    v      iv
  L1M4_orf2#LINE/    680 CTA--TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_3685676_36   4148 CAAGT--TGTATCTGATAAGG-ATTTGTATCTAGAGTATA-----AACC- 4188
                            i -- i            - i       i   i    -----   i-
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_3685676_36   4189 --ACA--------------------------CAGTTTAACAATGCGAAAA 4210
                         --   --------------------------  i  ?  v    v v   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_3685676_36   4211 ATATTTAAGTAAACATTATAGCCAAA-AGGATTTTTTAAATGGCCAATAA 4259
                         iv    i i  i     - vv     - i   v vi-             
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATT-TCTCCAAAGAAGATATAC-AAATGGCCAATAA 875

  chr2_3685676_36   4260 GCACAT---AAGATGATCAACATTATTTTTCAG 4289
                               ---      v       i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (95 / 67)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 8.11 (227 / 28)  


3268 26.54 0.55 0.55  chr2_3698268_3704550     4884  5791 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_3698268_37   4884 TGGAAGAACATTCCATGCTCCTGGGTAGGAAGAATCAATATCGTGAAAAT 4933
                              ii i  i     i  v   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_3698268_37   4934 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4983
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_3698268_37   4984 TACCAATGACTTTCTTCACGGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5031
                          v   iivi i  i  ii i   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_3698268_37   5032 TATGGAACCAAAAAAGAGCCTGCATCGCCACGTCAATCCTAAGCCAAAAG 5081
                                viiv  ii  v  v v  v    viv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_3698268_37   5082 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5131
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_3698268_37   5132 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5181
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_3698268_37   5182 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5229
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_3698268_37   5230 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5279
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_3698268_37   5280 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCT 5329
                           v  i  i              v      v  ?i  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_3698268_37   5330 GAAACTGGATCCCTTCCTCACACCTTATACAAAAATCAATTCAAGATGGA 5379
                            ii    i    v         v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_3698268_37   5380 TTAAAGACTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5429
                          i ?    i    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_3698268_37   5430 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5479
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_3698268_37   5480 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5529
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_3698268_37   5530 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5579
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_3698268_37   5580 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTCCT-CATCTGACA 5628
                           i     i   i             v  i    v-  v -i      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATA 745

  chr2_3698268_37   5629 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5678
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_3698268_37   5679 CAAACAAACAACCCCATCAAAAATTGGGCGAAGGATATGAACAGACACTT 5728
                         v i     i     v  i?    v     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_3698268_37   5729 CTCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5778
                            v           vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_3698268_37   5779 CATCACTGGCCAT 5791
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2086 23.61 4.83 2.04  chr2_3752509_3755311.rev     1107  1644 (1159)    L1M4_orf2#LINE/L1       12   564 (344)  

  chr2_3752509_37   1107 CCTGTGTTCATTCATTAGAAGATTCAATATTGTTAAAATGTCCATACCAC 1156
                           ii       vv   i     i i           i   v v    iv 
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chr2_3752509_37   1157 CCAAAGCAATCTACAGACTGAATGCCGACTCCATCAAAATCCCAATGGCA 1206
                              vii         i v  i  viv i i            iiv  -
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC- 110

  chr2_3752509_37   1207 TTTTTTTTAAAGAAATGGGAAAAACAATACTAAAATTCATATGGGACAAC 1256
                         -i      iv      v iv  ivii  v               i vvi 
  L1M4_orf2#LINE/    111 -CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_3752509_37   1257 AAAAGACACAAAAGAGCCAAAGTGATTTTGAGAACAAA---CAAAACTAG 1303
                           ii   v  i  v       iii  i    i  vi  ---    ii i 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_3752509_37   1304 AGGCATCACACTTTCTAATTTCAAAATATATTACAAAGCTACAGTAATTA 1353
                            vv        i i          iv  i                 i 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_3752509_37   1354 A-ACAGTATGATAATGACTGGCATAAAGACAGACATATAGACCAATAGAA 1402
                          -     i  i  ----         i  i           i    i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTA----CTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_3752509_37   1403 TAGAACCGAGAGCCCTAAAATAAACTCACACATATACAGTCAACTGATCT 1452
                              ii     i  vi        i  i    v  ii     i    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_3752509_37   1453 TCGACAAGGATACCAAGAACATACAATGGACAAGGGATAGTCTCTTCAAC 1502
                                  i i      v   v      iv  i i       i      
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_3752509_37   1503 ATATAATGCTGAAAAAATTAG----CCACATGTGAACAAATGAAATATGA 1548
                          v  ii     ii v  i i ----       ii  vi      i -  -
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT-TG- 453

  chr2_3752509_37   1549 CTGACTCCTATTTTATGTCATA--CAAAAACCAACTC------------- 1583
                         --   i    ii i iii    --      ii     -------------
  L1M4_orf2#LINE/    454 --GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_3752509_37   1584 ---TTAAATAATAAGACCTGAAATTGTAAAACTCCTAGAAGAAAACACAA 1630
                         ---i     i-     v  i   i i        i            i i
  L1M4_orf2#LINE/    502 GACCTAAATG-TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_3752509_37   1631 GGGGAAAGCTCCAT 1644
                          ? v   v  i i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGT 564

Transitions / transversions = 2.71 (92 / 34)
Gap_init rate = 0.02 (10 / 553), avg. gap size = 3.70 (37 / 10)  

1024 23.16 3.27 4.90  chr2_3752509_3755311.rev     1945  2311 (492)    L1M4_orf2#LINE/L1      548   908 (0)  

  chr2_3752509_37   1945 TAGGG--AAAGCTTCTTGACACTGGTCTTGGCAATAATTTCTTGGGTCTG 1992
                             ?--   v    v    vi   vi v      ii      i i v  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_3752509_37   1993 ACACCAAAATCAAGAGCAAGAGAACCAAAAAACAGACAAGTAGCATTACA 2042
                                  v  vi     v i  v-      i   i  i v v i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCA 646

  chr2_3752509_37   2043 TTAAACTGAAAAGCTTCTGCACAGCAAAAGAAACAATCAACAGAAGGAAA 2092
                          i   v v    i   i  ii vv    i  v  v     v i iv    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_3752509_37   2093 AGGCAATT-ATGGAATGAGA-AAAATATGTGTACTATCCACATATCTGAT 2140
                           i   ii- ii     i  -       v  i -- vi  i         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCA--AATCATATATCTGAT 744

  chr2_3752509_37   2141 AGAGGGTTAATTTCCA--ATATGTAGTTAAGA---CCTAGAACTCAATAA 2185
                          ii  ii vi v    --    i  ---    --- i  v          
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATA---AAGAACTCTTACAACTCAATAA 791

  chr2_3752509_37   2186 CAAAACAACAACAAAACAAAAATGATTTTTAAAATGGGCTAAGAACTTGA 2235
                         i    vi    - v   vv  -----  ?v         v   i i    
  L1M4_orf2#LINE/    792 TAAAAAGACAA-ATAACCCAA-----TTWAAAAATGGGCAAAGGATTTGA 835

  chr2_3752509_37   2236 ATAGACATTTCTTCAAAGA---CATATAAATGGTCAAGGTCAACAGGTAT 2282
                                     i      ---i   i      i   ------i i i i
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA------TAAGCAC 879

  chr2_3752509_37   2283 GTAAAAAAATGCTCAACATCACTAATTGT 2311
                         i i    i             ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (51 / 32)
Gap_init rate = 0.03 (12 / 361), avg. gap size = 2.50 (30 / 12)  


2231 25.56 6.91 2.59  chr2_3777961_3780789      918  1727 (1102)    L1M4_orf2#LINE/L1        1   845 (63)  

  chr2_3777961_37    918 TGGAAAAATGTTCCATGCTCATGGATAGGAAGAATTAATATTGTTTAAAT 967
                               i  i i     i        v      v           v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_3777961_37    968 TGTCATACTACCCAAAGCAATGTGCAGATTCAATGCTGTTTTTATCAAAC 1017
                         v iv     v      vii  v i         i  vi iii       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_3777961_37   1018 TACCAACGACATTTTTTACAGAATTAGA-AAACATATTCTAAAATTCATA 1066
                          v   i vi v      i     v v  -  i vv  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_3777961_37   1067 TGGAAA---AAAAAGCCT-GAATAGCCAAGACAATCCTAAGCAAAAAGAA 1112
                               ---  iiii  i-          i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_3777961_37   1113 GAAAGCTGGAGGCAC-CATACTACCCAACTTCAAACTATGCTACAAGGCT 1161
                         v    i      -  -  i   v     i      viv i      i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_3777961_37   1162 ATAGTTACCAAAACAGCATGGCAACAGTACAAAAACAGACACACAAACAA 1211
                          i   v i   i    ii   i vii i i  ii i     i i i i--
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT-- 297

  chr2_3777961_37   1212 ACCAACTGAACAGGTTAGAGAACCCAGAATGAAAACCACACACATAATGA 1261
                         --   iv   i  iv v    ii      vv   v   i   iv  -  i
  L1M4_orf2#LINE/    298 --CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGG 344

  chr2_3777961_37   1262 TC---TGATCTTTGACAAAG---TCAATGATAACAAGCAATGGGGAAAAA 1305
                           ---    i  i     i ---i   -  i--  vv           i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAA-GAC--CATTCAATGGGGAAAGA 391

  chr2_3777961_37   1306 GGCTTCCTATTTAATAAATGGTGCTGGGATAACTGGCTATCAATATGCAA 1355
                         ivvv  i -  i  i              i      v  ? v i      
  L1M4_orf2#LINE/    392 ATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_3777961_37   1356 AGGT-TAAAGCTGGAACACTTTCTTATACCATATA--------------- 1389
                          i v- i   i    v v  vi  i i        ---------------
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_3777961_37   1390 -----------GATTTAAATGTAAAATCAAAAACTTTAAAAACCCTAGAA 1428
                         -----------  ii         i v v      v     vi i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_3777961_37   1429 GAAAACCTAGA---AAATGCCACTCCA-GACATTGGCCCTGGCAAAGATT 1474
                               v   i---    ----  i i-   v    viiv     v i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_3777961_37   1475 TCAT-GATGAAGACTCTAAAAGCAATTGAAACAAAAACAAAAATTGACAA 1523
                           v -   - v   v i       vvv v       iv      v  i  
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_3777961_37   1524 AT-GGACTCTAATTAAACTAAAGAGCATCTGCACAGCAAAATAAATTATC 1572
                           -     - v  i   v v  i i v i  ii vv    iv v i    
  L1M4_orf2#LINE/    636 ATTGGACT-TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_3777961_37   1573 AAAAGAATAAATAGACAACCTATAGAATAGGAGAAAATATTTGTAAGTAA 1622
                           i i i i  v        i i     i              i  i v 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_3777961_37   1623 TGCATCTGACAAAGGTATAATATTCAGAATATCTATAAGGAGCT--TA-- 1668
                          ii      i  i  vv vi   i        --    i  i  --  --
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATAT--ATAAAGAACTCTTACA 782

  chr2_3777961_37   1669 ----AATAAGCGAGAAACAAC---CCCACTTTAAAAACATGCAAAAGACA 1711
                         ----     vvi i i    v---    v  ?     iiv     i  iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_3777961_37   1712 TGAGCAGATACCATTT 1727
                            ii   ---     
  L1M4_orf2#LINE/    833 TGAATAGA---CATTT 845

Transitions / transversions = 1.59 (126 / 79)
Gap_init rate = 0.03 (26 / 845), avg. gap size = 2.96 (77 / 26)  

 275 16.95 0.00 0.00  chr2_3777961_3780789     2279  2337 (492)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr2_3777961_37   2279 AGAGAAGACATACAAGTGGCCAACTAGCATATGAAAAAATATTAAACATC 2328
                          i      i      i       iv    i       i  ii v      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_3777961_37   2329 ACTAATCAT 2337
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 4.00 (8 / 2)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


3392 24.61 2.00 1.22  chr2_3903538_3908022.rev     3096  3993 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_3903538_39   3096 AAAGAGATCTCATGTTCATGTATTGGAAGAATTAATATTGTTGA------ 3139
                              v   i          v         v           i ------
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_3903538_39   3140 AATACTCATAACCCAAGT-GACCTATAGATTCAATGTGAAAGCTATCAAA 3188
                                ----     i -  i   i        i ii vvv        
  L1M4_orf2#LINE/     54 AATACTC----CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_3903538_39   3189 ATTCCAGTGACAGTTTTTTCACAAAAATAGAAAAAATGATTCTAAAATTC 3238
                           i    ivi --i     ii  i    v  v  iv    i         
  L1M4_orf2#LINE/    100 ATCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_3903538_39   3239 ACATGGAACTACAAAAGACCTCAGG-TAGCCAAAGCCACCTTGAGCAAAA 3287
                          i      v i   ii    -   i-        i v i     iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_3903538_39   3288 AGAGCAATGCTGGAGACATTACTCTATTTGACTTCAAAATATACTACAAA 3337
                            i   v i     ivv i  v  viiii i       iv         
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_3903538_39   3338 TCTACAGTAATCAAAACAGCATGATACTAGCATTAAAACAGACACATAGA 3387
                         v             i    ii  i    i    v ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_3903538_39   3388 CCAATGAGACAGAATAGAAAACTCATATATAAATCCACACAATTGTGGTC 3437
                         i     ii i     v  i iii  v v     i   i   v  i     
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_3903538_39   3438 AACTGAATTGTGACAAAATTGCCAGAAATACAAAATGGGGAAAGGATAGT 3487
                           i   v  vi     iiv     ii vi ivv           i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_3903538_39   3488 CTATTCAATAAATGGTTTTGAGATAACTGGATATCCATATGCA---GAAT 3534
                           v     i       vi  i  i         ?   i     ---    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_3903538_39   3535 ACAGGTACAGCCTTATCTCACACTACATACAAAAATCAATTCAAAATGGT 3584
                         iv  v iv v  i  i       i i          i  i         v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_3903538_39   3585 TTAAAGATTTAAATATAAGACATGAAACTGTAAAACTACTCGAAGGAAAC 3634
                          i ?   ii     i     vv i     i       vi v    i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_3903538_39   3635 AAGGGAG--AAGCTCCATGACATTGGTCTGGGCAATGACTCTTTTGAATA 3682
                          vi  ? --  v  i i    v    vi i       ii - i  ii   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAGATA 595

  chr2_3903538_39   3683 TGACCCCAGAACCACAGGTAATAAAAGCAAAAATAGACAAATGGAATTAC 3732
                             v   i  v    i i  i     v         i    v i i v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_3903538_39   3733 ATCAAA-TGAAAAAGCTTC-TGCTTAGCCAAGAAAACAATCAC--AGGT- 3777
                               - v     vi  i-     -- v   i v  v    v-- i  -
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTG 693

  chr2_3903538_39   3778 AAGAGACAACCTGCAGAATGGGAGAAAATATCTGCAAACTATACATCTGA 3827
                           i        ii                  i      ii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_3903538_39   3828 TAAGAAGTTAATACCTAAGATCTACACAGAAGGTAAATGACTCACTAGCA 3877
                             iiii vi  i i ii  v  i v    vvivv ii     v  ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_3903538_39   3878 AGAAAACAAATGACCTGCTTAAAAAATGAGCAAAGGACCTGAATAGACAT 3927
                          i  i      i   iiv  ?       i        ii           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_3903538_39   3928 TTACCAAAAGAAGACATGCAAATCACCAACAGGTATATGAAAAAACTGTT 3977
                           vi v        i  i     vi    i i i i       i -  i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr2_3903538_39   3978 GAACATCACTAATAAT 3993
                         v       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (147 / 70)
Gap_init rate = 0.02 (15 / 905), avg. gap size = 1.93 (29 / 15)  


2949 24.83 3.71 1.69  chr2_3927026_3931030.rev     2624  3513 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_3927026_39   2624 TGAAAATGTATTCTATGTTCATGGATTGGAAAAGTCAATATTGTTAAAAG 2673
                           i   vi   i i                 i v i           i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr2_3927026_39   2674 TATCTATGCTACCTAAAGAAATATATAGATTCAATACAATTCTTATCAAA 2723
                          iv v  i  v  i   vvi  v  i        ii    i i       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_3927026_39   2724 ATATCAATGACATTCTTCACAGAAATAGAAAAAAAAAATCCTAAAATTTA 2773
                           vi  iivi v  i  ii       v  v  ivvi -          i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCA 148

  chr2_3927026_39   2774 CATGGAACTGCAAAA-ATCCAGAATACCCAAAGACA-TACTGAGCAAAAA 2821
                         i      v     ii- i        v     -   - vi   i-   i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAA-AAAGA 196

  chr2_3927026_39   2822 AGAACAAAGCTGGAAAAATCACATTACCTGACTTCAAATTATACTACAAA 2871
                                  i    ii v     i v  ii i      viv         
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_3927026_39   2872 GCTATAAGTAAACAAAACCACATGGTACTGGCATG------------TAG 2909
                             i -    v   i  viii            i------------   
  L1M4_orf2#LINE/    247 GCTACA-GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_3927026_39   2910 ACTAATGGAGCAGAATAGAAAGCCCAAAAGTAAATC--TGCATTTAAATC 2957
                          ii      ii     v  i  i   i  i    i -- i      vivi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_3927026_39   2958 CAACTCATTTTTGACAAAGGTGCCAAGAATATACATTAGGAAAAGGACAG 3007
                            i v     i     i          vi  v  v i  i    i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_3927026_39   3008 TTTTCTTCAATAAATGGTGCTGAAA--ATTAGCAATCCATATACAGAAGA 3055
                          i  -     i           ii -- i i vv ?   i  i  i    
  L1M4_orf2#LINE/    396 TCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_3927026_39   3056 ATGAAACTGGACCCCTCACTTTCACTAGATGCAAAAATCAAGTGAAAGTG 3105
                              ii         vv  iv   i v  i       i  v v   i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_3927026_39   3106 G-TTAAAGACTTAAATCTAAGACCTGAAGCTATAAAACCATGGAAAGAAA 3154
                          - i ?    i     v     v  i  i         iv vii      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_3927026_39   3155 ACATTGAGGAAACTCTCCAAGACATTGGTCCAAACCAAGATTTCTTAA-- 3202
                             v i? v  v   i iv   v    vii ii v v i       i--
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_3927026_39   3203 --GACCCTCAACACACAGGCAACCAAAGCAAAAATAGACAAATGTGATGA 3250
                         --   v iv  vi    i     v    v         i    vv  ivv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_3927026_39   3251 CATGTAGTTTAAAACCTTCTGTACAGCAGAGGAAACAGTCAACAAACTGC 3300
                            vv iv      v   i   i vv  i    v  vi    v   v  v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_3927026_39   3301 ACAGACAACCCACAGAATGGGAGAAAATGTTTGCAAACCATTCACCCAAC 3350
                          v                          i        i   vi i ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_3927026_39   3351 AACATATGTTCTGATTAATAACCAGAACATGTAAGGAACTC--------- 3391
                           vi--------  i vi  v      i  i   i      ---------
  L1M4_orf2#LINE/    745 AAGG--------GACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_3927026_39   3392 AATAGAAAAAAAAAAAATCACCTGATT-AAAAATGGGTAAATGATCTGAA 3440
                             iv     i v    v   ii   -         i   v   i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_3927026_39   3441 TAGACAATTCTCAAAAGAAGATGTACAAATGGCCAAAAAATATATGAAAA 3490
                               v     v         i             v  ii i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_3927026_39   3491 AGATGTAGAACATCACTAATATC 3513
                         -    ivv       ????????
  L1M4_orf2#LINE/    887 -GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (133 / 85)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.82 (48 / 17)  


1158 26.41 10.80 5.15  chr2_4037103_4039510.rev      694  1295 (1113)    L1M4_orf2#LINE/L1        5   640 (268)  

  chr2_4037103_40    694 AAGATATCCTGTGTTCATGGATTGGAATTTTCAATATGGTTAAGATGTCA 743
                                  ii                vvi i     v         v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_4037103_40    744 CTATTTCCCAAATTGAACTATAGTGTCTATGAAATCCCAATCAAAATTC- 792
                         v  i i          v   i  vv  v i v      v        i -
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_4037103_40    793 AGCAAGCTATTTTCTAGATGTCAACAAATTGAT----------------- 825
                            viv  v    vi   vi ii    ii    -----------------
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_4037103_40    826 -AGGCAAGG-ACCTGGAACAATCCACACA-TACTGAA---GAATAGCAA- 868
                         - v      -   ii   i ii v v   - vi    ---   v i   -
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_4037103_40    869 TTTAGGGGATTT-CACCACCCTATTTAAAGAC--ATTGGAATGCCATAGT 915
                         v  i i   i i-   iv   v    v  i  -- i iv  v  i i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_4037103_40    916 AACGAAGATAGTGGGGTATTGGTGAAGAAATACACACATAG--------- 956
                           iv    i    v    i   iiv iii   v   i    ---------
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_4037103_40    957 -------------TCCAGCAA-AAATCCACATA-----AATAAATTGGTG 987
                         -------------     v  -   i   i i -----ii v     ---
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG--- 351

  chr2_4037103_40    988 ATTTTTCACAAAAGCACAAAGACATTTCAATTGAGAAAGTCTAGGGTTTT 1037
                              iv    ii ii v     vv      v i     vv   ------
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG------ 395

  chr2_4037103_40   1038 GTTTTTGTTTTTGTTTTTGTTTTAGTGAATGGTTCTGGTACATTTCAATG 1087
                         ------------- i   --- i iii      v    v   vi vi  i
  L1M4_orf2#LINE/    396 -------------TCTTT---TCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_4037103_40   1088 CTTATGTGAATAAAAAGTTGAACCTAGACACAAAACTTAAACTTTAAACA 1137
                         ?ii ii  v v  i  --    vi i   v vv v  i v  iv  v   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAA--TGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_4037103_40   1138 CAAATGTAACTCAACATGGATCATAGAACTAA-TGTAAAATGC-AAGACT 1185
                         v    -        v        ?   v    -     i -  -  i   
  L1M4_orf2#LINE/    478 AAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACT 525

  chr2_4037103_40   1186 ATAAAACT---AGAAGAAAACACAGGAGAAAATATATGAAAGACTGGGTT 1232
                                 ---           i   ? v    v vi vi vvi      
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_4037103_40   1233 TGGTTATGAGCTTCAT---TATAACATCAAAATCA-ATGCACATTAAATA 1278
                         v  iv   - i   v ---   i   i     v  - v   - iv   v 
  L1M4_orf2#LINE/    576 AGGCAATG-GTTTCTTAGATATGACACCAAAAGCACAAGCA-ACAAAAGA 623

  chr2_4037103_40   1279 AAAAATTAATAAGCTAG 1295
                               vi    ii i 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGG 640

Transitions / transversions = 1.20 (85 / 71)
Gap_init rate = 0.04 (24 / 636), avg. gap size = 4.00 (96 / 24)  

 540 21.45 4.29 12.54  chr2_4037103_4039510.rev     1614  1916 (492)    L1M4_orf2#LINE/L1      631   908 (0)  

  chr2_4037103_40   1614 GGTGAGCTGGATATTATTAAAATTAAAAACTTTTGT---TTAGGTAAAGA 1660
                          i i ii    iv i  i                  --- i ---  i  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA---AAGGA 677

  chr2_4037103_40   1661 CACTGTTTAGATAATGAAAAGGCAAGAAAAAAACAAACAAATTAAAGGCT 1710
                             i iv   v i       i   -------- vv   i v i------
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAA--------CCCACAGAATG------ 713

  chr2_4037103_40   1711 TGGAGAAAATATTTGCAAA--ACACATTTGACAAAGGTGATGTTTTTAAG 1758
                         -                  -- i i  i   i  i  vvv   v ii ii
  L1M4_orf2#LINE/    714 -GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_4037103_40   1759 ATATATAAAAAAATTCAAACTAAATAAAACAGTAATAACTTAATAA-AAA 1807
                                  i  -i  ---------------- v i    i     -   
  L1M4_orf2#LINE/    763 ATATATAAAGAA-CTC----------------TTACAACTCAATAATAAA 795

  chr2_4037103_40   1808 CTCAGAACAAA-AACTCAATTATAAATTAGGTGA-GGATTTGAATGAGCA 1855
                         --- ii     -   i     ?v   v i  ii -          iii  
  L1M4_orf2#LINE/    796 ---AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_4037103_40   1856 CCTC-ACAAAGAAGGTATACAGATGGC----AAGCATAAGAAATTATGTC 1900
                         ii  -v        i      i     ----     i v    vv   ii
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_4037103_40   1901 TAAAATTATTTGTCAT 1916
                         i  v  i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.56 (46 / 18)
Gap_init rate = 0.05 (13 / 278), avg. gap size = 3.92 (51 / 13)  


3075 25.43 0.98 2.28  chr2_4113904_4116440     1126  2045 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_4113904_41   1126 TAGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 1175
                          i    i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_4113904_41   1176 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCACCAAGC 1225
                            v     v      v i  i  i        i  v  i  i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_4113904_41   1226 TACCATTGACTTTCTTCACAGAACTAGAAAAAACT-ACTTTAAATGTCAT 1274
                          v   vivi i  i  ii     v v  v  i-  - iii    vv    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_4113904_41   1275 ATGGAGCCAGAAAGAGCCT-GTATAGCCAAGACTATCCTAAGCAAAAAGA 1323
                              iviiv  i ii  i- v        i  v   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_4113904_41   1324 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATTACAAGGCT 1373
                               i      vv   ii  v  ii i      viv  i     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_4113904_41   1374 ACAGTCACCAAAACAGCATGGTATT--CATACCAAAATAGATATGCAGAC 1421
                              v i   i    ii     i --    -- ii     i  ii   i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATATAGAT 297

  chr2_4113904_41   1422 CAGTGAAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCA 1471
                           i  i  i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_4113904_41   1472 TCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT--TC 1519
                         vi    i   i    ivv  v   i v  vv            i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_4113904_41   1520 CTTATTTAATAAATGGTGCTGGAAAAAGTGGCTAGCCATATGCGGAAAAC 1569
                         i  -- i  i            i v  v   v  ?   i    ii  i v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_4113904_41   1570 TGAAACTGGACCCCTTCTTCACACCTTATACAAAAATTAACTCAAGATGG 1619
                             ii         v i       v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_4113904_41   1620 ATTAAAGACTTAAATGTAACA-CTAAAACCATAAAAACCCTAGAAGAAAA 1668
                           i ?    i         v -       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_4113904_41   1669 CTTAGGCA-ATACCATTCAGGACATAGGAT-GGGCAAAGCCTTCATGACT 1716
                          v    ?i- v i -   iv   v v  i -i     v vi   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_4113904_41   1717 AAAACACCAAAAGCAATTGCAAGAAAAGCCAAAATTGACAAATGGGACCT 1766
                          vi            vvv    v     vv     v  i    v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_4113904_41   1767 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 1816
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_4113904_41   1817 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATATGAA 1866
                          v  i     i                 v       vii  vi  v   v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_4113904_41   1867 AAAGGTCTAGTATCCAGAGTTTACAAGGAAATTAAACAAATTTACAAAAA 1916
                           i  v  v         i v  i  i   v i--------      ---
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTC--------TTACAA--- 783

  chr2_4113904_41   1917 CAAAATAAAAACAAAAACAAAAACAAACCCCATCAAAAAGTGGGCAAAGG 1966
                          vv     v  -   i     v ---    v  i?    i          
  L1M4_orf2#LINE/    784 CTCAATAATAA-AAAGACAAATA---ACCCAATTWAAAAATGGGCAAAGG 829

  chr2_4113904_41   1967 ATATGAACAGACACTTCTCAAAAGCAGACATTTATGAGGCCAACAAATAT 2016
                           v    i     i     v    v   i  vi viv      i  ii i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_4113904_41   2017 ATGAAAAAAAGCTCATCATCACTGGTCAT 2045
                                i v     v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (135 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.00 (30 / 15)  


3038 21.63 8.75 1.42  chr2_4120343_4122241.rev      562  1407 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_4120343_41    562 TGAAAGGGAATACTATGTTCATG-ATCGGAAAATGTAACATTGTTATGAT 610
                           i  i iv  v i         -  i    i iv   i       v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_4120343_41    611 GGCAAGACTCTTCAAACTGATCTACAGATTCAGTAAACTCTGTATCAAAA 660
                              v    ii    i               iiiv v  iv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_4120343_41    661 TCCCAATGGCCTTTTTTTGAAGAATGGAAAAACTTACTTATCTTAAAATT 710
                              iiv         vv ii   v  v  i  v ----  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA----TCCTAAAATT 146

  chr2_4120343_41    711 CCTATGGAATTGCAAGGGGCCATGAACAGC-AAAACA-TGATGAAAAATC 758
                          v       v        i  vv   i   -      - vv       vv
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_4120343_41    759 ATAATA--GTTAGATGACTCACAATACACTGTTGTTTCAAAAGTT-TTAC 805
                          v  i --   i  v        v v v vi  ---      v  -i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATT---TCAAAACTTACTAC 243

  chr2_4120343_41    806 AAATATACAATAATCAAAATGGTATGGTACTGCTGTAAAGATACAAATAC 855
                            vv    i       i ii  i        vii   i    v v   i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_4120343_41    856 AGATGAATGGAATAAAATTGAAAGTCCAGAAATAAACTCAGACACCTATG 905
                             v         i      i               i  v   ii    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_4120343_41    906 GTCAATTGATTTTCAACAAGAATGCTGAGACCTTCCAATGGGGAGAGAA- 954
                                       i     ii   ii     v i         i    -
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_4120343_41    955 -----------CAAATGG---------------ATATCT----------- 967
                         -----------       ---------------   ? i-----------
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_4120343_41    968 ----------------TATCTCAAATCACATATAAAAATTAACTCAAAAA 1001
                         ----------------  i    v i  i   i                v
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_4120343_41   1002 GGATCAACAACCTAAATATAAAAGCCCGAAGTACAAAATTCTCAGAACAA 1051
                               ?vi        i   i   ivi  v  i    i   i    v  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_4120343_41   1052 ATCAAAGGC--AAATTATTGTGACCTTGTATTTGGCAATAGTTCCTTAAA 1099
                          v  v   ?--    iv i         vi  v      i   i    i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_4120343_41   1100 TATGACGTCAAGAACTGAAGTAACAGAAACAAAAGTTGGTAAGTTGCATA 1149
                               ii   i i vv   i    i  iv    i v i   i   v iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_4120343_41   1150 CCACCAAATTTTTTTAAATCCTGTCTGTT-----GAACACTATCACGAGA 1194
                         i  i    v  v---   v i v v  i ----- i         v  i 
  L1M4_orf2#LINE/    644 TCATCAAAATTA---AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_4120343_41   1195 TTGAAAAGAAAACCCACAAAATGAGATAAAATATTTGCAAATCTTGTAAC 1244
                         v        v        i    i  v                v i  v 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_4120343_41   1245 TGATAAGGT-CTAGTATTTAGAATTTTAAAAGAAATATTACAATTCAATA 1293
                                 v-  v    ii     v vv      v v      i      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_4120343_41   1294 ACAA---GACAAAATTA--TCAATT-AAAAATGGGAAAAAGACTTGAACA 1337
                          i  ---      --  --i     -         v   i  i     i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAA--TAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_4120343_41   1338 GAGAGTTGTTGAAGGAAGACATACAAATGGCCAACAATCACATAGAAAGA 1387
                           v v  v iv  i     i              i  v     ii     
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_4120343_41   1388 TGCTCAATATCATTAGTCTC 1407
                                i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (102 / 78)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.78 (86 / 18)  


2630 26.16 2.38 4.22  chr2_4125930_4128202.rev      857  1781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_4125930_41    857 TGGGTGGATATTCTAAGCTAAGGATTTAGAATATTCAATGAGGTTAAGAT 906
                            ivi     i i v i v v iv  i   v i i   ivv        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_4125930_41    907 AGTAATTTTCCTCAAGTTTATCTGTAGACTTTACATAATTCCTATCAAA- 955
                         i i   vi   i   i  v    ii   i iv  ii   i         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_4125930_41    956 CCCCAGCAGGCTGTTTTATAGAAATTGACAAGCTTATGCTAAAAT--ATA 1003
                         i      v v  v    ii               v  v       --   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_4125930_41   1004 TAGTGAATGTCAAAAAATACAGAATCAGAAAAACAAT-TTAGAAAAGGAG 1052
                          i -i    -   iii iv      vivv        -  ii     i  
  L1M4_orf2#LINE/    151 TGG-AAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_4125930_41   1053 ------GTTGTAGGAGATACAATAAACAATTTTAAAAGTTACTGTAAAAG 1096
                         ------    v    vvi   v vvv      i    v     ii   - 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-G 247

  chr2_4125930_41   1097 ATACAAAGTAATTAAGATAATGTGGTACTTGCATGAGGATAAACATATGA 1146
                         v    --     i    i i         v    i      i      ii
  L1M4_orf2#LINE/    248 CTACA--GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_4125930_41   1147 ATTAACAAAACATAACTGAGAATTCAGAAATAAACT--TGCATT-ACGGC 1193
                           i  iii  i v  i     i i           i-- i    - i  i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_4125930_41   1194 TGACCAATTTTCAGCAAAAGGCCCAATACATTTTAATTGACAAAGGATAG 1243
                         ii iii      ii   ii vv    v  vv  i   v iv    i    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_4125930_41   1244 TCTCTTCAATAAATAATTCTGAAACAATTTGATATCCAAGTACAAAGGA- 1292
                            i     i    ii v   ii    i v    ?   vi i    i  -
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_4125930_41   1293 CAGATTTCGATTCTCACCTCATGCCACACACAAAACATTCCCTCAAGATA 1342
                         iii v  v  ii ii      ii   i i      -   vv     i  i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATG 494

  chr2_4125930_41   1343 GATTCTAGACCTAAATATAAGAGCTTAAGCTATAAAATTTATGGAAGAAA 1392
                            iv?          i        v  i        i iv i       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_4125930_41   1393 ATGAAGGAGAAAGTTTTCATTTACCTTGAGTTATATAGAGAGCTATCAGT 1442
                          iiv   ? v  i i   i v-      i    vii iv ivi v i  v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_4125930_41   1443 GATTATATCTATAACACAATCCAAAAAAGACAAAATTAGTACATTAAACT 1492
                         v  v i i v v i     v v v      v     vii  v   ii   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_4125930_41   1493 CCATCAAAATTAAAA-CATCTG-ACTT-AAAAAACACCATTAAGGAATTA 1539
                         i              - v i  -i   -   ii    i  i   i  v i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_4125930_41   1540 AAAGGTCAAGCCACATAAAACATTTTAAACTCATATATCTGATTGTAGCA 1589
                            i v   v     v  ---------------------  --- v  v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAA---------------------TG---GGAGAA 719

  chr2_4125930_41   1590 AATATTTTCTTATTATATGTCTGAGCACTGAATAGAACTTGTCTCCAGGA 1639
                                v vv  i    i     ---- i i-- i      v     i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGA----TAAG--GGACTTGTATCCAGAA 763

  chr2_4125930_41   1640 TATATAAAGAAGACTTTCCACTCAATA-TAAAGAAGAGAAATAACCCAAT 1688
                                    vv   v v        -    -    v            
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAAATAACCCAAT 812

  chr2_4125930_41   1689 TTAACTGTAGGCAAAATGTTTGCATAGGCGTTT-TACAAAGTAAGATATA 1737
                          ?  vvi i      ivi    v    i i   - v     -        
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG-AAGATATA 861

  chr2_4125930_41   1738 TGGACAGCTAATATGAACATGA---GATGTTCAGCATTATTAGTCCT 1781
                         iii ii  i    v v      ---    i   i   i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (149 / 89)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.44 (61 / 25)  


2956 27.16 3.64 0.45  chr2_4183428_4189673     4875  5754 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_4183428_41   4875 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4924
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_4183428_41   4925 GGCCAT----------------------------GCCATCCCCATCAAGC 4946
                            v  ----------------------------  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_4183428_41   4947 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4994
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_4183428_41   4995 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTGAATCCTAAGCCAAAAG 5044
                                viiv  ii  v  v v  v     ivv    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_4183428_41   5045 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5094
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_4183428_41   5095 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5144
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_4183428_41   5145 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 5192
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_4183428_41   5193 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCCATGGGGAAAGGATTCC 5242
                          vi    i  i     ivv  vv  i v  vv v          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_4183428_41   5243 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5292
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_4183428_41   5293 GAAACTGGATCCCTTCCTTACACCTTATACGAAAATCAATTCAAGATGGA 5342
                            ii    i    v   i     v     i     i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_4183428_41   5343 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5392
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_4183428_41   5393 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5442
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_4183428_41   5443 AACACCAAAAGCAATGGCAAGAAAAGACAAAATTGACAAATGGGATCTAA 5492
                         i            vvi    v      v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_4183428_41   5493 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5542
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_4183428_41   5543 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5592
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_4183428_41   5593 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5642
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_4183428_41   5643 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5692
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_4183428_41   5693 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5742
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_4183428_41   5743 GTCACTGGCCAT 5754
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 6.00 (36 / 6)  


 581 32.37 1.66 0.83  chr2_4258243_4261162     1123  1363 (1557)    L1M4_orf2#LINE/L1        1   243 (665)  

  chr2_4258243_42   1123 TGAAAATGTATTTCATGCTGGTGAATTGGAAGAATTAATATTGTTAAATT 1172
                           i   vi   ii    i vi  i         v             iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_4258243_42   1173 G--AATATTACCCAAAGCAATTTACAGATTCAATGGAATTTTTATAAAAA 1220
                          --    i v      vii  i           i v   iii   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_4258243_42   1221 ATATTAATGATACTATTCACAAAAATAGGAAAAAAT-ATTCTAAAATGTA 1269
                         - vii iiviivi v  ii  i    -v  v  iv -  i       vi 
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chr2_4258243_42   1270 TATGGAATCACAAAAAGTTCTGAATAGCTAAAGCAATCCTGAGGAA-ATA 1318
                                vii   iiiiii v       i   i     i   ii  - vi
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_4258243_42   1319 AACAAACCAGGAGGCATCACACAGTCTGTCTTAAAAATACACTAC 1363
                               viv     vv      vvi iivi  v    ivi     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

Transitions / transversions = 1.79 (50 / 28)
Gap_init rate = 0.02 (5 / 243), avg. gap size = 1.20 (6 / 5)  

1686 23.80 3.82 7.93  chr2_4258243_4261162     1723  2428 (492)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_4258243_42   1723 AAAATATGCTACGGAGCTTTAATAATGAAATCAGCATTGTACTGGCATAA 1772
                             iv i    ii    vi i    v  iv   ii v            
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_4258243_42   1773 ACACAAACATA--GACCAACGCAACAGAAT--AG-GT---------AACC 1808
                         iv i i     --  i   i v  i     --  -  ---------    
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_4258243_42   1809 CAGATATTAATC-TCAACTCATTTTTGACAAGT-CACCAAGAACACACAT 1856
                           v i   v  v-    i v     i      v-ii      v  iv  v
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_4258243_42   1857 TGGGGAAGAAACAGTCTATTCAATAAATGGTGCCAGGAAAACTGGATAAC 1906
                                ii  i     v     i         ii   v         ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_4258243_42   1907 TGTATGCACAAGAATGAAACCACACCCCTATTTCTCACCATATA-ATAAA 1955
                         iii     v         iiiiv       ii  v         - v   
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_4258243_42   1956 TCAAATCAAAATGAGTTAAAGTCTTAAACCCAAGACCTAAAACTAAGAAA 2005
                          i  v        ii i ?  v i    ivi    v         vi   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_4258243_42   2006 TTACCATAAGAAAACATTGGGG-AAGTGTGTGAGGATATTGATCTGGGCA 2054
                         i vii v          v  ? -  i v vi -v  iv   ivi i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCA 580

  chr2_4258243_42   2055 AATAGTT-CTGGAGTAAAACATCAAAAGCGCAGGCCACCAAAGCAAACAT 2103
                          - i   -  viii  vi   i       i  i  v  v    v   v  
  L1M4_orf2#LINE/    581 A-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_4258243_42   2104 AGTCATA----GGATTACGTCAAGCTATAAATCTTTCACACAGTAAAGGA 2149
                           --   ----   i v i    iv vv   v    iiii vvi      
  L1M4_orf2#LINE/    630 AG--ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_4258243_42   2150 AACAATTAACAAAGTGAAGAGACAACCCACACAATGAGAGAAAATATTTG 2199
                         v  v  i  v        i            v    i             
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_4258243_42   2200 CAAACTACCCATATGATAAGGG-CTTAAGAATTAGAATAGATAGAATACA 2248
                             ii ivi  v         -   i-----------------------
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTG----------------------- 754

  chr2_4258243_42   2249 GAATAATACATAGAAATACATAGAATATATTAGAATGTAGAATTAGAAGC 2298
                         ----------------  ivi         ---  ---    i ----- 
  L1M4_orf2#LINE/    755 ----------------TATCCAGAATATAT---AA---AGAACT-----C 777

  chr2_4258243_42   2299 TTAAAAAACTCAACAGCAAAAATTCAAATAATATAATTTAAGCGTGG-CA 2347
                            v  --     i ii     vv       ivi    ?  ivi   -  
  L1M4_orf2#LINE/    778 TTACAA--CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_4258243_42   2348 AAATATCTGAATTCACATTTATCAGAGGAAGATATATAAATGCCCAACAG 2397
                           iv  i     vv      v  vi i         i     v    i i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_4258243_42   2398 CTACATAAAAA--TTTTCAACATCACTAATCAT 2428
                         vi    i    -- vi         ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (97 / 67)
Gap_init rate = 0.03 (21 / 677), avg. gap size = 3.95 (83 / 21)  


3321 26.76 0.44 0.44  chr2_4274189_4280467     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_4274189_42   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_4274189_42   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_4274189_42   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_4274189_42   5028 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_4274189_42   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_4274189_42   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_4274189_42   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_4274189_42   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_4274189_42   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_4274189_42   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_4274189_42   5376 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_4274189_42   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_4274189_42   5476 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5525
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_4274189_42   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_4274189_42   5576 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_4274189_42   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_4274189_42   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_4274189_42   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_4274189_42   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1546 28.55 10.91 2.66  chr2_4391737_4393957      934  1721 (500)    L1M4_orf2#LINE/L1       16   868 (40)  

  chr2_4391737_43    934 TGTTTATGAATTGGAATACCCAATGTTGTTAAAATGTTAATTCTCCCCAA 983
                             i   i       v  ii   i       i   vi   v        
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_4391737_43    984 ATTAATATTGATAGATTAATTCAATACAATTTCAAATGAAATCC-AGTGA 1032
                            i  v -- i     ----   ii    ii v vii      -  ivi
  L1M4_orf2#LINE/     66 ATTGATCT--ACAGATT----CAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_4391737_43   1033 CCTCTATCATAGATATTGAACAGCCTATTCTAAAATTTATATAGAAATTC 1082
                            i v iii   v     vv   iv  i        i    i     v 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_4391737_43   1083 AGAGAACATAGAATAAGCGTGGCAATT---AAAAGTAAAAACAG-TTTAA 1128
                          ii i  vi      iv ivii    i---    iv  i    i-v  ii
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_4391737_43   1129 AAAATTTAGCCTCCCTAATTTCAAGGTTTATTATAAAGTCACAGTAATCA 1178
                          ii i i vv  i  i        iii   i  i    ii          
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_4391737_43   1179 AGACACTGTTGTATGGGAGTGAAAATAATCACATA----------ATA-- 1216
                              v   v   iv  vi i ii   iv  i   ----------   --
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_4391737_43   1217 ----------CAGAAATGGACCCATACATATATGGTCAATTGAGTTTTGA 1256
                         ----------       ii          v             v   i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_4391737_43   1257 TAAAGGCTCTGAAGTAATTCAGTAGAGAAA---TATGT------------ 1291
                         i  i  iv ii iiiv     i i i    ---  -  ------------
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-GTCTTTTCAACAAA 408

  chr2_4391737_43   1292 TGGTGTCACAAAAATTGATAATTCACATGCAAAAGAATGAACCGCT--AT 1339
                              iiivi v  i  ivv ?i                  -- i -- i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA--GTTGGAC 456

  chr2_4391737_43   1340 CAGCATCTCAGATCCTGCATAACCTTTACCTCAAACTAGGCCATAGGTCT 1389
                          vvi i    v i v ii i  vvv   v      v i ii  ?  ii  
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_4391737_43   1390 AAATATAAACATCTATAAAAGTATAAAACTACAAGAAAAAAATAAAAA-- 1437
                             i   i- v   --   v         viv    i    i v ii--
  L1M4_orf2#LINE/    507 AAATGTAAG-AGCTA--AAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_4391737_43   1438 -AAAT-----TAACTTTGACTTAAGTA-TAATTTTTTATATAGGGCAC-A 1479
                         -    ----- i  i   iv   i i - ii   i   v   v i   - 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_4391737_43   1480 AAAGCATGAAACA-CAAAAGGCC---TAGTCA--CTGTATTTAATTAAAA 1523
                               i-  i  -      ivv---   vi --i  v i  v  i    
  L1M4_orf2#LINE/    604 AAAGCAC-AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_4391737_43   1524 TGTACAAACT---GCTCTTTGAAAGGCACTATTAAGAAAATAAAAAAAAA 1570
                          -  v     --- iv   ii  i i      i      i i    i --
  L1M4_orf2#LINE/    653 T-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA-- 699

  chr2_4391737_43   1571 GCAAGTCATACTGAATG--AAAATATATCTGCAGAAATACATATCTGATG 1618
                         -   vi  i --     -- i  v    i    -  vi i         i
  L1M4_orf2#LINE/    700 -CAACCCACA--GAATGGGAGAAAATATTTGCA-AATCATATATCTGATA 745

  chr2_4391737_43   1619 AAGAATCTA-----AGGGGAGTATCAAAAACTTTCAAAATTAGTTAAT-- 1661
                          i i ii i-----  iiv -   v  i    i i v  i viv    --
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATA-TATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_4391737_43   1662 -----CAT-TCTGCCAA---AAAAATGA--AAAAGAT--GGGTAGATGTT 1698
                         -----  v- vvv    ---       i--   i   -- ii    ii  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_4391737_43   1699 TCACCAA-GAAAATATTCAGATGG 1721
                           v    -   i    v  i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGG 868

Transitions / transversions = 2.14 (152 / 71)
Gap_init rate = 0.04 (36 / 853), avg. gap size = 2.97 (107 / 36)  


 216 34.25 0.00 0.00  chr2_4460990_4462583      428   500 (1094)    L1M4_orf2#LINE/L1       19    91 (817)  

  chr2_4460990_44    428 TTATAGGTTGAATGACTCAGTCCAGGTCAGATGTCAATTCTCCCAAAATT 477
                          i  i i   i v    i i viv v v     v    v     v     
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chr2_4460990_44    478 GAAGTACAAACCCAATATGGTCC 500
                           vv    i ii   iiiii   
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCC 91

Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.00 (0 / 0)  

1322 29.40 3.16 1.66  chr2_4460990_4462583      501  1102 (492)    L1M4_orf2#LINE/L1      298   908 (0)  

  chr2_4460990_44    501 CAATGGAACAGGAT--AGAATCTAGAAATAGACGCATACTTATATGGTTA 548
                                 i  i  --   i  i       i  v     v v      i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_4460990_44    549 ATTAAATTTTTACCAAGATGCAAATGAA-ATTCAATGGAGAAA--ATAAT 595
                            i v   iv  v i i   v  -  v-         i    --   i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGT 396

  chr2_4460990_44    596 ATTTTCCAGAGATGATGCTGAAACAATTGGACATTAATAAAACAATAACA 645
                         v     v v i   i     ii    i    i ?iv i vi-   ---- 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAA----A 441

  chr2_4460990_44    646 AAAACCAAAAATCTGGGTACATACTTTTATAATCTAAATAAAAATT---T 692
                          i  i--i  i -   iiv v   i i- i viv  v i       --- 
  L1M4_orf2#LINE/    442 AGAAT--GAAGT-TGGACCCCTACCTC-ACACCATATACAAAAATTAACT 487

  chr2_4460990_44    693 CAAACTAGTCCATAAAATTAAACTTAAAACCTAAAACTG-GAAATTTTCA 741
                             v i vi  ? i vi    iv   i v        i-i   i i i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_4460990_44    742 GAAGATAAAATAAAAGAAAATCTTCATAATATTGCATTAGAAAAT---TT 788
                              v  v   ii? v        i i iv   vi    iv   ---  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_4460990_44    789 TTTCACTGTAACATGAAATACGCAATCACTAAAAGTAAAAAT-GACAAAC 837
                         i  viv i i   iv   vi i   v  vi     v      -  i   i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_4460990_44    838 ACAATATCCTCACAATTAAAAAACACTGCCCTTTGAAAGATCCTGTTAAG 887
                         vvi iv  v   v         vivi  iv   ii  i  iv  i i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_4460990_44    888 AAAAGAAAAAGACAAATGACAGGCTATGACA---CATTTGCAAG--AAAT 932
                            ivi         viv    iv iv  v ---i        i-- v  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_4460990_44    933 ATGTGCTAAAGGACGTGCATCCAGAATATATAAATAATTCTCAAAATTCA 982
                           v  v   i    v  i                v  i   i v  i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_4460990_44    983 ATAATAGGAAAACACAAAATGCAATT-AAATTTTGGCTAATAATTTAAAC 1031
                               ii  i   v v  iv     -   vv v   v  vi    i  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_4460990_44   1032 AGATGCTTTACAAACGAAAATACACAGATGGCATATAAGCATTTAAAAGG 1081
                            iii  iv v  v   i   i   i     vv       iv i   i 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_4460990_44   1082 ATGCCTAACTTCATTATTCAT 1102
                             ii   v   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (102 / 72)
Gap_init rate = 0.03 (16 / 611), avg. gap size = 1.81 (29 / 16)  


3143 27.53 0.44 0.44  chr2_4625413_4630330     3519  4426 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_4625413_46   3519 TGGAAGAACATTCCATGCTCATTGGTAGGAGGAATCAATATCGTGAAAAT 3568
                              ii i  i     i    v i v   i  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_4625413_46   3569 GGCCATACTGCCCAAGGGAATTTATAGATTCAATGCCATCCCCATCAAGC 3618
                            v     v     ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_4625413_46   3619 TACCAATGACTTTCTTCACAGAATTGGAAAAAAATACTTTAAACTTCATA 3668
                          v   iivi i  i  ii     v v  v  ivvv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_4625413_46   3669 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 3718
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_4625413_46   3719 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 3768
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_4625413_46   3769 CAGTAACCAAAACAGCATGGTACTGGTAGCAAAACAGAGATATAGACCAA 3818
                               i   i    ii         i vv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_4625413_46   3819 TGGAACAGAAC--AGAGCCCTCAAAAATAATGCCACATATCTACAACTAT 3866
                              i    i--    i  -- i      vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_4625413_46   3867 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 3916
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_4625413_46   3917 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3966
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_4625413_46   3967 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 4016
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_4625413_46   4017 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 4066
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_4625413_46   4067 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 4115
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_4625413_46   4116 ACACCAAAAGCA-ATGCCAACAAAAGCCAAAACTGACAAATGGGATCTAA 4164
                                     - v  -        vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_4625413_46   4165 TTAAACTAAAGAGTTTCTGCACAGCAATAGAAACTACCATCAGCGTGAAC 4214
                          i   v v  i ii  i  ii vv   vi  v    i  vv iv     v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_4625413_46   4215 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAAGCTACTCATCTGACAA 4264
                           i     i   i             v       iii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_4625413_46   4265 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4314
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_4625413_46   4315 AAACAAACAACCCCAGCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 4364
                          i     i     v vi?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_4625413_46   4365 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 4414
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_4625413_46   4415 ATCACTGGCCAT 4426
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (142 / 104)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


1433 22.40 14.66 2.24  chr2_4706196_4708161      498   988 (978)    L1M4_orf2#LINE/L1      262   813 (95)  

  chr2_4706196_47    498 ACA-TGTGGTATTAGTGAGAGGACAAATACATAGATCAATGGAACAAAAC 546
                            -       i i iivi    i i i i              i i  i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_4706196_47    547 AGAGAGTCCA---ATAATCCCACACAAATATATAGTTAATTGATTTTTGA 593
                         v         ---    v    i   -- v   i  i          i  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACA--TTTATGGTCAATTGATTTTCGA 359

  chr2_4706196_47    594 CGAAGCTGCAAAGGCAATTCAA-------GGAATCATCTTTTCAACAAAA 636
                          i i v   v   i v      -------i    vi             v
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_4706196_47    637 GATGCTGG-ACAATTGAA-ATGCATATGCAACAAAATGAGCCT----CCC 680
                          i      -    i  i - ?v  i      v i     ivi ----   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_4706196_47    681 TGGAGCCTT---CCATAGCTCGTAAAGTTAAGTCAAA-TGGATCACAGGT 726
                          i---   i---     -- vvv   i    v     -       ?  ii
  L1M4_orf2#LINE/    460 TA---CCTCACACCATA--TACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_4706196_47    727 CTAAATGTAAAAGGCAAAACTGTAAA----------GAAACTAT------ 760
                                   i  vi      i    ----------    vi  ------
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_4706196_47    761 ------TTA-GACTTTGTGTGAGGTAATTAGGTTT--TAGATATGGCACC 801
                         ------ ii-   i   v  v   i   --     --        i    
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAAT--GGTTTCTTAGATATGACACC 602

  chr2_4706196_47    802 AAAAGCATGATCCGTTCAAAA-----AATTAATAAATTAGACTTCAGCAA 846
                                ii v vi--     -----   vi       i       v   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAA--CAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_4706196_47    847 AATTCAAAACTTTTGT--T---AAGAAAAATTTTAAAA------------ 879
                             v           -- ---   i v v v i  i ------------
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_4706196_47    880 ---CTATAGACTAAAAGCAAATATTTACAAGTTACATATCTGATGAAGAA 926
                         --- i i   v iii  v        i   i i i         i i i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_4706196_47    927 CTTATATCTAGAATATATGAAGCACTGTCA-AACTCAACAGTTAGAAAAC 975
                            i    i         i   v   v i -       i i v i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_4706196_47    976 ATGCAATCCAGTT 988
                          vii  i   i  
  L1M4_orf2#LINE/    801 AAATAACCCAATT 813

Transitions / transversions = 2.18 (74 / 34)
Gap_init rate = 0.04 (22 / 552), avg. gap size = 3.77 (83 / 22)  

 264 20.79 6.93 4.95  chr2_4706196_4708161     1376  1476 (490)    L1M4_orf2#LINE/L1      806   908 (0)  

  chr2_4706196_47   1376 ACCCAATTTTTTTTAAA---GGACAAAA-ATTTGAATAGATAATTCGCCA 1421
                                 ?-----   ---  i    i-           i v   v   
  L1M4_orf2#LINE/    806 ACCCAATTW-----AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_4706196_47   1422 GAGA---TGTATGGATAGAAAATATATACATGAAAAGAGACTCAACATGG 1468
                         i   --- i  iii  i vv    vii           vi        vi
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_4706196_47   1469 AGTCATTA 1476
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.04 (4 / 103), avg. gap size = 3.00 (12 / 4)  


3264 26.87 0.44 0.44  chr2_4910801_4917195     4996  5903 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_4910801_49   4996 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5045
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_4910801_49   5046 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_4910801_49   5096 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 5144
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_4910801_49   5145 ATGGAACCAAAAAAGAGCCCTCATCGCCAAGTCAATCCTAAGCCAAAAGA 5194
                               viiv  ii  v  vvv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_4910801_49   5195 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5244
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_4910801_49   5245 ACAGTAACCAAAACAGCATGTTACTGGTACCAAAACAGAGATACAGATCA 5294
                                i   i    ii  v      i iv ii i   v   i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_4910801_49   5295 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTA 5342
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_4910801_49   5343 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5392
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_4910801_49   5393 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5442
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_4910801_49   5443 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAA 5492
                           ii    i    v   i     v              i    i     v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_4910801_49   5493 TAAAGACTTAAACGTTAGACCTAAAACCATAAGAACCCTAGAAGAAAACC 5542
                         i ?    i    i  v   v       i    i vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_4910801_49   5543 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5592
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_4910801_49   5593 ACACCAAAAGCA-ATGCCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5641
                                     - v  -        vv     v  i    v   ii   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_4910801_49   5642 TTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCAACAGAGTGAAC 5691
                          i   v v  i i   i   i vv    i  v    i   v i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_4910801_49   5692 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTGCTCATCTGACAA 5741
                           i     i   i             v  ii   viiiivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_4910801_49   5742 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5791
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_4910801_49   5792 AAACAAAAAACCCCATCAAAAAGTGGGCAAAGGATATGAGCAGACACTTC 5841
                          i     v     v  i?    i            v   ii     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_4910801_49   5842 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5891
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_4910801_49   5892 ATCACTGGCCAT 5903
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2502 26.39 1.89 2.15  chr2_4980751_4984469.rev     2080  2871 (848)    L1M4_orf2#LINE/L1        4   793 (115)  

  chr2_4980751_49   2080 AGAGATATTCCACATTCATGGACAGGAAGAC--AATACTGCTAAAATATC 2127
                          i      i   ii        iv       --    i  i   i  iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_4980751_49   2128 AGTTCTTTACAACTTGACCTACAGATTCGATGCAGCCCCAATCAAAATCT 2177
                          i v  iiv   v    i          i i   ii   v         i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_4980751_49   2178 CAGCAAATTATTTTGTGGTTATCAACAAAATGATTCTGAAGTTAATATGG 2227
                             vivi v     ii vv  ii    iv    i  i  i  v      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_4980751_49   2228 AGAAGGAAAACACCCAGAACATCCAACACAATATC---AAAGA-GAGCAA 2273
                          i v v  iiv        i v    v     v i---     -  i   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_4980751_49   2274 ATCTGGCAGGCTGACACTACCCACCTTACAGAGCT-ACTCTAAAGCTACT 2322
                          vi   vi i  v     v    vi  -  i i  -   vi        v
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTT-CAAAACTTACTACAAAGCTACA 252

  chr2_4980751_49   2323 GTAAAAAAGACTGGGTGACTGTGTGGTCCTAGAAAAAGAACGGACAAATA 2372
                             vv     ------ --       v  i v v   i ii    v   
  L1M4_orf2#LINE/    253 GTAATCAAGAC------A--GTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_4980751_49   2373 GATCAGTGGCCCAGAGCAGAAAGACAAGAAATTGGTCCTCACAAATATAG 2422
                              i   vvi   iiv  i  v v      viii  vi   vv   i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_4980751_49   2423 TCAGTTTGATCTCTGACAAAGGAATAAAGGTAATTCAATGGAGAAAGGAC 2472
                            i  -   i ii     i  viiv   iiv         i     i i
  L1M4_orf2#LINE/    345 TCAATT-GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_4980751_49   2473 AGGTTTTTCCAAAAATGGTGCTGGGACAACTGGACGTCCACATGAAAAAA 2522
                           vi     v v                      ii?       v    i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_4980751_49   2523 AAAAAATGAATCTAGACACAGATCTTACATCTTACCCCAAAATGAACTCC 2572
                           ----    vi i   v vv i  i   i v  iv v     v     v
  L1M4_orf2#LINE/    444 AA----TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_4980751_49   2573 AA-----TAACAGAC-TACATGTAAAGTGCAAAAACTATACAACTTCTAG 2616
                           ----- v ?    -  v      - v  v         v    ii   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAA-GAGCTAAAACTATAAAACTCTTAG 538

  chr2_4980751_49   2617 AACAGAACACAGATGAAAATCTGAGTGACCT-GGGTTTGCTGATAATCTT 2665
                           v i    i  i? v      vv       -     v vii  ii i i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_4980751_49   2666 TTAGATACAACACCAAAAACACCATCCATGAAAGAAAAAAATCAGTAAGT 2715
                                ii         i   v v v ii          - vii   i 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAAT 637

  chr2_4980751_49   2716 TGGACTTCATTAAAATTAAACACGTATGCTCTGTCCAACG-TAGTATTAA 2764
                                   i         v  v v  iv  -  v  v -i v   i  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAA 686

  chr2_4980751_49   2765 AGTAATGAAGAGACAAGTCACAGATAGGAAGAAAATAGCTGTAAAACACC 2814
                         iiv i    i      vi      vv  i        vi  i   v  iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_4980751_49   2815 TATCTGATAAAGAACTTGTATTCAACATATATGAAGAATTCTTAAAAATC 2864
                                   i i        i  iv      i     i     v  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_4980751_49   2865 AACAACA 2871
                           i  i 
  L1M4_orf2#LINE/    787 AATAATA 793

Transitions / transversions = 1.31 (117 / 89)
Gap_init rate = 0.02 (16 / 790), avg. gap size = 2.00 (32 / 16)  

 431 16.82 4.67 0.00  chr2_4980751_4984469.rev     3121  3227 (492)    L1M4_orf2#LINE/L1      797   908 (0)  

  chr2_4980751_49   3121 AGA-AAACAACCCAATTAATAAATGGGCAACAGATCTGAACAGACATATC 3169
                            -   i         ? v          vi   i    i      v  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_4980751_49   3170 ACCAATAAAGATTTATCAAT----AACAAGCATATAAAAAGATGCTCATC 3215
                         v    vi     v  iv   ----  i     i  i            v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_4980751_49   3216 ATCATATGTCAT 3227
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.02 (2 / 112), avg. gap size = 2.50 (5 / 2)  


2419 26.71 1.16 5.68  chr2_5136720_5139310.rev     1149  2099 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_5136720_51   1149 TGGAAAAACATCCCAGGCTCACGAATTGGAAGAATCGATACCATTAAACT 1198
                               i i      v i   i i         v ii   iii    iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_5136720_51   1199 GACCATACTGCCCAAACCAATCTACAGATTCAACATAATTCCTATCAAAT 1248
                          i v     v      iii               ii   i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_5136720_51   1249 TACCAAAT-CATTGTCCATATAATTAGTAAAAAC-AATTCTGAAACTCAT 1296
                          v   iv - v  v iiii v  v v - v  i -i  i  i   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr2_5136720_51   1297 ATGGAACCAAAAAAAAACCTGAATAGTCAAAGAAATTCTAATCAAAAAGA 1346
                               viiv  iii v  v      i    iv   ii i vv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_5136720_51   1347 AAAAAGTTGGAGCCATCACATTACCTGATTTCAAGTTATATTACGAGGCT 1396
                          v          vvv     i v  ii       iviv  i   i i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_5136720_51   1397 ATAGCAAATGAAATATCATTTGCTATCCGAGTTTGATGCGGGATTTACCA 1446
                          i  i  --------   -----------  ---------------  vi
  L1M4_orf2#LINE/    250 ACAGTAA--------TCA-----------AG---------------ACAG 265

  chr2_5136720_51   1447 TGAAATATCATGATACTGGTATAAAAATAGACACATAGATTAATGAGATA 1496
                           --------  i      i    ii       i      i    ii   
  L1M4_orf2#LINE/    266 TG--------TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_5136720_51   1497 GAATAAAGAGCCCAGACAAAAAGCCACAGGCCCATAACCAACTGATCTTA 1546
                             vi    i     v v   v   i viiii  iii   i    i  v
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_5136720_51   1547 GACAAAGTCAACAAAAATATATACTGGAGAAAGA-CACCCTACTCAATAA 1595
                              i viiv   i vi  vi v   i      -i vi  vi    i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_5136720_51   1596 ATGGTACTGGGAAAATGAGATAGTCATTTGCAGAAGAATGAAATTGGACT 1645
                              i      v  ivi    ?i  iv    i         i      i
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_5136720_51   1646 CCTGTTTCTCACCAAATATAAAAATTAACTCAAGATGAATTAAAGATTTA 1695
                            iii  v     v   i              i   i  i ?   ii  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_5136720_51   1696 AGTGTAAGACCTGAAACTACAATAATCCTAGAAAAAAAGCTAGGAAAAAC 1745
                          i       v  i      i  v v  i     i    vv    ?iv  v
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_5136720_51   1746 TCTTCTGGACTTTGGCCTGGGCAAGTAATTTACGA-ACAAGTCCTCATAA 1794
                              vv   i    vi i     - ii   viv - i v v vi  v  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAA 606

  chr2_5136720_51   1795 ACAAAAACAACAAAAACAAAAATAGATGAATAGGACATAATTAAA-TTAA 1843
                         i  v  i        iv          i   v    v v  i   -    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_5136720_51   1844 AAAGCTTCTGCAGAGCAAAATAAGCAATCAACCTAGTAAACGGACAGCCT 1893
                            -   i  iivvv    iv vi v     vvv   i  vi    i  i
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_5136720_51   1894 ATAGA-TGGGAAAAAGTATTTGAAAACTATGCATCTGAAAGAGGGA-TAA 1941
                          i   -     i   i      v   ii  ii      v -     - vi
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA-AGGGACTTG 754

  chr2_5136720_51   1942 TATGTAGAGTCTACAGGAAACTCAAGCAACTCAACAACAACAACAACAAC 1991
                            vi   i v  i iii     vvi        i  i  -------  -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-------AA- 796

  chr2_5136720_51   1992 AAACAAAAAATCCCATTAAAAAGTGC-CAAAAGACATAAACAGATATTTG 2040
                          i     v  i  v   ?    i  v-    i  iv i  i   i    v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_5136720_51   2041 TA-AAAGAAGACAAACAAGTGGTCAACAA--ACATGAAAAAGTGTTCAAC 2087
                          v-        i v    i   i   i  --         ii  i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_5136720_51   2088 ATCACTAATCAT 2099
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (158 / 92)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.25 (65 / 20)  


1642 28.46 0.94 0.94  chr2_5158755_5160856      501  1034 (1068)    L1M4_orf2#LINE/L1      129   662 (246)  

  chr2_5158755_51    501 CAAGCTTATTATTAA-TTTATATGAAAATACAAAGGCCACAGGATAGCTA 549
                               v  iv v  -  i     i    i   i  v v   i     i 
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr2_5158755_51    550 AAAATAACCTTCAAAATGAAAAAGAAAGTGGAAAAAATCACTCCACCCAA 599
                            -i  i   v    v   i  v     v i ii v    v iv     
  L1M4_orf2#LINE/    179 AAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_5158755_51    600 TATTAAAGTCTATTATATAGCTGCATTAATTGAGACAGTGTGGTATTGGC 649
                          v i   iii  i  i v    i  v    ii             i    
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_5158755_51    650 AGAGAGATAAACACATAAATCGATTGAACAGAACAGAAAATCCAGAAATT 699
                          v ii    i   i   i   i  v   i    iv  i i         v
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_5158755_51    700 GACCAAAATAAATATGACCAACTGTTTTTTGTTGAAAGTGCTAAGGCAAT 749
                         i   v v i vv    ii   i  v    i vii ii    i   i v  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_5158755_51    750 GCATTTATAAATGAATACCCTTTTTAACAAATGGTGCTGGAGCAGTTTAA 799
                         v  v vivi  v     vi     i               ii  ii vi 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_5158755_51    800 TATTTAGAGTTAAAAAAAATAATTTTGACCTAAACTTCACACCTCATATA 849
                           ?ii v vvi    i  vv  v  v    ivv  i       vi   i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_5158755_51    850 ATAATTAACTCAAAGTAGATCTTGTACTTAAATATAAAATGTAACCTGAT 899
                          v            i i    v?iv  i     i   i vv   vviv  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_5158755_51    900 GAAACTTTTAGA-TAAAACATAAGAGGAAACCTCAGAGA--TTGACAGCT 946
                         i     i     -v        i ? v   i  iv v  --   i-- i 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG--GTT 575

  chr2_5158755_51    947 GGGCAATACGTTCTTAGACTTGACACCAAAACAAATAATCTACAGAAGGA 996
                         i      ivv        iv           -iv i  v v   i   i 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAA-GCACAAGCAACAAAAGAA 624

  chr2_5158755_51    997 CAAAGTAG-TAAATTAGACTTCATCAAAATGAAAATCTT 1034
                         -   i   -      i              v    v   
  L1M4_orf2#LINE/    625 -AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

Transitions / transversions = 1.37 (86 / 63)
Gap_init rate = 0.01 (8 / 534), avg. gap size = 1.25 (10 / 8)  

 638 24.92 6.73 3.37  chr2_5158755_5160856     1314  1610 (492)    L1M4_orf2#LINE/L1      602   908 (0)  

  chr2_5158755_51   1314 CAAAAAAAAAA--AAAAAAAAAAAAAAAAAAAAAA------------AAA 1349
                              iv v  --  v    i      v i v   ------------   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_5158755_51   1350 ATGAAAATCTTTGGCTCTGTAGAAAACCCCATTAACAGGATTAAAAAGGC 1399
                           v    v    v iv  vi i ii  v i  i  v i- v i     i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA-AGTGAAAAGAC 700

  chr2_5158755_51   1400 AAGCAATAGACTAGGAGAAAACACTTGTAAACTACATAGCTGTTAAGAAT 1449
                           v v i   v i        i i   i   ii i   v   v    i--
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG-- 748

  chr2_5158755_51   1450 GA---GTATCTAGAATAGAT---GAAATCTCAAAGCTTAATAGTAAAAGT 1493
                           ---     i      v  ---   v   i v i  i    i     iv
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_5158755_51   1494 ACAAATATTCCAATTACGAAGTGGGCCAAAAGACATGAAGAGACATTTCA 1543
                                vi      ?vi  i     -   i  iv    v         v
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGC-AAAGGATTTGAATAGACATTTCT 847

  chr2_5158755_51   1544 CCAAAGAGGATTGTGTAAACGCTCAATAAACACGTGAAATAAAAACATGT 1593
                                i   -i ii   i vi      i   -----  i    v   i
  L1M4_orf2#LINE/    848 CCAAAGAAGAT-ATACAAATGGCCAATAAGCAC-----ATGAAAAGATGC 891

  chr2_5158755_51   1594 TCAGGATCACTGGCTGT 1610
                            iv    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (43 / 30)
Gap_init rate = 0.03 (9 / 307), avg. gap size = 3.33 (30 / 9)  


3460 21.42 2.73 3.61  chr2_5189821_5192218.rev      992  1906 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_5189821_51    992 GAAAAGCT-TCCTATGTTCATTGATCACAAGACTTAACATTGTTAAGATG 1040
                          i    v -   i        v   iiv         i            
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_5189821_51   1041 GTATTATTCCTCAAACTGAGCTACAGATTCAATAAAATTCTCATCAGTAT 1090
                          i v  i   i    i   v            iiv   i ii    iv  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_5189821_51   1091 CTCAGCTGACTTCTTTATAAAAATTGACAAGCTGATTCTAAAGCTCATAT 1140
                          i      v   i   ii i                i     ii      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_5189821_51   1141 GGGATTTCAGGGAA-----ATTAGCCAAAACAATCTTTACAAAGGAAAAC 1185
                           i v v  i  i ----- v                v v    i i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_5189821_51   1186 CAAATAGAAGTAGTTATATTTCACGATTTCAAA--CTACTTCAAATCTGT 1233
                         v  i v i  v v i i i   v i        --i    v    v  ii
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_5189821_51   1234 AGTAACTAAGTTAGGGTGAAACTGACAAAAAGTCAATCACATAGAACAAT 1283
                              ii   vi  v   iv    i  v  i vi iv  i     v    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_5189821_51   1284 GGAATAAAACTGAAAGCACCCCAGAAGAAAATCTATGTATTTATGGTCAA 1333
                               i  i   i  i---      iv   i i  ii            
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGT---CCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_5189821_51   1334 ATGATAATCCATAAGAGTAC-AAAATTATTCAATGAGGAAAGAATAGCCT 1382
                         v    vv  v i   i  i -  i ii        i           i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_5189821_51   1383 TTTCAAAAAATGGTGCTGGAACAACTGTATAGCAACATGCAAGTGGATGA 1432
                               v            i       v   ? v        iv i    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_5189821_51   1433 AGCTGGACATTTACTTCACACCACATACAAAAATTGACCGAAAATGGATC 1482
                           i     vii   i        i           i  iv          
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_5189821_51   1483 A--GACCCAAATGTAAAAGCAAAATTTGTAAAATTCTTATGATAAAACAG 1530
                          --    i        i   v   vi i     i     vi v      v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_5189821_51   1531 AGTTAAATAAATCTTTACGACCTTAATTTTACCAAAGGAGTCCTACATAT 1580
                           --i?i        iii      iiv  viv   v  vv  i  v    
  L1M4_orf2#LINE/    549 AG--GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_5189821_51   1581 GACACCAAAAAGCACA-GCATCAAAATAAA---TATATAAGTTGCATTTT 1626
                                   -     -   v     v   ---  v    i   v i  i
  L1M4_orf2#LINE/    597 GACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_5189821_51   1627 ATCAAATATT-----TTTTTTCAAAGTGATGGCTTTCAAAG--CAGCATT 1669
                               -   -----i    -----   -----i       --  vi  i
  L1M4_orf2#LINE/    646 ATCAAA-ATTAAAAACTTTT-----GTG-----CTTCAAAGGACACTATC 684

  chr2_5189821_51   1670 AAGACAGTAAAACATCAACCTGAAGAATGGTAGAAAACATTTTTAAAGCA 1719
                             v   i   viv     iiv       v      i    vi   v  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_5189821_51   1720 TCTATCTG-CAAGAGACTCATTTCCAGAATATATAAAGAACTCTTACAAT 1768
                          v      -i   i    ii v                           i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_5189821_51   1769 TCAATAATAAA--GAAAAAGAACCTAATTTTTTAAAAAAAAAAAAAAAAC 1816
                                    --  v   v    i    ?--------------     -
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTW--------------AAAAA- 819

  chr2_5189821_51   1817 ATGAGCAAAGGACCTGAACAGACACTTCAGCATGTAAAACATACAAATGG 1866
                         -  i        ii    i     i   vv  viv  i i          
  L1M4_orf2#LINE/    820 -TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_5189821_51   1867 ACAACAAACACATGACAATGTGCTTGACATCATCAGTCAT 1906
                         v   i  i       v  vi    ii      ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (120 / 73)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 3.05 (58 / 19)  


2088 29.62 4.13 1.38  chr2_5194167_5196696.rev     1168  2038 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_5194167_51   1168 CACACTCATGGATAGGAAGAAACAATATTGTTAAAATGGCCATACTTCCC 1217
                           iii        v      vvi           i     v     i   
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_5194167_51   1218 CAAGCAATTCATAGATTCAATGTTATTCCTATGAAACTACTAGATACATT 1267
                         v  vii  ii i        i iv  i     v   v v i  v i v  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_5194167_51   1268 CTTCTCAGAACAAGGAAAAAAATAAACTTTTAAAAAATTTACATGGAAC- 1316
                         i  iv     -- vvi v  iv i v i ----      i i      v-
  L1M4_orf2#LINE/    114 TTTTGCAGAA--ATTGACAAGCTGATCCT----AAAATTCATATGGAAAT 157

  chr2_5194167_51   1317 -CAA-------AAAATAGCTAAGGCAGTCCTAAGTGAAAAGCACAAAGCT 1358
                         -   ------- i      i  ii  i  i i ivi i   v      i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_5194167_51   1359 GGAGACATTATGGTACCCAACTTCTAA-CTAAATCACAAGGCTACCAGAA 1407
                             ivv i iiv v     i   v  -  v v -    i     viv  
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACT-ACAAAGCTACAGTAA 256

  chr2_5194167_51   1408 CCAAAAACAGCATGGCACTGGTACAAAAACAGAAACATAGACCAATGGAA 1457
                         i   i -   ii   i     i i  ii i   v i     i        
  L1M4_orf2#LINE/    257 TCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_5194167_51   1458 CCAAACAAAGAGCCCAGAAATAAGTCTGAACACCTCCAACCAGTTGATCT 1507
                         ivi  ivi    i          ii iiv   ii viiii  i     i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_5194167_51   1508 TCAACAAAGCTAACAGAAACAAGCAATGGGAAAAGGGCTCCCTATTCAAT 1557
                           i    i v iv  ii v  vv       i    iiivvi  v     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_5194167_51   1558 A----GTGTTGAGATAATTGGCTAGT-ATATG-----GTGTAA----GGA 1593
                          ----   i  i  i  i   v  ?i- i   ----- vi i ----   
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_5194167_51   1594 CCCCTTCCTTACACCATATACTAAAAGCAACTTAAGATGAATTAAAGATT 1643
                              v   i           v    vi    i  i   i  i ?   ii
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_5194167_51   1644 TAAATATAAAACCCAAAACTATCAAAACTCT-AGAAGACAGCCTAAGCA- 1691
                              i   i v i        -        -      v i v  i ?i-
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_5194167_51   1692 ATACCATCCTGAATGTAAGAACAGGCAAAGATTTCAT-GATAAAGACACT 1740
                          v i v  v   viv ii v-i      v i    v -    v-     i
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT-GACACC 602

  chr2_5194167_51   1741 AGA-GCAGTTCCAACAAAAGCAAAAATTGACACATGTGATCTAATTAAAG 1789
                          i -   vvvv         v      v  i v  vv  ii v  i   i
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_5194167_51   1790 TAAAAAGCATCTACACAGGAAAATAAACCATTGGCAGGGTAAATAGACAA 1839
                          v    i v i iii vvv   iv v  i  iiiv ii  i  v      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_5194167_51   1840 CATACAGAATGAGAGAAAATTTTTGCAAACCATGCATCTGGCAAAGGTCT 1889
                          vi        i        v        i   ii     ii  i  v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_5194167_51   1890 AATAACCTGCATCTACAAAGAACTTAAACAAATTTATAA-----GGAAAA 1934
                         vi  v  v v  v  i        ivv    v iv    -----i  v  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_5194167_51   1935 ATAAAC--ATTAAAATGTGTGCAAAAGATATGAACAGACACTTCTCAAAA 1982
                             v --   ?   vi  v     i   v    i     i     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_5194167_51   1983 GAAGACATACATGTGGC-AAGAAGCATATCAAAAAAAACCTCAGCATCAC 2031
                              i     vi    -  v     i  v    i vi -   i     ?
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC-TCAACATCAZ 901

  chr2_5194167_51   2032 TGATCAT 2038
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.51 (153 / 101)
Gap_init rate = 0.02 (22 / 895), avg. gap size = 2.18 (48 / 22)  


2189 26.26 0.49 0.49  chr2_5232290_5233915.rev      501  1117 (509)    L1M4_orf2#LINE/L1      244   860 (48)  

  chr2_5232290_52    501 AAGGCTACAGTAACCAAAACAGGGTGGTACTGGTACCAAAACAGAGATAT 550
                           i          i   i    v          i iv ii i   v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_5232290_52    551 AGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTA 598
                                     i    i--    i  --        vv   i i  i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chr2_5232290_52    599 CAACTATCTGAACTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGG 648
                         iiiii vi   vi  i     ivv  vv  i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_5232290_52    649 ATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGA 698
                           vvi  v  i  i              v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_5232290_52    699 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAG 748
                          iiv    ii    i    v   i     v           i  i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_5232290_52    749 ATGGATTAAAGACTTACATGTTAGACCTAAAACCAAAACAACCCT-AGAA 797
                               i ?    i  v    v   v       i v  -   i  -    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAA 540

  chr2_5232290_52    798 GAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 847
                               v    ?i v viv   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_5232290_52    848 GTCTAAAACACCAAAAGCAATGGCAAAAAAAGACAAAATTGACAAATGGG 897
                         ivv  vi            vvi    v      v     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_5232290_52    898 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 947
                          ii v  i   v v  i i   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_5232290_52    948 GTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATC 997
                              v  i     i   i             v  i    vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_5232290_52    998 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACA 1047
                            i  i  i  vi          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_5232290_52   1048 AGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGA 1097
                          v     i     i     v  i?    i     i     iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_5232290_52   1098 CACTTCTCAAAAGAAGACAT 1117
                           i     v        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.29 (89 / 69)
Gap_init rate = 0.01 (4 / 617), avg. gap size = 1.50 (6 / 4)  


3102 26.98 1.67 0.45  chr2_5348807_5353266     3074  3970 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_5348807_53   3074 TGTAAAAACATTCCATGCTTATGGATAGTAAGAATCAATATAGTAAAAAT 3123
                           v   i i  i     i i      v v    v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_5348807_53   3124 GGCCATATTGCCCAAAGTAATTTATAGATTCAATGCTATCCTCATCAAGC 3173
                            v   i v      v i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_5348807_53   3174 TACCA-TTGACTTTTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 3221
                          v   -i  v      ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_5348807_53   3222 ATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAGA 3271
                               viiv  ii  v  v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_5348807_53   3272 ACAAAGCTGGAGGCAACATGCTACCTGACTTCAAATGATACTACAAGGCC 3321
                               i      vvv  ii  v  ii i      vvv        i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_5348807_53   3322 ACAGGAACCAAAGCGGCATGGTACTGGTACCAAAACAGAGATATAGATCA 3371
                             v  i   ii i ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_5348807_53   3372 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACTA 3419
                               i    i--    i  --        vv iii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_5348807_53   3420 TCTGATCTTTGATATACCTGACAAACACAAGCAATGGGGAAAGGATTCCC 3469
                         vi    i  i  i vivv  v   ivv  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_5348807_53   3470 TATTTAATAAATAGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTA 3519
                          v  i  i    i   i     v      v  ?   i     i  i v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_5348807_53   3520 AAACTGGACCCCTTCCTTACATCTTACACAAAAATTAA-----GATGGAT 3564
                           ii         v   i   i v  i           -----i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_5348807_53   3565 AAAAAACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 3614
                         v ? i  i    i      v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_5348807_53   3615 TAGGCA-ATACCATTCAGGACATAAGCATAGGCAAAGATTTCATGAATAA 3663
                             ?i- v i -   iv   v vi vv       v i    v ii   v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_5348807_53   3664 AACACCAAATG-----ACAACAAAAGCCAAAATTGGCAAATGGGATCTAA 3708
                         i        v -----i         vv     v ii    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_5348807_53   3709 TTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 3758
                          i   v v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_5348807_53   3759 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 3808
                           i     i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_5348807_53   3809 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 3858
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_5348807_53   3859 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATTTGAACAGACACTTC 3908
                          i     i     v  i?    i                 i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_5348807_53   3909 TTAAAAGAAGACACTTATGTGGCCAACAAACATATGAAAAAAAGTTCATC 3958
                          iv        i ivi vi       i  i  i       i v i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_5348807_53   3959 ATTGTTGGTCAT 3970
                           ii????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


 308 25.19 0.76 5.34  chr2_5370891_5373057      497   627 (1540)    L1M4_orf2#LINE/L1        4   128 (780)  

  chr2_5370891_53    497 AAATATATTTCATATTTATGAATTTTAATAATTAATATTATTAAAGTGCC 546
                            v    ii   i  i   i   vv  v v        i    ii  v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_5370891_53    547 TATACTACCCAAAT-AACACACAGATTCATTGTAATCTCTATCAAAATTT 595
                         v     v       -i ivi         vi i    i          ii
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_5370891_53    596 GAACAACATTCAACATTTTTTACAAAAGTAGA 627
                         ---  i -- --i v      i  i  i v  
  L1M4_orf2#LINE/    104 ---CAGC--T--GCCTTTTTTGCAGAAATTGA 128

Transitions / transversions = 1.75 (21 / 12)
Gap_init rate = 0.03 (4 / 125), avg. gap size = 2.00 (8 / 4)  

2687 23.74 2.86 1.77  chr2_5370891_5373057      944  1676 (491)    L1M4_orf2#LINE/L1      168   908 (0)  

  chr2_5370891_53    944 CAAAATAACCGAAGAAATCCTGAGAAAGTAAAACAAAGTTGGAGACCTCC 993
                           i    i  i  iv    i   i    v i             iv   v
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_5370891_53    994 CATTTTCTAATTTCAAATTATATTTAAAAGCTATATTAACCAACACAGTA 1043
                           i  i i         viv  i vv       i v   i   v     i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_5370891_53   1044 TGGTACTGAAATAAAAACAAAAACATAGACCTATGGAACAGAGTAGAGAG 1093
                                 iv    ii i i v i     i v      i   i v     
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_5370891_53   1094 CCCAGAAATAAACCCAAGAATATATAGTCAACTAATTTTTGACAAGCCTA 1143
                         i               viv  v   i     i i     i      vv i
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_5370891_53   1144 CCAAGAAGACACAACGGTGAAATGGCAGTCTCTTCAATAGATGCTATTGG 1193
                               vv iv   i  v    viii     i     i i   v ii   
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_5370891_53   1194 GAAAACTGGAAACTGGATATCCATATGCAAAAGAATAAAATTAGACCCTT 1243
                           --- ----         ?   i            i  i  i     i 
  L1M4_orf2#LINE/    418 GA---C----AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_5370891_53   1244 ATTTTACACCATACACAAAAATCAACTCAAAGTGGAATAAAGACCTAAGC 1293
                          ii i        i        i        i    vi ?        ii
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_5370891_53   1294 ACAAGACCTGAAATCATAAAACTCCTGGAATAAAACATAAGGGAAAATCT 1343
                         ii    v  i   ii         i i   v        i ? v      
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_5370891_53   1344 ------CCTTAA-TTA-----TGATTTTTGGGATATATCACCAAAAGCTC 1381
                         ------    ii-   -----  i   i vi     iv          v 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_5370891_53   1382 AGGCAGCAAAAATGAAAATAAATAAGTGGAACCACATCAAACTAAAAAGC 1431
                          i   i     ivi      i    i v i  iv       v v    i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_5370891_53   1432 TT-----CTCCAAAGCAAAGGA--AAAAAATTGTAAACAAAAAGGCAGCC 1474
                           -----  i     v v vv --  i   v  ------     i  i  
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTG------AAAAGACAACC 704

  chr2_5370891_53   1475 TATGGATTGAGAGAAAAATTTTGCAAATGATATATCTGATAAAGGCCTAA 1524
                         i ii  v  i       vv         v             i  v  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_5370891_53   1525 TAACCAAAATATAAAAAGAATTCCCACAACTTCACAGGAAAAA-ACAA-C 1572
                           v   i      v      i  ii      iv i iv     -    -i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_5370891_53   1573 AACCTGATTAAAAAATGAACAAAGGATCCAAATAGACATTTTTCTAAAGA 1622
                             ii   ?       ii        iii           i  i     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_5370891_53   1623 AGACATAAAAATGACCAACAGATATATGCAAAGGTGCTTAACATCTCTAA 1672
                            i   v     i    i iii i   v    i    i      v????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_5370891_53   1673 TCAC 1676
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.09 (115 / 55)
Gap_init rate = 0.01 (10 / 741), avg. gap size = 3.40 (34 / 10)  


3418 25.42 0.78 0.22  chr2_5578787_5580726      548  1448 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_5578787_55    548 GAAAAATATTCCACGTTCATGGATTAAAATAATCAATATTGTTAAAATGC 597
                             i    i   i           ii  v v i           i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_5578787_55    598 TCATACTACCCAAAACAATCTACAGGTTCAATGCAATCTCTATAAAAATA 647
                         iv     v      vii        i     i      i    v     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_5578787_55    648 TCAGTGAGATTCTTCAAAGAAATAGGAAAA--AATTCTAAAATTTATAGG 695
                         i   ivivv  i  iiv      v iv  i--i  i        i   v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_5578787_55    696 GACCCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAAAGAATA 745
                           vvii   ii                 i v   i   iv  i     i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_5578787_55    746 AAACTGGAGGAATCACATTATCTGACTTCAAATCATACTACAGAGCTCTA 795
                           ii       v     i vi ii i      v v       i    vi 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_5578787_55    796 ATAACCAAAATGGCATGGTACCAGAATAAAAAGAGACACCTAGACTGATA 845
                         i   i   i ii ii      ii v    ii v     iv    iii  i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_5578787_55    846 GAACAGAATAGAGAACCCAGAAATAAAGCCCTGTATCTACCGTGCACTCA 895
                            i     v    ii           v  v ii  i  iv  vv i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_5578787_55    896 TTTTTGACAAGGGTGCCAAGAACATCCACTGGGGGAAAGGACAGTCTCTT 945
                             i                v   i  v     -    i i     i  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTT 401

  chr2_5578787_55    946 CAATAAATGGTGGTGGGAAAACTGAATATCCAAATGAAGAAGAATGAAAC 995
                            i        v     v     i   ?   v   v i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_5578787_55    996 TAGACCCCT--CTCTCACCATATACAAAAATCAAATCAAAATAGATTAAA 1043
                          i       --   v                i  v       i   i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_5578787_55   1044 GCCTTACATCTAGGACCTCAAACTATGAAACTACTGAAAGAAAACATTGG 1093
                          v i  v  v  i  v  v       i     vi ii          v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_5578787_55   1094 GGAAACTGTCTAGGACATTAAATTGGTCAAAGATTTCTTGAGTAATACTC 1143
                         ? v  v v iiiv   v  iii  i v   v i      iii  vv  v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_5578787_55   1144 CACAAACACAGGCAACCAAAGCAAAAATGGACAAATTGGATCACATCCAG 1193
                           v  i    i     v    v      i  i        iiv    v i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_5578787_55   1194 -TTAAAAAGCTTCTGCACAGCAAAAGAAACAATCAACAGAGTGAAATGAC 1242
                         -       -   i  ii vv    i  v  v     v i       v   
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_5578787_55   1243 AATGGAAAGAAAGTGAGAAAATATTTGCAAGCTATCCATTTGACAAGAGA 1292
                           ivv v    v v                iii  vi  i   i   i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_5578787_55   1293 TCAATAACCAGAATATATAAGGAGCTCAAAAAACTCAACAGGAAAAAGTC 1342
                         iivi  v             i  i   vv v       i iv      v 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_5578787_55   1343 TAATAACCCAGTTTTAAAATGA-CAAAT-ATCTGAATAGACACTTCTCAA 1390
                         v         i  ?v      i-    v-  i          i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_5578787_55   1391 AAGAAGACATTCAAATGGCAAACGGGCATATGAAAAGGTGATCAGCATCA 1440
                                i  v        v  iii   i        i  v   i     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_5578787_55   1441 CTGATTAT 1448
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.01 (7 / 906), avg. gap size = 1.29 (9 / 7)  


 394 24.06 9.43 7.08  chr2_5665358_5671405      501   712 (5336)  C L1M4_orf2#LINE/L1   (20)   888   672  

C chr2_5665358_56    712 AAAAAAAACTACTGGGAAGATGAAAA--TTAGTCACAGAAT---AAAAAA 668
                            ii v    iiii   ii      --iv vi        --- i    
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

C chr2_5665358_56    667 ------------ATATAACGGACATAGGACTTGTATCCAGAATATGTATA 630
                         ------------     v v  i vi                   i  v 
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

C chr2_5665358_56    629 GAATTTCTACAAATCAAAAATAAAAATAAAAATAAAAAAACAAGCAAGCC 580
                            i ii     v    v        v v      -------------  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAA-------------CC 808

C chr2_5665358_56    579 CAGTT-AAAACTGGCTAAGCTGTGTGAACAGATACTTCTC--ATGGAGAT 533
                           i  -    v   vi  ivvi v    i   i i     -- v i    
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

C chr2_5665358_56    532 ACATGTAAATGGACAACAGACACAGGAGAAAA 501
                          i i--      v   i ii    v  i  i 
  L1M4_orf2#LINE/    859 ATAC--AAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.03 (7 / 217), avg. gap size = 5.00 (35 / 7)  

1193 27.62 8.64 4.32  chr2_5665358_5671405     1010  1657 (4391)  C L1M4_orf2#LINE/L1   (230)   678     3  

C chr2_5665358_56   1657 GAAAAATATTTCATACTTATGGATTG-----CT--ATGTAGTTATACTGG 1615
                             i    ii   ii i        -----  --  i v    viv   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

C chr2_5665358_56   1614 C-----TTCTGAGTTTTATCTAT-TACTCAGCATATTCCCAACCAAAATC 1571
                          ----- i iv iv  v     i-v i   i ii v    v i       
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

C chr2_5665358_56   1570 TTAGTAAGCTGTTTCATAGAAATTGACAAGCTGATTC---AATTTATACG 1524
                         ii  iviv  v   iii                  i ---    i   i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

C chr2_5665358_56   1523 TAAATGCAAAGTACTTTAAAAAGCCAAAACAGTTTTAAAATA-AAGAGCA 1475
                         v        i v  iivi  v          i i  i   v -    i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

C chr2_5665358_56   1474 AACTTGGAGGATGTACCGTATCTGATATCAGTATTATTTACTAGATAGCT 1425
                           v        ivi  vv vi ii  v   i- -- i      v v    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAA-A--ACTTACTACAAAGCT 249

C chr2_5665358_56   1424 TTAGTAATCAAAATAATG-AGT-------TAAGGATAGACGGATTTCTCA 1383
                         vi         i i i  -i  -------           iv  vvv   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

C chr2_5665358_56   1382 A--------AGTCAAG--TCAACTAATTCACCCTCACATGTTTACTGCGT 1343
                          -------- i ii  --  v vv   vv    vi    v v iv vvi 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

C chr2_5665358_56   1342 AGATTTTCAACAAAAGCAACAAGGCAATTCAGTGAAGGATACTAAAGTAT 1293
                         v       i    ii iiv    i v     i  i-   v vv v   v 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCT 398

C chr2_5665358_56   1292 TTTTGTCAAATGGTGCTGGGATA-C---ATAATTAGGT---AAAAAATTA 1250
                            iiv               i - ---   ?ii vi ---   i   v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

C chr2_5665358_56   1249 ACTTG-ACTTATGCCTCACACCAATTATGATTATATAATGATTA---TAT 1204
                          v   -  iiv i          --------    i  vi    ---i v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCA--------TATACAAAAATTAACTCAA 490

C chr2_5665358_56   1203 AATCATTCTATATAATTA--TATAATGACATAGAA-TATAACATTTCCAG 1157
                            viv  - ? v vi  -- i   -  vv  i  -     v i iii  
  L1M4_orf2#LINE/    491 AATGGATC-AWAGACCTAAATGTAA-GAGCTAAAACTATAAAACTCTTAG 538

C chr2_5665358_56   1156 AAAAATTGTTTTTTAAAAAAAG----AATCTATGTAACCTTTCAGGG--A 1113
                           i  ---------  v v i ----     vi  i     ---   -- 
  L1M4_orf2#LINE/    539 AAGAA---------AACATAGGNGTAAATCTTCGTGACCTT---GGGTTA 576

C chr2_5665358_56   1112 GGCAAAGATTTCCTAGACAGAGCAT-AAGAGCATTAGCCACAAAAGAAAA 1064
                              v i    i    i vii  i-  i    iv   v           
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

C chr2_5665358_56   1063 AAAAAGGATAACTTAGACTTCATAAAAATTAAAAACATTGGCTTATCAAA 1014
                           v --     v  i        v            v  v iviv     
  L1M4_orf2#LINE/    627 AATA--GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

C chr2_5665358_56   1013 AGGC 1010
                         i i 
  L1M4_orf2#LINE/    675 GGAC 678

Transitions / transversions = 1.30 (100 / 77)
Gap_init rate = 0.04 (29 / 676), avg. gap size = 2.90 (84 / 29)  

3609 22.47 2.58 0.56  chr2_5665358_5671405     4667  5556 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_5665358_56   4667 TGGAAATATATCCTATGGTCATAAGCTGGAAGACTTAATATTGTTAGTAT 4716
                               v      i   v    iiii                    iv  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_5665358_56   4717 GTTGACACTACCTAAAGCAATCTACAGATTCAGTACAATCCTTATAAAAA 4766
                          vii i   v  i   vii             iii      i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_5665358_56   4767 TCCCAATGACTTTTTTTTGCTGAAATAGAAAAAAGTTCATCTTGAATTTT 4816
                              iivi i      -  v     v  v  -- i v   i i  v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA--GCTGATCCTAAAATTC 147

  chr2_5665358_56   4817 ATATGGAATCTCAAGGAATCCTAAATAGCAAAAATATTTTTGAAAAAGAA 4866
                                 viv     i i  vi      v    i v i           
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_5665358_56   4867 ---CAAAGCTAGAGGACTCATACCTTTTGATTGCAAAGC--A-TATAAAG 4910
                         ---     i i         i  i iiii   v    i -- -  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_5665358_56   4911 CCACAGTAATCAA-ACAGAGTGGCACAGACATA----TAGACAGACAGAC 4955
                          i           -    v    i  v i    ----      v i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_5665358_56   4956 AAACAGACTAGAATACTGAGTCCAGAAATAAACC-GTAGTGTATATGGTC 5004
                         v  ii  v      vvv                 -i  -ii v       
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGTC 346

  chr2_5665358_56   5005 AAAAGATCTTCAACAAAAGTGCTAAGATCATTCAATATGGGAAGGAA-AA 5053
                           vv   i   i    ii    i    i        i-     i   - i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAG 395

  chr2_5665358_56   5054 TCACTTCAAGAAATAGTGGTGCAAAAATTTAATATCCACATGCAAAAGAA 5103
                           vi     v    i   v  vi v  i vi   ?               
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_5665358_56   5104 TGAAGCTGGACCTTTATCTTTTAGCATATATTAAAAGTAAC--AAAATGG 5151
                              i      ii  i  ivi v      iv    v    --       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_5665358_56   5152 ACTGAAGACATGAAT-TGACACCTAATACTATAAAACTCCTAGAAG---- 5196
                          iii?    v i   - i v v    v            i      ----
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_5665358_56   5197 CATAGGGGAAAAACTTCATGACACTGAATTTGACAATAATTTCTTGGCTG 5246
                               ? v   v    i    vi  ii  v i    ii      i v i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_5665358_56   5247 CGACACCAAAAGCACAGACAACAAAAACAAAAATAGATAAATGGTACTAC 5296
                         i               ii        iv              v v   v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_5665358_56   5297 ATCAAACTGAAAAACTTTTGTGCATAAAAGAGCACAATTAATAGAGTAAA 5346
                               v v              v v    ii   v  i  v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_5665358_56   5347 AAAA--ACCTACAGAATGGGAGAAAATATTTGTGAATAATACATCTGATA 5394
                           i --   i                      ii   v   i        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_5665358_56   5395 AAAGATTAATATCTGTGATATATAAATAACTCCTATAACTCACCTAC-AA 5443
                          ii  i vi    iivi         v     i  i      viv i-  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_5665358_56   5444 AAGCCAAATAACCCAATTAAAAAATAGATAAAAGGCTTGAATAGACATTT 5493
                            v              ?      i ii   i ii              
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_5665358_56   5494 CTCTAAAGTTGACATATAAATGTCCAATAAGTATATGAAAATATATTTAA 5543
                            i    vv  i   i     v        i i       v  ii i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_5665358_56   5544 CTTCATTAATCAT 5556
                          v   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (125 / 71)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.75 (28 / 16)  


3010 26.73 0.66 0.77  chr2_6188517_6193376.rev     3460  4368 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_6188517_61   3460 TGGAAACACATCCCATTCTCATGGAGGGGTAGAATCAATATTGTGAAAAT 3509
                               v i       vi       vv  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_6188517_61   3510 GACCACACTGCAAAAAGTAATCTACAAATTCAATGCAATTTCCATCAAAA 3559
                          i v i   v vv   v i       i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_6188517_61   3560 TATCA-CCATCATTATT-CAAAAAAAAACTGGAAAAAAAAATCCTAAAAT 3607
                          vi  - iii v  v  -  i   ----- v  v  ivvi          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA-----TTGACAAGCTGATCCTAAAAT 145

  chr2_6188517_61   3608 TCATACAGAATCAAAAAAGAGCCCACAA-AGCCAAAGCAAGACTAGGCAA 3656
                              ii   viiv  ii  -    v  -       i   vvi iiiv  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_6188517_61   3657 AAAGAACAAATCTGGAGGCATCACACTACCTGACTTCAAACTCTACTATA 3706
                         i         vi      vv       v  ii i      vii     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_6188517_61   3707 AGGCCATGGTCACCAAAAAAGCATGGTACTGATACAAATATAGGCACATA 3756
                          i  i ii  v i   i v  ii        ii i  iv    i  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_6188517_61   3757 GACCCATGGAACAGAATACAGAACCCAGAAATAAAGCCAAGTACTTACAG 3806
                           i v      i     vv   ii           v   vii i   ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_6188517_61   3807 TCAACTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAATGACA 3856
                             i    i  i     i vviv   i v   vv i        vi i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_6188517_61   3857 CCCTATTCAACAAATGGTGCTGGGATAATTGGGAAGGCCCATGTAGAAGA 3906
                         vi  v                    i  i   iv ?v v    i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_6188517_61   3907 ATGAACTTGGATCCTCATCTCTCACT-TATACAAAAATTAACTCAAGGCG 3955
                              v     i  ii i   v   i-                   iii 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_6188517_61   3956 GATCAAGGACTTAAATCTGAGACATAGAACCATAAAGGCTCT-AGACGAT 4004
                              ?i   i     v i   vv  i   i     -i    -   v  v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAA 543

  chr2_6188517_61   4005 AACATCAGGAAAACCCTTCTAGACATTGGCTTAGGCAAAAACTTAATGAC 4054
                              vi ?iv  vi    vv   v    v        viii  vv iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_6188517_61   4055 CAAGAACCCAAAAGCAAATGCAACAAAATCAAAGATAAATAGATGGGACT 4104
                         i v  vv         v v         vv   i   i   i  v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_6188517_61   4105 TAATTAAACTAAAAAGCTTCTTCGCAGCAAAAGAAATAATCAGCAGTGTT 4154
                          v  i   v v    i   i vi  vv    i  v iv    iv iv  v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_6188517_61   4155 AACAGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTACACATCTGA 4204
                           v              i           v  ii   vii i i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_6188517_61   4205 CAAAGGAGTAATATTCAGAATCTACAAAGAATTCAAACAAATCAGCAAGG 4254
                         i  i   v vi   i      v  i      i  vv    v   ii  vi
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_6188517_61   4255 AAAAAGCAAACAATCCA-TCAAAAAGTGGGCTAAGGACATGAATAGACAA 4303
                             ii    i  i   - i?    i     v     iv          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_6188517_61   4304 TTCTCAAAAGAAGATATACAAATGGCCAGAAAGCATATGGAAAAATGCTC 4353
                              v                      iv     i   i   i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_6188517_61   4354 AACATCACTAATTAT 4368
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (137 / 102)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


1375 24.61 11.37 3.58  chr2_6227910_6230020      501  1142 (969)    L1M4_orf2#LINE/L1      136   827 (81)  

  chr2_6227910_62    501 ATCCCAAAATTCATATTAAAGAGAAAAGGAATCAGAAT-----------T 539
                             i           vi  iv v  i   vi      ----------- 
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_6227910_62    540 TTT-AAAGACAAGAACTAAGTTAATGGACT-ATAC----CAGATTCAAGA 583
                         i  -   i v      v     iiv     - i  ----  iv     i 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_6227910_62    584 ---ATTATAAAGCTAGAGTAATCAAAGCAGTGTACAATTGG-AGAAAAAA 629
                         --- i  i       v         ii      ivv i   - v  ii v
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_6227910_62    630 AACCACATACATCAATGGCAAAGAA--AATAGTTCAGAAATTGATCCACA 677
                          iv  i   v        v v    --i v   i       vi i   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_6227910_62    678 TGTACACTGACAACTTATTTTTGACAAGGCTGCAAAGTCAAATCCATGGA 727
                         ii vi iv v   i v     i       v   v   v v v  v    i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_6227910_62    728 GAACACATAGACTTTTAGACAAATAGTGGCGAG-CAATTGCACATT-ACA 775
                            viv    v     vi      i   vi i -   i  v i ?i-   
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_6227910_62    776 CGTAAAAAAATAAAATGAAAGCAAACTCGTTCTATGCCCAGATCACTCCA 825
                         i i    i   i  i -----iii  i ---   ---  ---    v   
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGT-----TGGACCC---CTA---CC---TCACACCA 471

  chr2_6227910_62    826 TA-ATTAAAATTAAACCAAAATATATCATAGATTCACATGTAAACCCTAA 874
                           - iv        vi      iv    ?   iii v      ivv    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_6227910_62    875 AACTACAAAACTTCTTGAAAAAAACATAGA-------CTTCCAGTTAGAC 917
                              i      ii v   i         i-------    --  --   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC--GT--GAC 567

  chr2_6227910_62    918 AAGAATTT---TTAGACAATAATTTAT---ATATGATACGAAAAGCATGA 961
                         -----i  ---    i    ii   v ---      i  v       ii 
  L1M4_orf2#LINE/    568 -----CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_6227910_62    962 ----------------TAGATAGA--AGAATACAT-----TTAAAAACTT 988
                         ----------------      i --i  v v   -----          
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_6227910_62    989 CTGCTCTTTGAAAGACGCTTTTAAGAGACTAAAAAGACA--TCACAAACA 1036
                         i  iv   ii  i   i  v i    i v i        --i    i vv
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_6227910_62   1037 GGGAGAAACTATT-GCAAA--ACATATCCGATCTAGGTCTTGTATCTCTA 1083
                                 v    -     -- i     i   vvi  v        ivv 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_6227910_62   1084 ATATATAAAAAACTCTCAAAAATCAGCAATAAAAA-----ATAACA-AAT 1127
                                  i      i v  v   ii        -----     v-   
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_6227910_62   1128 TTAAAAATCATCAAA 1142
                          ?      viv    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAA 827

Transitions / transversions = 1.46 (92 / 63)
Gap_init rate = 0.04 (28 / 692), avg. gap size = 3.43 (96 / 28)  

 393 20.18 1.83 0.92  chr2_6227910_6230020     1511  1619 (492)    L1M4_orf2#LINE/L1      799   908 (0)  

  chr2_6227910_62   1511 ACAAATTAATTAATTAAAAAA--GTCAAAAATATTTGTACAGGCATTTTG 1558
                               v vii    ?     -- v    ii-     v i  i     iv
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGG-ATTTGAATAGACATTTCT 847

  chr2_6227910_62   1559 CCAAAGAAGATATTCTGATGGCAAATAAGTATATTAAAAGATGCTCAATA 1608
                                      v vi     v      i i  v             i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_6227910_62   1609 TTATTAGTCAT 1619
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.33 (12 / 9)
Gap_init rate = 0.02 (2 / 110), avg. gap size = 1.50 (3 / 2)  


3281 18.44 4.29 1.82  chr2_6319734_6321495      501  1270 (492)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr2_6319734_63    501 AAAAATGGAGAAGCCAATCCTCAAATTCACATGACATTGTAAGAGATCCT 550
                          i    v  v    ii     v       i   iv v  i   i  i  v
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_6319734_63    551 GAATAGCCAAAATAATCTTGAAAAAGAA---CAAACTTGGAGGACTCACA 597
                                     i               ---    v              
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_6319734_63    598 CTACCCAATCTCAAAACTTACTACAAAGTTACAGTAACAAAGTCTATGCG 647
                           v      i                  i        iv   v vi  i 
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_6319734_63    648 GTGCTGACAGATGGATA--CTCACAGTTCAGTGTATTAGAATCGAAGGTG 695
                           i   i  v v     -- vi i  v   i  v v      i  ii  v
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_6319734_63    696 CAGAGATGAAAACACAGAACAATTGTCAACTGCTTGTTGGTGTGGGCACC 745
                             i  i  vv  i v viv  v     i  v  v i iiiv   ii  
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_6319734_63    746 AAGAC-ATTCAATGGGGACAGAATGCCCTTTATAA--AATGATACTGGAG 792
                              -            v     ivi    vi  --    i i    ii
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_6319734_63    793 CAATTACATAGCCACATACAAA-GAATGAAGTTGGACACCTTCCTCATAC 841
                            i iv   ?      i    -              v   v     i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_6319734_63    842 AA-ATACAAAAATTAACACAAAATAGATGAAAAACCTAAATATAAGAGC- 889
                         v -              v      i   v ? i        i       -
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_6319734_63    890 AAAAC---------CTTAGGAGAAAACGGTGGGT---AATCTTCATGACC 927
                              ---------     i       i- i  ?---       i     
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACA-TAGGNGTAAATCTTCGTGACC 568

  chr2_6319734_63    928 TAGGATTTGGCAAAGACTTTTAGGATGTGACACCAAAGGCATGAAAACAA 977
                          v  i  v     v ii  i vi   i          i   i--  i   
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC--AAGCAA 616

  chr2_6319734_63    978 CAAAA------ATAGATAAATTGGACTTCATCAAAATATAAAGCTTTTAT 1021
                              ------                          vv   i     i 
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_6319734_63   1022 GCTTCAAAGGACGCCATCAAGAACATTGAAAAAAAAAACCTTACAACTCA 1071
                                     i i        - v      i ---------    i  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAA-AGTGAAAAGA---------CAACCCA 706

  chr2_6319734_63   1072 CAGAATGGGATAAAATATCTGCAAATTACATATCTAATAAGCATCTAGTA 1121
                                   v       i       i i      i     viv  v   
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_6319734_63   1122 TCCAGAATA-ATAAGGAACTCTTACAACAAAGCAATAAAAAGACAAATA- 1169
                                  -    i             vv ii                -
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_6319734_63   1170 CCCAATT-AGAAATGGGCAAAGGATTAGAGTA-ATAGTGTCTCAAAAGAA 1217
                                - i                v  i  - i v -    v      
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT-TCTCCAAAGAA 855

  chr2_6319734_63   1218 GATACACAAATGGCCAACAGCCATGTAAAACTATGCTCAACACCATCAGT 1267
                             i            i iv  ii i   vv          i  ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_6319734_63   1268 CAT 1270
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.53 (84 / 55)
Gap_init rate = 0.02 (19 / 789), avg. gap size = 2.47 (47 / 19)  


3092 28.30 0.44 0.44  chr2_6418464_6424323.rev     4461  5368 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_6418464_64   4461 TGGAAGAACATTCCATGCTCATGTATAGGAAGAATCAATATCGTGAAAAT 4510
                              ii i  i     i     v  v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_6418464_64   4511 GGCCATACTGCCCAAGGTAATTTATAGATGCAATGCCATCCCCATCAAAC 4560
                            v     v     iv i  i  i    v   i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_6418464_64   4561 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 4608
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_6418464_64   4609 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACCATCCTAAGCAAAAG 4658
                                 viiv  ii  v  viv  v     i  v   i i iv  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_6418464_64   4659 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTATAAGG 4708
                                 i      vv       v  ii i      viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_6418464_64   4709 CTACAGTAAACAAAATAGCATGGTACTGGTACCAAAGCAGAGATATGGAT 4758
                                  v   i i  ii         i iv iiii   v    i   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_6418464_64   4759 CAATGGAACAGAACAGAGGCCTCAGAAATAACATCTCACATCTGCAACCA 4808
                                 i    iv   ivii         vvi vi    i iiiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_6418464_64   4809 TCTGATCTTTGACAAACCTCATAAAAACAAGAAATGGGGAAAGGATTCCC 4858
                         vi    i  i     ivv vvi  i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_6418464_64   4859 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4908
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_6418464_64   4909 AAACTGGATCCCTTTCTTACACCTTATACAAAAATTAATTCAAGATGGAT 4958
                           ii    i    vi  i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_6418464_64   4959 TAAAGATTTAAATATTAGACCTAAAACCATAAAAACCCTGGAAGAAATCC 5008
                         i ?   ii     i v   v       i      vi i i       v v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_6418464_64   5009 TAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGACTAA 5057
                             ?i- v i -   iv   viv  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_6418464_64   5058 AATACCAAAAGCAATGGCAAAAAAAGCCAAAATAGACAAATGGGATCTAA 5107
                         i i          vvi    v     vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_6418464_64   5108 TTAAACTTCAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5157
                          i   v  v i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_6418464_64   5158 AGGCAACCTACAGAATGGGATAAAATTTTTGCAATCTACCCATCTGACAA 5207
                           i     i           v     v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_6418464_64   5208 AGGGCTAATA-CCAGAATCTACAAAGAACTTAAACACATTTACAAGAAAA 5256
                         i  i  vi  -       v  i        ivv   vv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_6418464_64   5257 AATCAAACAACCCCATCAAAAAGCGGGCAAAGGATATAAACAGACACTTC 5306
                          iv    i     v  i?    ii           v i  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_6418464_64   5307 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5356
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_6418464_64   5357 ATCACAGGTCAT 5368
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (153 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


1693 26.61 13.89 0.73  chr2_6466710_6470722      425  1108 (2905)    L1M4_orf2#LINE/L1        1   774 (134)  

  chr2_6466710_64    425 TGGAAATATATACTTTGT-CATAGAATGGAAGATTCGATGTTGTCAA--- 470
                               v    v iv   -   i  v       i ii  i    i  ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_6466710_64    471 -------CTCTCTCAATTTGTCTATAGATTCAACACAATTCCAATCAA-- 511
                         -------   i iv    vi    i         i    i  v     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_6466710_64    512 ------------TTTATATAGAAA--GACAAAGTAA--CTA--------- 536
                         ------------   v ii     --     iv i --   ---------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_6466710_64    537 ------------GAACCCATAATA--CAAA------TTGAAAAAGAAAAA 566
                         ------------ i     v    --    ------           i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_6466710_64    567 ACAAAGTTAGGAGGACTCACATT----GATGCCCAGATTTGATGTAAAGC 612
                         -       -            i ----i  vi v i i  iv ii     
  L1M4_orf2#LINE/    201 -CAAAGTT-GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_6466710_64    613 TACACCACTCAAGAC----TGACATTA-CAGAAAGAGTGGACATCTAGAT 657
                             vi v       ----  ii i i-  v  i  - i     v     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGAT 297

  chr2_6466710_64    658 CAATGGACAT-GAAT--AGAATCCACATATATAATCATGCGTATATGCCC 704
                                -  -    --   i    v v   v vi   i i v    vi 
  L1M4_orf2#LINE/    298 CAATGGA-ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_6466710_64    705 AGTTGATTTTTATCTAAGGTGCAAAGGCAATTCAGTGGAGATGGGATAGT 754
                          i        iiv v i     v   i v     i   i  vi i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_6466710_64    755 CTTT---ACAAATGATGCTGGAACAATCAGATTTCTATATGTAATACAA- 800
                             ---       i      i    iii   v? i i   i  v v  -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_6466710_64    801 GAAACCACAATCAATATCTTGCACTCTACACAAAAATTAACTCTATAAGG 850
                            iiii-i i vv  i  ii   iv  i              v v v  
  L1M4_orf2#LINE/    447 GAAGTTG-GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_6466710_64    851 ATCATAGACCTAAATACAAAACTGAAAATTACAAAATTTCTAGTTGAGAA 900
                             ?          ii  i viv    i  i    i ii   vv  i  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_6466710_64    901 CATAGGAGGAAATCTT-ATGAT-TTGAA--------------CTTAGAT- 933
                               ? v       -i   i-   ii--------------       -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_6466710_64    934 TAAATTCAAAAAAATCATCTATTAAAGAAAAAAT-GATAAATTGAATCTC 982
                          i vvi     iv iv v v iv           -         i ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_6466710_64    983 ATCAAAAGAAAGAACATCTACTCTTTAAAATATAGTATTGAAAGAAAGAT 1032
                                vv  i   v i iiv   i   iv i v   ii i i iv  v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_6466710_64   1033 AAGGCAGCT-ATACATTGGAA--AAATATTTTTAAATCACACATTTTGCG 1079
                            i  i i- i v v   i --        vi      i i  i viii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_6466710_64   1080 AAAGACTTGCATCCACAATATACAAAGAA 1108
                          ii      i     v      i      
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAA 774

Transitions / transversions = 1.89 (117 / 62)
Gap_init rate = 0.03 (27 / 774), avg. gap size = 3.70 (100 / 27)  

2707 25.14 4.53 1.70  chr2_6466710_6470722     1796  2678 (1335)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_6466710_64   1796 TGAAAACACATCC-ATGCTCATGGATATG--AGA------------AAG- 1829
                           i   v i    -   i        -  --   ------------   -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-TGGAAGACTTAATATTGTTAAGA 49

  chr2_6466710_64   1830 TGAACATACTGCCAAAAGCAATGTACACATTCAATGCAATTTTCATCAAA 1879
                           ivv     v  v   vii  v    v      i     iiii      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_6466710_64   1880 ATACCACTATGATGCCTC----ACAGAACCAGAAAAAAAC-AATCCTAAA 1924
                           v   ---- v     i----i     -- vvi v  i -i        
  L1M4_orf2#LINE/    100 ATCCCA----GCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAA 143

  chr2_6466710_64   1925 ATTCATATGGAATCAAAAAAAGAGCTCACA-TAGCAAAAGCAA----GAT 1969
                                     -- viv  i ii i  v -    v   i   ----  v
  L1M4_orf2#LINE/    144 ATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_6466710_64   1970 GAA-----ACAAATCTGGAGGCATCACATTACCTGATTTTAAACTATGCT 2014
                         i  -----     vi      vv     i v  ii    i   viv i  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_6466710_64   2015 ATAAGGCTATGGTCCTCAAAACAGCATGGTACTGGTGTAAAAATAGGCAC 2064
                          i  i    ii  vv    i    ii         ii   ii    i  i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_6466710_64   2065 ATAGACCAATGAAACAGAATAGAGAACCCAGAAATAAACCTAAACACTTA 2114
                              i     i  i     v    ii             i v   i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_6466710_64   2115 CAGCCAACTGATTTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGG 2164
                         ii i   i       i     i vviv   i v   vv i         i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_6466710_64   2165 ATATCCTATTCAACAAATGGTGCTGGCATAACCAGCAAGTCAGATGTAGG 2214
                            vi  v                  v i   ii vv ?i  v   i ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_6466710_64   2215 AGAGTGAAACTGGATCCTCATCTCTCACTTTATACAAAACTCAACTCAAG 2264
                            i    ii    i  ii i   v   iv         v i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_6466710_64   2265 ATGGATCAAAGACTTAAATCCAAGACCTGAAACCATAAAAATTCTAGAAG 2314
                                 ?    i     vi    v  i    i      v ii      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_6466710_64   2315 ATAACATCAGAA-AAATCCTTCTAGACATTGGCTTAGGCAAAGATTTCAT 2363
                          v     vi ?i-     -   vv   v    v        v i    v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_6466710_64   2364 -GACCAAGGAC-CCAAAAGCAAATGCAATGAAAACAAAGATAAATAGGTG 2411
                         -  i-- v   -         v v    ii   iv   i   i   ii v
  L1M4_orf2#LINE/    591 AGAT--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_6466710_64   2412 AGGCTTAATTAAACTAAAGAGATTTTGCATGGCAAAAGAAAC-AGCA-GA 2459
                         i i   v  i   v v  i iv     iiivv    i  v  - v  -  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_6466710_64   2460 A--TAAACAGACAATCCACAGGGTGGGAGAAAATATTCACAATCTGTACA 2507
                          -- i  v      i      ii              ii   viii  i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_6466710_64   2508 TCTGACAAAGGATTAATATCCAGAACCTACAAGCAACTCAAACAAATTAG 2557
                              i  i   i vi         iv  i  iv     vv    v ---
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--- 785

  chr2_6466710_64   2558 CAAGAA-AAAAAAACAAACGATGCCATCAAAAAGTGGGCTAAGGACATGA 2606
                            v  -     i     ii iv v  i?    i     v     iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_6466710_64   2607 ATAGACAATTCTCAAAAGGAGATATTCAAATGGCCAACAAACATGTAAAA 2656
                                v     v    i      v           i  i  ii i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_6466710_64   2657 A-ATGCTCAATATCACTAATTAT 2678
                          -        i    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (135 / 83)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.29 (55 / 24)  

 244 25.66 3.54 0.00  chr2_6466710_6470722     3412  3524 (489)    L1M4_orf2#LINE/L1      792   908 (0)  

  chr2_6466710_64   3412 TAAAAAAAGAGA-AAACAAACTAATAAATGCATAAAAGTTTTGAACAGAC 3460
                               i v i -  v v  i ? v     vii   i v      i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_6466710_64   3461 --TTCACAATATAAGATACATGGATGAAAAATAAACACATGTAAAGATGT 3508
                         --   v v v v      i iii   ivv     i      v       i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_6466710_64   3509 TCAACG-CAATTAGTCA 3524
                              i-  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (15 / 13)
Gap_init rate = 0.03 (3 / 117), avg. gap size = 1.33 (4 / 3)  


1754 23.92 7.92 0.17  chr2_6480563_6482123.rev      501  1081 (480)    L1M4_orf2#LINE/L1      283   908 (0)  

  chr2_6480563_64    501 GGTAGACATCTACCTCTATAAGACAGAACTGAGAATCCAAAAATAAATCC 550
                          i       v  vv  v  iii i    i     i    i       i  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_6480563_64    551 A--CAT---------ATTGATTTTTGACAAAAATGCCAAGGCAATTCATT 589
                          --   ---------         i     iii       i v     v 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_6480563_64    590 AGGGAAAGAACAGTGTGTTCAACAAATGGTGCCTGGACAACTGGATATAA 639
                         i         i   v v               iv             ?vv
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_6480563_64    640 A-ATCCAAAAAGATAAACTTAGACCT-----TCACATAAGTCAGAAAAAT 683
                          -  v     ii  i  v  i    i-----     iv vvi v      
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_6480563_64    684 TAATTCAAAATTGATTATATGAT-TACTTCTAAAAGCTAAAACAATAGAA 732
                            i       v   i ? -  i-  vv v   i         v   i  
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWA-GACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_6480563_64    733 CTTTTGG--GAAAAGATAGGAGAAAATCTTCAAGACATTGGGTTAAGGAA 780
                           i  i --     v     ? v        iv   v        i v  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_6480563_64    781 AAATCTCTTAGATTCTATACTGAAATCATAGTCTGTAAAAGAAAAAAATG 830
                         vii i        viv i  ii   v  i iv vii           vv 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_6480563_64    831 ATAAATTAGACTTTTTCAATGTTCAAAAATTTTGTACTGCAAAAGATAAT 880
                                i     iv    vi  v    v      i  v    i  i v 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_6480563_64    881 ATTAAAA---TAAAAATACAAACAGCAGACTG--AGAAAATAT--GCAAA 923
                           i  i --- i    v    v vi    v  --         --     
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_6480563_64    924 ACACATATCTAATAAAGATCTTGTATTCAAATTTTCAAAAGAAATGT-AT 972
                         v  i      i    i iv       i  i v v vv      v v - i
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_6480563_64    973 AACTCAATAA--AAAATAC------CCCAATAAGAAAGTGGGCAAAATGT 1014
                                   --    v  ------      v?i   i        ivi 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_6480563_64   1015 ATGAACTAACATTTCACCCAAGG---TATATA--TG---AATAAGTACAT 1056
                         v    ivi       v  v   i---    i --  ---      i    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_6480563_64   1057 GAAAA--TGGCTATCATTAGTCATTGG 1081
                              --  vii v   i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (73 / 62)
Gap_init rate = 0.03 (17 / 626), avg. gap size = 2.76 (47 / 17)  


1582 27.27 11.60 3.59  chr2_6495844_6498067.rev      897  1732 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_6495844_64    897 AGATATACTAAGGTCCTGTTTTGGAAAATTTAATATTGTTAGGATATGAA 946
                               v i v v  v  vv      i i            i   ivv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_6495844_64    947 TTATCATAAAATTGATATAGAGATTTAATACA--CTCAATCAAAATCTCA 994
                          vv  viv        v  v     i  ii  -- i v         i  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_6495844_64    995 GCAGTCTTTTTTGAAGCAATTGACA----GATTCTAAAATATATATTATA 1040
                           v i        v  v        ----   i       vi    viv 
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_6495844_64   1041 ATGCTAATCATCTAGACTCACCAAAAGAGTTTTGAAATAGTAAAACAAAT 1090
                             v ivv i i   v vi      v i i      v  v i      v
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_6495844_64   1091 CTGGAGGACTTAT--TGCCTGATCTGAAAAAT-ACT-----------GTA 1126
                         i         i i-- v  ii  i v    v -   -----------   
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_6495844_64   1127 ATCAGGACACCATGACAGAAGCTTAGGGTCATTAACATAGATAGATTAA- 1175
                             i    vii  ii vvi  v  i  --  vi     --     i  -
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGG--ATAGACATA--TAGATCAAT 301

  chr2_6495844_64   1176 ---GCAGAATTAAGAATTCAGAAATAGATACACACATACATAAGTAAGAC 1222
                         ---ii      i   i i        i iv  i    vi  iivi  vvv
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_6495844_64   1223 ATTTTCAACAAA-----------CATTGAAGTGGGAAAAAATGAGTGCTT 1261
                               i    i-----------    v  vv      i   -   -   
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT-AGT-CTT 399

  chr2_6495844_64   1262 TTCAACAAATGATGATGGACGAATTGGATGTATTTATCCA---------- 1301
                                    i  v   ivv  i     i?vivi  v  ----------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_6495844_64   1302 ---GCACCATTTCCTCATATAATTCATTTCCTCAGTAATTCAAAAATTAA 1348
                         --- v   vi v     i i----   ----------  v          
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACAC----CAT----------ATACAAAAATTAA 485

  chr2_6495844_64   1349 CTTGAAATACGTAACAAAATTAAA-----GAGC-AAAATGATAAAAAAAC 1392
                           ii    ivi v ? i vi    -----    -    iv      --- 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA---C 532

  chr2_6495844_64   1393 TTCTGCAAG----CATACAGACAAGATCATTGTGAATTTAAAGTAAACAC 1438
                          ii iv   ----    vi?ii  -   v i    vi  iiiv  ii  v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_6495844_64   1439 ACATTTCTTAG----GATACAAGAAGCATGAAC--CATGGGAAGAAATAA 1482
                         vvi        ----  i  v i     ii i --  vii   i     i
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_6495844_64   1483 ATAAAGTTGACAAATTTTA-AAAAATTA----CTTTTG------AAAGGC 1521
                              v v   ----  i -v       ----      ------     v
  L1M4_orf2#LINE/    632 ATAAATTGGAC----TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_6495844_64   1522 C-CTGTTACAAGATTAAAAGTACAGCCAA-ACATTAAGAGAAAATCTTCA 1569
                          -  i i vi i v i   iv   i  v - v v ii        v  ii
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_6495844_64   1570 CAATACATTTACCTGACAAGGGGATCATATTTAGAATATATAAGAAACTC 1619
                            vv   v  i    i     iv ii   ii           ii     
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_6495844_64   1620 TTACAGTGAAACAA--GAAGGGCTAAAACAGC-------AAAAAT----- 1655
                              iivv  i  --i  i i --   i i -------      -----
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGAC--AAATAACCCAATTWAAAAATGGGCA 825

  chr2_6495844_64   1656 ----ATTTGAATAGACCCTTCATTAAAGGAGATATATGGATGA--GAAAA 1699
                         ----            vi   vii    i       iii   i--i v  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_6495844_64   1700 ACACATGAAAAAATGTTCAGTATCATTGGTAAT 1732
                         i          i   i   ii    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (134 / 91)
Gap_init rate = 0.04 (32 / 903), avg. gap size = 3.97 (127 / 32)  


1978 27.56 1.89 0.94  chr2_6732650_6735634     1302  1936 (1049)    L1M4_orf2#LINE/L1        4   644 (264)  

  chr2_6732650_67   1302 AGAGATATTCCAAGTTCAGGAATAGAAAGATGCGATATTTTCAAGCTTTA 1351
                          i      i   v     v i  v i    ivii     v i   v vvv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_6732650_67   1352 ATTTCTTTCCAACTTGATCTATAGATTCAATGAAATCCCAGTCAAATTCC 1401
                          v v  ii    v        i        i v      vi     v   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_6732650_67   1402 CAG-TGAGTTATTTTTTGATATCGACAAAATGATTCTAAAGTTTATATGG 1450
                            -  vv  v   viv  v  i     iv    i     i  i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_6732650_67   1451 AGAGAAAAAAGACCCAGAATAACCAACTCAACATTGAAAGAGAATACCAA 1500
                          i viv  ii           i    vv   iv      i    v v   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_6732650_67   1501 TGTCTGAGAGCTGCCACTGTC-AACTTCAAGACT------AAAGCTACAG 1543
                         v  iv   ii  vv    vi -  i     i   ------          
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_6732650_67   1544 TCAACAATCAAAATAGTGTAGCACTGGTG-AACAAAAGACAAATAGATCA 1592
                          ----      i i     i i     ii-  vi v     v        
  L1M4_orf2#LINE/    254 T----AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_6732650_67   1593 GTTGGATGGAATACAGAGCCAAGAAATAGACTCATATAAATATAGTCACC 1642
                         i v i  i    vv    i v       i  i    i vv   i    vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_6732650_67   1643 TAATCTTTGACAAAGACGCAAAGACAAAACAATGGTGCAAAGACAGTATT 1692
                          i  i  i     i ii  v     v vv      v v  ii i   v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_6732650_67   1693 TTCAACAAACAGTACTGGAGCAACTGGATATCCTAAAGCCAAA-ACTGAA 1741
                                  ii  i    ii          ?  vv v  v   - v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_6732650_67   1742 TCTAGACACGGACCTGACACCCTTTTAGAAAACTGACTCAAAATGGACCA 1791
                         vi i   v vv    v     v v vvi    i i            i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_6732650_67   1792 TAAACCTAGATGTAA-AGCATAAAAATATTAAAGTCCTAAAAGATAACAT 1840
                         ? i     i      -   -     v   v   v  i  i    v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_6732650_67   1841 AGGAGAAAA-CTTAGCTAACTTTAGGTATAGCAATAAATTTTTTAATACA 1889
                            ? v   -   v - i  i  i   vvi     iiv  i  vi   ii
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_6732650_67   1890 CCACCAAAGGCATTATTCATGAAAGAAATAATTTATAAGCTGAACTT 1936
                         v       i   iv viv ii       v   vv    ii  i    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

Transitions / transversions = 1.10 (90 / 82)
Gap_init rate = 0.02 (10 / 641), avg. gap size = 1.80 (18 / 10)  

 668 23.22 7.87 4.12  chr2_6732650_6735634     2227  2493 (492)    L1M4_orf2#LINE/L1      632   908 (0)  

  chr2_6732650_67   2227 ATAAGCTGAATTTTATTAAAATTAAAAATGTTTAT-----AAAAGGCACT 2271
                             ii  i i  i  i           iv   i -----   i i    
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_6732650_67   2272 GTCAAGAGTGTGAGAAGACAAATCAAAGACTGAGA-AAAACATTTGCACA 2320
                         i      iv    i       vi  v   v  i  -    i       --
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-- 729

  chr2_6732650_67   2321 AGTCATGTCTTTCACGTCTTACAAAGAGCTGTTATCCAAAACATACAAAA 2370
                          i    i -------i   v i  i ii  vv      i  i   i   i
  L1M4_orf2#LINE/    730 AATCATAT-------ATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_6732650_67   2371 AAACTCTTAAAACTAAACAATAAAA---CA--TGAAC-------AAACTG 2408
                           -      v    v  i       ---  -- i v -------   v  
  L1M4_orf2#LINE/    773 AA-CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_6732650_67   2409 ---AAAAGACCTTAAGAGACATCTTACCAAGGAAAATATAACAGATGGAA 2455
                         ---   i  ii v  v      i iv    i   i     -  i    vv
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA-CAAATGGCC 870

  chr2_6732650_67   2456 AGTGTGTATACAAAAAGTTGCTCAACATCATATGTCAT 2493
                          i iv i i ii     v            ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.26 (43 / 19)
Gap_init rate = 0.04 (10 / 277), avg. gap size = 3.20 (32 / 10)  


2954 28.51 0.44 0.11  chr2_6777683_6779955      877  1781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_6777683_67    877 TGGAAACACAACCCATGCTCATGGATGGATAGAATCAATATTGTAAAACT 926
                               v i v      i        v iv   v i        v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_6777683_67    927 GATCATACTGCCAAAATCAATCTACAAATTAAATGCAATTCCCATCAAAA 976
                          iiv     v  v    ii       i   v  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_6777683_67    977 TACTTGCCATCATTCTTCACAGAACTAGAAAAAACAATCCCCAAATTCAT 1026
                          v iv  iii -  i  ii     v v  v  ivii    iv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_6777683_67   1027 ATGGGATCAAAAAAGAGCCCACATAACCAAAGCAAGACTAAGCAAGAAGA 1076
                             i viiv  ii  v  viv   i     i   vvi i iv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_6777683_67   1077 ACAAATCTGGAGGCATTACGTTACCTGACTTCAAACTATACTATAAGGCC 1126
                              vi      vv i  ii v  ii i      viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_6777683_67   1127 ATAGTCACTAAAACACCCC--TCCTGATATAAAAACAGGCATATAGACCA 1174
                          i   v ii  i   vivi-- v   ii    ii i  i        i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_6777683_67   1175 ATGGAACAGAATAGAAAACTCAGAAATAAAGCCAAATATTTACAGTTAAC 1224
                               i     v  i iii          v   v i     ii  i  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_6777683_67   1225 TGATCTTCGACAAAGCAGACAAAAACATAAAGTGGGGAAAGAACACCCTA 1274
                             i        i vv v   i v   vv i           i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_6777683_67   1275 TTCAACAAATGGAGCTGAGATAATTGGCAAGCCACATGTAGAAAAATGAA 1324
                                     v    i  i  i   vv ?       i i  i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_6777683_67   1325 ACTGAATCTTCGTCTCTCACTTTATACAAAAATCAACTCGAGATGGATCA 1374
                         ii  i i iiiii   v   iv           i     i i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_6777683_67   1375 AAGACTTAAATCTAAGACCTGAAATCATAAAGATTCTAGAAGATAAGATT 1424
                         ?    i     v     v  i   ii     iv ii       v  v  v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_6777683_67   1425 GGAAAAACCCTTCTAGACATTGGATTAGTCAAAGACTTCATGACCAAGAA 1474
                           ?iv  vi    vv   v    i    v   v ii   v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_6777683_67   1475 CCCTAAAGCAAGCACAGCAAAAACACAGATACATAGATGGGACTTACTGA 1524
                         v  v      vivi  i     iv v i   v   i  v      vv v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_6777683_67   1525 AACTGAAAAGCTTCTTCCCAGCAAAAGAAATAATCAGCAGAGTAAACAGA 1574
                           v v    i   i viv vv    i  v iv    iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_6777683_67   1575 CAACCCACAGAGTGGGAGAAAATCTTCACAATCTATATATTGGACAAAGG 1624
                                    i           v  ii   vii      iv  i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_6777683_67   1625 ACTAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAAGAAAAATC 1674
                            vi          v  i  i      vv    v   ii  v     vv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_6777683_67   1675 CAAACACCCCTATCAAAAAGTGGGCTATAGACATAAATAGATAATTCTCA 1724
                             i v   v  i?    i     v vi  iv i      i v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_6777683_67   1725 AAAGAAGATATACAAATGGCCAACAA--ACATGAAAAAATGCTTAACATC 1772
                                                i  --         i     i      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_6777683_67   1773 ACTATTTAT 1781
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.35 (146 / 108)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.67 (5 / 3)  


3918 16.58 3.42 6.74  chr2_6797787_6800129      917  1851 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_6797787_68    917 AAAATATCTCATATTAATGGGCTGGAAGACCTAACATTGTTAGGATGGCA 966
                           i     i   i  v    ii        i   i       i       
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_6797787_68    967 GTACTCCCCAAATTGATCTATAGGTTTAACACATTCCCTGTCAGATTTCC 1016
                         i                   i  i  i   i  v     i   i v i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_6797787_68   1017 AGATGACTTATCTGTAAAAATTTACGAGAGGATGCTAAA-TGCAGATAGA 1065
                           v  v   v i  i i     v  i  vv   v     - v  v  i  
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_6797787_68   1066 ATTGCAAGAGAGCCAAAATAGTCTCTCTCTCTCTCTCTCTCTCTCTCACA 1115
                          v      i  v   i     i ---------------------------
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCC--------------------------- 177

  chr2_6797787_68   1116 CACACACACACACACAAACACACATTGACACACACAATCTTGAAAAAGGG 1165
                         ---------------   ---------------               ii
  L1M4_orf2#LINE/    178 ---------------AAA---------------ACAATCTTGAAAAAGAA 197

  chr2_6797787_68   1166 ---CAA-GT---AGGACTCACACTTTCTCATTTGGAAACTTACTACAAGG 1208
                         ---   -  ---             i iv    vi             i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_6797787_68   1209 CAACAGTAATCAAGACAGCGCGGTACTGACATAAAGACAGATGTATATAG 1258
                          v                i i       i     i  i   ii    v v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_6797787_68   1259 CAATAGAATAGACTTGAGAGTCCAAAAAATGAACTCACACATCTATGGTT 1308
                             i       v           i   - i   i  i    i      i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGTC 346

  chr2_6797787_68   1309 AACCGACTTTTTGACAAGGGTGCCAGTACCATTCAACAGAAAAAGAATAG 1358
                           ii  -    i             iv         ii ii         
  L1M4_orf2#LINE/    347 AATTGA-TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_6797787_68   1359 TATCTTTAACAAATG-TGCTGGGACAACTGTATAGTCACCAACACAAGAA 1407
                          v i  i        -              v   ?i   vvi  v     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_6797787_68   1408 TGAAGTTGGACGCTTACATTACATCATATAAAAAAGTTAACTCAAAATGC 1457
                                    v i   v i   i      v    i             v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_6797787_68   1458 ATCA-ATACATAAATGAAAGAGCTAAAATTATAAAAGTCTTAGAAGAAAA 1506
                             - v  v      v           i       v             
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_6797787_68   1507 CATGAGAG-AAAGCCTCATGACCTTGGATCTGACAATATATTTTTAGATA 1555
                            ii ? -   v i  i         i iv i    ivv  i       
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_6797787_68   1556 AGACACCAAAAGCATGGGCAATTAAA---AAAAT-GATAACTTGAACTTT 1601
                         v             iii    iv   ---     -     v   i    i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_6797787_68   1602 ATCAAAATT---------TGTGCTTTAAAGGACAC-ATCAAAAAAGTGAA 1641
                                  ---------       i         -     i        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_6797787_68   1642 AAGACAATCAACAGAACAAGAAAAAATATTTGCAAATCATATATATAAGA 1691
                                i v      iii  i                      v i v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_6797787_68   1692 AGGGAATATCTTGTATATAGAATATACAAAAA---CTTAACACTCAGAAA 1738
                              ----       vi        i   i ---    vv     iv  
  L1M4_orf2#LINE/    746 AGGGA----CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_6797787_68   1739 TAACAAAACAA----CCCAATTTAAAAGTAGACAAATGATCTCAATAGAT 1784
                            v  i    ----       ?    i i i    v   i v      i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_6797787_68   1785 GTTTCCCCACATAAGTTATACAAATGGCCAATAAGCACATGAAAATATGC 1834
                         i    i   v v   v                             v    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_6797787_68   1835 CCAACATCATTAGCCAT 1851
                         i        ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (97 / 55)
Gap_init rate = 0.02 (18 / 904), avg. gap size = 5.28 (95 / 18)  


3045 27.97 0.44 0.44  chr2_6989801_6996839.rev     5640  6547 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_6989801_69   5640 TGGAAAAACATTCCACGCTCATGGATAGGAAGAATCGATATAGTGAAAAT 5689
                               i i  i   i i        v      v ii    v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_6989801_69   5690 GGCCATACTGCCCAAAGTAATTCGTGGATTCAATGCTATATCCATCAAGC 5739
                            v     v      v i  iiiii       i  v  vi i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_6989801_69   5740 TACCATCGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAATTTTA 5787
                          v   v vi i  i  ii     -   -- v  i  - iii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_6989801_69   5788 TTTGGAACCAAAAAAGAGCCCATAG-AGCCAAGACAATCCTAAGCAAAAA 5836
                          v     viiv  ii  -    v i-      i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_6989801_69   5837 GAACAAAGCTGGAGGCATCACGCGACCTGACTTCAAACTAGAGTACAAGG 5886
                                 i      vv    i vv  ii i      vivv v     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_6989801_69   5887 CTACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGATATATAGAC 5936
                                  i   i     i         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_6989801_69   5937 CAATGGAACAGAACAGAGGCCTCAGAAATCATGCCACACATCTACAACCA 5986
                                 i    iv   ivii       v vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_6989801_69   5987 TCTGATCTTTGAGAAACCTGACAAAAATAAGCAATGGGGAAAGGATTTCC 6036
                         vi    i  i  v  ivv  v   i vi vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_6989801_69   6037 TATTTAATAAATTGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 6086
                          v  i  i    v   i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_6989801_69   6087 AAATTGGACCCCTTCCTTACACCTTATACAAAAATTTATTCAAGATGGAT 6136
                           i          v   i     v            v i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_6989801_69   6137 TAAAGACTTAAACGTAAGACATAAAATCATAAAAACCCTAGAACAAAACC 6186
                         i ?    i    i      vv     ii      vi i     v     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_6989801_69   6187 TAGGCA-ATACCACTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 6235
                             ?i- v i -i  iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_6989801_69   6236 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 6285
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_6989801_69   6286 CTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTTTCATCAGAGTGAAC 6335
                         ii   v v  i i   i  ii vv    i  v   v   vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_6989801_69   6336 AAGCAACCTATGGAATGGGAGAAAATTTTTGCAATTTAGCCACCTGACAA 6385
                          ii     i ii              v       v i vvi i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_6989801_69   6386 AGGGCTAATACCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 6435
                         i  i  vi  i       v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_6989801_69   6436 AAACAAACAAACCCATCCAAAAGTGGGCAAAGGATATAAACAGACACTTC 6485
                          i     i  v  v  i?    i            v i  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_6989801_69   6486 TCAGAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGGTCAAC 6535
                           vi       i  vi vi       i  i  i       i v v     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_6989801_69   6536 AACACTGGTCAT 6547
                          v  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (147 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


3670 19.06 5.04 3.81  chr2_7029567_7031565.rev      618  1509 (490)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_7029567_70    618 AGACATCCCATGTTCGTGGAT-GGAAGAC--AATGTTGCTAAGATAGCAA 664
                            i           i     -       --   i   i      i    
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_7029567_70    665 CACCTTCCAAACTAATATATTAACAGATTGATTAATTGGTGAATAGATTA 714
                         i  iii     i i  v  ----      v -------------------
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTA----CAGATTCA------------------- 82

  chr2_7029567_70    715 CATGTAATTGCTATTAAAATCACAGCTGCCTTTTTTCAATAAAAATTGAC 764
                         - i i   iv    i      v              --ii i        
  L1M4_orf2#LINE/     83 -ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT--GCAGAAATTGAC 129

  chr2_7029567_70    765 AAGCTGATCCTAAAATTCACACAGAAATCCAAGAGACTCTTAGTAGCTAA 814
                                            i ii     v    i   i vv i    i  
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_7029567_70    815 AAGAACCTAGAAAA-GAAAAA-AAACTTGGGGGAGTTACACTTCTTAATG 862
                           v  i  v     -   i  -   v    i   v i       ii   v
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_7029567_70    863 TCAAAACTTACTATAAAGCTATATTAATCAAGATAGTGTAATAGTGACAT 912
                                      i       i v         i     ii  v  i   
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_7029567_70    913 AAGGACAGACATATGGATTAATAGATTAGAAGTGACAGTCCAAAAGTAAG 962
                              i        i   i   i  v     v   v      i  i   i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_7029567_70    963 CATCTACATTTCTGGTTAATTGATTCTTGACAAGAGTATCATGACATTTC 1012
                          viv       v    i        i i      i  ii  v   vv   
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_7029567_70   1013 AATGGGTAAATGATAGTGTTTTTTTTTTCAACGAATAGTGCTGAAA-AAC 1061
                               v   vi     ------i        i   i      ii -   
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGT------CTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_7029567_70   1062 TGAAT--CTAAACACAGA--------------------CCTTAAACCTTT 1089
                           i  -- i v ii  i --------------------   i v   v v
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_7029567_70   1090 CACAAAAATTAACAGCAAATGAATCATAGACCTAAATATAACAGCTAAAT 1139
                         i            vvv     i    ?          i   v       v
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_7029567_70   1140 TTATAAAACTCTTACAAATAAAACATAAAAGTAAATTTTTGTGATCACAG 1189
                         i             v  i-        ii?      i  i    i vii 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAG-AAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_7029567_70   1190 ATGAAGAAATGGTTTCTTAAATATGGTGCTAAAAGCTCAAACAA-----G 1234
                         i v i v            i     iii i      v   i   ----- 
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_7029567_70   1235 AAAAAATAGATACATTGTAATTCATCACAGTTAAAAATGTTTGCATGTCA 1284
                                     v    v v       v i       iv    iiiv   
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_7029567_70   1285 AAA-ATGCCATCAAGAGAGTAAAAAGACAACCCACAGAATGCAAAAGTGC 1333
                           i- ii i       i   i                    vi i ivii
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_7029567_70   1334 ATTTGCAAATCATATATCTGATAAAGGCCTCGGATTCAGAATATATGAAG 1383
                                                 i  v  i v  i          i   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_7029567_70   1384 AAT-------ACTTAACAATCCAAAGACAA----CCCAAATGTAAATATG 1422
                           i-------   i  i   vv        ----     - v?   v   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA-TTWAAAAATG 821

  chr2_7029567_70   1423 GGCAAAGGATTTAAATAGACATTTCTCCAAAGAAGATATTCAAATAGCCA 1472
                                     i                          v     i    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_7029567_70   1473 ATAAGCACAAGAAAAATTGCTCTACATGACTAACCAA 1509
                                  v     iv     v    v ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (109 / 58)
Gap_init rate = 0.02 (17 / 903), avg. gap size = 4.65 (79 / 17)  


 809 29.58 11.62 5.05  chr2_7040999_7045346.rev     3005  3856 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_7040999_70   3005 TGGATAGTGATACGATGTTCATGGATGAGAA-AGTCAATATCCCAG--AA 3051
                             v  vv  v v            vi   - v i     i--- --  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT---GTTAA 47

  chr2_7040999_70   3052 TATGCCAATTCTTTCTAAATTGACCTACAGAGTTAATGCAATCCA-AGCA 3100
                         v   v    v  ii i       i       v i  i       v- v  
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_7040999_70   3101 ACTTCCCAACAAGGGTTTGCTGCTGTTGTTAATGGTGCTATTAGTTCATA 3150
                          vv     ----------     iv  -  -----   - vv i  v i 
  L1M4_orf2#LINE/     98 AAATCCCA----------GCTGCCTTT-TT-----TGC-AGAAATTGACA 130

  chr2_7040999_70   3151 AACTAACTCTAAAATCTCTATAGAGG-GCAGAGGACCAGGTATAGCCAAA 3199
                          i  i ii       iiv   i  ii-   ii     vi v         
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr2_7040999_70   3200 CACCACC--AAATAAGAGGGAAAAGGTTGGAAG----------CCAAGTG 3237
                         -  v i --i  v    i i v  i      i ----------  v i v
  L1M4_orf2#LINE/    181 -ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_7040999_70   3238 CCAAAACTTACTAGAGAGCTGGAGTCATTAAGAGCAG-GCTGCATTGACA 3286
                         i            v i    iv   v  i    -   - iv i i  i  
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCA 278

  chr2_7040999_70   3287 CAGAGGTGGGCAACCTAACCAAGTTAATAAAGGAGA-CAGAGAA---AAA 3332
                         i ii i i i  ---  --i ii i   ii iv   -iv    i--- i 
  L1M4_orf2#LINE/    279 TAAGGATAGACA---TA--TAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_7040999_70   3333 AAAAAAAACATGAATACATGGAAACATGACACATAACAGAGTGTGCATTT 3382
                           v   vv   iv  vi    vv vv   ivivii   -  v    ---i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACA-AGGGTGC---C 369

  chr2_7040999_70   3383 CAGA----TAAATAGAGACAAAG--GGCCATTCAATAAATGTTACTACGT 3426
                         v   ---- v   i i  v i i-- v iv     i     v i  iv -
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG- 418

  chr2_7040999_70   3427 ATTATT---TTTCCTTATGAATAAAAACCACATTGGATTCCTCCATCACA 3473
                          iv i --- v?  vi   v v  i  iv vi     ii   v v     
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_7040999_70   3474 C-----ACAAAAGTTAATTCTAAAT---------ACTT-----------T 3498
                          -----      i    i  v    ---------  i -----------i
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_7040999_70   3499 TAAAACTATTAAA----TATAAGA--------GAGTGA--CTT-ATGACC 3533
                                  v   ----  v    -------- ?  i --   -i     
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_7040999_70   3534 TCAGAATACAGAAGAATATATTAAATAT-------AAGGCCCTAATTATA 3576
                          ii iv  viv  vii v v   i    -------  i  v v iiv i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_7040999_70   3577 AATGGGCAAGGCTGATATAGTCAGCAT-GTTAAAATCAAGAACTTCTAGT 3625
                           -i iv  iiiv    v v vii v -i i     i  i     i -  
  L1M4_orf2#LINE/    619 AA-AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT-GT 666

  chr2_7040999_70   3626 CATTAAAAAGATAACT-TACAGAAAGTGAAAATGGATGAC--ACAAACTG 3672
                         vv  v   i  i -  - vv            --  ii  --   i v  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACA-CTATCAAGAAAGTGAAAA--GACAACCCACAGAATG 713

  chr2_7040999_70   3673 GGAGGTAATATTT-----TTA-ACACTTGAAACAAACAACA-GTCTTCAG 3715
                             iv       ----- i - i ii   --i  ivi  v-  v i   
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGA--TAAGGGACTTGTATCCAG 761

  chr2_7040999_70   3716 AATACAGGAAAATGAGTTC----AAATCAATAAGAAAAATACAA----TC 3757
                             i vi  ---  ii  ----  v       v     v    ----i 
  L1M4_orf2#LINE/    762 AATATATAAA---GAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_7040999_70   3758 CAATAAAAAAACTAGACCAAAAATACGAGCAGTCATTT-TACAGTGGACA 3806
                             v?     - i i v  ii  vi  ii  v     - v  iv i v 
  L1M4_orf2#LINE/    809 CAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_7040999_70   3807 AA-ACAGATGGTGATTAAACATGGGGAAAGTAGCTCAATATTACTGGTAG 3855
                         v -   i    iv v   i  iiv i    vv      i  i ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_7040999_70   3856 C 3856
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.35 (143 / 106)
Gap_init rate = 0.05 (49 / 908), avg. gap size = 2.90 (142 / 49)  


 440 24.11 4.46 0.00  chr2_7171648_7173213       35   146 (1420)    L1M4_orf2#LINE/L1      169   285 (623)  

  chr2_7171648_71     35 AGACTAGCTAAAACCATCTTGAAAAA----AGCAAAGTTGAAGGACTTGC 80
                            v    i     v           ---- i        i      ii 
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_7171648_71     81 GCT-ACTGGTTTCAAGATCACCTATACAACTAAAGTAATGAAGACATTAT 129
                         i  -v iii      i iivv   i v i   v      v      v i 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_7171648_71    130 GGTTTTGGAATAAGGAT 146
                            vi   v        
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGAT 285

Transitions / transversions = 1.45 (16 / 11)
Gap_init rate = 0.02 (2 / 117), avg. gap size = 2.50 (5 / 2)  

1255 26.15 10.07 3.18  chr2_7171648_7173213      501  1066 (500)    L1M4_orf2#LINE/L1      288   892 (16)  

  chr2_7171648_71    501 ACAAATAGATCAAAAGAGCAGAATACAGAGGCCCGAAGTAGGCCCATATA 550
                            v         vi  ii     vv    v  v   i  ii      i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_7171648_71    551 TGTAGGATAAATAAGCTTTCAACAAAAGAGCC-----CA---------GA 586
                          v  v i v   viii    i    ii v   -----  ---------  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_7171648_71    587 AA----AGTGTTCTCAACAAATAGATCTG---TAACTGGGTAAGTACACG 629
                           ----   v  i         i vv   ---i      i  ?vi   i 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_7171648_71    630 GGAAAATCTGAACCTAGATAC-TACTTCACATCCTA-ATAGAG-TTAGTT 676
                         vi   ivv    vi i  iv -   i     i v  - i i i-   ii 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_7171648_71    677 CGTGATAGAGCATAGATTTAACT-TAAAAGCTA--------------CTA 711
                          ivi  i  v  ?   ii   v -   i     --------------i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_7171648_71    712 GAAGAAAACATAGAAGAATATATTTGTAACCTTGAGGTAAATAGGGACTC 761
                                      i? v v  v  i  i      -   ---    v v v
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTG-GGT---TAGGCAATG 583

  chr2_7171648_71    762 ATTTTTGAGA-A-GACAC-AAAAACA---GCCATAAGAGAACAAGATTGA 805
                         i   i v   - -     -    i  ---  v i  i    -  i  v  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA-AAAATAGA 632

  chr2_7171648_71    806 TAAATTGGATTTGTCATAACGAAACCTAAAACC---------CAAGACAG 846
                                  i  --   -- i   iiv     i---------   ---  
  L1M4_orf2#LINE/    633 TAAATTGGACTT--CAT--CAAAATTAAAAACTTTTGTGCTTCAA---AG 675

  chr2_7171648_71    847 GATGCCATTAAGAAAATTAAAAAGCAAGCCATAGAGTGGGAAAAAACATT 896
                           ii i  i      i v    ii   v   i   i     i    i   
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_7171648_71    897 CGCCA--TATAGTATCTGACAAAAGGCTTTGATCTGAAATATATAAAGAA 944
                         i  v --i   -       i  ii i   vv   iii             
  L1M4_orf2#LINE/    726 TGCAAATCATA-TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_7171648_71    945 CTCCTGGGAGTCAATAATGAAATGA-AACGAACCCAATTTAAAAAGTGGA 993
                            i ivi v        i   v  -  vv         ?     -   i
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGG 823

  chr2_7171648_71    994 TACAAGACTTCTTTCTATAGCCACATCACGAAAGGAAATATATGATTAGC 1043
                         i v i  ----   vv    v  iv  v v    i i     ii v i  
  L1M4_orf2#LINE/    824 CAAAGGA----TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_7171648_71   1044 CAATAAATATAAGAAAATATGTT 1066
                               ii i v     v   i 
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.67 (90 / 54)
Gap_init rate = 0.04 (25 / 605), avg. gap size = 3.00 (75 / 25)  


1852 27.03 7.29 2.70  chr2_7392862_7394704      501  1351 (492)    L1M4_orf2#LINE/L1       19   908 (0)  

  chr2_7392862_73    501 TCATAGATTAGGAAATTCAATATGGTTAAAATGTCAATTTTCACTTAAT- 549
                             i    i i i i i     v     i   v    vi  v iv   -
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chr2_7392862_73    550 GATCTATTGATTCAATGCAAATGAGATTAAAATCCCAAATGA--TTGTAG 597
                               iv       i    vivvv  i         iv  v--  v v 
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG 118

  chr2_7392862_73    598 TGGAAATAGATAAGCAAATTCTAGAATTTGTATTGAAA--------ATTC 639
                         ii     v  i    vi  i   i    ii   v    -------- ii 
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr2_7392862_73    640 AAAACAGCT----CA---TTGTA---GATAGGACAAAAT-GGAGGACTT- 677
                          i  i   i----  ---   v ---  -  i     i -        i-
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGA-AGAACAAAGTTGGAGGACTCA 217

  chr2_7392862_73    678 TACTT---AAATTCACCACTTACTAAAAAGCTACTACTATCAAGACAATT 724
                         i    ---  v    vv        v        viiv         i v
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_7392862_73    725 T--TA--AGT-TAAAAA--GATGTATAGACTAGTAGAACAAAAAAAGAGA 767
                          --  --i i-   ii --  ii      ii i i   i i  vv-    
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT-GAGA 316

  chr2_7392862_73    768 GTCTATAAATAAAACCATTTATATGTGGCTAATTGATTTTCAACAAAGGG 817
                            i v       v    vi  v i   ii           i    i  v
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_7392862_73    818 GGAAAAAGATTTAAATGGATAATGGGTAGATTTTTCAATAAATGGAGTTG 867
                          vv  i vvv  v     iv  v ii   vi       i      v i  
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_7392862_73    868 AAA-AATGAGATATTCATATGAAAATAAATAA-------TCCTTACCTCT 909
                         ii -  ivi    ?i  i   v   vi   i -------i  i      -
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC- 465

  chr2_7392862_73    910 AACCCTATGGTATACATAGAAAATTGAAACAAAATGAATCACT--CCATT 957
                         -  v i  ---     ---      i vv       i    ?v--  -- 
  L1M4_orf2#LINE/    466 -ACACCAT---ATACA---AAAATTAACTCAAAATGGATCAWAGACC--T 506

  chr2_7392862_73    958 AAATGGAAAAGTAAAAATTGTAATACTTCTGGA-GAAAATATAAAAAAAA 1006
                              v  i  iv    i i   v   ii i  -     i   ii?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_7392862_73   1007 ACTTTAATCAC-TGGGGTTTGGCAA-AATTTGATAGCTAAGACACAATAA 1054
                          ii  vi v  - v     v     -ii   vv   v  v     v v  
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_7392862_73   1055 GCAATTCCCATTAGAGAAAAAAT-GATAAAGCACATCTCATCAAAAGGTA 1103
                            vvvv v iv i         -      viiv ii         vvv 
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_7392862_73   1104 AAATTTCTGCCTTTAAAAAGACACC-TTAGAAAAATGAAAAGACAAGCCA 1152
                            i  i  ivi  v   i     i- i ii   i           v   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_7392862_73   1153 TATAGTGGCAGGAAATAACAGCAA--TGCATGTTTGACAAAGGACTTATA 1200
                         i v i   v  i     viv    --iii  i i   i  i      i  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_7392862_73   1201 TCCAGAATATGTAGCATAGAAAACCCTTACAAGTCAATA-TAAGGAGACA 1249
                                   -----   i i   i       v      -   ii     
  L1M4_orf2#LINE/    757 TCCAGAATAT-----ATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_7392862_73   1250 AACAACCCAATT-AAAAATA----------TTAAACAGGCACGAATTCAT 1288
                           i         -      i----------  i  i  i  i---   --
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT---TTC-- 846

  chr2_7392862_73   1289 ATACTAAAAAGGTGTATGAATCATCAATAAACACATGAATAACTGGTAGA 1338
                         - v v  i   i i  ii   vii      i        v iv  v vi 
  L1M4_orf2#LINE/    847 -TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_7392862_73   1339 CATCATGAATCAT 1351
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (138 / 89)
Gap_init rate = 0.04 (34 / 890), avg. gap size = 2.50 (85 / 34)  


3312 25.39 1.66 1.43  chr2_7502756_7505927.rev     1775  2680 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_7502756_75   1775 TGGAGAGATATTCCATGTTCATGGATAAGAAGACTCAATATTTTCAAGAT 1824
                             i      i              vi       i      v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_7502756_75   1825 GTTA----TTCTTAACTTGATTTATAGGTTCAGTGCAGTCCTAATCAAAA 1870
                          vi ---- i ii  v     i  i  i    ii   i   iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_7502756_75   1871 TCTTAGCAACTTATTTTGTGGATATCAAGAAACTGATTCTAAAGTTTATA 1920
                           ii   vi i v     ii  v  ii v  i     i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_7502756_75   1921 CAGAGAGGCAAAG-ACCCAGAACAACCAACACGGCATTGAAAAAGAAGAA 1969
                         ii  i v    i -        i i    v  iiiv              
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_7502756_75   1970 CAAAGTTTTAAGACTGACACTGCTCAACTTTAAGATTTATTATAAAGTTA 2019
                                vv i    v     v i   i  i  i i   i  i    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_7502756_75   2020 TAATCATCAAGAGAGTGTGGTATTGATGAAAGAATAGAGAAATAGATCAC 2069
                         i i v       v         i  iiiv   i     v v        v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_7502756_75   2070 TGGAACAGAATAGAGAGATTAGGAGTAGACACACATAAATATATTCGACT 2119
                              i     v     vii  i i  i  v  i i vv   iv  i i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_7502756_75   2120 GATCTTTGACAAAGA-GTAAGGATAATACAATGGAGAAGAAATCGTATTT 2168
                            i  i     i i- iv i  iv  v      i   ii   v  v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_7502756_75   2169 TCAACAAATGGTGCTGGAACAATTGGATATCCACATGCAAAAATTACATA 2218
                                          i    i      ?            i-------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG------- 443

  chr2_7502756_75   2219 AAATGAATCTAGACAAAGACCATACATCCTTCACAAAAATTAACTCAGTA 2268
                         -      vi i   vvvv   vi   i v vi               iv 
  L1M4_orf2#LINE/    444 -AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_7502756_75   2269 CGTATTACACATCTGAATATGAAATGTAAAACTATAAAATTCTTAGAAGA 2318
                         i v  i ? v i  i   i i i vv             i          
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_7502756_75   2319 GAACATAGGAAAAAATCTAGTATGACCTTGGGTTTGGTGATGACTTTTTA 2368
                         i        ?iv      -vii            v  ii   ii  i   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_7502756_75   2369 GGTGCAACAC-AAAAGC-CA--CAATTTTGAAAGAAAAAATGGATAAGCT 2414
                          i iii    -      -  --   i---i           i     ii 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAAC---AAAAGAAAAAATAGATAAATT 638

  chr2_7502756_75   2415 ATACTTTATTGCAATTAATA-TTTTTGCTCTGTGAATT-CATTGTCAAGA 2462
                         iv    i  iiv      v -i     iv  vii  vv-  i i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_7502756_75   2463 GAGTGAATAGACAAGCCACAAACTGGGAGGAAATATTTGCAGAAAGAAAT 2512
                         i      v      v     i v      i           -  vv v  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATCATAT 737

  chr2_7502756_75   2513 CTCTGATAACGGACCGCTACCCCAAATATACAAAAAACTCTTAAAACTAA 2562
                         v        v    ivv  i  vi      i   i        v    v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_7502756_75   2563 ATTGTAAGAAAATAAACAATTCAAT--AAAAGTGTCCTAAA-ATCTTAAC 2609
                           vi   i  i i   i  ii    --    i  vv v  i-  i v  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_7502756_75   2610 CAACACCTTGCCAAAGAAGATACACAGATGTCATGTAAGCATATGAAAAG 2659
                         vi   ii iv            i   i   v vvi      i        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_7502756_75   2660 ATACTCCACATCATATATAAT 2680
                           i   v      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (147 / 80)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  


 781 25.20 4.07 0.00  chr2_7550095_7555362.rev     2861  3106 (2162)  C L1M4_orf2#LINE/L1   (0)   908   653  

C chr2_7550095_75   3106 TTAAGAGTTTTTGCAA---AAAAGAAACTGTCATCAGACTGAACAGACAA 3060
                             i ii     iiv---   i  v   i   vv i v    v      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

C chr2_7550095_75   3059 CCTACAGAATGAAAGAAAAAATTTGCAATCTATCCATCTAATAAAAGCCT 3010
                           i        ii      v        vii  vi    i    ii v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

C chr2_7550095_75   3009 AATATCCAGAATCTATGATAAACT--TA-AACATATTTATAAG--GAAAA 2965
                         vi          v   i vi    --  -   vi v v    i--  v  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

C chr2_7550095_75   2964 ACAACTCCATTAAAAAGTGGACAAAGGGCATGAACAGACACTTCTCAAAA 2915
                          i   i v   ?    i   i      iiv    i     i     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

C chr2_7550095_75   2914 GAAGACATTTGTGTGGCCGACGA--ACATGAAAAAAAGCTCAACATCACT 2867
                              i  viivi     i ii --         i v           ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

C chr2_7550095_75   2866 CATCAT 2861
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.65 (38 / 23)
Gap_init rate = 0.02 (5 / 256), avg. gap size = 2.00 (10 / 5)  

2491 25.98 3.71 4.59  chr2_7550095_7555362.rev     3862  4777 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_7550095_75   3862 TGAAGAGACATATGACGTTCATGAATTGGAAACCTTAACATAGTGAAT-T 3910
                           i i   i  viv i       i       iv     i  v  v  v- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_7550095_75   3911 GTCAAATCTCCTCAAATTGACACACCATTTTAATGTAATTCCTATCATAA 3960
                          v   vv    i        ivi  viv  i  i i   i       v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_7550095_75   3961 TTCAAGCAAGATTTTTTGTTGACATAGAGGTGATTATTCCAAAATTTATA 4010
                          i v   vivv       iv  v  v  viv v v  i i      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_7550095_75   4011 TGGAACTACAAAGGCACTAGAATAGCTAAAATAGTTCTGAAAGAGAAGAA 4060
                              v i   i  vv i        i    i i ii     i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_7550095_75   4061 TAAAGTTGGAGAAA--GTGCTTTTCAAATTTTCAAGATTTAT--CAAGG- 4105
                         i          i v--iii   ii   --      i i   i--   i -
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAA--TTTCAAAACTTACTACAAAGC 248

  chr2_7550095_75   4106 TACACTAACCAAAACTGTGTGGTATTGATGGAGTATAA---TGGA-ATAA 4151
                             v   i   i  v        i  ----- i    --- i  -   v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTG-----GCATAAGGATAGACATAT 293

  chr2_7550095_75   4152 AGATCAATGAAACTGAATAGAGAATTTAAAAGTAGGTTTTCACAAGTATG 4201
                                  i  iv    v    i ii i  i  iiiiivi   vv    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_7550095_75   4202 GCCAACTAATTTTTGATGAAGGTAAAAAGA--ATTCAATGGAGGAAGAAT 4249
                          i   i i     i  ii i   ivv    --         i i      
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_7550095_75   4250 AGTCTTTGCAATAAATGGTGCTGGAGCAATTGAACATCTATAGGTTAAAA 4299
                                v   i            ii   i  i i ? i i v iv   i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_7550095_75   4300 ACTAAACCTTGATTTAAACCTTATAACC---TACTATAATTAACTTAAAA 4346
                          v i  vi v  iiivv    i i -  ---   v v        i    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACA-CCATATACAAAAATTAACTCAAAA 492

  chr2_7550095_75   4347 TGGATCATAAATTTAAATATTAATTATAAAACTACAAATCTTTTAAAAGG 4396
                                ? i ii     i v ivvv        i   v  i   i   i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_7550095_75   4397 TAATGTAGGAA-AAATCTTCAAGATTTACAGCATGG-TGAAGCA-----T 4439
                         v  ii    ?i-        iv  ii ------   - v i   ----- 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCT------TGGGTTAGGCAATGGTT 586

  chr2_7550095_75   4440 TCTTAGACATGACACCAAATGCATGATCCATAAAAGAGAAAATAG----- 4484
                                i           v   ii v v i      i       -----
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_7550095_75   4485 TTTGACTTTATCAAAATCAAAATTATCTTTTCGGTG-----AAAGATCCT 4529
                           v     i        i    -- -     --   -----  i  iv  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAA--A-CTTTT--GTGCTTCAAAGGACACT 681

  chr2_7550095_75   4530 GTAAAGAAGATAAAAAGGAAAGCTACAGACTGGGTGAAAATGTGTGAAAG 4579
                         i v     ii i     iv  v i     v    v      i v  v  i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_7550095_75   4580 CCACATATTTGACAAAGGCAATCATATCAAGAATATAATAGGAACTCTCA 4629
                         i  i    i   i  i  - v ii    v        vv i       i 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGG-ACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_7550095_75   4630 AAACACAATGGCAAAAAAAAAAAAAAAAAAAAACAAACAAGCCCAATCCA 4679
                         v   v    --------------  v     i     i  -      i? 
  L1M4_orf2#LINE/    781 CAACTCAAT--------------AATAAAAAGACAAATAA-CCCAATTWA 815

  chr2_7550095_75   4680 GGGAGAAAATGGGCAAGAAATATGAA--GGTATCTGTCATTGAGGGGAGT 4727
                         -----           iii  v    -- ii  i v  --ii i iiii 
  L1M4_orf2#LINE/    816 -----AAAATGGGCAAAGGATTTGAATAGACATTTCTC--CAAAGAAGAT 858

  chr2_7550095_75   4728 ATAAGGATGGCAGATAAGCATATGAAAAGATGATCTGCATCTTTAGAACA 4777
                            vii     vi       i           v  vi    v????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (152 / 82)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.92 (76 / 26)  


1569 27.16 6.75 0.63  chr2_7576731_7578358      501  1137 (491)    L1M4_orf2#LINE/L1      233   908 (0)  

  chr2_7576731_75    501 AAACTTTAACTACAA---TACAGTAGTGAAGACCGTATGGCAATGGAGAA 547
                               --       ---       i v     v  i   i v   viv 
  L1M4_orf2#LINE/    233 AAACTT--ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_7576731_75    548 AGGATAGACATGTAGATAAATGGGACAGAATGTAG---CCA--------- 585
                                    i     v     i i     vv  ---   ---------
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr2_7576731_75    586 -CATA--------GTTAATTGGGTTTTGAGAAATATGCAAAGGTAATTCA 626
                         -    --------  i     iv   i  v  ivi   v   iiv     
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_7576731_75    627 ATGGAATAAAAACAGTCTTTTCAACAAATGTTGCCAGAATAATTTCATAT 676
                             iiv  i  i                 v   ii i i  i vv   ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_7576731_75    677 CCATGTGAAATTGAATGAATCTCAATATACACCTCGCAACCTATA--AAA 724
                            ii  v  vv       vi vi ivivi     i  v v    --   
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_7576731_75    725 ATTAATT--AAATGGGTAATAGGCCTACATGTAAA--TTA----TAGAGA 766
                              i --      i v ?  i    v      i--i  ----  v i 
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_7576731_75    767 ACTCTGA-AAGAAATAACAGGAGAAAAATATTTGTGACTTTGAGTAAGGT 815
                              v -      vv i   ? v   - v  i     i   i  v   i
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGC 579

  chr2_7576731_75    816 ATGAATATTTTAGATACAACATGAAAATCAAGATCTATAAAAAGAAAGAC 865
                          vvii v i       ii   iv    v  vi v v i    ii   i i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_7576731_75    866 TGATTATTTCAATGTGACCAAAATTAAGAATATCTGCTCTTCACAGGACA 915
                         v   v v  vi iv v i         i  iv i  iv     v      
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_7576731_75    916 CTGTAAAGAGAATGAAATGGCAAGCCCCTCACTGTAAGAAAATATTCACA 965
                           i v    i i     v i   v  v vv v  vi          ii  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_7576731_75    966 AAT-ATCATAACTGATGAAGCACTGATATATATA-TATATATATATGTAT 1013
                            -  -   v     i i v   vi   vi v -      v v vv v 
  L1M4_orf2#LINE/    730 AATCAT-ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_7576731_75   1014 CAAGTCTCAAAAATAGTAA--CA--TAACCCAGTTTATAAACAGACAAAA 1059
                         i viv     v    iv  --  --       i  ? v   ii i    i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_7576731_75   1060 GCTTTGAACAGACATTTCACCAACAAAGATAGATAGATGGA-AATTAGCA 1108
                          v      i         v    vi      v i i    v-   v    
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_7576731_75   1109 AATAAAAATATGCTCAATAT-ATTTAGTTA 1137
                         v  i    v        i  - ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.04 (86 / 83)
Gap_init rate = 0.03 (18 / 676), avg. gap size = 2.61 (47 / 18)  


2311 24.54 8.05 1.45  chr2_7591149_7592824      427  1184 (492)    L1M4_orf2#LINE/L1      101   908 (0)  

  chr2_7591149_75    427 TTCCATTTACATTTTATGTATAA-TT-ACA--TTGGTGCCAAATATCCAC 472
                          i   vi i v    v  i v  -  -   --i  i v i   -  i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA-ATTCAT 149

  chr2_7591149_75    473 CAGGAAAAACTCTAAAGAGTCCTAGTTAGAATAACCAAAACAAACTTAAA 522
                         vv     vi ----   i v  i  ----    i         v   i  
  L1M4_orf2#LINE/    150 ATGGAAATGC----AAGGGACCCAG----AATAGCCAAAACAATCTTGAA 191

  chr2_7591149_75    523 TAAAAAAAAAAAAGCTGGAGGTATCACACTACCTGACTTCAAAATATACT 572
                         v  i  i  v    i      vv       v  ii i       iv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_7591149_75    573 ACAAAGATATAGTAACGTAAACAG-----------CATAAAAATGGACAC 611
                               v  i     ivv i    -----------     ii  i    i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_7591149_75    612 ATAGACCA--GGAACAGAGTAGGGAACCTAGAAATAAAACTACATATTTA 659
                              i  --    i   i v i  ii i         v i i i     
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_7591149_75    660 CAGCCAACTGATTTTTTAAAAAGGCGTCAATAACTTACATTAGGGAAAGG 709
                         ii i   i       iv v  i  i i   v v v v  v i       i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_7591149_75    710 GCAGTCTCTTTAATAAGTGGTTCCAGGAAAAGTAGATATCTATAGGCAGA 759
                         ii     i  i  i  i    v ii   v  v i    ? i i v   i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_7591149_75    760 AGAATAAAACTAGACCCTTGGCCCTCACCATACCCAAAAATTAACTCAAA 809
                              i  ii i     i iv i v       iv                
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_7591149_75    810 ATGGATTAAAGACTTAAATGTAAGACCCAAAACTATGAAACAACTAGAAG 859
                               i ?    i           v i        i    vvi      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_7591149_75    860 AAAACATAGGGG-AAATGTTTCTGGATACTTGT-CTGGGCAAAGATTTTA 907
                                   ? -    -i   vv  i-    v-i i     v i   iv
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CTTCGTGAC-CTTGGGTTAGGCAATGGTTTCT 589

  chr2_7591149_75    908 TGGTTAAGACCACAAAAACACA-GCAACAAAAGCAAAAATAAACAAAT-G 955
                          i v  v   vv     i    -          v       i i    - 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_7591149_75    956 AACCATATCAAACTAAAAAGCTTCTGTACAGCAAGGGAAAAGATCAACAG 1005
                         i  ivi      v v    i   i   i vv   i   v vv     v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_7591149_75   1006 AGTGAAACGGCAACCTTCA--------------ATT-------------- 1027
                                v i     iv  --------------   --------------
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_7591149_75   1028 ------AGAGATTAATGTCCAGAATATACAAAGAACTTAAACAACACAAT 1071
                         ------  i  i vi i           i        ivv     v    
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_7591149_75   1072 AA-----AG-CAAATAATGTGATTTTAAAATGGACAAGGAATCTGAATAG 1115
                           -----  -       ivii   ?v       i   i i  i       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_7591149_75   1116 CAATTTCTCAAAAGAAGACATACAAATGGCCAAGAAATACATGAAAAAAT 1165
                         vv       v        i              v  ii         i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_7591149_75   1166 ATTCAGCATCACTAATCAT 1184
                         ii   i     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (113 / 69)
Gap_init rate = 0.02 (18 / 808), avg. gap size = 4.00 (72 / 18)  


2653 26.02 2.43 2.43  chr2_7624974_7629245.rev     2874  3780 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_7624974_76   2874 GGAAACACCTTCCATGCTCATGGAAGGGTAGAATCAATATTGTGAAAATG 2923
                              v iv i     i       vv  v   v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_7624974_76   2924 ACCATACTGCC-AAAGCAATCTACCAATTCAATACAATTCCCATCAAAAT 2972
                         i v     v  -   vii      vi      ii    i  i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_7624974_76   2973 ACCACCATCATTCTTCACAGTACTAGAAAAAAACAATCTTAACATTCGTA 3022
                         v   v vv v  i  ii   v v v  v  iv-ii   i   v    i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATA 150

  chr2_7624974_76   3023 TA-AAATGAAAAAAGAGCCTGCGAAACAAGCAAGAC-----TAAGGAAAA 3066
                          i-     v  i-- ii  -- ii  i iv   i  ----- i ii  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAG--GGACC--CAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_7624974_76   3067 AGAACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATACTTTAAG 3116
                                 vi      vv     i v  ii i      viv    vi  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_7624974_76   3117 GCCATAGTCACCCAAACAACATGGTACTGGTATAAAAAGAGGCACATAGA 3166
                           i i   v i v i   iii         i    ii v  i  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_7624974_76   3167 CCAA-GAAACAGAATAGATAATCCAAAAATAAAGCCAGATAGTTACAGCC 3215
                         i   - i  i     v  v i    i       v   v i v   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_7624974_76   3216 AGCTGATCTTTGACAAAGCCAACAAAAACAT--AAAGAATGAAAGGACAC 3263
                          ii    i  i     i viiv   i v   --  v ii-     i i v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAG 395

  chr2_7624974_76   3264 CCTATTGAACAAATGGCGCTGGGATAATTGGCAAGCCACATGCAGAAGAA 3313
                         i  v  v         i       i  i   vv ?         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_7624974_76   3314 TGAAACTTGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATAG 3363
                             ii v  i  ii i   v    v           i       i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_7624974_76   3364 ATCAAAGACTTAAATCTAAGACCAGAAACCATAAAAATTCTAGAAGATAA 3413
                             ?    i     v     v vi    i      v ii       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_7624974_76   3414 CATCAG---AAACCCCACCCCCACCCCGCCCAGACATTGC-TTAGGCAAA 3459
                            vi ---   i ii----------  i---   v   v-        v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTT----------CGT---GACCTTGGGTTAGGCAAT 582

  chr2_7624974_76   3460 GACTTTGTGACACAGAAC-CCAAAAGCAAATACAACAAAAACAAAGATAA 3508
                          i-   v v v i vi  -         v vi        iv   i   i
  L1M4_orf2#LINE/    583 GG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_7624974_76   3509 ATAGATGGGACTTAATTAACAA--AAAAGCTTCTGCACAGCAAAATAAAT 3556
                            i  v      v  i  -  --    i   i  ii vv    iv v i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAA-AATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_7624974_76   3557 AATCAGCA--GTTAAAAGACAACATACAGAGTGGGAGAAAATCTTCACAG 3604
                         v    iv --  v          vi     i           v  ii  i
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_7624974_76   3605 TCTATATATCTGACAAAGGACGAATATCCAGAATCTACAAAGAATTCAAA 3654
                         vii          i  i    vvi          v  i      i  vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_7624974_76   3655 CAAATCAGTAAGAAAA---TAAATCAATCTGATCAAAAAGTGGGCTAAGG 3701
                            v   i   v    ---i    -  i ii  i?    i     v    
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGG 829

  chr2_7624974_76   3702 ACATAAATAGACAATTCTCAAAAAAAGATATACAAATGGACAACAAGCAT 3751
                          iv i        v     v   i               v   i     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_7624974_76   3752 ATGGAAAAATGCTTAACATCACTAATTAT 3780
                            i   i     i       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 2.20 (44 / 20)  


3809 18.56 2.20 0.98  chr2_7871609_7873386.rev      468  1286 (492)    L1M4_orf2#LINE/L1       80   908 (0)  

  chr2_7871609_78    468 TCAATATAAATCATTTTTCAACTCTGAGCTGCCTTTTTTGGCAGATATTG 517
                             iii  -  vi v iv  v  iv              -    v    
  L1M4_orf2#LINE/     80 TCAACGCAA-TCCCTATCAAAATCCCAGCTGCCTTTTTTG-CAGAAATTG 127

  chr2_7871609_78    518 ACAAGCC------AAAATTCATATGGAAAAGGACAGGGCCTAGTATAGCC 561
                               i------                v v vi  i  i  v      
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_7871609_78    562 AAAACAATCTTAAGAAAGAAGAACAAAGTTGGAGGACTCACAGTTACTGA 611
                                    i i                            v  v ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_7871609_78    612 TTTTACATCTTACTACAAAGATGCAATAATCAAGACAGTGTGGGACTGCC 661
                            i v v            v i  i                 v    v 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_7871609_78    662 ATGAGGATAGATATATA-ATCAGTGGAATACAATTGAGAGTCAAGAAAAA 710
                           i        i     -    i       v           v     v 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_7871609_78    711 AACTCATGTATCTAGGGTCAGTTGATTTTTGACAAAGCTACCAAGACCGC 760
                            i   ii  i  v     i        i     i v i        ii
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_7871609_78    761 TCAATGGGGGAAAGAATAGTCTCTTTAACAAACAGTTCTAAGAAGACTGG 810
                                  -            i  i      ii  v  ii  vi     
  L1M4_orf2#LINE/    378 TCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_7871609_78    811 CTATCTATCTGCAAAAGAATAAATGTGCACTCTTACCTCACACCAAACTA 860
                         v  ? i iv           i  vv  v  i i            v -  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA-TA 475

  chr2_7871609_78    861 AGAAGATTAACTCAAAATAAGTCA------TGAATGTAAGAGCTAAAACT 904
                         vi  i             iii   ------ i                  
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_7871609_78    905 ATAAAACCCTTAGAAGAAAACATAGAACTAAATCTTAGTGAC-TTGGATC 953
                                i                 i?v        v     -    i i
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_7871609_78    954 AGATAATAGTTTCTTAGATGTAACACCAAATGCATGAATGACAAAAAAGA 1003
                           ii   i           i i        v   ii iii      i i 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_7871609_78   1004 AAATA-ATAAAGTAGACTACATCAAAATTTAAAACTATTGTACTGCAAAT 1052
                              -     v i    v          v      v    i  v    v
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_7871609_78   1053 AATACT-TTAAGAAAGCAAGAAAACACCCCACAGAATGAGACAAT-TATG 1100
                         i i   - i       ii i  i   v           i  v  v-   v
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_7871609_78   1101 TGAAAATCATATAATGGCTAAATGACTTGCACCCAGAATATATAAAGAAC 1150
                           v          viv v   iv      i i                  
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_7871609_78   1151 ACCTTACAACTCAATATTTTCAAAAAG-CAAATAACACAATTTTAAAATG 1199
                         -i              v ---      -        v     ?v      
  L1M4_orf2#LINE/    776 -TCTTACAACTCAATAAT---AAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_7871609_78   1200 AACAAAGTATTTCAATAGACATTTTTCCAAATAGGATGTACAAATTGCCA 1249
                         ii     v    v           i      v i   i       v    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_7871609_78   1250 ATCATCCTATGAAAACACTCTCAATGTCATTAGTCAT 1286
                           v v vi       v iv     ii   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (88 / 61)
Gap_init rate = 0.02 (14 / 829), avg. gap size = 1.86 (26 / 14)  


3214 26.52 0.88 0.55  chr2_8217570_8222431     3466  4370 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_8217570_82   3466 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3515
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_8217570_82   3516 GGCCATACTGCCCAAGGTAATTTATAGATTCAAAGCCATCCCCATCAAGC 3565
                            v     v     iv i  i  i        v  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_8217570_82   3566 TACCAATGACTTTCTTCACAGAA-TTGAAAAAAACT-ACTTTAAAGTTCA 3613
                          v   iivi i  i  ii     -    v  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_8217570_82   3614 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3663
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_8217570_82   3664 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAAGC 3713
                                i      vv    i  v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_8217570_82   3714 TACAATCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGATC 3763
                             i v i   i    ii         i iv ii i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_8217570_82   3764 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCTCATATCTACAACT 3811
                                i    i--    i  --        vv  vi i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_8217570_82   3812 ATCTGATCTGTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGTTTCC 3861
                          vi    i vi     ivv  vv  i v  vv            iv vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_8217570_82   3862 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3911
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_8217570_82   3912 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3961
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_8217570_82   3962 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4011
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_8217570_82   4012 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4061
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_8217570_82   4062 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4111
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_8217570_82   4112 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4161
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_8217570_82   4162 AGGCAACCTACACAATGGGAGAAAATTTTCGCAACCTACTCATCTGAAAA 4211
                           i     i   v             v  i    vii ivi      v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_8217570_82   4212 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4261
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_8217570_82   4262 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAGCAGACACTTC 4311
                          i     i     v  i?    i            v   ii     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_8217570_82   4312 TCAAAAGACATTTATGCA----GCCAACAGACACATGAAAAAATGCTCAT 4357
                           v     - vv   i  ----     i ii          i       v
  L1M4_orf2#LINE/    847 TCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_8217570_82   4358 CATCACTGGCCAT 4370
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (135 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3146 27.39 0.55 0.66  chr2_8270563_8275192     3230  4138 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_8270563_82   3230 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3279
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_8270563_82   3280 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCGTCCCCATCAAGC 3329
                            v     v     iv i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_8270563_82   3330 TACCAATGACTTTCTTCACAGAA-TTGAAAAAAACT-ACTTTAAAGTTCA 3377
                          v   iivi i  i  ii     -    v  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_8270563_82   3378 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3427
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_8270563_82   3428 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3477
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_8270563_82   3478 TACAGTCACCAAAACAGCATGGGACTGGTACCAAAACAGAGATATAGATC 3527
                               v i   i    ii   v     i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_8270563_82   3528 AATGCAACAGAAC--AGAGCCCTCAGAAATAACACCTCATATCTACAACT 3575
                             v  i    i--    i  --        vv  vi i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_8270563_82   3576 ATCTGATCTGTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGTTTCC 3625
                          vi    i vi     ivv  vv  i v  vv            iv vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_8270563_82   3626 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3675
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_8270563_82   3676 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3725
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_8270563_82   3726 TTAAAGACTTAAATGTTAGACCTAAAGCCATAAAAACCCTAGAAGAAAAC 3775
                          i ?    i       v   v     i i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_8270563_82   3776 CTGGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTA 3824
                         v i  ?i- v i -   iv   v v  vv i i   v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_8270563_82   3825 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3874
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_8270563_82   3875 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3924
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_8270563_82   3925 CAGGCAACCTACACAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 3974
                         v  i     i   v             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_8270563_82   3975 AAGGGCTAATATCCAGAATCTACAATGCACTCAGACAAATTTACAAGAAA 4024
                          i  i  vi          v  i  v v    vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_8270563_82   4025 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAGCAGACACTT 4074
                           i     i     v  i?    i     i      v   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_8270563_82   4075 CTCAAAAGAAGGCATTTAGGCAGCCAAAAAAACACATGAAAAAATGCTTA 4124
                            v       ii  vi iiii     v  i-          i     i 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCA 894

  chr2_8270563_82   4125 TCATCACTGACCAT 4138
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1673 23.80 2.09 12.27  chr2_8298304_8302215     2518  3332 (580)    L1M4_orf2#LINE/L1        1   732 (176)  

  chr2_8298304_83   2518 TGGAAAGACATACCATGTTCATGGATGGGAAGATTCAACACAGTAAAGAT 2567
                                 i  v              v      i i  i iv  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_8298304_83   2568 GTCAGTTCTCCCCAGATTGATATAAAGGTTAAATGCAATTGCTATCAAAA 2617
                          v  i v       i      v  v  i  v  i     iv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_8298304_83   2618 TTGTAGCAAGATTTTGTGGTAGATATAGACAAGATTATTAAAACATTTAT 2667
                          ivi   v- vi   v v i   v  v      v v  ivv  v   i  
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_8298304_83   2668 ATGAAAATGCAAAGGAACTATAATGGCAAAAATAATTTTGAGAAAATATG 2717
                            i        i   v i v   i  v    i   i    i   ---- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA----G 195

  chr2_8298304_83   2718 AAGTGAAAATAATTAG----TTGATAC-----AACTTCAAGACATTTTAT 2758
                            --  v v i  i ----i v i  -----  i     i  v vi  i
  L1M4_orf2#LINE/    196 AAG--AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_8298304_83   2759 AC--CCACAGTAATCATGACTGTGTGGTATTCGTTGAGGGGAAGACATAT 2806
                          v-- i          v   v        i v ivv i  iv        
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_8298304_83   2807 AAGTCTAGGGAACACAATAGTAAATAGAGAAACAGATACACACAAATATG 2856
                          ii  v v    i v   v vi i vv     i i iv  i   vv    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_8298304_83   2857 CCCAACTGATTTTTGACAAAGGTAC-AGGAGCAATTCAATGAAGGAAGGG 2905
                         vi   i       i     i   i - i  v  -       ii i   ii
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAA 392

  chr2_8298304_83   2906 TAGCTTTTTTAAACAAATGGTGCTAGAGTAATTGGCCATCTATAGGCAAG 2955
                            - i    v             i iii  i   ---------------
  L1M4_orf2#LINE/    393 TAG-TCTTTTCAACAAATGGTGCTGGGACAACTGG--------------- 426

  chr2_8298304_83   2956 AATTCCAAAGTATCTCCAAAAATCTTCTATAACTAATATGCAAGTCTCAA 3005
                         ----------------------------   ? i -i      -------
  L1M4_orf2#LINE/    427 ----------------------------ATAKCCA-CATGCAA------- 440

  chr2_8298304_83   3006 GATAAAATATAAGCATGCAAAAATCAAGTATATTCCCACAACATCTTCAA 3055
                         ------------------  i   v    ----------------- vi 
  L1M4_orf2#LINE/    441 ------------------AAGAATGAAGT-----------------TGGA 455

  chr2_8298304_83   3056 CCTAAACTTCACAGCTTATACAAAATTTAAATCCAAATAGATCACAGGTT 3105
                           ivv  i     v v         v    v  v    i     ?  iii
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_8298304_83   3106 TAAATGGAAAAAC-AGAGCTATATAATGTATAGAAAACAA--TAAGAGAA 3152
                               v  i i - i i     v  iviv     i v  --  i ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_8298304_83   3153 AATTTTAG-GATCTCAGGCTAAGCAAAGATTTCTTAGACTA-GACACAAA 3200
                            i  v -  i  ii  i  i    v i         -  -     v  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAA 604

  chr2_8298304_83   3201 AAGCATGATCTATAAAAGAAAAAAATGGTAAACATGGATGTCATCGAAAG 3250
                              ii v v i           vv i    i-    iv     i   v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAAT-TGGACTTCATCAAAAT 653

  chr2_8298304_83   3251 TACAAACTTTTGCTCTGTAAAAGGCCTTGTTAAAAGGATAAAAAGACAAG 3300
                           v         iv  vi   i i vi i i  i iii i         v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_8298304_83   3301 CTACTGACTGGGAAAAAATCCAATTAGAAAAT 3332
                          i  v  v     i     ---   v v    
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAAT---ATTTGCAAAT 732

Transitions / transversions = 1.30 (108 / 83)
Gap_init rate = 0.03 (20 / 732), avg. gap size = 5.85 (117 / 20)  

 325 24.71 0.00 0.00  chr2_8298304_8302215     3336  3420 (492)    L1M4_orf2#LINE/L1      824   908 (0)  

  chr2_8298304_83   3336 CAAAAGCCATGAACAAATATTTCACTGCAATCAATATACAGATGGCAAGT 3385
                             i viv    i i i     v iiv ivvi       i     v i 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_8298304_83   3386 AAGTACATGAAAAGATGTTTAACATCATTATCCAT 3420
                            i             i i       ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.00 (0 / 0)  


2613 21.30 9.78 4.07  chr2_8871144_8875901     3408  4266 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_8871144_88   3408 TGAGGAGATATTCCATGTTCATGGGTAGGAAGACT--------------- 3442
                           iii      i            i v        ---------------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_8871144_88   3443 --CAATACT--------TGACCTAAAGATTTAACGCAATCTCAATGAAAA 3482
                         --       --------   i   v     i         i v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_8871144_88   3483 TCCCAGCAAGTT-----------ATT--CAAGGTGAATCAAAAGTTCATA 3519
                                vivi -----------   --    v   vi v   i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_8871144_88   3520 TGAGGA-GAAAAAGACCCAGAATAGCCAACACAGTATTGAAGGAGGAGAA 3568
                           iii - v  ii                v   i v     ii  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_8871144_88   3569 CAAAATAGGAGGACTGACACTACCCAACTTCAAGAA--A--ATAGAGCTA 3614
                             i v        v     v     i     i v-- -- i i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_8871144_88   3615 GAGTAATCAA-ACAGTGTGGTATGCGCAAACGAACAGACA---------- 3653
                         v         -           ivv   v v i i     ----------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_8871144_88   3654 ---AAGAGAA---AGAGCCCAGAAACAGACCTACACAAATATAGTCAATT 3697
                         ---  v    ---    i       i i   i i   vv   i       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_8871144_88   3698 GATCTTTGACAAGCG-GCAAAGGCAATACAATGC--AAGAAATAGCGTTT 3744
                            i  i      v -  v   i v  v     v--  ii     iv   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_8871144_88   3745 TTAACAAATGGTGCTGGAACAACTGGAAACAAAAAAAAAAAAAGAAAAGA 3794
                          i               i         v ---------------------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATA--------------------- 429

  chr2_8871144_88   3795 AGCAAGGAAGCAAGAAAGCAAGCAAGAAAA-GAATCTAGACACAT---TC 3840
                         -? -------  ------  v    i i  -   vi i   v v ---  
  L1M4_orf2#LINE/    430 -KC-------CA------CATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_8871144_88   3841 ACAC--TTCACAAAAATTAACTCAAAATAGCTCACAGACCTAAATGCAAA 3888
                             -- vi                   i v   ?           i  i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_8871144_88   3889 AG-------TATAAAACACCTAGAAAATGACAGAGGATAAAATCTAGGTG 3931
                           -------        v i     i vi   v   ?vv      vv   
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_8871144_88   3932 ACCGTAGGTTTGGTGTTAACTTTTTAGATAGGACACTAAAAGCAAGATCC 3981
                            v i    v  iiv iii  i       v     i       vi v v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_8871144_88   3982 ATGAAAGAAAGAATTAGTAAGCTAGACTTCATCAAAA------ATGTCTG 4025
                          ii       i   vii   ii i             ------ iv i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_8871144_88   4026 CTCTGCAAAAGACACTGTCAAGAGAATGAAAAG-CAACCAAAAGAATGGA 4074
                         iv  v    i      i      i i       -     v v       i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_8871144_88   4075 GCAAAATATTTGCAAAAAGCTTATCTGATAAAGGACCATTAGCCAAAATA 4124
                         iv              vviiv          i    ivv  v   i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_8871144_88   4125 CACAAAGAACTCTTAAAACTCAACAATAAGAAAATGAACAACCTGACTGA 4174
                         i i            v       i     i  i ii  i    ii i ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_8871144_88   4175 AAAATAAGCCAAGACCTTCA-CAGCCAATTCACCAAAGAAGACATACAGA 4223
                              ii  v   ivi  v -i  v  v   v          i     i 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_8871144_88   4224 TAGCAAATAAGCACATGAAAATATGCTCCACAACATGTGTAAT 4266
                          i  v                v      v   v  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (104 / 75)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 5.41 (119 / 22)  


3089 26.37 2.24 0.34  chr2_9002197_9004817     1239  2129 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_9002197_90   1239 TGGAAACACATCCTATGTTCATGGATGGGTAGAATCAGTATTACGGAAAT 1288
                               v i    i            v  v   v i i    iivi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_9002197_90   1289 GACCATACTCC-AAAAGCAATTTACAAATTCAATGCAATCCCCATCAAAA 1337
                          i v       -v   vii  i    i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_9002197_90   1338 TACCACCATCATTCTTCACAGAGTTAGAAAAAGCAGTTCTAAAATTCATA 1387
                          v   v vv v  i  ii    iv v  v  iviii i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_9002197_90   1388 TGGAACCAAAAAAGAGCCCGCATAGCCAAAGCAAGACTAAGCAAAAAGGA 1437
                              viiv  ii  v  v v         i   vvi i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_9002197_90   1438 CAAATCTGAAAGCATCACACTACCTGATTTCAAACTATACTATAAGGCCA 1487
                             vi  i i vv       v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_9002197_90   1488 TAGTCACAAAAACAGCATGGTACTGGCATAAAAATAGGCACACAAACCAA 1537
                         i   v iv  i    ii              ii    i  i i i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_9002197_90   1538 TGGAACAGAATAGAGAACCCATAAATAAACCCAAATACTTACAGCCAACT 1587
                              i     v    ii   v           v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_9002197_90   1588 GATCTTCAACAAAGCAAACAAAAACGTAAAATGAGGAAAGGACACCCTTT 1637
                            i   i    i vviv   i v i vv    i      i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_9002197_90   1638 TCAACAAATGG-------ATAATTGGCTAGCCACATGTAGGAGAATGAAA 1680
                                    ------- i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_9002197_90   1681 CTGCATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTAA 1730
                         i  v i  ii i   v    v           i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_9002197_90   1731 GGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATTG 1780
                         i   i    iv     v  i           v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_9002197_90   1781 GAAAAACCCTTCTAGACTTTGGCTTAGGCAAGGATTTCATGACCAAGAAC 1830
                          ?iv  vi    vv   i    v        v i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_9002197_90   1831 CCAAAAGCA-AAGCAATAAAAACAAAGATAAATAGTTGGGACCTATTTAA 1879
                                  -      i    iv   i   i   iv v    i vv i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_9002197_90   1880 ACTGAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAACAGGC 1929
                          v v  i i      iiivv    i iv  vi   iv i   i  v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_9002197_90   1930 AACCCACAGA------GAAAATCCTCACAATCTATATACATCTAACAAAG 1973
                                   ------      vi ii   vii     --   i i  i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATA--TCTGATAAGG 748

  chr2_9002197_90   1974 AAATAATATCCAGAATCTACAACGAACTC----AA-TCAGTAAGAAAAAA 2018
                         i v vi          v  i  v      ----  -   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_9002197_90   2019 AACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCT 2068
                          -    i  i  v  i?    i     v     iv          v    
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_9002197_90   2069 CAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCCCAACA 2118
                          v                       i  i  i       i    i     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_9002197_90   2119 TCACTAATGAT 2129
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.62 (143 / 88)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.88 (23 / 8)  


1848 23.90 11.64 0.47  chr2_9007098_9008725      501  1136 (492)    L1M4_orf2#LINE/L1      202   908 (0)  

  chr2_9007098_90    501 AAAGTTAGGGGAATTACATTACCTGATTTCAAGACTAAGTATGAAGCTTC 550
                               i i   v i   i v  ii       i   v v  ii     v 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_9007098_90    551 GGTAACCAAGACAGTATGACACTGGCCTAAGGTCAGACACATAGATCAAT 600
                         i    i         i  ii      v     vi     i          
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_9007098_90    601 G-AACAGAATAAAGAGTACAGAAATAAAGCCATACATAGATGGTGAATTG 649
                          -  i     vi     v          v        vv     v     
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_9007098_90    650 --------CAA--------------TTCAAAAGGAAAA----AGTATTTG 673
                         --------   --------------     vi  i   ----   v   v
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_9007098_90    674 CAACAAATAGTGCTGGGACAAATGAATATACATATAGAAAA-AATAAATT 722
                                 i            v  i   ?v  i  iv    -   i  v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_9007098_90    723 TCAACCCTTGTCTCTTAACATACACAAAAATTAACTCAATATGGATCATT 772
                          vi    i ii   vi v    i                v        ?v
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_9007098_90    773 GATCTAGGCATAAAAACTAGAACTGTAAAACTTCTAGGAGAAATTAT--- 819
                           i   iiii   i i   i    i       ii   i     vi  ---
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_9007098_90    820 ---------TCATAAACCAAGGGCAGGCACAGGTTTCTTAG-TAAAAGAT 859
                         ---------  i i v ivi  vi     vv          -  vi v i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_9007098_90    860 AAAAAGCTC------CAAACTAAAAAAT---TAAATTC-ACTTCATCAAA 899
                         v      v ------    vv       ---      v-           
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_9007098_90    900 ATTTAAAAGTTCTGCTCTTCAAAATTCACCACTAAGGAAAGGAAAAGGCA 949
                            v    v  i  iv       ivv   i ii   i  iv      i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_9007098_90    950 AAC-ATAGG-TTGAAAAAAATTTTCATAATTTATCTATCTGACAAAGGAC 997
                          v - i  i- v i i     v  iii  v i  v       i  i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_9007098_90    998 TTATATCCAAAACATAGAAATAA----------TGAATTATAAAAAAA-- 1035
                           i      i  i   v   v  ---------- v   v       i --
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_9007098_90   1036 AATTAAACCCAAC--------AGTCAACAGATATGAACAAA-ATGTCCCA 1076
                            --       i--------i v   vi   v    i i -  v  i v
  L1M4_orf2#LINE/    802 AAT--AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_9007098_90   1077 AAAGAAGATACACAATTAGTCAAACAGTACAGGAAAAAAATGTTTGACAT 1126
                                   i    v i i   vv  i   v     i -  i ii    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACAT 898

  chr2_9007098_90   1127 CATTAATCAT 1136
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (88 / 62)
Gap_init rate = 0.03 (18 / 707), avg. gap size = 4.28 (77 / 18)  


2753 22.60 3.09 0.81  chr2_9009721_9012150.rev      742  1356 (1074)    L1M4_orf2#LINE/L1        1   629 (279)  

  chr2_9009721_90    742 TGGAGAAGTATTTTATATTTATGAGTTGGAAGACTTTACATTGTTAAGAT 791
                             i ii   iii  i  i   ii           v i           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_9009721_90    792 GGCATTTCTTCACAAATTCATCTATAGATTTAATGCAATTCCTAACAGAA 841
                             v v  i v      v     i     i  i     i    v  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_9009721_90    842 ACACTGGCAGTTTTTTTTTTTGGTAGAAATTGATAAGCTTTTCCTAAAAG 891
                         v - ii  v ii      ---- i         i     vv        v
  L1M4_orf2#LINE/    101 TC-CCAGCTGCCTTTTTT----GCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_9009721_90    892 TTATATGGAAATACTAAGGACCTTAAGTAACCAAGATAATTTTGAAAAAG 941
                          i          i v i     ivi i  i    i i   i         
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_9009721_90    942 TATAACAGAGTTTGAAGATTTACACTCCTGTGTTTCAAAACTCAT----- 986
                         v v    i    v  i  i i     i ivvi          i i-----
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_9009721_90    987 -GCTACTGTGATCAAGACACTGTGCTATTGGCATAAGGATAGACATATAA 1035
                         -     v  i         v    v  i                     i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_9009721_90   1036 ATCATTGCAACAAAATTGAGAGTTCAGAAATAAACC------TTTATGGT 1079
                             v  v  i i          i            ------        
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_9009721_90   1080 CAGTTGATTTTTGACAAAAGTGCCAAGGCAGTT-----GGGAAAGGATAG 1124
                           i        i     ii        i vi  -----       i    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_9009721_90   1125 TTTTTTCAATACACAGTGCTGGGACAATCAGGTTTCTATATGCACAGAAA 1174
                          i       i v ii            iii i v? i i     v ii  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_9009721_90   1175 TGAACCTG-ACCCTTACCTCACATCATACATAAAAATCAACTCAAAATGC 1223
                             vi  -    i         i    i i      i           v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_9009721_90   1224 CTCTTAGTCCTCAATGTAGCAGCTAAACCTATAAAACT-TCAGAAGACAA 1272
                         v  v?  v   v      iv       v          - i      v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_9009721_90   1273 CACAGGAGAAATTCTCTGTGACTTGTGATTGGGCAAAGACTTCTTAGATA 1322
                           i   ? v  v   ii     i vv i  i     v ii          
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_9009721_90   1323 TGACAACCAAATAATTGCCCATAAAGAAAAAAAT 1356
                              v v   vv iviv v i   ii       
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

Transitions / transversions = 1.83 (88 / 48)
Gap_init rate = 0.01 (7 / 629), avg. gap size = 3.43 (24 / 7)  

 913 17.94 11.07 2.67  chr2_9009721_9012150.rev     1677  1938 (492)    L1M4_orf2#LINE/L1      625   908 (0)  

  chr2_9009721_90   1677 AAAATAAAAAAATTGAATACTCGTATTTCAGAATTTAAAACTTTTACTAT 1726
                               i v      i i-i  i ----  i    v         iivv 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGAC-TTCAT----CAAAATTAAAAACTTTTGTGCT 669

  chr2_9009721_90   1727 TCAAAAGACACCTTTAAGGAAATGAAGAGATAAGCCACAG---GAGA-AA 1772
                              i     iv i   i  i    i   i  v      --- i  -  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_9009721_90   1773 AATACTTGCAAAACATGTGTCTGATACAGGACTTGGATCCAGAAGATGTA 1822
                             i       v   i i       vi       v        v  i  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_9009721_90   1823 CAGAACTCGTACAA-TCAATACTAAGAAGACAA----CCCAATTTAAAGA 1867
                         v       v     -      v   i       ----       ?   i 
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_9009721_90   1868 TGGACA--GAATTGCTAGTTACACATTTC------------------ATG 1897
                            i  -- i   -- iiv  v       ------------------   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATT--TGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_9009721_90   1898 GCCAATATGCAAATTAAAAGATGCTCAAGATCACTAGCCAT 1938
                                v   v  v             v    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (27 / 19)
Gap_init rate = 0.03 (9 / 284), avg. gap size = 4.00 (36 / 9)  


1777 26.95 1.77 0.53  chr2_9021507_9023195.rev      500  1063 (626)    L1M4_orf2#LINE/L1      266   836 (72)  

  chr2_9021507_90    500 TATGGTACAGGTACAAAAACAGACACATAGACCAGTGGATCAGAATAGAG 549
                          i      v  i i  ii i     i     i  i    vi     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_9021507_90    550 ATCTCAGAAATAATACCACACATCTACAACCATCTGATCTTCAACA-GAC 598
                          vii         vv   i    i  iiii  vi    i   i   - iv
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_9021507_90    599 TGACAAAAGCAAGCAACGGGGAAAGGATTCCCTATTTAATAAATGGTGCT 648
                           v   i v  vv   i        i  vvi  v  i  i          
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_9021507_90    649 TGAAAAACAGGCTAGCCATGTGCAAAAAATTGAATCTGGATCCCTTCCTT 698
                         v i v   v  v  ?   ii       i v    vi    i    v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_9021507_90    699 ACACCTTATACAAAAATTAACTGAAGATGGATTAAAGACTTAAATGTAAA 748
                              v                v  i      i ?    i         i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_9021507_90    749 ACCCAAAACTATAGAAACCCTAGAAGAAAATCTAGGCAGTA--CCATTAA 796
                          v i         i  vi i          iv    ?-   --i -  vi
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN-GTAAATC-TTCG 563

  chr2_9021507_90    797 GGACATAGGCATGGGCAAAGATTTCATGACAAAAACATCAAAAGCAATTG 846
                         v   v v  vv i     v i    v iivv vi   i        vvv 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_9021507_90    847 CAACAAAAGCAAAAATTGACAAATGGGATATAATTAAACTAAAGAACTTC 896
                                  v      v  i    v   iv v  i   v v  i     i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_9021507_90    897 TGCACAGCAAAAGAAACTCATCAG---AGTGAACAGTCCACCTACAGAAT 943
                           ii vv    i  v   -    i---      v  v v   i       
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACT-ATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_9021507_90    944 GGGAGTAAATTTTTGCAATCTAACCATCTGACAAAGGTGTAATATCCGGA 993
                              v    v       vii vvi      i  i  vv vi     i  
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_9021507_90    994 ATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAACAAA--GCC--AT 1039
                           v  i  i     ivv    v iv i  v     i     --i  --  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_9021507_90   1040 CAAAAAGTGGGCAAAGGACATGAA 1063
                         i?    i           iv    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAA 836

Transitions / transversions = 1.14 (79 / 69)
Gap_init rate = 0.01 (8 / 571), avg. gap size = 1.62 (13 / 8)  

 288 20.00 0.00 0.00  chr2_9021507_9023195.rev     1128  1197 (492)    L1M4_orf2#LINE/L1      839   908 (0)  

  chr2_9021507_90   1128 GACACTTCTCAAAAGAAGACATTTATGTGACCAACAAACATATTAAAAAA 1177
                             i     v        i  vi vi  i    i  i  i  v    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_9021507_90   1178 AGCTCAACATCACTGATCAT 1197
                         v           ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.00 (0 / 0)  


2802 24.49 4.38 2.36  chr2_9039326_9044876.rev     4182  5071 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_9039326_90   4182 TGGAAAAACCTCTCA-GCTTATGGATTGGAAGAGTCAATGCCACTAAAAT 4230
                               i iv  i  - i i             v i   iiiii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_9039326_90   4231 GGCCATACTGCCCAAA------------------GCAATTTCTATCAAAC 4262
                            v     v      ------------------     ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_9039326_90   4263 TGCCAA-TGTCATTTTTTACAGAA-TTGGAAAAAACT-ATACTAAAATTC 4309
                          v   i-  i -      i     -   -- v  i  -  v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_9039326_90   4310 ATATGGAACCAAAAAAGAGCCCAAATAGCCAAAGCAATCTTAAGCAAAAT 4359
                                 viiv  ii  v  vi          i       i iv  i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_9039326_90   4360 GAACAAAGCTGGAGGCATCATACTACATGACTT-AAAACTATACTATAAG 4408
                                 i      vv   i   v vii i  -      -     i  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr2_9039326_90   4409 GATGCAGTAACCAAAACAGCATGATACTGGTACAAA-ACAGACACA--AA 4455
                          v i      i   i    ii  i      i i  i- i     i --i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_9039326_90   4456 CCAATGGAACAGAATAGAAGACTGCA-AAATAAAGCCACACACCTACAGC 4504
                         i        i     v  -  v v  -       v   i   ii  ii i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_9039326_90   4505 CATCTAATTGTCAACAAAATTGACAAAAATAAAGAGTGGGGAAAGGACTC 4554
                           vi i   v  i    iiv  v   i vi vvv i         i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_9039326_90   4555 CCTAGTCAATAAATGGTGCTGGTATAATTGGCTAGCCATATGCAGAAGAA 4604
                         i  vv    i            v i  i   v  ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_9039326_90   4605 TGAAACTGGACCCCTACCTTTCACCATGTACAAAAATTAACTCAAGATGG 4654
                             ii             iv      i                 i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_9039326_90   4655 ATTAGAGATTTAAATGTAAGACCTCAAACTGTAAGAACCCTGAAAAAAAA 4704
                           i ?   ii           v  v     i   -   i  v i  i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAA 544

  chr2_9039326_90   4705 AAAAGCA-AGGAACATCATTTTATCTGGGCATTGACCTTGGG------AA 4747
                          ----  -   ?ii -- ----    vv ---          ------  
  L1M4_orf2#LINE/    545 A----CATAGGNGTA--A----ATCTTCG---TGACCTTGGGTTAGGCAA 581

  chr2_9039326_90   4748 AGGATTTATGACTAAGTCCTCAAAAGCAATTGCAACAAAAACAAAAATTG 4797
                         v  v  iv iiv  v v vi        vvv         iv      v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_9039326_90   4798 ACAAGTGGAACCTAATTAGAACCAAAAAGCTTCTGCACAGCAAAAGAAAC 4847
                          i  i v i  i v  i i  ii     -   i  ii vv    i  v  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACAC 680

  chr2_9039326_90   4848 TGTCAAGA--GTAAACAGACCACCTACAGAATGGGAGAAAATATTTGCTA 4895
                          i      --  i  v    v   i                       v 
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_9039326_90   4896 ACTGTGGATTTGACAAAGGTTTAATATCCAGCATCTATAAGGAACTTAAA 4945
                          iii iv  i   i  i  vi vi       v  v     i     ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_9039326_90   4946 CAGTTGGACAGGCAAAAAGCAAATAATCCCATT-AAAAATGGGCAAAAGG 4994
                           ii vi i ivv    ii       i  v   -             i i
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_9039326_90   4995 CATGAAAAGACACTTTTCAAAAGAAGACATACAAGTGTTCAACAA--ACA 5042
                         iv    v     i  i  v        i      i  vi   i  --   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_9039326_90   5043 TGAAAAAATTACTGCACATTACTAATCAG 5071
                               i  -i  vv    i ????????
  L1M4_orf2#LINE/    881 TGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (135 / 80)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.40 (60 / 25)  


3259 26.76 0.55 0.55  chr2_9058242_9064007     4367  5274 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_9058242_90   4367 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4416
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_9058242_90   4417 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCGTCCCCATCAAGC 4466
                            v     v     iv i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_9058242_90   4467 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4514
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_9058242_90   4515 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCCAAAAG 4564
                                viiv  ii  v  viv        i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_9058242_90   4565 AATAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTAGAAGGC 4614
                           i    i      vv    i  v  ii i      viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_9058242_90   4615 TACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATATAGACC 4664
                                 i   i    ii i       i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_9058242_90   4665 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 4712
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_9058242_90   4713 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGCGGAAAGGATTCC 4762
                          vi    i  i     ivv  v   i v  vvv    v      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_9058242_90   4763 CTATTTAATAAATGGTGCTGGAAAAACTGGCTAGCCATATGTAGAAAGCT 4812
                           v  i  i            i v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_9058242_90   4813 GAAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4862
                            ii    i i  v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_9058242_90   4863 TTAAAGACTTAAATGTTAGACCGAAAACCATAAAAACCCTAGAAGAAAAC 4912
                          i ?    i       v   v v     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_9058242_90   4913 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4961
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_9058242_90   4962 AAACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5011
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_9058242_90   5012 AATAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5061
                          vi   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_9058242_90   5062 CAGGCAACCTACAGGATGGGAGAAAATTTTTGCAATCTACTCACCTGACA 5111
                         v  i     i    i            v       vii ivi i    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_9058242_90   5112 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5161
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_9058242_90   5162 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5211
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_9058242_90   5212 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5261
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_9058242_90   5262 CATCACTGGCCAT 5274
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3234 26.76 0.55 0.55  chr2_9128559_9134958     5001  5908 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_9128559_91   5001 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5050
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_9128559_91   5051 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5100
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_9128559_91   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5148
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_9128559_91   5149 TGTGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5198
                          i     viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_9128559_91   5199 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTAGAAGGC 5248
                                i      vv    i  v  ii i      viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_9128559_91   5249 TACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGAGATATAGATC 5298
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_9128559_91   5299 AATGGAACAGAAC--AGAGCCCTCAGAGATAATGCCTCATATCTACAACC 5346
                                i    i--    i  --   i    vv  vi i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_9128559_91   5347 ATCTGATCTTTGACAAACCTGACAATAACAAGAAATTGGGAAAGGATTCC 5396
                          vi    i  i     ivv  v   v v  vvv   v       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_9128559_91   5397 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5446
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_9128559_91   5447 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5496
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_9128559_91   5497 TTAAAGACTTAAATGTTAGACCGAAAACCATAAAAACCCTAGAAGAAAAC 5546
                          i ?    i       v   v v     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_9128559_91   5547 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5595
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_9128559_91   5596 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5645
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_9128559_91   5646 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5695
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_9128559_91   5696 CAGGCAACCTACAAAATGGGAGAAAATTTTCCCAACCTACTCATCTAACA 5745
                         v  i     i   i             v  iv   vii ivi    i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_9128559_91   5746 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5795
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_9128559_91   5796 AAAACAAACAACCCCATCAAAAAATGGGCGAAGGATATGAACAGACACTT 5845
                           i     i     v  i?          i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_9128559_91   5846 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5895
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_9128559_91   5896 CATCACTGGCCAT 5908
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1838 16.58 6.72 19.50  chr2_9261609_9263512      496  1418 (486)    L1M4_orf2#LINE/L1      104   908 (0)  

  chr2_9261609_92    496 CAG-TGTCTTTTT-GTAGAAATTAACAAGTTGATTCAAGAATTCATATGG 543
                            -  i      - i       i     i    i v i           
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_9261609_92    544 AAATGCAAAGAACCTAGAATAGCAAAAACAACTTTGAAAAAGAA---CAA 590
                                 i i   i        v       ii           ---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_9261609_92    591 AGT---AGGACTTGCAAAT----ATTT---GACTTATTATAAAGTTACAG 630
                            ---      ii  vv ----    ---i     i  i    i     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_9261609_92    631 TTATCAAGAC--TGTGGTACTGACATCA----AGACA----GATCCGTGA 670
                          v        --          i   v ----     ----    vi  i
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_9261609_92    671 AACAAAATAAAGAGTCCAGAAATAGATCCAGGCATACTT---GTCAAATA 717
                           i i   vi              i i   vi   --  ---     v i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACAT--TTATGGTCAATTG 351

  chr2_9261609_92    718 TTTTTTCCTATAGG---CAAAA---TTCAGT----------T-GTCATTT 750
                         v    ivvi vi  ---   i ---    i ---------- -   v   
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_9261609_92    751 CAAAAAATGGTGCTGGTACAACTGGATATTAATAGGCAAAATAATAAACT 800
                            v            v           ?iv i v      v   i  v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_9261609_92    801 TCAGTTCATATCTCACACCGTAAACAAAAATTAACCCAAAATGGATTATG 850
                          viiii v  i        i  v            i          ----
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT---- 497

  chr2_9261609_92    851 TTTTTGGTTTTTGTTTGTTTGTTTGTTTGTTTATGGAGATGGGGGCTTCT 900
                         --------------------------------------------------
  L1M4_orf2#LINE/    498 -------------------------------------------------- 497

  chr2_9261609_92    901 CACTATGTTGCCTAGTCTGGTCTTGAACTCCTGGCCTCAAGCGACCCGCC 950
                         --------------------------------------------------
  L1M4_orf2#LINE/    498 -------------------------------------------------- 497

  chr2_9261609_92    951 TGCCCCGGCCTCTCAAAGTGGTGGGATTACAGATGTGAGCCATCACACCT 1000
                         -------------  ?  ----------------------------    
  L1M4_orf2#LINE/    498 -------------CAWAG----------------------------ACCT 506

  chr2_9261609_92   1001 GGCCCCAAAATGGCCTCAATCATAAACTAAGGTATACAACCTAATACTGT 1050
                         -------     ---------------    ------- v    v   i 
  L1M4_orf2#LINE/    507 -------AAATG---------------TAAG-------AGCTAAAACTAT 527

  chr2_9261609_92   1051 AAAATGTATAGAAGAAGACAGAAGA--AAGTCATCATGACCTTTGATTAG 1098
                             iviv        i   v i ?--  i  v  i       v i    
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_9261609_92   1099 GCAAAGATTTCGTCAATAC-ACATGACAGGCACAATCCATAAAAGAACAT 1147
                             v i    v vi   i-   iv v i      v v i       v v
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_9261609_92   1148 GTTGATAAATTGTACTTTATCAAAAT-----ACTACTGTTCTTAGCAACA 1192
                         i v         v    i        -----   vi   v   viv iv 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_9261609_92   1193 CACTATTAAGAGA-TGAAAAGGTAATCCATGGACTAGGAGAAAATACTTG 1241
                               i    i -       ii  i   ii  v i          i   
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_9261609_92   1242 CAAATTAAATATCTGATGAAGGACTGGTATCTTGAATATATACACAAACT 1291
                              i v         i i     v     iv         v -i    
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA-GAACT 776

  chr2_9261609_92   1292 CTCAAAACTCAATCATAAGAAAATGA-TAACCCAAATTTTTAAAA--GGG 1338
                           i v        v    i  i ii -        ---  ?    --   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAA---TTWAAAAATGGG 823

  chr2_9261609_92   1339 CAAAAGACTT----AGACACTTCACCAAAGAAGACATATAGACAGCAGAT 1384
                             i  i  ----     i   v          i   i i ii  vi  
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_9261609_92   1385 AAGCACAAGAAAAGATGATCCA-ACCATTCTCCTC 1418
                                v         v  v - i  ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (90 / 59)
Gap_init rate = 0.04 (30 / 805), avg. gap size = 8.07 (242 / 30)  


3850 17.02 8.51 1.18  chr2_9310698_9312536.rev      502  1347 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_9310698_93    502 TGAAAAAAACTTCCAAGTTCATAGAT-AGAAGAGGTTATGATAGATTGTT 550
                           i   i vv i   v      i   -i     v-   --   --     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTA--ATA--TTGTT 45

  chr2_9310698_93    551 AAGATGTCTATACTCCCCAAATTGAACTACAGTGTCAACATAACCTCAAT 600
                               v v                v      vv     ii  i i v  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_9310698_93    601 GAAAATCTCAGCTGGCTTTTTTGCAGGAATTGAAAAGTTGATCCTAAAAT 650
                         v      i      v           i      v   i            
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_9310698_93    651 TCATATGGAAATGCAAGGGAGCCTCAATAGCCAAAACAATCTTGGGAAAA 700
                                             v  vv                   ii   i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_9310698_93    701 AAAAACAAAGTTGAAAGACTCACACTTCCTGATTTCCAAACATACCATAA 750
                           i          i i             ii     v    v   i i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_9310698_93    751 GGCCTACAGTTAATTAAGGCTTTATGGTACTAGCATAAAGGATAGGCATA 800
                         i  -      -   i   i vv i       i      -      i    
  L1M4_orf2#LINE/    246 AGC-TACAGT-AATCAAGACAGTGTGGTACTGGCATAA-GGATAGACATA 292

  chr2_9310698_93    801 AAGATCAATGGAACAGAACTGAGGGTCCAGAAATAAACTCATATATCAGA 850
                         v            i    i    i              i    i  iviv
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_9310698_93    851 AGTAAATCAACTTTTAAAAAGGATGCCAAGAGAATTCAA-----GAAGAA 895
                         i  v   ii i   ii v    i        vv      -----i     
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_9310698_93    896 AAGTCTTCCCAAGAAATGGTGCCAGGACAACTAGATATATCCATATGCAA 945
                         v      ii   v         ii        i    ?--   i      
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK--CCACATGCAA 440

  chr2_9310698_93    946 AAGAATGAAGTTGGACCCCTACCTCACATCATATACAAATATTAACTCAA 995
                                                     i          v          
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_9310698_93    996 AATGGATCAAAGACCTAAATGTAAGAACTGAAACTATAAAAC-------- 1037
                                  ?                i  i            --------
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_9310698_93   1038 -AGAATATAGGTGTAAATCTTTGTGAC--TGTATTATGCAA--------- 1075
                         - i  i     ?         i     --  vi   v    ---------
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_9310698_93   1076 ----------CCAAAGG----------------AAAAATGACTATTCTGG 1099
                         ----------     i ----------------      iiv  vvi   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_9310698_93   1100 ATGTCATCAAAATTAAAAAATTT-GTCCTTTGAAGGACACCATCAAATGA 1148
                          iv                v   -  v   ii        i     ivi 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_9310698_93   1149 GTGAAAAAACAATCTACAAAATGGAAATTATTACTTGCAAATTATATATC 1198
                                i    i i   i     i ivv v  i        i       
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_9310698_93   1199 TGATCTGGGTCTAATGTTCAGA---------------TTACAACTCAACA 1233
                             vv   v  vi i i    ---------------           i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_9310698_93   1234 ATAAAAAGACAAATAATCCAATATAAACATGG-CAAAGGATTTGAATAGA 1282
                                         i     v?   v    -                 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_9310698_93   1283 TAGTTCTCCAAAGAAGATACACACA--GCCA-TGGGCATATAAAACAACA 1329
                         i v                i   v --    - ii   i  i   vi ii
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_9310698_93   1330 CTCAAAATCATTAGTCAT 1347
                              v    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (88 / 52)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.56 (82 / 18)  


3804 22.20 1.79 0.45  chr2_9362536_9365521.rev     1603  2494 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_9362536_93   1603 AAGATATTCCATATTTGTGGACTGGAAGAATCAATATTGTTAAAATGTCC 1652
                                i    i  ii    i       v i           i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_9362536_93   1653 ATACTACCCAGAACGATTTACAGATTCAATGCAATCTCTATCAAAATACC 1702
                              v    i vi   i           i      i          v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_9362536_93   1703 AA-TGCTTTTCTTCACAGAAATAGAAAAAATAACCCTAAGATTTATATAG 1751
                          i-   i   i  -i       v  v  iv i i     i   i    i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_9362536_93   1752 AACCACAAAAGACCCAGAATAGCCAAAGCTATTCTAAGCAAAAAGAACAA 1801
                           vii   ii                 i v  ii i iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_9362536_93   1802 AACTGGAGGAACCACATTACCTTACTT--AAATTATACTATAGAGCTATA 1849
                          ii       vi    i v  iv i  --   i -     i i     i 
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACA 252

  chr2_9362536_93   1850 GTAGCCAAAACAGTATGGTACTGGCATAAAAACAGACACATAGACTAATG 1899
                            ii   i     i              ii i     i     ii    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_9362536_93   1900 GAATAGA-----GAACCCAGAAATAAATCCATACATTTACAGTGAACTCA 1944
                                -----  ii           i           ii  v  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_9362536_93   1945 TTTTTTACAAATGTGCCAAGAACATACACTGGGGAAAGGACAATTTTTTC 1994
                             iv    iv         v   v  v         i i i i     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_9362536_93   1995 AATAAATTGTGCTGGGAAGACTAAATATCCATGCTCAGAAGAATAAAACT 2044
                           i    v         vi   ii   ?   iiiv  i      i  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_9362536_93   2045 AGACCTCTATCTTTCACCATACACAAAAATCAAACCAAAATGGATTAAAG 2094
                         i    i   i  iv       i        i  vi          i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_9362536_93   2095 ACTTAAATCTATGACCTCAAACTATGAAACTCCTATAAGAAA---T-GGA 2140
                           i     v  v  v  v       i      i  v      --- -  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_9362536_93   2141 G-AAA-CTGCAGGACACTGGTCTGGGCAAAGAATTCTTGAGTAATGCC-C 2187
                          -   -  v iv   vi   vi i     v iv     iii  -  v - 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGACAC 601

  chr2_9362536_93   2188 CACAAGCACAGGCAACCAAAGCAAAAACAGATAAATGGGATCATATCAAG 2237
                           v       i     v    v     i        v   iivi     i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_9362536_93   2238 -TTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAAGAGAC 2286
                         -       -   i  ii vv       v  v     v        i    
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_9362536_93   2287 AACCCACAAAATGGGAGAAAATATTTGCAAACTATCCATCTGACAAGGAA 2336
                                 i                      ii  vi      i    i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_9362536_93   2337 TTAATAACCAAAATATGTAAGAAGCTCAAACAACTCTATAGGAAAAAATC 2386
                         i vi  v   i     i   ii i   vv       v   iv     iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_9362536_93   2387 TAATGATCCAATTTTAAAAAGGGCAAAAGATATAAATAGACATATCTCCA 2436
                         v   i i      ?v    v       i   v i         v      
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_9362536_93   2437 AAGAAGACATACAAATGGCAAACAGGCATACAAAAAGGTGTTCAACATCA 2486
                                i           v  i i   i ii     i  i         
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_9362536_93   2487 TTGATCAT 2494
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.08 (131 / 63)
Gap_init rate = 0.01 (13 / 904), avg. gap size = 1.54 (20 / 13)  


2424 16.92 4.04 1.73  chr2_9706303_9707924      603  1122 (500)    L1M4_orf2#LINE/L1      352   883 (25)  

  chr2_9706303_97    603 ATTTTCTATAAGTGTGAGAATTTCAGATCAAGGATAAATGAATTGTTATT 652
                               v i   v   vv  vvi  v-    v ivi  v    v  iv  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGTCTTT 400

  chr2_9706303_97    653 TCAACAAATGGTGCCAGGGCAATTGGATATCCACATGCAAAAGAATAAAA 702
                                       ii  i   i      ?                i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_9706303_97    703 TTGGACCTTTTCCTCACTCCATATGCAAAAAGGAACTCAAAATGGACTAA 752
                                ii v      v      i      vv             ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_9706303_97    753 AGACCTAAACACAGGAGCTAAAATGATAAAACT--TAGAAGAAATCATAA 800
                                  iii i         iv        --         v    i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_9706303_97    801 GTATATATCTTCATGACCTTGGACTAGGCAATGGTTTCTTAGATCTTATA 850
                          ?i  v      i         ii                    v v i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_9706303_97    851 CCAAAAACATAAGCAACCAAAAAAAAAAAA---AAA--GGACTTCA---A 892
                               i  i       v   i      v ---   --        --- 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_9706303_97    893 AATTAACAATGTTTCTGCTTCAAAGGACACTAACAAGA-----------C 931
                               v  iv   v                 v     ----------- 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_9706303_97    932 AATCCACAGAACGGGAGAAAAACATTTGCAAATCATCTATCTGATAAAGG 981
                           i        i         -i             v          i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGG 749

  chr2_9706303_97    982 TCTAGTATCCATAATATATTTAAAAAAAAAAAAGATTACAACCCAATGAT 1031
                         v  v       v       -------   i  vvv       i    i  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATAT-------AAAGAACTCTTACAACTCAATAAT 792

  chr2_9706303_97   1032 AAAAACACAAATAACCCAATTTTAAAACAAGCAAAGGATCTGAACAGACA 1081
                              v               ?v    iii         i    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_9706303_97   1082 TTTCTCCAAAGAGCATATACTAAAGGCCAATAAGTACATGA 1122
                                     iv      v  v          i      
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

Transitions / transversions = 1.15 (45 / 39)
Gap_init rate = 0.02 (8 / 532), avg. gap size = 3.75 (30 / 8)  


 404 27.97 0.00 3.50  chr2_9916956_9919369      589   731 (1683)    L1M4_orf2#LINE/L1        1   138 (770)  

  chr2_9916956_99    589 TGGTAAGATATACCACACTCATGGATTGAAAGACTCAATATTCTTTAAAC 638
                            v       v   iii          i      i      v  v i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_9916956_99    639 GCTAGTTCTCCCTCAAATTGATTCTCTAGATGCAATACAATAATATTCAA 688
                          vi i v     -         -  vi    v   ii    vvivv    
  L1M4_orf2#LINE/     51 GGCAATACTCCC-CAAATTGAT-CTACAGATTCAACGCAATCCCTATCAA 98

  chr2_9916956_99    689 CATCTTAGCAGGTCTTTTAAAAAAAAAATTTAATAAGCAGACC 731
                         v   ii   v vii    viv i   ---  i i    v  i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAA---TTGACAAGCTGATC 138

Transitions / transversions = 1.22 (22 / 18)
Gap_init rate = 0.02 (3 / 138), avg. gap size = 1.67 (5 / 3)  

2001 23.56 4.61 2.31  chr2_9916956_9919369      895  1501 (913)    L1M4_orf2#LINE/L1      165   785 (123)  

  chr2_9916956_99    895 ACATAGAATAGCCAAAACAATTGTGAA---GAGGAACAAAATTGGAAGAG 941
                           vi                 iv    ---  i       i     i  v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_9916956_99    942 TTATGCTCTCTGGTTTCAAAACTTACTATGAAGCTAATAGTAATCAAGAT 991
                          i ii  ii iii               ii      -i           i
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTA-CAGTAATCAAGAC 263

  chr2_9916956_99    992 AGTTTGGTATTCAAGTAAATTTTGACATACAGATCAATAAAACAGAATAT 1041
                            v     i vivi   ivv v      i        ii  i     vv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_9916956_99   1042 AAAATTCAGAAATAGACCCACCCACACATATGGTCAACTGATTTTCAGCA 1091
                          i i i        i     i--   iv         i        ii  
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCAT--ACATTTATGGTCAATTGATTTTCGACA 361

  chr2_9916956_99   1092 AACGTGTCAAGACAATTAAATGGGGGGAAAGA-CAATCTTTTCAATAAAA 1140
                          iv   i      v   v       --     -i i         i   v
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGG--AAAGAATAGTCTTTTCAACAAAT 409

  chr2_9916956_99   1141 GGTAGTGAAATCATTGGTTGACTCAATGTACAAAGATGAATCTTAACCT- 1189
                            iv  ii iv i   v i? ivv   i v  ii     vi vi   i-
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_9916956_99   1190 TACCTCACACCA-ATTCAAAAATTAACTTGAAGCAGATCATAAAC-TATA 1237
                                     -  v            ii  iii     ? i  -  v 
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_9916956_99   1238 TGTAAGAGCTAAAATTATAAACCT-TTAAAAAAAAACAGAAGA--AAATG 1284
                                       i      v  -   i  i      v i ?--    v
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_9916956_99   1285 TTAGTGATCCTGGGCAAGGCAACTATTTTAAAAATAGGGCACAAAAAGCA 1334
                           v    i i    iv      ivi   ivv i   v i   v       
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_9916956_99   1335 AAAACTACAAAAGAAAATACAAAACTACATCAAATTTGGACTTCATCAAA 1384
                         v  i v           -----  -  v  -     -             
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAA-----AA-TAGAT-AAATT-GGACTTCATCAAA 651

  chr2_9916956_99   1385 AATTAAAATGTCTGCTCTTTGAAA-ACACCATTAGGAAAATGAAAAGGCA 1433
                          v v    iv i  iv   ii  i-    i  i i    i       i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_9916956_99   1434 AGTCTCAT--TGG---------CTTGTA--CCAGACTAT---ATAAATGA 1467
                          vi v  v--   ---------i   i --i  v -   ---    iv  
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATA-TATCTGATAAGGGA 750

  chr2_9916956_99   1468 CTTGTA-CCAGAATATATAAAGAATTCTCATGGCT 1501
                               -                 i   i iii  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

Transitions / transversions = 1.92 (92 / 48)
Gap_init rate = 0.03 (21 / 621), avg. gap size = 2.00 (42 / 21)  

 437 18.94 8.33 2.27  chr2_9916956_9919369     1791  1922 (492)    L1M4_orf2#LINE/L1      769   908 (0)  

  chr2_9916956_99   1791 AAAGAATTCTCACAACACAGTAATGATAAAAGACAA----------TTAA 1830
                               i   i     v  i    i --        ---------- ?  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAA--AAAGACAAATAACCCAATTWAA 816

  chr2_9916956_99   1831 AATTGTGTATAAGATTTGAGCAGATATTTTATCAAAAAAAAT-CACAGAT 1879
                           v  v i v i       ii   i    ivi    i  i  -i   i  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_9916956_99   1880 GTCGAATAAGCACATGAAAAAAATGCTGAACATCATTAGTCAT 1922
                          v v                i -    v       ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.03 (4 / 140), avg. gap size = 3.50 (14 / 4)  


 414 23.23 7.74 3.87  chr2_9929394_9931617.rev      493   647 (1577)    L1M4_orf2#LINE/L1      242   402 (506)  

  chr2_9929394_99    493 ATAAATCATACAGTAATC----TAGTGTGATGC------AAGGATAGACC 532
                          i   v -          ----i      i i ------          v
  L1M4_orf2#LINE/    242 ACAAAGC-TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_9929394_99    533 AAAAAATTGACAGAACTGAATAGAAAGTCCAGAAACGGACTCATAAGTAC 582
                         v v i  ii ii   iv    v  i          iii  i    ---- 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA----C 336

  chr2_9929394_99    583 ATATAAAAT-AATCTGATTTACAACAAAGCTGCTACTAAAATTCAGTGAG 631
                           v  vii -   -      v i    i v   i vv vv     i  i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_9929394_99    632 GAAAGAATAG-CTTTTC 647
                                   -      
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTC 402

Transitions / transversions = 1.57 (22 / 14)
Gap_init rate = 0.04 (7 / 161), avg. gap size = 2.57 (18 / 7)  

 819 26.57 6.64 1.05  chr2_9929394_9931617.rev      946  1231 (993)    L1M4_orf2#LINE/L1      386   687 (221)  

  chr2_9929394_99    946 GAAAGAATAGT-TTTTCAATAAATGGTTCTGAATCAATCAGACATGCATA 994
                                    -       i       v   iiv   iii  i ?v  i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_9929394_99    995 TG--AGAAAATTA--TTG-ACCCCTTTCTCACACTGTACACAAAAATTAA 1039
                           -- i i   v --   -      vi       ii  i           
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_9929394_99   1040 TTCAAA-TAGATC------CTACATGTGATAGGTAAAACCATAAAGCTTC 1082
                         i     - i    ------   v    i v  v      i     i  ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_9929394_99   1083 TAGAAAAAAA-A-AGTGGTAAATATCTTTATGATTTGGTGT--GG-AATA 1127
                              i    - -  v?      --   ii   ii v v  --  -   i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_9929394_99   1128 GACTTCATCAACAGGGCACAAAAAGCACTACTCCTAAGAGAAAAGGTCAT 1177
                          -i   v vi i v i   v        v vivvi  i      ii viv
  L1M4_orf2#LINE/    584 G-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_9929394_99   1178 TACACTGGATTTCATTAAA-TTAAGAACTTCGATTCATCAGAAGACATTG 1226
                           v i    i     i   -    i     ivi v v   i i    i i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_9929394_99   1227 TTAGG 1231
                          i i 
  L1M4_orf2#LINE/    683 TCAAG 687

Transitions / transversions = 1.96 (49 / 25)
Gap_init rate = 0.04 (13 / 302), avg. gap size = 1.69 (22 / 13)  

 380 28.39 7.20 3.39  chr2_9929394_9931617.rev     1502  1737 (487)    L1M4_orf2#LINE/L1      664   908 (0)  

  chr2_9929394_99   1502 TGT-CTTTAAAAAAAATTAAAAAAAAAAAGACATAATTAAAG-CAAACTA 1549
                            -   i   ii v i  vv  i   iv  -------    -   v i 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGA-------AAAGACAACCCA 706

  chr2_9929394_99   1550 AAAACTGAGAGAAGAAATTCACAA--TACATATTCGACAAG--ACATGTA 1595
                         v i v  i     i v   ii   --i i    ii  i   --  v    
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_9929394_99   1596 ----------ACAAAGGTTTCCTACCGATCTATTAAGAAATAATAAACAA 1635
                         ---------- i    ivi  i   viv  v  v vi   vi i   i  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_9929394_99   1636 TCCAGTT-AAAAATAGGCAAAAAGATTTGAACAGGTATTTCATAAAAGAT 1684
                         i   i  -      i      i-        i  ii     viv     v
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAG-GATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_9929394_99   1685 AACAGCTAAATGGTCAATAAATATATGAAAATGTACGCAACGTCATTACT 1734
                         i i vvi      i      ii i       vi i v    i   ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_9929394_99   1735 TAT 1737
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.91 (44 / 23)
Gap_init rate = 0.03 (8 / 245), avg. gap size = 3.12 (25 / 8)  


3222 26.50 1.11 0.44  chr2_9951190_9957574     4992  5893 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_9951190_99   4992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5041
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_9951190_99   5042 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5091
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_9951190_99   5092 TACCAATGACTTTCTTCGCAGAATTGGAAAAA---A--CTAAAGTTCACA 5136
                          v   iivi i  i  i      v v  v  i--- --     i    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_9951190_99   5137 TGGAACCAAAAACGAGCCCTCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5186
                              viiv  iv  v  vvv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_9951190_99   5187 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5236
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_9951190_99   5237 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACCAA 5286
                               i   i    ii         i iv ii i   v   i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_9951190_99   5287 TGGAACAGAAC--AGAGCCATCAGAAATAATGCTGCATATCTACAACTAT 5334
                              i    i--    i --         vv iii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_9951190_99   5335 CTGATCTTTGACAAACCTGACAAAAACAAGCAAAGGGGAAAGGATTCCCT 5384
                         i    i  i     ivv  v   i v  vv   v        i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_9951190_99   5385 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5434
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_9951190_99   5435 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5484
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_9951190_99   5485 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5534
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_9951190_99   5535 AGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5582
                            ?-   --i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_9951190_99   5583 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5632
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_9951190_99   5633 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5682
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_9951190_99   5683 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5732
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_9951190_99   5733 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAGGAAAA 5782
                         i  i  vi          v  i  v      vv    v iv i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_9951190_99   5783 AAACAAACAACCCCAT-GAAATGTGGGCAAAGGGTATGAACAGTCATTTC 5831
                          i     i     v  -?   vi          i v    i  v      
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_9951190_99   5832 TCAAAAGAAGACATTTATGCAGCCCACAAACACATGAAAAAATGCTCATC 5881
                           v        i  vi viii   v i  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_9951190_99   5882 ATCACTGGCCAT 5893
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3210 26.70 1.56 0.11  chr2_10017849_10024512.rev     5278  6172 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_10017849_1   5278 TGGAAGAACATTCCATGGTCATGGATAGGAACAATCAATATCGTGAAAAT 5327
                              ii i  i     v        v    v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_10017849_1   5328 GGCCATGCTGCTTAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5377
                            v  i  v ii  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_10017849_1   5378 TACCAATGACTTTCTTCACAGAACTGGAAAAA---A--CTAAAGTTCATA 5422
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_10017849_1   5423 TGGAACCAAAAAAGAGCCCGCATTGCCAAAACAATCCTAAGCAAAAAGAA 5472
                              viiv  ii  v  v v  v            i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_10017849_1   5473 CAAAGCTGGAGGCATTACACTACCTGACTTCAAATTATACTACAAGGCTA 5522
                              i      vv i     v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_10017849_1   5523 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5572
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_10017849_1   5573 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5622
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_10017849_1   5623 GATCTTTGACAAACCTGACAAAAACAAGAAGTGGGGAAACGATTCCCTAT 5672
                            i  i     ivv  v   i v  vvv i        vi  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_10017849_1   5673 TTAATAAACGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5722
                          i  i   i    i     v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_10017849_1   5723 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 5772
                         i    i    v   i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_10017849_1   5773 AGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5822
                             i  v    v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_10017849_1   5823 GCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAAAC 5871
                          ?i- v i -   iv   v v  vv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_10017849_1   5872 ACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGACCTAATTA 5921
                                   vvi          vv        i    v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_10017849_1   5922 AACTAACAAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA---- 5967
                           v v v  i   i  ii vv    i  v    i  vv i      ----
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_10017849_1   5968 CAACTTACAGAATGGGAGAAAATTTTTTCAATCTACCCATCTGACAAAGG 6017
                             ii                 v   v   vii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_10017849_1   6018 GCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAAA 6067
                         i  vi          v  i        ivv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_10017849_1   6068 CAA----CCCCATCAAAAAGTGAGCAAAGGATATGAACAGACACTTCTCA 6113
                            ----   v  i?    i  i         v    i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_10017849_1   6114 AAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCATC 6163
                                 i  vi viii     i ii          i       v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_10017849_1   6164 ACTGGCCAT 6172
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.50 (15 / 6)  


3956 14.82 2.54 1.74  chr2_10338374_10341633.rev     1582  2330 (930)    L1M4_orf2#LINE/L1        3   757 (151)  

  chr2_10338374_1   1582 GAAAAAAATCCCATAATCATAGATCAGACAACTTAATTTTGTTAAGATGA 1631
                             i v       iv    i   ii  vi       v           i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_10338374_1   1632 CAGTACTCTCCAAATTGATCTACAGATTTAATGCAATTCCTGTCAAAATC 1681
                           i     i                   i  i     i   i        
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_10338374_1   1682 TCATCT---TTATTTGCAGAAATTGATAAGCCGACCCTACAAAATTCACA 1728
                         i  v  ---  v              i    i  i    --       i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA--AAATTCATA 150

  chr2_10338374_1   1729 TC------CAAGAGACCTGGAATAGTAAAAACA-TCATAAAAAAGAA--- 1768
                          v------    i    ii      iv      -  v i        ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_10338374_1   1769 CAAAGTTGGAGGGATTTCACTTCCCAATTTCAAA-CTTATTATAAAGCCA 1817
                                     iv iv                 -    i  i     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_10338374_1   1818 CAGTAACCACGACAATGTGATACTGGCATAAGACACAGACATATAGACCA 1867
                               i  v    i    i            i- i           i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAGACATATAGATCA 299

  chr2_10338374_1   1868 ATGGAATAGAATTGAGAGTCCAAAAATAAACCCTTACATTTATGGTCAAT 1917
                                               i          v                
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_10338374_1   1918 TGATTCTTGACAATGGATCCAAGACAATTCAATGGGGAAAGAGATTGTTT 1967
                              i i     v  vv       v                -  v  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCT 398

  chr2_10338374_1   1968 TTTCAACAAATGGTGCTGGGACAGCTGGATACGCACATTCAAAAGAAATT 2017
                                                i       ?v     v        - v
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TG 447

  chr2_10338374_1   2018 AATTTGGACCCCCATCCCACGCTATGAATAAAAATTAACTCAAAATAGAT 2067
                           v         i i i   i i  iv i                 i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_10338374_1   2068 TAAAGACCTAAATGTAAGAGTGAAAACTATAAAACTTTTAGAAGAAAACA 2117
                         i ?                 iv              i             
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_10338374_1   2118 TAGCCATAAATCTTCATGATTCCTGGAT-AGGTAAATAGTTTCTTAGATA 2166
                            v?i         i   i- i   i -   i  - i            
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAA-TGGTTTCTTAGATA 595

  chr2_10338374_1   2167 TGACACCAAAATCACAAATGATTTATAAAAAAA--GATAAATTGGACTTA 2214
                                    v     iii ivv vi      --              v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_10338374_1   2215 ATCATAACTTTCAAGAACCTTTTTTATGCTTCAGAAGAGACCATCAAGGA 2264
                             v  i ---  i   ---    i       i i  v  i      i 
  L1M4_orf2#LINE/    646 ATCAAAATT---AAAAAC---TTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_10338374_1   2265 AGTGAAAAGACAACCCACAGAATGAAAGAAAATATTTGCAAATCTTATAT 2314
                                                 ii                  v     
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_10338374_1   2315 CTACTAAG--ATTTTTAT 2330
                           iv    -- i  v   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTAT 757

Transitions / transversions = 2.09 (73 / 35)
Gap_init rate = 0.02 (16 / 755), avg. gap size = 2.00 (32 / 16)  

 604 17.16 3.73 2.99  chr2_10338374_10341633.rev     2627  2760 (500)    L1M4_orf2#LINE/L1      740   874 (34)  

  chr2_10338374_1   2627 CTACTAAGGGATTTTTTATTCAGAACATATGAAAGACTCTTACAACTCCA 2676
                           iv       -i  v   i     i    i  ii             v 
  L1M4_orf2#LINE/    740 CTGATAAGGGA-CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_10338374_1   2677 TCATTTAAAAAAAAC-----CCTCAATCAAAACATGGGCAAAGGATTTGA 2721
                          v  ---     i  -----v i    i?   v                 
  L1M4_orf2#LINE/    789 TAAT---AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_10338374_1   2722 ACAGAGGTTTCTCCAAAGAAAATACACCAATGGCCAATA 2760
                          i   vi             i   i  v           
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.02 (3 / 135), avg. gap size = 3.00 (9 / 3)  


4156 18.23 1.29 4.10  chr2_10598286_10601545     1861  2787 (473)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_10598286_1   1861 ATATTCCATGTTCATGGATTGGAAGACTCAATATGGTTATGATGGCAGTT 1910
                             i                       i     v    v       i v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_10598286_1   1911 CTCCTCAAAGTGATCTGTAGATACATTGCGATCATTATAAAAATCTCAGC 1960
                             i    v      ii    v  vi  i   vi   v      i    
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_10598286_1   1961 AAGCATTTTTGCAGAAATTGACAAGCTAATTCTATAATGTATATGAAAAT 2010
                         viv v                      i  i   v   vi     i    
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_10598286_1   2011 GCAAAAAACCCAGAAGAGCCAAAACAATTTTGAAAAAGAAGAAAAGAGTA 2060
                             iii        v            i              v i   v
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_10598286_1   2061 GGAGAATTCACACTTCCTAATTTCAAAATTTATTGTAAATCTATTGTAAT 2110
                             i i          i          i   i ii   v   iv     
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_10598286_1   2111 AAAGACAGTGTAGTACCGGCATAAAGATATGTATGTGTGTGTGTATATGT 2160
                         v          i    i       i    ------------------- -
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATA-------------------G- 287

  chr2_10598286_1   2161 ATACACATACATAAATATATATATGGAACTGGATTAAGAGTTCAGAAATA 2210
                         --   i   v  v   --------    iv i   i     i        
  L1M4_orf2#LINE/    288 --ACATATAGATCAAT--------GGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_10598286_1   2211 AAACCTTACATTTATGGTTAATTGCTTTTGAACAGAAGTACTGAGGCTAT 2260
                           v  v            i     v    vi   iii  i ii  i i  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_10598286_1   2261 TCCATGGAGAAAAAGAATAG-CTTTTTAACAAATGATGCTGGAATAATTG 2309
                           v    i    --      -     i        i      i i  i  
  L1M4_orf2#LINE/    378 TCAATGGGGAAA--GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_10598286_1   2310 TATACCCACATGCCAAAAGAA-GCATTCAGATCCTTACCTCACACCTTAT 2358
                         v   ?        -       - v v ii  i  i           v   
  L1M4_orf2#LINE/    426 GATAKCCACATGC-AAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_10598286_1   2359 AAAGAAATTAACTTATAATAGATCCTAGACCTAAGTGCAAGACCTTAAAC 2408
                          v i         i v   i    v?        i  i    v  v    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_10598286_1   2409 TATAAAACTTTTAGGAAAAAACATAGAA-TACAATCTTTATGACCTTGAG 2457
                                  i    i i         i?-  -      ii        i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTA-AATCTTCGTGACCTTGGG 573

  chr2_10598286_1   2458 TTAGGCAAAGAGTTCTCAGATA-----CCAAAAGTGCAAGTGGTAAAAGG 2502
                                 v iv    i     -----       ii    iiii     -
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG- 622

  chr2_10598286_1   2503 AAAAAATTGATAAATTGGACTTCATCAAGATGAAAACCTTTTGTGCTTCA 2552
                                v                    i  v    v             
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_10598286_1   2553 AAAGACAACATTAGGAGAATGGAAAGACAAGCCACAGACTAGTAGAAAAT 2602
                           i    vi  i i  i i  i        v       v i v       
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_10598286_1   2603 TTTTATAAAACATATACCTGATGAAGGACTTCTACCCAGAATATATGAAG 2652
                         v   ii   v      i     i i      v  i           i   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_10598286_1   2653 AACTCTTACAACTCAATAA---GACGACATACAACCCAATTTTAAAAATA 2699
                                            ---i v    v i         ?-      i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATG 821

  chr2_10598286_1   2700 GGCAAAATATTTGAATAGGCATTTTACCAAA-AATACAAATAAATGGCTA 2748
                               iv          i     iv     -  v i v i       i 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_10598286_1   2749 ATACACATATGATCAAAACCACTAGTCATCAGGGAAATG 2787
                            vi  i    --   ivii  viv     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGA--AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (107 / 58)
Gap_init rate = 0.02 (15 / 901), avg. gap size = 3.33 (50 / 15)  


2711 17.28 8.16 2.08  chr2_10988747_10990371.rev      501  1125 (500)    L1M4_orf2#LINE/L1      230   892 (16)  

  chr2_10988747_1    501 TCAAAACTTACTACAATATTGCAGTAATAAGGACTATAATCAAATATATA 550
                                         vii i       v i   --- i vvii  i---
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGAC---AGTGTGGTAC--- 273

  chr2_10988747_1    551 TGTCATAAAGACAGACATATAGATCAATAGAATA---------------- 584
                           v     i  i                i     ----------------
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_10988747_1    585 ---AAACCCTCACCTTTATTGTCAAATTGATTTTCAAAGAGGGTGACAAA 631
                         ---      vi  v     v     -         i vi      v   i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAA-TTGATTTTCGACAAGGGTGCCAAG 372

  chr2_10988747_1    632 ACAATTCAATGGAGAAAGAACAGTCTTTTTAACCAAAGGGGCTGGGA--- 678
                           v         i       i        i   v  v  v       ---
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_10988747_1    679 ------AATCATTTATGCAAAAGAATAAAGTTGGACCTTTACCTCACACC 722
                         ------ ?i  i--            i          ii           
  L1M4_orf2#LINE/    423 CTGGATAKCCAC--ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_10988747_1    723 ATATACAAAA-TTAACTCAAAACAGATCAAAGACCTGAATGTAAGAGGTA 771
                                   -           ii     ?      i          v  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_10988747_1    772 AAACTATAA--CTCTTAAAAGGAAACATAGGCA-ATATCTTAGTGGCCTT 818
                                  --      i   i         ?i- v     v   i    
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_10988747_1    819 AGATTAAGCAGTGAGATGCTTCTGAGAT--GACACTAAAAGCACAAATGA 866
                         i i   i   i  ---- i    v    --     i          iii 
  L1M4_orf2#LINE/    571 GGGTTAGGCAATG----GTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_10988747_1    867 CCAAAGAAAAAATAGATA----------CAT-----TTAGAA-CATTTGT 900
                          v                ----------   -----   i  - v     
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_10988747_1    901 GTGTCAAAGGACACTATCAAAAAAGTGACAAAAAGACCCATAGAATGGGA 950
                          iv                 i       v  i vi     i         
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_10988747_1    951 GTACATATATGCAAACCATGTATTTGATAAGTGGCTAGTATCCAAAATAT 1000
                          v v    v      i   i   i       v i  v       i     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_10988747_1   1001 ATGTTAGCCCCTTAGAACTCACCAATTAGAAGACAAATAGCCCAATTTAA 1050
                           ivviiv i    v      vi   v i          i       ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_10988747_1   1051 AAATGCTCAAAGGATGTGAATAAAAATTTCTCCAAAGAGACTATGCAAAT 1100
                              vv        v      i v             iiv   i     
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_10988747_1   1101 AGCCAACAAGCACATAACAA-ATGCT 1125
                         i     i        i v  -     
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.60 (64 / 40)
Gap_init rate = 0.02 (15 / 663), avg. gap size = 4.27 (64 / 15)  


3258 27.12 0.55 0.44  chr2_11087082_11093360.rev     4881  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_11087082_1   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_11087082_1   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_11087082_1   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_11087082_1   5029 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_11087082_1   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_11087082_1   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATT 5178
                                 i   i    ii         i iv ii i   v        i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_11087082_1   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_11087082_1   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_11087082_1   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_11087082_1   5327 GAAACCGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            iii   i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_11087082_1   5377 TTAAAGATTTAAACGTTAAA-CTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v i -       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_11087082_1   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_11087082_1   5476 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5525
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_11087082_1   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_11087082_1   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_11087082_1   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_11087082_1   5676 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_11087082_1   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_11087082_1   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


 755 32.04 13.44 3.02  chr2_11120871_11123635.rev     1489  2284 (481)    L1M4_orf2#LINE/L1       30   908 (0)  

  chr2_11120871_1   1489 AAGACCCAATATAAAAAAGATGTTAATTCTTCCAAAAATGATTCATAGAT 1538
                              ii     vivv      vi   v  i  v   v    ii i    
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGAT 79

  chr2_11120871_1   1539 TTAATGGAATTCCAACTTTAAAACTTCAGTAGGATTTTTCACTAAACTCA 1588
                          i  i v   i  v -- i    iii   iv vv     ii vi  v ii
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTA--TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chr2_11120871_1   1589 ATGAGCTTATTCTAAAATTTATATGGAAGAATAATAGACCAAGACCAGCC 1638
                          ii    v  i        i        ivii  vi    v   vi    
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_11120871_1   1639 TAAAAC--TCTTTGGA--GGAGGATGGGGGTGGGGG--TTGC-CCTCTGA 1681
                         -     --    vii -- i  i iiii v   i  -- ii - i  iv 
  L1M4_orf2#LINE/    178 -AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_11120871_1   1682 ATCTAGAAGCACATCACACAG----AG-----GGGGCAGTTTTGTG-TGG 1721
                           i vi  i vi ii   v  ----  -----ii i    v v  i-   
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_11120871_1   1722 GATCAGAAACAGGCAGGCA-AGCACAGAGAATAGAATTG-GAGGAACTCT 1769
                         v  v  i -i  i  vii - v  - vi           -   ------ 
  L1M4_orf2#LINE/    277 CATAAGGA-TAGACATATAGATCA-ATGGAATAGAATTGAGAG------T 318

  chr2_11120871_1   1770 CCA---ATGATTTGCAGGTGTGTAGAAACGGGCTACTGACTCAGCTGGCA 1816
                            ---  i vii-  viii v  ----i  v v i   i i--ii i  
  L1M4_orf2#LINE/    319 CCAGAAATAAACC-CATACATTTA----TGGTCAATTGATTT--TCGACA 361

  chr2_11120871_1   1817 A---TG--AAGGTCGT-----GGAAGAAGGACAGACTCTTTAATGAAGAG 1856
                          ---  --   ii i -----  iii   i i  v  i  i  ii  vi 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_11120871_1   1857 T--------AATTGATTAACTACAGGACAAACACTGAAATCGGATCTTTA 1898
                          --------  i  iv  ? i   v vv   v v    i i   i ii  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_11120871_1   1899 CTTTATCTCTTAATGTAAAAATAAATCTCAAA-TGGATTAAAGACTTAAT 1947
                          i i ivi v  - ii      v  -      -     i ?    i   v
  L1M4_orf2#LINE/    462 CCTCACACCATA-TACAAAAATTAA-CTCAAAATGGATCAWAGACCTAAA 509

  chr2_11120871_1   1948 TATTAAAGTCAAAACT-TAGA-------GAATATGATATAGGAGAATATC 1989
                          i v i  ii      -  i -------   v vi i     ? v v   
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_11120871_1   1990 TTCATGGTCTCGGGGTAGAAAAGAATT----AGTTA-------------- 2021
                            i  ii  i   v   iv  vii  ----  v  --------------
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_11120871_1   2022 -AAGCAACCCCTAACGGAAAAGATTAATACATTTG-CAGCATTAAAA--A 2067
                         -       ----  vi     i  vi   v   v - vv   i    -- 
  L1M4_orf2#LINE/    610 CAAGCAAC----AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_11120871_1   2068 AATA---TTGTTCATCCAAG--CTCTAT-AACAAAATTCAAA--TAAGAC 2109
                           v ---    v v  v   -- v    -  v   i vv   --i  vv 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_11120871_1   2110 ATGAATTAGCAGAAGGTATTATCAA--CACATGACTGACGAAAGA----- 2152
                          iii v i v    ii    vv   --  i  iv    ii ii  -----
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_11120871_1   2153 -TCTAGAATATATTAAAATTTCTAATAA---GATAAGAAAAAGCTC---- 2194
                         -  i         v  i vi   v i  ---i    v      viv----
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_11120871_1   2195 -CCCAATAGAAAAAAATACAAAAGA-------AAGCACTTTGCAGAAGAA 2236
                         -      v?     vivi    i  ------- ii  i  iv vi     
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_11120871_1   2237 G---CACAGATACCCGATTAATATGTGAAAAGCAACTGAAC--CATATTA 2281
                          ---i   i  iv  i  v ii ii       vvi  v   --  ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_11120871_1   2282 GCA 2284
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.64 (156 / 95)
Gap_init rate = 0.05 (43 / 879), avg. gap size = 3.05 (131 / 43)  


1098 29.63 10.39 3.19  chr2_11148771_11150653      549  1395 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_11148771_1    549 TAGAAAGACATCCTATGTTCTTTGATAGGGAAACACGACATCACTGAGAT 598
                          i      i    i      v v   v  i i  vii i  iii i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_11148771_1    599 GTTAGTTCTCCCTAAATTGAGGTATAGATGTAACACAATGCTAATGAAAA 648
                          vi i v     i       vv  i    vi   i    v iv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_11148771_1    649 TATCA-CCATTTTTTTTCTGGAGCTGAATAAGTTGATTATGAGGTTCATT 697
                          vi  - iiii      vii  iv vi i   i    iv i ii     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_11148771_1    698 TGAAGA---AAGAAACAAGCAAGAATAGCCAGGA-AATTTCTGAAAAGAA 743
                           i i ---   ii  --- v          ii -   i ivi       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_11148771_1    744 GAGTAGCAAG--AAAGAGCTC-TACATACCAATT---AAACT-ATT---- 782
                           ii --   --ii  ii   -i  v v      ---     - i ----
  L1M4_orf2#LINE/    198 GAACA--AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_11148771_1    783 --TTTCATTAA---AGA-AGTGTGATATTAGT----GAATGAATAGATAA 822
                         --i v  v   ---   -      i  i i i---- i  ii i v   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_11148771_1    823 GCCAATGGAACCAAATGGAAAAATTAAACTATAGAGCCATATATAGTATA 872
                         ii        ivi   v  i ivii i v-   i v     i  -v   i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAA-ATAAACCCATACAT-TTATG 343

  chr2_11148771_1    873 A--AATAAA-----GACA-GAATCTCAAG-----TCAATGGGGAGAAGAT 909
                         i--   vi -----    - ii vi    -----          i ii  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_11148771_1    910 GGACTTTTTAATAAATGAAATTAGTTAGTATAACTAAATAAACATAGGAA 959
                         i v     i  i     i--- - i i v i    ii   ?v  i v v 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGG---T-GCTGGGACAACTGGATAKCCACATGCA 439

  chr2_11148771_1    960 AAAAGATGAAATGAAATTGTATATTT--TTCATACCACACACCAGGATAA 1007
                            i-----      i   v ivii --i   i    i i  v ii  v 
  L1M4_orf2#LINE/    440 AAAG-----AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_11148771_1   1008 ATATTAAATGGAT---------AAACATAAAAAC-----CTTTATAAGTG 1043
                          iviv        ---------   ii   i i -----  v  v  v v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_11148771_1   1044 CTAGAAGAAAACAT--GAGTAAACTTCTCCATAATCTAGGAGTGAGAAAA 1091
                         i             -- ?     --   i i i i  v  iv ii v  v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_11148771_1   1092 ACTTCCTTAACAATGACTCAAAATCCAGAAACAATAAAGAAAAAGAAGGA 1141
                         iv  i    ivv     v v   vv  v  i   i   ii    i vi  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_11148771_1   1142 TAAATTTGACTACATAAAAATTTTAAAAAGATTTTGCATATCAAACAGCA 1191
                               v    v   v      ---    iv     iiiv     vii  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATT---AAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_11148771_1   1192 GAAGCAATGA---GAAAAGCAAATACCA----ATTTGAGAAA-TATTTT- 1232
                         vv v   vi ---      vv  i-   ----  vv      -     v-
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAAC-CCACAGAATGGGAGAAAATATTTGC 728

  chr2_11148771_1   1233 --ATCCTTTGTC--ACA-GGAA---------AAAATTTATGAAGAGCTTC 1268
                         --   v v i  -- i -  i --------- i   v   i    i  ii
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_11148771_1   1269 TAAAA---AATGAGATAAAAATACAAAGCAAACCCTGTAGAAAAATAGTG 1315
                           v  ---   i --      v     v--     vi v?      i vv
  L1M4_orf2#LINE/    779 TACAACTCAATAA--TAAAAAGACAAAT--AACCCAATTWAAAAATGGGC 824

  chr2_11148771_1   1316 TAAGAATATGAATAGGAAGTTCAC---AGAAAA-ATAAAAATGACTTTTA 1361
                         v   i  v       iv v   v ---    i -   v     i ivv  
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_11148771_1   1362 A-CAGTATGAAAAGATGCTTAACCTTGCTCATAAT 1395
                          -  -i             i   v ii????????
  L1M4_orf2#LINE/    875 AGCA-CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (153 / 95)
Gap_init rate = 0.05 (43 / 908), avg. gap size = 2.67 (115 / 43)  


1098 16.06 1.04 0.00  chr2_11178240_11181395      896  1088 (2068)    L1M4_orf2#LINE/L1        1   195 (713)  

  chr2_11178240_1    896 TGGAAAGCCATTCTATATTCGTGAATTATAAAACTTCATATTGTTAAGAT 945
                                vi  i i  i   i  i   iv  i    v             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_11178240_1    946 GGCAATACCCTCCAAATTGACCTACATATTCAATACAATCTCTATAAAAA 995
                                 i i         i     v      ii     i    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_11178240_1    996 TTCTAGCTGCTTTCTTT-CTGAAATTGACAAGATAA-CCTAAAATTCACA 1043
                          i i      i  i   - v            v i -           i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_11178240_1   1044 TAAAAATGCAAGGGCCCCAGAATACCCAAAACAATCTTGAAAAAG 1088
                          ii           v         v                    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

Transitions / transversions = 2.44 (22 / 9)
Gap_init rate = 0.01 (2 / 195), avg. gap size = 1.00 (2 / 2)  

3315 16.98 3.85 1.71  chr2_11178240_11181395     1964  2664 (492)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr2_11178240_1   1964 AAGTAGAACAAAGTTGGGGAATTTACACTTCCTGATTTCAAAATTTACTA 2013
                            v             i i i i        ii         i      
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_11178240_1   2014 CCAAGCTAGAGTAATTAAGACAATGTGGCACCCACATATGGATAAATACA 2063
                          v      v      i      i     i  ivi    v     i i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_11178240_1   2064 TAGATCAACGGAATAGGATGGACGGTCCAGAAATAA-CCCATACATCTAT 2112
                                 i       i  v  vi            -         i   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_11178240_1   2113 GGTCAATAGATTTCAGACA----TGACAA-----TTCAAAGGATAAAGAA 2153
                                v     iv    ----  v   -----     v  iv      
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_11178240_1   2154 GAATCTTTTCAGCAGACG-TGCTGGAACCATCATATAGTCCCACGCAAAA 2202
                         v i        i  i i -      i  v iiiv   ?i v  i      
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_11178240_1   2203 GAATGAACTTGGACCCTTACCACACCCCGT-TAGCAAAAATTACCTTAAA 2251
                                v        i    v   v  i -  -         v  i   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATA-CAAAAATTAACTCAAA 491

  chr2_11178240_1   2252 ATGGATGAAAGGCCTAAATATAAGAGCTAAAACTATAAAACTGTTACTCC 2301
                               v ?  i       i                      v   v---
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG--- 538

  chr2_11178240_1   2302 CCCAACACATACAAAAAAGCATAAATCTTTATAGCTTTGGATTAGGGAAT 2351
                         vvv  v     ------i ?i        ii ii i    i     v   
  L1M4_orf2#LINE/    539 AAGAAAACATA------GGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_11178240_1   2352 CGTTTCTTAAATATGACACCTAGAACACAAGCAGCTAGAGAAAAGATTCG 2401
                         v        i          v i i        i v i      i  -v 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT-AG 631

  chr2_11178240_1   2402 GTAAATTGGACTTTG---AAATTAAAAACGTTTGTGCTTCAAAGGACACT 2448
                         i            ii---           v                    
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_11178240_1   2449 ATTCCAGAAAGCGAAAAGACGACCCATGGAATGGGAAAAAATATTTGCAA 2498
                           - v      i        i     ii        i             
  L1M4_orf2#LINE/    682 AT-CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_11178240_1   2499 TCCATATATCTGA----GGA----TACTTAGAATATATAAAGAACTCTCT 2540
                         vi           ----   ----  iii                   iv
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_11178240_1   2541 CAACT---TAATAAAAAGACAAATGCCCCAACTAAAGAATCAGCAAAGGA 2587
                              ---                iv     i ?  i   vi        
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_11178240_1   2588 TTTAAATAGACATTTCTCCAAATATTATATAATAATGGCCAATCAG-ATA 2636
                            i                  v vv     vv          v  - i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_11178240_1   2637 TGAAAAGATGCTCGACCTCATTAACCAT 2664
                                      i  v   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (70 / 45)
Gap_init rate = 0.02 (15 / 716), avg. gap size = 2.60 (39 / 15)  


 755 24.56 2.63 5.26  chr2_11369386_11374881     3204  3431 (2065)    L1M4_orf2#LINE/L1        1   222 (686)  

  chr2_11369386_1   3204 TGGAGAGACAGTCCATGTTCTTGGATGTGAAGACTCAATGTTGTCAAGAT 3253
                             i   i vi        v     vv       i   i    i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_11369386_1   3254 ACCGGTTCTTCAAATATAGACCAAGTTGGTCTATATTTTCAATCCAATCA 3303
                         iv ii v  i ---------    i   i    i vv     iv     v
  L1M4_orf2#LINE/     51 GGCAATACTCC---------CCAAATTGATCTACAGATTCAACGCAATCC 91

  chr2_11369386_1   3304 CAAAAAAAACCCCAGTAAGTTATTTCACGGATATTGACAAACTGATTCTA 3353
                          v vv    i     ivivi v   ii i  v        i     i   
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr2_11369386_1   3354 AAGTTTATATGGAGAAGCAAAAGACCCAGAATAGCCAACAAAATATTAAA 3403
                           i  i       i v    ii                v v   v  i  
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_11369386_1   3404 ------GAACAGTCAGGTGCAGTGGCTCGCACCT 3431
                         ------     i--  v  v  - i   i   i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAA--AGTTGGAG-GACTCACACTT 222

Transitions / transversions = 1.43 (33 / 23)
Gap_init rate = 0.02 (4 / 222), avg. gap size = 4.50 (18 / 4)  

1904 21.95 12.68 2.11  chr2_11369386_11374881     3714  4328 (1168)    L1M4_orf2#LINE/L1      192   871 (37)  

  chr2_11369386_1   3714 AAGGAAGAACAAAATGGGAGGGATGAAACTATCCAACCTATAGACTTACT 3763
                           i          i v     iv v v   vi    ii vv i       
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_11369386_1   3764 ATAAAGCTACAGTAATCAAGACAATGTGATATTGGTGAAAGAAAAGACAA 3813
                          i                     i    i  i   iiv   i v     v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_11369386_1   3814 ATAGATCAATGAAACAGAATAGAGAGCCCAGAAATAGACCCACATAAATA 3863
                                    i  i     v     i         i     i i vv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_11369386_1   3864 TAGTCAACTGATCTTTGACAAAGGAGCAGAGGCAATACGATGGA------ 3907
                          i     i    i  i     i  v  vi  i v  v i    i------
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_11369386_1   3908 --------TTGAACAAATGTTGCTGGAATAACTGAATATCTACATGCAAA 3949
                         --------  v        v      i i     i   ? i         
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_11369386_1   3950 A----------------------------------AAAAA-------AAA 3958
                          ----------------------------------     -------   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_11369386_1   3959 AAGAATCA-AGACC--------AGACCTTA---TAT----CTTCTAGAGG 3992
                          v i    -     --------   v  v ---   ----  ii    i 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_11369386_1   3993 ATAGCATAGGAGAAAACCTAAATTATCTTGA-TTAGAGCAATGGTTTTTT 4041
                          v i      ? v   i  vvi v i    i-    -          i  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG-GCAATGGTTTCTT 590

  chr2_11369386_1   4042 AGATATAGCACCAAAGACATAACCCAAGAAAGAAAGAACTGATAACCTGA 4091
                               ii       ii  i  v v vi       i  iv     vi  i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_11369386_1   4092 ACTTCACTAAAATTCAAA--TTGTCTACTACTCAAAG-ACAATGTCAAGA 4138
                               ii      v   --  v v i  --      -   v i      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTATCAAGA 688

  chr2_11369386_1   4139 GGATGAGAAGAAAAACCAAAGACTGGGGGAAAATATTTGAAAAACACCCA 4188
                         iii   i    v  v   v   v    i           v   v  ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_11369386_1   4189 CCTGACAAAGGTCTATTATCCAAAAGAATTTGTTATACAAAGAACTCTCA 4238
                         i    i  i  v  vv      i  --------    i          i 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAA--------TATATAAAGAACTCTTA 780

  chr2_11369386_1   4239 AAACTAAACAATAAAAAAAAATAAACAACCCAATCAAAAAATGGGCCAAA 4288
                         v    v  i        i --i   i        i?          v  i
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_11369386_1   4289 GACCTGAACAGACACTTCATCAAAGAAGATATACA---GGCTA 4328
                           ii    i     i   vi               ---   i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.64 (82 / 50)
Gap_init rate = 0.02 (15 / 680), avg. gap size = 6.07 (91 / 15)  

 315 12.28 0.00 0.00  chr2_11369386_11374881     4948  5004 (492)    L1M4_orf2#LINE/L1      852   908 (0)  

  chr2_11369386_1   4948 AAAAGATATACAGATGGCAAATAAGTATATGAAAAGATGTTCCACATCAT 4997
                          i          i     v      i i           i  v      ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_11369386_1   4998 ATGTCAT 5004
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.00 (0 / 0)  


3146 26.06 1.67 0.56  chr2_11972441_11978827.rev     4998  5895 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_11972441_1   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATAAAAAT 5047
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_11972441_1   5048 GGCCATACTGCCCAAGATAATCTATAGATTCAATGCCATCCCCATCAAGC 5097
                            v     v     iv i     i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_11972441_1   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_11972441_1   5146 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5195
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_11972441_1   5196 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_11972441_1   5246 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5295
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_11972441_1   5296 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACT 5343
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_11972441_1   5344 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5393
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_11972441_1   5394 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAACCATA-----AAGC-T 5437
                           v  i  i              v      v  ?   i -----   v- 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_11972441_1   5438 GAAACAGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5487
                            iiv   i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_11972441_1   5488 TTAAAGACTTACATGTTAGACCTAAAACAATAAAAACCCTAGAAGAAAAC 5537
                          i ?    i  v    v   v       v      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_11972441_1   5538 CTAGGCA-ATACCATTCAGGACATACGCATGGGCAAGGACTTCATGTCTA 5586
                         v    ?i- v i -   iv   v vv vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_11972441_1   5587 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5636
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_11972441_1   5637 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5686
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_11972441_1   5687 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5736
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_11972441_1   5737 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACCAGAAA 5786
                          i  i  vi          v  i  v      vv    v iv iv v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_11972441_1   5787 AAAACAA----CCCCATCAACAAGTGAGCGAAGGATATGAACAGACACTT 5832
                           i    ----   v  i? v  i  i  i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_11972441_1   5833 CTCAAAAGAAGACATTCATGCAGCCAACAGACACATGAAAAAATGCTCAT 5882
                            v        i  v  viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_11972441_1   5883 CATTACTGGCCAT 5895
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (133 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2361 23.84 8.24 0.43  chr2_12039075_12040758      501  1192 (492)    L1M4_orf2#LINE/L1      163   908 (0)  

  chr2_12039075_1    501 GAACCTAGAATAGCACAGAACAATTTTTAAAAAGTAGAAGACAATTGGAA 550
                          i   i        -  i      i  v      v    v v i     i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGC-CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_12039075_1    551 GACTTATATGAGTTGATTTTAAGTCTTAACATAAAGCTACAATAATCCAG 600
                             i i ivvviii    i  iv    vi i         i     v  
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_12039075_1    601 AGAGTGTGGTATTGGCATAAAGGTAAACATATAGATCAATAGAATAGAAA 650
                          v         i        i i  i              i        v
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_12039075_1    651 -AAGAGTCTAGTAACAAACCCACACATAAATGGTGAATTGATTTTTGACG 699
                         -i      i  v  i       i    vv     v          i   i
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_12039075_1    700 AAGATGCGAAGACAATTCAAT----AAGAAATGTTCT--------AATTG 737
                          i i   v     v       ----  ii   iv   --------   v 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_12039075_1    738 TCAATTAGAACAATTTACAATACATATGCACAACAATGAACTTC-ATTTC 786
                          --ii i i    i vivv ?v  i     v  v      v  v- iii 
  L1M4_orf2#LINE/    412 T--GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_12039075_1    787 AACCTT-TACTGTACACAAAAGTTAATCTAAAATGGGCCATAGACCTAAA 835
                         v    i-i  ii  i      i    iii       ii  ?         
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_12039075_1    836 TGCAAAGCCTAAAACCATAAAACTTCTAGAGAAAAACATAGGAGAAATTC 885
                           i  iiv       i        ii    ii          ? v  v  
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_12039075_1    886 TTGGTGATCTTGGGATAGGCAAAGCTTTCTTAGATAAGACCCAAAAAGCA 935
                           v    i      v       v v           v   v v       
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_12039075_1    936 TTAATCATAAAAGAAAAAATAAATAAATTGGGC------ACAGT----AA 975
                         iv iiv i             i         i ------ v i ----  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_12039075_1    976 CTTCTATTTTTCAAAATATACT-TTGAGAAAATGAAATAAAAAGACACA- 1023
                            i i vi      iv i   - ii     i     vi v  vv    -
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_12039075_1   1024 --CGGGAGAAACTATTCAAAAAATGTATATCTAATACAAA-----TATTT 1066
                         --i        v    iiv   vii       i   viii-----   ii
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_12039075_1   1067 GGAATATA----AAACTCTTACAACTCAATAAGAA--------------- 1097
                         i       ----i                   v  ---------------
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_12039075_1   1098 ----TAAAAATTGACAAAAGACTTGAATATACACTTCAAAAAAGAAGAGA 1143
                         ----?      v i    i  i       v   i   vvv        v 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_12039075_1   1144 TACAAGTGGTCAATAAACACCTGAAAAGATGCCCAACATTATTAGTTAT 1192
                              i   i      i   v           i      i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (101 / 60)
Gap_init rate = 0.02 (14 / 746), avg. gap size = 4.29 (60 / 14)  


1326 26.78 1.37 1.64  chr2_12060164_12064846.rev     2820  3185 (1498)    L1M4_orf2#LINE/L1        1   365 (543)  

  chr2_12060164_1   2820 TGGAAAGACGTCACATGCTCATGGATTGGGAGACTTGACATCATTAAAAT 2869
                                 ii  v    i           i      i i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_12060164_1   2870 GACCATACTACTCAAGGCAATTTACATATTCAATGCAATCCCTATTGAAA 2919
                          i v     v i   ivii  i    v      i           ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_12060164_1   2920 TACCAG-TGTCAATTTTCACAGAAAT--ACAAAAAAAACC-ATACTAAAA 2965
                          v    -  i -v    ii       --    -----i i-  v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-----GCTGATCCTAAAA 144

  chr2_12060164_1   2966 TGTGTATAGAACCAAAAAAGAAGCTGAATAGTCAAAGCAATCCTGAGCAA 3015
                          vii   i   viiv  ii  vv v      i    i     i   iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_12060164_1   3016 AAAGAACAAAGCTGGAGGCATCATACTACCTGATTTCAAAATATATTACA 3065
                         i          i      vv   i   v  ii         iv  i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_12060164_1   3066 AGGTTATAATAATCAAAGCAGCATGGTATTGGTATAAAAAGGGGAGCATA 3115
                          i i  i i       ii   ii     i   i    ii vi ivii   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_12060164_1   3116 GACAAGTGGAATACAATAGAGCACACAGAAATAAATCCACATATTTACAG 3165
                           iv i       v   v   viiv          i   i i     ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_12060164_1   3166 CCA-TAGAGTTTTTACAAAGG 3185
                         i  - v  v   iv    i  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGG 365

Transitions / transversions = 2.38 (69 / 29)
Gap_init rate = 0.02 (6 / 365), avg. gap size = 1.83 (11 / 6)  

1542 23.36 5.29 5.84  chr2_12060164_12064846.rev     3644  4191 (492)    L1M4_orf2#LINE/L1      364   908 (0)  

  chr2_12060164_1   3644 GGTGCCAAGAATATACACTGGG-AAAGGACATCCTCTTCTATAAATGGTG 3692
                                   vi  v  v    -    i i vi  i   v i        
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_12060164_1   3693 CTGGGAAAATTAGAGCTCCATGAAGCTCTAATGCAGAAGCATGAACCTGG 3742
                               v  i i  vv?   i---------     i   v     vi   
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCAC---------ATGCAAAAGAATGAAGTTGG 454

  chr2_12060164_1   3743 ACCCCTAGGTTCACTGTAGATCTCATACCATATATTAATACAAAAACCAG 3792
                                -------------i    i        ------      ii i
  L1M4_orf2#LINE/    455 ACCCCTA-------------CCTCACACCATATA------CAAAAATTAA 485

  chr2_12060164_1   3793 CTCAAGATGGATCAAAGACTTAAACATAAGACCTGAAAATATAAAACTAC 3842
                              i        ?    i    ii     v  i   v         vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_12060164_1   3843 TA--------CATCAGGGAAACACTTCAGAACATTTGTCTAGGCAGAGAT 3884
                           --------   vi ? v  vv    ivi  v  v vi      iv i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_12060164_1   3885 GTTGAGGATAAGACCTCAACAGCACAA-------------AAATAGACAA 3921
                         v ivvi    v   vi   v       -------------       i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_12060164_1   3922 AAGAGACTTAACCTAAA----AAGCTTTTGCATAGCAAAGAAAACAACCA 3967
                          vvi     v i v   ----  i      iiivv     i v  v i  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_12060164_1   3968 ACAGAATGAAGAGATAACCTGATGAATGGAAGAAAATACTTGCAAACTAT 4017
                          v i i    i   i    iivv      i        i       ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_12060164_1   4018 TAATCTCACAAGGGGCTAATATCTAGAAAATACTCAAGGAACTCAAATAA 4067
                         vv    v i     i  vi    i    v   i--  i      vv i  
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATAT--AAAGAACTCTTACAA 783

  chr2_12060164_1   4068 CTCAGTGCAATAATAATA---ATAATCCCGTTGAAATGTGGGCAAAGGAC 4114
                             i --     v  v ---    i  vi  ?   vi           i
  L1M4_orf2#LINE/    784 CTCAAT--AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_12060164_1   4115 ATGAATAGACATGTCTCAAAAGATGACATACAAATGGCCAACAGGTATAT 4164
                         v           v    v     v  i              i i i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_12060164_1   4165 GAAAAAATGCTAACCATCATTAATAGT 4191
                              i     v v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (68 / 56)
Gap_init rate = 0.02 (10 / 545), avg. gap size = 6.10 (61 / 10)  


2942 22.88 3.54 6.02  chr2_12248588_12251823.rev     1814  2744 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_12248588_1   1814 TGAAAAGGCATCTCATGCTCATGGAGTTGAAGACTTAGTATTGTAAAGAT 1863
                           i    ii   i    i       v v         i      v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_12248588_1   1864 GGTACTTTTTACTAAATTGATTTATTGATTCCACACAATCCCTATCAACA 1913
                           i v vi iv i        i  iv     v  i             v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_12248588_1   1914 TCCTAGGAGAATTTTTAGTAGAAATTGACATGCTAA-CCTACA-TTTATA 1961
                            i  vv vv     v i           v   i -    v -  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_12248588_1   1962 TGAAAATACAAAGGATCTAGAAAAGCCAAAACCATTTTGAAAACAAAAAT 2011
                           i    i   i   i i    v         v  i       -- i  v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA--AGAAG 198

  chr2_12248588_1   2012 AATAAAGTTAGAGAAC----ATTATTTAATGCCAAAACTTACTATAACTC 2057
                           i      i   i  ---- i viii   vi            i  vv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_12248588_1   2058 TATAGTAATCAAGATAGTGTGG---------AAGGATAGGTACATCAACT 2098
                           i           i       ---------        ii i  vi ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_12248588_1   2099 AATGAAATAGAATTG-GTGTCCACAAA-AAACCT-TGTATTTATAGTCAA 2145
                             i          - v     v   -     i- ii      i     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_12248588_1   2146 CTGACATTGAGCAAAGATTCCAAAGCAACTCAGCAGGG------TAATCT 2189
                         i   iv  vii   i i v    ii v i   iii   ------  i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_12248588_1   2190 TTTCAATGAATTGCAAATGGTGCTAGGAAAATGGAAGATTCATATAAAAT 2239
                               -------           i   v  iv i v ?i  i  iv  -
  L1M4_orf2#LINE/    399 TTTCAA-------CAAATGGTGCTGGGACAACTGGATAKCCACATGCAA- 440

  chr2_12248588_1   2240 AAAAATGGAAAGGAAAATGGAAGATTCATATAAATTAAAAAAAAACCCTA 2289
                           i    ------------------------  i  i-------------
  L1M4_orf2#LINE/    441 AAGAATG------------------------AAGTTG------------- 453

  chr2_12248588_1   2290 GACTCTTATCTCACATCATACACAAAAATTAACTACAAATGGATCATATA 2339
                            i i  i      i    i             vv          ? v 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_12248588_1   2340 T-TAAATATAACTGTGAG---AAATGATAAGATTTCTAAAAGAACACATA 2385
                         i-     i   ----   ---   iv    i i ii  i     v     
  L1M4_orf2#LINE/    504 CCTAAATGTAA----GAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_12248588_1   2386 GGGGAAAACCTTTGAGATATTAG-TTAGACAAAGAGTTGTTGGATGCAAT 2434
                           ? v   i   i v  iv  i -    i   v iv  v  i   iii i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_12248588_1   2435 ACCAAATGCATGAGCCATAAAGGAAAAAAAGAAATGATAAATTGGACTCC 2484
                               v   ii   v i   i       vi----             i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATA----GATAAATTGGACTTC 645

  chr2_12248588_1   2485 ATTAAAATTTAAAATATTTGTGTTTCAAAAGATACCATTAAGATAACGAA 2534
                           i      v    iv      i      i  i  i  i    v ii   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_12248588_1   2535 AGAAACAAGCCACACATTGAAATAAAGTATTTGCAAACCATGTATCTGAT 2584
                          - i    v     v v  ii v   i          i   i        
  L1M4_orf2#LINE/    696 A-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_12248588_1   2585 GAAGCACATGCATC-AGAA-ATGTAAA-AACTCAT-TAACTCAAAAATAG 2630
                         i i v  v  i   -    -  i    -     v -i       v    i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_12248588_1   2631 GATGCCCAAAAAGCCAAATACAAAGTTGGCAAAAGACTTAAACAGATATT 2680
                         i v v v  v  v    v ?v   i v      i  i  i  i   i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_12248588_1   2681 TCACCAAAGAAGGCATATAAATGACTAACAGTCATCTGAAAAGGTGTTTA 2730
                           v         ii   i     i i  i iv  iv       i  i i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_12248588_1   2731 TCATTAGTAATTAG 2744
                         v   i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (138 / 71)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.87 (89 / 23)  


3840 19.31 3.01 1.67  chr2_12373145_12375431      900  1795 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_12373145_1    900 TAAAAAGATAATCTATATTTATGAATTAGAGCACTTAATATTGTAAAGA- 948
                          ii       vi i  i  i   i   i  iv            v    -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_12373145_1    949 ---AACTACTCCCTAAAAAAGATCTACAGAATCAATATAATCCCCATCAA 995
                         ---  -       i   vv-          v    iii      i     
  L1M4_orf2#LINE/     51 GGCAA-TACTCCCCAAATT-GATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_12373145_1    996 --------TGGCCTTTTTTCCCCTGAAAT-GACAAAGCTAATTCTCAAAT 1036
                         --------iv         v v--     -     -   i  i  v    
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCA--GAAATTGACAA-GCTGATCCTAAAAT 145

  chr2_12373145_1   1037 TCATATGGAATTTCAAGGTGCTCCAAATAGCCAAAACAATATTAAAACAA 1086
                                   v v     vi i vi               v  i   ---
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA--- 192

  chr2_12373145_1   1087 AATAAAAACAAAATTGGAGGCCTCACAAATTTTCAGTTTCAAAACTTACC 1136
                           v  i      i       v      v-  ii  i             i
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACAC-TTCCCAATTTCAAAACTTACT 241

  chr2_12373145_1   1137 ACAAAGCTGTGGTAATCAACACAGCATAGCACAGCCATAAGTATAGGCAT 1186
                                 iii        v    ii i i  v v      v    i   
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_12373145_1   1187 ATAGGCCAATGTAACAGAAT-GAGAATCCAGAAACAAACCCAAACATCTA 1235
                             ii     v  i     -    i        i       v    i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_12373145_1   1236 TGGCCAATTGATTTTCAGCAACGTTGCCAAGACCCTTCAACAAGGAAAGA 1285
                            i            ii   v v          v     iii       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_12373145_1   1286 ATAGACTCTTAAATAATTGGTGCTAGGATAACTAAAAAACCATATGCAAA 1335
                             v  i  v  i  v       i   i    ii v ?   i       
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_12373145_1   1336 AGAAGAAATTTGGACTCCTTTCTTCACTCCAAATATAAAAATTAACTCAA 1385
                             vi  v      i   vi  -   v   v   i              
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCT-CACACCATATACAAAAATTAACTCAA 490

  chr2_12373145_1   1386 AATTAATCAATGACCTAAGTATAAGAGCTAAAACAACAAAGCTGGTACAA 1435
                            vi    ?v       i i             v i   i  vv  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_12373145_1   1436 -ATAACACAGGGATAAATGTTCATGGCTTCTTGTTTGGCAATGGATTCTT 1484
                         - v    i   ?i     v   i  i i ivv   v        v     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_12373145_1   1485 AGATTTGGCATCAAAAGCTTAAGCAACAAAAGAAAAA---GACAAATTGG 1531
                             v  i  i       vi                 ---  i       
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_12373145_1   1532 A-TTAATAAAAATTAAAAATATTTGTGCCTCCAAATACATTATCAAGAAA 1580
                          -  v  v           iv       i  v  iv   i          
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_12373145_1   1581 GTGAAAAGACATTCTACAGAATGGTGGAAAATGTCTGCAAATCATATATC 1630
                                    vi i         vi      i i               
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_12373145_1   1631 TGATATAAAGGTCTAGTATCCAGATTATATAAAGAATTCTTATAATTTAA 1680
                              -- i  v  v         v           i     i  i i  
  L1M4_orf2#LINE/    741 TGATA--AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_12373145_1   1681 CAATAAAAAGAAAAACAATCTCCCAC-------ATGGACAAAG-ACTGGA 1722
                         i          v   i  ---    v-------    i     - i v  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAA---CCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_12373145_1   1723 GTAGATATTTCTCCAAAGAAAATATGAACACGTCCGACCAGTACATGAAA 1772
                         i    i              i    iv v i v  i iv  i        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_12373145_1   1773 AGAGATTCAACAGCACCAGCCAA 1795
                            vii      v  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (101 / 69)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.33 (42 / 18)  


3365 25.88 0.55 0.55  chr2_12612719_12616962.rev     2845  3752 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_12612719_1   2845 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2894
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_12612719_1   2895 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2944
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_12612719_1   2945 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2991
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_12612719_1   2992 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 3041
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_12612719_1   3042 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 3091
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_12612719_1   3092 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 3141
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_12612719_1   3142 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 3189
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_12612719_1   3190 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 3239
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_12612719_1   3240 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3289
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_12612719_1   3290 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 3339
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_12612719_1   3340 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3389
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_12612719_1   3390 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3439
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_12612719_1   3440 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3489
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_12612719_1   3490 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3539
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_12612719_1   3540 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 3589
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_12612719_1   3590 AAGGGCTGATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 3639
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_12612719_1   3640 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 3689
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_12612719_1   3690 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 3739
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_12612719_1   3740 CATCACTGGCCAT 3752
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (137 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2419 25.14 6.63 2.86  chr2_12701587_12703518      573  1447 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_12701587_1    573 TAGAGAGATACACCTTGTTCATAGGTCAGAAGACTCAATATTATTAAAAC 622
                          i  i     iv  v       i i ii       i      i    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_12701587_1    623 ATAAATTTGTTCCCAAATTACCCTGTAGATTCAAAGCAATCCA-ATCAAA 671
                         ivv   vi- i        ivi  ii        v       v-      
  L1M4_orf2#LINE/     51 GGCAATAC-TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_12701587_1    672 ACCCCCAAAAATA---TTTTAGTAGTAATCAACATATTGATTTCAAAATT 718
                          i   --- iv i---    v i  v   ii   vii    iii      
  L1M4_orf2#LINE/    100 ATCCC---AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_12701587_1    719 CATATAAAACTGCAAAGGACCAATAATTGCCAAAACAAATTTT--AAAAG 766
                              ii  v     i     v v   v          - i  --     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAG 195

  chr2_12701587_1    767 CAGAATAAATTTGAAAGACTACCACTCCCTGAATTTAATACTTATTATAA 816
                         v    i   v   i i    vv    i  ii v  i  v     i  i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_12701587_1    817 AAATGCAGTTATCCAGACAGTGTGGTATTAGTGCAAATATACAGAAAGAC 866
                          iv i    v   v             i i iii  iv   --  v v i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA--GACATAT 293

  chr2_12701587_1    867 AGATCAATAGAACAGAATAGGGACTTCAGAAATTGACCCCTATATATTTG 916
                                 i   i     v i  v i       vi    v  i  v v  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_12701587_1    917 GATAATGGATTTTCAGCA----TGC-AAGAGCAGTTCAGTAGAGAAAGAA 961
                          vi   v       ii  ----   -    v  -    i i i       
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAA 392

  chr2_12701587_1    962 TAGTCTTTTTAAGAAATGACACTGTAATGATTTGATATCCATATGCAAAA 1011
                                  i  v     iii   vi ii i v    ?   i        
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_12701587_1   1012 ATAAAATAAAATAAACTTAGATCTACATATTTCACCATATGTAGAAAT-A 1060
                         i--------   i  v  i  i ivi iv iv        ii i    - 
  L1M4_orf2#LINE/    443 G--------AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_12701587_1   1061 ACTCAAGATAAAGTATAGACCTTGATGTATTATAAAAGTGAAAACTATCA 1110
                               i  ii vi ?      vi     ----- i  iv        - 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTA-----AGAGCTAAAACTAT-A 528

  chr2_12701587_1   1111 AAATTCT-AGAAGAAA---T---------TCTCTGTCAGGTCAGGTCAGG 1147
                            i   -        --- ---------   ii  v vv ii   i   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_12701587_1   1148 AAA---------ATACATGATACTAAAACTAGGATCTATAAAAGAATAAA 1188
                         v  --------- v i    i  i    vi vi v v i       v   
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_12701587_1   1189 TTGATTACTTGAACTTCACCAAAGTTAAAAATTGCTGCTCTTTGAAAGAC 1238
                          v   v v   i      i    i       i vi  iv   ii  i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_12701587_1   1239 GTTA---AGAAAATTAAAAAAGAAAC-ACAAAGATGAGAAAAAATATTTA 1284
                         ii  ---     i v    i v  v -   i -   i  i         i
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGA-ATGGGAGAAAATATTTG 727

  chr2_12701587_1   1285 CAAAGCATATATCTGACAAAGGGCTTGTATC-AGAATACATAA----CTT 1329
                             v           i  i  i        -      i    ----  i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_12701587_1   1330 TTAAAAT---ACAATAAGAAAAC-----------TTAAAAAA-AGGCCAA 1364
                            v  i--- i     i  i  -----------  ?     -i   v  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_12701587_1   1365 ATATTTGAATAGACACTTCAATAAAGAAGATATAAGCACACAAAAAATAA 1414
                         iv             i   vvi            --  v iiivv     
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATA--CAAATGGCCAATAA 875

  chr2_12701587_1   1415 CCACATGAAAATAAGCTCTGTCTTATTAATCAT 1447
                         v          v v    viiv i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (138 / 79)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.07 (83 / 27)  


2736 23.62 4.72 0.54  chr2_12780061_12781793      501  1241 (492)    L1M4_orf2#LINE/L1      137   908 (0)  

  chr2_12780061_1    501 TCCTAAAATTCATTTGGAATAATG--AAAGACCCAAAATAACCAAGGCAA 548
                                      v     --   -- ii      i    i    ii   
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_12780061_1    549 TGCTGAGCAAAAAGAACAAAGCTGAAGG---CATCATTATTTGACTTTAA 595
                          vi   iv  i          i  i   ---  -  i viiii i  i  
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAA 233

  chr2_12780061_1    596 AGTGTATTACAAAGCTCTAGTAACCAAAACAGCATGGTAGTGGCATAAAA 645
                          iiv  i         vi     i   i    ii     v        ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_12780061_1    646 ATGGACACGTAGAACAATGGAACAGAATAGAGAGCCTACAG-------CA 688
                           i    ii    v        i     v     i i v i-------  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_12780061_1    689 AACA-------------GATTTTTGACAAAGATGCTAACAACACACATTG 725
                         v   -------------      i     i i   i  v v  iv  v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_12780061_1    726 GGAAAA----AGCCTCTTCAACAAATGGTACCTGGAAAATTAGATAACCA 771
                           i   ----  i  i             i iv   v  i i    ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_12780061_1    772 CATGAAAAAGAATGAGACTAGACCCCTACCTCTCACCATGTA-AAAAATC 820
                             v          iii i            v      i  -      i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_12780061_1    821 AACTCAAAACGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAACT 870
                                  i    i ?    i         i v i              
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_12780061_1    871 ACTAGAAGAAAACATAGGGGAAACATTTTATGACATTGCGCTGGGCAAAG 920
                         vi                ? v  vvi  ii    v   v i i     v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_12780061_1    921 ATTTTTTAAAATAAGAATTCAAAAGCAGAAGCAACAAAAGCAAAAATAGA 970
                         i   i   i -  v  vvi        v            v         
  L1M4_orf2#LINE/    584 GTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_12780061_1    971 AAAATAGAATTAAATCAAACTCAAAAGCTTTTGCACAGCAAAGGAAAGAA 1020
                         v    v i i vv      v i    i      ii vv       v vv 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_12780061_1   1021 TTAGCAAAGTGAAGAGATAATCTATGGAATGGTA-AAAATACTTGCAACC 1069
                          i iv        i   i  i i ii      v -      i      vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_12780061_1   1070 TACACATCTGACAAAAAGTTAGTATCCAGATTATATTAGGAACTTAAACA 1119
                         i i i      i  iiiii v         v     v i     ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_12780061_1   1120 ACTCAACAACAAT--GACAAG-AACCCAATT-AAATATGGGCAAAAGACC 1165
                               i  i  v--     i-         -   v         i  ii
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_12780061_1   1166 TTAATAGACATTTTTCAAAAGTGGACATACAAATGGCCAGCAGGTATTTG 1215
                          v           i  v    vi  i             ii i i iv  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_12780061_1   1216 AAAACATATCCAGTATTACTAATCAT 1241
                             v  iii  ii  i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (115 / 57)
Gap_init rate = 0.02 (13 / 772), avg. gap size = 3.00 (39 / 13)  


1365 29.48 7.34 2.61  chr2_13029186_13030981.rev      501  1304 (492)    L1M4_orf2#LINE/L1       67   908 (0)  

  chr2_13029186_1    501 TTGGCCTACAAATGGAACATAATTCTAAACAAAATCCCAGCAGACACTTT 550
                            ii     i  vv   ii   i iv v            v v vi   
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTT 116

  chr2_13029186_1    551 -GCGAAAATTGACAAGCTTATTCTAAATTTTGTATGAAAATG--AGAGGT 597
                         -  ii             v  i     v  ii    i     --  i ii
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr2_13029186_1    598 CAAGAATA--CAAT-TATTCTTGAACATAAAGATCAAA-CTGGATATAAT 643
                          v      --   v-i v       v vi    v    -i    vi- v 
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-ACT 215

  chr2_13029186_1    644 AACAGATACTAAC-----AATTT--TATAAATCTTTCATAATTAA----- 681
                         v   vv v i  i-----  i  --  i   v  vivi    i  -----
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_13029186_1    682 TGTAGTATTGGCATAAAAACTAATAAATAGAACAATGAAACAGAATGGAG 731
                            i   i        ii ivi i v     v     i  i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_13029186_1    732 AGCCCAGAAGCAG-CCTACCATGTTTACAAT-AATCAATTTATGACAAAG 779
                           i      ii i-  i i- ii    iii -   ii    vi     i 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCAT-ACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_13029186_1    780 A-AACAACTGA--ATTGTGATGGAGGAAAAGATTTTCTCTTCACTAATAG 826
                         i-iv   --  --   -ii    -     ii  vv   i    vi  vv 
  L1M4_orf2#LINE/    365 GTGCCAA--GACCATT-CAATGG-GGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_13029186_1    827 GAGCTGAGTCAATTGCATATCCACATGAAATAAAATAAATATTG------ 870
                          v    i v   i  v   ?       v  v i   i  -i   ------
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA-GTTGGACCCC 459

  chr2_13029186_1    871 TATTTTACTTTCTACATAAAAATAAGTTTCAGATGGATTGTACATCTCAA 920
                           ii i  viiv  i i      v ii iv i      ii? v i  v  
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_13029186_1    921 TGTGAAAAGAAAAACAATAAAGTATCTAGATGATAATAGAG-----AATC 965
                            i i ivv     v     iivii    v  v  i v  -----    
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_13029186_1    966 -----GATTTTGGGGTAAGTGGAATACTTTTT---ATAAGAGATCACAAT 1007
                         -----  ii     v  i i--   iv   i ---   v  v i  v  v
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGC--AATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_13029186_1   1008 CAGTAGAAACATGAAGAGAAAAGAT-TATAAACTGGACTTCATTGAAAT- 1055
                           vv  v    --- i      i  -v     i          ii    -
  L1M4_orf2#LINE/    608 CACAAGCAACA---AAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_13029186_1   1056 ACAA--TTTGGTTTATCAAAAGTCACAATATATAAACCAAGAAGGCAAAC 1103
                          v  --   v  viv     i v   v  vv v   vii i   i   v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_13029186_1   1104 CAACAAA---GAAAAATATATTTGTAAAATGTGTATTCAACAAAGGACTC 1150
                           -  i --- i i  v       i   vii i   iii i  i     i
  L1M4_orf2#LINE/    705 CA-CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_13029186_1   1151 ATATTCTGAATATGCAAGTAATATCTAGAAGTCAAGTAGAAAAAAATGCA 1200
                         i   i v      ii  iv  ivii  v  v    vv v     i --  
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CA 801

  chr2_13029186_1   1201 AA------ATTTTAAA--TGAACAACTCAATGAAATTTTAATGGACAATT 1242
                           ------ v  ?   --  ii   ------iii    v   i    v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAA------AGGATTTGAATAGACATTT 845

  chr2_13029186_1   1243 AACAAAAGGAGATATGCCAA-GGCTAATAAGTATGTGAAAATGTTTTCAA 1291
                         vv v    i      i v  -   i      i ii      vi vi    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_13029186_1   1292 CATCACTAGTCAT 1304
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.04 (34 / 842), avg. gap size = 2.35 (80 / 34)  


2821 26.61 2.34 1.22  chr2_13130791_13136929     4750  5647 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_13130791_1   4750 TGGAAA-ATATTCCATGCTCACGGATAGAAAGAATCAATATCGTGAAAAT 4798
                               -    i     i   i    v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_13130791_1   4799 GGCAATACTGCCCAAAGTAATTTATAGATCCAATGCTATTCCCATTAAAC 4848
                                  v      v i  i  i    i   i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_13130791_1   4849 TAT-AATTGACAATCTTCACAGAATTAGAATAAACT-ATTGTAAAATTAA 4896
                          vi- ii  v v- i  ii     v v  -i  i  -  iv       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chr2_13130791_1   4897 TATGGAATCAAAAAAGAGCTTGTATAGCCAAGATAATGCTAAGCAAAAAG 4946
                                viiv  ii  v iv v        i i   vi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_13130791_1   4947 AACAAAGCTGGAGGCATCATGTAACCAGACTTCAAACTATACTACAAGAC 4996
                                i      vv   iiivv  vi i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_13130791_1   4997 TACCGTA--TGAAACAGCATGGTACTGGTACAAAAGCAGACACATAGACC 5044
                            v   --ii i    ii         i i  iiii     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_13130791_1   5045 AATTGAACAGAGTAGAGAACTCAGAAATAAGACCACACATCTACAACCAT 5094
                            v   i   i v    iii         iv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_13130791_1   5095 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5144
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_13130791_1   5145 ATTTAATAAATGGTTCTGGGAGAACTGGCTAGCCATATGCAGAAAATTGA 5194
                         v  i  i       v      v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_13130791_1   5195 AACTGGACCCCTTCCTAACACCTTATACAAAAATTAACTCAAGATGGATT 5244
                          ii         v   v     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_13130791_1   5245 AAAGACTTAAATGTAAAACCCAAAACTATAAAAATCCTAGAAGAAAATCT 5294
                          ?    i         i v i            v  i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_13130791_1   5295 AGGCA-ATACCATTCA-GGCAT--AGTCATGGGCAA-AATTTC------A 5333
                            ?i- v i -   i- i v --i  i --     -ii    ------ 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATA 595

  chr2_13130791_1   5334 TGACAAAAATGCCAAAAGCAATTTCAACAAAACCCAAAATTGATAAACGG 5383
                              ------         vvvv        vvv     v      iv 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_13130791_1   5384 AATAGAATTAAACCAAAGAGCTTCTG--CAGCAAATCAAACTATCATCAG 5431
                         i ivvv  i   viv  i i   i  -- vv    vv v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_13130791_1   5432 AGTGAACAGGCAACCTTCAGAATGGGAGACAATTTTTTTAATCTATCCAT 5481
                               v  i     iv            v   v   vi  vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_13130791_1   5482 CTGACAAAGGTCTAATATCCAAAATCTACAAGGAACTTAAACAACT---T 5528
                             i  i  v  vi      i   v  i  i     ivv      --- 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_13130791_1   5529 TACAAAAAAACAAACAATACCATCAAAAATTGGGCAAAGGGTATGAACAG 5578
                         v i     i     i  iv v  i?    v          i v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_13130791_1   5579 ACACTTCTCAAAAGAAGACATTCATGCAACCAACAAACTTATGAAAAATA 5628
                            i     v        i  v  viiii    i  i vi       ivv
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_13130791_1   5629 GCTCAACATCACTGATCAT 5647
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.00 (32 / 16)  


3077 26.71 2.02 0.34  chr2_13153652_13157233.rev     2200  3090 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_13153652_1   2200 GAAATATATTGCATGCTTATAAATTGGAAGAATTAATATTCTTAAAATGT 2249
                             v    iv    i i  ii         v        v    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_13153652_1   2250 CAATACCACTCA--TTG---TACAGATTCAATTAAATCCCTATTAAAATG 2294
                               iv i  --   ---           ivv         i     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_13153652_1   2295 CCAATGAAATTCTTCCCAGATATAGAAAACACAATCTTAAAATTCAC-TG 2343
                            iivivv  i  iv    v  v  v  vvii   i         i-  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_13153652_1   2344 GAACCACAAAA-ACCCCTACTATCCACAGAAACTTTGAGCAAAAAGGTCA 2392
                            vii   ii-    vv v  v   v iv  ii    iv  i   iv  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_13153652_1   2393 GAGCTACAGGTGTCACACTAACTGATTTCAAATTTTATTACAAAGCTATG 2442
                         i  i iv   vv       vv ii        vi   i          ii
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_13153652_1   2443 CTATAGAAAATAGCATGGCATTGGCATAAAAACAGATACATAGACCAGTG 2492
                         v  vvv  i i  ii   i i        ii i   i i     i  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_13153652_1   2493 GAACAGAATAATAAGTCCAGAAATACATCCATGTATTTACAGCCAACTCA 2542
                            i     vivi            v i    ii     ii i   i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_13153652_1   2543 TTTTCAACAAAGGTACCAAGAACATACACTGAGGAAAAGACAGTCTTTTT 2592
                              i    i   i      v   v  v  i     ii i        i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_13153652_1   2593 AATAAATGGAGTTGGGAAAACTGGACGTTCATATGCAGAAATACGATTCT 2642
                           i      v i     v       ii?i  i     i  iv i  vvi 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_13153652_1   2643 AGACTCCTATCTCTCACCATACACAAAAA----CTCAAAATTGATTAAAG 2688
                         i   i    i   v       i       ----        v   i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_13153652_1   2689 ACTTAA-TGTACTACCTGAAATTATGAAACTACTAGAAGAAAACATTGAA 2737
                           i   -    vv v  i   i   i     vi             v i?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_13153652_1   2738 G-AAATGGTTCAGGACACTGCTCTAGACTATGACTTTTTGTGTAAGACAT 2786
                          -    v-   iv   vi  vvi   i v   ii  i  ivi  v    i
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_13153652_1   2787 CTAAAGTACAGACAACAAAAGCAAAGATAGACAAATTGGATTACATTAGG 2836
                          v    i   ii         v   i     i        i v   i ii
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_13153652_1   2837 CTAAAAAGCTTCTGCACAGCAAAGATAACATCATCAG---AGTAAAGAGA 2883
                         v v    i   i  ii vv     i--   ii    i---   i  i   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGG--ACACTATCAAGAAAGTGAAAAGA 699

  chr2_13153652_1   2884 TAACTTACAGAATGGAAAAAAATATTTCCAAATTATCCATCTGAGAAGGG 2933
                         i   ii         i i         v     i  vi      v     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_13153652_1   2934 ATTAATAACCACAATAGAGAAGAAACTCAAACAAA-CAAACACAAAAAAA 2982
                          i vi  v   v    v v  ii     vv    v-   vv i     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_13153652_1   2983 CAAATAATCCAATTAAAAAATCGGCAAAGGATCTGAAAAAACATTTCTCA 3032
                                i      ?      v          i    v i         v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_13153652_1   3033 AAAGAAGACATACAAATAATCAACAGGTGTATGAAA-GATACTCGACCTC 3081
                                 i        iii   i i iii      -   i   i  v  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_13153652_1   3082 ACTAATCAT 3090
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.66 (146 / 88)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 1.75 (21 / 12)  


1724 28.52 4.74 3.27  chr2_13263144_13265549.rev     1030  1916 (490)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr2_13263144_1   1030 TATCACAATATTCATTAGAT-GGAAGACTGAATATTAATAGTTTGTCAAT 1078
                             v  - i     -i   -        v      iv  ivv  v    
  L1M4_orf2#LINE/      9 TATCCCA-TGTTCAT-GGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_13263144_1   1079 TATCTGCAAATTGATCTATATATTCAACAAAATTCTAATTACATTTATAA 1128
                         vv  iv            i v       iv   i iv  i v v ivi i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_13263144_1   1129 CGGGCTTTCTTTTTGTATAAATGGATAAG-------TAAATAGTAATACA 1171
                          v v    ---    i v    v  i   -------    - v v   ii
  L1M4_orf2#LINE/    107 CTGCCTTT---TTTGCAGAAATTGACAAGCTGATCCTAAA-ATTCATATG 152

  chr2_13263144_1   1172 -AAATGCAAATTATGTAGAATAGTGAAAACTTTCTTAAGAAAGAAACACA 1220
                         -        ivv ivi       iv     vv    i i      iv   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_13263144_1   1221 AAGTTGAAGGACTTACACTGTATAGATTTAAGGCATAATGTAAAGTTTTA 1270
                               i      i     vivi iv  i  ii v  v ii    i vi 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_13263144_1   1271 TTTACTAAGACAGAATGTCACTGGCCAAAGAAAAATAGACATA--GAAGA 1318
                         v v ii       vi  vi      --- v  ii         --  vv 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGC---ATAAGGATAGACATATAGATCA 299

  chr2_13263144_1   1319 GTGGGAGACAA---AAATCTCAGAAATAGACTCACAGATATTTGGTTAAT 1365
                         i   i v v  --- i vii        i  i  i v  v v    i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_13263144_1   1366 TGATGCTTTG-TAAAAGGACCAATGCAACTTAATTG----AGTATAGTTA 1410
                             -i  i -i  ii vi    vi v i i   v ----  v     --
  L1M4_orf2#LINE/    350 TGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT-- 396

  chr2_13263144_1   1411 CCCTTTTCAGCAAATGATGCTGGAACAACAGGAAAAGTACATGGAAAAAT 1460
                         --       i      i      i     v   v ?vi     v    iv
  L1M4_orf2#LINE/    397 --CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_13263144_1   1461 TTGAAACTCAACTCCTTTCTCATACTATATGCAAAACAAAATTAATTCAA 1510
                         v    ii vi  i   vi    i  i    i     ----     i    
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAA----ATTAACTCAA 490

  chr2_13263144_1   1511 AATGGAATCTAGA---AAA-GCATAGAACCACAAACTGTGGTGCTTCTAG 1556
                               viv?   ---   - i -   i i -     i iivi  ii   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTA-AGAGCTA-AAACTATAAAACTCTTAG 538

  chr2_13263144_1   1557 AAGAAAATATAGAGAAATATATTTGTAACATTAATGTAGACAAATATATT 1606
                                i    i?iv v  v  i  i  v  iivv   i   vvi v i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_13263144_1   1607 TTAGAC-TAATACATAAAACTGTAACCA-TAAATGAAAAGCAAAT-GATA 1653
                              i- i i  -i    viii  v  -i   v     ---   -    
  L1M4_orf2#LINE/    589 TTAGATATGACAC-CAAAAGCACAAGCAACAAAAGAAAA---AATAGATA 634

  chr2_13263144_1   1654 AACAGGCCTTCATCAAAATTTATAA---TCATCCTTATCCAAAGATACCA 1700
                           iv  v             v v  --- ii v   -- v  i  i  i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTA 682

  chr2_13263144_1   1701 TTAAGAAAATAAACAGGGAATCCACTGACTG----AAAATATTCATAATA 1746
                          i      i i  v  iv  i    v  v  ----        iii  vv
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_13263144_1   1747 CATATACCT--TAAAATATGTTTGTCCAGAGTATATTTTAAAAA---CAT 1791
                               i  --   iiv iv v i      i     ---   i --- v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATAT---AAAGAACTCTT 779

  chr2_13263144_1   1792 ACAAATCAATAATGAGATGACTAGTAGCACAA---AAACATTGCCAAATT 1838
                             v        i i v   v i  i v   ---   v  v v    vv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_13263144_1   1839 TCTTCAGCCAATACTTCACAACAGAAGATATACCACCGATCACTAAGACC 1888
                         vi  v iivi i i   v v v           v vi ii  v    vv 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_13263144_1   1889 ACGAAAATAT-CTCAACATAATTAAACAA 1916
                          i     v  -        v ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (137 / 113)
Gap_init rate = 0.04 (32 / 900), avg. gap size = 2.22 (71 / 32)  


1030 29.15 8.48 5.14  chr2_13293646_13295487.rev      506  1342 (500)    L1M4_orf2#LINE/L1        1   865 (43)  

  chr2_13293646_1    506 TGGAGGAATGTACCATTTTAATATAATACAAGACTTAATATTGTAATAAT 555
                             iii  i v    v  v  iv v iv               v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_13293646_1    556 GTCACAT-TTGCCCAAATC---CTACCAGATTTACCCAATTCAATCTCTA 601
                          v  -  -i v       i---    -     ----   iv     i   
  L1M4_orf2#LINE/     51 GGCA-ATACTCCCCAAATTGATCTAC-AGATT----CAACGCAATCCCTA 94

  chr2_13293646_1    602 ATAAAAT---AG--------TTTGTTAATATTGCCAAGCCAATACTAAAA 640
                         vi     ---  --------    ivi v    v     ii  v      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_13293646_1    641 ATCATGTAGAAGGGCAAAGGACCAAGAATAATCAAAATTAATATTGAATA 690
                         v    i i   iv    i     v      ii     i-   v     v 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AATCTTGAAAA 193

  chr2_13293646_1    691 AGAAGAACAAAATGGGAAAACT-AGAC---CCTATTGGGTATTAAGAATT 736
                                    i v   ii   - v  ---  v   ----- i  i v  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT-----TCAAAACTT 238

  chr2_13293646_1    737 CTTGTAAAGTTACTATCATTAAGACAGCACAGTATTTGTGTAGAAATAAG 786
                         vi ii    i   vi v  i       iiii   i v ii  iii   ii
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_13293646_1    787 CAACTAGACCAATGAAACAAAATAATGAGCCCACTATGTGAGAAAGACAG 836
                           vv    i     i  i i   viv   i   ------  i v i  v-
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCA------GAAATAAACC- 331

  chr2_13293646_1    837 CACACGTACATGGATATTTAATAT---ACAAAATGTACCCTGAGAGTA-- 881
                           i  i vi    vi v  i  v ---    ii-  i  --i   vi --
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCC--AAGACCATT 378

  chr2_13293646_1    882 ----GAGGAAAAGTAACAGTGTTTTTTTTTTTCAATAAATGGTGCTGGAA 927
                         ---- i     i--  i   -------i       i            i 
  L1M4_orf2#LINE/    379 CAATGGGGAAAG--AATAGT-------CTTTTCAACAAATGGTGCTGGGA 419

  chr2_13293646_1    928 ATAGTTGG-TATTCATGTACACA--------------TCTATATCT-ATG 961
                         -i ii   -  ?i  ii i  v --------------i iv  i  - ii
  L1M4_orf2#LINE/    420 -CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_13293646_1    962 GCTTGTACTGAAATCAATTCCAT-TGGAGTGTAAGTCTGAATGTTAAGGT 1010
                         v v i   vi    i  i  v v-    vii? iii  i     -   --
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAG-- 515

  chr2_13293646_1   1011 AAGTAAAA----AAAGCT-TTAGAAATACAATACACAAAAATA--TTTTT 1053
                          iv     ----   i  -      i---  v   i ii?i  -- i  i
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAG---AAAACATAGGNGTAAATCTTC 562

  chr2_13293646_1   1054 A-GACTTCAATATAGGAAAATATTTCTCAAATAGAACATGTAAATCATTA 1102
                         i-   i iiivv    v  vvi     i i   vi   ivv   v  iv 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_13293646_1   1103 ATTA-GAAAGAAAATATTGATAAATGTTGATGGCATTAACAT-AAAGATA 1150
                         iiv -i        v  v       - v  ivv   i  v  -   i iv
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAAT-TGGACTTCATCAAAATTAAAAACT 661

  chr2_13293646_1   1151 TTT---CTTCTAAAAACAACATTAATTAAATAAAAAAGTAA-----ATAT 1192
                            ---    v  ii   vi  i  vv  i i    iii  ----- v v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_13293646_1   1193 TG--AAAATATATTTCTAACTTGTATCTTTGACAAAGAGATTGCATCTAC 1240
                           -- i  v      vi  v ii   v i   i  i iiv   i   i v
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_13293646_1   1241 AAGGTATAAATAAATGCTT-CAAGTCA-TAAGGCAAAGA-AAGGAACCAT 1287
                           vi      -i  iv   -   v   -   viv     -  iv    -i
  L1M4_orf2#LINE/    762 AATATATAAA-GAACTCTTACAACTCAATAATAAAAAGACAAATAACC-C 809

  chr2_13293646_1   1288 AGC--AAAAATATGCATAAGGCAATTGAATAG-CACTTCACAGATGAAGA 1334
                          ii--      iv   -    - v        -  i   v vi v     
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCA-AAGG-ATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_13293646_1   1335 TATACAAA 1342
                                 
  L1M4_orf2#LINE/    858 TATACAAA 865

Transitions / transversions = 1.65 (150 / 91)
Gap_init rate = 0.05 (46 / 865), avg. gap size = 2.48 (114 / 46)  


2031 25.49 8.38 3.26  chr2_13339700_13341582.rev      534  1392 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_13339700_1    534 AGAT-TACCATGTGTTTACATTGTAAGACATGTTATTGTTATAATGGAAA 582
                             - v      viv iv    v     v iv        vi    v  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_13339700_1    583 TTATAACCCAAAT-GATTTATAGATTCAA-----TCCTCAAGAAAATCAT 626
                          - ivv       -   i  i        -----   ii vv      vi
  L1M4_orf2#LINE/     56 T-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_13339700_1    627 AGCAGGTTTTTTTTTTCTGGAAACAGACAAGTAAATTCTAAAAGTTATAA 676
                            v ---ii      vii    iv      ivi  i      v i   v
  L1M4_orf2#LINE/    105 AGCTG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_13339700_1    677 AGAAATGCAAATGGTCCAGAATAGCCAACACTGTTTTTAAAAA------- 719
                         i         iv ii             v  vi i  v     -------
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_13339700_1    720 ----TTGTGGAATTTTTATTAACTAATTT--AAGTCTACTATAAAATTGC 763
                         ----   vi i i ivi i vv i     --  iii     i   ii i 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_13339700_1    764 AGTAAACAAGATGGTCTATTATTTGCATTAGGGT---------------- 797
                              v     ii  v iv  i v    v   i ----------------
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_13339700_1    798 GAAATAAA---------CCAAAAATAAATCCACACAT--ATGATTAGCTG 836
                          i    i ---------   i       i   i    --   i i ii  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_13339700_1    837 ATATTCAACAAAAGTGCCACAGCAATTCAATTTAAAAAATGACAGTTTCC 886
                           v   i    ii      vii v       vvii   i-i i   i ii
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTTT 400

  chr2_13339700_1    887 TCTACA----GTTTTGAAACAATTGGATATATGTGTATAAAATAATGAAC 932
                           v   ----  vi  ii    i      ?viiii ii    v      v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_13339700_1    933 TTTGACCCTTACTTTACAACATATTACCCAAATTA---CAAG-TAAGTCA 978
                           v     i   i i   v     -  vv      ---   i- iii   
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGATCA 499

  chr2_13339700_1    979 TAGGCTTAAAAGTAAACCAAAAAGTAAATTTGAAACCATAAAATGTCCAA 1028
                         ?  i i    v    i------  i----- i    i      iviii i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAG------AGC-----TAAAACTATAAAACTCTTAG 538

  chr2_13339700_1   1029 AAGAAA-CATAGGAGAAAATCTTCTTATCATTGGGTTAGGCAAAATATTC 1077
                               -      ? v        v iv v             vivv   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_13339700_1   1078 TTA--TATGAAATACAAAAGCATGAACCATTAAAAATGATAATTGATAAA 1125
                            --     v i-        i-  v  vi    ivi v   v      
  L1M4_orf2#LINE/    589 TTAGATATGACAC-CAAAAGCAC-AAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_13339700_1   1126 CTG-ACTTCTTTAAAATTAGAAACATTTTCTTCTCTAAAG-ACACTATGG 1173
                         i  -     v i       i    -    v v  ii    -       vi
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCA 685

  chr2_13339700_1   1174 GATAATTAAAATGA-AAGCCATAAACTTGAGGAATACATTTGCAAA-CAT 1221
                         iiv  v i   v  -  v   i i v v ii   v i         -   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_13339700_1   1222 ATAT-TGATAAAGAACTTATATCCAGAATATATAAAATACTATTACAACT 1270
                             -      i i    i                 iv   v        
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_13339700_1   1271 GAAGAATAA---GACAAAAAA---AAATACAAAATGGGCAAGAAACTTAC 1314
                         v  v     ---      v  ---  v ?v           iii i  iv
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_13339700_1   1315 ATAGACA---CTCCAAAAAAGAAAATATAAAAATCAAATGTCAAGTAAGC 1361
                                ---       i    ---    -----      v v i     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGA---TATA-----CAAATGGCCAATAAGC 877

  chr2_13339700_1   1362 AGATGAAAAAATGTTTAACACCTTTAGTTAT 1392
                          v       i   i i    i v????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (130 / 85)
Gap_init rate = 0.04 (32 / 903), avg. gap size = 3.12 (100 / 32)  


1492 26.60 5.47 2.58  chr2_13360644_13362288.rev      501  1158 (487)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_13360644_1    501 AAGAATTACCGTAAAGCTACAGTAATTAAGGCAGTGTAGTAT-------- 542
                           i v    iii              i   i      i   i--------
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_13360644_1    543 GGATAGATGTA-ACATTAAGTGAAATAAACAGACTAAAA-CACAGAAATA 590
                                ii  - v  i  -  i    i --- i i i -iv        
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAA-TGGAATAGA---ATTGAGAGTCCAGAAATA 327

  chr2_13360644_1    591 CACCCATACCTTTATGGTAAGCTGATTTTGTGCAATGATGCAAGGACAAC 640
                         v        v        v ii       vvi   v i   v i   -- 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC--C 375

  chr2_13360644_1    641 ATTCA---GGAAAAGA---GTCTTT-CAGTTAATGGAGCTGAAA-AACTG 682
                              ---  i     ---      -  iiv     v    ii -     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_13360644_1    683 GGTATCTGTATGGGACAAAATAAT-AAGT--GACTTTAA--TCAAAA-AT 726
                          i  ? iii   ---     v   -    --   iiiv --   v v-  
  L1M4_orf2#LINE/    426 GATAKCCACATG---CAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_13360644_1    727 AATCCAGAAAATAATTTTGAGAAGGATTTGTATTTCTACATATTTAAAAA 776
                          - v  i   v   i i-- i  v iv ii? vvi   v  i --  i i
  L1M4_orf2#LINE/    473 A-TACAAAAATTAACTC--AAAATGGATCAWAGACCTAAATGT--AAGAG 517

  chr2_13360644_1    777 TAAAAATTATAAGACTTCTAGAAGAAA-TATAGAGGTACGTCCTCGAGAC 825
                         iv    i     i   ii         -i    i?   vi  i   v   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_13360644_1    826 CTTGGGCTAGGCAAAGATTTCTTAGA-AGGACAAAGAAAATATTAACCAT 874
                               i       v i         - v    vvi   ii iv i v i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_13360644_1    875 GGAAAGAGAAAAGTGGCAATCTGGACTTCAT-ACAATTTAAA--TTTTCT 921
                         i-     i    vv ii  vi          - v    v   --    v 
  L1M4_orf2#LINE/    618 A-AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_13360644_1    922 GCTAGTCTGAAGATAGTAATAAGAAAATAAATAGGGAAGTCACAGAATGA 971
                            --  vi i  i v  vi      i i  v  iv  vi         i
  L1M4_orf2#LINE/    667 GCT--TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_13360644_1    972 AAGGAAATATCTTCTATGGACATATCTGAAAAATTACTACTATTTAGAAT 1021
                         i  i      i v v vvv i        v  ivv   vv   ii     
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_13360644_1   1022 ATAAAAATAAC----AGAACTCAATAGTAAAAAGAAAAACAACTCTAT-A 1066
                            v   v   ---- v         i        v   i   i v  -?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_13360644_1   1067 AAAAGCGGGAAGAAGTCATGAAACAATAACTCTTAAATAAAGATGTAGAA 1116
                             ii   v i i viv    vvi i vi   iv  vi     i  v  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_13360644_1   1117 ATGGCCAATAAACACATAAAAT--TGCTCAATTTCCCAATAACT 1158
                                    i     i   v--       iv  v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (100 / 71)
Gap_init rate = 0.04 (27 / 677), avg. gap size = 1.96 (53 / 27)  


1661 27.19 7.57 0.17  chr2_13382978_13384550.rev      501  1081 (492)    L1M4_orf2#LINE/L1      285   908 (0)  

  chr2_13382978_1    501 TAGACACATAGAGCAATGGAACAGAATAGAGAACCCAGAAACAAATCCAT 550
                               i     v        i     v    ii       i   i    
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_13382978_1    551 ACTTCTACAAGGAACTCATTTTCAATGAAGTTGACAAGAGCATACATTGG 600
                           v i  iiivv  i v      i ii i v  v     v   v  v   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_13382978_1    601 GGA--------------CGA-AAA----GCT-------------ATCCAT 618
                            -------------- i -   ----   ------------- ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_13382978_1    619 ATGTGGAAGAAGAAAACTAGATCCCTATC-CTTGCTATGTACAAAAATCA 667
                            iii     vi  ii i  i     i - vii i  i         i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_13382978_1    668 AATAAAAATAGACTAGTGACTTAAATCTAAGACCTCAAGTTATGAAACTA 717
                          v v     i  ii ?v   i     v     v  v  ii   i     v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_13382978_1    718 CTAAAAGAAAACATAAGGGAAATTCTCTAAGACATTAGTCTGGGTAATGA 767
                         i  i           i ? v  v   iiiv   v  i vi i  i    i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_13382978_1    768 TTTATTAAGTAATATCCCACAAGCACAGGCAACCAAAACAAAAATTGGCA 817
                            v   ii  vv iv   v       i     v   iv      v ii 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_13382978_1    818 AATGGAATCACATCAAG-TTAAAAAGCT--ACACAGCAAAGGAAAC---- 860
                            v i iiv      i-       vi --iii vv       v  ----
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_13382978_1    861 AACGAAGTAAAAAGACAATCAA-AGAATGAGAGAAAATATTTGCAGACTC 909
                           vi    i         i v -      i               i iiv
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_13382978_1    910 TCCATCTGATAAGGTCTTTATGCCCAGATTATATAAGGAGCTCAAACAAC 959
                          vi           vvi  i ii     v       i  i   vv     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_13382978_1    960 TCTATAGAATAAAATCTAATAATCCAATTTAAAAAATGGGCAAAATACCT 1009
                           v   iv v   iv v     i      ?     -        iv ii 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTT 833

  chr2_13382978_1   1010 AAAGAGACATTTCTC---AAAAGACAAAGAAATGGCAAACAGATGTAGGA 1056
                         i  v           --- i    i v v       v  i iiiii v  
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_13382978_1   1057 AAACGTGCTCAACATCACTGATCAT 1081
                            vi            ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (94 / 60)
Gap_init rate = 0.02 (11 / 624), avg. gap size = 4.09 (45 / 11)  


2541 28.07 1.43 2.19  chr2_13399957_13405792.rev     4433  5344 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_13399957_1   4433 AACAACATTCCATGCTCATGGAGAGGAGGAATCAATATCGTGAAAATAGC 4482
                           vi i  i     i       vv   i  v i     i  v  i  i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_13399957_1   4483 CATACTGCCCAAAGCAATTTATAGATTCAAAGCAATTTATAATCTATTCC 4532
                         v     v      vii  i  i        v     iiv  vivv v   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_13399957_1   4533 CATTTAACGACCTTTGAAATTCTTCACAGAATTAGAAAAAACT-ATTTTA 4581
                           ----i vi     -------  ii     v v  v  i-  -  ii  
  L1M4_orf2#LINE/    104 CA----GCTGCCTTT-------TTTGCAGAAATTGACAAG-CTGATCCTA 141

  chr2_13399957_1   4582 AAATTCATACGGAACCAAAAATCAGCTTGCATAGCCAAGGCAATCCTAAG 4631
                                  i    viiv  ivv v iv v        ii     i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_13399957_1   4632 CAAAAAGAACAAAGCTGGAGATATCACGCTACCTGAACTGAAACCATACT 4681
                         v  i          i     ivv    i  v  ii vi v   v v    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_13399957_1   4682 ACAAGCCTACAGTAATCAAAGCAGCACGATACTGGTACAAAAACAGGCAC 4731
                             iv             ii   iii i      i i  ii i  i  i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_13399957_1   4732 ATAGACCAATGGAATAAAATAAAGAACTGAGAAATAAAACCTCACAGCTA 4781
                              i          i   vi   iiiv         v  vi   vi  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_13399957_1   4782 AAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGG 4831
                         viii  vi    i  i     ivv  v   i v  vv      i     i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_13399957_1   4832 ATTCCCTATTTAATAAATTATGCTGGAAGAACTGGCTAGCTATATGCAGA 4881
                           vvi  v  i  i    vi      i v      v  ? i i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_13399957_1   4882 AAACTGAAACTGGTCCCCTTCCTTACACATTATACAAAAATCAACTTAAG 4931
                          i v    ii   v     v   i    vv           i    i  i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_13399957_1   4932 ATGGCATAAAGACTTAAATGTAAAACCCAAAACTATAAAAAACCTAGAAG 4981
                             vvi ?    i         i v i            vv i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_13399957_1   4982 AAAATCTAGGCA-ATACCATTCAGGACACAGACACGGGCAAAGATTT--T 5028
                             iv    ?i- v i -   iv   viv ivvii     v i   -- 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_13399957_1   5029 AATGATGAAATCGCCAAAA---CAAATTGCAACAAAAGTCACAATTGACA 5075
                          ivv    --- i      ---   ---          vv v   v  i 
  L1M4_orf2#LINE/    591 AGATATGA---CACCAAAAGCACAA---GCAACAAAAGAAAAAATAGATA 634

  chr2_13399957_1   5076 AACAGGATCTAGTTAAA-TTAAAGAGCTTCTGCACAGCAAAACAAACTAT 5124
                           iv   ii vi i   -     i -   i  ii vv    iv v     
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chr2_13399957_1   5125 CAC-AGAGTAAACAGGTAACCTACAGAATGGGAGAAAAT-TTTGCAATCT 5172
                           v- i   i  v  ii    i                 -       vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_13399957_1   5173 GCCCACCTGACAGAGGTTTAGTATCCAGAATCTACAAGGAACTTAAGCAA 5222
                         iivi i    i ii  vi v           v  i  i     ivvi   
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_13399957_1   5223 ATTTACAA-AAAAAAAAAAACAACCCCATCAAAAAGTAGGCAAAGGACAT 5271
                         v iv i  -     i v   i     v  i?    i i         iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_13399957_1   5272 GAACAGATATTTCTCAAAAAAAGACATACATGTGGCCAAAAAAACTATGA 5321
                            i   i       v   i    i     vi       v  ivvi    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_13399957_1   5322 AAA--CGCTCAGCATCACTGATCAT 5344
                            --i     i     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (150 / 102)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 2.06 (33 / 16)  


2611 27.46 5.79 0.58  chr2_13427641_13429876.rev      882  1744 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_13427641_1    882 TGGAAAAATCTCTCATGCTCATGGATTGGGAGAATCAATACTATTAAAAT 931
                               i  v  i    i           i   v i    i i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_13427641_1    932 GGCCATACTGGCCAAAGCAATCTACAGATTCAACACTATTCCTATTAAAC 981
                            v     vv     vii               i v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_13427641_1    982 TAGCA-CTGCCATTTTTCACAGAACTAGAAAAAACT-ATTCCAAAATTCA 1029
                          vv  -     -     ii     v v  v  i-  -  i i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_13427641_1   1030 TATGAAACCAAAAAAGAGCCCGAATTGCCAAAACAATCCTAAGCAAAAGG 1079
                             i  viiv  ii  v  v    v            i i iv  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_13427641_1   1080 AACAGAGCCTGAGGCATCACATCACCTGACTTCAAA-----CTATAAGGC 1124
                             i  iiv    vv     iiv  ii i      -----   i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_13427641_1   1125 TACAGTAACCAAAACAGCATGGTATCAGTACAAAAACAGACACACAAACT 1174
                                 i   i    ii     iii i i  ii i     i i i ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_13427641_1   1175 AATATAACAGAATAGAGAACCTGAAATTTAAGTCACACACTTAAAGCCAT 1224
                            iv  i     v    ii iii  v v  vi  i   i   vi i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_13427641_1   1225 CTGATCTTTGACAAAATTAAGAAAACTAAGCAATGGGGAAAGGACTCCCT 1274
                         i    i  i     iiv ivv  i  i vv            i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_13427641_1   1275 ATTCAATAAATGGTGCTGGGATCACTGGCTAGCTATATGCTGAAGAATGA 1324
                         v     i              iv     v  ? i i    vi        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_13427641_1   1325 CATTGGAACCCTACCTTTCACCATATATTAAAATTTAACTCAAGGTTGAT 1374
                         vi     v        iv         iv      -       ii v   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATT-AACTCAAAATGGAT 497

  chr2_13427641_1   1375 TAAATATTTAAAAAGTAAGACCTCAAACAATAAGAATTCTAGAAGAAAAT 1424
                         i ? v ii    v-      v  v    v    i v ii          i
  L1M4_orf2#LINE/    498 CAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_13427641_1   1425 CTAGG---AAACATTATATGAC--------------TAATTCCT------ 1451
                         v    ---   iv  -ii    -------------- ii  i  ------
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_13427641_1   1452 ------CAAAATT----TCAACAAAAACAAAAATTGATAAGTGGGACCTA 1491
                         ------     vi----v        iv      v     i v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_13427641_1   1492 ATCAAACTAAAGTGCTTCTGCACAGCAATATAAACTACCAACAGAGTAAA 1541
                               v v  ivi   i  ii vv   viv v    i   v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_13427641_1   1542 CACGCAACCTATAGAATGGGAGAAAATATTCACAAACTACGCATGTGACA 1591
                         v vi     i i                  ii    ii iii  v   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_13427641_1   1592 AAGGTCTAATATCCAGAATCCATAAGGAACTTGAGCAACCAAACAAGCAA 1641
                          i  v  vi          vi    i     ivvi    iv  i  vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_13427641_1   1642 AAAAGAAATAACCCTATT-AAAAATGGACAAAAGA-----ACAGATACTT 1685
                           i v         v   -        i    i  ----- i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_13427641_1   1686 GTTAAAAGAAGACATTCAAGGTGTCAA----CATACGAAAAAATGCTCAT 1731
                         v iv        i  v   ivv i   ----  i i     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_13427641_1   1732 TATCACTAATTAT 1744
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (147 / 88)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.67 (55 / 15)  


1811 24.89 8.26 8.26  chr2_13434149_13436602     1067  1962 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_13434149_1   1067 CCACATTCATGAGTTAGAAGTCTAATTATTGCTAAGATGTCAAGTCCCCC 1116
                            ii      ii  i    v  v v     i       v   vv i   
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_13434149_1   1117 CAA-TAGATCTATTGATGTAGTTCAATTCTGATCAATATCTCAGCAGACA 1165
                            - v      iv   vi iiv    i iv     v   i    v v v
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_13434149_1   1166 TTTT-GTAGGAATTGACAAACTGATTCTGAAATTCAAATGGAAATGTAAA 1214
                             - i  i         i     i  i       v         i  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_13434149_1   1215 AGAGCCAGAATAGCTAAAATAGCTTTGAAAAAGAAGAATGAAGTTGGAGA 1264
                         i  v          i    i iii              ii         i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_13434149_1   1265 ACTAAAATGACTTC---ATTCCATGGTTTATTATAAAGCCACAGTTATCA 1311
                            v v ---    ---   i  viii   i  i     i     v    
  L1M4_orf2#LINE/    213 ACTCACA---CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_13434149_1   1312 AGATAAAATGATAGTGGCCTTAAGTTATACTAACCAATCAATGGAACAGA 1361
                            i ivi  i  v    v v i v  v  vv ivi          i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_13434149_1   1362 ATGGAGCATCCCATAATATTGCCACACATATATGGTCAACT--------- 1402
                           v   vi   viv    vvv   i    v         i ---------
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_13434149_1   1403 ---------------CGTTTAATTGGAGAAAGTATAATCTTATCAACAAA 1437
                         --------------- i  i   -  i     v   i    v        
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_13434149_1   1438 TTGTGCTAGAATAATTAGATACACGTTTGAAAATAAAATATTGAACTAGC 1487
                          v     i i i  i i    ?v iiv  v   - i   i----------
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAA-AGAATG---------- 447

  chr2_13434149_1   1488 AATTTCAATCTATGTTTAACACTGTATAGAAAAATTATTTTAAAAGAGAT 1537
                           v  vi i iv iii v    ii    v        vi i    vi   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_13434149_1   1538 CCTGTACCTAAATGTAA-------AATT-TGAAACTT---GAAGAAAATG 1576
                          v?iv            -------  i - i     i---        ii
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_13434149_1   1577 TAGAAAAGAAATTTT--------TGAGTTAAGTA----TTTCT-ACTTAT 1613
                            i?i-v    i  --------  i    i i ----     - vv   
  L1M4_orf2#LINE/    548 TAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_13434149_1   1614 GACACCAAAAATCATGATCCATAAAATTAAAAATTACATACTTATATGTG 1663
                                   i-  ii v v i    vv      ----------------
  L1M4_orf2#LINE/    597 GACACCAAAAG-CACAAGCAACAAAAGAAAAAAT---------------- 629

  chr2_13434149_1   1664 TGTGTGTAAAGACATGTACTTATATATGTGTACATATATATTAAACT-CT 1712
                         ---------   ------------------------  v   ii   - v
  L1M4_orf2#LINE/    630 ---------AGA------------------------TAAATTGGACTTCA 646

  chr2_13434149_1   1713 TTAAGAATAAAAACTCCTGCCTTTTGAAAAGCATTA---AGAGAATGAAA 1759
                          i  i v        ii  ivi  ii  iii  i  ---   i i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_13434149_1   1760 AGTCAAGCCACAAAGTTAAGGAAGCAACTTTTAAGTCACATGTTTAATAA 1809
                           v   v     i i viii   ivv i  vi  i   i  i i i    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_13434149_1   1810 AGATTTTTGTATTCAGATTCCATAAAATACT-TTAAAGGT--ATGATAA- 1855
                         i ivi  -    i    v vi     iv   -   v iv --  i    -
  L1M4_orf2#LINE/    747 GGGACTT-GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_13434149_1   1856 --------TAACCTGAT---AAAATGATTGGCAAA--ATGTTAACAGAGA 1892
                         --------     ii  ---      ---      --  v v  i   v 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATG---GGCAAAGGATTTGAATAGACA 842

  chr2_13434149_1   1893 CATCACTAAATCAGATATAAATAAAAATGACAAATAAGCACATGAAAAGA 1942
                         iv  v i   vv       v ----    i v                  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACA----AATGGCCAATAAGCACATGAAAAGA 888

  chr2_13434149_1   1943 TGCTTAATCTCATTAGTCAT 1962
                             i  iv   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (134 / 86)
Gap_init rate = 0.03 (28 / 896), avg. gap size = 5.29 (148 / 28)  


 299 28.65 8.99 5.62  chr2_13439306_13441389.rev       15   192 (1892)  C L1M4_orf2#LINE/L1   (483)   425   242  

C chr2_13439306_1    192 ATAAATCTACAGTAATTAGAAGGCTGTGTTTTTCACGTAAG-------AC 150
                          i   v          i ii viv    v vi vi i    ------- i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

C chr2_13439306_1    149 ACAAATGCTATGTGAACAG----GAGAGTGGCCCAGGGAAAGACCCGTTT 104
                          i i  - v   -   i  ----      ---    ii v i    i vi
  L1M4_orf2#LINE/    292 ATAGAT-CAATG-GAATAGAATTGAGAGT---CCAGAAATAAACCCATAC 336

C chr2_13439306_1    103 ACCTGTGGACTCTTGACTTATTACATAGGCTGCATTGCAAAGTAATT--- 57
                          ii i   v vv    i  viv   -   v   ----   iiiv   ---
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACA-AGGGTGC----CAAGACCATTCAA 381

C chr2_13439306_1     56 --AGGCAAGGACAGACTTTTCTACAAAAGAAGCTGGGACAATTG 15
                         --i  v   i i  v      v     v iv          i  
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

Transitions / transversions = 1.43 (30 / 21)
Gap_init rate = 0.04 (8 / 184), avg. gap size = 3.25 (26 / 8)  

1391 26.62 3.24 3.06  chr2_13439306_13441389.rev      501  1056 (1028)    L1M4_orf2#LINE/L1      140   696 (212)  

  chr2_13439306_1    501 TAAAAT--ATATGTAA---CAAAAAAAGCCGCATAACCAATGCAATTCTA 545
                               --     v  ---   iii vv v v   i    vi    ii i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_13439306_1    546 AGCAAAAAGAACAAAGCTGGAGGCATCATGCTAACTCACTTCCAA--CTA 593
                          iv  i          i      vv   ii  v- i  v  i   --  -
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACT- 237

  chr2_13439306_1    594 TACTACAGGGCTACAATAACCAAAACGGCATGGTAATGGTATAGAAACAG 643
                                ii      i   i   i  i ii     v   i   iii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_13439306_1    644 ACACCTAGACCAATGGGACAGAATAGAGAACCCTAGAAATAAGACAGCAT 693
                            iv    i      i i     v    ii  -        iv --   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCC-AGAAATAAACC--CAT 334

  chr2_13439306_1    694 AC--CCACAACTATCTAATCTTTGACAAAGCAGACAAAAACAAGAAATGG 741
                           --ii iiiii vi i  i  i     i vv v   i v  vvv     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_13439306_1    742 GGAAAAGAT---CTATTCAATAAATACTGCTGGGATAACTGGCTAGCCAT 788
                              ii  ---  v     i    iv        i      v  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_13439306_1    789 ACGCAGAAGATTGAAAGTGGACCCCTTTCTTACACCACAAACAAAAATTA 838
                          i   i    v    iv         vi  i      i v          
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_13439306_1    839 AGTCAATATAGATTAAATACTTAAAGGTAAAACTCTGAACTATAAAAACT 888
                          v    v  i   i ? v  i    v    i viivi          -  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CT 533

  chr2_13439306_1    889 CT-GGAAGACAACCTAGGC---AATGCCATTCAGGACATAGGCACAGGAA 934
                           -i     v   v    ?---   -- -   iv   v v  vvi   v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCA 580

  chr2_13439306_1    935 AGAGTTCATGACAAA-GACATCAAAAGCAACTGCAACAAAAGTAAAAATT 983
                          vi   iv v v v -    i        vvv          v      v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_13439306_1    984 GAGAAATTGACAAATGGGACCTAATGAAACTGAAGAGCTTCTGAACAGCA 1033
                           v      --------   i v  v   v v  i i   i  vi vv  
  L1M4_orf2#LINE/    631 GATAAATTG--------GACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_13439306_1   1034 AAGGAAACCAT-AAGCAAAGGAAA 1056
                              v  i  -   v  iv    
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAA 696

Transitions / transversions = 1.23 (80 / 65)
Gap_init rate = 0.03 (17 / 557), avg. gap size = 2.06 (35 / 17)  

 352 27.27 12.30 0.00  chr2_13439306_13441389.rev     1406  1592 (492)    L1M4_orf2#LINE/L1      699   908 (0)  

  chr2_13439306_1   1406 ACAACATAAAGAATGGAAGAAAATTTGTGAAAGTTATGCATCAGGCAAAG 1455
                              vi v       i       v v  v  i i  ii   v ii  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_13439306_1   1456 GTCTAATATGTAGCATCTACAAGGAACTTAAACAA----AT--TTACAAG 1499
                          v  vi   vi  v  v  i  i     ivv    ----  -- v v   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_13439306_1   1500 A-AAGTA-------TGAAAA--GGTCA-------TAAACAGACACTTTTC 1532
                          -  i  ------- ?    --  v  ------- i  i     i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_13439306_1   1533 AAAAAAAGACATACTTGCCGCCAGCAATCATATGAATAAAAGCTCAACAT 1582
                         v   i    i    vviiv    ii  v  i     v i v         
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_13439306_1   1583 CACTATCATT 1592
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.17 (27 / 23)
Gap_init rate = 0.03 (6 / 210), avg. gap size = 3.83 (23 / 6)  


 490 19.42 0.00 0.00  chr2_13453369_13458235     1200  1302 (3565)  C L1M4_orf2#LINE/L1   (0)   908   806  

C chr2_13453369_1   1302 ATCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACCTCTCCAAAGAA 1253
                          i  v  i?    i            v    i     ii           
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

C chr2_13453369_1   1252 GACATTTATGTGGCCAACAAACATATGAAAAAAAGCTCATCATCACTGGT 1203
                           i  vi vi       i  i  i       i v     v     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

C chr2_13453369_1   1202 CAT 1200
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.00 (0 / 103), avg. gap size = 0.00 (0 / 0)  

2932 24.07 3.96 4.18  chr2_13453369_13458235     3466  4375 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_13453369_1   3466 TGGAAAGTTATT-----TTCATGGATTGGAAGAATCAATATTTTTAAAAT 3510
                                v   i-----                v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_13453369_1   3511 GCCCATGGTACCCAAAGCAATCTACAGAGGCAATGTACTGTATTTTGCAC 3560
                          v v  iv v      vii         vv   i i -------------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA------------- 87

  chr2_13453369_1   3561 TGTATTCCCTATCAAAATACCAAGGATATTCTTCACAGAAATAAAAAA-- 3608
                         ---  -            v   ivviiv  i  ii       vi v  --
  L1M4_orf2#LINE/     88 ---AT-CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC 133

  chr2_13453369_1   3609 --ATTCTAAAATTTATATAAAATCACAGAACATCCCAAATAGCCACAACT 3656
                         --  i        i    ii  vii  iiiv i  vi        v   v
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr2_13453369_1   3657 CTCCT----AAGCAGAA--------GAG---TCACATTACCTAATTTTAA 3691
                         v  i ----   v    --------   ---     i v  i     i  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_13453369_1   3692 ATTATGCTACAGAGCTGTAGTAACCAAAATGGCATGATACTGGCATAAAA 3741
                          viv i     i    ii     i   i ii ii  i           ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_13453369_1   3742 GCAGACACATAGACAAATGGAACAGAACAGAGAACCTGGAAACAAATCCA 3791
                         ii     i     iv       i    iv    ii ii    i   i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_13453369_1   3792 CATATCTACAACGAACTTATTGTTGACAAAGGAGCCAAGAACACATAGTG 3841
                         i i  i  iiiiv  i v   v i     i  v       v  ivi i  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_13453369_1   3842 GGGAAAATATAGTCTCTTCAATAAATAATGCTGAGGAAACTGAATATCCG 3891
                               iv       i     i    ii     i iv     i   ?  i
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_13453369_1   3892 TATGCATAAGAATGAAACTAGATCCATATCTCTTGCCATATACAAAGATA 3941
                         i     v         ii i  i  v  i   vii           i  -
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT- 482

  chr2_13453369_1   3942 TCAAATAAAAATGGATTAAACACTTAACTCTAAGACCTGAAACTATGAAA 3991
                         -i  v v         i ? v  i   v v     v  i       i   
  L1M4_orf2#LINE/    483 -TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_13453369_1   3992 CCACTATAAGAAAACATTGCAGAAATTCTCCATGACATTGGTCTGGGCAA 4041
                          ivi  v          v v? v  v   i i    v    vi i     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_13453369_1   4042 AAGTTTCTTCAGTAATAAC-CCACAGGCACAGGCAA----------AGTG 4080
                         vi       -  vv  i  -   v i     i    ---------- i i
  L1M4_orf2#LINE/    582 TGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_13453369_1   4081 GACAAATGAGATTATATCAAG-TTAAAAATCTTCTGCACTGCAAAGGAAA 4129
                           i    vi  i vi     i-       -   i  ii  v       v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA 679

  chr2_13453369_1   4130 CAAGCAACAAAGTGAAGAGACAACTCACAGAATGGGAGAAAATATTTGCA 4179
                          v v   v        i       i                         
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_13453369_1   4180 AACTATCCATCTGACAAGAGATTAATAACCAGGGTATAAAAACAAGCTCA 4229
                           ii  vi      i   i  i vi  v    ii    v   v  -   v
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTCT 778

  chr2_13453369_1   4230 AACAACTTTGTAGAAAAAAAAAACTAGTAATCTGATTTTAAAATTGGCAA 4279
                         v      ivi  -- v     i  v i   i ii   ?v     v     
  L1M4_orf2#LINE/    779 TACAACTCAATA--ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_13453369_1   4280 AAGATTTGAATAGACATTTCTCAACAGAGTTTTCTCAAAAGAAGAGATAC 4329
                          i                    -------------    -     v    
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTC-------------CAAA-GAAGATATAC 862

  chr2_13453369_1   4330 GAATGGCAAAGAGGCATATGAAAATATGCTCAATATCACTGATCTT 4375
                         i      v  v i   i       v        i    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (135 / 80)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.35 (74 / 17)  


1765 26.82 9.65 2.82  chr2_13458575_13461218.rev     1303  2152 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_13458575_1   1303 TGGAAA-ACATTCTATGC-CACTGACTGAAAGACCCCAATATTACTGACA 1350
                               - i  i i   i-  iv  i  i     ii-      ii i v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTT-AATATTGTTAAGA 49

  chr2_13458575_1   1351 ---CACTTTTCTCCCAAATTGATCTACAGATTTCATTCAATCTCAAATAA 1397
                         ---  v vi  -                    iv iv     i v vi  
  L1M4_orf2#LINE/     50 TGGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_13458575_1   1398 AATTCCATCAAACTGCTTTGTAGATATAGACAAACTTATTCTAAAGTTTA 1447
                            i   v viv  vi    i   v  v     i  v  i     i  i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_13458575_1   1448 AATAGAAAGGCAAAAGA-------TAGCCAAAAAAA----GAAAAA-AAG 1485
                         v  i    v    ii  -------         v  ----      -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_13458575_1   1486 TACAATGT-GGAG-ACACAAACTACCCAACTTCAGAACTTATAGTATAGC 1533
                         v    v  -    -  v  v   v     i    i      ivii v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_13458575_1   1534 TATAATAACCAAGATTATATGATACAGTTAAAAGAA---ACATATAAATC 1580
                           i i   i     ivi i  i   v vi v   i ---       i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_13458575_1   1581 AAAGAAA-------GAGAATATAGACATAGGACAAAATAAATATGATCAA 1623
                           v i  -------    i vi   v   iiv v v i vv    i    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_13458575_1   1624 CTGATTTTTAACAAGGACATAAAAGAAAGTTGAA-GGAGTGATGGCAGCC 1672
                         i       ii      iiiiv  -  vvi  v  -  i vi viii  i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTC 397

  chr2_13458575_1   1673 TTTCTCAAAAAATGATGCATCACCAATTAGATATCTATATTTAATAAAA- 1721
                            -    v     i   vvviv   i i    ? i i  vi  v i  -
  L1M4_orf2#LINE/    398 TTT-TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_13458575_1   1722 GAACCCAAACACAAATTTTACA--ATA-----AAATTAACTTAAAACAGA 1764
                            viiii  v vv ii i   --   -----         i    ii  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_13458575_1   1765 TCATACTTATAAATATAAAACGAAAAACTATAAAATGTCT---AAATACA 1811
                            ? vviv     i   i vvv            i-   ---  iv v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chr2_13458575_1   1812 TGTAAGAGAAAATCTGCGTGGGTGAACTGAGAAGTTTGGGT---GCAGTG 1858
                         ii  i ? v      v    -----  i-------      ---   i  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTG-----ACC-------TTGGGTTAGGCAATG 583

  chr2_13458575_1   1859 AGGAGTTTTTTTAAGATAAAACACTAAAAACACTTTCAA----AGAAAAA 1904
                         ----    i  --     vi    i    i   vvv   ----       
  L1M4_orf2#LINE/    584 ----GTTTCTT--AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_13458575_1   1905 AT-GACAGGT-GTACTTCATTAGAAGTAAAAACTTCTGTTCTGTGAAAGA 1952
                           -  i ii - v       i i  v         i   v  vii  i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_13458575_1   1953 CACTATTG-GAGTATTAAAA---AATGCACAGACTGGAAGAAAATATTTG 1998
                               ii-  ivi v    ---  iv      v   i            
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_13458575_1   1999 TGAAACACATACCTGATGAAGAAATTTTATCCAAAA-ATGTAAAGA---- 2043
                         ii  v  i   i     i i i v  v      i  -  i      ----
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_13458575_1   2044 ----------------------CAGACAACCCAATTAAAAAACTGGACAA 2071
                         ----------------------  i i         ?     -   i   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAA 826

  chr2_13458575_1   2072 AA-ATTTAAACAGTCGTCTAATCAAAGATGATGGGCAGATGGTCAATAAA 2120
                          i-    i  i  v i i vvi      v   ivi  i    i      i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_13458575_1   2121 CATATAAAAATATTCCCAATATCATTTGTCAT 2152
                           i  i    v  v i   i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 3.12 (106 / 34)  


2704 27.31 0.97 3.33  chr2_13512760_13519466.rev     5286  6215 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_13512760_1   5286 TGGAAAAAAAATCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5335
                               i v vi     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_13512760_1   5336 GGCCATACTACCCAAAGTAATTTATAGATTCAGTGCTATTCCCATCAAGC 5385
                            v     v      v i  i  i       ii  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_13512760_1   5386 TACCATTGACTTTCTTCACAGAATTAGAGAAACCTACTTTAAATTTCATA 5435
                          v   vivi i  i  ii     v v  v  i iv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_13512760_1   5436 TGGGACCAAAAAAGCGCTCATA-TAGACAAGACATTCCTAAGCAAAACAA 5484
                            i viiv  ii -i i  v -   v   i   v  i i --    v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGA--AAAAGAA 197

  chr2_13512760_1   5485 CAACAAAAACACAAACAAATGAAAACAAAGCTGGAGGCATCATGTTCCCT 5534
                         ----------------------i       i      vv   iii i  i
  L1M4_orf2#LINE/    198 ----------------------GAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_13512760_1   5535 GACTT-AAAACTATGCTACAAGGCTACAATAACCAAAACAGCATGGTACT 5583
                         i i  -      - i      i      i   i   i    ii       
  L1M4_orf2#LINE/    226 AATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr2_13512760_1   5584 AGTACAAAAACAGATATATTGACCAATGGAACAGAACAGAGGCCTCAGAA 5633
                         i i i  ii i   i    v  i        i    iv   ivii     
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr2_13512760_1   5634 ATAACACCACACATCTACAACCATCTGATCTTTGACAAACCTTACAAAAA 5683
                             vv   i    i  iiii  vi    i  i     ivv vv   i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_13512760_1   5684 CAAGCAATGGGGAAAGGATTCCCTGTTTAATAAATAGTGCCAGGAAAACT 5733
                           vv            i  vvi  v  i  i    i    ii   v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_13512760_1   5734 GGGTAGCCATATACAGAAAATAGAAACTGGACCTCTTCCTTACACCTT-T 5782
                           i  ?   i  i  i  i vv   ii      i  v   i     v - 
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_13512760_1   5783 ACAAAAATTAACTCAGGATTGATTAAACACTCCAATGTAAAACCTAAAAC 5832
                                        ii  v   i ? v  iiv       i v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_13512760_1   5833 CATAAAAACTCT-AGAAGATAACCCAGGCAGTA--CCATTCAGGACACAG 5879
                         i      -    -      v   vi   ?-   --i -   iv   viv 
  L1M4_orf2#LINE/    525 TATAAAA-CTCTTAGAAGAAAACATAGGN-GTAAATC-TTCGTGACCTTG 571

  chr2_13512760_1   5880 GTATGGGCAAAGACTTCATGACTAAAACACCAAAA--ACAATTGCAACAA 5927
                          vv i     v ii   v iiv  vi         --    --       
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GCAACAA 619

  chr2_13512760_1   5928 AACCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGTTTCTTCACA 5977
                           vvv     v  i    v   ii v  i   v v  i ii  i vii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_13512760_1   5978 GCAAAAGAAACTATCGTCAATGTGAACAGGCAACCTAAAGAATGGGAAAA 6027
                         v    i  v      ivv  v     v  i     i v         i  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_13512760_1   6028 AA-ATTTACAATCTATCCATCTGACAAAGACCTAATATCCAGAATCTACA 6076
                           -    i   vii  vi      i  i iv  vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_13512760_1   6077 AGGAACTTAAACAAATTTACAAGAAAAAAGCAAACAACCCCATCAAAAAG 6126
                          i     ivv    v iv i  v     ii    i     v  i?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_13512760_1   6127 TGTGTGAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGTGGC 6176
                           v ii      v    i     i     v        i  vi vi    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_13512760_1   6177 CAACAAACATATGAAAAAAAGCTCATCATCACTGGTCAT 6215
                            i  i  i       i v     v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (153 / 97)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  


1491 25.27 7.33 7.99  chr2_13541231_13545582.rev     2947  3860 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_13541231_1   2947 TGGAAAGACATT--GTGTTCATGGATTGGAAGAAACAGTATAGTAATGAG 2994
                                 i  i--i                  vvi i   v  v v  v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_13541231_1   2995 GCTAATTTTTTCTAAATCAATGCAGAGGTGCAATGTAATTCTTATCCAAA 3044
                          vi   vi ii i    ii  vi v  i v   i i   i i    -   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC-AAA 99

  chr2_13541231_1   3045 AT---AGC--CCATTTTTGTATAAAT--ATAGAATTATCACTGTAAAATT 3087
                           ---   --  v      i v    -- i iiv v   -  --      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-CT--AAAATT 146

  chr2_13541231_1   3088 TACATGGAA-TGCCCAGGGAACTAAACTAGCTAAAACAATTTCAAAAAGG 3136
                         i i      -   v-     v i i v    i        i ii    i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_13541231_1   3137 AAAAATAAAAAGGAATGAATTATTATATCTGATTTCAAGACTTATTATCT 3186
                           i  i   ivv i v  v i ivv vi ii       i     i  ivv
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_13541231_1   3187 ACATACATTAATTAATATTACGTGGTATTG------------ACACATAA 3224
                          vv    v    i  v ivii      i  ------------   i   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_13541231_1   3225 GCCAATGGAACAAGGTAGAGGGCCTAGAAACAGACCCATACAAT-ATACC 3273
                         ii        i iii v   i i i     i i         v -  ivi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_13541231_1   3274 TAACAAACTTTTGAGCAAGATGCAGGAACTA---AACTG--AAAGA-TGT 3317
                         i  ivi i   i  vv i i   viii  i ---  iv --     - iv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_13541231_1   3318 TCTTTTCAAGAAATGGTCCTGCGGCAATTGTTCATGCATAGACCAAAAGG 3367
                                  v       v   v i   i  ----- -   ?-   v v v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTG-----G-ATAK-CCACATGC 438

  chr2_13541231_1   3368 AAAAAAAAAAACAAAAGAAAAAGAATCCCAGCCTACATTTCATATAACAC 3417
                             i  v--------   ivv i i   vi   -  ivi      ----
  L1M4_orf2#LINE/    439 AAAAGAAT--------GAAGTTGGACCCCTACCT-CACACCATATA---- 475

  chr2_13541231_1   3418 ACAAACATTAAATCAAAATAAATTATATCCTTAAATGTAA-ATATATAAC 3466
                         -    v     v       ii  i ? vv i         - vv  v   
  L1M4_orf2#LINE/    476 -CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_13541231_1   3467 TAAAAAACATGTTTAAACTAAAAGAAAACA--------AACCTTCAGGAT 3508
                           v     --- i ----  i         --------  i    iv  i
  L1M4_orf2#LINE/    525 TATAAAAC---TCT----TAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_13541231_1   3509 CCAGAGGAAAGCTATAATTTCTCAGACTTGACATCAAAAGCACAATACAT 3558
                          iv i vv i  v  ii     i   iv     i           vvv i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_13541231_1   3559 AAAATAAAAAA-------ATT-------AT--AAACTATAAACTTTC-T- 3590
                             v      -------   -------  --   i  v       i- -
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_13541231_1   3591 CTTAGTGAAAACCAGTGTGAAAAGGATAGACAGACCAAGGTACATATTTG 3640
                            --ii  iiv  v i v  i iii ii v    -  vvi   v v v 
  L1M4_orf2#LINE/    668 CTT--CAAAGGACACTATCAAGAAAGTGAAAAGAC-AACCCACAGAATGG 714

  chr2_13541231_1   3641 GAGAAAACATTTA-AAATTATATATCTGAGAAAGGACTAGTATTTAGAAC 3689
                                i    i-    i          v  i     v    ii    i
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_13541231_1   3690 ATAAGAAAGACCTCTCTA-ACCTCAACAAAACAAAACTATACAGATTGCA 3738
                            -v     v    -  - v     i  ----------  -------- 
  L1M4_orf2#LINE/    765 ATA-TAAAGAACTCT-TACAACTCAATAA----------TA--------A 794

  chr2_13541231_1   3739 AAAGGTCTTGCAAAAATGAACTAGAAAAACCAATTAGAATATGGGCAAAA 3788
                             ------- v    -   --------      ?i  v         i
  L1M4_orf2#LINE/    795 AAAG-------ACAAAT-AAC--------CCAATTWAAAAATGGGCAAAG 828

  chr2_13541231_1   3789 GACATAAAGAGACATTTCAGTGAATAGGATATGCAGATGGCAAATAAGCA 3838
                           iv i  v         vvii  v i     i  i     v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_13541231_1   3839 TCATA---------TCAACATCATTGATCAC 3860
                         -   i---------         ????????
  L1M4_orf2#LINE/    879 -CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.05 (42 / 908), avg. gap size = 3.33 (140 / 42)  


2283 25.33 8.48 3.52  chr2_13552943_13556930     2664  3488 (500)    L1M4_orf2#LINE/L1        4   869 (39)  

  chr2_13552943_1   2664 AGAGATATTCCCTGTTTAAGGATTGGAAGACTCAATATAGTTAAACTGTT 2713
                          i      i  v    i v             i     v     iv  vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_13552943_1   2714 TAT-CTTCCCAATATGATCTACAGATTCA-CACAATCCTAAACCAAATTC 2761
                         v  -  i     vv               - i      iv v v    i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_13552943_1   2762 TAGCAAGTTACTTTGTAGTTATTACCAAATTCATTTTAAAGCTTACAAGA 2811
                         i   vivi vi    i  vv   iv   ii v  ii    ii i i v i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_13552943_1   2812 AGAGACAAAAAGACCCTAAATAACCAACACAATAGTTAAGACAAAGAATA 2861
                          i vi   ii-     vi    i    v     vv v  i vi     i 
  L1M4_orf2#LINE/    154 AAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_13552943_1   2862 AGATCAGAGGACTGACAACTGC--ATTTCAAAGCTTACTATAAAGTTACA 2909
                          ii ii       v   vi v --        i       i    i    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_13552943_1   2910 GTAAT---GA--------------------------------GATCAATG 2924
                              ---  --------------------------------        
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_13552943_1   2925 GAAGACAAT--AAGCTCCTGCAATA------------TATAGCCAATTGA 2960
                            v v   -- iiv   v v    ------------   i i       
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_13552943_1   2961 TCTCTGACAAAGGAGCAAAGACAATTTA-TGGACAAAGGATAGCCTTTCC 3009
                          i ii     i  v  v     v   i -   iv    i    i    i 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_13552943_1   3010 AACAAATGGGGCTTGAACAATTGGAGATCTATATGCTACAAAATTAATCT 3059
                                  v   v i    i    v ? i i    v v i   v  vi 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_13552943_1   3060 AGACACGTATCT-------TATACATAA--TAACTCAAAATAAAGCATAG 3100
                         i   v v  i  -------      v  --           ii v  ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_13552943_1   3101 AGCTACATGTAAAATGC-AAAACCATAAAACTTCTAGAAGAAAATATAGG 3149
                          v   v      i -  -     i        ii          i     
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_13552943_1   3150 AGACAATCTTGGTGATTTGGGACTTGGCAATGAGTATGTAGTTATAACAC 3199
                         ? vv      v    ii v  ii v       iv viv   v   i    
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_13552943_1   3200 CAAAAACACAGTCCTTGAAAGAAAAAAACTGGTAAGTTGGACTTCATTAA 3249
                              i    iv vvii          -iv i   i           i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAA 650

  chr2_13552943_1   3250 CAACAACCACCATCACCACAACAACAAAAAACAAATTTCTGTT---AAAG 3296
                         ----------------------  iv      v--   v  i ---  i 
  L1M4_orf2#LINE/    651 ----------------------AATTAAAAACT--TTTGTGCTTCAAAGG 676

  chr2_13552943_1   3297 ACACTGTTAAAAGCATGTAAAGACAAGTCACAGACTGGGTTAAAGTATTC 3346
                              i i  i ivi  v        vi      v    vv   i    i
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_13552943_1   3347 ATAAACACACATATTTGACAAAGGATTTGTATCTAAAATATACAAAGAGC 3396
                         ii   i-  i    i   i  i   i       i i      i     i 
  L1M4_orf2#LINE/    727 GCAAAT-CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_13552943_1   3397 ACTTAAACCTCAACA-TAAGAAAACAAGTCACTCAACT-AAAAATGGGCA 3444
                         v    v v     i -   i  i    i v  i   i -           
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_13552943_1   3445 ACAGACCTAAACAAAAACCTTACTAAGGAAAATAATA-AAATGGC 3488
                          vi  ii i  i i v ii iv i  i   i   -  -       
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATA-TACAAATGGC 869

Transitions / transversions = 1.57 (126 / 80)
Gap_init rate = 0.03 (22 / 866), avg. gap size = 4.50 (99 / 22)  


2690 25.66 2.54 1.97  chr2_13636417_13639302     1530  2394 (492)    L1M4_orf2#LINE/L1       39   908 (0)  

  chr2_13636417_1   1530 TACTATTAAGATGTCAGTTTTCTTCCAACTTGATCTATAGTTTCAATGCA 1579
                           i i        v  i vi  i-    v        i  v     i   
  L1M4_orf2#LINE/     39 TATTGTTAAGATGGCAATACTCC-CCAAATTGATCTACAGATTCAACGCA 87

  chr2_13636417_1   1580 CTACAAATCAAACCACTAGCAAATTAGTTTGTGGATATCAACAAATTGAT 1629
                         v v vv      viv i   vivi vv    ii  v  ii    ii    
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chr2_13636417_1   1630 TCTAAAAGT-ATA-GGAAAGGCAAAATGCCCAGAATAGCCATTTTGATAT 1677
                         i      v -   -     v    iivi             vvvii  v 
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_13636417_1   1678 TGAGAAC-AAGAACCAAGTCAGAGGACTGA-ATTATGTTACTTTAGCACT 1725
                            i  v-      v    ii       v - i viviv i  i iv   
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_13636417_1   1726 TACTATGAAACTACAATAATTAAGGCAATTTG-TACTAGTAAAAGAATAC 1774
                              ii  i     i    i   i  i v  -    i i v   i   v
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_13636417_1   1775 ACAAGTAGATTAACAGAACAAAAT----AGCCCAGAAATAGACCAACACA 1820
                            vi     i  ii   i i   ----  i         i   v i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_13636417_1   1821 AATACAATTAACTGACTGT-AACAAAGGCAAAAAAAA-ATTCAATGGAGA 1868
                         vv  iii i  i   i v -i    i  iivv  i v-         i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_13636417_1   1869 AAAAAAAATCTTTTCAGCAAATAGTGCTAGAACAAGTAGACAACTAGACA 1918
                           i  v i        i     i     i --------       i  i 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGG--------GACAACTGGATA 429

  chr2_13636417_1   1919 TCCATATCCTCTGCAGAA-AATCTA--TATACACACATCTTGCACTTTTC 1965
                         ?   i  -----   i  -   vv -- iv  v vi i  ii   iv vi
  L1M4_orf2#LINE/    430 KCCACAT-----GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_13636417_1   1966 ACAAAAGTTAACCCCAAATGGATCATAGGCCCAAATGTAAAATGC-AAAA 2014
                               i     i v          ?  i  i        i -  -    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAA 523

  chr2_13636417_1   2015 CCATAAACTTTCAAGGAAATAGCAT--GAGAAAATCTAGGTGACTTTGAG 2062
                          i     vi iiv  i i v i   -- ? v      vv     i   i 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_13636417_1   2063 TTTAGTGTTGACTTTTTGGATACAACACCAAAAATACAATCCATGACTGA 2112
                           vi iiv  ii  i  i    ii         ii    v v ii vv  
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_13636417_1   2113 ATAAATTGATAAGTAGGGCTTTATTAAA-TTAAAAAATGATCATTCTGCA 2161
                          v    v     i v  i   i  i   -       v v- ii v  v  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT-TTGTGCTTCA 672

  chr2_13636417_1   2162 AAAGACATTGTTAAGGAAATAAAAAGGCTACCCACA-ACTGGGAGAAAAT 2210
                           i    i i i   i  i i     i v       - v           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_13636417_1   2211 ACTTGCAAAACAAATAGCTGATAAAGGACTTGTTTCCAAAATATAAAAGG 2260
                          i       v  v   v       i        v    i      v  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_13636417_1   2261 AACTCTTA-AACATCAAAAATAAAAT--CAAAAAGCTTAATTTAAAAATG 2307
                                 -   -    v       v--    v i ii    ?       
  L1M4_orf2#LINE/    773 AACTCTTACAAC-TCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_13636417_1   2308 GGCAAATGATCTGAACAGGCATTTCACCAAAGAAGATATGCAAAAGGAAA 2357
                               v   i    i  i      v             i    v  vv 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_13636417_1   2358 ATAAACATATGGAAAGATGCTGAACATCATATGTCAT 2394
                             i  i   i         v       ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (134 / 84)
Gap_init rate = 0.03 (22 / 870), avg. gap size = 1.77 (39 / 22)  


1493 29.02 6.20 3.03  chr2_13690653_13692665      756  1513 (500)    L1M4_orf2#LINE/L1      114   895 (13)  

  chr2_13690653_1    756 TTTTGCTATAAATGGTCACACTGATTATAAAAGTGTTATTGAATAATAAG 805
                               - v    v v  vi     iv     v vv   v   vvii   
  L1M4_orf2#LINE/    114 TTTTGC-AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_13690653_1    806 ATACTTAAAAAAATTAAAA-AGT--TAAAAAAAAAAAA--------GAGG 844
                         iv  ii i  v iii    - i -- i     i  i  --------    
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_13690653_1    845 GCTGATACCAGCTGGCTTCAAGGCTTATTATAAAGCTAAAATTATCAAGG 894
                         i  v i  ivv iiii     ii    i  i       v i v      i
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_13690653_1    895 CAGTGTGATATTGGCATAGAGACAGACATTTATTTCAA------AGAAGT 938
                                i  i       ii  i      v  vv    ------    v 
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_13690653_1    939 G----TCAAGAAATTGATGCAC---TTTATGTAGCCATTTTATATTTTAC 981
                          ----  v      vi iv  i---      -- i  v  v  v  iv  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATG--GTCAATTGATTTTCGAC 360

  chr2_13690653_1    982 AATGATGCTAGGATACAAATGTTATTTAATAGAGAAAAAATTGTATTTTC 1031
                           v i   i i  i--------i   i   i i    i   v  v     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGAC--------CATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_13690653_1   1032 AACAAATGATACCAGAAATGTTGTAAATATACATGCATACATATGTGAAC 1081
                                 i i ii i vvii  v v ?vi       - v v -i    v
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGA-ATGAAG 450

  chr2_13690653_1   1082 GTGAACCTTT--CTTGTACCCTACACCAACATTTAGTGAAACTTTATTAC 1129
                         v  i   ii --  iii   v  i  v  v   v v v   v vv  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_13690653_1   1130 AGGACTAAATACAAAAGTTAAAAGTATGAAATGCGTGATAGGAAACATCA 1179
                           iv      ii  i  i     v   i   iv v iiv  i      vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_13690653_1   1180 AAGAAAATCTGTCTGACCTTCAATTATGCAAATGTTTTTGGTTGTTATAA 1229
                         i? v      viv       vii   v    vv    i -- v v   i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT--TAGATATGA 598

  chr2_13690653_1   1230 C-TCAAAAAGGCAAATAATATAAAAGAATAAAT-GATAAATTTTACTTCT 1277
                          -i     ivi   ii  i --      v    -        vv     v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACA--AAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_13690653_1   1278 TTGAAGTGAAAAATGTTT-TGCTTTTTCTAAAAG---CTTTTAAGAAAAT 1323
                          ii  i v     iv   -     i----   i ---  v i      i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTC----AAAGGACACTATCAAGAAAGT 692

  chr2_13690653_1   1324 GAAAGGACAGGCTTCCAACTGGCAGAAAATATTTTATAAA-CATATATTC 1372
                             i    iv iv vi v   v           -ii   -       ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCT 741

  chr2_13690653_1   1373 GGTAAAAGGACTTACATATTGAATGTATAAT--ACTTT---AATTCAATA 1417
                          i   i-      ii  viv    i     v--   i ---  i      
  L1M4_orf2#LINE/    742 GATAAG-GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_13690653_1   1418 ATTAGGACAAAAATGATTCAAC------ATGA-TAAAAGATTTGAGTATA 1460
                           v ii v v    i ii   i------   i-i   i       i  v 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_13690653_1   1461 CACTTCACCAAAGAAGATGTTTGAGTGAC-AATAAG-ATAAGAAATGATG 1508
                           i   v           i vii i  i -      - i v    v    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_13690653_1   1509 CTCAA 1513
                              
  L1M4_orf2#LINE/    891 CTCAA 895

Transitions / transversions = 1.44 (128 / 89)
Gap_init rate = 0.04 (28 / 782), avg. gap size = 2.50 (70 / 28)  


1168 26.81 4.20 4.20  chr2_13714003_13717565     1793  2221 (1342)    L1M4_orf2#LINE/L1        1   429 (479)  

  chr2_13714003_1   1793 TAAAGAGACATACTATGTTTGTGGATTGAAAGACTCAACATTGTAAAGAT 1842
                          ii i   i  v i     ii       i      i  i     v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_13714003_1   1843 ATCTATTTTCCCAAAATTGATCTTCAGGTTCAGTGCAATTTTAATTAAA- 1891
                         iv v  vi    v          v   i    ii     iiiv  i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_13714003_1   1892 TTCTAGGAGGGTTTATTTTATTTTATTTTTTAGAAATAGACAAGCGTTTT 1941
                          i i  -----------i iii  -    vi      v       vvv i
  L1M4_orf2#LINE/    101 TCCCAG-----------CTGCCTT-TTTTGCAGAAATTGACAAGCTGATC 138

  chr2_13714003_1   1942 ATAAAATGTGTATGGAAAAAAAAATATACTCA-AATATCT----CAATCA 1986
                         v      vii        viv  ivi-  i  -    v i----     v
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCT 187

  chr2_13714003_1   1987 TGAACAAGAAGAATAAAG-----GGAATTGTTCTACCTGATTACAATACT 2031
                             v        i    -----   v iiiv  v  ii   v   v   
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_13714003_1   2032 TATTATATACATACAGTAATCTAGACTCTGTAGCATTGGTGGAAAGATAG 2081
                           i  i v vv          v    vv   i i i   iiv  i     
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_13714003_1   2082 AACCATAGGTCAACTGAATAGAA----GAATACCATGCAATGGTCCCATG 2127
                          vvi    i    iv        ----  i -   - v   iiv     i
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGT-CCA-GAAATAAACCCATA 335

  chr2_13714003_1   2128 CA---AGGGTGACTTACTGTTTTTTGACAAACCCACAAAAACAATTCAAT 2174
                           --- v   v --- i  v    i     ivvii v  i  v       
  L1M4_orf2#LINE/    336 CATTTATGGTCA---ATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_13714003_1   2175 GGAGGAGAAATAGTCTTTTCTATAAATAGTGCTGGGACAATTGGCTA 2221
                           i i ii            v i    i            i   v  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

Transitions / transversions = 1.45 (68 / 47)
Gap_init rate = 0.03 (12 / 429), avg. gap size = 3.00 (36 / 12)  

 969 25.48 4.37 8.94  chr2_13714003_13717565     2552  3077 (486)    L1M4_orf2#LINE/L1      407   908 (0)  

  chr2_13714003_1   2552 AACAGT-CTGAGAGGACTAATACATATATCCTTAGGCAAAAAGAATTAAC 2600
                           ii  -   i  vi   ii-----   ?  vi v      -    v  v
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGG-----ATAKCCACATGCAAAA-GAATGAAG 450

  chr2_13714003_1   2601 ATCAACC--TAATCTTCACACATTAAACAAAAATTAATGCAAGATGGATT 2648
                         v vi   --  -- i      vv  v           iv   i      i
  L1M4_orf2#LINE/    451 TTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_13714003_1   2649 ATAGAATTAGATGTAAAATGTAAAACTATAAAATATCTGGAAAGAAACCA 2698
                          ?   vi  i      i vv             i-   vii      v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACA 547

  chr2_13714003_1   2699 TGGGAGAAACTCTTGGGGAACTCATGCTTGATGAGCAA--ATTT---AGA 2743
                          i  ? v  v    v v  v  iiv i v ----    --i   ---   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAG----GCAATGGTTTCTTAGA 593

  chr2_13714003_1   2744 TCTGACACAAATATTATGATCCATGCAATCTTTAAAAGAT-GATAAATTA 2792
                          v      v  v vi ii v v iiv  v----    i  -        i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAG----AAAAAATAGATAAATTG 639

  chr2_13714003_1   2793 TGCTTTGTCAAAATTAGAAACTTCTGCTTTGTGAAAGACCATGTTAAGAG 2842
                         vi   ii         i      i  ivi vii  i   vv i i    i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_13714003_1   2843 GATAAAAAGACAAGTTACAAACTC----AAAGTATTTGAAAAACCACATA 2888
                         ii i         vii   i v v----   i      v   -i  i   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATA 738

  chr2_13714003_1   2889 ACTATTAAAGGACTCATATCTGGAATATATAAAGAACTCTCAAAACTCAA 2938
                         v  iv   i     ii    ii                  i v       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_13714003_1   2939 CAGTAAAAAAAAAAAAACTGTAAAGAAAAACAAA-AACTAAAAACGAGCC 2987
                         i i      i -------------------    -   ----------  
  L1M4_orf2#LINE/    789 TAATAAAAAGA-------------------CAAATAAC----------CC 809

  chr2_13714003_1   2988 AGTTATAAAATCGGTAAAAG-CATGAACATATATTTTACCACAGGTGATA 3036
                          i  ?v     v  i   i -iv    i v i    iv   v  iv    
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_13714003_1   3037 TCCAGA--------AGGTACATGAAAACATATTCATCGTTATTGGACCA 3077
                          v  i -------- i i         v  ii   v i i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (77 / 53)
Gap_init rate = 0.04 (18 / 502), avg. gap size = 3.89 (70 / 18)  


2301 24.61 8.33 1.69  chr2_13722412_13724171      501  1268 (492)    L1M4_orf2#LINE/L1       90   908 (0)  

  chr2_13722412_1    501 CTCAATTTAAATCTTAGCAAGTTACTTTGTGGATATTGAAAAACTAATTC 550
                          i v  iv     ii   vivi vi    ii  v     v  i  i  i 
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_13722412_1    551 TAAAGTTTATTGAGAAAGGCAAAAGATCCAAAATCGTCAACACAGTATTA 600
                             i  i  vvi    v    ii  i   i   v i   v   i v  i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_13722412_1    601 AA------GAACAAAGTTGAAGGATTGCCACTACCTGACTTTAAGTCTTA 644
                           ------           i    i vv    v  ii i  i  iv    
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_13722412_1    645 TTATAAAGCTGTAAGAATAAAGACAGTGTGGTAATGGTGAAAGGATAGAC 694
                         i  i      ii iv   v              v   iiv          
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_13722412_1    695 AAACAGAGGAAGAAAACAGAATGGAAAGTCTGTGAACAAACCTACTGAAC 744
                          v i   vv  vii  i     v  i    iivi  i     i ivv vi
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_13722412_1    745 TATAGTCAACTGATCTT---------TGTCAA---------ATGAGTAAG 776
                            i     i    i  ---------  i   ---------   i v  i
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_13722412_1    777 GACAT-GTCTTTCCAATAAATGGTGCTGAGGCAAACTGGACATTCACATG 825
                           -  -      i   i           i i   -     i ?i      
  L1M4_orf2#LINE/    390 GA-ATAGTCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATG 437

  chr2_13722412_1    826 CAAAATGACGAGTCTAGAC----AC-TGACATTATA----------AGC- 859
                              vi i  ivi i   ----  - v   ii   ---------- i -
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_13722412_1    860 CAAAATGGATCATATACGCAAATGGAAAATCACAAAC-AGAAAATTTGTA 908
                                     ? v  vi     v  i v vv    - v    i iv  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_13722412_1    909 GAAGAAAACA-AGA---AAATCTAAGCTG--CTTGGAGT--GTCATGGTG 950
                                   -  i---      vv -  --     iv -- iv     -
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGT- 585

  chr2_13722412_1    951 AGTTAGTAAATACAACACCAAAAGCAAGATCCATGAAAGAAAAAA--GTT 998
                         --  vv  i   ii            vi v v ii          -- v 
  L1M4_orf2#LINE/    586 --TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_13722412_1    999 AAGTGTGAC--AATTAAAATTAAAAAGCTACTCCTCTGTG-----AAGGG 1041
                           i vv   --v  i           ------ i i    -----    i
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAA------CTTTTGTGCTTCAAAGGA 677

  chr2_13722412_1   1042 CACTGCTGAGAGAATGAAATGACAAATCCCATACTGGGAGAAAATAGTTT 1091
                             iiii   i i     v     vi v  v v            -   
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA-TTT 726

  chr2_13722412_1   1092 ACAAAACATCTTTTTGATAAAGGACTTGTATCCAATATGTACAAGCAACC 1141
                         i    v   v v i      i             iv  i  i  iv   i
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_13722412_1   1142 CTTAAAACTAAACAATAAGAGATCAAACAACCCAATTTAAAAATTGGCAA 1191
                             v    v  i     i iiv    i         ?      v     
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_13722412_1   1192 AGGATCTGAATGGATA-----CCACAGAAGATATACAAATGGCAAATAAG 1236
                              i     i  i -----   v                  v      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_13722412_1   1237 TGTATTAAAAGATGTTCATCATCATGCATCAT 1268
                         iii  v        i   v     ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (113 / 73)
Gap_init rate = 0.03 (23 / 819), avg. gap size = 3.35 (77 / 23)  


2542 24.36 3.56 2.56  chr2_13748739_13753552.rev     3424  4322 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_13748739_1   3424 TGAAAAAAAATTC-ATCCTCATGGACTGTGAAAA-TCAATATCATTAAAA 3471
                           i   i v  i -  vi       i  -   i - i     ii    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTG-GAAGACTTAATATTGTTAAGA 49

  chr2_13748739_1   3472 TGTTCATACTGCCCAAAGCAATCTACATTTTCAATATTATTTCTACCAAA 3521
                           viv     v      vii       vv     iiiv  ii   i    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_13748739_1   3522 CTACCAG-TATCATTGTTGACAGAATTAGAAAAAAAGTATTCTAAAATTA 3570
                         v v    - ii v  v   -     v v  v  ivv -  i        v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTG-ATCCTAAAATTC 147

  chr2_13748739_1   3571 ATCTGAA---GCCAAAAAAGGGCCCA-AATAGCCAAAGCAATCCTAAGTA 3616
                           v  i ---  ----  i  i    -          i     i i iv 
  L1M4_orf2#LINE/    148 ATATGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_13748739_1   3617 AAAAGAACAAAGTCCAAGTCATCA-AGTT----ATTTTACTTGAAACTAT 3661
                          i           ivi  vvv   - v  ----    i ----     - 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA----AAACT-T 238

  chr2_13748739_1   3662 ACTACAACGCTGTAATAACCAA-ATAGCTTGGTACTAGTACAAAAACAGA 3710
                                v   ii i   i   - i  iv       i i i  ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_13748739_1   3711 CACAAAGATCAATGTAACAGGATACAGAACCCAGAAATAAAGCCACACAC 3760
                           i v         v  i  i  vv   ii           v   i   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_13748739_1   3761 CTACCACCAACTGATCTTCAAAAAGGTTGACAACAAAAT-CAACGTAGAA 3809
                         i  ivii   i    i   i v    v  v   v vv  -   i vi   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_13748739_1   3810 AGGATTTCCTATTTAATAAATGGTGCTGGAATAACTGGCTAACCATATGC 3859
                           i  vvi  v  i  i            i i      v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_13748739_1   3860 AGAAGAATGAAAGCAGACCCCTACC-CATCATCATAAACAAAA-TTAAAT 3907
                          i         ivii          -  -  i    v      -    v 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACT 487

  chr2_13748739_1   3908 CAAGATGGATTAAAGAATTAAATGTAAGACCTCAAACTATAAAAATCCTA 3957
                            i      i ?   vi           v  v           v  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_13748739_1   3958 GAATAAAACCTAGG---AAATACTCCTATGGACATCTGCCTTGACAAATA 4004
                            v     v    ---    vi  v ---   v iv vi v i   - i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGT---GACCTTGGGTTAGGCAA-TG 583

  chr2_13748739_1   4005 ATTTAT--GACTAAGTTCTCAAAAGCAATTGCAAAAAAAAAAAAAAAAAA 4052
                         i   v --  -  v vivi        ----   iv  v    i      
  L1M4_orf2#LINE/    584 GTTTCTTAGA-TATGACACCAAAAGCA----CAAGCAACAAAAGAAAAAA 628

  chr2_13748739_1   4053 AAGA-AAGTGGAACCTAATTAAACTAAAGAGATTCTGCACAGCAAAAGAA 4101
                         v   -  i v i  i v  i   v v  i iv  i  ii vv    i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_13748739_1   4102 ACTATCAACAGAGTAAATAGAAAAAAACACAGAATGGAAGAAA-TACTCA 4150
                                 v i   i  v   v  vv-          i     -  i ii
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACC-CACAGAATGGGAGAAAATATTTG 727

  chr2_13748739_1   4151 CAAACTATGTATCTGATAAAGGTCTAATATCCAGAATCTATAAGGAACT- 4199
                             ii  i          i  v  vi          v     i     -
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_13748739_1   4200 TAACAAGCCAA--------AAACAAATAACCCTGTTAAACAGTGGGCAAA 4241
                          v    vi   -------- i           vi  ?  v i        
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_13748739_1   4242 GGGCCTAAATAGACACTTCTCAAAAGAAGACATACAAGTGGCCAACAGAC 4291
                           iii i        i     v        i      i       i ii 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_13748739_1   4292 ATATGAACAAATGCTCATCATCACTAATCAT 4322
                          i     v i       v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (126 / 90)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 1.90 (55 / 29)  


3255 26.35 0.77 0.66  chr2_13824236_13830507.rev     4874  5780 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_13824236_1   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCATGAAAAT 4923
                              ii i  i     i      i v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_13824236_1   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4973
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_13824236_1   4974 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5021
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_13824236_1   5022 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5071
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_13824236_1   5072 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5121
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_13824236_1   5122 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5171
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_13824236_1   5172 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5219
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_13824236_1   5220 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5269
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_13824236_1   5270 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5319
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_13824236_1   5320 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5369
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_13824236_1   5370 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5419
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_13824236_1   5420 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5469
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_13824236_1   5470 AACACCAAAAGCAATGGCAACAGAAGCCGAAATTGACAAGTGGGATCTAA 5519
                         i            vvi      i   vvi    v  i  i v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_13824236_1   5520 TTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACTACCATCAGAGTGAAC 5569
                          i   v v  i i   i vii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_13824236_1   5570 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5619
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_13824236_1   5620 AGGACTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5669
                         i     vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_13824236_1   5670 AAA-AAACAACCCCATCAAAAAGTGGGCCAAGGACATGAACAGACACTTC 5718
                          i -   i     v  i?    i     v     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_13824236_1   5719 TCAAAAGAAGACATT--AATGCAGCCAAAAGACACATGAAAAAATGCTCA 5766
                           v        i  v--    --     v ii          i       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_13824236_1   5767 TCATCACTGGCCAT 5780
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


1199 27.97 5.93 2.12  chr2_13873248_13875437      582  1053 (1137)    L1M4_orf2#LINE/L1       16   505 (403)  

  chr2_13873248_1    582 TGTTCATGGATATGAAGACTCAATATTGTCAAGA-AATAGTTTTCCCCAA 630
                                    vv       i        i    -iii i vi       
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_13873248_1    631 ATGAATCTAGTGATTCAATTTA-TTCCAATAAAACTTTCA-TTGAGTAAT 678
                           vi     vv       ivi - i  v  v   v ii  -i  vv v- 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT-T 114

  chr2_13873248_1    679 TTTATGAATATCAAAAAAA-GATCCTAAAATTTATATAAAGAGGCAAAAT 727
                            iiii v  ii v  iv-            i    ii i v    iiv
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr2_13873248_1    728 ATCCAGCATAACCAACACAACATTGTTGTGTGTTGAGAACAACAGAGCTG 777
                          i    v   i    v    iv   vvi------i    v    i  i  
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAA------AAGAAGAACAAAGTTG 208

  chr2_13873248_1    778 GAGGCCAGACAACACCAGACTTCAAGAGCTGACTATAAAGCTTCAGGAAT 827
                             v vv   viv  vi i     i -  v    i      v   v   
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAA-CTTACTACAAAGCTACAGTAAT 257

  chr2_13873248_1    828 GAAGAGAGTGTGGTATTGGTGAATTAACAGACAAATAGATTAATGGAACA 877
                         v    v         i   iiv vvi i     v      i       i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_13873248_1    878 GAATAGAGA-TCCCAAGACAGATCTACATAAATACAATTAAATTATGTTT 926
                             v    -   vi i i i i i i i vv  iii i  v v  v  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_13873248_1    927 GGCAAAGGAGCAAAAATAATATAATGGAGAAAAAATTGTCTTTTCAACAA 976
                          i   i  v  v  i iv  vi     i    i   v             
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_13873248_1    977 ATAATACTGGAAAACCTGCGA-ATCCACATAAAAAATGAATAAGGT---- 1021
                           ii i    i v v   -  - ?      iv    -    i i  ----
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTG-GATAKCCACATGCAAAA-GAATGAAGTTGGA 455

  chr2_13873248_1   1022 ---------CACAC---------AAATTAACTCAAAATAGAACATAGGCC 1053
                         ---------     ---------               i  v  ?  i  
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

Transitions / transversions = 1.36 (75 / 55)
Gap_init rate = 0.03 (13 / 490), avg. gap size = 2.92 (38 / 13)  

 669 25.16 21.43 0.62  chr2_13873248_13875437     1377  1698 (492)    L1M4_orf2#LINE/L1      520   908 (0)  

  chr2_13873248_1   1377 AAAATGATAAGACTCCTAGAAGATAACATAAGAAAATATCTACCTAATTT 1426
                             iv    i    i       v      i ?iv v    v v i ii 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_13873248_1   1427 TTGATATGGCAATCAATTTTTAGATATAATA-----------AGCAA--- 1462
                          v i vv      viv  i        i i -----------     ---
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_13873248_1   1463 --------------------AACTACATTAAAA--AAAAGCTTCTCCCCT 1490
                         --------------------i   v   i    --    i   i viv  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_13873248_1   1491 TTGAGAGGCACTGTCAAGAGAAT---AAG-----CCACAGACTAGGAGAA 1532
                          ii ii i    i      i i ---   -----       v i      
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_13873248_1   1533 CAAT-TTTGCAAAAGACACATCTGATACAGGACTGCCATCCAAAACATAC 1581
                         -   -        vv i i        vi     vvi     i  i   i
  L1M4_orf2#LINE/    720 -AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_13873248_1   1582 AAAGAAATATTAAAATTTGTTAACTAGAAAGCCAA-CAATCCAAT----- 1625
                               v v   v  i iiv   -  i    v   -i  i     -----
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAA 817

  chr2_13873248_1   1626 ---GAGCAAA--------------ACTTCATCAAAGAAGGTAGACAGAGG 1658
                         --- i     -------------- i   vi        i  v   i v 
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_13873248_1   1659 GTGAATAAACATAC-AAAAGATGTTTAACATCATATGCTGC 1698
                          iv     i  i i-        i i       ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (51 / 29)
Gap_init rate = 0.03 (12 / 389), avg. gap size = 5.92 (71 / 12)  


2752 28.03 2.35 0.56  chr2_13920664_13923600     1595  2486 (451)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_13920664_1   1595 TGGAAAAATATTCCATGCTCATGGATAGGAAGCATCAATATTGTGGAAAT 1644
                               i    i     i        v     vv i        vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_13920664_1   1645 GGCCATACTACCCAAAGTAATTTATAGATTCATTGCTTTTTCCATTAAAC 1694
                            v     v      v i  i  i       vi  vv ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_13920664_1   1695 TACCA-TTGACATTTTTGCAGAACTAGAAGAAATTATTTTAAAATTCATA 1743
                          v   -i  v v           v v  vi iv v  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_13920664_1   1744 TGGAACCCAAAAAGAGCCAGAATAGCCAAGAAAATGCTAAGCAA-AAGTA 1792
                              vivv  ii  v             i v   vi i iv  -   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_13920664_1   1793 CAAAGCTGGAGGTATCATGCTACCTGACTTCAAACTATGCTACAAGGATA 1842
                              i      vv   ii  v  ii i      viv i      i v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_13920664_1   1843 CAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCAA 1892
                               i   i    ii         i i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_13920664_1   1893 TGGAACAGAAT-AAGAACTCAGAAATAAGACTGCACACCTACAA-CAATC 1940
                              i     -i   iii         iv iii   ii  iii-    -
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT- 349

  chr2_13920664_1   1941 TGATTTTCAACAAAACTGACAAAAACAAGCAGTGGGAAAAGGATTCCCTA 1990
                                 i    iiv  v   i v  vv  i    i    i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_13920664_1   1991 TTTAATAAACAGTGTTGGGATAACTGGCTAGTCATATGCAGAACAATGAA 2040
                           i  i   ii   i     i      v  ?i  i     i  v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_13920664_1   2041 ACTAGAACTCTTCCTTACACCTTATACAGAAATTAACTCAAGATAGATTA 2090
                         ii i  v i  v   i     v      i            i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_13920664_1   2091 AAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTATAAGAAAATCTA 2140
                         ?    i         i v i            vi i  v       iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_13920664_1   2141 GGCAATATTATTCAGGACATAGACATGGGCAAAGATTTCATAACAAAAAC 2190
                           ?ivv v v   iv   v v ivv i     v i    v  ivv vi  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_13920664_1   2191 ATCAAAAGTAATTGTGACAAAAGAAAAAATTGACAAATGGGATCTAATTA 2240
                          i      i vvv ii              v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_13920664_1   2241 AACAAAAGAGCTTCTGCACAGCAAAATAAGCTATCCTCAGAGTGAACGGA 2290
                           vvv  i i   i  ii vv    iv vi     vvv i      vi  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_13920664_1   2291 CAACCTACAGAATGAGGGAAAATTTTAGCAATCTATTCATCTGACAAAGA 2340
                              i        i i      v  v    vii  vi      i  i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_13920664_1   2341 TCTAATATTCAGAGTATACTTAAACAAAT-TTACAGG--------AAAAA 2381
                         v  vi   i    i    --    v  v -     iv--------     
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATA--TAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_13920664_1   2382 AACACACAACCCCATTAAAAAGTCAGCAAAGGACATGAACAGATACTTCT 2431
                         i   v i     v   ?    i vi        iv    i   i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_13920664_1   2432 C---AAAAGCTAAACATCACTAATCATTAGGGAAATGCAAA-----TCAA 2473
                          --- i   v  v   -- v iii  v  i v v   v   -----    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACA--AATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_13920664_1   2474 AACCACTAATGAG 2486
                         v i  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (143 / 103)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.36 (26 / 11)  


2114 22.32 14.84 1.62  chr2_14003621_14005784      871  1672 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14003621_1    871 TAGAAAGGCATCCCATTTTCATTATTCAGAA-ACA-AATATTATTAAGAT 918
                          i     ii       v     viv ii   -  v-      i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14003621_1    919 AACAATACTGCCAAAGTTAAT--ACAAATTCATCACAATCTCTGATAAAA 966
                         ii       v  v  i  i  --   i     v i     i  ivi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_14003621_1    967 TCCCAGGTGAAATTTTTGCAGAAATTTGATA-GCTGTCTCTAAAATTCAT 1015
                               v  vvv              -  i -    vii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chr2_14003621_1   1016 GTCAAAACTTAAGGAGCACAGAATGGCCAAAGTAATTTTGACAAAGGA-- 1063
                         i vi   ivi    ii v      i      ii   i    v    i --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_14003621_1   1064 -TAGAGTTGGAGAAGTCATATCTCCAAGTTTCAAAACTTACTACAAAGCT 1112
                         -i i        i v   i ii   v i                      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_14003621_1   1113 GTGGCAATTAAGATAGTGACATATTGGCATATGGATAAAAATACAGAATA 1162
                         iii i   i    i    vvi  i       v     i v   i   vi 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_14003621_1   1163 AAGAAATAGAATTAAGTAGTC-AGATAAAAATCTTTACATTTTTGATAAA 1211
                          v i         i  -    -   v v   i iv       v  i v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_14003621_1   1212 TTAATTTATAACAAGGGTTCCAAGACCATTCAATGGGGGAAGAAAAATCA 1261
                           i    vii        v                   i     v i  v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_14003621_1   1262 TCTCAACAACTGTTGCAGGTATATCTGGATATCCACATATAAAAAAATAA 1311
                          i       v  v   v  v i v       ?      ii    i   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_14003621_1   1312 ATTAATTAAGTTGGACCCCTCACTTCATTCCTCAGACAAAAATTAACT-- 1359
                          --------           -  i   iv  vi v             --
  L1M4_orf2#LINE/    449 A--------GTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCA 489

  chr2_14003621_1   1360 ----------------TTAATTTAGAAGC--AAATTA----ATTTT---- 1383
                         ---------------- v   v  ii   --   i  ---- i i ----
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_14003621_1   1384 ---AAAT-------TAAATTT-------------------AAAAGTTT-- 1402
                         ---   i-------     i -------------------  vi    --
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_14003621_1   1403 TAAATTTAAT-TTAAAAAT--------TAAATTTAAAAGTTT-TAAATTT 1442
                           i  v i i-ii    ii--------i   vvv    i vv-      v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_14003621_1   1443 AATTT-A--AAAATTAAA-----------TTTAAAAG----TTTTAA--- 1471
                         i i  - --         -----------  i   i ---- v i  ---
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_14003621_1   1472 ATT-------TAATTTA-AAAATT-----AAAT--TTAAAAATCATATAT 1506
                          v -------i  iii - i   v-----    --  iv           
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_14003621_1   1507 TTGATAGTAAAATTTAGTATCCAGAATATATAAAAAACTCTTCCA-TTAA 1555
                         i     i-iii i  -                  i       v  -i v 
  L1M4_orf2#LINE/    740 CTGATAA-GGGACTT-GTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_14003621_1   1556 ACAATAAGAA---AAA-AACTCAATCAAAAAATGAGCAAATACTTTGAAG 1601
                          i     i  ---   -   i    i?       i     viv      v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_14003621_1   1602 AGATAATTCACCAAAAAAGATACACAAATGGCCAATATGCACATGAAAAG 1651
                            i v   v     i      i              v            
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_14003621_1   1652 ATGCTCAACATTATTAGCTAT 1672
                                    i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (113 / 64)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 3.88 (132 / 34)  


2496 26.73 0.43 0.58  chr2_14042466_14044157      501  1192 (500)    L1M4_orf2#LINE/L1      201   891 (17)  

  chr2_14042466_1    501 CAAAGCTGGAGGCATCACGCTACCTGACTTCCAACTATACTGCAAGGCTA 550
                              i      vv    i  v  ii i   v  viv    i   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_14042466_1    551 CAGTAACCAAAACAGCATGGTACTGGTACCAAACCAGAGGTATAGACCAG 600
                               i   i    ii         i iv iivi   vi      i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_14042466_1    601 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT 648
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_14042466_1    649 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 698
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_14042466_1    699 ATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 748
                         v  i  i   i          v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_14042466_1    749 AGCTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGATT 798
                           i    i    v   i   i v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_14042466_1    799 AAAGACTTACATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAACCT 848
                          ?    i  v    v   v       i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_14042466_1    849 AGGCA-ATACCATTCAGGACATAGGCCTGGGCAAGGACTTCATGTCTAAA 897
                            ?i- v i -   iv   v v  vi i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_14042466_1    898 ACACCAAAAGCAATGGCAACAAAAGCCAACATTGACAAATGGGATCTAAT 947
                                     vvi          vv  v  v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_14042466_1    948 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 997
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_14042466_1    998 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 1047
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_14042466_1   1048 GGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAAA 1097
                           i  vi          v  i  v      iv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_14042466_1   1098 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 1147
                         i -    i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_14042466_1   1148 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGC 1192
                           v        i  vi viii     v  i          i    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

Transitions / transversions = 1.45 (107 / 74)
Gap_init rate = 0.01 (5 / 691), avg. gap size = 1.40 (7 / 5)  


2199 26.85 12.93 1.11  chr2_14052970_14056020.rev     1748  2559 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14052970_1   1748 TGATAAGATATTCTATGTTCATGAATTAGAAGAATTAATACAGTTATTAT 1797
                           iv       i i         i   i     v      iv    vv  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14052970_1   1798 GATAACACAATTCAAAGCAACTTACAGATTCCATGAAATTTCTATCAAAA 1847
                          ii  i  vvii    vii ii         v i v   ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_14052970_1   1848 TACCAATGACTTTCTTCACAGAAATAGGAAAAACAATTTTTAAATTTATA 1897
                          v   iivi i  i  ii       v iv  ivii  ii v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_14052970_1   1898 TGGAAA-----AGAACCCATAATAGCCAAA-------------------- 1922
                               -----i i     v          --------------------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_14052970_1   1923 --------------TCA--------------------------------- 1925
                         --------------   ---------------------------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_14052970_1   1926 --------------GCATGGTACTGGACTAAGCACAGATACATAGGCCGC 1961
                         -------------- ii         vv    v i   i i    ii iv
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_14052970_1   1962 AGGAAAATAATAAAAAGTTCAGAAACAAATCCACAAACTTACAGCCAACT 2011
                         v    v v   vi i   i      i   i   i v i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_14052970_1   2012 GATATTTGACAAAGGCATCACAAACATACAATAGAATGGAAATA-TCTCT 2060
                            v  i     i  iii  vi v   v    i iiviii    -   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_14052970_1   2061 TTAATAAATGGTACTGCGA-AACTGGATAACTATATGCAGAAGACTGAAA 2109
                          i  i       i   v  -         ? i i     i    v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_14052970_1   2110 CTAGACTCTTATATCTCACTATATGCAAAAATCAAACCACAATGGATTAA 2159
                         i i   i i  iv  v   i    i       i  vi  v       i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_14052970_1   2160 ATAACTTAATGTTACACCCCTATTTATGAAACTTCTAGAAGAAAACATAG 2209
                          v v  v     v v v ivv vi   i     ii               
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_14052970_1   2210 GGGAAACACTTCAGGCCACTGGTCTAGGCAAAGATTTTATGGATA-AACT 2258
                          ? v  vv    iv v vi   vi       v i   iv i    -i  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_14052970_1   2259 GCAAAAGCACAGTCAACAAAAATAAATATAGGCAAATGAAATTATATC-- 2306
                         v          iv        iv   v    ii    vii i vi   --
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_14052970_1   2307 --CCAAAAAATTTTGCACAGCAAAGGAAACAATCATCAGA---TGAAGAA 2351
                         --ii     v     ii vv       v  v    --   ---    i i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--AGAAAGTGAAAAG 698

  chr2_14052970_1   2352 ACATCCTACAAAATGGGAGAAAATATTTGCAAACTATTCATCTGACAAGG 2401
                            v  i   i                      ii  vi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_14052970_1   2402 GATTAATAACCAAAATATGTAAGGAACTCAGACAACTCAATAGCAAAACC 2451
                           i vi  v   i     i   i      vv           ii    --
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA-- 796

  chr2_14052970_1   2452 CAAATAATTTGATAACTTAATGAAAAAATG--------ATCTGAATAAAT 2493
                         - i i  ----     ii   v?       --------  i      i i
  L1M4_orf2#LINE/    797 -AGACAA----ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_14052970_1   2494 ATTTTGCAAAAGAAGACATATAAATAGCTGATAGGTATATGAAAA-ATGC 2542
                             iv v        i   i    i  ii   i i i       -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_14052970_1   2543 TCAACATCACTAATCAT 2559
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (138 / 76)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 8.77 (114 / 13)  


2975 25.81 1.00 1.11  chr2_14084905_14087415     1121  2019 (492)    L1M4_orf2#LINE/L1       11   908 (0)  

  chr2_14084905_1   1121 TCCCATGCTCACAGATGGGTAGAATTGATATTGTAAAATTGACCATACTG 1170
                                i   ii   v  v   v  i       v  iv  i v     v
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chr2_14084905_1   1171 CCAAAAGAAATATATATATTTGATGCAATTCCCATCAAAATACCACCATC 1220
                           v   vvi  v  i v   ii i     i  i        v   v vv 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr2_14084905_1   1221 ATTCTTTACAGAACTAGAAAAAA-AATCCTAAAATTCATATGGAACCAAA 1269
                         v  i   i     v v  v  iv-i                    viiv 
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_14084905_1   1270 AAAGAGCCCACATAGCCAAAGCAAGGCTAAACAAAAAGAACAATTCTGGA 1319
                          ii  v  viv         i   vvi i  v  i        vvi    
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_14084905_1   1320 GGCATTACATTACCTGACTTCAAACCTATACTATAAGGCCATAACAACAA 1369
                           vv i   i v  ii i      v  -     i  i  i i ii  iv 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCA 259

  chr2_14084905_1   1370 AAACAGCATGGTACTGGTATAAAAATAGGCACACAGACCAATGGAACAGA 1419
                          i    ii         i    ii    i  i i   i        i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_14084905_1   1420 ATCAAGAACCCAGAAATAAAACCAAATACTTACAGCCAACTGATTTTTGA 1469
                           ii   ii           v   v i i   ii i   i       i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_14084905_1   1470 CAAAGCAAACAAAAAC-TTCAAGTGGGGAAAGAACACCCTATTCAACAAA 1518
                            i vviv   i v -     -           i vi  v         
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_14084905_1   1519 TGGTACTGGAATGACTGGCAAGCCAC-TGTAGAAAAATAAAACTGGATCT 1567
                             i    i ii     vv ?    -  i i  i   i  ii    i i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_14084905_1   1568 TCATCTCTCACCTTATACCAAAATCAACTTATGATGGATCAAAAACTTAA 1617
                         ii i   v    v     v     i    i vi        ? i  i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_14084905_1   1618 ATCTAAAATCTGAAACCGTAAAGATTCTGGAGGATGCCATTAGAA-AAAC 1666
                           v   i v  i    ii    iv ii i  i  viv   vi ?i-   i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_14084905_1   1667 CCTCCTACACATTGGGTTAGGCAAAGACTTC-AAGACCAAGAACCCAAAA 1715
                          i  v i-  v             v ii   -v   -i v  vv      
  L1M4_orf2#LINE/    559 CTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAA 606

  chr2_14084905_1   1716 GCAAAAGCAACAACA-AAAAAATAAATAGATGGGACTTAATTAAA-CTAA 1763
                            v         v -        i   i  v      v  i   -i   
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_14084905_1   1764 AACCTTCTGCACAGCAAAAGAAATAACCAGCAGAGTTAACAGATAACCCA 1813
                           v   i  ii vv    i  v iv i  iv i   v  v   i      
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_14084905_1   1814 CAGAGTGGGAAAAAA-ATCTTCACAATCTATACATCTGACAAAGGACTAA 1862
                             i     i    -  i v  -    -   i      i  i     vi
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGATAAGGGACTTG 754

  chr2_14084905_1   1863 TATCCAAAATCTACAAAGAACTCAAACAAATCAGTGATAGAAAAACAAAC 1912
                               i   v  i         vv    v   i i   i   i     -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA- 803

  chr2_14084905_1   1913 TAACCCA-TCAAAAAGTGAGCTAAAGACATGAATAGGCAATTCTTAAAAG 1961
                                - i?    i  i  v  i  iv       i  v    iv    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_14084905_1   1962 GAGATATATAAATGGCCAACAAGCATATGGAAAAAAAACGCTCAACATCA 2011
                         i       i          i     i   ---    i i           
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATG---AAAAGATGCTCAACATCA 900

  chr2_14084905_1   2012 CTAATTAT 2019
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.68 (143 / 85)
Gap_init rate = 0.02 (17 / 898), avg. gap size = 1.12 (19 / 17)  


2591 28.33 4.47 0.34  chr2_14089538_14093601     2703  3574 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14089538_1   2703 TGGAAAGATACTCTATGTTT-------------CTT--TATTGTTAATAT 2737
                                   ii i     i-------------   --         v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14089538_1   2738 GTAAACATTAATGAAAGCAATCTACAGATGCAATAAAACCCTTA-CAATA 2786
                          vv  i i vviv   vii          v   iiv  i  i  -   v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_14089538_1   2787 TTTCAATGGTATTTTACACAGAACTAGGAAAAAAAAATTCTAAAATTGCT 2836
                          ii  iiv iv    vii     v -v  v  ivvi  i        vv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_14089538_1   2837 ATGGAACCAGAAAAGATCTTGCACAGCTAAAGCAATCTTGAGCAAGAAGA 2886
                               viiv  ii  i iv v i   i   i         iv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_14089538_1   2887 ACAAAGTTGGGAAAATAAAATGTATTGATTTTAAATTATATTACAAAGCT 2936
                                   iii v v v iv viii    i   viv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_14089538_1   2937 ACAATAATTAAAAGAGTACAGTACTGTCATAAAAACAGAGATATAATCCA 2986
                            i    i  i v   iii      v     ii i   v     ivi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_14089538_1   2987 ATGGAACAGAACGGAAAACTCATAGATAAACCCAAGCATATATGGCCAAT 3036
                               i    iv  i iii  v i         vi   v     i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_14089538_1   3037 AAATTGTCAACAGGGGCACTCAGAAAACACAATGGGGAAA-AACAGTTTC 3085
                         vi   v  i   i   ii iv   vv iv           -  i   i i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_14089538_1   3086 TTTAATAAATGGTGTTAGAA-ATCTAGATATTCACATA-AAAAGAA---A 3130
                           i  i        i i i - v  i    ?i     i-       --- 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_14089538_1   3131 ATTGCATTCTTATCTCACACTATACAAGAAAATGAACTCAAGATGGGTTA 3180
                         i   v ii i  i       i   i vi     v       i    i i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_14089538_1   3181 ATGACTTAAATGTAATTTCTGAATTCATAATACTTCTTGAAGTAAACTTA 3230
                         ?v   i         vvv  i  vii    v   ii v    v    v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_14089538_1   3231 GG-GTAAGAGCTCTATGACAATGGTCCTGGCAATTGTTTTTTGAATATAA 3279
                           -    - v  iii    vv   viiv      v    i  ii    i 
  L1M4_orf2#LINE/    550 GGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_14089538_1   3280 CAC---------AAGCAATAAAAGCAAAAATAAACAAGTGGGACTATATT 3320
                            ---------      i     v       i i  i v     vi  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_14089538_1   3321 AAACTGCAAAGCTTTGCAGCAGCAAGGGAAAC----AACAGAGTACAAGC 3366
                            v vv   i    vvv  vv   i   v  ----  v i   iv  iv
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_14089538_1   3367 ACAACCTATGAAATGGGGGAAAATATTTGCAAACCATATACTCCATTATG 3416
                               i iii      i               i      iiiv  v v 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_14089538_1   3417 GTTTTAATAGCCACAATATTTAAATGACTCATA-AACTCAATAGCAATAA 3465
                          vi  i-  v   v     v    vi    v  -         ii  v  
  L1M4_orf2#LINE/    749 GACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_14089538_1   3466 AACAAAAAACCCAATTAAAAAGTGGGCAA-GGATGTAAATTGATTTTTTT 3514
                         i     v         ?    i       -    v i   v  iv   i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_14089538_1   3515 CTAA-GAAGACATAAAAATAGCCAACAGGTATATGCAAAGGTGCTCAATA 3563
                          i  -     i   v    i     i i i i   v    i       i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_14089538_1   3564 TTGCTAATCAT 3574
                          ii????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.62 (42 / 16)  


3207 27.97 0.11 0.11  chr2_14189357_14195767     5012  5919 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14189357_1   5012 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5061
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14189357_1   5062 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5111
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_14189357_1   5112 TACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 5161
                          v   iivi i  i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_14189357_1   5162 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5211
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_14189357_1   5212 CAAAGCCAGAAGCATCACGCTATCTGACTTCAAACTATACTACAAGGCTA 5261
                              iii  i vv    i  vi ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_14189357_1   5262 CAGTAACCAAAACAGCATGTTACTGGTACCAAAAGAGAGAAATAGATCAA 5311
                               i   i    ii  v      i iv ii v   v v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_14189357_1   5312 TAGAACAGAACAGAGACCTCAGAAATAATGCCACATATCTACAACTATCT 5361
                          i   i    iv    vii         vv   i i  i  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_14189357_1   5362 GATCTTTGACAAACCTGAGAAAAACAAGCAATGGGAAAAGGATTCCCTAT 5411
                            i  i     ivv  vv  i v  vv       i    i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_14189357_1   5412 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAG 5461
                          i  i              v      v  ?   i   i i  iiv     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_14189357_1   5462 CTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGATTAA 5511
                         i    i    v   i    iv              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_14189357_1   5512 ACACTTAAATGTTAGACCTAAAACCATAAAAACCGTAGAAGAAAACCTAG 5561
                          v  i       v   v       i      vi v           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_14189357_1   5562 GCG-ATATCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAAAAC 5610
                          ? - v   -   iv   v v  vvii     v ii   v ivv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_14189357_1   5611 ACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTA 5660
                                   vvi          vv     v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_14189357_1   5661 AAATAAAGAGCTTCTGCACAGCAAAAGAAAGTACCATCAGAGTGAACAGG 5710
                             v  i i   i  ii vv    i  v v  i  vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_14189357_1   5711 CAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAGG 5760
                              i   i             v  ii   vii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_14189357_1   5761 GCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAA 5810
                         i  vi          v  i  v      vv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_14189357_1   5811 CAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGATACTTCTCA 5860
                             i     v  i?    i     i      v    i   i i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_14189357_1   5861 AAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATC 5910
                                 i  vi viii     v  i          i       v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_14189357_1   5911 ACTGGCCAT 5919
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.40 (146 / 104)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 1.00 (2 / 2)  


2675 25.63 3.30 3.41  chr2_14319791_14321995.rev      805  1713 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14319791_1    805 TGGAAAAACATTCCATGCTCTTCGATAGAAAGAATCAGTATTTTTTAAAT 854
                               i i  i     i  v v   v i    v i i    v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14319791_1    855 GGCCATACTGCCCAAAGCAATTTCACAGATTCAATGCTATTTCTATCAAA 904
                            v     v      vii  i -          i  v  ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCT-ACAGATTCAACGCAATCCCTATCAAA 99

  chr2_14319791_1    905 CTACCAATTACATTTTTCACAGAATTAGAATAAACT-ATTTCAAATGTCA 953
                         v v   ii i v     ii     v v  -i  i  -  iii   vv   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chr2_14319791_1    954 TATAGAACCAAAAAAAAGCTTGAATAGCTAAAGCAATCCTAAGGAAAAAA 1003
                            i   viiv  iii v iv       i   i     i ---      i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT---GAAAAAG 195

  chr2_14319791_1   1004 AAATGAAACAAAGATGAAGGCCTCATGATACCTAACTTTAAAATACATTA 1053
                           i---       v  i   v    iiv v  i  i  i    ivi i  
  L1M4_orf2#LINE/    196 AAG---AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_14319791_1   1054 CAGGGCTACAGTAACCAAAACAGCATAGTACTGGTACAAAAACAGACACA 1103
                           ii          i   i    ii i       i i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_14319791_1   1104 TAGACTAATACAACAGGTTAGAGATCCCAGAAAGAAAGCCATAAACCTAC 1153
                             ii   iv  i  iv v    vi       v   v     v ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_14319791_1   1154 AACCATCTGATCTTTGACAAAACTGACAAAAACAAGCAACAGGTAAAAGA 1203
                         iii  vi    i  i     iiv  v   i v  vv   ii  v   ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_14319791_1   1204 C--TCCATATTCAACAAATGATGCTGGGATAACTGGCTAATCATATGCAG 1251
                         i--  -- v           i        i      v  ?i  i     i
  L1M4_orf2#LINE/    393 TAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_14319791_1   1252 AAGATTGAAATTAGATTCTTTCCTTTCACCATTTATAAAAATCAACTCAA 1301
                             v    i  i  ii i v   iv      v  i      i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_14319791_1   1302 GATAGATTAAAGACCTAAATGGAAAACCTCAAACTGTAAAAACTCT-AAA 1350
                         i  i   i ?           v  i v  v     i     -    - i 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGA 539

  chr2_14319791_1   1351 AGGAAACCTAGG---AAAT----ATCACCTTGGACAGAGGCCCTGACAAA 1393
                           i    v    ---    ----i v       ii-v    ------  v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGC------AAT 582

  chr2_14319791_1   1394 GATTT------TATGACAAAGCTTTCAAAAGCCTTTGCAACAAAAACAAA 1437
                          i   ------       ------i       vivv         iv   
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_14319791_1   1438 AATTGACAAATGGGACCTAATTAAACTAAAGAGCTTCTGCACAACAA--- 1484
                            v  i    v    i v  i   v v  i i   i  ii vv   ---
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_14319791_1   1485 -------CAAAAATTGAGTAAACAGATAATCTACAGAATGGGAGAAAATA 1527
                         -------   i  ---   i  v   i  i i                  
  L1M4_orf2#LINE/    677 ACACTATCAAGAA---AGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_14319791_1   1528 TTTGCAAATTTTGCATCCCACAAAGGTCTAATATGAAGAATATATAAAGA 1577
                                  iv ii   iv i  i  v  vi   vv              
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_14319791_1   1578 ACTTCAACAAATTAACAA-ACAAGGAGTGAACAACCCTATCCAAAAATGT 1626
                            iiv    v i  i  - v  i  -ii  i     v  i?       v
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGG 822

  chr2_14319791_1   1627 GCAAAGAAGACGAACAGACACTTCTCAAAGGAAGACATATG--TGGCCAA 1674
                               i vvi   i     i     v  i     i   ii--       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_14319791_1   1675 AAAACATATGAGAAAAAAATGCTTATCATCACAAATATT 1713
                         v  i  i    ---   i     i v     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGA---AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (149 / 81)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.90 (61 / 21)  


 495 25.57 4.55 1.70  chr2_14339530_14341838.rev      759   934 (1375)    L1M4_orf2#LINE/L1        3   183 (725)  

  chr2_14339530_1    759 GAGAAATATC--ATGTACCAAGCTTAGAAAACTCAATATTTCTAAAATGG 806
                           i i     --    v vvi v  i   i   i      vi   i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_14339530_1    807 CA-CACTTCCTCAGTTTGACCTATCAATTCA-TACAAACTCAG--AAAAT 852
                           -i   i  -  iv    i   ivi     -ii   v i vi--     
  L1M4_orf2#LINE/     53 CAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_14339530_1    853 ACTTCAGCAGTCTATTTTG-AGACATTGACAAGCT-ATTATAAAATAAAT 900
                         v --    v i  v     -   v           -  iv      vv  
  L1M4_orf2#LINE/    102 CC--CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_14339530_1    901 GTAGAAATGCAAAGGACTTGTAATAGTCAAATCA 934
                         i i         i    iiiv     i    v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

Transitions / transversions = 1.50 (27 / 18)
Gap_init rate = 0.04 (8 / 181), avg. gap size = 1.38 (11 / 8)  

1413 26.06 6.58 5.62  chr2_14339530_14341838.rev     1103  1831 (478)    L1M4_orf2#LINE/L1      173   908 (0)  

  chr2_14339530_1   1103 TAGTCAAAGTGATTTTAAATAAGAAAAACAAAATAAGAG---TCACACTA 1149
                            i    iii  i  i  v     i      i vi   ---       v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr2_14339530_1   1150 CTTAACTTTAAGACTTATTATAAAACTACACCAAGCAAAAAAGTGTT-TA 1198
                          ii  i  i  i     i  i   i     vi  v   i v     v-  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_14339530_1   1199 TTGAAACAAGCATTGACA---AG------GGCACAGAAA-AAGATTCCCG 1238
                         i  iv i   v  v    ---  ------  v i    v-i   v   v 
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_14339530_1   1239 GAATAGATGTATATATGTATGTGCAATTGATTTTCCAAAAAGATGCCAAA 1288
                         i    i ivi   i  v    vv            v v  i i      i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_14339530_1   1289 GTTACTCAATTGG-AAATCATAAGCCTTTCTATCAAATGTTACTGGAACA 1337
                         iii i     v  -   vv   - i    ii v      v i    i   
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATA-GTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_14339530_1   1338 ACTGAATATCCACCTG----AAAATAAAACTCAATCCTTAAATAATGCCA 1383
                             i   ?    v  ---- i   i  ii vi i  i  vv v ii   
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_14339530_1   1384 TACATA----TCAATTCAACATGGATAATATACTCATACCTAA-ATCTAA 1428
                           i i ---- i  i    v      v ? v  ii v iv   - v    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_14339530_1   1429 AACTATAAAACTTCTAGAAGAATATATAGGAAATGATGTTTATGATCTTG 1478
                                     ii        v i     ?ivvi  v  ii   i    
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_14339530_1   1479 GAGGTAGTCATATA--TGCTCAG----GACATAAAATGTGCAAATCATAA 1522
                          - v   v  -  i-- v  i  ----    iv   v ii   iiv i  
  L1M4_orf2#LINE/    572 G-GTTAGGCA-ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_14339530_1   1523 AATAAATAGATTGATGAATAGGACTGTATTAGAATTAAGAACATTTTCT- 1571
                           v   - i  v   i   v     vi  i i      i   -    v -
  L1M4_orf2#LINE/    620 AAGAAA-AAATAGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTG 667

  chr2_14339530_1   1572 CTTTGTATAACACCA--AAAAAATATAAAAAGAAAAACCACAATCTGGAA 1619
                            iiv vi    i --  i   -i i      v  v     ivv   i 
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAA-GTGAAAAGACAACCCACAGAATGGGA 716

  chr2_14339530_1   1620 AAAGTAGTTGCAATAGTTTGCATATTTTGATATTTGCTACATAAGTG--- 1666
                         i  --------    -      v  iv -    i  ----     v ---
  L1M4_orf2#LINE/    717 GAA--------AATA-TTTGCAAATCAT-ATATCTG----ATAAGGGACT 752

  chr2_14339530_1   1667 TGTGTGCATATGTGCATATAATAAAAGATTTTAATTTAAAAAATTACAAC 1716
                            i v  ----- v     -    ii i i ------------      
  L1M4_orf2#LINE/    753 TGTATCCA-----GAATATA-TAAAGAACTCT------------TACAAC 784

  chr2_14339530_1   1717 TCAATTATGG---GACAATCAATCCCATTTAAAACTGTGAAAAAATATTT 1763
                              v  ii---     vi  i  v   ?    v  v v   ii-    
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG-ATTT 833

  chr2_14339530_1   1764 GAAAAGACA---CTTTACAAAAGATACA------GCAAATAAGCATATTA 1804
                            v     ---  ii v i      i ------  v        i  v 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_14339530_1   1805 AAAAAATTCCTTGTCATTAGTCATCAC 1831
                            i -- v  iiv   i ????????
  L1M4_orf2#LINE/    884 AAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (112 / 74)
Gap_init rate = 0.04 (32 / 736), avg. gap size = 2.78 (89 / 32)  


2612 25.25 4.26 2.36  chr2_14459551_14463921     3005  3895 (476)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14459551_1   3005 TGGAAAAAAATCCCATGTTCATGGATAGGAAGAATCAATATTCTTAAAAT 3054
                               i v                 v      v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14459551_1   3055 GGCCATATTGCCCAAGCAACAAAGCAATTTACAGATGTAATGCTATTCCT 3104
                            v   i -   ------    vii  i       vi  i  v  i   
  L1M4_orf2#LINE/     51 GGCAATACT-CCC------CAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr2_14459551_1   3105 TTCAAACTACCAATGACATTCTTCACAAAACCAGAAAAAAATTATTTTAA 3154
                         v     v v   iivi v  i  ii  i  viv  v  iv- v  ii   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAA 142

  chr2_14459551_1   3155 AGTACGTATGGAACCAATA-AAGGAACT--GAATAGCCAAGGCGATCCTA 3201
                          i v i       ---  i-    i  i--          ii i   i i
  L1M4_orf2#LINE/    143 AATTCATATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_14459551_1   3202 AGCAAAAAGAACAAATCTGGAGACATCACGTTACCCGACTTTGAACTATA 3251
                          iv  i         vi     ivv    ii v   i i  ii  viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_14459551_1   3252 GTACTGGGTTACAGTAACCAAAACAGTGTGGTCCTGGTACACAAATAGAC 3301
                         v   vii i        i   i          v    i i vii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_14459551_1   3302 ACATAGACCAATGGAACAGAATAGAAAGCCCAGAAATAAGGCTGCACACC 3351
                          i     i        i     v  i  i          iv iii   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_14459551_1   3352 TACAA-CAACCTGATCTTTCACAAGGCTGACAAAAACAAGCAATGAAGAA 3400
                           iii-   i-    i  iv      v  v   i v  vv     ii   
  L1M4_orf2#LINE/    340 TATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_14459551_1   3401 AAGAC--TCCTTGTTCAGTAAATGGGGCTGGGATAACTGGCTAGCCATAA 3448
                          ii i--  i  --   ii      v       i      v  ?   i v
  L1M4_orf2#LINE/    389 AGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_14459551_1   3449 GCAGAAGACTGAAGCTGGACCCCTTCCTTACAGCATATACAAAAAATCAA 3498
                            i    v     i         v   i   v            - i  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAA 485

  chr2_14459551_1   3499 TTCAA----GATTAAAGACTTAAATGTAAAACCTAAAAGTATAAAAACCT 3544
                         i    ----   i ?    i         i v      v       vi  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_14459551_1   3545 TGGAACACAATCTAGGAGATACTGTCCTGGACATAGGAACAGGAAAAGAT 3594
                          i   v v  iv    ? vv v v i vv   v v  ivi   v  v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_14459551_1   3595 TTTATTGACAAAGACACCAAAAGCA--ATTTGCAATGAAGGCAAAAATTG 3642
                           iv v  i v-             -- ---    ii  i v      v 
  L1M4_orf2#LINE/    586 TTCTTAGATAT-GACACCAAAAGCACAA---GCAACAAAAGAAAAAATAG 631

  chr2_14459551_1   3643 A-AAAGTGGG----ATC-----TAAGAGCTTCTGCACAGCAAAAGAAACT 3682
                          -   v   i----   -----   i i   i  ii vv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_14459551_1   3683 AACAACAGAGGAAACAGACAACG-ATGGAATGGGGGAACATTTTTGCAAA 3731
                          v   v i  vi  v       v- ii       i   v  v        
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_14459551_1   3732 CTATGTATCTGACAAAGGCCTTATATCCAACATCTATAAGGAACTGAAAC 3781
                         ii  i       i  i  v   i      iv  v     i     vvv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_14459551_1   3782 AAATT-----TACAAGGAAAAA-AAC---ATTAAAAAGTGGGAAAATGAC 3822
                           v i-----  v  i  v   -   ---   ?    i    v   v  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_14459551_1   3823 ATGAACAGACACTTCTGTAAAGAAGACATACA--TG--CAGTAAACAAAC 3868
                         v    i     i    vi        i     --  --  i   i  -- 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA--C 879

  chr2_14459551_1   3869 AT-AAAAGA-GATCAATATCACTGATCAT 3895
                           -      - v    i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (130 / 91)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.19 (59 / 27)  


 657 31.49 7.13 4.48  chr2_14473369_14475360      645  1514 (478)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_14473369_1    645 TGCTCATGAATTTAAAAAACTCACTCTC-CTAAG-TAGATTAGCATTCCC 692
                           i     i   -ii  i   i v v i-i    - i --i ii i    
  L1M4_orf2#LINE/     16 TGTTCATGGATT-GGAAGACTTAATATTGTTAAGATGG--CAATACTCCC 62

  chr2_14473369_1    693 ACAAAT-AATCCATATAT-CAGAACTATTTAAATCAAAATTTCAACATGA 740
                         -     -i   i i v  -  ivi v  iivv        ii  i -  v
  L1M4_orf2#LINE/     63 -CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGC 110

  chr2_14473369_1    741 -TTTTTCATGGAGCTAAACAGACTAATTCTAAAATGAAT-TGAAA--GCA 786
                         -     iiii  iv vi   ii  i  i       vv  -  i  --   
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_14473369_1    787 ATTATTTAATATTCTCCAAAATAATTCTAAAAACTAAACAAGAAGTAAGG 836
                          vviviiv v v vv      i   ii i    vv  iv vi    vi i
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_14473369_1    837 TAACTTTCGCTACTAGACTT-AAGACTT--TATAAAGATATGGTAATTAA 883
                         vi   iv i  v ivi i  -  i    --  i    v  ii     i  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_14473369_1    884 AATATT----TA--GACA-GAGGTT-GAGAAGTAGACCAATAAAGGAAAT 925
                         i i v ----  -- i  -i   v -  v vi    i    ---    vv
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT---GGAATA 307

  chr2_14473369_1    926 CAGTAGAGATACTGGAAACAGACTCAAGCATATGTGGGGATTAGTACCTG 975
                         v i v    vv ii    i i  i  vi   v i   --- i i ---  
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGG---TCAAT---TG 351

  chr2_14473369_1    976 CTGTCC-ATA-GCATACAAATCAGTATGCAGTGGTAAA--------CTCT 1015
                         v v i - i - vi i v  v- vi  v  i   vi  --------  i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_14473369_1   1016 TCATAAAAATGTATAGTGACTCAGTTGGCTTTCCTTATG---GAGAATAG 1062
                            - v     -i iv  ivv  ii   v v?  vi   ---i     ii
  L1M4_orf2#LINE/    401 TCA-ACAAATG-GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_14473369_1   1063 AGTCTAGAGCACCACTTCATATCACACATACAAAAA--AACTTCCACATG 1110
                            - i  v v i  i   i i  i --        --    - v v   
  L1M4_orf2#LINE/    449 AGT-TGGACCCCTACCTCACACCATA--TACAAAAATTAACT-CAAAATG 494

  chr2_14473369_1   1111 CATTAAACATCTGAATTATAAAATC-AAACTTGTAATGCACCTATAAGAA 1159
                         v  i ? v i  i   -i   i v -   vi i   vi v i  v     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_14473369_1   1160 AATGTAG-----AATGTTTTTAAGCACTGCTGAGAATGTAAAAATTTCTT 1204
                           ii   -----   v  iv i v viv v v  --- i  vii      
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAG---GCAATGGTTTCTT 590

  chr2_14473369_1   1205 AGCTAAAACAC----ATTAATAACAACAAAAAGAATAAATTAATAAATGT 1250
                           v  vi    ---- vi vv i        -   v    vi      vv
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTG 639

  chr2_14473369_1   1251 GA--TCATATGAGATTTTAAAGTTCTATAATATAAAAG-TGCCATATACA 1297
                           --    -ii i   vv   v  i i iv vi   i -ii i  vv v 
  L1M4_orf2#LINE/    640 GACTTCAT-CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_14473369_1   1298 AAGTTAAAA-ACAGATCA--AATTGGCAGAAGATATTTCCAA----TATA 1340
                             v    -   ivi  --i v   v    i      v   ----    
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_14473369_1   1341 TATAACCAAGAGTTTTAGTCTACAGAAAAGAAAAAGAATGCCTACAAGTC 1390
                          v i i-   i vi  -  v v     v v v      iv i     v  
  L1M4_orf2#LINE/    739 TCTGAT-AAGGGACTT-GTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_14473369_1   1391 AATATTTAAGACAAAAATAATCTACTAGAAAAAATGTGCAAAGTAACTAA 1440
                             v v  i v v      i i v -v?       v      -----i 
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAAT-TWAAAAATGGGCAAAG-----GA 830

  chr2_14473369_1   1441 TTTAACTGAACAGGCAATTC-CCAGTGGAGA-----AAATAGCGAATAA- 1483
                            ----   i  i  v   -   iv i   -----    i  v     -
  L1M4_orf2#LINE/    831 TTT----GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_14473369_1   1484 -ATATGAAAATGCATGCAACCTCACAGAAAAT 1514
                         - i       viiiiv    v   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (151 / 120)
Gap_init rate = 0.06 (51 / 893), avg. gap size = 1.98 (101 / 51)  


3212 25.03 0.77 0.66  chr2_14499677_14504650     3576  4482 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14499677_1   3576 TGGAAACATATCCCATGCTCATGGATGGGTAGAATCAGTACTGTGAAAAT 3625
                               v          i        v  v   v i i  i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14499677_1   3626 GACCATACTACCCAAAGCAATCTACAAATTCAGTGCAATCCCAATCAAAA 3675
                          i v     v      vii       i     ii        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_14499677_1   3676 TACCATCATCATTCTTCACAGAATTAGGAAAAAAAATTTTAAA-TTCATA 3724
                          v   v vv v  i  ii     v v iv  ivvi  ii    -      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_14499677_1   3725 TAGAACCAAAAAAGAACCTGCATAGCCAAAGCAAGACTAAGCAAAAACAA 3774
                          i   viiv  ii  v  v v         i   vvi i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_14499677_1   3775 CAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAAGCCA 3824
                             vi      vv       v  ii        viv     i     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_14499677_1   3825 CAGTCACCAAAACAGCATGGTACTGGTATAAAAACAGACACACAGACCAA 3874
                             v i   i    ii         i    ii i     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_14499677_1   3875 TGGAACAGAATAAAGAACCCAGAAATAAAGCCAAATACTTACAGCCAACT 3924
                              i     vi   ii           v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_14499677_1   3925 CATCTTTGACAAAGCAAACAAAAACATAAAGTGAGGAAAGTACATCCTTT 3974
                         v  i  i     i vviv   i v   vv i  i      v i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_14499677_1   3975 TCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGACAATGAAA 4024
                                            i  i   v  ?       i ii v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_14499677_1   4025 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGACTAA 4074
                         i    i  ii i   v    v           i       i     ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_14499677_1   4075 GGACTTAAATCTAAGATGTGAAACTATACAAATTCT-AGATGATAACATT 4123
                         i   i     v     vv i        -   i   -   v  v     v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATA 549

  chr2_14499677_1   4124 GGAGAAACCCTTCCAGACATTGGCTTAGGCAAGGATTTCATGACCAAGA- 4172
                           ? v  vi    vv   v    v        v i    v iivi v  -
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_14499677_1   4173 ACCCAAA-CACAAATGCAACAAAAACATAGATAAATAGTTAGGACTTAAT 4221
                            v   -     --         iv v i   i   iv v      v  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_14499677_1   4222 TAAACTAAAGAGCTTTTGCACGGCAAATGGA-ATGGTCAGCAGAGTAAAC 4270
                         i   v v  i i      ii vv    -   - ivi   iv i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAA 696

  chr2_14499677_1   4271 AGACAACCTACAGAGTAGGAGAACATCTACACAACCTACACGATCTGACA 4320
                                 i     i i      v  v vii   vii i i-      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATA 745

  chr2_14499677_1   4321 AAGGACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGTAAGAAA 4370
                          i     vi          v  i  v      vv    v   i   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_14499677_1   4371 AA-ACAAATGAACCCA-TCAAAAAGTGGGCTAAGGACATGAATAGACAAT 4418
                           -      -      - i?    i     v     iv          v 
  L1M4_orf2#LINE/    796 AAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_14499677_1   4419 TCTCAAAAAATGATATACAAATGACCAACAAACATATGAAAAAATGCTCA 4468
                             v   i v            i    i  i  i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_14499677_1   4469 TCATCACCATTGAT 4482
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (126 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.08 (13 / 12)  


3114 21.98 5.98 1.50  chr2_14559600_14566294      493  1361 (5334)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_14559600_1   1361 TGGAAATATATCCCATGTTCGTGGATTGGAAGACTTAATATTGTTAAAAT 1312
                               v             i                          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_14559600_1   1311 GTCCATAAAACCCAGAGTGATCTACAGATTCCATGCAATCTCTGT-AAAA 1263
                          v v   vvv    i v              v i      i  i -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_14559600_1   1262 TTCCAATTAAGTTTCTTTTTGT-GAAATAGAAAAGACAATCCCAAAATTT 1214
                          i   ii -- ii -      i-     v  v   vii    i      i
  L1M4_orf2#LINE/    101 TCCCAGCT--GCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

C chr2_14559600_1   1213 ATATGGAACAACCAAGGACCTTGAATAGCCAAAGTAATCTTGAGCAAAAC 1164
                                 vvi v i     iv           ii        iv  i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chr2_14559600_1   1163 GAACAAAGT-AAAGGCATCAGACTACCTGATTTGAAAATCTATTAAATAT 1115
                                  -ii   vv   v   v  ii    v    -  ------  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA-CT------TAC 240

C chr2_14559600_1   1114 TACAAAGTTAAAGTTATTAAAACAGTATGGTAGTGGAATAAATACAGACA 1065
                                i  v   v  i  i     i     v   v    iv i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

C chr2_14559600_1   1064 TATACATCAGCGGAACATAATAGAGAGCTCAGAAAGAAATCCAGTCATAT 1015
                             v    ii    i v   v     ii      v   i   vv   v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

C chr2_14559600_1   1014 ATGGCCAAT--------------GATGCCAAGAGTACACAATGGAGAAAG 979
                             i    -------------- i        vi iv      i     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

C chr2_14559600_1    978 GTCAATCTCTTCAATAAATAGTGCTGTGAAAATTGGATATCCACATGGCA 929
                         ivi i   i     i    i      v  v  i      ?       -  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CA 439

C chr2_14559600_1    928 AAAGAATAAA-TTA-ATCCTT--CCCACACTATATACAAAAGTCAACACA 883
                                i  -  i- i  i -- i     i          i i   v  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

C chr2_14559600_1    882 CAGTGAATTACACACTTAAACATAAGAGCTGAAACTA--AAACTACTAGG 835
                         v i  i  i ? v  i    ii        i      --     vi   i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

C chr2_14559600_1    834 AGAAAACATAAGGAAAAATTTCCATGACATTAGTCTGAGCAAATATTTTT 785
                                   i ?iv    i i i    v  i vi ii    vvi   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

C chr2_14559600_1    784 TGTACTATGACACCACAAGCAGAGGCAACAAAA-ACAAAATAGACAAATG 736
                          iv -          v     v i         - v        i    v
  L1M4_orf2#LINE/    590 TAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

C chr2_14559600_1    735 GGATT------AAACTAAAAAGCTTCAGCAGAGCAAAGGAAACAATCAGC 692
                            i ------   i      -   iv iivvv       v  v    iv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

C chr2_14559600_1    691 AAAGTGAACAAACAAACTACTAAATATGTGAATATATTTGCACATCATA- 643
                                 v i    v i  vi   iv v   v         v      -
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

C chr2_14559600_1    642 ATCTGATAGGGGACTTATATCCAAAATATATAAGAAATTCAAACAACTAA 593
                                 i       i      i         ii  i  vv      v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

C chr2_14559600_1    592 ATAGTAAAAAAACAAATAA--------------------AGGACCAGACT 563
                            i      i        --------------------    iiv  v 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

C chr2_14559600_1    562 AGACATCTCTCATATAAAGACATACAAATGGCCAACAGTTAAATGAAA-G 514
                               i    vv vi    i              i ivi v      - 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

C chr2_14559600_1    513 TTCCTCAACATCACTAATCAT 493
                         v v          ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (109 / 79)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.25 (65 / 20)  

1564 29.02 1.76 1.37  chr2_14559600_14566294     4974  5483 (1212)    L1M4_orf2#LINE/L1        1   512 (396)  

  chr2_14559600_1   4974 TGAAAAAATATTCTATACTCATGGATTGGAAGAATCAATATCATTAAAAT 5023
                           i   i    i i  ii               v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14559600_1   5024 GGCTGTACTGCCCAAAGGAATCTACAGACTCAGTACTATTTCTAGCAAAC 5073
                            vi    v      vvi         i   iii v  ii   v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_14559600_1   5074 TACCAA-TGTCTTTTTCTCACAGAATTGGAAAAAAAAAAATACGCTGAAA 5122
                          v   i-  i      iv  v -     --- v  ivvi  - -  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAGCTGAT-C-CTAAAA 144

  chr2_14559600_1   5123 TTCATATGTAAA----AAGGCCTCA--ATAGCCAAAGATATCCTAAGCAA 5166
                                 v   ---- i  v i  --         ivv   i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_14559600_1   5167 AAAT--TAAAACTGGAGGCATCATACTACCTGGCTTCAAACTATACTACA 5214
                         i  v--i   ii      vv   i   v  iiii      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_14559600_1   5215 AGCCTATAGTAAACAAAACAACGTGGTACTGGTACAAAAACAGACAAATA 5264
                          iv   i     v   i   ii          i i  ii i     v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_14559600_1   5265 GACCAATGGAACAGAACAGAAAAAACAGAAATAAAGCTGCACACCTACAG 5314
                           i        i    iv  i ivv          v iii   ii  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_14559600_1   5315 CCATCTGATCTTCAACAACATCAACAAAAATAAAAGATGGAATAAAGGAC 5364
                         i  vi    i   i    viviiv   i vi vvvi    ii-    i i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAAT 393

  chr2_14559600_1   5365 CCCTTATTCAACCAAAGGTACTGGAATAGCTGGCTAGCCACATGCAGAAG 5414
                         vvii v      v  v   i    i i i    v  ?         i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_14559600_1   5415 TATGAAACTGAACCCCTGTCTTTCACCATATACAAAAATTAACTTATCAT 5464
                         v     ii  i      ii  iv                     i vv  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_14559600_1   5465 GGATTGAAGAGGCAAGTGT 5483
                             ii?   vvi  i   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGT 512

Transitions / transversions = 1.81 (94 / 52)
Gap_init rate = 0.02 (9 / 512), avg. gap size = 1.78 (16 / 9)  

1073 26.81 3.03 1.86  chr2_14559600_14566294     5775  6203 (492)    L1M4_orf2#LINE/L1      475   908 (0)  

  chr2_14559600_1   5775 ACAAAAATCAA----AAGTGGATTAAAGGCTTACATATAAGACTTAAGAG 5820
                                 i  ----  i     i ?  i i  v  i     vi   i v
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_14559600_1   5821 TATAAAAATCCTTGGTGAAGACCTAAGA-CATACCATTCTGGACATTGGC 5869
                                v  i v iv   i  v  i ?-i v i -   vv   v    v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

  chr2_14559600_1   5870 CTTGGCAAATAATTTATTACTAAT-T--CCCCAAAAGCAATTGCAAAAAA 5916
                         i v     - ii   v   --i  - -- v         vvv    v   
  L1M4_orf2#LINE/    574 TTAGGCAA-TGGTTTCTTA--GATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_14559600_1   5917 AAACAAAAGTTGACAAGGGGGACCTAATTAAACTAAAAAGCTTCTGCACA 5966
                          i -    i v  i  ivv    i v  i   v v    i   i  ii v
  L1M4_orf2#LINE/    621 AGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_14559600_1   5967 GAAAAAGAAGCCATCAACAAAGTATACAGGCAACCCACATAA-GGGTAAT 6015
                         vv   i  vi i     v     iv v  i         v  -   vi v
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_14559600_1   6016 AATATTCTCAAATTATGCATCTGACAAAGGTCTAATATACACAACCTATA 6065
                               iv     i  ii      i  i  v  vi   v  v  iv    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_14559600_1   6066 AATAGTAACTT----AATTCAGCAAGCAAAAACCAAATAACCCTTTTTAG 6111
                           -- -    i----  i   ii  vv    iv          vv  ? i
  L1M4_orf2#LINE/    770 AA--G-AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_14559600_1   6112 AAATGGGCAGAGGACGTGCACACATACTTCTCAAAAGAAGAAATACATGT 6161
                                  i    iv  v i v i i     v        v     vi 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_14559600_1   6162 GGCCAACAAATACATGGAAAAATGTTCAACATCACTAATCAT 6203
                               i  ii     i   i   i         ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (60 / 52)
Gap_init rate = 0.03 (12 / 434), avg. gap size = 1.75 (21 / 12)  


 414 22.35 0.00 0.00  chr2_14573205_14576354     1886  1970 (1180)    L1M4_orf2#LINE/L1        1    85 (823)  

  chr2_14573205_1   1886 TGGAAAAACATTGCATCCTCATGGATAGGAAGAATCAATATTGTTAAAAT 1935
                               i i  iv   vi        v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14573205_1   1936 GGCCATACTATCCAAAGCAATTTATAGATTCAATG 1970
                            v     vi     vii  i  i        i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACG 85

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.00 (0 / 0)  

2180 27.60 1.14 2.42  chr2_14573205_14576354     1974  2676 (474)    L1M4_orf2#LINE/L1      215   908 (0)  

  chr2_14573205_1   1974 TCATGCTACCTGACTCCAAACTATACTGCAGGGCTACAGTAACCAAAACA 2023
                            ii  v  ii i i    viv    i  ii          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_14573205_1   2024 GTATAGTACTGGTAAAAAACAAAAAAACAAAGACCATATAGACTAATGGA 2073
                           i i       -------  v  ii i i ---        ii      
  L1M4_orf2#LINE/    265 GTGTGGTACTGG-------CATAAGGATAGA---CATATAGATCAATGGA 304

  chr2_14573205_1   2074 ACAGAACAGAGAATCCAGAAATAAGAATATATACCTACAACTATCTGACC 2123
                          i    iv    i           ivvi   i ii  iiiii vi   ii
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_14573205_1   2124 TTCAACAAAGTTGACAAAAACAAGGAATGGGAAAAGAATTCCCTGTTCAA 2173
                            i    i v  v   i v  vvv      i       vvi  v     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_14573205_1   2174 TAAATGGTGCTGCAAGAACTGACTAACCACATGCAGAAGATTAAAACTGA 2223
                         i           vi v     iv  ?         i    v i  ii  i
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_14573205_1   2224 ACTCCTTCTTTATATCATATACAAAAATTAACTGAAGATGGATTAAAGAC 2273
                           i   v i i i i                  v  i      i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_14573205_1   2274 TTAAATGTGAAAGCCAGAACTATAAAAACCCTGAAAGATAATCTAGGC-C 2322
                         i       i i   i i          vi i ii    v  iv    ?-i
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_14573205_1   2323 ATACCACTCAGGACTTAGGCCTGGGCAAAGATTTCATGAAGAAGACACCA 2372
                          v i -i  iv   i v  vi i     v i    v ii v v       
  L1M4_orf2#LINE/    555 AAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_14573205_1   2373 AAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTAATTAAACT 2422
                               vvv          v      v  i    v   ii v  i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_14573205_1   2423 AAAGAGCTCCTGCACAGCAAAAGAAATTATCAACAGAGTAAACGGACAAC 2472
                         v  i i  ii  ii vv    i  v i      v i   i  vi      
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_14573205_1   2473 GTATAGAATGGGAGAAAATGTTTGCAAACTGTGCATCTGACAAAGATGTA 2522
                         vi i               i        iii ii      i  i ivv v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_14573205_1   2523 ATATCTAGCATTTATAAGGAACT--TACATTT--ACAATAAAAAAAC--- 2565
                         i    i  v  v     i     --    vi -- i        i  ---
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_14573205_1   2566 TGACCCCATAAAAAAGTGGGGAAAGGATATAGACAGACAGTTTTTAAAAG 2615
                          i    v  v?    i    v       v ii i     v  i iv    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_14573205_1   2616 AAGACATAAATGTATCCAACAATCATGCGAAAAAAAAAAAAAACTCAACA 2665
                             i   v vi iv    i  v  iii     i vi------       
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATG------CTCAACA 897

  chr2_14573205_1   2666 TCACTGAATCA 2676
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.88 (124 / 66)
Gap_init rate = 0.01 (8 / 694), avg. gap size = 3.12 (25 / 8)  


3080 27.94 0.44 0.55  chr2_14592424_14598831.rev     5008  5916 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14592424_1   5008 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5057
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14592424_1   5058 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5107
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_14592424_1   5108 TACCAATGACTTTCTTCACC-AAATTGGAGAAAACT-ACTTTAAAGTTCA 5155
                          v   iivi i  i  ii v-      iv--  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chr2_14592424_1   5156 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5205
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_14592424_1   5206 AGCAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5255
                          i     i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_14592424_1   5256 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATG 5305
                                 i   i    ii        vi iv ii i   v        v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_14592424_1   5306 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5353
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_14592424_1   5354 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5403
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_14592424_1   5404 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5453
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_14592424_1   5454 GAAACTGGATCCCTTCCTTACAACTTATACAAAAATTAATTCAAGATGGA 5503
                            ii    i    v   i   v v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_14592424_1   5504 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5553
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_14592424_1   5554 CTAGGCATTACCATTCAGGACATACGCATGGGCAAGGACTTCATGTCTAA 5603
                         v    ?i v viv   iv   v vv vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_14592424_1   5604 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5653
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_14592424_1   5654 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAGTACCATCAGAGTGAAC 5703
                          i   v v  i i   i  ii vv    i  v v  i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_14592424_1   5704 AGGCTACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5753
                           i v   i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_14592424_1   5754 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5803
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_14592424_1   5804 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATACAAACAGACACTT 5853
                          i -    i     v  i?    i     i      vii  i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_14592424_1   5854 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5903
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_14592424_1   5904 CATCACTGGCCAT 5916
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (148 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3111 27.62 0.88 0.55  chr2_14874294_14880699.rev     5010  5914 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14874294_1   5010 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 5059
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14874294_1   5060 TGCCTTACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5109
                         v  vv    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_14874294_1   5110 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 5157
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_14874294_1   5158 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGACAAAAG 5207
                                viiv  ii  v  v v  v     iv     i i i v i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_14874294_1   5208 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5257
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_14874294_1   5258 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATATATC 5307
                                 i   i    ii         i iv ii i   v     v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_14874294_1   5308 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5355
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_14874294_1   5356 ATCTGATCTTTGACAAAGCTGAGAAAAAACAAGCAATGGGGAAAGGATTC 5405
                          vi    i  i     i v  vv  i v-  vv            i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAG 395

  chr2_14874294_1   5406 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5455
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_14874294_1   5456 TGAAACTGAATCCATTCATTACACCTTATACAAAAATTAATTCAAGATGG 5505
                             ii  i i  v v v i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_14874294_1   5506 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5555
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_14874294_1   5556 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5605
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_14874294_1   5606 AAACACCAAAAGCAGTGGCAACAAAAGCCAAGATTGACAAATGGGATCTA 5655
                         vi            vvi          vv  i  v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_14874294_1   5656 ATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5705
                           i   viv  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_14874294_1   5706 CAGGCAACCTACAAAATGGGAGAACATTTTCACAACCTACTCATCTGACA 5755
                         v  i     i   i          v  v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_14874294_1   5756 AAGGGCTAATATCCAGAGTCTACAATGAACTCAAACGAATTTACAAGAAA 5805
                          i  i  vi        i v  i  v      vv  i v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_14874294_1   5806 AAAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5851
                           i    ----   v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_14874294_1   5852 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5901
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_14874294_1   5902 CATCACTGGCCAT 5914
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


1735 25.38 3.72 5.58  chr2_14885568_14887808.rev      607  1197 (1044)    L1M4_orf2#LINE/L1        7   586 (322)  

  chr2_14885568_1    607 GATACACAATATTTATGAATTGGTAAATTCAATATTGTTAAGATGTAAAT 656
                             iv v  i  i   i     v i i i               vv   
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_14885568_1    657 GTTTCTCAAAT----CTATAGAGTCAAGGTAAACTCAATCAAAATCCCAG 702
                         ii i i     ----   i   v    v i  v i v             
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_14885568_1    703 CAGTCACTTTATGTAGAAACTAACAGCTTGGTTCCAAAATTCATATGGAA 752
                          v i vi   -  i     i i   ivi  i i i               
  L1M4_orf2#LINE/    107 CTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_14885568_1    753 GTGTGAATGACA-AAAATAGTCAAAATAACTTTGGAAAGGAAGAATGAAG 801
                         i  ii iv   v- i     i     i  ii   i   i      ii   
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_14885568_1    802 TTGTAGAACCTTCCCTATCTGACTTCAAGAATCACTATAATGCTTCACTA 851
                            v  i  iiv v  vi ii i     i v i    i  v   v  v  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_14885568_1    852 ACCAAGGCAGCATATAGTGCTGTCA-------AGACA----GATAAATGG 890
                          i    i   -- i i  i   v  -------     ----   v     
  L1M4_orf2#LINE/    256 ATCAAGACAG--TGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_14885568_1    891 AACAGAAAAGAGGCTCCAAAACTAGACCCACCACATATATGGTCAGTTCC 940
                           i    vv   iv    i  v  i     i-    v        i  vv
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGGTCAATTGA 352

  chr2_14885568_1    941 TCATCAACAAATTTTCCATAGCAATTCAGTGGAGAAAGAATATTCTTTTC 990
                          iv  i    ivv v   vii v     i   i         v       
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_14885568_1    991 AACAAATGGTTCTGGAATGAATTGGGCATCCATGTGCAAAAAACACAAAC 1040
                                   v    i i-  i   ii ?   ii       i - ii  v
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGAC-AACTGGATAKCCACATGCAAAAGA-ATGAAG 450

  chr2_14885568_1   1041 TTTAACAC-TACCTTATATAATGTTACAAAAATTAA-----ACTATATCA 1084
                           vi  v -     i i iv  i -           ----- v iv    
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGATCA 499

  chr2_14885568_1   1085 TAGACCTGAATGCAAAACTTCTAAATCATAAAACTTCTAAATCATAAAGA 1134
                         ?      i    i  i vi v-   ii        ii  i ------   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGA------AGA 542

  chr2_14885568_1   1135 AATCATAAAACTTCTAAAAGACATACAGAAGAATATTTATGACTTCGAGT 1184
                           v    ------------ i?i  ------   v  ii    i i i  
  L1M4_orf2#LINE/    543 AAACATA------------GGNGTA------AATCTTCGTGACCTTGGGT 574

  chr2_14885568_1   1185 TAGGCCAGTGGTT 1197
                              - i     
  L1M4_orf2#LINE/    575 TAGGC-AATGGTT 586

Transitions / transversions = 2.00 (98 / 49)
Gap_init rate = 0.03 (17 / 580), avg. gap size = 3.24 (55 / 17)  

 709 21.86 14.79 4.82  chr2_14885568_14887808.rev     1439  1749 (492)    L1M4_orf2#LINE/L1      567   908 (0)  

  chr2_14885568_1   1439 CTTTGGGTTAGGCAAATGTCTTTTTGATATAACACCAAGA---------- 1478
                          i             vv  i i  v     i       i ----------
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_14885568_1   1479 --------------------TTTTACTTGAATAAAGTTAAGAAATTCTCT 1508
                         --------------------  vv    v vi   i    i  v  i v 
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_14885568_1   1509 CATTTGAAAGAAACT--TAAGAAAATGAAA-GTCAAAGCATAGGCTAAAA 1555
                         vv  ii  i  v   --i      i     - v   vv  i  iv iii 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_14885568_1   1556 -AAATTATTTGCAAAT--TATATCTGATAAAGGGCTTGTATCCAGAATAT 1602
                         -   v           --            i  i                
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_14885568_1   1603 ATATATATATGTAAAATCTTGGCATTTCAAAACTCCATAATAATAAG--- 1649
                            v -------i  v    -------- v     v       v   ---
  L1M4_orf2#LINE/    767 ATAAA-------GAACTCTT--------ACAACTCAATAATAAAAAGACA 801

  chr2_14885568_1   1650 ------CCAATAAATATATGGACCAAT-ATTTGAATAGACATTTCACCAA 1692
                         ------     v? v v    i v  v-                 v    
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_14885568_1   1693 AGAAGGCATATAGGTAGCAAATAAGCATGCACAAAGATTTTCATCATTAG 1742
                              ii   i ii i  v        iiiiv      vi   v   i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_14885568_1   1743 ATATTAT 1749
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.09 (35 / 32)
Gap_init rate = 0.03 (9 / 342), avg. gap size = 6.78 (61 / 9)  


2546 27.60 0.41 0.27  chr2_14892022_14893764.rev      499  1230 (513)    L1M4_orf2#LINE/L1      128   860 (48)  

  chr2_14892022_1    499 ATAAACT-ACTTTACAGTTCATATGGAACCAAAAAGGAGCCTGCATCGCC 547
                          i  i  - iii  v i           viiv  i   v  v v  v   
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_14892022_1    548 AAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGA 597
                           iv     i i ivv i          i      vv       v  ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_14892022_1    598 CTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGGACTGGT 647
                         i      viv        i          i   i    ii   v     i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_14892022_1    648 ACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAA 695
                          iv ii i   v                i    i--    i  --     
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAA 325

  chr2_14892022_1    696 TAATGCCGCATACCTACAACTATCTGATCTTTGACAAACCTGAGAAAAAC 745
                            vv  ii i ii  iiiii vi    i  i     ivv  vv  i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_14892022_1    746 AAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTG 795
                          vv            i  vvi  v  i  i              v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_14892022_1    796 GCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATA 845
                          v  ?   i   i i  iiv    ii    i    v   i     v    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_14892022_1    846 CAAAAATCAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACC 895
                                i  i    i      i ?    i    i  v   v       i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_14892022_1    896 ATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCAT 945
                               vi i           v    ?i v viv   iv   v v  vv 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_14892022_1    946 GGGCAAGGACTTCATGTCCAAAACACCAAAAACAATGGCAACAAAAGCCA 995
                         i     v ii   v ivvi vi         i  vvi          vv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_14892022_1    996 AAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAA 1045
                             v  i    v   ii v  i   v v  i i   i  ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_14892022_1   1046 GAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTT 1095
                           v    i  vv i      v  i     i   i             v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_14892022_1   1096 CGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAAC 1145
                         i    vii ivi      i  i  i  vi          v  i  v    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_14892022_1   1146 TCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCG 1195
                           vv    v iv i  v     i     i     v  i?    i     i
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_14892022_1   1196 AAGGACATGAACAGACACTTCTCAAAAGAAGACAT 1230
                              iv    i     i     v        i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.41 (116 / 82)
Gap_init rate = 0.00 (3 / 733), avg. gap size = 1.67 (5 / 3)  


1012 29.55 16.46 3.24  chr2_14926268_14928471.rev      915  1716 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14926268_1    915 TGGAAAAATACTCCATGTCCATGAATTAGAAGACTTAATCTAAGAAAGTT 964
                               i   ii      i    i   i           v vivv   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14926268_1    965 ATCAATTCTTCCTAAATGTATCTACATATTTGATGTGATCCCCATCAAAA 1014
                         iv    v  i  i    vv       v   ii i ii     i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_14926268_1   1015 TCCAA--TGGTTTGTGTG-----ACTGTACGCAGAATTATGCTA---TTT 1054
                            v --  vi  v v  ----- i  ---i  iiv v  v   ---  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_14926268_1   1055 ATATGGAATAATAGAGGGCTTCACATAGCTAATATA-TCTT--------- 1094
                                 vvii ii  i iiviv     i  v i -    ---------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_14926268_1   1095 ---CT--GCTAGA-----TATA------AA-----AAACTTGTTTTAAAG 1123
                         --- v-- i i  -----i i ------  -----      ii vi    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_14926268_1   1124 CTACAGTACTTAAGATAG-------CTGGTTAAAATATAGATGAATAG-T 1165
                                 v i    i  -------    ivv  iv     iiv    - 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_14926268_1   1166 CAAATGTAATAGAATATG-GAATGCAGGAA-AA---------------GT 1198
                            -  v        -  -  i v   i  -  ---------------  
  L1M4_orf2#LINE/    298 CAA-TGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_14926268_1   1199 CA---------CGCACACGG-----AAGAGCACTTGAT------------ 1222
                           ---------  -   v  -----    v  i ii  ------------
  L1M4_orf2#LINE/    346 CAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_14926268_1   1223 ---TT--------ATGTTGCTGCAACGATTGGATATCCACATGGGAGAAA 1261
                         ---  --------   v     vi  i i      ?       vi i i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_14926268_1   1262 AGAAACTTG--CTATTAACTTCAAGATATATGCAAAA-TCAATTCCAGAT 1308
                          vi  v   -- ivi  - i   vivi    i     - i  i  v i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_14926268_1   1309 AAATCATAGACCTTTACATGAGAGTCAAAATACTCAAATTTATCAAGGCA 1358
                         ii    ?      vv ii i    ii    ivv v   i iv vi i v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_14926268_1   1359 AATTTGGAAGAATATCTTC-TATCTTTGGGGTAG-C-----TTATTTAAA 1401
                           iv i i? v v      - iv i     v   - -----  vi   i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_14926268_1   1402 AAAACCTA-GACACAAAAAGCATTAAC--CATGAGATAAAATTTATAG-T 1447
                         ------  -     v       iv i --  vi   v     vv   i- 
  L1M4_orf2#LINE/    594 ------TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_14926268_1   1448 TGTAACACAATAAAATGAAAAACTTCTATCCATCAATAATCACCATTAAA 1497
                           v viv  vi     v        i i v v    viiv   i  i  i
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_14926268_1   1498 ACAGTAAAAACAAAACAAAAGCTATTTATAGAGTGAGAG----TACATGT 1543
                          v   i    ---i    ------iii i   i  i   ----  iv  i
  L1M4_orf2#LINE/    688 AAAGTGAAAA---GACAA------CCCACAGAATGGGAGAAAATATTTGC 728

  chr2_14926268_1   1544 AAAT---------AACAAAAACCTCTTA--CAGAAAATACAAAGATCTCT 1582
                             ---------i i  iiiv  iv  --     v   i     v    
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_14926268_1   1583 TGTAAATCAATAAGATAAAGATAGACCACCCAGTGGAAAAATAAATGGAC 1632
                          ii  v       v v     i i iv     i v?      ----  i 
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT----GGGC 824

  chr2_14926268_1   1633 AAGATATTGCAACAGCCATTCCACAAAATAAGTTATCTAAATGATTACCA 1682
                           iiv   vv  i  v    i v v   v   v   vi     iii vi 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_14926268_1   1683 CACAGATGGAAAGGCATTCAACTTTATGCCTTTA 1716
                         vi  v   i    iiii     v i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.04 (38 / 908), avg. gap size = 4.16 (158 / 38)  


3010 27.65 1.67 0.45  chr2_14938287_14944555     4881  5777 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_14938287_1   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_14938287_1   4931 GGG---------CAGGT-AATTTATAGATTCAATGCCATCCCCATCAAGC 4970
                           v---------  ii -i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_14938287_1   4971 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5018
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_14938287_1   5019 TAAGGAACCAAAAAAGAGCCCGCACCGCCAAGTCAATCCTAAGCCAAAAG 5068
                           v    viiv  ii  v  v v iv     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_14938287_1   5069 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5118
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_14938287_1   5119 TACAGTAACCAAAACAGCATGGGACTGGTACCAAAACAGAGATATAGATC 5168
                                 i   i    ii   v     i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_14938287_1   5169 AATGGAACAAAAC--AGAGCCCTCAGAAATAATGCCGCATACCTACAACT 5216
                                i i  i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_14938287_1   5217 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5266
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_14938287_1   5267 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5316
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_14938287_1   5317 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5366
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_14938287_1   5367 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5416
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_14938287_1   5417 CTAGGCATTACCATTCAGGACATAGGCATGGG-AAGGACTTCATGTCCAA 5465
                         v    ?i v viv   iv   v v  vv i  -  v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_14938287_1   5466 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5515
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_14938287_1   5516 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5565
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_14938287_1   5566 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5615
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_14938287_1   5616 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5665
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_14938287_1   5666 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5715
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_14938287_1   5716 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5765
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_14938287_1   5766 ATCACTGGCCAT 5777
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  


3155 25.39 1.88 1.22  chr2_15036638_15040720     2690  3591 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_15036638_1   2690 TGAAAAGATATTCTATGCTTATGGACTGAAAGAACTAATATTGTTAGGAT 2739
                           i        i i   i i     i  i    vi           i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_15036638_1   2740 GACAATACTACCTAAAACAATTTATAGATTCAATGCAATCCTCGTCAAAA 2789
                          i       v  i   vii  i  i        i       iii      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_15036638_1   2790 TACCAATGACATTATTCACAGAAATAGAAAAAAAAATCTTAAAATGTATA 2839
                          v   iivi v  v  ii       v  v  ivvi   i      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_15036638_1   2840 CAGAACCACAAG--ACTCGGAATAGCCCAG-CAATCCTTGGCAAA-AAGA 2885
                         ii   vii    --  i i        v i-     -   iv   -    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAAGAAGA 199

  chr2_15036638_1   2886 ACAAAGGTGGAGGCATCACATCTTTACTGCAAAGTGGCTTCAAAATTTAC 2935
                               v      vv     ii ii----   -----i       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCC----CAA-----TTTCAAAACTTAC 240

  chr2_15036638_1   2936 TACAAAGCTA--GTAACCAAATTACCATAGCACTGGCATAAAAACAGATA 2983
                                   --    i   ivi vii i i          ii i   i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_15036638_1   2984 CATAGATCAATGGAACAGAATAAAGCACCCAAATATAAATCCACACACTT 3033
                         i              i     vi  vii   i v     i   i   i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_15036638_1   3034 ACAG---ATTTATCTTCAACAAAAGCACCAGAAACATACAATGGTAAAAG 3080
                          ii ---   v  i   i    ii ii   ii v   v      vi    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_15036638_1   3081 AACAGGCTTTTCAACAAATGATACCAAGAAAACTGAATAACCAT-TTCAG 3129
                           i  v              i i iii  v     i   ?   i- v  i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_15036638_1   3130 AAGAATGAAACTAGACCCCTATAACTTGCCACACACAAAAATCAAATCAA 3179
                                  ii i        ivv vii   i i        i  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_15036638_1   3180 ATTGGATTACAGACTTAAAC-TAAGACTTGAAACTACGAAACTTCTAGAA 3228
                          v     i ?    i    i-     vi i      ii     ii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_15036638_1   3229 ACAACAATAGGGAAAACACTCCAGGACACTGGTTTTGGCAAATAATTT-T 3277
                         iv  vv     ?iv  vv  i iv   vi   v  v     - ii   - 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chr2_15036638_1   3278 TGTGTAAGATCTCAAAAGCACAGGTAACCAGAGCAAAAGTAGACAAATTT 3327
                          ivi  v  ivi          i i   v i  v    i    i     v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_15036638_1   3328 GATTTAATCAAGCTAAAAAGCTTCTGCACAGCAAAGCAAACAATCAA--- 3374
                           i  v     iv v    i   i  ii vv     v v  v     ---
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_15036638_1   3375 AGTGAAAAGACAATTCACATAATGGGAGAAAA-ATTTGCAGACTGCCCAC 3423
                                      ii    v            -       i iiiivi i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_15036638_1   3424 GTGATAAGTGATTGATAACCAGAATATATAACAAGCTCAAAAAACTCAAT 3473
                         v       v  i vi  v             vi i   vv v        
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_15036638_1   3474 AGCAAAAA-ACAAATAACATAATTTTAAAATGGGCAAAAGATCTCAATAG 3522
                          ii     -         vi    ?v            i   i v     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_15036638_1   3523 ATATTTCTCAAAAGAAGACATACATATGGCCAACAGGTATGTGAAGCAAT 3572
                          i       v        i     v        i i i ii    ivi  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_15036638_1   3573 GCTCAACATCACCAATCAT 3591
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (149 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.87 (28 / 15)  


2097 23.65 15.27 1.20  chr2_15056500_15059596     1384  2051 (1046)    L1M4_orf2#LINE/L1        1   762 (146)  

  chr2_15056500_1   1384 TGGAGAAACATATTGTGTGTATGAACTGGAATACTGAATATTACTAAGGT 1433
                             i i i  viii   vi   i i     v   v      ii    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_15056500_1   1434 ATCAGTTCTTCCCCAAACTGATATATAGATTCAATGCAATTTCAATCAAA 1483
                         iv  i v  -       i    v  i        i     ii v      
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_15056500_1   1484 CTACTAGCAGAATTTTTTTTATAGAAA-------GCCAGTTTCAAAATTC 1526
                         v v i   v --ii      ii     -------  iii iii       
  L1M4_orf2#LINE/    100 ATCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_15056500_1   1527 ACACGGAAATTCTAAGGATCTAGAATAGACTAAACAACTTTGAAAAAGAG 1576
                          i i      v v i   i i       v v      ii          i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_15056500_1   1577 ---CAAAGTTGTAAGACTGATACTACCCGATTTCAAGACTTTTTATAAAG 1623
                         ---        v i    v i   v   i       i    vi  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_15056500_1   1624 CTACAGTAATCACACCAAGCCTCCACTGGCATAAAGATAGACAAATAGAT 1673
                                     viv  ivvivvi          i        v      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_15056500_1   1674 AAAGAAAACAGCATAGAAAAGTTAGAAA-AGGAATATACATAGTTAATGA 1722
                         v  vii  i  v  v  i ivii     - iivvi      --   -  i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT--TTA-TGG 344

  chr2_15056500_1   1723 CCAATT-ATT---GACAAAGGTAC-AAGAGCACC---------------- 1751
                         i     -   ---     i   i -    v  ii----------------
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_15056500_1   1752 ------TCAGTAAA------------AACT----ATTCACATGCAAAA-- 1777
                         ------   ii   ------------    ---- ?i           --
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_15056500_1   1778 ------------------------------------ATTAACTTAAAATG 1791
                         ------------------------------------       i      
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_15056500_1   1792 GAACATATACCTAGAGGTAAAAGTTAAAACTA-AAATTTCTTAGAAGAAA 1840
                           v  ? v     i v    i  i        -   vi            
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_15056500_1   1841 GGATAGGATTAAATCTCTGTGGCCTTGGGTTAGGGAAAGGTCTCTTAGCT 1890
                         iv     ?v       ii   i            v  v   i      v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_15056500_1   1891 ACAATATCAAAAGCACAAACAGTAAAGGAACAAA-AGATAAATTGGACTT 1939
                          ii i i           i  ii   i   v   -               
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_15056500_1   1940 AATCAAAATCAAAA-CTTTTGTACTATAAGCAATATCATCGACAAAG--- 1985
                         v        i    -       i  vi  ivi i ii   i v    ---
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_15056500_1   1986 ----GTAATCCACAGAATGGAAAAAAATATATTTGCAAGTCATGTATGGA 2031
                         ----ii  i           i i       --      i    i   vvi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATAT--TTGCAAATCATATATCTG 742

  chr2_15056500_1   2032 GTAAGGGACTTGTATGCAGA 2051
                         i              v    
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGA 762

Transitions / transversions = 2.04 (104 / 51)
Gap_init rate = 0.02 (19 / 762), avg. gap size = 5.79 (110 / 19)  

 741 13.07 0.65 2.61  chr2_15056500_15059596     2459  2611 (486)    L1M4_orf2#LINE/L1      759   908 (0)  

  chr2_15056500_1   2459 CAGAATATATAAAGAACTCTTACAATTCAATAATCAAAAGACAAAGAACC 2508
                                                  i        v          v    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_15056500_1   2509 CAATTTAAAAGTTGGCAAAGTCTCTAAATAGTCATGGTCTCCAAAGAATG 2558
                              ?    i v       vv i i     v   -v           vi
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACAT-TTCTCCAAAGAAGA 857

  chr2_15056500_1   2559 TATACAAATAAC-AATAAGGGTATGAAGAGATGCTCAACAACTTCATATG 2607
                                  ii -      vii     i            ---   ????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA---TCAZZZZ 904

  chr2_15056500_1   2608 CCCC 2611
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 1.67 (5 / 3)  


3136 24.61 2.33 1.66  chr2_15114941_15116959.rev      626  1527 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_15114941_1    626 TGGAAAAACATTCCATCCTCATGGATAAGAAGAATCAATATAGTTAAAAT 675
                               i i  i    vi        vi     v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_15114941_1    676 GTCCATATTACCCAAAGCAATTTACAGATTCAATGCTATTCCTATCGAAC 725
                          v v   i v      vii  i           i  v  i      i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_15114941_1    726 TACCAATGACATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 774
                          v   iivi v  i  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_15114941_1    775 ATGGAA---CAAAAAAAGCCCA-AATAGCTAAAGCAATCCTAAGCAAAAG 820
                               ---   iii --    -      i   i     i i iv  i i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_15114941_1    821 GAACAAAGCTGGAAGAATCACATTGCCCGACTTCAAACTGTACTGCAAGG 870
                                 i    i  v     i v   i i      viv    i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_15114941_1    871 CAATGGTAACCCAAACAGAATGGTAATGGTTCAAAAACAGACACATAGAC 920
                          v ii    i v i    vi     v   ivi  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_15114941_1    921 CAATGGAACAGAATAGAGAGCCCAGAAATAAAGCCACACACCTACAACCA 970
                                 i     v     i           v   i   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_15114941_1    971 TCTGATCTTTGATAAAGCTGGCAAAAACAAGCAATGGGGAAAGGAT--TC 1018
                         vi    i  i  i  i v  v   i v  vv            i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_15114941_1   1019 CTTATTCAATAAATGGTGTTGGGATAACTGGCTAGCTATACGCAGAAGAT 1068
                         i  --    i        i     i      v  ? i i i   i    v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_15114941_1   1069 TGAAACTGGACCTCTTTCTTATACCATATACAAAAATCAACTCAAGATGG 1118
                             ii      i  vi  i i               i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_15114941_1   1119 ATTAAATATACCTAAATGCAAAATCTAAAACTATAAAAC-CTTGGAAGAT 1167
                           i ? v --        i  i v               -   i     v
  L1M4_orf2#LINE/    496 ATCAWAGA--CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_15114941_1   1168 AACCTAGG---AAATACCATTTTG-GACATTGGAACTAGCAAAGATTTTA 1213
                            v    ---    ----i  i -   v    ivivi    v i   iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_15114941_1   1214 T-GATGAAAACATCAAAAGCAATTGCAACAGAAGCAAGCATTGACAAATG 1262
                          -   - vi   i        vvv      i   v  iv  v  i    v
  L1M4_orf2#LINE/    590 TAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_15114941_1   1263 GGACCTAATTAAACTAAAGTGCTTCTGCACAGAAAAGGAAACTATGAACA 1312
                             i v  i   v v  ivi   i  ii vvv      v     v  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_15114941_1   1313 GGGTAAACAGTCAATCTACAGAATGGGAGATAATATTTGCAAACTGTACA 1362
                         ii  i  v  v   i i             v            iii  i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_15114941_1   1363 TCTGATTAAGTTCTAATATCCAGAATATACAG-GAACTTAAATGAACATT 1411
                               v i vv  vi             i i-     i--- v vv i 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC---TTACAACT 785

  chr2_15114941_1   1412 CAA--GCAAAAAG-CA--TTGCCCA-TTACAAAGTGGGCAAAGGATATGA 1455
                            --ii      -  -- vi    -  ?v   i            v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_15114941_1   1456 ACAGACACTTTTCAAAAGAAGACATACATGCAACCAAAAAGCATTTTAAA 1505
                          i     i  i  v        i     viiii    v     iv v   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_15114941_1   1506 A-ATGCTCAATATCACTAATCAT 1527
                          -        i    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (137 / 82)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.71 (36 / 21)  


3273 23.85 5.18 0.58  chr2_15154356_15157837     2123  2990 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_15154356_1   2123 TGGAAAGATGCTACATGTTTATGGATTGGAAGACTTGTTACTGCTAAATT 2172
                                  iiiv      i                iv  i  i   iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_15154356_1   2173 GCCCCTACTAAATAAAGCAATCTACAGATTCAACACTATCTCCATCAAAA 2222
                          v vv    vvvi   vii               i v   i i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_15154356_1   2223 TCCCAATGACATTTTTTACAGACATAGA-AA----ATCCTAAAATTAATA 2267
                              iivi v      i    v  v  -  ----           v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_15154356_1   2268 TGGAACCACAAAAT-CCCTGAGTAGCCAAAGCAATC-----AAAGAAGAA 2311
                              vii   iiv-   v  i        i     -----         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_15154356_1   2312 CAAAGTTGGAGGCCTCATACTTCCTGATTTCAAAATATATTACAAAGTTA 2361
                                     v    i      ii         iv  i       i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_15154356_1   2362 TAGTAAACAAAATTGTATGCTACTGACATGCAGACAGAAATAAAGACCAA 2411
                         i     v   i iv  i  v     i   ivi  i   v   v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_15154356_1   2412 TGGAACAGAATAAATAGCCCAGAAATAAACACACACATTTACAGTCAATT 2461
                              i     vi v  i            v  i       ii       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_15154356_1   2462 GCTCTTTGACAAGGGTGCCAAGACTACACAATGAGGAAAGGACAATCTCT 2511
                          v i  i                 i iv     i      i i i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_15154356_1   2512 TCAACAAATAGTACTGGGAAAACTAGATACCTACATGCAGAAAAAAATGA 2561
                                  i  i      v    i    ? i       --   i     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA--AAAGAATGA 448

  chr2_15154356_1   2562 AATTGT-TCCTTATCTTATACCGTACATAAAAGTAAAGTCAAAATGGATT 2610
                          i   v-i  i  i  i i   i  i i    i v  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_15154356_1   2611 AATGATTTATACTTAAGACCTGAAATTAT------TTTA--------C-T 2645
                          ?v  ii  v iv     v  i   i   ------i   -------- - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_15154356_1   2646 AGGAA-AAACCTTCATGACATTGATCTCGGCAATTATTTCTTGGATTTGA 2694
                            ?i-   i    i    v   ivi v      vi      i   v   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_15154356_1   2695 CACCAAATGCATAGTCAGCAAAAACAAAACCAAGCAAATGGGACTATATC 2744
                                v   i iv  i     iv    vi iii    v     vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_15154356_1   2745 AAA-CCAAAAA-------GGATTAAGAAAAACCATCAC-ACAGTGAAAAG 2785
                            -ii     ------- vv i  iii v  i    v- v         
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_15154356_1   2786 GCAACCTATGAAATGGGAGAAGATATTCACAAACCATACATTTGTTAAGG 2835
                         i     i iii          i     ii    i    i  i  v     
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_15154356_1   2836 GGTTAATATCCAAAACACATAGGGAAATCATATGACGCAAGAGCAAGAAA 2885
                          ii vi      i  i i   ii   v  v  ii  v   v ii  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_15154356_1   2886 ACAA----TCCAATTAAAAAATAAGTAAAGGATT-GAACAGACATTTCTC 2930
                             ----i      ?      ii i        -   i           
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_15154356_1   2931 CACAGAAGACATACATGTGAACCACAAGCACGTTTTTAAAAAAT---CGA 2977
                           v      i     vi  iv v i      i v---    i  --- i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATG---AAAAGATGCTCAA 895

  chr2_15154356_1   2978 CATCACTAATCAT 2990
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (136 / 67)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.94 (50 / 17)  


3065 27.67 0.88 0.77  chr2_15337447_15341942     3098  4004 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_15337447_1   3098 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3147
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_15337447_1   3148 GGCCATACTGATGCCCAAAGTAATTTACAGTTTCAATGCTGTCACCATCA 3197
                            v     v---      v i  i     v     i  vi  v i    
  L1M4_orf2#LINE/     51 GGCAATACTC---CCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_15337447_1   3198 AGCTACT-GTTGACTTTCTTCACAGAAGTGGAAAAAAACT-ACTTTAAAT 3245
                          iv v i- i  v    i  -i     i v  v  i--  - iii    v
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAA 144

  chr2_15337447_1   3246 TTCATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAA 3295
                                    viiv  ii  v  viv  v     i      i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_15337447_1   3296 AAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACA 3345
                         i          i      vv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_15337447_1   3346 AGGCTACAGTAACCAGAACAGCATGGTACTGGTACCAAAACAGAGATATA 3395
                          i          i  ii    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_15337447_1   3396 GACCAATGGAACAAAACAGAGGCCTCAGAAATAACGCCACACATCTACAA 3445
                           i        i i  iv   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_15337447_1   3446 TCATCTGATCTTTGACAAACCTGACAGAAACAAGCAATGGGGAAAGGATT 3495
                            vi    i  i     ivv  v  ii v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_15337447_1   3496 CCCTATTTAATAAATGATGTTGGGAAAACTGGCTAGGCATATGCAGAAAG 3545
                         vi  v  i  i     i  i     v      v  ?v  i     i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_15337447_1   3546 CTGAAACTGGATCCCTTCCTTACACTTTAAACAAAAATTAACTCAAGATG 3595
                         v    ii    i    v   i    iv  v                i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_15337447_1   3596 GATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAA 3645
                            i ?    i    ii     v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_15337447_1   3646 ATCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTAATGAC 3694
                          iv    ?i- v i -   iv   v v  vv i     v ii  vv iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_15337447_1   3695 TAAAACACCAAAAGCAATGGCAACAAAAGCCGAAGTAGACAAATGGAATC 3744
                           vi            vvi          vvi  i    i    v i ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_15337447_1   3745 TAACTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 3794
                          v ii   v v  i i   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_15337447_1   3795 AACAGGCAGTCTACAGAATGGGAGAAAATTTTTGCTATCTATCCATCTGA 3844
                           v  i  ii i                 v     v vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_15337447_1   3845 CACAGGGCTAATATCCAGAATCTACAAAAAACTTAAGCAAATTTACAAGA 3894
                         i vi  i  vi          v  i   i    ivvi   v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_15337447_1   3895 AA----TAAACAACCTCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 3940
                           ----i   i    iv  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_15337447_1   3941 ATCTCAAAAGTAGACATTTATGCGGCCAACAAGCATATGAAAAAA-GCTC 3989
                         v    v    v   i  vi vii      i     i       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_15337447_1   3990 ATCATCACTGTTCAT 4004
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2542 27.21 3.02 1.34  chr2_15345540_15348611.rev     1688  2580 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_15345540_1   1688 TGGAAACACATCCCATGCTCAAGGATAGGTAGAATCAATATTGTGAAAAT 1737
                               v i        i   v    v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_15345540_1   1738 GACCATATTGCCAAAAGCAGTCTATAAATTTAATACAATTCCCACCAAAA 1787
                          i v   i v  v   viii    i i   i  ii    i  i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_15345540_1   1788 TACGATCATCATTCTTGACAGAACTAGAAAAAA-AATCCTAAAATTCATA 1836
                          v v v vv v  i  vi     v v  v  iv-i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_15345540_1   1837 CAGAACCCAAAAAGAGTCTTCATAGCCAAAGCAA----GACTAAACAAAA 1882
                         ii   vivv  ii  vi vvv         i   ----  --   vi  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chr2_15345540_1   1883 AACAAATCTGGAGGCATCATATTACCTAACTTCAAACTATACTATAAAGC 1932
                               vi      vv   i i v  i  i      viv     i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_15345540_1   1933 TATATTAATAGTTACCAAAACAGCACTGTACTCGTATGAAAATATGCATA 1982
                           i v    ------   i    iiiv     v i  i ii   vi    
  L1M4_orf2#LINE/    249 TACAGTAAT------CAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_15345540_1   1983 TAGACCAATGGAACAGAATGGATAACCCAGAAACAAAGCCAAATACTTAC 2032
                             i        i     v  v ii       i   v   v i i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_15345540_1   2033 AGCCAACTGATCTTTGACAAAGCAAACAAAAACA--AAGTGGGGAAAGGT 2080
                         i i   i    i  i     i vviv   i v  --v i         iv
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_15345540_1   2081 CACTCTATTCAACAAATGGTGCTGGGATACTTCATTGGCAAGCCACCTGT 2130
                         i v   v                    i ---- i   vv ?    v  i
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACA----ACTGGATAKCCACATGC 438

  chr2_15345540_1   2131 AGAAGAATGAACCTGACTCCTCATCTCTAACCAAATACAAAAATTAACTC 2180
                          i         vi  ivi  ii i   vv    v                
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_15345540_1   2181 AAGATGGTTCAAGGACTTAAATCTAACACCTGAAGC-ATAAAAATTCTAG 2229
                           i    v   ?i   i     v   v v  i  i -      v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_15345540_1   2230 AGGATAACGTTGGAAAAACTCTTCTAGACATTGGATTAGGCTAAGA---C 2276
                          i  v   i v  ?iv  v     vv   v    i      v v i--- 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_15345540_1   2277 CAAGA------ACCCAAAGCAAATGAAACAAAACCAAAGATAAATAGATG 2320
                         iv   ------   v      v v v       vv   i   i   i  v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_15345540_1   2321 GTACCTAATTAAACTAAAAAGCATCTACACTGCAAAAGAAATGATCA-GC 2369
                          v  i v  i   v v    i v i iii  v    i  v iv    - v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_15345540_1   2370 TACTCAA----CAACCTACAGAGTGGGAGAAAATATTCACAAACTAAGCA 2415
                         v v v  ----     i     i              ii    ii vii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_15345540_1   2416 TCTGATAAAGGACTA--ATCCAGAATCTACAAGGAACTCAAACAGATCAG 2463
                                 i     v--         v  i  i      vv   iv   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_15345540_1   2464 CAAGAAGCAAGCAAACAATCCCATCAAAAAGTAAGCAAAG-ACATGAATA 2512
                         i  v  iv ii    i  i  v  i?    i ii      - iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_15345540_1   2513 GATACTTCTCAAAAGGAGATACACCAGTGGCCAAAAA--ACAAGAAAAAA 2560
                           i i     v    i     i  v i       v  --   v     i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_15345540_1   2561 TGTTCAACATCACTAATTAT 2580
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (132 / 107)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.79 (39 / 14)  


3145 26.88 1.33 0.88  chr2_15406477_15412875     5004  5907 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_15406477_1   5004 TGGAAGAATATTCCATGCTTATGGATAGGAAAAATCAATATAGTGAAAAT 5053
                              ii    i     i i      v    i v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_15406477_1   5054 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5103
                            v     vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_15406477_1   5104 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5151
                          v   iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_15406477_1   5152 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5201
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_15406477_1   5202 AACAAAGCTGGAAGCATTACGTTACCTGACTTCAAACTATACTACAAGGC 5251
                                i    i vv i  ii v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_15406477_1   5252 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5301
                           i     i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_15406477_1   5302 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 5349
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_15406477_1   5350 ATCTAATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT--T 5397
                          vi i  i  i     ivv  v   i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_15406477_1   5398 CCTTATTTAACAAATGGTGCTTGGAAAACTGGCTAGCCATATGTAGAAAG 5447
                          i  -- i             v   v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_15406477_1   5448 CTGAAACTGGATCCCTTCTTTACACCTTATACAAAAATTAATTCAAGACG 5497
                         v    ii    i    v i i     v              i    i i 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_15406477_1   5498 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5547
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_15406477_1   5548 ACCTAGGCA-ATACCATTCAGGACATAGGCCTGGGCAAGGACTTCATGAC 5596
                           v    ?i- v i -   iv   v v  vi i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_15406477_1   5597 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAAGGGGATC 5646
                           vi            vvi          vv        i   vv   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_15406477_1   5647 TAATTAAACTAAAGACCTTCTGCATGGCAAAAGAAACCACCATTGGAGTG 5696
                          v  i   v v  i v   i  iiivv    i  v  i i  vvii    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_15406477_1   5697 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 5746
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_15406477_1   5747 CAAAGGGCTAATATCCAGAATCTACAAAGAACTGAAACAAATCTACAAGA 5796
                         i  i  i  vi          v  i        vvv    v  v i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_15406477_1   5797 AAAAAAGCAAACAACCCCATCAAACAGTGGGCAAAGGATATGAACAGACA 5846
                             i -    i     v  i?  v i            v    i     
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_15406477_1   5847 CTTCT-----GAAAACATCTATGCAGCCAACAGACACATGAAAAAATGCC 5891
                         i    -----   i i  vi viii     i ii          i    i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_15406477_1   5892 CATTATCACTGGCCAT 5907
                           vi    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (150 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


1151 29.48 7.26 4.31  chr2_15495946_15497986      706  1587 (454)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_15495946_1    706 TAGAACAACATCCGCTATTATTGGATAAGATGACTGAACATTATACAAAT 755
                          i   vi i    vv i  vv     vi  v    v  i   i vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_15495946_1    756 ATTGGT-CTCCCTAAGTTAATGTACAAATTCAATGCAATCACAAT-AAAA 803
                         iviii -     i  i  i  v    i      i      v v  -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_15495946_1    804 TACCAATAAGCAATTTTATGAAAGTAGACAAACTGTTACTAAAGTTCAGA 853
                          v   iiviv vv    iiii  i v     i   v v     i    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_15495946_1    854 TAGAAAAACAA---ATATACAATAACATGTAAAAAAAAAAAACAAAACAA 900
                          i    vi   --- ivi v    i ----------------        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGC----------------CAAAACAA 184

  chr2_15495946_1    901 -----AAAAACATGAGGAAAAAAACCCACAGAGGAATACTACCTCCTCAG 945
                         -----     ---  i   v   iii---i     v vvi  i   -  -
  L1M4_orf2#LINE/    185 TCTTGAAAAA---GAAGAACAAAGTT---GGAGGACTCACACTTCC-CA- 226

  chr2_15495946_1    946 ACATTAAAACACACTA-AAATCTCTA-TAATTAAAATCATGAAGTACTAG 993
                          iv i     vi    -   v  vi -    i  i ivi  vi     i 
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_15495946_1    994 TGCATGGACAGACA----GACCAGTAGAATATA---GAAACTCTAGAATT 1036
                         iii v   i     ----  i  i i     v ---  i v  i    v 
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_15495946_1   1037 AAACCCATGTACAGATGG-AAATTTAGGTATATGACAAAGGTGGCATTTC 1085
                                 ii ivv    -v    -- i v vi     i    v  vvv 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATT--GATTTTCGACAAGGGTGCCAAGAC 374

  chr2_15495946_1   1086 AAATCACTAGGGTAATGGTAAACTTTTTAATAAATGATGCTGGAACAACT 1135
                         v v   v i   v  vii  iv     i  i     i      i      
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_15495946_1   1136 GCGTGGTCATTTGGGAAA--ATAAAATCAGATCCATGTCTCACA--ATAC 1181
                          vi i?i  iv  vi   --  i  i ii  i  v ii      --   i
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_15495946_1   1182 AAAAGAATAAACTCCAAATAAATTGGGAAGA-------GAAAAA--TAAA 1222
                          v  i   v     v    ii  ii--?   ------- v  i --    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCA--WAGACCTAAATGTAAGAGCTAAA 522

  chr2_15495946_1   1223 ACCATGCAAGTACTAGAAGAAAACGTGAGAG-AATTCTTCCTTAACTCTG 1271
                           i  iv  v vi           i ii ? -  v     v -i  ii  
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACCTTG 571

  chr2_15495946_1   1272 AGT-ATGAAAAGGCTTTCCAACTATTACTCAAAATACAGAGGCAGTAAAA 1320
                         i  - v v  v  i  iii iv   v  v v   vi  v i   ii    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_15495946_1   1321 GA-----TCGAACAATTTGACTACACAAAAATTAAAAA-----GTGAAAA 1360
                           ----- v  vv    v    v  iv           -----   ----
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG---- 667

  chr2_15495946_1   1361 CATTGTATGACACAATAAACAAAGTCAAAAGACAACTGACCAACTGGGAG 1410
                          v iiv v     v  v  v     v          iv  vi v      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_15495946_1   1411 AAA-TATT----AAT-ATATGCCACAGAGAAAGGGTTAGT-TACACGAAT 1453
                            -    ----   -    ii v--  v  i  ii v  - v  -    
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCT--GATAAGGGACTTGTATCCA-GAAT 764

  chr2_15495946_1   1454 ATGTAA-GAATTCCTAAAAATTAA-GGTACAAAGGAACAAA-AACCCTAT 1500
                           i   -   i  i  v  v i  -ii  v    --     -     v  
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAG--ACAAATAACCCAAT 812

  chr2_15495946_1   1501 CGAAGAATGGAGTAAGGACAGGAATAAA---TTCACAAGAGAGG-TA--- 1543
                         i?  i     ivv     ivv     i ---   v v i   i -  ---
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_15495946_1   1544 --ATGCCTATCTAACATATCGGAAAATGTTAAAACTCTTAATTAGA 1587
                         --   v i viv i  i  vii  i   i v  vv  v????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (141 / 115)
Gap_init rate = 0.04 (39 / 908), avg. gap size = 2.62 (102 / 39)  


3306 26.65 0.55 0.55  chr2_15529723_15536138     5017  5924 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_15529723_1   5017 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5066
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_15529723_1   5067 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5116
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_15529723_1   5117 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5164
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_15529723_1   5165 TATGGAACCAAAAAAGAGCCTGCAACA-CCAAGTCAATCTTAAGCCAAAA 5213
                                viiv  ii  v  v -  i -    iv       i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAG-AATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_15529723_1   5214 GAACAGAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGG 5263
                              i  i      vv   i   v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_15529723_1   5264 CTACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATATAGAT 5313
                                  i   i    ii     i   i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_15529723_1   5314 CAATGGAACAGAAC--ACAGCCCTCAGAAATAACGTCGCATATCTACAAC 5361
                                 i    i-- v  i  --        vvi ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_15529723_1   5362 TATCTGATCTTTGATAAGCCTGAGAACAACAAGCAATGGGGAAAGGATTC 5411
                         i vi    i  i  i   vv  vv  v v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_15529723_1   5412 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGC 5461
                         i  v  i  i              v      v  ?   i   i ii iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_15529723_1   5462 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5511
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_15529723_1   5512 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAACCCCTAGAAGAAAA 5561
                           i ?    i    i  v   v       i       i i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_15529723_1   5562 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGATTTCATGTCTA 5611
                          v    ?i v viv   iv   v v  vv i     v i    v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_15529723_1   5612 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGGATCTA 5661
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_15529723_1   5662 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5711
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_15529723_1   5712 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5761
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_15529723_1   5762 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5811
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_15529723_1   5812 AAAACAAACAATCCTGTCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5861
                           i     i  i  vi i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_15529723_1   5862 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5911
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_15529723_1   5912 CATCACTGGCCAT 5924
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 388 21.84 0.00 0.00  chr2_15942737_15946257.rev     1842  1928 (1593)    L1M4_orf2#LINE/L1       19   105 (803)  

  chr2_15942737_1   1842 TCATGAATCAAAAGAATTAATATTGTTAAAATGACTATCTTGCCCAAAGC 1891
                              i  iii    v             i   i v  vi v      vi
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chr2_15942737_1   1892 AATCTACAGAGTCAATGAAATCACTATCAAAATACCA 1928
                         i         v    i v    v          v   
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.00 (0 / 0)  

2838 23.98 4.08 0.51  chr2_15942737_15946257.rev     2246  3029 (492)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr2_15942737_1   2246 AAAATTTCA------TTCTTCACAGAGTTAGAGAAAACAGTTCTGAAATT 2289
                              ii  ------  i  ii    iv v  v  iviii i  i     
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_15942737_1   2290 GATTTGGAACCAAAAAAGAGCCCGAATAGCCTAAGCAATCCCGAGTAAAA 2339
                         v  v     viiv  ii  v  v        v  i     ii  iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_15942737_1   2340 AGAACAAAGTTGGAGGCATCACATTACCTGACTTCAAAATATGTTATATG 2389
                                         vv     i v  ii i       iv ii  i vi
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_15942737_1   2390 GCTGTAGTAACCAAAACAGCATGGTATTGGTATAAAAATAGACACATAGA 2439
                            ii     i   i    ii     i   i    ii       i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_15942737_1   2440 CCACTGGAATAGAATAAAGAACCCGGAAATAAAGCCACATGTTTACAGGC 2489
                         i  v           vi   ii  i        v   i ii    ii v 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_15942737_1   2490 AACTGATCTTCAACAAAGCCAACAAGAACTTACACTGGGGAAAGGACACT 2539
                           i    i   i    i viiv     v v v  v         i i v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_15942737_1   2540 CTCTTCAATAAATGGTGCTGAGAAAATTTGATAGCCAAATGCAAAAGAAT 2589
                           i     i           i  v  i v    ?   v            
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_15942737_1   2590 GAAACTGAACCCCCATCTCTCAGCATATACAAAAATCAACTCAAAATGTA 2639
                            ii  i     i i   v  v             i           v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_15942737_1   2640 CTGAAGACTTAAA-------------ACTACAAAAATACTGGAAGAAAAC 2676
                         iii?    i    -------------    i    v vi i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_15942737_1   2677 CTAGGAAAAACTATTCTGGAC-----ATTAGGCAAAGAA--CTTATGACT 2719
                         v    ?iv  v v   vv   -----i        v iv--    -  - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GA-T 594

  chr2_15942737_1   2720 AAGACCTCAAAAGCACAAGCAACAAAAACAAAAATGACCAAATTGCACTA 2769
                          v   vi                    iv      iivi      v   v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_15942737_1   2770 TATTAAACTAAAAAGCTTCTGC-CAGCAAAAGAAATAACCAACAGAGTGA 2818
                         i  i   v v    i   i  i- vv    i  v iv i   v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_15942737_1   2819 AGAGACAACCTGTTGAATGGGAGAAAATATTTGCAAACTATTCATCTGAC 2868
                          i        iiiv                       ii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_15942737_1   2869 AAGAGACTAATATCCAGAATATACAAGGAAC-CAAGCAACTCAACAG-AA 2916
                            i    vi             i  i    - vvi        i i-  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_15942737_1   2917 AAAAAAAAAT--CCCA-TTTAAAAATGGGCAAAGGACAGGATTAGACATT 2963
                            i v    --    -  ?                ivv  v        
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_15942737_1   2964 TCTCAAAAGAAGACATATAAAAATGGCCAACAATTATGTGAAAAAATGCT 3013
                             v        --    v          i  vi ii      i     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGA--TATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_15942737_1   3014 CAACATCACTAATCAT 3029
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (115 / 69)
Gap_init rate = 0.01 (12 / 812), avg. gap size = 3.00 (36 / 12)  


 410 26.02 3.25 0.81  chr2_15993295_15999572     4273  4395 (1883)    L1M4_orf2#LINE/L1        1   126 (782)  

  chr2_15993295_1   4273 TGGAGAGAAATAT-ATATTCATGGATTGAATGACCCAATATCCTTAAGAG 4321
                             i   v  vi-  i           i v   ii     iv      v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_15993295_1   4322 GTCAGTTCTCACTAAATTGTTC--CAAACTCAACACACTTTCAAT-AAAA 4368
                          v  i v   v i      v  --  i i     i  v ii v  -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_15993295_1   4369 TTCTAGCAAGCTTCTTTGGTAGAAATT 4395
                          i i   v-  i i   v i       
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATT 126

Transitions / transversions = 1.46 (19 / 13)
Gap_init rate = 0.03 (4 / 126), avg. gap size = 1.25 (5 / 4)  

1635 25.88 4.25 2.22  chr2_15993295_15999572     4719  5259 (1019)    L1M4_orf2#LINE/L1      122   673 (235)  

  chr2_15993295_1   4719 AAATTGACATGTTAATTCTAAAATTAATATGAAAATTTAAAA-ATTTAAA 4767
                                  v i i  i        v     i    vi  ii- iii i 
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_15993295_1   4768 ATA-CCAAAGTAATTTTGAAAAATAA---CAAAGCTGGAA-ACTGGTCTT 4812
                            -     ii   i        v  ---     i    i-   viivi 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_15993295_1   4813 GCCTGACTTTGAGACTTGT---AAAGCTATAAAAATTAAGACAGTGTGAT 4859
                         v  ii i  ii i    ii---       i iv   i           i 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_15993295_1   4860 AATAATCTCAAACTATACAAATAGTTAAATATGACAGAA---------CA 4900
                          v iiiv v iiv  v   v    v v   ivi i    ---------  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_15993295_1   4901 GG--TAGACCCACATATATATAGATAGCTGATTTTCAAGAGACATGCAAA 4948
                          i--  i     i i  v   i vi ii        i v iivi   v  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_15993295_1   4949 GTTAATTCA-TGGGCAAAAAGATAGTCTTTTCAATAAATGGTGTTAAAAT 4997
                          viv     -    v   i -             i        i iii i
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_15993295_1   4998 AA-TGGTTATTCATATGCAAAAAAAATGAACATTGATCCATACATCACAC 5046
                           -   v  ?i  i        i  -    vv v  i  v   v      
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACAC 469

  chr2_15993295_1   5047 CATACACAAAATTTAACTCAAAATGTATTGGAGACTTAAATGTAAAACCT 5096
                             i      v             v  ii?    i         i v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_15993295_1   5097 AGAACTACAAAAAACTTAGAAGAAAAAAATAGAAAAAGATCTTTGTGGTC 5146
                          i     i    vv            v -   i?iv i     i   ii 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACA-TAGGNGTAAATCTTCGTGACC 568

  chr2_15993295_1   5147 TTGAGTTAAGCAACAATCTCTTAGATACAATACCAAAAACACAATACATG 5196
                            i    i    iii i         ii i       i     ------
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA------ 612

  chr2_15993295_1   5197 AGGGGAAAAAAAACAAAAACAGATAAAT-GGACTTCTTCAATATTAAGAA 5245
                         --- v  v    iv     i        -       v    v     i  
  L1M4_orf2#LINE/    613 ---GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_15993295_1   5246 CCTCTTCTCTTCAA 5259
                          i i viv      
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAA 673

Transitions / transversions = 2.04 (92 / 45)
Gap_init rate = 0.03 (14 / 552), avg. gap size = 2.50 (35 / 14)  

 772 19.51 8.94 3.25  chr2_15993295_15999572     5543  5788 (490)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr2_15993295_1   5543 AAAA--AAAAATTTCTGTTCTGCTCTTCAAAAT-CACTGTTAC------- 5582
                             --     i  i   ---   --     iv-    i i v-------
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGT---GCT--TCAAAGGACACTATCAAGAAAGTG 693

  chr2_15993295_1   5583 AAAATACAAGCCACAGGCTAGGGGAGAATATTTGCAAAGCACATATGTGA 5632
                             v    v      iv i  i  i            v  i    v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_15993295_1   5633 TAAAGCACTTGTATTCGCAATATACACAGAATTCTCAAAACTGGATAATA 5682
                            i v        i iv      i v    i   i v    vi      
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_15993295_1   5683 AGAAAACCAACAACTTCACAAT---AAAATGAGCAAAAGATATGAACA-- 5727
                          i  i  v  i   i---    ---      i     i   v    i --
  L1M4_orf2#LINE/    794 AAAAGACAAATAACC---CAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_15993295_1   5728 -AT------AAAGAAGATATATGGATGGCAAATATGCACATGAAAATAAG 5770
                         -  ------            iii     v    v           v v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_15993295_1   5771 CTCAGCATTGTTTGTCAT 5788
                             i   ii????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (30 / 18)
Gap_init rate = 0.03 (9 / 260), avg. gap size = 3.33 (30 / 9)  


1812 25.47 5.16 3.59  chr2_16411554_16414279     1027  1666 (1060)    L1M4_orf2#LINE/L1        1   650 (258)  

  chr2_16411554_1   1027 TGGAGAAATATACTATGTTCATGGATCAGAGGAAGAATAAATAGTGTTAT 1076
                             i i    v i            i---      v v    v     v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT---GGAAGACTTAATATTGTTAA 47

  chr2_16411554_1   1077 AATGTAAATTATGCTGAAATTTGTCTATAGATACAATACAATTGAAATAA 1126
                         i   vv   vv v iv     vi    i    v   ii    ivvv  v 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_16411554_1   1127 AAATTCTAGTAGGCTTTTCT-TAAAAATAGATTTTGACAAGCTGATTCTA 1175
                             i i  iv v     i -i i    ------            i   
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAAT------TGACAAGCTGATCCTA 141

  chr2_16411554_1   1176 AAATTTATATAAAAATGTGAATGACCTAGCATAGACAAAACAATGTTTAA 1225
                              i    ii     ii iv    i  v    v         v  v  
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_16411554_1   1226 AAAAAAGAATAAAGTTAAAG--TTTATACTGCCTGATTTTGTGACTTAAT 1273
                            i     i      ii  --i i i   v  ii    iivi     v 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_16411554_1   1274 ATAAAGTTACAGTAATCATGATATCACGGTATCAGTA-AAGGTTATATAT 1322
                          i    i           v  i viii    iii i -    v  v i  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_16411554_1   1323 ACAGATCA-CAAGACAGGATAGAGAGTTCTGAAATAAACCCACACATATA 1371
                          i      -iiii i  i  v      i v            i    v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_16411554_1   1372 TGGCCAATTAATTTGTGATAAAGATTTCAA-----TTCAATAGAGAGAGG 1416
                            i     i    vi  i  i i vi   -----      i i  i  i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_16411554_1   1417 GGAATCTTTTCCACAAATGATGGTGAAACAACTCTGACAGGAA---ACAA 1463
                         iv i       v       i  v  ii      v-  i ?vv ---i   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTG-GATAKCCACATGCAA 440

  chr2_16411554_1   1464 ATGAATAAACAAACATCAG-CTCTTACCCC-CACTGTACACAAAAAATTA 1511
                          v    i  -----i ii - i i    i -   ii  i       -   
  L1M4_orf2#LINE/    441 AAGAATGAA-----GTTGGACCCCTACCTCACACCATATACAAAAA-TTA 484

  chr2_16411554_1   1512 ATT-AAAGTGGATGATTGATCTAAATGAAAGAGCTACAACTA--AAAGTT 1558
                          i -   i     v ?v  i       v        v     --   v i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_16411554_1   1559 TT-GATGTGAAACATAATAAAAAATCTTTGTGACTATGGGATCTAAGAAG 1607
                           -  v -i       iv?iv       i     iv    v ------  
  L1M4_orf2#LINE/    535 TTAGAAG-AAAACATAGGNGTAAATCTTCGTGACCTTGGGTT------AG 577

  chr2_16411554_1   1608 ACAAATATTTTTTAGAT----CACTAAAAGTACAA--AACATAAAAA--- 1648
                         i   vvi   i      ----   i     i    --    v  i  ---
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_16411554_1   1649 -----TAAATTAGATTTCGCCAA 1666
                         -----      i  i   ii   
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAA 650

Transitions / transversions = 1.86 (104 / 56)
Gap_init rate = 0.03 (21 / 650), avg. gap size = 2.67 (56 / 21)  

 459 19.03 14.98 6.48  chr2_16411554_16414279     1988  2234 (492)    L1M4_orf2#LINE/L1      641   908 (0)  

  chr2_16411554_1   1988 ATTTTATCAACATTTAAAAGAAAAGCACAATGTTTT---CTTCAAAAGAC 2034
                          i  i     v   ------    i ------    ---       i   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATT------AAAAAC------TTTTGTGCTTCAAAGGAC 678

  chr2_16411554_1   2035 AC-----AGCTAAATTAAAACATGAACCACAGA------GAAAATATTTG 2073
                           -----  v-  i v    v ii v       ------           
  L1M4_orf2#LINE/    679 ACTATCAAGA-AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_16411554_1   2074 CAAGCTCCT-T-TTTGACAAAAGA-----ACGCAGAATGTATGAAGAACT 2116
                            i-  v - - i   i  ii  ----- iv      i   i       
  L1M4_orf2#LINE/    728 CAAA-TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_16411554_1   2117 ATTAGAACTTCAA----AACAAGATAA---------TTTAAAAATGGACA 2153
                         v   v    -   ----  v    i  ---------  ?        i  
  L1M4_orf2#LINE/    777 CTTACAACT-CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_16411554_1   2154 ACTGGCTTGAAAAGACACTTCACAAAAGAAAAGACACTTCATG---AAAA 2200
                          vv ii     v     i   v v      i v i  v-v   ---  v 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA-AATGGCCAATA 874

  chr2_16411554_1   2201 AGCACATGGCAAAATGTTCAACCTCATTAGTTAC 2234
                                 iv  i   i     v   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (25 / 21)
Gap_init rate = 0.06 (15 / 268), avg. gap size = 3.53 (53 / 15)  


3106 24.97 4.81 0.80  chr2_16444254_16447673     2058  2930 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_16444254_1   2058 TAAAAAGACATCCCCTGCTCATGTATCAGAAGAATTAATATTATTAAAAT 2107
                          ii     i     v  i     v  ii     v        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_16444254_1   2108 GGCCATACTGCCCGAAGCAATCTACAGATTCAGTGGAATTCTTATCAAAA 2157
                            v     v   i  vii             ii v   i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_16444254_1   2158 TACCAA-TGTCATTTTTTACATGAAATAGAAAAAATAATCCCAAAATAAG 2206
                          v   i-  i -      i  -     v  v  iv i    i     vvi
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCA-GAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_16444254_1   2207 TATGGAATCAAAAAAGTGCTCA-AATAGCCAAAGCAATTCTGAACAAGAG 2255
                                viiv  ii -i i  -          i    ii    v    -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGA- 196

  chr2_16444254_1   2256 AGAACAAAGCTGGAGGCATCACACTATCCAA------AATATACTACAAG 2299
                                  i      vv       vi    ------  iv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_16444254_1   2300 GC----------AAAACAGAATGGTATTGGTATGAAAACAGACACACAGA 2339
                           ----------  i    vi     i   i  i ii i     i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_16444254_1   2340 TCAATGGA-CAGAATAGAGAATCTAGAAATAATTCCATGCATCTATAGCT 2388
                                 -i     v    i  i        vi    i   i   i ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_16444254_1   2389 GACTGCTTTTTGATAAAGGTGTCAAGAACATATACTGGGGTAAAGACACA 2438
                         i i  v    i  i  i    i     v   vi v     v  ii i vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_16444254_1   2439 CTCTTCAATAA-TAGCTCTGGAAAAATTGAATGTCCGTATGCAGAAGAAT 2487
                           i     i  - i iv    i v  i  i  i?  ii     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_16444254_1   2488 GAGACTGGATCCCTATCTCTCACCATAAACAAAAATCAACTAAAGATGGA 2537
                           iii    i     i   v       v        i    v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_16444254_1   2538 TTAAAGACTTA---GTAAGATCTGAAACTATAAAACTACTAGAAGAGAAC 2584
                          i ?    i  ---      v  i             vi       i   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_16444254_1   2585 ATAGAG--AAAACAATTCAGGACAATGGTTTAGACAAAGATTTTATGACT 2632
                             i?--   v --   iv   vv   v    i   v i   iv iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_16444254_1   2633 AAGACCTTGAAAGCACAGACAATGAAAACAAAAATAGGCAAATGGAAGTC 2682
                          v   viii        ii   ii   iv        ii    v i v i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_16444254_1   2683 TGTTAAA-TTAGAAGTCTTCTTTGCAACAAAGAAAACAATCAGTAGAATG 2731
                         ii i   -   i  i-   i v   vv     i v  v    iv i i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_16444254_1   2732 ATGAAA-AACTTGTTGAATGGGAGAAAATATCTGCAAATCATTCACCTAA 2780
                          vi i -   iiiiv                i          vi i  i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_16444254_1   2781 CAAGAGACTAATATCCAGAATA---------------CCACTCAATAGTA 2815
                         i   i    vi           --------------- v        i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_16444254_1   2816 TAGAAACAAGTAATTCCATTAAAAAGTGGGCAAAGGACATTAATAGACAT 2865
                         v i i    i   ii v   ?    i           iv v         
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_16444254_1   2866 TTTTCAAAAGAAGACATACAAATGGCTAACATGTATATGAAATAATTCTC 2915
                           i  v        i           i  i v i i      vi  v   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_16444254_1   2916 AACATAATTATCAGG 2930
                              v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (144 / 70)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.88 (49 / 17)  


2707 25.05 2.16 4.10  chr2_16643843_16645774      515  1440 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_16643843_1    515 TGGAGAGATTTACTACTATTTTTTTATGGATCAGAAAACACAATATGGTT 564
                             i    v v i ----- v  i      ii   i  vi     v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCA-----TGTTCATGGATTGGAAGACTTAATATTGTT 45

  chr2_16643843_1    565 TATATGTCTATTTTCCCCAAATTAATATATATATATTCTAAGGATCCTCA 614
                         v v   v v  vi          i  v  i v  --  v v v vi i v
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGAT--TCAACGCAATCCCT 93

  chr2_16643843_1    615 ATAAAAGTCTCAACGGGATAATTTTTTGGTAGGAATTGACAAGGTAATTC 664
                           v   i  i  i ---- ivi     v i  i          v i  i 
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGC----TGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_16643843_1    665 TAAAATTCATAAAGGAATTGAGAGCATCCAGAACAGCCAAAATTAATTTG 714
                                    vi i   vv ii v i      i        iv vi   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_16643843_1    715 AAAATGAAAAA---AATTGGAGGATTTCCATTATCTGAGTTCAAGATTTA 761
                             v   i  --- i        i iv  i vi ii v     i i   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_16643843_1    762 TTATCAAGCTACATTAATCAAGACAGTGTAGTATTTACGCTAAGTTATTA 811
                         i  iv        v               i   i vi i-    v-  --
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGG-AT-- 285

  chr2_16643843_1    812 AGTTATACAGATCAATGGAACTAACT--AGGATCTGGAATTAGATCCACA 859
                           vi   i            ivi v --  ii  ii   v  i i   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_16643843_1    860 CATATACAGTCAATTTATATTTGACAAAGATGCAAAGGCCATTCAGTGGA 909
                            v  ii       v  v  i     i i   v   i       i   i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_16643843_1    910 GAAAGGACAGTCTT--CAGCAG-TTACATAAGAACTACTGGA-ATCCTTA 955
                              i i      --  i  i- viiiivi i  v      - ?  vi 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_16643843_1    956 TGCAAA-TAATGAAATTCAAACCATCCCTAACACCATAGACACAAATAGA 1004
                               -v      i  vi v  v v   v        v   v    ---
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT--- 482

  chr2_16643843_1   1005 CAAACACTAACACAAA-TTGATTATGGACCTAAATGTAAAACCTGAAACG 1053
                         -------    v    - v   i ?i             i v  i    v
  L1M4_orf2#LINE/    483 -------TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_16643843_1   1054 TTAAATCTTTTAGAAGAAAACTTAGGAGATTATGTTTGTGACATTGGGTT 1103
                         v    v  i            v    ? vvv  v  i     v       
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_16643843_1   1104 AGACAG-AATTTTTTAGATACAACTCCAAAAGT----GCAATAGAAGAGA 1148
                           i  i-ii   i       ii  v       i----    i i    i 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_16643843_1   1149 AAAAGAGTTGATAAATTGGACTTCATCAGAATCAACAAGTACTGATTTTC 1198
                            ---- v                   i   i  v  v vi  vvi   
  L1M4_orf2#LINE/    626 AAA----TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_16643843_1   1199 TAAAGCTACTGTAAAGATAATGAAATGACAACC-ACAGACTATGAGAAAA 1247
                         v  i vi   i v    v i     v       -     v iv       
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_16643843_1   1248 TATTTGAAAATCTTGTATCTGATAAAGGACTTGTATTCATTACACATAAA 1297
                               v     v i          i          i  vv i i     
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_16643843_1   1298 TAAGTCTCAAAACCCAATAATAAGAAAACAATGAAGACAATAACAAAA-- 1345
                         v  v   i v   i         i  i    vv  vv    v?v    --
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_16643843_1   1346 -GCAGAAGATACGAACAGACTCTTTACCAAACAAACAAACAAGACATATG 1394
                         -   i i   vi   i    vi  iv     v  --------  i   ii
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAA--------GATATACA 863

  chr2_16643843_1   1395 AATAGCAAATAAAGTACATGAATATACTCTAAACACCATTAGTCTT 1440
                            i  v     - i       v v iv  v    i  ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAA-GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (125 / 103)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.76 (58 / 21)  


1832 27.15 8.35 3.13  chr2_16682798_16684750      606  1467 (486)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_16682798_1    606 GGAAAGATGTGCTATATTCACAGATAGGAAAAATCAATATTACACACATG 655
                                 i v i  i    ii   v    i v i      iivv v   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_16682798_1    656 GCAATTCTCCCCTAATTGTTCCATAGATTTGATGCAATTATAATCAATAT 705
                              v      v     v  i i     ii i     iviv     v  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_16682798_1    706 CCCAGTAGAATTTTTTATTGTAGAAACTAAGGA-CTAATTAGAAAATTTA 754
                              iv --ii    -   i     i i vi -  i  ivv      i 
  L1M4_orf2#LINE/    102 CCCAGCTG--CCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_16682798_1    755 CTTAGAAAAGTAAAGGAGTTAGAATAGCCAAAACAGTCTTCCAAAAGA-- 802
                         iv i    v i  i   vii               i    vv      --
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_16682798_1    803 ------GTTAAAAGACTTACTCTTTCTTGACTCTAAGACCTATT-----G 841
                         ------   ii i    i  v   i i-i i ii  i  i  i ----- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCC-AATTTCAAAACTTACTACAAAG 247

  chr2_16682798_1    842 TTT--GTTAT-------ATTTGGTATTAATTGGTGAGAAGGTAGATCAAT 882
                         i v--  v  -------i v     i ----  iivi i i    ivv  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACT----GGCATAAGGATAGACATAT 293

  chr2_16682798_1    883 AGAGTAATCAGAGAAAACAGAGAGTCCTGAAGTAGCCCATATCACACATA 932
                            vi   vii v i  iv        v   i  iv  ----  i    -
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC----CATACAT- 338

  chr2_16682798_1    933 TTACAATTAGCAAATTT---ACAAAA-TG----GAC-ATT--------AA 965
                            iii i iivi    ---    ii-  ----   -   --------  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_16682798_1    966 AG--CAATC----CACC---TG-TGCTACTACAATATTATGGAC-----T 1000
                           --i i  ----  v ---  -    ivv    i----    i-----i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC----TGGATAKCCAC 434

  chr2_16682798_1   1001 ATGAAAAAATAATAAACCTA-ATACCTTTCTCACAACATATGCAAAAATT 1049
                            v    i-   i  vi i- iv   vi      v     i        
  L1M4_orf2#LINE/    435 ATGCAAAAG-AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_16682798_1   1050 AGTTGAAGATCAGTCACTGATCTAAATGTAA-AGCTTAAAACAATACAGC 1098
                          ii v  i  vii   ?v  i          -    -     v   v i 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAAC 532

  chr2_16682798_1   1099 TTTCAGAAGAAAACAAAGCAAAATATCTTTGTGACCTTGGTATAGGTCAT 1148
                          i i           v  v?iv v     i          vv    iv  
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_16682798_1   1149 AATTTCTTAGA----ATACAGAAAGTGCTTAGCA-TAAAATTTAAAAATT 1193
                         ii         ---- i  vi    ii v-    -i    v--     v 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACA-AGCAACAAAAG--AAAAAAT 629

  chr2_16682798_1   1194 A--TAAACTGTACTTCATCAAAATTTGAAACTTCCATTCATGAAAAGATA 1241
                          --    i  v              vi      iii v v v   i  i 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_16682798_1   1242 TCAATAAGAAAATAAGTAGGTAAGCCTAC----TAGGTAAAAATATTTGC 1287
                         ii vi      i i iv  ii  -  i  ---- i  vi           
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAA-CCCACAGAATGGGAGAAAATATTTGC 728

  chr2_16682798_1   1288 AAG--ATATAGCTTACAAAACACATGTATACAAAGTACAATAAAGAATTC 1335
                           i--     v  v i  iiv  v     v  i i  i -       i  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATA-TAAAGAACTC 777

  chr2_16682798_1   1336 CTACAATTTACCAATACAAAGACGAACAACCTAATT-AAAACTAGGCAAA 1384
                         i     i i vi    v      i  i    i    -    v i      
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_16682798_1   1385 AGACATGACAAGATATTT-TCTTAAATAGATAAGCAACTATACAATAAGC 1433
                         i  iv   vv   i    -  iv  iv     vi   v ivv        
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_16682798_1   1434 ACATGAAAAAGAGCTCAACACTGTCAGTTATTAT 1467
                                  iiv        ---   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACA---TCAZZZZZZZZ 908

Transitions / transversions = 1.73 (147 / 85)
Gap_init rate = 0.04 (38 / 907), avg. gap size = 2.61 (99 / 38)  


3275 27.09 0.44 0.44  chr2_16696875_16703154.rev     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_16696875_1   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_16696875_1   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_16696875_1   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_16696875_1   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_16696875_1   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_16696875_1   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_16696875_1   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_16696875_1   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_16696875_1   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_16696875_1   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_16696875_1   5377 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_16696875_1   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_16696875_1   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_16696875_1   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_16696875_1   5577 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_16696875_1   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_16696875_1   5677 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_16696875_1   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_16696875_1   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 476 20.16 0.00 0.00  chr2_16798092_16801491.rev      218   346 (3054)  C L1M4_orf2#LINE/L1   (0)   908   780  

C chr2_16798092_1    346 ACAAATGAACAAGAAAAAAACAAATAATCCCATCAAAAAGTAGGGAAAAG 297
                             v v  i  v     i        i  v  i?    i i  v   i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

C chr2_16798092_1    296 ACATAAACAGACATTTCTCAAAAGAAGATATGCAAATGGCAAAATAACAG 247
                          iv i  i           v           i        v  vv i  v
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

C chr2_16798092_1    246 ATGAAAAAATGCTCAATATCACTAATCAT 218
                                i        i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (14 / 11)
Gap_init rate = 0.00 (0 / 129), avg. gap size = 0.00 (0 / 0)  

 934 28.16 2.53 0.72  chr2_16798092_16801491.rev     1239  1515 (1885)    L1M4_orf2#LINE/L1        1   282 (626)  

  chr2_16798092_1   1239 TGGAAATACATCCCATACTCATGAATTTGAAGAATCGATATTGCGAAAAT 1288
                               v i       ii     i   v     v ii      iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_16798092_1   1289 GACCATATTCCCCAAAGCAATCTATAGATTCAAAGTAATTCCTATCAAAA 1338
                          i v   i        vii     i        v i   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_16798092_1   1339 TACCAACATCATTTTTCACACAGAAA-----AAAATG--TCTAAAATTCA 1381
                          v   i vv v     ii  --    -----  iv  --i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA--GAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_16798092_1   1382 TATTGAACCAAAAAAGAGTCCAAATAGCCAAAGCAATCCTAAGTGAAAAG 1431
                            v   viiv  ii  vi vi          i     i i ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_16798092_1   1432 GTTAAATCTAGAGGCATGACATTACTTGACTTCAAATTATACTACAAGAC 1481
                         ivi   vi i    vv v   i v iii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_16798092_1   1482 TATAGTAACCAAAACAGCATGGTACTTGTATTAG 1515
                           i     i   i    ii       v i  v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

Transitions / transversions = 1.79 (50 / 28)
Gap_init rate = 0.01 (3 / 282), avg. gap size = 3.00 (9 / 3)  

 962 22.87 0.28 12.67  chr2_16798092_16801491.rev     1864  2226 (1174)    L1M4_orf2#LINE/L1      270   587 (321)  

  chr2_16798092_1   1864 GTACTGGGATAAAAGTAGATACATGGATCAATGGAACAGAATATAGAATC 1913
                                v    iii    i i  i           i     vv   i  
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_16798092_1   1914 TAGAAATAACGCATCTAGAAATAATGTATTCTAATCTAGAAATAGAGATT 1963
                         i        --- i i ------- ii   i----------  i -----
  L1M4_orf2#LINE/    320 CAGAAATAA---ACCCA-------TACATTT----------ATGG----- 344

  chr2_16798092_1   1964 CTAAAAATAAAGCCCAACCAACTGATCTTTGACAAAGCATACAAAAAC-A 2012
                         -----------------i   i    i  i     i -i i v  i  - 
  L1M4_orf2#LINE/    345 -----------------TCAATTGATTTTCGACAAGG-GTGCCAAGACCA 376

  chr2_16798092_1   2013 TAAATTGGGGTAAAGGATACCATTTATTCAATAAATGGTGTTGGGAAAAC 2062
                          vv v     -    i   --i i v     i        i     v   
  L1M4_orf2#LINE/    377 TTCAATGGGG-AAAGAATA--GTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_16798092_1   2063 TGAATAGCCACATGTAGAACAATGAAACTAGATCTCTATTTTTCACAACG 2112
                           i   ?       i i  v      ii i  i i   ii iv   v ii
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_16798092_1   2113 TACAAAAATCAACTCAAGATGGATTAAAGACTTAAATCTAAGAACTGAAA 2162
                                  i       i      i ?    i     v     i  i   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_16798092_1   2163 CCACAAAAATTCTAGAAGAAAACCTAGGAAAAACTCTTCTCGACACTGGA 2212
                          i i    v ii           v    ?iv  v     vi   vi   i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_16798092_1   2213 AGAGCAAATAATTT 2226
                         vv  vv   ii   
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTT 587

Transitions / transversions = 2.48 (57 / 23)
Gap_init rate = 0.03 (8 / 318), avg. gap size = 5.88 (47 / 8)  

1047 23.68 1.32 0.33  chr2_16798092_16801491.rev     2605  2908 (492)    L1M4_orf2#LINE/L1      602   908 (0)  

  chr2_16798092_1   2605 CAAAAGCAACAAA-AACAAAAACAAAAATAAATAAATGGAACCTAATTAA 2653
                                 -   i-       iv       i      v i  i v  i  
  L1M4_orf2#LINE/    602 CAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_16798092_1   2654 ACTAAAAATCTTCTGCAATGCAAAAGAAATAATCATCAGAGTAATCGGAC 2703
                          v v    v   i  iiv v    i  v iv    vv i   i vvi   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_16798092_1   2704 AACTCACAGAATGGGAGAAAATGTTTGCAAACTATGCATCTGACAAAGGA 2753
                            i                  i        ii  ii      i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_16798092_1   2754 CTAATATCCAGAATCTACAGGGAGCCC--AAAACAGTATAAGAAAGA-AC 2800
                           vi          v  i ii  i i -- v   vvv    v   i -  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_16798092_1   2801 AAATAAACCCATCAAAAAGTGAGCAAATGACATGAGCTGGCACTTCTCAA 2850
                               v  v  i?    i  i     v  iv   iiv i  i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_16798092_1   2851 AAGAAGATATACAGATGGCCAACAAGCATATGAAAAAATATTCAACGTCA 2900
                                      i        i     i       i  ii     i   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_16798092_1   2901 TTAATCAT 2908
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.63 (44 / 27)
Gap_init rate = 0.01 (4 / 307), avg. gap size = 1.25 (5 / 4)  


 272 16.42 5.97 0.00  chr2_17119402_17121810.rev      652   718 (1691)    L1M4_orf2#LINE/L1        1    71 (837)  

  chr2_17119402_1    652 TGTAAAGACA--CCATGGTCATGGATTTCA-GACATAATGTTTTTAAGAA 698
                           v     i --     v         vv -   v    i  v      v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_17119402_1    699 GGCAATA-TGCCCGAATTGAT 718
                                - v   i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT 71

Transitions / transversions = 0.38 (3 / 8)
Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.33 (4 / 3)  

3193 21.72 4.25 1.94  chr2_17119402_17121810.rev     1096  1919 (490)    L1M4_orf2#LINE/L1       66   908 (0)  

  chr2_17119402_1   1096 ATTAATCTTTAGATTCAATGCAATCTCTATCAAAACTCTGAATGTCTTTT 1145
                            i    vi        i      i         ii iiiv  i     
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_17119402_1   1146 TCTTTGGTGAAATCAACAAGCTTGCTTTGAAATTAATACAGAGAAGCAAA 1195
                          ---  vv     ii       viiii i     v   ii  i v    i
  L1M4_orf2#LINE/    116 T---TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_17119402_1   1196 CAAACCAAAATAAGCAATACAGTCTTGAAAAAGAAG-------TTGTAGG 1238
                         vi v   i    iv   v   i              -------   v   
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_17119402_1   1239 ACTTACACTTCCTAATTTTCAGACTTGCTTGAAAGCTACAGTAATCAAG- 1287
                            i        i     iv i    i  vv                  -
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_17119402_1   1288 CAATGTGTTAATGGCATAAGAAAAGAGACATTGATCAATAGGATAGAATT 1337
                           i    v  v         i v   v i  v       i i        
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_17119402_1   1338 GAGGATTCAGAAATAAATACTTA-ACT-ATAGTCAATTGATTTTTGATAA 1385
                            ii i          iv v  - i -  i             i  i  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_17119402_1   1386 ATATGCCAAGATAATTCAGTAGGGAAACAATAGTCTCTTCAACAAATTGT 1435
                         ivi        iv     i i      v        i          v  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_17119402_1   1436 ACTTGGATAAATGTATATTCACATATAAAA--ATGAATTTGGGCTCCTGT 1483
                         i  v   i  v  v   ?i     ii    --     v    i i   ii
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_17119402_1   1484 CTTATATTGTATG--GACATTCTCTCTCCCTCTCCAAAA-AGATTGTAGA 1530
                           i i iii   i--i v   vv   ---------    -i   ii?   
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTC---------AAAATGGATCAWAGA 503

  chr2_17119402_1   1531 CCTCAATACAAGAAATAAAACTATAAA-TACCTAGTAGAAAATATAGAAG 1579
                            v   ii    iv            -iv i   v      i    i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_17119402_1   1580 TAAATGTTTATGAACTTGGGTTAGGCAAAATCTTCTTAGATACAACAACA 1629
                              v  ii   v              vivi          ii   v  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_17119402_1   1630 AAAGCATATGTGA-AAAAGAAAGCATAGATAA-TTGAACTCCATAAAAAT 1677
                               i v ii -        iv        -   i   i   v     
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_17119402_1   1678 TAAAAAGTTTTATTCGTAAAAGAACACTATGAATAAAGTGAAA-GATCAC 1726
                               v    i v v v    i       v  v         -  iv  
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_17119402_1   1727 TCACAGAATAGAAAATAGTAGTTGCAAA--------------AGGG-CTT 1761
                         i        i i i v i  v       --------------    -   
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_17119402_1   1762 GTACCTAGAATCCATAAGGAACTCTTACTATTATGCAGTAATAAGAAGAC 1811
                            i i     vi    i          v i ---  i      i     
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAAAAAGAC 800

  chr2_17119402_1   1812 AAATTACCCAATT-AAAAATGAGCAAGGGACCTGAATAGAAGTTTCTGTA 1860
                             v        -       i    i   ii        vi     vi 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_17119402_1   1861 AAGAAAAACATACAAATTGTGAATAAGCACTTGAAAAGATGTTCAACATT 1910
                              i -i        v iv         v          i       i
  L1M4_orf2#LINE/    851 AAGAAGA-TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_17119402_1   1911 GTTAGTCAT 1919
                         i????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.84 (114 / 62)
Gap_init rate = 0.02 (18 / 843), avg. gap size = 2.83 (51 / 18)  


2647 28.25 2.47 0.67  chr2_17125371_17127279.rev      526  1417 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_17125371_1    526 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATT---AAAAT 572
                               i i  i     i        v      v i      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_17125371_1    573 AGCCATGCTGTCCAAAGCAACTTACAAATTAAATGCTATTTCTATCAAAC 622
                         i  v  i  vi     vii ii    i   v  i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_17125371_1    623 TGTCAATGACATTCTCCACAGAACTAGAAAAAAACT-ATTTTAAAATTCA 671
                          vi  iivi v  i iii     v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_17125371_1    672 TAGAGAACTTAAAAAGA-------TAGCCAAGGGAATCCTAAGCAAAAAG 714
                           vi   v vv  ii  -------       iiv    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_17125371_1    715 AACAGAGCTCGTAGCATCATATTACTCAACTCCAGACTATGCTACCAGTT 764
                             i  i v vi vv   i i v i   i i  i viv i    v ivi
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_17125371_1    765 TACAGTAACTAAAACAGCATGGCACTGTCACAAAAACAGACATATAGACC 814
                                 ii  i    ii   i    v  i  ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_17125371_1    815 AATGGAACAGAATAGAGAGCCCAGAAATAATGCCACACGCATATAACCAT 864
                                i     v     i          vv   i  iiv   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_17125371_1    865 CTAATAACTGTCAAAATTGACAAAAACAAGCACTGGGGAAAGAA-ATTTC 913
                         i i  vvii v   iiv  v   i v  vv  v           - v ii
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_17125371_1    914 TTTTAATAAATGGCTCTGGGATAACTGGCTAGCCATCTGCAGAACATTGA 963
                            i  i      iv      i      v  ?   iv    i  v v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_17125371_1    964 AACTGGACTCCTTCCTTACACCCTACACAAAAATAAACTCAAGATGAATT 1013
                          ii     i   v   i     v  i        v       i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_17125371_1   1014 AAAGACTTAAATGTAAAACCTAAAACTATGAACACTCT-GGAAGATAACC 1062
                          ?    i         i v          i  -     -i     v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chr2_17125371_1   1063 T--GCAAAATACCATTATGTACCAAGGACCTGGCAAAGGTTTCAT-GATG 1109
                          -- ?iv  - i v ii  -   vv  iiiv     v      v -   -
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr2_17125371_1   1110 AAGACACCAAAAGCAATTGCAACAAAACCAAAAATTGACACACAGGACTT 1159
                          v             vvv         vv      v  i v iv      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_17125371_1   1160 -----AACTGAAGAGCTTCTGCATAGCAAAAGAAACTATCAACAGAGTAA 1204
                         -----  v v  i i   i  iiivv    i  v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_17125371_1   1205 ACAGACAACCGACAGAATGGGAGAAAATATTTGCAAACTGTGCCATTGGC 1254
                          v        v                          iii iivvi  ii
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_17125371_1   1255 AAAGGTCTGATATCCAGAACCTATAATAAACTTAAACAAATTTACAAGCA 1304
                           i  v  vi         iv     vi    ivv    v iv i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_17125371_1   1305 AAACACAAAGAAGCCTATTATAAACTGGGCAGAAGACATAAACAGATACT 1354
                            v     v  v  v   ?v   v      i i  iv i  i   i i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_17125371_1   1355 TTTCAAAAGAATACATACACAAGGCCAATAAGTCTGTAAAGA-ATGCTCA 1403
                          i  v      v i     v v          ivii i  i -       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_17125371_1   1404 ACACCACTAATCAT 1417
                            i  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (144 / 104)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  


 343 27.66 0.00 0.00  chr2_17197338_17200745.rev      168   261 (3147)    L1M4_orf2#LINE/L1      140   233 (675)  

  chr2_17197338_1    168 TAAAATTAATATTAAAATGCAAAGAAATGAAAATAGTCAAAACACTTTTG 217
                                v    vi        i i viv i     i       v i   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_17197338_1    218 GGAATGAAAAACAAAGTTGGAGAGTTAATACCACCTGACTTCAA 261
                         ii  v   i             iii v i  iv  ii i     
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

Transitions / transversions = 2.25 (18 / 8)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  

1784 22.81 7.13 10.09  chr2_17197338_17200745.rev     2016  2927 (481)    L1M4_orf2#LINE/L1       24   908 (0)  

  chr2_17197338_1   2016 GGTCAGAAGATTTAATATCGTTAAGATGCGAAGTA-TATCCAAATTTATC 2064
                          i ii     i       i         - v i  - vi       v   
  L1M4_orf2#LINE/     24 GATTGGAAGACTTAATATTGTTAAGATG-GCAATACTCCCCAAATTGATC 72

  chr2_17197338_1   2065 TATAGATTCAAAGTAATTGCAATAAAAATTCTAGTAGGCTTTT--ACTAG 2112
                           i        v i   iv v  v     i i  iv v     --i -  
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC-AG 121

  chr2_17197338_1   2113 AAATAGACAAGTTA----TAAAATTGATACTAAAATGCAAAGAAATTAAA 2158
                             v      i i----       v   ivi        i i vii i 
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_17197338_1   2159 ATAGAC----CACTTTTAGGAGTGAAAAACAAAGTTGGAGATTTTTTATT 2204
                             v ----  v i  iii iv   i             i---------
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG--------- 212

  chr2_17197338_1   2205 ATTATTATACTTTA-AGTTTTAGGGTACATGTGCACAACGTGCAGGTTTG 2253
                          i --i i    iv- i   -------------  v   --------  i
  L1M4_orf2#LINE/    213 ACT--CACACTTCCCAATTT-------------CAAAAC--------TTA 239

  chr2_17197338_1   2254 TTACACCTGACCCCACACCAAACTAT--TATCTAAGACCATGTGATACTG 2301
                         i    --------------  i   i--  vii     vi    i     
  L1M4_orf2#LINE/    240 CTACA--------------AAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_17197338_1   2302 ACAACAAGATAAA----TAGGTCAATGAAACAGAGTAGAAAGTCCAGAAT 2347
                         i  vv i    i ----   i      i  i   i v  i         v
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_17197338_1   2348 CAGACTCATTCTGATAGGTGCAGTAATATGAATGATTGAGTTTTAATCAA 2397
                         i i  i   ----------i  v --    ivii     v   ii iv i
  L1M4_orf2#LINE/    326 TAAACCCAT----------ACATT--TATGGTCAATTGATTTTCGACAAG 363

  chr2_17197338_1   2398 GTTGCAAAGACAATTCAATTGAATTTTGATTTTCTTTTCAATAATGAAAA 2447
                          v   v     v       v i-----------------------    i
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGG-----------------------GAAAG 390

  chr2_17197338_1   2448 AATGATTTTATTTTCAATAAATGGCAC--GGA-------ATATTGAGATG 2488
                            ii i  ---     i      ii --   -------   ?iv v   
  L1M4_orf2#LINE/    391 AATAGTCTT---TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_17197338_1   2489 CAAAA-AATAAACCTAAATTCATTCCTCTCATCATATA--AAAATTAATT 2535
                              -   i  vi ii ii v v    v  i      --        i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_17197338_1   2536 CAAAATGGATCATAGACCTAAATATAAAA-CT----TTATAAAACT---- 2576
                                     ?          i   i -  ----i         ----
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_17197338_1   2577 GAAAATAA-ATGGGAGAAAATATTTGTGAACTTGGGTAAGGCAAAGATTT 2625
                            i v  -  i  ? v    v  i    v       v      v i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_17197338_1   2626 CTT----------CCAAAAACATTACCTGTAAAAGAACAGATTGACAAAC 2665
                            ----------      i  iv v vii       v i  v  i   i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_17197338_1   2666 -GAACTTCATCAAAATCAAAACATAGTCTCCTT-AAAGGAAATTATTAAA 2713
                         - i             i    vv vv v v   -      v i   i  i
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_17197338_1   2714 AGATTGAAAAGACAATCTGTAGACTGAGATAAAATATATTTGCAAACTGT 2763
                          i v           i iii   v  i  v       --       iii 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT--TTGCAAATCAT 735

  chr2_17197338_1   2764 GTATCTGATAACAGA-----ATCCA-----CATAAAGATCTTTTAGAAGT 2803
                         i          vi  -----     -----i       v  i   v  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_17197338_1   2804 CAACAGTAGGAAAATCGACAA-CAGCCCAATTAAAAACTGG-CAAAAGAT 2851
                            i i  --    --     -i i       ?    v   -    i   
  L1M4_orf2#LINE/    786 CAATAATA--AAAA--GACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_17197338_1   2852 TAAAGCAGACACGTTACTGAAGAAGAACTAACAATGGAAAATAAGCACAA 2901
                          vi ii     iv iv ii       vv  vv     vv          v
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_17197338_1   2902 AAAAAAA-GTTTGTCATCTTTAGTTAC 2927
                         i    i - i iiv    v????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (128 / 76)
Gap_init rate = 0.04 (37 / 885), avg. gap size = 4.24 (157 / 37)  


1857 25.00 6.25 1.29  chr2_17312276_17316642.rev     2674  3217 (1150)    L1M4_orf2#LINE/L1        1   571 (337)  

  chr2_17312276_1   2674 TGGAAAGATATCCCATGTTCGCGGATTGGAAGAATCAATATTGTCAAGAT 2723
                                             ii           v i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_17312276_1   2724 GTCCATACTACCCAATGTGAACTAAAGGTTTAGTGTAATTCCTATGAAAA 2773
                          v v     v     vv   v   v  i  i ii i   i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_17312276_1   2774 TTCGAATGGCATTTTTCACAGGAATAGAAAAAAAAATCCTAAAATTTGTA 2823
                          i v iiv  v     ii   i   v  v  ivvi           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_17312276_1   2824 TAAAACTATAAAAGACCCCGAAAAGGTAAAGCACTGTAGAATAAGAAGAA 2873
                          ii  v ii  ii     v   v  vi   i  v v v   v        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_17312276_1   2874 CAAAGACAGAGGCATCACACCTCCCAATTTCAAATAATATTACAAAACTA 2923
                              vii    vv      i             vvv  i      i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_17312276_1   2924 TAGCAATCAAA--------------GCAT-----------TATAGACCAA 2948
                         i  i      i--------------    -----------      i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_17312276_1   2949 TGGAAAAGAATAGAAATCCCCCAAATAAGCTCATGCATATATGGTCAACT 2998
                              v     v  i vi  vv      i i   i   v         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_17312276_1   2999 AATCTTTGACAAAGATGCTAAGAATATACAATGGAAAAAAGATAATTGCT 3048
                         i  i  i     i i   i    vi  v      ii   ii   i ivi 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_17312276_1   3049 TCAATAAATGGTGCTGGGAAAACTGG-TATGTACATGTAATTTAAAAAAG 3097
                             i              v      -  ?vi     i  ---  i  v 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA---AAGAATG 447

  chr2_17312276_1   3098 CAAATTGTATCCTTGT-----ACCATA--CAGAAACTCCAACTGAAAATG 3140
                         -  i   v i  i ii-----      --  i   i --    v      
  L1M4_orf2#LINE/    448 -AAGTTGGACCCCTACCTCACACCATATACAAAAATT--AACTCAAAATG 494

  chr2_17312276_1   3141 GATTAAAGAT-TAAACATGAGACCTGAAATTGTAAAACACCTAAAAGAAA 3189
                            i ?   i-    ii i   v  i   i i      v i  i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_17312276_1   3190 ACATGAAGAAAAAGCTCCATGGACATTG 3217
                             iii?iv   v  i i  -  v   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTG-ACCTTG 571

Transitions / transversions = 1.71 (84 / 49)
Gap_init rate = 0.02 (10 / 571), avg. gap size = 4.10 (41 / 10)  

1146 22.75 1.12 4.49  chr2_17312276_17316642.rev     3520  3875 (492)    L1M4_orf2#LINE/L1      565   908 (0)  

  chr2_17312276_1   3520 GGCATTGGTTTGGACAAAGATTTTTTGGCTACGACACTAAAATCATAGGC 3569
                          i v    v  i i   v i   i  i v  i     i    v  i i  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_17312276_1   3570 AACAAAAGTAAAAATAAATAAGAGAGACTACAT-AAAACCAAAAAGTTTC 3618
                                 v       i    ivvi    v   -    ii     v   -
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT- 663

  chr2_17312276_1   3619 TGCACAGCAAAGGAAACCATCAGTAAAATATAAAAGA--ACCCACGGAAT 3666
                           ii vv       v  i    iv   i i-      --      i    
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTG-AAAAGACAACCCACAGAAT 712

  chr2_17312276_1   3667 CG-AGATAAATGTTTGGAAACTATATATTCAATGAGGGGTCAATATCCTA 3715
                         v -   -    i    v   ii      iii  i    iiivi     vi
  L1M4_orf2#LINE/    713 GGGAGA-AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_17312276_1   3716 TATATATTAGGAACTAATACAACTCAGTAGAAAAACAAAACAAAACAAAA 3765
                         v      v i     vv         i  ----- i    -- i     -
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATA-----ATAAAA--AGACAAA- 803

  chr2_17312276_1   3766 CAATTAACCTGATTAAAAAATGGACCAAGGACTTTGAATAGACATTTTTC 3815
                         ----     ii   ?        i v     -               i  
  L1M4_orf2#LINE/    804 ----TAACCCAATTWAAAAATGGGCAAAGGA-TTTGAATAGACATTTCTC 848

  chr2_17312276_1   3816 CCAGGAAGACGTACAGATGGCCAACAGGTATATGGAAAAGTGATCCATAT 3865
                          v i     ii    i        i i i i   i   ii  v  v i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_17312276_1   3866 CACTAATCCT 3875
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.08 (54 / 26)
Gap_init rate = 0.03 (10 / 344), avg. gap size = 2.00 (20 / 10)  


2787 26.92 2.11 1.11  chr2_17468152_17472393.rev     2852  3750 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_17468152_1   2852 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTCAAAAT 2901
                               v i        i        v  v   v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_17468152_1   2902 GACCATACTGCCAAAA-------GCAA--TCAATG-AAT---TATAAAAC 2938
                          i v     v  v   -------i  i--    i -   ---   v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_17468152_1   2939 TACCATCATCATTCTTCACAGAACTAGAAAAAAAAATCATAAAATTGAGA 2988
                          v   v vv v  i  ii     v v  v  ivvi   v       v v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_17468152_1   2989 TGGAACCCAAAAAGAGCCTGCATAGCCAAAGCAAGTCTAAGCAAAAAGAA 3038
                              vivv  ii  v  v v         i   vii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_17468152_1   3039 TAAATCTGGAGGCATTACATTACCCATTTTCAAAATATACTATAAGGCTA 3088
                         i   vi      vv i   i v    v        iv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_17468152_1   3089 TAGTCACGAAAATAGCATGGTATTGGTATAAAAATAGGCATATAGATCAA 3138
                         i   v iv  i i  ii     i   i    ii    i            
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_17468152_1   3139 TGGAACAGAACAGAGAATTCAGAAATAAAGCCAAATACTTACAGCCAACT 3188
                              i    iv    i i          v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_17468152_1   3189 GATCTTTAACAAAGCAAACAAAAACATAAAGTGGGGAAAAGGACACCCTA 3238
                            i  ii    i vviv   i v   vv i        - i i vi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTT 399

  chr2_17468152_1   3239 TTCAACAAATGGTGCTGGGATAATTGGCTAGCTGCATGTAGAAGAAGGAA 3288
                                             i  i   v  ? ii    i i     v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_17468152_1   3289 ACTAGAACCTCATCTCTCACCTTATACAAACAAACAAA--AACTCAAGAT 3336
                         ii i  v  ii i   v    v        ------  --       i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAA------AATTAACTCAAAAT 493

  chr2_17468152_1   3337 GGATCAATGACTTAAATCCTAGACCTGAAACCATAAAAATTCTAGAAGAT 3386
                               ?v   i     viv   v  i    i      v ii       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_17468152_1   3387 AACATCAGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCAT-GA 3435
                              vi ?iv  vi    vv   v    v        v ii   v -  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_17468152_1   3436 TCAAGA-ACCAAAAA-ACAAATATAACAAAAAGAAAGATAAATAGATGGG 3483
                          - v  -       i-    ii --      ii   i   i   i  v  
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCA--ACAAAAGAAAAAATAGATAAATTGG 640

  chr2_17468152_1   3484 ACTTAATTAAA-CTAAAAAGCTCTGCACAGCAAAAGTAATCATCAGCAGA 3532
                             v  i   -i      vi i  ii vv    i vv ii    iv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_17468152_1   3533 GTAAATAGACAAACCTCAGAGAGGGAGAAAATCTTCACAGACTATGTATC 3582
                           i  v      v  v    iv          v  ii  i ii  i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_17468152_1   3583 CAACAAAGGACTAATACCCAGGGTCTACAAGGAACTCAAACAAATGAGCA 3632
                         ii i  i     vi  i    ii v  i  i      vv    v v ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_17468152_1   3633 AGAAAAAAATGAATAATCCCATCAAAAAGTGGGCTCAGGACATGAGTAGA 3682
                          v     i ii     i  v  i?    i     vv    iv   i    
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_17468152_1   3683 CAATTTGCAAAAGGAGGTATACAAATGTCCAACAAACATACGAAAAAATG 3732
                           v  iv v    i  i          v    i  i  i i     i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_17468152_1   3733 CTCAACATCACTAATGAT 3750
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.23 (29 / 13)  


3081 27.20 0.59 0.59  chr2_17473049_17475077      677  1529 (500)    L1M4_orf2#LINE/L1        1   853 (55)  

  chr2_17473049_1    677 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATCGTGAAAAT 726
                              ii i  i     i i    i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_17473049_1    727 GGCCATATTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 776
                            v   i v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_17473049_1    777 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 824
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_17473049_1    825 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGTCAAAAG 874
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_17473049_1    875 AACAAAGTTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 924
                                       vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_17473049_1    925 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 974
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_17473049_1    975 AATGGAACAGAAC--AGAGCCCTCAGGAATAACGCCACATATCTACAACT 1022
                                i    i--    i  --  i     vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_17473049_1   1023 ATCTGATCCTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1072
                          vi    ii i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_17473049_1   1073 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1122
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_17473049_1   1123 GAAACTGGATCCCTTCCTTACACTTCATACAAAAATCAATTCAAGATGGA 1172
                            ii    i    v   i    ivi          i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_17473049_1   1173 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1222
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_17473049_1   1223 CTAGGCTTTACCATTC-TGAACATAGGCATGGGCAAGGACTTCATGTCTA 1271
                         v    ?v v viv   -   v v i  i- i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr2_17473049_1   1272 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1321
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_17473049_1   1322 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1371
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_17473049_1   1372 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTTATCTGACA 1421
                         v  i     i   i             v       vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_17473049_1   1422 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAG 1471
                          i  i  vi          v  i  v      vv    v iv i  v  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_17473049_1   1472 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 1521
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_17473049_1   1522 CTTAAAAG 1529
                           iv    
  L1M4_orf2#LINE/    846 CTCCAAAG 853

Transitions / transversions = 1.56 (139 / 89)
Gap_init rate = 0.01 (7 / 853), avg. gap size = 1.43 (10 / 7)  


 563 29.51 10.49 3.28  chr2_17497364_17498961      497  1106 (492)    L1M4_orf2#LINE/L1      255   908 (0)  

  chr2_17497364_1    497 AAGTAAAACCATATGGTATGGGTAAATGGGTTTACAAAGAAATCAATGAA 546
                           vi  i  vi i     iv  i v v  i vv   v v i       i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_17497364_1    547 ATATAGCTGAATGTCTAGAAATAGAATCAATTGCAT--ATGG--AATTCA 592
                            v ii   iv   i       i vi  -- i   --    --    v 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAATTGA 352

  chr2_17497364_1    593 GTATATTAATAAGCAGCACTGCAAA-----TCAGTGGGGGAAAGAAAAA- 636
                         v - - ii i   -i ii --   i-----   i     -      v i-
  L1M4_orf2#LINE/    353 TT-T-TCGACAAG-GGTGC--CAAGACCATTCAATGGGG-AAAGAATAGT 396

  chr2_17497364_1    637 -----CAGTAAATGATGTTGGAGTAATCTGATATTCACATTATAACAAAA 681
                         -----  ii     i  i   iii  iiv    ?i     ----i     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT----GCAAAA 442

  chr2_17497364_1    682 GA-TAAAACTAGGTTATT-TCTCACATCATACACCAGAAAAAA---AAAG 726
                           - i  ii i iiivi -i      i    i  v i  vv  ---   i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_17497364_1    727 TGTATTATGAGATATTTAAATGTAAAAATGGAAAACATACAAATACTAGA 776
                           v  i ?-   i--i         i iivi   vi   v  v vi    
  L1M4_orf2#LINE/    493 TGGATCAW-AGAC--CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_17497364_1    777 AGAAAGCAT--GAGTAAATCCTCTATAATCT-GAAAGAGGAAAAA----C 819
                              i   -- ?       i  -i i i  - iivv   v  vi---- 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_17497364_1    820 TTA--------------AG---AAGCAATAAAGGAACAGATTAATAAACA 852
                            --------------  ---      i   i   v i  vi     iv
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_17497364_1    853 CAAGAT---ATAACAATTTAAAAAATATGG-----CAAAAATAAATCTTA 894
                         --i  i---  v v    -     v v v -----    iivv v v i 
  L1M4_orf2#LINE/    639 --GGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_17497364_1    895 AATATAATGAAAA---AAATGACAAACTGGAA-AAAATTTTTGCAACTTA 940
                          iv - i      ---  viv   i v   i -     v       v i 
  L1M4_orf2#LINE/    686 AGAA-AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_17497364_1    941 TATGACAGAAAAGAG-TTGGTATCCCTAAAATAGAAAGA--TTGTCTAAT 987
                            iv v  v   i -i v      vv  v   v     -- iv vi  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_17497364_1    988 ---AGAAGAAAAACTCCAATAACTCTATTGAAAAATGAACAAGAGATATA 1034
                         --- v  v     vv v      i v   ?       ii   ii   v i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_17497364_1   1035 AATATAGACTTAACAGAAAAAGAAAGGCAGATGGCCCTTTA--ACATGAA 1082
                             v v i  vv vi  i    v vi  i      vv v --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_17497364_1   1083 AATATGCTCAACGTCATTCATAAT 1106
                           v         i   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (100 / 76)
Gap_init rate = 0.05 (33 / 654), avg. gap size = 2.55 (84 / 33)  


3328 24.78 1.87 1.87  chr2_17506327_17508851     1126  2033 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_17506327_1   1126 TGGAAAGACATCTCACACCCATGAATCAGAAGAATTTATATTGTTAAAAT 1175
                                 i   i  iiii    i  ii     v  v          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_17506327_1   1176 AACAATACTACCCAAAGAAATCTACTGATTCAATGCAATGCTTATCAAAA 1225
                         ii       v      vvi      v       i     v i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_17506327_1   1226 TATCAATGACATTCTTCATAGAAATAGAAAAAAAAGGGTTT---AATTTA 1272
                          vi  iivi v  i  iii      v  v  iv--v i ii---    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chr2_17506327_1   1273 TATGGAACTATGAAAGACCCTGAATAGCCAAAGCAATCCTGAGCAAAAAG 1322
                                v iii ii     v           i     i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_17506327_1   1323 AATAAAGCTAGAGGCATCACACTATTTTTCAAAATATAGATTTCAAAATA 1372
                           i    i i    vv       --- ii   --------        iv
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACT---TCCCAA--------TTTCAAAACT 237

  chr2_17506327_1   1373 TACTACAAAGCTATAGTCACCAAAACAGCATGATACTGGCATAA----AA 1418
                                      i   v i   i    ii  i           ---- i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_17506327_1   1419 ACATTCATAGATGAATGGAACAGAATGGAGAACCCATAAATTAACCCATA 1468
                             --      v       i     v    ii   v    v        
  L1M4_orf2#LINE/    288 ACAT--ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_17506327_1   1469 TATGTACAGCTAACTGATTTTTGACAAAAGCACCAAGAACACTCATTGGG 1518
                         i  v  ii ii  i       i     ii ii      v  i   v    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_17506327_1   1519 GAAAGGACAGCCTCTTTAAGAAATGATGCTGGGGAAACTGAATATCCATA 1568
                              i i  i  i  i  v     i       iv     i   ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_17506327_1   1569 TACAGAAGAATGAAACTGGGCCCCCACTCCTCACTTTATACAAAAATTAC 1618
                          i  i         ii   i    i  ii v   iv             v
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_17506327_1   1619 CTCTAAATGGATCAAAGACATATGTGTAAGAACCAAAACTATAAAACCAC 1668
                            v          ?    v  vi       i i             ivi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_17506327_1   1669 TAGAAGAAA-CATAGGGA-AAATGCTTGTGACATTTGTCTGGGAAAGGAC 1716
                                  -      ?i-    vi i     v  v vi i  v  v ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_17506327_1   1717 TTTATGAATAAGACCTCAAAAGCATAGGCAACAAAAGCAAAAATAAACAA 1766
                           iv ii   v   vi        i i          v       i i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_17506327_1   1767 AAAGGATTATATCAAA-CTAAAGACCTTT-TGCCTACCAAAGGAAACAAT 1814
                          vv   i vi      -i    i  i   -   i --       v  v  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTAT 683

  chr2_17506327_1   1815 CAACAGACTGAAAAGACACCCTACACGATGGGAGTAA---CCTACA--CT 1859
                            v i v          v  i   vi       v  ---ii i  --ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_17506327_1   1860 ATTCACTTGACAGAGG-TTTATATTCAGAATATACACAGGACTCAAACAT 1908
                           vi ii   i ii  -i  i   i         i v  i    vv   v
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_17506327_1   1909 CTCAGCAACAAACAAACAAACACTCTACTTTAAAAATAAGCAACAGATCA 1958
                             ii  i   v i     i vi i v  ?      ii    vi   iv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_17506327_1   1959 GAACAGACGTTTTTCAAAATAAGACATACAAATGGCTAAAAAATGTATGA 2008
                            i    i   i  v   v    i           i  v  iiii    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_17506327_1   2009 AAATACGTTCAACATCACTAATCAT 2033
                            v i i         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (150 / 71)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.43 (34 / 14)  


2816 27.27 2.58 0.67  chr2_17551781_17554353     1191  2081 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_17551781_1   1191 TGGAACAACATTCCATCCTCAGGGATAGGAAAAATCAGTATGGTGAAAAT 1240
                              vi i  i    vi   v    v    i v i i   v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_17551781_1   1241 GGCTATACTGGCCAAAGTAAT-TATAGATACAATGCTATTCCCATCAAAC 1289
                            v     vv     v i  -  i    v   i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_17551781_1   1290 TACCATTGACATTCTTCACAGAATTAGAAAAAAACT-ACTTTAAAATTCA 1338
                          v   vivi v  i  ii     v v  v  i--  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_17551781_1   1339 TATGGAA-CAAAAAAGAGCCTGCGTAGCCAAGACAATCCTAAGCAAAAAG 1387
                                -iiv  ii  v  v vi       i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_17551781_1   1388 AACAAAACTGGAGGCATCACGCTACCTGACTTCACACTATACTACAAGGC 1437
                               ii      vv    i  v  ii i    v viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_17551781_1   1438 TACACTAACCAAAACAGCATAGTGCTGGTACCAAAGA-AGACATATAGAC 1486
                             v   i   i    ii i  i    i i-  i  -           i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGAT 297

  chr2_17551781_1   1487 CAATGGAACAGAATAGAGACCTCAGAAATAAGACCACACATCTACAACCA 1536
                                 i     v    vii         iv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_17551781_1   1537 TCTGATCTTCAACAAACCGGACAAAAGCAAGCAATGGGGAAAGAATTCCC 1586
                         vi    i   i    ivvv v   i v  vv               vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_17551781_1   1587 TATTTAATAAACGGTGCTGGGAAAACTGACTGGCCATATGCAGACAACTG 1636
                          v  i  i   i          v     iv i?   i     i vi v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_17551781_1   1637 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGGTAGAT 1686
                           ii    i    v   i     v                   ii i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_17551781_1   1687 TAAAGACTTGAATGTAAGACCCAAAACCATAAAAACCCTAGAAGAAAACC 1736
                         i ?    i i         v i     i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_17551781_1   1737 TAGACA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTT-------- 1777
                            i?i- v i -   iv   v v  vv i     v i   i--------
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_17551781_1   1778 ---ACCATGAAATCACCAAAAACAATTGCTAAAATTAACAAATGGGATCT 1824
                         ---    --   v   v iv     vv vv     vi i    v   ii 
  L1M4_orf2#LINE/    597 GACACCA--AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_17551781_1   1825 AATCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGCGA 1874
                         v      v v  i i   i  ii vv    i  v       vv i  i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_17551781_1   1875 ACACACAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 1924
                          v v      i                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_17551781_1   1925 AAAAGTCTAATATC--GA-----CAAGAAACTTAAACAAATTTACAAGAA 1967
                           ii v  vi    --  -----i  ii    ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_17551781_1   1968 AAAAACAGACAACCCCATCAAAAAGTGGGCAAAGGATATAAGCAGACACT 2017
                            i   i i     v  i?    i            v i ii     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_17551781_1   2018 TCTCAAAAGGAGACATTTATGCAGCCAACAAACATATGAAAAGAAGCTCA 2067
                             v    i   i  vi viii     i  i  i         v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_17551781_1   2068 TCATCACTGGTCAT 2081
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  


3117 24.83 4.21 0.80  chr2_17571115_17573318.rev      835  1712 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_17571115_1    835 TGGGAAGATAGCCCATGCCCATAGATTGGAAGAACTGATGTTGTTAAAAT 884
                            i      v      ii   i          vi i  i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_17571115_1    885 GTTCATACTACCCAAAGCAATCTACAGATTCAATGTAATCCATATAAAAA 934
                          viv     v      vii              i i     v   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_17571115_1    935 TTCCAATGACATTATTTTACAGAAAT-----AG--------AAAATATGT 971
                          i   iivi v  -    i       -----  --------     vii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_17571115_1    972 ATGGAACTATGGCAGATCCTGACTAGACAAAGCAATCTTTAGCAAAAAGA 1021
                               v iiiivi  i  v  v   v    i       v iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_17571115_1   1022 ACAAAACTGAAGGCATCAGACTACCTGATTTCAAAATATGCTACAAAGCC 1071
                              ii  i   vv   v   v  ii         iv i         i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_17571115_1   1072 ACAAAGTTGTCAAAACAGCATGGTACTTCTATAAAAACAGACACGTAGAC 1121
                            --  vi    i    ii       vvi    ii i     ii    i
  L1M4_orf2#LINE/    250 ACA--GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_17571115_1   1122 CAATGGAATGGAATAAAGAGACCATAAATAAACTCACAAATTTAAAGTCA 1171
                                  i    vi    v   v        i  i v     vi    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_17571115_1   1172 ATTGATTTTTGAAAAAGGTACCAAGAACATACAATGGCGGAAAGAACTGT 1221
                                  i  v  i   i      v   v      -        iv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGT 396

  chr2_17571115_1   1222 CTCTCCAATAAATGATAGTAGGCAAATTGGATATCCACATGCAGAAGAAT 1271
                           i i   i     i iv i  vv  i      ?         i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_17571115_1   1272 AAAATTGGACCCTTATATCATGCCATATAAAAAAAATCAACACAAAATGG 1321
                         i  i        i  iv   ii       v     - i   v        
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGG 495

  chr2_17571115_1   1322 ATTAAAAACTTAAATGTAAGACCAGAAACTGTGAAAACACT-GTAAGAAA 1370
                           i ? i  i           v vi     i -     v  -iv      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAA 544

  chr2_17571115_1   1371 ACGTAGGGGAAAAGCTCCACAACACTGGTGTT-GGCAATAATTTTTTGGA 1419
                           i    ? v   v  i iii  vi   -   -      ii   i  i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGA 593

  chr2_17571115_1   1420 TATGACCCCAAAAGCACAAACAATGAAAATGAAAATACACAAACAGGATT 1469
                               v            i   ii   ivi      v i   iv   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_17571115_1   1470 ACATCAAC-CCAAAAGAGCTCATACAGCCAGGAAAATAATCAATAGAGTG 1518
                         v      v-ii    ivvi ii i vv v i i v iv     v i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_17571115_1   1519 AAGTGACAACCTAGAGAATGAGGGAAAATATTTGTAAACCA--------- 1559
                           iv       i v      i i           i   i  ---------
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_17571115_1   1560 -AAGAGGTTAGTATCTAAAATGTAAAAGAAACTCAAACATCTCAGTAGCC 1608
                         -   i ii v     i i   i  v  ii     vv   v    i  iiv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_17571115_1   1609 AGAA----AATAGCCTGATTAAAAACTGA-------ATTTGAATAGACCT 1647
                          i  ----    i  ii   ?    v  i-------            v 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_17571115_1   1648 GTCTCAAAAGAACACATACTAATGCCTAACAGATATATGAAAAAATGCTC 1697
                         v    v      v i    v    v i  i iii i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_17571115_1   1698 AACATCAATAATAAT 1712
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (137 / 77)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.14 (44 / 14)  


2686 26.58 5.06 0.58  chr2_17591609_17594516.rev     1548  2416 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_17591609_1   1548 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCGATATCGTGAAAAT 1597
                               i i  i     i        v      v ii    i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_17591609_1   1598 TGACATAGTGCCCAAAGTAATTTATAGATTCAATGCTAACCCCATCAAGC 1647
                         v vv   v v      v i  i  i        i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_17591609_1   1648 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 1696
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_17591609_1   1697 ATGGAACCAAAAAAAGAGCCAGTATAGCCAAGACAATCCTAAGCAAAAAG 1746
                               viiv  ii-  v    v        i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_17591609_1   1747 AACAAAGCGGGAGGCATTACACTACCTAACTTCAAACTATACCAAAAGGT 1796
                                iv     vv i     v  i  i      viv   i v  i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_17591609_1   1797 TACAGTAA-CAATAACAGCATGGTACTGGTACCA----AAACAGATAGAC 1841
                                 -   -i    ii         i iv ---- i   v     i
  L1M4_orf2#LINE/    249 TACAGTAATCAA-GACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_17591609_1   1842 CACTGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 1891
                           v     i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_17591609_1   1892 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATTCCC 1941
                         vi    i  i     ivv  v   i v  vv      i     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_17591609_1   1942 TATTTAATAAATGGTGTTGGGAAAACTAG----CCATATGCAGAAAACTG 1987
                          v  i  i        i     v    i ----   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_17591609_1   1988 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 2037
                           ii         v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_17591609_1   2038 TAAAGACTTATACATAAGACCTAAAACAATAAAAACCCTAGAAGAAAACC 2087
                         i ?    i  v ii     v       v      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_17591609_1   2088 TAGGCA-ACACCATTCAGGACATAGGCATGGGCAAAGACTTCA-AGATTA 2135
                             ?i- v i -   iv   v v  vv i     v ii   v-    - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr2_17591609_1   2136 AAACACCAAAAGTAATGGCAACAGAAGCCAAAATTGACAAACGAG----- 2180
                         vi          i vvi      i   vv     v  i   ivi -----
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_17591609_1   2181 --CAAAA---GAAACTAT----CCTCAGAGG----------------GAA 2205
                         --     ---i     v ---- i   i   ----------------   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_17591609_1   2206 CAGGCCACCTACAGAATGGGAGAAAATGTTTGCAGTCTATCCATGTGAGA 2255
                         v  i v   i                 i      ivii  vi  v   v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_17591609_1   2256 AAGGGCTAATATCCAGATTCTACAAGGAACTTAAACAAATTTACAAGAAA 2305
                          i  i  vi        v v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_17591609_1   2306 AAAA--AGCAACTCTATCAAAAAGTGGGTGAAGGATATAAATAGACACTT 2353
                           i -- ii   i v  i?    i    ii      v i        i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_17591609_1   2354 CTCAAAATGAGACATTTATGCGGCCAACAAACATATGAAAAGAAGCTCAT 2403
                            v   vi   i  vi vii      i  i  i         v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_17591609_1   2404 CATCACTGGTCAT 2416
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.06 (49 / 16)  


 702 27.57 20.96 2.39  chr2_17668884_17670552.rev      489  1199 (470)    L1M4_orf2#LINE/L1       66   908 (0)  

  chr2_17668884_1    489 ATTAGTATAAACACTCAATTCAATTCTAATAAAAATCCCAAGTATATTTT 538
                            ii v  v v i    iv    i iv  v         iv iiv    
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_17668884_1    539 TTAT-GAAGTT-------------TAA---CCAAATGAAAAAGCAAAAGG 571
                           ii-   i  -------------   ---i  v   i   v    ii i
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_17668884_1    572 TC-AGTAATATTTAAGACAACTTTGAG---GAAGACCACGGATAGTG--T 615
                         i -  -    vii  i    ii    i---     v  vi v i v --i
  L1M4_orf2#LINE/    166 CCCAG-AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_17668884_1    616 TC-TACTCCATTAAATATCTAAGCTTATTATAAAGCCACACTATTTAATA 664
                           -i   i vi--   v  v  i    i  i     i   v  v i  v 
  L1M4_orf2#LINE/    215 TCACACTTCCC--AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_17668884_1    665 CAGTTTGGTACTGATAAAATAATGGAAAAATACA-AAATGGCAATAGAAC 713
                             v        ii v  vi  i  v v   v -v     -       i
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG-AATAGAAT 311

  chr2_17668884_1    714 AGAGAG-------------CTAAACATTTG-GGAC--TTTACATGTGATA 747
                         v     ------------- i v      i-  v --  v iv vi  i 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_17668884_1    748 GTGGGTGCCTAATACAA--CAACAGAGAAAGAAAAATATATTCAATAAAA 795
                         i-       -  v  v --   ii i       v i v v     i   -
  L1M4_orf2#LINE/    362 A-GGGTGCC-AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA- 408

  chr2_17668884_1    796 CTGTGTTAGGATAACTGAATGTCTACAGGGCAAAA--ATAAAATTAGATT 843
                         iv   i i   i     i  i? i   v -     --  i  i  i  ii
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAATGAAGTTGGACC 457

  chr2_17668884_1    844 TCAACCTCACACCA-AT-----------CTCAAAA------ATACGTTTC 875
                         i v           -  -----------       ------ ? viii v
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_17668884_1    876 A--GTTAGA-TTAAAACCC--AAACTT---------AACACAG---TA-- 906
                          --  v   -i      iv--     i---------    i  ---  --
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_17668884_1    907 --TT------------TTAAATCATGGT---------------------- 920
                         --  ------------   iiiv     ----------------------
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_17668884_1    921 ---------------AAGAGGTTGATAAATCCAACTATCTCAAAATTTAA 955
                         ---------------  i ii v       ivi   viv        v  
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_17668884_1    956 AA-TTTTGTTTTTAAGACAAAAGCAACCATAAACAAAGTTAAA---TAAG 1001
                           -      vi  ----    i vv  i  v  v     v   ---i  v
  L1M4_orf2#LINE/    658 AACTTTTGTGCTT----CAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_17668884_1   1002 TGACAGACAAAGAGATAATATCTGCAA----TGTATATAACAAATAGTTT 1047
                         iv     vvii    v     i     ---- i   v i i  iviii  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_17668884_1   1048 GCATTCAGAATTTATAAGGAATTC---CAAATGATGGATAAGAAAAAGAC 1094
                          i  i      v     i   i  ---   v v ---    v        
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCA---ATAATAAAAAGAC 800

  chr2_17668884_1   1095 AAACAATCCTATTAAAAAATAGGCAAGGCCTGTGAATAAGTAATT-TACA 1143
                            i  i  v   ?      i     i vv v      iii v  - v  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_17668884_1   1144 GAGAAGAAA-ACCTAAATGGCCACTAAAGAT-TAAGAAAATGA--AAAAT 1189
                         i      v -  --         v   iv i- i i  i   v--  v  
  L1M4_orf2#LINE/    851 AAGAAGATATAC--AAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_17668884_1   1190 TATGAAGGAC 1199
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.41 (113 / 80)
Gap_init rate = 0.05 (42 / 843), avg. gap size = 3.95 (166 / 42)  


3833 17.73 7.07 1.85  chr2_17885776_17887633      510  1372 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_17885776_1    510 TGGAAATACATTCCATGTTCATGAATCAGAAGAC---ATA------AGAT 550
                               v i  i           i  ii      ---   ------    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_17885776_1    551 GACCATACTCCCCAAACTGATCTACAGGTTAAATGTAATTCCCATTAA-- 598
                          i v            i          i  v  i i   i  i  i  --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_17885776_1    599 TTCCAGCTGGTTTCTTTGC--------------TGATTCTAAAATTCATA 634
                          i       vi  i     --------------    i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_17885776_1    635 TGGAAATTTCAGGAACACAGAATATTAGGAAGAATCTTGAAAGAG----- 679
                                viv   i  v       vivii  v          i  -----
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_17885776_1    680 ----TTTGAATGACCCACCCTTCCTGATTTTAAG---TA-TACAGAACTA 721
                         ----v   i v   i   v     ii    i  i---  -    i i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_17885776_1    722 CAGTAATGAAT---GTGTTGTACTGGTATAAAGGTAGACATATAGGTCAA 768
                                v  v---    v       i    i i           -----
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG----- 295

  chr2_17885776_1    769 TATAGATCAATGGCATAGAATTGAGAATTCAGAAAAAAAGCCTTCACGTT 818
                         -----        v            i i      v   v  v -  i  
  L1M4_orf2#LINE/    296 -----ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATT 339

  chr2_17885776_1    819 TATGGTCAGTTGATTTTAAACCAGAGTGCCAAGACAATTCAATGGGAAAA 868
                                 i        vi  v  i          v          i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_17885776_1    869 GGAAACAGTCTTTGAACCAACTGTCTTCTGGATCTATTGGATATCTATGT 918
                          --  i       vv v   v  v- v    iv v i      ? i ii 
  L1M4_orf2#LINE/    390 G--AATAGTCTTTTCAACAAATGG-TGCTGGGACAACTGGATAKCCACAT 436

  chr2_17885776_1    919 AAAAAAGAGTGACATTTGATTCCTACTTCACATGATATTTAAGAAGTAAC 968
                         iv      i   vi  v  ii     i     iv    vi  i  v    
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_17885776_1    969 TTAAGATGGATCAAATACCTAAATGTAAG--CTAAAGCTATAAAACTCTT 1016
                          i  i        ? v             --     i             
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_17885776_1   1017 AGAAGAAAACATAGACGTAAATCTTTGTGACTTTGGATTAGGCAAGGATT 1066
                                       i?         i     i    i        v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_17885776_1   1067 TCTTAAATAT---ACCCAAAGCATAGGCAACAAAAGAGAA--TACACAAA 1111
                              i    ---   v      i i           i  --  v i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_17885776_1   1112 CTGGACTTCATCAAAACTAAAAACTGTTGT--TTGAAATGACACCATCAA 1159
                         i               i        v    --  v   v     i     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_17885776_1   1160 GAAAGTGAAAAGACAGCTTACAGAATGGGAGAAAATATTTGCAAATCATA 1209
                                        i ii                               
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_17885776_1   1210 AATGTGATAAGGGACTTGTATCTTGGTGGTATATAAAGAACTCGTA--AC 1257
                         v  v                  iv i--i              v  --  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGA--ATATATAAAGAACTCTTACAAC 784

  chr2_17885776_1   1258 TCAATTATAAAAAGACAACT-------TT--GAAATGGGCAAAATAGCTC 1298
                              v            v -------  --i           iv vi v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_17885776_1   1299 AACAGGCTTTTCTGCAAAGAAGAAATACAAATGACCAAGAAGCACATTTA 1348
                           i  i v     v         v         i    v        vv 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_17885776_1   1349 AAAATTTTCAGTACTATTACTCAT 1372
                           i  vi   ii ii ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (90 / 60)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.85 (77 / 20)  


2432 25.79 4.05 4.84  chr2_17999946_18001826.rev      502  1389 (492)    L1M4_orf2#LINE/L1       28   908 (0)  

  chr2_17999946_1    502 GGAATAATCAATATCATTAAAATGGTCATACAACTCAAAGCAATCTACAG 551
                             v v i     ii    i    iv    vv i    vii        
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chr2_17999946_1    552 ATAGATTCAATGCTATTCCTATCAAACTATTAA-TGTCATTTTTAAAGAA 600
                           ----    i  v  i         v vii i-  i v     iv    
  L1M4_orf2#LINE/     78 AT----TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAA 123

  chr2_17999946_1    601 TTAGACAAAACT-ACTTTGAAATTCATATGGAACCAAAAAAAGAGCCTGA 649
                         v v     i-  - iii i              viiv  ii-  v  v  
  L1M4_orf2#LINE/    124 ATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGG-GACCCAGA 171

  chr2_17999946_1    650 ATAGCCAAAGCAATCTTAAGCAAAAAAAAAAAAAAAAACCTAGAGGCATC 699
                                  i       i -----    i  i  v   vi i    vv  
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGA-----AAAAGAAGAACAAAGTTGGAGGACTC 216

  chr2_17999946_1    700 ACATTACTGACTTT--AAGCTATACTACAAGGCTACAGTAACTAAAACAG 747
                            i v iv v   --  i  -        i          ii  i    
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_17999946_1    748 CATGGTACTGGTATAAAAACAGACACACAGACCAATGGAAGAGAACAGAG 797
                         ii         i    ii i     i i   i        v    iv   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_17999946_1    798 AACCCAGAATTGAAGCCACATACCCACAACCATCTGATCTTCAACAAAGT 847
                          ii      v i  v   i i iii iiii  vi    i   i    i v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_17999946_1    848 CAACAAAAATAAGCCATAGGGAAAGGAC--TCCCTAATCAATAAATGGTG 895
                         iiv   i vi vv v  i       i i--  ii --    i        
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGTG 413

  chr2_17999946_1    896 CTGAGATAACTGGCTAACCATATGCAGAAGAACAAATTTGAACCCCTACT 945
                            i  i      v  ?   i     i     ii  v   i        i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_17999946_1    946 TATAACCATGTACAAAAATTAACTCAAGATGGATTAAAGTCTTAAATGTA 995
                          vvv     i                 i      i ?  v i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_17999946_1    996 AGACCTCAAACCATAAAAATCCTAGAAGAAAACCTGGGTTTTCTTTCTAG 1045
                            v  v    i      v  i           v -------------  
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-------------AG 550

  chr2_17999946_1   1046 AAGTCATTTATTAAAGGAAATACCTTTCTCAACATCAGCCTTGGCAAAGA 1095
                         i?  -------------    ---i   vii  v ii vi v     v i
  L1M4_orf2#LINE/    551 GNGT-------------AAAT---CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_17999946_1   1096 ATTTGTGGCTAAGTCCTCAGAAGTAATTTTAACAAAA---ATAATTGACT 1142
                         v  iv i v  v v vi  i   i vvvvi       --- v   v  iv
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_17999946_1   1143 AGTGGGACCTAATTAAACTAAGGAGATTCTGCACAGTAAAAGAAACAATC 1192
                          i v    i v  i   v v ii iv  i  ii vvi   i  v  v   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_17999946_1   1193 AA-AGAGTAAACAGACAGCCTATAGAATGGGAGAAAAAAATTGCAAATTA 1241
                           - i   i  v     i  i i              v v        i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_17999946_1   1242 TGCATCTGACAGAAGACTAACATCCAGAATCTATAAGAAATTT----AAA 1287
                          ii      i iii    vii         v     ii  i i----  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_17999946_1   1288 TTGACAACAAAGA-ACAAATAACCCCATT--------------------- 1315
                          ii i  i   i -           v   ---------------------
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_17999946_1   1316 AACAGACACTTCTCAAAAGAGGACATACAAGTGGCCAACAAACATATGAA 1365
                           i     i     v     i  i      i       i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_17999946_1   1366 AAAATGCTCATCATCACCGATGAT 1389
                           i       v     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (145 / 81)
Gap_init rate = 0.02 (18 / 881), avg. gap size = 4.39 (79 / 18)  


3304 26.43 0.55 0.55  chr2_18006606_18008323.rev      320  1227 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_18006606_1    320 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCATTATTGTGAAAAT 369
                              ii i  i     i        v      v i v      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_18006606_1    370 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 419
                            v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_18006606_1    420 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 467
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_18006606_1    468 TATGGAACCAAAAAAGAGCCCGCATTACCAAGACAATCCTAAGCCCAAAG 517
                                viiv  ii  v  v v  vi    i      i i ivvvi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_18006606_1    518 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 567
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_18006606_1    568 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 617
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_18006606_1    618 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACGACC 665
                                i    i--    i  --        vv   i    i  i ii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_18006606_1    666 ATCTGATCTTTGACAAACCTGACAAAAAGAAGAAATGCGGAAAGGATTCC 715
                          vi    i  i     ivv  v   i vv vvv    v      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_18006606_1    716 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 765
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_18006606_1    766 GGAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 815
                          i ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_18006606_1    816 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAGGAAAAC 865
                          i ?    i       v   v       i      vi i    i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_18006606_1    866 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 914
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_18006606_1    915 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 964
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_18006606_1    965 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1014
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_18006606_1   1015 CAGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTACTCATCTGACA 1064
                         v  i     i              v  v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_18006606_1   1065 AAGGGCTAATATCCAGAATATACAAAGAACTCCAACAAATTTACAAGAAA 1114
                          i  i  vi             i         iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_18006606_1   1115 AAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTT 1164
                           i     i     v  i? v  i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_18006606_1   1165 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 1214
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_18006606_1   1215 CATCCCTGGCTAT 1227
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3185 27.19 0.55 0.99  chr2_18086278_18092473.rev     4794  5705 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_18086278_1   4794 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4843
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_18086278_1   4844 GCCA-TACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4892
                          v  -    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_18086278_1   4893 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4940
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_18086278_1   4941 TATGGAATCAAAAAAGAGCCCACATTGCCAAGTCAATTCTAAGCCCGAAG 4990
                                viiv  ii  v  viv  v     iv    ii i ivvv    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_18086278_1   4991 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTATAGGGC 5040
                                i      vv    i  v  ii i      viv     i ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_18086278_1   5041 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5090
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_18086278_1   5091 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5138
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_18086278_1   5139 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5188
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_18086278_1   5189 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5238
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_18086278_1   5239 GATCTGCATCAGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAG 5288
                           ----- viv   i    v   i     v              i    i
  L1M4_orf2#LINE/    447 GA-----AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_18086278_1   5289 ATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAG 5338
                               i ?    i       v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_18086278_1   5339 AAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCCTG 5388
                              v    ?i v viv   iv   v v  vv i     v ii   i i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_18086278_1   5389 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5438
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_18086278_1   5439 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5488
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_18086278_1   5489 TGAACAGGCAACCTACAGAATGGGAGAACATTTTTGCAACCTACTCATCT 5538
                             v  i     i              v  v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_18086278_1   5539 GACAAAGGGCTAATATCTAGAATCTACAATGAACTCAAACAGATTTACAA 5588
                           i  i  i  vi    i     v  i  v      vv   iv iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_18086278_1   5589 GAAAAAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGAC 5638
                         v     i     i     v  i? v  i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_18086278_1   5639 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGC 5688
                          i     v        i  vi viii     v ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_18086278_1   5689 TCATCATCCCTGGCCAT 5705
                            v    v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  


3238 26.94 0.44 0.99  chr2_18115163_18121418.rev     4852  5764 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_18115163_1   4852 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4901
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_18115163_1   4902 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4951
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_18115163_1   4952 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4999
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_18115163_1   5000 TATGGAATCAAAAAAGAGCCCACATTGCCAAGTCAATTCTAAGCCCGAAG 5049
                                viiv  ii  v  viv  v     iv    ii i ivvv    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_18115163_1   5050 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTATAGGGC 5099
                                i      vv    i  v  ii i      viv     i ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_18115163_1   5100 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5149
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_18115163_1   5150 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5197
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_18115163_1   5198 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5247
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_18115163_1   5248 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5297
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_18115163_1   5298 GATCTGCATCAGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAG 5347
                           ----- viv   i    v   i     v              i    i
  L1M4_orf2#LINE/    447 GA-----AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_18115163_1   5348 ATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAG 5397
                               i ?    i       v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_18115163_1   5398 AAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCCTG 5447
                              v    ?i v viv   iv   v v  vv i     v ii   i i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_18115163_1   5448 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5497
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_18115163_1   5498 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5547
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_18115163_1   5548 TGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCT 5597
                             v  i     i   i             v  i    vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_18115163_1   5598 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAGATTTACAA 5647
                           i  i  i  vi          v  i  v      vv   iv iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_18115163_1   5648 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAAAC 5697
                         v     i     i     v  i?    i     i     iv    i i  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_18115163_1   5698 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGC 5747
                          i     v        i  vi viii     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_18115163_1   5748 TCATCATCACTGGCCAT 5764
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.17 (13 / 6)  


1112 26.04 10.68 3.67  chr2_18161358_18162948.rev      501  1099 (492)    L1M4_orf2#LINE/L1      268   908 (0)  

  chr2_18161358_1    501 TAGTATTAGTATTAGTATAAAGGAATA---CAACAGAATAGAAT-GA--- 543
                          i   i i i  v  v   i viv   ---   ii         -  ---
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_18161358_1    544 -CCAGAAATAGACCAACACCTTTATGGACTTTTGGTTA-CTACAAAGGCA 591
                         -         i   v i  v       v vv   i  v- v    i  ii
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_18161358_1    592 ACACTGAAGACCAATTAAAATGGGGCA--------TTTTTAAATAAATGG 633
                         v  ----      v i  --     v --------i    v  i      
  L1M4_orf2#LINE/    368 CCA----AGACCATTCAA--TGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_18161358_1    634 TACT-------CT---TTTCCACATAGAAAAAAGTAAACTTTGACCTTTA 673
                          i  -------  --- v?      iv    i i i  v  v    ii  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_18161358_1    674 TTACACACCAGGCCCAAAATTCAATTACAGGTG-ATTGTGGGTTGACATT 722
                         iiv       viiv     v i  i vv ii  -  ii?i iiiv v  v
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_18161358_1    723 TAAAGAATAAAACAATAAAGCT-TTAAAACACAACACAGGATGATACCTT 771
                            iiiv      v     i  -   i  v v    i   ?vv v i   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_18161358_1    772 TATGAAGATGGTTTAGGCAAAGATTCCCTTAAA-AGGATACAAAAATCA- 819
                         ii   vvv   v        v i  i -   i - v  i  v    v  -
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGACACCAAAAGCAC 610

  chr2_18161358_1    820 --ATAACCTAAATGGTAAAAATGGATACGTTGGACTTCTTTAAAATTAAT 867
                         --ii   --   v i-      i    vi         v i        -
  L1M4_orf2#LINE/    611 AAGCAAC--AAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAA- 656

  chr2_18161358_1    868 AAACTTTCACGTATTAAAG-ACACCTAGTCAA-AGAGT------------ 903
                                iii iv i    -    -  -    - i   ------------
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACAC-TA-TCAAGAAAGTGAAAAGACAACC 704

  chr2_18161358_1    904 -ACAAAATG----------TTTG-AAATACATATAATTGACCAAGAACTC 941
                         -   i    ----------    -    -      vi   iv i i   i
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAAT-CATATATCTGATAAGGGACTT 753

  chr2_18161358_1    942 ATATTCAGAATGTATGAAGAAGTTCTGTTATAAATCAGTATGACAAAGGC 991
                         i   i      i   i     ---  v   i  v   i  vv v    i 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAA---CTCTTACAACTCAATAATAAAAAGAC 800

  chr2_18161358_1    992 AAACAAGCCAATTATTTTTAAATTG--TAAAGTATTTAACTAGACACTTC 1039
                            i  v      ?v----   v  --i    v    i v      i   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWA----AAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_18161358_1   1040 ATTATAAAGGATATTCAAATGGTCAA---GTATATAAAAATGATACTCAA 1086
                         vii v i i     v       i   --- i i  i    -   i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAA 895

  chr2_18161358_1   1087 CATTACCAGTCAT 1099
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (90 / 62)
Gap_init rate = 0.05 (30 / 641), avg. gap size = 2.87 (86 / 30)  


2585 26.14 1.35 7.16  chr2_18242237_18248677.rev     4986  5949 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_18242237_1   4986 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCTTGAAAAT 5035
                              ii i  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_18242237_1   5036 GGCCAGACTGTCCAAGGTAATTTATAGATTCAATGCCAACCCCAT--AAA 5083
                            v v   vi    iv i  i  i        i  v v   i  --   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_18242237_1   5084 TCTACCATTAACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGT 5131
                           --   vivi i  i  ii     -   --- v  i  - iii    i 
  L1M4_orf2#LINE/    101 TC--CCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAAT 145

  chr2_18242237_1   5132 TCATATGGAATCAAAAACAAGTCCGCATTGCCAAGACAATCCTAAGCAAA 5181
                                   viiv  ivi vi v v  v     i      i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_18242237_1   5182 AAGAACAAAGCTGGAGACATCACACTACCTGACTTCAAACTATACTACAA 5231
                                   i     ivv       v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_18242237_1   5232 GGCTACAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 5281
                         i          v   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_18242237_1   5282 ACCAATAGAACAGAACAGAGGCCTCAGAAATAACACCAAACATCTACAAC 5331
                          i    i   i    iv   ivii         vv   v    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_18242237_1   5332 CATCTGATATTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5381
                           vi    v  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_18242237_1   5382 CCTATTTAATAAATGGTTTTGGGAAAACTGGCTAGTCGTACATAGAAAGC 5431
                         i  v  i  i       vi     v      v  ?i ii iii i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_18242237_1   5432 TGAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGGTGA 5481
                             ii    i    v   i    iv              i    ii  i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_18242237_1   5482 ATTAAAGATTTACATGGTAGACCTAGAACCATAAAAAACCTAGAAGAAAA 5531
                           i ?   ii  v   vv   v   i   i      vv i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_18242237_1   5532 CCTAGGCA-ATACCATTCAGGACATAGGTATGAGCAAGGACTTCATGACT 5580
                          v    ?i- v i -   iv   v v  vv ii    v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_18242237_1   5581 AAAACACCAAAAGGAATGGCAACAAAAGCCATAATAGACAAATGGGATCT 5630
                          vi          v vvi          vv v      i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_18242237_1   5631 AATCAATCTAAAGAGCTTCCGCACAGCAAAAAAAAAAAAAAAAAAAAAAA 5680
                         v     vv v  i i   ii ii vv    ii -----------------
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGA----------------- 677

  chr2_18242237_1   5681 AAAAAAAAAAAAAGAAAAAAAAAAGAAAAGAAAAGAAAGAAAAAACACCA 5730
                         ---------------------------------------------   i 
  L1M4_orf2#LINE/    678 ---------------------------------------------CACTA 682

  chr2_18242237_1   5731 TCAG---AGTGAACAGACAACCTACAGAATGGGAGAAAATTTTTTGCAAT 5777
                            i---      v        i                 v   -    v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAA 731

  chr2_18242237_1   5778 CTACCCATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAAC 5827
                         ii ivi      i  i  i  vi          v  i        ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_18242237_1   5828 AAATTTACAAGAAAGAAA-----AACCCCATCAACAAGTGGTCAAAGGAT 5872
                           v iv i  v   i i -----     v  i? v  i   v        
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_18242237_1   5873 ATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACAT 5922
                         v    i     i     v        i  vi viii     i ii     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_18242237_1   5923 GAAAAAATGCTCATCATCACTGGTCAT 5949
                              i       v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 7.45 (82 / 11)  


3140 27.16 1.11 0.44  chr2_18265364_18272054.rev     5298  6199 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_18265364_1   5298 TGGAAAAACATTTCACGCTCATGGATAGGAAGAATCGATATTGTGAAAAT 5347
                               i i  ii  i i        v      v ii       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_18265364_1   5348 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCTATCAAGC 5397
                            v     v      v i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_18265364_1   5398 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 5445
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_18265364_1   5446 TATGGAAGCAAAAACAAGCCCGCATAGCCCAGACAATCCTAAGGAAAAAG 5495
                                iiiv  ivi v  v v      v i      i i ii  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_18265364_1   5496 AACAAAGCTAGAGGCATCATGCTACCTGACTTCAA---T--CTGCAAGGC 5540
                                i i    vv   ii  v  ii i     --- --  i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_18265364_1   5541 TATAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGATATATAGATC 5590
                           i     i   i i  ii         i iv ii i   i         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_18265364_1   5591 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTAAAACCAT 5640
                                i    iv   ivii         vv   i    i  viii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_18265364_1   5641 CTGATCTTTGACAAACCTGACTAAAAGAAGCAATGGGGAAAGGATTCCCT 5690
                         i    i  i     ivv  v v i vv vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_18265364_1   5691 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAGTTGA 5740
                         v  i  i        i     v      v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_18265364_1   5741 AACTGGATCCGTTCCTTACACCTTATACAAAA-TTAACTCAGGATGGATG 5789
                          ii    i  v v   i     v         -        ii      v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_18265364_1   5790 AAAGACCTAAATGCAAGACCTAAAACCATAAAAACCCTAGAAGAAATTCT 5839
                          ?           i    v       i      vi i         viv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_18265364_1   5840 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 5888
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_18265364_1   5889 ACTCCAAAAGCAGTGGCAACAAAAGCCAAAATTCACAAATGGGATCTAAT 5938
                           v         vvi          vv     vv i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_18265364_1   5939 TAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAGCA 5988
                         i   v v  i ii  i  ii vv    i  v       vv i     iv 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_18265364_1   5989 GGCAATTTACAGAATGGGAGAAAATTTTTGCAATCTATCTATCTGACAAA 6038
                          i   iii                 v       vii  v       i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_18265364_1   6039 GGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 6088
                           i  vi          v  i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_18265364_1   6089 AACAAACAACCCA-TCAAAAAGTGGGCCCACGATATGAACAGACACTTCT 6137
                         i     i      - i?    i     vv v   v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_18265364_1   6138 CAAAAGAAGACATTTATGTAGCCAACAAACATTTGAAAAAAAAGCTCATC 6187
                          v        i  vi vi i     i  i  iv      i v-     v 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAAC 896

  chr2_18265364_1   6188 ATCACTGGTCAT 6199
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


3125 25.54 3.97 0.91  chr2_18309328_18311989.rev     1290  2170 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_18309328_1   1290 TGAAAAGCTATTTCATGTTCGTGGATTGGAAGATTCAATATCATCAAGAT 1339
                           i    v   ii       i            i i     ii i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_18309328_1   1340 GTCA---TTTCTCAATTTTATCAATAAATTCAATGCATTCTCAATCAAAG 1386
                          v  ---i i i   v  v   v i i      i   v  i v      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_18309328_1   1387 TCTCAGCAAGTTATTTTGTGGATATTGACAAAGC--ATC-TACAGTT-AT 1432
                           i    vivi v     ii  v        -  --   -  v i  -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_18309328_1   1433 ATAGAGA-ACAAGAGACTCAAAATAGCCAACACAATATTAAAGCAGAAAG 1481
                           i  i -i    i   i  i         v     v  i  iv    ii
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_18309328_1   1482 AGAAAGTGAAAGGATTGATACC-CCCAACTTTGAGG----------GGGT 1520
                          v     vii    i v i  i-     i  ii ii----------i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_18309328_1   1521 ACAGTAATCTAGACAGTATGGTATTAATGGAAGAATAAATAC-T---TCA 1566
                                  v       i     i iiiiv   i   i i i- ---   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_18309328_1   1567 ATATAATTGAATAAAGAGTCCAGAAATAAATCCACATGAATATAGTCAAT 1616
                           iv   v    vi                i   i iivv   i      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_18309328_1   1617 TGATCTTTGGCAAAGGAGCAAAGACAACGTAATGGAGAAAAGATAGTCTT 1666
                             i  i i   i  v  v     v ivi     i    ii        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_18309328_1   1667 CTTGAGAAATGGTGCTGCAACAACTAGACATTCACATGCTAAAGAGTGAA 1716
                         i ii v           vi      i  i ?i       v     i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_18309328_1   1717 ACCAGACACAGGCCTTATACTATTTATAAAAATTAACCCCAAATGGATTG 1766
                         iiii   v vvi   i i  i  v  i          i v        ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_18309328_1   1767 TAGGCTTAAATGTAAAACAGAAAACTATAAAACTTTTAGAAGGTAACA-- 1814
                         ?  i i         i vvv              i       iv    --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_18309328_1   1815 -GTATAAAATCTAGATGACCT-GAGTATGGCAATGACATTTTAGCTACAA 1862
                         - ?i    -   vvi      - i  vv       iiv i    v  ii 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_18309328_1   1863 CATTAAGGACACAATCCGTGAAAGAAGTAACTGATAAACTGGACTTTATT 1912
                           ii  iii     v viii      iv  iv      i       i  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_18309328_1   1913 GAAATTTAAAA--TTTCTACTTGGCAGAAGACACTGTCAAGAAAATAAGG 1960
                         i     v    --   v i   --  i i      i        i i ii
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_18309328_1   1961 AGGCAAGCCACAAACTGAGAGAAAGCATTTGCAAAAGACATAGCTGATTA 2010
                           i   v     i v  i      ii         vv i   v     v 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_18309328_1   2011 G---CTATTATCCAAAATATACAAATAATTCTTAAAACTCAACAA---AA 2054
                          ---  vv      i      i   v  i     v       i  ---  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_18309328_1   2055 AGATGAACAACTTAACTTAAAAAAATGGGGGCAAAAGACCTGAAGAGACA 2104
                            ii  i   ii  i ?     --    --    i  ii    v     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAA--TGGG--CAAAGGATTTGAATAGACA 842

  chr2_18309328_1   2105 CCTCACCAAAGAAGATATACAAATGGAAAGTAAGTCTATGAAAAGATGCT 2154
                         ii  v                     vv i    ivi             
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_18309328_1   2155 CCATATTATGAAATAC 2170
                          v i  i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (151 / 70)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.26 (43 / 19)  


2266 24.10 2.53 5.33  chr2_18520759_18522501.rev      500  1250 (492)    L1M4_orf2#LINE/L1      179   908 (0)  

  chr2_18520759_1    500 AAACAATCCTGAGAAAACTGAACAAAGCTGTAGGTATTATATTACCAGAC 549
                                 i   i   ivv        i  v   vv i i i v  vi i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr2_18520759_1    550 TTCAAATTATACTACAAAGCTAGAGTAACCAACACAGCATG-TACTGCCA 598
                               viv             v     i   v    ii  -     ---
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG--- 275

  chr2_18520759_1    599 AACACACACACACACACACACACACACACACACACACACACACCAAGGGA 648
                         ---------------------i  i viv i v   i i v i   v   
  L1M4_orf2#LINE/    276 ---------------------GCATAAGGATAGACATATAGATCAATGGA 304

  chr2_18520759_1    649 ACAGAATAGATAATCCAGAAATAAACTCATGCTTTTACAGTCATCTCATT 698
                          i     v  v i             i   i v    ii    vi v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_18520759_1    699 TTTGACAAAGGCACCAATAACATACATTGGGGAAAAGGTAATCTCTTTAA 748
                           i     i  ii    v v   v  v        iii  i   i  i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_18520759_1    749 TAAATGCTGCTGGAGAAACTGGATACTCATACGCA---GAATACAACTAG 795
                         i     v      iiv         ?i  i i   ---    iv ii i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_18520759_1    796 ACCCC-ATCTCTCACTGTATACAAACAAATAAAATCAAAATGGACTAAAG 844
                              - i   v   ii        --   v  v          ii ?  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAA--AATTAACTCAAAATGGATCAWAG 502

  chr2_18520759_1    845 ACTTAAATTTAAAACCAGAAACTATAAAACTAGATATAAAACCACTAGGA 894
                           i     v   i v vi             ---------- i--   i 
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACT----------CT--TAGAA 540

  chr2_18520759_1    895 GAAAACATTGGCAAAACTCTCTAGGACATTTGTATGGGCAACAATTTCTT 944
                                 v  ?iv  v   iiiv   v  v vv i     iii      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_18520759_1    945 ---T----TACTAAGACTTCACAGCAACCAAAGCACATATGGACAAATGG 987
                         --- ----i  i  i viv  -      v    v v v  i  i    v 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_18520759_1    988 GATCACATCAAGCTAAAAAGCTTCTGCACAGCAAAGGGAACAATCAACAA 1037
                           iiv      iv v    i   i  ii vv      iv  v     v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_18520759_1   1038 AATGAAGAGACAACCCACAGAATGGGAGAAAAGATTTGCAAACTACCCTT 1087
                          i    i                         v         ii iviv 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_18520759_1   1088 CTGACAAGGGATTAATAACCAGGATATATAAGGAAGCTAAACAACTTGAT 1137
                             i      i vi  v    i        i   viivv      ii  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_18520759_1   1138 AGGAAAAA-----ATAATCTAATTTGAAAATGGGCAAACAATCTGAACAA 1182
                          iv     -----    i i    ?i            vi  i    i i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_18520759_1   1183 ATATTTCTTAAAAGAAGACATACAAA-GACCA-TAAGGTACATGAAAAAA 1230
                          i      iv        i       - i   -    -i         i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGA 888

  chr2_18520759_1   1231 TGCTTAACATCAGTAATCGT 1250
                             i       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (109 / 68)
Gap_init rate = 0.02 (14 / 730), avg. gap size = 4.21 (59 / 14)  

 595 21.62 0.68 4.05  chr2_18520759_18522501.rev     1297  1444 (298)  C L1M4_orf2#LINE/L1   (765)   143     1  

C chr2_18520759_1   1444 TGGAAAGAAAGCCGATGGTCATGGATTGAAAGACATAATTAGTATTGGCA 1395
                                 v v  v   v          i     ----   i     vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC----TTAATATTGTTA 46

C chr2_18520759_1   1394 AGATGTCAATACTACCCAAAGTAATCTACAGGTTTAGTGCAATTTCTATC 1345
                              v       v      v i        i  i ii     ii     
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

C chr2_18520759_1   1344 AAAATTCCAA-TGATTTTTTTTTTCGGAAATAGAATAACCCATTTTAAA 1297
                              i   i-  --ii      v i     v  vv i iv  ii    
  L1M4_orf2#LINE/     97 AAAATCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

Transitions / transversions = 1.46 (19 / 13)
Gap_init rate = 0.02 (3 / 143), avg. gap size = 2.33 (7 / 3)  


2137 27.89 2.17 0.58  chr2_18549636_18551306      488  1179 (492)    L1M4_orf2#LINE/L1      206   908 (0)  

  chr2_18549636_1    488 TTTGAGAAATCTC-CACTACTGGATTTCAAGTTATACTACAAGGCTACAG 536
                           v   i --   -    v ivi       iviv        i       
  L1M4_orf2#LINE/    206 TTGGAGGA--CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_18549636_1    537 TAAGCAAAATGGCATGACACTGGTACAAAAACAGACATATAGACCAATAG 586
                            v   i ii ii  ii     i i  ii i           i    i 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_18549636_1    587 AACAAGTTAGAGAACCCAGATATAAAGTTGCACACCTACAGCCATCTGAT 636
                           i iiv v    ii     v     viiii   ii  ii i  vi    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_18549636_1    637 CTGTGACAAAGTCAATAATAACAAGCAA-GAGAAAAGAACTCTCTATTCA 685
                         i vi     i viivi  v v  vv   - i i      ivv   v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_18549636_1    686 ATAAATGGTGTTGGGATAACTGGTTGGCCACAGACAGAAGAATGAAACTA 735
                          i        i     i      v i?     vi  i         ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_18549636_1    736 GACCCCTACCTTTCACCATACACAAAAATCCACTCAAGATAGATTAAAGA 785
                                    iv       i        iv      i  i   i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_18549636_1    786 CTTAGATGTAAGACCTAAAACTCTAAAAATCCTAAAAGA---CCTAGGA- 831
                          i  i        v        v     v  i  i    --- v    ?-
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_18549636_1    832 CATACCATTCCAGATATAGGCCTTGGCACAGATTTCATGAGGAAGTCTCC 881
                         i v i -   vv  iv v  vi v    vv i    v iiiv v v v  
  L1M4_orf2#LINE/    554 TAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_18549636_1    882 AAACGCAATTGCAACAAAA-ACAAAATAGACAAGTGGGACCAAATCAAA- 929
                            v   vvv         - v        i  i v    ivv      -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_18549636_1    930 TGAAGAGCTTCTGCAGAGCAAAAGAAACTATCAACAGAGTAAACAGACAA 979
                          v  i i   i  iivvv    i  v        v i   i  v      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_18549636_1    980 CCTATAGGATAAGAGAAAATATTTGCAAGCTATGCACCCGACAAGAGTCT 1029
                           i i  i  ii                iii  ii i i  i   i v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_18549636_1   1030 AATATCCGGAATCTATCAGGAACTTAAACAAATCAACAAGCAAAAAATCA 1079
                         vi     i    v   v i     ivv    v    i  -i     iv  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAGACA 801

  chr2_18549636_1   1080 AACAGCCCCATTAAAAAATGGGCAAAGGAC----ATGGACAATTCTAAAA 1125
                           i i   v   ?                i----  i    v    vv  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_18549636_1   1126 AGAAGACATATGCATGACTA-TCAATAC--GAAAAAATGCTTAACATTAC 1172
                               i   iiv   i i - v ii  --     i     i     i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_18549636_1   1173 TAATCAT 1179
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.62 (117 / 72)
Gap_init rate = 0.02 (12 / 703), avg. gap size = 1.58 (19 / 12)  


3107 26.26 2.12 0.67  chr2_18561364_18567717.rev     4968  5862 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_18561364_1   4968 TGGAAGAATATTCCATGCTCATGCATAGGAAGAATCAATATCATGAAAAT 5017
                              ii    i     i     v  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_18561364_1   5018 GGCCATACTGCCCAAAGTAATTTACAGTTTCAATGCTACCCTCATCAAGC 5067
                            v     v      v i  i     v     i  v i  ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_18561364_1   5068 TATCAATGACTTTCTTCACAGAATCAGAAAAAACT-ACTTTAAATTTCAT 5116
                          vi  iivi i  i  ii     viv  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_18561364_1   5117 ATGGAACCAAACAAAGAGCCC-GCATAGCCAAGACAATCCTAAGCAAAAA 5165
                               -- vi   i ii   - v        i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_18561364_1   5166 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATTACAAGG 5215
                                 i      vv   ii  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_18561364_1   5216 CTACAGTAACAAAAACAGCATGGGGTACTTGTACAAA-ACAGATATATAG 5264
                                  iv  i    --  v      v i i  i- i   i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAG--TGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_18561364_1   5265 ACCAATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATCTACAAC 5314
                          i        i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_18561364_1   5315 CATCTGATCTTTGACAAACCTGATAAAAACAAGCAATGGGGAAAGGATTC 5364
                           vi    i  i     ivv  vi  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_18561364_1   5365 CCTATTTAACAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 5414
                         i  v  i           i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_18561364_1   5415 TGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGGTGG 5464
                             ii         v   i     v                   ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_18561364_1   5465 ATTAAAGACTGAGATGTAAGACCTAAAAC---------CCTAGAAGAAAA 5505
                           i ?    iv i        v       --------- i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_18561364_1   5506 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACT 5554
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_18561364_1   5555 AAAACA--AAAAGCAATGGCAACAAAACCCAAAATTGACAAATGGGATCT 5602
                          vi   --       vvi         vvv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_18561364_1   5603 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAGACTATCAG---AGTGA 5649
                         v  i   v v  i i   i  ii vv    i  v       i---     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_18561364_1   5650 ACAGGCAACCTACAGAATGGGAGCAAATTTTTGTAATCTATCCATCTGAC 5699
                          v  i     i            v    v    i  vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_18561364_1   5700 AAAGGGCTAATATCCAGAATCTACAAAGAACTTGAGCAAAGTAACAAGAA 5749
                           i  i  vi          v  i        ivvi   vvi  i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_18561364_1   5750 AAAAACAAACAACCCCATCAAAAAGTGGGGGAAGGATATGAACAGACACT 5799
                            i     i     v  i?    i    vi      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_18561364_1   5800 TCTCAAAAGAATACATTTATGCAGCCAACAAACATATGAAAAAA-GCTCA 5848
                             v      v i  vi viii     i  i  i       i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_18561364_1   5849 TCATCACTAGATTA 5862
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (139 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.08 (25 / 12)  


 404 26.17 0.00 1.87  chr2_18609751_18612292.rev      677   783 (1759)    L1M4_orf2#LINE/L1        1   105 (803)  

  chr2_18609751_1    677 TGGAAGAATATACTGTGTTTATGATATCTGGAAGACTTCATATTTTAAAA 726
                              ii    v ii    i   i-  -          v     v v  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGG-AT-TGGAAGACTTAATATTGTTAAG 48

  chr2_18609751_1    727 ATGTTGATTCTTCCCAAATTGGCTTATAGGTTCAGTGCAATGTCAATCAA 776
                            vii  v  i         iii  i  i    ii     vi v     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_18609751_1    777 AATTCTA 783
                            i i 
  L1M4_orf2#LINE/     99 AATCCCA 105

Transitions / transversions = 2.50 (20 / 8)
Gap_init rate = 0.02 (2 / 105), avg. gap size = 1.00 (2 / 2)  

 290 31.14 10.06 6.19  chr2_18609751_18612292.rev      988  1504 (1038)    L1M4_orf2#LINE/L1      126   662 (246)  

  chr2_18609751_1    988 TGACAAG-TAGTTTTTAAATGTATATGGAAAAGCAAAAGGAGAAGAGTGA 1036
                                - ii ii v    vi         v    ii ivvv   i ii
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr2_18609751_1   1037 CAAAGACATTCTAGAAAATAACAAATGAAG----AGTATTTGC--TTTAA 1080
                          v  i   v   v     vi vi  ii   ----  v i ii --  ivv
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_18609751_1   1081 AGGAAATAAATACTTTCTGTGAAGCTATAATAATTAAGAC--TGTGGTAT 1128
                          -- vv v  v    v  iii      i i    i     --       i
  L1M4_orf2#LINE/    226 A--ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr2_18609751_1   1129 TGGTTCAGGG--------------CAAGGAAGTAGCA--AACAGTACAAC 1162
                            ivi i  --------------   v i i   v --i v   v  i-
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG- 322

  chr2_18609751_1   1163 TCAAACAAAATTATGTACATATGAACCCTTGAACTGTGATAGAAGTTGCA 1212
                         --   i   vii  ii iv    iv vv    vi vi  i iii  vv  
  L1M4_orf2#LINE/    323 --AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_18609751_1   1213 TTTTATTTCATTAAATG----AAACATATTATTTTCAATAAATGATGCAT 1258
                         ---- vvi    v    ----  iv   v v       i     i   - 
  L1M4_orf2#LINE/    371 ----AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC-T 415

  chr2_18609751_1   1259 AAGTATATTGACCAACAATATGGAAAAG--TGAAATCAGACTGTTATCTC 1306
                         ii vvv i  ivi ? v i   v     --    i ii   ivi  i   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_18609751_1   1307 ACTTGGTATGCAAAAATTGTTGCATGTCATTTAAAT--ATCTAAGAGAGA 1354
                           vivi   i        i---- i-   ---    --   ---- ?   
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTA----AC-TCA---AAATGGATC----AWAGA 503

  chr2_18609751_1   1355 TGAAACTATATAAATGAAATAAAATTATATAAATGTTTTCTATAATAATA 1404
                         ivv  --  i   --  iv     i    -   i- i  vv vi v  i 
  L1M4_orf2#LINE/    504 CCTAA--ATGTAA--GAGCTAAAACTATA-AAAC-TCTTAGAAGAAAACA 547

  chr2_18609751_1   1405 TAAGAGAATATCTTCATGGTCTTGGAATAAAGAA---------------G 1439
                           i ? v v      i  ii     iv  iiv  --------------- 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_18609751_1   1440 ACA--AAAATTTATATGAGTCATAAAAGAAACAACTAG-TAA-TTTAACG 1485
                            --    ---ii ii  iv i        v  -   -   -  vi  v
  L1M4_orf2#LINE/    598 ACACCAAAA---GCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACT 643

  chr2_18609751_1   1486 TTATTAAAAATAAGAGCTT 1504
                          i  i    v   i i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTT 662

Transitions / transversions = 1.47 (94 / 64)
Gap_init rate = 0.05 (27 / 537), avg. gap size = 3.11 (84 / 27)  

 319 22.88 8.86 9.59  chr2_18609751_18612292.rev     1780  2050 (492)    L1M4_orf2#LINE/L1      640   908 (0)  

  chr2_18609751_1   1780 GACTCCATCTCAAAAAAAAAAAAACTTCTATGTATCAAAGA----TATCA 1825
                             i    ----    vv        i i  iv      i----     
  L1M4_orf2#LINE/    640 GACTTCATC----AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_18609751_1   1826 AAGTTAAAAAGATAACACTAAAAGTAAAACTACAAACCACTGAATTGAA- 1874
                          i------------------     i   vv    v    v    v i -
  L1M4_orf2#LINE/    686 AG------------------AAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_18609751_1   1875 -AAGTATCTGCAGCACATACAACTGACAAATATCAGCCATCCAGAACATT 1923
                         -  i   i    ivv    i v    i  iviv vvvi        i  v
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_18609751_1   1924 TAAAGAACTACATACATCCTGAAGAAAAAAAGAAACAAATGAATACAA-- 1971
                                  - v    -v  v  v  v    - i      -  iv   --
  L1M4_orf2#LINE/    768 TAAAGAACT-CTTACA-ACTCAATAATAAAA-AGACAAAT-AACCCAATT 813

  chr2_18609751_1   1972 -AAAGATAATGAAAAGATATGAACTGGTCTTTCT-------AAAT----- 2008
                         -   i  iivv   i   v    iv iiv     ------- i  -----
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_18609751_1   2009 --TGGCCA-TAAGCTTATGAAAAGTGGTTTAACTTCAGTGGCAAT 2050
                         --      -     vi        vv i i   v   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.94 (30 / 32)
Gap_init rate = 0.04 (12 / 269), avg. gap size = 4.17 (50 / 12)  


 374 24.38 11.25 5.00  chr2_18672708_18676087     1712  1871 (1509)    L1M4_orf2#LINE/L1        2   171 (737)  

  chr2_18672708_1   1712 GGAGAAATA--CCATGTCCATGGACAGAAAGACTTAATATTGTTAAGATA 1759
                            i i   --      i      iv i                     i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_18672708_1   1760 TCTATTATCCCAAGATCTAGCTATAAATAAAATAAAAATAAAAAATTCTT 1809
                         v v  vv    v i  iv v   i i  ---- v  vii  ---- i i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGAT----TCAACGCAA----TCCCT 93

  chr2_18672708_1   1810 GTAAAAATT---------TTTCCCCCAGAAAT----AAACT--TCTTAAA 1844
                         i v     i---------   iiiv       ----  i  --  i    
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_18672708_1   1845 -TCTATATGAAAGTGCAAGGGAATCAGA 1871
                         - ii     i  i         vi    
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGA 171

Transitions / transversions = 2.00 (26 / 13)
Gap_init rate = 0.04 (7 / 170), avg. gap size = 3.71 (26 / 7)  

 265 28.00 1.33 0.00  chr2_18672708_18676087     2290  2364 (1016)    L1M4_orf2#LINE/L1      232   307 (601)  

  chr2_18672708_1   2290 AGAACT-ACTATAAAACTACAATAATCAAGACAATGTAATATTGATAAAG 2338
                          i    -    i   i     i           i   ii  i  ii v i
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_18672708_1   2339 GGATGAATATCTGTATTAAAGGAACA 2364
                             ii i  v iv  i  v    i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATA 307

Transitions / transversions = 4.25 (17 / 4)
Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1)  

1486 24.57 3.40 4.16  chr2_18672708_18676087     2366  2894 (486)    L1M4_orf2#LINE/L1      384   908 (0)  

  chr2_18672708_1   2366 GGCAGAAAATCACCCTTTTCAACAAATAATGCTTGAACAATTAAGATATC 2415
                           v i i   - vi             ii    v i    i i-    ? 
  L1M4_orf2#LINE/    384 GGGAAAGAAT-AGTCTTTTCAACAAATGGTGCTGGGACAACTG-GATAKC 431

  chr2_18672708_1   2416 CAGGAAATTAGGATAAGGAGGAAAAATGAACCACAACTTGTGCTTTGCAC 2465
                           ------i v vv  i  ivi  iv  i   v ------ i i ii   
  L1M4_orf2#LINE/    432 CA------CATGCAAAAGAATGAAGTTGGACCCC------TACCTCACAC 469

  chr2_18672708_1   2466 AA-ATACCATA-TTGACTCAAAATAGATGATAATCCTAA--GTAAGAAAC 2511
                         v -    v v -  i         i   v ? iv     --      i--
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG-- 517

  chr2_18672708_1   2512 CTAAAACCATAAAATTTCTATATAAAAAGTCTGGAGATAA-TCCTTGTGG 2560
                                i      i ii  v - i   iiv i i?i   -  i i   i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGA-AGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_18672708_1   2561 CCTTGGATTAGGCAAAGATTTCTTATATATGACATTAAAAGCACAATTTC 2610
                               i        v i       v        ii          vivv
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_18672708_1   2611 TAAGAGAAAAAATTGATAAATCTGACTTCATCAAAATTATAAGTTTCTGC 2660
                         i  i         v       iv                v  ii  i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_18672708_1   2661 TCACTGAAAAGCACTG-AAAGATGTTAGAATGAAA-GACAAGC-ACAGGC 2707
                         v viii  iii    i-v    -----i i     -     v -    iv
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGA-----AAGTGAAAAGACAACCCACAGAA 711

  chr2_18672708_1   2708 TGAGAGAAGATATTTGTAAAACACACACCTGATAAAGGATGAGTATCCAA 2757
                           i     i       i   v  i i i       i   ivv       i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_18672708_1   2758 AACATATGAGGAACTCTCAGAAGTTGATAACAAAC---CAAA-AACCCAA 2803
                           i    i i       i v  v ii    i   v---    -       
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_18672708_1   2804 T---AAAATAAGGAAAATATTTGAACAGGTACTTCACCAAAGAAGATATG 2850
                          ---     ii v   iv       i  ii i   v             i
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_18672708_1   2851 TGA-TGGAAAA-AAGCAC-TGATAAGATGCTCAGTAACATTTGTCAT 2894
                         ii -   vv  -      -   v          ii v  ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (85 / 42)
Gap_init rate = 0.04 (20 / 525), avg. gap size = 2.00 (40 / 20)  


2987 26.19 1.66 0.89  chr2_18679848_18683439     2200  3100 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_18679848_1   2200 TGGAAAAACATCCCATGATCATGAATAGGAAGAATCAATTTTGTTAAAAT 2249
                               i i        v     i  v      v i   v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_18679848_1   2250 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 2299
                            v     v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_18679848_1   2300 TACCAATGACATTTTTCACAGAATTAGAAAAAACT-ATTTGGAAATTCAC 2348
                          v   iivi v     ii     v v  v  i-  -  iivi       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_18679848_1   2349 ATGGAATCAAAAAAGAGCTGGAATAGCCAAAGCAAAACTTAGCAAA-AAG 2397
                               viiv  ii  v ii           i   v-   iiv   -   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAG 198

  chr2_18679848_1   2398 AACAAAGCTGGAAGTATTATATAACCAAACTTCAAACTATACTACAAAGA 2447
                                i    i vv i i ivv  v  i      viv          v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_18679848_1   2448 TACAATAACTAAAACAGCATGGTGCCGGTATAAAAACAGACACATAGACC 2497
                             i   ii  i    ii    i i  i    ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_18679848_1   2498 AATGGAACAGGTTAGAAAACCCAGAAATAAAGCCACACACCTACAACCAT 2547
                                i  iv v  i ii           v   i   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_18679848_1   2548 CTGATCTTCAACCAAGTCAAGAAAAACATGCAATGGGGAAAGGACTCTGT 2597
                         i    i   i  v i viivv  i v   v            i ivv v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_18679848_1   2598 ATTCAATAAATGGTGCTGGGATAACTGGCTAGCTATATGCCAAAGATTGA 2647
                         v     i              i      v  ? i i    v     v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_18679848_1   2648 AATGGGACCCCTTTCTTTCACCAGATACAAAAATTAACTCAAGATGGATT 2697
                          i v        vi  iv     v                  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_18679848_1   2698 AAAGACTTAAACATAAAACTCAAAGCCC--AAGCCCT-AGAGGAAAACCT 2744
                          ?    i    ii   i vii   i iv--  i i  -   i      v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_18679848_1   2745 AGG---AAATACCATTCTGGACA--GGCTTTGGCAAAGATTTCAT-GATG 2788
                            ---    -- -   vv   v--  v  v     v i    v -   -
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr2_18679848_1   2789 AAGACACCAAAAGCAATTGCAACAACAAGAAAAAATTGACAAATGGGAGC 2838
                          v             vvv       -          v  i    v   vi
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAA-AAGAAAAAATAGATAAATTGGACT 643

  chr2_18679848_1   2839 TAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCAACAGAGTA 2888
                          v  i   v v  i i   i  iiivv    i  v        v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_18679848_1   2889 AACAGACAGCCTATAAAATGGAAGAAAATATTTTCAAACTATGCATTTAA 2938
                           v     i  i i i     i           v    ii  ii  i i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_18679848_1   2939 CAAAGGTCAAAAATCCAGAATTTGTGAGGTATTTAAACAGATTAACAAGC 2988
                         i  i  v vviv         v i i i v i ivv   iv i  i  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_18679848_1   2989 AGAA-ACAAA---CCTCATTAAAAACTGGGCAAATGACATGAATAGACAC 3034
                          i  -     ---  iv   ?    v        v  iv          i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_18679848_1   3035 TTCTCAAAAGAAGACATACATGCAGCCAACAAGCGTATGAAAAAAATGCT 3084
                              v        i     viii     i    ii       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr2_18679848_1   3085 TAACCTCACTAATCAT 3100
                         i   v   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.44 (23 / 16)  


 350 25.49 0.00 1.96  chr2_18735832_18740670.rev     3334  3435 (1404)    L1M4_orf2#LINE/L1        1   100 (808)  

  chr2_18735832_1   3334 TGGAAAAACATTCCATGCTCATGGATAAGAAGAATCAATTATCATTAAAA 3383
                               i i  i     i        vi     v i   -  ii    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT-ATTGTTAAGA 49

  chr2_18735832_1   3384 TGCCCATACTGCCCAAAACAATTTATAGATTTTATACTACTCCATCTCAA 3433
                           v v     v      vii  i  i     iv ii - v   v v    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAA 98

  chr2_18735832_1   3434 AA 3435
                           
  L1M4_orf2#LINE/     99 AA 100

Transitions / transversions = 1.60 (16 / 10)
Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.00 (2 / 2)  

2733 25.88 4.79 1.25  chr2_18735832_18740670.rev     3471  4347 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_18735832_1   3471 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATTATCACTAAAA 3520
                               i i  i     i        v      v i   -  iii   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT-ATTGTTAAGA 49

  chr2_18735832_1   3521 TGGCTATACTGCCCAAAAAAATTTATAGATTTTACGCTATTCTCATTAAA 3570
                             v     v      vvi  i  i     iv    v  i ii  i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_18735832_1   3571 CTAAC-GTTGACATTCTTCAAACAGAA-TT-AGAAACT-ATTTTAAAATT 3616
                         v vv - i  v v  i  ---i     -  - v  i  -  ii       
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_18735832_1   3617 CACATGGAAC--CAAAAAACAGCTTGAATAGCCAAGGCAATCTTAAGCAA 3664
                           i      v--   iii  -- iv          ii       i i-  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAA-AA 193

  chr2_18735832_1   3665 AAAAAAACAAAGGTGGAGACATCCTGCTACCCAACTTCAAACTATACTTC 3714
                          i  i       v     ivv  vii  v     i      viv    v 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_18735832_1   3715 AAGGCTACAGTAACCAAAATGGCATGGTACTGGTACAAGAACAGACACAT 3764
                           i          i   i ii ii         i i   i i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_18735832_1   3765 AGACCAATGAAAAAGAATAGAGAACCCAGAGATAAGATCATGCACCTACA 3814
                            i     i  v     v    ii     i    ivi   i  ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_18735832_1   3815 ACCATCTGATCTTTAACAAACCTGACAAAAACAAGCAACAGGGAAAGGGT 3864
                         ii  vi    i  ii    ivv  v   i v  vv   ii       ii 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_18735832_1   3865 TCCCTATTTAACAAATGTTGCTGGTAGAACTGGCTAGCCATAATCAGAAA 3914
                         vvi  v  i        v      v v      v  ?   i vv  i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_18735832_1   3915 ATTGAAACTGGACTCCTTCCTTACACCATATACAAAAACTAACTCAAGAT 3964
                          v    ii     i   v   i                i        i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_18735832_1   3965 GGATTAAAGACTTAAATGTAAAAACAAAAACTATAAAAAGCCTAGAAAAA 4014
                             i ?    i         i i v            vv i     i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_18735832_1   4015 AACCTGGGCA-ATACCATTCAGGACATAGGCATAGACAAAGATTTCATAA 4063
                            v i  ?i- v i -   iv   v v  vv   i   v i    v  i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_18735832_1   4064 CGAAGATGCCCAAAGCA----------------AAATTGACAAATGGGAT 4097
                         vv v  ii  v      ----------------    v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_18735832_1   4098 ATAATTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAATCATCAAAAGAG 4146
                         v v  i   -     i -   i  ii vv    i  v ii     i i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_18735832_1   4147 TAACCAGATAACCTACAGAATGGGAGAAAATTTCCACAAACTATGCATCT 4196
                          i vv   i    i                 v iii    ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_18735832_1   4197 GACAAAGGTCTAATATCCAGCATCTATAAGAAAAT--TA-AATTTA---- 4239
                           i  i  v  vi       v  v     ii  v --  -  i i ----
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_18735832_1   4240 --------CAAAAAA---AATTAAAAAGTGGGCAAAAGGACATGAACAGA 4278
                         --------    v  ---    ?    i        -   iv    i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA-GGATTTGAATAGA 840

  chr2_18735832_1   4279 CATTTCTCAAAAGAAGACATATATGTGGCCAAAAAACATATAAAAAAAAA 4328
                                 v        i   i vi       v  i  i  i    i v-
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT- 889

  chr2_18735832_1   4329 GCTCCACATCACTGATGGT 4347
                             v      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (140 / 83)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.65 (53 / 20)  


1810 22.73 1.62 12.18  chr2_18772713_18778397.rev     3899  4637 (1048)    L1M4_orf2#LINE/L1        1   661 (247)  

  chr2_18772713_1   3899 TGGAAATACATTCCATGTTTATGAGTTGGAAGAATCAATTTCATAAGAAT 3948
                               v i  i       i   ii        v i   v ii v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_18772713_1   3949 GACTATACTGCCCAGAGCAATCTACAGATTCAATGCAATTCCTATGAAAA 3998
                          i v     v    i vii              i     i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_18772713_1   3999 TACCAACATCATTTTTTATACTGCCCAAAGCAATTTACAGATTCAATGCA 4048
                          v   i --------------    --------   -----  ---    
  L1M4_orf2#LINE/    101 TCCCAGC--------------TGCC--------TTT-----TT---TGCA 120

  chr2_18772713_1   4049 ATTCCTATGAAAATACCAACATCATTAACAATTAAGATTGTTATTTCTAA 4098
                         --------    ------------  i    -------- ------  i 
  L1M4_orf2#LINE/    121 --------GAAA------------TTGACAA--------G------CTGA 136

  chr2_18772713_1   4099 TTTCTAAAAAGAAAAAATAATATTTTTTGGTTTATAGGGAACCAAAAAAG 4148
                          i-      ---------------------  i   v    viiv  ii 
  L1M4_orf2#LINE/    137 TC-CTAAAA---------------------TTCATATGGAAATGCAAGGG 164

  chr2_18772713_1   4149 AGCCCAAATAGCCAAAGCAATACTAAGCCAAAAGAATAAATCTGGAGGCA 4198
                          v  vi          i    vi i ivv i     i   vi      vv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_18772713_1   4199 TCATATTACCCAACTTCAAATTATACTACAAGGCTATAAATACCCAAACA 4248
                            i i v     i      viv        i    i ivv i v i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_18772713_1   4249 GCACGGTACTGGTATAAAAGTAGACACATAGATCAATGGAACAGAATAGA 4298
                          iii        i    iii      i              i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_18772713_1   4299 GAATCTAGAAATAAATCCAAACATTTACAACCAATTGAGATTTGACAAAG 4348
                           i  i         i   v       iiii       vv  i     i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_18772713_1   4349 CATACAAAAAC-AT-CAATTGGAGAAAGGACATCCTATTCAATTAATGGT 4396
                         -i i v  i  -  -    -  i     i i vi  v     iv      
  L1M4_orf2#LINE/    365 -GTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_18772713_1   4397 TCTGGGAAGTTTGGATAGCTACATGTAGAAGAATGAAACTGCATCTCTAT 4446
                         v      vivi      ? i     i i         ii  v i i   i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_18772713_1   4447 CTCTCACCATACACAAAAGTTAACTCAAGATGGATT-------CAAATAT 4489
                            v       i      i         i      i-------i    i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_18772713_1   4490 AAGACCTTAAACCACATAAATTCT-GGAATGAAACCTA--AGTAAAACTT 4536
                             v  v    i i -   i   -i   vi    v  --?     v   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_18772713_1   4537 CTGGACATTGGCCTAAGCAGAGAATTTATGACTAAGATCCCAAAAGCAAA 4586
                          vv   v    vi  i   iv iv  iv iiv  v  iv         v 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_18772713_1   4587 TGCTAACAAAAACAAAAATAAATAAGTGAGACCTTATTAAGCTAAAAAGC 4636
                         v  -       iv       i    i vi   i i  i  iv v    i 
  L1M4_orf2#LINE/    612 AGC-AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_18772713_1   4637 T 4637
                          
  L1M4_orf2#LINE/    661 T 661

Transitions / transversions = 1.77 (106 / 60)
Gap_init rate = 0.03 (19 / 661), avg. gap size = 5.37 (102 / 19)  

 709 20.77 9.18 0.48  chr2_18772713_18778397.rev     4987  5193 (492)    L1M4_orf2#LINE/L1      684   908 (0)  

  chr2_18772713_1   4987 CAAACAAACAAACAGACAACCTACAGAATGGGAGAAAATACTTGGAAATT 5036
                            iv  iii  v        i                  i   v    i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_18772713_1   5037 ATGCTA-CTGACAAAGGACTAATATCCAGAATCTACAAGGAACTCAAGCA 5085
                           i-  -    i  i     vi          v  i  i      vvi  
  L1M4_orf2#LINE/    734 ATA-TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_18772713_1   5086 CGTCAGCAAGAAAACAACAAATAATCCCATTAAAAAGTGAGCAAAAGACG 5135
                         vv   ii  v    vi        i  v   ?    i  i     i  iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_18772713_1   5136 TGAATAGA-----------------TATAC-AATGGCCAATAAAGATTTT 5167
                                 -----------------     -            iv iv v
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_18772713_1   5168 TAAAAATGCTCAACATCACTAATCAT 5193
                         v   i             ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (25 / 17)
Gap_init rate = 0.02 (4 / 225), avg. gap size = 5.00 (20 / 4)  


1650 25.76 7.46 0.85  chr2_18793698_18795276      498  1087 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_18793698_1    498 AATAACAGACACAAAGACTGATGAAACAGAATAGAGAACTCAGTAATAAA 547
                           vi i     i v   iii   i  i     v    iii   v      
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_18793698_1    548 CCCAAGCATATACAATCAACTAAATTTTGACAAGACCACCAATAAAGCAA 597
                             vi   v  iii    i i v   i      ivii    --i v  v
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA--GACCAT 377

  chr2_18793698_1    598 -AAATGGTGAAAGGAT-------TCAACAAGTGGAAATGGGAAAATTGGG 639
                         -v     v     i  -------       i   viv     v  i   i
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_18793698_1    640 TATGTACATG-AAAAGAATGACACTGGATCCTTAAATGGTATCCTACACA 688
                           ?vi     -          vii    i  i  vv vii i v  i   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_18793698_1    689 AAAATCAAATCAAAATGTATTAAAAACCTCAGTATAAGATCTAAAACTGT 738
                              i  v        v  i ? i    v i i     v        i 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_18793698_1    739 AAAAATTCCTGGAAGAAAATATACAGAGGAAAAGCTTCTTGACATTGCCC 788
                             -i  i i        i   -- i? v   v    v    v   vvi
  L1M4_orf2#LINE/    528 AAAA-CTCTTAGAAGAAAACATA--GGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_18793698_1    789 TTGGCAATTAGTTTTTGGATTTCACAACAAAAGCTCAGTGAATAAAAACA 838
                          v      viv  i  i   v v   v       v  ivv  i    iv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_18793698_1    839 AAAATAAATAAGTGGGACTATATCAAA-CTAAAAAG----GTTCTCCAAA 883
                               i    i v     vi      -i      v----  v  i    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_18793698_1    884 ------TAGCAAAAGA---AAAAGACAGCTTATGGTTTGGGAGACAATAT 924
                         ------  v   i i ---        i ii ii vv       v     
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_18793698_1    925 TTGCAAACTATACATCTGATAAGAGATTAACTCCCAAAATATATAAGGAA 974
                                ii   i          i  i viivi   i         i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_18793698_1    975 GTC--ACA---CAATAGCAAAAAAA-AAGT-------TTAAAAAATGAGC 1011
                         v  --   ---     ii     i -  i -------  ?       i  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_18793698_1   1012 AAAA-ATCTG----GACATTTTTCT---GAACACATAAAAATATCCAACA 1053
                            i-  i  ----       i  i---   v i   v    iv    i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_18793698_1   1054 GGTATATGAAAAGGTGCTCACCATCAGTAATCAT 1087
                         i i i        i      v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (92 / 56)
Gap_init rate = 0.03 (17 / 629), avg. gap size = 2.88 (49 / 17)  


3087 26.55 1.22 0.77  chr2_18795344_18801731.rev     4993  5896 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_18795344_1   4993 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5042
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_18795344_1   5043 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5092
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_18795344_1   5093 TACCAATGAATTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5140
                          v   iivivi  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_18795344_1   5141 TAGGGAATCAAAAAAGAGCCCGCATTTCCAAGTCAATACTAAGCCAAAAG 5190
                           v    viiv  ii  v  v v  vv    iv    vi i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_18795344_1   5191 AACAAAGCTGGCGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5240
                                i   v  vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_18795344_1   5241 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5290
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_18795344_1   5291 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5338
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_18795344_1   5339 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5388
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_18795344_1   5389 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGAA 5438
                           v  i  i              v      v  ?   i   i -      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAA 445

  chr2_18795344_1   5439 -GAAACTGGATACCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5487
                         -   ii    iv   v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_18795344_1   5488 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAA 5536
                           i ?    i       v   v       i      -    -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr2_18795344_1   5537 ACCTTGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5585
                           v v  ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_18795344_1   5586 TAAAACACCAAAAGCAATGGTAACAAAAGCCAAAATTGACAAATGGGATC 5635
                           vi            vvi i        vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_18795344_1   5636 TAATTAAACTAAAGAGATTCTGCACAGCAAAAGAAACCACCATCAGAGTG 5685
                          v  i   v v  i iv  i  ii vv    i  v  i i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_18795344_1   5686 AACAGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTACTCATCTGA 5735
                           v  i     i              v  v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_18795344_1   5736 CAAAGGGCTAATATCCAGAATCTACAAGGAACTCAAACAAATTTACAAGA 5785
                         i  i  i  vi          v  i  i      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_18795344_1   5786 AAAAAACAA----CCCCATCAACAAGTGGGCAAAGGATATGAACAGACAC 5831
                             i    ----   v  i? v  i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_18795344_1   5832 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5881
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_18795344_1   5882 ATCATCACTGGCCAT 5896
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (136 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


2558 24.97 2.91 5.27  chr2_18959436_18961720.rev      865  1793 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_18959436_1    865 GGAAAACCATTCCATGTTCATAAATAGGAGGAATAAATATTGT-AAAATG 913
                              ivi  i          ii  v   i  v v        -  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_18959436_1    914 GCCATACTCCCCAAAGAAATTTATAGATTCAATGCTATTCCTA-CAAAAC 962
                           v            vvi  i  i        i  v  i    -     -
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA- 100

  chr2_18959436_1    963 TACCAA-TGTCACTTTTTACAGATCTTT-TAAA--AAATCTAAAATTCAT 1008
                          v   i-  i -i     i    vv  v-i  i--i vi           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_18959436_1   1009 ATTGAAACAAATAAGAACTGGAATAGCCAAGGTGATCCTAAACTAAAAGA 1058
                           v    iiv vii  v ii          iiii   i i  vv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_18959436_1   1059 ACAAAACTGGAGGCATCACACTACTGAACTTCAAACCACAGTAAATGGTT 1108
                              ii      vv       v iv  i      v vi v  v vi i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_18959436_1   1109 ATAGTAACGAAAACGGCATG-TAATGGTACAAAAATAGACACATAGACCA 1157
                          i     iv  i  i ii  -  v   i i  ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_18959436_1   1158 GTGTAACAGGTTAGAGAACCCCGAGGTAAAGCCGTACATCTACAACTATC 1207
                         i  v  i  iv v    ii  v  ii    v  i     i  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_18959436_1   1208 TAATCTTTGAAAAAGTTGATAATAACAAGCAATAAGGAAAGAAT--TCAC 1255
                          i  i  i  v  i v  vi  v v  vv    ii         --  vi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_18959436_1   1256 AATTCAGTAAATGTTTCTGGGGTAACTGGCTATCTATATGCAGAAGATTG 1305
                         --    ii     v v     ii      v  ? i i     i    v  
  L1M4_orf2#LINE/    400 --TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_18959436_1   1306 AAACTGGACCCCAACTATTCACCATATACAAAAATCAACTCAAGAGAGAT 1355
                           ii        v  iviv                i       i vi   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_18959436_1   1356 TAAAGACTTAAATTTAAGACCTAAAACTGTGTGTGTGTATATATATATAA 1405
                         i ?    i     v     v        ------------------    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACT------------------ATAA 529

  chr2_18959436_1   1406 AATCTAGGAGTTTACAGTTAAGAGGAAAACCTAGG---AAATACCTTTCT 1452
                           -  -----i   -------  i      v    ---    ---i   v
  L1M4_orf2#LINE/    530 AA-CT-----CTTA-------GAAGAAAACATAGGNGTAAAT---CTTCG 563

  chr2_18959436_1   1453 CAACATAAGCCTTGGCAACAATTT--TAG----GACA---AAATCTCCCA 1493
                         ii  v vi vi v     iii   --   ----    ---   v v ---
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC--- 610

  chr2_18959436_1   1494 AAGCAACTGCAAAAATACCCCCAAAATAGACAAGTAGGACCTAATTAAAC 1543
                                ---    iv -----        i  i v    i v  i   v
  L1M4_orf2#LINE/    611 AAGCAAC---AAAAGAA-----AAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_18959436_1   1544 TAAAGAGCTTCTGCATACCAAAATAAACTATTAACAGAGTAAATAGACAG 1593
                          v  i i   i  iiivi    iv v     i  v i   i  v     i
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_18959436_1   1594 CCTACAGAATGAGAGAAAATACTTTCAAACTATGCATCCAACAAAGGTCT 1643
                           i        i         i  v    ii  ii   ii i  i  v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_18959436_1   1644 AATATCCAGAATCTGCAAGGAACTT----AAATCAACAAGCAAAA-ACAA 1688
                         vi          v ii  i     i----  v    i  vv    -    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_18959436_1   1689 ACAACTCCATTAAAAAATGGGCAAAG-ACATGAACAGACACTTCTCCAAA 1737
                          i   i v   ?              - iv    i     i         
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_18959436_1   1738 GAAGACATACATGTAGCCAACAAGCATATAAAAAAATGCTCAACATCACT 1787
                              i     vi i     i     i  i    i             ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_18959436_1   1788 AATCAT 1793
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.79 (147 / 82)
Gap_init rate = 0.03 (25 / 907), avg. gap size = 3.04 (76 / 25)  


1058 25.55 0.62 4.98  chr2_19040631_19043198.rev      883  1203 (1365)    L1M4_orf2#LINE/L1        4   310 (598)  

  chr2_19040631_1    883 AGAGATACACTGTGTTCATA-ATTTGAAAACTGAATATTGTTAAAATGCT 931
                          i     iv ii       i-   v   i   v           i   vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_19040631_1    932 AATTTTTCCCAAAATGACCTGTAGATTCAATGCAATTTCAATTAAACATA 981
                            vi i      v   i  ii        i     ii v  i   --- 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA---A 100

  chr2_19040631_1    982 TCGTTTTTGTTTGTCTGTTTGTTTTAATATAATTGGACAGGCTGATTCTA 1031
                           --------iiiv   ii v    i-i v  v v    i      i   
  L1M4_orf2#LINE/    101 TC--------CCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTA 141

  chr2_19040631_1   1032 CAATTCAAATAGAAATACAAAGGACCTATGTAGAAGAGCCAAAACAACTT 1081
                         v      v  i     i   i     i ----   v           ii 
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCA----GAATAGCCAAAACAATCT 187

  chr2_19040631_1   1082 TTTCAAAGATAAA-AAAGTTGGAGGATTTACATTATCTGATTCCAAACCT 1130
                          vvv     vi  -            i i   i vi ii   i    v  
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_19040631_1   1131 TATTATAAAGCTACAGCAATTGAGACAGTGTAATATTTATCTAAATACAG 1180
                           i  i          i   ii         ii  i viiv   iv i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_19040631_1   1181 ACAAATGGAATAATAGAATAAAA 1203
                            v  i  vi   i     i  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAA 310

Transitions / transversions = 2.15 (56 / 26)
Gap_init rate = 0.02 (6 / 307), avg. gap size = 3.00 (18 / 6)  

1142 27.30 9.22 3.30  chr2_19040631_19043198.rev     1502  2076 (492)    L1M4_orf2#LINE/L1      300   908 (0)  

  chr2_19040631_1   1502 ATAAAAAAAAAAGGAGA-TTCAGAAATAGGTCCACACATATATGTGTAAC 1550
                           ii  v i  vv    - i        iii   i    v    -  v v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG-GTCAA 348

  chr2_19040631_1   1551 TTATTTTTCCACAAAGGTTCAAAGGCAATTCAGTGGGAAAAGAATATATT 1600
                           iv     v    i   v v   i v     i    i        -i i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-GTC 397

  chr2_19040631_1   1601 TTTTTAACCAAT----C--AGAAAACTAAA----------CAAAAAAGT- 1633
                             i   v   ---- --i  v    ii ----------     i i -
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_19040631_1   1634 ---TTCAATTCATACATTTAGCCATGCACAAAAATTAACTCAAAATTGAT 1680
                         ---  vi ii v   v ivvi    ii                   v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_19040631_1   1681 TTTATACCTTAATTTATAAATTAAAATCATAA--CTTTCAGATTAAAACA 1728
                         iv? v    v   v  vi ii     ii    --  i i   vv      
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_19040631_1   1729 CTGGAGAAAACTTTTGTGGTTTTGAGT---ACATTTAAGTTATTTCAA-- 1773
                         iv  ? v   ii  i   iii   i  ---i  v --i   vi  vi --
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT--GGTTTCTTAGATA 595

  chr2_19040631_1   1774 --ACATTGATAACTTGGGTTATTATTTAAGTTATTTCAAACATTTGATAA 1821
                         --   iii v i viii iv iv ---   -------   v v v     
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAA---AAG-------AAAAAATAGATAA 635

  chr2_19040631_1   1822 CCTGGGTGTCATCAAAATTAAAAACCTCTCTTTTTGA---GACACTGTTT 1868
                         vi   iiv                 i i v vi  v ---      i i-
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC- 684

  chr2_19040631_1   1869 AAAGATAAGGAAAA------CCACAAACTTGGAGAAAATATTTGATAAAG 1912
                         -    v iv     ------     i v v              -i   v
  L1M4_orf2#LINE/    685 -AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG-CAAAT 732

  chr2_19040631_1   1913 AACATATATCTGATAAAGAACTTG-ATTTCAAGTTTATAAAAAAGTTTCA 1961
                         --              i i     -  iivi i v      i  v i i 
  L1M4_orf2#LINE/    733 --CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_19040631_1   1962 AAATTCAATTATAAGGAAACAAGCAACTCAAT----------ACAAA--A 1999
                         v  i     v    ii i    ii   i    ----------i    -- 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_19040631_1   2000 TCTGAACAGATATTTTATTGATGAAGATGTACAAATAAA-AATAAGCCCA 2048
                          i    i   i    iviii v      i       iiv-       v  
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_19040631_1   2049 TGAAAAGATGTTCAATATTATGAATCAT 2076
                                   i    i  i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (98 / 57)
Gap_init rate = 0.04 (22 / 609), avg. gap size = 3.27 (72 / 22)  


3187 26.43 0.66 1.10  chr2_19117678_19123760.rev     4680  5591 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_19117678_1   4680 TGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATCATGAAAAT 4729
                              ii i  i     i     i  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_19117678_1   4730 GGCCATACTGCCCAAGGTAATTTATAGGTACAATGCCATCCCCATCAAGC 4779
                            v     v     iv i  i  i  i v   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_19117678_1   4780 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAAACTTCA 4827
                          v   iivi i  i  ii     -   -- v  i  -  ii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_19117678_1   4828 CACTGAACCATAAAAGAGCCCGCATAGCCAAGACAATCCTAAGCAACAAG 4877
                         i iv   viii  ii  v  v v        i      i i iv  v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_19117678_1   4878 AACAAAGCCGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4927
                                ii     vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_19117678_1   4928 TACAGTAACCAAAATAGCGTGGTACTGGTACCAAAACAGATCTATAGACC 4977
                                 i   i i  i          i iv ii i   iv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_19117678_1   4978 AATGGAACACAACAGAGGCCTCAGAAATAACACCACACATCTATAAGCAT 5027
                                i v  iv   ivii         vv   i    i   iiv  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_19117678_1   5028 CTGATCTTTGACAAATCTGACAAAAACAAGCATTGGGGAAAGGATTCCCT 5077
                         i    i  i     ivv  v   i v  vv  v         i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_19117678_1   5078 ATTCAATAAATGATGTTGGGAAAACCAGCTATCCATATGCAGAAAACTGA 5127
                         v     i     i  i     v   ii v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_19117678_1   5128 AACTGGACCCCTTCCTCACACCTTATAGAAAAATTAACTCAAGATGGATT 5177
                          ii         v         v    v              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_19117678_1   5178 AAAGACTTAAACATAAGACCTAAAAGCATAAAAATCCTAGAAGAAAACCT 5227
                          ?    i    ii     v      vi      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_19117678_1   5228 AGGC---AATGCCATTGAGGACATAGGCATGGGCAAAGACTTCATGTCTA 5274
                            ?---   -- v i v iv v i  i- i     v ii   v ivv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--CTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr2_19117678_1   5275 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5324
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_19117678_1   5325 ATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGTGTGAA 5374
                           i   v v  i i   i  ii vv    i  v       vv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_19117678_1   5375 GAGAGTGAACAACCTACGGAATGGGAGAAAATTTTTGCAATCTATCCATC 5424
                         i   -----     i  i              v       vii  vi   
  L1M4_orf2#LINE/    696 AAGA-----CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_19117678_1   5425 TGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACA 5474
                            i  i  i  vi          v  i        ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_19117678_1   5475 AGAAAAAAA-AAACAACCCCATCAAAAAGTGGGCAAAGGATATAAACAGA 5523
                          v     i -   i     v  i?    i            v i  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_19117678_1   5524 CACTTCTGAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAGAAG 5573
                           i    vv        i  vi viii     i  i  i         v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_19117678_1   5574 CTCATCATCACTAGTCAC 5591
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


3187 26.43 0.66 1.10  chr2_19136180_19142262.rev     4680  5591 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_19136180_1   4680 TGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATCATGAAAAT 4729
                              ii i  i     i     i  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_19136180_1   4730 GGCCATACTGCCCAAGGTAATTTATAGGTACAATGCCATCCCCATCAAGC 4779
                            v     v     iv i  i  i  i v   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_19136180_1   4780 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAAACTTCA 4827
                          v   iivi i  i  ii     -   -- v  i  -  ii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_19136180_1   4828 CACTGAACCATAAAAGAGCCCGCATAGCCAAGACAATCCTAAGCAACAAG 4877
                         i iv   viii  ii  v  v v        i      i i iv  v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_19136180_1   4878 AACAAAGCCGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4927
                                ii     vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_19136180_1   4928 TACAGTAACCAAAATAGCGTGGTACTGGTACCAAAACAGATCTATAGACC 4977
                                 i   i i  i          i iv ii i   iv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_19136180_1   4978 AATGGAACACAACAGAGGCCTCAGAAATAACACCACACATCTATAAGCAT 5027
                                i v  iv   ivii         vv   i    i   iiv  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_19136180_1   5028 CTGATCTTTGACAAATCTGACAAAAACAAGCATTGGGGAAAGGATTCCCT 5077
                         i    i  i     ivv  v   i v  vv  v         i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_19136180_1   5078 ATTCAATAAATGATGTTGGGAAAACCAGCTATCCATATGCAGAAAACTGA 5127
                         v     i     i  i     v   ii v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_19136180_1   5128 AACTGGACCCCTTCCTCACACCTTATAGAAAAATTAACTCAAGATGGATT 5177
                          ii         v         v    v              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_19136180_1   5178 AAAGACTTAAACATAAGACCTAAAAGCATAAAAATCCTAGAAGAAAACCT 5227
                          ?    i    ii     v      vi      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_19136180_1   5228 AGGC---AATGCCATTGAGGACATAGGCATGGGCAAAGACTTCATGTCTA 5274
                            ?---   -- v i v iv v i  i- i     v ii   v ivv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--CTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr2_19136180_1   5275 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5324
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_19136180_1   5325 ATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGTGTGAA 5374
                           i   v v  i i   i  ii vv    i  v       vv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_19136180_1   5375 GAGAGTGAACAACCTACGGAATGGGAGAAAATTTTTGCAATCTATCCATC 5424
                         i   -----     i  i              v       vii  vi   
  L1M4_orf2#LINE/    696 AAGA-----CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_19136180_1   5425 TGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACA 5474
                            i  i  i  vi          v  i        ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_19136180_1   5475 AGAAAAAAA-AAACAACCCCATCAAAAAGTGGGCAAAGGATATAAACAGA 5523
                          v     i -   i     v  i?    i            v i  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_19136180_1   5524 CACTTCTGAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAGAAG 5573
                           i    vv        i  vi viii     i  i  i         v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_19136180_1   5574 CTCATCATCACTAGTCAC 5591
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


2553 25.83 3.32 6.00  chr2_19210158_19216530     4949  5881 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_19210158_1   4949 TGGAAGAACATTCCATGCTCATAGATAGGAAGAATCAATATCATGAAAAT 4998
                              ii i  i     i    i   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_19210158_1   4999 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5048
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_19210158_1   5049 TACCAATGACTTTCTTCACAGAACTGGAAAAACT-ACATTAAACTCCATA 5097
                          v   iivi i  i  ii     v v  v  i  - ivi    v i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_19210158_1   5098 TGGAACCAAAAAATAGCCCACATAGCCATGACAATCCTAAGCCAAAAGAA 5147
                              viiv  iiv v  viv       vi      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_19210158_1   5148 CAAAGCTGGAGGCATCATGTTACCTGACTTCAAACTTTTTTTTTGTCAAT 5197
                              i      --------------   -  v    ii-------    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG--------------ACT-CACACTTCC-------CAAT 228

  chr2_19210158_1   5198 TTTTACCACTTGTTACTAAATAAAATGTTTGTCAAACTTTGTTACTACAA 5247
                           ----  -------------------------      ----       
  L1M4_orf2#LINE/    229 TT----CA-------------------------AAACTT----ACTACAA 245

  chr2_19210158_1   5248 GGCTACAGTAACCAAGACAGCATGGTACTGGTACCAAAACAGATATATAG 5297
                         i          i        ii         i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_19210158_1   5298 ACCCATGGAAGAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAC 5347
                          i v      v    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_19210158_1   5348 CATCAGATCTTTGACAAACCTGACAAAAATAAGCAATAGGGAAAGGATCC 5397
                           viv   i  i     ivv  v   i vi vv    i       i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_19210158_1   5398 CCTATTTAATAAATGGTGCTGGGAAAACCGGCCAGCCATATGTAGAAAGC 5447
                         i  v  i  i              v   i  vi ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_19210158_1   5448 TGAAACTGGATCCCTTCCTTATACCCTATACAACAATTAACTCAA----- 5492
                             ii    i    v   i i   v       v           -----
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_19210158_1   5493 ------GACCCAAA-------------ACCATAAAAACCCTAGAAGAAAA 5523
                         ------    i   -------------  i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_19210158_1   5524 CCGAGGCA-ATACCATTCAGGACATAGGCATGGGTGAAGACTTCATGACT 5572
                          vv   ?i- v i -   iv   v v  vv i  ii v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_19210158_1   5573 AAAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCT 5622
                          vi    v       vvi          vv     v  i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_19210158_1   5623 AATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5672
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_19210158_1   5673 ATGGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5722
                          vi i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_19210158_1   5723 AAAGGGCTAATATACAGAATATACAAAGAACTTAAACAAATTTACAAGAA 5772
                           i  i  vi   v         i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_19210158_1   5773 AAA-----ACAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5817
                            ----- i   i v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_19210158_1   5818 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5867
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_19210158_1   5868 TCATCACTCGTACA 5881
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 7.25 (87 / 12)  


2780 25.46 2.12 0.00  chr2_19281938_19283630.rev      495  1201 (492)    L1M4_orf2#LINE/L1      187   908 (0)  

  chr2_19281938_1    495 TTGCAAAAAAATAACAACGTTGGAGGTTTCATACTTCTTGATTTCAGATT 544
                            v    i  v     v        vi   i     iii      i vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_19281938_1    545 ATACTACAAACCTATTGTAACCAAAACAGTATGGTATTGGCATAACAACA 594
                         v         v   iv    i   i     i     i        vi i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_19281938_1    595 GACACATAGACTAATGGAAAAGAATAGAGCGCCCAGAAATAAACCCATGC 644
                             i     ii       v     v   v i                i 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_19281938_1    645 ATATATGGCCAACTGATCTTTGACAAAAACATCAAGAATACACAATGG-- 692
                           v     i   i    i  i     iiiiii     vi iv      --
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_19281938_1    693 AAAAAAT---CTCTTAAATAAGTGGTGCTGGGAAAACTGAATATCCACAT 739
                            i   ---  i  v  i  i           v     i   ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_19281938_1    740 GCAAAAGAATGAAATTGTACCCTTATTTTACACAGTACACAAAAATCAAT 789
                                      i   v    i  ii i    vi  i        i  i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_19281938_1    790 TCGGAATAGATTAAAGACTTAAACATAAGACCTGAAACTATAAAACCTCT 839
                           ii   i   i ?    i    ii     v  i            iii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_19281938_1    840 AGCAGAAAACATAGCGAAAAACTTCCTTGACGTTAGTCTTGGAAGCACAT 889
                           v           v?iv   ii i v    v  i vi v  v iiivv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_19281938_1    890 TTTTGAATATGCTGTGGAAAACACAGGCAATAAAAGCAAAAGAAAGCAAG 939
                          i  ii     viiivi   i    i    i     v    iv iii  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_19281938_1    940 TGGGATTACATCAAACTAAAACGTTTCTGCACAGTAAAGAAAACAGTCAA 989
                          v   i v       v v   vii  i  ii vvi    i v  vi    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_19281938_1    990 CAAAATGAAAAGGCAACCTTTGGCATGGGAGAAAATATTTGTAAACCATA 1039
                         v   i       i     ivii v                 i   i    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_19281938_1   1040 TATCTGATAAAGAATTAATATTTAAAATA----AATAATTTATATAATT- 1084
                                   i i i vi   ii i    ----  v  i iv  i  i -
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_19281938_1   1085 ---AGTAAAAA-ACAGATAACCCT-TTAAAAAGTGAGCAAAAGACCAGAA 1129
                         --- i      -   i       v-  ?    i  i     i  iiv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_19281938_1   1130 TAGGCATTTTTCCAAAGAAGACATACAAATGGCCAACAGGTACCTGAAAA 1179
                            i     i           i              i i i  v      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_19281938_1   1180 GAGACTCAAAATCACTAATGAT 1201
                           vi     v    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.26 (122 / 54)
Gap_init rate = 0.01 (6 / 722), avg. gap size = 2.50 (15 / 6)  


2424 25.39 5.63 5.41  chr2_19301104_19305381.rev     2881  3786 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_19301104_1   2881 TGGAAACACATCCCATGGTCCTGGATGGGTAGAATCAATATTTTGAAAAT 2930
                               v i        v  v     v  v   v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_19301104_1   2931 GACCATATTGCCAAAAGCAATCTACAAATTCAATGCAATTTCCATCAAAA 2980
                          i v   i v  v   vii       i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_19301104_1   2981 TACCACCATCATTCTTCACAGAACTAAGAAAAAGC-AATCCTAAAATTCA 3029
                          v   v vv v  i  ii     v --vi v    -i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCA 148

  chr2_19301104_1   3030 TATGGAACCAAAAAGTAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAG 3079
                                viiv  i v v  viv         i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_19301104_1   3080 AACAAATCTGGAGGCATCACTCTACCAGACTTCAAACTATACTGTAAGGC 3129
                               vi      vv    v  v  vi i      viv    ii  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_19301104_1   3130 CATAGTCATCAAAACAGCATGGTACTGGTATAAAAATAGAGACATAGACC 3179
                         i i   v     i    ii         i    ii     v i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_19301104_1   3180 AATGGAACAGAATAGAGTACCCAGAAATAAAGCCAAGTACTTAGAGCCAA 3229
                                i     v   vii           v   vii i   vi i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_19301104_1   3230 CTGATCTTTGACAAAGCAAACACAAACATAAAATGGGGAAAGGA------ 3273
                         i    i  i     i vviv  vi v   vv           i ------
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_19301104_1   3274 -----------------------------------CATGTAGAAGAATGA 3288
                         -----------------------------------    i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_19301104_1   3289 AACTGGATCCTCATATCTCACCTTGTACAAAAATCAACCCAAAATGAATC 3338
                          ii    i  ii iv  v    v i         i   i       i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_19301104_1   3339 AAAAACTTAAATCTAAGACCTGAAACCATAAGGATTCTAGAAGATAACCC 3388
                          ? i  i     v     v  i    i    iiv ii       v   vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_19301104_1   3389 TGGAA-AAATCCTTCTAGTTGCTGGCTTAGGCAAAGACTTCCAAGAACCA 3437
                         v  ?i-     i iv iiii-i   v        v ii   i--------
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCT-------- 589

  chr2_19301104_1   3438 AAAAACCAAAGCAAATGTAAATGCAACAAAGAACCAAAAACCCAAAAGCA 3487
                         -----------------  i  iii   -------------         
  L1M4_orf2#LINE/    590 -----------------TAGATATGACA-------------CCAAAAGCA 609

  chr2_19301104_1   3488 AATACAACAAAAACAAAGATAAATAGATGGGACTAAATTAAACTGAAAAG 3537
                         v vi        iv   i   i   i  v     vv  i   v v    i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_19301104_1   3538 CTTCTGCACAGCCAAAGAAATAATCACAAGAGTTAACAGACAACTCACAG 3587
                            i  ii vv v  i  v iv    vi i   v  v       i     
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_19301104_1   3588 AGTGGGAGAAAATCTTCACAA--------TCTAACGAGGGGTTAATATCC 3629
                          i           v  ii   --------   i ii    ii vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_19301104_1   3630 AGAATCTACAAGGAACTCAAACAAATCAGTAAGAAAAAAAAAAAAGAAAA 3679
                              v  i  i      vv    v   i   v     i v   ------
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA------ 803

  chr2_19301104_1   3680 AATAAACCCATCAAAAAATGGGCTAATGACATGAATATGTAATTCTCAAA 3729
                         --   v  v  i?          v  v  iv      vii v     v  
  L1M4_orf2#LINE/    804 --TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_19301104_1   3730 AGAAGATATGCAAATGGCCAAAAAGCATATGGAAACATGCTCAATATCAC 3779
                                  i           v     i   i   v        i    ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_19301104_1   3780 TAACTAT 3786
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.34 (130 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 11.11 (100 / 9)  


3197 26.19 1.22 0.55  chr2_19426729_19433001     4881  5781 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_19426729_1   4881 GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATG 4930
                             ii i  i     i      i v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_19426729_1   4931 GCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCT 4980
                           v     v     iv i  i           i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_19426729_1   4981 ACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                         v   i-       i  -i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_19426729_1   5028 TATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_19426729_1   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_19426729_1   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_19426729_1   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_19426729_1   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_19426729_1   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_19426729_1   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_19426729_1   5376 GTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                         vi ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_19426729_1   5426 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACCTCATGTCTAA 5475
                         v    ?i v viv   iv   v v  vv i     v iii  v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_19426729_1   5476 AACACCAAAAGCAGTGGCAACAAAATACAAAATTGACAAATGGGATCTAA 5525
                         i            vvi         v v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_19426729_1   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGACACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i       i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_19426729_1   5576 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_19426729_1   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAGATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv   iv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_19426729_1   5676 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5721
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_19426729_1   5722 TA-AAAGAAGACATTTATGCAGCCAAAAAACA-ATGAAAATATGCTCATC 5769
                          v-        i  vi viii     v  i  -       v       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_19426729_1   5770 ATCACTGGCCAT 5781
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 1.60 (16 / 10)  


 670 30.81 8.49 6.74  chr2_19438424_19440562.rev      777  1636 (503)    L1M4_orf2#LINE/L1        1   875 (33)  

  chr2_19438424_1    777 TGGATATACATTCCCAGTTTTTGTATGGAATGACTTAATATTATCAAGCT 826
                             v v i  i  vv   iv  v  v i v           i i   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_19438424_1    827 G----T-CTCCCCAAATTAACTTATAAATTCAATATAATTCCATTTAAAA 871
                          ---- -           i ii  i i      iii   i  vv i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_19438424_1    872 TTCTAGTGGGGTATTTTGAAGACCTTGATACAAAC--ATTCTAAAACTTA 919
                          i i  iv vv v     v   vv    --   i --  i      i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCA 148

  chr2_19438424_1    920 CATAGAAGAATTAAGGTCCTTGAATAGCTAGGTCAATCTTAAAAAATA-G 968
                         i  i   iviiv i  v  iv       i iiv       i     v - 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_19438424_1    969 AGAAAAG-----AGATT-----TT-----TTTTGG--CCTGATACTAAGA 1001
                          iv    -----i  i -----  -----   iii-- i iv   v   v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_19438424_1   1002 TATATTA--CAA--C-GTGTGATATTTATATAAAGA--GACTAATAATCC 1044
                           i v  --   -- -     i  i vii    i  --   vv   ivi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_19438424_1   1045 AGTAGAACAGAATAGAGAACCCGGACACATATATCTACATCTGTATTTCC 1094
                          i i   i     v    ii  i  - -   v i i i i----    --
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGA-A-ATAAACCCATAC----ATTT-- 340

  chr2_19438424_1   1095 ATGTCTAAATATCTATATTCATATCTATGTATATTTGTACCCACATC--- 1141
                            vii  v i---  v   i--------- i vvv  i  v v i ---
  L1M4_orf2#LINE/    341 ATGGTCAATTG---ATTTTCG---------ACAAGGGTGCCAAGACCATT 378

  chr2_19438424_1   1142 ---TGGGAAACTAATA-----TTAAAGAAAACTGGCATAACAAGTCAATG 1183
                         ---    i  vv    -----  v  v   --   -- iviii v   iv
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAA--TGG--TGCTGGGACAACT 424

  chr2_19438424_1   1184 GGATAGG-AGAGATAAGTAGCTTAGTAGTTAGATTTGGAAAAACTGCCTC 1232
                              ?v- v vii  i-  vv - v    i  iii-------  i    
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAA-AGAAT-GAAGTTGGACCC-------CTACCTC 465

  chr2_19438424_1   1233 ATAATATAAATTTTTTTGACAACATACAAAGGTAAACTTTAGGTGGATTA 1282
                          i vi   ----------------      ii v    iv ii     i 
  L1M4_orf2#LINE/    466 ACACCATA----------------TACAAAAATTAACTCAAAATGGATCA 499

  chr2_19438424_1   1283 AAGTCTTAGATATTGAAGGAAATGCTATAACGTTAATGAAAGAAAATATA 1332
                         ?  v i  i  i vii  vv  vi      vii vv ii       i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_19438424_1   1333 GGAG--AATATTTTTGATGTCTGGAAAGAAAAATCACTTCTTCAATAAAA 1380
                           ? --   v  iv   iv iv  vv  iv  - vii     vi   vi 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGA 598

  chr2_19438424_1   1381 CCTTTAAAATACAATGTATGAAATAAAAAAGAATTGATAAATTTGACTAC 1430
                          viiv   ii    - i vv   -- i   i   v        v    v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAA-GCAACAAA--AGAAAAAATAGATAAATTGGACTTC 645

  chr2_19438424_1   1431 ATCAAATTTAAGAAAATCATAAGT---AAAG----CTAACAACA--GTGT 1471
                               v    -   v iv iv i---    ----   v   v --   v
  L1M4_orf2#LINE/    646 ATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_19438424_1   1472 AAAAAT-----------TGGGATAATATTCTTGTAA--TGT-TATT--AC 1505
                            i i-----------     v  v  vi   i  --ii -   i-- i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_19438424_1   1506 AAGATATTAATATCTAGGACATAAAAACAACTCTTGTAAATTAATATGTG 1555
                            iv i vi    i  i i   v   v       ii  v i    -i i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATA 793

  chr2_19438424_1   1556 AAAGAGAGGAAC--CCCAGTAGAATAATGAGCCAAGGATATGTACAACCA 1603
                            -   vi  i--    i v?  v    i  v      v  v i iv  
  L1M4_orf2#LINE/    794 AAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_19438424_1   1604 ATTTACTCAAGAAAAGATCCAAAAGGTCAGCAA 1636
                         v  iv iv     i v  v    v  i  ii  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

Transitions / transversions = 1.33 (149 / 112)
Gap_init rate = 0.05 (43 / 875), avg. gap size = 3.05 (131 / 43)  

1384 27.34 1.68 1.20  chr2_19438424_19440562.rev     1637  2053 (86)    L1M4_orf2#LINE/L1      250   668 (240)  

  chr2_19438424_1   1637 ATAGTCACCAAAACAGCATGGTACTGATAATAGAAGTAGATAAATAGACT 1686
                          i   v i   i    ii        ii -  iiii    i v     ii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATC 298

  chr2_19438424_1   1687 AATGGAACAGAATAGAGGGCCCAGAAGTAAAGCCAAATACTTAACAACTG 1736
                                i     v   i i      i    v   v i i   -iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCA 347

  chr2_19438424_1   1737 ATTGATATTCCACAAAGCATACAAAAAC-ATAAATTGGGAAAAGGACA-- 1783
                               v   v    i -i i v  i  -  vv v    i    i i --
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_19438424_1   1784 CCTCAGTCAATAAATGGTCCTGGGAAAACCAGATAGCCACATGTAGAAGA 1833
                          i i--    i       v      v   ii    ?       i i    
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_19438424_1   1834 ATGAAACTGGATCCCTATCTCTCAATATATACAGAAATCAACTCAGAATT 1883
                              ii    i     i   v  vi       i    i      i   v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_19438424_1   1884 GATTAAAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGGAGAAA 1933
                            i ?    i     v     v  i    i      v ii   i     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_19438424_1   1934 ACCTAGAAGAAACTATTCTGAACGTTGGTTTAGGCAAAGAATTTATGACT 1983
                           v   i? v  v v   vvi  v    v        v iv  iv iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_19438424_1   1984 AAGATCCCAAAAGCAAAGGCAACAAAAATGAA----GATAAATTGGATCT 2029
                          v  iv         v i         ivi  ----           ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_19438424_1   2030 AGTTAAACTAAAAAGCTTCTGCAC 2053
                         vi i   v v    i   i  ii 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGC 668

Transitions / transversions = 1.92 (73 / 38)
Gap_init rate = 0.02 (7 / 419), avg. gap size = 1.71 (12 / 7)  


3194 26.25 1.45 0.67  chr2_19505611_19508325.rev     1325  2223 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_19505611_1   1325 GGAAGATCATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAATG 1374
                          i     -  i     i        v      v i        v  i   
  L1M4_orf2#LINE/      3 GAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_19505611_1   1375 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAGGCT 1424
                           v     v     iv i  i  i        i  v     i    iiv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_19505611_1   1425 ACCAATGACTTTCATCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 1472
                         v   iivi i  iv ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_19505611_1   1473 ATGGAACCAAAAAAGAGTCCGCATTGCCAAGTCAATCCT-------AAGA 1515
                               viiv  ii  vi v v  v     iv     i -------    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_19505611_1   1516 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 1565
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_19505611_1   1566 ACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGACCA 1615
                                i   i    iii        i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_19505611_1   1616 ATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACA-ATCTACAACCA 1662
                               i    i--    i  --        vv   i -  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_19505611_1   1663 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 1712
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_19505611_1   1713 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGCTG 1762
                          v  i  i              v      v  ?   i  ii i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_19505611_1   1763 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 1812
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_19505611_1   1813 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1862
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_19505611_1   1863 TAGGCA-ATACCATTCAGGACATAGGCACGAGCAAGGACTTCATGTCTAA 1911
                             ?i- v i -   iv   v v  vviii    v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_19505611_1   1912 AACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCTAA 1961
                         i            vvi          vv i   v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_19505611_1   1962 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAGCTACCATCAGAGTGAAC 2011
                          i   v v  i i   i  ii vv    i  vi   i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_19505611_1   2012 AGGCAACATACAGAACGGGAGAAAATTTTTGCAATCCACTCATCTGACAA 2061
                           i    vi      i          v       vi  ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_19505611_1   2062 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTATAAGAAAA 2111
                         i  i  vi          v  i  v      iv    v iv    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_19505611_1   2112 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 2161
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_19505611_1   2162 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 2211
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_19505611_1   2212 ATTACTGGCCAT 2223
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (141 / 91)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.90 (19 / 10)  


3556 23.65 1.55 1.22  chr2_19604338_19606475.rev      742  1646 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_19604338_1    742 TGAAAATATATCCCATGTTCATAAATTAGAAGAAATAATATTGTTAAAAT 791
                           i   v               ii   i     vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_19604338_1    792 GTCCATACTACCAAAA--GATGTCTAATGATTCAATGCAATCTCTATCAA 839
                          v v     v  v   --   --   vv       i      i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT--CTACAGATTCAACGCAATCCCTATCAA 98

  chr2_19604338_1    840 AATTCCAATGGCATTTTTTTCACAGATATAAAAAAC-AATCCACAAATTT 888
                            i   iiv  v      v  v i  - i v  i -i    vv     i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTC 147

  chr2_19604338_1    889 ATATAGAACCACACACACACACAAACAGAACAGCCAAAGCAATCCTAAGT 938
                             i   vii  - viv  - ---     i       i     i i iv
  L1M4_orf2#LINE/    148 ATATGGAAATGCA-AGGGAC-C---CAGAATAGCCAAAACAATCTTGAAA 192

  chr2_19604338_1    939 AAGAAGGACAAAACTTAGAGGCATCACACTTTCTGATTTCAAATTATATT 988
                               i     i-  i    vv        i ii        viv  i 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_19604338_1    989 ATAAAGCTATAGTAGTCAAGCCAGTATGGTACTGACGTAGAAATAGACAC 1038
                          i       i    i     v    i        i i  iii       i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_19604338_1   1039 ATAAACCAATGGAACAGAATAGAAGGTCCAGAAATAAACCCACACGTATA 1088
                            i i        i     v  ii                 i  i v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_19604338_1   1089 TGATCAACTAATTTTTGACCAGGGCATCAAGAATGCACAA-GGAGAAAAA 1137
                           i    i i     i   v    iii     viiiv   -  i    i 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_19604338_1   1138 ATAGTCTCTTCAATAAATGGTGTTGGGAAAATTGGTTATCCACAGGAAAA 1187
                                i     i        i     v  i   v  ?     v v   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_19604338_1   1188 CAAATGAAATTGCACCC-TGTTTTACACCATACGCAAAAATCAACTCAAT 1236
                         vi      i   v    - iii i        ii       i       v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_19604338_1   1237 ATTGATTAAAGACTTAAACATAAAATCTGAAACCATAAAACTCCCAGAAG 1286
                           v   i ?    i    ii   i v  i    i         ii     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_19604338_1   1287 AAAACATGGGGAAAAAGTCTCTTGACATTGGTTCTGGCAATAATGTTTTG 1336
                                i  ?iv   vii  v    v    v iv      ii v i  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_19604338_1   1337 AATATGACACCAAATGCACAGACAACAGAAGCAAAAAATAAACAAGTAGG 1386
                         i             v     ii     i   -        i i  i v  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGG 640

  chr2_19604338_1   1387 ATTACATCAAA-TTAAACAGCTTCTTCACAGCAAAGGAAGCAATCCACAA 1435
                          i v       -     - i   i vii vv       vi v   v v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_19604338_1   1436 AATGAAAAATCAATCTGTGGAATGGGAGAAAATATTTGCAAACCATACAC 1485
                          i      iv   i iiii                       i    i i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_19604338_1   1486 CTGATAAAGGGTCAATAACTAAAGTATACAATGAATTTCTATAACTAAAG 1535
                                i  iiivi  v i i i    i  v   i ii  i    v  v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_19604338_1   1536 GGCAAAAATA-AAATAATTCAATT-AAAAATAGGGAAAGAACCTGAATAG 1583
                         iii     v -      ii     -      i  v    i ii       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_19604338_1   1584 ACATTTCTCCAAAGAAGACAT------GACCAACAGGTGTATGAAAAGGG 1627
                                           i  ------ i    i i iii        iv
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_19604338_1   1628 GCTCAACATTACTAATCAT 1646
                                  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (146 / 65)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.56 (25 / 16)  


2982 26.33 1.55 1.11  chr2_19632778_19637384.rev     3212  4115 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_19632778_1   3212 TGGAAACACATCCGTTGCTCATGGATGGGTAGAGTCACTGTTGTGAAAAT 3261
                               v i    vv  i        v  v   v i v i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_19632778_1   3262 GACCATACTTCCAAAAGCAATCTATAAATTCGATGCAATTCCCATCAAAA 3311
                          i v     i  v   vii     i i    i i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_19632778_1   3312 TACCA-TTATCATTGTTCACAGAGCTAGAAAAAA-AATTCTAAAACTTTT 3359
                          v   -i ii -  v  ii    iv v  v  iv-i  i      i iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_19632778_1   3360 ATGGAACCAAAAAAGAGCTCACATAGCCAAAGCAAGACTAAGCAAAAAGA 3409
                               viiv  ii  v iviv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_19632778_1   3410 ACAAATCTGGAGC-CTCACATTACCCGACTTCAAACTATACTATAAGGCC 3458
                              vi     v-      i v   i i      viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_19632778_1   3459 ATAGTTATAAAAACAGCATGGTACCAGTATAAAAATAGGCATATAGACCA 3508
                          i   v  v  i    ii      ii i    ii    i        i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_19632778_1   3509 ATGGAACAGAATAGAAAACCCAGAAATAAAAGTCAAATTCTTACAGCCAA 3558
                               i     v  i ii           v-i  v ivi   ii i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTTATGGTCAA 348

  chr2_19632778_1   3559 CTGATCTTTGACAAAGCGAACAAAATAAAAAAATAAAATGGGGACAGGAC 3608
                         i    i  i     i - vi ----i  i vv  vv        v  i i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGC----CAAGACCATTCAATGGGGAAAGAAT 393

  chr2_19632778_1   3609 ACGCTATTCAACAAATGTTGCTGGGATAATTGGCAAGCCACATGTAGAAG 3658
                          vv  v           v        i  i   vv ?       i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_19632778_1   3659 AATGAAACTGGATCCTCATCTCTCACCCTATACAAAAATCAACTCAAAAT 3708
                               ii    i  ii i   v    v           i          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_19632778_1   3709 GGTTCAAAGACTTAAATCTAAGACCTGAAGTCATAAAGATTCTAGAAAAT 3758
                           v   ?    i     v     v  i  iii     iv ii     i v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_19632778_1   3759 AACATCA-TGAAAGCCTTTCTAGACATTGGCTTAGGCAAAGACTTCATGA 3807
                              vi-? v  ii   iv -   v    v        v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_19632778_1   3808 CCAAGAACCCAACAGCAAATGTTACAAAAACGAAGATAAATAGATGGGAC 3857
                         vi v  vv    v    v v iv      ivi  i   i   i  v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_19632778_1   3858 TTAATTAAACTAAAAAACTTCTCCACAGCAAAAGAAATAATCAATAGAAT 3907
                           v  i   v v        i vii vv    i  v iv     v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_19632778_1   3908 AAACAGACAACCTACAGAGTGGGAGAAAATCTT--CACATTCTATTCATC 3955
                         i  v        i     i           v  --  v  iv   --   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATC 740

  chr2_19632778_1   3956 TGACAAGGGACTAATATCCAGAATCTACAAATAACTC----AAATCAGCA 4001
                            i        vi          v  i   v     ----  v   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_19632778_1   4002 AGGAAAA-ACCAAT--CCCA-TAAAAAAGTGGGCTAAGGACATGAATAGG 4047
                          vi    -  v   --    - v?    i     v     iv       i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_19632778_1   4048 CAATTCTCAGAAGAAGATATACAAATGGCCAACAAGCATATGGAAAAATG 4097
                           v     vi                      i     i   i   i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_19632778_1   4098 CTCAGCATCACTAATGAT 4115
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.60 (24 / 15)  


2583 29.90 1.00 0.78  chr2_19702321_19707898     4184  5086 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_19702321_1   4184 AAAAACATTCCATGCCCGTAGATAGGAAGAACCAATATCATGAAAATGTC 4233
                            i i  i     ii i i   v      vii     ii v  i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_19702321_1   4234 CATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGCTAC 4283
                         v     v      v i  i  i        i  v     i     iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_19702321_1   4284 CATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCATATG 4332
                           vivi i  i  ii     v v  v  i-  - iii    v        
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATG 152

  chr2_19702321_1   4333 GAACCAAAAAAGAACCCATATAGCCAAGACAATCCTAAGCAAAAAAAACA 4382
                            viiv  ii  v  viv        i      i i iv  i  i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_19702321_1   4383 AAGCTGAAGTCATCATGCTACCTGACTTCAAACTACATTAAAAGGCTATG 4432
                            i  i  vvv   ii  v  ii i      vivi i  v  i    ii
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_19702321_1   4433 GTAACCAAAATAGCATGGCATTGACACCAAAAGAGATATA-AGACCAATG 4481
                             i   i i  ii   i i  i  iv ii v   i   -   i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_19702321_1   4482 GAACACAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCATCTGA 4531
                            i v  iv   ivii         vv   i    i  iiii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_19702321_1   4532 TCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTACCTATTT 4581
                          i  i     ivv  v   i v  vv            i  vii  v  i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_19702321_1   4582 AATAAATT-TATTTATTAACAAATAGAGAATAAATATGCAGAAAACTGAA 4630
                           i    v- ii vi--i    v i  v ?iv -i     i  i v    
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGG--GACAACTGGATAKCCA-CATGCAAAAGAATGAA 449

  chr2_19702321_1   4631 ACTGGACCACTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 4680
                         ii      v  v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_19702321_1   4681 AAGACTTAAACATATGACCTAAAACCATAAAAACCTTAGAAGAAAATCTA 4730
                         ?    i    ii  v  v       i      vi            iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_19702321_1   4731 GGCAGTACTATTCAGGATATAGGCATGGGCAAAGACTTCAT-GACCTAAA 4779
                           ?ivv v v   iv  iv v  vv i     v ii   v -  iv i -
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA- 598

  chr2_19702321_1   4780 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAACT 4829
                                    vvi          vv     v  i    v   ii v ii
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_19702321_1   4830 AAACTAAAGAGCTTCTGCACAACAAAATAAATTTTCATCAGAGTGAACAG 4879
                            v v  i i   i  ii vv    iv v i v   vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_19702321_1   4880 GCAACCTACTGAATGGGAGAACATCTTTGCAATCTATACATGTGACAAAG 4929
                         i     i  v           v  v       vii   i  v   i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_19702321_1   4930 GGCTCATATCCAGAATCTACAAGGAACTTAAACAAATTTGCAACAAAAA- 4978
                          i  ii          v  i  i     ivv    v ivii  i     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_19702321_1   4979 --AAA-AACCCA-TCAAAAAGTGGGCGAAGGATATGAACAGATACTTTTC 5024
                         --   -      - i?    i     i      v    i   i i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_19702321_1   5025 AAAAGGAGACATTTATGCAGCCAACAAACATATGGAAAAAAAAGTTCATC 5074
                         v    i   i  vi viii     i  i  i   --    i v i   v 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATG--AAAAGATGCTCAAC 896

  chr2_19702321_1   5075 ATCACTGGTCAT 5086
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (163 / 103)
Gap_init rate = 0.01 (12 / 905), avg. gap size = 1.33 (16 / 12)  


4003 17.89 5.73 1.61  chr2_19888652_19891539     1526  2397 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_19888652_1   1526 TGGAAAGATATCCTGTGCTCATGGTTCAGAAGATGTAATACTGTCAAAGT 1575
                                      ii  i      v ii     iv     i   i  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_19888652_1   1576 GTCAATACTACTCAAAGAAGTCTACATATTCAATACAATCCCCATCAAAA 1625
                          v       v i    vvii      v      ii       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_19888652_1   1626 TTCCAATGGCCTTTTGTGCATAA-TGGAAAATTCAATCCTTAAATTCATA 1674
                          i   iiv       v    v  - v  v  viii     v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_19888652_1   1675 TGAAATTTCAAGGGGCTCCAAATAGTCAAAACTGTCTTGAAAAAGAAGA- 1723
                           i  v v      i i vi     i      vi               -
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_19888652_1   1724 CA--GTAGGAGGACTGACACTTGCCTATTTCAAAACTTACTATAAAACTA 1771
                           --  v        v      v  v                i   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_19888652_1   1772 TAGTAATCAAGACAGGGTGGCACTGGCATAAGGATAGACACATAGACTTA 1821
                         i              v    i                   i     iiv 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_19888652_1   1822 CAGAATAGAATTGGGAATCCAGAAATAACCCTATA-ATTCTATCACTAAC 1870
                         ii           i  i           v  i   -   -   viii  -
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGGTCAA- 348

  chr2_19888652_1   1871 TTTTATTTTTAACAACAGTTTTAAGACCATTCAATGGAGAAAGAATACTC 1920
                         -  v     ii    vi  vii               i         v  
  L1M4_orf2#LINE/    349 -TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_19888652_1   1921 ACTCCAACAAATGGCTCTGAAACAACTGAATATCCACATGCAAATGAATC 1970
                         vi i          iv   ii       i   ?           v    v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_19888652_1   1971 ACGTTAGACCC-TACCTTATACCACGTACAAAAATTAACTCAAAGTGGAT 2019
                          v   i     -     i i    ii                  i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_19888652_1   2020 CAATGACTTATATATAAGACCTAAACCTACAAAATTCTTTGAAGAAAACA 2069
                           ?v   i  v  i     v     v   i    i    v          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_19888652_1   2070 TAGGGGTAAATCTTCGTGACTGTGGATTTGGCAATGGATTCTTAGTTATG 2119
                             ?               iv   i  v        v       v    
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_19888652_1   2120 CTTAGATATCTAA-GAATAAGCAACAAAAGAAAAAACAAATACATTAGAC 2168
                         ----- i i v  - v i                  i i   v   i   
  L1M4_orf2#LINE/    598 -----ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_19888652_1   2169 CTCGTCAAAATAAAAAAAAAAGTTGTGGATCAAAAAAAGAACATTATCAA 2218
                         i  i       v     vv--v     vv     ---- i   i      
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACT--TTTGTGCTTCAAA----GGACACTATCAA 686

  chr2_19888652_1   2219 GAAAGTAAAAGAAAAACCTACAGAATAAGAGGATATATTTACAAATCATG 2268
                               i   ii v    i       ii   i v      i        i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_19888652_1   2269 TATCTGATAAGG-----------------------------------CTC 2283
                                     -----------------------------------   
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_19888652_1   2284 AA------AAAGACAAACAACTCAAAT-AAAAATGGGCAATGGACTTGAA 2326
                           ------         i   i   v -            v   i     
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_19888652_1   2327 TAGGCATTCCTCTAAAGAAGATATACAAATGGCCAA-ACACACATGAAAA 2375
                            i    i   i                       - vi          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_19888652_1   2376 GATGTTCAACATCTTAGTCATT 2397
                             i        v????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (94 / 59)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.27 (64 / 15)  


2985 27.60 1.56 0.11  chr2_20036845_20043869     5639  6533 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_20036845_2   5639 TGCAAAAACATTCCATGCTCATGGATAGGAAGAACCAATATCATCAAAAT 5688
                           v   i i  i     i        v      vii     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_20036845_2   5689 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCAATCAAGC 5738
                            v     v      v i  i  i        i  v     v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_20036845_2   5739 TACCATTGACTTTCTTTACAGAATTAGA-AAG--AACTTTAAATTTCATA 5785
                          v   vivi i  i   i     v v  -   --i iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_20036845_2   5786 TGGAACCAAAAAAGAGCCCGCATAGCCAACACAATCCTAAGCAAAAAGAA 5835
                              viiv  ii  v  v v        v      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_20036845_2   5836 CAAAGCTGGAAGCATCACACTAACTGACTACGAACTATACTACAAGGCTA 5885
                              i    i vv       vv ii i v i  viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_20036845_2   5886 CAGCAACAAAAACGGCACGGTACTGGTACCAAAACAGATATATAGACCAA 5935
                            i  iv  i  i iii        i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_20036845_2   5936 TGGAACAGAATAGAGGCCTCAGAAACAACGCCAAACATCTACAACCATCT 5985
                              i     v   ivii      i  vv   v    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_20036845_2   5986 GATCTTTGAGAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 6035
                            i  i  v  ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_20036845_2   6036 TTAATAAATGATGTTGGCAAAACTGGCTAGCCATATGCAGAAAGCTGAAA 6085
                          i  i     i  i   v v      v  ?   i     i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_20036845_2   6086 CTGAATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAA 6135
                         i  i i    v   i     v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_20036845_2   6136 AGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 6185
                             i    i      v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_20036845_2   6186 GCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATAACTAAAAC 6234
                          ?i- v i -   iv   v v  vv i     v ii   v  iv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_20036845_2   6235 ACCAAAAGCAGTGGCAACAAAAGCCAAAATAGAAAAATGGGATCTGATTA 6284
                                   vvi          vv        v    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_20036845_2   6285 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTGAACTGG 6334
                           v v  i i   i  ii vv    i  v        v i      vv i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_20036845_2   6335 CAACCTACAGAA--------AATTTTTGCAACCTACCCATCTGACAAAGG 6376
                              i      --------   v       vii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_20036845_2   6377 GCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAAA 6426
                         i  vi          v  i        ivv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_20036845_2   6427 CAAATAACTCCATCAAAAAGTGGGTGAAGGATATGAACAGAAACTTTTCA 6476
                                 i v  i?    i    ii      v    i   v i  i  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_20036845_2   6477 AAAGAAGACATTTTTGCATCCAACAA--ACATGAAGAAAAGCTCATCATC 6524
                                 i  vivviiiv    i  --       i i v     v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_20036845_2   6525 ACTGGTCAT 6533
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.50 (15 / 6)  


1858 24.59 4.10 0.41  chr2_20149520_20153199     1571  2058 (1622)    L1M4_orf2#LINE/L1        1   506 (402)  

  chr2_20149520_2   1571 TGGAAAAAGATTCCATGCTCACAGATAGGAAGAATCAATATTGTTAAAAT 1620
                               i v  i     i   ii   v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_20149520_2   1621 GGCCATACTGCCCAAAGCAGTTTACAGATTCAATGCTATTCCTATTAAAC 1670
                            v     v      viii i           i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_20149520_2   1671 TACCAA-TGGCATTTTCACAGAATTAGAAAAAACT-ATTTCAAAATTCAT 1718
                          v   i-  v v    ii     v v  v  i-  -  iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_20149520_2   1719 ATGGAACCA-AAAAAAGCCTGAATAGCCAAGGCAATCCTAAGCAGAAAGA 1767
                               vii-  iii v  v          ii     i i iv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_20149520_2   1768 ACAAAGCTGAAGGCATCACATTATCCAACTTCAAACTATACTACAAGACT 1817
                               i  i   vv     i vi    i      viv        ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_20149520_2   1818 ACAGTAATCAAAACAGCATGGTACTGGTACAAAAACAGACA----GACCA 1863
                                    i    ii         i i  ii i     ----  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_20149520_2   1864 ATGGAACCAAATACAGAACCCAGAAATAAAGCCATACAAACTACAGCCAT 1913
                               ivi   vv   ii           v       v-i  ii i  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-TTATGGTCAA 348

  chr2_20149520_2   1914 CTGATCTTCAATAAAGTTGACAAAAATAAGTAATGGGGAAAGGA----CT 1959
                         i    i   i i  i v  v   i vi vvi           i ----  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_20149520_2   1960 ATTCAATAAATGGTGCTGGGATAACTGGTTAGCCAAATGCA---GATTAG 2006
                         v     i              i      v  ?   v     ---  v ii
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_20149520_2   2007 AACTAGAC----ACCTT-CACCATATATAAAAAT-AACTTAAGATGGATT 2050
                          ii i   ----    i-         i      -    i  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_20149520_2   2051 AAAGACTT 2058
                          ?    i 
  L1M4_orf2#LINE/    499 AWAGACCT 506

Transitions / transversions = 2.11 (80 / 38)
Gap_init rate = 0.02 (11 / 506), avg. gap size = 2.00 (22 / 11)  

 781 25.30 2.41 3.01  chr2_20149520_20153199     2470  2801 (879)    L1M4_orf2#LINE/L1      501   830 (78)  

  chr2_20149520_2   2470 AAACCTAACTGAAAAAAC-AAAACAAACAAAACCCCTAGAAGGACACCTA 2518
                          i      v  v  i i -     v -i     i i      i v  v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTA-TAAAACTCTTAGAAGAAAACATA 549

  chr2_20149520_2   2519 AG---AAATACCATTCTGGATGTAGGCCCTGGCAAAGATTTCATGAGGAA 2565
                         i ---    -- -   vv  iv v  viiv     v i    v iiiv v
  L1M4_orf2#LINE/    550 GGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_20149520_2   2566 GACACCAAAAGCAACTGCAACAAAAACAAAAATTGACAAATGGGACCTAA 2615
                                      vvv         iv      v  i    v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_20149520_2   2616 TTAAACTAAAGAGCTTCTCTGCTCTGCTAAAGAAACTATCAACAGAGCAA 2665
                          i   v v  i i   i v    i-- v  i  v        v i  ii 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGA 694

  chr2_20149520_2   2666 CCAGACAACCTACAGAATGGAAGAAAATATTTGCAAACTATGGATATGAC 2715
                         vv        i         i                ii  iv  v   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_20149520_2   2716 AAAGGTCTAATATTCAGAATCTATAAGGAACTTAAGCAA---AA-AACAA 2761
                           i  v  vi   i      v     i     ivvi   ---  -  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_20149520_2   2762 AACAACAACAACAACAACAACATTAAAAGTGGGCAAAGGA 2801
                           vi    -- i   v-   i- ?    i           
  L1M4_orf2#LINE/    795 AAAGACAA--ATAACC-CAAT-TWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.13 (44 / 39)
Gap_init rate = 0.03 (11 / 330), avg. gap size = 1.64 (18 / 11)  

 450 13.19 3.30 0.00  chr2_20149520_20153199     3098  3188 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_20149520_2   3098 AAAAATTGGTAAAGGACATGAACAGACACTTCTC---AAAAGACATACAC 3144
                               v  i      iv    i     i     --- i    i     v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_20149520_2   3145 ATGGCCAATAAGTAAATGAAAAAATGCTCAACATCACTAACCAT 3188
                                     i v       i             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 3.00 (3 / 1)  


 322 29.97 10.09 5.34  chr2_20280436_20282143.rev      138   474 (1234)    L1M4_orf2#LINE/L1      231   583 (325)  

  chr2_20280436_2    138 CAAAACATATTATGAAGTTAGAG-AATTAAAA----ATAATATAGGATTA 182
                               v  i  ii   i  v  -   i  i ----i ii  iv  vv  
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_20280436_2    183 A--ATAGACAAATAGACCAAAGTAATAGGATAGTGAGTGCACAAACAGAC 230
                          --       v     i   v v     i  v v    v  v   i i  
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr2_20280436_2    231 CCTCGAATATGTAGAAACTTAGTGTATGATACAGTTGGTATTTCAGATGA 280
                           ----   ii ------   -----  i -  i   i v  iv v v i
  L1M4_orf2#LINE/    331 CC----ATACAT------TTA-----TGGT-CAATTGATTTTCGACAAGG 364

  chr2_20280436_2    281 GTGACAAAAC-ATTCAATTA------AATA----TTTTAGGA-------- 311
                            v   i  -       vi------    ----   i iv --------
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_20280436_2    312 -GAAACAACTGCAGA---AAATG--AAAG--TCAAGTTTAATTTCTACTT 353
                         - ii       v v --- v   --    -- v     vi iii    i 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_20280436_2    354 CACACCAGTCATAATAATAAATTCCAGGTTACTTAAAGAACTAAATATAT 403
                                vvi i  v   v  i  v ii viv i ?   v      i  v
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_20280436_2    404 CTTTTTAAACTGCAAAAGAATTAGGATAAAATGTAGGAGATTGTTTTTGT 453
                         vvvi v     ii    vvv    i v    ii    ? vvvi i  i  
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_20280436_2    454 GGTTTTGTGATAAAGCATATG 474
                          iii   - i v i   -   
  L1M4_orf2#LINE/    565 GACCTTG-GGTTAGGCA-ATG 583

Transitions / transversions = 1.20 (54 / 45)
Gap_init rate = 0.05 (16 / 353), avg. gap size = 3.25 (52 / 16)  

2515 24.83 2.65 1.67  chr2_20280436_20282143.rev      501  1217 (491)    L1M4_orf2#LINE/L1      185   908 (0)  

  chr2_20280436_2    501 TTTTGAAAAAGAAGAACTAAGTGGGAA---TTAGTCTACCCAATTCCAAG 547
                          i               v    v   i--- i vv  v       i   i
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_20280436_2    548 A--TGTTATATAGCTATGATAATTAGGACTGTGTGATATTGGTGGAGGGA 595
                          -- ii  i v     iii    i i   v     i  i   iiv i   
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_20280436_2    596 TGGAAGCATAAATCAATGGGAAAGGATGGAAAATCCAGAAATAGACCTAC 645
                          i  vii   i        i v  i  v  i i          i   i i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_20280436_2    646 ACAGATATGCGCAACCGAGTTTTGAAAAAGATGCAAACGCAATCCAATGG 695
                            vv    vv   ii  v   i  v  i i   v  vi v  i      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_20280436_2    696 ATGAAGGATAGCCTTGTAAACAAATGGTCCTGGAACCACTGAACATCCAT 745
                         ivi   i    i   v v          v    i  v    i i ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_20280436_2    746 AGGTAAAAG--TGAACCTTGACCTAGACTCCAGGCTGTATAAAAAAATTA 793
                          v i     --    vi v    ivv  ii  vi ii    v        
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_20280436_2    794 ACTCAAAATGAATCACAAACATAAATGTGAAACCTAAAACTACAAAACTT 843
                                   i    ? i  v       i i v         i      i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_20280436_2    844 TTAGGAAGAAAATACATGGGAGAAACATTTTTGTGGTTTTGGGCTAGACA 893
                             -       --   i  ? v  -  i  i   iii     i   i  
  L1M4_orf2#LINE/    535 TTAG-AAGAAAA--CATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_20280436_2    894 --GAGTTCTCAGCCTTGACACCAAAAGTATTATCCATAAAAGGAAACATC 941
                         -- iv    i  viv            i iv v v i     i   v  v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_20280436_2    942 AATAAATTGGGCTTCATCAAAACTGAAAACTTTTGCTTTGTGAAAGACCC 991
                         i         i           i i          ivi vii  i   v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_20280436_2    992 TGTACAGAGAATAAAAAGACAATCTAAAGATTGGGAGAAGATATTTGCAA 1041
                          i vv   i i i         i i v   v        i          
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_20280436_2   1042 AACACA-----GA----GGACTAGAGCCTAGAATACATACATTTCTCTCA 1082
                          v  i -----  ----     v vii i      i   v vvv    i 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_20280436_2   1083 AAACTGAACAATAAAAA-ACAAAGAATCGAATTCAAAAATGGGCAAAAGA 1131
                         v    v  i        -     v  i v    ?             i  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_20280436_2   1132 CATGAACAGACATTTAGCCAAAGAGAGTGTACTCCTGGTACTCCTGGTTA 1181
                         iv    i        vv       iii i   vvv   ----  v---- 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG----CCA----A 872

  chr2_20280436_2   1182 TAAGCACATGAAAAGATGGTCAACATCCTTAGCCAT 1217
                                           v        v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (104 / 70)
Gap_init rate = 0.02 (12 / 724), avg. gap size = 2.58 (31 / 12)  


2894 19.88 6.82 0.00  chr2_20358527_20360192.rev      501  1174 (492)    L1M4_orf2#LINE/L1      189   908 (0)  

  chr2_20358527_2    501 GAAACAAACAAACAAAACCAGAGGTATCACGTTTCCTGATTTCAAAACTT 550
                             v i vi      iiii    vv    ii    ii            
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_20358527_2    551 ATTAGAAAGCTACAGTAATCCAAACAGTGTGGCACTGGCATAAAGACAGA 600
                          i  v               v i         i          i  i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_20358527_2    601 CATACAGACCGAAGGAAGAGAATAGACAGACCAGGGAGAAACCCTCGCAT 650
                             i   i i v    v     v  v  v    ii v      vii   
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_20358527_2    651 ATATGGTCAAGTGATCTTCCACAAGGGTGCCAAGACCGTCCAATGAGGAA 700
                         v         v    i   v                 i i     i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_20358527_2    701 ACAACAGTCGTTGCAACAAGTG------------------------ATGC 726
                          v  i    v  v      i  ------------------------    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_20358527_2    727 AAAAG-------TTGGTCCCTTACCTTACATCATATACAAAA-CTAACTA 768
                              -------    v   i     i   i           -i     v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_20358527_2    769 AAAATGGATGA-AGATCTAAACGTAAGACCGAAAACTGTGAAACCCT-AT 816
                                  v -   i     i      v v      i i    i  - v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_20358527_2    817 AAGAAAATGTAGGGGGAAAGCTTCGTGATGTTGGATTTGGCAGTGATTT- 865
                                ii    ? v   v        iv    i  v    i  i   -
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_20358527_2    866 --GGCTATGACAGCAAAAACACATGCAA---AAGCAAAACTAAATAAATG 910
                         --i v       v     i    v    ---   v    v  i      v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_20358527_2    911 AGACTACATCAAACTTTAAAATGTCTGTGCACCAAAGGAAACAATCAACA 960
                         i    v       v  v    iv i     vi       v  v     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_20358527_2    961 AAGTGGAAAGGCAATCTACAGACTGGGAGAAAATATTTGCAAAT-ATGTA 1009
                              i    i   i i     v                     -  i  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_20358527_2   1010 AATAATAAAGGGTTAATATTCAGAATACATAGACA---CCTACAACTCAA 1056
                         vv i    i  ii vi   i       i   i v --- i          
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_20358527_2   1057 CAACAACAAAA--AACAACGTGATTTTAAAATGGACAAAGGACTTAAATA 1104
                         i  i  v  i --  i   vii   ?v       i       i  i    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_20358527_2   1105 GACATTTCTCCAAAGATGATATATAAATGGCCAAGAAGAATGTGAAAAGA 1154
                                         v      i          v   v ii        
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_20358527_2   1155 TGCTCAATGTCATCAGTCAT 1174
                                ii   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (78 / 54)
Gap_init rate = 0.01 (10 / 720), avg. gap size = 4.60 (46 / 10)  


3206 26.05 1.44 0.78  chr2_20579192_20585922     5338  6239 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_20579192_2   5338 TGGAAAAACATTCCATGCTCACGGATACGAAGAATCAATATTGTGAAAAT 5387
                               i i  i     i   i    vv     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_20579192_2   5388 GGCCATACTGCTCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 5437
                            v     v i    v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_20579192_2   5438 TACCATTGACTTTCTTCACAGAATTAGAAAAA--AATTACTTTAAATATC 5485
                          v   vivi i  i  ii     v v  v  i--i  -- i v    -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT--CCTAAAAT-TC 147

  chr2_20579192_2   5486 ATATGGAACCAAAAAAGAGCCCGTATAGCTAAGACAATCCTAAGCAAAAA 5535
                                 viiv  ii  v  v v     i  i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_20579192_2   5536 GAACAAAGCTGGAGGCATCACGTTACGTGACTTCAAACTATACTACAAGG 5585
                                 i      vv    ii v vii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_20579192_2   5586 CTACAGTGACGAAAAGAGCATGGTACTGGTATCAAGACAGATATATAGAC 5635
                                i iv  i v  ii         i  v i  i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_20579192_2   5636 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCAAACATCTACAACCA 5685
                                 i    iv   ivii         vv   v    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_20579192_2   5686 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGGAAGGAT--TC 5733
                         vi    i  i     ivv  v   i v  vv        i   i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_20579192_2   5734 CTGATTTAATAAATGGTGTTGAGAAAACTGGCTAGCCTTATGCAGAAAAC 5783
                         i --  i  i        i  i  v      v  ?  vi     i  i v
  L1M4_orf2#LINE/    398 TT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_20579192_2   5784 TGAAACTGGACCCCTTCCTTATACCTTAGACAAAAATTAACTCAAGATGG 5833
                             ii         v   i i   v  v                i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_20579192_2   5834 A-------CTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5876
                          ------- i           v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_20579192_2   5877 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGAAAAGACCTCATGAGT 5925
                          v    ?i- v i -   iv   v v  vv i  v  v iii  v iii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_20579192_2   5926 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5975
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_20579192_2   5976 AATTAAACTAAAGAGCTTCTGCGCAGCAAAATAAACTATCATCAGAGTGA 6025
                         v  i   v v  i i   i  i  vv    iv v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_20579192_2   6026 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCATCTGAC 6075
                          v  i     i                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_20579192_2   6076 AAAGGGCTAATATCCAGAATCTGTAAGGAACTTAAACAGTT-ATTAAGAA 6124
                           i  i  vi          v i   i     ivv   ii - v   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_20579192_2   6125 AAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAAGAGACAC 6174
                            i -    i     v  i?    i    ii      v    v     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_20579192_2   6175 TTCTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTC 6224
                              v        i  vi vi       i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_20579192_2   6225 ATCATCACTAGTCAT 6239
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (136 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


3238 11.03 1.25 25.40  chr2_20727601_20730550.rev     1263  2459 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_20727601_2   1263 TAAAAAGACATTCCATGTTCATTGATTAGAAGACTTGATATTGTTAAAAT 1312
                          ii     i  i          v    i        i          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_20727601_2   1313 GACAGTAATCTCCAAATAGATCTACAGATTTAATGCCATGCTTATCAAAA 1362
                          i  i  v  i      v            i  i  v  v i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_20727601_2   1363 TCCCAATGTGATGTTTTTACAGAAATGGAAAAGCTAATCCTAAAATTTGT 1412
                              ii-  viv     i       v  v     i           ii 
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_20727601_2   1413 ATGGAATTACAAGGGACCCTGAATAGCTAAAGCAATCTTCAAAAAGAAGA 1462
                               v i          v       i   i       v          
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_20727601_2   1463 GCAAAGTTGGAGGACTTATACTTCCCAATTTCAAAAGTCACTACAAAGTT 1512
                         i               i i                 v i         i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_20727601_2   1513 ACAGTAATCAAAACAGTGTGGCACTGGCACA-GGATAGACATATAGATCA 1561
                                    i         i       i -                  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_20727601_2   1562 ACTGGATGGAATTAAGAGTCCAGATATAAACTCATACACGTGTGG-CACT 1610
                          iv i  i     i          v      i      iv i   -  v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_20727601_2   1611 TGATTTATGACAAGGGTGCCAAGACCATTCCATGCAGAATAGCCTCCCAA 1660
                               vi                      --------------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTC-------------------- 379

  chr2_20727601_2   1661 GAAATTGTATTGGAGGGGACATCCACGTGTAAAAGAATGAAGTCAGAGGC 1710
                         --   ---------     -------------      --    ------
  L1M4_orf2#LINE/    380 --AAT---------GGGGA-------------AAGAAT--AGTC------ 397

  chr2_20727601_2   1711 CAGGTGTGGTGGCTCATGCCTGTAATCCCAGCACATTGGGAGGCTGAGGT 1760
                         --------------------------------------------------
  L1M4_orf2#LINE/    398 -------------------------------------------------- 397

  chr2_20727601_2   1761 GGGCAGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGT 1810
                         ------------------------   -------------i     ----
  L1M4_orf2#LINE/    398 ------------------------TTT-------------TCAACA---- 406

  chr2_20727601_2   1811 GAAACCCTGTCTCTTCTAAAAATACAAAAATTAGCTGGGCATAGTCATGG 1860
                         ----------------------------   ------------------ 
  L1M4_orf2#LINE/    407 ----------------------------AAT------------------G 410

  chr2_20727601_2   1861 GTGTCTGTAACTCCAGCTACTCAGGAGGCCAAGGCAGGAGAATTGCTTGA 1910
                            -   -----------------------------   v  i  -----
  L1M4_orf2#LINE/    411 GTG-CTG-----------------------------GGACAACTG----- 425

  chr2_20727601_2   1911 ACCTGGGAGGTGGAGGTTGCAGTGAGCTGAGACCACACCACTGCACTCCA 1960
                         -------- i i?-------------------     ----    -----
  L1M4_orf2#LINE/    426 --------GATAK-------------------CCACA----TGCA----- 439

  chr2_20727601_2   1961 GCCTGGGCGATGGAGCAAGACTCTGTCTCAAAAAAAAAAAAGAATGAAGT 2010
                         --------------------------------------            
  L1M4_orf2#LINE/    440 --------------------------------------AAAGAATGAAGT 451

  chr2_20727601_2   2011 TGCACCC-TACCTCATACCATATGCAAAAATTAACTCAACATAAATCAAA 2059
                           v    -       i       i               v  ii    ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_20727601_2   2060 GACCTAAATATAAGAGCTATTACTATAAAACTCTTAATA-AAAATATAGG 2108
                                  i         vv               iv -    i     
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_20727601_2   2109 -GTAAGTCTTCATGACCTGAGATTTGGCCATGGATTATTAGATATGACAC 2157
                         -    i     i      vi i  v   v    v  v             
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_20727601_2   2158 CAAGAGCACAAGCGGCCAAAAAAAAATAAAAAGATAAATTGATGAATTTA 2207
                            i         ii -    i    --  v          --  v  i 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAAC-AAAAGAAAA--AATAGATAAATTG--GACTTCA 646

  chr2_20727601_2   2208 TCGAAACTAAAAACTTTTGTGCTTCCAAGGACAACATCAAGAGAGTGAAA 2257
                           i   i                  v       vi       i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_20727601_2   2258 -GACAACACAAAGAATAGGACAAAATGTTTGCAAACCATATATCGTTTAA 2306
                         -      v  v     i   v     i        i        vvv   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_20727601_2   2307 GGATCTAGTGTCTAGAATATATAAAGAACTCCTACAACTCAACAA----- 2351
                           iv  v  i  i                  i          i  -----
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_20727601_2   2352 ---CAAATAACCCAATTTAAAAATTGGCATAGGATTTACATAGGCATTTA 2398
                         ---              ?      v    v       iv    i     v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_20727601_2   2399 TTCAAAGAAAATATACAAA-GGACAACAAACACATGAAAATATGTTCAGT 2447
                          i       i         -  v   i  i          v   i   ii
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_20727601_2   2448 GTCTTTTTGTCT 2459
                         i  v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (81 / 48)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 12.27 (319 / 26)  


3190 24.70 2.41 2.85  chr2_20839044_20843276     2831  3741 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_20839044_2   2831 GAAAAGATATCCCATGCTCATGGATTGGAAGGGTTAATATCATTGAAATG 2880
                          i              i              iv       ii  i i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_20839044_2   2881 TTA-TATGACCCAAAGCAATCTACAGATTCAATGCAATCTCTCTCAAAAT 2929
                         vi -  ivv      vii              i      i  v       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_20839044_2   2930 ACTAATGACATGCTTCACAGAAATGGAGAAAACAATCCTAAAATTTGTAT 2979
                         v i iivi v vi  ii       v  v  ivii           ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_20839044_2   2980 GGAATCCCAAAAGACGCCGAATTGCTAAGG-AATCCTAAGGAAAGGAAAA 3028
                             viv   ii   v v    v  i  ii-    i --------     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--------GAAAA 193

  chr2_20839044_2   3029 AACAAAAACAAAAAAACAAAGCTGGAAGCATCATACTACCTGACTTTAAA 3078
                          i---------  i       i    i vv   i   v  ii i  i   
  L1M4_orf2#LINE/    194 AG---------AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_20839044_2   3079 TCATGCTACAAAGCTATAGTAATTAAATCAACATGATACTGGCATAAAAG 3128
                         v v i           i      i  iv  iii  i           iii
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_20839044_2   3129 CAGACACA--GACCAATGGAATGTAATAGAGAACTCAGAAATAAATCAGT 3176
                         i     i --  i         iv   v    iii          i vi 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_20839044_2   3177 ATACTTACAGCCAACTTGTTTTCAACAAAGGCACTAAGAACACACATTGG 3226
                          i i   ii i   i vi     i    i  ii i    v  iv  v   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_20839044_2   3227 GGAAAGGATAGTCTCTCTAATAAACATTATTGA---AACTAGATATCCAT 3273
                               i       i ii  i   iiv ii  i---    i    ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_20839044_2   3274 ATGCAGAAGAATGAAGCTAGATCGATCCTATCTTTTACCATATACAAAAA 3323
                              i          i i  i ---    i  ivi              
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACC---CCTACCTCACACCATATACAAAAA 481

  chr2_20839044_2   3324 TCAACTCAAA-TGGATTAAAGACTTTAAT---AGGAC-------ATGAAA 3362
                          i        -     i ?    i v   ---  ii -------  i   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_20839044_2   3363 CTACTAAAAGAAAACATTAGGGGGAATGCTACAGGACATTGGTCTGGGGA 3412
                           vi  i          -   ? v  vv  v iv   v    vi i  v 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_20839044_2   3413 AAGATTTTTTTCGGGTAAGACCTCAAAAACACAGGCAACAAAAGCGAAAA 3462
                          v i   i  --i i  v   vi     i    i          -i    
  L1M4_orf2#LINE/    581 ATGGTTTCTT--AGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAA 627

  chr2_20839044_2   3463 ATAGACAAATGGGATTACACCAAGCTAAAAAGCT---ACACATAGAAAAG 3509
                              i    v   i v  i   iv v    i  ---iii v v--    
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC--AAAG 675

  chr2_20839044_2   3510 TAAACAATCAACAAAGTGAAGAAACAGTCTACAGCATGGGAGAAAATATT 3559
                         v v  v     v        i i   ii i    v               
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_20839044_2   3560 TGCAAACTATCCATCTAACAAGGGATTAATAACCAGGATATTTAGGGAAC 3609
                               ii  vi    i i      i vi  v    i    v  ii    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_20839044_2   3610 TCAAACAACTCAATAGCATGATGACAAATAATCTGAATAAAACATGGACC 3659
                           vv           ii vi v         i ii v ?   v    i v
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_20839044_2   3660 AAAGACCTGAATAGAAATTTCTCAAAGGAAGACATACAAATGGCCAACAA 3709
                           i  ii        v       v  i     i              i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_20839044_2   3710 GTACATAAAAA-ATGCTCAGCATCACTATCAGG 3741
                          i    i    -       i     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (151 / 70)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 3.00 (48 / 16)  


2898 24.92 4.53 1.70  chr2_20984697_20987044      974  1856 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_20984697_2    974 TGGAAAAACATTCCATGCTCATGGATAGGAAAAATCAATAGTGTCACAGT 1023
                               i i  i     i        v    i v i    v   i vii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_20984697_2   1024 GACCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAATC 1073
                          i v     v      vii  i           i  v  i        vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_20984697_2   1074 TACCAATTGAATTGTTCACAGAATTAGAAAAAAAACT-ATTTTAAAATTC 1122
                          v   ii  vv  v  ii     v v  v  i---  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_20984697_2   1123 ATATGGAACCAGAAAAAACTT-GAATAGCCAAGGCAATCGTAGGCAAAAA 1171
                                 viiv  iii  ii-          ii     v iiiv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_20984697_2   1172 GAACAAAGTTGGAGGCATCACATTACATGACTTCAAACTATACTGCAAAG 1221
                                        vv     i v vii i      viv    i     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_20984697_2   1222 CTACAATAACCAAAACAGCATGATACTTGTACAAAAACAGACACACAGAC 1271
                              i   i   i    ii  i    v i i  ii i     i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_20984697_2   1272 CAATGGAACAAAAT--AGAG-----AAATAATGCTGCACACCTACAACTA 1314
                                 i i   --    -----      vv iii   ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_20984697_2   1315 CCTGATCTTTGACAATATTCACCAGAAAAAGCAATGGGGAAAGGAC--TC 1362
                         vi    i  i     viv vv v   vv vv            i i--  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_20984697_2   1363 TTTATTCAATACATGGTGCTGGGATAACTGGCTAGTCACATGCAGAAGAT 1412
                            --    i v            i      v  ?i        i    v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_20984697_2   1413 TGAAGCTGGACCCCTTCCCTACACCATATACAAAAATTGACTCAAGATGG 1462
                              i         v  ii                  i      i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_20984697_2   1463 ATTAAAGACCTAAATCTAAAATTGAAAACTATTAAAACCCT-AGAAGATA 1511
                           i ?          v   i viv        -     i  -      v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAA 544

  chr2_20984697_2   1512 ATTTGGG---AAATT-------CCT-------GGCAAATACTTCAT-GAT 1543
                          iv i  ---    i-------   -------     vvii   v -   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_20984697_2   1544 AAAAACACCAAA-GCAATTGTGACAAAAACAAACATCGACAAACAGGACC 1592
                          vi -       -   vvv ii      iv   v  v  i   iv    i
  L1M4_orf2#LINE/    595 ATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_20984697_2   1593 TAACTAAACCTAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAATA 1642
                          v ii   vi   i i   i  ii vv    i  v        v i i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_20984697_2   1643 AACAGACAACCTAACAGAATGGGAGAAAATATTTGCAAACTATGCATCTG 1692
                           v        i -                         ii  ii     
  L1M4_orf2#LINE/    694 AAAAGACAACCCA-CAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_20984697_2   1693 ACAAAAGGTCTAATATCCGGAATCTATAAGGAACTTAAATTTGCAAGCCA 1742
                          i  i-  v  vi     i    v     i     i----  i   vi  
  L1M4_orf2#LINE/    743 ATAAG-GGACTTGTATCCAGAATATATAAAGAACTC----TTACAACTCA 787

  chr2_20984697_2   1743 A--------AACCAAACAACCGTATTAAAAAGTGGGCAAAGAACATGAGC 1784
                          -------- iv    i    vv   ?    i         i iv   ii
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_20984697_2   1785 AGACAGTTTTT-AAAGAACCACATTCAAGTGGCCAACAAGTATATGGAAA 1833
                              v  i i-      v- i  v   i       i   i i   -   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAGCACATG-AAA 885

  chr2_20984697_2   1834 AAATGCTCAACATTACTAATCAT 1856
                          i           i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.50 (55 / 22)  


3257 25.49 0.54 2.48  chr2_21027093_21033500.rev     4991  5916 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_21027093_2   4991 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5040
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_21027093_2   5041 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATTCCCATCAAGC 5090
                            v     v     iv i  i           i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_21027093_2   5091 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_21027093_2   5139 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5188
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_21027093_2   5189 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5238
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_21027093_2   5239 TACAGTAACCTAAAAGGCTACAGTAACCAAAACAGGATGGTACTGGTACC 5288
                                 i ------------------  i    vi         i iv
  L1M4_orf2#LINE/    249 TACAGTAATC------------------AAGACAGTGTGGTACTGGCATA 280

  chr2_21027093_2   5289 AAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAA 5336
                          ii i   v                i    i--    i  --        
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAA 328

  chr2_21027093_2   5337 TGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGACAAAAACAAG 5386
                         vv  ii i  i  iiiii vi    i  i     ivv  v   i v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_21027093_2   5387 AAATGGGGAAAGGATTCCCTATTTAATAAATGATGCTGGGAAAACTGGCT 5436
                         v           i  vvi  v  i  i     i        v      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_21027093_2   5437 AGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAA 5486
                          ?   i   i i  iiv    ii    i    v   i     v       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_21027093_2   5487 AAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATA 5536
                                i    i      i ?    i       v   v       i   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_21027093_2   5537 AAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGG 5585
                            vi i           v    ?i- v i -   iv   v v  vv i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG 577

  chr2_21027093_2   5586 GCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAA 5635
                             v ii   v ivv  vi            vvi          vv   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_21027093_2   5636 ATTGACAAATGGGATCTAATTTAACTAAAGAGCTTCTGCACAGCAAAAGA 5685
                           v  i    v   ii v  iv  v v  i i   i  ii vv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_21027093_2   5686 AACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTG 5735
                         v    i  vv i      v  i     i                 v    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_21027093_2   5736 CAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTC 5785
                            vii ivi      i  i  i  vi          v  i         
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_21027093_2   5786 AAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGTGAA 5835
                         vv    v iv i  v     i     i     v  i?    i    ii  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_21027093_2   5836 GGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGACAAAAAAC 5885
                             v    i     i     v        i  vi viii v   v  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_21027093_2   5886 ACATGAAAAAATGCTCATCATCACTGGCCAT 5916
                                  i       v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.50 (28 / 8)  


3068 27.10 0.70 0.23  chr2_21213631_21215476      500  1355 (491)    L1M4_orf2#LINE/L1       49   908 (0)  

  chr2_21213631_2    500 ATGGCCATACTGCCCAATGTAATTTATAGATTCAATGCTATCCCCATCAA 549
                              v     v     vv i  i  i        i  v     i     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_21213631_2    550 GCTACCATTGATTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTC 598
                         iv v   viviii  i  ii     v v  v  i-  - iii    v   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr2_21213631_2    599 ATATGGAATCAAAAAAGAGCCAGTATAGCCAAGACAATCCTAAGCAAAAA 648
                                 viiv  ii  v    v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_21213631_2    649 GAACAAAGCTGGAGGTATCTTGCTACCTGACTTCAAACTATACTGTAGGG 698
                                 i      vv  vii  v  ii i      viv    ii ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_21213631_2    699 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 748
                                  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_21213631_2    749 CTATGGAAGAGAACAGAGGCCTCAGAAATAATGTCACACATCTACAACCA 798
                          v      v    iv   ivii         vvi  i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_21213631_2    799 TCTGGTCTTTGACAAACCTGACAAAAACAGGCAATGGGGAAAGGATTCCC 848
                         vi  i i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_21213631_2    849 TATTTAATAAATGGTGTTGGGAAAACTGGCTATCCATATGCAGAAAACTG 898
                          v  i  i        i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_21213631_2    899 AAACTGGACCCCTTCCTTACATCTTAGACAAAAATTAACTCAAGATGGAT 948
                           ii         v   i   i v  v                i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_21213631_2    949 TAAAGACTTAAATGTAAGACCTAAAGCCATAAAAATTCTACAAGAAAACC 998
                         i ?    i           v     i i      v ii  v        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_21213631_2    999 TGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCTTGACTAA 1047
                          i  ?i- v i -   iv   v v  vv i     v ii     iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_21213631_2   1048 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTAA 1097
                         i            vvi          vv     v  i    v i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_21213631_2   1098 TTAAACTAAAGAGCTTCTG-ACAGCAAAAGAAACTATCATCAGAATGAAC 1146
                          i   v v  i i   i  -i vv    i  v       vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_21213631_2   1147 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 1196
                           i     i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_21213631_2   1197 AGGGCTAATATCCAGAATCTACAAAGAGCTTAAACAAATTTACAAGAAAA 1246
                         i  i  vi          v  i     i  ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_21213631_2   1247 AAA-AAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACACTTC 1295
                          i -   i     v  i? v  i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_21213631_2   1296 TCAAAAAAAGACATTTATGTGGCCAATAA--ACATGAAAAAAAGCTCATC 1343
                           v   i    i  vi vi          --         i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_21213631_2   1344 ATCGCTGGTCAT 1355
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.01 (7 / 860), avg. gap size = 1.14 (8 / 7)  


2276 23.28 7.01 4.28  chr2_21261092_21262925.rev      501  1342 (492)    L1M4_orf2#LINE/L1       44   908 (0)  

  chr2_21261092_2    501 TTAAGGTATCAATTCTCCCCAAAGTCACCTACAGAACTGACATAATCCCA 550
                              i iv    v         v v i       viii  ii      v
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr2_21261092_2    551 ATCAAAATCCTGGGATGCATTTTG-GTAGAAATT--CAAACGCGATTCTA 597
                                   ii v-   v    v- i       --   i -i   i   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTA 141

  chr2_21261092_2    598 AACCTTTTATGGAAATGCAAAGGAAC-AGAACGGTCTAAATAGGTTATAA 646
                           vi iv             i   v -    ii i v   i ivi - i 
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT-TGA 190

  chr2_21261092_2    647 AAAAATAAACTGAAAAAGATTAAAATTTGAGAACTTATGCTTACCTGAGT 696
                             -------   i  ---i   i  v   i   i ii   -  ii v 
  L1M4_orf2#LINE/    191 AAAA-------GAAGAA---CAAAGTTGGAGGACTCACACTT-CCCAATT 229

  chr2_21261092_2    697 TTAAGACTAATTATAAAGTTACAGCACTCAAGACACTGTGGTACTGGTGT 746
                          i  i   v i  i    i     i v        v           ii 
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_21261092_2    747 AGTACTGGTGTGGAAATATAATTCACTGGAACAGA--TCAGAATGCAGAA 794
                          i----  -i i  v     iv   v     i   -- v   i v     
  L1M4_orf2#LINE/    280 AA----GG-ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr2_21261092_2    795 ATAAGACCTAGATAAAGTCAATAAAAGATAAAATGATTTTCAACCAAGGT 844
                             -   i v i --- iv  ---- i v  v        i  v i   
  L1M4_orf2#LINE/    325 ATAA-ACCCATACA---TTTAT----GGTCAATTGATTTTCGACAAGGGT 366

  chr2_21261092_2    845 GCCAG-------CAAT------------------TCGACAAATGATGCTG 869
                             i-------    ------------------  i       i     
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_21261092_2    870 TAACAGCTGGATAGCCATACGCTTAAAAGAGGGAAA--AAA-----ACTG 912
                         vi   i       ?   i i  --      iv   i--ii -----  iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGC--AAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_21261092_2    913 ---ACCATATGCAAAAATTTATTCTAAATGGAATATAAACCCACATATAA 959
                         ---       i        v i  v       vi ? i   i v  i   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_21261092_2    960 GAACTAAATGTATAAAACTTCTCAGAAAAAAACAGA-----AAATCATAG 1004
                           i     vv         -  i    i      v -----     v v 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_21261092_2   1005 GTACCTTGACGT--GGCAAAGACATCTTAAATAGGACACAAAAAATTCAA 1052
                         vv      i-  --     v iiv     i   v     v    iiv   
  L1M4_orf2#LINE/    564 TGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_21261092_2   1053 ACTGCTAAAGAGGGACAAAATCAATACATCAAAGTTTATCAAAATTAAAA 1102
                         i vi v     i----     vi   v  iii v  i             
  L1M4_orf2#LINE/    613 GCAACAAAAGAA----AAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_21261092_2   1103 TATTTTGCTCCTCCAAAGACACAATAAAAAGACT--AAAGGCAAGCCTGA 1150
                         vv     iv i  v  i     v  v  i i v --    i   v  vv 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_21261092_2   1151 GAGAGTGAGAAAATACTTACAAAACATATAGCC--TA--GAACCTGTCTC 1196
                           iv v         i  i    v      v i--  -- i  i   v  
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_21261092_2   1197 TAAAATATATAAAGAACTTTTACAACTCAATAATAAAAAAA-AAAT---C 1242
                         i i               i                    i -    --- 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_21261092_2   1243 CAATTTAAAAATAGGTAAAAGATTT-AGCAGCCACTTTACCAAAGAAGAT 1291
                              ?      i  i   i     - ii  v  i  iv           
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_21261092_2   1292 TTATTGATGGAAAATTCGCATTTGAAAAAGATGCTTAATATCATTGTTAT 1341
                         v  ivi    vv   vv   iv      -      i  i    ???????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZZ 907

  chr2_21261092_2   1342 C 1342
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.51 (116 / 77)
Gap_init rate = 0.04 (33 / 865), avg. gap size = 2.88 (95 / 33)  


 415 21.51 0.00 0.00  chr2_21303788_21305697.rev      251   343 (1567)  C L1M4_orf2#LINE/L1   (0)   908   816  

C chr2_21303788_2    343 AGAAAGGGGAAAGGACCTGAATAGACATTTCTTGAAAGAAGACATACAAA 294
                          i  v   v      ii               iv        i       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

C chr2_21303788_2    293 TAGTTGACAGGCATATAAAAAGGTGATTAGCATCACTAATCAT 251
                          i iii i i   i  i     i  v i i     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.00 (16 / 4)
Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.00 (0 / 0)  

3238 25.06 1.22 0.55  chr2_21303788_21305697.rev      517  1418 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_21303788_2    517 TGGAAACACATCCCACGCTCATGCATTGGTAGAATAAATATTGTGAAAAT 566
                               v i      i i     v     v   v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_21303788_2    567 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 616
                          i v     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_21303788_2    617 TACCACCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCATA 666
                          v   v vv v  i  ii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_21303788_2    667 TAGAAACAAAGAAGAACCTGCATAGCCAAAGCAAGACTAAGCAAGAAGAA 716
                          i    iiv iii  v  v v         i   vvi i iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_21303788_2    717 CAAA-TCAGGGGA-TCACATTACCCAACTTCAAACTATACTACAATGCCA 764
                             - ii i   -     i v     i      viv        v  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_21303788_2    765 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGTGCATAGACCAA 814
                         i   v i   i    ii         i    ii    iiii     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_21303788_2    815 TGGAACAAAATGGAGAACCTAGAAATAAAGCCAAATACTTAACAGCCAAC 864
                              i i   v    ii i         v   v i i   -ii i   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAAT 349

  chr2_21303788_2    865 TGATCTTCAACAAAGCAAACAAAAACATAAGATAAGGAGATGACACGCTA 914
                             i   i    i vviv   i v   vvi  ii   i vi i vv  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_21303788_2    915 TTCAACAAATGGTGCTGGGATATCTGGCAAGCTACATTTGGAAGAATGAA 964
                                             i v    vv ? i    viii         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_21303788_2    965 ACTGGATCCTCATCTCTCACCTTATACAAAGATCAACTCAAGATGGATCA 1014
                         ii    i  ii i   v    v        i  i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_21303788_2   1015 AAGACTTAAATCTAAGAACTGAAACCATAAAAATTCTAGAAGATAACCTC 1064
                         ?    i     v     i  i    i      v ii       v   v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_21303788_2   1065 AGA--AAATCCCTTCTTGACACTGGCTTAGGTAAAGACTTCAT-GATCAA 1111
                         i ?--     --   v    vi   v     i  v ii   v -   - v
  L1M4_orf2#LINE/    550 GGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr2_21303788_2   1112 GAATCCAAAAGCAAATACAACTAAAACAAAGATAAATAGATGGGACTT-- 1159
                           vv         v vi    v   iv   i   i   i  v      --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_21303788_2   1160 ---AAACTAAAAAGCTTTTGCACAACAAAAGAAATAATCAGCAGAGCTAA 1206
                         ---   i      -      ii vv    i  v iv    iv i  iv  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_21303788_2   1207 CAGACAATCCACAGAGTAGGAGAAAATCTTCACAATCTATACATCTGACA 1256
                         v      i       i i         v  ii   vii   i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_21303788_2   1257 AAGGACTAATATCCAGA-TCTACAAAGAACTCAAACAAATCAGCAAGAAA 1305
                          i     vi        - v  i         vv    v   ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_21303788_2   1306 AGAACAAATAATCCCATCAAAAAGTGGGCTAAAGACATGAATAGACAATT 1355
                          ii        i  v  i?    i     v  i  iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_21303788_2   1356 CTCAAAAGAAGATATACAGATGGTCAACAAGCATATGGAAAGATGCTAAA 1405
                            v              i    i   i     i   i         v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_21303788_2   1406 CATCACTAATTAT 1418
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (133 / 89)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3216 26.65 0.55 0.55  chr2_21322512_21324493.rev      583  1490 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_21322512_2    583 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGCAAAAAT 632
                              ii i  i     i      i v      v i       iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_21322512_2    633 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 682
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_21322512_2    683 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACCTCAAAGTTC 729
                          v   i-       i  -i     -   -- v  i  - i ii   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_21322512_2    730 ATATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAA 779
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_21322512_2    780 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 829
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_21322512_2    830 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGAT 879
                                  i   i    ii         i iv ii i   v  i     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_21322512_2    880 CAATGGAACAGAAC--AGAGCCCTCAGAAAGAATGCCGCATATCTACAAC 927
                                 i    i--    i  --     v  vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_21322512_2    928 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 977
                         i vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_21322512_2    978 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTACAAAGC 1027
                         i  v  i  i              v      v  ?   i   i v  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_21322512_2   1028 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 1077
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_21322512_2   1078 ATTAAAGACTTAAGTGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1127
                           i ?    i   i   v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_21322512_2   1128 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1177
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_21322512_2   1178 AAAGACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTA 1227
                         vi v          vvi          vv    iv  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_21322512_2   1228 ATTAAACTAAAGAGCGTGTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1277
                           i   v v  i i v v  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_21322512_2   1278 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 1327
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_21322512_2   1328 AAGGGCTAATATCCAGAATCTACAATGAATTCAAACAAATTTACAAGAAA 1377
                          i  i  vi          v  i  v   i  vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_21322512_2   1378 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 1427
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_21322512_2   1428 CTCAAAAGAAGACATTTATGCAGACAAAAAACACATGAAAAAATGCTCAC 1477
                            v        i  vi viii v   v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_21322512_2   1478 CATCACTGGCCAT 1490
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3222 27.09 0.33 0.33  chr2_21343349_21349761.rev     5014  5921 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_21343349_2   5014 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5063
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_21343349_2   5064 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5113
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_21343349_2   5114 TACCAATGACATTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5162
                          v   iivi v  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_21343349_2   5163 ATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGA 5212
                               viiv  ii  v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_21343349_2   5213 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5262
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_21343349_2   5263 ACAGTAACCAACACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5312
                                i   v    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_21343349_2   5313 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTA 5360
                               i    i--    i  --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_21343349_2   5361 TCTGATCTTTGACAAACCTAAGAAAAACAAGCAATGGGGAAAGGATTCCC 5410
                         vi    i  i     ivv ivv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_21343349_2   5411 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5460
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_21343349_2   5461 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5510
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_21343349_2   5511 TAAAGACCTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5560
                         i ?         ii v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_21343349_2   5561 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5610
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_21343349_2   5611 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5660
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_21343349_2   5661 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5710
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_21343349_2   5711 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5760
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_21343349_2   5761 GGACTAATATCCAGAATCCTCAATGAACTCAAACAAATTTACAAGAAAAA 5810
                              vi          vivi  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_21343349_2   5811 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 5860
                         i     i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_21343349_2   5861 CAAAAGAAGACATTTATGCATCAAAAAAACACATGAAAAAATGCTCATCA 5910
                          v        i  vi viiiv v  v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_21343349_2   5911 TCACTGGCCAT 5921
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.37 (140 / 102)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


1874 25.20 6.96 3.41  chr2_21370560_21372286.rev      502  1263 (464)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr2_21370560_2    502 AGAAATTGAGAAGCTGGTTCTTAGATTTACATCAAAACACAAAGTACCTA 551
                                  v      i i  v i   i i  vi   ii   i v   i 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_21370560_2    552 GGCTAGCCGAAACAA-CTTCTAAAAG--GAACAAAATTGGAAAACTAATG 598
                          iv     i      -   vv     --       i     ii   v ii
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_21370560_2    599 CTACCTTTTATCAAGTCTTAACACAGAATTAAAGGAATCAAGATGGTTTG 648
                           v  ivv v    iv    vi   i ii  v  v        ii  v  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_21370560_2    649 GTAGTGGCATAAGGATGGCCACACAGATATACTGAATAGAATGCAGAGTC 698
                            v            i v  i i    vv iv         vv      
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_21370560_2    699 CAAAAATA----TATACATACATGCTCAATTGATTTTTAACAAG--TGCC 742
                           i     ----i      vi   v            ii     --    
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_21370560_2    743 AAGGTAATTCAATTTG-AAAGGATGCTTTTTTTCAATAAATGATGCTGAA 791
                            iiv       vv -    i  iv i    -   i     i     ii
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTT-CAACAAATGGTGCTGGG 418

  chr2_21370560_2    792 AGAACTGGATATTCATTTAAAACAAATACGAACTTTGATTCTTACCACAC 841
                          v         ?i  iv iv  v i - i   v  v  ii i    v   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGA-ATGAAGTTGGACCCCTACCTCAC 467

  chr2_21370560_2    842 CTCATACACACAATAAATAGTGAGAAGTAAATCAGAGACCTAAACATAAA 891
                         vi    i   -  -  v  iivvi  i ii    ?         ii   i
  L1M4_orf2#LINE/    468 ACCATATACA-AA-AATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_21370560_2    892 AAGCTAGAATGTTAAAACTTTCTGAAGAAAATATAGGAAAAAACATGTAT 941
                          -    i  ivv       i iv        i     ?iv   iv vii 
  L1M4_orf2#LINE/    516 A-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_21370560_2    942 AATGTTGGAATAGGCAAAAATTCCTTAGATAGCATGGCAAAGTCTTAAAC 991
                         i iv    iv       vii  i        vv iiv    iv vi  i 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_21370560_2    992 TCTAAAAGAA----TAG--------GATTCCGTCAACTGATTAAGA---T 1026
                         vvi       ----   --------  i i i    --i     i --- 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAA--AATTAAAAACTT 662

  chr2_21370560_2   1027 CTGCTCTTTGAAAAACAACATGAAGAAA---------------ACAAAGT 1061
                         i  iv   ii  ii   vi  v      ---------------   i i 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_21370560_2   1062 GGCAGAA--TATTT-CAATAAATGTATCTGATAAAG-ACTGGTATCCAGA 1107
                           v    --     -   vvv  i          i -   v         
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_21370560_2   1108 ACATAGTATTTTTTAAG----CCTACAATTCAAGAATAAAACAACAAATA 1153
                          i   -  ------   ---- i     i    v       vi       
  L1M4_orf2#LINE/    763 ATATA-TA------AAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_21370560_2   1154 ACCCAAATTTTAAAATGGGCAAAC--TTTGGAAAAGACACTTAAGCACAG 1201
                               -  ?v            v--    -  v     i  --- v vi
  L1M4_orf2#LINE/    806 ACCCAA-TTWAAAAATGGGCAAAGGATTTG-AATAGACATTT---CTCCA 850

  chr2_21370560_2   1202 AAAAAGATGTTCAATGTGACCAGTAA---TAAGAACAAAATGCAATTTAA 1248
                           i     i v   -i  i   i   ---i v   -  i    ---- v 
  L1M4_orf2#LINE/    851 AAGAAGATATACAA-ATGGCCAATAAGCACATGAA-AAGATGC----TCA 894

  chr2_21370560_2   1249 ACTATTAATTTGATG 1263
                           -  i ????????
  L1M4_orf2#LINE/    895 AC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (113 / 75)
Gap_init rate = 0.04 (30 / 789), avg. gap size = 2.63 (79 / 30)  


3117 28.24 0.78 0.22  chr2_21469963_21476337     4981  5883 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_21469963_2   4981 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5030
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_21469963_2   5031 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAA-G 5079
                            v     v     iv i  i  i        i  v     i     -i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_21469963_2   5080 CACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5127
                         iv   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_21469963_2   5128 TATGGAACCAAAAAAAAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5177
                                viiv  iii v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_21469963_2   5178 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5227
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_21469963_2   5228 TACAGTAACCAAAGCAGCATGGTACTTGTACCAAAACAGAGATATAGACC 5277
                                 i   ii   ii       v i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_21469963_2   5278 AATGGAACAGAACGGAGCCCTCAGAAATAATGCCACATATCTACAACTAT 5327
                                i    iv   vvii         vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_21469963_2   5328 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5377
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_21469963_2   5378 ATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTACAAAGCTGA 5427
                         v  i                 v      v  ?   i   i v  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_21469963_2   5428 AACTGGATCCCTTCCTTACACCTTATAGAAGAAGTAATTCAAGATGGATT 5477
                          ii    i    v   i     v    v  i  v   i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_21469963_2   5478 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5527
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_21469963_2   5528 AGGCATTGCCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5577
                            ?i viviv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_21469963_2   5578 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5627
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_21469963_2   5628 AAACTAAAGAGCCTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5677
                            v v  i i i i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_21469963_2   5678 GCAACCTACAGAATGGAAGAAAATCTGTGCAACCTACTCATCTGACAAAG 5727
                         i     i         i       v v     vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_21469963_2   5728 GGCTAATATCCAGAATCTACAATGAACTCAAGCAAATTTACAAGAAAAAA 5777
                          i  vi          v  i  v      vvi   v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_21469963_2   5778 GCAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCTC 5823
                         i   ----   v  i?    i    ii      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_21469963_2   5824 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 5873
                         v        i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_21469963_2   5874 CACTGGCCAT 5883
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.49 (150 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.80 (9 / 5)  


3546 19.64 4.24 1.45  chr2_21514546_21516362      501  1325 (492)    L1M4_orf2#LINE/L1       61   908 (0)  

  chr2_21514546_2    501 CTCAAAGCAGTCTGTAGATTCAACATAATCTCCATCAAAATCCCAGTGGC 550
                          i    viii   ii         ii    i i             iv  
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr2_21514546_2    551 ATTTTTTTCAGAATTAGAAAAATTCATTTTAAAATAAATATGGA--TTCA 598
                         v      v     v v  v  ii v  ii      vv       -- v  
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_21514546_2    599 AAGGACCCTGAATAGACAACAAAATATTTAAAAAGAA---CAAAGCTAGA 645
                          i      v      v   v v   v  v        ---     i i  
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_21514546_2    646 GGTGTCACAATCTTTAATTTTAAAACTTACTACAA-GCTATGGTAATCAA 694
                           vv     v iiii     i              -    ii        
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_21514546_2    695 AAAAATTAGTATGGTACTGGAATAAAGATAGACATA--GACCAGTGAAAT 742
                         i ----i   i         v    i          --  i  i  i   
  L1M4_orf2#LINE/    261 GA----CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_21514546_2    743 AGAATAGAGAGTCCATAAATAAATCCTGGTTTATATGATCAAATAATCTT 792
                              v         v       i  vviiv v    i    v i  i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_21514546_2    793 TGCGAAAAGTGCTAAGATCATGCAAAGGGAAAAGA---GCTTTTTCAACA 839
                         i vv  ii    i    i   v   v   i     --- ii         
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_21514546_2    840 ACTGGTGTTGGGAAAACTAGATATCCACATGCAAAAGAATGACATT---- 885
                          v     i     v    i    ?                  vi  ----
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_21514546_2    886 -CTTATCGCT-----TATACAAAAATTAACTCAAACTGGATTAAAGACTT 929
                         - i  i v v-----                    v     i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_21514546_2    930 AAACATGAGACCAAAAACTATAAATCTCCTAGAAGAAAACATAGGGGCAT 979
                            ii i   v v           v   i                ? i -
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA- 555

  chr2_21514546_2    980 AGGGGAAAAGCTTCATGACAATGAGTATGACAATGAATTTTTGGATATGT 1029
                         -------  v    i    vv  i  vv i     iv  i  i      v
  L1M4_orf2#LINE/    556 -------AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_21514546_2   1030 CATCAAAAACACAGGCAACAAAAGTAAAAATAGACAAATGGGACTGCATC 1079
                           i     i    i          v         i    v     v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_21514546_2   1080 AAACTTAAAAATTTCTGTGCATCAAAGAACGCCATCAATGGAGTGAAAAG 1129
                            v       i  i     v      i  i i     vii         
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_21514546_2   1130 GCAAACTACAGATTGGGAGAACATATTTTCAAATC-------TGATAAAG 1172
                         i   v i     v        v      v      -------      i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_21514546_2   1173 GGTTAATATGTAGAATACATAAAGAAATCTTGCAATTCAACAATAAAAA- 1221
                          ii vi   vi      i        v    i   i    i        -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_21514546_2   1222 ----ATAACACAACTAAAATATGGGCAAAGATCTTGAATAGACATTTATC 1267
                         ----     v   i ?   v          ivi              v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_21514546_2   1268 CAAAGATAATATACAAATGGCCAATAAGCA--TGAAGAGATGCTCAACGT 1315
                               vi                      --    i           i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_21514546_2   1316 CACCAATCAT 1325
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.39 (92 / 66)
Gap_init rate = 0.01 (12 / 848), avg. gap size = 3.92 (47 / 12)  


1884 28.46 1.99 3.86  chr2_21591450_21593169.rev      477  1228 (492)    L1M4_orf2#LINE/L1      171   908 (0)  

  chr2_21591450_2    477 AAAAGTCAAGAAATATTTT-ATAGGGAGGAACAAAGTTGGAGAATTTATA 525
                           v  i   i v -  i  - v ii  i              i i i i 
  L1M4_orf2#LINE/    171 AATAGCCAAAACA-ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_21591450_2    526 GCATTTGATTTCAAAACTTACTATAAAGCTACACTAATCAAGAAACTCTG 575
                         viviiii                i         v         v v v  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_21591450_2    576 ATATTGATGTCTTACAAATAAATTATATCTATAAGTGATATAGGTCAATA 625
                         i  i  i--- v  vii   i i--------------      i     i
  L1M4_orf2#LINE/    270 GTACTGG---CATAAGGATAGAC--------------ATATAGATCAATG 302

  chr2_21591450_2    626 AAACAACAT----AGCCCAGAAAAAGGGCCTCACAT--ATGGTAAGCTGA 669
                         i  i iv  ----  i       v iiv  vi    --     v ii   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_21591450_2    670 TTCACGACAGTGGCATGAAGGCAATTCAGTAGGGAAAATGTCATCTTTTC 719
                           iv     iv  iiiv   i v     i i      ivi vi       
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_21591450_2    720 AATACATGGTGCCAGAACAACTGAATATCTGTATGAAAAATATATTAACT 769
                           i v       ii i       i   ? iii   v    v -  v  v 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-ATGAAGT 451

  chr2_21591450_2    770 GCAATCCTTACCTCACACCATACATAAAAGTTCATTTTAAATGGATCATA 819
                         vvi i  i              i i    i  v i iv          ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_21591450_2    820 AACCTAAATTTAAAAGC-AACTCTACAAAACTTCTAGCAGAAAAAATGAG 868
                         i        v   i   -  vv   i      ii   v      v  ii 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_21591450_2    869 AGAATATCTTTGTGACCTCAAGATATGCAA-GATTTATTACATAGAAAAC 917
                         ? v v     i       iii v  v    - i   v   v   vi v  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_21591450_2    918 CAAAAATATAAACTTTAAAAGTAAATAATTGCTGTATTGGACTTTACCAA 967
                              ii i  i vvi     v   -   v v iv         i i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAA 650

  chr2_21591450_2    968 AAT-AAAAACTTTAGATTTTTGAAAGATATGGGTAAGGAAATGAAAAAGC 1016
                            -         v vvi  ii  i  i ivivi   i  i      ii 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_21591450_2   1017 AGTTCCAAGACACAATGAAATATAATATATAAAAATACTATACGTATGTG 1066
                          iii ----   v    ii v v     v iv    --i   --   v  
  L1M4_orf2#LINE/    701 AACCC----ACAGAATGGGAGAAAATATTTGCAAAT--CATA--TATCTG 742

  chr2_21591450_2   1067 GCAAAGAATTTGTATTGCAAATATATAAAGCATTCCCACAAATTAGCAAC 1116
                         ii  i i i      ivvi           v i  ii    v i ii  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_21591450_2   1117 AAAAAT-TAAGCCATACAATAAGAAATTGAGTGAAACACTTGAATGAACA 1165
                              v-i  iiv iv    v?i   v  i ii  iv i      ii   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_21591450_2   1166 CTTTATAAATAAAAGATACACATACGGCCAA---G-ACATGGAAAGATGC 1211
                         i  iviv  - i      i   v i      --- -     i        
  L1M4_orf2#LINE/    843 TTTCTCCAA-AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_21591450_2   1212 TCAATGTCATTAATCAT 1228
                             ii   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (136 / 74)
Gap_init rate = 0.02 (18 / 738), avg. gap size = 2.44 (44 / 18)  


3194 26.71 0.77 0.55  chr2_21655769_21662114.rev     4949  5854 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_21655769_2   4949 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4998
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_21655769_2   4999 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5048
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_21655769_2   5049 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5096
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_21655769_2   5097 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5146
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_21655769_2   5147 AACAAAGCGGGAGGCCTCACACTACCTGACTTCAAACTATACTACAAGGC 5196
                                iv     v        v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_21655769_2   5197 TACAGTAACCAAAACAGCATGGTACTGCTACCAAAATAGAGATACAGACC 5246
                                 i   i    ii        vi iv ii     v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_21655769_2   5247 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACA-ATCTACAACT 5293
                                i    i--    i  --        vv   i -  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_21655769_2   5294 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5343
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_21655769_2   5344 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5393
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_21655769_2   5394 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5443
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_21655769_2   5444 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5493
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_21655769_2   5494 TGAGGCA-ATACCATTCAGGACATAGGTATGGGCAA-GACTTCATGTCTA 5541
                         vv   ?i- v i -   iv   v v  vv i     - ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_21655769_2   5542 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5591
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_21655769_2   5592 ATTTAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5641
                           iv  v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_21655769_2   5642 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5691
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_21655769_2   5692 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5741
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_21655769_2   5742 AAAACAAACAACCCCACCAACAAGTGGGTGAAGGATATGAACAGACACTT 5791
                           i     i     v ii? v  i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_21655769_2   5792 CTCAAAAGAAGACACTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5841
                            v        i ivi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_21655769_2   5842 CATCACTGGCCAT 5854
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2878 25.83 2.00 1.33  chr2_21716914_21718877.rev      571  1472 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_21716914_2    571 TGGAAAAACATTCCATGATCATGGATAGGAAGAATCAATAAAGTGAAAAT 620
                               i i  i     v        v      v i    vv  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_21716914_2    621 GGCCATACTGCCCCAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 670
                            v     v   v  v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_21716914_2    671 TACCA-TTGACTTTCATCACAGAATTAGGAAAAAACT-ACTTTAAATTTC 718
                          v   -i  v    i- ii     v v -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_21716914_2    719 ATATGGAACCAAAAAAAGCCCATAG-AGCCAAGGCAATCCTCAGCAAAAC 767
                                 viiv  iiii    v i-      ii     i v iv  i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_21716914_2    768 GAACAAAGCTGGAGGCATCATGCTACCTGACTTGAA---T--CTACAAGG 812
                                 i      vv   ii  v  ii i  v  --- --      i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_21716914_2    813 CTATAGTAACTAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 862
                            i     ii  i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_21716914_2    863 CAATGGAACAGAACAGAGACCTCAGAAATAAGACCACAAATCTACAACCA 912
                                 i    iv    vii         iv   i v  i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_21716914_2    913 TCTGATCTTTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAG 962
                         ----  ---    i  i     ivv  v   i v  vv            
  L1M4_orf2#LINE/    348 ----AT---TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_21716914_2    963 GATTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAG 1012
                         i  vvi  v  i  i        i     v      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_21716914_2   1013 AAAACTGAATCTGGACCCCTTCCTTATACCTTATACAAAAATTAACTCAA 1062
                           i v    vi         v   i i   v                   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_21716914_2   1063 GATGGATGAAACACTTAAATATTAAGA-CTAAAACCATAAAAACCCTAGA 1111
                         i      v ? v  i     i -    -       i      vi i    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_21716914_2   1112 AGAAAACCAAGGCA-ATACCATTCAGAACATAGGCATGGGCAAAGACTTC 1160
                                vv   ?i- v i -   ivi  v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_21716914_2   1161 ATGACTAAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATG 1210
                         v iiv  vi            vvv          vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_21716914_2   1211 GGATCTAACCAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCA 1260
                            ii v i    v v  i i   i  ii vv    iv v       vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_21716914_2   1261 GAGTAAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCA 1310
                         i   i  v  i     i                 v       vii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_21716914_2   1311 TCTGACAAAGTGCTAATATCCAGAATCGACAAAGAACTTAAACAAATTTA 1360
                              i  i vi  vi          vv i        ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_21716914_2   1361 CAA-AAAAAAA-----AACCACATCAAAAAATGGGTGAAGCATATGAACA 1404
                         i  -     i -----    vv  i?         ii   v  v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_21716914_2   1405 GACACTTCTCAAAAGAAGACATTTATGTGGCCAAGAA--ACATGAAAAAA 1452
                             i     v        i  vi vi       v  --         i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_21716914_2   1453 AGCTCATCATCATTGGTCAT 1472
                         v     v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (127 / 102)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


2692 27.89 1.22 0.67  chr2_21731427_21733548.rev      731  1630 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_21731427_2    731 AAAAAAATCC-ATGATCATGAATAGGAAGAATCAATATAGTGAAAATGGC 779
                            i v    -   v     i  v      v i     v  v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_21731427_2    780 CACACTGCCCAAGGTAATTTGTAGATTCAATGCTATTCCCACCAAGCTCC 829
                         v i   v     iv i  i ii        i  v  i  i i   iv   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_21731427_2    830 --ATTGACTTTCTTCACAGAACTAGAAAAAACT-ACTTTAATTTTCATAT 876
                         --ii  v    i  -i     v v  v  i-  - iii   vv       
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr2_21731427_2    877 GGAACCAAAAAAGTGCCTGAATAGCCAAGACAATCCTAAGTGAAAAGAAC 926
                             viiv  ii vv  v          i      i i ivi i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_21731427_2    927 AAAGCTGCAGGTATCATGACATCT-GACTTCAAAATATACAACAAGGTTA 975
                             i  v   vv   i-  v  i-i i       iv   v    i i  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_21731427_2    976 CAATAACAAAAACGGCAAGGTACTGGTACCAAAACAGACACATTGACCAA 1025
                           i   iv  i  i iiv        i iv ii i     i  v  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_21731427_2   1026 TGTAACAGAATAGAGGCCTCAGGAATAACACCACACATCTAAAATCATCT 1075
                           v  i     v   ivii   i     vv   i    i  vii   vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_21731427_2   1076 GATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAAAGGACTCCCTAT 1125
                            i        ivv  v   i v  vv            i ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_21731427_2   1126 TTAATAAATGGTGCTGGGAAAACTGGCTGACCACATACAGAAAACAAAAA 1175
                          i  i              v      v i?      i  i  i vvi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_21731427_2   1176 TTGAACCCCTTCTTTATACCTTATACAAAAATTAACTCAAAATAAACTAA 1225
                            i      v i i i   v                      ii ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_21731427_2   1226 AGATTTAAACATAAAACCTAAAAGCATAAAAACTCT-AGAATAAAACCTA 1274
                            ii    ii   i v      vi      -    -    v     v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATA 549

  chr2_21731427_2   1275 GGCA-ATACCATTCCGGGCATAGGCATGGGCAAAGACTTTATAGCTAAAA 1323
                           ?i- v i -   vv i v v  vv i     v ii  iv   v  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_21731427_2   1324 CACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGA-TCCAAT 1372
                                    vvv          vv     v  i    v   - i  vi
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_21731427_2   1373 TAAATGAAAGAGCTTCTGCACAGCAATAGAAACTATCATCAGAGTGAACA 1422
                         v    v   i -   i  ii vv   vi  v       vv i      v 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_21731427_2   1423 GGCAACCTATAGAATGGGACAAAATTTTTGCAATCTATCCATCTGACAAA 1472
                          i     i i         v     v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_21731427_2   1473 GGTCTAACATCCAGAATCTACAAGGAACTTAAACGAATTTACATTTACAA 1522
                           v  vii         v  i  i     ivv  i v iv i v v v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_21731427_2   1523 GAAAAAAAA---AATAAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 1569
                           v   v  ---   v?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_21731427_2   1570 CAAAAGAAGACATTTATGTAGCCAACAAACATATGAAAAAATGCTCATCA 1619
                          v        i  vi vi i     i  i  i       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_21731427_2   1620 TCACTGGTCAC 1630
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.27 (138 / 109)
Gap_init rate = 0.02 (14 / 905), avg. gap size = 1.21 (17 / 14)  


3608 22.70 0.76 2.59  chr2_21745784_21750080.rev     2881  3805 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_21745784_2   2881 TGGAAAAATATTCCATGTTCATGGATTGTAAGAATCAATGTTGTTAAAAT 2930
                               i    i                v    v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_21745784_2   2931 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTATGAGAA 2980
                          v v     v      vii              i           v i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_21745784_2   2981 TACCAATGATATTCTTCACATAG---GGCAAACCTA-CCTAAGATTTATA 3026
                          v   iiviiv  i  ii  v i--- i   i iv -     i   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_21745784_2   3027 TGGAACCACAAAAGAGACCCAGAATAGCCAAAGCTATCCTAAGCCAAAAA 3076
                              vii   -- i                 i v   i i --------
  L1M4_orf2#LINE/    151 TGGAAATGCAA--GGGACCCAGAATAGCCAAAACAATCTTGA-------- 190

  chr2_21745784_2   3077 AAAAAAAAAAAAAAAACTGGAAGAATTATATTACCTGACTTCAAATTATA 3126
                         -    i  i  v   ii    i  v i i i v  ii i      viv  
  L1M4_orf2#LINE/    191 -AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_21745784_2   3127 CTACAGAGCTATAATAACAAAAACAGCATGGTACCAGCATAAAATCAGAC 3176
                              i     i i   iv  i    ii      ii      iivi    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_21745784_2   3177 ACATAGACCAATGGAACAGAATAGAGAACCTAGAAATAAATACACACACC 3226
                          i     i        i     v    ii i         iv  i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_21745784_2   3227 TATAGGGAACTCATTTTTGACAAAAGTGCCAAGAACATACACTGGGGAAA 3276
                            i vv  i v     i     ii         v   v  v        
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_21745784_2   3277 AGACAGTCTCTTCAATAAATGATGTTAGGAAAACTGGATATCCATATGCA 3326
                         ii i     i     i     i  i i   v         ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_21745784_2   3327 GAAGAATTAAACTAGACTCCTATCTCTTGCCATATATAAAAATCAAATAA 3376
                         i      v  ii i   i    i   vii       i      i  v --
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT-- 487

  chr2_21745784_2   3377 AATCAAAATTGATTCAAGACATAAATCTAAGACCTCAAACTATGAAACTA 3426
                         ---      v   iv?    v     v     v  v       i     v
  L1M4_orf2#LINE/    488 ---CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_21745784_2   3427 CTACAAGAAAACATTGGGGAAATTCTCAAAGACATTGGTCTGGGAAAAGA 3476
                         i  v          v  ? v  v   iviv   v    vi i  v  v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_21745784_2   3477 TTTTTTGAGCAATAGC-CCAAAAGCATAGGCAACCAAAGCAAAAATGGAC 3525
                            i  -  vv  ii -         i i     v    v      i  i
  L1M4_orf2#LINE/    585 TTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_21745784_2   3526 AAATGGGATCACATCAAG-TTAAAAAAAGTGTCTGCACAGCAAAGGATAC 3574
                             v   iiv      i-       ---iv i  ii vv       i  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAA---CTTTTGTGCTTCAAAGGACAC 680

  chr2_21745784_2   3575 AATCAACAAAATAAAGAGACAACCCACAGAATGGGAGAAAATATTTGCAA 3624
                         v     v   i i  i                                  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_21745784_2   3625 ACTACCCATCTGACAAGGGATTAATAACCAGAATATATAAGGAGCTCAAA 3674
                          ii ivi      i      i vi  v             i  i   vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_21745784_2   3675 CAACTCTACAGGAAAAA-ACATCTAATAATTCTATTTAAAAAATAGGCAA 3723
                               v i iv     -   ---     ii v   ?     - i     
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACA---AATAACCCAATTWAAAAA-TGGGCAA 826

  chr2_21745784_2   3724 AAGATTTGAATAGACATTTTGCAAAAGAAGACATACAAATGTCCAACAGG 3773
                          i                 iv v        i         v    i i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_21745784_2   3774 CATATGAAAAAGTGCTCAACATCATTGATCAT 3805
                           i       ii            ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (134 / 72)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


3284 22.89 4.44 1.03  chr2_21815245_21818392     1780  2657 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_21815245_2   1780 TGGAAATGCACCTTATGTTCAAGGATCGGAAGAAGACTTAATATTGTTAA 1829
                               vii i ii       v    i      ---              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA---CTTAATATTGTTAA 47

  chr2_21815245_2   1830 GATATCAATATCATTCAAAGCAACCTACATATTCAATGTGATTCCCATCA 1879
                            iv     iivii    vii i     v      i ii  i  i    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_21815245_2   1880 AATTTCCAATGACTTTTTTTGCAGAA-TAGAAAAATCCATCCTATAATGT 1928
                           v i   iivi i            - v  v  iiiv      v   vi
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_21815245_2   1929 ATATGGAATCTCAATGAATGTCAAATAGCCAAAACAATCTTGAAAATGAA 1978
                                 viv   v i ivivi                       v   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_21815245_2   1979 ---CAAAACTAAACAACTCACACTT----------------ACAACAAAG 2009
                         ---    ii ii vi          ----------------  v      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_21815245_2   2010 TTACAGTACTCAAAACAGTGTGATATTGGGATAAAAACAGACATATACA- 2058
                         i       v    i        i  i   v    ii i         v -
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_21815245_2   2059 CAAAGAAACATAATAGAGAGCCCAGAAATAAACCTTAATATATATGATAA 2108
                            v i  i v   v     i             ivv i  v    i v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_21815245_2   2109 AATAATTTT-GACAAAGGTGGCAAGACCATTCAGTGGTTAAAGGGGAATC 2157
                          v i     -     i    v            i   vv    iiv i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_21815245_2   2158 TTT-AAACAAATGGTTCTAGGAAAGCTGGATATCTTAATGCGAAAGATAG 2206
                            -v          v  i   v i       ? ivv    i     vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_21815245_2   2207 AAGTTGGACCTGTACTTAACACTGTATAAAAAAATTAACTCAAAATAGAT 2256
                                   iv   i v    ii    v                 i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_21815245_2   2257 CAAAGACCTAAGTGTAACACTTAAATCTATAAAATTCTTAGAAGAAAACA 2306
                           ?        i     v vi    v        i               
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_21815245_2   2307 TAGGATGATAGATTTACAGTG---TTAGATTTTGCAGTGATTTCTTGGAT 2353
                             ?--i  i  i v -   ---  i i  vv   i  i      i   
  L1M4_orf2#LINE/    548 TAGGN--GTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_21815245_2   2354 ACGGCAACAAAGGCACATGAAACAACCAAAAAAATTGATGAGTTACATTT 2403
                          i i  v    i     v v     vvi       v   i i  iv i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_21815245_2   2404 TATGAAAAATTTTAAAAA---TTGTATGTCAAAAGACACTGTTAACAAAG 2450
                         i  v    ---       ---    iiv     i      i i  v    
  L1M4_orf2#LINE/    645 CATCAAAA---TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_21815245_2   2451 TAAGAATGCAAACTATA---TG--AGAAAATATTTTTAAGT-ATGTATTT 2494
                          i i  vi   v i i ---  --           vi  i -  i   i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_21815245_2   2495 GCTAAGGGATTAATATTAAGAATATATAGAAAACTTTTAGCTTTCAACAA 2544
                          v       i vi   iv          i i    i   vvvi    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_21815245_2   2545 GAAA----CAAACAACCTGATTAAAAAATGAGCAAAGAACTTGAATAGAC 2590
                         v   ----    i    ii   ?       i      i i          
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_21815245_2   2591 ATTTCTGCAAAGAAGTTATGCAAATGGCCTATAAACATAAGAAAAAACAC 2640
                               v        v   i         v    i  i v     i ii 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_21815245_2   2641 TCAACATCCCTAATTAT 2657
                                 v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (120 / 77)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.00 (48 / 16)  


2986 26.10 2.81 0.79  chr2_21876530_21878552.rev      646  1534 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_21876530_2    646 GGAAAAATAATCCATGCTCATGGACTGGAAGAATCAATATTGTTAAAATG 695
                              i   vi     i       i       v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_21876530_2    696 GACATATGGCCCAAAGCACTTTGCAGATTCAATGTTATCACTATCAAAAT 745
                          vv   ivv      viiv i i         i iv   v          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_21876530_2    746 ------------TTTCAGAGAATTAGAAATATCT-ATTTTAAAATTCATT 782
                         ------------   iiv    v v  v - v  -  ii          v
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATA 150

  chr2_21876530_2    783 TAGAACCAAAACAGTGCCCA-AATAGCCACAA--ATTCTAAGCAAAAAGA 829
                          i   viiv  vi -i    -        v  --  ii i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_21876530_2    830 ATAAAGCTGGAGGCATCACATTACTTTACTTCAAACTATACTATAAGGCT 879
                          i    i      vv     i v iiv i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_21876530_2    880 ATAGTAACCAAAACATCATGGTACTGGTATGAAAACAGACACATAGGCCA 929
                          i     i   i   vii         i  i ii i     i    ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_21876530_2    930 ATGAAATAGAATAGAGAACCCAGAAATAAACCCACACATGTACAACCATC 979
                            i        v    ii               i    v  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_21876530_2    980 TGATCTCTGGTAAATTTGACAAAAAGTAAGCAATGGGAAAAGGACTTCCT 1029
                             i ii ii  ivv  v   i v-i vv       i    i ivvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCT 398

  chr2_21876530_2   1030 ATTCAATAAATGGTGCTGAGATAACTGGTTAGCCATATGCAGAAGAATGA 1079
                         v     i           i  i      v  ?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_21876530_2   1080 ATTTGGACCACCACCTCTCACATTACACAAAAATTAACTACAGATGGATT 1129
                          v       v i     v   vv  i             vv i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_21876530_2   1130 AAAGACTTAAACGTAAGTCCTCGAACTATAAAAATCCTAGAAGAAAACCT 1179
                          ?    i    i     vv  vi          v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_21876530_2   1180 AGGT---AATACGCTTTTTGACATAGGATTTGGTGAAGAATTTTTGGCTA 1226
                            ?---   ---   iv    v v  i  v  ii v iv  i  i v  
  L1M4_orf2#LINE/    549 AGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_21876530_2   1227 AGTCCCCAAAAGCAATTGGAACAAAAATGAAAAAAGACAAGTGGGACCTA 1276
                         v v v         vvv v       ivi    v   i  i v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_21876530_2   1277 ATTTAA-TTAAAGAGCTCCTGCACAGCAAAAGCTAGTATCAA-AGAGTAG 1324
                           iv  -     i -  ii  ii vv    i vi v      - i   ii
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_21876530_2   1325 ACAAACAGCCTACAGAATGGGAGAAAATATTTGCAAACCATGCACCTGAT 1374
                          v i   i  i                          i   ii i     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_21876530_2   1375 AGAGGCCTAATATCCAGAATCTACAAGTAACTT----AAATCAATAAGCA 1420
                          ii  v  vi          v  i  iv    i----  v       vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_21876530_2   1421 AAAACCAAAAAATCAAATTAAAAACTAGGCAAAGGACATGAACAGACACA 1470
                            iv    v  i v    ?    v i         iv    i     iv
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_21876530_2   1471 TTTCAAAAGAAGATAAACAAATGGCTAACAAACATTTGAAAAAATGCTTA 1520
                          i  v          v         i  i  i  iv      i     i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_21876530_2   1521 TCACTAATCAGATA 1534
                         v  ii ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (134 / 94)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 2.46 (32 / 13)  


2672 22.90 2.29 2.67  chr2_21991779_21993564.rev      501  1286 (500)    L1M4_orf2#LINE/L1       83   865 (43)  

  chr2_21991779_2    501 ATGCAATCTCTATCAAAATATCAA-TGCCATTCTTTACAAAAATAGAAAA 549
                          i      i          vi  i-    -  i   i  i    v  v  
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAA 131

  chr2_21991779_2    550 AA-AATTCTAAAATCCATATGGAACCGCAAAG-ACCCCGAACAGCCTAAG 597
                         iv-i  i       i         vi    i -    v   i    v  i
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr2_21991779_2    598 CAATTTTGGGCAAAAAGAACAAAGCTGGTAGCATCACACTACCTGACTTA 647
                             i   iiv  i          i   vi vv       v  ii i  -
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT- 230

  chr2_21991779_2    648 TTAAATGCTATAAGCATACTACAAAGTTGTAGTAAACAAAACAGCATGGT 697
                         -i   -i  -------          i ii     v   i    ii    
  L1M4_orf2#LINE/    231 -CAAA-ACT-------TACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_21991779_2    698 AGTGGAATAAAAGAAGACATA--GATCAGTGGAACAGAATGCAAAGCCCA 745
                          v   v    iiiv       --     i     i     vv i  i   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_21991779_2    746 GAAAGAAACCCAAGCATCTACAATCAAGTGTCTTTCAACAAACACGTCAA 795
                             v       vi   i  iii    v  vi    i    ivii i   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_21991779_2    796 GTATACGCAATGGGGAAAGGACAGCCTCTCCAACAAATGGTCATGGGAGA 845
                          vvi iv            i i  i  i i           vv     v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_21991779_2    846 ACTGGATCTCAACATGAAGAAGAATGAAACTAGACCC-TATCTCTCACCA 894
                                v? v     v i         ii i     -  i   v     
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_21991779_2    895 TATACAAAAATTAACTCAAAATGGATTAACAACTTGAATGTAAGACCTAA 944
                                                   i ?vi  i i         v    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_21991779_2    945 ACCTATGAAAGTACTGGAAGAAAACATAGGTGAAAATTTCTGTAACATTA 994
                          v    i   v vi i              ? v    i ii  i  v  i
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_21991779_2    995 GTCTAACCAATAATTTTCTTA-ATAAAACTGCAAAAGCATAGGCAACAAA 1043
                          vi  iv    ii   -    -   vi  vv        i i        
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTT-CTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_21991779_2   1044 AGCAAATACAGATAAATGGGATTACATCAGACTAAAAAAGCTT----CTT 1089
                           v   v i        v   i v     i v v     vi  ----   
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_21991779_2   1090 CACAACAACAAAAATCAACAAAGCAAAGAAACAACCTACAGATTGTGAAA 1139
                           -  vi   vv -    v    ii  i i      i     v  v  i 
  L1M4_orf2#LINE/    671 CA-AAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_21991779_2   1140 ATAAATATACTTGCAAACTGTACATCTATTAAAGGGTTAATATTCAAAAT 1189
                          --     --       iii  i    iv   i  ii vi   i  i   
  L1M4_orf2#LINE/    719 A--AATAT--TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_21991779_2   1190 ATACAAGGAACTCTTACAACTCAACAATAAAAA---AAAAAACCTGATT- 1235
                            i  i                 i        ---   v    ii   -
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_21991779_2   1236 AAAAATGGGCAAA--ATTACAATAATCTACATTTCTAGAATAAAGA-ATA 1282
                                      --   vv    i---        vv  vi    -   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAG---ACATTTCTCCAAAGAAGATATA 861

  chr2_21991779_2   1283 GAAA 1286
                         v   
  L1M4_orf2#LINE/    862 CAAA 865

Transitions / transversions = 1.64 (110 / 67)
Gap_init rate = 0.03 (21 / 783), avg. gap size = 1.86 (39 / 21)  

 527 13.16 4.39 1.75  chr2_21991779_21993564.rev     1390  1503 (283)    L1M4_orf2#LINE/L1      792   908 (0)  

  chr2_21991779_2   1390 TAAAAATA-AAAT----TAATTTTAAAATGAGCAAAAGATCTGAATAGAC 1434
                               v -    ----i    ?v      i     i   i         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_21991779_2   1435 ATTTCTCCAAAGAAGACATACAAATGGCCAACAGGTATATGAAAAAAAAT 1484
                                         i              i i i i       i -- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--T 889

  chr2_21991779_2   1485 GTTCAATATCACTAATTAT 1503
                          i    i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 6.00 (12 / 2)
Gap_init rate = 0.03 (3 / 117), avg. gap size = 2.33 (7 / 3)  


2486 21.90 2.58 12.59  chr2_21997746_21999763.rev      518  1526 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_21997746_2    518 TGGAAAGATGCCCTGTGTTCATGAATTAAAAGGATTAATACTGTTA---T 564
                                  ii  ii        i   ii   iv      i     --- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_21997746_2    565 AACACACATACTATCCCAAGTGATCTACAGATTGAATGAAATCCCTGCCA 614
                         ii  ---     vi  v  v             v  i v       ii  
  L1M4_orf2#LINE/     51 GGCA---ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_21997746_2    615 AAATTTCCATTACTTTTTATACAGAAATAGAAAAATAG--CCTAAAATTT 662
                             ii vii i i    v i       v  v  iiv --         i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_21997746_2    663 ATTTGGAACCACAATAGACCCTGAATAGTCAAATCA----TGAGCAAACT 708
                           v     vii   vi     v      i    v  ----   iv  ivv
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_21997746_2    709 AAACAAGGTTGGAAGCATCATACTACCTGATTTTAAA-CATACTACAAAG 757
                         i     i      i vv   i   v  ii    i   - v          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_21997746_2    758 CAATAATAATCAAATTAGCATGTTACTGGACTAAGAACAGCCATATCGAC 807
                          v i i       ivi  ii  v      vv    i i  v     v  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_21997746_2    808 CAA-GGAAAAGAATAAAGAGCCCAGAAATAAATTTACATATGTATGGTCA 856
                            -    v     vi    i           iii i i  v        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_21997746_2    857 TATTTGTTCTTGACAAAGCTGTCAAGAACACATAACAGGGAAAGGGCAGT 906
                         -   vi  i i     i v  i     v  ivi  ii       iii   
  L1M4_orf2#LINE/    348 -ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_21997746_2    907 CTCTTTAATAAATGGTGTTGGGAAATCTGGATATCCACAGGCAGAAGAAG 956
                           i  i  i        i     v v       ?     v   i     v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_21997746_2    957 GCA-TTAGGCCTTCTTCTCACACTGTATACATAAATGAACTCAAAATGAA 1005
                          v -  i i  iiivi       ii      v    v           i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_21997746_2   1006 TTAAAAACTTAAACGTAACATCTGAAACTGTAAAACT---AGAGAAAAAA 1052
                          i ? i  i    i    v v  i     i       ---   ii    v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_21997746_2   1053 AT----GAAAAACATTGTTGATATTGTTTTTGGCAGTACTTTTTAAAAAA 1098
                           ---- v   v v i  -  iv   vv  v    i iv   i v i --
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA-- 593

  chr2_21997746_2   1099 TAGGTCTTCAAAAGCACAAGCAACAAACACAAAGTTAG-TAAATAGGATT 1147
                           v v vi                   viv   iv   -     v   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_21997746_2   1148 ACATCAAGCTACAAAGCTTCTGCACAGCCATGGAAAACAATCAACAGAGG 1197
                         v      iv vv   i   i  --------  ------------------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTG--------TG------------------ 667

  chr2_21997746_2   1198 GAAGAGACAAAAAAAATAGGTCTTCAAAAGCACAAGCGACAAACACAAAG 1247
                         ---------------------       i ------------    ----
  L1M4_orf2#LINE/    668 ---------------------CTTCAAAGG------------ACAC---- 680

  chr2_21997746_2   1248 TTAGTAAATAGGATTACATCAAGCTACAAATTTTCTGCACAGCCGTGGAA 1297
                         ----------------i      ---------------------------
  L1M4_orf2#LINE/    681 ----------------TATCAAG--------------------------- 687

  chr2_21997746_2   1298 AACAATCAACAGAGGGAAAAGACAACCTGTAAAATGTGAGAAAATAGTTG 1347
                         ---------- i  v            iii i    v         v   
  L1M4_orf2#LINE/    688 ----------AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_21997746_2   1348 TGAACTATATATCTGA--AAGGATTTAATATTCAATACATATAA-TAACT 1394
                         ii  ii          -- i   i  i-   i  iv i      -v    
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACT 776

  chr2_21997746_2   1395 C--A-AACTCAATAGCAAAACCAATCAAATAATTCAATTTAAAAATAAGC 1441
                          -- -         ii    -- iv       ii     ?      ii  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAA--AGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_21997746_2   1442 TAAGTATCTGTGTAAACATTTCTCAGAATGATACATACAAATGGCCAACA 1491
                         v   v  i  vi  i         vi  vi v i              i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_21997746_2   1492 GGTATATGAAAAAAATGTTCAACATTACTAATAAT 1526
                         i i i       i -  i       i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (138 / 80)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 6.12 (153 / 25)  


2074 30.06 3.88 0.14  chr2_22001505_22003268      551  1272 (492)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr2_22001505_2    551 AAAAAACCT-GAATAGCCGTACCATTCT-GATAAAAAAGAACAAAGCTGG 598
                           iii   i-        iv v  v   -  v   i          i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_22001505_2    599 AAGCATCACACTACCTGGTTTCAAAATATATTAAAATACTATAGTAACAA 648
                          i vv       v  iii        iv  i  v  vi   i     iv 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_22001505_2    649 AAACAGCGTAACATTGCTATAAAAACAGACACGTAGGCCAATGGGCGAAA 698
                          i    i  iii i  vi    ii i     ii   ii      ivv i 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_22001505_2    699 ACAGAGAAACAAGAAATGAATCCACATATTTACAGACAACTAATTTTTCA 748
                          iv    iv v      i  i   i i     ii v   i i     iv 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_22001505_2    749 TGAAGGCACCAAGAATGTGCATTGGGAAAAGGACACCCTCTCTAGTAAAT 798
                         ii i  ii      vii v  v    i    i i vi  i ii ii    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_22001505_2    799 GATGCTGGAAAAATTAGATACTCGTGTGAGGAAGAATACAAGTGGACCCC 848
                          i      i v  i i    ?i iii  vii      iv iv        
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_22001505_2    849 TATCTCTCACCATATACAAGTATT----CAAGATGGATTAAAGACTTAAA 894
                           i   v            iv   ----   i      i ?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_22001505_2    895 CATTAGACCCCAAACTATAAAAATACTAGAAGAAAACATGAAAG-ACA-C 942
                         ii v   v iv           v vi             iii? - v - 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_22001505_2    943 TTTAGGACATCAGTCTAGGCAAAGATTTTATGGTTAAGACCTCGAAAGCA 992
                           iiv   v ii vi       v i   iv i v  v   vi i      
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_22001505_2    993 CATGCAACAAAAATGAAAATAGACAAATGGGACTACATTAAACTAAAATG 1042
                           v         ivi        i    v     v   i   v v   vi
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_22001505_2   1043 TCTCTGTAGAGCAAATGAAACAGTTGACAGATTGATCAGACCACATGTTG 1092
                         ii i   ivvv    v  v  vi ii v i v   vv    v  viiiv 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_22001505_2   1093 GATTGGAGAAAATTTTAGCAAA----GTATTCAGCAAGGGGCTAATATTC 1138
                         i  v         v  v     ----i   iiiii     i  vi   i 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_22001505_2   1139 AGAATATATAATAAACTT----AACT--------GGAAGA-AAATTAC-- 1173
                                    vi    i----    --------ii    -    v  --
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_22001505_2   1174 -GTTTAAATGTGAGCAAAGGACATGAACAGACATTTCTCAAAAAAAAGAC 1222
                         -i  ?   vi  i        iv    i           v   i  -  i
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-GAT 858

  chr2_22001505_2   1223 ATATAGTTGGCCAACAGGTATATGTAAATATTTTCAACATCAGTAATCAT 1272
                            i iv       i i i i   v   v  vi         ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (137 / 76)
Gap_init rate = 0.01 (11 / 749), avg. gap size = 2.64 (29 / 11)  


2529 27.49 3.96 1.58  chr2_22006857_22009399.rev     1168  2051 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_22006857_2   1168 AAAAACTTTCCATGCTCATGCATAGGCAGAATAAATATCGTTTAAAAGGC 1217
                            i iv i     i     v  v  v   v v     i   v i v   
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_22006857_2   1218 CACATTGCCCAAAGCAATTTATAGATTTGACACTATTCCTGTCAAACTAC 1267
                         v i i v      vii  i  i     ii  i v  i   i     v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_22006857_2   1268 CAATGACATTTTTCACAGAATTAGAAAAACT-ATTTTGAAAACTATATGG 1316
                           iivi v     ii     v v  v  i  -  ii i   vii      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_22006857_2   1317 CACCAAAAAAGAGCATGGATAGTTAATGCAATTCTAAACAA-AATAACAA 1365
                         v viiv  ii  v vv i    ii  vi    ii i  v  -  v     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_22006857_2   1366 AGCTGGAGGCATCATATTATCCAATTTCAAACTATACTACAAGTCTACAG 1415
                           i      vv   i i vi           viv        iv      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_22006857_2   1416 TAACCAAAACAGCATGGCACTGGTACAAAAACCGA------GACTAATGG 1459
                            i   i    ii   i     i i  ii iv  ------  ii     
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_22006857_2   1460 AACAGAAT--AGA---CAG---CACACCTACAGCCATCTAT--------- 1492
                           i     --   ---   ---i v   i i --   i   ---------
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATA--CATTTATGGTCAATTG 351

  chr2_22006857_2   1493 -TCTTTGACAAAGCTGACCAAAACAAG-CAATGGAGAAAGGACTTTATAT 1540
                         - i  i     i v  -    i  v v-      i     i ivv v v 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_22006857_2   1541 TCAGTAAATTGCACTGAGATAACTGGATAGCCACGTGCAGAAGATTGAAG 1590
                            ii    v ii   i  i         ?    i    i    v     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_22006857_2   1591 CTGGATCCT--CCTTATTCTAACATATACAAAAATCAAGTCAAGATGGAT 1638
                         i    i  i--   i iv ---             i  v    i      
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACAC---CATATACAAAAATTAACTCAAAATGGAT 497

  chr2_22006857_2   1639 TAAAGACTTAAATGTGAAACATAGAATTATAAAAAACCCTTC-AAGAAAA 1687
                         i ?    i       i i vv  i  i       -- i   v-       
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA--CTCTTAGAAGAAAA 545

  chr2_22006857_2   1688 CCTAGG---AAATACCATTCAAGACCTAGGCCCTGGCAAAGATTTTATAA 1734
                          v    ---    -- -   iv     v  viiv     v i   iv  i
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_22006857_2   1735 TGAGGATGCCAAAAGCAATTGAAACAAAAACAAAAATAGACAAATGAAAC 1784
                         vv v  ii         vvv v       iv         i    vii  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_22006857_2   1785 CAAATTAAACTAAGGAGCTTCTGTATAGCAAAAGAAGCTATCAACAATAT 1834
                         ivv  i   v v ii i   i   iivv    i  vi       v  vi 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_22006857_2   1835 AAACAGATAACCCACAAAATGGGAAAAAAATTTTTGCAAACCATGAATTT 1884
                         i  v   i        i       i    - v        i   iv  i 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCT 741

  chr2_22006857_2   1885 AATAAAGGTCACCTATA--CAGAATCTGTAAGAAACTTAAATGAATTAAC 1932
                         i    i  --  i i  --      v i   ii    ivv ii v i  i
  L1M4_orf2#LINE/    742 GATAAGGG--ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_22006857_2   1933 AAGCAAAAACCAAACAAGTCCATTAAAAAGTGAACAAAGGACATGAACAG 1982
                           vv    iv    i  vi v   ?    i  ii       iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_22006857_2   1983 ACACTTTTCAAAAGAAGACATATATGTGGCCAATAAGCATATGAAAAAAT 2032
                            i  i  v        i   i vi             i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_22006857_2   2033 GTTCAACATCATTAATCAT 2051
                          i         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (149 / 91)
Gap_init rate = 0.02 (20 / 905), avg. gap size = 2.45 (49 / 20)  


3265 26.44 1.00 0.55  chr2_22038096_22044368.rev     4878  5781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_22038096_2   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_22038096_2   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_22038096_2   4978 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5024
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_22038096_2   5025 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5074
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_22038096_2   5075 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5124
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_22038096_2   5125 CTACAGTAGCCAAAACAGCATGGTACTGGTACCAAAACAGAGATATGGAT 5174
                                 ii   i    ii         i iv ii i   v    i   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_22038096_2   5175 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAAC 5222
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_22038096_2   5223 TATCTGATCTTTGACAAACCTGAGAGAAACAAGCAATGGGGAAAGGATTC 5272
                         i vi    i  i     ivv  vv ii v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_22038096_2   5273 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5322
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_22038096_2   5323 TGAAGCTGGATCCCTTTCTTACACGTTATACAAAAATCAATTCAAGATGG 5372
                              i    i    vi  i    vv           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_22038096_2   5373 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5422
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_22038096_2   5423 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5472
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_22038096_2   5473 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5522
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_22038096_2   5523 ATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5572
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_22038096_2   5573 CAGGAAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5622
                         v  iv    i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_22038096_2   5623 AAGGGCTAATATCCAGAATCTACAATGAACTTCAACAAATTTAGAAGAAA 5672
                          i  i  vi          v  i  v     iiv    v iv v  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_22038096_2   5673 AAAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5718
                           i    ----   v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_22038096_2   5719 CTCAAAAGAAGACATTTATGCAGTCAAAAAACACATGAAAAAATGCTCAT 5768
                            v        i  vi viii i   v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_22038096_2   5769 CATCACTGGCCAT 5781
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


1561 20.95 2.38 2.86  chr2_22210952_22212876.rev      488   907 (1018)    L1M4_orf2#LINE/L1      270   687 (221)  

  chr2_22210952_2    488 GTACTGAAATAGAATAGGGATAGACATGCAGATCAATTCAATAGAATTGA 537
                               ----- v   i          ii        vv           
  L1M4_orf2#LINE/    270 GTACTG-----GCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_22210952_2    538 AGAGTCTAGAAGTAAAGCCACACATTTATTATCAATTGATTTTTCAACAA 587
                         -     i    i    v   i        vi            - i    
  L1M4_orf2#LINE/    315 -GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT-CGACAA 362

  chr2_22210952_2    588 GAGTGCCAAGGCAATTAAATGAGGGAGACAATTATATTTTAAACAAATGG 637
                          i        i v   v    -    i v   vi v    v         
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_22210952_2    638 TACTGAGACAACTCTATACCCACACACAAAAATTTGAGTTTGGAATC-TA 686
                          i   i       vv   ?     ii     ivv   iv     vi -  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_22210952_2    687 TCTTACACCATATACAAAAATTAGCTTATAAAGGATCAAGGAGTTAA-TG 735
                         i  i                   i  i v  v      ?i  vi   -  
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_22210952_2    736 TAAGAGATAAAATAATACAACTGTTTGAAGAA--CGGAAATGTAA-TTTT 782
                               v     iv   v    v  v      -- iv ii?    - i  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_22210952_2    783 CAAGATCCTGGTTTAGGCA----TTTTTTAAAAATACAACATTAGATGCA 828
                          iv  i i   v       ----   i   i --  ii   ii i v   
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGA--TATGACACCAAAAGCA 609

  chr2_22210952_2    829 CCCAAGTGTGATAAGGAAAAATAGATAAATTGAACTATATCAAAATGAGA 878
                          --   iivv v   i                i   vi        v i 
  L1M4_orf2#LINE/    610 C--AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_22210952_2    879 AAATCTTGTGCTTCAAAG-ACATAATAAAG 907
                           v i             -   iv  v   
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAG 687

Transitions / transversions = 1.30 (48 / 37)
Gap_init rate = 0.03 (12 / 418), avg. gap size = 1.83 (22 / 12)  

 831 16.28 5.58 0.47  chr2_22210952_22212876.rev     1219  1433 (492)    L1M4_orf2#LINE/L1      683   908 (0)  

  chr2_22210952_2   1219 TTAAAAAAGTGAAAAGACA-CCTA-ACTATGGGA--AAATATTAACAAAT 1264
                          i  i              -  i - vv      --       vi     
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_22210952_2   1265 TATATATCTGATGA-AAATCTGTATGTAGAATATATAAGAAACTTTTA-A 1312
                         i           i -ii ii     vi           ii    i   - 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_22210952_2   1313 ACTCAACAA----AAAACACATGATGTCAATTAAAAAATGGGCAAAAGAT 1358
                               i  ----  i   v  i i-i     ?             i   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAAC-CCAATTWAAAAATGGGCAAAGGAT 831

  chr2_22210952_2   1359 ATGAATAGTAATTTTTCCAAAGAAGATTTAAAAATGGCAAATAACCATAT 1408
                         v       vv    i            v  v       v     v  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_22210952_2   1409 GAAAA--TGCTCAACATCATTAATAAG 1433
                              --            ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (22 / 12)
Gap_init rate = 0.04 (8 / 226), avg. gap size = 1.62 (13 / 8)  


2657 29.37 2.13 0.45  chr2_22224849_22229062.rev     2835  3726 (488)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_22224849_2   2835 GGAAAATTACTCCATGCTCTTGGATTGGAAGAATCAATGTAATTAAAATG 2884
                              iv  ii     i  v            v i   i vi    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_22224849_2   2885 GTTGTACTGCTTAAAGCAATTTACAGATTCAGTGCTATTCATATCAAACT 2934
                          ivi    v ii   vii  i          ii  v  i v       v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_22224849_2   2935 ACCAATATCATTTTTTACAGAATTAGAAAAATCTATTCTCAAATTCATAT 2984
                         v   iivv v      i     v v  v  iiiv  i  v          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_22224849_2   2985 GGAAAAAAAAAGGATCCCAAATAGCCCAAGAAATTCTAAGCAAAAAGAAC 3034
                              viv  i   i  vi       v  iv   ii i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_22224849_2   3035 AAAGCCAAAGGCAACACATTGCCCAACTTCAAACTATAGTACAAGGTTAC 3084
                             iiii   vvv    i v     i      viv  v     i i   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_22224849_2   3085 AGTAAACAAAACAGCATGGAACTGGTACATAAATAGATACACAGACCAAT 3134
                              v   i    ii   v     i i vii     i i i   i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_22224849_2   3135 GGAACAGAATAGAGAGTCCAGAAATAAACTAGCGCACCTACAACCAGGTG 3184
                             i     v                  iviii  ii  iiii  iv  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_22224849_2   3185 ATCTTCAACAAAGTCTACAAAAAAAAGCAATGGAGAAAAGACTACCTATT 3234
                           i   i    i vivv   i vv vv      i    ii ivii  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_22224849_2   3235 TAATAAATGATTCTGGGATAACTGACTAGCCATATGCTGAAGAATAAAAC 3284
                         i  i     i v      i     iv  ?   i    vi      i  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_22224849_2   3285 TGGATCCCTACCTGTCACCACATACAAAAATTAA-----GATGAATTAAA 3329
                             i        vv     i             -----i   i  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_22224849_2   3330 GACTTAAATGTAAGACCTTACACTATAAAAATCCTAGAAGAAAACCTAGG 3379
                            i           v  v v         v  i           v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_22224849_2   3380 ---AAATACCCTTCTTAATATCAGCCTCAATAAAGAATTTATGGCTGT-- 3424
                         ---    ---    v i iv ii vi viii  v iv  iv i v i --
  L1M4_orf2#LINE/    552 NGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_22224849_2   3425 TATCAAAAGCAATTGTAACAGAAACTAAAATAGACAAGTGACACCTCATT 3474
                         i i        vvv i    i  ivv        i  i viv  i    i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_22224849_2   3475 AAAG-----AGCTTCAGCACAGCAAGATAAACTATCAAGGGAGTAATTAG 3519
                            i----- i   iv ii vv   iiv v         ii   i vv  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_22224849_2   3520 ACAACCTAAAGAATGCGAGAAAGTATTCAGAAATTAGACATCCAACAAAG 3569
                               i v      v      i    iiv    i v i   ii i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_22224849_2   3570 GTCTAATATCCAGAATCTTTAAGTAGCT--TA-AACACATAAACAAGCAA 3616
                          v  vi          v v   iv i  --  -   v  vv  i  iv i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_22224849_2   3617 A-AAATAACAGTATTAAAAAGTGGGCAAAGGACATGAACAGATATTTGTC 3665
                          -       vvv   ?    i           iv    i   i    v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_22224849_2   3666 AAAAGAATGCATACAAGCAGCCAACAAATATATGAAAAAAATGCTCATCC 3715
                         v      vii      iii     i  ii i       i -      v v
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACA 897

  chr2_22224849_2   3716 CCACTAATCAT 3726
                         i  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.56 (158 / 101)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 2.56 (23 / 9)  


3302 20.54 6.66 4.18  chr2_22245471_22247524      677  1562 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_22245471_2    677 TAGAAAAATATCCTGTGTTTATGAATTGGAAGAC--AATATTCCTGGGGT 724
                          i    i      ii    i   i          --      vi ii i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_22245471_2    725 GACTATGTTCTTTATACTGATCTCCAGATTTACTGTAATTATTATCAAAA 774
                          i v  ii  iii v i      v      i vi i   ivi        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_22245471_2    775 TCCTGG-TGGAATTTTTGCAGAAATTTACCTGCTGATCCTAAAATTCATA 823
                            ii -  vvv              v  vv                   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_22245471_2    824 TGGATATTCATGGTACCCAGAATAGTTAAGA--GTCTTGA---------- 861
                             v  v  v  v           ii  i --i      ----------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_22245471_2    862 ---------------------------TTTTAAAACTTTCTACAAAGCTA 884
                         ---------------------------   i       v           
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_22245471_2    885 TACTAATCAAGATAGGGTG-TACTGGTCTCAAGACAGACAAACAGATCAA 933
                         i v         i  v   -      iv v i  i     v i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_22245471_2    934 TTAAATAGAATTGAGTGTCCAGAAGTAAATGCATAC-TTTGTGGTGAATT 982
                          vi            v        i    iv     -   i    v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_22245471_2    983 GATTTCTGCCAAAGGTACCAAAACAACTCAACAGGGAGGAAATGGTATTT 1032
                              ii v   i   i    i  v i    ii    iii   i  ---i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT---C 397

  chr2_22245471_2   1033 TTTTTAAGAACTGATGATGGAATAACTGGATATCCGCATGCAAAAGGATG 1082
                             i  v  v  i  v   i i         ?  i          i   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_22245471_2   1083 CAGTTGGAGTCTT----CATAGAATATACAATCATTAACTGACAATAGCT 1128
                         v       vi i ----  i vv        vv       v v   i v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_22245471_2   1129 T-TGAATC---ATTTAACTACTAAAACTATGATTAC-CTTAGAGGAAAAC 1173
                         i-?ii i ---  v   vvi          i v-  -      i      
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chr2_22245471_2   1174 ----GAGTGAATATTTTTGTGACTTTGTATGTGGCGATGGTTTCTTAGAT 1219
                         ---- ?  i   --i  i     i   vi vv   i              
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_22245471_2   1220 ATGACATCTAAGGCTAAAGCAATAAAATTAAAAATAGATAAATTGGACTT 1269
                               i v  i  vv      i    vv                     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_22245471_2   1270 TGTCAGAATTAAAAACCTTTGTATTTCAAATAGCAGTTATCAAGAAAGTG 1319
                         ii   i          i     ii      vii  -i             
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGAAAGTG 693

  chr2_22245471_2   1320 AAAGGACAACTTACAGAACGGGGTAAAATATTTGCAAATCACATATCTCA 1369
                            i      ii      i   iv                 i      v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_22245471_2   1370 TGAAG--TTTAATATCTACCCCCCAGAACATATACATATGTTCTGAAGAA 1417
                          i i --i  i-    -------     i     -----------     
  L1M4_orf2#LINE/    744 TAAGGGACTTG-TATC-------CAGAATATATA-----------AAGAA 774

  chr2_22245471_2   1418 ATATATATATTTCTTACTACTCAATAATAAAAGGGCAGATAACCTAATTT 1467
                         ----------i      v              i i  i      i    ?
  L1M4_orf2#LINE/    775 ----------CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_22245471_2   1468 AAAAATGGGCAAAGAATTTGAAATAAGGTGTCTCTAAAAGATGATAGATA 1517
                                       i       vvi vi v    i   -  v    v i 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA-GAAGATATACA 863

  chr2_22245471_2   1518 AAAGGTCAATTAGCATGAGAAAAGATGTTTAACATCATTAATCAT 1562
                           v  i    v    iiv         i i       ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (113 / 65)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.57 (96 / 21)  


1742 26.21 14.78 1.99  chr2_22280431_22284517.rev     2791  3595 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_22280431_2   2791 TGGAGA-ACATCCCATGGTCATGTACCATAATGTACAAGTATGGTTAAAA 2839
                             i - i        v     v iiiv  viivi  -   v     i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAA-TATTGTTAAGA 49

  chr2_22280431_2   2840 AGACCATACTTTGCAAAGCAATCCACAGATTCAACACAATCCTGGTCAAA 2889
                         v i v     iiv    vii   i           i      ivi     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_22280431_2   2890 TTACCA-TTGTTATTTTTCACAGAATTATTT-TAAG--AATCATAGAATT 2935
                         v v   -i  ii-     ii     --   v-i   --i   v  i    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATT 146

  chr2_22280431_2   2936 TATATGGAATCAAAAAAGAGCCCAAATATCCAAATCAATCATAAGTACAA 2985
                         i        viiv  ii  v  vi    v     v     v i iv vi 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_22280431_2   2986 AGATCAAAGCTGGAGGCATCACATTATCTGACTTCAAATTATATTACAAG 3035
                            v     i      vv     i vi ii i      viv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_22280431_2   3036 GCTATAGTAACTAAAACAGCATGGTACTATTATGAAAATAGATACATAGA 3085
                             i     ii  i    ii       ivi  i ii     i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_22280431_2   3086 TCAATGAAACAGAAT---AAACCCAGAATAAAAGCCA--CAT-------- 3122
                               i  i     ---i ii      vv   v   --   --------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_22280431_2   3123 ------------AC-------CTAAAACCA-------------------- 3133
                         ------------  ------- i  i    --------------------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_22280431_2   3134 -------------------------ACTG-ATAT---------------- 3141
                         -------------------------    -   ?----------------
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_22280431_2   3142 -AAGTCTGAGCCCATATATCTCACCATATTAAAAAAATTAGTTCAGGATG 3190
                         -    -  ii   v  iv  v        - v        ii   ii   
  L1M4_orf2#LINE/    447 GAAGT-TGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATG 494

  chr2_22280431_2   3191 TATTAAAGACCTAAACATAAAACCTGAAAGTACATAAATTCT-AGAAGAA 3239
                         v  i ?         ii   i v  i   v  i -   i   -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAA 543

  chr2_22280431_2   3240 AACCCAGGAAAAAATCTTTTGGACATTGGCCTAGGCACACAATTT----- 3284
                            vi   ?iv       ivv   v    vi      - iii   -----
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAG 592

  chr2_22280431_2   3285 --ATGACAGTCCTCAAAACCTAATGCAATAAAAATAAAAAAAGGCAAATG 3332
                         --      --- iv   i vi  -    i    iv     v  ii    v
  L1M4_orf2#LINE/    593 ATATGACA---CCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATT 638

  chr2_22280431_2   3333 GGAATT------AATTAAAA--TATTAT-CCACAAAAGAAGTAACAATCA 3373
                            v  ------        -- v  i - iv    i  v---  v    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC---ACTATCA 685

  chr2_22280431_2   3374 ACAAAGTAAACAGACAACTCACAGAATGGAA--AAATATTTGCAAACAAT 3421
                          v     i  v       i          i --             iv  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_22280431_2   3422 GCATTCCACAAAGGGATAATACCCAGAATTTACAAGGAACCCAAACAGCT 3471
                         ii  iiv i  i  iv vi  i       v  i  i    i vv   i  
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_22280431_2   3472 CAGCAAGAAAAAAAACTAATAATCCCATTACAAAATGGGCAAAGAACATG 3521
                           ii  v     i - v     i  v   ?v             i iv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_22280431_2   3522 AACGGGCATTTTTCAAAAGAGGACGTACTAGCAGCCCACAAACATATGAA 3571
                           ii i     i  v     i  ii   v iii   v i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_22280431_2   3572 AAAATGCTCAATATCACTAATCAT 3595
                           i        i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (133 / 74)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 4.82 (135 / 28)  


3308 26.49 0.66 0.44  chr2_22290467_22296741     4878  5783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_22290467_2   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4927
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_22290467_2   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGTCATCCCCATCAAGC 4977
                            v     v     iv i  i           i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_22290467_2   4978 TACCAATGACATTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi v  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_22290467_2   5026 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_22290467_2   5076 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5125
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_22290467_2   5126 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_22290467_2   5176 AATGGAACAGAAC--ACAGCCCTCAGAAATAAGGCCGCATATCTACAACT 5223
                                i    i-- v  i  --        iv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_22290467_2   5224 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5273
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_22290467_2   5274 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_22290467_2   5324 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5373
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_22290467_2   5374 TTAAAGACTTAAACGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?    i    i  v   v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_22290467_2   5424 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA- 5472
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_22290467_2   5473 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5522
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_22290467_2   5523 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAGTACCATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv    i  v v  i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_22290467_2   5573 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5622
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_22290467_2   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5672
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_22290467_2   5673 AAACAAACAACCCA-TCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5721
                          i     i      - i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_22290467_2   5722 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5771
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_22290467_2   5772 ATCACTGGCCAT 5783
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2913 26.82 1.66 1.43  chr2_22393899_22398162.rev     2867  3772 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_22393899_2   2867 TGGAAATACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2916
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_22393899_2   2917 GACCATCCTGACAAAAGCAATCTACAACTTCAATGCAATTATCATCAAAA 2966
                          i v  v  vv v   vii       iv     i     ivii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_22393899_2   2967 TACCA-CAATCATCCCTCACAGAATTAGACAAAAACAATTCTAAAATTCA 3015
                          v   - vii - iii ii     v v     iv-ii  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chr2_22393899_2   3016 TATGGAACCA-AAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAG 3064
                                vii-  ii  v  v v         i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_22393899_2   3065 AACAAATCTGGAGGCATCACATTGCTGAATTTCAAACTATACTATAGGGC 3114
                               vi      vv     i v iv         viv     i ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_22393899_2   3115 CATAGTCTCCAAAACACCAAAACAGCATGGCACTGGTATGAAAATAGGCA 3164
                         i i   ------  i--   i    ii   i     i  i ii    i  
  L1M4_orf2#LINE/    249 TACAGT------AAT--CAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_22393899_2   3165 CAAATACCAATGGAACAGAATGGAGAACCCAGAAATAAACCCAAACACTT 3214
                         i v v i        i     v    ii               v   i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_22393899_2   3215 ACAGCCAACTGATCTTAGATGAAGCAAACAAAAACATAAAGTAGGGAAAG 3264
                          ii i   i    i  v  ii i vviv   i v   vv i i       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_22393899_2   3265 GATACCCTATTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAG 3314
                         i   vi  v                    i  i   v  ?       i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_22393899_2   3315 AAGAATGAAACTGGATCCTTATCTTTCACCTTATACAAAAATCAACTCAA 3364
                                  ii    i  i  i  iv    v           i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_22393899_2   3365 GATGGATTAAGGACTTAAATCTAAGACCTGAAAATATAAAAATTCTATCA 3414
                         i      i ?i   i     v     v  i   v       v ii  vv 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_22393899_2   3415 ATTAACATTGGAATAACCCTTCTAGACACTGGTTTAGGCAAAGATTTTAT 3464
                         ivv     v  ?i   vi    vv   vi   v        v i   iv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_22393899_2   3465 GACCAAGAACCCAAGAGCAAATGCAATAAAAACAAATATAAATAGGTAGG 3514
                         iivi v  vv    i    v v    i    iv   v   i   ii v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_22393899_2   3515 ACTTAATTATAACTAAAGAGCTTTTGCACAGCAAAAG----TAGTAGCAG 3560
                             v  i v  i    i -      ii vv    i ----  vi iv i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_22393899_2   3561 AGTAAACAGACAACCCATAGAGTGGGA-AAAATATCTTCACAGTCTATAC 3609
                            i  v          i   i     -       i v  - i  -   i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATAT 737

  chr2_22393899_2   3610 ATCTGACAGAGGGCTAATATCCAGAATCTACAACAAGCTCAAACAAACCA 3659
                               i ii  i  vi          v  i  vi i   vv    vi  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_22393899_2   3660 ACAAGAAAAAAAT------CCT--CTCAAAATTGGGCTAGGGACATAAAT 3701
                          i  v     i i------  i--i ?    v     v i   iv i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_22393899_2   3702 AGACAATTCTCAAAAAAAGATACACAAATGTCCGACAAACATATGAAAAA 3751
                              v     v   i      i       v  i i  i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_22393899_2   3752 ATGTCCAACATCACTAATGAT 3772
                            ii        ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.15 (28 / 13)  


2443 28.69 4.57 0.80  chr2_22724066_22729656     4225  5099 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_22724066_2   4225 TGAAAAAACGTTCCATGCTCACGAGTAGGAAGAATCAGTATCGTGAAAAT 4274
                           i   i ii i     i   i ii v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_22724066_2   4275 GGCCATACTGCCCAAAGTAGTTTATAGATTCAATGCTATTCCTATTAAA- 4323
                            v     v      v ii i  i        i  v  i     i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_22724066_2   4324 --CAAACATTGACATTCTTCACAGAATTAGAAAAAAACT-ATTTTAAAAT 4370
                         -- v i --  v -  i  ii     v v  v  i--  -  ii      
  L1M4_orf2#LINE/    101 TCCCAGC--TGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAAT 145

  chr2_22724066_2   4371 TCATATGGAACCAAAAAAGAGCACGTATAGCCAGGACAATCCT------- 4413
                                   viiv  ii  v vv v       ii      i -------
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_22724066_2   4414 -------AAGCTGGAGGTATCATGTTACCCGACTTCAAA----------- 4445
                         -------   i      vv   iii v   i i      -----------
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_22724066_2   4446 --CCATAGTAACCAAAACAGTATGGTGCTGGTATAAAAACAGACACATCG 4493
                         -- i i     i   i     i    i    i    ii i     i  v 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_22724066_2   4494 ACCAATGGAACAGAATAGAGAAGTCAGAGATAAGACGGCACACCTACAAC 4543
                          i        i     v    ivi    i    iv vii   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_22724066_2   4544 CACCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGGAAGTGTTC 4593
                           vi    i  i     ivv  v   i v  vv        i   vi vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_22724066_2   4594 CCTATTTAAAAACAGGTGCTAGGAGAACTGGCCAGCCATACACAGAAAAT 4643
                         i  v  i  v  vv      i   v      vi ?   i ii  i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_22724066_2   4644 TAAAACTGGAACCCTTTCTTACACCTTATACAAAAATTAACTCAAGATGG 4693
                          i  ii    v    vi  i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_22724066_2   4694 ATTCAAGATTGAAATGTAAAACCCAAAACTATAAAAACCCTA-AAGAAAA 4742
                           iv?   iiv        i v i            vi i  -       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_22724066_2   4743 TCTAGCCA-ATACCATTCAGGACATAGGCGTAGGTGACGATTTTATAATG 4791
                         iv   v?i- v i -   iv   v v  vv    ii i i   iv  ivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_22724066_2   4792 AAGATGTCAAAAACTACT-GCAACAAAAGTAAAAATTGACAAATGGGATC 4840
                          v  iii     i -  v-          v      v  i    v   ii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_22724066_2   4841 TAATTAAACTAAAGAGCCTCTGCAAG-CAAAAGAAACTATGATCAGAGCA 4889
                          v  i   v v  i i i i  iivv-    i  v     v vv i  ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_22724066_2   4890 AACAGATAACCCACAGAATGGAAAAAAAAAATTGCAATCTAGCCATCTGA 4939
                           v   i              i i    v v      vii vvi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_22724066_2   4940 CAAAGGTCTAATATCCAGAGTCTAGAAGGAACTTAAACAAATTTGCAAGA 4989
                         i  i  v  vi        i v  v  i     ivv    v ivii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_22724066_2   4990 AAAAAA-AAACAACCCCATTAAAAAGTGGGCAA--GACATGAATAGACAC 5036
                             i -   i     v   ?    i       --  iv          i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_22724066_2   5037 TTCTCAAAAGAAGACATTTATGTGGCCAGGAAACAT-TAAAAAAAAG-TC 5084
                              v        i  vi vi      iv  i  i- i    i v -  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_22724066_2   5085 AACATCACTGAGCAT 5099
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.76 (47 / 17)  


1489 24.62 10.46 1.85  chr2_22792502_22794092      442  1091 (500)    L1M4_orf2#LINE/L1      181   886 (22)  

  chr2_22792502_2    442 ATAAACTGGAAAATGAA-AACATTTGTGTGGAGGACATAAGCAGCCTTAT 490
                          i  v  v     v   -    vv-  -        vi vi vv  iv  
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAA-GT-TGGAGGACTCACACTTCCCAAT 228

  chr2_22792502_2    491 AGTAAGAC--AATATAAAGTTATAATAATCAAGACAGT------CTAAAA 532
                         vvi  i  -- v  i    i  i i             ------  iiv 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_22792502_2    533 TAAAG-TAAATACATATATAAATAAAACAGAATAGAAAGCCTGGAAATAA 581
                            i -  i i i   v  v   ii  i     v  i  i ii       
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_22792502_2    582 TACAGCCACACAAT-ATAGCCAAGTGATTTT-GACAAAGGCGCAAAGAC- 628
                         -  --   i   v -  i i   v       -     i  i  v     -
  L1M4_orf2#LINE/    329 -AC--CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_22792502_2    629 ----AACGGGAAAAGA-TAATCTTTTCAACAAATTGTGCTGGAACAATTG 673
                         ----  i   i     -  i              v       i    i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_22792502_2    674 AATGTTCATTTGCAGAAAAA--AAGT-----------CTTATATCTT-CA 709
                         i  i?i  iv    i  i  --    -----------  i i i v -i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_22792502_2    710 CAAAAATTAACTCA----------TACACTAAAATGTAAAGTGC-AAAAC 748
                                       ----------? v  iv        - v  -     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA-GAGCTAAAAC 524

  chr2_22792502_2    749 TA--AAGCTTCGAGAAAAAAA--TAGA---AAATCTATATGACCATGGGT 791
                           --  i  iiv    i    --   i---      vii     v     
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_22792502_2    792 TTGGTGACA-TTTTTTAGACACAACACCAAAAATATGACCTATCAAAGAA 840
                          v  ii ii-   i     i ii         ii ii v v iv      
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_22792502_2    841 AAATTTGATACATTAGGTTTTATTACAATTTTTAAAATTATTCT-CTGCA 889
                            v v    v   i ii  i  i v    v--    i v  v -  v  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTA--AAAACTTTTGTGCTTCA 672

  chr2_22792502_2    890 AAAGATATGGCTCATCAAA----TGAAAATACAAGC-ACAGACTAGGAGA 934
                           i  i ---  -     i----      v    v -     v i     
  L1M4_orf2#LINE/    673 AAGGACA---CT-ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_22792502_2    935 AAATTCTTGCAAAACACGTAACTGAAAATGAACTTGTGCCTCAAATATAC 984
                             vi       v  ii  v    v  v i      ii ivi      i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_22792502_2    985 AGAGAACTCTTAAAAT--AACATTAAGAAAA-AAATTA---AATTGAAAA 1028
                          i          v  i--  i v   i  i -    v ---    ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_22792502_2   1029 ATGGACAA--TATCTGAACAGACACCTTGACAAGGAATATATATGGATGG 1076
                             i   --v  i    i     ii ivv   i   v     iii    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_22792502_2   1077 T-AA--AGCATATGAAAA 1091
                         i-  --    i       
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAA 886

Transitions / transversions = 1.75 (100 / 57)
Gap_init rate = 0.05 (34 / 706), avg. gap size = 2.35 (80 / 34)  

 212 31.34 5.97 0.00  chr2_22792502_22794092     1081  1147 (444)  C L1M4_orf2#LINE/L1   (432)   476   406 *

C chr2_22792502_2   1147 AAATACTGTTGGGAAAACTGAATATTCACTTGCAAAACTAGGAAATTTGA 1098
                             iv  i     v     i   ?i   v       vv v   i  v  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

C chr2_22792502_2   1097 TTCTTGTTTT----CATATGC 1081
                         ii i iii i----     i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATAC 476

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.01 (1 / 71), avg. gap size = 4.00 (4 / 1)  

1275 27.44 6.92 0.00  chr2_22792502_22794092     1169  1558 (33)  C L1M4_orf2#LINE/L1   (482)   426    10  

C chr2_22792502_2   1558 ATCCAGTGTTTCTGAACTGAAAGAATTAATATCATAGTAATGTACATACT 1509
                             vi    iv  i i  i    v       ii vivi   vvv     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

C chr2_22792502_2   1508 ACCCAAAGTGAT--------TCAAAGGGATCTCTATCAAAATTCCAATGG 1467
                         v      v    --------    v vi   i          i   iiv 
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

C chr2_22792502_2   1466 CATTTTTAACAGAAAT--AAAAGTAAACTCTAAAATTTGTGTAAAACCAC 1419
                          v     vi       -- v   ivi ii        ii i ii  vii 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

C chr2_22792502_2   1418 AAAGAACCCA-AATAGCCAATGCAATTTTGA-------GAACAAAACTGA 1377
                           i i     -         vi    i    -------       ii  i
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

C chr2_22792502_2   1376 AGACATCACATTTCCTGATTTCACACTATATTACAATGCTATAGTAATCA 1327
                           ivv     i    ii      v viv  i     v    i        
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

C chr2_22792502_2   1326 AAACCATATGGCACTGCCATAAAAAT-GAAACATAGTCCAATGGAACAGA 1278
                          i  vi i   i    v     ii  -  v i    vi        i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

C chr2_22792502_2   1277 AC--AGAG-CCTGGAATAAACCCATGCATATTTGGTCAACTGATCTCTGA 1231
                          i--    -  v i           i   v v       i    i ii  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

C chr2_22792502_2   1230 CAAGGGTGCCAACAATATACAACAGGAAA----CAGTACCTTTAATAAAT 1185
                                     v vi  v   ii  i  ----i   vii  i  i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

C chr2_22792502_2   1184 GCTACTGAG-TAATCGG 1169
                          v i   i -i  ii  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGG 426

Transitions / transversions = 1.89 (70 / 37)
Gap_init rate = 0.02 (9 / 417), avg. gap size = 3.00 (27 / 9)  


2503 28.25 1.56 0.67  chr2_22843992_22848232.rev     2854  3752 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_22843992_2   2854 GGAAAAAAATTTCATGTACCTCGATAGGAAAAATCAATATTGTTAAAATG 2903
                              i v  ii     v v v   v    i v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_22843992_2   2904 ATTATATTGCCCAAAGAAATCTACAGATGCAAGAAAATTCCTATTAAATT 2953
                         iiv   i v      vvi          v   viv   i     i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_22843992_2   2954 ACCAAGATCATTTTTCACAGAATTAGAAAAAAAGATTCTAAAATT-ATTT 3002
                         v   ivvv v     ii     v v  v  ivv   i        -  v 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_22843992_2   3003 GGAAGTAACAAAGAGCAT-GAAGAGCCCAAACAACACTAAGCAAAAACAA 3051
                             i -i   i ii vi-   v    v      ivi i iv  i  v  
  L1M4_orf2#LINE/    152 GGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_22843992_2   3052 CAAAGCTGGAGGCATTACATTACCCAATTTCAAACTATAATACAGGGCTA 3101
                              i      vv i   i v            viv  v    ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_22843992_2   3102 TAATA-TCAAAAACATCATGATACTGGCAGAAAAATTAATCTGCAGATAA 3150
                         i i  -    i -  vii  i        v  ii  vi iv ii    v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_22843992_2   3151 ATTGATTAGAATAGAGAACCCA-AAATAAAGTCACACACCTAAAATCACC 3199
                           v  v      v    ii   -       vi  i   ii  vii   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_22843992_2   3200 TAATCTTTGACAAAGTTGACAAAAATAAACATTGAGGAAAAGCTACCCTA 3249
                          i  i  i     i v  v   i vi vv  v  i     iiv  vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_22843992_2   3250 TTCAATAAATGTTGCTGGTAAAACTGGCTAGCCATATGCAAAAGAATGAA 3299
                              i     v      v v      v  ?   i               
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_22843992_2   3300 ACTGGACCTCTACCTCTCATTACATACGAAAATCAACCCCAAATCAATTA 3349
                         ii      i       v  ii i    i     i   i v    vi  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_22843992_2   3350 AAGACTTAAATGTAAGGCCTGAAGCTATAAAACTACTAGATGAAAACCTA 3399
                         ?    i          iv  i  i          vi    v      v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_22843992_2   3400 GGAAAAACTCTTCTGGAAATTAGCCTTGGCAAATAATTTATGAGGAA-GA 3448
                           ?iv  v     vv  vv  i vi v     - ii   v v  iv -  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGA 598

  chr2_22843992_2   3449 CCTTAAAAGCAAATGCAACAAAAACAAAAACAGATAAATGTGACTAAATT 3498
                          vii       v v         iv     i        vv    vv  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_22843992_2   3499 AAACTAAAGAACTTCTGTAGAGTAAAAGGA-ATAAACAAGA--GTTAACA 3545
                            v v  i     i   - vv v      - iv v     --  v  v 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGT-GCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_22843992_2   3546 GGTAATCTATAGAATGGGAGAAAATATTTGCAATCTATGAATGTGACAAA 3595
                          ii  i i i                       vii  iv  v   i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_22843992_2   3596 GAACTAATATCCAGAGTCCATAAAGAACTTGAACAAATCAACAAGAAAAA 3645
                          i   vi        i vi          ivv    v    i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_22843992_2   3646 TACA--TAACTCCATTAAAAAGTGCACATAAGACATCAACACACACACTT 3693
                         v   --    i v   ?    i  vi  v i  iv v  i v   --i  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA--TTT 845

  chr2_22843992_2   3694 CTC---AAAATATATAGAAGCAGCCAACAAACTTA-AAAAAAATGCTCGT 3739
                            --- i  v     v  iii     i  i vi -i    i      iv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_22843992_2   3740 TACTAAATCATCT 3752
                         i ii ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (134 / 116)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 1.33 (20 / 15)  


3068 25.39 2.80 1.23  chr2_22857536_22859988     1069  1962 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_22857536_2   1069 TGGAAAGGTATTCCATGTTCATGGATTGGAAGAATTAATATTGTTAAAAA 1118
                                i   i                     v             i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_22857536_2   1119 GTCCATACTACTGAAAGTTATCTATAGATTCAATGTAATTCCTATCAAAA 1168
                          v v     v iv   v v     i        i i   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_22857536_2   1169 TCCCAA-TGTCATTTCCTACAGAAAGAGAAAAAAAAATTCCAA--CTCAT 1215
                              i-  i -   ii i      vv  v  ivvi  i i  --i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_22857536_2   1216 ATGGAATCAAG-AAAAGACTCTCAATATTCCAAGTAATCTTGAGCAAAAA 1264
                               -- v -  ii   i vv    vi v  ii        iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_22857536_2   1265 GTACAAAGCTGGAGGCATCACACTTCCTGATTTCAAAATATGTCATAAAG 1314
                          v      i      vv          ii         iv iii i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_22857536_2   1315 CTATTGTAATCAAAATAGCATGGTACCCTCACAAC-AGAAACACTCCCAC 1363
                            iv        i i  ii      ivv  i  v- v i   ivivv i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_22857536_2   1364 TAGTAGAACATGATATAAAGCCCAGAAATAAACCAAGGTATTTATAGTCA 1413
                         i i i   i vi  vv i  i             v vii      i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_22857536_2   1414 ATTGATTTTTGACAAAAGTGCCAAAAATATACTATGAGGAACAGACAACC 1463
                                  i     ii       i vi  v v   i    vii i ii 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_22857536_2   1464 TCTTTAATACATGGTGGTGGGAAAACTATATATCCACATGCAGAATAATA 1513
                          i  i  i v      v     v    iv   ?         i  v   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_22857536_2   1514 AAATTAAATCTTTATCTCACACCATATACAAAAATCAACTCAAAATAGAT 1563
                           i  ii i ii  i                    i          i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_22857536_2   1564 AAAAGACTGAAATGTATGATCTGACACTGTTATGTTACCAGAAGAACACA 1613
                         v ?    iv       v  v  i v   i v vii vii       v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_22857536_2   1614 TAGAA--AAAGCTCTGAAACGTTGGTTTGGTTAGCGATTTTTTGGATAGG 1661
                            i?--   v  ii vi  v    v  i vi ii i   i  i    v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_22857536_2   1662 AGTCCAAAAGCACAGGCAACAAAACAAAAA-CAGGTAAATGAGACTGTGT 1710
                          vv           i         v     -i  i     vi    vii 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_22857536_2   1711 TAAA--TGAAAAGCCTTCTGCACAGCAAAGGAATCAATTAACAAAGTGTA 1758
                         i   -- i    --   i  ii vv       vv v  i  v      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_22857536_2   1759 GATACCATACCA-AGATTGTGAAAGAATATTTGCAAACCATATATCTTAT 1807
                         i v  v i-   -   v  v  i i            i         v  
  L1M4_orf2#LINE/    696 AAGACAAC-CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_22857536_2   1808 AAGAGGCTAATAAACCAAAATATATAAGGAACTCAAACAACTCAATAGTA 1857
                            i i  vi  v-   i         i      vv           i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTAT-CCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_22857536_2   1858 AAAAAAAAAA-AACCCAGTTAAAAAATAGACAAAGGGTCTACACAGGCAT 1906
                             i v   -      i  ?      i i      i i iv i  i   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_22857536_2   1907 TTCTCAAAAGAAGAGATGT----------TAAATATATGTTTTAAA---T 1943
                              v        v  ii----------   ii i   ----   --- 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG----AAAAGAT 889

  chr2_22857536_2   1944 GTTCAACATCTCTAATCAG 1962
                          i        v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (137 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


2208 25.43 4.85 7.00  chr2_22904147_22908362     2797  3724 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_22904147_2   2797 TGCAGAGATATACTGCATTCA------GGAAGACTCACTATTGTTAAGAT 2840
                           v i      v iiii    ------        i v            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_22904147_2   2841 CTCATTTCTCCCCAAATT-ATCTACATGTTCAATAAAATCTTTGCCAAAA 2889
                         vv  v v           -       vi     iiv    ii ii     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_22904147_2   2890 TTAGAGCAAGATTTTCTTTGCAGAAATTAGAAAACCAATTCTAAAATT-A 2938
                          ivv   --viii  i            iiv  i ii  i        - 
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_22904147_2   2939 TATAGAAAACCAATGGATCAATAATAGCCAAATTAACTCTGAA---GAAG 2985
                            i    vv   v   i v v          vi  iii    ---    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_22904147_2   2986 GATATAGTTGGAGAATTAATAATACCTGATTCTAAAACTTATCATAAAGC 3035
                         i i v        i i v i v v  ii   ii        ii i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_22904147_2   3036 TACTACAACCAAGACTTTGTTTTACT-----------AGACAAATAGTTC 3074
                            vii  i      vv   vv    -----------     v    v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_22904147_2   3075 AATGAAATAGAATGAAGAGTCCTGTAAAAAGCACACACATATATG-TAAA 3123
                             i        vi       v v  v  i v  i    v    - v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_22904147_2   3124 CTTGATTTTTGAAAAAGCTTTGCAAAGGTAATTCAGTAGATAAATTATGG 3173
                         -        i  v  i v --  v   iiv     i i iv   vv  i 
  L1M4_orf2#LINE/    349 -TTGATTTTCGACAAGGGT--GCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_22904147_2   3174 TATCTTCAACAAATGATGCATGAACAACTGAATATCTGTAGGCAAACAAA 3223
                          v i           i   vv i       i   ? iii v     vi  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_22904147_2   3224 --AAGCT---TCAATGTTTC-CACTGTAAGTAAACATTAACTCAAAATGG 3267
                         --   i ---i vv iii  -   ii  vii   v               
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_22904147_2   3268 ATTGTAAACCTAAATATAAAATCTAAATCTTTAAAACTAAATTAAGAAAA 3317
                           ii? i        i   i v     v  v       ------------
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT------------ 533

  chr2_22904147_2   3318 TTTCTAAGCCTATAGAAGTAAGTGTGAAACCTAAATCCATAAAATCTATA 3367
                         ---------  -      --------------------------------
  L1M4_orf2#LINE/    534 ---------CT-TAGAAG-------------------------------- 541

  chr2_22904147_2   3368 GAAAGGAAACTTAGGAGGAAATCTCAGGGACCTTTAGTTTGGCAAATGTT 3417
                         -----i    v    ? v      iv v      vi   v     vv   
  L1M4_orf2#LINE/    542 -----AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_22904147_2   3418 TTTTAAGTAGTATATAAAAAGCACACATTCTAAAAGAAAATATCAATAAA 3467
                          i   ii  vv i iv         viivvi         v  vi     
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_22904147_2   3468 TTAGACTTCATCAAAACCAAAAATTTTTACTCTT-ATAAGACACTGTTAA 3516
                           i             ii     i    iiv   - v i      i i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_22904147_2   3517 GAGTATTTAATGTTAAGCCATAGAATGAGAGAAAATGTTTGAAAATCACT 3566
                           ivi vv  v vi  v   i      i        i    v      iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_22904147_2   3567 TGTCTGATGAAGGACTAATATTCCCA-TACATGAAGAATTATTAAGAT-- 3613
                          i      i i     vi   i vv -  i  i     i v   vi i--
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_22904147_2   3614 ---------AAGA--AACAATCCAAT-AGACTATGAACAAAATACATACA 3651
                         ---------    --  i  i     -?i vv   ii    iv iv iv 
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_22904147_2   3652 CAGATACTTCACTATAGGTGATATAAAGATGGCAGATAAGCACATGAAAA 3701
                         i   i i   v i v  iv      v i     vi               
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_22904147_2   3702 AGGTTTTCAACATCATCAGTCAC 3724
                         - i vi         ????????
  L1M4_orf2#LINE/    887 -GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (134 / 98)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 5.24 (110 / 21)  


1824 26.03 8.90 5.25  chr2_23069164_23073953     3428  4303 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_23069164_2   3428 TGGGTACACATTACATGTTTATGAAT-GGAAGACTCA-TAATGTTAA--- 3472
                            iv v i  iv      i   i  -        i -  v      ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_23069164_2   3473 -----TTCTCTCCAAATTGATCTATCAATTTCAACTGAA--CCTA---AA 3512
                         ----- v   i             -  iv      vv  --    ---  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTA-CAGATTCAACGCAATCCCTATCAAA 99

  chr2_23069164_2   3513 TTCTCAGCAGAATGCTTTA-AGAAAGTGAC---TTGTTTCCCAAGTATAT 3558
                         v  i    v vv vi   i-     v    ---i  v i iv  i vi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_23069164_2   3559 ATGAAAATTTAAGAAATATAGAATACTTAAAACAATTTTAGAAAA----A 3604
                            i    vi   ii ivi      vii        i  ii    ---- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_23069164_2   3605 ATAAAAACAGAACAATTATACAACCTAATTTCAAGATTTACTATAAACTT 3654
                          i   ivii  iv v i i  vv  i        i i      i   vi 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_23069164_2   3655 ATAGTAA------------------GACATAGAAATAGACACATAGATCA 3686
                          i     ------------------ i    iii       i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_23069164_2   3687 ATAAGAAAGAATTTCAAGCCTA-AAATACACACACACTATATATACATAT 3735
                           iii v      vvi  i i -     v  ----- i   i  v--   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAAC-----CCATACATT--TAT 342

  chr2_23069164_2   3736 AGTCAACTAATTTTTA-----GATGCCAAGGTAATTCAATTGGGAAATAA 3780
                         i     i i     ii----- i       iiv       v      v  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_23069164_2   3781 TTATTTTCCCAGCAAATGATGCTGGAACAACCAAATATCCATATGGAAAA 3830
                          vi i  ii  i      i      i     iii   ?   i   v    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_23069164_2   3831 ATACAAAGCCCAACCAGTTACCTCACACCTTAACTATCACACATAAAAGC 3880
                         iv ii   iivi   v-i           --------- i i i    ii
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCC-CTACCTCACACC---------ATATACAAAAAT 482

  chr2_23069164_2   3881 TAATGTGAAGTG-ATCATGGGCTTAAGTATAAAAACTTAAAACTCTGAAA 3929
                            ivii  i  -    ?i i i   i i   i i  -      v i   
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAA 531

  chr2_23069164_2   3930 CT-TTGGAAGAAAGCATAGGAAAAAATCTTTGTGACTTTAGATTGCTTAG 3978
                           -  i       i      ?iv       i     i  i i  ------
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT------ 575

  chr2_23069164_2   3979 ATAGAATCAAAAAACTTATTGTTTTGATAGGAC--CAAAGATTTCTTAGA 4026
                         --  i--   ----- vi  vi  v    v   --    iii------- 
  L1M4_orf2#LINE/    576 --AGG--CAA-----TGGTTTCTTAGATATGACACCAAAAGC-------A 609

  chr2_23069164_2   4027 TAAGGCAAAAAAAGTAAACACTGATAATTTGGATTTCATCCAAATTTCAA 4076
                         i   -   v     v   v iv     v     i      v     vv  
  L1M4_orf2#LINE/    610 CAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_23069164_2   4077 ACATTTGTTCTTCAAAATGCGCGAATCAA-ATAGCG---------CTAAT 4116
                           v     v       ivi i v -    - v  i --------- iv i
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_23069164_2   4117 AGGCTATGTTCATATATTTTCAATACATACATCTGACAAATGATTTCTAT 4166
                           iv iv vvv v      v   vv    i      i  iv  i  v   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_23069164_2   4167 CCAGAATATATACCATACTCTTACGATTCAACAATATGAAGACAAACAAT 4216
                                     vviv        i i    i    vi        i  i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_23069164_2   4217 GCAATTTTTTAAAA--GGGCAACACATTTAAACAGAAATAT----AAAAG 4260
                         v     ?---    --      viv    i  i   v  v ----   ii
  L1M4_orf2#LINE/    808 CCAATTW---AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_23069164_2   4261 AGAGAGA---------AGTAA--ACCTGAAAAGATGCTTAAAACCCTTAG 4299
                            v v --------- i   --  v            i  v i v????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_23069164_2   4300 TCAT 4303
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.76 (124 / 33)  


2990 27.04 3.28 0.57  chr2_23118178_23124438     4886  5769 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_23118178_2   4886 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAAGCAATATCATGAAAAT 4935
                              ii i  i     i      i v      vvi     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_23118178_2   4936 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4985
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_23118178_2   4986 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5033
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_23118178_2   5034 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGGCAATCCTAAGCCAAAAG 5083
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_23118178_2   5084 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5133
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_23118178_2   5134 CACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5183
                         i       i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_23118178_2   5184 AATGGAACAGAAC--AGAGCCCTCAGAAATAAGGCCGCATATCTACAACT 5231
                                i    i--    i  --        iv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_23118178_2   5232 ATCTGATCTTTGACAAACCTGAGAAAAAACAAGCAATGGGGAAAGGATTC 5281
                          vi    i  i     ivv  vv  i v-  vv            i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAG 395

  chr2_23118178_2   5282 CCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGC 5331
                         i  v  i  i              v      v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_23118178_2   5332 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5381
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_23118178_2   5382 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5431
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_23118178_2   5432 TCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCTA 5481
                         iv    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_23118178_2   5482 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5531
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_23118178_2   5532 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCA------T--- 5572
                           i   v v  i i   i  ii vv    i  v    i  ------ ---
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_23118178_2   5573 -----------CAGAGTG-----AAATTTTCACAACCTACTCATCTGACA 5606
                         -----------    i  -----    v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_23118178_2   5607 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5656
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_23118178_2   5657 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGGACAGACACTT 5706
                           i     i     v  i?    i           iv  i i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_23118178_2   5707 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5756
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_23118178_2   5757 CATCACTGGCCAT 5769
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (144 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.78 (34 / 9)  


2654 20.77 2.80 3.24  chr2_23144665_23146372.rev      514  1192 (516)    L1M4_orf2#LINE/L1      196   871 (37)  

  chr2_23144665_2    514 AAGAACAAAGCTG-AGGCCTCATATTTCCAGATTTCAAA--TTACATTAC 560
                                   i  -   v    i i    vi        --    --   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TAC 243

  chr2_23144665_2    561 AAAGCTAAAGTAATCAAAACTGTATAGTGCTGGTATAAATATAGACACAC 610
                                v         i  v  i i  i    i    iv       i i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_23144665_2    611 AGACCAATGGGACAAAATAAAGAGCCAAGAAATAAATCTATGCATGTAAG 660
                            i      i i i   vi    i v         i i  i   v  v 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_23144665_2    661 GTTAACTGATTTTCAACAAGAGCACCAAGAGTA--CAAACTGGTGAAAGA 708
                           i  i        i     i ii      vi --   --   v      
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGA 391

  chr2_23144665_2    709 ATAGTTTCTTCAATAAATGGTGTTGGGAAAACTGGATCTCCACATGCAAA 758
                              i i     i        i     v        v?           
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_23144665_2    759 AGAGTGAAATTGGATCCTTAT-----AACATACACAAAAATGAACTCAAA 803
                            i    i     i  i  i----- v    i        v        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_23144665_2    804 ATGGACTCA-AGACTTAAATGTAACACCTGAAAACATAAAACCTCTAGAA 852
                              -   -    i         v v  i   vi       iii     
  L1M4_orf2#LINE/    492 ATGGA-TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_23144665_2    853 GAAAACACAGGAGAAAAGCTCTGTGACAGTGGTCTTGGAAATACATTTTT 902
                                i   ? v   v  ii     vv   vi v  v   ivv  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_23144665_2    903 GGATATAACAGCATGAACACAGGCAACAAAAGCCAAAATAAGCAGAGTTG 952
                         i     i   v  vi i    i          vv      iii i -   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA-TTG 639

  chr2_23144665_2    953 -----TGTCAAACTAGGAAGCTTCTGTACAGCAAAGGAAACAATTGGCAA 997
                         -----ii     v vii  i   i   i vv       v  v  iiiv  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_23144665_2    998 AATGAAAAAA-AACT-ACAGAGTGGCAGAAAATATTTGCAAACTATATAT 1045
                          i      i -   i-     i   v                ii      
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_23144665_2   1046 CTGATAAGGGGTTAATATCCAAAATGTATAAGGAACTCATACAACTCAAT 1095
                                   ii vi      i   i     i      v           
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_23144665_2   1096 AGCAAAAAACCAACCAAACAAAATAAGTTAAGTCAAT-AAAAAATGGGCA 1144
                          ii     i--------     ------   vi    -?           
  L1M4_orf2#LINE/    790 AATAAAAAG--------ACAAA------TAACCCAATTWAAAAATGGGCA 825

  chr2_23144665_2   1145 AAGGACCTCAACAGCCATTTCTCCAAAAAAGACATGCATCAGTGATCA 1192
                              ii v  i  v            i    i  i  -- i  ii  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA--AATGGCCA 871

Transitions / transversions = 2.14 (94 / 44)
Gap_init rate = 0.02 (16 / 676), avg. gap size = 2.56 (41 / 16)  


1144 22.29 1.81 11.85  chr2_23305572_23311968        1   498 (5899)    L1M4_orf2#LINE/L1      252   699 (209)  

  chr2_23305572_2      1 AGTAATCAAGACATT-TAGTACTGGCATCAAGATAGACAAATAGAC--AT 47
                                      v - i          v i        v     i--  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_23305572_2     48 GGAACAAAATATAGAATCCAGAATTAGACCCAAAAAATTGAAAACAAATC 97
                             i i   vv   i       v  i     v v v  -----------
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT----------- 340

  chr2_23305572_2     98 AATTTTCAATTGATTTTTTTACAAAAGTGTTAGG-CAATTCAGTGAAGAA 146
                         -  vv            iv-    ii   ii i - v     i  ii   
  L1M4_orf2#LINE/    341 -ATGGTCAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_23305572_2    147 AGGATGGTATTCCCAACAAATGGCACTGGAAAAATTAAGCATCCATATGC 196
                           i  i  v  ii          ii    i v  i iiii ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_23305572_2    197 ATGCATCAATTAGTTAATTAATGAATTTCAATCCATAAATTATGTGAACT 246
                          ------  --  ------      v  vi i  v  ----------- i
  L1M4_orf2#LINE/    439 A------AA--AG------AATGAAGTTGGACCCCTA-----------CC 463

  chr2_23305572_2    247 GAAATCATATGGATTGCATCATATATACAAATTTACTCAAAATAGGTCAT 296
                         ----   ---------  i      i v     v         i i   ?
  L1M4_orf2#LINE/    464 ----TCA---------CACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_23305572_2    297 GGGAATAAACATAAAATCTAAAATTATAATGCCTCTAGAAAATTAAAGCA 346
                         i ivv    ii   i v      i     vi iii     i ---  i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA---AAACA 547

  chr2_23305572_2    347 CAGGATGAAATCCCTTTTTACCT-AGATTAAGCAAAGATTCTTCAAATAT 395
                         i   ?vv     i- iv v    -i i   i    v i  ii i i    
  L1M4_orf2#LINE/    548 TAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_23305572_2    396 GATGCCAAAA---CAAGAATTCATGAAAGAAAAAAATTTATAAATGGGAC 442
                           ii      ---    v --- ii          - vv      v    
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCA---ACAAAAGAAAAAA-TAGATAAATTGGAC 642

  chr2_23305572_2    443 TTTATCAAAATTTAGAACTTCTGCTTTTCAAAGG-CACTGTTAAGAAAAT 491
                           i         v i     i  ivi        -    i i      i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_23305572_2    492 ATAAAGA 498
                         iv     
  L1M4_orf2#LINE/    693 GAAAAGA 699

Transitions / transversions = 2.00 (72 / 36)
Gap_init rate = 0.04 (18 / 448), avg. gap size = 3.78 (68 / 18)  

3137 26.06 0.76 2.17  chr2_23305572_23311968     4985  5905 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_23305572_2   4985 TGGAAGAACATTCCATGTTCATGGATAGGAAGAATCAATATTGTGAAAAT 5034
                              ii i  i              v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_23305572_2   5035 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTTATCAAGC 5084
                            v     v     iv i  i  i        i  v    i      iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_23305572_2   5085 TACCAATGACTTTCTTCACAGA--TTGGAAAAAACTGCTT-TAAAGTTCA 5131
                          v   iivi i  i  ii    --   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_23305572_2   5132 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGACAATCCTAAGCCAAAAG 5181
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_23305572_2   5182 AACAAAGCTGGAGGCATCATGCTAACTGACTTCAAACTATACTATAAGGC 5231
                                i      vv   ii  vv ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_23305572_2   5232 TACAGTAACCAAAACAGAATGGTACTGGTACCAAAACAGAGATATAGACA 5281
                                 i   i    vi         i iv ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_23305572_2   5282 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5329
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_23305572_2   5330 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5379
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_23305572_2   5380 CTGTTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5429
                           v  i  i       i      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_23305572_2   5430 GAAACTGGATCCCTTCCTTACACCTTTATACAAAAATTAATTCAAGATGG 5479
                            ii    i    v   i     v -             i    i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCAT-ATACAAAAATTAACTCAAAATGG 495

  chr2_23305572_2   5480 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5529
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_23305572_2   5530 CCTAGGCA-ATACCATGCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5578
                          v    ?i- v i - v iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_23305572_2   5579 AAAACACCAAAAGCAGTGGCAACAAAGCCAAAACT-GACAAATGGGATCT 5627
                          vi            vvi        ivv    v -  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_23305572_2   5628 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGA 5677
                         v  i   v v  i i   i  ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_23305572_2   5678 ATAGGCAACCTACAGAACGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5727
                          v  i     i      i          v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_23305572_2   5728 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5777
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_23305572_2   5778 AAAATCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5827
                            iv    i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_23305572_2   5828 TCTCAAAGAAATGTCTTCAAAAGAAGACATTTATGCAGCCCACAGACACA 5877
                             -------------    -     i  vi viii   v i ii    
  L1M4_orf2#LINE/    845 TCTC-------------CAAA-GAAGATATACAAATGGCCAATAAGCACA 880

  chr2_23305572_2   5878 TGAAAAAATGCTCATCATCACTGGCCAT 5905
                               i       v     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.45 (27 / 11)  


3284 26.87 0.44 0.44  chr2_23359627_23365909.rev     4884  5791 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_23359627_2   4884 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATCGTGAAAAT 4933
                              ii i  i     i      i v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_23359627_2   4934 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4983
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_23359627_2   4984 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5031
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_23359627_2   5032 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5081
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_23359627_2   5082 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5131
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_23359627_2   5132 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5181
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_23359627_2   5182 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATACCTACAACT 5229
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_23359627_2   5230 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5279
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_23359627_2   5280 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5329
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_23359627_2   5330 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5379
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_23359627_2   5380 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5429
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_23359627_2   5430 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5479
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_23359627_2   5480 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5529
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_23359627_2   5530 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5579
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_23359627_2   5580 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5629
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_23359627_2   5630 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5679
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_23359627_2   5680 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5729
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_23359627_2   5730 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5779
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_23359627_2   5780 ATCACTGGCCAT 5791
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2713 25.79 6.53 0.93  chr2_23401384_23403281.rev      550  1406 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_23401384_2    550 AGAGATATAAACCATGTTCATGGGTCAAAAGACACAATAGTCGTAAGATG 599
                          i      v--            i iii     vi    v vv       
  L1M4_orf2#LINE/      4 AAAGATATC--CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_23401384_2    600 TCAGTTCTCTCCAAATTGATGTGTAGATTCATCATAAGTCCAA-AGAAAT 648
                         v  i v   i          v ii       v ii  vi  v -vi    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_23401384_2    649 CTCAGCAGCTTTCTTTTCCTAAATATTTATAAGCCCATTTTAAAATTTAT 698
                          i    v  i  i   v -- i v   v i    iv  ii       i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGC--AGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_23401384_2    699 ATGGAAATGCACAGAATCTAGAAGAGCCAAAGCAACATTGAAAAC-AGGA 747
                                    vi i i i    v       i   iv       v- i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_23401384_2    748 ACAAAGTTTGA-----------------TTTCAAA-TTTGTTATAAAGCC 779
                                 v  -----------------       -i  ii  i     i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_23401384_2    780 ACAATAATCAAGAAAGTATAGCATTGACATAA--ATATATACTTAGATAA 827
                            i         v   i i i i  i     --   v i iv     v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_23401384_2    828 ATGGAACAGAAGAAAGAGTAGAGAAATAGATATACACATTTTTGATTAAC 877
                               i    vvi     vv       i ivi i      v  i i  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_23401384_2    878 TGATTTCCTAT---GGTCTCAATGCAGTTTAGTTGGAAAATGAGATTTTT 924
                               i v i---   vi   vi vi  i i v  i   vi v v i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_23401384_2    925 CTCCATTAAATGATGCCAGAGCAATTG-----CAATTTGCAGAAAAATGA 969
                         i  v i-     i   ii ii   i  ----- v iv    i  i     
  L1M4_orf2#LINE/    400 TTCAAC-AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_23401384_2    970 ATTTTGATCTTTACCTCACGCCATATGCAAAAATAAACTTGAAATGAATG 1019
                          v  v  i ii        i      i       v    ii     i  v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_23401384_2   1020 ATAGGCCTAAATGCAAGAGTTAAA-TGACAGAGCTTTTAACAGATAACAT 1068
                          ?  i        i     i    -iv i i i  i   iv   v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_23401384_2   1069 AGGAGAAAGTCTTCATA--CTTGGGTTTGGCAAAGGTTTCTTAAGTACG- 1115
                            ? v  i     i i--        v     v         ii  i -
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_23401384_2   1116 TACCAAAGAGAACAAATTACAAAC--ACAAATAGA--AATAGAAAATTAT 1161
                         i      -  v    iiv     v-- v       --   v i vv i  
  L1M4_orf2#LINE/    599 CACCAAA-AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_23401384_2   1162 CAGAATTACAAATTCTTATTCTTCAAAAGA-----------------AAA 1194
                           i     v   i i  i v       i  -----------------   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_23401384_2   1195 GGCAGGCCATAGGCTACAAGAAAATATTTGCAAAACATGTATCTGACTTA 1244
                          i  iv   i  iv ivi                v   i       ivvi
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_23401384_2   1245 GGACTTTTATGAAGATTATATGAA-AACTCCTCCCACTCAATTGTAAAAA 1293
                               v   vv   v     i  -     i v v       vi      
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_23401384_2   1294 GACAAATGACCCAATTAAAAAAAGTACAAAAGATTTTCACCGACTCTTCA 1343
                                i        ?     v vi    i     vv iv   vi   v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_23401384_2   1344 CCAAAGAAGTTATATATCAGTGGCAGGAAAATACCTGAAAATATACTTAA 1393
                                  --     iv i    viiv  ii  v      v  i  i  
  L1M4_orf2#LINE/    848 CCAAAGAAG--ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_23401384_2   1394 CATCATTAGTTAT 1406
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (131 / 87)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 3.37 (64 / 19)  


3216 26.87 0.55 0.55  chr2_23870590_23876986     4998  5905 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_23870590_2   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5047
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_23870590_2   5048 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCAATCAAGC 5097
                            v     v     iv i  i  i        i  v     v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_23870590_2   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_23870590_2   5146 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAACCAAAAG 5195
                                viiv  ii  v  v v  v     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_23870590_2   5196 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_23870590_2   5246 TACAGGAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5295
                              v  i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_23870590_2   5296 AATGGAACAGAAC--ACAGCCCTCAGAAATAATGCCACATATCTACAACT 5343
                                i    i-- v  i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_23870590_2   5344 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5393
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_23870590_2   5394 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5443
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_23870590_2   5444 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5493
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_23870590_2   5494 TTAAAGACTTAAACGTTAGCCCTAAAACCATAAAAACCCTAGAAGAAAAC 5543
                          i ?    i    i  v  vv       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_23870590_2   5544 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACGTCATGTCTA 5592
                         v    ?i- v i -   iv   v v  vv i     v iiv  v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_23870590_2   5593 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5642
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_23870590_2   5643 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACGACCATCAGAGTGAA 5692
                           i   v v  i i   i  ii vv    i  v  v i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_23870590_2   5693 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5742
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_23870590_2   5743 AAGGGCTAATATTCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5792
                          i  i  vi   i      v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_23870590_2   5793 AAAACAAACAACCTCATCAAAAAGTGGGCGAAGAACATGAACAGACACTT 5842
                           i     i    iv  i?    i     i   i iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_23870590_2   5843 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5892
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_23870590_2   5893 CATCACTGGCCAT 5905
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 323 30.10 10.38 7.96  chr2_23939858_23941676.rev      461  1327 (492)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr2_23939858_2    461 ATGAATGGTAAGACTTTAAATT-CAAAGGCTGTGAGGTTTTTTCCTAAAT 509
                            i  v v       v v   -iv   iiv ii --- vi i  i    
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAA---TACTCCCCAAAT 67

  chr2_23939858_2    510 TAATGTATAAATTAAGTACAGTTCTAATTATAATCTC--CTCAAAACTTA 557
                          i  v  i i   v iii  i i iv  i v    i --  ---iv   v
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT---GCCTTT 114

  chr2_23939858_2    558 GGGGGAGAAGTTAAAAAAAAAGAGTTCTGTTTCTTCTAGAAAATAAATAT 607
                         vvv v    i  i v  i--------   v i  -----     vv    
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAG--------CTGATCCT-----AAAATTCATAT 151

  chr2_23939858_2    608 GAGAGTAGCAAGG-----AGAAT-----------TCTAGAGGAAAAAGTG 641
                          ii i -      -----     -----------   v  ii  i   vi
  L1M4_orf2#LINE/    152 GGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_23939858_2    642 TCA--TTAGGG----CGCCCTACCAAAATTGTAAGGGTGTAATAGAGTTA 685
                         iv --  i i ---- i v  v  v  v  vv  ivv iiv i i  i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_23939858_2    686 CAGTAATAAAGAAAGTATG---CCTGTGCAAGAGTAGACA----AAGTAA 728
                                v    v   i  --- iv iii   ii      ----i vi  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_23939858_2    729 TAGAACAGAA--GAGACTATTCATGCTTAGACTTGTGTAGAAGTAGAATT 776
                          i   i    --    --i i  vivv  i  iii ii ---------  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGA--GTCCAGAAATAAACCCATACA---------TT 339

  chr2_23939858_2    777 TGATGGTTA--TGA----CCACAATGGCG--ATGACATTTCATATCAGTA 818
                          -     i --   ---- v    v  i -- v   ----   -   i i
  L1M4_orf2#LINE/    340 T-ATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC----CAT-TCAATG 383

  chr2_23939858_2    819 GATGGAAGAAATGGATTATTTACCAAATGGT-CTTGGAAAACTGGCAAGC 867
                          --    ii   i vi v  i v        -  v   v      vv ? 
  L1M4_orf2#LINE/    384 G--GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_23939858_2    868 TCCTCCAGTAGGGGAAAAAGCAAAACAAATAAAACTGGGATTTCCTACTT 917
                         iv -------------- v      -i   i  ii   i--ii     i 
  L1M4_orf2#LINE/    432 CAC--------------ATGCAAAA-GAATGAAGTTGGA--CCCCTACCT 464

  chr2_23939858_2    918 TTTTCTGTAGCCCAAAATAAACTCTACATGGGC----------AGTG--- 954
                         iviv ii  vv v     v     v v    ii---------- i  ---
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_23939858_2    955 ------GAACTATAAAAGTACTGGAAAAATTCACAAG-GTCAGTATATTT 997
                         ------i          v vi i   i  vv  i i -  v --  v  i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA--ATCTTC 562

  chr2_23939858_2    998 ATTATCTTATGTGTGAAAGTAATTTCTAAGCAATG-CACAAAAACTAGAA 1046
                         i v i   iv  vv iv i ii     v  vv   -   v    vi v  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_23939858_2   1047 --AACATAAAGATA---TGAAGGAATTTGATTATAT-AAAATTTTAAA-- 1088
                         --    -     v --- ii vi    v  i vi  -      vv   --
  L1M4_orf2#LINE/    613 GCAACA-AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_23939858_2   1089 -TTGCACATGGCAAAAAGCATTCTTTAGATTAAATTAATAGATA-----T 1132
                         -   ii v --    iii  i v iv   --  i v  v   i -----i
  L1M4_orf2#LINE/    662 TTTGTGCTT--CAAAGGACACTATCAAGA--AAGTGAAAAGACAACCCAC 707

  chr2_23939858_2   1133 AGTCTGGGAAAAAGTATATTTGTAG--CAGATATGTTGAGAACAAGTTT- 1179
                           vv     i   --       i i--  v    -i   v  viiii  -
  L1M4_orf2#LINE/    708 AGAATGGGAGAAA--ATATTTGCAAATCATATAT-CTGATAAGGGACTTG 754

  chr2_23939858_2   1180 --TCTA-AATATGGGCAAATAC-CTTAAAA-TCAGTAAGAAGAAAGAATA 1224
                         --  i -     iviv i -  -    v  -   i   v  -     vv 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGA-ACTCTTACAACTCAATAATAA-AAAGACAA 802

  chr2_23939858_2   1225 GCAATCTAATATAAAAATTGGCAAA--ATAGAAACATGCTATTTATG-GG 1271
                         ii  i i   v?      v      --  vvi  i - vi    v v-ii
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA-GACATTTCTCCAA 851

  chr2_23939858_2   1272 GGAAAATA-AAAAGTAACCAATAAAAATGTGAAAAGATTCTAAGCTTCAC 1320
                         i   i   - v  i ii       iv ii         v  v i v   ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_23939858_2   1321 TTAAGTG 1327
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.33 (148 / 111)
Gap_init rate = 0.06 (53 / 888), avg. gap size = 3.00 (159 / 53)  


1046 22.42 16.12 1.26  chr2_23985834_23990358     2263  2659 (1866)    L1M4_orf2#LINE/L1        1   456 (452)  

  chr2_23985834_2   2263 TGAACAGAATTACCATGTTCATAGACTGAAAGACG-AATA-----AGGAT 2306
                           i v   vv v          i  i  i     v-    ----- i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_23985834_2   2307 G-CAATTCTTCCCAAATAGATCGAAGGATTAATTGCAATCCCAAATAAA- 2354
                          -    v  i       v    v vi    v vi        v vi   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_23985834_2   2355 TCCCAACAGTCTTTTCTAAAGAAACTGACAAGAGGCTTTAGAAATGTAAA 2404
                              i v i     i iv     i       vv v iivi    vi v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_23985834_2   2405 TGGAAAGATAA------TAGA-TGACTACAACAATTCTGAAAAAGAA--- 2444
                               vii  ------i   - ii i v      ii          ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_23985834_2   2445 CAAATTTGGAGGACTTATACT----------AAAA-TGA----------A 2473
                             v          i i   ----------    - v ---------- 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_23985834_2   2474 CATTAATCAAGACAGTG--------GTATAAGGATAGACCTGTAGATCAA 2515
                           v              -------- i            v i        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_23985834_2   2516 TGGAATC-AACTAACAAATCTAGAAATAGAC--ACACATTTATATGGTCA 2562
                               v-  i i -i i  i       i  -- i        --     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACATTTAT--GGTCA 347

  chr2_23985834_2   2563 ATT----TTTGTCAAAGACGTGCCAAGAA-ATTTAAC----AAAG--TAA 2601
                            ----  i v   i --         v-   i  i----    --  i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG--GTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_23985834_2   2602 ACTCTTCAATATATGGTTCTGGAACAAATGAGTATCTGTAT--AAAAAAA 2649
                         v  i     i v     v    i    v  ii  ? iii  --    i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_23985834_2   2650 T-AGGCTGGGC 2659
                          - i i   i 
  L1M4_orf2#LINE/    446 TGAAGTTGGAC 456

Transitions / transversions = 1.59 (54 / 34)
Gap_init rate = 0.05 (22 / 456), avg. gap size = 3.14 (69 / 22)  

 297 22.99 0.00 2.30  chr2_23985834_23990358     2997  3083 (1442)    L1M4_orf2#LINE/L1      441   525 (383)  

  chr2_23985834_2   2997 AAAAATTAACTTAAACCCTCACCTCTTACTGATACACAAACATTAACGTA 3046
                           i   v  v  ii    ii     vi  i-   i     v      vi 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACC-ATATACAAAAATTAACTCA 489

  chr2_23985834_2   3047 AAATGAATCATTGACTTAAATATTAAGAGCTAACACT 3083
                              i    ?v   i     i -         v   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACT 525

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.00 (2 / 2)  

 220 28.84 7.44 4.19  chr2_23985834_23990358     3379  3593 (932)    L1M4_orf2#LINE/L1      513   734 (174)  

  chr2_23985834_2   3379 AAAAGCTAACGCTATTAATATTTTCAAAGAAAACATCCAAGAAAATTATT 3428
                           i      vi    v  vv i  vi          vvi? v    iv i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_23985834_2   3429 GCCACACTTAT-TTAGGCAACT-TTTCTCAAGCAGAACACAAAAGGCACA 3476
                          iv  -   iv-        iv-     i iii vi    v   i     
  L1M4_orf2#LINE/    563 GTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_23985834_2   3477 GATA-CATTTTTTAAA-------TCTATATGGTGG-CTTTATCAAAATTC 3517
                         iii -  ------   ------- vv   viv   -   i         v
  L1M4_orf2#LINE/    612 AGCAACA------AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_23985834_2   3518 AAA--TCCTGACTCTTCAAAAGTC-CTAACTAAGCAAACAAAGATACAAG 3564
                            -- ii  -iv       i v -   v -   v  iii  i v    v
  L1M4_orf2#LINE/    656 AAAACTTTTG-TGCTTCAAAGGACACTATC-AAGAAAGTGAAAAGACAAC 703

  chr2_23985834_2   3565 CCAGAACACTGGAAAAAA-ATTT-CAAAACA 3593
                            v iv iv   i    -    -    v  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCA 734

Transitions / transversions = 1.10 (32 / 29)
Gap_init rate = 0.06 (13 / 222), avg. gap size = 1.92 (25 / 13)  

 321 17.07 6.71 9.15  chr2_23985834_23990358     3870  4033 (492)    L1M4_orf2#LINE/L1      749   908 (0)  

  chr2_23985834_2   3870 GACTCTGTCTCAAAAAAAAAAAAAAAAC----ACAAGGACTACAACA-CA 3914
                             -   v  v i  v v v   i   ----    ---  -   i -i 
  L1M4_orf2#LINE/    749 GACT-TGTATCCAGAATATATAAAGAACTCTTACAA---CT-CAATAATA 793

  chr2_23985834_2   3915 ACAAGACACACAATCTAATTTCTAGTTTTAAAAAATGGCGCAAAAGATTT 3964
                          v      v i  i i    ?---------        -     i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTW---------AAAAATGG-GCAAAGGATTT 833

  chr2_23985834_2   3965 --ACAGACATTTCACAAATGAAAATATATAAACAGGCAATAAACACA--- 4009
                         -- i         v v  v   i     i   ii v      i    ---
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_23985834_2   4010 -AAGATGCTCAATATTATTGGATTA 4033
                         -           i  i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (16 / 11)
Gap_init rate = 0.06 (9 / 160), avg. gap size = 2.89 (26 / 9)  


3092 26.53 1.44 0.67  chr2_24231584_24235545     2570  3470 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_24231584_2   2570 TGGAAGAATATTTCATTCTCATGGATAGGAAGAATCAATATCATGAAAAT 2619
                              ii    ii   vi        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_24231584_2   2620 GGCCACACTGCCCAAAGT-ATTTATAGATTCAATGCCATCCCCATCAAGC 2668
                            v i   v      v -  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_24231584_2   2669 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGATCA 2716
                          v   iivi i  i  ii     -   -- v  i  - iii    iv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_24231584_2   2717 TATGGAACCAAAAAAGAACCCCCCATTACCAAGACAATCCTAAGCAAAAA 2766
                                viiv  ii  -   vvv  vi    i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_24231584_2   2767 GAACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAGG 2816
                                 i      vv   vi  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_24231584_2   2817 CTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGATACATAGAC 2866
                                  i   i    iii        i iv ii i   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_24231584_2   2867 CAATGGAACAGAA--AAGAGGCCTCAGAAATAACACCACACATCTACAAC 2914
                                 i    --i    v  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_24231584_2   2915 CATCTGATCTTTGACAAACCTGACAAATACAAGCAATGGGGAAAGGATTC 2964
                           vi    i  i     ivv  v   ivv  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_24231584_2   2965 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3014
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_24231584_2   3015 TGAGACTGGATCCCTTCCTTACACCTTATA-AAAAATTAATTCAAGATGG 3063
                            iii    i    v   i     v    -         i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_24231584_2   3064 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3113
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_24231584_2   3114 CCTAGGCA-ATACCATTCAGGACGTAGGCATGGGCAAGGACTTCATGACT 3162
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_24231584_2   3163 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAAGGGATCT 3212
                          vi            vvi          vv     v  i   vv   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_24231584_2   3213 AATTAAACGAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAGTGA 3262
                         v  i   vvv  i i   i  iiivv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_24231584_2   3263 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTGCCCATCTGAC 3312
                          v  i     i                 v       viiiivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_24231584_2   3313 AAAGGGCTAATATCCAGAATCTACAAATAACTCAAACAAATTTACAAGAA 3362
                           i  i  vi          v  i   v     vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_24231584_2   3363 AAA---AAAT--CCCA-TCAAAAAGTGGGTGAAGGATATGAACAGACACT 3406
                            ---    --    - i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_24231584_2   3407 TCTCAAAAGAAGACATCCATGCAGCCAACAGACACATGAAAAAATGCTCA 3456
                             v        i  v  viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_24231584_2   3457 TCATCACTGGTCAT 3470
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


2477 23.69 3.06 3.82  chr2_24239468_24244718     3975  4759 (492)    L1M4_orf2#LINE/L1      130   908 (0)  

  chr2_24239468_2   3975 AAGCT-ATTTTGAAATTCATATGGAACCAAAAAAGAGCTCGAATAGCTAA 4023
                              -  ii i              viiv  ii  v iv       i  
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_24239468_2   4024 GGCAACCCT----AAG-----CAAAGCTGAAGGCATCACCTTACCCAACT 4064
                         ii   i i ----   -----     i  i   vv    vi v     i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_24239468_2   4065 TCAAACTATATACTACAGGGCTACAGTAACCAAAACAGCATGGTACTGGT 4114
                              -- iv       ii          i   i    ii         i
  L1M4_orf2#LINE/    230 TCAAA--ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_24239468_2   4115 ACAAAAACAGACATATAGACCAATGGAACAGTAGAGAGAGCCCAGAAATA 4164
                          i  ii i           i        i  v vv     i         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_24239468_2   4165 ATGCCATACACCTATAACCATCTGATCTTCAACAAAGTTGACAAAAAAAA 4214
                          vv       ii   iii  vi    i   i    i v  v   ------
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA------ 371

  chr2_24239468_2   4215 AGAGTAATGGCAAAAAAAAAAAAAAAAAGCAATGGAAAGTACTCCTTATT 4264
                         -  vi v --   viiii   i  ---------------  v  i  -- 
  L1M4_orf2#LINE/    372 -GACCATT--CAATGGGGAAAGAA---------------TAGTCTTT--T 401

  chr2_24239468_2   4265 CAATAAATGGTGCTAGAATAAATGGCTAGCCACATGCAGAAGATTGAAAT 4314
                            i          i i i  v   v  ?         i    v    i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_24239468_2   4315 TTGACCCCTTCCTTACACCATATACAAAA-TCAACTCAAGATGGATTAAA 4363
                          v       v   i               - i       i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_24239468_2   4364 GACTTATGTGTAAAAACTCAAACTATAAAAACACTGGAAGATAACCTAGG 4413
                            i  vi     i i  v           vivi i     v   v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_24239468_2   4414 A-CATGCCATTCTGGACATAGGACTTGGTGAAGATTTCATAATGAAGACA 4462
                         ?-i vii -   vv   v v  ii v  ii v i    v  ivv v    
  L1M4_orf2#LINE/    552 NGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_24239468_2   4463 CCAAAAGCAATTGCAACGAAACAAAAATT-GACAAATGGCATGTAATTAA 4511
                                  vvv     i   v     v -  i    v v iv v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_24239468_2   4512 A-TTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTAAACAGA 4560
                          -     i -   i  ii vv    i  v        v i   i  v   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_24239468_2   4561 CAACCTAC----TGAGAGAAAATATTTGCAAACTATACATCTGACAAAGG 4606
                              i  ----  i                 ii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_24239468_2   4607 TCTAATATCCAGAATCTATAAGGAACTTAAACAAATT-----TACAAGCA 4651
                         v  vi          v     i     ivv    v i-----  v  iv 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_24239468_2   4652 AAAACAACCCCATCAAAAAGTGGGCAAAGAACATGAACAGACACTTTTCA 4701
                         v   i     v  i?    i         i iv    i     i  i  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_24239468_2   4702 AAAGAAGACATATATGCAGCCAAAAAGCATATGAAAA-ATGCTCAACATC 4750
                                 i   i viii     v     i       -            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_24239468_2   4751 ACTAACCAT 4759
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.56 (111 / 71)
Gap_init rate = 0.02 (17 / 779), avg. gap size = 3.18 (54 / 17)  


3235 26.56 1.33 0.44  chr2_24328196_24333660.rev     4074  4973 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_24328196_2   4074 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4123
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_24328196_2   4124 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4173
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_24328196_2   4174 TACCAATGACTTTCTTCACAGA--TTGGAAAAAACT-ACTTTAAAGTTCA 4220
                          v   iivi i  i  ii    --   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_24328196_2   4221 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 4270
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_24328196_2   4271 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4320
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_24328196_2   4321 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4370
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_24328196_2   4371 AATGGAACAGAA--AAGAGCCCTCAGAAATAATGCCGCATATCTACAACC 4418
                                i    --i    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_24328196_2   4419 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4468
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_24328196_2   4469 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4518
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_24328196_2   4519 GAAACTGGATCCCTTCCTTACACCTCATACAAAAATTAATTCAAGATGGA 4568
                            ii    i    v   i     vi             i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_24328196_2   4569 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAAC 4618
                          i ?    i  v    v   v       i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_24328196_2   4619 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTC---AAT-- 4663
                         v    ?i v viv   iv   v v  vv i     v ii   ---i  --
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_24328196_2   4664 --TACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4711
                         --i          vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_24328196_2   4712 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAGTACCATCAGAGTGAAC 4761
                          i   v v  i i   i  ii vv    i  v v  i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_24328196_2   4762 AGGCAACCTACAGAATGCGAGAAAATTTTTGCAACCTACTCATCTGACAA 4811
                           i     i        v        v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_24328196_2   4812 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4861
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_24328196_2   4862 AAACAAACAACCCCATCAAAAAGTGGGTGAACGACATGAACAGACACTTC 4911
                          i     i     v  i?    i    ii  v  iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_24328196_2   4912 TCAAAAGAAGACATTTATGCAGCCAAAAATCACATGAAAAAATGCTCATC 4961
                           v        i  vi viii     v  v          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_24328196_2   4962 ATCACTGGCCAT 4973
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


2885 23.51 1.61 3.96  chr2_24367974_24369774      502  1309 (492)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr2_24367974_2    502 AAAAAGTGATTCTAAAACTGATTCTAAAAGTTTATACGGAGAGGCAAAAG 551
                          i   v   i----  i     i      -  i   i   i v    ii 
  L1M4_orf2#LINE/    120 AGAAATTGAC----AAGCTGATCCTAAAA-TTCATATGGAAATGCAAGGG 164

  chr2_24367974_2    552 ACCCAGAATAGCCAACAAAAAAATTAAAGGAGAAGAATAAAACTGAAGAA 601
                                        -  v  vv  i  ii       i   ii  i  i 
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAA-AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_24367974_2    602 CTGACACTACCTGACCTCAAGACTTACTAGAAAGCTGCAGTAATCAAGCC 651
                           v     v  ii ii    i        v      i           v 
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_24367974_2    652 AGTGTGATACTGGCCAAAGAATACACAAATAGATCAATGAAACAGAAT-- 699
                               i       vv   i   v   v           i  i     --
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_24367974_2    700 AGAGCCCAGAAATAGACCCATATAAATAGAGTCAACTGACCTTTGACAAA 749
                             i         i       i vv  vi     i   ii  i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_24367974_2    750 GGAGCAAAGGCAATACAATGGGGCAAAGATACTCTTTTCAACAAATGATG 799
                           v  v   i v  v        v  ii   v               i  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_24367974_2    800 CTGGAACAACTGGCCATCCAAATGCGAAAAAAAAAAAAGAAATTGTCTTT 849
                             i        vi ?   v    ---------       ---------
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGC---------AAAAGAA--------- 445

  chr2_24367974_2    850 AAAATGAAATATAGACACAGGTCTC-TACTGTTCGCAAAAATCAACTCAA 898
                         ----    i - i   v vvii   -i  ii vii       i       
  L1M4_orf2#LINE/    446 ----TGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_24367974_2    899 AATGCATCACAAACCTAAATCTGAAACACAAAACTATAAAGCTCCCAGAA 948
                             v    ? i        v i i vvi           i   ii    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_24367974_2    949 AATAGTGTAAGCGAAAATCTAGATAACCTTGGGTTTAGTGATGACTCTTT 998
                         i v iii  i ? v      vvi i          vi ii   ii ii  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_24367974_2    999 AGATATGATACCAAAGACACAATCCATGAAAGAAAGAGTTGATAAGCTGG 1048
                                 i      ii     v v ii       i i v     ii   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_24367974_2   1049 ACTTCATTAAATGTAAACACTTTCATTCTGCAAAAGATGTGGTCAAGAGA 1098
                                i   vv    v     ii v  v    i  iiivi      i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_24367974_2   1099 ATGAGAAGACAAGGCACAGACTGAAAAAAAAT--TTGCAAAAGACGTATC 1146
                         i   i       vv      v  ii i     --       vv ii    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_24367974_2   1147 TGATAAAGAACTATTTTTCAAAATATGGAAAGGACTCTTTTAACAGTTCA 1196
                               i i   vv v i  i     iv    i      ---   ii   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT---ACAACTCA 787

  chr2_24367974_2   1197 ACAATAAGAAAACAAATAA--------AAAAATGGGCCAAAGACCTTAAC 1238
                          i     i  i        --------          v  i  ii v  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_24367974_2   1239 AGATGCCTCATGGAAAAAGATATGCAGATGGCAAATAAGCATATAAAAAG 1288
                            iiii  vivi  i       i  i     v        i  i     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_24367974_2   1289 ATGCTTTGCATCATACGTTGT 1309
                              ivi     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (126 / 61)
Gap_init rate = 0.01 (11 / 789), avg. gap size = 4.09 (45 / 11)  


1188 22.81 3.16 0.70  chr2_24421816_24425133.rev     1351  1635 (1683)    L1M4_orf2#LINE/L1        1   292 (616)  

  chr2_24421816_2   1351 TGGAAAGATACTCCATGTTCATGTATTGGAAGAATTAATATT-TTAAAAA 1399
                                   ii           v         v        -    i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr2_24421816_2   1400 TTATCTGTACTACCCAAAGCAATATACAGATTCAACACAAT----ATCAG 1445
                         - iv vi    v      vii  v            i    ----    i
  L1M4_orf2#LINE/     50 -TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_24421816_2   1446 AATTCAAATAGCATTTT-CACAGAAATAGAAAAAGCAATTTTAAAACGTA 1494
                            i v iiv  v    -ii       v  v  ivii  ii     ivi 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_24421816_2   1495 TATGGAATCACAGAAGACTTCAAATAGCCAAAGCAATCTTGAGAAAGAAA 1544
                                vii  iii   iivi          i         i      i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_24421816_2   1545 AACAAAGTTGGAAGCATCACACTGCCTGTTTGCAAA---TATTATGAAGC 1591
                                     i vv       v  iiv  v    ---  i  ii    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_24421816_2   1592 TATAGTAATCAGAACAGTGTGGTACTGGCATAAAAACAGACATA 1635
                           i        ii                    ii i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

Transitions / transversions = 2.10 (44 / 21)
Gap_init rate = 0.02 (5 / 292), avg. gap size = 2.20 (11 / 5)  

2455 22.80 5.24 0.00  chr2_24421816_24425133.rev     2235  2826 (492)    L1M4_orf2#LINE/L1      286   908 (0)  

  chr2_24421816_2   2235 AGACATACAGACTTATGAAATAGAATAGAGAGCCCAAAAATAAACCCAAG 2284
                                i   iiv   i        v     i   i           vi
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_24421816_2   2285 TGTATATGGTCAACTAATTTTTGACAAGGGTATCAAGAAGACACAATGGG 2334
                         ii v         i i     i         ii     vv iv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_24421816_2   2335 AAAAGG-TAGCCTCTTCGATAAATGGTATTGGGAAAACTGGATATCCACC 2383
                         i    i-   i  i   i i       ii     v         ?    v
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_24421816_2   2384 TGCAAAAGAATGAAATTGGA-----GCCTTATACCATACTCAAAAATCAG 2428
                                       i     -----i   i i      iv       i i
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_24421816_2   2429 CTCAAAATGGAT--------TAAACATAAGACATGAAACCGTAAAACTCC 2470
                                     --------    ii     vv i    ii        i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_24421816_2   2471 TAGAAGAAAACATTGACA-AAAGCTCTTTGACATTGGCCTTGGCAGTGAT 2519
                                      v i?i-   v  iiv    v    vi v    i  i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_24421816_2   2520 TTTTTGGATATTACACCAAAAGCTCAGGAAACAAAA------ATAAACAA 2563
                           i  i     v           v  i v       ------   i i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_24421816_2   2564 GTGGGACTTCATCAAACTAAAAAGTTTCTGCACAGTAAAGGAAACAATCA 2613
                         i v             v v    ii  i  ii vvi      v  v    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_24421816_2   2614 AGA---TGAAAAGGCAGTCTGTGGAATGGGAGAAAATACTTGTGAGCCAT 2660
                            ---       i  ii iiii               i   ii ii   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_24421816_2   2661 GTATCTGATAAGTGGTTTATATCCAAAATACA--AGGAATATATATAACT 2708
                         i           v ii  i      i    i -- i   iviv  i    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_24421816_2   2709 CAATACCAAAAA-----ACAACCCAATTTCAAAATGGGCAAAGGACCTGA 2753
                              vi     ----- i         ?v               ii   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_24421816_2   2754 GTGGACATTTCTCCAAAGAAGACCTAAAAATGGTAAAGAGATATTTAAAA 2803
                         i i                   iv  v      iv  v iii iv i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_24421816_2   2804 AGGGACTCAACATTATTAATCAT 2826
                           ivi        i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (93 / 39)
Gap_init rate = 0.01 (8 / 623), avg. gap size = 3.88 (31 / 8)  


3179 26.16 1.66 1.00  chr2_24666228_24671849.rev     4229  5130 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_24666228_2   4229 TGGGAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4278
                            i ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_24666228_2   4279 GGCCATACTGCCTAAGGTAATTTATGGATTCAATGCCATCCCCATCAAGC 4328
                            v     v  i  iv i  i  ii       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_24666228_2   4329 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTCA 4376
                          v   iivi i  i  ii     -   -- v  i  - iii i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_24666228_2   4377 TATGGAACCAAAAAAGAGCCCACAAT-GCCAAGACAATCCTAAGCCAAAA 4425
                                viiv  ii  -    v   -     i      i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_24666228_2   4426 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAA--CTATACTACAAG 4473
                                 i      vv   ii  v  ii i     --  -        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr2_24666228_2   4474 GCTACAGTAACCAAAACAGCATGGTAATGGTACCTAA--ACAGATATACA 4521
                                   i   i    ii     v   i --   -- i   i   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATA 294

  chr2_24666228_2   4522 GACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAA 4571
                           i        i    iv   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_24666228_2   4572 CCATCTGATCTTTGACAAACCTGATGAAAACAAGCAATGGGGAAAGGATT 4621
                         i  vi    i  i     ivv  vii i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_24666228_2   4622 CCCTATTTAATAAATGGTGCTGGGAAAGCTGGTTAGCCATATGTAGAAAG 4671
                         vi  v  i  i              v i    v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_24666228_2   4672 CTGAAACTGGATCCCTTCCTTATACCTTATACAAAAATTACTTCAAGATG 4721
                         v    ii    i    v   i i   v             vi    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_24666228_2   4722 GATTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 4771
                            i ?   ii       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_24666228_2   4772 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 4820
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_24666228_2   4821 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACAGGATC 4870
                           vi            vvi          vv     v  i   iv   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_24666228_2   4871 TAATTAAACTAAAGAGCTTCTGCATGACAAAAGAAACTACCATCAGAGTA 4920
                          v  i   v v  i i   i  iiivv    i  v    i  vv i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_24666228_2   4921 AACAGGCAACCTACAGAATGGAAGAAAATTTTTGCAA--TATACCCATCT 4968
                           v  i     i         i       v       --i   i--    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCT 741

  chr2_24666228_2   4969 GACAAAGGGCTAATATCCAGAATCTACAAAGAATTTAAACAAGTTTACAA 5018
                           i  i  i  vi          v  i      i ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_24666228_2   5019 GAAAAAAACAA----CTCCATCAAAAAATGGGCAAAGGATATGAACAGAC 5064
                         v     i    ---- i v  i?                 v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_24666228_2   5065 ACTTCTCAAAAGAAGACATTTATGTAGCCA-CAGACACATGAAAAAATGC 5113
                          i     v        i  vi vi i    -i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_24666228_2   5114 TCATCATCACTGGTCAT 5130
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (148 / 84)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.60 (24 / 15)  


3019 24.94 5.03 1.14  chr2_24822524_24824424.rev      536  1409 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_24822524_2    536 TAGAAAAACATCCCATGCTCATGAATAGGAGGAATAAATATCATTAAAAT 585
                          i    i i        i     i  v   i  v v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_24822524_2    586 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 635
                            v     v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_24822524_2    636 TACCAATGACATTTTTCACAGAACTGGAAGAAATTATTTCAAAATTCATA 685
                          v   iivi v     ii     v v  vi iv v  iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_24822524_2    686 TGGAACCAAAAAAGAGCCCAAATAGCCAAGGCGATCCTAAGCAAAAAGAA 735
                              viiv  ii  v  vi         ii i   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_24822524_2    736 CAAAGCTGGGGGCATCATGTTATCTAACTTCAAACTATATTACAGGGGTA 785
                              i   i  vv   iii vi i  i      viv  i    ii v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_24822524_2    786 CAGTAACAAAAACAGTATGGTAC------------------------CAA 811
                               iv  i     i      ------------------------   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_24822524_2    812 ---AATAGAATACCGAGCCTAGAAATAGGGCGGCACACCTACAGCCATCT 858
                         ---        vvv   i i       iiv vii   ii  ii i  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_24822524_2    859 GATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGACTCCCTAG 908
                            i  i     i v  v   i v  vv            i ivvi  vv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_24822524_2    909 TCAATAAATGGTGCTGTGATAACTGGATAGCCATATGCAGAAGATTAAAA 958
                             i           v  i         ?   i     i    v i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_24822524_2    959 CTGGACCTCTTTCTTACACCATATACAAAAATCAACTCAAGATGGATTAA 1008
                         i      i  vi  i                 i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_24822524_2   1009 AGACTTAAATGTAAAACCCAAAACTATAAAAAACT-TTGGAAGACAACTT 1057
                             i         i v i            --  -  i     v   v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA--CTCTTAGAAGAAAACAT 548

  chr2_24822524_2   1058 AGGC---AATACCACTCTG-GACATAGGAATGGGCAAAGATTTCAT-GAT 1102
                            ?---   ----  ii -   v v  iv i     v i    v -   
  L1M4_orf2#LINE/    549 AGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_24822524_2   1103 GAAGATGCCAAAAGTGATCAA--AACAAAAGCAAAAATTGACAAATGGGA 1150
                         - v  ii       ii--   --        v      v  i    v   
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_24822524_2   1151 CCT-----AAATATAAGATCATCTGCACAGCAAAAGAAACTGTCAAGAGA 1195
                          i -----    -   i v v i  ii vv    i  v   i      i 
  L1M4_orf2#LINE/    642 CTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_24822524_2   1196 GTAAACAGGCAACCTACAGAATCGGAGAAAATATTTGCAAACCATGCATC 1245
                           i  v  i     i       v                  i   ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_24822524_2   1246 TGACAAAAGTCTAATATCCAGTATTCATAAGGAACTTAAACAAATTTACA 1295
                            i  ii v  vi       v  vi    i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_24822524_2   1296 AGGAAAAAACAA----CCCCATTAAAAAGTGGGCAAAGGACATCAACAGA 1341
                          vi    i    ----   v   ?    i           iv v  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_24822524_2   1342 CACTTTTCAAAAGAAGACACACATATGGCCAACAAGCATGTGAAAAAAAG 1391
                           i  i  v        i i   v        i     ii      i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_24822524_2   1392 CTCAATATCACTGATTAT 1409
                              i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (134 / 80)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.86 (54 / 14)  


3201 26.68 0.55 0.44  chr2_24935098_24941491.rev     4996  5902 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_24935098_2   4996 TGGGAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5045
                            i ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_24935098_2   5046 GGCCATACTGCCCAAGCTAATTTATGGATTCAATGCCATCCCCATCAAGC 5095
                            v     v     ii i  i  ii       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_24935098_2   5096 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTCA 5143
                          v   iivi i  i  ii     -   -- v  i  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_24935098_2   5144 TATGGAACCAAAAAAGAGCCCCCATTGCCAAGACAATCCCATGCCAAAAG 5193
                                viiv  ii  v  vvv  v     i      iiivivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_24935098_2   5194 AACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGGC 5243
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_24935098_2   5244 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5293
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_24935098_2   5294 AATGGAACAGAACAGA-AGCCTCAGAAATAATGCCACATATCTACAACTA 5342
                                i    iv  -  i -         vv   i i  i  iiiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chr2_24935098_2   5343 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAGGATTC-CC 5391
                         vi    i  i     ivv  v   i v  vvv         i  v v-i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_24935098_2   5392 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5441
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_24935098_2   5442 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5491
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_24935098_2   5492 TAAAGACTTAAAAGTTAGACCTAAAACCATACAAATCCTAGAAGAAAACC 5541
                         i ?    i    v  v   v       i   v  v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_24935098_2   5542 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5590
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_24935098_2   5591 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGGATCTAA 5640
                         i            vvi          vv     v  i   iv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_24935098_2   5641 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5690
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_24935098_2   5691 AGGCAACCTACAGAATGGGAGAAAATTTTTCCAATCTACTCATCTGACAA 5740
                           i     i                 v   v   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_24935098_2   5741 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATGTACAAGAAAA 5790
                         i  i  vi          v  i  v      vv    v vv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_24935098_2   5791 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5840
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_24935098_2   5841 TCAAAAGAAGACATTTCTGCAGCCAAAAGACACATGAAAAAATGCTCATC 5890
                           v        i  vivviii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_24935098_2   5891 ATCACTGGCCAT 5902
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


2241 24.93 3.37 2.64  chr2_25583585_25586437.rev     1226  1907 (946)    L1M4_orf2#LINE/L1        1   687 (221)  

  chr2_25583585_2   1226 TGAAGAGGTATGCCATATTGATGGATTAAAAGATTTAATATTGTTAGGAT 1275
                           i i  i   v    i  v       ii    i            i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_25583585_2   1276 GGCAGAT-TTTCCTAAATTGATCTATAGATTTAATACCAATTC------A 1318
                             -  -i i  i           i     i  ii -   i ------ 
  L1M4_orf2#LINE/     51 GGCA-ATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAA 98

  chr2_25583585_2   1319 AATCTCAACAGGCTTTTTTATAGAAATTAGCAAACTGTTTTTAAAATGTA 1368
                             i  i v v       ii       ii   i   v ii      vi 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_25583585_2   1369 TTTGGAGAACCAAAGGACCTAGAATAACCATAACAGTCTTGAAAAAGAAA 1418
                          v    i vv   i     i      i   v    i             i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_25583585_2   1419 AACAAAGTTGGCAGACTTA-A--TCCTACTTGACATTAAGACTTACTATA 1465
                                    vi    i - --   i v  ---- i  i        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATT----TCAAAACTTACTACA 244

  chr2_25583585_2   1466 AAGCTATAGTAATCAAGAAAGTAAGATACTGGCAAAAGGATGAACAAATA 1515
                               i           v   iv i        v      ii   v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_25583585_2   1516 AATCAAAGGAACAGAATAGAGTATCCATAAAAGACACTCATG--TGTAAG 1563
                         i     v    i     v   vi    -i   v v  i   i-- v  v 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATG 343

  chr2_25583585_2   1564 GTCAAATGACTTTCAACAAAGGTAAGAAG-CAAATCAGTCAGAAAAGGAA 1612
                              v   i    i    i   ivv   - v v   i vi i    i v
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_25583585_2   1613 ACTCTTTCTATTTTTAACAAATGCTGTTGGAACAACTGGATATCTACACA 1662
                          v     ------ i        v  i   i           ? --    
  L1M4_orf2#LINE/    394 AGTCTTT------TCAACAAATGGTGCTGGGACAACTGGATAKC--CACA 435

  chr2_25583585_2   1663 GGGAAGAAAA-GAATCTCAACCCCTGCCTCATACCATACAAATAAATCAA 1711
                         v v  i i  -   vi vi      i     i      i v v    i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_25583585_2   1712 TTTGAAATGTATCATAAACTTAAACATAAAAGCTAAAACCATAAAGCTAC 1761
                         i ii     v    ? i  i    ii   i         i     i  vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_25583585_2   1762 TAAAAG----TATAGGAGAATAATTCTTCATTCTCTTAGGAAGAATAAAA 1807
                           i   ----i     ? --   v     i vvi   i  vviiii  vi
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNG--TAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_25583585_2   1808 ATTCATTAGAGTTTATA--GGGATCACAAACCATT---TTAAAAATTGAT 1852
                         i  iv     vv v i --iii v     i v iv---vv      v   
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_25583585_2   1853 AAATTAGACCCTATCAAATGTAAAATCTTTTGCTCATTAGAAGATACTAT 1902
                              i   iii      vv     v      iv v i i i  i     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_25583585_2   1903 TCAAG 1907
                         -    
  L1M4_orf2#LINE/    684 -CAAG 687

Transitions / transversions = 1.74 (106 / 61)
Gap_init rate = 0.03 (18 / 687), avg. gap size = 2.28 (41 / 18)  

 841 19.16 6.07 1.40  chr2_25583585_25586437.rev     2148  2361 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_25583585_2   2148 AAGAAAAAGAAAAACAGACAAACCACTATCTGAAAGAAAATATTTGCAAA 2197
                               iv     ---     v    vivv  ii                
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAA---GACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_25583585_2   2198 --ACATGTCTGACAAAGGAC--------AGAATATATAAAGAATTCCTGC 2237
                         -- i  i     i  i    --------               i  i i 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_25583585_2   2238 ACCTCAGCAATAAAAAGACAAGC--CTTTTTTAAAAAATGAGCAAAAGAC 2285
                          v    ii             ii-- iivv  ?       i     i  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_25583585_2   2286 TTGAACAGATATTCC-ACAAAGAAGATATGCCAGTGGCCAATAAGCACAT 2334
                              i   i   i -v            i v i                
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_25583585_2   2335 GAAAATGTGCTTGATATCATTAATCAT 2361
                              vi    ii i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.64 (29 / 11)
Gap_init rate = 0.02 (5 / 224), avg. gap size = 3.20 (16 / 5)  


 809 25.79 13.95 3.95  chr2_26240240_26242942      502   881 (1822)    L1M4_orf2#LINE/L1      112   529 (379)  

  chr2_26240240_2    502 TTTTATGTAAATATAGACAAGCTTATCCTAGTATTTATATGGGAAGGCTA 551
                             v  i i v  v        v      iv   i      i  v  v 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_26240240_2    552 GGG--------TAGCTAAAACAAT-TTGACAAAGTAAAATAA-GTGGGAA 591
                            --------    i        -    v    v i  i  -  v   i
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_26240240_2    592 GAATCAATCTATCTGGTTGTAAAGCTTTTTATTTAACCATAGTAATCTAG 641
                           v   vv  vi iii  vi   i   vi  ivv i i i       - i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC-AA 260

  chr2_26240240_2    642 GACAGTATGGTAATGG----AGGAGGCCTAGACACATAGGAGATTGCAAC 687
                               i     v   ----    ----      i    ivv v  v  i
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGA----TAGACATATAGATCAATGGAAT 306

  chr2_26240240_2    688 AGAATAAAGAACCCAGACACAGATTGA-ACTGTGGTATGGCCTGCAGATT 736
                              vi   ii     v i i iiv -  vv --     i viiv    
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAATTGATT 354

  chr2_26240240_2    737 TTTGACAAAGGTACAAAAGCAATTCAATGGAGCAAGGTTATTACTTCGAC 786
                           i     i   i v  ii v         i v   iv  v -   ----
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT-CTT---- 399

  chr2_26240240_2    787 ATTTCAAGCAAATGGTGCTTGAGCAATAGGA------CATTCATAGAAAT 830
                         --     -           v ii   iv   ------   v  v ii   
  L1M4_orf2#LINE/    400 --TTCAA-CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_26240240_2    831 G---------TCCTATTT-------------GAAATTAACTCAAAATGTA 858
                          ---------i    ii -------------i                v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_26240240_2    859 CCATCGGTTTAA----------TAAAACCATAA 881
                         i  ?v iii   ----------      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

Transitions / transversions = 1.37 (56 / 41)
Gap_init rate = 0.04 (15 / 418), avg. gap size = 4.53 (68 / 15)  

 206 25.00 0.00 0.00  chr2_26240240_26242942     1184  1227 (1476)    L1M4_orf2#LINE/L1      524   567 (341)  

  chr2_26240240_2   1184 CCATAAGGCTTTTAGAAGAAAATACAGGAGAAAATCTTTGGAAC 1227
                          i    ii  i           i i   ? v       i vi  
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

Transitions / transversions = 4.00 (8 / 2)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.00 (0 / 0)  

 716 25.42 2.97 3.39  chr2_26240240_26242942     1547  1782 (921)    L1M4_orf2#LINE/L1      572   806 (102)  

  chr2_26240240_2   1547 GACTAGGTGAAGAATTCTTAGACATAACACTAAACACATGATCTGTAAAA 1596
                          ii    ii v iv        i  i    i   vi  ii v vii    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_26240240_2   1597 GAAAAAAAAATCAGTAAATTAATTAGACTTTCACAAAATTAAAAGCTTCC 1646
                                -------  i  v    i     ivv           i   ii
  L1M4_orf2#LINE/    622 GAAAAAA-------TAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_26240240_2   1647 TCTCTACAAAATACCCTGTCAAGGGAATGAAAAGACTAGCTACAGACTTG 1696
                         viv  v    iv  v  i     ii i         v v i     v v 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_26240240_2   1697 GAGAAAATATTTACAAGCCAGTGTATCTGACAAAGGACTTCTGT------ 1740
                                     i   ii  - i       i  i      v i ------
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCA-TATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_26240240_2   1741 -ATAAAAAGAACTTTCAAAAGTCAGCAGTAAAAAGACAAAAAA 1782
                         -   v        i i v  v   ii i            v  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

Transitions / transversions = 1.73 (38 / 22)
Gap_init rate = 0.01 (3 / 235), avg. gap size = 5.00 (15 / 3)  

 403 23.39 0.81 0.00  chr2_26240240_26242942     2089  2212 (491)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr2_26240240_2   2089 CCCAAAAACAAAAA-ACTAACAATCCAATTAGAAAATGGGCAAAAAAAAA 2137
                          i   v  i     -  v  i  i      ?i            ii vvv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_26240240_2   2138 AACCAGACATTTCACCAAAGAGGACATGTGGATGGCAAATAAACACATGA 2187
                         i vi         v       i  i  iiii     v     i       
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_26240240_2   2188 AAAAATGTTCACCATCTTAGCCACA 2212
                            i   i   v    v????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.01 (1 / 125), avg. gap size = 1.00 (1 / 1)  


 245 25.76 1.52 0.00  chr2_26259373_26261700.rev      496   561 (1767)    L1M4_orf2#LINE/L1       89   155 (753)  

  chr2_26259373_2    496 TCCCC-TTAAGATCCCAATGACAATTTTTGCAGAAATAGAAAGATCTATC 544
                             i- i  i      iivi vv             v  v iiiiv   
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chr2_26259373_2    545 CAAAAATTCATATGGAA 561
                          v               
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAA 155

Transitions / transversions = 1.43 (10 / 7)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1)  

2645 18.45 6.50 0.35  chr2_26259373_26261700.rev      897  1465 (863)    L1M4_orf2#LINE/L1      204   807 (101)  

  chr2_26259373_2    897 AGCTGGGGGAGTCA--------AATTTCAGAACTTACTGCAAA------- 931
                           i   i   v   --------       i        i    -------
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_26259373_2    932 ---TCAAAA-AGTGTGGAACTGGCATAAAGACAGATACACAGACTAATGG 977
                         ---    i -       v          i  i   i i i   ii     
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_26259373_2    978 AATGGAATAGAGAGCCCAGAAATAAATCCTCACATACTTAGTCAAATGAC 1027
                            i    v     i           i  vi    viv i     v   i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_26259373_2   1028 CCTCGACAAGGATGCCAAAATCAGTCAATAGGGAAAGGACAGTCTTTTCA 1077
                         ii         i      i i  v     i       i i          
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_26259373_2   1078 ATAAATAGCACTAGGAAAACCAGATATCCACATGCAAAACAATGAAGCTG 1127
                          i    i ii  i   v   ii    ?            v       i  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_26259373_2   1128 GATCCTTATTTTAAACCATATAAAAAAATTAACTTGAACTAGATCAAAGA 1177
                           i  i  ii i v        v           ii  v i     ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_26259373_2   1178 CCT-----------C--AAACTATAAAACTCTTAGAAGAAAACATAGGGA 1214
                            ----------- --                               ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_26259373_2   1215 -AAAGCTTCAGGACACTGGATTTGGCAATGGTTTCTTTGACATGATACCA 1263
                         -   v    iv   vi   i  v              v  i    i    
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_26259373_2   1264 AAAGCACAGGCAATAAAAGAAAAAGTAGTTAAACTGTACTTCATCAAAGT 1313
                                 i    i          i   v    i  v           i 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_26259373_2   1314 TAAAAACTACTGTGCAACAAAGGACGCTATCAAGAGAATGAAAAGACTAC 1363
                                 vi     vv        i         i i         v  
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_26259373_2   1364 CCACAAAA-AGGAGGAAATATTTGTAAATCATGTATTTGA-AAGGGAATA 1411
                              i  -i    i         i       i   i   -      v v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_26259373_2   1412 ATACCTAGAATATATAAAAAACACCTAAAACTCCTAACAACAACAAAA-- 1459
                         i  i i            i   v i  v     --  i  i  v  i --
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTC--AATAATAAAAAGACA 801

  chr2_26259373_2   1460 AATGAC 1465
                            i  
  L1M4_orf2#LINE/    802 AATAAC 807

Transitions / transversions = 2.52 (73 / 29)
Gap_init rate = 0.02 (10 / 604), avg. gap size = 3.90 (39 / 10)  

 472 13.51 5.41 0.00  chr2_26259373_26261700.rev     1726  1836 (492)    L1M4_orf2#LINE/L1      792   908 (0)  

  chr2_26259373_2   1726 TAAAAAAAAAAAAAA---AA---AAAAGCAAGCAAAGGATTTGAATAGAC 1769
                               i v   v  ---  ---    iiii                   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_26259373_2   1770 ATTTCTTCAAAGAAGATATACAAACAAACAATATGCACATGAATAGATGC 1819
                               i                 iiiv     v         v      
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_26259373_2   1820 TCAATATCACTAAGATT 1836
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.02 (2 / 117), avg. gap size = 3.00 (6 / 2)  


4334 17.25 3.49 1.13  chr2_26285982_26289951     2592  3478 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_26285982_2   2592 TGGAAAGACATCCCATATTCATGGGTTAGAAGACTTAATATTGTTAAACT 2641
                                 i       i       i  i                   iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_26285982_2   2642 GTCCATACTACTCAAAGTACTCTACAAATTCAATGCAACCCCTCTCAAAA 2691
                          v v     v i    v iv      i      i    i    v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_26285982_2   2692 ATCCCCATGGCATTTTTTTGATAAATAGAAAAAAAAAT--TAAAATTCAT 2739
                         -    viiv  v      vv v    v  v  ivvi  --          
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_26285982_2   2740 G-AGTAATATCAAAGGACCCAGAACAGCCAAAAGAATT------------ 2776
                         i-i v   i-   i          i        v   i------------
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_26285982_2   2777 -ACAAAGTTGGAGGATTTACACCTACTTCCTGATTTTAAAACTTACTACA 2825
                         -              i i    ----    ii    i             
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACAC----TTCCCAATTTCAAAACTTACTACA 244

  chr2_26285982_2   2826 AAGCTACAGTAATCAAAATAGTATGGTATTGGCATAAAGACAGACATATA 2875
                                         i i   i     i        i  i         
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_26285982_2   2876 GACCAATGGAACAGAATAGAGAGCCCAGAAATAAAGCCTCATGTTATATG 2925
                           i        i     v     i           v  vi ii  -    
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATG 343

  chr2_26285982_2   2926 GTCAAAGAATCTTTGACAAGGGTGCCAAAGCTACACAATGAGGAAAGATT 2975
                              vvi  i  i              ii i iv     i       v 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_26285982_2   2976 AGCCTCTTCAATAAATGGTGCTGGGAAAATTGGATATCCACATGCAAAAG 3025
                           i  i     i              v  i      ?             
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_26285982_2   3026 AATGA---TGAATCCTTATCGTATACTATATACAAAAATTAATCCAGAAT 3072
                              ---  i i  i  i vi i  i               ii  i   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_26285982_2   3073 -----AAAGGCCTAAATATA-GACCTAAAATTATAAAACTCCTAGAAGAA 3116
                         ----- ?  i       i  -  v      i          i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_26285982_2   3117 AACATAGGGGAAAAATCTTCGTGACATTGGACTTGGCAATGCTTTCTTGG 3166
                                 ? v   -          v    ii v       v      i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_26285982_2   3167 ATATGACACCAAAAGCACAGATAACAAAAGCAAAA-TAGGACAAATTGAA 3215
                                            iii        v    -   - i      i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG-ATAAATTGGA 641

  chr2_26285982_2   3216 CTACATCAAACTTAAAAACTTTCA-----CACAGCAAACAATCAAAAGAG 3260
                           v       v           ii-----  v  v v  v     i i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_26285982_2   3261 TGAAAAAGCAACCTACAGAATGGGAGGAAAATATTTGTAAACCATATATC 3310
                               ii     i            -          i   i        
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAG-AAAATATTTGCAAATCATATATC 740

  chr2_26285982_2   3311 AGATAAGGGAATAATATCCAGAATATATAAAGAGCTCCTGTAACTCAATA 3360
                         v         v vi                   i   i ii         
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_26285982_2   3361 GTACAAAACTAAATAATCTTATTTTAAATTGGGCAACAGACTTGAATAGA 3410
                         i  v   ivi      i iv   ?v   v       vi  i         
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_26285982_2   3411 CATTTCTCCACAGAAAACATACAGATGGTCAACAAACACAAGAAAAGATG 3460
                                   v    i i     i    i   i  i    v         
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_26285982_2   3461 CTCAACATCACTAATCAT 3478
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (98 / 51)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.73 (41 / 15)  


1047 22.45 1.22 2.45  chr2_26559691_26562116.rev      687   931 (1495)    L1M4_orf2#LINE/L1        3   244 (664)  

  chr2_26559691_2    687 GGAAGATATCCTGTGCTTATGAACTGGATGACTCAATATTGTTAAAAATG 736
                          i         ii  i i   i i    v    i           i -  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-TG 51

  chr2_26559691_2    737 TCCATACTATACAAAGTGATCTATAGATTCAGTGCAGTCCTTAACAAAAT 786
                         v v     viv    v       i       ii   i   i  v      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_26559691_2    787 CCCAACATCATTTTTTGTGGAAATAGGAAAACC-ATCCTAAAATTTGTAA 835
                             i vv v       ii     v iv  i i-           ii  -
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA- 150

  chr2_26559691_2    836 AATTCAGAATCTCAAGAGACTCCAAATTGCCAAAATAGTCTTGAGAAA-- 883
                         ----ii   viv    i   i vi   v       i i      i   --
  L1M4_orf2#LINE/    151 ----TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_26559691_2    884 AGAACAAAGTTGGAGGCCCCACATTTCCTGGTTTCAAAACATACTACA 931
                                         v i    i    iii         v       
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

Transitions / transversions = 2.06 (37 / 18)
Gap_init rate = 0.02 (4 / 242), avg. gap size = 2.25 (9 / 4)  

2528 17.44 5.04 8.50  chr2_26559691_26562116.rev     1242  1935 (491)    L1M4_orf2#LINE/L1      239   908 (0)  

  chr2_26559691_2   1242 ACTGCAAAGAGCAACAGGAATTAA-AGAATGTTGTACTGACATAAAAATA 1290
                            i     -- v    v   i  - v i   v      i     ii   
  L1M4_orf2#LINE/    239 ACTACAAAG--CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_26559691_2   1291 GATATATAGACCAAGGGAAC----TAGAGAGCCCAGAAATAAACCCCTAC 1336
                           i       i   v    i---- v     i              v   
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_26559691_2   1337 ATATATGACCAAATGGCTTT-GACAAGGGTCAAAATGATAAATGAATGAT 1385
                           v    ii   v  ii   -         --------------------
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGT-------------------- 366

  chr2_26559691_2   1386 ACATAAACCCCTGCATCTATGGTCAAATGACTTTTGACAAGACTATACAG 1435
                         ------------  -----------------------      i  v  i
  L1M4_orf2#LINE/    367 ------------GC-----------------------CAAGACCATTCAA 381

  chr2_26559691_2   1436 TGGAGAAAGGATAGTCTCTTCAACAAATGATGTTGAGAAAACTGGATATT 1485
                            i     i       i           i  i  i  v         ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_26559691_2   1486 CACAGGCAAAAGAATGAAGTTGGGTCCTTACCTTATACCATATACAAAAA 1535
                             v                  ii  i     i i              
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_26559691_2   1536 T-AACTCAAAATCGATTAAAGACCTAAA-------------ACTATTAAA 1571
                          -          v   i ?         -------------     v   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_26559691_2   1572 CTCCTAGAAGAAAATATAGAGGACAAGCTTTCTGCACATTGGATTTGGCC 1621
                            i          i    i? vv  v   iv  -  v    i  v   v
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCA 580

  chr2_26559691_2   1622 ATAATTTCTTGGATATCACACCAAAATCCCAGGCAGCAAAATCAAAAATA 1671
                           ii      i     v         v v  i   i     vv       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_26559691_2   1672 GACAAACGGGGCTGCACCAAACTCAAAAATGTTTGCACATCAAAAAAAAA 1721
                           i   iv  i  v  i    v i     iv    ii v     ii v v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_26559691_2   1722 -ATCAAGAC--TAAGAAGGCAATATACGGAATAGGAAATCATAATTGAAA 1768
                         -       v-- i i   i   ivi  i    i   i vv   v   v  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_26559691_2   1769 ATCATATATCTGATAAGGGGTTAATGTCCAAAATACATAAAGAACTTCTA 1818
                                            ii vi i    i    i          ii  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_26559691_2   1819 TAACTCAA------------AAACAACCCAATTTAAAAATAAGCAAAGGA 1856
                         i       ------------   i         ?      ii        
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_26559691_2   1857 TTTAAATAGACATTTCTCCAAAGATGATATACAAGTGACCAATAAACACA 1906
                            i                    v         i  i       i    
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_26559691_2   1907 TGAAAAACATGCACAACATCTCTAATCGT 1935
                               i-    v       v????????
  L1M4_orf2#LINE/    881 TGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (74 / 43)
Gap_init rate = 0.02 (13 / 670), avg. gap size = 7.23 (94 / 13)  


 888 23.61 1.85 0.00  chr2_26679277_26683283.rev     2026  2241 (1766)    L1M4_orf2#LINE/L1        1   220 (688)  

  chr2_26679277_2   2026 TAGAAA-ATAGATTATGTTTATGGACT-GAAGATTCATAATTGTTAAGAT 2073
                          i    -   vvii     i     i -     i i vv           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_26679277_2   2074 GACAATTCTCCACAAAATGATCTATAGACTGAATGCAATCCTAATAAAAA 2123
                          i    v    v    v       i   i v  i       iv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_26679277_2   2124 TCACAACAAACTATTTTGTAGAAATTGA-AAACT-ACTTTAAAATTTATG 2171
                           v  i viv  v     i         -  i  - iii       i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_26679277_2   2172 TGGACATGCAAATGATCTAGAATAGCTAAAGCAGCCTTGAAAATGGAGAA 2221
                             v      iv  i i        i   i  ii        v i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_26679277_2   2222 GAGAATTGGAGGGTTCACAC 2241
                         v i i       ii      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACAC 220

Transitions / transversions = 1.83 (33 / 18)
Gap_init rate = 0.02 (4 / 220), avg. gap size = 1.00 (4 / 4)  

1638 20.44 9.12 8.68  chr2_26679277_26683283.rev     2837  3516 (491)    L1M4_orf2#LINE/L1      226   908 (0)  

  chr2_26679277_2   2837 AATTATAAGTCTAACTATAAAGTTAAAGGAATTAAGAAAGTGTGGCATTG 2886
                             vi  iv  v    i    i  v  v   i    v       i i  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_26679277_2   2887 GTCTAAGAATAGACATATAGACCAATGGAGCAGAAT--AGTGTCCAGAAA 2934
                          iv    i             i       ii     --  v         
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_26679277_2   2935 TAAACTCTGTACATATAAAATCAATTGATTTTCAATCAAGGTGT------ 2978
                              i -i     v  vii             i iv i    i------
  L1M4_orf2#LINE/    326 TAAACCC-ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_26679277_2   2979 -------TGG-------ATA-TCT--------------------AGAACT 2993
                         -------   -------   -   -------------------- v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_26679277_2   2994 AGGTATCTATATGGAGAAAAAATGAACTTCAAACTCCTACCTCATACCAT 3043
                         i i  ? i i   v -   i      v  -ii  i         i     
  L1M4_orf2#LINE/    425 GGATAKCCACATGCA-AAAGAATGAAGTT-GGACCCCTACCTCACACCAT 472

  chr2_26679277_2   3044 CCACAAAAATTAATGTAAGATGGATTATAGAATTAAACATTAAAAACT-- 3091
                         vi           ivi  i      i ?   vi    ii -  i i  --
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAA 521

  chr2_26679277_2   3092 ---TATAAG-CTTCTAGAAGAAAATATAGA---ACATCTTTTTTTGTATT 3134
                         ---     i-  ii          i    i--- v     i----  ivi
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC----GTGAC 567

  chr2_26679277_2   3135 CTTGGGTTAGGCAAAGGTTTCTTAAAGAAAAATTTTAAAAGACTAAA--C 3182
                                       v         i ---------  vi v  i   -- 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGA---------TATGACACCAAAAGC 608

  chr2_26679277_2   3183 ATAAGAAATAAATTTCACTAAAAACTTGCATTTCTTAAAAATTGGAAACT 3232
                          i   v  i   ---- vv     -- iv  -------        ----
  L1M4_orf2#LINE/    609 ACAAGCAACAAA----AGAAAAAA--TAGAT-------AAATTGGA---- 641

  chr2_26679277_2   3233 CTCTTTGGCTAGTCACAGAGTAAAAAAAATTGAAAACTCCTATTCATAAA 3282
                         --   ii-----   -----------     i      ii i v v v  
  L1M4_orf2#LINE/    642 --CTTCA-----TCA-----------AAATTAAAAACTTTTGTGCTTCAA 673

  chr2_26679277_2   3283 AAAATCACATTTAAGAAGGCAAGAGAAGGCAAGTCACACACAGGAAGAAA 3332
                          ii -   vv i     i i--  i   i   vi    v vv  i     
  L1M4_orf2#LINE/    674 AGGA-CACTATCAAGAAAGT--GAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_26679277_2   3333 ATATT--CA---CATTTATCTGACAAAGGACTTGTAGCCAGAATATATAA 3377
                              --  ---   v       i  i         v             
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_26679277_2   3378 AGAATCCCTATAAGTCAATAATAATAAGACAAATTATGAAATTTTTTATG 3427
                             ii i  i  v          v         v ivv    ?vvv -i
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA-A 819

  chr2_26679277_2   3428 TAGGCAAAAGACTTGAAGAGACA---CTCCATAGAATAAGATAGACGTAT 3474
                          i      i  i     v     ---     v    ---    v  iv  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA---GATATACAAAT 866

  chr2_26679277_2   3475 GGCCAATAAACATGTGAAAATGTGATCAACATCCTGAGTCAT 3516
                                  i  ii      vi  v        v????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (84 / 52)
Gap_init rate = 0.04 (28 / 683), avg. gap size = 4.32 (121 / 28)  


2987 25.40 5.49 0.12  chr2_26798066_26799876.rev      501  1319 (492)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr2_26798066_2    501 AAAATGTCAGTTCTTCCCAACTTAACCTATAAATCCAACACAATCCCAAT 550
                           i   v  i v  i     v  i i   i i  i    i       v  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_26798066_2    551 AGAAATCCCAGCAAGTTATTTTGTGGATTTCAACAAATTGATTTAAAAAT 600
                         vi          vivi v     ii  vv ii    ii    iiv     
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_26798066_2    601 TTATATAGAGAGGCAAAG-ACCCAGAATAGCCAACACAATACTGAAG--G 647
                          i    i  i v    i -               v     vi    i-- 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_26798066_2    648 AAGA-CAATGTCAGAGGACCGACACTACCTGACTTTAAGA--TACTGTAA 694
                             -   v  ii      iv     v  ii i  i  i --    ii  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_26798066_2    695 ATCTATGGTAATCAAAATAGTATGGTACTGGTGAAAGAATAGATGCATAG 744
                          v   ii        i i   i         iiv   i     iii    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_26798066_2    745 ATCAATAGAATAGAATAGAAAGCCTAGAAATAGACTAACACAAATATAGC 794
                               i         v  i  i i       i  iv i   vv   i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_26798066_2    795 CAATTCATCTTTGACAAAGGAGAAAAGGTAATTTAATGGAGAAAAGGTAG 844
                              v  i  i     i  v vv   iiv   i     i    iii   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_26798066_2    845 TCTTTACAACAAATAGTGCTGGAACGATTGGGCA--CAGATGCAAAATCA 892
                              v        i       i  i i   ii --  v        v- 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-A 444

  chr2_26798066_2    893 ATGACTCTAGATACAGACCTTATACCCTTCACAAAAATTACTATAAAATG 942
                             vvi i  iv vv    i i   v vi          vivi      
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_26798066_2    943 GATCATAGACCTAA--GCAAAATTCAAAACCACAAGGTTTTTAGAAGATA 990
                              ?        -- i  i vii     i i  iii i        v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_26798066_2    991 ACATGGGAGAAAATCTAGGTGACCTTGGGTTTGGTGAGGATGTTTTAGAT 1040
                             i  ? v      vv             v  ii v i v i      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_26798066_2   1041 ATAACACAAAAAACATGATTCATGAAAGAAAAAATTGCTAAGCTGTACTT 1090
                           i    v    i  ii viv ii           v v   ii  v    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_26798066_2   1091 CATTAAAATTAAAAATTTCTGCTCTGTGAAGAACACTGTTAAGAGAATGA 1140
                            i           i  i  iv  vii   i     i i    i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_26798066_2   1141 AA-GACAAGCCACAGAGTGGGAGAAAATGTTTGCAAAACACATATCTGAT 1189
                           -     v       i           i        v  i         
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_26798066_2   1190 AAAATACTTTAATCCAAAATACAAAAAGGACT---------------TAA 1224
                           iiv    vv     i    i v    i   ---------------   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_26798066_2   1225 AA----------CCCAATTTTAAAA---GC------TCTGAATAAGCACC 1255
                           ----------       ?v    ---  ------ i      ii  ii
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_26798066_2   1256 TAAATAAAGAAGACACACAGGTGGTAAATAAGCATATGAAAATATGTCCA 1305
                          vvvi        i i   ii   iv        i       v   ii  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_26798066_2   1306 ACATCATATACCAC 1319
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (137 / 68)
Gap_init rate = 0.01 (12 / 863), avg. gap size = 3.83 (46 / 12)  


 230 17.95 0.00 0.00  chr2_26966527_26971109     2911  2949 (1634)    L1M4_orf2#LINE/L1        7    45 (863)  

  chr2_26966527_2   2911 GATATTCTACGTTTATGGATAGGAAGACTCAATACTGTT 2949
                              i i i   i      v        i    i    
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT 45

Transitions / transversions = 6.00 (6 / 1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.00 (0 / 0)  

3040 21.93 4.72 1.53  chr2_26966527_26971109     3244  4091 (492)    L1M4_orf2#LINE/L1       34   908 (0)  

  chr2_26966527_2   3244 CTCAATACTGTTAAGATGTCAACTCTTCCCAATTTTATCTATGGATTCAA 3293
                           i    i          v   iv  i     v  v     ii       
  L1M4_orf2#LINE/     34 CTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAA 83

  chr2_26966527_2   3294 CACAATCCCTATTACATTACCAGCAAGTTATTCTGTGGATATCAGCAAAC 3343
                          i          i v v v     vivi v  i  ii  v  iii   i 
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC 133

  chr2_26966527_2   3344 TGATTCTAAAATTTATGTGGAAAGGCAAAAAACCCAGAATAGCCAACAAA 3393
                             i        i  i      v    iii               v v 
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr2_26966527_2   3394 ATACTGAA---GACTATCCAAG--GGTAGAC----ACCACCCAACTTCAA 3434
                           vi    ---  vv v v   --  vi   ----  iv     i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_26966527_2   3435 GACTTACTATAAAGCTACTTTAATCAAGACAGTATGCTATTGATGAAAGA 3484
                         i        i        vv             i  v  i  iiiv   i
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_26966527_2   3485 ATAGACAAATTGATCAATGGAACATAATAGAAAGCCCAGAAAAAGACAAC 3534
                                v  v           i v   v  i  i       v i  v- 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC-C 332

  chr2_26966527_2   3535 AGATCTTTAACAAGGCAACTGATCTTTAACAAGGA-GCGAAGGCAATTAA 3583
                          v iv    v--i v   i    i  ii      i-  v   i v   v 
  L1M4_orf2#LINE/    333 ATACATTTAT--GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_26966527_2   3584 GTAAGAGAATGGATAGT-TTTTCAAAGAA----GCT------ACTGGACA 3622
                         i ii -   v i     -       vi  ----   ------      i 
  L1M4_orf2#LINE/    381 ATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_26966527_2   3623 TACATAATGTAAAAACAATGAATTGAGACACTGACCTTACACCTTTCACA 3672
                         ?v  i -  i    i-      v vi   v iv    i     v vi   
  L1M4_orf2#LINE/    430 KCCACA-TGCAAAAG-AATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_26966527_2   3673 AAAATCAACTCAAAATGGATCATAGACATAAATGTAAAATGC-AAAACTA 3721
                              i                ?    v         i -  -       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTA 526

  chr2_26966527_2   3722 TAAAACT---AGAAGGTTACATAGAAGAAAATCTAGGTGACTTTGGGTT- 3767
                                ---     ivv      i? v      vv     i       -
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_26966527_2   3768 GACAATGAGTTTTTAGATACAACAGTAAATGCATGAACCATGAAAGGAAC 3817
                          i     iv  i       ii   vi   v   ii i v ii    i  v
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_26966527_2   3818 ATT-GATAAGCTGGACATTATTAAAATTAAAATCTTCTCCTTGGTCTGT- 3865
                          v -     ii     v i  i          v   ----   vv  vi-
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTT----TTGTGCTTCA 672

  chr2_26966527_2   3866 ---GACACT--TAAGAGAATGAAAAGACAAGCCACAAACTAGAAAAAAAA 3910
                         ---      --i    i i           v     i v i i i    -
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA- 721

  chr2_26966527_2   3911 TATTTTCAAA--ATATATCTGATAAAGGACTTATATTTAAA---TCTAAA 3955
                              v    --             i      i   ii i --- v    
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_26966527_2   3956 AAACTCCTAAAACTCAACAA-AGAAAG-CAAACGACCCTAATTTAAAAAT 4003
                         i     i  v       i  - i    -    ii    -    ?      
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCC-AATTWAAAAAT 820

  chr2_26966527_2   4004 GGGCAAAAGATCTGAACAGACACCTCACCAAACAAGATATACAGATGATG 4053
                                i   i    i     ii  v     v          i   iiv
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_26966527_2   4054 AATAATCATATGAAAAGATGCTCAACATCATATATCAT 4091
                              v  i                     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (109 / 73)
Gap_init rate = 0.03 (26 / 875), avg. gap size = 2.04 (53 / 26)  


 681 28.38 16.22 4.67  chr2_27002125_27003947.rev      519  1332 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_27002125_2    519 TGAAACAAATAT---ATGCTTA--GACAGGAAGACATAATATCGT-AAAA 562
                           i  - i    ---   i i --  iv       v      i  -  i 
  L1M4_orf2#LINE/      1 TGGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_27002125_2    563 TGTCAATTTTCTCCAAATTAGTATATAGA---AGTG-AATACCCA----- 603
                           v    vi  i       ii v  i   --- ii -   v  i -----
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_27002125_2    604 AT----G-TGTTTCTTTTG---AAATAGATAA--------TAA------- 630
                           ---- -  ii i     ---    v  i  --------   -------
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_27002125_2    631 -TGGAATTGAGAGGAGTTGAGAA----------AATTATAAAAAGGAATA 669
                         -     v  vi   iiiiv    ----------   iv i    i   v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_27002125_2    670 GTGTGGGGAAGATGAAGGGCTT-C-CTTAGTAGATATTACAATATGCTCT 717
                         iii-----   v  i   i  i- -   vvi ---   v   v iviv  
  L1M4_orf2#LINE/    200 ACA-----AAGTTGGAGGACTCACACTTCCCA---ATTTCAAAACTTACT 241

  chr2_27002125_2    718 ATGAAATCACCGTAGTTAAAACTGTATGGTATCAACAGATAAGGAGAG-C 766
                          ii  iii  v   i i  i  v  i     iiii  --      v  - 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGAC 289

  chr2_27002125_2    767 A------------GAATAGAGTGCTTGGTAG--CAGA------------- 789
                          ------------       i ---  iv  --    -------------
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAAT---TGAGAGTCCAGAAATAAACCCATAC 336

  chr2_27002125_2    790 -TTT-----CAATTAAATC-CAACAGAAGTGATATTTCAATTCAGTGGGG 832
                         -   -----     i v i- i   iii   vi vvv v     i     
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_27002125_2    833 AAA--ATGACTTATGCAATGAATGATGTGGGCACAACTGGTTATTCATCT 880
                            --  iiii v v   ii    i  iv  v        v  ?i  iv 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_27002125_2    881 GGAAGAAAATTAAATTGGCTCCCTACCTTACAGCATATATCAAAATCTGT 930
                          v  i i   v  i    vi        i   v      iv     --- 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT---T 483

  chr2_27002125_2    931 AA-TCCATCTGGA--ATTTATTTAAATGTAAAACATAAAACAATAAAAAG 977
                           -  v vv    -- ?vv ii         i vv      v      vv
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_27002125_2    978 ACTAGAAGACAACCTGGGAG-A---CTGCGTACCACCAAGGAGTAGGGGA 1023
                         vi       v   v i  ? - ---  v   i--   vv  iv    vi 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTG--ACCTTGGGTTAGGCAA 581

  chr2_27002125_2   1024 TCGCTTTTAACTCAG-TCTGCAAACTCAGAGGCCACACACACACACAAAG 1072
                          v i  ----  i  - v  - v  iv i  --    vi  -   -    
  L1M4_orf2#LINE/    582 TGGTTT----CTTAGATATG-ACACCAAAAG--CACAAGCA-ACA-AAAG 622

  chr2_27002125_2   1073 ACACAAT-------TCCGACTTGATAAAAATGTTTAAATTTTTATCAAGA 1115
                          v v   ------- iv     v  v     - vv   i    i --- v
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTTTGT---GC 668

  chr2_27002125_2   1116 AATGAAAGATACTATAGAAATAAATCAATAGATAAATGATAAAGAGTCTG 1165
                         vvii  i  i     vi i -  i v  v   i  viv i --  i vv 
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGA-AAGTGAAAAGACAACCCACA--GAATGGG 715

  chr2_27002125_2   1166 AGAAAACATGTGCAGCGCATAT-----------GAC--------AG---- 1192
                               i  v    ivv     -----------   --------  ----
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_27002125_2   1193 --CAAGGAGCTCTTA--ACATATTGATTGGAAAAAGACAAACAACC-AAG 1237
                         --i  i  i      --  vi v i  ---           i    -  v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAAT---AAAAAGACAAATAACCCAAT 812

  chr2_27002125_2   1238 AGAAAGATGGGCATAGGACATCAGTAAGTGATACACAGAAGAACAAAGCT 1287
                         v?   i       v    iv v i  iiiiv v v vi     v v vvi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_27002125_2   1288 AAATAACCAACAA-CATATGAGATGATGTTCAGCCTCTGCAGTAGT 1332
                             ii    i  -  i    i v    i   i v  v????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (126 / 101)
Gap_init rate = 0.06 (50 / 908), avg. gap size = 3.40 (170 / 50)  


2459 18.11 7.41 14.71  chr2_27008032_27009663.rev      171  1142 (490)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_27008032_2    171 ATATATCATGTTTCTAGATTGCAAGAACAGATATTGTTAAGATGTCCATT 220
                             vi      iv i     v    vivi              v v  v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_27008032_2    221 CTTTCCAATCTGATCTACAGATTCAACACACCCTCAATCAAAATCCTAAT 270
                           ii    vi                 i  vi i v          i ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_27008032_2    271 AGGCCTTTTTGTGGATATTGATAAGCTCATATTAAA-TTTATATAAAATA 319
                         v v i      ii  v     i     v  vi    -  i    ii  - 
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA-A 156

  chr2_27008032_2    320 TGTACG--ACCTAGAACAGGCAAACCAATTTTGGAAAAGAACAAAGGTGG 367
                           i v --   i    i  v    v    i   i       ---------
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA--------- 197

  chr2_27008032_2    368 AATCAATCAAACCCAGAGATCAGCAGCCACACCTCTCACCACCTCCCAGA 417
                         ------------------------------------------------  
  L1M4_orf2#LINE/    198 ------------------------------------------------GA 199

  chr2_27008032_2    418 ACGCAGGTCTCCCTGCAAAGGCTGGGCCTCCTGGGACACCTGGAAAATGC 467
                           ---------------  i i   i-------    -------------
  L1M4_orf2#LINE/    200 AC---------------AAAGTTGGA-------GGAC------------- 214

  chr2_27008032_2    468 CACATGAAGTCAGACACCTCCTGCTTTTTTAAAACCTTATTTCAAGACAT 517
                         ---------   --   i   ii---------------       i  v 
  L1M4_orf2#LINE/    215 ---------TCA--CACTTCCCA---------------ATTTCAAAACTT 238

  chr2_27008032_2    518 ACTGTAAAGCTACAGTTATCAAGACAGTGTGGTATTGCTGTAAG-ATAGA 566
                            ii           v                 i  vii    -     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_27008032_2    567 TGAATATGTGGATGATACAGAATAGAGATTCTAGAAATAGACCTACATAT 616
                         iiv   vi vi   iv i     v    v  i       i   --    i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATAC 336

  chr2_27008032_2    617 ATATATGATCATTTGATTTTTGACAAACGTACCAAGGTAATTCAATGCGG 666
                           v    i   v        i     iv  i     iiv        -  
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GG 385

  chr2_27008032_2    667 GAAAGAGTAGTCTTT-CAACAAATGATGCTAGAACAAATGGATATCCATT 715
                               i        -         i    i i    v      ?   iv
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_27008032_2    716 TGGGGAAAAA---AGT-GGAC-------------------------TTAA 736
                           vii  i  ---   -    -------------------------    
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_27008032_2    737 ------ATGGATCATAGACCTAATCATAGATGCTAAC-CTATGAA-CTCC 778
                         ------        ?        vii  iiv     v-    i  -   i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_27008032_2    779 TAGGAAAAAATATAGGAGAAAGTCTTTAGGATCTTGGGTTAGG------- 821
                            i i    i     ? v  i    iiv  i           -------
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_27008032_2    822 ------------ACATAAAAAGCATGAACCCTAAAAGATAAAATTGTTAA 859
                         ------------   iv       ii i vvi      v     v v   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_27008032_2    860 ATGAAACTTTTATCGAAATTTAAAACTTGTGTTCTTCATAAGATCCTGTT 909
                           vii    i-   i     v       v   v     v i  iv  i i
  L1M4_orf2#LINE/    636 ATTGGACTTC-ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_27008032_2    910 AAGAAAATGAAAAAGCAAGCCATAGACTGGGATAAAACATTTGCAACACA 959
                               i      ii   v   i   v     v    i        vv  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_27008032_2    960 TAGATCTGATAAAGGACTTATATCCAGAATATAAAGATAATTCTTACAAC 1009
                           v         i      i             v i v  i         
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_27008032_2   1010 TCAATAATACAATG-CAATTAA--------AAAAATGAGCAAAAGATTTG 1050
                                  v  v -   v   --------       i     i      
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_27008032_2   1051 AAGAGACACTTGAAGAGACACTATTTGTATCTACAAAAAAGATA--CAAG 1098
                           v     i  -------------------  v    i      --   i
  L1M4_orf2#LINE/    835 AATAGACATTT-------------------CTCCAAAGAAGATATACAAA 865

  chr2_27008032_2   1099 TAGTAAATAAGCACATAAAAAAAATGCTCAACATAATTGGTTAT 1142
                          i iv           i    i -          v ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (106 / 67)
Gap_init rate = 0.03 (26 / 901), avg. gap size = 8.27 (215 / 26)  


2650 14.59 15.84 0.53  chr2_27532097_27534403      402   963 (1344)    L1M4_orf2#LINE/L1       52   699 (209)  

  chr2_27532097_2    402 GTAATACTCCCCCAGTTGATCTACAGATTCTGCATAACCCCTATAGAAA- 450
                          i          v i               vi ii  i      vi   -
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_27532097_2    451 CCCAGGTGCCTTTTGTGCAGAAATTGACAAATTAATCCTAAAATTTAGAT 500
                              v        v               ii i           i v  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_27532097_2    501 GAAAA-ACAA----------------------ATTTTAAAAA-------C 520
                          i   -i   ----------------------  i  i    ------- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_27532097_2    521 A-------------------------TTTCAAAACGTACTAAAAAGCTAC 545
                          -------------------------         v     v        
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_27532097_2    546 AGTAACCAAGATAGTGTATTACTGGCATAGGGA----CATGTAGACCAAT 591
                              i     i     iv          i   ----   i    i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_27532097_2    592 GAAATGGACTTGAGAGTTCAGAAATAAAACCCTCACATTTACGGTCAATT 641
                          i   i  v        i          -   vi       i        
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTCAATT 350

  chr2_27532097_2    642 TATCTCTGACAATGATGCCAAGATAATTCAATGGGGGAAAAGAACAGTGG 691
                         v  i ii     v i        iv           --      i   vv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAAGAATAGTCT 398

  chr2_27532097_2    692 TTTAAACAAATAGTGCTGGGACAACTTGATATCCACACACAAAAGAATGA 741
                            v       i              v    ?     ii           
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_27532097_2    742 AGTTGGATCACTCCCTCATACCATTCACAAAAATTCACTCAAAATGGATC 791
                                i v  v     i     vi         v              
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_27532097_2    792 ACAGA---------AACAGCTAAAACTATAAAACTCTTAGAAGAAAACCT 832
                          ?   ---------  v                               v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_27532097_2    833 AAGAGAAAATTCTCGTGACTTTGGGTTAGGCAA-AGCTTCTTAA------ 875
                          i ? v    ii       i             -i i      i------
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_27532097_2    876 ---CAAAAACA-----AACAAAC---AAAATAGACAAATTGGACTTTATC 914
                         ---     i  -----      v---        i           i   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_27532097_2    915 AAAAGTAAAAACTTTTGT--TTCAAAAGACACCATCAAGAAAGCAAAAAG 962
                             v             --      i     i          ii     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_27532097_2    963 A 963
                          
  L1M4_orf2#LINE/    699 A 699

Transitions / transversions = 1.93 (52 / 27)
Gap_init rate = 0.02 (14 / 648), avg. gap size = 6.57 (92 / 14)  

 968 10.80 6.57 1.41  chr2_27532097_27534403     1609  1821 (486)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_27532097_2   1609 AAGAAAGC-AAAAG----TCCACAAAAATTGGAGAAAAGATTTGCAAATC 1653
                                i-     ----i     i  - v        v           
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAA-TGGGAGAAAATATTTGCAAATC 733

  chr2_27532097_2   1654 ATATATCTAACAA---ACTTGTATCCAAAACACATAAAGAACTCTTACAC 1700
                                 i i  ---           i  i i                v
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_27532097_2   1701 ATCAAAAGACAAAAAGACAA----TCCAATT-AAAAATGGACAAAGACTT 1745
                         v    v - i          ----i      -        i     iv  
  L1M4_orf2#LINE/    784 CTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_27532097_2   1746 TGAACAGACATTTCTCCAAAGAAGATACACAAATGTCCAATAAGCACAT- 1794
                             i                      i       v             -
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_27532097_2   1795 AAAAGATGTTCAAACATAAGGCCTGGC 1821
                                 i    -   v ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.04 (9 / 224), avg. gap size = 1.89 (17 / 9)  


1492 19.71 14.50 13.82  chr2_27722000_27724209.rev      828  1710 (500)    L1M4_orf2#LINE/L1        2   890 (18)  

  chr2_27722000_2    828 GGGAAAATATAGCATGTTCATAAATCAGAAAACTCAATATTGTTAAAATA 877
                           i  i    vv         ii  ii   i   i           i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_27722000_2    878 GCAATTTTCCCCAACGGAATCTATAGATTCAATATAATACCAATCAATA- 926
                              vi       vvvi     i        iii   v  v     v -
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_27722000_2    927 CTCAGCAAGCTTCTTTTAATAGATATTGGCAACCCAATTCTATACTTCTT 976
                          i    v-  i i    i-i   v    i   v ii  i   v v   v 
  L1M4_orf2#LINE/    102 CCCAGCT-GCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_27722000_2    977 ATAAAAACGCAAAGAACTGAGAATAACCAAAACAATTTTGAAAAAGAACA 1026
                           ii   i    i i  iv      i          i           v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_27722000_2   1027 CTAAAGTTAGAGGACTTAC------TGATTTCAAGA-------------- 1056
                         vi      i       i  ------ii       i --------------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_27722000_2   1057 --------------------------GTCTAA--ATAAACAT------CA 1072
                         -------------------------- iv   --   i    ------  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_27722000_2   1073 GTAGAACAGAATAAGGAGAGTCCAGAAACAGACCTACACATATACATGTC 1122
                         i i   i     --v             i i   i i    v  --  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAAT--TGAGAGTCCAGAAATAAACCCATACATTTA--TGGT 345

  chr2_27722000_2   1123 CAAGTGAAGTTTGACAAAGATGCCAAGGCAATTCAGTAGGGAAAGAAAAC 1172
                            v   vv  i     i i       i v     i i         v v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_27722000_2   1173 TCTTTCCAACAA------CTGGGTATA--TAAATAG------AAAAAAAA 1208
                              i      ------     - i -- ii   ?------iv    i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGG-ACAACTGGATAKCCACATGCAAAAGA 444

  chr2_27722000_2   1209 GTCAACATTGACCCTTACCATAAAACATTCACAGAAATTAACTCTAAATG 1258
                         i v  vv v     i    vi v v   vi   i          v     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_27722000_2   1259 AGTCACAGACCTAAATATAA------AACCTATAAAACTTCTAGGAGAAA 1302
                         ii   ?          i   ------  v          ii   i     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_27722000_2   1303 AGACCACAGAAAATCTCTGCAATTAGGGAGGCAAAAGTTTCTTTTTTTTA 1352
                          ------------------  --    ?-- i   ----    i------
  L1M4_orf2#LINE/    545 A------------------CA--TAGGN--GTAAA----TCTTC------ 562

  chr2_27722000_2   1353 ATTATTATTATTTCTTAAGACGGAATCTCGCTCTGTCGCCCAGGCTGGAG 1402
                         --------------------------------------------------
  L1M4_orf2#LINE/    563 -------------------------------------------------- 562

  chr2_27722000_2   1403 TGCAGTGGCACCACCTTGACTCGCTACGACCTCCAGGGAGGCAAAGGTTT 1452
                         ----   -----      i--- i  -------------     v     
  L1M4_orf2#LINE/    563 ----GTG-----ACCTTGG---GTTA-------------GGCAATGGTTT 587

  chr2_27722000_2   1453 CTTAAATAGGATACATAAAAGCATGA--AATGTAAGAAAAAAATGATAAA 1500
                             i   v  i  -i       ii --  iiv         vv      
  L1M4_orf2#LINE/    588 CTTAGATATGACAC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_27722000_2   1501 TT---------------TAAAC-CTTTTGCTCTTCAAAAGACATCATTAA 1534
                           ---------------    v-      iv       i    ii  i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_27722000_2   1535 GAAAATGAAA-GACAAACCA--GACTGGAAGGAAGTAT----AA--CA-- 1573
                             i     -     v   --  v   i  i  i   ----  --  --
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_27722000_2   1574 -----GACAAACGAGTTGTATTCAGGACAGATTTTTTTAAATACC----A 1614
                         -----  i  iv  v      i   i i v  ------   v v ---- 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATAT------AAAGAACTCTTA 780

  chr2_27722000_2   1615 CAATTCAATAA----------GATAACCCACTTTTTTTAATGGACAAAAA 1654
                            i       ----------i        v  ?vvv-     i    ii
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGG 829

  chr2_27722000_2   1655 ---TG--TAAACATTTTACAAAAGTAGACACACAAATGGCCAATAAGAAT 1699
                         ---  --  i      iv v    v   i i                v i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_27722000_2   1700 AGGAACAGATG 1710
                          v   v     
  L1M4_orf2#LINE/    880 ATGAAAAGATG 890

Transitions / transversions = 1.70 (107 / 63)
Gap_init rate = 0.04 (37 / 889), avg. gap size = 6.76 (250 / 37)  


 695 27.67 9.01 11.20  chr2_28036633_28038358.rev      470  1246 (480)    L1M4_orf2#LINE/L1      149   908 (0)  

  chr2_28036633_2    470 TACAAAAACGTATGTAGAACACAGGGTTAAGCAAGACAATTTTTAAGAAT 519
                           iii   i i v -- i  v   ii - iv   i     i  v  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG--GGACCCAGAAT-AGCCAAAACAATCTTGAAAAAG 195

  chr2_28036633_2    520 TAGAACAAGATGGAAGGGGGGAATTTGTCCTACTGGCTATCATGACATTT 569
                         v       ii v i   ----- i iiiv  v iviv v   vi  v vi
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGG-----ACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_28036633_2    570 CACAAGACTGTAATAGTTAAGAAAGTATGGAACTGGCACAAGGACAG--- 616
                         i    ii  ii i  i i    v   i   v       i     i  ---
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_28036633_2    617 TG-AGGCTGACTGACCAAAACAGAAAGCCTGGCAACAGGCCCATG----T 661
                          i-  iiii iv  vi i  iv  i  i ii v  i ii     i---- 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_28036633_2    662 GTGAT--ATAAACTT--GACA----T-------CCAT------GGGCAAG 690
                         i  i --  vi i  --    ---- -------    ------   v   
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_28036633_2    691 GATGGCCTTCTCAATAAATGAGGCTAGGTCAACCAATTATCCATACGGTG 740
                         i  i i   i    i     iv   i  v    iiiv  ?   i i v--
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-- 438

  chr2_28036633_2    741 GGGGGGGTGGGGGAGACAATATCTCTATCTCACTCCATATTACAGAAAAA 790
                         iiii ii  ii vv i---- i i   i     v      -   ---   
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGG----ACCCCTACCTCACACCATAT-ACA---AAA 480

  chr2_28036633_2    791 ATAAATTCCCA-T---TTAAAGACCAAAAAAGGAAACAGG-AAAACTTTA 835
                           v  i  vv - --- i ?     v   --v v  v  v-      v  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAA--TGTAAGAGCTAAAACTATA 528

  chr2_28036633_2    836 AAATTCGTA-AAGAAA-----GATGT--------GTGACTTTTGGATAGG 871
                            i  v  -      ----- i?  --------     i  v  v    
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_28036633_2    872 CCCAGATTTCTTAAAACTCTCTTTCTCTCTCTCTCTCTCTCTCTCACACA 921
                          vvv i       i -------------------------- v v    -
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGA--------------------------TATGACAC- 601

  chr2_28036633_2    922 CACACACACACACAAACACACACACGTGCACACAGGCACATATATTCAAA 971
                         ----------  v  i    vi  -------------   -------   
  L1M4_orf2#LINE/    602 ----------CAAAAGCACAAGCA-------------ACA-------AAA 621

  chr2_28036633_2    972 TCTAAAAAAGAAAATACTGTAGAATATAACTTCATCAAAATCAAAA-CTC 1020
                         ---i     iv i   ------   vvi             i    -  i
  L1M4_orf2#LINE/    622 ---GAAAAAATAGATA------AATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_28036633_2   1021 TTGGATGTCAGGGG-CACTA------AAATAAGAATATATGCCACAGACT 1063
                            viiv   ii  -     ------  i i i  v i vv       v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_28036633_2   1064 TTGTGCAGATATTTGTAATACATGTAATTACCAAAAGATCAGTATCCAAA 1113
                         vv v v i       i  vv   i  vi ivi  ii  iiv       i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_28036633_2   1114 ATACACAAAGAATGCTTTAAAATCTATAG-AAATATACAAACAATCCACT 1162
                            i i      iv   vv  v  v   i-   v v     i  i   v 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_28036633_2   1163 TAAAAGACGAACAAAGGAT----AT--------CCCAAAGGAAGAAATCT 1200
                          ?   i i ii        ----  -------- i v  i     v  vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_28036633_2   1201 GAATTGCCAATAAGCATATTAAAAGACTTTTCACCA-CAATGAGATA 1246
                         i   v           i  v      - vi   v  -  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (129 / 82)
Gap_init rate = 0.05 (36 / 760), avg. gap size = 4.36 (157 / 36)  


2544 24.15 7.03 4.31  chr2_28107934_28110972     1670  2551 (488)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_28107934_2   1670 GAGATATATAATATATTCAAGGATGGGAAGACTCAACATAGTTAAGATGT 1719
                           i v    vvi  i    v    v        i  i  v         -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG- 51

  chr2_28107934_2   1720 TTTCCCTAATTAGTTTTAATTAGTTTCCTAAGTCAATTTTCCCTAAATTA 1769
                         ------------------------------- -    vi    i     i
  L1M4_orf2#LINE/     52 -------------------------------G-CAATACTCCCCAAATTG 69

  chr2_28107934_2   1770 ATGTACACTATTTAGTGTAATCCCCATCAAAATCCCAGCAGGATTGG--G 1817
                           v    v-   i ii i      i              v vv  vv-- 
  L1M4_orf2#LINE/     70 ATCTACAG-ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG 118

  chr2_28107934_2   1818 TAGATATTGACAAGATGATTTTAAAATTTACGTGGGAA-GCAAAGAATT- 1865
                         i   v         v    ii       i ii   i  -    i i ii-
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr2_28107934_2   1866 AAAATAGCCAAAACAATTTTGGAAAAGAACAATAAAAATGGAGGAGTCAG 1915
                          i               i   i       v  i   iv       v   v
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_28107934_2   1916 ACTACTCAGTTTGAAGACTTATTA--------------TCAAGGCAGTGT 1951
                            v i  i   v  i     i  --------------     i      
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_28107934_2   1952 GATATTGGCAAAAGAAGAGCCATA--GATCAATAGAACAAAAT----AGT 1995
                          i  i     v   i v  v    --       i   i i   ----   
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_28107934_2   1996 CCAATAATAGATCCATATAAATATGGTCAAT-GATTTTCCACAAAAACGC 2044
                            iv    i i     i vv          -       v    iiii  
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_28107934_2   2045 AAAGGCACTTCAATGGCAAAAGGA--GTCTTCTCAGCAAGTAG------- 2085
                         v   i vv        vi    i --     i   i   i i -------
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_28107934_2   2086 --------ACATCTACATGCAAAAAAAAGGACCTTGACTTATATTTCAAA 2127
                         -------- i ? i          i  v i vi v   iiv  ii   v 
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_28107934_2   2128 CCATGTTCAAAAATTGG-------TGAATCACATTCTTAAATGGAAAATT 2170
                             i v        ii-------  i    ? vv i      v  i vi
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_28107934_2   2171 TCAAACCATAAAAATCCAAGAAGTAACCATAGAAGGAAGGCTTTGTGAC- 2219
                          v    i      v  iv     v  v     i? v  iv   i     -
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_28107934_2   2220 TTGGGCTGGGCATTGAGTT---AGATACAACAGTAGAAACATAATCCATA 2266
                              i i    v  iv  ---     ii   vi i  i  i  v v i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_28107934_2   2267 AAAGAAAAAAGTTGATAAATTGGATTTCACTGAAGCTTAAAACTTTTGCT 2316
                                   - v           i    iii  ii v          iv
  L1M4_orf2#LINE/    619 AAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_28107934_2   2317 CTGCTGAAGAGACTGTTAAGAGGAAGAGGAG-GACAAGAAGCAG--TAAG 2363
                           v vi i  v   i i    --   v i i-     vvvi   -- ii 
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGA--AAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_28107934_2   2364 AGAAAATATTTGCAAATCATGTATCTAACAGAGAACAAATTTCAAGAATA 2413
                                             i     i i ii i  vvi v  v      
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_28107934_2   2414 TGTAG----CTTTCAAAAGTCAACATTAAGAAAACCAACAAC--AATAAA 2457
                          i  i----  i i v  v    i v   i  i  v  i   --   v? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_28107934_2   2458 AAAAATGGGGAACAGATCTGAACAGATACTCCACCAAGGAATATATACAG 2507
                             -    v  vi   i    i   i i i v    i   v       i
  L1M4_orf2#LINE/    816 AAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_28107934_2   2508 GTAGCAAATAAACACATGAAAAGATGCTCAACTTTATTAGTCAT 2551
                         i i  v     i                    v i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (129 / 80)
Gap_init rate = 0.02 (22 / 906), avg. gap size = 4.55 (100 / 22)  


2476 24.59 2.04 2.31  chr2_28252489_28254218.rev      503  1238 (492)    L1M4_orf2#LINE/L1      175   908 (0)  

  chr2_28252489_2    503 GCCAAGACAATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCATGCTACG 552
                              i      i i iv  i          i      vv   ii  v v
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr2_28252489_2    553 TGACTCCAACCTATACTACAAGGCTACAGTAACCAAAACAGCATAGTACT 602
                         ii i i   vviv        i          i   i    ii i     
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr2_28252489_2    603 GGTACCAAAACAGACATACAGACCAATGGAGCAGAATAGACACCTCAGAA 652
                           i iv ii i       i   i       ii     v  v vii     
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr2_28252489_2    653 ATAACACCACACATCTACAACCATCTGATCTTCGACAAACCTGACAAAAA 702
                             vv   i    i  iiii  vi    i        ivv  v   i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_28252489_2    703 CATGTAATGGGGAAAGGATCTCCTATTCAGTA--TGTTGCTGGGAAAACA 750
                            vi           i  vvi  v    ii --  v        v   v
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_28252489_2    751 GGCTAGCCATATGCACAAAACTGAAACTGGACCCCTTCCTTACACCTTAT 800
                           v  ?   i     v  i v    ii         v   i     v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_28252489_2    801 ACAAAAATTAACTCAAGATGGATTAACAACTTAAATGTAAAACCCAAAAC 850
                                         i      i ?vi  i         i v i     
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_28252489_2    851 CATAAAAACCCTAGAAGAAAACCTAGACA-ATACCATTCAGGACATATGG 899
                         i      vi i           v   i?i- v i -   iv   v -   
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT-TGG 572

  chr2_28252489_2    900 G-----CAAAAGCTTC------ATGACAAAAATGCCAAAAGCAATTGCAA 938
                          -----   vi i   ------      ------         vvv    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAA 616

  chr2_28252489_2    939 CAAAAGCCAAAATTGAAAATTGACAAATGGGATTTAATTAAACTAAAGAG 988
                               --    -----   v  i    v   i  v  i   v v  i i
  L1M4_orf2#LINE/    617 CAAAAG--AAAA-----AATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_28252489_2    989 CTTCTACACAGCAAAAGAAAGTATCGTTGGAGTGAACAGGCAACCTACAG 1038
                            i iii vv    i  v v    ivvii      v  i     i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_28252489_2   1039 AATGGGAGAAAATTTTTG-AAATCTACCTATCTGACAAAGGGCTAATATC 1087
                                      v    -     - iv       i  i  i  vi    
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGGGACTTGTATC 758

  chr2_28252489_2   1088 CAGAGTTTACAAGGAACTTAAACATATTTACAAGAAAAAAAACAAACAAC 1137
                             i v  i  i     ivv   - i i vv iv     i     i   
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACA-ACTCAATAATAAAAAGACAAATAAC 807

  chr2_28252489_2   1138 CCTATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGG 1187
                           v  i?    i            v    i     i     v       i
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_28252489_2   1188 CATTTGTTTGGCCAACAAACATATGAAAAAGAGCTCAACATCACTGGTCA 1237
                         i  viivv       i  i  i       iiv           ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_28252489_2   1238 T 1238
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.53 (107 / 70)
Gap_init rate = 0.02 (12 / 734), avg. gap size = 2.67 (32 / 12)  


3141 26.09 1.67 0.67  chr2_28311645_28315883     2856  3752 (487)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_28311645_2   2856 GAAAAACAGCCTACCCTCATGAATCAAAAGAATTAATATTGTTAAAATGA 2905
                             i i v  i ivi     i  iii    v             i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_28311645_2   2906 CTATACTACTCAAAGCAATCTACAGATTCAATGTAATCTGTATCAAAATA 2955
                          v     v i    vii              i i    iv         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_28311645_2   2956 CCAA-TGTCATTTTTCACAGAATTAGAAAAAACTATCCTAAAATTCATGT 3004
                            i-  i -     ii     v v  v  iviv              i 
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_28311645_2   3005 GGAACCAAAAATTAGGCTGAATAACCAAAGGAATCCTGAGCAAAAAGAAC 3054
                             viiv  ivv vv v     i     iv    i   iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_28311645_2   3055 AAAGCTGAAGGCATCACACTACCTAACTGCAAAATATATTACAAGACTAT 3104
                             i  i   vv       v  i  i v     iv  i     ii   i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_28311645_2   3105 GGTAATCAAAACAGCATGATACTGGTATGA-AACAGACACATAGACCAAT 3153
                         i        i    ii  i      i  i -i i     i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_28311645_2   3154 GGAACAATATAAAGAATCTAGAAATAAATCCTTGTATTTACAGCCAACTG 3203
                             i iv  vi   i  i         i  v ii     ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_28311645_2   3204 GTTTTTGACAATGCCACCAAGAACATACATTGCAGAAAGGACATTCTCTT 3253
                         i    i     v vii      v   v  v  vi     i i v   i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_28311645_2   3254 CAATAAATAGTGCATGGAAAACTGGATCTCCATATGCCACGGAACGAAAC 3303
                            i    i    vv   v        v?   i    v vi   i   ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_28311645_2   3304 TAGACCCCTATCTCTTGTCACATACAAAAATCAACTCAAAATGGAGTGAA 3353
                          i        i   viii  i          i             vii? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_28311645_2   3354 GAC-TAAACATAAGACCTGAAGCTATAAAACTACTAGAAGAAAACGTAG- 3401
                            -    ii     v  i  i          vi           i   -
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_28311645_2   3402 AGCAAATGCTACAGGACATTGGTTTAGGCAAAGATTT-TAAGTCTGTGGC 3450
                         ? i    -  v iv   v    v        v i   - v  -v i  i 
  L1M4_orf2#LINE/    552 NGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-ATATGAC 599

  chr2_28311645_2   3451 CTCAAAAGCACAGGTAGCAAAAACAAAAATAGGCACATGGGACTATATTA 3500
                         vi          i i i     iv        ii v  v     vi  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_28311645_2   3501 AA--TAAAAAAGCTTCTGCACAACAAAGGAAACAAATCAACAGAGTAAAG 3548
                           --      --   i  ii vv       v  -v     v i   i  i
  L1M4_orf2#LINE/    650 AAATTAAAAA--CTTTTGTGCTTCAAAGGACAC-TATCAAGAAAGTGAAA 696

  chr2_28311645_2   3549 AGACAATCTGTTGAATGGAAGAAAACATTGACAAACTATTCATCTGCCAA 3598
                               i iiiv      i      i   vi    ii  vi     vi  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_28311645_2   3599 GG-ACTAATATCCAAAATATGCGAGGAACTCAAACAAC-----AGCAAAA 3642
                           -   vi      i     iii i      vv     ----- ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_28311645_2   3643 AGAAAAAAAATCACATTAAAAAGTGGGCAAAG-ACATGAATGTACATTTT 3691
                            v   v  i vv   ?    i         - iv     iv      i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_28311645_2   3692 TCAGAAGAAGATACGCAAATTGTCAACAGGTATACAAAAA-ATGCTCAAT 3740
                           vi         ii     v i   i i i i ii    -        i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_28311645_2   3741 GTTACTAATCAT 3752
                         i i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (151 / 79)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 1.40 (21 / 15)  


 918 25.30 4.17 8.04  chr2_28576611_28578793.rev      427   762 (1421)    L1M4_orf2#LINE/L1      162   484 (424)  

  chr2_28576611_2    427 GGGACCCTGTCTCAACAAAACAA-----AACAACAAGAACAAAATATGTA 471
                                v vv viv        -----  v  v         i -----
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT----- 206

  chr2_28576611_2    472 TATGCAGTACCCCATGGAGCATCCGTCTTCACTACCTGAATT-AGAACTT 520
                         --------------     v ii i----    v  ii v  - i     
  L1M4_orf2#LINE/    207 --------------TGGAGGACTCA----CACTTCCCAATTTCAAAACTT 238

  chr2_28576611_2    521 GCTGTAAAGCTATTGTAATCATGACAATAAGATATTGGTGTCAGAATAGA 570
                         i  ii       iv       v    i iv i  i   ii v  i     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_28576611_2    571 CAAGGAGATCAAGGAAACAGAATAGAAAGCCTAGGAGTGAGACCATGTGT 620
                           viv       v i  i     v  i  i i  i i i iv    iii 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_28576611_2    621 ATGTGCTCAACTGACTCCCAACAAAGGCACCAATGTGATTCAATGGGGGA 670
                         v i  v    i   i ii i    i  ii    viiv           - 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-A 387

  chr2_28576611_2    671 AAGGAAAGTCTTTTTAATTTTAAATGATGCTAGAACATCTGGATATT--- 717
                            i v        i  i---     i    i i   v       ?i---
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAAC---AAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_28576611_2    718 -----AAAAAATGAGCATTGACCCTTACCTCACATCATACTCAAAAATTA 762
                         -----   i     ivv v     i         i    iv         
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

Transitions / transversions = 1.90 (55 / 29)
Gap_init rate = 0.02 (7 / 323), avg. gap size = 5.86 (41 / 7)  

 485 21.76 4.15 8.29  chr2_28576611_28578793.rev     1078  1270 (913)    L1M4_orf2#LINE/L1      490   674 (234)  

  chr2_28576611_2   1078 AGATGGATTATAGACCTAAACAAAAAATCTAAAACTATAAAGCTTCTAAA 1127
                          i      i ?         iiv  i v             i  ii  i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_28576611_2   1128 AAAGAACAGAAGAGAGAATTTTCATGACTTTTGGGTAGGCAAAGTTTTCT 1177
                          i i    v i ? vi   i   i    i  v  v       v v     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_28576611_2   1178 TAAACAGATCACACACAAAGAAAAACAATCACAAACTATTAAAAAATGAA 1227
                           i i -- v    -    -------- v     i ----  v   v   
  L1M4_orf2#LINE/    590 TAGATA--TGACAC-CAAA--------AGCACAAGC----AACAAAAGAA 624

  chr2_28576611_2   1228 ATAATTTGTAGATTGGACATTATCAA--TT------TTTTGTTGTTTTAA 1269
                          v   vvi  i       v i     --  ------      - i  i  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT-GCTTCAA 673

  chr2_28576611_2   1270 A 1270
                          
  L1M4_orf2#LINE/    674 A 674

Transitions / transversions = 1.50 (24 / 16)
Gap_init rate = 0.04 (7 / 185), avg. gap size = 3.43 (24 / 7)  

 611 21.01 5.46 4.20  chr2_28576611_28578793.rev     1454  1691 (492)    L1M4_orf2#LINE/L1      668   908 (0)  

  chr2_28576611_2   1454 CTTGGAAAGACGTTTTTAAGAAAAT----AGGCAAGTCA--GTCTGTGAA 1497
                            vi  i   ii v i      i ----  i   vi  -- vv  - i 
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG-GGA 716

  chr2_28576611_2   1498 AAAAATATTCACACAAAACATATATCTGACAAAGTTCTGGTATCTAGAAT 1547
                         i        ii  --  v           i  i vv  v     i     
  L1M4_orf2#LINE/    717 GAAAATATTTGCA--AATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_28576611_2   1548 ATATAAATA---CTCACAAATCAAGAATAAAATGATTTTTTAAA--GCCT 1592
                                v ---  i    v    v       v  i-----   --i  i
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGAC-----AAATAACCC 809

  chr2_28576611_2   1593 AATAAATAAAAGGGAGCAAAGGACATGAACAGACACGTCACAAAAGAACA 1642
                            v? -    v  -        iv    i     iv  v v      v 
  L1M4_orf2#LINE/    810 AATTWA-AAAATGG-GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_28576611_2   1643 T-TACAAAGGGCCAGTAAACAAATGAAAAT-TGCTCAGCCTCATTGTGCT 1690
                          -      v     i   i  v       v-      i v   ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_28576611_2   1691 T 1691
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.04 (25 / 24)
Gap_init rate = 0.05 (11 / 241), avg. gap size = 2.09 (23 / 11)  


3936 17.48 1.08 0.14  chr2_28616427_28618156.rev      501  1238 (492)    L1M4_orf2#LINE/L1      164   908 (0)  

  chr2_28616427_2    501 GACCCCGAATAACCAAAACAATGTTGGAAATAAAGAACAAAGCTAGAGAA 550
                              v     i          v   i   vi          i i   i 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_28616427_2    551 CTCACACTTACTGATTTCAAAGCTTACTACGAAGCTATAGTAGTCAGAAC 600
                                  v ii        i        i      i    i   ii  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_28616427_2    601 ACTGTGGTACTGGCATAAAGACAGACACATAGACCAATAGAATAGGATAC 650
                          v                i  i     i     i    i      i  vv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_28616427_2    651 ACAGTCCAGAAACAAACCCTCTCATATATAGTTAAATGGTTTTCAGCAAG 700
                          v          i      viv   v   i  i  v  i     ii    
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_28616427_2    701 GGTGC-AAGACCATTCAATGGAGGAAAGGACAGTCTTTTCAACAAATAAT 749
                              -               -      i i                ii 
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_28616427_2    750 GCTGGGAAAACTGAATATCT-CATGCAAACGAACGAAGCTGGGCCCTTAC 798
                                v     i   ? i-        v   i    i   i   i   
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_28616427_2    799 CTAATGCCATATACAAAAATGAACTCGAAATGGATCAAAGACCTAAATGT 848
                           v ii              v     i          ?            
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_28616427_2    849 AAGACCAAAAACTCTAAAACTTTTAGGAGAAAGCATAGGGCAAAAGTTTT 898
                             v v      v       i    i     i      ?vv   vi  i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_28616427_2    899 ATGACATTGGATTTGGCAGTGATTTCTTGAATATGACACTAACAG-ACAG 947
                         i    v    i  v    i  i      ii         i  v  -   i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_28616427_2    948 GAAATAA-GGAAAAAATAGACAAATTGGACTTCATGAAAATTTAAAAGTT 996
                          v  i  -i           i              v      v    v  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_28616427_2    997 TTGTGCATCAAAAGACACTATCAATAGAATGAAAAGGCAATCTATGCAAT 1046
                               v     i           v i i       i   i i iiv   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_28616427_2   1047 GGGAGAAAATATTTGCAAATTATATATCTGATAAGGGATTGATATCCAGA 1096
                                             i                 i vi        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_28616427_2   1097 ATATACACAGGATGCCTAAGACTCAACAACAACAAAACAA----CCCAAC 1142
                              i v  i iv i  vi      i  i  v  i    ----     i
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_28616427_2   1143 TCAGTAATGAGCTAAGGACTTGGATAAACATTTCTCCAAGGAAGATATGC 1192
                          ? iv    i  v     i   i   i            i        i 
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_28616427_2   1193 AAATGGTCAATAAGCACATGAAAAGATGCTTAACACCACTTATCAC 1238
                               i                       i    i  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (86 / 39)
Gap_init rate = 0.01 (6 / 745), avg. gap size = 1.50 (9 / 6)  


4243 16.28 6.98 1.40  chr2_28703473_28707189     2366  3225 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_28703473_2   2366 TAGAAAAACATCTGACACTCATGGATTAGAAGATTTAATATTCTTCA--- 2412
                          i    i i   iv iii         i     i        v  v ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_28703473_2   2413 --TAATACTCCCCACATCAATCTACGGATTCAATGTGATCCCTATCAAAA 2460
                         --i           v  ii      i       i ii             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_28703473_2   2461 TTCCAGCTAGCTCCTTTGCAGAAATTTGCAAGCTGACCCTAAAATTCATG 2510
                          i      iv  ii            vi        i            i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_28703473_2   2511 TGGAAATTCAAGGGACCCAGAATATCCCAAGAAATCTAGAAAA----GAA 2556
                                v                v  v  iv     v     ----   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_28703473_2   2557 CAAATTCAGAGGATTCATACTTACCAATTTCAAAAGTTACTATAAAGCTA 2606
                             v ii     i   i    v            v      i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_28703473_2   2607 TAGTAATCAAGAC---GTGGTACTAGCATGAGGATAGACATATCGAACAG 2653
                         i            ---        i    i             v  v  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_28703473_2   2654 TGGACTAAGATTGAGAGTC-AGAAATTAAACTCTCATATTCATGGTTAAC 2702
                             v  ii          -      -    i vi i   i     i  i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAAT-AAACCCATACATTTATGGTCAAT 349

  chr2_28703473_2   2703 TCATTTTCAGCAAGGATGCCAAAACCA----ATGGGGGAAAGAATCGTCT 2748
                          v      ii     i      i    ----      -       v    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCT 398

  chr2_28703473_2   2749 TTTCAATAAACTGTGCTGAGACAACTAGATAGTTACACACAGAAAAATGA 2798
                               i   iv      i       i    ?ii   ii  i  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_28703473_2   2799 GGTTGAACTCCTACCTCACACTTTATACAAAAATTCACTCAAAATGAATC 2848
                         i    i  i            iv            v          i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_28703473_2   2849 ATAGACCTAAATGTAAGAGCTAAAACTA----ACTCTAGGAAGAAAATAC 2894
                          ?                          ----     vi        i i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_28703473_2   2895 AGGAGCAAATCTTTATGATCTTGAGCTAAACAAAGTCTTCTTAGATATGC 2944
                            ? i       ii   i    i i  ii   v vi            v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_28703473_2   2945 CACTAAGA---CAAGTGACAAAAGAAAAAA-----AAATCGA-------- 2978
                            i  i ---    ii             -----    i i--------
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_28703473_2   2979 -----TA-----TTTTGCGCTTCAAAGGATGTCATATCATATATCAAAGA 3018
                         -----  -----     i           --------  i-      -  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGA--------CAC-TATCAA-GA 688

  chr2_28703473_2   3019 AAGT--AAAGACAGCCCAAAGAGTGGAAGAAAACACTTGCCAATCCTATA 3066
                             --       i    v   i   i      i i    v    v    
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_28703473_2   3067 TCTAATAAGAAACTTACGTCTAGAAATTATAAAGAACTCTTAGAACTCAA 3116
                            i     ii    iii  i    vv               v       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_28703473_2   3117 ------AAAGA----TAACCCAGTT-AAAATCGGGCAAAGGATCTGAATA 3155
                         ------     ----       i  -    vi           i      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_28703473_2   3156 GACATTTTTCCACAGAAGATATGCAAATGACTAGTAAGCACTTGAAAATA 3205
                                i    v         i      i i i       v      v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_28703473_2   3206 TGCTCAACATCAGTAGCCAT 3225
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.70 (100 / 37)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.79 (72 / 19)  


1463 25.42 11.88 0.48  chr2_28871821_28873843.rev      501   921 (1102)    L1M4_orf2#LINE/L1      122   590 (318)  

  chr2_28871821_2    501 AAATTGACAAGTTGACTCTTAAATGTATATAGAACCGCAAAAGATCTAAA 550
                                    i   ii  v    vi    i   vi    ii  i i i 
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_28871821_2    551 ATAGACAAGACCATCTTGAAGAGAAAGAACAAAGTTGGTGGATT-ATACT 599
                             v   i  v        i ii              v   i - i   
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_28871821_2    600 ATCAGATTTTAAAATTTAATATGAAATTACAGTAATTAAGACAGTGTGAT 649
                         vi vi    i    i   v  ii  ii         i           i 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_28871821_2    650 ATTAGTACGAGAACAGACA----AATCAATAGAAGAGAGTATAGAGTTCA 695
                          i i i ii  i i     ----i      i   v   i vv     i  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_28871821_2    696 GAAATAGACTCACATATATATAGT-------------------------- 719
                               i  i  i i  v   i  --------------------------
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_28871821_2    720 -----------GGGGAAAAGATGGTCTTTTCAATAAATGATTCTGGAGTA 758
                         -----------       ii  i          i     i v    iii 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_28871821_2    759 ATTGGATAGTCTTATAAAAAAATAATGAGCTTTGGCCTTT-TTTCATACC 807
                          i      ?i vi  iv    i-     iv  v i  ii -ii   i   
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAG-AATGAAGTTGGACCCCTACCTCACACC 470

  chr2_28871821_2    808 ATATGTGAAAAATTAACTTGAGATGGATCATAGACCTAAATG-----GC- 851
                             ii-           ii i        ?           -----  -
  L1M4_orf2#LINE/    471 ATATAC-AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_28871821_2    852 AAAACAATAAAGCTTCT-GAAGAATACATGGAAGAATATCTTCATGACTT 900
                              v     i  ii -      v    i i? v v      i    i 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_28871821_2    901 TATGGCAGTCAAAGATTTCTT 921
                          iv vi  v   v i      
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 3.00 (78 / 26)
Gap_init rate = 0.02 (9 / 469), avg. gap size = 5.78 (52 / 9)  

 687 23.64 14.55 2.91  chr2_28871821_28873843.rev     1257  1531 (492)    L1M4_orf2#LINE/L1      602   908 (0)  

  chr2_28871821_2   1257 CAAAAAAACTAACCATAAAAGGAAAGATTGATAA-TTGGA-TTCATTAAA 1304
                              iv  v i v i     i   i  v     -     -     i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_28871821_2   1305 AATAAGAACTTTT-----TC---------------------GAAAGGGCA 1328
                          v   i       -----  ---------------------    i i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_28871821_2   1329 AGTCACAGACTGAGAGAAAGTATTTGCAATCCACCTCTCTCTT------T 1372
                          vi      v  i      i         vi  iv v   vv ------i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_28871821_2   1373 CTCTCTCCA------ATGAAGAATTTAAATTCTATAAACCAATAAGGAAA 1416
                         i v v    ------  i     i i-----i  i  vi      vi   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTC-----TTACAACTCAATAATAAAA 796

  chr2_28871821_2   1417 AGACAGACAACCCAATTATAAAATGGGCAAAACACTTGAACAAGCATTTC 1466
                              i i         ?v            iv i     i ii      
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_28871821_2   1467 ACAGAAGAGGATGTCCAAATATCTAGTAAGTATGTGAAAAAGGTACTTAA 1516
                         v vi    i   i v     iv i i    i ii      - i i  i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAA 895

  chr2_28871821_2   1517 GACATCATTAGTCAC 1531
                         --     ????????
  L1M4_orf2#LINE/    896 --CATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (42 / 22)
Gap_init rate = 0.03 (9 / 307), avg. gap size = 5.33 (48 / 9)  


2843 25.23 3.94 1.69  chr2_28929577_28932819.rev     1864  2751 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_28929577_2   1864 TGGAAAAACATTCCATGCTCATGGAT-AGAAGAATCAATATTGTTAAAAT 1912
                               i i  i     i        -i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_28929577_2   1913 CTCCATACTGCCCAAAGTAGTTTACAGATTCAATGCTCTTCTTATCAAAC 1962
                         vv v     v      v ii i           i  vv i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_28929577_2   1963 TACCAA-TGTCATTTTTCACAGCATTAGAAAAGAACTT-TTCTAAAATTC 2010
                          v   i-  i -     ii   v v v  v   --  v- i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_28929577_2   2011 ATATGAAATTGAAAAAGAGCCCGAATAGCCAAAGCA-TCCTAAGCAAAAA 2059
                              i  v  v  ii  v  v           i  -  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_28929577_2   2060 GAACAAAGCCAGAAGCGTCACACTACCAAACTTCAAGGTACATTATAAGG 2109
                                 iii  i vv       v  v  i     iiivi i  i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_28929577_2   2110 CTTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAAA 2159
                           -       i   i    ii         i iv ii i         i 
  L1M4_orf2#LINE/    248 CT-ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_28929577_2   2160 CCAATGGAACAGGATGGAGGAGCCAGAAATAAAGCTGTACTCCTGCAACC 2209
                         i        i  i  v   iiv           v ii   vii iiiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_28929577_2   2210 ATCTGATCTTGAACAAAGTCAACAATAACAAGCAATGGAGAAGAGACTGC 2259
                          vi    i  vi    i viiv   v v  vv      i   iii iv i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_28929577_2   2260 CTATTTGATAAATGGTGCTAAGATAACTGGCTAGCCATATGCAGAAGACT 2309
                           v  ii i          ii  i      v  ?   i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_28929577_2   2310 GAAACTGGACCCCT--TTCAC--CATACACAAAAATTAACTCAAGATGGA 2355
                            ii         --i    --    i                i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_28929577_2   2356 TTAAAGATTTAAATATAAGACCTCACACTATAAAAACCCTAGAAGAAAAC 2405
                          i ?   ii     i     v  v v         vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_28929577_2   2406 CTAGG---AAATACCATTCTGGACACTGTCCTTGGGAAATAATTTAT--G 2450
                         v    ---    -- -   vv   vi  vv-  i  v   ii   v -- 
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAG 592

  chr2_28929577_2   2451 ACCAAGTCCCCAAAAGCAACTGCAACCAAAACAATGATTGACAAGTGGGA 2500
                          i- v v v         vvv     v   iv  vi  v  i  i v   
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_28929577_2   2501 C-----CAAAATAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCAA 2545
                          -----      ----    i -   i  ii vv    iv v        
  L1M4_orf2#LINE/    642 CTTCATCAAAAT----TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_28929577_2   2546 CAGAATAAACAGACAACCTATAGAATGAGAGAAAATA----CAAACTATG 2591
                         v i i i  v        i i      i         ----    ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_28929577_2   2592 CATCCAACAAAGGTCTAATATCCAGACTCTATAAGGCATTT----AATTC 2637
                         i   ii i  i  v  vi        v v     i v i i----  i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_28929577_2   2638 AACAATCAAAAAACAA----CCCCATT-AAAAATGGGCAAAGGACATGAA 2682
                           i   v    i    ----   v   -                iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_28929577_2   2683 CAGACACTTCTCAAAAAACAAACGTGCA----GCCAACAAATATATGAAA 2728
                         i     i     v   i - i ii i  ----     i  ii i      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_28929577_2   2729 AAATGCTCATCATCACTATTAAT 2751
                          i       v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (141 / 81)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.08 (50 / 24)  


2988 13.52 4.56 4.89  chr2_28967548_28969153      501  1114 (492)    L1M4_orf2#LINE/L1      297   908 (0)  

  chr2_28967548_2    501 TCCATGGAATAGAAGTG----TCCAGAAATATACCGTCACAATTATGTTC 546
                           v           v  ----          v   vvi   v     v  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_28967548_2    547 AATTGAATTTTGACAAGGGTGCCAAGAAAATTCAATGGGGAAAATGTAGT 596
                               v   i                vv              ivi    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_28967548_2    597 CTTTTCAACAAATGGTGCTATGACAACTGGATATCTACAAGCAAAAGAAT 646
                                            iv            ? i   v          
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_28967548_2    647 GAAGCCGAACCTCTGGTTTATACCATATATAAAAATTAACTCAAAATGGA 696
                             ii i   i  ivi i i        i                    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_28967548_2    697 TCAAAGACCTAAATGTAAAACCTAAAACCATAAAACTCTTAGAAGAAAAC 746
                            ?              i v       i                     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_28967548_2    747 ATAGGGGTAAGTCTTCGTGACCTTGAATTAGG------TTTCTTAGACAT 790
                              ?    i              ii     ------         i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_28967548_2    791 GATACCAAAAGTAACATGTAACAAAAGAAAATATA---AAAT-AGACATC 836
                           i        i -  v i            v   ---    -i   v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_28967548_2    837 ATCAAAATTAAAACCTTTTGTCCTTCAAAGGATACCA-------AGTGAA 879
                                      v       v          i  i -------      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_28967548_2    880 GAGATGACCTATAAAATGAAAAAAATTTTTTGCAAGTCATCTATTTGATA 929
                         i   ii   i i i    ii i   v v       i    v   i     
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_28967548_2    930 AGGGTCTTGTATCTAGAA-ATATAAAGAGCT-TTACAACTTAATAATAAA 977
                             v        i    -         i  -        i         
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_28967548_2    978 AAGACAA-----TCAATTTAAAAAATGGGCAAATAATCCAAATAGACATT 1022
                                -----i     ?     -        vi  iii          
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATT 844

  chr2_28967548_2   1023 TCTCCAAAGAAGGTATGCAAATTGCTAAAACACACACACACACACACACA 1072
                                     i   i     v  i  v vi    --------------
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACA-------------- 880

  chr2_28967548_2   1073 CACACACACACACTTGAAAAGATGTTCAACATCATTAGCTGT 1114
                         --------------          i         ????????
  L1M4_orf2#LINE/    881 --------------TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (51 / 28)
Gap_init rate = 0.02 (11 / 612), avg. gap size = 5.27 (58 / 11)  


3537 22.83 3.04 0.90  chr2_29232979_29235039.rev      681  1569 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_29232979_2    681 TGGAGAGATATTTCATGTTTGTGGATCAGAAGACTCAATAATGTCAAAAT 730
                             i      ii      ii     ii       i    v   i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_29232979_2    731 GACAGTTCTTCCCAGCGTGATCTGTAGATTTAGCACAATCCCAATCAAAA 780
                          i  i v  i    ivv      ii     i i i       v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_29232979_2    781 TTCCAGCAAATTATTTTGTACATGTTGACAAACTGATTCTGAAGTTTCTG 830
                          i     vivi v     i v vi       i     i  i  i  iv i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_29232979_2    831 TGGAAAGGCGAAAGACCCCAAATAGCTAACACAATCTTAAA------GAA 874
                               v  i ii     vi      i  v        i  ------   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_29232979_2    875 CAAAGTCAGAGGATTGACACT--ACAGGCTTAAAGATATACTACAAAGCT 922
                               ii     i v     --v  ivi i   - iv            
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-ACTTACTACAAAGCT 249

  chr2_29232979_2    923 ACAGCCATCAAGAC--TGTGGAATTGGCAGAAGAATACACAAATAAATCA 970
                             iv        --     v i     v   i   v   v   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_29232979_2    971 ATGGAATCTAATAAAGGGCTCAGAAATATACTCACTCAAATATAGTCCAC 1020
                                vv   vi  i ii        v  i  iv  vv   i   v i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_29232979_2   1021 TGAT----AACACAGGAGCAAAGACAATTCAATGGAAAAAAAGGATAGTC 1066
                             ----i   vi  v  v     v         ii   i --      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA--ATAGTC 397

  chr2_29232979_2   1067 TTTTAAATAAATGGCCCTAGAACAACTGGACAACCACATACGAATAAATG 1116
                             v  i      iv  i i         i ?      i i  vi    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_29232979_2   1117 AATCCAGACACAGATCTTACACCTTTTACAAAAATTAACTCAAAATGGAT 1166
                           viii   v vv i  i     v v                        
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_29232979_2   1167 CGTGGACATAAACGTAAAATTCAAAACTATAAAACATCTATCTAGAAGAT 1216
                          i?i   v    i    i vii             -   ---       v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCT---TAGAAGAA 543

  chr2_29232979_2   1217 AACATAGGAGAAAATCTAAGTGACCTTGGGTTTGCTGATGACTTTTTAGA 1266
                                 ? v      vv             v vii   ii  i     
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_29232979_2   1267 TACAACACCAAAGGCATAATTAATGAAAGAAAAAACTGACAAGTTGAACT 1316
                           ii        i   i  vi  ii          iv  i  i   i   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_29232979_2   1317 TCATTATATTTTTTCAATTCTGTTCTGTGAAAAATCCTGTTAAGACAATG 1366
                             i v v  vvvv v  i   v  vii  ii iv  i i    v i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_29232979_2   1367 AAAAGACAAGCCACAGACTAGGAGAAAATCTTTGCAAAACACATGTCTGG 1416
                                  v       v i         v        v  i  i    i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_29232979_2   1417 TAAAG-ACTGTTATCCAAAATATACAAGG----CTTAAAATT---TAATA 1458
                            i -   vv      i      i  i ----    v  i ---     
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_29232979_2   1459 AAAAGA-AAAT---TCAATTGTTTAAATGGGCAAAAGATCTGAACAGACA 1504
                               -    ---i     -?vv           i   i    i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_29232979_2   1505 CCTCACCAAAGAAGATATACAAATAGCAAATAAGCATGTGAAAAGATGCT 1554
                         ii  v                   i  v        ii            
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_29232979_2   1555 -AACATCATATGTCAT 1569
                         -       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (123 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.33 (35 / 15)  


1004 28.16 10.23 5.86  chr2_29245544_29247672.rev      772  1641 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_29245544_2    772 TGGAGAGATA---CA-G--CATGGATAGGATGACTTTACATTGTAAAAGT 815
                             i     ---  - --       v   v     v i     v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_29245544_2    816 A-------TCC---ATTTAGTCTCCAAAGTAAATGTTATGGCAACCAAAA 855
                         i-------   --- v  ii   v  i v v  i iv  vv v i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_29245544_2    856 TTCCAGCAGAAACTAAATTTTTAGGGAACTCAACAAACTTAC---AAAAT 902
                          i     v v--  ---     ivi   v ii    i  v i---     
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CT---TTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_29245544_2    903 ATATAAGGAGA---AATAAATTTTAAACAGTTAAGTCAATTAT-AAAAAC 948
                         vi   v   i ---  vii iiivi  i  ii  iv    iv -     v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_29245544_2    949 CAGAGCAGACCTGCCATGCCAGATATT-----ATGTCA----TTGCCACA 989
                         v   i  i vi  v- v v vv i i -----  v   ----  i i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGG-AGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_29245544_2    990 ------TAGTAATAAAAATATTATGGTACTGGTATA-GGA---ACACATA 1029
                         ------i      v  i i v i         i   -   ---   i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_29245544_2   1030 GAGCAAATAGGAAACAGAATGAAGAACTCAGGAGCAGACCCACGTATAAA 1079
                           v   - i --  i     vi   iii   i ii i     iii  vv 
  L1M4_orf2#LINE/    295 GATCAA-TGG--AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_29245544_2   1080 TGCTACCTCCATTTAC-ACAAAGGTGGTACCACAGA----TCAATGAGAA 1124
                           v vvv iv    v -    i    ---   -   ----      i i 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTG---CCA-AGACCATTCAATGGGGA 387

  chr2_29245544_2   1125 AAATATAAATTATTTAGAAGACGGCATTCGGGA-AACTGGCTTTAATTTA 1173
                           iv   ivi v  i iv i i  iii -    -      v --- ?ii 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCT-GGGACAACTGGAT---AKCCA 433

  chr2_29245544_2   1174 T---CAAGGAAAAATAAAGTTGAGAGCCCCATGTTCTGCCATATACAAAG 1220
                         i---   --  i   i      -  v   i iv ivii           i
  L1M4_orf2#LINE/    434 CATGCAA--AAGAATGAAGTTG-GACCCCTACCTCACACCATATACAAAA 480

  chr2_29245544_2   1221 GTGAACTCCAGATAAATGGCAGACCTACATATGA----------TACAAA 1260
                         i v     v i  ii  vi?       v  i i ----------  i   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_29245544_2   1261 A---------GAAAATGCAGGAGACTATCTCTATAATGT-GGGTTAGG-A 1299
                          ---------     iii   ? vvv    iii i iv -        - 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_29245544_2   1300 AT--TTACTTC-ATAAAACAGGTTTGCAAAAGCACAATCCTTGAAGCAAA 1346
                           --  v   v-   vi   v-----           v ----- i    
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACAC-----CAAAAGCACAAGC-----AACAAA 620

  chr2_29245544_2   1347 A-AAAAATTGTATGACTTG-ACTGCATCACAATTAAGGG-TTCTGT---T 1390
                          -     v iv  i v   -   v     v      iii-  i   --- 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_29245544_2   1391 CAGTTAAGAATACCATAGAAAAAATTAACAGATGGCTGACAAATTGGAAG 1440
                           ---   i i  i  vi i   i v  v   iii iv   i v   i  
  L1M4_orf2#LINE/    671 CA---AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_29245544_2   1441 AAAACATGTGC------TATGTTCAAAAGCAACTAGGGATTAATATCTGA 1484
                             i  v   ------   i iii v ------     i vi    iii
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATA------AGGGACTTGTATCCAG 761

  chr2_29245544_2   1485 AATGCATGAGGAACTTTTCACAAATCAAAAGGAAGTCAATATAAAATATT 1534
                            ii  i i     i  -    v    v iv  i--  v i   -----
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTT-ACAACTCAATAATAAA--AAGACAAA----- 803

  chr2_29245544_2   1535 TTAAAGGCCAATATAAAAATGAGAAAAGTATAAGAATAGACAATTCACAG 1584
                         -   v--     v?       i v    v  vv         v   v vi
  L1M4_orf2#LINE/    804 -TAAC--CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_29245544_2   1585 AAGGAAA-AGCCAGAATGGCAAGCAAGCAT-TAAAGAGATGCTCAACCCC 1632
                            i i - vv  -      v ii     i- i  i           vi 
  L1M4_orf2#LINE/    851 AAGAAGATATACA-AATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_29245544_2   1633 ACTTGTAAT 1641
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.06 (50 / 908), avg. gap size = 2.80 (140 / 50)  


2933 25.31 2.56 1.34  chr2_29271787_29275068.rev     1894  2790 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_29271787_2   1894 TGGAAAAACACTCCATGCTCATGGACTGGAAGAATCAGTATCATTAAAAT 1943
                               i i ii     i       i       v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_29271787_2   1944 GTCCACATTGCCCAAAGCAATTGACAGTTTCAACAGTCTTCCTATCAAAT 1993
                          v v i i v      vii  iv    v      ivvv i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_29271787_2   1994 TTCCAACATCGTTTTTCACAGGATTAGAAAAAACTG-TTCTAAAATTCAT 2042
                          i   i vv v     ii   i v v  v  i-   - i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_29271787_2   2043 ATGGAGCCAAAAAAAAAAAAGAGCCCA-AATAGCCAAAGCAATCCTAAGC 2091
                              -------  viv  i ii    -          i     i i iv
  L1M4_orf2#LINE/    150 ATGGA-------AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_29271787_2   2092 AGAAAGAACAGAAGCCAGAGGCATCACATTACCTGACTT-AAAATTATAC 2140
                          ii       -   iii    vv     i v  ii i  -    i -   
  L1M4_orf2#LINE/    193 AAGAAGAACA-AAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TAC 240

  chr2_29271787_2   2141 TACAAGACTCCAGTAATCAAAACAGCATGATATTGCTAAAAAAAATAGAC 2190
                              ii  v          i    ii  i  i  vi v  ii -     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGAC 289

  chr2_29271787_2   2191 ATATAGACCAATGAAACAGAATAGAGACCCCTGAAATAAAGCCACACAC- 2239
                                i     i  i     v    vi  v        v   i   i-
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_29271787_2   2240 ---AACCAACTGATCTTTGACAAAGCTGACAAAAATAAACAGTAGGGAAA 2286
                         ---iii   i    i  i     i v  v   i vi vv  i i      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_29271787_2   2287 GGACACTCTACTCA-TAGATGGTGCTGGGAAAACTGGCTAGCCATATGCA 2335
                          i i v   vi   -i i            v      v  ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_29271787_2   2336 GAACAATGAAACTGGACCCCCACTACTCACTATATACAAAAATTAACTCA 2385
                         i  v      ii        i  iv v   i                   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_29271787_2   2386 AGATGGATTTAAAATTTAAATGTAAGACCTCGAACTACAAAAATCCTAGA 2435
                          i      iv? i ii           v  vi     i    v  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_29271787_2   2436 CGAAAACCTAGGAAATACTCTTCTAGGCATTGGCTTAGGCAAAGAATT-T 2484
                         v      v    ?ivv v     vv i v    v        v iv  - 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_29271787_2   2485 GGGACTAAGTCCTCAAAAGCGAAGGCAACAAAAACAAAAATTGTCAAACA 2534
                         vi  -  v v vi       iv i         iv      v vi   iv
  L1M4_orf2#LINE/    590 TAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_29271787_2   2535 GGACCTCATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACA 2584
                             i    i   v v  i i   i  ii vv    i  v        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_29271787_2   2585 GAGTAAACAGACAACCTACAGAATGGGTAAAAATA----CAAACTATGCA 2630
                         i   i  v        i          vi      ----    ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_29271787_2   2631 TCCAACAAAGGACTAATATCCAGAATCTATAAGGAATGTAAACAAATCAA 2680
                           ii i  i     vi          v     i   ivivv    v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_29271787_2   2681 CAAGAAAAA---AAAT--CCCA--TTAAAAAGCGGCAAAGAACATGAACA 2723
                         i  v     ---    --    -- ?     vv       i iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_29271787_2   2724 GACACTTCTCAAAAGAAGACATACAAGCAACCAACAA--ATATAAAAA-A 2770
                             i     v        i      iiii    i  -- i  i    - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_29271787_2   2771 TGCTCAACGTCACTAATCAT 2790
                                 i   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (138 / 85)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.94 (35 / 18)  


3191 24.40 2.98 0.48  chr2_29304422_29306397.rev      637  1476 (500)    L1M4_orf2#LINE/L1        1   861 (47)  

  chr2_29304422_2    637 TGGAGAGATAGTCCATGTTTATAGGTAAAAAGACTAAATATT---AACAT 683
                             i     vi       i  i i vii      v      ---  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_29304422_2    684 GTCAGTTCTTCCCAACTTGATCTATATAGTCAATGCAATCCCAATTAAAA 733
                          v  i v  i     v        i v v    i        v  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_29304422_2    734 TCCCAGCAAGTTATTTTATGGATATTGACAAACTGATTATGAAGTTTATA 783
                                vivi v    iii  v        i     iv i  i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_29304422_2    784 TACACAGGTGAAAGGCCTAGAATAACCAACACAACATTGAAGAAGCAGAT 833
                          iv v v ii ii i  i      i    v    iv     i   v   v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_29304422_2    834 CAAAACCAGAGGATTGACACTACTCAACCTGAAGAATTACTATAAAGCTA 883
                             iiii     i v     v i   ii v  i v      i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_29304422_2    884 CAGTAATCAAGACAGTGTGGTACTGGCA-AAAGATGAGACAAATAGATCA 932
                                                     -  i   -     v        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGATCA 299

  chr2_29304422_2    933 ATGAAACAGAACGGAGAGCCCAGAAATAGCCCAATATAAAT-TAGTCAAC 981
                            i  i    iv     i         iv  v   i vv - i     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_29304422_2    982 TGATCTTTGAAAAAAGAGCAAAGGCAATTCAATGGAAAAAAGACAGTCTT 1031
                             i  i  v  ii v  v   i v         ii   ii i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_29304422_2   1032 TTCAACACCTAATACTCGAACAACTGGACATTCACATGTGAAAAAAAAAA 1081
                                vv ii i  v i         i ?i      ii   i  vi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_29304422_2   1082 ATCTAGACACAGACCCTCACATCTTACCCAAAAATTAACTCAAAATGGAT 1131
                         i - i   v vv   -     i v  iv                      
  L1M4_orf2#LINE/    450 GT-TGGACCCCTACC-TCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_29304422_2   1132 CATAGATCT---TATAAGACACAAAACTATAAAACTCCTAGAAGATAACA 1178
                           ?   i  --- i     vvi               i       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_29304422_2   1179 CAGGACAAAAATCAGAGTGATCTTGGGTTTGATGATGACTT-TTAGATAA 1227
                         i   ?-iv     vvv    i        v iii   ii  -       v
  L1M4_orf2#LINE/    548 TAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_29304422_2   1228 AACACCAAA-GCACAATTCACAAAATAAAAAACTGATAACTCGGACTTCA 1276
                         i        -      viv      v      iv     v i        
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_29304422_2   1277 TTAAAACTAAAAGCTTCTGCTCTGTGAAATACACTGTTAAGAGAATGAAA 1326
                          i    i     i   i  iv  vii  iv     i i    i i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_29304422_2   1327 AGACAAGTCACAGACTGGGGGAAA-TAGTTGCAAAACACATGTCTGATAC 1375
                               vi      v    i    -  v       v  i  i       v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_29304422_2   1376 ATGTTTGGTATTCAAAATATACAAAGAAC-----------AACAAGAAAA 1414
                         iv vi v    i  i      i       -----------  i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_29304422_2   1415 TAGCAAACAG---AATTTTAAAATGAGCAGAAGATGTGAACAGGCACATC 1461
                         vii    i i---    ?v      i   i i   v    i  i  iv  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_29304422_2   1462 ATCAAAGAAGATACA 1476
                         vi           i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATA 861

Transitions / transversions = 1.64 (125 / 76)
Gap_init rate = 0.02 (13 / 861), avg. gap size = 2.23 (29 / 13)  


1439 24.16 21.71 4.39  chr2_29606440_29608656      952  1725 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_29606440_2    952 TGAAAATTTATCATGTGTTAA-GGACTGGAAGACTCACTATAGTTAGAAT 1000
                           i   vv    vii    v -   i         i v   v    ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_29606440_2   1001 GTCAGGTCTCCTCAAAT----CTGTAGATTAAACTTAATCCCAATCAAAA 1046
                          v  ivv    i     ----  ii     v   vi      v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_29606440_2   1047 TCTCAGCAGAATTGTGTGTATTTGTACTGTGTGACAATTTATGAGATGAT 1096
                           i    -----  iv v -    i ------  -    v ii  v    
  L1M4_orf2#LINE/    101 TCCCAGC-----TGCCTTT-TTTGCA------GA-AATTGACAAGCTGAT 137

  chr2_29606440_2   1097 TCTAAAATACACGTAGAAATGCAAAAGGCAAAGCATGGCAAAGATGATCT 1146
                         i       v  ii i         ii i vv  v  i  v  i ii    
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_29606440_2   1147 TGAA------GAACAAAGTTGGAGCACTTACAGTACCAGATATCAAGACA 1190
                             ------              v   i   v v  vi  v    i  v
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_29606440_2   1191 TATTATAAAGCTCCTGTATTTAAAACAGTGTGGTACTTGTGCAAATATAG 1240
                           i  i      v v   v i  i             v iii  iv    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_29606440_2   1241 ACAAACAGA-----GAAGTTTGTCTTCTCTGAAT-GA-AGTCCAGGAACA 1283
                            v i   ----- i i v----------    -  -       i  i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATA----------GAATTGAGAGTCCAGAAATA 327

  chr2_29606440_2   1284 AACCTATTC--TTAAAACCACCTGATTCACAGCAAAGATGCCATTGCAAT 1331
                             i  v --   viii  vi     iv ii   i i     vvi v  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_29606440_2   1332 GCAGTGGAGAAAGGAGAATCTTTTCAACA--------------------- 1360
                         v  i   i     i v i           ---------------------
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_29606440_2   1361 TA--------------AATGAG------CCTATACCTC--------TAC- 1381
                           --------------     i------  iv      --------   -
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_29606440_2   1382 ----TTAATGCTAAATGAATTATAGACCTAAATGTGAAAGGAAAAACAAT 1427
                         ----    iv v     i  i ?            i i  vv     v  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_29606440_2   1428 AAAGTTTCTAGAAGATGACATAGAAGAATATATTTATGATATCAAGGTAA 1477
                            ii ii       vi      i? v v  v  ii   iv iii v  i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_29606440_2   1478 GTAAAGATTTCTTGAATAGGATATAAAAAGCA------------------ 1509
                          i  v i      ii   v  i iv       ------------------
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_29606440_2   1510 -------------------------------------GT----------- 1511
                         -------------------------------------  -----------
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_29606440_2   1512 -----------AAATGGAAAGGCAAGCCACAGATTTGGAGAAAATATCTG 1550
                         -----------  i  i    i   v       v v           i  
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_29606440_2   1551 CAATATTCACAATGTATACATCT--TAAGG-ACTGTTGTCTGTAATATAT 1597
                            -  i--------   i    --     -   vv i  iiv       
  L1M4_orf2#LINE/    728 CAA-ATC--------ATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_29606440_2   1598 AAAGAAGCCCTAAAA-TCATTAAGAAAAATACAAACAATACAAC--AAAA 1644
                               vi i  v  -   v   v     v     i  iv   i--    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_29606440_2   1645 AAGGGTAAAAAGACTTGCACAGGAC----CTTCACAAAAGA------AAT 1684
                          v   i   i-  i   v i  -  ----  i  v i    ------   
  L1M4_orf2#LINE/    819 ATGGGCAAAG-GATTTGAATAG-ACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_29606440_2   1685 ATTCAATAAGCATATGAAAGG-TGTTCAAAATCATTACTCAT 1725
                         ivi         i      i -  i    v    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (110 / 75)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 6.73 (202 / 30)  


1001 23.06 14.44 1.11  chr2_29646222_29648928      144   503 (2204)  C L1M4_orf2#LINE/L1   (0)   908   501  

C chr2_29646222_2    503 AGACCTAAAC--AAAATCTAAAGCTATTATAACATTTCTGGAATAAAACA 456
                                  i--  i v     --- i     v i ii i   v      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAA---ACTATAAAACTCTTAGAAGAAAACA 547

C chr2_29646222_2    455 TAAGAGAAAATTATTGCAGACTTGGGTAAGAAAAAACTTTTTTAGATAGC 406
                           i ? v    iv i iiiv       v  iv  viv   i       vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

C chr2_29646222_2    405 ATACAAAAAGCATAAACTATAAAACAAAATATTGATCAATAGGAATTTAT 356
                          i  v       i  i v i    v    v  v   v   v   v  i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

C chr2_29646222_2    355 CAAAATTTAAAACTTTTAAATATTCAAAAGATTCCATTTGAAAAATCAAA 306
                                v         ivii-      i  iv i  ivii   i v   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGAAA 696

C chr2_29646222_2    305 ATACAAGCCACAGTGTGGGAGAAAATATTAGCTATACTTACATCTGA-AA 257
                          v    v      vi              v  v vv v  i      -  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chr2_29646222_2    256 AGAACTTGTACCCA------------------------------------ 243
                         i i       i   ------------------------------------
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chr2_29646222_2    242 ----------CCCAATT---AAGTGGGCAAAATATTTTAATAGACGTTAC 206
                         ----------       ---  i        iv    v       i  v 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chr2_29646222_2    205 ACTAAAGAAGATATACAAATGGCCATGAAACATATGAAAAGATGCTCAAC 156
                         v i                      vv  i  i                 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chr2_29646222_2    155 ATCGCTAGTCAT 144
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (43 / 39)
Gap_init rate = 0.01 (6 / 408), avg. gap size = 9.33 (56 / 6)  

3279 26.46 0.66 0.55  chr2_29646222_29648928     1309  2215 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_29646222_2   1309 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1358
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_29646222_2   1359 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCGTCCCCATCAAGC 1408
                            v     v     iv i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_29646222_2   1409 TACCAATGACTTTCTTCACATAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1456
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_29646222_2   1457 TACGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 1506
                           i    viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_29646222_2   1507 AACAAAGTTGGAGGCATCACACTACCTGACTTCAA--CTATACTACAAGG 1554
                                       vv       v  ii i     --  -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_29646222_2   1555 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 1604
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_29646222_2   1605 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 1652
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_29646222_2   1653 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 1702
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_29646222_2   1703 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1752
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_29646222_2   1753 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 1802
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_29646222_2   1803 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1852
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_29646222_2   1853 CCTAGGCATTACCATTCAGGACTTAGGCACGGGCAAGGACTTCATGTCTA 1902
                          v    ?i v viv   iv   i v  vvii     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_29646222_2   1903 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 1952
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_29646222_2   1953 ATTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 2002
                           i   v v  v i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_29646222_2   2003 CAGGCAACCCACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 2052
                         v  i         i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_29646222_2   2053 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 2102
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_29646222_2   2103 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGAAATGAACAGACACTT 2152
                           i     i     v  i?    i           vv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_29646222_2   2153 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 2202
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_29646222_2   2203 CATCACTGGCCAT 2215
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


 321 16.46 2.53 1.27  chr2_29768275_29771869     1389  1467 (2128)    L1M4_orf2#LINE/L1        1    80 (828)  

  chr2_29768275_2   1389 TGGAAAGA-ATACTAAGTTCATGGATTGGAAGTCTTAATATAGTAAAGTT 1437
                                 -  v i v                v        v  v   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_29768275_2   1438 GTCAAT-TTCCCCAAAATAGATATATAGGTT 1467
                          v    -i        - v   v  i  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATT 80

Transitions / transversions = 0.44 (4 / 9)
Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.00 (3 / 3)  

1955 22.76 7.17 9.87  chr2_29768275_29771869     2212  3103 (492)    L1M4_orf2#LINE/L1       41   908 (0)  

  chr2_29768275_2   2212 TTGTTACAGCGGCCACACG----AAACTAATACA-AGGTTTAGCACAATT 2256
                               viii   v i  v----   i i  vi -  i  i i i    i
  L1M4_orf2#LINE/     41 TTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chr2_29768275_2   2257 CCTATCAGAATCCCAG--------------GAA-----------GATTCT 2281
                                i        --------------   -----------   i  
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_29768275_2   2282 --------TGTGAAAA----AGGAACT-AGAATAGCTAAAATACTTCTGA 2318
                         -------- i  i   ----   i  i-        i    i v ii   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_29768275_2   2319 AAAAGAAGAATAAAGTGGGAAGAATTGCTTTACCTGAATTCAAGA--TAC 2366
                                   i     v   i  v ii vi v  ii v     i --   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_29768275_2   2367 TATATAGCTACAGTAATCAAGACA-TGTGGTGTTGGGGGAGGAATATACA 2415
                           i v                   -      ii   viv i i   v   
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_29768275_2   2416 CATAGATCAATGGAAT-GAAATGAGAACACAGAAACAGACACATACAAAT 2464
                         i               -   v     iiv      i i  v      vv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_29768275_2   2465 ATGCCCA-T--ATTCTTGATAAAGGTACAAAAACAGCTCAATAGAGGAAG 2511
                            vi  - --   i i  i  i   i v  i  vii     i i i   
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_29768275_2   2512 GATAGGCTTG-CAACAAATAATAAATGGTCTTGGAGCAATTGGACATCCA 2560
                         i    v   v-        -------   vi   ii   i    i ?   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAAT-------GGTGCTGGGACAACTGGATAKCCA 433

  chr2_29768275_2   2561 GAGGCCAAAAATAAAGAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA 2610
                         v v  ---------------------------------------------
  L1M4_orf2#LINE/    434 CATGC--------------------------------------------- 438

  chr2_29768275_2   2611 AAAGAAAAGAAAAGAAAGATAAAGAAAAATGGAGAAGAAACAAATGACCT 2660
                         ---------       --- i   v----    ------- ------  i
  L1M4_orf2#LINE/    439 ---------AAAAGAA---TGAAGT----TGGA-------C------CCC 459

  chr2_29768275_2   2661 TAGGTCAGAATTTTTAGTTAATAAAAGCTAACTCAAAATGAATCATGGAC 2710
                           vv   v viv v  -----i    ii            i    ?i   
  L1M4_orf2#LINE/    460 TACCTCACACCATATA-----CAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_29768275_2   2711 TTAAATGTAAGATGTAAAATTATAACACT-TTAAAAAAA----TAGGATA 2755
                         i           vv     i     v   -   i  i  ----    ?vv
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_29768275_2   2756 AAATTTTGAGGAAGTAGGGCAACAGAAAGAGTTCTTAGACTTGGCACCAA 2805
                             i  viv  vv v   iv viv  v iv        iv  i      
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_29768275_2   2806 AAAACACTATCTATAAAAGAAAAATTTGGTAAATTAGATTTCATCAAAAT 2855
                           i-   v v v i          v v i      i  i           
  L1M4_orf2#LINE/    605 AAG-CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_29768275_2   2856 TAAAAACTTTTGCTCTGCAAAAAGATCCTGTTTATAGGATGAAAAGATAA 2905
                                     iv  v    i-  iv  i iv v iii        i  
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_29768275_2   2906 GCTGCAGACTGGGAGAAAATATTTACAAACCACACTTCTGAGAAAAGACT 2955
                         v ii    v               i    i  i iv     v  ii    
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_29768275_2   2956 AGTATCTAGAATATTTAAAAACCTC--AAAATTCAACAATTAAAA----- 2998
                         v     i       v    i v   -- v  i    i   v    -----
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_29768275_2   2999 ATATTCAAATTAGAAAACAGGCAAAAGATTTAAAGGCACATTGTATCAAA 3048
                            vi v    ?i    ii      i     i  viv     vivi    
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_29768275_2   3049 AAGGATAAACAGCTGGAAAATAAGCACACGAAA-GATGTTAAATATCATT 3097
                         i i    v   iv   vv          i    -    i v  i    ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_29768275_2   3098 AACTAT 3103
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.49 (119 / 80)
Gap_init rate = 0.03 (27 / 868), avg. gap size = 5.63 (152 / 27)  


3587 22.48 2.06 1.49  chr2_29994492_29998527     2665  3536 (500)    L1M4_orf2#LINE/L1        5   881 (27)  

  chr2_29994492_2   2665 AAAATATCCTGTATTCATGGATTAGAAGAAT--GTCTTCTTAAAATGTCT 2712
                           i      ii i          i     v --i v  v    i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_29994492_2   2713 GTACTACCCAAAGTGATCTACAGATTCAATGCAACCCCTATCAAAATTCC 2762
                         i    v      v                i    i            i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_29994492_2   2763 AATGACATTTTTTCACAGACATAGAGAAAGCAATCCTAAAATTCATATAG 2812
                          iivi v      -i    v  v  v  ivii                i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_29994492_2   2813 AACCAGAAAAGACCCAGAATAGCCAAAGCAATCTTGAGAAAAAAAAA--- 2859
                           viiv  ii                 i         i   i  i  ---
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_29994492_2   2860 AACTGGGGGCATCACACTACCTGATTTTAAAATGCACTACTAAGCTTTAG 2909
                          ii   i  vv       v  ii    i    ivi     v     vi  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_29994492_2   2910 TAATCAAAACA---TCATACTGGCACAAAAACAGATGTATAGAGCAATGG 2956
                                i   --- vi        i  ii i   ii      v      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_29994492_2   2957 AACAGCAA--GAGAGCCCAGAAATAAATCCACACATTTCCAGTTAATTGA 3004
                           i  -  --     i           i   i      vii  i      
  L1M4_orf2#LINE/    304 AATAG-AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_29994492_2   3005 TCTTTGACAAAGGTACCAAGAACATACAATGAGGAAAAGGATAGTCTGTC 3054
                          i  i     i   i      v   v     i     - i       v i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTT 401

  chr2_29994492_2   3055 TAAGAAAGAGCATTGGGAAAACTGGGTATCCATACGCAGAAGAATAAA-T 3103
                         i  v   vi iii     v      i  ?   i i   i      i  - 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_29994492_2   3104 TGGATCTTTATCTCGCCCCATATACAAAAATCAACTTGAAATGGATTAAT 3153
                             i ii  i   i v              i    ii        i ?v
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_29994492_2   3154 GACTTAAATGTAAGACCTGAAACTGTAAAACCACAAGAAGAAAACATAGA 3203
                            i           v  i     i      iviv              i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_29994492_2   3204 GGAAAAGCTTTTTGACATTCATTTGGGCAATGTTTTCTTGGATATAACTT 3253
                         ? v   v   iv    v  viv  i       v      i     i  vi
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_29994492_2   3254 CCAAAGCATGGGCAACAAAAGCAAAAACAGACAAAAGAGATGGCATCAAA 3303
                          v      iii          v     i   i   vvi  ivv       
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_29994492_2   3304 --TAAAAAGTTAAGCTGCTTCTACACAGTGAAAGAAACAATCAACACAGT 3351
                         --      v  vv -      --------i  i  v  v     v v   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTG-TGCTTC--------AAAGGACACTATCAAGAAAGT 692

  chr2_29994492_2   3352 GAAGAGACAGCCTGTGGATTGAGAGAAAATACTTGCAAACCATACATGT- 3400
                            i     i  iiii  v  i         i       i    i  v -
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_29994492_2   3401 ATAAAGTGGTTAATGTCCAAAACGTATAAAGTACTCAAACAACTTAATAG 3450
                             i - ii vi i    i  ii       v    vv      i    i
  L1M4_orf2#LINE/    743 ATAAGG-GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_29994492_2   3451 TAAGAA----AATGACCCAATTTAAAAATGAGCAAATGACCTGAAAAGGT 3496
                            i  ----   i        ?       i     v  ii    v  ii
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_29994492_2   3497 ATTTCTCAAAAGAAGATATACAAATGGCCAATAAGAATAT 3536
                                v                           v i  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 1.91 (126 / 66)
Gap_init rate = 0.02 (14 / 877), avg. gap size = 2.21 (31 / 14)  


 814 23.10 7.59 1.27  chr2_30093412_30095713      211   526 (1776)    L1M4_orf2#LINE/L1      526   861 (47)  

  chr2_30093412_3    211 ATAAAAATCTTAGAAGAAAATCTAGGAAAAACTCTTCTGGACATTGGCCT 260
                               v             iv    ?iv  v     vv   v    vi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_30093412_3    261 CAGCAAATAATTTAT--GACTAAGACCTCAAAAGCAAATGCAACAAAACC 308
                         vi    - ii   v --  -  v   vi        v v         vv
  L1M4_orf2#LINE/    576 AGGCAA-TGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_30093412_3    309 AAAAATAGACAAATGCAACTTAATTAAACTAAAAAGATTCTGTATGGCAA 358
                                  i    vvi    v  i   v v    iv  i   iivv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_30093412_3    359 AAGA-A--ATCAATAGAGTAAATAGATGATCTAAAGAATGGGAGAAAATA 405
                          i  - --     v i   i  v   ii i i v                
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_30093412_3    406 TTTGTAAACTATGTGTCAGACAAAGGACTAATATCCAGAATCTACAATGA 455
                             i   ii  i i  v  i  i     vi          v  i  v  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_30093412_3    456 ACT-----AA----ACAAGAAAAA-ACAAATAATCTCATTTAAAAGTAGA 495
                            -----  ---- i  v     -        i iv   ?    i i i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_30093412_3    496 CAAAG-ATTTACAATAG--------CCAAAGAATGAAATA 526
                              -    i-     --------        -  v   
  L1M4_orf2#LINE/    824 CAAAGGATTTG-AATAGACATTTCTCCAAAGAA-GATATA 861

Transitions / transversions = 1.09 (37 / 34)
Gap_init rate = 0.04 (12 / 336), avg. gap size = 2.33 (28 / 12)  

 822 26.18 2.18 3.64  chr2_30093412_30095713      620   894 (1408)    L1M4_orf2#LINE/L1        2   272 (636)  

  chr2_30093412_3    620 GAAAAAATATTCTATGTTCATGGATTAGAAGAATCAATATTGTTATTAAT 669
                          i   i    i i             i     v i          -----
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA----- 46

  chr2_30093412_3    670 AAAATAGCCATACTGCTCAAAGCAATTTATAGATTCAATGCTATTCCTAT 719
                         - i  i  v     v i    vii  i  i        i  v  i     
  L1M4_orf2#LINE/     47 -AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_30093412_3    720 CAAAACACAAACATCATCTCTCACAAAATTAGAAAAATATATTCTAAAAT 769
                              iv v i vv v i i ii  i  v v  v  iivv  i       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_30093412_3    770 TCATACAGAA--CCAAAGAACACCCAAAATAGCCAAAGAAATCCTAAGCA 817
                              ii   --v   i i  --   i          iv    i i -- 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGA--A 191

  chr2_30093412_3    818 AAAAAAGAA---AGTTGGAGGCATCACATTACTTGACTTCAAACTATACT 864
                            i     ---         vv     i v iii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_30093412_3    865 TTAAGAATACAATAACCTGGCCAG-GTGGTA 894
                         vi  iiv    i   i vi v   -      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

Transitions / transversions = 1.77 (46 / 26)
Gap_init rate = 0.02 (6 / 271), avg. gap size = 2.67 (16 / 6)  

2225 25.00 4.88 0.30  chr2_30093412_30095713     1155  1810 (492)    L1M4_orf2#LINE/L1      223   908 (0)  

  chr2_30093412_3   1155 CTCCATTTCAAAA---A--AAAAAGGACTACAATAACCGAAACAGCAGGG 1199
                          i v         --- -- v    --     i   i i i    iiv  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAG--CTACAGTAATCAAGACAGTGTGG 270

  chr2_30093412_3   1200 TGCTAGTACAAAAACAGACACATAGCCCAGTGGAACAGAATACAGAACCT 1249
                          i  i i i  ii i     i    vi  i     i     vv   ii i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_30093412_3   1250 ACACATAAACCTGCACACCTATGACCATCTGATCTTCAATGAAATCAATA 1299
                          v v       iii   ii    ii  vi    i   i ii iiviivi 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_30093412_3   1300 AAAATAAGCAGTAGGTAAAG--TA-----TTTAATAAATGGCGCTGGGAT 1342
                          i vi vv  i i  v    --  -----  i  i      i       i
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_30093412_3   1343 AACTGGCTAGCCATATGCTGAAGAATGAAACTGGACCCCTACCTCTCACC 1392
                               v  ?   i    vi         ii              v    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_30093412_3   1393 ATATACAAAAATTAACTCAAGATGGATTAAAGATTTAAATGTAAGACCTA 1442
                                             i      i ?   ii           v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_30093412_3   1443 AAACTATAAAA-TCCTAGAATAAAACCTACGAAATACTCTTCTTGACATC 1491
                                    -  i     v     v  v ?ivv v     v    v i
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_30093412_3   1492 AGCTTGGGCAAAGAATTTATGGCTAAGTCTCCAGAAGCAACTGCAACTAA 1541
                         i v  i     v iv  iv i v  v v v   i     vvv     v  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_30093412_3   1542 AACAAAAATTGACAAATGGAACCTAATTAAA-CTAAAA---TCTGCATAG 1587
                          iv      v  i    v i  i v  i   -i     --- i  iiivv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_30093412_3   1588 CAAAAGAAATTGCCAACAGAA--AACAGAGAGCCTACAGAATGGGAGACA 1635
                             i  v i ii   v i i--  v   v i  i             v 
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_30093412_3   1636 ATATTTGCA---------TCTGACAAAGGTCTAATATCCAGAATCTGCAA 1676
                                  ---------     i  i  v  vi          v ii  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_30093412_3   1677 GGAACTTAAACATGTCAATAAGCAAAAAACAAATAACACAATTAAAACAT 1726
                         i     ivv   vv       vv    i         v     ?   v  
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_30093412_3   1727 AGGCAAAGGATACGAACAGACACCTCTCAAAAGAAGACATACAAATGGCC 1776
                         i          vi   i     ii    v        i            
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_30093412_3   1777 AA----CATATGACAAGATGCTCAACATCACTATTCAT 1810
                           ----  i    v                ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (96 / 64)
Gap_init rate = 0.02 (11 / 686), avg. gap size = 3.09 (34 / 11)  


3155 26.78 1.44 0.56  chr2_30133164_30139298     2197  3096 (3039)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_30133164_3   2197 TGGAAGAACATTCCATGCTCGTGGGTAGGTAGAATCAATATCATGAAAAT 2246
                              ii i  i     i  i   i v  v   v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_30133164_3   2247 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2296
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_30133164_3   2297 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2344
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_30133164_3   2345 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 2394
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_30133164_3   2395 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 2444
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_30133164_3   2445 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGGCC 2494
                                 i   i    ii         i iv ii i   v      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_30133164_3   2495 AATGGAACAGAAC--AGAGTCCTCAGAAATAATGCTGCATATCTACAACT 2542
                                i    i--       --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_30133164_3   2543 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2592
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_30133164_3   2593 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAGCT 2642
                           v  i  i              v      v  ?   ii  i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_30133164_3   2643 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGACGGA 2692
                            ii    i    v   i     v              i    i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_30133164_3   2693 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2742
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_30133164_3   2743 CTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 2791
                         v    ?i- v   -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_30133164_3   2792 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCAA 2841
                         vi            vvi          vv     v  i    v   iivv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_30133164_3   2842 ATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 2891
                           i   viv  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_30133164_3   2892 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCT---A 2938
                         v  i     i                 v       vii ivi    --- 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_30133164_3   2939 AGGG-CTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 2987
                             -  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_30133164_3   2988 AAAACAA----CCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTT 3033
                           i    ----   v  i? v  i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_30133164_3   3034 CTCAAAAGAAGACATTTATGCAGCCCAAAGACACATGAAAAAATGCTCAT 3083
                            v        i  vi viii   v v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_30133164_3   3084 CATCACTGGCCAT 3096
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  

4131 16.96 7.77 0.82  chr2_30133164_30139298     4795  5643 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_30133164_3   4795 TGGAAGGATATTCTGTGTTCATGTACTGGAAGACTTACTTTTATTGTTAT 4844
                              i     i ii        v i           v ---       -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT---ATTGTTA- 46

  chr2_30133164_3   4845 TAAGAGTTTAATACTTGCCAAATTGATCTACAGATTTAACATAATCCGTG 4894
                         --   vvvi      iv                   i   ii     v i
  L1M4_orf2#LINE/     47 --AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_30133164_3   4895 TCAAAATCCCAGCTGGCTTTTTTGGAGAAATTGATAAGCTGATGTTAAAA 4944
                                        v        v         i        vi     
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_30133164_3   4945 TTTATATGAGTATGTAGGGAATTCAAAATAGCTAAAACCAATCTTCATAA 4994
                           i     iiv   i i  i ii  i      i     -      v v  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AATCTTGAAAA 193

  chr2_30133164_3   4995 AGAA---CAAAGCTAGAGAACCTAC------CAATTTTAAAACTTAGTAC 5035
                             ---     i i   i  ii  ------      i        v   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_30133164_3   5036 AAAGTGACAGTAACCAAGGTACTGTAGTACTGTCATAAAAACAGACATGT 5085
                             iv       i    ii v   i      v     ii i      i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_30133164_3   5086 ACATCACTGGAATACATTTGAGAATCTAGAAATAAACCCTTACACTTATG 5135
                          v    v       v v      i  i            v    i     
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_30133164_3   5136 GTCAACTGATTTTTGACAAAGGGGCCAAGACAATTCAATGAGGAAAGAAC 5185
                              i       i     i  v        v        i        i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_30133164_3   5186 AGTCTTTTCAACAAATGGTGTTGGGGCACTTGGGCATCCACATGCAAAAT 5235
                                             i    i  vi   ii ?            v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_30133164_3   5236 AATGAAGTTGAACCACTACTTCACATCGTACGTAATAATTAA-----AAT 5280
                                   i   v    i     i i  iii  v      -----   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_30133164_3   5281 AAATAAAAAACCTAAATGTAAGAGCCAAAACTATATAACTCTTAGAAGAA 5330
                         ii  v ? i                i         v              
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_30133164_3   5331 AACACAGGTGTAAATCTTTATGACCTTAGATTAGACAATAGTTTTTTCGA 5380
                             i   ?         ii       i i    i    i    i  v  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_30133164_3   5381 TATGACGCCAAAAGTAAATGCAACCAAAGGAAAAA-AGA--AATTGGACT 5427
                               i       i v v     v    i     -   --         
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_30133164_3   5428 ACATCAAAATTATGAACTTTCGTGTTTCTAAGAACACTAAAAAGAAAGTG 5477
                         v           vi      i   i   v   i      vv         
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_30133164_3   5478 AAAGGACAA---------TGGG-----------------------TCTAA 5495
                            i     ---------    -----------------------   i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_30133164_3   5496 TA-----------TCCAGAATATATGAAGAATTCTCACAAC-----AACA 5529
                           -----------            i     i   i     -----  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_30133164_3   5530 TAAAGAAAAATAATCTAATTTTAAAATCAGCAAAGAATGTGTACAGACAT 5579
                         v     v      i i    ?v     vi      i  v  v i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_30133164_3   5580 TTCCACCAGAAAGACAGACAAATG-CCAATAAGCACATGAAAAGATGCTC 5628
                            iv v ii    i v       -                         
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_30133164_3   5629 AACATCATTAGCCAT 5643
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (92 / 48)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 5.62 (73 / 13)  


 658 27.06 15.36 2.56  chr2_30152362_30153900      501  1047 (492)    L1M4_orf2#LINE/L1      292   908 (0)  

  chr2_30152362_3    501 ATAGGCCAATAGAAT-GCAC--AGAGTC-AGAAACAGACCT-TG-ATGTA 544
                             ii    i    - v i--      -     i i   i- i-  v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_30152362_3    545 TAGGGAATTTGATAAATGATAGAGGTGGCAT-----TTCAAATAAGAAGA 589
                          i vv    -   vvvi  i ii    v  v-----     - ----- i
  L1M4_orf2#LINE/    342 TGGTCAATT-GATTTTCGACAAGGGTGCCAAGACCATTCAA-T-----GG 384

  chr2_30152362_3    590 GGAAAGA-TGGATTACTCAAAAGATGGTATTAGAGCAGATAGGCTCTCTA 638
                                - i vi vi    v i     ii i ii  - iv  v v? i 
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA-ACTGGATAKCCA 433

  chr2_30152362_3    639 TTTGGGGAAG---GAAAATAGATACCTGTCTCATATGA-ATAAAGAAAAT 684
                         iv  vii   ---   iv i  iv   ii    i iv -   v -     
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA-AAAAT 482

  chr2_30152362_3    685 T---TCTAGACGGAAAAAATACCTAAATGTAAAA-CCAAGCTACTTTAAA 730
                          ---  v i i   vv ? v            i - i  i--   v    
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA--ACTATAAA 530

  chr2_30152362_3    731 AAG--TGAAAGAAAATATA-----ATATTTTTATATCCTTGCGGTAAGG- 772
                          vv-- ii       i   ----- v  i  ii iv     -   v   -
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG-GGTTAGGC 579

  chr2_30152362_3    773 -ATG-----TTAAA------ATCAAAAATCATAA-------------AGA 797
                         -   -----   i ------ i     i-  i  ------------- i 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAG-CACAAGCAACAAAAGAAAAAA 628

  chr2_30152362_3    798 TAGATAAATCTGACTTTTTCAAGTGCTA--------TGTACT--AAAATA 837
                                  iv     iv    i-ii  --------   i  --   iv 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_30152362_3    838 TAGCATCAAATAATTTCAA-GA-AAC--------TGAGAGAAAATATTTG 877
                         i vi     iv  v vv  -  -   --------  i             
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_30152362_3    878 CAAAT-AC-TATC----AAAGAACTTGTACTCAGAATATGCAGAGAACTC 921
                              - i-    ----  i i       ii        ii i       
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_30152362_3    922 CTAGAAATCTATAAGAAAAGGACAAACTATCCAAT-AGAAAATAGTCTGC 970
                         i  v  v  v    v    i      iv i     -?i     i v viv
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_30152362_3    971 AGATATGAAAAAACAGTTCTT---GGAAGGTTTACAAATGAGGAATAAAT 1017
                         i   v    v i   v    i---i    i v        ivv     ii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_30152362_3   1018 AAATAGAAA-ATGCTCAGTCTCACTAAAAGG 1047
                          v  ii   -       iiv   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (90 / 55)
Gap_init rate = 0.06 (37 / 617), avg. gap size = 2.65 (98 / 37)  


3112 25.80 1.10 0.99  chr2_30234209_30236467.rev      861  1767 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_30234209_3    861 TAGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 910
                          i    v i        i        v  v   v i        v  ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA--- 47

  chr2_30234209_3    911 GATGACCATACTGCCAAAAGCAAACTACAGATTCAATGGAATTCCCATCA 960
                             i v     v  v   vii v            i v   i  i    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_30234209_3    961 GAATACCACCATCACTCTTCACAGAACTAGAAAAAACAATCCTAAAACTC 1010
                         i   v   v vv vi i  ii     v v  v  ivii         i  
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_30234209_3   1011 ATATGGAACCAAAAGAGAGACCACATAGCCAAAGCAAGACTAAGCAAAAA 1060
                                 viiv   i  vv viv         i   vvi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_30234209_3   1061 TAACAAATCTGGAGGCATCGCATTACGTGATTTCAAAGTATACTGTAAGG 1110
                         v      vi      vv  i  i v vii        iiv    ii  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_30234209_3   1111 CCATAGTCACCAAAACAGCTTGATGCTGGTATAAAAATAG-CACATAGAC 1159
                          i i   v i   i    iv  i i    i    ii    -  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_30234209_3   1160 CAATCGAACAGAATAGAGAACCCAGAAATAAAGCTAAATACTTACAGCCA 1209
                             v   i     v    ii           v i v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_30234209_3   1210 ACTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCC 1259
                          i    i   i    i vviv   i v   vv i         i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_30234209_3   1260 TATTCAACAAATGGTGCTGAGATAATTGGCCAACCACCTGTAAAAGAATG 1309
                          v                 i  i  i   vi ?    v  i         
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_30234209_3   1310 AAGCTGGATCCTCATCTCTCATCTTACACAAAAATCAACTCAAGGTGGAT 1359
                            i    i  ii i   v  i v  i        i       ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_30234209_3   1360 CAAAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACA 1409
                           ?    i     v     v  i    i      v ii       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_30234209_3   1410 TTGAAAAAACCCTTCTAGACACTGGCTTAGGAAAAGACTT------TATG 1453
                          v i?iv  vi    vv   vi   v     v  v ii  ------    
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_30234209_3   1454 ACCAAGAACTCCAAAGCAAATGCAACAAAAACAAAGATAAATAGATTGTA 1503
                           -----  - v      v v         iv   i   i   i    v 
  L1M4_orf2#LINE/    598 AC-----AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_30234209_3   1504 CTTAATTAAACTAAAAAGCTTCCGCATAGCAACAGAAAC-ATCAGCAGAG 1552
                            v  i   v v    i   ii iiivv   vi  v  -    iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_30234209_3   1553 TAAACAGACAACCCACAGAGTGGGAGAAAATCTTTGCAATCTATATATCT 1602
                          i  v              i           v       vii        
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_30234209_3   1603 GACAAATAACTAATATCCAGAACCTAGAAGGAGCTTAAATAAATTAGCAA 1652
                           i  ivi   vi         iv  v  i  i  ivv i  v i ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_30234209_3   1653 GAAAAA-ACAAACAATCCCACCAAAAAGTGGGCTAAGGACATGAATAGAC 1701
                         v     -     i  i  v ii?    i     v     iv         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_30234209_3   1702 AATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAA-ATGC 1750
                          v     v                       i  i  i       -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_30234209_3   1751 TCAACATCACTAATGAT 1767
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  


 756 25.78 11.92 8.03  chr2_30349361_30351117      500  1271 (486)    L1M4_orf2#LINE/L1      107   908 (0)  

  chr2_30349361_3    500 CTGCTTTGTTTTG---AACTAGACAATCTGATCTCAAAATTCCCTTGGAA 546
                             i  -     ---  v v     v      ii       viv     
  L1M4_orf2#LINE/    107 CTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_30349361_3    547 GCACAAAGGGCCAAGAATAACTGAGAAACAATTTTGAAAAAGTA---CAA 593
                         iii   i  i  v      i ii --      i         v ---   
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAA--AACAATCTTGAAAAAGAAGAACAA 203

  chr2_30349361_3    594 GGTGGAAGAACTTGCCCTACCAGATATCAAGATTTATTATCAAAATATTT 643
                         i  v i  i   ii v  v  vi  v    i i   i  -    ii- vi
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA-CAAAGC-TAC 251

  chr2_30349361_3    644 AGAAAAGAAGACAATATAGT-CTGCGCACAAGGATA-------AG--TAA 683
                           v  vv      i i i  -   -   i       -------  --i  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTG-GCATAAGGATAGACATATAGATCAA 300

  chr2_30349361_3    684 GGGAGCAGAATAAAGGGCCCAGTCACTGGCCTGCCCATGTTTGG--AAAG 731
                         v   ii     vi  i i    vv ivii  iiiv   v v   --  vv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_30349361_3    732 AAGATGGGGCAGAGATGATGTTACACGCCAGTGGGGAAAGGGTATTCTAT 781
                         i vv vv i  ii i  viivv  vvvi  i         ii  v   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_30349361_3    782 CTGATAAATGAGTGCTAGGAGCAACCTT---TATCCATATGGAAAATAGT 828
                         iii i     -     i   -    -- ---  ?   i   v    v i 
  L1M4_orf2#LINE/    401 TCAACAAATG-GTGCTGGGA-CAAC--TGGATAKCCACATGCAAAAGAAT 446

  chr2_30349361_3    829 A------GATTTCTACATCAGATCATTCCTGGGTGATCTTAAAAAAAAAA 872
                         i------  iii    v   v i   ---------  ----- v     v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCAT---------AT-----ACAAAAAT 482

  chr2_30349361_3    873 AAAAGCACAACTTTAAAACTTAAAAACTTAAAAAAAAAAGC-ACAACTTT 921
                         v  vv  v  --- ii -- i ? i  i    viv  i   - v    v 
  L1M4_orf2#LINE/    483 TAACTCAAAA---TGGA--TCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_30349361_3    922 AAAAC----AGAAGATGAAGACATAGAAAAATTCTTTGTAATTCTTTGTG 967
                              ----      --- i      i?---------    v    i   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGA---AAACATAGGN---------GTAAATCTTCGTG 565

  chr2_30349361_3    968 ACTTTAAGATG---AAGAGTTCATTTAAA---AACACTGAAAATAGAAAC 1011
                           i  ii v i---  vi   i-i   i ---i    ii   ii v  i 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTT-CTTAGATATGACACCAAAAGCACAAGC 614

  chr2_30349361_3   1012 TTGGGGTAAGTTTAATTTTAAAAGTGGTAATGTGGACTAGTACATTAAAA 1061
                         --iiviv   ---  ----    vv i   vv      -- -   i    
  L1M4_orf2#LINE/    615 --AACAAAAG---AA----AAAATAGATAAATTGGACT--T-CATCAAAA 652

  chr2_30349361_3   1062 CTCA---CTTTTGTACAACAAAGGCCATGAG-AACAAAGTGAAAAC-CAA 1106
                         i v ---       i vv      v  iv v-  v          v-   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_30349361_3   1107 GCCATAGACTGGAAGATAATATTTGCAA----------TGA--------- 1137
                         v   i   v   i   v           ----------   ---------
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_30349361_3   1138 ---ATACA--ATATGCAAAGCGATATCTCT---AATT-AATAAGAAAAAG 1178
                         ---  v  --    ii    ---- v    ---  i -     v      
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAG----AACTCTTACAACTCAATAATAAAAAG 798

  chr2_30349361_3   1179 ACAACATA-------TGGGGGAAAATGGACAAA--ACT---AT---CAAT 1213
                             -   ------- ?i---       i    -- i ---  ---  v 
  L1M4_orf2#LINE/    799 ACAA-ATAACCCAATTWA---AAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_30349361_3   1214 TCAC---AGAAAAACTCCA---GGTCAATAAAAATATAAAAAGATGCTTA 1257
                           v ---    i vv v  ---  i      iv i  i          i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_30349361_3   1258 CTTTCACTATTAAA 1271
                         viv   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (111 / 84)
Gap_init rate = 0.06 (49 / 802), avg. gap size = 3.14 (154 / 49)  


2743 24.55 7.78 0.60  chr2_30433293_30435119.rev      504  1338 (489)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_30433293_3    504 CATGTTTATGGATTGGAATCCTTCTTGAAGTTAAGATACCAATTCTCCGC 553
                               i           vv   vv ivv        iv    v    v 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_30433293_3    554 AAATTGAACTGTAGATGTAACACAATCCCAAGCCAAGGCACAGCAGGATT 603
                                v  ii    vi   i       v v v  iv v    v vv  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_30433293_3    604 CTTTGTGGATACAGGCAAGTGAATTCTAACACTTATATGAGAAGGTAA-- 651
                         i    ii  v iv i    ivi  i    v i i     ii  v i  --
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_30433293_3    652 ----------AGCCAAGGCAATTTTGGGAAAGAA---CAAATTTGGAG-A 687
                         ----------      ii    i   ii      ---    v      - 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_30433293_3    688 CTCACACTACCTGAT----------ACTATCAAGCTACAGTCATGCAAAC 727
                                 v  ii  ----------    iv          v  vv i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_30433293_3    728 AGTGTGGTATTGGTGAAAGGATAGACA------------GAATAAA---- 761
                                  i   iiv           ------------     i ----
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_30433293_3    762 -GAGTCTAGAAATAGACACACACAAATATGGTCAATTGATTTTTGGCAAA 810
                         -     i       i  v  i   vv                 i i   i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_30433293_3    811 GATATATAAAGGGAATTCAATGGAAAAAGGACAGTCTTTTTAATAAATGA 860
                          i iiv--   ivv         ii    i i        i  i     i
  L1M4_orf2#LINE/    364 GGTGCC--AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_30433293_3    861 TGTTGGAGAAATTTGATATCC-TATGCAAAAACAATTACCCTTGACCTGT 909
                           i   iiv  i v    ?  -i        i-   v vvi v    iv 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAG-AATGAAGTTGGACCCCT 460

  chr2_30433293_3    910 GCCTCACGT--TATAGAAAAGTGAATTAAAAATAGATCATGGACCTAGAT 957
                         i      ii--    v    i v  i v     i     ?i      i  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_30433293_3    958 GTAA-AGTATGTAACTATAAAACTCTTAGAAGAAAACA--GGAGAAAATC 1004
                             -  i- iv                          --  ? v     
  L1M4_orf2#LINE/    511 GTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_30433293_3   1005 GTTGTAATCTTGACTTAAACAAAGAGTTCTTAGATACGACAACCAAACCA 1054
                         v i  i i    iv   ii   v iv          i    v v   v  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_30433293_3   1055 TGCTCTATAAAAGAAAAAC--AATAAATTGGACTTTATCAAAATTAAACA 1102
                         iivv v i          v--i             i            v 
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_30433293_3   1103 CCTTTACTCTTGTGAAAGACATTTTAAAGAGAATGAGAAGAAAAGCTGCA 1152
                          i   iiv   -ii  i    i v v    i i   i    v  v ii  
  L1M4_orf2#LINE/    660 CTTTTGTGCTT-CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_30433293_3   1153 AACTGGGGGGAAATACTTGCAGATCACATATCAGACAACAGAC----ATC 1198
                         i v    i i     i     i    i     v  i  vi   ----   
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_30433293_3   1199 TAGACTATAAAAAGAACTCGTAAAAGT-AA-GATCAGAA-ACAACCAATT 1245
                         i   v    v         v  v  v -  -i  v i  -    vi  ii
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_30433293_3   1246 T--TTAAAAACTAGGCAA--GATTTGAAAAGATGCTTCACCAATTAAGAT 1291
                         i--  ?    v i     --        v   iii   v    vv     
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_30433293_3   1292 ATAGAAATGGCAAACGAATACATGAAAAGATGCTCA---TTAGTGATTAA 1338
                            v       v  ii ii                 --- i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (118 / 83)
Gap_init rate = 0.02 (22 / 895), avg. gap size = 3.18 (70 / 22)  


3176 26.43 0.66 0.66  chr2_30730410_30733583.rev     1775  2682 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_30730410_3   1775 TGGAAAAACACTCCATGCTCATGGATTGGAAGAATCAATATCGTGAAATT 1824
                               i i ii     i               v i     i  v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_30730410_3   1825 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCCATTAAAC 1874
                            v     v      vii  i           i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_30730410_3   1875 TGCC-GTTGACATTCTTCATAGAATTAGAAAAAACTC-TTTTAAAATTCA 1922
                          v  - i  v -  i  iii    v v  v  i-  v- ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_30730410_3   1923 TATGGAACCAACAAAAAGCCCATA-TAGCCAAGACAATCTTAAGCAAAAA 1971
                                vii-   iiii    v -       i        i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_30730410_3   1972 GAACACAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAGGG 2021
                              v  i      vv     i v  ii i      viv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_30730410_3   2022 CTACAGTAACCAAAATAGCATGGTACTGTTACAAAAACAGACACATAGAC 2071
                                  i   i i  ii        vi i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_30730410_3   2072 CAATGGAACAGAATAGAGAACTCAGAAATAAGTCCGTGCAACTACAGCCA 2121
                                 i     v    iii         ii  i i  vi  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_30730410_3   2122 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 2171
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_30730410_3   2172 TATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAACTG 2221
                          v  i  i              v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_30730410_3   2222 AAACTGGACCCCTTCCTTACACCTTATGCAAAAATTAACTCAAGATGGAT 2271
                           ii         v   i     v   i               i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_30730410_3   2272 TAAAGACTTAAATGAAAAACCCAAAACTATAAAAACCCTAGAAAAAAATC 2321
                         i ?    i      v  i v i            vi i     i    iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_30730410_3   2322 TAGGCA-ATACCATTCAGGACATAAGCATGGGCAAAGATTTCAT-GATGA 2369
                             ?i- v i -   iv   v vi vv i     v i    v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr2_30730410_3   2370 AGATGACAAAAGCAATTGCAACCAAAGCAAAAATTGACAAATGGGATCTG 2419
                         v  iiv        vvv     v    v      v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_30730410_3   2420 ATTAAACTAAAGGGCTTCAGCACAGGAAAAGAAACTATCATCAGAGCAAA 2469
                           i   v v  iii   iv ii vvv   i  v       vv i  ii  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_30730410_3   2470 CAGACATTCTACAGAAAGGGAGAAAATTTTTGCAATCTATCCATCTGACA 2519
                         v     vi i      v          v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_30730410_3   2520 AAGGTCTAATACTCAGAGTCAACAAGAAACTTAAACAAATTTACAAGAAA 2569
                          i  v  vi  ii    i vv i  ii    ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_30730410_3   2570 AAAA-AAACAACCCCATTAAAAAAGTGGGCAAGGGACATGAACAGACTCT 2618
                           i -   i     v   ?     -       i   iv    i    vi 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATT 844

  chr2_30730410_3   2619 TCTCAAAAGAAGACATTTATATGGCTAATAAACTTATGAAAAAAAGCTCA 2668
                             v        i  vi v     i     i vi       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_30730410_3   2669 ACATCACTGATCAT 2682
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.00 (12 / 12)  


3195 26.16 1.22 0.55  chr2_30740048_30742013      573  1474 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_30740048_3    573 TGGAAAAACACTCCATGCTCATGGATTGGAAGAATCAATATCGTGAAATT 622
                               i i ii     i               v i     i  v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_30740048_3    623 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCCATTAAAC 672
                            v     v      vii  i           i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_30740048_3    673 TGCC-GTTGACATTCTTCATAGAATTAGAAAAA--ACTCTTAAAATTCAT 719
                          v  - i  v -  i  iii    v v  v  i--iv  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_30740048_3    720 ATGGAACCAACAAAAAGCCCATA-TAGCCAAGACAATCTTAAGCAAAAAG 768
                               vii-   iiii    v -       i        i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_30740048_3    769 AACACAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAGGGC 818
                             v  i      vv     i v  ii i      viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_30740048_3    819 TACAGTAACCAAAATAGCATGGTACTGTTACAAAAACAGACACATAGACC 868
                                 i   i i  ii        vi i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_30740048_3    869 AATGGAACAGAATAGAGAACTCAGAAATAAGTCCGTGCAACTACAGCCAT 918
                                i     v    iii         ii  i i  vi  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_30740048_3    919 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 968
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_30740048_3    969 ATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAACTGA 1018
                         v  i  i              v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_30740048_3   1019 AACTGGACCCCTTCCTTACACCTTATGCAAAAATTAACTCAAGATGGATT 1068
                          ii         v   i     v   i               i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_30740048_3   1069 AAAGACTTAAATGAAAAACCCAAAACTATAAAAACCCTAGAAAAAAATCT 1118
                          ?    i      v  i v i            vi i     i    iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_30740048_3   1119 AGGCA-ATACCATTCAGGACATAAGCATGGGCAAAGATTTCAT-GATGAA 1166
                            ?i- v i -   iv   v vi vv i     v i    v -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr2_30740048_3   1167 GATGACAAAAGCAATTGCAACCAAAGCAAAAATTGACAAATGGGATCTGA 1216
                           iiv        vvv     v    v      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_30740048_3   1217 TTAAACTAAAGGGCTTCTGCACAGGAAAAGAAACTATCATCAGAGCAAAC 1266
                          i   v v  iii   i  ii vvv   i  v       vv i  ii  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_30740048_3   1267 AGACATTCTACAGAAAGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 1316
                              vi i      v          v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_30740048_3   1317 AGGTCTAATATTCAGAGTCAACAAGAAACTAAAACAAATTTACAAGAAAA 1366
                         i  v  vi   i    i vv i  ii    vvv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_30740048_3   1367 A-----ACAACCCCATTAAAAAAGTGGGCAAGGGACATGAACAGACACTT 1411
                          ----- i     v   ?     -       i   iv    i     i  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTT 845

  chr2_30740048_3   1412 CTCAAAAGAAGACATTTATATGGCTAATAAACTTATGAAAAAAAGCTCAA 1461
                            v        i  vi v     i     i vi       i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_30740048_3   1462 CATCACTGATCAT 1474
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


2638 25.09 3.58 3.35  chr2_30832516_30834435.rev      556  1420 (500)    L1M4_orf2#LINE/L1       28   894 (14)  

  chr2_30832516_3    556 GGAAG-CCCAATATT---AGGATGTCAATTCGCTCCAAATTGATCTATAC 601
                              - ii      --- i    v    v v i             i v
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chr2_30832516_3    602 ATTTGATTCAATTTCAATAAAACTCTCTGC-AAATTTTTAATAGAAATTG 650
                            ii iv    ii v  v   v  i v  -ivv     vii        
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chr2_30832516_3    651 ACAATCTGAGGCTAAAATTTGTATGGAAAGGCAAAGGAACTGGAATAGCC 700
                             v    vv        ii        v    i   v ii        
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_30832516_3    701 AAAACAATTTGGGAGAAAACAAAAGCAAAGTTGGAGGAACCATGCTACCT 750
                                 i v i --   v  i i             vi  ii  v  i
  L1M4_orf2#LINE/    178 AAAACAATCTTGAA--AAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_30832516_3    751 GATTTCAGGACTTACTATATTTATCATAAAACTATAGCAATGAGGTCAGT 800
                         i      ii        i ---------  i   i  i   v i v    
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACA---------AAGCTACAGTAATCAAGACAGT 266

  chr2_30832516_3    801 GTATGATTTTGGAGGGAAAAAGAAAAAAATAGATATGTCAATGGTACAGA 850
                           -- i vi   v--- v  i  v i v   --  vi       v i   
  L1M4_orf2#LINE/    267 GT--GGTACTGGC---ATAAGGATAGACATA--TAGATCAATGGAATAGA 309

  chr2_30832516_3    851 ATATAGAGTCCAGAAATAGATACACACAT--ATAGTCAACAACTTTTTTA 898
                           vv              i iv  i    --  i     iviv    iv 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_30832516_3    899 CACAAATACAAAGGAAATTCAGTAGAGAAAGGATAGTCTTTTCA-CAAAT 947
                           viii i v   ivv     i i i     i            -     
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_30832516_3    948 GGTGCTGAAACAATTAAATATGCATAGGCAAAA-AGTAAACCTCCAATCC 996
                                ii    i ii   ?v  i v      - i i  vi v-i i  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG-GACCC 458

  chr2_30832516_3    997 ATACTTCCCACTCCA-ATGTAAAAACTACCACAAAATGGATCATAAACCT 1045
                         v   i  v   --  -  ii     i  v v            ? i    
  L1M4_orf2#LINE/    459 CTACCTCACAC--CATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_30832516_3   1046 TAATGTAA-------AATTATAAAACTTCTAGAAGGAA-CACAGAAGAAA 1087
                         v       -------  i         ii      i  -  i  i? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_30832516_3   1088 ATCTTTGTGACTTTGGGCTAGGCAAAAATGTCCTCAACTCAATACTAGAA 1137
                              i     i     i       vii v  i vi ivii i  i i  
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_30832516_3   1138 GCATGATTCAGAAAAGAAAAAAATTGCTAAGTTG-ATTTCATCAAAACGT 1186
                            ii viv v           - v v   i   - i          -- 
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAA--T 653

  chr2_30832516_3   1187 TAATAACTTCTGTTGTTTGAAAGACACTGATAAGAGAGTGAAAAGACTAA 1236
                            v     i   vv  ii  i      ivi    i           v v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_30832516_3   1237 CCACAGACTGGCAAAAAACATTGGCAAATCACATATCCAAGAAAGGATTC 1286
                                v   v i    i   v        i     ii v  i   i i
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_30832516_3   1287 GTATCCAGAATATAAAAAGAACCCTCAAAACTCAATAGTAAGTAAAGAAG 1336
                                       v       i  i v         i   iv i v  i
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_30832516_3   1337 CAACTGAAATTTTTAAAAGGGAGGGCAAAT-ACTTG--TAA--------- 1374
                         i   iv  ---  ?    iv --      v- i   --  i---------
  L1M4_orf2#LINE/    804 TAACCCAA---TTWAAAAATG--GGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_30832516_3   1375 CAAAATAGATTTGTAGATGGCAAATAACTACTTGAGAAGGTGTGCA 1420
                             iv    v ii i     v     vi  v   i   i  iv  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.60 (131 / 82)
Gap_init rate = 0.03 (24 / 867), avg. gap size = 2.50 (60 / 24)  


3702 17.96 7.07 0.60  chr2_30860226_30862587     1036  1870 (492)    L1M4_orf2#LINE/L1       20   908 (0)  

  chr2_30860226_3   1036 CATGGAACAAAAGATTTTATATTGTGAAGATGGCAATATTCCCCAGATTG 1085
                               viii    i  v       v            i      i    
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chr2_30860226_3   1086 ACCTTTAGATTTAATGTAATCTCTATCAAAATCCCAG------------- 1122
                          i  vi     i  i i    i               -------------
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chr2_30860226_3   1123 --AAGCTGATAAATTGATTCTAAAATTTATATGTAAATGCAAGGAACCCA 1170
                         --  ii   i  ii    i        i     v          i     
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_30860226_3   1171 GAAGAGCCAAAATAGTCTTGAAAA-GTAAAATAAAGTTGGAAAACTCACA 1219
                            v        i i         - v i  i         ii       
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_30860226_3   1220 CTTCCTAATTTCAAAAGTTACTATAAAATTGTAGCAATCAACAAAGTGTG 1269
                              i          v      i   ii ii  i      v v      
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_30860226_3   1270 ATACTGGCATAAG-ATACACACATAAATCAATTGAACAGAAAGGAACGTC 1318
                         i            -   v   i   i      v   i    vv  iv   
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_30860226_3   1319 CATAAATACATTC------TTATATTAAATTGATTTTTGAAAAGGGTTCC 1362
                           v     v ii ------    iv v          i  v      v  
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_30860226_3   1363 AAGACAAAGAAACAGGAGAATGAATAGTTTTTTCAGCAACTGGTGCTGGG 1412
                              v vvv  ii  -   v       i      i   v          
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_30860226_3   1413 ACAAATGAATGA----ATGCAAAAGAATGAAATTAGAACGTTACTTCACA 1458
                             v  i  i?----               i  i  v vi   i     
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_30860226_3   1459 CCATATA-AAAAATGATCTCAAAATGGATCAAAGACCTAAATGTAAGAGC 1507
                                -      v v              ?                  
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_30860226_3   1508 TAAA-CTATAAAAC----AGAATAAA---TAG---------TT--TGACC 1538
                             -         ----    v   ---   ---------  --     
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_30860226_3   1539 TTGGGTTGGGCAATGATTTCTCAGCTATACCACCAAAAATAT--GTGACA 1586
                                i       i     i  v   iv        ii i-- ii   
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_30860226_3   1587 AAAGAAAACAATAGATAAATTAGACTCCATCAAAATTAAAGACTCATATG 1636
                                 -            i    i             i   iv i  
  L1M4_orf2#LINE/    619 AAAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_30860226_3   1637 CTACAGATGATGGCATCAA-AAACTGCAAAGACAACCTGCAGAAGGGGAG 1685
                           v  i v  iivi     -   v  v          ii     v     
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_30860226_3   1686 AAAAATTTTGCAAATCACATAT---ATAAGGAATTCGTATCTACAATATA 1732
                             vv           i    ---      i i i     i v      
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_30860226_3   1733 CAAAGAACATCTATAACTCCTCTGTAGTAAAAATATAAGTAACCCAGCTT 1782
                         i       vii  i     v---i  i      v i  i       ii ?
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCA---ATAATAAAAAGACAAATAACCCAATTW 814

  chr2_30860226_3   1783 AAAAATGGACAAAGAACT-AAATGAACATTTCGCC---GAAGATATA-AA 1827
                                 i     i i -i   ii       v  ---         -  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_30860226_3   1828 ATAACCCACAAGCAC-TGAAAAGATGCTCAAAATCATTAGTCAT 1870
                           ii  v i      -               v    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (96 / 51)
Gap_init rate = 0.02 (21 / 889), avg. gap size = 3.05 (64 / 21)  


3022 21.64 6.94 1.85  chr2_30926153_30929326     1819  2682 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_30926153_3   1819 TGGAGAGATATATCCGGTTCATTTATTGGAAGGCTCAATACTGCCAAGAT 1868
                             i      vi vv      vv        i  i    i  ii     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_30926153_3   1869 GGCAGTTTTTTCCAAATTTCTCTATAGGTTCAATACAATCCTAACCAAAA 1918
                             i vi ii       vv    i  i     ii      iv i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_30926153_3   1919 TTCTAGCATGCTTTTTTTTTGTTAGAAATTGATAAGCAGATTCTAAGATT 1968
                          i i   -   i      -- i-         i    v   i    i   
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTT--GC-AGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_30926153_3   1969 TATATCTAAATGCGAAGAACCTAGAATAACCAAAGCAATTTTATAAAAAG 2018
                         i    vv      i i i   i      i     i    i  i-      
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-AAAAAG 195

  chr2_30926153_3   2019 AAGAA-AAAACTGAAGGACTTACCCAACCTGACTTCAATACATATTATAA 2067
                              -   ii  i      i  v vv  ii i     v  v  i  i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_30926153_3   2068 AGCTAC--------------TGT---ACTGGCAAAAATATAGACAAATAG 2100
                               --------------   ---       v  iv       v    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_30926153_3   2101 ATCAATGGAGAAGGGTAGAGAATCTAGAA-TAAATCAACACATATATGGC 2149
                                  iv  ii v    i  i    -    i v i    v     i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_30926153_3   2150 CAATTAATTT--GAGAGAGGTTTCAAGGCAATTCAATGGGGGAAAGAAAA 2197
                              i    --  v ii   vi    i v           -      v 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chr2_30926153_3   2198 GTCTTTCCAAAAAAATGGTGCTGGATCAACAGGATTTCTAAATGGGAAAA 2247
                               i   v   -         iv    v    v? i v   v-    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGC-AAAA 442

  chr2_30926153_3   2248 GTACAAACAAACATGGATCT-TACTTCACACCACACACAAAAACCAAGTC 2296
                          ----  ii  vv    i i-   i        i i       ii  v  
  L1M4_orf2#LINE/    443 G----AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_30926153_3   2297 AAAATG-ATCACAGACCTAAAGGTAAAA-CTTAAATTATAATACTTTCAG 2344
                               -    ?         v    i -  v   i     v   i i  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_30926153_3   2345 AAGAAAACAT------------TTGCAAACTTGGGGTAGGTAAATGTGTT 2382
                                   ------------ i ii v      v    i  vv  v i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_30926153_3   2383 TTTGATAGAATACAAAAAATATGAGCCATACAAGAAAAAAAATTGATAAA 2432
                           v    vi i  v    ii ii   - -    i i       v      
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGC-A-ACAAAAGAAAAAATAGATAAA 636

  chr2_30926153_3   2433 TTAGACTTCATCAAAGTT----------------TAAAAGACACCATTAA 2466
                           i            i  ----------------i   i     i  i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_30926153_3   2467 AAAAACAAAAATGCAAATTTCAGACTACGTGAAAATATTTGCAGCACGTA 2516
                         i   iii    vi   viiv    v iv v             ivv i  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_30926153_3   2517 TATCAGACAAAGGACTTGAATCCACAACATATAAAGAACTCTTACAAATC 2566
                             v  i  i       v     v  i                   v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_30926153_3   2567 AATAATCAGAA---AAAAAACCCACT---AAAATGGCCAAAAGATTTGAA 2610
                               v i  ---   v      v ---       v    i        
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_30926153_3   2611 --GACACATCACCAAAGAGTATATAAAAACAAGCAATAACCCAACTTGAA 2658
                         --    iv  v       iv     v   iiiv      v --  v    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC--ACATGAA 884

  chr2_30926153_3   2659 AAGATGTTCCACATCATAAGTTAT 2682
                               i  v      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (112 / 73)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.17 (76 / 24)  


3181 27.32 1.00 0.55  chr2_30948960_30954093     3739  4642 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_30948960_3   3739 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATAGTGAAAAT 3788
                              ii i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_30948960_3   3789 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3838
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_30948960_3   3839 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3886
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_30948960_3   3887 TATGGAACCAAAAAAGAGCCTGTATCACTAAGTCAATCCTAAGCCAAAAG 3936
                                viiv  ii  v  v v  vi i  iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_30948960_3   3937 AACAAAGCCGGAGGCTTCATGCTACCTGACTTCAAACTATACTACAAGGC 3986
                                ii     vi   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_30948960_3   3987 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGATC 4036
                                 i   i    ii         i iv ii i   i         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_30948960_3   4037 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 4084
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_30948960_3   4085 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4134
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_30948960_3   4135 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4184
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_30948960_3   4185 GAAACTGGATCCCTTCCTTACTCCTTATACAAAAATTAATTCAAGATGGA 4234
                            ii    i    v   i  v  v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_30948960_3   4235 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4284
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_30948960_3   4285 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4333
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_30948960_3   4334 AAACACCAAAAGCAATGGCAACAAACGCCGAAATTGACAAATGGGATCTA 4383
                         vi            vvi        v vvi    v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_30948960_3   4384 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 4433
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_30948960_3   4434 CAGGCAACCTACAGAATGGGAAAAAATTTTTGCAACCTACTCATCTGACA 4483
                         v  i     i           i     v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_30948960_3   4484 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4533
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_30948960_3   4534 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAAGAGTCACCT 4579
                           i    ----   v  i?    i    ii      v    v  v  ii 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_30948960_3   4580 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 4629
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_30948960_3   4630 CATCACTGGCAAT 4642
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3512 20.33 4.35 1.65  chr2_30976857_30978863      667  1517 (490)    L1M4_orf2#LINE/L1        1   874 (34)  

  chr2_30976857_3    667 TGAAAAGACATACCATGTTCACGTATTAGAAGACTTCATCTTGTTAAGAT 716
                           i     i  v         i v   i        v  v          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_30976857_3    717 GGCAATACTACTCAAGTTGATCTACAGGTTAGGTG------------AGA 754
                                  v i   i           i  viii ------------ i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_30976857_3    755 TCTCAGTTGCTCTTTGTGTGCAAATTTGTAAGCTTGTACTAAAATTAATA 804
                           i   i   ii   v  iiv     vii     vi v        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_30976857_3    805 TGGAAATGCAAATTACCCAGAATAGCCAAAACAATCTTAAAAAAGAATG- 853
                                    ivv                        i        vi-
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_30976857_3    854 CGA--TTGGAGGACTTACATTTCACAATTTCAAAATTAACTACAAAACTA 901
                          i --          i   i   v           i v        i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_30976857_3    902 TAGTGATCAAGACTCTATGTTACTAGCATAAGCATAGACATAAAGATCAG 951
                         i   i        vv i  v    i       v         v      i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_30976857_3    952 ----ATACATGTTTA----TCAGAAATAAACATGTATGTTTTTGGTCAAT 993
                         ----   v -i  v ----i           vii  ii   v        
  L1M4_orf2#LINE/    301 TGGAATAGA-ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_30976857_3    994 TGATTTTCAACAAGGGTGTCAGTACAATAAAGTGTGGAAAGAATAGTCTT 1043
                                 i         i  iv  v  vv i  v               
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_30976857_3   1044 TTCAACAAATGATCCTGAGATAGAAAATGATCCTGGCTATCCACATATGA 1093
                                    i v   i  i i---------    v  ?      iii 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAA---------CTGGATAKCCACATGCAA 440

  chr2_30976857_3   1094 AAGAATTAAGTTGTAATTCCACATAACACTATTTACATAAAAATTAACTC 1143
                               v      v vii i  v v    i  v    --           
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACA--AAAATTAACTC 488

  chr2_30976857_3   1144 CCAATGGATCAAAGACCTAAA-----GAGCTGAAACCATGAATGTCTTAT 1188
                         vv         ?         -----     i    i  i  vv     v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_30976857_3   1189 ATCTATATTTTTTTCTAAGTCTTCATAATGCTGCATTAAGCCGTAGTTTT 1238
                          vvv v iv vvv?v   i     i i ivi  vi   i  vi i    i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_30976857_3   1239 TTTTAGCTATGACACCAAAAGCACAATCAATCAAAGAAAAAGTAGATATA 1288
                           --  v                   v   iv         i      v 
  L1M4_orf2#LINE/    589 TT--AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_30976857_3   1289 TTAGACTTCATTGAA-TTATAAACTTTAGTGCTGCAAAGGACAGTATCAA 1337
                           i        ii  -   v       v     v         v      
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_30976857_3   1338 GAAAGTGAATAGATAGCACACAGAATGAGAGAGAATATTTGCAACT-ATA 1386
                                  v   i i v         i    i           v -   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_30976857_3   1387 CAAATGAT--GAGTCTAGTGTCTATAACATATAAATAACCATTACAACTA 1434
                         i vv    -- i v  v  i  i v  i       v   iv        v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_30976857_3   1435 AACAATTAAAAGACAA----CCCAATTTAAAAATGGGCAAAATATTTGAA 1480
                           i   v         ----       ?             iv       
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_30976857_3   1481 CAGACATTTCTTCAGATAAGATATACAC-TGGATAATA 1517
                         i          i  i v          v-   vi    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.11 (89 / 80)
Gap_init rate = 0.02 (15 / 874), avg. gap size = 3.40 (51 / 15)  


2264 26.58 0.57 1.15  chr2_31008697_31010383.rev      500  1195 (492)    L1M4_orf2#LINE/L1      217   908 (0)  

  chr2_31008697_3    500 ACACTCTACCAGACTTCAAACTATACTATAAGGCTACTATAACCAAAACA 549
                              - v   - i      viv     i  i     vi   i   i   
  L1M4_orf2#LINE/    217 ACACT-TCCCA-ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_31008697_3    550 GCATGGTACTGATACAAAAAAAAAGACATATAGACCAATGGAACAGAATA 599
                          ii        i--  v  ii v           i        i     v
  L1M4_orf2#LINE/    265 GTGTGGTACTGG--CATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_31008697_3    600 GAGAACGCAGAAATAAGATTGTACATCCACAACCATCTGATCTTTGACAA 649
                             iiv         iviii     ii iiii  vi    i  i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_31008697_3    650 ATCTGACAAAAACAAGCAGTGGAGAAAGGACTCCCTATTCAACAAATGGT 699
                         ivv  v   i v  vv  i   i     i ivvi  v             
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_31008697_3    700 GTTGGGATAACTGGCTATCCATTTGCAGAAAATTAAAACTGGACCCCTTT 749
                          i     i      v  ?   iv    i  i v i  ii         vi
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_31008697_3    750 CTCCCACCTTATACAAAAATTAACTCAAGATGGATTAAATGCTTAAATGT 799
                            v    v                   i      i ? vi i       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_31008697_3    800 AAAACCCCAAACCATAAAAACCCTAGAAGAAAATCTAAGCCAATACCATT 849
                           i v iv    i      vi i          iv  i ?vv v i -  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TT 561

  chr2_31008697_3    850 CAGGACATAGGCAAGGGCAAAAATTTCACA---ATGAAATTGCCGAAAGC 896
                          iv   v v  vvvi     vii    vi ---    v ---  i     
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA---CCAAAAGC 608

  chr2_31008697_3    897 AATTGCAACAGGAGCAAAAATGGATAAATGGGATCTAATTAAACTAAAGA 946
                          vvv      ii  v      i       v   ii v  i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_31008697_3    947 GCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAGGCAACCTACA 996
                         i   i  ii vv    i  v       vv i      v  i     i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_31008697_3    997 TAGTGGGAGAAAATTTTTGCAATTTATCCATCCAACAAAAGTCTAATATC 1046
                         v i           v       v i  vi   ii i  ii v  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_31008697_3   1047 CAGAATTTACAAGGAACTCAAACAAATTTACCAGAAATAAACAAACAACC 1096
                               v  i  i      vv    v iv iv v   v i     i    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_31008697_3   1097 CCATT-AAAAATGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGAC 1145
                          v   -                iv    i     i     v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_31008697_3   1146 ATTCATGCAGCCAACAAACATAGGAAAAAAAGTTCAACATCACTCATCAT 1195
                           v  viii     i  i  i v     i v i         ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (105 / 77)
Gap_init rate = 0.01 (7 / 692), avg. gap size = 1.71 (12 / 7)  


3295 26.98 0.44 0.44  chr2_31038216_31044488     4874  5781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31038216_3   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4923
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31038216_3   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4973
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31038216_3   4974 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5021
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_31038216_3   5022 TATGGAACCAGAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5071
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_31038216_3   5072 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5121
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_31038216_3   5122 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGATC 5171
                                 i   i    iii        i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_31038216_3   5172 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5219
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_31038216_3   5220 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTTG 5269
                          vi    i  i     ivv  vv  i v  vv            i  vvv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_31038216_3   5270 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5319
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_31038216_3   5320 GAAACTGGATCCCTTCCTTACACCTTATACAAAATTCAATTCAAGATGGA 5369
                            ii    i    v   i     v         v i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_31038216_3   5370 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5419
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_31038216_3   5420 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAA 5469
                         v    ?i v viv   iv   v v  vvii     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_31038216_3   5470 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5519
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_31038216_3   5520 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5569
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_31038216_3   5570 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5619
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_31038216_3   5620 AGGGCTAATATCCAGAATCTACAATGAACTCAGACAAATTTACAAGAAAA 5669
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_31038216_3   5670 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5719
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_31038216_3   5720 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5769
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_31038216_3   5770 ATCACTGGCCAT 5781
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 607 31.99 13.73 2.45  chr2_31233220_31235687.rev     1161  1976 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31233220_3   1161 TGGAAAGAT------TGCTCATGGATGGAAAAAC--AATA-------GAC 1195
                                  ------  i        v i  i  --    -------  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31233220_3   1196 ATCATT-CTATTTAAGTTAATTTATAAATCAAACACAATCTAAATAAAAG 1244
                         iv  v -  viii  i  i  i  i i  iv   i     ivv  v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31233220_3   1245 TATCAATAGATAATTTTCTAAAACTAGTTAAGTTTGTTTTAAAGTTCAAA 1294
                          vi  iiv vivv    vi i  v v vi   i vi ii    i    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_31233220_3   1295 TAAAAAGGTAAATAA----AAATAG--AAAA--ATTCTGAAAAA----AC 1332
                          ii   v i  ivi ----i     --    --  ii       ---- v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_31233220_3   1333 CCATATGAGGTGACTGGCGCTACTAGATATTGAA-TTTATTATAGTGTGT 1381
                          v vi vi iv    vi i  v ivi  v ii  -i   i  i iv ivv
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_31233220_3   1382 CATTTATTGAAACTGTGTGCTACAGAGACA----TGCACACATAGTTAAA 1427
                           v v  ii i  v     v   v iv i ---- iv   i    v v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_31233220_3   1428 AGGAACCAAGTGGTTAGTCCAGAAATAGATCCAAATGCATATGATCATTT 1477
                         v    ivi i v vv            i i   v iiiv    i   v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_31233220_3   1478 AGTATTTGACAAAGGTAGCATCTTAAATCATTGAA--GGAAAAGATTAAA 1525
                         ii v  i     i   iv  ---- i i    v  --  i     v  i-
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGAAAGAATAG- 395

  chr2_31233220_3   1526 TATGTTC--CA-------CTGGGATATCTGG-TAGCCCTGTGGGTGAAAA 1565
                          v v   --  -------      i v    -  ?  vii  vivi i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_31233220_3   1566 TAAAATTGTATCCATACCTCACACCATGTATACACCAAGATAAGATTCCA 1615
                          i  i   v i  v             --     --  i  v - i  v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCAT--ATACA--AAAATTA-ACTCAA 490

  chr2_31233220_3   1616 AATGAAAACGAAATGTAAAGGTAAAAGC-AAGACTATGAAAGTACCAGAA 1664
                             i vvv? i iv    v    i   -  i     i   v vii    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_31233220_3   1665 GGAAACACACAGG---------GTGCCTTT---CTAACCAA-GA---CTT 1698
                          i     i vi? ---------   v i  ---i  iv   - i---   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_31233220_3   1699 AAATCTTGAAACCA-------------TAAAATAAAAATCTGATATAACT 1735
                          i  v -  v    -------------i    v     viv    -  i 
  L1M4_orf2#LINE/    591 AGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA-AATT 638

  chr2_31233220_3   1736 G-AGTAAATAAAAATTGAAGG------------AAAAAAATCTTCTAAGT 1772
                          - v vv  v      i  ii------------   ii vv  vii   v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_31233220_3   1773 A-GCAAAAAGA--ATCTACATAA-----GTAAAC---TGAAAAG-ACACA 1810
                          - ii      -- i i   v  ----- v   i---  v   v- i i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_31233220_3   1811 T--GACAAAGGCCTAAT---CAACTTAAATAAAGAGTTCCAAAGGGTCAA 1855
                          --  i  i  v  vi ---  ivv  v       ii  iv viiv    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_31233220_3   1856 TAA-----AAATGAATTTCAATCCAATAGAAAATAATAGGCAAAGGATAT 1900
                            ----- i ii   ---  i     v?    --  i          v 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAAT---AACCCAATTWAAAA--ATGGGCAAAGGATTT 833

  chr2_31233220_3   1901 AAACGGGCAATGCACAGAAAAAGAAATATGAATAGACC--TAAATTTGTT 1948
                         i  ii i  v v v vi  i    v   ii   i -  --   iivii v
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGG-CCAATAAGCACATG 882

  chr2_31233220_3   1949 AAAAGATGTACTTAACATTACCTCATCA 1976
                                 --  i     i ????????
  L1M4_orf2#LINE/    883 AAAAGATG--CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (149 / 108)
Gap_init rate = 0.05 (42 / 908), avg. gap size = 3.14 (132 / 42)  


 840 29.38 7.42 4.90  chr2_31252870_31254489      497  1129 (491)    L1M4_orf2#LINE/L1      260   908 (0)  

  chr2_31252870_3    497 AAAAAGTATGACATTGCCATAGTAAAAGACAAAGAGGTCCATGGAA---A 543
                          i v   i  ii i  v    ivi v     v v  i  v      --- 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_31252870_3    544 ATGGAGTTCCCAGAACTAGAACCCA-ATATTTATGGGAAATT-ATAT--G 589
                           v   vvi      v  -      - i        vv    -  v -- 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATA-AACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_31252870_3    590 ACAAAGTGGTC--TTTTAATTAGTGGGGGAAGTGATGGCTTATTTAATTA 637
                             i vv i --vvii v i i     i   -i  i ii v  i  iv 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAA 407

  chr2_31252870_3    638 ATGATGTTGACACAAATGACTATTCATTTTGGAAGAAAATACAGTTGAAT 687
                            i  i  iv    v  iv  ?i  iv - v  i i   iv     i i
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAATGAAGTTGGAC 456

  chr2_31252870_3    688 CCCTACCTCAAACCTGACATAAAAATAAATCCCAGATGGACCTAAGATTT 737
                                   v   vv i i      v  ii v i     i v?   ii 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_31252870_3    738 AAAAGTTTAAGAAAAAAAAATCATATAAAAGT-------GGAAATTT-GG 779
                            v  --    ivv    -- -       v ------- i   iv -  
  L1M4_orf2#LINE/    507 AAATGT--AAGAGCTAAAA--C-TATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_31252870_3    780 GATAT-TCTATGTACAATCTAGGACTTA--CGATGATCTTTTTAATCAAG 826
                         ?i  v-   vi  i-- i  v  i-   -- i   i i i  ------  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTG--ACCTTGGG-TTAGGCAATGGTTTCTT------AG 592

  chr2_31252870_3    827 ACAGGGCATT-----CATGAGCTATTTTTTGAAAAGACATATTCGAC--- 868
                          i v i  ii-----  ii   v i------      v v v v  i---
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAAC------AAAAGAAAAAATAGATAAA 636

  chr2_31252870_3    869 -TGTATTTT-TCAAAGCCAAAAAGTTATATGG--CAATATATACCAT--- 911
                         -  v i  i-     iii     v  v i  v--   viv i  i  ---
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_31252870_3    912 -AAAGTCAACAGT--ATTAACAAATTAATCAGAAAAAA-ATCTGCAA--C 955
                         -     v  v  v-- iiv   i ---  vi  i    -  i     -- 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGA---ATGGGAGAAAATATTTGCAAATC 733

  chr2_31252870_3    956 ATATATGACTAATAAAGAACT---ATCAATAACATGCAAAGAGCTCTTTT 1002
                               --  i    i i   ---   v v  i  ii     i     vi
  L1M4_orf2#LINE/    734 ATATAT--CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_31252870_3   1003 A-CTTGGCAACAAAAAGATAAACCGTACAGTAGAAAAATAGGGAGAGGAT 1051
                          -  iiii  i       i   iviiv  i v?      i  v i     
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_31252870_3   1052 ATGAATAGACCCCTCATAGAAGGGCAAGATCCTTACATG--CAATAAACA 1099
                         v         vii  vivi   ---     vivi v   --      i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAG---AAGATATACAAATGGCCAATAAGCA 878

  chr2_31252870_3   1100 TATGAGAACATACTCAACCTCTCTGGTAAT 1129
                         i    i  v  i      v  v????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (107 / 75)
Gap_init rate = 0.05 (33 / 649), avg. gap size = 2.36 (78 / 33)  


3317 26.43 0.55 0.55  chr2_31316132_31318615     1085  1992 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31316132_3   1085 TGGAAGAACATTCCATGCTCATGGGTTGGAAGAATCAATATCGTGAAAAT 1134
                              ii i  i     i      i        v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31316132_3   1135 GGCCATACTGCCTAAGGCAATTTATAGATTCAATGCCATCCCCATCAAGC 1184
                            v     v  i  ivii  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31316132_3   1185 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1232
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_31316132_3   1233 CATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1282
                         i      viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_31316132_3   1283 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1332
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_31316132_3   1333 TACAGTAACCAAAACAGCATGGTACTGGAACCAAAACAGAGATATAGATC 1382
                                 i   i    ii         v iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_31316132_3   1383 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCTTGTCTATAACT 1430
                                i    i--    i  --        vv  iivii i   iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_31316132_3   1431 ATCTGATCTTTGACAAACCTGACAAAAACAAACAATGGGGAAAGGATTTC 1480
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_31316132_3   1481 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1530
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_31316132_3   1531 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1580
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_31316132_3   1581 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1630
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_31316132_3   1631 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 1679
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_31316132_3   1680 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAAAAATGGGATCTA 1729
                         vi            vvi          vv     v  v    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_31316132_3   1730 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTGAA 1779
                           i   v v  i i   i  ii vv    i  v   ii  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_31316132_3   1780 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 1829
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_31316132_3   1830 AAGGGCTAATATCCAGAATCTACAATGAACTCACACAAATTTACAAGAAA 1879
                          i  i  vi          v  i  v      vi    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_31316132_3   1880 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 1929
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_31316132_3   1930 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 1979
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_31316132_3   1980 CATCACTGGCCAT 1992
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3134 26.23 0.55 1.31  chr2_31440310_31444587.rev     2872  3786 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31440310_3   2872 TGGAAACGCATCCAATGCTCATGAATGGGTAGAATCAATATTGTGAAAAT 2921
                               vii    v   i     i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31440310_3   2922 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCAACAAAA 2971
                          i v     v  v   vii       i      i     i  i v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31440310_3   2972 TGCCACCATCGTTCTTCACAGAACTAGAAAGAACAATCCTAAAATTCATA 3021
                          v   v vv v  i  ii     v v  v iivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_31440310_3   3022 TGAAACCAAAAAAGAGTGTGCATAGCCACAGCAAGACTAAGCAAAAAGAA 3071
                           i  viiv  ii  vivv v       v i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_31440310_3   3072 CACATCTGGAGGCATCACATTACCTGATTTCAAAGTATACTATAAGGCTA 3121
                           v vi      vv     i v  ii        iiv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_31440310_3   3122 CAGTCACCAAAACAGTAAGGTACTGGTATGAAAATAGGCACATAGCCCAA 3171
                             v i   i     iv        i  i ii    i  i    vi   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_31440310_3   3172 TGGAACAGAATTGAGAACACAGAAACAAACCCAAACACTTACAGCCAACT 3221
                              i          iiv      i       v   i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_31440310_3   3222 GATCTTCAACAAAGCAAACAAAAA-ACTTAAAGTGGGGAAAGGGCACCCT 3270
                            i   i    i vviv   i v- i i  --         iii vi  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTCT 398

  chr2_31440310_3   3271 ATTCAACAAATGGTGCTGGAATAATTGGCTAGCCACATGTAGGAGAATGA 3320
                         v                  i i  i   v  ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_31440310_3   3321 AACTAGATCCTCATCTCTCACTTTATACAAAAATCAACTCAAGATGGAAT 3370
                          ii i  i  ii i   v   iv           i       i     vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_31440310_3   3371 G-AGGCTTAAATCTAAGACCTGAAACTTTATAGTTTTATAAATTCT-AGA 3418
                         i-  i i     v     v  i     --   -------   i   -   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACT--ATA-------AAACTCTTAGA 539

  chr2_31440310_3   3419 AGATAACATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCA 3468
                            v     v  ?iv  vi    vv   v    v        v i    v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_31440310_3   3469 TGACGAAGAGTCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGGCAG 3518
                          iivv v  vv         v v    i    iv   i   i   iiiv 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_31440310_3   3519 AATTTAATTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAG 3568
                         i i  v  i   v v  i i      iiivv    i iv  vi   iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_31440310_3   3569 AGTAAACAGACAACCCACAGAGTGGGAGAAAATCTCCACAATCTATACAT 3618
                            i  v              i           v iii   vii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_31440310_3   3619 CTGACAAAGGACTAATATCCAGAATCTACAATGAACTCA-ACAAATTAGC 3667
                             i  i     vi          v  i  v      v-    v i ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_31440310_3   3668 AAGAAAACAAACAAAAAATCCAATC-AAAATTGGGCTAAGGACATGAATG 3716
                           v    - i     v  i     i-    v     v     iv     i
  L1M4_orf2#LINE/    790 AATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_31440310_3   3717 GACAATTCTCAAAAGAAGATATGCAAATGGTCAACAAGCATAAGAAAAAA 3766
                             v     v           i       i   i     i v     i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_31440310_3   3767 TACTCAACATCACTAATGAT 3786
                          i          ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


2986 23.54 5.61 3.81  chr2_31524778_31526858.rev      698  1589 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31524778_3    698 TGGAGAGATATTTCTTTTTCATGAATAAGGAGACTGAATAT-GTCAAGAT 746
                             i      ii v v      i  vi i     v     -  i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31524778_3    747 GTCAGTTGTTCCCAA------CTGTAGACTCAATGCAATCCCAATCAAAA 790
                          v  i vv i     ------  ii   i    i        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31524778_3    791 TCCCAGTAAATTATTTTGTGGCTATCAACAAATTGATCCTAAGGTTTATA 840
                               ivivi v     ii vv  ii    ii         ii  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_31524778_3    841 TGGAGAAGAACAAGATCCAGAATAGCCAACTCAATATTGAAGGAGAATAG 890
                             i v v vii  i             vv    v     ii    ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA--- 197

  chr2_31524778_3    891 AGAACAAAGTCAGAGGACTGACACTACCCAATTTCAAGATTTACTACAAA 940
                         -         ii       v     v           i i          
  L1M4_orf2#LINE/    198 -GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_31524778_3    941 GCTGCAGTTATCAAGACAGTGTAGTATGGACACTGTCCATACTACAAAAA 990
                            i    v             i   i-----------------------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTAC----------------------- 273

  chr2_31524778_3    991 GAATGGACAAAAGAATGGACAAAGAGATCAATGGAACAGAATAGAGAGCC 1040
                         ---   -  v   i  i    v v            i     v     i 
  L1M4_orf2#LINE/    274 ---TGG-CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_31524778_3   1041 CAGAAATAGACCAACATAAATACAGTCAACTGATGTTTCACAAAGAAGAA 1090
                                 i   v i i vv  ii     i    v  iv    i iv vv
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_31524778_3   1091 AAGGCGATACGATGGAGCAAAGATTGTCTTTTTAATAAATGGTGCTGCAA 1140
                            i v  v i    i v  ii  v       i  i           vi 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_31524778_3   1141 CAGTTGGACATTCACATACAAAAAAAAATGAATCTAAACACAGACCTTAT 1190
                           ii    i ?i     i     i  --    vi ii  v vv    i i
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAA--TGAAGTTGGACCCCTACCTCAC 467

  chr2_31524778_3   1191 AC-ACTTCTCAAAATTAACTCAAAATGAATCATAAACCTAAGTGTAA--- 1236
                           - iv viv                 i    ? i      i     ---
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_31524778_3   1237 ----AGCAATAAAACTCCTAGAAGATGACATAGGAGAAAACCTAGATGAC 1282
                         ---- i v         i       vi       ? v   i  vvi    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_31524778_3   1283 CTTGGAAT-GATGATGACTTTTTAGATGCAACACCAAAGGCATGATCCAT 1331
                              iv - iii   ii  i      iii        i   ii v v i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_31524778_3   1332 AAAAGAAATAAT-TATAAGCTGGACTTCATTAAAATTTAATA-------- 1372
                                 v   -v    ii          i      v  v --------
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_31524778_3   1373 -----------ACGAT---GAA--TGAGGAGACAAGCGGTACACTGGGAG 1406
                         -----------  v  ---   --   ii      v vii v v      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_31524778_3   1407 AAAAATATTTGCAAAAGACACATCTTGTAAAGTACTT--ATCCA-AATAT 1453
                             -          vv i i    vi   i v    --     -     
  L1M4_orf2#LINE/    718 AAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_31524778_3   1454 ACAAAGAACTTATAAAACTCAGCAATAAGACAATGAACAACTAAATTAAA 1503
                          i        iv  v      ii     i vi ii  i   iv    ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_31524778_3   1504 AAATGGGTAAAAGACCTGCACAGCTACCTCACCAAAGAAGGTATATGGAT 1553
                                i   i  ii  v i  vi ii  v         i    iii  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_31524778_3   1554 GGCCAGTAAGCATATAA------GTTCGACATCATATGCCAT 1589
                              i      i  i ------ i  i      ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (132 / 74)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.94 (84 / 17)  


2792 27.42 1.90 0.89  chr2_31614095_31619259.rev     3777  4673 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_31614095_3   3777 GACAAATTTTCCATGCTCATGAATAGGAATAATTAATATCATGAAAATGG 3826
                           v i  v i     i     i  v    v v       ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_31614095_3   3827 CCATGCTGCCCAAAGCAATTTACAGATTGAATGTTATC---ATCAAACTA 3873
                          v  i  v      vii  i        v  i iv   ---      v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_31614095_3   3874 C-AATGACATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCTTAT 3921
                          - iivi v  i  ii     v v  v  i-  -  ii        v   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr2_31614095_3   3922 GGGACCAAAAAAGAGTCTGAATAGCCAAGGAAATCGTAAGCAAAAAGGAC 3971
                           i viiv  ii  vi v          iiv    v i iv  i   i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_31614095_3   3972 AAAACTGGAGGCATCATGTTACCCAACTTCAAACTACACTACAGGGATCC 4021
                            ii      vv   iii v     i      vivi      ii v v 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_31614095_3   4022 CATAACCAAAGCAATGTGGTACTGGTACAAAAAACGGCACATAGACCAGT 4071
                         vi   i   ii  i           i i  ii vv i  i     i  i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_31614095_3   4072 GGAACAGAATAGAGAGACCAGAAATAAGGCTAGACACCTATGACCACCTG 4121
                             i     v     v          iv i v   ii    ii  vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_31614095_3   4122 ATCTTCGACAAAGCTGACAAAAACAAGCAATGGGGAAAAGACTCCCTATT 4171
                           i        i v  v   i v  vv           ii ivvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_31614095_3   4172 CAATAAATGGTGCTGGGATAAGTGGCTAGCCAGATGCGGAAGATTGAAGC 4221
                            i              i  v   v  ?   v    ii    v     i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_31614095_3   4222 TGGACCTCTTTTTTACATCATACACAAAAATCAACTGAAGATGGATTAAA 4271
                               i  vii i   i    i        i    v  i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_31614095_3   4272 GATATAAATGTAAAACCCAAAACTATGAAAACTCT-GGAAGACAACCTAG 4320
                           iv         i v i        -        -i     v   v   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAG 550

  chr2_31614095_3   4321 GCAATACCATCTT-G-GACATAAGAATGGGTAAACATCTCAT-GACA-GA 4366
                          ?i-  v-     - -   v vi iv i  i  vvi i  v -  i -  
  L1M4_orf2#LINE/    551 GNG-TAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_31614095_3   4367 GCCATCAAATCTATCA-CAACAAAAGCAAAGATTGATGTGTGGGATCTAA 4415
                         --  i    vvi iv -         v   i  v   ivi v   ii v 
  L1M4_orf2#LINE/    599 --CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_31614095_3   4416 TTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTAT-AAGCAGAATAAA 4464
                          i   v v  i i   i  iiivv    i  v     -   - i i i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAA 695

  chr2_31614095_3   4465 CAAACATCCTACAGAATGGGATAAAATATTTGCAAACTATGCATCTGACA 4514
                         v i   v  i           v              ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_31614095_3   4515 AAGGTCCAATATTCAATATCTGTAAGGAACT--TA-AATTTA-TAAGAGG 4560
                          i  v ivi   i  iv  v i   i     --  -  i i -   v ii
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_31614095_3   4561 AAAACAAACAACCCCATTAAAAAGTGGGCAAAGGATATGAGCAGACACTT 4610
                           i     i     v   ?    i            v   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_31614095_3   4611 TTCAAAAGAAGACAAACATGCAGCCAACAAGCATATGAAAAAAATACT-A 4659
                         i  v        i v   viii     i     i       i - i  - 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCA 894

  chr2_31614095_3   4660 ACATCACTAGTCAT 4673
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (150 / 92)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 1.19 (25 / 21)  


3179 27.31 0.55 0.55  chr2_31630379_31636720     4943  5850 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31630379_3   4943 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4992
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31630379_3   4993 GGCCATACTGCCCAAGGTAATGTATAGATTCAATGCCATCCCCATCAAGC 5042
                            v     v     iv i  v  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31630379_3   5043 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5089
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_31630379_3   5090 ATATGGAACCAAAAAAGAGCCCGCATCATCAAGTCAATCCTAAGCCCAAA 5139
                                 viiv  ii  v  v v  vii   iv     i i ivvvi  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_31630379_3   5140 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTGCAAGG 5189
                                 i      vv    i  v  ii i      viv    i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_31630379_3   5190 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGAT 5239
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_31630379_3   5240 CAATGCAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5287
                              v  i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_31630379_3   5288 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATCC 5337
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_31630379_3   5338 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5387
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_31630379_3   5388 TGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGG 5437
                             ii    i    v   i     v  i           i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_31630379_3   5438 ATTAAAGACTTAAACATTAGGCCTAAAACCATAAAAACCCTAGAAGAAAG 5487
                           i ?    i    ii v  iv       i      vi i         i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_31630379_3   5488 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5537
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_31630379_3   5538 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5587
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_31630379_3   5588 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGGA 5637
                           i   v v  i i   i  ii vv    i  v    i  vv i    i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_31630379_3   5638 CAGGCAACCTACAGAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5687
                         v  i     i                 v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_31630379_3   5688 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5737
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_31630379_3   5738 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGCATATGAACAGATGCTT 5787
                           iv    i     v  i?    i         v  v    i   iii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_31630379_3   5788 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACGTGAAAAAATGCTCAT 5837
                            v        i  vi viii     v ii   i      i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_31630379_3   5838 CATCACTGGCCAT 5850
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 944 19.82 1.84 0.00  chr2_31644619_31647993      144   360 (3015)  C L1M4_orf2#LINE/L1   (0)   908   688  

C chr2_31644619_3    360 AAAATGAAAAGACAACTGACATAATGGAAGAAAATAATTACAAGCTATTT 311
                            i            iv   v     i        v  i   iii  v 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

C chr2_31644619_3    310 ATCTAATAAGGAGTTAATATCCAAAATATATAAGGAACTCATATAACTCA 261
                             i      iii vi      i         i      v  i      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

C chr2_31644619_3    260 ATAGCAAAAGAACAAATAACCCCATTAAATAATGGACAAAGGACTTAAA- 212
                            ii    ii           v   ?  v     i       i  i  -
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

C chr2_31644619_3    211 ---CATTTTTCCAAAGAAGACATAAAAGTGGCCAAAAAATATCTGAAAAG 165
                         ---     i           i   v  i       v  ii iv       
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

C chr2_31644619_3    164 ATACTGAACACCACTAATCAC 144
                           i  v    i  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (30 / 12)
Gap_init rate = 0.00 (1 / 221), avg. gap size = 4.00 (4 / 1)  

2279 28.59 1.62 2.37  chr2_31644619_31647993     1681  2481 (894)    L1M4_orf2#LINE/L1        1   795 (113)  

  chr2_31644619_3   1681 TGGAGAGACATATGATGTTCATGGAATGGAAGATTTAATCTTGATAAGAT 1730
                             i   i  viv           v       i     v   v      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31644619_3   1731 GCCAATTCTCCCCAGATTGAGCAATAGTTACAATGCAATACAAATCAAAA 1780
                          v    v       i     v v i  v v   i     v vv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31644619_3   1781 TCTCAAAGATCTATTTCATAGATAATAAGGAGCTAAATCTAAAACTTACA 1830
                           i  ivvii  v   iii   v v i vi    i vi      i i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_31644619_3   1831 TGGAAAGACAAAGGAATTAATACAGCCAGAACAGTTTTGAAAAAGAA--- 1877
                               vi   i   vii iv i     i    i i           ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_31644619_3   1878 -AAAGTTGGACCACCCACACTACTTAATATCAAAACTCGT---AAGTTTA 1923
                         -         vv  i      v ii   v        iii---  ivi  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_31644619_3   1924 AAGTTATCAATATATTGTGGTATTCGTAAAAAATATACACATACAGATCA 1973
                         v   v     v i v       i v i v  ii-   v     i      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAGACATATAGATCA 299

  chr2_31644619_3   1974 GTCATATAAAATAAAAAATGCAGAAATAGATTC-TACAAATATAGTCAAC 2022
                         i viv   i   vi i i v        i ii -    vv   i     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_31644619_3   2023 AGATTTTTGGCAAATGTGCAAAAGCAAACCAATACAGAAGAGTTCCTCTT 2072
                         v      i i   iv    v  ii v vi    ivi   iiiv vv    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_31644619_3   2073 TTCAACAAATGATGTTGAAGCAATTGGGTAGTCATCAGGAAAAATACAAG 2122
                                    i  i  iii   i   i  ?i  i--------  i   i
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCAC--------ATGCAAA 441

  chr2_31644619_3   2123 AACAGAAAGTTA-ACCTCAATCTGTATCTTACATGTTACACAAACATTAA 2171
                          iv vi     i-   i ------  i  i   ivv  i     v     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCC------TACCTCACACCATATACAAAAATTAA 485

  chr2_31644619_3   2172 CTCAAAATGCGCCATAGAATAAAAT-TAAAAAGTGTATCTATAAAGCATC 2220
                                  vii  ?   viv    -   i iv iv v       i vii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_31644619_3   2221 TAAAAGAAAACAAATAAGAAAATCTTTATAACCTTGAGTTAAGCAAAGAG 2270
                           i         v vi? v       ii i      i    i    v - 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-G 584

  chr2_31644619_3   2271 TTATTTAGCTATAACACCAGACGTATGATCCATAAAAGAAATAAATTAAT 2320
                           vi    v   i      i v i ii v v i        -    vi  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGAT 633

  chr2_31644619_3   2321 AAATTAGACTCCATTTAAATTAAAATTTTTTACCTGTT---AAAAACACT 2367
                              i    i   iv         vi    i--  i ---  ii     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTG--TGCTTCAAAGGACACT 681

  chr2_31644619_3   2368 CTTACACGAATGAAAAGACAAGGCACAGGCTGGTAGAAAATATTTTCAAT 2417
                         v i vivi i           vv     iv   v           v   v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_31644619_3   2418 AGATACATTTGACTGAACACTTGTATTCAAAATATGTAAATAGCTCTCAA 2467
                         vv   i  i   iviiiv        i  i     i    v i    i v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_31644619_3   2468 AACTCAACAGTAGA 2481
                                i i  i 
  L1M4_orf2#LINE/    782 AACTCAATAATAAA 795

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.02 (12 / 795), avg. gap size = 2.67 (32 / 12)  

 358 23.73 6.78 0.85  chr2_31644619_31647993     2766  2883 (492)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr2_31644619_3   2766 CTCAGCAATAAGAAAACGACACAATTTTTTT---AAATGAGGAAAG-ATC 2811
                             ii     i  i  i - i  iiivv  ---     i v    -  i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAA-ATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_31644619_3   2812 T----AGACACTTCACTAATGAGGAAATATGGATGGCAAATAAGCATACG 2857
                          ----     i   v i  v  i  v   iii     v        i i 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_31644619_3   2858 AGAAGATGCCCAACATCATTACACAT 2883
                          i       i        ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (21 / 7)
Gap_init rate = 0.03 (4 / 125), avg. gap size = 2.25 (9 / 4)  


1115 21.18 3.82 1.04  chr2_31680047_31685712     2746  3033 (2633)    L1M4_orf2#LINE/L1        1   296 (612)  

  chr2_31680047_3   2746 TGGAAA-ACATTCCATGTTCATGGACTGGAAGAC--AATATTTTTCAAAT 2792
                               - i  i             i        --      v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31680047_3   2793 GTCCATACTACCAACA-CAATCTATTGACTCAATACAATCCCTATCAAAA 2841
                          v v     v  v v -ii     iv  i    ii               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31680047_3   2842 TTCCAATGACTTTTTTTTTTCAGAAATAAAACAGTCCACTATAAAATTCA 2891
                          i   iivi i      --v       vi vv  iiv iiv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_31680047_3   2892 AATGGAATCTCAAGAGACATCAAAA-AGCCAAAACAATTTTGAAAAAGGA 2940
                         v      viv    i   -i  i  -            i         i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_31680047_3   2941 GAAAAAATATTGAGGACTCTCATTTCCTGATTTCAAATCTTACTA-AAAA 2989
                            v   vv v        v  i    ii        v       -   i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_31680047_3   2990 CTATAGTAATCAAAGCAATATAGTACTGGCATA----TAGACA-ATAAA 3033
                            i         ii  i i i           ----      -   i 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

Transitions / transversions = 1.54 (37 / 24)
Gap_init rate = 0.03 (9 / 296), avg. gap size = 1.56 (14 / 9)  

 424 20.45 0.00 0.00  chr2_31680047_31685712     3819  3906 (1760)    L1M4_orf2#LINE/L1      286   373 (535)  

  chr2_31680047_3   3819 AGGCACATAGACCTGTGAAATACAATACAGAGTCCAGAAATAAACCCTAA 3868
                           i  i     i vi  i    v   vv                   vv 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_31680047_3   3869 TATATATGGTTAAATGATTTTTGACAAGGGTGCTATGA 3906
                         i  v      i  v       i           i v  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

Transitions / transversions = 1.00 (9 / 9)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.00 (0 / 0)  

2508 17.77 3.78 0.76  chr2_31680047_31685712     4646  5174 (492)    L1M4_orf2#LINE/L1      364   908 (0)  

  chr2_31680047_3   4646 GATGTCAAGACCATTCAGTGGAGAAAGAACAGTCTTTTCAGCAAATCATG 4695
                          i  i            i   i       i          i     vi  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_31680047_3   4696 CTGGGAAAACTGGATATCCATATGCAAAATAAATAAATTAGACCCTTACC 4745
                               v         ?   i        v  vv  i  i     i    
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_31680047_3   4746 TAATACTATATAGAAAAATTAACTCAAAATTGATCAAAGACCTAAATATA 4795
                          v i  i     v                 v     ?          i  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_31680047_3   4796 AGAAA-AAAACTATAAAATTCTTAAAAGAAAACGTAGGACAAAAGCATCA 4844
                            iv-            i     i        i    ?vv   v v  i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_31680047_3   4845 TGATACTGTATCTGGCAGTGATTTCTTGGATATGCTACCAAAGGTGCAGC 4894
                            ivi  vi iv    i  i      i      vi      i ii  iv
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_31680047_3   4895 CAACAAAAGAAAAAACAGAAAAACTGAACTTCATGGAGAATCTTTAAAA- 4943
                                        i   v   i  i       vi i ----      -
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA----TTAAAAA 659

  chr2_31680047_3   4944 ---TTGTACATCAAAG-ACACTATTAATAGAGGAAAAGGGCAACCCACAG 4989
                         ---    i v      -       i  v i  vi   i i          
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_31680047_3   4990 AATGGGAGAAAGTATTTGCAAAGCATATATCTGACAAGAGATTGACATCC 5039
                                    i          v           i   i  i vii    
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_31680047_3   5040 AGAATATATAAAGCACTCCTAAAACTCAACAACAA-----CAA------C 5078
                                      v    i  v       i  i  -----   ------ 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_31680047_3   5079 AA---AAAATTGGGCAATGGACTCGAATAAATGTCTCTCCAAAGAAGCTA 5125
                           ---    v       v   i i     i ii i            v  
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_31680047_3   5126 TGCAAATGGCCCATAAGAACCTGAAAAGATGCTCAACATCACTAATCTT 5174
                          i         v     v  v                    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (58 / 33)
Gap_init rate = 0.01 (7 / 545), avg. gap size = 3.43 (24 / 7)  


 335 25.77 0.00 0.00  chr2_31706150_31709000       59   155 (2696)  C L1M4_orf2#LINE/L1   (0)   908   812  

C chr2_31706150_3    155 TTTAAAAATAGGAGAATTATATGAACAGATACTTTGCCAAAGAAAACGTA 106
                           ?      i  vi  vv  v    i   i i  iv        i ii  
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

C chr2_31706150_3    105 TGATTGGCAAACAAGAACATGAAAGGATGCTCATTATTAGTGATTAG 59
                         ii v    v  i   v        i        vi  i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (15 / 9)
Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.00 (0 / 0)  

 978 21.74 3.77 8.99  chr2_31706150_31709000      159   503 (2348)    L1M4_orf2#LINE/L1      362   688 (220)  

  chr2_31706150_3    159 AAGGTGCAAAGGCAGTTCATTGGACAAAAAGTAGTATTTTCAACAAATGG 208
                          i     v   i vi    v   iv   i i    v              
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_31706150_3    209 TACTAAAACAATTGACTGTCCACATGCAAAAAACAAAAAACAAAAAAAAA 258
                          i  iii    i  iv i?            i ---------- vi  iv
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGA----------ATGAAGT 451

  chr2_31706150_3    259 AAAACACAACAAAAAAACTTTGATTCAAACTTGGAAACCTACTTTAAAAA 308
                         vii  ------------ ii ivi   v  i----- iv   ---     
  L1M4_orf2#LINE/    452 TGGAC------------CCCTACCTCACACC-----ATATAC---AAAAA 481

  chr2_31706150_3    309 TTAATTCAAAATGTGTCATAGACCTGAAAT-TAAAACCTAAAACTACAAA 357
                             i        vi   ?      -    -   i v         i   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCT-AAATGTAAGAGCTAAAACTATAAA 530

  chr2_31706150_3    358 TCTTGTAGAAGGAAATATAAGAGAAAATCACTGTGACCTTAGATTAGGCA 407
                         v  iv      i   i   i ? v     vii        i i       
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_31706150_3    408 AAAATTTTTTAGATATCACATCAAAAGC--------CAAAG--AAAAATG 447
                          vii   i        v   i       --------    i--      i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_31706150_3    448 GAAAAATTAGACTTCATCAAAATTAAACATTTCTGTTTTTCAAAAGACA- 496
                           v     i                  v i  i   vi      i    -
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_31706150_3    497 -GTTAAGA 503
                         -i i    
  L1M4_orf2#LINE/    681 TATCAAGA 688

Transitions / transversions = 2.13 (49 / 23)
Gap_init rate = 0.03 (9 / 327), avg. gap size = 4.89 (44 / 9)  

3021 26.89 1.44 0.78  chr2_31706150_31709000     1460  2359 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_31706150_3   1460 GAAAAACATTCCATGCTCATGGATAGAAAGAATCAATATTGTTAAAATGG 1509
                             i i  i     i        v i    v i           i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_31706150_3   1510 CCATACTGCC-AAAGCGATTTACAGATTAAATGCTATTCCTATCAAACTA 1558
                          v     v  -   vi   i        v  i  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_31706150_3   1559 CTGATGACATTCTTCACAGAATTAGAAAAAAACT-ATTTTAAAATTCATA 1607
                          iiiivi v  i  ii     v v  v  i--  -  ii           
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chr2_31706150_3   1608 TGGAATCAAAAAAGAGCTGGGATAACCAGG-CAATCCTAAGAAAAAAGAA 1656
                              viiv  ii  v ii i   i   ii-     i i i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_31706150_3   1657 CAAAGCTGGAGGCAC-CACATTACCTGACTTCAAACTACACTACAAGGCT 1705
                              i      -  -    i v  ii i      vivi       i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_31706150_3   1706 ACAGTAACCAAAACAGCGTGGCACTGGTACAAAAACAGACATATAGACCA 1755
                                i   i    i    i     i i  ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_31706150_3   1756 ATGGAACAGGATAGAGTGCCCAGAAACAATGCTGCATACCTACAACCATC 1805
                               i  i  v   v i       i  vv iii i ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_31706150_3   1806 TGATATTTAATACAGTTGACAAAAGCAAGTAACAGGGAAAGGACTCCCTA 1855
                             v  ii i vi v  v   i v  vvi  ii       i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_31706150_3   1856 TTCAA--AATGGAGCTGGGATAACTGACTAGCCATATGCAGAAAATTGGA 1903
                              --     v       i     iv  ?   i     i  i v  i 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_31706150_3   1904 ACTGGACCACTACCTTACACCACATACAAAAATCAACTCAAGATGAATTA 1953
                         ii      v      i      i          i       i   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_31706150_3   1954 AAGACTTAAATGCAAAACCTAAAACCATAAACACCCT-AGAAGAAAACCT 2002
                         ?    i      i  i v       i     -  i  -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACAT 548

  chr2_31706150_3   2003 AGA---AAATGCCATTCTGGACATAGGATCTGGCAAAGACCTCATGACAA 2049
                           i---    -- -   vv   v v  i iv     v iii  v iivv 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_31706150_3   2050 AGACACCAAAAGCAATTGCAACGTAACCAAAAATTGACAAATAGGACCTA 2099
                         v             vvv     iv  vv      v  i    v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_31706150_3   2100 ATTAAACTAAAGAGCTTCTGCACAGGAAAAAAAACTATCAAGAGAGTAAA 2149
                           i   v v  i i   i  ii vvv   ii v          i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_31706150_3   2150 CATGCAACTTACAGAATGGGAAAAAATATCTGCAAACTGTGCATCTGACA 2199
                         v vi    ii           i       i      iii ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_31706150_3   2200 AAGGTCTAATATCCAGCATCTATAAGGAATTTAAACTAATTTACAAGCAA 2249
                          i  v  vi       v  v     i   i ivv  v v iv i  vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_31706150_3   2250 AAACCAAACAATTCAATT-AAAAGTGGGCAAAGGACATCAACAGATACTT 2298
                           iv    i  ii     -    i           iv v  i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_31706150_3   2299 TTCAAAACAAGATATATG--TGGCCAACAAGGATATGAAAAAATGCTCGG 2346
                         i  v   v        ii--       i   v i       i      ii
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_31706150_3   2347 CATCACTAATCAT 2359
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (155 / 85)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 1.43 (20 / 14)  


2313 26.74 5.79 0.69  chr2_31731589_31734933     1990  2853 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31731589_3   1990 TGGAAACATAGCTCAAGCTCATGGATGGGTAGAATCAATATTGTGAAAGT 2039
                               v   v i  v i        v  v   v i        v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31731589_3   2040 GACCACCCTGCCAAAAGCAATCTACAAATTCAATGAAATTCCCATCAAAA 2089
                          i v iv  v  v   vii       i      i v   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31731589_3   2090 TACCACCATCATTTTTTCACAGAATTTTTAAAA--AATACTAAAATTAAT 2137
                          v   v vv v      -i     v  vvv  i--i  v        v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_31731589_3   2138 ATGGAACCAAAAAAGGG-CCCACT-CAACCAAAGCAAGACTAAACCAAAA 2185
                               -- viv     -    vv-i i     i   vvi i  vv i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_31731589_3   2186 GAACAAGTCTGGAGGCATCACATTACACAACTTCAAA-----CTATA--- 2227
                               ivi      vv     i v v   i      -----   i ---
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_31731589_3   2228 CTACAGT---CA--------TGGTACTGATTTAAAAACAGACACATAGAC 2266
                                ---  --------        iiv   ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_31731589_3   2267 CAATGGAACAAAATAGATAACTCAGAAATAAAGCCAAATACTTATAGCCA 2316
                                 i i   v  v iii          v   v i i    i i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_31731589_3   2317 ACTGATCTTTGACAAAGCAAACAGAAACA--AAGTGGAGAAAGAACACCC 2364
                          i    i  i     i vviv  ii v  --v i   i       i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_31731589_3   2365 TACTCAACAAATGGTGCTGGGATAATTGGCAAACCACATGTAGAAGAATG 2414
                          vi                   i  i   vv ?       i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_31731589_3   2415 AAACTAGATCTGCATCTCTCACCTAATACAAAT-TCAACTGAAGATGGAT 2463
                           ii i  i ivi i   v    vv       v- i    v  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_31731589_3   2464 CAAAAACTTAATTCAAAGATCAGAAACCATAAAAATTCTAGAAGATAAAA 2513
                           ? i  i   v vv    v vi    i      v ii       v  v 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_31731589_3   2514 TAAAAAAAAAACTCTTCTAGACATTGCCTTAGTCAAAGAGTTCATGAGTA 2563
                           ii?iv   --     vv   v   vv    v   v iv   v iii  
  L1M4_orf2#LINE/    548 TAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_31731589_3   2564 -------AAAATC--------CAAAAACAAAGATAAATATATGGGACTT- 2597
                         -------    v --------     iv   i   i   v  v      -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_31731589_3   2598 ----AAACTAAAAAGCTTCTGCATAGCAAAAGAAACAATCAGCAGAGTAA 2643
                         ----   i      -   i  iiivv    i  v  v    iv i   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_31731589_3   2644 ACAGGCAATGCAAAGAGTGGGAGAAAATCTTCACAATCTATACATCCAAC 2693
                          v  i   iv  v   i           v  ii   vii   i   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_31731589_3   2694 AAAGGACTGATATCCAGAAACTACAAGGAAATCAAACAAATCAACAAGAA 2743
                           i     vi         vv  i  i   v  vv    v    i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_31731589_3   2744 AAAAACAA----TCTCATCAAAAAGTGGGCTAAGGACATGATTAGACAAT 2789
                            i    ----i iv  i?    i     v     iv   v      v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_31731589_3   2790 TTTCAAAAGAAAATACACAAATGGCCAAGAAACATATTAAAAAATGCTCA 2839
                          i  v      i   i            v  i  i  v    i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_31731589_3   2840 ACATCACTAATGAT 2853
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (122 / 105)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.29 (56 / 17)  


3652 23.33 1.33 0.67  chr2_31748553_31750644      701  1600 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_31748553_3    701 GAAATATAGTTCATGTTCATGGATTGGAAGAATTAATATTGTTAAAATGT 750
                             v   vii                    v             i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_31748553_3    751 CTACACTAACCAAAGTAATCTGCATATTTAATGCAATTTGTATTGGAATT 800
                          v i   vv     v i    i  v   i  i     iiv   iii   i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_31748553_3    801 CCA--TGTCATTTTTCACAGAAATGGAAAAAACAATCCTAAAATTTATAC 848
                            --  i -     ii       v  v  ivii           i   i
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_31748553_3    849 GGAGTTACAAAAGACTGTAAACGCCCAAAGCAATCTTGAGCAAAAAGAAC 898
                            iv i   ii   ivvi  iiv     i         iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_31748553_3    899 AATGCTGGAAGGATCACACTGACAGATTTCAAAATATATTACAAACCTAC 948
                           v i    i iv       vv vi         iv  i      v    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_31748553_3    949 TGTAATCAAAACAGCATGCTATTGGAATTTAAAAA-AGGCATTTTGACCG 997
                         v        i    ii  v  i   v  --  ii -  i   v v  i i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGATCA 299

  chr2_31748553_3    998 AGGGAACAGGATAGAAAGCCCAGATATAAACTTAAATATTTGCAGTTAAT 1047
                          v    i  i  v  i  i     v      ii v i    iii  i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_31748553_3   1048 TGATTTTCAACAAAGGTGCCAAGAACACACCATAGGGAAAGAACAGTCTC 1097
                                 i    i          v  iv v  i         i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_31748553_3   1098 TTCAATAAATGGTGTAGAGA-AACTGGACATCCACATGCAGAAGAATGAA 1146
                              i        iv i  -       i ?         i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_31748553_3   1147 ATTGGACCCTTATTTCATACCATATACAAAAATTAACTTAAAATGAATAA 1196
                         i        i  ii   i                    i      i  v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_31748553_3   1197 GAGACTGAAACATAAGGCTTAAAACTGTAAAGCTACTGAAAGAAAACAGA 1246
                         ?    iv   ii    ivi       i    i  vi ii         v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_31748553_3   1247 AGGGTAAAACTTCATGACATTGAGCTGGTTAATGACTTCTTGGATAGGAC 1296
                         i ?     v    i    v   i i i vi    ii     i    v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_31748553_3   1297 TCCAAAAGTACATGAAACAGAAGCAAAAATATACAAACGGGATTGTATCA 1346
                         v       i   v v    i   v       v i   iv   i vi    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_31748553_3   1347 AACTAAAAAGCTTCTGCACAACAAAGGAAAC----AACAGAATAAAGAGA 1392
                           v v    i   i  ii vv       v  ----  v i i i  i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_31748553_3   1393 CAACCCACAGATTGGGAGAAAATATTTACAAACCATACATCTGATAAAGA 1442
                                    v               i    i    i         i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_31748553_3   1443 ACCAATATAAAAAA-ACACACAAGAATCTCAAACAACTCAATGGATAAAA 1491
                           ivi   vv i  - i i -     -   vv          i-      
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATA-AAGAA-CTCTTACAACTCAATA-ATAAAA 796

  chr2_31748553_3   1492 AAGCAAA--ACCCAACTAAAAAATGAGCAAAGAGTCTGAACAGACATTTC 1539
                          ii    --      i ?       i      ii i    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_31748553_3   1540 TCAAAAGAAGAGATATGAATAGCCAACAGATATATGAAAA-ATGCTCAAT 1588
                           v        v   ii   i     i iii i       -        i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_31748553_3   1589 ATCATTAGTCAT 1600
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (138 / 68)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 1.50 (18 / 12)  


3175 27.42 0.55 0.55  chr2_31761331_31766201.rev     3471  4378 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31761331_3   3471 TGGAAGAACATTCCATGCTCATGGATGGGAAGAATCAATATGGTGAAAAT 3520
                              ii i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31761331_3   3521 GGCCATAGTGCCCAAGGTAGTGTATAGATTCAATGCCATCCCCATCAAGC 3570
                            v   v v     iv ii v  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31761331_3   3571 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCG 3618
                          v   iivi i  i  ii     -   -- v  i  - iii    i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_31761331_3   3619 TATGGAACCAGAAAAGAGCCTACATAGCCAAGACAATCCTAAGCAAAAAT 3668
                                viiv  ii  v  viv        i      i i iv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_31761331_3   3669 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAATTATACTGCAAGCC 3718
                                i      vv       v  ii i      viv    i   iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_31761331_3   3719 TACAGTAACCAAAACAGCATTGTACTGATACCAAAACAGAGATATAGATC 3768
                                 i   i    ii v      ii iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_31761331_3   3769 AATGCAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 3818
                             v  i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_31761331_3   3819 CTGATCTTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCCCT 3868
                         i    i  i     ivv  v   i vv vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_31761331_3   3869 GTTTAATAAATGTCGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3918
                         v  i  i     vi       v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_31761331_3   3919 AACTATGTCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGATT 3968
                          ii ivii    v   i    iv              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_31761331_3   3969 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTGGAAGAAAACCT 4018
                          ?    i       v   v       i      vi i i         v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_31761331_3   4019 AGGCA-ATACCATTCAGGACATAGGTATGGGCAAGTACTTCGTGACTAAA 4067
                            ?i- v i -   iv   v v  vv i     vvii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_31761331_3   4068 ACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAAT 4117
                                     vvi          vv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_31761331_3   4118 TAAACTAAAGAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGGACA 4167
                         i   v v  i     i  ii vv    i  v    i  vv i    i v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_31761331_3   4168 GGCAACCTACAGAATGGGACAAAATTTTTGCAA--TATACCTATCTGACG 4215
                          i     i           v     v       --i   --       ii
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA--TATCTGATA 745

  chr2_31761331_3   4216 AAGGGTTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 4265
                          i  ii vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_31761331_3   4266 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 4315
                           iv    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_31761331_3   4316 CTCAAAAGAAGACATTTGTACAGCCAACAGACATATGAAAAAATGCTCAT 4365
                            v        i  viiv ii     i ii  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_31761331_3   4366 CATCACTGGTCAT 4378
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2973 24.80 2.91 1.45  chr2_31771521_31774523.rev     1617  2511 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31771521_3   1617 TGGAAAGCTACTCAATGCTCTTGGATTGGAAGAAATAATAGTGT-AAAAT 1665
                                v  ii v   i  v            vv     v   -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31771521_3   1666 GATAATACTACCCAAGGAAATACACAGATTCAATGCAATCTGTATAAAAA 1715
                          ii      v     ivvi  vi          i      iv   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31771521_3   1716 ----AATGACATTCTTCACAGAAATAGAAAAAA-AATCCTAAAATTTATA 1760
                         ---- iivi v  i  ii       v  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_31771521_3   1761 TGGAATAACAAAAGTTCCTGAACAGGCAAAGCAGTCCTGAGCAAAAACAG 1810
                              vvi   ii vi  v   i  v    i  i  i   iv  i  v i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_31771521_3   1811 CAAAGCTAGAAGCCTTACACTACTTGACTTCAAACTTTGCCACAAAGATA 1860
                              i i  i v  i     v iii i      vi  i i      v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_31771521_3   1861 CAGTAA------CATCATAGAATTGGCATAAAAATAGACTCCTAGACCAA 1904
                               ------  vii i v i        ii      viv    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_31771521_3   1905 TGGAACAGAATACAGTATCCAGATATAAATGCATTCATTTACAATTAACT 1954
                              i     vv  vi      v     iv   v      iii i  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_31771521_3   1955 CATCTTTGAAAGGAGTACCAAGAACATACAATGGGAAAAGAAAATCCTTT 2004
                         v  i  i  v i i  i      v   v       i      v vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_31771521_3   2005 TCAATAAATTGTGTTACGAAAATT--------ACATGAAAAAGAAAAAAT 2046
                             i    v   i iv  v  i --------     v       vi  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_31771521_3   2047 CTACACCTCTATCTTTCAGCATACACAAAATTTAAATCAAAATGTATTGA 2096
                         i iv   i   i  iv  v    i      v    v        v  ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_31771521_3   2097 AGACTTAAATATAAGATCTGAAACTATGAAACTACTAGAAGAAAATAATG 2146
                             i     i     v  i       i     vi          i vv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_31771521_3   2147 GAG-AAATGTTCTAGGACGTTGGTCTGGGCAAAGATTTTTTTGGCATAAC 2195
                          ? -    v   -iv   v    vi i     v i   i  v ii  i  
  L1M4_orf2#LINE/    551 GNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_31771521_3   2196 ACCTCAAAAGTACAGGCAACTGAAGTAAAAG-AGACAA-TTGGGATTTAT 2243
                            --     i   i     vi   v    i-   i  -    iv  i  
  L1M4_orf2#LINE/    600 ACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_31771521_3   2244 TTAGTAAATAAAGCTAAAATACTTCTAAAAAGCAAAGGGAGCAATCAACA 2293
                         i--------   ii     -    i ivivvv      ivi v     v 
  L1M4_orf2#LINE/    648 C--------AAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_31771521_3   2294 AAGTGAAGAAACAATCCACAAAATGAGAGAAAATATTTGCAACT-ATCCA 2342
                                i i    i     i    i                v -  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_31771521_3   2343 TCTGCCAAGGGATTAATAACAAGAATATATAAGGAACTCAAACAACTCTG 2392
                             vi      i vi  v v           i      vv       vi
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_31771521_3   2393 TAGGAAAAAAATCTAATAATCCAATTAAAGAA-GGGAAAAAGATCTGAAT 2441
                           iv     i - v     i      ?  i  -   v   i   i     
  L1M4_orf2#LINE/    789 TAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_31771521_3   2442 AGACATTTCTCAAAAGAAGATATACAAATGGCCAACAGGTATATAAAAA- 2490
                                    v                       i i i i  i    -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_31771521_3   2491 ATGCTTAACATCACCTATCAT 2511
                              i       ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (130 / 89)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.44 (39 / 16)  


3025 24.97 1.53 2.08  chr2_31806072_31810408.rev     2933  3845 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31806072_3   2933 TGGAAACACATTG-ACATT-ATGGATTTGAAGAATCAATATTATGAAAAT 2980
                               v i  iv- ii  -       v     v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31806072_3   2981 GACCATATTACCTAAAGCAATCTACAGATTCAATGCAATTCCTATCAAAA 3030
                          i v   i v  i   vii              i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31806072_3   3031 TACCAACATAATTTTTCATAAAATTAGAAAAAACAATTCTGAAATTCATA 3080
                          v   i vvvv     iii i  v v  v  ivii  i  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_31806072_3   3081 TG-AAACCCAGAAAGAGCCCA-AATAGCCAAAGAAATCCTAAGCAAAAAG 3128
                           -   iv  -- i ii    -          iv    i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCA--AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_31806072_3   3129 AACAGATCTGGAGGCATCACATTACCAAACTTCAAATTATACTACTAAGG 3178
                             i vi      vv     i v  v  i      viv      v   v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_31806072_3   3179 TATAGTTACCAAAACAACATGGTA------TAAAAGTAGACACGTAGACC 3222
                           i   v i   i   iii     ------   iii      ii    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_31806072_3   3223 AATGAAAAATAACAGAGAACCCAGAAATAAAGCCAAATACTTACAACCAA 3272
                             i  v v  iv    ii           v   v i i   iiii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_31806072_3   3273 CTGATCTTTGACCAAGCATACAGAAAT-ATAAATTGAGGAAAGGACACTC 3321
                         i    i  i   -   vi i vi i i-  vv v  i      i i v  
  L1M4_orf2#LINE/    349 TTGATTTTCGAC-AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_31806072_3   3322 TATTTAATAAATGGTGCTGGGAAAACTGGATAGCCACATGTAGAATAATG 3371
                          v  i  i              v         ?       i i  v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_31806072_3   3372 AAACTGGATCACTATTTCTCACCTTATTAAAAAATAAACTCAAGATGGAT 3421
                           ii    i v   ii  v    v   vv      v       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_31806072_3   3422 CAGAGACCTTCAGATCTTAAGTCCAAGACCTGAAACCGTAAAAATCCTAG 3471
                           ?      ---------  i vi    v  i    ii     v  i   
  L1M4_orf2#LINE/    498 CAWAGACCT---------AAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_31806072_3   3472 AAGGTAACCTAGGA--AAACCTCTACTGAACATTGGCCTAGGCAAAGAAT 3519
                            iv   v    ?--   i  iii-   v -    vi       v iv 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCG-TGACC-TTGGGTTAGGCAATGGTT 586

  chr2_31806072_3   3520 TTATGACTAAGACCCCCAGAACAAATGCAACTAAAGCAAAAATAAATAAA 3569
                          iv iiv  v   v  v i i  v v     v    v       i     
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_31806072_3   3570 TGGAACCTAATTAAA-CTAAAAGCTTCTGTACATCAAAAGAAATAATCAT 3618
                          v i  i v  i   -i     i   i   i v     i  v iv    v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_31806072_3   3619 CAGAATAAACAGACAACTCACAGAGTAGGAGAAAATATTTGCAAACTGTG 3668
                         v i i i  v       i      i i                  iii i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_31806072_3   3669 CATCTGACAAAGGACTAATATCCAGAATCTACAAGGAACTCACACAAATC 3718
                         i      i  i     vi          v  i  i      vi    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_31806072_3   3719 AGCAAGAAAAAAAACCCACAAATAATCCCATCAAAAAGTGGACAAATGAC 3768
                          ii  v     i -----       i  v  i?    i   i    v  i
  L1M4_orf2#LINE/    787 AATAATAAAAAGA-----CAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_31806072_3   3769 ATGAATAGACATTTCTTCAAAGAATATATACAAATGGCCAACAAACATAT 3818
                         v               i       v                i  i  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_31806072_3   3819 GAAAAAATGCTCAACATCACTAATCAT 3845
                              i             ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.36 (33 / 14)  


2844 19.77 1.14 4.41  chr2_31813365_31815041      485  1187 (490)    L1M4_orf2#LINE/L1      229   908 (0)  

  chr2_31813365_3    485 TTCAAAACTTAATATCATATACTACAAAGCTATAGCAACAAAAACAGCAT 534
                                    ----------           i  i  iv  i    ii 
  L1M4_orf2#LINE/    229 TTCAAAACTTA----------CTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_31813365_3    535 GTTACTGGCATGAAAGCAGACACATAGACCAATGAAACAGTAA--GAGAA 582
                          v         i iiii     i     i     i  i  -  --    i
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG-AATTGAGAG 317

  chr2_31813365_3    583 GCCAGAAATATATCCACACGTTTACAGTCAACTGATTTTTAACAAAAGTG 632
                         v         v i   i  i    ii     i       ii    ii   
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_31813365_3    633 CCAAAGATATACAATGGGAAAATGACAGTCTCTTCAATAAATGGTGTTGG 682
                             iivi  v       i   vi i     i     i        i   
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_31813365_3    683 GAAATCTGGATATCCACATGCAGAAGAATGAAATTAGACCCTTATCTTTT 732
                           v v       ?         i         i  i     i  i  ivi
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_31813365_3    733 ACCATATGCAAAAATTAACCCAAAATGGATTAAAGACTTAAATTTAAAAT 782
                                i           i          i ?    i     v   i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_31813365_3    783 CCAAAACTATAAAACTGCTAGAAGGAAACATAGGAGAAAACCTTCATGGC 832
                          i              vi      i         ? v   i    i  --
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-- 565

  chr2_31813365_3    833 ATCT---GTCGGAGCAATGATTTTTTTGGATATGACCTCAAAACCATAGG 879
                          i  ---  ii -      i   i  -i        vi     v  i i 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAG-GCAATGGTTTCTT-AGATATGACACCAAAAGCACAAG 613

  chr2_31813365_3    880 CA-CAAAAGCAAAAATAGACAAATGGGATTACATCAAA-CTAAAAAGTTT 927
                           -      v         i    v   i v       -i      v   
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_31813365_3    928 -ATGCATGGTGAAGGAAGTAATCTACAGAGTAAAGAGACAACCTATAGAA 976
                         -i   v --ii     viiv   v v i   i  i        i i    
  L1M4_orf2#LINE/    664 TGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_31813365_3    977 TGGGAGAAAATATTTGAAAACTATACATATAACAAGGGCTTAATATCTAA 1026
                                         v   ii   i  v i i     vi vi    i i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_31813365_3   1027 AATATATAAGGAACTCAAACAACTCAATAGCAAGAAAACAAATAACCCAA 1076
                                  i      vv           ii  i  i             
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_31813365_3   1077 TCTTAAAAATGGTTAAAGGACCTTAATATACTCAAAAGAAGACATTAATC 1126
                          - ?        vi      ii v    ------------      vv  
  L1M4_orf2#LINE/    812 T-TWAAAAATGGGCAAAGGATTTGAATA------------GACATTTCTC 848

  chr2_31813365_3   1127 AAAAGAAGACATACAAACGGCCAATAGGTATATGAAAAAAATGCTCAATA 1176
                         v        i       i        i i i       i -       i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACA 897

  chr2_31813365_3   1177 TAACTAATTAT 1187
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.65 (98 / 37)
Gap_init rate = 0.02 (14 / 680), avg. gap size = 2.79 (39 / 14)  


3193 26.11 1.33 0.88  chr2_31815064_31821384.rev     4926  5829 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31815064_3   4926 TGGAAGAACATTCCATGCTCATGGATGGGAAGAATCAATATCATGAAAAT 4975
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31815064_3   4976 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATGAAGC 5025
                           iv     v     iv i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31815064_3   5026 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5072
                          v   -   v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_31815064_3   5073 ATATGGAACAAGAAAAGAGCCC-GCTTAGCAAAGACAATCCTAAGCAAAA 5121
                                 - v v  i ii   - vv    v  i      i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_31815064_3   5122 AGAATAAAGTTGGAGGCATCACACTACCTGACCTCAAACTATACTACAAG 5171
                             i           vv       v  ii ii     viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_31815064_3   5172 GCTACAGTAACCAAAACATCATGGTACTGGTACCAAAACAGATATATAGA 5221
                                   i   i   vii         i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_31815064_3   5222 CCAATGGAACAGAACAGAGGCCTCCGAAATAACACCACACATCTACAACC 5271
                         i        i    iv   ivii v       vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_31815064_3   5272 ATCTGATCTTTGACAAACCTGATAAAAACAAGAAATGGGGAAAGGAT--T 5319
                          vi    i  i     ivv  vi  i v  vvv           i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_31815064_3   5320 CCTTATTTAATAAATGGTGCCGGGAAAACTGGCTAGCCATATGTAGAAAG 5369
                          i  -- i  i         i    v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_31815064_3   5370 CTGAAACTGGATCCCTTCCTCACACTGTATACAAAAATTAACTCAAGGTG 5419
                         v    ii    i    v        ii                   ii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_31815064_3   5420 GATTAAAGAGTTAAATGTCAGATCTAAGACCATAAAAACCTTAGAAGAAA 5469
                            i ?   vi       v   v    i  i      vi           
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_31815064_3   5470 ACCTAGGCAATACAAT--TCATGACATAGGCATGGGCAAAGACTTCATGA 5517
                           v    ?i-  -   --  i    v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    545 ACATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_31815064_3   5518 CTGAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5567
                         v ivi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_31815064_3   5568 CTAATTAAACCAAAGAGCTTCTGCACAGGAAAAGAAACTATTATCAGAGT 5617
                         i v  i   viv  i i   i  ii vvv   i  v     i vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_31815064_3   5618 GAACAGGCAACCAACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTG 5667
                            v  i     v                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_31815064_3   5668 ACAAAGGGATAATATCCAGAATCTACAAAGAACTTAAACAGATTTACAAG 5717
                          i  i  iv vi          v  i        ivv   iv iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_31815064_3   5718 AAAAA----AATAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACC 5763
                              ----      i v  i?    i            v    i    v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_31815064_3   5764 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCT 5813
                         i     v        i  vi viii     i ii  i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_31815064_3   5814 TATCATCATTGGTCAT 5829
                         i v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (142 / 90)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


3084 26.50 1.22 0.55  chr2_31854734_31860307     4183  5084 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31854734_3   4183 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4232
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31854734_3   4233 GGCCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCCATCAAGT 4282
                            v     v      vii  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31854734_3   4283 TACCATTGGCTTTCTTCACAGAATTAGAAAAACT-ACTTTAAATTTCATA 4331
                          v   viv  i  i  ii     v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_31854734_3   4332 TGGAACCAAAAAAGAGCTCGTATAGCCAAGAAAATCCTAAGCAAAAAGAA 4381
                              viiv  ii  v iv v        i v    i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_31854734_3   4382 CAAAGCTGGAGGCATCACATTACCTGACTT-AAAATTATACTACAAGGCT 4430
                              i      vv     i v  ii i  -    i -        i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr2_31854734_3   4431 ACAGTGACCAAAACAACATGGTACTGGTACCAAAACAGATACATAGACCA 4480
                              i i   i   iii         i iv ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_31854734_3   4481 ATAGAACAGAAC--AGAGTCCTCAGAAATAAGACCACACATCTACAACCA 4528
                           i   i    i--       --        iv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_31854734_3   4529 TCTGCTCTTCGACAAGCCTGACAAAAACAAGCAATGGAAAAAAGATTCTC 4578
                         vi  v i         vv  v   i v  vv      ii   ii  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_31854734_3   4579 TATTTAATAAATGGTGCTGGGAAAATTCGCCAGCCATATGCAGAAAACAA 4628
                          v  i  i              v  i v vi ?   i     i  i vvi
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_31854734_3   4629 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 4678
                           ii         v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_31854734_3   4679 TAAAGACTTAAATGTAAAACCTAAAATAATAAACACCCT-AGAAGAAAAC 4727
                         i ?    i         i v      iv     -  i  -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chr2_31854734_3   4728 CTAGGCA-ATACCATTCAGGACATAGGCATAGGCAAAGACTTTATGGCTA 4776
                         v    ?i- v i -   iv   v v  vv       v ii  iv i v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_31854734_3   4777 AAATACAAAAAGCAACTGCAAAAAAAGCCAAAATTGACAAATGGGATCTA 4826
                         vi i  v       vvv    v     vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_31854734_3   4827 ATTAAACCAAAAAGCTTCTCCACAACAAAAGAAACTATCATCAGAGTAAA 4876
                           i   viv    i   i vii vv    i  v       vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_31854734_3   4877 CAGGCAACCTACAGAATGGGAGAAAAGTTTTGCAATCTATCCATCTGACA 4926
                         v  i     i                vv       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_31854734_3   4927 AAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAA 4976
                          i  i  vi          v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_31854734_3   4977 AA-----ACAACCCCATCAAAAAGTGGGCAAAGGATATGAAAAGACACTT 5021
                           ----- i     v  i?    i            v    v     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_31854734_3   5022 CTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGTTTAT 5071
                            v        i  vi vi       i  i  i       i v i i v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_31854734_3   5072 CATAACTGGTCAT 5084
                            v ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


 920 28.63 0.38 0.00  chr2_31915630_31922230      243   504 (6097)    L1M4_orf2#LINE/L1      130   392 (516)  

  chr2_31915630_3    243 AAACT-ATTTTAAAATTCATATAGAACCAAAAAAGAGCTCATATAGCCAA 291
                           i  -  ii            i   viiv  ii  v iviv        
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_31915630_3    292 GACAATCCTAAGCAAAAGGAACAAAGGTGGAGGGATCACACTACTGGACT 341
                         i      i i iv  i i        v      iv       v ivi i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_31915630_3    342 TCAAACTATACTACAAGGCTACAGTAACCAAAACATGATAGTACTGGTAC 391
                              viv        i          i   i   vvi i       i i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_31915630_3    392 AAAAACAGACACATAGACCAATGGAACGGAATAGAGAACTCAGAAATATA 441
                           ii i     i     i        ii    v    iii        v 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_31915630_3    442 ACTGTACATCTACAACCATCTGATCTTCAACAAACCTGACAAAAACAAGC 491
                         v ii     i  iiii  vi    i   i    ivv  v   i v  vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_31915630_3    492 AATGGGGAAAGGA 504
                                    i 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAA 392

Transitions / transversions = 2.12 (51 / 24)
Gap_init rate = 0.00 (1 / 263), avg. gap size = 1.00 (1 / 1)  

1153 28.08 2.29 0.29  chr2_31915630_31922230     3825  4173 (2428)    L1M4_orf2#LINE/L1        3   358 (550)  

  chr2_31915630_3   3825 GGAAGACATTCCATGCACATGGATAGGAAGAATAAATATTGTTAAAATGG 3874
                          i    i  i     iv       v      v v           i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_31915630_3   3875 TCATACTACCCAAAGTGATTTACACATTCAATGCTATTCCAATTA----- 3919
                         iv     v      v    i    v      i  v  i  v  i -----
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_31915630_3   3920 CCAATGACATTCTTCACAGAACTAGAAAAA--AATTTTTTAAATTCATAT 3967
                            iivi v  i  ii     v v  v  i--i  ii v-          
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA-AAATTCATAT 151

  chr2_31915630_3   3968 GGAACCAAAACAGAGCCCGAATAGGCAAAGCAATCCTAAGCAAAAAGAAC 4017
                             viiv  vi  v  v      v    i     i i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_31915630_3   4018 AAAGCAGGAGGCATCACACTACCTGACTTCAAACTATACTACATGGGTAA 4067
                             iv     vv       v  ii i      viv       vi v  v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_31915630_3   4068 AGCAAACAAAATAG-ATGGTACTGGTACAAAAACAGACACATAGACCAAT 4116
                           i  v   i i  -i         i i  ii i     i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_31915630_3   4117 GGAAGAGAATAAAGAGCCTGGAAATAAGGGCACACACCTACAATCGTCTG 4166
                             v     vi    i ii       ivv  i   ii  iii  ivi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_31915630_3   4167 ATATTTG 4173
                           v  i 
  L1M4_orf2#LINE/    352 ATTTTCG 358

Transitions / transversions = 1.51 (59 / 39)
Gap_init rate = 0.01 (4 / 356), avg. gap size = 2.25 (9 / 4)  

1688 26.04 1.04 0.42  chr2_31915630_31922230     5233  5712 (889)    L1M4_orf2#LINE/L1      346   828 (80)  

  chr2_31915630_3   5233 CAATAGATATTTAATAAAGTTGACAAAAATAAGCAACAGGGAAAGGACTC 5282
                             v   v  ii i  i v  v   i vi vv   ii       i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_31915630_3   5283 CCTATTCAATAAATGGTGCTGGAATAACTGGCTAGTCAAATGCAGAAGAT 5332
                         i  v     i            i i      v  ?i  v     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_31915630_3   5333 TGAAACTGGACCCCTTCCTTACACCATATACAAAAATCAACACAAGATGG 5382
                             ii         v   i                 i   v   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_31915630_3   5383 GTTGAAGATTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGATAA 5432
                         i ii?   ii         i v i            vi i       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_31915630_3   5433 CCTAGGA-TATACCATTCTGGACATAGGAACTGGCAAAGATTTCATGACA 5481
                          v    ?-  v i -   vv   v v  iviv     v i    v iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_31915630_3   5482 AAGACACCAAAAGCAATCGCAACAAAAGCGAAAATTGACAAATGGGATCT 5531
                          v             vvv          vi     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_31915630_3   5532 AATTAAACTTAAGACCTTCTGCACAGCAAAAGAAACTATCAAGAGAGTAA 5581
                         v  i   v    i v   i  ii vv    i  v          i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_31915630_3   5582 ACAGACAACCTACAGAATAGGAGAAAATATCTGCAAACTATGCATATGAC 5631
                          v        i       i           i      ii  ii  v   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_31915630_3   5632 AAAGGGCTAATATTCAGCACATATAAGAAACTTAAACAAATTTACAAGGA 5681
                           i  i  vi   i   v i      ii    ivv    v iv i  v- 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-A 793

  chr2_31915630_3   5682 AAAAGACAA----CCCCATTAAAAGGTGGGCAAAG 5712
                                  ----   v   ?   ii         
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.28 (68 / 53)
Gap_init rate = 0.01 (4 / 483), avg. gap size = 1.75 (7 / 4)  

 375 18.58 5.31 1.77  chr2_31915630_31922230     5997  6109 (492)    L1M4_orf2#LINE/L1      792   908 (0)  

  chr2_31915630_3   5997 TAAAAAAATAAA------AATAAAAAAATTGGGCAAAGGATGTGAACAGA 6040
                               i i   ------   v?      -           v    i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAAT-GGGCAAAGGATTTGAATAGA 840

  chr2_31915630_3   6041 AACTTTTCAAAAGAAGACATATATGCAGCCCATAAGCATATGAAAAAAAA 6090
                         v i  i  v        i   i viii   v       i       i v-
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT- 889

  chr2_31915630_3   6091 GCTCAATATCACTGATCAC 6109
                               i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.03 (3 / 117), avg. gap size = 2.67 (8 / 3)  


1858 18.26 0.41 26.04  chr2_31923402_31928162     3051  4271 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31923402_3   3051 TGGAAGGATATTCCATGTTAATGGATTGGAAGAATCAATATCATTAAAAT 3100
                              i     i       v             v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31923402_3   3101 GTCCATACATACTACCCAAAGTAATCAACAGATTCAATACAATTCCTATC 3150
                          v --- -     v      v i   v          ii    i      
  L1M4_orf2#LINE/     51 GGC---A-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_31923402_3   3151 AAAATACCAATGGCATTCTTCACAGAAATAAAAAAAA-AATCCTAAAATT 3199
                              v   iiv  v  i  ii       vi v  iv-i           
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_31923402_3   3200 TATATGAAACCACAAAAGACACAGAAGAGCCAAAGTCACCCTGAGCAAAA 3249
                         i     i  vii   ii   v     v       iiv i i   iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_31923402_3   3250 CTAACAAAACTGGAGTAATCACATTACCTTACTTCACACTAGACTACAGA 3299
                         vv      ii     v v     i v  iv i    v vivv      i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_31923402_3   3300 GCTATAGTAACCAAAACAGTAATGGTACTGGCATAAAAACAGACACACAG 3349
                             i     i   i     i-              ii i     i i  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTG-TGGTACTGGCATAAGGATAGACATATAG 295

  chr2_31923402_3   3350 ACCAATAGAACACAATAGAGAACGCAGAAACAAATTCATACATCTACAGT 3399
                          i    i   i v   v    iiv      i   ii       i  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_31923402_3   3400 GAACTCATTTTCAACAAAGGTGTCAAGAACATACACTGGGAAAAGGACAG 3449
                         v  i v      i    i    i     v   v  v    i    i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_31923402_3   3450 TCTCTTCAATAAATGTTGCCGGGAAAAGTGGATATCCATATGCAGCAGAA 3499
                            i     i     v   i    v  v      ?   i     iv    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_31923402_3   3500 TGAAACTAGACTCCTATCACTTGCTATTAAAAAAATAAAATAAAATCAGC 3549
                             ii i   i    i --------------------------------
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACC-------------------------------- 463

  chr2_31923402_3   3550 CGGGCATGGTGGCTCAAGCCTGTAATCCTAGCACTTTGCAAGGCCAAGGT 3599
                         --------------------------------------------------
  L1M4_orf2#LINE/    464 -------------------------------------------------- 463

  chr2_31923402_3   3600 GGGTGGATCACTTGAGATCAGGAGTTCAAGACCAGCCTGGCCAACATGGC 3649
                         -------    -------------------    ----------------
  L1M4_orf2#LINE/    464 -------TCAC-------------------ACCA---------------- 471

  chr2_31923402_3   3650 AAAACGCTGTCCACACTAAAAATACAAAAATTAGCTGGGCATGGTGGCAT 3699
                         ----------------  ----           i  --------------
  L1M4_orf2#LINE/    472 ----------------TA----TACAAAAATTAACT-------------- 487

  chr2_31923402_3   3700 GCACCTATAATCCCAGCTATTTGAGAGGCTGAGGCACCTGAATCATTTGA 3749
                         --------------------------------------------------
  L1M4_orf2#LINE/    488 -------------------------------------------------- 487

  chr2_31923402_3   3750 ACCTAGGAAGTGGAGGTTGCAGTAAGCCAAGAATGCACCACTGCACTCCA 3799
                         --------------------------------------------------
  L1M4_orf2#LINE/    488 -------------------------------------------------- 487

  chr2_31923402_3   3800 GCCTGGGTGACAGAACAAGACTGTCTCAAAACAAGCAAACAAAAAAATCA 3849
                         --------------------------------------------------
  L1M4_orf2#LINE/    488 -------------------------------------------------- 487

  chr2_31923402_3   3850 AATCAAAATGGATGAAAGACTTCAATCTAAGACTTCAAACTATGAAACCT 3899
                         ---          v ?    i v   v     vi v       i    ii
  L1M4_orf2#LINE/    488 ---CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_31923402_3   3900 CTATAAGAAAACATTAGAGAAACTCTCCAGGACATCGTAGTGGGCAAATA 3949
                         i  v          vi ? v  v   i iv   v i viv i     - i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TG 583

  chr2_31923402_3   3950 ATTTCTTGAGTAATATCCTACAAGCACAGGCAATCAAAGCAAAAATGGAC 3999
                         i      iii  vv iv i v       i    iv    v      i  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_31923402_3   4000 AAATGGGGTTATATCAAG-TTAAAAAGCCTCTGCACAGAAAAGAAAATAA 4048
                             v  ii vi     i-       - i i  ii vvv    i v iv 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA 682

  chr2_31923402_3   4049 TCAGTAGAGTGAAGAAACAATGCACAGGC--GGAGAAAATATTTGCAAAC 4096
                            iv i      i i    iv     iv--                  i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_31923402_3   4097 TAACAATCCGACAAGGGATTAATAACCAGAATATATAAGGAGCTCAAACA 4146
                         i vvv   i  i      i vi  v             i  i   vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_31923402_3   4147 ACTCTATAAGAAAAAATCTAATAATCCAATTTAAAA-TGGGCAAAATATT 4195
                             v    v     iv v     i      ?    -        iv   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_31923402_3   4196 TGAAGAAACATTTCTCAGAAGAATACATATAAATGGCAAACAAGTATATG 4245
                             v i         vi     v i   i       v  i   i i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_31923402_3   4246 AAAAGGTGCTCAGCATAACTGATCCT 4271
                              i      i   v ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (134 / 85)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 23.07 (323 / 14)  


3028 27.17 2.82 0.45  chr2_31931558_31937908     4973  5859 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_31931558_3   4973 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATGGTGAAAAT 5022
                              ii i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31931558_3   5023 GGCCATACTGCCCAAGGTAATGTATAGATTCAATGCTATCCCTATCAAGC 5072
                            v     v     iv i  v  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31931558_3   5073 TACCAATGACTTTCTTCACAGAATTGGAAAAAACCACTTTAAAGTTCATA 5122
                          v   iivi i  i  ii     v v  v  iviv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_31931558_3   5123 TGGAACCAGAAAAGAGCCCACATTA-CCAAGACAAGCCTAAGCAAAAGGA 5171
                              viiv  ii  -    v v  -    i    v i i iv  i i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_31931558_3   5172 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGCT 5221
                               i      vv       v  ii i      vivi       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_31931558_3   5222 ATAGTAACCAAAACAGCATGGTACTGGTAGCAAAACAGAGATATAGACCA 5271
                          i     i   i    ii         i vv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_31931558_3   5272 ATGGAGCAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCA 5319
                              ii    i--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_31931558_3   5320 TCTGATCTTTGACAAACCTGACAAAAACAATAAATGGGGAAAGGATTCCC 5369
                         vi    i  i     ivv  v   i v  v v           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_31931558_3   5370 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5419
                          v  i  i        i     v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_31931558_3   5420 AAATTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGAC 5469
                           i     i    v   i    iv              i    i     i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_31931558_3   5470 TAAAGACTTAAATGTCAGACCTAAAACAATAAAAACCCTAGAAGAAAACC 5519
                         i ?    i       v   v       v      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_31931558_3   5520 TAGGGA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTTCTGTCTAA 5568
                             ?i- v i -   iv   v v  vv i     v ii  ii ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_31931558_3   5569 AACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATATAA 5618
                         i            vvi      i   vv     v  i    v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_31931558_3   5619 TTAAACTAAAGAGCTTCTACACAGCAAAAGAAATTACTATTGGAGTGAAC 5668
                          i   v v  i i   i iii vv    i  v i  ii vvii      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_31931558_3   5669 AGGCAACCTATGGAATGGAAGAAAAT-----------------CTGACAA 5701
                           i     i ii      i       -----------------    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_31931558_3   5702 AGGGTTAATATCCAGAATCTACTAAGAACTCAAACAAATTTACAAGAAAA 5751
                         i  ii vi          v  iv        vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_31931558_3   5752 AAACAA----CCCCATCAAAAAGTAGGCAAAGGATATGAACAGACACTTC 5797
                          i    ----   v  i?    i i          v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_31931558_3   5798 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGTTCATC 5847
                           v        i  vi viii     v ii          i   i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_31931558_3   5848 ATCACTGGCCAT 5859
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.62 (29 / 8)  


1967 25.40 3.72 4.21  chr2_31966427_31968780.rev      668  1285 (1069)    L1M4_orf2#LINE/L1        1   615 (293)  

  chr2_31966427_3    668 TGAAGATATATACCTTCTGCATGGGCTGGAAGACTCAATATTTTTAAGAT 717
                           i i v    v  v v v     ii         i      v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_31966427_3    718 ATCAGTTCTCCTCAAATTGATTTATAGATTCAACATAATCCCAACCAAAA 767
                         iv  i v    i         i  i         ii      v i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_31966427_3    768 TCTCAGCAGACTTA---AAAAAAAATGGGAA-CTGGC----AAGCTGGTA 809
                           i    v v   v---iv i   v  iv  -   ii----  ii vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_31966427_3    810 TGGGAATGCCAAGGACCTAGAATAACTGCCACAA-CTTCAGAAGAAGAAG 858
                            i     v i     i      i iivv    -   ----------- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT-----------G 189

  chr2_31966427_3    859 AAAAAAAAGAACAAAGTTGAAAGGCT-ATACTATTGGATTTTAACCATTA 907
                              i             i i i  - i   viivi    i  vvv   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_31966427_3    908 TTATTAAAATATAATAATCAAAACAGGGTGGTATTGGCATGAAGATAGAC 957
                         i  iv  iv  i i       i    v      i      i i       
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_31966427_3    958 AATTACACTAAAGAAGCGGAATAGATAACTCTGAAATAGACCCACACAT- 1006
                          vv  v ii  v i iii    v  v iii v      i     i    -
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_31966427_3   1007 ---GGACAATGACTTTTTTAGAGTGGTACAAAGGTAATGCAATGGGAACA 1053
                         ---  v    viv    iv v iv   i v   iiv  v       i v 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_31966427_3   1054 GTGTAGATTTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATCT 1103
                          vi   - i                    i    i      ?   i  --
  L1M4_orf2#LINE/    390 GAATAG-TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-- 436

  chr2_31966427_3   1104 CTATCTATATGTATATAAAGGAACTTGGATTGATGCCATGCAACATATAC 1153
                         ---------- i v vi  v   v     iivv i  vii  v       
  L1M4_orf2#LINE/    437 ----------GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_31966427_3   1154 AAAAACTAACTCAAAATAGGTCATATATGTCAATGTAAAACCTAAA---- 1199
                              i           i i   ? v iv v       i v     ----
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_31966427_3   1200 -----CTCTTAGAAGAAAACATGGGAGAAAACCTTTGTAACCTTCGGTTC 1244
                         -----                 i  ? v   i   i  i     v    v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_31966427_3   1245 AGCAAATATTTCTTAGATAAAACACCAAAATCGGCCAGGCA 1285
                         i    vvi           vi         v i--  i   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCA--CAAGCA 615

Transitions / transversions = 1.41 (90 / 64)
Gap_init rate = 0.02 (11 / 615), avg. gap size = 4.45 (49 / 11)  

1307 16.44 7.19 1.03  chr2_31966427_31968780.rev     1571  1862 (492)    L1M4_orf2#LINE/L1      599   908 (0)  

  chr2_31966427_3   1571 CACCAAAATCACAACCAATAAAAGGATGAATTGATAAATTAGACTTCATC 1620
                                 v     v   i     i vi   v        i         
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_31966427_3   1621 AAAATTTAAAATTTCTATTTTTCAAAG-ACACTATTAAGAGAATGAAAAG 1669
                               v    i  i i vi       -       i    i i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_31966427_3   1670 ACAAGCCACATAGTGAGATAAAATCTTTGGCCAGA--ATATATTTGATAA 1717
                             v     v i  i  v     v    --  i --      i      
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTG--CAAATCATATATCTGATAA 746

  chr2_31966427_3   1718 AGGACTTG------------------GACACTTGAAACTCAACAATAAGA 1749
                         i       ------------------i  v   iv       i     i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_31966427_3   1750 AAACAAATAACCCAATTAAAATAATGGGCTAAAGATTTGAACAGACATTT 1799
                          i               ?   -       v  i        i        
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_31966427_3   1800 CTCCAAAGAAGATATATAGATGACAAGTAATTGCATGAAAAGGTGCCCAA 1849
                                         i i   i v i   vii         i   i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_31966427_3   1850 TATCATTACTCAT 1862
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (32 / 15)
Gap_init rate = 0.02 (5 / 310), avg. gap size = 4.80 (24 / 5)  


3168 26.28 0.54 1.95  chr2_32237432_32243803.rev     4960  5880 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_32237432_3   4960 TGGAAGAACATTCCATGCTTATGGATAGGAAGAATCAATATCATGAAAAT 5009
                              ii i  i     i i      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_32237432_3   5010 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5059
                            v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_32237432_3   5060 TACAAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5107
                          v v iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_32237432_3   5108 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5157
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_32237432_3   5158 AACAAAGCTGGAGGCATCGTGCTACCTGACTTCAAACTATACTACGAAGG 5207
                                i      vv  iii  v  ii i      viv      i   v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_32237432_3   5208 TACAGTAATCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGACC 5257
                                     i    ii        ii iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_32237432_3   5258 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5305
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_32237432_3   5306 ATGTGATCTTTGACAAACCTGACAAAAACAATAAATGGGGAAAGGATTTC 5355
                          vv    i  i     ivv  v   i v  v v           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_32237432_3   5356 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAAACGTACAAAGCT 5405
                           v  i  i              v      v  ?   v i i v  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_32237432_3   5406 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5455
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_32237432_3   5456 TTAAAGACTTAAATGTTAGTTCTAAAACTATAAAAACCCTAGAAGAAAAT 5505
                          i ?    i       v  vv              vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_32237432_3   5506 CTAGGCA-ATACCATTCAGGACACTGGCATGGGCACTGGCATGGGCAAGG 5554
                         v    ?i- v i -   iv   -  ----    i------- i     v 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGAC-CT----TGGGT-------TAGGCAATG 583

  chr2_32237432_3   5555 ACTTCATGCCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAC 5604
                         ii   v ivv  vi            vvi          vv     v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_32237432_3   5605 AAATGGGATCTAATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTAC 5654
                             v   ii v  i   v v  i ii  i  ii vv    i  v    i
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_32237432_3   5655 CATCAGAGTGAACAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCT 5704
                           vv i      v  i     i i               v       vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_32237432_3   5705 ACCCATCTGACAAAGGGCTGATATCCAGAATCTACAAAGAACTTAAAAAA 5754
                          ivi      i  i  i  vi          v  i        ivv v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_32237432_3   5755 ATTTACAAGAAAAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGTATA 5804
                         v iv i  v     i -    i     v  i?    i         v  v
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_32237432_3   5805 TGAACAGATGCTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATG 5854
                             i   iii     v        i  vi viii     v ii      
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_32237432_3   5855 AAAAAATGCTCATCATCACTGGCCAT 5880
                             i       v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


3456 23.32 3.25 1.68  chr2_32259019_32261501     1100  1991 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_32259019_3   1100 GAGAGATATTCCATGTAAATGGACAGGGAGACTAAATATTATTGAGATGT 1149
                           i      i      vv     iv  i     v      i  i     v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_32259019_3   1150 CAGTTCTTCCCAAGTTCATATATCGATTCAGTGCAGTCCCAGTCAAA-CC 1198
                           i v  i     i  v  v  iv      ii   i    vi     -i 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_32259019_3   1199 CCAGCCAGTTATTTTGTGGATACTGGCAAACT------AAAGTTTATATG 1242
                              iivi v     ii  v i  i   i  ------   i  i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_32259019_3   1243 AAAAGGCAAAAGACCTAGAACAGCCAACACAGTATTGAA---GAAGAAAA 1289
                         i   v    ii    i    i      v   i v     ---      v 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_32259019_3   1290 AAGTCAGAGGACTGAAACTACCCAATTTCAAGACTTACTGTAAAGCTACA 1339
                             ii       v v   v           i       ii         
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_32259019_3   1340 TTAATCAAGACAGCATGTCATTGGCAAAAGAATAGACAAATAAATCAGTA 1389
                         v            ii  vi i     v   i       v   i    i i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_32259019_3   1390 GAATTGGACAGAGAGCCTAGAAATCAACCCACACAGATAAAGTCAACTGA 1439
                             v i iv     i i      v      i   vv  vi     i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_32259019_3   1440 TCTTTGGCAAAGGGACAAAGACAATTCAGTGGAGAAAAGATAGCCTTTTC 1489
                          i  i i   i  vi v     v     i   i    ii    i      
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_32259019_3   1490 AACAAATGGTA-TAGGACAACTGGACATCCACATGCAAAAAAGTTAATCT 1538
                                   i- i           i ?            i i v  vi 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_32259019_3   1539 AGACACAGACCTGACAACTTTCACAAAAAT-------AAATGGATCATAG 1581
                         i   v vv    v   v v vi        -------          ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_32259019_3   1582 ACCTAAATGTAACATGC--GAACTG--AAACTTCTAGAGGATAACATAGG 1627
                                     v -  --i    i--     ii    i  v        
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_32259019_3   1628 AGAAAATCTAGGATAACATGAGAAAAATTTTTGGTTTGGCAGTGACTTCT 1677
                         ? v      ---- -- i   ------ii  v    v    i  ii    
  L1M4_orf2#LINE/    552 NGTAAATCT----T--CGTGA------CCTTGGGTTAGGCAATGGTTTCT 589

  chr2_32259019_3   1678 TAGGTACAATACCAAAA-CATGATCCTTGAAAAAAAAAATCAGTATGTTG 1726
                            i  ii i       -  ii v vvii   i       vii  vi   
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_32259019_3   1727 AACTTTGTTTAAATTATAAACTTCTGCTCTGTGTAAGATGCTGTTAGGAG 1776
                         i    ii iv      v      i  iv  viiv i  ii  i i i  i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_32259019_3   1777 AATGAAAAGACATGCAGCAGAGTGGGAGAC----TTTACAAAATTCAT-T 1821
                          i          vv vi    i       v----   i    --    - 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA--TCATAT 737

  chr2_32259019_3   1822 ATCTGATGAAGGACCAGTATCCAAAATATACAAAGAACTTTTAAAACTCA 1871
                                i i    iv       i      i        i   v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_32259019_3   1872 ACAATAAGAAAATATACAACCCAGTTAATAAATGGGCAAAATATCTGAAC 1921
                          i     i  i i v i      i  ? v           iv  i    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_32259019_3   1922 AGACACCTCACCAAGGAAGATAGATAGATGAC-AACAAGCATATGAATAT 1970
                              ii  v    i       v i i   i -  i     i     v v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_32259019_3   1971 ATGCTCAACATCATGTCGTTA 1991
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (134 / 70)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 2.75 (44 / 16)  


2393 26.53 5.40 1.68  chr2_32274657_32276484.rev      504  1336 (492)    L1M4_orf2#LINE/L1       45   908 (0)  

  chr2_32274657_3    504 TAAAATGACTATACTGCCCAAAGCAATTTACAGATTCAATGGTATTTCTA 553
                            i   i v     v      vii  i           i vv  ii   
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_32274657_3    554 TCAAACTATCAATGTTG--TTTTTCACAAAATTAGAAAAAAATATTCTAA 601
                              v vi  -- i  --     ii  i  v v  v  ivvv  i    
  L1M4_orf2#LINE/     95 TCAAAATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr2_32274657_3    602 AATTCATATGGAA--GCAAAAAAAGAGTCCA-AATAGACAAAGCAATCCT 648
                                      --    iii ----i   -     v    i     i 
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTT 188

  chr2_32274657_3    649 AAGCAAAAAGAACAAAGCTGTAAGTATCACGTTACCTGACTTTAAACCGA 698
                         i iv  i          i  v i vv    ii v  ii i  i   v vv
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_32274657_3    699 ACTACA------CAGCAGCCCAAACAGCATAATTCTGGTATAAAAACAGA 742
                               ------   i ii v i    ii ii v    i    ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_32274657_3    743 CACACAAACCAAAGGAACAGGACAGAAAATTGAGAAATAAAGCCACACAC 792
                           i i i i   v    i  i iv  i i iv         v   i   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_32274657_3    793 CTATAACCATCTGATCTTTGATAAGACTGACAAAAACAAGCAATGAGGAA 842
                         i   iii  vi    i  i  i   iv  v   i v  vv     i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_32274657_3    843 AAGGACTCCCTATTCAATAAATGGCATGGGGATTACTGGCTAGCCATATG 892
                          - i ivvi  v     i      iiiv    iv     v  ?   i   
  L1M4_orf2#LINE/    389 A-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_32274657_3    893 TAGAAAAATGAAACTGGACCCTTACTTTTCACCATATACAAAAATTAACT 942
                         i i  i      ii       i   i iv                     
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_32274657_3    943 CAAGGTGGATTAAAGATTTAAATGTAAGATCTCAAAGTATAAAAATGCTA 992
                            ii     i ?   ii           v  v   v       v vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_32274657_3    993 GAAGAAAAC-TAGG---AAATACACTTCTTGACATCAGCCTCAGAAAGAA 1038
                                  -    ---    ---    v    v ii vi vi v  vii
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_32274657_3   1039 ATT-TTGGCTAAGTCCCCAAA--CACAATTGCAACAAAAATAAAAATTGA 1085
                         v  -  i v  v v v     --     --         iv      v  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGA 632

  chr2_32274657_3   1086 CAAGTGGGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAAGAACCA 1135
                         i  i v    i v  i   v v  i i   i  ii vv    iiiv  i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_32274657_3   1136 TCAACAGAGTAAACAGACAATCTACAGAAC-------------TGCA--- 1169
                             v i   i  v      i i      i-------------    ---
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_32274657_3   1170 ------TCTAACAATGGTCTGATATCCAGAATCTATAAGGAATTCAAACA 1213
                         ------   i i  v  v  vi          v     i   i  vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_32274657_3   1214 ATTGAACAAGCTAAAAACACACAACCCTATTAAAAAATGGGTAAAAAGGA 1263
                          i v  i  vvv   i   v i     v   ?         i   --   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA--GGA 830

  chr2_32274657_3   1264 AATGAATAGACACTTCTC---AAAAGACATACGAGGGGACAACAA--ACA 1308
                         vv          i     --- i    i    i iv  v   i  --   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_32274657_3   1309 TGAAAAAATGCTCATCATCACTAACCAT 1336
                               i       v     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (133 / 85)
Gap_init rate = 0.02 (18 / 864), avg. gap size = 3.28 (59 / 18)  


4073 15.25 4.25 5.34  chr2_32915615_32918114.rev     1091  2008 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_32915615_3   1091 TGTAAAGACATTCCATGTTCATGGATCAAAAGACTTAATATTATTAAGAT 1140
                           v     i  i              iii             i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_32915615_3   1141 GGCAGTACTCCCCTTATTCACCTGCAGATTCAA---------TAT-AAGG 1180
                             i        vv   v i  i         ---------   -  ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_32915615_3   1181 TC-----------TTTTGGGGAAATTTACAAAGCTAA----AAATCCCAT 1215
                           -----------     vi      v    -   i ----   vii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_32915615_3   1216 AGGAAAATTCAAGGAATGCTGAATAGCCAAAACTATCTTGTAAAGGAAGA 1265
                          v i    v     i iv v             v      v   i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_32915615_3   1266 ACAAAGTTGGAGTACTCACAG----CATTTTCAAAACTTACTACAAAGTT 1311
                                     v       v----  v                    i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_32915615_3   1312 TCTGTAAACAAGACAGTGGAATATGCACAGACCTATAGTCAATGAAATGT 1361
                         v v    v          vii  ---- v i v  -  -----  v ---
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTA----CTGGCATA-AG-----GATA--- 286

  chr2_32915615_3   1362 GACATACAG-TCAATGAAATGTGATTGATGGACCATAAATACATCCTTAC 1410
                               i  -      i   ivi     vi v   v     ---------
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA--------- 327

  chr2_32915615_3   1411 ATTACAGTCAATTAATTTTTGACCACTTACATTTACAGTAAACTGATTTT 1460
                         -------------  i------   --        ii  v  i       
  L1M4_orf2#LINE/    328 -------------AAC------CCA--TACATTTATGGTCAATTGATTTT 356

  chr2_32915615_3   1461 TGACCAGAGTGACAAGACTATT-AATAGGAAAAGAATAGTCTTTTCAACA 1509
                         i   v  i   v      i   -   i  i                    
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_32915615_3   1510 AA--GTTTTGAGACAACTGGATATCTACATGTAAAAGAATGAAGTTGGAC 1557
                           --  vi  i            ? i     i                  
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_32915615_3   1558 CCCTTCCTTATATCATAAATAAAA-TTAACTTAAAATGGTCCCTAGACCT 1606
                             v   i i i    v i    -      i       vi v?      
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_32915615_3   1607 TAATGAAAGAGTTAAAACTATAAAACTCCTAGCAGAAAAGATAGGAGTAC 1656
                         v    v     i                i   v      v     ?   v
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_32915615_3   1657 ATCTTTGTGACTTTGGATTTGGCAATGGATTCTTAGATATTGTACCAAAA 1706
                              i     i    i  v        v           vii       
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_32915615_3   1707 GTATGAGCAACAAAAGAAAAAACAGGTAAGTTGGACCTCATCAAGATTAG 1756
                          i ii                 i  i   i      i       i    i
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_32915615_3   1757 G--CTTTTGTGCTTTAAAGTGCACAATCAATAGAGAGAAAAAAAAAAAAC 1804
                         i--           i    vi   v     v i  v     i v  --- 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA---C 703

  chr2_32915615_3   1805 TTAACAGAATGGGAGAAAATATTTGCAAATCATTTGTCTGACAAGGGACT 1854
                         ii -                             v i     i        
  L1M4_orf2#LINE/    704 CCA-CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_32915615_3   1855 TGTAGCTAGAATATAGAAAGAACTCTTACAACTCAATGATAAAAGGATAC 1904
                             v i        v                     i      i  i v
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_32915615_3   1905 ATGACCCAATTTTAAAAATGGGTAA-GGATGTGAATAGACATTTC--CAA 1951
                           i        ?-         i  -    v              --   
  L1M4_orf2#LINE/    803 ATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_32915615_3   1952 AGAGGATATACGAATGGCCAAGAAGCATGTGAAAAGATGCTCAACATCAT 2001
                            i       i         v     ii                    ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_32915615_3   2002 TAGCCAT 2008
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.52 (82 / 54)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.83 (88 / 23)  


 459 18.18 0.00 1.14  chr2_32932825_32935246      207   294 (2128)    L1M4_orf2#LINE/L1        1    87 (821)  

  chr2_32932825_3    207 TGGAAACACATCTCATGTTCATGGATTGAAAAACTTAACATTGTTAAGTT 256
                               v i   i               i  i      i         v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_32932825_3    257 GTCAGTACTACCCAAAGTGATGTCTGGAATTCAGCGCA 294
                          v  i    v      v    v vii -     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAG-ATTCAACGCA 87

Transitions / transversions = 1.29 (9 / 7)
Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1)  

1142 21.34 2.51 0.00  chr2_32932825_32935246      518   756 (1666)    L1M4_orf2#LINE/L1      112   356 (552)  

  chr2_32932825_3    518 TTTTTCTCAGAAATAGAAAAACCTATCCTAAAATTCAAATGGAATCTCAA 567
                              iv       v  v  i iv             v      viv   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_32932825_3    568 GAGACCCTGGATGGCCCAAACAACTTTTAAAAAGAACAACAAAGCTAGGG 617
                          i     v i  i   v      ii  v        v       i i i 
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_32932825_3    618 GACTCATGCTTCCTGATTTCAAAACTTACCACAAAACTGTAGTAGTCAAA 667
                               ii     ii              i     i  ii    i    i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_32932825_3    668 ACAGTGTGGAACTGGCATAAAGACAGACATACAGACCAATAGAATTGAAC 717
                                  v          i  i       i   i    i    v   i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_32932825_3    718 TAAAAGCTCAGAAAT----CTGTGTAT--ATGGTCAAAGGATTTT 756
                          i i  ii       ---- ii ii  --        vv      
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 2.40 (36 / 15)
Gap_init rate = 0.01 (2 / 245), avg. gap size = 3.00 (6 / 2)  

2878 16.07 1.79 1.07  chr2_32932825_32935246     1371  1930 (492)    L1M4_orf2#LINE/L1      345   908 (0)  

  chr2_32932825_3   1371 TCAAATGATTTTTGACAAGGGTGCCAAGACTATTCAATGGGGAAA----- 1415
                             v       i                 i              -----
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_32932825_3   1416 ----TTTCAACAAATTGTCCTGGGAAAACTGCATATCCACATGCAAAAGA 1461
                         ----           v  v      v     v   ?              
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_32932825_3   1462 ATAAAGTTGGACCCTTACCTAACACTGTATACACATGCTAACTCAAAATG 1511
                           i           i     v    ii      v vii            
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_32932825_3   1512 AATCAAATACTTAAATTTAATAGCTACAACTGTAAAACTCTTAAAAGTAA 1561
                         i    ? v  i     v   v     v    i           i   v  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_32932825_3   1562 ACATAGGGCAAGAACTTTATAACGGTAGATTTGGCAATGATTTCTTGGAT 1611
                                ?vv i v   ii i  vv i i  v       i      i   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_32932825_3   1612 ATGACACCAAAAGCACAGGCAATAAAAAGAAAAAACAGACAAATTGGACT 1661
                                          i    i    -       i   i          
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACT 643

  chr2_32932825_3   1662 TTGTGAAAATTTAAAAATTTTGTGCACCAAAA-ACAGTATCAACGGAGTA 1710
                          ii v      v    v        vi    i-   v      vii   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_32932825_3   1711 AAAAGCCAACTCACAGAATGGAAGAAAATATTTGCAAGTAATATATCTGA 1760
                              v    i          i               i v          
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_32932825_3   1761 TAAGGGAATAATATCCAGAATATATAGAGGACTTCTAAAATTCAATGACA 1810
                                v vi               i  i   ii  v  i     i i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_32932825_3   1811 ACAAAACCCCCCAAACAGCCCAATTAAAAAATGTGCAAAGGAGTTGAATA 1860
                          v  i  -----   i i       ?       v        v       
  L1M4_orf2#LINE/    794 AAAAGAC-----AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_32932825_3   1861 GACATTTCTCCAGAGAAGATAAACAAATGAACAATAAGCACATGAAAAGA 1910
                                     i        v       iv                   
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_32932825_3   1911 TGTGCAGCACCACTAATCAT 1930
                           iv  i  i  ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (50 / 36)
Gap_init rate = 0.01 (4 / 564), avg. gap size = 4.00 (16 / 4)  


2242 11.51 1.93 29.98  chr2_33042186_33044209      501  1534 (490)    L1M4_orf2#LINE/L1      165   908 (0)  

  chr2_33042186_3    501 ACCCAGAATAACCAAAACAATCTTGAAAATGAA---CAAAATTGAAG-AT 546
                                   i                  v   ---    i   i  - i
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_33042186_3    547 TCATACTTCCTGATTTCAAAACTTACTACAAAGCTTAAGTAAACAAGGCA 596
                            i      ii                       vv     v    i  
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_33042186_3    597 GTGTAGTGCTGGCA-GAGACTAGGCATAGAGACTAATGGAGCAGAATTGA 645
                             i  i      -i  iv   i    v   ii      ii        
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_33042186_3    646 GATTCCAAAAATAAACCCATACATCTATGGT-AATTGATTTTCAACTAGA 694
                           v    i                i      -           i  v  i
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_33042186_3    695 ATATCAAGCCCATTCAATAGGTTAAGAATGTTTCTTTTCAACAATTGGTG 744
                         i ii    v         i  vv      iv -           v     
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGT-CTTTTCAACAAATGGTG 413

  chr2_33042186_3    745 CTGGTACAACTGCTTATCCACAGGCAAACAAATGAATCTGGAACCCTACC 794
                             v       vv  ?     v     vi      vi    v       
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_33042186_3    795 TCACACCATATACAAGAATTAG-----AATGGATCAAAAGACCCAAGTGT 839
                                        i     i-----         ? -    i  i   
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWA-GACCTAAATGT 512

  chr2_33042186_3    840 AAAAGCTAAAAGTGTAAAACCCTTAGAAGCAAACA--GGTATATATCTTT 887
                           i        v i      i        v     --  ?i  v     i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_33042186_3    888 GCGACCTTGGATTTAGCAATTTTGTTTTTGTTTTTGTTTTGAGACAGAAT 937
                          i        i  -------------------------------------
  L1M4_orf2#LINE/    563 GTGACCTTGGGTT------------------------------------- 575

  chr2_33042186_3    938 CTTGCTCTGTCACCCAGGCTGGAGTGCAGTGGTGTGATGTGGGCTCCCTG 987
                         --------------------------------------------------
  L1M4_orf2#LINE/    576 -------------------------------------------------- 575

  chr2_33042186_3    988 CAACCTCTGCCTCCCGGGTTCAAGCGATTTTCCTGCCTCAGTCTCCTGAG 1037
                         --------------------------------------------------
  L1M4_orf2#LINE/    576 -------------------------------------------------- 575

  chr2_33042186_3   1038 TGGCTGGGACCACAGGTGTGGGCCACCACACCCAGCCAATTTTTTTATTT 1087
                         --------------------------------------------------
  L1M4_orf2#LINE/    576 -------------------------------------------------- 575

  chr2_33042186_3   1088 TTAGTCAAGATGGAGTTTCACCATGTTGGACATGCTGGTCTTGAGCTCCT 1137
                         --------------------------------------------------
  L1M4_orf2#LINE/    576 -------------------------------------------------- 575

  chr2_33042186_3   1138 GACCTCAAGTAATCTGCCTGCCTCAGCCTCCCAAAGTGCTGGGATTACAG 1187
                         ------------------------------------------------  
  L1M4_orf2#LINE/    576 ------------------------------------------------AG 577

  chr2_33042186_3   1188 GCGTGAGCGACTGCACCTGGCTGGCAATGGTTTTTTAGTTATGATGTTGA 1237
                           -----------------------        i    v     iiiii 
  L1M4_orf2#LINE/    578 GC-----------------------AATGGTTTCTTAGATATGACACCAA 604

  chr2_33042186_3   1238 AAGCACAAGCAACTAAA-AAAAGAGAGAAAAATCAGATTTCATCAAAATT 1286
                                      v   -    i v   v    ii  i            
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_33042186_3   1287 AAACATTTTTGTGTGTCAAAAGAGACTATCAAGAAAGTAAAAAAACAACC 1336
                            v i       iv     i  v              i    i      
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_33042186_3   1337 TACAGAATGGGAGAAAATATATGCAAATCTTATATTGGGTAAGGGTCTAG 1386
                         i                   v        v     iv i      v  v 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_33042186_3   1387 TATCTAAAATATATGAAGGACTCTTACTATTCAACAATAAAGAGACAAAT 1436
                             i i       i   i        v i    i      i        
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_33042186_3   1437 AGCTCAACTTAAAAGTGGTCAAAACATGTGAATAGACACTTCTCTAA--- 1483
                          i i   i ?    i   v    iv  v          i     i  ---
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_33042186_3   1484 ---TATACGAATGGCCAATACACACATGAAAAGATGCTCTACATAATTAG 1530
                         ---     i           vi                 v    v ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_33042186_3   1531 CCGT 1534
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.74 (73 / 42)
Gap_init rate = 0.02 (12 / 744), avg. gap size = 27.50 (330 / 12)  


 407 22.12 0.96 2.88  chr2_33198278_33199894.rev       11   114 (1503)    L1M4_orf2#LINE/L1      175   276 (632)  

  chr2_33198278_3     11 GTCAAAAAGTGGTTTTGAAAATGCAGAACAAAATTG-AGGGCTTACACAA 59
                          i     --iii i       v v        i   -   i  i    vv
  L1M4_orf2#LINE/    175 GCCAAAA--CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr2_33198278_3     60 CTTGATTTGAAGACTTACTTTTGAAGCTACAGTACTCAAGACAGTGTGGG 109
                          iii    v  i       vi-i           v              v
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTAC-AAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_33198278_3    110 ACAGG 114
                           v  
  L1M4_orf2#LINE/    272 ACTGG 276

Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.33 (4 / 3)  

1533 23.80 7.35 5.27  chr2_33198278_33199894.rev      500  1125 (492)    L1M4_orf2#LINE/L1      270   908 (0)  

  chr2_33198278_3    500 GTACTAGCATAAGGATCAACA-ACAGATCAACAGAATAGC-TGGAAACTC 547
                              i          vi   - i       ii      v- v  i v  
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_33198278_3    548 CC-AAATAGACTCACATATATATGGTCAACTGATTTTTTGATAAAAGGTG 596
                          v-     i  i  i i  v         i       i-  i  i-    
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTC-GACAAG-GGTG 367

  chr2_33198278_3    597 CCAA-AGCATTCCAACGGAGAAAAGAAACTCTTTTCAACAAATGATCCTG 645
                             - v     -  i  i    ii v v               i v   
  L1M4_orf2#LINE/    368 CCAAGACCATTC-AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_33198278_3    646 A-ACAACTAGATATCAGTATAAAGAAAAAAAATGAAGCATCCTGGATTCT 694
                         i-      i    ? vii  --- v    i       i----    ii i
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACAT---GCAAAAGAATGAAGT----TGGACCCC 459

  chr2_33198278_3    695 CACCTTACAC--TACACTCAAGTGAACTCAAAGTTAATCCTAGACCTAAA 742
                         i    i    --  i  vv  i v        i vi   v?         
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_33198278_3    743 CACAGAAGCTAAAACAACAAAGCTCT-AGAAGAAATCATAGGAAAATATC 791
                         iii ii         v i   i    -        v      ?iv v   
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_33198278_3    792 TTTATAATTTGAGAGTAGGCAAAGATTTATT-GA-GCGACACACAGAAAT 839
                           ii i ii vi iv       v i   v  -  -ii     -  i  ii
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC-CAAAAGC 608

  chr2_33198278_3    840 -----CAATAATC------ATACA-AAATCAGACCTCAACAAAATTAAAA 877
                         -----   i  vv------   v -    ii   i   v           
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_33198278_3    878 ACT-----GCTCACCAAAAGACACTGTTAAGAAAACTAA---------CA 913
                            -----   i--    i      i i      iiv  ---------  
  L1M4_orf2#LINE/    659 ACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_33198278_3    914 CAGTAAGAGGAAAAAAATGCTGTGTGTGTGTGTGTGTATGAGACAGAGAG 963
                            -  vi   i    ---- i v  iivi -ii i   ---- v  ---
  L1M4_orf2#LINE/    707 CAG-AATGGGAGAAAA----TATTTGCAAAT-CATATAT----CTGA--- 743

  chr2_33198278_3    964 ATAAAAGATTGATATCCAGGATATATACTAATAAAAAATTC---CAACTC 1010
                         -   ii  i vi       i       ------  i  i  ---      
  L1M4_orf2#LINE/    744 -TAAGGGACTTGTATCCAGAATATATA------AAGAACTCTTACAACTC 786

  chr2_33198278_3   1011 ATTAAGAAAAAAA------AGCTGATTAATAAATGAGCAATATATTC-AA 1053
                          v   v     i ------ v ii   ? v     i    viv   i-  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_33198278_3   1054 TAGACATTTCACAAAGGGGAATATACAGATGGTTAATATGTACATTAAAA 1103
                                   v v  i iii       i    ii    v i    v    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_33198278_3   1104 GCTATTCGATATCATTAGTCAT 1125
                          v ii  i i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (99 / 46)
Gap_init rate = 0.05 (30 / 639), avg. gap size = 2.63 (79 / 30)  


3196 27.10 0.88 0.44  chr2_33306232_33312633     5007  5910 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_33306232_3   5007 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5056
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_33306232_3   5057 GGCCATACTGCCCAAGGTAATGTATAGATTCAATGCCATCCCCATCAAGC 5106
                            v     v     iv i  v  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_33306232_3   5107 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5154
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_33306232_3   5155 TATGGAACCAAAAAAGAGCCCGCATCGCAAAGTGAATCCTAAGCCAAAAA 5204
                                viiv  ii  v  v v  v  v  ivv    i i ivv i  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_33306232_3   5205 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5254
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_33306232_3   5255 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5304
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_33306232_3   5305 AATGGAAGAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5352
                                v    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_33306232_3   5353 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5402
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_33306232_3   5403 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5452
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_33306232_3   5453 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGAA 5502
                            ii    i    v   i     v              i    i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_33306232_3   5503 TTAAAGACTTAAACGTTAGACCTAAAACCATAGAAACCCTAGAAGAAAAC 5552
                          i ?    i    i  v   v       i   i  vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_33306232_3   5553 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5602
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_33306232_3   5603 AACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCTAA 5652
                         i            vvi          vv i   v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_33306232_3   5653 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5702
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_33306232_3   5703 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5752
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_33306232_3   5753 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5802
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_33306232_3   5803 AAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 5848
                          i    ----   v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_33306232_3   5849 TCAAAAGAAGCCATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5898
                           v       vi  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_33306232_3   5899 ATCACTGGCCAT 5910
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


 902 21.55 5.60 0.00  chr2_33819694_33822641.rev      284   515 (2433)    L1M4_orf2#LINE/L1      118   362 (546)  

  chr2_33819694_3    284 GCAGAAA-----AAGAT-ATTCTAAAATTCATATGGAACCACAAAAGACA 327
                                -----   v -  i                 vii   ii   v
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_33819694_3    328 ATGAATAGCCAAATGAATCCAGAGAAGGAAGAACAAAGTTGGAGGCATCA 377
                         vv           vv    iv  i  i                  vv   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_33819694_3    378 AATGTACTAATTTCAAAATATATTACAAAGCTACAGTAATCAAAACAGTA 427
                         v iv v i          iv  i                    i     i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_33819694_3    428 TGTTACTGGCATAA----AGACAGATAGGTTAATGAAACAGAA---AGGG 470
                           v           ----     v    i i    i  i    ---  i 
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_33819694_3    471 ACCAAAAATATACCCACTCATATGCAGTTAAGCAATCTTCAACAA 515
                         v   i     v     iv   v iii  i  vii  i   i    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

Transitions / transversions = 1.38 (29 / 21)
Gap_init rate = 0.02 (4 / 245), avg. gap size = 3.25 (13 / 4)  

3509 23.72 1.56 0.67  chr2_33819694_33822641.rev     1559  2456 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_33819694_3   1559 GAAAGATAATCCATTCTCATGGGAGGAGAAGAATTGATATTGATAAG-TG 1607
                                 vi    vi      - vvi     v  i      v    -  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGG-ATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_33819694_3   1608 ACAATACTACCCAAAGCCATTTACAGATTCAATGCTATCCCTGTCAAAAT 1657
                         i       v      viv  i           i  v      i       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_33819694_3   1658 ACCAATGACATTCTTCACAGAAATAGAAATAAAAGCTG----TACAATTG 1703
                         v   iivi v  i  ii       v  v ----     ----  v    v
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACA----AGCTGATCCTAAAATTC 147

  chr2_33819694_3   1704 ATGTGAAACCACAAAACACCTCGAATTGCCAAAGCAATACTGAGCAAAAA 1753
                           i  i  vii   iiv   iv    v      i    vi   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_33819694_3   1754 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAAATTTATTATAAAG 1803
                                 i      vv       v  ii i       i   i  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_33819694_3   1804 CTAAAGTAACCAAAACAGCATGTTACTGGTATAAA-ACAGGCACATAGAC 1852
                            v     i   i    ii  v      i    i- i  i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_33819694_3   1853 CAATGGAACAAAATAGAGAACCCGGATATAAATCCATGCATTTACAGCCA 1902
                                 i i   v    ii  i  v     i    i      ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_33819694_3   1903 ACTCATCTTCAACAAAAGCACAAAGAGCATACAATGGGGCAAAGATAATC 1952
                          i v  i   i    ii ii v    v   v        v  ii   i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_33819694_3   1953 TTCTCAATA----GTGATGGAAAAACTGGAGAATTATATGCAGAAGAAAG 1998
                           i    i ----   v   i v       v ?ii i     i     v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_33819694_3   1999 GAACTAGACCCC-ATTTCTCATCATTCATCAAAATCAAATCAAAATGGAC 2047
                         i ii i      - ii  v  i   vi iv     i  v          i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_33819694_3   2048 TAAAGACTTAAACCTGAGACCTGAAACTCTGAAACTACTAGACGAAAACA 2097
                         i ?    i    iv i   v  i     v i     vi    v       
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_33819694_3   2098 TTGGGGAAACACTCCAGGACATTGGCCTGGGCAAAGATTTTTTGTATAAG 2147
                          v  ? v  vv  i iv   v    vi i     v i   i  iv   v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_33819694_3   2148 ACTTCAAAATCATAGACAACAAAAGCAAAAATAAACAAATAGGATTATAT 2197
                           vi     v  i ii         v       i i    v   i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_33819694_3   2198 TAAA-TTAAAAAGCTTCTGCATTGCTAAGGAGACATTCAACAAAGTGAAG 2246
                         i   -       -   i  iii v v     v  vv    v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_33819694_3   2247 CGACAACCCACAAAATGGGAGAAAATATTTACAAATGATCCATCTGACAA 2296
                         v           i                 i     v  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_33819694_3   2297 GAAACTAATAACCAGAATATATAAGGAGCTCAAACAACTCAATCACAAAA 2346
                          ii   vi  v             i  i   vv          v i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_33819694_3   2347 A-ACAAATAATCTAATTTTAAAATGGGCAAAAGATCTGAACAGACATTTC 2395
                          -        i i    ?v            i   i    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_33819694_3   2396 TTAAAAGAAGATATACAAATGGCCAACAGGTATATGAAAA-ATGCTCAGC 2444
                          iv                       i i i i       -       i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_33819694_3   2445 ATCACTAACCAT 2456
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (130 / 79)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.82 (20 / 11)  


3101 25.69 1.00 0.44  chr2_33875352_33879935.rev     3190  4092 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_33875352_3   3190 TGGAAACACATCCCATGCTTATGGATGGGTAGAATCAATATTGTGACAAT 3239
                               v i        i i      v  v   v i        v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_33875352_3   3240 GACCATACTGTCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 3289
                          i v     vi v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_33875352_3   3290 TACCACCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCATA 3339
                          v   v vv v  i  ii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_33875352_3   3340 TGGAACCAAAAAAGAGCCTACATAGCCAAAGCAAGACTAAGCAAAAAGAT 3389
                              viiv  ii  v  viv         i   vvi i iv  i    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_33875352_3   3390 TAAACGTGGAGGCATCACATTACCTGACTTCAAACTATACTATAAGGCCA 3439
                         i   vv      vv     i v  ii i      viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_33875352_3   3440 TAGTCACTGAAACAGCATGGTACTGGTATAAAAATAGGCACACAGACCAA 3489
                         i   v iii i    ii         i    ii    i  i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_33875352_3   3490 TGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACCGCCAACT 3539
                              i     v    ii           v   v i i   iv i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_33875352_3   3540 GATATTCAGCAAATCAAACAAAAACATAAAGTGGGGAAAGGACACCCTAT 3589
                            v   ii   ivvviv   i v   vv i         i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_33875352_3   3590 TCAACAAATGGTGCTGGGATAATTGACAAGCCTCATGTAGAAGAATGAAA 3639
                                            i  i  ivv ?  v    i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_33875352_3   3640 CTGGATCCTCATCTTTCACCTTATACAAAAATCAACTCAAGATGGATCAA 3689
                         i    i  ii i  iv    v           i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_33875352_3   3690 AGACTTAAACCTAAGACCTGAAACCATAACAAATCT-AGAAGATAACATT 3738
                             i    iv     v  i    i    -  v   -      v     v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACATA 549

  chr2_33875352_3   3739 GGAAAAACCCCTCTAGACATTGGCTTAGGCAA-GACTTCATGACATAGAA 3787
                           ?iv  vi i  vv   v    v        - ii   - v v   vi 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGA 598

  chr2_33875352_3   3788 C-CCAAAAGAAAATGCAACAGAAACAAAGGTAAATAGATGGGACTTAATT 3836
                          -       v v v      i  iv   ii  i   i  v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_33875352_3   3837 AAACTAAAAAGCTTCTGCACTGCAAAAGAAAC-AGCA-GAA--TCAACAG 3882
                            v v    i   i  ii  v    i  v  - v  -   -- v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_33875352_3   3883 ACAACCCA--GAGTGGGAGAAAAATCTTCACAATGTATACATTTGAAAAA 3930
                                 --  i          - v  ii   vvi   i  i   v  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAG 747

  chr2_33875352_3   3931 GGACTAATATCCAGAATCCACAAAGAACTCAAACAAATCAGCAAGAAAAA 3980
                              vi          vi i         vv    v   ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_33875352_3   3981 AATCAAACAATACCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTC 4030
                         i -    i  iv v  i?    i     v     iv          v   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_33875352_3   4031 TCAAAAGAAGACACACAAATGGACAACAAGCATATGGAAAAATGCTCAAC 4080
                           v        i i        v   i     i   i   i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_33875352_3   4081 ATCACTGATTAT 4092
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (129 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.18 (13 / 11)  


2876 26.78 3.05 0.45  chr2_33963686_33965954.rev      893  1777 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_33963686_3    893 TGGAAAAACATTCCATGCTCATGTATAGGATGAATAAATATTGTTAAAAT 942
                               i i  i     i     v  v   v  v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_33963686_3    943 GACCATACTGCTCAAAGCAACTTACAGATTCAATGCTATTCCTATCAAAC 992
                          i v     v i    vii ii           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_33963686_3    993 TACCAATGACATTCTTCACAGAATTCGAAAAAACT-ATTTTAAAATGTAT 1041
                          v   iivi v  i  ii     v i  v  i-  -  ii      vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_33963686_3   1042 ATGGAACCAAAAAGAGCTCA-AATAGCCAAGGAAATCCTATGCAAAAAGA 1090
                               viiv  i ii i  -         iiv    i iviv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_33963686_3   1091 ACAAAGCTAGAGGCATCACA-TTACCAACTTCAAACTGTATTATAAAGCT 1139
                               i i    vv     -  v    i      viv  i  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_33963686_3   1140 ACAGTAATGAAAACAGCAATGGTACTGGTACAAAAACAGACACACGCACC 1189
                                 v  i    ii-         i i  ii i     i iiv i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTG-TGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_33963686_3   1190 AATGGAACAGAGTAAAGAGCCCAGAAATACAGCTGTACACCTACAACCAT 1239
                                i   i vi    i         v v ii    ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_33963686_3   1240 CTTATCTTTGACAAGGTTGACAAACACAAGCAATGGAGAAAGGACTCCCT 1289
                         i v  i  i       v  v   ivv  vv      i     i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_33963686_3   1290 GTTCAATAAACAGTGCTGGGATAACTGGCTAGCCCTATGAAGAAGACTGA 1339
                         v     i   ii         i      v  ?  vi   v i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_33963686_3   1340 AACTGGACCCTTTTCTTATTCTATACACAAAAATCAATTCAAGGTGGATT 1389
                          ii       i vi  i iv i   i        i  i    ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_33963686_3   1390 AAATACTTAAA-GC-----CTAAAACTATAAAAACCC-AGACGATAACCT 1432
                          ? v  i    - i-----              vi i-   v  v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_33963686_3   1433 AGGAAATACTATTCTGGAAATGGGCCCTGGCAAAGATTCCAT-GACAGAG 1481
                            ?ivv v v   vv  vv v  viiv     v i  i v -  i v- 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-G 597

  chr2_33963686_3   1482 ACACCAAAAGCA--ATTGTTAAAAAACAAAAATTAACAAATGGGACCTAA 1529
                                     -- viivi    i -      vi i    v    i v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCA 646

  chr2_33963686_3   1530 TCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTCTCAACAGAGTAAAT 1579
                              v v  i i   i  ii vv    i  v   v    v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_33963686_3   1580 AG----CCTACAGAATGAGAGAAAATATTCGCAAACTGCACATCTGACAA 1625
                           ----  i        i           i     iiii i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_33963686_3   1626 AGGTCTAATATCCAGCATCTATAAGGAACT-TAACAA-------GCAAAA 1667
                         i  v  vi       v  v     i     - v    -------ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_33963686_3   1668 AG-CAAATAACCCCATTAAAACATGGGCAAAGGACATGAACAAACACTTT 1716
                           -          v   ?   v            iv    i i   i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_33963686_3   1717 TCTAAAGAAGACGTACACAAGGCCAACAAGCATATGAAAA-ATGTTCAAC 1765
                           i        ii    v v      i     i       -   i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_33963686_3   1766 ATCACTAATCAA 1777
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.82 (31 / 17)  

1325 28.57 0.54 0.54  chr2_33963686_33965954.rev     1898  2268 (1)    L1M4_orf2#LINE/L1        1   371 (537)  

  chr2_33963686_3   1898 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATAAATATCGTGAAAAT 1947
                              ii i  i     i      i v      v v     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_33963686_3   1948 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 1997
                            v     v     iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_33963686_3   1998 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2045
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_33963686_3   2046 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 2095
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_33963686_3   2096 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2145
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_33963686_3   2146 TACAGTAACCAAAACAGCATGGTACTGGTAGCAAAACAGAGATATAGACC 2195
                                 i   i    ii         i vv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_33963686_3   2196 AATGGAACAGAACAGAGCCTTCAGAAATAATGCCGCTTATCTACAACCAT 2245
                                i    iv   vv i         vv  iivi  i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_33963686_3   2246 CTGATCTTTGACAAACCTGACAA 2268
                         i    i  i     ivv  v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAA 371

Transitions / transversions = 1.72 (67 / 39)
Gap_init rate = 0.01 (3 / 371), avg. gap size = 1.33 (4 / 3)  


3351 17.91 3.95 0.56  chr2_34011632_34013330.rev      501  1209 (490)    L1M4_orf2#LINE/L1      176   908 (0)  

  chr2_34011632_3    501 CCAAAATGATTTTGAAAGAGAA---CAGAGTTAGAGGACTCACATTTTTC 547
                               ii  i      i    ---  i    i           i  ii 
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_34011632_3    548 CATTTTAAGACTTACTACAAAGCTACAATAATCAAGAC--TGTGGTACTG 595
                         v    i  i                  i          --          
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_34011632_3    596 GAAGGGTGGTAAACATGGAGATCAATGGAATCAGACTAAGAGTCAAGAAA 645
                          v viiv i  i    iv             vii i i      v     
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_34011632_3    646 TAAACCTTCACATTTATAACCCGTTGATTTTTGACAAGGGTGCCAAGATA 695
                               ivi        iii vi        i                iv
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_34011632_3    696 ATTCAGTGGGAGGAAGAATAGTCTTTTCAACAAATGATTCTAGGACAACT 745
                              i    - i                       i v  i        
  L1M4_orf2#LINE/    376 ATTCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_34011632_3    746 GGATTTTCACATGCCAAAAAAATGAAGTTGGACCCCTACATAACACCATA 795
                             v?i       -    i                   v v        
  L1M4_orf2#LINE/    425 GGATAKCCACATGC-AAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_34011632_3    796 TGCAAAAATTAACTCAAAATGGGTCTTCAACTAAAATATAA-------AA 838
                          i                    i  v?vi  iv    i   -------  
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_34011632_3    839 CTATGAAACTTTTATTAAAAAAAAAT--GGGTAAATCTTTATGACCTTGG 886
                             i     i   v-  i    v  -- ?         ii         
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAG-AAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_34011632_3    887 ATGATGCAGTGGTTTCTTTAACAGGACACCAAAAACCCAAGCAAAAAAAG 936
                         i v v   i         vi i v          i v       v     
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_34011632_3    937 AAAAAATA----AATTGAACTATAGTGAAAATTTTAAA---TGGTGATTC 979
                                 ----     i   vi - v      vv   --- v   v   
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCA-TCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_34011632_3    980 AAAAGACACCATCAAGAAGGTAAAAATAAAACCTACAAAATGGGA--AAA 1027
                            i     i        i  i    v v    i   i       --   
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_34011632_3   1028 TATGTATAAATCAAATATCTGTTAAAAAACTTAT-TGCAGACCATATAAA 1076
                            v ii      v       v   iii    i - v    vi       
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_34011632_3   1077 GCACACTTATAATGCAATAATAAAGTGACAA----CCCAATTTAAAAATG 1122
                          v  v    i  iv          iv     ----       ?       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_34011632_3   1123 GGTAAAAGATCTAAGTAGAGATTTCTCCAAAGAAGATATGCAAATAGCCT 1172
                           i   i   i i i    v                   i     i   v
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_34011632_3   1173 ATAAGCACATAAAAAGATGCCCAATATAATTAGTCAT 1209
                                   i         i   i  v ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (78 / 45)
Gap_init rate = 0.02 (13 / 733), avg. gap size = 2.46 (32 / 13)  


 371 24.11 0.89 0.89  chr2_34220962_34223247.rev      691   802 (1484)    L1M4_orf2#LINE/L1       35   146 (762)  

  chr2_34220962_3    691 TTAATATTGTTAAAATGTCTATACTACTCAAAGTCATCTACATATTCAAT 740
                                      i   v v     v i    v v       v      i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr2_34220962_3    741 GCAATTCCTATCAAAATTCTAATGATATTCTTCACAGATATAGAAAAAA- 789
                              i           i i iiviiv  i  ii    v  v  v  iv-
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr2_34220962_3    790 AATCCTCAAAATT 802
                         i     -      
  L1M4_orf2#LINE/    135 GATCCT-AAAATT 146

Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.02 (2 / 112), avg. gap size = 1.00 (2 / 2)  

2163 24.50 7.83 1.14  chr2_34220962_34223247.rev     1093  1794 (492)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr2_34220962_3   1093 AAAAGATCCCAAGTAGCTAAAGCAATCTTGAACAAAAAGAGCAAATCCAG 1142
                           ii  i  vi i    i   i          v  i    i    viii 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_34220962_3   1143 TGGCACT-GCACTACCTAACTTCGAAATATACAACAAAGTTATAGTAACC 1191
                         v  -   -i    v  i  i   i   iv   v      i  i     i 
  L1M4_orf2#LINE/    210 AGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_34220962_3   1192 AAAACAGCATGGTACTGGTATA--TACAAACACAAAGACCAATGGAA--- 1236
                           i    ii         i   --v i i   i v   i        ---
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_34220962_3   1237 -----------CACAAATAAATTCATGCGTTTACAGCCAACTGATTTTTG 1275
                         -----------  v       ii   i i    ii i   i       i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_34220962_3   1276 AC--------CAA-------CAATGAGAAAAGAAAAGTCTTGTCAATAAA 1310
                           --------   -------     i i      v      v    i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_34220962_3   1311 TAGTGTTGGAAAAACTGGATATCCACATTTAGAAAAGTAAAATTAGACTC 1360
                          i   i   i v         ?      vi i  i i i  i  i   i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_34220962_3   1361 TTACCTACCAACCTATACAGAAAACCAGCTCAAAATGTATTA--GTCTTA 1408
                         i     vv  v v      -    ii i         v  i -- v i  
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACA-AAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_34220962_3   1409 AATATAAGACCCAAAACTATGAAACTACTAGAAAAAAAACATACAGGAAA 1458
                            i     v i        i     vi     i    -    vi? v  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGTAA 556

  chr2_34220962_3   1459 AGCCCAATCACATTGGTCTGGGCAATGATTTTCTGGGTATAATCTCACAA 1508
                          v iivi v  v    vi i       i   ii i i   i ivi  v  
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_34220962_3   1509 ACACAAGCACCAAAATCAAAAATAAACAAATGGTTATATTTCA----AAC 1554
                         i        v     vv       i i    --- iv i    ----  i
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAAT---TGGACTTCATCAAAAT 653

  chr2_34220962_3   1555 TAAAAAGCTTCTGCATGGCAAAGAA-AC----AACAAAGTAAAGAAAGAA 1599
                               -   i  iiivv     i -  ----  v     i  i i v  
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_34220962_3   1600 GCTACAGAATGAAA-AAAATATTTACAACATT-TATATCTGATACGGTGG 1647
                         v i        ii -         i   -  i-           v  viv
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATAAGGGAC 751

  chr2_34220962_3   1648 TAATATTCAAAACATATAAGGAACTC----AACTCCATCTCAATAAAACA 1693
                          vi   i  i  i      i      ----     v  vvi  v  i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_34220962_3   1694 AATAAC----TTTAAAAATGGGCAAAAGACCCATATAGACATTTCTCAAA 1739
                               ----  ?             i  iiiiv             v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_34220962_3   1740 AGAAGATATACACATAGTCAACAGATATATAAAAA--TACTCAACAACAC 1787
                                     v  i i   i iii i  i    -- i       v  ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_34220962_3   1788 TAATCAT 1794
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.25 (117 / 52)
Gap_init rate = 0.03 (20 / 749), avg. gap size = 3.15 (63 / 20)  


2205 27.14 0.16 0.32  chr2_34445006_34446630.rev      496  1125 (500)    L1M4_orf2#LINE/L1      263   891 (17)  

  chr2_34445006_3    496 CAGTGATAGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC 545
                              - i       i iv ii i   v                i    i
  L1M4_orf2#LINE/    263 CAGTG-TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_34445006_3    546 AGAGCCCCCAGAAATAATGCCGCATATCTACAACTATCTGATCTTTGACA 595
                         v   vvi          vv  ii i  i  iiiii vi    i  i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_34445006_3    596 AACCTGAGAAAAAAAAAGCAATGGGGAAAGGATTCCCTATTTAATAAATG 645
                          ivv  v-v  i vv vv            i  vvi  v  i  i     
  L1M4_orf2#LINE/    362 AGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_34445006_3    646 GTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCT 695
                                  v      v  ?   i   i i  iiv    ii    i    
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_34445006_3    696 TCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAAT 745
                         v   i     v              i    i      i ?    i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_34445006_3    746 GTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCAT 795
                           v   v       i      vi i           v    ?i v viv 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_34445006_3    796 TCAGGACATAGGCATGGGCAAGGACTTCCTCTCTAAAACACCAAAAGCAA 845
                           iv   v v  vv i     v ii   i vvv  vi            v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_34445006_3    846 TGGCAACAAAAGGCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGC 895
                         vi          iv     v  i    v   ii v  i   v v  i i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_34445006_3    896 TTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAA 945
                           i  ii vv    i  v    i  vv i      v  i     i   i 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_34445006_3    946 ATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCA 995
                                     v  i    vii ivi      i  i  i  vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_34445006_3    996 GAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCAC 1045
                             v  i  v      vv    v iv i  v     i     i    vv
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_34445006_3   1046 ATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACAT 1095
                           i?    i           iv    i     i     v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_34445006_3   1096 TTATGCAGCCAA-AAACACATGAAAAAATAC 1125
                         vi viii     -  i          i  i 
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGC 891

Transitions / transversions = 1.32 (95 / 72)
Gap_init rate = 0.00 (3 / 629), avg. gap size = 1.00 (3 / 3)  


 585 23.08 0.00 0.70  chr2_34512503_34514542.rev      502   644 (1396)    L1M4_orf2#LINE/L1      274   415 (493)  

  chr2_34512503_3    502 TGGTCTACAAAATTGACAAATAGATCAATGGAACAGAATAGAGAGTCTAG 551
                            iv  - ii  v    v              i     v       i  
  L1M4_orf2#LINE/    274 TGGCATA-AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_34512503_3    552 AAATATACCCACAAAAATATAGTCGATGTATCTCTGACAAAGGAGCAAAA 601
                              v     i v vv   i   i  vv  i ii     i  v  v  i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_34512503_3    602 GCAATTTAATGGAGAAAGGATAGTGTTTGTAACAAATGGTGCT 644
                         i v   i     i     i     v   vi             
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

Transitions / transversions = 1.20 (18 / 15)
Gap_init rate = 0.01 (1 / 142), avg. gap size = 1.00 (1 / 1)  

1562 23.94 2.82 1.81  chr2_34512503_34514542.rev     1052  1548 (492)    L1M4_orf2#LINE/L1      407   908 (0)  

  chr2_34512503_3   1052 AACAGTGCTAGGGGAACAACTAGACATCCAAATGCAAAAAAGTTTGTCTG 1101
                           ii     i  ---      i  i ?   v        i i vvivi  
  L1M4_orf2#LINE/    407 AATGGTGCTGGG---ACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_34512503_3   1102 AACATTGACTTTTCAC-ATTTCACAACTAATAACTCAAAATGGGTTATAT 1150
                         i  viiv  i iv   -  v -    vv v             i i ? v
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_34512503_3   1151 ACCTAAAAGTAAAATGC-AAAACTATAAAATTCT-AGAAGATAACATAGG 1198
                                v    i -  -            i   -      v        
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_34512503_3   1199 AGAAAATTTAAGTTACCATGGGTTTGGCAATTACTTTCTT-GATGACAAC 1247
                         ? v    i vv  v   v      v      vi-      -   - ii  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGAT-ATGAC 599

  chr2_34512503_3   1248 ACCAAAAGAACAATCCATAGAA--AAAAATCAGTAAGT-GGATTTCATTG 1294
                                 v    v v i i  --      vii   i -   i     ii
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_34512503_3   1295 AAATTAAAAACATCTGCTCTGTGAAAAAAATGGTCTAAGATAATGAGAAG 1344
                                    v i  iv  vii  ii v ivi  -    v i   i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATC-AAGAAAGTGAAAAG 698

  chr2_34512503_3   1345 ATAATCCATAAACTAAAAGAAAATG---GCAAAACATATAGCTGATAAAG 1391
                          i  i   i i v iii       i---     v      v       i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_34512503_3   1392 GATGTGTATCTAAGATATGCAAAGAATTCTTA-AACTT--CAATAAGAAA 1438
                           iv      i ii    ii      i     -    i--i     i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_34512503_3   1439 ACAAACAACCCAACT-GAAAATAAGTAAAAAAATCTGAACAGACATCTCA 1487
                              i       i -i     ii i   ii - i    i      i  v
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGA-TTTGAATAGACATTTCT 847

  chr2_34512503_3   1488 CCAGAAAAGACATATAAATGTCAAATAAGTATATCAAAAGATGCTCAACA 1537
                            i i    i   i     v v      i i  v               
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_34512503_3   1538 TCATATGTCAT 1548
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.97 (77 / 39)
Gap_init rate = 0.03 (17 / 502), avg. gap size = 1.35 (23 / 17)  


3217 26.22 1.56 0.67  chr2_34586278_34589956.rev     2289  3188 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_34586278_3   2289 TGGAATGATATTCCTCATTCATGGATTAGAAGAATCAATATTGTTAAAAT 2338
                              v     i  vii          i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_34586278_3   2339 GTCTGTAATACTG---AAAGCAATCTAAAGATTCAATGCAATCTCTATAA 2385
                          --- i      v---   vii     v        i      i    v 
  L1M4_orf2#LINE/     51 G---GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_34586278_3   2386 AAATACCAATAACATGCTTTACTGAAATAGAAAAACATAACCCTAAAATT 2435
                             v   iivi v vi   i v     v  v  i - i i         
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATT 146

  chr2_34586278_3   2436 TTTATGAAACCACAAAACACCCAAAATAGTTAAAGCCATCCTGAGCAAAA 2485
                         iv    i  vii   iiv     i     ii   i v   i   iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_34586278_3   2486 AGAACAAAACTGGAGAAATCATAATACCTGACTTCAAATTATACCACAGA 2535
                                 ii     i v   i v v  ii i      viv   i   i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_34586278_3   2536 GATATAATAATCAAAACAGCATGGCACTGGCATAAAAACAGTCACATAGA 2585
                          v  i i       i    ii   i          ii i  v  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_34586278_3   2586 CCTGTGGAACAGAAAAGAGAAACCAGAAATAAATCTATGCGCCTATAGTT 2635
                         i vi     i    vv    iv           i i  i iii   i  i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_34586278_3   2636 AACTCATTTTTTACAAAGGTGCCAAGAACACACAGTGGGGAAAGGAAAGT 2685
                           i v     iv    i          v  iv  i         i v   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_34586278_3   2686 CTCTTCAATAAATGGTGGTGGGAAAACCATATATCCATATGTGCAAGAAT 2735
                           i     i        v     v   iiv   ?   i   iiv      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_34586278_3   2736 GACACTAGACCCCTATCTTTTGCCATCTACAAAAATTAAATAAAAATGGA 2785
                           vii i        i  ivii    v            v v        
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_34586278_3   2786 TTAAAGACTTAAATCTAAGACCTCAAACTATGAAACTGCTTC-AGGAAAA 2834
                          i ?    i     v     v  v       i     -   v- i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAA 545

  chr2_34586278_3   2835 CTTTGGTGAAGCTCTCAAAGACATTGGTCTGGGTAAAGATTTTTTGAGTG 2884
                          v v  ? v iv   iviv   v    vi i  i  v i   i  iii -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr2_34586278_3   2885 AT-ACCCCACAAGCACAGGTAACCAAAGCAAAAATGGACAAATTGCATCA 2933
                           -  v   v       i i   v    v      i  i      v iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_34586278_3   2934 CATCA---TTAAAAAGCTCTGCACATCAAAGGAAACAACTGACAATGTTA 2980
                              ---       vi i  ii v        v  v iii v  v  v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_34586278_3   2981 -----CAACCCAAAGAATGGGAGAAACTATTTGCAAACCAC-CATTTGAC 3024
                         -----       v             v          i  i-i  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_34586278_3   3025 AAATGATTAATAACCAGAATATATAAGGAGGTGAAATAATTCTATAGAAA 3074
                           iv  i vi  v             i  iv vvv i  i  v   iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_34586278_3   3075 CAAATTTAATAGTTTGATTAAAAGATGGGTAAAATATTTGAATAGACATT 3124
                         v  iviv    iiiii   ?   i     i   iv               
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_34586278_3   3125 TCTCAAAAGAAGACATACAAATGACAAACAGGCATGTGAAATGGTGCACA 3174
                             v        i         i v  i i   ii     v i   v  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_34586278_3   3175 ACATCGCTGATCAT 3188
                              i????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (143 / 89)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2968 27.13 1.11 0.55  chr2_34602444_34609125     5288  6190 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_34602444_3   5288 TGGAAAAACATTCCATGCTCATGGATAAGTAGAATCAATATCATTAAAAT 5337
                               i i  i     i        vi v   v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_34602444_3   5338 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCTTCAAAC 5387
                            v     v      v i  i  i        i  v     iv     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_34602444_3   5388 TACCATTGACTTTCTTCACAGAATTAGAAAAAAATACCTTAAATTTCATA 5437
                          v   vivi i  i  ii     v v  v  ivvv i i    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_34602444_3   5438 TGGAGCCAAAG-AAGAG-CTCATA-TATCCAAGACAATCCTAAGCAAAAA 5484
                             ---  v -   i - i  v -  v    i      i i iv  i  
  L1M4_orf2#LINE/    151 TGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_34602444_3   5485 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACGAGG 5534
                                 i      vv   ii  v  ii i      viv      i i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_34602444_3   5535 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGAC 5584
                                  i   i    ii         i iv ii i   v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_34602444_3   5585 CAATGGAACAGAACAGAGGCATCAGAACTAATGCCACACATCTACAACCA 5634
                                 i    iv   ivvi     v   vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_34602444_3   5635 TCTGATCTTTGACAAACCTGACCAAAAAAAG-CAATTGGGAAAGGATTCC 5683
                         vi    i  i     ivv  -    i vv v-    v       i  vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_34602444_3   5684 CTATTTAATAAATGGTGCTGGGAAAACTGGTAAGCCATATGCAGAAAACG 5733
                           v  i  i              v      vv ?   i     i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_34602444_3   5734 GAAACTGGACACCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 5783
                            ii     v   v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_34602444_3   5784 TTAAAGACTTAAATGTAAGACCTAAAACTATAAAAATCCTAGAAGAAAAC 5833
                          i ?    i           v              v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_34602444_3   5834 CTAGGCAATAGCATTCAGGACATAGGCATGGGAAAAGACCTCATGTCTAG 5883
                         v    ?ivv iiv   iv   v v  vv i  v  v iii  v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_34602444_3   5884 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATCTAA 5933
                         i            vvi          vv     v  i i  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_34602444_3   5934 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCATCATCAGAGTGAAC 5983
                          i   v v  i i   i  ii vv    i  v  i    vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_34602444_3   5984 AG-TGACCTGCAGAATGGCAGAAAATTTTTGCTATCTGTCCATCTGACAA 6032
                           -ii   ii        v       v     v viii vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_34602444_3   6033 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACACATTTACAAGAAAA 6082
                         i  i  vi          v  i        ivv   vv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_34602444_3   6083 AAAAAAA-AACC---TTCAAACAGTGGGCAAAGGATATGAACAAACTCTT 6128
                          i v   -    ---  ?   - i            v    i i  vi  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_34602444_3   6129 CTCAAAAGAAGACATTTATGCAGCCAACAAATATATAAAAAAA-GCTCAT 6177
                            v        i  vi viii     i  ii i  i    i -     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_34602444_3   6178 CATCACTGGTCAT 6190
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (135 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


1537 25.36 1.25 2.08  chr2_34717436_34719898.rev        1   481 (1982)  C L1M4_orf2#LINE/L1   (25)   883   407  

C chr2_34717436_3    481 AATGGTTTGGGGAAAATTGGATACCCACATGTAGAAGAATGAAACTGAAT 432
                               viv    v  i      ?       i i         ii  i i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

C chr2_34717436_3    431 CCCTATCTCTCACCTTATACAAAAGTCAACTCAAACTGGATCAAAGGCTG 382
                              i   v    v         i i        v       ?  i iv
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

C chr2_34717436_3    381 AAATCTAACATCTGAAACTATAAAAATTCTAAAAGATAACCTAGAAAAAA 332
                             v   v v  i           v ii  i    v   v   i?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

C chr2_34717436_3    331 CTCTCTG-GATATTGGCCCAGGCAAATAATTTA-TGGCTAAGACCCAAAA 284
                         v   ii -  iv    vii      - ii   v- i v  v   v v   
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAA 605

C chr2_34717436_3    283 AGCAAATGCAACAAAAATAAAAATAAATA----GGACATCATTAAACTAA 238
                             v v         iv       i   ----    v    i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

C chr2_34717436_3    237 ACAGCTTCTGTACCACAAAAGATAAGAGGACAGACAAGACCAGAGGACAG 188
                          v i   i   i iv    i  i ------ viv     -v  v i v  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACA------CTATCAAGA-AAGTGAAAAG 698

C chr2_34717436_3    187 ACAAGCCACAGAATAGAAGAAAATATCTGTGAACTATGCATCCGTCAAAG 138
                             v         i i         i  ii  ii  ii   i vi  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

C chr2_34717436_3    137 GACTAATATCCAGAATCTACAATGAACTCAAAAAAAAATCAGCAAGAAAT 88
                             vi          v  i  v      --vv v  v   ii  v   v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCAATAATAAAA 796

C chr2_34717436_3     87 AAATAAATAACCCCATCCAACAGTGGGCAAATGACATGAACAGATATTTC 38
                          i i         v  i?  v i        v  iv    i   i     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chr2_34717436_3     37 TTAAAAGAAGATTTACAAATGACCAACAAACATATGA 1
                          iv         v        i    i  i  i    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

Transitions / transversions = 1.27 (66 / 52)
Gap_init rate = 0.01 (7 / 477), avg. gap size = 2.29 (16 / 7)  

2100 26.08 2.96 7.07  chr2_34717436_34719898.rev     1025  1971 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_34717436_3   1025 TGGAAATATATATTGCAT-TTCCTGAATTGGAACAC--AATATAACAATA 1071
                               v    vi--   -   v  i       v  --     ----- i
  L1M4_orf2#LINE/      1 TGGAAAGATATCC--CATGTTCATGGATTGGAAGACTTAATAT-----TG 43

  chr2_34717436_3   1072 CATTTAACATGTTACTTTTCCCCAAATTCATGTATAGGTTGACTATAGTC 1121
                         ---    v   vi v vi          v  v  i  i  v viii i  
  L1M4_orf2#LINE/     44 ---TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chr2_34717436_3   1122 CTAAATAAAATCCCTGTGGTATTAGCTTGTACATGTAGTCAACCTGATTC 1171
                          iv vi        v iv iv  -vi   i v vi v v   v     i 
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_34717436_3   1172 TAAAGTTTATGTGGAAAGGGAATGGAAGTAAAACA-CTGAAATAATTTTA 1220
                             i  i  i      v v  v   vvi i  i - ii   i   i  i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_34717436_3   1221 AAAT----GAATAAATTTGGAAGATTCATACTACCTGGTTTTAATGTTTA 1266
                            v----   i   v     i  i   i   v  iii   i  vii   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_34717436_3   1267 TTATAAAGCTTGAGTAGTCAAGACGATGTGGCATTGG-AGAGGTGA-AAA 1314
                         i  i      vv    i       ii     i i   - v i -  - i 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGA 288

  chr2_34717436_3   1315 CATATAGATCAATGAAACAGAAT--AGAGTCCAGAAATACATTCACACAA 1362
                                       i  i     --              v ii  i   v
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_34717436_3   1363 ATACAGTCAATTCACTTTTGACGAAAATACAAAGATAATTCAATGGAGCA 1412
                         v  ii       v i   i   i iii i v    iv         i v 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_34717436_3   1413 AGGGTAGTCTCTGTAATAAATGATACTGCAACAATTATGCATCTATATGT 1462
                           ii      i vi  i     i i   vi    i ivii ? i i   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_34717436_3   1463 AAAAAGAT-AAGT-AAACCTCAACCTAACCTTCATACTGCATCCAAAA-T 1509
                             ii  -    -ii   ----    -- i   i  iii  v     - 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACC----CCTA--CCTCACACCATATACAAAAAT 482

  chr2_34717436_3   1510 TAACTGAAAATAGATTTAAAATCTACATGTAAAATGTAAAACTCCAAAAT 1559
                              v     i   iv? i i   v      i vv       vi    i
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_34717436_3   1560 T-TTAGGAAAAAACATCATAGGAGAAAATCTATGTGACCTTAACATTGGC 1608
                          -    i i       ---   ? v      vi        ii-i  i v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACAT---AGGNGTAAATCTTCGTGACCTTGG-GTTAGG 578

  chr2_34717436_3   1609 CAAAAGTT-CTTATATGGGACATAATAAGCATGATTCATAAAATAAAATG 1657
                            vi   -    v  iv    iv v     ii viv i    v    vi
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_34717436_3   1658 TTGGTATGTTTCACTTCATTAAAA----AAATGTTTACTGTGTGAAAGTT 1703
                          v i  vi  vv       i    ----   iv   i-  iv v    vv
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGA 677

  chr2_34717436_3   1704 T-CTGGTAAGAGAATGAAAAAACAGGCTATAGACGATGAAAAAATATTTG 1752
                         i-  ivi    i i      i   iv i i   vviv  i          
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_34717436_3   1753 CAAATCACATA-CTGAACAAAGGATTTTTGTTGAATCAAAGGCCTACATA 1801
                                i   -    -i  i   i  v i i----  i ----- i   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGA-TAAGGGACTTGTATC----CAGA-----ATATA 767

  chr2_34717436_3   1802 TTCTGGGCAAGCAAAGGACTAT-ACA-TTCTTGGTAAATATATAAAGCAT 1849
                          -----------    i   v -   -i  ------    -     ----
  L1M4_orf2#LINE/    768 T-----------AAAGAACTCTTACAACTC------AATA-ATAAA---- 795

  chr2_34717436_3   1850 TCTCAGAACTCAAGAGTAAACAATTCAATT-AAAGATGAGCA--GATTTT 1896
                         -----------    -i   i  ii     -   i   i   -- iv   
  L1M4_orf2#LINE/    796 -----------AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_34717436_3   1897 CCACTGGCACTTAACCAAAGAAAATACACAAATGGCAAATGAGCACATTA 1946
                         vv iv i  i  vv        i   i         v   i       v 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_34717436_3   1947 AGAGAAGTTCAATGTCATTAAGTAC 1971
                          i   v i    ii   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (155 / 89)
Gap_init rate = 0.04 (37 / 908), avg. gap size = 2.57 (95 / 37)  


2630 18.26 6.81 5.65  chr2_34725838_34728971.rev     1419  2108 (1026)    L1M4_orf2#LINE/L1        1   698 (210)  

  chr2_34725838_3   1419 TAGAAAGGAATCCCATGATCATGGA--------CTTA------TTAAGAT 1454
                          i     iv        v       --------    ------       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_34725838_3   1455 GATAATACTTTATAAATTGATCTATAGATTCAACACAACTCCTATCGGAA 1504
                          ii      iivi           i         i   ii      ii  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_34725838_3   1505 TCCCAACTGATCTTTTTTTTTGAGGGGGTGGGGGCAGAAATTGCCAACCT 1554
                              i   -- i      --------------          v   v  
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTT--------------GCAGAAATTGACAAGCT 134

  chr2_34725838_3   1555 GCTCCTAAAATTATTGAGAAAATGCAAGAGGCTCAGAATAGCTAAAAGGA 1604
                          v          vv iv i         i i i         i    ---
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA--- 181

  chr2_34725838_3   1605 AATAATCATGAAAAAGAA---CAGAGT-AGTGGACTCACACTTCAGAATG 1650
                         --i    v          ---  i   -i v             vv   v
  L1M4_orf2#LINE/    182 --CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_34725838_3   1651 TAAAAAGTTATTGCAAAGCTACCTTAATCAAGACAGTTTTTTACTGACAT 1700
                          v    v   i i         vv             v vv     i   
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_34725838_3   1701 AAAAATAGACATACAAATCAATGGAATACAATTGAGAATCCAGAAATAAA 1750
                           ii         i i            v        i            
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_34725838_3   1751 CCCTAACATTTATGTGATCAATTGATCTTTGACAAGGG--CCAGGATAAT 1798
                            vv         --i         i  i        --   i  iv  
  L1M4_orf2#LINE/    330 CCCATACATTTATG--GTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_34725838_3   1799 TCAATG-------AACAGCCTTTTCAACAAATAGTGCTGAGACAACTAAA 1841
                               -------  i  i             i      i       ii 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_34725838_3   1842 TGTTTACCTG-AAAAAAATAAATAAATAAAAAATAACATTCAACCCCCTT 1890
                          i?ii  v  -    i   i  ---------------i  vi     ivi
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAA---------------GTTGGACCCCTAC 462

  chr2_34725838_3   1891 CTTCCAGCATGCACAAAAAATTAACTCAAAATGTATCAAAGAGTTAAATG 1940
                           iv  v   ii       -             v    ?   vi      
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_34725838_3   1941 TAAGAGCCAAA--CATAAAATTCTTTCAATACA-CACAGAATTAAATATA 1987
                                i   --i      i    vv  v v -  i  i?v     v v
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_34725838_3   1988 TGAGACCTTGGGTTAAGCAATGATTTCTTAG---------------CACA 2022
                         i v            i      i        ---------------    
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_34725838_3   2023 AACAATCAAAGAGAAGATTTATAATTTGTATTTAATCAAAATTGAAGTCA 2072
                          i   iv     i  i  vv    v   v i  v         i  iv v
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_34725838_3   2073 TTTGTGTTTCAAAG-ACATCATCCAGAAAGTGAAAAG 2108
                               i       -   ii   v             
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

Transitions / transversions = 1.51 (74 / 49)
Gap_init rate = 0.02 (17 / 698), avg. gap size = 5.06 (86 / 17)  

 948 16.98 5.66 0.00  chr2_34725838_34728971.rev     2431  2642 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_34725838_3   2431 AAGAAAGTGAA--GACAACCCTCAGACTGGCAGAAAATATTTTCAGGTCA 2478
                                    --        v    v   v           v  ii   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_34725838_3   2479 TATAGCTGATAAGGGACTTGCACTCAGAATTTATAAAGAATTAATAAAAC 2528
                             v               i ii      v         i vv  v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_34725838_3   2529 TCAATAAT-----TATAAATAACC--AGTTACAAATGACCAAAGGATTTG 2571
                                 -----v i        -- v ? v     iv           
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_34725838_3   2572 AATAAACATTTCTCCAAGTAAGATATATGAATGGTTAAT---CTTGTTAA 2618
                             i            iv        ii     ii   --- vii v  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_34725838_3   2619 ATGATCCTCAACACCACTGGTCAT 2642
                          v   v       i  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.94 (17 / 18)
Gap_init rate = 0.02 (4 / 224), avg. gap size = 3.00 (12 / 4)  


3026 23.91 4.04 2.13  chr2_34764302_34767089     1406  2296 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_34764302_3   1406 TAGAAAGATATTCTGTGTTTTTGGAATAGAGGAGTTAATATTGTTAAAAT 1455
                          i         i ii    iv    v i  i  v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_34764302_3   1456 GTCTACGGTACCCAAAGCAATCTATAGACTCAATGCAATTCATATTAAAA 1505
                          v v iiv v      vii     i   i    i     i v   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_34764302_3   1506 TACCAGTGAAATTCTTAACAGAAATAGTAAACAAA--AATCCTAATATTC 1553
                          v    ivivv  i  vi       v ---    i--i       v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_34764302_3   1554 ACATGGAACCACAAAAAACCCCAAGTAGCCAAAGCAATCTTGATTAAAAA 1603
                          i      vii   iii    vi i        i         vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_34764302_3   1604 GGACAAAGCTGGATGCATCATACT-ACCAACTTCAAAACATACTACAGTG 1652
                          i      i    v vv   i   -v    i        v       iv 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_34764302_3   1653 CTATAGTAGCCAA-ACAGCATAGTCCTGGCATAAAAACAGACCCAATGGC 1701
                            i    ii   -    ii i  v         ii i    vi vv ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_34764302_3   1702 CAATGCAACAGAAT--AGAGCCCAGAAAGAAATTTACTACATTCATGGCC 1749
                              v  i     --    i       v   iii -      i    i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTATGGTC 346

  chr2_34764302_3   1750 AATTGATTTTCAACAAAAGAATCAAGTACATACAATAGGGGAAAGATAAT 1799
                                    i    ii vii    vv   v    i   i  ii   i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_34764302_3   1800 TACTTCCATAAATGGTGTTAGGAAAAATGGATATCCACATGCAGAAGGAT 1849
                         ivi   v i        i i   v  v      ?         i   i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_34764302_3   1850 TAAATTAAACCTTTATCTCTCACCATGTATAAAAAC-AACT-GAAATGG- 1896
                         v  i  ii   ii  i   v      i  i     i-    -i      -
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_34764302_3   1897 TAATA-ACTTAAATGAAAGACCTAAAACTGTTAGA------AAAAAAAAC 1939
                          v ? -  i      v    v        i v i ------i  i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_34764302_3   1940 ATAGGGGAAAAGTTCCATGACATTGGTCTGAGCAATGTTTTTTTCTAGAT 1989
                              ? v   vi i i    v    vi ii      v   i  --    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--AGAT 594

  chr2_34764302_3   1990 ACATAATGGTTTTCTCAAAAGCACAA-------AAGCAAAAATAGACAA- 2031
                          -- i ii------i           -------   v         i  -
  L1M4_orf2#LINE/    595 A--TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_34764302_3   2032 TAGGATTATTTAAAACTTAAAATCTTCTGTACTTCAGAGGAAACAATTAA 2081
                          v   i viv v   v      v   i   i     i    v  v  i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_34764302_3   2082 CAAAATGAACAGACAACCTACAAAATGGAAGAAAATATTTGCA------- 2124
                         v   i    v        i   i     i              -------
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_34764302_3   2125 --TCTTATAAGGAGTTCATAGCCAAAATATACAAGGAACTCAAACAACTC 2172
                         --   v      iii ii  v   i      i  i      vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_34764302_3   2173 AATAGCAAGAAAACAAACAAAAAAATTTAAAAAATGGGCAAAAGACCTGA 2222
                             ii  i  i     i  vvv    ?     -        i  ii   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGA 835

  chr2_34764302_3   2223 ATAGCTATTTCTCAAAAGAAGACATA--AATGGCTCACA-GTATATTTTT 2269
                             vi       v        i   --      iv i - i i  v---
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG--- 882

  chr2_34764302_3   2270 TAAAAAATACTCATCATCACTATTCAT 2296
                         -    i  i    v     ????????
  L1M4_orf2#LINE/    883 -AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (135 / 74)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.62 (55 / 21)  


3125 27.19 0.55 0.99  chr2_34771530_34777945     5013  5924 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_34771530_3   5013 TGGAAGAACATTACATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5062
                              ii i  iv    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_34771530_3   5063 GGCCATACTGTCCAAGGTCATTTATAGATTCAATGCCATCCCCATCAAGC 5112
                            v     vi    iv v  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_34771530_3   5113 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5160
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_34771530_3   5161 TATGGAACCAAAAAAGAGCCTGTATCGCCATGTCAATCCTAAGCCAAAAG 5210
                                viiv  ii  v  v v  v    viv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_34771530_3   5211 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTGCAAGGC 5260
                                i      vv       v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_34771530_3   5261 TACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGATC 5310
                                 i   i     i         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_34771530_3   5311 AATGGAACAGAA--GAACAGAGCCCTCAGAAATAATGCTGCTTATCTACA 5358
                                i    --  ---   i  --        vv iiivi  i  ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGA---GAGTCC--AGAAATAAACCCATACATTTATG 343

  chr2_34771530_3   5359 AACTATCCGATCTTTGACAAACCCAACAAAAACAAGCAATGGGGAAAGGA 5408
                         iv v  i-   i  i     ivviiv   i v  vv            i 
  L1M4_orf2#LINE/    344 GTCAATT-GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_34771530_3   5409 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 5458
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_34771530_3   5459 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 5508
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_34771530_3   5509 TGGATTAAAGAGTTACATGTTAGACCGAAAACCATAAAAACCCTAGAAGA 5558
                              i ?   vi  v    v   v v     i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_34771530_3   5559 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGTAAGGACTTCATG 5607
                             v    ?i- v i -   iv   v v  vv i  i  v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_34771530_3   5608 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5657
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_34771530_3   5658 TCTCATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5707
                         ii    i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_34771530_3   5708 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATTT 5757
                             v  i     i                 v  i    vii ivi  i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_34771530_3   5758 GACAAAGAGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 5807
                           i  i ii  vi          v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_34771530_3   5808 GAAAAAAACAAACAACCCCATCAACAAGTGGACGAAGGATATGAACAGAT 5857
                         v     i     i     v  i? v  i   i i      v    i   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_34771530_3   5858 ACTTCTCAAAAGAAGACATTTATGCCGCCAAAAAACACATGAAAAAATGC 5907
                          i     v        i  vi viiv     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_34771530_3   5908 TCACTATCACTGGCCAT 5924
                            vi    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2384 24.61 1.58 2.37  chr2_34808809_34813256     2724  3357 (1091)    L1M4_orf2#LINE/L1        1   629 (279)  

  chr2_34808809_3   2724 TGAAAGGATATTCCACGTTTGTGGATTGGAAGAATCAATATTGTTAAAAT 2773
                           i  i     i   i   ii            v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_34808809_3   2774 TCCCATACTACCCAAATCAATCTACAGATTCAATGCAGGATATGAAATCA 2823
                         vv v     v       ii              i   -------------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA------------- 87

  chr2_34808809_3   2824 AATCCCTATCACAATATCAATGGCATTCTTCACAGAAACAGAAAAAATAA 2873
                         -          v   vi  iiv  v  i  ii      iv  v  iv i 
  L1M4_orf2#LINE/     88 -ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr2_34808809_3   2874 TCTTAAAATTTATATGGAACCACAAAAGACCCAGAATAGGCAAAGCAATC 2923
                           i       i        vii   ii            v    i     
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_34808809_3   2924 CTGAGCAAAAAGAACAAAACTGGAGAAATCATATTATCTCACTTCAAATT 2973
                         i   iv  i         ii     i v   i i vi iv i      vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_34808809_3   2974 ATACTACAGAGCTA----AACCAA-ACAGCATGGTACTGGCATAA--ACA 3016
                         v       i     ----  i   -    ii              -- i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_34808809_3   3017 GACACACAGACCAATGGAACTGAATAGACAATACAGAAATAAATCTACCC 3066
                             i i   i        iv    v  v i v          i i iv 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_34808809_3   3067 ATCTACAGTGAACTTATTTTCGACAATGGTGCCAAGAACATACATTGGAG 3116
                           i  ii  v  i v           v          v   v  v   i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_34808809_3   3117 AAAACACAGTCCT--CAATAGTTGGTGCTGGGGAAACTGGGTATCCATAT 3164
                            iv i    i --   i iv          iv      i  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_34808809_3   3165 GCAGAAGAATGACACTGCACTTCTGTTGCTTGCCATAGACAAAAATCACA 3214
                            i        vii  v  ii  iiiv vii     v        i vv
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_34808809_3   3215 ACAAAATGGATTAAAGACTTAAATCTAATAATTCAGCCTATGAAACTTCT 3264
                         v          i ?    i     v   v ii v iv    i     ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_34808809_3   3265 AAAAGAAGTAATTGAAGAAACTCATCAAAACACTGCAGTT-GGCAAAGGT 3313
                          i     ivv  v i? v  v  v  ivi  vi  -i   -     v   
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG-GGTTAGGCAATGGT 585

  chr2_34808809_3   3314 TTCTTGAATATTACACCACAAGCACAGGCAACCAAAGCAAAAAT 3357
                              ii    v      v       i     v    v      
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

Transitions / transversions = 1.59 (94 / 59)
Gap_init rate = 0.01 (7 / 629), avg. gap size = 3.57 (25 / 7)  

1037 21.92 0.38 0.77  chr2_34808809_34813256     3697  3956 (492)    L1M4_orf2#LINE/L1      650   908 (0)  

  chr2_34808809_3   3697 AAGTTAAAACCTTTCTGCACAACAAAGGAAACAATCAACAAAGTGAAGAG 3746
                           i      v    -  ii vv       v  v     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_34808809_3   3747 ACAACCCACGGAATAGGGGAACATATTTGCAAACTATTCCTCTGACAAGA 3796
                                  i    i  i   v           ii  viv     i   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_34808809_3   3797 GATTAATAGCCAGAATATATAAGGAACTCAAATAATTCAATAGGAAAAAA 3846
                           i vi  v             i      vv i  i      iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_34808809_3   3847 ATCTAATAATCTGATTTTTAAGTGGGTAAA-AATTGAAATAGACATTTCT 3895
                          - v     i ii   ?vv  i    i   -i   vi             
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_34808809_3   3896 CAAAATAAGATATACAAATAGCAAACAGGTATCTGAAAAAGTGCTCAACA 3945
                          v   v             i  v  i i i iv      ii         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_34808809_3   3946 TTACTGGTCAT 3956
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (34 / 22)
Gap_init rate = 0.01 (3 / 259), avg. gap size = 1.00 (3 / 3)  


2236 28.06 3.45 2.34  chr2_34970662_34973592     1574  2471 (460)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_34970662_3   1574 TGGGAAAACATTTCACACTCATGAATTGGAAGAACTAATCTCATTAAAAT 1623
                            i  i i  ii  iii     i         vi    v ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_34970662_3   1624 GTTCATATGGCTCTAAGCAATCCACAGATTCAGTGCTATTCCTATCAAAC 1673
                          viv   ivv i v  vii   i         ii  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_34970662_3   1674 TACCAA-TGCCATTTTTTCATAGAATTAGAAAAAACT-ATTTTAAAATTC 1721
                          v   i-    v     v  v -    i-- v  i  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_34970662_3   1722 ATATGGGACAAAAAAAACGAGCCTGAATAGACAAAGCAATCCTAAACAAA 1771
                               i -- viv  iv  v  v      v    i     i i  v  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_34970662_3   1772 AAGAACAAACCTGGAAGCATTATATTACCTAACTTCAAACTATACTACAA 1821
                                  vi    i vv i i i v  i  i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_34970662_3   1822 GACTGCAGTAACCAAAACAGCACAGTACTGTTACAGAAGCAGACACATAG 1871
                         ii  i      i   i    iiii      vi i iiiii     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_34970662_3   1872 AATAATGGAACAGAATAGAGAACTCAGAAAGAAAGCAGCATATCTACACT 1921
                          vi       i     v    iii      v   v vii i  i  iiv 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_34970662_3   1922 -ACCTGATCTTCAAGAAAGTCAATAAGAAAAG-CAATGTGGAGAGAAATT 1969
                         - vi    i   i v  i viivi    vv v-     v   i    vvv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_34970662_3   1970 TCTATTCAATAAATGGTTCTGGGATAACTGACTATCCGTAAGTAGAAGAA 2019
                            v     i       v      i     iv  ?  ii v i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_34970662_3   2020 AGAAACTGGACCTCTATCTATCACCATATACAAAAATTAACTGAAAAAGG 2069
                         v   ii      i   i  vv                     v    v  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_34970662_3   2070 ATGAAAGTCTTCTTATCCAT-TGAGAACTCCATCTATAAAAATCCTAAAA 2118
                           v ?  v --  v ---  - i   i  vv v        v  i  i  
  L1M4_orf2#LINE/    496 ATCAWAGAC--CTAA---ATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_34970662_3   2119 GAAAACCCAGAAAATACTCTTCTCAACATTAGTCTTGGCAAAGAATT--T 2166
                               vi  i?ivv v     vii  v  i vi v     v iv  -- 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_34970662_3   2167 AGAAGCAAGCCTTCACAAGCAACTGCAATAAAAACAAAAA-AGACAAGTG 2215
                            --i v v vi  v     vvv    i    iv     -   i  i v
  L1M4_orf2#LINE/    591 AGA--TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_34970662_3   2216 GGGCATAATTAAA-TGAAAGAGCTT----CTTCACAGTAATAGAAATTGT 2260
                           i v v  i   - v   i vi  ----     v  -----  v i i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-----GACACTAT 683

  chr2_34970662_3   2261 CAATAGAG--GAAACACAACCTACAGAATGAGAGGAAATATTTGCAAACC 2308
                            v i  --i   v      i        i   i             i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_34970662_3   2309 ATG-ATTTGATAACAGTCTAATATCTAGAATTTATAAACAATTT----AA 2353
                           i-  i      vi v  vi    i     v      v  i i----  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_34970662_3   2354 ATCAACAAGCAA----TAAATGACCCCATTAAAAAGTGGGCAAAGGACAA 2399
                         v    i  vv  ----i    i    v   ?    i           ivv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_34970662_3   2400 GTATAGACACTTCTC-AAAAAAAAGACACG------CAATAAAAATATTT 2442
                          v       i     -   i  i v i  i------      iv i  --
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-- 881

  chr2_34970662_3   2443 TTAAAATGATTCTTATTATTATTCACCAG 2471
                         --i   v   v  i vi  i ????????
  L1M4_orf2#LINE/    882 --GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (142 / 106)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.26 (52 / 23)  


3110 24.86 2.20 2.31  chr2_34993223_34997831     3211  4119 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_34993223_3   3211 TGGAAGAATACTCCATGTTTATGCATTGGAAAAATCAATATTGTTAAAAT 3260
                              ii   ii       i   v       i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_34993223_3   3261 GTTCTTATTACCCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 3310
                          vivv  i v      vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_34993223_3   3311 TAGCAATAACATTCTTCATGAGGAAA--AAAAA----ATTCTAAAGTTTA 3354
                          vv  iivi v  i  --  vi    --i v  ----  i     i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT--TGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_34993223_3   3355 TATGAAATAACAAAAGACCAAGAATAGCCAGAGCTATCCTAAGCAAAAAA 3404
                             i  vvi   ii    v          i i v   i i ------- 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-------A 191

  chr2_34993223_3   3405 AAAAAAAAACAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACT 3454
                            i  i      ii       v     i v  ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_34993223_3   3455 ACAGAGCAATACTAACCCAAACAGCATGGTACCTGTATAAAAACAGATAC 3504
                            i   v i v   i v i    ii      iv i    ii i   i i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_34993223_3   3505 AAAGACCAATGGA-CATAATACAGAACCCAGATGCAAATTCACACACCTA 3553
                          v   i       -i v   vv   ii     vii   ii  i   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_34993223_3   3554 CAGTGAACTCATTTCTGACAAAGGTGCCAAGAACCTACACTGGAGGAAAG 3603
                         ii  v  i v    ii     i          v v v  v   i i  ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_34993223_3   3604 ATTGTTTCTTCAATAAACGGTGCTGGGAAAACTAGATGTGTATATGCAGA 3653
                           v  i i     i   i          v    i   i?vi i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_34993223_3   3654 AGAATGAAACTAGACCCTTATCTCTCACCATATACAAATATCAAATCAAA 3703
                                 ii i     i  i   v             v  i  v     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_34993223_3   3704 ATTAATTAATAACTT-----TAATACCTGAAACTATGAAACTACTACAAG 3748
                           vi  i ?vi  i -----   v v  i       i     vi  v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_34993223_3   3749 AAAACTTTAGAGAAAATCACCAGGACATCAATCTTGGGTCTTGGCAAAAG 3798
                              v vi ? v     vi iv   ------       - v     vi 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGAC------CTTGGGT-TAGGCAATGG 584

  chr2_34993223_3   3799 TTTCTTGAGCAATAAC-CCACAAACACAGGCAACTAAAGAAAAAATGGAC 3847
                               -  vv  i  -   v  i    i     v           i  i
  L1M4_orf2#LINE/    585 TTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_34993223_3   3848 AAATGGGATCACATCAAGTTGAAAAGCTTCTGCACAGCAAAGGAAACAAT 3897
                             v   iiv      iv v    i   i  ii vv       v  v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_34993223_3   3898 CAACAAAGTGAAGAGACCACCCACACAATGGGAGAAAACATTTGCAAACT 3947
                            v        i    v       v            i         ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_34993223_3   3948 ACCAATCTCACAAAGGGTTAATAACCAGAATGTGTAAGTAGCTCAAACAA 3997
                          ivv    v i  i  ii vi  v       i i   iv i   vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_34993223_3   3998 CT-----ATGGGAAAACATTGAATAATTTAATT-AAAAATGGACAAAAGA 4041
                           -----  iii  i   ---     iii    -        i    i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACA---AATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_34993223_3   4042 TTTGAGTAGACATTTCTCAAAAGAAGACATACAAATGAT-AATCAGGCAT 4090
                              i            v        i         ii-   - i   i
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCAC 879

  chr2_34993223_3   4091 ATGAAAAGGTGGTTAACATAATTGATCAT 4119
                                 i  v i     v ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (142 / 81)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.73 (41 / 15)  


2348 25.09 11.70 2.17  chr2_35022319_35024553.rev      916  1744 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35022319_3    916 TGGAAAAATATTCCATGTTCAAGGACTAAAAGATTCAATATAGTTAAAAT 965
                               i    i         v   i ii    i i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35022319_3    966 GTTTATACTACCATGAGCAATCTACAGATTTAATGCAATCCCTATCAAAA 1015
                          viv     v  vvi vii           i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35022319_3   1016 TGCCAATAATATTCTTGACAGAAATAGGAAAAGC-AATACAAAAAATT-T 1063
                          v   iiviiv  i  vi       -v  v    -i  v v    v i- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_35022319_3   1064 ATGGAGCAACGAAAGACCAAGAACAGCAAAATCTTTTCTAAGCAAAGAGA 1113
                              ivvi i ii    v    i   v   v vv ii i iv  ii   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_35022319_3   1114 ACAAAACTGGAGTAATCACATTGCCTGACTTCGAATTATACTACAGAGCT 1163
                              ii     v v     i v  ii i   i  viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_35022319_3   1164 GTAGTAAACAAAACGGAATGATACTGGCATAAAAACCAGCAAATAGACCA 1213
                         ii     v   i  i vi  i           ii ivii  v     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_35022319_3   1214 AGGGAACAGAATAGAGAACCCAGAAACAAATGTCCGTAC--TTACAATGA 1261
                          v    i     v    ii       i   i--  i   --   iii v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAAC--CCATACATTTATGGTCA 347

  chr2_35022319_3   1262 ATTCTTTTTTGACAATGGTGCCAAGAACATACTCTGGAGAAAAGACAATC 1311
                            vv    i     v          v   v vv   i    ii i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_35022319_3   1312 TCTTCAATAAATAGTGCTGGGGAAACTGGAAATACATATGCCGAAGAATG 1361
                          i     i    i        iv       v ?v  i    vi       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_35022319_3   1362 AAACTAGACCTCTATCTCTTACCATATACAAAAATCAAATCAAGATGGAT 1411
                           ii i    i   i   vi               i  v    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_35022319_3   1412 TAAAGTGTTAAATCTAATACCTCAAACTATAAAACTACTACAAGAAAACA 1461
                         i ?  vvi     v   v v  v             vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_35022319_3   1462 T-TATGGAAACATTCTGGAGTAA---TGGG----GCAAACATATCTTGAG 1503
                          -vi? v   iv   ----  i ---    ----    vvi v    iii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTC----GTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_35022319_3   1504 CAATACCCCACAAGCATAGGCAACCAAAG--------------------- 1532
                         i vv  v   v     i i     v    ---------------------
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_35022319_3   1533 ----CAAAA----------------------------------------- 1537
                         ----     -----------------------------------------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_35022319_3   1538 -----------------ATGGGAGAAAATATTTGCAAACTATCCATCTGA 1570
                         -----------------                     ii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_35022319_3   1571 CAAGGGATTAATA-CTAGAATATATAAGAATATAAAAGGAGCTCAAAAAA 1619
                         i      i vi  - i           i----------  i   vv v  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAA----------GAACTCTTACAA 783

  chr2_35022319_3   1620 CTCTATAGGAAAAAAATATAATAATCTAATCAAAAACTGGGCAAAATATT 1669
                            v   iv     i i -     i i   i?    v        iv   
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_35022319_3   1670 TGAATAGACATTTTTCAAAAGAAGACATGTAAATGAAAAATAGGCATATG 1719
                                      i  v        i  ii     ivv    i   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_35022319_3   1720 GAAAGGTGATCAACAT-ATTGATCAT 1744
                         i    i  v       - ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (122 / 82)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 7.67 (115 / 15)  


2235 25.49 4.75 3.71  chr2_35088469_35090743      924  1786 (489)    L1M4_orf2#LINE/L1       37   908 (0)  

  chr2_35088469_3    924 AATATTTTTAAGATAAAAATTCTCTAAAAGTTTATTTATAGATTTAATAA 973
                               v       iiv   v   ivv  i  v  i  i     i  iiv
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chr2_35088469_3    974 AATCACTATTAAAATCATAGCAGGCTTTAATTTTATTCTCTGTAGAATTT 1023
                             v    i      vi   v v    ---------- i  i    v  
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTT----------TTTGCAGAAATT 126

  chr2_35088469_3   1024 GACAAACTGGTCCCAAGATTGA---AGTAATATGAAAAACCTAGAATAGC 1070
                              i   i   i  i   v ---i v   iii iii   i        
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr2_35088469_3   1071 TGCAATGATTTTGTAAAAGAA---CAATGTTGAAGGACATACACTTACCA 1117
                         iiv  ii  i   v       ---   v    i     vi      v   
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_35088469_3   1118 ATATCATAACTTTTTA--AGGCTGTGGGAATTAGTATGGGGTGGTACTGG 1165
                           v   v     vi  -- i   iii v   i iv ii v          
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_35088469_3   1166 TGTAAGAATTGGCATATAGATCAGTGGAACACAATGGAGAGTTCAGAAAT 1215
                         ii    i  v i           i     i v   v      i       
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_35088469_3   1216 AAACCCCATATGTACAAGTTCAATCAATTTTAAGCAAAGATGTCAGGGAA 1265
                               -   ii vi v v     ii     vii   i i  i  i ivv
  L1M4_orf2#LINE/    327 AAACCC-ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_35088469_3   1266 ATTCAATGAGTAAA-AGTAGTCTTGTTAAAAAATTGGGTTGATGACACAA 1314
                                 i v   - i       v i  v    --   - v  iv    
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT--GGT-GCTGGGACAA 422

  chr2_35088469_3   1315 TAGTATAACCAC---TAAAA--ATG---T----CTTTTAC-TAACACCAT 1351
                         iv v   ?    ---i    --   --- ---- iii   - v       
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_35088469_3   1352 ACTAATGCCCAATAAATTTGGCTCATAATGGATCATGAATCTAAATGTAA 1401
                          -  -----   -     -ii    v         ?ii i          
  L1M4_orf2#LINE/    473 A-TA-----CAA-AAATT-AACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_35088469_3   1402 GAGCTAGAACTATAAAACTATTTGTTCTTACTGAACGAAATATGGGAG-A 1450
                               i            -------    --   vi   i  i  ? - 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACT-------CTTA--GAAGAAAACATAGGNGTA 555

  chr2_35088469_3   1451 AATGTTT-TGATCATGGATTGAGTAAAAAGGTATTAAATGCAATATCAAG 1499
                            v  i-   i v   i  ii i  viivv v   i  iii i i   i
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_35088469_3   1500 AGCAT--GCATTAG--TGAAAAATTCATAAATTAAAATTCACTGGAACTA 1545
                             i--   vi i--vi      vv       ii v    iiii  i  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_35088469_3   1546 GAA--CTTTGTTCTTCAAAATACATTATTAAGAAAGTAAAAATATAAGCC 1593
                         i  --i     v       iv   i   i        i    v i  v  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_35088469_3   1594 ACATATTTTTGATAAAAT--TAGCAAATTATACATCTGACAATGAATTTG 1641
                            v v vv-  v     -- v      i   i      i  v i i   
  L1M4_orf2#LINE/    706 ACAGAATGG-GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_35088469_3   1642 CATTGAGAATTTATAAAGAATCCTTATG--TCAATGTTGATATGACAAA- 1688
                         i  iv     v         ii    ii--     iv i v v      -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_35088469_3   1689 -ATCCAAT--AACAA-GTTCAAAAGACTTCAATAGACATTTCAATAAAGA 1734
                         - i     --  v  - vv    i  i  v            vvi     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_35088469_3   1735 AGAC-TACCCATGACTAACAA-TACATTAAAACATGCTTAACACTATTAG 1782
                            i-   vv   i i  i  -i    v    v     i    ii ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_35088469_3   1783 AAAT 1786
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.68 (136 / 81)
Gap_init rate = 0.04 (32 / 872), avg. gap size = 2.28 (73 / 32)  


2886 24.04 4.51 2.03  chr2_35118598_35121142.rev     1168  2053 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35118598_3   1168 TAGAAAAACACCCAATGCTTATGGATTGGAAGAATTAATAT----AAAAT 1213
                          i    i i i  v   i i             v       ----  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35118598_3   1214 GATCATACTACTCAATGTAATCTA-AAATCCCATGCAATTCTTATCAATA 1262
                          iiv     v i   vv i     - i  i v i     i i      v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35118598_3   1263 TTCCA-TTGTCATTTTTCACAGAATTAGAAAAAA-AATCCTAAAATTCAC 1310
                          i   -i  i -     ii     v v  v  iv-i             i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_35118598_3   1311 ATGGAACTGCAAAAGACACCTAATAACCAAAACAATTCTAATCAAAAATA 1360
                               v     ii   v vv    i          ii i vv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_35118598_3   1361 ACAAAGCTAGAGGCAGCACATTACCTTACTTCAAACTATACTACAAGGCT 1410
                               i i    vvv    i v  iv i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_35118598_3   1411 ATAGTAATCAAAGCAGCCTGTTACTGGTACAAAAATAGA--------TCA 1452
                          i         ii   iv  v      i i  ii     --------   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_35118598_3   1453 ATGGAACATAATAGGGAACCCAGAAATAAAGCCATATATCTACAATCAAC 1502
                               i v   v i  ii           v     i  i  iii    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_35118598_3   1503 TGATTTTTGGCAAAGGTAACTAAAACATTCGCTG---AAAGGATACCCTA 1549
                                i i   i   iv v i v     iv  ---    i   vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_35118598_3   1550 TTCAATAAATGGTGTTGGGAAAATTGGATAGCCATATGCAGAATAATGAA 1599
                              i        i     v  i      ?   i     i  v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_35118598_3   1600 AGCGGATCCCTATCTC-CATTGTATACGAAAATTAACTCAAGTTGGATTA 1648
                         ivi   i     i   -  iii     i             iv     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_35118598_3   1649 AAGACTTAAATATAAGACATTAAACTATGAAAATTCTAGAACAAAATAT- 1697
                         ?    i     i     vv v       i   v ii     v    i  -
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_35118598_3   1698 --TTTAAAAACTCTTTAGGACCTGGACCTAGACAAAGAATTTATGATTAA 1745
                         --?v    ---    iiv     v ivi   i   v iv  iv iiv  v
  L1M4_orf2#LINE/    550 GGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_35118598_3   1746 GATCTCAAAAGCAAATGCAACAAAAACAAAAAGAGACAAATGGAACTTAA 1795
                           ivi        v v         iv     v   i    v i    v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_35118598_3   1796 TTAAACTAAAAAGCTTCTGC----CAGAAAA-ACTAATAATCAA-CAAAC 1839
                          i   v v    i   i  i----  i ii -    vi  vv  -ii  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_35118598_3   1840 AGACAACCTACACAATGGGAGAAAATATTTGCAAACTTCTGCATGTATG- 1888
                                 i   v                      i-----   i   v-
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAAT-----CATATATCT 741

  chr2_35118598_3   1889 GACAAAGGACTGATATCCAGAATCTACCAGGAATGC--A-AACTCAATAA 1935
                           i  i     vi          v  iv i   iv -- -          
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_35118598_3   1936 GGAAAATAATGACACAACAAATAACC---TTAAAAAATCAGAAAAAGACA 1982
                         vi    ---------i          ---  ?      vi v   i  iv
  L1M4_orf2#LINE/    792 TAAAAA---------GACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_35118598_3   1983 TGAAAAGACGGTTTTC---AGAAGACATACAAATAGCCAACAA--ACATG 2027
                             v    iv  i  ---      i        i     i  --     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_35118598_3   2028 AAAAAATGCTCAACATCACTAACCAT 2053
                             i             ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (129 / 80)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.76 (58 / 21)  


2960 28.10 1.22 0.77  chr2_35148666_35155057     4997  5900 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35148666_3   4997 TGGAAGAACATTCCATGCTCATAAGTAGAAAGAATCAGTATCATGAAAGT 5046
                              ii i  i     i    iii v i    v i i   ii v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35148666_3   5047 GGCCATACTGCCTAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     v  i  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35148666_3   5097 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT---CCTTTAAAGTT 5142
                          v   iivi i  i  ii     -   -- v  i  ---   --   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCT--AAAATT 146

  chr2_35148666_3   5143 CATATGGAACCAAAAAATAGCTGGCATTGCCAAGTCAATCCTAAGCCAAA 5192
                                  viiv  iiv v ii v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_35148666_3   5193 AGAACGAAGCTGGAGGCATCACGCTACCTGACTTCAAACTGTACTACAAG 5242
                              i   i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_35148666_3   5243 ACTAAAGTAACCAAAACAGCATGGTACTGGTAACAAAACAGAGATATAGA 5292
                         i   v     i   i    ii         i vv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_35148666_3   5293 CCAATGGAACAGAAC--AGAGCCCTCATAAATAATGCCGCTTATCTACAA 5340
                         i        i    i--    i  -- v      vv  iivi  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_35148666_3   5341 CCCTCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5390
                         i vvi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_35148666_3   5391 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5440
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_35148666_3   5441 CTGAAACTGGATCCCTTCCTTACACCTTATACAAATATTAATTCAAGATG 5490
                         v    ii    i    v   i     v        v     i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_35148666_3   5491 GATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5540
                            i ?    i    ii v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_35148666_3   5541 ACCTAGGCA-ATACCATTCAGGACATAGGCATTGGCAAGGACTTCATGTC 5589
                           v    ?i- v i -   iv   v v  vv v     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_35148666_3   5590 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5639
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_35148666_3   5640 TAATTAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTACCATCAGAGTG 5689
                          v  i   v v  i i  ii  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_35148666_3   5690 AACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAATCTACTCATCTGA 5739
                           v  i     i                 v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_35148666_3   5740 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTGCAAGA 5789
                         i  i  i  vi          v  i  v      vv    v ivii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_35148666_3   5790 AAAAAACAA----CCCCATCAGCAAGTGGGCAAAGGATATGAACAGACAC 5835
                             i    ----   v  i?iv  i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_35148666_3   5836 TTCTCAAAAGAAGACATCTATGCAGCCAAAAGACACATGAAAAAATGCTC 5885
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_35148666_3   5886 ATCATCACTGGCCAT 5900
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (149 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


1546 30.01 7.18 1.97  chr2_35185973_35187865.rev      539  1401 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35185973_3    539 TAAAAAGCCATACCATATTCATGGATTGAAAGGCTCAATGTAGT-AAATT 587
                          ii    vi  v    i           i   i  i   i v  -  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35185973_3    588 GTCATTTCTTCTGAAATTGATGTACAAGTTTAACACAGCATTTATCAAAA 637
                          v  v v  i iv        v    ii  i   i  iivii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35185973_3    638 TCCCTGG-ACAATTTTTGTAAATATAGACATGATTATTCTAAAATGTATA 686
                             v v-i vv      i i v  v    v v v  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_35185973_3    687 GGGAAATCAAAGGAAGTAATAAAAGT--AAACAATTTTATAAAAGGATAA 734
                         v      vv    i viv v  v  i--       i  iv     i v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_35185973_3    735 CCTAATCTTATGAATCACTCTTAACAGTTTCAAGAC--------AAGTTG 776
                          vv i ivv v  v    v   vv  i      i  --------   i -
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT- 249

  chr2_35185973_3    777 GTACAGTAATC------------------CACAA--------------AT 794
                         --         ------------------  i  --------------  
  L1M4_orf2#LINE/    250 --ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_35185973_3    795 GAATGGAATAGAATAGAGTACTCAGAATTAACCCTATGCAAATACA-CCA 843
                         v             v   viii     v   v  i  i  vv  ii-i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_35185973_3    844 ATTTGAGTTTTGATA----TGTTAAAAAACAGTGCAATAGAGGAAGAATA 889
                            -  v   i  i ----  ii  i -- vi v    i i i       
  L1M4_orf2#LINE/    348 ATT-GATTTTCGACAAGGGTGCCAAGA--CCATTCAATGGGGAAAGAATA 394

  chr2_35185973_3    890 ATCTTTTCAACACATCACGCTGGGAAAATTGGATATTGAAAT---AAAAA 936
                         i           v  vii       v  i      ?iv v  ---   i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_35185973_3    937 ACAAATGTTTA---TCTAAGCCACGTAAATTACAGAACATTTCTCTCAAA 983
                          ii  -   vi---i   vvi   iiv vv    i  -   vv-      
  L1M4_orf2#LINE/    445 ATGAA-GTTGGACCCCTACCTCACACCATATACAAAA-ATTAA-CTCAAA 491

  chr2_35185973_3    984 ATTTATCATAGATTTAAAAGTAAAATGTAACATTTTAAAACTTCTGTAAA 1033
                           vv    ?   ii    v    i vv   v i v       ii iv  i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_35185973_3   1034 AAATCATAGGAAAAAATATTT-CAGTCCTGGATCTTCACAAAAAGATGTT 1082
                            v      ?iv    v  i-iiii i   i - vvi   viivv v  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTT 590

  chr2_35185973_3   1083 AC-CATGGTACCAAAAGCATCATTCATAAAAATAATATTTCACAACTTGG 1131
                          v-i   ii          iv viv i    iv  v v vv i  v    
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_35185973_3   1132 ACTTCATCAGAATTTAAAATTTTTG--CTGTATAAGACTTGGTTAAGAAG 1179
                                  i    v    i     --  vi v i   vivi i     i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_35185973_3   1180 ACAAAAATATAAGGTGAAATCTAGGAAAATAAGAGTTTCTGATCACATAT 1229
                         iii    v i  vviiv ivv i   i  -  v v  v vi    i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCATATAT 739

  chr2_35185973_3   1230 CTGAAAAAGGAATTAT-TTTAGATTATATAA-GAACTCTTAAATCTCAAC 1277
                             v  i   v  i - ii   v       -         v v     i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_35185973_3   1278 AATAAGAAAAAAATACAAATATCTCTATTAGAAAGTGGACAGAAGACATG 1327
                              -----   v       v i v   ?i   i   i  i i  iv  
  L1M4_orf2#LINE/    790 AATAA-----AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_35185973_3   1328 GAGATACATCTAACTAAACA-GTTATACAGATAACAGGTAAGCACATATA 1376
                         i v v    i vv i   v - v      i  ii vii         i- 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-A 883

  chr2_35185973_3   1377 AAAGATACTGAACATCACTAGCCAT 1401
                               i  v       ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (135 / 120)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.04 (79 / 26)  


 491 25.90 1.44 0.72  chr2_35205171_35210432     3652  3790 (1472)    L1M4_orf2#LINE/L1        1   140 (768)  

  chr2_35205171_3   3652 TGGAAGAACAATCCATGCTCATGGATT-GAAGAATCAATATCATTAA-AT 3699
                              ii i vi     i         -     v i     ii    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35205171_3   3700 GTTCATACTGCCCAAAGCAATCTGAAAATTCAATGCTATTCCTATCAAAC 3749
                          viv     v      vii    iv i      i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35205171_3   3750 TACCAACTTCATTTTCCACAGAACTGGAACAAACTATTCCT 3790
                          v   i  v v    iii     v v -    i  iv    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCT 140

Transitions / transversions = 1.40 (21 / 15)
Gap_init rate = 0.02 (3 / 140), avg. gap size = 1.00 (3 / 3)  

2284 27.69 1.69 2.54  chr2_35205171_35210432     3944  4770 (492)    L1M4_orf2#LINE/L1       89   908 (0)  

  chr2_35205171_3   3944 TCCCCACCTCAAATAGATCCTAGTGTCTGTTGTTTCCTTTTTCATAGAA- 3992
                             i --     ---    i  ---   ------       iii    -
  L1M4_orf2#LINE/     89 TCCCTA--TCAAA---ATCCCAG---CTG------CCTTTTTTGCAGAAA 124

  chr2_35205171_3   3993 ----CAGACT-ATTCTAAAATTAACTTGAAAC--CAAAAGGCC--AAATA 4033
                         ----  ii  -  i        v iv  i  v--   ii i  --i    
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr2_35205171_3   4034 TCCAAAGCAATTCTAAGCAAAATAAACATAGTTGGAGGCATCACATTATC 4083
                         v     i    ii i iv  i vi    v         vv     i vi 
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr2_35205171_3   4084 AAACTTCAAACTATACTATCAGGATACAGTAATCAAAACAGCATGGTACT 4133
                         v  i      viv     iv i v            i    ii       
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr2_35205171_3   4134 GGTATAGAAACAGACACATAGACCAATGGAACAGAATTGATAACCCAGAA 4183
                           i   iii i     i     i        i        v ii      
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr2_35205171_3   4184 ATAAAGCTACACAAATACAGCCACCAAATATTCAACTAAGTTGCCAAAAA 4233
                              v i i   vv  ii i  vivi  v   i  v i v      i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_35205171_3   4234 TAAGCAATGAGGAAAGGACTTTCTATTCAACAAATGGTGCTGGGATACTT 4283
                         i vv     i      i ivv   v                    i vi 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_35205171_3   4284 GTGTAGCCATATGCAGAAGAATAACACTGGATCCATATCTTTCACAATAT 4333
                          vi  ?   i     i      i vii    i  v  i  iv   v    
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_35205171_3   4334 ATAAAAATTAACAGATGATGGATTAAAGAATTAAATGTAAGACATCAACC 4383
                          i          vv vi      i ?   vi           vv v  v 
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_35205171_3   4384 TAAAAAAACCCTAGCAGAAAACCCAGG----AACCATTCTGAATATCAGC 4429
                           v    vi i   v       vi   ----  i v iv   viv vi i
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_35205171_3   4430 CACGGGAAAGGATTTATGACTAAGTCCTCAAAAGCAATTGCAACAAAAGC 4479
                         i -  v  v  v  iv iiv  v v vi        vvv          v
  L1M4_orf2#LINE/    575 TA-GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_35205171_3   4480 AAAAATTGACAAGTTGGGACACAATTAAACTAAAGAGGTCCTGCACAGAA 4529
                               v  i  i    -  viv  i   v v  i iv ii  ii vvv 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGG-ACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_35205171_3   4530 AAAGAAACTTATCAACAGGGTAAACAGGCAACCTACAGAATGGGAGAAAA 4579
                           i  v   -     v ii  i  v  i     i                
  L1M4_orf2#LINE/    673 AAGGACACT-ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_35205171_3   4580 TATTCACAAACTATGTATGCATCTAACAGAGGTCTAATATCCAGAATCTA 4629
                             ii    ii  i   ----  i i ii  v  vi          v  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATAT----CTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_35205171_3   4630 TCTGAAACTTAAGCAAATCAACCAGCAAAAACCAAATAACCCCATTAAAA 4679
                          vvii    ivvi   v    iv vv    iv          v   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_35205171_3   4680 AATGTGCAAAATACCTGAATAGATACTTCTCAGAAGAAGACAAACAAGAA 4729
                             v     iv ii        i i     vi       i v    ivi
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_35205171_3   4730 GTCATCAAGTATATAAAAAAATGCTCCACATCAGTAATCAT 4770
                          i  vi   i i  i    i      v      ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (129 / 97)
Gap_init rate = 0.02 (13 / 820), avg. gap size = 2.69 (35 / 13)  


 309 28.57 5.00 2.86  chr2_35219336_35221677      638   777 (1565)    L1M4_orf2#LINE/L1        6   148 (760)  

  chr2_35219336_3    638 AGGTATATCATATTTACAAATGTGAAGTTCTAATACAGTAATAATATCAC 687
                           i   vi   i  i iii  vv    vii     iv  v vi  iv  v
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_35219336_3    688 TTCTTCCCAAATTGATATGCAGATT-AACACAATACCTACCAAAAATCCC 736
                          v  i           v i      -   i    v    i     -    
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCC 104

  chr2_35219336_3    737 AGAACAATGTTTTGTATGGAAA------AGCTTATATTTAAATTTCA 777
                           -- viiv    v iii    ------    v  -ii    v    
  L1M4_orf2#LINE/    105 AG--CTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCA 148

Transitions / transversions = 1.35 (23 / 17)
Gap_init rate = 0.03 (5 / 143), avg. gap size = 2.20 (11 / 5)  

1486 27.36 5.50 3.95  chr2_35219336_35221677     1134  1842 (500)    L1M4_orf2#LINE/L1      150   869 (39)  

  chr2_35219336_3   1134 ATTAAAATGCTA---ACATAAAAT-GCTAACAAAAATTTAAAAAACAATA 1179
                           vi      v ---  vi i   -  i  v v  vi  i     v  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_35219336_3   1180 ACAAAGTGAGAAGA-----ATTGCTCAATTTTACGCTGAGATTTATCATA 1224
                                vi  i  ----- i v i      i ----- i i   ii i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCA-----AAACTTACTACA 244

  chr2_35219336_3   1225 TGTCTGCAGTTGTTAAGTCAATATGGTTTTGCTGAAGGAATAGACATACT 1274
                         viv  i    vi i   v  i i    vi  viiv i i         iv
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_35219336_3   1275 GGCCAATGGAATAGA-----GAATGCAGAAACAGACTGACACAAATATGA 1319
                          ii            -----  i v      i i  iv i   vv    i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_35219336_3   1320 CCATTCTATATTTGAGGAAGGTGCAAAAGCAATTAAAATGAATAATGGAT 1369
                         i  v iv  v  i  vi i     v  ii v   v  -  iiv  v i  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAAT 393

  chr2_35219336_3   1370 AGGCTTTTCAATAAATGGTGCTGGAACAATTAGATATCAGTAGACAAAAA 1419
                           v        i            i    i i    ? vii vi     i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_35219336_3   1420 AGGAGAAATAAGAACAAATAATTTTACATAACCTAGACAACATACACAAA 1469
                          iv-   i vi  v ----------- v  -   v-   v    i     
  L1M4_orf2#LINE/    444 AAT-GAAGTTGGACC-----------CCTA-CCTC-ACACCATATACAAA 479

  chr2_35219336_3   1470 AATTAA-----AATAAACCATGGACTTAAATGTAAAACTTAA-----TAA 1509
                               -----   ii i  ?i   i         i vi   -----   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_35219336_3   1510 A-CTTTGAGCAGAAAGCAGAGGA-TAACATCTTTGGAACCAAGTGCTAAA 1557
                          -  i v  v     i  v   ?-   -     i vi   vv v i  ii
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGG 578

  chr2_35219336_3   1558 CAAAGGATTCTTACACACGACATGAAAAACGTGATCCGTAAAATAA---- 1603
                            v  v      v i i    iv    i iii v vii    v  ----
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_35219336_3   1604 TA-ATAAATTGGACTTCATCAAAATTCAACA-TTTTGTTCTAGGAAAGAC 1651
                           -                       v  v -      v  vvi  i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_35219336_3   1652 CCAGTTAAGAAAAAGAAAGGAAATGACAACT-ACAGATTTAGAAAAAATA 1700
                         v vi i      iv    i  -----    i-     v vi  i      
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGA-----CAACCCACAGAATGGGAGAAAATA 723

  chr2_35219336_3   1701 TTTATAAACCACATATCTGA-AAAAGTCTGGTATCTAGAATATACAAATA 1749
                            ii   i  i        -  ii v  v     i        i   v 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_35219336_3   1750 ATTC--ACAAATCTCAACAGCAAAAA--CAAGCAATTCAATTATAAAATG 1795
                          i  --    --     i ii     --   ii  ii     ?v      
  L1M4_orf2#LINE/    774 ACTCTTACAA--CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_35219336_3   1796 GACAT-GTATAAAAATATAAATTTTACCAAAGAGGAAAGACGTATGGC 1842
                          i  v- v  vvi    v v    iv       i  v v  iv     
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

Transitions / transversions = 1.41 (111 / 79)
Gap_init rate = 0.03 (25 / 720), avg. gap size = 2.68 (67 / 25)  


3218 26.60 0.66 0.44  chr2_35243819_35250226.rev     5011  5916 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35243819_3   5011 TGGAAGAACATTACATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5060
                              ii i  iv    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35243819_3   5061 GGCCATACTGCCCAAGGTAATTTACACATTCAATGCCATCGCCATCAAGC 5110
                            v     v     iv i  i    v      i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35243819_3   5111 TACCAA-TGACTTTCTT-CACAAATTGGAAAAAACT-ACTTTAAAGTTCA 5157
                          v   i-  v    i  -  v      -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_35243819_3   5158 TATGGAACCAAAAAAGAGCCCCCATCGCCAAGTCAATCCTGAGCCAAAAG 5207
                                viiv  ii  v  vvv  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_35243819_3   5208 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5257
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_35243819_3   5258 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5307
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_35243819_3   5308 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5355
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_35243819_3   5356 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5405
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_35243819_3   5406 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5455
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_35243819_3   5456 GAAACTGGATCCCCTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5505
                            ii    i   iv   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_35243819_3   5506 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAACAC 5555
                          i ?    i    ii v   v       i      vi i        v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_35243819_3   5556 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5605
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_35243819_3   5606 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAA-TGGGATCTAA 5654
                         i            vvi          vv     v  i  - v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_35243819_3   5655 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5704
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_35243819_3   5705 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5754
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_35243819_3   5755 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAGAA 5804
                         i  i  vi          v  i  v      vv    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_35243819_3   5805 AAACAAACAACCCCATCCAAAAGTGGGCAAAGGATATGAACAGACACTTC 5854
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_35243819_3   5855 TCAGAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5904
                           vi       i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_35243819_3   5905 ATCACTGGCCAT 5916
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (136 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2497 25.46 6.83 1.74  chr2_35335804_35338116.rev      958  1821 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35335804_3    958 TGGAGAAATTCTCCATATTCATGTAT---AAGA-------------GGAT 991
                             i i  vii    i      v  ---    -------------i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35335804_3    992 GTCAGTTCTTCTCAAATTGACCTATAGATTTAATATCATCCAAGTTGAAA 1041
                          v  i v  i i        i   i     i  iiiv    vvi ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35335804_3   1042 TTCTAGCAAGCTATTTTGTAAATATTGAAAAACTGGTTCTAAAAAATATA 1091
                          i i   viv  v     i i v     v  i   i i      vvi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_35335804_3   1092 AAGAAAGGCAAAAGACATAGAATAGTCAATAC-----TGAA---GTAGAA 1133
                         vi    v    ii   vi       i   v  -----    --- v    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_35335804_3   1134 CAAAGTTAGAGGACAGATATTACTCAACTTCAAGACTTACTGTAAAGCCA 1183
                                i      vv i i v i   i     i       ii     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_35335804_3   1184 CAGTGATCAAGACAATGTC-TATTTGTGACAGAACAGACAGACG--TCAT 1230
                             i         i   v-  i v iivv  i i     v ii--   v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_35335804_3   1231 CTGAACAGA-----GAGCCCAAAAATAAACCCATACAAATATTGTTAACT 1275
                         iv   i   -----   i   i               vv   v  i  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_35335804_3   1276 GATCTTTGACAAAGGAAAAAAGACAATCCAAGTGAAAAAAAAAAAATTGT 1325
                            i  i     i  vivv     v  i   -  iii   i  v ---  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATA---GT 396

  chr2_35335804_3   1326 CCTTTTGACAAATGGTTCCTGGAACAGATGGACATCAACATGCCCAAAAA 1375
                          i   ii         v -   i   iv    i ? v      ----   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGC-TGGGACAACTGGATAKCCACATGC----AAA 441

  chr2_35335804_3   1376 AAAAAAAAATTGTCAACACATACCTTACGTCTTTCACAAAAATTAACTCA 1425
                          i  vi  i   --i  v v     i  ii v vi               
  L1M4_orf2#LINE/    442 AGAATGAAGTTG--GACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_35335804_3   1426 AAATGGATCATATACCTAAGT-TAAAATC-AAAACAATAAAATGTCTAGA 1473
                                   ? v      i -   i v -     v      ivii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_35335804_3   1474 AGGTATCTT-GGAG--AATATTGAAGTGACCTTGGATTTGAAAAGAGTTT 1520
                           iv v v -  ? --   v  v--          i  v iv  vi    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTC--GTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_35335804_3   1521 -TAAGATGTAATACCAAAAGAATGATTTGTAAAG--AAAAGTTGATAAGT 1567
                         - v    i i i        v ii vivii   i--    i v     i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_35335804_3   1568 TGGACTTCATTAAAATTAAAAACT---GCTCTGCAAAAGAAACTGGTAAT 1614
                                   i             --- iv  v    i  v   ivi  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_35335804_3   1615 AGAACGAAAGGACAAGCCACAGAGTGGGAGAAAATGT--AAAAACGACGC 1662
                          i ii    i     v       i           i --iv   i-- ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT--CAT 735

  chr2_35335804_3   1663 ATATCTGATAAACAACTTGTAAACAAAATATACAAAGAACTC--AAACCT 1710
                                    ivi       vv  i      i         -- v v  
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_35335804_3   1711 CAGCAGCAAGAAAACAA----CCTAATTACAAAGTGGGTAAAAGATCTGA 1756
                           ii ii  i  i    ----  i    ?v   i    i   i   i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_35335804_3   1757 -CAGAAACCTCTCCAAAGA---TACACAAATGAC----AAGCCTATTAAA 1798
                         -i   v ii          ---  i       i ----    vi  v   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_35335804_3   1799 AGATGCTAACTATCATATGTCAT 1821
                                v vi    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (136 / 80)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.74 (74 / 27)  


2416 30.30 1.55 0.78  chr2_35373483_35378043     3171  4071 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35373483_3   3171 TGGAAAAAGCATTCCATGTTCATGGATAGAAAGAATCAATACCATTAAAA 3220
                               i -i  i              v i    v i    iii    i 
  L1M4_orf2#LINE/      1 TGGAAAGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_35373483_3   3221 TGGCCATATTTCCTGAAGCAATTAATATATTCAATGCTATTCTTATTAAA 3270
                             v   i i  ii  vii  iv i v      i  v  i i   i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_35373483_3   3271 AGTATCAATGACATTCCTCACAGAACTAGAAAAAAATATTTTAAAATTCA 3320
                          - vi  iivi v  ii ii     v v  v  ivvv  ii         
  L1M4_orf2#LINE/    100 A-TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_35373483_3   3321 TATAGATCCAAAAAGGAGCCCGAATAGCCAAGGCATTCCTAAGCAAAAAG 3370
                            i  vviiv  i   v  v          ii  v  i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_35373483_3   3371 AACAAAGCTGGAGAAATCACACTACCTGACTTCAAACCATTCTACAGGGC 3420
                                i     i v       v  ii i      v v v     ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_35373483_3   3421 TATAGTAACCAAAACA-CATGATTCTGGTACAAAAACAAACATA--ACCC 3467
                           i     i   i   -ii  i v    i i  ii i i     --ivi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_35373483_3   3468 AATGGAACAGAATAGAGAACCCAGAAATAAGGATACGCACCTA-AACTAT 3516
                                i     v    ii          ivvi ii  ii  -iiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_35373483_3   3517 CTGATCTTTGACAAACCTGAAAAAAATAAGCAATGGGGAAATGACTCCCT 3566
                         i    i  i     ivv  vv  i vi vv           vi ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_35373483_3   3567 ATTTAATTAATGGTGCTGGGATAACTGGAAGGCCATTTGCAGAGCATCCA 3616
                         v  i  iv             i       vi?   iv    i iv viv 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_35373483_3   3617 AACTGGAACCCATCCTTACATAATATATAAAAATTAACTCAAGATGGATT 3666
                          ii    v   vv   i   iv     i              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_35373483_3   3667 AAAGACTTAAATGTAAAACCAAAAACTATAAAAAACCCTGGAAGAGAACC 3716
                          ?    i         i v v            v-i i i     i   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACA 547

  chr2_35373483_3   3717 CAGGCAATACTATTCTGGACATAGGAATGGGCAAAGATGTCAT-GATGAA 3765
                         i   ?ivv v v   vv   v v  iv i     v i v  v -   - v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr2_35373483_3   3766 GATGCTAAAGGCAATTGCAACAAAAGCAAAAATTGACAAAT--GACATCT 3813
                           ii i   i   vvv          v      v  i    --   v  -
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC- 645

  chr2_35373483_3   3814 AATTAAA-TGAAAGAGTATCTGCAGAGCAAAGGAAACTATCAACAGAGGG 3862
                         -  i   - v   i v - i  iivvv       v        v i  v 
  L1M4_orf2#LINE/    646 -ATCAAAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_35373483_3   3863 AACAGACAACTTACAGAATGGGAAAAAAT----GCAAACTGTGCATCAGA 3908
                           v       ii           i     ----     iii ii   v  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_35373483_3   3909 TAAAGGTCTAATAACCAATATCTATGAGAAACAA--ACAAATTAACATGA 3956
                            i  v  vi  v   iv  v   i ii   vv--    v i  i vv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_35373483_3   3957 GAAAAACTTACAACTGCATTAAAAAGTATGCAAAAGACATGAACAGATGC 4006
                         i   i  vv i   ivv   ?    i iv     i  iv    i   iii
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_35373483_3   4007 TTTTCAAAAGAAGATATGCATGAGGCCAACAAACGTATGAAGAAATGTTC 4056
                           i  v           i  viv      i  i ii     i i   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_35373483_3   4057 ATCATGACTGATCAT 4071
                          v   v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (160 / 109)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


2496 28.86 3.38 1.01  chr2_35404378_35408868.rev     3113  3999 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35404378_3   3113 TGGAAAGACATTTTGTGTTCATGGATTTAAAGAATTAATATTGTTATAAT 3162
                                 i  iiii            vi    v            vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35404378_3   3163 ATCTGTATCACCCAAGC-AATCTAAAAATTTGATACAATCC-TATCAATG 3210
                         iv vi  iiv     ii-i     v i   ii ii      -      vi
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35404378_3   3211 TATTGATGACATTCTTCATAGAAATAGAAAAAAAAAATCCTAAAATT--- 3257
                          viiiiivi v  i  iii      v  v  ivvi -          ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_35404378_3   3258 -TGGGACCACAGAAGACCTCACATAGCCTAAGCAATCTTGAGCAAAAA-- 3304
                         -   i vii  iii    iviv      v  i         iv  i  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_35404378_3   3305 ACAAAGTGGGAGACATCACACTACCTGACTTCAAAATATACTACAAAGCT 3354
                                v    ivv       v  ii i       iv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_35404378_3   3355 ACAATAATCAAAACAGCATTTCACTGACATCAAAACA-ACACATACACCA 3403
                            i       i    ii vvi    i   v ii i -   i   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_35404378_3   3404 ATGGAACAGAAGAGAGAACCTGGAAATAA-TCCAAGCATCTACAAACAAC 3452
                               i    vv    ii ii       -i   vi   i  iiiv   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_35404378_3   3453 TTATTTTCAACAAAGTTGCCCAGAAAA--CAAATTGAAAACAGGACAGTT 3500
                          v      i    i v    v   vv --   --  iii v  i i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTC 397

  chr2_35404378_3   3501 TCTTCAATAATTGATTCTAGACAAATTGGATATTCACATTCAGATGAATG 3550
                          i     i  v  i v  i ivv  i      ?i     v  i v     
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_35404378_3   3551 AAACTGGACCCCTACCTTTCACCAT---CAACA-TCAACTTATGATGAAT 3596
                           ii             iv      ---   v - i    i vi   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_35404378_3   3597 TAAAGATGTAAATGCAAAAACTGAAAGTATAAAACTACTAGAAG------ 3640
                         i ?   iv      i  i i  i   v         vi      ------
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_35404378_3   3641 ------TAAATGCTTTCTAAAGTTGGACTGGGCAAAGATTTTTTGAGTAC 3684
                         ------     -   iv i vv    ii i     v i   i  iii  i
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_35404378_3   3685 GAATTCAAAAGCAGAGGCAACAAATGCAAAAATGAAAAGATAGGATTACA 3734
                           vvi        v i        v v      ii v i  v   i v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_35404378_3   3735 ACATATTTTAAAAGCTTCTGCACAGGGAAAAAAAAGCAATCAAGAGAGTG 3784
                         v  v v  -    i   i  ii --vvv   ii vi v       i    
  L1M4_orf2#LINE/    647 TCAAAATT-AAAAACTTTTGTGC--TTCAAAGGACACTATCAAGAAAGTG 693

  chr2_35404378_3   3785 AAAAGACAACCTACAGAATGGGAAAATATATTCAGAAACTACACATTTAG 3834
                                    i           i  v     iiv   ii i i  i ii
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_35404378_3   3835 CAAGGGATTAGTATCCATAATATATAAGAAACTTAAGCAAATCAATAGCA 3884
                         i      i v       v         ii    ivvi   v      ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_35404378_3   3885 ACAAAATGATTA-TCCAATTAAAATACAATCAAAAAACTGGCATAGTCAT 3933
                          v  i ii v  -i      ?   v iiiv    ii i v v    v   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_35404378_3   3934 TTATCAAAAGAAGGCATAGAAATG-CAAAGAGGTATGTGAAAAAAAATAC 3982
                           v  v       ii   v     - v  v i i ii      i -- i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGC 891

  chr2_35404378_3   3983 TCAACATCACTAATCAT 3999
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (163 / 90)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.17 (39 / 18)  


2676 27.67 1.76 1.65  chr2_35415049_35417400.rev      954  1860 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35415049_3    954 TGGAAAAACTTTCCATGCCCATGGATAAGAAAAATTCATAGTGTTAAGAT 1003
                               i iv i     ii       vi   i v  v   v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35415049_3   1004 GGTCATACTCCCTAAAGCAATTTATAGATTCAGTGCTATTCCTATCAAAC 1053
                           iv        i   vii  i  i       ii  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35415049_3   1054 TACAAATGACATTCCTCACATAATTAGAAAAAACT-ATTCTAAAATTTAC 1102
                          v v iivi v  ii ii  v  v v  v  i-  -  i        i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_35415049_3   1103 ATGGAACCAAAAAAGAGCCTGACTAGCCAAGGCAATCCTAAGCAAAAAGA 1152
                               viiv  ii  v  v  v       ii     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_35415049_3   1153 GGAAAGCTGGAGGCATAATGTTACCCAACTTCAAACAATACTACAAGGCG 1202
                         iv    i      vv v iii v     i      vvv        i  v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_35415049_3   1203 ACTATAACCAAAACAGCATGGTGCTCATACAAAAACAGACACATAGACCA 1252
                           vi   i   i    ii    i  vii i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_35415049_3   1253 ATGGAGCAGAATAGATAGCCAAGAAATAAAGCTGTACACCTAAAACCATC 1302
                              ii     v  v  i v         v ii    ii  viii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_35415049_3   1303 TAAGTTTTGATAAAGTTGACACAAACAAGCAACAGAGAAAGGACTCCCTA 1352
                          i v   i  i  i v  v  vi v  vv   ii i     i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_35415049_3   1353 TTCAATAAATGGTGCTAGGATACCTGGCTAGCCATATACTGAAGATCAAA 1402
                              i          i   i v    v  ?   i  i vi    vii  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_35415049_3   1403 ACTGGACCTCTTCCTTAC--CATATACAAAAATCAATTCAAGATGGATTA 1450
                         ii      i  v   i  --             i  i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_35415049_3   1451 AATGCTTTAATGAAAAACCTAAAGTTATAAAAACTCT-GGAAAATAACCT 1499
                         ? vi i v    v  i v     ii       -    -i   i v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr2_35415049_3   1500 AGG---AAATACAATTCTGGACATAGGCCCTGGCAAAGATTCC------A 1540
                            ---    - --   vv   v v  viiv     v i  i ------ 
  L1M4_orf2#LINE/    549 AGGNGTAAAT-C--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_35415049_3   1541 TGACAAAGTTGCCAAAAGTAATTGCAACAAAAACAAAAATTGTCAAATAG 1590
                              ------       i vvv         iv      v vi    v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_35415049_3   1591 GACCTAATTAAACTAACAAGCTTCTGTGCAGCAAAATAAACTATCAACAG 1640
                            i v  i   v v v  i   i     vv    iv v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_35415049_3   1641 AATAAAGAGACTACTTACAAAATGAGAGAAAATATTTGCAAATTTTGCAT 1690
                          i i  i    v  ii   i    i                  iv ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_35415049_3   1691 CTGACAAAGGGCTAATATTCAGAATCTTTAAGCAACTTCAGAGAACAAGC 1740
                             i  i  i  vi   i      v v   iv    - vv v   --v 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACT-CTTACAAC--TC 786

  chr2_35415049_3   1741 AAAAAAAAAAAAACCAATA--CCA-TTAAAAAGTGAACAAAGGACATGAA 1787
                           v  v     i  v    --   -  ?    i  ii       iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_35415049_3   1788 TAAACAGTTTTCAAAAGAAGATATACATGCAGCCCACAAGCATATTTAAA 1837
                           i   v  i  v              viii   v i     i  v-   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAA 885

  chr2_35415049_3   1838 AAATGCTCAACATCACTAATCAT 1860
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.07 (31 / 15)  


3170 27.02 1.00 0.55  chr2_35456726_35460858.rev     2739  3641 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_35456726_3   2739 GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAATG 2788
                             ii i  i     i      i v      v i     ii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_35456726_3   2789 GCTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 2838
                           v     v     iv i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_35456726_3   2839 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 2886
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_35456726_3   2887 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 2936
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_35456726_3   2937 ACAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATACTACAAGGCT 2986
                               i      vv   ii  v  ii        viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_35456726_3   2987 ACAGTAACCAAAACAGCATGGTACTGGTACCACAACAGAGATATAGACAA 3036
                                i   i    ii         i iv vi i   v       iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_35456726_3   3037 ATGGAACATAAC--AGAGCCCTCAGAAATAATGTCATGTATCTACAACCA 3084
                               i v  i--    i  --        vvi   ii  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_35456726_3   3085 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 3134
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_35456726_3   3135 TATTTAATAAATGTTGCTGGGAAAACTGGTTAGCCATATATAGAAAGCTG 3184
                          v  i  i     v        v      v  ?   i  ii i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_35456726_3   3185 AAACTGGAACCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 3234
                           ii    v    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_35456726_3   3235 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 3284
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_35456726_3   3285 TAGGCA-ATACCATTCAGGACATAGGCATGGATAAGGACTTCATGTCTAA 3333
                             ?i- v i -   iv   v v  vv i ii  v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_35456726_3   3334 AACACCAAAAGCAATGGCAACAAAAGCTAAAATTGACAAATGGGATCCCA 3383
                         i            vvi          vv     v  i    v   iii  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_35456726_3   3384 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3433
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_35456726_3   3434 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 3483
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_35456726_3   3484 ACGGCTAATATCCAGAATCTACAATGAACTC----AAATTTACAAGAAAC 3529
                         iv i  vi          v  i  v      ----  v iv i  v   v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_35456726_3   3530 AAACAAAGAACCCTATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 3579
                          i     v     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_35456726_3   3580 TCAAAAGAAGACATTTATGTAGCCAACAGACACATGAAAAAATGCTCATC 3629
                           v        i  vi vi i     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_35456726_3   3630 ATCACTGGCCAT 3641
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 1.75 (14 / 8)  


3224 24.49 3.85 0.91  chr2_35462730_35464781      679  1560 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35462730_3    679 TGGAAAGACATTCTTTCTTCCTGGATTGGAACATTTGAGGACGTTAATAT 728
                                 i  i iv v   v          v i  i vivi     v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35462730_3    729 GTCTATGCATCCCAAAGCAACTTACAGATTCTATGCAATCTCTATCAAAA 778
                          v v  i vi      vii ii         v i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35462730_3    779 TGCCAATGGTCTTTTTTTTGCTGAAATAGAAAAGCTAGTCTTCAAAGTCA 828
                          v   iiv i       --  v     v  v     ii  i v   v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_35462730_3    829 TGTGAAATTGCAAGAAACCCTGAATAGCCAAAAAAAATACTGAAAAATAA 878
                          i  i  v      ii    v            v  - vi       v  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAA 197

  chr2_35462730_3    879 TAAT---GTTGGAGGGCTTACATTTCCTGACTTCAAAACGTACT-----G 920
                         v  i---        i  i   i    ii i        v    ----- 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_35462730_3    921 CTA-AGTGATCAAAAGGGTGTAGTACTGGCATAAGGATAGGCACATAGAC 969
                            -   i     i vi    i                  i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_35462730_3    970 TAATACAAGAGTGCTGAGAGTTGATGAATAAACTCATATGATCTATAGCC 1019
                         i   iv  v  vii       iv vi       i    i-  i   i i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC-ATTTATGGTC 346

  chr2_35462730_3   1020 AATTGACTTTTGA-AAG--TGTCACAGCCACTCATTGGCGAAAGAGTAGT 1066
                               i   i  -   --  i  vii   i   v   v      i    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_35462730_3   1067 CTCTTTAACAAATGGT--TGTAATAGTTACGTATC---ATGCAAAATAAC 1111
                           i  i          --  vi i ii ivi  ? ---        v  i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_35462730_3   1112 AAAGTTGATTCTTTATTTCACATCACATACAAAAATTAACTCAGA-TGCA 1160
                         i      ivi ii  ii     i  i                 i -  v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_35462730_3   1161 TTGAAAAAGTAAATAAAAGAGCTAAAACTCTAAAACTCCTAAGATAGAAC 1210
                          ii? i vv     iv             v        i  ii v i   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_35462730_3   1211 A--GAAATAAATCATTACAACCTTGGATTTTACAATAGCTTTTTAGGTAT 1258
                          -- i?i      v iiii       i  vvi    i i  i    i   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_35462730_3   1259 AGTACCCAATGCACAAGCAACAAAAGAAGGA---GA-AAATCATAATTCA 1304
                         iii   v  v                  ii ---  -    iiv v    
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_35462730_3   1305 CAAAAATGTTTAAAAAA----ATACATCAAAGGACACTAGAAAAACAGTG 1350
                         iv     ---      v----i i v             vv  i v    
  L1M4_orf2#LINE/    647 TCAAAAT---TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_35462730_3   1351 AAAAGACAATCCATAGAATAGGAGAAAATATTTGCAA-TCATATGTCTGA 1399
                                  i   i     i                 -      i     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_35462730_3   1400 TAGATGTCTATTATGTACAGTACATGAAACATT-TCACTGCTCAACAACA 1448
                           iiv v  vv   vi v i  i  i  iv i - i  vi     i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_35462730_3   1449 AAAGGACAAACAATGTCATTTAAAAAATGGGCAGAAGAC--GAGTAGACA 1496
                            i      i  i-i  v  ?           i i  i--  i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAAC-CCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_35462730_3   1497 TTTCTCCAGAGACTA-AT-CACGTGTTCAACAAGCAAATAAAAAGATGTT 1544
                                 i   vv -  -  vi  vi   i     v  i        i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_35462730_3   1545 CAATGTCATTTGTTAA 1560
                            ii   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (140 / 72)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.91 (42 / 22)  


 791 29.21 6.74 1.12  chr2_35494378_35496567      497   852 (1338)    L1M4_orf2#LINE/L1      131   506 (402)  

  chr2_35494378_3    497 AGCT-ATCCTAAAACTTACATGCAAGGGCAAATAAACTGGAATAATTTCA 545
                             -         i i i   v  iv    ivi v ii     iiivv 
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr2_35494378_3    546 ACAATTT--AAAAAGAAG--CAAGGTCAAAAGAATCACCATACCTGATTT 591
                              i --         --   i  iii i  v    vv v  ii    
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr2_35494378_3    592 TACGATTTACTATAAATCTACTCTAATAAAGAAAATG--GTATTGG--TG 637
                         i vi i      i   v    vv    v    v i  --   i   -- i
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_35494378_3    638 AAGAAAGA-A-ATAGGTTCCTGAAATGGAAT-AAGCAGCATATGCATAGA 684
                          i  v   - -    i ivv  i   i    -i  -  ivi viv   i 
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAG-AGTCCAGAAATAAA 329

  chr2_35494378_3    685 CTTGAACAAATTTA--GCCATTTGATATTTGACAAAGGT--TAAA--CA- 727
                          iiiv   --    -- i  v     v  i     i   --i  i--  -
  L1M4_orf2#LINE/    330 CCCATACA--TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_35494378_3    728 --AATAA--AAAGGATAGTCTTTGCAGCAAATGGTATTGAAACAATTGGT 773
                         --   ii--    i         v  i        ii  ii    i   v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_35494378_3    774 TCTCTATAGGCAAAAACAATGAACTATGACCTAAACTTCAAACT-CATGA 822
                          v? i i v      i-      v vv    ivv  i   v  i-i  iv
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAG-AATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_35494378_3    823 AAAAGTCAACTCAAAATAGATCACAGATTT 852
                             i i          i     ?   ii 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCT 506

Transitions / transversions = 1.83 (66 / 36)
Gap_init rate = 0.05 (17 / 376), avg. gap size = 1.65 (28 / 17)  

1059 26.41 2.93 1.22  chr2_35494378_35496567     1290  1698 (492)    L1M4_orf2#LINE/L1      493   908 (0)  

  chr2_35494378_3   1290 TAGATTACAGATTTAAATGTAAAATGAAAAACTATAAAAATTTTAGAATA 1339
                          i   i ?   ii         i vvv            v i      v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_35494378_3   1340 AA-CTCAGTAGAAAATTATCATAACCCAGAATCAGGACTAGAGTT-CTGA 1387
                           - vi  v? v    iv  i i   iv ii i   - v vi   -  v 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTA 591

  chr2_35494378_3   1388 GAAACAATCCTAATAGCATGTTCTATGACA---AACAT-GATAAATAAGA 1433
                           v ii iv i  v    iivv v ii v ---  v  -       vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_35494378_3   1434 GTTTACCAAACTTACAAGCTTTTGTTCTGTCAAAG-ATACTATCAAGAAA 1482
                         v  i i    v   v  i       v  -      - i            
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAA 690

  chr2_35494378_3   1483 GTGAAGAAACAAGATATGGATTGAAATAAAATATTTCCAAACCATATATC 1532
                              i i    vvi ii  v  ii v         v    i        
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_35494378_3   1533 C-AGAAAGAATTTGGTATCAAGTCCACACAGAGAACTCTCAAAAACTCAA 1581
                         i- v  i i i   -    v  vvi i i i        i v  -     
  L1M4_orf2#LINE/    741 TGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAA-CTCAA 788

  chr2_35494378_3   1582 TTAACAAGACAACAAATAAT----TTAAGAAATGAACAAAAGACTTGAAT 1627
                          -  i  i vi        i----  ? i     ii    i  i      
  L1M4_orf2#LINE/    789 T-AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_35494378_3   1628 ACACTGTTTACCAAAGATAATATAAGAATGGCAAATAATCACATAAAAAG 1677
                          v  vv  iv       vi     vi      v     v     i     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_35494378_3   1678 ATGTCCAACATCATTAGCTAC 1698
                            ii        ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (60 / 45)
Gap_init rate = 0.03 (12 / 416), avg. gap size = 1.42 (17 / 12)  


2616 25.87 0.42 0.42  chr2_35550029_35551740.rev      506  1220 (492)    L1M4_orf2#LINE/L1      194   908 (0)  

  chr2_35550029_3    506 AAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTTATACTATACTAC 555
                          i          i      vv       v  ii i  i v viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_35550029_3    556 AAGGCCACAGTCACCAGAACAGCATGGTACTGGTACCAAAACAGAGATAT 605
                           i  i     v i  ii    ii         i iv ii i   v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_35550029_3    606 ACATCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTA 653
                          v          i    i--    i  --        vv   i    i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chr2_35550029_3    654 CAACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGG 703
                         iiiii vi    i  i     ivv  v   i v  vvv           i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_35550029_3    704 ATTCCCTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGA 753
                           vvi  v  i                 v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_35550029_3    754 AAGCTGAAATTGGATCCCTTCCTTACACCTTATACAAAACTTAATTCAAG 803
                          iiv    i     i    v   i     v         v    i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_35550029_3    804 ATGGATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAG 853
                               i ?    i  v    v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_35550029_3    854 AAAACGTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 902
                              i    ?i- v i -   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_35550029_3    903 GTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 952
                         ivv  vi            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_35550029_3    953 ATCTAATCAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGA 1002
                          ii v      v v  i i   i   i vv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_35550029_3   1003 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTAGTCATC 1052
                              v  i     i                 v       vii vvi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_35550029_3   1053 CTACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACG 1102
                         iv i  i  i  vi          v  i         vv    v iv ii
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_35550029_3   1103 AGAAAAAAACAAACAACTCCATCAAAATGTGGGCAAAGGATATGAACAGA 1152
                          v     i     i   i v  i?   vi            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_35550029_3   1153 CACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAGAAATG 1202
                           i     v        i  vi viii     i ii        i i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_35550029_3   1203 CTCATCATCACTGGCCAT 1220
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (103 / 78)
Gap_init rate = 0.01 (4 / 715), avg. gap size = 1.50 (6 / 4)  


2578 27.93 3.43 0.59  chr2_35614052_35620155     4760  5604 (500)    L1M4_orf2#LINE/L1        1   869 (39)  

  chr2_35614052_3   4760 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATAAATATTGTGAAAAT 4809
                               i i  i     i        v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35614052_3   4810 GGCCATACTGCCCCAAGGAATTCATAGATTCAATGCTATCCACCTCAAGC 4859
                            v     v   v  vvi  ii i        i  v    viv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35614052_3   4860 TACCA-TTGTCTTTCTTCACAGAATTAGAAAGAACT-ACTTTAATTTTCA 4907
                          v   -i  i    i  -i     v v  v - i  - iii   vv    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chr2_35614052_3   4908 TATGAAACCAAGAAAGAGCCCGTATAGCCAAGAAAATCTTG--------- 4948
                             i  viivi ii  v  v v        i v       ---------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_35614052_3   4949 ----------GAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4988
                         ----------    vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_35614052_3   4989 TACAGCAACCAAAACAGCATGGCACTGGTATCAAAACAGATATGTAGGCC 5038
                              i  i   i    ii   i     i  v ii i   i  i   ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_35614052_3   5039 AATGGAACAGAAC--AGAGTCCTCAGAAATAACACCATACATCTACAACC 5086
                                i    i--       --        vv        i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_35614052_3   5087 ATCAGATCTTTGGCAACCTGACAAAAACTAGCCA-TGGGGAAAGGATTCC 5135
                          viv   i  i i   vvvvi v  i  i vi  -         i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_35614052_3   5136 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTATATGCAGAAAACT 5185
                           v  i  i              v      v  ? i i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_35614052_3   5186 GAAACTGGACCCCTTCCTTAAACCTTATACAAAAATTAACTCAAGATGGA 5235
                            ii         v   i v   v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_35614052_3   5236 TTAAAGACTTGAATGTAAAACCTAAAACTATAAAAACCCTAGAAGAAAAC 5285
                          i ?    i i       i v              vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_35614052_3   5286 CTAAGCA-ATACCGTTCAGGGCATACACGTGGACAAAGACTTCATGACTA 5334
                         v  i ?i- v i -   iv i v vvivv i i   v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_35614052_3   5335 AAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5384
                         vi            vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_35614052_3   5385 ATTAAACCAAACAGCTTCTGGACAGCAAAAGAAACTATCATCAGAGTGAA 5434
                           i   viv  v i   i  vi vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_35614052_3   5435 TAGGCAAACTACCAAATGGGAGAAAATTTTTGCAATCTATCCATCTGACA 5484
                         v  i   v i  vi             v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_35614052_3   5485 AAGGTCTAATATCCAGAAACTACAAGGAACTTAAACAAATTTACAAGAAA 5534
                          i  v  vi         vv  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_35614052_3   5535 AAAAAAAAAAAC---ATCAAAATGTGGGCAAAGGATATAAACAGACACT- 5580
                           i v   v   ---  i?   vi            v i  i     i -
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_35614052_3   5581 CTCAAGAGAATACATTTATATAGC 5604
                            v i    v i  vi v  i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGC 869

Transitions / transversions = 1.23 (128 / 104)
Gap_init rate = 0.01 (12 / 869), avg. gap size = 2.83 (34 / 12)  


1113 28.17 8.92 5.01  chr2_35623030_35624653.rev      497  1135 (489)    L1M4_orf2#LINE/L1      245   908 (0)  

  chr2_35623030_3    497 AAACTATAGTAATCAAGACAGTA-AATAT----ATAAGGATATAAA-ATG 540
                           i   i               i-ii  i----         v v -  i
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_35623030_3    541 GATCAATGAAGTAGAAGAGAAAGTTCAGAAGTAGGCCTGCACATCATGTA 590
                                 i i     vv  i   i     i  ii  iii    i---  
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT---TA 341

  chr2_35623030_3    591 TCTTTAACAGATTTTCAACAAAGGCACTAAGTTAATTCAAAGGAGAAGAA 640
                          vv i  iv       i    i  ii i   viv      v  i   - i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AG 390

  chr2_35623030_3    641 AATATTTATTTCAACCAATAACGTTGAATAAATAAAAAGATACCTATAGG 690
                             v iv       v   iii i  i-----------  i v  ---- 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGG-----------GACAACT----G 425

  chr2_35623030_3    691 GATATCCATATGTAAATATATAAAATTATATTTATGCTTTGCTCCACATG 740
                             ?   i   i   viv  i  i  iv iiiv i i ii v   i  i
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_35623030_3    741 CATAAATGATCACCAAATGGAACAAAGACACAGATGTGAAGCCTAAAAC- 789
                           v    v v v v       v  ?    vi i    i iiv       -
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_35623030_3    790 GTAGAACTTCTAAAATACATTATAGTAGAATATGTTTGTG-TTTTGTAAT 838
                         i  i    ii  i  v v vi    v? v v  v  i   -ii   -ii 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG-GGT 574

  chr2_35623030_3    839 TAGAAAACTATT-CTTATACATGATATGAAGAGCACAAATCATTTTTTAA 887
                            iv  ivi  -    v i    i iv  i       iiv i-----  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-----AA 619

  chr2_35623030_3    888 A--------TATGACTAATTTGTCTTAATTTAAATAAAAAGCTTCTGTTT 929
                          --------  -  iv    v v   v  iv    v    i   i   vi
  L1M4_orf2#LINE/    620 AAGAAAAAATA-GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_35623030_3    930 TTTTTGAAGATATTTTTAAGACTAAGT----------CTCATTG--TAGC 967
                           iv-i i  i i v i    --    ---------- i  iv -- i v
  L1M4_orf2#LINE/    669 TTCA-AAGGACACTATCAAGA--AAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_35623030_3    968 ATAAAATATTTGCAAAACACTTATTTGATAAGG----------------- 1000
                          v              v  iv   i        -----------------
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_35623030_3   1001 -------AACCCTCAAAAGTCAATAATTAAAAAAAATCAAGCAGTACAAT 1043
                         -------   i  i v  v        --     i -   ii iiv    
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAAT--AAAAAGA-CAAATAACCCAAT 812

  chr2_35623030_3   1044 --AAAAATGTGTGAAATTCTTGAACAGGTTCTTCACCAAAGAAGATAAAG 1091
                         --       v ii  ivvi     i  iivi   v            v v
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_35623030_3   1092 AAA--GCAATTAAGCAAATAAAAAGATGCTCAACACTGTTAGTCAC 1135
                            --  v v      v  i               iii????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (111 / 66)
Gap_init rate = 0.03 (23 / 664), avg. gap size = 3.87 (89 / 23)  


2353 26.61 9.19 0.84  chr2_35660397_35664595.rev     2870  3707 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35660397_3   2870 TGGAAAAATATTCCATATTCATGGACTGGGAGAATCATTATTGTTAAAAT 2919
                               i    i    i        i   i   v i v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35660397_3   2920 GCCCAGACTATCCAAAGTAATCTGCAGATTCCATGCCATCTCTATCCAAA 2969
                          v v v   vi     v i    i       v i  v   i     v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35660397_3   2970 TACCAATGACATTCTTCACAGAAACAGAAAAAAATATATATAAAATTTAT 3019
                          v   iivi v  i  ii      iv  v  ivvv  vi-       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC-TAAAATTCAT 149

  chr2_35660397_3   3020 ATGGAACCCCCAAAGACCCAGAATAACCAAAACTATCCTGAGCAAAAACA 3069
                               viv v ii           i       v   i   iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_35660397_3   3070 ACAAACCTGGAGGAATCATATTACCTGA--------------------CT 3099
                              vi       v   i i v  ii --------------------  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_35660397_3   3100 ATTGTAACCAAAAT-GCATGGTATTGGCATAAAAAGAGACACATAGACCA 3148
                          iv    i   i i- ii     i        ii v     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_35660397_3   3149 GTAGAGCAAAAT--A-----CAGAA------------------GG-CAA- 3171
                         i i  ii i   -- -----     ------------------  -   -
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_35660397_3   3172 ---------ACAAAGGTGTCAAAAACATACTATGAAAAAAAAAAATGGTC 3212
                         ---------    i    i   i v   v v   iii   i  -- i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA--TAGTC 397

  chr2_35660397_3   3213 TCTTCAACAAATGGTGCTGGGAAAATTGAATATTCATATGCATGAGAATG 3262
                          i                    v  i  i   ?i  i     vi      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_35660397_3   3263 AAAAT--ATC---ACTTT---TCATATGCAAAAGTCAAATAAAAATGGAT 3304
                           iv -- i ---  i i---i     i     i i  v v         
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_35660397_3   3305 TAAATGCTGAAATCTAAGACATTATACTATGAAAGTACTAGAAGAATACA 3354
                         i ? vi iv    v     vv v v     i   v vi        v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_35660397_3   3355 TTAGGGAAGCTCTCCATG-----GGACTGGACAGAGATTTCTTGAGTAAT 3399
                          vi ? v iv   i i  -----  ii i i  iv i      iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_35660397_3   3400 ATTCCAGGAGTACAGGCAACCAAAACAAAAGTGGGCAAACGAAATCACAT 3449
                          iv   ii  i   i     v   iv    i i ii   ivii iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_35660397_3   3450 CAAG-TTAAAAAGCTTCTGCACAGCAAAGAAAATAATTTTAAAAG-GAAA 3497
                            i-       -   i  ii vv     i v iv  ivvi    -    
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_35660397_3   3498 ---CAGCCCACAGAGTCAGACAAAATAATTGCAACCTACTCATCTGACAA 3544
                         ---  i        i vi  v      v      vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_35660397_3   3545 GGGATTAATAACCAGAATAT-TAAAGGAGCTCAAACAACTCTATAGGAAA 3593
                             i vi  v         -     i -   vv       v   iv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATAATAAA 795

  chr2_35660397_3   3594 GAGAATCTAATCATCCAATTGAAAAATCAGCCAAAGATTGGAATACACAT 3643
                         i   -- v   v i      ?      vi  v  i    v     v    
  L1M4_orf2#LINE/    796 AAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_35660397_3   3644 TTCTCAAAAGAA-ACATGCAAATGGCAAACAGGCATATGAAAAGGTGCTC 3692
                              v      - i  i        v  i i   i        i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_35660397_3   3693 AACATCATTGATCAT 3707
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (135 / 84)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.00 (84 / 21)  


2514 25.66 0.73 0.44  chr2_35668658_35670327.rev      493  1178 (492)    L1M4_orf2#LINE/L1      221   908 (0)  

  chr2_35668658_3    493 TTTCCAGTTTCAAACTATACTACAAGGCTATAGTAACCAAAACAGCATGG 542
                           i   i       viv        i    i     i   i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_35668658_3    543 TACTGGTACCAAAACAGAGATATAGATCAATGCAACAGAAC--AGAGCCC 590
                               i iv ii i   v             v  i    i--    i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_35668658_3    591 TCAGAAATAATCCCACATATCTACAACCATCTGATCTTTGACAAACCTGA 640
                         --        v    i i  i  iiii  vi    i  i     ivv  v
  L1M4_orf2#LINE/    321 --AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_35668658_3    641 CAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAAGGGTGCTGGG 690
                            i v  vv            i  vvi  v  i  i   v         
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_35668658_3    691 AAAACTGGATAGCCATATGTAGAAAGCTGAAACTGGATCCCTTACTTACA 740
                          v         ?   i   i i  iiv    ii    i    vv  i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_35668658_3    741 CCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGACC 790
                           v              i    i      i ?    i       v   v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_35668658_3    791 TAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGAC 839
                               i      vi i           v    ?i- v i -   iv   
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGAC 567

  chr2_35668658_3    840 ATAGACATGGTCAAGGACTTCGTGTCTAAAACACCAAAAGCAATGGCAAC 889
                         v v ivv i v   v ii   v ivv  vi            vvi     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_35668658_3    890 AAAAGCCAAAATTGACAAATGGGATCTAATTAAGCTAAAGAGCTTCTGCA 939
                              vv     v  i    v   ii v  i  iv v  i i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_35668658_3    940 CAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAG 989
                          vv    i  v    i  vv i      v  i     i   i        
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_35668658_3    990 AAAATTTTCACAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTA 1039
                              v  ii   vii ivi      i  i  i  vi          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_35668658_3   1040 CAAAGAACTCAAACAAATTTACAAGAAAAAAACAAACGACCCCATCAAAA 1089
                         i         vv    v iv i  v     i     ii    v  i?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_35668658_3   1090 AGTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCA 1139
                          i     i      v    i     i     v        i  vi viii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_35668658_3   1140 GCCAAAAA--ACATGAAAAAATGCTCATCATCACTGGCCAT 1178
                              v  --         i       v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (102 / 70)
Gap_init rate = 0.01 (5 / 688), avg. gap size = 1.60 (8 / 5)  


1015 28.85 12.31 3.33  chr2_35690026_35691863.rev      571  1350 (488)    L1M4_orf2#LINE/L1       59   908 (0)  

  chr2_35690026_3    571 TCCTTTAATTTATCTG-AAATTCAATGCAATTTTGATCAAAATACCAACA 619
                            iiv    v    i- i      i     iiiv        v   i v
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_35690026_3    620 GGGTTTTTCATGAATCTTGACAAACTGATTTGAAACTTTATCTGGAGGAG 669
                          vv     iiiii vv       i     iiv   v  i  v    iiv 
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_35690026_3    670 CAAAAGACCAAAAATGGCCAAAAC-----TGAAGAA------------TG 702
                            ii    v i   i        -----    i  ------------  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_35690026_3    703 TA----TCCTAC----CAGCTATCAATGTATATTATAAACCTCTAGTGAT 744
                         v ----  vi  ----  ii -    viiv  i  i   v  vi   i  
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATT-TCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_35690026_3    745 AAAGTCAATATGTTATTGGCACAGAAATACAAAAACATTGACCCATGGAA 794
                         v   v  i i  v  i     i iii   --i v i  v  i v      
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATA--GACATATAGATCAATGGAA 305

  chr2_35690026_3    795 CAGAATGAAGA-TCTGGGAAATAGACT-GTGT-TTTACAACTTAATATAT 841
                         i     vi   -  ii -     i  i-i ii-    iii- i   vv  
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAG-AAATAAACCCATACATTTATGG-TCAATTGAT 353

  chr2_35690026_3    842 CT----CAAAGGTGCAACTGAAGATCATC--GTGGAATAAAGAGTA---- 881
                         i ----   i     -- --    i   i--i   ii-     i  ----
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGC--C--AAGACCATTCAATGGGG-AAAGAATAGTCT 398

  chr2_35690026_3    882 -TTCAAAATGTGAGACTGA-ACAATTAACTGCCCAC--GTAAATTGGATC 927
                         -     v vi  ivi   i-    i iiv i?    -- i   --i  --
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA--AGA-- 444

  chr2_35690026_3    928 CTTAAATTGGATTCTTACTTTCCACCATAC-CAATAAGTTAATTCTAGAT 976
                         v v  i     ii i   i iv       i-   -  i    i  v i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAA-AAATTAACTCAAAAT 493

  chr2_35690026_3    977 AGGATAAGGGG----AATGGTTCAAGGGG-AATATT-TGAGAC-CTTAAA 1019
                         -    v ?i i----    ---i   i v-  v i - i i  -    i 
  L1M4_orf2#LINE/    494 -GGATCAWAGACCTAAATG---TAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_35690026_3   1020 AGAAAATA-AGAAATAACATTTTTTTCTAAATTTGAGCTAGGGAA----- 1063
                               i -  i?i   -  i  iv --i vi   i i    v  -----
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAA-ATCTTCGT--GACCTTGGGTTAGGCAATGGTT 586

  chr2_35690026_3   1064 ----AGACA--A-ATTAAAA-TACATGTTA----AGCATTTAAAATGGAC 1101
                         ----   i -- - ii    -i   v iv ----  v ---     i  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA---AAAATAGAT 633

  chr2_35690026_3   1102 AAATTTCACTATATGTTCATTAAAAACTTCTTTCCCACAGAAAAATACC- 1150
                              vv   vi  vvvv           i v v iv  -  ii i  i-
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTA 682

  chr2_35690026_3   1151 TAAAGACAGTGAAAAGACAAAACACAAAC-------AAATGTCTGCAG-- 1191
                          v    v             vv    i v-------    i i    i--
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_35690026_3   1192 CACAT---------GAAATTTGCA--AAGGAT-TAGGAAGA-CTCTTACA 1228
                           i  --------- ii i   i --v  i  -  vi    -        
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_35690026_3   1229 AATCAATTAGAAAAGGACAAA--ACTCAATAGAAAATTGAAAAAAGGACA 1276
                          v     v v    i      --  i    v?    v  iiv      iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_35690026_3   1277 CAAACAGGCATCTCACAGAAGAGGA-A-ACATGTTGCAAACAAGCTCATG 1324
                         ii  i  i   i  v vi    i  - -   vi v  v  i    v    
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_35690026_3   1325 AAAAGATGTTTAACTTTATTAGTTCT 1350
                                 i i   v i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (144 / 77)
Gap_init rate = 0.06 (50 / 850), avg. gap size = 2.44 (122 / 50)  


3085 27.56 0.66 0.55  chr2_35700031_35706422.rev     4994  5900 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35700031_3   4994 TGGAGGAACATTC-ATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5042
                             iii i  i -   i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35700031_3   5043 GGCCATAATGCCAAAGGTAATTTATAGATTCAATTCCATCCCCATCAAGC 5092
                            v   v v  v  iv i  i  i        iv v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35700031_3   5093 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTTA 5140
                          v   iivi i  i  ii     -   -- v  i  - iii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_35700031_3   5141 TATGGAACCAAAAAATAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5190
                                viiv  iiv v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_35700031_3   5191 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5240
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_35700031_3   5241 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5290
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_35700031_3   5291 AATGCAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5338
                             v  i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_35700031_3   5339 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5388
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_35700031_3   5389 CTATTTAATAAATGTTGCTGGGAAAACCGGCTAGCCATATGTAGAAAGCT 5438
                           v  i  i     v        v   i  v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_35700031_3   5439 GAAACTGGATCCCTTACTTACATCTTATACAAAAATTAATTCAAGATGGA 5488
                            ii    i    vv  i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_35700031_3   5489 TTAAAGACTTACATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5538
                          i ?    i  v        v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_35700031_3   5539 CTAGGCA-ATACCATTCAGGACATAGGCATGATCAAGGACTTCATGTCTA 5587
                         v    ?i- v i -   iv   v v  vv iiv   v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_35700031_3   5588 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5637
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_35700031_3   5638 GTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCCTCAGAGTGAA 5687
                         i i   v v  i i   i  ii vv    i  v  i i vvv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_35700031_3   5688 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5737
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_35700031_3   5738 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5787
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_35700031_3   5788 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5837
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_35700031_3   5838 CTTAAAAGAAGACATTTATGCAGCCAAAAAGCACATGAAAAAATGCTCAT 5887
                           iv        i  vi viii     v             i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_35700031_3   5888 CATCACTGGCCAT 5900
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2734 26.63 3.54 1.37  chr2_35706531_35710739.rev     2843  3717 (492)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_35706531_3   2843 ATGACTATGGATTGGAAAAATTAAGATTGTTAAAGTAGGCATACTACCCA 2892
                            vii           i v    v        ii i vv     v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_35706531_3   2893 AAGTCATATACAGATTGAGTGCAATTCTTATCAAA-CACCAATGACATTC 2941
                           v v  v        v ii     i i       -iv   iivi v  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr2_35706531_3   2942 TTCATAGAAATAGAAACATCTACCCTAAAATTCATATGGAACCACAAAAG 2991
                           iii      v  v viiiv i                  vii   ii 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr2_35706531_3   2992 ATCCTGAATAGCCAAATAAATACTGAGCCAAAAGAACAAAGCTGGATGCA 3041
                          i  v           vv   vi   ivv i          i    v vv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_35706531_3   3042 TGACACTACCTGACTTCAACATATACTACAAAGCTGTAGTAACCAAAACA 3091
                          v     v  ii i     v iv            ii     i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_35706531_3   3092 GCATGACACTGGT-CAAAAACAGACACATGGACCAATGGAGCAGAATAGA 3140
                          ii  ii     i-i  ii i     i  i  i       ii     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_35706531_3   3141 GTACCCAGAGGTAAATCCACATATTTACAGCCAACTGAATTTCAACA--- 3187
                          vii     ii    i   i i     ii i   i   v    i   ---
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_35706531_3   3188 -TGC-------ATT----AGGGAAGGGACACCCTCTTCAATAAATTCTGC 3225
                         -   -------   ----i     i i i vi  i     i    vv   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_35706531_3   3226 TGAGAAAGCTGGATATTCATAGGCAGAAGAATGAAAGTAGATCCCTATAT 3275
                           i  v i       ?i  i v   i         iv i  i     iv 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_35706531_3   3276 CTCCACATTTACAAATATCAATTCAAAATGGATTAAGTACTTAAATGTAA 3325
                          v vv   v      v  i  i           i ?iv  i         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_35706531_3   3326 CA-CTGAAGCTATAAAACTATTAGAAGAAAACATACGGG--AATGCTTCA 3372
                         v -  i  i          v               v ? --   -    i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCG 563

  chr2_35706531_3   3373 GGGCATTGGAATGCACATATACTTTAT-GGGTAAGACTTCAAATGCACAG 3421
                         v i v    iv ivi  -  iv   v -i i  v   vi    v     i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCA-ATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_35706531_3   3422 GCAACAAAA----AAGTGGACAAATAGGACTATATCAAA--CAAAAAATC 3465
                                  ----  i i  i    v     vi      --i     -- 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA--C 660

  chr2_35706531_3   3466 TTCTCCACATCAAGGAAATCAATGAATAGAATGAAGTCAAAACCTGTAGA 3515
                           i vii v    i i vv v  v  v i i    ivv v    iii   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_35706531_3   3516 ATGGGAGAAAGTGTG-GCATGCTTTTCATCC---AAGAGACAAATATCTA 3561
                                   i i v-   viiiv vi   i---   i   vvi    i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_35706531_3   3562 GAATACACAGAGAACTCAACAGCAAAAACTCAACAGCAAAACAACAACAA 3611
                              i i i       -----iv v       i ii    - i--    
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTC-----TTACAACTCAATAATAAAA-AG--ACAA 802

  chr2_35706531_3   3612 ATAATCTGATTTAAAAATGGGCAAACGTTTTGAATATATATATTTTAAAA 3661
                             i ii   ?             v v        v i  v i iv   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_35706531_3   3662 GAAGATATACAAAAGGCCAAAAAGTACATGAGGAAATGCTCAATATCACT 3711
                                      v      v   i      ii i        i    ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_35706531_3   3712 AATCAT 3717
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.66 (143 / 86)
Gap_init rate = 0.02 (18 / 894), avg. gap size = 2.39 (43 / 18)  


2963 28.37 0.66 0.55  chr2_35807142_35811825.rev     3287  4192 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_35807142_3   3287 GAAAAGATATTTCATATTCATGAATTAGAATAATAAATATAGTGAAAATA 3336
                          i        ii   i      i   i   v v v     v  v  i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_35807142_3   3337 TTTAAACTACCCAAAGCAATCTACAGATTCAATGCAATTACTATCAAAAT 3386
                         viv v   v      vii              i     iv          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_35807142_3   3387 ACCAATGACATTCTTCACAGAAATAGAAACACT-ATTTTAAAATTTATAT 3435
                         v   iivi v  i  ii       v  v vi  -  ii       i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_35807142_3   3436 GGAACCACAAAAGTCCCAGAATAGCCAAAGTCATCCTGAGCAAAAACACC 3485
                             vii   ii v               iiv   i   iv  i  v v 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_35807142_3   3486 AAACTGGAAGGAAGAATCATATTACTTGACTTCAAATTATGCTATAGCAC 3535
                            v v i    ---v   i i v iii i      viv i   i ivi 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGA---CTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_35807142_3   3536 TATAGTTACTAAAACTGCATGGTACTGGCATAAAAA-ACACACATACATC 3584
                           i   v ii  i  v ii              ii - v   i   v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_35807142_3   3585 AGTAGAACAGAATAGAGAACCCAGAAATTAATCCGTACATCTACAATGAG 3634
                          i i   i     v    ii        v  i  i     i  iii v i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_35807142_3   3635 CTCATTTTCAACAAAGGTGCCAAGAACATGCTTTGGGGAAAGAAAAGTGT 3684
                         i v      i    i          v   v vv           v   v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_35807142_3   3685 CTTCAATAAGTGGTGCTGGGAAAACTGGATATTCATATGAAGAAAAATGA 3734
                         i     i  i           v         ?i  i   v i  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_35807142_3   3735 AACTAGACCCCTATCTCTTGTCATATACTAAAATCAAATCAAAATAGATT 3784
                          ii i        i   viii       v     i  v       i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_35807142_3   3785 GAAGACTTTAATCTAAGACCTGGAACTATGAAACTGCTGCAAGAAAATAT 3834
                         i?    i v   v     v  ii      i     vi iv       i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_35807142_3   3835 TGGGAATACCCTCCAGGATGTTGATCT-GGCAAAGATTTCTTGAGTAATA 3883
                         v  ?ivv vi  i iv  iv   ivi -     v i      iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_35807142_3   3884 CCCCACAAACACAGGCAACCAAAGCAAAAATGGACAAATGGGATCACATC 3933
                          v   v  i    i     v    v      i  i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_35807142_3   3934 AA-GTTAAAAAGCTCCTGCACAGCAAAGAAAAGAACCCACAAGGTAAAGA 3982
                           -i       -  ii  ii vv     i v vv i v v  i  i  i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_35807142_3   3983 GACAACC-ACAGAATGGGAGAGAAATATTTTCAAACTATCCATCTGACAA 4031
                                -             -        v    ii  vi      i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGA-AAATATTTGCAAATCATATATCTGATAA 746

  chr2_35807142_3   4032 GAGATTAATAAGCAGAATATATAAGGAACTCAAACAACTGTATAAAGTAA 4081
                          i  i vi  vv            i      vv      vv    viv  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_35807142_3   4082 AACTAAACAATCTGATTAAAATACCAGCAAAAGA-ACAAATGGAGATTTC 4130
                          ivi   i  i ii   ?   v ivi     i  -vii   i  v     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_35807142_3   4131 TCAGAATAAGACATGCAAATGGTAATCAGGTATTTGGAAAATTTCTCGAT 4180
                           vi  v    i  i       iv vi i i iv  i   iv v   i i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_35807142_3   4181 ATCATAGATCAT 4192
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (153 / 100)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 1.22 (11 / 9)  


 356 20.69 9.20 1.15  chr2_35882261_35889173     3230  3316 (3597)    L1M4_orf2#LINE/L1        3    96 (812)  

  chr2_35882261_3   3230 GAGAGAAATCCTATATTCATGGAT--GAA------ACGTTACAAAAATTG 3271
                           i   v    i  i         --   ------ ii  iiv  i  v 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_35882261_3   3272 CAACATTCTCCCAAATTGACCTATAGATTCAGTGAAATCCCTATC 3316
                            i i  -          i   i       ii v          
  L1M4_orf2#LINE/     53 CAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

Transitions / transversions = 3.50 (14 / 4)
Gap_init rate = 0.03 (3 / 94), avg. gap size = 3.00 (9 / 3)  

 706 19.43 4.57 3.43  chr2_35882261_35889173     3317  3491 (3422)    L1M4_orf2#LINE/L1        5   181 (727)  

  chr2_35882261_3   3317 AAAACTTCCTATATTCATGGAT--GAA------ATGTTATAAAAATTGTA 3358
                           i iv   i  i         --   ------  i  i v  i  v i 
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_35882261_3   3359 ACATTCTCCCAAATTGATCTACAGATTCAATGAAATACCTATCAAAACTT 3408
                          i i  -                       i v   v          iii
  L1M4_orf2#LINE/     55 ATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_35882261_3   3409 CAGCTGACTTCTGTGCGGAAATTGACAAGCTTATCCTCATATTCATATAG 3458
                               v   i v   i              v     v v        i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_35882261_3   3459 AAAGTCAAGTGATATCATACTGAATGGGCAAAA 3491
                            vv    v  i-i  ----    i v     
  L1M4_orf2#LINE/    154 AAATGCAAGGGAC-CCA----GAATAGCCAAAA 181

Transitions / transversions = 1.43 (20 / 14)
Gap_init rate = 0.03 (5 / 177), avg. gap size = 2.80 (14 / 5)  

3134 27.17 0.66 0.77  chr2_35882261_35889173     3942  4850 (2063)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35882261_3   3942 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3991
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35882261_3   3992 GGCCGTACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4041
                            vi    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35882261_3   4042 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4089
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_35882261_3   4090 TATAGAACCAAAAAAAGAGCCCACATT-GCCAAGTCAATCCTAAGCCAAA 4138
                            i   -- viv  i ii    v v -     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_35882261_3   4139 AGAACAAAGCTGGAGTCATCACGCTACCTGACTTCAAACTATACTACAAG 4188
                                  i     vvv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_35882261_3   4189 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 4238
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_35882261_3   4239 CCAATGGAACAGGAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAA 4286
                         i        i  i i--    i  --        vv iii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_35882261_3   4287 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 4336
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_35882261_3   4337 TGCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGACATATGTAGAAAG 4386
                         vv  v  i  i              v      v  ?v  i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_35882261_3   4387 CTGAAACTGGATCCCTTCCATACACCTTATACAAAAATTAACTCAAGATG 4436
                         v    ii    i    v  vi     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_35882261_3   4437 GATTAAAGACTTACATGTTAGACCTAAAATCATAAAAGCCCTAGAAGAAA 4486
                            i ?    i  v    v   v      ii      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_35882261_3   4487 ACCTAGGCA-ATACCAGTCATGACATAGGCATGGCCAAGGACTTCATGTC 4535
                           v    ?i- v i -v  i    v v  vv i v   v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_35882261_3   4536 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 4585
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_35882261_3   4586 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 4635
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_35882261_3   4636 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACTCATCTGA 4685
                           v  i     i                 v      ivii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_35882261_3   4686 CAAAAGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGA 4735
                         i  ii i  vi          v  i  v      iv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_35882261_3   4736 AAAAAACAAACAACCCCATCAAAAAGTTGGCAAAGGACATGAACAGACAC 4785
                             i     i     v  i?    i v         iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_35882261_3   4786 TTCTCAAAAGGAGACGTTTATGCAGCCAAAAAACACATGAAAAAATGCTC 4835
                              v    i   ii vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_35882261_3   4836 ACCATCACTGGCCAT 4850
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  

2204 17.29 4.44 13.69  chr2_35882261_35889173     5589  6421 (492)    L1M4_orf2#LINE/L1      153   908 (0)  

  chr2_35882261_3   5589 GAAAGTCAAGTGATAGAGCATAGCCACACACACAC---ACAAAAATGAGC 5635
                             vv    v  ivv  v       v -   vv --- v   i v  i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGAAC 201

  chr2_35882261_3   5636 TAAATTAGAGGACTCACACTTAAAGATTTCAAAACTTACTACAAAACTAC 5685
                         v  i  i              vvvi                    i    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_35882261_3   5686 AATAATAAAAACAGTATG-TACTGGCATAAGGATAAACGTGTGTGTGTGT 5734
                          i    v  i     i  -                i  i i --------
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT-------- 293

  chr2_35882261_3   5735 GTGTGTGTGTGTGTGTGTGTGTATGTGTGTATTTTAACTAAAAAGGATTA 5784
                         ------------------------------ vv i  ivi  v  i   i
  L1M4_orf2#LINE/    294 ------------------------------AGATCAATGGAATAGAATTG 313

  chr2_35882261_3   5785 AAA-TCCACAAAATAAACTTTTACATGTATGGTGAATCAATTTCTGAAAA 5833
                          i -    -i        iiv     v      v   ii    ii  v  
  L1M4_orf2#LINE/    314 AGAGTCCA-GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_35882261_3   5834 TGGGGCCAAGACAATTCGAAGAGAAAAAGCATAGTCTTTTCAACAAATGG 5883
                         v  v        v    -  vi ii    v                    
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTC-AATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_35882261_3   5884 TGCTGGGGCATTTGCATAGCCACATGAAGAAGGAAAAAGTTAGACCCGTT 5933
                                i  vi  v   ?       v i   i vi     i     v v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_35882261_3   5934 TCTCACACCAGACACAAAATCTA---CAAAAATTGGATCACAGACCTAAA 5980
                         i         v i      vi  ---     --       ?         
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAA--TGGATCAWAGACCTAAA 509

  chr2_35882261_3   5981 TATAAGAACTAAAATTATAAATCTCCTAGAAGAAAATATATAAATATATA 6030
                          i     i      i      v   i          i   ----------
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA---------- 549

  chr2_35882261_3   6031 TGTATATAAGACCTCAATATGAGAAAATTATAAATCTCCTAGAAGGAAAT 6080
                         --------------------------------------------  ?i--
  L1M4_orf2#LINE/    550 --------------------------------------------GGNG-- 553

  chr2_35882261_3   6081 ATATAAATCTATATCTGTATGATTTTTGGTTACATAAAGCCTTTTTAAAT 6130
                         ---       ---  ---i   ii  v     vii  v vi  i   i  
  L1M4_orf2#LINE/    554 ---TAAATCT---TC---GTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_35882261_3   6131 ACAACACCAAAAGCATAATCAACAAAAGAAAATATACA-AAATTGGGTTT 6179
                          ii            i  v             v   v -       ii  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_35882261_3   6180 ----AAGATTCA------TTGTGCTTCAAATGATATGACATTAACAAAGT 6219
                         ----  i   v ------            v  i i--i  i  v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC--TATCAAGAAAGT 692

  chr2_35882261_3   6220 GAAAA-ACA--CCATGGAA---ATAAAAATATTTAAAAATAATATATTTG 6263
                              -   --   ii   ---ivi         iv    v      i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_35882261_3   6264 ATAAAGGAAGGACTTTTATTTAGAATATGTGAA-AATTATTACAACTCAA 6312
                             i   ----   v   ii       i i  -  i v           
  L1M4_orf2#LINE/    743 ATAAGGGA----CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_35882261_3   6313 TAATAAAA---CAATT-------TTTGAAAATGTGTAAAAAATGTGCATA 6352
                                 ---   v -------  ?i      v i   ii  v  v   
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_35882261_3   6353 GACATTCCTCCAGAGAAGATATACAAATGGCCAA-ATGCACATGACAAGA 6401
                               i     i                     - v        v    
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_35882261_3   6402 TGCTCAATATCATTAGACAT 6421
                                i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (81 / 59)
Gap_init rate = 0.03 (25 / 756), avg. gap size = 6.04 (151 / 25)  


1106 22.97 0.34 6.08  chr2_35889646_35894251.rev     2896  3191 (1414)    L1M4_orf2#LINE/L1        1   279 (629)  

  chr2_35889646_3   2896 TGAAAAGATACTTCATGTTCATGGATTGGAAGAATCAGTAGTGTTAAAAT 2945
                           i       iii                    v i i  v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35889646_3   2946 ATCCATACTACCCAAAGCAATCTACATATTCAATGCAGTCCCTAT-AAAG 2994
                         iv v     v      vii       v      i   i       -   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35889646_3   2995 TATCAATAACATTTTTCACAGAAATAGAAAACAAACAAACAAACAAAAAA 3044
                          vi  iivi v     ii       v  -------   i vi i------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-------CAAGCTGAT------ 137

  chr2_35889646_3   3045 ACAGCCCTAGAATTTATGTGGAACTGCAAAAGACTCAGAACACCCAAAGC 3094
                         -----    i    i  i     v     ii   i     i v     i 
  L1M4_orf2#LINE/    138 -----CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_35889646_3   3095 TATCCTAAGCAGAAAGAACAAAACTGGAGGAATCACATTACCTGATTTCA 3144
                         v   i i iv ii         ii       v     i v  ii      
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_35889646_3   3145 AATTATACTACCCAGCTACAGTAACTAAAACAGAATGGTACTGGCAT 3191
                           viv      vv           ii  i    vi            
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

Transitions / transversions = 1.96 (45 / 23)
Gap_init rate = 0.01 (3 / 279), avg. gap size = 6.33 (19 / 3)  

2213 26.57 1.57 0.79  chr2_35889646_35894251.rev     3480  4115 (490)    L1M4_orf2#LINE/L1      268   908 (0)  

  chr2_35889646_3   3480 TGGTACTGGCATTAAAACAGACACATAGACCAATGGAACAGA-TAGAGAA 3528
                                     v ii i     i     i        i   - v    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_35889646_3   3529 CCCAGAAACAAATCCACCCACCTATAGTAAACTTACTTTTGACAAAGGTG 3578
                         i       i   i   iv  ii   i  v  i v i   i     i    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_35889646_3   3579 CCAAGAATCTACACTGGGGAAAAGACAGTCTCTTCAATAAATGGTGCTAG 3628
                               viv v  v        ii i     i     i          i 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_35889646_3   3629 GAAAACTGGATATCCATGTGCAAAAGAATGAAACTAGACTCCTATCTCTC 3678
                           v         ?   ii              ii i   i    i   v 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_35889646_3   3679 TCCATATACAAAAATAAAGTCAAAGTGGATT-------TAAATTTAAGAT 3721
                         v              v  v     i     i-------     v     v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_35889646_3   3722 GTCAAACCATGAAACCATCACAAGAAAACACTGGGAAAAACAACCAGGTC 3771
                         v v    i  i    iv i v         iv  ?iv   ivvi iv v 
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_35889646_3   3772 ATTGGTCTGGGCAAAAATTTCTTGAGCAATACCTCATAAGTGCAGGCAAC 3821
                         v    vi i     vii      iiii vv  vi  v   ii  i     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_35889646_3   3822 CAAAACAAAAATGGACACAAATGAGATAACAT--AAGTTAAAAAGTTTCT 3869
                         v   iv      i  i --   vi  ivv   --  i       v   - 
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATA--AATTGGACTTCATCAAAATTAAAAACTTT-T 664

  chr2_35889646_3   3870 GCACAATAAAGGATACAACCAACAAAGGGAAGAGACAGCCCACAGAATGG 3919
                          ii vvi      i  v i   v    v   i     i            
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_35889646_3   3920 GAGAAAATATTCAAAAACTACCCTTCTGACAAGGAATTAATAACCAAAAT 3969
                                    iiv   ii iviv     i    i i vi  v   i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_35889646_3   3970 ACATAAAGAGTTCAAACAATTTTATGGCAAAAAAAATCTAATGATCTGAT 4019
                          i       ii  vv    i iv  iii     i -- v   i i ii  
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CAAATAACCCAAT 812

  chr2_35889646_3   4020 CAAAAGATGGGTGAGAGATTTGAACAGACATTTCATAAAAGAATACATAC 4069
                         i?   i     ii ii        i         viv      v i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_35889646_3   4070 AAATGGCAAACAGGCATAGGAAAAGGTGCCCAACATTTCTGATCAT 4115
                                v  i i   i v      i   i      iv????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (107 / 59)
Gap_init rate = 0.01 (6 / 641), avg. gap size = 2.50 (15 / 6)  


3067 27.23 0.99 0.88  chr2_35902661_35908760     4702  5608 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_35902661_3   4702 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATTTTGTAAAAAC 4751
                              ii i  i     i      i v      v i   v    v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_35902661_3   4752 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCGTCAAGC 4801
                            v     v     iv i  i  i        i  v     ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_35902661_3   4802 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4849
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_35902661_3   4850 TATGGAACCAAAAAAGGGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4899
                                viiv  ii iv  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_35902661_3   4900 AACAAAGCTGGAGTCATCACACTACCTGACTTCAAACCATACTACAAGAC 4949
                                i     vvv       v  ii i      v v        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_35902661_3   4950 TACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATACACC 4999
                                 i   i    ii    i    i iv ii i   v     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_35902661_3   5000 AATGGAACAGGAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACT 5047
                                i  i i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_35902661_3   5048 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGATTC-C 5096
                          vi    i  i     ivv  vv  i v  vvv            v v-i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_35902661_3   5097 CTATTTAATAAACAGTGCTGGGAAAACTAGCTAGCCATATGTAGAAAACT 5146
                           v  i  i   ii         v    i v  ?   i   i i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_35902661_3   5147 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 5196
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_35902661_3   5197 TTGAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAACAAAAC 5246
                          ii?    i       v   v       i      vi i     v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_35902661_3   5247 CTAGGCA-ATACCATTCAGGACATAGGCATGTT---CAAGGACTTCATGT 5292
                         v    ?i- v i -   iv   v v  ---   ---   v ii   v iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGG---GTTAGGCAATGGTTTCTTAG 592

  chr2_35902661_3   5293 CTAAAACACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5342
                         v  vi    i       vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_35902661_3   5343 CTAATTAAACTAACGAGCTTCTGCACAGCAAAAGAAACCATCATCAGAGT 5392
                         i v  i   v v vi i   i  ii vv    i  v  i    vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_35902661_3   5393 GAACAGGCAACCTACAGAATGGGAGAAAACTTTTGCAACCTACTCATCTG 5442
                            v  i     i                iv       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_35902661_3   5443 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAG 5492
                          i  i  i  vi          v  i  v      iv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_35902661_3   5493 AAAAAAACAAACAACCCCATCAAAAATTGGGTGAAGGATATGAACAGACA 5542
                              i     i     v  i?    v    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_35902661_3   5543 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCT 5592
                         i     v        i  vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_35902661_3   5593 CATCATCACTGGCCAC 5608
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


2653 27.28 0.74 1.36  chr2_35985354_35987108      454  1263 (492)    L1M4_orf2#LINE/L1      104   908 (0)  

  chr2_35985354_3    454 CAAATGCCTTTTCTGCATCTATTGAGATAATCATGTGGTTTTTGTCCAAG 503
                           iv        i    vvv     --i  v ---  i ii ----v  i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGA--CAAGC---TGATCCT----AAAA 144

  chr2_35985354_3    504 TTCATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCA 553
                                    viiv  ii  v  viv  v     i      i i ivv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_35985354_3    554 AAAGAACAAAGCTGGGGGCATCACGCTACCTGACTTCAAACTATACTACA 603
                         i          i   i  vv    i  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_35985354_3    604 AGCCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 653
                          iv         i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_35985354_3    654 GACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTAC 701
                           i        i    i--    i  --        vv   i    i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chr2_35985354_3    702 AACCATCTGATCTCTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGA 751
                         iii  vi    i ii     ivv  v   i v  vvv           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_35985354_3    752 TTCCCTATTTAATAAGTGGTATTGGGAAAACTGGCTAGCCATATGTAGAA 801
                          vvi  v  i  i  i    ii     v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_35985354_3    802 AGCTGAAACTGGATCCCTTCCTTACAACTTACACAAAAATTAATTCAAGA 851
                         iiv    ii    i    v   i   v v  i           i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_35985354_3    852 TGGATTAAAGACTTACGTGTTAGACCTAAAACCATAAAAACCCTAGAAGA 901
                              i ?    i  vi   v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_35985354_3    902 AAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCACGT 951
                             v    ?i v viv   iv   v v  vv i     v ii   viiv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_35985354_3    952 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 1001
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_35985354_3   1002 CTAATTAAACTAAAGACCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 1051
                         i v  i   v v  i v   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_35985354_3   1052 GAACAGGCAACCTACAAAACGGGAGAAAATTTTTGCAATCTACTCATCTG 1101
                            v  i     i   i  i          v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_35985354_3   1102 AAAAAGGGCTAATATCCAGAATCTACAAAGAATTCAAACAAATTTACAAG 1151
                          v  i  i  vi          v  i      i  vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_35985354_3   1152 AAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 1197
                              i    ----   v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_35985354_3   1198 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCT 1247
                         i     v        i  vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_35985354_3   1248 CATCATCACTGGCCAT 1263
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (124 / 93)
Gap_init rate = 0.01 (6 / 805), avg. gap size = 2.83 (17 / 6)  


3362 24.97 1.21 1.32  chr2_36026189_36030407.rev     2820  3728 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_36026189_3   2820 TGGAAAGATATTGCATGTTCATGGATTAGAAGAATCAGTATTGTTAAAAT 2869
                                    iv              i     v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_36026189_3   2870 GTCCATACTACTCAAAGCAATATACGGCATCAATGCAATCCCTCTAAAAA 2919
                          v v     v i    vii  v   i vv    i         v v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_36026189_3   2920 TACTGATGACATTCTTCACAAAAATTTAAAAAATAATCTTAAAGTTTTTG 2969
                          v iiiivi v  i  ii  i     v v  iv i   i    i  iv i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_36026189_3   2970 TAGAACCACAAAAGACCCAGGATAGCCAAAGCCACCTTGAATAAAAAGAA 3019
                          i   vii   ii       i         i v i      v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_36026189_3   3020 CAAAACTGGAGGAAACACGTGACCTGACTTTAAA--TTATCCTACAGATC 3067
                             ii       vv   iivv  ii i  i   --   --     i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGC 248

  chr2_36026189_3   3068 TATAGTAACCCAAACAACATAGTACTGGCATAAAAACAGACACAGAGACC 3117
                           i     i v i   iii i            ii i     i v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_36026189_3   3118 AATGCAACAGAACAGAGAACCTAGAAATTAATCCACGCATCTACAGTCAA 3167
                             v  i    iv    ii i      v  i   ii   i  ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_36026189_3   3168 TTTATTTTTAACAAAGATGTCAAGAACCTACACTGGGGAAAGGACAGTCT 3217
                           v     ii    i i  i     v v v  v         i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_36026189_3   3218 TGTTAATAATTGGTGCTGGGAGAACTGGATATCCACATACAGAAGAATGG 3267
                          v i  i  v           v         ?      i  i       i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_36026189_3   3268 AACTAGACCTGTATCTCTAACCATATACAAAAATCAAATCAAAATATATT 3317
                          ii i    iv  i   vv               i  v       iv  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_36026189_3   3318 GAAGACTTAAATCTAATACCTGAAACTATGAAACTACTAAAAGAAAACAT 3367
                         i?    i     v   v v  i       i     vi  i          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_36026189_3   3368 -TGTGCAAACTCTCTAGGATATTGGTCTGGGCAAAGATTTCT-GGA-GTG 3414
                         -v ? i   -   iiiv  iv    vi i     v i     -i  -i  
  L1M4_orf2#LINE/    549 AGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_36026189_3   3415 ATATTCCAAAAACACAGGCAACCAAAGCACAAATGGACAGATGGGA-TTC 3463
                          i --      i    i     v    v v    i  i i  v   -   
  L1M4_orf2#LINE/    598 ACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_36026189_3   3464 ATCAAG-TTAAAAAGCTTCTGAACAACAAAGGGGAC----AACAAAGTGA 3508
                              i-       -   i  vi vv      iv  ----  v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_36026189_3   3509 AGAGAAAACCCACAAAATTTGAGAAAATATTTGCAAACTATTCATTTGAC 3558
                          i   v        i   vv                 ii  vi  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_36026189_3   3559 AAAGGATCAATAAATAACCAGAATATATAAAGAGCCCAAACAAGCCAATG 3608
                           i   iivi  -- --                i i vv    vi    i
  L1M4_orf2#LINE/    745 AAGGGACTTGTA--T--CCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_36026189_3   3609 GGAAAAATAATTGAATAATCTGATTTAAAAATGGGTAAAATATCTGAATA 3658
                         iv     v --ii     i ii   ?         i   iv  i      
  L1M4_orf2#LINE/    791 ATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_36026189_3   3659 GACATTTCTTAAAAGAAGACATACAAATGGGAAACAGGTATATGAAAAAG 3708
                                  iv        i          vv  i i i i       ii
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_36026189_3   3709 TGCATAACATCTTGGATTAT 3728
                            vi      v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (145 / 78)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


3035 26.64 4.59 0.34  chr2_36037887_36044242.rev     4994  5864 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_36037887_3   4994 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5043
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_36037887_3   5044 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCTTCAAGC 5093
                            v     v     iv i  i  i        i  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_36037887_3   5094 TACCAATGATTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5141
                          v   iiviii  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_36037887_3   5142 TATGGAACCAAAAAATAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5191
                                viiv  iiv v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_36037887_3   5192 AACAAAGCTGGAGGTATCATGCTACCTGACTTCAAACTATAGTACAAGGC 5241
                                i      vv   ii  v  ii i      viv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_36037887_3   5242 TACAGTAACCAAAGCAGCATGGTACTGGTACCAAAATATAGATATAGACC 5291
                                 i   ii   ii         i iv ii   v v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_36037887_3   5292 AATGGAACAGAACAGAGCCTTCAGAAATAATACCACACATCTGCACCCAT 5341
                                i    iv   vv i         vv   i    i iiivi  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_36037887_3   5342 CTGATCTTTGACAAACTTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5391
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_36037887_3   5392 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5441
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_36037887_3   5442 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5491
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_36037887_3   5492 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5541
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_36037887_3   5542 AGGCA-ATACCATTCAGGACATAGGCATGGTTAAGGATTTCATGACTAAA 5590
                            ?i- v i -   iv   v v  vv i vi  v i    v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_36037887_3   5591 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT--- 5637
                                     vvi          vv     v  i    v   ii ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_36037887_3   5638 -------------------------------ACCATCAG---AGTGAACA 5653
                         -------------------------------  i    i---      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_36037887_3   5654 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5703
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_36037887_3   5704 GGGCTAATATCCAGAATCTACAAAGAACTTAGACAAATGTACAAGAAAAA 5753
                           i  vi          v  i        ivv    v vv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_36037887_3   5754 ATCAAACAACCCCACCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5803
                         iv    i     v ii?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_36037887_3   5804 TAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTCATCA 5853
                         iv        i  vi viii     i ii  i       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_36037887_3   5854 TCACTGGCCAT 5864
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 6.14 (43 / 7)  


 698 31.91 8.70 2.73  chr2_36108781_36110357.rev      501  1086 (491)    L1M4_orf2#LINE/L1      288   908 (0)  

  chr2_36108781_3    501 ACATGTAA--CAATGGACTGGAATAGTGGGCTTAAAAATGGATTCATGCT 548
                             i  i--       v i    v v i iii i    ii ii   i -
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC- 336

  chr2_36108781_3    549 CAAATATGA-AAGTATGATAATTAA-AGGAACTGGTGT---GGCTGAACA 593
                         - vv    i-v i -    vv ii - i ----    i--- i iivv  
  L1M4_orf2#LINE/    337 -ATTTATGGTCAAT-TGATTTTCGACAAG----GGTGCCAAGACCATTCA 380

  chr2_36108781_3    594 GAGAGTAAAAAAGGGACTCCTCAATAAATGATACTGGGAATACTGTTGA- 642
                         iv i v   i  vi v  ii    i     i i      vv    --  -
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG--GAT 428

  chr2_36108781_3    643 ------ATGGAAAGG--TGAATATGAATCTCTACTTCATAACATACACAA 684
                         ------   v   i --    vv  i i i    i   i v    i    
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_36108781_3    685 ACATCAAATTCAATTGGAACAATAAC--AAATAACAGAAGTAAAATTGTA 732
                          v  i  v iv  v    v  ?vi  --    ivv   iv     i i  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_36108781_3    733 AAACT-TCAGAAAAGAACAAGGGAGAATAAAGGCACAT--CCTTGCAGTA 779
                              - i    i i    vi  ? --    vviv i --     -i  -
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNG--TAAATCTTCGTGACCTTG-GGT- 574

  chr2_36108781_3    780 TAG---AGGAATTTTTATACAAGACACAAAGAGCTCTTATGATAAG-GAA 825
                            --- v iv  i   v i v     v  i   v vviii i  i-   
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_36108781_3    826 AAGACTGAGAAATTTGCTTATATTCAAATGAAAAACTTCTGGTCTTCAAA 875
                           i iv  v     v vi vi  iv    v        i  vv       
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_36108781_3    876 AGTGACCATTGAGAGA---AAGAGATAAGCCA------------AGCTAT 910
                         i vv  i  ii   i ---  i   i  v   ------------ iv   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_36108781_3    911 TTGATAAACATCATAACCAAGATATTATTAATACCCATACTATATAAAGA 960
                            vv  v   -   v ii v vivv i vi  i   v v          
  L1M4_orf2#LINE/    725 TTGCAAATCAT-ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_36108781_3    961 ATGCCTATAAATT-----TAAAAAGGCAA----CATTGTAGAAAAATGGG 1001
                          iv i  i  v i-----       i   ---- vivi v?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_36108781_3   1002 CAATAAGTATATATAGATACTTTTTGCTAGGGGAAATATGCA--TGACCC 1049
                            viii v iv     i i  i -- i ii i i    i  --  i  v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCT--CCAAAGAAGATATACAAATGGCCA 871

  chr2_36108781_3   1050 ACAAACATATGAAAATATGCTTAGCCTCCTTAGTAGT 1086
                          i  i  i       v     i i v  v????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (107 / 77)
Gap_init rate = 0.04 (25 / 621), avg. gap size = 2.68 (67 / 25)  


4427 16.01 3.72 1.35  chr2_36120160_36122299      762  1648 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_36120160_3    762 TGGAAAGGCATTCCATGTTCATGAA----AATATTTCACATTATAAAGAT 807
                                ii  i           i ----  v i  v i   i v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_36120160_3    808 AGCAATATTCCTCAACTTTTTCTGCAGATTCAATGCAATCTCTATCAAAA 857
                         i      i   i   v  vv   i         i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_36120160_3    858 CCCTAGCTGCCTCTGTTTGCAGAAATTGGCAAGATGATATTAAAATTCAT 907
                         i  i        i -             i    v    vi          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_36120160_3    908 ATGGAAATGCAAAGGACTCAGAACAGTCAAAACAATTTTGAAAAAGAA-- 955
                                     i    i     i  i         i           --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_36120160_3    956 -CAAAGTTAGAGAACTCAAACTTTAAGATTTTAAA-CTTACTACAGAGTT 1003
                         -       i   i     v    ivvi    i   -         i  i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_36120160_3   1004 ACCATAATCAAGACAGAGTGGTATAGACATAAGGATAGACATAGACCAAT 1053
                           vi            v      iv i                ------ 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA------T 293

  chr2_36120160_3   1054 AAATCAATGGAACAGAATTTAG-TTTCAGAAATAAACCCTCACATTTATG 1102
                          i          i      v  -v i             vi         
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_36120160_3   1103 TCCAACTGATTTTCAACAGAAGGGCCAAGACAATTCAATATGAAAAGAAT 1152
                         vi   i        i   iii v        v       iv i       
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_36120160_3   1153 AATCTTTTTAATAGATATTGCTGGTACA-TTG-----CCAAATGCAGAAG 1196
                          i      i  i i  iv      v   -i  -----   v     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_36120160_3   1197 GATCAA-TT--ACCACTACCCTCATACCACATACAAAAATTAACTCAAAA 1243
                         i  v  -  --   v     -   i    i                    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACC-TCACACCATATACAAAAATTAACTCAAAA 492

  chr2_36120160_3   1244 TAGATCAAAGACCTAAATGTAAGAGCTA------TAAAACTCTTAAAAGA 1287
                          i     ?                    ------           i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_36120160_3   1288 AAACAAAGGCATAAATCCT--TGGCCTTGGGTTAGGCAATGGGGTTTCTT 1335
                              v   ?i      i --  i                  --      
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG--TTTCTT 590

  chr2_36120160_3   1336 AAATATGACCCCAAAAGCATAAGCAACAAAAGACAAA-----TAAATTGT 1380
                          i       v         i             v   -----       v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_36120160_3   1381 ATTTCATCAAAAGCAAAAGCTTTTGTACTCCAAAGGATACTATTAAGAAA 1430
                          i          vi    i       i  i       i     i      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_36120160_3   1431 GTAAAAAGATAGCCCACAGAATTGGAGATAATATTTGCAGGTCATATATT 1480
                           i      i i          v     v          ii        i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_36120160_3   1481 TCATTTGGGACATAAATGCAGAATGTAAAAAGAACACTTGTAACTCAATA 1530
                          v  vv     v iv  v      i  v       v   ii         
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_36120160_3   1531 ATGAAAGGACAGATAACCCCATTTTTAAAAA--AGCAAAGAATTTGAATA 1578
                           i   i    i       v   ?--     --i      i         
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATA 838

  chr2_36120160_3   1579 GCCAATTTTCTAAATAAGATTTACAAATGGTCTATAAGTACATGAAAAGT 1628
                          v  v  i  i   v     v         i v     i          v
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_36120160_3   1629 TGTTTAAAATCATTAGTCAT 1648
                           i i  v    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (90 / 49)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.65 (45 / 17)  


3005 27.09 1.21 1.21  chr2_36200778_36205225     3049  3956 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_36200778_3   3049 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3098
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_36200778_3   3099 GGCCATACTGCCCAAGGTAATTTATAGAT-CAATGCCACCCCCGTCAAGC 3147
                            v     v     iv i  i  i    -   i  v i   ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_36200778_3   3148 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAACTA--CTTAAAATT 3194
                          v   iivi i  i  ii     -   ---- v  i  i-- i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr2_36200778_3   3195 TCATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATACTAAGCCAA 3244
                         -         viiv  ii  v  v v  v     iv    vi i ivv i
  L1M4_orf2#LINE/    147 -CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_36200778_3   3245 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAA 3294
                                   i      vv   ii  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_36200778_3   3295 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 3344
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_36200778_3   3345 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATGTCTACA 3392
                          i        i    i--    i  --        vv  ii ii i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr2_36200778_3   3393 ACTATCTGATCTTTGACAAACCCAACAAAAACAAGAAATGGGGAAAC--T 3440
                         iii vi    i  i     ivviiv   i v  vvv          v-- 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_36200778_3   3441 ATTCCTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGA 3490
                          v  i  -- i  i              v      v  ?   i   i i 
  L1M4_orf2#LINE/    394 AGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_36200778_3   3491 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAG 3540
                          iiv    ii    i    v   i     v              i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_36200778_3   3541 ATGGATTAAAGACTTACATGTTAGACCTAAAACCATAGAAACCCTAGAAG 3590
                               i ?    i  v    v   v       i   i  vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_36200778_3   3591 AAAACCTTGG--TAATACCATTCAGGACATAGGCATGGGCAAGGACTTCA 3638
                              v v  --   - i -   iv   v v  vv i     v ii   v
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_36200778_3   3639 TGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGG 3688
                          ivv  vi            vvi          vv     v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_36200778_3   3689 GATCTAATTAAACTAAAGAGCTGCTGCACAGCAAAAGAAACTACTATCAG 3738
                           ii v  i   v v  i i  vi  ii vv    i  v    ii vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_36200778_3   3739 AGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCAT 3788
                               v  i     i                 v       vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_36200778_3   3789 CTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAATAAATTTAC 3838
                             i  i  i  vi          v  i  v      vv i  v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_36200778_3   3839 AAGAAAAA-ACGAACAACTCCATCAAAAAGCGGGCAAAGGATATGAATAG 3887
                           v     -  i  i   i v  i?    ii           v       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_36200778_3   3888 ACACTTCTCAAAAGAAGACATTTATGCAGACAAAAGACACATGAAAAATT 3937
                            i     v        i  vi viii v   v ii          iv 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_36200778_3   3938 GCTCGTCATCACTGGCCAT 3956
                             iv     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


3185 25.67 1.33 0.44  chr2_36207634_36209673      650  1549 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_36207634_3    650 TGGAAAAACCTCCCATGTTCACAAATAGGAAGAATTAATAGTGTTAAGAT 699
                               i iv           iii  v      v      v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_36207634_3    700 GATCATACTACTCAAAGCAATCTACAGATTCAATGCAATCACTATCAAAA 749
                          iiv     v i    vii              i      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_36207634_3    750 TACCAG-TGTCGTTCTTCGCAGAAATAGAAAAAA-AATCCTAAAATTCGT 797
                          v    -  i -  i  i        v  v  iv-i            i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_36207634_3    798 ATGCAACCACAAAAGACTCCAAATAGCCGAAGTAATCCTGAGCAGAAAGA 847
                            v  vii   ii   i vi       i  ii    i   iv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_36207634_3    848 ACAAAGCTGGAAGA---ATAC---CAAACTTCAAAATATATTACAAAGCG 891
                               i    i  --- i  --- v  i       iv  i        v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_36207634_3    892 ATAGTAACTAAAAGAGCATGATACTGGCATAAAAGCAGATGCATAGACCA 941
                          i     ii  i v  ii  i           iiii   iii     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_36207634_3    942 ATGCAACCACACAGAAAGCCGCAAAATTAATCCATACATCTATAGCCAAC 991
                            v  iviv iv  i  i vvi    v  i        i   i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_36207634_3    992 TGAAATTTT--ACAAAGGCCTCAAGGACATTCATTAAAGAAAGGATAGTC 1039
                            --    --    i  ivi    iv      v iii     i      
  L1M4_orf2#LINE/    350 TGA--TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_36207634_3   1040 TTGTAAATAAATGGTATTATGAAAACTGGATATCCATATGCAGAAGAATG 1089
                           v v  i       ii iv  v         ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_36207634_3   1090 AAACTAGACCACCACCTCTCACCCTATA-AAAAATAAACTCAAAATGGAT 1138
                           ii i    v i     v    v    -      v              
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_36207634_3   1139 TACAGACCTAAATGTAAGATCCAAAACTATAAAACTACTAAAAGAAAACA 1188
                         i ?                v i              vi  i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_36207634_3   1189 TAGGAAAAACACCTCAAAACATTTGTCTGGAAAAAGATTTTGTGAGTAAG 1238
                             ?iv  vv i  ivi  v  v vi i iv  v i   iv iii  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_36207634_3   1239 ACCTCAAAAGCACAGGCAACAAAAGCAAAAATAAACAAATGTGATTAAAA 1288
                           vi          i          v       i i    vv  i vv v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_36207634_3   1289 CAAACTAAAAAGCTTCTGCACAGAAAAAGAATCAATCAACAGAATGAAAA 1338
                             v v    i   i  ii vvv   i  vv v     v i i      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_36207634_3   1339 GAGAACTTAGAGAAGAGGAGAAAATATCTGCAAACTATTCATTCAA-AAG 1387
                           v   ii v    vi           i      ii  vi  iii -   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_36207634_3   1388 AGAATTAATATCCAGAATATACAAAGAATTCAAACATCTGAATAGAAAAA 1437
                         i  v  i-             i      i  vv   v  v    iv    
  L1M4_orf2#LINE/    748 GGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_36207634_3   1438 AACTAAACAGTCTGATTTAAAAATTAGCAAGTGACCTGAACAGACATTTC 1487
                          ivi   i ii ii   ?      vi    iv  ii    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_36207634_3   1488 TCAAAAGAAGACATACAAATAGACAACAAATATATGAAAAAATGTTCGAC 1537
                           v        i        i v   i  ii i       i   i  i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_36207634_3   1538 ATCGCCATCATC 1549
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (145 / 82)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3150 27.45 0.55 0.44  chr2_36235903_36241705     4408  5314 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_36235903_3   4408 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4457
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_36235903_3   4458 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4507
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_36235903_3   4508 TACCAATGACTTTCTTCACAGACCTGGAAAAAACT-ACTTTAAAGTTCAT 4556
                          v   iivi i  i  ii    vv v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_36235903_3   4557 ATGGAACCAAAAAAGAGCCCGCATTGCCAACTCAATCATAAGCCAAAAGA 4606
                               viiv  ii  v  v v  v     vv     v i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_36235903_3   4607 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 4656
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_36235903_3   4657 ACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGATCA 4706
                                i   i    ii         i  v ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_36235903_3   4707 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTA 4754
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_36235903_3   4755 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGAGGAAAGGATTCCC 4804
                         vi    i  i     ivv  vv  i v  vv     i      i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_36235903_3   4805 TATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCATCTGTAGAAAGCTG 4854
                          v  i  i              v      v  ?   iv  i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_36235903_3   4855 AAACTGGATCCCTTCTTCACACCTTATACAAAAATTAATTCAAGATGGAT 4904
                           ii    i    v i       v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_36235903_3   4905 TAAAGACTTAAACATTTGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4954
                         i ?    i    ii vv  v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_36235903_3   4955 TAGGCATTA-TCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5003
                             ?i v -  -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_36235903_3   5004 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5053
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_36235903_3   5054 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5103
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_36235903_3   5104 AGGCAACGTACAGTATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5153
                           i    vi    v            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_36235903_3   5154 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATGTACAAGAAAA 5203
                         i  i  vi          v  i  v      vv    v vv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_36235903_3   5204 A-ACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5252
                          -     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_36235903_3   5253 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAGAAAATGCCCACC 5302
                           v        i  vi viii     v ii       i  i    i  v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_36235903_3   5303 ACGACTGGCTAT 5314
                          iv ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3301 26.87 0.44 0.44  chr2_36251553_36257831.rev     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_36251553_3   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 4929
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_36251553_3   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_36251553_3   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_36251553_3   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_36251553_3   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_36251553_3   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_36251553_3   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_36251553_3   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_36251553_3   5276 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_36251553_3   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_36251553_3   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_36251553_3   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_36251553_3   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5525
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_36251553_3   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_36251553_3   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_36251553_3   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_36251553_3   5676 AAACAAACAACCGCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i    vv  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_36251553_3   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_36251553_3   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2782 11.57 3.74 25.30  chr2_36612391_36615339.rev     1308  2457 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_36612391_3   1308 GACATCCCGTGTTCATGGATTGAAAGAC--AACATTGTTTAAATGGAAAT 1355
                           i     i             i     --  i      v i    v   
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_36612391_3   1356 ATTCCCCAAATTGATCTACATGTTCAATGCAATCTCTATCAAACTCCTAG 1405
                          i                  vi     i      i        v   i  
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_36612391_3   1406 CTGGCTCTTTTGTAGAAATTGATAAGCTGATCATAAAATTCATATGAAAA 1455
                            v  i     i         i         v             i   
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_36612391_3   1456 TGCAAGGGACCCAGAATTGCCAAAACAATCTT-AAAAGGGAGAACAAAGT 1504
                                          v              -    i i          
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_36612391_3   1505 TAGAGAACTCCTACTTCCTAATTTCAAAACATAATACAATGCTATAGTAA 1554
                          i   i    vi      i           v  v     v    i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_36612391_3   1555 TCAAGACTATGTGGTACTGCCACAGGGATAGATATATAGTTCAATGGAAT 1604
                                vi          v  i i       i      v          
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_36612391_3   1605 -----TGAGAGTTCAGGAATAAACT-ATCACATTTACAGGTATTTTGACA 1648
                         -----       i   i       i-  -       --------------
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTA-------------- 341

  chr2_36612391_3   1649 AGATGGCCAAGACTCAGTGGGGTTCAAAGTCTTTTTTTTTTTTTTTTTTT 1698
                         ---   i   ------------  v -------------------    i
  L1M4_orf2#LINE/    342 ---TGGTCAA------------TTGA-------------------TTTTC 357

  chr2_36612391_3   1699 GATATAGAGTCTCACTCTGTCACCCAGGCTGGAGTGGAGTGGCGTCATCT 1748
                           i -  i  --------------------------------- i  ---
  L1M4_orf2#LINE/    358 GACA-AGGGT---------------------------------GCCA--- 370

  chr2_36612391_3   1749 GAGCTCACTGCAACCTTTACCTCCTGGGTTCAAGTGATTCTCCTGCCTCA 1798
                         -  vi  ---------------------     -----------------
  L1M4_orf2#LINE/    371 -AGACCA---------------------TTCAA----------------- 381

  chr2_36612391_3   1799 GCCTCCCAAGTATCTGGGACTACAGGTGCATGACACCATGCCCAGCTAAT 1848
                         --------------    i-------------------------------
  L1M4_orf2#LINE/    382 --------------TGGGG------------------------------- 386

  chr2_36612391_3   1849 TTTTGTATTTTTAGTAAAGACCATGTTGGCCAGGCTGGTCTTGAACTCCT 1898
                         ---------------     --  i------------     --------
  L1M4_orf2#LINE/    387 ---------------AAAGA--ATA------------GTCTT-------- 399

  chr2_36612391_3   1899 CTGACCTCAAGTGATCCAACCACCTTGGCCTCCCAAAGTGCTAGGATGAC 1948
                         -----i    ------   --------------- vi     i   ii  
  L1M4_orf2#LINE/    400 -----TTCAA------CAA---------------ATGGTGCTGGGACAAC 423

  chr2_36612391_3   1949 AGGTGTGAGCCACCATGCCAGGCCTGAGGTTGAAAGTCTTTTGCATTATC 1998
                         ------------------------------  i ------------  ? 
  L1M4_orf2#LINE/    424 ------------------------------TGGA------------TAKC 431

  chr2_36612391_3   1999 TACATGCAAAAGAATAAAGAAGAAAACCCTATGCCTCACACCATATACAA 2048
                         i              i   vv i v-     --                 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGAC-CCCTA--CCTCACACCATATACAA 478

  chr2_36612391_3   2049 AAATTAACTCAAAATGAATCATAGAGTTATGATCTAAATACAACAGCTAC 2098
                                         i    ?   -------i      ii  v     v
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGA-------CCTAAATGTAAGAGCTAA 521

  chr2_36612391_3   2099 ACCTACAGTGCTCTTAGAAGGAAGCATAAGAGTTAATCTTTGTGGCCTTT 2148
                          v   i ivi          i  i    i ?  v      i   i    v
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_36612391_3   2149 GATTAGGGAGTGGTTTCTTAGATGTGACATTCAAAGCATAAGCAACAAAG 2198
                          i     v i             i     iiv      i          i
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_36612391_3   2199 GAACAAAACAGATAAACTGGACTTCATCAA----------TTTTGGGACT 2238
                            -    i       i             ----------     v -  
  L1M4_orf2#LINE/    622 GAA-AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG-CT 669

  chr2_36612391_3   2239 TAAAAGGACACCATCAAAAAGGTAAAAAGACAACCCTACAGATTGGGAGA 2288
                          v         i     i  i  i            -     v       
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC-ACAGAATGGGAGA 718

  chr2_36612391_3   2289 AAGTATTTGCAA-TCATATATCTGATTTAAAAAAACTGGTACC------- 2330
                           i         -             ---  iii   v   i -------
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGAT---AAGGGACTTGTATCCAGAATA 765

  chr2_36612391_3   2331 ----GAGAACTCCCATAATTAAACGATAAAAA------TAATCTAATC-- 2368
                         ----i       ii i  i v  ii       ------   i i   i--
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_36612391_3   2369 AAAACGGGCAAACC-TTTGAACAGACACTTCTTCAAATAAGACAGA--AA 2415
                             i       vv-      i     i    i    v    i v --  
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_36612391_3   2416 TGGACAATAAACACATGAAAAGATGCTCGA-ATCATTAGTCAC 2457
                            v      i                 i -    ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.42 (92 / 38)
Gap_init rate = 0.04 (36 / 902), avg. gap size = 9.28 (334 / 36)  


3805 23.16 0.33 0.66  chr2_36779078_36783410     2931  3841 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_36779078_3   2931 TGGAAAGATATTCCACGTTCGTAGATTGGAAGAATCAATGTTGTTAAATT 2980
                                    i   i    i i          v i   i       iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_36779078_3   2981 GTCCATACCACCCAAAGCAATCTATAGATTCAATGCAATCCCTATCAAAA 3030
                          v v    iv      vii     i        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_36779078_3   3031 -AACAATGAAATTCTTCACAGAAATAGAAAAAAACAATCCTAAAATGTAT 3079
                         -vv  iivivv  i  ii       v  v  -ivii          vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_36779078_3   3080 ATGAAAGCATAAAAGACCCAGACTAGACAAAGCTATCCTGAGTTAAAAGA 3129
                            i  iiii  ii        v   v    i v   i   ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_36779078_3   3130 ACAAAACTGGAGGAATCATATTACCTGACTTCAAATTATACTACAGAGCC 3179
                              ii       v   i i v  ii i      viv       i   i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_36779078_3   3180 ACAGTAACCAAAACAGCATGGTACTGGCATAAAAATAGACACATAGACCA 3229
                                i   i    ii              ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_36779078_3   3230 ATAGGAAAGAATAAAGAACCTAGAGATAAATCCATACATCTACAGTCAAC 3279
                           i i v     vi   ii i   i     i        i  ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_36779078_3   3280 TCATTTTCAACAAAGGTGCCAAGAACATACACTGGAGAAAGGACAGTCTC 3329
                          v      i    i          v   v  v   i     i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_36779078_3   3330 TCCAATATATGCTGCTGGGAAAACTGGATATCCACATGCAGAAGAATGAA 3379
                          i   i v   v        v         ?         i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_36779078_3   3380 ACTAGACCCTTATCTATTGCCATATACATAAATCATATCAAAATGGATTA 3429
                         ii i     i  i  vvii         v    i vv           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_36779078_3   3430 AAGAATTAAATCTAAGACCTCAAACTATGAAACTACTACAAGAAAACATT 3479
                         ?   vi     v     v  v       i     vi  v          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_36779078_3   3480 GGGAAAACTCTTCAGGACATTGGACTGGGCAAAAGTTTCTTGAGTAATAC 3529
                           ?iv  v     iv   v    ii i     vi       iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_36779078_3   3530 TCCACAAGCACAGACAACCAAAGCAAAAATGGACAAACAGGATCACATCA 3579
                         v   v       ii    v    v      i  i   iv   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_36779078_3   3580 A-GTTAAAAATTTTCTGCACAGCAAAGGAAACAATCAAAAAAATGAAGAG 3628
                          -i       i   -  ii vv       v  v     i   i    i  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_36779078_3   3629 ACAACCCACAGAATGGGAGAAAATATTTGCAAACTACTCATCTGACAAAG 3678
                                                          ii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_36779078_3   3679 GATTAATAACCAGAATATATAAGGAGCTCAAACAACTCAATAGGAAAAAA 3728
                           i vi  v             i  i   vv           iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_36779078_3   3729 AAATCTAGTAACATGATTAAAAGACTGGCAAGAAATCTAAATAGACATTT 3778
                          --- v i    vii   ?   i iv     iii  i i           
  L1M4_orf2#LINE/    799 A---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_36779078_3   3779 CTCAAAAGAAGACATACAAATGGC-AATTAGCTATATAAAAAGGTGTTCA 3827
                            v        i           -   v   - i  i     i  i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGC-ACATGAAAAGATGCTCA 894

  chr2_36779078_3   3828 ACATCACTGAATTT 3841
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (134 / 73)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3015 26.37 2.23 0.78  chr2_36882869_36887071.rev     2817  3711 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_36882869_3   2817 TGGAAAAATATTCCATGCTCATGGAGTGGAAGAATCAATATTGTTAAAAT 2866
                               i    i     i       v       v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_36882869_3   2867 GACCATACTGCCCAAAGCAATGTACAGATTCAACATTATTTTTATCAAAC 2916
                          i v     v      vii  v            iiv  iii       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_36882869_3   2917 TGCCAATGAAATTTTTCACAGAATTAGAAAAAACT-ATTCTAAAATTCAT 2965
                          v   iivivv     ii     v v  v  i-  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_36882869_3   2966 ATGGAATAATAAAAGAGCCTGAAGAGCCAAAAAAACTCTAAGCAAAAAGA 3015
                               vvii  ii  v  v   v        v  iii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_36882869_3   3016 AAAAAGCTGGAGGTATCACATTATCAGACTT-AA----TACTACAAGGCT 3060
                          v    i      vv     i vi vi i  -  ----        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_36882869_3   3061 ACAGCAATCAAAACAACATGGTGTCAGTACAAAAACCGGACATGTAGA-C 3109
                             i      i   iii    iiii i i  ii i-i     i    - 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGATC 298

  chr2_36882869_3   3110 GACGGAAAAGAATAGAAAACTCAGGAATAAAGCCATACACCTGCAACTAT 3159
                         i i    v     v  i iii   i      v       ii iiiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_36882869_3   3160 CTGATTGTCCACAAAGTTGACACAAATAAGCAATAGGGAAAGGATTCCCT 3209
                         i     v  v    i v  v  vi vi vv    i       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_36882869_3   3210 ATTCAATAAATAGTGCTGGGGATAACTGGCTATCCATATGCAAAAGAATG 3259
                         v     i    i        - i      v  ?   i             
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGG-ACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_36882869_3   3260 AAACTGGATCCCTCCCTATCAACATATACAAAAATTAACTCAAGATGGAT 3309
                           ii    i    v   vv  v                     i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_36882869_3   3310 TAAAGACTTACATGTAAGACTTCAAACTATAAAAATCCTAGAAGAAAACC 3359
                         i ?    i  v        vi v           v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_36882869_3   3360 TAGG---AAATACCCTTCTCGACATTGGTCTTGGCAAAGAATTTATGTCT 3406
                             ---    ---    vi   v    vi v     v iv  iv ivv 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_36882869_3   3407 AAGTCCTCAAAAGCAATTGCAACAAAAACAAAAATTGATGAGCAGGATCT 3456
                          v v vi        vvv         iv      v   i iiv   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_36882869_3   3457 AATTAAA-CTAAAGAGCTCTGCACAGCAAAAGAACCTATCAGTGGAGTAA 3505
                         v  i   -i    i vi i  ii vv    i  vv      ivii   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_36882869_3   3506 ATAGAAAACCTATAGAAAGAGAGAAAATATTTGCAAACTATGCATCCAAC 3555
                          v   v    i i    v i                 ii  ii   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_36882869_3   3556 AAAGGTCTAATATCCAGAATCTATAAGGGACTT----AATCAAACAATCA 3601
                           i  v  vi          v     i i   i----  iiv  i   v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_36882869_3   3602 AAAAACAA-----CCACGTTAAAAAGTGGGCAAAGGACACAAACAGACAT 3646
                            i    -----   -i  ?    i           ivii  i      
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_36882869_3   3647 TTCTCAAAAGAAAACATACAAGCAGCCAACAAACATATGAAAAAATACTC 3696
                              v      i i      iii     i  i  i       i  i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_36882869_3   3697 ATCATCACTAATCAT 3711
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (145 / 88)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.08 (27 / 13)  


2659 23.72 4.10 2.05  chr2_37000932_37006311.rev     3713  4492 (888)    L1M4_orf2#LINE/L1        1   796 (112)  

  chr2_37000932_3   3713 TGGAAAAACATTCCATGCTCATGGATAGAAAGAATC--TATTGTTAAAAT 3760
                               i i  i     i        v i    v i--         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_37000932_3   3761 GGCCGTACTGCCCAAAGCAATTTACAAATTCAATGCTATTCCTATCAAAC 3810
                            vi    v      vii  i    i      i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_37000932_3   3811 TACCAA-TGACATTCTAACAGAATTAGAAAAAATG--TTTAAAATTCATA 3857
                          v   i-  v v  i vi     v v  v  iv  --ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_37000932_3   3858 TGGAAA---------CCC-GAAGAGCCAAGGCAATCCTAAGCAAAAAGAA 3897
                               ---------   -   v      ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_37000932_3   3898 CAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAGGGCTG 3947
                              i      vv     i v  ii i      viv       ii   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_37000932_3   3948 TAGTAACCAAAACATCATGGTACTGGTACAAAAACAGAAGCATAGACCAA 3997
                         i     i   i   vii         i i  ii i   vii     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_37000932_3   3998 TGAAACAGAATAGAGAGCCCAGAAATAAAGCTGCACACTTATAACCGTCT 4047
                           i  i     v     i           v iii   i    iii ivi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_37000932_3   4048 AATCTTCGACAAAGTTGACAAAAGCA----ATGGGGAAAGGACTCCCTAT 4093
                         i  i        i v  v   i v  ----          i ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_37000932_3   4094 TCAATAAATGATGCTGGGATAAATGGCTAGCCATATGCAGAAGATTGAAA 4143
                             i     i        i  v   v  ?   i     i    v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_37000932_3   4144 CTGGACCCCTTCCTTATACCATATATAAAAATCAATTCAGA-CGGATTAA 4192
                         i         v   i i        i      i  i   i -i    i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_37000932_3   4193 AGACTTAAATGCAAAACCTAAAACTAAAAAAAGTT--GAAGAAAACCTAG 4240
                             i      i  i v         v    vvi --         v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_37000932_3   4241 GGA-ATACCATTCTAGACATATGCCCT-GGCAAAGATTTCAT-GATGAAG 4287
                          ?i- v i -   vv   v -  vvi -     v i    v -   - v 
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr2_37000932_3   4288 ACACCAAAAGCAATTGCAA-CAATGACCAAAAAAAAAAAT-GACAAATGG 4335
                                     ----   -   ----     i       -  i    v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCA----CAAGCAA----CAAAAGAAAAAATAGATAAATTG 639

  chr2_37000932_3   4336 GACCTAATTTAACTGAAGAGCTTCTGCACACATT---AGAACG--ATCAA 4380
                            i v  iv  v v  i i   i  ii ---  ---  i  i--     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGC---TTCAAAGGACACTATCAA 686

  chr2_37000932_3   4381 CAGCGTAAATAGACAACCCACAGAATGAGAGAAAATATTTGCAAACTATG 4430
                         v iv  i  v                 i                 ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_37000932_3   4431 AATCTGACAAAGGACCAATATCCAGAATCTGTAAGGAACCTAAACAAATT 4480
                         v      i  i    ivi          v i   i    iivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_37000932_3   4481 AACAAGCTAAAA 4492
                           i  --     
  L1M4_orf2#LINE/    787 AATAA--TAAAA 796

Transitions / transversions = 1.80 (117 / 65)
Gap_init rate = 0.03 (22 / 796), avg. gap size = 2.18 (48 / 22)  

 431 18.05 4.51 3.01  chr2_37000932_37006311.rev     4756  4888 (492)    L1M4_orf2#LINE/L1      774   908 (0)  

  chr2_37000932_3   4756 ACTC---CATCTCAAAAAAAAAAAAGAATAAAAACAACCCCATTAAAAAG 4802
                             ---  v     v  v     i---- v   i     v   ?    i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAG----ACAAATAACCCAATTWAAAAA 819

  chr2_37000932_3   4803 TGGGCAAAGGACGTGAACAGATAGTTTCCAAAAGAAGACATACATGCGGC 4852
                                    iv    i   i v  ii v        i     vii   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_37000932_3   4853 CAACAG--ACATGAAAA-ATGCTCATCATCACTTATTAC 4888
                            i i--         -       v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.03 (4 / 135), avg. gap size = 2.50 (10 / 4)  

 412 17.56 2.29 3.05  chr2_37000932_37006311.rev     4894  5024 (356)    L1M4_orf2#LINE/L1      779   908 (0)  

  chr2_37000932_3   4894 TGCAAATCAAAAATTAACAAGCAAAAAACAACCCCATTAAAAAGTGGGCA 4943
                          i   v    v   -  v   -- v   i     v   ?    i      
  L1M4_orf2#LINE/    779 TACAACTCAATAAT-AAAAAG--ACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_37000932_3   4944 AAGAACATGAACAGATAGTT-TCCAGAAGAAGACATACATGTGGCCAACA 4992
                            i iv    i   i v  -    -       i     vi       i 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCA-AAGAAGATATACAAATGGCCAATA 874

  chr2_37000932_3   4993 G--ACAGGAAAAAATGCTCAACAACACTTATTAT 5024
                         i--   v     i          v  ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (12 / 10)
Gap_init rate = 0.04 (5 / 130), avg. gap size = 1.40 (7 / 5)  


1365 20.92 14.40 1.09  chr2_37211903_37214100      561   928 (1270)    L1M4_orf2#LINE/L1        1   417 (491)  

  chr2_37211903_3    561 TGGAGAGATATATCATGTCCATAGGGTGGAAGACTTAATATTATTAGGAT 610
                             i      vi     i   i iv                i   i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_37211903_3    611 GGCAATTCTCTCCAAATT------------CAATGCAACCTGAATCAAAA 648
                               v   i       ------------   i    i ivv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_37211903_3    649 TCCCAACATGGTATTTTTGCAGACATTGACAA------------------ 680
                              i -  viv          v        ------------------
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_37211903_3    681 ---------------ACCTAGACTGGGCAAAACAATTTTGAAAAAGAA-- 713
                         ---------------   i   v i v         i           --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_37211903_3    714 -CAAAGTTGGAGGGCTAACAGCACCTGATTTCAACACTTATTACAAAGGA 762
                         -            i  v   viv  ii       v     i       vv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_37211903_3    763 ACTGTAATGAAGAAAA-GTGTTGTTGGCATCAAGATAGACAAATGGATCA 811
                           v     v    v i-   v ii      v i        v  i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_37211903_3    812 ATGAAACAGCACAGAGAGTCCAAAATTATACCTACACATATACACACAAC 861
                            i  i  v iv         i  v  v   i i    v  iivv   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_37211903_3    862 TGATTTTCAACAAAGGGTGTAAACGGA--GTTTAGTGAAGAAAAGATAGG 909
                                 i    -     iv  --  --i  i i  ii    ii    v
  L1M4_orf2#LINE/    350 TGATTTTCGACAA-GGGTGCCAA--GACCATTCAATGGGGAAAGAATAGT 396

  chr2_37211903_3    910 CTTTTCGA--AATGGTACTGG 928
                               i --      i    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGG 417

Transitions / transversions = 1.48 (46 / 31)
Gap_init rate = 0.02 (9 / 417), avg. gap size = 6.33 (57 / 9)  

1542 22.34 7.10 1.46  chr2_37211903_37214100     1228  1706 (492)    L1M4_orf2#LINE/L1      403   908 (0)  

  chr2_37211903_3   1228 AAGAAATGGTACTGGAAGAAGTGGATATCCATATTGAAAAAAAAAACAAA 1277
                           v       i    i v  v      ?   i  ---iv    i  ii  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACAT---GCAAAAGAATGAA 449

  chr2_37211903_3   1278 AAATTTTGATTCAAACCTTGCAACATATACAAAAATTAACTCAAAATGGA 1327
                         i---  v  ii vv    ii  v                           
  L1M4_orf2#LINE/    450 G---TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_37211903_3   1328 TCACATATCTAA--GTA-----TAAAACTATAAAACTTCTAGAAGGAAAC 1370
                            ? v i    --   -----               ii      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_37211903_3   1371 ACAGGA-CAAA---------CCCTGGTTTACGAAATGTTTCCTTAGATAC 1410
                          i   ?-i   ---------  i   v   v v    v  i        i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_37211903_3   1411 AACACCAAAAGCACAATCCATATAAGAAAAATT-GATACACTGGAT---- 1455
                         i               v v i v        v -    v i    i----
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_37211903_3   1456 --GAAATTCAAAATCTCTTTTCCTTACAAGGCACTGTTTAGAGAATAAAG 1503
                         --i     v    ii i v v i i v i i    i iv   i i i  i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_37211903_3   1504 AGACAGGCCACCCATTGGGA-AAAATATTTGTAAATCACATATCTGATAA 1552
                              iv    vv v     -          i      i           
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_37211903_3   1553 AGGAATATGTA--AAAAACCTATAAAACACTCTCAAAAGTCAATAATTAT 1600
                         i   v -    --v i  iv      iv     i v  v        v v
  L1M4_orf2#LINE/    747 GGGACT-TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_37211903_3   1601 AAAACAA----CCCAATAAAACAATGGACAAAAGATT-GAGCACATCCTT 1645
                           i    ----      v?  v     i    i    -  ii v ivi  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_37211903_3   1646 CTTCGAAGAAGATATG--GATGGCAAATAAGCACCTGAAAATATGCTTAT 1693
                           i i          i--i     v         v      v     i v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_37211903_3   1694 CATTAGTCATCAC 1706
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (60 / 43)
Gap_init rate = 0.03 (14 / 506), avg. gap size = 2.93 (41 / 14)  


2864 27.85 2.59 0.23  chr2_37345087_37349329     2866  3752 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_37345087_3   2866 TGGAAACGCATCCCATGTTCATGGATGGGTAGAATCGATATTGTGAAAAT 2915
                               vii                 v  v   v ii       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_37345087_3   2916 GACCATACTGCCAAAAGCAATCTATAAATTTAATGTAATTCCCATCAAAA 2965
                          i v     v  v   vii     i i   i  i i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_37345087_3   2966 TGCCATCATCATTCTTCACAGAACTAGGAAAAAAAATCCTGAAATTCATA 3015
                          v   v vv v  i  ii     v v iv  ivvi     i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_37345087_3   3016 TGGAACAAAATAAGAG--CCTGCATAGCCAAG-CAAGACTAAACAAAAAG 3062
                              -- vii   i --  v v        i-   vvi i  v  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_37345087_3   3063 AACAAATCTAGAGGCATCTCATTACCTGACTTCAAACTATACTACTAGGC 3112
                               vi i    vv  v  i v  ii i      viv      v i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_37345087_3   3113 TATTGTTACCAAAATAGCATGGTACTTGTACAAAAACAGGCACGTAGACC 3162
                           iv  v i   i i  ii       v i i  ii i  i  ii    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_37345087_3   3163 AATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAACCAT 3212
                                i     v    ii           v   v i i   iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_37345087_3   3213 CTGATCTTTGACAAAGTAAACAAAAACA--AAGTGGGGAAAGGACACCCT 3260
                         i    i  i     i vviv   i v  --v i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_37345087_3   3261 ATTGAACCATTGGTGCTGGGATAACTGGCAAGCCACATGTAGGAGAATTA 3310
                         v  v   v v           i      vv ?       i ii     v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_37345087_3   3311 AACTGGATCCTCATTTCTCACCTTATGCAGAAA---ACTCAAGATGGATC 3357
                          ii    i  ii ii  v    v   i  i   ---      i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_37345087_3   3358 GAAGACTTAAAGATAAGACCTGAAACTGTAAAAATTCTAGAATATAACAT 3407
                         i?    i    vi     v  i     i     v ii     v v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_37345087_3   3408 TGGAAAAACTCTTCTAGACATTGGCTTAAGTA--GAGTTCATGACCAAGA 3455
                         v  ?iv  v     vv   v    v   i i -- iv   v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_37345087_3   3456 ACCTAAATGCAAATGCAACAAAA--ACAAATAGATG----GGACTTAATT 3499
                         vv i   v   v v         -- v        i----      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_37345087_3   3500 AAGCTAAAAAGCGTCTGCATAGCAAAATAAATAATCAGCAGAGTAAATAG 3549
                           iv v    i v i  iiivv    iv v iv    iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_37345087_3   3550 ACAACCCATAGAGTGGGAGAAAATCTTCGTAAACTATGCATCTGAGAAAG 3599
                                 i   i           v  i i   ii  ii      v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_37345087_3   3600 GACTAATGTCCAGAATCTATAAGGAACTCAAAAAAGTCAGCAAGAAAAAA 3649
                             vi i        v     i      vv v  v   ii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_37345087_3   3650 ACAA----TCCCATCAAAAAGTGTGTTAAGGATATGAACAGACAATTCTC 3695
                             ----i  v  i?    i  v iv      v    i     v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_37345087_3   3696 ---AAAAGATATACAAATGGTCAAGAAACATATGAAGAAATGCTCAACAT 3742
                         --- i               i   v  i  i     i i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_37345087_3   3743 CCCTGATTAT 3752
                          v????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.34 (139 / 104)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.50 (25 / 10)  


4416 17.63 1.31 2.50  chr2_37537418_37539918.rev     1091  2009 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_37537418_3   1091 TAGAAAGATATCCCACATTCATGGATTGGAAGATTTAATATTGTAAAGAT 1140
                          i             ii                i          v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_37537418_3   1141 GGACACAGTCCATAAATTGATGTACAGACTCAACATACCCCCAATCAATA 1190
                           vv i v   vi        v      i     ii vi   v     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_37537418_3   1191 TCTCACCAGGCCTTTTTACAGAAATTGACAAGCTAATCCTAAACTTTATA 1240
                           i  v v v i     i                i        v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_37537418_3   1241 TGGAAATCTAAGGGATCCAAAACAGCCAAAGAAATCTTGAAAAAACAAAA 1290
                                vi      i   i  i       iv            iv i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_37537418_3   1291 --AACTTAGATAACTTATACTTCCTAATTTGAAATTTTATTAGAAAGCTA 1338
                         --  v  i  vi   i i      i     v   vi   i  v       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_37537418_3   1339 TAATAACGAAGAGAGTGTAGT-CTAGCATAGGGA--GACATATAGG-CAA 1384
                         i i   iv    v     i  -  i     i   --         i-   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_37537418_3   1385 TGGATCAGAATTAAAAGTCCGAAAACAAATCCTTACATC-ATGGTCAGTT 1433
                             vi      i i     ii   i   i  v     i-       i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_37537418_3   1434 TATTTTCAACAAGGGTTCCCAAACAATTCAACAGAGAAAAAACAGTCTTT 1483
                         v      i        v  v i  v      ii i    i  i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_37537418_3   1484 TCAACAAATGGTACTGGACCAACTG-ATATCCTCATGTAAAAGAATGAAT 1532
                                     i    iv      -   ?  v    i           v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_37537418_3   1533 CTGGACCCTCTAACTTCATACCACATATACAAATTAATTCCAAATGGATT 1582
                         i       -   - i   i    i   i v       i  v        i
  L1M4_orf2#LINE/    451 TTGGACCC-CTA-CCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_37537418_3   1583 AAAGACCACTTAATCCAGTTATGTTTTAGTAAGAGCTAAAAACCATAAAA 1632
                          ?     ---   -------    ------           - i      
  L1M4_orf2#LINE/    499 AWAGACC---TAA-------ATGT------AAGAGCTAAAA-CTATAAAA 531

  chr2_37537418_3   1633 CTCTAAGAAGAAAATATGGAAATAA-CCCTCATGACCTTGGGTT-GGCAA 1680
                             v         i  i i?i   -i i  i            -     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_37537418_3   1681 TAGATTCTTAGATATGACACTAAAATTCACAAGCAACAAAAGAAAAAATA 1730
                          i v                i    v-                       
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAG-CACAAGCAACAAAAGAAAAAATA 630

  chr2_37537418_3   1731 GATAAATTGAACTTCATCAAAATTAAGAACTTTTCTGCTTCAAAAAATAC 1780
                                  i                i       v         ii i  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_37537418_3   1781 CATCAAGAAGGTGAAAAGACAACTCATGAAATGGGGGAAAATGCTTGCAA 1830
                         i        i             i  iii      i      ii      
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_37537418_3   1831 GTCATGTATCAGTTATAGGTCTTGTACTCAGAATATGTAAGGATCTCTTG 1880
                         i    i    v v  vi  v      ii        i   i  v     i
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_37537418_3   1881 TTAACTCAATAATAAGAAGCCACATAATGCAATGAAAAAGTAGGCCAAAA 1930
                         i-             i   v  v    iv    v?    i i   v  ii
  L1M4_orf2#LINE/    781 C-AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_37537418_3   1931 AGCTGAATGGACATTTTTTCAAAGAAGTTATATATAAATGGTCAATAAGT 1980
                          vi     i       i i        --     i      i       i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAG--ATATACAAATGGCCAATAAGC 877

  chr2_37537418_3   1981 ATATGAA--GATGCTCAACATCATTAATCAT 2009
                          i     --              ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.22 (109 / 49)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.94 (35 / 18)  


1805 27.49 2.24 0.00  chr2_37568115_37572702.rev     2864  3354 (1234)    L1M4_orf2#LINE/L1        1   502 (406)  

  chr2_37568115_3   2864 TGGAAATACATTCCATGATCTTGCCTGGGCAGAATCAATATTGTGAAAAT 2913
                               v i  i     v  v  vv v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_37568115_3   2914 GACAATACTGCCAAAAGCAACCTACAAATTCAATGCAATTCCCATCAAAG 2963
                          i       v  v   vii i     i      i     i  i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_37568115_3   2964 TACCACCATCATTCTTCACAGAATTAGAAAAACCAATGCTAAAGTTCATG 3013
                          v   v vv v  i  ii     v v  v  i ii  v     i     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_37568115_3   3014 TGGAACTAAAGAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 3063
                              v iv iii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_37568115_3   3064 CAAATCTGGAGGCATCACAGTATCTGATTTCATCCTATAC-ATAAGGCCA 3112
                             vi      vv     v vi ii      vvviv   - i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_37568115_3   3113 CAGTCACCAAAACAGCATGATACTTGTATAAAACTAGGCACATAGACCAA 3162
                             v i   i    ii  i    v i    iiv   i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_37568115_3   3163 TAGAACAGAATAGAGTACCCAGAAATAAACC--TAAAT--------AACT 3202
                          i   i     v   vii             --  v  --------  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_37568115_3   3203 GATCTTTGACAAAGCAAACAAAAACATCAAGTGGGGAAAGGACACCCTTT 3252
                            i  i     i vviv   i v   iv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_37568115_3   3253 TCAACAAATGGTGCTGGGATAATTGGGTAGTCACATGTAGGAGAATGAAA 3302
                                            i  i   i  ?i      i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_37568115_3   3303 CTGGATCCTCATCTCTCACCTTATATAAAAATCAACTCAAGATGGATCAA 3352
                         i    i  ii i   v    v    i      i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_37568115_3   3353 GG 3354
                         i 
  L1M4_orf2#LINE/    501 AG 502

Transitions / transversions = 1.56 (81 / 52)
Gap_init rate = 0.01 (3 / 502), avg. gap size = 3.67 (11 / 3)  

1245 26.51 1.93 0.72  chr2_37568115_37572702.rev     3682  4096 (492)    L1M4_orf2#LINE/L1      489   908 (0)  

  chr2_37568115_3   3682 AAGATGGATCAAGGACTT-----TAAGACCTGAAACTATAAAATTTCTGG 3726
                           i        ?i   i -----     v  i           i ii i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_37568115_3   3727 AAGATAATAACATTGGAAAAACCCCTCTGGACATTGGATTACACAAGGAT 3776
                             -  --    v  ?iv  vi i  vv   v    i   vi   v i 
  L1M4_orf2#LINE/    539 AAGA-AA--ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_37568115_3   3777 TTCATGACCAAGAACCCAAAAGCAAATGCCATAAAAACAAAGATAAATAG 3826
                            v iivi v  vv         v v  v i    iv   i   i   i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_37568115_3   3827 CTAGGACTTAATTAAACTAAAGAGCTTTTGCATGGCAAAAGGAAGAGTCA 3876
                         v v      v  i   v v  i i      iiivv    i iv vvi   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_37568115_3   3877 GCAGAGTAAACAGACGAC--ACA-ATTGGGAGATAATCTTGACAATCTAT 3923
                         iv i   i  v    i  --   - v       v   v  vi   vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_37568115_3   3924 ACATCTGACAAAGGACTAATATCCAGACTCTACAACAAACTCAAACAAAT 3973
                          i      i  i     vi        v v  i  vi     vv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_37568115_3   3974 CAGCAAGATAAAAACAAACAATCCCATCAAAAAGTGGGCTAAAGACATGA 4023
                           ii  v v   i     i  i  v  i?    i     v  i  iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_37568115_3   4024 ACAGACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAA 4073
                          i     v     v                       i  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_37568115_3   4074 AAATGCTCAACATCACTAATGAT 4096
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (58 / 49)
Gap_init rate = 0.01 (5 / 420), avg. gap size = 2.20 (11 / 5)  


2294 25.88 8.71 1.88  chr2_37600918_37603449.rev     1192  2041 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_37600918_3   1192 TGAAGAGATATACTATGTTCATGAATCAAAAGATTCAACATTATAAATCG 1241
                           i i      v i         i  iii    i i  i   i v  -- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA--G 48

  chr2_37600918_3   1242 ATA--AAT-TTCCCTGAAGTGATCTATAGATACAATGGAATTCTAATAAA 1288
                           i--   -i    ii  v       i    v   i v   i iv  v  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_37600918_3   1289 AATCCCAGGAAGCTTTTTAAAAGAAATTGACAGGGTGTTTTTGAAATTTA 1338
                                 vviv      viv           i v  v ii i     i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_37600918_3   1339 TGGTGATATAATGCAAAGAACCAAGATTGGTAAAAGCAATTTTAGAAAGG 1388
                          ivv  ---       i i   v   v i iv   i    i  ii   i 
  L1M4_orf2#LINE/    149 TATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_37600918_3   1389 AA--------TTTGAG-----------------------ACTTTCTATAA 1407
                           --------  v   -----------------------    v   i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_37600918_3   1408 AGCTACAGAAATGGAGACAGTGTGATATTTACATAAGGATAGACATATAA 1457
                                 v   vi          i  i vi                  i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_37600918_3   1458 ATAAATGGAACACAATAGGCAGTCAAAAAATATAACTACCCA---ATGGT 1504
                           v       i v   v iv    v i     v v i iv  ---     
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_37600918_3   1505 AAATTGACTTTTAACAAGGATGTAGAGATAATTCAATAAGTAAAGGATAG 1554
                         v      i   ii      i  ivi   iv       ii v    i    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_37600918_3   1555 TGTTTTCAACACA--GTTCTTGAAAAACCAGAT-CCCATATTTTTAACAA 1601
                          v         v --  v  v i v   ii   -?   i  viv-  vi 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGA 444

  chr2_37600918_3   1602 ATAAACCTTGACCCTTACCTCGCACTATAAACAAAAATT----------- 1640
                           i  vi v     i      i   i   v         -----------
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_37600918_3   1641 GATCATAGA---AATTG---AAGCTAAAACTGTAAGACTTCTAGAAAAAT 1684
                              ?   ---  v  ---i          i   i   ii     i  v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_37600918_3   1685 ATGCAGAAGAAAATCTTTGTGACTATGGGGTAGGAAAGATTTTTTTAGAC 1734
                          iii  i? v       i     iv    v    v  viv   i     i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_37600918_3   1735 ATAACAGATAAAAAGAACAAACCATAAAATGAAAAAGTA--TAAATGAAA 1782
                           i   --iv     v    i v i    -      i  --     vii 
  L1M4_orf2#LINE/    595 ATGACA--CCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGA 641

  chr2_37600918_3   1783 CATTATCAAAATTAATGACTTCTA-G--TCCAAAGATATCAT-AAAAGAA 1828
                          v i           vi    i i- --  v  i  i ii  -  i i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_37600918_3   1829 TAAACAGGCAATCCACAGACTGGGAAAAAAAATATTCACCATATACATAC 1878
                          i  v  i   i       v     i    --    ii v vvi i   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAA--TATTTGCAAATCATATAT 739

  chr2_37600918_3   1879 CTACTGCAGGTCTTGTATTGAGACTATTTAAAGAACT---ATAATCCAAC 1925
                           iv ivi  v       iv   v   v         --- i  ii   i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_37600918_3   1926 AG------GAAAAATATGTT--TTAAAATGCTTAATGGGCAGAAGATTTG 1967
                          i------  v     vvii--  ?   -----        i i      
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAA-----AATGGGCAAAGGATTTG 834

  chr2_37600918_3   1968 AACAGATAGTTTACAAAAGGAGAAATATAAATGTCTAATAAATGAATGAA 2017
                           i   i v  iv v    i   v   i     v i     iiiv     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_37600918_3   2018 AATATGCTCAACATCCTGATCATC 2041
                           v            v????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (132 / 84)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.75 (90 / 24)  


1985 26.22 0.18 0.18  chr2_37630714_37635301.rev     1446  1998 (2589)    L1M4_orf2#LINE/L1      356   908 (0)  

  chr2_37630714_3   1446 TTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAAT 1495
                          i     ivv  vv  i v  vv            i  vvi  v  i  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_37630714_3   1496 AAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGA 1545
                                       v      v  ?   i   i i  iiv    ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_37630714_3   1546 TCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATT 1595
                         i    v   i     v           i  i    i      i ?   ii
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_37630714_3   1596 TAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-A 1644
                             i  v   v       i      vi i           v    ?i- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_37630714_3   1645 TACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAACACCAA 1694
                         v i -   iv   v v  vv i     v ii   v ivvi vi       
  L1M4_orf2#LINE/    556 AATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_37630714_3   1695 AAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTA 1744
                              vvi          vv     v  i    v   ii v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_37630714_3   1745 AAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACC 1794
                           i i   i  ii vv    i  v    i  vv i      v  i     
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_37630714_3   1795 TACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAA 1844
                         i   iv            v  i    vii ivi      i  i  i  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_37630714_3   1845 TATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAAC 1894
                                   v  i  v      vv    v iv i  v     i     i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_37630714_3   1895 AACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAAAAGA 1944
                              v  i?    i     i      v    i     i     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_37630714_3   1945 AGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGG 1994
                            i  vi viii     v  i          i       v     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_37630714_3   1995 CCAT 1998
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.20 (77 / 64)
Gap_init rate = 0.00 (2 / 553), avg. gap size = 1.00 (2 / 2)  

2506 26.26 4.16 4.81  chr2_37630714_37635301.rev     3182  4095 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_37630714_3   3182 TGGAAAAGGATTTCATGCTCATAGATTGGAAGAATTAATATCATTAAAAT 3231
                               iiv  ii    i    i          v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_37630714_3   3232 GGCCATACTGCCCAAAGCAATCTACAGATTCAGTGCTATTCATATCAAAT 3281
                            v     v      vii             ii  v  i v       -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr2_37630714_3   3282 TATGATATTCAATGCTATTCACATCAAGTGCTATTCATATCAAAATGTCA 3331
                         ----------------  i ----  iv   i------------------
  L1M4_orf2#LINE/    100 ----------------ATCC----CAGCTGCC------------------ 111

  chr2_37630714_3   3332 TTTTTCACCAAATTAGAAAAA--AATTCTAAAATTCAT-TAGAACCAAAA 3378
                              ii vi  v v  v  i--i  i           - i   viiv  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_37630714_3   3379 AAGAGTATGAACAGCCAAGCCAATCCTAAGCAAAAAGAACAAAGCCAAAG 3428
                         ii  vivv   i      iv     i i iv  i          iiii  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_37630714_3   3429 GTATCACATTACCTGACTTCAAACTATACTACAAGGCTACAGCAACCAAA 3478
                          vv     i v  ii i      viv        i       i  i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_37630714_3   3479 ACAGCATGGTACTAGTACAAAAATAGACATGTAGACCACTGGAAGAGAAT 3528
                             ii       i i i  ii        i    i  v     v     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_37630714_3   3529 AGAGAACTTAGAGATACAGCTGCACACCTCCAACCAACTGATCTTTGACA 3578
                         v    iiii   i   v v iii   ii viiii   i    i  i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_37630714_3   3579 AAGTCAACAAAATAAG-CAACAGAGAAAGGACTCCCTATTCAATAAATGG 3627
                          i viiv   i iv v-   ii i     i ivvi  v     i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_37630714_3   3628 TGCTGGGAAAACTGGCTAACCA-------------GAAACTGGACCCCTA 3664
                                 v      v  ?   -------------   ii          
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_37630714_3   3665 CCTATCATCATATATACAAAAATTGACTCAAGATGGATTAAATAC--AAA 3712
                            vv  i      --        i      i      i ? v  --   
  L1M4_orf2#LINE/    462 CCTCACACCATATA--CAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_37630714_3   3713 TGTATAACCTCAAACTATAAAAATCCTAGAAGAAAAGCTAGG---AAATA 3759
                             vi v  v           v  i          vv    ---    -
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT- 558

  chr2_37630714_3   3760 CCCTTCTGGACATCAGCCTAGGCAAAGAATTTATGACTAAGCCCTCAAAA 3809
                         --    vv   v ii vi       v iv  iv iiv  v v vi     
  L1M4_orf2#LINE/    559 --CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_37630714_3   3810 GCAATTGCAACAAAAATAAAAATTGACAAGTGGAACCTAATTAAACTAAA 3859
                            vvv         iv      v  i  i v i  i v  i   v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_37630714_3   3860 GAGCTTCTACACAACAAAAGAAACTATCAACA----GAATAAACAACCTA 3905
                         i i   i iii vv    i  v        v ----   v i      i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_37630714_3   3906 CAAAATGGGGGGAAATATTCACAAACTATGCATCTGACAAAGGGCTAATA 3955
                           i      i i       ii    ii  ii      i  i  i  vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_37630714_3   3956 CCCAGAACCTATAAGGACCTTAAACAAATCAA-----------CTAATAA 3994
                         i      iv     i  v  ivv    v    ----------- v     
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_37630714_3   3995 CCCCATTAAAAAGTGGGCAAAG-ACATGAACAAATATTTTTCGAAAGAAC 4043
                            v   ?    i         - iv    i i i    i  v      v
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_37630714_3   4044 ACATAAATGTGGCTATCAAGCATATGACAAATAGTTCAACATCACTGATC 4093
                          i   v vi    i vi     i    v  ivv i         ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_37630714_3   4094 AT 4095
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 5.86 (82 / 14)  


 286 25.22 14.78 2.61  chr2_37656593_37658651.rev      499   613 (1445)    L1M4_orf2#LINE/L1      148   276 (632)  

  chr2_37656593_3    499 ATATGAAAACACAAAAGACCCA----------AGCATTCTGTTAAAAGAA 538
                              i   ii   ii      ---------- i  v   vvv       
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_37656593_3    539 GAACAAGGTTGGG------ACACTTACCTGATTTCAAAAAATATTTTATA 582
                               i     i------      -  ii         vv  i -- i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACT--ACA 244

  chr2_37656593_3    583 AAACTCTGATAATAAAAGCAATATGG-GCTGG 613
                           i  viii    v  ii  i i   -i    
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

Transitions / transversions = 2.62 (21 / 8)
Gap_init rate = 0.04 (5 / 129), avg. gap size = 4.00 (20 / 5)  

1696 24.61 5.76 2.96  chr2_37656593_37658651.rev      930  1571 (487)    L1M4_orf2#LINE/L1      249   908 (0)  

  chr2_37656593_3    930 TAAAATAA--AAGTCAGTATGATACTGGTGAAAAGACAGACATATAAATT 977
                           v i   --   v    i  i      iiv  i  i         i  i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_37656593_3    978 TATAGAAAAGAATAGAGAATACAGAAATAAACCACATACAT--ATGGTCG 1025
                         v  i   v     v    i v            -       --      i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACC-CATACATTTATGGTCA 347

  chr2_37656593_3   1026 ATTTGTTGTTTTTTGTTTTTTTTACAAAAATACTAAGGTAATTCGATGGG 1075
                            ---- v    i --------    iii i i   iiv    i     
  L1M4_orf2#LINE/    348 ATT----GATTTTCG--------ACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_37656593_3   1076 GAAAGGAT-----TTTCAACAAATGATGTTGG-ACACATTG----TTCAG 1115
                              i  -----            i  i   -   - i  ----?i  v
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA-ACTGGATAKCCAC 434

  chr2_37656593_3   1116 A--AAAAAAAATTAATATGGTCCTTTACCTCACACCATCCACAAAAATTA 1163
                          --v    i   v  vv   v  ii             vi          
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_37656593_3   1164 ACTCAAAGTA-ATCATAGTCCTAACTTTGAAACATAAAACTCTAAAATTT 1212
                                i i-    ?  v     v v i i vv       v     i i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_37656593_3   1213 TTTACAAAAAGCGCAGGAG--AAT-TACAT---CTTGGGGTAGGCAAACA 1256
                           viv i   i ii   ? --   - v i ---      v       vvi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_37656593_3   1257 TTTCTTGGCTAGAACACAAAAAGCATGAGCCATAAAAGAAAAAA--AATA 1304
                               i v  vi    v       ii   v i           --i   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_37656593_3   1305 A-CTGATCTTCGACCAAATTTTAAGTGTTTTACTATCTGAAAGACACCAC 1353
                          -i  iv    - i    v  v  ivv    iivv iii  i     i i
  L1M4_orf2#LINE/    635 AATTGGACTTC-ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_37656593_3   1354 TAAGAAAACAAAACTGCAAGCCACAGACCTGG-GAAAATATTTACTAAAC 1402
                         i      iii   vvi   v       viv  -          i v  v 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_37656593_3   1403 ATATATCAGACAAGTT-CTTGCA--CAGAAAATATATTTGAAAATT-TTA 1448
                                v  i   vv-    i --     v     ---i i  i -   
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATA---AAGAACTCTTA 780

  chr2_37656593_3   1449 TCACTCAACAGTAAGAAGACAAACAATCCAATTTTTAAAATAAGTAAAAC 1498
                         iv      i i   i        i  i      ?v-     ii i   iv
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGG 829

  chr2_37656593_3   1499 ATTT--ATATAC--TTTACCTAAAAGGACCTATAGTTGGCTCAGAAGCAT 1544
                             --   v  --  iv  v  i i  iv  i iv    iv v     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_37656593_3   1545 ATGAAAAGA-GCTCA-TATTGTTAGTCAT 1571
                                  -     -i  ii????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (94 / 60)
Gap_init rate = 0.04 (27 / 660), avg. gap size = 2.07 (56 / 27)  


3012 26.81 3.28 0.57  chr2_37733237_37739618.rev     5007  5890 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_37733237_3   5007 TGAAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATAGTGAAAAT 5056
                           i  ii i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_37733237_3   5057 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 5106
                            v     v     iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_37733237_3   5107 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5154
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_37733237_3   5155 TGTAAAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCCAAGCCAATAG 5204
                          i ii  viiv  ii  v  v v  v     i      iii ivv iv  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_37733237_3   5205 AACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTACAAGGT 5254
                                i     ivv   ii  v  ii i      viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_37733237_3   5255 TACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGATATGTAGACC 5304
                                 i   i    ii        vi iv ii i   i  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_37733237_3   5305 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTA----C 5348
                                i    i--    i  --        vv   i    i  ---- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_37733237_3   5349 AGATGATCTTTGACAAAAA---CAAG------CAATGGGGAAAGGGTTCC 5389
                          iv    i  i     iii---    ------            ii vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_37733237_3   5390 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5439
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_37733237_3   5440 GAAACTGGATCCCTTCCTTACACCTTATACTAGAATTAATTCAAGATGGA 5489
                            ii    i    v   i     v     v i      i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_37733237_3   5490 TTAAAGACTTAAATGTTAGACCTAAAACCAC------CCTAGAAGAAAAC 5533
                          i ?    i       v   v       i i------ i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_37733237_3   5534 CTAGGAGATACAT-TTAG-GACATAGGCATGGGCAAGGACTTCATGACTA 5581
                         v    ? -  v  -  v -   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_37733237_3   5582 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5631
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_37733237_3   5632 ATTAGACTAAAAAGCTTCTGCATAGCAAAAGAAACTACTATCAGAGTGAA 5681
                           i i v v    i   i  iiivv    i  v    ii vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_37733237_3   5682 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACA 5731
                         v  i     i                 v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_37733237_3   5732 AAGGGCTAATATCCATAATCTACAGTGAACTCAAACAAATTTACAAGAAA 5781
                          i  i  vi      v   v  i iv      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_37733237_3   5782 AAAACAA----CCCTAACAAAAAGTGGGCAAAGGATATGAACAAACGCTT 5827
                           i    ----   v vi?    i            v    i i  ii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_37733237_3   5828 CTCAAAAGAAGATATCTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5877
                            v           vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_37733237_3   5878 CATCAGTGGTCAT 5890
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (146 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.62 (34 / 13)  


1870 25.76 8.59 6.94  chr2_37851960_37855755.rev     2449  3298 (498)    L1M4_orf2#LINE/L1        2   865 (43)  

  chr2_37851960_3   2449 GGAGAGACATTCAATGTTTATGAGGTAGAAGACTCAATGTTGTTAAGATA 2498
                            i   i  i v     i   iiv i       i   i          i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_37851960_3   2499 TTTATTTTCCTCAGATTTATTTGTGAATTTAATACAGTC---ATCAAAAT 2545
                         viv  vi   i  i   v  i iiii   i  ii  i  ---        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_37851960_3   2546 TTCAGTAGGACTTTTTAGAGAAATTTACAAGCTGAACCTATAACTGATAT 2595
                         ii   iv vvi     iv       v         v    v  i v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_37851960_3   2596 GAAAATGC-----------------CAAAGCAATCTTGAAAAA----ATT 2624
                          i      -----------------    i             ---- vi
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_37851960_3   2625 AAAGTTGGAAGATTTATAATACCCAGTTCTAAAACCGAATAT---GTTAG 2671
                                  i  i i i v v    i  ii     iv v  i--- i  v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_37851960_3   2672 ACTAATCAATGCATTGCAGTATTGACGTGAAGATAGACAAATACATCAAG 2721
                          v       vi  v  ii   i  i i i i        v   v     v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_37851960_3   2722 AGAACAGAATCCAGAAATAGACTCATATGTATAGACTTAATTAATTTTTT 2771
                         i   i     iv   -------------  vi   -------   -----
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGA-------------GTCCAGA-------AAT----- 326

  chr2_37851960_3   2772 AAAACGCTTTATTAGAGTAGTTTTAGGTTCACATCAAGATTAGAATCAAC 2821
                         -    v ---  ------------------    -----   vii    i
  L1M4_orf2#LINE/    327 -AAACCC---AT------------------ACAT-----TTATGGTCAAT 349

  chr2_37851960_3   2822 TGATTTTTAACTGAATGTGACAAGGTGATTTCATGAAGAAAAGA-AGACT 2870
                                ii  -i iv   v    iiv   iv   ii    ii -  v  
  L1M4_orf2#LINE/    350 TGATTTTCGAC-AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_37851960_3   2871 TGTTAACAAGTGGTGCTGGAACAACTGGATGGCCATATAAAAAACAAACA 2920
                          v i     i         i          i?   i  iv    -i  ii
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATG 447

  chr2_37851960_3   2921 AAAAACTTGACTCCTGTCACACGCCATACAATAAAAT-AGTTTGAGATAA 2969
                           i--i v   i   ii v   i     i vv     - ii ii i  ii
  L1M4_orf2#LINE/    448 AAG--TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_37851960_3   2970 A-CATAGAACAAAATATAAC--CTAGAATAATAAAGTTTCTAGTAGAAAG 3016
                          -  ?   v v    i   v--   i  iv     ii ii   v     i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_37851960_3   3017 CATAAAAGAGTAA--CTTTACAACCTTGGAGTAGGCAA-ATTTTTTTAGA 3063
                             i-- ?    --   iiii       iv       -iv   i     
  L1M4_orf2#LINE/    546 CATAG--GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_37851960_3   3064 CAGAACACAAAAAGCACGAACTATGAAA-----AAT-GATAG-CTGGTTT 3106
                         i vi    v        i i v ii   -----   -    i-i   vi 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_37851960_3   3107 TCATTAAAAC-AAAAATTTCTGTGTACCAAAAGATACCATTAAGAAAATG 3155
                             i    i-     i  i    ivi    i  i  i  i      i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_37851960_3   3156 AATATGCAAATCA--------------------GTA---CATATATCTGA 3182
                           v vi   vi  -------------------- i ---           
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_37851960_3   3183 CAAAGGGCATGTATGCATTGTATATAAAGAACTCTTTCAAATCAATAATA 3232
                         i  i  i v     v  vvi                v   v         
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_37851960_3   3233 T---GACAATTTAATTTTTTT----AATGGGCAAAAGATTGAAGCTGTCA 3275
                         v---     v -  iiivv  ----          i    vi iiv v  
  L1M4_orf2#LINE/    794 AAAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_37851960_3   3276 TTTCACAAAAAAAGATACATAGA 3298
                             v v   i      i i i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAA 865

Transitions / transversions = 2.04 (145 / 71)
Gap_init rate = 0.03 (29 / 864), avg. gap size = 4.55 (132 / 29)  


3233 26.93 0.66 0.44  chr2_37861451_37867834     4987  5892 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_37861451_3   4987 TGGAAGAACATTTCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5036
                              ii i  ii    i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_37861451_3   5037 GGCCATGCTGCCCAAGGTAATTTACACATTCAATGCTATCCCCGTCAAGC 5086
                            v  i  v     iv i  i    v      i  v     ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_37861451_3   5087 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5134
                          v   iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_37861451_3   5135 TATGGAACCAAAAAAGGGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5184
                                viiv  ii iv  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_37861451_3   5185 AACAAAGCTGGAGGCATCATGCTACCAGACTTCAAACTATACTACAAGGC 5234
                                i      vv   ii  v  vi i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_37861451_3   5235 TACAGTAACCAAAACAGTGTGGTACTGGTACCAAAATAGAGATATAGA-C 5283
                                 i   i               i iv ii     v       - 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_37861451_3   5284 AATGGAACAGAACAGAGACCTCAGAAATAATACCACACATCTACAACCAG 5333
                                i    iv    vii         vv   i    i  iiii  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_37861451_3   5334 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT--TCC 5381
                         i    i  i     ivv  v   i v  vvv           i  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_37861451_3   5382 TTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5431
                           -- i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_37861451_3   5432 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5481
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_37861451_3   5482 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACACTAGGAGAAAAC 5531
                          i ?    i    i  v   v       i      vivi   i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_37861451_3   5532 CTAGGCACTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5581
                         v    ?iiv viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_37861451_3   5582 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAGAAATGGGATCTAA 5631
                         i            vvi          vv     v  v    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_37861451_3   5632 TGAAACTAAAGAGCTTCTGCAAAGCGAAAGAAACTACCATCAGAGTGAAC 5681
                          v   v v  i i   i  iivvv i  i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_37861451_3   5682 AGGCAATCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5731
                           i   i i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_37861451_3   5732 AGGGCTAATATCTAGAATCTACAAAGAACTCCAGCAAATTTACAACAAAA 5781
                         i  i  vi    i     v  i         ivi   v iv i  i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_37861451_3   5782 A-ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5830
                          -     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_37861451_3   5831 TCAAAAGAAGACATTTATGCAGCCAACAGACACAAGAAAAAATGCTCATC 5880
                           v        i  vi viii     i ii    v     i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_37861451_3   5881 ATCACTGGCCAT 5892
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3042 27.01 1.21 1.10  chr2_37943037_37945397.rev      963  1869 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_37943037_3    963 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1012
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_37943037_3   1013 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1062
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_37943037_3   1063 TACCAATGACTTTCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCG 1110
                          v   iivi i  i  ii     -   -- v  i  - iii    i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_37943037_3   1111 TATGGAAGCAAAAAAGAGCCTGTGTCACCAAGTCAATCCTAAGCCAAAAG 1160
                                iiiv  ii  v  v vi vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_37943037_3   1161 AACAAAGCTGGAGGCAC-CACGCTGCCTGACTTCAAATTATACTACAAGG 1209
                                i      -  -   i  v  ii i      viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_37943037_3   1210 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAACCAGAGATATAGAT 1259
                                  i   i    ii         i iv iivi   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_37943037_3   1260 CAATGGAACAGAAC--AGAGCCCTCAGAAATGATGCCGCATATCTACAAC 1307
                                 i    i--    i  --      i vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_37943037_3   1308 CATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAAGATTC 1357
                           vi    i  i     ivv  vv  i v  vv           ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_37943037_3   1358 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1407
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_37943037_3   1408 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 1457
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_37943037_3   1458 ATTAAAGACTTACATGTTAGACCTAAAACCATAATAACCCT-AGAAGAAA 1506
                           i ?    i  v    v   v       i    -   i  -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAA 544

  chr2_37943037_3   1507 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCGTGTC 1555
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_37943037_3   1556 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGGATC 1605
                           vi            vvi          vv     v  i   iv   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_37943037_3   1606 TAATTAAACTAAAGACCTTCTGCACAGCAAAAGAAACCACCATCAGG--- 1652
                          v  i   v v  i v   i  ii vv    i  ---   i    i ---
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA---CACTATCAAGAAA 690

  chr2_37943037_3   1653 GTGAACAGGCAACCTACCAAATCGGAGAAAATTTTCGCCACCTACTCATC 1702
                              v  i     i  vi   v         v  i  v vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_37943037_3   1703 TGACAAAGGGCTAACACCGAGAATCTACAATGAACTCAAACAAATTTACA 1752
                            i  i  i  vii i v     v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_37943037_3   1753 AGAAAAA-ACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGA 1801
                          v     -     i     v  i?    i           iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_37943037_3   1802 TACTTCTCAAAAGAAGACATTTATGCAACCAAAAGACACATGAAAAAATG 1851
                         i i     v        i  vi viiii    v ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_37943037_3   1852 CTCATCATCACTGGCCAT 1869
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


3072 26.45 1.21 1.54  chr2_38074938_38081650.rev     5311  6221 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_38074938_3   5311 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5360
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_38074938_3   5361 GGCCACACTCCTCAAAGTAATTTACAGATTCAATGCTATTCCCATGAAGC 5410
                            v i     i    v i  i           i  v  i  i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_38074938_3   5411 TACCATTGACTTTCTTCACAGAATTAGAAAAAAGCT-ACTTTAAATTTCA 5459
                          v   vivi i  i  ii     v v  v  --   - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr2_38074938_3   5460 TATGGAACCAAAAAGGAACCTGTATAGCCAAGACAATCCTAAGCAAAAAG 5509
                                viiv  i   v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_38074938_3   5510 AACCAAGCTGAAGGCATCATGCTACCTGACTTCAAA-----CTATA---C 5551
                            v   i  i   vv   ii  v  ii i      -----   i --- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_38074938_3   5552 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5601
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_38074938_3   5602 AATGGAACAGAACAGAGGCTTCAGAAATAACACCACACATCTACAACCAT 5651
                                i    iv   iv i         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_38074938_3   5652 CTGATCTTTGACAAACCTGACAAAAACAG-CAATAGGGAAAAGATTCCCT 5700
                         i    i  i     ivv  v   i v  v-    i      ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_38074938_3   5701 GTTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAAAAAAAAAC 5750
                         v  i  i        i     v      v  ?   i        i  ---
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--- 445

  chr2_38074938_3   5751 TGAAACTGGACCCCTTCCTTACACCTGATACAAAAAATTAACTCAAGATG 5800
                             ii         v   i     vv         -         i   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATG 494

  chr2_38074938_3   5801 GATTGGATTAAAGACTTAAGCGTTAAGACCTGAAAACCATAAAAACCCTA 5850
                            i----- ?    i   ii  -    v  -     i      vi i  
  L1M4_orf2#LINE/    495 GATC-----AWAGACCTAAATGT-AAGAGCT-AAAACTATAAAACTCTTA 537

  chr2_38074938_3   5851 GAAGAAAACCTGGGCA-ATATCATTCAGGACATAGGCATGAGCAAAGACT 5899
                                  v i  ?i- v   -   iv   v v  vv ii    v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_38074938_3   5900 TCATGACTAAAACACCAAAAGCAATTGCAGCAAAAGCCAAAATTGACAAA 5949
                           v iiv  vi            vvv   i      vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_38074938_3   5950 TGGGATCTAATTAAACTAGAGAGCTCCTGCACAGCAAAAGAAAGTATCAT 5999
                          v   ii v  i   v vi i i  ii  ii vv    i  v v     v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_38074938_3   6000 CAGAGTGAACAGGCACCCTACAGAATGGGAGAAAATTTTTGCAATCTATT 6049
                         v i      v  i  v  i                 v       vii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_38074938_3   6050 CGTCTGACAAAGGGCTAATATTAAGTATCTACAAGGAACTTAAACAAATT 6099
                         ii     i  i  i  vi   iv  v  v  i  i     ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_38074938_3   6100 TACAAGAAAAAAGCAAACAACCCCATCAAAAAGTGGGCAAAGGATATAAA 6149
                         v i  v     ii    i     v  i?    i            v i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_38074938_3   6150 CAGACACTTTTCAAAAGAAGACATTTATGTGGCCAACAAATATAAGAAAA 6199
                         i     i  i  v        i  vi vi       i  ii i v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_38074938_3   6200 AAAGCTCATCATCACTGTTCAT 6221
                         i v     v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.08 (25 / 12)  


2984 27.23 1.79 0.45  chr2_38092243_38101888.rev     4801  5696 (3950)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_38092243_3   4801 TGGAAAAACACTCCACACTCATGGATACAAAGAATCAGTATTGTGAAAAT 4850
                               i i ii   iii        vvi    v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_38092243_3   4851 GGCCATACTGCCCCAAAT-AATTTATAGATTTAATGCTATTCCCATCAAG 4899
                            v     -        -i  i  i     i  i  v  i  i     i
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_38092243_3   4900 CTACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAACTTCA 4948
                         v v   vivi i  i  ii     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_38092243_3   4949 TATGAAACCAAAAAAGAGCCCATATAGTCAAGACAATCCTAAACAAAAAG 4998
                             i  viiv  ii  v  viv    i   i      i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_38092243_3   4999 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGC 5048
                                i      vv       v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_38092243_3   5049 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5098
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_38092243_3   5099 AATGGAATAGAACAGAGGCCTCAAAAATAACACCACACATCTACAACCAC 5148
                                     iv   ivii  i      vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_38092243_3   5149 CTGATCTTTGACAAACCTGACAAAAACAAGCAA-GGGGAAAGGATTCCCT 5197
                         i    i  i     ivv  v   i v  vv   -        i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_38092243_3   5198 ATTTAATAAATGGTATTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5247
                         v  i  i       ii     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_38092243_3   5248 AACTGGACCCCTTCCTTATACCTTATACAAAAATCAACTCAAGAAGGATC 5297
                          ii         v   i i   v           i       i v     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_38092243_3   5298 AAAGACTTAAATGATTAAACCTAAAGCCATAAAAACCCTAGAAGAAAACC 5347
                          ?    i      - v i v     i i      vi i           v
  L1M4_orf2#LINE/    499 AWAGACCTAAATG-TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_38092243_3   5348 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAAACTTCATGACTAA 5396
                             ?i- v i -   iv   v v  vv i     viii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_38092243_3   5397 AACACCAAAAGCAATTGCAACAAAAGTAAAAATAGACAAATTGGATCTAA 5446
                         i            vvv          v         i        ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_38092243_3   5447 TTAAACTACAGAGCTTCTGCACAGTAAAAGAAACTATCATCAGAGTGAAC 5496
                          i   v vv i i   i  ii vvi   i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_38092243_3   5497 AGGCAACCTACAGAATGGCAGAAAATTTCTGCAATCTATCCATCTGACAA 5546
                           i     i         v       v i     vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_38092243_3   5547 AGGGCTAATATCAAGAATCTACAAGGAACTTAAATAAATTTACAAGAAAA 5596
                         i  i  vi    v     v  i  i     ivv i  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_38092243_3   5597 AACCAAACAACCCTATCAAAAAGTGGGTGAAGGATATCAACAGACACTTC 5646
                          iv    i     v  i?    i    ii      v v  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_38092243_3   5647 TTAAAAG--------CA----GCCAACAAACATACGAAAAAAAGCTCATC 5684
                          iv    --------  ----     i  i  i i     i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_38092243_3   5685 ATCACTGGTCAT 5696
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (147 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  

4338 20.55 0.55 0.77  chr2_38092243_38101888.rev     8245  9154 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_38092243_3   8245 TAGAAAGACATGCCATGTTTGTGGATTTGAAAGTTTA-TAATGTTAAGAT 8293
                          i      i  v       ii      v   iii   -  v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_38092243_3   8294 GTCAATCCTACCCAAAATAATCTACAGATGCAATGCAATCCCTCTGAAAA 8343
                          v    v  v      v i          v   i         v v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_38092243_3   8344 TCCCAATGATATTTTTTGTACAAATAGAAAAATCTATCCTGAAATTCATT 8393
                              iiviiv       i v    v  v  iiiv     i        v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_38092243_3   8394 TGGAATTCCAAGACACCCGAAATGGCCAAAATAATCTTGAAAAATAAAAA 8443
                              v v    iv    ii   i       i            v  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_38092243_3   8444 CAAAGTTGGAGGTCTCACACCTCCTGATTTTCAAACCTACTACAAAGCTA 8493
                                     v       i   ii    iv    i             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_38092243_3   8494 CAGTAACCAAAACAGTATGGTACAGTGTGGTGTAAAGACAGATGTATAGG 8543
                               i   i     i      ----   ii   i  i   ii     i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTAC----TGGCATAAGGATAGACATATAGA 296

  chr2_38092243_3   8544 CTGGTGAAAGAAAATGGAAAGCCCAGAAGTCAACC-ACACATATATGATC 8592
                         iiii  i  v i   v  i  i      i v    - i    v    i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_38092243_3   8593 ACATGACTTTTGACAAAGGTTCCAAGACCATTCAATGGAGAAAGGGTAAT 8642
                          vv   i   i     i   v                 i     ii  i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_38092243_3   8643 CTCTTCAACAAATGGTGTTGAGAAAACTGGATATCCACATATAAAAGAAT 8692
                           i              i  i  v         ?      ii        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_38092243_3   8693 GAAGTAAGACCATTACTTAACATCACACACAAAAATTAACTCAAAATGCA 8742
                              vi    vi   i v   i  i i                    v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_38092243_3   8743 TCAAAGACCTAAATATAAAACCTAAAGCTATAAAACTCTTAAAAGAAAAC 8792
                            ?          i   i v     i              i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_38092243_3   8793 ATAATGCAAAAGCTTCACAACAGTGGATTTGGCAATGATTTATTGGATGT 8842
                            iv?vv   v    iii  vv   i  v       i   v  i   i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_38092243_3   8843 GGCACTAAAAGCATAGGCAATAAAAGAAAAAATTGATAAACTAGACTACC 8892
                          i   i       i i    i            v      i i    v v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_38092243_3   8893 TCAAAACCGAAAACTTCTATGGATCAAAGGACATAATCAACAGAGTAAAA 8942
                               iii       i i  vv          iv     v i   i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_38092243_3   8943 AGGCAACCCACACATTGGGAGAAAATATTTGCAAATTATATCTTTTTTAA 8992
                           i         v v                     i    v i vv   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_38092243_3   8993 AGGGTTAATATCCAAAATATATAAAGAACTCCTACAAATCAACAA---AA 9039
                         i  ii vi      i                i     v    i  ---  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_38092243_3   9040 AAACAAACAACCTGATTTAAAAAAAAGGATCAAGGGACTTGAATTGGCAT 9089
                          i     i    ii   ?     vii ---   i   i      v i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGG---CAAAGGATTTGAATAGACAT 843

  chr2_38092243_3   9090 TTCTCCAAAGAAGATATACAAATGGGCAGCAGTCACACGAAAAGATGTTC 9139
                                                  v  ii iv    i         i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_38092243_3   9140 AATGTCACTAATCAT 9154
                           ii   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (121 / 62)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.40 (12 / 5)  


3130 27.64 0.44 0.44  chr2_38143747_38150152.rev     5007  5914 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_38143747_3   5007 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5056
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_38143747_3   5057 GGCCATACTGACCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 5106
                            v     vv    iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_38143747_3   5107 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTAAAGTTCA 5154
                          v   iivi i  i  ii     -   -- v  i  - i i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_38143747_3   5155 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5204
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_38143747_3   5205 AACAAAGCTGGAGGCATCATGCTACCAGACTTCAAACTATACTACAAGGC 5254
                                i      vv   ii  v  vi i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_38143747_3   5255 TACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5304
                               v i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_38143747_3   5305 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACC 5352
                                i    i--    i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_38143747_3   5353 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACGATCCC 5402
                          vi    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_38143747_3   5403 CTACTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5452
                           vi i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_38143747_3   5453 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5502
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_38143747_3   5503 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAAC 5552
                          i ?    i  v    v   v       i      vi i   i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_38143747_3   5553 TTAGGCACTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTGTAA 5602
                         v    ?iiv viv   iv   v v  vv i     v ii   v ivi  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_38143747_3   5603 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTCACAAATGGGATCTAA 5652
                         i            vvi          vv     vv i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_38143747_3   5653 TGAAACTAAAGAGCTTCTGCACAGCAAAAGAACCTACCAACAGAGTGAAC 5702
                          v   v v  i i   i  ii vv    i  vv   i   v i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_38143747_3   5703 CGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5752
                         v i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_38143747_3   5753 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5802
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_38143747_3   5803 AAACAAACAACCCCATCAAAAAGTGGGCACAGGATATGAACAGACACTTC 5852
                          i     i     v  i?    i      v     v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_38143747_3   5853 TCAAAAGAAGACATTTATGCAGACAAAAGACACATGAAAAAATGCTCATC 5902
                           v        i  vi viii v   v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_38143747_3   5903 ATCACTGGCCAT 5914
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3204 26.98 0.44 0.44  chr2_38271456_38277885.rev     5031  5938 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_38271456_3   5031 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5080
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_38271456_3   5081 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5130
                            v     v      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_38271456_3   5131 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5179
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_38271456_3   5180 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5229
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_38271456_3   5230 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5279
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_38271456_3   5280 ACAGTCACCAAAACAGCATGGTACTGGTACCAAACCAGAGATATAGATCA 5329
                              v i   i    ii         i iv iivi   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_38271456_3   5330 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACCA 5377
                               i    i--    i  --        vv iii i  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_38271456_3   5378 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATCCCC 5427
                         vi    i  i     ivv  v   i v  vvv          vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_38271456_3   5428 TACTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5477
                          vi i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_38271456_3   5478 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5527
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_38271456_3   5528 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5577
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_38271456_3   5578 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5626
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_38271456_3   5627 AACACCAAAAGCAATGACAACAAAAGCCAAAATTCACAAATGGGATCTAA 5676
                         i            vvii         vv     vv i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_38271456_3   5677 TGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5726
                          v   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_38271456_3   5727 AAGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5776
                          ii     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_38271456_3   5777 AGGGCTAACCTCCAGAATCTACAATGAACTCAAACAAATTTATAAGAAAA 5826
                         i  i  viiv        v  i  v      vv    v iv    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_38271456_3   5827 AAACAAACAACCCCATCAAAAAGTGGGCACAGGATATGAACAGACACTTC 5876
                          i     i     v  i?    i      v     v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_38271456_3   5877 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5926
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_38271456_3   5927 ATCACTGGCCAT 5938
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2574 24.67 10.76 1.21  chr2_38343859_38345693      517  1343 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_38343859_3    517 GAGAGATAGC--ATATTTATGGATTACAAAACTCTATATTGTTAAAATGG 564
                           i     v --  i  i       iv  i   iv          i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_38343859_3    565 CAATGCTGCCCAAATTCCTCCCAAGATTCAACACAATTCCAATCAAAATT 614
                             i  v        vv  ivv         i    i  v        i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_38343859_3    615 TCTATAAGCATTCTTATAAAAATTGACAAGCTGATTCTAATATTTGTATG 664
                         i viiviv v  i  ii i                i    v   ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_38343859_3    665 AAAATTCAAGGAACCTAGAATAGCCAAAGTAAT-TCGAACAA--AGAACA 711
                         i    v     i   i            ii   - i   v  --      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_38343859_3    712 TAGTTGAAGGACTTACTCTATTTGACTTCAGTACTTACTATAAAGCTATA 761
                         v     i      i  v  viiii i    iv        i       i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_38343859_3    762 GTAATTCGTTCTGTTTAATATTATGGTAAAGGTAGGCATATAGATCAATG 811
                              ivivv v  v ii  i ivvi   i i   i              
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_38343859_3    812 AAACAGAAT--ACAGTCCAGAAATAGACC---------------AGCTGA 844
                         i  i     -- v            i   --------------- ii   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_38343859_3    845 GTTTTGACAAACAAGCCAAGGCAACTCAATGGGGGAAAATAAAGTCTTTT 894
                         v   i     iviv      i v i         i  i - v        
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTT 401

  chr2_38343859_3    895 TAATAAATGTCATT----CAATAAACTATCCATTTTTTTAAAAAAAATCA 940
                         i  i     viii ----   iviiv  ?   iv vi---    i   v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGC---AAAAGAATGA 448

  chr2_38343859_3    941 A-------TCCTACTCCCTACCATACACAAAAATCAACTAAAAATATATT 983
                          -------i     ii vi      i        i    v     iv  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_38343859_3    984 CCACATCTTAATGTGAAATGTGAAACTATGAAACTTCTAGAAGAAAACAC 1033
                         v? v i  v     i i vv i       i     ii            i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_38343859_3   1034 AGGAA-AAATATTTGAGATCTTAAGGCAAGCAAAGATTTCTTAGATGTGA 1082
                            ?i-    v  i v  i   ii vi i    v i          i   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_38343859_3   1083 CACCGAAATCACTATCCATAAGAGAAAAAATGTTGGTAA-TTGAACTTTA 1131
                             i   v   v v v i  i         i-- i   -   i    i 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTCA 646

  chr2_38343859_3   1132 TCAAAATTTAAAACTTTAACTCTTTGGAAAGCACCAATAAGAAAAC-AAA 1180
                                 v        viiv   iii iii   i vi      ii-   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_38343859_3   1181 AGAC---TCATA---------AAAATATTTACAA--CATATTTATCTGGT 1216
                             ---i  i ---------         i   --     --     i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGAT 744

  chr2_38343859_3   1217 AAAGAACTCACATCTAAAATACAGAAAGAATGCTTATAACTC-------- 1258
                           i i   iii   i i    i v      iv    i     --------
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_38343859_3   1259 ---GACAAA---------------ATG-----------TAAACAGACTTT 1279
                         ---      ---------------   ----------- i  i    v  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_38343859_3   1280 TGACCAAAGTCAAGATATG--AATGGACAATCAACACATGAAAAGATGTT 1327
                          vv      --       i--     v    v i              i 
  L1M4_orf2#LINE/    845 TCTCCAAAG--AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_38343859_3   1328 CAACATCATTTGTTAT 1343
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (135 / 66)
Gap_init rate = 0.02 (22 / 906), avg. gap size = 4.50 (99 / 22)  


 987 30.00 12.25 2.96  chr2_38374619_38376254      435  1144 (492)    L1M4_orf2#LINE/L1      133   908 (0)  

  chr2_38374619_3    435 CTAGTTCTCAAATT-ATATGGAGGAACAAAGACCTAAGAGTAAATAAAGC 483
                           ii i  v     -       iivi   i iv iv   i  ivi   i 
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_38374619_3    484 ACTCCTGAAAAGGAATA------------------------------TCA 503
                          v  i      i   v ------------------------------   
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_38374619_3    504 AGACTTATTCCAAAGCTAAAATAACAAAGACAGTGCTGTACTGGCACAGA 553
                          i     i v        v i   iv         iv         i ii
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_38374619_3    554 AATAGACAAATTGCCCAATGGAACAGACTAGAGAAACAGAGACAGAGAGA 603
                         i       v  v vi        i   v v    iv -----    i v 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTC-----CAGAAATA 327

  chr2_38374619_3    604 AAG--AGAGAAGGGTGGGTACTTGAGGATGGAAGAGAAGGCACTGCGGAT 651
                           v-- v v vvvi   vi v    vvv v  vi  --  ii ii-i  i
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAG--GGTGCCA-AGAC 374

  chr2_38374619_3    652 GA--CAA---GGAAACAATGAACTCTTCAATAAATAGTGCAAGGCCA-CT 695
                         v --   ---     v   iiv  i     i    i    vi  v  -  
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_38374619_3    696 GGTTACCTACATGGGGGGGAAAATACTGTGACTA-ATCCCTGCTTTGCAC 744
                           v  ? i     v-----    v v  viii i- i    i i ii   
  L1M4_orf2#LINE/    425 GGATAKCCACATGC-----AAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_38374619_3    745 CATGCAGAAGAATCAAATGCTAGCAGATTTAAGATTTAAATACACAAGGC 794
                            ii v  i   i  v vvv iii   iv?   ii     ii vi  vi
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_38374619_3    795 AAAACTCTAAAACTTTT-GAAGGCAACATGGGAGAATATCTTTAGAACAT 843
                               v       i  -    iv     i  ? v v     iivi  v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_38374619_3    844 CAGAG-AGGTGAAGGTTTCTTAAA---------GAAAACACAAAACTATG 883
                         ii iv-   ii v         i ---------i   i     i- v ii
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG-CAACA 618

  chr2_38374619_3    884 AAAGAAAAA-TA-ATAAATTTGGCTACATTCAAATTAAGAACTTCTGT-- 929
                                  -  -       v i  v   iv       i     i   --
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_38374619_3    930 TTAACAGTAGACCCCATGAAGAAAGTGATCAGAAAAGCAACAATGTAGGA 979
                           v v  --   v i  v          vv   v  v v   ivi i   
  L1M4_orf2#LINE/    669 TTCAAAG--GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_38374619_3    980 GAAGATATTTGCAATATATATAACCAATA--TAATCTACATAAAGATGAT 1027
                            i          vvi     v ii   --vi ii ii  vv   --  
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA--AT 764

  chr2_38374619_3   1028 GTAT------TTTTTAAAATCTT-----TTCAAAG--------TTCAAT- 1057
                         i   ------i i   v  -  i----- vv    --------ii    -
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAA-CTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_38374619_3   1058 ---AAATAAGTTAA-----TAAATACACAGTTCACAGAGCAGAAAATATG 1099
                         ---    ii iv  ----- i    v   v   v vi --    i    i
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA--AGAAGATATA 861

  chr2_38374619_3   1100 --AATAGCCCATAAATATATAAAAGAATACACAACCTCATTAGTAAT 1144
                         --   i   v    ii i  i   ii  i v    v   ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (122 / 88)
Gap_init rate = 0.04 (29 / 776), avg. gap size = 3.72 (108 / 29)  


2030 25.57 3.06 1.99  chr2_38532605_38534243      501  1153 (486)    L1M4_orf2#LINE/L1      249   908 (0)  

  chr2_38532605_3    501 TATAGTAACCAAAACAGCACGGTAGCAGTACCAAAACAGACACATAGACC 550
                           i     i   i    iii    vii i iv ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_38532605_3    551 AATGGAACAGAATAGAAAGCCCAGAAATAATGCCACACTCCTACAACCAT 600
                                i     v  i  i          vv   i  vii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_38532605_3    601 CTGATCTTTGACAGAGTTGACAAAAACAAGCAATGGGGAAAGGACTCCCT 650
                         i    i  i    ii v  v   i v  vv            i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_38532605_3    651 ATTCAATAAACGGTTCCAGGATAACTGGCTAGCTATATGTGGAAGATTGA 700
                         v     i   i   v ii   i      v  ? i i   iii    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_38532605_3    701 AACTGGACCCCTTCCTTACACCATATATAAAAATCAACTCAAGACCAATT 750
                          ii         v   i          i      i       i ivi  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_38532605_3    751 AAAGATTTAAACATAAAACCTAAAACCATAAAAACCTTGGAAGATAACCT 800
                          ?   ii    ii   i v       i      vi   i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_38532605_3    801 AGG---AAATACCATTCTGGACATAGGACTGGGCAAAGATTTC------A 841
                            ---    -- -   vv   v v  ii i     v i    ------ 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_38532605_3    842 TGACAAAAATGCCAAAAACAACTGCAACAAAAACAAAAATTCATAAATGG 891
                              ------      i  vvv         iv      vv      v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_38532605_3    892 AACCTAATTGAACT--AAAGTTTCCACACAGCAAAAGAAACTATCAACAG 939
                         i  i v  ii  v --   ii  iiiii vv    i  v        -- 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA--G 687

  chr2_38532605_3    940 AGTAGTAAACAGACAACCTACAGAATGGGAGAAACTATTTGCAAACTATA 989
                          i-   i  v        i               v          ii   
  L1M4_orf2#LINE/    688 AA-AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_38532605_3    990 C-TCGTGACAAAGGTCTAATAACCAGAATCTATAAGGAACT--TA-AATT 1035
                         i-  -   i  i  v  vi  v       v     i     --  -  i 
  L1M4_orf2#LINE/    737 TATC-TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_38532605_3   1036 TA-CAAGCAAAAAACAAACAACTCCATTAAAAAGTGAGCACAGGACAAGA 1084
                         i -i  vv    i     i   i v   ?    i  i   v    ivv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_38532605_3   1085 ACAGACACTTTTCAAAAAAAGACATACATGTGGCCAACAAGC-CACAAAA 1133
                          i     i  i  v   i    i     vi       i    -  ii   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_38532605_3   1134 ---TGCTCAACGTTACTAATCAC 1153
                         ---        i i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (109 / 55)
Gap_init rate = 0.02 (15 / 660), avg. gap size = 2.20 (33 / 15)  


 490 24.77 0.00 0.00  chr2_38652286_38654641      501   609 (1747)    L1M4_orf2#LINE/L1      181   289 (619)  

  chr2_38652286_3    501 ACAATATTGAAGGAGGAGAACAAAGTTAGAGGACCGACACTATCTGACTG 550
                              v     ii  i           i      iv     vi ii i v
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr2_38652286_3    551 CAGGAGTTACTATAAAGTTGCAGCAACCAAGACAGTGTGGCATTGGCAAA 600
                           ii v      i    i i   i  i             i i     v 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_38652286_3    601 ACAATAAAC 609
                          vi   i  
  L1M4_orf2#LINE/    281 AGGATAGAC 289

Transitions / transversions = 2.86 (20 / 7)
Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.00 (0 / 0)  

1091 25.64 0.96 1.28  chr2_38652286_38654641      916  1227 (1129)    L1M4_orf2#LINE/L1      280   590 (318)  

  chr2_38652286_3    916 AAGGATAAACAAAGAGATCAATGAAACAGAATAGAGATCTCAGAAACAGA 965
                                i   v v         i  i     v    vii      i i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_38652286_3    966 CCCATATAAATATAGTCAATTGATGTTTGACCAAAAAAACAAAGGCAATA 1015
                               i vv   i          v  i  -   iiivi v   i v  v
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGA-CAAGGGTGCCAAGACCATT 378

  chr2_38652286_3   1016 CAATGGGGAAAAGAAAATCTTTTCAAAAAATGGTACTGGGACGA---GAC 1062
                                    ii v i         v       i       i ---  i
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_38652286_3   1063 ATTTATATTCAAAAAAAAGGAATGAAGACATAGATCTCATACCCTTCACA 1112
                          ?ii i  v     i  v i i v-i   vivv i    i   v vi   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTT-GGACCCCTACCTCACACCATATACA 477

  chr2_38652286_3   1113 AAAAAATTAACTCTAAATAGATCACAGACCTAAATGTAAAACACAAAATG 1162
                             --       v    i     ?              i vvi    iv
  L1M4_orf2#LINE/    478 AAAA--TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_38652286_3   1163 GTAAGACTCTTAGAAAATAACATAGGAGAAAATCTAGATAACCTTGGCTT 1212
                         i   i          i v        ? v      vvi i       v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_38652286_3   1213 TGGTAGTGACTTTTT 1227
                         v  i i  ii  i  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTT 590

Transitions / transversions = 1.48 (46 / 31)
Gap_init rate = 0.01 (4 / 311), avg. gap size = 1.75 (7 / 4)  

1137 24.46 2.14 0.31  chr2_38652286_38654641     1542  1868 (488)    L1M4_orf2#LINE/L1      576   908 (0)  

  chr2_38652286_3   1542 AGGTTATGACTTTTTTGACATGACACCAAAGGCATGATCTATGAAAGAAA 1591
                            iv   ii  i  v  i           i   ii v v ii       
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_38652286_3   1592 ACACTGATAAGCTAGACTTCATTAAAATTAGAAACTTCTGTTCTGTAAAA 1641
                          v iv     ii i        i       i      i   v  vi   i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_38652286_3   1642 AATACT--TATGATAATATAAAGAAAAGCCACACACTGGGAGAAAATATT 1689
                         i i   --i v  v i iv     v  v     v v              
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_38652286_3   1690 TGCCAAAGATGTATTTGATATGGGGCTATTATCCAAAACATAAATAAAAC 1739
                            v  vv  i   i     v   i  vv      i  i   v v i   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_38652286_3   1740 TCTTAAAACTCAACAGTAAGGAAACAAACAACC-AATT-AAAAATGGGCC 1787
                              v       i i   ii i     i    -    -          v
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_38652286_3   1788 AAGACATT--AAGAGAGAGTTCACCGCAAAAGACATACAGGTGGCAAATA 1835
                            i-   --  v   v v   v  iv i    i     ii    v    
  L1M4_orf2#LINE/    826 AAGG-ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_38652286_3   1836 AGCATACGAAA-GATGCCCCACGACGTATGTCAT 1868
                             i i    -     i v  iv i????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (47 / 33)
Gap_init rate = 0.02 (6 / 333), avg. gap size = 1.33 (8 / 6)  


 905 17.41 1.34 9.82  chr2_38685573_38687187.rev       18   241 (1374)    L1M4_orf2#LINE/L1        7   211 (697)  

  chr2_38685573_3     18 GATATATCTTGTTCATGAGTCAGAAGACTCAATATAGTTAACATGTCAGT 67
                              vi v        ii ii       i     v     v   v  i 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_38685573_3     68 TATCCCTGAATTGACCTATAGATTTAATGCGATCTCTGTCAAGATCCCAG 117
                         vv    ii      i   i     i  i  i   i  i    i       
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_38685573_3    118 CAGGTCTTTTTTTTTTTTTTTTTTTTTTTAAGGTAGAAATTTATAAGCTG 167
                          -v i       -------------------- i       v i      
  L1M4_orf2#LINE/    107 C-TGCCTTTTTT--------------------GCAGAAATTGACAAGCTG 135

  chr2_38685573_3    168 ATTGTAAAAATTCATATG-AAATGCAAAGGACCTAGAATAGCCAAAACAA 216
                           iv     -        -        i     i                
  L1M4_orf2#LINE/    136 ATCCTAAAA-TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_38685573_3    217 CTTTGAAAACAAA--CCAGAGTTGGAG 241
                         ii       vi  --v  i        
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAG 211

Transitions / transversions = 2.25 (27 / 12)
Gap_init rate = 0.02 (5 / 205), avg. gap size = 5.00 (25 / 5)  

1833 20.84 10.58 3.58  chr2_38685573_38687187.rev      481  1123 (492)    L1M4_orf2#LINE/L1      221   908 (0)  

  chr2_38685573_3    481 TTCC--ACCTCAAAACTTA-TACA--GCTATAGTAATCAAGAC--TGTGG 523
                             -- ii          -    --    i            --     
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_38685573_3    524 TA--GGTGTGTAAAATAAA-A-ATAGATCAATGGGACAGAAT-----AT- 563
                           --  ii i- ii   i - -            i i     -----i -
  L1M4_orf2#LINE/    271 TACTGGCATA-AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_38685573_3    564 -AGATATAAAGCCACACATATTGATAATGCATACTGATTTGTTACAAATA 612
                         -   v     v   i    -  -  ii -  - i      viv    ivi
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACAT-TT-ATGGT-CA-ATTGATTTTCGACAAGGG 365

  chr2_38685573_3    613 TGAAAAGAA-ATGCAGTGGAAAAAGGACCCTCTTTTCAACAAATGTTGTT 661
                           vv    v-  v  i   ii    i ivv               v  i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_38685573_3    662 GGAACAACTGGAAATACATATGCAGAAA----------GACCCCTTCTAG 701
                           i         v ?v  i     i  i----------       v i--
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC-- 463

  chr2_38685573_3    702 CCATGTTCTGTTCCATATGCAACAATTAACTCAAGATGGGTGAAAGACTT 751
                         i  ii-------      i   v           i    i v ?    i 
  L1M4_orf2#LINE/    464 TCACA-------CCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_38685573_3    752 AAATGCAAGAGCTAAAATTATGAATCTTATAGATGAAAAC---------- 791
                              i           i   i  v  iv    v      ----------
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_38685573_3    792 -TTTTTGTGACCTTTTTTTGAGTAATGATTTCTTACA----ACACCAAAA 836
                         - i  i        vvv  ii i    i       v ----         
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_38685573_3    837 ACATTGGTCTATTAAAAAAATCCAAAACCCA-AACTCATAAACT-CAGCA 884
                         i  ivi i-- vi    i  ---    ivv -  v -- ii   -  v  
  L1M4_orf2#LINE/    607 GCACAAGC--AACAAAAGAA---AAAATAGATAAAT--TGGACTTCATCA 649

  chr2_38685573_3    885 AAATGTAAAACTTCTG--CTCTAATAGA---------GAAGG--AAAAGA 921
                             vv       i  --  ii  vi  ---------   i --      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_38685573_3    922 CAAGCTACAGATTAAGAGAAGATATTTGCAA--CATATATTTCTGATATA 969
                            v i     v ii     i          --       --      vi
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT--CTGATAAG 747

  chr2_38685573_3    970 GGACTTGTATCTAGAAAATACAAAGAATTCTCAAAACTCAACAA------ 1013
                                    i    v   i      i   i v       i  ------
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_38685573_3   1014 GA-AAATGACCCTATTAAAACTTGGCAAAAAGATTAGAATCTACATTTTA 1062
                           -    i    v   ?   vv   vv   i    v    vv      iv
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_38685573_3   1063 CTGAAGAAGATACATAAAAGATGAATAAGCACATGGAAAGATGCTTAACA 1112
                          ii         i i   v iiv            i         i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_38685573_3   1113 TCATTATCCGT 1123
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.67 (82 / 49)
Gap_init rate = 0.05 (32 / 688), avg. gap size = 2.84 (91 / 32)  


1001 28.44 15.19 1.80  chr2_39215712_39217469      490  1266 (492)    L1M4_orf2#LINE/L1       28   908 (0)  

  chr2_39215712_3    490 GGAAGTACCATAATATC-TCAAGATGTCAAT-TGTCCTA---TACTCTAA 534
                              -  i-      i- i      v    -ivi  i --- iv    v
  L1M4_orf2#LINE/     28 GGAAG-ACT-TAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chr2_39215712_3    535 ACATT----ATAATTCCTATTAAAATTGAAACAA--TTTTCTG-AAAAAT 577
                          v   ----ii   i     i     ivv i vi--    i  - i    
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr2_39215712_3    578 TGAGATGCTGATCCTAAA-TTTA----GAA-------GAGCCAAGAACAA 615
                            v v            -  i ----   ------- ii  v    i i
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr2_39215712_3    616 CTAAGGCACTCCT---AAAGAAAAATCAGGC-AAAAAACT-ATTTTTCCT 660
                          i  ii  v  i ---      i  iv i i-ii ii   - ivi    -
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC- 224

  chr2_39215712_3    661 GCCAGATAAAGACATGATTAC---GCTACAGTGATTAAGATACTAAGATA 707
                         - v vv v  i  - v i   ---        i  i    i v iv i  
  L1M4_orf2#LINE/    225 -CAATTTCAAAAC-TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_39215712_3    708 TTAGT----GCAGAAACAGAAAGACCACCGTAATGGA-----GAGCTTGT 748
                         i i i---- v v i   v v   i  vi v   i  -----   iiiiv
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_39215712_3    749 ATACAGATCT-----TGTATGA--AAATAATATAAAACAAGAG--CCAGT 789
                          v i i i i----- v    i--  v i  v vvi     i --   iv
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_39215712_3    790 AGTATAGATTCATGAGGAAAGGATGGATCATCCAATATATAGTGCTAGGA 839
                          vi  --- iv   i      i  i viiv i   i v  i     i   
  L1M4_orf2#LINE/    373 ACCAT---TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_39215712_3    840 CA-TTGG-----------CAAA----TTA--TT----CCCTATCACATAC 867
                           -i   -----------    ---- v --  ----     i v  i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_39215712_3    868 CATATATAAAAACCAACTGAAGATGGATCAAGTACATAACGGTGATAAGC 917
                               i     ii    v  i        ?iv  v   vv  i -i   
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA-GAGC 518

  chr2_39215712_3    918 AAAAGATTCAGAAACTTTTAGTA-AAAGCATAGCAGGATATCTTTATAAC 966
                         v   - i vvi     i    v -   i     v? v v     ii i  
  L1M4_orf2#LINE/    519 TAAA-ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_39215712_3    967 CT-GAGTTAGGAAAGAATTTATTTAGAAA-GACACAAGAAGTATAA--AA 1012
                           - i      v  vii   -i     v -     v i   i i  --  
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTT-CTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_39215712_3   1013 TGAA-GAAAAATT---CTAATTCAATTTCAT------TAAGAACTACTG- 1051
                         ii  -      v ---iv    vi i     ------   i    vi  -
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_39215712_3   1052 -CTT-AATCAACA-TATCACAAAAAGTGGAAAGATAAGTCACACACTGGG 1098
                         -   -  vvi   -     - i      i     i  vi    v v    
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCA-AGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_39215712_3   1099 A-----------CA---CATATAACCTATAAAGGAA--ATATCCAGGATA 1132
                          -----------  ---      v iv    i   v--i       i   
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_39215712_3   1133 AATAA-TAAC----AAAGTTT--TAATAAAAA--CAAATC-CTCAGTTTT 1172
                         v    -v   ---- v ii i--         --     v- i  i  ?v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_39215712_3   1173 CTAAAATGGGCAAAAGTCATGTACAGACATTTCATGGAAGGGGAAACACA 1222
                         --            i viv  v i         vivi   ii  v i   
  L1M4_orf2#LINE/    816 --AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_39215712_3   1223 ACTGCCCCATAAATAT-TAGAAAGGTGCTCAGCCTCAATCTCAAT 1266
                          v  v  v    ii i- ii    i      i v   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (133 / 85)
Gap_init rate = 0.06 (52 / 881), avg. gap size = 2.54 (132 / 52)  


3783 18.13 2.31 1.82  chr2_39241281_39243682      689  1510 (892)    L1M4_orf2#LINE/L1        4   829 (79)  

  chr2_39241281_3    689 AAAGCCATTCTGAGTTATTGAGTAGGAAGACTTAATATTGTTGACAT--C 736
                             vi  i iiv   vv  ii v                  i v  -- 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_39241281_3    737 AATACTACCTAGAGCAATGTACAGATTCGATGCAATCTCTATCAAAATTC 786
                               v  i i vii  v         i i      i          i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_39241281_3    787 CAAAATCTTTTCTTGCAGAAACGGAAATGCTGACCCTCAAATTCACA--G 834
                           ivvv i   i         iv  v v     i   v       i -- 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_39241281_3    835 AGCTGCAAGGGACACTGAAAAGCCAAAACAATCAAGAAAAAAAA-----A 879
                          iv          v v   v             vv      i  ----- 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_39241281_3    880 AGTTGGAACACTCACACTTTCTGACTTCAGAACTTACTACAATGCTACAG 929
                                iv          i ii i    i            v       
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_39241281_3    930 TAATCAAAATAATATGGTACTGAAA-AAGCATAGACATATAGACCAACAG 978
                                i i i i        iv -   v             i   ii 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_39241281_3    979 CATAAAACTGAGCATACCAAAATAAACTGATACATCTATGACCAACTGAT 1028
                         v   i  i    vi v vi        iv      i    ii   i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_39241281_3   1029 TT---------GTGCCAAGTCCATTCAATGGAGAAATAAGACCCTGCTCA 1069
                           ---------        v           i    v  v vi  vi   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_39241281_3   1070 ACAAATGGTGCTGGGACAACTGGATTTCCACAAGCAAAAGAATGACGTTG 1119
                                                  v?     v            v    
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_39241281_3   1120 GACTCCTAACTCATACCAAACACAAAAATTAACTGAAAATATATCAATGA 1169
                            i    v    i    v i             v     iv    ?v  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_39241281_3   1170 CCTAAATATAAGAGCTAAAACCATAAATCTCTTAGAAGAAAACATAGGGG 1219
                                i             i     v                    ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_39241281_3   1220 CAAATCCTCATGACCTTGGATTTGGCAATGAATTCTTAAGATCTGACACA 1269
                         i     i  i         i  v       iv      -   v      v
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GATATGACACC 602

  chr2_39241281_3   1270 AAAAGCACAAGACAATGAAAGAAAAAACAGATAAATCTGACTTCGTCAAA 1319
                                    -   ii          i        iv      i     
  L1M4_orf2#LINE/    603 AAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_39241281_3   1320 ATTAAAAACTTTCGTTCATCAGAGGACATTATCAAGAAACTAAAAAGATA 1369
                                     i  v v   i      i          v i      i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_39241281_3   1370 AACTTTTGATTGGGTTTAAATGAGAGAAAATATTTGCAAATCATATATTG 1419
                          v i---- iv ------    i                         iv
  L1M4_orf2#LINE/    702 ACCC----ACAG------AATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_39241281_3   1420 GATAAAGGTCTAATATCAAGAATATATAATAAGGATCTCCTAAAACTCAA 1469
                              i  v  vi    v           --  i -   i  v       
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAA--AGAA-CTCTTACAACTCAA 788

  chr2_39241281_3   1470 CATCAAAAACACAAACAACCAAATTAAAAAATGGGCAATGG 1510
                         i vi     v     i    v    ?            v  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.27 (81 / 64)
Gap_init rate = 0.01 (11 / 826), avg. gap size = 3.09 (34 / 11)  

 627 11.20 5.60 0.00  chr2_39241281_39243682     1786  1910 (492)    L1M4_orf2#LINE/L1      777   908 (0)  

  chr2_39241281_3   1786 CTT-CATCTCAA--ATAAATAAATAAATAACT-AATTTAAAAAGGGGCAA 1831
                            -  v     --     v i i       i-    ?     v      
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_39241281_3   1832 TGAATTTGAATAGACATTTCTATAAAGA---CATACAAATGGCCAATAAG 1878
                         v i                  vi     ---i                  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_39241281_3   1879 CACATGAAAAGATGCTTAATATCATTACTGGT 1910
                                         i  i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.03 (4 / 132), avg. gap size = 1.75 (7 / 4)  


3044 24.40 4.09 1.02  chr2_39335221_39340516     3924  4804 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_39335221_3   3924 TGGAAACACATCCTATGCTCATGGATGGGTAGAATCAATATTGTGAAGAC 3973
                               v i    i   i        v  v   v i        v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_39335221_3   3974 GACCATACTGCCAAAAGCAACCTACAAATCCAATGCAATTCCCATCAAAA 4023
                          i v     v  v   vii i     i  i   i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_39335221_3   4024 TACCC--CCATCATTCTTCACAGAACTTGAAAAAACAATCCTAAAATTCA 4071
                          -   -- iii -  i  ii     v    v  ivii             
  L1M4_orf2#LINE/    101 T-CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_39335221_3   4072 TATAGAACCAAAAAAAGAGCCCAC--TAGCCAGAGCAAGACTAAGCAAAA 4119
                            i   -- viv  i ii    v--      i i   vvi i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_39335221_3   4120 AGAACAAATCTGGAGGGATTATCCTACCTGACTTCAAACTATACTATAAG 4169
                                 vi      iv i iv  v  ii i      viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_39335221_3   4170 GCCATAGTCATCAAAGCAGTATGGTATTGGTATAAAAACAGGCATATAGA 4219
                           i i   v     ii    i     i   i    ii i  i        
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_39335221_3   4220 CCAATGGAACAGAATAGAGAAACCAGAAATAAAGCCAAATACTTATAGTC 4269
                         i        i     v    iv           v   v i i    i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_39335221_3   4270 AAATGATCTTTGACAAAGCAAACAAAAACATAAAGTGATGAATGGACACC 4319
                           v    i  i     i vviv   i v   vv i  iv   v i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_39335221_3   4320 TTATTAAACAAATGGTGCTGGTATAATTGGCAAGCCACATGTAGAAGAAT 4369
                         i v  v               v i  i   vv ?       i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_39335221_3   4370 GAAACTGGATCCTCACCTCTCACCTTATACAAAAATCATCTCAAGATGGA 4419
                            ii    i  ii     v    v           i v     i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_39335221_3   4420 TCAAAGACTTCAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAAC 4469
                            ?    i v   v     v  i    i      v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_39335221_3   4470 AC---------------------TGGCTTAGGCAAAGACTTCTCATGACC 4498
                          i---------------------   v        v ii    i -  i-
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GAT- 594

  chr2_39335221_3   4499 AAGAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGAACTT 4548
                          v  vv         v v         iv   i   i   i  v i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_39335221_3   4549 -----AAACTAAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGT 4593
                         -----   i      --   i  ii vv    i  v iv    iv i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_39335221_3   4594 AAACAGACAACCCACAGTGTGGGAGAAAATCTTCACAATCTATACATCCA 4643
                         i  v             vi           v  ii   vii   i   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_39335221_3   4644 ACAGAGGACTAATATCCAGAATCTACAAGCAACTC----AAATCAGCAAG 4689
                          i ii     vi          v  i  iv     ----  v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_39335221_3   4690 AAAAA-ACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACA 4738
                              -     i  i  v  i?    i     v     iv          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_39335221_3   4739 TT-CTCAAAAGAAGATATACAAATGGCTAACAAAAACATGAAAAAAATGC 4787
                           -   v                    i  i  iv         i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chr2_39335221_3   4788 TCAACATCACTAATTAT 4804
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (132 / 80)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.21 (45 / 14)  


 206 31.51 8.22 0.00  chr2_39374898_39378900     1964  2036 (1967)    L1M4_orf2#LINE/L1        2    80 (828)  

  chr2_39374898_3   1964 GGAGAAAAATGCCATGTTCATGGATTTGAAAACCCAGCA------AGATA 2007
                            i i v  v               v   i  ii ii ------    i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_39374898_3   2008 TCAGCTTTTCATAAATTCATCTATAAACT 2036
                         v  iivi i vi     v     i i i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATT 80

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.01 (1 / 79), avg. gap size = 6.00 (6 / 1)  

 882 17.28 7.31 8.31  chr2_39374898_39378900     2335  2635 (1368)    L1M4_orf2#LINE/L1       62   359 (549)  

  chr2_39374898_3   2335 CCAAAATGA---ACAAAATTAAACAAAATTAATTCCTTATACAAATTCCA 2381
                              v   ---   i -  v   iv   -----  i   vv    i   
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGA-TTCAACGCAAT-----CCCTATCAAAATCCCA 105

  chr2_39374898_3   2382 ACAGGCTTTATTTGGACAGAAATTGA-AA-------CTAAGATTTATACG 2423
                         i v v    -    --          -  -------    i   i   i 
  L1M4_orf2#LINE/    106 GCTGCCTTT-TTTG--CAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_39374898_3   2424 GAAATGCATACGACCCAGAATAGCCAAATCAACTTTGAAAAAGAA---CA 2470
                                 viv                 v   ii           ---  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_39374898_3   2471 AATTTAGAATATTTATATTAAAAATTTATCTTAAATTTGACTTAAAATTT 2520
                           v  i  iv i i i i ---------  ii  -   ----i    i  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACT---------TCCCAA-TTT----CAAAACTT 238

  chr2_39374898_3   2521 TACTATAAAGTTATGGTAAATCAAGAC--TGTGGTACCAGCATAA----A 2564
                         -    i    i  ii    -       --        ii      ---- 
  L1M4_orf2#LINE/    239 -ACTACAAAGCTACAGTAA-TCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_39374898_3   2565 GACATATA--TCAATGAAACATAATAATGAGTCAAGAAATAAACCCTTCT 2612
                                 --      i  i v   viv     v            v vi
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_39374898_3   2613 ATTTATGGTCAATTGACTTTTAA 2635
                                         i   ii 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGA 359

Transitions / transversions = 1.89 (34 / 18)
Gap_init rate = 0.05 (16 / 298), avg. gap size = 2.94 (47 / 16)  

2292 19.79 1.74 3.99  chr2_39374898_39378900     2947  3522 (481)    L1M4_orf2#LINE/L1      346   908 (0)  

  chr2_39374898_3   2947 CAACTGACTTTTGACAAAGTTGCTGCAGCAATTCGACAAGGAAAGAATAG 2996
                            i   i   i     i v   iivii v    i iii           
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_39374898_3   2997 TCTTTTCAACAAATGATACTAGGACCATTGGATATCCATATGCAAAACAA 3046
                                        i i  i    v i      ?   i        -i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GA 444

  chr2_39374898_3   3047 ACAACAAACACACACAGT-AGACAGACACCTCACACAATATAGCAAAATT 3095
                          ii -----------   -i   vvvi         v     vv      
  L1M4_orf2#LINE/    445 ATGA-----------AGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_39374898_3   3096 AACTCAAAATGGA-CAAAGACCAAAATGTAAGCATTAAAACTGTATAACT 3144
                                      -  ?     v         vii       i  v    
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_39374898_3   3145 TCTAGAAAAAAAAAAAGAGGAGAAAAATCTTTGTGACTTTCAGTTATGCA 3194
                         ii     i    v v  i? v---       i     i  vi    v   
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGT---AAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_39374898_3   3195 --GATTTCTTAGATATGACACCATAAGCATGATTCATAAAAGAAAAAATA 3242
                         -- i                   v     ii viv i             
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_39374898_3   3243 GATAAAATGGAATTTATCAACATTAAAATCTTTTGCTCCTCAAAAAATTT 3292
                               v    v  i     v       v      iv i     ii ---
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA--- 677

  chr2_39374898_3   3293 CCCCATTAAGAAAATGAAAAGCTAAGCCACAGACTAAAGAAAAATATTAG 3342
                          v i  i      i       vi  v       v iiiii        v 
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_39374898_3   3343 CAAATCTTATATCTGATAAAATATTTGTATCCAGAATACATAGAGAGCAT 3392
                               v            iiv i              i   i   -- i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA--AC 775

  chr2_39374898_3   3393 GCTTACAACTCAATAG---GAGGTTAAACAACCCAATTTAAAAATGGACA 3439
                         v              i---i i vi   i         ?        i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_39374898_3   3440 AAAGATGTGAATAGACATTTTACCAAAGA---TACACAAATGTCTACTAA 3486
                           i   v             iv       ---  i       v i v   
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_39374898_3   3487 GCACATGAAAGGATGCTGTTAGCCATTAGGGAAGTG 3522
                                   i      --i i -  i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCT--CAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (71 / 39)
Gap_init rate = 0.02 (12 / 563), avg. gap size = 2.75 (33 / 12)  


 895 21.93 3.35 5.95  chr2_39523738_39526738.rev      581   849 (2152)    L1M4_orf2#LINE/L1       16   277 (631)  

  chr2_39523738_3    581 TGTTCATGGATTGGAAGACTCCACATAGTAAATATGTCAGTTCTTTCCAA 630
                                             iv i  v  v  v   v  i v  ii    
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_39523738_3    631 ATTGATCTATAGATTTAATGTACTTCCAAATAAAAGTCCCAACAGCAGAT 680
                                  i     i  i i v i  v vi    -     i v  ---i
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCCAGCTGC---C 111

  chr2_39523738_3    681 TTTTTTTTTTAAACAGACAAGCTGG--CTCAAATTTATATGGAAAGGCAA 728
                               vivv   iv         i--  v     i         v    
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_39523738_3    729 AGGACCTTTGTT-GCCAAAGCAACTTTGAAAAAGTA----AAAGTTGGAG 773
                         i     ivviv -      i   ii         v ----          
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_39523738_3    774 GAATCACAAAATTATTGTGATTGTAAATTTAAAATTTACTATAAAACTAC 823
                           v     ------i ---- ivi  v  i    i      i   i    
  L1M4_orf2#LINE/    212 GACTCACA------CT----TCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_39523738_3    824 AATAATC--GGCCGGGCGTGGTGGTGGC 849
                          i     -- i --i i     iv    
  L1M4_orf2#LINE/    252 AGTAATCAAGAC--AGTGTGGTACTGGC 277

Transitions / transversions = 1.46 (35 / 24)
Gap_init rate = 0.03 (9 / 262), avg. gap size = 2.78 (25 / 9)  

1415 24.34 3.34 2.63  chr2_39523738_39526738.rev     1138  1556 (1445)    L1M4_orf2#LINE/L1      244   665 (243)  

  chr2_39523738_3   1138 AAAATTACACTAATCAAGACTGTATAGTGTAGGTA-AGAGATAAACACAC 1186
                            ii    v          v  i i  iiv  i - ii    i   i -
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA- 292

  chr2_39523738_3   1187 AATCACTAGATCAAT---ATAGA-TCAACATGGGGTCCAGAAATAGATCC 1232
                         ------         ---     - ii ---- i           i i  
  L1M4_orf2#LINE/    293 ------TAGATCAATGGAATAGAATTGA----GAGTCCAGAAATAAACCC 332

  chr2_39523738_3   1233 ACACAAATATAGCCAATTCATTTTTGACAAAGGTGG-AAGTCAGTTCAAT 1281
                          i   vv   i i     v     i     i    v-   v vi      
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_39523738_3   1282 GAAAGGAAAATTGACTTTTCCACAAATGATAA-GAAAGAGTTGGACATAT 1330
                          iiiii i   v v      v       i iv- ii v ii    i ?vi
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_39523738_3   1331 ACATGCAAAAAAATGTACCTAAACTTAAACTGTACACCTTACACAAAAAT 1380
                                   i    v vi ii  iivv  ivi     v  i        
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_39523738_3   1381 GATCTCAAAATGTATCATGAAACTAAATGTAAAAAC-------ATAAAAC 1423
                         v v         v    ?ii v          i i -------       
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_39523738_3   1424 TTTTAGAAGAAAACACAGGAGAAAATATTTGTGACCTGGAGTTAAGCAAA 1473
                          i             i   ? v    v  i       v i    i    v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_39523738_3   1474 AAGATCTTGGATGTGATACCAAAAGCACAATTCATAAAAGAAACTATTGA 1523
                         iivv    i   i   i             viv i        vv  v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_39523738_3   1524 TAAATTGGACTTTATCAAAAATAAAAACTTTTG 1556
                                     i       v            
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.68 (62 / 37)
Gap_init rate = 0.02 (8 / 422), avg. gap size = 3.12 (25 / 8)  

 359 18.83 8.79 16.32  chr2_39523738_39526738.rev     2283  2521 (480)    L1M4_orf2#LINE/L1      688   908 (0)  

  chr2_39523738_3   2283 AGAGTGAAACTTCGTCTCAAAAAA----AAAAAAAAATTGCAAATCATAT 2328
                          i       vvv iv i  v i  ---- i    v v             
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_39523738_3   2329 ATCTGACAAAGGACTCATATATAGAATATATATATATATATATATATATA 2378
                               i  i     ii   vi          ------------------
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATA------------------ 769

  chr2_39523738_3   2379 TATATATATATATATATGAAGAACGCTCATAACTCAGTAAGAAAA---TA 2425
                         ------------------      v  i i      i   v    ---i 
  L1M4_orf2#LINE/    770 ------------------AAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_39523738_3   2426 AATATTCCAGTTAAAAACATGGATGAAAGACTGGAA--AACAGTTCATCA 2473
                             vi   i  ?    -    iii  i  i v   --i   v   vi  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_39523738_3   2474 AAGGA----------TGGCAGGTAAGCACATGAATAGA--CTAAGAGCAT 2511
                            i ----------    vii            v   --  v i--   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA--CAT 898

  chr2_39523738_3   2512 CATTAGTCAT 2521
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.59 (27 / 17)
Gap_init rate = 0.04 (8 / 221), avg. gap size = 7.50 (60 / 8)  


3213 26.74 0.88 0.55  chr2_39714062_39720443.rev     4986  5890 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_39714062_3   4986 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5035
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_39714062_3   5036 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5085
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_39714062_3   5086 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ATATTAAAGTTCAT 5134
                          v   iivi i  i  ii     v v  v  i-  -  vi    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_39714062_3   5135 ATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCTAAAGA 5184
                               viiv  ii  v  v v  v     iv     i i ivvvi    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_39714062_3   5185 ACAAAGCTGGAGGCATCATGCTATCTGATTTCAAACTATACTACAAGGCT 5234
                               i      vv   ii  vi ii        viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_39714062_3   5235 ACAGTAACCAAAACTGCATGGTACTGGTACCAAAACAGAGATACTCACCA 5284
                                i   i  v ii         i iv ii i   v   ivv i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_39714062_3   5285 ATGGAACAGAAC--AGAGTCCTCAGAAATAATACCACATATCTACAACTA 5332
                               i    i--       --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_39714062_3   5333 TCTGATCTTTGACAAACGTGACAAAAACAAGAAATGGTGAAAGGATTCCC 5382
                         vi    i  i     iv   v   i v  vvv     v     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_39714062_3   5383 TATTTAACAAATGGTGCTGGGAAAACTGGCTTGCCATATGTAGAAAGCTG 5432
                          v  i                 v      v v?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_39714062_3   5433 AAACTGGATCCCTTCCTTACACCTTATACAAAAAATTAATTCAAGATGGA 5482
                           ii    i    v   i     v          -    i    i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGA 496

  chr2_39714062_3   5483 TTAAAGACTTAAACGTTAGAGCTAAAACCATAAAAACCCTAGAAGAAAAC 5532
                          i ?    i    i  v           i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_39714062_3   5533 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5581
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_39714062_3   5582 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5631
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_39714062_3   5632 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5681
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_39714062_3   5682 CAGGCAACCTGCAGAATGGGAGAAAATTTTTGCAATCTACTTATCTGACA 5731
                         v  i     ii                v       vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_39714062_3   5732 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5781
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_39714062_3   5782 AAAACAA----CCCCATCAATAAGTGGGTGAAGGATATGAAGGGACACTT 5827
                           i    ----   v  i? v  i    ii      v    vi    i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_39714062_3   5828 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5877
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_39714062_3   5878 CATCACTGCCCAT 5890
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (137 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3180 26.64 1.00 0.33  chr2_39946740_39953422.rev     5291  6191 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_39946740_3   5291 GGAAAAATATTCCATGCTTATGGATAGAAAGAATCAATATCGTGAAAATG 5340
                              i    i     i i      v i    v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_39946740_3   5341 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGCT 5390
                           v     v      v i  i  i        i  v  i  i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_39946740_3   5391 ACCATTGACCTTCATCACAGAATTAGAAAAAACT-ACTTTAAATTTCATA 5439
                         v   vivi    iv ii     v v  v  i-  - iii    v      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr2_39946740_3   5440 TGGAACCAAAAAATAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAGAA 5489
                              viiv  iiv v  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_39946740_3   5490 CAAAGCCGGAAGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5539
                              ii   i vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_39946740_3   5540 CAGTAACCAAAGCAGCATGGTTCTGGTACCAAAACAGACAAATAGACCAA 5589
                               i   ii   ii    v    i iv ii i     v     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_39946740_3   5590 TGGAACAGAACAGAGGCCTCAGAAGTAACACCACACATCTACAACCATCT 5639
                              i    iv   ivii     i   vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_39946740_3   5640 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 5689
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_39946740_3   5690 TTAATAAATGGTGTTGGGAAAACTGGATAGCCATATGCAGAAAACTGAAA 5739
                          i  i        i     v         ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_39946740_3   5740 CTGGACCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGGATTAA 5789
                         i         v   i i   v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_39946740_3   5790 AGACTTAAACGTAAGA-CCAAAACCATAAAAACCCCAGAAGAAAACCTAG 5838
                             i    i      - i     i      vi ii          v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_39946740_3   5839 GCA-ATGTCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAAC 5887
                          ?i- vi  -   iv   v v  vv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_39946740_3   5888 ACCAAAAGCAATTGCAACAAAAGCCAAAACTGACAAATGGGAT---AT-- 5932
                                   vvv          vv    iv  i    v   i---  --
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_39946740_3   5933 -AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGCATGAACAG 5981
                         -       i -   i  ii vv    i  v       vv ivi    v  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_39946740_3   5982 GCAACCTACAGAATGGGAGAAATTTTTTGCAGTCTATCCATCTGACAAAA 6031
                         i     i               v v      ivii  vi      i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_39946740_3   6032 GGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAA 6081
                          i  vi          v  i  i     ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_39946740_3   6082 ACAAACAACCCCATCAAAAACTGGGCAAAGGATATGAACAGACCCTTCTC 6131
                              i     v  i?    v            v    i    vi     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_39946740_3   6132 AAAAGAAGACATGTATGCAGCCAATAAACATATGAAAAAAAGCTCATCAT 6181
                         v        i  ii viii        i  i       i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_39946740_3   6182 CACTGATCAT 6191
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 1.50 (12 / 8)  


1786 22.29 4.09 1.84  chr2_39964031_39970719.rev        2   490 (6199)    L1M4_orf2#LINE/L1      331   830 (78)  

  chr2_39964031_3      2 CCACACATATACAGTCAATTGATTTTCAACAAAAGTGCCAAGAACATGCA 51
                            i    v  ii              i    ii         v   v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_39964031_3     52 GTGGATAAAGGACA-TATCTTTAATTAATAATGTTGGAAAAACTGAATAT 100
                         i   iv    i i - v i  i  iv   ii  i   i v     i   ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_39964031_3    101 CCACATGCCAAAAAATGAAATTAGACCCCTACTTCATGCCATATATAAAA 150
                                 v   i      i  i         i   ii       i    
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_39964031_3    151 ATCATCCCAAAATTGATTA-------AAACATAAGATCTGAAACCATGAA 193
                           i v i      v   i -------   ii     v  i    i  i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_39964031_3    194 ATTACTAGAAGAAAACATAGGAGGAAAGCTCTACGAAAC------TTGGG 237
                          i vi                ? v   --   v  vi  ------  i  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGG 578

  chr2_39964031_3    238 CAATGATTTTTTTTTGGAAATGAACCCAATAGTACAGGCAACACAAGAAA 287
                              i   i  ---i  v    vv    v  i   i      v      
  L1M4_orf2#LINE/    579 CAATGGTTTCTT---AGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_39964031_3    288 AAAAAATACACAAGTGGGATTACATCAAA-CTAAAAA----TGT-CTACA 331
                            ---  v i  i v   i v       -i      ----   -  v  
  L1M4_orf2#LINE/    626 AAA---TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_39964031_3    332 CAAGAAATAAAACAGCAAAATGAAGAGACAACCTATGGAATGGTAGAAAA 381
                         v i  v iv v-  iv   i    i        i ii      v      
  L1M4_orf2#LINE/    673 AAGGACACTAT-CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_39964031_3    382 TATTTCCAAACCATACATCTGATAAGGGTTTAATATTCAAAATATGTAAG 431
                              v    i    i            vi vi   i  i     i   i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_39964031_3    432 AAACTCAAACAACTCAATAGAACAAAAACAAATAACTCAATTTAAAAATA 481
                         i     vv           iv v   i         i     ?      i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_39964031_3    482 GGCAAGAGA 490
                              ii  
  L1M4_orf2#LINE/    822 GGCAAAGGA 830

Transitions / transversions = 1.86 (69 / 37)
Gap_init rate = 0.02 (10 / 500), avg. gap size = 2.90 (29 / 10)  

2880 27.90 2.59 0.45  chr2_39964031_39970719.rev     5309  6197 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_39964031_3   5309 TGGAAAAACATTTCATGCTCATGAATAGGAAGAATCAATATTATGAAAAT 5358
                               i i  ii    i     i  v      v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_39964031_3   5359 GGCTATACCGTCCAAAGTAATTTACAGATTCAATGATATCCCCATCAAG- 5407
                            v    ivi     v i  i           i vv     i     i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_39964031_3   5408 --TTAGCATTGACTTTCATCACAGAATTAGAAAAAATTATTTTAAATTTC 5455
                         --ii   --  v    i- ii     v v  v  iv v  ii    v   
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_39964031_3   5456 ATATGGAACCAAAAAAGAGCCTATGTAGTCAAGACAATCCTAAGCAAAAA 5505
                                 viiv  ii  v  vivi   i   i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_39964031_3   5506 GAACAAAGCTGGAGGCATCGTGCTACCTGACTTCAAACTATACTACAAGG 5555
                                 i      vv  iii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_39964031_3   5556 CTACAGTAACCAAAACATCATGGTATTGGTAGCAAAACAGATATATAGAC 5605
                                  i   i   vii     i   i vv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_39964031_3   5606 CAATGGAACAGAGCAGAGGCCTCAGAAATAACACCACACATCTA----CA 5651
                                 i   iiv   ivii         vv   i    i  ----  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_39964031_3   5652 A---ACCT--GACAAAAA---CAAG------CAATGGGGAAAGGTTTCCC 5687
                          --- ii --     iii---    ------            iv vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_39964031_3   5688 TATTTAATAAATGGTGTTGGGAAAAATGGCTAGCCATATGCAGAAAACAG 5737
                          v  i  i        i     v  v   v  ?   i     i  i vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_39964031_3   5738 AAACTGGACCCCTTCCTTATACCTTATACAAAAATTAACTCAGGATGGAT 5787
                           ii         v   i i   v                  ii      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_39964031_3   5788 TAAAGCCTTAAATATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5837
                         i ?  v i     i     v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_39964031_3   5838 TAGGAAACAACATTCAGGATACAGGCATGGGCAAAGACTTCGTGACTAAA 5887
                             ?ivv  iv   iv  iviv  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_39964031_3   5888 ACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATATAAT 5937
                                     vvv          vv     v  i    v   iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_39964031_3   5938 TAAACTAAAGAGCTTCTGCACCACAAAAGAACCTATCATCAGAATGAACA 5987
                         i   v v  i i   i  ii iv    i  vv      vv i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_39964031_3   5988 GGCCACCTACAGAATAGGAGAAAATTTTTGCAATCTAGCCATCTGACAAA 6037
                          i v   i       i         v       vii vvi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_39964031_3   6038 AGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACTAGAAAAA 6087
                         i i  vi          v  i  i     ivv    -i i v  iv    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAAA 796

  chr2_39964031_3   6088 AGA--AACCCCCCTGTCAAAAAGTGGGCAAAGGATATGAGCAGACACTTC 6135
                            --  ivv   vi i?    i            v   ii     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_39964031_3   6136 TCAAAAGAAGACATTTATGTGGCCAAGAAATATATGGCAAAAAGCTCACC 6185
                           v        i  vi vi       v  ii i   iv  i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_39964031_3   6186 GTCACTGGTCAT 6197
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.70 (27 / 10)  


2745 26.28 3.45 0.71  chr2_40073909_40076001      759  1599 (493)    L1M4_orf2#LINE/L1        3   866 (42)  

  chr2_40073909_4    759 GAAAAATACTTCGTGCTTATGGATTGGAAGAATTGGTATCATTAAAATGG 808
                             i   iii i  i i             v  ii   ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_40073909_4    809 CCATACTGCCCAAAGCAATCTACAGATTCAGTGCTACTCCTATGAAGCTA 858
                          v     v      vii             ii  v ii     v  iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_40073909_4    859 CCAACATCATTTTTCACAAAATTAGAAAAACATATTCTAAAATTCATATG 908
                            i vv v     ii  i  v v  v  i vv  i              
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_40073909_4    909 GAA---CCAAAAAGCCGGAATAGCCAAAGCAACCTTAAGCAAAAAGAACA 955
                            --- v iii v  i           i   i   i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_40073909_4    956 AAGCTGGAGGCATCACATTACCTGACTTCAAA--TTA-TACAAGGCTACA 1002
                            i      vv     i v  ii i      --   -     i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_40073909_4   1003 GTAACCAAAACAGCATGGTACTGGTAAAAAAAACAGACACATAGACAAAT 1052
                             i   i    ii         i v  ii -i     i     iv   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAAT 301

  chr2_40073909_4   1053 GGAACAGAATAGAGAACTCAGAAATAAAGC--TACATTCCTACAGCCATC 1100
                             i     v    iii          v --      --  ii i  vi
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAAT 349

  chr2_40073909_4   1101 TGATCTTTGACAATGTTGACAAAAATAAGCAACAGGAAAATAACTCCCTA 1150
                             i  i     v v  v   i vi vv   ii  i   v  ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_40073909_4   1151 TTCAATAAATAGTGCTGGGATAGCTGGTTAGCTGTATGCAGAAGAATCAA 1200
                              i    i         i i    v  ? iii     i      v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_40073909_4   1201 ACTTTACCCTGACCTTTCACCATATATAAAAATTAA-----GATAGATTA 1245
                         ii vv    iv    iv         i         -----i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_40073909_4   1246 AAGATTTAAATGTAAGACCTCAAAGTACAAA--TCCTAGAAGAAAACCTA 1293
                         ?   ii           v  v   v  i   --  i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_40073909_4   1294 GGAAACAACATTCTGGACATTGGCCTTGGGACAGAATTTATGGCTAAGTC 1343
                           ?ivv  iv   vv   v    vi v  v vv iv  iv i v  v v 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_40073909_4   1344 CTCAAAAGCAGTTGCAACAAAA----AAATTGACAAGTGGGACCTAATTA 1389
                         vi        vvv         ----    v  i  i v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_40073909_4   1390 A--CTAAAGAGCTTCTACACAGCAAAAGAAATTATGAACAGAAT--AAAG 1435
                          --i    i -   i iii vv    i  v i   v  v i i --    
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_40073909_4   1436 ACAACCTACAGAATGGGAGAAAATATTTGCAAATTATTCATGTTACAAAG 1485
                               i                           i  vi  v v i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_40073909_4   1486 GTCTAACATACAGAATTTATCAGGA--TCTTAAGCAATTGGATATGAAAA 1533
                          v  vii  v      v   v i  --     --   i vi   vv    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAAA 796

  chr2_40073909_4   1534 AATCAAATAACCCCATTATAAAATGAGCAAAAAACATGAA----CAATTC 1579
                          iv          v   ?v      i     ii iv    ----  v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_40073909_4   1580 TCAAAAGAAGACATACAAGT 1599
                           v        i      i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAAT 866

Transitions / transversions = 1.36 (125 / 92)
Gap_init rate = 0.02 (15 / 864), avg. gap size = 2.33 (35 / 15)  


 269 21.21 1.52 0.00  chr2_40147641_40153910.rev        1    66 (6204)  C L1M4_orf2#LINE/L1   (31)   877   811  

C chr2_40147641_4     66 ACTTAAAAAT-AGCAAAAGACGTGAACAGACACTTCTCAAAAGAAGACAT 18
                          i ?      -i     i  iv    i     i     v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

C chr2_40147641_4     17 GCAAGTGGCCAAAAAAC 1
                         i   i       v  i 
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGC 877

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1)  

3112 27.20 0.66 0.66  chr2_40147641_40153910.rev     4871  5778 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40147641_4   4871 TGGAAGAACATTCCATGCTCATGGGTAGGAAGACTCAATATCATGAAAAT 4920
                              ii i  i     i      i v        i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40147641_4   4921 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4970
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40147641_4   4971 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5018
                          v   vivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_40147641_4   5019 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5068
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_40147641_4   5069 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAAGGC 5118
                                i      vv    i  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_40147641_4   5119 TACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGATC 5168
                                 i   i    ii        ii iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_40147641_4   5169 ATTGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5216
                          v     i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_40147641_4   5217 ATCTGATCTTTGACAAACCTGAGAAAAAGAAGCAATGGGGAAAGGATTCC 5266
                          vi    i  i     ivv  vv  i vv vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_40147641_4   5267 CTATTTCATAAATGGTGCTGGGAAAACTGGCTAGCCCTATGTAGAAAGCT 5316
                           v  iv i              v      v  ?  vi   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_40147641_4   5317 GAAACTGGATCCCTTCCTTACACCTTATAGAAAAATCAATTCAAGATGGA 5366
                            ii    i    v   i     v    v      i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_40147641_4   5367 TTAAAGACTTAAACGTTAGACCTAAAACCATACAAACCCT-AGAAGAAAA 5415
                          i ?    i    i  v   v       i   -    i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAA 545

  chr2_40147641_4   5416 TCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5465
                         iv    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_40147641_4   5466 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA-TCC 5514
                         vi            vvi          vv     v  i    v   - i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_40147641_4   5515 ACTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5564
                          iiv   i    i -   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_40147641_4   5565 ACAGGCAACCTACAAAATGGGAGAAAAATTTTGCAACCTACTCATCTGAC 5614
                          v  i     i   i            vv       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_40147641_4   5615 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5664
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_40147641_4   5665 AAAAACAAACAAGCCCCTCAAAAAGCGGGCGAAGGACATGAATAGACACT 5714
                            i     i  v  vv i?    ii    i     iv          i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_40147641_4   5715 TCTTAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5764
                            iv        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_40147641_4   5765 TCATCACTGGCCAT 5778
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2771 28.35 1.21 1.43  chr2_40205683_40211727.rev     4650  5559 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40205683_4   4650 TGGAAAAACATTTCATGTTCATGGATAGGAAAAATCAGTATCATGAAAAT 4699
                               i i  ii             v    i v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40205683_4   4700 GGCCATACTGCCCAAAGCAATTTATTGATTCAATGCTCTTCCTATTAAAC 4749
                            v     v      vii  i  iv       i  vv i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40205683_4   4750 TACCA-CTGACATTCATCACAGAACTAGGAAAAAAAACT-ATTTTAAAAT 4797
                          v   -   v v  i- ii     v v ---- v  i  -  ii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTG----ACAAGCTGATCCTAAAAT 145

  chr2_40205683_4   4798 TCACATGGAACCA-AAAGGAGCCTGAATAGTCAAGACAATCCTAACCAAA 4846
                            i      vii-  i   v  v      i   i      i i vv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_40205683_4   4847 AAGAACAAAGCTGGAAGCATCACGCTACCCAATTTCAAACTATACTACAG 4896
                                   i    i vv    i  v            viv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_40205683_4   4897 GGCTGCAGTAGCCAAAACAGCAAGATACTGGTTCAAAAGTGCACACATAG 4946
                         i   i     ii   i    iiv i      ivi  iii iv   i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_40205683_4   4947 ACAAACGGGACAGAATAGGGAACCCAGAAATAAGACTGCATACCTGCAAC 4996
                          iv  i  i i     v i  ii          iv iii i ii iiiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_40205683_4   4997 TATCTGATCTTTGACAAACCTGACAAAAATGAGCAAGGAGGAAAGAAT-- 5044
                         i vi    i  i     ivv  v   i viivv   v i         --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_40205683_4   5045 TCCATATTCAGTAATTGGTGCTCCGATAACTGGCTAGCCATATGCAGAAG 5094
                           -- v    ii  v       vv  i      v  ?   i     i   
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_40205683_4   5095 ATTGAAACTTGACCCCTTCCTTACAACTTATACAAAAATTAACTCAAGAT 5144
                          v    ii v       v   i   v v                   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_40205683_4   5145 AGATTAAAGACTTAAATGTAAAACTCAAAACTATAAAAACCCTGGAAGAC 5194
                         i   i ?    i         i vii            vi i i     v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_40205683_4   5195 AACCTGGGC--AAAACAATTCAAAACATAGGCATGAGCAAAGATTTCAT- 5241
                            v i  ?--   v --   ivi  v v  vv ii    v i    v -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_40205683_4   5242 GATGAAGACATGAAAAGCAATTGCAACAAAAGCAAAAATTAACAAATGGG 5291
                            - v    iv       vvv          v      vi i    v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_40205683_4   5292 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTATCAACAAA 5341
                          ii v  i   v v  i i   i  ii vv    i  v i      v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_40205683_4   5342 ATAAACAGACAACCAACAGAATGGGAGAAAACTTTTGGGAACTATGCATC 5391
                         i i  v        v                iv    vi  ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_40205683_4   5392 TGACAAAGTTCTAATATCTAGCATCTGTAAGGAACTTAAATAAGTTTGCA 5441
                            i  i vv  vi    i  v  v i   i     ivv i  v ---  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CA 787

  chr2_40205683_4   5442 AGAATCAAA---CAAGCAATCCCATTAAAAAGTGGTCAAATAACATGAAT 5488
                          v   v   ---   ii  i  v   ?    i   v    vi iv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_40205683_4   5489 AGTTGCTTCTCAAAAGAAGGCATACATGTGGTCAGCAATCATCTGAAAAA 5538
                           viii     v       ii     vi   i  ii  v  iv      i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_40205683_4   5539 AAGCTCAACGCTACTGATTAT 5559
                          v       iii ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (153 / 101)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


3022 27.44 1.33 0.44  chr2_40211905_40216023.rev     1278  2177 (1942)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40211905_4   1278 TGGGAAAACATTCCATGCTCATGGATAAGAAGAATCAATATTATGAAAAT 1327
                            i  i i  i     i        vi     v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40211905_4   1328 GGCCATACTGCCCAAGGTAATTTAAAGATTCAGTGCTATCCTTATCAAGC 1377
                            v     v     iv i  i  v       ii  v    i      iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40211905_4   1378 TTCCATTGACTTTCTCCACAGAATTAGAAAAAACTGCTT-TAAATTTCAT 1426
                          i   vivi i  i iii     v v  v  i-   v i-    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_40211905_4   1427 ATGGAAC--CAAAAAATAGCCCATA-TAGCTAAGACAATCCTAAGCAAAA 1473
                               v--   iii ---    v -    i  i      i i iv  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_40211905_4   1474 AGAACGAAGCTGGAG---TCAT-CATGCTGACTTCAAACTATACTACGAG 1519
                              i   i     ---   i- v v ii i      viv      i i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_40211905_4   1520 GCTACAGTAACCATAACAGCATGAACCTGGTACCAAAACAGATATATAGA 1569
                                   i  vi    ii  ivv    i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_40211905_4   1570 CCAATGGAACAGAACAGGGGCCTCAGAAATAACACCACACATCTACAACC 1619
                         i        i    iv i ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_40211905_4   1620 ATCTGATCTTTGACAAACCTGACACAAACAAGCAATGGGGAAAGGATTCC 1669
                          vi    i  i     ivv  v  vi v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_40211905_4   1670 CTATTTAATAAATGGAGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 1719
                           v  i  i      v i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_40211905_4   1720 GAAACTGCACCCCTTCCTTACACCTTATACAAATATTAACTCAAGATGGA 1769
                            ii  v      v   i     v        v          i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_40211905_4   1770 TTAAAGACTTTAAAGTAAGACCTAAAACCATAATATCCCTAGAAGAAAAC 1819
                          i ?    i v  v      v       i    v ii i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_40211905_4   1820 CTAGGCAATAACATTCAGGACATAGGCATGGGCAAAGACTTCATGACGAA 1869
                         v    ?ivv  iv   iv   v v  vv i     v ii   v iivv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_40211905_4   1870 AACACCAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGGGATCTAA 1919
                         i            vvi          iv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_40211905_4   1920 TTAAAATAAAGAGCTTCTGCACAACAAAAGAAACTATCATCAGAGTGAAC 1969
                          i     v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_40211905_4   1970 AGGCAACCTACAGAATGGGAGAAATTTTTTGCCATCTATCCATCTGACAA 2019
                           i     i               v v     v vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_40211905_4   2020 AGGGCTAATATCCAGCAAGTATAAGGAACTTG---AATTTA-CAAGAAAA 2065
                         i  i  vi       v vi     i     iv---  i i -i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_40211905_4   2066 AAACTAACAACCCCAACAAAAAGTGGGCAAAGGATATGAAAAGACACTTC 2115
                          i  v  i     v vi?    i            v    v     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_40211905_4   2116 TCAAAAGAAGACACTTATGTGGCCAAAAAACACATGAAGAAAAGCTTATC 2165
                           v        i ivi vi       v  i        i i v   i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_40211905_4   2166 ATCACCGATCAT 2177
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  

2599 26.79 7.52 0.82  chr2_40211905_40216023.rev     2777  3627 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40211905_4   2777 TGGAAAAACATTCCATGCTCATAAATTGGAAGAATCAATATTGTTAAAAT 2826
                               i i  i     i    ii         v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40211905_4   2827 GGCCATTCTGCCCAAAGCAATCTACAGATTCAACACTATTTCTACCAAGC 2876
                            v  v  v      vii               i v  ii   i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40211905_4   2877 TACCAA-TGTCACTTTTCACAGAATTAGAAAAAACTG-TTCTAAAATTCT 2924
                          v   i-  i -i    ii     v v  v  i-   - i         v
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_40211905_4   2925 TATGGCATTATAAAAGAGTTCGAAGGGCTAAAACAATCTTAAGCACAAGA 2974
                              v v ii  ii  viiv   vi  i           i iv vi ii
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_40211905_4   2975 AACAAAGCCAGAGACATCACATTATCCAACTTCAAACTATATTACAAGGC 3024
                                iii   ivv     i vi    i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_40211905_4   3025 TACAGTAACCAAAGCTGCATGATACTGGCATGAAAACAGATACACAGATC 3074
                                 i   ii v ii  i         i ii i   i i i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_40211905_4   3075 AACGGAAAATAATAGAGATCCCAGAAATAAAGTGGCACAGCTACAGCCAT 3124
                           i    v v   v    vi           vivii   vi  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_40211905_4   3125 CTGATCTTTGACAAAGTTGACAAAAATAAACGATAGGGAAAG----GTCT 3170
                         i    i  i     i v  v   i vi vv i  i       ----    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_40211905_4   3171 CTGTCTTCAATAAATGGTGC--AGATAGTTAGCTAGCTATATGCAGAAGT 3218
                         i ----    i         --i  i ii i v  ? i i     i   v
  L1M4_orf2#LINE/    399 TT----TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_40211905_4   3219 ATGAAGCTGGACCCTTACCTTTCTGTATATACAGAAATTAACTCATGATG 3268
                               i       i     iv vvi       i           vi   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_40211905_4   3269 GATTCAAGATTTAAATGTAGGACCTGAAAACTATAAACATCTTAGGGGGA 3318
                            iv?   ii        i  v  -           vv      ii i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAA 543

  chr2_40211905_4   3319 AA---AAAAAAAAA--------AC-------TAGGAGATACCCTTCTGGG 3350
                           --- ii?iv   --------  -------    vi  ivii ii i i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_40211905_4   3351 TATTA--------GCCTTGGCAA--------AGAATTTGTGA-TTA-AGT 3382
                            v --------  vivi    -------- i   vvi i -  i- v 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_40211905_4   3383 TC-TCAAAA---ACAATT-----GCAACAAAA------AT-AAAAAAGTA 3416
                           -      --- v  i -----  vv    i------  -  i     i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_40211905_4   3417 AACAGACAACCTAAAGGATGGCAGAAAATATTCACAAACTATGCATCAGA 3466
                           v        i v  i    v          ii    ii  ii   v  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_40211905_4   3467 CAAAGGTCTAATGTTCAGAATCTATAAGAAACTT----AATTCAAAAAAC 3512
                         i  i  v  vi i i      v     ii    i----  i    v  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_40211905_4   3513 AAAAAACAAATAACCCTATTAAAAAGTGGACAAAGGACATGAACAGACAC 3562
                             i           v   ?    i   i       iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_40211905_4   3563 TTCTCAAAAGAAAACATACAAGTGGCCAATAAACATATGAAAAAATGCTC 3612
                              v      i i      i          i  i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_40211905_4   3613 AGTGTCACCAATCAT 3627
                          iii   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (151 / 73)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.38 (71 / 21)  


3026 26.15 2.12 0.67  chr2_40219791_40224036.rev     2860  3754 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40219791_4   2860 TGAAAAGATATTCCATGTTCATGGATTGGTAGAATCAATCTTTTTTTAAT 2909
                           i        i                 v   v i   v  v  vvi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40219791_4   2910 GTCCATACAACCCAAAGCAATATACATATTTAATGCAATCACTATCAAAA 2959
                          v v    vv      vii  v    v   i  i      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40219791_4   2960 TACCAATGACATTATCCACAGAAGT--ATAAAAAAATCCTAAAGTTTATG 3007
                          v   iivi v  v iii     i -- i  ivvi        i  i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_40219791_4   3008 TGAAAA----AAAGACCCAGCATAGCCAAAGCTATCCTAAGCAAAAGAAA 3053
                           i   ---- ii       v         i v   i i iv  i ii  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_40219791_4   3054 CAAACCTGGAAGAACCACATTACCTAACTTTAGCTCACACTACAAAACTA 3103
                             vi    i  vi    i v  i  i  i ivv vi        i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_40219791_4   3104 TAATAACCAAAACATCATGATACTGGCATGAAAAAAGACATATA-ACCAA 3152
                         i i   i   i   vii  i         i ii v         - i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_40219791_4   3153 TGACATAGAATAAAGAACCCAGAAACAATTCCATACATCTACAGTGAATG 3202
                           iv       vi   ii       i  vi        i  ii  v   v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_40219791_4   3203 CATTTTCAACAACAGTGACAATAACATACATTGGGAAAAGAA--GTCTCT 3250
                         v      i    vi   v   v v   v  v    i      --    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_40219791_4   3251 TCAATAAATAGTGCTGGTAAAACTAGATATCCCTATGTGGAAGGATGAAA 3300
                             i    i       v v    i    ?  vi   iii   i     i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_40219791_4   3301 CTAGACTCCTATCTCTCACCAAATACAAAAATCAAATCAAAATGGAATAA 3350
                         i i   i    i   v     v          i  v          vi ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_40219791_4   3351 AGACTTCAATCTAAGACCTCAAACTATGAAACTACTACAAGAAAACTTTG 3400
                             i v   v     v  v       i     vi  v        v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_40219791_4   3401 AGGAAACTCTCCAGGACATTGCACTTGGTAAAGATTTCTTGAGTAACACC 3450
                         i? v  v   i iv   v   vii v  i  v i      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_40219791_4   3451 CCATAATCACAGGCAACCAAACTAAAAATGGACAAATGGGATCACATCAA 3500
                            v  v    i     v   vv      i  i    v   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_40219791_4   3501 TCAATTTAAAAACCTCTGCACCGCAAAGTGA----ATCCACATAGTGAAA 3546
                         --    -      i i  ii iv     -  ----   v v v       
  L1M4_orf2#LINE/    651 --AATT-AAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGAAA 696

  chr2_40219791_4   3547 ACACAGCTTACAGAATGGAAGAAAGTATTTGCAAACTATCCAGCTGACAA 3596
                          v   i ii         i     i          ii  vi v    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_40219791_4   3597 GGGTTTAATAACCAGAATACATAAAGAGCTCAAACACCTCTATAAGAAAA 3646
                            vi vi  v        i       i   vv   v   v    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_40219791_4   3647 AATCTAATA-TCTGATGAAAAAGTGGGCAAAAGATCTAAAAAGACATTTC 3695
                          iv v    -i ii  v?    i        i   i i  v         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_40219791_4   3696 TT-----AAGACATACAAATGGCAAACAAGTGTCTGTATAAGGGTGTTTA 3740
                          i-----    i           v  i   iiiv  - -  i i  i i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATG-A-AAAGATGCTCA 894

  chr2_40219791_4   3741 ACATCATTGATCAT 3754
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.08 (25 / 12)  


2160 27.24 3.89 1.17  chr2_40355045_40356713.rev      407  1177 (492)    L1M4_orf2#LINE/L1      117   908 (0)  

  chr2_40355045_4    407 TGTAGAGAA-GAGAAGC--ATCCAAGAAACTATACAGGA---CAAAGGAA 450
                           i   i v-  v    --    v i  vii   ii i ---   i   -
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA- 165

  chr2_40355045_4    451 AAGCCTA--ATA---AAAACTGAAGCCC--AAAGGAAAGATTCAGGTCAA 493
                         ---  i --   ---     --  v ii--   i   ii ivv  v vi 
  L1M4_orf2#LINE/    166 ---CCCAGAATAGCCAAAAC--AATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_40355045_4    494 GAAATAACATGCACCTGACTTCAAATTATACTACAAGCCTACAGTAATCA 543
                          i v v   ivi-  ii i      viv        iv            
  L1M4_orf2#LINE/    211 GGACTCACACTT-CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_40355045_4    544 AAACAGCATGGTACTGGTACCAAAACAGATATATAAACCAATGGAACAAA 593
                          i    ii         i iv ii i   i     i i        i i 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_40355045_4    594 ACAGAGACCTCAGAAATAACACCACACATCTACAACCATCAGATCTTTGA 643
                          iv    vii         vv   i    i  iiii  viv   i  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_40355045_4    644 CAAACCTGACAGAAACAAGCAATGGGGAAATGATATCCTATTCAATAAAT 693
                            ivv  v  ii v  vv           vi   vi  v     i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_40355045_4    694 GGTGGTAGAAAAACTGGTTAGCCATATGCAGAAAACTGAAACTGGACCAC 743
                             v i i v      v  ?   i     i  i v    ii      v 
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_40355045_4    744 TTCCTTACACCTTATACAAAAATCAACTCAAGATGGATTCAAGACTTTAA 793
                          v   i     v           i       i      iv?    i v  
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_40355045_4    794 TGTAAAACCCCAAACCATAAAAACCCTAAAAGAAAACCTAGGC---AAT- 839
                              i v iv    i      vi i  i        v    ?---   -
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_40355045_4    840 ------ATCTAGGCATGGGCAAAGACTTCATGACGAAAACACCAAAAGCA 883
                         ------ i  v  vv i     v ii   v iivv vi            
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_40355045_4    884 ATGGCAACAAAAGTCAAAATTGAGAAATGGGATCCAATTAAACTAAAAAG 933
                         vvi          vv     v  v    v   iiiv  i   v v    i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_40355045_4    934 CTTCGGCATAGCAAAAGAAACTATCCTCAGAGTGAACAGGCAACCTACAG 983
                            iv iiivv    i  v      vvv i      v  i     i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_40355045_4    984 AATGGGAGAAAATTTTTGCGATCCATCCATCTGACAAAGATCTAATATCC 1033
                                      v     i vi   vi      i  i iv  vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_40355045_4   1034 AGAATCTACAAAGA--TTGTAAACAAATTTACAAGAAAAA----AATAAC 1077
                              v  i     -- iv  --   v iv i  v     ----      
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTA--CAACTCAATAATAAAAAGACAAATAAC 807

  chr2_40355045_4   1078 CCCATCAAAAAGTGGGCGAAGGATCTGAACAGACACTTC-CTAAAGAAGA 1126
                           v  i?    i     i      i    i     i   - i        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_40355045_4   1127 CATTCATGCAGCCAACAAAAATATGAAAAGAAGCCCAACATCACTGGTCA 1176
                         i  v  viii     i  iv i         v  i        ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_40355045_4   1177 T 1177
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.42 (121 / 85)
Gap_init rate = 0.02 (15 / 792), avg. gap size = 2.60 (39 / 15)  


3158 27.25 0.33 0.55  chr2_40371638_40377918.rev     4880  5789 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40371638_4   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4929
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40371638_4   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40371638_4   4980 CACCAA-TGCCTCTCTTCACAGAATTGGAAAAAAGTACTTTAAAGTTCAT 5028
                         iv   i-     i i  -i     v v  v  ivvv iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_40371638_4   5029 ATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAGTCCTAAGCCAAAAGA 5078
                               viiv  ii  v  v v  vi    iv  i  i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_40371638_4   5079 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATATACTACAAGG 5128
                               i      vv    i  v  ii i      -- iv        i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAG 247

  chr2_40371638_4   5129 CTACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGAT 5178
                                  i   i    ii        ii iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_40371638_4   5179 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5226
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_40371638_4   5227 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5276
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_40371638_4   5277 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5326
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_40371638_4   5327 TGAAACTGGATCCCTTCCTGACACCTTATACAAAAATCAGTTCAAGATGG 5376
                             ii    i    v   v     v           i ii    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_40371638_4   5377 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5426
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_40371638_4   5427 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTA 5476
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_40371638_4   5477 AAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGAACTA 5526
                         vi            vvii         vv     v  i    v   vi v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_40371638_4   5527 ATTAAAATAAAGAGCTTCTGCACAGGAAAAGAAACTACCGTCAGAGAGAA 5576
                           i     v  i i   i  ii vvv   i  v    i ivv i  v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_40371638_4   5577 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5626
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_40371638_4   5627 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5676
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_40371638_4   5677 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5726
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_40371638_4   5727 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5776
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_40371638_4   5777 CATCACTGGCCAT 5789
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1751 29.13 6.31 2.18  chr2_40452078_40454576.rev     1136  2007 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40452078_4   1136 TAGACAGATATGCC-T-TTCACAGGTCAGAAAACATCATATTTTTAAGAT 1183
                          i  v      v  - -    ii i ii   i  v v     v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40452078_4   1184 AATCGTTCTTCCCAAATTGATCTAGAGATTCAATGTAATTCCAGTGAAAA 1233
                         iiivi v  i              v        i i   i  vi v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40452078_4   1234 TCCCAATAAGCATTTTTTTTTTGGTGTAAATTTTTCAAGCTTTTTCTAAA 1283
                              ----  - vii       vv -     vv-      vv i     
  L1M4_orf2#LINE/    101 TCCCA----GC-TGCCTTTTTTGCAG-AAATTGA-CAAGCTGATCCTAAA 143

  chr2_40452078_4   1284 GTTCATGTATAAATACAGAGGACCTAAAATAGCTAAAATACCACTGGAAA 1333
                         i     i iv    i  ii     i i      i    i vivi  i   
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_40452078_4   1334 AAAAGAACAAA-----AGGA-TAACACTACTTGATTTCAAGATTTATTTT 1377
                          i         -----    - v     v iii       i i   i vi
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_40452078_4   1378 ATTGTTTCAGGTACCAAGCTAGTGTGGTAGTGGCATAAAAATAGAAATA- 1426
                          vv i v   vv i    vi         v        ii     v   -
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_40452078_4   1427 AG-TGATTAGAATGGAAT--AAACTATGGAAATAGATCCACACATATATG 1473
                           - v v i    i    -- i v vii      i i   i    v    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_40452078_4   1474 AATAAACTGGTTTTGGATTTTGTTGTTGTTGTTATTCTAACAAAAATACA 1523
                         i- v  i  i    v  ivvv v  iiivviii    -  iiiii --- 
  L1M4_orf2#LINE/    344 G-TCAATTGATTTTCGACAAGGGTGCCAAGACCATTC-AATGGGGA---A 388

  chr2_40452078_4   1524 AGGCAAT--TCTGTGCAGAACAAATGCTTCCCGAAATATTGTATATGCAG 1571
                           --   --   v v  --       v v iv i vv i  v   ?v  -
  L1M4_orf2#LINE/    389 AG--AATAGTCTTTTCA--ACAAATGGTGCTGGGACAACTGGATAKCCA- 433

  chr2_40452078_4   1572 CAAATAAAA-AATGAATTTTGATCTATTACTTCACACTATATGCACAAAT 1620
                           vii    -      v  v  i i-i   i      i    i  v    
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCC-CTACCTCACACCATATACAAAAAT 482

  chr2_40452078_4   1621 T----CCAAATGTATCTGAAACCTAA-TAAAAAACCTCAA-TTATA---T 1661
                          ---- v     v   v? i      - iv  i v  v  -i    ---i
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_40452078_4   1662 TTTTTTCAAAAAACGGTGAAGAAAGTCTTTGAGAACTTAGGTTAGGCAAA 1711
                          i  vvv i     ivv i? v  i    i v  v   i          v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_40452078_4   1712 GATTTCCTAGATTCTTTATCCAAAACATTATCTATTT--TTAAAAATTGA 1759
                          i    i     vivvi i v   i  iv v v ivv--vv      v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_40452078_4   1760 TAA---------CAT-----TTAAA--CCTTT-TACTCTGAAATATGTTG 1792
                            ---------   -----     -- i   - i  iii  iv iii i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_40452078_4   1793 TTCAGTGAAGGAAAAGACAGGCTA--GACTGAAAGAAAATACTGGCAAAT 1840
                          iv  vi iv         iv i --  v  ii        i v      
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_40452078_4   1841 AGTATATCTAACAAAATATTTATATC-AGAATATTTAATTAATGCTCAAA 1889
                         vi       i i  iiv i  i    -       v   vv  iv  i v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_40452078_4   1890 ATTTAACAATTAAGAAAACA--CAGC------AAAAAATTGGTCAAATAT 1931
                          i i  i   -  i  i   --i i ------?      v  iv  iv  
  L1M4_orf2#LINE/    783 ACTCAATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_40452078_4   1932 TTGAGCAGATATTTCACTAAAGAAAATATATGT-TAACAAATAAGCACAT 1980
                             ii   i     v i      i     iiv- ii v           
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_40452078_4   1981 GGAAATATGCTCAACATCATTTACTCA 2007
                          i   v             ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (145 / 105)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 2.11 (74 / 35)  


3179 26.46 0.88 0.77  chr2_40630109_40632047      541  1447 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40630109_4    541 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 590
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40630109_4    591 GGCCATACTGCC-AAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 639
                            v     v  -  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40630109_4    640 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 687
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_40630109_4    688 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 737
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_40630109_4    738 AACAAAGCTGCAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 787
                                i  v   vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_40630109_4    788 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 837
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_40630109_4    838 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 885
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_40630109_4    886 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 935
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_40630109_4    936 CTATTTTATAAATCGTGCTGGGAAAACTGGCTAGCCATATCTAGAAAGCT 985
                           v  iv i    v         v      v  ?   i  vi i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_40630109_4    986 GAAACTGGATCCCTTCCTGACACCTTATACAAAAATTAACTCAAGATGGA 1035
                            ii    i    v   v     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_40630109_4   1036 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1085
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_40630109_4   1086 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGAACTTCATGTCAAA 1135
                         v    ?i v viv   iv   v v  vvii     viii   --- i i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC---TTAGA 593

  chr2_40630109_4   1136 ---AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 1182
                         ---i            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_40630109_4   1183 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 1232
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_40630109_4   1233 AACAGGCAACCTACAAAATTGGAGAAAATTTTCGCAACCTACTCATCTGA 1282
                           v  i     i   i   v         v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_40630109_4   1283 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 1332
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_40630109_4   1333 AAAAAACAAACAACCCAATCAAAAAGTGGGCAAAGGACATGAACAGACAC 1382
                             i     i        i?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_40630109_4   1383 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 1432
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_40630109_4   1433 ACCATCACTGGCCAT 1447
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


3410 25.55 0.33 0.77  chr2_40641715_40644013      896  1807 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40641715_4    896 TGGAAAATTAATCCATAATCATGGATTGGAAGAACCAATATTGTTAAAAT 945
                               iv  vi    iv               vii           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40641715_4    946 ATCTGTATTACCCAAAGCAATCTATAGAGTCAATGCAATTCCTATCAAAA 995
                         iv vi  i v      vii     i   v    i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40641715_4    996 TGCCGATGACATTCTTCACTGAAATAGAAAAAATAGTCCTAAAATTTATG 1045
                          v  iiivi v  i  ii v     v  v  iv ii          i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_40641715_4   1046 TGAGACTACAAAAGACCCAGAATAGCTGAAGCTATCCTAAGCAA-AAGAA 1094
                           ii v i   ii             ii  i v   i i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_40641715_4   1095 CAAAACTGGAGGAATCACATTACCTGGCTTCAAATTATAATGCAGAGCTA 1144
                             ii       v     i v  iiii      viv  v i  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_40641715_4   1145 GAGTAAATAAAACAGCAGGTTACTGGCATAAAAACAGACACATAGACCAA 1194
                         v     vi  i    iiv v           ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_40641715_4   1195 TGGAACAGAATAGAGAACCCAGAAACAAATCCACACACCTATAGATAGTG 1244
                              i     v    ii       i   i   i   ii   i vi i v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_40641715_4   1245 AACTCAGTTTTACAAAGTTGCCAAGAACATACACTGGGAAAAAGACAGTC 1294
                         i i ---  iv    i v        v   v  v    i   ii i    
  L1M4_orf2#LINE/    351 GATT---TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_40641715_4   1295 TCTTCAGTAAATAGGCCTAGGAAAACTGAATATCCATATGTAGAAGAATG 1344
                          i    ii    i vv  i   v     i   ?   i   i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_40641715_4   1345 AAACTGGACCTCTGTCTCTCGCTAAATACAACAATCAAATAAAAATGGAT 1394
                           ii      i  ii   v i i v      v   i  v v         
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_40641715_4   1395 TAGAGACTTAAATCTAAGACCTCAAACCATGAAACTACTACAAGAAAACC 1444
                         i ?    i     v     v  v    i  i     vi  v        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_40641715_4   1445 TTGAAGAACATCTCCAGCACATTGGTCTGGGCAAAGATTTCTTGAGCAAT 1494
                          v i? v v    i ivv  v    vi i     v i      iiii vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_40641715_4   1495 ACCCCACAAGCACAGGCAACCAAAGCAAAAATGGATAAATGGGATCACAT 1544
                           v   v       i     v    v      i       v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_40641715_4   1545 CAAT-TTAAAAAGCTTCTGTACAGCAAATAATACAATCAACAAAGTGAAG 1593
                            v-       -   i   i vv    vi i  v     v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_40641715_4   1594 AGGCAACACACAGAATGAGAGAAAAATATTTGCAAATTACCCATCTGACA 1643
                           i    v         i       -           i ivi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATA 745

  chr2_40641715_4   1644 AGGAATTAATAACCAGAATATATAAGGAGCTCAAACAACTCTATGAGATA 1693
                            i i vi  v             i  i   vv       v  i v v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_40641715_4   1694 CATTCTAATAATCAGATTTTTAAAAATGG-CAGCAGATTTGAATAGACAG 1742
                         v vv v     i vi   ?--        -  ivi              v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_40641715_4   1743 TTCTCAAAAGAAGACATACAAATGGTAAACAAGCATATGAAAATGTGCTC 1792
                              v        i          iv  i     i       vi     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_40641715_4   1793 AACACCACTGATCAT 1807
                             i  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3778 16.24 2.34 10.15  chr2_40655174_40658403.rev     1754  2738 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40655174_4   1754 TGGGAAAAGACCCCATGTTCATAGATCAGAAGACTTAACATTGTTAAGAT 1803
                            i  i v i           i   ii          i           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40655174_4   1804 -----TATTCCCTAAAATCATCTACAGATTCAACATAATTTCTATCAAAA 1848
                         -----  i    i   v v               ii   ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40655174_4   1849 TCCTCGCTGATACTATTT---AGAAGTTGACAACCTGGTTCTAAAACTCA 1895
                            iv    v--  v   ---    i       v   i i      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_40655174_4   1896 TATTAAATTTCAAATAACCCCAGATAGCCAACA-AATATTGAAACAGAA- 1943
                            vi  v v   ivi    vii        v -   v      v    -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_40655174_4   1944 --CCAAGTTGAAGGACTCATAGTTCCTGATTTCAAAATTTACTACAAAGC 1991
                         -- v      i        i v    ii         i            
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_40655174_4   1992 CACGGTAATCAAAACAA-ATGATACTGGCATAAGGATAGACCTGCAGATC 2040
                         i  i        i   i-i  i                   v ii     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_40655174_4   2041 AAAGGAATAGACGTCCATTCAGAATTCCATTCCAGAAATAAACATCCAGA 2090
                           v        -----   v   i ------            -------
  L1M4_orf2#LINE/    299 AATGGAATAGA-----ATTGAGAGT------CCAGAAATAAAC------- 330

  chr2_40655174_4   2091 AATAAATTCAACATCTAGAAATAAGCCCATACATCTGTGTTCAATTGATT 2140
                         --------------------------        i i  v          
  L1M4_orf2#LINE/    331 --------------------------CCATACATTTATGGTCAATTGATT 354

  chr2_40655174_4   2141 TTCAACAAGGATAGCAAGTTTATTAAATGCAGAAACGAATAGTCTT--CA 2188
                            i      i iv    vii   v    vi    -          --  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTCA 403

  chr2_40655174_4   2189 ACTAATGGCATTGGGACAACTAGATATTCATGTGCAGAAGAATGAAGTTG 2238
                           v     iii          i    ?i  ii    i             
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_40655174_4   2239 GATTCCTATCTCATATCATACACAAAAACTAACCCCAAATGGATTAGAGA 2288
                           ii    i    i i    i       i    i v        i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_40655174_4   2289 CCTAATTGTAAGAGCTAAAATCACAAAACTCTTAGAAGAAAACATAGGAG 2338
                              v              ii i                        ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_40655174_4   2339 TAAATATTCATGACCTTCCTTAGCTTTGGCAACAGATTATTGGATAATAA 2388
                              v   i       ----i v  v     ii v  v  i    - i 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTT----GGGTTAGGCAATGGTTTCTTAGATA-TGA 598

  chr2_40655174_4   2389 TCTGTTGGATTATAATTATTGGATAAGCATGAGCAAAAGAAATAAATAAT 2438
                         i------- ii v  ----- v i     ---i         -     --
  L1M4_orf2#LINE/    599 C-------ACCAAAA-----GCACAAGCA---ACAAAAGAAA-AAATA-- 630

  chr2_40655174_4   2439 AGATAAATTGGATTTCACCAAAATTGCAATGGCTACAAGAAAAATAAAAA 2488
                         -           i    i       -------------------------
  L1M4_orf2#LINE/    631 -GATAAATTGGACTTCATCAAAATT------------------------- 654

  chr2_40655174_4   2489 TAAAAACTTTTGTTCTTCAAAGACCAGCATCAGGAAAGTGAAAAAATAAT 2538
                         -            v        iv  vi    i           i i  i
  L1M4_orf2#LINE/    655 -AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_40655174_4   2539 CCACAGAGTGGAAAAAAGTATTTGTAAATCACATATCTGATAAGGGTCTT 2588
                                i   i i   i      i      i              v   
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_40655174_4   2589 GTATCAAGACTATATAAAGA-----CATGACTCAATCATAAAA-GACAAA 2632
                              v   v          -----i ii       v      -      
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_40655174_4   2633 TAACCTGATT-AAAAATCAGCTAAGGATCTTAATAGCCACTTCACTAAGA 2681
                              ii   -      vi  v      i v     v  i   v i  ii
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_40655174_4   2682 AAGACGTACACATGGCCAATGAGC-CATAAAAAAAAGCTACTTAACATTA 2730
                             ii    v         i   -   i    i --- i  i     i 
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGA---TGCTCAACATCA 900

  chr2_40655174_4   2731 TTAGTCAT 2738
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.27 (109 / 48)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 5.12 (123 / 24)  


3324 16.65 5.48 9.80  chr2_40723999_40726364.rev      926  1874 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40723999_4    926 TGGAAAGGCATTCTGTGTTGAAACATTAGAACACTTTGTATTGTTATGAT 975
                                ii  i ii    v viv   i   v    vi        v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40723999_4    976 G----TACTCCTCAAACTGATCTATAGATTCTATGCAATCTGTATGAAAA 1021
                          ----      i    i       i      v i      iv   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40723999_4   1022 TCGCAACTGG--TTTTTGCAGAAATTGACAAGTCAATCCTGAAAGTCATA 1069
                           v  i   v--                    iii     i   v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_40723999_4   1070 TGAAAACTCAAAGGACCCATAAAAGTCAAAACAATCTTGAAAAAGAA--- 1116
                           i   iv   i       v  v  i                     ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_40723999_4   1117 CAAAGTTGGAAG-CTCACACTTCTTGATATTAAAACTTAGTACAAAGCTG 1165
                                   i -          iii  v i        v         i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_40723999_4   1166 CAGTAATTAAGACTCCAGGGTACTGGCATAAGAACAGACATATAAAACAA 1215
                                i     -------------------------------------
  L1M4_orf2#LINE/    251 CAGTAATCAAGAC------------------------------------- 263

  chr2_40723999_4   1216 CTGAATAGAATTGTAAGTCCAGAAGTAAAACTATATGTCCAATTCAAGAC 1265
                         -----------------------   i-----------------------
  L1M4_orf2#LINE/    264 -----------------------AGTG----------------------- 267

  chr2_40723999_4   1266 TCCATAGTACTGGCATAAGGATAGACGTATAAATCAACTGAATAGAATAG 1315
                         ---- i                    i    i     iv         v 
  L1M4_orf2#LINE/    268 ----TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_40723999_4   1316 GAAGTCCACAAGTAAACCTATGCATATATGGCCAATTAAGTTTTGACAAG 1365
                         ii      v  i      i  i   v     i     i v   i      
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_40723999_4   1366 GGTGCCAAGACCATTCAGTGTGCAGGGAATAGTCTTTTCATCAAGTGTGG 1415
                                          i  v v ii              v   i  vv 
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_40723999_4   1416 CTAGGACAAATGGCTACACAAATGCAGAATAATGAAGTT----------- 1454
                           i      v   v  ?v  v     i  v         -----------
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_40723999_4   1455 -CATGTAATTTACAAAAATTAATTCAAAA-AAATGGAAGAT----ATGTT 1498
                         -  iiiv  v            i      -ii  vi?   i----    -
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT- 512

  chr2_40723999_4   1499 AAGAGCTAAAACTATAAAATCATTAGAAGAAAACA--GGTAAAAATATTT 1546
                                            iiv             --  ?iv    v  i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_40723999_4   1547 GTGACCTTGAATAAGTTGATGGATTTTTAGACACTGCATTAAAATCACAA 1596
                                  ii v  vii    v  i     i ivi  ii    v     
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_40723999_4   1597 ATAACCAAAGAAAAA-TAGATTAATTGGACCTTTTCCAAATTAAAAAGTA 1645
                         ii   v         -     v        i iv  v          v v
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_40723999_4   1646 TAGTCCTTAAAAGGATACTATTAATAAAGTGAAAAGACAACCCAGAGAAT 1695
                          v  v   v      i     i  v                   v     
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_40723999_4   1696 GGGATAAACTATTTACAAAT---ATATCTGATAAGAGTCTAGTACTCAGA 1742
                             v   v     i     ---            i v  v   ii    
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_40723999_4   1743 ATATATTTTTAAAAAAAC----ACAACTCAATAA-----AAACAAA-AA- 1781
                               -----   i   ----            ----- i     -  -
  L1M4_orf2#LINE/    763 ATATAT-----AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_40723999_4   1782 --AATTGAAAAATGGGCAAAAGATGGGAATAAACATTTCTCTGAAGAATA 1829
                         --    ?             i   vv     i         ii     v 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_40723999_4   1830 TATG-AAACTGTCAATAAGCACA-----AGATTCTTGACATCATTAATCA 1873
                            i-   iv i           -----    v  ii      ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_40723999_4   1874 T 1874
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.44 (91 / 63)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 7.25 (145 / 20)  


1714 24.36 17.44 1.03  chr2_40760421_40762206      515  1294 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_40760421_4    515 TGGAGAGAGATAGCATGTTTATGGATCAGAAAATTTAAT-TTTTTAAGCT 563
                             i   v  vv      i      ii   i i     -  v     v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40760421_4    564 GTGAAGTCTCCCCAAAT-GACTTCTAGATTCAGTGCAATCCTAATCAAA- 611
                          vv  vv          -  ii vi       ii       iv      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_40760421_4    612 --TCAAAT-CAATTTTAATAAGAGTCAATACACTGATTCTAAAATTGGTA 658
                         --i  iv - vv    vii ii i ii i vi     i        vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_40760421_4    659 TGGAAATACAAAGGATGTAGGATAGATAAAACAATT-----AAAGAAAAG 703
                                i   i   ivi  i    vi        i-----      i i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_40760421_4    704 T----TTGAAAGATTTAC-CCTACGGATTTAAATCCTTATTA-------- 740
                         i----   i i  i i  - i v vi    v  vv    i  --------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_40760421_4    741 ---TAATCAA----------------CATA------GACAAATAGATCAA 765
                         ---       ----------------    ------    v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_40760421_4    766 TTGAGGTGGAGAAAGAATCCTGAATCAAA---AAACATT-------AATT 805
                          v  ivv i vvi   i   v   vi   --- v     -------    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_40760421_4    806 GATTTTT-ATAAAATTGC-AA----ATTCAATTGGTGAAGAA-AGT---- 844
                               i- i  iiv   -  ----       v  vi     -   ----
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_40760421_4    845 ---ACAA-T----CTG-----ACTAGA------------AAAAAGTGAAC 869
                         ---    - ----   -----   i  ------------   i i    v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_40760421_4    870 ACTT--ACACATATTTTGTAGTATACATAAAAATTAACT-AAAATAAATA 916
                         --  --  v v  ii iii vi   i i           -     ii  v
  L1M4_orf2#LINE/    451 --TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_40760421_4    917 ACAGATCTACATGTAAAATCTAAAATTATAAAACACATTGAATAATACAT 966
                          ?   i   v      i v      i        v v v   v  v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_40760421_4    967 AGGAAAAAATATTTGTGACCTTGGGTTAAGCAAAGAATTCTTAA----GA 1012
                            ?iv    v  i              i    v iv      i----  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_40760421_4   1013 CACCAAAAGCATGATCCATTAAAGAAAAAAGTGATACATTAGACTTCATC 1062
                                    ii v v iv          vv    v   i         
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_40760421_4   1063 AAAATTAAGAATTTCTGCTCTT---------------AGAAAATGAAAAG 1097
                                 i  i  i  iv   ---------------     i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_40760421_4   1098 ACAAGCCGCAGGCCAGAAGACTACAATTGTAACTTATATATCTAATAGAG 1147
                             v  i   ivii i   vv i v   i  v i        i   ii 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_40760421_4   1148 AATTTGTATGAATAATATATATA---TTTTTAAATCTCAA--ATCTCAAG 1192
                         i i      vv v        v ---i i   v v     --  ---  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT---AAA 795

  chr2_40760421_4   1193 AAGAGAAGCAATTTAATTTAAGAAATACGCAAAAGATTTGAATGGACACT 1242
                             v  ii  iii    ?  -    iv     i         i    i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_40760421_4   1243 TC----ATGAAGGTAATTGTAAA--GCCAAT--------GAAAAGATGTG 1278
                           ---- v    i  -- ii   --      --------         iv
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATA--TACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_40760421_4   1279 TAACATCATTAATCAG 1294
                         i       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (112 / 75)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 4.24 (144 / 34)  


2967 27.46 1.58 0.68  chr2_40820176_40824232     2673  3557 (500)    L1M4_orf2#LINE/L1        1   893 (15)  

  chr2_40820176_4   2673 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 2722
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_40820176_4   2723 GGCCATACTGCCCAAATTAATTTATAGATTCAATGCCTATCC--ATCAAG 2770
                            v     v        i  i  i        i  v-    --     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA-ATCCCTATCAAA 99

  chr2_40820176_4   2771 CTACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 2819
                         v v   iivi i  i  ii     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_40820176_4   2820 TATAGAACCAAAAAAGAGTCTGTATAGCCAAGACAATCCTAAGCAAAAAG 2869
                            i   viiv  ii  vi v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_40820176_4   2870 AACAAAGCTGGAGGCATCATGCCACCTGACTTCAAACTATGCTACAAGGC 2919
                                i      vv   ii iv  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_40820176_4   2920 TACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGATATATAGACC 2969
                                 i   i   iii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_40820176_4   2970 AATGGAACAGAACGGAGGCCTCAGAAGTAATGCCACACATCTACAACCAT 3019
                                i    iv   ivii     i   vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_40820176_4   3020 CTGATATTTGACAAGCCTGACAAAAACAAACAATGGGGAAATGAT--TCC 3067
                         i    v  i      vv  v   i v  vv           vi  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_40820176_4   3068 TTATTTAATAAATGGTGTTGGAA-AATTGACTAGCCATGTGCAGACAACT 3116
                           -- i  i        i   i -  i  iv  ?   ii    i vi v 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_40820176_4   3117 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGGA 3166
                            ii    i    v   i i   v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_40820176_4   3167 TTAAACACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3216
                          i ? v  i    i      v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_40820176_4   3217 CTAGGCA-ATACCATTCAGGATGTAGGCATGGGCAAAAACTTCGTAAGTA 3265
                         v    ?i- v i -   iv  iv v  vv i     viii   v  ii  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_40820176_4   3266 AAACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGGA---- 3311
                         vi            vvi          vv     v  i    v   ----
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_40820176_4   3312 -TCTAAATAAAGGGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 3360
                         -  v    v  iii   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_40820176_4   3361 GAGATGACCTACAGAATAGGAGAAGATTTTTGCAATCTATCCCTCTGACA 3410
                         i   ii   i       i      i  v       vii  viv     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_40820176_4   3411 AAGGGCTAATATCCAGAACCTACAAGGAACTTAAACAAATTTACAAGAAA 3460
                          i  i  vi         iv  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_40820176_4   3461 AGCACAAACAACCCCCTAAAAACAGTGGGCAAAGTATATGAAAAGACACT 3510
                          iv     i     vv v?   - i         v  v    v     i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACATT 844

  chr2_40820176_4   3511 TCTTAAAAGAACACATTTATGCGACCAACAA--ACATGAAATAAAGCTC 3557
                            iv      v i  vi vii i    i  --        vi v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (12 / 893), avg. gap size = 1.67 (20 / 12)  


1821 24.35 12.71 1.53  chr2_40908141_40909784.rev      501  1153 (491)    L1M4_orf2#LINE/L1      183   908 (0)  

  chr2_40908141_4    501 AATCTTGACCAA--AGAACAAAGCTGA--GACATCACACAAATTGACTGC 546
                                 vv  --         i  i--   -      vvviii i v 
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTC 231

  chr2_40908141_4    547 AAAATATATTATGAAGCTATAGTAATCAAAACATTATGGTACTGGCATAA 596
                             iv  i  ii      i         i   v i              
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_40908141_4    597 AAACAGACAGACACATTGACCAGTGGAATAGGATGGATAGCCTGGAAATA 646
                         i----  i     i  v  i  i        i  v  v  i ii      
  L1M4_orf2#LINE/    282 G----GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_40908141_4    647 AACCCAGACATC-AGAGTCAATTGATTTTTGACAAAGGTGCCAATAATAT 695
                               v    i- vi             i     i        v vi  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_40908141_4    696 ACAATGC-------ACAGTGTCTTTAA-AAATGGTGTTGGGAAAACCAGA 737
                         v     v------- i   v i  i  -        i     v   ii  
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_40908141_4    738 TATACATGTACAGAAGGA-------------------------------- 755
                           ?v  ii i  i   i --------------------------------
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_40908141_4    756 ------------AAATGGATTAAATATTTAAATGCAATTCCTGAATCTAT 793
                         ------------        i ? v ii      i  vvv  i  v    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_40908141_4    794 ACTACAGATACTAGAAGAAAGCACAGGGGGAAATCTCCATGGTATTGGTC 843
                          vv  --- vi         i  i   ? v      i i  iiv    vi
  L1M4_orf2#LINE/    528 AAAAC---TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_40908141_4    844 TGGACAATAATTTCTTGTGTGTAATCCCAAAAGCACAGGAAACAAAAGCA 893
                          i i    ii      ivi i i iv           i v        v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_40908141_4    894 TAAATAGACAAACATGATTCCATCAAACTAAAAAGCTTCTGCAC--AAAA 941
                         v       i   ivv  i i       v v    i   i  ii --v   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_40908141_4    942 GGACACAATT------GTGTCAAGAGAAAATGCACAGATTAAGA-AAAGT 984
                               v  i------   --  i   v  iv      v ii  -   i 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTG--AAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_40908141_4    985 AT--AAAAATTATACATCAGATAATGGGCTCTTTTACAAAATATACAAGA 1032
                           --iv    i   i   v     v  i  iv v v  i      i  ii
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_40908141_4   1033 AACTC--A-AACT----AATCCAAA-----ACAATCCTATT-AAAAACGG 1069
                              -- -    ----   vv   ----- i  i  v   -     i  
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_40908141_4   1070 GCAAAGAACTCAAATAGACATTTCTTAAAAGAAGACACACAAATTGCCAA 1119
                               i i ii             iv        i i      v     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_40908141_4   1120 TAGTTATATGAAAA--TGTTCAACATCTCTAATCAT 1153
                           ivi i       --  i        v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (98 / 58)
Gap_init rate = 0.03 (20 / 726), avg. gap size = 4.65 (93 / 20)  


2933 25.90 1.33 0.24  chr2_40937448_40939287.rev      519  1348 (492)    L1M4_orf2#LINE/L1       70   908 (0)  

  chr2_40937448_4    519 ATCTAAAAATTCAACGCAAACCCCATCAGAATACGACCATCATTCTTCAC 568
                              v i           v   i    i   v v v vv v  i  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chr2_40937448_4    569 AGAATTAGAAAAA--AAATGTAAAATTAATATGGAACCAAAAAGAGCCCA 616
                             v v  v  i--i viv       v        viiv  i ii    
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_40937448_4    617 CA-TAGCCAAAGCAAGACTAAGCAAAAAGGATAAATCTGGAGGCATCACA 665
                         v -        i   vvi i iv  i   i i   vi      vv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_40937448_4    666 CTACCTGATTTCAA--CTATATTATAAGGCCATAGTCACCAAAACAGCAT 713
                           v  ii       --  -  i  i  i  i i   v i   i    ii 
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_40937448_4    714 GGTACTGGTATAA----AGGCACATAGACCAATGGAACAGAAGAGAGAAC 759
                                 i    ----  i  i     i        i    vv    ii
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_40937448_4    760 CCAGAAATAAACCCAAATATTTACAGTCAACTGATCTTCGACAAAGCAAA 809
                                        v i     ii     i    i        i vviv
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_40937448_4    810 CAAAAACATACTATGGGGAAAGGACACCCATTTTAACAAATGGTGCTGGG 859
                            i v   v v          i i vi v   i                
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_40937448_4    860 ATAACTGGATAGTCACATGTAGGAGGATGAAACTGGAATCTCATCTCTCA 909
                          i         ?i      i ii  i     ii    vi ii i   v  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_40937448_4    910 CCTCATACAAAAATCAACTTGAGATGGATTAAGGACTTAAACCTAAGACC 959
                           vi          i    ii i      i ?i   i    iv     v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_40937448_4    960 TGAAAGTATAAAAATTCTAGAAGATAACTTTGGAAAAACCCTTCTAGACA 1009
                          i   v       v ii       v   v v  ?iv  vi    vv   v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_40937448_4   1010 TTGGCTTAGGCAAGGACTTCATGAGCAAGAACCCGAAAGCAAATGCAATA 1059
                             v        v ii   v iiii v  vv  i      v v    i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_40937448_4   1060 AAAACAAAGATAAATAGCTGGGACCTAATTAAACTAAAGAGCTTCTGCAC 1109
                            iv   i   i   iv v    i v  i   v v  i i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_40937448_4   1110 AGCAAAAGGAACAGTCAGCAGAGTAAACAGACAACATACAGAGTGGGAGA 1159
                         vv    i iv  vi   iv i   i  v       vi     i       
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_40937448_4   1160 AAATCTTCACAATCTATACATCTGACAAAGGACTAATATCCAGAATATAC 1209
                             v  ii   vii   i      i  i     vi             i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_40937448_4   1210 AACGAACTCAAACAAATCAATAAGAAATAAAACAAACAATCCCATCAAAA 1259
                           v      vv    v       v   -  i     i  i  v  i?   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAA-AAGACAAATAACCCAATTWAAA 817

  chr2_40937448_4   1260 AGTGGGCTAAGGACATGAATAAACAGTTCTCAAAAGAAGATACACAAATA 1309
                          i     v     iv      i   v     v          i      i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_40937448_4   1310 GCCAACAA--ACATGAAAAAATGCTCAACATTACTAATGAT 1348
                              i  --         i           i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (126 / 85)
Gap_init rate = 0.01 (7 / 839), avg. gap size = 1.86 (13 / 7)  


1400 26.99 5.52 4.91  chr2_40984387_40986369.rev      418  1069 (914)    L1M4_orf2#LINE/L1      150   805 (103)  

  chr2_40984387_4    418 ATTAAAATACAAGTTGAAGGAT--AAAATGGCAGAAAACTGCAAAT---- 461
                           vi    i    -----   i-- i   i  v-     ----   ----
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG-----GGACCCAGAATAGCC-AAAAC----AATCTTG 189

  chr2_40984387_4    462 AAAAGGTTGGATAAAGTAAAAGGGAAATCAGTCTACTACATTTCAAGATA 511
                             i vv i i     vii   -- v   vv  v ivv       i iv
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGG--ACTCACACTTCCCAATTTCAAAACT 237

  chr2_40984387_4    512 T-TTACATAGCTACATTAATCAAGAC--TATGGTAACAGCAGAGGAATAA 558
                          -i    v       v          -- i     vii   v i i   i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_40984387_4    559 ACTCATAGAGCAACACAATTAAGTAAAAAATTCAGAAATAGATGCATAAA 608
                           vi     v   iiv   vi i vi i i i        i iv    v 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_40984387_4    609 AATATG-CCAGACTGATTTTTGATAACA-TGACATAACTAATCGAATTCA 656
                         vv    -i  - i       i  i  vi-  v  vi  i ------    
  L1M4_orf2#LINE/    338 TTTATGGTCA-ATTGATTTTCGACAAGGGTGCCAAGACCA------TTCA 380

  chr2_40984387_4    657 ATGGAGGAAAGATGGTCTTTTCAACAAACGATGAGGGAGCAATGAGCAAG 706
                             i i  ii  i              i i  vv  ii   iv----- 
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT-----G 425

  chr2_40984387_4    707 GA-AGCAAGCAAGCAAGAGAGAAAAG---AACCTTCAGTTAAGTTACGTA 752
                           - ? v -  v    i   ivi   ---i   iii vi ------ ii 
  L1M4_orf2#LINE/    426 GATAKCCA-CATGCAAAAGAATGAAGTTGGACCCCTACCT------CACA 468

  chr2_40984387_4    753 TCTTATACAGAAATTGATCTAAAATTAATTATGGACTTAAGTGTAAAACA 802
                         i v      i     i iii     vi  i ?i   i   i     i vv
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_40984387_4    803 TAAAAGTATAAAATCTTTAGAAAAAAGCATAGGAG-ATATTTTT-TAACC 850
                              v       iii      i   i      ? - v  i  i- i   
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_40984387_4    851 TAGGACTAGGCA--GAGTTCTTAGACTTGATGCAGAATGTATAATCAATC 898
                          v  ii      -- iv        iv   ii vi  v i i  v   - 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA-C 617

  chr2_40984387_4    899 AAAAGAAAAATT-GATAAATTGGACTTTATTAGAAC-GTAAACTTTTGTA 946
                                   v -              i  i i  i-iv          i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_40984387_4    947 TTATGAAAGGCTCTATT-------T--AAAG-----CTACAGACTGGAAG 982
                         i vii  i i v    i------- --    ----- i     v   i  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_40984387_4    983 AAAATATTTGCAAACCCCATATTTGATAAAAGGCTAGTATCTACAATATA 1032
                                       i vi    i      ii i  v     i v      
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_40984387_4   1033 GGAAGAAC-CTCAAAATTCAACAGTAAAAACTCAAACA 1069
                         vi      -  i v  i    i i      vv    i 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

Transitions / transversions = 1.93 (114 / 59)
Gap_init rate = 0.04 (27 / 656), avg. gap size = 2.52 (68 / 27)  

 308 16.67 7.94 8.73  chr2_40984387_40986369.rev     1366  1491 (492)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr2_40984387_4   1366 CTCAA-AACAAAAACAAAAACAAAAAACAGTCTGTCCAATTAGAACCTGG 1414
                              -  i     ----i     v   -------      ?i  vv   
  L1M4_orf2#LINE/    784 CTCAATAATAAAAA----GACAAATAAC-------CCAATTWAAAAATGG 822

  chr2_40984387_4   1415 -CAAAAGA-----AGAAATATTTCACCAAAGA---TATATAGATGGTAAG 1455
                         -    i  ----- v i i     v       ---    i i    iv i
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_40984387_4   1456 TTAGTACATGAAAAGATGTTCAATATCACTATTAGT 1491
                          v  i             i    i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.05 (6 / 125), avg. gap size = 3.50 (21 / 6)  


2048 26.44 2.42 0.15  chr2_41030155_41031801      501  1162 (484)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_41030155_4    501 AAAATTGACTACAGAGCTATAGTAATCAAGATAGTATGGTATTAAGA-AA 549
                             i v      i     i           i   i     i iiv -  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_41030155_4    550 GAATAGACAAATAGATCAATCGAACAGTATAAAGAGCCCAGAAAAAAATA 599
                          i       v          v   i  v  vi    i       v   iv
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_41030155_4    600 CATATAAATATAATCAGCTGATTT-CGACAAGTCTACAGAGGCAATGCAA 648
                             i vv   ii   ii      -       vv i vi  i v  v   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_41030155_4    649 TGG----AGGAGAGTCTTTTCCAGAAATTCTGCTTTAACAAGTGGATATG 694
                            ----  i v         v v    vv    vvi    v      ?v
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_41030155_4    695 CACATGTAAGAAAGTGAATCTCTAGACAGATCTCATGCCCTTCACAAAAA 744
                               i  i i i    vi vv vv vv i    ii  v vi       
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_41030155_4    745 TTAATTCAAAATAGATTACAGATTTAAATGTAAAATGAAAAACTACAACA 794
                             i       i   i ?   ii         i vvv       i  v 
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_41030155_4    795 TTCATAGAAAATAGCA---GAGAAAACATAGATGACCTTGGGCATGACAA 841
                         i  v     i v i  --- ? v   iv vvi          ivv i   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_41030155_4    842 TGATATGTAAAATATAACACCAAAGGCATGATCCATCAGAGAAATAATTG 891
                           i v v v i    i        i   ii v v iv i     v   v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_41030155_4    892 AGAAGCTG-ACTTCATGGAAATTAGAAACGTCTTCTCTACAAAAGACAC- 939
                          v  ii  -       vi      i    v i viv  v    i     -
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_41030155_4    940 ATCAAGAGTGTAAAAAGAGAAGCCACAGA-TGGGGAGAAATAGTTGTAAA 988
                                iv  i      v  v       -    iii     v   i   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_41030155_4    989 --AGACATCTGAAAAATTATTGTTATCCAAAAATATACAAAGAACTCTTA 1036
                         -- v i      v  ivv i vv      i  -    i            
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAA-TATATAAAGAACTCTTA 780

  chr2_41030155_4   1037 AAATTCAACAACAAGAAAACTAACAACCTGATT-AAAAATAAGCTAAAGA 1085
                         v  i    i  i  i  i  v  i    ii   -      ii  v  i  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_41030155_4   1086 TCTGAAGAAACACCTCACCAAAGAAGATATATACATGGCATATATGCATA 1135
                          i    v i   ii  v              i v     vv   v   i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_41030155_4   1136 TTAATAGATGCTTCCCAT-ACTATGTCA 1162
                          v  v       ivv   - ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (90 / 82)
Gap_init rate = 0.02 (11 / 677), avg. gap size = 1.55 (17 / 11)  


2893 27.53 0.77 0.77  chr2_41231584_41233709      727  1634 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_41231584_4    727 TGGAAAAACATTCCATGCTCACGGTTAGGAAGAATCAGTATCGCGAAAAT 776
                               i i  i     i   i  v v      v i i   i iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_41231584_4    777 GGCCATACTGTCCAAAGTAATTTACACATTCAATGCTATCCCCACCAAGC 826
                            v     vi     v i  i    v      i  v     i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_41231584_4    827 TACCA-TAAACTTTCTT-CAAATAATTAGAAAAAAACT-ACTTTAAAGTT 873
                          v   -iviv    i  -  i -    i--- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAGCTGATCCTAAAATT 146

  chr2_41231584_4    874 CATGTGGAACCAAAAGAGAGCCCATATAGCCAAGACAATCCTAAGCAAAA 923
                            i     viiv   i  v  viv        i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_41231584_4    924 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACAACAAG 973
                                  i      vv    i  v  ii i      viv   v    i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_41231584_4    974 GCTACAGTAACAAAAGCAGCATGGTACTGGTACCAAAACAGATATATAGA 1023
                                   iv  ii   ii         i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_41231584_4   1024 CCAATGCAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACC 1073
                         i     v  i    iv   ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_41231584_4   1074 ATCTGATCTGTGACAAACCTGAAAAAAACAAGCAATGGGGAAAGGATTCC 1123
                          vi    i vi     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_41231584_4   1124 CTATTTAACAAATGCTGTTGGGAAAACTGGCTAACCATATGCAGAAAACT 1173
                           v  i        v  i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_41231584_4   1174 GAAACTGGGTCCCTTCCTTATGCCTTATACAAAAATTAACTGAAGATGGA 1223
                            ii   ii    v   i ii  v                v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_41231584_4   1224 TTAAAGACTTCAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1273
                          i ?    i v  ii     v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_41231584_4   1274 CTAGGCA-ATACCATTCAGTACATAGGCATGGGCAAAGATTTCAT-GATG 1321
                         v    ?i- v i -   ivv  v v  vv i     v i    v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr2_41231584_4   1322 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 1371
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_41231584_4   1372 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTATCAGAGTGA 1421
                         v  i   v v  i i   i  ii vv    i  v     i vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_41231584_4   1422 ACAGGCAACCTACAGAATGGGAGACAATTTTTGCAATCTATCCGTCTGAA 1471
                          v  i     i             v   v       vii  vii     v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_41231584_4   1472 AAAGGGCTAATATCCAGAATCTGCAATCTACTTAAACAAATTCACAAGGA 1521
                           i  i  vi          v ii  vvv   ivv    v iv i  vi 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_41231584_4   1522 AAAAAGAAACAACTCCATCAAAAATTGGGCAAAGGTTATCAACAGACACT 1571
                            i v   i   i v  i?    v          v v v  i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_41231584_4   1572 GCTCAAAAGAAGACATTTAAGTGGCCAACAA--ACATGAAAAAAAAGCTC 1619
                         v   v        i  vi  i       i  --         i v-    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTC 893

  chr2_41231584_4   1620 ATCATCACTGATCAT 1634
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (139 / 107)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


2450 24.50 8.05 2.10  chr2_41449734_41451757.rev      682  1538 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_41449734_4    682 TGGAGGGATATGCTATATTCATGCATCAAAAGAC--AATATTTTAAAGAT 729
                             ii     v i  i      v  iii     --      v v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_41449734_4    730 GTTAATTCTCACCCATGTGATCTGTAGATTCAACACGTCAACCTCAATCG 779
                          vi   v   v  v vv      ii         i ---  i i v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC---AATCCCTATCA 97

  chr2_41449734_4    780 CAATTGCAGCATGGATTTTT-GTAGTAATTGACAAGCTAATTCTAAG-TG 827
                         v   iv    -  vv     - i  v            i  i    i- v
  L1M4_orf2#LINE/     98 AAATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_41449734_4    828 CATATAAAATTTAAAAGAACCTGGAATAACCAAAACA-TCTCTGAAGACG 876
                              ii  v vv  i i   ii     i        -   -    i v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT-TGAAAAAG 195

  chr2_41449734_4    877 AAAAACAGAGTTGGAGGAATTGCACTACCCGATTATAAGATTTATTACAA 926
                           i    i          v ii    v   i   vi  i i   i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_41449734_4    927 AGCTGCAGTAAT-AAGACTCTGTGGTGTTGGAAT--GGATTTAGACAAGC 973
                             i       -     vv      ii   v  --    --     vii
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT--AGACATAT 293

  chr2_41449734_4    974 AGATCAATGAAACAG---TGAAGGAGACATAGAA-TGGAACCACACATAT 1019
                                  i  i  ---   --   v -i    - ii v   i    v 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGA--GAGTC-CAGAAATAAACCCATACATTT 340

  chr2_41449734_4   1020 ATGGTCAATTGATATTTGACGAAGGTACTAAAGTAATTCAAGAGGAAAAG 1069
                                      v  i   i i   i i  iiiv      vi  i    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_41449734_4   1070 GTGAATATTGTCCTTTT------T--TATTG----AAT---ATGGCCATA 1104
                         ---    --   i   i------ -- ii  ----  i---  i?   i 
  L1M4_orf2#LINE/    391 ---AATA--GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_41449734_4   1105 TTCAATAAAATAATCTTCAACCCACATATCACATCATATGTAAAA-TTAA 1153
                          v   v i   i vv  vi    vi iv     i     ii    -    
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_41449734_4   1154 CTCAAAATGGAT-ATAGAGGTAAATGTAAGAGCTAAAA--ATAAAATATT 1200
                                     - ?   vv                  --      i- i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TC 534

  chr2_41449734_4   1201 CTAGAATAAAACA-------AATATTTTAGTGACCCTGGGTT-------- 1235
                         i     v      -------  -  i  v      i      --------
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_41449734_4   1236 -----TTAAACTATAACATAAAAGGCATGA--------AGGAAAATTTGG 1272
                         -----   i -   i   iv   i   ii --------  i    v v i
  L1M4_orf2#LINE/    584 GTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_41449734_4   1273 TAAATTGGACTTCATAAAAAGTAAAAAACTT-GCTCTTCAAAA-ACATTG 1320
                                        v    v      vi  - iv       i-   i i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_41449734_4   1321 TTAGGAAAATGTAAATGCAAGTCATAG----GAAGAAAATATTTGACAAT 1366
                          i i    i  v   vi   vi  i  ---- i            vv   
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_41449734_4   1367 TATATGTTGGACAGAAGATGTGTATTTGAAATATATATAGGACCCTCCCA 1416
                         i    i iv  i iii  iv     iiii        v  i  i  iv  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_41449734_4   1417 ACTCTATAATAAGA-GACACACATTTCAAT--ATAAATGGGAAAAATATT 1463
                             v       i -    v i vii    -- v       v   iv   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_41449734_4   1464 CAAA-AGACACCTCATCATAGAAGATGTATAGATAGCAAGTCTGTATCTG 1512
                         ii  -     ii  vi  v       i  i i  i  v i vv i iv  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_41449734_4   1513 GAAAGATGTCCATTATTATTAATCAT 1538
                         i       ii  vi  i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (134 / 74)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 2.49 (87 / 35)  


3310 21.22 2.92 1.06  chr2_41530656_41532417.rev      517  1270 (492)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr2_41530656_4    517 AAAATTTATGTAAGTTTGCAAGAGACCCTGAATAGCCAAAGCAGTCTTAA 566
                               i  i iiivv      i     v           i  i    i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_41530656_4    567 AGAAAAGGAACACATTTGCAGGTCTCATATTTCCTTATTTCAAAACTTAT 616
                          i  i i     v v   v   v    i i    iv             i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_41530656_4    617 AACAAAGCTACAATAATCAAAACAGTGTGATACTGGCATAAAGATAGACA 666
                         v           i       i        i           i        
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_41530656_4    667 TCTAGACCAGTAGAATATAAT--AGATATCAGGAATAAGCCCTTGCGTAT 714
                          v    i  i i     v   --   vvi   i     i   v i i v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_41530656_4    715 ACAGTCAACTTATTTTTGACAAGGGTGCCAAGATCATTCAAGGGGGAAAG 764
                          ii     i v     i                i       v        
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_41530656_4    765 TGTAGTTTGTCCAACAAATGGTGTTGGGAAAACTGGATATCCACATGCAG 814
                         vi    i v i            i     v         ?         i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_41530656_4    815 AAGAATGAGATTAGAACCTTATCTCATACTATATATGCAAATCAACTCAA 864
                                 ii  i  v  i  i    i  i     iiv    i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_41530656_4    865 AATCCATTTGAGAGTTAACTATGAGACATGAAACTTTAAAACTACTAGAA 914
                            vv  iv?   vi   v i i   vv i     v       vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_41530656_4    915 GAAAACATATGGGAAAATCTCCATGACATTGGTCTGGGCAATGATTTTTT 964
                                  v ? v      i i    v    vi i       i   i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_41530656_4    965 GGA------------AGCACAGGCAGCAGAAGTAAAACTAGGTAAATTTA 1002
                         i  ------------      i   i  i   v    v   i      vi
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_41530656_4   1003 ACCACATCAAAATTAAAACTTTCTGTTCATCCAAGATCACAATTAACACT 1052
                           iv              vi  i   v v  v   iv   v  i  v vv
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_41530656_4   1053 GTGAAAAGGCAACCTATGGGGTGGGAGACAATATTTGCAA-TTATATATC 1101
                                 i     i ii ii       v           - i       
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_41530656_4   1102 TGATAAAGGGTTAAAAACCAAAATATCATGTATAAAGAACTTCAACAACT 1151
                               i  ii viv v   i     -----          iiv      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATAT-----ATAAAGAACTCTTACAACT 785

  chr2_41530656_4   1152 CAACAACAATAAAACAA----CCCAAATAAAAAATGGGACAAGAACTTAA 1197
                            i  i  v  i    ----     v ?         vv   i i  i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_41530656_4   1198 TATAGACGTTTCTTCAAAGAGGATATATGAGTGGCCTGAATA--CGTATG 1245
                         -      i     i      i      ii i     --    -- ii   
  L1M4_orf2#LINE/    836 -ATAGACATTTCTCCAAAGAAGATATACAAATGGCC--AATAAGCACATG 882

  chr2_41530656_4   1246 AAA-GATGCTCAACATCACTAATCTT 1270
                            -              ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (99 / 57)
Gap_init rate = 0.01 (9 / 768), avg. gap size = 3.33 (30 / 9)  


 528 30.94 1.10 0.00  chr2_41534974_41536682.rev       17   197 (1512)  C L1M4_orf2#LINE/L1   (722)   186     4  

C chr2_41534974_4    197 AATGACATCACATGCTCGTGAATTGTAAGAATTAAAATTGTTAAAATGAT 148
                           v  i   v    i  i  i    v    v    v        i   ii
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

C chr2_41534974_4    147 CATACTACCTAAAGAAATGTATAAAGTCAATGCAATCACTATCAAAATAT 98
                         v     v  i   vvi  v  i i v    i      v          vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

C chr2_41534974_4     97 CAATGACATTCTTCTTAGACATAGAAAAA--AATCCTAAATTTCAAATGG 50
                           iivi v  i  ivi   v  v  v  i--i        v    v    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

C chr2_41534974_4     49 AGCCATAGAAGACCTTAAATAGTCATAGCAATC 17
                          iviii iii    ivi     i  v i     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

Transitions / transversions = 1.33 (32 / 24)
Gap_init rate = 0.01 (1 / 183), avg. gap size = 2.00 (2 / 1)  

2161 24.20 3.34 2.64  chr2_41534974_41536682.rev      501  1219 (490)    L1M4_orf2#LINE/L1      185   908 (0)  

  chr2_41534974_4    501 TCCTGAGCAAAAAGAACAAAGCTGGAGG---CATCACTACCAGACTTCAA 547
                           i   iv  i          i      ---  -    v  vi i     
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAA 233

  chr2_41534974_4    548 AATACACTGCAAGGCCATAGTATACAAAACAGCATGGTTCTGGCATAAAA 597
                           ivi   i   i  i i    vv   i    ii    v         ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_41534974_4    598 ACAGACACATAGACCAAATAGAACAGAATAGAGAATGCAGAAATTAATCC 647
                          i     i     i   - i   i     v    i v       v  i  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAA-TGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_41534974_4    648 ATCTATCTACTGCCAACTTACTTTTGACAAAGACATCAAGAAGATTCATT 697
                           vi  i  iv i   i v i   i     i iiii     vv     v 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_41534974_4    698 GGGGGAAAGGAC-GCCACCTTAAATACATGGTGCTGGGAAAACTGGATAT 746
                             -    i i- i -ii  v  i v            v         ?
  L1M4_orf2#LINE/    383 GGGG-AAAGAATAGTC-TTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_41534974_4    747 CCATA-GCAGAAGAATAAAACTAGACCCTCGTCTTTCAACCTATACAAAA 795
                            i -   i      i  ii i     iiii  iv  v v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_41534974_4    796 ATCAACTCAAAAT-----AAAGACCTAAATGTAAGACCTAAAACTATAAA 840
                           i          ----- ?                v             
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_41534974_4    841 ACTACTAGAAGAAAACATAGAGGAAACACTTTAGGACATTGGG--A---A 885
                            vi               i? v  vv   iiv   v     -- --- 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_41534974_4    886 AAGATTTTATAAACAAGACCTCAAAATCACA-GCAA-AAAAGTCAAAATA 933
                          v i   iv  i i v   vi     v    -    -     vv      
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_41534974_4    934 AACAAATGAAATTATATTAAACTAAAAAGTTTCTGCACAACAAAGGAAAC 983
                         i i    vii i vi  i   v v    ii  i  ii vv       v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_41534974_4    984 AA-CAGGA---TGGAAAGGTAACTGACAGAATTGGGGAAAATATCTTCTT 1029
                         v -  i  ---  i    ii   iv       v  i        ------
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT------ 724

  chr2_41534974_4   1030 GCTCTCTCTTGCAAACTATTTATCTGACAGGAGATTAATATCCAGAATAT 1079
                         --------       ii  v       i i i  i vi            
  L1M4_orf2#LINE/    725 --------TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_41534974_4   1080 GCAAGGAACTCAAACATCTCAACAGCAAAAAAAAAAAAAAAAAAGATTAA 1129
                         ii  i      vv   v     i ii     i v   v  vvv -   ? 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA-ATTWA 815

  chr2_41534974_4   1130 AAAATGAGCAAATGACCTGAACAG-CATTTCTGAAAAGAAAACATAAAAA 1178
                               i     v  ii    i  -       vv      i i   v   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_41534974_4   1179 TGGTCATGAA--ATATAAAAAAAAGTTCAACATAACTAATCAT 1219
                            i  vv  -- i  i    i v i       v ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (106 / 64)
Gap_init rate = 0.02 (18 / 724), avg. gap size = 2.39 (43 / 18)  


2139 25.87 4.97 6.00  chr2_41545669_41547560.rev      527  1392 (500)    L1M4_orf2#LINE/L1        2   858 (50)  

  chr2_41545669_4    527 GGAGACATATGACTTGTCCATGGGTTGAAAGAATTAATATTGTTAATGTG 576
                            i v    vv v   i     i   i    v             vi  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_41545669_4    577 TTGATTTCCCTCAAATTCATCAGTAGATTGAATGTAATCCCAATAAAAAT 626
                         vii  vii  i      v   vii     v  i i      v  v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_41545669_4    627 TCCAGC------------AAAACTTAGCAATCTCATTCTAAAATGCAAAT 664
                         i     ------------ i  v  ii   v  v  i       v  v  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_41545669_4    665 GGAAATGCAAAT-ACTTAGAATCACCCAAATAACTTTGAAAAA--AGAGC 711
                                   iv-  ii     vi  v   i  ii        --   i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_41545669_4    712 AAAATTGGAGGACTTGCACTACCTGACTCGGAGACTTATTATAAA-CTAC 760
                            i          ii    v  ii i ivi i     i  i   -    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_41545669_4    761 ACCAATCAAGATGGCGTGATATTAGTGTCAAGACAGAAAAATAGGTCAAC 810
                          vi        ii i   i  i i ii v i  i   v v    i    i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_41545669_4    811 AGCAAAGAACTGAGAATTCAGAAATAGACTCGGCCATACATGGTC---TA 857
                         i v v    i     i i        i  i ivv   vi      --- i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_41545669_4    858 ATCTTTCTACAGAGATTCCAACGTAATTCAATGGAAAAAGGATGACATTT 907
                           -    v   ii i v    viiv         ii    i  iiiv   
  L1M4_orf2#LINE/    352 AT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_41545669_4    908 TCAAGAAATTGTGAAATAATTGTGTACTGTCTGCAGAAAAATCCAAACCT 957
                             v    v   -----------------   -- i v  - iii -- 
  L1M4_orf2#LINE/    401 TCAACAAATGGTG-----------------CTG--GGACAA-CTGGA--T 428

  chr2_41545669_4    958 AACCAAATAACACAACAAAAACAGTAACAAAATCCCTCCAAAAGCATTTC 1007
                          ?   v  i------     i---------   -------i   ---  v
  L1M4_orf2#LINE/    429 AKCCACATG------CAAAAG---------AAT-------GAAG---TTG 453

  chr2_41545669_4   1008 AATCTACATGTCATACTATATATAAAAATTAACTCAAAATGAACCATAAA 1057
                         i i ivi iv   i  i     i                  i i  ? i 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_41545669_4   1058 CCTAAAT-TACAAACATAAAATGGCAAA-----CAGAA--AAGCACAGG- 1098
                                -  vi i -     ivii   -----i    --  i  i   -
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_41545669_4   1099 --AAAT----ATG---TTCAGTTAGAAAAAAAATTCCTTAGATACACCAC 1139
                         --    ----i  ---  vi     iv  vii-  i        iiv   
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGACAC 601

  chr2_41545669_4   1140 CAAATGCATAAACCAAAAAAGAAAAATTTGATAAACTGGGTTTCATCAGA 1189
                             v   i  i v v          v v      i   ii       i 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_41545669_4   1190 GTTAAGAACATCTGCTCCTTGAAATATACTTTTAACAGAACGAAAAGGCA 1239
                         i    i   v i  iv i ii  iv i   v i  v i ii      i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_41545669_4   1240 AGCCACAGATTTGGAAAAAAATGTTTAAAAATTACATATCTGATAGAGAA 1289
                          v       v -  i i     i   iv    i i          ii i 
  L1M4_orf2#LINE/    702 ACCCACAGAAT-GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_41545669_4   1290 CTTACATTCAGAACA-ATACAGAACTTTCAAAATTCAATAATAAAAACG- 1337
                            ii  i     i -   v      i i v  i             vi-
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_41545669_4   1338 AAACAAACCAATTTGAAAAATTGACTAAAGATTTG----GGTACTTGACC 1383
                            i  v      ?-      v i v  i      ---- ii i  vv  
  L1M4_orf2#LINE/    801 AAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_41545669_4   1384 AAAAGAGAT 1392
                            ii    
  L1M4_orf2#LINE/    850 AAAGAAGAT 858

Transitions / transversions = 2.11 (150 / 71)
Gap_init rate = 0.03 (27 / 857), avg. gap size = 3.52 (95 / 27)  


2095 25.79 2.67 0.31  chr2_41560366_41562861.rev      502  1137 (1359)    L1M4_orf2#LINE/L1      258   908 (0)  

  chr2_41560366_4    502 CAAAACAGCATGGTACTGGTATAAAAACAGGTACCTAGACCAATGGAACA 551
                            i    ii         i    ii i  ii iv    i        i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_41560366_4    552 GAATAGAGAACCCAGATATAAACCCAAATATGTAATTCCAACTGATCTTA 601
                             v    ii     v         v i  v  vvvi   i    i  v
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_41560366_4    602 GACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCATATTCAACAA 651
                              i vviv   i v   vv i         i i viv v        
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_41560366_4    652 ATGGTGCTGGGATAACTGGCAAGCCACATGTAGGAGAATGAAACTGGATC 701
                                     i      vv ?       i ii        ii    i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_41560366_4    702 CTCATCTCTTATCTTATACAAAAATCAACTCATGATGGATAAAGGACTTA 751
                          ii i   vi i v           i      vi      v ?i   i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_41560366_4    752 AATCTAAAACCTGAAACTATAAAAATTCTAGAAGATAATATCAGAAAAAC 801
                            v   i v  i           v ii       v  i  vi ?iv  v
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_41560366_4    802 CCTTCTAGAAATTGGCTTACACAAAGATTTCATGACCAAGAACTCCAAGG 851
                         i    vv  vv    v   vi   v i    v iivi v  vvi v  i 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_41560366_4    852 CAAATGCAACAAAAGCAAAGATAAATAGGTGGGACTTAATTAAACTAAAG 901
                           v v          v   i   i   ii v      v  i   v v  i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_41560366_4    902 AGCTTCTGCACAGCAAAAGGAACAGTCTGCAGAGTAAA----CAACCCAC 947
                          i   i  ii vv    i iv  vi  viv i   i  ----        
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_41560366_4    948 AGAGTGGGAGAAAA-ATCTTCACAATCTATACATCTGACAAAGGACTGAT 996
                            i          -  i v  -    -   i      i  i     vi 
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGATAAGGGACTTGT 755

  chr2_41560366_4    997 ATCCAGAATCTACAAAGAACTCT--------AAT--TAGCAAGAAAAA-A 1035
                                  v  i          --------   --  iv    v   - 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_41560366_4   1036 ATCCCATCAAAAAGTGGGCTAAAGACATGAAGAGAAAATTCTCAAAGGAA 1085
                          i  v  i?    i     v  i  iv    v   v v     v  i   
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_41560366_4   1086 GATATACAAATGGCCAACAAACA-AGAAAAAAATGCTCAACATCACCAAT 1134
                                          i  i  - vi    i             ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_41560366_4   1135 GAT 1137
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.29 (90 / 70)
Gap_init rate = 0.01 (8 / 651), avg. gap size = 2.38 (19 / 8)  

2973 24.60 4.41 0.73  chr2_41560366_41562861.rev     1194  2010 (486)    L1M4_orf2#LINE/L1       62   908 (0)  

  chr2_41560366_4   1194 CCAAAGTGATCTACATATTGATTGCAATCCTTATGAAAACCCCAGTGGCA 1243
                              v         v   v vi       i   v    i     iv  v
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_41560366_4   1244 TTTGCTATGGCAGTAGAAAAAAAAATCTGGAAATTCATGTAGAACCACAG 1293
                            vi iii v i v  v  ivvi   ivi        i i   vii  i
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_41560366_4   1294 AAGAATCCCAG--TAGCCAAAGCAATCTTCAGAAAGAACAATGAAGT-GC 1340
                         ii  --     --        i       v i      v  ii    - v
  L1M4_orf2#LINE/    162 GGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_41560366_4   1341 AAGAATCAAATTATCTGTCTTCAAAATATACTACAAAATGATAGCAATCA 1390
                          i  v   v i vi iivi       iv         iiv i  i     
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_41560366_4   1391 AAGCAGTGTGGTACTGGCATAAAAAAAAGAGACACAGACCAATGGAACAG 1440
                          ii                   ii v -  v i i   i        i  
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATA-GACATATAGATCAATGGAATAG 308

  chr2_41560366_4   1441 AATAGAGAACCCAGAAATAAACCCACTCATCTATAGTCAACTGATCT--- 1487
                            v    ii               iv   i   i     i    i ---
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_41560366_4   1488 GTAAAGGTGCCATGAACACAAAATGGGAGAAGGATAATCTTTTTAA---- 1533
                         ii  i       v  v  ivv      ii   i   i      i  ----
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_41560366_4   1534 TGGTGTTGGGAAAACTGGATGTCCACATGCAGAAGAATGAAATTTGACCC 1583
                              i     v        i?         i         i  v     
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_41560366_4   1584 TTGGATTATACCATATATAAAAATCAACTAAAAATGGATTTAAAAACTTA 1633
                         i ivv i i        i      i    v         i- ? i  i  
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATC-AWAGACCTA 507

  chr2_41560366_4   1634 AAAGTAATACCTGAAACTATAAAAATACTAGAAGAAAACACATGGGAAGA 1683
                           v    v v  i           v vi            i v ? v i 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_41560366_4   1684 GCTTCTTGACATTTGTCTGGGCAGTGGATTTTTGGATATAACACCAAAAG 1733
                         v    v    v  v vi i    i   v  i  i     i          
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_41560366_4   1734 CACAGAAAACGGAAGCAAAAATAGAGAAATGGGATTACATCAAGCTGAAA 1783
                             iiv   ii   v         v    v   i v      iv v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_41560366_4   1784 AGCTTATGCATTTCAACAGGGACA--ATCCACACAGTGAAAAGGCAAC-- 1829
                          i   v  iii     --i     --   v v v         i    --
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAA--AGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_41560366_4   1830 ------------GAAATATTTGCAGACCATAC--CTGATAGGGGGTTAAT 1865
                         ------------i           i i    i--      i   ii vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_41560366_4   1866 CCGCAAAATACATAAGAAGCTCATACAAGTCAATAGCAAAAA-------- 1907
                         viv  i    i    ii i   v     v      ii     --------
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_41560366_4   1908 ACCTGTTTAAAAAATTGGCAAAGGACCTGATTAAACGTTTCTCAAAAGTT 1957
                            iiv  ?      v         ii   v  i  i      v    vv
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_41560366_4   1958 GATATACAAATAGTCAACAAGTATATGAAAAGGTGCTCATAATCCCTAAT 2007
                                    i i   i   i i        i      vv   v?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_41560366_4   2008 CAT 2010
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.63 (122 / 75)
Gap_init rate = 0.01 (12 / 847), avg. gap size = 3.50 (42 / 12)  


3145 26.66 0.44 1.74  chr2_41575037_41579252.rev     2806  3724 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_41575037_4   2806 GAAAAAATATTCCATGTTTACGGATTGGAAGAATCAATATTGTTAAAATG 2855
                          i   i    i       i i           v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_41575037_4   2856 TCCATACTACCCAAAGCAGTCTATAGATTCAATGCAATTAGTATAAAAAT 2905
                         v v     v      viii    i        i     ivv   v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_41575037_4   2906 ACCAATGACATTCTCCACAGAAGTAGCAAAAAC-AATCCTAAAATTTATA 2954
                         v   iivi v  i iii     i v - v  i -i           i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCATA 150

  chr2_41575037_4   2955 TGGAACCACAAAAGACCCCAAATAGCCAAAGCTATCCTAAGCAAAAAGAA 3004
                              vii   ii     vi          i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_41575037_4   3005 CAAAACAGCAGGAAATCACATTACTTGACTTCAAATTATATGACCGAGCT 3054
                             iiv v    v-     i v iii i      viv  iv  vi    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_41575037_4   3055 ATAGTAACCAAAACAGCATGGTGCTGGCATAAAAACAGACACAAAGTCCA 3104
                          i     i   i    ii    i         ii i     i v  vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_41575037_4   3105 ATGGAACAGAATAGACAACTCAGAAAGAAATCCACACACCTACATTGAAC 3154
                               i     v  v iii      v   i   i   ii  iiv v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_41575037_4   3155 TCATTTACAGTAAAGATGCCAAGAACATACACTGGGAAAAAGACAGTCTC 3204
                          v    v iii  i i        v   v  v    i   ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_41575037_4   3205 TTCAATAATAAATGGTGCTTGGAAAACTGGCTATCCATACACAGAAGAAT 3254
                              i  ---        v   v      v  ?   i ii  i      
  L1M4_orf2#LINE/    400 TTCAACAA---ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_41575037_4   3255 GAAACTAGGTCCCTATCTCTTGCCATATACAAAAATAAAATCAAAATGTA 3304
                            ii i ii     i   vii              v  v        v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_41575037_4   3305 TTGAAGACTTAAATCTAAGACCTCAAACCATGAAAATACTATGGGAAAAC 3354
                          ii?    i     v     v  v    i  i   v vi  vii      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_41575037_4   3355 ATTAAGGAAACTCTCTAAGACATTGGTATGGGCAAAGATTTCTTGAGAAA 3404
                           vii? v  v   iiiv   v    vv i     v i      --- i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT---AGA 593

  chr2_41575037_4   3405 CATGCCAC---AGGCACTGGCAACCAAAGCAACAATGAACAAATAAGATC 3451
                         i   v   --- i    vi     v    v  v   ii i    vi  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_41575037_4   3452 ACATTAAATAAAAAAAACTTTTGAATAGCAAAGGATACAGTCAACAAAGT 3501
                         v   i   - vv           viivv       i  vi    v     
  L1M4_orf2#LINE/    644 TCATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_41575037_4   3502 GAAGAGAAAACTCACCTAATGGGAGAAAATATTTGTAAACTATCCATCTG 3551
                            i   v   i   vv                  i   ii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_41575037_4   3552 ACAAGGGATTAATAACCAGAATATATAAGGAGCTCAAACAATTCTATAGA 3601
                          i      i vi  v             i  i   vv    i  v   iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_41575037_4   3602 AAAAAAATCTAATTGTTTGATCAAAAGATGGGCAAAAGACTTAAATAGAC 3651
                              i - v   viiiii  i?   i         i  i  i       
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_41575037_4   3652 TTTTTTTTTTTTTAAAAAAAGACATACAAATGGCAAACAGACCTATGAAA 3701
                         v   i ii------   i    i           v  i ii vi      
  L1M4_orf2#LINE/    842 ATTTCTCC------AAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_41575037_4   3702 AAGTGCTCAACATCATTGATCAT 3724
                          ii            ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (154 / 87)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 2.22 (20 / 9)  


1461 27.86 1.20 1.00  chr2_41587296_41589218      501   999 (924)    L1M4_orf2#LINE/L1      284   783 (125)  

  chr2_41587296_4    501 ACAGACACATACAGCAATGAAACAGAATAGAGAACCCAGGAATAAGGCTA 550
                          i     i   v v     i  i     v    ii    i     iv i 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_41587296_4    551 CACCCCTACAACCGTCTGATCTTCAACAAAGCTGACAAAAACAAGAAATG 600
                         i  vii  iiii ivi    i   i    i v  v   i v  vvv    
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_41587296_4    601 GGGAAAGAACTCTCTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCA 650
                                  ivv   v     i              i      v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_41587296_4    651 TATGCACAAGATTGAAACTGCACCCCTTCCCTAAACCATAGACAAAAATC 700
                         i     v    v    ii  v      v  ii v      v        i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_41587296_4    701 AGCTTCAGATGGAGTA-AGACTAAAATTTAAAACCCAAATCTATAAAAAT 749
                          i  iv i     vi -    iv    v   i v i   v        v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_41587296_4    750 CCTAGAAAACTACCTAGGCAATACTATTCTGGACATAAGAATGGGCAAAG 799
                          i     i vv  v    ?ivv v v   vv   v vi iv i     v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_41587296_4    800 ATTTCATAATGAATATG---CCAAAAGCAATTGCAACAAAAGCAAAACTT 846
                         i    v  ---i     ---         vvv          v    v v
  L1M4_orf2#LINE/    584 GTTTCTTA---GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_41587296_4    847 GGCAAATAGGAACCAATTAAACTTAAGAGCCTTTGCACAGCAAAAGAAGC 896
                          ii    v   viiv  i   v    i i i    ii vv    i  vi 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_41587296_4    897 TAT-AAGCAGAGTAAACAGACGACCTACAGAATGGGAGACAAAT-TTTGC 944
                            -   - i   i  v    i   i             -    -     
  L1M4_orf2#LINE/    681 TATCAAG-AAAGTGAAAAGACAACCCACAGAATGGGAGA-AAATATTTGC 728

  chr2_41587296_4    945 AAACTATGCATCTCACAAAGCCCTAATATCCAGCATCTATAAGGACCTTA 994
                            ii  ii    v i  i vv  vi       v  v     i  v  iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_41587296_4    995 AACAA 999
                         v    
  L1M4_orf2#LINE/    779 TACAA 783

Transitions / transversions = 1.08 (71 / 66)
Gap_init rate = 0.01 (7 / 500), avg. gap size = 1.57 (11 / 7)  

 464 20.54 2.68 0.00  chr2_41587296_41589218     1320  1431 (492)    L1M4_orf2#LINE/L1      794   908 (0)  

  chr2_41587296_4   1320 AAAAAACAAA---CTTTATTAAAAAGTGGACAAAGGACATGTACAGACAC 1366
                             i     --- iiv   ?    i   i       iv  v i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_41587296_4   1367 TTTTCAAAAGAAGACATACCTGTGGCCAATAAGCATATGTAAAAAAGTTC 1416
                           i  v        i    vvi             i   v   i v i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_41587296_4   1417 AACATCACTGATCGT 1431
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.01 (1 / 115), avg. gap size = 3.00 (3 / 1)  


2825 25.23 4.91 1.26  chr2_41692192_41695156.rev     1604  2479 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_41692192_4   1604 TGGAAAAACATCTCATGCTCCTGGATAGGAAGAATCATTATAATTAAAAT 1653
                               i i   i    i  v     v      v i v   vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_41692192_4   1654 GGCCATAGTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAA- 1702
                            v   v v      vii  i           i  v  i         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_41692192_4   1703 ---CAAC-----------CAA----TGACA------TCCT-----TTATA 1723
                         ---  i -----------  i----     ------    ----- i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_41692192_4   1724 TAGAACCAGAGAAGATCACAAATAGCAAAGGCAATCCTAAGCAAAAAGAA 1773
                          i   viiv iii  i vvi      v  ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_41692192_4   1774 CAAAGCTGGGAGCATCACATTACCTGACTTCAAATTATATACTACAGTGT 1823
                              i   ii vv     i v  ii i      -- iv       iv i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAGC 248

  chr2_41692192_4   1824 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACTGGGACATAGAGC 1873
                                 i   i    ii         i i  ii iv iv i     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_41692192_4   1874 AATGAAACAGAATGGAGAGCCCAAAAATAAGGGTACACACGTACAACCAC 1923
                             i  i     v     i   i      ivvi i   iv  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_41692192_4   1924 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAAGAC--TCC 1971
                         i    i  i     ivv  v   i v  vv           ii i--  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_41692192_4   1972 TTATTCAATAAATGGTGCTGGAATAACTGGCTAACCATAAGCAGAAGATT 2021
                           --    i            i i      v  ?   i v   i    v 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_41692192_4   2022 GAAGCTGCACCCCTTCCTTACACCGTATACAAAAATCAACTCAAGAGTGA 2071
                             i  v      v   i     i           i       i vv  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_41692192_4   2072 TTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACTCT-AGAAGACAA 2120
                          i ?    i         i v i            -    -      v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr2_41692192_4   2121 CTTAGGC---AATGCCATCCTGAACATAGAGAATGACCAAAAATTTCATG 2167
                          v    ?---   -- v  v   v v i ivv v --   vii    - v
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGG--CAATGGTTTC-TT 590

  chr2_41692192_4   2168 AGAAA-AACACCAAAAGCAATAGCAACAAAAGCACAAATTGACAAATGGG 2216
                            v -i            vv           v v    v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_41692192_4   2217 ATCTAATTAAATTTAAGAGCTTCTGTACAGTCAAAGAA-ACTATCAACAG 2265
                          ii v  i   v    i i   i   i -v      i -        v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAA 689

  chr2_41692192_4   2266 AATAAACAGGCAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCAC 2315
                          i i  v  i     i                          ii  ii i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_41692192_4   2316 CCAACAAAGGCCTGATATCTAGCAT-CATAAGAAACTTAAACAAATTTGC 2364
                          ii i  i  v  vi    i  v  -i    ii    ivv    v ivii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_41692192_4   2365 AAGAGAAAAACAA----CTCCATTGAAAAGTGGGCAAAGGAAAAGAACAG 2410
                           v i   i    ---- i v   ?    i           vvv   i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_41692192_4   2411 ACATTTTTAAAAAGAAGACGTACAAATGGCCCATAAGCATATGAAAAATT 2460
                               i vv        ii           v       i       iv 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_41692192_4   2461 GATCAATGTCACTAATCAT 2479
                          v    ii   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (134 / 83)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.84 (54 / 19)  


2113 19.93 10.05 4.45  chr2_41813242_41815474.rev     1127  1733 (500)    L1M4_orf2#LINE/L1      241   881 (27)  

  chr2_41813242_4   1127 TATAAAACTACAGTAATTAA-ACAGTATGATACTGGCATAAAGGTAGACA 1175
                           i   i          i  -     i  i           i i      
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_41813242_4   1176 TATTAGATCAATGGAACAAA-----GAACCCAGAAACAAACCCATGCATA 1220
                            -            i i -----  ii       i        i   v
  L1M4_orf2#LINE/    291 TAT-AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_41813242_4   1221 TATGGTCAACTGACCAAAATATGCAAGGATATCTGACAAGGATACAAAAA 1270
                                  i   ---------------- v ii       i i v  i 
  L1M4_orf2#LINE/    340 TATGGTCAATTGA----------------TTTTCGACAAGGGTGCCAAGA 373

  chr2_41813242_4   1271 ATATGCAATGGGAAAA--ATAGTCTCTTCAGGAAATTGGTATTGGAAAAA 1318
                         vi  v       i   --       i    iv    -   ii   i v  
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT-GGTGCTGGGACAA 422

  chr2_41813242_4   1319 CCAGGTATCCACGTGCAAAA-AATGAAATTGATCTCCTACCT-------- 1359
                          ii i  ?    i       -      i   iv i       --------
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_41813242_4   1360 ----AAAAAT-----------GGATTAAAGACTTACAGGTAAGACCTGAA 1394
                         ----      -----------    i ?    i  v v      v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_41813242_4   1395 ACTATAAAATCCCTAGGAGAAAATACATAGG---AAACACTTCTTCGTA- 1440
                                  ii i   i      --      ---   ----       i-
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAA----TCTTCGTGA 566

  chr2_41813242_4   1441 --TTGATCTTGGCAATGGTTTCTTGGATGTGACACCAAAAGCACAGGCAA 1488
                         --   ivi v              i   i                i    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_41813242_4   1489 CAAAAGCGTAAATAGACAAGTGAGACTATATCAAACTAGGAAGCTTTTGC 1538
                               viv       i  i vi    vi      v vii  i      i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_41813242_4   1539 ATAATAAAGGAAAC----AACAGAATGAAAAGGCAACCTCTGGAATGGGA 1584
                         iivvi      v  ----  v i i       i     ivii        
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_41813242_4   1585 GAAAGT-TCTGTAAACCATATGTCTGATAAGGGGTTAATGTCTAAAATAG 1633
                             i - i  i   i     i           ii vi i  i i    v
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_41813242_4   1634 ATAA----------CA---CAAAAGCAAGAAAGCAAATAA-----TTAAA 1665
                             ----------  ---   v ii  i  ii       -----  ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_41813242_4   1666 AAATGTGCAAATGACTTGAACAGACATTTGTCCAAAGAACAAGATATACA 1715
                              v     v  i     i        v         ---        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA---GATATACA 863

  chr2_41813242_4   1716 AAAGGCCAACAGATATAT 1733
                           v      i iii i  
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACAT 881

Transitions / transversions = 2.81 (87 / 31)
Gap_init rate = 0.03 (19 / 641), avg. gap size = 4.63 (88 / 19)  


3033 25.61 5.19 0.58  chr2_41820820_41822752.rev      576  1442 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_41820820_4    576 GGAGAGCCATTCCACGTTTATGAATAGGAAGACCCAATACTGTAAACATA 625
                            i  vi  i   i   i   i  v       ii    i   v  v  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_41820820_4    626 TGAGTTCTTTCCAACTTGATCTATAGATCCAATGCAATCTCAGTCACAAT 675
                         vv i v  ii    v        i    i   i      i vi   v   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_41820820_4    676 CTCAGCCAGTTATCTTGTGAATACTGACAAACAAATTCTAGTGTTTATAT 725
                          i    iivi v i   iii v i      i vi  i   ivi  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_41820820_4    726 GGAGAGGCAAAATGATCCAGAATAGCCAACATAATATTGAA---GGAGAA 772
                            i v    ii-  i             v i   v     --- i    
  L1M4_orf2#LINE/    152 GGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_41820820_4    773 CAAAATTGGAGGACTGACACTGTCAGACTTCGA--CTTACTATAAAATTA 820
                             i          v     vi vi i   i --       i   ii  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_41820820_4    821 CAATAATAAAGACAGTGTGGTATTAGTGAAAGAATGGACA----AATCAG 866
                           i    v              i i iiv   i  i    ----i    i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_41820820_4    867 TAGAACAAAGTAAAGAGCTCCCAAATGAACCCACATAAATACAGTCAACT 916
                          i   i i i vi    ii vv    i      i i vv  ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_41820820_4    917 AAT---AGACAAAGGAGCAAAGACAACACAGTGGAGAAAAGATAGTCTTT 963
                         i  ---v     i  v  v     v iv  i   i    ii         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_41820820_4    964 TTGACAG-TGGTGCTGGAACAACTGAACATCCACATGTAAAGAAATAAAT 1012
                          ii   i-         i       i i ?       i   ii   i  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_41820820_4   1013 CCAGAC----AC---AGACCAT-TACAAAGATTATCTCAAAATGGATCAC 1054
                         iii   ----  --- v     -      i    v              ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_41820820_4   1055 AGACCTGCATGTAA-----AACAC----AAGCTCCTAGAAGAAAACA--A 1093
                               iv      -----  v  ----  i   i            --i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_41820820_4   1094 GAGACAATTGAGGTGATCTTGAGTTTGGCAATGACTTTTTGGGTATGACA 1143
                          ? vv   ivvv    i    i   v       ii  i  i i       
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_41820820_4   1144 CCAATGGCATGATCTATGAAAGAAATAATTGATAAGCTGGACTTCATTAA 1193
                             vi   ii v v ii       v   v     ii          i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_41820820_4   1194 AAGTAAATATTTCTGTGGTGTTAAATATGCTGTGAAGGAA-TAAAAAGAC 1242
                           v    v i  i    v viv  iv ii  i v   i  - i       
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_41820820_4   1243 AAGTCAGAGACTAGAAGAACATATTTGCAAAAACCATATA-------AGG 1285
                           vi  v   v i i    v           --i      -------   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAA--TCATATATCTGATAAGG 748

  chr2_41820820_4   1286 --CCTGTTATCCAAAATATAAAAGGAACTCTTAAAACTCAACAATAAGAA 1333
                         -- i   -     i      v  i         v       i     i  
  L1M4_orf2#LINE/    749 GACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_41820820_4   1334 AACGAACAACATGATTAGAAAAGGGGCCAAAAACCTCAACAGACA---CT 1380
                         i  i  i   vii   ?i    v    v  ii ii v  i     ---  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_41820820_4   1381 ACCACAGAAAATAAACAGATGGCAAATAAACATGCAAAAAGGTGCTCCAC 1430
                         -   v    i   v   i     v     i  iiii     i     v  
  L1M4_orf2#LINE/    848 -CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_41820820_4   1431 ATCCTATGTCAT 1442
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (147 / 71)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 2.63 (50 / 19)  


1185 23.66 0.00 0.38  chr2_41934769_41936686.rev        1   262 (1656)    L1M4_orf2#LINE/L1       16   276 (632)  

  chr2_41934769_4      1 TGTTCATGGACAGGAAGGCTCAATCTTGTTGAGATGTCAACTCTTCCTAA 50
                                   iv     i  i   v     i     v   iv  i  i  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_41934769_4     51 ATTGATCTATACCTGCAACACAATCCCAGTAAAAATCCTTGCAAATTATT 100
                                  i vv v    i       vi v       iv  vivi v  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_41934769_4    101 TTGTGGATATCAACAAACTGATTCTAAAGTTTTATATGGAAAGACAAAAG 150
                            ii  v  ii    i     i     i  -i         vi   ii 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATT-CATATGGAAATGCAAGGG 164

  chr2_41934769_4    151 ACCCAGAATATTCAATAAAATATTGAAGAGGAAGAGCAAAGTCAGAAGAC 200
                                   vi   v v   v     i i     i      ii  i   
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_41934769_4    201 TGACACTACATGGCTTCAAGTCTTACTATAAAGCTTCAGTAATCAAGACA 250
                          v     v viiii     iv       i      v              
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_41934769_4    251 GTGTGGTACAGG 262
                                  v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGG 276

Transitions / transversions = 1.48 (37 / 25)
Gap_init rate = 0.00 (1 / 261), avg. gap size = 1.00 (1 / 1)  

1076 23.53 5.04 3.64  chr2_41934769_41936686.rev      501   857 (1061)    L1M4_orf2#LINE/L1      271   632 (276)  

  chr2_41934769_4    501 TATTGGTAAAAGAATAGACA----GATTGATGGGACAAAATAGAGAGCCT 546
                           i   i v   i       ----   ii    i i i   v     i i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_41934769_4    547 AGAAATAGATCCACAAAAT-ACAGTCA-CTGGTCTTTGACAAAGAAGGAA 594
                                i i   i v v - ii    -i  i i  i     i iv vv 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_41934769_4    595 AGGCAATACAAAGGAGAAAGAATAGTCCTTTCAGCAAATGGTGCTGAAAC 644
                           i v  v   v  i            i     i            ii  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_41934769_4    645 AACTGGATATCTAAATGCAAAAAAAAAAAAAAAAAAATCTAGATACAGAC 694
                                  ? i v        i  vi  i--------i i  iv vv  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAG--------TTGGACCCCTAC 462

  chr2_41934769_4    695 CTTACAGCTTTCACAAAAATTAA-----AATGGATCACAGGCCTAA-TTT 738
                           i   v v vi           -----         ?  i     - v 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_41934769_4    739 AAAATGC-AAAATTATAAAACTTCTGGAAAGTAACAGA-----AAATTTA 782
                           i -  -    i         ii i   iiv    v -----    i v
  L1M4_orf2#LINE/    513 AAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_41934769_4    783 GTTGACTTTGAGTTTGGCAATGAGTTTTTAGATAAAACACCAAAAGCATA 832
                         vv    i   i   v       iv  i       vi            i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_41934769_4    833 ATTAATCAATGGAAGAAAACATTGA 857
                          vi  -   ---       v  v  
  L1M4_orf2#LINE/    612 AGCAA-CAA---AAGAAAAAATAGA 632

Transitions / transversions = 1.73 (52 / 30)
Gap_init rate = 0.03 (11 / 362), avg. gap size = 2.82 (31 / 11)  

 795 21.14 12.20 4.07  chr2_41934769_41936686.rev     1181  1426 (492)    L1M4_orf2#LINE/L1      643   908 (0)  

  chr2_41934769_4   1181 TTCATTCAAATTAAAAATTTTGGCTCTGCAAAAATTAATTTCATGCACTG 1230
                              iv          i   v iv  v    ii----------i    i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG----------ACACTA 682

  chr2_41934769_4   1231 TTAAGAGATTCAAAAGACAGGTCACAGACTGAGAGGGGATATTTGCAAAA 1280
                          i    i v v        ivi      v  i   iii           v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_41934769_4   1281 CACATATCTGATAACAG-CTTGTATCCAAAATATGCAAATAATTCTGAAA 1329
                           i           vi -          i     ii   v  i   v v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_41934769_4   1330 ATTCAACAATAAGAAAACAA----CCCAGT-------------------- 1355
                          i    i     i  i    ----    i --------------------
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_41934769_4   1356 -----AGATGCTTCACCAAAGAAAATATACAGATGGCAAATAAGCATATG 1400
                         -----   iii   v        i       i     v        i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_41934769_4   1401 AAAAAAAGCTTAGCATTATAGTCATC 1426
                             i v   i i   i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (36 / 16)
Gap_init rate = 0.02 (4 / 266), avg. gap size = 10.00 (40 / 4)  


2839 24.75 4.50 2.36  chr2_41960807_41963651     1465  2353 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_41960807_4   1465 TAGAGAAACATATCATGTTCATGGACTGAAAGATCCAACATAGTAAAGAT 1514
                          i  i i i  vi            i  i    iii  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_41960807_4   1515 GTCAATTCTCCCCAAACTGACATACAGATTTGACCTAA---CTATCAAAA 1561
                          v    v         i   iv        ii  vi  ---         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_41960807_4   1562 ATCCAGCAAGACTGTTTTATAGATATGGACAAGAATATTCTAAAACGAAT 1611
                         vi     v- v  v    ii   v  v      vvv  i      ivv  
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_41960807_4   1612 ACATGGAAAGACAAAAGAACTAGAATAGCTAAAATAA------------- 1648
                          --      vi   ii  v i        i    i  -------------
  L1M4_orf2#LINE/    150 A--TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_41960807_4   1649 AAATAAAGTGATAGGAATC---TGTCTTATTTTCAAGACTTATAATATTG 1695
                         i  i     viv    v  ---iv  ii v      i     iv i vv 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_41960807_4   1696 CTACCATAATCAAGACTCTGTGGTACTGGTGGAAGGAGAGACATATAGAT 1745
                             vi          vv           iiv     v            
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_41960807_4   1746 CAATGGGACAGAATAAAGACTGCAGAAATAGAACCACGCAAATATACCCA 1795
                               i i     vi   v v        i v   ii  vv   ivi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_41960807_4   1796 ACTCATTTTTGACAAAGGAACAAAAGCAATTCAATAAAGAAAAGACAGCC 1845
                          i v     i     i  vi v  ii v       iii    ii i  i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_41960807_4   1846 TTTTCAGCAAATGGTGCTGGAAGAATTGGACATCTATAGGCCAAAAAAAG 1895
                               i             i v  i    i ? i i v  v   i  v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_41960807_4   1896 ATCCTTGACC--TAATCCTCACATCTTATAC------TGACTCAAAATGG 1937
                          vvi v    --  --       i v     ------ i           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_41960807_4   1938 AACAAAGACCCTTAAATATAAACCATAAAACTATAAAACTTTTAGAAAAT 1987
                          v  ?     --     i   ivvv               i      i -
  L1M4_orf2#LINE/    496 ATCAWAGACC--TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA- 542

  chr2_41960807_4   1988 AAAACTTGGGAGAAAATCTTCAGGATCCAGGGATAGGCAAAGAATGTTTA 2037
                         -    v i  ? v        iv  i iv   v       v iv vi   
  L1M4_orf2#LINE/    543 -AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_41960807_4   2038 GACTTGTCACCAAAAGCATGATCCATTAAAGGAAAAAAT-GATAAATTGG 2086
                           iv  v           ii v v i-   i        -          
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGG 640

  chr2_41960807_4   2087 ACTTCATCAAAATTTAAAA--TTTGCTCTGCGAAAGACTGTTGCTGAGGG 2134
                                       v    --    iv  v i  i   -ii iiii  ii
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC-ACTATCAAGAA 689

  chr2_41960807_4   2135 GATGAAAAGACAAGCTACATAATGGGAGAAAATATTTGCAAACCATAATC 2184
                         ii           v i   v                      i    ---
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA--- 736

  chr2_41960807_4   2185 AAACCAATAGTCAACAAACGACTGTTATCTAGAATGTGAAAAGAACTCTC 2234
                         -------  viii i  iv    vv    i     i iv          i
  L1M4_orf2#LINE/    737 -------TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_41960807_4   2235 AAAATGTGACAATTAAGAAACA-----TCAGATAAGAAAATGAGAAAA-- 2277
                          v  ivii i   v  i i   -----i vi  v?i      i v   --
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_41960807_4   2278 --TTACATAGACATTTCATCAAAAAGGATATACAGATGACAAATAAGCAC 2325
                         --  iv           vi    i i        i   i v         
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_41960807_4   2326 ATAAAAATATTTTCA-CATCAGTAGCCAT 2353
                           i    v  vi   -     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (127 / 89)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.39 (61 / 18)  


1803 20.48 6.78 11.90  chr2_42258020_42261504.rev     1742  2405 (1080)    L1M4_orf2#LINE/L1        1   630 (278)  

  chr2_42258020_4   1742 TGAAAAAAGACTTTGTGCTCATGGATTGAAAGACTCAATATTGTTAAGAT 1791
                           i   i v iiiii  i          i      i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_42258020_4   1792 GTCAGTTTTCCCCTAATAGATCTGTAGATTCAATGCAATCCTCATCAAAA 1841
                          v  i vi     v   v     ii        i       ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_42258020_4   1842 TTCCAGTAGGCTTTCCCCTCTCAGAAACTGGCAAACTTATTCTAAAATTC 1891
                          i    iv v    i--- iv      i  i   i  v  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT---TTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_42258020_4   1892 A------AGCTTAA----TCTAGAAT--TCATATTTTTCTTAGAAAA--A 1927
                          ------ iivi  ----i i     --i  v vivv    ii    -- 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_42258020_4   1928 GAATAAAGTTAGA-----------------TTTCAAGACTTGCAATAAAG 1960
                            i      i  -----------------      i    i v i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_42258020_4   1961 CTACAGTAATCAAGACAATTTTTATTTGTCTTGACAAATACCCAGACAAA 2010
                                          i -------------------------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGT------------------------------- 266

  chr2_42258020_4   2011 TTATATTTGTCTTAATACAAATACCCAATTTGATATTTGTATTGAGATAG 2060
                         --------  --------------------- i  i v i  vii     
  L1M4_orf2#LINE/    267 --------GT---------------------GGTACTGGCATAAGGATAG 287

  chr2_42258020_4   2061 AAAAATAGATCAATGTAACAGAATAGAGAATCCAGAA-TAGACCCACAAA 2109
                          v v           v  i     v    i       -  i     i v 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_42258020_4   2110 TATATGGTCAATTGTCAATTGACTTTCAACAAAAGTGCAAAGACACTTCA 2159
                          v            ------- i    i    ii    v     vv    
  L1M4_orf2#LINE/    338 TTTATGGTCAATTG-------ATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_42258020_4   2160 GTAGATAAAGATCAGTCTTTTCAATAAATGGTGCTAGAACTATTGGATAT 2209
                         i i iv     vi           i          i i  v i      ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_42258020_4   2210 TCATAGATTATAGACAAAAAACTAAACATCATTCTAAACTTTGCATTATA 2259
                         i  i viiv v   - vi  ii ii  ----ii   -- i ii  ii   
  L1M4_orf2#LINE/    431 CCACATGCAAAAGA-ATGAAGTTGGAC----CCCTA--CCTCACACCATA 473

  chr2_42258020_4   2260 TACAAAAATTAACTCAAAAT-------AGACTTAAATATAAAATCTAAAC 2302
                                             -------    i     i   i v     v
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_42258020_4   2303 GTATAAAAATTTTGGAAGCAAACA--GGAGAAAATCTCTGTGACCTTGGG 2350
                         v       v i  i    v     --  ? v      ii           
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_42258020_4   2351 TTAGGTAAAGATTTCTCAGAT----CACCAAACGCACCATCCATGCAAGA 2396
                              i  v i     i    ----       v    v v v iiv    
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_42258020_4   2397 AAATTAATA 2405
                            --    
  L1M4_orf2#LINE/    624 AAA--AATA 630

Transitions / transversions = 1.98 (89 / 45)
Gap_init rate = 0.03 (17 / 630), avg. gap size = 7.29 (124 / 17)  

 733 24.24 6.06 3.03  chr2_42258020_42261504.rev     2697  2993 (492)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr2_42258020_4   2697 AAAAAAAAAAAAAAGAAAAAAGAAAACTAATAAATTGCATTGCATCAAA- 2745
                             iv v  iv  v    i i    ivi        v i v       -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_42258020_4   2746 TTAAGAATTTCTGTTCTTGAAAGG-CATTGTTAAGGAAATAAAAAGAT-- 2792
                             i  i  i   v   v     -  i i i   i  i i      i--
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_42258020_4   2793 ---------TAGGAGAAAGGATTTGCCAATCATATATCTTACCAAGGAGT 2833
                         --------- i       iv      v            v iv i   v 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_42258020_4   2834 TGTTTGCAGTATATATAGA---CTCTTAAAACTCAACAGTTAAGAAAAAG 2880
                            v v   v       i ---      v       ----   v      
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAA----TAATAAAAAG 798

  chr2_42258020_4   2881 CAAAACAAAACCCTGGTTAAAATATAAGCAGAAGGCATGAA-AGATTCGT 2929
                         vv   i  ---  iii  ?   v  ii   i i iiv    -   iviv 
  L1M4_orf2#LINE/    799 ACAAATAA---CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_42258020_4   2930 CACCAGAGAAGATACAAGGATGGCAAATATGCCCATGAAA-GATTTTTTC 2978
                          v   i        i vii     v    v  v       -   vi -- 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT--C 893

  chr2_42258020_4   2979 AACCTCAGTAGTTAT 2993
                            v   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (39 / 32)
Gap_init rate = 0.03 (9 / 306), avg. gap size = 3.00 (27 / 9)  


 891 29.01 18.09 2.22  chr2_42429071_42431190      533  1118 (1002)    L1M4_orf2#LINE/L1        2   680 (228)  

  chr2_42429071_4    533 GGAGGGATGTTACATAATCATGGATAGGA-GAC--GATG-----AAGACG 574
                            ii   i iv   iv        v   -   --i  i-----    i 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_42429071_4    575 TCACT--TTTGCATATTGAGCTATATATACATTTAGCAGA----GTCAAA 618
                         v  v -- iiv  v     v   i v  v  vi--   iv----i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAAC--GCAATCCCTATCAAA 99

  chr2_42429071_4    619 A-CTCAGCT------TTCATAGGAGTTGACAAACTGA-------ATATAT 654
                          - i     ------  iii  i i       i    -------  vi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_42429071_4    655 GTGGAAATATGAAGGGGAAGAAATAGGGAATAGCCA---CAATTGTAAAG 701
                         i       ii-     ------ ivvi         ---    iv i  i
  L1M4_orf2#LINE/    150 ATGGAAATGC-AAGGG------ACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_42429071_4    702 AAAAAGAATAAGGTCAAAGCACATAAAATATAAAATATCAAGACTTAT-- 749
                           i     i  i  iii  v  vi v v vivv   v    i     i--
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_42429071_4    750 ----------GTAATTAAGACATTGTGATAC------------AAACATA 777
                         ----------     i      v    i   ------------ i     
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_42429071_4    778 --GATCAGTGGAA-------GAGAATATAGAAACAGGTTACACAAATC-- 816
                         --     i     -------    i vi     i iiii-  i v  i--
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC-CATACATTTA 341

  chr2_42429071_4    817 -AGTTGCTTGACTTATGCCAAAGGTGGCGA-----TGCAGTAGGCGCAGA 860
                         -i  iiv    i  vi v   i    v i ----- v  i i  viv   
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_42429071_4    861 ATAATGTTTTCAGTGAATGGTGCTGGCTTAATTGGATACTCATATGAAAA 910
                            i v      iii           vvi  i      ?i  i   v   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_42429071_4    911 AAAAATTACCTTG-ACCCCTCCCTCACAGCATTCAGAAAAATCAGTTTTA 959
                          i  - v vv   -      v       v   vi v      i ii iv 
  L1M4_orf2#LINE/    442 AGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_42429071_4    960 GATGGATTATGCATCTTAGCATGAAAGGTAAAAAACAGTAAAGCTTTTAG 1009
                         i      i ?iv i  v iii i i  v     -- vi    i  i    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAA--CTATAAAACTCTTAG 538

  chr2_42429071_4   1010 AAGAAAATACAG-----AAC-------ACCTTTA--TAAGTA--GATTTC 1043
                                i i  -----  i-------     vi--  i i -- i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_42429071_4   1044 TTAA----GGCATATAAAGTACTAACCATAATGGGAGAAAAAGATAAAT- 1088
                            i---- i  ivv    i  v i v i  vi i i   v        -
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_42429071_4   1089 ------CAT----GTTAAAAACTTCTCTTTATCAA--GACAC 1118
                         ------   ----i          i v viv    --     
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

Transitions / transversions = 1.80 (108 / 60)
Gap_init rate = 0.04 (30 / 679), avg. gap size = 3.97 (119 / 30)  

 420 30.81 7.58 0.00  chr2_42429071_42431190     1431  1628 (492)    L1M4_orf2#LINE/L1      696   908 (0)  

  chr2_42429071_4   1431 AAGACACCTTTAAGAGTGTGAGAAAATATTTGTGATACATACTTCCAACA 1480
                               v iivv   i  v             ii vv    iv  ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_42429071_4   1481 AAACACTCATATTCTGAATATATAAGCA--TCT-ATAGTTCAGTAAGAAA 1527
                          iiv   ii   i v          iv --   - i ii   i   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_42429071_4   1528 AAGACAGTTT------TTTAAACA---GCAAAAGACTT---CCGGCACTA 1565
                               iv v------  ?   v ---     i  i  ---iv i  i v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_42429071_4   1566 CATAAAACAGGGTGTCCAGGTGATTAATAAGCATATGTAAAGGTACACAA 1615
                          viv   v i i i v  ii  iii        i   v    i i v   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_42429071_4   1616 CCTCATTAATTAT 1628
                          v   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (37 / 23)
Gap_init rate = 0.02 (5 / 213), avg. gap size = 3.00 (15 / 5)  


2648 16.28 11.68 1.81  chr2_42447938_42449528.rev      492  1099 (492)    L1M4_orf2#LINE/L1      241   908 (0)  

  chr2_42447938_4    492 TACAGAATCCCATAATGATTACAAC--TATGGTAACTGGCATAAGCACAG 539
                             i i-- i i i i  i vi  -- i     -          v i  
  L1M4_orf2#LINE/    241 TACAAAG--CTACAGTAATCAAGACAGTGTGGTA-CTGGCATAAGGATAG 287

  chr2_42447938_4    540 ATATATATACATATTTATGGAACAGAATTCAAAGTCCAGAGAAAATCTCA 589
                          i     v ---- iv      i      v i        i v  v i  
  L1M4_orf2#LINE/    288 ACATATAGA----TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_42447938_4    590 TACATCTTTGGCCAATTTGTTTTCAAAAATGGTGCCAATACTATTCAATG 639
                              i v   i     vi     i v  v        v  i        
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_42447938_4    640 GAGAAAGAGAAGTCTTTTCAACAAATGGTGCTG---TAACTGAATATCCA 686
                          i      iv                       ---i     i   ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_42447938_4    687 CATACAAAAGAATGAAGTTGGACACCTACTGGGCCATACTATATATGAAG 736
                            i                   v     i---i  i  i     ii  i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACC---TCACACCATATACAAAA 480

  chr2_42447938_4    737 ATTAACTCAAGACGAATTGGAGACCTAAAGGTAAGAGCTAAAACTATAAA 786
                                   i i i  ii?         v                    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_42447938_4    787 ACTCTTAGAAGAAAACATAGAAGTAAATATTTATG--------------- 821
                                             i?      v  ii  ---------------
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_42447938_4    822 -------CTTA--------------------AGAAACAAGAGAAAGAACA 844
                         -------    --------------------  v     i     i  i 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_42447938_4    845 GATAAACTAAACTACATCAAAACTTAAAACTCTGGTGCTATTAA----CA 890
                               i ii   v        i v      i v     - i  ----  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACA 679

  chr2_42447938_4    891 ACATCAAGAAAGTGAAAAGACCACCCTCAGAATGAG-GAAAATATTTGAA 939
                         vi                   v    v       i -           v 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_42447938_4    940 AA----AGATCTG-TAAGGAACT-GTATCCAGAATATATAAAAAACTCTT 983
                           ---- v     -     i   -                  i       
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_42447938_4    984 ACAA-------------GAACAGACAACCCAATTCAAAGATGGGCACAGG 1020
                             -------------ii   i i         ?   i       v   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_42447938_4   1021 ATTTCAACATACATTTCTCTAAAGAGGATATACAAGTGGCCAATAAGTAC 1070
                             v  i v         i     i         i           i  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_42447938_4   1071 TTGAAGAAATGCTCAACATCATTAGCCAT 1099
                         v    i i             ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.28 (66 / 29)
Gap_init rate = 0.02 (15 / 668), avg. gap size = 5.47 (82 / 15)  


 737 19.76 2.40 1.80  chr2_42572197_42574940      604   770 (1974)    L1M4_orf2#LINE/L1        3   170 (738)  

  chr2_42572197_4    604 GAAAGGCACCTCATATTCATAGATTAGAAGACTTAATATGAATAAGATG- 652
                              ii i i   i     i    i             viv       -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_42572197_4    653 C--TAC-CCCCTAATTTATCTACAGATTCAATGTATTCACTGTCAAAATT 699
                          --   -    v    v              i i v  v  i       i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_42572197_4    700 CCAACTAAATTTTTTTGCAGAAATGGACACACCAAACCTAAAATTCATAT 749
                            i  iv-i              v    vi ii v              
  L1M4_orf2#LINE/    103 CCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_42572197_4    750 AGTAATACAAGGAATGGCCAG 770
                         i v   i     i i--    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGAC--CCAG 170

Transitions / transversions = 2.00 (22 / 11)
Gap_init rate = 0.03 (5 / 168), avg. gap size = 1.40 (7 / 5)  

 237 20.00 0.00 0.00  chr2_42572197_42574940     1114  1173 (1571)    L1M4_orf2#LINE/L1      141   200 (708)  

  chr2_42572197_4   1114 AAAATAAACAAAGAAATACAAGGGACCCAGAATAGCCAAAATAATTTTTA 1163
                              vv i vi     i                       i   i  v 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_42572197_4   1164 AAAAAGGGAA 1173
                             iii   
  L1M4_orf2#LINE/    191 AAAAGAAGAA 200

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.00 (0 / 0)  

1578 16.72 7.33 2.35  chr2_42572197_42574940     1274  1614 (1130)    L1M4_orf2#LINE/L1      190   547 (361)  

  chr2_42572197_4   1274 AAAAAAAAAAAAAAGGTAAGAGAGACTCACACTTCCTGATTTCCAAACTT 1323
                              i  i  v  i  vi   -             ii     v      
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAG-GACTCACACTTCCCAATTTCAAAACTT 238

  chr2_42572197_4   1324 ACTACAAAGATACA---ATC-------TTTTGTTCTGGCATAAAAATCAA 1363
                                  v    ---   ------- v v  v         ii  vi 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_42572197_4   1364 CACATAGATCACTAGAATAGAATTGAGAATCTAGAAATAAACCCACACAT 1413
                           i        v i              i  i             i    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_42572197_4   1414 CTATGGTCAATTGATTTTTGTCAAAAGTGCCAATACCATTACATGGGGAA 1463
                         i                 i v   ii       v      vv        
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_42572197_4   1464 AGACTGATCTTTTCAACAA---------------CTGGATATCTACATGC 1498
                            v ii            ---------------       ? i      
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_42572197_4   1499 AAAAAATAAACAAATAAAATTGGACTCCTACTTCATAACAGATGCAAAAA 1548
                             i -------  i  i      i     i   i v  v  i      
  L1M4_orf2#LINE/    439 AAAAGA-------ATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_42572197_4   1549 TTAACTAAAAATGGATCAGAGACCTAAAGACAGGCATTAACACTATAAAA 1598
                               v           ?         vii i vii   v         
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_42572197_4   1599 CTCTTAAGAGAAAACA 1614
                               ii        
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACA 547

Transitions / transversions = 1.75 (35 / 20)
Gap_init rate = 0.01 (5 / 358), avg. gap size = 6.60 (33 / 5)  

1234 16.41 8.33 5.21  chr2_42572197_42574940     1904  2287 (457)    L1M4_orf2#LINE/L1      513   908 (0)  

  chr2_42572197_4   1904 AAAAAATAAAA---TAAAATTCTTAAGAAAACACATAGGAGTAAATCTTC 1950
                           i iv     ---     i     ii i  v       ?          
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_42572197_4   1951 ATGACCTT--------CACT---TTATTAGATATGACACCAGAAGCAAAA 1989
                         i       --------  v ---  v               i     v  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_42572197_4   1990 GAGACAAGAGAAAAAACAGATAAATTGGGAAACATCAAAATTTAAAA--T 2037
                          vi    i        i           ivvv          v    -- 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_42572197_4   2038 GTGTGCTGCAAATGATACATACCACTAAGAAAGTGAAAAGACAACCCTCA 2087
                         v      v    v  i  -  i  ---                    v  
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACAC-TATCA---AGAAAGTGAAAAGACAACCCACA 708

  chr2_42572197_4   2088 GAATAAGAGAAAATATTTACAAATCATATATTTGA-AAAGGATCTGTATC 2136
                             ii            i            i   -  i   ii      
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_42572197_4   2137 CAGAATA----AACAACTCTTAAAATCCAACAACTTTTTTAAAAA----- 2177
                                ----  v        v  ii   i  ------      -----
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAA------TAAAAAGACAA 802

  chr2_42572197_4   2178 ---ACCTATTTTTTTAA-GGGCAGGGG-TTTAAGTAGACATTTCTCCAAA 2222
                         ---   i v  ?vvv  -     ii  -   i i                
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_42572197_4   2223 GAATAGATGAAAAGATGACCAACA-GCATTGTCATTAGGGAAATGCAAGT 2271
                            --   iv v i   i    i -   ----   v ii- i    --- 
  L1M4_orf2#LINE/    853 GAA--GATATACAAATGGCCAATAAGCA----CATGAAA-AGATGC---T 892

  chr2_42572197_4   2272 CATAATCACAGGGAGA 2287
                           vv    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (36 / 25)
Gap_init rate = 0.04 (17 / 396), avg. gap size = 3.06 (52 / 17)  


2218 23.01 0.37 2.97  chr2_42867000_42869305.rev      573  1111 (1195)    L1M4_orf2#LINE/L1        1   525 (383)  

  chr2_42867000_4    573 TGCAAAGATATCCCATATTCATGGATTGGAAGAATCGATACTGTTAAAAT 622
                           v             i                v ii   i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_42867000_4    623 GTCCATACTAACTCAAAGCAATCTATGGATTCAATGCAATGCCTATCAAA 672
                          v v     v- i    vii     ii       i     v         
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_42867000_4    673 ATACCAATGATGTTCTTCGCAGAGATAGAAATAATAGTCCTAAAATTTAT 722
                           v   iiviiv  i  i     i  v  v viv ii          i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_42867000_4    723 ATGGAATCACAAAAGACCCAGTATAGCCAAAGCTATTCTGAACAAAAGGA 772
                               vii   ii       v         i v  ii    v  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_42867000_4    773 ACAAAACTGGAAAAATCAC--TTCATCTGACTTCAAATTATACTACAGAG 820
                              ii    ii v    --   -- ii i      viv       i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTC--CCAATTTCAAAACTTACTACAAAG 247

  chr2_42867000_4    821 CTATGGTAAGCAAAACAGCATGGTACTGGCATAAAAACAGACATACAGAC 870
                            ii    v   i    ii              ii i       i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_42867000_4    871 CAATGGAACAGAATGGAGAACCCAGAAACAAATCTATACATCTACAGTAT 920
                                 i     v    ii       i   i i      i  ii  v-
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC- 346

  chr2_42867000_4    921 AAACTCATTTTAAACTCATTTAAAACAATGGTGCCAAGAACATACATTGG 970
                         -  i v     ----- i------    v          v   v  v   
  L1M4_orf2#LINE/    347 -AATTGATTTT-----CG------ACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_42867000_4    971 AGAAAATATAGTCTCTTCAATAAATGGCACTGGGAAAACTGGATAGCCAT 1020
                         i    iv       i     i      ii      v         ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_42867000_4   1021 ATGCAGAATAATAAAACTAGACCCCTCTTTCTTGCCATATACAAAAATCA 1070
                              i  v   i  ii i       vii  vii              i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_42867000_4   1071 AATCAAAATAAATTAAATACTTCAATCTAAGACCTCAAACT 1111
                          v       ii  i ? v  i v   v     v  v     
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

Transitions / transversions = 2.05 (82 / 40)
Gap_init rate = 0.01 (6 / 525), avg. gap size = 3.00 (18 / 6)  

1419 23.27 2.05 0.77  chr2_42867000_42869305.rev     1424  1814 (492)    L1M4_orf2#LINE/L1      513   908 (0)  

  chr2_42867000_4   1424 AAAAACTCAAACTGTGAAACTAATAAAAGAAAACACTGGAGAAACTTTCT 1473
                           i i  v     i i     vv  i         iv  ? v  v i ii
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_42867000_4   1474 AGGACATTGTTCTGGGCAAATATTTCTTGAGTA--ATATCCACAGGCACA 1521
                         iv   v   vvi i     vvi      iii  -- i -   v i     
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA-CCAAAAGCACA 611

  chr2_42867000_4   1522 GGCAACCAAAGCAAAAATAGACAAATTAGATCATATCAA-GTTAAAAAGC 1570
                         i     v    v         i     i  iivi     -i       - 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-C 660

  chr2_42867000_4   1571 TTTTGCACAGCAAAAGAAACAGTCAACAAAGTGAAGAGACAATGCACAGA 1620
                              ii vv    i  v  vi    v        i      iv      
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_42867000_4   1621 ATGGGAGAAAATATCTGC----TATCCATCTGACAAGGGATTAATAGCTA 1666
                                       i   ----i  vi      i      i vi  v i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_42867000_4   1667 GAATATATACGGAGCTCAAACAACTCAATAGGAAAACAATCTAATAATCT 1716
                                  vi  i   vv           iv    vi - v     i i
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCC 809

  chr2_42867000_4   1717 GATT-AAAAATGGGCAAAAGGTGTGAAAAGACATTTCTCAAAAGAAGACA 1765
                         i   -             i i v    v           v        i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_42867000_4   1766 TACAAATGGCAAACAGGCATATGGAAAGGTGTTCAACACCAATGATCAT 1814
                                   v  i i   i   i    i  i      i  ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (55 / 35)
Gap_init rate = 0.02 (7 / 396), avg. gap size = 1.57 (11 / 7)  


 200 24.19 9.68 1.61  chr2_42954580_42957221.rev      369   430 (2212)    L1M4_orf2#LINE/L1        3    69 (839)  

  chr2_42954580_4    369 GAGAGGTATGCTGTGTTTATGGAATCAGAAGAC---ACACTTTTAAGAAG 415
                           i  i   v ii    i    -  ii      --- i i v      v 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGG-ATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_42954580_4    416 GTAAT---TCTCAAATTG 430
                          i   ---i i       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTG 69

Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.04 (3 / 67), avg. gap size = 2.33 (7 / 3)  

2427 21.14 6.43 4.71  chr2_42954580_42957221.rev      830  1529 (1113)    L1M4_orf2#LINE/L1       29   740 (168)  

  chr2_42954580_4    830 GAAGAC---ATATTTTGAAGAAGATAATTCTCCTCAAATTGTTGAACGTC 876
                               ---     v v    v ii   v    i       ---------
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG--------- 69

  chr2_42954580_4    877 TTGATCAATACATTTAACAGAATTTCTATCAAAATCCAAGCAGAACTTTT 926
                         ---   v i v   i   iv   ii            v   v vvi    
  L1M4_orf2#LINE/     70 ---ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTT 116

  chr2_42954580_4    927 CATAGAAATTGGTAAACTGAACCTAAAATTTATATGAAAATGTAAAGGAC 976
                         iii        ii  i    v         i     i     i  i    
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr2_42954580_4    977 CTGCAATGGCCAAAAGCATTTTGAAAGAGAAGAACAAAATTGGAGAACTT 1026
                          iiv   i       vv  i      i           i      i   i
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr2_42954580_4   1027 ATAATACCTGGTTTCCAAACTTACTCTAAATCTACAGTAATCACCACAGT 1076
                          i v v  iii    v         vi   v            vv     
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_42954580_4   1077 GTAGTGTTGGCATAACACCATACTGACAGGTCAATAGAATAGAAC-GATA 1125
                           i  ii        vivi v  vv i  i     i        i-  v 
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_42954580_4   1126 GTACAGCAATAGAGCAACACATTTATGGACAGCTTGTTTTTGATAAGA-T 1174
                           v   v    i v v i          v  ii vi    i  i   i- 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_42954580_4   1175 GCCAAGGCAATTTGATCAGGAAAGAATAAGCTTTTCAACAAATGGTGCC- 1223
                               i v   ii  vi          iv                  i-
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_42954580_4   1224 --ATAATTTAGATACTCACATACCCCAACCCCCCTCAAAATGA-----GA 1266
                         -- i  i -i    ?i     i ---  v------- i     -----  
  L1M4_orf2#LINE/    417 GGACAACT-GGATAKCCACATGC---AAA-------AGAATGAAGTTGGA 455

  chr2_42954580_4   1267 CCTTTACCTCACACCATACACAAAAATTAAGTCAACTCAAAATGGAGCAT 1316
                           ii              i           -----           v  ?
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAA-----CTCAAAATGGATCAW 500

  chr2_42954580_4   1317 AAACCTAAATATAAGAACTAAA----------TCATGGA------C-TA- 1348
                          i        i     i     ----------  v i  ------ -  -
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_42954580_4   1349 ----AAATCTTGGTGACCTTGAGTTAAACAAAGGTTATTTAGATATAGCA 1394
                         ----       v         i    ii   v    vi        ii  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_42954580_4   1395 CCAAAAGTACAATCAATAATGGGTAAAGAAATCAATGAATTGAACTTCAT 1444
                                i    v   i  vi ---  i    vi  i     i       
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAG---AAAAAATAGATAAATTGGACTTCAT 647

  chr2_42954580_4   1445 CAAAATGTTAAGA--TTTTGCTCGTTAACAGATATTA----GAAAATGAA 1488
                               --   i --     iv v i  vi  i i  ----    i    
  L1M4_orf2#LINE/    648 CAAAAT--TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_42954580_4   1489 AACCCAAGCCACAAACTGGAAGTAA----TTACAAATTATATATC 1529
                           vv   v     i v   i  v  ----  i     i       
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

Transitions / transversions = 1.70 (92 / 54)
Gap_init rate = 0.03 (19 / 712), avg. gap size = 4.11 (78 / 19)  

 323 29.46 2.68 0.00  chr2_42954580_42957221.rev     1815  1926 (716)    L1M4_orf2#LINE/L1      716   830 (78)  

  chr2_42954580_4   1815 AAAAAATATACGTA--TTATATATCCAACAAGGGAACTACATCTAGATTA 1862
                          i       vi i -- i       ii i      vi ii   i   v  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_42954580_4   1863 TACAGAAAATCTCTACAACCCAATAATGAAAAGAGAAACAACTCAAT-AA 1911
                           i i i  iiii      i       i      v   i   i    -? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_42954580_4   1912 AAAGCAGACAGAAGA 1926
                            iii i  i i  
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGA 830

Transitions / transversions = 7.00 (28 / 4)
Gap_init rate = 0.02 (2 / 115), avg. gap size = 1.50 (3 / 2)  

 287 22.64 6.60 0.00  chr2_42954580_42957221.rev     2045  2150 (492)    L1M4_orf2#LINE/L1      796   908 (0)  

  chr2_42954580_4   2045 AAAACAAG-ACCCCATCTCAAAAA----CAAAAAAC--AAAAAAATACTT 2087
                           i    i- v    vi ?     ----    ii i--i  v i i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_42954580_4   2088 CACCAAAGAGGATATATTAATGTCTAATAAGCATATGAAAAGCTACTCAA 2137
                          v       i      iv    v i        i        v i     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_42954580_4   2138 CATTATTAATGCA 2150
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.03 (3 / 113), avg. gap size = 2.33 (7 / 3)  


1163 21.17 2.92 1.46  chr2_43127767_43134043       85   358 (5919)  C L1M4_orf2#LINE/L1   (509)   399   122  

C chr2_43127767_4    358 AAATTGAGAAACTAATTCTAAAACTCATATGGAAGTGCAAAGAAAT--GA 311
                                v  i  i  i      i          i     i i vi--  
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

C chr2_43127767_4    310 ATAATCACAACAACTTTTGAA---GAAGCATAAAGTTGAAAGACAAACAC 264
                            ii  v     - i     ---    v i       i i   vv    
  L1M4_orf2#LINE/    172 ATAGCCAAAACAA-TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

C chr2_43127767_4    263 CATCTGATTTTAACACTTATTATAAAG-TGCAGTAATCAAGACAGTGTGA 215
                         ivi ii    i  v     i  i    - i                   i
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

C chr2_43127767_4    214 TATTGGTATAAAGACAGACAAACAGATCAATGGAACAGAATTGAAAGTCC 165
                           i   i    i  i     v i            i        i     
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

C chr2_43127767_4    164 AGAAATAGACCCATA--TTTAAATGGACAAGTGATTTCTAACAAAGGCAT 117
                                i       --    --   v   v      iii    i  iii
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTA--TGGTCAATTGATTTTCGACAAGGGTGC 368

C chr2_43127767_4    116 AAAGGCAATGCAGTACAAGAAAGGATAGTCTT 85
                         v   i v  v  i i-ii     i        
  L1M4_orf2#LINE/    369 CAAGACCATTCAATG-GGGAAAGAATAGTCTT 399

Transitions / transversions = 3.14 (44 / 14)
Gap_init rate = 0.03 (7 / 278), avg. gap size = 1.71 (12 / 7)  

3260 26.24 0.66 0.55  chr2_43127767_43134043     4879  5785 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_43127767_4   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGACTCAATATCGTGAAAAT 4928
                              ii i  i     i      i v        i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_43127767_4   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_43127767_4   4979 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5025
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_43127767_4   5026 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5075
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_43127767_4   5076 GAACAAAGCTGGAGGCATCACACTACCTGACTGCAAACTATACTACAAGG 5125
                                 i      vv       v  ii i v    viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_43127767_4   5126 CTGCAGTCACCAAAACAGCAGGGTACTGGTACCAAAACAGAGATATAGAT 5175
                           i    v i   i    iiv        i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_43127767_4   5176 CAATGGAACAGAAC--AGAGCCCTCAGAAATGACGCCGCATATCTACAAC 5223
                                 i    i--    i  --      i vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_43127767_4   5224 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5273
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_43127767_4   5274 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGC 5323
                         i  v  i  i              v      v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_43127767_4   5324 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5373
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_43127767_4   5374 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCCAGAAGAAAA 5423
                           i ?    i    i  v   v       i      vi ii         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_43127767_4   5424 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5473
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_43127767_4   5474 AAACACCAAAAGCAATGGCAACAAAAGCCAAATT-GACAAATGGGATCTA 5522
                         vi            vvi          vv   v -  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_43127767_4   5523 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5572
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_43127767_4   5573 CAGGCAACCTACACAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5622
                         v  i     i   v             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_43127767_4   5623 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5672
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_43127767_4   5673 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5722
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_43127767_4   5723 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5772
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_43127767_4   5773 CATCACTGGCCAT 5785
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3044 11.89 5.68 18.53  chr2_43150643_43153180.rev      664  1613 (925)    L1M4_orf2#LINE/L1        2   829 (79)  

  chr2_43150643_4    664 GGAAAGACACCCTGTGTTCATGGATTGGAAGACTTAATATTGTTAAAATG 713
                                i i  ii                                i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_43150643_4    714 GCAATATTCCTGGAAATGATCTACAGGGTCTATGCAATCCCTATTAAAAT 763
                               i   ivi  v          iv  v i           i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_43150643_4    764 CT-AGCTGCCTTTTTTTTGCAGAAACTGA-AAGCTGATCC---------- 801
                          i-             --       i   -          ----------
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_43150643_4    802 -----------------CTAGAATAGCAAAAACAATCCTGAAAAGAAAGA 834
                         ----------------- i        v         i      ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_43150643_4    835 ACGAAGTAGGGAGACTCACACTTCTCTCTTTCAAAACTTATTACTAAGCT 884
                           i    v  ii            i vv            i   v     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_43150643_4    885 ATAGTAATCAAGACAGTGTGGTACTGGTATAAGGATATGCCTGCACATAT 934
                          i                         i         ----- -      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-----G-ACATAT 293

  chr2_43150643_4    935 AGATCAGTGGAACAGAATTGAGC-TCTAAAAATGAACCCTTACATATATG 983
                               i     i         v-  i i    i     v     v    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_43150643_4    984 GTTAACTGGATGTTCAGCAAGGGTGTCAATACAATTCAATGGAGGAAAGA 1033
                           i  i  -  v   ii        i   v  v         -       
  L1M4_orf2#LINE/    344 GTCAATTG-ATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGA 391

  chr2_43150643_4   1034 ATAGC----------------GCTGGGACAACTGGATATTCACATTCAAA 1067
                             i----------------                 ?i     v    
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_43150643_4   1068 AAGTATTA--TTGAATCCTTACCTCACATCATATA--AAAACTAACTCAA 1113
                          - v  v --   i i  i         i      --    i        
  L1M4_orf2#LINE/    442 A-GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_43150643_4   1114 AATGGCTCATAAGAGGAAAAAATGCCATAACATAGTTATTAAATGTAAAA 1163
                              v   ? ----  -------  -------------         i 
  L1M4_orf2#LINE/    491 AATGGATCAWA----GA-------CC-------------TAAATGTAAGA 516

  chr2_43150643_4   1164 AGTAAATGAAAGTAAAAAGTAAAAAGAAAGTAAAAAGTAAAGAAAAATAA 1213
                         --------------------------------------------------
  L1M4_orf2#LINE/    517 -------------------------------------------------- 516

  chr2_43150643_4   1214 AAGTAAAGTAAAAAGAAAGTAAAAAGTAAAGAAAAATAAAAGTAAAGTAA 1263
                         ------------------------- i---------     v  ---   
  L1M4_orf2#LINE/    517 -------------------------GC---------TAAAACTA---TAA 529

  chr2_43150643_4   1264 AAAGAAAAGTAAATGAAAATGGATCCAAAAGTAAAAAGAAAATGGATCCT 1313
                           ----------------------- --------------------  i 
  L1M4_orf2#LINE/    530 AA-----------------------C--------------------TCTT 536

  chr2_43150643_4   1314 AGAACTAAACGTAAGAGCTAAAACTAGAATACTTCATGACCTAAGATGAA 1363
                             vv    i  i ? -    ------- -    i      vi i v i
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNG-TAAA-------T-CTTCGTGACCTTGGGTTAG 577

  chr2_43150643_4   1364 ACATTGGTTTCTTAGATATGACACCAAAAGCACAAGCAAAAAAAGAAAAA 1413
                         i  v                                   v          
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_43150643_4   1414 CTAGATACTTTGGATTTCATCAGG-TAAAAAACTTTTGTGCTTCAAAGAA 1462
                         v      vv     i       ii- v                     i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_43150643_4   1463 CAGCAGCAAGAAAGTAAGAAATATGACCTACAGAATGGGAGAAAATGTTT 1512
                           vi v         i -   v ii   i                 i   
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGA-AAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_43150643_4   1513 GCAAATCCTGTGTCTGATAAGGAACTTGTATCCAGAATATAAAAATAACT 1562
                                v i i          i                  v   v    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_43150643_4   1563 CTTATAATTCAACAGTGA---GACAAAAAATCCAATTTTAAAAATATGCA 1609
                             i  i    i i i ---      v  i      ?-      iv   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCA 825

  chr2_43150643_4   1610 AAGG 1613
                             
  L1M4_orf2#LINE/    826 AAGG 829

Transitions / transversions = 1.87 (71 / 38)
Gap_init rate = 0.03 (28 / 828), avg. gap size = 8.21 (230 / 28)  

 563 10.58 0.00 1.92  chr2_43150643_43153180.rev     1943  2046 (492)    L1M4_orf2#LINE/L1      807   908 (0)  

  chr2_43150643_4   1943 CTCAATAAAATAAAGTGTGCAAAGGATTTGAAAAGACATTTCACCAAAGA 1992
                          i    v?  --  i  v              v         v       
  L1M4_orf2#LINE/    807 CCCAATTWAA--AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_43150643_4   1993 AGATAAACAAATGGCCAGTAAATACATGAAAAGATGCTCAACATCATTAG 2042
                              v           i   ii                       ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_43150643_4   2043 CCAT 2046
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.00 (5 / 5)
Gap_init rate = 0.01 (1 / 102), avg. gap size = 2.00 (2 / 1)  


 741 17.97 8.29 4.15  chr2_43447806_43450570        2   218 (2547)    L1M4_orf2#LINE/L1      683   908 (0)  

  chr2_43447806_4      2 TTAAGAAAATGAAAAGGCAAGCCACAGCCAGGTAAAAACTGT--GCAAAA 49
                          i      i       i   v      vvv  v i   v i --     v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_43447806_4     50 CATTTACCTGTATAAAGGGCTTGTATTTAGAA-------AAAACTCTTAC 92
                            v  i   -    i  i       ii    ------- i         
  L1M4_orf2#LINE/    733 CATATATCTG-ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_43447806_4     93 AACCCAGTAA------GACAAACAACTCGAATTTAAAAAGCAATGTATAA 136
                            i  i   ------      i   i -    ?     ----  vii  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCC-AATTWAAAAA----TGGGCAA 826

  chr2_43447806_4    137 AAGATGTGAATAGGCACTTTACCAAAAAAGACATACA--TAGTCAAACAT 184
                          i   v       i  i  iv     i    i     -- i i   --- 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA---T 873

  chr2_43447806_4    185 GA-CACATGAAAAGATGCTCAACATTATCAGCCAT 218
                         i -                      i ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.45 (27 / 11)
Gap_init rate = 0.04 (9 / 226), avg. gap size = 3.00 (27 / 9)  

3796 16.16 4.28 5.26  chr2_43447806_43450570     1063  1879 (886)    L1M4_orf2#LINE/L1        1   809 (99)  

  chr2_43447806_4   1063 TGGAAAGACATCCAGTGTTTGTGGATTTAAAGACATCATATTGTTATGAT 1112
                                 i    vi    ii      vi     v v         v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_43447806_4   1113 GGCAGTACTCTTCAAATTGATCTACAGATTTAATGCAATCCCTATCAAGA 1162
                             i     ii                  i  i              i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_43447806_4   1163 TTCCAGCTGGCTTTTTCTTTCCTCCCTCCCTCCCTCCCTCCCTTTCCCGC 1212
                          i       v      ---------------------------- v v -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT----------------------------TGCAG- 121

  chr2_43447806_4   1213 CCCCCCCCCAAA----CAAGCTGATCCTAAAATTCATGTGAAAATGCAAG 1258
                         ---------   ----                     i  i         
  L1M4_orf2#LINE/    122 ---------AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_43447806_4   1259 GAACCCAGAATAGGCAAAGCAATGTTGAAAAATGAAGAA-------AGAG 1301
                          i           v    i    v        -      -------i   
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAA-GAAGAACAAAGTTGGAG 211

  chr2_43447806_4   1302 GACTCACACATCCTGATTTCAAG--TTACTATGAAGTAATGATAATCAAG 1349
                                  v   ii       i--      ii   iv iii        
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_43447806_4   1350 ACAGTGTGCTCCTGGCATAAGGATAGATACATAGATCAATGGAATACAAT 1399
                                 v v                i i                v   
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_43447806_4   1400 TAAGAATCGAGAAACAAACCCCTA-ATTTATGGTCAACTGACTTTTTGAC 1448
                          i   i  v     i      v  -            i   -    i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA-TTTTCGAC 360

  chr2_43447806_4   1449 AAGGGTGCCATGACAATTCAATGGGGAAAGGATAGTCTTTTTGAAATACA 1498
                                   v   v               i          ii v v ii
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_43447806_4   1499 GTGCTAGGACAAATGGATAGTCACATATGCCAAAGGAATGAGGCTGAATC 1548
                              i      v      ?i     i---    i      i i  i i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATG---CAAAAGAATGAAGTTGGACC 457

  chr2_43447806_4   1549 TGTACCTCCTATCAGATATAAAAATTAACTCAACATGGATCATAAACTTA 1598
                         iv      vi i  v   i              v        ? i  i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_43447806_4   1599 --TG----AACTAAAACTGTAAAACTTCCAGAGGAAAACATGGGTGCAAA 1642
                         --  ---- i        i       iii   i        i  ? i   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_43447806_4   1643 TCTTTGTGACTTTGGATTAGGCAATTATTT--TAGACATGAAATCAAATG 1690
                             i     i    i         vi   --    i    v i    v 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_43447806_4   1691 CACAAGCAATAAAA-----AACAGATACAATGGACTTCA---AAACTAAA 1732
                                  i    -----  i     v v         ---   i    
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_43447806_4   1733 AACTTTTGTCCATCAAAGGATATTATGAAGACAGTAAAAA-----TCCAC 1777
                                  v v        i i   v    v   i    -----i    
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_43447806_4   1778 AGAAAGGGAGAAAATATTTGCAAACTGTGTGTCTTATAAGGGATTAATAT 1827
                             v                   iii i i   v        i vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_43447806_4   1828 CTTGGACATAAAAAGAACCCTTACAACTTGAGAATAAAAAGAGAAATAAC 1877
                          iv i i   v       i         ii v          v       
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_43447806_4   1878 TC 1879
                         i 
  L1M4_orf2#LINE/    808 CC 809

Transitions / transversions = 2.07 (87 / 42)
Gap_init rate = 0.02 (15 / 809), avg. gap size = 5.20 (78 / 15)  

 453 18.33 4.17 0.00  chr2_43447806_43450570     2159  2278 (487)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr2_43447806_4   2159 CTCAAAAA-AAAAAAAGAGACAACTCACTT-AAAAATGCGCAAAGGATCT 2206
                              v  -     i v i i   i  v  -       v         i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_43447806_4   2207 GAAGAGACCGTTCTTT---GAAGATATATAAATGACCAACTAGCACTAGA 2253
                            v    vv    ii---         i     i    iv     vv  
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_43447806_4   2254 AAAGATGCTCAAACTCATTAGTCAT 2278
                                     vv   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.83 (10 / 12)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 1.67 (5 / 3)  


1103 23.88 3.81 2.42  chr2_43673385_43675681.rev      501   789 (1508)    L1M4_orf2#LINE/L1      205   497 (411)  

  chr2_43673385_4    501 GCTGGAGGTAACATACTACCAGACTTCAAAATATACTACAAACCTGTAGC 550
                          i      vvv  i   v  vi i       iv         v  ii  i
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_43673385_4    551 AA-CAAAAAAGTGTGGTACTGGTGTACAAACAGACACATAGACCAGTGGA 599
                           -   i v             ii  vii i     i     i  i    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_43673385_4    600 ACAGAATAGAGAACCCAGAAATTAA----TGTATCTACCGCCAACTGATT 645
                          i     v    ii        v  ---- ii  i  iv i   i     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_43673385_4    646 TTCGATAAAGGCTCCACGAACTCTCATTGGGTAAAGGACTGTC----CAA 691
                              i  i  iv   v  v vi   v    v    i iv   ----   
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_43673385_4    692 TAAACGGTGCTGGGAAAACTGAGTATGCTTTCTTCATATGCAGAAGGATG 741
                         i   i          v     ii  -------?i  i     i   i   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATA-------KCCACATGCAAAAGAATG 447

  chr2_43673385_4    742 AAACTAGACCC--ACCTCTCACTCTATACAAAAATCAACTCAAAATGAAT 789
                           ii i     --     v   iv           i           i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

Transitions / transversions = 2.09 (46 / 22)
Gap_init rate = 0.02 (5 / 293), avg. gap size = 3.60 (18 / 5)  

 254 20.51 6.84 7.69  chr2_43673385_43675681.rev     1074  1190 (1107)    L1M4_orf2#LINE/L1      475   590 (318)  

  chr2_43673385_4   1074 ACAGAAATTAACTCAAAATGGATAAAAGACCTTCAAAACAATAAATGGTA 1123
                            i                   v ?      ---   ii-   iv v  
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCT---AAATG-TAAGAGCTA 520

  chr2_43673385_4   1124 AAGACTACTATAAAACTACTT-GAA-------TAGTGGTATTTATTCAGG 1165
                           ----           -   -   -------   v?   vv v   iv 
  L1M4_orf2#LINE/    521 AA----ACTATAAAACT-CTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_43673385_4   1166 ACATTGATCTGGGAAAAGATTTTTT 1190
                           v   ivi i  v  v i   i  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 0.83 (10 / 12)
Gap_init rate = 0.05 (6 / 116), avg. gap size = 2.83 (17 / 6)  

 776 26.79 8.33 0.60  chr2_43673385_43675681.rev     1470  1805 (492)    L1M4_orf2#LINE/L1      547   908 (0)  

  chr2_43673385_4   1470 ACAGGCGTGAGCCACCG----CCTGGCCTGGGAAAACATTTTTATAAATA 1515
                          i   ?  i ii vi  ---- i   vi i  v  vvi   i -  i   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT-TAGATA 595

  chr2_43673385_4   1516 AGACCTCAAAAGCATAGACAACAAAA--------AG-TAAGTGGGATTAT 1556
                         v   vi        i ii        --------  -   i v   i vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_43673385_4   1557 ATCAAACTAAAAACCTTCTGCACAGCAAAGGAAAC----AACAGAGCCAA 1602
                               v v    v   i  ii vv       v  ----  v i  iv  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_43673385_4   1603 AAGATAAACTTCAGAATGGGAGAAAAAAATTTGTAAACTATTCATCTGAC 1652
                             i  v iv               v -    i   ii  vi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATA-TTTGCAAATCATATATCTGAT 744

  chr2_43673385_4   1653 A--GGATTAATGTCCAAAATGTACAGGGACCTCAAACATCTCAACAGCAA 1700
                          --   i vi i    i   i  i ii  v   vv   v     i ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_43673385_4   1701 AAAAAAAAAAAA---AAAAAAAAAAAGGACAAATGATCTGAACAGACATT 1747
                            i v   v  ---  vv?     v  i    v   i    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_43673385_4   1748 TCTCAAAAACAGA------AATGACGAACAAATATATGAAAAAATGTTCA 1791
                             v   iv   ------    i v  i  ii i       i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_43673385_4   1792 ACATCACAAATCAG 1805
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (53 / 35)
Gap_init rate = 0.02 (9 / 362), avg. gap size = 3.33 (30 / 9)  


3022 27.01 1.10 0.99  chr2_43681916_43688128.rev     4815  5721 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_43681916_4   4815 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAGT 4864
                              ii i  i     i      i v      v i     ii v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_43681916_4   4865 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4914
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_43681916_4   4915 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTACAGTTC 4961
                          v   i-       i  -i     -   -- v  i  - iii  v i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_43681916_4   4962 ATATGGCACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5011
                               v viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_43681916_4   5012 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATGCTATAAGG 5061
                                 i      vv   ii  v  ii i      viv i   i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_43681916_4   5062 CTACAGTAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGATATAGAT 5111
                                  i   i    i          i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_43681916_4   5112 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACTCTTATCTACA 5159
                                 i    i--    i  --        vv   iv --  i  ii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATAC--ATTTATG 343

  chr2_43681916_4   5160 ACTACCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGGAGAGGA 5209
                         iii vi    i  i     ivv  vv  i v  vv        i -  i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAA 392

  chr2_43681916_4   5210 TTCCCTATTTAATAAATGGTGCTGGGAAAACAGGCTAGCCATATGTAGAA 5259
                          vvi  v  i  i              v   v  v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_43681916_4   5260 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 5309
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_43681916_4   5310 CGGATTAAAGACTTAAACTTTAGACCTAAAACCATAAAAACCCTAGAAGA 5359
                         i    i ?    i    iv v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_43681916_4   5360 AAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 5409
                             v    ?i v viv   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_43681916_4   5410 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5459
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_43681916_4   5460 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5509
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_43681916_4   5510 GAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTG 5559
                            v  i     i   i             v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_43681916_4   5560 ACAAAGGGCTAATATGCAGAATCTACAATGAACTCAAAACAAATTTACAA 5609
                          i  i  i  vi   v      v  i  v      vv -   v iv i  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAA 791

  chr2_43681916_4   5610 GAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGA- 5654
                         v     i    ----   v  i?    i           iv    i   -
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_43681916_4   5655 ACTTCTCAAAAGAAGACATTTATGCAGCCAGAAAACACATGAAAAAATGC 5704
                          i     v        i  vi viii    iv  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_43681916_4   5705 TCACCATCACTGGCCAT 5721
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


 797 16.88 5.84 0.00  chr2_43763775_43766380      501   654 (1952)    L1M4_orf2#LINE/L1      206   368 (540)  

  chr2_43763775_4    501 TTGGAAGACT------TTGCAATTTCAAAGCTTACTACAAAGCTA--GTT 542
                              i    ------ iv          i               --  v
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_43763775_4    543 ATCAAGACAGTGTGGTACTGACTTAAAGACAGACATATATATCCATGGAA 592
                                             i v   i  i         v   v      
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_43763775_4    593 TAGACTTGAGAGTGCAGAAATAAAGCCTCATATTGACAGTTAGTTGATCT 642
                             v        v          v  vi i   v ii  i i     i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_43763775_4    643 TCAACA-GGATAC 654
                           i   -  i i 
  L1M4_orf2#LINE/    356 TCGACAAGGGTGC 368

Transitions / transversions = 1.60 (16 / 10)
Gap_init rate = 0.02 (3 / 163), avg. gap size = 3.00 (9 / 3)  

1676 18.18 0.61 0.61  chr2_43763775_43766380      968  1297 (1309)    L1M4_orf2#LINE/L1      366   695 (213)  

  chr2_43763775_4    968 TACAAAGAACTTTTAATGGAGAAAAAACAGTCTTTTCAACAAATGATACT 1017
                          i v    v v  i     i    i  i                 i i  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_43763775_4   1018 GGAACAACTGGATATCCATATACAAAGGAATGAATTTGAACCCCTATCTC 1067
                           i           ?   i  i    i       v   i       i   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_43763775_4   1068 ATTCCATATATAAAAAATAATGGGGAAAATGAATCAAATACCTAAATGTA 1117
                          iv       i     v   ivv--      i    ? v           
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTC--AAAATGGATCAWAGACCTAAATGTA 513

  chr2_43763775_4   1118 AGAGCAATAGCTCTAAAACTATTAGAAGAAAA--TAGGCATAAGTCTTCA 1165
                              v v i  v       v           --    ?i   i     i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_43763775_4   1166 TGACCTTGCATTAGGCAACTGTTTCTTAGATATGACACCTAGAGCACCAA 1215
                                 vi        iv                   v i     v i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_43763775_4   1216 TGACAAAAGAAAAAGCCGATAAACTGGAATTTGTCAAAATTTAAAAATAT 1265
                         ii            iiv      i    v  ii        v    v v 
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_43763775_4   1266 TGTCCTTCAAAGGACACCATCAAGAAAGTAAA 1297
                            v             i           i  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

Transitions / transversions = 1.48 (34 / 23)
Gap_init rate = 0.01 (2 / 330), avg. gap size = 2.00 (4 / 2)  

 773 11.20 0.00 0.00  chr2_43763775_43766380     1576  1700 (906)    L1M4_orf2#LINE/L1      685   809 (99)  

  chr2_43763775_4   1576 AAGAAGGTAAAAAGACAACACACAGAATAGGAGAAAATATTTCCAAATCC 1625
                              i  i          v        i             v      v
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_43763775_4   1626 TGTATCTGATAAGGGAATTGTATCTAAGATACATAAAGAACTCTTACAAC 1675
                          i              v       i ii   i                  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_43763775_4   1676 TCAATAATAAAAAGACAGATAACTC 1700
                                          i     i 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCC 809

Transitions / transversions = 2.50 (10 / 4)
Gap_init rate = 0.00 (0 / 125), avg. gap size = 0.00 (0 / 0)  

 545 16.53 0.83 0.00  chr2_43763775_43766380     1996  2116 (490)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr2_43763775_4   1996 AAAAAAAAAAAAAAAGATAACTCGAATGAAAAATTAGCAAATGACCTGAA 2045
                           v  v     i v i     i i v ?      vi     v  ii    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_43763775_4   2046 TAGAC-TTTCTCCAAAGAAGATATGCAAATGGACAATAAGTACATGAAAA 2094
                              -                  i       v       i         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_43763775_4   2095 GATGCTTAACATTGTTAGTTGT 2116
                               i     ii????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 1.00 (1 / 1)  


2905 11.55 3.50 23.20  chr2_43778987_43782060.rev     1150  2179 (895)    L1M4_orf2#LINE/L1        3   829 (79)  

  chr2_43778987_4   1150 GGAAGAAATTGTATATTCATGGATTAGAAGACTTAATATTGTGAAGATGG 1199
                          i    v  ivi  i          i                v       
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_43778987_4   1200 CAATACTTGC-AAATGGCTATATACACACAATGCAATCTCTATCAAAGTT 1248
                                iv -    v v v  i v iv   i      i        i i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_43778987_4   1249 GCAACTGCATTTTTTGCAGAAATTGACAAGCTGATC--AAACTTTGCCTG 1296
                         v  i    v                           --   v  iiiv  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_43778987_4   1297 GAAATTCAAGGGCTGAAGAATAGACAAAATAAAATTGAAAA--------- 1337
                              v      vivv       v     i  vv       ---------
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_43778987_4   1338 --GTTGGAGGACTCACATGTTACTATTTCTAAACTTACTACAAAGCTATA 1385
                         --               iv iv v     v                  --
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA-- 250

  chr2_43778987_4   1386 CAGTAGCTTGATTAC-ACAGTGTGGTACTTGCATAAAGATAGATATATAG 1434
                              -----  i v-             v      i      i      
  L1M4_orf2#LINE/    251 CAGTA-----ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_43778987_4   1435 ATAAACAGAATAAAGTTAAG--TCCAGAATTAAAGCCTCACATT------ 1476
                           v  ii     i i  i  --       v    v  vi     ------
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_43778987_4   1477 -----GATTTTTGGCAAGAGTGATAAGATCATCCAATGGGGGAAAGAATA 1521
                         -----      i i    i   vi    i   i        -        
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chr2_43778987_4   1522 GTCTTTTCAACAGATGATGCTGGGACAACTGGATATCCATATGTAAAAGA 1571
                                     i   i                  ?   i   i      
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_43778987_4   1572 ATGAATGTGGACCCATACCTCATACCATATATACACAGTAACACAAAATG 1621
                              vv       v       i        i v v v    v       
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_43778987_4   1622 GATCACAAACTTACAGGTACCAGCCAAAGCTCTAAACCAGGGGTGTCCAA 1671
                              ? i  ----------------------------------------
  L1M4_orf2#LINE/    495 GATCAWAGAC---------------------------------------- 504

  chr2_43778987_4   1672 TCTTTTGACTTCCTTGGGCCACGTTAGAAGAAGAATTGTCTTGAGCCACA 1721
                         --------------------------------------------------
  L1M4_orf2#LINE/    505 -------------------------------------------------- 504

  chr2_43778987_4   1722 CATAAAATACACTAACACTAAAGGTAGCTGATGAGCTAAAAAAAAAAATT 1771
                         -----------------     v   i-----         ---------
  L1M4_orf2#LINE/    505 -----------------CTAAATGTAA-----GAGCTAAAA--------- 523

  chr2_43778987_4   1772 GCAAAACAAATCTCATAATGCTTTAAGAAAGTTTACAAATTTGTTTTGGG 1821
                         -----------  -    --------------------------------
  L1M4_orf2#LINE/    524 -----------CT-ATAA-------------------------------- 529

  chr2_43778987_4   1822 CCACATTCAAAGCCATCCTGGGCTGCCTGTGGCCTGCAGGCCACAGGTTG 1871
                         --------------------------------------------------
  L1M4_orf2#LINE/    530 -------------------------------------------------- 529

  chr2_43778987_4   1872 GACACGCTTGCTCTAAACTCTTAGAAGAAAAGA--GGTATAAATCTTCAT 1919
                         ---------------                v --  ?i         i 
  L1M4_orf2#LINE/    530 ---------------AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_43778987_4   1920 GACCTTGGATTAGGCAACAGATTCTTAGATATGACACCTAAAGCACAAGG 1969
                                 i        ii v                 v          v
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_43778987_4   1970 AATCGAAGAAAAAATAGATAAATTGGACTTCATAAAAATTTTTAAATTTT 2019
                           ivi                            v      vv-   i   
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA-AAACTTT 663

  chr2_43778987_4   2020 TGTCCTTCAAAGGACACTATCAAGAAAGTGCAAAGATAACCCACAGAATG 2069
                            v                          v     i             
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_43778987_4   2070 GGA-AAAATAGTTGCAAATCATGTATCTCA---GGGATTTGTGTCTAGAA 2115
                            -      v           i     v ---    i    i  i    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_43778987_4   2116 TATATAAAGGACTCTTAGGACTCAACGATAAAAAAA--GATAACCCAATT 2163
                                  i       vi      ii       i --i           
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_43778987_4   2164 AAACAATGGGCAAAGG 2179
                         ?  v            
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGG 829

Transitions / transversions = 1.17 (62 / 53)
Gap_init rate = 0.02 (19 / 827), avg. gap size = 14.47 (275 / 19)  

 435  7.46 4.48 13.43  chr2_43778987_43782060.rev     2483  2616 (458)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr2_43778987_4   2483 AATAATAAATTAAAAATAAATAA----AT--AAAAATGGGCAAAGTATCT 2526
                                  ---  i i      ----  --              v  i 
  L1M4_orf2#LINE/    787 AATAATAAA---AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_43778987_4   2527 GAATAGAGATTTATCCAAAGAAGATATACAAATGGCCAATAAGCACATTA 2576
                                v    v                                   --
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-- 881

  chr2_43778987_4   2577 TTTGCTATGAGAGAAAATGCAAATCAAAGTCACAACAACA 2616
                         ----------  i  i    ---    vi   ????????
  L1M4_orf2#LINE/    882 ----------GAAAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (6 / 4)
Gap_init rate = 0.04 (5 / 122), avg. gap size = 4.80 (24 / 5)  


 672 18.32 4.46 4.95  chr2_43799511_43805790.rev      103   304 (5976)    L1M4_orf2#LINE/L1      708   908 (0)  

  chr2_43799511_4    103 AAAATGAGATACTAGAAAA-ATTAGTGCAAA--ACACATCTGATAAAAGA 149
                          i    i  -----     -   --      -- i i         ii  
  L1M4_orf2#LINE/    708 AGAATGGGA-----GAAAATATT--TGCAAATCATATATCTGATAAGGGA 750

  chr2_43799511_4    150 CTTGTATCCAGAATATATAAGGAATTTTTACAATTCAAGAATA------C 193
                                             i   i i      i    v    ------ 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_43799511_4    194 AAATAACCCCATTTTTAAAAATGCTAAAAGGATTTAGACAGATACTTTAC 243
                                  v   ?--       vvv         ii i   i i  iv 
  L1M4_orf2#LINE/    801 AAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_43799511_4    244 CAAAAAATAAATATGGATAGCAAGTTAAATACGTAAAAAGATGGTCAACA 293
                             i  v v   iii  i  v i -  ii  i i        v      
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAAT-AAGCACATGAAAAGATGCTCAACA 897

  chr2_43799511_4    294 TCATTAGTCAT 304
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.60 (26 / 10)
Gap_init rate = 0.03 (7 / 201), avg. gap size = 2.71 (19 / 7)  

3316 26.65 0.44 0.44  chr2_43799511_43805790.rev     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_43799511_4   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_43799511_4   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_43799511_4   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_43799511_4   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_43799511_4   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_43799511_4   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_43799511_4   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATACCTACAACT 5226
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_43799511_4   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_43799511_4   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_43799511_4   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGAA 5376
                            ii    i    v   i     v           i  i    i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_43799511_4   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_43799511_4   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCTAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_43799511_4   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_43799511_4   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv v      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_43799511_4   5577 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_43799511_4   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_43799511_4   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_43799511_4   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5776
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_43799511_4   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2293 27.26 0.30 0.30  chr2_44004242_44005897      501  1164 (492)    L1M4_orf2#LINE/L1      245   908 (0)  

  chr2_44004242_4    501 AGGCTACAGTAACCAAAACATCATGGTACTGGTACCAAAACAGAAATATA 550
                          i          i   i   vii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_44004242_4    551 GATCAATAGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTAC 598
                                i   i    i--    i  --        vv  ii i  i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chr2_44004242_4    599 AACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGA 648
                         iiii vi    i  i     ivv  vv  i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_44004242_4    649 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 698
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_44004242_4    699 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGA 748
                         iiv    ii    i    v   i     v           i  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_44004242_4    749 TGGATTAAAGAGTTAAACATTAGACCTAAAACCATAAAAGCCCTAGAAGA 798
                              i ?   vi    ii v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_44004242_4    799 AAACCTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGT 848
                             v    ?i v viv   iv   v v  vvii     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_44004242_4    849 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 898
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_44004242_4    899 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 948
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_44004242_4    949 GAACAGGCAACCCACAAAATAGGAAAAAATTTTCGCAACCTACTCATCTG 998
                            v  i         i   i   i     v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_44004242_4    999 ACAAAGGGCTAATATCCAGAATCTACAATGAAGTCAAACAAATTTACAAG 1048
                          i  i  i  vi          v  i  v   v  vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_44004242_4   1049 AAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAATAGACA 1098
                              i     i     v  i?    i     i     iv          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_44004242_4   1099 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 1148
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_44004242_4   1149 CACCACCACTGGCCAT 1164
                           v  i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (104 / 73)
Gap_init rate = 0.00 (2 / 664), avg. gap size = 2.00 (4 / 2)  


 551 14.95 0.00 2.80  chr2_44392753_44394766      499   605 (1409)    L1M4_orf2#LINE/L1      192   295 (613)  

  chr2_44392753_4    499 AGAGAAGAACAAAATTGAAGGACTCATGCTTACTAATTTCAAAACCTTAC 548
                          i           i   i        ii   v i           -    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC-TTAC 240

  chr2_44392753_4    549 AAACAAAGCTAACAGTAATCAAAACAATGTGATACTGATATAAAAATAGG 598
                         -v         -          i   i    i     ii    ii    i
  L1M4_orf2#LINE/    241 -TACAAAGCTA-CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_44392753_4    599 CATATAG 605
                                
  L1M4_orf2#LINE/    289 CATATAG 295

Transitions / transversions = 7.00 (14 / 2)
Gap_init rate = 0.03 (3 / 104), avg. gap size = 1.00 (3 / 3)  

3128 14.26 2.88 2.08  chr2_44392753_44394766      899  1522 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_44392753_4    899 AAAAAAAGGCATATAGATCAATGGAATAGAATTCAGAGTCCATAAATAAA 948
                           ii v  i                        v        v       
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_44392753_4    949 CCCATACATCTATGGTCAATTGATTATCACCCAGGGTGAAAAGGCCATCA 998
                                  i               v  iv v      vv   i    iv
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_44392753_4    999 AACGGGGAAAGAATACTCTGTTCAATAAATGGTGCTGGGACAACTGGATA 1048
                           i            v   v     i                        
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_44392753_4   1049 TACACATGCAGAAGAATGAAGTTGGATTCCTAT-TCACACCATATACAAA 1097
                         ?v        i               ii    i-                
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_44392753_4   1098 AATTAACTCAAAATGGATCA---ACTTAAATATAAGAGCTAAAACCATAA 1144
                                             ---  i     i             i    
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_44392753_4   1145 AATTCTTACAAAAAAAAACATAGGGGCAAATCTTTATGATCATGGATTTG 1194
                           i     --i  i          ? i       ii   i v   i  v 
  L1M4_orf2#LINE/    530 AACTCTTA--GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_44392753_4   1195 GCAGTGAA-----AGATAGGACATCAAAA-CACATGAAACTAAAGAAAAA 1238
                            i  iv-----     v    i     -    v v   v         
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_44392753_4   1239 -TAGATAAATTGAGCTTCATCAAAATTAAATACTTTAGTGCAACAAAGGA 1287
                         -           ii                v     v    vv       
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_44392753_4   1288 CACCATGAAGAAAGTGAAAAGA--GTCTACATAATGAGAGAAAATATTTG 1335
                            i  v               --ii i   v    i             
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_44392753_4   1336 CAAATCATATAGCTGATAAGGGGCTAACATC-AGAATATATAAATAATGC 1384
                                    v          i  vii   -            v  iv 
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_44392753_4   1385 TTACAACTCACCAA---AAAGACAAAACAGCACCATTTAAAAATAGGCAA 1431
                                   vi  ---         -i i v v   ?      i     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAA 826

  chr2_44392753_4   1432 AACCCAGTTAAAAATTTGAATAGACATCTCTCCAAAGAAGATAT-TAAAT 1480
                          i----------i              i                -i    
  L1M4_orf2#LINE/    827 AG----------GATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_44392753_4   1481 GGCCAACATGCATACATAGGGATGCTCAACATCATTAGTCAT 1522
                               i v   i iiv ii              ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (52 / 34)
Gap_init rate = 0.02 (12 / 629), avg. gap size = 2.58 (31 / 12)  


 386 22.55 1.96 0.00  chr2_44402026_44405283     1280  1381 (1877)    L1M4_orf2#LINE/L1        2   105 (803)  

  chr2_44402026_4   1280 GAAAAGAGATACCATGTTCTTGGAT-GTAAGA-TTAATATTGTTAAGATG 1327
                          i     v  v        v     - v    -                 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_44402026_4   1328 TCAATTATCCACAAATTGATTTATAGATAAAATAAAATTCTTGACAGAGT 1377
                         v    vv   v         i  i    vv  iiv   i i iv  i i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_44402026_4   1378 CTCA 1381
                          i  
  L1M4_orf2#LINE/    102 CCCA 105

Transitions / transversions = 0.92 (11 / 12)
Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2)  

 974 26.47 2.06 4.41  chr2_44402026_44405283     1648  1987 (1271)    L1M4_orf2#LINE/L1       70   401 (507)  

  chr2_44402026_4   1648 ATTTATAGATTAAATAAAATCTA-ATGAAAATTCTACTAGCCATTTTTTT 1696
                           i  i     v  iiv    iv-  v     i i viv   --      
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC--TTTTTT 117

  chr2_44402026_4   1697 GGGGTAGAGTTTGACAAGCTGATTGTAAAATGTATTTTAAATCTTAAATA 1746
                          ---i   iv             iv      vi  v vi  ---------
  L1M4_orf2#LINE/    118 G---CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA--------- 155

  chr2_44402026_4   1747 ATGCAAGTGACCTTGAATAGCCAAAACAACTTTGATAAAG--GGATTAAA 1794
                                v    iv               ii    v    -- i iv  i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_44402026_4   1795 TTGGTGGATTCATATTACTGGATTACAAGAATTCCTATAAAGTTGTGGCA 1844
                             v   i   i i v ivi   v   i v  v   i    i iii i 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_44402026_4   1845 ATTAAGATAATGTGGTTTTGGTGTCAGGAT---C-TATATATCAAGGGAA 1890
                           i    i i      vi   ii v     --- -    v     v    
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_44402026_4   1891 CACAATAGAGAATCTTGAAATAGACCTGTACATATATGGTCACTTGAGTT 1940
                         i v   v    i  iv      i   ii     v        v    v  
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_44402026_4   1941 TTAACAAAAATGACATGGGAATTCAATAGCAGAAAGGAAAGTTCTTT 1987
                          ii    iii  v  v ivv       i -i     i v   ii   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTT 401

Transitions / transversions = 1.50 (54 / 36)
Gap_init rate = 0.02 (8 / 332), avg. gap size = 2.75 (22 / 8)  

1301 23.05 9.22 5.21  chr2_44402026_44405283     2283  2781 (477)    L1M4_orf2#LINE/L1      390   908 (0)  

  chr2_44402026_4   2283 GAAAAGTCTTTTTAACAAATGGTTTTGGAACAAATGTGTAGCCATATGCA 2332
                            v        i          vi   i    v  vi  ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_44402026_4   2333 ACTACAACAGTAACAGCAAAATCAACCTTGACCTTCTTATCTCATGCCAC 2382
                          ----------  -----i   v  vi v    -- i  i    ii   i
  L1M4_orf2#LINE/    440 A----------AA-----GAATGAAGTTGGACC--CCTACCTCACACCAT 472

  chr2_44402026_4   2383 A--CAAGAATTAACTAGCAATTAATCACAGACTTAATGACAAGAGCTAAA 2430
                          --   i        viv   vi    ?    i   vvii          
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_44402026_4   2431 ACTA--AAATTTCTAGATGATAACAGTGGAGGAAATCTTTGTGACCTTGA 2478
                             --   i ii    v  v    vv  ? v       i         i
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_44402026_4   2479 GTTAGGCAACA----CTCAGGTAAGATACAGAAAACATAAGAATAAGTAC 2524
                                  ii----  i  i  v  i  vi   i  i   -------- 
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG--------C 614

  chr2_44402026_4   2525 CATAAAAGAAATTACTGGTGAATTCGATTTAATAAAAATTAGAAACTTCT 2574
                         v i        vv iv i i    v  i  v  v       i      i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_44402026_4   2575 ACTCTTCAAGAGAAACTGTCAAGAAAATTAAAAGTCAAGCCTTAG----- 2619
                         iiv      ii  v   i        i v     v   v  vi  -----
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_44402026_4   2620 ------------GCAA--CACATATCTGATAAATAACTCATACTTA---T 2652
                         ------------    --  i           ivi   ii  iii --- 
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_44402026_4   2653 A-AGAAACAACTTTTACAACTCAGTAACAAAAAGCAGAAATAGG-----T 2696
                          - v   v    i          i   i      - v     iv----- 
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAG-ACAAATAACCCAATT 813

  chr2_44402026_4   2697 AAAATATTG-CAAAA---TTGAATGAGCATTTCACTAAGGAAGATATACA 2742
                         ?   v  v -    i---      iii      v i  i           
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_44402026_4   2743 AATGGCAAATAAACGC-TAA-----TGTTCAAAGTTATTGGCCTT 2781
                               v     i i - i -----  i    vi i ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (69 / 42)
Gap_init rate = 0.03 (17 / 519), avg. gap size = 4.24 (72 / 17)  


3431 13.47 2.17 2.79  chr2_44427030_44429977.rev      615  1260 (1688)    L1M4_orf2#LINE/L1        1   642 (266)  

  chr2_44427030_4    615 TGGAAAGACATCTCATGTTCATGAATTGGAAGACTTAACAT----AAGAT 660
                                 i   i          i              i  ----     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_44427030_4    661 GGCTATGTTCCCCAGAGTGAACCACAGATTCAATGCAATCCCTATCAAAA 710
                            v  ii      i v   v i          i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_44427030_4    711 CCACAGCAGGCTTCTTTGCAAACATTGTCAAGCTGACTCAGAAATTCACA 760
                         i v    v v   i      i v    v        ii vi       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_44427030_4    761 TGGAAATCCAAAGGACTTGGAATAGT-GAAACAATACTGAAAAAGAA--- 806
                                v   i    iii      i-i       vi          ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_44427030_4    807 CAAAGTTGTAGGATTCTCACTTCCCGATTTCAAAACTTACTACAAAGCGC 856
                                 v    i  v        i                      vv
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_44427030_4    857 TAGTAATTCAGACAGTGTGTGGTACTGACATAAGGACAGACATATAGATG 906
                         i      iv          --      i        i            v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTG--GTACTGGCATAAGGATAGACATATAGATC 298

  chr2_44427030_4    907 AATGGAACAGAACTGAGAGTCCAGAAATAAACCCATGCATTTATGGTCAA 956
                                i    i                       i             
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_44427030_4    957 TTGATTTTCAACAAAAGTTGCCA-GACAATTCAGTAGGGAAAGAATAGTA 1005
                                  i    ii  -    -   v     i i             v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_44427030_4   1006 TTTTTAA-ACATACGTGATTGGAATAACTGAATAGCCACATGCAAAAAAA 1054
                             i  - v  i-   -i   i i     i   ?            i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATG-GTG-CTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_44427030_4   1055 AAAAAAAAAAGTCGGACAGCTTACCTTCACACCCTATATAAAAATTAACA 1104
                         vi  ------  i    v- i     -      v    i          v
  L1M4_orf2#LINE/    446 TGAA------GTTGGACC-CCTACCT-CACACCATATACAAAAATTAACT 487

  chr2_44427030_4   1105 AAAAATGGATCACAGACAATCTAAAATGTAAGA-CTAAAACTGTGAAACT 1153
                         v           ?    ---     -       -        i i     
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGAC---CTAAA-TGTAAGAGCTAAAACTATAAAACT 533

  chr2_44427030_4   1154 G--AGAAGAAAACATAGGAGTAAATCTTCATGACCTTGGATTAAGCAATG 1201
                         v--               ?          i         i   i      
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_44427030_4   1202 GTT-CTTAGATACGACACTAAAGGCACAAGCAACAAAAGAAAAAAATAAA 1250
                            -        i     i   i                      -  i 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGA 632

  chr2_44427030_4   1251 TAAATTGGGC 1260
                                 i 
  L1M4_orf2#LINE/    633 TAAATTGGAC 642

Transitions / transversions = 2.23 (58 / 26)
Gap_init rate = 0.03 (18 / 642), avg. gap size = 1.78 (32 / 18)  

 666 14.79 0.70 2.82  chr2_44427030_44429977.rev     1521  1662 (1286)    L1M4_orf2#LINE/L1      602   740 (168)  

  chr2_44427030_4   1521 CAAGAGCATAACTCTGTCTCAAAA-AACAAATAAATAAATAGGACATCAT 1569
                            i    i  ---- ivv     -  v     i      v    v    
  L1M4_orf2#LINE/    602 CAAAAGCACAA----GCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_44427030_4   1570 CAAAATTAAAAACGCTTGTGCTTCAAAAGGCACCATCAAGAAAGTAAAAA 1619
                                      vi            i i   i           i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_44427030_4   1620 GACAACCAACAGAATAGGAAAAATTATTTGTAAATCATGTATC 1662
                                v       i   i   v      i       i    
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.01 (2 / 139), avg. gap size = 2.50 (5 / 2)  

 350 10.77 7.69 0.00  chr2_44427030_44429977.rev     1990  2054 (894)    L1M4_orf2#LINE/L1      760   829 (79)  

  chr2_44427030_4   1990 AGAATATGT-AAGAACTTTTACAACCCAATAATAAAAAGACAA----CCC 2034
                                i -       i       i                 ----   
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_44427030_4   2035 TGTTTAACAATGGGCAAAGG 2054
                         vi  ?  v            
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 2.00 (4 / 2)
Gap_init rate = 0.03 (2 / 70), avg. gap size = 2.50 (5 / 2)  

 504 14.29 4.51 2.26  chr2_44427030_44429977.rev     2325  2457 (491)    L1M4_orf2#LINE/L1      773   908 (0)  

  chr2_44427030_4   2325 AACTCT---ATCTCAAAAA-AAATAAATAAATAAAAATGAAAT--AAAAA 2368
                               --- v     v  -   v i i      ---ivv   --     
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAA---CCCAATTWAAAAA 819

  chr2_44427030_4   2369 TGGGCAAAGGATTTAAATAGACATTTCTACAATGCAGATATACAAATGAA 2418
                                       i             v   v v             iv
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_44427030_4   2419 CTATAAGCACATAAAAAGATGTTCAACGTCTTTAGCCAT 2457
                          v          i        i     i  v????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.73 (8 / 11)
Gap_init rate = 0.03 (4 / 136), avg. gap size = 2.25 (9 / 4)  


2362 19.00 9.73 7.47  chr2_44445894_44448016.rev      751  1634 (489)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_44445894_4    751 AAGATACATCTGTCTTCATGGATTAGAAGAC-----------AAGATGGC 789
                               i-i ii v          i      -----------        
  L1M4_orf2#LINE/      5 AAGATAT-CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_44445894_4    790 ATGATTGCCAAAAATGATAAACAGATTCAATGCAATCCCTATCAAAATCC 839
                          vv i v  v   v    vv          i                   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_44445894_4    840 CAGTTGGCTATTCTA---AAATTTATATGGAAATCCTAAAATTCACATGG 886
                            i  v  v  i i---     v i v vvi             i    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_44445894_4    887 AAATATAAGGTACCCAGAACAGCTAAAACAATCTTGAAAAATAA---CAA 933
                             ii    v        i   i                 v  ---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_44445894_4    934 AGTTGGAGGACCCATACTTCTCTATGTCAAAACTTACTA---AGCTACAC 980
                                    i  i     i v  v             ---       v
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_44445894_4    981 TAATCAACTCAGGGTGTT-CAGGCATAGAGACAGACATATAGAT-----G 1024
                                vv   v   v - v      ii  i            ----- 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_44445894_4   1025 AACAGAACTGAGAGTCTGGAAATCTAATCAACTGATTTTCTTTTTTTTGT 1074
                           i    i        ii     --  ---  iv  ---viv   v v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAAT--AA---ACCCAT---ACATTTATGGT 345

  chr2_44445894_4   1075 T--TTGTTTTACATTTAGAGACGGGGTCTCACTCTGTCACCCAGGCTGGA 1122
                         i--   v   v -----  v v   ---------  i  ---  i ii--
  L1M4_orf2#LINE/    346 CAATTGATTTTC-----GACAAGGG---------TGCCA---AGACCA-- 376

  chr2_44445894_4   1123 GTTCACCCTGGAGTG--TAATCATGGCTCAAGGCAAACTTGAACTCCTGG 1170
                         -    vivv   iv --  i  v --i    --    --  i-- v    
  L1M4_orf2#LINE/    377 -TTCAATGGGGAAAGAATAGTCTT--TTCAA--CAAA--TGG--TGCTGG 417

  chr2_44445894_4   1171 GCTCAACT-----CCCACCTCAGCCTCCCAAAGTGCTGGGATTTCAGATG 1215
                          v-     -----?    v --  -----   i----- i  ----  v 
  L1M4_orf2#LINE/    418 GA-CAACTGGATAKCCACAT--GC-----AAAA-----GAAT----GAAG 450

  chr2_44445894_4   1216 T-GAGCCACCACGCCCA-GCC---TACAATCAGTTGATTTTTCAACAAAG 1260
                          - ii  v i  - i  -i  ---     -v i  i i ---   v vi 
  L1M4_orf2#LINE/    451 TTGGACCCCTAC-CTCACACCATATACAA-AAATTAACT---CAAAATGG 495

  chr2_44445894_4   1261 ATTCCATGATAATCC--AATG---AAGCAAAGA--ATAGTCTTTTTAGCA 1303
                           i----- ? iv  --    ---i   v  i --   ivvi i    v 
  L1M4_orf2#LINE/    496 ATC-----AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_44445894_4   1304 TGTGGTGCTGGAATAAATA-----GACC-------AGGCAATGGTTTCT- 1340
                         viviiiiiv  ?i     v-----    -------              -
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_44445894_4   1341 -AATATAACACTAAAAGTACAAGTAACAACA---ACAACAAAACAACTGG 1386
                         -i    i    i     i     i     v --- v  i i vv  i   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_44445894_4   1387 ACTTCATAAAAATTAAAAACTTCTGTGCTTTTCAAGGGACACTATCAAGA 1436
                                v              i       --   i              
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGA 688

  chr2_44445894_4   1437 AAGTGACATGAAAGCCCACAGAATGGGAGAAAATACTTGCAAATCAC--- 1483
                               v v  v i                     i          i---
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_44445894_4   1484 -CT--------------ATCCAGTATATATCAGGAATTCTTACAACTAAA 1518
                         -  --------------      v      v i   i          v  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_44445894_4   1519 CAATAAAAAGACAA----CCAAATTTAATTATAGGCAAAGAATCTGAACA 1564
                         i             ----  v    ?  vv  i       i  i    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_44445894_4   1565 GACATTACTCCAAATAAGACATGCAGATGTCCAATAAGCACATGAAAATA 1614
                               v       v    i  i  i   v                  v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_44445894_4   1615 CCCTCAACAAAATTAGCCAT 1634
                         iv       vv ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (88 / 76)
Gap_init rate = 0.05 (44 / 904), avg. gap size = 3.45 (152 / 44)  


3106 25.11 1.10 1.54  chr2_44522516_44526839.rev     2921  3832 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_44522516_4   2921 TGGAAACACATCCCATGCTCATGGATAGGTAGAATCAATATGGTGAAAAT 2970
                               v i        i        v  v   v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_44522516_4   2971 GACCATACTGCCAAAAGCAATCTACAAATTCAATTCAATCCCCATCAAAA 3020
                          i v     v  v   vii       i      iv       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_44522516_4   3021 TACCACCATCATTCTTCACCGAATTAGAAAAAACAATTCTAAAATTTATA 3070
                          v   v vv v  i  ii v   v v  v  ivii  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_44522516_4   3071 TGGAACCAAAAAAGAACCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 3120
                              viiv  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_44522516_4   3121 CAAATCTGGAGGCATCACACTACCTGATTTCAA--CTATACTATAAAGCC 3168
                             vi      vv       v  ii       --  -     i     i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr2_44522516_4   3169 ACAGTCACTAAAACAGCGTGGTACTGATATAAAAATAAGCACAGAGACCA 3218
                              v ii  i    i         ii    ii   ii  i v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_44522516_4   3219 CTGGAACAGAATAGAGAAACCAGAAATAAATCCAAATACTTACAGCCAAC 3268
                         v     i     v    iv           i   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_44522516_4   3269 TGATCTTTGACAAAGTAAACAAAACAA---AAAGTGGGGGAAAGGACACC 3315
                             i  i     i vviv   i  v ---  --     -    i i vi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGG-AAAGAATAGT 396

  chr2_44522516_4   3316 CTTTTCAACAAATGGTGCTGGAATAATTGGCTAGCTATATGCAGA-GAAT 3364
                                              i i  i   v  ? i i     i -    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_44522516_4   3365 GAAACTGGATACTCATATCACCTTATA---AAAAATCAACTTAGGATGGA 3411
                            ii    iv ii iv    vii   ---      i    i ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_44522516_4   3412 TTGAGGACTTAAATCTAAGACCTGAAACTATCAAAATTCT-AGAAGATAA 3460
                          ii?i   i     v     v  i       -    i   -      v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chr2_44522516_4   3461 CATTGGAAAAACTCTTCTAGACATTGTCTTAGGCAAGGATTTCATGACCA 3510
                            v  ?iv  v     vv   v   vv        v i    v iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_44522516_4   3511 AGAACCCAAAAGCAAATGCAAAAAAAAAAAAAAAAAAAAGATAAATAGCT 3560
                         v  vv         ----   iv  v    i      v        --- 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCA----CAAGCAACAAAAGAAAAAATAGATAAAT---T 638

  chr2_44522516_4   3561 GAGATCTAATTAAACTAAGGAGCTTTTGTACAGCAAAAGGAACAGTCAGC 3610
                          -  ii v  i   v v ii i       i vv    i iv  vi   iv
  L1M4_orf2#LINE/    639 G-GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_44522516_4   3611 AGAGTAAACAGACAACCCAGAGAGTGGGAGAAAATCTTCACAATCTAAAC 3660
                          i   i  v          v   i           v  ii   vii v i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_44522516_4   3661 ATCTGACAAAGGCCTAATATTCAGAATCCACAACGAACTCAAACGAATCA 3710
                               i  i  v  vi   i      vi i  v      vv  i v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_44522516_4   3711 GTAAGAAAAAAACAAACAATCCCATCAAAAAGTGGACTAAGGACATGAAT 3760
                         i   v     i     i  i  v  i?    i   i v     iv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_44522516_4   3761 AGACAATTCTCAAAAGAAGATATACAAATGGCCAACAAATATATGAAAAA 3810
                              v     v                       i  ii i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_44522516_4   3811 AATGCTCAACATCACTAGTGAT 3832
                          -            ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (131 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


 589 29.73 8.90 4.93  chr2_44534176_44535794      491  1119 (500)    L1M4_orf2#LINE/L1      232   885 (23)  

  chr2_44534176_4    491 AAAAC--AATGTAAAGCTACA-CAATTAAAATAGTGTGGCATTATTGCAG 537
                              -- v ii         -i   i  i i       i i i--   v
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG--GCAT 279

  chr2_44534176_4    538 AA--ATACACATATAAATCAAT---ATTTTTAGAATAAAGTGTTCACAAA 582
                           --   v       i      ---  ----     vi  v  i  v   
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAAT----AGAATTGAGAGTCCAGAAA 325

  chr2_44534176_4    583 --GACCTAAATATATGTG---ACTTAACATATGATGAAGATAC-AATTTT 626
                         --i   i v i  v i  --- v  i iv vi  ii i i i -  vvii
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_44534176_4    627 AGTAAGAGAGGAAAGGATGGATTCTTTAATAAATAGTATTGGGACCATTG 676
                          v v iv i      i  i vi i  i  i    i  ii      v i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_44534176_4    677 CCTAGGAATTTAGGAAACTAATAAAGCTGACTCCCTCCTATATACTATAT 726
                         vv  ?vv iv - v   vv   i   i  ivi    v ivi i  i    
  L1M4_orf2#LINE/    426 GATAKCCACAT-GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_44534176_4    727 GCCAAAATAAATTTAATATGGGTTAAGTATTTAA---------TTAAAAA 767
                         i v     v  i i  v    i i ?iv ii   ---------i     v
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_44534176_4    768 CATAACACTCTTAGA------TATTTCAGATGAATAATTTTAAT-ATATT 810
                         i    v         ------i  ---  i? v -   i  vi - iv  
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACAT---AGGNGTA-AATCTTCGTGACCTT 570

  chr2_44534176_4    811 GAAATCAAG-AA-GGTCCTTCTAAG-TGCGA-GTCAAA--CAC---CA-T 850
                          ii- i i -  -   --    v  - ii  -ii    --   ---  -i
  L1M4_orf2#LINE/    571 GGG-TTAGGCAATGGT--TTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_44534176_4    851 GAATTTAAAGGTTAATAGATTG-ACTAATTTAAGATTTAAAGACCCTT-T 898
                         i  vvv   ii vi   i    -   vvv i  i   -   i  ii  - 
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT-AAAAACTTTTGT 666

  chr2_44534176_4    899 A-TTCAAAAAGCGC-ATCAAAAAAATTGAAATACAAATTACACACTGGCA 946
                         i-      iii i -     i   i vi   v    vii   v v   v 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_44534176_4    947 ATTATTATTTATGA--CATATATTCAGATGAAGA---TGTATTTTC---- 987
                         ivv v     iii --       - v   i i i---     i-- ----
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATAT-CTGATAAGGGACTTGTATC--CAGAA 763

  chr2_44534176_4    988 TTTATAAAGAGCTCTTACAAATCCATAATAAAAAGACAATCTGAAAACCT 1037
                          v        i         v  v               ---- v    i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA----ATAACCC 809

  chr2_44534176_4   1038 GTAAGATAGAGAAAAACGTAGCCAAAAATTTAAGAAGAGGTATTTCACAA 1087
                         --- iv ?---     i -i  v  ii    --   v  ii     v v 
  L1M4_orf2#LINE/    810 ---AATTW---AAAAATG-GGCAAAGGATTT--GAATAGACATTTCTCCA 850

  chr2_44534176_4   1088 GAGAA---ATAGCAATGTTCTGTATGTACATCAAA 1119
                         i    ---   vv    vi vi  v i    v   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

Transitions / transversions = 1.58 (112 / 71)
Gap_init rate = 0.06 (40 / 654), avg. gap size = 2.17 (87 / 40)  


3080 24.63 3.41 0.34  chr2_44564527_44566848      951  1831 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_44564527_4    951 TGGAAAAACATTCCATGCTCATGTACTGGAAGAATCGATATCATTAAAAT 1000
                               i i  i     i     v i       v ii    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_44564527_4   1001 GCCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTTCTATGAAAT 1050
                          v v     v      vii  i           i  v  ii    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_44564527_4   1051 TACCAA-TGTCACTTTTCACAGTATTAGAAAAACT-ATC-TAAAATTCAT 1097
                          v   i-  i -i    ii   v v v  v  i  -   -          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_44564527_4   1098 ATGGAACCAAAAAAGAGCCCAAGTAGCCAAAGCAAGCCTAAGCAAAAAGA 1147
                               viiv  ii  v  vi i        i   v i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_44564527_4   1148 ACAAAACCAGAGGCATCACATTACACAATTTTAAACTAAACTACAGGGCT 1197
                              iiii    vv     i v v      i   vivv      ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_44564527_4   1198 ACAGTAACCAAAACAGCATGGAACTGGTACAAAAATAGACACATAGACCA 1247
                                i   i    ii   v     i i  ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_44564527_4   1248 ATGGAACAGAATAGAGAATCCTGAAATAAAGCCATATACCTACAACCAAC 1297
                               i     v    i   v        v     i ii  iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_44564527_4   1298 TGATGTTCTACAA---TGTCAA-------CAATGGGGGAAGGATACCCTA 1337
                             v   v    ---  i   -------        i   i   vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_44564527_4   1338 TTCAATAAATGGTGCTGGGAAAACTGGTTAACCATATGCAGAAGAATGAA 1387
                              i              v      v  ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_44564527_4   1388 AT--GACATCTACCTCTGACCATATACAAAAACTAACTTAAGATGGATTA 1435
                         i --   vi       vv              i     i  i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_44564527_4   1436 AAGATTTAAATATAAGATCTCGAACCATAAAAATTCTAGTAGAAAACCTA 1485
                         ?   ii     i     v  vi   i      v ii   v       v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_44564527_4   1486 GGAAATACTCTTCTGGACATTGGCCTAGGCAAATAATGTAC--GACCAAG 1533
                           ?ivv v     vv   v    vi       - ii v vi--  i- v 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT-ATG 597

  chr2_44564527_4   1534 TCCTCAAAAACAAATGCAACAAAA----AAATTGACAA-TTGGTCCTAAT 1578
                         v vi     i  v v         ----    v  i  -    v i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_44564527_4   1579 TAGACAAAAGAACTTCTGCACAGCAAAATAAACTATCAACAGATTAAACA 1628
                         i i vvv  i     i  ii vv    iv v        v i v i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_44564527_4   1629 GACAACATACAGAATGGGAGAAAATATTTGAAAGCTACACATTTGACAAA 1678
                               vi                      v  iii i i  i   i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_44564527_4   1679 AGACTAGTATCCAGAATCTATAAGGAATGTAAACAAATCAACAAGAAAAA 1728
                         i    v           v     i   ivivv    v    i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_44564527_4   1729 ---AAATG--CCA-TTGAAAAGTGGGCAAAGGACACGAACAGATACTTCT 1772
                         ---    i--   -  ?    i           ivi   i   i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_44564527_4   1773 CAAAAGAAGACATCCAAGTGGCCAACAA--ACATGAAAAAATTCTCAACT 1820
                          v        i  v   i       i  --         i  v      v
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_44564527_4   1821 TCGTGAATCTA 1831
                           i????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (127 / 86)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.06 (33 / 16)  


2349 24.86 3.83 2.32  chr2_44605877_44607550      451  1182 (492)    L1M4_orf2#LINE/L1      166   908 (0)  

  chr2_44605877_4    451 CTCAGAAAAA--AAAACAA----AAAAAAACAAAGCCAAACCAACAAAC- 493
                          i     v i--       ----i     i--   -------      v-
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAG--AAG-------AACAAAGT 206

  chr2_44605877_4    494 --AAAAACTCACCACCACCACCA---CCAAAATATACTACAAAGCGACAG 538
                         --i ii      -  iv  --  ---i     iv           v    
  L1M4_orf2#LINE/    207 TGGAGGACTCAC-ACTTCC--CAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_44605877_4    539 TCAGCAAAACAATATGGTACTGGCATGAAAACTAACATGTAGACCAATAG 588
                          v v   i   i i            i ii ivi    i    i    i 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_44605877_4    589 AATACA-----GAACCAAGAAATAAGTTTGTGTATCTATAGCCAACTGAT 633
                             v -----  ii v        iiiii ii  i   i i   i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_44605877_4    634 TTTTGAGAAAGGTATTCCAAAAATATGTTGA--GGGGAAGGACAGTCTCT 681
                            i  v  i   i--    i vi  - ii --   i   i i     i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTG--CCAAGACCAT-TCAATGGGGAAAGAATAGTCTTT 400

  chr2_44605877_4    682 TCAGTAAATAGTGGTGGGAAAACTGGATATCCATATGTAGAAGAATGAAA 731
                            ii    i   v     v         ?   i   i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_44605877_4    732 CTAGACTCCTAGTTCTCACCATGCACAAAAATCATCTCAAGATGGATTAC 781
                         i i   i    vi  v      ii        i v     i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_44605877_4    782 GGACTCAAATATAAGACCCAAAACTATGAAACTACCAGAAGAAAGTATGG 831
                         i   ii    i     v i        i     vii        ii  i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_44605877_4    832 GAG-AAATGCTTCAGGGCATTGGTCTGGGCAAAGATTTTATGGCTAAGAC 880
                          ? -    -    iv i v    vi i     v i   iv i v  v   
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_44605877_4    881 CTCAAAAACATAGGCAACAAAAGCAAAAATAGACAAATAGTATTATAT-A 929
                         vi     i  i i          v         i    v v i vi  - 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_44605877_4    930 AAACTAAAAAGCTTTTGCACAACAGAATAAACAATCAACAGAGTGAAAAG 979
                            i      -      ii vv  i iv v  v     v i         
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_44605877_4    980 ACAACTGGAAGAATGGGAGACAATATTTGCAAAC----TATCCAACAAGA 1025
                              iviv           v            i----    ii i   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_44605877_4   1026 GTTTAATATCCAGAATATACAAGGAACTCA-ACAATTCAACAGCAAAAAA 1074
                          vi vi             i  i      v-    i    i ii     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_44605877_4   1075 GCAAATAATCTAAC--AAAAATGAGGCTATAATCTGAATAGATATTTTTC 1122
                         i       i i  i--       i vvv vi  i        i    i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_44605877_4   1123 AGCAGAAGTCATATTAAAGGCCAACAAGTATATGAAACAATGTTCCACAT 1172
                         viv     vi   iv  v      i   i i      vi   i  v    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_44605877_4   1173 CACTGGTCAT 1182
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.31 (125 / 54)
Gap_init rate = 0.03 (19 / 743), avg. gap size = 2.37 (45 / 19)  


2239 26.46 3.89 2.08  chr2_44622479_44624264      516  1286 (500)    L1M4_orf2#LINE/L1      112   896 (12)  

  chr2_44622479_4    516 TTTTTGGTAGAAACTGACAAAC-GATTTTAACGTTTATATGAAAATGTAA 564
                              v i     i      i -   ii   vi  i     i     i  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_44622479_4    565 AGAACCAATAATAGTCAAAATCATCTGGAAGAAAAGGAAGAAAGTTGGAA 614
                         i i   v v     i     iv    v   i  i i   v         i
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_44622479_4    615 GATTTACACTACCAGATATCAAGGCTTGTTATAAAGCTACAGTAATTAAG 664
                           i i     v  vi  v    ii   ii  i              i   
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_44622479_4    665 ATAGCGTGGTATTGGTGTAAGGATTGA--TGAAAGTCAA----ATAAAAT 708
                          i  i      i   ii       v  -- iv ii    ----   i   
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_44622479_4    709 GATAAGGAGTCCAAAAATATACCCACATATATGTGGAAACTTGATTTTAT 758
                         -- i  -      i     v     i i  v i   vv v        -i
  L1M4_orf2#LINE/    312 --TGAG-AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT-C 357

  chr2_44622479_4    759 AACATAGGTAGCACTGCAAAACAATGAAGATGGA-TGGTATTTTTAATAA 807
                         i   vi   iv  vvi v vv     ii  vi  - i  v    i  i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_44622479_4    808 AATATTCTGATTCAACTGGATAACCTCATGAAAAAAAATCA---TGGTCC 854
                          vvi v   ivv          ?  v    v    i   v ---   v  
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_44622479_4    855 TCTACCTCATACCATATACAAATATCAATTTCAGATTTCTATTTAGACTA 904
                         i        i            v  i  i iv i  --------i  ii 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAAT--------GGATCA 499

  chr2_44622479_4    905 TAAGTCTAAATATAGAGGGTAAAGCAGTAAAGCTTCTAACATTAATGCAT 954
                         ? iii      i  iii v    i vi    i  ii  iv vv  -i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA-ACAT 548

  chr2_44622479_4    955 AAGAATA--TCTTCATGACCCTGAGTTAGGTAAGGATATCTTAAATAGGA 1002
                          i ?i  --     i     i  i      i  v i v     i   v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_44622479_4   1003 CAAAAAAAAAAAAACCATACA---GAAAAGATTGATAAATTGGTCTATGT 1049
                           vv    iv v  v  -   ---     i  v          v  vii 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCA-ACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_44622479_4   1050 TATAATTAGGAATTTCTGTTATT-GAAGGACACTATTTAGAAAGTAGAAA 1098
                         i v     ii  i  i   vv  -i           iv       ii   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_44622479_4   1099 TGTAAGTTACAGAGTAGGAGGCGGTATTTG-AAATGCATATAACTAA--- 1144
                         vii  vii     i i    ivii      -    -      v  i ---
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAAT-CATATATCTGATAA 746

  chr2_44622479_4   1145 -GGACTTATTTTCAGAATATATAACAAATTCTTACAAATCAACAGGAAAA 1193
                         -      i v i            vi  i        v    i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_44622479_4   1194 A---AAAGAACCTAATTTCACAAATGTGAAAAACAT--GAACAGGCACTT 1238
                          ---   v    i    ?v -     v v   iv  --   i  i  i  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_44622479_4   1239 C-ACGAACAGTATATCCAAATGGCCGATAAACAGA--AAAAGATACTAAA 1285
                          -v i  v iv    v         i    i  v --       i  v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_44622479_4   1286 C 1286
                          
  L1M4_orf2#LINE/    896 C 896

Transitions / transversions = 1.63 (124 / 76)
Gap_init rate = 0.03 (22 / 785), avg. gap size = 2.09 (46 / 22)  


 628 20.51 0.00 0.00  chr2_44672164_44676717     2848  2964 (1590)    L1M4_orf2#LINE/L1        1   117 (791)  

  chr2_44672164_4   2848 TGGAAAGATATTCCATGTTTGTGGGTCAGAAGAATTAATATTGTTAAAAT 2897
                                    i       ii   i ii     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_44672164_4   2898 GACCATACTACCCAAAGAAATCTGTAGATTCAATGCAGTCCCTATTAAAA 2947
                          i v     v      vvi    ii        i   i       i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_44672164_4   2948 TACCAACTTTTTTTTTT 2964
                          v   i  vii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT 117

Transitions / transversions = 2.43 (17 / 7)
Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.00 (0 / 0)  

2901 27.00 0.50 0.88  chr2_44672164_44676717     3265  4064 (490)    L1M4_orf2#LINE/L1      112   908 (0)  

  chr2_44672164_4   3265 TTTTTCGTAGAAATAGAAAAAATAATCCCCAAATTTGTATGGAACCAAAA 3314
                              i i      v  v  iv i    iv     ii       viiv  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_44672164_4   3315 AAGAGCCTGAATAGGCAAACCAATCCTGAGCAAAAAGAACAAAGCTGGAG 3364
                         ii  v  v      v    v     i   iv  i          i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_44672164_4   3365 GCATCATACTACCTGACTTTAAAGTATATTACAAGGATATAGTAACCCAA 3414
                          vv   i   v  ii i  i   iiv  i     i v  i     i v i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_44672164_4   3415 ACAGCATGGTATCAGTATAAAAATTGACGTATAGACCAATGGAACAGAAT 3464
                             ii     iii i    ii  v   i      i        i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_44672164_4   3465 AGAGAACCCAGAAGTAAATGCACATATTTACAGCCAACTGATTTTTGACA 3514
                         v    ii      i    iv  i i     ii i   i       i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_44672164_4   3515 AAGGCAACAAGAATATACATTAGT---AGGACAGTCTCCTCAATAAATGG 3561
                          i  iiv     vi  v  v i v---  i i     ii    i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_44672164_4   3562 TACTGGGAAAGCTGGATATTTATATGCAGAAGAATGAAACTGGACCCATA 3611
                          i      v i       ?ii i     i         ii       v  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_44672164_4   3612 TCTCTCTCCACGTACCAAAAAGCCAACTCCAGATGGATTAAGGACTTAAA 3661
                         i   v v   ii   --    iii     v i      i ?i   i    
  L1M4_orf2#LINE/    462 CCTCACACCATATAC--AAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_44672164_4   3662 TATCAGATCCCAAACTATGGAACTATTAGATGAAAACATAGGGGAAACAG 3711
                          i v   v iv       ii    v     v           ? v  vvv
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_44672164_4   3712 TTTAGGACACTGGTCTAGGCAAAGATTTTATAGTTAAGACCTCCAAAGCA 3761
                           iiv   vi   vi       v i   iv   v  v   vi v      
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_44672164_4   3762 TAGACAACAAAAACAAAAATGTACAAATGGGACAATATTAAACTAAAAAG 3811
                         i ii        iv      iv i    v    vvi  i   v v    i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_44672164_4   3812 CCTCTGCACAGCAAAGGAAACAATCAACAGAATAAAGGCATAACCTTCTG 3861
                          i i  ii vv       v  v     v i i i  iiv i    iv v 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_44672164_4   3862 AATAGGAGAAAATATTTGCAAACTATTTATCTGACAAGGGACTAATATCC 3911
                            i                  ii  v       i        vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_44672164_4   3912 AGAATATACAAGGAATTCAAACAACTCAACAGTAAAACAAACAAACAAAC 3961
                                 i  i   i  vv         i i     ----- i     i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAA-----AGACAAAT 804

  chr2_44672164_4   3962 AGTTCCATTAAAAAGTGAG-AAGGGACATGAATATACATTTATCAGTAGA 4010
                          iii v   ?    i  i -  i   iv      v      v  viv   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_44672164_4   4011 AGACATACAAATGGCCAGTAGGTATATGAACAAATGTTTCACATGACTAA 4060
                            i             i  i i i     v i   i iv    v ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_44672164_4   4061 TCAT 4064
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.79 (136 / 76)
Gap_init rate = 0.01 (4 / 797), avg. gap size = 2.75 (11 / 4)  


3213 27.32 0.88 0.44  chr2_44728798_44730859.rev      667  1570 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_44728798_4    667 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 716
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_44728798_4    717 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCAACCCCATCAAGC 766
                           iv     v     iv i  i  i        i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_44728798_4    767 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 814
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_44728798_4    815 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 864
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_44728798_4    865 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 914
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_44728798_4    915 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGATC 964
                                 i   i    iii        i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_44728798_4    965 AATGGAACAGGAC--ACAGCCCTCAGAAATAACGCCACATATCTACAACT 1012
                                i  i i-- v  i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_44728798_4   1013 ATCTGATCTTTGACAAACCTGAGAAAAATAAGCAATGGGGAAAGGACTCC 1062
                          vi    i  i     ivv  vv  i vi vv            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_44728798_4   1063 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1112
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_44728798_4   1113 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1162
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_44728798_4   1163 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1212
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_44728798_4   1213 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1262
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_44728798_4   1263 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 1312
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_44728798_4   1313 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1362
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_44728798_4   1363 AGGCAACCCATAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 1412
                           i       i i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_44728798_4   1413 AGGGCTAATATCCAGAATATACAATGAACTC----AAATTTGCAAGAAAA 1458
                         i  i  vi             i  v      ----  v ivii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_44728798_4   1459 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 1508
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_44728798_4   1509 TCAAAGGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 1558
                           v  i     i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_44728798_4   1559 ATCACTGGCCAT 1570
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (150 / 93)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3149 26.31 1.90 0.67  chr2_44732352_44734353      614  1510 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_44732352_4    614 TGGAAAAACATTCCATGCTCATGGATAGGAAGAGTCAATATTGTGAAAAT 663
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_44732352_4    664 GGCCATACTGCCCGAAGTAATTTATAAATTCAATGCTATCCCCATCAAGC 713
                            v     v   i  v i  i  i i      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_44732352_4    714 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 761
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_44732352_4    762 TATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAG 811
                                viiv  ii  v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_44732352_4    812 AACAAAGCTGGAAGCATCACGCTACCTGACTTCAAACTACGCTACAAGGC 861
                                i    i vv    i  v  ii i      vivii      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_44732352_4    862 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 911
                          i      i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_44732352_4    912 AATGGAACAAAACAGAGGCCTCAGAAATAACACCACACATCTAAAACCAT 961
                                i i  iv   ivii         vv   i    i  viii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_44732352_4    962 CTGATCTTTGACAAACCTGACAGAAACAAGCAATGGGGAAAGGATTCCCT 1011
                         i    i  i     ivv  v  ii v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_44732352_4   1012 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGGAAGCTGA 1061
                         v  i  i              v      v  ?   i     ii iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_44732352_4   1062 AACTGGATCCCTTCCTTACACCTTAGACAAAAATTAACTCAAGATGGATT 1111
                          ii    i    v   i     v  v                i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_44732352_4   1112 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1161
                          ?    i           v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_44732352_4   1162 AGGC---AATGCCATTCAGGACATAGGCATGGGCAAAGACTTTATGACTA 1208
                            ?---   -- -   iv   v v  vv i     v ii  iv iiv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_44732352_4   1209 AAACACCAAAAGCAATGGCAACAAAATCCAAAATTGACAAGTGGGATCTA 1258
                         vi            vvi         vvv     v  i  i v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_44732352_4   1259 ATTAAA-TGAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 1307
                           i   - v   i -   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_44732352_4   1308 ACAGGCAACCTACAAAATGGGAGAAAACTTTTGCAATCTATCCATCTGAC 1357
                          v  i     i   i            iv       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_44732352_4   1358 AAAGGGGTGATATCCAGAATCTACAAAGAACT--TA-AATTTA-CAAGAA 1403
                           i  iv vi          v  i        --  -  i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_44732352_4   1404 AAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACGGACGCC 1449
                            i    ----   v  i?    i    ii      v    ii   iii
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_44732352_4   1450 TGTCAAAAGAAGACGTTTATGCAGCCAGCAA--ACATGAAAAAA-GCTCA 1496
                          v  v        ii vi viii    ii  --         i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_44732352_4   1497 TCATCACTGTTCAT 1510
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (145 / 87)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  

 260 20.75 0.00 0.00  chr2_44732352_44734353     1948  2000 (2)    L1M4_orf2#LINE/L1        1    53 (855)  

  chr2_44732352_4   1948 TGGAAAAACATTGCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 1997
                               i i  iv    i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_44732352_4   1998 GAC 2000
                          i 
  L1M4_orf2#LINE/     51 GGC 53

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.00 (0 / 0)  


2914 22.32 2.68 5.26  chr2_44763538_44767352.rev     2392  3323 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_44763538_4   2392 TGGAGTGAGATATCATTATTATGGATCAAAAGACTCAATATTATTAAGAT 2441
                             iv  v  vi   vv i      iii      i      i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_44763538_4   2442 GTGAATTATCTTCTCTTTAAATTCATCTATGAATTCAATGCAATCCCAAT 2491
                          vv   - ----   iii     v     iii      i        v  
  L1M4_orf2#LINE/     51 GGCAAT-A----CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_44763538_4   2492 TAAAATCACAACAGCCTTCTTCTTTTGATTTTTTAGAGATTGCCAACCTG 2541
                         i      v  i v     ----     ------i   i    v   v   
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTT----TTTTG------CAGAAATTGACAAGCTG 135

  chr2_44763538_4   2542 ATTCTAACATTTATATG-AAATACAAAGGACCTAAAATATCCAAAACCAA 2590
                           i    v   i     -    i   i     i i    v       -  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AA 184

  chr2_44763538_4   2591 TGTGGAAAAAGTAGAACAAAATTAGATGACTTACAGTACCTGATTTAAGG 2640
                          v v       v        i  i  v    i   v v  ii    v ii
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_44763538_4   2641 ACTTGT---AAATCTACAGTAATCAAAACAGTATGGTATTGGCATAATGG 2687
                             ii---   v             i     i     i        v i
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_44763538_4   2688 TAGACATACAGATTAAGGGAATAGAAAAGACAGTCCAGTAAGAGATCTGG 2737
                                 i    i  v         vv  v       v  v i i iiv
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_44763538_4   2738 ACATTTACA-TCAATTAATTTTCAACAATA-TGTAAAAGTAATTCAATGG 2785
                                ii-      i      i    vi-  iv  iiiv         
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_44763538_4   2786 GAGAAAAGATGATCTTTTCACCAAGTAATGCTAGAACAACTGGATATCGG 2835
                          -    ii  ii        v   i ii    i i           ? vi
  L1M4_orf2#LINE/    385 G-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_44763538_4   2836 TACGGAAAAAAAATGAACCTCGACCCTTACCTCACACTGTAT-TAAAAAT 2884
                         i i v    i  -    vi v     i          ii   -i      
  L1M4_orf2#LINE/    434 CATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_44763538_4   2885 AATATTCAAA-TATATCACATTCCTAAACATAAATGCTAAAGCTTTAAAA 2933
                         v - i     - iv    ? vv      ii   iv      i  v     
  L1M4_orf2#LINE/    483 TA-ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_44763538_4   2934 TATCCAAATTAAAACATAGGAGAAAAATCTTCATGATGTTTGTGTGAG-C 2982
                         iviii i vv          ? v   -     i   i-i   v  v  - 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGAC-CTTGGGTTAGGC 579

  chr2_44763538_4   2983 AA-AACTTTTTAGA----ACACAAAATGCACTAGCCATAAAAGAAAAAAA 3027
                           -iii  i     ----    v   v    v   v i           v
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_44763538_4   3028 AGATAACTTAGATTTTATAAAAACTAAAATCTTCTGCTCTTAAAAAGACA 3077
                               v  i  i  i  v    i     v   i  iv   v   i    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_44763538_4   3078 GTATTAATAAAATAAAAAGGCAAGCCAAAGACTGGGAAAAAATCTGCAAT 3127
                         v   i  v   i i     i   v   v   v     i     -------
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT------- 722

  chr2_44763538_4   3128 ACTTACATTTAACAACTGATTTGTTAAATATATGTATTTATTAAATGTAT 3177
                         ------------------     i-    -i  i   i iv   iv - i
  L1M4_orf2#LINE/    723 ------------------ATTTGC-AAAT-CATATATCTGATAAGGG-AC 751

  chr2_44763538_4   3178 TTGTAT--AGGTTATATACAGAATTATTGCAATT---TAATAAAAAGGTA 3222
                               --  iv      v    i v  i   i ---          ii 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_44763538_4   3223 TCCAATTCAACTAAAAACTGTACAAAAGATTTGAA----CATGTC-CCAA 3267
                         vvi  ii   i ?    v  vi    i        ----   v  -    
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_44763538_4   3268 AAAATATATACAAATGGTCAATAAACACATGAAAAAA-ATTCAACATCAG 3316
                          i  v            i      i          i -ii         ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_44763538_4   3317 CAATCAT 3323
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.65 (127 / 77)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.64 (74 / 28)  


3233 24.33 2.34 1.00  chr2_44864671_44868200.rev     2143  3038 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_44864671_4   2143 TGGAAAAACATTCCAGGCTCATGGATGAGAAGAATCAATGTTGTAAAAAT 2192
                               i i  i   v i        vi     v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_44864671_4   2193 GGCCATACTGCCCAAAGCAATTTACAGGTTCAAGGCCATTCCTATTAAAC 2242
                            v     v      vii  i     i     v  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_44864671_4   2243 TACCAA-TGTCATTCTTCGCAGAATTAGAAAAAGGTTATTTTAAAATTCA 2291
                          v   i-  i -  i  i      v v  v  - v v  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr2_44864671_4   2292 TATGGAACCAAAAAAAGAGTCCA-AATAGCCAAAACAATCCTGAGCAAAA 2340
                                -- viv  i iii   -                i   iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_44864671_4   2341 AGAACAAAGCCAGAGGCAC-CACACT-ACTGACTTCAAGCTATACTATAA 2388
                                  iii    -  -      -v ii i     iviv     i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_44864671_4   2389 AGCCATAGTCACCAAAACAGCTTGGTACTGGTATAAAAATAGACACATAG 2438
                            i i   v i   i    iv         i    ii       i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_44864671_4   2439 ACCAATGGAACAGAATAGAAAGCTCAGAAATAAAGCCGCACACTTGCAAC 2488
                          i        i     v  i  ii          v  ii   i  iiiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_44864671_4   2489 CATCTGATCTTCAACAAAGCTGACAAAAACAAGCAAGGGGGAAAGGACAC 2538
                           vi    i   i    i v  v   i v  vv   v        i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_44864671_4   2539 CCTGTTCAATAAATGGTGCTGAGATAACTGGCTAACCATATGCAGAAGAA 2588
                         i  v     i           i  i      v  ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_44864671_4   2589 TAAAATTGGACCCCTACCTATTGCCATATACAAAAATTAAATCAAAATGG 2638
                          i  i              vvii                 v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_44864671_4   2639 ATTACGGTTTTAAATGTAAGACCTCAAACTACAAAAATCCTGGAAGACAA 2688
                           i ?i vii           v  v      i    v  i i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_44864671_4   2689 CCTAGG---AAATACTCTCTTGACATTGGCCTTGGCAAATAATTT-TTGG 2734
                          v    ---    -  -  v    v    vi v     - ii   -  i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CT-TCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAG 592

  chr2_44864671_4   2735 CTAAGTCTCCAACAGCAACTGCAACAAAAACAAAAATAGACACGTGTGAC 2784
                         v  v v v    v    vvv         iv         i vi vv   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_44864671_4   2785 CTGATTACACGAAAGAGCTTCTGTATATCAAAAGAAACTACCAACAGGGT 2834
                         i v  i v vvv  i i   i   iiv     i  v    i   v ii  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_44864671_4   2835 AAATGGACAATACACAGAATGGGAGCACATATTTGTAAACTATGCATCCA 2884
                         i  vi     iv             v v       i   ii  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_44864671_4   2885 ACAAAGGCATAATATCTAGAATCTCTAGGGAACTT---------AATAAG 2925
                          i  i  vv vi    i     v v  ii     i---------     v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_44864671_4   2926 CAAAAAACAA-TAACCTCATTTAAAAA-GGGCAAAGGACGTGAACGGACA 2973
                         v    i    -     iv   ?     -          iv    ii    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_44864671_4   2974 CTTCTCAAAAGAAGATACACCAAGCGGCCAACAAACATATAAAAA-ATGC 3022
                         i     v          i  -  ii      i  i  i  i    -    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATAC-AAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_44864671_4   3023 -CAGCATCACTAATTAC 3038
                         -  i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (132 / 83)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.58 (30 / 19)  


3420 22.61 2.17 3.59  chr2_44999880_45004180     2890  3809 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_44999880_4   2890 GGAGAGATATTCCATGATCATGGATAGGAAGACTCAATATTGTTAAAATT 2939
                            i      i     v        v        i           i  v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_44999880_4   2940 TCAGTTTTTCCCAATTTGATCTATAGATTCAGCACAACCCCGATCAAAAT 2989
                         v  i vi i     v        i       i i   i   v        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_44999880_4   2990 CCCAGCAAGCTATTTTGTAGATATTGATGAACTGATTCTAAAGTTTATAT 3039
                               viv  v     i   v     ii i     i     i  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_44999880_4   3040 AGAGAGGGAAAAGACCCAGAACAGCCAACACAATATTGAAGGAAAAGAAC 3089
                         i  i v v  ii         i      v     v     ii i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_44999880_4   3090 GAAGTTGGAGGACTGACACTACTTGACTTCAGGACTTACTATAAAGCTAC 3139
                         i             v     v iii i    ii        i        
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_44999880_4   3140 AGTAATCAAGACAGTGTGGT----GAAAAAAAATAGACTAATAGATTAAT 3185
                                             ---- v v  ii      vv      i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_44999880_4   3186 GG----GGCCTAATAGCCCAGAAATAGACCCATGTGAACATAGTCTACTG 3231
                           ---- ivi i v  i         i      iiivvi  i   v i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_44999880_4   3232 ATCTTTGACAAAAGAGCAAAGGAAATACAATGGAAAAAAGACTGTCTTTT 3281
                           i  i     ii v  v   ivv  v      ii   ii iv       
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_44999880_4   3282 TCAACCAATGATACTGGAATAACTGAACATCCACAGGCAAAATTAATAAT 3331
                         -    v    i i    i i     i i ?     v      v-------
  L1M4_orf2#LINE/    402 -CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG------- 443

  chr2_44999880_4   3332 AATAATAATAATAATAATAAGGAATCTAGACACAGACC-T-TACAAAATT 3379
                         ------   i - i -- --   vi iviv v  v   - -       v 
  L1M4_orf2#LINE/    444 ------AATGA-AGT--T--GGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_44999880_4   3380 TATCTCAAGATGAATCACAGACCTAAATGTAAAATACAAAACTATAAAAC 3429
                           v     i   i    ?              i vvi             
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_44999880_4   3430 TTTTAGAAGATAATATAAGAGAAAATCTAGATGACCTTGGGTATGGTGGT 3479
                          i        v  i   i ? v      vvi           vv  iii 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_44999880_4   3480 GACTTTTTGGATATAACACCAAAAGCACAATCCATGAAAGAAATAATCCT 3529
                          ii  i  i     i               v v ii       v   ---
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT--- 629

  chr2_44999880_4   3530 GAACTTCATTAAATAAGCTGAACTTCATTAAAATTAAAACCTTCTGCTCT 3579
                         ---------- i    ii  i       i          v   i  iv  
  L1M4_orf2#LINE/    630 ----------AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_44999880_4   3580 GTGAATGGCAATGTCAAGAGAAT---AAGATAAGCCACAGAATGGGAGAA 3626
                         vii  v i  v i      i i ---    i  v                
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_44999880_4   3627 AATATTTTGTAAA--AAATATCTGATATAGAACTGTTATTCAAAATGTAC 3674
                                - i   -- v          vi i   vv   i  i   i  i
  L1M4_orf2#LINE/    720 AATATTT-GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_44999880_4   3675 CAAGAACTATTAAAACTCAAAAATAGGAAAATAAATAACCTAATTAAAAA 3724
                         v       v   v       v    ii  i i        i    ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_44999880_4   3725 ATGAACAGAT-ACCTAAACAGATACCTCGGCAAAGAAGATATACAGATGT 3773
                            ii  i v- ii i  i   i ii  vv               i   v
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_44999880_4   3774 ----TAAGTATATTAAAAGATATTCCGCATTATTTGTCAT 3809
                         ----    i i  v       ii  vi   i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (131 / 73)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 3.53 (53 / 15)  


3175 27.21 0.88 0.44  chr2_45198602_45204877.rev     4881  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_45198602_4   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_45198602_4   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_45198602_4   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_45198602_4   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAACCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     ii   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_45198602_4   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_45198602_4   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_45198602_4   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_45198602_4   5227 GTCTGATCTTTGACAAACCCGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                         ivi    i  i     ivvi vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_45198602_4   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_45198602_4   5327 GAAACTGGATCCCCTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i   iv   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_45198602_4   5377 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_45198602_4   5427 CTAGGCATCACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_45198602_4   5477 AACACCAACAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i       v    vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_45198602_4   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_45198602_4   5577 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_45198602_4   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACGAAAAAA 5676
                         i  i  vi          v  i  v      vv    v iv ii v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_45198602_4   5677 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5722
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_45198602_4   5723 TCAAGAGAAGACATTTATGCAGCCAAAAACCACATGAAAAAATGCTCATC 5772
                           v i      i  vi viii     v  v          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_45198602_4   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3217 27.42 0.44 0.44  chr2_45214035_45220314     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_45214035_4   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_45214035_4   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_45214035_4   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_45214035_4   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAACCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     ii   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_45214035_4   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_45214035_4   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_45214035_4   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTGCAACT 5226
                                i    i--    i  --        vv  ii i  i iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_45214035_4   5227 GTCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                         ivi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_45214035_4   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_45214035_4   5327 GAAACTGGATCCCCTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i   iv   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_45214035_4   5377 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_45214035_4   5427 CTAGGCATCACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_45214035_4   5477 AACACCAACAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i       v    vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_45214035_4   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_45214035_4   5577 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5626
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_45214035_4   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAGA 5676
                         i  i  vi          v  i  v      vv    v iv i  v  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_45214035_4   5677 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_45214035_4   5727 TCAAAAGAAGACATTTATGCAGCCAAAAACCACATGAAAAAATGCTCATC 5776
                           v        i  vi viii     v  v          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_45214035_4   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (149 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2491 26.43 6.29 2.63  chr2_45238769_45241311.rev     1186  2059 (484)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_45238769_4   1186 GAGAGACA-CACATGTTCACAGATTGGATGACTCAATATCGTTAAGACAT 1234
                           i   i - v        ii       v    i     i       iiv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_45238769_4   1235 TAATTCTTCCTGAACTGATATATAAGTTCAATAAAATCACAATCAAAATC 1284
                         i   v  i  ii  i    v  i ii     iiv    v v         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_45238769_4   1285 CCAGAAAGTTTATGGTTGTTGAAATTGACAAGTTGGTTCTGAATTTTACA 1334
                             vvivi  v --   iv            i  i i  i  v  i i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTT--TTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_45238769_4   1335 AGGAAATGCAAGAGACCTAGAATTGCTAAGACAGCCTTGAA------GAA 1378
                         v           i    i     v  i  i   ii      ------   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_45238769_4   1379 CAAAATTGGAGAATTTACAGTACAAAATGTTGAGTCTTACAAAAATGACA 1428
                             i      i i i   v v vv   v ii iv     ----- -   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC-----T-ACA 244

  chr2_45238769_4   1429 AAGCTTTAGTAACTAAGACAGCATGGTATTGGTGAAAGAATAGATAAGTT 1478
                              vi     ii       ii     i   iiv   i     i vi v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_45238769_4   1479 GATCAGTGTTATAAAATTCAGTG--CAGAAATAGACCCA--CATATATGC 1524
                              i  vv   i    v  v --        i     --   v    v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_45238769_4   1525 TCACCTGATTCACAAAGACAATACCAATGTAATTCAGTGGAGGAAAGAAT 1574
                            vi     iv i vi vii i    viiv     i   -         
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAAT 393

  chr2_45238769_4   1575 TATCTTTTCAACAGCTGGTGCTGAAAC--TTGAATAGG-----GCAAAAA 1617
                         vi           iv        ii  --i  i   ?v-----      i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_45238769_4   1618 AACTAAGTGTGAACCCCTACCTCCTACAATGCACAGAAATTAATGTGAGA 1667
                           iv    -  i           vi  v  ii   i       ivii i 
  L1M4_orf2#LINE/    444 AATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_45238769_4   1668 TGGATCATAGACTTAAATATGAAAGATAAAACAATAAAGTTTCCAAAGGG 1717
                                ?    i     i i i  v      v     ii iii i i i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_45238769_4   1718 AAATAGAATAGT-----TTCAAGACCTTGGAGGAAGCCAAGATTTCTTAG 1762
                            i v iv?  -----   iv        ivv i  v v i        
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_45238769_4   1763 G-ATG-CAATAAATTAGTAGCCTTAAATTAAAAAAAAAAAACCTGATTAA 1810
                         i-   -  vi   --  i ----i  iiv v    i     viv   v  
  L1M4_orf2#LINE/    593 ATATGACACCAAA--AGCA----CAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_45238769_4   1811 TTGAACTTCACTAAAATTGAAGACTTCTGTTCATCAACAGAAATCATTAA 1860
                            i      ii      i  i    i   v v    vi  v ii  i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_45238769_4   1861 GAGAATAAAAAAGCAAGTCTCAGAC-------AAATATCT-----TTGTA 1898
                           i i i    ii   vi v    v-------      i ----- ii  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_45238769_4   1899 CAGGTAATAAAAAGGACTCATATCTGAAATATATGAACAACTCCTACAAA 1948
                         i vv i    i--     ii    iii       i  v     i     v
  L1M4_orf2#LINE/    737 TATCTGATAAG--GGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_45238769_4   1949 TCAACGAGAAAA---CAAA----CCAATTTTAAAATGTGTAAA------- 1984
                             ii v    ---    ----      ?v      v i   -------
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_45238769_4   1985 AATA----TTTCACTTAAAAGGAGAGAATATCCAAATGGCTAACAAGCAT 2030
                             ----    v i--    i   ---   v        i  i     i
  L1M4_orf2#LINE/    835 AATAGACATTTCTCC--AAAGAAGA---TATACAAATGGCCAATAAGCAC 879

  chr2_45238769_4   2031 GTGAAAAAATACTGCACGTTATACTACTT 2059
                         i      i  i  vv  i i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (149 / 78)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 3.12 (78 / 25)  


4112 16.27 5.73 1.72  chr2_45244041_45246399      995  1867 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_45244041_4    995 TGAAAAGTTATTCAAT-TACAATTGATTGGAATATTTCAAATATTATTAT 1043
                           i    v   i v  - v  - v        v i  --      i   v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCA-TGGATTGGAAGACTT--AATATTGTTAA 47

  chr2_45244041_4   1044 GATATCAATACTCCCCAAATTGATCTACAGATGCAGCGCAATCCCTATCA 1093
                            iv                           v  i              
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_45244041_4   1094 AAATTCCAGATGGCTTTTCTGTAGGTATTAGTAAGCTCATTATAAAATTC 1143
                             i    v  v     i  i  iv   iii     v  iv        
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_45244041_4   1144 ATGTGGAAATTCAAGGGACCCAGAGGAACCAAAACAATACTGAAAAAGAA 1193
                           i       v             iv i          vi          
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_45244041_4   1194 ---CAAACTTGGAATACTCACACTTTCTACTTTAAAAAC-----ACAAAG 1235
                         ---    v     iv          i i v   v     -----      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_45244041_4   1236 CTATAGTGATCAAGACTGTGAAGTATAGGCATAAAAATAGACATACACAT 1285
                            i   i        v   vi   iv       ii         i v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_45244041_4   1286 CCACATCGACGGAATAGAATTGAGAATCCAGACAAAAAAAAACCTCTTAC 1335
                          ------i i               i      ----  v     - v   
  L1M4_orf2#LINE/    298 C------AATGGAATAGAATTGAGAGTCCAGA----AATAAACC-CATAC 336

  chr2_45244041_4   1336 ATTTTTGGTCAATTGATTTTTGACA--------------------TGGGG 1365
                             v               i    --------------------     
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_45244041_4   1366 GAA--ATAGTCTTT-CAACAAATGTTGCTGAGACAACTG-ATATCCACAT 1411
                         i  --         -         v     i        -   ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_45244041_4   1412 GCAAAAGGGTGAACTTGGATCCTTATCTCTC--TATGTACAAAAGTTAAC 1459
                                ii    v     i  i  i   v --i  i       i     
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_45244041_4   1460 TGAAAA-GGGCCAGAGACCTTCATGTGAGAGCTGAAAATACAAAACTTTT 1508
                          v    -  ii  ?      vv    i      i   v  i      i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_45244041_4   1509 AGAAGAAAATATAGATGTGAATCTTCATGTCCTCAGATTAGGCAATGGTT 1558
                                  i    i?  i       i  v   ii i             
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_45244041_4   1559 TCTTAGCCATGACACCAAGAGCACAAGTTGCAAAG--AAAAATG--TAAA 1604
                               vi          i        ivi    i--      i--    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_45244041_4   1605 TTGCACTTCATCAAAGTAAAACACTTTTGTGCTTCAAAGAATATAATCAA 1654
                            v           i v   v                 i i iv     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_45244041_4   1655 TAAAGTGAAAA-----CCCACAGAATGAGAAAGAAGTTTTGTAAATCATA 1699
                         v          -----           i  i i  vv    i        
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_45244041_4   1700 CATTTCATAAGGGACTTGTATCCAGAATA---AAAAATGTATATACAATG 1746
                         i  i v                       ---   i vv v -     iv
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAACT 785

  chr2_45244041_4   1747 CTACAATAAAAAGAAAAATAATCCAATTTTAAAATGGGCAAAAGATTGGA 1796
                          v i          v      i      ?v            i    v  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_45244041_4   1797 ATAAGCATTTCTCCAAAGAGGATATATAAATGGTCAA-AAACACATGAGA 1845
                            ii              i      i      i   -  i       i 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_45244041_4   1846 AAATGCTCA-CATTATTAGGGAA 1867
                          i       -   i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (85 / 53)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.10 (65 / 21)  


3964 18.73 1.23 2.34  chr2_45353659_45356394     1348  2244 (492)    L1M4_orf2#LINE/L1       22   908 (0)  

  chr2_45353659_4   1348 TGAGTTAAAAGACTTAATATTGTTAACATGTGCATATAATCC--AAAATG 1395
                           ii  ii                  v   -   -   v   --   v  
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATG-GCA-ATACTCCCCAAATTG 69

  chr2_45353659_4   1396 ATCTACAGATTTAATATAATCCTTCTCAAAATCC-AAATGCCATTTTTTG 1444
                                    i  iii     i v         - iv    -       
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTG 118

  chr2_45353659_4   1445 CAGATATAGCAAAAACAATCCTAAAATT--TATGGAACTAAAAAGGACCC 1492
                             v  v vv  ivii           --       v iv  i      
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr2_45353659_4   1493 TGAATAGCTAAAACAATCTTGAGGAAGAAGAACAAACCTGGAAGCCTCAC 1542
                         v       i             ii            vi    i v     
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_45353659_4   1543 ACTTCTTGACTTCAAAACATATTCCAA-GCTACAGTAATTAAAACAGTAT 1591
                              iii i        v  i v   -           i  i     i 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_45353659_4   1592 GGTAATGGCATAAGGTCAGACATGTATAGACCAATGGAACAGAAGAGAGA 1641
                             v          vi      --     i        i    vv    
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACAT--ATAGATCAATGGAATAGAATTGAGA 316

  chr2_45353659_4   1642 GCCTCAAAATATACCTATGCATAGACAGTCAAATGACCTTTACCTAAAGT 1691
                          i ivi     v   i  i   vv ii     v   ii  iiv v ii  
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_45353659_4   1692 ACCAAGACTACACATTGGAGCAAGGATAGTCTTCTCAATAAATGGTGCTG 1741
                         i       i iv  v   i v   i        i    i           
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_45353659_4   1742 GGAAAACTGGAAAACCACATGCAAAAGAATGAAATTGGACCTTTATCTTA 1791
                            v       v ?                   i       ii  i  i 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_45353659_4   1792 CACCATACACAAAAATTAACTCAAAATAGATTAAAGATCTAAACATAAGT 1841
                                i                   i   i ?   i     ii    -
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG- 515

  chr2_45353659_4   1842 TATGTGAAACTATAAAACTCCTAGAAGAAAACATAAGGGAAAACCTTCAC 1891
                         - vv i              i              i ? v   i    ii
  L1M4_orf2#LINE/    516 -AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_45353659_4   1892 GGCATTAGATTTGGCAATGATTTCTTGGCTATGACACCAAAA--ACAGAC 1939
                          i v  i i  v       i      i v             --   ii 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_45353659_4   1940 AACAAAAGCAAAAATAGACAAGT-GGACCAACATCAAA-TGAAAAAGTTT 1987
                                 v         i  i -    i-v       - v     v   
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACT-TCATCAAAATTAAAAACTTT 663

  chr2_45353659_4   1988 CTGCACAGCAAAGGTAACAATCAATAGAGTGAAAAGGCAACCTATGGAAT 2037
                         -  ii vv      vv  v     v i         i     i ii    
  L1M4_orf2#LINE/    664 -TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_45353659_4   2038 GAGAGAAAATATTTTCAAACCATATAACTGATAAGGGCTTAATAAGCAAA 2087
                          i            v    i      v          vi vi  vv  i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_45353659_4   2088 ATATATTTTTTAAAAACTCCTACAACTCAATAACCACACAACAAAAGTAA 2137
                               ----v  i     i             --------i    iv v
  L1M4_orf2#LINE/    763 ATATAT----AAAGAACTCTTACAACTCAATAA--------TAAAAAGAC 800

  chr2_45353659_4   2138 AAATAACTTGATTAAAAAGCAGGCAAAGGACTTCAATAGAGTTTTCTCCA 2187
                                iii   ?    iii         i  v      vv        
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_45353659_4   2188 AAGAAGATATACAAATGGCCAATAAGTATATGAAAAGATGC-CAACATCA 2236
                                                   i i            -        
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_45353659_4   2237 CTAATCAC 2244
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.69 (103 / 61)
Gap_init rate = 0.02 (17 / 887), avg. gap size = 1.88 (32 / 17)  


 648 28.30 15.61 1.89  chr2_45383948_45385646      503  1085 (614)    L1M4_orf2#LINE/L1      227   889 (19)  

  chr2_45383948_4    503 ATATCAAAACATAATATAAAGCTATGAGAAATAAAACACTGTGCTATTGG 552
                           v       v  v  i       iiiv  vi  i   v    v  i   
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_45383948_4    553 TGTAAGGTTTAAAAAATAGCTCAATAGAACAGAAAAGGGAATCTAGAAGT 602
                         ii     v vi v v    v     i   i    vv i  i  i    i 
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_45383948_4    603 AGAGTCATGGATATATGGTGAATATATTATATGACAAATGTGGCACTTCA 652
                          i vi   iv  v      v   vv   v -i     iv   v  vvv v
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTT-CGACAAGGGTGCCAAGACC 375

  chr2_45383948_4    653 AATAAATGGGGAAAAGATAAACTGTCCA---------GTCGGGA------ 687
                          v v          ii   iv  v i  --------- ii    ------
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_45383948_4    688 ----------------AAAATTAATTTACATCACTACTTTTAACTAT-TG 720
                         ---------------- i   v  v  iv i v    i ivv  i  - i
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_45383948_4    721 -AAAAATATAAGTTTCAGAA-GGTTTAAAGACCTAAACA-AAGTGC-AAC 766
                         -      -   --i   i  -  v i ?         ii-   v  -  v
  L1M4_orf2#LINE/    476 CAAAAAT-TAA--CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_45383948_4    767 ACTATAAAA-TATTA-AAGAAAATATTAGAG---AT----GCCACATAGG 807
                                  - v   -       i  vi ? ---  ---- iv  v v  
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_45383948_4    808 GTAAGCC--------------TATG----CAAAAACT------ATAGAAG 833
                           v  v --------------    ----     i v------ i i   
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_45383948_4    834 AAAAAGGGGTTAAATTTCACTTTGTCAA---TAAAA--TTCTATCAATGA 878
                              ivi v      vv    ii    ---     --  i i vvv v 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_45383948_4    879 AAGTG-ACCATAAATATACT-ACAAGAAAAGTAACAAATTAGGAAAAGAT 926
                            vi-  i  v  v v v - v    v  viv   i v i   i  i  
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_45383948_4    927 ATTTGC---TCATATAC--AACAAAGGGTTGATATTCAAAACATATAAGG 971
                               ---       i--i i  i  ii vi   i  i  i      i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_45383948_4    972 AACTC-----ATTCAAGAA---AAAGACAAATAGCTCAATAGAAAAATGG 1013
                              ----- i    v  ---           i i    v?        
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_45383948_4   1014 GTGAAAGATATGAATTGGTAATTCATATAAGACAAAGTACATATCCAGAA 1063
                          ii  i   v     v ii v   vi------     v v    v  -  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTC------CAAAGAAGATATACA-AA 865

  chr2_45383948_4   1064 T--CTACAAGGAACTTAAAAAAAT 1085
                          -- i vv i v  v i    i  
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGAT 889

Transitions / transversions = 1.02 (82 / 80)
Gap_init rate = 0.04 (28 / 663), avg. gap size = 3.64 (102 / 28)  

 275 19.83 6.61 7.44  chr2_45383948_45385646     1087  1207 (492)    L1M4_orf2#LINE/L1      789   908 (0)  

  chr2_45383948_4   1087 TACTAGAAAAA-AAAT--CCCCATCAAAAAGTAGGCAAAAGCTATGAACA 1133
                           v  i   i -    --   v  i?    i i      i v v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_45383948_4   1134 GACACTTCTCAAAAAAAAAAAAAAAAGACATTTACGTGGCCAACAA--AC 1181
                             i     v   i  ---------  i  vi vi       i  --  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAA---------GATATACAAATGGCCAATAAGCAC 879

  chr2_45383948_4   1182 ATGAGAAAAAGCTCA---TCACTGGTCAT 1207
                             i  i v     ---   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.04 (5 / 120), avg. gap size = 3.40 (17 / 5)  


 267  5.13 5.13 0.00  chr2_45515512_45518043      112   150 (2382)    L1M4_orf2#LINE/L1        1    41 (867)  

  chr2_45515512_4    112 TGGAAAGACAGCCCATGTTCATGGATTGGAAGAC--AATAT 150
                                 i v                       --     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT 41

Transitions / transversions = 1.00 (1 / 1)
Gap_init rate = 0.02 (1 / 41), avg. gap size = 2.00 (2 / 1)  

1025 19.00 1.36 2.26  chr2_45515512_45518043      476   696 (1836)    L1M4_orf2#LINE/L1       20   238 (670)  

  chr2_45515512_4    476 CATGAATATGGAGGGCTGACTGTTCTATTAAGA-GGCTATATCCCCCCAA 524
                             i  -    i i  v v i  --i      -   v   - i      
  L1M4_orf2#LINE/     20 CATGGAT-TGGAAGACTTAATATT--GTTAAGATGGCAATA-CTCCCCAA 65

  chr2_45515512_4    525 ATTGACCCACATATTCAACACAATCCCTATTAAGATCTCAGCTGACTTCT 574
                              i i   v       i          i  i   i      v   i 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_45515512_4    575 CTGCAGAAATTGACAAGTTGGTCCTAAAATCCATACGAAAATGCAAGGAA 624
                         i                i  i         i    i i          i 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_45515512_4    625 CCCAGAATAGCCAAAACAACCTTGAGAATGAAAAACCAGCTGTGGTGG-C 673
                                            i     i  v   i   v iv -   v  - 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT-TGGAGGAC 214

  chr2_45515512_4    674 TTACATCTGT-AATCCCAGCACTT 696
                          i   ii vi-   ii  iv    
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTT 238

Transitions / transversions = 2.82 (31 / 11)
Gap_init rate = 0.03 (7 / 219), avg. gap size = 1.14 (8 / 7)  

2151 13.50 5.91 16.46  chr2_45515512_45518043      951  1661 (871)    L1M4_orf2#LINE/L1      190   825 (83)  

  chr2_45515512_4    951 AAAAGGGAAAACAAAATTGGAGGATTGGAGGATTCACACTTCTCAATTTC 1000
                             i i i      i        i --------        i       
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACT--------CACACTTCCCAATTTC 231

  chr2_45515512_4   1001 AAAATATACTACAAAGCTCCAGTACTCATGACAGTATGGTACTGGCATAA 1050
                             iv            v     v   v      i              
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_45515512_4   1051 ACACAGACATA---ATAAATTGATTGGAATTGATC-TCTAGAA-----CA 1091
                         iv i       ---  v   v  v i       vv-  i    ----- v
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_45515512_4   1092 CATACATCTATGGTCAACCGATTATTGACAAAGGTACCATGACAATTATT 1141
                                i         ii    v i     i   i   v   -------
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC------- 374

  chr2_45515512_4   1142 AGTTTGGTGCAAAAGTAATTGCGTTTTAATTACTTTTTTTAAGTAAAGTT 1191
                         --------------------------------------------------
  L1M4_orf2#LINE/    375 -------------------------------------------------- 374

  chr2_45515512_4   1192 TTTATAAATGCCATTAAATGGCAAAAAACACAATTACTTTTGCAGCAACC 1241
                         -----------    ---------------    ----------------
  L1M4_orf2#LINE/    375 -----------CATT---------------CAAT---------------- 382

  chr2_45515512_4   1242 TAATAATTGGGGAAAGAATTGTCTTTTCAACAAAGAATGTAGGGACAACT 1291
                         --------           v              vii  iv         
  L1M4_orf2#LINE/    383 --------GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_45515512_4   1292 GGATATGCATAGGCAAAAGAATCA-GTGTGGACCTCTACCTCATTCCACA 1340
                              ?v  i v          v -  -      i        iv   i 
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGT-TGGACCCCTACCTCACACCATA 473

  chr2_45515512_4   1341 TGCAAA--TTAATTCAAAGTGGATCAGATACCTAAATTTAAGAGCTAAAA 1388
                          i    --    i     i       ? v        v            
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_45515512_4   1389 CTATTAAACAC----AAGAAAACAGAGGCATAA-TTATCCTGACCTTGGA 1433
                             v    v ----         v   ?i   - iv  v         i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_45515512_4   1434 TTAGGCA-TG-TTTATTAAAT--GATACCAAAAGCTCAAGCC-CAAAAGA 1478
                                -  -   v   i  --  i         v     v-       
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_45515512_4   1479 AAAAA---ATAAATTGACCCTCATACCAATTAAACA-TTTTGTGCTTCAA 1524
                              ---        iv i    vvv       v -             
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_45515512_4   1525 AAGGCACTATTAAGAAAGTGAAAAGAAAACTCACAGAATGGGATAAAGTT 1574
                          i i      i               v   i            v   i v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_45515512_4   1575 TTT-------ATTTATCTGATAAGAAACTTGTATTTAGAATATATAAAGA 1617
                            -------  v           ii        ii              
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_45515512_4   1618 ACTCCCACAATGTAGTAA---------AAATAACCTAATATAAAATATGG 1658
                             ii    ivi i   ---------        i   v?    -    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA-ATGG 822

  chr2_45515512_4   1659 TCA 1661
                         v  
  L1M4_orf2#LINE/    823 GCA 825

Transitions / transversions = 1.19 (50 / 42)
Gap_init rate = 0.03 (21 / 636), avg. gap size = 7.57 (159 / 21)  

 414 17.70 11.50 0.00  chr2_45515512_45518043     1933  2045 (487)    L1M4_orf2#LINE/L1      783   908 (0)  

  chr2_45515512_4   1933 ACTCCATCTCAAAAAAAAAAAAAA--------AAATATGGTCAGAG--TC 1972
                             v  vvi     i v   v  --------   v    v  i  -- i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_45515512_4   1973 TGAATAGACATTTCTTCAAAGA---TATGCAAATGACCAATAAGCATATG 2019
                                        i      ---   i      i          i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_45515512_4   2020 AAAAAATGCTCAATGTTGTTATTCAT 2045
                             i        ii ii????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.02 (3 / 126), avg. gap size = 4.33 (13 / 3)  


3406 25.06 1.43 1.21  chr2_45637537_45640528.rev     1595  2500 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_45637537_4   1595 TGGAATAATATTCCATGCTCCTAGATTGGGAGGATTAATATTGTTAAAAT 1644
                              vi    i     i  v i      i  iv             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_45637537_4   1645 GTCTTTACTACCCAAAGTGATCTACAGATTCAGTGCAATACCTATCAAAA 1694
                          v vv    v      v               ii     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_45637537_4   1695 TACCAATGACATTCTTCATAGAAGTAGAAAAAA-AATACTAAAAATTCAA 1743
                          v   iivi v  i  iii    i v  v  iv-i  v      -    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCAT 149

  chr2_45637537_4   1744 ATGAAACAACAAAAGACCCCAAATAGCTAATGCAATCCTTAGCAAAACGA 1793
                            i  vvi   ii     vi      i  vi     i v iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_45637537_4   1794 ACAAAGCTGAAGGCATCACACTACCTGATTTCAAAGTATACTACAAAGCT 1843
                               i  i   vv       v  ii        iiv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_45637537_4   1844 GTTATAACCAAAACAGCATGATACTGGCATAAAAACAGACACATAGACCA 1893
                         iivi   i   i    ii  i           ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_45637537_4   1894 ATGGAACAGAAGAGAGAACCCAGAAGTAGATCTGTACACGTGGAGTCAAC 1943
                               i    vv    ii      i  i i ii    iv ivi     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_45637537_4   1944 TCATTTT-GACAGTGGTGCCAAGAACACACACTGGGGAAAGGACAGCCTC 1992
                          v     -    iv          v  iv  v         i i  i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_45637537_4   1993 TTTAATAAATGATGCTGGGAAAACTGGATATCCATTTGCAGAAGAATGAA 2042
                           i  i     i        v         ?   iv    i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_45637537_4   2043 ACTAGATCCCCGTTTTTTACCATATATAAAAATTAACTAAAAATGGATTA 2092
                         ii i  i   iiii ivi        i           v         i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_45637537_4   2093 AAGACTTAAATGTAAGACCTGAAACTATAAAACTGCTAAAAGAAAACATT 2142
                         ?    i           v  i             vi  i          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_45637537_4   2143 GGGGGAAATGCTGC-CGATCAGTGGTCTGGGCAAAGATTTTTGGGGTAAG 2191
                           ? v    -  v -i  i -v   vi i     v i   i vi i  v 
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_45637537_4   2192 ACCTCAAAAGCACAGACAA----AGCAAAAATAGACAAATGGGATTACAT 2237
                           vi          ii   ----  v         i    v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_45637537_4   2238 CAAGCTAAAAAGCTTCTGCACAGCAAAGGAAACAGTCAACAAAGTGAAGA 2287
                            iv v    i   i  ii vv       v  vi    v        i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_45637537_4   2288 AGCAACCTACTGAATGGGAGAAATTATTTGCAAACTATCACA------AA 2331
                         ii     i  v            v          ii  - i ------  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-ATATCTGATAA 746

  chr2_45637537_4   2332 GGGATTAATAACTAGAACATATAAGGAAGTGAAACAGCTCAATAGCAAAA 2381
                             i vi  v i    i      i   v vvv   i       ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_45637537_4   2382 GAAAACCCACAAATACTGTGATTAAGAAATAGTCAAAAGACCTGTACAAA 2431
                         ii ------      vivii   ? i    i v    i  ii  v i i 
  L1M4_orf2#LINE/    797 AGA------CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_45637537_4   2432 CATTTCTCAGAAGAAGACATACAGATAACCACTAGATATATTAAAGAAAT 2481
                                 vi       i     i  ii   v  iii i  v   - i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGAT 889

  chr2_45637537_4   2482 GCTAAGCATCACTAATCAT 2500
                            v i     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (144 / 79)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.18 (24 / 11)  


1908 21.40 5.54 11.64  chr2_45771709_45773602      501  1402 (492)    L1M4_orf2#LINE/L1       62   908 (0)  

  chr2_45771709_4    501 CCAAAATGATTTTATAGACTTGATG-AATAAGAATCAAAATATTAGCAGG 549
                              v    i - i   i ii i -   vvvv        vii   v v
  L1M4_orf2#LINE/     62 CCAAATTGATCT-ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr2_45771709_4    550 ATTTTTTA-AAACATAAGCAAGCTGATTCTAAAATGTATATGAAAAGGCA 598
                         v      i- i v  vii         i       vi     i   v   
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_45771709_4    599 AAGGACATAGAATAAACAAAACAAT-TTGAAAAAGAAGAATAGAGTTAG- 646
                          i    vi      iv         -              i i    i -
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_45771709_4    647 ---CTCACCCTAACCA-TTTTAAAACTTAGTCTAAAGCGAAGTATAATAA 692
                         ---     v  vv   -   i        v vi     ----  i i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC----TACAGTAA 256

  chr2_45771709_4    693 TTTTAAGACCCTGTGGTATTG--ATGAAACTATACACACAATGATCAATG 740
                          i--     vv       i  --  i iiv  v   i i --        
  L1M4_orf2#LINE/    257 TC--AAGACAGTGTGGTACTGGCATAAGGATAGACATATA--GATCAATG 302

  chr2_45771709_4    741 GAACAAAATAGGCAATCCAGGAATAGATCCACAAAAATATGATCAATTGA 790
                            i i   v iv i     i    i i   i v vv    i        
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_45771709_4    791 TTTTTGAAGATAGATTTTTTTATTGAGATAAAATTGACATAAAATACATC 840
                             i  -------------------------------------------
  L1M4_orf2#LINE/    353 TTTTCGA------------------------------------------- 359

  chr2_45771709_4    841 ATTTTAACCATTTTAAAGTACAAAATTGACAATTTTTGAAAAAGGTATTA 890
                         --------------------   i-------------------   iii 
  L1M4_orf2#LINE/    360 --------------------CAAG-------------------GGTGCCA 370

  chr2_45771709_4    891 AGGCAATTCAATGGATAAAGGATAATCTTTTCAACAAATGG------AAC 934
                           i v         iv    i   i                ------i  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_45771709_4    935 AACTGAACATCCATATGCAAAAAAATGAACCTTAAGCTATATATCAGAGT 984
                              i i ?   i        i      vi vi v iv  iv   v vi
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_45771709_4    985 ATAATCTATAGAAAAATTAACCTCAAATGGATCATAGATCTAAATGCAAA 1034
                            -----  v          iiv          ?   i       i  i
  L1M4_orf2#LINE/    471 ATA-----TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_45771709_4   1035 A-CTAGAAACTA--ACATGTTTATTTTAAAACATA--TGT---TTTT--- 1073
                          -   -      -- v ivi   vvvv        --?  --- i  ---
  L1M4_orf2#LINE/    516 AGCTA-AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_45771709_4   1074 ------------GATAATG----TTTAGCTATGACATCAAAATC-CAATT 1106
                         ------------ ii    ----i    v       i     v -   vi
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_45771709_4   1107 CATAAAAGCAAAAAAAGATAAATTAGACTTAATCAAAATTAATTTTTTTT 1156
                         v i     v     v         i     v           vvvi    
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_45771709_4   1157 TGGCT---AAAAACATTGTTAAGTATTTAAGAATTAAAAGAACAAGCTGT 1203
                         vv   ---  ii   i i i   ------ i i v      -   v iii
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAG------AAAGTGAAAAGA-CAACCCAC 707

  chr2_45771709_4   1204 AAACTGGGATCAAATATTAGCAAATTGTATATCCAACACAGGATTTGTAT 1253
                          i v     vv       v      ii      ii i vi   i      
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_45771709_4   1254 CCAGAATATGTAAATAACTTTCAAAAC--AATAATAAGAAAACAA-CAAT 1300
                                  i    v    i i v   --        i  i    -i  i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_45771709_4   1301 ACAATTTTAAAAATAGGCAAAATATGCGAATGAACATTTCAACAAAGAAG 1350
                         v     ?-      i      iv  vi    ii       vv        
  L1M4_orf2#LINE/    808 CCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_45771709_4   1351 TTACGCAGATGGCAGATAAAGATATGAAAAGTTGCTCAAAATCATTAGCC 1400
                         v  ii  i     vi    iv i        v       v    ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_45771709_4   1401 AT 1402
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.45 (112 / 77)
Gap_init rate = 0.03 (28 / 847), avg. gap size = 5.54 (155 / 28)  


2724 21.39 2.76 10.13  chr2_46133330_46137988.rev     3191  4167 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_46133330_4   3191 AGAGATATACCGTATTCATGGATAGAAAGACTCAGTATTTGTCAAGATG- 3239
                          i      v  i i         v i      i i    -  i      -
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-GTTAAGATGG 52

  chr2_46133330_4   3240 ---T-CTTTCCAAACTCGATCTATATATTCAACGCAACCTTAATCAAAAT 3285
                         --- -  ii     i -      i v           i iiv        
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATT-GATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_46133330_4   3286 CCCAGC-AAGTTATTTATGGATATCGACAAACTCATTCTAAAGTTTATAT 3334
                               -ivv  v   iii  v  i     i  v  i     i  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_46133330_4   3335 GGAGAGGCAAAAGACCCAGGCAAAAGACCCAAGCAAAAGGCTAACACAAT 3384
                            i v    ii       ----------------  vi  i  v     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAG----------------AATAGCCAAAACAAT 185

  chr2_46133330_4   3385 ATTGAAGAAAAAGAACGAAGTCAGAAGACTGACACTACCCAATTTCAAGA 3434
                         v     i  i      i    ii  i    v     v           i 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_46133330_4   3435 CTTACTATAAAGCTGAAGTAATCAAGACAATGTGGAATTGGCAAAACATC 3484
                                i      iv             i     v i     v  ----
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA---- 281

  chr2_46133330_4   3485 AATGGAACAGACAAATAGATCAATGGAACAGAACAGACAGCCCAGAG-CA 3533
                         ---- i i     v              i    iv  v  i     i-i 
  L1M4_orf2#LINE/    282 ----GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_46133330_4   3534 GACCCGCACAAATACAGCCAACTGATCTTTGACAAAGAAGCAAAGGCAAT 3583
                         i    ii   vv  ii i   i    i  i     i iv  v   i v  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_46133330_4   3584 AAAATGGAGCAAAGACAGT--TTTCAACAAATGGTGCTAGAAAAACTAGA 3631
                         vv     i v  ii i   --                 i i v    i  
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_46133330_4   3632 ------CATGCAAAACAGTGAATCTAGACACAAACCTTACGATCTT-CAC 3674
                         ------         v i    vi i   v vv    i  - i v -i  
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC-ACCATATAC 476

  chr2_46133330_4   3675 AAAAATGAATCCAAAATGGACTGTAGACCTAAATGTAAAAGGCAAAACTA 3724
                               v  ii         iii?              i  vi       
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_46133330_4   3725 TGAAACTCCTTGAAGATAATATAGAAGAAAATATAGGTAACCTTGG-CTA 3773
                          i      i v     v  i    i? v    v vv  i       -i  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_46133330_4   3774 CACAGATAACTTTCTT-GATGCAACACCATGATGCATGGACATGATCCAT 3822
                         vi  -  ii-      -   iii      vi -   iiii  ------ i
  L1M4_orf2#LINE/    577 GGCA-ATGG-TTTCTTAGATATGACACCAAAA-GCACAAGCA------AC 617

  chr2_46133330_4   3823 GAAAAAAAGAGCTGATAAGCTGAACTTCATTAAAATAAAAAACTTTTGCT 3872
                         i   i   i iiv     ii  i       i     v           --
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG-- 665

  chr2_46133330_4   3873 CTGTCCCCCACCTCCCCAAACTAAAACAAACAAACAAACAAACAAAAAAC 3922
                         -  --------  i ----------------------------   ii  
  L1M4_orf2#LINE/    666 -TG--------CTTC----------------------------AAAGGAC 678

  chr2_46133330_4   3923 AAACAAAACCAAACCACACACTGCCAATAGAATAAAAAGACAAGTAACAG 3972
                          -------------------  ii   v i i i         viv    
  L1M4_orf2#LINE/    679 A-------------------CTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_46133330_4   3973 ACTGGGAGAAAGTATTTACAAAAGACATATATGATAATATATGCCTATAT 4022
                          v         i     i    vv i    v      viv -- i i   
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA--CTTGTAT 757

  chr2_46133330_4   4023 TATCCAATATAGGCAACAAACTCTTA-AACTTAACAATAACAAAATGAAT 4071
                         ---   iv   vii  vi        -    i  i     v  i ii   
  L1M4_orf2#LINE/    758 ---CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_46133330_4   4072 AACCCAAT--------GGGCAAAAGACTTGAGCATACACCTCGCCAAAGA 4113
                                 --------       i  i    ii v   ii  v       
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_46133330_4   4114 AGATATTCAGATGGTAAATAAGCATAGGAGAAGATGCTCCACTTCATGTG 4163
                               v  i    iv        i v  i         v  v   ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_46133330_4   4164 TCAT 4167
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.04 (139 / 68)
Gap_init rate = 0.03 (26 / 905), avg. gap size = 4.85 (126 / 26)  


 932 31.62 7.67 3.67  chr2_46278276_46280211      577  1449 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_46278276_4    577 TGGAAAGACACAAAGTATTATTGGATAAGAAGGGAAGACTCAACATCATA 626
                                 i ivvvi i  vv     -----v        i  i  ii v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-----TGGAAGACTTAATATTGTT 45

  chr2_46278276_4    627 AAAATATCAACTCTCCCTAAGTTAATTTATAACTTTAAACATATTCACAA 676
                           i  iv   iv     i  i  i  i  i iv  i  - ii v  v v 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTA 94

  chr2_46278276_4    677 TAAAGACATCACCAGGATTGTTTTTT------AACTAGACAAA-TGATTC 719
                          v  i --  -    --i  ii    ------  v v     i-    i 
  L1M4_orf2#LINE/     95 TCAAAA--TC-CCAG--CTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_46278276_4    720 TAAAGTTCATATGGAAAAATAAA----CAGGAATGGCCAGGA-AATTTTG 764
                             i            vii  i---- vi    i    ii -   i   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_46278276_4    765 AAAAATAATAATA----TGTAG-ACTGGTACTACCAAGTGTTAAAAGGCA 809
                              v  v  i ----  v  -   vii   v  v i v i    vvi 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_46278276_4    810 TTATAAACCTGCAATAATTAAAAGAGTGTGGTAT-------AGAGT-GAC 851
                         i  i   v  i  i    i  i v         i-------  ii -   
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_46278276_4    852 GTTATAGAATAAAAGATACAGGA---AAAATCCA--AGTGCACATGAGGA 896
                         i -     vi  vi  - i  i --- i i    -- i iv  viiviv 
  L1M4_orf2#LINE/    290 AT-ATAGATCAATGGA-ATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_46278276_4    897 TTTA--GT--ACTAGTATTTGATAAAGGTGGTATT-TCAATCAGTGAGGA 941
                             --  -- i ii v  i  i  i    vi vv-i  v   i  i   
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_46278276_4    942 AAAGATGACCTATTCAACGTAAGGGACTGGGACAACTTACTAAGTTTCTG 991
                           ii  iii  v      iv v  vi           viv  ?viviv  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_46278276_4    992 AAAACAAGTGAAGTTGGATATGGATCACACATCTTTTATCAGAACAAGTC 1041
                         v   vi i          ivivv i v    i v v  iv i  iv iii
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_46278276_4   1042 CCAGATATATCAGAGACTTACATTTACCAAATGAAAACATAAAAGTACTG 1091
                          v i  iv    ?    i  v  v  vv iv i   vi      v vi i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_46278276_4   1092 GGAGAAACCCTGGGAGAATACTTTTATAACTTTGAAATGGGTAA-AGCCT 1140
                          i     v v i  ? v v ii  ii i  i   iiv i  i  -i ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_46278276_4   1141 TTCAAATTAAGACAT-AAAATC-CAAACC-CATGATATAAAACA--TCAG 1185
                         i i i  - v    i-    v -   i v-  vi v v    i -- v i
  L1M4_orf2#LINE/    588 CTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_46278276_4   1186 TTCAATTACATAAAAAT-AAATAATATTG-GCATGACAAAACCACCAT-A 1232
                           vi i v   v     -   v v v   -  v v v ii  -  i  - 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC-ACTATCA 685

  chr2_46278276_4   1233 AGCAATGCCAAAAGTCAAACAAAAAACTGGGATAAG-TATTTGCAATTCT 1281
                           v  - iv     v   v v v i v     v  i-         v  v
  L1M4_orf2#LINE/    686 AGAAA-GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_46278276_4   1282 TATCTTCCTGTATGCCCTTTCATGCATGAAGTTTGTTTCC-TAATATAGA 1330
                            v --   -----------  -- v iiii    v   -v      v 
  L1M4_orf2#LINE/    735 TATAT--CTG-----------AT--AAGGGACTTGTATCCAGAATATATA 769

  chr2_46278276_4   1331 ATGAGCTCCTAAAAATCGATAA----AAAACAAACACCACAAAAGAAAAA 1376
                          v  i   i  v  v  i    ----  i     i v v   vv?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_46278276_4   1377 TGGGCAA--------------CAATTCATGGAAAAAAATA--CAGATCTC 1410
                                --------------  v   vivi  i  i   --  i  vv 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_46278276_4   1411 TTTTGAATACATGAAAACATGCTCGAAC-TTACAGAGAAA 1449
                         ivv i ii         v      -   - i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTC-AACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (152 / 120)
Gap_init rate = 0.05 (41 / 908), avg. gap size = 2.41 (99 / 41)  


3136 27.35 0.89 0.33  chr2_46357911_46362315     3011  3913 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_46357911_4   3011 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3060
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_46357911_4   3061 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCCTCCCCATCAAGC 3110
                            v     v     iv i  i  i        i  vv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_46357911_4   3111 TACAAATGACTTTCTTCACAGAATTGGAAAAA---ACTTTAAAGTTTATA 3157
                          v v iivi i  i  ii     v v  v  i--- iii    i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_46357911_4   3158 TGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAGAA 3207
                              viiv  ii  v  viv  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_46357911_4   3208 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 3257
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_46357911_4   3258 CAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGATATAGACCAA 3307
                               i   i    ii           iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_46357911_4   3308 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCAT 3355
                              i    i--    i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_46357911_4   3356 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 3405
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_46357911_4   3406 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3455
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_46357911_4   3456 AACAGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3505
                          iiv   i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_46357911_4   3506 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3555
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_46357911_4   3556 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 3604
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_46357911_4   3605 ACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAT-GGATCTGAT 3653
                             v       vvi          vv     v  i    -   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_46357911_4   3654 TAATCTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTGAACA 3703
                         i  vv v  i i   i  ii vv    i  v    ii vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_46357911_4   3704 GGCAACATACAAAATGGGAGAAAATTTTTACAATCTACCCATCTGACAAA 3753
                          i    vi   i             v   i   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_46357911_4   3754 GGGCTAATATCCAGAATCCACAAAGAACTTAAACAAATTTACAAGAAAAA 3803
                           i  vi          vi i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_46357911_4   3804 ATCAAACAACTCCACGAAAAAGTAG-TGAAGGATATGAACAGACACTTCT 3852
                         iv    i   i v iv?    i i -ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_46357911_4   3853 CAAAAGAAGACATTTATGCAGCCAATAGGCACATGAAAAAATGCTCATCA 3902
                          v        i  vi viii       i           i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_46357911_4   3903 TCAATGGCCAT 3913
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3031 26.32 1.76 1.76  chr2_46385343_46387424.rev      691  1598 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_46385343_4    691 TGGAAAAATATCCCATGCTCATGGATATGAAAAATCAATATTGTTAAAAT 740
                               i          i        vv   i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_46385343_4    741 GGCCATACTGCCCAAAGCAACCTATAGATTCAATGTTATTCTTATCAAGC 790
                            v     v      vii i   i        i iv  i i      iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_46385343_4    791 TACCAATGACATGTTTCACAGAACTAGAAAAAACT-ACTCTAAAATTTAT 839
                          v   iivi v v   ii     v v  v  i-  - ii        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_46385343_4    840 GTGGAAGCAAAAAAGAGCCCAAATAGCCAAAGCAATCCTAAGCAAAAAGA 889
                         i     iiiv  ii  v  vi          i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_46385343_4    890 ACAAAGCTGGAGGTATCACATTACCTGACTTCAAACTATACTACAAGGCT 939
                               i      vv     i v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_46385343_4    940 ACAATAACCAAAACAGCATGGTACTGGTACAAAAACAGATACATAGACCA 989
                            i   i   i    ii         i i  ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_46385343_4    990 ATGGAACAGAATAGAAAACCCAGAAATAAAGCCACACACCTACAA-CAAT 1038
                               i     v  i ii           v   i   ii  iii-    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_46385343_4   1039 CTGATTTTCAACAAAGTCAACAAAAATAGGGAATGGGAAAAGGACTCCCT 1088
                         -        i    i viiv   i vi vvv      i    i ivvi  
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_46385343_4   1089 ATTCAATAAATGGTACTAGGATAGCTGGCTGGCTACATGCAGGAGAATGA 1138
                         v     i       i  i   i i    v i? i       ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_46385343_4   1139 AACTGTACCCTTACCTTTAACTGTATAGAAAAATTACCTCAAGATGGGTC 1188
                          ii  v    i     ivv  ii    v        v     i    i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_46385343_4   1189 AAAGATTTAAATATAAGACCTCAAACTATAAGATTCCTAGGAAACACCAT 1238
                          ?   ii     i     v  v         i i  i   i i v v   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_46385343_4   1239 -TCTGGACATC-----AGCCTTGGG------AAAGAATTTATGACTAAGT 1276
                         -vv? v v   -----ii       ------  v iv  iv iiv  v v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_46385343_4   1277 TCTCAAAAGCAATTGCAACAAAACCAAAAATTGACACATGGAGCCTAATT 1326
                         ivi        vvv         vv      v  i v  v ii i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_46385343_4   1327 AAACTAACAAGCTTCTGCACAGCAAAAGACACTATCAGCAGATTAAACAG 1376
                            v v v  i   i  ii vv    i          iv i v i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_46385343_4   1377 A--GCCTACAGAGTGGGAGAAAATATTTGCAAACTATGAATCTGACAAAG 1424
                          --i  i     i                    ii  iv      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_46385343_4   1425 GTCTAATATCCATAATATGTAAGGAACTTAAACAAATCAACAAGCAACAA 1474
                          v  vi      v     i   i     ivv    v    i  vv  v i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_46385343_4   1475 ACAAATAATCCCATTTAAAAATGGGAAAAGACATTGAACAGACACTTCTC 1524
                                 i  v   ?         v    ivv     i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_46385343_4   1525 AAAAGAAGACTTATAACAACAATCATTGTGGCCAACAAGCATACCAAAAA 1574
                         v        --    ----   -----i       i     i iv    i
  L1M4_orf2#LINE/    849 CAAAGAAGA--TATA----CAA-----ATGGCCAATAAGCACATGAAAAG 887

  chr2_46385343_4   1575 AAGCTCAATGTAATCACTAATCAT 1598
                          v      i---    ????????
  L1M4_orf2#LINE/    888 ATGCTCAAC---ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (145 / 90)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.67 (32 / 12)  


3062 27.37 0.99 0.77  chr2_46611088_46617403.rev     4919  5824 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_46611088_4   4919 TGGAAGAACATTCCATGCTCATGGATAGGAATAATCAATATCGTGAAAAT 4968
                              ii i  i     i        v    v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_46611088_4   4969 GGCCATACTTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5018
                            v     i     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_46611088_4   5019 TATCAA-TGACTTTCTTCAAAAAATTAGAAAAAAAAAACT-ACTCTAAAG 5066
                          vi  i-  v    i  vv i     i------ v  i  - ii     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG------ACAAGCTGATCCTAAAA 144

  chr2_46611088_4   5067 TTCATATAGAACCAAAAAAGAGCCCACATTGCCAAGACAACCCTAAGCCA 5116
                                i   viiv  ii  v  viv  v     i    i i i ivv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_46611088_4   5117 AAAGAACAAAGCTGGAGGCATTACACTACCTGACTTCAAACTATACTACA 5166
                         i          i      vv i     v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_46611088_4   5167 AGGCTACAGTAACCAAAACAGCATGATACTGGCACCAAAACAGAAATATA 5216
                          i          i   i    ii  i        iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_46611088_4   5217 GATCAATGGAACAGAACAGAGCCTTCAGAAATAATACCACACATCTACAA 5266
                                    i    iv   vv i         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_46611088_4   5267 CCATGTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGATTC 5316
                         i  vv    i  i     ivv  v   i v  vv             v v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_46611088_4   5317 -CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5365
                         -i  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_46611088_4   5366 CTGAAACAGGATCCCTTCCTTACACCTTATACAAAAATTAGTTCACTATG 5415
                         v    iiv   i    v   i     v             ii   vv   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_46611088_4   5416 GATTAAAGACTTTAATGTTTGACCTGAAACCATAAAAACCCTAGAAGAAA 5465
                            i ?    i v     vv  v  i    i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_46611088_4   5466 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCACGAC 5514
                           v    ?i- v i -   iv   v v  vv i     v ii   viiiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_46611088_4   5515 TAAAACACCAAAAGCGATGGCAACAAAAGCCAGAATTGACCAATGGGATC 5564
                           vi           ivvi          vv i   v  iv   v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_46611088_4   5565 TAATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5614
                          v  i   viv  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_46611088_4   5615 AACAGGCAACCTACAGAATGGGA-AAAATGTTTACAATCTACCCATCTGA 5663
                           v  i     i           -     i   i   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_46611088_4   5664 CAAAGGGCTAATATCCAGAATCCACAAAGAACTTAAACAAATTTACAAGA 5713
                         i  i  i  vi          vi i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_46611088_4   5714 AAAAATCAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 5759
                             iv   ----   v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_46611088_4   5760 TTCTCAAAAGAAGACATTTATGCAGCCAATAGACACATGAAAAAATGCTC 5809
                              v        i  vi viii       ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_46611088_4   5810 ATCATCACTGGCCAT 5824
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


4081 20.83 0.65 1.64  chr2_46655055_46657044      582  1498 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_46655055_4    582 TGGAAAGACATCCCATGTTCATATGTTGGAAGAACTAATATTGTTAAAAT 631
                                 i             ivi        vi            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_46655055_4    632 GTCCATACTAACCAAAATGATCCACAGATTCTGTGCAATCCCTATCAAAA 681
                          v v     vv     v     i        vii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_46655055_4    682 TCCT-GATGCTGTTTTTTGCAGAAATAGGGTGGGAGAATTCTAAAATTCA 730
                            i- v   i-              -v iiii vvi  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chr2_46655055_4    731 TATAGAATCACAAAGGACCCCAAATAGCCAAAAACAATCTTGAGAAAGAA 780
                            i   vii   i      vi           -         i      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAA 197

  chr2_46655055_4    781 CAACAAAGCTAAAGGTCTCACATTTCCTGACTTCAACATATACTACGAAG 830
                         v       i ii   v      i    ii i     v iv      i   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_46655055_4    831 TTAAAGTAATTAAAACAGTATGGTACTGGCATAAAGCTAGATATATAGAC 880
                         i  v      i  i     i              i v    i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_46655055_4    881 CAATGGAAAAGAATGAAGAGCCCAGAAATAAACCC-CACATTTACAATCA 929
                                 v     vi    i              -i       iii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_46655055_4    930 AATGATCATCAATAAGGGTGCCAAGACTACATAATGGGGGAAAGATAGCC 979
                          v    iv  i i              i ivi       i  ii    i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_46655055_4    980 TCTTCAATAAATGGTGTTGGGAAAACTAGATATCCACATGCAAAAGAATG 1029
                          i     i        i     v    i    ?                 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_46655055_4   1030 AAATTGGACCCTTATTTTA-AGCATACACAAAAATCAACTAAAAATTGAT 1078
                           i        i  ii i - v    i        i    v     v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_46655055_4   1079 TGAAGACTTAAATGTAAGGCCTGAAACGATAAAATTCCTAGAAAGAAACA 1128
                         ii?    i          iv  i    v      i  i     ii     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_46655055_4   1129 AACGGGAAAAGCTTCATAACACTGGTCTTGCCAATGATTTCTTGGATATG 1178
                         v v ? v   v    i i  vi   vi v v     i      i      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_46655055_4   1179 ACAGAGAAAGCACAGACAACAAAAGCAAAAATAGACAAATGAGATTGCAT 1228
                            vvi        ii         v         i    vi  i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_46655055_4   1229 AAAATTTAAAAGCATCTATGCAGCAAATCAAACAATCCACAGAGTGAAAA 1278
                         v   v      i v i i   vv    vv v  v   v v i        
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_46655055_4   1279 GGTCACCAATGGAGTGGGA-AAAATATCTGCAAACCGTATATCTCATAAG 1327
                          iiv   v ii  i     -       i      i i       v     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_46655055_4   1328 AAGTTAATATCCAGAATACATAAGGAACTTTTACAACTCAA-AGCAAAAG 1376
                         iiii vi           i    i     i           - ii    i
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_46655055_4   1377 CAACAACAACAACAAACTTGATTTTAAAATGGGCAAAACACCTGAGTAGA 1426
                         -------i    vv   iii   ?v            iv ii   i    
  L1M4_orf2#LINE/    798 -------GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_46655055_4   1427 CATTTCTCTAAAGAAGACATACAAA-GGCCAACAGGCATAGGAAAACATC 1475
                                 i        i       -      i i   i v     v  -
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT- 889

  chr2_46655055_4   1476 ATGTGCTCAACATCAATCATCAA 1498
                         ----           ????????
  L1M4_orf2#LINE/    890 ----GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (122 / 65)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.91 (21 / 11)  


3019 25.64 2.90 1.67  chr2_46661283_46663508.rev      838  1734 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_46661283_4    838 TGGAAAAACATTCCATTCTCATGGATAGGAAGAATCAATATCATGAAAAT 887
                               i i  i    vi        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_46661283_4    888 GCCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATTCCCATTAAAC 937
                          v v     v      v i  i  i       ii  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_46661283_4    938 TACCATTGACATTCTTCACAGAA-TTAAAAAAAAACT-ATTTTAAATTTT 985
                          v   vivi v  i  ii     -  i v  i---  -  ii    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_46661283_4    986 ATATGGAA-T-CAAAGAAGACCCCATATAGCCAAGATAATCCTAAGCAAA 1033
                                 - -   i --     viv        i i    i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_46661283_4   1034 AAGAACCAAGCTGGAGGCATCACACTACCTGACTTCAAACTATGCTACAA 1083
                               v   i      vv       v  ii i      viv i      
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_46661283_4   1084 GGCTACAGTAACCAAAACGGCATGGTACTGGTACCAAAACAGACATATAG 1133
                         i          i   i  i ii         i iv ii i          
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_46661283_4   1134 GCCAATGGAGCAGA-----GACCTCAGAAATAACATCGCACATCTACAAC 1178
                         ii       ii   -----  vii         vvi ii    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_46661283_4   1179 CATCTGATCTTCGAAAAACCTGACAAAAACAAGCAATGGGGAAAGGATCT 1228
                           vi    i     v  ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_46661283_4   1229 CCTATTCAGTAAGTGATGCTGGGAAAACTGACTAGCCATATGCAGAAAAC 1278
                         i  v    ii  i  i        v     iv  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_46661283_4   1279 TGAAACTGGACCCCTTCCTTACACCTTATGTAAAAATTAACTTGAGATGG 1328
                             ii         v   i     v   ii           ii i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_46661283_4   1329 ATTAAAGACTTAAATGTAAAACCCCAAACCATAAAAACCCTAGAAGAAAA 1378
                           i ?    i         i v iv    i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_46661283_4   1379 CCTAGGCAATACAATTTAG-GACATAGGAATGGGCAAAGACTTC------ 1421
                          v    ?i-  v vi  v -   v v  iv i     v ii   ------
  L1M4_orf2#LINE/    546 CATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_46661283_4   1422 ATGACAAAAATGCCAAAAGCAATTGCAACAAGAGCCAAAATTCACAAATG 1471
                               ------         vvv       i  vv     vv i    v
  L1M4_orf2#LINE/    595 ATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_46661283_4   1472 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCA 1521
                            ii v  i   v v  i i   i  ii vv    i  v       vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_46661283_4   1522 GAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTTCAATCTACTCA 1571
                         i      v  i     i                 v   v   vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_46661283_4   1572 CCTGACAAAGGTCTAATATCCAGAATTTACGAGGAACTTAAACATATTTA 1621
                         i    i  i  v  vi          v  ii i     ivv   - i --
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACT-- 785

  chr2_46661283_4   1622 CAAT--TAAAAAAA-----AAC---ATCAAAAAGTGGGCAAAGGATATGA 1661
                             --      i -----   ---  i?    i            v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_46661283_4   1662 ACAGACATTTCTCAAAAGAAGACATTTACATGGCCAATGAACATATGAAA 1711
                          i           v        i  vi v         i i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_46661283_4   1712 AAAAGCTGAATATCACTGATCTT 1734
                          i v   v  i    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (138 / 88)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.56 (41 / 16)  


 496 25.74 2.94 0.00  chr2_46765007_46767880.rev      547   682 (2192)    L1M4_orf2#LINE/L1        1   140 (768)  

  chr2_46765007_4    547 TGGAAAAACATTCCAAGCTCATGAGCTAGAAGAATCAATATCATTAAAAT 596
                               i i  i   v i     iii i     v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_46765007_4    597 GGCCATACTGCCCAAAGCAATCCACAGATTCAATGCTATTCCTATCAAAC 646
                            v     v      vii   i          i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_46765007_4    647 TACAAACATCATTTTTCACAGAATTAGAAAA----ATCCT 682
                          v v i vv v     ii     v v  v  ----     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 1.33 (20 / 15)
Gap_init rate = 0.01 (1 / 140), avg. gap size = 4.00 (4 / 1)  

1170 24.23 8.08 1.67  chr2_46765007_46767880.rev      989  1347 (1527)    L1M4_orf2#LINE/L1      136   517 (391)  

  chr2_46765007_4    989 ATTCTAAAATTCATATGGAA-----------CCAAAA------AATCAAT 1021
                           i                 -----------   i  ------  v    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_46765007_4   1022 CCTAAGCAAATAAAACAAAGCTG-AGGTATCACATTACCTGAGTT--AAA 1068
                          i i iv  iv i       i  -   vv     i v  ii v  --   
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_46765007_4   1069 CTATACTATAAGGAAGCTACAGTAACCAAAACAGCATGGTACAGATATAA 1118
                           -     i  ---           i   i    ii      v ii    
  L1M4_orf2#LINE/    236 CT-TACTACAA---AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_46765007_4   1119 AAACAGACCCATAGACCAATGGAATGGAAC--AGA---CAGAAATAAAGC 1163
                         ii i    vi     i         i   i--   ---          v 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_46765007_4   1164 TACACACCTACAGCCATCTGACCTTTGACAAAGTTAACAAAAATAAGCAA 1213
                         i i   ii  ii i  vi   ii  i     i v iv   i vi vv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_46765007_4   1214 CAGAGAAAGGATTCCCTAATTCAATAAATGGTGCTGGAACAGCTGTCTAG 1263
                         ii i     i  vvi  v-     i            i   i   vv  ?
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_46765007_4   1264 CCATATGCAGAAGACTCAAACTGGACCCCT--TTCAC--CATATATATAA 1309
                            i     i    v v  ii         --i    --      i -  
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA-AA 479

  chr2_46765007_4   1310 AATTACCTCAAGATAGATTAAAGATTTAAATATAAGGG 1347
                              v     i  i   i ?   ii     i    i 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

Transitions / transversions = 2.54 (61 / 24)
Gap_init rate = 0.03 (12 / 382), avg. gap size = 2.92 (35 / 12)  

 804 28.06 1.94 1.61  chr2_46765007_46767880.rev     1647  1956 (918)    L1M4_orf2#LINE/L1      499   809 (99)  

  chr2_46765007_4   1647 AAAGATTTAAATGTAAGACTTCAAGCTATAAGAGTCCTAGAAGAAAACCT 1696
                          ?   ii           vi v  i      i v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_46765007_4   1697 ACGAAATAACATCT--G-GACATCAGCTATGGGAAAGAA---CTTACGGC 1740
                          - i?i   -    -- -   v ii v - i  v  vii---    -- v
  L1M4_orf2#LINE/    549 A-GGNGTAA-ATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTA--GA 593

  chr2_46765007_4   1741 TAAGTCCTCAAAAGCAATTGCAACAAAAACAAAAATTGACAAGTGGAACC 1790
                           v v vi        vvv         iv      v  i  i v i  i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_46765007_4   1791 TAATCAAACTAAAGAGCTTCTGCACCGCAAAAGGAACTATCAATACAGTA 1840
                          v      v v  i i   i  ii iv    i iv        v v   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_46765007_4   1841 AACAGACAACCTACAGAATGGGAGAGAATATTCACAAACTGTGCATCTGA 1890
                           v        i             i      ii    iii ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_46765007_4   1891 AAAAGGTCTAATGTCCAAAATCTATAAGGAACTAAAACAATTCAGAAAAC 1940
                         v  i  v  vi i    i   v     i     vvv    i   iv  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_46765007_4   1941 GAAAACCAAGTAACTC 1956
                         i   iv   i    i 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCC 809

Transitions / transversions = 1.30 (48 / 37)
Gap_init rate = 0.02 (7 / 311), avg. gap size = 1.57 (11 / 7)  

 385 18.52 3.70 0.00  chr2_46765007_46767880.rev     2275  2382 (492)    L1M4_orf2#LINE/L1      797   908 (0)  

  chr2_46765007_4   2275 AAACAAA-AACCC-ATTAAAAAAATGCCAAAAGACTTGAACAGACACTTC 2322
                          i     -     -   ?     vv v    i  i     i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_46765007_4   2323 TCAAAAGACAACATACAAGCGGTTAACAA--ACATGAAAAAATGCTCAAC 2370
                           v     vi i      ii  ii  i  --         i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_46765007_4   2371 ATTACTAATCAG 2382
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.80 (14 / 5)
Gap_init rate = 0.03 (3 / 112), avg. gap size = 1.33 (4 / 3)  


 281 31.25 10.62 1.25  chr2_46798417_46800945.rev      492   651 (1878)    L1M4_orf2#LINE/L1      102   276 (632)  

  chr2_46798417_4    492 CTCAG--GCCCTTTTTG--GAATCTGATAAA-TCATTTAAAAAATTTCAC 536
                          i   --   i      --   vi   i  i- v  iiv    --    i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA--TTCAT 149

  chr2_46798417_4    537 AGGGAAGAGTTAACAGCAAAGAATAGACAAGATACTTCTAAAGAAGAAAA 586
                          v    iv iv ivii vv       v   i i v ii i  i     i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_46798417_4    587 A---------AGGACTTATCCTGACAGATATCAAGACTTATTTCTAAGCT 627
                          ---------      i iv  vv vi  v    i     i v v     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_46798417_4    628 ATAGAAATGGGAAC--TGTGG-GCTGG 651
                          i  v   viii  --     -i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGG 276

Transitions / transversions = 1.50 (30 / 20)
Gap_init rate = 0.04 (7 / 175), avg. gap size = 2.71 (19 / 7)  

 206 27.12 6.78 5.08  chr2_46798417_46800945.rev      918  1035 (1494)    L1M4_orf2#LINE/L1      223   342 (566)  

  chr2_46798417_4    918 CTCCATCTCAAAA---ACAAAAAAGA-ACAAAAAAAAAGAAATAGGAACT 963
                          i v  i      ---  v v    v-   iv  vv    --i  ---- 
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA--CAG----T 266

  chr2_46798417_4    964 GTGTTGTTGGTGCAGGGACATAAAAATACACCAGTGGAATAA----GAGA 1009
                            v ii   iii i   i v v v   v i  i       i----    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_46798417_4   1010 GCCTAGAAACAGACCCACATATTTAT 1035
                          i i     i i     i i      
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTAT 342

Transitions / transversions = 1.67 (20 / 12)
Gap_init rate = 0.04 (5 / 120), avg. gap size = 2.80 (14 / 5)  

 868 30.47 7.36 1.64  chr2_46798417_46800945.rev     1549  2037 (492)    L1M4_orf2#LINE/L1      392   908 (0)  

  chr2_46798417_4   1549 ATAGTCTATTCAATGAATGACACTGGAA--ACTTGGTTTCCATGAATATG 1596
                                v     ii    iii    i --   v i v?   i----   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC----ATG 437

  chr2_46798417_4   1597 AAAAAAAATGAA------TCCCTGCC-------ATATACAAAAA------ 1627
                         v    i      ------i    i  -------           ------
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_46798417_4   1628 ---AATGAA------ACTTAAATGTAAAAGGCACAATTTTAAATATCTTT 1668
                         ---    i ------  i         i  vi v  i v    - -  i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-A-CTCT 535

  chr2_46798417_4   1669 TAAAAGAAACTACAGA---AAAACTTTAGGAATTCAGCATAGGAAAGAAT 1715
                           i      vi i  i---   v   iiv  vi ii vv    v  vii 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_46798417_4   1716 GTCTCTGATAAGTCACAAAAGACACAAACCAGAAAGGAAATGGTTAATAC 1765
                         v   iv    v v   v   ii     i v v   i    vii vi   v
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_46798417_4   1766 ATTTT-CTCCATTAAAATTTTAAATGTATATTCATCACAATTCATTTTTA 1814
                            vv-  i   i      vv   iv v i v v   v ivv  i v i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_46798417_4   1815 AAATAGTGAAAAGACATGCCACAATCTGGGAAAAATTATTTGCAGTTTAT 1864
                          i v            vv     ivv     i   v        iv i  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_46798417_4   1865 GTAACTGGCAAAGGGTTAACATCTAGAATATATGAAGGAAACCAATGAAT 1914
                         i  v   ii  i  ii vii   i         i   i vv iv ii v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_46798417_4   1915 CAATAAGAAAAAATGAAACACTGCAATAGGAAAGTGGACAAAAGACACAA 1964
                               v     ivv   i viv    v?i   i   i    i  ivii 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_46798417_4   1965 ACTGGCATTCA--CAGAAAAGAAAACCAAATGGGCAGTGAAGAAGTGGAA 2012
                          iv i    iv--  i i    v vv       v  i i iv vi  i  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_46798417_4   2013 AGATGCTCAACCTATCAGTAATAAG 2037
                                    --    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAAC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (82 / 65)
Gap_init rate = 0.02 (12 / 517), avg. gap size = 3.67 (44 / 12)  


1990 24.78 9.79 2.35  chr2_46849668_46851497.rev      533  1339 (491)    L1M4_orf2#LINE/L1       42   908 (0)  

  chr2_46849668_4    533 TGTTAAGATGTTAATTTTCTCCAA-----TTCATAGATTCAAATGCAACC 577
                                   vi   vi  i    ----- ii i        -i    i 
  L1M4_orf2#LINE/     42 TGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAATC 90

  chr2_46849668_4    578 CTAATAAAAATTCCAAAAGGCTTTTTTGTAGATATTGATAAGCTGATTAC 627
                          iv  v     i   ivv v        i   v     i        ivi
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_46849668_4    628 AAAATTTATGTGCAAATGTACAATACCTAAAAAAAGTCTAAACAATCTTG 677
                               i  i  v     i viiv   i i  v - i v           
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATA-GCCAAAACAATCTTG 189

  chr2_46849668_4    678 AAAAATAAGAACTAAACTGGAGAAGTTCTATTACCTTATTTCAAGACTTA 727
                              v      v  ii     i v ivi i v  iv       i     
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_46849668_4    728 AT-----GCTATGGTAAATCAAGACAGTGTCATAGTGGCAGAAAGACAAA 772
                         v -----    ii    -            vi  v     v  i  i i 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAA-TCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_46849668_4    773 CA----GAT-----GAACAGAAT--AGAGTTTAGAGACAGATCCACAC-- 809
                           ----   -----   i     --     ii   i i i i   i  --
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_46849668_4    810 TTAC--TCCATTAACTGCGCTTTAACAAGG-TGCCAAAGCAATT-AATGC 855
                            i--  v   i i ----  ii      -      ii v   -    v
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATT----TTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_46849668_4    856 GGAAAGGGAAGTAT---------ACTGTGTTGGAACAATTAGCTATCTAT 896
                               iiv   v --------- iv   i   i    i i v  ? i i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_46849668_4    897 ATGGGGGCAAAA--AT-----------CTAATCTTA-ACCA-ATACACAA 931
                            ----     --  ----------- iv i  i -    -     v  
  L1M4_orf2#LINE/    435 ATG----CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_46849668_4    932 --TA-CACAAAATT-ATCA----CCTCAATACACAAAAATTATCACCATA 973
                         --  - v      v-    ----   v   ii -- i ii  vv  i   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTA--AGAGCTAAAACTATA 528

  chr2_46849668_4    974 AAGCATCTGGAAGAAAACA---GGATAATATCTTCACAACTGTGGGGGTG 1020
                           i vii i          --- ?i   -      iii  iv    vvv 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAG 577

  chr2_46849668_4   1021 GCAAAGATT-CTTAGACAGGAC-CCAGAAAAACACTAGCA-TAAGAGGAA 1067
                             v i  -      i v   -   --   i   v    -i  i  i  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCA--AAAGCACAAGCAACAAAAGAAA 625

  chr2_46849668_4   1068 ATATTGATAAAATAGAC--CA-CTAAATTCAAAACTTTTGTTCATCGAAA 1114
                          v  v      v i   --  - v     v           v v  i  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_46849668_4   1115 GATGCCACCAAAACAATGAACAGTCAAGCCACAGACTGGAAGAAAA-ATC 1163
                           ii i i   i v i    v  v   v       v   i      -  i
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_46849668_4   1164 TCTAACACATTTATGTGTCAAAGAAGTTGCATCCAATTAATATACAAA-- 1211
                          vi  vv   v   v  vi  i i v   i     i--      i   --
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAG--AATATATAAAGA 773

  chr2_46849668_4   1212 --TCCTAAAACTTAACAGTAAAATGACA--TAA---AATTGGTAACTGGT 1254
                         --  i  v    i  i i     v    --   ---    ?iv  v   v
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_46849668_4   1255 TAA-TGCCTTGAACAGACATATCACTAAGGATGATATGCAAAATAGCCTA 1303
                         i  -v vi     i      v  v i  i  v     i    - i   v 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAA 872

  chr2_46849668_4   1304 TAAGCACATGACAAAATGCATGACATCGATACTCAC 1339
                                    v  i    vii     i????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (119 / 78)
Gap_init rate = 0.04 (39 / 867), avg. gap size = 2.51 (98 / 39)  


2361 21.60 3.70 2.31  chr2_46932465_46934104      501  1148 (492)    L1M4_orf2#LINE/L1      252   908 (0)  

  chr2_46932465_4    501 AGTAATCACGACTAT-TGGTATTGGCATAAGGACAGAAATATAAATCAAT 549
                                 v   vi -     i           i   v     i      
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_46932465_4    550 AGAACAGAAT--AGAGTCCAAATATAGACCCACACTTATTTGGTCAATTG 597
                         i   i     --        i v   i     i  v v v          
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_46932465_4    598 ATTTTCAACAAGGTTGCCAAGGCAATTTAATGAGGAAAGGATGTTCTTTT 647
                               i      v       i v   i    i      i  iv      
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_46932465_4    648 CAAGAAGTGGTTCCAGAACAATAAGATATC---ATGTAGAAGAAGACAAA 694
                            v  i    v ii i    ivi    ? ---   i i     --ii  
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--TGAA 449

  chr2_46932465_4    695 CTTTGACCCTTACCCCACACCACATA--AAAGTTTACTTGAAATGGATTA 742
                         v  v     i    i       i   --   i  v   ii        i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_46932465_4    743 TAGACCTAAATGTAAAAGCGAACACTGTAAAACAGCAAGATGAAAACACA 792
                         ?              i   v  v   i      vviv   v       i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_46932465_4    793 GGAGAAAA-CTTCAGCCATCTCTGGATGGATAAAGATTTCTTAGATAGGA 841
                           ? v   -    - iv i  iv  v i ii  v i           v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_46932465_4    842 CACAAAAAACACAAACTATAAAAGGAAAATT-GATAAATTTGATTTCATA 890
                            v    i     i v i     i    v -        v  i     v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_46932465_4    891 AAAATTAAAATTTTCTACTCTTTAA----CACCGTTAAGGAGATAAAAA- 935
                                   vi  i iiv   i  ----   ii i   i ii i    -
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_46932465_4    936 ---AGCTACAGACTTGGAAAAAATATTGGTAATACATGTATCTTACAGTG 982
                         --- v i     v v   i        v i  vv   i     v i iv 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_46932465_4    983 GAATTGTATCTTGAACACCTAAAGAACTCTTACTAGTCAATTATTGGTAG 1032
                           v       iv   i iv              v v     v  viiv  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_46932465_4   1033 GCAAATA-CCCAATTTTAAAGTGGGCTAATTATTT---TAAACTAATTTA 1078
                         i      -       ?v   i     v  vv    ---  i  --    -
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC--ATTT- 845

  chr2_46932465_4   1079 AATCCAGACTCTCATAGAAGATATACAAATGTCAAATAAGCACA--AGAA 1126
                         --------   -  v                v v          -- i  
  L1M4_orf2#LINE/    846 --------CTC-CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_46932465_4   1127 GATACTCTACATTATTAATCAT 1148
                            i   v    i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (77 / 59)
Gap_init rate = 0.02 (16 / 657), avg. gap size = 2.44 (39 / 16)  


1566 17.23 3.21 26.52  chr2_47273238_47278716.rev     3803  4986 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_47273238_4   3803 TGAAGAGATTTCCCGTG------GATAGGAAGA-TCAATATTGTCAAGAT 3845
                           i i    v    i  ------   v      - i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_47273238_4   3846 GTCAGTTCTTCCCAATTTGATCTTTAAATTCCATGCAATCCCAATAATAA 3895
                          v  i v  i     v       vi i    v i        v  v v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_47273238_4   3896 TTAGAGAATGT-TATTTTGTGGCTATCAACAAACAG--TCTAAAGTATAT 3942
                          ivv  v-  i- v     ii vv  ii    i v --i     i vi  
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_47273238_4   3943 ATGGAAAGGCAAAA-ACCTAGAATAGCCAACACAATGATGAAGGAGAATA 3991
                                v    ii-   i           v     vv    ii    v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_47273238_4   3992 GCAAAGTTAGAGGACTGACACTACCTGACTTCAAGGCCTACTTAAAAGCT 4041
                         i       i       v     v  ii i     ii i    vv      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_47273238_4   4042 ACAGTAATCTAGAGAGTATTATATTGGCA-AAGAATAGACAAATAGATCA 4090
                                  v   v   i vi  i     -   i       v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_47273238_4   4091 ATGGAACAGAATAGAGAATACAGAAATAGACACACAAAAATATAGTCAAC 4140
                               i     v    i v        i  v  i v vv   i     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_47273238_4   4141 TGAATTTTGACAAAGGAGCAGAGTCAATACAACAAAGAAAAGATAGTTTT 4190
                            v   i     i  v  vi  v v  v   iiii    ii     i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_47273238_4   4191 TTCAACAAATGGTGCTGGAACAACTGGATATCCACATTCAAAAAAGAAGA 4240
                                           i           ?      v     -------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA------- 442

  chr2_47273238_4   4241 GGCTGGGCGTGGTGGTTCATGCCTGTAATCCTAGCACTTTGGGAGGCCGA 4290
                         --------------------------------------------------
  L1M4_orf2#LINE/    443 -------------------------------------------------- 442

  chr2_47273238_4   4291 GGCAGATGGATCACTTGAGGTCATGAGTTCAAGACCAGCCTGGCCAATAT 4340
                         --------------------------------------------------
  L1M4_orf2#LINE/    443 -------------------------------------------------- 442

  chr2_47273238_4   4341 AGTGAAACCCCATCTCTACTGAAAATATAAAAATTAGCCAGACGTGGTGG 4390
                         --------------------   ---------------------------
  L1M4_orf2#LINE/    443 --------------------GAA--------------------------- 445

  chr2_47273238_4   4391 CGGGTGCCTGTAATCCTAGCTACTTGGGAGGCTGAAGCAGGAGAATCGTT 4440
                         --------------------------------     ------------ 
  L1M4_orf2#LINE/    446 --------------------------------TGAAG------------T 451

  chr2_47273238_4   4441 TGAACCTGGGAGGTGCAGGTTGCAGTGAGCTGAAATTACCCCACTGCACT 4490
                           i   ---------------------------------  i  iv   v
  L1M4_orf2#LINE/    452 TGGACC---------------------------------CCTACCTCACA 468

  chr2_47273238_4   4491 CCAGCCTGGGTGACAGAGTGAGACTCTTCCTCCAAAATAAAAATAAAAAA 4540
                            -----------------------------------------------
  L1M4_orf2#LINE/    469 CCA----------------------------------------------- 471

  chr2_47273238_4   4541 GAGGAAAAGAATCTAGACACAGACCTTAAACCCTTCACAAAATGAACTCA 4590
                         -------------  v   -------------------     v      
  L1M4_orf2#LINE/    472 -------------TATACA-------------------AAAATTAACTCA 489

  chr2_47273238_4   4591 AAGTTGATTACAAAACTTAAATGTAAAAAGCAAGACTATACAACTTCTAG 4640
                           i v   i -? i  i         i ivi  i      v    ii   
  L1M4_orf2#LINE/    490 AAATGGATCA-WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_47273238_4   4641 AAGGTAACATAAGA--AAATCTAGACGACTTTGAGTT------------- 4675
                            iv      i ?--      vvii   i   i   -------------
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_47273238_4   4676 -TAGATCCTACACCAAAAGCATGATCCATGAAAGAAATAATTAATAAATT 4724
                         -     viv            ii v v ii       v   vi       
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_47273238_4   4725 GGATTTCTTTGGAACTAAAA--TTTTCTGCTCAGCAAAAGACACTG--AA 4770
                            i   v iii  i     --    v    i--    i      i--  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAA 686

  chr2_47273238_4   4771 GAGAATGAAAAGACAAGTGACTAACTG--AGAATATATTTGCAAAAGATA 4818
                           i i           viv  vi v  --    v           vv   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_47273238_4   4819 TATCTGAGAAAGAACTGTTGACCAAAATATACAAAGAACTCTGAAAACCC 4868
                                v  i i   vv iv   i      i          v v   i 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_47273238_4   4869 AGCAATAAGAAAACAA----CTCAATTAAACAATTGGCCAAACTCCTTAA 4914
                          ii     i  i    ---- i     ?  v   v   v  ivvii v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_47273238_4   4915 TATACACCTCTCCAAAGAAGACATACAGATGTCAAAAAAGCATATGAAAA 4964
                           v   ii             i     i   v v  v     i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_47273238_4   4965 AACGTTTCACATCATATGTCAT 4986
                         i i i iv      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (114 / 86)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 16.76 (352 / 21)  


3277 26.43 0.55 0.55  chr2_48049612_48051768.rev      758  1665 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_48049612_4    758 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 807
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_48049612_4    808 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 857
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_48049612_4    858 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 905
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_48049612_4    906 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 955
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_48049612_4    956 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1005
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_48049612_4   1006 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAGC 1055
                                 i   i    ii         i iv ii i   v       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_48049612_4   1056 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 1103
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_48049612_4   1104 ATCTGATCTTTGACAAACCTGACTAAAACAAGAAATGGGGAAAGGATTCC 1153
                          vi    i  i     ivv  v v i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_48049612_4   1154 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1203
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_48049612_4   1204 GAAACTGGATCCCTTCCTAACACCTTATGCAAAAATTAATTCAAGATGGA 1253
                            ii    i    v   v     v   i          i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_48049612_4   1254 TTAAAGACTTAAATGTTAGACCTAACACCACAAAAACCCTAGAAGAAAAC 1303
                          i ?    i       v   v    v  i i    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_48049612_4   1304 CTAAGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 1352
                         v  i ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_48049612_4   1353 AAACACCAAAAGCAATGGCAACAAGAGCCAACATTGACAAATGGGATCTA 1402
                         vi            vvi       i  vv  v  v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_48049612_4   1403 ATTAAACTAAAGAGCTTCTGCCCAGCAAAAGAAACTACCATCAGAGTGAA 1452
                           i   v v  i i   i  iv vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_48049612_4   1453 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 1502
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_48049612_4   1503 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 1552
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_48049612_4   1553 AAATCAAACAACGCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1602
                           iv    i   v v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_48049612_4   1603 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 1652
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_48049612_4   1653 CATCACTGGCCAT 1665
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2065 28.90 0.49 0.32  chr2_48093507_48095570      501  1116 (948)    L1M4_orf2#LINE/L1      145   761 (147)  

  chr2_48093507_4    501 TTTACAGGGAATCAAAAAAGAGCCTGAATAGCCGAGGCAATCCTAAGCAA 550
                           i i v    viiv  ii  v  v        i ii     i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_48093507_4    551 AAAGAACAAAACTGGAAGCATTATGTTACCTGACTTCAAACTATACAACA 600
                         i         ii    i vv i iii v  ii i      viv   v   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_48093507_4    601 GGGCTACAGAAACCAAAACAGCATGGTACTGCTACAAAAACAGGCATATA 650
                         ii       v  i   i    ii        vi i  ii i  i      
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_48093507_4    651 GACCAATGGAACAGAACAGAAAGCGCAGAAATAAGGCCACATACCTATGC 700
                           i        i    iv  i  iv         iv   i i ii    v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_48093507_4    701 CCCTCTGATCTTCAACAAAG-TGACAAAAACAAGCAATGGAGAAAAGACT 749
                         i vvi    i   i    i -  v   i v  vv      i    ii iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_48093507_4    750 CCCTATTCAATAAATGGTGCTGGGATAACTGGCTGGCCATATGCAGAAAA 799
                         vi  v     i              i      v i?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_48093507_4    800 TTGAAGCTAGCCTCCTTCCTTACACCATATACTAAAATCAACTGAAGGTG 849
                         v     i i v i   v   i           v     i    v  ii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_48093507_4    850 GATTAAAGACTTAAATGTAGAACCCCAAGGTATAAAAACCCTGGAAGACA 899
                            i ?    i        ii v iv  iv       vi i i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_48093507_4    900 ACCTAGGCAATACCATCTT-G-GACAAAGGAATGGGCAAAAATTTCATGA 947
                           v    ?i-  v-     - -   vvv  iv i     vii    v ii
  L1M4_orf2#LINE/    545 ACATAGGNG-TAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_48093507_4    948 CAAAGACACCAAAAGCAATTGCAATGAAAGCAAAAATGGACAAATGGGAT 997
                         vv v             vvv    ii    v      i  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_48093507_4    998 CTAATTAAACTTAAGAGCTCCTGCACAGCAAAAGAAACTATTAACATAGT 1047
                         i v  i   v    i i  ii  ii vv    i  v     i  v v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_48093507_4   1048 AAACAGACAACCTACAAAATGGGAGAAAATATTTGCAAACTATACATTTG 1097
                         i  v        i   i                      ii   i  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_48093507_4   1098 ACAAAGGTCTAATATCCAG 1116
                          i  i  v  vi       
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAG 761

Transitions / transversions = 1.73 (111 / 64)
Gap_init rate = 0.01 (5 / 617), avg. gap size = 1.00 (5 / 5)  

 435 26.45 1.94 0.00  chr2_48093507_48095570     1418  1572 (492)    L1M4_orf2#LINE/L1      751   908 (0)  

  chr2_48093507_4   1418 CTAATATCCAGCATCTGTAAGCAACTTAAATAAATTTATAAGAGAAAAAC 1467
                           vi       v  v i   iv    ivv i  v iv    v i   i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_48093507_4   1468 AAACCACACCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAA 1517
                            iv  v v   ?    i           iv    i     i  i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_48093507_4   1518 AAAAAGACATACCTGCAGCCAA-AA--ACGTGAAAAAAAGTTCAATATCA 1564
                           i    i    vviii     -  --  i      i v i    i    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_48093507_4   1565 CTGATAAT 1572
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.35 (23 / 17)
Gap_init rate = 0.01 (2 / 158), avg. gap size = 1.50 (3 / 2)  


3567 24.01 0.66 0.66  chr2_48096743_48101336     3195  4102 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_48096743_4   3195 TGGAAAAATACTCCATGTTCATGGATTGGAAGAACCAATATTGTTAAAAT 3244
                               i   ii                     vii           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_48096743_4   3245 GTCCACACTATCCAAAGCAATCTACAAATTCAGTGCAATCCCTGTCAAAA 3294
                          v v i   vi     vii       i     ii         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_48096743_4   3295 TACCAATGAAATTCTTCACAGAAATAGAAAAAAACAATCCTAAAATTTAT 3344
                          v   iivivv  i  ii       v  v  -ivii           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_48096743_4   3345 ATGGAACAACCAAAGACCCAGAATAGTCAAAGCTATCCTAAGCAA-AATA 3393
                               vvi v ii            i    i v   i i iv  -  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_48096743_4   3394 ATAAAATTGGAGGAATCACACTACCTGACTTCAAATTACACTACATAGCT 3443
                          i   i        v       v  ii i      vivi      v    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_48096743_4   3444 ATAGTAACCAAAACAGCATGATCCTGGCATAAAAACAGAGACATAGACCA 3493
                          i     i   i    ii  i v         ii i   v i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_48096743_4   3494 ATGAAACAGAATAGAGAACCCTGAAATAAATCCATGCACCTATAATGAAC 3543
                            i  i     v    ii  v        i    i  ii   ii v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_48096743_4   3544 TCATTTTCATCAAAGTTGCCAAGAACTTACACTGGGGAAAAGATAGTCTT 3593
                          v      iv   i v        v v v  v        ii        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_48096743_4   3594 GTCAATAAATGGTGCTGGGAAAACAGCATATCTGTATGCAAAAGAATGAA 3643
                         v    i              v   v v   ? iii               
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_48096743_4   3644 ACTAGACTCCTATCTCAC--CATATACACAAATCAAATCAAAATGAATTA 3691
                         ii i   i    i     --        v    i  v        i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_48096743_4   3692 AAGACTTAACTCTAAGATCTCAGCCTATGAAACTACTACAAGAAAATATT 3741
                         ?    i   v v     v  v iv    i     vi  v       i  -
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT- 548

  chr2_48096743_4   3742 AGGAA-AACTCTCCAGGACATTGGACTGGGCAAAAATTTCTTGAGCAATA 3790
                            ?i-  v   i iv   v    ii i     vii      iiii vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_48096743_4   3791 CCCCACAAGCACAGGAAACCAAAGCAAAAATGGACAAAATGAGATCACAT 3840
                          v   v       i v   v    v      i  i   v  -  iiv   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG-GACTTCAT 647

  chr2_48096743_4   3841 CAA-CTTAAAAAGCTTCTGCACAGCAAAGAATACAATCAACAAGGTGAAT 3889
                            -v       -   i  ii vv     i i  v     v  i     v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_48096743_4   3890 AGACAACCCACACAATGGGAGATAATATTTGCAAACTACCCATCTGACAA 3939
                                     v         v            ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_48096743_4   3940 ATAATTCATAATCAGAATATGTAAGGAGCTTAAACAACTCTACAGGAAAA 3989
                         ivi i ii  vi        i   i  i  ivv       v i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_48096743_4   3990 AAAATCTAATAATCCAAT-AAAAAATGGGCAGATTATTTGAATAGACATT 4038
                          i -- v     i     -?           i vv               
  L1M4_orf2#LINE/    797 AGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_48096743_4   4039 TCTCAAAAGAAAGCATACAAATGGCAAACAGGCATATGAAAAGGTGCTCA 4088
                             v      iii           v  i i   i        i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_48096743_4   4089 ACATTATTGATCAC 4102
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (133 / 81)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.20 (12 / 10)  


3015 26.10 1.10 1.10  chr2_48109466_48112428     1564  2471 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_48109466_4   1564 TGGAAACACAACCCATGCTCATGGATGAGTAGAATCAATATTGTGCAAAT 1613
                               v i v      i        vi v   v i        vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_48109466_4   1614 GGCCATACTGCTAAAAGCAATCTACAAATTCAGTGCAATCCCCATCAAAA 1663
                            v     v iv   vii       i     ii        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_48109466_4   1664 TACCACCATTATTCTTCACACAGTTAGAAAAAACAATTCTAAAATTCATA 1713
                          v   v vviv  i  ii  v iv v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_48109466_4   1714 TGAAACCAAAAAAGAGCCCGCATAGCCAAAGCAAGACTAAGAAA-AAGAA 1762
                           i  viiv  ii  v  v v         i   vvi i i   -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_48109466_4   1763 TAAACCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGCAA 1812
                         i   vi      vv       v  ii        viv     i  i  v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_48109466_4   1813 AAGTCACCAAAACAGTGTGGTACTGGTATAAAAACAGCCACATAGACCAA 1862
                         v   v i   i               i    ii i  v  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_48109466_4   1863 TGGAACAGAATACAGAACCCAGAAATAAACCTAAATGCTTACAGCCAACT 1912
                              i     vv   ii             i v iii   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_48109466_4   1913 GATCTTTGACAAAGCAAACAAAGAC-ATGAAGTGGGAAAAGGACACCCTT 1961
                            i  i     i -ivi v     -  vv i    i    i i vi   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_48109466_4   1962 TTCAACAAATGGTGCTGGAATAATTGGCTAGCCACGTGTAAGAAAATGAA 2011
                                           i i  i   v  ?    i  i  i i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_48109466_4   2012 ACCGGATCCTCACCTCTCACCTCATACAAAAATCAGCTCAAGATGGATTA 2061
                         iii   i  ii     v    vi          i i     i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_48109466_4   2062 AGGACTTAAACCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACATT 2111
                         ?i   i    iv     v  i    i      v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_48109466_4   2112 GGAA-AAATCCTTCTAGCCATTGGCTTAGGCAAGGAATTCAT-GACCTAG 2159
                           ?i-     i iv ii  -    v        v iv   v -  --  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGA--TAT 596

  chr2_48109466_4   2160 AAC-CCAACAGCAAATGCAAG-AACAACACAGATAAATAAATAGCTGGGA 2207
                         i  -    v    ----    -     v v i -     i   iv v   
  L1M4_orf2#LINE/    597 GACACCAAAAGCA----CAAGCAACAAAAGAAA-AAATAGATAAATTGGA 641

  chr2_48109466_4   2208 CCTAATTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAAAAAAGCAGA 2257
                          i v  i   v v  i i      iiivv    i iv  v vv   - i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAA 690

  chr2_48109466_4   2258 GTAAACAGATGACCCACAGAGTTGGAGAAAATCTTCATAATCTATACATC 2307
                           i  v   ii         i v         v  iii  vii   i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_48109466_4   2308 TGACAAATGTCTAACGTCCAGAATCTACAACAAACTC----AAATCAGTA 2353
                            i  iv v  viii        v  i  vi     ----  v   i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_48109466_4   2354 AGAAAAAACAAAAAAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGA 2403
                          v     ivv   v  i  v  i?    i     v     iv        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_48109466_4   2404 CAATTCTCAAAAGAAGATACACAAATGGCCAACAAACACAAGAAAAAATG 2453
                           v     v          i            i  i    v     i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_48109466_4   2454 CTCAAAATCACTAATGAT 2471
                              v    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


3188 26.07 0.77 0.88  chr2_48191923_48197709.rev     4387  5295 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_48191923_4   4387 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCAAGAAAGT 4436
                              ii i  i     i        v      v i     iivv  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_48191923_4   4437 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4486
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_48191923_4   4487 TACCAA-TGACTTTCTT-CATACAATTGGAAAAAACT-ACTTTAAAGTTC 4533
                          v   i-  v    i  -  v -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_48191923_4   4534 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAA 4583
                                 viiv  ii  v  viv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_48191923_4   4584 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTGTACTACAAGG 4633
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_48191923_4   4634 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAG 4683
                                  i   i    ii         i iv ii i   v       v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_48191923_4   4684 CAATGGAACCGAAC--AGAGCCCTCAGAAATAATACCACTCATCTACAAC 4731
                                 iv   i--    i  --        vv   iv   i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_48191923_4   4732 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 4781
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_48191923_4   4782 CCTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGC 4831
                         i  v  i  i              v     iv  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_48191923_4   4832 TGAAACTGGATCCCTTCCTAACACCTTATACAAAAATTAATTCAAGATGG 4881
                             ii    i    v   v     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_48191923_4   4882 ATTAAAGACTTAAATGTTAGACCTAACACCATAAAAACCCTAGAAGAAAA 4931
                           i ?    i       v   v    v  i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_48191923_4   4932 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 4980
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_48191923_4   4981 AAAACACCAAAAGCAATGGCAACAAGAGCCAACATTGACAAATGGGATCT 5030
                          vi            vvi       i  vv  v  v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_48191923_4   5031 AATTAAACTAAAGAGCTTCTGCCCAGCAAAAGAAACTACCATCAGAGTGA 5080
                         v  i   v v  i i   i  iv vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_48191923_4   5081 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5130
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_48191923_4   5131 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5180
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_48191923_4   5181 AAAATCAAACAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5230
                            iv    i   i v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_48191923_4   5231 TCTCAAAAGAAGACATTTAT-TGCAGCCAACAGACACATGAAAAAATGCT 5279
                             v        i  vi v-  --     i ii          i     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCT 892

  chr2_48191923_4   5280 CATCATCACTGGTCAT 5295
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (134 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2932 23.89 3.94 2.59  chr2_48296508_48301020     2826  3637 (876)    L1M4_orf2#LINE/L1        3   825 (83)  

  chr2_48296508_4   2826 GAAAAACATCCCTTGCTCATGGACTGGAAGAATTAATATTGTTAAAATGA 2875
                             i i     v  i       i       v             i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_48296508_4   2876 CCATACTACCTGAAGCAATCTACAGACTCAATGCAATCCCTATCAAAATA 2925
                          v     v  ii  vii         i    i                 v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_48296508_4   2926 CCAATGACATTCTTCACAGAAATAGAAAAAACAATCCTAAAATTCATATG 2975
                            iivi v  i  ii       v  v  ivii                 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_48296508_4   2976 GAGCCACAAAACACCCTGAATAGCAAAAACAATACTAAGCAAAAAGAATA 3025
                           ivii   iiv    v       v        vi i iv  i     i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_48296508_4   3026 AAGCTGGAGGTATCACACTATCTGACTTCAAAATATACTACAAAGTTGTA 3075
                            i      vv       vi ii i       iv          i ii 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_48296508_4   3076 ACAATCAAAATAGCATGGCATTGGTATGAA----------------AATG 3109
                         ii      i i  ii   i i   i  i i----------------    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_48296508_4   3110 AAACAGA-----GAACCCAAAAATAAATCCACATATTTACAGCCAACTGA 3154
                         i  i   -----  ii   i       i   i i     ii i   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_48296508_4   3155 CTTTTGACAAAGGTGCCAAGAGTATACAATGGG-AAAGGACATCCTTTTT 3203
                         i   i     i          vi  v       -    i i vi     i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_48296508_4   3204 AA---ATGGTGCTAGGAAAACTGGATATTCATATGCAGAAAAATCAAAT- 3249
                           ---        i   v         ?i  i     i  i   v  i -
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_48296508_4   3250 AGACCTGTATCTCTCACCGTATACAAAAATCAACTCAAAAATGGATTAAA 3299
                         i    iv  i   v    i           i         -     i ? 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGATCAWA 501

  chr2_48296508_4   3300 GACTTATTAAATCTTATTAAATCATAAGATTCAAAACTC---AACTGCTA 3346
                            i  -------------   -i     vii      v---    -  -
  L1M4_orf2#LINE/    502 GACCTA-------------AAT-GTAAGAGCTAAAACTATAAAACT-CT- 535

  chr2_48296508_4   3347 CTAGAAATAAACATAGGAG-AAACGTGTTAGGACATTGGTCTAGGTAA-- 3393
                         -     iv         ? -   iv - iiv   v    vi    i  --
  L1M4_orf2#LINE/    536 -TAGAAGAAAACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATG 583

  chr2_48296508_4   3394 GTCATTTATGGCTAAGACTTCAAAAGCATAGGCAACGGAAACAAAAATAG 3443
                           ivi   -- v  v   vi        i i     ii  iv        
  L1M4_orf2#LINE/    584 GTTTCTTA--GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_48296508_4   3444 ACAAATGGGACCATGTTAAACTAAAAAACTTCTGCACAGTAAAGGAAACA 3493
                          i    v    ivii i   v v        i  ii vvi      v  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_48296508_4   3494 ACCAACAGAGTGAAGAGACAATCTATAGAATGGGAGAAAATATTTATAAA 3543
                          i   v i      i      i i i                   ii   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_48296508_4   3544 CTATTTCTCCAACAAGTGACTAACATTCAGAATATATAAGGAGGTCAAAC 3593
                         ii  v v  ii i   v    vii  i            i  iv  vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_48296508_4   3594 AACTCAATAGCAAAAACACAAATAATCCCATTAAAAAGTGGGCA 3637
                                  ii     v        i  v   ?    i      
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 2.28 (132 / 58)
Gap_init rate = 0.02 (15 / 823), avg. gap size = 3.53 (53 / 15)  

 397 19.42 0.00 2.91  chr2_48296508_48301020     3919  4021 (492)    L1M4_orf2#LINE/L1      809   908 (0)  

  chr2_48296508_4   3919 CAACTAAATAAGTGATCCAATGATTTGAACAGACTTTTCTCAAAACTAGA 3968
                            i ?  -  i  iv v  v        i    v      v   vv   
  L1M4_orf2#LINE/    809 CAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_48296508_4   3969 CATACAAATGGCCAACAGGTATATGAAAAAACATGTTCTACATCACGAGT 4018
                         i              i i i i       i --  i  v      ?????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAACATCAZZZZZ 905

  chr2_48296508_4   4019 CAT 4021
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.38 (11 / 8)
Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.50 (3 / 2)  


2929 28.46 0.66 0.11  chr2_48435740_48442688.rev     5555  6457 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_48435740_4   5555 TAGAAAAACCTTCCATGCTTATGGATAGGAAGAATCAATATCGTGAAAAA 5604
                          i    i iv i     i i      v      v i     i  v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_48435740_4   5605 GGCCACACTGCCCAAAGTAATCCACAGATTCAGTGCTATTCCCATCAAGC 5654
                            v i   v      v i   i         ii  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_48435740_4   5655 TACCATTGACCTTCTTCAGAGAATTAGAAAAAATTACTTTAAATTTCATA 5704
                          v   vivi    i  iiv    v v  v  iv v iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_48435740_4   5705 TGGAACCAAAAACGAGCCCATATAGCCAAGACAATCCTAAGCATAAACAA 5754
                              viiv  iv  v  viv        i      i i iv vi  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_48435740_4   5755 CAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTACAAGCTTA 5804
                              i     ivv   ii  v  ii i      viv        ivi  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_48435740_4   5805 CAGTAACCAAAACAGCGTGGTACTAGTACCAAAACAGAAATATAGACCAA 5854
                               i   i    i        i i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_48435740_4   5855 TGGAATAGAACAGAGGCCTCAGAAATAACACCACAGCTCTACAACCATCT 5904
                                   iv   ivii         vv   i vv i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_48435740_4   5905 GATCTTTGACAGACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 5954
                            i  i    iivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_48435740_4   5955 TTAATAAATGGTGCTGGGAAAACTGGCAATCCATATGCAGAAAACTGAAA 6004
                          i  i              v      vv ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_48435740_4   6005 CTGGACCCATTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAA 6054
                         i       v v   i     v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_48435740_4   6055 AGAATTAAATGTAAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 6104
                            vi         i v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_48435740_4   6105 GCA-ATACCATTTAGGACATAGGCATGGGCAAAGACTTCATGACTAAAAC 6153
                          ?i- v i -  iiv   v v  vv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_48435740_4   6154 ACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAAGGGATCTAATTA 6203
                                   vvi          vv     v  i   vv   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_48435740_4   6204 AACTAAAGAGCTTCTGCATAACAAAAGAAACTATCATTAGAATGAACAGG 6253
                           v v  i i   i  iiivv    i  v       vv i i    v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_48435740_4   6254 CAACCTACAGAGTGGGAGAAACTTTTTTCAATCTATCCATCTGGCAAGGG 6303
                              i     i         v v   v   vii  vi     ii     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_48435740_4   6304 TCCAATATCCAGAATCTAAAAAGAACTTAAAGAAATTTACAAGAAAAAAG 6353
                         v ivi          v  v        ivv v  v iv i  v     ii
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_48435740_4   6354 CAA----CCCCATCAAAAAGTAGGCAAAGGATATGAACAGACACTTCGCA 6399
                            ----   v  i?    i i          v    i     i   v v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_48435740_4   6400 AAAGAAGACATTTATGGGGCCAACCAACACATGAAAA-ATGTTGATCATC 6448
                                 i  vi viv      iv i          -   i v v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_48435740_4   6449 ACTGGTCAT 6457
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.20 (138 / 115)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.75 (7 / 4)  


1156 25.29 5.00 1.76  chr2_48508853_48511455.rev      924  1263 (1340)    L1M4_orf2#LINE/L1        6   356 (552)  

  chr2_48508853_4    924 AGACATCCCATACTCATGGATAGGAAAAATTAGTATTGTTAAAATGACAA 973
                            i       ii        v    i v   i         i   i   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_48508853_4    974 TACTACCTCCAAAGCAATCTATAAATTC-----------TATCAAAATAC 1012
                             -- i     vii     i i    -----------         v 
  L1M4_orf2#LINE/     56 TACT--CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_48508853_4   1013 CAATGATATCCTTCACGGAAAT--ATAAAATAATCCTGAAAGTTGTATGG 1060
                           iiviiv ii  ii i     -- i  iv i     i   v ii     
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_48508853_4   1061 AACTACAAAAGACCCCAAATAGGCAAAAGAATCTTGAGCAAAAAGAACAA 1110
                           v i   ii     vi     v     v        iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_48508853_4   1111 AACTGGAGG---CAAAATACAAACAGACCTCAAAATATACTACAAAGCTG 1157
                          ii      ---  v v v --- vi ii      iv            i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTC---CCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_48508853_4   1158 TAGTAACCAAAAAAGCAAGGTACTGGCATAAAAATAAGACACATAGACCA 1207
                         i     i   i v  iiv             ii   -    i     i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGATCA 299

  chr2_48508853_4   1208 ATGGAACAGAATAGAGAACCTGGACATTAATTGACATATTTACAGCCAAC 1257
                               i     v    ii ii  v  v  iiv i i     ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_48508853_4   1258 T-ATTTT 1263
                          -     
  L1M4_orf2#LINE/    350 TGATTTT 356

Transitions / transversions = 2.58 (62 / 24)
Gap_init rate = 0.02 (7 / 351), avg. gap size = 3.29 (23 / 7)  

1703 25.05 2.78 2.23  chr2_48508853_48511455.rev     1565  2103 (500)    L1M4_orf2#LINE/L1      348   889 (19)  

  chr2_48508853_4   1565 ACTGATTTTTGACAAAGGTGCCAAGAATACTAACTGGGGGAAAGACAGTT 1614
                          i       i     i          vi i v v     i  ii i   i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_48508853_4   1615 TCTTCAATAAATGATACAAAAGAAATTGGATATATATCTACAGGCAGAAG 1664
                          i     i     i i viiiiv  i      ?---- i   v   i   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAK----CCACATGCAAAAG 443

  chr2_48508853_4   1665 AATGAAACGAGACTCCCACTTGTCACCCTATACAAAAATCAGCTCAAAAT 1714
                               iivi   i  i  i vv    v           i i        
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_48508853_4   1715 GGATCAAAGACCTAAATGTAAGAACTGAAACGATAAAACTACCAGGAGAA 1764
                               ?                i  i    v        vii  i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_48508853_4   1765 AACAAAGATGAAACACTTCAGGACATTGGTCTGGGAAAAGATTTTATGAA 1814
                             v  i? v  vv    iv   v    vi i  v  v i   iv ii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_48508853_4   1815 TGAGACCTCAAAAACATAGGTAACAAAAGCAAAAATAAACGTAATTA--- 1861
                          iv   vi     i  i i i        v       i ii-    i---
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA-AATTGGAC 642

  chr2_48508853_4   1862 --TATCAAACTAAAAAGCTTCTG-----CACAGGAAAGAAACAACA--GT 1902
                         --i      v v    i   i  -----  v    v vv v   v --  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_48508853_4   1903 GAAATGACAACCTACAGAATGA-ATAAAATATATGCAAACTACTCATCTG 1951
                             v       i        i- v       v      ii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_48508853_4   1952 ACAGGGGATTAACATCTACAATATAAAAGGAACTCAAGCATCTCAACAGG 2001
                          i i    i vii   i v      v  i      vvi  v     i iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_48508853_4   2002 AAAACAAACAAACCAAAATCCTCTAATTTAAAAATGGGCAAATGATCAGA 2051
                             - i     i---  i  ---    ?             v   iv  
  L1M4_orf2#LINE/    793 AAAA-AGACAAAT---AACCC---AATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_48508853_4   2052 ACAGACATTGCTCAAAAGAAGACATACAAATGGTCAAGAA--ATTTAAAA 2099
                          i       v   v        i          i   v  -- iv i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_48508853_4   2100 AAAT 2103
                          i  
  L1M4_orf2#LINE/    886 AGAT 889

Transitions / transversions = 1.62 (81 / 50)
Gap_init rate = 0.02 (10 / 542), avg. gap size = 2.70 (27 / 10)  


 290 22.06 7.35 0.00  chr2_48614989_48617677.rev      544   611 (2078)    L1M4_orf2#LINE/L1        1    73 (835)  

  chr2_48614989_4    544 TGGAAAAACATACTATGTTCATGAATCAGATGACT-AA----GCTTAGAT 588
                               i i  v i         i  ii  v    -  ---- i v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_48614989_4    589 GGCAATACTCCCTGTATTAATTT 611
                                     iiv   i  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCT 73

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.03 (2 / 73), avg. gap size = 2.50 (5 / 2)  

3009 11.76 1.59 25.91  chr2_48614989_48617677.rev     1067  2197 (492)    L1M4_orf2#LINE/L1       53   908 (0)  

  chr2_48614989_4   1067 CAACCCTCTCCAAAATGATCTACAAGTTCAATGCAATCCCTATCAGAATC 1116
                            iv   i     v         ii     i             i    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_48614989_4   1117 CCAACTGACTTCTTTGTAGACATCAACACAAGCTGATTCTAAAATTCATA 1166
                            i   v   i    i   v  ii   --       i            
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACA--AGCTGATCCTAAAATTCATA 150

  chr2_48614989_4   1167 CGGGATTGCAAGGGACCTCAAATAACCAAAACAATCTTGAAAAAAAAAAA 1216
                         i  i v           ivi    i                   i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_48614989_4   1217 AAAAGTAGGAGGGCTCACGCTTCCTAATCTCGAAATTTGCTATAAAGCAA 1266
                         v     v     i     i     i   i  i   i  i   i     v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_48614989_4   1267 CAATCATCAAGATATTATGGTACTGGTGT--GGACAGA--------TCAA 1306
                           i v       i v i         ii --   i   --------    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_48614989_4   1307 TGAAATAGACCTGAGAATCCAGAAATAAATCCATATATCTACAGTCAACT 1356
                           i      vi     i            i     i  i  ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_48614989_4   1357 GATTCTCCACAAGGGTACCCAGACCATTCAATAAGGAAAGAATAGGCTTT 1406
                             i  v        i  v            ii           v    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_48614989_4   1407 TCAGCAAATGGTGCAGGGACAACTGCATAGGCACAGGCACCATATACAAA 1456
                            i          v          v   ?---------   i  i    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAK---------CCACATGCAAA 441

  chr2_48614989_4   1457 AATTAAAATGAGGTTGGGTGTGGTGGCTTATGCCTGTAATCCCAGCATTT 1506
                          i----     i     ---------------------------------
  L1M4_orf2#LINE/    442 AG----AATGAAGTTGG--------------------------------- 454

  chr2_48614989_4   1507 TGGGAGGCCGAGATGGGCAGATCACCTGAGGCTAGGAGTTCGAGACCAGC 1556
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chr2_48614989_4   1557 CTGGCCAACATGGTGAGACCCCCATCTCTACTAAAAAATGCAAAAATTAG 1606
                         -----------------     i i   ----------------------
  L1M4_orf2#LINE/    455 -----------------ACCCCTACCTC---------------------- 465

  chr2_48614989_4   1607 CCAAGTGCAGTGGCGCACACCCGTAGTCCCAGCTACTCGGGAGGCTGAAG 1656
                         ----------------     -----------------------------
  L1M4_orf2#LINE/    466 ----------------ACACC----------------------------- 470

  chr2_48614989_4   1657 CAGGAGATCACTTAAATCCGGGAGGCAGTTTGCAGCGAGCTGAGAGTGTG 1706
                         ---------------  ---------------------------------
  L1M4_orf2#LINE/    471 ---------------AT--------------------------------- 472

  chr2_48614989_4   1707 ACACTGCACTCCAGACTGGGTGATAGAGTGAGACTCTGTCTAAAAAAAAA 1756
                          i  ----------------------------------------------
  L1M4_orf2#LINE/    473 ATAC---------------------------------------------- 476

  chr2_48614989_4   1757 AAAAAAAAAAAAAAATTAATTCAAAATTAATCATAAACCTAAGTGTAAGT 1806
                         ----------         i       vi    ? i      i      -
  L1M4_orf2#LINE/    477 ----------AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG- 515

  chr2_48614989_4   1807 AAGAGTTAAAACTATAAAACGCTTAGAAGAAAACACAGG-GTAAGTCTTC 1855
                         ---  i              v              i   -    i     
  L1M4_orf2#LINE/    516 ---AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_48614989_4   1856 ATAACCTCAGATTTGACAGCAGATTCTTAGATATGACATCAAAAGCATCA 1905
                         i i    ii i  v i  iii v               i        iv 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_48614989_4   1906 GCAACAACAACAACAAAAATGGG-AAACTGGACTTCATCAAAATTGAACA 1954
                                -  v  --     i i-   i                 i  v 
  L1M4_orf2#LINE/    613 GCAACAA-AAGAA--AAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_48614989_4   1955 TTTTTGTTCCTCAAAGGACACTATCAAGAAAGTTAAAAGACAACCTATAA 2004
                         i      v i                       v           i i i
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_48614989_4   2005 AATGGAAGAAAATATT-GCAAATCATATATCCAATAAGTGACTTGTATGT 2053
                              i          -              ii     v         vi
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_48614989_4   2054 ATAATACATAAAGAACTCTTATAACTCAATAATAAACAGACAA----CCT 2099
                          v    i              i              v      ----  i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_48614989_4   2100 AACTGAAAAATGGAGAAAAGATCTCAATAAATATTTCTCCAA-GAAGATA 2148
                           i ?        iv   i   i v    i i          -       
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_48614989_4   2149 TACAAATGGCCAATAAGTACATTAAAAGATAGTCAACATCACTCGCAAT 2197
                                          i    v       iv         ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.82 (96 / 34)
Gap_init rate = 0.02 (18 / 856), avg. gap size = 17.28 (311 / 18)  


2361 23.36 1.71 2.80  chr2_48763602_48766322.rev     1010  1651 (1070)    L1M4_orf2#LINE/L1        1   635 (273)  

  chr2_48763602_4   1010 TGGGAAAATA-CCCATGTTCATGGACTGGAATAACTGATATCATTAAAAT 1058
                            i  i   -              i     v vi i    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_48763602_4   1059 GTCCATACTACCCAAAGCAAAATATGGATTCAACAAAATCTCTTATCAAA 1108
                          v v     v      vii vv  ii        iv    i  -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT-ATCAAA 99

  chr2_48763602_4   1109 ATTCCAATGACTTTCTTTATAGAAAT--ACAAAAAAAAGTCTAAAATTCA 1156
                           i   iivi i  i   ii      --    ivvi -vi          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCA 148

  chr2_48763602_4   1157 TATGGAA---CAACAGAACACATTAAATA-CCAAAGCAATTCAGAGGGGA 1202
                                ---   -i i  v  --i    -     i    iiv  -----
  L1M4_orf2#LINE/    149 TATGGAAATGCAA-GGGACCCA--GAATAGCCAAAACAATCTTGA----- 190

  chr2_48763602_4   1203 AGAAAAAAAAAGCAGAGTTGGAGGTATCACATTTTCTTGTTT-AAAACTA 1251
                         --    i  i i  i         vv     i  i ivi   -      -
  L1M4_orf2#LINE/    191 --AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT- 237

  chr2_48763602_4   1252 TATTGCAAACCTGTAGTAATCAAAACAGTATGGCACTGACA--AAAACAG 1299
                           i i    v  ii         i     i   i    i  -- ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_48763602_4   1300 ACACAAAGACCAGCAGAACAGTATAGAGAGCCCAGAAATAAACCCAAACA 1349
                            i v   i  iii   i  v  v     i               v   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_48763602_4   1350 CATATGGTCAACTGATTTTCAACAAGGGTGCTAAGAGGACACAATGGGGA 1399
                         iv         i        i          i    vv iv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_48763602_4   1400 AAGGATAGTTTCTTCAATAAATGGTTGTTGGTGGAAGAAGTGAATTTCCA 1449
                            i     i i     i       ---- v   i v  v  i  v?   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGT----GCTGGGACAACTGGATAKCCA 433

  chr2_48763602_4   1450 CACACAAAAGAATGAAAT-GGACTCTTATTTTCATACCATACATAAAAAT 1498
                           ii            i -    i i  ii -  i      i i      
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCT-CACACCATATACAAAAAT 482

  chr2_48763602_4   1499 CAATTCAAAATAGACAAAAGACCTAACCATAAGACCTTAAACCATAAAAC 1548
                         i  i       i  iv ?        vii     v  v    i       
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_48763602_4   1549 TCCAAGACAAAAACACAGAGGAAAACCTGTTTGACAATGGCCTTGGCAAT 1598
                           iv   vi      i  i? v   i  viv    vv   vi v      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_48763602_4   1599 GATTTTTTGGATATCACACCAAAAGCTCGGGCTACAAAAGCGAAAATAAA 1648
                          i   i  i     v           v ii  v       vi      i 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_48763602_4   1649 TAA 1651
                            
  L1M4_orf2#LINE/    633 TAA 635

Transitions / transversions = 2.06 (99 / 48)
Gap_init rate = 0.02 (15 / 635), avg. gap size = 1.93 (29 / 15)  

 935 22.30 2.03 1.35  chr2_48763602_48766322.rev     1934  2229 (492)    L1M4_orf2#LINE/L1      611   908 (0)  

  chr2_48763602_4   1934 AAAAAATAAAATAAAATA-AAATAAATACAGAC---ATCAAA-TTAAAAA 1978
                           iv  i    v    v - i      -ii   ---      -       
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAAT-TGGACTTCATCAAAATTAAAAA 659

  chr2_48763602_4   1979 GCTCCTGCACAGCAAAGAAAACAAATAACAAAATAAAACAGCAGCCAACA 2028
                         -  ii  ii vv     i v  v vi  v   i i   vii  i  v   
  L1M4_orf2#LINE/    660 -CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_48763602_4   2029 GATACGGAGAAAATATTTGCAAACCATATATCTGATAAAGGGCTTAATAT 2078
                           vvv                  i              i  i   i-   
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG-TAT 757

  chr2_48763602_4   2079 CCAAAATATATTAAAAGATTTACACAACTCAATAACAGAAAAACAAATAA 2128
                            i       -   ii i ivi            i i   i        
  L1M4_orf2#LINE/    758 CCAGAATATAT-AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_48763602_4   2129 CCTT-TTCAAAAATTGGCAAAGGACTTGAATAGATCTTTTTCCAAAGACA 2177
                           iv-  ?      v         i         iv   i        vi
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_48763602_4   2178 ACATAAAAACAGCTAACAGGTATACAAAAAGGTGCTCAACATCACTATTC 2227
                          i   v   ii  i  i i i i ii     i            ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_48763602_4   2228 AT 2229
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.25 (45 / 20)
Gap_init rate = 0.03 (8 / 298), avg. gap size = 1.25 (10 / 8)  


3066 25.80 2.21 1.66  chr2_48777039_48779242      816  1718 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_48777039_4    816 TGGGAAAACATCCCACGCTCATGGGTAGGAAGAATCAATATTATTAAAAT 865
                            i  i i      i i      i v      v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_48777039_4    866 GGCCATACTACCCAAAGCAATGTACAGATGCAATGCTATTCCTATCAAAT 915
                            v     v      vii  v       v   i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_48777039_4    916 TACCAATGAAATTCTTCACAGAGCTGGAAAACACT-ATTTTAAAACTCAT 964
                          v   iivivv  i  ii    iv v  v  -i  -  ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_48777039_4    965 ATGGAGCTAACAAAGAACCT-GAATAGCCAAGGCAATCCTAAACAAAAAG 1013
                              iv i-   i i   i-          ii     i i  v  i   
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_48777039_4   1014 GACAAAGCTGGAGGCATCACATTACCTGACTT-AAAACTATACTACAGGG 1062
                         i      i      vv     i v  ii i  -      -       ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_48777039_4   1063 CCACAGTAACCAAAACAGCATGGTACTGGTACAA--ACAGACCCATAGGC 1110
                          i       i   i    ii         i i  -- i    vi    ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_48777039_4   1111 CAATGGAACAGAATAGACAGCCAGGAAATAAGGCTGCACACCTGTAGCCA 1160
                                 i     v  v  i vi       iv iii   ii i i i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_48777039_4   1161 TCTGACCTTTGACAAAGTCAACAAAAGTAAGCAATGGTGAAAGCACTCCC 1210
                         vi   ii  i     i viiv   i vi vv      v     -------
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG------- 390

  chr2_48777039_4   1211 AATAA-------AATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAG 1253
                             i-------  i              i      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_48777039_4   1254 AAGACTGAAGCTGGACCCCTTTCTTACACCACATACAAAAATCAACTCAA 1303
                             v     i         vi  i      i          i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_48777039_4   1304 GATGGATTAAAGACTTAAATATAAAACCCCAAACTGTAAAAAACCCTAGA 1353
                         i      i ?    i     i   i v iv     i     v-i i    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGA 539

  chr2_48777039_4   1354 AAACAACCTAGGCAATACCATCTT-G-GACATAGGAACAGGCAAAGATTT 1401
                          i v   v    ?i-  v-     - -   v v  ivi      v i   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNG-TAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_48777039_4   1402 CATGACAAAGACACCAAAAGCAATCA--CAAGAAAAGCAAAAATTTACAA 1449
                          v iivv v             --  --   v     v      vv i  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_48777039_4   1450 GTGAGATCTAATTAAACTTAAGAGTTTCTGCACAGTGAAAGAAACTATCA 1499
                         i vi  ii v  i   v    i ii  i  ii vvii  i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_48777039_4   1500 ACAGAG-GAAG---CAGCCTACAGAATGGAAGAAAATATTTGCAAACTAT 1545
                          v i  -   i---  i  i         i                ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_48777039_4   1546 GTATCTGACAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAAT 1595
                         i       i  i  v  vi       v  v     i     ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_48777039_4   1596 TTACAAGAGAAGAACAAACAGTCCCGTTAAAATGTGGATAAAGGACATGA 1645
                         iv i  v i  ii     i ii  vi  ?   vi   ii      iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_48777039_4   1646 ACAGACACTTTTCAAAAGAAGACATACATGCAGCCAACAAGCATATGAAA 1695
                          i     i  i  v        i     viii     i     i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_48777039_4   1696 AAAAGCTCAATATTACTGATCAT 1718
                          i v      i  i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (153 / 76)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.94 (35 / 18)  


2742 20.25 2.76 0.77  chr2_48794737_48796370.rev      491  1142 (492)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr2_48794737_4    491 AAAATTAAAA-AATAAAACCAGTGTGTTATTAATGTATAGACAGGTGTAT 539
                            ii  v i-   v  iv       v  i iiii  vi  i  iii   
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_48794737_4    540 ACACCAATAAAATAAA-----GATCCCAGCAACAAACCGTTACATAAAAC 584
                          v i    ii    i -----  vi    v  i     vv     vv vv
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_48794737_4    585 GTCAATT----TTCCATAAGGGTAACAAGACCATTCAATGTGGAATGGAC 630
                                ----   v i      iv               v    v i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_48794737_4    631 AGTCTTTTCAACAAATCATTTTGGGAAAACTAG-CA-CCACATTGAAAAT 678
                                         vi vi     v    i -i -      vv    v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_48794737_4    679 AATGGAGTTGAACCCTAAATTTATACCATCTACGAAAATTAACTCAAAAT 728
                             i     i    iv vi i i     v   i                
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_48794737_4    729 GGATCAAAGAGCTAAAGATAAGAACTAAAACTATAAATCTCTTAGAGGAA 778
                               ?   v     vi     i             v        i   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_48794737_4    779 AACAGGTGGTGAAAAT-TTCATGACATTGGATTTGAAAATAATTTATTGG 827
                             vi-  ? v    -   i    v    i  v iv   ii   v  i 
  L1M4_orf2#LINE/    544 AACATA-GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_48794737_4    828 ATATGACACCAAAAGCATAGGCAACAAAAGAAAAAAATAGATAAAATGGA 877
                                          i i                -        v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGA 641

  chr2_48794737_4    878 CTTCACCAAAATCAAAACCTTTTGTGCT-CAAAAGACATTATTAACAGAG 926
                              i      i    v          -    i    i   i  v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_48794737_4    927 AGTAAAGGCAACCCATAAAATGGGAGAAAATATTTGCAAATCATACATCT 976
                         v v    i       i i                           i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_48794737_4    977 GATAAGAGGTGAATATCCAGGATATATAAAGAACT---ACAAGTCAACAA 1023
                               i iivvi       i              ---    v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_48794737_4   1024 CAACAGAGCAAACAGTCCAATTTTAAAAAAATGGGCAAAGGACTTGAATA 1073
                         i  v iii    i ii      ?---                i       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTW---AAAAATGGGCAAAGGATTTGAATA 838

  chr2_48794737_4   1074 GACTTCTCTACAAAGAATGCATACAAGTGGCCAG-AAGAACATAAAACAA 1122
                            v i   v       vii      i      i-   v    i   vi 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_48794737_4   1123 TGTTCAACATCACTAATTAT 1142
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (79 / 50)
Gap_init rate = 0.02 (12 / 665), avg. gap size = 1.92 (23 / 12)  


 495 29.28 10.30 7.94  chr2_48814768_48816573.rev      501  1306 (500)    L1M4_orf2#LINE/L1       63   887 (21)  

  chr2_48814768_4    501 CAAATT---TTATTAATTTAATGTGATCTCAATGAAAATACCAACAGGGT 547
                               ---i  ivi   i  i ii   i v  v     v   i v vv 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_48814768_4    548 TTTATTTTGAACCAGACAAGTTGATTCTGGAGTTAATATGAAAA----AT 593
                            v viv   viv      i    i  ii i  v     i   ---- v
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_48814768_4    594 GAACA-AGAATATCCAGGAAAACTCTGCAAAAAAATTAGTAAAG---AAT 639
                          i  v-      v   ii v  iii  v    i  v- ii    ---i v
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG-AACAAAGTTGGAG 211

  chr2_48814768_4    640 TACTAAC-CTTACCAG-------AC--ATTAAAAATCT-TAATAATTAAA 678
                         v   v  -   v   i-------  -- i  v   v  -i i    i  i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_48814768_4    679 TCAGAGTAGCATAGGCCTATGGACAGACA----AACCAATGGAACAAAAC 724
                         v   v  i i iv   v  v   i     ----i i        i i  i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_48814768_4    725 AGAAAATCAATAAGTAGACCCAAATACATTTA-GA--AATGCAGT---AG 768
                         v  i i  v v  i  i     --        - i--   vv v ---ii
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAATTGATTTTCGA 359

  chr2_48814768_4    769 CA--GATGATAA-ATCATGTCTTAACATTAGGGACGAAATAGATTTCTTA 815
                           -- i  vi  - i   --- i  --- i    vii     vi  i i 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCAT---TCAA---TGGGGAAAGAATAGTCTTTTCA 403

  chr2_48814768_4    816 AAAAATG---TTAGGAAGATTGAGTAGCCACCTGGAAAAAAAAAAATAAA 862
                          v     ---i i   vi i  ii  ?    v  v    i  ---- i  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA----TGAA 449

  chr2_48814768_4    863 AAGTTGAAACCATATGTTACATTATACACCAAGACAAACACCAAATGAAT 912
                         --    i v  v  iv i   ii   i  v  i iv   v v     i  
  L1M4_orf2#LINE/    450 --GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_48814768_4    913 CA-AGACTTGAGTATATAGATATAGATATAGATATAGATGATATAGATAT 961
                           -    i i i i  ----------------------------   ---
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTA----------------------------AGA--- 516

  chr2_48814768_4    962 AGATATAGATATATAGATATATATGAAATACTT-GAAGAAAACATGAGCT 1010
                         - v  v iv    ------------   iv   -           ii ?v
  L1M4_orf2#LINE/    517 -GCTAAAACTATA------------AAACTCTTAGAAGAAAACATAGGNG 553

  chr2_48814768_4   1011 TC--CCTTTAAAACTCTGAGGTAAGAAAGAACTTTTTATTCATGGCTCAA 1058
                          v--i   iivi  ii  i v  i v  viii  i   vvi   i v v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_48814768_4   1059 AATGCAGAAGACATAAAATTAAAGATTGACAGATC---------CAAAAT 1099
                           v   v   vv i    vv   i  v  i i  i---------      
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_48814768_4   1100 CTACA--TATTG------AAAAGAAA-----AAGCAA-TGAAAA--TAAC 1133
                         iv v -- v   ------   i  v -----   v  -      --i   
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_48814768_4   1134 T----GAGT---AAAAAGTACTT-C------TGTGTATAACAAAAAGCTC 1169
                         i----  i --- i   i  i  - ------ i i v i i  iiii  -
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT- 752

  chr2_48814768_4   1170 ATTTTCTCCAAAATA-ATATTGAGCTCTTAGAGATCACTAAATATAAGAC 1218
                         -- v v    i    -   vv  i      v iv   v   vv v     
  L1M4_orf2#LINE/    753 --TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_48814768_4   1219 CAAATAATCCAATTTTTTAAATAGACAAAGATTATGAACAAACAGTTCAC 1268
                         -      i      ?vv-    i i     iv v    i i   v   v 
  L1M4_orf2#LINE/    801 -AAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_48814768_4   1269 AAAATGTAA-ATACAAAAGGCCCTTTAACATATGGAAAG 1306
                         v   vivi -       v    vv v i  i   i    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

Transitions / transversions = 1.33 (133 / 100)
Gap_init rate = 0.05 (42 / 825), avg. gap size = 3.50 (147 / 42)  


3257 27.42 0.22 0.22  chr2_48878130_48884397     4869  5776 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_48878130_4   4869 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4918
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_48878130_4   4919 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4968
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_48878130_4   4969 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5016
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_48878130_4   5017 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5066
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_48878130_4   5067 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5116
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_48878130_4   5117 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5166
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_48878130_4   5167 AATGGAACAGAACTGAGCCCTCAGAAATAACACCGCATATCTACAACTAT 5216
                                i    i    vvii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_48878130_4   5217 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5266
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_48878130_4   5267 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5316
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_48878130_4   5317 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5366
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_48878130_4   5367 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCC 5416
                          ?    i    i  v   v       i      vi i           vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_48878130_4   5417 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5466
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_48878130_4   5467 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCCAATT 5516
                                    vvi          vv     v  i    v   iiiv  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_48878130_4   5517 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGGGAACAG 5566
                            v v  i i   i  ii vv    i  v    i  vv i  v   v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_48878130_4   5567 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 5616
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_48878130_4   5617 GGCTAATATCCACAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5666
                          i  vi      v   v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_48878130_4   5667 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5716
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_48878130_4   5717 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAGTGCTCACCAT 5766
                         v        i  vi viii     v  i          ii      v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_48878130_4   5767 CACTGGCCAT 5776
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


3035 27.32 0.87 1.64  chr2_48900610_48907316.rev     5301  6215 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_48900610_4   5301 TGGAAAAACATTCCATGCTTATGGATAGGAAGAATCAATATCGTGAAAAT 5350
                               i i  i     i i      v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_48900610_4   5351 GGCCATACTGCCCAAAATAATTTGTACATTCAATGTTATTTCTATCAAAC 5400
                            v     v      v i  i ii v      i iv  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_48900610_4   5401 TACCATTGACTTTCTTCACAGAATTGGAAAAACT-ACTTTATATTTTATA 5449
                          v   vivi i  i  ii     v v  v  i  - iii  v v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_48900610_4   5450 TGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGTAAAAAGAG 5499
                              viiv  ii  v  v v        i      i i iv  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_48900610_4   5500 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATTACAAGGCTA 5549
                              i      vv   ii  v  ii i      viv  i     i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_48900610_4   5550 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5599
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_48900610_4   5600 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5649
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_48900610_4   5650 GATCTTTGACAAACCTGAGGAAAACAAGCAATGGGGAAAGGATTCCCTAT 5699
                            i  i     ivv  vvi i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_48900610_4   5700 TTAATAAACGGTGCTGGGAAAACTGGCTAGCCCTATCTGGAAAGCTGAAA 5749
                          i  i   i          v      v  ?  vi  viii  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_48900610_4   5750 CTGGATCCCTTCCTTACAAAACTGGATCCCTTCCTTATACAAAAATTAAC 5799
                         i    i    v   i   --------------  v               
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACA--------------CCATATACAAAAATTAAC 486

  chr2_48900610_4   5800 TCAAGATGGATTAAAGGCTTAAAGGTAAGACCTAAAAACATAAAAACCCT 5849
                             i      i ?  i i    v      v      vi      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_48900610_4   5850 AGAAGAAAACCTAGGCA-ATACCATCCAGGACATAGGCATGGGCAAAGAC 5898
                                   v    ?i- v i - i iv   v v  vv i     v ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_48900610_4   5899 TTCATGACTAAAACACTAAAAGCAACGGCAACAAAAGCCAAAATTGACAA 5948
                            v iiv  vi    i       vvi          vv     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_48900610_4   5949 ATGGAATCTAATTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTATCA 5998
                           v i ii v  i   v v  i i      ii vv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_48900610_4   5999 TCACAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTAA 6048
                         vv v      v  i     i                 v       vii v
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_48900610_4   6049 CCATCTGAAAAAGGGCTAATATCCAGAATCTACAAAGAACGTAAACAAAT 6098
                         vi      v  i  i  vi          v  i       vivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_48900610_4   6099 TTACAAGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAAGATATGA 6144
                         iv i  v     i    ----   v  i?    i        i   v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_48900610_4   6145 ACAGACACTTCTCAAAAGAAGACATGTATGCAGCCAACAA--ACATGAAA 6192
                          i     i     v        i  ii viii     i  --        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_48900610_4   6193 AAATGCTGGTCATCAGAGAAATG 6215
                          i     viv     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 3.83 (23 / 6)  


 650 25.76 0.00 5.56  chr2_48971345_48977963.rev     2862  3059 (3560)    L1M4_orf2#LINE/L1        1   187 (721)  

  chr2_48971345_4   2862 TGAACATATATTCCATGTTCATCAAGTGGAAGAATCAATATTGAATCAAT 2911
                           i v v    i          vi v       -- --------- i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA--C---------TTAAT 39

  chr2_48971345_4   2912 ATTGTCAAAATATCCATATTACTCAAAGCAATCCACAAATTCAATGTAAT 2961
                              i  i  iv v   i v i    vii   i   i      i i   
  L1M4_orf2#LINE/     40 ATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

  chr2_48971345_4   2962 CCCTATCAAAATGTCAATAACATGCTTCACAGAAATAGGAAAAACAATCC 3011
                                     vi  iivi v vi  ii       v iv  ivii    
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_48971345_4   3012 TAAAATGTATATGGAAGCTCAAAAGACCCAGAATAGCCAAAGCTGTCT 3059
                               vi        iiv   ii                 i vi   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

Transitions / transversions = 1.83 (33 / 18)
Gap_init rate = 0.01 (2 / 187), avg. gap size = 5.50 (11 / 2)  

2427 26.36 1.29 1.81  chr2_48971345_48977963.rev     5354  6127 (492)    L1M4_orf2#LINE/L1      139   908 (0)  

  chr2_48971345_4   5354 CTACAATTCACAATGAGATTTGGATGGGGAC-----ACAGCCAAATCATC 5398
                            v      i vv  i  -- v -i     ----- i       v  --
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAAT--GCA-AGGGACCCAGAATAGCCAAAACA-- 183

  chr2_48971345_4   5399 ACTATCCTAAGCAAAAAGAAAAAAACAGGAGGAAACATATTACCAGACTT 5448
                         ---   i i iv  i     v   iiv      vv  i i v  vi i  
  L1M4_orf2#LINE/    184 ---ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr2_48971345_4   5449 CAA--TTTATGTTACAGAGCTATACTAACCAAAACAGCATGGTATGAGTA 5496
                            --i   i--    i     i v   i   i    ii     ivi i 
  L1M4_orf2#LINE/    231 CAAAACTTAC--TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_48971345_4   5497 TAAAAACAAATGCATAGACCAATGAAATAAAACAGAGAA-ACAGAAACAA 5545
                            ii i i iii     i     i    i  iv    i-v      i  
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_48971345_4   5546 ATCCATACTTCTACAGTGAACTTATTTTTAACAAAGGTGCCAAGGAACAT 5595
                          i      v i  ii  v  i v     ii    i         - v   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG-ACCAT 377

  chr2_48971345_4   5596 ACATTGGAGAAAGGACAGTCTCTTCAATAAACGGTGCTGGGAAAACTGAA 5645
                         v  v   i     i i     i     i   i          v     i 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_48971345_4   5646 TATCCACATGCAGAAGAATGAAACTAGACCCGTATCTTTC-CCATATGCA 5694
                           ?         i         ii i     v  i  iv -      i  
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_48971345_4   5695 AAAATCAAATCCAAATGAATTACAGGCTTAAATCTAAGACCCCAAACTCT 5744
                              i  v  v     i  i ?  i i     v     v iv     v 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_48971345_4   5745 GAAACTACCACAAGAAAATACCAAGAAAACTTTCCAGGACAATGGTCTGG 5794
                         i     vii v       i ivii?iv  v i i iv   vv   vi i 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_48971345_4   5795 GCAAAATTTTCTTGAGTAATAGC-CCAAAAGCACAGGCAACCAAAGCAAA 5843
                             viv      iii  - ii -           i     v    v   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_48971345_4   5844 AAAGAACAAACAAGATCACATCAAGCTAAAAAGCTTTTGCATATCACTGA 5893
                           vii i   ivi  iiv      iv v    i      iiiv   vv i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_48971345_4   5894 AGACAATCAACAAAGTAAAAAGAAAACCCACAAAATGGAAGAAAATATTT 5943
                          v  v     v     i      v        i     i           
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_48971345_4   5944 TCAAACTACCCGTTTCACAAGGGATTAATAATCAGAATATAAAAGGAGCT 5993
                         v    ii ivii i v i      i vi  vi         v  i  i  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_48971345_4   5994 CAAACAACTCTATATGAAAAATATCTAATAATCCAATTTCAAAATGGGAA 6043
                          vv       v   vv     v - v     i      ?v        v 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCA 825

  chr2_48971345_4   6044 AAAGGATCTGAATAGACATTTCTCAAAAGATAACATACAAATGGCAAACA 6093
                           -    i                v     vi i           v  i 
  L1M4_orf2#LINE/    826 AA-GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_48971345_4   6094 GGCATATGAAAATGCGCTTGACATCACTGATCAT 6127
                         i   i       vii   ii      ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (125 / 75)
Gap_init rate = 0.02 (13 / 770), avg. gap size = 1.85 (24 / 13)  


 434 23.85 0.92 0.00  chr2_49193883_49199401     3724  3832 (1686)    L1M4_orf2#LINE/L1        1   110 (798)  

  chr2_49193883_4   3724 TGGAAAAACATCCCAAGCTCATGGATGTGAATAATCAGTATTGTTAAAAT 3773
                               i i      v i        vv   v v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49193883_4   3774 GACCTTACTAACTAAAGCAATCTAAAGATTCAATGCAATTACTATCAAAA 3823
                          i vv    vv i   vii     v        i     iv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49193883_4   3824 TACCAA-TGC 3832
                          v   i-   
  L1M4_orf2#LINE/    101 TCCCAGCTGC 110

Transitions / transversions = 1.00 (13 / 13)
Gap_init rate = 0.01 (1 / 110), avg. gap size = 1.00 (1 / 1)  

2139 22.03 2.74 11.30  chr2_49193883_49199401     4152  5027 (491)    L1M4_orf2#LINE/L1      108   908 (0)  

  chr2_49193883_4   4152 TGCCGTCATTCACAGAAGTAGAAAAAAAAATTT--AAATTTGTACGGAAC 4199
                             v i-  ii     i v  v  ivvi  ii--     ii  i    v
  L1M4_orf2#LINE/    108 TGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_49193883_4   4200 CACAAAACATCCTGCATGGCCAAAGTAAGCCTAATCAAAAAAGAACAAAG 4249
                         ii   iiv i  v v  i      ii  v i i -v   i          
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAGAACAAAG 205

  chr2_49193883_4   4250 TTGGCAGCATCAAACTACCAGACTTCAAAATATAATACAAAGTTATAGTA 4299
                             vi vv   v   v  vi i       iv  v       i  i    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_49193883_4   4300 ACCAAAACAGCATGGTACTGGGGGAAAAAAAAAACAGACAAATAGACCAA 4349
                          i   i    ii         v----- v  ii i     v     i   
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGC-----ATAAGGATAGACATATAGATCAA 300

  chr2_49193883_4   4350 TGGAACAGAATAGAGAATCCGTAAATTAATGCACGTATCTATAGCCAACT 4399
                              i     v    i   iv    v  iv  iii  i   i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_49193883_4   4400 GATTTTTGACAAAGGTGCCAAGAACATTCACTGGAGAAAGGACGGT---T 4446
                               i     i          v      v   i     i ii  --- 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_49193883_4   4447 TCA-TAAATGATGCTGGGAAAACTGGATATCCACATGTAGAAGACTGATA 4495
                            -i     i        v         ?       i i    v   --
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA-- 448

  chr2_49193883_4   4496 CTATTAGGCTGGTGCAAAGGTAACTGTGATTTTTGCTATTAGAAAGTAAT 4545
                         -----------------  -------------------  i  -------
  L1M4_orf2#LINE/    449 -----------------AG-------------------TTGGA------- 455

  chr2_49193883_4   4546 GGCAAAAACTGCAATTACTTTTATATCAACCTAACAGATGCCCCCTTTCA 4595
                         -----------------------------------------     --- 
  L1M4_orf2#LINE/    456 -----------------------------------------CCCCT---A 461

  chr2_49193883_4   4596 CCTCTCATTCTATACAAAAATCAACTCAACATGGATCAAATTCCTAAATA 4645
                             v  iiv           i       v        ? vv       i
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_49193883_4   4646 TACGTCCAAAAATGATAAAACTGCAAGAAGAAAACAT-GGAGGAAGTGCT 4694
                           v vv v    iv        viv            -  ? v  i -  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CT 560

  chr2_49193883_4   4695 TGAGGACTTTGGTTTCGGAAAAGATTTCATGAATAAGACATCAAAAGCAC 4744
                          viv   i    v  v  v  v i    v ii   v    i         
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_49193883_4   4745 AGGAAACAAAATCAAAAATA----AAGGGGATTATATCAAACCAAAAAGC 4790
                          i v       vv       ----  vv   i vi      viv    i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_49193883_4   4791 TGCAGAGC--CAATGAA-ACAATCAATATAGTGAAAAGACAACC-ACAGA 4836
                          viv v  --   v i -  v     v v               -     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_49193883_4   4837 ATGGGAGAATATGTTTGCCAAGTACTCATTTGACAGGGCATTAATATCCA 4886
                                  v  i     v  vi ivi  i   i i  v i vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_49193883_4   4887 GAATATATAAGAAACTCAAACAA---------AAAAATACCAAAAAAATT 4927
                                   ii     vv    ---------     v  --   v  ii
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC--AAATAACC 808

  chr2_49193883_4   4928 TGATTAAAATATAAGCAAGTGATCTGAACAGATATTTCTGAAAAGAAGAC 4977
                         ii   ?   v  ii    iv   i    i   i      vv        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_49193883_4   4978 ATATAAATGGCCAACACATATATGGAAAAATGCTCCACATCACTAATCAT 5027
                            i          i vii i   i   i      v      ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (107 / 82)
Gap_init rate = 0.02 (18 / 801), avg. gap size = 6.83 (123 / 18)  


2429 24.89 3.52 0.98  chr2_49200406_49202108      501  1211 (492)    L1M4_orf2#LINE/L1      180   908 (0)  

  chr2_49200406_4    501 AGCAACCCTGAGCAAAAAGAATAAAGCTGAAGGCATCACAGTACAGGACT 550
                          i   i i   iv  i     i    i  i   vv     v v vvi i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_49200406_4    551 TAAAAATATACTACAAAGCTATAGTAATCCAAACAACGTGCTATGGTCAT 600
                          v    iv             i       v i   ii   v  iv v   
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_49200406_4    601 AAAAACCAAACCATATGCA--GGTGGCACAGAA---A------AGAAATA 639
                           ii i- i  -    iv --ii   v i    --- ------       
  L1M4_orf2#LINE/    280 AAGGAT-AGAC-ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_49200406_4    640 AACCTACATATTTATAGTGAAGTGATTTTCAACAAAGACATTGAGAACGT 689
                             i i i      i  v  v        i    i iiiiii   v i 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_49200406_4    690 TCATTGGGGAAAGGAAAATCTCTTCAATGAGTTGTGCTGGGACAACTGGA 739
                            v         i v i   i     ii i v                 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_49200406_4    740 TATTCACATGCAGAA-AAGGAAACTGGATATCTATATTTCACCATATACA 788
                           ?i        i  -  v   ii    ivi   iv iv           
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_49200406_4    789 AAAGTCAACTCAAAATGGATTAAAGACTAAAATGTAAGATCTGAAACTAT 838
                            i i              i ?    iv          v  i       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_49200406_4    839 ATAAAACTTCTGGAAGAAAACATTGGGA-AATTCTTCAGAAAATTGATCT 887
                          --     ii i           v  ?i-  v     ivi vv   ivi 
  L1M4_orf2#LINE/    528 A--AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_49200406_4    888 GTGTGAAGATTTTTATGGAGAAGACCTCAAAAGCACAGGAAATAAAAGGA 937
                         iv ii v i   i - i  v v   vi          i v  i     i 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCT-TAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_49200406_4    938 AAAACAGACAAATGGCATTATGTTAAA-TTAAAAAGCATCTGTAGAGCAA 986
                             i   i    v v i vii i   -       - v i   ivvv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chr2_49200406_4    987 AGGAAACAACCGAG----TGAAGAGCCAACCTTCAGAATGGGAGAAAATA 1032
                             v  v i i  ----    i  v     iv                 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_49200406_4   1033 TTTGGAAACTACTCATC----AAAGGATTAGTATCCAGAATATACAAGGA 1078
                             v   ii ivi   ----  i   i v              i  i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_49200406_4   1079 ATTCAAACAACTCAACAGCAAAA---TTAATAATCAAATTTAAAAATGAT 1125
                          i  vv         i ii    ---iv     i v    ?       iv
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_49200406_4   1126 CATATGGGTCAAATAGACATCTCTCAAAAGAAGACATACAAATGGTCAAT 1175
                           v v iv ii         i    v        i          i    
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_49200406_4   1176 AGGCATATGAAAAAACTGTTCAACATCACTAATTAT 1211
                          i   i       i -  i         ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (111 / 62)
Gap_init rate = 0.02 (15 / 729), avg. gap size = 2.13 (32 / 15)  


2725 25.70 4.85 2.48  chr2_49211418_49213701      932  1818 (465)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49211418_4    932 TGTAAAGACATCCCATGTTCATGGATCAGAATAATTAATATTGTTAAAAT 981
                           v     i                 ii   v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49211418_4    982 GACTATACCACCCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 1031
                          i v    iv      vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49211418_4   1032 TGGCAATGACATTCTTTATAGAAATAAAAAAACT-----TAAAATTT-TG 1075
                          vv  iivi v  i   ii      vi v  i  -----       i- i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_49211418_4   1076 TGGAACCACAAAAGATACTGAATAACCAAAGCATTCT-AAGCAAAAAGAA 1124
                              vii   ii  iv v     i     i  v   -i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_49211418_4   1125 CAAAATTATATGCATCACA-TTCTCAGACTTCAAAATATACTACAAAGCT 1173
                             i  iv v vv     -   i  - i       iv            
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCT 249

  chr2_49211418_4   1174 ATAGTAACCAAAACAACAAGGTATTGGCATGAAAATAGAAACATAGACCA 1223
                          i     i   i   iiiv    i      i ii     v i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_49211418_4   1224 GAAGAACAGACTAGAGAACCCAGAAAATAATCCATGTATTGACATTCAAC 1273
                         ivi   i   v v    ii       vv  i    ii   v iiv    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_49211418_4   1274 TAATTTTTGACAAAGGTGTCAAGAACACTCACTGGGGAAAGGACAGTCTC 1323
                          i     i     i    i     v  i   v         i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_49211418_4   1324 TTCAATAAATTCTGCTGGGAAAATTGTAGATCCCTAGGCAGAAGAGTGAA 1373
                              i    vv        v  i  v v ?  vi v   i    i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_49211418_4   1374 ACTATACTTCCACCTCTCATTCTATATAGAAATGACCACAAAATGACTCA 1423
                         ii iv  ii i     v  iiv    i i    v v v       iv   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_49211418_4   1424 GAGACCTAAATATAAGACCTGAAATGATAAAACTACTAGAAGAAAATGTA 1473
                         ?          i     v  i   iv        vi          ii  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_49211418_4   1474 GAAGTG---CTTCAGAGCATTGGTCTGGGAAAAGGTTTTATGAGTAAGAC 1520
                          i?  i---    ivii v    vi i  v  v     iv iii  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_49211418_4   1521 TTCAGAAGCACAGGAAACAAAAGGAAAAATAAACAAATGGGATTATGTCA 1570
                         vi  i       i v        i       i i    v   i vii   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_49211418_4   1571 AACCAAAAAGCTTCTTCACAGCAAAGAAAACAAAAAACAGAATGAAAAGA 1620
                           viv    i   i vii vv     i v  v vv  v i i        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_49211418_4   1621 TAACCTATAGAATGGAAGAAAATATTTGCCAACTACCCATTTGACAGAAG 1670
                         i    i i       i             v  ii ivi  i   i iii 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_49211418_4   1671 ATT--------------------AACTCAAACATCTCAACAGCAAAAAAA 1700
                          i --------------------     vv   v     i ii     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_49211418_4   1701 CAACAAATCACCACCAACAAAAAAGTTGATTAAGAAAATAAGCAAATGAT 1750
                            ---  v   -----   ---------  ? -     ii     v   
  L1M4_orf2#LINE/    800 CAA---ATAACC-----CAA---------TTWA-AAAATGGGCAAAGGAT 831

  chr2_49211418_4   1751 CTGAACAGACATTTCCCAAAAGAAAACA-ACAAAT-----------ACAT 1788
                         i    i         i v      i i -      -----------    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_49211418_4   1789 AAAACAGGTTCCCTGATCATCAGGAAAATT 1818
                         i   -  i v i -- v     ????????
  L1M4_orf2#LINE/    882 GAAA-AGATGCTC--AACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (143 / 81)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.33 (65 / 15)  


 926 28.97 9.08 6.21  chr2_49216818_49219406     1228  2097 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_49216818_4   1228 CACATTTATAAGTGGTAAGTTTCAATGTTGTGAAGATAATCAGTTTAATC 1277
                           ii  i  iii v v   vi i   i    v     ii-  i vivvi 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG-CAATACTCCC 62

  chr2_49216818_4   1278 CACATCAGTATATAAATTGAAGGCAAAACCCATCTAAAGCACAGTTGTTT 1327
                           v  iii v  i i   v  v    vv  i   v   v v   i  ii 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_49216818_4   1328 TTTTGTTTGTTTTTGTATGGGTATGTGGAAATTAACTGGCTGAT--TAAT 1375
                             -------------------  ii      i  vi      --   v
  L1M4_orf2#LINE/    113 TTTT-------------------TGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_49216818_4   1376 AGTTATATGGAAGAGCAAGTTTTAAAGAAAAGCTAAAGCAATTTTAAAGA 1425
                          v i        iv     vvvivv    v   i   i    i  i  i 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_49216818_4   1426 AGTAGATCAAGATTGAGGGGATTGGCA--TACCAG----GAAATATGATT 1469
                           v   v   ii   - i   i vi  -- v   i----i   i----  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTG-GAGGACTCACACTTCCCAATTTCAAAAC----TT 238

  chr2_49216818_4   1470 TTTCTAAAGTTAGAGTGATTAAAATATTATGATATCGACA--GGGATTTA 1517
                         vi vi    i  v   i  i  i i v i  i  ii i  --i    -- 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT--A 286

  chr2_49216818_4   1518 AAAAAATAGACCAATGGAAGAAAATAAAGAGCACGGAAATAAACCACAAA 1567
                         i v v     i        v i   vi    iv i          -  v 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC-CATA 335

  chr2_49216818_4   1568 CA---AAGG--AATATGATAAATGACA-GTGTATCATCAAA--AATCAGT 1609
                           --- v  --   -    vvvi    - v  ii  -- i -- v   i 
  L1M4_orf2#LINE/    336 CATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCA--AGACCATTCAAT 382

  chr2_49216818_4   1610 GGTGGACAATATGGACTAATCAATAAAGGATGCTAAGACTATTGATTTTC 1659
                           -   v iv  i v  vv    i   v i    ii   v i  iv v? 
  L1M4_orf2#LINE/    383 GG-GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_49216818_4   1660 CTTGTG-----GAGTAACCTAAGACCTTTGCTTATTACCACAT-TAAATC 1703
                          vii  -----  i i vv vi    ii i i vvi    i  -i   vv
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_49216818_4   1704 TCAATTCCAATTTTACTAAAGATATAAATAGGAAAAATTAAGACTTTAAA 1753
                          i  i  v  v vv ii ?   iv     - v  i ii   i   v    
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAA 530

  chr2_49216818_4   1754 ACTTTTA------AATA-------AAATGTCTGT----TCAGA--AGAC- 1783
                            i   ------  i -------    v ii  ---- ii i--  i -
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_49216818_4   1784 ----TTTTTTAAAAA-AACACACAAAAATCCC-GCACTAAAATTGAAAAA 1827
                         ----   i   i v -i    -     iiv v-   vi    --      
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACAC-CAAAAGCACAAGCAACAAAA--GAAAAA 627

  chr2_49216818_4   1828 TTA-ATAAATTTAAGTACACTAAACTTAAAA-TTTCTGTAAAACAAAG-A 1874
                         v  -       vi v v  ii   v      -i  i   ivvv     - 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_49216818_4   1875 TAC-ATAAACTGAACTGTAGTTTATGTGTAAGCGTTAGACTGGAGAAAGA 1923
                         i  -  v  --   ----   vv vivii  v vvi   v   iii  i 
  L1M4_orf2#LINE/    678 CACTATCAA--GAA----AGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_49216818_4   1924 TATTTGCAA--CACATGCCAG-TAAAG---------------TATATAAA 1955
                                  --  i  ii v -   i ---------------        
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_49216818_4   1956 GAAATTT----GCTAAATAATAAGAGAAATACAAACAACCCAGTAGAAAA 2001
                            v i ----i  v        ---   v     i      i v?    
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAA---AAAGACAAATAACCCAATTWAAAA 818

  chr2_49216818_4   2002 ATTGGCAAAAGATATGAACAGGCAATTT---ATAGAAGATAAAATGCAAA 2048
                           v      i   v    i  i  v  i--- v        --- i    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA---TACAAA 865

  chr2_49216818_4   2049 CGATCAATAAACATGTAAAAAAAAGAAGATGTTCATCTTCAGTAGTAAT 2097
                         i ii      i  ii i    ------    i   v v   ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAA------GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (146 / 103)
Gap_init rate = 0.05 (43 / 895), avg. gap size = 3.09 (133 / 43)  


1113 28.43 6.48 1.50  chr2_49229161_49232489.rev     1679  2079 (1250)    L1M4_orf2#LINE/L1        1   421 (487)  

  chr2_49229161_4   1679 TGGAAAGCCATACTGTGTTGTGTTCATA-ATCAGAAAATTCACTATAGTT 1727
                                --   --- viii       i-  ii   i i i v   v   
  L1M4_orf2#LINE/      1 TGGAAAG--ATA---TCCCATGTTCATGGATTGGAAGACTTAATATTGTT 45

  chr2_49229161_4   1728 AA--------TTCTCCTCAAACTGATCTGTAGGTT-AACATAATTACAAA 1768
                           -------- v    i    i      ii  i  -   ii   iv v v
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_49229161_4   1769 CAAAATCCCTGAAGGATTTTTTGTAGATACAGATTAGCTGATTCTAAAAT 1818
                                  v vv vv       i   v iv  iv       i       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_49229161_4   1819 TTATATGAAAAGGTAAAGGGATTAAAACAGTCAAAATAATTTTGACAAAG 1868
                          i     i   v i  i  ivii i  i  i     i   i    v    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_49229161_4   1869 AAGAACCAAATCAGAGAACTCATGTTAACCAATTTAAAGACTTACTATAA 1918
                               v  i ii   i     iii vv       v  i        i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_49229161_4   1919 AACTGCAATAATCAAGAAAACATAACATTGGCAAAA----AGACTCATAG 1964
                          i  i  i         v iii iii i     v  ----    vi    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_49229161_4   1965 ATCTATCCA------TTTAG----CAGAA-CAGACCCACAAAATTATAGC 2003
                            v  vv ------  v  ----     -i i     i v v    i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_49229161_4   2004 TAATTAATTTTTGACAGAAAT-CTAACGTAATTCATCAGCAAAAGGATAG 2052
                         i    i     i    iiii - i  viiv     vii vi    i    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_49229161_4   2053 TATTTTTAAACAAATAGCACTGGAGCA 2079
                          v    i  -     i ii    ii  
  L1M4_orf2#LINE/    396 TCTTTTCAA-CAAATGGTGCTGGGACA 421

Transitions / transversions = 2.17 (78 / 36)
Gap_init rate = 0.03 (11 / 421), avg. gap size = 2.91 (32 / 11)  

1351 24.20 3.20 0.91  chr2_49229161_49232489.rev     2403  2840 (489)    L1M4_orf2#LINE/L1      461   908 (0)  

  chr2_49229161_4   2403 ACCTCATACCGTACACAAAAATTCTCCCAAATTGTATCATAAATCTAAAT 2452
                               i   i  i         vv i    v  v    ? i i      
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_49229161_4   2453 ATAAAACATAAAAGCTATAAAAAACTTAGACAAAAACACTAGAGAAAATC 2502
                         i   i vv     -        vv      vi      ivi ? v     
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_49229161_4   2503 TCCATGATTTT-----AGGCAAAGAGTTTTAAAACATGACATCAAAAACA 2547
                          i i   ii  -----      v iv  i v i i      i     i  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_49229161_4   2548 CAATCCATTAAAAAAAAAATGG-TAAGTTGGACTTCATCGAAATGTAAAA 2596
                            v v iv   i       i -   i            i    vv    
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_49229161_4   2597 CTTTTGTTCTATGTAAGCTACTATCAAGAGAATGAAG-GACAAACTACAG 2645
                                v  viiv i vi          i i    i-     v i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_49229161_4   2646 ATAGGGAGATAATATTTGTAAACCCTATGTCTAAAAAAGGACTTCTATCT 2695
                          vv      v        i   i v   i   i v  i      v    i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_49229161_4   2696 AGTATATATAGAGAATTCTCAAAACTCCAGAAAGAAAACAAGAAAAAAAA 2745
                           v       i    i   i v     - iv  v    --   v   v  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTC-AATAATAAAA--AGACAAATAA 806

  chr2_49229161_4   2746 TTTT-TTTAATCATGGG-AAAGAATC-----AGTCACTTCACCAAAAAAA 2788
                         iiiv-  ?  vv     -    i  i-----  v  i   v     i  i
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_49229161_4   2789 ATATAAGAATGACAAATAAGCACAACAAAACATGCTCAGCACTAAGGAAA 2838
                              vi    i v          vv    v       i  ii ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_49229161_4   2839 CA 2840
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.24 (57 / 46)
Gap_init rate = 0.02 (9 / 448), avg. gap size = 2.00 (18 / 9)  


4145 16.48 2.81 1.34  chr2_49233355_49235165      501  1319 (492)    L1M4_orf2#LINE/L1       78   908 (0)  

  chr2_49233355_4    501 ATTTAATACAATTTCTATCAAAACGCTAGCTGCTTTTATTTTTCTTGGCA 550
                            i  ii    ii         iv i      i   ---   ----   
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT---TTT----GCA 120

  chr2_49233355_4    551 GAAATTGAGAAGTTGATTCTAAAATTTACAAAAATATGCAAGAAACCCAT 600
                                 v   i    i        i i vii v       ii     v
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr2_49233355_4    601 AATGGTCAAAATAATTTTGAAAAAGAG---CAAAGTTG-AGGACTCATAC 646
                            i i     i   i          i---        -        i  
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_49233355_4    647 TTCATGATTTCAAAATTCACTACAGAGCTACAGTAAT-AAGA---TGTGG 692
                            vii         i i      i            -    ---     
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_49233355_4    693 TAGCAGTGGCACAAAGACAAACATATAAGTCAATGGAATAGAATTGAGAG 742
                           - --     i  i  i i       ii                     
  L1M4_orf2#LINE/    271 TA-C--TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_49233355_4    743 TCCGGAAATAAGCCCATCCACTTATGGGTAACTGATTTTTGACAAGGGTG 792
                            i       i     v  i      vi  i       i          
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_49233355_4    793 --ATGACATTTTAATAGGGGAAAGAATAGTCTTTTGAATAAATGGTGCTG 840
                         -- v   vv  i   -                   v  i           
  L1M4_orf2#LINE/    368 CCAAGACCATTCAAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_49233355_4    841 GGACAACTAAATAGGCACATTCAGAAGAAGGAAATTGAATCCCTACCTCA 890
                                 ii   ?v     v  i     v   i   i i          
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_49233355_4    891 CATCGTTTGTAAATATTAACTCGAAATTGATTAAAGATCAAATTGTAAGA 940
                           i i v ii   v        i    v   i ?   i v  v       
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_49233355_4    941 GCTAAAACTATAAAACTTTTTGAAGAAAATATGAAAGTAAATATATGTGA 990
                                          i  v        i  iii?      v vi    
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_49233355_4    991 CCTTGGATTAGTCAATTGTTTCTTAAATATGATGCCCAAAGCATAA---A 1037
                               i    v    v        i      ii  v      i  --- 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_49233355_4   1038 CAAAAGAAAAAGTAGATACATTGGACTTAATCAAAATTAAAAATATTTGT 1087
                                    i      v         v              iv     
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_49233355_4   1088 GCATCAAAAGACACTACCAAGAAAGCAAAAAGACAACCCACAAAAT---- 1133
                           v     i       i        ii               i   ----
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_49233355_4   1134 -AAAATATTTGCAAATCATGTATCTGAGAAAGGTCTTTTATCAAGAATAT 1182
                         -                  i       v  i  v   v    v       
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_49233355_4   1183 ATGAAGAACTGGTACAACCCAACAACAAAGGGACAA----CCCAGTTTTA 1228
                           i       vv      i   i  i   ii     ----    i  ?v 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_49233355_4   1229 AAATGGGTGAAG-ATTTGAAAATATATTTCTCCAGTAAAGATATACAAAT 1277
                                ii   -       v v i         ivi             
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_49233355_4   1278 AGCCAATAGACATATGAAAAGATGCTCAATATCATTAGTCAT 1319
                         i       ii  i                i    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.27 (91 / 40)
Gap_init rate = 0.02 (14 / 831), avg. gap size = 2.43 (34 / 14)  


3025 28.24 1.11 0.55  chr2_49271678_49273616      545  1447 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49271678_4    545 TGGAAGAACATTCCATGCTCATACATAGAAAGAATCAATATCATCAAAAT 594
                              ii i  i     i    iv  v i    v i     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49271678_4    595 GGCCATGCTGCCCGAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 644
                            v  i  v   i iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49271678_4    645 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 692
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_49271678_4    693 TATGGAACCAAAAAAGAGCCCTCATTGCCAAAACAATCCTAAGCAAAAGG 742
                                viiv  ii  v  vvv  v            i i iv  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_49271678_4    743 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTATAAGGC 792
                                i      vv       v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_49271678_4    793 TACAATAACCAAAACAGCACGGTACTGATACCAAAACAGAGATATAGACC 842
                             i   i   i    iii       ii iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_49271678_4    843 AATGGAACATAAC--AGAGCCCTCAGAAATAATACCATACATCTACAACC 890
                                i v  i--    i  --        vv        i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_49271678_4    891 ATCTGATCTTTGACAAACCTGACAAAAAAAAGCAATGGGGAAAGGATTCC 940
                          vi    i  i     ivv  v   i vv vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_49271678_4    941 CTATTTAATAAATGGTACTGGGAAAATTGGCTAGCCATATGTAGAAAGCT 990
                           v  i  i       i      v  i   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_49271678_4    991 GAAACTGGATTCCTTCCTTACACCTTATACAAAAGTTAATTCAAGATGGA 1040
                            ii    ii   v   i     v         i    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_49271678_4   1041 TTAAAGGCTTAAATGTTAGATGTAAAACC-TAAAAACCCTAGAAGGAAAC 1089
                          i ?  i i       v   vv      i-     vi i      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_49271678_4   1090 CTAGGCA-ATACCATTAAGACCACAGGCATGGGCAAGGGCTTCATGACTA 1138
                         v    ?i- v i v iiv    vii  i- i     v  i   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr2_49271678_4   1139 AAACACCAAAAGCGATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1188
                         vi           ivvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_49271678_4   1189 ATTAGACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGAA 1238
                           i i v v  i i   i  iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_49271678_4   1239 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGATA 1288
                         v  i     i                 v   i   vii ivi        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_49271678_4   1289 AAGTGCTAATATCCAGAATCTACCAAGAACTTAAACAAATTTACAAGAAA 1338
                          i vi  vi          v  iv       ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_49271678_4   1339 AAATCAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1384
                           iv   ----   v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_49271678_4   1385 CTCAAAAGAAGACATTTATGCAGCCAACAGACACAAGAAGAAATGCTCAT 1434
                            v        i  vi viii     i ii    v   i i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_49271678_4   1435 CATCACTGGCCAT 1447
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (158 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2899 27.06 2.93 0.56  chr2_49319569_49324488.rev     3543  4429 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49319569_4   3543 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATCAAAAT 3592
                               i i  i     i        v      v i     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49319569_4   3593 AGCCATACTGTCCAAAGTAATTTATAGATTCAATGCTATCCCAGTCTAGC 3642
                         i  v     vi     v i  i  i        i  v     vi  v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49319569_4   3643 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 3690
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_49319569_4   3691 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAGTCCTAAGCAAAAAC 3740
                                viiv  ii  v  viv        i   i  i i iv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_49319569_4   3741 AACAAAGCTGGAAGCATCACACTACCTGACTTCAAACTATACTATAAGGC 3790
                                i    i vv       v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_49319569_4   3791 TACAGTCACCAAAACAGCATGGGACTGGTACCAAAACAGAGATATAGACC 3840
                               v i   i    ii   v     i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_49319569_4   3841 AATGGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 3890
                                i     v   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_49319569_4   3891 CTGATCTTTCACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT--TCC 3938
                         i    i  iv    ivv  v   i v  vv            i  --  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chr2_49319569_4   3939 ATATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATCCGGAAAGCT 3988
                         - v  i  i          i   v      v  ?   i  v ii  iiv 
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_49319569_4   3989 GAAACGGGATCCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGGA 4038
                            iiv   i    v   i     v  i                i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_49319569_4   4039 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4088
                          i ?    i           v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_49319569_4   4089 CTTGGCA-ATACCATTCAGGACATATGCATGGGCAAAGACTTCATGACTA 4137
                         v v  ?i- v i -   iv   v vv vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_49319569_4   4138 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTG 4187
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_49319569_4   4188 AATAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 4237
                          vi   v v  i     i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_49319569_4   4238 CAGGAAACCTACAGATTGGGAGAAAATTTTTGCAATCTATCCATCTGACA 4287
                         v  iv    i     v           v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_49319569_4   4288 AATGGCCAATATCTAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 4337
                          iv i ivi    i     v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_49319569_4   4338 AA--------ACCCCATCAAAAAGTGGGCAAAGGACATGAACGGACACTC 4379
                           --------    v  i?    i           iv    ii    i i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_49319569_4   4380 CTCAAAAGAAG------------CCAGTAAACATACGAAAAAA-GCTCAT 4416
                            v       ------------   i   i  i i     i -     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_49319569_4   4417 CATCCCTGCTCAT 4429
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.10 (31 / 10)  


2953 26.94 0.97 3.12  chr2_49348196_49354485     4871  5798 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49348196_4   4871 TGGAAGAACCTTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4920
                              ii iv i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49348196_4   4921 GGCCATGCTGCCCAAAGTAATTGATAGGTTCAATGCCATCCCCATTAAGC 4970
                            v  i  v      v i  iv i  i     i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49348196_4   4971 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACTACTTTCACATGTA 5019
                          v   iivi i  i  ii     -   --- v  i  iv ii------  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCC------TA 141

  chr2_49348196_4   5020 ACTATTTCATTTGGTTAATAT--GGAACCAAAAAAGAGGCCACATTGCCA 5067
                          -- v     v   v-   ii--  i   v i  ---------- v    
  L1M4_orf2#LINE/    142 A--AATTCATATGGA-AATGCAAGGGACCCAGAA----------TAGCCA 178

  chr2_49348196_4   5068 AGACAATCCTAAGCAAAAAGAACTAAGCTGGAGGCATCACACTACCTGAT 5117
                          i      i i iv  i      v   i      vv       v  ii  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr2_49348196_4   5118 TTCAAACTATATTACAAGGCTACAGTAACCAAAATAGCATGCTACTGGCA 5167
                               viv  i     i          i   i i  ii  v        
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_49348196_4   5168 CCAAAACAGAGATATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAA 5217
                         iv ii i   v       i        i    iv   ivii         
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_49348196_4   5218 CACCACACATCTACAACCCCCTGATCTTTAACAAATGTGACAAAAACAAG 5267
                         vv   i    i  iiii vvi    i  ii    iv   v   i v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_49348196_4   5268 AAATGGGGAAAGGATTCCCTGTTTAATAAATGGTGCTGGGAAAACTGGCT 5317
                         v           i  vvi  v  i  i              v      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_49348196_4   5318 AGCCATATGTAGACAGCTGAAACTGGATCCGTTGCTTGCACCTTGTACAA 5367
                          ?   i   i i viiv    ii    i  v vv  ii    v i     
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_49348196_4   5368 AAATTAATTCAAGATGGATTAAAGACTTAC-TGTTAGACCTAAAACCATA 5416
                                i    i      i ?    i  v-   v   v       i   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_49348196_4   5417 AAAACCTTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGG 5465
                            vi             v    ?i- v i -   iv   v -----   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT-----TGG 572

  chr2_49348196_4   5466 GCAAGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCG-CAAAA 5514
                          iv   -   v ii   v ivv  vi            vvi  i-     
  L1M4_orf2#LINE/    573 GTTAGG-CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_49348196_4   5515 GCCAAAATAGACAAATGAGATCTAATTAAACTAAAGAGCTTCTGCACAGC 5564
                          vv        i    vi  ii v  i   v v  i i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_49348196_4   5565 AAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGGAAA 5614
                            i  v    i  vv i      v  i     i            i   
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_49348196_4   5615 TTTTTGCAATCTACCCATCTGACAAAGAACTAATATCCAGAATCTGCAAA 5664
                          v       vii ivi      i  i i   vi          v ii   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_49348196_4   5665 GAACTTATACAAATTTACAAGAAAAAAAT---CAACCCCATCAAAAAGTG 5711
                              iv     v iv i  v     i i---i     v  i?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_49348196_4   5712 GGTGAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCA 5761
                           ii      v    i     i     v        i  vi viii    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_49348196_4   5762 ACAGACATGTGAAAAAATGCTCATCATCACTGGTCAG 5798
                          i ii  ii      i       v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (151 / 95)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.71 (38 / 14)  


2947 26.72 1.77 1.11  chr2_49381692_49386862     3778  4679 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49381692_4   3778 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATCAATATCTGG-ATAA 3826
                               i    i     i        v      v i     -  v- vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-TGTTAAGA 49

  chr2_49381692_4   3827 TGGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTTTCCCCATCAAT 3876
                             v     v      v i  i  i       ii  vv    i     v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_49381692_4   3877 CTACCA-CTGACTTTCTTGACAGAATTGGAAAACCCTACTTTAAAGTTCA 3925
                         v v   -   v    i   -     v v  v  v iv iii    i    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_49381692_4   3926 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAA 3975
                                viiv  ii  v  v v  v     i      i i i-   i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAA 197

  chr2_49381692_4   3976 GAACAAAGCTGGAGGAATCATGCTAGCTGACTGAATTCAAACTATACTAC 4025
                                 i       v   ii  vv ii i --- iv     -      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATT---TCAAAACT-TACTAC 243

  chr2_49381692_4   4026 AAGGCTACAGTAACCAA-ACAGCATGGTACCGGTACCAAAACAGATATAT 4074
                           i          i   -    ii      i  i iv ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_49381692_4   4075 AGACTGATGGAACAGAACAGAGGCCTCAGAAATAACACCACAGATCTACA 4124
                            iii      i    iv   ivii         vv   i v  i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_49381692_4   4125 ACCATCTGATCTTTGACAAACCTGACAAAATAAA-AAATGGGGAAAGGAT 4173
                         ii  vi    i  i     ivv  v   i iv v-v           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_49381692_4   4174 TCCCTATTTAATAAATGGTGCTGGCAAAACTGGCTAGCCATATGTAGAAA 4223
                         vvi  v  i  i            v v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_49381692_4   4224 GCTGAAACTGGATCCCTTCTTTACACCTTATCCAAAAATTGACTTCAGAT 4273
                         iv    ii    i    v i i     v   v        i   iv i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_49381692_4   4274 GGATTAAAGACTTAAATATAAGA-CTAAAACCATAAAAACCCTAGAAGAA 4322
                             i ?    i     i     -       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_49381692_4   4323 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 4371
                            v    ?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_49381692_4   4372 CGGAAACACCAAA----CAATGGCAACAAAAGCCAAAATAGACA--TGGG 4415
                         vvivi        ----   --          vv        i -- v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_49381692_4   4416 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAGCAGA 4465
                          ii v  i   v v  i i   i  ii vv    i  v       iv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_49381692_4   4466 GTGAACAGGCAACCTACAGATTGGGAAAAAAGTTTTGCAATCTATCCATC 4515
                              v  i     i     v     i    vv       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_49381692_4   4516 TGACAAAGGGCTAATATCCGTAATCTACAAGGAACTTAAACAA---AATT 4562
                            i  i  i  vi     iv   v  i  i     ivv    ---   v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_49381692_4   4563 AGAAGGAAA-AAACAACCCCATAAAAAAATGGGTGAAGGATATGAACAGA 4611
                          v  ii i -   i     v  v?         ii      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_49381692_4   4612 CACTTCTCAAAAGAAGACATTTATGCAGCCAATGAACTTACGAAAAAATG 4661
                           i     v        i  vi viii      i i vi i     i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_49381692_4   4662 CTCATCATCACTGTTCAT 4679
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.53 (26 / 17)  


2566 25.67 11.19 0.73  chr2_49436766_49443094     5016  5837 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49436766_4   5016 TGGAAGAACATTCCATGCTCATGGACAGGAAGTATCAATATTGTGAAAAC 5065
                              ii i  i     i       iv     vv i        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49436766_4   5066 AGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATTCCCATCAAGC 5115
                         i  v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49436766_4   5116 TCC-AACTGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TGAAGTTC 5162
                            - i   v    i  -i     -   -- v  i   v i- i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_49436766_4   5163 ATGTGGA------------------------------------------- 5169
                           i    -------------------------------------------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_49436766_4   5170 -------------------------------------------TACAAGG 5176
                         -------------------------------------------     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_49436766_4   5177 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACTCAC 5226
                                  i   i    ii         i iv ii i   v   ivv i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_49436766_4   5227 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGTCAGACATCTACAAC 5274
                                 i    i--    i  --        vvi  v    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_49436766_4   5275 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAGGGATTC 5324
                         i vi    i  i     ivv  vv  i v  vv          i i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_49436766_4   5325 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5374
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_49436766_4   5375 TGAAATTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5424
                             i     i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_49436766_4   5425 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5474
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_49436766_4   5475 CCCAGGCA-ATACCATTCAGGATATAGGCATGGGCAAGGACTTCATGACT 5523
                          vi   ?i- v i -   iv  iv v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_49436766_4   5524 AAAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCT 5573
                          vi            vvi     v    vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_49436766_4   5574 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5623
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_49436766_4   5624 ACAGGTAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5673
                          v  ii    i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_49436766_4   5674 AAAGGGCTAATATGCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 5723
                           i  i  vi   v      v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_49436766_4   5724 AAAAACAAACAACCCCATCAAAAATTGGGCAAAGGAAATGAACAGACACT 5773
                            i     i     v  i?    v           vv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_49436766_4   5774 TCTCAAAAGAAGATATTTATGCAGCCAACCAACACATGAAAAAATGCTCA 5823
                             v           vi viii     iv i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_49436766_4   5824 TCATCACTGACCAT 5837
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (122 / 85)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 9.80 (98 / 10)  


3261 27.57 0.55 0.00  chr2_49450472_49456123     4258  5160 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49450472_4   4258 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCATGAAAAT 4307
                              ii i  i     i      i v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49450472_4   4308 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4357
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49450472_4   4358 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 4402
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_49450472_4   4403 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAATAGAA 4452
                              viiv  ii  v  v v  v     iv     i i ivv iv    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_49450472_4   4453 CAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGGCTA 4502
                              i      vv   vi  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_49450472_4   4503 CAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGACCAA 4552
                               i   i    ii         i i  ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_49450472_4   4553 TGGAACAGAACAGAGCCTTCAGAAATAATGCCACATATCTACAACTATCT 4602
                              i    iv   vv i         vv   i i  i  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_49450472_4   4603 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 4652
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_49450472_4   4653 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 4702
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_49450472_4   4703 CTAGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGATTAA 4752
                         i i  i    v   i i   v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_49450472_4   4753 AGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 4802
                             i       v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_49450472_4   4803 GCATTACCATTCTGGACATAGGCATGGGCAAGAACTTCATGTCTAAAACA 4852
                          ?i v viv   vv   v v  vv i     viii   v ivv  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_49450472_4   4853 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATTTAATTAA 4902
                                  vvi          vv     v  i    v   i  v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_49450472_4   4903 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 4952
                          v v  i i   i  ii vv    i  v    i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_49450472_4   4953 AACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTAACAAAGGG 5002
                             i                 v       vii ivi    i i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_49450472_4   5003 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAATC 5052
                           vi          v  i  v      vv    v iv i  v     iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_49450472_4   5053 AAACAATCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAA 5102
                            i  i  v  i?    i     i      v    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_49450472_4   5103 AAGAAGACATTTATGCAGCCAAAAGACACATGAAAGAATGCTCACCATCA 5152
                                i  vi viii     v ii         ii       v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_49450472_4   5153 CTGGCCAT 5160
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.50 (5 / 2)  


3493 19.68 5.57 2.28  chr2_49464347_49466661      945  1823 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49464347_4    945 TAAAAAGATATCCTATGTTCATGGGTTGAAA-ACTTTGTATTGTTAAGAT 993
                          ii          i          i   i  -    vi            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49464347_4    994 G----------TCAAAGCAATCTACAGATTCAATGCAATCCCTATTGAAA 1033
                          ----------i    vii              i           ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49464347_4   1034 TCCCAAC--ATTTTCTTGGAGAAATAG-CACACTTCATTCCAAAATTTGT 1080
                              i --vi   i   v      v -  vi  v-  i i      ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chr2_49464347_4   1081 ATGAAATCTCAAGGGACTTCAAATAGCTAAAACAATCTTGAAAAAGAA-- 1128
                            i  viv        iivi      i                    --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_49464347_4   1129 -TAAAGTTGGATTACAAATACTTCTAGATTTCACAATTAAGTGTTAAGCT 1177
                         -i         vv  vv i     ivi      v  i v v iiv     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_49464347_4   1178 AAAGTAATCAAAACAGTGTGGTTTTAACATAAAGATAGACATATA----- 1222
                          v         i          vi ii     i            -----
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_49464347_4   1223 -TGCAAATAAAATAGAAAATCCAGAAATTGACCC-T-CATTGCGTATGGT 1269
                         -  -i    i   v  i i         vi    - -    ---      
  L1M4_orf2#LINE/    300 ATG-GAATAGAATTGAGAGTCCAGAAATAAACCCATACATT---TATGGT 345

  chr2_49464347_4   1270 TGAATGTTTTATTGACAACGGTGCCA-GAC---TCAACAGAGAAATTATA 1315
                         ii v  v   - i     v       -   ---    ii i    vv   
  L1M4_orf2#LINE/    346 CAATTGATTT-TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_49464347_4   1316 CCCTTTTCAATAAATGGTGCTGGGAAAAATGGAAATCCATATGCAAAAGA 1365
                         vi        i              v  v    v ?   i          
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_49464347_4   1366 ATG------GACCTTTATATACAAACT-TATACAAATATTAACTCAAAAT 1408
                            ------    ii  iv -  v  i-        v             
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCT-CACACCATATACAAAAATTAACTCAAAAT 493

  chr2_49464347_4   1409 GTATCAAAGACATAAGTGTAAAAGCTACAACTATAAAACT-TTAGAAGAA 1457
                          v    ?    v   i     i     v            -         
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_49464347_4   1458 AGCATA----TAAGAGCTTTTTGACATTGGATTTGGCAATGATTTCTTGA 1503
                          i    ----   - v   iv    v    i  v       i      ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_49464347_4   1504 CTATGACACCAAAG--ATAGGCAACCAAAGGAAAAATAAACAAATCAGAC 1551
                         v            i-- i i     v    i       i i    ii   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_49464347_4   1552 TTCACCAAAATCTAGATTTTTTTTTTTTTGCATCAAAAGACACTATCAAC 1601
                             i      iv i vi    v -----  v     i           v
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGT-----GCTTCAAAGGACACTATCAAG 687

  chr2_49464347_4   1602 AGAGTAAAAATGCAACCCACAGAATGGGAGGAAATATTTGCA--TCAGAT 1649
                          i   i    vi                  i           --   v  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_49464347_4   1650 GTCTGGCAAGGGATTAATATGTAGAATATATGCAGAACTCTTAAAATTCG 1699
                         i    ii      i vi   vi         iv          v  i  i
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_49464347_4   1700 ACAACAATAAAACAA----CCCAATTTATAAATAGGCAAAAGACCTAAAG 1745
                          i  i  v  i    ----       ? v    i      i  ii i  v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_49464347_4   1746 AAACATTTATCCAGAGAATGTGTACAGATAGCTAATAAGCACATACAAAA 1795
                          i      v    i    vi i    i  i  i           iv   i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_49464347_4   1796 TATTAATATGCTCAGCCTCACAGATATT 1823
                         -------       i v   ????????
  L1M4_orf2#LINE/    888 -------ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (108 / 62)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.76 (69 / 25)  


 815 22.35 0.59 0.00  chr2_49525956_49530478      332   501 (4022)  C L1M4_orf2#LINE/L1   (396)   512   342  

C chr2_49525956_4    501 TAGCCAATTGATTTTCAACAAACTTGTCAGGAATACACATTGGGGAAAAG 452
                          i i            i    ivv  i  i  vi iv  v        ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

C chr2_49525956_4    451 ACAGTCTTTTCCATAAATGATGCTGGGAAAATTATATAACCACATGCAGA 402
                          i         v i     i        v  i iv   ?         i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

C chr2_49525956_4    401 AGGATGACATTAGACCCCTAACTCTGACCATATACAGAAATCAACTCAAA 352
                           i    vi  i        v   vv          i    i        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

C chr2_49525956_4    351 ATG-ATTAAAGAGTTAAATGT 332
                            -  i ?   vi       
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGT 512

Transitions / transversions = 1.77 (23 / 13)
Gap_init rate = 0.01 (1 / 171), avg. gap size = 1.00 (1 / 1)  

2905 25.98 2.91 1.23  chr2_49525956_49530478     3139  4031 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49525956_4   3139 TGGAAAGACATTCCATGTTGATGGATAGGAAGA----ATATTGTTAAAAT 3184
                                 i  i       v      v      ----          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49525956_4   3185 GGCCATATCACTCCAAGCAATTTACAGATTCAATGCTACTGCTATCAAAC 3234
                            v   iiv i v  vii  i           i  v iiv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49525956_4   3235 TACCAATGACATTCTTCCCAGAA-CTG-CAAATATCT-ATTTTAAAATTC 3281
                          v   iivi v  i  iv     -i  -   i---  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_49525956_4   3282 ATATGAAACCAAAAAGAGCCTA-AATAGCCACGTTAATCCTAACCAAAAA 3330
                              i  viiv  i ii  i -        vivi    i i vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_49525956_4   3331 GAACAAAGATGGAAGTATCACATTACCCGACTT-AAAACTATACTACCGG 3379
                                 v    i vv     i v   i i  -      -      vii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr2_49525956_4   3380 GACACAGTAACCAAAACAACATGGTACTGGTACAAAAACAGATACATAGA 3429
                          vi       i   i   iii         i i  ii i   i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_49525956_4   3430 CCAATGGAACAGAAATGACAGACCAGAAATAATGCCACACACCCACAACC 3479
                         i        i    v   v  v          vv   i   iii iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_49525956_4   3480 ATGAGATCTCCAACAAAACTGACAAAAACAAGCAATGGGGAAAGGACTCC 3529
                          vvv   i i i    iiv  v   i v  vv            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_49525956_4   3530 CTATTCAATAAATGGTGCTGGGATAAATGGCTAGCCATATACAAAAGATT 3579
                           v     i              i  v   v  ?   i  i       v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_49525956_4   3580 GAAACTGGACCTCTTCCTTACATCATATACAAAAATCAACTCAAGATG-A 3628
                            ii      i  v   i   i             i       i   - 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_49525956_4   3629 TTAAAGACTTAAATGTAAAACACAAAACTATAAAATCCTTGGAAGACAGC 3678
                          i ?    i         i vvi            ii   i     v i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_49525956_4   3679 CTAGG---AAAT----ATCATTTTGGACATAAGAAATGACGAAGGTCTCA 3721
                         v    ---    ----i v ii    ii-  i v    ------  i  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATG------GTTTCT 589

  chr2_49525956_4   3722 TGATTAAGACGCCAAAAGTAATTGCAACAAAAGCAAAAATTGGCAAATGG 3771
                          iiv  v   i       i vvv          v      v ii    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_49525956_4   3772 GATCTAATTAAACTAAATAGCTTCTGTACAGTAAAAGAATCTATCAACAG 3821
                           ii v  i   v v  v i   i   i vvi   i  vv       v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_49525956_4   3822 AGTAGACAGACAACCTACAGAATGGGAGAATATATTTGCAAACTATGTAT 3871
                            ii v        i              v           ii  i   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_49525956_4   3872 CTGATAAAAGTCTAATATCCC-----TATAAGGAACT--TA-AACACACT 3913
                                ii v  vi     v-----     i     --  -   v  v 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_49525956_4   3914 TATAAGCAAA-AAACAACTCCATTAAAAAGTGGGCAAAGTACATGAACAG 3962
                         v    iv i -   i   i v   ?    i         v iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_49525956_4   3963 ACACTTTTCAAAAGAAGACATATATCCATCCAACAATCATAAGAAAAAAA 4012
                            i  i  v        i   i vviiv    i  v  i v     i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_49525956_4   4013 GCCCACTATCACTGATTAT 4031
                           i  vi    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.18 (37 / 17)  


2988 27.45 0.88 0.77  chr2_49619261_49625020     4362  5268 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49619261_4   4362 TGGAAGAACATTCCATACTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4411
                              ii i  i    ii      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49619261_4   4412 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4461
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49619261_4   4462 TACCAATGACTTTCTTCACAGAT-TTGGAAAAAACT-ACTTTAAAGTTCA 4509
                          v   iivi i  i  ii    v-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_49619261_4   4510 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 4559
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_49619261_4   4560 AACAAAGTTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4609
                                       vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_49619261_4   4610 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACTCACC 4659
                                 i   i    ii         i iv ii i   v   ivv i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_49619261_4   4660 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 4707
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_49619261_4   4708 ATCTGATCTTTCACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4757
                          vi    i  iv    ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_49619261_4   4758 CTATTTAATAAATGGCTCTGGGAAAACTGACTAGCCATATGTAGAAAGCT 4807
                           v  i  i      iv      v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_49619261_4   4808 GAATCTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4857
                            vi    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_49619261_4   4858 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAAACCCTAGAAGAAAA 4907
                          i ?    i  v    v   v       i      v-i i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chr2_49619261_4   4908 CCTA--CGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 4955
                          v  --? i  - i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_49619261_4   4956 TAAAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATC 5005
                           vi            vvii         vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_49619261_4   5006 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTG 5055
                          v  i   v v  i i   i  ii vv    i  v  i i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_49619261_4   5056 AACAGGCAAACTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 5105
                           v  i   v i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_49619261_4   5106 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTAGAAGA 5155
                         i  i  i  vi          v  i         vv    v iv v  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_49619261_4   5156 AAAAAG--AACAACCCCATCAAAAACTGGGCAAAGGATATGAACAGACAC 5203
                             ii--  i     v  i?    v            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_49619261_4   5204 TTCTCAAAAGAAGACATTTATGCAGACAAAACACACATGAAAAAATGCTC 5253
                              v        i  vi viii v   v vi          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_49619261_4   5254 ATCATCAGTGGCCAT 5268
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3246 26.59 0.77 0.99  chr2_49631894_49636149     2855  3764 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49631894_4   2855 TGGAAACATATCCCATGCTCATGAATCAGAAGAATTAGTATTGTTAAAAT 2904
                               v          i     i  ii     v   i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49631894_4   2905 GGCCATAGTAATCAAAATAATCTACAGAAGCCATGCAATCCCTGTTAAAT 2954
                            v   v vvi    v i         vv v i         i i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr2_49631894_4   2955 ATCT--ATCACGTTTTTTCACAGAAATAGAGAAAACAATTCCTAAAACTT 3002
                            i--iiii v      -i       v  v  ivii  -       i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGAT-CCTAAAATTC 147

  chr2_49631894_4   3003 GTGTGGAACCCACAATGATCTCA-AATAGCCAAAGCAATACTGAGCAAAA 3051
                         i i     vi-i   v iv i  -          i    vi   iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_49631894_4   3052 AGAATAAAGCTGGAGGCATTTCACCACTTGACTTCAAAATATACTATAAA 3101
                             i    i      vv iv   iv iii i       iv     i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_49631894_4   3102 GCTGTAGTAACCAAAACAACATGGTACTGGCATAAAAGCAGACACATAGA 3151
                            ii     i   i   iii              iiii     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_49631894_4   3152 CCAAAAAAACAACCGAATAGAAAATCCATAAATAAATTCATATATTTACA 3201
                         i   vii  i ---    v  i i    v       ii    i     ii
  L1M4_orf2#LINE/    297 TCAATGGAATA---GAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_49631894_4   3202 GCCAACTGATTTTTGGCATAGGAACCAAGAACATACATTGGGAAAATGAC 3251
                          i   i       i i  vi  vi      v   v  v    i   vi i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_49631894_4   3252 ACCCTCTTCAATAAATGGTACTGAGAAAACTGAATATGCATTTGCAGAAG 3301
                          vi  i     i       i   i  v     i   ?v  iv    i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_49631894_4   3302 AATGAAATTAAGCCTCTATCATTTACCATATACAAAAGTCAATTCACAAT 3351
                               i  iii  i   i vivi             i i  i   v   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_49631894_4   3352 GGATTAAAGACTTGAACATAAGATCCAAATCTATAAAATTACTAGAAGAA 3401
                             i ?    i i  ii     v i   v        i vi        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_49631894_4   3402 AACATAGTGGGAATACTCCAGGATATTGGTCTAGGGAAGGATTTTATGGC 3451
                                v? v  vv  i iv  iv    vi    v  v i   iv i v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_49631894_4   3452 TAAGACTTTAAAAGAACAGGCAACAAAACCAAAAATGGACACATGGGTGC 3501
                           v   vii     v   i         vv      i  i v  v  -i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG-AC 642

  chr2_49631894_4   3502 ATTTATGAAACTAAAAAGCTTCTGCACAGTGAAGGAAACAATCAACAACG 3551
                         -  i  v   v v    i   i  ii vvii     v  v     v  v 
  L1M4_orf2#LINE/    643 -TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_49631894_4   3552 TGAAGAGATAACCACTAGAATGAAAGAAAATATTTGCAAACTATTAATTC 3601
                             i   i    vvi      ii                ii  vv  ii
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_49631894_4   3602 AACAAAGAACTAATATATAGAATATTCAAGGAACTT----AAATCAACCA 3647
                         i i  i i   vi   vi       vi  i     i----  v    iv 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_49631894_4   3648 CAAAAATACAAATTATTCCATTAAAAAGTGGGCAACAGATTTGGATAGGC 3697
                         i     v      v ii v   ?    i       vi      i    i 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_49631894_4   3698 ATTTCTCAAAAGAAGATATACAAATGGCCAACAGGTATATGAAGAAATGT 3747
                                v                       i i i i     i i   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_49631894_4   3748 TCAACATCAGTAATCAT 3764
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (154 / 84)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2556 27.96 2.68 1.12  chr2_49784965_49787450.rev     1101  1994 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49784965_4   1101 TGGAAAAAC-TTCCATGCTCAGGGACTGGAAGAAAAAATATCATTGAAAT 1149
                               i i- i     i   v   i       vvv     ii  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49784965_4   1150 GTCCATACTGTCCAAAGCAACCTACAGATTCAATGCTATTCCTATCAAAC 1199
                          v v     vi     vii i            i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49784965_4   1200 TACCAATATCAATTTTCACAGAATTAGAAAAAAAACT-ATCCTAAA-TTC 1247
                          v   iivv vv    ii     v v  v  i---  -        -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_49784965_4   1248 ATATGGAA-TGAAAAAAGAGTCCA-AATAGCCAAAGCTATCCTAAGCAAA 1295
                                 -  v  i-- iii   -          i v   i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_49784965_4   1296 AAGAATAAAGCCAGAGGCATCACATTACCCAATTTCAAAATATACTATAA 1345
                              i    iii    vv     i v             iv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_49784965_4   1346 AGCTACAATAACAAAAACAGCATGGTAATAGAACAAAAACAGACACATAG 1395
                                i   iv  i    ii     v i v i  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_49784965_4   1396 -CCAATGGAACAGAATGGAAAAAGTC-AGAGGTGA---CATAC--CTACA 1438
                         -i        i     v  i --   -   ii i ---     --i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGA--GTCCAGAAATAAACCCATACATTTATG 343

  chr2_49784965_4   1439 GCCTTCTGATTGTTGATAAAGCCAACAAAAATAAGCAATGGGGAAATGAC 1488
                          i vvi     v i  i  i viiv   i vi vv           vi i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_49784965_4   1489 --TCCATATTCAATAAATGGTGCTGGGACAGCTGGCTAGCTAAATGCAGA 1536
                         --  -- v     i                i    v  ? i v     i 
  L1M4_orf2#LINE/    394 AGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_49784965_4   1537 AGAATAAAACTAGATCTCTACCTTTCACCATATACAAAAATTAACTCAAG 1586
                              i  ii i  i i      iv                        i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_49784965_4   1587 ATGAATTAAAGATTTACATGTAAGACCTCAAACTGTAAGAATCCTAGAAG 1636
                            i  i ?   ii  v        v  v     i   i v  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_49784965_4   1637 AAAACCTAAGAAGCACTATTCTGGGCATTGGCCTTAGGAAAAAAATTAT- 1685
                              v  i ?ivv v v   vv i v    v-     v  viiv  v -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTT 590

  chr2_49784965_4   1686 GGTTAAGTCCTTAAAAGCAATAGCAACAAAAACAAAAATTGTTAACTGGG 1735
                         i v  v v vii       vv          iv      v v   v v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_49784965_4   1736 ACCTAATTAAGCTAAAGAGATTCTGCACAGCAAGAAAAATAATCAACAGA 1785
                           i v  i  iv v  i iv  i  ii vv   iii v iv     v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_49784965_4   1786 GTACAGAGGCAACCTATAGAAGGGGAAAACATATTCACAAACTGTGCATC 1835
                           iv i  i     i i    v    i  v     ii    iii ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_49784965_4   1836 CAACAAAGGTATAGTATCTAGAATCTTTAA-GAA--------ACTTAATA 1876
                         ii i  i  vv v     i     v v   -   --------   i    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_49784965_4   1877 AGCCAAAAACAAGTAAACCCTTTAAATAGTGGGGAAAAGACATGAACAGA 1926
                          vvv   i    i   v  vv  ?  v i    v   i  iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_49784965_4   1927 CACTTGTCAAAAGAAGAGACACATGCAGCCAACAAACGTAAGAAAAAAAG 1976
                           i  v  v        v i   viii     i  i ii v     i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_49784965_4   1977 CTCAGCATCACTAATCAC 1994
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.89 (34 / 18)  


 357 28.16 5.83 0.00  chr2_49822739_49825051      551   653 (1659)    L1M4_orf2#LINE/L1        1   109 (799)  

  chr2_49822739_4    551 TAGAATAACATTCCATGCTCATGGATTGGAAGAATCAATATTGTTAAAAT 600
                          i   vi i  i     i               v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49822739_4    601 AGCCATATTGCCTGATATGGTTTG--GCTTTGTC----TCCCCACCCAAA 644
                         i  v   i v  ii vv  i i i-- v  iiv ----    i i v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49822739_4    645 TCTCACCTG 653
                           i  v   
  L1M4_orf2#LINE/    101 TCCCAGCTG 109

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.02 (2 / 109), avg. gap size = 3.00 (6 / 2)  

2362 27.03 2.06 2.86  chr2_49822739_49825051      949  1821 (491)    L1M4_orf2#LINE/L1       43   908 (0)  

  chr2_49822739_4    949 GTGAAAATGTACTAATACACAGCACAAAACAATTTATAGATGAAATGCTT 998
                           v  i   -i -     v -- v    vii  i  i    vv  i  vv
  L1M4_orf2#LINE/     43 GTTAAGATG-GC-AATACTC--CCCAAATTGATCTACAGATTCAACGCAA 88

  chr2_49822739_4    999 TTTCTATTAAATTGCCAAGGTAA-TTTTTCACAGAA--TAAAAAGCAACT 1045
                          ii    i   v v   - v iv-     ii     -- i v    vi--
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTG-- 135

  chr2_49822739_4   1046 ATCCTGTAATTCATATGGAACCAAAAAAGGGCCTGCATAGCCAAAGCAAT 1095
                              iv             viiv  ii iv  v v         i    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_49822739_4   1096 CCTCGTCAAGAAGAAGAAAGCCAGAAGCATCTCATTACCCACCTTCAAAC 1145
                          i vivv        v    iii  i vv  v  i v    vi      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_49822739_4   1146 TGTACTACAAGGCTACAGTAACCAAAAGAGCATGGTACTAGTACGTGGAC 1195
                         iv        i          i   i v  ii       i i iiv   -
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA- 284

  chr2_49822739_4   1196 TAGTACATAGACACATAGACCAATACTTCAGAATGAAGACCCTTGGAATA 1245
                         -------      i     i    ivvvi     vi   vi iv i    
  L1M4_orf2#LINE/    285 -------TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_49822739_4   1246 AAGCTGCATACCTACAACCAACTGATCTTCAACAAGCTTGACAAAAATAA 1295
                           v iii i ii  iiii   i    i   i     vv  v   i vi v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_49822739_4   1296 AACAATGGGGAGAGGATACCCTATTCAATAAGTGGTGCTGGGATAAATGG 1345
                         v-         i  i   vi  v     i  i           i  v   
  L1M4_orf2#LINE/    378 T-CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_49822739_4   1346 CTAACCATATGCAGAAGAATGAAACTGGACAGCTACGTCTTACCAAATAC 1395
                         v  ?   i     i         ii     vv    v  vi    v    
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_49822739_4   1396 AAAAATTAACTCAAGATGGATTAAATACTTAACTGTAAGATCTCATATTA 1445
                                       i      i ? v  i   v       v  v v i  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_49822739_4   1446 TAAAAATCCTAGAAGATGACCTAGG---AAATGCCTTTCTGGACATTGGC 1492
                              v  i       vi  v    ---    --   iv  -  v    v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTG-ACCTTGGG 573

  chr2_49822739_4   1493 CTAGGCAAAGA------AGTTACGAGCAAGTCCTTAAAAGCAAATGCAAC 1536
                         i       v i------  v  i  -  ---  --       v v     
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGA-CA---CC--AAAAGCACAAGCAAC 617

  chr2_49822739_4   1537 AAAACCAAAAATTGACAATTGAGACCTAATTAAACTAAAGAGCTTCGGCA 1586
                             vv      v  i  v vi   i v  i   v v  i i   iv ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_49822739_4   1587 CAGCAAAAGAAACTGTCAACAGAGTAAGCAGACAAAAAACAGAATGGGAG 1636
                          vv    i  v   i    v i   i iv      vvv            
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_49822739_4   1637 AAAATACTCACAAACTATGCATCTGGCAAAGGACTAATATCTGGAATCTA 1686
                               i ii    ii  ii     ii  i     vi    ii    v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_49822739_4   1687 GAAGGAACTCAAACAAATCAACAAGAAAAAAACAA----CCTCATTAAAA 1732
                         v  i      vv    v    i  v     i    ----  iv   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_49822739_4   1733 AGTGGGCAAAGGACACGAATA--CACTTACCAAGAGATGACATACACATG 1780
                          i           ivi     --  i  vi v i   v  i     v   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_49822739_4   1781 GCCAAGAAACAGGAAGAAAAATTTTCAGCATCACTAATCAT 1821
                              v  i  vivii   i  vi   i     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (129 / 104)
Gap_init rate = 0.02 (18 / 866), avg. gap size = 2.39 (43 / 18)  


1491 25.11 4.75 4.90  chr2_49828124_49829788.rev      501  1173 (492)    L1M4_orf2#LINE/L1      237   908 (0)  

  chr2_49828124_4    501 TTACTATA--TCTATGGTAGTCAATACTGTGTGGTATTGGC-TAAGGGCT 547
                               i --v   ii   i    v  v        i    -     i- 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-T 285

  chr2_49828124_4    548 AAACACATAGATTAAAACAATAGACCAGCTAATCCAGAAATAGATTCGTA 597
                          i   i      i  viv      viv vv i          i ii i  
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_49828124_4    598 CAAATATACCCAACT--TTTCTGACAAAAGATGTACATG-CAATTCAATC 644
                           vv   ivi   i --   ii     ii -  i-  v - v       -
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGG-TGC-CAAGACCATTCAAT- 382

  chr2_49828124_4    645 AAGGAAAGA-TATTCTTT-CAA--AATG-TGTTGAAACTATTGGACATCT 689
                         ii       -  v     -   --    -  i  ii  v i    i ? i
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_49828124_4    690 ATAGTAAAAAAAAAAAAAAAAAAACCTCAACTTAATTATCAAATCTTATT 739
                          i - iv    i  vi  ivvii   i v  i ------  v i v   v
  L1M4_orf2#LINE/    433 ACA-TGCAAAAGAATGAAGTTGGACCCCTACCT------CACACCATATA 475

  chr2_49828124_4    740 CAAAAGTTAACTCAAAATAGATCATGGATTTAAATGTAAAACATTAAAA- 788
                              i            i     ?i  ii         i -ii     -
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAAC 524

  chr2_49828124_4    789 TATAAAAGTATTAGGAAAAATATATAGTAGAAAAATCGTTGGAATCTAGG 838
                                v v    i i   - i    v? v   -  v i vi i  v  
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAA-ACATAGGNGTAAA-TCTTCGTGACCTTGG 572

  chr2_49828124_4    839 GAAAGGCAAAAAGTTCTTAAGAGTTCACACCATAAACATATTCCATAAAA 888
                          vv      viiv      -  vv v      v  i  i vv v i    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTA-GATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_49828124_4    889 GGCAAAATC----AATTAGACATCATCAAAAGTTATAAAATTT---ATTT 931
                          iv     v----    i   v         -   v   v   ---ii  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAA-TTAAAAACTTTTGTGCTT 670

  chr2_49828124_4    932 --AAAGATCTTGTCAAAAATAATGAAACGATAGGCTACAAAGTGGT-GAA 978
                         --  i  ivi i    i  - i     v  i iv i   i i   v-   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAA-AGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_49828124_4    979 AATACCTGCAAACCTCATAGCCAACAAAGAACTATTATCTAGAATGTATC 1028
                             ii      i vi   v ii i  i i   vv    i     i   -
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT- 768

  chr2_49828124_4   1029 ATAAACTCTTTTTTTCATAAACTCTTAAAATTCAATAGTAAAAGAACAA- 1077
                         --   -------------i        v  i      i     ii    -
  L1M4_orf2#LINE/    769 --AAA-------------GAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_49828124_4   1078 ---TCTAATTAAAAAATGGGCAAACAAAT-GAAGAGGCATTTCACCAAAG 1123
                         ---i i    ?             vi v -   v  i      v      
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_49828124_4   1124 A-----TTCATATAGCAAATAAGCACATGAATAGATGTTCGATATTACTA 1168
                          ----- v  v  i  v              v     i  i i  i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_49828124_4   1169 GCCTT 1173
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.58 (101 / 64)
Gap_init rate = 0.04 (30 / 672), avg. gap size = 2.17 (65 / 30)  


1838 28.40 8.45 1.88  chr2_49860058_49862159      760  1611 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_49860058_4    760 TGGAGAAACATACAATATT-AT---TTTGAAAAC--AATATTATT----T 799
                             i i i  v v  i  -  ---  v   i  --      i  ---- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_49860058_4    800 T-CAATTTTCCCCCATTTGATGTATATATTTCATGCAATTCA-ATCAAAA 847
                         v-    vi     v v     v  i v   iv i     i v-       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_49860058_4    848 TCTCAGTTATACTTTT-GTAGAAATTGATAAGTTAAATGTAGAATACAAA 896
                           i   i iivi    - i         i   i i viv  i   v  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_49860058_4    897 TGAAAACG----GGACCTGGAATAGCCTACACA-CATTGAAAACAATGAG 941
                           i   i ----     ii        v v   -iv       vi v  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_49860058_4    942 CAAATTTAGAGGACTTACA-TGCCTATTTTCAAGACTTGTTATAAAGGTA 990
                             v  i       i   - v  i v      i    ii  i    v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_49860058_4    991 CATTAATCAAGACAGTGTGGTATTAGAATAACAGCATATTTACAGGTCAA 1040
                           v                   i i v    viii v iv  i  i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_49860058_4   1041 CATAGCAAAATAGGAAATCCAAAAATAGATTAACACATATATGGTTAACT 1090
                         iiv ii i   v ii i    i     i iiv i    v      i  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_49860058_4   1091 GATTTTCAACAAAGAGATCAATGCACCTCAATGGGGAAAAAAT---CATT 1137
                                i    i ivii   vi vvi            i   --- v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_49860058_4   1138 TCAACAAATGATGCTGGTTAAAAGTGTGGG---------GGAAGAAAGTG 1178
                                   i      --i v ii-   i--------- v  i i i  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGG--GACAAC-TGGATAKCCACATGCAAAAGAATG 447

  chr2_49860058_4   1179 AACCTCAACCCA-ACCTCACACCACACACAA----TAATTTGAGATGATT 1223
                           vi vi    v-           i i    ----   i ii i   iv 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_49860058_4   1224 CATAAGCTTACACATAAAACTTAACA-TATAAAGCTTCT-GAAGAGT-CA 1270
                           ? ii i  v ii   i vi   v -      i  ii -     iv-  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_49860058_4   1271 TAAAAGAACAACTTTATGTTCTGAAGT-ATGCAAAAAAATTCCTGGGCA- 1318
                           ii? v v v   ii  vi  vii  - v    viiv-   i i ii -
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATAT 596

  chr2_49860058_4   1319 -----CAAAAGCACGAATTCAAAATAGAAAAAAATAAAGGAAGGGTTATA 1363
                         -----         i i--   v v ii        i vi  ---  iv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAG--CAACAAAAGAAAAAATAGATAAA---TTGGA 641

  chr2_49860058_4   1364 TAAGTTTTACCAAAATTAAGAACTTCTGCTTATTGAAAGCTGCCATTAAT 1413
                         i----  i i         i     i  iviv ii  i vii i  i  v
  L1M4_orf2#LINE/    642 C----TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_49860058_4   1414 AAAGT-------CAAATCACTGGATTGGAGAATATAGTTTCAAGACATGA 1456
                              -------   vi   v i  v      v   v  v   iv   iv
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_49860058_4   1457 ATTTTACAACAGAC--ATATTCAGACTATATAATGAATTCCTATGAATCA 1504
                           i v i  vi   --i   i    v       v   i  i  ii v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_49860058_4   1505 GCAATATAAAGA-AGACAACCAAATTTTTTAAATGG-C------TGTGA- 1545
                         ii    v     - i i    v    ?vv-      - ------ v   -
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAA 836

  chr2_49860058_4   1546 --GACAAATTTTTCAAAAAAGA-----AAATTATCCAATAAGCATATGAA 1588
                         --    v-  i i    i    -----    vi-          i     
  L1M4_orf2#LINE/    837 TAGACAT-TTCTCCAAAGAAGATATACAAATGG-CCAATAAGCACATGAA 884

  chr2_49860058_4   1589 AA-ATGCTTCACATCTTCAGTCAC 1611
                           -     iv     v????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (152 / 87)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 2.44 (88 / 36)  


3140 26.05 1.22 0.78  chr2_49961388_49966573.rev     3793  4694 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_49961388_4   3793 GAAAAATATTCCATGCTTATGGACAGGAAGAATCAATACCATGACAATGG 3842
                             i    i     i i     iv      v i    iii v vi    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_49961388_4   3843 CCATACTGCCCAAAGTAATTTATAGATTCAGTGCTACTCCCATCAAAATA 3892
                          v     v      v i  i  i       ii  v ii  i        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_49961388_4   3893 CCATTGACATTCTTCACAGAATTAGAAAAAACTAATT-TACATTTCATAT 3941
                            vivi v  i  ii     v v  v  i-  i  i-  v v       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr2_49961388_4   3942 GGGGAAT-CAAAGAAGATCCCATATAGCCAAGGCAATGCTAAGCAAAAAG 3990
                           i-   -   i --  i  viv        ii    vi i iv  i   
  L1M4_orf2#LINE/    152 GGA-AATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_49961388_4   3991 AACAAAGCTGGAGGCATCATACTACCTGACTTCAAACTACACTACAAAGA 4040
                                i      vv   i   v  ii i      vivi         v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_49961388_4   4041 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGGCACATAGACC 4090
                                 i   i    ii         i iv ii i  i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_49961388_4   4091 AATGGAACAGAACAGAGACCTCAGAAATAACACCACACATTTACAACCAT 4140
                                i    iv    vii         vv   i       iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_49961388_4   4141 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT--TTT 4188
                         i    i  i     ivv  v   i v  vv            i  -- i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_49961388_4   4189 CTACAATACATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAACTGA 4238
                         i v   i v            v      v  ?   i   iii  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_49961388_4   4239 AACTGGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGTTGGATT 4288
                          ii         v   i     v           i       iv     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_49961388_4   4289 CAAGGCTTAAATGTAAAACCCAAAACCATAAAAACCCTATAAGAAAACCT 4338
                         v?  i i         i v i     i      vi i  v        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_49961388_4   4339 AGGCA-ATACCATTCAGGACAT-AGGTTGGGCAAAGACTTCATAATGAAA 4386
                            ?i- v i -   iv   v -i    i     v ii   v  ivv vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_49961388_4   4387 ACACCAAAGGCAATTGCAACAGAAGCCAAAATTGACAAATGGGATCTAAT 4436
                                 i   vvv      i   vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_49961388_4   4437 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTAAACA 4486
                         i   v v  i i   i  ii vv    i  v       vv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_49961388_4   4487 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATTTGACAAA 4536
                          i     i                 v       vii ivi  i   i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_49961388_4   4537 GATCTAATATCCAGAATTTACTAGGAACT-TTACAAATTAACAAGAACAA 4585
                          iv  vi          v  iv i     -      v i  i  v  -  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AA 796

  chr2_49961388_4   4586 AAACAAACAACCCCATTAAAAAGTGGTCAAAGGATATGAACAGACACTTC 4635
                          i     i     v   ?    i   v        v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_49961388_4   4636 TCAAAAGATGTTTATGCA----GCCAACAAACATATGAAAAAAAGCTCAA 4681
                           v     v v -  i  ----     i  i  i       i v      
  L1M4_orf2#LINE/    847 TCCAAAGAAGAT-ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_49961388_4   4682 CATCACTGATCAT 4694
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (139 / 92)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 1.38 (18 / 13)  


2898 27.83 1.21 1.32  chr2_50020188_50026880     5293  6201 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_50020188_5   5293 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAG 5342
                               i i  i     i        v      v i        v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_50020188_5   5343 AGGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAG 5392
                         -   v     v      v i  i  i        i  v     i     i
  L1M4_orf2#LINE/     51 -GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_50020188_5   5393 CTACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTT 5439
                         v v   -   v    i  -i     -   -- v  i  - iii    v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chr2_50020188_5   5440 CATATGGAACCAAAAAAATAGCCCTCATAGCTCAGACAATCCTGGGCAAG 5489
                                  viiv  iii- v  vvv     iv i      i  iiv   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_50020188_5   5490 AAGAACAAAGCTGGAGGCATTTGAAGTCACTACCTGACTTCAAACTATAC 5539
                                   i      - i ii----    v  ii i      viv   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGG-ACTCA----CACTTCCCAATTTCAAAACTTAC 240

  chr2_50020188_5   5540 TACAAGGCTACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGATA 5589
                              i          i   i i  ii         i iv ii i   i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_50020188_5   5590 TATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAACACTACACATCT 5639
                               i        i    iv   ivii         vv i i    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_50020188_5   5640 ACAATTACCTAATCTTTGACAAACCTGACACAAACAAGCAATGG--AAAA 5687
                          iii i vi i  i  i     ivv  v  vi v  vv      --   i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_50020188_5   5688 CATTCCCTATTTAATCAATTGTGTTGGGAAAATTGGCTAGCCATATGTAG 5737
                         v  vvi  v  i  iv   v   i     v  i   v  ?   i   i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_50020188_5   5738 AAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAAATCAACTCA 5787
                           i v    ii         v   i     v          - i      
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCA 489

  chr2_50020188_5   5788 AGATAGATCAAAGACTTAAACATAAGACGTAGGACCATAAAAATCCTAGA 5837
                          i  i     ?    i    ii     vv  ii  i      v  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_50020188_5   5838 AGAAAACCTGGGCA-ATACCATTCAGGGCACAGACATGGGTAAAGACTTC 5886
                                v i  ?i- v i -   iv i viv ivv i  i  v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_50020188_5   5887 ATGACTAAATCACCAAAGGCAATGGCAACAGAAGCCAAAATTGACAAATG 5936
                         v iiv  viv       i   vvi      i   vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_50020188_5   5937 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCA 5986
                            ii v  i   v v  i i   i  ii vv    i  v    i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_50020188_5   5987 GAGTGAACAGGCAACCTGCAGAATGGGAGAAAATTTTTGCAATCTATCCA 6036
                         i      v  i     ii                v       vii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_50020188_5   6037 TCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTA 6086
                              i  i  i  vi          v  i        ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_50020188_5   6087 CAAGAAAAA-----ACAACCCCATCGAAAAGTGGGCAAAGGATATCAACA 6131
                         i  v     ----- i     v  i?    i            v v  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_50020188_5   6132 GATACTTCTCAAAAGAAGTCATTTATGCAGCCAACAGATATATGAATAAA 6181
                           i i     v       vi  vi viii     i iii i     v i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_50020188_5   6182 TGTGCATCATCATTGGTCGT 6201
                           iv  v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (151 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


2250 24.49 3.29 9.88  chr2_50029425_50032571.rev     1692  2663 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_50029425_5   1692 TGAAGAAATATTCCACGTTCATGGATTTAGAGACCCAATATTGTCAAGAC 1741
                           i i i    i   i           vii    ii        i    -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr2_50029425_5   1742 ATCAGTTCTTTCCAGATGTCAGTTTCTTCCCAATTTGATCTATGGGTCCA 1791
                         ----------------  v  i v-  i     v        ii i i  
  L1M4_orf2#LINE/     50 ----------------TGGCAATA-CTCCCCAAATTGATCTACAGATTCA 82

  chr2_50029425_5   1792 ATGTGATCCCAATAAAAATATCAGCAA--------GTGGATATTGA-AAA 1832
                          i ii     v  v     vi    vi-------- ii  v     -  i
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG 132

  chr2_50029425_5   1833 CTGACTGTGAAGTTTTTATAGAG-TGTCAAATACCCATAATAGCCTACAT 1881
                             iiv i  i  iv   i  i-  iv iiv     v       v v i
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_50029425_5   1882 AACATTGAAGGAGAATAATAAATTAGGAAGAGT---ATTATATGACTTCA 1928
                           iv     ii    v  i   v v   i  v --- i vivii i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_50029425_5   1929 AGACTTTTTATAAAGTCACAGCAATCAAGACAGTGTGATATTGGTATAAA 1978
                          i    vi  i    ii    i               i  i   i    i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_50029425_5   1979 AACAGACAATTAGATCAAAGAAACAGAATAGGGAGCCCAGAAACAAACTC 2028
                         i i     vv        v i  i     v i   i       i    i 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_50029425_5   2029 TCATAAATATGGTTAAGTAATCTGTGACAAAGGAGAAAAGGCAATACAAT 2078
                         vi i vv      i  v i  i vi     i  v vv   i v  v    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_50029425_5   2079 AGAGCATAGATAGTCTTTTAAACAAATGGTTCTGAAACAATTGGTTATCC 2128
                         i i v vii          v          v   ii    i   v  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_50029425_5   2129 ACATCCAAAAAAAAGTATACTTAGATACACT-CCTCATGCTCTTTGCAAA 2177
                             v     i  -- iv v  i  iv -  -     ii iv v i    
  L1M4_orf2#LINE/    433 ACATGCAAAAGAA--TGAAGTTGGACCC-CTACCTCACACCATATACAAA 479

  chr2_50029425_5   2178 AATTAATTCAAAATGAATCAGAGACCTAAATGTAAAATGTAAAAATATAA 2227
                               i        i    ?              i vv     v     
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_50029425_5   2228 AACTGCTAGAAGACAGCATAGAAGAAAATCTAGATAGCCTTAA-TCATGA 2276
                             vi       v i     i? v      vvi ii    ii- i - i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA-GG 578

  chr2_50029425_5   2277 AAATGTCTTTTTAGATATAGCACTAAGGGCATAATTCATAAGATTAGTAC 2326
                         v    vi  i        ii   i  ii   i  ----------------
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAA---------------- 612

  chr2_50029425_5   2327 TTAATTAATCACAACAAACCCCTGTGACATTAGTTAACCTATATAACAAA 2376
                         ----------i       -------------  vv  vv  v    ----
  L1M4_orf2#LINE/    613 ----------GCAACAAA-------------AGAAAAAATAGATAA---- 635

  chr2_50029425_5   2377 CCTGCACATGTACCTGAACCTAAAATAACAGTTAAAAACAACAGCAACAA 2426
                         -------  -----  i  i -------  - i    vi  ---------
  L1M4_orf2#LINE/    636 -------AT-----TGGACTT-------CA-TCAAAATTAA--------- 656

  chr2_50029425_5   2427 AAAAACTTCTGCTCTGCAGAAGACACTCTCAAGAGAACAAAAAAAC---- 2472
                         --      i  iv  v  i i      v      i iii    i  ----
  L1M4_orf2#LINE/    657 --AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_50029425_5   2473 -------TAGAAAAAAATATTTGCCAAAGGTATATCAGATAAAGGACTCT 2515
                         ------- i i i           v  vvi      v     i     iv
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_50029425_5   2516 TGTCCAAAATATACCAAAAACCCTTAAAACTCAACAATAAGAAAATGAAC 2565
                          i    i      iv  i   i    v       i     i  i ii  i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_50029425_5   2566 AACCTAATT-AAAAATGGGCCAAAGATCTTAACA---ATCTCACCAAAAA 2611
                             i    -          v  i   i v  i ---  i  v     i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_50029425_5   2612 A--TAAACAGAGAATGAATAATCATATGAAAAGATGCTACATATTACATA 2659
                          --  v   i viiiv     v  i             vv i  i ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_50029425_5   2660 TCAT 2663
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.80 (151 / 84)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 5.82 (128 / 22)  


1002 29.73 12.14 3.76  chr2_50042600_50045688.rev     1779  2602 (487)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_50042600_5   1779 TGTTAATGGACTAGAA--CCCAATATCAAAATTCCATATCATAAAAT--- 1823
                             v     i i   -- ii     ---------- i --   i  ---
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATAT----------TGT--TAAGATGGC 53

  chr2_50042600_5   1824 AATTCTGCCCAAATTGATCTACAAATTGAGTGCAATTTCAATCAAAATCC 1873
                            v  v                i   v ii     ii v          
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_50042600_5   1874 CGAGTAGTTGGCTGTTGCTACTGATCTTGATAAACTGATTCTAAAATTAA 1923
                          ----  i  v  v  -i i v  vv    i  i     i        v 
  L1M4_orf2#LINE/    104 C----AGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_50042600_5   1924 CATGGAAGAGCAGAGGGTCAAATATAGCCTAGAGACTCCTGAAAAAAAA- 1972
                         i      iv   ii  ii v iv      v i v v  i       i  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_50042600_5   1973 AGCAAAGTTGG----CTGACAT-----GACTACCAGG-----TATAAAGC 2008
                          i         ----  v   i-----i i v v ii-----  i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_50042600_5   2009 AGCCATTTTTGAGACA-CATAGAATTGGTGCAGGCTTCGATAAGTAGAGC 2057
                         vi vi vv ii     -ii i v i   iii i vv v  i vi    v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_50042600_5   2058 AATGAAATGAAAC----AATC-------AAATCCACACAGTTTGAAACAA 2096
                             i   ii  i---- i  -------   i   i   v  vviiv   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_50042600_5   2097 --GATTTATGATAACTGGCAATTGAGA----TCAGAGGCAAAAGAAAAGA 2140
                         --     vi  i  --  vviiii   ----   iv  vi      v  v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAA--GGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_50042600_5   2141 ATTT----------GTTCTTGGACAATTGATTATTCACATGGAAAAATTA 2180
                         v   ----------  v  v      i  iv  ?i      v    iv- 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-A 445

  chr2_50042600_5   2181 TGCAACTAGACTTA-ACCTCCTGACAGATATAAAAGTCAATTCCATGTGC 2229
                           v ii i   iiv-     viiv  v   i    i i  i  v vi  v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_50042600_5   2230 ACTAAAGATTTAAACGTGA-AGCCAAAAGGGTGAAACATTTATAAGATAA 2278
                          ii ?   ii    i  i -   i    vvi i    vi   v    v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_50042600_5   2279 TATAGTTGTAA--CTGCTTGAT----AATTAAG----GCTTTCTTTCAAA 2318
                         i    v?    --  v v   i----ii   i ---- v      --- i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT---AG 592

  chr2_50042600_5   2319 AAGTGAT-TCAACATCACAAATTATAAATAAAAAGATTGATACATT---- 2363
                          vi   i-i   v v     iiv i   vi    i  v    v   ----
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_50042600_5   2364 --TATTAAATTATAATACCTTCTGTTCATAACATTTAACAAA-ATCATTA 2410
                         --i  i   v -   v v   i   v ------  i  vii - ii  i 
  L1M4_orf2#LINE/    643 TTCATCAAAAT-TAAAAACTTTTGTGC------TTCAAAGGACACTATCA 685

  chr2_50042600_5   2411 A-AATGTGAATGGATATACCATAGATTAGACAAAGAAATGTGCAA----T 2455
                          -  v     vi  i vv   i   v i ivi  i v  v     ---- 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_50042600_5   2456 ACAT-------GGGA-TTG------------ATAAATAATTGATACA-CA 2484
                          i  -------    -   ------------     v  i vv    - v
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_50042600_5   2485 TAA-AATACTAAAACTTCTAAGTCAATTAAAAAAAAAGCTTAC-ATGTAA 2532
                         i  -    vv  i  vvv   vi     ?     vii  vv v-  v i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_50042600_5   2533 ATAGGCACTTCAC--AAGAGAATATA--AATTCCCAGTAAGCACATGAGA 2578
                             i  i   v --    ii     --   vv   i           i 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_50042600_5   2579 ACATTACTCAAGCTCATTAGTAAT 2602
                          v  -i     vv   ????????
  L1M4_orf2#LINE/    886 AGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (136 / 105)
Gap_init rate = 0.04 (40 / 893), avg. gap size = 3.27 (131 / 40)  


2269 26.03 4.73 0.79  chr2_50129348_50132108     1066  1699 (1062)    L1M4_orf2#LINE/L1        7   665 (243)  

  chr2_50129348_5   1066 GATATTCCATGTTCAT-------------TATTATTGTCAAAATGTCAGT 1102
                              i          -------------  v      i  i   v  i 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_50129348_5   1103 TCTTCCCAACTTGATTTATAGCTTCAATGCAATCCCAATCAAAATCCTGG 1152
                         v  i     v     i  i  v     i        v          ii 
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_50129348_5   1153 CAAGTTATTTTGTGGATGTTGACAAACTGATTCTAAAGTTTATATGGAGA 1202
                          vivi v     ii  vi       i     i     i  i       i 
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_50129348_5   1203 GGCAAAAGAACTGGAATGGCTAACAAAATATTGAAGGAGAAGAACAAAGT 1252
                         v    ii  v ii    i  i  v v   v     ii             
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_50129348_5   1253 TGAAGGACTGACATCATCTAACGTCAAGCCTTACTATAAAGTTATAACAT 1302
                           i      v   iivi i  iv    iv       i    i  i ii v
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_50129348_5   1303 TCAAGACAGTGTGGTATTAATGAAGGAATAGGCAAATAGATTAATGGAAG 1352
                                         i iiiiv i i    i  v      i       v
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_50129348_5   1353 AGAA----GAACCCAGAAACAGACCTAGATAAATATAATCAACTGATCTT 1398
                             ----  ii       i i   i v i vv   ii    i    i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_50129348_5   1399 TGATATAGA-GCAAAGGTTACATAATAAAGCAAAGATAGTCTTTTCAACA 1447
                         i  i vi i-  v   iii ivi   iii v  ii               
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_50129348_5   1448 AACGGTGCTAGAACAACTAGACATCCATATGAAAAATAAT----TTAGAG 1493
                           i      i i      i  i ?   i   v    v   ----  i  v
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_50129348_5   1494 ----AC---AGACAATTGACAAACATTAACTCAAAATGGATCAAACCCTT 1536
                         ----  --- v  v  vv     v                   ? vv i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_50129348_5   1537 AAGTGTAAAATGAAAAACCATAAAACTCTTAGAAGACGACACAGGAGAAA 1586
                           i     i vvv     i                 vi   i   ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_50129348_5   1587 AACCTAGATGACCTTGGGTATGGCACTGACTTTTTAGATACAAAACCAAA 1636
                          v i v -           vv    v  ii  i       ii v      
  L1M4_orf2#LINE/    557 ATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_50129348_5   1637 GG-ATGATCCATGAGAGAAATAATTAATGAGCTCTACATCATTAAAATAA 1685
                         i - ii v v ii i     v   vi  i ii vv  v    i     v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_50129348_5   1686 AGAAAAAACTTTTG 1699
                          ----         
  L1M4_orf2#LINE/    656 A----AAACTTTTG 665

Transitions / transversions = 1.75 (103 / 59)
Gap_init rate = 0.01 (9 / 659), avg. gap size = 3.89 (35 / 9)  

 682 20.68 10.90 1.13  chr2_50129348_50132108     2004  2269 (492)    L1M4_orf2#LINE/L1      617   908 (0)  

  chr2_50129348_5   2004 CAAAAAACAAAAACAAACAAA----AC---AACAACAAT-----ACTTCT 2041
                              i -     i i i   ----  --- v   -   -----    i 
  L1M4_orf2#LINE/    617 CAAAAGA-AAAAATAGATAAATTGGACTTCATCAA-AATTAAAAACTTTT 664

  chr2_50129348_5   2042 GTTATCTGAAAAACTCTGTTAAGAAAATGAGAAGACAAGCCACAGACTAG 2091
                           vv iii  ii  v  i i      i   i       v       v i 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_50129348_5   2092 CAAAAAATACTTGCAAAAGACCTATCTGATAAAAGACT-GTGATCCAAAA 2140
                         v i      i       vv iv          ii    -  -     i  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT-ATCCAGAA 763

  chr2_50129348_5   2141 TATACAAAGAACTCGTAAAACTCAACAATGATAAAACAAA---------- 2180
                             i         v  v       i   i v  i     ----------
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_50129348_5   2181 --AAAAGGGCCAAA--ATCTTAACAGACACCTGACCAAA-AAGAGATATA 2225
                         --    v  v    --  i v  i     ii vv     -    v   i 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_50129348_5   2226 GATGGCAATTGAGCACATGAAA-GATGCTCCACATTATACACCAT 2269
                         i     v v i           -       v    i ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (33 / 22)
Gap_init rate = 0.04 (11 / 292), avg. gap size = 2.91 (32 / 11)  


1738 28.03 2.39 0.60  chr2_50390072_50393912.rev     2064  2566 (1275)    L1M4_orf2#LINE/L1        1   512 (396)  

  chr2_50390072_5   2064 TGAAAAAGCATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 2113
                           i   iii  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_50390072_5   2114 GGCCATACTGCCCAAAGCAATTTATAGTTTAAATACTATTCCCATTAAAC 2163
                            v     v      vii  i  i  v  v  ii v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_50390072_5   2164 TACCATTGACATTCTTTACAGAATTAGAAAAAACCATTTTAAAATTCATA 2213
                          v   vivi v  i   i     v v  v  iviv  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_50390072_5   2214 TGGAACCAAAAAAGAATCTGTATAGCTAAGACAATCCTAAATGAAGAGAA 2263
                              viiv  ii  vi v v     i  i      i i  vi ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_50390072_5   2264 TAAACCTGGAGGCATCACGTTACCTGACTTTAAACTATACTACAAGGCTA 2313
                         i   vi      vv    ii v  ii i  i   viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_50390072_5   2314 CAGTAACCAA-ACAGCATGGCAC--ACACA------GACACATAGACTAA 2354
                               i   -    ii   i  --i  i ------    i     ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_50390072_5   2355 TGGAACAGTTTAGAGATCTCAGAAATAAGACTGCACATCTACAACCACCT 2404
                              i  vv v    vii         iv iii    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_50390072_5   2405 GATCTTCGACAAACCTGACAAAAAGATGCAATGGGGAAAGGAT--TCCCT 2452
                            i        ivv  v   i vv  v            i  --  ii 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_50390072_5   2453 AATTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATACAGAAAATGGA 2502
                         -- i  i        i     v      v  ?   i  i  i  i vv  
  L1M4_orf2#LINE/    401 --TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_50390072_5   2503 AACTGGACCCCGTACTT-ACACCTTATACAAAAATTAACTCAAGATGGAT 2551
                          ii        -   i -     v                   i      
  L1M4_orf2#LINE/    449 AGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_50390072_5   2552 TAAAGATATAAATGT 2566
                         i ?   iv       
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGT 512

Transitions / transversions = 1.84 (90 / 49)
Gap_init rate = 0.01 (7 / 512), avg. gap size = 2.14 (15 / 7)  

1053 27.91 2.09 0.93  chr2_50390072_50393912.rev     2920  3349 (492)    L1M4_orf2#LINE/L1      474   908 (0)  

  chr2_50390072_5   2920 TAAAAAAGTTAA---AAAA-AAA--AAAGACTTAAATGTAAAACCCAAAA 2963
                           v    i    ---    -ii -- ?    i         i v i    
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_50390072_5   2964 CTGTAAAAACCCTAGAAGAAAATCTAAGCA-ATACCATTCAGGACATAGG 3012
                           i     vi i          iv  i ?i- v i -   iv   v v  
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGG 572

  chr2_50390072_5   3013 CATAGGTAAAGATTTCATGACAAAAACATAAAAAGAAATGGCAACAATAG 3062
                         vv    i  v i    v iivv vi   iv     v vvi       v  
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_50390072_5   3063 CAAACATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA 3112
                         v   v  v  i    v   ii v  i   v v  i i   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_50390072_5   3113 AAAGAAACTATCATCAGAGTGAACAGACAACCTGCAGAATAGGAGAAAAC 3162
                           i  v       vv i      v        ii      i        i
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_50390072_5   3163 TTTTGCAATCTATCCATCTGACAAAGGTCTAATATCCAGAATCTACAAGG 3212
                         v       vii  vi      i  i  v  vi          v  i  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_50390072_5   3213 AACCTGGGCAAATTTACAAAAACAAACAAACAAAAAAAC--ATTAAAAAC 3260
                            iivvi   v ---   v  i   v i     v  v --   ?    v
  L1M4_orf2#LINE/    773 AACTCTTACAACT---CAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_50390072_5   3261 TGGGCAAAGGGCATTAACAGACATTTGTCAAAAGAAAACATTTATGCTGC 3310
                                   iiv v  i        v  v      i i  vi viiv  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_50390072_5   3311 CAACAATCATATGAAAAAACGTTCAACATCACTGATCAT 3349
                            i  v  i       i i i         ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.13 (62 / 55)
Gap_init rate = 0.02 (7 / 435), avg. gap size = 1.86 (13 / 7)  


2981 29.72 0.33 0.00  chr2_50496073_50502792     5324  6228 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_50496073_5   5324 TGGAAAAACATTCCATGCTCATGGATAGAGAGAATCAATATCGTGAAAAT 5373
                               i i  i     i        v ii   v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_50496073_5   5374 GGCCATACTGCCCAAAGTAATTTATGCATTTAATGTTTTTCCCATCAAGC 5423
                            v     v      v i  i  iiv   i  i ivv i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_50496073_5   5424 TACCATTGACTTCCTTTACCAAATTAGAAAAAAGTACTTTAAATTTCATA 5473
                          v   vivi i ii   i vi  v v  v  ivvv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_50496073_5   5474 TGGAATAAAAAAGTACCCCGTACAGCCAAGACAATCCTAAGCAAAAAGAA 5523
                              vviv  i v    v v i      i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_50496073_5   5524 TAAAGCTAGAGGCATCACGCTACCTGACTTCAAA--CTA-TACAAGGTCA 5570
                         i    i i    vv    i  v  ii i      --i  -     i ii 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_50496073_5   5571 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 5620
                               i   i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_50496073_5   5621 TGGAATAGAATAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5670
                                    v   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_50496073_5   5671 TTTCTTTAACAAACCTGATGAAAACAAGCAATGGGGAAAGGATCCCCTAT 5720
                         vv i  ii    ivv  vii i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_50496073_5   5721 TTAATAAATGGTGTTGGGGGAACTGGCTAGCCATATTCAGAAAACTGAAA 5770
                          i  i        i    iv      v  ?   i  v  i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_50496073_5   5771 CTGGACTCCTTCCTTATGCCTTATACAAAAATTAACTTGATATGGATTAA 5820
                         i     i   v   i ii  v                ii v      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_50496073_5   5821 AGATTTAAACGTAAGACCTAAAACCATAAAAACCTTAGAAGAAAACCTAG 5870
                            ii    i      v       i      vi             v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_50496073_5   5871 GCAATAACATTCAAAACATAGGCATGGACAAAGACTGCATGACTAAAACA 5920
                          ?ivv  iv   ivi  v v  vv i i   v ii v v iiv  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_50496073_5   5921 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGTTCTGATTAA 5970
                                  vvi          vv     v  i    v  vii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_50496073_5   5971 ACTAAGGAGCTTCTGCACAGCAAAAGAAACTATCATCAAAGTGAACAGGG 6020
                          v v ii i   i  ii vv    i  v       vv        v  iv
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_50496073_5   6021 AACCTAAAGAATGGGAGGAAATTTTTGCAATCTATCCATCTGGCAAAGGG 6070
                             i v          i    v       vii  vi     ii  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_50496073_5   6071 CTAATCTCTAGAATCCACAAGGAACTTAAACAAATTTACAAGAAAAAAAC 6120
                           vi v  i     vi i  i     ivv    v iv i  v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_50496073_5   6121 AAACAACCCCATCAAAAGGCGGGCAAAGGATATGAACAGACACTTTTCAA 6170
                            i     v  i?   iii           v    i     i  i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_50496073_5   6171 AAGAAGACATTTATGCAGCCAATAAACACATGTAAAAAAGCTCATCATCA 6220
                                i  vi viii        i      v   i v     v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_50496073_5   6221 CTGGTCAT 6228
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.45 (157 / 108)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 1.50 (3 / 2)  


2574 25.32 1.98 1.70  chr2_51186284_51189552.rev     1336  2042 (1227)    L1M4_orf2#LINE/L1        1   709 (199)  

  chr2_51186284_5   1336 TGGAAAAATGTCTCATGTTCATGGACTGGAAGAATTAACATTGTTAAAAT 1385
                               i  i  i            i       v    i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_51186284_5   1386 GGCCATCTTACCCAAAGTGATCTACGGACCTAATGCAATCTCTATCAAAA 1435
                            v  vi v      v        i  iii  i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_51186284_5   1436 TATCAATGACATTCTTCACAGAAATAGAAAAAACAATTCTAACATTCATA 1485
                          vi  iivi v  i  ii       v  v  ivii  i    v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_51186284_5   1486 TGGAACCACAAAATACTAAGAACAGCCAACTGAATCCTGAGCACAAAGAA 1535
                              vii   iiv  iv    i      vvv    i   iv vi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_51186284_5   1536 CAAAGCTAGAGGCATCATATTACCTGACTCAAAAATATGCTACAAAGCTG 1585
                              i i    vv   i i v  ii i iv    iv i          i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_51186284_5   1586 TAGTAACCAAAACAACATGGTACTGGAACAGAAACACATACATAGACTAA 1635
                         i     i   i   iii         v i iii i v i i     ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_51186284_5   1636 TAAAACCGAATAGAGTGTCCAGAAATAAATTCAAACAAGTACAGTCAACT 1685
                          ii  iv    v   v             ii  v   vv  ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_51186284_5   1686 GATTTTCTTCAACAAAGGTGTCAAGAACACATGTTGGGGGAAAGAA-AGT 1734
                                ---i    i    i     v  iviiv     -      -   
  L1M4_orf2#LINE/    351 GATTTTC---GACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGT 396

  chr2_51186284_5   1735 CTCTT----AAAGGGTGCTGGGAGAACCAGATATCCACATGCAGAAGAAT 1780
                           i  ----   v          v   ii    ?         i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_51186284_5   1781 AAAACTAAGCCCATACTTCTCATCATATAGAAAAATTGACTCAAAATGGA 1830
                         i  ii iii   v   i  v  i      v       i            
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_51186284_5   1831 TTAAAGACAAGACTTAAGTGTAAAACCCATAACTATTAAACTACTAGAAG 1880
                          i ?    -----i   i     i v i v      v     vi      
  L1M4_orf2#LINE/    497 TCAWAGAC-----CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_51186284_5   1881 AAAACATAGGAAAAATTCTTC---ACATTGGGCTGGGCAAGAATTTTTAA 1927
                                   ?iv  v     ---  v     i i     vii   i v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_51186284_5   1928 AATAAGACCTCAAAAGCACAG-----AGAAGAAAGCAAATAAATAAATGA 1972
                         i   v   vi          i----- i      --     i      vi
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAA--AAATAGATAAATTG 639

  chr2_51186284_5   1973 AATTGCATCAAA-CTAAAAGCTTTTTGCACAGCAAAGGAAACAATTAGAT 2021
                         i i v       -i     i     - ii vv       v  v  i iiv
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGA 688

  chr2_51186284_5   2022 AAGTGAAAAGAAAGTCTACAG 2042
                                    v ii i    
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAG 709

Transitions / transversions = 1.93 (116 / 60)
Gap_init rate = 0.01 (10 / 709), avg. gap size = 2.60 (26 / 10)  

 780 20.00 0.44 4.44  chr2_51186284_51189552.rev     2558  2782 (487)    L1M4_orf2#LINE/L1      693   908 (0)  

  chr2_51186284_5   2558 GAAAAGCCTGGTCTACAGAATAGGAGAAAACAGCTGCAAATTATACATCT 2607
                               v -iii i       i        i vi       i   i    
  L1M4_orf2#LINE/    693 GAAAAGAC-AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_51186284_5   2608 GCCAAGGG-CTTGATATCCACAATATATAAATGAGTTAAACACCTCAACA 2656
                          vi     -    -      v          vi v ivv   v     i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_51186284_5   2657 AAACAAACAAAAAAAAGATATAAACCCAATTTAAAAATGGGCAAAACACC 2706
                          v -----    i v i   ---        ?             iv ii
  L1M4_orf2#LINE/    791 ATA-----AAAAGACAAATA---ACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_51186284_5   2707 TGAATAGACATTTCTCAAAAGGACATATAGAAATGGCCAATAGGTATATT 2756
                                         v    i v     v            i i i  v
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_51186284_5   2757 TTAAAATGCTCAATGTAACTAATCAA 2782
                         vv  i        ii v ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (25 / 19)
Gap_init rate = 0.02 (5 / 216), avg. gap size = 2.20 (11 / 5)  


3735 21.52 2.47 1.12  chr2_51197824_51202269     3067  3958 (488)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_51197824_5   3067 AAGGCATCCCATATCCATGGATTAGAAGACTTAGTATTTCTAAAATGTCA 3116
                            ii       i i        i         i    vi   i   v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_51197824_5   3117 ATATTACCCAAACCAATCTATAAATTTAATGCAA-ACCTACCAAAATTCC 3165
                            i v      iii     i i   i  i    -v    i      i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_51197824_5   3166 AAGGCTG--TGTTTTGCACAGATGGAAAAGACAATTCTTAAATTCATCTG 3213
                          --    -- v       v i  v  v   vii  i  v        v  
  L1M4_orf2#LINE/    105 A--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_51197824_5   3214 GAGTTGCAAGAGACCCTGAATAGTGAAAACAATCTTGAAAATAAA----A 3259
                           iv      i     v      iv                vi  ---- 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_51197824_5   3260 AGATTAAAAGAATTACACTTCCTGATTTCAAAACTTACTAAAAACCTACT 3309
                          ii  ii i  v i        ii                v   v    v
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_51197824_5   3310 GTAATCAAAATATTGTGATACTAGCATAAAGACAGACATATAGACCAATG 3359
                                 i i v    i    i      i  i           i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_51197824_5   3360 GATTAGAATTGAAAGTCTAGAAAT----CCATGTATTTATGCCTAATTAA 3405
                           v         i    i      ----    ii       vii    i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_51197824_5   3406 TTTTTTGTAAGAGTGTTAACACCATGCAATGAAGGACAGAACAGTGCCTT 3455
                             ivii   i   ii  v     v     i-   v    i   vii  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTT 401

  chr2_51197824_5   3456 CAACAAATGGTACAAAAACAACTGGATATTAACATGCAAAGGAATGAAAT 3505
                                    i viii           ?iv         i       i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_51197824_5   3506 AAAACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATTAAT 3555
                         vii                                           i ?v
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_51197824_5   3556 GACCTAAATATAAGTGTTAAAATTGTAAAACTATTAGAAAAACAAATA-- 3603
                                  i    v i     i i       v      i  v v   --
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_51197824_5   3604 --TTATTTTTCATGATCTTCAATCTGGTGATGGATGCTTAGATATGCCAT 3651
                         -- v v i   i   i   vii iv  ii    v v          v  i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_51197824_5   3652 GAAAAATATGAACAACAAAAGAAAAAAATTGTTAGATAGGGCTTCATCAA 3701
                         v    ii ii i               - v v  i  v  i         
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAA 650

  chr2_51197824_5   3702 AATTAAAAACTCTTATGCATCAAATGATGTTATCAGGAACATGAAAAGAA 3751
                                    i  i   v     v  iii     i   vi        v
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_51197824_5   3752 AACCTAGAGAATGAAAGACAATGTTT-TAAATCATGTATATGATAAGCGC 3800
                             i v      ii   v   i   -i       i   v       v v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_51197824_5   3801 CTATTATCCAGAATATATTTTTAAA--ATTCTTACAACTC--TGAGTCAA 3846
                           vv              ----   -- i           -- i --i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATAT----AAAGAACTCTTACAACTCAATAA--TAA 794

  chr2_51197824_5   3847 AAGGACCAACCACCCCATTTTAAAAAGAAGAAAAC-CTTGAATAGCCATT 3895
                           i   v  iv    v   ?v    v iiv   iv-i        v    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_51197824_5   3896 TCTCTAGAAAAAATGGACAAACGACCAAGAAACTCATGAAA-GATGCTCA 3944
                             i i i  i  iv     i i    v  i v       -        
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_51197824_5   3945 ACCTTATTAGGTAT 3958
                           v i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (120 / 69)
Gap_init rate = 0.02 (15 / 904), avg. gap size = 2.13 (32 / 15)  


3030 27.09 0.66 0.66  chr2_51317974_51322195     2823  3730 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_51317974_5   2823 TGGAAACACGTCTCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2872
                               v ii  i    i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_51317974_5   2873 GACCATACGGCCGAAAGCAATCTACAAATTCAATGTAATTCCCATCAAAA 2922
                          i v    vv  v   vii       i      i i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_51317974_5   2923 TACCACCATCATTCATCACAGAACTAGAGAAAC-AATCCTAAAGTTTATA 2971
                          v   v vv v  iv ii     v v  v  i -i        i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_51317974_5   2972 TGGAGCCAAAAAAGAGCCTGCATTGCTAAAACAAGACTAAGCAAAAATAA 3021
                             iviiv  ii  v  v v  v  i       vvi i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_51317974_5   3022 CAAATCTGGAGGCATCACATTACCCAACTTTAAA--CTACAGTGTAAGGC 3069
                             vi      vv     i v     i  i   --i   -- ii  i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGC 248

  chr2_51317974_5   3070 TATAGTCACCAAAACAGCATGGTATTGGTATAAAAATAGGCACATAAGCA 3119
                           i   v i   i    ii     i   i    ii    i  i   iiiv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_51317974_5   3120 AATGAAACAAAATAGTGAACCCAGAGATAAACCCAAATACTTACAGCCAA 3169
                             i  i i   v v  ii     i         v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_51317974_5   3170 CTGATTTTTGACACAGCAAACAAAAACATAAAGTGGGGAAAGTACACCCT 3219
                         i       i    vi vviv   i v   vv i         v i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_51317974_5   3220 GTTCAACAAATGCTGCTGGGATAATTGGCAAGCCACATGTAGGATAGTGA 3269
                         v           v        i  i   vv ?       i ii v i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_51317974_5   3270 AACTGTATCCTCATCTCTCACCTTATATAAAAATCAACTGAAAATGAAGG 3319
                          ii  v i  ii i   v    v    i      i    v      i vv
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_51317974_5   3320 AAAGACTTAAGTGTAAGATCTTAAATCATAAAAATTCTAGAAAATAATAT 3369
                          ?    i   i       v  v   ii      v ii     i v  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_51317974_5   3370 TGGAA-AAACCCTTGTAGACATTGGCTTAGGCAAAGAATTTATTAC-TAA 3417
                         v  ?i-   i i i  -   v    v        v i-   v   v-  v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGG-TTTCTTAGATAT 596

  chr2_51317974_5   3418 GAACCCAAAAGCAAATGAAACAAAAACAAGGATAAATAGATGGGACTTAA 3467
                           vv         v v v       iv  ii   i   i  v      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_51317974_5   3468 TTAAACTAAAAAGCTTCTGCACAACAAAAGAAATAATCAGCAGAGTTAAC 3517
                          i   v v    i   i  ii vv    i  v iv    iv i   v  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_51317974_5   3518 AGACAACCCACAGAGTGGGAGAAAATATTTGCAAACTATGCCTCTGACAA 3567
                                       i                    ii  iiv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_51317974_5   3568 AGGACTAATATCCAGAATCTA-GGGGAAATCAAACAAATCATCAAGATAA 3616
                         i     vi          v  -iii   v  vv    v   vi  v v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_51317974_5   3617 AAACAAACAATCCCATCAAAAAGTTAGCTAAGGATATGAACAGATGCAAT 3666
                          i     i  i  v  i?    i vi  v      v    i   --  v 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA--CATT 844

  chr2_51317974_5   3667 TCTCACAAGAGGATATGCAAATGGCCAACAAACATATGAAAAAATGCTCA 3716
                             vv    i     i           i  i  i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_51317974_5   3717 ACATCACTAATTAT 3730
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2513 26.67 2.91 1.21  chr2_51327287_51332946.rev     4344  5168 (492)    L1M4_orf2#LINE/L1       70   908 (0)  

  chr2_51327287_5   4344 ATC-ACAGATTCAATGCTATTCCCATTAAACTACCAATGACATTCTTCAC 4392
                            -          i  v  i  i  i   v v   iivi v  i  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chr2_51327287_5   4393 AGAATTAGAAAAAACTAGTT-TAAAATTCATATGGAAC--CAAAAGACAG 4439
                             v v  v  i-  ii i-                v--   ii   --
  L1M4_orf2#LINE/    120 AGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGGGAC-- 166

  chr2_51327287_5   4440 ACCATAA-AGCCAAGACAATCCTAAGCAAAAAGAACAAAGCTGGAGGCAT 4488
                         -   v  -      i      i i iv  i          i      vv 
  L1M4_orf2#LINE/    167 -CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_51327287_5   4489 CACACTACCTGTTTTTAA---------CAATGCTACAGCAACCAAAACAG 4529
                               v  iiv   i  ---------   v       i  i   i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_51327287_5   4530 GATGGTACTGGTACAAGAAGAGACACATGGACAGACCAATGGCACAGACT 4579
                         vi         i i   i v     i  ----   i      v i   v 
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATAT----AGATCAATGGAATAGAAT 311

  chr2_51327287_5   4580 GGAGAACACAGGAATAAGACCAAACAGCCACAACCACCTGATCTTCAACA 4629
                         v    iiv   i     iv   v   vii iiii  vi    i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_51327287_5   4630 AACTTGACAAAAACAAGCAATGGAAAAAGGAC--TCTATTTAATAAATGG 4677
                          ivv  v   i v  vv      ii    i i--   v  i  i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_51327287_5   4678 TTCTAGGAGTGCTGGCTAGTCATATGCATAAAATTGAAACTGGATCTTT- 4726
                          v  i   vvi    v  ?i  i     v  i v    ii    i ii -
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_51327287_5   4727 TTTTACACCATATACAAAAATTAACTCCAGATGGATTAAAGACTTACGTG 4776
                         ii i                       v i      i ?    i  vi  
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_51327287_5   4777 TGAAACTCAAAACTATGAAAACCCTAGAAGAAATTCTAGGCA-ATATCAT 4825
                          i i vii        i   vi i         viv    ?i- v   - 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-T 560

  chr2_51327287_5   4826 TCAGGACATAGGCATGAGCAAAGATTTCATGAAAAAAACACCAAAAGCAA 4875
                           iv   v v  vv ii    v i    v ii v vi            v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_51327287_5   4876 TTACAACAAAAGCAAAAATTGACAAATGGGATCTACTTAAACTAAAGAGT 4925
                         vvi         v      v  i    v   ii vv i   v v  i ii
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_51327287_5   4926 TCCTGCACAGCAAAATAAACTATCTCAGA--GTAAACAGACAACCAACAG 4973
                          ii  ii vv    iv v      -v   --  i  v        v    
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATC-AAGAAAGTGAAAAGACAACCCACAG 709

  chr2_51327287_5   4974 AATGGGAGAAAAT-TTTGCAATTTATCTATCTGACAAAGGTCTAATATCT 5022
                                      -       v i  v       i  i  v  vi    i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_51327287_5   5023 AGAGTCTACAAATAACTTAAACAAATTTACAAGAAAAAAATAAA--ACCC 5070
                            i v  i   v    ivv    v iv i  v     i i   --    
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_51327287_5   5071 A-TTAAAAAGCAGGCAAAGGACATGAACAGATACTTCTCAAAAAACGATA 5119
                          -  ?    iii         iv    i   i i     v   i v    
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_51327287_5   5120 TACATGTGGCCAACAAACATATGAAAAAAAGCTCAACATCACTGACCAT 5168
                             vi       i  i  i       i v           ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (128 / 88)
Gap_init rate = 0.02 (17 / 839), avg. gap size = 2.00 (34 / 17)  


3126 25.63 1.31 2.29  chr2_51392036_51396255     2812  3728 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_51392036_5   2812 TGGAAAGATATCCCATGCCCACGGATTGAAAGAATTAATATCATTAACAT 2861
                                          ii  i      i    v       ii    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_51392036_5   2862 GACCATACTACTGAAAGCAATCTATAGATTCAATACAATCCCTTTCAAAA 2911
                          i v     v iv   vii     i        ii        v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_51392036_5   2912 TATCAGT--CATTTTTCACAAAAGTAGAAAAA--AATCCTGAAATTCATA 2957
                          vi   i-- v     ii  i  i v  v  i--i     i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_51392036_5   2958 TGGAATAAAAAAAGAGCCAGAAAAGCCAAAGCAATCCTGGGCAAAAAGAA 3007
                              vviv  ii  v      v       i     i  iiv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_51392036_5   3008 CAAAACTGAAAGTCATCACATTACCTGACTTGAAAATATATTATGG-GTT 3056
                             ii  i i v -     i v  ii i  v    iv  i  iii- i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_51392036_5   3057 ACAGTAACCAAAACAGCATGCCACTAGTATAAAAATAGACATGTAGACCA 3106
                                i   i    ii  vi   i i    ii        i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_51392036_5   3107 GTGGAACAGAATAGAAAACCCATAAAAGGATTCATATATTTACAGCTGAC 3156
                         i     i     v  i ii   v   vii ii    i     ii iii i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_51392036_5   3157 TGATCTTCATAAAAGCTGTCAAGGACATACATTGGAGAAAGGACGCCCTC 3206
                             i   ivv  i v  i    iv   v  v   i     i iivi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_51392036_5   3207 TTCAATAAATGGGGCTGGGAAAACTGGTTAACCATATGCAGAAGAATGAA 3256
                              i      v       v      v  ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_51392036_5   3257 ACTAGACCGCTATCTCTCACCATATACAAAA-TCAACTCAAGATGGATTA 3305
                         ii i    v   i   v              - i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_51392036_5   3306 AATACTTAAACATA-GACCTGAAACAATTAAACAACTAGAAGAAAACACA 3354
                         ? v  i    ii  -  v  i    v  v    vvi            i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_51392036_5   3355 GGGAAAACTCTTCAGGACATTGGTCAAGGCAAAGATTTTATGGCTAAGAC 3404
                           ?iv  v     iv   v    viv      v i   iv i v  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_51392036_5   3405 CTCAAAGGCACAGGCAACAAAGCAAAAAATAGACAAATGGAATTATATTA 3454
                         vi    i     i        iv          i    v i i vi  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_51392036_5   3455 AACTAAACAGCATCTGTGCAGAGAAAGAAACAATCAACAGAGTGAAGAAA 3504
                           v v  v i v i     vvvi  i  v  v     v i      i i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_51392036_5   3505 CAGCCTCTTGAATGGGAGAAAATATTTGTAAACTACTCATCCAAC--GGG 3552
                           i  iviv                   i   ii ivi   ii i--   
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_51392036_5   3553 ATTAATATCCATGATTT-CAAGGAACTCAGTAGTAAAACAAAAACAAACA 3601
                          i vi      vi  v -i  i      -- --  v   v--------  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTC--T--TACAACT--------CA 787

  chr2_51392036_5   3602 ATAACAACAACGAAAAACAAACAAAAACCCA--TTAAAAGTGGGCAAAGG 3649
                             i  -----   i     i  ---    -- ?    i          
  L1M4_orf2#LINE/    788 ATAATAA-----AAAGACAAATAA---CCCAATTWAAAAATGGGCAAAGG 829

  chr2_51392036_5   3650 ACATGAATGGACATGTCTCAAAAGGAGACATACAAATGACTAACAGGTAT 3699
                          iv     i     v    v    i   i         i i  i i i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_51392036_5   3700 ATGAAGAAATGCTGAACATCACCAATCAT 3728
                              i i     v       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (152 / 79)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.36 (33 / 14)  


3079 27.62 0.88 0.55  chr2_51451747_51458134.rev     4992  5896 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_51451747_5   4992 TGGAAGAATGTTCCATGCTCATGGGCAGGAAGAATCAATATCGTGAAAAT 5041
                              ii  i i     i      iiv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_51451747_5   5042 GGCCATACTGCACAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5091
                            v     v v   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_51451747_5   5092 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5139
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_51451747_5   5140 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5189
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_51451747_5   5190 AACAAAGCCAGAGGCATCACACTACCTGACTTCAAACTATACTACAGGGC 5239
                                iii    vv       v  ii i      viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_51451747_5   5240 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5289
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_51451747_5   5290 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACC 5337
                                i    i--    i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_51451747_5   5338 ATCTGATCTTTGACAAACCT-CAGAAAACAAGCAATGGGGAAAGGATTCC 5386
                          vi    i  i     ivv - vi i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_51451747_5   5387 CTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATAAGTAGAAAGCT 5436
                           v  i  i   i          v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_51451747_5   5437 GAAACTGGATGCCTTCCTCACACCTTATACAAAAATTAATTCAAGATGGA 5486
                            ii    iv   v         v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_51451747_5   5487 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAAC 5536
                          i ?    i  v    v   v       i      vi i   i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_51451747_5   5537 CTAGGCA-ATACCACTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5585
                         v    ?i- v i -i  iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_51451747_5   5586 ATACACCAAAAGCAAAGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5635
                         vv            v i          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_51451747_5   5636 ATTAAACTAAAGAGCTTCTGCACAGCAAAAAAAACTACCATCAGATTGAA 5685
                           i   v v  i i   i  ii vv    ii v    i  vv i v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_51451747_5   5686 CAGGCAACCTATGAAATCGGAGAAAATTTTCGCAACCTACTCGTCTGACA 5735
                         v  i     i iii   v         v  i    vii ivii     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_51451747_5   5736 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTGACAAGAAA 5785
                          i  i  vi          v  i  v      vv    v ii i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_51451747_5   5786 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5835
                           i     i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_51451747_5   5836 CTCAAAAGAAGACATTTATGCAGCCAA--AGCACATGAAAAAATGCTCAT 5883
                            v        i  vi viii     --            i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_51451747_5   5884 CATCACTGGCCAT 5896
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (150 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


1909 25.37 13.48 2.21  chr2_51486940_51489330     1085  1900 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_51486940_5   1085 TGGAGAGATATGTCATGTTCATGTGTCAGAAGATTCAGTATTGTTAAGAT 1134
                             i      vi          vi ii     i i i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_51486940_5   1135 GTAAATTCTCTCCTAATTGATTTATAGGTTCAAAAAAATCCCAATAACAA 1184
                          vv   v   i  v       i  i  i     viv      v  v v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_51486940_5   1185 TTTCAGTAGCCTCTTTTTGTAGAAATTAGGCAA-TTGATTATAAAATTCA 1233
                          ii   iv    -      i       - i   -i    iv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCA 148

  chr2_51486940_5   1234 TATAGAAATGCAAAG-ACCCAGAATATCCAGAACAATTTTGAAAAAGAA- 1281
                            i         i -          v   i      i           -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_51486940_5   1282 --TGAGGTTGGAGGACTAATACAACTTGATATCAAAAATTATTACAAACC 1329
                         --ii i           v i  vv iii  v      v   i      v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_51486940_5   1330 TCTGGTAATCAAAACAATGCAGAATTAAGATTAAGGTAGACA----AATG 1375
                          vii        i   i  ii v i iiv  v i i      ----i  v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_51486940_5   1376 AATGAAATGAAATAGAGGGTTCAGAAATAGAT------ATTTGTAGATAA 1419
                             i   ii   v   i  i        i i------    i i vi  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_51486940_5   1420 GTGTTTTCC--TAAGTATGGAAAAAC-ATCTCAGTGGAGAAGTGATAGTC 1466
                         v  v   i --i   vi  vv  i  -  -   i   i   ivi      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGTC 397

  chr2_51486940_5   1467 TTTTGAAAAAATAATGTTGAACCAATTGGCCATTTACCATTTACATGCAA 1516
                             v  v    ii  i  iiv   i   --  ----- ?ii        
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGG--AT-----AKCCACATGCAA 440

  chr2_51486940_5   1517 GAAGAAAGAACTTTAATTCATTTCTCATAGCATATACAAAAATTGAATGA 1566
                         -     v   v  vi ii v vi    i v              i v v 
  L1M4_orf2#LINE/    441 -AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_51486940_5   1567 AAATGGATCACGGGTCTTAAAATTGGGAAAAGC-AAAG---TGAAA---- 1608
                                   ?i ii  --    -- v  i   -   i--- i   ----
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCT--AAAT--GTAAGAGCTAAAACTATAAAACTCT 535

  chr2_51486940_5   1609 TGAAAGA-----TAAGAAACAACCATTATAATTTTGTGCTGGGCAAAAGT 1653
                          ii    -----  i ?ivv  i v ii i ii   v i i     vi  
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_51486940_5   1654 GTCTTAGCTATAACACCAAAAGTA-------------------------- 1677
                         v      v   i          i --------------------------
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_51486940_5   1678 -TTG----CCA-CAGAGTT-------TTTG--CTCTATAAAATA-TAT-- 1709
                         -   ----i  -  i i  -------    --  ii v ii i -   --
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_51486940_5   1710 -GAGAATGA----------CATAGAAGAAAAGGAAATATTTGCAAATCAC 1748
                         -  i i   ----------  i    viii  i                i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_51486940_5   1749 ATATCTGTGAAAAAGTTTGTA-----AATACTAGGTAAAGAACTCTCAAA 1793
                                vv  iiiii     -----    -  --           i v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATA-TA--TAAAGAACTCTTACA 782

  chr2_51486940_5   1794 AC---------AGAATACAA-TA-------TTAAAAACAGGCAAAAGATT 1826
                           --------- i  v    -  ------- ?     ii      i    
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_51486940_5   1827 TTA-CAGGAAGCTA-ACAAAGGAAATATTAGAATATCAAATACACACATA 1874
                          v -i  iv vi v-v     i i    vvi   iv v    vi     i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_51486940_5   1875 AAAAGATACTCAACTTCGTTAAACCC 1900
                                i      v  i????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (134 / 69)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 3.66 (128 / 35)  


2972 26.89 0.88 1.21  chr2_51529673_51536173     5099  6009 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_51529673_5   5099 TAGAAAATCATTCCATGCTCATGGATAGGAAGAGTCAATATTGTGAAAAT 5148
                          i    ivi  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_51529673_5   5149 GGCCATACTGCCCAAAGTATTTTATAGGTTCAGTGCTATTCTCATCAAGC 5198
                            v     v      v iv i  i  i    ii  v  i ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_51529673_5   5199 TATT-GTTGACTTTCTTCACAGAATTAGAAAAAAAAAAACT-ACTTTAAA 5246
                          vii- i  v    i  -i     v v  v  i------  - iii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG------CTGATCCTAAA 143

  chr2_51529673_5   5247 TTTCGTATGGAACCAAAAAAGGG-CCCATA-TAGCCAAGACAATCCTAAG 5294
                         v   i       -- viv     -    v -       i      i i i
  L1M4_orf2#LINE/    144 ATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_51529673_5   5295 CAGAAAGAACAAAGCTGGAAGCATCACACTACCTGAATTCAAACTATACT 5344
                         v ii          i    i vv       v  ii v      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_51529673_5   5345 ACAAGCCTACCGTAACCAAAACAGCAGGGTGCTGGTACCAAAACAGATAT 5394
                             iv    v    i   i    iiv   i    i iv ii i   i  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_51529673_5   5395 ATAGACCAATGGAACAGAACAGAGACCTCAGAATTAACACCACACATCTA 5444
                              i        i    iv    vii     v   vv   i    i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_51529673_5   5445 CAACCATCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGTAAAAGA 5494
                         iiii  vi    i  i     ivv  v   i v  vv      vi     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_51529673_5   5495 ATTCCCTTTTTAATAAATGCTATTGGGAAAACTGGCTAGCCATATGCAGA 5544
                           vvi     i  i     v ii     v      v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_51529673_5   5545 AAACTTAAAATGGAGCCCT-TCTTACACCTTATACAAAAATTAACTCAAG 5593
                          i v v  iv    v    -i  i     v                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_51529673_5   5594 GTGGATTAAAGACTTAAATTTAAGACCTAAAACTGTAAAAACCCT-GAAG 5642
                         i     i ?    i     v     v        i     vi i -    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_51529673_5   5643 AAAACCTAGGCA-ATACCATTCA-GAACATAGGCATGTTAATACACTTCA 5690
                              v    ?i- v i -   i-  v v i  ivv vi   i-ii   v
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG-GTTTCT 589

  chr2_51529673_5   5691 TGACTAAAATAGCAAAAGCAATGGCAACAAAAGCCAAAAGTGACAAATGG 5740
                          iiv  vi i v        vvi          vv    vv  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_51529673_5   5741 GATCTAATTAAACTAAAGAGCTTCTGCAAAGCAAAAGAGACTATAATCAG 5790
                           ii v  i   v v  i i   i  iivvv    i  v     v vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_51529673_5   5791 AGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCAT 5840
                               v  i     i                 v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_51529673_5   5841 CTGACAAAGGGCTAATATCCAGAATCTACAAGGAACATAAACAAATTTAC 5890
                             i  i  i  vi          v  i  i    vivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_51529673_5   5891 AAGAAAAATACAAACAACCCGAACAAAAAGTGGGCAAAGGATATGAATAG 5940
                           v     v     i     i vi?    i            v       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_51529673_5   5941 ACACTTCTCAAAAGAAGACATTTATGTGGCCAAGAAACATATGAAAAAAA 5990
                            i     v        i  vi vi       v  i  i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_51529673_5   5991 GCTCATCATCACTGGTCAT 6009
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (136 / 105)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


2674 26.75 3.27 0.79  chr2_51542914_51546006.rev     1716  2601 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_51542914_5   1716 TAAAGAGATATTCCATGTTTATGACTTGTAAGATTCAATATTGTCAAGAT 1765
                          ii i      i       i   iv   v    i i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_51542914_5   1766 GTCAGTTCTTCTTATCCTGCTCTATAGATTCAGTGGAATCCAAATGAAAA 1815
                          v  i v  i ii vvi  v    i       ii v     vv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_51542914_5   1816 TCC-ATCTAAGATATTTTGCAT---TTAACAAACTTATTCTAGAGTTTAT 1861
                            - v  ivvv -       v---  i    i  v  i   i i  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_51542914_5   1862 TTGAAGA-GCTAAAACTACAAAATAGGCAACACA-TATTGAAGGAGAAGT 1909
                         v  i i -  v iiiviv  i     v   v   - v     ii     v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_51542914_5   1910 AAAAAGCTGGAGGA-TGACACTGTCTCTCTTCAAGATGTACGATAAAGCT 1958
                          v    i       - v     vi ivvi     i iv   v i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_51542914_5   1959 GTAATAATTTTGATAGTGTGGCATTGGCGGAAGAACAGGCAAATAAATCA 2008
                         ii i    ivv  i       i i    iv   i i  i  v   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_51542914_5   2009 ATGTAACAGAATAGAGAGTGCAGAAATAGATCCCTATAAATAT----AAT 2054
                            v  i     v      v        i i  v  i vv   ----   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_51542914_5   2055 T----------AAGAGAGCAAAGGCAATACAATAAAGCAAAAA-ACTCTT 2093
                          ----------   i v  v   i v  v    iii v  i  - v    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_51542914_5   2094 TACAACAAATAGTATTGTAACAACTAGACATCCACATGAAAAAAAATGAA 2143
                          v        i  ii  vi      i  i ?       v    i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_51542914_5   2144 TCTAGACATAAACTTTAAACACTTTTCAAAAATTAACTTAAAATGGATCA 2193
                         vi i   vivv  i i v  vv v v            i           
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_51542914_5   2194 TAGATATGAATGTAAAAGGCAAAACTATAAAACTCTTAGAAGATAACATA 2243
                         ?   iv i       i  vi                       v      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_51542914_5   2244 GGATGAAACCTAGATAACCTTGAGTATGGTGATGGCTTCTTAGATACAAC 2293
                           ?vv   i  vvi i      i  vv  ii    i          ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_51542914_5   2294 AAAAAAGGCATGCTCCACGAAATAAATAATTGATAAACTGGACTTTATTA 2343
                          vv   i   iivv v  i   v   v   v      i       i  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_51542914_5   2344 CATTTTAAAACTTCTGTG--TGAAAGAAAA-TGT--AGACAG-AATACAA 2387
                         v v  v       i    -- v    i v - i --   v  -i v vi 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_51542914_5   2388 CAAGCCATATATTGATAGAAAAAATATTTTCAAAAGACACACCTAATCAA 2437
                            v   i v v  i--  i         v    vv i i i  i  v i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGG--GAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_51542914_5   2438 GGACTATTATCCAAAATATACAAAGAACTCTGAAAACTCAACAATAAGAA 2487
                              vv      i      i          v v       i     i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_51542914_5   2488 AGCAAACAATCTAATTAAAAAATGGACCAATGACCTTAAAT-GACACTTC 2536
                         ii    i  i i    ?        i v  v  i-  i   -    i   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGACATTTC 846

  chr2_51542914_5   2537 ATAAAAGAACATATATATCAGATGGAAAATACTCATATAAAAAGATGTTC 2586
                         viv      v     ---  i    vv    vv  i  i        i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATA---CAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_51542914_5   2587 CACGTCATATGTCAC 2601
                         v  i   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (127 / 106)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


2231 24.72 5.43 4.77  chr2_51666854_51669150.rev      904  1805 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_51666854_5    904 TGGTAAAA-ATCCCACGTTCATAGATAGAAAGATTCAATAATTCTTTTGA 952
                            v  i -      i      i   v i    i i    -  v  --- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA-TTGTT---A 46

  chr2_51666854_5    953 TCTCTCCCCAAATTGCGA-ACTCACCCTAAATTGATCTATTGATTCAAAA 1001
                         --------- i  v  i -    --  i           iv       vi
  L1M4_orf2#LINE/     47 ---------AGATGGCAATACTC--CCCAAATTGATCTACAGATTCAACG 85

  chr2_51666854_5   1002 AAGTCTCCATGAGCTTATCAG--ATTTTTTGGGTAGAAATTGACAAGCCT 1049
                         v i  i i  v ivv vi   --iii    vv i              iv
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chr2_51666854_5   1050 ATCATTACAATTATTATGTAAATATAATAGCTTTAAAATAGTCAAAAAAA 1099
                            -i  v    vv    v    ii  vi viii i     i     v  
  L1M4_orf2#LINE/    136 ATC-CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_51666854_5   1100 TTTTTAAAAAGAA---CAAAGTTGGAAAGCATAGGATACCTGACTTCTAA 1146
                          i  v        ---          iii vi viv v  ii i   v  
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_51666854_5   1147 ACTT--T-CAAAG-TACAGTAATAAAGACAATGTAATCATAATGTACATA 1192
                             -- -     -         v      i   ii --- v  -i    
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT---ACTG-GCATA 280

  chr2_51666854_5   1193 CAGATAAGCATATAGACTAACTGGACCA-AATTCAAAGTTTGGAAATAAA 1241
                         vi    ii        ii  -    vi -    v i   iii        
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAA-TGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_51666854_5   1242 CTCTTA-ATTT--GGTTA-----TTTTTAGTAAAGAATCAAAGATAATTA 1283
                          i v  -    --   i -----    iiii  i ivv v    iv   v
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_51666854_5   1284 AATGGTGAGAGAATGGGCTTTTGAAGAAATAGTAATAGAACAACTTAGTA 1333
                              v  i     i v     v  v    i  iv i i      vii  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_51666854_5   1334 TTCCTATGCAAAAACAACAGAAAAGAAGAATAAAGAACTTAGCAACTTAC 1383
                         ?i vi        --------------    i   ---  i vvv i   
  L1M4_orf2#LINE/    430 KCCACATGCAAAA--------------GAATGAAG---TTGGACCCCTAC 462

  chr2_51666854_5   1384 CCCACACTATACACAAAAATTAAATCAAAATGGGTCACAGATGTAAATAT 1433
                          i     i   i           v         i   ?   iv     i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_51666854_5   1434 TGTATAAGAACTAATACTATAAAACTTCTGGA-GAAAACCTAGGAGATAA 1482
                         -----    i    v           ii i  -      v    ? vv  
  L1M4_orf2#LINE/    513 -----AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_51666854_5   1483 TCTTTATGGCCTTTGGATAGGCAAAAATCTCTTGGCTACAGTAC-AAAAA 1531
                             ii  i    v  v       vii i    i v  iiii  -    i
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_51666854_5   1532 TATGATTTATTAAA--AACATTATATTG-TTGAACTTCATGAACATTAGA 1578
                         i ii viv iv   --  v v  v  vi-   i       v  v    i 
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_51666854_5   1579 AACTTTTATACTTGAAAC-ACAACAT----AAAATGAAA-TACAAGCCA- 1621
                                i i   v   v-   vi  ----   i     -v    v   -
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_51666854_5   1622 --------------TATTTATAAGTCATATATCTGATAAAGGACTTACAT 1657
                         --------------     ii  i               i      ii  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_51666854_5   1658 CTAGAAAATATCAATA--TTTT-CAAATCAATATTTAAAAGACATAAATT 1704
                          i    v    v  v -- i  -   v      v v        v v vi
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_51666854_5   1705 CCAAGTAAACGATAGTTGAAATATTTGAATAAACATTTTACCAAAGAACA 1754
                             v ?  vi  i vii  iv         i      iv        v 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_51666854_5   1755 CATATGAATGCCTAATATGCACATGAAAAGATGCTCAATATCACTAGTAA 1804
                         i   ii    v i    v                    i    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_51666854_5   1805 T 1805
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.46 (130 / 89)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 2.88 (92 / 32)  


2810 27.79 1.14 1.82  chr2_51678857_51680715      502  1379 (480)    L1M4_orf2#LINE/L1       37   908 (0)  

  chr2_51678857_5    502 AATATCATGAAAATGGCCATACTGCCCAAGGTTATTTATAGATTCAATGC 551
                              ii v  i     v     v     iv v  i  i        i  
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chr2_51678857_5    552 CATCCCCATCAAGCTACCAATGACTTTCTTCATAGAA-TTGGGAAAAACT 600
                         v     i     iv v   iivi i  i  iii    -   -- v  i  
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCT 134

  chr2_51678857_5    601 -ACTTTAAAGTTCATATGGAACCAAAAAAGAACCCACATTGCCAAGACAA 649
                         - iii    i           viiv  ii  v  viv  v     i    
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_51678857_5    650 TCCTAAGCAAGAAGAACAAAGCTGGAGGCATCATGCTTCCTGACTTCAAA 699
                           i i iv             i      vv   ii     ii i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_51678857_5    700 CTATTCTATGAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAA 749
                         viv v   ii i          i   i    ii         i iv ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_51678857_5    750 CAGAGATATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCAC 799
                         i   v       i        i    iv   ivii         vv   i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_51678857_5    800 ACACCTACAACCATGTGATCTTTAACAAACCTGACAAAAACAAGAAATGG 849
                            ii  iiii  vv    i  ii    ivv  v   i v  vvv     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_51678857_5    850 AGAAAGGATTCCCTATTTAATAAATAGTGCTGGGAAAATTGGCTAGCCAT 899
                         i     i  vvi  v  i  i    i         v  i   v  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_51678857_5    900 ATGTAGAAAGCTGAAACTGGATCCCTTCCTAACACCTTATACAAAAATTA 949
                            i i  iiv    ii    i    v   v     v             
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_51678857_5    950 ATTGAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACC 999
                          i v  i      i ?    i       v   v       i      vi 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_51678857_5   1000 CTAGAAGAAAACCTAGGC---AATGCCATTCAGGACATAGGCATGGGCAA 1046
                         i           v    ?---   -- -   iv   v v  vv i     
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAA 581

  chr2_51678857_5   1047 GGACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTG 1096
                         v ii   v iiv  vi            vvi          vv     v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_51678857_5   1097 ACAAATGGGATCTAATTAAACTAAAGAACTTCTACATAGCAAAAAAAGAA 1146
                          i    v   ii v  i   v v  i     i iiiivv    ii v---
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC--- 678

  chr2_51678857_5   1147 AAAAAAAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAA 1196
                         --------    i  vv i      v  i     i   i           
  L1M4_orf2#LINE/    679 --------ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_51678857_5   1197 ATTTTTGCAATCTACCCATCTGACAAAGGGCTAATATCCAGAATCTACGA 1246
                           v       vii ivi      i  i  i  vi          v  ii 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_51678857_5   1247 AGAATTTAAACAAATTTACAAGAAAAAATCAA----CCCCATCAAAAAGT 1292
                             i ivv    v iv i  v     iv   ----   v  i?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_51678857_5   1293 GGGCAAAGGATATGAAGAGACCCTT-TCCAAAGAAGACATGTATGCAGCC 1341
                                    v    v    vi  -           i  ii viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_51678857_5   1342 AACAGACACATGAAAAAAGGCTTAGTAACTTTTTTCTA 1379
                           i ii          i v   i ii v v????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (9 / 872), avg. gap size = 2.89 (26 / 9)  


2590 23.01 3.29 7.21  chr2_51705148_51707474.rev      893  1835 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_51705148_5    893 GAAACTGATATTCCATGTTCATAGATTGGATGAATTAACATTGTTAAAA- 941
                             --     i          i       v  v    i        i -
  L1M4_orf2#LINE/      3 GAAA--GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_51705148_5    942 -ATCATACTTTCTAAAGTGATCTATGGATTTAGTGCAATTCCTTTCAAAA 990
                         -iiv     ii i   v       ii    i ii     i   v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_51705148_5    991 TATGAATGATTTTCTTCAAAGAAATAGAAAAAC-AATACTAAATGTCATA 1039
                          viv iiviii  i  iiv      v  v  i -i  v     vv     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_51705148_5   1040 TGGAACCACAAAAGTCACCAAATAACCAAAGCGATACTGAGGAAAAAAAG 1089
                              vii   ii v v vi    i     i i  vi   --    i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chr2_51705148_5   1090 AACAAAGCTGAAGGCATCATACTCCCTGGCCTCAAAAATATACTACAAAG 1139
                                i  i   vv   i   i  iiiii      v -          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_51705148_5   1140 CTA-ACCAAGCAACACAGAG-----CTGGTATAAAAACAGACACATGGAA 1183
                            - vi  v   v    v -----    i    ii i     i  i  v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_51705148_5   1184 CAATGGAAAAGGATAGAGAACCCAGAAATAAATCCACACATCAAGAGCCA 1233
                                 v  i  v    ii           i   i    iv vi i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_51705148_5   1234 ACTGATTTTTTTACAAAG-TGCCAAAACACATT----GGAAAAAGAACCA 1278
                          i       iv-    i -      i  -    ----  ii      ivi
  L1M4_orf2#LINE/    348 ATTGATTTTCG-ACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAG 395

  chr2_51705148_5   1279 TCTCTTCAATAAATGGTGCTGGGA-AATTGGATACCCACATGCAGAAGAA 1327
                            i     i              -  i      ?         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_51705148_5   1328 TGAGACTAGAAACCTCTGTCTCAC--TATATTAAAAATAATCAAGAGAGA 1375
                            iii i  --  i  ii     --i    - v   -   i  ------
  L1M4_orf2#LINE/    446 TGAAGTTGGA--CCCCTACCTCACACCATAT-ACAAA-AATTAA------ 485

  chr2_51705148_5   1376 AACTCCATCTCAAAAAAAAAAATAATGATCAACCAAAAAGTGGATTAAAG 1425
                         --------       -------------------------     i ?  
  L1M4_orf2#LINE/    486 --------CTCAAAA-------------------------TGGATCAWAG 502

  chr2_51705148_5   1426 AC--AAACGTAGG-GCACAAAACAATGACACTAGTATAAGAAAACATGGG 1472
                           --   i   i -  -i     v  i v   vv  v          i  
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_51705148_5   1473 GG--AATACTTAATGACAATGGACTAGGCAAGAACTTTTTTTAAA---GA 1517
                         ? --   -   vi    vv   ii       vii--   i   i ---  
  L1M4_orf2#LINE/    552 NGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGG--TTTCTTAGATATGA 598

  chr2_51705148_5   1518 CCTCAAAAACTTGGACAACGAAAGCAAAAATAGGCAACAAAACTAAAATA 1567
                          vi     i viiii    i    v        ii  ---- i ii ---
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA----ATTGGA--- 641

  chr2_51705148_5   1568 CTCACATCAAACTAAAAAGCTTCTGCACAGCAAAGAAAACAATCAACAAA 1617
                           i-       v v    i   i  ii vv     i v  v     v   
  L1M4_orf2#LINE/    642 CTT-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_51705148_5   1618 TTGAGGAGACAATCTACAAAATGGGAGAAAATATTTGTAAAGTATACATC 1667
                         v   ii      i i   i                  i   vi   i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_51705148_5   1668 CGACAAAAGTTTAATATCCAGAATATACAG-GAATCCAAACAACTCAATA 1716
                         i  i  ii vi vi             i i-   ii vv           
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_51705148_5   1717 GCAAAATAAAAAGA-AAACAATTTAATTTTTTAAATGGGCTAAAGACCTA 1765
                         -----         -   i  iii    ?vv-        v  i  ii i
  L1M4_orf2#LINE/    791 -----ATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTG 834

  chr2_51705148_5   1766 CGTAGACACTTCTC---AAAAGACA-ACAAATAGCCAATGGGTATATGAA 1811
                         vi      i     --- i    i -      i      ii i i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_51705148_5   1812 AAAATTTTCAACATCACTAGTCAT 1835
                           i  vi         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (149 / 64)
Gap_init rate = 0.04 (34 / 906), avg. gap size = 2.91 (99 / 34)  


2715 27.26 2.91 1.45  chr2_51739039_51744701.rev     4276  5170 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_51739039_5   4276 TAGAAAAACTTCCCATGCTCACTGATACAAATAATCAATATTGTGAAAAT 4325
                          i    i iv       i   iv   vvi  v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_51739039_5   4326 GACCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTTCTATCAAAT 4375
                          i v     v      v i  i  i        i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_51739039_5   4376 TACCATTGACATTCTTCACA-AAATTAATTAGAAAAAACT-ATTTTAAAA 4423
                          v   vivi v  i  ii  -     i i------  i  -  ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC------AAGCTGATCCTAAAA 144

  chr2_51739039_5   4424 TTCATATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAC 4473
                                    viiv  ii  v  viv        i      i i iv v
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_51739039_5   4474 AAAGAACAAAGCTGCTGAAGGCCTTTCACTACCTAAATTCAAACTATACT 4523
                         i          i  ---i   v  iv    v  i  v      viv    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTG---GAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_51739039_5   4524 ATAAAGCTACATTAACCAAAACAGCATGGTACTGGTACAAAAAACAGACA 4573
                          i         v   i   i    ii         i i  ii -i     
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACA 290

  chr2_51739039_5   4574 CATAGACCAACAGAACAGAATAGAGAACTCAGAAATACGACCACACTTCC 4623
                         i     i   ii   i     v    iii        viv   i  v ii
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_51739039_5   4624 ACAGCCATCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAG 4673
                          ii i  vi    i   i    ivv  v   i v  vv            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_51739039_5   4674 GAT---------------TGGTGCTGGGAGAACTAGCTAGCCATATGCAG 4708
                         i  ---------------           v    i v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_51739039_5   4709 AAAATTGAAACTGGACCCCTTCCTTACAGCTTATACAAAAGTTAACTCAA 4758
                           i v    ii         v   i   v v         i         
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_51739039_5   4759 TATGGATTAAAGATTTAAATGTAAAATCCACAACTGTGAAATCCCTAGAA 4808
                         v      i ?   ii         i v i v    i i   ii i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_51739039_5   4809 GAAAATCTAGGCA-ATACCATTTAGGACACAGGTATGAGCAAAGATTTCA 4857
                              iv    ?i- v i -  iiv   viv  vv ii    v i    v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_51739039_5   4858 TGACAAAAACACCAAAAGCAATGACAGCAAAAGCAAAAATTGACAAAC-G 4906
                          iivv vi            vvii  i      v      v  i   i- 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_51739039_5   4907 GACTCTAATTAAACTAAAGAGCTTCTGCAGAGCAAAAGAATCTATCATCA 4956
                             - v  i   v v  i i   i  iivvv    i  vv      vv 
  L1M4_orf2#LINE/    640 GACT-TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_51739039_5   4957 GAGTAAACAGACAACCTACAAAATGGGAGAAAATATTTGCAAACTGTGCA 5006
                         i   i  v        i   i                      iii ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_51739039_5   5007 TCTGACAAAGGTCTAATACCCAACATCTAAAAGGAACTTAAACAAATTTA 5056
                              i  i  v  vi  i   iv  v  v  i     ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_51739039_5   5057 CAAGAAAGAAAACAAAAAACCTAATTAAAAAGTGGG-AAAGGAC------ 5099
                         i  v   -  i     v    i    ?    i    -      i------
  L1M4_orf2#LINE/    789 TAATAAA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_51739039_5   5100 AAACACTTCTCAAAAGACAACATTTATGCAGCCAACAAACATATGAAAAT 5149
                          i   i     v     vi i  vi viii     i  i  i       v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_51739039_5   5150 AAGCTCAACATCACTGAGAAC 5170
                          v           ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.00 (39 / 13)  


1123 28.71 6.94 4.10  chr2_51903322_51904922      491  1124 (477)    L1M4_orf2#LINE/L1      257   908 (0)  

  chr2_51903322_5    491 TTAAATCAGTGCGTAGTACTGACATAAATATACAAATAAAAAAGATAAAC 540
                          i  iv     -- i      i     iv   v v   v ---   v  i
  L1M4_orf2#LINE/    257 TCAAGACAGTG--TGGTACTGGCATAAGGATAGACATATA---GATCAAT 301

  chr2_51903322_5    541 AGAAGAGAACAGAGAGTCCACAAACAGATCCACACATATATGAACAACTG 590
                         i   v    iv         v   i i i   i    v    iv   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_51903322_5    591 ATTTATAACTCAGGTAAAAAAAAAAAAAAACAATTCAGTGGAGATTGGAT 640
                             vii  vvi   ivv  i -------- v     i   i  vv i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGA--------CCATTCAATGGGGAAAGAAT 393

  chr2_51903322_5    641 TTTGTTTTCAAGAAATAATGACAGAAATCAATTATTTACCCACAAGCGTA 690
                         vv v       v    ii  vii i --   i ivv  ?     v  iv 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGA--CAACTGGATAKCCACATGCAAA 441

  chr2_51903322_5    691 AAAATAAAAT---------ACCTCACACCATTGATTAAAATTAACTAAAA 731
                          i   i  i ---------            vv iv          v   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_51903322_5    732 A---ATCATAGACCTACATATAAAACCTAAAATTACA----TCT-AGAAG 773
                          ---    ?       v  i   i v      i  i ----   -     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_51903322_5    774 AACACACAGGAAAATAACCTCTGTAACCTTAAAATAAG-AACTATTTTT- 821
                           v   i   ?iv -  i  ii  i     iiiv  i -  ivi   i -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_51903322_5    822 -GATACAATAT-ATAAGTGTGATTCATATTAGAACAAATGGATAAATT-- 867
                         -    ii i i- v   iiii viv i vv    v    i        --
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_51903322_5    868 ----TATC----TTCAA---TTTCATCCTT-AAAG-------TTAGGAGA 898
                         ----i   ----  v  ---   ii v   -    ------- i i  i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_51903322_5    899 AT-AAAAGGCCAGCCACAGAGCAACAAAAACTATTTCTACTATATATATC 947
                         i -     i v v       iiiiv i   v     vi vvvi       
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_51903322_5    948 TGGTGAAGGAATAATAATTAGAATATGTCTGGAACTCTTAAAATTCATTG 997
                           i i i   v vi  vii       i vvi         v  i   v i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_51903322_5    998 ATAGTAAG-CTAACAACCCAATTAAAGGACAAGGGCAAAAAACTTGAACA 1046
                            iv   - v  i         ?  ii i--       ii i     i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAAT--GGGCAAAGGATTTGAATA 838

  chr2_51903322_5   1047 GCCACATTACCAGAGTAGGTGTACTTATTTGATGGCAAAGAAGCACGTGA 1096
                          v  iv iv   i  v  i i   -- ---i     v  v      i   
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATAC--A---AATGGCCAATAAGCACATGA 883

  chr2_51903322_5   1097 AAAGACATAAGTACACATTAGTTATTAG 1124
                              iii--- vv    i ????????
  L1M4_orf2#LINE/    884 AAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (107 / 71)
Gap_init rate = 0.04 (23 / 652), avg. gap size = 3.04 (70 / 23)  


2788 27.67 1.20 2.29  chr2_51908071_51914488.rev     5009  5926 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_51908071_5   5009 TGGAAGAACATTCCATGCTAATGGGTAGGAAGAATCAATATCATAAAAAT 5058
                              ii i  i     i v    i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_51908071_5   5059 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_51908071_5   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_51908071_5   5157 TATGGAACCAAAAATGAGCCCACAAT-GCCTAGATAATCCTAAGCCGAAA 5205
                                viiv  iv  -    v   -   v i i    i i ivvii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_51908071_5   5206 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTGCAAGG 5255
                                 i      vv   ii  v  ii i      viv    i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_51908071_5   5256 CTACAGTAACCAAAAAAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5305
                                  i   i v  ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_51908071_5   5306 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5353
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_51908071_5   5354 CATCTGATCTTCAAAAAATCAGAAAGAAAGAAAGAAACAAACAAGAAATG 5403
                           vi    i   i -----  ---  iiv vv ii v  vv   ----  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGA-----CA---AGGGTGCCAAGACCATTCAA----TG 383

  chr2_51908071_5   5404 GGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCA 5453
                                i  vvi  v  i  i              v      v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_51908071_5   5454 GATGTAGACAGCTGAAACTGGATCCCTTCCTTACACCTTATACTAACATT 5503
                         v   i i viiv    ii    i    v   i     v     v  v   
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_51908071_5   5504 AATTCAAGACGGATTAAAGACTTACATGTTAGACCTAAAACCATAAAAAC 5553
                           i    i i    i ?    i  v    v   v       i      vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_51908071_5   5554 CCTAGAAGAATACCTAGGC---AATGCCATTCAGGACATAGGCATGGGCA 5600
                          i        v  v    ?---   -- -   iv   v v  vv i    
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCA 580

  chr2_51908071_5   5601 AGGACTTCATGACTAAAACATCAAAAACAATGGCAACAAAAGCCAAAATT 5650
                          v ii   v iiv  vi   i     i  vvi          vv     v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_51908071_5   5651 GACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAC 5700
                           i    v   ii v  i   v v  i i   i  ii vv    i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_51908071_5   5701 TACCATCAGAGTGAACAGGCAACCTAAAAAATGGGAGAAAATTTTTGCGA 5750
                           i  vv i      v  i     i v i             v     i 
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_51908071_5   5751 TCTACCCATCTGACAAAGGGCTAATATTCAGAATCTACAAGAAACTGAAA 5800
                         vii ivi      i  i  i  vi   i      v  i  ii    vvv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_51908071_5   5801 CAAAATTTACAAGAAAAAATCAAACAACTCCATCTAAAAGTGGGTGAAGG 5850
                            v- iv i  v     iv    i   i v  i?    i    ii    
  L1M4_orf2#LINE/    781 CAAC-TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_51908071_5   5851 ATATGAACAGACACTTCTCAAAAGAAGACGTTTATGCAGCCAG---ACAC 5897
                           v    i     i     v        ii vi viii    i---i   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_51908071_5   5898 ATGAAAAAATGCTCATGATCACTGGCCAT 5926
                                i       vv    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (152 / 98)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.13 (32 / 15)  


2581 26.69 1.20 3.59  chr2_52003769_52005952.rev      775  1692 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_52003769_5    775 CCATGCTCATGGATGGGTAGAACGAATATTGTGAAAATGACCACACTTCC 824
                              i        v  v   viv        v  i   i v i   i  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_52003769_5    825 AAAAGCAATCTGTAAATTCAATGCAATTCCCATCAACATGCCA--TGATC 872
                         v   vii    ii i      i     i  i     v  v   --  -- 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG--C 110

  chr2_52003769_5    873 ATTCATCACAGAATTAGAAAAAAGC-AATCCTATAACTCATATGGAACCA 921
                         v  iv ii     v v  v  --  -i      v  i          vii
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCATATGGAAATG 158

  chr2_52003769_5    922 AAAAAGAGCCCACATAGCCAGACAAAGCAAAAAAAAAAAAAATTTATATA 971
                         v  ii  v  viv       i vv  v vvi     i  i  i-------
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC------- 201

  chr2_52003769_5    972 TATATATATATATATATCTGGAGGCATCGCATTACCTGACAT-GAAACTA 1020
                         ------------- v vi      vv  i  i v  ii iv -i     -
  L1M4_orf2#LINE/    202 -------------AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT- 237

  chr2_52003769_5   1021 CAGTATAAGGCCATAGTCACCAAAACAGTATGGTACTGGTATAAAAATAA 1070
                         i v  i  i  i i   v i   i     i         i    ii   i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_52003769_5   1071 GCACATAGACAAATGGAACAGAATAGAGAACTCAGAAATAAACCCAAATA 1120
                         i  i     iv       i     v    iii              v i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_52003769_5   1121 CTTACAGCCAACTGATCTTCGACAAAGTAAACAAAAACATAAAGTGGGTA 1170
                         i   ii i   i    i        i vviv   i v   vv i    v 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_52003769_5   1171 AA-AACACCGTGTTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATG 1219
                           -  i viv v                    i  i   vv ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_52003769_5   1220 TAGAAGAATGAAATTGGATCCTCATTTCTCACCTTATACAAAACTCAACT 1269
                         i i         i     i  ii ii  v    v         v i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_52003769_5   1270 CAAGATGGATCAAAGACATAAATCTAAGACCCGAAACCATAAAGATTCTA 1319
                            i        ?    v     v     v ii    i     iv ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_52003769_5   1320 GAACAAAACATTGGAA-AAACCCTTGTATACATTCGCTTCGGCAAAGACT 1368
                            v       v  ?i-   i i i  i-  v  v v  v     v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTT 586

  chr2_52003769_5   1369 TCATGACCAAGAACTCAAAAGCAAATGGAACAAAAGCAAACATAAATAGA 1418
                           v iivi v  vvi        v v v        v   v   i   i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_52003769_5   1419 TGGGACTGAAATAAACAAAAAAGCTTCTGCATAGTAAAAAAAAAAAAAAA 1468
                          v     vv vi   vvv    i   i  iiivvi   ii v vv ----
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA---- 682

  chr2_52003769_5   1469 AAATCAGCAGAGTTAACAGACAACCCATAGAGTGGGAGAAAATCTTCACA 1518
                         ---   iv i   v  v          i   i           v  ii  
  L1M4_orf2#LINE/    683 ---TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_52003769_5   1519 ATTTATACATCCAACAAAGGACTAATATCCAAAATCTACTAGGAAATCAA 1568
                          v i   i   ii i  i     vi      i   v  iv i   v  vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_52003769_5   1569 ACAAACCAGCAAGAAAAAAA-----AATCCCATCAAAAAGTGGGCTAAGC 1613
                             vi  ii  v     i -----  i  v  i?    i     v   v
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_52003769_5   1614 ATGTGAATAGACAATTCTCAAAAGAAGATATACAAATGGCTAAGAAGCAC 1663
                           v          v     v                    i  v      
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_52003769_5   1664 ATAGAAAAATGTTCAACATCATTAATTAT 1692
                           ii   i   i         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (136 / 105)
Gap_init rate = 0.01 (12 / 896), avg. gap size = 3.67 (44 / 12)  


2171 28.42 1.97 1.45  chr2_52020595_52024095.rev     1806  2565 (936)    L1M4_orf2#LINE/L1       13   776 (132)  

  chr2_52020595_5   1806 CTGTGCTCATGGATATGAAGAATCAATATTGTTAAAATGGCCACAGTGCC 1855
                          ii  i        vv     v i           i     v i v v  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_52020595_5   1856 AAAAGCAATTTACAGATTCAATGCTGTTCCTATCAAAATACCAATGAAAT 1905
                         v   vii  i           i  vi i           v   iivivv 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_52020595_5   1906 TTGTCACAGAA-TT----AGCTAACACTCTTCTAAAACTTATATGGAACA 1950
                           v ii     -  ----    i ----- i      i i        vv
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGA-----TCCTAAAATTCATATGGAAAT 157

  chr2_52020595_5   1951 AAAAAACAGCTGGAATGGCCAAATCAATCCTAAACAAAAACAACAAAGTT 2000
                         iv  iiv v ii    i      v     i i  v  i  v         
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_52020595_5   2001 GGAAGCATGATATTACCTGACTTCAAACTATAGTATAAGGCTACAATAAC 2050
                            i vv v i i v  ii i      viv  v  i  i      i   i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_52020595_5   2051 CAAAACAGCATGCCACTGGTACAAAAA--GACACATA--TCAAAGGAACA 2096
                            i    ii  vi     i i  ii --    i   --    v    i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_52020595_5   2097 TCATACAGAGCCCAGAAATAAAGCTGCACAGGTACAACCATATAACCTTC 2146
                         vv  vv    i           v iii   vv  iiii  vv i ii   
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_52020595_5   2147 AAAAAAGTCAACATAAACAAGCAATGGGGAAAGGACTCCCTATTCAATAT 2196
                         i v  i viiv  vi v  vv            i ivvi  v     i v
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_52020595_5   2197 ATGGTGCTGAGATTATTGGCTAACTGTATGCAAAACATTGAAATTGGATC 2246
                                  i  iv i   v  ? iii        v v    i     i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_52020595_5   2247 TCTTCCTTACACCATATACAAAAATCAACTCAAGATGGAATAGTGACTTA 2296
                         i  v   i                 i       i     vi ?v   i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_52020595_5   2297 AATGTGAAAACTAAAACTGTAGAAACACTT-GAAATCAACCTAGG---AA 2342
                              i i i        i  -    v   -   ivv   v    ---  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_52020595_5   2343 ATACCAGTCTGGGCATAGGTTTCAGCCAA-GGTTTCATGAAAAAGATGAC 2391
                           viiv  -- iv v i    --  v   -      v ii v v  iiv 
  L1M4_orf2#LINE/    557 ATCTTCGT--GACCTTGGGTT--AGGCAATGGTTTCTTAGATATGACACC 602

  chr2_52020595_5   2392 AAAAGCAATTGCAACAAAAACAAAAATTCACAAATGGGACCTAATTAAAC 2441
                                vvv         iv      vv i    v    i v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_52020595_5   2442 TAGACAGCTTCTGCACAGAAAATGATATTATCAATAGAGTAAATAG-CAA 2490
                          vi v i   i  ii vvv   v  i i      v i   i  v  -   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_52020595_5   2491 GCCCACAGAAGGGGAGAAAATATTTGCAAAATATACATCTGACAAAAGTC 2540
                         -         v                   vi   i      i  ii v 
  L1M4_orf2#LINE/    703 -CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_52020595_5   2541 TAACATCTAGAATCTATAAGAAACT 2565
                          vii   i     v     ii    
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.30 (121 / 93)
Gap_init rate = 0.02 (13 / 764), avg. gap size = 2.00 (26 / 13)  

 471 21.88 0.78 0.00  chr2_52020595_52024095.rev     2882  3009 (492)    L1M4_orf2#LINE/L1      780   908 (0)  

  chr2_52020595_5   2882 ACAAGCTAAAAACAAACGAACAAAAATCCTCATTATAAAGTGGGCAAAGG 2931
                             vii  v  i   vii     v v  iv   ?v   i          
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_52020595_5   2932 AAATGAACGGATACTTTTCAAAAGAAGATATACACATGGCCAAGAAGCAC 2981
                          vv    ii  i i  i  v              v        v      
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_52020595_5   2982 ATGAAGAAA-GCTCAATATCACTGATAAT 3009
                              i i -      i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.01 (1 / 129), avg. gap size = 1.00 (1 / 1)  


2925 26.13 1.87 1.76  chr2_52051597_52055959     2981  3887 (476)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_52051597_5   2981 TGAAAACATATTTCATCTTCATGGATAGGAAGAATCAATATTGTGAAAAT 3030
                           i   v    ii   v         v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_52051597_5   3031 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 3080
                            v     v      v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_52051597_5   3081 TATCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTACATTTCAT 3129
                          vi  vivi v  i  ii     v v  v  i-  - iii  v v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_52051597_5   3130 ATGGAA-TCAAAGAAGAACCCATA-TAGTCAAGATAATCCTAAGCAGAAG 3177
                               - vv   -- i     v -   i   i i    i i iv ii i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_52051597_5   3178 GAACAAAGCCGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 3227
                                 ii     vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_52051597_5   3228 CTACAGTAACCAAAACAGCATGGTACTGATAACAAAACAGACATATGGAC 3277
                                  i   i    ii        ii vv ii i        i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_52051597_5   3278 CAATGGAACAGAAGAGAGACCTCAGAAATAACACCACACATCTACAACCA 3327
                                 i    vv    vii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_52051597_5   3328 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGCATTCCC 3377
                         vi    i  i     ivv  v   i v  vv            v  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_52051597_5   3378 CATTTAGTAAATG---TTGGGAAAACTGGCTAGACATATGCAGAAAACTG 3424
                         iv  i ii     ---i     v      v  ?v  i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_52051597_5   3425 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 3474
                           ii         v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_52051597_5   3475 TAAAGACTTAAACATAAGACCTAAAACCGTAAAAACCTTAGAAGAAAACA 3524
                         i ?    i    ii     v       ii     vi              
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_52051597_5   3525 TAGGCA-ACACCATTCAGGACATAGGCATGGGCAAAGACTTC------AT 3567
                             ?i- v i -   iv   v v  vv i     v ii   ------  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_52051597_5   3568 GACAAAAACAGCAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGA 3617
                             vv  v    ---   --          vv     v  i    vi  
  L1M4_orf2#LINE/    597 GACACCAAAAGCA---CAA--GCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_52051597_5   3618 TCTAGTTAAACTAAAGAAGTTTCACATAGCAAAAGAAACTATCATCAGAG 3667
                         ii vi i   v v  i  v   iiiiivv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_52051597_5   3668 TGAACAGGCAACCTACAGAATGGGAGAAAATTCTTGCAATCTACCCATCT 3717
                             v  i     i                 vi      vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_52051597_5   3718 GACAAAGGTCTAATATCCAGAATTTACAAGGAACTTAAAGAAATTTATAA 3767
                           i  i  v  vi          v  i  i     ivv v  v iv    
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_52051597_5   3768 GAAAAAAACAA----CCCCATTAAAGAGTAGGCAAAGGAGATGAACAGAC 3813
                         v     i    ----   v   ?  i i i         vv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_52051597_5   3814 ACTTCTCAGAAGAACACATTTATGTGGCCAACAAACATAGGAAGAAAATG 3863
                          i     vi     v i  vi vi       i  i  i v   i -----
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA----- 886

  chr2_52051597_5   3864 TGATACATATACATCACTGATAAT 3887
                         -   i vi -      ????????
  L1M4_orf2#LINE/    887 -GATGCTCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (134 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.36 (33 / 14)  


2182 27.60 0.47 0.95  chr2_52150877_52155417.rev     2854  3487 (1054)    L1M4_orf2#LINE/L1        2   632 (276)  

  chr2_52150877_5   2854 GGAAACACAACTCATGCTTATGGATAAGTAGAATCAATATTGTGAAAATA 2903
                              v i v i    i i      vi v   v i        v  i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_52150877_5   2904 ACCATACTGGTAAAAGCAGTCTACAAATTCAATGCAATTCCCATCAAAAT 2953
                         i v     vviv   viii      i      i     i  i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_52150877_5   2954 ACCACCATCATTCTTCACAGAGTTAGAAAAAACAATTCTAAAATTTATAT 3003
                         v   v vv v  i  ii    iv v  v  ivii  i        i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_52150877_5   3004 GAAACCAAAAAAGAACCCTCATAGCCAAAGCAAGACTAAGCAAAAAGAGC 3053
                          i  viiv  ii  v  vvv         i   vvi i iv  i    i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_52150877_5   3054 AAATCTGGAGGCATGACACTACTTGGTTTCAAACTGTACTACAAGGCCAT 3103
                            vi      vv v     v iiii       viv        i  i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_52150877_5   3104 AGTCACCAAAACAGCATGGTACTGGTATAAAAATGGGCACATAAACCAAT 3153
                            v i   i    ii         i    ii  i i  i   i i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_52150877_5   3154 GGAACAGAAT-GAGAACCCAGAAATAAAGCCAAATACTTACAGCCAACTG 3202
                             i     -    ii           v   v i i   ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_52150877_5   3203 ATCTTTGACAAACCAAACAAAAACACAGAATGGGAAAAGGACACCCTTTT 3252
                           i  i     ivvviv   i v  ivv      i    i i vi     
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_52150877_5   3253 CAACAAATGGTGCTGGGATAATTGGCTAGCCATATGGAGGAGAATGAAAC 3302
                                           i  i   v  ?   i   v ii        ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_52150877_5   3303 TGTATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATCAAA 3352
                           v i  ii i   v    v           i       i        ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_52150877_5   3353 GACTTAAACCTAGGAGCTGAAACTATAAGCACTCT-AGAAGATAACATTG 3401
                            i    iv  i     i         i-     -      v     v 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAG 550

  chr2_52150877_5   3402 GAA-AAACCTTTCTAGACATTGACTTAGGCAAGGATTTATTTAATGACCA 3450
                          ?i-   i   iv -   v   iv        v i   v  vi  ---- 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGAT----A 595

  chr2_52150877_5   3451 AGAACCCAAAAGAAAATGCAATAAAAAGAAAGATAGA 3487
                         v  vv       v v v    i    ii   i     
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

Transitions / transversions = 1.57 (105 / 67)
Gap_init rate = 0.01 (6 / 631), avg. gap size = 1.50 (9 / 6)  

 919 21.78 3.63 1.65  chr2_52150877_52155417.rev     3748  4050 (491)    L1M4_orf2#LINE/L1      600   908 (0)  

  chr2_52150877_5   3748 ACCAAAA--AAAAACCAAAACAAAAGCAAAAATATATAGTTGGGACTTAA 3795
                                -- v  i ---        v       v   iv v      v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGC---AACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_52150877_5   3796 TCAAACGAAAGAGCTTTT---CTTGGCAAAAGAAACAGTCAGCAGAGTAA 3842
                              vvv  i i     ---   --    i  v  vi   iv i   i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGA 694

  chr2_52150877_5   3843 ACAGACAACCCACAGAGTGGGAGAAAATCTTCCCAACATATACATTTGAC 3892
                          v              i           v  iv   vvi   i  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_52150877_5   3893 AACAGACTAATATCCAGAATCTGCAACAAACTC----AAATCAGTAAGAA 3938
                           vi    vi          v ii  vi     ----  v   i   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_52150877_5   3939 AAAAACAGACAATCCTATCAAAAAGTTTGCTAAGGACATGAATAGACGAT 3988
                            i   i i  i  v  i?    i vv  v     iv         iv 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_52150877_5   3989 TCTCAAAAGAAGATATACAAATGTCCAA-AAAC-CATGAAAAAATGATCC 4036
                             v                  v    -  i -        i   v  v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_52150877_5   4037 ACATCGCTAATGAT 4050
                              i????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 0.97 (32 / 33)
Gap_init rate = 0.02 (7 / 309), avg. gap size = 2.29 (16 / 7)  


3180 27.53 0.44 0.44  chr2_52178455_52184841.rev     4988  5895 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_52178455_5   4988 TGGAAGACCATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5037
                              iivi  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_52178455_5   5038 GGCCACACTGCCCAGGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5087
                            v i   v    iiv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_52178455_5   5088 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5135
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_52178455_5   5136 TATGGAACCAAAAAAGAGCTCGCATCACCAAGTCAATCCTAAGCCAAAAG 5185
                                viiv  ii  v iv v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_52178455_5   5186 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5235
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_52178455_5   5236 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5285
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_52178455_5   5286 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5333
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_52178455_5   5334 ATCTGATCTTTGACAAACCTGAAAAAAACAAGCAATGGGGAAAGGATTCC 5383
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_52178455_5   5384 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5433
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_52178455_5   5434 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5483
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_52178455_5   5484 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5533
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_52178455_5   5534 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAA 5583
                         v    ?i v viv   iv   v v  vvii     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_52178455_5   5584 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5633
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_52178455_5   5634 TTAAACTAAACAGCTTCTGCACAGCTAAAGAAACTACCATCAGAATGAAC 5683
                          i   v v  v i   i  ii vv v  i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_52178455_5   5684 AGGCAACCCACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5733
                           i         i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_52178455_5   5734 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5783
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_52178455_5   5784 AAACAAACAACCCCATCAAAAAGTGGACGAAGGACATGAACAGACACTTC 5833
                          i     i     v  i?    i   i i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_52178455_5   5834 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5883
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_52178455_5   5884 ATCACTGGCCAT 5895
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2680 25.69 9.00 0.36  chr2_52200910_52202658      425  1257 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_52200910_5    425 AGAGATCGCCTATGTTCATGAATTAGAA-------TATTGCTAAAATTTT 467
                          i    vv  i         i   i   -------     i   i  vvi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_52200910_5    468 CATACTACCCAAA------------------GCAATTCCTGTTAAAATTC 499
                         v     v      ------------------     i   i i     i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_52200910_5    500 TA--------------------------------------ATTTGTTTAG 511
                         i --------------------------------------   ii v i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_52200910_5    512 AACCACAAAAGACCCCAAATAGCCAAAGCAATCTTGAGAAAAAAGAATAA 561
                           vii   ii     vi          i         i   i     i  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_52200910_5    562 A-CTGAAGGCATCACACTACCTGATTTCAAAATAAAC-ATAAATTTATAA 609
                          -i  i   vv       v  ii         ivv  - i   vi  i i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_52200910_5    610 TAACCAACACACCATTGTACAGTCATAAAGACCAACAAGTAGACTAGTGG 659
                            i   v   vii v    v v     i  ivi   vi    ii i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_52200910_5    660 AAGAGAATGGAGAACCCAGAAATAAATTCATCTATTTATAATCAATTAGT 709
                           v     v    ii           ii   vi      ii      ii 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_52200910_5    710 TTTTGACAAGA-TGCCAAGGACACACAATAAGGAAGACATAGTTTCTTTA 758
                            i      i-       iv  iv    ii    iiv     i i  i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_52200910_5    759 ACAAGTGGTGTTGAGAAAACTGGACATCCTCATCCAAAATAATAAAATTA 808
                             i     i  i  v       i ?  v   v     v   i  i  i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_52200910_5    809 GACTC--ATCTCACACCATATACAAAAATCAACTCAGAATGGATTA-AGT 855
                            i -- i                    i      i       i -  v
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_52200910_5    856 CTCACTTATAAGACCTAAAACTGTAAAACCGCTAATAGAAAACAAAGAA- 904
                          ii vv i     v        i      ivi  iv        v  i?-
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_52200910_5    905 -AAAGCTTCATGATATTGATCTGGGCAATCATTT-TTGCGTATGATCCAA 952
                         -   v    i   iv   ivi i      vi   -  ivi     iv v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_52200910_5    953 AAAGCACAAGCAACATAAACAAACAGAAAAGACAAATGTGATTATAT-GA 1001
                                        v  iv   ---  v   i    vv  i vi  -i 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAA---AATAGATAAATTGGACTTCATCAA 650

  chr2_52200910_5   1002 AATAAGACGCTTTTGCACAGAAAAAGATACAATCAACAGAGTGAAGAGAC 1051
                            v i vi      ii vvv   i  i  v     v i      i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_52200910_5   1052 AAGCTACGACACGGGAGAAAATATTTTTAAACCATACATCTGACAAGG-A 1100
                           v i  iiv i              vi   i    i      i    - 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_52200910_5   1101 CTTA-ATATAAATTATGTGAGAAACTCAAACAACTCAACGGCAAGAAAAC 1149
                            i-  vi i v   i i ii     vv         iiii  i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_52200910_5   1150 AAATAAAACAGTTAAAAAATGGGCAAAGGACCTGAACAGACATTTCTCAA 1199
                               vv  i  ?                ii    i           v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_52200910_5   1200 AAGAAGGCATACAAATGACCAACAGGTAGATTTAAAAATTCTCAATATCA 1249
                               ii         i    i i i v  vv   i  v     i    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_52200910_5   1250 CCAATCAT 1257
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.89 (138 / 73)
Gap_init rate = 0.02 (14 / 905), avg. gap size = 5.57 (78 / 14)  


 590 30.99 0.00 0.00  chr2_52239380_52243213.rev     2118  2288 (1546)    L1M4_orf2#LINE/L1        6   176 (732)  

  chr2_52239380_5   2118 AGACATTGCATGTTTATGGACAGGAAAGCTCTATATTATTAGAAAGTAAA 2167
                            i  iv      i     iv    ii  iv     i   ii v vv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_52239380_5   2168 TTCTTCTGAACTTAATTTATATACTCAATGTAATTCCAATCAAAATCTCA 2217
                          v  i iv  v  i  i  i v i    i i   i  v         i  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_52239380_5   2218 GTAAGTTATTTTATAAATATTGATAAACTGATTCTAAAGATTATTTAGAG 2267
                          ivivi v    ii i v     i  i     i     iv i  v i  i
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_52239380_5   2268 AGGCAAAAGACCCAGAATAGC 2288
                          v    ii             
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGC 176

Transitions / transversions = 1.94 (35 / 18)
Gap_init rate = 0.00 (0 / 171), avg. gap size = 0.00 (0 / 0)  

2030 26.19 5.02 2.04  chr2_52239380_52243213.rev     2606  3342 (492)    L1M4_orf2#LINE/L1      150   908 (0)  

  chr2_52239380_5   2606 ATGAAAATG-----GACTAATATAATAGCCAACACAAT-TTGAAGGAGAA 2649
                            i     -----   i--i v         v     -     ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACC--CAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_52239380_5   2650 GAACATAGTTGGAAGACTGGCACTGCCCAATCTCAAAACTTACTATAATG 2699
                              v       i    vi    v      i             i  v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_52239380_5   2700 CTAGAATAATCAAGACAATGTGATATTGGTGAAAGAATAGACAAGGAGAT 2749
                            v i           i    i  i   iiv   i       viv    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_52239380_5   2750 CAATAAAACAGAAC--AAAGTCCAGAAATAGACCCACATGAATATAGACA 2797
                             ii  i    i-- i            i     i iivv   i v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_52239380_5   2798 TGTGATGTTTGACAGTGGAACAAAGGCAATGCAATGGAGAAAATATAATA 2847
                         vv    v  i    iv  vi v   i v  v      i    iv   i v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_52239380_5   2848 TTTTGATTAAGTGATGCTGGAACAACT---TA---ACATGCAAAAAAAAT 2891
                             v vi  i  i      i      ---  ---          i  - 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-T 446

  chr2_52239380_5   2892 GAATCTAGACAAAGACCATACATTCTTTACAAAAACTAACTCAAAATAGA 2941
                            vi i   vvvv   vi   iiv v        i           i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_52239380_5   2942 TTA-AAACTTATTTGTCAAA--TACCAAATTGTAAAACTCCTAGAAGATA 2988
                          i - i  i  vv   v i --  --   i i        i       v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTA--AAACTATAAAACTCTTAGAAGAAA 544

  chr2_52239380_5   2989 ATATAGGTGAAAATCTACACAACCAACAGTTTGGTAATGATTCTTTACAC 3038
                          i     ? v      v iii   vvvi   v  i    i  ii   v -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA- 593

  chr2_52239380_5   3039 ACATATATAACAT-GTAAGAATGAACCATAAAAGAAACAAGAAGCCAAGA 3087
                         -----   i   i-iv   v ii i v i        v  v i---- v 
  L1M4_orf2#LINE/    594 -----TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG----ATA 634

  chr2_52239380_5   3088 AGCTGGAATTCATGGATATTAAAAAATTCTACTCTGTGAAACGCATTATG 3137
                          ii    v     vi v        v  i iiv  vii  ivi  i   v
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_52239380_5   3138 AAGAGAATTAAAA---AAGCAAGAGACTGGGAGAAAATATTTGCAAA--A 3182
                             i i v    ---  v v v   v                    -- 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_52239380_5   3183 TA---CT-ATAA----------TCCAAAATATTCAAGGGACACTTAAAAC 3218
                           ---  -    ----------    i     vi  i i  v    v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_52239380_5   3219 TCAACAGTAAGAAAAGAGGCATTCCTATTTAAAAATGGACCAAAGAGCTT 3268
                             i i   i  i v iii vi  v   ?        i v  i  vi v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_52239380_5   3269 AACAAATATCTCACCAGAGAAAATGTTCGCATGACAAATAATCATATAAA 3318
                           i i i  i  v   i    i  i v iv   i v     v  i  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_52239380_5   3319 ACGGTGTTCCACATTATATGTCCT 3342
                          v i  i  v    i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (112 / 79)
Gap_init rate = 0.02 (18 / 759), avg. gap size = 2.89 (52 / 18)  


1734 27.38 10.35 1.23  chr2_52261563_52263216.rev      442  1175 (479)    L1M4_orf2#LINE/L1       76   876 (32)  

  chr2_52261563_5    442 AGAATCAACCCAATCCCACTCAAAATTGTAGCAGAATATTATGTAGATAT 491
                            v     v       vv       ivi   v vv v  v  i   v  
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr2_52261563_5    492 TAATAAGCTTATTCTAAGATTAATATAACAAAGCAAA-----TAGAAAAG 536
                          i i     v  i    i   v    iiv  v    i-----i    v  
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr2_52261563_5    537 CTAAAATAAACT--GAAAAGGAGAATAAAGCTGAAGGATTTATATTACTC 584
                          i    i  v  --i     i    i    i  i    i i i i v i 
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_52261563_5    585 AAGTTTAATACTTAATAAAAAATTACAACAATCAAGACAGTATAACACTG 634
                           v  i  v     v  v   ii    ii            i iii    
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_52261563_5    635 GGGAAAGGAAAGATACATTGGTCAATGGTATAGAAT--ACAGCCCAGAAA 682
                          viv     v   i i  v i       v       -- v  i       
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_52261563_5    683 TAGGTTCATGC--------TTAAATGAGTTTTGACAAAGTTGAAAAGCTG 724
                           iiii   i -------- i  v   v   i     i v  vv   viv
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_52261563_5    725 AATCAATGGAGACAGGATAGTCTTTTCAACAAATGTTGCTGAAAAAATAG 774
                          v       i  v  i                   v     ii v  iv 
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_52261563_5    775 GGCATCCATAT-CATAAAAATGAACCTCATTTCATAATTCACACTGCATC 823
                          ii ?   i  -  v  i      vi vivii v  vi      iii  v
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_52261563_5    824 TCAAACTTAACTCAAAATGAGTTAAGTGTAAATCCTAAATATAAGTTGTA 873
                         iv   v             ii i ?---- i -       i    vvv  
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAW----AGA-CCTAAATGTAAGAGCTA 520

  chr2_52261563_5    874 AAGTTATAAAACTTCTAGAAGGAAATACAGGATAAAATCTTTGTAAACTG 923
                           ii         ii      i   i i   ?vv       i  i v  v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_52261563_5    924 GAATTAGA-----GTT----AGGCAATGACT---GAATCACAATCTATTA 961
                          ii    i-----   ----  ii -    v---i  v     v v i- 
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATA-TGACACCAAAAGCACAAGCAAC-A 618

  chr2_52261563_5    962 AAAG------CTGATAAAT-------CA--AAAGTTGATAAATATTTTTG 996
                             ------iv       -------  --   i  i -   iv   v  
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA-AAACTTTTGTG 667

  chr2_52261563_5    997 CT----------CTGT--------------GACAAGCCATAAAACAGGAG 1022
                           ----------  i --------------     v   i i  ii    
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_52261563_5   1023 AAGATATTTGCAAA-CATTTACCTGCTAGGTAACTCTTATCCAGAAAAT- 1070
                           i           -   v  i   v  i vi   iv         v  -
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_52261563_5   1071 TAGAAGAATATTGAAAACTTGATGTTAATAA----AATATCTCTATTAAA 1116
                           -     ivi v v    ii  iv   v  ----    v i v   ?  
  L1M4_orf2#LINE/    768 TA-AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_52261563_5   1117 AAATAGACAAAACAGTTGAGCAGATATTTCACCAAA-AAGCTATTCCGAT 1165
                             i i    iv v    ii   i     v     -   v   v vi  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_52261563_5   1166 GACAAGTAAG 1175
                          i v i    
  L1M4_orf2#LINE/    867 GGCCAATAAG 876

Transitions / transversions = 1.37 (114 / 83)
Gap_init rate = 0.03 (23 / 801), avg. gap size = 3.70 (85 / 23)  


2854 19.78 12.26 2.06  chr2_52289818_52291837      705  1528 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_52289818_5    705 TGGAAAGAC-TTTCACATTCATGAAGTAGAAGAA--AATATTGT-AAGAT 750
                                 i- ii  ii      i v i     v--        -     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_52289818_5    751 GTCAGTGCTACCCAAGATGATCTA-AAATTCAATATGATCCCTATAAAAA 799
                          v  i i  v     iv       - i      iiii        v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_52289818_5    800 TCCCAATGATGTCATTTGCAGAAGTTGGAACAAA--AATACTAAAATGT- 846
                              iiviiv iv         i   --    i--i  v       vi-
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_52289818_5    847 TATGAAATCTCAAGGTATCCTGAACTCTTTTTCACAAAGTTCTTTTTGGA 896
                             i  viv     v i  v   ---- vvi  v  viv    ----  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAA----TAGCCAAAACAATCTT----GA 190

  chr2_52289818_5    897 GCAAAAAGAACAAAGCTGAAGATCTCACATTTCCTGATTTCAAA-CTTCC 945
                         iv  i          i  i  iv      i    ii        -   v 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_52289818_5    946 TA-AAAGTCTACAGTAATAAAAAGAGTGGGGTACCGGCATAAAAGCAGAC 994
                           -    -          v  i v    v     i       iiii    
  L1M4_orf2#LINE/    241 TACAAAG-CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_52289818_5    995 ATACATACCTCCATAGA----------GAGTCCCAAAATAAACCCTCATA 1034
                            i v --  v  i  ----------      vi          vi i 
  L1M4_orf2#LINE/    290 ATATAGA--TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_52289818_5   1035 CGTATGGTCAAGAGATTTTCAACAAGGGTGCCAAGATCATACAGTGGGAA 1084
                         iv         vv       i               i   v  i    i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_52289818_5   1085 AAGAAGAGTCTTTTCAACAAATGGTGCTGAGAAAACTGGATATT------ 1128
                              v                       i  v         ?i------
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_52289818_5   1129 -AAAAAAA-------------------------------AAAAA------ 1140
                         -    i  -------------------------------     ------
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_52289818_5   1141 -------GATCAAAAGTATAAATGTAA-ACCTAACATTATAAAACTCTTA 1182
                         -------     ? iiiv         - v    v i             
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_52289818_5   1183 GAAGAAAACAGAGGA-CAAAGCTTTACAACCTTGGGTATGGCACTGATTT 1231
                                   v   ?-i   v   iiii         vv    v  i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_52289818_5   1232 CTTTGATATGACAACAAAGGCATATGCAAGAAAAGAAAAAAATTAACAAA 1281
                            v         v    i   i v    v           - vi i   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAA 636

  chr2_52289818_5   1282 TTGGACTTTATACAAATTTTGAAAACTTCTG--CATCAAAAGACACTATC 1329
                                 i  -    v  -i       i  -- v     i         
  L1M4_orf2#LINE/    637 TTGGACTTCAT-CAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_52289818_5   1330 AAAACACTAAAAAC-CAACCCACTGAATGGGAGAAATTATTTGTAAATTA 1378
                           i v v i    v-        v            v      i    i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_52289818_5   1379 TATACCTGATA-GGGATTAATATCCAGAATATATGGAGA-----CACAA- 1421
                             i      -    i vi              ii   -----i    -
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_52289818_5   1422 --AATA-------------CAATCTGATTCAAAAATGGTCGAAGGACTTG 1456
                         --    -------------i  i ii   ?        v i     i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_52289818_5   1457 AACAGACATTTCTTCCATAGAAGATATTCAAACAAC---TAAGTGCATGA 1503
                           i          -   v         v    iii ---    ii     
  L1M4_orf2#LINE/    835 AATAGACATTTCT-CCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_52289818_5   1504 AAAGGTACTCAACACCACTAATCAT 1528
                             i i       i  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (99 / 60)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 3.93 (118 / 30)  


2525 26.13 6.16 0.93  chr2_52324136_52326123      637  1497 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_52324136_5    637 GAAAGATATTCCATGTTCAAGAATTGGAAGAAGTAATATTATTAAAAT-- 684
                                  i         v i         vv       i    i  --
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_52324136_5    685 -----------------ATCCATAGTATCCAAAGCAATC----TGAAGAT 713
                         -----------------   i i  -  i   v      ---- v  i  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAG-ATTCAACGCAATCCCTATCAAAAT 101

  chr2_52324136_5    714 ---A------TTTTTCCCAGAAATAGAAGAAAAAAATTCGAAAATTGTTA 754
                         --- ------     iv       v  v-  ivvi  i v      vv  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCATA 150

  chr2_52324136_5    755 TGAAACCAACAAGGATCTCGAA-AGC-AAAGCAAACTCTAGTAAAAATAA 802
                           i  viivv i   i iv   -   -   i   v  iv iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_52324136_5    803 CAAAGGTGAAGGTATCAAAGTATCTGATTTCAAAATATACGACAAAGGTA 852
                              v  i   vv   v v vi ii         iv   v      v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_52324136_5    853 TAGTAAAAAAGA----ATGGCACTACCATAAAAACAGCCACATAGATTAA 898
                         i     vv    ----i   i   iv     ii i  v  i      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_52324136_5    899 TGAAACAAAATAGAAAGCCCAGAAATAAATTCG-GCATTTACAGTCAATT 947
                           i  i i   v  i  i           ii i-i      ii       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_52324136_5    948 CATCTTTGACAAAGTTTTCAGTAATACACAATGAGGAAAAGACAGTCTCT 997
                         v  i  i     i v vi  iv vi iv     i     ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_52324136_5    998 T----GAATAGTGTCAGAAAAATTAGATATCCACATGTGTAAGAATAAAA 1043
                          ----i   i   iii i v  i i    ?       iiv      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_52324136_5   1044 TTGGATCTTTATATTATACAACACACAGAAATAAATAAACTCAAAAATCA 1093
                              i ii  iv i i  v i i   i    ---   -       - vi
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAAT---TAA-CTCAAAA-TGG 495

  chr2_52324136_5   1094 ATGAAAGAC----ACATAAGACCCAAAACTATAAAACTCCTGAAAGAAAA 1139
                           v ?    ---- ii     v i               i ii       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_52324136_5   1140 CACAGAGAAAAAGCTTCTCGACATTGATCTAGACAATGATTTTTCA-ATA 1188
                           i  i?iv   v    vi   v   ivi   i     i   i i -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_52324136_5   1189 TGACTCCAAAAGCAGAGGCAACTAAAGCAACGATAAACAAATGGGATTGC 1238
                             v         v i     v    v  vi   i i    v   i v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_52324136_5   1239 ATCAGA-TAAAAAGCTTCTGCACAGCAAAG-ACA--ATCAACAAAATGAA 1284
                             i - v    i   i  ii vv     -   --     v   i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_52324136_5   1285 GAGACAACTTACAGAATGGGAGAATACATTTGCAAAGCATACATCTAATA 1334
                         i       ii              v i         v    i    i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_52324136_5   1335 AAAAGTTAATATCCAACATATGCAAGGAATTCAAGCAACTCAA-AAGAAA 1383
                          iiiii vi      iv    ii  i   i  vvi        -  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_52324136_5   1384 AAAACAAAACATTCTGATTTAAAAATGGGCAAAACACCTGAATAGACATC 1433
                           i     -i vi ii   ?             iv ii           i
  L1M4_orf2#LINE/    796 AAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_52324136_5   1434 TCCTAAAAGAAGACATACAATCAGCCAACAAACACATGAAAAAATGTTTA 1483
                           iiv        i      vii     i  i          i   i i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_52324136_5   1484 ACATCTCTAATTAT 1497
                              v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (145 / 76)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 2.90 (61 / 21)  


 307 12.50 5.36 0.00  chr2_52466588_52469039      678   733 (1719)    L1M4_orf2#LINE/L1        1    59 (849)  

  chr2_52466588_5    678 TGGAAAGATATCCCCTGTTCAGGGATTGTAA---TTAATATTGTTAAAAT 724
                                       v      v      v  ---             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_52466588_5    725 GTCCATGCT 733
                          v v  i  
  L1M4_orf2#LINE/     51 GGCAATACT 59

Transitions / transversions = 0.40 (2 / 5)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 3.00 (3 / 1)  

2382 23.47 1.20 9.93  chr2_52466588_52469039     1049  1964 (488)    L1M4_orf2#LINE/L1       73   908 (0)  

  chr2_52466588_5   1049 TATACATTCAATGGAATCTCTAACAAAATACCAATGATGTTCTCCATAGA 1098
                           i v      i v    i   v      v   iiviiv  i iiii   
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chr2_52466588_5   1099 AATAAAAAAAAAAATCCTCAAATTCATGTAGAATGACAAAAGACCCTGAA 1148
                            vi v  ivvi     v        i i   vvi   ii     v   
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr2_52466588_5   1149 TAGCCAAAGAAATCTTGAGCAGAAAATAAACAAACCAAACCAAACAAAAA 1198
                                 iv        ---------------------------    i
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGA---------------------------AAAAG 195

  chr2_52466588_5   1199 AACAGAACAAAAAACCCAACAACAAACAAAACAACAACAACAACAACAAA 1248
                           --       ---------------------------------------
  L1M4_orf2#LINE/    196 AA--GAACAAA--------------------------------------- 204

  chr2_52466588_5   1249 GCTGGAGGCATCACACTGGCTGATTTCAAAATATGCTTCAAAGCTAGAGT 1298
                          i      vv       vv ii         iv i  v        v   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_52466588_5   1299 AACCAAAACAGTATAGTATTACTACAAGAACACAGATACACATACCAGTG 1348
                           i   i     i i   i ivi i   i i --  i i i v i  i  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATA--GACATATAGATCAATG 302

  chr2_52466588_5   1349 GAACAGA-T--AGAGCCTAGAAATAAATCCACAAATCTCCAGCTAACTGA 1395
                            i   - --    i i         i   i v  i vii ii  i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_52466588_5   1396 CTTTCAATAAAGGTGCCAAGAAAATCGGATT--ATGGAAAAAGAATAATC 1443
                         i    i i  i          ---i --   --    ii        i  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGA---CC--ATTCAATGGGGAAAGAATAGTC 397

  chr2_52466588_5   1444 ATTTTAATAAATGGTACTAGAAAAATTGGATAACCATATGCAGAAAAATA 1493
                         v   i  i       i  i i v  i      ?   i     i  i   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_52466588_5   1494 AAACCAGACCCTTATATTTTACCATATTTAAAAATCAACTGTAAATGGAT 1543
                           iiii     i  iv ivi       vi      i    vv        
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_52466588_5   1544 TGAAGATTTAAATGCAAGACCTGAAACTATTAAACTACTAGAAAAAAACA 1593
                         ii?   ii      i    v  i       v     vi     i      
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_52466588_5   1594 TATAGGGGAAATGATTCATGACGTTGGACTACGCAAATATTTTTTGGATA 1643
                           -i ? v    v-   i    v    ii  v    vvi   i  i    
  L1M4_orf2#LINE/    548 TA-GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_52466588_5   1644 AGAGCTCAAAAGCATAATGAACAAAAGCAAAAATAGATAAATGGGATTAC 1693
                         v  vvi        i  vv        v              v   i v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_52466588_5   1694 ACTAAACTTAAAAAACCTTCTGCACAGAAAAGGAAACAATAAACAGAATG 1743
                          ii   v       --   i  ii vvv      v  v  v  v i i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_52466588_5   1744 AAGAGACAACCTAAAGAATGAGAGAAAATATTTCCAACCTTTATATCTGG 1793
                           i        i v      i            v   viiv        i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_52466588_5   1794 CAAAGG--TTACTATCCAGAATATATAAGAAATTCGAACAATTCGAAAGC 1841
                         i  i  --  i-                ii  i  vv    i  ------
  L1M4_orf2#LINE/    744 TAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTC------ 786

  chr2_52466588_5   1842 AAATAATAATAGTAATAATAGTATCCTGATTTAAAAACTGTACAGAACAC 1891
                         -        v i-i i  --i  v  ii   ?     -  vi  i iv i
  L1M4_orf2#LINE/    787 -AATAATAAAAA-GACAA--ATAACCCAATTWAAAAA-TGGGCAAAGGAT 831

  chr2_52466588_5   1892 CTTAGCAGACATTTTTCCAAAGAAGATATACAAAAGACCGACAGGTATAC 1941
                         i v ii        i                   v i  i i i i i i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_52466588_5   1942 GAAAAAATGCT----ATCACTAATTAT 1964
                              i     ----    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (141 / 70)
Gap_init rate = 0.02 (19 / 836), avg. gap size = 5.37 (102 / 19)  


3048 22.04 3.40 4.06  chr2_52582923_52587074.rev     2749  3660 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_52582923_5   2749 GAAAGATACCTTCTGTTTGTGGATGGTAGGACTTAATATTGTCAATATGG 2798
                                 i iiv    ii     v v i             i  v    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_52582923_5   2799 CAATATTCCTCAAAATAATCTACACATTCAATACA-TCACTCTAAAAGGC 2847
                              i   i    v i       v      ii  -  v  v v   iv 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_52582923_5   2848 TCATCTGTGAGCTT----GAAGAAATTGACAAGTTTATCTTAAAATTTAT 2893
                         i  v   i---   ---- v             i v   i       i  
  L1M4_orf2#LINE/    103 CCAGCTGC---CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_52582923_5   2894 GTAAGAATGTAAATGA---AAAGTAGTAGTCTAAATC--TTTT-----AG 2933
                         i iii    i  iv  --- i i   ---- i   v -- i  -----  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAG----CCAAAACAATCTTGAAAAAG 195

  chr2_52582923_5   2934 AAAAACAGAGTTAAATGATTATAACTTTCTGATTTTAAA-CTT----CAA 2978
                           i    i    ii v  i vvv    i ii    i   -   ----   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_52582923_5   2979 AGATAAAGTTATCAAGACAGTATGGCACAAGAATAGGGATAGAAATACAG 3028
                           v  v   v           i   i  vi v   i       v   i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_52582923_5   3029 ATTCATGAAGTACAATTGGATGTGTAGAAGCAAACCCCCATATTTATTGG 3078
                           iv   i i  v     iiv  vi    ii      vi i      -  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT-GG 344

  chr2_52582923_5   3079 TTAATTGATTTTTGACAAGTGTGTTAAGGCAATTCAATGGGGAA-GAATA 3127
                          i          i      v   ii   i v             -     
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_52582923_5   3128 -TATTTTCAACCACTAGTAC-AGAATGGCTGTTTATCTTTATGGGAAAGA 3175
                         - v        v v i  i -i i iii   vv  ? ivi   vi     
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_52582923_5   3176 ATACAGTTGTGCCTGTTATCTCAAAAAAAAAAAAAAATATATATATATAT 3225
                           iv     vi  i-i  i    ----------------i i-i     i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCC-CTACCTCA----------------CAC-CATATAC 476

  chr2_52582923_5   3226 ATATATATATACTGGAAATGGATAATAGACCTAAATGTAAGAGCTAAACC 3275
                          v v  -  -   vi        v ?                      v 
  L1M4_orf2#LINE/    477 AAAAAT-TA-ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_52582923_5   3276 TACATGCCTGGTTCAAGAAAA-ATAGGAGTAAATCCTCATGATCTTTAGT 3324
                           i viv  vv vv       -     ?       i  i   i   vi  
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_52582923_5   3325 TAGA-AAT--TTTATTAACTACGACACCAAAAGCAAAAGCAACAATATAA 3371
                            i-   --   v   iv  i             v         v v  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_52582923_5   3372 A---TAGATACCTTAAATGCCATCAAA-TTAAAAACTTTTGTGCTTCAAA 3417
                          ---      vv  ii ivi       -                      
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_52582923_5   3418 GGACATCATGCAGAAAATGAAAATGGAACAGAAAGAATGGGAGAAAATAT 3467
                              ii  vv     i      viv   vv v                 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_52582923_5   3468 TTACAAATCATATACTTGAAAAGAGACCAGTATCGAGAATGTATAAAACA 3517
                           i           ii   v   i   iv     v     i      ---
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA--- 771

  chr2_52582923_5   3518 GCTTGAATGTATAAAAACTCAACAATAAAAAAGATACATAAACTATTTCC 3567
                         ----   i- v v v       i        -  i v    v i v  ?v
  L1M4_orf2#LINE/    772 ----GAAC-TCTTACAACTCAATAATAAAAA-GACAAATAACCCAATTWA 815

  chr2_52582923_5   3568 AAAATGGATACAGGATCTGAGGAGACATTTCTCCAGAGAAAATTAACAAA 3617
                                ii v     i   iv             i    i  vv     
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_52582923_5   3618 TGTTCAGTAAGCACATGAAAAGATGCTCAAAATTATTAGTCAT 3660
                           vi  i                       v  i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (113 / 84)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 2.62 (68 / 26)  


2053 27.97 3.11 5.79  chr2_52626139_52631685.rev     4135  5067 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_52626139_5   4135 TGGAAAAATATTTCATGCTCATGGAT----AGAATAAATATTGTGAAAAT 4180
                               i    ii    i        ----   v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_52626139_5   4181 GCCCATACTGCCCAAAATGATTTATAGATTTGATGCTATTCCTATTAAAC 4230
                          v v     v      v    i  i     ii i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_52626139_5   4231 TGCCA-TTGACATTCTTGACAGAA--TGAGAAAAAACT-ATTTCAAAATT 4276
                          v   -i  v v  i   -     --   v  i---  -  iii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAG---CTGATCCTAAAATT 146

  chr2_52626139_5   4277 CATATGAGAACAGAAAAAAAACA-AATAGCCAAGACAATCCTAAGCAAAA 4325
                               ii  iiv  iii vv  -         i      i i ------
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------ 190

  chr2_52626139_5   4326 AAAAAAAAAAAAAAAAAAAAAAAAGCTGGAGGCATCACACTACCTGACTT 4375
                         ----------    i  i  v    i      vv       v  ii i  
  L1M4_orf2#LINE/    191 ----------AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr2_52626139_5   4376 CAAACTATACTATAAGGCTACAGTGGCCAAAATAGTGTGGTACTGGTACA 4425
                             viv     i  i        iii   i i             i i 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_52626139_5   4426 AAAACAAACACATATACCAATGGAACAGAATAGAGAACTCGTAAACAAGA 4475
                          ii i i   i   v i        i     v    iii iv   i  iv
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr2_52626139_5   4476 CTGCACACCTACAACCATCTGAACTTCAACAAGCCTGACAAAAGCAAGCA 4525
                          iii   ii  iiii  vi   vi   i     vv  v   i v  vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_52626139_5   4526 ACGAGGAAAAGACTCCCTACTTAATAAGGACTCCTTATTAATAAATAGGC 4575
                          i i     ii ivvi  vi i  i  iviv v  vi--i i  v -  v
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG--GACAACT-GGA 427

  chr2_52626139_5   4576 TAGCGATATGCAGAAAATTAAAACTGGACCCCTTCCTTACACTTTATAGA 4625
                           ? v i     i  i v i  ii         v   i    iv    v 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_52626139_5   4626 AAAAATAA-----GATAGAAGAAAGACTTAAATATAAAACTCAAAACTAT 4670
                             v   -----i  i  vv ?    i     i   i vii        
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_52626139_5   4671 AAAAGCTGTAGAAGAAAATCTAGGCA-ATACCATTCAGGACATAGGCATG 4719
                             viiv          iv    ?i- v i -   iv   v v  vv i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTA 576

  chr2_52626139_5   4720 GGCGAAGATTTCATGGCAAAAATGCTAAAAGGAATTGCAACACAAACAAA 4769
                            i v i    v i vv vi ii i     v vvv      v  iv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_52626139_5   4770 AATTGACAAATGCAATCTAATTAAA-CTGAAGACCT--GCACAGCAAAAA 4816
                            v  i    vvi ii v  i   -i i  i  i -- ii vv    ii
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_52626139_5   4817 ATACAAAACCACACAATTACATGAAAATTGAACTATCATAAGAGTGAACA 4866
                          i  -----------------------------     vi i      v 
  L1M4_orf2#LINE/    677 ACAC-----------------------------TATCAAGAAAGTGAAAA 697

  chr2_52626139_5   4867 GACAACCTACAGAACTGGAGAAAATTTTCGCAATCTATCCATCTGAAAAA 4916
                                i      iv         v  i    vii  vi      v  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_52626139_5   4917 AGTTTAATATCCAGCATCTACAAGAAACTTAAACAAAATATACAAGGAAA 4966
                         i vi vi       v  v  i  ii    ivv    vvi - i  vi   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-ATAATAAAA 796

  chr2_52626139_5   4967 AAACAAAT--CCCA-TTAAGAAGTGGGCAAAGGACATGAACAGACACTTC 5013
                          i      --    -  ? i  i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_52626139_5   5014 TTAAAAGAAGACATTCTTGTGGCCAACAA--ACATAA------GCTCAAC 5055
                          iv        i  v vvi       i  --    i ------       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_52626139_5   5056 ATCACTTATCAT 5067
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (158 / 99)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.95 (83 / 21)  


2372 25.21 3.39 3.15  chr2_52653054_52654868      501  1325 (490)    L1M4_orf2#LINE/L1       82   908 (0)  

  chr2_52653054_5    501 AATGTGATCCCTATAAAAATTCCAATTACATTTTTTATTGAAGAAGT--A 548
                           i ii        v     i   ii i v      --- v    i -- 
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT---GCAGAAATTGA 128

  chr2_52653054_5    549 AAAG-TAATTCTAAAATTCATATGGTATTACAAAAGTCCCA-AATAGTCA 596
                         v   - i  i               v v i   ii v    -     i  
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr2_52653054_5    597 AAGCGATATTGAGCAAGAAGAACCAAGGTGGAGGCATCACACTTCCTGAT 646
                           i i  v    iv         v   v      vv          ii  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr2_52653054_5    647 TTCAAATTATATTACAAAGCCATAATAAACAA-ACAGTACAGT-CTGACA 694
                               viv  i        i i i   v   -     iii  -   i  
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_52653054_5    695 CAAAAACAGACATACAGACCAATGTAACA--ATAAAAAACCCAGAAATAA 742
                         i  ii i       i   i     v  i --  vi i ii          
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_52653054_5    743 ACT--TACATTTATATATTCAACTAATTTTGGACAAAGATACCAAGAATA 790
                           i--         iv--    i i     v     i i i      vi 
  L1M4_orf2#LINE/    329 ACCCATACATTTATGG--TCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_52653054_5    791 CACAATGGAGAAACGATAGTTCTTT-GGTAAGTG-TGCTGAGAAAACTGA 838
                         iv      i    vi     ii   -iii  i  -     i  v     i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_52653054_5    839 ATATCTACGTGCAAAAACATTAAAACTGGACCCTTATCTTACATCATAAA 888
                            ? i  i       iv  -i  ii       i  i  i   i    v 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAAT-GAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_52653054_5    889 CAGAAATCAACTAAAAGTAGAATAAATATGTAGACATAAAGCCTGCAACC 938
                           i    i    v   i i  vi ? v iv  i ii   iiv  iv   i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_52653054_5    939 AGAAAACTAGTAGAACACAATGTAAAAGAAAAGCTCCTTGACATTGGTTT 988
                          v      vv     v v  ii  ii? v   v  i v    v    v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_52653054_5    989 TGGCAATTTTTTTTTA--TATGACACCAGAAACACAGGCAATATAACCAA 1036
                         v      vv   i   --          i  i    i    i v  vv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_52653054_5   1037 AA-TAAACAAGTAGGATCATATCAAAATAAAAAGCTTCTGCCCAGGAAAC 1085
                           -  i i  i v   iivi        v    i   i  iv vvv   v
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_52653054_5   1086 AAAACATTCAACAAAATGAACAGGCAACTTA-----TGGAAGTAAAGATT 1130
                         i v  vv    v   i    v  i    ii -----   i  v   v   
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_52653054_5   1131 TGCAAAACACGTATCTATCTGATAAGGG--TTACTATACAAAATACATAA 1178
                               v  --   --            --  i-   v  i    i    
  L1M4_orf2#LINE/    726 TGCAAATCA--TAT--ATCTGATAAGGGACTTG-TATCCAGAATATATAA 770

  chr2_52653054_5   1179 GAAACTCATACAACTGAATAGCAAAACAGACCCAAACAAAAACCAAATAA 1228
                         ii     v       v    ii    -    -------------      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAA-AGAC-------------AAATAA 806

  chr2_52653054_5   1229 CCTTAAC--AAAAATGGGCAAAG-ACCTGAGTA---ATTTGTCTAAAAAC 1272
                           i-  i--              - ii   i  ---    v  i   i v
  L1M4_orf2#LINE/    807 CCC-AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_52653054_5   1273 GACATACAAATATGTAACAGATATATTAAGAAGTGCTCAACATTGCTAAT 1322
                           i        ivvi  i iii i  v  i ii          ii?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_52653054_5   1323 GAT 1325
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.85 (133 / 72)
Gap_init rate = 0.03 (25 / 827), avg. gap size = 2.16 (54 / 25)  


2646 27.53 4.55 1.25  chr2_52705874_52709928.rev     2685  3563 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_52705874_5   2685 TGAAAAAACACTCCATGTTCATGGATAGGAATAATCAATATTATTAGAAT 2734
                           i   i i ii              v    v v i      i   ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_52705874_5   2735 GATCATACTATCCAAAGCCATTTGCAGATTTAATGCTATTCCTATCAAGC 2784
                          iiv     vi     viv  i i      i  i  v  i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_52705874_5   2785 TACTAATGACATTCTTTACCACATTAGAAA-----AAACT-ATTTTAAAA 2828
                          v i iivi v  i   i ------     -----  i  -  ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGC------AGAAATTGACAAGCTGATCCTAAAA 144

  chr2_52705874_5   2829 TTCATAAGGAAC--CAAA------AAAATAGCCAAGGCAATCTCAAGCAA 2870
                               v    v--   i------ i         ii      ii iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_52705874_5   2871 AAAGAACAAAGCTGGAGGCATCACATTACCGTACTTCAAACTATACTACA 2920
                         i          i      vv     i v  vv i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_52705874_5   2921 AGTCTACAGTAACCTAAACAGCATGGTATTGGTACAAAAACAGTCACATA 2970
                          iv         i v i    ii     i   i i  ii i  v  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_52705874_5   2971 GACCAATGGAACAAAGTAGAGATCCCAGAAATAAAGCTGCACACCTACAG 3020
                           i        i i i v    vi           v iii   ii  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_52705874_5   3021 CCATCTAATTTTTGACAAAGTTGATGAAAACAAGCAGTAGAAAAAGGAC- 3069
                         i  vi i     i     i v  vii i v  vv  i i ii    i i-
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_52705874_5   3070 -TCCTTAGTCAATAAATAGTGCTGAGATGACTGGCTGGCCAAATGTAGAA 3118
                         -  i  --    i    i      i  ii     v i?   v   i i  
  L1M4_orf2#LINE/    395 GTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_52705874_5   3119 TATTGAAGCTGGACCCCTTCCTTACACCA----CACAAACCAACTCAAGA 3164
                         v v     i         v   i      ----  v   ii       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_52705874_5   3165 TGAATTAAAGACTTAAAC--AAAAACTAAAAACTATAAAACCCG-GGAAG 3211
                           i  i ?    i    i--  i i      -         i v-i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAG 541

  chr2_52705874_5   3212 ACAACCTAGGTG-ATACCATTCTTGACATAGGAACAGGTGAAGATTTTAT 3260
                          v   v    ? - v i -   v    v v  ivi   ii v i   iv 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_52705874_5   3261 -GATGAAGATGCCAAAAGCAATTGCAATGGAAGCAAAAATTGATGAATGG 3309
                         -   - v  ii         vvv    iii   v      v   i   v 
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_52705874_5   3310 GATCTAATTAGACTAAAGAGCTTCTG-----CACAGCAGACTAGCAACAA 3354
                           ii v  i i v v  i i   i  -----  v  v v    v   v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_52705874_5   3355 AGTAAACAGGCATCCTACAAAATC--AGAAAATGTTTGCA--CTATACAA 3400
                            i  v  i  v  i   i   v--       i      --ii   i v
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_52705874_5   3401 CTGTGAAAGGTCTAATATCTAGCATCTGTAAGGAACTTAAACAGATTTAC 3450
                            vv  i  v  vi    i  v  v i   i     ivv   iv iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_52705874_5   3451 AAGAAAAAAA------ACCTAATTAAAAAGTGAGCAAAGGACATGAACAG 3494
                           v     i ------   i    ?    i  i        iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_52705874_5   3495 ACACTTTTCAAAAGAAGACAAATATGTGGCCAACAAGCATATGAAAAAAA 3544
                            i  i  v        i v i vi       i     i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_52705874_5   3545 GCTCAGTATCACTGATTAT 3563
                              ii    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (153 / 85)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.68 (51 / 19)  


2081 24.52 4.86 8.88  chr2_52713014_52718014.rev     3566  4511 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_52713014_5   3566 TGGAAAAACAGTG-ATGCTCATGGATTGGAAGAATCAGTATCATTAAAGT 3614
                               i i viv-   i               v i i   ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_52713014_5   3615 GACCATACTGCCCAAAGCAATCCATAGATTCAATGCAATTTCTGTCAAA- 3663
                          i v     v      vii   i i        i     ii  i     -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_52713014_5   3664 --CTA-CTATCATTCTTTG-ATAAATAGAAAAAA-AATT---AAATTTAC 3705
                         -- i -  ii -  i    - v    v  v  iv-i  i---     i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_52713014_5   3706 ATGGAAATGAAAAAGGGTCCA-AATAGCCATCGCTATCCTAAGCAAAAAG 3754
                                  v  i-  ii   -        vvi v   i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_52713014_5   3755 AATAAAGCTACAGGTATCACATTACCTGACATCAAATTATACTACAAAGC 3804
                           i    i iv   vv     i v  ii iv     viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_52713014_5   3805 TATAGTAACAAAAACACCATGATACTAGTATAAAAATAGACACACAGATA 3854
                           i     iv  i   vii  i    i i    ii       i i    v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_52713014_5   3855 AATGGAACAGAGTAGAGAACCCAGAAATAAAGCCACATATCTAAAACGAA 3904
                                i   i v    ii           v   i i  i  viiiv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_52713014_5   3905 ATGATCTTTTACAAAGCCAGCAAAAATATACACTGGGGAAAGGA-AACCT 3953
                         v    i  iv    i viiv   i vi  v  v         i - ii  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_52713014_5   3954 AATTCAATAAGTGGTGCTGGGATAACTGCTGAGCCATATGCAGGTAAATA 4003
                         v-     i  i           i     vvv ?   i     iivi   i
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_52713014_5   4004 AAACTAGACCTGTATCTCTCACCATATTCAAAAATTAACTCATA-TGGAT 4052
                           ii i    iv  i   v        v              v -     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_52713014_5   4053 --------TAAATGTTAGACTTGAAGTTATAAAAACCCAAGAAGA----- 4089
                         --------       v   vi i  ii       vi iv      -----
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_52713014_5   4090 ----------TCTTT-TGCCCATTGTTCTAGGCAAATAATTT---AGGAC 4125
                         ----------    i-  v  -   vvi       - ii   ---  ivv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAA-TGGTTTCTTAGATA 595

  chr2_52713014_5   4126 TGAATTTTCAAAAGAAAATGCAACAAAAACAAAAATAGGCAAATGAGACT 4175
                            --ivi      v v v         iv        ii    vi    
  L1M4_orf2#LINE/    596 TGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_52713014_5   4176 -----AAAACTAAAAATCTTCTGCACAGCAGAAAATTATAAAAGAAGTAA 4220
                         -----    i      -   i  ii ---------  -i   i  viiv 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGC---------TT-CAAAGGACACTA 682

  chr2_52713014_5   4221 TCAACTGAGTAAACAGACTATCTACAGAATGGGAGAAAATATTTCCAAAC 4270
                             vvi   i  v    v i i                     v    i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_52713014_5   4271 TATGCATCTGAGAAAGTACTAATTCCCAGAATCTACAAGGAACGCAACAA 4320
                         i  ii      v  i v   vi vi       v  i  i    v --iv 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--TTA 780

  chr2_52713014_5   4321 CAACAAAAAAAACCATCAAAAAATATTTGCAAACTATGCATCTGAGAAGG 4370
                             -----------    v  -------------------- i i   -
  L1M4_orf2#LINE/    781 CAAC-----------TCAATAA--------------------TAAAAAG- 798

  chr2_52713014_5   4371 TACTAATTCCCAGAATCTACAAGGAACTCAACAAAAAAACACCCATCAAA 4420
                         ------------------    iv   i   -------------- i?  
  L1M4_orf2#LINE/    799 ------------------ACAAATAACCCAA--------------TTWAA 816

  chr2_52713014_5   4421 AAGTAGGCAAAGGACATGAACAGAAATTGTTCAAAAGATGACATAAAAGC 4470
                           i i         iv    i   v   vi  v     v  i   v  ii
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_52713014_5   4471 AGCCAATACACATATGAAAA-ATGCTCAGCATTGCTAATCAT 4511
                         i       vi  i       -       i   ii????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (147 / 83)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 4.48 (130 / 29)  


3073 26.57 1.10 0.99  chr2_52726643_52731409.rev     3369  4275 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_52726643_5   3369 TGGAAAAACATTCCATGCTCATGGATAAGAAGAATCAATATTGTGAAAAT 3418
                               i i  i     i        vi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_52726643_5   3419 GGCCATACTACCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 3468
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_52726643_5   3469 TACCAGTGACTTTCTTTGCAGAATTAGAAAAAAACT-ACTTTGAATTCCA 3517
                          v    ivi i  i         v v  v  i--  - iii i  v i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_52726643_5   3518 TATGGAACAAAAAAAGAGCCCGCACAGCCAAAACAATCCTAAGCAAAAAG 3567
                                vviv  ii  v  v v i             i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_52726643_5   3568 AACAAACCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3617
                               vi      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_52726643_5   3618 TACAGTAACCAAAACAGCGTGGTACTAGTACCAAAACAGATATATACACC 3667
                                 i   i    i        i i iv ii i   i     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_52726643_5   3668 AATGGAAGAGAACAGAGACCTCAGAAATAACACCACACATCTACAACTAT 3717
                                v    iv    vii         vv   i    i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_52726643_5   3718 CTGATCTTCAAAAAACTTGACAAAAACAAGCCATGGGGAAAGGAT--TCC 3765
                         i    i   i v  ivv  v   i v  vv v          i  --  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chr2_52726643_5   3766 ATATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAA-AAC 3814
                         - v  i  i              i      v  ?   i     i  -  i
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_52726643_5   3815 AAAAACTGCTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGA 3864
                         i  ---- i         v   i     v                   i 
  L1M4_orf2#LINE/    447 GAA----GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_52726643_5   3865 TGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGA 3914
                              i ?    i         i v i            vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_52726643_5   3915 AAACTTGGCAATA--CCATTTAGGACATAGGCATGGGCAAAGACTTCATG 3962
                             v i v?i  --i -  iiv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_52726643_5   3963 ACTAAAACACTGAAAGCAATTGCAACAAAAGTCAAAACTGACAAATGGGA 4012
                         iv  vi    ii      vvv          vv    iv  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_52726643_5   4013 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCACCAGAG 4062
                         ii v  i   v v  i i   i  ii vv    iv v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_52726643_5   4063 TGAACATGCAACCTACAGAATGGGAGAAAATTTCTGCAAGCTACCCATCT 4112
                             v vi     i                 v i     iii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_52726643_5   4113 GACAAAGGTCTAATACCCAGAATCTACAAGGAATTTAAACAAATTTACAA 4162
                           i  i  v  vi  i       v  i  i   i ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_52726643_5   4163 GAAAAA---AAAAAACCCA-TCAAAAAGTGGGCAAAGGATATGAACAGAT 4208
                         v     ---   v      - i?    i            v    i   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_52726643_5   4209 GCTTCTCAAAAGAAGACATTTATGCAGCCAACCAACATATGAAAACAAGC 4258
                         ii     v        i  vi viii     iv i  i       v v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_52726643_5   4259 CCATCATCACTAGTCAT 4275
                         i  v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


1741 29.38 5.92 2.37  chr2_52771820_52774244.rev     1082  1925 (500)    L1M4_orf2#LINE/L1        1   874 (34)  

  chr2_52771820_5   1082 TGGCGATACATCCCATGTTTATAGTTTGTAATACTCAAAACTGTTAAAAA 1131
                            vi v i          i  i v   v  v   i  v i      i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_52771820_5   1132 GTCATTTTTTTCCAAATAAATTTACAGATATTATTCAATCCC-AGTAAGA 1180
                          v  v vi ii      vi  i       viv iv       - vi  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_52771820_5   1181 TACATAG--AACATTTTGATAGAAATCAGTAAGTTGATTCTAAAATTTAT 1228
                          v -i  --iv v    vii      iiii   i    i        i  
  L1M4_orf2#LINE/    101 TCC-CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_52771820_5   1229 ATGGAAATGCAAATTACTT-GAAAAAACAAAACAAGTTTGAAAATAAAAA 1277
                                     ivv  ii-   v iv        vi       vi  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_52771820_5   1278 TCCAAGTCAGAGTATCTACATTAGCTGATT-CAGGACTTACATATTAA-- 1324
                         v v    ii   v iii   i vv ii   -  ii      -  iv  --
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC-TACAAAGC 248

  chr2_52771820_5   1325 --CACTAATTAGGATTGTTTGTTATTAATACAAGAATAGACAAATGGATA 1372
                         --  v    i i  iv  v  v  i iii i   i       v  i   v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_52771820_5   1373 AAAGGAATC--ATT-----T------ATAAAATCACACGTATTTAGTCTA 1409
                           v     v--   ----- ------     vi  i  i v v i   v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_52771820_5   1410 TTGATTTTTGAAAAAGGTGT-AATAGTGGTTATATGGGGGAAGGAAAGGG 1458
                                 i  v  i    i-  v viiv i -      i   i v  --
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAGAATAG-- 395

  chr2_52771820_5   1459 ATATCTCTTCAACAAATGATTCTGGAACAACTACGTGTCTGTATTCATA- 1507
                         ---   i           i v    i      ivi i? iii  v  v -
  L1M4_orf2#LINE/    396 ---TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_52771820_5   1508 ---TGA-------CTTCTACCTTGCACCAGGCACAAAAATTAATATAAGA 1547
                         ---   ------- ii      ii     vii           ivi  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_52771820_5   1548 TAAATGAATGACCCAAATGAATAAATTAAAAATACTAAGACT---GGAAG 1594
                          ii  v ?v    i     v vi ii     v  -   i   ---i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTA-TAAAACTCTTAGAAG 541

  chr2_52771820_5   1595 AAAACACAGGATGATATTTTTATAATCTGTGGTTTAAAAAATG-TTTCTT 1643
                               i   ?vv v  i  ii i i  -   v   iiv    -      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTT 590

  chr2_52771820_5   1644 AAATAGAA----GAAAGCAGAGAGTAATAATTATAAGAACAAACTGATTA 1689
                          i   vi ----i      v -  i  i  ----     v   iv   - 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACA-AGCAACAA----AAGAAAAAATAGAT-A 634

  chr2_52771820_5   1690 AATAATAATG-ATCAAAATTTAAAACTTCTGCTCATCAGAAAAAAAAACC 1738
                            viv v v-         v       i  iv v   ---  ii v  i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA---AAGGACACT 681

  chr2_52771820_5   1739 ATTAAGAAAG-AAACAGATTGGTCATAGGCTGGGAGAACATATTCACGAT 1787
                           i       -i  v   ivivi  i  iv        v     ii i v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_52771820_5   1788 AGATATAATTGTCAAATAACTCATTTGCAGGATATATAAATGATTGCTAC 1837
                         vv     vi  vi  ivi   ii v v   i         vi i vi   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_52771820_5   1838 AAATCAACAA---GAAGACAAATAATCTAATT--ATAGTGAGCCAAGGAC 1882
                           v    i  ---i           i i    -- v i  i  v     i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_52771820_5   1883 TTGAGCAGACCATTC-ACATGGCAAAATTTACAAATGGTCAGTA 1925
                             ii    vv   -v  vi -  i  v         i  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAG-AAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.03 (30 / 874), avg. gap size = 2.33 (70 / 30)  


2468 25.69 2.02 1.76  chr2_52799914_52803294     1666  2459 (922)    L1M4_orf2#LINE/L1        4   799 (109)  

  chr2_52799914_5   1666 AAAAATGTACTTTGTTCATGGATTAGG-GACTCAAAATATTTAAGATTTC 1714
                            i  i v iv            i i-    i  v  vv       vv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_52799914_5   1715 AGTTAC-CCCAAAATTTATCTATAGATTCAACACATTCTCAATCAAAATT 1763
                          i -  -   v     v     i         i  v  i v        i
  L1M4_orf2#LINE/     54 AAT-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_52799914_5   1764 CCAGCAGTTTTCTTTTTGGTAGAAATTGACAAGATGATTCTAACACTCAG 1813
                              v i---      v i             v    i    v i   v
  L1M4_orf2#LINE/    103 CCAGCTGC---CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_52799914_5   1814 ATGAAAATGCAAAAGGATATCGATTAGCCAAAACAAATTTCAAAATTAA- 1862
                            i        i-   iviv  v            vi  v    vv  -
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_52799914_5   1863 --CA--TTTGGAGGACTAACATTACCTGACTTTAAAGCTTCTTATAA-GC 1907
                         --  --v          v   i v  ii i  i   i   vi  i  -  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_52799914_5   1908 TACAGTTATCAAAACCATGACAAATTTTCTTAAAGATAAAGGACAAATCA 1957
                               v     i  vi  vviv i vv v   i    ---    v  vi
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA---GACATATAG 295

  chr2_52799914_5   1958 GTCAATGGAACATA---GACGGTACAGAAATAGATT--TACGTATATATT 2002
                         i         i v ---  vi  v        i ii--   i v   iv 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_52799914_5   2003 TAATTGAGTTTTGGTAAAGGTACAAAGGCAATTCAATAGAAAAATAAGAA 2052
                         i      v   i ii  i   i v   i v       i ii   ---   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA---GAA 392

  chr2_52799914_5   2053 GATTCTTTTCAATAAAATAGTGTTATAATAATTAAATATTCATAAGTTAA 2102
                         v v         i   - i   i ivi i  i ii   ?i  i v iv  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_52799914_5   2103 AAAGTTAACTTCAATCCATATATCACACCACATACAAAAATTAACTCAAG 2152
                          i i v  v  vi i  v  iv        i                  i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_52799914_5   2153 ATGGATTACAGGTCTAAATTTAACACCTAAAACCATAACTGTTCTGGGAG 2202
                               i ?  ii      v   v v       i    vvv ii i i  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_52799914_5   2203 AATACGGAGGATAAAATCCTTGTGACCTTGGATAAGGCAAAGATTTCTTA 2252
                           v  iv   ?vv     i i          i v      v i       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_52799914_5   2253 GATATGACACCAAATACATTATGCT-TAAAAGAAGATATTGATAAATTGG 2301
                                       vi  iv -  v-i       i v  v          
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_52799914_5   2302 ACTTCACCAAAATTAACATCCTTTTCTTTTCTAATAAC-TTAGTAAGAAA 2350
                               i         v v i   vivi   v  vi  -i  vi      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_52799914_5   2351 ATAAAAAGAAAAGCCACC-ACTTTGAAAAAATATTTTTGATTCTTATACC 2399
                         i i      v  v    v- v vv  i         vii v  v    i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_52799914_5   2400 TGATAAAGGCCTTTTTTCTAGAATAAATTAAAAACTCTCAAAACTTAGTA 2449
                               i  v   v v  i      v  v  i      i v    i i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_52799914_5   2450 ATAGAAAAGA 2459
                            -      
  L1M4_orf2#LINE/    791 ATA-AAAAGA 799

Transitions / transversions = 1.14 (107 / 94)
Gap_init rate = 0.02 (18 / 796), avg. gap size = 1.67 (30 / 18)  

 243 26.83 4.88 1.63  chr2_52799914_52803294     2767  2889 (492)    L1M4_orf2#LINE/L1      782   908 (0)  

  chr2_52799914_5   2767 AACTTAGTAATAGAA-GACAAATAGCTCAAATTATTAAATAGGAAAAAAA 2815
                             i i     i  -        i i   v ? v-    i  v   ii 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGA 830

  chr2_52799914_5   2816 CCC----AGATTCTTCACTAAAGAAGATACGTGCTTGACAACATAAACAC 2861
                         iii----   ivi   v i          iiiivv  i v -    i   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA-ATAAGCAC 879

  chr2_52799914_5   2862 ATGAAATAAGG-TAAACATCATTAGTCAT 2889
                               vi v - v       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (21 / 11)
Gap_init rate = 0.04 (5 / 127), avg. gap size = 1.60 (8 / 5)  


2815 25.17 5.86 1.49  chr2_52821417_52824369     1592  2461 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_52821417_5   1592 TGGAAAACAATCTTATGCTCATGGATCAGAAGAATTAATATCACTAAAAT 1641
                               ivv   ii   i        ii     v       iii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_52821417_5   1642 AGCCACACTACCCAAAG-AATCTACAGATTCAATGCACTCCCTATAAAAA 1690
                         i  v i   v      v-i              i   v       v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_52821417_5   1691 TACTAATATGATTTTTTTTTCACAGAAATAGAAAAAAAGAATTCTAAAAG 1740
                          v i ii-  vi      ---i       v  v  ivv  - i      v
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTT---GCAGAAATTGACAAGCTGA-TCCTAAAAT 145

  chr2_52821417_5   1741 TCTGATGGAATCAAAAAAGTGTCTAAATAGCCAAAGCAATCCTGAGCAGA 1790
                           vv      viiv  ii vvi vi          i     i   iv ii
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_52821417_5   1791 AAGGACAAAGTTGAGAGCATCACA--------TTTCAAAATATATTATAT 1832
                            i         iii vv     --------        iv  i  i v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_52821417_5   1833 GGCTACAGTAACCAAAACAGTACGGTATTAGTACAAAAGCAGGCACATAG 1882
                         i          i   i     ii    i i i i  iiii  i  i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_52821417_5   1883 ACTAATGAAATAGAATAGAAAATCCAGAAGTAAATCCACATATTTACAGC 1932
                          ii    i        v  i i       i    i   i i     ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_52821417_5   1933 CAACTAATCTTTAACAAAGCTGTCAGGAACATATGTTGGGGAAAGGATAT 1982
                            i i  i  ii    i v  i  i  v   viiv         i   -
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA- 394

  chr2_52821417_5   1983 GGTCTT--CAATAAATGGTGCTGGGAAAACTGGATAACAACATGCAGAAG 2030
                         -     --   i              v         ? v       i   
  L1M4_orf2#LINE/    395 -GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_52821417_5   2031 AATAAAACTGGATTTCTATCTCTCATCATGTATAAAAATCTACTGAAGAT 2080
                            i  ii    iii   i   v  i   i  i      iv   v  i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_52821417_5   2081 AAATTAAAGACTTAAATGTAAGACTTGAAAGTACACATCTACTAGAAGGA 2130
                         ii  i ?    i           vi i   v  i v v  vi      i 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_52821417_5   2131 AACCTAG-TGAAAACTCTTG-GACATTGGTCTATGCAAAGATTTTATAGC 2178
                            v   -? v   iii i -   v    vi  v    v i   iv   v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_52821417_5   2179 TAAGACCTCAAAAGCACAGACAACAACA-ATAAAATAGACAAATGAGACT 2227
                           v   vi          ii      v - v        i    vi    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_52821417_5   2228 ATATTAAA-CTAAAAATATCTTGTGCACAGCAAAATAAACAAGCAAGAGA 2276
                         vi  i   -i      i- i      vi--    iv v  v v     i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAAC-TTTTGTGCTT--CAAAGGACACTATCAAGAAA 690

  chr2_52821417_5   2277 GTGAAGAGACAACCTCTTGAGTGTGAGAAAATATCTGAAAACTCATCACA 2326
                              i        iviv  i  v          i  v   -    - i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCAT-ATA 738

  chr2_52821417_5   2327 -CTG----GAAACTAATAGCGAGAATATATAAGAAACTCACACAACCTAA 2371
                         -   ---- ii   vi  v v           ii     vi     ii  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_52821417_5   2372 CAGTAAAACAGA--AATAA-----------------------------AT 2390
                         i i     -   --     -----------------------------  
  L1M4_orf2#LINE/    789 TAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_52821417_5   2391 CCACATTTCTCAAAAGAAGACATACAAATGACCAATAGGTGTATGAAAAA 2440
                         vv         v        i         i      i iii       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_52821417_5   2441 ATGCTCAACATTACTAATCAT 2461
                                    i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (144 / 72)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.20 (64 / 20)  


 494 27.22 1.27 1.27  chr2_52907898_52912646     3079  3236 (1513)    L1M4_orf2#LINE/L1        1   158 (750)  

  chr2_52907898_5   3079 TGAAAAAAGCACTCCATGTTCATGGATAGGAAAAATCAATATTGTTAAAA 3128
                           i   i -i ii              v    i v i           i 
  L1M4_orf2#LINE/      1 TGGAAAGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_52907898_5   3129 TGGCCATACTGCCCAAAGCAATTTA-ATATTCACTACTGTACCTATCAAA 3177
                             v     v      vii  i  - v     vii vi v         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_52907898_5   3178 CTACCAATGATATCCTTCACAGAATTAGAAGAAACT-ATTTAAAAATTCA 3226
                         v v   iiviiv ii  ii     v v  v-  i  -  iiv        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCA 148

  chr2_52907898_5   3227 TATGGAAGTG 3236
                                i  
  L1M4_orf2#LINE/    149 TATGGAAATG 158

Transitions / transversions = 1.53 (26 / 17)
Gap_init rate = 0.03 (4 / 158), avg. gap size = 1.00 (4 / 4)  

2201 25.68 4.73 0.95  chr2_52907898_52912646     3518  4257 (492)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr2_52907898_5   3518 AAAATTCATATGGAA-T-CAAAAGAGCTTGAATAGCAGAGGTAATCCTAA 3565
                                        - -   ii  v iv       vi iii    i i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_52907898_5   3566 GCAAAAAGACCAAAACTGAAAGCATCTCATTCCTGGACTTCCA----TAC 3611
                         iv  i    v    ii  i i vv  v  i i ivi i   v ----   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_52907898_5   3612 TGCAAGTCTACAGTGACCAAAACAGCAAGGCACTGGCACAAAAACAGAAA 3661
                          i   iv       i i   i    iiv  i       i  ii i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_52907898_5   3662 CGTAGACCAATGGAACAGAACAGAAAGCCCAGAAGTAATGCCACACAGCT 3711
                         ii    i        i    iv  i  i      i   vv   i   vi 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_52907898_5   3712 ACAATCATATGATCGTCCACAAAGTGGACAAAAGCAAGGAATCGGGAAAA 3761
                          iii   vv    iv  v    i vv v   i v  vvv   -   i   
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAA 389

  chr2_52907898_5   3762 GACT--TCCTAATCAATAAATGGTGCTGGCATAATTGGCTAACCATATGC 3809
                           v --  i v-    i            v i  i   v  ?   i    
  L1M4_orf2#LINE/    390 GAATAGTCTTT-TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_52907898_5   3810 AGAAGATTGAAGCTGGGCTCCTTCCTTACACCATATACAAAAATCAACTC 3859
                          i    v     i   i i   v   i                 i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_52907898_5   3860 AAGGTGGAATAAAGACTAAAATCTAAAACCAAAAACTACACAAACTTT-- 3907
                           ii    vi ?    iv    v   i v v       i -     i --
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTA 537

  chr2_52907898_5   3908 GCAGTATAACCTAGG----AATTGT--TGACC-------ATGTAAAGATT 3944
                          v  v -   v    ----   iv --     ------- v i  v i  
  L1M4_orf2#LINE/    538 GAAGAA-AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_52907898_5   3945 TCAT-GATGATGATGCCAAAAGCAATTGCAACAAAAACAAAAATTGACAA 3993
                           v -   -    ii         vvv         iv      v  i  
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_52907898_5   3994 ATGGGACCT----AAAG--AAGAACTTTTGCATAGCAAAAGAAATGATCC 4037
                           v    i ----   i--  i        iiivv    i  v iv   v
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_52907898_5   4038 ACACAGTAAACAACCAACCTACAGAATGGTAGAAAATTTTTGCAACCTAT 4087
                          v v   i  v iv     i         v       v       vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_52907898_5   4088 GCATCTGACAAAGGTCTGATATCCAGAATCTATTAGGAACTTAAACAAAC 4137
                         ii      i  i  v  vi          v   v i     ivv    - 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-C 784

  chr2_52907898_5   4138 TTA-CAAGCAAAAAACAG----CCCCATTAAAAAGTGGGCAAAGGACATG 4182
                          i -i  vv    i   i----   v   ?    i           iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_52907898_5   4183 AATACAAACTTTTCGAAAGAAGACATACACATGGCCAAGAAGCATAGGGA 4232
                             v v i  i  v        i     v        v     i v - 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-A 883

  chr2_52907898_5   4233 AAAAATGTTCATCATCACTATCATT 4257
                            i   i   v     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (106 / 81)
Gap_init rate = 0.03 (20 / 768), avg. gap size = 2.10 (42 / 20)  


1739 25.60 4.56 8.03  chr2_52924930_52929554.rev     3216  4137 (488)    L1M4_orf2#LINE/L1       19   908 (0)  

  chr2_52924930_5   3216 TTATGGAT-GAAAGAC--AATACTCAGTATAAGGTATATACATTCTCCTT 3262
                          i      - i     --    i --  -    i i-ii -  v    ii
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATT--GT-TAAGATG-GCA-ATACTCCCC 63

  chr2_52924930_5   3263 AAAATGATTTATAGATTAAATGCAATTTCAGATATAATCAAAGTAG--TA 3310
                            v    i  i     v  i     ii vivi v    vv  iv -- v
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_52924930_5   3311 TTTTAAAATAAAATTAAGAAGCTAATTCTTACATTTACCTGGAAATGTA- 3359
                             iv i--     i v     i  i  v v   i iv        i -
  L1M4_orf2#LINE/    114 TTTTGCAG--AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_52924930_5   3360 ------CA-AACAGCTAAACCATCAAACTTGACAAAGAATAA------TG 3396
                         ------  -  i   i   -- -   v     v      v  ------  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAA--A-CAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_52924930_5   3397 TCACATTTACATTACTTGATTTTAAGA-TTACTATAAAGTGACAGTAATC 3445
                         vviv i i   i v iii    i  i -      i    iv         
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_52924930_5   3446 AAGATGACAATATGTTGTTGATATAATGATGG-CAAATAGATCAATGGAA 3494
                             ---  i i  v ii  ii    v   i -  v              
  L1M4_orf2#LINE/    259 AAGA---CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_52924930_5   3495 CAAAAC--AGGATCAACAGAAGTTGATCCACATGTACACAGTTGAACCGA 3542
                         i i  i--  ii  --     i vi i   i ii vi ii  i-  ii  
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTC-AATTGA 352

  chr2_52924930_5   3543 AAAGTGACAAAGGTAAAAAG-TTATTCAGTGGAGAATGAAATAAT--TTT 3589
                         vvvvi     i   ivv   -ii     i   i   v   -  i --   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTTTT 401

  chr2_52924930_5   3590 CAACAAATGTTGGTAAAACAATGGGGTAATTATATGGAAAAAAAGAAACA 3639
                                  v  v iii    iv  i  ?ii i   v    i  vi  vv
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_52924930_5   3640 CGTACCTCTGCTTCATCCCATATAGAAAAATTCATTTGATATGTATCGTA 3689
                         i v   i  i i   iv       v       v i ii v   v   i? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_52924930_5   3690 GACCTAAACTTAAAAGCTAAA-CTCTAAAGGTCATTGAACAACAACAACA 3738
                                 iv   i       -  v    iv  v v   v  --------
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA-------- 543

  chr2_52924930_5   3739 ACAAATATATATTTTTATATATATAAATATATATATAAATATATATTTAT 3788
                         -------------------------  i   vi?i     ----------
  L1M4_orf2#LINE/    544 -------------------------AACATAGGNGTAAAT---------- 558

  chr2_52924930_5   3789 ATATATTTATTTATATATGACTTGGGAGTAGGCAAAGATTT-TTAAGCAG 3837
                         ---------i  ---ii    i v  iv       v i   -   iii v
  L1M4_orf2#LINE/    559 ---------CTT---CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_52924930_5   3838 TAC-TCAGAAGTA---ACTACAGAAGAAAAATTGGA--AATTAGACTTCA 3881
                         v  -i  i   i ---i v   i        v i  --    i       
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_52924930_5   3882 TCAAAGTTAAAAACATATGTCCATCAAAGGATATCATTAA-AAATTGAAA 3930
                              i        v v   v v        i ii  i  -   v     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_52924930_5   3931 AGGCAAGACACATGCTAGAAAAATATATATGCAAAACATATATTTTTCAT 3980
                           i   vv    viv i i i  v    v      v       i v--  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG--AT 744

  chr2_52924930_5   3981 AAGCT-CTTGTATCCAGACTATAAAAAGAACT---GAAACTCAACAATAA 4026
                            vv-            v    v        ---iv       i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_52924930_5   4027 AAAATCAAATAACCCAGCAAAAAAACAGGTAAAG-ACTGGAAGAAATATT 4075
                            iv           iiv?     ii  i    - i v   v i i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_52924930_5   4076 GCACAAAAGAACATATTCAAATGGCCAACTCACACATAAGAAGGCACTCA 4125
                         v v v      v    v           ivvi     i i   iii    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_52924930_5   4126 TC--CATATTTTTC 4137
                         v --  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (140 / 92)
Gap_init rate = 0.04 (36 / 890), avg. gap size = 3.22 (116 / 36)  


2285 27.68 7.52 0.60  chr2_52981861_52985244.rev     2061  2898 (486)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_52981861_5   2061 CTATATTCATGGATTGAGAGACTTAATGTTGTTAAAAAGTGAATTTTTCA 2110
                          i  i           ii         i       i v vv   vi i v
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_52981861_5   2111 TAAAGTGATATATAGATTAAAGACAATCTCAGGCAGAACTTCCACTGATT 2160
                         i   v    v  i     v  vi     i viv  i  iii vi   vi 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_52981861_5   2161 TTTTT-TAGTAATTGGCAAGTTAACTTTAG---TAACATGGAAATGCCAA 2206
                              -i  v     i    i i iii  i--- v i          v i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_52981861_5   2207 AGACTTAGAATAAACAAAACAGTTTTTTTAAA--------AAGTCGCCGA 2248
                         i   ii      iv       i i  vvv   --------    i vv i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_52981861_5   2249 ATTTATATTACCTAATTTCAAAACTTACTATAAAGCCACAAAAATCAAGG 2298
                          i i i i v  i                 i     i   iv       i
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_52981861_5   2299 CAGTGTGGTATAAGTTTAAAGATAAA-GTATAGATTAATGG--------- 2338
                                   ivi iv   i    i -i       i     ---------
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_52981861_5   2339 -----TCTAGGAAAAGATCCTTACATTTATGGTCAATTTATTTTCAGTAA 2383
                         -----  i  i  v i i  v                 v      iii  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_52981861_5   2384 CACTGCCTAGACAAGTCAATGAAGAAGGCACAATCTCTTCAACAAGTGTT 2433
                         viv    v    v v      ii   i v i i   i        i  v 
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_52981861_5   2434 GCTGAAATTATTAGATAGTCATATATAAAA-AATTAATCTAAACTTTTAC 2482
                             ii iv i i    ?i  i  ii    -   v  vi ii  iii   
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_52981861_5   2483 CTTATATTATATAAAAATAATAATTCAAAATGACTCA--AACCAAAATGT 2530
                           i i ii     v   v v   i        iv   --i   v      
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_52981861_5   2531 TAGTGCCTTAACTATAAAACTTTTAGAAAAAAATGTAGAAGAAAAAATTT 2580
                         v  v  ivv            i      i    ii   i? v   vv  i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_52981861_5   2581 -TGATATTATATGAGGCCAGGATTTCTTAAATAGAACACAAAGATTATGA 2629
                         -   iv  ivi v    v v i       i   vi    v  i vi ii 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_52981861_5   2630 ATATTAAAGGTGAAAAATC-ATAAATTGGACATTATCAAAATTAAAAGCT 2678
                         ii vi   i -i      v-           v i             i  
  L1M4_orf2#LINE/    613 GCAACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_52981861_5   2679 TTTGCTCTTCAAAGAACATTTGCTGATAAAATAATAA---AAGCCACAGA 2725
                             iv        i   i -iiii v   i i v  ---  v       
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACT-ATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_52981861_5   2726 TTTGGAGAAAATATTTGCAAA--ACATATCAAGGAAATGACTT-CACTTA 2772
                         v v                  -- i     viiv  iv     -i iii 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_52981861_5   2773 GAGTATATACA--ACATTTAAAA---AATAATAGAA-------TAAGTCA 2810
                           i      v --  vi   v  ---       i  -------   vi  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_52981861_5   2811 ATTAAAACA-----AAAAAAATTG----GACAATTCACTAAAGGAAATGT 2851
                            ?   v -----   ii v   ----    v   v i    i i  i 
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_52981861_5   2852 ATAAAAGAC----AAGGGCATGAAAAACTGTTCAACAATTTTAACCATTA 2897
                          i   v i ----   vi        iv  i      --- i ???????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA---TCAZZZZZZZ 907

  chr2_52981861_5   2898 G 2898
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.79 (147 / 82)
Gap_init rate = 0.02 (21 / 896), avg. gap size = 3.24 (68 / 21)  


2691 25.31 3.06 1.93  chr2_52985915_52991671.rev     4385  5265 (492)    L1M4_orf2#LINE/L1       18   908 (0)  

  chr2_52985915_5   4385 TTCATGGATAGGAAGAATCAGTGTTATTAAAATGGTCATACTGCAGAAAT 4434
                                  v      v i i i  i    i    iv     v vv    
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr2_52985915_5   4435 TAATTTATAGATTCAATGCTGTTCC-ATCAAACTACCATTGACATTCTTC 4483
                          i  i  i        i  vi i  -      v v   vivi v  i  i
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr2_52985915_5   4484 ACAGAATTAGAAAAAAACTAA-ATGAAAATTCATATGGAACCAAAAAAAG 4532
                         i     v v  v  i--  i -viv               -- viv  i 
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAG--CTGATCCTAAAATTCATATGGAA--ATGCAAGG 163

  chr2_52985915_5   4533 AGCCCACA-TAGCCAAGAAAATCCTAAGCAAAAAGAGCAAAGGTGGAGGC 4581
                         ii    v -       i v    i i iv  i    i     v      v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_52985915_5   4582 ATCAGACTACCTGACTTCTA---TT-CTACAAGCCTACAATAACCAAAAC 4627
                         v   v   v  ii i   v ---  -      iv     i   i   i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_52985915_5   4628 AGCATGGTACTGGTACCAAAACAGACATATAGACCAATGGAACAAAACAG 4677
                           ii         i iv ii i           i        i i  iv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_52985915_5   4678 AGACCTCAGAAATAAGACCACACATCTACAAGGATCA---GATCTTCAAC 4724
                            vii         iv   i    i  i--- i   ---   i   i  
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTAT---GGTCAATTGATTTTCGAC 360

  chr2_52985915_5   4725 AAACCTGACAAAAACAAGGACTGGGGAAATA-TCCCCTATTTAATAAATG 4773
                           ivv  v   i v  vvv v        v - vvi  v  i  i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_52985915_5   4774 GTGCTGGGAAAACTGGCTAGCCATAGGCAGAAAACTGAAACTGGACCCCT 4823
                                  v      v  ?   i v   i  i v    ii         
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_52985915_5   4824 TCCTTACACCTCATACAAAA-TTAACTCAAGATGGATGAAAAACTTAAAT 4872
                         v   i     vi        -         i      v ? i  i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_52985915_5   4873 ATAAAACCCAAAACTATAAAACCCT-AGAAGAAAACCTAGGCA-ATACCA 4920
                         i   i v i             i  -          v    ?i- v i -
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC- 559

  chr2_52985915_5   4921 CTCAGGACATAGGCATGTGCAAAGACTTC------ATGACAAAAAAATCC 4964
                         i  iv   v v  vv iv    v ii   ------      -------  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA-------CC 602

  chr2_52985915_5   4965 AAAA--ACAATTGCAACAAAAGCCAAATTTGATAAATGGGATCTAATTAA 5012
                             --    --          vv   v v       v   ii v  i  
  L1M4_orf2#LINE/    603 AAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_52985915_5   5013 ACTAAAGGGCTTCTGCACAGCAAAAGAAACTCTTGTCAGAGTGAACAGGC 5062
                          v v  iii   i  ii vv    i  v   v iivv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_52985915_5   5063 AACCTACAGAATGGGAGAACATTTTTGCAATCTACCCATCTGACAAAGGT 5112
                             i              v  v       vii ivi      i  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_52985915_5   5113 CTAATATCCAGAACTTACAAGGAACTAAAACAAATCTGCAAGAAAAA--- 5159
                           vi         iv  i  i     vvv    v  vii  v     ---
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_52985915_5   5160 --ACAACCCCATCAAAAAGTGGGAAAAGTACATGAACAGACACTTCTCAA 5207
                         -- i     v  i?    i    v    v iv    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_52985915_5   5208 AAGAAGACATTTATGTGGCCAATAAACACATGAAAAAAAGCTCAACATCA 5257
                                i  vi vi          i          i v           
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_52985915_5   5258 CTGATCAT 5265
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.23 (121 / 98)
Gap_init rate = 0.02 (19 / 891), avg. gap size = 2.32 (44 / 19)  


2195 24.88 5.72 3.73  chr2_52993628_52995392      470  1273 (492)    L1M4_orf2#LINE/L1       89   908 (0)  

  chr2_52993628_5    470 TCCTTACTCACAAAGAATAGCTATTTCTTTTA-AAAAATT-ACAA----- 512
                            i  -   -   vvvi    iii i    i- i     -    -----
  L1M4_orf2#LINE/     89 TCCCTA-TCA-AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr2_52993628_5    513 ------AATTGGTATAGAACTACAAAAGATACAAAATAGCCAAAGCAATT 556
                         ------    vi   i   v i   ii  iv  i          i    i
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_52993628_5    557 CTGAGCAA-------AAAGCTGGAGGCATCACACTACCAGACTTCAAAAT 599
                         i   iv  -------    i      vv       v  vi i       i
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_52993628_5    600 ATACTACAAAACTATAGCAACTAAAACAGCACGGTAGTGACATAAACACA 649
                         v         i   i  i  ii  i    iii    v  i     iv i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_52993628_5    650 AACACAGAGACCAAAGAAACAGAATATAGAACACAAAAACTAATCTATG- 698
                         i   i v   i   v i  i     vv   iiv  i   iv  i i  i-
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_52993628_5    699 -TCTATAGTCAACTGATTTTT-ACAAAGGTG---------------GGGG 731
                         - i   i     i       i-    i    ---------------    
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_52993628_5    732 AAG---T--TCTCTTCAATAA-CAGTGTTAGGAAAACTGGATACCCATAT 775
                           i--- --   i     i  -ii   i i   v         ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_52993628_5    776 GCAGAAAAATGAAACTAGACCCCCCACCTCACACTCTATATAAAAAACAA 825
                            i  i      ii i      i-         iv    i     vi  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAA 485

  chr2_52993628_5    826 CTCAAAATGAATTAAAAAACTAAATATAGGACTCAAAACTTTAAAACTAC 875
                                  i  i ? i v      i  i  vii      v       vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_52993628_5    876 TAGAAGAAAACACAGGGA-AAATGCTTCAGGACATTAATTTAGGAAAAGA 924
                                     i   ?i-    -    iv   v  iiv     v  v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_52993628_5    925 TTTTATGAGCAAAGATCCCAAAAGCACAGGCAACAAAAGCAAAAATAAAC 974
                            i- v  vv v  iv           i          v       i i
  L1M4_orf2#LINE/    585 TTTC-TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_52993628_5    975 AA-TAGGAGTATATCAAACCAAAAAGTTTCTACACATCTGAGGAAACAGT 1023
                           - v   v vi      viv    ii  i iii v  vi    v  vi 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_52993628_5   1024 TAACACTGTGAGAAGGCAACCTGCAGAAATAGGAGAAAATATTTGCAAAC 1073
                         i  v vv    i   i     ii     - i                  i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAA-TGGGAGAAAATATTTGCAAAT 732

  chr2_52993628_5   1074 TACTGTTTCCACAGGGGATACAAACTCCACAGGGGATACTACTGTTTCCA 1123
                         i - i v  i------    ----------    ---   --   v    
  L1M4_orf2#LINE/    733 CA-TATATCT------GATA----------AGGG---ACT--TGTATCCA 760

  chr2_52993628_5   1124 GAGTATACAAGGAACTCAAACATCTCAACAGAAAAGAAACAAACAGTCCA 1173
                           i    i  i      vv   v     i iv   i i     i ii   
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_52993628_5   1174 ATTAAAAAACAGTTAAATCATCTAAACAGATATTTATCAAAAAAAGAGAC 1223
                            ?     ii vi   vv  i i  i   i    v  v   i    --i
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA--T 858

  chr2_52993628_5   1224 ATACAAATAGCCAAGAAATATAAGAAAAAATGCTCGACATCACTTATCAT 1273
                                 i     v  ii i v     i      i      ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (133 / 63)
Gap_init rate = 0.03 (24 / 820), avg. gap size = 3.17 (76 / 24)  


 374 19.78 12.09 0.00  chr2_53066579_53070535      382   472 (3485)    L1M4_orf2#LINE/L1        4   105 (803)  

  chr2_53066579_5    382 AAAGACACCTGATTTTCATGGACTGAAAGACTCA---TTATTAA-ATG-- 425
                              i i iv  v        i  i      i ---  i    -   --
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_53066579_5    426 --TAC---CCAAAGCAATCTACAGATTCAATGTAGTCTCTATTAAAATCT 470
                         --   ---     vii              i i i  i    i      i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_53066579_5    471 CA 472
                           
  L1M4_orf2#LINE/    104 CA 105

Transitions / transversions = 5.00 (15 / 3)
Gap_init rate = 0.04 (4 / 102), avg. gap size = 2.75 (11 / 4)  

2052 20.62 3.70 1.75  chr2_53066579_53070535      482   995 (2962)    L1M4_orf2#LINE/L1      234   757 (151)  

  chr2_53066579_5    482 AACTTATAACAATATTGCC-TAATCAAAACAGTGTGGTGGTACTGGCATA 530
                               iv    vii i v-       i          ---         
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT---ACTGGCATA 280

  chr2_53066579_5    531 AAGACAGACATATAGACCCATGGAATGCAGA---GAGAGCCTGGAAATAA 577
                          i  i           i v       --   ---     i ii       
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAAT--AGAATTGAGAGTCCAGAAATAA 328

  chr2_53066579_5    578 ACCCTCACATATATGGTAAAATAATCTTTAACAAGCATGCCAACACCACA 627
                             vi    v      v  v i  i  ii     vi      v    iv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_53066579_5    628 CAA-GAGG---GAAT-GCCTCTTCAAAAAATGGTATTGGGAAAACTAGAT 672
                            - i  ---    - i  i     v       ii     v    i   
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_53066579_5    673 ATTCATATGCAAAAGAATGAGGTTGGACCCTTATTTTATACCATATGCAA 722
                          ?i  i              i         i  ii i i       i   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_53066579_5    723 AAATT----CAAAATGAATTAAAGAAAAATGTAAATGTCAAATTTTAAAC 768
                              ----       i  i ?   ----iv       v i vi v    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGA----CCTAAATGTAAGAGCTAAAAC 524

  chr2_53066579_5    769 TATAAAAATCT-AGAAATAAACATAGAGAAGAAGGTTTGTGATTTTGGAT 817
                                v   -    iv        i?ivi  vv  i    ii    i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_53066579_5    818 TTGGCAATGATTTCTTGTACATAACACCAAAAGCATTGGCAACAAAAGCA 867
                          v       i      iv i  i            ivi          v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_53066579_5    868 AGGTTAGATAAGTGGAACTACATAAAACTTAAAATCTTCTGTACATCAAA 917
                          iiv       i v i   v   v   v      v   i   i v     
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_53066579_5    918 GGAAAAAAT--AAACAGTGAAATG-CAACCAACAGAATTGGAGAAAATAT 964
                            v vv  -- i v       v -     v       v           
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_53066579_5    965 TTGAAAATCAGATAGCTGATAAGGGG--TGTAT 995
                            v      v   v          i--     
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTAT 757

Transitions / transversions = 1.40 (60 / 43)
Gap_init rate = 0.02 (13 / 524), avg. gap size = 2.15 (28 / 13)  

 679 17.49 3.83 4.92  chr2_53066579_53070535     3283  3465 (492)    L1M4_orf2#LINE/L1      728   908 (0)  

  chr2_53066579_5   3283 CAAACCATA------ACAAGGGGGCTATATTTAGAATATCTAA-GAATTT 3325
                             i    ------ i     ivi i   ii       v   -   i i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_53066579_5   3326 CTACAAATCTACAACAACAGCAACAAAACAAATGACCTGATTTTTAAAAA 3375
                         i     --  ----   i ii  v  i      i   ii   ?--     
  L1M4_orf2#LINE/    778 TTACAA--CT----CAATAATAAAAAGACAAATAACCCAATTW--AAAAA 819

  chr2_53066579_5   3376 TAGAAAAAGGACTTCAATAGACATTTCTCCAAAAAGGGTACACAAATGGC 3425
                          i iv      i  v                  i i i  i         
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_53066579_5   3426 CAAACAAGCAAATGAAAAGATGCTCAACATCATTAATCAT 3465
                            -i     v                     ????????
  L1M4_orf2#LINE/    870 CAA-TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.17 (25 / 6)
Gap_init rate = 0.03 (6 / 181), avg. gap size = 2.67 (16 / 6)  


2502 28.92 3.36 1.57  chr2_53177674_53181528.rev      835  1726 (2129)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53177674_5    835 TGAAAAAACATTTCATGCTCATGAATTGAAGGGATTAATATCTTTAAAAT 884
                           i   i i  ii    i     i    i i iv       iv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53177674_5    885 GGCCATACTGCCCAAAGCAATATATAGGTTTAATGCTATTTTTATCAGAC 934
                            v     v      vii  v  i  i  i  i  v  iii     i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53177674_5    935 TACTAA-TGTCATTTT--CCAAAGTTAGAAAAC--A-CTTAAAAAATTCA 978
                          v i i-  i v    -- vi  i  iiv  i -- - i     --    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA--TTCA 148

  chr2_53177674_5    979 TATGTAAC--CAAAACACAGCGTGAATAGTGAAAGCAATCCTAAGCAAAA 1026
                             v  v--   iiv  -- vv      iv   i     i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_53177674_5   1027 AGGACAAAGCCAGTGGCGTCACATTATTCAATTTCAAAATATACTGTAAG 1076
                           i      iii v  vv     i vii           iv    ii  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_53177674_5   1077 GCTAGAGCAACCAAAACAGCATCATACTGGTAGAAA-ACAGACATATGGA 1125
                             v  i  i   i    ii vi      i v  i- i        i  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_53177674_5   1126 CTAATAGCACAGAATAGAGAACCCATAAATAAAGTTACATGTCTACAGCC 1175
                         ii   i v i     v    ii   v       vii i ii i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_53177674_5   1176 ATCTGATCTTC---AAGGCTGACAAAAATAAGCAGTGGAGAAAGAACTCC 1222
                          vi    i   ---    v  v   i vi vv  i   i       ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_53177674_5   1223 CTAGTCATTAAATAGTCCTGGGATAACCGGCTAGGTATATCCAGAAAAAT 1272
                           vv   vi    i  v      i   i  v  ?vi i  v  i  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_53177674_5   1273 GAAACTGGACCCCTAGCTTTCACCATATACAAAAATTAAGT-----TGGA 1317
                            ii          v  iv                   v -----    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_53177674_5   1318 TTC--GATTTAAATGTAAGATCTCAAACTATAAGAATCCTACAAGAAAGC 1365
                          iv--  ii           v  v         i v  i  v      i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_53177674_5   1366 TTAGG---AAACCCCATTCTGGACATCAGCCTTGAGAAAGAATT------ 1406
                         v    ---   i ---   vv   v ii vi v iv  v iv  ------
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_53177674_5   1407 TATGACTAAGTGCTCAAAAGCAATTGCAACAAAAACAAAGTTTGACAAGT 1456
                               -- ----i        vvv         iv   iv v  i  i 
  L1M4_orf2#LINE/    594 TATGAC--A----CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_53177674_5   1457 GGGACCTAATTAAACCAAACAGCCTCTGCAGAGCAGAAGAATCTGTCAAC 1506
                         v    i v  i   viv  v i i i  iivvv  i i  vv  i    v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_53177674_5   1507 AGAGTAAACAGATAACCTACAGAGTGGGAGGAAATATTCACAAACTATGC 1556
                          i   i  v   i    i     i      i       ii    ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_53177674_5   1557 ATCCAGCAAATGTCTAATATGCAGAATTTATAAGGAACTTAAACAATTCA 1606
                            iiii  iv v  vi   v      v     i     ivv    i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_53177674_5   1607 ACACTTAAAAACCAAATAACTGCA--TAGAAAGTGGGCAAAAGATATGAA 1654
                          i v v    iv        i-  -- ?i   i        i   v    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_53177674_5   1655 CAGACACTTCTCAAAAGATGACACACAGGCAGCCAATGAACATATGAAAA 1704
                         i     i     v     v  i i   iiii      i i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_53177674_5   1705 CGTGCTCAACATCACTAATCAT 1726
                         vi            ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (161 / 95)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.44 (44 / 18)  

1471 26.99 11.39 0.94  chr2_53177674_53181528.rev     2128  2768 (1087)  C L1M4_orf2#LINE/L1   (0)   908   201  

C chr2_53177674_5   2768 CAAAGATATGGAGAGCTGACTGTAATTGATTTCAAGGCTTAGTATGAAGC 2719
                              - -     ii  v  vv vviii       ii    v  ii    
  L1M4_orf2#LINE/    201 CAAAG-T-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr2_53177674_5   2718 TATAATATTCAAGACAATATGGTATTGGCATAGCAATGTCCAGAGAGG-- 2671
                           i i  v        i i     i       ivi  ivv  v v  i--
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr2_53177674_5   2670 AATGGAATGGAAT--AGAGTTCAAAAATACACTCATACACATATGAT-AA 2624
                                 i    --     i  i     v  i      iv    i -  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

C chr2_53177674_5   2623 TTGATTTTGAACAAAGGTGT-AAGGTTATTCAATGGGGAAAGAATA---- 2579
                                 vi    i    i-   iii                   ----
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

C chr2_53177674_5   2578 --TTAACATGTAGTAATGGAAAAATTATATATCCACTTTGAAAAAAGTAA 2531
                         -- i    vi i  iv   i v  i iv   ?    v vv    i i i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

C chr2_53177674_5   2530 ACCTTGATTCTTATATTCTATCTCACACAAAAAATAGCTTGATGTGCATC 2481
                          vi v  ii i  iv ivi i vi i       v  i  ii vi  v   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

C chr2_53177674_5   2480 ATAGTCCTAAAACTATAGGTTAAA-CTAGAAAATGTCTAGATGAAAATAT 2432
                          ?  v      vv  vii i    -   v    ivii    v     i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

C chr2_53177674_5   2431 GGCAGAAAATTTTTGTGATGCTGGGATAGGCTCAA--ATTTCCAAAGTAG 2384
                         i v? v    i  i    ivi    v     --  --i    iv ii  v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGC--AATGGTTTCTTAGATAT 596

C chr2_53177674_5   2383 GACTTAGAAAAGTACAGATTA-AAAAGAAAAACATA-ATAAATCAGACTT 2336
                            viv-     i   iiiv -          -   -      ii     
  L1M4_orf2#LINE/    597 GACACC-AAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTT 644

C chr2_53177674_5   2335 CATC-----CAAAAAC-----------AAA--ACTCAGTTAAAAAA-TGA 2305
                             -----i      -----------   --  v vi i  i   -   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

C chr2_53177674_5   2304 AAAG-----CTAAAGAATAA-ACAAAACAC--ACTA--CATATATTTGAC 2265
                             ----- i v     ii- v    i i--i v --       i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

C chr2_53177674_5   2264 AGATGACTTGTATCCAAACTGCATAAAGAAATCTTACAATTTAATTGTAA 2215
                          iiv            i v ii        v        i i   vi   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

C chr2_53177674_5   2214 GAATACAACCAACCCAAC-----AATGAG---AAGATTTGAACAAAAAGT 2173
                         i  v    vi       i-----    i --- i        i i v v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chr2_53177674_5   2172 TATTAAACTAAGATATACAGA-------------------AAGAGGCTCA 2142
                          v iv  vv          i -------------------    v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chr2_53177674_5   2141 ACATCATCAGTCAT 2128
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (106 / 64)
Gap_init rate = 0.04 (25 / 708), avg. gap size = 3.16 (79 / 25)  

 722 25.00 0.88 5.26  chr2_53177674_53181528.rev     3076  3303 (552)  C L1M4_orf2#LINE/L1   (687)   221     4  

C chr2_53177674_5   3303 AGAGATATATCATCTCCATTGAACTGAAGAATCAATATTGTTAAAATTG- 3255
                          i      vi   v i   v  viv     v i           i  v -
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

C chr2_53177674_5   3254 AATTTTTTTCCCAAGTTGATTTATAGATTTAATGCAATCCCTCCCACTCC 3205
                            vi i--     i     i  i     i  i         vi  ----
  L1M4_orf2#LINE/     54 AATACTC--CCCAAATTGATCTACAGATTCAACGCAATCCCTATCA---- 97

C chr2_53177674_5   3204 TAAAAAAATCCCAGGAGACTTTTTAACAAGAAATTTATATGTTGATTCTA 3155
                         -----         vv v      vi  -      v i v i    i   
  L1M4_orf2#LINE/     98 -----AAATCCCAGCTGCCTTTTTTGCA-GAAATTGACAAGCTGATCCTA 141

C chr2_53177674_5   3154 ATATTTGTATGGAAATG-AAAAGATCTAGAATAACTAAAATAGTTATCAA 3106
                          v   ii          -  ii  i i      i i    i i iv v  
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

C chr2_53177674_5   3105 AAAATAGGACAAAATTAGGGAACTTATGCT 3076
                            iv  i     i  i i i   i ii  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACT 221

Transitions / transversions = 2.00 (38 / 19)
Gap_init rate = 0.02 (5 / 218), avg. gap size = 2.80 (14 / 5)  


 218 27.27 0.00 0.00  chr2_53183361_53185745.rev       29    83 (2302)    L1M4_orf2#LINE/L1        1    55 (853)  

  chr2_53183361_5     29 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCGTGAAAAA 78
                              ii i  i   i i      i v      v i     i  v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53183361_5     79 GACAA 83
                          i   
  L1M4_orf2#LINE/     51 GGCAA 55

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.00 (0 / 0)  

2904 25.57 1.52 4.24  chr2_53183361_53185745.rev      990  1908 (477)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_53183361_5    990 ATGTTTGTGAGTTGAAAGAATGAATGTTGTTTAAATGTCTGTACTACCCA 1039
                              ii  ii   i    v v   i     v i   v vi    v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_53183361_5   1040 AAGTGATCTATAGATTCAATGTAATTTCTGTCAGAATTCCAATGTCATTT 1089
                           v       i        i i   ii  i   i   i   -- iiiii 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA--GCTGCCT 112

  chr2_53183361_5   1090 TTTTTACTGAAATACAAAAAAAAATTCATAAAATTT-TATAGAACCAGAA 1138
                              i v     vv v  ivvi  i -       i-   i   viiv  
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCC-TAAAATTCATATGGAAATGCAA 161

  chr2_53183361_5   1139 AAGACCCCTAAAAACCCAAACAATCTTATCAAA-AAGAACAAAAGTGGAG 1187
                         ii     vv  v i  v          ivv   -         iv     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_53183361_5   1188 GCATTC-CACTCCTTGATTCCAAAATATGACATAAAGCTTTTGTAATCAA 1236
                          - i  -    i iii   i     iv ivi i      viv        
  L1M4_orf2#LINE/    212 G-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_53183361_5   1237 AACACCATGGTTCTGGCATACAAACAAAGATATTGACCAATGAGACCACA 1286
                         i   vii    v        vii i i v    v  i     ii iviv 
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_53183361_5   1287 TAGAATGCCTAGAAATCAACTCAAGTATTTAAGATTAATTGACTCTTGAC 1336
                          v  iv i i      v   i  vii     v i i      i i i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_53183361_5   1337 GAAAGTGTCAAGACTATACAATGGGAAAAGAACAGTCTCTTCAGTAAATG 1386
                         i ii   i      i  v       i      i     i    ii     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_53183361_5   1387 ATGTTGGGAAAACTTGATATCCACATGCAAAAGAATGAAATTGGACCCTT 1436
                         i  i     v    v    ?                   i        i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_53183361_5   1437 ATCTCACATCATATCCAAACAGTCAACTCAAAATGGATAAAAGCCTTAAA 1486
                          i      i     v    - i i              v ?  v i    
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAA-AATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_53183361_5   1487 CTTAAGATGTGAAACTGTAGACTTACCAGGAGAAACCATAGTGGAAAACT 1536
                         iv     vv i     i  i vi vii  i     v     v? v   - 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-T 558

  chr2_53183361_5   1537 CTAC-TAAATTTGT-CTGGGCAGTCATTTTGTGGATAAAACTGTGAAAGC 1584
                           v - i vi   v-i i    i vi   iv i    vi  vvii     
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_53183361_5   1585 AGAGACAACAAAAGCAATAATAAACAAATGGGATTGCATCAAACTGAAAA 1634
                          v ii         v  v    i i    v   i v       v v    
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_53183361_5   1635 GCTTCTGCATAGCAAAAGAAACAATTAACAGAGTGAAGAGACAACATGTG 1684
                         i   i  iiivv    i  v  v  i  v i      i       viiii
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_53183361_5   1685 GATTGGGGGAAAATATTTGCAAACAATACATTCTATAAGAGACTACAATT 1734
                           v    i               iv   i  iiv     i    ------
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT------ 752

  chr2_53183361_5   1735 GGCTCCCTGTATGTATCTATTTTGCATAAAATATATAAAGGAACTC---- 1780
                         -----------      i ---------i           -     ----
  L1M4_orf2#LINE/    753 -----------TGTATCCA---------GAATATATAAAG-AACTCTTAC 781

  chr2_53183361_5   1781 AACTCAGTAGCAAGAA----AATAACCCAATT-AAAAACAAGCAAAGGAT 1825
                               i  ii  i  ----            -     iii         
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_53183361_5   1826 CTGAACAGACATTTCTCAAAAGATGAGCTATGAATGATTAATAGATATAT 1875
                         i    i           v     v  vv  ii    iii    iii i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_53183361_5   1876 GAAAAAATACCATCTCTAATCATCAGGGAAAAT 1908
                              i  i ----  -  -     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGC----TC-AA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (152 / 80)
Gap_init rate = 0.02 (19 / 894), avg. gap size = 2.79 (53 / 19)  


3217 23.05 5.28 1.15  chr2_53211878_53213755.rev      518  1389 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53211878_5    518 TGGAGAGACATTTTATAATAATGGATTGAAGGAATTAATGTTGTTAAAAT 567
                             i   i  iii  iv v        i i  v     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53211878_5    568 GTTCCTACTACCCAAAGCAATCTACAGATTCAATATAATACCTATCAAAA 617
                          vivv    v      vii              iii   v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53211878_5    618 TTGC-GATAACTT------AGAAA-----AAA---ATCCTAAAATTTCTA 652
                          iv - v iv   ------     -----  i---           iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_53211878_5    653 TAGAACCACAAAAGACTCAAAATAACCTAAGCAATTTTGATCAAGAA--- 699
                          i   vii   ii   i  i    i  v  i    i    vv     ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_53211878_5    700 CAAAACTGAACACATTACACATCTTGATTTTAACATTTATAACAAAGCTA 749
                             ii  i vivv i    v  iii    i  v i   iv         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_53211878_5    750 TAATGATCAAAACAGTATGGTACTAACATAAAAACAGATATATAGATCAC 799
                         i i i     i     i       ii     ii i   i          v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_53211878_5    800 TGAAACAGCATAGAGAACTCAGAAATAAAGTCATACATGTATGGTCAACT 849
                           i  i  v  v    iii          vi       v         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_53211878_5    850 TATTTTTGGCAGAAGTGTCA---TCACTTAATGGGGAAAGAATAGTCTCT 896
                         v     i i  iii   i  ---i  i i                   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_53211878_5    897 TCAACAAATGGTTTTAGGAAAACTGAAAATCTACATGCAGAAGAATGAAA 946
                                     vi i   v     i v ? i       i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_53211878_5    947 TTGGTCCCCGATTCTACACCACATACAAAAGTCAACTAAAAATGAATTA- 995
                             v    v iiii      i        i i    v      i  i -
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_53211878_5    996 -GAC-TCAACATAAGACCTGACACCATAAA-CTCTTAGAAGAAAACATAG 1042
                         -   - v  ii     v  i v  i     -                   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_53211878_5   1043 AGTAAAAGCTTCTAGATATTGGCTTTGGCAATGATTTCTTAGATATGACA 1092
                         i?vv   v    vv  iv    v  v       i                
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_53211878_5   1093 GCAAA-GCACAGGCAAAAAAAAGCAAAAATTAGACAAATGGGATTGTATC 1141
                         v    -     i    v    i--     v    i    v   i vi   
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAG--AAAAAATAGATAAATTGGACTTCATC 648

  chr2_53211878_5   1142 ACACTAAAAAGTTTCTGTACAGCAGAGGAAAC-----AGAAAATGAA--G 1184
                          v v v    ii  i   i vv  i    v  -----     i    -- 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_53211878_5   1185 ACAACTTA------------AAACATTTGTAAATCATATATCTAATAAAG 1222
                              ii ------------   i     i             i    i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_53211878_5   1223 GGTTAATATCCAAAATATATAAGGAAGTCCTACAACTCTATCAAAAAACA 1272
                          ii vi      i         i   v  i        v  -  v   --
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-AATAAA-- 795

  chr2_53211878_5   1273 ACTAAAACAAA-AACCATGATTTAAAAATAGGCAAAAGAGTGGAAGTGAT 1321
                         ---  i     -    -ii   ?      i      i  v v   vv  i
  L1M4_orf2#LINE/    796 ---AAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_53211878_5   1322 ATTTCTCAAAGAAAGACATACAGATGGCCAACAGGTATATGAAAAAAATG 1371
                                v  ii    i     i        i i i i       i -  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chr2_53211878_5   1372 TTCAACAGCTTTAATAAT 1389
                         i      v v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (130 / 68)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.95 (56 / 19)  


3087 24.69 3.37 1.46  chr2_53216215_53220742     3146  4036 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53216215_5   3146 TGGAAAGATATCCCATGTTCAGGGACTGGAAGAATTACTATTGCTAA-AT 3194
                                              v   i       v   v     i   -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53216215_5   3195 GCTCATACTACACACAGCAATCTACAGATTCAATGTAATCCTTATAAAAA 3244
                          viv     v v  v vii              i i     i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53216215_5   3245 TACCAATTACATTCTTAATAGAAATAGAAAAA---ATCCTGAAGTTTGTA 3291
                          v   ii i v  i  vii      v  v  i---     i  i  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_53216215_5   3292 TGAAATCTTAAAAGACCTTGAATAGCCAAAGCAATCTTGAGCAAAAAGAA 3341
                           i  vivi  ii    iv           i         iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_53216215_5   3342 CAAAGCTGGAGGA-TCACACTGCCTGACTTCAAAACATACTACAGAGCTA 3390
                              i       -       v  ii i        v       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_53216215_5   3391 AAGTAACCTAAATAGTTTGGTAGAGTCATAAAAACAGACATGTAGACAAA 3440
                         v     i v i i   v     vv v     ii i      i    iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_53216215_5   3441 TGGAACAGAAC-AAAAATCTCAGAAATAAATCCATGCATCTACGCCTAAC 3489
                              i    i-i i i  -          i    i   i  i vii  i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_53216215_5   3490 TGATTTTTGACAAAGTTGTCAAGAACAAACACTGGGGAAAGGATAGTCTC 3539
                                i     i v  i     v  vv  v         i       i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_53216215_5   3540 TTCAATACATGATGCTGAGAAAACTGAACACCCACATGCGGAAGAATAAA 3589
                              i v   i     i  v     i i ?        ii      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_53216215_5   3590 ACTAGACTCCTGACTCTCACAATATA--AAAATTAACTCAAA-TGAATTA 3636
                         ii i   i   iv   v   v     --              -  i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_53216215_5   3637 AAGACTTAAATGTGAGACTTGAAATCATGAAATTACTAGAGGGAAATG-- 3684
                         ?    i       i   vi i   ii  i   i vi    i i   ii--
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_53216215_5   3685 ---------CTTCATGACATTGGTCTGGACAAGGATTTTCAGGATAAGAC 3725
                         ---------    i    v    vi i i   v i   iivi    v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_53216215_5   3726 CTCAAAAGCACAGATAACTAAAGCAGAAATAGACAA-TGAGATTGCATCA 3774
                         vi          iii   v    v i       i  - vi  i v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_53216215_5   3775 AA-CTAAAATGCTCTGCGTAGCTAAGGAAAT----AACAGAATGAAGAGG 3819
                           -i     vvi i  i ivv v     v i----  v i i    i  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_53216215_5   3820 CAACTTACAGATCGATCGGGAGAAAACATTCACAAACTATACATCTGACA 3869
                             ii     ---  -         i   ii    ii   i      i 
  L1M4_orf2#LINE/    700 CAACCCACAGA---AT-GGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_53216215_5   3870 GGTGGCTAATATCCAGATTATACAAAGAACTCAAATAGCTCAATAGTAAT 3919
                         i v i  vi        v    i         vv i i       i   v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_53216215_5   3920 AATAATAATAATAAT--AATTTGTGAAAGTAGAACAAAAGACTTGTACAG 3967
                           -i i  --    i--    ?i--   i i i-    i  i   v i  
  L1M4_orf2#LINE/    796 AA-GACAA--ATAACCCAATTWA--AAAATGGG-CAAAGGATTTGAATAG 839

  chr2_53216215_5   3968 AAATTTCTCAATAAAATACATAAAAATG-TCAACAGGTATATGAAAAAAT 4016
                          v       v v i  v i   v     -i   i i i i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_53216215_5   4017 -CACAAATCATCAGGAGAATG 4036
                         - v   --     ????????
  L1M4_orf2#LINE/    890 GCTCAA--CATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (146 / 71)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.05 (43 / 21)  


1802 25.40 3.40 1.62  chr2_53244496_53246104      500  1117 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_53244496_5    500 AAAAACAGACACAAAGAGCAATGGAAGAGAACAGAGAACCCAAAAATAAG 549
                           ii i     i v   v        v    iv    ii   i      i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_53244496_5    550 ACTGCACACCTACAGCTATCTGATCTTTGACAAACCTGGCAAAAACAAAA 599
                         v iii   ii  ii ii vi    i  i     ivv  v   i v  vvv
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_53244496_5    600 AAATGGGGGAAGGA--GTCCCTATTCAATAAATGGTGCTGGGATAACTGG 647
                           -     i   i --   -- v     i              i      
  L1M4_orf2#LINE/    380 AA-TGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_53244496_5    648 TTAGCCATATACAGAAGATTGAAACTACACCTCTTCCTTACACCATATTA 697
                         v  ?   i  i  i    v    ii iv   i  v   i         - 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT-A 475

  chr2_53244496_5    698 AAAAAATTAACTCAAGATGCGTTAAAGACTTAAATGTAAAACCCAAAACA 747
                         v              i   vi i ?    i         i v i     v
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_53244496_5    748 ATAAAAACCCTGGAATACAACCCAGGTG-ATACCATTTTG-GACATATGA 795
                               vi i i   v v   vi   ? - v i --  i -   v vv i
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGG 573

  chr2_53244496_5    796 AAAGGCAAAGATTTCGT-GATGAAGACACCAAAAGCAATTGCAACGAAAG 844
                         vv      v i    v -   - v             vvv     i    
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_53244496_5    845 CGAAAATGGACAAATGGGGTCTAGTTAAACTAAAGAACTTCCGCACAGCA 894
                         vi     i  i    v  iii vi i   v v  i     ii ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_53244496_5    895 AAGGAAGCTATCAACAAAATAAACAGACAACCTACAGAATGGGAGCAAAT 944
                              vi       v   i i  v        i            v    
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_53244496_5    945 GTTTGCAAA-CACTGCCTCTGACAAAGG-------TCCACCATCTATAAG 986
                         i        -  - iiv     i  i  -------    vv  v     i
  L1M4_orf2#LINE/    723 ATTTGCAAATCA-TATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_53244496_5    987 GAACTTAAGCAAATTTACGAGAAAAAAA-----AATCCCATTAAAAAGTG 1031
                              ivvi   v iv ii v     i -----  i  v   ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_53244496_5   1032 GGCAAAAGAAATGAACAGACACTT-TCAAAAGAAGATATATG--TGGCCA 1078
                               i  vv    i     i  -  v            ii--      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_53244496_5   1079 AAAGGCACATGAAAGAAAAAACTCAACATCACTGATCAT 1117
                          v i          -- i vi          ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAA--AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (89 / 64)
Gap_init rate = 0.03 (16 / 629), avg. gap size = 1.94 (31 / 16)  


2859 25.71 4.10 0.80  chr2_53260738_53264922.rev     2815  3693 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53260738_5   2815 TGGTAACACATCCAATGCTTAGGGATGGGTAGAATCAATATTGTGAAAAT 2864
                            v  v i    v   i i v    v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53260738_5   2865 GACCATACTGTCAAAAGCAATCTGCAAATTCAATGTAATGCCTATCAAAA 2914
                          i v     vi v   vii    i  i      i i   v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53260738_5   2915 TAGCA-CTGTCATTCTTCACAGAA--TGAAAAAAGC-AATCCTAAAA--- 2957
                          vv  -   i -  i  ii     --   v  --  -i         ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTC 147

  chr2_53260738_5   2958 ------------AAAGAGCCCACA-TAGCCAAAGCAAGACTAAACAAAAA 2994
                         ------------  i ii    v -        i   vvi i  v  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_53260738_5   2995 GAACACATCCAGAGGCATCACATTACCTGACTTCAAA--TTACATTAAAA 3042
                              v viii    vv     i v  ii i      --    --  v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAA 245

  chr2_53260738_5   3043 GGCCATAGTCATCAAAACAGCATGATACTGGTATGAAAATAGGCACATAG 3092
                         i  i i   v     i    ii  i      i  i ii    i  i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_53260738_5   3093 ACAAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAGC 3142
                          iv       i     v    ii           v   v i i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_53260738_5   3143 CAACTAATCTCTGACAAAGCAAACAAAAATATAAAGTGAGGAAAGGACAT 3192
                            i i  i ii     i vviv   i vi  vv i  i      i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_53260738_5   3193 CCTATTCAACAAATGGTGCCGGGATAATTGGCAAGCCGCATGTAGAAGAA 3242
                         i  v               i    i  i   vv ?  i    i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_53260738_5   3243 TGAAACCAGATCCTCATCTCTCACCTTA-----AAATCAACTCAAGATGG 3287
                             iiii  i  ii i   v    v  -----    i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_53260738_5   3288 ATCAAAGTCTTAAATCTAAGACCTGAAAACT-TAAAAGTTCTGGAAGATA 3336
                             ?  v i     v     v  -      -     v ii i     v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAA 544

  chr2_53260738_5   3337 ACATCAGAG-AAATCCTTCTAGACATTGGGTTAGGCAAAGACTTCATGAC 3385
                             vi ? -     -   vv   v             v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_53260738_5   3386 CAAGAACTCAAAAGGAAATGCAACAAAAACAAAAATAGATG----GGATT 3431
                         i v  vvi      v v v         iv          i----   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_53260738_5   3432 TAATTAAGCTAAAAAGCTTCTGCACAGCAAAAGATACAATCAGCAGAGTA 3481
                          v  i  iv v    i   i  ii vv    i  i  v    iv i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_53260738_5   3482 AACATACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGA 3531
                           v v            i           v  ii   vii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_53260738_5   3532 CAAAGGACTAATATCCAGAATCTACAAGAAACGCAAACGAATCAGCAAGA 3581
                         i  i     vi          v  i  ii   v vv  i v   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_53260738_5   3582 AAAA---AAGCAATCCCATCAAAAAATGGGCTAAGGGCATGAATAGACAA 3628
                             ---  ii  i  v  i?          v    iiv          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_53260738_5   3629 TTCTCAAAAAAAGATATACCAGCGGCCAATAAACATATGAAAAAATGCTC 3678
                              v   i         v ii         i  i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_53260738_5   3679 AACATCACTAATGAT 3693
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (136 / 86)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.69 (43 / 16)  


3212 26.87 0.66 0.66  chr2_53301054_53305422     2970  3877 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53301054_5   2970 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3019
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53301054_5   3020 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 3069
                            v     v     iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53301054_5   3070 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3117
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_53301054_5   3118 TATGGAACCAAAAAGGAGCCCGCATTGCCAAGTCAATCCTAAGCCGAAAG 3167
                                viiv  i   v  v v  v     iv     i i ivvii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_53301054_5   3168 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3217
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_53301054_5   3218 TACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGCTATAGACC 3267
                                 i   i    ii   i     i iv ii i   vv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_53301054_5   3268 CATGGAGCAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 3315
                         v     ii    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_53301054_5   3316 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATAGGGAAAGGATTCC 3365
                          vi    i  i     ivv  v   i v  vvv   i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_53301054_5   3366 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 3415
                           v  i  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_53301054_5   3416 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATAGA 3465
                            ii    i    v   i     v           i  i    i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_53301054_5   3466 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3515
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_53301054_5   3516 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3564
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_53301054_5   3565 AAACACCAAAAGCAATGGAAACAAAAGACAAAATTGACAAATGGGATCTA 3614
                         vi            vvi v         v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_53301054_5   3615 ATTACA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGA 3663
                           i v -     i -   i  ii vv    i  v    i  vv i i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_53301054_5   3664 ACAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 3713
                          v  i     i i               v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_53301054_5   3714 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 3763
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_53301054_5   3764 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 3813
                            i     i     v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_53301054_5   3814 TCTCGAAAGAAGACATTTATGCAGCCAAAAGACACATGAAGAAATGCTCA 3863
                             v        i  vi viii     v ii        i i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_53301054_5   3864 TCATCACTGGCCAT 3877
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2820 25.50 2.91 1.34  chr2_53406481_53411972     4107  5000 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53406481_5   4107 TAGAAAACTATTTCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4156
                          i    iv   ii    i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53406481_5   4157 GGCCATACCTCCCAAAGCAATTTATAGATTCATGGTATTCCC-ATTATAC 4205
                            v    ii      vii  i  i       vv i v    -  i v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53406481_5   4206 TACCATTAACGTTCTTCACAGGTCTAGAAAAAAAAAAACTG-TTTTAAAA 4254
                          v   vivi v  i  ii   ------   vvi v  i   - ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG------AAATTGACAAGCTGATCCTAAAA 144

  chr2_53406481_5   4255 TTCATATGGAACCAAAAAAAGAGCACA-AATAGCCAGGGCAATCCTAAGC 4303
                                    -- viv  i ii v  -        iii     i i iv
  L1M4_orf2#LINE/    145 TTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_53406481_5   4304 AAAAAGGACAAAACCGTAGGCATCACGCTACCTGACTTCAAACTATACTA 4353
                           i   i     iii v   vv    i  v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_53406481_5   4354 CAGGGCAACAGTAGCCAAAACAGTGTGGTA------TAAGAACAGACACA 4397
                           ii  v      ii   i           ------    i i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_53406481_5   4398 CAGAACAATAGAACAGAACAGAGAACCTAGAAATAAGACTGCACACCTAC 4447
                         i   v    i   i    iv    ii i        iv iii   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_53406481_5   4448 AACTATCTGGTCTTCAACAAACCTGAGAAAAACAAGCAATGGGGAAAGTA 4497
                         iiii vi  i i   i    ivv  vv  i v  vv            v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_53406481_5   4498 CTCCCTATTCAATAAATGGTACTGAAAGAACTAGCTAACCATATGCAGAA 4547
                         ivvi  v     i       i   ii v    i v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_53406481_5   4548 AATTGAAACCGGACACCTTCCTTACACCATATGCAAAAATTAACTCAAGA 4597
                         i v    iii    v   v   i         i               i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_53406481_5   4598 TGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACTCT-GGAAG 4646
                              i ?    i         i v i            -    -i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAG 541

  chr2_53406481_5   4647 AAAACCTAGGCA-ATACCATTCTGGACATAGGCATAGGCAAAGATTTCAT 4695
                              v    ?i- v i -   vv   v v  vv       v i    v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_53406481_5   4696 -GATGAAGACACCAATAGCAGTTGCAACAAAAGCAAAAATTGACAAAT-G 4743
                         -   - v        v    vvv          v      v  i    - 
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_53406481_5   4744 G----CATCTAA-TTAAAGAGCTTCTGCACAACAAAAGAAACTATCAACA 4788
                          ----    v  -     i -   i  ii vv    i  v        v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_53406481_5   4789 GAGTAAACAGACAACGTACAGCATGGGAGAAACT-TTTGCAAACCATGCA 4837
                         i   i  v       vi    v          v -        i   ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_53406481_5   4838 GCTGACAAAGGTCTCAGATCCAGCATCTATAAGGAACT--TA-AATTTAC 4884
                         v    i  i  v  iiv      v  v     i     --  -  i i v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_53406481_5   4885 AAAGAAAAAAACAAATGACCCCATAAAAAAGTGGGCAAAGGAC----ATT 4930
                         v  v     i      i    v  v?    i           i----  v
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_53406481_5   4931 AACGCTTTTCAAAAGAAGACATACATGTGGCCAACAATCACATGGAAAAA 4980
                         i  ii  i  v        i     vi       i  v      i   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_53406481_5   4981 AGCTGAACATCACTGATAAT 5000
                         v   v       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (132 / 92)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.90 (38 / 20)  


3324 22.32 1.37 5.79  chr2_53431476_53435632     2716  3665 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53431476_5   2716 TAGAAAGATATTCCATATTCATGGACTGGAAGAATCATTATTGTTAAAAT 2765
                          i         i    i        i       v i v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53431476_5   2766 GTCCATACTACCCAAAGCAATCTATAAATTCTATGCAGTC--TATCAAAA 2813
                          v v     v      vii     i i    v i   i  --        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53431476_5   2814 TACCAATGGCATTATTCACAGAAATAGAAAAAAAAATTCTTAAATTTATA 2863
                          v   iiv  v  v  ii       v  v  ivvi  i  v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_53431476_5   2864 TGGAACAACAGAAGACCTAGAATGGCCAAAGCTATCCTAAGCAAAAAGAA 2913
                              vvi  iii    i     i      i v   i i ---       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAA 197

  chr2_53431476_5   2914 CAAAACCGCCTCGAATAAAGGGGAATATATAAAAAAGAAAAACCTGGAGA 2963
                         ------------   i    -----------------------i     i
  L1M4_orf2#LINE/    198 ------------GAACAAAG-----------------------TTGGAGG 212

  chr2_53431476_5   2964 AATCACATTACCTGACCTTAAATAGTAACTACAGTTACCATACAGAGCTA 3013
                          v     i v  ii ii i   -----   -----   --    i     
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAA-----ACT-----TAC--TACAAAGCTA 250

  chr2_53431476_5   3014 TAGTAACCAAAACAGGGTAGTACTGGCATAAAAATAGACACATAGACCAA 3063
                         i     i   i    v  i            ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_53431476_5   3064 TGAAACAGAATAGAGAACCCAGAAACAAATCCACACACCTGCAATTAACT 3113
                           i  i     v    ii       i   i   i   ii iiii i  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_53431476_5   3114 CATTTTCAACAAAGATGCCAAGAGCATACACTGAGGAAAAGGCAGTGTCT 3163
                         v      i    i i        v   v  v  i     iiii   v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_53431476_5   3164 TCAATAAATGGTGCTGGGAAAACTGGATATCCTTATGTAGAAGAATGAAA 3213
                             i              v         ?  vi   i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_53431476_5   3214 CTAGACCTCTATCTCTCACCATATATAAAAATCAAATCAAAATGAATAAA 3263
                         i i    i   i   v         i      i  v        i  v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_53431476_5   3264 AGACTTAAATGTAAGACCTCAAACTATGAAACTACTATAAGACAACATTG 3313
                             i           v  v       i     vi  v    v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_53431476_5   3314 GAGACAATCTCCAGGACACTGGTCTGGGCAAAAATTTCTTGAGTAATCCC 3363
                          ? vv     i iv   vi   vi i     vii      iii  - vv 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGAC 599

  chr2_53431476_5   3364 AC-ACAAGCACAGGTAACGAAAGCAAAAATGGACAAAG-GGAGTCACATT 3411
                           - v       i i   i    v      i  i   v-   v i-   i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATC 648

  chr2_53431476_5   3412 AAGGTAAGAAGCTTCTG-------AAGCACA--GTCAACAAAGTGAAGAG 3452
                           ii v i  i   i  -------   v   --i    v        i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_53431476_5   3453 ACAGCCCACAGAACGAGAGAAAATTTTTGCAAACTACCCATCTAACAAGG 3502
                            i         i i        v        ii ivi    i i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_53431476_5   3503 GATTAATAACAAGAATATATAAGGGGCTCAAACAACTCTATAGGAAAAAA 3552
                           i vi  v v           i ii   vv       v   iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_53431476_5   3553 ATTTAATAATCTGATTTTAAAAATGAGCAAGAGATTTGAGTAGACCTTTC 3602
                          iv-     i ii   ?-       i    ii       i     v    
  L1M4_orf2#LINE/    799 ACA-AATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_53431476_5   3603 TAAAAAGGAAGACATACAAATGGCAAACAGCCATATGAAAAGGTGCTCAA 3652
                          vv    -    i           v  i iv  i        i       
  L1M4_orf2#LINE/    847 TCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_53431476_5   3653 CATCATTAATCAT 3665
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (139 / 69)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.25 (68 / 16)  


 215 25.40 0.00 3.17  chr2_53475525_53479007.rev      123   185 (3298)  C L1M4_orf2#LINE/L1   (54)   854   794  

C chr2_53475525_5    185 AAAAAACAAATAATCTGAGTTTTTTCAATGGGCGAAAGATCTAAATAGAC 136
                             i        i ii --  ?vvv       i  i   i i       
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAA--TTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chr2_53475525_5    135 ATTTTTTTAAAAA 123
                             i ii   i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGA 854

Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.02 (1 / 61), avg. gap size = 2.00 (2 / 1)  

1075 28.32 8.01 2.15  chr2_53475525_53479007.rev      503  1014 (2469)    L1M4_orf2#LINE/L1      189   730 (178)  

  chr2_53475525_5    503 GAAAGAAAACACCAAAGTTTGAGTATTTTGACTACTTTATTTTAGA--TT 550
                             i i  v v       v   v i ivv   v iiv    i i --  
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_53475525_5    551 ATTAGAAAGTTATAATAAGCAAGA-----TGGTATTGATATAA----AAA 591
                          i  v    i  i i   v     -----     i  ii    ---- i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_53475525_5    592 CAAATATATTACTGAAAT----CTG---TTCCAATGACAAACAGAGAATC 634
                           v   v  i v  i   ----i  ---v    ivi i    ------i 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC------CC 332

  chr2_53475525_5    635 TTGAATTTGTGCTATAATGACTCTTGACAAAGCCACCAAATTAATTCAGT 684
                         v iv    i  v vv v   i i i     i vii    iviv     i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_53475525_5    685 GGAGGAAAGGACAAT-TTTTCAACAAATAG----GGAAGAACTGGATATC 729
                           -      i i i -            i ----  i v         ? 
  L1M4_orf2#LINE/    383 GG-GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_53475525_5    730 TGTATGGAAAAAAA---ACCACAATTCCTATATCATACCATTTATAAGAA 776
                         iii   v    i  --- vivvi ii    iv   i     v  i  i  
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_53475525_5    777 TTAATTTGATATGAATCATAAACCTAAACATGAAGTGC-AAAGCTATAAG 825
                             i ii v   i    ? i       ii -   v  -   i      i
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAA 530

  chr2_53475525_5    826 GGTTATAAAATAAAACATGGAAG--AATATTTGATGACCT------AG-- 865
                         iv iv  i  v       i i? --   v  i -      ------  --
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGC 579

  chr2_53475525_5    866 AA-GTTTTCTT-GACAGAACTCAGAAAGCACTAACCTTACAAGATAAAAG 913
                           - v      -  i vi  v vi       v i vvi v    -    i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAAA 628

  chr2_53475525_5    914 TA-ATAAATTGGACTTTATCAACATTGAAAAGTTTTGCTCATCAAAAGAC 962
                           -             i     v   i    v     iv v     i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_53475525_5    963 ATCATTAAGGAAATGTACACGA-AAGCCACAGATTAACATAAAGTATCCA 1011
                          ii  i   i  i  - v v  -  v       v iiv v   i   iii
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTG-AAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_53475525_5   1012 CAA 1014
                            
  L1M4_orf2#LINE/    728 CAA 730

Transitions / transversions = 1.58 (87 / 55)
Gap_init rate = 0.04 (22 / 542), avg. gap size = 2.36 (52 / 22)  

 416 31.93 1.81 0.00  chr2_53475525_53479007.rev     1328  1493 (1990)    L1M4_orf2#LINE/L1      740   908 (0)  

  chr2_53475525_5   1328 CTGA-AAAAAATTTTTATTTTGATTACATAAACAATT--TATAATTTAAT 1374
                             -  iii i  v   iiv  v  i     v  i --  i  i i   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_53475525_5   1375 AACAAGAATATTTCCAATCCTCCCAAAAAATAGATGAAAGATTTAAATAG 1424
                           i  i  v ivvvi  i  vvii?      i iii  i     i     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_53475525_5   1425 ACACTTCACCAAGAAAGCTAAGCAAATCGCCAATTAGTCCATGGAAAAGT 1474
                            i   v    ii   v  vi     v      v  iv    i   ii 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_53475525_5   1475 GTTTAGCATTATTGATCAT 1493
                          i i i   i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (36 / 16)
Gap_init rate = 0.01 (2 / 169), avg. gap size = 1.50 (3 / 2)  

3821 18.15 5.34 0.71  chr2_53475525_53479007.rev     2149  2991 (492)    L1M4_orf2#LINE/L1       27   908 (0)  

  chr2_53475525_5   2149 TGAAAGACTTAA-ATTTTATAAAATGGCAATATTCT---------TCTGC 2188
                           i         -   v -   i         i  i---------   i 
  L1M4_orf2#LINE/     27 TGGAAGACTTAATATTGT-TAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chr2_53475525_5   2189 AGATTCAATGGAA-CCTAATCAAA-TCCCAGCTGCTGTTTTGGGGGACAG 2236
                                 i v  -  iv      -          iv    v ----   
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG----CAG 121

  chr2_53475525_5   2237 AAATTGACAAGATAATCC--AAATTTGTATGGAGACTTAAGGGACCCAGA 2284
                                    v i    --     ii      i ivi            
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_53475525_5   2285 ATAGCCAAAGCAATCTTGAAAAAGAAGAACAAAGTTGGAGTACTCATGTT 2334
                                  i                              v     iii 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_53475525_5   2335 TCATGATTTCAACACTTACTGTAAAGTTATAGTAATCAACATAGTGTGAT 2384
                           vii       v       ii    i  i         v i      i 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_53475525_5   2385 ACTAGAATAATTATGGGCACATAGATTAACAGAATAGAATTGAGAGTCCA 2434
                            i v    vv  i i  i      i  ii                   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_53475525_5   2435 GAAATAAACCCTTACATTTTTAGTCAACTAATTT-CAACAAAGGTACCCA 2483
                                    v       v i     i i    - i    i   i  v 
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_53475525_5   2484 AATCATTCAGTGGGGGAAAGAATCGTATT------AAGTGATTCTGGGA- 2526
                         i i      i     -       v  v  ------  i  i v      -
  L1M4_orf2#LINE/    372 GACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_53475525_5   2527 AACGAGATATCCACAGGCAGAAGAAATTAATTGG----CTGCCTCAACCC 2572
                            vi    ?     v   i     vvv i    ----  i     vv  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_53475525_5   2573 ATACACAAAAATTAACTCAAAATGGCTCACCAGCCTAAATGTAAGGATCA 2622
                            i                     v   ?vii            iiii 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_53475525_5   2623 AAAGGATAAAACCTTTAGATGAAAAGA--GGAGTAAATATTTATAAGCTT 2670
                            vv       ii     v     v --  ?      v  ii i v   
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_53475525_5   2671 CAGTTAGGAAATGGTTTCTGAGTTATGACAGCAAAAGTACAAGCAACAAC 2720
                         vi      v          v  v       v      i           v
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_53475525_5   2721 A-ATAATATAGATAAATTGGA-TTCACCACAATTAATAGCTTTTTTGCTT 2768
                          - v  v              -    i  v      v i     v     
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_53475525_5   2769 -AAATG---CTATTAAG---GTAAAAAGACAACCCATAGACTATGCAA-- 2809
                         -   v ---    i   ---  i             i   v iv vi --
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_53475525_5   2810 ---TTTCCAAATCATATATTTGATATGGGATTTTTGTACAGAATGTATAA 2856
                         ---   v            i     v    i  v i v      i     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_53475525_5   2857 AGAACTCTTACAAAACAATAATGAAAACGTAAGTAACCCAATT-AAAAGT 2905
                                      vv       i    vii  i          -    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_53475525_5   2906 GGGCAAAGGATCTGAATAGATGTATTTTCAAAGACCATGTGCACATGGCT 2955
                                    i        ii v i i      vv  i i  v     i
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_53475525_5   2956 AACAG--ACATGAAAAGATGCTCAATATCATTAGTCAT 2991
                           i i--                  i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (89 / 61)
Gap_init rate = 0.02 (21 / 882), avg. gap size = 2.43 (51 / 21)  


 243 23.53 5.88 1.18  chr2_53479209_53482524.rev      426   510 (2806)  C L1M4_orf2#LINE/L1   (0)   908   820  

C chr2_53479209_5    510 TGGG---AGGAT--GCAGGAACATTTCTTAAAATAAGACATACAAATAAT 466
                             ---     -- v vii        iv   v    i        iii
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

C chr2_53479209_5    465 CTACAGGGATATGAAAAAAATACACAGCATCACTCATCAT 426
                          v i i v i       i - i v  i     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.03 (3 / 89), avg. gap size = 2.00 (6 / 3)  

 603 26.40 6.18 0.56  chr2_53479209_53482524.rev     1583  1760 (1556)    L1M4_orf2#LINE/L1        1   188 (720)  

  chr2_53479209_5   1583 TGGAAAAAGATTTCATGCTTGTGGATAGGAAGAATCAATATTGTTAAAAT 1632
                               i v  ii    i ii     v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53479209_5   1633 GGCCATTCTGCCCAAAGCAATTTATAGATTC----------CTATCAAAC 1672
                            v  v  v      vii  i  i      ----------        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53479209_5   1673 AGCCAATGACATTCTTCACAGAACTAGAAAAAGGTATTCTAAAATTCATA 1722
                         vv   iivi v  i  ii     v v  v  ivvv  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_53479209_5   1723 TG-AAACATAAAGGAGCCCAAATAGCCAAGGCAATTCTT 1760
                           -   iii  i   v  vi         ii    -   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTT 188

Transitions / transversions = 1.35 (27 / 20)
Gap_init rate = 0.02 (3 / 188), avg. gap size = 4.00 (12 / 3)  

2538 26.26 1.77 0.68  chr2_53479209_53482524.rev     2090  2824 (492)    L1M4_orf2#LINE/L1      166   908 (0)  

  chr2_53479209_5   2090 CCCGGCCTAGCCAAGGCAATTATAAGCAAAAATAACAGAGCTGGAGGCAT 2139
                            i vv       ii    iv i iv  i  v    i  i      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_53479209_5   2140 CATACTACCCAACTTCAAACTGTACTACATGGCTACAGTAATCAAAACAG 2189
                           i   v     i      viv       vi              i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_53479209_5   2190 CATGGTACTGGTACAAAAACAGACACATAGACCAATGGAACAGAATAGAG 2239
                         ii         i i  ii i     i     i        i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_53479209_5   2240 GGCCCAGAAATAGAGCCATGCACCTACAATCACCTGATCTGCAACAAAGC 2289
                         i i         i v    i  ii  iii   vi    i v i    i v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_53479209_5   2290 TGACAAAAACAAGCAATGGGGAATGGACTTCCTGTTCAATAAGTGGTACT 2339
                           v   i v  vv          v i ivvi  v     i  i    i  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_53479209_5   2340 GAGACAACTGGCTAGCCGTATGCAGAAAATTGGAACTGGATCTCTTTCTT 2389
                          i         v  ?  ii     i  i v  i ii    i i  vi  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_53479209_5   2390 ATACCATATA-AAAAGTTAACTAGAGATGGATTAAAGACTTAAATGTAAA 2438
                          i        -    i      vi i      i ?    i         i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_53479209_5   2439 ACCCAAAACTATAAAAACCCTGGAAGACAACCTA--TGCAATACCATCCT 2486
                          v i            vi i i     v   v  --? i  - i v  v 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGT 564

  chr2_53479209_5   2487 GGACATAGGAACAAACA--GATTTCATGAGGAAGACGCCAAAAGTAATTG 2534
                          -  v v  ivi ii  -- i    v iiiv v   i       i vvv 
  L1M4_orf2#LINE/    565 G-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_53479209_5   2535 CAACAAAAGCAAAAATTGACAAATGGCGTCTAATTAAA-CTAAGAGCTCT 2583
                                  v      v  i    v viii v  i   -i   i i  i 
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_53479209_5   2584 GCATG-GCT--AAAGAA-ACTATCAAGAAAGTAAACAGACTACCTACAGA 2629
                         ---  -   --    i -              i  v    v   i     
  L1M4_orf2#LINE/    664 ---TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_53479209_5   2630 ATGGGAGAAAACTTTTGGAAACTATGCATCTGACAAAAGTCTAATATCTA 2679
                                    iv    v   ii  ii      i  ii v  vi    i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_53479209_5   2680 GCATTTATAAGGAACTTAAACCAATTTATAAGCAAAAAACC--CAACCCC 2727
                          v  v     i     ivv  v v iv    vv    i  v--i     v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_53479209_5   2728 ATTAGAAAGTGGGCAAAGGACATGAAGAGACATTT-TCAAAAGGAAACAC 2776
                            ?i   i           iv    v        -  v    i i i i
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_53479209_5   2777 ACATGTGGTCAACAAGCATATGAAAAAAAGCTTAACATCACTGATCAG 2824
                            vi   i   i     i       i v   i       ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (119 / 70)
Gap_init rate = 0.02 (12 / 743), avg. gap size = 1.50 (18 / 12)  


2771 26.03 4.82 0.69  chr2_53531750_53535949     2838  3709 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53531750_5   2838 TAGAAAGATATAATATATTCATGGACGGAGAGACTGAGCATCATAAAGAT 2887
                          i         vvi  i        iv ii     v ii  ii v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53531750_5   2888 GTCCATTTTCCCAAAATTGAGGTGTAGATATAAGGCAATTCCTCTAAAAA 2937
                          v v  vi    v       vv ii    vi  v     i   v v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53531750_5   2938 TCTCAGCAAGATTTTTTTTGTAAATATAGATAATATTATTCTAAAATTTA 2987
                           i    --viii       i i v  v  i  vv v  i        i 
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_53531750_5   2988 TATGGAAAGGCAAAGGAACTAGAATGGCTAAAACAAT-TTGGAAAAGGAG 3036
                                 v    i   v i     i  i        -   i     i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_53531750_5   3037 ATTAAAGTGGGAGGAATC-CATTTACCGG---CAAGATTTATTATATAGC 3082
                          vi     v      v  -  i  v  ii---   i i   i  i v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_53531750_5   3083 TACAGTAATCATGACTGTGAGGTATTGTCAGAGAGTTAGACACATAGATC 3132
                                    v   v   v    i  v  v ii v      i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_53531750_5   3133 AATGGAGCAAAATAGAAAACCCAGAGACAGACCCATACAAATATATTCAA 3182
                               ii i   v  i ii     i i i         vv   iv    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_53531750_5   3183 CTGATTGTTGACAAAGGTGCAAAAGCAATTCAGCTGAGGAAATA-TATCC 3231
                         i     v i     i     v  ii v     i-  i     v -  vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTC 397

  chr2_53531750_5   3232 TTTTCAATAAATGGAGCTGGAGCAATTGGACATCTAGAAGAAGAAAAA-- 3279
                                i      v     ii   i    i ? i v v v i  i  --
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_53531750_5   3280 AAATTAA---TCTAAGTTTCATCCTATATATAAAAATTAATTCAAAG-GG 3325
                           i  ii---i   --ii   iv i     i         i     i-  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_53531750_5   3326 ATCACAGGCTTAA-TGAAAAAAGTACAACTATAAAACTTTTAGTA-AAAA 3373
                             ?  i i   -  v  i iv  v            i    v -    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_53531750_5   3374 CATACGAGAAAATGTTCAGGATCTAGTGCTAAGCAAAAGTT-CTTAAATC 3422
                             v ? v    v   iv  i  v v i  i    vi   -    i  v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_53531750_5   3423 TAACACCAAATGCAAAAGCTATTTTTAGAAAAGTTA-ATAGATTGAATTT 3471
                          i        v   v    v ivvv-      iv  -   i    i i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAA-AGAAAAAATAGATAAATTGGACTT 644

  chr2_53531750_5   3472 CATCAAAATGGACAACATTTGCTCAT-AAAAGACACTGGAAAGAGAATGA 3520
                                  vi v   v    iv v -   i      ivv    i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_53531750_5   3521 ATGGACAAGGTACAGTGTAGGAGAAAATACGTGCAAGCTACATATCTAAG 3570
                          vi     vvi    vi i          iv     iii i      i v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_53531750_5   3571 AAAAGGCTGCTATTTACAATACATAAAGAAC-------ATTCAA------ 3607
                           ii i  vv   ii v    i         ------- i    ------
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_53531750_5   3608 ---AACA-----TCCAATTAGAAAATGGGCAAAAGACAAGAAGAGGTATT 3649
                         ---i   -----i      ?i            i  ivv   v  ii   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_53531750_5   3650 TCACCAAAGGGGATATACAGTTGAC----AAACACATGACAAGAAACTCA 3695
                           v      ii        iv  i ----  i       v    vi    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_53531750_5   3696 ACATCTACCCTAAG 3709
                              v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (132 / 91)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.40 (48 / 20)  


2330 26.10 5.29 5.29  chr2_53556680_53561703.rev     3631  4538 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53556680_5   3631 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATCACTACTGTTTAACT 3680
                               i    i     i        v      v i v  i    v iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53556680_5   3681 GGCCATACCGACCAAAGCAATTTATAGATTCAATGCTGTTCCTATC---- 3726
                            v    ivv     vii  i  i        i  vi i      ----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53556680_5   3727 TACCAATGATACTTTTCACAGAA-TTAAAAAAATTATTCTAAAATTTATT 3775
                          v   iiviivi    ii     -  i v  iv v  i        i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_53556680_5   3776 TGGAACCAGAAAAGGAGCCCATA-CAGTCAGAGCAATCCTAAACAAAAAG 3824
                              -- viv    ii    v -i  i  i i     i i  v  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_53556680_5   3825 AAAAAAGCTGCAGGTATCAC--TACCTGATTTCAAGCTATACTGCAAGGC 3872
                           v    i  v   vv    -- v  ii       iviv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_53556680_5   3873 TACAGTAACTGAAACAGCATAGTACTGATACAAAAACAGACATGTAGACC 3922
                                 iii i    ii i      ii i  ii i      i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_53556680_5   3923 AATGGAACAGGTTAGATAACCTAGAAATAAAGTTGCACACCTACAACCAT 3972
                                i  iv v  v ii i         viiii   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_53556680_5   3973 CTGATCTTCAAAAAATCTGACAAAACAAG-CAATGGGGAAAGGATTCCCT 4021
                         i    i   i v  ivv  v   i  v v-            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_53556680_5   4022 ATTCAATAAATGGTACTGGGATAACTGACTTGTCATATGCAGAAGATTGA 4071
                         v     i       i      i     iv v?i  i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_53556680_5   4072 AACTGGATCCCTGAATTTTACCATATATAAAAATTTACCCAAGATGGATT 4121
                          ii    i    ivv ivi        i       v  i   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_53556680_5   4122 GAAGACTTAAACGTAAAACCTAAAACTATAA-----------GAAAACTT 4160
                         i?    i    i    i v            -----------      v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_53556680_5   4161 AGG---AAATACCATTCTGGAAATAGGAACTGGCAAAGATTTC------A 4201
                            ---    -- -   vv  vv v  iviv     v i    ------ 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_53556680_5   4202 TGATG---AAGTCACAAAAAACAATTGCAACAATTGACAAATGGGACCTA 4248
                            ii---  iv     iv     vv v  v   v  i    v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_53556680_5   4249 ATTAAACTAAAGAGATTCTGCACAGCAAAAAACAAACAAAAAAACCCAAA 4298
                           i   v v  i iv  i  ii vv    ii   ----------------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA---------------- 679

  chr2_53556680_5   4299 ACAAAAAAAAGCAAACAAAAAAACCCCCAAAACAAATAATAAACAGACAA 4348
                         ----------- v v   i   i---------------- i  v      
  L1M4_orf2#LINE/    680 -----------CTATCAAGAAAG----------------TGAAAAGACAA 702

  chr2_53556680_5   4349 CCTACAGAATATGAGAAAATATTTGCAAACCATGCGTTTGATAAAGGTCT 4398
                           i       iv                 i   iii i      i  v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_53556680_5   4399 AATATTGATAACCTATAAGAAACTC--AGAAATCAATA-TG------CAA 4439
                         vi   iv v  iv     ii     -- v  v      - i------   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_53556680_5   4440 AAAACCCA--TTAAAAATGGGCAAAGGATGTGAA----CACTTCTCAAAA 4483
                          v      -- ?                 v    ----  i     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_53556680_5   4484 GAAGACATGGATGTGGCCAA-AAACATATGAAAGAATTCTCAATATGACT 4532
                              i  iv vi       -  i  i      ii  v     i  v ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_53556680_5   4533 TATCAT 4538
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.57 (143 / 91)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.80 (96 / 20)  


3273 27.10 0.66 0.22  chr2_53725322_53731587     4871  5774 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53725322_5   4871 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4920
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53725322_5   4921 GGCCATACTACCCAAGGTAGTTTACAGATTCAATGCCATCCCCATCAAGC 4970
                            v     v     iv ii i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53725322_5   4971 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5018
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_53725322_5   5019 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5068
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_53725322_5   5069 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGCC 5118
                                i      vv       v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_53725322_5   5119 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5168
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_53725322_5   5169 AATGGAACAGAACAGAGACCTCAGAAATAATGCCGCATATCTACAACTAT 5218
                                i    iv    vii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_53725322_5   5219 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5268
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_53725322_5   5269 ATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCTGA 5318
                         v  i  i              v  i   v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_53725322_5   5319 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5368
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_53725322_5   5369 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5418
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_53725322_5   5419 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5468
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_53725322_5   5469 CACCAAAAACAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5518
                                 i  vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_53725322_5   5519 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5568
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_53725322_5   5569 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5618
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_53725322_5   5619 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5668
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_53725322_5   5669 ACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5714
                             ----   v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_53725322_5   5715 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 5764
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_53725322_5   5765 CACTGGCCAT 5774
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.00 (8 / 4)  


3062 26.72 1.55 0.89  chr2_53801321_53806216     3503  4404 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_53801321_5   3503 TGGAAGAACATTCCATGCTTATGGATAGGGAGAATCAGTATCGTGAAAAT 3552
                              ii i  i     i i      v  i   v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_53801321_5   3553 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 3602
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_53801321_5   3603 TACTATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 3650
                          v i vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_53801321_5   3651 TATGGAACCAAAAAAGACTC-GCATAGCCAAGACAACCCTAAGCAAAAAG 3699
                                viiv  ii   i - v        i    i i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_53801321_5   3700 AACAAAGTTGGAGGCTTCACTCTACTTGACTTCAAACTATACTACAA-GC 3748
                                       vi    v  v iii i      viv        -  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_53801321_5   3749 TACAGTAACCAAAACAGCATGGTACTGGTACCCAACAGAGATATATAGAC 3798
                                 i   i    ii         i iv- iv v   i       i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATA-AGGATAGACATATAGAT 297

  chr2_53801321_5   3799 CAATGGAACAGAACAGAGGCCTCAGATATAACACCACCACACATGTACAA 3848
                                 i    iv   ivii    v    -   --  i    v  iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAA-ACC--CATACATTTATGG 344

  chr2_53801321_5   3849 CCATCTGATCTCTGACAAACCTGACAAAAGCAAGAAATGGGGAAAGGAT- 3897
                         i  vi    i ii     ivv  v   i v  vvv           i  -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_53801321_5   3898 -TCCTTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAAAA 3946
                         -  i  -- i  i        i     v      v  ?   i        
  L1M4_orf2#LINE/    395 GTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_53801321_5   3947 AGCTGAAATTGGATCCTT-CCTTACACCTTATACAAAAATTAACTCAAGA 3995
                         iiv    i     i  i -   i     v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_53801321_5   3996 TGGATTAACGACTTAAAAATAAGACCTAAAACCATAAAAACCCTAGAAGA 4045
                              i ?v   i    vi     v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_53801321_5   4046 AAACCTAGGCAATATTATTCAGGACGCAGGCATGGGCAAACACTTCATGA 4095
                             v    ?ivv v v   iv   viv  vv i     vvii   v ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_53801321_5   4096 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGCAT 4145
                         v  vi            vvi          vv     v  i    v v i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_53801321_5   4146 CTAATGAAACTAAGAAGCTTCTGCACAGCAAAATAAACTATCGTCAGAGT 4195
                         i v  v   v v i  i   i  ii vv    iv v      ivv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_53801321_5   4196 GAATAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTG 4245
                            v  i     i                 v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_53801321_5   4246 ACAAAGGGCTAATATCAAGAATCTACAAAGAATTTAAACAGATTTACAAG 4295
                          i  i  i  vi    v     v  i      i ivv   iv iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_53801321_5   4296 AAAAA-------AACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACA 4338
                              -------     v  i?    i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_53801321_5   4339 CTTTGAAAAAGAAGACATTTATACAGCCAAAAAACATATGAAAAAATGCT 4388
                         i  ivvv        i  vi v ii     v  i  i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_53801321_5   4389 CATCATCACTGGTCAT 4404
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


 281 24.39 0.00 4.88  chr2_53858760_53863983     3245  3326 (1898)    L1M4_orf2#LINE/L1       16    93 (815)  

  chr2_53858760_5   3245 TGCTCACGGATTGCAAAAATCAATATCATTTTAAAAAATACCCATACTGC 3294
                           i   i      v  i v i     ii  ----  i  iv v     v 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTT----AAGATGGCAATACTCC 61

  chr2_53858760_5   3295 CCAAAGCAATCTATAGATTCAACACTATTCCT 3326
                              vii     i         i v  i   
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCT 93

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.01 (1 / 78), avg. gap size = 4.00 (4 / 1)  

2150 24.14 2.21 7.72  chr2_53858760_53863983     3531  4346 (878)    L1M4_orf2#LINE/L1       59   829 (79)  

  chr2_53858760_5   3531 TCCCTGAAGTGTCATTTTTATGCTTCAATGCTATTCCTATCAAACTACCG 3580
                             ii  v  --  i vi - v     i  v  i         v v  i
  L1M4_orf2#LINE/     59 TCCCCAAATTG--ATCTACA-GATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_53858760_5   3581 ACACCATTTTTTACAGAATTAGAAAAAAAATTTCTTAAATTCATATGGAA 3630
                         i vv v      i     v v  v  ivviv i  v              
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_53858760_5   3631 CCAAAAAAGGG-CACA-AATAGCCAAAGCAATACCAAGCAAAAAGAATAA 3678
                         -- viv     - v  -          i    viii iv  i     i  
  L1M4_orf2#LINE/    156 --ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_53858760_5   3679 AGCTGGAGGTATCACATTACCCAATTTCAAACTCTACTTTAAGGCTACAG 3728
                           i      vv     i v            vii    vi  i       
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_53858760_5   3729 TAACCAAAACAGCATGGTCCTGGTACAAAAACAGACACAAAGACCAATGG 3778
                            i   i    ii    v    i i  ii i     i v   i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_53858760_5   3779 AATAGAATAGAGAATCCAGAAATACAGCCATGCACCTACAGCCATCTGAT 3828
                                 v    i          v v    i  ii  ii i  vi    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_53858760_5   3829 CTTTGACAAAGTTGACAAAAATAAGCAATGAGTTAGAGACT--CCTTATT 3876
                         i  i     i v  v   i vi vv     i v- i   v --i   -  
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTT-TT 401

  chr2_53858760_5   3877 CAATAAACGGTGCTAGTATAGCTGGCTAGCTACATGTAGAAGAATGAAAC 3926
                            i   i      i v i i    v  ? i     i i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_53858760_5   3927 TGGAACCCTATCTTTCACTATATACAAAAATCAACTCAAGATGGATTAAA 3976
                             v     i  iv   i            i       i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_53858760_5   3977 AGTTTAAATGTAAGACCTCAAACTATAAAAATCCTAGTTAGAAAAAAAAA 4026
                         iiii           v  v           v  ----      i    v 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTC----TTAGAAGAAAACA 547

  chr2_53858760_5   4027 T--GAGAAAACACTGTTCTGGACATCGGCCCTGAGAAAGAATTTATGACT 4074
                          -- ? v   --- v   vv   v i  viiv iv  v iv  iv iiv 
  L1M4_orf2#LINE/    548 TAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_53858760_5   4075 AAGTTCTCAAAAGCAATTGCAACAAAAACAAAAATTGGTAAGTGGGACCT 4124
                          v vivi        vvv         iv      v i   i v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_53858760_5   4125 AATTAATCTCTTTAGATTAATTAAGCTCTTTAGCTTCTGTAAAA------ 4168
                         v  i  --------i     --  i  i  vv     ---   i------
  L1M4_orf2#LINE/    645 CATCAA--------AATTAA--AAACTTTTGTGCTTC---AAAGGACACT 681

  chr2_53858760_5   4169 --CAGAAGAATCCACAGACAACCCACAGAATAGGAGAAAATATTTGCTAA 4216
                         --  ii i i vv v                i               v  
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_53858760_5   4217 CTAGGTATCTTTATAGATTCTGGATATTACACAAAGGTCTTTATCTTAAC 4266
                         ii --------    ---    -------- i  i  -----------  
  L1M4_orf2#LINE/    732 TCA--------TATA---TCTG--------ATAAGGG-----------AC 751

  chr2_53858760_5   4267 TTTGTCCAATATCTAGAATCTATAAGGAACTTAAACAATTCAACAAGCAA 4316
                           ------i    i     v     i     ivv    i    i  vv  
  L1M4_orf2#LINE/    752 TT------GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_53858760_5   4317 AAAACAA----CCCCATTAAGAACTGGGCAAAAG 4346
                           i    ----   v   ? i  v        i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.35 (111 / 82)
Gap_init rate = 0.03 (21 / 771), avg. gap size = 3.86 (81 / 21)  

 393 19.15 0.00 0.00  chr2_53858760_53863983     4639  4732 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_53858760_5   4639 AAAATTGGGCAAAAGACATGAAAAGATACTTCTCAAAAGAAGACATAGAA 4688
                             v        i  iv    v   i i     v        i   v  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_53858760_5   4689 GCAGCCAACAAACACATGAAGAATTGCTCAACATCACCAATCAC 4732
                         iii     i  i        i iv            ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3402 23.28 1.75 2.73  chr2_53971117_53973708     1187  2101 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_53971117_5   1187 GAAAGATATCCTGTCTTCATGGATTGGAAGAAT-AAGATTGTTAAAATGT 1235
                                    ii v                v -  v        i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_53971117_5   1236 CCATACTACCCAAATCAATCTACTACTCAAAGGATTCAATGCAATC--TA 1283
                          v     v       ii      --------i       i      --  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTAC--------AGATTCAACGCAATCCCTA 94

  chr2_53971117_5   1284 TTAAAATTCCAATGACCTGTTTCACAAAAATAGGAAACACT-ATCCTAAA 1332
                          i     i   iivi   v   ii  i    v iv  -i  -        
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAA 143

  chr2_53971117_5   1333 ATTCATATGAAACCATAAAAGACCCCCAAATAGCCAAAGTACCCCCAAAG 1382
                                  i  viii  ii     v-i          ii ---------
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCA-GAATAGCCAAAACA--------- 183

  chr2_53971117_5   1383 ACCCCCAAATAGCAAAAAGAACAATGCAAGAGGCATCACACTACCTGATA 1432
                          i iiv   ----  i        v ivi    vv       v  ii  v
  L1M4_orf2#LINE/    184 ATCTTGAAA----AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_53971117_5   1433 TCAAAATCTACTACAA-GCCA---TAATCAAAGCAGCATGCTATTGACAT 1478
                               ii        -  i ---       ii   ii  v  i  i   
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_53971117_5   1479 AAAAACAGATCTGTAGACCAACAAAACAGAATAGAAAGCCCAGAAATAAA 1528
                           ii i   iv i    i   iii  i     v  i  i           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_53971117_5   1529 TCTACATATTTCTGGTCAATTGATTTTCAACAAAGATGCCAATAACACAC 1578
                         i i i i    v                i    i i      v v  iv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_53971117_5   1579 AATGGGGAAGCAACAGTCTCTTCAATAC----TGTTGATA-AACAGTATA 1623
                                  iv  i     i     i v----  i  iv -   v v   
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_53971117_5   1624 TCCACATGCAGAAGAATGTCACTGGGCCTTTATCTCACTCCATATAAAAC 1673
                         ?         i       vvii   i  ii  i     v       v  v
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_53971117_5   1674 AATCCACTGAAAATGGAGTA-AGATTTAAATGTAAGACCTGAAACTGTGA 1722
                            iv   v        vi -   ii           v  i     i i 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_53971117_5   1723 AACTACTAGAAAAAAACAAAGGGGAAAAGTTCCATGACATTGGTTTGGGC 1772
                             vi     i      v   ? v   vi i i    v    v  i   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_53971117_5   1773 AATAATTGTTTTGAATATGACCCCAAAAGCATAGGCAACAAAAGCAAAAG 1822
                            ii  - i  ii       v         i i          v    i
  L1M4_orf2#LINE/    580 AATGGTT-TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_53971117_5   1823 TAGATAAATGAGATTACATTAAACTAAAAAGCTTCTGCACAAAAGAGGGA 1872
                                  vi  i v   i   v v    i   i  ii vvv i   iv
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_53971117_5   1873 ACAATCAACAGTGTGAAAAAGACAACCTATGGAATGGAAGAAAATATTTG 1922
                           v     v iv       -       i ii      i            
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAA-GACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_53971117_5   1923 TAAACTATGTATCTGATAAGGAGTTAATATCCAAAATATATAAGGAATTC 1972
                         i   ii  i            iii vi      i         i   i  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_53971117_5   1973 ACACACCTCAATAGCAAGAAAA-AATTAACCAGATTTTACAATGGGCAAA 2021
                         vi   v       ii  i  i -  v     vi   ?v v          
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_53971117_5   2022 GGAACTAAATAGACATGTCTCAAAAGAAAACATACAAATGGCCAACAGGT 2071
                            vi i         v    v      i i              i i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_53971117_5   2072 ATATAAAAAAAGG-TCAGCATCGGCCGGGCG 2101
                          i  i    i v -   i    i????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (140 / 70)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 2.41 (41 / 17)  


3553 12.19 2.78 16.47  chr2_54211176_54213076      476  1410 (491)    L1M4_orf2#LINE/L1      102   908 (0)  

  chr2_54211176_5    476 CCCAGCTACCTTTTTTAAAAGTGGAAAATT--TAAGCTGATTCTAAA-TT 522
                                i        ---- ii    -  --i        i     -  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT----GCAGAAA-TTGACAAGCTGATCCTAAAATT 146

  chr2_54211176_5    523 CATATGGAAATGCAAGGTACTCA----------AACAATCTTGAGAAAGA 562
                                          v  i  ----------           i     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_54211176_5    563 A---CAAAGTAGAAAGACTCACACTTCCTAATTTCAAGACTTACTACAAA 609
                          ---      v i i             i        i            
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_54211176_5    610 GGTACATTAATCAAGTGAGTGTGGTACTGACAAAAGGCTAGACTTAT-GA 658
                          v    v        vv            i  v    v     v   -  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_54211176_5    659 TCAGTAGACTAGAATTGAGAGTTCAGAAATAAACTCTTATATTTACAGTC 708
                            i i  v             i           i v  i     ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_54211176_5    709 AATTGATTTTTTGACAACGGCGCTAAGACAATTCAATGGGAAAAGAATAG 758
                                   i-     v  i  i     v          i         
  L1M4_orf2#LINE/    347 AATTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_54211176_5    759 TCTTTTCAGCAAAATGGTGCTGGGACAACTGGGTATCTACATACAAATGA 808
                                 i    -                  i  ? i    i    v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_54211176_5    809 ATGAAGGCGGACTCTGACTTCACACCATATGTAAGAATAAATCAAAATGA 858
                               vi    i iv  i           --------------------
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATAT-------------------- 474

  chr2_54211176_5    859 GCCAGGTGTGGTAGTGCATGCCTGTAGTCCCAGCTACTTGGGAGGCTGAG 908
                         --------------------------------------------------
  L1M4_orf2#LINE/    475 -------------------------------------------------- 474

  chr2_54211176_5    909 GTGGGAAGATCTCTTGAGCCCAGGAGTTTGAGTCCAGCCTGGGCAATGTA 958
                         --------------------------------------------------
  L1M4_orf2#LINE/    475 -------------------------------------------------- 474

  chr2_54211176_5    959 GGGAGACCATACCTAAGGAAAAAAAAAAAATTAACTCAAAATGGATCAAA 1008
                         ----------  -------------                       ? 
  L1M4_orf2#LINE/    475 ----------AC-------------AAAAATTAACTCAAAATGGATCAWA 501

  chr2_54211176_5   1009 GACCTAACTACCAGAGCTAGAAGTACAAAACTCTTGGAAGAAAACATAGA 1058
                                v iiv       i  v  i         i             i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_54211176_5   1059 TGTAACTCTTTATGACTTTGGAA-AGGCAATGCTTTCTTGGGTTTGACAC 1107
                         ?    v    ii    i    iv-        v      i i v      
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_54211176_5   1108 CAAAAACACAAGCAACAAAAGGAAAAAGTAAATAAATTGGATTTTGTGAA 1157
                              i               i     -  i          i  ii v  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAA 650

  chr2_54211176_5   1158 CATTTAAAATTTTTGTGTTTCAAAAGACACCACCATCAAGAAAGTGAAAA 1207
                         v   v    i       i      i     i ---               
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTA---TCAAGAAAGTGAAAA 697

  chr2_54211176_5   1208 GGCAACTCATAGAAGGGGAGAAAATTTTTGCAAACCTTATATCTGATAAG 1257
                          i    i  i    v          v        i v             
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_54211176_5   1258 GAACTTATACCTAGAATATGTAAATAACTATTACAACTCAAAAATAAA-- 1305
                          i    i  i i       i    v    v           v      --
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_54211176_5   1306 GACAA------TGATTAAAAAATGGGCAAAAGGTCTGAACAAAGATTTCT 1349
                              ------ii   ?             i i i    i i v      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_54211176_5   1350 TCAAAGAAGATTTACAAATGGCCAATAAGCACATGAAAAGTTGCTTGATG 1399
                         i          v                            v    ii ii
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_54211176_5   1400 TCTGATGTCAT 1410
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.06 (74 / 36)
Gap_init rate = 0.02 (16 / 807), avg. gap size = 11.25 (180 / 16)  


 947 28.84 13.63 2.73  chr2_54279352_54280942.rev      410  1106 (485)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr2_54279352_5    410 ATCTTAAAGTTAAGAGAGGAA-ACAAATGCCCAAGAA-AGCAAATAAAAG 457
                            i    i  v v vi i  -i   iv v  v    -   ---i    v
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC---CAAAAC 182

  chr2_54279352_5    458 AATC------AAAAAGAACA--GTGAGAGGA------------------- 480
                             ------  i       --  vi     -------------------
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_54279352_5    481 -AATATACTGTGGAGATAGTATAATTAAATCAATATGGTATACTGATGTA 529
                         -  iv    iiii  v  vvi    i  iv  i i     --   iii  
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA--CTGGCATA 280

  chr2_54279352_5    530 GGAACAGAGAAATAGATCAGTGGAACAGAATAGAGAATTCAGAAATAAAA 579
                         i i i   v v        i     i     v    i i          -
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA- 329

  chr2_54279352_5    580 TCCAGTCTATATGAGATT--TTAACGTATGACAAAAATGT-ATTTCAATG 626
                         i   - vi  v iv i i--  i iv vi     iii  i- vvv v  v
  L1M4_orf2#LINE/    330 CCCA-TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_54279352_5    627 CAATGGGGGAAAGAGTGATTATTT-AGTAAGTGGCGCCAGGACAACTGGC 675
                                 -     i ii iv   - ii  i   i  ii          v
  L1M4_orf2#LINE/    379 CAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_54279352_5    676 TATTCATCTGGTAGAAAAT--AGTTGGTCCAATATCTCATCTTTTAAATA 723
                           ?i  iv  vv i i   --      v  vv  i    iviiv  v i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_54279352_5    724 AAAAACAAATTCCAGATGGAGTAAATGCTTAAATGTAATAAATAGAGC-A 772
                             vi  -i  v i     vi ? vi i         v iv  i i - 
  L1M4_orf2#LINE/    478 AAAATTAA-CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_54279352_5    773 TCAAG---TTAGAAGAAAACCTGGGCGACAACACTTACAATCT------- 812
                          v  i---            v i  ? vv  ivi iiii i  -------
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_54279352_5    813 -------GTTTCTTA--------ACCAGAG-------------AGAAAAA 834
                         -------        --------    i i------------- ii    
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_54279352_5    835 AATAGCCATATTTGAGTTAATAAAAATGAAAAACAATTTATGTTGCAAAG 884
                              vi v   v  v  v  v     v      v-   i  i v     
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACT-TTTGTGCTTCAAAG 675

  chr2_54279352_5    885 ----CTATCATAGACGAAACCAATAGGCAAATTATAGATTTGG-GAAAAT 929
                         ----      -   --  iiv  v  i   vii i   v v  -      
  L1M4_orf2#LINE/    676 GACACTATCA-AGA--AAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_54279352_5    930 ACCTGCAAAAGCA-ATAACAGATAATGGGTTAGTAACCATAACCAATATA 978
                          ii      -v  -   v v     v  ii v   v   v  ----    
  L1M4_orf2#LINE/    723 ATTTGCAAA-TCATATATCTGATAAGGGACTTGTATCCAGAA----TATA 767

  chr2_54279352_5    979 CAAAGAGCTTTTAAAAATTGGCAA----GAGACAAGCAACTCGATAGAAA 1024
                         i     i  i   v  v iiii  ----i      ii   i i  v?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_54279352_5   1025 AATGGGTAAAGGATGTGAAAAGGGAGTTCATGAGAACAAATTCACA---G 1071
                               i       v    v  iv v   viv i iv i  vi   --- 
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_54279352_5   1072 AC--ATAAGCATA----AAGATGCTCCAAC-TTACTAGTCAT 1106
                         i --       i ----         -   - i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTC-AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (117 / 80)
Gap_init rate = 0.04 (34 / 773), avg. gap size = 3.35 (114 / 34)  


3698 22.28 0.99 1.32  chr2_54838145_54842152     2606  3516 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_54838145_5   2606 TAGAAAGAGATTCCATGTTCATGGATTAGAAGAATTAATATTGTTAAAAT 2655
                          i      v  i               i     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_54838145_5   2656 GTCCATACTACCCAAAACAATCTACAGATTCAATGGAATCCCTATCAAAA 2705
                          v v     v      vii              i v              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_54838145_5   2706 TATCAAGGACGTTCTTCACAGAAATAGAAGAAAAACAG-TCCTAAAATGT 2754
                          vi  ivvi v  i  ii       v  ---v  i v -         vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA---CAAGCTGATCCTAAAATTC 147

  chr2_54838145_5   2755 ATATGGAATCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAATA 2804
                                 vii   ii                 i v   i   iv  iv 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_54838145_5   2805 GAACAAAATTGGAAGAAACACATTACCTGACTTTAAATTATAGTACAGAG 2854
                                i     i  vv    i v  ii i  i   viv  v    i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_54838145_5   2855 CTATTGTAAACAAAATGACGTGGTACTGGAATAAAAACAGATATGTAGAT 2904
                            iv    v   i iiii          v    ii i   i  i     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_54838145_5   2905 CAGTGGAACAGAACAGAGAGCCTAGAA-TAAATCCACACATCTACAGCAA 2953
                           i     i    iv     i i    -    i   i    i  ii iv 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_54838145_5   2954 ACTTGTTTTCAACAAAGGTGCCAAGAACATACACTGGGAAAAGGACAGCC 3003
                          i vi     i    i          v   v  v    i    i i  i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_54838145_5   3004 TCTTCAGTAAATTGT-CTGGGAAAACTGGATATCCATATGCAGAAGAATG 3052
                          i    ii    v  -      v         ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_54838145_5   3053 AAACTAGACCCCATCTCCCTATCTCTTGCCATATA-AAAAATAAAATCAA 3101
                           ii i      -------  i   vii       -      v  v    
  L1M4_orf2#LINE/    448 AAGTTGGACCCC-------TACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_54838145_5   3102 AATGGATTAAAGACTTATATTTAAGACCTCAACCTATGAAACTACCAAAA 3151
                                i ?    i  v  v     v  v  v    i     vii i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_54838145_5   3152 TAAAACATTAGGGAAACTCTCCAGGACATTGGACTGGGCAAAGATTTCTT 3201
                         v       vi ? v  v   i iv   v    ii i     v i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_54838145_5   3202 GAGTAATAAC-CCACAAGCACAGGCAACCAAAGCAAAAATGGACAAATGG 3250
                         iii  - i  -   v       i     v    v      i  i    v 
  L1M4_orf2#LINE/    591 AGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_54838145_5   3251 GATCACATCGA-GTTAAAAAGCTTCTGTACAGCAAAGGAAACAATCAACA 3299
                           iiv    i -i       -   i   i vv       v  v     v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_54838145_5   3300 AACTGAAGAGATAACCCACAAAATGGGAGAAAATATTTGCAAACTATCCA 3349
                           v    i   i        i                      ii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_54838145_5   3350 TCTGATAAAGGATTAAAAT-CAGACTATATAAACAACTCAAACAACTTCA 3398
                                 i   i viv  -    v        v     vv      iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_54838145_5   3399 TAG-GACTAGTCTAATAATCCAATT-AGAAATGGGCAAAAGATCTGAATA 3446
                           i-i vv  v v     i      - i           i   i      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_54838145_5   3447 GACATTTCTCAAAAGAAGACACAAAAATGGCCAACAGGGATATGAAAAGC 3496
                                   v        i i v          i i v i        v
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_54838145_5   3497 TGTTCAACATCATGGATCAT 3516
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (121 / 79)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


1467 19.23 4.97 21.29  chr2_54892729_54894951.rev      657  1722 (500)    L1M4_orf2#LINE/L1        1   892 (16)  

  chr2_54892729_5    657 TAGAGGGATATATCATTTTCATGGATTGGAAGACTCAATATTATAAAGAT 706
                          i  ii     vi   v                  i      i v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_54892729_5    707 GTCAATTCTCTCCAAAGTGATTTATACAATCAATATAATCTCAATCAAAA 756
                          v    v   i     v    i  i v v    iii    i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_54892729_5    757 TATCAGCAGG-TTTTTAATGGAAATTGACAGATCAATTCTAAAACTGATA 805
                          vi    v v-     viii          iiiii  i      i v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_54892729_5    806 CAGAAATACAAAGGACGCAGAATACTCAAGACAACTCTGAAGAAGTACCA 855
                         ii     i   i    v       vi   i    iii    i   v vv 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_54892729_5    856 CAAAGTCAGAGAGGTTATA-TTCTCAGAGTTCAAA-------------CT 891
                               ii   iiv i i -   i  - v      -------------  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCT 249

  chr2_54892729_5    892 GCAGTAATTAAAACAGCGTGGCGTCAGTGCAAGGAT-GA-----AGACTA 935
                         i       i  i    i    iiiii iii      -  -----   ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_54892729_5    936 ATGGATCAGAAT--GGAATCCAGAAACAGACTTAT-----TAGGGCTGCC 978
                              vi     --i  i        i i  ii  -----  v  iiivi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_54892729_5    979 TGATTTATGACAAGGTTGCCA---CTAGTTCAATGGGTTAAAAAATGATC 1025
                               vi       v     --- i -         v-   i   ii  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGG-AAAGAATAGTC 397

  chr2_54892729_5   1026 TTTTCAATAA-TAGATCTGGGTTAACTGTATATCTGTATTTAAAAAACAA 1074
                                i  - i vv     vi     v   ? iii  vi    i ---
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA--- 444

  chr2_54892729_5   1075 ATTGCTAATCATGACCATCTCATAAAATCATTTCCATTGGATCACAGACC 1124
                         ---------------------  i  i ---------    i -----  
  L1M4_orf2#LINE/    445 ---------------------ATGAAGT---------TGGACC-----CC 459

  chr2_54892729_5   1125 TAAATTTTAAAGGTAAATCAATAAAGTTTCTGGAACTGTGGTATCCATTG 1174
                           --------------------------i  --------------  ---
  L1M4_orf2#LINE/    460 TA--------------------------CCT--------------CA--- 466

  chr2_54892729_5   1175 TGGTAACCACTAGCTACATGTGACTAACTACATTTAATTTTGAATTAATT 1224
                         -------   i ------------  --    ---  -----      i 
  L1M4_orf2#LINE/    467 -------CACCA------------TA--TACA---AA-----AATTAACT 487

  chr2_54892729_5   1225 AAAATCTAATAAAATTTAAAATTTAGCTTTCACTAACCACATTTTAAGTG 1274
                         v   ----  ii ----------------   ?vi   ------------
  L1M4_orf2#LINE/    488 CAAA----ATGGA----------------TCAWAGACC------------ 505

  chr2_54892729_5   1275 GCCAGTAGCCAAATGTGACTAGTGGGCTACCACTGGACAGTACAAAC-AT 1323
                         ---------i      i ----- i    --------------    -  
  L1M4_orf2#LINE/    506 ---------TAAATGTAA-----GAGCTA--------------AAACTAT 527

  chr2_54892729_5   1324 AGAACATTTCTGCACTTCAGAAAGTTCTACTGGACAGTGCCGTTTTGAGA 1373
                          i   ------------------------------------- i  -   
  L1M4_orf2#LINE/    528 AAAAC-------------------------------------TCTT-AGA 539

  chr2_54892729_5   1374 AGATTACATAGGA--AAATCTTTACATAACCCTGAATTGGGGAAATATTT 1421
                            vv       ?--       -- i i   i  ii  i  v  vvi   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTT--CGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_54892729_5   1422 CATTAACAGGAC-CCAGACAGCACTAATCATAAAGTAAAAGATTGATAAA 1470
                          v vi i v   -   i -     -  v  ----ii      -----   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAA-AGCAC-AAGCA----ACAAAAGA-----AAA 626

  chr2_54892729_5   1471 GATTGATAAATTGGACTTCA-CTAAATAAAGAATGTCTGATCATCAAAGA 1519
                         i  v                - v    v  i  iv i  vv v      i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_54892729_5   1520 ATAC--------AAATG------CAAGCCACAGAATGGGAGAAGATATTT 1555
                          i  --------  i  ------   v                i      
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_54892729_5   1556 G-AAAT-ATAGAATTGACAAAGTACTCATATCCAGTATATATAAATAACT 1603
                          -    -   v vi   i  i v   ii       v         v    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_54892729_5   1604 CATATATATCAATAAGAAAAAGACAGGCAACCCAGTTATTTCAAATGGTC 1653
                          v  i vv       v         iii      i  ?v--v      v 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA--AAAATGGGC 824

  chr2_54892729_5   1654 AAAAAGACCTGAAGAGGCACTTCACAAAAGAGGGTATCAAAATGGTCACT 1703
                            i-  ii    v  i  i   v v     i i   vv      i  v 
  L1M4_orf2#LINE/    825 AAAG-GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_54892729_5   1704 AAGCACATGAAAAGGTGCT 1722
                                       i    
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.91 (132 / 69)
Gap_init rate = 0.05 (44 / 892), avg. gap size = 6.36 (280 / 44)  


3421 23.05 3.95 1.36  chr2_55058368_55061604     1861  2745 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_55058368_5   1861 TGGAAAGAGATCCTGTGTTCATGGAGTGGAAGAACTAATATTGTTAAAAT 1910
                                 v    ii          v       vi            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_55058368_5   1911 GTTCACACTACCCAAAAAATAATCTGCAGATTCAATGTAATCCTTATCAA 1960
                          viv i   v      v-- i    i         i i     i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT--TGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_55058368_5   1961 AATTCCAAAGGCATTTTTTTCACAAAAATTGGAAAAACAACCTTAAAATG 2010
                            i   ivv  v      --i  i      iv  ivii i i      v
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_55058368_5   2011 TGTATGTAACCACAAAAAACCT-GAATAGCCAAAGCAATCCCAAGAAAGA 2059
                         ii    v  vii   iii   i-           i     iii i     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_55058368_5   2060 A---TAAAGCTGGAAGTGTCACACTTTGAAATATACATTTCAAACTATAT 2106
                          ---i    i    i vv        ivv   -----  iv     -  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAAT-----TTCAAAACT-TAC 240

  chr2_55058368_5   2107 TACAAAGCTATAGTAATCAAAAT-GTATGGTACTGACATAA----AAACA 2151
                                   i         i i-  i        i     ---- i   
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_55058368_5   2152 CATAGACCAATGAAACAGAATAAAGATGCCAGAAATATATCCATATATAT 2201
                         i     i     i  i     vi   vv         v i     i  - 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-T 339

  chr2_55058368_5   2202 TATA--TAGTCCATCTTTGACAAGGATACCAAAAATATACGGTAAGGAGA 2249
                            i--i i iv  i  i       i i    i vi  v ii ii   i 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_55058368_5   2250 AGACAGTCTCTTCAATGAGTGGTGTCAGGGAAACTGGATATCTACATTCA 2299
                         ii i     i     ii i     iii  iv         ? i    v  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_55058368_5   2300 AAAGAATGAATTTGGACTT-TATCTCACACCATTTAAAAAAATTAACCCA 2348
                                   v      ii-  i          v  v          i  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_55058368_5   2349 AAGTGGATTAAAGACTTAAATGTAAGACATGAAATCATACAACTCCTAGA 2398
                           i     i ?    i           vv i   ii   v     i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_55058368_5   2399 AGAAAATATAA----AGAGCTCCTTGACATTGGTCTTGGCAGTGATTTCT 2444
                               i   i---- i v  i v    v    vi v    i  i     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_55058368_5   2445 TGGATGTAACAGCCAAAGCACAAGCAA--AAACAAAAG-----CAAGTGA 2487
                          i   i i   v v             --   v    i-----i  i vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_55058368_5   2488 GACAACATCAAA-CTAAAAAGCTTTGCATGGCAAATGAAACAATCAACAA 2536
                            vv       -i      vi    iiivv    v  v  v     v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_55058368_5   2537 AATGAAAAGGCAGCCTATCAAATGGGA-AAAATAATTGCAAACCATGTTT 2585
                          i       i  i  i ivi       -      v       i   i v 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_55058368_5   2586 CTGATAAAGGGTTAATATACAAAATATATAATGAATT-TTACAACTCAAT 2634
                                i  ii vi   v  i         v   i -            
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_55058368_5   2635 AGCAA---------TAACTATGATTTTAAAACAGGCAAATGACTTGAATA 2675
                          ii  ---------    i-ii   ?v    ii      v  i       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_55058368_5   2676 GACATTTCTCCAAAGAAGACATAGAAATGGCCAACAGGTATGTGAAAAGA 2725
                                            i   v          i i i ii        
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_55058368_5   2726 TGTTCAACATCACTTTTTAG 2745
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (139 / 62)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.47 (47 / 19)  


 203 16.28 4.65 0.00  chr2_55175994_55177812       36    78 (1741)    L1M4_orf2#LINE/L1        4    48 (860)  

  chr2_55175994_5     36 AGAGATATCACAT--TCATGGGTTGAAAGATATAATATTGTTGAG 78
                          i       v   --      i   i    iv          i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.02 (1 / 45), avg. gap size = 2.00 (2 / 1)  

2424 22.32 6.56 3.46  chr2_55175994_55177812      500  1337 (482)    L1M4_orf2#LINE/L1       45   908 (0)  

  chr2_55175994_5    500 TAAGACGTCACTTATCCCCCCTACTAATCTCTAGATTCAATGCAATCCCA 549
                              i v  v - ii    vv i i    vi        i        v
  L1M4_orf2#LINE/     45 TAAGATGGCAAT-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr2_55175994_5    550 ATCAAATTCATAACAGGCATTTT-ATAGAAATGAACAAGCTGATTCTGAA 598
                               v  vi i v v v    -ii      vi          i  i  
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_55175994_5    599 ATTTATGCAGAAATACTAAGGGACCTAGAAGACACAAAACAATTTTGAAA 648
                            i  iii     i -        i    v vv         i      
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_55175994_5    649 AA--AGATCAAACTTGCAG---TCATACTACTTAATTTTACGACTTGCTA 693
                           --   v    v   v  ---   i   v ii     i vi    i   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_55175994_5    694 TAAAACTACAATAATCAAG---------TATTGGCATAAGGATAGACA-- 732
                         i   i     i        ---------  i                 --
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_55175994_5    733 --AATCAGTAGAACAAAATAGATA-TATATAAATAGACACACTTCAT--A 777
                         --i    i i   i i   v  v - vi v     i  v  - v   -- 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTA 341

  chr2_55175994_5    778 TGGTCAATTTCTTTTCC-CAAAGGCACCAAAGCAATTCAATAGAAAGAGA 826
                                  vv     v-   i  ii    ii v       i ii i   
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_55175994_5    827 AAAATATTTTCAAAAAACTCTGCTGGGAAAACTGCTTATTATATGTATGG 876
                          v i v       v   ivv        v     vv  ?i---iii   v
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC---CACATGC 438

  chr2_55175994_5    877 AAAAGAAACAAATAAATCTGGATCTATGGTAACTCATACCATAGACAAAA 926
                                ----- i  vi    i iv --- v    i      v      
  L1M4_orf2#LINE/    439 AAAAGAA-----TGAAGTTGGACCCCT---ACCTCACACCATATACAAAA 480

  chr2_55175994_5    927 ACTACCTCAAAACGGATCA-AGAC--AAAC--AAAAGCTAAAACTATCAA 971
                          i  v       i      -    --   i--  i            v  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_55175994_5    972 GCTTCTAGAAGAAACCA-AAGTGT----CTTCACAATCCTGGAAGGAGGC 1016
                         i  ii         v  - i ?  ----    iii i i   i-vv    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGC 579

  chr2_55175994_5   1017 AAAGATGTCTTAGACATCACAAAGAAAGCACTAACCATGAAAGAAAAAGT 1066
                           v i v       i  v   vvi       v i v ii         i 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_55175994_5   1067 A-----ATTATGACTTC-TCAAAATTAAAAA--TTTATACTCATCAAAAG 1108
                          -----   i-      -             --   i i  --     i 
  L1M4_orf2#LINE/    630 AGATAAATTG-GACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGG 676

  chr2_55175994_5   1109 A----ATCAATAAAATTAATAGGCAAGCTACAGACTAGGAGAATATATTC 1154
                          ----     v   i v  v  i   v i     v i      v     i
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_55175994_5   1155 ACAACACATGTATCAGACCAAAGATTTGTATTCATAATATATAGAGAGAA 1204
                         i   vv   i    v  iv ii  i      i  v        i   -- 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA--A 774

  chr2_55175994_5   1205 CTCTTACAAAT--ATGTAGGAAAAAAAAAGGCATACAACACAATTTAAGA 1252
                                  v --  ------  v      i  v i   v     ?  i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAAT------AATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_55175994_5   1253 ATGGGCAAATTACTTGAACAGACACTTCACCAAAGAAAACACACA----- 1297
                                  vv i     i     i   v        i i i   -----
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_55175994_5   1298 -CAA--AGGACATGTAAAAGTCCTCTAATTCATTAGTCCCTAG 1337
                         -   --  v     v   ii v   -  --   i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTC-AA--CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (108 / 76)
Gap_init rate = 0.04 (33 / 864), avg. gap size = 2.55 (84 / 33)  


2719 24.29 1.98 6.37  chr2_55262712_55265724      654  1563 (1450)    L1M4_orf2#LINE/L1        1   870 (38)  

  chr2_55262712_5    654 TGGAAAACACATCCCATGCTCATGGATAGGAAGAATCAGTATCATTAAAA 703
                               i- i        i        v      v i i   ii    i 
  L1M4_orf2#LINE/      1 TGGAAAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_55262712_5    704 TGGCTATACTGGCCATAGCAATTTACAGATTCAATGCTATTCCTATCAAA 753
                             v     vv   v vii  i           i  v  i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_55262712_5    754 CTACCAACAATCTTC---ACAGAACTAGAAAAAAACT-ATTTTAAAATTT 799
                         v v   i vii   i---i     v v  v  i--  -  ii       i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_55262712_5    800 ATATGGAACAAAAAAAGAGCCTGAATAGTGAAGGCAATCCTAAGCAAAAA 849
                                 vviv  ii  v  v      iv  ii     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_55262712_5    850 GAACAAAGTTGGAAGTATCACATTATGCAAGTTTAAATTATACTACAAGG 899
                                      i vv     i viv   v  i   viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_55262712_5    900 CTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGGCACATAGAC 949
                                  i   i    ii         i i  ii i  i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_55262712_5    950 CAACGGAACAGAATGGAGAGCCCAGAAATAAGGCCACATATCTATGATCA 999
                            i    i     v     i          iv   i i  i    i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_55262712_5   1000 TCTGATCTTCAACAAAACTGACAAAACCAAGCAATGGGGAAAAGACTCCC 1049
                         vi    i   i    iiv  v   i    vv           ii ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_55262712_5   1050 TGTTCAATAAATGATGCTGGGATAACTGGCTAGCCATATGCGGAAGATTG 1099
                          v     i     i        i      v  ?   i    ii    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_55262712_5   1100 AAAATGGACCCCTTTCTTATACCATACACAAAAATCAATTCAATAATGCA 1149
                           iv         vi  i i      i        i  i    -------
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA------- 490

  chr2_55262712_5   1150 GACTGCTGCACAAAACAAAAGAAAAAAATTCAACTAAAGATGAATTAAAG 1199
                         --------------------------------------i   i  i ?  
  L1M4_orf2#LINE/    491 --------------------------------------AATGGATCAWAG 502

  chr2_55262712_5   1200 TCTTAAAAGTAAAATGC-AAAACTATAAAAACCCTGGAAGACAACCTAAA 1248
                         v i    v    i -  -            vi i i     v   v  ii
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_55262712_5   1249 CA-ATACCATCCTGGACATAGGAATGGGCAAAAATTTCATGAGAAA-GAC 1296
                         ?i- v i v  v  -  v v  iv i     vii    - v   v -   
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTC-TTAGATATGAC 599

  chr2_55262712_5   1297 ACAAAGAGCTATCGCAACGAAAGCAAAAATTGACAAGTGGGATCTAATTA 1346
                           v  i   vvvv     i    v      v  i  i v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_55262712_5   1347 AACTTAAGAGCTCT-GCACAGCAAAAGAAACTATCAATGGTAAACAGAAT 1395
                           v    i i  i - ii vv    i  v        -- v  iiii  -
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA--GAAAGTGAAA- 696

  chr2_55262712_5   1396 GGGAGA-AACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCTGA 1444
                         ---   -    i                          ii  ii      
  L1M4_orf2#LINE/    697 ---AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_55262712_5   1445 CGAAGGTCTAATATCCAGCACCTATAAGGAACTTGAACAGATTTA----T 1490
                         ii i  v  vi       v iv     i     ivv   - i i ---- 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCAATAAT 792

  chr2_55262712_5   1491 AAGAGGA-AAACAACCCCATTAAAAAGTGGGCGAAGGAAATGAACAGATA 1539
                           i i  -   i     v   ?    i     i     vv    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_55262712_5   1540 CTTCTCAAAAGAAGACATA----TGGCC 1563
                         i     v        i   ----     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCC 870

Transitions / transversions = 1.71 (137 / 80)
Gap_init rate = 0.02 (19 / 870), avg. gap size = 4.00 (76 / 19)  

 229 16.39 0.00 3.28  chr2_55262712_55265724     2461  2521 (492)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr2_55262712_5   2461 AAAGAAGACATATATGCAGCCAACAAGCATATGGAAAAGAAAGCTCAATA 2510
                                 i   i viii     i     i   -      -v      i 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGA-TGCTCAACA 897

  chr2_55262712_5   2511 TCACTGATCAT 2521
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 4.00 (8 / 2)
Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2)  


1612 19.01 6.73 0.58  chr2_55330837_55332836      501   842 (1158)    L1M4_orf2#LINE/L1      208   570 (338)  

  chr2_55330837_5    501 GAAGGAATCACTCTTCT-GATTTCAAAACTTACTACTAAGCTACAGTAAT 549
                          i    v    v    i-i                 v             
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_55330837_5    550 CAAGATAGTATACTACTGGCGTGGGG-TGGACATCTAGAGCAATGGGATA 598
                              i   i iv       i ii  - i     v    v      i   
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_55330837_5    599 GAACTGAAAGTCAAGAAATAAACTCTAAATATTTATAGTCAATTGATTTT 648
                            i   i    v          i - v i      i             
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCC-ATACATTTATGGTCAATTGATTTT 356

  chr2_55330837_5    649 TGACAAAGAGGTCAAAA---TTCAATGGATACAAAGTA-TTTTCCCAACA 694
                         i     i iv i   i ---        iv v i i  - i  ii     
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_55330837_5    695 A--GGTGCTGGGAAAACCAGATTATCCTTAAGCAAAAGAATGAAACTGGA 742
                          --          v   ii   - ?  vi v             ii    
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGAT-AKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_55330837_5    743 CCCCTACCTCACATCATACAGAAAAATTAACCAAAAGTAGATCATGTATC 792
                                      i    i v          iv   i i     ?iv i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_55330837_5    793 TGAATGTG-------------TAAAACTCTTAGAAGAAAACA--GGAGTA 827
                          i     i-------------                     --  ?   
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_55330837_5    828 GATCTCTGTGACTTT 842
                         i    ii     i  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTT 570

Transitions / transversions = 2.65 (45 / 17)
Gap_init rate = 0.02 (9 / 363), avg. gap size = 2.78 (25 / 9)  

1392 17.03 2.97 6.22  chr2_55330837_55332836     1139  1508 (492)    L1M4_orf2#LINE/L1      551   908 (0)  

  chr2_55330837_5   1139 GGACAGATCTCTATGATCTTAAGTTAGGCAAAGATTTCATAGCTACAACA 1188
                          ?ii i    iii   i   ii         v i    v   v  ii   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_55330837_5   1189 CAAAAGGCA-AAGCCATAAAAGAGAAAATTCATAAGTGGAACTT-ATCAA 1236
                          v   i   -    v i      i     vv    i v i    -     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_55330837_5   1237 AATTAAAAACTTTTA-ACTTCAAAAGAAACCAGTGAAACACTTTTTTTTT 1285
                                       i-i       i  -----------    --------
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGA-----------CACT-------- 681

  chr2_55330837_5   1286 TAAATTAAAAAGAGTGAAAAGACAACCCACAGTTGGGAAAAAAATATTTG 1335
                         ---  i  i  -                    vvv  i i          
  L1M4_orf2#LINE/    682 ---ATCAAGAA-AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_55330837_5   1336 CAAATCAAGTATCAAATA-GGGTTTTA-ATTCAGACTATATAAGGAACTC 1383
                                vi    vi   -   vi  i-  i    v       i      
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_55330837_5   1384 TTAAAACTCAATAATAAAAACACAAAAAACACAATTTACAAATGAGCAAA 1433
                            v                v     v   v     ? v     i     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_55330837_5   1434 GGAC------AGACATTTCTCCAAAGAAGACATACAAATGGCCAAGAGAC 1477
                            i------                    i              v ii 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_55330837_5   1478 AAGTGAAAAGATGCCTAACATTACTAGTCAT 1508
                          vi           ii     i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (39 / 22)
Gap_init rate = 0.03 (9 / 358), avg. gap size = 3.78 (34 / 9)  


3301 24.61 0.72 0.48  chr2_55338168_55343660     3794  4622 (871)    L1M4_orf2#LINE/L1        1   831 (77)  

  chr2_55338168_5   3794 TGGAAACATATGCCATATTCATGGATTGGAAGAATCAGTATTGTTAAAAT 3843
                               v    v    i                v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_55338168_5   3844 GTCTATACTACCCAAAGCAATCTACAGATTTAATGCAATCCCTATCAAAA 3893
                          v v     v      vii           i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_55338168_5   3894 TACCA--TGAAATTCTTCACAGAAATAGAAGAATCAACTCCCAAATTTAT 3941
                          v   --  -vv  i  ii       v  vi iiii ii iv     i  
  L1M4_orf2#LINE/    101 TCCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_55338168_5   3942 ATGGAACCACAAAAGACCCAGAATAGCCAAAAACCATCCTAAGCAAAAAG 3991
                               vii   ii                  - v   i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAG 198

  chr2_55338168_5   3992 AACAAAACTGGAGGAATCACATTATCTAACTTCAAATTCTACTACAGAGC 4041
                               ii       v     i vi i  i      vii       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_55338168_5   4042 TATAGTAACCAAAACAGCACGGTAATGGAATAAAAACAGATGCACAGTCC 4091
                           i     i   i    iii    v   v    ii i   iii i  vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_55338168_5   4092 AATGGAACAGAATAGAGAACCCAGAAACAAATGCACATACCTAAAGTGAA 4141
                                i     v    ii       i   iv  i i ii  vi  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_55338168_5   4142 CTCACTTTTGACAAAGGTGACAAGAACATATACTGGGGAAAAGACAGTCT 4191
                         i v i   i     i    v     v   vi v        ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_55338168_5   4192 CTTCAGTAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAAAATGA 4241
                         i    ii              v         ?   i     i  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_55338168_5   4242 AACTAGGCCCCTATCTCTTGTCATAGA-AAAAACCAAATCAAAATGGATT 4290
                          ii i i      i   viii    v -     ii  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_55338168_5   4291 AAATATTTAAATCTAAGACCTCAAACTATGAAAC-CATACAAGAAAACAT 4339
                          ? v ii     v     v  v       i    - v  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_55338168_5   4340 TGGGGAAATTCTCCAGGACATTGGTCTCGGCAAAAATTTCTTGCATAATA 4389
                         v  ? v  v   i iv   v    vi v     vii      iv   vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_55338168_5   4390 CCCCATAAGCACAGGCAATTGAAGAAAAAAATGGACAAATGGGATCACAT 4439
                          v   v       i    ivi         - i  i    v   iiv   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCAT 647

  chr2_55338168_5   4440 CAAGGTAAAAAGCTTCTGCAC-AGAAAGGATACAATCAACGAAGTGAAGA 4488
                            ii v    i   i  ii -vv      i  v     vi       i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_55338168_5   4489 GACAACCCACAGAATGGGAGAAAATATTTGCAAACTACCCACCTAACAAG 4538
                                                           ii ivi i  i i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_55338168_5   4539 GAGTTCATAACCAGAATACATAAGGAGCTCAAACAACTCCATAGGAAAAA 4588
                          iii ii  v        i    i  i   vv       v   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_55338168_5   4589 AATCTAATAATCTGATT-AAAAATGGGCAAAAGAT 4622
                         i - v     i ii   -             i   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.91 (132 / 69)
Gap_init rate = 0.01 (9 / 831), avg. gap size = 1.11 (10 / 9)  

 490 14.89 0.00 0.00  chr2_55338168_55343660     4908  5001 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_55338168_5   4908 AAGAAAAGGCAAAAGATTTGAATAGACATTTCTCAAAAGAAGACATACAA 4957
                           i  vi      i                    v        i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_55338168_5   4958 ATGGCAACCAGGCATATGAAAATGTGCTCCACATCATTGATCAT 5001
                              v vi i   i       vi     v      ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (8 / 6)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3236 27.20 0.44 0.44  chr2_55580394_55586784     4992  5899 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_55580394_5   4992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5041
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_55580394_5   5042 GTCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5091
                          v v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_55580394_5   5092 TACCAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTTCA 5139
                          v   iivi i  i  ii  -      -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_55580394_5   5140 TATGGAACTAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5189
                                v iv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_55580394_5   5190 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5239
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_55580394_5   5240 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGATC 5289
                                 i   i    ii         i iv ii i   v v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_55580394_5   5290 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5337
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_55580394_5   5338 ATGTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5387
                          vv    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_55580394_5   5388 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5437
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_55580394_5   5438 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAGTTCAAGATGGA 5487
                            ii    i    v   i     v             ii    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_55580394_5   5488 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5537
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_55580394_5   5538 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5587
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_55580394_5   5588 AACACCAAAAGCAATGGTAACAAAAGCCAAAATTGACAAATGAGATCTAA 5637
                         i            vvi i        vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_55580394_5   5638 TTAAACTAAAGAGCTTCTGCACAGCAAAAAAAACTACCATCAGAGTGAAC 5687
                          i   v v  i i   i  ii vv    ii v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_55580394_5   5688 AGGCAACCTACAACATGGGAGAACATTTTCGCAACCTACTCATCTGACAA 5737
                           i     i   iv         v  v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_55580394_5   5738 GGGGCTAATATCCAGTATCTACAATGAACTCAAACAAATTTACAAGAAAA 5787
                            i  vi       v  v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_55580394_5   5788 AAACAAACAACCCCATCAAAAAGTGGGCTAAGGGTATGAACAGACACTTC 5837
                          i     i     v  i?    i     v    i v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_55580394_5   5838 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5887
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_55580394_5   5888 ATCACTGGCCAT 5899
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3177 26.82 1.21 0.99  chr2_55600455_55606842     4991  5896 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_55600455_5   4991 TGGAAGAACATTCCATGCTCACGGATAGGAAGAATCAATGTCATGAAAAT 5040
                              ii i  i     i   i    v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_55600455_5   5041 GTCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATTCCCATCAAGC 5090
                          v v     v     iv i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_55600455_5   5091 TACCAATGACTTTCTTCACA-AAATTGGAAAAAAACT-ACTTTAAAGTTC 5138
                          v   iivi i  i  ii  -      --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_55600455_5   5139 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACACTCCTAAGTAAAAA 5188
                                 viiv  ii  v  viv  v     i   v  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_55600455_5   5189 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCGAACTATACTACAAGG 5238
                                 i      vv   ii  v  ii i   i  viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_55600455_5   5239 CTGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGGTATAGAC 5288
                           i      i   i    ii         i iv ii i   vi      i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_55600455_5   5289 CAGTGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAAC 5336
                           i     i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_55600455_5   5337 CATCTGCTCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT-- 5384
                           vi  v i  i     ivv  v   i v  vvv           i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_55600455_5   5385 TCCATTTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5434
                           --    i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_55600455_5   5435 GCTGAGACTGGATCCTTTCCTTACGCCTTATACAAAAATTAATTCAAGAT 5484
                         iv   iii    i  i v   i  i  v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_55600455_5   5485 GGATTAAAGACTTAAATGTTAGATTTAAAACCATAAAAACCCTAGAAGAA 5534
                             i ?    i       v   vi      i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_55600455_5   5535 AATCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGA 5583
                           iv    ?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_55600455_5   5584 CTAAAACACCAAAAGCAATGGTAACAAAAGCCAAAATTGACAAATGGGAT 5633
                         v  vi            vvi i        vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_55600455_5   5634 CTAGTTAAACTAAAGAGCTTCTGCACAGCAAATGA-ACCATCAA---AGT 5679
                         i vi i   v v  i i   i  ii vv    v  -  i     ---   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_55600455_5   5680 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTG 5729
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_55600455_5   5730 ACAAAGGGCTAATATCCAGAATCTACAAAGAATGTAAACAAATTTACAAG 5779
                          i  i  i  vi          v  i      ivivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_55600455_5   5780 AAAAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 5829
                              i -    i     v  i?    i            v    i    
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_55600455_5   5830 ACTTCTCAAAAGAAGATATTTATGCAGCCAACAGACACATGAAAAAATGC 5879
                          i     v           vi viii     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_55600455_5   5880 TCATCATCACTGATCAT 5896
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (152 / 87)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


1061 20.70 1.32 0.44  chr2_55608043_55612662     1587  1813 (2807)    L1M4_orf2#LINE/L1        3   231 (677)  

  chr2_55608043_5   1587 GAAAGAATTCACATATTTATGGTTTGGAAGACTTGATCTTGTAAAGATGA 1636
                               vv  v   i  i    v           i  v    v      i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_55608043_5   1637 CACTGTTCCCCAAAGTGATCTACAGATTCAGAGCAATTCCTGTCAAAATC 1686
                           v ii        v               iv     i   i        
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_55608043_5   1687 CAAA--ACCTTTGCTGCAGAAATGGAAAAAGTCTATCCTCAAATGCATAT 1734
                          v i--i     vi         v  v  - iiv     v    v     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATAT 151

  chr2_55608043_5   1735 GTGATCTCAAGGCACCCCAAAT-GTCAAAACAATCTTGGGAAAGGAAGAC 1783
                          vi viv     v    vi   - i             ii    i ii  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_55608043_5   1784 AAAATTGGAGGACCCACACTTCACAATTTC 1813
                            i         i        v       
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTC 231

Transitions / transversions = 1.14 (25 / 22)
Gap_init rate = 0.01 (3 / 229), avg. gap size = 1.33 (4 / 3)  

 316 11.11 0.00 3.70  chr2_55608043_55612662     2123  2176 (2444)    L1M4_orf2#LINE/L1      220   271 (637)  

  chr2_55608043_5   2123 CCTCACAATTTCAAAACTCACTACAAAGCTACAGTAATCAGGGCCGCGTG 2172
                          i  v             i                     i i --v   
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC--AGTG 267

  chr2_55608043_5   2173 TGGT 2176
                             
  L1M4_orf2#LINE/    268 TGGT 271

Transitions / transversions = 2.00 (4 / 2)
Gap_init rate = 0.02 (1 / 52), avg. gap size = 2.00 (2 / 1)  

1573 14.99 1.73 6.92  chr2_55608043_55612662     2420  2766 (1854)    L1M4_orf2#LINE/L1      210   538 (370)  

  chr2_55608043_5   2420 AAGACTC-CATTTCAAAAAACAA---CAACAATGACAACAAAAGCTACAG 2465
                          i     -  i   v-----   ---   v v v  v     -       
  L1M4_orf2#LINE/    210 AGGACTCACACTTCC-----CAATTTCAAAACTTACTACAAA-GCTACAG 253

  chr2_55608043_5   2466 TAATCAAAACACTGTGGTACTGGCATAAG-AGAGACATATGGATCAGTGG 2514
                                i   v                 - v        i     i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_55608043_5   2515 AATAGAATTGAGCATCCAGAAATAAACC-ATACATCTATGGCCAATTGAT 2563
                                     vi              -      i     i        
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_55608043_5   2564 TTTCATCAAGGGTGCTAAAACAATTCAGTGAGGGAGAAAACAGTCTTTTC 2613
                             iv         i  i  v     i  -    i i  i         
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTTC 402

  chr2_55608043_5   2614 AATAAGTAGGGCTGGAAGAATTGGATACTCACATGCAAAAGAATAATCTT 2663
                           i  i i v     i v  i      ?i               i vv  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_55608043_5   2664 GGACTATTACTGCATACCATCTATAAAAATTAACTCAAGATGGACAAAAG 2713
                             ivi   iv  i     v  i              i     iv ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_55608043_5   2714 ACCTAAATGTAAGAACTATGAAAGTAGGAAAATGTAAAATATAAAACTCT 2763
                                       i   -----------------   v           
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTA-----------------AAACTATAAAACTCT 535

  chr2_55608043_5   2764 CAG 2766
                         i  
  L1M4_orf2#LINE/    536 TAG 538

Transitions / transversions = 1.63 (31 / 19)
Gap_init rate = 0.02 (8 / 329), avg. gap size = 3.75 (30 / 8)  

 798 13.92 7.59 0.63  chr2_55608043_55612662     3132  3289 (1331)    L1M4_orf2#LINE/L1      530   698 (210)  

  chr2_55608043_5   3132 AACTCTCAGAAGAAAACACAGGCAAACATCTTCTTGGCCTTGGATTTGGC 3181
                               i           i   ?iv v      v  i      i  v   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_55608043_5   3182 AGT-----CTTAGGTATGACACCAAAA-----AGCAACAAAAGAAAAGAA 3221
                          i -----     i             -----               -  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AA 628

  chr2_55608043_5   3222 TAAGTAAATAGAGCTTCATTAAAATTAAAAA--TTTGTGTATCAAAGGAC 3269
                           ii     v ii      i           --      iv         
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_55608043_5   3270 ACTATCAAGAGAGTAAAAAG 3289
                                   i   i     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAG 698

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.02 (4 / 169), avg. gap size = 3.25 (13 / 4)  

 671 19.01 0.70 0.00  chr2_55608043_55612662     3612  3753 (867)    L1M4_orf2#LINE/L1      686   828 (80)  

  chr2_55608043_5   3612 AGAAAGTAAAAAGAAAACCCACAGAGAGGGA-AATATATTTGTAAATTAT 3660
                                i      v          iv    -  v       i    i  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_55608043_5   3661 ACCTCTGATAAGTATCTAGTATCCAGAATATGTACAGAACTCCTACAGCT 3710
                          iv         viv  v             i  v       i    i  
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_55608043_5   3711 GAACGATTAAAAGACAAAGAGCTCCATTTGAAAATGGGCAAAG 3753
                         v  ii  v          v i i v   ?i             
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.17 (14 / 12)
Gap_init rate = 0.01 (1 / 143), avg. gap size = 1.00 (1 / 1)  

 604  9.57 0.00 0.00  chr2_55608043_55612662     4035  4128 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_55608043_5   4035 AAAAATGGGCAAAGGACTTGAATGCACATTTCTCCAAAAAAGATATACAA 4084
                                         i      iv             i           
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_55608043_5   4085 ATAGCCAACAAGCACATGAAAGGATGCTCAATATTATTAGTCAT 4128
                           i     i            i         i  i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 8.00 (8 / 1)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3089 21.44 6.31 3.10  chr2_55678152_55681185.rev     1671  2542 (492)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr2_55678152_5   1671 TATTCCATGTTTATGGACAGGAAAACTCAAT---GTCAAGATGTCAGTTC 1717
                            i       i     iv    i   i   ---  i      v  i v 
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr2_55678152_5   1718 TTCCCAACATGATCTACAGATTCAATACAATATCAATCAAAATTTCAGCA 1767
                          i     vv                ii    vi v        ii    v
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_55678152_5   1768 AGTTATTTTGTGGATACTGACAAACAGATTCTAACATTTATATGGAGAGG 1817
                         ivi v     ii  v i      i v   i    v   i       i v 
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_55678152_5   1818 CAAAACACCCAGAATAGCCAACACAATATTGAA------GAACAAAATTG 1861
                            iiv               v     v     ------       i   
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_55678152_5   1862 GAGGACTGACACTACCCAACTTGGAGACTT----CAAA-CTACAGTAATC 1906
                                v     v     i  vi i    ----    -           
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_55678152_5   1907 AAGAGAGTGTGGTATTTGCAAAAGAATGGAGAAATAGATCAACAGAACAT 1956
                             v         i v   v   i  i  v v         ii   i v
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_55678152_5   1957 AATAGAGAGCCCAGAAATAAACTCACATAAATATAATCAATTTATCTTTG 2006
                            v     i            i  i i vv   ii      v  i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_55678152_5   2007 ACAAAGGAGCAAAGGCAATACGGTGAGGAAAGGA-------------AAA 2043
                             i  v  v   i v  v ii  i      i -------------   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_55678152_5   2044 TGG-------ACATCTGAA-A-------GAAAAAATATGAATCTAGACAC 2078
                            -------   v   i - ------- v    iv     vi i   v 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_55678152_5   2079 AAACTTTACACCCTTCACAAAAAATAATTCAAAATAGATCACAGACCTAA 2128
                         vv  i i     v vi       v   i       i     ?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_55678152_5   2129 ATGTAAAATGTAAAACTATAAAAATCCTAGAAGATAACATAGGAGGAAAT 2178
                               i vv             v  i       v        ? v    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_55678152_5   2179 TTAGGTGACCTTGGGTATGGTGATGACTTTTTTGATACAACACCAAAGGC 2228
                         i vv            vv  ii   ii  i  v    ii        i  
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_55678152_5   2229 ACACCCTATGAAAGACATAATTAATAAGCTGAACTTCATTAAAATTT--- 2275
                            vv v ii     v v   vi    ii  i       i      v---
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_55678152_5   2276 -CTGCTATGT---AAAAGACAGTATCAAGAGGATGAGAAGACAAGCCACA 2321
                         -  vi i  i---   i    v        iii   i       v     
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_55678152_5   2322 GACTGGAAGAAAATATTTTCAGAAGACACATCTGATAAAGGACTGTTATT 2371
                           v   i           v  i vv i i         i     vv   i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_55678152_5   2372 CAAAATATACAAAGAACACTTAAAATTCAACAATAAGAAAATGAACCCAA 2421
                           i      i       v    v  i    i     --------------
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAA-------------- 794

  chr2_55678152_5   2422 TTAACAAAAAGAAAACAAACAACCCAAC--AAATATAATGGGTCAAAAAC 2469
                         -------     ---    i       i--   ---      iv  ii i
  L1M4_orf2#LINE/    795 -------AAAGA---CAAATAACCCAATTWAAA---AATGGGCAAAGGAT 831

  chr2_55678152_5   2470 CTTAACAGACTCATCACCAAAGAAGATACATAGATGAC----AAGCATAT 2515
                         i v  i    viv  v            i i i   i ----     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_55678152_5   2516 GAAAAGATGCTCCACATCATGTCATCA 2542
                                     v      ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (107 / 78)
Gap_init rate = 0.02 (15 / 900), avg. gap size = 5.47 (82 / 15)  


3205 26.98 0.55 0.55  chr2_55875397_55881679.rev     4884  5791 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_55875397_5   4884 TGGAAGAACATTCCATGCTCATGTGTAGGAAGAATCAATTTCGTGAAAAT 4933
                              ii i  i     i     vi v      v i   v i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_55875397_5   4934 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4983
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_55875397_5   4984 TACCAA-TGCCTTTATTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5030
                          v   i-       -  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_55875397_5   5031 ATATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAA 5080
                                 viiv  ii  v  viv  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_55875397_5   5081 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5130
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_55875397_5   5131 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5180
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_55875397_5   5181 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATACCTACAAC 5228
                                 i    i--    i  --        vv   i i ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_55875397_5   5229 TATCTGATCTTTGACAAACTTGAGAAAAACAAGCAATGGGGAAAGGATTC 5278
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_55875397_5   5279 CCTATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGC 5328
                         i  v  i  i          i   v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_55875397_5   5329 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5378
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_55875397_5   5379 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5428
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_55875397_5   5429 CCTAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTA 5478
                          v    ?i v viv   iv   v v  vv i i   v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_55875397_5   5479 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5528
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_55875397_5   5529 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5578
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_55875397_5   5579 CGGGCAACCTACAAAATGGGAGAACATTTTCGCAACCTACTCATCTGACA 5628
                         vi i     i   i          v  v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_55875397_5   5629 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTGACAAGAAA 5678
                          i  i  vi          v  i  v      vv    v ii i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_55875397_5   5679 AAAACAAACAACCCCATCAAAGAGTGGGTGAAGGACATGAACAGACACTT 5728
                           i     i     v  i?  i i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_55875397_5   5729 CTCAAAAGAAGATATTTATGCAGCCAAAAAACACAGGAAAAAATGCTCAC 5778
                            v           vi viii     v  i    v     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_55875397_5   5779 CATCACTGGCCAT 5791
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3095 27.24 1.11 0.55  chr2_55927155_55933547.rev     4999  5901 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_55927155_5   4999 TGGAAGAACATTCCGTGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5048
                              ii i  i  i  i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_55927155_5   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_55927155_5   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_55927155_5   5147 TATGGAACCAAAATAGGGCACACATT-GCCAAGTCAATCCTAAGCCAAAG 5195
                                viiv  -i  i v  v v -     iv     i i ivv i i
  L1M4_orf2#LINE/    149 TATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_55927155_5   5196 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5245
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_55927155_5   5246 CTACAGTAACCAA-ACAGCATGGTACTGGTACCAAAACAGAGACATAGAA 5294
                                  i   -    ii         i iv ii i   v i     v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_55927155_5   5295 CAATATAACAGAAC--AGAGCCATCAGAAATAATGCCACATATCTACAAC 5342
                             iv  i    i--    i --         vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGT 345

  chr2_55927155_5   5343 TATCTAATCTTTCACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5392
                         i vi i  i  iv    ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_55927155_5   5393 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGC 5442
                         i  v  i  i              v      v  ?   i  ii i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_55927155_5   5443 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5492
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_55927155_5   5493 ATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAA 5542
                           i ?    i  v    v   v       i      vi i   i      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_55927155_5   5543 CCTAGGCAATAAGGTTCAGGACATAGCCATGGGCAAGGACTTCATGTCTA 5592
                          v    ?ivv  vv   iv   v v vvv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_55927155_5   5593 AAACACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5642
                         vi    i       vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_55927155_5   5643 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5692
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_55927155_5   5693 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5742
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_55927155_5   5743 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTGACAAGAAA 5792
                          i  i  vi          v  i  v      vv    v ii i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_55927155_5   5793 AAAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5838
                           i    ----   v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_55927155_5   5839 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5888
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_55927155_5   5889 CATCACTGGCCAT 5901
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2991 28.44 1.33 0.44  chr2_55952319_55960775     4974  5873 (2584)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_55952319_5   4974 TGGAAGAACATTCTGTGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5023
                              ii i  i ii  i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_55952319_5   5024 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5073
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_55952319_5   5074 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 5121
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_55952319_5   5122 TATGGAACCAAAATAGAGCACACATTGCCAAGTCAATCCTAAGCCAAAGG 5171
                                viiv  vi  v vviv  v     iv     i i ivv i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_55952319_5   5172 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5221
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_55952319_5   5222 TACAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGAGATATAGAAC 5271
                                 i   i    ii       i i iv ii i   v       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_55952319_5   5272 AATGGAACAGAAC--AGCGCCATCAGAAATAATGCCGCATATCTACAACT 5319
                                i    i--  v i --         vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTC 346

  chr2_55952319_5   5320 ATCTAATCTTTCACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5369
                          vi i  i  iv    ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_55952319_5   5370 CTATTTAATAAATGGTGCTGGGAAGACTAGCTAGCCATATATAGAAAGCT 5419
                           v  i  i              vi   i v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_55952319_5   5420 CAAACTGGATCCCTTCCTTACACCTTATACAAAAATGAATTCAAGATGGA 5469
                         v  ii    i    v   i     v           v  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_55952319_5   5470 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAAC 5519
                          i ?    i  v    v   v       i      vi i   i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_55952319_5   5520 CTAGGCAATAAGGTTCAGGACATAGCCATGGGCAAGGACTTCATGTCTAA 5569
                         v    ?ivv  vv   iv   v v vvv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_55952319_5   5570 AACACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5619
                         i    i       vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_55952319_5   5620 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5669
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_55952319_5   5670 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTGATCTGACAA 5719
                           i     i                 v  i    vii ivv      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_55952319_5   5720 AGGGCTAATATCTAGAATCTACAATGAACTC----AAATTGACAAGAAAA 5765
                         i  i  vi    i     v  i  v      ----  v ii i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_55952319_5   5766 AAACAG----CCCCATCAAAGAGTGGGTGAAGGACATGAACAGACACTTC 5811
                          i   i----   v  i?  i i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_55952319_5   5812 TCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5861
                           v           vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_55952319_5   5862 ATCACTGGCCAT 5873
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (149 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  

3670 22.33 2.69 0.79  chr2_55952319_55960775     7075  7965 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_55952319_5   7075 TGAAAAGACATCCTGTGTTTATGGATTGGAATAACTAATATTATTAAAAT 7124
                           i     i    ii    i           v vi       i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_55952319_5   7125 GTGCA-TACTATCTAAAGTGATCTATAGAGTCAATGCAATCCCAATTAAA 7173
                          -   -    vi i   v       i   v    i        v  i   
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_55952319_5   7174 ATC------------TTCACAGAAATAGAAAAA--AATCTTAAAACTTAT 7209
                            ------------  ii       v  v  i--i   i     i i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_55952319_5   7210 ATGGAACTACAAAA-ACCCTGAAAAACAATAGGAATCTTGAACAAAAAGA 7258
                               v i   ii-    v   v i v v iv         v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_55952319_5   7259 ACAAAGCTGAAGGCATCACACTTCCTGATTTCAAAATATATTATAAACTG 7308
                               i  i   vv          ii         iv  i  i   viv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_55952319_5   7309 ATAGTAATCCAAACAGCATAGTACTGGCATAAAAACAGACATA--GACCA 7356
                          i       v i    ii i            ii i       --  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_55952319_5   7357 GTGAAATAGAATGGAGGGACCAGAACTAAATCTACACATT-ATAGTCAAC 7405
                         i  i        v   i v      v    i i i     -  i     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_55952319_5   7406 TGATCTTCAATAATGGTGCCGAGAACACACAATAGGGAAAGGATCACATC 7455
                             i   i i  v      i   v  iv    i       i  viiv i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_55952319_5   7456 TTTAATAAACAGTGTTGGGAAAATTGGATATCCACAGGTAGAAGAATGAA 7505
                           i  i   ii   i     v  i      ?     v i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_55952319_5   7506 ATTGGACCCTTATCTCATATCATATACAAAA-TGAACTGAAAATGGATTA 7554
                         i        i  i    i i           - v    v         i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_55952319_5   7555 GTGAGTTAAGTGTAAGACCTGAAACCACAGAACTACTGCAAGGAAACATA 7604
                         ?v  vi   i       v  i    i i i    vi iv   i       
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_55952319_5   7605 GTGAAAAAGCTTCTTGACATTGGTCTGGGCAATGATTTTTTGGATATTAC 7654
                          v?iv   v    v    v    vi i       i   i  i     v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_55952319_5   7655 ACCAAAAGCACAAGCAACAGAAGTAAAAATAGACAAGTAGGATTGCATCA 7704
                                            i   v         i  i v   i v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_55952319_5   7705 AA-CTAAAAGTTTCTTCACAGCAAAGAAAAAAACCAATAGAGTGAAAAGA 7753
                           -i     ii  i vii vv     i v vv i   v i          
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_55952319_5   7754 CAATCTAGAGCATAGGAGAAAATATTTGCAAACTATATATCTGATAACTG 7803
                            i i v  v  i                  ii             vv 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_55952319_5   7804 GTTAATTTCCAAAATATATAAAGAATAACTCTTACAAATCAATAGCAAGA 7853
                         ii vi v    i             ---         v      ii  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAA---CTCTTACAACTCAATAATAAAA 796

  chr2_55952319_5   7854 AAACAAACATCCTGATTTAAAAAATGGG--AAGGACTTGAACAGATGTTT 7901
                          i     i v  ii   ?     -    --     i     i   ii   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTT 845

  chr2_55952319_5   7902 CTCAAAGAGAAGACAATA-AAATGGCCAATGGCTATGTAAAAAGATGCTC 7950
                            v  -      i -  -           iivi ii i           
  L1M4_orf2#LINE/    846 CTCCAA-AGAAGATA-TACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_55952319_5   7951 AACATCACTAGTCAT 7965
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (130 / 65)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.07 (31 / 15)  


3173 26.60 0.77 0.55  chr2_55965163_55976963.rev     5000  5905 (5896)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_55965163_5   5000 TGGAAGAACATTCCATGCTTACGGATAGGAAGAATCAATATTGTGAAAAT 5049
                              ii i  i     i i i    v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_55965163_5   5050 GGCCATACTGCTCAAGGTGATTTATAGATTCAATGCCATCCCCATCAAGC 5099
                            v     v i   iv    i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_55965163_5   5100 TACCAA-TGACTTTCTT-CACGAATTGGAAAAATCTACTTTAAAGTTAAT 5147
                          v   i-  v    i  -  vi     - v  iiiv iii    i  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr2_55965163_5   5148 ATGAAATCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAACAAAAAGA 5197
                            i  viiv  ii  v  v v        i      i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_55965163_5   5198 ACAAAGATGGAGGCAATCATGCTACCTGACTTCAAACTATACTACAAGGC 5247
                               v      - v   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_55965163_5   5248 TACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGAAC 5297
                                 i   i    ii        ii iv ii i   v       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_55965163_5   5298 AATGGAACACAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5345
                                i v  i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_55965163_5   5346 ATATGATCTTTGACAAACCTGACAAAAACAAGCAATAGGGAAAGGGTTCC 5395
                          vv    i  i     ivv  v   i v  vv    i       ii vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_55965163_5   5396 CTATTTAATAAATAGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5445
                           v  i  i    i         v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_55965163_5   5446 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5495
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_55965163_5   5496 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5545
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_55965163_5   5546 CTAGGCA-ATACCGTTCAGGACACAGCCATGGGCAAGGACTTCATGACTA 5594
                         v    ?i- v i -   iv   viv vvv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_55965163_5   5595 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5644
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_55965163_5   5645 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5694
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_55965163_5   5695 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5744
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_55965163_5   5745 AGGG-CTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5793
                             -  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_55965163_5   5794 AA-ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGATACTT 5842
                           -     i     v  i?    i            v    i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_55965163_5   5843 CTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTCAT 5892
                            v        i  vi viii     i ii  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_55965163_5   5893 CGTCTGTGGTCAT 5905
                          i  v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.20 (12 / 10)  

2810 28.21 2.23 1.00  chr2_55965163_55976963.rev     6714  7610 (4191)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_55965163_5   7610 TGGGGAAACATTCTATACTCATGGATAGGAAGAATCCATTTTGTTAAAAT 7561
                            ii i i  i i  ii        v      v iv  v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_55965163_5   7560 GGCCATACTACCCAAAACAATTTACAGATTCAATGCTATTCCTATCAAAC 7511
                            v     v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_55965163_5   7510 TACCAATGATATTCCTCACAGAA-TTACAAAAAAAATTTTAAAATTCATA 7462
                          v   iiviiv  ii ii     -  ivv  ivvi  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr2_55965163_5   7461 GAGAACCACAAAAGAGCCGGAATAGGCAGAGCAATCCTAAAGAAAAAGAA 7412
                         vi   vii   ii  v  i      v  i i     i i  i  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chr2_55965163_5   7411 CAAAGCTGGAGGCATTATGTTACCTTGTTACCTGACTCCAAACAATAAAG 7362
                              i      vv i iii v  ivi  v vvi   i---  v i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT---ACTACAAAG 247

C chr2_55965163_5   7361 GCTACAGTAACCAAAGCTGCATGATACTGGTACAAAAACAGACACATAGA 7312
                         -         i   ii v ii  i      i i  ii i     i     
  L1M4_orf2#LINE/    248 -CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chr2_55965163_5   7311 CCAATGTAACAACATAGAAAGTCCAGAAATAATGTCGCAGTCCTACAACC 7262
                         i     v  i iv  v  i             vvi ii vvii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

C chr2_55965163_5   7261 ATCTGATCTTTGACAAAGTTGACAAAAACAAGCACTGGGGACAGGAC--T 7214
                          vi    i  i     i v  v   i v  vv  v      v  i i-- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chr2_55965163_5   7213 CCTT-CAATAAATGGTGTTGGGATTACTGGCTAATCATATGCAGAAAATT 7165
                          i  -   i        i     iv     v  ?i  i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chr2_55965163_5   7164 GAAACTAG-CCACTGTCCTTACACCATATACAAAAATCAATTCAAGATGG 7116
                            ii i -  v  i-   i                 i  i    i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAATGG 495

C chr2_55965163_5   7115 ATTAAAGACTTAAATGTAAAACCTAAAAGTATAAGAACCCTGGAAGATAA 7066
                           i ?    i         i v      v     i vi i i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

C chr2_55965163_5   7065 TGTAGGAAATACTATTCTGGACATAGGCCCTGGCAAAGATTTCAT-GATG 7017
                         ii    ?ivv v v   vv   v v  viiv     v i    v -   -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

C chr2_55965163_5   7016 AAGATGGCAAAAGCAATAGCAACAAAACAAAAA-TGGACAAACGAGACTT 6968
                          v  iiv        vv          v     - i  i   ivi     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

C chr2_55965163_5   6967 AATTAAA-TCAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGCA 6919
                         v  i   - i   i -   i  ii vv    i  v        v i  ii
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

C chr2_55965163_5   6918 AACAGACAGCCTACAGAATGGGAGAAAATATTTGCAAACTAGGCATCTGA 6869
                           v     i  i                          ii vii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

C chr2_55965163_5   6868 CAATGATCTAGTAACAAGCATTTATAAGGAACT------------TAACA 6831
                         i  v iv  v   v v  v  v     i     ------------   i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

C chr2_55965163_5   6830 GGCAAAAACAAAGAGCTTCATTAAAAAGTGGGCAAAGGACGTGAACAGAT 6781
                         i--   i     v i iiv   ?    i           iv    i   i
  L1M4_orf2#LINE/    794 A--AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chr2_55965163_5   6780 ACTTTTCAAAAGAAGACATGCACGCAGCCAACAGGCATATGGAAACATAC 6731
                          i  i  v        i  i  viii     i i   i   i   v  i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

C chr2_55965163_5   6730 TCAACATTATAAATCAT 6714
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (159 / 90)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.07 (29 / 14)  


3092 25.22 2.79 1.45  chr2_56142229_56146714.rev     3130  4025 (461)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_56142229_5   3130 TAGAGAGATAGCCCATGTTCCTGAGTAAGAAAACT--ATATTGTCAAGAT 3177
                          i  i     v         v  ii vi   i   --       i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_56142229_5   3178 GTCAGTTCTTCTTAATTTGAACTATAGATTCAAAGAAGTCCCAATCAAAA 3227
                          v  i v  i ii  v    v   i        v v i    v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_56142229_5   3228 TCCCAGAAAGTGATTTTGTGTATATTGACAAACCAATTCTAATGTTTATG 3277
                               vvivivv     iiv v        i ii  i    vi  i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_56142229_5   3278 TGTAGAGGTAAAAGATCCAGAATA-CCAACTCATTATTCAA---GGAGAA 3323
                           v i v i  ii  i        -    vv  v v  v  --- i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_56142229_5   3324 TAAAATTGGAGGACTGACACAACCTGACTTCAAGACTTACTGTATCACTA 3373
                         i   i          v    vv  ii i     i       ii vvi   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_56142229_5   3374 CGGCAGTCAAGCCAGTGTAGTACTGATGAAAGAATAGGTGAATAGATTAA 3423
                          i i i     v      i      iiiv   i    iiiv      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_56142229_5   3424 TGGAACATAATAGAAGGCCTAGATATAGACCCACACAAGCATGGTTAGCT 3473
                              i v   v  ii i i   v   i     i   vvi     i ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_56142229_5   3474 GATCTTTGACAAAGGAGCAAAGGCAATACAATGGAGCAAAGA---GTCTT 3520
                            i  i     i  v  v   i v  v      i -     ---     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTT 399

  chr2_56142229_5   3521 TTCAAGAAATAGTGCTGGAGCAACTGGACATCCACATGCAAAAAATAATA 3570
                              v    i       ii        i ?            i -----
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA----- 444

  chr2_56142229_5   3571 ATAATAATCTCGACACAAATCTTATATCCTTCACAAAAGTTA-CTCATAG 3619
                           i - i - v   v vv i  i i i v vi      i   -    v i
  L1M4_orf2#LINE/    445 ATGA-AGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_56142229_5   3620 TGGTTCATAGGCCTAAATACAAAATGC-AAAACTATAAAACTCCTGGAAG 3668
                            v   ?  i       ii  i -  -               i i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAG 541

  chr2_56142229_5   3669 ATAACACAAGAGAAAA-CTTAGATGACCTTCGGCATGACATTGACTTTTT 3717
                          v    i i ? v   -   v -       v  ivv i  v  ii  i  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_56142229_5   3718 AGATATAACCCCAAAGGCACGACCTATGAAAGAAATAATTGATAAGGTGG 3767
                               i  v     i    i v v ii       v   v     iv   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_56142229_5   3768 GCTTCATTAAAATGTAAAACTTCTGCTCTGCAAAAGATTATGTTAAGAGA 3817
                         i      i     vv       i  iv  v    i  ivv i i    i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_56142229_5   3818 TAGTGAGTAGATAAGCCACAGACTGGGAGAAAATATTTGCAAAAAAAA-A 3866
                         --    iv   i  v       v                    vv v - 
  L1M4_orf2#LINE/    691 --GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_56142229_5   3867 TCTGATAAAGAATTGTTATCTAAAATACACAAAGAACACTTAAAACTGAA 3916
                                 i i i vv    i i    i i       v    v    v  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_56142229_5   3917 CAATAATAAAATGAA---CCCAATCTAAAAATGGGCAATATACCTGAATA 3963
                         i     v  i ii  ---      i?            viv ii      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_56142229_5   3964 GACATATCACCAAAGAAGATATAATAAGT--------AGCATATGAAA-G 4004
                              v  v              -i  i --------    i      - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATA-CAAATGGCCAATAAGCACATGAAAAG 887

  chr2_56142229_5   4005 ATTTTTGATATTGTATGTCAT 4025
                           vi ii i  ii????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (135 / 87)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.00 (38 / 19)  


3133 26.75 0.76 1.64  chr2_56231584_56237250     4260  5175 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_56231584_5   4260 TGGAAAAACATTCCATGCTCATGGACAGGAAGAATCAATATCGTGAAAAT 4309
                               i i  i     i       iv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_56231584_5   4310 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 4359
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_56231584_5   4360 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4407
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_56231584_5   4408 TGTGGAACCAGAAAAGAGTCCACATTGCCAAGAAAATCCTAAGCCAAAAG 4457
                          i     viiv  ii  vi viv  v     i v    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_56231584_5   4458 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTGTACTACAAGGG 4507
                                i      vv    i  v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_56231584_5   4508 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGA--TATAGACG 4555
                                 i   i    ii         i iv ii i   --      iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_56231584_5   4556 AATGGAACAGAAC--ATAGCCCTCAGAAATAATACCACACATCTACAGCC 4603
                                i    i-- v  i  --        vv   i    i  ii i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_56231584_5   4604 ATCTGATCTTTGATAAACTTGACAAAACAAAACAAAAACAAGAAATGGGG 4653
                          vi    i  i  i  ivv  v   i  ----------  vvv       
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGAC----------CATTCAATGGGG 386

  chr2_56231584_5   4654 AAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCTTAT 4703
                             i  vvi  v  i  i              v      v  ?  vi  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_56231584_5   4704 GTAGAAAGCTGAAACTGGATCCCTTCCTTATATCTTATACAAAAATTAAT 4753
                          i i  iiv    ii    i    v   i i i v              i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_56231584_5   4754 TCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAGCCATAAAAACCCT 4803
                             i      i ?    i       v   v     i i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_56231584_5   4804 AGAAGAAAACCTAGCCATTACCATTCAGGACATAGGCATGGGCAAGGACT 4853
                                   v   v?i v viv   iv   v v  vv i     v ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_56231584_5   4854 TCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAA 4903
                           v ivv  vi            vvi          vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_56231584_5   4904 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAT 4953
                          v   ii v  i   v v  i i   i  ii vv    i  v    i  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_56231584_5   4954 CAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACC 5003
                         v i      v  i     i                 v   i   vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_56231584_5   5004 CATCTGACAAAGGGCTAATATCCAGAATCTCCAAAGAACTCAAACAAACT 5053
                         i      i  i  i  vi          v vi         vv    -  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CT 785

  chr2_56231584_5   5054 TA-CAAGAAAAAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGA 5102
                         i -i  v     i     i     v  i? v  i            v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_56231584_5   5103 ACAGACACTTCTCAAAAGAAGACGTTTATGCAGCCAACAGACACATGAAA 5152
                          i     i     v        ii vi viii     i ii         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_56231584_5   5153 AAATGCTCACCATCACTGGCCAT 5175
                          i       v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.44 (22 / 9)  


3127 26.97 1.44 0.67  chr2_56276179_56279038.rev     1468  2368 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_56276179_5   1468 TGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 1517
                           i  ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_56276179_5   1518 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1567
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_56276179_5   1568 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTAAAGTTCA 1615
                          v   iivi i  i  ii     -   -- v  i  - i i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_56276179_5   1616 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 1665
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_56276179_5   1666 AACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAAGC 1715
                                i      vv   vi  v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_56276179_5   1716 TACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1765
                                 i   ii   ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_56276179_5   1766 AATGGAACAGAAT--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 1813
                                i     --    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_56276179_5   1814 ATCTGATCTTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCC 1863
                          vi    i  i     ivv  v   i vv vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_56276179_5   1864 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1913
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_56276179_5   1914 GAAACTGGTTCCCTTCCTTACACCTTATACAGAAATTAATTCAAGATGGA 1963
                            ii   vi    v   i     v      i       i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_56276179_5   1964 T--------TAAATGTCCAACCTAAAACCATAGAAACCCTAGAAAAAAAC 2005
                          --------       vvi v       i   i  vi i     i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_56276179_5   2006 CTAGGCA-ATACCATTTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 2054
                         v    ?i- v i --   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_56276179_5   2055 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 2104
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_56276179_5   2105 AATTAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 2154
                         v  i  iv v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_56276179_5   2155 ACACGCAACCTACAGAATGGGAGAAAATTTCTGCAATCTACTCATCTGAC 2204
                          v vi     i                 v i     vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_56276179_5   2205 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 2254
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_56276179_5   2255 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 2304
                            i     i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_56276179_5   2305 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTTA 2354
                             v        i  vi viii     v ii          i     i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_56276179_5   2355 TCATCACTGGCCAT 2368
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  


2948 13.02 4.25 20.96  chr2_56362990_56365064.rev      501  1583 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_56362990_5    501 GACATCCCATGTTAACAAGCCAGAAGATTTAATATTGTTAGGATGGCAAT 550
                           i          v iiiiiii     i            i         
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_56362990_5    551 AGTCTTCAAATTCATCTACAGATTCAATGCAATCCCTTTCAAAATCCCAA 600
                          v  ii      v              i         v           i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_56362990_5    601 TTGCCATTTTTGCAGATAATGACAAGCCTACACTAAAAGACATATGGAAA 650
                         i    v          v v        iv iv      vv          
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_56362990_5    651 TTCAAAAGAACCAGAATAACCAAAGTAACCTTGGTGTGGGGTAA-ACAGT 699
                          v   ii  v        i     ii  i    ivivi iiv  - v   
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_56362990_5    700 TAAAAGACTCATATTTCCTGATTTCAAAACTTACTACACAGGTACAGTAA 749
                          ii i      i i    ii                  v  v        
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_56362990_5    750 TAAAGACACTCTGGTACTGGCATAAGGAGAGGCATATAGGTCAATGAAAT 799
                          v      v v                 v  i       i      i   
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_56362990_5    800 GGAATAAAGAGTC-AGAAATAAACCCCGACATTTATGGTTAATAATTTTT 848
                         i    vi      -            vv           i   -------
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT------- 349

  chr2_56362990_5    849 TTTTTGAGACGCACTCTCCTTCTATTGCACAGGATGGAATGCAGTGGCGC 898
                         --------------------------------------------------
  L1M4_orf2#LINE/    350 -------------------------------------------------- 349

  chr2_56362990_5    899 AGTCTCGGCTCACTGCAAGCTCCACCTCCTGTGTTCAAGTGATTCTCCTG 948
                         ---------------------------------------     i  ---
  L1M4_orf2#LINE/    350 ---------------------------------------TGATTTTC--- 357

  chr2_56362990_5    949 CCTCAGCCTCCCAAGTAGCTGGGATTACAGGCATGCACCACCACGCCAAG 998
                         ----------------------  ----------------------    
  L1M4_orf2#LINE/    358 ----------------------GA----------------------CAAG 363

  chr2_56362990_5    999 CTAGTTGTTTATATAATTTTAGTAGAGATGGGGTTTCACCATATTGGCCA 1048
                         -------------------------------   ------------    
  L1M4_orf2#LINE/    364 -------------------------------GGT------------GCCA 370

  chr2_56362990_5   1049 GGCTGATCTCGAACTCCTGACCTCGTGATCTGCCCACCTCAACATTCAAT 1098
                         i ---------------------------------   -----       
  L1M4_orf2#LINE/    371 AG---------------------------------ACC-----ATTCAAT 382

  chr2_56362990_5   1099 CAGGAGTAAATAGTATTTTCAACAAATGGTGCTGGGACAACTGGATATCC 1148
                         vi   ivi      v                                ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_56362990_5   1149 ACACACAAACAAATGAATTTG------CACTTCATG--AAAAAAAAAAAT 1190
                            ii    vi      v   ------i  i   ii-- v v v      
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_56362990_5   1191 GAAC-AAAAATGGATTGTAGACCCAACTATAATAACTAAAACTATAAATA 1239
                         v   -v         ii?     i  v i   v i             vv
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_56362990_5   1240 TCTTAGAAGAAATAATAGGTATATATCTTCATAAACTTAGGTGAAGCAAT 1289
                                     vv     ?i  v      i i v   i   v i     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_56362990_5   1290 GGTTTCTTAGCTATGACTTTAAAAGCATG-GCAATAAAAGAAAAAACAGA 1338
                                   v      vii       ii-    i           i   
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_56362990_5   1339 ---------CTTCATCAAAATTAAAAGCTTTTCTGCTT----G------- 1368
                         ---------                 i     v     ---- -------
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_56362990_5   1369 -TAAGAAAATGAAAACACAACCCACAGAATGAGAAACAACTATTTGTACA 1417
                         -i      i      v               i  i v  -      i v 
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAA 731

  chr2_56362990_5   1418 TCATATATCTGATAAGGGACTTAGATCTAAAACATACATAAAGAACATTT 1467
                                               iv   i i  i   --        vi  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATA--TAAAGAACTCTT 779

  chr2_56362990_5   1468 ATAACTCAATAATAAAAAGACAAA----CCAATT-AAAAATGGG-AAAAG 1511
                          i                      ----      -         -   i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_56362990_5   1512 ACTTGAATAGACATTTCTCCAAAGAA--TATACAA----TCAATAA-CAC 1554
                          i                        --       ----i      -   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_56362990_5   1555 ATGAAAGGATGCTCAACATCATTAATCAA 1583
                               i              ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (85 / 53)
Gap_init rate = 0.03 (24 / 902), avg. gap size = 11.38 (273 / 24)  


1913 24.08 9.78 5.38  chr2_56419965_56422799.rev     1518  2335 (500)    L1M4_orf2#LINE/L1       25   878 (30)  

  chr2_56419965_5   1518 ATGAGAAGATTTCATATTATTAAAATA---------------------TA 1546
                           vi     i  v     i    i  i---------------------  
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr2_56419965_5   1547 TAGACACAACACAATCCAAATCAAAACATCAGT--CTTTCTTTGTAGAAA 1594
                         i   iv    i      vv       ivi   i-- i  i    i     
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr2_56419965_5   1595 TTGATACAATTACTTTAA------TAT----ATAC--TTGACCTCAAATT 1632
                             i viv v iii   ------   ----  i --vv    ivi   v
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr2_56419965_5   1633 GTTGAAATAATCTTAATCAACAACAACAAAAATGTAGAGGACTCACACTA 1682
                          iii   i      i vv  v  v      iv  --             v
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG--GAGGACTCACACTT 222

  chr2_56419965_5   1683 TTTGATTTCAGGACTTACTACAAAGCTACAGTTATCAAGACAGTGTTGTA 1732
                         iiii      ii                    v             v   
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_56419965_5   1733 TTAATGTAAGGACAGACAAACATAACAACAGAAT------------CTAA 1770
                         i iiii      i     v i v v   ii    ------------ i i
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_56419965_5   1771 AAAAAGATCCACACATATATGGCCAATTGATCTTTGACAAGGGTGCCAAG 1820
                            v i i   i    v     i        i  i               
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_56419965_5   1821 GTAATTCAATGGAGGAAAGAACAGTCTTTTCAACAAATTGTAC------- 1863
                         iiv         -        i                v  i -------
  L1M4_orf2#LINE/    373 ACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_56419965_5   1864 -CTCGATATCCATAAAAAAAAAACTCTCAAAATT-------TTCCTCACA 1905
                         -  v    ?   i viv    i v ---i  i  ------- v       
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAAT---GAAGTTGGACCCCTACCTCACA 468

  chr2_56419965_5   1906 TGTTAGGAACTAATAATAATAAC--AAAATGGATCACAGACCTAAAGATG 1953
                         ivv  v--  v  -   --    --           ?         vi i
  L1M4_orf2#LINE/    469 CCATAT--ACAAA-AAT--TAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_56419965_5   1954 AAATCTAAAATAATTAAAGTTGTAGTTAAAAACATAGGGAATAACATTTG 2003
                          i v      iv  v   v iv   vvi          ?ivv  iv  i 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_56419965_5   2004 CAATCTTAGAGTATGCAAAGATTTCTTAG----GATAC---AAGTACAGA 2046
                         ii i   i iv  v    v i        ----  i  ---   i   ii
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_56419965_5   2047 CCACAAAATTTTTAAATGGATATACTGAACTTCATCAAAATTAAGGATTC 2096
                          v      vvvv-    i    v i  i                ii i i
  L1M4_orf2#LINE/    614 CAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_56419965_5   2097 TTCTTCATCTAA--ACACCACTAAGAAAATGACAGGTCAAGCTACAGATT 2144
                           v v v  v  --    i ii      i   v i v   v i     v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_56419965_5   2145 GAGAGAAAACATTCTTATTCACTATTATTTACATATATCTGACAAATATG 2194
                          i       ----------------     i  -----------   ---
  L1M4_orf2#LINE/    713 GGGAGAAAA----------------TATTTGCA-----------AAT--- 732

  chr2_56419965_5   2195 TATATAGCTTTGAAAAAATACTTGATTACAGAATATATAAAGAACTCTAA 2244
                         i     -- i   v  iiv     vv v                    v 
  L1M4_orf2#LINE/    733 CATATA--TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_56419965_5   2245 AAATTCA-TGA--AAAAGATAAACAGCT-AATCAAAAAA--GGCAAAATC 2288
                         v  i   - i --      i   i i i-   i?     --      ivv
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_56419965_5   2289 CATGAACAGACACTTCACTAAAAAAGAC-CACAAATGGCTGATATGCA 2335
                         iv    i     i   v i   i    i-i         ii   v   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

Transitions / transversions = 1.51 (116 / 77)
Gap_init rate = 0.03 (28 / 854), avg. gap size = 4.43 (124 / 28)  


3103 27.48 0.66 0.66  chr2_56458859_56461841     1586  2491 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_56458859_5   1586 GAAGAACGTTCCATGCTCGTGGATACGAAGAACCAATATTGTGAAAATGG 1635
                            ii ii i     i  i     vv     vii        v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_56458859_5   1636 CCATATGGCCCAAGGTAATTTCTAGATTCAATTCCATCCCCATCATGCTA 1685
                          v   ivv     iv i  i vi        iv v     i    viv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_56458859_5   1686 CCAATGACTTTCTTCACAGAATAGGATAAAACT-ACTTTAAAGTTCATAT 1734
                            iivi i  i  ii     vvv  i  i-  - iii    i       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr2_56458859_5   1735 GGAACCAAAAAAGAGCCCGCATTGCCAAGATAATCCTAAGCCAAAAGAAC 1784
                             viiv  ii  v  v v  v     i i    i i ivv i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_56458859_5   1785 AAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAGGCTAC 1834
                             i      vv   vi  v  ii i      viv        i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_56458859_5   1835 AGTAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGATATAGACCAAT 1884
                              i   i    i          i iv ii i   v       i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_56458859_5   1885 GGAACAGAAT--AGAGCCCTCAGAAATAATACCACACATCTACAACCATC 1932
                             i     --    i  --        vv   i    i  iiii  vi
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_56458859_5   1933 TGGTCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 1982
                           i i  i     ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_56458859_5   1983 TTTAATAAATGTTGCTGGGAAAACTGGCTAGCCATACGTAGAAAGCTGAA 2032
                           i  i     v        v      v  ?   i i i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_56458859_5   2033 ACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTA 2082
                         ii    i    v   i     v           i  i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_56458859_5   2083 AAGACTTAAATGTTAGACCTAAAGCCATAAAAACTCT-AGAAGAAAACCT 2131
                         ?    i       v   v     i i      -    -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr2_56458859_5   2132 AGGCA-AAACCATTCA-GGCCATAGGCATGGGCAAGGGCTTCATGTCTAA 2179
                            ?i-   i -   i- i  v i  i- i     v  i   v ivv  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT 596

  chr2_56458859_5   2180 AACACCAAAAGCAATGGCAGCAAAAGCCCAAATTGACAAATGGGTTCTAA 2229
                         i            vvi   i      vvv    v  i    v  vii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_56458859_5   2230 TTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACCACCATCAGAGTGAAC 2279
                          i   v v  i i   i vii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_56458859_5   2280 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 2329
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_56458859_5   2330 AGGGCTAGTATCCAGAATCTACAAAAAACTCAAACAGATTTACAAGAAAA 2379
                         i  i  v           v  i   i     vv   iv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_56458859_5   2380 AATCAAACAACCCCATTAAAAAGTGGGTGATGGATATGAACAGACAATTC 2429
                          iv    i     v   ?    i    ii v    v    i     v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_56458859_5   2430 TCAAAAGAAGATGTTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 2479
                           v         i vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_56458859_5   2480 ATCACGGGCCAT 2491
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.20 (12 / 10)  


2758 23.53 7.41 1.65  chr2_56533157_56537435.rev     2943  3792 (487)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_56533157_5   2943 ATCCTATGTTCATAGATAGGAACAATCAATATTGTTACCAAAT--CAGTT 2990
                             i        i   v    v v i          -- i  --  i v
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA--AGATGGCAATA 57

  chr2_56533157_5   2991 CTTCCTAACTTGATC------------------CCAATCAAAATCC-AGC 3021
                           i  i  v      ------------------  v          -   
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_56533157_5   3022 AAGTTATTTTGTGAAATATTGACAAACTGATTATAAAGTTCATGTGGAGA 3071
                         vivi v     iii  -        i     iv    i     i    i 
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_56533157_5   3072 GGCAAAAGGCCTGGACTAGTCAACACAATATTGAA---GAAGAACAAAGT 3118
                         v    ii i  ii  v   i   v     v     ---            
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_56533157_5   3119 GAGAGGACCAGCATTACTCAACTTGAAGACTTAGTAAAAAGCTATAGTAA 3168
                         vi      ivi  i v i   i  v  i     v  v       i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_56533157_5   3169 TCAAGACAATGTGGTACTGGCATAAGAACAAACA----GATCAATGGAAT 3214
                                 i                 i i i   ----            
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_56533157_5   3215 AGAATAGAGAGCCAAGAAACAGACCCATGCAAATACAGTCAAATAATCTT 3264
                              v     i v     i i      i  vv  ii     v i  i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_56533157_5   3265 AGACAAAGGATCAAAGACAATTCAATGGACTAAAGA---GTCTTTTTGAC 3311
                         v     i  vv v     v         iv-     ---       ii  
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAAC 405

  chr2_56533157_5   3312 AAATGGTAATGGGGCAACTGGACATTCACATGCAAAAAAAAAAGAATCTA 3361
                                iv    i        i ?i           i  v--   vi i
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT--GAAGTTG 453

  chr2_56533157_5   3362 GACATGTAACTTAACACCCTTTACAAAAATTAACTCAAAATAAATTATAA 3411
                            viv  v  i -    v v                    ii  i ? i
  L1M4_orf2#LINE/    454 GACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_56533157_5   3412 ACCTAAATGTAA-AGTTCAAAACTCTACAACTCCTAGAAGATTACAGTAG 3460
                                     -  i -      v  v     i       vv   vvi 
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_56533157_5   3461 AGAAAACCTAAATGGCCATGGGGATT-GTCAGTGACTTTCTAGATACAAT 3509
                         ? v   i  vvi  i  v    --  - v  i  ii  ii      ii i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_56533157_5   3510 ATCAAAGTCATGATTTAT----TAAAAAGTTGATAAGTT-----TAATTA 3550
                          i    iv  ii viv i----v     i v     i  ----- v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_56533157_5   3551 AAATTAAAAACAT----------AAAAACAATGTCACGAGAATAAGAAAA 3590
                                    v ----------  ii   v i   v  i i i i  i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_56533157_5   3591 CAAGCAACAGACTGATAGAAAATATTTTCAAAAGCTACATCTGAAGAGGG 3640
                            v v     v  iv           v    vvv  i      vi    
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_56533157_5   3641 ACTGTTATCCAAAATATACAAAAAAAAACCCCTCA-AACTTAACAATAAG 3689
                            vv      i      i   i  ---- i  i -    i  i     i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAA----CTCTTACAACTCAATAATAAA 795

  chr2_56533157_5   3690 AAAAGCAACAATACAATTTAAAAATGGGCAAAAGAT----------ACCT 3729
                           i vv  i  iv     ?             i   ---------- ii 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_56533157_5   3730 CATCAAAAAAGATATACAGATGGCAAGTAAGTATATGAAAATATGTCCAA 3779
                          vi    i          i     v i    i i       v   ii   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_56533157_5   3780 TGTTGTAAATTGC 3792
                         ii ii????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (120 / 76)
Gap_init rate = 0.02 (21 / 899), avg. gap size = 3.67 (77 / 21)  


3670 17.62 2.50 3.81  chr2_56552984_56556326.rev     1639  2478 (865)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr2_56552984_5   1639 TGGAAAGCCATCCCATCTTTGCAGATTGGAAGACTTAATATAATAGTATT 1688
                                vi       v  iiii                  ----- i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-----TGTT 45

  chr2_56552984_5   1689 ATGTTGACAATGCTCCCCAAATTTATCTACAGAGTCAACACAATTCTTAT 1738
                          v v  i    i           v         v     i    i i   
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_56552984_5   1739 TAAAATCCTAGTTGCTTTTTTTTTGGCAGAAACTGACAAGTTGATCCTAA 1788
                         i       i  i   i      ---       i       i         
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAA 142

  chr2_56552984_5   1789 TATTCATATGGAATTGCAAGGGACCCAGGATAGCCAAA-CAACATTGAAA 1837
                         v            v              i         -   iv      
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_56552984_5   1838 ATGAAAAACAAAGTAGGAAAA-----AATTCTCAATTTCAAAACTTACAA 1882
                          v   i        v   ii ----- v   i                v 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_56552984_5   1883 CAAAATTACTATAATCAAGTACACAGTGTAGTACTCGCATAAG-ATAGGC 1931
                             ii   vi        ---       i     v       -    i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAG---ACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_56552984_5   1932 ATAAAGAACAATGAAATACACT--A-----CAGAAATAAACCTATACATT 1974
                            v   v     i    v v -- -----            i       
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_56552984_5   1975 TATGGTCAATAGGCTTTTGACAAGGGTACAAAGATAATTTATTAGGGGAA 2024
                                   v ii   i         i v    iv   i v -      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAA 388

  chr2_56552984_5   2025 AGAATATTCTTTTCAATATAGAGGCTTGAGTTAAATGGATATCAACACAC 2074
                               v         i v vi vvi  i vi  v      ? -------
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC------- 431

  chr2_56552984_5   2075 ACACACACACACACACACACACACAAATTGAACCCATACCTTACACCCCA 2124
                         -------    ii  v viv ii-  i   i    v     i     vi 
  L1M4_orf2#LINE/    432 -------CACATGCAAAAGAATG-AAGTTGGACCCCTACCTCACACCATA 473

  chr2_56552984_5   2125 CACAAAAGTTAGTTTCAAATGGATCATAGACCTAAATGTATATGCTAAAA 2174
                         i      i   ii iv          ?             viv       
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_56552984_5   2175 CTATAATAAACTTTTGAAAAAAAAATGTAGGCTCAAGTCTTCATGACATT 2224
                               --    i  - i  i    ii    ?vi  i     i    v  
  L1M4_orf2#LINE/    524 CTATAA--AACTCTT-AGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_56552984_5   2225 GGATTAGGCAAGGGTT-CTTAAATATGACACCAGAAGCACAAGCAAACAA 2273
                           i        v    -    i           i            -   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA-CAA 619

  chr2_56552984_5   2274 AACAAAACAGTCAACAAATTAGAC---ATCAAAATTCAAAATATTTGT-- 2318
                           v    - i vi i     i   ---         v    iv     --
  L1M4_orf2#LINE/    620 AAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_56552984_5   2319 TTTAAAGGAGACTATAAAGAAAGTGAAAAGACAACCCCCAGAGTGGAAAA 2368
                           i      v     v                     v    i   i i 
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_56552984_5   2369 AACTATTTGCAAAGCATATGTCTAATAAAGGACTAGTATATAGCATATAT 2418
                           v          v     i   i    i     v    vi  v      
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_56552984_5   2419 ATAGAACTCT-ACAATTCAACAACAAAACCATAAACAAACCAATTTTAAA 2467
                          v        -    i    i  i    vv i   i  v      ?v   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_56552984_5   2468 ATGAGCAAAGG 2478
                            i       
  L1M4_orf2#LINE/    819 ATGGGCAAAGG 829

Transitions / transversions = 1.48 (86 / 58)
Gap_init rate = 0.02 (19 / 829), avg. gap size = 2.79 (53 / 19)  

 542 10.87 0.00 0.00  chr2_56552984_56556326.rev     2760  2851 (492)    L1M4_orf2#LINE/L1      817   908 (0)  

  chr2_56552984_5   2760 AAATAAGCAAAGGACTTGAATAGAAATTTCTCCAAAAAAGATAAGCAAAT 2809
                             ii        i         v           i      vi     
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_56552984_5   2810 GGCCAAGAAGCACATGAAAAGATGCTTGACATCATTATTAAT 2851
                               v                   ii      ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.00 (0 / 0)  


 331 25.27 0.00 0.00  chr2_56559344_56565741      357   447 (5951)  C L1M4_orf2#LINE/L1   (78)   830   740  

C chr2_56559344_5    447 CTGGTACAGGTCTAATATCCAGAATCTATAAGTAACTTAAACAAGCCAAC 398
                            i  vi  v  vi          v     iv    ivv    vi   i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

C chr2_56559344_5    397 AAGCAAACAACAAATAATTCCATTTAAAAATGGGCAAAGGA 357
                           vv   vi        ii v   ?                
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 0.83 (10 / 12)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.00 (0 / 0)  

2986 26.58 1.09 2.18  chr2_56559344_56565741     4989  5906 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_56559344_5   4989 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5038
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_56559344_5   5039 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5088
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_56559344_5   5089 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5136
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_56559344_5   5137 CATGGAACCA-AAAAAAGCCTGTATTGCCAAGACAATCCTAAGCCAAAAG 5185
                         i      vii-  iii v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_56559344_5   5186 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5235
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_56559344_5   5236 TACATTAACCAAAACATAATGGTACTGGTACCAAAACAGAGACATAGATC 5285
                             v   i   i   vvi         i iv ii i   v i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_56559344_5   5286 AAAGGACCAGAATGGAGCCCTCAGAAATAATACCACACATCTACAACCAT 5335
                           v   vi     v   vvii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_56559344_5   5336 CTGAACTTTGACAAACCTGACAAAAGCAAGAAATGGGGAAAAGATTCCCT 5385
                         i   vi  i     ivv  v   i v  vvv          ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_56559344_5   5386 ATTTAATAAATGGTGCTGGTA-AACTGGATAGGCATATGTAGACAGCTGA 5434
                         v  i  i            v -         ?v  i   i i viiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_56559344_5   5435 AACTGGATCCCTTCCTTACACCTTATACAAAAAT-----CAAGATGGATT 5479
                          ii    i    v   i     v           -----   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_56559344_5   5480 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5529
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_56559344_5   5530 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGTAGGACTTTATGACT 5578
                            ?i- v i -   iv   v v  vv i     - i vvii   -  - 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA-GA-T 594

  chr2_56559344_5   5579 AAAGCACCAAAAGCAATGACAATAAAAGCCAAAATTGACAAATGGGATCT 5628
                          vii           vvii   i     vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_56559344_5   5629 AATTAAACTACAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5678
                         v  i   v vv i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_56559344_5   5679 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACATTTGACAA 5728
                          v  i     i                 v   i   vii i  -------
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT------- 737

  chr2_56559344_5   5729 TCTACCCATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAA 5778
                         -------      i  i  i  vi          v  i        ivv 
  L1M4_orf2#LINE/    738 -------ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_56559344_5   5779 CAAATTTATAAGAAAAAATCAAGCAACCCCATCAACAAGTGGGCAAAGGA 5828
                            v iv    v     iv   ii     v  i? v  i           
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_56559344_5   5829 TATGAACAGACACTTCTCTAAAGAAGACATTTATGCAGCCAACAGACAGA 5878
                          v    i     i     i        i  vi viii     i ii  v 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_56559344_5   5879 TGAAAAAATGCTCATCATCACTGGCCAT 5906
                               i       v     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.50 (30 / 12)  


2272 26.29 5.37 3.15  chr2_56603485_56608767     3927  4782 (501)    L1M4_orf2#LINE/L1        1   875 (33)  

  chr2_56603485_5   3927 TGGAAAAACATCCCATGCTTATGGATTGGAAGAATCAAT---GTTAAAAT 3973
                               i i        i i             v i   ---     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_56603485_5   3974 GTTCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 4023
                          viv     v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_56603485_5   4024 TACCAA-TGTCATTTTTCACATAATTAGACAAAAAATTCTAAATTTAAAA 4072
                          v   i-  i -     ii  v  v v     i-----  i --------
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-----CTGA-------- 136

  chr2_56603485_5   4073 AATTCTAAATTTAACATGGAACCAAAAGAGAGCCCCA---TAGCCAAAAC 4119
                         -- i     v  v i      viiv   i  --    ---          
  L1M4_orf2#LINE/    137 --TCCTAAAATTCATATGGAAATGCAAGGGA--CCCAGAATAGCCAAAAC 182

  chr2_56603485_5   4120 AATCCTAAGCAGAAAGAACAAAGCTGGAGGCATCACATAACCCAACTTCA 4169
                             i i iv ii          i      vv     ivv     i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_56603485_5   4170 AACTGTACTACAAGGCTACAATAA-CACAAACAGCAGGGTACTCATACAA 4218
                           viv        i      i   -  - i    iiv      vii i  
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCA-AGACAGTGTGGTACTGGCATAA 281

  chr2_56603485_5   4219 AAACAGGAACATA-ACCAATGAAACAGAATAGAAATCCCAGAAATAAAGC 4267
                         ii i  iv i   - i     i  i     v  i vi           v 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_56603485_5   4268 GGTATGCCTACAACCACTTAATTTTTGACA-GACTCAACTAAAATAAGT- 4315
                         vi  iiii  iiii  v  i     i    - iv --i i  i iv v -
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGT--GCCAAGACCATTC 379

  chr2_56603485_5   4316 AATGGGGAAA----AG--------ACA----GTGCTGGGATAACTGGCTA 4349
                                   ----  --------   ----         i      v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_56603485_5   4350 TCCATATGGAGAAGAATGAAACTGGACCCCTACC-CATGACTGTATACCA 4398
                         ?   i   v i         ii            -  i-  ii     v 
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC-ACCATATACAA 478

  chr2_56603485_5   4399 AAATTAACTCAAGATGGTTGAAAGACTTAAATGTAAGTCTTCAAAAC-AT 4447
                                     i    v v ?    i          vvi -     -  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTAT 527

  chr2_56603485_5   4448 AAAAATCCTGGGAGAAGACCTAAA---AAATACCCATCTCAATTTTGGCC 4494
                             v  i i i    i  v  ii---    --- v  vii ii    vi
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGT 574

  chr2_56603485_5   4495 TCGGTAAATAATTTAT-GGGTAAGTCCTCAAAAGCGATTGCAACAAAACA 4543
                          v  i  - ii   v -i i  v v vi       ivvv         v 
  L1M4_orf2#LINE/    575 TAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_56603485_5   4544 AAAATTGATTAAGTGGGACCCAATTAAACCAAAGTGCTTCTGCACAGCAA 4593
                             v iiv   i v    iiv  i   viv  ivi   i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_56603485_5   4594 GAGAAACTGTCAACAGAGTAAA----CAACCTACAATATAGAAGGAAGTA 4639
                         ii  v   i    v i   i  ----     i   iv  i i  i  i  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_56603485_5   4640 TTCACAAACTATGCATCCAACAAAGGTCTAATATCCAGAATCTGTAAGAA 4689
                           ii    ii  ii   ii i  i  v  vi          v i   ii 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_56603485_5   4690 ACTTAAACAAATCAACAA-------ACAAAAAACATCATT-AAAACTGGG 4731
                            ivv    v    i  -------     v   viv   -    v    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_56603485_5   4732 CAAATAACATGAAAAGACATGTCTCAAAAGAAGACATATACACG-CCAAC 4780
                             vi iv    v      v    v        i   i v i -    i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_56603485_5   4781 AA 4782
                           
  L1M4_orf2#LINE/    874 AA 875

Transitions / transversions = 1.72 (141 / 82)
Gap_init rate = 0.03 (28 / 875), avg. gap size = 2.61 (73 / 28)  


3051 28.41 0.44 0.44  chr2_56690635_56697031.rev     4998  5905 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_56690635_5   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 5047
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_56690635_5   5048 GGCCATACTGCCCAAGGTAATTCATAGATTCAATGCCATCCCCATCAAGT 5097
                            v     v     iv i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_56690635_5   5098 TACCAATGACTTTCTTCACAGAACTGGAAAAAACTGCTT-TAAAGTTCAT 5146
                          v   iivi i  i  ii     v v  v  i-   v i-    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_56690635_5   5147 ATGGCACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAGA 5196
                             v viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_56690635_5   5197 ACAAAGCTGAAGATATCACACTACCTGACTTCAAACTATACTACAAGGCT 5246
                               i  i  ivv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_56690635_5   5247 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGATCA 5296
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_56690635_5   5297 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACTA 5344
                               i    i--    i  --        vv iii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_56690635_5   5345 TCTGATCTTTGACAAACCTGAGAAAAGCAAGAAATGGGGAAAGGATTCCC 5394
                         vi    i  i     ivv  vv  i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_56690635_5   5395 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCTG 5444
                          v  i  i              v      v  ?i  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_56690635_5   5445 AAACTGGATCGCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGCT 5494
                           ii    i v  v   i     v              i    i    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_56690635_5   5495 TAAAGACTTAGACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACA 5544
                         i ?    i  i ii v   v       i      vi i            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_56690635_5   5545 TACGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5594
                           v ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_56690635_5   5595 ACACCAAAAGGAATGGCAATGAAAGCCAAAATTGACAAATGGGATCTAAT 5644
                                   v vvi    ii    vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_56690635_5   5645 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5694
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_56690635_5   5695 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTA-ATCATCTGACAA 5743
                          i     i   i             v  i    vii -  -      i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAA 746

  chr2_56690635_5   5744 AGGGCTAATATCCAGAATCTACAATAAACTCAAAGAAATTTACAAGAAAA 5793
                         i  i  vi          v  i  vi     vv v  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_56690635_5   5794 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTT 5843
                          i     i     v  i?    i    ii     iv    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_56690635_5   5844 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5893
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_56690635_5   5894 ATCACTGGCCAT 5905
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (151 / 103)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2556 24.44 5.02 3.68  chr2_56715438_56719721     2897  3792 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_56715438_5   2897 TGAAACCATGTCCTGTACTCTTGGATCAGAAGAATTAATATCATTTAAAT 2946
                           i  vv  i   ii ii  v     ii     v       ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_56715438_5   2947 GACCACACTACCCAAAGCAAT----AAA---AATGCGATCTCTATTAAAA 2989
                          i v i   v      vii  ---- i ---  i  i   i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_56715438_5   2990 TACCCACATTATTTTTT----AGAAGATTAGCAGAAAAACCCCAAAACCT 3035
                          -    -ii iii    ----    -   ----  v  i i---i v   
  L1M4_orf2#LINE/    101 T-CCCA-GCTGCCTTTTTTGCAGAA-ATT----GACAAGCT---GATCCT 140

  chr2_56715438_5   3036 AAAGTTCATTTAGAA--GCAAAAAAAAAAAAAGCCCA-AATAGCCAAAGC 3082
                            i     v i   --    iii --------    -          i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGA--------CCCAGAATAGCCAAAAC 182

  chr2_56715438_5   3083 AATCCTGAACATAAAGAACAAAGCTAGAGG-----CATCTC---ACTTCA 3124
                             i    v vi          i i    -----  ii  --- i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_56715438_5   3125 AAATATATTACAAGGCTATAGTAACCCAAACAACATGGTATTGGTATAAA 3174
                            iv  i     i    i     i v i   iii     i   i    i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_56715438_5   3175 GACAGACACATAGATTAATGGAACA---T--AGAGTCCAGAAGTAAATCA 3219
                           i     i      i       i --- --           i    i v
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_56715438_5   3220 GTGTTTTTAC--CCCACTGACTTTTGAGAAAGGTGCCAAGAACAAACACT 3267
                         i iiv    i--i v i   i   i  v  i          v  vv  v 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_56715438_5   3268 GGGCAAAGGTCACCGTCTT--CAATAAGTAGTGCTGGGAAAATGGAATAT 3315
                            v    i-- iv     --   i  i i         v  iv i   ?
  L1M4_orf2#LINE/    383 GGGGAAAGA--ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_56715438_5   3316 CCATATGCAGAAGA-TGAAACAGGACTCATATATCTC-CCAGTATGCAGA 3363
                            i     i    -    iiv    i v  iv  v -   -   i  i 
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA-TATACAAA 479

  chr2_56715438_5   3364 AATCAACTAAAAATGGATTAGAGACTTAAATGTAACACCAAACACTATAA 3413
                            i    v         i ?    i         v v v  v       
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_56715438_5   3414 AACTAGTAGGAGAAAAAAAACTAGAGATAGAGTTAACACTTCAAGACATT 3463
                             vv   ----  i     -----    i?v   vv    iv   v  
  L1M4_orf2#LINE/    530 AACTCTTAG----AAGAAAAC-----ATAGGNGTAAATCTTCGTGACCTT 570

  chr2_56715438_5   3464 AGTGTAAGCAAAGATATCATGGCTAAGAGCTAAAAAGCACAG---ACAAA 3510
                         i vv  i    v i v  v i v  v  vviv         i---     
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_56715438_5   3511 CCTAACAAAAGTAGACAGATGGGACTACATTAATCTAAACAACTTCTGGC 3560
                         --- iv    i    i i  v     v   i  vv v  v     i  vv
  L1M4_orf2#LINE/    621 ---AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_56715438_5   3561 CAGCAAAGAAAACAATCAACAGGGTGAAGAAACAACTTGTTGCATGGGGG 3610
                          vv     i v  v     v ii     i i     iiiiv v     i 
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_56715438_5   3611 AAAATATTTGCAAACTATTCATCCAAAAAGGGACTAATATCCAGAATATA 3660
                                       ii  vi   ii v        vi             
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_56715438_5   3661 TAAGAAAC----ACAAA-CAATG-TGAAAAACCAAATAATTCCATTAAAA 3704
                            ii   ----    v-    i- i    iv       ii v   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_56715438_5   3705 AGTGAGCAGAGGGCATGGATAGACATTTCTC---AAAAGACATCCAAATA 3751
                          i  i   i   iiv  i             --- i    i  v     i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_56715438_5   3752 TGCAAAAGGCACATGAAAAAATGCTCAACATCACTAGTCAT 3792
                         vv   v i           i             ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (135 / 80)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.69 (78 / 29)  


3220 26.54 0.77 0.77  chr2_56770274_56776678.rev     5006  5913 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_56770274_5   5006 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5055
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_56770274_5   5056 GGCCATACTGCCCAAGGTAATTCATAGATTTAATGCCATCCCCATCAAGC 5105
                            v     v     iv i  ii i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_56770274_5   5106 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5153
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_56770274_5   5154 TATGGAACCAAAAAAGAGACC--GCATCGCCAAGTCAATCCTAAGCCAAC 5201
                                -- viv   i    -- v  v     iv     i i ivv iv
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_56770274_5   5202 AGAACAAAGCTGGAGGCATAACACTACCTGACTTCAAACTATACTACAAG 5251
                                  i      vv v     v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_56770274_5   5252 GCCCCAGTAACCAAAACAGCATGGTACTGGTACCAAATCAGAGATATAGA 5301
                           iv      i   i    ii         i iv iivi   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_56770274_5   5302 CCAATGGAACAGAAC--AGAGCCCTCAAAAATAATGCCACATATCTACAA 5349
                         i        i    i--    i  -- i      vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_56770274_5   5350 CTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5399
                         ii vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_56770274_5   5400 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5449
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_56770274_5   5450 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5499
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_56770274_5   5500 GATTAAAGACTTAAATGTTAGACTTAAAACCATAAAAACCCTAGAAGAAA 5549
                            i ?    i       v   vi      i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_56770274_5   5550 ATCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGGCTTCATGTC 5598
                          iv    ?i- v i -   iv   v v  vv i     v  i   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_56770274_5   5599 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5648
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_56770274_5   5649 TAATTAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTACCATCAGAGTG 5698
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_56770274_5   5699 AACGGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCGACTCATCTGA 5748
                           vi i     i                 v       viv ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_56770274_5   5749 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5798
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_56770274_5   5799 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAC 5848
                             i     i     v  i?    i     i     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_56770274_5   5849 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5898
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_56770274_5   5899 ATCATCACTGGCCAT 5913
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2119 24.27 7.94 6.38  chr2_56832619_56836145     2142  3035 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_56832619_5   2142 TGGTGAGATGTATCAAGTTCTTGCATTGTAAGTTTTACCGTTGTTGAGCT 2191
                            vi    i vi  v    v  v    v   vi   vii     i  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_56832619_5   2192 ATCAAT-CTCCCTAAATCAGTTCATAGTTTCAATGTAATCCTAACTAAAA 2240
                         iv    -     i    iii ii i  v     i i     iv ii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_56832619_5   2241 TCCCTGCAGGCTGTTGTTTGGGGAGGATGGCAGTACTTGCTAACTAGATT 2290
                             ----i    iiv   -------- v    v v   vi  viv   i
  L1M4_orf2#LINE/    101 TCCC----AGCTGCCTTTT--------TTGCAGAAATTGACAAGCTGATC 138

  chr2_56832619_5   2291 CTAAAATGTATATGGAAACACAAAGGATCTAGAATAGGCAAAA-ACGTTT 2339
                                vi         ii   i   i i       v     - vvi  
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr2_56832619_5   2340 GAAAAAGAAGAAAAAAG----AGCACTTACACTATCTGACTTCCAAACTT 2385
                                     v    ----  v   i     vi ii i   v      
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_56832619_5   2386 ATTATAAAGCTAGTATAATATGGATATTGTGGTTTTGCTTTAAAAAATGG 2435
                          i  i       vvi    vvi  i v      ------------ v   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGT------------ACTGG 276

  chr2_56832619_5   2436 CACTAAAGGCAAATATCAATGTCAGTGTGACATAATAGAGATTCCAGAAG 2485
                           -   i ii i i  vv vi   i  vi i v   v    v       i
  L1M4_orf2#LINE/    277 CA-TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_56832619_5   2486 TAAACCCAAACATATTAATAATAATACTTAATAAATGATCAACTGATTTT 2535
                                 v    --------------   -----  i    i       
  L1M4_orf2#LINE/    326 TAAACCCATACAT--------------TTA-----TGGTCAATTGATTTT 356

  chr2_56832619_5   2536 TCACAAGCATATTGAGGCAATTCAGTGGGGAAA--ATA-CCATTTTAACA 2582
                         iv     vi iiii  i v     i        --   -i v   i    
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_56832619_5   2583 AATTTTTGCAGGAAATATTGAATAACCACATGAAAAACAA--AACCTCAA 2630
                            vv -  v  i vv i  i   ?       v    v  --  vi vi 
  L1M4_orf2#LINE/    407 AATGGT-GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_56832619_5   2631 CACATATTTTATTTCATATTTTTAAAAACCT-CTCAAAATAGATCATAGA 2679
                          v v  ii i ivi     vi--     iiv-        i     ?   
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATAC--AAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_56832619_5   2680 TTTACTTGTATGTAAGAGCTAAAGGTATAAAACTCCCAGATAAACGTATG 2729
                         ii  v----              iv          ii   vi  vii  i
  L1M4_orf2#LINE/    504 CCTAA----ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_56832619_5   2730 GGAG-----------------GAGTT-GGCAAAGATTTATTAGCTACAAT 2761
                           ? ----------------- i   -     v i   v    v  ii i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_56832619_5   2762 ACCCAAAGCACAATC--CAAAG-----------TAAATTGGACTTCAT-A 2797
                            v         v --    i-----------               - 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_56832619_5   2798 AAATTAAAATATTTTCCTTTTCAAA--ATGCT--CAAAATGAGAATGAAA 2843
                                  vv    vivi      -- ii  --   ---  i i     
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA---GAAAGTGAAA 696

  chr2_56832619_5   2844 TTGTCAGCCACAGACTGGGGAGAAGATGTTTGCAAAACTTATATCTGACA 2893
                         vviiv v       v    -    i  i        v v         i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGG-AGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_56832619_5   2894 AATGACTGCTCTGTAAACTGTATTAGGAATTTCTATAACT---TAATAAG 2940
                          iv    vv v vi i v i   v i   i ii  i    ---      i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_56832619_5   2941 AACACA-------CAA-----AAATGGGCAGAAGATCAGAAGAGA--TTC 2976
                           v   -------   -----         i i   iv   v   --  i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_56832619_5   2977 CTTACTAAAGAAGTGATA------ACAAATAAGCACATGAAAAAATGCTC 3020
                           -- i       vv   ------i v                i      
  L1M4_orf2#LINE/    846 CT--CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_56832619_5   3021 AACATCATTAGACAT 3035
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (122 / 92)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 4.13 (128 / 31)  


3182 26.07 0.99 1.64  chr2_56862929_56865192.rev      860  1772 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_56862929_5    860 GGAAGAACATTCCATGCTCATGGATAGGAAGAATCAACATTGTGAAAATG 909
                             ii i  i     i        v      v i  i     v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_56862929_5    910 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 959
                           v     v      v i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_56862929_5    960 ACCAATTATTTTCTTCACAGAA-TTGGAAAAAACCTACTTTAAAGTTCAT 1008
                         v   ii iii  i  ii     -   -- v  i iv iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_56862929_5   1009 ATGGAACCAAAAAGAGCCC-GTATTGCCAAGACAATCCTAAGCCAAAAGA 1057
                               viiv  i ii   - v  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_56862929_5   1058 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAAGGAT 1107
                               i      vv    i  v  ii i      vivi       i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_56862929_5   1108 ACATTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAAAA 1157
                            v   i   i    ii         i iv ii i   v       vv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_56862929_5   1158 ATGGAACAGAAC--AGAGTCCTCAGAAATAATACCACACATCTACAGCCT 1205
                               i    i--       --        vv   i    i  ii i v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_56862929_5   1206 TCTGATCTTTGACAAACCTGACAAAATGAAACAAAAACAAGAAATGGGGA 1255
                         vi    i  i     ivv  v   i i----------  vvv        
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGAC----------CATTCAATGGGGA 387

  chr2_56862929_5   1256 AAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCTTATG 1305
                            i  vvi  v  i  i              v      v  ?  vi   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_56862929_5   1306 TAGAAAGCTGAAACTGGATCCCTTCCTTATATCTTATACAAAAATTAATT 1355
                         i i  iiv    ii    i    v   i i i v              i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_56862929_5   1356 CAAGATGGATTAAAGACTTAAATGTTAGACCTAAAGCCATAAAAACCCTA 1405
                            i      i ?    i       v   v     i i      vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_56862929_5   1406 GAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGATT 1454
                                  v    ?i- v i -   iv   v v  vv i     v i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_56862929_5   1455 TCATGTCTAAAACACCAAAAGCAATGGCAATAAAAGCCAAAATTGACAAA 1504
                           v ivv  vi            vvi    i     vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_56862929_5   1505 TGGGATCTAATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTACCAT 1554
                          v   ii v  i   viv  i i   i  ii vv    i  v    i  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_56862929_5   1555 CAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACC 1604
                         v i      v  i     i                 v   i   vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_56862929_5   1605 CATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTC--A-AACTT 1651
                         i      i  i  i  vi          v  i  v      -- -    i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_56862929_5   1652 A-CAAGAAAAAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAA 1700
                          -i  v     i     i     v  i? v  i            v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_56862929_5   1701 CAGACACTTCTCAAAAGAAGACATTTATGCAGACAACAGACACATGAAAA 1750
                         i     i     v        i  vi viii v   i ii          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_56862929_5   1751 AATGCTCATCATCACTGGCCAT 1772
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 2.18 (24 / 11)  


2470 28.12 2.23 1.00  chr2_56994126_56999635.rev     4129  5024 (486)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_56994126_5   4129 GGAAAAACATTCCATGCTCATGCATAGGAAGAATCAATATTGTTAAAATG 4178
                              i i  i     i     v  v      v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_56994126_5   4179 GCTATACTGTCAAAAGTAAATTACAGATTCAATACTATTCCTATAAAACT 4228
                           v     vi v   v i vi           ii v  i     v   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_56994126_5   4229 ACCAATGACATTTGT--CAGAGAATTAGAAAAAAACTTCTAAAATTCAAA 4276
                         v   iivi v   v --    -    iiv  ivviv i          v 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_56994126_5   4277 AGGAACCCAAAAAGTGCCTGAATAGCGAAAGAAATCCTAAGCAGAAAGAG 4326
                         v    vivv  ii vv  v       v   iv    i i iv ii    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_56994126_5   4327 CAAAACTAGAGACATCACACCATCTGACTTCAAGCTACACTGCAAGGATA 4376
                             ii i   ivv      ivi ii i     ivivi   i   i v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_56994126_5   4377 CGGTAAACAAAACAACATGGTACTGGTATAAAAATAGACATATAGACCAA 4426
                          i    v   i   iii         i    ii             i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_56994126_5   4427 TGAAATAGGTTAGAGAATC-AGAAATAAAGCCACATACCTATAACCATTT 4475
                           i     iv v    i  -         v   i i ii   iii  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_56994126_5   4476 GAAGTTTGACAGGGTCAACAATAACAAACAATGGAGAAAGGACTCCCTAT 4525
                           vv  i    i  viiv   v v  vv      i     i ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_56994126_5   4526 TCAATGAATGGTGCTGGGATACCTAGCTAGCCATATACTGAAAATTGAAA 4575
                             ii             i v  i v  ?   i  i vi  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_56994126_5   4576 CTGGACTCTTTCCTTACATCATACACAAAAATCAACTCAAGATAAATTAA 4625
                         i     i i v   i   i    i        i       i  ii  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_56994126_5   4626 AGACTTAAATGTAAAAGCTAAAACTATAAAAACCCCAGAATAAAAGCTAG 4675
                             i         i                vi ii    v    vv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_56994126_5   4676 A---AAATACCATTCTGAACACAGGCCCTAG-CAAAGATTTTAT-GATGA 4720
                         i---    -- v iv   v vii  i--   -   v i   iv -   - 
  L1M4_orf2#LINE/    551 GNGTAAAT--CTTCGTGACCTTGGGT--TAGGCAATGGTTTCTTAGAT-A 595

  chr2_56994126_5   4721 AGACTCCAAAAGCA------ACAAAAACAAAAATTTACAACTGGGAACTA 4764
                         v   v         ------      iv      vv i  v v   vi v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_56994126_5   4765 ATTAAACTAAAGAGCTTTCCACACAGCAAAAGAAACTATCAACAGAGTAA 4814
                           i   v v  i i    i-iii vv    i  v        v i   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_56994126_5   4815 ACAGGCAATCTACAGAATTACAACAAATATTTACAAACTATACATTCATC 4864
                          v  i   i i       viv iv        i    ii   i  iiivi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_56994126_5   4865 AAATG---TATATCAAAAATCTATAAGGAGCTTAAAGAAATCAACAAACA 4911
                           iv --- i    v i   v     i  i  ivv v  v    i  -i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TA 793

  chr2_56994126_5   4912 CAAAAACGAATATCCCCATTTAAAAAATGGGCAAAGGACATGAACAGACA 4961
                         v   i  i    v   v   ?     -           iv    i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chr2_56994126_5   4962 CTTATCAAAAGAAG-CATACAAGTTGCCAATAA--ACAAGAAAAAATGCT 5008
                         i  v  v       -i      i v        --   v     i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_56994126_5   5009 CAACCTCCCAAATCAT 5024
                             v  v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (145 / 104)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 1.81 (29 / 16)  


2219 30.19 1.80 2.13  chr2_57015504_57018723     1830  2720 (500)    L1M4_orf2#LINE/L1        1   888 (20)  

  chr2_57015504_5   1830 TGGAAAAACCATTCCATGATAATGCATAGGAAGATTCAATATCACTGAAA 1879
                               i i-  i     v v   v  v      i i     iii i i 
  L1M4_orf2#LINE/      1 TGGAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_57015504_5   1880 TGATCATACTGTAAAAAGCAATTTACCAATGCAATGCTATTGCTATCAAA 1929
                           iiv     vivv   vii  i   vi  v   i  v  iv        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_57015504_5   1930 ---CTAATGACATTCTTCACAGAACTAGA-AAACTCTATTTTAAGATTCA 1975
                         --- i iivi v  i  ii     v v  -  i  v-  ii   i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCA 148

  chr2_57015504_5   1976 TATTGAA-TG--AG---CCCA-AATAGCCAAGGTAATCCTAAGTAAAATG 2018
                            v   -  --  ---    -         iii    i i iv  i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_57015504_5   2019 AGCAAAGCCAGAGGCATCACACTATCTGACTTCAAACTATATTACAGGGC 2068
                          i     iii    vv       vi ii i      viv  i    ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_57015504_5   2069 TACAGTAACCAAAACAGCATAATACTGGTACAAAAACAGAAACATAGACC 2118
                                 i   i    ii ii      i i  ii i   v i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_57015504_5   2119 AAAGGGACAGAAA-AAAAGCCCAGAAATAAGGCCATACACTTAAAACCAC 2167
                           v  i i    v-i i  i          iv       i   viii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_57015504_5   2168 CTGATCTTTGACAAAGCCGACAAAAACAAGCAATGGGGAAAAGACTGCCT 2217
                         i    i  i     i vi v   i v  vv           ii iv i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_57015504_5   2218 ATTCAATAAATGGTGTTGTGATAACTGCCTAGCCATATGCAGAAAATTAA 2267
                         v     i        i  v  i     vv  ?   i     i  i v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_57015504_5   2268 AACTGGACTTCTTACTTACACTATTTACTAAGATCAACTGAAGAGGGAAT 2317
                          ii     ii  vv  i    i  v   v  i  i    v  i v   vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_57015504_5   2318 AAAGAATCAAA---AAACCCCAAAACTATAAAAACTCT-GGAAGACAACC 2363
                          ?   vii   ---  ivv i            -    -i     v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr2_57015504_5   2364 TGGGCAATACTATTCTGGACATAGGAACTGGCAAAGATTTCATAACGAAG 2413
                          i  ?ivv v v   vv   v v  iviv     v i    v  ivv v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_57015504_5   2414 ATGCCAAAAGCAATTGCAGCCAAAAGCAATTGCAACCAAACAAAAATGGA 2463
                          ii         --------   --    ---   --  iv      i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCA--------CAA--GCAA---CAA--AAGAAAAAATAGA 632

  chr2_57015504_5   2464 CAAATGAGGTCTAATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTA 2513
                         i    vi iii v  i   v v  i i   i  ii vv       v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_57015504_5   2514 TCAACAGAGTAAGCAGAAAATCTACACGATGGGAGAAAATAACAGCAAAT 2563
                             v i   i iv   v  i i   vi             viv      
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_57015504_5   2564 TATGCATCCATCAAAGGTCTAATATTCAGAATCTGTAAGGAATGTAAACA 2613
                         i  ii   iivi  i  v  vi   i      v i   i   ivivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_57015504_5   2614 AATTTACAAGAAAAAACCGAAAGAACCCCATTAAAAAGTGGGTAAAGGAC 2663
                          v iv i  v     iv -   v     v   ?    i    i      i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_57015504_5   2664 ATAGAGAGAAACTTTTCAAAAGAAGACATACATGCAGCCAAGAAGCATAT 2713
                         v ii v   v i  i  v        i     viii     v     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_57015504_5   2714 AAAAAAA 2720
                         i    i 
  L1M4_orf2#LINE/    882 GAAAAGA 888

Transitions / transversions = 1.57 (162 / 103)
Gap_init rate = 0.02 (17 / 888), avg. gap size = 2.06 (35 / 17)  


3331 26.24 0.55 0.88  chr2_57079537_57083712.rev     2778  3684 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_57079537_5   2778 AAAAAATTCCATGTTAGTGGATCGGAAGAATCAATATTGTTAAAATGTTC 2827
                           i v  i       vi     i      v i           i   viv
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_57079537_5   2828 ATACTACTCAAAGCAGTCTACAGATTCAACGCAATCCCTACCAAAATACA 2877
                              v i    viii                        i      v v
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_57079537_5   2878 AATGATATTCTTCACAGAAACAGAAAAAACAATCCTAAAGCTTATATGGA 2927
                          iiviiv  i  ii      iv  v  ivii        ii i       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_57079537_5   2928 ACTACAGAAGACCCAAAATATCCAAAGCTATCCTAAGCAAAAAGAGCAAA 2977
                          v i  iii      i    v     i v   i i iv  i    i    
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_57079537_5   2978 ATTAGAGGAATCACATTACCTGACTACAAGTTATACTATAA-GCTACAGT 3026
                         i  i     v     i v  ii i v   iviv     i  -        
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_57079537_5   3027 AACCAAAACAGCATGGCACTGGCATAAAAACAGACATATAGACCAATGGA 3076
                           i   i    ii   i          ii i           i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_57079537_5   3077 ACAGAAGAGAGAACCCACAAATGAATCCACATGCCTATAGTGAACTCATT 3126
                          i    vv    ii   v    i  i   i iiii   i  v  i v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_57079537_5   3127 TTTGATGAAGATGCCAAGAACACACACAGCGGAAAAGACAGTCTCTTCAA 3176
                           i  ii i i        v  iv  vv v     ii i     i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_57079537_5   3177 TAAATGTTGCAGGAAAAACTGGATATTCATATACGGAAGAATGAAACTAG 3226
                         i     v   v  i v         ?i  i  i ii         ii i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_57079537_5   3227 ATCCTTATGTCTCACCATATACAAAAATTAAATCAAAATGCATGAAAGAC 3276
                          i  i  iv  v                   v        v  v ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_57079537_5   3277 TTAAACCTAAGTTTTCAAACTATGAAACTACCACAAGAAAACACTGGGGA 3326
                         i    iv    vvi v       i     vii v         iv  ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_57079537_5   3327 AAACCTCCAGGACATTGGTCTGGGCAAACGTTTTTTTAG-TAATACCCCA 3375
                            i  i iv   v    vi i     -i v   i    -  vv  v   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCA 603

  chr2_57079537_5   3376 CAAGCACAGACAACCAAAACAGTAATGGACAAATAGGATTACATCAAG-T 3424
                         v       ii    v   iv iv   i  i    v   i v      i- 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_57079537_5   3425 TAATAAGCTTCTGCAAAGCAAAGGATACAATCCACAAAGTGAAATGACAA 3474
                            -  i   i  iivvv       i  v   v v         v     
  L1M4_orf2#LINE/    654 TAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_57079537_5   3475 CTCATAAAATGGGAGAAAATATTTGCAAACTACGAATCTGACAAGGGATT 3524
                          i  i i                      ii iiv      i      i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_57079537_5   3525 AATAACCAGACTATGTAAGGAGTTCAAACAACT--GTGAAGGAAAAACAA 3572
                         vi  v     v   i   i  ii  vv      --i i vii   i    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_57079537_5   3573 AATCTAATAATCTGATCAAAGATTGGATAAAAGATTTAAATAGATGTTGC 3622
                          ------   i ii  i?  i v   ii   i     i      ii  v 
  L1M4_orf2#LINE/    803 A------TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_57079537_5   3623 TCAAAAGAAGACATACAAATGGCAAACAGGCAAATGAATAGTTGTTCAAC 3672
                           v        i           v  i i   v     v  v  i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_57079537_5   3673 ATCACTGATCAT 3684
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (151 / 83)
Gap_init rate = 0.01 (7 / 904), avg. gap size = 1.86 (13 / 7)  


2800 27.83 1.21 1.54  chr2_57087508_57092274.rev     3367  4275 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_57087508_5   3367 GAAAAACATTCCATACTCATGGATGGAAAGAATCAATCTCATTACAGTGG 3416
                             i i  i    ii        v i    v i   v ii   vii   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_57087508_5   3417 CCATACTGCCCAAAGCGATTTATGGATTCAATGCAATTGCTATCAAACTA 3466
                          v     v      vi   i  ii       i     iv        v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_57087508_5   3467 CCAA-TGTCTTTCTTCACAGAACTTGAGAAAACT-ATTTTAAAATTTATA 3514
                            i-  i    i  -i     v    v  i-  -  ii       i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr2_57087508_5   3515 TGGAAGTAATAAAGAGCCAGAATAGCCAAGGCAATTCTAAGTAAAAAGAA 3564
                              i ivv ii  v             ii    ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_57087508_5   3565 CAAAGCAGGAGAGCTCGTGTTACTTGACTTCAAAATATATTACAGGGCTA 3614
                              iv    ii   iiii v iii i       iv  i    ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_57087508_5   3615 CAGCAACCAAAACAGTACCATTCTGGTACAAAAATAGACACATACACCAA 3664
                            i  i   i     iivi v    i i  ii       i   v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_57087508_5   3665 TGGAACAGAGTAGAGAGCCCAGAAATAAAGCTGTACAACTACAACCATCT 3714
                              i   i v     i           v ii    vi  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_57087508_5   3715 GATCTCCAA-AAGAGCTGACAAAAACAAGCAATAGGAAAATGACT--CCC 3761
                            i i i -   i -  v   i v  vv    i  i   -  v --i i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGAAA-GAATAGTCT 398

  chr2_57087508_5   3762 TATCAAATAAATGGTTCTGGGATAACTGTTTAGCCATATTCAGATGGTTG 3811
                          v    -i       v      i     vv  ?   i  v  i v iv  
  L1M4_orf2#LINE/    399 TTTCAA-CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_57087508_5   3812 AACTTGGATATCTTTCTTCCACTATATACAAAAATCAACTCAAGATGGAT 3861
                           v     ivi  vi  iv   i            i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_57087508_5   3862 TAAAAACTTATATGTAAAACCAAAAACTACAAAAACCTT-GAAGACAACC 3910
                         i ? i  i  v      i v v       i    vi   -     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_57087508_5   3911 TAG---TCAATACCATTCTGGTCATAGGAACAGGCAAAGATTTCATGACA 3957
                            --- v   -- v iv  ii v i  v-i      v i    v iivv
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--CTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_57087508_5   3958 AAGACACCAAAAGT-CATTGCAAAACAAAGCAAAAATTGACTAATGGGAT 4006
                          v           i-  v-    v -    v      v  iv   v   i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA-GCAACA-AAAGAAAAAATAGATAAATTGGAC 642

  chr2_57087508_5   4007 CCAATTAAACTTAAGAGTTTCTGAAAAGCAAAAGAAGCTATTAACAGAGT 4056
                         iiv  i   v    i ii  i  vivvv    i  vi    i  v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_57087508_5   4057 AAACAGACAATCTACAGAATGAGATAATATATTTGCAAATTATGTGTCCA 4106
                         i  v      i i        i  v  v            i  i i  ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_57087508_5   4107 ACAAAGGTCTAATATTTAGAATCTATAAGGAACTTAAAGAAATTTACAA- 4155
                          i  i  v  vi   ii     v     i     ivv v  v iv i  -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_57087508_5   4156 AAAAAAATTACCAAACAACTCCATTAAAAAGTGGGCAAAGGATACAGACT 4205
                              i ----    i   i v   ?    i            viii iv
  L1M4_orf2#LINE/    793 AAAAAGA----CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_57087508_5   4206 GACACTTTTCAAAAGAAGACATACATGCAGCCAACAACCATATGAAAAAA 4255
                             i  i  v        i     viii     i  v  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_57087508_5   4256 AGCTCAATATCACTGATCAT 4275
                         v      i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (160 / 90)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 1.39 (25 / 18)  


2484 28.46 2.33 1.77  chr2_57149535_57151561      652  1554 (473)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57149535_5    652 TGGAGAAGTATTTCATATTCATGAATAGGAAGACTCAATATTGATAAGTT 701
                             i ii   ii   i      i  v        i       v    v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57149535_5    702 GTCAATTCTTCACAACTTGATCTGTAGATTCAATGCAATGCCACTCAAAA 751
                          v    v  i v   v       ii        i     v  vv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57149535_5    752 TACCAGGAAGTTATTTTGTAGATATCAACAAATTGATTTTACAGGTTATA 801
                          v    vvivi v     i   v  ii    ii    ii  v iv i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_57149535_5    802 TGGAGAAACCAAAGACCTGGAATAGTGAACGCATTATTGAA------GAA 845
                             i vi v ii    ii      iv  vi  v v     ------   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_57149535_5    846 CAAAGTTGAAAGAGTAAGACTACCAAATTTCAACACTTATGATAAAGCTA 895
                                 i i  v v v   v  v        v     iv i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_57149535_5    896 CAGTAGTTGAGATAGTGTGATATTGGTG-AAGAATGGGAAAA-AAA--AA 941
                              i ii   i      i  i   ii-   i  i iv v - i --  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_57149535_5    942 TGGAGGAGAATAGAGAGCCCAGAGAAAAACCTACATAAATACAGTCA-CT 990
                             iv     v     i     i v     i i i vv  ii    -i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_57149535_5    991 GATAGTTGACAAAGGAACAAAGTTAATACAATGAAACAAAGATAACCTTT 1040
                            vv i     i  vi v   viv  v     iiiv  ii   ii    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_57149535_5   1041 TCAAGACATGGTTCTAAAACAATTGGAAATCCACAAGCCAAAAAAAAAAA 1090
                             v v     v  iii    i    v ?     v  v   i  vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_57149535_5   1091 TCTAGACACAGACCTTATATCTTCCACAAAACTTAATTCAAAATGGATCT 1140
                          - i   v vv    i i i v vi      v    i            v
  L1M4_orf2#LINE/    451 T-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_57149535_5   1141 TAGGCCTAAGCGTAAAA-C--AAGTTGTACCACTCT---AAGAAAATTAT 1184
                         ?  i     ii    i - --  ii i  vv     ---       i-  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC-AT 548

  chr2_57149535_5   1185 TGGAGAAAATCTAGATAACCTTGGATATAGTGATGACATTTTAGATACAA 1234
                         v  ? v      vvi i       i vvi ii   iiv i       ii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_57149535_5   1235 CACCAAGGGCATGATCTATCAAAGAAATAATAGATAACCTGAACTTTATT 1284
                               ii   ii v v iv       v         vi  i    i  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_57149535_5   1285 AAGAATTTAAAAGCAAACTCATGCTCTATGGTAAACAATGCTAAGAGAAT 1334
                           i --      i v--i ii    ii vi --i   v iii    i i 
  L1M4_orf2#LINE/    649 AAAA--TTAAAAACT--TTTGTGCTTCAAAG--GACACTATCAAGAAAGT 692

  chr2_57149535_5   1335 AAAAAGACAAGCCACAGAATGGGAGAAAATATTTCCAAAGGACACATCTG 1384
                         i         v                       v    vv i i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_57149535_5   1385 ATAAAAAACTGTTATCCAAAAAGTACCAA-AACTAGTAACACCTCAACAA 1433
                             iii   vv      i  vi  iv  -    vv  -  v     i  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAA 791

  chr2_57149535_5   1434 TATGAAAACAAAAATCCTAAT-GAAAATTCGACCTAAAACCTTAACATAC 1482
                           vi  i     v v  i   -?    v v i vv ii ii v  i v  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_57149535_5   1483 ACTTCATTAA-GAAAACAGACAGATGACATATAGGCATATGAAAAGTGAA 1531
                          i   vii  -   i i v   i   i vv   i   i        ----
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG---- 887

  chr2_57149535_5   1532 CCTATG-TCATCAGCAAAATGTAA 1554
                         ---   -   v  v  ????????
  L1M4_orf2#LINE/    888 ---ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (150 / 103)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.95 (37 / 19)  


2995 26.50 1.67 0.56  chr2_57194058_57198608.rev     3162  4059 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57194058_5   3162 TGGAAAGATATTCCATGTTGATGTATTGAAAGGATAAATATTGCTAAAAT 3211
                                    i       v   v    i   iv v       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57194058_5   3212 GTCCTTACTAACCAAAGAAATCTACAAATTCTGTGTAATTCCTATCAAAC 3261
                          v vv    vv     vvi       i    vii i   i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57194058_5   3262 TACCAAAGACATTCTTCACAGAAATAGATGAAACAATCCTAAACTGTATA 3311
                          v   ivvi v  i  ii       v  ii ivii        v vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_57194058_5   3312 TAGAATCACACAAGACCCAAAATAGCTAAAGCTATCCTGAGCAAAATGAT 3361
                          i   vii  vii      i      i   i v   i   iv  i v  v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_57194058_5   3362 CTAAACTGGAAGAATAACATTGCCTGATTTCAAACTGTACTACAGAGCTA 3411
                          v  ii    i  v v   i v  ii        viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_57194058_5   3412 TAGTAACCAATACAGTATAGCATTGGCATCAAAACAGTCACATAAACCAG 3461
                         i     i   v     i i i i      v ii i  v  i   i i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_57194058_5   3462 TTCAACA-AACAGAGAACATGAAAACAAATTCATACCCATATAATGAACT 3510
                          vv  i -  iv    iiviii   i   ii     viv   ii v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_57194058_5   3511 CATTTTTCACAAAGCTTCCAAAAACATACACCTG--AAAGAACAGTCTTG 3558
                         v     iv    i v v    i v   v  viv --      i      v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_57194058_5   3559 TCAGTGAATAGTGCTGGGAAAGCTGCATAACCATATGCAGAAGAATGTAA 3608
                            iii   i         v i   v   ?   i     i       v i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_57194058_5   3609 CTTGATCCCTATCTCTCTCACCTTATATAAAAATCAAATCATAATAGATT 3658
                         i v  i     i   v --   v    i      i  v   v   i   i
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCAC--ACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_57194058_5   3659 AAAGGTTTAAATGTAAAACCTTAAACTATGAAACTACTATAAGAAAACAT 3708
                          ?  iii         i v  v       i     vi  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_57194058_5   3709 TGGAGAAACTCTCCAGGACATTGGTCTTGGCAAAAATTTCT-AGA-ATAA 3756
                         v  ? v  v   i iv   v    vi v     vii     -   -  i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_57194058_5   3757 TACCTCAACGGCACTGGCAACCAAAGCAAAAATGGGCAAATTGGA----- 3801
                         i   --  vi    vi     v    v      i ii        -----
  L1M4_orf2#LINE/    599 CACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_57194058_5   3802 TCAAG--TCAAAATATTTCTGCATAAAAGGGAAACAAGCAACAAAATGAA 3849
                             i-- v    iv   v   v v     - v  v v   v   i    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGG-ACACTATCAAGAAAGTGAA 695

  chr2_57194058_5   3850 GACACAACCCACAGAATGGGAGAAAATATTTGCAAACTACCCATCTGACA 3899
                         i v                                 ii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_57194058_5   3900 AGGCATTCATAATCAGAATATATAAGGAGCTCAAACAACTCTACAGGAAA 3949
                            v i ii  vi            i  i   vv       v i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_57194058_5   3950 AAATCTAATAATCCAATT-AAGTATGGTCAAAAGATTTGAATAGCTATTT 3998
                           iv v     i      -  iv    v    i           vi    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_57194058_5   3999 CTAAAAAGAAGA-A-AAAAATGGCAAACAGGCATATGAAAAAGTGCTCAA 4046
                           vv        - - v       v  i i   i       ii       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_57194058_5   4047 CATCATTGATCAT 4059
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (133 / 102)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


3047 25.22 1.42 2.29  chr2_57237017_57241281.rev     2858  3773 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57237017_5   2858 TAAAAAGATATTCCATGTTAATATAGTGGAAGAAACAATATTGTTGAAAT 2907
                          ii        i       v  iv v       vvi         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57237017_5   2908 TTCTATACTCCTCAAAGTAAACTACAGATTCAAAGCAATTACTTTCAAAA 2957
                         vv v       i    v i v            v     iv  v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57237017_5   2958 TACCAATGACATTCTTCACAGAAATAGAAAAA---ACTCCCAAATTTATA 3004
                          v   iivi v  i  ii       v  v  i--- ii iv     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_57237017_5   3005 TGGAAC--CAAAAGACACAGAATCATCAAAGCTATCCTGAGCAA-AAGAA 3051
                              v--   ii   v      vii    i v   i   iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_57237017_5   3052 CAAAATTGAAAGAATAACATTACCTGACTTTAAGTTATGCTACAAAGCTT 3101
                             i   i i  v v   i v  ii i  i  iviv i          v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_57237017_5   3102 TAGTAACCAAAAGAGCATGGCACTAGCATAAAAACAGCAACATAGACCAG 3151
                         i     i   i v  ii   i   i      ii i  vv i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_57237017_5   3152 TGGAACAGAACAGAGAA--CTGAAACAAATCCACATACTTACAGTGAACT 3199
                              i    iv    i-- v    i   i   i i i   ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_57237017_5   3200 CATTTTTGACAAAGGTGTCAAGAACATCTACTGGAAAAAAAACAGTCTCT 3249
                         v     i     i    i     v   ii v   ii   i  i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_57237017_5   3250 TCAATAAATGTTTTTCGGAAAACTGGATGTCCATATAAAGAAGAATGAAA 3299
                             i     v vi v   v        i?   i  iv i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_57237017_5   3300 CTAGACTCCTATCTCTCACCATGTACAAAAATCAA-TCAAAATGGTTTAA 3348
                         i i   i    i   v      i         i  -         v i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_57237017_5   3349 GGACTTAAATGTGAGACCTCAAATGAAAAAAAAAAAACAAAACACACTAC 3398
                         i   i       i   v  -----------    vv i     v -i  -
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCT-----------AAAACTATAAAACTC-TTA- 537

  chr2_57237017_5   3399 AAAAAAAACATGTGGG-AACTCTCCGGGATATCGATCTGGGCAACAATTT 3447
                         i  i       iv ? -  v   i  v  iv i ivi i     iii   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_57237017_5   3448 CTTGAGCAATAAC-CTACCAGCACAGGCAACCAACCAAAGCAAGAATGGA 3496
                            -  vv  i  - i vv      i     -  ---   v  i   i  
  L1M4_orf2#LINE/    588 CTT-AGATATGACACCAAAAGCACAAGCAAC-AA---AAGAAAAAATAGA 632

  chr2_57237017_5   3497 CAAATGAGATCACATCAAG-TTAAAAAGATTCTACACAGCAAAGGACACA 3545
                         i    vi  iiv      i-       v-  i iii vv          v
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACT 681

  chr2_57237017_5   3546 ATCCACAAAGTGAAATGACAACCCATATAATGGGAGAAAATATTTGCAAA 3595
                            v v         v         i v                      
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_57237017_5   3596 CTACTTCTCTGACAAGGGATTAATAACCAAATTATATAAGGAATGCAAAC 3645
                         ii iv v     i      i vi  v   i v       i   iv vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_57237017_5   3646 AACTCTACAGGGAAAAAAAATTAATAATCTGATGAAAACATGGGCAAAAT 3695
                              v i iv--     i iv     i ii  v?   v         iv
  L1M4_orf2#LINE/    782 AACTCAATAAT--AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_57237017_5   3696 ATTTGAATAGATATTTCTCAAAAGAAGATATATAAATGGCAAACAGGCAT 3745
                                    i       v            i       v  i i   i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_57237017_5   3746 ATGAAAAG-TGCTCAACATCATTGATCAT 3773
                                 -            ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (141 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


2487 28.68 1.88 1.33  chr2_57285432_57291577     4752  5654 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57285432_5   4752 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTAAAAAT 4801
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57285432_5   4802 GGCCATACTGCCCAAAACAATTTGTAGATTCAATGCTATTCCCATTAAAC 4851
                            v     v      vii  i ii        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57285432_5   4852 TACCATTGACATTCTTCACAGAA-TTAGGAAAAACT-ATTTTAAAATTCA 4899
                          v   vivi v  i  ii     -  --  v  i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr2_57285432_5   4900 CATGGAACCAAAAAGAGCTCACA-TAGCAAAGACAATACTAAGCAAAATT 4948
                         i      viiv  i ii i  v -    v  i     vi i iv  i vv
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_57285432_5   4949 AACAAAGCCAGAGGCATCACACTACCTGACTTCAGACTATACTACAAGAC 4998
                                iii    vv       v  ii i    i viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_57285432_5   4999 TAAAGTAACCAAAACTGCATAGTACTGGTACAAAAACAGACACATAGACC 5048
                           v     i   i  v ii i       i i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_57285432_5   5049 AATGAAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACATCCAT 5098
                             i  i    iv   ivii         vv   i    i  iivi  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_57285432_5   5099 CTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGACTTCCT 5148
                         i    i   i    ivv  v   i v  vv            i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_57285432_5   5149 GTTTAATAAGTCGTGCTGGGAGAACTGGCTAGCCATATACAGAAAATTGA 5198
                         v  i  i  i v         v      v  ?   i  i  i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_57285432_5   5199 AACTGGACCCCATCCTTACACCTTATACAAAAATCAACTCAAGATGAATT 5248
                          ii        vv   i     v           i       i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_57285432_5   5249 AAAAACTTAAGTGTAAAACCCGAAACTGTAAGAGCCCTAGAAGAAAATCT 5298
                          ? i  i   i     i v ii     i   i vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_57285432_5   5299 AGGCA-ATACCATTCAGGACAT-GGGCATGGCAAAGATTTTAT-GATGAA 5345
                            ?i- v i -   iv   v -   ivv     v i   iv -   ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_57285432_5   5346 ATCGCCAATAGCAATTGCAACAAAAGCAATAATTGAAAAATGGTATATAA 5395
                          - i    v    vvv          v  v   v  v    v v iv v 
  L1M4_orf2#LINE/    598 A-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_57285432_5   5396 TTAAA-CTAAGAGCTTCAGCACAGCAAATGAAACTATCATCA---T-AAC 5440
                          i   -i   i i   iv ii vv    v  v       vv --- -  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_57285432_5   5441 AGACAACCCACAGAATGTGAAATAAT--TTGCAATCTATTCATCTGTCAA 5488
                                          v  i v   --      vii  vi     vi  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_57285432_5   5489 AGGTCTAATACGCTTTGTCAGAATCCACAAGGAACTTAAGCAAATTTACA 5538
                         i  v  vi  i------i      vi i  i     ivvi   v iv i 
  L1M4_orf2#LINE/    747 GGGACTTGTAT------CCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_57285432_5   5539 AGGAAAAAACAA----CCCCATTAAAAAGTGAGCAAAGGATATGAACAGA 5584
                          vi    i    ----   v   ?    i  i         v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_57285432_5   5585 AACATCTCAATAAAAGACATACATGCAGCCAAAAAAAAAATACAAAAAAA 5634
                         v iv    v v i    i     viii     v  iv v  i--    i 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG--AAAAGA 888

  chr2_57285432_5   5635 AGCTCGACGTCACTGATCAT 5654
                         v    i  i   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (150 / 105)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.81 (29 / 16)  


1959 22.67 3.11 14.79  chr2_57323373_57326453     1572  2599 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57323373_5   1572 TGAAGAAACACTTCAGGTTGATGGATTGAAATAATCTGTATTGTTAAAAT 1621
                           i i i i iii  v   v        i  v v ivi         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57323373_5   1622 GGTCATACTACCCAAAACAATCTACAGATTCAATGCATTTCCTATCAAAC 1671
                           iv     v      vii              i   v i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57323373_5   1672 TACCAA-TGTCATTTTTCTCAGAACTGGAAAAAAACT-ATTCTAAAGTTT 1719
                          v   i-  i -     iv     v v  v  i--  -  i     i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_57323373_5   1720 GTATGGAA-TCCAAAG-AGCAAAAATA-CCAA---------GCAAAA--A 1755
                         i       - v   i - v v i    -    --------- v    -- 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_57323373_5   1756 GAACATAGCTGGAAGCATAGCATTACCTGACTTCAAAGTATGCTATAAGA 1805
                              v  i    i vv vi  i v  ii i      iiv i   i  ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_57323373_5   1806 CTACAATAACCAAAACAGCATGGTACTGGTATAAAAACAGATACATAGAC 1855
                              i   i   i    ii         i    ii i   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_57323373_5   1856 CAATGAAACAGAATAAAGAACCCAGAAATAAAGCCACAAACCTACAGCCA 1905
                              i  i     vi   ii           v   i v ii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_57323373_5   1906 -----TCTTTGACAAATTTCACAAAACTGAGCAATGGGAAAAGGACTCCC 1950
                         ----- i  i     ivv vv   i  iivv       i    i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_57323373_5   1951 TATTGAAAAAATGGTGCTGG-ACAAGCTGGCTAGCCAAATGCTGAAGAAT 1999
                          v  v  v            -    -    v  ?   v    vi      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAAT 446

  chr2_57323373_5   2000 AAAACTGAACTCCTACCCTTCACCATACATAAAAATAAACTCAAGAGGGA 2049
                         i  ii  i  i      iiv       i i      v       i v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_57323373_5   2050 ATAAAGATTTAAATATAAGACCATGAACTATAAAAATTGTAGAAGAAAAC 2099
                         vi ?   ii     i     v vvi          v iv           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_57323373_5   2100 CTAGGAAACACCATTCTGGACATCACCTTTTCAAAGGAATTTGTGACCAA 2149
                         v    ?----------- v v   ---------------  i      --
  L1M4_orf2#LINE/    547 ATAGGN-----------GTAAATC---------------TTCGTGACC-- 568

  chr2_57323373_5   2150 GTCCTCAAGAGAAATTGTAACAAAAAGAAAAATTAAGGAATCAGGAAAAA 2199
                         --------------------------------------------------
  L1M4_orf2#LINE/    569 -------------------------------------------------- 568

  chr2_57323373_5   2200 TAGCTAGTGTATGCTGGGCATAATACCTAGGTGATGGATTGATAGATGCA 2249
                         -------------i    i--------    ii    v  vv     iii
  L1M4_orf2#LINE/    569 -------------TTGGGT--------TAGGCAATGGTTTCTTAGATATG 597

  chr2_57323373_5   2250 GCAAACCACCATGGCACATGTTTACCTATGTAACAAACCTGCACATCCTG 2299
                         i  --   -- vi     --------- - i      -------------
  L1M4_orf2#LINE/    598 ACA--CCA--AAAGCACA---------A-GCAACAAA------------- 620

  chr2_57323373_5   2300 CACATGTACCCTGGAACTTAAAATAGAAATAAAAAAAGTGAGTCCTAATT 2349
                         ------------i   ---        --    ----- vi v i v  i
  L1M4_orf2#LINE/    621 ------------AGAA---AAAATAGA--TAAA-----TTGGACTTCATC 648

  chr2_57323373_5   2350 AAACTAAATAGCTTTGGCACAGCAAAAGAAACTATCAACAGAGTAAACAG 2399
                            v v  v i    v ii vv    i  v        v i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_57323373_5   2400 ACAACTTACAAGATAGGAGAAAATATTCTCAAACTATATATTCAACAAAG 2449
                              ii   ii  i            iv    ii      iii i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_57323373_5   2450 GTCTAATATCCCGACTCTATAAGGAGCTTACGCAATTCAACAGTCGAAAA 2499
                          v  vi     v  v v     i  i  ivii   i    i i vi   i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_57323373_5   2500 ACAA----CCCCATTAAAAAGTGGCCAAAAGA----AATGGACATTTCTC 2541
                             ----   v   ?    i   v    i  ----   i          
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_57323373_5   2542 AAAATAAGACATACAAAGGGCCAAGAAACATATAAAAAAA-GTTTA-TAT 2589
                         v   v    i       v      v  i  i  i    i - i i -i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_57323373_5   2590 CAATAACCAT 2599
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.73 (145 / 84)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 6.57 (184 / 28)  


2644 23.01 7.86 2.89  chr2_57375846_57379603     2403  3267 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57375846_5   2403 TGGAAATATATCTCATGTTCATAAATTAGAA---TTAATATTGTTAAAAT 2449
                               v     i         ii   i   ---             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57375846_5   2450 GTTCAAATTCCCCAGAGTGAACCAAAGATGTAATGCAACACCTATCACAT 2499
                          viv v i      i v   v i v    vi  i    iv       v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57375846_5   2500 TTGTAA-TACAATTTTTCACGGACAGATGAAAAAAT--TCTTAAAACTGT 2546
                          ivi i- i v-     ii i  - iv   v  iv --  i     i --
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATT-- 146

  chr2_57375846_5   2547 CA---GGAACCACAAAATATCCTGAATAGCCAAAA-AATCTTAGCAAATA 2592
                           ---    vii   iiv i  v            -      iiv   v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_57375846_5   2593 -GATCAAAA------GACT--------------TCAAAATATACTGCAAA 2621
                         -  v    i------    --------------      iv    i    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_57375846_5   2622 GTTTTGGTAATCAAAACAGCATGGTACTGGTATAAAAACAAACAGATCAT 2671
                          i vii        i    ii         i    ii i i   v  viv
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_57375846_5   2672 TCAATGGAAAAGAATAGAGAGCCCAGAAATAAATCCACATTTTTAAGGTC 2721
                                  v     v     i           i   i iv    v    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_57375846_5   2722 AACTGATTTTTGACAAAGGTGCCAAGAACCCAT--GATGGGGAAAAGACA 2769
                           i       i     i          --    --i         ii i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGA--CCATTCAATGGGGAAAGAATA 394

  chr2_57375846_5   2770 ATCTCGTCAATAAATGTTGTCAGGAAAA-TGAATATCCACATGCA----- 2813
                         i   iv    i     v  iii   v  -  i   ?         -----
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_57375846_5   2814 -T---------CCCTTACATCACACCACACACAAAA-CCAACTCAAAATG 2852
                         - ---------   i   v        i i      -ii           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_57375846_5   2853 AATTAAAGACTTAAACCTAAGACCTGAAACTATAAAACTGCTAGAAGAAA 2902
                         i  i ?    i    iv     v  i             vi         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_57375846_5   2903 ACATAGTTGAAAAGCTTCA------------AGACAATGATTTGTTGGCT 2940
                               v? v   v    i------------  i     i   v  i v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_57375846_5   2941 CTGACTCCAAATGCACAGCCAACAAAAACCAAAATAAGCACATCATTTTG 2990
                         v    v     v     iv        ivv      iii v  iivvi v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_57375846_5   2991 CATCAAACTGAAAAACGTTTTCTAAGCCAA-GGAAACAATCAACAGAGT- 3038
                                v v      -    v ivvi   -   v  v     v i   -
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_57375846_5   3039 -AAAGATAACCCTATTGAATGGGAGAAAATATTTCTAATCCATACATTTG 3087
                         -     i     - iv                  vi  vi    i  i  
  L1M4_orf2#LINE/    694 AAAAGACAACCC-ACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_57375846_5   3088 GTAAGAGGTCAATATTTAAAATACATAAGGAATTGAAACAACTGGATAGG 3137
                         i    i iiivi   ii i    i    i   i vvv      vi   --
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-- 790

  chr2_57375846_5   3138 AAGATACACATAAACTTAAAGATACACATAA---AATTAAAAAATGGGCA 3184
                         ---------     ----    --  v    ---    ?           
  L1M4_orf2#LINE/    791 ---------ATAAA----AAGA--CAAATAACCCAATTWAAAAATGGGCA 825

  chr2_57375846_5   3185 AAGGATCTGAATAGACATTTCTTAAAATAAGACATACAAATTGCCAGCAG 3234
                               i               iv   v    i        v    ii i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_57375846_5   3235 GTATTTGAAAAAAAGTTCAACTTCCTTATCATC 3267
                          i iv      i v i     v  v????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (118 / 77)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.58 (93 / 26)  


2968 27.05 1.55 0.89  chr2_57409898_57415403.rev     4113  5014 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57409898_5   4113 TGGAAGAAAATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4162
                              ii v  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57409898_5   4163 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4212
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57409898_5   4213 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4260
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_57409898_5   4261 TATGAAACCAAAAAAGAGCCCACATTGTCAAGAAAATCCTAAGCAAAAAG 4310
                             i  viiv  ii  v  viv  v i   i v    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_57409898_5   4311 AACAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4360
                                i i    vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_57409898_5   4361 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGATC 4410
                                 i   i    ii         i iv ii i   v i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_57409898_5   4411 AATGGAACAGAAT--AGAGCCCTCAGAAATAATACCACACATATACAACC 4458
                                i     --    i  --        vv   i    v  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_57409898_5   4459 ATGTGATCTTTGGCAAACCTTACAAAAACAAGAAATGGGGAAAGGATTCC 4508
                          vv    i  i i   ivv vv   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_57409898_5   4509 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4558
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_57409898_5   4559 GAAACTGGATCCCTTCCTTACACCTTATACAAAAAT-AATTCAAGATGGA 4607
                            ii    i    v   i     v           -  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_57409898_5   4608 TTAAAGACTTAAATATTAGATCTAAAACCATAAAAACCCTGGAAGAAAAC 4657
                          i ?    i     i v   v       i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_57409898_5   4658 CTAGGCA-ATACCATTCAGGACATAGG--CATGCCAAGGTCTTCATGTCT 4704
                         v    ?i- v i -   iv   v v  --i v  v v   -   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGAT 594

  chr2_57409898_5   4705 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACATATGGGATCT 4754
                          vi            vvi          vv     v  i v  v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_57409898_5   4755 ------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGTGTT 4798
                         ------       i -   i  ii vv    i  v    i  vv iv  v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_57409898_5   4799 AACAGGCAACCTCCAGAATGGGAGAAAATTTTTACAGTCTACCCATCCGA 4848
                           v  i     iv                v   i  ivii ivi   i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_57409898_5   4849 AAAAGGGCTAATATCCAGAATCTACAAAGAACACAAACAAATTTACGAGA 4898
                         v  i  i  vi          v  i       v vv    v iv ii v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_57409898_5   4899 AAAAAATCAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACA 4948
                             i -    i     v  i? v  i            v    i     
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_57409898_5   4949 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCT 4998
                         i     v        i  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_57409898_5   4999 TGTCATCACTGGCCAT 5014
                         iiv     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


2513 28.60 2.31 2.42  chr2_57417158_57419179      637  1545 (477)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57417158_5    637 TGAAAAGATATCCCATTCTTATGCATTGGAAGAATTAATATTGCTAAAAT 686
                           i             vi i   v         v         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57417158_5    687 ATAAACACCACCCAAAACAATTTAGAAATTGAGTGCAATATCTATCAAAG 736
                         ivv  i  iv      vii  i  v i   v ii     vi        i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57417158_5    737 TGTCAATAACATTTTTTATAGAAATAGAAAAAACAACACTAAAATTCACA 786
                          vi  iivi v      ii      v  v  ivii iv          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_57417158_5    787 CAAAAA----------CCA-AATAGCCAAAGCAACCCTGAGATAAAAGAT 825
                         iii   ----------   -          i   i i   i v i    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_57417158_5    826 CAAAGCTGGAGGCATGGCACTACCTGACTTTGAAGTATACCGTAAAGCCA 875
                              i      vv vi    v  ii i  ii  iiv   iii     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_57417158_5    876 TAGTAACCAAAAGAGCAAGGGGGTGGCATAAA-ACAGAAACTTAGACTAG 924
                         i     i   i v  iiv  viv        i- i   v iv    ii i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_57417158_5    925 CAGAACAGAACAGATAACCCAGAAATACATTTATGTATTTACATCCAATT 974
                         ii   i    iv  v ii         v iii  ii     iivi     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_57417158_5    975 CATTTTTGACAAAGACCTCAAGAACATATATTGGGCAAATGGCAGTCTCT 1024
                         v     i     i iivi     v   vi v    v   viii     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_57417158_5   1025 TCAATAAGTTGTGCTGGAAAAACTGAATAGCCATAGGTGGAAGAATAAAA 1074
                             i  i v       i v     i   ?   i v iii      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_57417158_5   1075 CTACACCCCTATCTCTCACCATATACAAAAATTAAACCACAATG-ATTAA 1123
                         i iv       i   v                   vi  v    -  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_57417158_5   1124 AGACTTAAATCTAAGACCTGAAACTATGAAACTACTAGAAGAGGACAT-G 1172
                             i     v     v  i       i     vi       ii    - 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_57417158_5   1173 GAGTCTGTCCACCCAGT-ACATTGATCTGGACAAACCTTTTTTGGCCAAT 1221
                          ?  vvi  iv ---  -  v   ivi i i   vvv   i  i vi vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTC---GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_57417158_5   1222 ATTCCCAGAGCACAGAAAAAAAAAGAAACATTAGACAAATGGGATTACAT 1271
                          iv  v i      iiv  v        v v    i    v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_57417158_5   1272 CAAGCTAAAAAGCCTCTGCACCACAAAGAAAACAATCAACAAAGTGAAGA 1321
                            iv v    i i i  ii iv     i v  v     v        i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_57417158_5   1322 GAATGAATAACCTCTGAATAACCTACAGAATGAGAGAACTCTTTCACAAA 1371
                           ----------------i    i        i     vviv  ii    
  L1M4_orf2#LINE/    698 GA----------------CAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_57417158_5   1372 CTATCCATCTGCAAAGAGATTAATAACCAGAATATATAGAAAATTTAAAC 1421
                         ii  vi     vv   i  i vi  v            i i  i ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_57417158_5   1422 AACTCCATAGCAAAAAAAAAAA-AG---AATT--AAAATGGGCAAAAGCT 1465
                              v   ii     i v   - i---    --            i v 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_57417158_5   1466 CTCAATAGACATTTCTCAAAAGAAGACATGGAAGTGTCTAATGGGTATAT 1515
                         i v              v        i  iv  i  v i   ii i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_57417158_5   1516 AAAAAAAAAACCCATGACATCACTAATCAT 1545
                         i    i vi- i  --      ????????
  L1M4_orf2#LINE/    882 GAAAAGATG-CTCA--ACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (163 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.31 (43 / 13)  


3186 26.90 0.88 0.77  chr2_57420747_57425027     2883  3789 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57420747_5   2883 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2932
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57420747_5   2933 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2982
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57420747_5   2983 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3030
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_57420747_5   3031 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 3080
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_57420747_5   3081 AACAAAGCTGGAGGCATCACACTATCTGACTTTAAACTATACTACAAGGC 3130
                                i      vv       vi ii i  i   viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_57420747_5   3131 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGATC 3180
                                 i   i    ii         i iv ii i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_57420747_5   3181 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3228
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_57420747_5   3229 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAGAGGAT--T 3276
                          vi    i  i     ivv  vv  i v  vvv        i  i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_57420747_5   3277 CCCTATTATTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3326
                          ii - i vi              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    397 CTTT-TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_57420747_5   3327 TGAAACTGGATCCCTTCCTTACACATTTTACAAAAATCAGTTCAAGATGG 3376
                             ii    i    v   i    vv v         i ii    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_57420747_5   3377 ATTAAAGACTTAAACGTTAGACTTAAAACCATAAAAACCTTAGAAGAAAA 3426
                           i ?    i    i  v   vi      i      vi            
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_57420747_5   3427 CCTAGGCATTACCATTCAGGACATAAGCATGGGCAAGGACTTCATGTCTA 3476
                          v    ?i v viv   iv   v vi vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_57420747_5   3477 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 3526
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_57420747_5   3527 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3576
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_57420747_5   3577 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAA--CATACTCATCTGA 3624
                         v  i     i                 v  i    --    i--      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chr2_57420747_5   3625 CAAAGGGTTAATATCCAGAATCTACAATGAACTCAAACAAATTGACAAGA 3674
                         i  i  ii vi          v  i  v      vv    v ii i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_57420747_5   3675 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACAC 3724
                             i     i     v  i?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_57420747_5   3725 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 3774
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_57420747_5   3775 ACCATCACTGGCCAT 3789
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (148 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2181 27.39 3.59 4.89  chr2_57455188_57458306     1708  2627 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57455188_5   1708 TGGCAAAGCATTCCATGGTCATAGATAGCAAGAATCAATATTGTCAAAAT 1757
                            v  iii  i     v    i   v v    v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57455188_5   1758 AGCCATATTGCCCAAAGCAATTTATAGATACAATGCTATTCCTATCAAAC 1807
                         i  v   i v      vii  i  i    v   i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57455188_5   1808 TACCAATGACATTCTTCACAGAATTAGAAAAACTCTCTCTCTCTCTCTCT 1857
                          v   iivi v  i  ii     v v  v  i  v---------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--------------- 135

  chr2_57455188_5   1858 ATCTCTCTCTCTCTATA---TATATATATATATTAGATAAATATATATAT 1904
                            ---------   v ---i    iv v  iiv  iv vvi v -   v
  L1M4_orf2#LINE/    136 ATC---------CTAAAATTCATATGGAAATGCAAGGGACCCAGA-ATAG 175

  chr2_57455188_5   1905 CTAAGGCAATCCTAAACAAAAAGAACAATGCTGGAGGCATCACATGGCCA 1954
                          i  ii     i i  v  i        v i      vv     ivv  v
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_57455188_5   1955 TACTTCAAACTATGCCACAAGTCTACAGTAACCAAAACAAACACGGCATG 2004
                         v i      viv i i    iv         i   i   ------ ii  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA------GTGTG 269

  chr2_57455188_5   2005 GCATATGTGTCAGGTATGAAAACAGACACATAGACAAACGGAACTGAATA 2054
                          i ------- v  i  i ii i     i     iv  i    iv    v
  L1M4_orf2#LINE/    270 GTA-------CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_57455188_5   2055 GAGAGCCCAGAAATAAGGCTGTACACCTACAACCATCTAATCTTCCACAA 2104
                              i          iv ii    ii  iiii  vi i  i   v    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_57455188_5   2105 AATCAACATAAACAAGCAGTGAGGAAAGGATTCCCTGCTCAATACATGGT 2154
                         iiviiv  vi v  vv  i  i      i  vvi  vi    i v     
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_57455188_5   2155 G----------------GCCACATGCAGAAGATTGAAACTGGACCACTTT 2188
                          ----------------?         i    v    ii      v  vi
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_57455188_5   2189 TTTATACCATATACAAAAATCTACTCAAGATGGATTAAACACTTAAATCT 2238
                         i i i               iv      i      i ? v  i     v 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_57455188_5   2239 GAAACCAAAACCTATACAAAC-CTTGGAAGATAACCTAGG---AAATACC 2284
                         i i v v   v     -    -   i     v   v    ---    -- 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAGGNGTAAAT--C 559

  chr2_57455188_5   2285 ATTCTGGACCTAGGACTTGGCAAATACTTCACCACAAA-GGTGCCAAAAG 2333
                         -   vv     v  ii v     vvii   -ii v v - iii       
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGACACCAAAAG 607

  chr2_57455188_5   2334 C-CATTGAAACAAAAACAAATATTGACAAATTGGGTCT------AATTAA 2376
                          -  v- v       iv   v  v  i       iii ------      
  L1M4_orf2#LINE/    608 CACAA-GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_57455188_5   2377 AGAGCTTCTGTGCAGCTAAAGAAACTATCAACAGAGTAAACAGACAATCT 2426
                          i -   i     vv v  i  v        v i   i  v      i i
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_57455188_5   2427 ACAGACTGGGAGAAAATATTTTCAAATTATACACCCATCAAAGGTCTAAT 2476
                              v               v     i   i i iivi  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_57455188_5   2477 ATCCAGAATCTATATGGAATTTAAACAAATTTACAAGCAAAA-ACACACA 2525
                                  v    vi   i ivv    v iv i  vv    -   v i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_57455188_5   2526 ACCCCATTATAAAGTGGGCAAAGGATATGAACAGACACTTTTCAAAAATG 2575
                             v   ?v   i            v    i     i  i  v   ivi
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_57455188_5   2576 GACATTCATGTAGCCAACAAGCATGTAAAAA-ATTCTCAACATCACTGAT 2624
                           i  v  vi i     i     ii i    -  v          ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_57455188_5   2625 CAT 2627
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.33 (142 / 107)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.90 (78 / 20)  


2084 29.65 0.28 0.14  chr2_57491775_57493487.rev      507  1221 (492)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr2_57491775_5    507 AAAAATAACAAACCTGGAGACATCACACTACCTGACTTCAAACTACACTA 556
                           i  v      vi     ivv       v  ii i      vivi    
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_57491775_5    557 CAAGGCTACAGTAAACCAAACCACATGGTACTGGTACCAAAGCAGATATA 606
                            i          v v i  viii         i iv iiii   i   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_57491775_5    607 CAGACCAATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTAC 656
                         i   i        i    iv    vii         vv   i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_57491775_5    657 AACCATCTGATCTTCAACAAACCTGAAAAAAACAAGCAATGGGGAAAGGA 706
                         iii  vi    i   i    ivv  vv  i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_57491775_5    707 TTCCCTATTCAATAAATGATGCTGGGAAAACTGGCTAGCCATATGCAGAA 756
                          vvi  v     i     i        v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_57491775_5    757 CACTGAAACTGGACTCCTACCTTACGTATTATACAAAAAATAACTCAAGA 806
                         v v    ii     i       i  iivv          v        i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_57491775_5    807 TGGATTAAAAACTTAAATATACAACCCCAAACCATAAAAACCCTAGAAGA 856
                              i ? i  i     i  vi v iv    i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_57491775_5    857 AAACTTAGTCA-ATACCATACAGGATGTAGGCATGGGAAAAGACTTCATG 905
                             v   v?i- v i v - iv  iv v  vv i  v  v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_57491775_5    906 ACAAAAACACCAAAAGCAATTTCAATAAAAGCCAAAATTGATAAATTGGC 955
                         ivv vi            vvvv   i     vv     v          v
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_57491775_5    956 TCTAATTAACCTAAAGAGCTTCTGCACAGTGAGAGAAACTGTCATCTGAG 1005
                         ii v  i  vv v  i i   i  ii vvii ii  v   i   vvvi  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_57491775_5   1006 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCT 1055
                             v  i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_57491775_5   1056 GATAAAGTTCTAATACCTAAAATCTACTAGAAACTTAAACAAATTTACAA 1105
                              i vv  vi  i i i   v  iv ii    ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_57491775_5   1106 GAAAAAAACCAACAACCCCAACAAAAAGTGTGCAA-GGATATGAATAGAC 1154
                         v     i  v  i     v vi?    i  v    -    v         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_57491775_5   1155 ACTTCTCAAAAGAAGACATTTATGTGGCCAACAAACATAAGAAAAAAAGC 1204
                          i     v        i  vi vi       i  i  i v     i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_57491775_5   1205 TCATCATCACTGATCAT 1221
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (113 / 95)
Gap_init rate = 0.00 (3 / 716), avg. gap size = 1.00 (3 / 3)  


3167 26.66 1.11 0.66  chr2_57556997_57563260     4869  5772 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57556997_5   4869 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4918
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57556997_5   4919 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCGTCAAGC 4968
                            v     v     iv i  i           i  v     ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57556997_5   4969 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5016
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_57556997_5   5017 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5066
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_57556997_5   5067 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5116
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_57556997_5   5117 TACAGTAAGCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGTTC 5166
                                 v   i    ii         i iv ii ii  v      v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_57556997_5   5167 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5214
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_57556997_5   5215 ATCTGATCTTTCACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT--T 5262
                          vi    i  iv    ivv  vv  i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_57556997_5   5263 CCTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5312
                          i  -- i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_57556997_5   5313 CTGAAACTGGATCCCTTCCTTAGACCTTATACAAAAATCAATTCAAGATG 5362
                         v    ii    i    v   i v   v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_57556997_5   5363 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5412
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_57556997_5   5413 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5462
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_57556997_5   5463 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATAT 5512
                          vi            vvi          vv     v  i    v   iv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_57556997_5   5513 AATTAAACTAAAGAGCTTCTGCCCAGCAAAAGAAACCACCATCAGAGTGA 5562
                         v  i   v v  i i   i  iv vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_57556997_5   5563 ATAGGAAACCTACAAAATGGGAGACAATATTCGCAACCTACTCATCTGAC 5612
                          v  iv    i   i         v      i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_57556997_5   5613 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTGACAAGAA 5662
                           i  i  vi          v  i  v      vv    v ii i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_57556997_5   5663 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5708
                            i    ----   v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_57556997_5   5709 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5758
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_57556997_5   5759 CCATCACTGGCCAT 5772
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


1815 23.93 2.44 14.26  chr2_57605399_57607408.rev      495  1518 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_57605399_5    495 AGGTATTTTCATGCTCATGGGTAGGAAGAATAAATATCATGAAAATGGCC 544
                           i   ii-    i      i v      v v     ii v  i     v
  L1M4_orf2#LINE/      6 AGATATCC-CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_57605399_5    545 ATACTGCCCAAAGCAATTTACAAATTCAGCGCTATTCCTAACAAACTACC 594
                              v      vii  i    i     i   v  i    v    v v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_57605399_5    595 AA-TGTCATTTTT-CACAGATTAAGAAAAAAAAAAGATTCTAAAATTTTT 642
                          i-  i v     -  v i   i v  ivv-----   i        iv 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCT-----GATCCTAAAATTCAT 149

  chr2_57605399_5    643 GTGGAA-TAAAAAGAGCCC-TAAGAGCCAAAGCAATCCTAAGCAAAAAAA 690
                         i     - iv  i ii   -v  v       i     i i ---    i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGA 196

  chr2_57605399_5    691 AAAACAAAGTCAGAGGCATCATGTTACCTGACCT-GAAACTATACTGCAA 739
                          i        ii    vv   iii v  ii ii -i     -    i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chr2_57605399_5    740 GGCTGCTGTAACCAAAACAGCATGGCACTGTTCCAAAAACAGACAGGTAG 789
                         i   i v    i   i    ii   i    vivi  ii i     vi   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_57605399_5    790 ACCAATGGAACAGAATAGAGAAGCCAGAAATAAATCTGCACACCTAAAA- 838
                          i        i     v    iv           i iii   ii  vii-
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_57605399_5    839 CAATCTGATCATTGACAAAGTCAACAAAAATAAACAATGGGGAAAAGAC- 887
                             -    iv i     i viiv   i vi vv           ii i-
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_57605399_5    888 -TCCTCATTCAATAAATGGTGCTAGGATGACTGGCTATCCATATGCCGAA 936
                         -  i --     i          i   ii     v  ?   i    vi  
  L1M4_orf2#LINE/    395 GTCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_57605399_5    937 GAAGGAAACTGGATCTCTACCTTTCACCCTATACAAAAATTAATGGAAGT 986
                            v   ii    i i      iv    v              ivv  iv
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_57605399_5    987 CAGATTAAAGAC--AAATGTTAGACAGGAAAAATAACTAATGGGTACAAG 1034
                         ii   i ?    --      v   --------------------------
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGA-------------------------- 516

  chr2_57605399_5   1035 GCTTAATACCTGGGTGACAAAATAATCTGTACAACAAACCCCCATGATAC 1084
                            ---------------    ----------------------------
  L1M4_orf2#LINE/    517 GCT---------------AAAA---------------------------- 523

  chr2_57605399_5   1085 AAGTTTACCTATATAACAAGCCTGCACATGTACCCCTGAACTTAAAAGTT 1134
                         --------     v   ---------------------------------
  L1M4_orf2#LINE/    524 --------CTATAAAAC--------------------------------- 532

  chr2_57605399_5   1135 AAATTAAAAAAAAAAGATTCTAGAAGAAAACATAGAAA-AACTCCTTCTC 1183
                         ----------------- ii               i?i-  v  -   vi
  L1M4_orf2#LINE/    533 -----------------TCTTAGAAGAAAACATAGGNGTAAATC-TTCGT 564

  chr2_57605399_5   1184 AATATTGGCCCTAGCAAAAAATTTATGGCTAAATCCTCAAAAGCA---AC 1230
                         i iv    viivi    viiv  iv i v  viv vi        ---i 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_57605399_5   1231 TACAACAACAACACATTGACAAATAGGACCTAATTAAACTAAAGAGTGTC 1280
                         v    -  v  v v  v  i    v    i v  i   v v  i iiv i
  L1M4_orf2#LINE/    615 AACAA-AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_57605399_5   1281 TGCACAGCAAGAGAAACTA--AAGAGAGTAAACAGACAACCTATAGAATG 1328
                           ii vv   ii  v    --    i   i  v        i i      
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_57605399_5   1329 GGAGAAAATATTTGCAAACTATGCATCTGACAAAGGCCTAATATCCAGAA 1378
                                           ii  ii      i  i  v  vi         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_57605399_5   1379 TCTATAAGCAACTT----AAATCAACAAGCAAGAAACA--TACCCCA-TT 1421
                          v     iv    i----  v    i  vv  i i   --  v    -  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_57605399_5   1422 AAAAAGCAGGCAAAAGGGCACAAACACACACTTCTCAAAAGAAAACATAC 1471
                         ?    iii      -  iivii  i v   i     v      i i    
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAA-GGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_57605399_5   1472 AAGCAGCCAACAAATATATTTTTAAAA--TGCTCATAATCACTAATCAT 1518
                           iii     i  ii i  v---    --      vv    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATG---AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (155 / 86)
Gap_init rate = 0.03 (29 / 903), avg. gap size = 5.90 (171 / 29)  


 234 27.87 0.00 0.00  chr2_57643751_57645639.rev      424   484 (1405)    L1M4_orf2#LINE/L1       13    73 (835)  

  chr2_57643751_5    424 CCGTGTTCATGGATTAGAAGAGTTAGTATAGCAGCAATTCCAATTCCTCC 473
                           i            i     v   i   v ivivi  vv    v ii  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_57643751_5    474 CAAATGGATTT 484
                              v   i 
  L1M4_orf2#LINE/     63 CAAATTGATCT 73

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.00 (0 / 0)  

 587 28.27 13.99 0.89  chr2_57643751_57645639.rev      501   836 (1053)    L1M4_orf2#LINE/L1      280   659 (249)  

  chr2_57643751_5    501 AGGGGTAGGCATA--GAACAAAGGAACAGAATAGAGAACTCAGAAATTGA 548
                          i  i   i    --  v   v    i     v    iii       vi 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_57643751_5    549 TT-ACAAAATTCTGCCCAACTTATTTCTTTA-AAATGTGCAAAAGCAATT 596
                         ii- i v v  v  vi   i v    - iv -  iv    v  ii v   
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTT-TCGACAAGGGTGCCAAGACCATT 378

  chr2_57643751_5    597 GAATAGAGGAAAGATAGTATTCTCAACAAATAGTGCTAGAGCAATTTAAC 646
                         v   i i i  ii     v  i         i     i ii   i vi i
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_57643751_5    647 ACCCA------------------------------TTACA------ATAA 660
                          ?   ------------------------------ i   ------ i  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_57643751_5    661 ACTTTAACTCAAATTGGATCATCTACTTAAATATAAAACATAAAACTATA 710
                          vv          v       ?vv  i     i   i vv          
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_57643751_5    711 AAACACTTAGACAAAAA--TAGGA-TAATATCTGGGGGATGTAGACTTAG 757
                             v      vi    --    ?-   -    vv v  iv v iv    
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAG 577

  chr2_57643751_5    758 CAAACAGTT-CTTAAACTTGAAAACAAAAGCATGTTTCATAAGAGAAAAA 806
                         vv  ii   -    i iv   v v        iivviv i  i       
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_57643751_5    807 CAT-GATTAACTGAACTCTATTAAAA--AAAAA 836
                         -  -   v  i  i   ii  i    --     
  L1M4_orf2#LINE/    628 -ATAGATAAATTGGACTTCATCAAAATTAAAAA 659

Transitions / transversions = 1.30 (52 / 40)
Gap_init rate = 0.03 (13 / 380), avg. gap size = 3.85 (50 / 13)  

 597 27.80 4.69 1.44  chr2_57643751_57645639.rev     1122  1398 (491)    L1M4_orf2#LINE/L1      623   908 (0)  

  chr2_57643751_5   1122 AAAAAATA-ATAATAATAAATTTTA--AAAA--AACAACTTTTG--CTCC 1164
                                 -    - v ii i  i --    --  v        --  i 
  L1M4_orf2#LINE/    623 AAAAAATAGATAA-ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_57643751_5   1165 ATGAAGAACCTCATTAAGAAGATAAATAGACAAGCTACAGGGTGAAAGAA 1214
                          --   i  vii  i     ii i  v      v i    ii  ii    
  L1M4_orf2#LINE/    672 A--AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_57643751_5   1215 AATATTTACAAACCCTATATGCAACAAATTACTAAGATGTAGACTATATA 1264
                                i    i v     vii i  ivv   viv  vi   v      
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_57643751_5   1265 AAGGATTCATAAAACTTAATAGTAAG----CAAA-AATCCAATTATGGAA 1309
                            i i  v  v    i    i   i----    -  i      ?vii  
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_57643751_5   1310 TGAACAAAAAACACAAAGAAGTAACTTCTC-AAAAAGAATATATAGATGA 1358
                           ii    ii ivii  v iii -i     -   i ii     i i   i
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACA-TTTCTCCAAAGAAGATATACAAATGG 868

  chr2_57643751_5   1359 CAAATAAGCTTATAAAAACATGTTTAACATCGTTAGCCAT 1398
                          v       vi  i    v   i i      i????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.62 (55 / 21)
Gap_init rate = 0.03 (10 / 286), avg. gap size = 1.70 (17 / 10)  


2748 26.94 1.94 4.20  chr2_57658957_57661673.rev     1308  2235 (482)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_57658957_5   1308 GAAAAAATATTTTATGTTTATGAATTAGAAGAATCAGTATTGTTAAAATG 1357
                          i   i    iii     i   i   i     v i i         i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_57658957_5   1358 TCCATACTATCCAACACGATCTACAGATTCAATGCAGTTTCTATCAAAAT 1407
                         v v     vi    vvi               i   i ii          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_57658957_5   1408 ACT-GATATCATACTTCACGGAAATAGAATAAAAC--ATTTTTAAATATG 1454
                         v i- v ii v -i  ii i     v  v--  i --  ii v    vii
  L1M4_orf2#LINE/    102 CCCAGCTGCCTT-TTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chr2_57658957_5   1455 TATGGGAACACAAAAGACCCAGTATAGCCAAAGTCATCCTGAGGAAAAAG 1504
                              i  ii   ii       v         iiv   i   ii  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_57658957_5   1505 AACAAAACTAGAAAACTCACATTTCCTGATTTCAAATTACACAACAGTGT 1554
                               ii i  ii       i    ii        vivi  v   iv i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_57658957_5   1555 TATAGTAACC--TACAGATTGCTAACGGCAAAGAAAACACAACAAAACAA 1602
                           i     i --v    vv  v  vi    --------------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA-------------------- 278

  chr2_57658957_5   1603 CAACAACAAAAGAAAAACAGTCACATGGACCAATAGGTAAGAACAGAGAA 1652
                         -----------v  ii i  v  i  i  i    i ivv    iv    i
  L1M4_orf2#LINE/    279 -----------TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_57658957_5   1653 CCCAAAAATAAATCCATAAATATACCATGAATTCATTTTTGACAATGGTG 1702
                         i   i       i     v  v  ivi v    v     i     v    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_57658957_5   1703 TCAAGAACATGCA-TTTGGAAAGGACAGTTTATTTAATACCTGATACTGA 1751
                         i     v   v  - vv      i i   i v  i  i vv  i i   i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_57658957_5   1752 GAAAACTGGATATTTATATG-GGAAGAATGAAACTATGTCTCTATCTCTT 1800
                           v         ?ii i   -ii         ii ivii i   i   vi
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_57658957_5   1801 GCTATATTCAAAATTCAAATCACAATGGATTAAAGACTTAAATCTAAGAC 1850
                         i i    v     v i  v   v       i ?    i     v     v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_57658957_5   1851 CTAAAACTATGAAACTACTAAAAGAAAACATTGAGGAAACTAGCCAGGAC 1900
                                   i     vi  i          v i? v  v vvi iv   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_57658957_5   1901 ATTGGTCTGGGCAAATATTGCTTGAGTAATATCTCAAAACCACAGGCAAC 1950
                         v    vi i     vvi  v   iii  vv ivi     v    i     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_57658957_5   1951 CAAAGCAAAAATGAACAAATGGGAGTTTGTCACATTGTGTTATAAAGCTT 2000
                         v    v      ii i    v   v  ii   v ----i   -   i   
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAA----ATTA-AAAACTT 662

  chr2_57658957_5   2001 CTGCACAGCAACAGAAGCAATCAAAAGAGTGAAGAGGCAATCTACAGAAT 2050
                         i  ii vv   vi  vi v     i i      i  i   i i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_57658957_5   2051 GAGAGGAAATATTTGCAAATTAACCATCTGATAAGG-ATTAATAACTAGA 2099
                          i   i              i vvi           - i vi  v i   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_57658957_5   2100 ATATATAAGAAGCTCAAACAAATCAATT-TAAAAAATCTAATAATTCAAT 2148
                                 ii i   vv    v     v-      iv v     ii    
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_57658957_5   2149 TAAAAAATGGGCAAAAGATCTGAATAGACATTTCTC-----AAGACACAC 2193
                          ?             i   i                -----    i i  
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_57658957_5   2194 AAATGGCAAACAGGTGTGTGAAAA----CTAGGCACCATTATTTAT 2235
                                v  i i iiii      ----  vii  i  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (157 / 89)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 4.07 (57 / 14)  


2077 25.00 2.38 4.37  chr2_57663959_57665691.rev      486  1241 (492)    L1M4_orf2#LINE/L1      168   908 (0)  

  chr2_57663959_5    486 CAGAATATTTGGATAAAAGCAATCCTAAGCAAAACAACAACAAAAACACC 535
                                ---- vi    -     i i --    v  v      ------
  L1M4_orf2#LINE/    168 CAGAATA----GCCAAAA-CAATCTTGA--AAAAGAAGAACAAA------ 204

  chr2_57663959_5    536 CAGAGCTGGAAGCATCACCTTACATAACTTCAAATTATACTACAAGGCTA 585
                         ---- i    i vv    vi v vi  i      viv        i    
  L1M4_orf2#LINE/    205 ----GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_57663959_5    586 TAGTAACCAAAATATCTTAGTACTGGTATAAAAATAGACTGATAGATCAA 635
                         i     i   i i viv i       i    ii      vv         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_57663959_5    636 TAGAACAAAATTGAGAACCCAGAAATAAAGCCACCTGTCTACAACCAACA 685
                          i   i i        ii           v   ivii i  iiii   iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_57663959_5    686 GATCT---ACACAGTCAACAAAAATATACACTGGGAAAATGACACCCTAT 732
                            i ---   vi viiv   i vi  v  v    i   vi i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_57663959_5    733 TCAATAAACGGTGCCGGGAAAATTGGAAAGCCATATGCAGAAGAGTGAA- 781
                             i   i     i    v  i    v ?   i     i    i    -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_57663959_5    782 CTGGACCAATATCTCTCAACACATTCAAAAATTAACTCAAGATAGGTTAA 831
                         i      vv  i   v  v  i  v               i  i i i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_57663959_5    832 AAACCTAAATGTAAGACCAGAAACCATAAAAATCCTGGAAGAATATTTAG 881
                          i              v vi    i      v  i i      v iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_57663959_5    882 G---AAATACACTTCTGGACATTGGCCTAGGCAAAGGATTTACGAGCAAG 928
                          ---    ---    vv   v    vi       v  v  iviiiii v 
  L1M4_orf2#LINE/    551 GNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_57663959_5    929 CTCTCAAAAGCAAATGCAACAAAAACAAA----GACAAATGGTACTTAAT 974
                         vivi        v v         iv   ----  i    v v    v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_57663959_5    975 TAAA-TTAAAAAGGTCTGCACGCCAAAAAACAAAAAACAAAACAATCAAC 1023
                         i   -       vv i  ii vi    ii   ---------- v     v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACA----------CTATCAAG 687

  chr2_57663959_5   1024 AGAATAGATAGACAACCTACAGAATAGGAGAAAATATTTATAAACCATTT 1073
                          i i ii v        i       i             ii   i   v 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_57663959_5   1074 ATCTGACAAAAGGCTAATATCCAGAATTTACAAGGAA---TGAAAACATT 1120
                               i  ii i  vi          v  i  i   --- v v   -- 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC--T 785

  chr2_57663959_5   1121 CAACAACAAAAAAGCCAAATAACCTCCTTAAAAAGTGGTCAAAGGACACA 1170
                            i  i     - v         ivv  ?    i   v       ivii
  L1M4_orf2#LINE/    786 CAATAATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_57663959_5   1171 AAGATACAGTTTTCAAAAGAAGGTATGCAAGTG-CCAAAAA--ATATGAA 1217
                           v v   v  i  v       i   i   i  -    v  -- i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_57663959_5   1218 AAAATGCTCAATATCACTAATCAC 1241
                           i        i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (111 / 75)
Gap_init rate = 0.02 (16 / 741), avg. gap size = 3.19 (51 / 16)  


1758 28.70 6.48 3.36  chr2_57678721_57680903.rev      877  1740 (443)    L1M4_orf2#LINE/L1       18   908 (0)  

  chr2_57678721_5    877 TTTAAAGATTGGCAAACTTGATTTTATTGAGATGTCATTTCTCCT-AAAT 925
                           i vi      v i    i  v  i  i     v  v v    i-    
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr2_57678721_5    926 TTATCTATAATTTCAAGACAATTCCAACAAAAATTACAGCAGAATTTTCT 975
                          v     i iv     vi    i  v iv     iv    v vv    i 
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr2_57678721_5    976 GTGGAAATTGACATGTAGATTGAAGAAACTTATTTAAAAATGAAAACTTC 1025
                          ii          v iv   ivv -   i i  v ii     v  i----
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTA-AAATTCATATGGAAATGCAAG---- 162

  chr2_57678721_5   1026 ATTATGTGGCTCTTGACTAGCCAACACAATCTTGAAGGAGAAACACAAAA 1075
                         -------  vi iv  v       v           ii    iv     i
  L1M4_orf2#LINE/    163 -------GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_57678721_5   1076 TTGGAGGATTT-TAGTACCAGATTTTGGTACATATTGTAAAACTAGAATA 1124
                                 i i-i v v  vi    iiiv  v  i ii   i   v i  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_57678721_5   1125 AGTAAGACA---TGATGCTGGTGGAGTTAGGATAAAAAAAAATACCAATA 1171
                          vi      ---  i i    iiv ---      i v v v v i    i
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATA---AGGATAGACATATAGATCAATG 302

  chr2_57678721_5   1172 GCACAAAATAGATATTCTAGGCCTAGATCTCCACACATGTAATCGGCTGA 1221
                          v i i   v  v v  i  ivv  i i ivi   iv i ii  iii   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_57678721_5   1222 TTTT---------TGTCAA----ACTTAATCTGAGAAAGGAGATTATTTT 1258
                             ---------  i   ---- i i   v- i     i v v v    
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTT 401

  chr2_57678721_5   1259 CAGTAACTAATAGTGGAACAACTAGATAATTATATGGAAAAACTTGAAGT 1308
                           ii  v ii iv   i      i    ?ii i   v    ivv      
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_57678721_5   1309 T---TTCTTATATCACAC-----ACAAAACAGTAATTTGAGATGGTTCAC 1350
                          ---ii i  iv      -----      - v   i ii i    v   ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATGGATCAW 500

  chr2_57678721_5   1351 AGGCCTAAATGTAAAAGTTAAATCTATAAATATTCT-ATAATAAAATATG 1399
                           i           i  i    v       - i   - v  v    i  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATA 549

  chr2_57678721_5   1400 ----------TTCATAAGTTTTGGGTTGGAAAACA-TTTCTTAGGT--GA 1436
                         ----------   i i -ii       i iv  ii-        i --  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGA-CCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_57678721_5   1437 GATCAAGCGTCACTAATAATAAACAGAAACAT---TTAATCGGACTTAGC 1483
                         v i   iv -   v ii  i   vii   v  --- v   i      vii
  L1M4_orf2#LINE/    599 CACCAAAAG-CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_57678721_5   1484 TAAAATGTAAATATTTT---GCTTATCAAAAAACAATATTGCAAAAGTGA 1530
                         i     -    v i   ---    --    ii   v   iivi       
  L1M4_orf2#LINE/    648 CAAAAT-TAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGA 694

  chr2_57678721_5   1531 AA-GTCAAGCCACAGATTTGGAAAAGGTATTTTTAAAACATGTATCTGAC 1579
                           - v   v       v v   i  ii     vi   v   i       -
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA- 743

  chr2_57678721_5   1580 TCTTAG---CTTTTATTAAGGTTATATGAAGAACACCTGTAACTTAATTA 1626
                         -- v  ---   v   iv  iv     i      v i ii    i   v 
  L1M4_orf2#LINE/    744 --TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_57678721_5   1627 TGAAAAGAAAAACAACACAATTAAAACATGGACGAAAGAGTC---TA-AC 1672
                          i      v   i   v     ?   v    i i  i  v i---  -  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_57678721_5   1673 ATTTTACCAAATCTTTATATAAGAATTCCCAC--AGCACATATGAAAAGT 1720
                             iv     vvvv-     vi   vv   v--       --      v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAGCACAT--GAAAAGA 888

  chr2_57678721_5   1721 TGTTTGGTGCCACTGAATCA 1740
                           i iiiiii  ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.03 (31 / 891), avg. gap size = 2.74 (85 / 31)  


1048 18.01 0.74 4.04  chr2_57722543_57730973      491   762 (7669)  C L1M4_orf2#LINE/L1   (0)   908   646  

C chr2_57722543_5    762 ATTAAAAATAAAAATATTTTTTAAACTTGTGTAGCAAATCACATTTTCAA 713
                           i    v      i---    ivi   ------    vv   i v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAAC---TTTTGTGCTT------CAAAGGACACTATCAA 686

C chr2_57722543_5    712 GAAAGTGAAAAGACAATCCAGAGAGTGGGAGAAA-TATTTTACAAATCAC 664
                                         i   v   i         -     -i       i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCAT 735

C chr2_57722543_5    663 GTATCTCATAAGGGACTCCTATGCAGAAAATACAAAGAATATTTAAAACC 614
                         i     v          iv   v     v   i      ivi   v   i
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

C chr2_57722543_5    613 CAATATTACAAAGACAAATAACCAGTTTTGAAAATGAGCAAAGGATCTGA 564
                              v  v              viv  ?i      i         i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

C chr2_57722543_5    563 ATGGATATTCATCCAAAGTGGATATACAAACAGCCAATAGACACATGAAA 514
                           i  i   iv       vi          ii       ii         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

C chr2_57722543_5    513 AT-TGTGTCAACATAATTAGTACT 491
                          v-  i-       v ????????
  L1M4_orf2#LINE/    886 AGATGC-TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (28 / 20)
Gap_init rate = 0.02 (6 / 263), avg. gap size = 2.17 (13 / 6)  

2978 21.19 1.83 0.76  chr2_57722543_57730973     1266  1921 (6510)  C L1M4_orf2#LINE/L1   (245)   663     1  

C chr2_57722543_5   1921 TGGAAAGACACGCAGTGTTCATGGGTAGAAATGCCTAGTATTGTAAAGAT 1872
                                 i iv vi         i v i  vi i  i      v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_57722543_5   1871 GCTAGTGCTTCCCTAAACAATCTATATATTCAAATGTGACCCCTATCAAA 1822
                          vi i i  i   v  vii     i v      -i ii i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAA 99

C chr2_57722543_5   1821 ATTTTAATGGCCATTTTTGCCAAAATGAAAAAGCTAATCCAAAAAATTCA 1772
                           iii iiv   v       vi    vi v     i    v    -    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCA 148

C chr2_57722543_5   1771 TATGGAATTGCAAGGGACAC----TAGCCAAAATGATTTTGAAAAAGAAA 1726
                                v          v ----         ii  i           i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr2_57722543_5   1725 AACAAAGTTGGAGGACTCTCACTTTTAAGTTTCAAAATGTATTACAAGGC 1676
                                           v     iiv i        iv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr2_57722543_5   1675 AGCAGTAATAAAAAC--TGTGGTATTAGCATAATGGTAGACATATAGACC 1628
                         vi       v  i  --       i i      v i            i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr2_57722543_5   1627 AATAAGAACATAACTGAGAATTCAGAA-----CCCATATATCTATAGTCA 1583
                            i-   i v  i     i i     -----      i  i   i    
  L1M4_orf2#LINE/    299 AATG-GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

C chr2_57722543_5   1582 ACTGATTTTCAACAAAGGTGCCAACACTATTCAGAGGGAAAAGAATAGTG 1533
                          i        i    i        v  i     iv   i          v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chr2_57722543_5   1532 TCTTTAACAAACGGTGATGAGACAATTGGATACCTATATGTAAAAAGAAT 1483
                          i  i      i    v  i     i      ? i i   i    -    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAAT 446

C chr2_57722543_5   1482 GACTTTTGACCCCTACCTTAATACCATATACAAGAATTCACTCAAAAGGA 1433
                           vv  v           i -i           i    v        v i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATGG 495

C chr2_57722543_5   1432 ATAAGAAATCTAAATATAAAAATAGAAAGTATAAAACTCTTAGAAGAAAA 1383
                           v ? i i      i   i iivi   v                     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

C chr2_57722543_5   1382 TATAAGAGTAAATCTTGATGATTATGGATTTGGCAATAGATTCTTAGATA 1333
                         i   i ?         vi   iiv   i  v      i v          
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chr2_57722543_5   1332 TGACACATAAAG-ACACCCAACAAGAGAAAAAGACAATACATTGGACTTT 1284
                               vv    -   vv      i       ivvi   v         i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chr2_57722543_5   1283 ATCAACATTAAAAATTTT 1266
                              v        i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTT 663

Transitions / transversions = 1.83 (88 / 48)
Gap_init rate = 0.01 (9 / 663), avg. gap size = 1.89 (17 / 9)  

3264 26.65 0.55 0.55  chr2_57722543_57730973     7032  7939 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57722543_5   7032 TGGAAGAACATTCCGTGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 7081
                              ii i  i  i  i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57722543_5   7082 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 7131
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57722543_5   7132 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 7178
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_57722543_5   7179 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCAAAGCCAAAA 7228
                                 viiv  ii  v  v v  vi    iv     ivi ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_57722543_5   7229 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTGTACTACAAGG 7278
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_57722543_5   7279 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 7328
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_57722543_5   7329 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAAC 7376
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_57722543_5   7377 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 7426
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_57722543_5   7427 CCTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 7476
                         i  v  i  i  i           v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_57722543_5   7477 TGAAACTGGATCCCTTCCTTACACCTTATACAAACATCAATTCAAGATGG 7526
                             ii    i    v   i     v        v  i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_57722543_5   7527 ATTAAAGACTTAAACATTAGATCTAAAACCACAAAAACCCTAGAAGAAAA 7576
                           i ?    i    ii v   v       i i    vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_57722543_5   7577 CCTAGGCATTACCATTCAGGACATAGACATGGGCAAGGACTTCATGTCTA 7626
                          v    ?i v viv   iv   v v ivv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_57722543_5   7627 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTC 7676
                         vi            vvi          vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_57722543_5   7677 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 7726
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_57722543_5   7727 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 7776
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_57722543_5   7777 AAGGGCTAATATCCAGAATCTACAATGAATTCAAACAAATTGACAAGAAA 7826
                          i  i  vi          v  i  v   i  vv    v ii i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_57722543_5   7827 AAAACAAACAACTCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 7876
                           i     i   i v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_57722543_5   7877 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 7926
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_57722543_5   7927 CATCACTGGCCAT 7939
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2679 25.72 2.03 1.20  chr2_57744650_57746474      498  1333 (492)    L1M4_orf2#LINE/L1       66   908 (0)  

  chr2_57744650_5    498 ATCAATTTATAGATTCGATGCTATTTCCATCAAACTACCA-CTGACATTC 546
                           ii  i  i      i i  v  ii i      v v   -   v -  i
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTT 114

  chr2_57744650_5    547 TTTGCAGAACGAGGAAAAGCT-ACTTTAAATTTCATATGGAA-T-CAAAG 593
                                  -ivv  v     - iii    v           - -   i 
  L1M4_orf2#LINE/    115 TTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_57744650_5    594 AAGATCCCATATAGCCAAGACAATTCTTAGCAAAAAGAACAAAGCTGGAG 643
                         --  i  viv        i     ii v iv  i          i     
  L1M4_orf2#LINE/    164 --GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_57744650_5    644 GTGTCATGCTACCTGATTTCAAACTATACTACAAGGCTACAGTAAGCAAA 693
                          vv   ii  v  ii        viv        i          v   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_57744650_5    694 ACAGCATGATACTGGTACCAAAACAGACATATAGACCAATGGAACAGAAC 743
                             ii  i      i iv ii i           i        i    i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_57744650_5    744 AGAGACCTCAGAATTAGCACCACACACCTACAACCATCTGTTCTTCAACA 793
                         v    vii     v  ivv   i   ii  iiii  vi  v i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_57744650_5    794 AACCTGACAAAAACAAGCAGTGGGGAAAGGATCTCCTACTCAATAAATGG 843
                          ivv  v   i v  vv  i         i  vvi  vi    i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_57744650_5    844 TGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAACTAGACCCTTT 893
                                 v      v  ?   i     i  i v    ii i     i v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_57744650_5    894 CCTTCACAT--TATACAAAAATTAACTCAATATGGATTAAAGACTTAAAT 941
                            -    i--                   v      i ?    i     
  L1M4_orf2#LINE/    462 CCT-CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_57744650_5    942 GTAAAACGC-AAAACCATGAAAACCCTAGAAGAACACATAG---TCAATA 987
                             i -  -     i  i   vi i        v      --- v   -
  L1M4_orf2#LINE/    511 GTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT- 558

  chr2_57744650_5    988 CCATTCAGGATGTAGGTATGGGCAAAGACTTCAT-GATAAAAATGCCAAA 1036
                         - -   iv  iv v  vv i     v ii   v -    vi -ii     
  L1M4_orf2#LINE/    559 -C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-CACCAAA 605

  chr2_57744650_5   1037 AGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATATAATTAAACTAA 1086
                             vvv          vv     v  i    v   iv v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_57744650_5   1087 ACAGCTTCTGAACAGCAAAAGAAACTATCATCAGAGTGAGCAGGCAACCT 1136
                          v i   i  vi vv    i  v       vv i     iv  i     i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_57744650_5   1137 ACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAGGTCTAAT 1186
                                          v       vii ivi      i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_57744650_5   1187 ATCCTAAATTTATAAGGAACCTAAACAAATTTACAAGAAAAA---AAAAA 1233
                             vi   v     i    iivv    v iv i  v     ---   v 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_57744650_5   1234 AC---ATCAAAAAGTAGGCAAAGGATATAAAAAGATACTTCTCAAAATAA 1280
                           ---  i?    i i          v i  v   i i     v   v  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_57744650_5   1281 GACATTTACACAGCCAACAAACATATGAAAAAAAGCTCAACATCACTGAT 1330
                           i  vi v ii     i  i  i       i v           ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_57744650_5   1331 CAT 1333
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.36 (122 / 90)
Gap_init rate = 0.02 (18 / 843), avg. gap size = 1.50 (27 / 18)  


3196 26.21 0.77 0.77  chr2_57747134_57753385     4853  5760 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57747134_5   4853 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4902
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57747134_5   4903 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCGTCCCCATCAAGA 4952
                            v     v     iv i  i           i  vi    i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57747134_5   4953 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4999
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_57747134_5   5000 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCAAAGCCAAAA 5049
                                 viiv  ii  v  v v  vi    iv     ivi ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_57747134_5   5050 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5099
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_57747134_5   5100 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5149
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_57747134_5   5150 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAAC 5197
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_57747134_5   5198 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5247
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_57747134_5   5248 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5297
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_57747134_5   5298 TGAAACTGGATCCCTTCCTTACACCTTATATAAACATCAATTCAAGATGG 5347
                             ii    i    v   i     v    i   v  i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_57747134_5   5348 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCC-AGAAGAAAA 5396
                           i ?    i    ii v   v       i      vi i-         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_57747134_5   5397 CCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGCCT 5445
                          v    ?i- v   -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_57747134_5   5446 AAAACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5495
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_57747134_5   5496 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCCGAGTGA 5545
                         v  i   v v  i i   i  ii vv    i  v    i  vvvi     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_57747134_5   5546 ACAGGCAACCTACAAAATGGGAGAACATTTTCGCAACCTACTCATCTGAC 5595
                          v  i     i   i          v  v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_57747134_5   5596 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTGACAAGAA 5645
                           i  i  vi          v  i  v      vv    v ii i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_57747134_5   5646 AAAAACAAACAACTCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5695
                            i     i   i v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_57747134_5   5696 TCTCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAAAATGCTC 5745
                             v        i  vi viii     v  i-          i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTC 893

  chr2_57747134_5   5746 ATCATCACTGGCCAT 5760
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


2854 26.22 2.43 1.99  chr2_57825332_57830794     4068  4971 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57825332_5   4068 TGGAAAAACAATCCATGTTCATGAATTGGAAAAATGAGTATTGTTAAAAT 4117
                               i i vi           i       i v v i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_57825332_5   4118 ATTTATGCTGCCCAAAGCAATCTACACATTAAATGCTATTCTTATCAAA- 4166
                         iviv  i  v      vii       v   v  i  v  i i       -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_57825332_5   4167 TCACCAA-TATCATTTCT-CAAAGAATTAGAAAAAACT-ATTTTAAAATT 4213
                           -   i- ii v   i -  i -    i-- v  i  -  ii       
  L1M4_orf2#LINE/    101 TC-CCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATT 146

  chr2_57825332_5   4214 TATTTGGAACCAAAAAAGTGCCGGAATAGCCAAAGCAATCTTGAGTATAA 4263
                         i  v     viiv  ii vv  i           i         iv vi 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_57825332_5   4264 AGAACAAAGCCAAGGGCATCACATTACCCACCTTCAAACTATACTACAAG 4313
                                  iiiii  vv     i v    vi      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_57825332_5   4314 GCTACAGTAAACAAAACAGCATGGTGCTGATTCCAAAAATAGATACATAG 4363
                                   v   i    ii    i   ii-vi  ii     i i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGACATATAG 295

  chr2_57825332_5   4364 ATCAATGGAA-AGAATCAAGAACTCAGAAATAAATCACCATATCTACAAT 4412
                                   -     ii   iii          i vvi i  i  iii 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_57825332_5   4413 CTACTGATCTTCAACAAGATTAACAAAAATAAGCAATGTAGAAAGGATTC 4462
                          v i    i   i     iv iv   i vi vv     vi     i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_57825332_5   4463 CCTATTCAGTAAATGGTGCTGGGAAAATTGGCTATCCCTATGCAGAAGAA 4512
                         i  v    ii              v  i   v  ?  vi     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_57825332_5   4513 TAAAACCGGACCCTGATCTATCGCTGTACATATACGAAAATTCACTCAAG 4562
                          i  iii      iv i  vv i ----       i      v      i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACAC----CATATACAAAAATTAACTCAAA 491

  chr2_57825332_5   4563 ATCAATTAAAGACTTAAATGTAAGACTTCAAACTCTAAAAATACTAGAAG 4612
                           vi  i ?    i           vi v     v     v vi      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_57825332_5   4613 GAAACCTAGGAA-ATATCCTTCTGAATATCAACCTTGA--CA---AATAA 4656
                         i    v    ?i- v   i iv   -------     i--i ---   ii
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGA-------CCTTGGGTTAGGCAATGG 584

  chr2_57825332_5   4657 TTTATGAG-CAAGTCCTCAAAAGCAATTGCAACAAAA----AAATTGACA 4701
                            v v  -i v v vi        vvv         ----    v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_57825332_5   4702 GGTGGGATCTAATTAAAGTAAAGAGCTT-----CTTCACAGAAGAAACTA 4746
                         ii v   ii v  i   i v  i i   -----     v  --  v    
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG--GACACTA 682

  chr2_57825332_5   4747 TCAACAGATTAAACAGACAACCTACAGAATGGGGGAAAATATTCACAAAC 4796
                             v i v i  v        i          i         ii    i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_57825332_5   4797 TATGAACCCAACAAAGGGCTATTATCCCGAATCTATAAGGAACTTTAAAA 4846
                         i  iv i ii i  i  i  vv     v    v     i     i v v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_57825332_5   4847 AATCAACAAGAAGAAAACAAATAACTCCATTCAAAAGTGGGCAAAGGACA 4896
                          v    i  v  i  i         i v   ?    i           iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_57825332_5   4897 TGAACAGACACTTCTTAAAAGAAGACATACAAACAGCCAACAAACATGTA 4946
                             i     i    iv        i       ii     i  i  ii i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_57825332_5   4947 AAAA-ATGCCCAGCATCACTAATCAT 4971
                             -    i  i     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (149 / 84)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.11 (40 / 19)  


2488 17.57 4.79 4.31  chr2_57856812_57858429      501  1126 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_57856812_5    501 AAAGACAGACATATAGATCAATGGAATAGTATAGAAAGCCCAGAAATAAA 550
                           i  i                       v  v  i  i           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_57856812_5    551 CTCTTGCATATATAACCAAATGACTTT-GACAAGAATGCTA-GAT-ATTC 597
                          i v i   v   iii   v   i   -      ii   i -  i-    
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_57856812_5    598 AATCAGAAAAGTATAGTTGTTTTTGACAAATGATGTTAAGAAAACTGGAT 647
                            vi i    v     i-    ii       i  i ii  v        
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTC-TTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_57856812_5    648 ATTCACATGCAAAAGAATGAGGTTGGACCCGTACCTTACTCCATATACAA 697
                          ?i                 i         v     i  v          
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_57856812_5    698 AA-TTAATTCAAAATGGATTAAAGACATGTAAAGAGATGTAACAGTTAAA 746
                           -    i           i ?    v ------ i      v  i    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCT------AAATGTAAGAGCTAAA 522

  chr2_57856812_5    747 ACTATAAAACTGTTAAAAGAAAACATAAGATAAAAACTTCATGACACTGG 796
                                    v   i           i ?vv   v    i    vi   
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_57856812_5    797 ATTTGGCAAAGAT--CTTGGATATGATACCAAAAG-----GCAGCAAAAG 839
                         i  v     v i --   i       i        -----   i      
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_57856812_5    840 CAAACAGAGATAAATTGCACTTCATCAAAATCTAAAAA-TTCTGCACATC 888
                         v   v v          v             -      -  i  ii v  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTTTGTGCTTC 671

  chr2_57856812_5    889 TAACAACATCTATCTTTCTATAGCTACTATCAACAGAGTATAAAAGGCAA 938
                         v  vi   ------------------       v i   i-     i   
  L1M4_orf2#LINE/    672 AAAGGACA------------------CTATCAAGAAAGTG-AAAAGACAA 702

  chr2_57856812_5    939 CATATGGAAT-----AAAATATTTGCAAATCATAT-TCTAATAAGGGTTC 982
                          vi ii    -----                    -   i       vii
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_57856812_5    983 AATATCCAGAATATATGAACAACTCATAGAACTCAACAACAA-------- 1024
                         vi              i  v     v  v       i  i  --------
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_57856812_5   1025 ----CCCAATTTAAAAACAGTTAAAGGACTTGAATAGACTTTTCTCACAA 1070
                         ----       ?     ii vi      i          v      vv  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_57856812_5   1071 GAAGATATATAGTTGGCCACTAAGAACATAAAAAGATGTTTAATATCACT 1120
                                  i iv      v    v    i        i i  i    ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_57856812_5   1121 AACCAT 1126
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.65 (66 / 40)
Gap_init rate = 0.02 (15 / 629), avg. gap size = 3.80 (57 / 15)  


2240 27.62 3.03 0.88  chr2_57868133_57869901.rev      484  1276 (492)    L1M4_orf2#LINE/L1       99   908 (0)  

  chr2_57868133_5    484 AATCACCATGGTGTCATTCTTCGCAGAACTAGAAAAAAACT-ATTTTAAA 532
                             -   - v  i -  i  i      v v  v  i--  -  ii    
  L1M4_orf2#LINE/     99 AATC-CCA-GCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAA 143

  chr2_57868133_5    533 ATTCATATGGAACCAAAAGAGAGCCTGAATAGCTAACACACTCCTAAACA 582
                                     viiv   i  v  v       i  v   v  i i  v 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_57868133_5    583 A----AACAAAGCTGGAGGCATCACACTACCCAACTTCAAACTATACTAC 628
                          ----       i      vv       v     i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_57868133_5    629 AGGGTTATAGTAACCAAAACAGCATAGCACTAGTACAAAGACAGACATAC 678
                          ii i  i     i   i    ii i i   i i i  i  i       i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_57868133_5    679 AGACCAATGGGACATAATAGAGAACCCAGAAATAAGGCTGCACACCTA-- 726
                            i      i i v   v    ii          iv iii   ii  --
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_57868133_5    727 --CAAGT-ATTTTTGACAAATCTGACAAAGACAAGCAATGGAAAAAGGAT 773
                         --   v -     i     ivv  v   iiv  vv      ii    i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_57868133_5    774 TCCCTACTTCATAAATGGTGCTTGAATAACTGGCTAACCATATGTAGAAG 823
                         vvi  vi iv i          v i i      v  ?   i   i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_57868133_5    824 ACTGAAACTGGACCCCTTCCTTACACCTT-TACAAAACTTA-CTCAAGAT 871
                          v    ii         v   i     v -       v   -     i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_57868133_5    872 GGATTAAAGACTTAAA----ACA--CAAAACTATAAAAACCCTGGAAGAC 915
                             i ?    i    ---- v --i            vi i i     v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_57868133_5    916 AACCTAGGTAATACTATTCAGGACATAGGAACAGGCAAAGATTTCATGAC 965
                            v    ?ivv v v   iv   v v  ivi      v i    v iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_57868133_5    966 AAAGACACCAAAAGCAATTGCAACAAAACAAAAATT-GACAAATGGGATC 1014
                         v v             vvv         v     v -  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_57868133_5   1015 TAATTAAACTTAAGAGCTTCTAAACAGCAAATGAAACTATCAA-----TA 1059
                          v  i   v    i i   i ivi vv    v  v        ----- i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_57868133_5   1060 AACAGACAACCTATAAAATAAGAGAAAAAAATTTTAAACTATGTATATGA 1109
                           v        i i i   ii       v v  vi   ii  i   v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_57868133_5   1110 CAATGATCTAATATCTAGCATCTATAAGGAACTTAAACAAATTTACAAGT 1159
                         i  v iv  vi    i  v  v     i     ivv    v iv i  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_57868133_5   1160 AAAAACCAAACAATTCTATTAAAAAGTGGGCAAACGACAGGAACAGATAC 1209
                             iv    i  ii v   ?    i        v  ivv   i   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_57868133_5   1210 TTTTAAAAAGAAGACATGCATGTGGACAGAAATCATATGAAGAAAAAAGG 1259
                           i vv        i  i  vi   v  iv  v  i     --  i v v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA--AAGATGC 891

  chr2_57868133_5   1260 TCAGTATCACTGATCAT 1276
                            ii    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (120 / 95)
Gap_init rate = 0.02 (15 / 810), avg. gap size = 2.07 (31 / 15)  


3047 25.34 3.25 1.46  chr2_57962440_57966697     2876  3767 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_57962440_5   2876 TAGAAAGGTATACTATATTTCTGGATTGGAAGAATCAAACAACTTTATAT 2925
                          i     i   v i  i  iv            ---------   v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA---------CTTAATAT 41

  chr2_57962440_5   2926 TGTTAAAAATGCCCATACTATTCAAAGCAATCTGCAGACTTAATGTAATT 2975
                               i -  v v     vii    vii    i    i i  i i   i
  L1M4_orf2#LINE/     42 TGTTAAGA-TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chr2_57962440_5   2976 CCTACCAAAACTCCAA-TGGCATTTTTACAGAAATAGAAAAAA-AATACT 3023
                             i     ii   i-  v v     i       v  v  iv-i  v  
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_57962440_5   3024 AAAATACATATGGAACCACAAAATACACCGAATAGTCAATGCAATCTTGA 3073
                              v         vii   iiv  v v      i   vi         
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_57962440_5   3074 GGAAAAAAGTACAAAGTTAAAGGAACCACATTTTCTGATCTCATACCATA 3123
                         i-   i   v        ii    vi    i  i ii  i   v v v  
  L1M4_orf2#LINE/    191 A-AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_57962440_5   3124 TTACAAAGCTATAGTAATCAACACTGCATGGTAATGCCATAAAAACAGAT 3173
                         i          i         v  v ii     v  v     ii i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_57962440_5   3174 A---------ATTGAAAATAATAGAGAGCTCAGAAACAAATCCCATGCAT 3214
                          ---------  v   v v   v     ii      i   -     i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACAT 338

  chr2_57962440_5   3215 TTATA-TCAATTGATTT-CAACAGAGGTATCAAAATCATACAATGAAAAA 3262
                             i-           - i   ii   ii   i i   v     iii  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_57962440_5   3263 AGGACAGTTTCTTCAATAAATAGTGCTAAGAAAACTGGGTATCTACATGT 3312
                           i i   i i     i    i     ii  v      i  ? i     i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_57962440_5   3313 AGCAGAAAAAAATTGCACCCTTAACTCAAACTACATACAAAAATCAACTC 3362
                          iv    vi  i   v    i  v    v  i i          i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_57962440_5   3363 AAAACGAA-----GATTTAAACACAAGGTTTGAAATGATAAAACTACTAA 3407
                             i i -----  ii    iii   ivi i   iv        vi  i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_57962440_5   3408 AAGAAAACA-AAGGATAAAGACTTCTTGACATTGATCTGGAAAATTACTT 3456
                                  - i ?i    v-    v    v   ivi i iv   vii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_57962440_5   3457 TTTGGAT----C-CCAAAAGCATACACAACAAAAGCACAAACAGACAAAT 3501
                         i  i   ---- -         i vi         v v   i   i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_57962440_5   3502 GGGA-TGAAACCAATCTAAAGGTTTCTGCAAAGCAGAGGAAAT----AAC 3546
                         v   - vv v v  vi    iii  i  iivvv  i    v i----  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_57962440_5   3547 AGAGTAAAAAGACAACCTATGGCATGGGAAAAAATAATTGCAAACCTTCC 3596
                          i   i           i ii v      i      v       i v vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_57962440_5   3597 ATATGATAAGAGGTTAATATATAAAATATATAAAGAACTCAAACAACTCA 3646
                           v       i ii vi   vi i                vv        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_57962440_5   3647 ATAGCAAACAAACAGGTAACCTGATCTAAAAATGGGCAAAGGACCTGAAT 3696
                            ii   v i   ii     ii  i?                ii     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_57962440_5   3697 AGACATTTTTCAAAAGAAGTCATACAAATGGCCAATAGGCATATAAAAAA 3746
                                 i  v       vi                i   i  i    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_57962440_5   3747 ATACTTAACATCGCTAATCAT 3767
                           i  i      i????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (149 / 74)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.62 (42 / 16)  


3225 26.03 1.56 0.56  chr2_58061767_58066166.rev     3010  3908 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_58061767_5   3010 TGGAAAGGCATTCCAAGTTCTTGGATTGGAAGAATCAATATTGTTAAAAT 3059
                                ii  i   v    v            v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_58061767_5   3060 GTCCATTCTAGTGGAAACAATCTACAAGTTCAATGCAGTCCCTATCAAAA 3109
                          v v  v  vvivi  vii       ii     i   i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_58061767_5   3110 TACCGATGACTTTCTTCACA-AAATAGAAAAAATAATTCTAAAATTTATA 3158
                          v  iiivi i  i  ii  -    v  v  iv i  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_58061767_5   3159 TGGAATCACAAAAGACCTAGAATAGCCAAAGCTATCCTAAGCAAAAAGAA 3208
                              vii   ii    i            i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_58061767_5   3209 CACTACTGAAGGAATCACATTACCTGACTTCAAAGTATACAGCAGAGGTG 3258
                           vvii  i    v     i v  ii i      iiv   vi  i  v i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_58061767_5   3259 TAGTAACCGAAATGGCATGGTACTGACATACAAACAGACACAGAGATCAG 3308
                         i     i i i ii ii        i    vii i     i v      i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_58061767_5   3309 AAGAACGGAAGAGAGAACACAGAAATAAATTCACACATCTAGAATAGACT 3358
                         vi   ii   vv    iiv          ii  i    i  vii vi i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_58061767_5   3359 CATTTTTGACAAAGGTGCCAAGAACATACATTATGGAAAGGAAAGTCTCT 3408
                         v     i     i          v   v  v iv      i v     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_58061767_5   3409 TCAATAAATGTTGCTGGTAAAACTGGATATCCATACGCATAAGAACGAAA 3458
                             i     v      v v         ?   i i   v     i   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_58061767_5   3459 CTAGACCCCTATCTCTCCCCATA--CAAAAATCAAATAAAAATGAATTAA 3506
                         i i        i   v v     --       i  v v      i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_58061767_5   3507 AGACTTAAATCTAAGAACTGAAACTG--AAACTACTAAAGGGAAACCTTG 3554
                             i     v     i  i     i--     vi  i i i    v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_58061767_5   3555 GAG-AAATTCTCTAGACATTGTAATGGGCAAAAATTTCTTGAGTA--ATA 3601
                          ? -    ii  vv   v   viv i     vii      iii  -- i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_58061767_5   3602 TCCACAAGCAAAGGCAACCAAAGCAAAAGGGGATAAACGGGA--TCA-CA 3648
                         -   v     v i     v    v    ivi      iv   --   -  
  L1M4_orf2#LINE/    601 -CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_58061767_5   3649 ACTAACTAAAAAGCTTCAGCACAGCAAAGGAAACAA--AAAAAGGTGAAG 3696
                          --  i      -   iv ii vv       v  v --  i  i     i
  L1M4_orf2#LINE/    650 A--AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_58061767_5   3697 AGACAACCCACAGAATGGAAGAAAATATTTGCAAACTATGCATCTGACAA 3746
                                           i                ii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_58061767_5   3747 GAGATTAATAATCAGAATATATAAGAAGTTCAAACAACTTTATGG-AAAA 3795
                          i  i vi  vi            ii ii  vv      iv  ii-    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_58061767_5   3796 AATCTAATAATCTGATTTAAAAACAGACAAAAGATCTGAATAGACATTTC 3845
                          iv v     i ii   ?     ii i    i   i              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_58061767_5   3846 TCAAAAAAAAAACATACAAATGGCAAACAGGCATATGAAAAGGTACTCAA 3895
                           v   i  i -i           v  i i   i        i i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGA-TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_58061767_5   3896 CATCATTGGTCAT 3908
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.99 (153 / 77)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


2741 25.26 1.94 1.81  chr2_58069658_58071430.rev      510  1281 (492)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr2_58069658_5    510 ATCCTAAAATTTGTATGAAAACACAAAAGATCATAAATAGCTATAGCAAT 559
                                    ii    i   ii   ii  i vvi      i v i    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_58069658_5    560 CTTATAGAGTAAGAAAAACAAAGAAGTAGGCATCACACTTCTTGATTTCA 609
                            ---  iv     i       vv v   vv         iii      
  L1M4_orf2#LINE/    186 CTT---GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_58069658_5    610 AA--TTATTTACAAATCCATAGTAATCAAAGCAGCATGGTACTGCCATAA 657
                           --   i -     v i i         ii   ii        v     
  L1M4_orf2#LINE/    233 AAACTTACT-ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_58069658_5    658 AAACAGACGTATAGATCAATGCAACAGAATAGAAAGTTCAGAAACAAACC 707
                         ii i    i            v  i     v  i   i      i     
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_58069658_5    708 TATGTACGTACATTCAACTAATTTTTGACAAAGGCACCAAAAATACACAA 757
                         i  ii iv  iiv    i i     i     i  ii    i vi iv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_58069658_5    758 TAAGTAAAAGGTAGTCTCTTCCATAAATGATGTTGAGGAAACTGAATATA 807
                          ii v   iii      i   v i     i  i  i iv     i   ?v
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_58069658_5    808 CATATACCAAAAAAAAAAAAAAAGAAAGTTG-ATCCCTATGTTACACCAC 856
                           i  i ---------    i  vi      - i     iv i      i
  L1M4_orf2#LINE/    432 CACATGC---------AAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_58069658_5    857 ACACAAAAATCAACTCAAAATGGAT-AGAGAACTGAAGCACAAGATTGGA 905
                          i        i              - ?   v  i  -iii    vivi 
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA-TGTAAGAGCTAA 521

  chr2_58069658_5    906 AGCTATAAATCTCTTAGAGGAAAAT----GAGAAAATGTCCATGACATCG 951
                          i       v        i     i---- ? v    v i i    v i 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_58069658_5    952 ATCTTGGTGATAATTTTTTGGATATGATACCAAAACCACAGGTGACAAAA 1001
                         ivi v  ii  ii   i  i       i       v    i ii      
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_58069658_5   1002 GCAAAAACA---AAGTGGGACTATATCGAACTAATACATTTCTGCACAGC 1048
                          v     i ---  i v     vi   i  v v v v i  i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_58069658_5   1049 AAAATA-ACAGTCAACAAAAGGCAAAGGCACACTATGGAATGAGATAATA 1097
                            iv -  vi    v   iv v    i  vv i ii     i  v  v 
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_58069658_5   1098 TATTTGCAAACCGTATACCTGATATGGGGTTAATATTCAGAATATCTAGA 1147
                                   i i    i      v   ii vi   i        v  i 
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_58069658_5   1148 GAACTCATACAACTCAGTAGCAAAAAATCAAGTAAAC--ATTAAAAATTG 1195
                               v         i  ii     iv   i   v --   ?    v  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_58069658_5   1196 GGCAAAGGATCTGAATAGATATTCCTCAAAAGAAGA-ATACAAATAGCCA 1244
                                   i        i   i   v        -        i    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_58069658_5   1245 ATAGGTGTATTAAAAGGGGCTCAACATCACTAATCAT 1281
                            i iii  v     iv           ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (130 / 61)
Gap_init rate = 0.02 (12 / 773), avg. gap size = 2.42 (29 / 12)  


 703 20.28 12.68 12.39  chr2_58124505_58126701      528   882 (1314)    L1M4_orf2#LINE/L1        1   356 (552)  

  chr2_58124505_5    528 TAGAAAAATATGCCATGCTCATAGGTTGAAAGACATAATGTTGTTAAGAT 577
                          i    i    v     i    i i   i     v    i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_58124505_5    578 T-CAATATTCTTTAAATGTCAGCTTCTTCAAACTGATAGATCTAATATAG 626
                         v-     i  iii    ----------------    ----   ------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT----------------TGAT----CTA------ 74

  chr2_58124505_5    627 ATTTTGGACTCAATATAGATTCAATACATTTCCAATCAAAATTCCAGCAA 676
                         ---------------i        ii  v i  v        i     v-
  L1M4_orf2#LINE/     75 ---------------CAGATTCAACGCAATCCCTATCAAAATCCCAGCT- 108

  chr2_58124505_5    677 GATTTCTTTATAGAAATCAGCACACTAATTCTGAAATTTATATGGAAA-G 725
                          vi  i   ii      iii  vi  i  i  i     i         - 
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_58124505_5    726 CCAAGGAATTAGAAAAGTCAAAACAATTTTGAAAAA--AGAATAACATTT 773
                          v i   vii    v  i         i        --    i  vi  v
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_58124505_5    774 GAAGACTTATATTACCTGATATCAAGACT----ATAAAGCCACA-TA--- 815
                           i    i i i v  ii  v    i   ---- i     i   -  ---
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_58124505_5    816 --------------------------TATACATATA--TT--TGCAACAA 835
                         --------------------------  v       -- i--  v  i i
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_58124505_5    836 AA--AAGACTTCAGAAATAGACCCACTA-ATACATAGTTCAATCGATTTT 882
                           --i   v i        i     -  -  vi  i  -    i      
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCA-TACATTTATGGT-CAATTGATTTT 356

Transitions / transversions = 2.79 (53 / 19)
Gap_init rate = 0.04 (16 / 356), avg. gap size = 5.56 (89 / 16)  

1459 22.97 11.20 0.77  chr2_58124505_58126701     1188  1705 (491)    L1M4_orf2#LINE/L1      337   908 (0)  

  chr2_58124505_5   1188 ATTTTTGA-CAATTGATTTT-GACAAAAATGC-AAAACTAATTGTTAGAT 1234
                             v  i-           -     iii   -  i  i v iiv i iv
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_58124505_5   1235 AAAGGATAATATTTTTTAAAAATTGTGTTGGAAAAACTGGATATACACAT 1284
                             i   i v    iv v    v   i   i v         ?v     
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_58124505_5   1285 GCAAAAAAATATAAACTTCCTTTCCTACCTCACACCATATACAAAAATTA 1334
                               i   i--  v  vvvii                           
  L1M4_orf2#LINE/    437 GCAAAAGAATG--AAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_58124505_5   1335 AATCCAAACGGATGACAGACATAAAAGTAAAACCTGAAACCA-------- 1376
                          v  v   i    v ?    v    v    i v  i    i --------
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_58124505_5   1377 ----GAGAAAACAT------------------CCATAGGAAAAAAAATG- 1403
                         ----i         ------------------  v i  vv iiv    -
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_58124505_5   1404 ------AAATAT-----CAAAAGCATAAAATATTATAAGAAAAGTTA-AC 1441
                         ------ i    -----        i  i-i vi v       iv  - i
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGAT 633

  chr2_58124505_5   1442 AAATTGAACTTTATCAAAATCAAAAAATTCTTCTCTCTGAAGGTGCTTAT 1491
                               i    i        i     v  i viv  iii    vvvi   
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_58124505_5   1492 ------AATAAAACAACAAACCACAAACCAAGAAAAAAATCTATGCAAAT 1535
                         ------ i i   vi    v     i viii  i    - v v       
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAAT 732

  chr2_58124505_5   1536 TATGTATCTGATAAAGGACTTGTATCCAGAATATATAAACAACTCTCAAA 1585
                         i  i          i                        v      i v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_58124505_5   1586 ACTCAGTAA---GAAGACAAACAATCCAAT--AAAAATGGGCAAAAC-TC 1629
                              i   ---i        i  i     --             iv- i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_58124505_5   1630 TGAACAAATACTTCACAGATGAAAATATACATATGGCAAATATGCACATG 1679
                             i i i i   v vi v   i       v     v    v       
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_58124505_5   1680 AAAAGGTGTTCAAGATCATTAGTAAT 1705
                              i  i    v    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (69 / 48)
Gap_init rate = 0.03 (15 / 572), avg. gap size = 4.13 (62 / 15)  


2843 23.03 5.70 2.17  chr2_58209348_58212168.rev     1453  2329 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_58209348_5   1453 TGGAGAGATACATCATGTTCATAAATAGGAAGACTCACTCATATTCTTAA 1502
                             i     ivi         ii  v        i ---     v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTA---ATATTGTTAA 47

  chr2_58209348_5   1503 GATGTCAGT-CTCCTCAACTTGATATATAAAGTCAAAGCAATACTAATAA 1551
                             v  i -    i   v     v  i i v    v     v iv  v 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_58209348_5   1552 AAACACAAGTTA----TGTTGTGGATATCAACAAATTGATTCTAAAGTTT 1597
                            iv v  i i---- v   ii  v  ii    ii    i     i  i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_58209348_5   1598 GTACATAAAGGCAAAAGATCCAGAACAGCAAACACAATACTGAA------ 1641
                         i  iiv   v    ii  i      i   v  v     vi    ------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_58209348_5   1642 GAACAAAGTCAGAGGACTTGCACTATTCAAGTTCAAAGCTTTCTATAAA- 1690
                                  ii       ii    vii   v      i   v   i   -
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_58209348_5   1691 ---CAATAATTAAGAAAATGTGGTACTGCAAAAAAAATAGACAAATAGAT 1737
                         ---  i    i    v i          vv v  ii       v      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_58209348_5   1738 CAATGTAATAGA-T----AGCCTAGAAATAGACCCGATATAGTCAAATAT 1782
                              v      - ----  i i       i    -   i v i -----
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCC-ATACATTTA----- 341

  chr2_58209348_5   1783 AAATAGGCAGTCAATCTTT-ACAAAAAAGCAAAGGCAATTCAATAGACGA 1831
                         --- i v  i ii  i  i-    iiiv  v   i v       i ivi 
  L1M4_orf2#LINE/    342 ---TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_58209348_5   1832 AGTGTAGTCTTTTCAGTAAATGGTACTAGGAC---TGGACACTCACATGC 1878
                           vi           ii       i  i    ---    i ?i       
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_58209348_5   1879 AAAAATGTGAATCTAGACACTGATCTT---TCATA----AAAATTAACTC 1921
                             ivi    vi i   v iv i  i---i    ----           
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_58209348_5   1922 AAAATGGATCATAAACCTAAATGTACAATGCAAAAACGATAAA-CTTCTG 1970
                                    ? i           vi -  v     v     -  ii i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTA 537

  chr2_58209348_5   1971 GAAGATAACACAGATGAAAATCTGGGTGACCTAAGG----GTAATGAGTT 2016
                              v    i  i? v      vv       vi  ---- i    iv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_58209348_5   2017 TTTACAGATATAATACCAAAAGCATAATCCATGCAAGAAAAGAACTGTTA 2066
                         i   --     i i          i  v v iiv       -  iv v  
  L1M4_orf2#LINE/    588 CTTA--GATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATA 634

  chr2_58209348_5   2067 AATTGGACTTCATTAACATTAAAAA-TTTTCTGCTCTGTCAAAG-ACACT 2114
                                      i  v        -    v    ---      -     
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCT---TCAAAGGACACT 681

  chr2_58209348_5   2115 GTTAAGAAAATAATAAGATAAATCACAGTCTGGGAGGAGATATTTGCAAA 2164
                         i i      i i v    i  vi     vv      i i           
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_58209348_5   2165 ----ACATCTGACAAG--AC--ATATCAAAAATATACAAAATATTCTTAA 2206
                         ---- i      i   --  --i    v i      i   iv i     v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_58209348_5   2207 AACTCAACAATAAAAA-ATGAACAACTCATTTTAAAA-TGAGCAAAATAT 2254
                                i        - ii  i   i  v  ?    -  i     iv  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_58209348_5   2255 TT-AACAGAAACTTCTA-AAAAAAGATGTAAAGGTGTAAAATAAACATAC 2302
                           -  i   v i    v-   i     i  v ii  vvv     i  i i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_58209348_5   2303 GAAAAGATGCTTAACATCATATATAAC 2329
                                    i       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (127 / 71)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.46 (69 / 28)  


3310 26.32 0.55 0.55  chr2_58231701_58233583.rev      484  1391 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_58231701_5    484 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATCAGAAT 533
                              ii i  i     i        v      v i     ii i ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_58231701_5    534 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 583
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_58231701_5    584 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 631
                          v   iivi i  i  ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_58231701_5    632 TATGGAACCAAAAAAGGGCCTGCATTGCCAAGACAATCCTAAGACAAAAG 681
                                viiv  ii iv  v v  v     i      i i i v i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_58231701_5    682 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGGC 731
                                i      vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_58231701_5    732 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 781
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_58231701_5    782 AATGGAACAGAAC--AGAGCCCTCAGAAATAATATCACACATCTACAACC 829
                                i    i--    i  --        vvi  i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_58231701_5    830 ATCTGATCTTTGAGAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 879
                          vi    i  i  v  ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_58231701_5    880 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 929
                           v  i  i              v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_58231701_5    930 GAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGA 979
                            ii    i    v   i    iv              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_58231701_5    980 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1029
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_58231701_5   1030 CTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGACTA 1078
                         v    ?i- v i -   iv   viv  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_58231701_5   1079 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1128
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_58231701_5   1129 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1178
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_58231701_5   1179 CAGGCAACCTACAAAATGGGAGAACATTTCCGCAACCTACTCATCTGACA 1228
                         v  i     i   i          v  v ii    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_58231701_5   1229 AAGGACTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 1278
                          i     vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_58231701_5   1279 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1328
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_58231701_5   1329 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1378
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_58231701_5   1379 CATCACTGGCCAT 1391
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (144 / 91)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3169 24.77 3.04 0.79  chr2_58240523_58244743     2842  3729 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_58240523_5   2842 TGGAAAAACATTCCATGCTTATAGATCAGAAGA------ATTGTTAAAAT 2885
                               i i  i     i i  i   ii     ------        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_58240523_5   2886 GAGCACAGTGCCCAAAACAATCTGCAGATTCAGTGCAATCTCTATCCAAA 2935
                          ivv i v v      vii    i        ii      i     v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_58240523_5   2936 TACAAGCATCATTTTTCACAGAATTAGACAAAACCATCCTGAAATTCACA 2985
                          v v   vv v     ii     v v     iviv     i       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_58240523_5   2986 TAGAACTGAAAAGGGGGCCTGAATAGCCAAAGCAACCCTAAGCCCAAAGA 3035
                          i   v  v  -   iv  v           i   i i i ivvvi    
  L1M4_orf2#LINE/    151 TGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_58240523_5   3036 ACAAAGCTGGAGGCATCACATTACCTGACCACAAATTATACTGCAAGGCT 3085
                               i      vv     i v  ii iiv    viv    i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_58240523_5   3086 ATAGTAACCAAAACAGCATGGTTCTGGTATCAAAATAGACACATAGATCA 3135
                          i     i   i    ii    v    i  v ii       i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_58240523_5   3136 GTGGAACAGAATAGAGAACCAATAAATAAAGCTACATATCTACACCCAAG 3185
                         i     i     v    ii v v       v i i i  i  iivi   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_58240523_5   3186 TGATTGTTGATAGAGTCAACAAAAATGCACACTGGGGAAAGGACACCCTG 3235
                              v i  i ii viiv   i viiiv  v         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_58240523_5   3236 TTCAATAAATTGTGCTGGGAAAATTGGATTGCCATATACAGAATAATGAA 3285
                              i    v         v  i     v?   i  i  i  v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_58240523_5   3286 AATGGACCCCTATCTCTCACCATATACAACAGTCAACTCAAGATGGATTA 3335
                         iv          i   v            v i i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_58240523_5   3336 AAGACCTAAATGTAAGGGCTGAAACTATAAAAAATACTAGAAGTAAAACA 3385
                         ?               i   i           v- vi      -      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAG-AAAACA 547

  chr2_58240523_5   3386 -AGGGAAAGCTCTT-GTGGACATTGGTCTAGGTAAATAATTA--TAGACT 3431
                         -   ?iv iv    -   -  v    vi    i  - ii  v--    - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAA-TGGTTTCTTAGA-T 594

  chr2_58240523_5   3432 AAGACCTGAAAAGCTTAAGCAACAAAA------ATAGACAAGTGGGATTT 3475
                          v   viv      vi           ------     i  i v   i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_58240523_5   3476 AATTAAACTGAAAAACCTCTGCACAGCAAGAGAAACAATCAACCAAGTGA 3525
                         v  i   v v      i i  ii vv   ii  v  v     vv      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_58240523_5   3526 ACAGACAACCTGCAGAGTGGAAGAAAATATTTGCAAACAATGCATATGAC 3575
                          v        ii    i   i                iv  ii  v   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_58240523_5   3576 AAAGGGCTAATATCCAGAATCTATAAGGAACT-TGACAA---------GA 3615
                           i  i  vi          v     i     - v    ---------i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_58240523_5   3616 AAAAA-AAATAACCCCATTAAAAGATGGGCAAAAGACATGAACAGATATT 3664
                            i -         v   ?   i         i  iv    i   i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_58240523_5   3665 GTTTAAAATAAGACATAAAAATAGCCAATAAATATATGGAAAAAATGCTC 3714
                         vi iv   v    i   v    i        ii i   -    i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTC 893

  chr2_58240523_5   3715 AACATCACTAATCAT 3729
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (132 / 84)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.27 (34 / 15)  


2164 27.18 7.68 3.56  chr2_58286570_58290907.rev     2980  3851 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_58286570_5   2980 TGCAGAGAAGTACCAGGTTTATGCACTGGAGGAGTCGACATTGTTGGGAT 3029
                           v i   vi v   v   i   v i    i  v ii i      ii   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_58286570_5   3030 GCCAGTTCTCCATAAACTCATCTTTACACTTAATGTACTCCCAGTCAATA 3079
                          v  i v    vi   i v    vi v i i  i i v    vi    v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_58286570_5   3080 TCCCATTGTGCATTTTTTGGTGGAAACTAACAAGCTGCTTCTTAAATTT- 3128
                              vi-   v       -ii    i i        v i  v     i-
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_58286570_5   3129 TATGGAGGAGACTAGG-ACCTAAAATGGCCAATACATTTTTGAAAGAAAA 3177
                               i- vi v   -   i i   i     v   v i      i i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_58286570_5   3178 TAAAAGGATTAAAGAACT---ATT--CTAATTTCAGAACTTGCTGTAAAG 3222
                         v  v iii  ii  i   --- i -- i       i     i  ii    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_58286570_5   3223 CGACAGTAATTGATGCAGTGTGGTGTTGGTGTAAGGAGAGACAAGTAGA- 3271
                          v        ii vi         ii   ii      v     vi    -
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_58286570_5   3272 --ATAGAAGAAAAT--AGAGCCCAGAAATAGGCTCACACAC--ACAGTTA 3315
                         --  i   v i   --    i         ii i  i   i-- ii  i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_58286570_5   3316 GCTGACTTTTGAAAAGGGCTCCAAAGAAATTCATTAGGAACA------TC 3359
                         ii   i   i  v     iv    iivv     v i  i v ------  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_58286570_5   3360 TTTTCAATAAATGATGGTG---CAA-------ACTATATGAAAAAGA--G 3397
                                i     i  v  ---   -------? i i   v      -- 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_58286570_5   3398 AACCTCAACCTCCACCTCACACAATACACATGAATTGATTTGAGATGGCT 3447
                           vi vi   i i         v   i   vi    i i ii i    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_58286570_5   3448 CATAGAACCAACAATGAAAGCTAAAACCATGAGCCTTGTATAGAAATATA 3497
                           ?   v i  vvi i i         i  i iv  iv  v ii  v i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_58286570_5   3498 TAGCAAAATAA--CTTTGTGACCTTGAGGTAGGCAAAGGTTTCTTAGGTA 3545
                            --i?i   --   i         i v       v          i  
  L1M4_orf2#LINE/    548 TAG--GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_58286570_5   3546 TCTTTACAG-AAAAACAAACAAACGACAAAAAAACTATTAAAATATTGAT 3594
                          v---   v-    i  --   i i      i  -----      --   
  L1M4_orf2#LINE/    596 TG---ACACCAAAAGCA--CAAGCAACAAAAGAA-----AAAATA--GAT 633

  chr2_58286570_5   3595 AAATTGAACTTCAAATAAAAAAACAAATAATATAAAAAGCTTCTGCACAT 3644
                               i      -- -------    ----  v    i   i  ii v 
  L1M4_orf2#LINE/    634 AAATTGGACTTCA--T-------CAAA----ATTAAAAACTTTTGTGCTT 670

  chr2_58286570_5   3645 CCTAAGATACTATGAATTAAATGATTAGGCAGGCCGCATGCTAGGAGAGG 3694
                          vv i  i     v  vv  i   vv  i  iv  i  viv i     ii
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_58286570_5   3695 ATATCCATAATACAGATATCTGATAAGG---------------------- 3722
                             iiii  vv  v             ----------------------
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_58286570_5   3723 ---ACTCCTGTGGCTTAACAATAAAAAGACAAATATCCAAAT--AAAAAT 3767
                         ---    i iiii  i  i                v  v   --      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_58286570_5   3768 ---TAGAACACTCGACAAAGAAACTTTGTAAGAACAGATATATGAAAGGT 3814
                         ---i i iv i i  - v   v i  iviv i iv       ii  v  i
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGA-ATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_58286570_5   3815 CAGTAAAAACGTGAAAG--TGCTCAAACTTAATTAGACA 3851
                           i   iv  i     i--       vv i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (153 / 81)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 3.38 (98 / 29)  


3232 27.86 0.22 0.22  chr2_58309901_58316328     5029  5936 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_58309901_5   5029 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5078
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_58309901_5   5079 GGCCACACTGCCCAACGTACTTTATAGATTCAATGCCATCCCCATCAAGC 5128
                            v i   v     vv iv i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_58309901_5   5129 TACCAGTGACTTTCTTCACAGAATTGGAAAAATCTACTTTAAAGTTCATA 5178
                          v    ivi i  i  ii     v v  v  iiiv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_58309901_5   5179 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5228
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_58309901_5   5229 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5278
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_58309901_5   5279 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5328
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_58309901_5   5329 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAC 5376
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_58309901_5   5377 CTGATCGTTGACAAACCTGAGAAACACAAGCAATGGGGAAAGGATTCCCT 5426
                         i    iv i     ivv  vv  ivv  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_58309901_5   5427 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTATATGTAGGAAGCTGA 5476
                         v  i  i              v      v  ? i i   i ii iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_58309901_5   5477 AACCGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5526
                          iii   i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_58309901_5   5527 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5576
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_58309901_5   5577 AGGTATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5626
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_58309901_5   5627 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5676
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_58309901_5   5677 AAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGAACAG 5726
                            v v  i i   i iii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_58309901_5   5727 GCAACCTACAAAATGGGAGAACATTTTCGCAACCTACTCATCTGACAAAG 5776
                         i     i   i          v  v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_58309901_5   5777 GGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAA 5826
                          i  vi          v  i         vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_58309901_5   5827 ACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 5876
                              i     v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_58309901_5   5877 AAAAGAAGACATTTATGCAGCCAAGAAACACATGAAAAAATGCTCATCAT 5926
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_58309901_5   5927 CACTGGCCAT 5936
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


4259 18.32 2.65 2.43  chr2_58439861_58442084.rev      836  1741 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_58439861_5    836 TGGAAACAGACCCCATATATATAAATTGGAAGGAAGGTTTAATACTACTA 885
                               v v i     i vi  ii        i----i      i ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA----CTTAATATTGTTA 46

  chr2_58439861_5    886 AGATAGTAATACTCCCAATACAAATCTACAGATTCAGCACAATTCCTATC 935
                             i i         v v ivi             i i    i      
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_58439861_5    936 AAAATCTCAGTGGATTTCCTTGTACAACTTAGCAAGCTGATTCTAAAATG 985
                               i   iv vi  ii   i v  v  ii         i       v
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_58439861_5    986 TCCATGGAACTGCAAGAGACCCAAATTAGCGAAAACAATCTTGAAAAAGA 1035
                         ivi      v      i      i v    v                   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_58439861_5   1036 AGAACCAAGTTAGAGGAC------------AT---AAAACTCATTACAAA 1070
                              v     i      ------------  ---      i i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_58439861_5   1071 GCCACAGTTATCTAGAGAGTGTGGTACTGGCACAATGATAAACATATAGA 1120
                           i     v   v   v               i  v    i         
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_58439861_5   1121 TCAATGGAATGGAATTGAGAGTCCAGAAATAAATCTATGTGCCAACGGTC 1170
                                   i                      i i  iiiiiv i    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_58439861_5   1171 AACTGATTTTTAGCAAGGGTCCCAGGACCATTTAATAGGGAAA-AATTGC 1219
                           i       iii       v   i       i   i      -   v i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_58439861_5   1220 CTTTTTGACAAATGTTGCTGGGGCAAATGA----CCACATGCAAAAGAAT 1265
                              ii       v       i   v  i----                
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_58439861_5   1266 AAGGGTGGAACCTTACCTCACACTGTATACAAACATCAATACAAA-TGGG 1314
                         i i v    v  i          ii        v  i  iv    -   i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_58439861_5   1315 TCAAAGACCTAAATGTAAGAGCTAAAACTACAAAACTATTAAAAGAAAAC 1364
                            ?                          i      v   i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_58439861_5   1365 ATAGATGTAAATCTTAATGACTTCAGATTTGGCAGTGGATTCTTCGATAT 1414
                             i?         vi    i ii i  v    i   v     v     
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_58439861_5   1415 AACAAAAATTTTGATGAAGTCCAATCTATTTTTGCTATTATTGTGCAAGC 1464
                         i   vv  --------   iv   ---------  v iv vv viv  ii
  L1M4_orf2#LINE/    597 GACACCAA--------AAGCACAA---------GCAACAAAAGAAAAAAT 629

  chr2_58439861_5   1465 AAATAATTTTGGACTTCATCAAAATTAAAAACTTTAGTTCTTCAAAGGAC 1514
                          i    v  -                         v  v           
  L1M4_orf2#LINE/    630 AGATAAATT-GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_58439861_5   1515 ACTA-CAAAAAGGTGAAAAGACCACCCATAGAATGGAGGAACATATTTAC 1563
                             -   i  i          v     i       ii   v      i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_58439861_5   1564 AAATCATATATCTGATAAGAAGCTTGTAACTAGAATATACAAAGAACTCT 1613
                                            iii      v i        i          
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_58439861_5   1614 TACAACTCAGTAATAAAAAGATAAACAACCAAATT-AAAAATGGACAAGC 1662
                                  i           i   i    v    -        i   iv
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_58439861_5   1663 AATCTGAATTTTGATTTCTCTGAAGGAGTTATACAAATAGCCAATAAGCG 1712
                         i  i     vvvv       ii   i  v         i          i
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_58439861_5   1713 CATAAAAAGATG-TCATTATTAGTCACTGG 1741
                            i        -   vi  i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (107 / 57)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.83 (46 / 12)  


2354 20.72 1.74 5.80  chr2_58505696_58507375      501  1190 (490)    L1M4_orf2#LINE/L1      247   908 (0)  

  chr2_58505696_5    501 GCAACAGCAATCAAGACAGAA--GTATCTGA-ATAAAAAAAAAGAGACAT 547
                           v    i           vi--   -   i-    ii ----v      
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTA-CTGGCATAAGGA----TAGACAT 291

  chr2_58505696_5    548 ATACATAAATGGAACTGAATAGACAATCCAGACATAAACCCACAAATTTA 597
                            v  v       iv    v  v i      v         i v     
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_58505696_5    598 TGCTCAAGTGCTATTTGACAATATTTCTAAGAAAATTCAATTGAGAAAGA 647
                           v    v  v v  i     viv v i    vv       v i      
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_58505696_5    648 ATAATTTTTTCTACAAATTATGCTGGGACAACTGAGAATCTTCATGCAAA 697
                            i i     v      vi              iiv ? iv        
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_58505696_5    698 AAAAAAAAAGAAAGAAAGAAAAGAAAAAGAAAAGAAAAGAAATTAGATGA 747
                          i  v---------------------------------   i  i  ivv
  L1M4_orf2#LINE/    442 AGAAT---------------------------------GAAGTTGGACCC 458

  chr2_58505696_5    748 ATTCTTTCTACCACACAGATAAATTCACTCGAACTGGATTTTTGACCTAA 797
                         v v i ivi    i i v v     v    i  v     iv?v       
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_58505696_5    798 ATATGAGAGATAAAACTATAAAAAATCTTAGAAGAAAATATGGGAATAAA 847
                           i i    v             v-             i  i  ?i    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_58505696_5    848 TCTCCATGACATTTGGTTAGGCACTCATTTCTAAGATATGACAAGGAAAA 897
                            i i    v  v         v vi     v          vv-    
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC-AAAA 606

  chr2_58505696_5    898 GCATACGTGATAAA-GAAGAAACAGTTAAATTGAACTTTGTCAAA-TTAA 945
                            i v ii i   -   i   i  v       i    ii     -    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_58505696_5    946 AAGCTTTTGTGCTGCAAATAATACCACAAAGGAAGTGAAA-GACAGCCCA 994
                           i          v    vi i  i iv   i        -    i    
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_58505696_5    995 CAGAATGGGAGAAAATATTTGCAGATCATATATTTGTTAAGGAACTTGTA 1044
                                                i         i  v     i       
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_58505696_5   1045 CCTAGAATATAAAAAGACCTCTTAAAATGCAATTATGAAAAAA-AAACAG 1093
                         i i        v     v      v  iv    v  i    i -   i i
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_58505696_5   1094 ----ATTTTAAAATGAGCAAAGGATTTTAACTGACCTTTCCCCAAAGAAT 1139
                         ----   ?v      i           v  iv   v    i        v
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_58505696_5   1140 ATGTATCAAGAAATGATAAGCACATGAAAATATG-TCAACATTCTTGATT 1188
                           i  iv  viivii               v   -       iv??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_58505696_5   1189 AT 1190
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.11 (73 / 66)
Gap_init rate = 0.02 (13 / 662), avg. gap size = 4.00 (52 / 13)  


3310 26.33 0.88 0.44  chr2_58520578_58526852.rev     4880  5783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_58520578_5   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4929
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_58520578_5   4930 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_58520578_5   4980 TACCAA-TGCCTTTCTTCACAGAATTGGAGAAAACT-ACTTTAAAGTTCA 5027
                          v   i-       i  -i     v v  v  i-  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_58520578_5   5028 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_58520578_5   5078 AACAAAGCTGGAGGCATCACGCTCCCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv    i  i  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_58520578_5   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_58520578_5   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCACATCTACAACT 5225
                                i    i--    i  --        vv iii    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_58520578_5   5226 ATCTGATCTTTGACAAACCTGAGAAACACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  ivv  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_58520578_5   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_58520578_5   5326 GAAATTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            i     i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_58520578_5   5376 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_58520578_5   5426 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAAGACTCCGTGTCTAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii i v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_58520578_5   5476 AATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i i          vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_58520578_5   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_58520578_5   5576 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5625
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_58520578_5   5626 AGGGCTAATATCCAGAATCTACAATGAACTC----AAATTTACAAGAAAA 5671
                         i  i  vi          v  i  v      ----  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_58520578_5   5672 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTA 5721
                          i     i     v  i?    i           iv    i     i  v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_58520578_5   5722 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5771
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_58520578_5   5772 ATCACTGGCCAT 5783
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


3145 25.64 1.90 0.67  chr2_58827346_58833171     4438  5334 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_58827346_5   4438 TGGAAAAACATTCCATGCTCATGGCTAGGAAGGATCAATATCGTGAAAAT 4487
                               i i  i     i      v v     iv i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_58827346_5   4488 GGCCATACTGCCCAAAATAATTTATAGATTCAGTGCTATCCCCATCAAGC 4537
                            v     v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_58827346_5   4538 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 4585
                          v   -   v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_58827346_5   4586 TCTGGAAC--CAAAAAACAGCCTGTATAGCCAAGACAATCCTCAGCAAAA 4633
                          v     v--   iii  --  v v        i      i v iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_58827346_5   4634 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTAGAAG 4683
                                  i      vv   ii  v  ii i      viv     v  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_58827346_5   4684 GCTGCAGTAACCAAAACAGTGTGGTACTGGTACCAAAACAGATATATAGA 4733
                            i      i   i               i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_58827346_5   4734 CCAATGGAACAGAACAGAGGCCTCAGAAATAATACCACATATCCACAAGC 4783
                         i        i    iv   ivii         vv   i i  ii iiiv 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_58827346_5   4784 ATCTGATCTTTGACAAACCTGACCAAAACAAG-CAATGGGGAAAGGATTC 4832
                          vi    i  i     ivv  -    i  v v-            i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_58827346_5   4833 CCTATTTAATAAATGGCATTGGGAAAACTGGCTAGCCATATGCAGAAAAC 4882
                         i  v  i  i      iii     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_58827346_5   4883 TGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGT 4932
                             ii         v   i     v                   i   v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_58827346_5   4933 TTTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4982
                         v i ?    i           v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_58827346_5   4983 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACT 5031
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_58827346_5   5032 AAAACAGCAGAAGCAATGGCAACAAAACCAAAAATTGACAAATGGGATCC 5081
                          vi   v  i     vvi         vv      v  i    v   iii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_58827346_5   5082 AATTAAACTAAAGAGCTTCTGCGCAGCAAAAGAAACTATCAG---AGTGA 5128
                         v  i   v v  i i   i  i  vv    i  v       i---     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_58827346_5   5129 ACAGGCCACCTACAGAATGGGAGAAAAATTTTGTAATCTATCCATCTGAC 5178
                          v  i v   i                vv    i  vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_58827346_5   5179 AAAGAGCTAATATCCTGAATCTACAAAGAACT--TA-AATTTA-TAAGAA 5224
                           i ii  vi     v    v  i        --  -  i i -   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_58827346_5   5225 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGTATATGAACAAGCACT 5270
                            i    ----   v  i?    i         v  v    i ii  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_58827346_5   5271 TCTTAAAAGAAGACATTTATGCGGCCAAAAAACATATGAAAAAAAGCTCA 5320
                            iv        i  vi vii      v  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_58827346_5   5321 TCATCACTGGCCGT 5334
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (133 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.53 (23 / 15)  


3161 25.77 1.44 1.00  chr2_59225785_59232172.rev     4993  5896 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_59225785_5   4993 TGGAAGAATATTCCATGCTCTTGGGCAGGAAGAATCAATATTGTGAAAAT 5042
                              ii    i     i  v   iiv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_59225785_5   5043 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5092
                            v     vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_59225785_5   5093 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5140
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_59225785_5   5141 TATGCAACCAAAAAAGAGCCCACACT-GCCAAGTCAATCCTAAGCCAAAA 5189
                             v  viiv  ii  -    v v -     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_59225785_5   5190 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAAGG 5239
                                 i      vv    i  v  ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_59225785_5   5240 CTACAGTACCCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5289
                                 vi   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_59225785_5   5290 CAATGGTACAGAAC--AGAGCCCTCAGAAACAATGCCACATATCTACAAC 5337
                               v i    i--    i  --     i  vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_59225785_5   5338 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGA--G 5385
                         i vi    i  i     ivv  v   i v  vvv           i -- 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_59225785_5   5386 TCCCTATTTAATAAATTGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5435
                           -- v  i  i    v         v      v  ?   i   i i  i
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_59225785_5   5436 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 5485
                         iv    ii    i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_59225785_5   5486 GGATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCTTAGAAGAA 5535
                             i ?    i  v    v   v       i      vi          
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_59225785_5   5536 AACCTAGGCA-ATACCATTCAGGAGATAGGCATGGGCAAGGACTTCATGT 5584
                            v    ?i- v i -   iv  vv v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_59225785_5   5585 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA- 5633
                         v  vi            vvi          vv     v  i    v   -
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_59225785_5   5634 ----TCTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5679
                         ----  v   i    i -   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_59225785_5   5680 TGAACAGGCAACCTGCAGAATGGGAGAAAATTTTTGCAACCTACTCATCT 5729
                             v  i     ii                v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_59225785_5   5730 GACAAATGGCTAGTATCCAGAATCTACAATGAACTCAAACAAATTTACAA 5779
                           i  iv i  v           v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_59225785_5   5780 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 5829
                         v     i     i     v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_59225785_5   5830 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGC 5879
                          i     v        i  vi viii     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_59225785_5   5880 TCATCATCACTGGCCAT 5896
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (134 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


 238 38.66 0.00 0.00  chr2_59268963_59270963        1   119 (1882)    L1M4_orf2#LINE/L1      100   218 (690)  

  chr2_59268963_5      1 ATGCCACCTTTCCTTTTGGTAGTAATTGGTAACTTTTTAATAAAATTTAC 50
                           v   v  vi i    v i  v     ii  vi vv vv       i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_59268963_5     51 CCAGTAATGCAAATGACATAGGGTAATCAAAGTGATTATAAACTAGAAGC 100
                         vii v       iv   vi  ii  ii    iii  iv i  vv     v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_59268963_5    101 ATAATATTGCAGAATTTAC 119
                          i  vi   v  i i i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCAC 218

Transitions / transversions = 1.30 (26 / 20)
Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.00 (0 / 0)  

1681 22.84 6.45 5.34  chr2_59268963_59270963      469  1011 (990)    L1M4_orf2#LINE/L1      183   731 (177)  

  chr2_59268963_5    469 AATTTTG-----GAAGGACACAGTTCAGTCCACAGCACTTAGAGTATCTT 513
                            i   -----    i   v    -i -----  v   i v v vi iv
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTT-GG-----AGGACTCACACTTCCCA 226

  chr2_59268963_5    514 ATTTCACAACGTAATGCTTACTATAAAGTCATAGTAATTAAGGAAGTA-G 562
                               v   -------      i    ii i      i   iv   i- 
  L1M4_orf2#LINE/    227 ATTTCAAAAC-------TTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_59268963_5    563 ATACTGGCCTAAAGATAGAAATGTAGATCAGATA-AACAGAAC----AGT 607
                         i       v   i      v  i       -  i-  i    i----   
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCA-ATGGAATAGAATTGAGAGT 318

  chr2_59268963_5    608 CTATAAGTAAATC-ACACATTTGTGGTCAATTGATTTTTTACAAAGTTGC 656
                          i v  i    i - i      i               iv    i v   
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_59268963_5    657 CAAATTAATTCAGTGGGGAAGGA-TGATCTTTTCAACAAATTGTGCTGAA 705
                            iviv     i       i  - ii              v      ii
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_59268963_5    706 ACAACTGGACATCCAAATGTAAAAATGTATGAAGCATTAG--CTTTGCTT 753
                                  i ?   v   i    -- v      --  i -- ii i i 
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAA--GAATGAAG--TTGGACCCCTACCT 464

  chr2_59268963_5    754 TACATCATCTACAAAATTTAATTCAAAATAGATTATAGTCCTCAACCTAA 803
                         i   i   v       v    i       i   i ?  v   v  iv   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_59268963_5    804 -AGCTACAACTATAAAATTTCTAGAAAGAACCAC-GGGATAATATCTTTA 851
                         -     v          i ii     ii  v  i-  ?i   -     ii
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCG 563

  chr2_59268963_5    852 TGATCTTGGGTTAAGCAAAGTCTTCTTAGACAGGGCAC-----ACTTATT 896
                            i         i    v vi        i v i   -----i vi vv
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_59268963_5    897 CATTAAAA------ATA------TTAGATTTTATCAAAATAAAAACTAAC 934
                           vi    ------   ------  i  i  i        v    -----
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA----- 658

  chr2_59268963_5    935 TTATAACTTCTGTTCTTTGGAAGAT-CTCTTAAGAAAATGAAGTGGTAAA 983
                         -----    i   v   iii i  i-  v i      i    iv ii  v
  L1M4_orf2#LINE/    659 -----ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_59268963_5    984 TCACAAAGTGAGAGAAAACATTTGCGAA 1011
                         i    i i  i       i      i  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAA 731

Transitions / transversions = 2.27 (84 / 37)
Gap_init rate = 0.04 (21 / 549), avg. gap size = 3.05 (64 / 21)  

 397 22.99 0.57 9.20  chr2_59268963_59270963     1338  1511 (490)    L1M4_orf2#LINE/L1      750   908 (0)  

  chr2_59268963_5   1338 ATTTTTATTCAGAATGTATAAA-AACTATTATAAATCTACTGTAAGAATA 1386
                          i  v   i      i      -    v   i  v  v ivi   i  v 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_59268963_5   1387 CTAACTATCCAATTAATTTTTTTAGACAGTCAAAAACTTTCAAAAGACTT 1436
                          v  iv i      ? ----------------    ivvv    i  i  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWA----------------AAAATGGGCAAAGGATTT 833

  chr2_59268963_5   1437 GACCAGAAACGTCATGAAAGAAGATATTTGAATGGCCAATAAATACATGA 1486
                           vi   v iv  viv           vii            ii      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_59268963_5   1487 AAAGATGCTCGTCATAATCTTCATA 1511
                                   iv   v ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.05 (20 / 19)
Gap_init rate = 0.01 (2 / 159), avg. gap size = 8.50 (17 / 2)  


3160 26.92 0.66 0.88  chr2_59399697_59404148     3051  3960 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_59399697_5   3051 TGCAAGAACGTTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3100
                           v  ii ii i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_59399697_5   3101 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3150
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_59399697_5   3151 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3198
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_59399697_5   3199 TATGGAACCAAAAAGGAGCCCGCATTACCAAGTCAATCCGAAGCCAAAAG 3248
                                viiv  i   v  v v  vi    iv     ivi ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_59399697_5   3249 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3298
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_59399697_5   3299 CACAGTAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGCTATAGACC 3348
                         i       i   i    i          i iv ii i   vv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_59399697_5   3349 AATGGAACAGAAC--AGGGCCCTCAGAAATAATGCCACATATCTACAACT 3396
                                i    i--  i i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_59399697_5   3397 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 3446
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_59399697_5   3447 CTATTTAATAAATGCTGCTGGGAAAGCTGGCTAGGCATATGTAGAAAGCT 3496
                           v  i  i     v        v i    v  ?v  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_59399697_5   3497 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGC 3546
                            ii    i    v   i     v                   i    v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_59399697_5   3547 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAGCCTTAGAAGAAAAC 3596
                          i ?    i  v    v   v       i      vi             
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_59399697_5   3597 CTAGGCA-ATACCATTCA-GGTCATAGGCATGGGCAAGGACTTCATGTCT 3644
                         v    ?i- v i -   i- ii v i  i- i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_59399697_5   3645 AAAACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3694
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_59399697_5   3695 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3744
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_59399697_5   3745 ACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCACCTGAC 3794
                          v  i     i                 v  i    vii ivi i    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_59399697_5   3795 AAAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAAAAG 3844
                           i--  i  vi          v  i  v      vv    v iv v  v
  L1M4_orf2#LINE/    745 AAG--GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_59399697_5   3845 AAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATACGAACAGACA 3894
                              i     i     v  i?    i            vi   i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_59399697_5   3895 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAGAAAATGCT 3944
                         i     v        i  vi viii     v  i       i  i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_59399697_5   3945 CATCATCACTGGCCAT 3960
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2373 25.93 5.87 0.77  chr2_59449514_59451290.rev      503  1285 (492)    L1M4_orf2#LINE/L1       86   908 (0)  

  chr2_59449514_5    503 CAGTCCCAATGAAAATCTCAACAAGATATTTTGAGGGTATCAACAAAGTT 552
                           i    v  v      i  i vivv v     vi iv  ii    iv v
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chr2_59449514_5    553 ACTCTAAAATTTTTATGGAAAGGTAAAATATC-AAAATAGCCAACATAAT 601
                          ii        iv        v i  iiv i - i         v i   
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_59449514_5    602 ACTGAA---GAAGAACACCGTTGAATGAGTAACAATACGCAACTT-GAAA 647
                         vi    ---        vv    i v  v v   v v v   i  -i   
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_59449514_5    648 C--AATAAAAAATTGCAGTAATCAAGACAGGCTAAGATTAGCAAAATAAT 695
                          -- v  v   ii i               vv iiv i i   v  vi  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_59449514_5    696 AGGCA---AAATCAATGGAACAGGATAGAAAGCTCATACATAGACCAACA 742
                           i  --- i          i  i  v  i  ii  v v   i   v i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_59449514_5    743 CA---------AAT--ATCTTTGATAAAGG----AAAACTGGCAATTCAA 777
                           ---------   --  i  i  i  i  ----  i  i----      
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC----ATTCAA 381

  chr2_59449514_5    778 TGAAGAGATGATAGTCTTTTCAATAAATGTTGCTAGAACAATTTGATGCC 827
                           ii  i vi             i     v    i i    i v   i? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_59449514_5    828 CATATGCAAAAGAAAAAAATCTAGACACAGACCTCACACCTTTCATAAAA 877
                           i           vi  i - i   v vv          v vi i    
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAA 480

  chr2_59449514_5    878 GTTAGCTCAAAATCAGTCATAAACCTTAATATAAGACACAATACTGTAAA 927
                         i   i        vii   ? i    v   i     vvi  v   i    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_59449514_5    928 ATCTCTAGAAAAAAATGTAGGAGGTAATCTATGTGACTTTAGGTTTGGCA 977
                          iiii     i    ii    ? vv     vi     i  i    v    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_59449514_5    978 ATGAGTTTTTAGGAACAACACCAAAAGCATAATCTATGAAAGAAAAAAAA 1027
                            iv  i    iv ii            i  v v ii          v 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_59449514_5   1028 TGATAAATTGCACCTT-TCGAA--TG-----TTTTGCTCTGAAAATTACA 1069
                         -         v  i i-  i  -- i-----     iv  vv   vv   
  L1M4_orf2#LINE/    631 -GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_59449514_5   1070 TTTTTAAGAGAACAAAAAGACAAGTCACAATCTGGGAGAAAATATTTACA 1119
                         i v i    i iii         vi    ivv               i  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_59449514_5   1120 AAACAAATATTTGATAAGGCAGTTGTATTCACAATACACAAAGAACTCTT 1169
                           v  v    i        v v      i  v    i i           
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_59449514_5   1170 A-------ACAATAAGAA----AATAACCCCCCCAAAAAATGGGCAAAAT 1208
                          ------- i     i  ----        vvii?             iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_59449514_5   1209 ATCTGAAGAGATATCTCACCGAGGAAGAGATACAGATGTCAAATAATCAT 1258
                           i    v   i  i  v  i i     v     i   v v     v  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_59449514_5   1259 ATAAAAA--TGCTCAATATCATTTGTTAT 1285
                           i    --       i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (118 / 81)
Gap_init rate = 0.02 (17 / 823), avg. gap size = 3.06 (52 / 17)  


3183 27.20 0.66 0.66  chr2_59464594_59470989     4997  5904 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_59464594_5   4997 TGCAAGAACGTTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5046
                           v  ii ii i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_59464594_5   5047 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_59464594_5   5097 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5144
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_59464594_5   5145 TATGGAACCAAAAAAGAGCCTGCATAGCCAAGTCAATCCTAAGCCAAAAG 5194
                                viiv  ii  v  v v        iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_59464594_5   5195 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5244
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_59464594_5   5245 CACAGTAACCAAAACAACATGGTACTGGTACCAACACAGAGCTGTAGACC 5294
                         i       i   i   iii         i iv iv i   vv i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_59464594_5   5295 AATGGAACAGAAC--AGGGCCCTCAGAAATAATGCCGCATATCTACAACT 5342
                                i    i--  i i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_59464594_5   5343 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5392
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_59464594_5   5393 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5442
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_59464594_5   5443 GAAACTGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5492
                            ii  i i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_59464594_5   5493 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCTTAGAAGAAAAC 5542
                          i ?    i  v    v   v       i      vi             
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_59464594_5   5543 CTAGGCA-ATACCATTCA-GGTCATAGGCATGGGCAAGGACTTCATGTCT 5590
                         v    ?i- v i -   i- ii v i  i- i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_59464594_5   5591 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5640
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_59464594_5   5641 AATTAAACTAAAGAGTTTCTGCACAGCAAAAGAATCTACCATCAGAGTGA 5690
                         v  i   v v  i ii  i  ii vv    i  vv   i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_59464594_5   5691 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5740
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_59464594_5   5741 AAAGGGCAAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5790
                           i  i vvi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_59464594_5   5791 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATAGGAACAGACACT 5840
                            i     i     v  i?    i            vv   i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_59464594_5   5841 TCTCAGAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5890
                             vi       i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_59464594_5   5891 CCATCACTGGCCAT 5904
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (149 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1824 24.33 5.38 5.65  chr2_59513494_59515229      501  1244 (492)    L1M4_orf2#LINE/L1      167   908 (0)  

  chr2_59513494_5    501 CCGTAATAGCTAAAACAATTTTGAAAAGGA----TACAGTGGAAGAAAGC 546
                           iv      i        i       i  ----i v   v i  i vv 
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr2_59513494_5    547 ATTCTACTTGATTTCCAGACTTATTATATAGCTACAGTAATGAAGACACA 596
                          iv  v iii     v i     i  i v            v      -i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA-G 265

  chr2_59513494_5    597 TGTAAT--TGGCAAAGAAATAGAGACACAGATTAATTGACTAGAATACAC 644
                            ii --     v iii     v i i    i   v  v      vv v
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_59513494_5    645 AACTCAGAAATAGACCCACACAAATATGCCCAATTGATTTT-GACAAAGG 693
                          iii        i     i   vv    vi           -     i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_59513494_5    694 GGCAAAAACC-TTCAATGGAGTCAAAATAGACTTTTCAACAAGTGGTGCT 742
                         v  v  i   -        i vv i     v           i       
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_59513494_5    743 GGGGAAATTCAACATACATTGTTTAAAAAAATAAACCTTTACCTAAGTCT 792
                            iv  i vi i ?v  i-i vi    i   i  vi vv   ivvii  
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCAC-ATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_59513494_5    793 CACTCCTTATACAAATAAAAACTGAAAATGGGTCACATAATTGAATGTGA 842
                            v  v        v vv    v       i   ? v vi i     i 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_59513494_5    843 AATATAAAATTATAAA-TTTTTAGAA-AAAACAGAAGA--AAATCTTCCT 888
                         i vv     i      -i i      -      v i ?--        v 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_59513494_5    889 GATCTATGTCTAAGTAAAGAGTGTTTTTGACTTGACAGCAAAATCACAAT 938
                           i  vv vi  i i  v -  v i  v  iv     v     v     v
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATG-GTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_59513494_5    939 TCATGTAAGCAAACATTGAT----TAGATTTTATAAAAAATAAAGACTTT 984
                         iv iiv   v   v  v   ---- i  i  i  v    v    i     
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_59513494_5    985 TTTTAAATGTGAAAGACCCTGTTAAAAGAATGAAAAAACAAGCTACAGAT 1034
                          v --iv vii  i   v  i i  i i i      i    v i     v
  L1M4_orf2#LINE/    664 TGT--GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_59513494_5   1035 TAGGAGAAAATATTTGCAAAACCATCTGAGGCAGGAGAAAGGATGGTAAA 1084
                          i                  ----  ----------------------- 
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAA----TC-----------------------A 734

  chr2_59513494_5   1085 TATTTGAAAATCATCTGGTAAAGGATAATTATTTAGAATACTTAAAGAAC 1134
                            ---------     i   i   ivvv   ii      iv        
  L1M4_orf2#LINE/    735 TAT---------ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_59513494_5   1135 TCTGAAAACTCAACATTTAAAA---AAATG--CCA-TTCGAAAACGGACA 1178
                            v v       i v v    ---    i--   -  ?i    i  i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_59513494_5   1179 AA------------AC------CGGAAAAAGAGTATGCAGATGGAAAATA 1210
                           ------------  ------ vi  i    -   i  i    vv    
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGA-TATACAAATGGCCAATA 874

  chr2_59513494_5   1211 AGCACATGAAAAGATGTTCAACATCATTAACGAT 1244
                                         i         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (97 / 80)
Gap_init rate = 0.03 (21 / 742), avg. gap size = 3.90 (82 / 21)  


2891 26.23 3.14 1.35  chr2_59516957_59521576     3237  4128 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_59516957_5   3237 TGAGAAGACATTCCATCCTCATGGATTAGAAAAATTAATAATGTTAAAAT 3286
                           ii    i  i    vi         i   i v      v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_59516957_5   3287 TAGAATACTACCCAAAGCAATCTACAAATTAAATACGATCCCTTTCAAGA 3336
                         viv      v      vii       i   v  ii i      v    i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_59516957_5   3337 CACGAATTATAATTTTCACAGAAATAAATAGAGAAAC-AATCCTAAAATG 3385
                         iv v ii iivv    ii       --- -  v  i -i          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT---T-GACAAGCTGATCCTAAAATT 146

  chr2_59516957_5   3386 TGCATGGAAGCAAAAAAGAGCCCAAATAGACAAAGCAATCAGAACCAAAA 3435
                         iii      iiiv  ii  v  vi     v    i     vvi --    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAA 194

  chr2_59516957_5   3436 GAA--ACAAAGCTGGAGGCATCACATTACCTGACTTCAAAATATATTACA 3483
                            --      i      vv     i v  ii i       iv  i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_59516957_5   3484 AGGCTACAGTAACCAAAACAACATGGTATTGGAATAAAAGCAGACACACA 3533
                          i          i   i   iii     i   v    iiii     i i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_59516957_5   3534 GACCAATGGAATAGATTGGAGAACCCAGAAATAAATTCAATTATTTACAG 3583
                           i            v v    ii           ii  vvi     ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_59516957_5   3584 CCAAATGATTTTCAACAAAGGCACCAAGAACACATACGAGGGAAAGGACA 3633
                         i   v        i    i  ii      v  ivi vvi       i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_59516957_5   3634 TTTTCTTCAATAAATGGTGCTGGAAAAAAATGAATCTCCATATGCAGAAG 3683
                         v i i     i            i v  v-  i  v?   i     i   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAAC-TGGATAKCCACATGCAAAAG 443

  chr2_59516957_5   3684 AATAAAATTTAGTTCCTTTCTCTCAACATATA-AAAAGTAAATTCAAAAT 3732
                            i  i  viiii   vi   v  v      -    i v  i       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_59516957_5   3733 GAATTAAAGATTTAAATGTAAAACCTATAATTATAAATGTATTAGAAGAA 3782
                          i  i ?   ii         i v   v  i      vv v         
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_59516957_5   3783 AACATAGGGG-AACTCTTCAGGATATTTGTCCAGTCAA------------ 3819
                                 ? -  v     iv  iv  v vii  v   ------------
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_59516957_5   3820 ---GACTTTAAAAGT-TAGCTAACAAAAACAAAAATAGACAAATGGGACT 3865
                         ---   vii     i-i ivi       iv         i    v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_59516957_5   3866 ATATTGAACT---GAACTTCTGCACAGCAAAGGAAACAGGTAACAGAGTG 3912
                         vi  ii  v ---i     i  ii vv       v  vivi  v i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_59516957_5   3913 AAGAGACACCCTGTTGAATGGGACAAAATATTTGTGAACTATTCATCTGA 3962
                           i     v  iiiv        v          ii  ii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_59516957_5   3963 C--GGGACTAATATCTAAAATATACAAGGAACTCAAAACAACTCACCAAC 4010
                         i--      vi    i i      i  i      vv -       --- i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCA---AT 789

  chr2_59516957_5   4011 AATAAAAAT-CAAATAATTTCACTAAAATGTGGGCAAAA-ATCAGAATAG 4058
                                 v-       iiiv i ?   vi        i-  iv      
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_59516957_5   4059 ATATTTCTCAAAAGAAAACATACAAATGGCCAACAGGTATATGAAAAAAA 4108
                          i       v      i i              i i i i       i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA- 888

  chr2_59516957_5   4109 TTTTCAACATCACTAAACAT 4128
                          vi         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (150 / 80)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.35 (40 / 17)  


1003 24.92 4.79 2.56  chr2_59541369_59546309      225   537 (4404)    L1M4_orf2#LINE/L1      243   562 (346)  

  chr2_59541369_5    225 CAAAGCTATAATAATTAAAATAGTATGCTACCAGCA-AAAAATAGGAACA 273
                                 i i    i  i i   i  v   ii   -  ii    iv i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_59541369_5    274 TTGACCAATGAAACAGAATAGAGAGCCCAAAAATGAACCCATGCATGTAG 323
                          v  i     i  i     v     i   i    i       i   v  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_59541369_5    324 AGTCAATTGATTTTCAATAAAGTTGCCAAGAACATGCAATGGAAAAAGGA 373
                         i              i i  i v        v   v      ii    i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_59541369_5    374 CAGTTCCTTCAATAAATGGAGTTGGAA-AACTGGACATCTATATATAAAA 422
                         i   iii     i      v i   i -       i ? i i  ii    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_59541369_5    423 GAACAGAACTGAGCCCTTATCTCACAGCATATACAAAAA---GCTCGAA- 468
                            iii ii  ii   i  i      v            ---i   i  -
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_59541369_5    469 --GA-CAAAGTCTTCAAAT-TAACACAATTCAACAAAGACAAAAAAGA-- 512
                         --  -  ?  v i -    -   v -------i v  i  v v   iv--
  L1M4_orf2#LINE/    493 TGGATCAWAGACCT-AAATGTAAGA-------GCTAAAACTATAAAACTC 534

  chr2_59541369_5    513 --ATAAGAAAACATAAACA-AAGTCTTC 537
                         -- v           ii?i-  i     
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTC 562

Transitions / transversions = 3.17 (57 / 18)
Gap_init rate = 0.03 (10 / 320), avg. gap size = 2.30 (23 / 10)  

2476 27.31 5.44 0.35  chr2_59541369_59546309     3586  4449 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_59541369_5   3586 TGGAAACAAATCCCATGCTCATGGAAGGGTAGGATCAATGTTGTGAAAAT 3635
                               v v        i       vv  v  iv i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_59541369_5   3636 GACCATACTGCCAAAAGCCACCTACCAAATCAATGCAATTCCCATTGAAA 3685
                          i v     v  v   viv i    vi v    i     i  i  ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_59541369_5   3686 TATCACCATCATTCTTCACAGAAATAAAAAAATT---TCTAAAGTTCATA 3732
                          vi  v vv v  i  ii       vi v  ii ---i     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_59541369_5   3733 TGAAACCAAAAAAGAGCCTGCATAGCCAAAGCAAAAATAAGCAAGGAGAA 3782
                           i  viiv  ii  v  v v         i   vvv i iv   i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_59541369_5   3783 CAAATCTGGAGGTATCACATTACCTGATATCAAA-----CTATAAGGCTA 3827
                             vi      vv     i v  ii  v     -----   i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_59541369_5   3828 TAGTCACCAAAACAGCATGATACTGGTATAAAAATAGACACATAGACCAA 3877
                         i   v i   i    ii  i      i    ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_59541369_5   3878 TGGAACAGAATAGAGAACCCAGAAATAAACCCAAATGCCTACAGCAAACT 3927
                              i     v    ii               v iiii  ii iv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_59541369_5   3928 GATCATTGACCAGG----CAA-AC-------------AAAAAC---CT-- 3954
                            iv i   v   ----   -  -------------  i  i---  --
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_59541369_5   3955 -----AAA--GTGCTAGGAAAATTGGCTAGCCACATGTAGGAGAATAAAA 3997
                         -----   --     i   v  i   v  ?       i ii     i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_59541369_5   3998 CTGGATCCTCATGT-ATGACATTATACAAAAATCAACTCGAGTTGGATTA 4046
                         i    i  ii iv - iiv   -          i     i iv     i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCAT-ATACAAAAATTAACTCAAAATGGATCA 499

  chr2_59541369_5   4047 AGGACTTAAATCTAAGACCTGAAACTACAAAAATTCTGAAAGATAACATT 4096
                         ?i   i     v     v  i      i    v ii ii    v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_59541369_5   4097 GAAAGAAACCCTTGTAGACATTGGCTTAGGCAAGGATTTCAT-GATG-AA 4144
                          i?iv   i i i  -   v    v        v i    v -   i-i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_59541369_5   4145 TAACCAAAGAAAATGCAATAAAAACAAAGATAAATTACCGGGACTTATTC 4194
                         i v v    v v v    i    iv   i   i  v viv      vv  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_59541369_5   4195 AAACTAAAGAGCTTCTGCACGGCAAAAGGAACAGTCAGCAGAGTAAACAG 4244
                            v v  i i   i  ii vv    i iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_59541369_5   4245 AGAACCCACAGAGTGGGACAAAATCTTCACTATCTATACATCTGACAAAT 4294
                          v          i     v     v  ii v vii   i      i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_59541369_5   4295 GACTAAAATCCAGAATCTACAATGAACTCAAACAAATCAACAAGAAAACA 4344
                             viv         v  i  v      vv    v    i  v    vi
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_59541369_5   4345 ACAAA----CCGATCAAAAATTGGGCTAGGAAAATAAATAGACAATTCTC 4390
                              ----  i  i?    v     v i i vv i        v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_59541369_5   4391 AAAAGAAGATATACAAATGGCCAACAA--ACATGAAAAAAATGCTAAATA 4438
                         v                       i  --         i -    v  i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACA 897

  chr2_59541369_5   4439 TCACTAATGTT 4449
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.39 (135 / 97)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.12 (50 / 16)  


2867 26.75 2.00 1.22  chr2_59547538_59551768.rev     2839  3739 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_59547538_5   2839 TGGAAACAAATCCCATGCTCATGGAAGGGTAGAATCAATATTGTGAAAAT 2888
                               v v        i       vv  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_59547538_5   2889 GACCATACTGCCAAAAGCCACCTACCAAATCAATGCAATTCCCATTGAAA 2938
                          i v     v  v   viv i    vi v    i     i  i  ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_59547538_5   2939 TATCACCATCATTCTTCACAGAAAT-AAAAATCTGA------AATTCATA 2981
                          vi  v vv v  i  ii       -i v  v    ------        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_59547538_5   2982 TGAAACAAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAGAAGAA 3031
                           i  vviv  ii  v  v v         i   vvi i iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_59547538_5   3032 CAAATCTGGAGGCATCATATTACCTGATTTCAAACTATACTATAAGGCTA 3081
                             vi      vv   i i v  ii        viv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_59547538_5   3082 TAGTCACCAAAACAGCATGATACTGGTATAAAAATAGGCACATAGACCAA 3131
                         i   v i   i    ii  i      i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_59547538_5   3132 TGGAACAGAATAGGGAACCCAGAAATAGACCCAAATACTTCCAGCAAACT 3181
                              i     v i  ii         i     v i i  vii iv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_59547538_5   3182 GATATTTGACATGACAAACAAAAACCTAAAGTGGGGAAAGGACACCCTAT 3231
                            v  i    v ivviv   i v v vv i         i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_59547538_5   3232 TCAACAAATGGTGCTAGGATAACTGGCTAGCCACATGTAGGAGAATGAAA 3281
                                        i   i      v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_59547538_5   3282 CTGTATCCTTATGTCTGACAT--TATACAAAAATCAACTCAAGATGGATT 3329
                         i  v i  i  iv  --   i--           i       i      i
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTC--ACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_59547538_5   3330 AAGGACTTAAATCTAAGACCTGAAACTATAAAATTCC-AGAAGATAACAT 3378
                          ?i   i     v     v  i           i  i-      v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_59547538_5   3379 TGGAAAAGCCCTTCCAGACATTGGCTTAGGCAAGGATTTC------ATGA 3422
                         v  ?iv ivi    vv   v    v        v i    ------    
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_59547538_5   3423 CAACAAACTCAAAGGCAAATGCAATAAAAACAA-AGGCAAATTGCTGGGA 3471
                           v    vv  v i    ---   v i   v  -  ii      ----  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAA---CAAAAGAAAAAATAGATAAATTG----GA 641

  chr2_59547538_5   3472 CTT-ATTTAAACTAAAGATTTTTTGCACGGCAAAAGGAGCAGTCAGCAGA 3520
                            -  iv   i    i i    - ii vv    i ivi vi   iv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_59547538_5   3521 GTAAACAGGGAACCCACAGAGTGGGACAAAATCTTCACGATCTATACAGC 3570
                           i  v  iv          i     v     v  ii i vii   i v 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_59547538_5   3571 TGACTAAAGTTTAGTATCCAGAATCTACAACACACTCAAACAACTTATCA 3620
                            iv ii vi v           v  i  viv    vv      i vi 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_59547538_5   3621 AGAAGAAAACAAACAATCTTACCAAAAAGTGGGCTAAGGAAATGAATTCT 3670
                          v  i  i     i  i iv ii?    i     v     vv     vvv
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_59547538_5   3671 CAGTTCTCAAAAGAAAATACACAAAATGGCCAACAAACATATGAAAAAAT 3720
                           v     v      i   i     -       i  i  i       i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACATGAAAAGAT 889

  chr2_59547538_5   3721 GCTCAACATCACAAATGAT 3739
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (134 / 103)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  


3010 26.17 2.82 0.23  chr2_59617775_59619623      506  1357 (492)    L1M4_orf2#LINE/L1       35   908 (0)  

  chr2_59617775_5    506 TTAATAGTGTTAAAATGTTCACACTTGCCAAAGTGATCTACAGATTCAAT 555
                               v      i   viv i   iv     v                i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr2_59617775_5    556 GCCATCCTTATCATAATATCAAAGACATTCTTCACAGAAATAGAAAGACC 605
                           v    i     v   vi  ivvi v  i  ii       v  v ii i
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr2_59617775_5    606 AATTCTAATATTTGTATGGAACCACAAAAACCTCA-AATAGCCAAAGCAA 654
                         i  i    v   ii       vii   iiiv i  -          i   
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_59617775_5    655 TATTGAGCAAAAGGAACAAAACTGGAGGCCTCACACTATCTTATTTGAAA 704
                          v    iv  i i       ii      v        vi iv    v   
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_59617775_5    705 ATATACCATAAAGCTATCATAACCAAAACACCATAAT-TTGACACAAAAA 753
                          iv   i i       ivi   i   i   vii ii -i  i  i  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_59617775_5    754 TAAACA----GACCAATGGAACAGAATTGAGAGCCTAGAAAGAAATCCAG 799
                           i   ----  i        i           i i     v   i   v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_59617775_5    800 GAATTTATAATCAACTGATATTAG-CAAAGATGCCAAAACACAT--ATTG 846
                         iv      ii    i    v  v -   i i      i  -   -- v  
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATG 383

  chr2_59617775_5    847 AGAGAAAGACAGTCTTTTACATAAATGATG-TGGTAATACTGAATATTCA 895
                         i ii  ii i        vv i     i  -   v vv    i   ?i  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_59617775_5    896 TATACAAAAGAA----ATTAAACCTTTAC-TCTCATCACATGCAAAAATC 940
                         i  i        ----i  ii   ii   -  v  i  i  i       i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_59617775_5    941 AACTCAAAATGAATTAAGCATTTAAATGTAAGATCCAAATCTACGAAACT 990
                                    i  i ?iv ii           v i   v   ii     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_59617775_5    991 ACTAGAAGAAAGCATAGGGG-AACTGCTTCGTGATGTTGGCATGGGCAA- 1038
                         vi         i      ? -  v -        iv    vv i     -
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_59617775_5   1039 GAATTGTTGGATAAGACCTCAAAATCACAGGTAACAAAAGCAAAATTCAA 1088
                          iv  v  i    v   vi     v    i i        v    v vi 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_59617775_5   1089 CAAATAAGATTACATCAAACTGAAAAGCTTCTGCACAGCAAAGAA-ACAG 1137
                         i    vi  i v       v v    i   i  ii vv     i -  vi
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_59617775_5   1138 TCAGCAGAGGGAGAAGACAACCTACAAAATGGAAGAAAATATTTGCAAAC 1187
                            iv i  v  i         i   i     i                i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_59617775_5   1188 TACCTGTATAACAAGGGATTAATATTTAAAATATATAAGGAACTC--ATA 1235
                         i iv i v i i      i vi   ii i         i      -- i 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_59617775_5   1236 ACTCAACAGCAAGAAAACAAATAAACCCATTTAAAAATGGGTAAAAGACT 1285
                               i ii  i  i        v  v   ?         i   i  i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_59617775_5   1286 TGAATAGATACTTCTTAACAGAAGACATACCA---GCTAACAGGTATATA 1332
                                 i i    iv v      i    v ---  i  i i i i  i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_59617775_5   1333 AAAA-ATGTTCAACATTACTTATATA 1357
                             -   i       i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (149 / 70)
Gap_init rate = 0.02 (16 / 874), avg. gap size = 1.62 (26 / 16)  


2639 27.38 3.70 1.80  chr2_59632794_59636940.rev     2768  3658 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_59632794_5   2768 TGGAAAAGCATTCCATGCTCACTGGTTGGAAGAATCAGTATTGTTAAAAT 2817
                               iii  i     i   iv i        v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_59632794_5   2818 GGTCACACTGCCCAAAGCAGTCTACCAATTCAATGCTATTTCTATCAAAC 2867
                           iv i   v      viii     vi      i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_59632794_5   2868 TAACAA-TGTCATTTTTCACAGAACTAGAAAAACT-ATTATAAAATTCAT 2915
                          vv  i-  i -     ii     v v  v  i  -  iv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_59632794_5   2916 ATGGAACTCAGCAAGAAGCC--AAATAGTCAAAGCAATCCTCAGAAAAAA 2963
                               v --     iii  --i     i    i     i v i   i  
  L1M4_orf2#LINE/    150 ATGGAAAT--GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_59632794_5   2964 GAGCAAAGCTGGTGGCATTATCTTACCCAACTTCAAACTGCAGTATAAGG 3013
                           i     i   v  vv i ivi v     i      vivi v  i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_59632794_5   3014 CCACAGTAACCAAAAGAGCATGGTACTTATAAAAAAACAGAAACACAGAC 3063
                          i       i   i v  ii       vii v  ii i   v i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_59632794_5   3064 CAATGCAACAGAATAGAGAATCCAGAAGTAAAGCTGCACTTCTACAGCCA 3113
                              v  i     v    i       i    v iii  v i  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_59632794_5   3114 TCTGCTCTTTGACAAAATCAACAAAAGTAAGCAATAGGAAAAGGAC--TC 3161
                         vi  v i  i     iiviiv   i vi vv    i  i    i i--  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_59632794_5   3162 TTTATTCAATAAATAGTGTTGCAATAGCTGGCTATCCATATGCAGAAGAA 3211
                            --    i    i   i  vi i i    v  ?   i     i     
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_59632794_5   3212 TGGAATAGGACCCCTACCTTTCAGCATATACAAAAATTAACTCAAGATGG 3261
                           i i v            iv  v                     i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_59632794_5   3262 ATTAAAGGTTTAAATGTGAGACCTCTAGCTATAAGAATGCT--GAAGAAA 3309
                           i ?  iii       i   v  vv i      -  iv  --       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAA 544

  chr2_59632794_5   3310 ACCTAGAAA-ACACCATTCTGGACATCAGCCTTAGGAAATAATTTAT--G 3356
                           v   i?i- v i -   vv   v ii v-     v   ii   v -- 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAG 592

  chr2_59632794_5   3357 ACTAAGTCCTCAAAAGCAGTTGCAATGAAA------ATTGACAATTGGGA 3400
                          -  v v vi        vvv    ii   ------  v  i  v v   
  L1M4_orf2#LINE/    593 A-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_59632794_5   3401 CCTAATTAAACTAAAGAGCTTCTAT----CAAGGGAGAGAAACTATCAAG 3446
                          i v  i   v v  i i   i i ----   i   v ----        
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA----CTATCAAG 687

  chr2_59632794_5   3447 GGAGTAAACAGACAACCTATAGAACAG-AGAAAATATTC---------AT 3486
                         ii   i  v        i i    ii -          i---------  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_59632794_5   3487 ATCCAACAGAGGTCTAATATCCAGAATCTATAAGAAACTTAAACAATTCA 3536
                            ii i ii  v  vi          v     ii    ivv    i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_59632794_5   3537 GAAACCAGAAAACAAATAATTCATTTAACAAGTGGGCAAGGGACATGAAC 3586
                         iv  iv i  i        ii  v  ? v  i       i   iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_59632794_5   3587 AGACTATCTCTTGAAAGAAGACATGCA--TGAGCCCAAAAAAATATGAAA 3634
                             -  i   iv        i  i  --  -   v v  iv i      
  L1M4_orf2#LINE/    838 AGAC-ATTTCTCCAAAGAAGATATACAAATG-GCCAATAAGCACATGAAA 885

  chr2_59632794_5   3635 AAAATTCTCATCACTAATCATCAG 3658
                          i - v    v  ii ????????
  L1M4_orf2#LINE/    886 AGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (154 / 86)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.13 (49 / 23)  


 263 15.91 0.00 0.00  chr2_60151504_60154216     1040  1083 (1630)    L1M4_orf2#LINE/L1        6    49 (859)  

  chr2_60151504_6   1040 AGACATCCTGTGTTCATGAATTGGAAGACTTACTGTTTTTAAGA 1083
                            i    ii        i             v i  v      
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.00 (0 / 0)  

3699 20.00 3.13 0.36  chr2_60151504_60154216     1384  2213 (500)    L1M4_orf2#LINE/L1       46   898 (10)  

  chr2_60151504_6   1384 AAGAAGTCAACACTACTCAAAGTAATCTACAAATTTAATGCAATCCCTAG 1433
                             v v   i   v i    v i       i   i  i          v
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_60151504_6   1434 CAAAATCCCAGTGGCATTGTTTGAAGAAATGTAAAAATCCACCCTAAAAT 1483
                                    iv  v  v    v      vv v  iiiv i        
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_60151504_6   1484 TTACATG-ATATCTCAATGACCTTAACTATCCTAAATAATCTTGTAAAAG 1532
                          i i   - v  viv iv    ivi v  v  v   i       v     
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_60151504_6   1533 AAGGACAAAGTTG-AGGTATCCCAATTTCTAATTTCAAAACCTA------ 1575
                            i         -   vv  v  v  i i           i  ------
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_60151504_6   1576 AGCTGCAATAATCAGAATAGCGTGGTATTGCCATAAA-ACAAACATATAG 1624
                             i  i      ii i  i      i  v     i- i i        
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_60151504_6   1625 ACCAATGGAACAGAACAGAGAACCCAGAAATAA-CCCTTGCAGATATGGC 1673
                          i        i    iv    ii          -   v i  vv     i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_60151504_6   1674 TAAATGATTTT-GACAAGGATGCAAAGACCATTCAATAGGAAAA----AG 1718
                         i  v       -       i   v             i  i   ----  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_60151504_6   1719 TCTTTTCAACAAATGATGCTGGAA-AACTGGATACCCACATGCAAAATAA 1767
                                        i      i -         ?            v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_60151504_6   1768 TGAAGTTGGGCTCTTACTGTACACCATCTACAAAATTTAACTCAAAATGG 1817
                                  i i i   ivi       v       v              
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_60151504_6   1818 ATCA--AACTTAAACATAAGACCTAAAACTATAAAATGCTTAGAAGAAAA 1865
                             --i  i    ii     v              iv            
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_60151504_6   1866 ATATAAGGAAAAAGCTTCATGACATTGGGTTTAACAGGGATTTCCTGGAT 1915
                         -i   i ?iv   v    i    v       vii  iv i    i i   
  L1M4_orf2#LINE/    546 -CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_60151504_6   1916 ATGACACCAAAACCACAGGCAACACAAGTGAAAACAGAACAACTGGACTA 1965
                                     v    i      v   vi    i   vv  i      v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_60151504_6   1966 TATCCAAATTATAAACTGCTGTGCATTAAAGGACACAATCAACAAAGTAA 2015
                         i   v      v     vi     v i         v     v     i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_60151504_6   2016 AAAGGCAACCCGCAAAATGGGAGAAAATATGCGCAAACCATATATCTAAT 2065
                             i      i  i               vi     i         i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_60151504_6   2066 AAGGAGATCCTATGTC--AAATACATAAAGAATTCCTTCATTGCAACAAC 2113
                             -  - i i i  --i    i        i  i v  viv   i  i
  L1M4_orf2#LINE/    745 AAGG-GA-CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_60151504_6   2114 AAATA------TAACCCAATTTAAAAATGGACAAACAACTTGAATAGACA 2157
                            v ------          ?        i    vi i           
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_60151504_6   2158 TTTTTTCAAATGTGATAAACAAATGGCCAGAAAGCATATGAAAAGATGCT 2207
                            i i    viv    v           iv     i             
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_60151504_6   2208 CAACAT 2213
                               
  L1M4_orf2#LINE/    893 CAACAT 898

Transitions / transversions = 1.47 (97 / 66)
Gap_init rate = 0.02 (14 / 853), avg. gap size = 2.07 (29 / 14)  


3230 27.20 0.44 0.44  chr2_60221949_60228228     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_60221949_6   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAAAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_60221949_6   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_60221949_6   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_60221949_6   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_60221949_6   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_60221949_6   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_60221949_6   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_60221949_6   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_60221949_6   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_60221949_6   5327 GAAACTGGATCCCTTCCTTACACCTTATAGAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v    v      i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_60221949_6   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_60221949_6   5427 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vvii     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_60221949_6   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_60221949_6   5527 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_60221949_6   5577 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_60221949_6   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_60221949_6   5677 AAACAAACAACCCCATCAAAAAGTGGGCCAAGGACATGAACAGTCACTTC 5726
                          i     i     v  i?    i     v     iv    i  v  i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_60221949_6   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5776
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_60221949_6   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


4000 17.68 2.24 5.54  chr2_60246697_60248650.rev      524  1462 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_60246697_6    524 TGGAAAGACACCCTACATTTATGGATTGGAAGACTTAATATTGTTAAGAT 573
                                 i i  i ii  i                              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_60246697_6    574 GTCAATACTACTCAAAGTGATCTACAGATTTAATGCAATCCCTTTAAAAA 623
                          v       v i    v             i  i         v v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_60246697_6    624 TTCCAATGTTTTTTTTTGCAGAAATAGAAAAACTCATTCTAAAATTCATA 673
                          i   iivvii              v  v  i  v  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_60246697_6    674 ATCCACATAGAATTTTAAGGGACCCCAAATAGTCAAAATAATCCCGAAAA 723
                         ------- i   v vi         vi     i     i    ii     
  L1M4_orf2#LINE/    151 -------TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_60246697_6    724 AGAAAAA---AGCTAGAGGATTCACACTTCTGGATTTCAAAACTTTCCAT 770
                             i  ---  i i     i         ivi            v i i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_60246697_6    771 AAAGCTA-----ATCAAAACAGTGTGGTACTGGCATAAAGACAGCCAGAT 815
                                -----     i                    i  i  v  v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_60246697_6    816 AAACAAAAGGAATAGAGTATGGG-GTCCATAAATAAACCCTTATATATAT 864
                          i iv  v        i -  i -     v          ----   i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAAT-TGAGAGTCCAGAAATAAACCC----ATACAT 338

  chr2_60246697_6    865 ATGTGATCAAATGATTTT-GACAAGCAT--CAAGACC-TTCAGTGGGGGA 910
                         v i  i    v       -      vi --       -    i     i 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_60246697_6    911 AAAGACAGTCTTTTCAACAAACGGTGCAGAGAAAACTGGATATCTACATG 960
                          i - i               i     v i  v         ? i     
  L1M4_orf2#LINE/    389 AGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_60246697_6    961 CGAAAGAATAAAGTTGGACTCTTATCTAACACCATACACAATCATTAACT 1010
                          i       i         i i  i  v        i    vv       
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_60246697_6   1011 CAAAATCGATCCATGACCCAAATGTAAGACCTAAAACTACAGAACCCTTA 1060
                               v    v?v    i          v         i i   i    
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_60246697_6   1061 GCAGAAGACATAGAGCAAAATCCCCATGACAGTGAATTTTGCAGTAACTT 1110
                          v    i      i?vv     ii i    vv  ii  vv   i iii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_60246697_6   1111 ATTGGATATGACACCAGAGGCACAGGCAACAAAAGAAAAAATAGACAAAT 1160
                         v  i            i i     i                    i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_60246697_6   1161 TGAACTTCATTATA--TAACA----TTGTGCATCCAAAGACACTATCATC 1204
                           i       i v --   v ----      v  v  i          --
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA-- 685

  chr2_60246697_6   1205 AGATATCAGCTCTGGTATGAAAAAAACCACTATCAATGCAGTAAAGTGGC 1254
                            v -----------i      i ------------------------ 
  L1M4_orf2#LINE/    686 AGAAA-----------GTGAAAAGA------------------------C 700

  chr2_60246697_6   1255 AAACCCACAAAATAGGAGAAAATATTTGCAAATCATGTATCTGATA-GGT 1303
                           -      i   i                      i         -  v
  L1M4_orf2#LINE/    701 AA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_60246697_6   1304 ACTAACA-CCACGCTATGCAGACAACTTCTAAAACTCAACATCAAAAACC 1352
                            vii -   viv   ii i v    ii  v       i vi     vv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_60246697_6   1353 CAAACAATCCAATTCAAAACTGGGCAAAGGACTTGAATAGATATTTCTCT 1402
                             i  i      ?    v           i         i       i
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_60246697_6   1403 AAAGAAGGTGTGTGAATGGCTGATTAAACACATGAAAAGATGCTCAGCAT 1452
                                i i iii      ii  -  i                  i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAAT-AAGCACATGAAAAGATGCTCAACAT 898

  chr2_60246697_6   1453 CACTAATCAT 1462
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.95 (107 / 55)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.84 (73 / 19)  


2975 25.65 1.08 2.81  chr2_60269212_60275635.rev     5009  5932 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_60269212_6   5009 TGGAAGAAAATTCCATGCTCATGGGTAGGAAGAATGAAGAGCTTG--AAA 5056
                              ii v  i     i      i v      v v  v --   --  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA--TTGTTAAG 48

  chr2_60269212_6   5057 ATGGCCATACTGCCCAAGGTAATTTATGGATTCAATGCCATCCCCATCAA 5106
                              v     v     iv i  i  ii       i  v     i     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_60269212_6   5107 GCTGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 5154
                         iv v   iivi i  i  ii     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chr2_60269212_6   5155 CATATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAA 5204
                                  viiv  ii  v  v v  v     i      i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_60269212_6   5205 GGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5254
                         i        i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_60269212_6   5255 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGA 5304
                                   i   i    ii         i iv ii i   v v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_60269212_6   5305 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAACACAACACATCTACAA 5352
                         i        i    i--    i  --        vv v i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_60269212_6   5353 CCATCTGATCTCTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 5402
                         i  vi    i ii     ivv  v   i v  vvv           i  -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT- 393

  chr2_60269212_6   5403 CCCTATTTACTAAATTCCCTTTAAATAAATAAAGGTGCTGGGAAAACTGG 5452
                         ------------ i -- i   v  i    ---          v      
  L1M4_orf2#LINE/    394 ------------AGT--CTTTTCAACAAAT---GGTGCTGGGACAACTGG 426

  chr2_60269212_6   5453 CTAGCCATATGCAGAAAGCTGAAACTGGATCCCTTACTTC-CACCTTATA 5501
                         v  ?   i     i  iiv    ii    i    -  i  -    v    
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCT-ACCTCACACCATATA 475

  chr2_60269212_6   5502 CAAAAATTAATTCAAGATGGATTAAAGTCCTAAATGTTAGACCTAAA-CC 5550
                                   i    i      i ?  v         v   v     - i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_60269212_6   5551 ATAAAAACCCTAGAAGAAAACGTAGGCA-ATACCATTCAGGACATAGGCA 5599
                               vi i           i    ?i- v i -   iv   v v  vv
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT 574

  chr2_60269212_6   5600 TGGGCAAGGGCTTCATGAATAAAACACCAAAAGCAATGGCAACAAAAGCC 5649
                          i     v  i   v ii   vi            vvi          vv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_60269212_6   5650 AAAACTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 5699
                             iv  i    v   ii v  i   v v  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_60269212_6   5700 AGAAACTACCATCAGGGTGAACAAGCAATCTACAGAATGGGAGAAAATTT 5749
                         i  v    i  vv ii     v ii   i i                 v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_60269212_6   5750 TTGCAATCTACCCATCTGACAATGTGCTAATAACCAGAATCTCCAAAGAA 5799
                               vii ivi      i  v vi  vi  v       v vi      
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_60269212_6   5800 CTTAAACGAATTTACAAGAAAATATCAAATAACCCCATCAAAAAGTGGGC 5849
                           ivv  i v iv i  v    viv          v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_60269212_6   5850 AAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 5899
                                v    i     i     v        i  vi viii     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_60269212_6   5900 GACACATGAAAA-ATGCTCATCATCAGTGGTCAT 5932
                         ii          -       v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.25 (36 / 16)  


3343 26.54 0.44 0.44  chr2_60279478_60285757     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_60279478_6   4881 TGGAAGAACATTCCATGTCCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i      i     i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_60279478_6   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_60279478_6   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_60279478_6   5029 TATGGAACCAAAAAAGAGCGCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v vv v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_60279478_6   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_60279478_6   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_60279478_6   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5226
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_60279478_6   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_60279478_6   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 5326
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_60279478_6   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_60279478_6   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAGAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i   i  vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_60279478_6   5427 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAA 5476
                         v    ?i v viv   iv   v v  vvii     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_60279478_6   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5526
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_60279478_6   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_60279478_6   5577 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_60279478_6   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTGATAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v ii    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_60279478_6   5677 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_60279478_6   5727 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCACC 5776
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_60279478_6   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3301 26.21 0.66 0.66  chr2_60327310_60337576     4878  5785 (4482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_60327310_6   4878 TGGAAGAACATTCCGTGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i  i  i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_60327310_6   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_60327310_6   4978 TACCAATGAATTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivivi  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_60327310_6   5026 TATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_60327310_6   5076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5125
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_60327310_6   5126 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_60327310_6   5176 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5223
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_60327310_6   5224 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5273
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_60327310_6   5274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 5323
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_60327310_6   5324 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5373
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_60327310_6   5374 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_60327310_6   5424 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5473
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_60327310_6   5474 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGGCAAATGGGATCTAA 5523
                         i            vvi          vv     v ii    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_60327310_6   5524 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5573
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_60327310_6   5574 AGGCAACCTACAAAATGGGAGAAACTTTTTGCAA--CATACTCATCTGAC 5621
                           i     i   i           v v       --    i--      i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGAT 744

  chr2_60327310_6   5622 AAAGGGCTAATATCCAAAATCTACAATGAACTCCAACAAATTTACAAGAA 5671
                           i  i  vi      i   v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_60327310_6   5672 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5721
                            i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_60327310_6   5722 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5771
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_60327310_6   5772 CCATCACTGGCCAT 5785
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  

1218 25.67 13.37 0.00  chr2_60327310_60337576     6764  7137 (3130)    L1M4_orf2#LINE/L1        1   424 (484)  

  chr2_60327310_6   6764 TAGAGAGATATTCTGTATTCATGGATT----------AT--------GAT 6795
                          i  i      i ii i          ----------  --------   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_60327310_6   6796 GCCAATTCTTCCCAACCTGTTTTATAGATTCAGCACAATCCAC-TCAAAA 6844
                          v    v  i     vi  v i  i       i i      vi-      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_60327310_6   6845 CCCCAGTAAGCTATTT-GTAAATATTGGTAAACTGCACCCAAAAATTATA 6893
                         i     iviv  v   - i i v    ii  i   vv  i    v i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_60327310_6   6894 TGGAAG-GCAAAAGATTTATAAGAGCCAATACAATACTGAAGAATAACAA 6942
                              i-    ii  iii v  v      v     vi    i  v  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_60327310_6   6943 CAAAGTTGGAGGATTCAC----------------------TATAAAGCTA 6970
                                      i    ----------------------  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_60327310_6   6971 CAATAATCAAGA-------ACACTGGTGAAAGAATAGATACATAGATCAA 7013
                           i         -------ii     iiv   i     i i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_60327310_6   7014 TCAAACACAACAGAGAGCCCAGAAATTGACCCAAACAAATATAGTTGACT 7063
                          vi  i v  iv     i        vi     v   vv   i  ii i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_60327310_6   7064 GGTCTTTGAGAAAGGAGCAAAGGAAATTCAATAGAGAAAAGCTAGTGTAT 7113
                          i i  i  v  i  v  v   ivv       i i    iiv    v v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_60327310_6   7114 TCAACAAATGATGCTGGAACAATT 7137
                                   i      i    i 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACT 424

Transitions / transversions = 1.82 (62 / 34)
Gap_init rate = 0.02 (7 / 424), avg. gap size = 7.14 (50 / 7)  

2909 26.72 1.09 2.07  chr2_60327310_60337576     7862  8778 (1489)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_60327310_6   8778 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATGTCATGAAAAT 8729
                              ii i  i     i        v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_60327310_6   8728 GGCCATACTACCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 8679
                            v     v      v i  i  i        i  v  i  i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

C chr2_60327310_6   8678 GATCCTTG--AAATTTTTCACAGATTTATAAAAAACT-ACTTTAAATTTC 8632
                         -    iv --ivv     ii    vv - i v  i  - iii    v   
  L1M4_orf2#LINE/    100 -ATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTC 147

C chr2_60327310_6   8631 ATGTGAAACCAAAACAGAGCCCATATAGCCAAGAGAATCCTAAACAAAAA 8582
                           i  i  viiv  vi  v  viv        i v    i i  v  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chr2_60327310_6   8581 GAAGAAAGCTGGAGGCATCATGCTGTCTGTCTTCAAACTATACTACAAGG 8532
                            v    i      vv   ii  vi iivi      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chr2_60327310_6   8531 CTACAGTAACCAAAACAGCATGCTACTGGTACCAAAACAGATATATCGAC 8482
                                  i   i    ii  v      i iv ii i   i    v  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chr2_60327310_6   8481 CAATGGAACAGAACAGAG-GTGTCAGAAATAACACCATGCATCTACAACC 8433
                                 i    iv   -  -i         vv    i   i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGT-CCAGAAATAAACCCATACATTTATGGTC 346

C chr2_60327310_6   8432 ATCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAGGATTCC 8383
                          vi    i  i     ivv  v   i vi vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chr2_60327310_6   8382 CTATTTAATAAATGGTGCTGGGAAAACTTGATAGCCATATGCAGAAAACA 8333
                           v  i  i              v    v    ?   i     i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chr2_60327310_6   8332 GAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGA 8283
                            ii    i    v   i    iv                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chr2_60327310_6   8282 TTA-AAACTTAAATGTAAAACCCAAAACCATAAAAACTCT-AAAAGAAAA 8235
                          i - i  i         i v i     i      -    - i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

C chr2_60327310_6   8234 TCTAAGCA-ATACCATTCA-GGTCATAGGCATGGGCAAGGATGAAAGTCT 8187
                         iv  i ?i- v i -   i- ii v i  i- i     v i ------- 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGT-------T 586

C chr2_60327310_6   8186 TTTCATGATGAAAAGACCAAAAGCAATTGTAATAAAAGCCAAAATTGACA 8137
                          i i -   - vi v          vvv i  i     vv     v  i 
  L1M4_orf2#LINE/    587 TCTTA-GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

C chr2_60327310_6   8136 AAT--GGTTTCCAATTAAACTAAGGAGCTTCTTCACAGCAAAAGAAACTA 8089
                            -- ii   --  i   v v ii i   i vii vv    i  v    
  L1M4_orf2#LINE/    635 AATTGGACTTC--ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

C chr2_60327310_6   8088 TCATCAGAGTGAAAAGGCAACCTAGAGAATGGGAGAAAATTTTTGCAATC 8039
                            vv i         i     i v               v       vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

C chr2_60327310_6   8038 TGCCCATCTGACAAAGATCTAATATCCAGAATCTACAAGGAACTTCAACA 7989
                         iiivi      i  i iv  vi          v  i  i     iiv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

C chr2_60327310_6   7988 CCTTTATATGAAAAAAACAAACAACCCCCATCAAAAAATGGGCAAAGGAT 7939
                         v  iv   vv     i     i     v-  i?                 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGAT 831

C chr2_60327310_6   7938 ATGAACAGACAGTTTTCAAAAGAAGACATTTATGCAACCAACAAACATAC 7889
                         v    i     v  i  v        i  vi viiii    i  i  i i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

C chr2_60327310_6   7888 GAAAAAAAGCTCATCATCACTGATCAT 7862
                              i v     v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (150 / 92)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.53 (29 / 19)  

1433 27.59 3.33 2.15  chr2_60327310_60337576     9266  9776 (491)    L1M4_orf2#LINE/L1      392   908 (0)  

  chr2_60327310_6   9266 ATAGGTTTGTCA-TAAATGATGCTAGAATAATTACATGTTTATATGTGAA 9314
                             vi  v   -i     i    i i i  i iv  i?ii i   i-  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-AA 440

  chr2_60327310_6   9315 AAAAATGGAACAGGATATAGTTCTCACACCTTTCACAAAAATTAATT-AA 9363
                           i    i iiv   ivivvvi        v vi           i -  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_60327310_6   9364 AATGGGTCATAGAACTAACTATGAAATTCAAAACTATAAAGCTTCTAGGA 9413
                              i   ?   v    v i i i vii           i  ii   i 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_60327310_6   9414 GAAAATATAAGTG--AGTTTTAGT---------TTAG-CAATGAGTTTTT 9451
                              i   i ? -- i i  v  ---------    -     iv  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_60327310_6   9452 ATACA-GACAATGTAAATAGAAAAGCATAAGACATGAAAGAGAAAATTTG 9500
                          v i -    vi--------       i   vv ii     i     v- 
  L1M4_orf2#LINE/    591 AGATATGACACC--------AAAAGCACAAGCAACAAAAGAAAAAATA-G 631

  chr2_60327310_6   9501 GTAAACTGGACTTTATTAAAATTTAAGACTTCTCCTCTGTAAAAGACACC 9550
                         i    i       i  i      v  i    i viv  vi   i     i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_60327310_6   9551 GTTAAGTGAATAAATGTGTGAGCCACAGACTGGGAGAAAATATTTGCAAA 9600
                         i i   vi i i  viviii v       v                    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_60327310_6   9601 ACATGTGTCT-ATAAGGGTCTTCTATCCAAAATGTACCAC-AACCCTTAA 9648
                         v   i i   -       v   v      i   i  iv v-   i    v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_60327310_6   9649 AACTTAAACAATAAGAAAACAAACAATCCAACTTAAAAAAGCACAAAAGA 9698
                             i  -i     i  i     i  i    i ?     v vi    i  
  L1M4_orf2#LINE/    782 AACTCAA-TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_60327310_6   9699 TCTGAACACACACCTCATCAAAAAAGATATAACGATTGCAAATAAGCTTA 9748
                          i    i v   ii  vi    i        vvi  v  v       vi 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_60327310_6   9749 TGAAAATATAGTTAATGTCTTATACCAT 9776
                               v  iv i  ii  v????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (90 / 47)
Gap_init rate = 0.02 (12 / 517), avg. gap size = 2.33 (28 / 12)  


2877 27.47 0.54 3.11  chr2_60339940_60347054.rev     5692  6623 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_60339940_6   5692 TGAAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5741
                           i   i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_60339940_6   5742 GGCCATACTACCCAAAGTAATTTATAGATTCAATCCTATTTCCATTAAAT 5791
                            v     v      v i  i  i        iv v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_60339940_6   5792 ACCC--TTGAAATTCTTCACAGAATTAGAAAAATCTACTTTAAATTTCAT 5839
                         v   --i  vv-  i  ii     v v  v  iiiv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_60339940_6   5840 ATGGAACCAAAAAGTGCCT-GTATAGTCAAAACAATCCTAAGCAAACAGA 5888
                               viiv  i vi  i- v    i          i i iv  iv   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_60339940_6   5889 ACAAAGCTGGAGGCGTCATGCTACATGACTTCAAACTATGCTACAAGGCT 5938
                               i      vv   ii  v vii i      viv i      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_60339940_6   5939 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATCTACCA 5988
                                i   i    ii         i iv ii i   i    vv i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_60339940_6   5989 ATGGAACAGAATAGAGGCATCAGAAA-AAACACCATGCATCTACAACCAT 6037
                               i     v   ivvi      -    -    i   i  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTTATGGTCAA 348

  chr2_60339940_6   6038 CTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAGAATTCCCT 6087
                         i    i  i     ivv  v   i vi vv               vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_60339940_6   6088 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACAGA 6137
                         v  i  i              v      v  ?   i     i  i ----
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA---- 444

  chr2_60339940_6   6138 AACTGAGCCATGTGCAGAAAACAGAAACTGAATCCCTTTCTTACATCTTA 6187
                         ---------   ------------  ii  i i    vi  i   i v  
  L1M4_orf2#LINE/    445 ---------ATG------------AAGTTGGACCCCTACCTCACACCATA 473

  chr2_60339940_6   6188 TACAAAAATTAACTCAAGGTGAATTGAAGACTTAAAAGTAATACCTAAAA 6237
                                          ii  i  ii?    i    v    v v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_60339940_6   6238 CCATAAAAACCCTAGAAGATATCCTAGGCA-ATACCATTCAGGACACAGG 6286
                          i      vi i       v v v    ?i- v i -   iv   viv  
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGG 572

  chr2_60339940_6   6287 CATAGGCAAAGACTTCATGACTAAAACACTAAAAGCAATTTCGACAGAAG 6336
                         vv       v ii   v iiv  vi    i       vvvv i   i   
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_60339940_6   6337 CCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTTGGCACAGCA 6386
                         vv     v  i    v   ii v  i   v v  i i    v ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_60339940_6   6387 AAAGAAGCTATCATCAGAGTGAAGAGGCAACCTACAGAATGGGAGAAAAT 6436
                           i  vi      vv i      i  i     i                 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_60339940_6   6437 TTTTGCAATCTATTCATCTGACAAAGGGCTAATATCCAGAATCTACAAGG 6486
                         v       vii  vi      i  i  i  vi          v  i  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_60339940_6   6487 AACTTAAACAAAGTTATGAGAACAAAACCAAACAACCCCACCAAAAAGTG 6536
                             ivv    vviv  i v  v  i  -   i     v ii?    i  
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATG 821

  chr2_60339940_6   6537 GGTGAAGGATATGAACAGACACTTTTCAAAAGAAGACGTTTATGTGGCCA 6586
                           ii      v    i     i  i  v        ii vi vi      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_60339940_6   6587 ATAAACATATGAAAAAAAGGTCATTATCAGTGCTCAT 6623
                             i  i       i v v   vi    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (149 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.40 (34 / 10)  


1751 22.29 10.62 0.83  chr2_60553414_60555505.rev      501   980 (1112)    L1M4_orf2#LINE/L1       64   590 (318)  

  chr2_60553414_6    501 AAATTGATCAATAG--TCAATGCAAATCCAATCAAAATCCCAGCAGGCTT 548
                                  v i  --    i    vi  v              -v  i 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCT 112

  chr2_60553414_6    549 TTTTTGTTGAAATTGACAAACTGATTCTAAAATGTATGTGGAAATGCAAA 598
                               iv           i     i       vi  i           i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_60553414_6    599 TG-CCTAAAATAGTTAAAGCAATTTTGAAAAAGAAAAACACATTTGGAGG 647
                         v -  i i     ii   i    i           i    v v       
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_60553414_6    648 ACTTATACAGTGCTAT-------CTGACTTCAAAACT------------- 677
                            i i  vviv v  -------  v   v    i  -------------
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_60553414_6    678 ---TGTGGTGTTAGTGTACAGACAGACA---GGATCAATAGAACAAA--- 718
                         ---      ii i ii  vi  i     ---i       i   i i ---
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_60553414_6    719 ----GTCCAGAGATAGACCCATGCATATAAGATTAACTGAATTTTGACAA 764
                         ----       i   i      i   v  v i i  i   v   i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_60553414_6    765 AGATGCACAAG-CAGTTTAATGGGGGAAAGGGCAATCTTTTCATCAAA-G 812
                         i i   -    - vi  i       -    iii i        v    - 
  L1M4_orf2#LINE/    363 GGGTGC-CAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATG 410

  chr2_60553414_6    813 GAGCTGGAATAATTAGA-ATTTATATGCAAAAAAA-GAACTTCAACCTAC 860
                          v     i i  i i  - ?ii i        i  -   v  vi   ivi
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_60553414_6    861 AAGTCACACCACACACAAAAGTTAACTTAAAGTGGATCACAGATCTAAAT 910
                          vv        i i      i      i   i       ?   i      
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_60553414_6    911 GCAGG-GCAACAACTATAAAA---------GAAAACAT-GGAGAAAATCG 949
                          i i -  v v          ---------        -  ? v     v
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_60553414_6    950 ATGTGACCTTGCATTAGAGAAATGCTTTTTT 980
                         vi         vi    - v    v   i  
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAG-GCAATGGTTTCTT 590

Transitions / transversions = 1.97 (69 / 35)
Gap_init rate = 0.03 (17 / 527), avg. gap size = 3.24 (55 / 17)  

1283 20.67 3.91 2.79  chr2_60553414_60555505.rev     1243  1600 (492)    L1M4_orf2#LINE/L1      547   908 (0)  

  chr2_60553414_6   1243 ACAGGCGTGAGCCACCGTGCCC--GGCCTGAGAAATAATTT-TTAAATAG 1289
                          i   ?  i ii vi    v  --  vi ii v   ii   -   i   v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_60553414_6   1290 GACAC-ACATGCACACACAAACCAAACTATTAAATAAAAAATTGATAAAT 1338
                              - v v     vi   --    ------- v       v       
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAA--CAAA-------AGAAAAAATAGATAAAT 637

  chr2_60553414_6   1339 CAGGCATTATCGAAGTTTAAAACTTTTGCTCTTCGAAAGACACTGTTAAT 1388
                         ii i v i   i  i  v          iv    i  i      i i  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_60553414_6   1389 AAAGTAAAAAGACAAG--ACAGACTGGGAGAAAGTTTTTGCAAAAAATAC 1436
                              i         v--     v         i v        vv   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_60553414_6   1437 ATCTGATAAAGAACTTGTATCCGGAATAAATAAAGCACTCTCAAAAGTCA 1486
                                  i i          i     v      v     i v  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_60553414_6   1487 ATAGTAAGAAATCAATGCAACACAAT--GAAAATGAGCGAAAGATTTGAA 1534
                            i   i  iv   -ii   v    --i      i  i  i        
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_60553414_6   1535 CAGACATTCCACCAAAGAAGGCAT------GGCAAATAAACACATGGAAA 1578
                         i       i v         ii  ------   v     i      i   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_60553414_6   1579 GATGCTGAACATCATTAGTCAT 1600
                               v       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (45 / 28)
Gap_init rate = 0.02 (9 / 362), avg. gap size = 2.67 (24 / 9)  


2856 24.88 5.90 1.04  chr2_60862294_60864945     1297  2160 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_60862294_6   1297 GAGAGACATACCATGTTCATGGATTGGAAGACTCAAAATAACAAAGATGT 1346
                           i   i  v                       i  v  viiv      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_60862294_6   1347 TAGTTCCCTCCAAAATTTATCCACAGGTTTTATGCAATTCCTATAAGAAT 1396
                         i i v i i     -  v   i    i  iv i     i     v i   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_60862294_6   1397 CCTAAAAAGGTTTCTTGCAGACATAGACAAGCTTATTCGAACATTTATAT 1446
                           i ivvivv   i       v  v        v  i v  v   i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_60862294_6   1447 GGAAAGGCACAGGTCCTAGAATAGCTCAAACAATCTTGAAAAAGAAGAA- 1495
                              v   vi  v  i        iv                      -
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_60862294_6   1496 ACAG--AAAAGAATCACTCTACCAAATATTAAGTCTTACTATTTAGCTGC 1543
                          v  --ii i  v    v  v  v   v i  iv       ivv    i 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_60862294_6   1544 AGTAATCAA-AT-GAGTGATATTGGTG-AAGGA---ACA----------- 1576
                                  - i- v   i  i   ii-     ---   -----------
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_60862294_6   1577 -----------GAGAATCCAGAAATAGACCCACACAAATGTGGCAAATTG 1615
                         -----------    i          i     i   vv i   iv     
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_60862294_6   1616 ATTTTTGACAACAGTATGAAAGCAATTCAATGGAGGAAGGATAGCCTTTT 1665
                              i     vi  iiv  ii v         i i   i    i     
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_60862294_6   1666 TAACAAATGATGCTGGAGCA-TTGAACATGCATAGGCAAA-TAATGAACC 1713
                         i        i      ii  -i  i i ?v  i v     -v      vi
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_60862294_6   1714 TCAACCTAAACGTCATATCTTCTATAAAATTTCAC-AAAAATAAATCATA 1762
                          vi   ivv  v   i i v v  i    v  v  -v     ii    ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_60862294_6   1763 GACTTAAATGTAAAATGTAAAACTATAAAACTTTTAAAAAAAAG--TAAG 1810
                            i         i vv               i   i  i   i--  i 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_60862294_6   1811 AGAAAGTCTTTGGGATCTCAGGCTAGACAAAGGATTCTTACACTTAACAC 1860
                         ? v  i    i v  i  ii  i   i   v  v      v iv i    
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_60862294_6   1861 CAAAAGCATGAT--------GGAAAAATTGACAACTTGGCCCTCATCAAA 1902
                                 ii v-------- i      v  i  v    v i        
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_60862294_6   1903 ATTAAAATATTTTTTGCTTTATGAAAGACACTGTTAAGAGAATATAAGTA 1952
                                vv    v     i --  i      i i    i i iv  iv 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_60862294_6   1953 AAAGCTACAGACTGTAGGGGGAAATATTGGCAAAGTTTACATCAGACAAA 2002
                         v  v i     v  --  i i       v     viv  i   v  i  i
  L1M4_orf2#LINE/    700 CAACCCACAGAATG--GGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_60862294_6   2003 GGACTAATATCTAAAATATATTTTTAAAAACCCCTCAAAACTCGAAAGTA 2052
                              vi    i i       ----   i v i  i v     i v i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATAT----AAAGAACTCTTACAACTCAATAATA 793

  chr2_60862294_6   2053 AAAATACAAA----CCAATT---ACGTGGGCACAAGATATAAACAGACAT 2095
                             v     ----      --- vi      v i   v i  i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_60862294_6   2096 TTCATCAAAGAAACTATTCAGAAGGCAAAAAGGCACATGAATAGATGTCC 2145
                            vi       iv   v  i v   v  v i         v     ii 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_60862294_6   2146 AACACCACTGGCCAT 2160
                             i  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (122 / 90)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 3.33 (60 / 18)  


3819 21.76 2.57 1.23  chr2_61071448_61074914.rev     2080  2975 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_61071448_6   2080 TGCAAAAATATCCCACATTCATAGATTGGAAGACTTAATATTGCTAAAAT 2129
                           v   i        ii     i                    i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_61071448_6   2130 GTCCATACTAACCAAAGTGATCTAAAGATTCAGTGCAATCCCTGTCAAAA 2179
                          v v     vv     v       v       ii         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_61071448_6   2180 TTCCAATGATATTTTCCACAGAAATCGAAAAAACAATCCTAAAATTCATA 2229
                          i   iiviiv    iii       i  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_61071448_6   2230 TGGAACCACTAAAGACCCTGAATAGCCAAAGCAATCTTGAGCAAAAAGAA 2279
                              vii v ii     v           i         iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_61071448_6   2280 CAAAGCTAGAGATATCACAATACCTGATTTCAAAA-TTACTACAAAGCCA 2328
                              i i   ivv     v v  ii         -            i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_61071448_6   2329 TAGTAATCAAAACATTTTTGTACTGGCATAAAAACAGACACTTAAACCAA 2378
                         i         i   v v v            ii i     iv  i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_61071448_6   2379 AAGAATAGGAAAGAGAGCCCAGGAATAAATCCATATATTTACAGCCAGCT 2428
                         vi      i vv     i    i      i     i     ii i  ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_61071448_6   2429 GATTTTTTACAAACGTGTGAAGAA-ACTTAATGGGAAAAGA-CAGTCCCT 2476
                               iv    iv   iv    v- i i      i     -i    ii 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_61071448_6   2477 TTAATAAATTGTGCTGGGACAACTGGATATCCACATACAGAATAATGAAG 2526
                          i  i    v                   ?      i  i  v       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_61071448_6   2527 TTAGACCCTTATCTCACACCATATTAAAAACTCAACTGACAGTG------ 2570
                           i     i  i            vv    v i    v v i  ------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_61071448_6   2571 --ACCTAAATCTAAGACCCAAAACTGTAAA-CTATTAGAAGAAAACGTAG 2617
                         --        v     v i      i    -  v            i   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_61071448_6   2618 AGAAAAAGCTCCATGACACTGGTCTGGGCAATTATTT---GAATATGACC 2664
                         i?iv   v  i i    vi   vi i      vi   ---ii       v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_61071448_6   2665 CTAAAAGCACAGGTAACAACAACAAAAAAAAGACAAATCAAATGGGACTA 2714
                          i         i i     -----  i    i i i  -    v     v
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAA-----AAGAAAAAATAGAT-AAATTGGACTT 644

  chr2_61071448_6   2715 TATCAAA--CAAAAGCTTCTGCACTGCAAAGGAAACTATCAACAGAGTGA 2762
                         i      --i    i   i  ii  v       v        v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_61071448_6   2763 AGAGACAACTTATGGAATGGAATAAAATATTTATAAGCCATACATCTAAT 2812
                          i       ii ii      i v         ii  ii    i    i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_61071448_6   2813 GAGGGGTTAATATCCAAAATATACAACGAACTCCAACAACTCAATACCAA 2862
                         i    ii vi      i      i  v      iv           vi  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_61071448_6   2863 GAAAACAG----CCTGATTAAAAGATGGGGAAAGGACCTGAGTAGACATT 2908
                         i  i   i----  ii   ?   i     v      ii   i        
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_61071448_6   2909 TCTCAAAAGAAGACATACAAATGGCCAACAGGTTTAAGACATGCAAA--T 2956
                             v        i              i i i-----     v   -- 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGC-----ACATGAAAAGAT 889

  chr2_61071448_6   2957 GCTTACCATCACTTACCAG 2975
                            i v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.20 (132 / 60)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.83 (34 / 12)  


3150 27.27 1.11 0.44  chr2_61172626_61179287     5269  6170 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_61172626_6   5269 TGGAAGAACATTCCATGCCCATGGATAGGAAGAATCAATATCATGAAAAT 5318
                              ii i  i     ii       v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_61172626_6   5319 GGCAGTACTGCCCAAGGTAATTTATAGATGCAATGCTATCCCCATCAAGC 5368
                             i    v     iv i  i  i    v   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_61172626_6   5369 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5415
                          v   -   v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_61172626_6   5416 ATATGGAACCAAAAAAGAGCCAACATAACCAAGACAATCCTAAGCAAAAA 5465
                                 viiv  ii  v   iv   i    i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_61172626_6   5466 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5515
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_61172626_6   5516 CTACAGTAACCAAAACAGCATGGTGCTTGTACCAACACAAATATATAGAC 5565
                                  i   i    ii    i  v i iv iv i i i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_61172626_6   5566 CAATGGAACAGAACAGAGGCCTCAGAAATAATACC---ACATCTACAACC 5612
                                 i    iv   ivii         -   ---    i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTC 346

  chr2_61172626_6   5613 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATAGGGAAAGGATTCC 5662
                          vi    i  i     ivv  v   i v  vvv   i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_61172626_6   5663 CTATTTAATAAATGGTGCTGGAAAAACTGGCTAGCCATATGTAGAAAGCT 5712
                           v  i  i            i v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_61172626_6   5713 GAAACTGGATTCCTTCCTTACACCGTATACAAAAATTAACTCAAGATGGA 5762
                            ii    ii   v   i     i                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_61172626_6   5763 TTAAAAACTTAAATGTAAGACTTAACACCATAAAAACCCAAGAAGAAAGC 5812
                          i ? i  i           vi   v  i      vi iv        i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_61172626_6   5813 CTAAGCA-ACACCTTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5861
                         v  i ?i- v i    iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_61172626_6   5862 AACACCAAAAACAATGACAACAAAAGCCGGAATAGACAGATGGGATCTAA 5911
                         i         i  vvii         vvii      i i  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_61172626_6   5912 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAACCTATCATCAGAGTGAAC 5961
                          i   v v  i i   i  ii vv    i  vv      vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_61172626_6   5962 AGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTACCCATCTGACAA 6011
                           i     i                 i       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_61172626_6   6012 AGGGCTAATGTCTAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 6061
                         i  i  vi i  i     v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_61172626_6   6062 A---AAACAACCCCATCAAAAAGTAGGCAAAAGATATGAACAGATACTTC 6108
                          ---   i     v  i?    i i      i   v    i   i i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_61172626_6   6109 TCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAATGCTCATC 6158
                           v        i  vi viii     i  i  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_61172626_6   6159 ATCACTGGTCAT 6170
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (156 / 86)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2162 24.52 4.11 2.50  chr2_61250574_61254619.rev     2359  3039 (1007)    L1M4_orf2#LINE/L1        1   692 (216)  

  chr2_61250574_6   2359 TGGAGAGATATTCCATGTTCATGGATGGGAAGAACTGCCATTGGAAAAAA 2408
                             i      i              v      vi ivi    vv  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_61250574_6   2409 AAGGAATTCACCCCAAATTGGTATATGGGTTCAACACAATCCCAACAAAA 2458
                         i- v   v v          i v  ii i      i       v iv   
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_61250574_6   2459 ATCCCAAAAAGATA-----TTTGTAGAAATATCCACACAGACTCTAAAAT 2503
                               ---- v i-----    i      vvv  vi v  ii       
  L1M4_orf2#LINE/    100 ATCCCA----GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_61250574_6   2504 TTGTA-GAAAATGCAACGTACCTTGAAAGGCCAAAATAAT-TTAAAATTA 2551
                          ii  - i        v v   iv   vi       i   -  i   vvi
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_61250574_6   2552 AAGAATAATTTTGGAGGACTCACACCACCAGGTTTCAAGACTCACTA-AA 2600
                              i  vv               iv  vii      i   i    -  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_61250574_6   2601 ATCTACAAAAATTAA--CAGTGTGGTATTGATATGCTGATGTAAAGAAAG 2648
                          v     iv   i  --          i  ii  --------  i  v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCAT--------AAGGATAG 287

  chr2_61250574_6   2649 ACATAAGAATCAATGGAAGAAAAC--ACAGTTTGGAAATGGGGCCACATG 2696
                              vii          v i  i-- v   iii     iiiv   i ii
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_61250574_6   2697 TAAATGGTCAACCGATTTTTAACA----TGCCAAGGTAATCCAATATGTT 2742
                          vv        ii      ii   ----       iiv  i    iv --
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-- 385

  chr2_61250574_6   2743 AGAACAGAATAGTCTTTTCAATAAACGGTGCTGGAACAACCGGCTATGCC 2792
                         -   -                i   i        i     i  v  ?v v
  L1M4_orf2#LINE/    386 -GAA-AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_61250574_6   2793 TATGGAAAAAAAGGAAGCTTGACCCTTAACTCATACAA-----AAAAATT 2837
                         i   v    i  v    i v     i  v    i  v -----       
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_61250574_6   2838 AACCTGAATGGGATCATAATCTTAAATA-AAAAGCTAAAATCATACAACT 2886
                            iii  vv      ? iv i     i-  i        ii   v    
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_61250574_6   2887 TCTAGAAGAAAACACAGCAGAAAATCTTTGTGACTTTGAGGTAGGCAAAT 2936
                         ii            i  v? v       i     i   i v       vv
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_61250574_6   2937 ACTTCTTAGCTATTAAAT-AATGGAACA--TAA-AAAGGAAAAACTAAA- 2981
                         ii       v   v v i-  vi v   --i  -   i      v  i -
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_61250574_6   2982 AAATTAGAATTCA-CAAAATTTAAAACTTTAGCTCTTCAAAATACATCAT 3030
                              i  v    -       v        v iv       iv   ii  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_61250574_6   3031 TAAGAAAAT 3039
                         i      i 
  L1M4_orf2#LINE/    684 CAAGAAAGT 692

Transitions / transversions = 1.45 (97 / 67)
Gap_init rate = 0.03 (19 / 692), avg. gap size = 2.37 (45 / 19)  

 778 20.45 3.64 1.82  chr2_61250574_61254619.rev     3338  3557 (489)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_61250574_6   3338 AAGAAAATTAAAAGGCAAGGCATAGACTAGGGGAAA-TATTGAGAAA-CA 3385
                               i v     i   vv  i   v i  i    -    viv   -  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_61250574_6   3386 TATGGCTGACAAAAAAGACTTAGATCTAAAGTATATACAAAGAAATCTTA 3435
                            iv    i  --ii     iv   i i i      --     v     
  L1M4_orf2#LINE/    735 TATATCTGATAA--GGGACTTGTATCCAGAATATATA--AAGAACTCTTA 780

  chr2_61250574_6   3436 CAATTCAATAATAA---GGCAAATGATCCAAT--AAAAATGGGCCAAAGA 3480
                            i          --- i     i i     --          v  i  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_61250574_6   3481 TTTAAACAAACACTTC-ATAAAAAAGATATATAAATGGTCAGTAAAAACA 3529
                            i  i i   i   -vi   i        i      i  i   iv   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_61250574_6   3530 TGAAAAGTTGCTTAACACTATCTACCCA 3557
                                v    i    ii ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.46 (32 / 13)
Gap_init rate = 0.03 (7 / 224), avg. gap size = 1.71 (12 / 7)  


4829 15.73 3.15 1.12  chr2_61268728_61271714     1606  2495 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_61268728_6   1606 TGGAAAGACATTCTATGTTCATGGATCATAAGACTTAATGTTATTAAGAT 1655
                                 i  i i            iiv          i  i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_61268728_6   1656 GGGAGTATTCCTCAACTTAATCTACAGATTCACCACAGTCTCTAGCAGAG 1705
                           v i  i   i   v  i             v i  i  i   v  i i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_61268728_6   1706 AGACTTGTGAGAGACTCTCTTCCTTGTAGAAATTAACAAGCTGATTCTAA 1755
                         ----- viv  ---  vi   ii   i       i          i    
  L1M4_orf2#LINE/    101 -----TCCCAG---CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr2_61268728_6   1756 AATTTATGTGAAAACTCAAGGGATTCAGAATAGCCAAAACAATTTTGGAA 1805
                             i  i  i   iv       ii                  i   i  
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_61268728_6   1806 GACAA---CAAAGTTAGAAGATTTACACTTTCCCATTTCCAATCTTACTA 1852
                         i v  ---       i  i  i i      i  v     v  v       
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_61268728_6   1853 CAAAGCTACAATAGTCAAGACAGTGCAGTACTGGTATAAGGATAGACATA 1902
                                   i  i           ii       i               
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_61268728_6   1903 CAGATCAATGGAACAGGATTGGGAGTCCAGAAATAAACCCACATTTCTAT 1952
                         i            i  i    i                   i iv i   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_61268728_6   1953 GGTCAACTGATTTTCATCAAGGGTG--AA---------------AAAGAA 1985
                               i        iv        --  ---------------      
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_61268728_6   1986 TAGTCTTTTCTACAAATGGCACTAGGATAGCTAGACAGGCTAATGCAAAA 2035
                                   v        ii  i   i i  i  i ?v vv        
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_61268728_6   2036 TAATCAAGTTGGATCCTTACATCACACCATATGTAAAAATTGATGCAAAA 2085
                         v   v        i  i   v           ii       i iv     
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_61268728_6   2086 TGGATCAAAGACCTAAATGTAAGAGTCAAAACTGTAAAACTCTTACAAGA 2135
                                ?                 ii      i           v    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_61268728_6   2136 AAGCATAGGGGTAAATCTTCGTGACCTTGGATTTGGCAA-GGATTCTTAG 2184
                           i      ?                    i  v     -  v       
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_61268728_6   2185 ATAAGACAATAAAAGCACAAGCAACAAGCAAACAAATAAATAAATTGGAC 2234
                            v    vi                 ivi  v     i           
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_61268728_6   2235 ---ACCAAAATTAAAAACTTTTATGCTTCAAAGAACA---TCAAGAAAGT 2278
                         --- i                 i          i   ---          
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_61268728_6   2279 GAAAAGATAGCTTACAGAATGTGAGAAAATGTTTACAAAGTATGTATCTG 2328
                                i i ii        v        i   i    vi  i      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_61268728_6   2329 ATAAGGAAACGTGTATCCAGAATGTATAAAGAATGCCTACAACTCAACAT 2378
                               i - v            i         iv i          i v
  L1M4_orf2#LINE/    743 ATAAGGGA-CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_61268728_6   2379 TTAAAAGAAAAATAACCCAATTTTTAAAATGG-TGAAAGACTTGAATAGA 2427
                          v      v             ?v-       -ii  i  i         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGA 840

  chr2_61268728_6   2428 CATTTTTCCAAAGAAGATATACAAATGGTCAGTAAGCGCATGAAAAGTTG 2477
                              i                      i  i     i         v  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_61268728_6   2478 CTCAACATCATTGGCCAT 2495
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.49 (97 / 39)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.45 (38 / 11)  


 225 30.05 11.62 4.80  chr2_61337180_61339108.rev     1048  1443 (486)    L1M4_orf2#LINE/L1      486   908 (0)  

  chr2_61337180_6   1048 CTCAAAAAAAA--AAGGACTTAATTGTGAAA---AAAATCATTGAAATAT 1092
                                vii -- ?i   i   v   i i ---    ii  vi  v v 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_61337180_6   1093 TAAAGGAAAACATAACATCACATGAATACCACCATGAGATTTGAA--AGA 1140
                           i i         i----i?i i   -- vi i   v-i   ii--  i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAG----GNGTAAAT--CTTCGTGAC-CTTGGGTTAGG 578

  chr2_61337180_6   1141 CCATG-CTACCTAG----GACACAAAACCCAGAAACAATAAGA-----AG 1180
                          v   -i v i   ----     v   vv  v  i   i  i ----- i
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_61337180_6   1181 TTGAAAGTTTTGACTACATAAAAATTGAAAA------TACTACATGGTGA 1224
                          v  v iv  v    v   v      i    ------ i  v  ----i 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA----AA 674

  chr2_61337180_6   1225 AAATGCCATAAACTGAATTAAAACACAA---ACAGCTAATTGG-GAAAAT 1270
                         ii ii i  v  vvi i v    v    ---    --   v  -      
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAG--AATGGGAGAAAAT 722

  chr2_61337180_6   1271 GTTTGCATACT---TAACAGATAAACAGCCAACACTGCCA--ATATATAC 1315
                         i      v ii---  v v     ivii ivii i--   --       v
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTAT--CCAGAATATATAA 770

  chr2_61337180_6   1316 CAAATTTTTAGGATT---TGGTAAGATGATGAAGAACGTTAAGT--AAAA 1360
                         vi  i i   vi i --- ii   i v  ii  v   -ii  v --    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAAC-CCAATTWAAAAA 819

  chr2_61337180_6   1361 TCAGCAAAGGACATGAATAGGCAGTTT--------AGACACAAAAAAGTG 1402
                          vi        iv       i  v  i--------   i i v   --  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA--TG 867

  chr2_61337180_6   1403 TTTGGTAACCACATGAGAAGTTGCCCAGAC-TTACTAATAAA 1443
                         viiii   v       i   v   i  -  - i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (73 / 44)
Gap_init rate = 0.06 (24 / 423), avg. gap size = 2.71 (65 / 24)  


1628 22.88 4.98 2.95  chr2_61497911_61501364        5   546 (2908)    L1M4_orf2#LINE/L1      171   723 (185)  

  chr2_61497911_6      5 AATAGCCAGAACAGTCT-GAAAAAGATGACTTTGAAACTTGCAAAAAGAA 53
                                 i    i   -        v  vi---   v   v ii vvv 
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAAC---AAAGTTGGAGGACTCA 217

  chr2_61497911_6     54 AA------AAAAGAAAAA---AC-AAAAAGCAACAGTAGTAATTAAATAG 93
                         v ------  vvvv    ---  - v     v      i v -- i i  
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA--AGACAG 265

  chr2_61497911_6     94 TATGGTACTGACATAAGGACACACATGTAGGCCAGTGGAGAAGAATGCAG 143
                          i        i        i v    i   ii  i    iv     vv  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_61497911_6    144 ATCCCAAAAATAAACCTTCATATGAAAAAGGTCAACTGACTTTCAACCAA 193
                          vi   i         --    iivvv v      i   i    i  -  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACC--CATACATTTATGGTCAATTGATTTTCGAC-AA 362

  chr2_61497911_6    194 GGTTGCCAAGGCCATTTAATGGGGGAAGGACAGTTTTTTCAACAAATGGT 243
                           v       i     i       i   i i   i               
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_61497911_6    244 GTTAGGAAAACTGAATATTTACATGTAAAAAGAATAAAGTTTAATCTTTA 293
                          i i   v     i   ?ii     i    -    i     vi i ii  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAAGTTGGACCCCTA 461

  chr2_61497911_6    294 CCTTACACCACATGTAA----CAAATCAAAACACATCAAATACTTAAAAG 339
                            i      i  ii  ----i  v      iiv    ? v  i    v 
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_61497911_6    340 AAAAATCTTTTTTTA-AAAACCCTTAGAAGGAAAAGATAAGGATTGTAAT 388
                         v  i v  vvvvi  -     i        -    v   i ?i v--   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAG-AAAACATAGGNGTA--AAT 558

  chr2_61497911_6    389 CTTCATGACATTGGATTTGAAAATTATTTCTTGGGTATGACGCCAAAA-- 436
                             i    v    i  v iv   vi      i i      i      --
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_61497911_6    437 ATAGTCAACAACAACAAA----GATATGTTAGACTTCATCAAAATTAAAA 482
                          i iv      v iv   ----    vi  i                   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_61497911_6    483 ACTTTTGTGCATCAAAGGACACTAG-AAGAA--TGAAAA--TAAACCATA 527
                                   v             v-     --      --i  v   i 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_61497911_6    528 GATCACACAGCAAAAAATA 546
                           ---- ii v i      
  L1M4_orf2#LINE/    709 GA----ATGGGAGAAAATA 723

Transitions / transversions = 1.37 (70 / 51)
Gap_init rate = 0.03 (19 / 553), avg. gap size = 2.26 (43 / 19)  

 434 19.47 4.42 2.65  chr2_61497911_61501364     1433  1545 (1909)    L1M4_orf2#LINE/L1        1   115 (793)  

  chr2_61497911_6   1433 TAAAAAGACATTCCATATTCATGCACTGAAGGAA-AAATATCATTAAAA- 1480
                          ii     i  i    i      v i  i i  v-v     ii    i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_61497911_6   1481 GTCCATACCACCCAAA---ATCTACAGAGTCAACGCAATCCCTATCAAAA 1527
                          v v    iv      ---         v                     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_61497911_6   1528 TCTCAATGGCAGTCTTTT 1545
                           i  ---  v i     
  L1M4_orf2#LINE/    101 TCCCA---GCTGCCTTTT 115

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.03 (4 / 115), avg. gap size = 2.00 (8 / 4)  

 543 29.52 1.81 0.60  chr2_61497911_61501364     1839  2004 (1450)    L1M4_orf2#LINE/L1      102   269 (639)  

  chr2_61497911_6   1839 CTCAATGGCATTCCTTACAAAAATAGAAAAAACAGCCCTAAAATTCATAC 1888
                          i  iiv  v  ii  i  i    v  v  iviiii             i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_61497911_6   1889 AGAACCACAAAAGGCCCCAAATAGCAAAAAACAATCTTGAG---TAAGAA 1935
                         i   vii   ii i   vi      v    -         i---v     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAA 200

  chr2_61497911_6   1936 TAGAGTTGGAAGTATCACACTTTTTAATTCCAAAATACATTACATGACTA 1985
                         i i       i vv        iii    i     ivi i    vii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_61497911_6   1986 CAGTAATCAAAACAATATG 2004
                                   i   i i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTG 269

Transitions / transversions = 2.77 (36 / 13)
Gap_init rate = 0.01 (2 / 168), avg. gap size = 2.00 (4 / 2)  

2229 23.03 2.63 3.25  chr2_61497911_61501364     2316  2962 (492)    L1M4_orf2#LINE/L1      266   908 (0)  

  chr2_61497911_6   2316 TATGGCACTGGCATAAAAACAGACATATGGACCCATAGAACA-AATAAAA 2364
                          i   i          ii i        i  i v  i   i -   vi i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_61497911_6   2365 ACCCCAGAAACAAATCCATGCATCTACAATCAACTGATCTTCCAGAAGGA 2414
                          vi       i   i    i   i  iii    i    i   v v    i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_61497911_6   2415 TGCCAAGAACATATGATAGGGAAAGGACAGTCTCTTCAACAAAAGGTGAT 2464
                                 v   vii  i       i i     i         v    v 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_61497911_6   2465 GGGAAAACCTGATATCCACATACA---GAATGAAACTGGATCCTTATCTT 2511
                             v   iv    ?      i  ---       ii    i  i  i  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_61497911_6   2512 ATACCACACACAAAAATCAACTCAAAATGGATTAAAAACTTCAAAGTACA 2561
                          i    i i        i              i ? i  i -   -----
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT-AAA----- 509

  chr2_61497911_6   2562 TTTAAGACCTGAAATTGTAAAACTACTAGAAGGTGACACAGGTTAAAAAG 2611
                          v     v  i   i i       vi      ivi   i   ?-iv   v
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN-GTAAAT 558

  chr2_61497911_6   2612 CTTCTTGACAATGGTCTAGGAAATAATTTTTTTGACAGGA-ACTATTAGC 2660
                             v    vv   vi    v   ii   i  v  i v  -  i vv   
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_61497911_6   2661 ATAGGCAACATAAGCCAAAATATACAATTGAGATTTCATCAAACCAACAA 2710
                          i i      v   vv      v i  v vi  i         viv v  
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_61497911_6   2711 GCTTCTGCACAGCAAAGGAAAC----AACAGAGTGAAAAAGCAACCTACA 2756
                         i   i  ii vv       v  ----  v i        ii     i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_61497911_6   2757 AAATGGAATAAAATATTTACAAACCATGTAT-TGATTAGGGGTTAATATC 2805
                         i     i v         i    i   i   -    v    ii vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_61497911_6   2806 CAGAATATTTAAGAAACTCATACAACTCAATAGCAAAAAAATAATAAATA 2855
                                 v   ii     v            ii     i i  ---   
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA---ATA 805

  chr2_61497911_6   2856 AATAAATAAATAAATAACCCTATGTAGGGCAAAGAA----AATAGACATT 2901
                          viv   v? v    -----------        i ----          
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAAT-----------GGGCAAAGGATTTGAATAGACATT 844

  chr2_61497911_6   2902 TCTCAAAAAAAGACAAACAAATAGCCAATAGGTATA---AAAGCTGCTCA 2948
                             v   i    i v      i       i i i ---    v      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_61497911_6   2949 ATATCACTAATCAT 2962
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (94 / 51)
Gap_init rate = 0.02 (12 / 643), avg. gap size = 3.17 (38 / 12)  


2723 27.33 1.28 0.93  chr2_61731335_61733184      499  1358 (492)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr2_61731335_6    499 AAAATGGCTATACTGCCCAAAGTAATTTAAAGATTCAATGCTATTCCCAT 548
                           i     v     v      v i  i  v        i  v  i  i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_61731335_6    549 CAAGCTACC-TTTGACTTTCTTTGTAGAGTTAGAAAAAACT-ACTTTAAA 596
                            iv v  -vi  v    -    i   iv v  v  i-  - iii    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTT-TTTGCAGAAATTGACAAG-CTGATCCTAAA 143

  chr2_61731335_6    597 TTTCATATGGGACCAAAAAAGAACCTGTATAGCCAAGACAATTCTAAGCA 646
                         v         i viiv  ii  v  v v        i     ii i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_61731335_6    647 AAAAGCACAAAGCTGGAGGCATCACGTATCT-GACTTCAAACTATACTAC 695
                          i   v      i      vv    iiv  i-i i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_61731335_6    696 AAGGCTACAGTAACCAAAACAGAATGGTACTGATACCAAAACAGATATAT 745
                           i          i   i    vi        ii iv ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_61731335_6    746 AGAACAATGGAGCAAAACAGAGACCTCAGAAATAACACCACACATCTGCA 795
                            v       ii i  iv    vii         vv   i    i iii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_61731335_6    796 ACCATCTGATCTTTGGCAAACCTAACAAAAATAAGCAATGGGGGAA-AGG 844
                         ii  vi    i  i i   ivv iv   i vi vv        i  - iv
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_61731335_6    845 AGTCCGTATTTAAGAAATGATGCTGGGAAAACTGGCTAGCCACTTGCAGA 894
                             -- v  i  v     i        v      v  ?    v    i 
  L1M4_orf2#LINE/    394 AGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_61731335_6    895 AAACAGAAACTGGACCTCTTCCTTACACCTTATACAAAAATTAACTCAAG 944
                          i vv   ii      i  v   i     v                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_61731335_6    945 ATGGATTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAG 994
                               i ?    i         i v i     i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_61731335_6    995 AAAACCTAGGC---AATCCCATTCAGGACATAGGCATGGGCAAAGGCTTC 1041
                              v    ?---    ---   iv   v v  vv i     v  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_61731335_6   1042 ATGACTAAAACATCAAAAGCAATTGCAAGAAAAGCCAAAATTGACAAAGG 1091
                         v iiv  vi   i        vvv    v     vv     v  i   vv
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_61731335_6   1092 GGATCTAATTAAACTAAAGAGCTTCTGCACAACGAAGAA-ACTATCATCA 1140
                            ii v  i   v v  i i   i  ii vv i   i -       vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_61731335_6   1141 GAGTGAACAGGCAACCTA-AGAATGGAAGAAAAGTTTTGCAATCTACCTA 1189
                         i      v  i     i -       i      vv       vii iv  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_61731335_6   1190 TCTGACAAAAGTCCAATATCCAGACTCTACAAGGAACTTTAACAAATTTA 1239
                              i  ii v ivi        v v  i  i     i v    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_61731335_6   1240 CAAGGAAAAAAACAAACAACCTTATCAAAAAGTGGGCGAAGGATATGAAC 1289
                         i  v-     i     i    iv  i?    i     i      v    i
  L1M4_orf2#LINE/    789 TAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_61731335_6   1290 AGACACTTCTCAACAGAAGACATTTATGCAGCCAACAA--ACGTGAAAAA 1337
                              i     v v      i  vi viii     i  --  i      i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_61731335_6   1338 AAGCTCATCATCACTGGTCAT 1358
                          v     v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (133 / 98)
Gap_init rate = 0.02 (13 / 863), avg. gap size = 1.46 (19 / 13)  


1157 24.91 0.37 0.00  chr2_62119192_62124778.rev     3858  4126 (1461)    L1M4_orf2#LINE/L1        1   270 (638)  

  chr2_62119192_6   3858 TGAAAAGATATTCCATGTTCATGGATTGGAAGAATCAATATTGTTGAAAT 3907
                           i        i                     v i         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_62119192_6   3908 GTCTATACTATGCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 3957
                          v v     viv    vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_62119192_6   3958 TACCAATGACATTCTTCACAGAAACAGAAAAAC-AATCCTAAAATGTATA 4006
                          v   iivi v  i  ii      iv  v  i -i          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_62119192_6   4007 ATGAACCATAAAAGACCCAGAATCGCCAAAGCTATCCTGAGCAAAAAGAA 4056
                         vv   viii  ii          v      i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_62119192_6   4057 CAAAACTGGTGGAATCACATTACCTGACTTCAAATTATACTACAGAGCTA 4106
                             ii   v   v     i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_62119192_6   4107 TAGTAACTGATATGGTTTGG 4126
                         i     iii v ii  v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGG 270

Transitions / transversions = 1.68 (42 / 25)
Gap_init rate = 0.00 (1 / 270), avg. gap size = 1.00 (1 / 1)  

2503 22.87 2.63 0.62  chr2_62119192_62124778.rev     4449  5095 (492)    L1M4_orf2#LINE/L1      249   908 (0)  

  chr2_62119192_6   4449 TACAGTAACCAAAACAACATGGTACTGGCATAAAAACAGACACACAGACC 4498
                                 i   i   iii              ii i     i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_62119192_6   4499 AGTGGAACAGAATAGAGAACCCAGAAACAAATCCATCCATGTACAGTGAA 4548
                          i     i     v    ii       i   i    v   v  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_62119192_6   4549 CTCATTTTCGACAAAAGTGCCAAAAC--------AGAGAAAAGACAGTCT 4590
                         i v           ii       i  --------i i    ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_62119192_6   4591 CTTCAATAAGTGGTGCTAGGCAAACTGGATATCAACATGCAGAAGATCTG 4640
                         i     i  i       i  vv         ? v       i    -v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-ATG 447

  chr2_62119192_6   4641 AAACTAGACCCCTATCTCTCGCCATGTACAAAAATCAAATCAAAATGGAT 4690
                           ii i        i   v i    i         i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_62119192_6   4691 GAGAGACTTAAATCTAGGACCTCAAACTATGAAACT---ACAAGAAAACA 4737
                         v ?    i     v  i  v  v       i     --- v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_62119192_6   4738 TTGGGGAAACTCTTCAGGCCATTGGACTGGGCAAAGATTCCTTGAGTAAA 4787
                          v  ? v  v     iv v v    ii i     v i  i   iii  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_62119192_6   4788 TACCCCACAAGTACAGGTAACCAAAGCAAAAGTGGACAAATGGGATCACA 4837
                         -  v   v   i   i i   v    v    i i  i    v   iiv  
  L1M4_orf2#LINE/    598 -ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_62119192_6   4838 TTAAG-TTAAAAGGCTTCTGCACAGCAAAGGAAGCCATCAACAAAGGGAA 4886
                          i  i-      i-   i  ii vv       vi i     v    v   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_62119192_6   4887 GAGACAATCCACAGAATGGGAGAAAATATTTGTAAACTATCCATCTGACA 4936
                         i      i                        i   ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_62119192_6   4937 AGAGATTAATAACCAGGATA-A-AAGGGGCTCAAACAACTCTACAGGACA 4984
                           i  i vi  v    i   - -  i ii   vv       v i iv v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_62119192_6   4985 AAT-CTAATAACCCAATTTTAAAATGGGCAAAAAAAGCTGAACAGACATT 5033
                           v- v            ?v            ii -vi    i       
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGA-TTTGAATAGACATT 844

  chr2_62119192_6   5034 TCTCAAAAAAAGAAATAAAAAAGGCAAACA--TACATGAAAAGATGCTCA 5081
                             v   i    v   v   v   v  i --i                 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_62119192_6   5082 ACATCATTGATCAT 5095
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (92 / 52)
Gap_init rate = 0.02 (11 / 660), avg. gap size = 1.91 (21 / 11)  

1107 27.25 0.00 0.00  chr2_62119192_62124778.rev     5168  5501 (86)    L1M4_orf2#LINE/L1      575   908 (0)  

  chr2_62119192_6   5168 TGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAGAAGAC 5217
                          i     v ii   v ivvi vi            vvi      i    v
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_62119192_6   5218 AAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 5267
                              v  i    v   ii v  i   v v  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_62119192_6   5268 AGAAACTACCATCAGAGTGAACAGGCAACCTACAACATGGGAGAAAATTT 5317
                         i  v    i  vv i      v  i     i   iv            v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_62119192_6   5318 TCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAA 5367
                          i    vii ivi      i  i  i  vi          v  i  v   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_62119192_6   5368 CTCAAACAAATTTACAACAAAAAAACAAACAACCCCATCAAAAAGTGGGC 5417
                            vv    v iv i  i     i     i     v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_62119192_6   5418 GAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCTAAAA 5467
                         i     iv    i     i     v        i  vi viii  i  v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_62119192_6   5468 AACACATGAAGAAATGCTCATCATCACTGGCCAT 5501
                          i        i i       v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (53 / 37)
Gap_init rate = 0.00 (0 / 334), avg. gap size = 0.00 (0 / 0)  


 609 25.00 4.65 1.16  chr2_62513707_62515986      485   656 (1624)    L1M4_orf2#LINE/L1      179   356 (552)  

  chr2_62513707_6    485 AAACAAT---GGAGGAGCCAAAACAAAGCTGGAGGCATCACATTACCTGA 531
                                --- i ii  v- i       i      vv     i v  ii 
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGA-AGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_62513707_6    532 CTTTA-----TACTACAAAGTTGTAGTAACCAAAACAACGTGGGACTGGT 576
                         i  i -----          i ii     i   i   ii    v     i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_62513707_6    577 ATAAAATCAGACCCACAGACCAATGGAAACCAAATAGAGAACCCAGAAAT 626
                             iivi    vi i   i        -ivi   v    ii        
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAA-TAGAATTGAGAGTCCAGAAAT 326

  chr2_62513707_6    627 AAACGCACACATTTACAGTCAAGTCATTTT 656
                             v  i       ii     v v     
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 2.58 (31 / 12)
Gap_init rate = 0.02 (4 / 178), avg. gap size = 2.50 (10 / 4)  

 656 23.38 1.95 0.65  chr2_62513707_62515986      920  1073 (1207)    L1M4_orf2#LINE/L1      344   499 (409)  

  chr2_62513707_6    920 GTCAACTCATTTTTGACAAAGGCACCAAGAACATAAATTAGGGAAAGGAC 969
                              i v     i     i  ii      v   vv v i       i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_62513707_6    970 A-CCTTTTTAATAAATGATGTTAGGAAAAT--GATAATCATATGCAGAGG 1016
                          -i     i  i     i  i i   v  i--    ?i  i     i i 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_62513707_6   1017 AATGAAACTAGACCCCTATTTCTCACCATATACAAGAATCAAATAAAAAA 1066
                               ii i        ii  v            i   i  v v    -
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA- 492

  chr2_62513707_6   1067 TGGATCA 1073
                                
  L1M4_orf2#LINE/    493 TGGATCA 499

Transitions / transversions = 2.89 (26 / 9)
Gap_init rate = 0.02 (3 / 156), avg. gap size = 1.33 (4 / 3)  

1411 23.72 3.18 0.49  chr2_62513707_62515986     1380  1788 (492)    L1M4_orf2#LINE/L1      489   908 (0)  

  chr2_62513707_6   1380 AAAAAGGATCAAAGACCTAAATGTAAGA--------CATGAAACTACTAG 1421
                             v      ?                --------i  i     vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_62513707_6   1422 AAGAAAACATTGGAG-AAATGCTTCAGGGACAATAGGCTGGGCTAAGATT 1470
                                   v  ? -    -    - v   vv i  i i   v v i  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT-CTTC-GTGACCTTGGGTTAGGCAATGGTT 586

  chr2_62513707_6   1471 TCTTGAGTAAGACCTCAACAGCACAGGTAACCAAAGCAAAAACTGACAAA 1520
                             iii  v   vi   v      i i   v    v     iv  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_62513707_6   1521 TGTCATTAGATCAAGCTAAAAAGCTTCTGCACAGCAGATAAAACAATCAA 1570
                          vvv i vv     iv v    i   i  ii vv  i vi v  v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_62513707_6   1571 CAAGGTGAAGAGACAACTTATAAGATGGGAGAAAATACTTGAAAACTACT 1620
                         v  i     i       ii i ii             i   v   ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_62513707_6   1621 CATCTGGTGAAGAATTAATAACCAAAATATAGAAAGAACTCAAACAACTC 1670
                         i     i i i i i vi  v   i      v         vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_62513707_6   1671 AATAACAAAAAAA-AAAT---CTGATTTAAAAATATGTAAAAGATCTGAA 1716
                              i     i -    --- ii   ?      iv i   i   i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_62513707_6   1717 TAGACATTTCTCAAAAGAAGACATAAAAATGGCTAACAGGTATATGAAAA 1766
                                     v        i   v       i  i i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_62513707_6   1767 AATGCTCAACATCACTAAGCAT 1788
                         i             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (57 / 37)
Gap_init rate = 0.01 (6 / 420), avg. gap size = 2.50 (15 / 6)  


3529 24.56 1.22 0.56  chr2_62557523_62561788     2875  3774 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_62557523_6   2875 GAAAAATATTTTGTGTTTATGAATTGGAAGAATTAATATCGATAACATGT 2924
                             i    iiii    i   i         v       i v   v   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_62557523_6   2925 CCATACTACTCAAAGCAATCTACAGATTCAGTGCAATCCTTACCAAAATA 2974
                          v     v i    vii             ii       i  i      v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_62557523_6   2975 CCAATGACATTTTTCACAGAAATAGAAAAAACT-ACCGCAAAATTTATAT 3023
                            iivi v     ii       v  v  i-  - i vi      i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr2_62557523_6   3024 GAAACTACAAAAGGCCCA--ATTGCCAAAGCTATCCTCAGCAAAAAGAAC 3071
                          i  v i   ii i    --  v      i v   i v iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_62557523_6   3072 AAAACTGGAGGAATCCACATTACCTGACTTCGAATTATATTACAGAGCTA 3121
                            ii       v  -   i v  ii i   i  viv  i    i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTC-ACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_62557523_6   3122 CAGCAACCAAAACAGCATGGTACTGGCATAAAAACAGACACATAGACCAA 3171
                            i  i   i    ii              ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_62557523_6   3172 TGGAACAGAATAGAGAACCCAGAAACAAATCCACACAGCTCCAGTGAACT 3221
                              i     v    ii       i   i   i   vi vii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_62557523_6   3222 TATTTTCAACAAAGGTGCCAAGAATATACAGTGGGGAAAAGACGGTCTT- 3270
                         v      i    i          vi  v  i        ii ii     -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_62557523_6   3271 -CAATAAATGCTGCTGGGAAAACTGGATATTCATATGCAAAAGAATGAAG 3319
                         -   i     v        v         ?i  i                
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_62557523_6   3320 CTAGGCTGCTACCTCTCATCATATACAAAATTCAAATAAAAATGGATTAA 3369
                         i i i iv       v  i           v i  v v         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_62557523_6   3370 AGATGTAAGTCTAAGACCTCAAACTATGAAACTACTTC-AAGAGAACATT 3418
                            iv   i v     v  v       i     -   v-    i     v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATA 549

  chr2_62557523_6   3419 GGGGAAAATCTCCAGGACATTGGTCTGGACAAAAATTTCATGAGCAGTAC 3468
                           ? v      i iv   v    vi i i   vii    v iiii vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_62557523_6   3469 CCCACAAGCACAGGCAACCTAAGCAAAAATGAACAAATGGAATCATATCA 3518
                         v   v       i     vv   v      ii i    v i iivi    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_62557523_6   3519 AG-TTAAAAGGCTGCTGCACAGCAAAGGATACAGTCAACAAAGTGAAGAG 3567
                          i-      i-  vi  ii vv       i  vi    v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_62557523_6   3568 ACAACTCACAGAATGGGAGAAAATATTTGCAAACTACCCATCTGACAAGG 3617
                              i                           ii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_62557523_6   3618 GATTAATCACCAGAATATATAAGGAGCTGAAACAACTATATAGGGAAAAA 3667
                           i vi vv             i  i  vvv      vv   ivi    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_62557523_6   3668 ATAAAATAATCCAATCAAAAAATGAGCAAAAGATTTGAATTGACATTTCT 3717
                          i   -   i     i?       i     i         v         
  L1M4_orf2#LINE/    799 ACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_62557523_6   3718 CAAAAGAAGACCTA----TGGCACACAGGCATATGAGATGGTACTTAACA 3763
                          v        iv  ----    vv i i   i    i v i i  i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_62557523_6   3764 TTATCAATCAT 3774
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.45 (16 / 11)  


3126 27.01 0.77 0.66  chr2_62654558_62660937.rev     4982  5888 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_62654558_6   4982 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATGAATATCGTGAAAAT 5031
                              ii i  i     i        v      v v     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_62654558_6   5032 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5081
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_62654558_6   5082 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5129
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_62654558_6   5130 TATGGAACCAAAAAAGAGCCGGCATTGCCAAGACAACCCTAAGCCAAAAG 5179
                                viiv  ii  v  i v  v     i    i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_62654558_6   5180 AACAAAGATGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5229
                                v      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_62654558_6   5230 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 5279
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_62654558_6   5280 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGTCACACATCTACAACC 5327
                                i    i--    i  --        vvi  i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_62654558_6   5328 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAACTGGGGAAAGGATTCC 5377
                          vi    i  i     ivv  vv  i v  vvv v         i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_62654558_6   5378 CTATTTAATAAATGGTGCTGGGAAAACTGACTAGCTACATGTAGAAAGCT 5427
                           v  i  i              v     iv  ? i     i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_62654558_6   5428 CAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGA 5477
                         v  ii    i    v   i    iv              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_62654558_6   5478 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5527
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_62654558_6   5528 CTAAGC-CATACCATTCAGGACATAGGCATGTGCAAGGACTTCATGACTA 5576
                         v  i ?-i v i -   iv   v v  vv iv    v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_62654558_6   5577 AAACACCAAAAGCAATGGCAACAAA-GCCAAAATTGACAAATGGGATCTA 5625
                         vi            vvi        - vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_62654558_6   5626 ATTAAACTAAAGAGCTTCTGCACAGCAAATGAAACTACCATCAGAGTGAA 5675
                           i   v v  i i   i  ii vv    v  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_62654558_6   5676 CAGGCAACCTACATAATGGGAGAAAAC-TTTTCAATCTACCCATCTGACA 5724
                         v  i     i   v            i-   v   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_62654558_6   5725 AAGGACTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5774
                          i     vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_62654558_6   5775 AAAATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 5824
                           i -    i     v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_62654558_6   5825 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5874
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_62654558_6   5875 TTATCACTGGCCAT 5888
                         vi    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3125 26.78 1.67 0.78  chr2_62719929_62726272.rev     4953  5852 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_62719929_6   4953 TGGAAGAACACTCCATGCTCATGGATAGGAAGAATTAATATCGTGAAAAT 5002
                              ii i ii     i        v      v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_62719929_6   5003 GGCCATACTGCCCAAGGTAATTTATAGATTCCATGCCATCCCCATCAAGC 5052
                            v     v     iv i  i  i      v i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_62719929_6   5053 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5100
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_62719929_6   5101 TATGGAACCAGAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5150
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_62719929_6   5151 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTATAAGGC 5200
                                i      vv    i  v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_62719929_6   5201 TACAGTAACCAAAACCGCATGGTACTGGTACCAAAACAGAGATATAGACC 5250
                                 i   i  v ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_62719929_6   5251 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACTTCTACAACT 5298
                                i    i--    i  --        vv   i  v i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_62719929_6   5299 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGTGAAAGGAT--T 5346
                          vi    i  i     ivv  v   i v  vvv     v     i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_62719929_6   5347 CCTTATTTAACAAGTGGTGCTTGGAAAACTGGCTAGCCATATGTAGAAAG 5396
                          i  -- i     i       v   v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_62719929_6   5397 CTGAAACTGGATCCCTTCCTTACACATTATACAAAAATTAATTCAAGATG 5446
                         v    ii    i    v   i    vv              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_62719929_6   5447 GATTAAAGACTTACATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAA 5496
                            i ?    i  v    v   v  i    i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_62719929_6   5497 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5545
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_62719929_6   5546 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATGGACAAATGGGATC 5595
                           vi            vvi          vv     i  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_62719929_6   5596 TAATTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTACCATCAGAGTG 5645
                          v  i   v v  i i   i  ii vvi   i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_62719929_6   5646 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 5695
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_62719929_6   5696 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 5745
                         i  i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_62719929_6   5746 AAAA--------ACCCCGTCAACAAGTGGACGAAGGATATGAACAGACAC 5787
                             --------    vi i? v  i   i i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_62719929_6   5788 TTCTCAAAAGAAGACATTTATGTAGCCAAAAGACACATGAAAAAATGCTC 5837
                              v        i  vi vi i     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_62719929_6   5838 ATCATCACTGGCCAT 5852
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.20 (22 / 10)  


3177 27.31 0.66 0.66  chr2_62743524_62749914     4992  5899 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_62743524_6   4992 TGGAAAAACATTCCATGCTCATGGGTGGGAAGAATCAATATCATGAAAAT 5041
                               i i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_62743524_6   5042 GGCCATACTGCCCAAGGTAATTTATAGATTGAATGCCATCCCCATGAAGC 5091
                            v     v     iv i  i  i     v  i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_62743524_6   5092 TACCAATGACTTTCTTCACAGAATTGGAAAAGACT-ACTTTAAAGTTCTT 5140
                          v   iivi i  i  ii     v v  v   -  - iii    i   v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_62743524_6   5141 ATGGAACCAAACAAGAG-CCCACATT-GTAAAGTCAATCCTAAGCCAAAA 5188
                               -- vi    i -    v v - iv  iv     i i ivv i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_62743524_6   5189 GAACAAAGCTAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5238
                                 i i    vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_62743524_6   5239 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5288
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_62743524_6   5289 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGTGTATCTACAAC 5336
                                 i    i--    i  --        vv ii ii  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_62743524_6   5337 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5386
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_62743524_6   5387 CCTGTTTAATAAATGTTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5436
                         i  v  i  i     v        v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_62743524_6   5437 TGAAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGG 5486
                             ii    i    v   i     v i            i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_62743524_6   5487 ATTAAAGACTTAAATGTTAGACCTGAAAACATAAAAACCCTAGAAGAAAA 5536
                           i ?    i       v   v  i   vi      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_62743524_6   5537 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5585
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_62743524_6   5586 AAAACACTGAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5635
                          vi    ii      vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_62743524_6   5636 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAGCTACCATCAGAGTGA 5685
                         v  i   v v  i i   i  ii vv    i  vi   i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_62743524_6   5686 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5735
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_62743524_6   5736 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5785
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_62743524_6   5786 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 5835
                            i     i     v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_62743524_6   5836 TCTCAAGAGAAGACATTTATGCAGCCAGCAGACACATGAAAATATGCTCA 5885
                             v i      i  vi viii    ii ii          v       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_62743524_6   5886 TCATCACTGGCCAT 5899
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3119 26.82 0.77 0.55  chr2_62755446_62762015.rev     5173  6078 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_62755446_6   5173 TGGAAAAACATGCCATGCTCATGGATAGGAAGAATCAACATCGTGAAAAT 5222
                               i i  v     i        v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_62755446_6   5223 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCTCCATCAAGC 5272
                            v     v      v i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_62755446_6   5273 TACCA-TTGCCTTTCTTCACAGAATTAGAAAAATCTACTTTAAATTTCAT 5321
                          v   -i       i  -i     v v  v  iiiv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_62755446_6   5322 ATAGAACCAACAAAGAGCCCACA-TAGCCAAGACAATCCTAAGCAAAAAG 5370
                           i   vii-   i ii    v -       i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_62755446_6   5371 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAAGC 5420
                                i      vv   ii  v  ii i      vivi          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_62755446_6   5421 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5470
                          i      i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_62755446_6   5471 AATGGAACAGAATACAGGCCTCAGAAATAACACCACACATCTACAA-CGA 5519
                                i     vv  ivii         vv   i    i  iii- i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_62755446_6   5520 TCTGATCTTTGACAAACCTGACATAAACAAGCAATAGGGAAAGGCCTCCC 5569
                          -    i  i     ivv  v  vi v  vv    i       ivivvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_62755446_6   5570 TATTGAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC-- 5617
                          v  v  i        i     v      v  ?   i     i  i v--
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_62755446_6   5618 AAACTGGACCCCTTCCTTACACCTTACATGAAAATTAACTCAAGATGGAT 5667
                           ii         v   i     v  i ii             i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_62755446_6   5668 TAAAGACTGAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5717
                         i ?    iv   ii     v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_62755446_6   5718 TAGGC--AACACAATTCAGGAGATAGGCATGGGCAGAAACTTCATGACTA 5765
                             ?--  vv --   iv  vv v  vv i    iviii   v iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_62755446_6   5766 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5815
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_62755446_6   5816 ATTAAACTAAAGAGCTTCGGCACAGCAAAAGAAACTATCATGAGAGTGAA 5865
                           i   v v  i i   iv ii vv    i  v       v  i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_62755446_6   5866 CAGGCAAGCTTCAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACA 5915
                         v  i   v iv                v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_62755446_6   5916 AAGGGCTAATATCCAGAACCTACAAAGAACTTAAACAAATTTACAAGAAA 5965
                          i  i  vi         iv  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_62755446_6   5966 AAAACAAACAACCCCACCAAAAAGTGGGCAAAGAATATGAACAGACACTT 6015
                           i     i     v ii?    i         i  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_62755446_6   6016 CTTAAAAGAAGATATTTATGCAGCCAACAAACATATGAAAAAAAGCTCAT 6065
                           iv           vi viii     i  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_62755446_6   6066 CATCACTGCTCAT 6078
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1020 16.18 2.94 9.56  chr2_62765142_62767971.rev      955  1226 (1604)    L1M4_orf2#LINE/L1        1   254 (654)  

  chr2_62765142_6    955 TGGAAAGACATTTG--GTTCATGGAGCGGAAGAC--AATATTGTTAAAAT 1000
                                 i  iiv--         vi       --           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_62765142_6   1001 GTTCATACTACACAAACATGGGAGATCCACAACGCACAAGATTCACAAGA 1050
                          viv     v v    i-  ----   i   --------      -----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TG----ATCTACA--------GATTCA----- 82

  chr2_62765142_6   1051 TTAAATGCAATCCCTATTAAAATCCCAATGGCATTATTTTTTGGCAGAAA 1100
                         ---- i           i         iiv  ----i     v       
  L1M4_orf2#LINE/     83 ----ACGCAATCCCTATCAAAATCCCAGCTGC----CTTTTTTGCAGAAA 124

  chr2_62765142_6   1101 TAGAAAA----ATCCTAAAATTCATATGGAACCTCAAAGGACCTTGAAAA 1146
                          v  v  ----                    viv   i     iv   v 
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr2_62765142_6   1147 GCCAAAATAATCTTGAATAAGAAAAACAAAGTTGGGTGCCTCACATGTCA 1196
                                i         v     i           iv v      iv  v
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr2_62765142_6   1197 TGATTTCAAAACATATTACAAAGCTATAGT 1226
                         ii          v  i          i   
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGT 254

Transitions / transversions = 1.20 (24 / 20)
Gap_init rate = 0.03 (8 / 254), avg. gap size = 4.25 (34 / 8)  

2911 19.53 2.96 1.63  chr2_62765142_62767971.rev     1663  2338 (492)    L1M4_orf2#LINE/L1      224   908 (0)  

  chr2_62765142_6   1663 CCACTCTCACCAATCTT-CTACA----TACAGTAACCATAACAGTCTGGT 1707
                            v i   --  v   -     ----        i  vi     v    
  L1M4_orf2#LINE/    224 CCAATTTCA--AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_62765142_6   1708 ACATGCACAAGGAGGCACATACAGACCAATGGAACAGAATAGAAAACCTA 1757
                           vv   i     viv     i   i        i     v  i ii i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_62765142_6   1758 AAAATAAACACTGACATATATGGTCAGATAATCTTTGACAAAGGTGCCAA 1807
                         i        v vv    v        iv i  i  i     i        
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_62765142_6   1808 GGT---------GGGAAAGGATAGTTCCTTCAACAAATGGTGCTGGAAAA 1848
                          ii---------       i     iii                  i v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_62765142_6   1849 AACT--ATATCTACATGCAAAAGAAGGAAGCTAGACCTTTGTCTTACATC 1896
                          -  --   ? i             v    i i    ii ii  i   i 
  L1M4_orf2#LINE/    422 A-CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_62765142_6   1897 ATATAAAAACATTAACTCAAAATGCATTAAAATGTTAAATGTAAGGCCCA 1946
                              v   v              v  i ? ivvi          iv i 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_62765142_6   1947 AAACTATAAAACTCCTAGAAGAAAATACATAGAG--AAATCTTCATGGCA 1994
                                       i          --     i?--        i  i v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATCTTCGTGACC 568

  chr2_62765142_6   1995 TTGGATTTGGCAGTGATTTCTTGAATATGATACCAAAAGCACAGACAACA 2044
                             i  v    i  i      ii      i            ii     
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_62765142_6   2045 AAAGCAAAAATCTACAAAGGAAACCACATCAAACTCAAAAA-TTCTGTGC 2093
                             v      vv i   vvii  iv       v i     -  i     
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_62765142_6   2094 AGCAAAGGAAACAATCACCAGAGTTAAAATGGCAACCTATAAAATGGGAG 2143
                         vv       v  v    vv i   v    - i     i i i        
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAA-GACAACCCACAGAATGGGAG 717

  chr2_62765142_6   2144 AAAATATTCACAATCCATATATCTGATAAGGTGTTAATATCCAGAATGCA 2193
                                 ii   vi                vii vi          ii 
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_62765142_6   2194 TAAAGAACTCCTACAACTCAACAACACAACAACAAAACAAATAATTCAAT 2243
                                   i          i  i ----  -  i        ii    
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATA----AA-AAGACAAATAACCCAAT 812

  chr2_62765142_6   2244 TTAAAAATGG-CAAAGAACTTGAAAAGTCATTTCTCCAAAGAAGATATAC 2292
                          ?        -     i i     v  v                      
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_62765142_6   2293 AAATGGCCAATTAGCATGTGAAAAAATGCTTAATGTCACTAATCAT 2338
                                    v    ii      i     i  ii   ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (84 / 44)
Gap_init rate = 0.02 (13 / 685), avg. gap size = 2.38 (31 / 13)  


2764 26.81 3.73 1.02  chr2_62771284_62778251     5594  6477 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_62771284_6   5594 TGAAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5643
                           i   i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_62771284_6   5644 GACCATACTGCCCAAAGTAACTGATAGATTCAATGCTCTCCCCATCAAA- 5692
                          i v     v      v i iiv i        i  vv    i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_62771284_6   5693 -CTCAATGACTTTCTTCACAGAATTAGAAAAAAAACT-ACTTTAAATTTC 5740
                         - i  iivi i  i  ii     v v  v  i---  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_62771284_6   5741 ACATGGAACCAAAAAAGAGCTCATATAGCCAAGACAATCCTAAGCAAAAA 5790
                          i      viiv  ii  v iviv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_62771284_6   5791 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAAG 5840
                                 i      vv       v  ii i      viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_62771284_6   5841 TTGCAGTAACCAAAAGAGTATGGTGCTGGTACCAAAACAGAGATGTAGAC 5890
                         i i      i   i v   i    i    i iv ii i   v  i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_62771284_6   5891 CAATGGAACAGAACAGAGACCTTGGAAATAATGCCACACATCTACAACCA 5940
                                 i    iv    viiii       vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_62771284_6   5941 TCTGATCTTTGACAAACCTGACATAAGCA----ATTGGGAAAGGATTCCC 5986
                         vi    i  i     ivv  v  vi v  ----  v       i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_62771284_6   5987 TAGTTAATAAATGGTGTTGGGAAAAATGGCTAGCCATATGCAGAAAACTG 6036
                          vv i  i        i     v  v   v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_62771284_6   6037 AAACTGGACTCCT---TGA-GTTA-ATACAGAAGTTAACTCAAGATGGAT 6081
                           ii     i   --- v -iii -     i  i         i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_62771284_6   6082 TAAAGACTGAAACATAAGACCTAAAACCATAAAAATGCTAGAAGAAAACC 6131
                         i ?    iv   ii     v       i      v vi           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_62771284_6   6132 TAGGCAGTA--CCATTCAGGACCT--AGTCATAGGCACAGACTTCATGAC 6177
                             ?-   --i -   iv     --i  --      vv ii   v iiv
  L1M4_orf2#LINE/    548 TAGGN-GTAAATC-TTCGTGACCTTGGGT--TAGGCAATGGTTTCTTAGA 593

  chr2_62771284_6   6178 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 6227
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_62771284_6   6228 T------AATTAAAGAGCTTCTGCACAGTAAAAGAAACTATCATGAGAGT 6271
                          ------       i -   i  ii vvi   i  v       v  i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_62771284_6   6272 GAACAGGCAAGCTTCAGAATGGGAGAAAATTTTTGCAATCTATCCATCTG 6321
                            v  i   v iv                v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_62771284_6   6322 ACAAAGGGCTAATATCCAGAATCTACAAGGAACT--TA-AATTTA-CAAG 6367
                          i  i  i  vi          v  i  i     --  -  i i -i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_62771284_6   6368 AAAAAAA-----AACCCA--TCAAAAATGAGCTAAGGATATGAACAGAAA 6410
                              i -----      -- ?       i  v      v    i   v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_62771284_6   6411 CATCTCAAAAGAAGACATTTATGCAGCCAAGGAACATATGAAAAAAAAGC 6460
                         iv    v        i  vi viii     vi i  i       i v-  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GC 891

  chr2_62771284_6   6461 TCATCATCTCTGGTCAT 6477
                            v    v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (144 / 89)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.10 (42 / 20)  


 780 29.49 0.85 0.85  chr2_62784751_62791012.rev        3   236 (6026)  C L1M4_orf2#LINE/L1   (674)   234     1  

C chr2_62784751_6    236 TGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATCGTGAAAAT 187
                              ii i  i     i     i  v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_62784751_6    186 GGCCATACAGCCCAAGGTAATTTATTGATTCAATGCCATCCCCATCAAGC 137
                            v    vv     iv i  i  iv       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_62784751_6    136 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 89
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chr2_62784751_6     88 TATGGAACCAGAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 39
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr2_62784751_6     38 AACAAAGCTGGAGGCGTCACGCTACCTGACTTCAAA 3
                                i      vv    i  v  ii i      
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

Transitions / transversions = 1.76 (44 / 25)
Gap_init rate = 0.01 (3 / 234), avg. gap size = 1.33 (4 / 3)  

3190 27.23 0.55 0.55  chr2_62784751_62791012.rev     4864  5770 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_62784751_6   4864 GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCATGAAAATG 4913
                             ii i  i     i      i v      v i i   ii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_62784751_6   4914 GCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCT 4963
                           v     v     iv i  i           i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_62784751_6   4964 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 5011
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_62784751_6   5012 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGA 5061
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_62784751_6   5062 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5111
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_62784751_6   5112 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5161
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_62784751_6   5162 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATTTACAACTA 5209
                               i    i--    i  --        vv  ii i     iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_62784751_6   5210 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAACGATTCCC 5259
                         vi    i  i     ivv  vv  i v  vv           vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_62784751_6   5260 TATTTAATAAATGGTGCTTGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5309
                          v  i  i          v   v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_62784751_6   5310 AAACTGGATCCCTTCCTTACACTTTATACAAAAATCAATTCAATATGGAT 5359
                           ii    i    v   i    iv           i  i    v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_62784751_6   5360 TAAAGACTTAAACGTTTGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5409
                         i ?    i    i  vv  v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_62784751_6   5410 TAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAAA 5459
                             ?i v viv   iv   v v  vv i i   v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_62784751_6   5460 ACACTGAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGGTCTAAT 5509
                             ii      vvi          vv     v  i    v  iii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_62784751_6   5510 TAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATGAGAGTGAAT 5558
                         i   -     i -   i  ii vv    i  v  i i  v  i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_62784751_6   5559 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5608
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_62784751_6   5609 AGGGCTAATATCCAGAATCTACAATCAACTCAAACAAATTTACAAGAAAA 5658
                         i  i  vi          v  i  vv     vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_62784751_6   5659 AAACAAACAATCCCATGAAAAAGTGGGCGAAGGACACGAACAGACACTTC 5708
                          i     i  i  v  v?    i     i     ivi   i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_62784751_6   5709 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5758
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_62784751_6   5759 ATCACTGGCCAT 5770
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 1.43 (10 / 7)  


3136 26.79 0.66 0.55  chr2_62888020_62894423.rev     5006  5912 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_62888020_6   5006 TGCAAGAACATTCCACGCTCATGGATAGGAATAATGAATATCATGAAAAT 5055
                           v  ii i  i   i i        v    v v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_62888020_6   5056 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCC-ATCAAGC 5104
                            v     v     iv i  i  i        i  v     -     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_62888020_6   5105 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5152
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_62888020_6   5153 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5202
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_62888020_6   5203 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5252
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_62888020_6   5253 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5302
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_62888020_6   5303 AATAGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5350
                            i   i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_62888020_6   5351 ATAAGATCTTCGACAAACCTAACAAAAACAAGAAATGGGGAAAGGACTCC 5400
                          vvv   i        ivv iv   i v  vvv           i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_62888020_6   5401 CTATTTAATAATTGGTGCTGGGAAAAGTGGCTAGCCATAGGTAGAAAGCT 5450
                           v  i  i  v           v  v   v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_62888020_6   5451 GAAACTGGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAGATGGA 5500
                            ii    i    v   i     v    i         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_62888020_6   5501 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5550
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_62888020_6   5551 CCAGGCA-ATACCATTCAAGACACAGGCATGGGCAAGGACTTCATGTCTA 5599
                         vi   ?i- v i -   iv   viv  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_62888020_6   5600 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGTACTTA 5649
                         vi            vvi           v     v  i    v v    v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_62888020_6   5650 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATGAGAGTGAA 5699
                           i   v v  i i   i  ii vv    i  v  i i  v  i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_62888020_6   5700 CAGACAACCTACAGAATGGAAGAAAATTTTTGCAACCTACTTATCTGACA 5749
                         v        i         i       v       vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_62888020_6   5750 AAAGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAT 5799
                          ii i  vi          v  i         vv    v iv i  v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_62888020_6   5800 AAAACAAACAACTCCATCAACAAGTGGGCAAAGGATATGAACAGACACTT 5849
                           i     i   i v  i? v  i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_62888020_6   5850 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5899
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_62888020_6   5900 CATCACTGGCCAT 5912
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3292 26.65 0.55 0.55  chr2_62973765_62980037     4874  5781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_62973765_6   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4923
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_62973765_6   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGG 4973
                            v     v     iv i  i           i  v     i     ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_62973765_6   4974 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5021
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_62973765_6   5022 TATGGAACCAAAAAAGGGCTTGCATTGCCAAGACAATCCTAAGCCAAAAG 5071
                                viiv  ii iv iv v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_62973765_6   5072 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5121
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_62973765_6   5122 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5171
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_62973765_6   5172 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5219
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_62973765_6   5220 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAATC- 5268
                          vi    i  i     ivv  vv  i v  vv            -   v-
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAG 395

  chr2_62973765_6   5269 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGC 5318
                         i  v  i  i              v      v  ?   i   i ii iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_62973765_6   5319 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5368
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_62973765_6   5369 ATTAAAGACTGAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5418
                           i ?    iv   ii     v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_62973765_6   5419 CCTAGGCATTACCATTCAGGACTTAGGCATGGGCAAGGACTTCATGTCCA 5468
                          v    ?i v viv   iv   i v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_62973765_6   5469 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5518
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_62973765_6   5519 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5568
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_62973765_6   5569 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5618
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_62973765_6   5619 AAGGGCTAATATCCAGAATCTACAGTGAACACAAACAAATTTACAAGAAA 5668
                          i  i  vi          v  i iv    v vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_62973765_6   5669 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5718
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_62973765_6   5719 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5768
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_62973765_6   5769 CATCACTGGCCAT 5781
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (147 / 91)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1778 25.18 4.36 7.17  chr2_62984913_62987181      718  1428 (841)    L1M4_orf2#LINE/L1        1   691 (217)  

  chr2_62984913_6    718 TGGAGAGATAACCTGTGTTCATAGATTAGAAGATACAGTATTGTTAAGAT 767
                             i     v  ii       i    i     ivi i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_62984913_6    768 ATCATTTTTCCTCAAATCAATCTGTAAATCCAACTCAATGCCAGTCATAA 817
                         iv  v vi   i     ii    ii i  i    v    v  vi   v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_62984913_6    818 TCCTAGCAGGTGTTTTTTAAAAATAAAGAAATTCAAAAG-TGATTCTAAA 866
                            i   ---  ii    v---- iv       v v   -    i     
  L1M4_orf2#LINE/    101 TCCCAGC---TGCCTTTTT----TGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_62984913_6    867 GTATATTTGGGGATGCAAAG---------TAACCAAAAGAATATTGAGAA 907
                         i vi  v   ii      i ---------  i      v   v    i  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_62984913_6    908 AGAA---CTGAATTATAATAGTAATGCTACCTGACATGAAAATTTACTAT 954
                             --- vi i  iv iv v v ii  v  ii iv v    i      i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_62984913_6    955 AAAGCTGTAGTAATCAAGATAGTGTCAAATTGGCATA-GGATAAA----T 999
                               ii           i     viv i       -     i ---- 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_62984913_6   1000 AGATCAACAGAACAAAAC--AAAGTCCTGAAATATACCCAAGC-TT---G 1043
                                ii   i i  i-- i     v      v     vi -  --- 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_62984913_6   1044 GCCAATTAATTT-CAACAAAGTTGTCAGCATAATCCAGTGGGGGAAAAG- 1091
                          i     i    - i    i v  i  iv iv  i  i     i  i i-
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_62984913_6   1092 -GTCTTTTCAATAAATGATGCTGA-ACAACTGGATGTTTGTATGGAAAA- 1138
                         -          i     i     i-          i?iiii   v    -
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_62984913_6   1139 AATGAACCTCAACCCCCACCTCTCCACATACATTAATTCAGTGTGTTCAT 1188
                               vi vi     i     -------   ii ---------------
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTC-------ACACCA--------------- 471

  chr2_62984913_6   1189 TATAATTAATAGCAAACATTAATTCAAGATAGATCATAGACCTAAATACA 1238
                             --------    v     i    i  i     ?          ii 
  L1M4_orf2#LINE/    472 TATA--------CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_62984913_6   1239 AAACTGTAAAATGATGAAGCTTCTGAAAAAAAGCAAAACAAAAACCTAGA 1288
                          i vi-     iv  i  i  ii ---- i   -      v ii?v  --
  L1M4_orf2#LINE/    514 AGAGC-TAAAACTATAAAACTCTT----AGAAG-AAAACATAGGNGTA-- 555

  chr2_62984913_6   1289 AACCTGTGTTTCTGACCTCATGGTAGGCAGAGGGTTTTAACAGATGACAC 1338
                           i  vi  ----     iiv v      iv  v  i v v v       
  L1M4_orf2#LINE/    556 AATCTTCGT----GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_62984913_6   1339 AGAAAGCAATAACCAGGAAGGAAAAATTTGATAGATTAAACTTAGTCAAA 1388
                         vi      vv i v vi  i      v v    i   ii    vi     
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_62984913_6   1389 ATTTAAAACTT--ACACTAATCAAAATAGATTATTTAAAAAG 1428
                            v       --iii  --     iv v i   iv i    
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCT--TCAAAGGACACTATCAAGAAAG 691

Transitions / transversions = 1.89 (115 / 61)
Gap_init rate = 0.03 (24 / 691), avg. gap size = 3.42 (82 / 24)  

 559 25.42 4.66 4.24  chr2_62984913_62987181     1550  1785 (484)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr2_62984913_6   1550 AAAGAAGACCATTAAGAAAATGTACGAGCAAGTCATAGATTAGAAGAAAA 1599
                             i v  i  i      i  v viii   vi  i   v i i      
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_62984913_6   1600 TAGTCACAAAGCATATATCTGTCACAGATCTTGTTTCCAGAACAGATTTT 1649
                           v ii    v          vi vi iv     v       i ------
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA------ 765

  chr2_62984913_6   1650 TATAAAAATGCCTTACAGCTAAATAATAAAAAAGACATGTGACCTTATTT 1699
                               i vvi      i  v           -    vi i   iv   ?
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAA-GACAAATAACCCAATTW 814

  chr2_62984913_6   1700 TTTTAAAATGGACAAAG-ATTTGGACATATGGTTCAC----AAAGATCTA 1744
                         v---       i     -     i i v iiv   v ----i     v  
  L1M4_orf2#LINE/    815 A---AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_62984913_6   1745 TCACTAGCCAAATGGCACATCAAAAA----TC--CATCACTTTTAAT 1785
                         iv v i     vvi      v    i----  --     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (33 / 26)
Gap_init rate = 0.03 (7 / 237), avg. gap size = 3.00 (21 / 7)  


1374 25.60 9.13 3.17  chr2_63005584_63008345      792  1295 (1467)    L1M4_orf2#LINE/L1        1   534 (374)  

  chr2_63005584_6    792 TGGGAAAAAATACAATGGCCATGGATTCAAAGATATAA----GTTA---- 833
                            i  i v  v v   vi        vi    iv   ----    ----
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63005584_6    834 --------TTTTCAG-TCAATTTATAAATTCAGTGCCATCCCAATCAAAA 874
                         -------- iii  i- ii  i  i i     ii  v     v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63005584_6    875 TTTTAGCATGC--TTTTTAAAAAAATAATTTGTCA-GCTGTTTATAAAAT 921
                          iii   -   --     iv i    ----  v  -    v iv      
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAAT----TGACAAGCTGATCCTAAAAT 145

  chr2_63005584_6    922 GTATGTGGAAATGAAAGGGACTTAGAATAATCAAAACAACTTTGAAAAAG 971
                         vi  i        v       ii      ii        ii         
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_63005584_6    972 AG---CAAAATTTGAGGATTTATACTATCTGATTTTAAAACT-------- 1010
                          i---    i  v     i i i   vi ii    i      --------
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_63005584_6   1011 -----CATTAACCAAGACAGTGTGGTATTAGTTTACTAATAGAC-TGTAG 1054
                         -----  v   i               i i iv  vvi      - i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_63005584_6   1055 GTGACTGGAA-------GAGAGCCTGGAATTAGATTCATACATATATTGC 1097
                         i v v     -------     i ii   v  i ii       v   v i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_63005584_6   1098 CAATTTATTTTTGACAAAGCTAGCAAAGAAAAT-CAATTAGGAAATGATA 1146
                              v     i     i v -  v    vv  -    vi     vi   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_63005584_6   1147 ATCTTTTCAAGAAATGATGCTAGAACAATTAAATGTCCATATGCCCCTCC 1196
                         i         v     i    i i    i ii  i?   i    ------
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC------ 438

  chr2_63005584_6   1197 TCAACAAAAAAAAAGCTACAATTCTTACCTTCCACTGTATAAAACATTTA 1246
                         --  -  i  vi   i i-i ii i     iv   ii    v  v v   
  L1M4_orf2#LINE/    439 --AA-AAGAATGAAGTTG-GACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_63005584_6   1247 TCTAAAAATAGATCACACAACTAAAAGTAAGAATAAAAACTG-AAGATTC 1295
                         v  v     i     ? v v     v      iiv      i-  i i  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

Transitions / transversions = 1.89 (83 / 44)
Gap_init rate = 0.03 (17 / 534), avg. gap size = 3.65 (62 / 17)  

 880 25.83 2.95 0.37  chr2_63005584_63008345     1592  1862 (900)    L1M4_orf2#LINE/L1      520   797 (111)  

  chr2_63005584_6   1592 AAAACTG-AAGATTCT-AGAAGAGGACATAGGAAAAAGTCTTAGTGACTT 1639
                               i-  i i   -      ii       ?iv  i    v     i 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_63005584_6   1640 TGTATTTGGGA--GATTTCTTAAGTAGAATGCAACAAAACACAAAGGATA 1687
                           vi  v  v -- i       ii  vi ii v -   i     ivi i 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCA-AAAGCACAAGCAACA 618

  chr2_63005584_6   1688 AAACAAAAAATGGTTAATTTGTACTTCATCAATATTAAAACGTTTTTCTC 1737
                            v       i v   v   v          v       vv    viv 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_63005584_6   1738 TTTATAAAACTCT--TACAAAAATGAAAAAGCAAGCCACAGTTTGGCAGA 1785
                           i v ii  v  --i vi   i      ii   v      vv   v   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_63005584_6   1786 AATGATTTGCAATACCTGCATCTGGCAAAAGAC--GTATCCAGAATATGT 1833
                           vv        vv v ii     ii  ii   --             i 
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_63005584_6   1834 AAAGAACTCTTTTAACTCAGTAATAAGAA 1862
                                    vi      i      i  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAA 797

Transitions / transversions = 1.30 (39 / 30)
Gap_init rate = 0.02 (6 / 278), avg. gap size = 1.50 (9 / 6)  


2576 22.92 3.36 7.89  chr2_63013766_63019950     4743  5693 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63013766_6   4743 TAGAAAAACATTATATGCTCATGGATCGGAAAAATCAATATT---AAAAT 4789
                          i    i i  ivi   i        i    i v i      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63013766_6   4790 GGCCTTATTGCCTAAAGCAATTTGCAGATTCAATGCTATTTCTATCAAAA 4839
                            vv  i v  i   vii  i i         i  v  ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63013766_6   4840 TTACCAA-TGAATTTTTCACA-AAATTAGAAAAAAAAAACT-ATTCCAAA 4886
                          i-   i-  vv     ii  -     i------ v  i  -  i i   
  L1M4_orf2#LINE/    101 TC-CCAGCTGCCTTTTTTGCAGAAATTG------ACAAGCTGATCCTAAA 143

  chr2_63013766_6   4887 ATTCATATGGAAAAACAACAACAACAACAAATAGCCTGGATAGCCAATGC 4936
                                      vi   vii-----  ------  v i        vi 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGG-----AC------CCAGAATAGCCAAAAC 182

  chr2_63013766_6   4937 AATCCTAAGCAAAGAGAACAAAGCTTGAGGCATCACACTATCTGACTTTA 4986
                             i i iv  ii         i v    vv       vi ii i  i 
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_63013766_6   4987 GACTATACTAGAAGGGTACAGTAATCAAAACAGCATGGTACTGG------ 5030
                         i viv     v  i v            i    ii         ------
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_63013766_6   5031 --TAGACGCACAGACCAATGGAACAG--TTAAGAGAACTCAGAAATAAAG 5076
                         --     ii i   i        i  --  i    --ii          v
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAG--TCCAGAAATAAAC 330

  chr2_63013766_6   5077 CCACACAACTACGACCATCTGATCTTTGAGAAAGTTGACAAAAACAAGCA 5126
                            i   vi  i ii  vi    i  i  v  i v  v   i v  vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_63013766_6   5127 ATGGGGAAAGGAT--TCATTATTCAACAAGTGGTGCCAGGTTAACTGGAT 5174
                                   i  --  -  -        i      ii  vi        
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTC-TT-TTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_63013766_6   5175 AGCCATGTAAAGAAGATTGAAACTGGACCCCTTCCTTTCACCACATACAA 5224
                          ?   ii iv i    v    ii         v   iv     i      
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_63013766_6   5225 AAATTAACTCAAGATGCATTAAAGACTTAAATGTAAAACCTAAAACTATA 5274
                                     i   v  i ?    i         i v           
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_63013766_6   5275 AAATTATAACCCTAGAAGAAAGCCTAGG---AAATACCATTATGTGATAT 5321
                            i ----- i         i v    ---    ----i vi    iv 
  L1M4_orf2#LINE/    529 AAACT-----CTTAGAAGAAAACATAGGNGTAAAT----CTTCGTGACCT 569

  chr2_63013766_6   5322 TGGCCCTGATGAAGATTTC------ATGACAAAAACTCCAGTAGCAATTG 5365
                            viiv iii v i    ------      ------   iv    v---
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACA------CCAAAAGCAC--- 610

  chr2_63013766_6   5366 TGAAAAAAAAAAAAAAGAAAATTGATAAATGAGACCTAATCAAA-CTAAG 5414
                         ---  iv  v    i i     v       vi   i v      -i   i
  L1M4_orf2#LINE/    611 ---AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_63013766_6   5415 AGCTTCTGCACAGCAAAAAAGAAAGAAACAAAAAACAAAAAACAAAAACT 5464
                          i   i  ii vv    i------  v  v v---   i   --------
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAG------GACACTAT---CAAGAAA-------- 690

  chr2_63013766_6   5465 CTTGCCAGAGTAAACAGACAATCTACAGAATTGGAGAAAATATTTTCCAA 5514
                         ---------  i  v      i i       v             v v  
  L1M4_orf2#LINE/    691 ---------GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_63013766_6   5515 CTACATATCTGAGAAAGGTCTAATATCCAAAATCCATAGGTAACTT---- 5560
                         ii i        v  i  v  vi      i   vi   iiv    i----
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_63013766_6   5561 AAATTAACAAGCAAAAAACAACCGACCAACCCCATTAAACAATGAGCAAA 5610
                           v i  i  vv    i    --- i-     v   ?  v    i     
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAA---AT-AACCCAATTWAAAAATGGGCAAA 827

  chr2_63013766_6   5611 GAACATGAAAAGACACTTCTCAAAAGAATACATACATGTGGCCATCGAGT 5660
                          i iv    v     i     v      v i     vi      vii  i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_63013766_6   5661 ATATGAGAAAAAATGCTCAACATCAGTAATCTT 5693
                          i    --   i             ????????
  L1M4_orf2#LINE/    878 ACATGA--AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (138 / 77)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.82 (107 / 28)  


2440 27.26 9.77 0.24  chr2_63062502_63065857     2056  2884 (472)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63062502_6   2056 TGGAAAGTCATCCCAACCTCATGGATCAGATGA----ATATCATTAAAAT 2101
                                vi      vvi        ii  v  ----    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63062502_6   2102 GACCATGTAGCCCAAAGCGATCTACAGATTAAATGCAATATCTATCAAAA 2151
                          i v  iivv      vi            v  i     vi         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63062502_6   2152 TACCAATTACATTCTTCACAGAAATAGA-AAATAAAAAACAGAATTTATA 2200
                          v   ii i v  i  ii       v  -  iivi vvvi i    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_63062502_6   2201 TGAACCCACAAAAGACCTCAAATAGCTAAAGCAATCATGAGCAAAAATAA 2250
                           i vvii   ii    ivi      i   i     v   iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_63062502_6   2251 CCAAGCTGGACGTATAACACTACCAGACCTCAAAGTGTATGACAAAACTA 2300
                          v   i    v vv v     v  vi ii     iiv  iv     i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_63062502_6   2301 TTCTTACCAAAACAGCATGGTACTAGCATAAAAGCAGACACATAGACCAA 2350
                         ivv v i   i    ii       i      iiii     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_63062502_6   2351 TGAAATAGAATAGAGAACCCAGAAATTAATTCACATATCCACAGTGAACT 2400
                           i        v    ii        v  ii  i i  ii ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_63062502_6   2401 GATTTGTGACAAAGACACCAAGGACACTCATTGGGGAAAGA-TAGTCTCT 2449
                              vi     i iii     iv  i   v          -      i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_63062502_6   2450 TCAATTAATTGTGCTGGGAAAACTGGATATTC-------------TGGAA 2486
                             iv   v         v         ?i -------------  i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_63062502_6   2487 CTAGACTGCCACCTC---------------------TCAAAATGGATCAA 2515
                         i i   iv i     ---------------------             ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_63062502_6   2516 AGACTTAAATGTAAGACCTGAAGCATTGAAACTACTAGTAGAAGACATAG 2565
                             i           v  i  i vv i     vi   v    i      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_63062502_6   2566 TGGAAACACTTCAAGACCT------------------------------- 2584
                         v? v  vv    iv     -------------------------------
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_63062502_6   2585 -CAAACGCATAGGCAGCAAAAGCATAAATAAACAAATGGGATTACATCAA 2633
                         -    v   i i   i      v v     i i    v   i v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_63062502_6   2634 ACCAAAAAGCTTCTGCACAGCAAAGAAAAC----AGCAGAGTGAAAAGAC 2679
                          viv    i   i  ii vv     i v  ---- iv i           
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_63062502_6   2680 AACCTACAGAATGGAAGAAAATATTTGCAAACTACTCATTCGATGGAGGA 2729
                             i         i                ii ivi  ii   iii   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_63062502_6   2730 TTAATACCCAGAATATAAAAGAAACTGAAACATCCCAATAGCCAAAAAAC 2779
                         i vi  i          v  ii    vvv   v i     iiv    i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_63062502_6   2780 AATTGAACTCAAAT-----ATGGGCAAATGACCTGAACAGATATTTCTCA 2824
                           v -   i   v -----         v  ii    i   i       v
  L1M4_orf2#LINE/    801 AAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_63062502_6   2825 ATAGAAGACATACAAATGACCAAAAAATATATTTTTTACATGTCCAACAT 2874
                          v      i         i    v  ii i  vvvv- v   ii      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATGCTCAACAT 898

  chr2_63062502_6   2875 TACTAATCAT 2884
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.62 (138 / 85)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 8.30 (83 / 10)  


3935 18.98 3.11 2.33  chr2_63066910_63070570     2269  3169 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63066910_6   2269 TGGAAAGATATCCCGTGTTCTTGGCTTAGAAAACTTAATATTGTTAACAT 2318
                                       i     v   v  i   i               v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63066910_6   2319 ATCAATACCACCCAAAGATATCTAAAGATTTAATGCAATTCTTATAAAGA 2368
                         iv      iv      vvv     v     i  i     i i   v  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63066910_6   2369 TCCCAATAATGTTTTTTGTAAAAAT--ACAAA--AATCCATGTTAATATT 2414
                              iiviiv       i i    --    i--i    ----   v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC----TAAAATT 146

  chr2_63066910_6   2415 CATTTGGAATTTTAAAGAACCCAGAATAACCAAAAACAAGCCTCGAAAA- 2463
                            v     v vi  i i          i      -   -i  i     -
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAA-TCTTGAAAAA 194

  chr2_63066910_6   2464 ---GAACAAGAGTGGAAGACTCACACTTTCTGATTTTAAAACTTACTGCA 2510
                         ---      iiv    i           i ii    i          i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_63066910_6   2511 CAGCTACAGTAATCAAGACAGTATGGTACTGGCATGA----AGACATATA 2556
                         v                     i            i ----         
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_63066910_6   2557 GACCAAC--AATGGAATAGAGAGTCCAGAAACAAACCTCTGCATATAATA 2604
                           i   i--   i    v             i     iv i   v  - -
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-T- 342

  chr2_63066910_6   2605 AGGTCAGT-GATTTTCAACAAGAGAGTCAGGACTATGGAGAAAAATGGAG 2653
                         -     i -       i     i v i  i   i  vv -----    i 
  L1M4_orf2#LINE/    343 -GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA-----ATGGGG 386

  chr2_63066910_6   2654 AAAAGACCATTTTTTCAACAAATAATATTGGAA-AATTAGAT-GTCACAT 2701
                            ii ivi i            ii ii   i -  i i   -?i     
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_63066910_6   2702 GCAAAAGAATGAAGTTGGACCCTTACCTAACACCATATACAAAAAGCAAC 2751
                                               i     v                vi   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_63066910_6   2752 CCAAAATGGATTGAAGACTTCAATGTAAGGGCTAAGACCATAAATCTCTT 2801
                         i          ii?    i v        i     i  i     v     
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_63066910_6   2802 AGAATAAAACATAGGGCAAAAAC---AAAACATTGGATTTGGGAGTGATT 2848
                             v          ?vv   v ---ivi  v    i  v  v i  i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_63066910_6   2849 TCTTGGGTA-GACACCAAAGGCACAGACAGCAAAAGAAAGAA--GACAAA 2895
                             i i  -         i     ii  i         i  --  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_63066910_6   2896 TTAGACTTCATGAAAATTTAAAACTTTTGTGCCTCAAAGAACACAATCAA 2945
                           i        v      v             i      i    v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_63066910_6   2946 CAGAGGGAAAATATTTCTTGCCTACAAAATGGGAGGA--TATTTTAAAAT 2993
                         v i  v     v iv----i  i   i        i --     vv    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACA----ACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_63066910_6   2994 AACATATCTGTTAAGAAGGGATTTATATCCAGCATATATAGGAAACTCTT 3043
                         v i       --- v      i  i       v       iii       
  L1M4_orf2#LINE/    733 CATATATCTG---ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_63066910_6   3044 AAAACT---TAACCAAAAACCAAACAACCCAGTTCAAAAATAGGCAAAGG 3090
                          v    ---   iv    iv    i      i  ?      i        
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_63066910_6   3091 CCTTGAATAGATATTTATCCAAAGAACACATACAGATAGCCAACTAGTAT 3140
                         vi         i    v         v i     i  i     iv  i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_63066910_6   3141 ATGAAAAGATGCTCGACATCACTAATTAT 3169
                                       i      ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (111 / 56)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.33 (49 / 21)  


3714 17.15 5.53 5.09  chr2_63213795_63215794.rev      605  1508 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63213795_6    605 TGGAAAGACATCCAATGTTCATGAGTTGGAAGACTTAATACTGCTAAGAT 654
                                 i    v         ii               i  i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63213795_6    655 ---AATACCACCCAAAGCAATACACAGATTCAAT----------TCAAAG 691
                         ---     iv      vii  vi          i----------     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63213795_6    692 ACCCAATAGCATTTTTTGCAGAAATAGAAAAGTCCATCCTAAAATTTATA 741
                         v    iiv  v              v  v   iiv           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_63213795_6    742 TGAAATTCCAAAGGTCCCAGAAGAGCAAAAACAATCTTGAAAAAAAATGA 791
                           i  v v   i  v       v   v                 i  vi 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_63213795_6    792 CAAAGTTGGAGGACTTGCACATTCTGATTTCAAAAGCTACAAATATGCCT 841
                                        ii   v i ii         -------------  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA-------------CT 237

  chr2_63213795_6    842 TAAATATACACAATAAAATTTATTTTTTAAATGCTATAAATAATGGAAAA 891
                           -------- v i   ---------------    i i-    vi i v
  L1M4_orf2#LINE/    238 TA--------CTACAAA---------------GCTACAG-TAATCAAGAC 263

  chr2_63213795_6    892 AGTATAGTACTGGCATAAAGACATACATAAAGACCAATGCGATAGAC--- 938
                            i i            i  i v     v   i     vi     v---
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_63213795_6    939 --AGCCTAGAAATAAACCTTAGAGCACCTT----GTCAAATGATTTTTGA 982
                         --  i i           i----ii  v  ----     v       i  
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCC----ATACATTTATGGTCAATTGATTTTCGA 359

  chr2_63213795_6    983 CAAGGATGCCAAGACCATTCAATTGGTAAAAGACAGTCTTTTTCAACAAA 1032
                              i                 v  v   ii i        -       
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT-CAACAAA 408

  chr2_63213795_6   1033 TGGTGCTGGAAAACCTGGATATCCACATGCAAAAGAATGAAGTT---CTC 1079
                                  i v v       ?                      --- i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_63213795_6   1080 TTACTTTACACCACATACAAAAATTAACTCAAAATGGATCAAAGACCTAA 1129
                         i   i i      i                           ?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_63213795_6   1130 ATATAAGACCTAAAATTACAAAACTCTTAGGAAAAAAAA-AGGGAGAAAT 1178
                           i     v      i  i           i i    v -   ?iv    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_63213795_6   1179 CATCATGACACTGAATTTAGCAATAATTTATTGGATATGATACCAAAAGC 1228
                          v  i    vi  ii  vi     ii   v  i       i         
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_63213795_6   1229 ACAGCCAACAAACTAAACAAATAGATAAATTGAACT-------------- 1264
                            iv       vv   -              i   --------------
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_63213795_6   1265 ---------ACTTCAAAATATACTCTCAGCAGAGTGAAACAGCAACCAAC 1305
                         ---------i       iv i   v   iv i       vii     v  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_63213795_6   1306 AGAATGGGAGAAAATATTTCCAAATCATATATCTGATAAGG-ACTTAATA 1354
                                            v                     -    i-  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG-TA 756

  chr2_63213795_6   1355 TCCTGAACACATACAGAATTCCTACAATTCAACAACATAAAAACAAACAA 1404
                            v   i i   v    i  i     i    i  i v   i     i  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_63213795_6   1405 TCTGACTTTTAAAATGGACACAGGACTTAAATAAACCTTTCTCCAAAGAA 1454
                         i ii -  ?v       i  v    i  i    i  v             
  L1M4_orf2#LINE/    807 CCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_63213795_6   1455 AATATACACATGGCCAACAGGCACATGAAAAAGATGCTCACCATTACTAA 1504
                         i       v        i i           -        v   i ????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZ 904

  chr2_63213795_6   1505 TCAT 1508
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.80 (97 / 54)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 5.33 (96 / 18)  


3029 25.45 2.12 0.78  chr2_63222775_63224824.rev      663  1558 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63222775_6    663 TAGAAAAGCATTCCATGCTCATGAGTTGGAAAAATCAATATGATTCAAAT 712
                          i    iii  i     i     ii      i v i     vi  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63222775_6    713 GTCCGTACTGCTCAAATTAATATACAGATTCAATGCT-TTCCTATCTAAT 761
                          v vi    v i      i  v           i  v- i      v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63222775_6    762 TACCAGTAACATTTTTCCTAGAATTAGAAAAACTA--CTTAAAATTCATA 809
                          v    ivi v     ivi    v v  v  i  i-- i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_63222775_6    810 TGGAACCAAAAAATTAGACC--AAATAGCCAAGGTAATCTTAAGCAAAAA 857
                              viiv  ii---    --i         iii      i iv  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG---GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_63222775_6    858 GAATAAAGCCAAAGGTATCACATTACCTGACTTCAAACAATACTACAAGG 907
                            i    iiii   vv     i v  ii i      vvv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_63222775_6    908 CTACAGTAACCTAAACAGCATAGTACTGGTATAAAAATATACACATAGAC 957
                                  i v i    ii i       i    ii   v   i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_63222775_6    958 CAATGAAACAGAATAGAGACCCCTGAAAGAAAGTCACACACCTA-AACCA 1006
                              i  i     v    vi  v    v   vi  i   ii  -iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_63222775_6   1007 ACTGATCTTCAACAAAGTTGACAAAAATAAACAATGAGGAAAAAATACCT 1056
                          i    i   i    i v  v   i vi vv     i     i    vii
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_63222775_6   1057 TCTTCAAGAAATAGTGCTAGGAAAACTGGCTAACCACACGCAGAAGAAAG 1106
                          i     v    i     i   v      v  ?     i   i     v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_63222775_6   1107 AAATATTGGACTCCTGCTTCTTACCATGTATAAACATTAACTCAAGATGA 1156
                           i --     i   i i  vi     i  i   v          i   i
  L1M4_orf2#LINE/    448 AAGT--TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_63222775_6   1157 ATTAAAGACTTAAATGTAAGACCTGAAACTATAAAAAATCCTAGAAGACA 1206
                           i ?    i           v  i           v-  i       v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAA 544

  chr2_63222775_6   1207 ACCAAGAAATAC-TCTTCTAAACAGTGGCCTAGGCAAAAAATGTAT-GAT 1254
                           vv  i?i  v-     vvi  vv   vi       viiv viv -   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_63222775_6   1255 GAAGATCCCCAAAGCAAATGCCACAAAATAAAAAATAAACAAACAGGACT 1304
                         - v  iv  v      v v  v      v        i i   iv     
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_63222775_6   1305 TAATTAAACTAAAGCGCTTCTGCACAGCAAAAGAAACTATGAACAGAGTA 1354
                          v  i   v v  ivi   i  ii vv    i  v     v  v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_63222775_6   1355 AACAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGGATCCAA 1404
                           v        i                          ii  iv   ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_63222775_6   1405 CAACAGACTAATATCCAGAGTCTATAAGGAACTT----AAATCAATAAGA 1450
                         i  vi    vi        i v     i     i----  v       v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_63222775_6   1451 GAAAAACAAA-AATCCCATTAAAAAATGGGCAAAGGAT----ATAGACAC 1495
                         i   i     -  i  v   ?                 ----       i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_63222775_6   1496 TTCTCAAAAGAAGACATACAG-CAGCCAACAAACATATAAAAA-ATGTTC 1543
                              v        i     i-ii     i  i  i  i    -   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_63222775_6   1544 AACATCACTAATCAT 1558
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  


3216 27.42 0.44 0.44  chr2_63226711_63231639.rev     3530  4437 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63226711_6   3530 TGGAAGAATGTTCCGTGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3579
                              ii  i i  i  i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63226711_6   3580 GGCCATAGTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCCTGC 3629
                            v   v v     iv i  i  i        i iv     i   vviv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63226711_6   3630 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3677
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_63226711_6   3678 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3727
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_63226711_6   3728 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3777
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_63226711_6   3778 TACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGAGATATATATC 3827
                                 iv  i    ii         i iv ii i   v     v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_63226711_6   3828 AATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCACATATCTACACCT 3875
                                i    i-- v  i  --        vv   i i  i  iivii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_63226711_6   3876 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCT 3925
                          vi    i  i     ivv  vv  i v  vv            i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_63226711_6   3926 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3975
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_63226711_6   3976 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4025
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_63226711_6   4026 TTAAAGACTTAAACGTTATTCCTAAAACCATAAAAACCCTAGAAGAAAAC 4075
                          i ?    i    i  v vvv       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_63226711_6   4076 CTAGGCATCACCATTCAGGACATAGGCATGGGCCAGGACTTCATGTCTAA 4125
                         v    ?i v viv   iv   v v  vv i   v v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_63226711_6   4126 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 4175
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_63226711_6   4176 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4225
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_63226711_6   4226 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 4275
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_63226711_6   4276 AGGGCTAATATCCAGAATGTACAATGAACTTAAACAAATTTACAAGAAAA 4325
                         i  i  vi          i  i  v     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_63226711_6   4326 AAACAAACAACTCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 4375
                          i     i   i v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_63226711_6   4376 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 4425
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_63226711_6   4426 ATCACTGGCCAT 4437
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3177 25.06 3.76 0.34  chr2_63239258_63242941.rev     2315  3192 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63239258_6   2315 TGGAAAGACATCCCATGCTCATGGACTGGAAGAATTAATCTCATTAAAAT 2364
                                 i        i       i       v     v ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63239258_6   2365 GACTAAACTGCCCAAAGCAATCTATAGATTCAATATAATCCCTATCAAAA 2414
                          i v v   v      vii     i        iii              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63239258_6   2415 TACCAA-TGTCTTTTTTATAGAA-TTAAAAAAA-AATCCTAAAATTCATA 2461
                          v   i-  i       ii    -  i v  iv-i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_63239258_6   2462 TGGAACAAGAAAGGAGCATGAATAGCCAAAGCAATCCTGAGCAA-----A 2506
                              vviv  i   v vv           i     i   iv  ----- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_63239258_6   2507 CAAAGTGAGAGGCATCACATTGCCTGACTTCAAAATATATTAAAAGGCTA 2556
                               vi    vv     i v  ii i       iv  i  v  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_63239258_6   2557 TAGTAACCAAAACAGCATGGTATTGGTATAAAATCAGACATACAGACCAA 2606
                         i     i   i    ii     i   i    iivi       i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_63239258_6   2607 TGAAACAGAAGAGGGAACCAAGAAATAAATCCACATGTTTACAGCCAACT 2656
                           i  i    vv i  ii v         i   i ii    ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_63239258_6   2657 AATTTTCAATGAAGGCACCAAGAACATATATTGGGGAAAGAACACGATCT 2706
                         i      i ii i  ii      v   vi v           i vvv i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_63239258_6   2707 TGAATAAATGGTGCTGGGAAAACTGAATATCTATACACACAGGAATGAAA 2756
                          v  i              v     i   ? i i ii  v i       i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_63239258_6   2757 CTGGACCCTT--CTC-TAC-GTGTA---AAATCAACTCAAGATTAATTAA 2799
                         i       i --   -i  -i i  ---    i       i  vi  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_63239258_6   2800 AGACTTAAATATAAGACCCCAAGCCATAAAACTACTGGAAGAAGACATAG 2849
                             i     i     v iv  i i        vi i      i      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_63239258_6   2850 GGGAAACACTTAAGGACAATTGG--TAGGCA--GATTTTATGCCTAAGAC 2895
                          ? v  vv   viv   v-    --      -- i   iv ivv  v   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_63239258_6   2896 CTCAAAAGCACAGACAATAAAAACAAAAATAGACAAATGGGACTATATTA 2945
                         vi          ii   i    iv         i    v     vi  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_63239258_6   2946 AACCAAAAAGCTCCTGCACAGCAAAGGAAACAATCAACAGAGTGAAGAGG 2995
                           viv    i  ii  ii vv       v  v     v i      i  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_63239258_6   2996 CAACTTGTTGAATGGGAGAAAATATTTGCAAATTATTCACCTAATAA--- 3042
                             iiiiv                        i  vi i  i    ---
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_63239258_6   3043 ACTAACATCCAGAATATACAAGAAATTCAAACAAC-----------AGGA 3081
                            vii            i  ii  i  vv     ----------- i  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_63239258_6   3082 AAAAAAATCCCCTGAAACAATGGGCAAAGGATCTGAATAGACATTTGTTA 3131
                         v   v  i  vv v?  v              i             v iv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_63239258_6   3132 AAAGAAGACAAACAAATGGCTAAGAAGTTTATGAAGATAAAAGTTCAACA 3181
                                 i v         i  v   ivi     i --i v i      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAA--GATGCTCAACA 897

  chr2_63239258_6   3182 TCACTAATTAT 3192
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.81 (139 / 77)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.57 (36 / 14)  


1571 16.06 1.75 30.02  chr2_63251160_63253847.rev      734  1879 (809)    L1M4_orf2#LINE/L1        3   824 (84)  

  chr2_63251160_6    734 GGAAGATATTCCATATTCATAGATAGGAAGACTTAATATTATCAAGACAT 783
                          i       i    i     i   v               i i    iiv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_63251160_6    784 CAGT-TTTTCCAACTTGATCTATAAATTCAATGCCATCCCAATCAAAATC 832
                           i -i ii    v        i i      i  v     v         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_63251160_6    833 CCAACAAGTTATTTTGTAAACATGAACAAACCAATTCTAATGTTTATATG 882
                            i vivi v     i i v  vi    i ii  i    vi  i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_63251160_6    883 CAGAGGCAAAAGACTCAGAATAGCCAATACAATATTGAA---GGGGCATA 929
                         v i v    ii   i            v     v     --- ii v i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_63251160_6    930 AAGTTAGAGGACTGACACTACTCAACTTAAAGACTTACTGTAACACTACA 979
                              i       v     v i   i  v  i       ii  vi     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_63251160_6    980 ATAATCAAGACAGTGTGGTACTGGTG-AAGGA----CAAATAGGTCAATG 1024
                         i                       ii-     ----  v    i      
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_63251160_6   1025 GAATAGAATAGAGAGCACAGAAACGGAGCCACTAAAT--ACAGTCACCTA 1072
                                  v     iv      iii v   -  v  -- ii    vi i
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTATGGTCAATTG 351

  chr2_63251160_6   1073 ATCTTTGACAAAGGAGCAAAGGCAATACATTGTAAAAAAAAAAAAAAAAA 1122
                           i  i     i  v  v   i v  v  v  vii   i  ---------
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA--------- 392

  chr2_63251160_6   1123 AAAAAAAAAATATATATATATATATATATATAGCCTTTCCAATAAATGAT 1172
                         ------------------------------   i    i   i     i 
  L1M4_orf2#LINE/    393 ------------------------------TAGTCTTTTCAACAAATGGT 412

  chr2_63251160_6   1173 GTTGGAACAA-TGGACACCCACATGCAAAAGA-TGAATCTGGGCCGGGTG 1220
                          i   i    -    i ?              -    vi   i  -----
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC----- 457

  chr2_63251160_6   1221 CAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGACCGAGGTGGGCGG 1270
                         ------------   ---------------------   -----------
  L1M4_orf2#LINE/    458 ------------CCT---------------------ACC----------- 463

  chr2_63251160_6   1271 ATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACC 1320
                         -    -------------------    ----------------------
  L1M4_orf2#LINE/    464 -TCAC-------------------ACCA---------------------- 471

  chr2_63251160_6   1321 CCATCTCTACTAAAAAAGATACAAAAATTAGCTGGGCGTGGTGGCAGGCG 1370
                         --------------------------------------------------
  L1M4_orf2#LINE/    472 -------------------------------------------------- 471

  chr2_63251160_6   1371 CCTTAATCCCAGCTACTTGGGAGGCAGAGGCAGGAGAATCATTTGAACCC 1420
                         --------------------------------------------------
  L1M4_orf2#LINE/    472 -------------------------------------------------- 471

  chr2_63251160_6   1421 AGGAGGCGGAGGTTGCAGTGAGCTGAGATCAAGCCATTGCACTCAAACTT 1470
                         --------------------------------------------------
  L1M4_orf2#LINE/    472 -------------------------------------------------- 471

  chr2_63251160_6   1471 GGGGGACAAGAACGAGATTTCTCTTATTAAAAAAAAAAAAAAGATAAATT 1520
                         ------------------------   -----------------------
  L1M4_orf2#LINE/    472 ------------------------TAT----------------------- 474

  chr2_63251160_6   1521 TAGAGGAAGACCTTCACAAAAATTAACTCAAAATGTATCACAAGCCTTAA 1570
                         ---------------                    v    ? ii   v  
  L1M4_orf2#LINE/    475 ---------------ACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_63251160_6   1571 TGTAGAATACAAAACTATAAAACTCCTAGAAGATAACA--GGAGAAAATC 1618
                             ii vvi               i       v    --  ? v     
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_63251160_6   1619 TAGATGACCTTAGATTTGGTGATGACTTTTTAGATGTGACACTGAAGACA 1668
                          vvi       i i  v  ii   ii  i      i      ii  ii  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_63251160_6   1669 TGATTTATAAAAGAAAAGAGTCAATTAGCTGGATTTCATTAAAATTAAAC 1718
                         ii viv i         i - vi  v ii    i     i         v
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_63251160_6   1719 ATTTCTGCTCTACAAAAGACACTGCCAAGAGAATGAAAACATGGTC-ACA 1767
                          i  i  iv  v    i      ii     i i      v iiii -   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_63251160_6   1768 GACTAGGAGAAAATATTTGCAAAAGACCTATCTCATAAAGGACTATTATC 1817
                           v i                  vv iv     v    i     vv    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_63251160_6   1818 CAAAATATACAAAGAATTCCCAAAACTCAAAAATAAGAAAACAA----CC 1863
                           i      i      i  ii v       v     i  i    ----  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_63251160_6   1864 CAATTAAAAAATGGAC 1879
                              ?        i 
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGC 824

Transitions / transversions = 2.05 (121 / 59)
Gap_init rate = 0.02 (19 / 822), avg. gap size = 19.16 (364 / 19)  

 252 23.02 7.94 0.79  chr2_63251160_63253847.rev     2071  2196 (492)    L1M4_orf2#LINE/L1      774   908 (0)  

  chr2_63251160_6   2071 ACTC---CATCTCAAAAAAAAGAAAAAAAAAAA-------AAGAAAAGGA 2110
                             ---  v     v  v  i  i v   v  -------? i   v  i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_63251160_6   2111 CCAAAGACCTTAACAGACTTCTCACCAAAGAAGACATAGAGATGCAAAAA 2160
                          v  i  ii v  i    v i  v          i   v i   -ivv  
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG-GCCAA 872

  chr2_63251160_6   2161 AAAGCATATGAAAAGATGCTCCACATCATATGTCAT 2196
                         v     i              v      ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.87 (13 / 15)
Gap_init rate = 0.02 (3 / 135), avg. gap size = 3.67 (11 / 3)  


2864 16.59 4.07 1.46  chr2_63253852_63255450.rev      495  1109 (490)    L1M4_orf2#LINE/L1      278   908 (0)  

  chr2_63253852_6    495 ATACAAACAGACATATAGACCAATTGAAGA-AATACAGAGCCAAGAAATA 543
                            vii i           i    v   v -   vv    i v       
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_63253852_6    544 AACCT-TAGAGTATATGGTCAAATTATTTTTGATGAGGGTGCCAAGACCA 592
                             i-  v v -         v v     i  ii               
  L1M4_orf2#LINE/    328 AACCCATACATT-TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_63253852_6    593 TTAAATGGGGAGGGAAAGGGCAGTCTTTTCAACATATGCTGCTGCTGGGA 642
                           v        ii   ----i             v   -- -        
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAA----TAGTCTTTTCAACAAATG--G-TGCTGGGA 419

  chr2_63253852_6    643 AAACTGGATATCCACATGCAAAAGAATGAAGTTGGACCCTTACCTTATGC 692
                         v         ?                            i     i ii 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_63253852_6    693 CATATACAAAAAT-AACTCAAAAGTGATCAAAGACCCAAACATAAGACCT 741
                                      -         vv     ?     i   ii     v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_63253852_6    742 GAAAATATAAAACTATTAGAAGAAAACACAAGG--AAAGCTTCTTTACAT 789
                         i   v         v             i i ?--   v    v v  v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_63253852_6    790 TTGATTTGGTGATGATTTCTTGGATAT-------AAAGCCCA-GCAACAA 831
                          v i  v  ii   i      i     -------     v  -       
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_63253852_6    832 AAGTAAAAACAGATAAACTGGACTCCA----AATCAAAAACTTCTGTGCA 877
                            v     i       i      i  ----   i        i     v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_63253852_6    878 TCAAAGGACACTACCAGCAGATTGAAAAAGCAGTCTATGAAATGGAAGAA 927
                                      i  iv i v      ii  ii i iii     i    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_63253852_6    928 AACATTTGCAAGTCATAT--CTGATAAGGGCTTAATATCTAGACTATATA 975
                           i        i      --          vi vi    i   v      
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_63253852_6    976 AAGAACTCCTACAACTCACACAAAAAATAGCAAAATA------TTTTTAA 1019
                                 i         - i  v   v  vv     ------  ?vv  
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCA-ATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_63253852_6   1020 ATGGGCAAAGAACTTGAACAGACATTTCTCCAAGGAAGATATACAAATGG 1069
                                   i i     i              i                
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_63253852_6   1070 CCAATGAGCACATGAAATAATGCTCAACATTGCTAATGTA 1109
                              i           vi           ii????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (59 / 39)
Gap_init rate = 0.02 (14 / 631), avg. gap size = 2.43 (34 / 14)  


2899 18.78 2.60 3.21  chr2_63267853_63269963.rev      485  1139 (972)    L1M4_orf2#LINE/L1       73   723 (185)  

  chr2_63267853_6    485 TACAGAACTCTCCACTCAATTCCTATCAAAATCTCAATATATCTTT---G 531
                               ---i  v  v    i            i  ii- ii    --- 
  L1M4_orf2#LINE/     73 TACAGA---TTCAACGCAATCCCTATCAAAATCCCAGC-TGCCTTTTTTG 118

  chr2_63267853_6    532 CAGAAATAGAAAAAAAAAATACTCATCCTTAAATTAATATGGAAAATCAA 581
                                v  v  i-------  v     v     v         vv   
  L1M4_orf2#LINE/    119 CAGAAATTGACAAG-------CTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_63267853_6    582 GGGACCTTGAAAAGCCAAAACAATCTTGAAAACAAACAATAAAGTTGAAG 631
                               iv   v                    vi  v  i       i  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_63267853_6    632 AACTCACACTTTCTGACTTCAAAATTTACTACAAAGCTACAGTAATCAAA 681
                         i          i ii i       i                        i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_63267853_6    682 ATA---TGGTGCTAGCATAAAGACAGACATATAGAACCATGGAACAGAAT 728
                          i ---    i  i      i  i           v v      i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_63267853_6    729 CGAGAACCTAAATA-AAACCTTTGTGTATGTGGATAAATGATTTCTGACA 777
                         i    ii i i v -     iv iii v i   vi  v      ii    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_63267853_6    778 AGGGTGCCAAGACCATTTAATGGGGGAAAAGACAGTCTTTTCATCAAATA 827
                                          i       i  i - i          v     i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACAAATG 410

  chr2_63267853_6    828 TTGCTGGGAAAACAGGATGTCCATATGCAAAAGTATGAAGTTAGACTCTT 877
                         v        v   v    i?   i         v        i   i i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_63267853_6    878 ACCTTACACCATATACAAAAATCAACTCAAAATGTATCAAAGATCTATAC 927
                             i                 i           v    ?   i   v i
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_63267853_6    928 ACAGGC-CTAAAACTATAATTCTCTTGGA-GAAAACGTAGGAGAAAAT-- 973
                         ii i v-            vv     i  -      i    ? v    --
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_63267853_6    974 --GTAGCATTGAATTTGGCAACGATTTCACAGGTAAGACACCAAAAGTAC 1021
                         --  ii v   ii  v     i i    vi  i  v           i  
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_63267853_6   1022 AGGCAATAAAAACAACAACAAAAAAACAGATAAACTAGACTTCACTAAAA 1071
                          i    i    i--------      i       i i       ii    
  L1M4_orf2#LINE/    611 AAGCAACAAAAG--------AAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_63267853_6   1072 TTA----TTGTTTGTCCATCAAAGGATACTATCAACAGAGTAAAAAGGCA 1117
                            ----i -     v v        i        v i   i     i  
  L1M4_orf2#LINE/    653 TTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_63267853_6   1118 ACCCACACAACAGGAGAAAATA 1139
                                v  ii          
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATA 723

Transitions / transversions = 2.08 (81 / 39)
Gap_init rate = 0.02 (13 / 651), avg. gap size = 2.92 (38 / 13)  

 438 14.04 23.39 2.92  chr2_63267853_63269963.rev     1449  1619 (492)    L1M4_orf2#LINE/L1      703   908 (0)  

  chr2_63267853_6   1449 CCCACAAATACTGAGCGACAACTGTATTTGCAAATCACATATATAATAAG 1498
                               i - -  i v  v  ---             i    v i     
  L1M4_orf2#LINE/    703 CCCACAGA-A-TGGGAGAAAA---TATTTGCAAATCATATATCTGATAAG 747

  chr2_63267853_6   1499 TGACAAATAACCAGAATATA-GAAGAACT---ACAACCCAATAAAAAAAT 1544
                         v   vvi  v          -i       ---     i      v    v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_63267853_6   1545 G-----TAA-------------TGTGCAAAGAACTT-------------- 1562
                          -----   -------------  v      i i  --------------
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_63267853_6   1563 CCAA----GATATACAAATGGACAAAAAGTACATGAAATGATGTTCAACA 1608
                             ----             v   v   i        v    i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_63267853_6   1609 TCACTAATTGT 1619
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 0.85 (11 / 13)
Gap_init rate = 0.04 (9 / 206), avg. gap size = 5.00 (45 / 9)  


3247 24.89 1.56 0.33  chr2_63277859_63282743.rev     3498  4393 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_63277859_6   3498 GGAAACACATCCCATGCTCATGAATGGGTAGAATCAATATTGTGAAAATG 3547
                              v i        i     i  v  v   v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_63277859_6   3548 ACCATACTGCCAAAAGCAATCTACAAATTCAATGTAGTCCCCATCAAAAT 3597
                         i v     v  v   vii       i      i i i    i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_63277859_6   3598 ACCACCATCATTCTTCACAAAATTAGAAAAAACAATTCTAAAATTCATAT 3647
                         v   v vv v  i  ii  i  v v  v  ivii  i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_63277859_6   3648 GGAACCAAGAAAGAG-CCCA-CACAGCCAAAGCAGAC-TAAGCAAAAAGA 3694
                             -- v v   i -    -v i       i  iv - i iv  i    
  L1M4_orf2#LINE/    152 GGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_63277859_6   3695 ACAAATCTAGAGGAAGCACACTACCTGATTTCAAACTATAATATAAGGCC 3744
                              vi i     vv      v  ii        viv  v  i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_63277859_6   3745 ATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCATACAGATCA 3794
                          i   v i   i    ii         i    ii    i    i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_63277859_6   3795 ATGGAACTGAATAGAGAACCCAGAAATAAATGCAAATACTTACAGCCAAC 3844
                               iv    v    ii           iv  v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_63277859_6   3845 TGATTTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTT 3894
                                 i    i vviv   i v   vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_63277859_6   3895 TTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAA 3944
                                             i  i   v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_63277859_6   3945 ACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTA 3994
                         ii    i  ii i   v    v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_63277859_6   3995 AGTACTTAAACCTAAGTCGTGAAACTATAAAAATTTTAGAAGATAACATT 4044
                         ?iv  i    iv    vvv i           v i        v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_63277859_6   4045 GGAAAAACCCTTCTAGACATTGGCGTAGGCAAAGATTTCATTACCAAGAA 4094
                           ?iv  vi    vv   v    vv       v i    -   vvv vi 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGA 598

  chr2_63277859_6   4095 C-CCAAAAGCAAATGCAATAAAAACAAAGAGAAATAGCTGGGACCTAATT 4143
                          -         v v    i    iv   i v i   iv v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_63277859_6   4144 AAACTAAAGAGCTTTTTCACAGCAAAAGAAACAGTCAGCAGAATAAACAG 4193
                            v v  i i     vii vv    i  v  vi   iv i i i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_63277859_6   4194 ACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTAACAAAG 4243
                                     i           v  ii   vii   i    i i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_63277859_6   4244 GACTAATATCCAGAATCTACAACAAACTC----AAATCAGTAAGAAAAAA 4289
                             vi          v  i  vi     ----  v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_63277859_6   4290 ACAA----TCCCATAAAAAAGTGGGCTAAGGACATGAATGGACAATTCTC 4335
                             ----i  v  v?    i     v     iv     i    v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_63277859_6   4336 AAAAGAACATATACAAATGGCCAACAA--ACATGAAAAAATGCTCAACAT 4383
                         v      v                i  --         i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_63277859_6   4384 CACTAATGAT 4393
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.31 (124 / 95)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 1.89 (17 / 9)  


 608 25.40 2.82 8.06  chr2_63293200_63297749.rev     2972  3219 (1331)    L1M4_orf2#LINE/L1       14   248 (660)  

  chr2_63293200_6   2972 CGTGTTTACGGTTTGGA---CTCAATATAGTAAAGATGTCAGCTGTCTCC 3018
                          i    i i  v     ---  i     v  v      v  i- i-    
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA-TA-CTCC 61

  chr2_63293200_6   3019 TGACTAATCTAAAGATTTCTGATTAATCTAAAGATTTGATAAAATTCTGA 3068
                         -------- i   ---------  i     v     ii iiv   i iv 
  L1M4_orf2#LINE/     62 --------CCAAA---------TTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_63293200_6   3069 TCAAAATCCCAGAAGGATTTTTTAAAGATATCAACAAGCTGATTCTAAAA 3118
                                     vv vv      iv   v  ii          i      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_63293200_6   3119 TTTATACAAAGAGACAAAGAAGCTAGAATAACAAAAAACATTTTGAAAAA 3168
                           i   iii i vi   i i v i      i v    vv  i        
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_63293200_6   3169 GGAAAATAATGTTGGAAGGATCATACAT---GATCTTAGGACTT-TTGCT 3214
                          i i  i  v      i iv   i  v ---i  i i ii    -i i -
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC- 243

  chr2_63293200_6   3215 AAAGC 3219
                              
  L1M4_orf2#LINE/    244 AAAGC 248

Transitions / transversions = 2.00 (42 / 21)
Gap_init rate = 0.03 (8 / 235), avg. gap size = 3.38 (27 / 8)  

2131 23.45 5.43 2.02  chr2_63293200_63297749.rev     3424  4067 (483)    L1M4_orf2#LINE/L1      243   908 (0)  

  chr2_63293200_6   3424 CAAAGCTATAACTAATCAAGAAATTACAGTATTAGTAAAAGGACAGACAC 3473
                                 i i-         v v iii   i i i v     i     i
  L1M4_orf2#LINE/    243 CAAAGCTACAG-TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_63293200_6   3474 ACAGATTAATGAAACAGAACATATAACCCAGAAATAGACCCATATAAATA 3523
                          i    i    i  i    ivv v ii         i       i vv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_63293200_6   3524 TGCCCAGCTGATTTTTGACAAAAGTACAAAGGTAATTCAATGGAGAAAGG 3573
                           vi  ii       i     ii  i v   iiv         i     i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_63293200_6   3574 ATAGT-TTTTCAACAAATGGTATTGGCACAA-TACACATCTATGCACACA 3621
                              -               ii   v    - iv i ? ----    ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC----CACATG 437

  chr2_63293200_6   3622 CAGACACACAAAGAATCTCAAACTAAACCTCACAC-AT-TACTCTCAAAA 3669
                           i --- v  v   vi vi v ivv         -  -   ----    
  L1M4_orf2#LINE/    438 CAAA---AGAATGAAGTTGGACCCCTACCTCACACCATATAC----AAAA 480

  chr2_63293200_6   3670 ATTAACTAAAAATAAATCATAGATCTAAATATAAAATGTAAAACTATCAA 3719
                                v     ii    ?   i      i   i vv         v  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_63293200_6   3720 ACTTTTAGAAGAAAGCATAGGAGGAAATATTTGTGACCTGGGATTAA-CA 3768
                            i          i      ? v    v  i       v  i   i-  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_63293200_6   3769 AAGAATTCTCCAACTA-GACACCAAAAGCATGATCCATTTTA-AAAAAAT 3816
                          v iv    ivi -  -             ii v v ivvv -       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_63293200_6   3817 TGGTAA------CTTCATCAA---------CTGTTGTTCCTCAAAAGGCA 3851
                         v i   ------         ---------  v    v i     i i  
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_63293200_6   3852 CTATTAGGAGCCTGAAAAGACAAGCTACATGATGGGAGCAAATATTTGCA 3901
                             i i  ivv           v i   vi       v           
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_63293200_6   3902 AGTCACATATCCAGCAAAGGAGTTGTATCCAGAATATATACAGAACTCTC 3951
                          i   i     iiii  i   v                  v        i
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_63293200_6   3952 AAAGCTCAACAGTAAGAAAACAAATAGCCCAACT--ACAGTGGTCAAAAG 3999
                          v i     i i   i  i       i     i -- v i   v    i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_63293200_6   4000 ACTTGGACGGACATTTCAATAAGGA-GATATATGGATAGC----AAACAA 4044
                          i   i ii        vvi  i  -      iii  i  ----  i  v
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_63293200_6   4045 ATAAA------TTTAATATCATGAGCTAT 4067
                           i  ------i i  i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (97 / 51)
Gap_init rate = 0.03 (18 / 666), avg. gap size = 2.67 (48 / 18)  


1858 22.20 8.64 2.37  chr2_63309146_63310727      501  1090 (492)    L1M4_orf2#LINE/L1      282   908 (0)  

  chr2_63309146_6    501 GAATAGACATATAGATCAATAGAGCAGAATGACAAATCCAGAAATAAACA 550
                          i                  i  ii     vivi i             v
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_63309146_6    551 CTTAACACCTATAGTCAGTTGATTTTTGATGAAGGTGTAAAGGCAATTCA 600
                          v  -  ii   i    i        i  ii i    iv   i v     
  L1M4_orf2#LINE/    332 CATA-CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_63309146_6    601 GTGGGGAAA--ATGAGTTTTTTTTCTTCCTCAAAAAA--ATACTGGGGAA 646
                         i        --  -   i    --------   v   --i i     iv 
  L1M4_orf2#LINE/    381 ATGGGGAAAGAAT-AGTCTTTT--------CAACAAATGGTGCTGGGACA 421

  chr2_63309146_6    647 ACGTGTATTTCTATGTACTACATAATGACCTTAGACCCTTAT-TCACATC 695
                           -  v  v? i ii i v v v     vv  i     i  i-     i 
  L1M4_orf2#LINE/    422 AC-TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_63309146_6    696 CTACATAAAAATTAACTCAAAATGGA-------CTT-----TAAGAGCTG 733
                         v  i i                    ------- i -----        i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_63309146_6    734 GAACTATAAAACTTCTAGAAGAAAACAT--GAGAAAATATCCACATTTTC 781
                         i            ii             -- ? v    v i iiivii i
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_63309146_6    782 AGATTAGAAAGAAATTT---AAGTACAACACATAAAAG-ACAATCAAAAA 827
                         i i    iv ivii   --- ii  ii    -i     -    v   v  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACAC-CAAAAGCACAAGCAACAA 619

  chr2_63309146_6    828 AAGAAAAAATTGCTATCCTTGGCTTCACCAAAATTTGGAAACTTTTGCAC 877
                                   v v  vvi v i     i       -ii         ii 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATT-AAAAACTTTTGTGC 668

  chr2_63309146_6    878 TTCAAAAGACACTA-CTGGAAAATGAAAAGGCAGATCACAGAC--GGAGA 924
                               i       - vi    i       i  ivi      v--     
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_63309146_6    925 AAATACTTGCACATCAGGTATTTAATAAGGAACTTGTATTCAGAATACAT 974
                              i     v    vi   i i      i        i       i  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_63309146_6    975 AGAAGTA-TCTTACAATTCAATAACAA---GACAACTAA---------AG 1011
                          -   v -        i       i  ---     v   --------- i
  L1M4_orf2#LINE/    769 A-AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_63309146_6   1012 AATGGACAACAAATTTGAATAGCTATAACAACAAAGAA----------TG 1051
                              i   vii          vi  vv vv       ----------  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_63309146_6   1052 -CTAATGAGCAAATAAGAA-ATGTTCAACATCATTAGTTGT 1090
                         - i   i    v  i i  -   i         ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (87 / 42)
Gap_init rate = 0.04 (23 / 627), avg. gap size = 2.83 (65 / 23)  


3306 19.26 4.66 3.19  chr2_63314459_63318176.rev     2001  2815 (903)    L1M4_orf2#LINE/L1        3   829 (79)  

  chr2_63314459_6   2001 GAAAGACATCCAATATTCATGGATTGGAATACTTCATGTTGTTAAAATGT 2050
                               i    v  i              v    v  i       i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_63314459_6   2051 CAGTATTGCCCAAGGTAATCTACCAATTCAGTGCAATCCCTATCAAAATC 2100
                           i  i v     iv i      vi     ii                  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_63314459_6   2101 CCAA-TGGCATCTTTGGAAATATAGAAAAATCCATTTAAAAATTCATATG 2149
                            i-  v v i    v i v  v  v  iiiv  iiv            
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_63314459_6   2150 GAATCACAAGAGATGCTGAATAGCCAGAACAATCTTCAAAAGGGAAAA-- 2197
                            vii    i  iv v         i         v    i i i  --
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_63314459_6   2198 -----AGAGG--TC----TTTCTGATT-CAAAACATATTACAAGGCTACA 2235
                         -----i    --  ----  i ii   -      v  i     i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_63314459_6   2236 GTAATCTAAACA-T-TAGTACTGGCATAAACACAGACATATAGACCAACA 2283
                               v i   - - i            iv i           i   ii
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_63314459_6   2284 AAAATGAACAGAATTGAGAGCCCAGATATAAACCATTAACCAT--ATGGT 2331
                         -----   i           i     v       vv  --   --     
  L1M4_orf2#LINE/    303 -----GAATAGAATTGAGAGTCCAGAAATAAACCCATA--CATTTATGGT 345

  chr2_63314459_6   2332 CAAACAATTTTTGACA--GATGTCAACACCATTCAATGCAAAAGGAACTA 2379
                            vii     i    -- i  i   v           vii  i   ivi
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_63314459_6   2380 TCTCTTCAACAAACGTTGCTGGGA-AACTGGATATCCCCATGCAAAAGAG 2428
                            i         i v        -         ?  v           i
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_63314459_6   2429 C-AAGTTGGACCCTTTTGTTACACCACAAACAAAAATTAACTCAAAATGA 2477
                         i-           i viv i      i v                    i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_63314459_6   2478 ATTAAAGACCTAAACATAAGAAACAAAAGTATAAAACTGCTAGAAGAAAA 2527
                           i ?         ii     ivi    v         vi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_63314459_6   2528 CATTAGAGAAAAGCTTCATGATATTGGATATGACAATGATTTCTTGTATG 2577
                            vi ? v   v    i   iv    i vv i     i      iv  i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_63314459_6   2578 TGACACCAAAAGCATAGGCAACAAAAGCAAAA-TAGACAAATGGGACTAC 2626
                                       i i          v    -    i    v     v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_63314459_6   2627 AAATGGGGCTTAATCCAACTTAAAAACTTTTATGCATTAAAGGACACAAT 2676
                          ------------  v  v            i   v i         ---
  L1M4_orf2#LINE/    646 A------------TCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC--- 680

  chr2_63314459_6   2677 AAAGTACCAATAAAGTGAACAGACAGCCTAAGGAATGGGAGAAAATATTT 2726
                         ----  i   v        v     i  i vi                  
  L1M4_orf2#LINE/    681 ----TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_63314459_6   2727 GCAAATC-------TGACAAAGCATTAATATCTAGACTACATACAGAGCT 2769
                                -------   i  i v i vi    i   v  i   v   i  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_63314459_6   2770 CCTACAACT------TAAAAACAAAAACAACCTAATT-AAAAATGGGCAA 2812
                          i       ------      v v   i    i    -            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_63314459_6   2813 GGG 2815
                         i  
  L1M4_orf2#LINE/    827 AGG 829

Transitions / transversions = 1.61 (95 / 59)
Gap_init rate = 0.02 (19 / 827), avg. gap size = 3.37 (64 / 19)  

 469 20.59 0.00 0.00  chr2_63314459_63318176.rev     3125  3226 (492)    L1M4_orf2#LINE/L1      807   908 (0)  

  chr2_63314459_6   3125 CTCAAAGAAAAAAAGGACAAGTGACTTGAATCCACATTTCTTCAGTGAAG 3174
                          i   vv?     v  i   iv  i      vv        i  iv    
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_63314459_6   3175 GTATACAAATGACCAACAAGCATATAAAAAGATGCTCAGTATCACTTATT 3224
                         i          i    i     i  i            ii    ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_63314459_6   3225 AG 3226
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.00 (0 / 0)  


2495 23.99 5.26 5.81  chr2_63319214_63323435.rev     2818  3730 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63319214_6   2818 TGGAAAAACCTCCCATGTTCATGGATCACAAAAATCAATATCATTAAAA- 2866
                               i iv                iiv  i v i     ii    i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63319214_6   2867 AAAAA------CCATACAGATGTATAGATTGAATGTAATTCCTATTTTTA 2910
                         iiv  ------   v iv   v  i     v  i i   i     i--- 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC---A 97

  chr2_63319214_6   2911 AAATGTAA------TTTTTCATAGAATTAGAAAAAACAATCCTAAAATTC 2954
                             viv ------     iii    v v  v  ivii            
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_63319214_6   2955 ATATAGAATGAAAAAAGAGCCTGAATATCCAAAGCAATTGTAAGCAAAAA 3004
                             i   vviv  ii  v  v     v     i    iv i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_63319214_6   3005 GAACAAAGCTGGAGGCATCACATTACCTGACTTCAAATTATACTATGAGG 3054
                                 i      vv     i v  ii i      viv     ii i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_63319214_6   3055 TTACAGTAACCAAAACAGCATGGTACTTGTATAAAAATAGACATACAGAT 3104
                         i        i   i    ii       v i    ii         i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_63319214_6   3105 CAATGTAACAGAATAGAGAACTCAGAAATAAAGCCATATACCTACAGACA 3154
                              v  i     v    iii          v     i ii  ii v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_63319214_6   3155 ACTGATCTTTGACAA---TGTCAACACAAACATACCCTGAGGAAAGGACA 3201
                          i    i  i     ---  i   v  ---   v vv  i      i i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAAAGAATA 394

  chr2_63319214_6   3202 TCCTTTACAATAAGTGGTGCTAGGAAAATTGGATTACC-TGTGCAGAAGA 3250
                         vi    v   i  i       i   v  i     v?  -ii    i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_63319214_6   3251 ATGAAACTGGACTTCTGTCTCTCACCATCTACAAG--CCAACTCAAGATC 3298
                              ii     ii  ii   v      v     i--ii       i  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_63319214_6   3299 AATTAAAAGCTTAAATGTAAGACCTGAAACTATAAAAATACTAGAAGAAA 3348
                         i  i ? ii i           v  i           v vi         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_63319214_6   3349 ACCTACGGAAAACTCCTCTGGACATTGGCCTAGATGAGCAAT------TT 3392
                           v  v ?iv  v  i  vv   v    vi   ----     ------  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAG----GCAATGGTTTCTT 590

  chr2_63319214_6   3393 ATGACTAAGGCCTCGAAAGCAAATGCAACAAAAACACAAATAGACAAATG 3442
                          -  -  v i vi i      v v         iv v       i    v
  L1M4_orf2#LINE/    591 A-GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_63319214_6   3443 GGACTTAATTCAACTAAAGAGCTTCTG-----CAAAGCGA-A-----AAG 3481
                               v  iv  v v  i i   i  -----     -  - -----   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAG 687

  chr2_63319214_6   3482 AAATAAGAGAACAGACAATGTGTAGAATGGGAGAAAACATTTACAAACTA 3531
                            --- v   v      iviii              i    i    ii 
  L1M4_orf2#LINE/    688 AAA---GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_63319214_6   3532 TGCATACAACAAGGGACT---------AATATACAAGGAACTCAAACAAC 3572
                          ii  vii i        ---------      i  i      vv     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_63319214_6   3573 TCAACAACAACAAAAACAAATAAAAGAACATAAATATTTTCTCATCCTTT 3622
                             i  i  -   i        ---------------------------
  L1M4_orf2#LINE/    785 TCAATAATAA-AAAGACAAATAA--------------------------- 806

  chr2_63319214_6   3623 ACCCACCTCCTACACTACTGAATGGGCAAAGAACATGAATAT---TTTTT 3669
                         -    -------- i ?vvi           i iv      v---   i 
  L1M4_orf2#LINE/    807 -CCCA--------ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_63319214_6   3670 CAAAAGAAAACATACAAATGTCTAACCTGCATATGAAAAAATTTTTAACA 3719
                          v      i i         v i  ivv   i       i  vi i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_63319214_6   3720 TCACTCACAAT 3730
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.69 (135 / 80)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.59 (101 / 22)  


2989 24.46 3.61 0.84  chr2_63342589_63345582.rev     1322  2151 (843)    L1M4_orf2#LINE/L1        1   853 (55)  

  chr2_63342589_6   1322 TAGAAAGATATTCCATGTTCATGGATTGGAAGAATCAATATTGATAAAAT 1371
                          i         i                     v i       v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63342589_6   1372 GTCCATACTACCAAAAC-AATCTACATATTCAATGCAATCCATATCAAAA 1420
                          v v     v  v   i-i       v      i       v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63342589_6   1421 TACCA-CTGACATCCTTCACAGAAATAGAAAAAA-AATCCTAAAATTTAC 1468
                          v   -   v - ii  ii       v  v  iv-i           i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_63342589_6   1469 ATGGAACCACAAGAGACGCAGAGTAGCCAAAGCAATCCTAAGCAAAAAGA 1518
                               vii    i   v    i        i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_63342589_6   1519 A--------------TCATATTACCTTACTT-AAAATTATACTACAGAGC 1553
                          --------------   i i v  iv i  -    i -       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_63342589_6   1554 TATAGTAACCAAAACAACATGGTACTGGCATAAAAATAGACATGCAGACC 1603
                           i     i   i   iii              ii        ii   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_63342589_6   1604 AATGGAACAAAATAGCTAA-CCAGAAACAAATCCACGCACCTCCAGTGAA 1652
                                i i   v vv i-       i   i   ii  ii vii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_63342589_6   1653 CTCATTTTCAACAAAGGTGACAAAAGCATACACTGGGGGAAAGACAATCT 1702
                         i v      i    i    v   i v   v  v     i  ii i i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_63342589_6   1703 CTTCAATAAATGGTACTGGGAAAACTGGATATCCATATGTAGAAGAATGA 1752
                         i     i       i      v         ?   i   i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_63342589_6   1753 AACTAAACCTGTATCTCTTGCCATATACAAAAATCAAAATAAAATG-ACT 1801
                          ii ii   iv  i   vii              i  vvi      - ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_63342589_6   1802 GAAGACTTAAATCTACAACCTCAAACTA--ATAC------AAGAAAATAT 1843
                         i?    i     v  vi v  v      -- v  ------       i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_63342589_6   1844 TGGGG-AAATGCTCCAGGGCATTGGTCTGGGTAGAAACTTCTTAAGTAAT 1892
                         v  ? -    -  i iv i v    vi i  i iviii      ii  vv
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_63342589_6   1893 ACCCCACAAGCACAGGTAACTAAAGCAAAAATGGACAAATGGGATCATAT 1942
                           v   v       i i   v    v      i  i    v   iivi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_63342589_6   1943 CAAGTTTAAAAGCTTCTACCCAGCAAAGGAAACAATCCACAAAGTGAAGA 1992
                            iv      i   i iiv vv       v  v   v v        i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_63342589_6   1993 GACAAGCCACAGAATGGGGGAAAATACC-GCAAACTACCCATCTCACAAG 2041
                              v            i       ii-     ii ivi    v i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_63342589_6   2042 GGATTAATAACCAGAATATATAAGGAATTTAAACAACTCTGTATGAAAAA 2091
                            i vi  v             i   i ivv       vi  -iv    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAAA 796

  chr2_63342589_6   2092 AAACATGTAATAATCCTATTTAAAAATGAGCTAAAGATTTAAATAGACAT 2141
                          i   ---     i  v   ?       i  v  i     i         
  L1M4_orf2#LINE/    797 AGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_63342589_6   2142 TTCTCAAAAG 2151
                              v    
  L1M4_orf2#LINE/    844 TTCTCCAAAG 853

Transitions / transversions = 1.80 (128 / 71)
Gap_init rate = 0.02 (16 / 853), avg. gap size = 2.31 (37 / 16)  


2807 23.23 1.01 9.29  chr2_63348756_63355254     5018  6007 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63348756_6   5018 TGGAAGAACATTCCATGCTCACGGATAGGAAGAATCAATATCATGAAAAT 5067
                              ii i  i     i   i    v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63348756_6   5068 GGCCATACTGCCCAAGGTAATCTATAGATTCAAGGCCATCCCCATCAAGC 5117
                            v     v     iv i     i        v  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63348756_6   5118 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5165
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_63348756_6   5166 CATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAG 5215
                         i      viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_63348756_6   5216 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGGC 5265
                                i      --------------   i------     v -----
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG--------------ACTC------ACACTTC----- 223

  chr2_63348756_6   5266 TACAGTAACCAAAACAGAGATATAGACCAATGGATCAGAACAGAGCCCTC 5315
                         --------------------------     ----------------i  
  L1M4_orf2#LINE/    224 --------------------------CCAAT----------------TTC 231

  chr2_63348756_6   5316 AGAAATAACCCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAAT 5365
                          -----------------     -        i          i   i i
  L1M4_orf2#LINE/    232 A-----------------AAACT-TACTACAAAGCTACAGTAATCAAGAC 263

  chr2_63348756_6   5366 AGCATGGTGCTGGTACCAAAACAGAGATATAGAACAATGGAACAGAAC-- 5413
                           ii    i    i iv ii i   v       v        i    i--
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_63348756_6   5414 AGAGCCCTCAGAAATAATACCGCATATCTGCAACCATCTGATCTTTGACA 5463
                             i  --        vv  ii i  i iiiii  vi    i  i    
  L1M4_orf2#LINE/    314 AGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_63348756_6   5464 AACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGG 5513
                          ivv  v   i v  vvv           i  vvi  v  i  i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_63348756_6   5514 TGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTT 5563
                                 v      v  ?   i   i i  iiv    ii    i    v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_63348756_6   5564 CCTTACACCTTATACAAAAATTAATTCAAGATGGATTTAAAGACTTAAAT 5613
                            i     v              i    i      i- ?    i     
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATC-AWAGACCTAAAT 510

  chr2_63348756_6   5614 GTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCAGTA--CC 5661
                           v   v       i      vi i           v    ?-   --i 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN-GTAAATC 559

  chr2_63348756_6   5662 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGC 5711
                         -   iv   v v  vv i     v ii   v ivv  vi           
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_63348756_6   5712 AATGGCAACTAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGA 5761
                          vvi     v    vv     v  i    v   ii v  i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_63348756_6   5762 GCTTCTGCACAGCAAAAGAAACTACCATCAGGGTGAACAGGCAACCTACA 5811
                         i   i  ii vv    i  v    i  vv ii     v  i     i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_63348756_6   5812 GAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAGGGCTAATATC 5861
                                       v       vii ivi      i  i  i  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_63348756_6   5862 CAGAATCTACAAAGAACTCAAATAAATTTACAAGAAAAAAACAA----CC 5907
                               v  i         vv i  v iv i  v     i    ----  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_63348756_6   5908 CCATCCAAAAGTGGGCAAAGGATATGAACAGACATTTCTCAAAAGAAGAC 5957
                          v  i?    i            v    i           v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_63348756_6   5958 ATTTATGCAGCCAAAAGACACATGAAAAAATGCTCGTCATCACTGGCCAT 6007
                           vi viii     v ii          i      iv     ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (138 / 88)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 6.38 (102 / 16)  


2372 27.15 4.86 2.15  chr2_63389270_63392937     2293  3176 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63389270_6   2293 TGGAAAAAC-TTCCACGTGCCTGGATTGGAAAAATCAATATCATTAAAAT 2341
                               i i- i   i  v v          i v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63389270_6   2342 GTCCATACTGCCCAAAGCAATCTATGGATTCAACTCTGTATCTATCAAAC 2391
                          v v     v      vii     ii        v vi vi        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63389270_6   2392 TACCAAGGTCATTTTTCATAGAAATAGAACAAAAACC-ATTCTAAAATTC 2440
                          v   ivvv v     iii      v  -   i-- i-  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAG--CTGATCCTAAAATTC 147

  chr2_63389270_6   2441 ATATGGAACCAAAAAAGAGCCCAGA-TAACCAAAGCAATCCTAAGCATGA 2489
                                 viiv  ii  -      -  i     i     i i iv v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_63389270_6   2490 AGAACAGAGCTGGAGGGATCACCATTACCCAACTTTAAACTATACTACAA 2539
                               i  i      iv    - i v     i  i   viv        
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_63389270_6   2540 GTCTGCAGTAACCAAAACAACATAGTAGTAGTACAAAAACAGACACAGAG 2589
                         iv  i      i   i   iii i   v i i i  ii i     i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_63389270_6   2590 ACCAATGTAACAAAATAGAGAACACTGAAATAAAGCCACACATCTACAGG 2639
                          i     v  i i   v    iiv v        v   i    i  ii v
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_63389270_6   2640 CATCTGATCTTCGACA-----GTCAAGAAAAG-AAGTTGGGAAAGGACTC 2683
                           vi    i       ----- i     vv v-v i v       i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_63389270_6   2684 CCTATCCAATAAATGGTTCTGGAATAGCTTGCTAGCCATAT--------- 2724
                         i  v i   i       v    i i i  v v  ?   i  ---------
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_63389270_6   2725 ----------------CTTTTCACCATATACAAAAATTAACTTAAGATTA 2758
                         ---------------- i iv                     i  i  vi
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_63389270_6   2759 ATTAAATAATTAAATGTATGACCTCATACCATATAAGAATCCTAGAAGAA 2808
                           i ? v vi        v  v  v v  --     i v  i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAAC--TATAAAACTCTTAGAAGAA 543

  chr2_63389270_6   2809 AACCTAGG---AAATGTCCTTCTGGACATTGGCCTTGGTAAAAAATTTAT 2855
                            v    ---    ---    vv   v    vi v  i  viiv  i--
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTC-- 588

  chr2_63389270_6   2856 GATTAAGTAAGTCCTCAAAAATAAATGCAACAATAACAAAAATTGACAAG 2905
                         --   ii  v v vi     ii v v       v iv      v  i  i
  L1M4_orf2#LINE/    589 --TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_63389270_6   2906 TGGGGCCCAATTAAACCAAAGAGCTTCTGCACATCAAAAAA-ACTATCAA 2954
                          v  i iiv  i   viv  i i   i  ii v     ii -        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_63389270_6   2955 CAAAGTAAACAGACAGCCTACAGAATGAGAGAAAATATTTGCAAACTATG 3004
                         v     i  v     i  i        i                 ii  -
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT- 735

  chr2_63389270_6   3005 CTATGCATTTAACAAAGGACTAATAAGCAGAATCTATGAAAAACTTG--- 3051
                         --  --  i i i  i     vi  vv      v   i  i    iv---
  L1M4_orf2#LINE/    736 --AT--ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_63389270_6   3052 AAATCAACAAGATAAAAACAAATAAGTCCATTAAAAAGCATGAAAATGAC 3101
                           v    i  v v   i        vi v   ?    iiiv v   v  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_63389270_6   3102 ATGAACAATCATTACTCAAAAGCAGACATACAAGCAGTCAACAA--ACAT 3149
                         v    i iv    v   v    v   i      iii i   i  --    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_63389270_6   3150 GAAAAAATGCTCAATGTCACTAATCAA 3176
                              i        ii   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.26 (62 / 19)  


2943 22.85 4.24 3.01  chr2_63402753_63407018     2879  3775 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63402753_6   2879 TGGAAAGATATCCCATATTCATGGATTAGTAGAAACAGTAGTGTTAAAAT 2928
                                         i          i v   vvi i  v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63402753_6   2929 GTTCATACTACCCAAAGTAATGTACTAATTCATTGCAATTCCTATCAAAA 2978
                          viv     v      v i  v   vi     vi     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63402753_6   2979 TTCCAA-TGTCATTTTTTTTTAGCAAAATAGAAAAAACAGTCCTAAAATC 3027
                          i   i-  i --      vi  --    v  v  iviii         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAG--AAATTGACAAGCTGATCCTAAAATT 146

  chr2_63402753_6   3028 AATATGGAACCAGATAATACCCTAGAGAGCCAA--CAATCTTGCACAAAA 3075
                         v        viiv viiv    vii v      --        v v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_63402753_6   3076 GGAACAAAGCTGGAGGCAACACAAT----AACTTCAAAACATATTATAAA 3121
                         i        i      vvv    v ----  i        v  i  i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_63402753_6   3122 GCTATTGAAACAAAAGCAGCATAGTACTGGCATAAAAACAGACACATTGA 3171
                             iv v  iv  ii   ii i            ii i     i  v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_63402753_6   3172 AGAATGGTACAAGATAGAAAGCCCAGATACAAATCCAAGTATTTATGGTC 3221
                         vv     v i ii  v  i  i     v i   i   vii          
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_63402753_6   3222 AGTTGATTTTCAACAAAGCAGCCAAGAACATGCAATGGG-AAAGAACAAT 3270
                          i         i    i vv       v   v       -      i --
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-- 394

  chr2_63402753_6   3271 TTATTGTCCTTTCCAATTTATTTAATAAATGGTGTTGGGAAAACTGGATA 3320
                         -----   i    ----------  i        i     v         
  L1M4_orf2#LINE/    395 -----GTCTTTTC----------AACAAATGGTGCTGGGACAACTGGATA 429

  chr2_63402753_6   3321 TTCATGTGCAGAATAATAAAATTGGACCCTTACATCAAACCACATATAAA 3370
                         ?i  ii    i  v   i  i        i   v   v    i   i   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_63402753_6   3371 AATCAACTCAAAATGGATAAAAGA--TAGTATGTTAAGCAC-AAGACT-T 3416
                            i              v ?   --  i-    -   vi -  i   - 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAA-ATGT-AAGAGCTAAAACTAT 527

  chr2_63402753_6   3417 GAAACT-TGAGGAGGA-------GGGAAAAACTCCTCAACATTTGCCTGG 3458
                         i     - v  i  i ------- ? v   v  i vii  v  v vi i 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_63402753_6   3459 GCAATGATTTCTTGGCTAGGATTCCAAAAGCACAAGCAGCAAAAGCAAAA 3508
                               i      i v  v  iv               i      v    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_63402753_6   3509 ATAGATAAATGAGACTGCAATGAA-TGAAAAAGATTATGGACAGCAAAAG 3557
                                   vi    v  vii  - v     vv  -  vi vv    i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGG 676

  chr2_63402753_6   3558 A----AGGAAGTAACAGTGAAGAGATAAACCATGTATTGGGAGAAAATAT 3603
                          ---- vv   -  -      i   i  v   iiv v             
  L1M4_orf2#LINE/    677 ACACTATCAAG-AA-AGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_63402753_6   3604 TTACAAACCATACATCTGATAAGGGGCCAATATCCAAAATATATAAGGAA 3653
                           i    i    i            i ivi      i         i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_63402753_6   3654 TTCAAACAACTCAATAGTAAGAA-------AACTCAGTTAAAAGCTGGTA 3696
                         i  vv           i   i  -------   i  i  ?   iv   vv
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_63402753_6   3697 AAAGTATCTGAGCAGACATTTCTCAAAAGAGAGGTAGAT-----GCCAAC 3741
                             v  i   ii           v     -  i  v i-----     i
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGA-AGATATACAAATGGCCAAT 873

  chr2_63402753_6   3742 AGATACATGAAAA-ACACTCAACATCTCTAATCAC 3775
                          iii         - ii         v????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (117 / 84)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.71 (65 / 24)  


 353 27.27 8.39 0.00  chr2_63414618_63420528     4162  4304 (1607)    L1M4_orf2#LINE/L1        1   155 (753)  

  chr2_63414618_6   4162 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATAGTGGAAAT 4211
                               v i        i        v  v   v i     v  vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63414618_6   4212 GGCCATACTGTCAAAAGCAATC-A-------AAAGCAGTC--TAC--AAA 4249
                            v     vi v   vii   - -------  v   i  --  i--   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63414618_6   4250 TACCACCATCATTCTTCACAAAACTAGAAAAAACAATCCTAGAATTCATA 4299
                          v   v vv v  i  ii  i  v v  v  ivii      i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_63414618_6   4300 CGGAA 4304
                         i    
  L1M4_orf2#LINE/    151 TGGAA 155

Transitions / transversions = 0.95 (19 / 20)
Gap_init rate = 0.03 (4 / 155), avg. gap size = 3.00 (12 / 4)  

2525 24.77 1.87 1.47  chr2_63414618_63420528     4673  5419 (492)    L1M4_orf2#LINE/L1      159   908 (0)  

  chr2_63414618_6   4673 CAAG---CCCACAG-AGCCAAAGCAA----GACAAAGCAAAAAGAACAAA 4714
                             ---    v i-       i   ----  v    ----         
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG----AAGAACAAA 204

  chr2_63414618_6   4715 TCTGGAAGCATCACATTACCCAACTTCAAACCATACCCTAAGACTACAGT 4764
                         vi    i vv     i v     i      v v   ivi  ii       
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_63414618_6   4765 CACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCAATGGA 4814
                         v i   i    ii         i    ii    i  i     i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_63414618_6   4815 ACAGAATAAATAACCCAGAAATAAAGGCAAATATTTACAGCTAACTGATC 4864
                          i     vi v ii           vv  v i     ii ii  i    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_63414618_6   4865 TTCAACAAAGCAAACAAATACATAAAGTGAGGAAAGGACACCCGTTTCAA 4914
                            i    i vviv   ivv   vv i  i      i i vi v      
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_63414618_6   4915 TAAATGGTGCTGGGATAATTGGCTAGCTACATGCAGAA-AATGAAACTGG 4963
                         i              i  i   v  ? i       i  -      ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_63414618_6   4964 ATTATCATCTCTTACTTTATACAAAAATCAACTCAAGATGGATTGAAGTC 5013
                          iivii i   vi  iv           i       i      ii?  v 
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_63414618_6   5014 TTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATCAGAGA 5063
                         i     v     v  i           v ii       v     vi ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_63414618_6   5064 AACCCTTCTAGACAGTGGCTTAGGCAAAGACTTCATGACTACAAC-CCAA 5112
                           vi    vv   vv   v        v ii   v iiv  ii  -    
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_63414618_6   5113 AAGCAAATGAAACAAAAACAAAGATAAGTAGATGGGACTTAATTAAACTA 5162
                              v v v       iv   i   ii  i  v      v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_63414618_6   5163 AAAAAGTTTTTCTGCACTGGAAAAGAAATAATCAGCAGAGTTAACAGACA 5212
                              v    --- ii  vv   i  v iv    iv i   v  v     
  L1M4_orf2#LINE/    655 AAAAACTTTT---GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_63414618_6   5213 ACCCACAGAAAGGGAGAAAATCTTCACAATCTATACATCTAACGAAGGAC 5262
                                   v          v  ii   vii   i    i ii i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_63414618_6   5263 TAATATCCAGAATCTACAAAGAACTC----AAATCAGCAAGAAAAAAAAA 5308
                          vi          v  i         ----  v   ii  v     i --
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-- 799

  chr2_63414618_6   5309 CCCAACAATCCCATAAAAAAAGTAGGCTAAGGACATGAATAGACAATTCT 5358
                         - v  i  i  v  v?     - i   v     iv          v    
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_63414618_6   5359 CAAAAGAAGATAAACAAATGGCCAACAAGCATATGGGAAAATGCTTAACA 5408
                          v          v            i     i   ii  i     i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_63414618_6   5409 TCACTAATTAT 5419
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (106 / 75)
Gap_init rate = 0.01 (10 / 750), avg. gap size = 2.50 (25 / 10)  


1676 25.76 0.25 0.00  chr2_63476037_63479285.rev     1478  1873 (1376)    L1M4_orf2#LINE/L1        6   402 (506)  

  chr2_63476037_6   1478 AGATATTCCATGTTTGTAAATTGGAAGAATTAATATAGTTAAAATCACAA 1527
                               i       ii ii         v       v     i  vi   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_63476037_6   1528 TACTGCCCAAGGCAATTTACAGATTCAATGTTATCCCTATCAAAATACCA 1577
                             v     ivii  i           i iv              v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_63476037_6   1578 ATGACATTTTTCACAAAAATAGAAAAAA-AACTATAAAATTTATATGGAA 1626
                         iivi v     ii  i    v  v  iv-i iiv       i        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_63476037_6   1627 CCACAGAAGACCCTGAATAGCCAAAGCAATCCTGAACAAAAAGAACAAAG 1676
                         vii  iii     v           i     i    v  i          
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_63476037_6   1677 CTGGAGTCATTACACTACCTGACTTCAAAATTTACTACAAAGCCATAGTA 1726
                         i     vvv i     v  ii i       i            i i    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_63476037_6   1727 ACTGAAACAGCATAGCACTGGTATAAAAACAGACACATAAACCAATGGAA 1776
                          iii i    ii i i     i    ii i     i   i i        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_63476037_6   1777 CAGAATAGAGAACCCTGATATAAATTCACACTTTTATAGACAAGTCATTT 1826
                         i     v    ii  v  v     ii  i  v     i v   v v    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_63476037_6   1827 GCGATACAGACACCAAGTACATATAATGGGGAAAGGACAGTCTTTTC 1873
                         v   i vi iii     vv   vi           i i         
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

Transitions / transversions = 2.19 (70 / 32)
Gap_init rate = 0.00 (1 / 397), avg. gap size = 1.00 (1 / 1)  

1810 25.15 1.55 0.97  chr2_63476037_63479285.rev     2241  2757 (492)    L1M4_orf2#LINE/L1      389   908 (0)  

  chr2_63476037_6   2241 AGGAGAGTCTTTTCAATGAATGATGCTGGGAAGACTGGATTACTCTTTGA 2290
                           i v           ii    i        vi       v? iviv  v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_63476037_6   2291 AGAACAATGAAGGTAGACCCC-ATCTCTCACCATACACAAAAATTAAATT 2339
                          i  v       v i      - i   v       i           v i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_63476037_6   2340 AAAATGGATTAAATACTTAAACCCAAGACCTGAAAGTATAAAACTACTAG 2389
                                  i ? v  i    ivi    v  i   v         vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_63476037_6   2390 AAGGTATCATTAGGGAAAGGCTCTGGGATATTGGTTTTTGAGAAGACATT 2439
                            iv v   vi ? v  iv  ii v  iv    v  vv vi v iiv i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_63476037_6   2440 TTGTGTAAGACCTCAAAAGCACAGGTAACCAAAACAAAAATAGACAAATG 2489
                           ivi  v   vi          i i   v   iv         i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_63476037_6   2490 AGATTACCTCAAG--CAAAAAAGTTTCTGCATAGCAAAAGAGATGATCAA 2537
                         i  i v v    i--i     vv   v   v --    i  v iv     
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAA 686

  chr2_63476037_6   2538 CAAAGTGAAGAGCCAGTCCACAGAATGGGAGAAAATATTTGCAAATTATT 2587
                         v        i  v  ii                             i  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_63476037_6   2588 CATTTGACAAGAGATTAATAATCAGAATATATAAGGAGCTCAAATAACTT 2637
                         i  i   i   i  i vi  vi            i  i   vv i    i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_63476037_6   2638 AATAGCAAAAA---AAAT--CCTATTTTTTTTAAATGGGCAAAAGATCTG 2682
                             ii     ---    --  i v  ?vv--           i   i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAA--AAATGGGCAAAGGATTTG 834

  chr2_63476037_6   2683 AATAGACATTTTTCAAAAGAAGACATACTAATGGCCAACATATATGTGGA 2732
                                    i  v        i    v         i vii ii  i 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_63476037_6   2733 AAAACTGTTCAACATCACTAATCAG 2757
                           i -  i         ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (71 / 55)
Gap_init rate = 0.01 (7 / 520), avg. gap size = 1.86 (13 / 7)  


2578 22.25 10.18 2.96  chr2_63522424_63525746     1995  2839 (484)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_63522424_6   1995 GAAGGGTA--CTACTTTTATGGATTAGGAGACTCAATATTGTTAAGA-AT 2041
                            i i  -- i iv  i       i i     i             -iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_63522424_6   2042 CATTCCTCCCTAAAATGATCTATAGATCCAACACAATCTCAGTCAAAATC 2091
                           v v     i   v       i    i    i     i vi        
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_63522424_6   2092 CCATCAG--------GT-GAAA----CAAGCCAGTTTCAAAACTTATATA 2128
                            v v -------- i-    ----     iii iii    i i    i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_63522424_6   2129 GACATGGAAAGGATCTAGAATAGTCAAAATAATAG-GAAAAAGAAGAATA 2177
                           v   v  i   i i       i     i   vv-            i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_63522424_6   2178 AAGTTGAAGGACTAACAGTACCTGATTTCAAGACTTACTGTAAAGCCACT 2227
                               i      v   v v  ii       i       -----------
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT----------- 241

  chr2_63522424_6   2228 TACTGTAAAGCCACAGGAATCAAGTCAGAATGGTACTTGCTTAAGGTACA 2277
                         -  ---     i    v       v   vi       v  v     - i 
  L1M4_orf2#LINE/    242 -AC---AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATA 286

  chr2_63522424_6   2278 GACATTTAATTCACTAAAA--GA----------CA-----------ATAC 2304
                              v  iv   v ii  --  ----------  -----------    
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_63522424_6   2305 AGTTAT-------TGAT---------AGAT--CAAAGTAATTCAATGGGA 2336
                          v    -------    ---------i i --   iiiv          -
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG- 385

  chr2_63522424_6   2337 GAAAGAATACTCTTTCTGACAATTGGTGCTGGAACAA-TAAATATTTATA 2385
                                  v     iii    v         i    - ii   ?ii i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_63522424_6   2386 T-TAAAA--ATTAATCTCAACCCATACCTCATACCATATGCAAAAAATTA 2432
                          -i    --  v  vi vi    v       i       i      -   
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTA 484

  chr2_63522424_6   2433 ACTTGAAGTAGACCATCAACCTAAATGTAAGAGCTAAACCCACAAAACTT 2482
                            ii  i i  i  ?vi                    v i i      i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_63522424_6   2483 CTATAAGAAAA------------TCCTTGTGACCCTGCGTCAAAGAGT-- 2518
                         i  v       ------------  i i      i  v  i iiv i --
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_63522424_6   2519 TTTCTTAG----GACGTGAAAAGCAAAAGCCATAAAACAAAGAACATTAT 2564
                                 ----   iiv       v    v i    v   i  i v-  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG-AT 633

  chr2_63522424_6   2565 GAACTGAATTTCATTAAAATTAAAAACTTCTGCTACTTTATAA-ACAATG 2613
                         i  i  i i     i              i  - i   i v i-   v i
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTA 682

  chr2_63522424_6   2614 GTAAAATAATGAAAGGGTAAACTACAGGCTGAAAGAAAATATTCACAATA 2663
                         vi  i v i     i ii  v i    iv  ii          ii   vv
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_63522424_6   2664 CAAGTATCTTACAAAGGCCTTGTATTCATAAAATATACATAAAAAATCTC 2713
                           vi     v i  i  v       i  --i      --    i  -   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCA--GAATATA--TAAAGAA-CTC 777

  chr2_63522424_6   2714 TTACAACTCAAGAATAAGTAAAGAAAAAATCCAATT-AAATTTGGGCAAA 2762
                                    v     iv i v   v  i      -   vv        
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_63522424_6   2763 AGATTTGAAGACATACTTCATCAGACAAGATATACAA----CAAATAAGC 2808
                         i        v v i i   vi  i v           ---- v       
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_63522424_6   2809 ACATGAAAAGATGCTTGATTCCAACAGTCAC 2839
                                        ii ivi  ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (122 / 64)
Gap_init rate = 0.03 (31 / 906), avg. gap size = 3.58 (111 / 31)  


 450 29.27 0.00 0.00  chr2_63526516_63533582      258   380 (6687)    L1M4_orf2#LINE/L1        1   123 (785)  

  chr2_63526516_6    258 TGGAAAAACATTCAAAGCTCATGGATAGGTAGAATCAATATCATTAAAAT 307
                               i i  i v v i        v  v   v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63526516_6    308 GACTTTACTGCCCAAAGCAATTTACAGATCCAGTGCTATTCCTATCAAAC 357
                          i vv    v      vii  i       i  ii  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63526516_6    358 TACCAATGACATTCTTCACAGAA 380
                          v   iivi v  i  ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA 123

Transitions / transversions = 1.57 (22 / 14)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.00 (0 / 0)  

3433 26.21 0.33 0.33  chr2_63526516_63533582     4170  5077 (1990)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63526516_6   4170 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4219
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63526516_6   4220 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4269
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63526516_6   4270 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4317
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_63526516_6   4318 TATGGAACCAAAAAAGAGCTTGCATTGCCAAGACAATCCTAAGCAAAAAG 4367
                                viiv  ii  v iv v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_63526516_6   4368 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4417
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_63526516_6   4418 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4467
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_63526516_6   4468 AATGGAACAGAACAGAGGCCTTGGAAATAACACCACACATCTACAACCAT 4517
                                i    iv   iviiii       vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_63526516_6   4518 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 4567
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_63526516_6   4568 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAACTGA 4617
                         v  i  i              v      v  ?   i v i i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_63526516_6   4618 AACTGGATCCCTTCCTTACACCTTATACAAAAGTTAATTCAAGATGGATC 4667
                          ii    i    v   i     v         i    i    i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_63526516_6   4668 AAAGATTTAAATGTTAGGCCTAAAACCATAAAACCCCTAGAAGAAAACCT 4717
                          ?   ii       v  iv       i       i i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_63526516_6   4718 AGGCA-ATACCATTCAGGACATAGGCATAGGCAAGGACTTCATGTCTAAA 4766
                            ?i- v i -   iv   v v  vv       v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_63526516_6   4767 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 4816
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_63526516_6   4817 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATTAGAGTGAACA 4866
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_63526516_6   4867 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 4916
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_63526516_6   4917 GGGCTAATATCAAGAATCTACAAAGAACTCAAATAAATTTACAAGAAAAA 4966
                           i  vi    v     v  i         vv i  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_63526516_6   4967 AACAAACAACCCCATCAAAAAGTGGGCAAAGCATATGAACAGACACTTTT 5016
                         i     i     v  i?    i         v  v    i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_63526516_6   5017 CAAAAGCAGACATCTATGCAGCCAATAGACACATGAAAAAATGCTCATCA 5066
                          v    v   i  vi viii       ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_63526516_6   5067 TCACTGGTCAT 5077
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  

2152 25.74 6.33 0.94  chr2_63526516_63533582     5834  6575 (492)    L1M4_orf2#LINE/L1      127   908 (0)  

  chr2_63526516_6   5834 GAAAAACTAATT-TAAAATTCATATGGAACCAAAAAAAGAGTCTGAATAG 5882
                           v  i  i  i-                viiv  ii-  vi v      
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG-GACCCAGAATAG 175

  chr2_63526516_6   5883 CTAACACGATCCTAAACAAAAAGAACAAAGCTGGAGGCATCACAACATAC 5932
                          i  v  i   i i  v  i          i      vv     - v - 
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA-CTT-C 223

  chr2_63526516_6   5933 CCAACTTCAAACTATACCACAATGATGCAATGACCAAAACAGCATGGTAC 5982
                             i      viv   i    v v i  i i i   i    ii      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr2_63526516_6   5983 TGGTACAAAAACAGACACAGAGACCAATGAAACAGAATAGAGAGCCCAGA 6032
                            i i  ii i     i v   i     i  i     v     i     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_63526516_6   6033 AATAATGCTACACACCTACAACCATATGATCTT-GACAAAGTCAACAAAA 6081
                              vv i i   ii  iiii  vv    i  -     i viiv   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr2_63526516_6   6082 ACAAGCA--GGGAAAGGACT--TCTTATTCAGTATATTGTACTGGGATAA 6127
                         v  vv  --   i  i  v --    -    ii v  v  i      i  
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAA 422

  chr2_63526516_6   6128 CTGGCTAGCCATATACAGAAGATTGAAACTGGACCCCATCTTTACACCAT 6177
                             v  ?   i  i  i    v    ii        vv i i       
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_63526516_6   6178 ACAGAAAAATCAATTAAAGATGGATTAAAGACTTAAATGTAAAACCTAAA 6227
                          i v      i  i v  i      i ?    i         i v     
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_63526516_6   6228 ACTATGAAAACCCTGCAAGGTAACCTAGG---AAATACCATTTG-GGCAC 6273
                              i   vi i iv   iv   v    ---    -- -  i - i vi
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCT 569

  chr2_63526516_6   6274 AGGCCCTGGCAAAGATTTCATGACAAAGGCGCCAAAAACAGTTGTGACAA 6323
                         v  viiv     v i    v iivv v i i      i  vvv ii    
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_63526516_6   6324 AACCAAACATTGACAAATGAGACT-------------------------- 6347
                           vv   v  v  i    vi    --------------------------
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_63526516_6   6348 --AAAGAA-ACAATCAACAGAGTAAACAGACAACCTACAGAATAGGAGAA 6394
                         --    i -  v     v i   i  v        i       i      
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_63526516_6   6395 GATATTTGCAAATTATGCATCTGACAAAGGTTTAGTATCCAGAATCT-TA 6443
                         i            i  ii      i  i  vi v           v -  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_63526516_6   6444 AGGAACTTAAACAAATGAACAACCAAAACACAAACAACCCCATTAACAAT 6493
                          i     ivv    v v  i  iv    v     i     v   ? v  v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_63526516_6   6494 TGGG-AAAGAAC----ATAGACATTTC--AAAAGAAGACATACATGCAGC 6536
                             -    i i----           --v        i     viii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_63526516_6   6537 CTACAACCATATGAAAAAATGCTCAACATCACTAATTAT 6575
                          v i  v  i       i             ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (113 / 75)
Gap_init rate = 0.02 (18 / 782), avg. gap size = 3.00 (54 / 18)  


2309 26.87 0.48 0.32  chr2_63549769_63553374     1904  2532 (1074)    L1M4_orf2#LINE/L1        1   630 (278)  

  chr2_63549769_6   1904 TGGAAACACATCCCATGCTCATCGATGGGTAGAATCAATGTTGTGAAAAT 1953
                               v i        i    v   v  v   v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63549769_6   1954 GACCATACTGCCAAAAGCAATCTACAAATTCAATCCAATCCCCATCAAAA 2003
                          i v     v  v   vii       i      iv       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63549769_6   2004 TACCACCATCATTCTTCATGGAATTAGAAAAAC-AATTCTAAAATTCATA 2052
                          v   v vv v  i  iiii   v v  v  i -i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_63549769_6   2053 TGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGATTAAGCAAAAAGAA 2102
                              viiv  ii  v  viv         i   vv  i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_63549769_6   2103 CAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGCCA 2152
                             vi      vv       v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_63549769_6   2153 TAGTCACCAAAAGAGCATGGTACTGGTATAAAAATATGCACACAGGCCAA 2202
                         i   v i   i v  ii         i    ii   vi  i i  ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_63549769_6   2203 TGGAACAGAATAAAGAATCCAGAAATAAACCCAAATACTTACAGCCAACT 2252
                              i     vi   i                v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_63549769_6   2253 GATCTTCGACAAAGCATACAAAAAC-ATACAGTGGGAAAAGGACACCCTA 2301
                            i        i -i i v  i  -  v  i    i    i i vi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_63549769_6   2302 TTCAACAAATGATGCTAGGATAATTGGCTAGCCACATGTAGAAGAATGAA 2351
                                    i    i   i  i   v  ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_63549769_6   2352 ACTGGATCCTCATCTCTCACCTTGTACAAAAATCAACTCAAGATGGATGA 2401
                         ii    i  ii i   v    v i         i       i      v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_63549769_6   2402 AGGACTTAAACCTAAAACTTGAAACTATAAAAATTCTAGAAGATAACATT 2451
                         ?i   i    iv   i vi i           v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_63549769_6   2452 GGAA-AAATCCCTCTGGACATTGGCTTAGGCAAGGATTTCATGACCAAGA 2500
                           ?i-     -i  vv   v    v        v i    v iivi v  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_63549769_6   2501 ACCCGAAGTCAAATGCAATAAAAACAAAGATA 2532
                         vv  i  iv  v v    i    iv   i   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

Transitions / transversions = 1.55 (101 / 65)
Gap_init rate = 0.01 (5 / 630), avg. gap size = 1.00 (5 / 5)  

 889 21.12 4.62 3.30  chr2_63549769_63553374     2812  3114 (492)    L1M4_orf2#LINE/L1      602   908 (0)  

  chr2_63549769_6   2812 CAAACAAACAAACAAACAAAAACAAAGATAAATAGCTGGGACTTAATTAA 2861
                             viv    i -       iv   i   i   iv v      v  i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_63549769_6   2862 ACTAAAGAGCTTTTG-----CAAAGAACAAAAGGAACAGTCAGCAGAGTA 2906
                          v v  i i      -----     i   ------- vi   iv i   i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACA-------CTATCAAGAAAGTG 693

  chr2_63549769_6   2907 AACAGACAACCCA----GTGGGAGAAAATCTTCACAATCTGTACATCTGA 2952
                           v          ----i           v  ii   viii  i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_63549769_6   2953 CAAAGGATTAATATCTAGAATCTACAACGACCTCAAACAAATCAATAAGA 3002
                         i  i   i vi    i     v  i  v  v   vv    v       v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_63549769_6   3003 AAAAAA-AAAT--CCCA--TAAAAAAAGTGGGCTAAGGACAGGAATGGAC 3047
                             i -    --    -- ?     --     v     ivv    i   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATAGAC 841

  chr2_63549769_6   3048 AATTCTCAAAAGAAGATACAGAAATGGCCAACAAACATATGAAAAAATGC 3097
                          v     v          i v          i  i  i       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_63549769_6   3098 TCCACATCACTAATGAT 3114
                           v      ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (35 / 28)
Gap_init rate = 0.03 (8 / 307), avg. gap size = 3.00 (24 / 8)  


 332 24.68 0.00 0.00  chr2_63563975_63568882     3717  3793 (1115)    L1M4_orf2#LINE/L1        1    77 (831)  

  chr2_63563975_6   3717 TGGAAAAACATTCCATGCTCAGAGATTGGAAGAATCATTCTTGTTAAAAT 3766
                               i i  i     i   vi          v i v v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63563975_6   3767 GGCCATAATGCCCAAAGCAACCTAGAG 3793
                            v   v v      vii i   v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAG 77

Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.00 (0 / 0)  

1500 28.41 1.61 3.85  chr2_63563975_63568882     3794  4416 (492)    L1M4_orf2#LINE/L1      300   908 (0)  

  chr2_63563975_6   3794 ATGGAACAGAATAGAGAACCCAGAAAAAAAGTCACACACCTACAACCATC 3843
                               i     v    ii       v   vi  i   ii  iiii  -v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA-A 348

  chr2_63563975_6   3844 TTGTTCTTCAACAAACTTGACAAAAATAAGCAATGGGGAAAACACTCCCT 3893
                            v i   i    ivv  v   i vi vv           iv ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_63563975_6   3894 ATTCAATAAATAGTGTTAGGATAGCTGGCTATTCATGTGCAGAAGAATGA 3943
                         v     i    i   i i   i i    v  ?i  ii    i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_63563975_6   3944 AACTGGAACCCCT-CCTATCAGCATAAACAAAAATTAATTCACGATTAAA 3992
                          ii    -     -   vv  v    v           i   --------
  L1M4_orf2#LINE/    449 AGTTGGA-CCCCTACCTCACACCATATACAAAAATTAACTCA-------- 489

  chr2_63563975_6   3993 TTAAACAAAAATTAATTCACTTAAAAAACTTAAAGGTAAGACCTCAAACT 4042
                         --------    vi  i------ ? i  i    v      v  v     
  L1M4_orf2#LINE/    490 --------AAATGGATC------AWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_63563975_6   4043 ATAAATATCCTACAAGGAAACCTAGGAAACACCCTTCTCAATATCAGTCT 4092
                              vv  i  v   i    v    ?ivv vi    vii iv ii vi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_63563975_6   4093 TAGCAAAGAATTTATGGTAAAGTCCTCAAAAGCAAATACAAGAAAAACAC 4142
                         vi    v iv  iv i vv v v vi        v vi   v    iv v
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_63563975_6   4143 AAAT---TAAGAGGGGCCTAATTAAACTAAAGAGCTTCTACACAGCAAGA 4189
                             ---   ivv  i i v  i   v v  i i   i iii vv   ii
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_63563975_6   4190 AACACTATAAAGAGAGTAAACAGACAACCTACAGAATGAGAGAAAATATT 4239
                         i       v    i   i  v        i        i           
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_63563975_6   4240 TGTAAACTGTGCATCCAACAAAGGTCTAATACATAGGATCTATAAGGAAC 4289
                           i   iii ii   ii i  i  v  vi  ivi  i  v     i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_63563975_6   4290 ATAAACAAATCAAGAAGCAAAAAACAAATAACCTCTATAAAAAGCGGGCA 4339
                         vivv    v    v  vv    i          ivvv ?    ii     
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_63563975_6   4340 AAGGACATGAAT------TTCTCAAAAGAAGACATACAAATCGCCAACAA 4383
                              iv     ------     v        i        v     i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_63563975_6   4384 ACATATGAAAGAATGCTCATAATCACTAATCAT 4416
                         i  i      ii       vv    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (97 / 76)
Gap_init rate = 0.01 (7 / 609), avg. gap size = 4.86 (34 / 7)  


2727 25.54 5.15 1.15  chr2_63595330_63598744     2060  2932 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63595330_6   2060 TGAAAAGAAAATACCATGCTCATGGATTAAAAGAATTAACATAGTTAAAA 2109
                           i     v - v     i         ii    v    i  v     i 
  L1M4_orf2#LINE/      1 TGGAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_63595330_6   2110 TGACCATACTATCCAAAGCAATCTACAGATTGAATGTAATACCCAT---- 2155
                           i v     vi     vii           v  i i   v  i  ----
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_63595330_6   2156 ------GCCAC--TTTTCACAGACATAGAAAAAATAATCCTAAAATTTGT 2197
                         ------  ii --    ii    v  v  v  iv i           ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_63595330_6   2198 ATGGAACCAAAAAAGAACCCAAACAGCCAAAGCAATCCTGACCAAAAAGA 2247
                               viiv  ii  v  vi  i       i     i   vv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_63595330_6   2248 ACAAATCTGGAGGCATCACACTACCTGACTTCAAAACATATTACAAGGAT 2297
                              vi      vv       v  ii i        v  i     i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_63595330_6   2298 ATAGAAACCAAAACAGCATGATATTCGTGTAACAACAGACACATAGATCA 2347
                          i  v  i   i    ii  i  i v ii   vi i     i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_63595330_6   2348 ATGGAACAGACTAGAGA-CACAGAGATAAATCCACATATTTACAGCCAAC 2396
                               i   v v    -iv    i     i   i i     ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_63595330_6   2397 TGATCTTCTCCATAGCCCTCAAGAACATACACTGGGGAAAGAAAACCCTC 2446
                             i   vv  vi vivi     v   v  v           v vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_63595330_6   2447 TTCAATAAATGATA-----ACCACT---TATTCTTCTATATGTAGAAGAA 2488
                              i     i i-----  v   ---  ?i ---- i   i i     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCC----ACATGCAAAAGAA 445

  chr2_63595330_6   2489 TGAAACTGGACCCCTATCTCTCACAATATACAGAAGTCAACTCAAGATGG 2538
                             ii          i   v   v       i  i i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_63595330_6   2539 ATTA--AACCCAAAAGTA-----TAAAACTACTAGAAAT---AGTAGTAG 2578
                           i --i   i   v   -----        -  i  v ---  v  v i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTA-TAAAACTCTTAGAAGAAA 544

  chr2_63595330_6   2579 TTCTAGGGAAAACTCTTCAGGACATTGGTTTAGGCAAAGATTTTATGGCT 2628
                         viv    ?iv  v     iv   v    v        v i   iv i v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_63595330_6   2629 AAGACCTCAAAAGCACAGGCAACAAAAACAAAAATAGACAAATGAGAGTA 2678
                          v   vi          i         iv         i    vi  v v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_63595330_6   2679 TATTAAATTTACATGCTTCTGCACAGCAAAAGAAACAATCAACAGAGTGA 2728
                         i  i   v   v vi   i  ii vv    i  v  v     v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_63595330_6   2729 AGAAACAACCTCTTGTATAGGAGAAAATGTTTGCAAATTACTCATCCAAT 2778
                          i i      iviv v  i         i         i ivi   ii  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_63595330_6   2779 AGGGGACTACTAATACCCAGCACATACAAGGAATTCAGACATCTCAACAG 2828
                          i      -- i-  i    v i   i  i   i  vv   v     i i
  L1M4_orf2#LINE/    745 AAGGGACT--TG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_63595330_6   2829 TTAAAA---AAAAAACTCATTTAAAAAAATGAGCAAAGTACATGAATAGA 2875
                          v    ---   v   i  v  ?     -  i      v iv        
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGA 840

  chr2_63595330_6   2876 CATTTCTC---AAAAGACATACATATAGACAAGAGGTATATGA------- 2915
                                 --- i    i     v  i v   v i i i    -------
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_63595330_6   2916 CT-AACACCACAATGTGA 2932
                           -    i  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (132 / 88)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.06 (55 / 18)  


3330 16.69 2.68 5.97  chr2_63601790_63603560      459  1279 (492)    L1M4_orf2#LINE/L1      115   908 (0)  

  chr2_63601790_6    459 TTTGTTTAAATGGAGAAGAGTTGAGCCTGTTTAAAAGCTGAC-TGGGAAT 507
                             ivv    v  v   --i   v   -----   ii v i-   i   
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAG--CTGATCCT-----AAAATTCATATGGAAAT 157

  chr2_63601790_6    508 ATCAAGGGCCCCCCAGTAGTCAAAACCATTTTGAAAAAGAAGAACAAAGT 557
                         i-      v   vv i   i      v  i                    
  L1M4_orf2#LINE/    158 G-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_63601790_6    558 TGGAGGATTCGCATTTCCTGATTTCAAAATATATTACAAAACTA-----A 602
                                i  i  i    ii         iv  i      i   ----- 
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_63601790_6    603 TCAAAAACAGTGTGGTTCTGGCATAAAAACAGACACATAAACCAGTGGAA 652
                             i -         v         ii i     i   i i  i     
  L1M4_orf2#LINE/    257 TCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_63601790_6    653 CAGAAAAGAGATCCCAGGAATAAATCCTCACATAAATGGTCAAATGATCT 702
                         i    vv    vi    i      i  vi    vv        v    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_63601790_6    703 TCCACAAGGGTGCCAAGACTATTCGATGGGGAGAAAGAACAATCTTTTCA 752
                           v                i    i       --     i i        
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGA--AAGAATAGTCTTTTCA 403

  chr2_63601790_6    753 ACAAACGATGCTGAGAAAACTGGATATTCATATGCAAAAGAACGAAGTTG 802
                              i i     i  v         ?i  i           i       
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_63601790_6    803 AACCT-TACCTTACATAATATACAAAAATTAACTCAAAATGGATTAAAGA 851
                         i   i-     i   iv                           i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_63601790_6    852 CAGAAATGTAGAGAGAGAACCCTGGAAAAGCAAAGTATCACGGACCCAAT 901
                          vv       ---    ----  --    ---------------------
  L1M4_orf2#LINE/    504 CCTAAATGTA---AGAG----CT--AAAA--------------------- 523

  chr2_63601790_6    902 CTATAAAACTTCCAGAAGAAAAGAGAGGA--AAAGCTTTATGACATTGGG 949
                                   iii         v v   ?--   v   ii    v     
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_63601790_6    950 GTGGACTTCATGATTTCTTGCATATGACACCAAAAGCACATACTACAAAA 999
                         v i i --v   i      iv                   vi v      
  L1M4_orf2#LINE/    574 TTAGGC--AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_63601790_6   1000 GCAAAAACAAACAAATGGGAC---ATCAAACTTAAAAACCTTTAGGTATC 1046
                          v     i i i    v    ---      v        i   iv iv  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_63601790_6   1047 AAAAGACACAATCAACAAAATGAAAAGGTAACCTACAGAATGGGAGAAAA 1096
                            i     v     v   i       ii    i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_63601790_6   1097 TATTTGCAAAACATAT----GA-AAGAG--TTA-ATCCTCAAAATACATT 1138
                                   v     ----  -   i --  i-    -- i    i  -
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCC--AGAATATAT- 768

  chr2_63601790_6   1139 TTAAA--ACTCCTACAATTCAACAACGAAAAAATCAGATAATCCAACTTA 1186
                         --   --    i     i    i  ii    i -  i    i    i ? 
  L1M4_orf2#LINE/    769 --AAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWA 815

  chr2_63601790_6   1187 AAAATGGGCAAAGGACTTAAATAGACATTTCTACAAAGATGATATATAAA 1236
                                        i  i             v      v      i   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_63601790_6   1237 TACCCAACAAGCATATGAAAAGATACTCAACATTACTAATCAT 1279
                          iv    i     i          i        i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (89 / 44)
Gap_init rate = 0.03 (23 / 794), avg. gap size = 3.09 (71 / 23)  


3395 25.96 0.22 0.33  chr2_63616366_63620435     2670  3578 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63616366_6   2670 TGGAAATACATCCCATGCTCATGGATGGGTAGAATCAATATCATGAAAAT 2719
                               v i        i        v  v   v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63616366_6   2720 GGCCATACTGCCAAAAGCAGTCTACAAATTCAATGTAATTCCCATCAAA- 2768
                            v     v  v   viii      i      i i   i  i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63616366_6   2769 TACCA-CCACCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCAT 2817
                          v   - ii  -  i  ii     v v  v  ivii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_63616366_6   2818 ATGGAACCAAAAAAGGGCCCGCATAGCCAAAGCAAGACTAAACAAAAAGA 2867
                               viiv  ii iv  v v         i   vvi i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_63616366_6   2868 ACAAATCTGGAGGCATCACATTTCCTGACTTCGAACTATAATACAAAGCC 2917
                              vi      vv     i    ii i   i  viv  v        i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_63616366_6   2918 ATAGTTACCAAAACAGCGTAGTGCTGGTATAAAAATAGGCACATAGACCA 2967
                          i   v i   i    i  i  i    i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_63616366_6   2968 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAAC 3017
                               i     v    ii               v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_63616366_6   3018 TGATCTCTGACAAAGCAAACAAAAACATACAGTGGGGAAAGGACACCCTA 3067
                             i ii     i vviv   i v   v  i         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_63616366_6   3068 TTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGAAGAATGAA 3117
                                             i  i   vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_63616366_6   3118 ACTGGATTCTCATCTCTCACCTTATACAAAAATCAACTTAAGATGGATTA 3167
                         ii    ii ii i   v    v           i    i  i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_63616366_6   3168 AGGACTTACACCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATT 3217
                         ?i   i  v iv     v  i           v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_63616366_6   3218 GGAAGAACCCCTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAA 3267
                           ?iv  vi i  vv   v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_63616366_6   3268 CCCAAAAGCAAATGCAATAACAACAAAGATAAATAGCTGGGACCTAATTA 3317
                         v         v v    i  v iv   i   i   iv v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_63616366_6   3318 AACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAGA 3367
                           v v  i i      ii vv    i iv  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_63616366_6   3368 CAACCCACAAAGTGGGAAAAAATCTTCACAATCTATACATCTGACAAAGG 3417
                                  i i     i     v  ii   vii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_63616366_6   3418 ACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGTAAGAAAAAAA 3467
                            vi          v  i  v      vv    v   i   v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_63616366_6   3468 ACAAACAATCCCATAAAAAAAGTGGGTTAAGGACATGAATGGACAATTTT 3517
                         -    i  i  v  v?     -    iv     iv     i    v  i 
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_63616366_6   3518 CAAAAGAAGATATACAAATGGCCAGCAAACACATGGAAAAACGCTCAATA 3567
                          v                      ii  i      i   i i      i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_63616366_6   3568 TCACTAATGAT 3578
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.58 (142 / 90)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


3226 27.08 1.11 0.33  chr2_63645835_63651437     4211  5111 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63645835_6   4211 TGGAAAAACATTCCATGCTCATGGATGGAAAGAATCAATATCATGAAAAT 4260
                               i i  i     i        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63645835_6   4261 GGCCATACTTCCCAAAGTAATTTATAGATTCAATGGTATTCCCATCAAGC 4310
                            v     i      v i  i  i        i vv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63645835_6   4311 TACCATTGACTTTCTTCACAGAATTAGA-AAACTACTACTTTAAATTTCA 4359
                          v   vivi i  i  ii     v v  -  i  i-- iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCA 148

  chr2_63645835_6   4360 TATGGAACCAAAAAAGAGCCCGTAGAGCCAAGACAATCCTAAGCAAAAAG 4409
                                viiv  ii  v  v v v      i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_63645835_6   4410 AACAAAGCTGAAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4459
                                i  i   vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_63645835_6   4460 TGCAATAACCAAAACAGCATGGTACTGGTACCAAAGCAGATATATAGACC 4509
                          i  i   i   i    ii         i iv iiii   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_63645835_6   4510 TATGGAACAGAACAGAGGCCTCAGAAATAATACTACACATCTACAACCAT 4559
                         v      i    iv   ivii         vv i i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_63645835_6   4560 CTGGTCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 4609
                         i  i i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_63645835_6   4610 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 4659
                         v  i  i              v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_63645835_6   4660 AACTGGACCACTTCCTTACACCTTATACAAAAATTAACTCATGATGGATT 4709
                          ii      v  v   i     v                  vi      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_63645835_6   4710 AAAGATTTAAACGTAAGACCTAAAACTATGAAAACCCTAGAAGAAAACAT 4759
                          ?   ii    i      v          i   vi i             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_63645835_6   4760 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 4808
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_63645835_6   4809 ACACTACAAGCAATTGCAACAAAAGTCAAAATTGACAAATGGGATCTAAT 4858
                             i v     vvv          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_63645835_6   4859 TAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAGTGAACA 4908
                         i   v v  i i   i  iiivv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_63645835_6   4909 GGCAACCTACAGAATGGGGGAAAATTTTTGCAATCTATCCATCTGACAAA 4958
                          i     i          i      v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_63645835_6   4959 GGGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTA-CAAGAAAAA 5004
                           i  vi          v  i        --  -  i i -i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_63645835_6   5005 ----AGTAACCCCATCAAAAAGTGGGCAAATGATATAAACAGACACTTTT 5050
                         ---- i      v  i?    i        v   v i  i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_63645835_6   5051 CAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCATCA 5100
                          v        i  vi viii     i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_63645835_6   5101 TCACTGGTTAT 5111
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.61 (148 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3324 26.98 0.44 0.44  chr2_63669012_63675409     4999  5906 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63669012_6   4999 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAGAT 5048
                               i i  i     i        v      v i     i  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63669012_6   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63669012_6   5099 TACCAATGACTTTCTTCACAAAATTGGAAAAACT-ACTTTAAAGTTCATA 5147
                          v   iivi i  i  ii  i  v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_63669012_6   5148 TGGAACCAAAAAAGACCCGGCATTGCCAAGACAATCCTAAGCCAAAAGAA 5197
                              viiv  ii     i v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_63669012_6   5198 CAGAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5247
                           i  i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_63669012_6   5248 CGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5297
                          i    i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_63669012_6   5298 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCAT 5345
                              i    i--    i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_63669012_6   5346 CTGATCTCTGACAAACCTGACAAAAACAAGAAATGGAGAAAGGATTCCCT 5395
                         i    i ii     ivv  v   i v  vvv     i     i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_63669012_6   5396 ATTACAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5445
                         v  -   i          i   v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    399 TTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_63669012_6   5446 AAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCGAGATGGAT 5495
                           ii    i    v   i    iv              i  i i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_63669012_6   5496 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAACC 5545
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_63669012_6   5546 TAGGCA-ATACCATTCAGAACATAGGCATGGGCAAGGACTTCATATCTAA 5594
                             ?i- v i -   ivi  v v  vv i     v ii   v  vv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_63669012_6   5595 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5644
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_63669012_6   5645 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAGCAGAGTGAAC 5694
                          i   v v  i i   i  ii vv    i  v    i  iv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_63669012_6   5695 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACGCATCTGACAA 5744
                           i     i                 v      ivii iii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_63669012_6   5745 AGGGCTAATATCTGGAATCTACAAGGAATTTAAACAAATTTACAAGAAAA 5794
                         i  i  vi    ii    v  i  i   i ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_63669012_6   5795 AGTCAAACAATCCCATCAAAAACTGGGCGAAGGATATTAACAGACACTTC 5844
                           v    i  i  v  i?    v     i      v v  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_63669012_6   5845 TCAAAAGAAGACATCTATGCAGCCAATAGACACATGAAAATATGCTTATC 5894
                           v        i  vi viii       ii          v     i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_63669012_6   5895 ATCACTGGCCAT 5906
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


3246 25.92 1.90 0.45  chr2_63761317_63765872     3170  4064 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_63761317_6   3170 TGGAAAAACATTCCATGCTCATGGATGGGAAGAATCAATATCGTGAAAAT 3219
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63761317_6   3220 GGCCATACTGCCTAAAGTAATTCATAGATTCAATGCTATCCCCATCAAGC 3269
                            v     v  i   v i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63761317_6   3270 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 3318
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_63761317_6   3319 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAATA 3368
                               viiv  ii  v  viv        i      i i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_63761317_6   3369 ACAAAGCTGGAGGCAC-CATGCTACCTGACTTCAAATTATACTACAAGGC 3417
                               i      -  -  ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_63761317_6   3418 TACAGTAACCAAAACAGCATGGTACTGATACTAAAACAGATATATAGACC 3467
                                 i   i    ii        ii iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_63761317_6   3468 TATGGAACAGAACTGAGGCCTTAGAAATAAGGCCATACATCTACAACCAT 3517
                         v      i    i    iviii        iv        i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_63761317_6   3518 CTGATCTTTGACAAACCTGACAAAAACAAGCAGAGGGGAAAGGATTCCCT 3567
                         i    i  i     ivv  v   i v  vv  iv        i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_63761317_6   3568 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 3617
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_63761317_6   3618 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 3667
                          ii         v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_63761317_6   3668 AAAGACTTAAATGTAAGACCTAAAACCGTAAAAACCCTGGAAGAAAACCT 3717
                          ?    i           v       ii     vi i i         v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_63761317_6   3718 AGGCA-ATATCATTCAGGACATAGGCATGGGCAAAGACTTCATGACCAAA 3766
                            ?i- v   -   iv   v v  vv i     v ii   v iivi vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_63761317_6   3767 ATACCAAAAGCAACGGCAACAAAAGCTAAAATTGACAAATTGGATCTAAT 3816
                          i          vvi          vv     v  i        ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_63761317_6   3817 TAAACCTAAGAGCTTCTGCACAGCAAAATAAATTATCATTAGAGTGAACA 3866
                         i   vi   i i   i  ii vv    iv v i     vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_63761317_6   3867 GGCAACCTACAGAATGGGAGAAAATATTTGCAATCTATCTATCTGACAGA 3916
                          i     i                         vii  v       i - 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA-A 746

  chr2_63761317_6   3917 GGGA-TAATATTCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 3965
                             - vi   i      v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_63761317_6   3966 A-----ATAACCCCATTAAAAAA--------GGATATGAACAGACACTTC 4002
                          -----       v   ?     --------    v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_63761317_6   4003 TCAAAAGAAGACATTTATGCAGCCAATAAACATATTTTAAAAAGCTCATC 4052
                           v        i  vi viii        i  i  vvv  i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_63761317_6   4053 ATCACTGGTCAT 4064
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (137 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


 955 21.20 3.69 0.46  chr2_63774950_63776979       56   272 (1758)    L1M4_orf2#LINE/L1        1   224 (684)  

  chr2_63774950_6     56 TGGAAAGATATCCCATGTTCATGGATTGGAAGA----ATATTGTTAAAAT 101
                                                          ----          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_63774950_6    102 GTCCATACTATCCAAAGTGATCAATAGATTCAATACAATCTTTGTCAAAA 151
                          v v     vi     v     v i        ii     ii i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_63774950_6    152 TTTTATCATCATTTTTCATAGAAATAGTAAAAAC-AATATTAAAATTTGG 200
                          iii v vv v     iii      v - v  i -i  vi       iiv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr2_63774950_6    201 ATGGAACCACAAAGGACCCAAAACACCCAAAGCAATCTTGAGAAAAAA-- 248
                               vii   i       i  i v     i         i   i  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_63774950_6    249 -CAAAGCTGGTGGCATCACACTTCC 272
                         -     i   v  vv          
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCC 224

Transitions / transversions = 1.56 (28 / 18)
Gap_init rate = 0.02 (4 / 224), avg. gap size = 2.25 (9 / 4)  

1518 27.32 2.68 0.00  chr2_63774950_63776979      491   900 (1130)    L1M4_orf2#LINE/L1      215   635 (273)  

  chr2_63774950_6    491 TCACACTTCTTAATTTCAAACTACATTACAAA----TAGTAAT-AAAACA 535
                                  ii         vivi i      ----i      -  i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_63774950_6    536 GTACAATACTGGCCTAAAAACAGACACACCAAGCAATTGAACAGAATACA 585
                           iiii       v   ii i     i ivi v    v   i     vv 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_63774950_6    586 GAGCCCAGAAATAAACCCACACATGTACAGTCGACCAGTCTTTGACAAGG 635
                            i               i    v  ii   i iiii i  i       
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_63774950_6    636 GCTTCAAGAATACACAATGAAGAAAGA-TAATATCTTCAAAAAACAGTGT 684
                          ivi     vi iv     ii      -  i v i     v   ii   i
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_63774950_6    685 TGGGA-AACAGGATATCCACATGCAAGGAAATGAAACTGTATCCCCACTT 733
                              -   v     ?          iii      ii  v i   i  i 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_63774950_6    734 TACATCACTTCCAAAAATTAACTCAAATTGGATTTAACATTTAAGTGTAA 783
                         i   i  iv v                v     iv? v ii   i     
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_63774950_6    784 AACTCGAAATTGTAAAACTCCTAGAAGAAAA----AGAGAAAAGCTCCTT 829
                         i viii   i i        i          ----i ? v   v  i v 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_63774950_6    830 GACATTAGTCTTGGCAGTGATATTTTGGCTATGACACGAAAGGCACAGGC 879
                            v  i vi v    i  i v i  i v        v   i     i  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_63774950_6    880 AGTAAAAGCAAAAACAAACAA 900
                          ii     v     i i i  
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAA 635

Transitions / transversions = 2.41 (77 / 32)
Gap_init rate = 0.01 (5 / 421), avg. gap size = 2.20 (11 / 5)  

 693 19.22 4.80 12.61  chr2_63774950_63776979     1206  1538 (492)    L1M4_orf2#LINE/L1      602   908 (0)  

  chr2_63774950_6   1206 CAAAAAAACAAA-AACAAAGAAACAAACAAAAAAAACCAGTGG-CTACAA 1253
                              iv    i-      ii  v   i i v   ----v   -  v  v
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA----TTGGACTTCAT 647

  chr2_63774950_6   1254 CAGAAAAAAAAAAAAAAAAGCTTTTGCACAGCAAACTAAACAATCAACAA 1303
                           i  vv     --------      ii vv    vv v  v     v  
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--------CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_63774950_6   1304 AATGGAAAGGCAACCTACAGAATGGGAGAAAATAT-------------AT 1340
                          i  i    i     i                   -------------  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_63774950_6   1341 CTGATATAAGGGACTAACAACTAAAATGTATAAGGAACTCATACAGCTCA 1390
                               --       vii v i i   i     i      v    i    
  L1M4_orf2#LINE/    740 CTGATA--AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_63774950_6   1391 ATAGCAAAACAAACAGACAAACAAAAAAACAATAAATACACAAATAATCT 1440
                            ----------------- i     i    -----------    i i
  L1M4_orf2#LINE/    788 ATA-----------------ATAAAAAGACAA-----------ATAACCC 809

  chr2_63774950_6   1441 GGTTTCAAAATGGGCAAAAGACCTGAATGAATATTTTTCCAA-GAAGATA 1489
                         ii  ?v            i  ii     ii i    i     -       
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_63774950_6   1490 CACAAATGGCCAGCAGATACAGGAAAGGGTACTAAACATCACTAACCAT 1538
                         i           ii iii   v    i i i  v       ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (42 / 21)
Gap_init rate = 0.03 (9 / 307), avg. gap size = 6.44 (58 / 9)  


1618 28.78 5.60 3.91  chr2_63884279_63887870.rev     1184  1951 (1641)    L1M4_orf2#LINE/L1       23   803 (105)  

  chr2_63884279_6   1184 GAACTAGAAGATTCTATATTATAAAGATATCTGTTGTCCCTAATTTGATC 1233
                          i i i     i iv     i v     iv vi vv    i  v      
  L1M4_orf2#LINE/     23 GGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATC 72

  chr2_63884279_6   1234 TACAGAATCAATGCAATCTCAATCAAA-TCTCTGATAGATTTTGTTTAAA 1282
                               v    i      i v      -  i v v ivv    v vi i 
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chr2_63884279_6   1283 AAGTCAAACATGACCATCATATTCTAAAATGTATATGGAATAACAAAGGA 1332
                           - ------    v v vv  i       vi        vvi   i   
  L1M4_orf2#LINE/    123 AA-T------TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_63884279_6   1333 CCAAAAATAGCCAAAACACTCTTAAAGAGGACAAATGAGTTTG------T 1376
                           v i             v    i  i i  vi  ii iv   ------ 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_63884279_6   1377 C---CTACCAGCTTTCAGGAC--ACTAATAAAGCTGTGGTTCTTAAGATA 1421
                          ---  v  viv     ii  --    -i      iii  vv i    i 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTA-CAAAGCTACAGTAATCAAGACA 264

  chr2_63884279_6   1422 GTACAGTATTAGTGCT-GGATAGACAAATAGATCTATGGAACAGAATTAA 1470
                           iii   i i iiiv-         v       v      i      i 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_63884279_6   1471 -AGCCCAGAAATAGACACTGACATATATAGATACTAGATATATGATGGAA 1519
                         -  i         i  v vv    v   i vi v v   v vi  iiiii
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_63884279_6   1520 GTGGTATTGCAGAT-----GACAGGAAAATGATGAGTTTTTCAATAAATG 1564
                            vi ----   i-----i ii  i   vi  iivi       i     
  L1M4_orf2#LINE/    365 GTGCCA----AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_63884279_6   1565 GTACTGG-ATAA--AGATATCCATATGGGAAAAAATTATATTGAGTCTCT 1611
                           i    - i  --i    ?   i   vi   i   v vi   iii i  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_63884279_6   1612 ACCTCACACTATAAACAAAA-------TAAAATTTTGGGAGAATCAAAGA 1654
                                  i   v      -------i     ------- i    ?   
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAAT-------GGATCAWAGA 503

  chr2_63884279_6   1655 CCTAAAAGTAAAAGGCAAAACCA--AAGCCTTTAAAAAAATACATAGGAA 1702
                               v    i  vi     i --  i ii   i  i  v       ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_63884279_6   1703 AATATCCTCATGGCAACAGAGTACAGAAGGATTTCTTGAACAAAGTACAA 1752
                         v v   i  i  i vvii iv  viv  v i      ii i viii  v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_63884279_6   1753 AAAG-ACAA---ACAGGTGAAAGATT-GAAAATTTAAACTAAATTAAAAT 1797
                             -    ---   iiv    i v -  v  v  ii   vv  i     
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_63884279_6   1798 TAAGAATTTTAGATATGTTTCAGATCATCAAAGGACAACAT--AAAAAGT 1845
                            i  i   --- i  i    --------       vi  -- i     
  L1M4_orf2#LINE/    654 TAAAAACTTT---TGTGCTTCA--------AAGGACACTATCAAGAAAGT 692

  chr2_63884279_6   1846 GCAAAGACAAGTTACAAATTAGTAGAAAATATTTGTAG--CATATGT-TA 1892
                          v        vii   i v i v            i i--     i - i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_63884279_6   1893 CTAAGAT-CTAACATCTATAGTATGCAA-GAGCTGCTACAAATCAGTGGG 1940
                         v    iv-  vii   i v i   ii  -  i  vi     v   i iiv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_63884279_6   1941 AAAATGACAAA 1951
                             v      
  L1M4_orf2#LINE/    793 AAAAAGACAAA 803

Transitions / transversions = 1.66 (136 / 82)
Gap_init rate = 0.03 (26 / 781), avg. gap size = 2.81 (73 / 26)  

 303 15.94 0.00 0.00  chr2_63884279_63887870.rev     3032  3100 (492)    L1M4_orf2#LINE/L1      840   908 (0)  

  chr2_63884279_6   3032 ACATTTCACAAAAGAAGAAACTCAAATGGCCCATAAACATATGAAAACAT 3081
                                v v        v iv         v    i  i       v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_63884279_6   3082 GCTCACCTTCATTAGTGAT 3100
                              v v   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.38 (3 / 8)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.00 (0 / 0)  


2451 21.05 5.80 10.74  chr2_63905876_63907798.rev      501  1431 (492)    L1M4_orf2#LINE/L1       24   908 (0)  

  chr2_63905876_6    501 GATTG-AAGACTTGATATTTTTAAGACATCAATTATCCCCAATTTCATCT 549
                              -       i     v      iiv    vv       v  v    
  L1M4_orf2#LINE/     24 GATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCT 73

  chr2_63905876_6    550 ATAAATTCAATGCAACCCCTATCAAAATTTCAGCAGATTTTTT---AAAA 596
                          i i      i    i            ii    v vi     --- i  
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAA 123

  chr2_63905876_6    597 GTTGACAGATTGACTCTAAAACTCATA--AAAATGCAGAGGACCTGGAAT 644
                         i      iii   ii      i     --i       ii     ii    
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chr2_63905876_6    645 AGCCAAAACAATTTGGAAAAAAAAAAAAAAGGAACAAAAATGGCACACTT 694
                                     i v      i  -------       iv   viv   i
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAA-------GAACAAAGTTGGAGGACTC 216

  chr2_63905876_6    695 ATACTGTCTGA--------CTTA-------------------AAGATAGT 717
                          i   vi ii --------    -------------------    i   
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_63905876_6    718 G--------GCATAAAAATAGTCAAATAGTTCAATGGTATAAAATAGAGA 759
                          --------      ii    v  v    v       v   i   v    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_63905876_6    760 CTTCAGAAATAGGCCTACACATGTATGGTCCATTGATTTTTAACAAAAGT 809
                         v i        ii  i i    v       v         ii    ii  
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_63905876_6    810 ACAAAGTCAATTCAG-GAAAAAAGCATAGTCATTTTCAACAAAAGGTACT 858
                         i v   v v     i- iii    v      -           v   i  
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTC-TTTTCAACAAATGGTGCT 415

  chr2_63905876_6    859 AGAACAATGGGACATTTATTTGCAAATAAATGAACTTTGGTCCATACCTT 908
                         i i    iv   i ?ii iv      vi      v  v ii  v     i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_63905876_6    909 CTACCATAAATAAAA-TCAACTAAAAATTGATCATAGACCTGAATATAAA 957
                         vi      v i    - i    v     v     ?      i   i   i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_63905876_6    958 ACCTAAAATATGAAACTTATTTTTTGTTGTTTTTAAAATTGTTCTTTTTG 1007
                          -------------------------------------------------
  L1M4_orf2#LINE/    516 A------------------------------------------------- 516

  chr2_63905876_6   1008 GTTGTTGTTGTTATTTTCCTAGGCATCAACCTCAACTTAACTAAAACTAT 1057
                         ---------------------------------------i          
  L1M4_orf2#LINE/    517 ---------------------------------------GCTAAAACTAT 527

  chr2_63905876_6   1058 AAAACTTCTGTAAGGAAAAATTAAGAGAAAATCTTGGTAACCTTGGGCTA 1107
                               ii iv   i   v  - i ? v       v  i        i  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_63905876_6   1108 AACAAAGCTTCCTTAGATACCATATGAAAGAGATGATCCATTTAA--AAA 1155
                         ii   v v  i        iv i iv   iiv ii v v ivv  --   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_63905876_6   1156 TTTTGATAAATTAAACTCTATCAAAATTGAGA-CATTT-TGCTGATAGAA 1203
                         vv v        ii   ii         i i - v   -    -- vi  
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAA 674

  chr2_63905876_6   1204 AGACACCA--AAGAGAGTGAAAAGCCA---CACAGA-CAGGACAAAATAT 1247
                         i     i --    i         v  ---      -ii   v       
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_63905876_6   1248 TTGCATATCACATATCAAATAAAGGACTTCTATCTAGAATACATAAAGAA 1297
                              v    i     vi    i      v    i      i        
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_63905876_6   1298 TTCTTGAAACTCAACAATAAGAACACACATA-CACAAATAAACCTACAGA 1346
                         i    iv       i     i  v   v   - v   v ?  vv- ii i
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA-ATGGG 823

  chr2_63905876_6   1347 TAAGATATTTGAACAGACTTTTTGTCAAAGAAGATATTCAGATGGCAAAT 1396
                         i  iiv       i    v   ivi            v  i     v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_63905876_6   1397 AAGCACATAAAAAGATGTTCATCATCATTGATCAT 1431
                                 i        i   v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (120 / 72)
Gap_init rate = 0.02 (21 / 885), avg. gap size = 7.33 (154 / 21)  


1694 22.64 15.55 0.20  chr2_64042166_64047117     3351  3858 (1094)    L1M4_orf2#LINE/L1        7   592 (316)  

  chr2_64042166_6   3351 GATATACCTTGTTTGTGGATCAGGAGACCCAATA--------ATGTCAAT 3392
                              v  v    ii     ii i    ii    --------   v    
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_64042166_6   3393 -TTCACCCCAACTGATCTATACATTCAACGCAATTTCAATCAAAATCTGA 3441
                         -i  -   v  i       i v            ii v         iv 
  L1M4_orf2#LINE/     57 ACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_64042166_6   3442 GCAGCCTTTTTGGTAGTATTTGATAAGCTGATATAAAATTTTATAGGGAA 3491
                           v        v i  v v    i        viv   v  i   v    
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_64042166_6   3492 AAGCTAAGGACCTAGAATAGCCAAAACAATTTTGAAAAAGAA---CAAAA 3538
                          v  v i     i                 i           ---    i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_64042166_6   3539 TTAGTGAGCTCACATTATCTTATTTCAAGATTTACAATAATGCTGGAGTA 3588
                           i v ii      i vi iv       i i    v i  v   iv    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_64042166_6   3589 GCTAAGACAGTGTGGTACTGG------AACAGA-ATATA-ATC------- 3623
                         iii                  ------i i   -     -   -------
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_64042166_6   3624 -----TCAAAA--CCAAACAAAAAC----------------AGTTGATTT 3650
                         ----- ii i --   i v v    ---------------- i       
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_64042166_6   3651 TTAACAAAGGTGCCAG----------TGGAGAAATGATAGTCTTTTTAAC 3690
                          ii    i       i----------   i    vi          i   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_64042166_6   3691 AAAAGGTGCTGG---AACT----------ATG---AAAAATGAACACTGA 3724
                            v        ---    ----------   ---  i      vviv  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_64042166_6   3725 CTTATACTTTGCATTATATATAAATATCAACTAGAAATGAATCATAGCCT 3774
                          iiv   i ii  ii     i   v  i    vi     i    ?  v i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_64042166_6   3775 TAAATATAAAACCTAAAACAATAACATTCT-AGAAAAAAA-ATTGGAGAA 3822
                              i   i v       v    v i   -    i    -  v  ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_64042166_6   3823 TATCTTTGTAAC-TTGGGTTATACAAAGATTTCTTGG 3858
                         v     i  i  -        vi   v i      i 
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

Transitions / transversions = 1.69 (71 / 42)
Gap_init rate = 0.03 (17 / 586), avg. gap size = 4.71 (80 / 17)  

1000 19.08 11.18 1.64  chr2_64042166_64047117     4158  4461 (491)    L1M4_orf2#LINE/L1      576   908 (0)  

  chr2_64042166_6   4158 AAGAAAAGATTTCTCAGGATAGGACAC---AAGCAGCATG-AACAGAA-A 4202
                          i v  v i     i  -   v     ---     -  v -    i  - 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAG-ATATGACACCAAAAGCA-CAAGCAACAAAAGA 623

  chr2_64042166_6   4203 ATAAATAAATAAACTGAATTTCATCAAAATCAAAAATT-----GCTCTAA 4247
                          v     i     i  i i           i     i -----   ii  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_64042166_6   4248 --GACACTGTTCATGAAAG-GAGAAGACAAGCCACAAACTGGGAGAAAAT 4294
                         --      i -  v     -  i       v     i v           
  L1M4_orf2#LINE/    674 AGGACACTAT-CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_64042166_6   4295 ACTTAGAAACCACATA-CTGATACAGAATTTGTATCTAAGATATATAAGG 4343
                          i  iv   i  i   -      vi i i       i ii        i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_64042166_6   4344 AACACTTATAA--------------GACAAACAACCTAATATTTTTAAAT 4379
                            v    i  --------------      i    i   -- ?vv    
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT--TWAAAAAT 820

  chr2_64042166_6   4380 GAGCAAGAAATCTGAGCAGACACTTTACCAAAGA-----TATGAATGGCA 4424
                          i    iii  i   ii     i  iv       -----  ii      v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_64042166_6   4425 AACAAGCACATGAAAAGATGCTTAACAT-ATCTGTAAT 4461
                           i                   i     - ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.80 (42 / 15)
Gap_init rate = 0.04 (14 / 333), avg. gap size = 2.79 (39 / 14)  


 293 26.79 4.46 0.89  chr2_64062970_64064579      249   360 (1250)    L1M4_orf2#LINE/L1      139   254 (654)  

  chr2_64062970_6    249 CTAAAATGTATATGGATTTGTAAAAGACCAAGAAGAGTTGAGGCAATCCT 298
                                vi       vv  i  ii    v    v  iii ii     i 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr2_64062970_6    299 ---AAAGAAGAA-AAATTGGGAGAAATTA-ATCTCCCAGATATTAATATG 343
                         ---         -   v v    i v i - ii     -  v i  v iv
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACT 237

  chr2_64062970_6    344 GATTAAAAAGCTACAGT 360
                         v i  v           
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGT 254

Transitions / transversions = 1.31 (17 / 13)
Gap_init rate = 0.03 (4 / 116), avg. gap size = 1.50 (6 / 4)  

1216 27.84 9.33 3.89  chr2_64062970_64064579      488  1130 (480)    L1M4_orf2#LINE/L1      231   908 (0)  

  chr2_64062970_6    488 CAAAAGCTATCGTAA--CTACAGTAACTATGACAATTTTACTTAATGGTA 535
                              vi  iiii  --         ii v    i --------i     
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGT--------GTGGTA 272

  chr2_64062970_6    536 CTGGTGTAAAGACAGA-A---AAATGAACGAAATAGA-------GTCCAG 574
                             ii   i  i   - --- i  v  i i      -------      
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_64062970_6    575 AAACAGA----TACGCCTATCTGAATATTTGATTTATGTCAAGAGTGACA 620
                            i i ----   iii   -- ivi v       vi v    i   v  
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTAT--GGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_64062970_6    621 TTATAGAGCAGT-----AGGAAAGA-CAGCCTTTTCAATAAATGGTGCAA 664
                         ----   v  v -----i       -i  i        i         vi
  L1M4_orf2#LINE/    371 ----AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_64062970_6    665 GGTCAAAAACATATCCATATGGGAAAAAA---ATCTTAACCC-----TCA 706
                           v   vviv   ?   i   vi   i  --- vi vi    -----   
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_64062970_6    707 TACTAAACATAAAAATCAATTCTAGATGGATTGTAGGTCTTAATGTGAAA 756
                         i  i v i i      i  i  v i      ii?  ii  v     i i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_64062970_6    757 AAGACAGTAACAAAGTTTCTAGACAGTAACCA---GAAAACATCTTCAAG 803
                         ivv v iiv i   ii ii    -  v  v  --- ?iv v      iv 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGA-AGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_64062970_6    804 TCTTTAAGGTAGAGAAAGATTTCTTAAACAGGACACAAAGAAGCATAAAT 853
                         v i  ii v   iv  v i       i i v     v  -     i  ii
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA-AAGCACAAGC 614

  chr2_64062970_6    854 CATAAAGGAAAGTAATGAATCA--TAGAATT-AT----ATTAAGAACTTT 896
                         v i   i    i-   ii  v -- i  v  -  ----     i      
  L1M4_orf2#LINE/    615 AACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_64062970_6    897 TGTTCACCAAAAAACCCAAT-AAGA--GTGAAAAGTCAATACAGAAAGTG 943
                            v vi    ii  v v  -    --        v   iv  v i i  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_64062970_6    944 GGAGAAGATATCTGCAA--TATGGACAACTGGCAAAAGGTTTGTG-CTGA 990
                               i    i     --i  -- i v   ii  ii ii    i- iii
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCAT--ATATCTGATAAGGGACTTGTATCCAG 761

  chr2_64062970_6    991 CATAATATAAACAACCTTCACAGATCAA---------GACAAA----CCA 1027
                         v   -      v   ii i   iv    ---------      ----   
  L1M4_orf2#LINE/    762 AATA-TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_64062970_6   1028 ACAGAAAAATGGGTAAAGGCCTTGAATAGGCACTTCATAGAAAAGGACAT 1077
                          iv?         i     vi        i  i   vivi  i i  i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_64062970_6   1078 CCCAGAAGCCAATGAATGTATGAAAAGGTGCTCTCCTAACAATCATCAGG 1127
                         v v ivi      i iiii        i     ----    -   ?????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTC----AACA-TCAZZZZZ 905

  chr2_64062970_6   1128 GAA 1130
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.07 (118 / 57)
Gap_init rate = 0.04 (29 / 678), avg. gap size = 2.93 (85 / 29)  


3321 25.84 1.45 0.33  chr2_64064804_64071202     5010  5907 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_64064804_6   5010 TGGAAAAACATTCCATGCTCATGGATAAGAAGAATCAATATTGTGAAAAT 5059
                               i i  i     i        vi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_64064804_6   5060 GGCCTTACTGCCAAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5109
                            vv    v  v   v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_64064804_6   5110 TACCA-CTGACTTTCTTCACAGAAATGAAAAAAACTA---CTAA------ 5149
                          v   -   v    i  -i       vi v  i-  i---    ------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_64064804_6   5150 --TGGAACCAAAAAAGAGCCCGCATAGCCAAGACAATCCTGGGCAAGAAG 5197
                         --     viiv  ii  v  v v        i      i  iiv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_64064804_6   5198 AACAAAGCTGGAGGCATCATGCTACCTGACGTCAAACTATACTACAAGGC 5247
                                i      vv   ii  v  ii iv     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_64064804_6   5248 TACAATAATCAAAACAACATGATACCGGTACCAAAACAGATATATAGACC 5297
                             i       i   iii  i   i  i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_64064804_6   5298 AATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATCTACAACCAT 5347
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_64064804_6   5348 CTGATCTTTGACAAACCTGACACATACAAGCAATGGGGAAAAGATTCCCT 5397
                         i    i  i     ivv  v  vivv  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_64064804_6   5398 ATTTGATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5447
                         v  ii i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_64064804_6   5448 AACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGATC 5497
                          ii         v   i                 i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_64064804_6   5498 AAAGACTTAAACGTAAGACCTAGGACCATAAAACTCCTAGAAGAAAACCT 5547
                          ?    i    i      v   ii  i         i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_64064804_6   5548 GGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAAA 5596
                         i  ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_64064804_6   5597 ACACCAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGGGATCTAAT 5646
                                     vvi          iv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_64064804_6   5647 TAAACGGAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 5696
                         i   vvv  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_64064804_6   5697 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5746
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_64064804_6   5747 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 5796
                           i  vi          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_64064804_6   5797 AGCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5846
                         ii    i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_64064804_6   5847 CAAAAGAGGACATTTATGTGGCCAAAAGACATATGAAAAAATGCTCATCA 5896
                          v     i  i  vi vi       v ii  i       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_64064804_6   5897 TCACTGGTCAT 5907
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (136 / 92)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


3015 20.20 4.35 0.84  chr2_64075006_64076689      480  1192 (492)    L1M4_orf2#LINE/L1      171   908 (0)  

  chr2_64075006_6    480 AAAAGTCAAAATACAATCGTAAA------GAATGAAGTATGGAAGTCTTA 523
                           v  i     --     v i  ------   ii    -    i v  i 
  L1M4_orf2#LINE/    171 AATAGCCAAAA--CAATCTTGAAAAAGAAGAACAAAGT-TGGAGGACTCA 217

  chr2_64075006_6    524 TAAT-CCTGATTTCAAAACTTAC---AAGACTATGGTAATCATAACAGTG 569
                         i v -  ii              ---  ii   ii       vi      
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_64075006_6    570 TGGTATTGGCATAAAGAGTGACATATAGA--------ATAGA---GAGAG 608
                              i        i  vv          --------     ---     
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_64075006_6    609 CCCACAAATGAACTCTCACATATACAGTAAAATGTTTTTTGACAAGGGTG 658
                         i   v    i   i vi    v  ii  v  v  v    i          
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_64075006_6    659 GCAAGACCATTCAATGCAGAAAGGTCAGTCTTTTCAACAAATGATACTCG 708
                         v               vi     ivi                 i i  v 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_64075006_6    709 GAAAACTGAATATCCACATGCTAAAGAATGAAAGTAGACCGCTGTCTTAT 758
                           v     i   ?        v          iv i    v  ii  i i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_64075006_6    759 ACCACCTATAAAAACAAACT-AAAGTCAATTAAAGGCCTAAATATAAGCT 807
                             iv  i     iv    -   i vi  i ?  i       i    vv
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_64075006_6    808 CTAAAAATATAAAATTCTTACAAGAAAATACAGGGAAAAAGCTTCAGGAC 857
                               v       i     v       i i   ?iv   v    iv   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_64075006_6    858 ACTGGATTTGGCATTGATTTCTTGGATATGAAATGAAAAACATAGGTGAC 907
                         vi   i  v    v  i      i       v iv    i  i i ii  
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_64075006_6    908 AACA-AAAAAATAGACAAATTGGACTACATCAAAATAGAAAAACTTCTAT 956
                           v -          i          v         -v        i i 
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTTTGT 666

  chr2_64075006_6    957 GCATCAAAAGACACCATTAACAGAGTAAAAAGGCAACCTGCGGAATGGGA 1006
                           v     i     i  i  v i   i     i     ii i        
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_64075006_6   1007 GAAAATATTTGTAAATCACGTATATGATAAAAGGTTAATATCCAGAATAT 1056
                                    i      ii   v      ii ii vi            
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_64075006_6   1057 GTAAAGAACTTCTACAACTCAACAACAAAAAAACCAAACCACCCCATTAA 1106
                         i         ii          i  i     i  -   iv    v   ? 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTWA 815

  chr2_64075006_6   1107 ATAATAGGCAAA-----TAAA---ATATTTTTCCAAAAAAGACATAAAAA 1148
                          v   i      ----- i  --- i    i      i    i   v   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_64075006_6   1149 TGCCCAATAAGCACATAAAAAAGATGCTCAACATCACTCATCAT 1192
                           v             i    -              ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (92 / 48)
Gap_init rate = 0.02 (14 / 738), avg. gap size = 2.64 (37 / 14)  


3034 24.13 2.27 0.80  chr2_64111696_64114331.rev      958  1707 (929)    L1M4_orf2#LINE/L1        1   761 (147)  

  chr2_64111696_6    958 TGGAGAGATATTTCATATATGTGGATAGGAAGGCTCAATATTGTCAAGGT 1007
                             i      ii   i vii     v     i  i        i   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_64111696_6   1008 GTCTCTTTTTCCCAACTTGATCAATAGAGTCAACATAATCCTGATTAAAA 1057
                          v vv vi i     v      v i   v     ii     iv  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_64111696_6   1058 TCCTAGCAGTTGGTTTCTTG--GATATTGA-AAACTGACTCTAAAGCTTA 1104
                            i   v ii--   i   --  v     -  i    ii     ii i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_64111696_6   1105 TATAGAAA---AAG--ACCCAGAATAGCTAACACAGTATT--AAAAGAGG 1147
                            i    ---   --            i  v   i v  --      i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_64111696_6   1148 AACAAAGCTGGAGGACTGATACCACTCAGTTTGAAGTTTTGCTATAAAGC 1197
                                i         v i  iv i  i   v  ivi  i   i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_64111696_6   1198 TACAGTAATCAAGACAATGTCATATTGGTGAAAGAACAGACATATGGGTC 1247
                                         i   vi  i   iiv   i i        i i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_64111696_6   1248 AGTGGAACAGA-----GAACCCAGAAATAGACCCACACAAATACAATCAA 1292
                          i     i   -----  ii         i     i   vv  iii    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_64111696_6   1293 CTGATTTTTAACAAAGGGGCAAAGGTAATTCAGTAGAGAAAGGATAGTTG 1342
                         i       ii    i  v  v   iiv     i i i     i     iv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_64111696_6   1343 TTTGAACAAATGGTACTGAAACAACTATACATCCACATACCAAAGAGAAA 1392
                            v          i   ii      iv i ?      i --  i    v
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC--AAAAGAAT 446

  chr2_64111696_6   1393 GAATATAGACATACCACCTTGCACTATTCATGGAAATTAGCTCAAAGTTG 1442
                            vv i   vi- i    ii   i  vi iii      i      i v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_64111696_6   1443 ATGATAGACCTTAATGTAAAATGC-AAAACTATAAAACTTCTAGATGATA 1491
                           v ?      v       i -  -              ii    v  v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_64111696_6   1492 ACATAGGAGAAAATCTAGGTAACCTTGGGTTTGGTAATGGCTTTTTAGAT 1541
                                ? v      vv  i          v  i     i  i      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_64111696_6   1542 ATGAAAG-AAAAGCACAATCCATGAAAGAAAAAATTGAAAAGTTGAACTT 1590
                             v v-          v v ii           v  v  i   i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_64111696_6   1591 CATTAAAATTAAAAAGTTCTACTCTGTGAAAGACACCTTTAAGAGAATGA 1640
                            i           v  i iiv  vii  i     iv i    i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_64111696_6   1641 AAAAACAAGCCAAAGACTGGGAGAAAATACTTAGAAAACACATATCTGAT 1690
                            i    v   v   v            i  iv   v  i         
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_64111696_6   1691 ACAGGATTGGTGGTCAG 1707
                          vi   i v  ivi   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAG 761

Transitions / transversions = 1.97 (118 / 60)
Gap_init rate = 0.02 (12 / 761), avg. gap size = 1.92 (23 / 12)  

 609 18.07 1.20 2.41  chr2_64111696_64114331.rev     1983  2148 (488)    L1M4_orf2#LINE/L1      745   908 (0)  

  chr2_64111696_6   1983 AAGGGACTGGTACCAAAAATAAACAAAGGA--GTTAAAACTCAACAACAA 2030
                                 v   i v i    v i    i --v   v       i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_64111696_6   2031 CAAAACAAACAGCCAAATTAAAAAATGAGTAAAGGACTTTGAATAGACCT 2080
                         v  i     i i  v    ?       i i      -           v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA-TTTGAATAGACAT 843

  chr2_64111696_6   2081 TTTCCCAAAAAAAGATATAGAAGTGTGCAATTAGCACATGGAAAGATGGT 2130
                           ii     i  -      v  i  vv    v        i       v 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_64111696_6   2131 CAACATAGCAAATAATTT 2148
                               --  ????????
  L1M4_orf2#LINE/    893 CAACAT--CAZZZZZZZZ 908

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.02 (4 / 164), avg. gap size = 1.50 (6 / 4)  

 368 15.62 4.17 3.12  chr2_64111696_64114331.rev     2183  2278 (358)    L1M4_orf2#LINE/L1      812   908 (0)  

  chr2_64111696_6   2183 TTAAAAAATATGAGCAAAAGATCTAAATA----CCTCACCAAAGAAGATA 2228
                           ?      -- i     i   i i    ----ii  v            
  L1M4_orf2#LINE/    812 TTWAAAAAT--GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_64111696_6   2229 ATGCAGATGGCAAATAAGCATATAAAAAGATGCTAAATATCAAATGTCAT 2278
                         - i  i     v        i  i          v  i    ????????
  L1M4_orf2#LINE/    860 -TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.03 (3 / 97), avg. gap size = 2.33 (7 / 3)  


2603 26.29 7.28 0.82  chr2_64125137_64127721.rev     1263  2114 (471)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_64125137_6   1263 GGAAAGATATTCTGTGTTCATGGATTGGAAGAATCAATATTGTTAAAATG 1312
                                   i ii                  v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_64125137_6   1313 TCCATACTAACCAAAGCAATCTACAGATTCAGTGTATTCCCTATCAAAAT 1362
                         v v     vv     vii             ii i v             
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_64125137_6   1363 ACCAATTAAATTCTTCAGAGAAATAGAAAAAACAATCTTGAAATTTATAT 1412
                         v   ii ivv  i  iiv      v  v  ivii   i i     i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_64125137_6   1413 AGAACCACAAAAGACTTGGAATAAACAAAGCTATCCTATGCAAAAAAAAG 1462
                         i   vii   ii   iii     iv    i v   i iviv  i  i  v
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_64125137_6   1463 AAAATTGGAAGAACCGCATGATGTGATTTCAAA--TTA-TACAA--C--- 1504
                            i     i  vi i  ivvivii        --   -     -- ---
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_64125137_6   1505 ------------------GTATTGGCATATAACCAGACACATAGAACAGT 1536
                         ------------------   i       viivi     i     v  i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_64125137_6   1537 GGAACCAAGTAGAGAACCCAGAAATAAATCCATTCATCTACAGTGATCTC 1586
                             ivi i v    ii           i    v   i  ii  v vi v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_64125137_6   1587 ATTCTTAACAAAGG-------ACAATCT--TGGGGAAAAGGACAGTCTCT 1627
                            i ii    i  -------  v  ii--        - i i     i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTT 400

  chr2_64125137_6   1628 TCAATAAATTGTGCTGGGAAAACTAGATATCCATGGATAGAACAATGAAA 1677
                             i    v         v    i    ?   iivii i  v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_64125137_6   1678 CTGGACCC-TATTTCGC--CATATACAAAAAT------AAAATGGATGCA 1718
                         i       -  ii  i --             ------         vv?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_64125137_6   1719 AGACTTAAATCTAAGACTTCAAACTATGAAACAACGAAAAGAAAGCCTTG 1768
                             i     v     vi v       i    vviv i      i v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_64125137_6   1769 GGGAAAATGTCCAGGTCATTGAAGTGAGCAAGGATTTCTTGAATAAATAC 1818
                          ? v    v i iv v v   iiv ii    v i      ii   vi-  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG-AC 599

  chr2_64125137_6   1819 CCCACAAGCACAGGCAACCAAAGCAAAAATGAACAAATGGAATCACATCA 1868
                         v   v       i     v    v      ii i    v i iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_64125137_6   1869 AG-TTACAAAGCTTCTGCACAGCAAAGGAAAC----AACAAAGTGAGGAG 1913
                          i-   -   i   i  ii vv       v  ----  v       ii  
  L1M4_orf2#LINE/    650 AAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_64125137_6   1914 ACATCCCACAGAATGGGAGGAAAATATTTGCAAACTACCCATCTGACAAG 1963
                            v               -              ii ivi      i   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAG-AAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_64125137_6   1964 GGATTAATAACAAGAATATATAGGGAGCTCAAACAACCTTATAGATAAAA 2013
                            i vi  v v          ii  i   vv     iiv   -      
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAAA 796

  chr2_64125137_6   2014 ATCCAA-TATGTTGATTAAAAGATGGGCAAAATATCTGAATAGATATTAC 2062
                          vv   -  vviii   ?   i         iv  i        i   v 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_64125137_6   2063 TCAAGAGAAAACATGCAAATGGC--------ACATG----GGTGTATTTA 2100
                           v i    i i  i        --------     ---- i  i-- i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC--TCA 894

  chr2_64125137_6   2101 TCATCAGAGGAATG 2114
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (138 / 82)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 3.45 (69 / 20)  


1107 28.62 6.90 4.19  chr2_64437583_64439491      546  1429 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_64437583_6    546 TGAAAAAAAAGGTCATGTTCAAGGATAAAAAGACCCAATATCATGAAGAT 595
                           i   i v vvi        v    vii     ii     ii v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_64437583_6    596 --CAATTTGTCCCAAGTTTATCTATCATTTCAATCAGAATCTCAATAGAA 643
                         --    vivi     i  v     iviv     - iv    i v  vi  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAA 99

  chr2_64437583_6    644 ATATTTTA--TGGATATTATGCAGACAAATC--CTAGCTGCTTATAAAAT 689
                           --iii --  vv v  v      --   i-- v     v iv      
  L1M4_orf2#LINE/    100 AT--CCCAGCTGCCTTTTTTGCAGA--AATTGACAAGCTGATCCTAAAAT 145

  chr2_64437583_6    690 GTATATGGAAGGGCAAAGAACAAGAAAGAGGAAAGAGAATCTTGAAGGAG 739
                         vi        iv    i i  vvii  v  vv  i v         ii  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_64437583_6    740 GAGGG--AAG-----GGACTTGC-CATAGCAGATATCAAGAACTTACTAT 781
                         i  ii--   -----     ii - v vv  -  v    -         i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAA-AACTTACTAC 243

  chr2_64437583_6    782 AAAGCCCCAGCAGTTAAGCCAAAGGGGAGGGGAGGATGTATGAGAAATAA 831
                              iv   i i i   v  iv v  vivv ----- i  i  i -  i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTG-----GCATAAGGA-TAG 287

  chr2_64437583_6    832 ACAGAGAGACCAATGCAATGGAA--AAGAGCTTAGACATAAACTCAC-CA 878
                            v v   i     v   i   --i    iii   v      i  i-  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_64437583_6    879 TATAAGAAAAAATTCATTCATAACAGAGCAGCCATTATACAT-CAGTAAG 927
                          v  v ivv  -  v   ivii   ii vv    vv i-   -  i ii 
  L1M4_orf2#LINE/    338 TTTATGGTCAA-TTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGG 385

  chr2_64437583_6    928 GAAAGGAATGGAGTGCTCAA-AAATGGGGCTGGGACAAT--AATCACCCC 974
                              -   i vv vi    -      v          i--i  v?  v 
  L1M4_orf2#LINE/    386 GAAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_64437583_6    975 TCCCTAAAAAAAGGAAAGAAAAATTGGATTTCTACCTCATACTATATACA 1024
                         viv -    i  v   i------     iii        i  i       
  L1M4_orf2#LINE/    435 ATGC-AAAAGAATGAAG------TTGGACCCCTACCTCACACCATATACA 477

  chr2_64437583_6   1025 CAAATCAATTCTACATAGATTAAATGA---AAGTTTAAAAATGACAAAAC 1071
                         v    i  i  v v  i   i ? -  ---  i v   i -- vi     
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWA-GACCTAAATGTAAGA--GCTAAAAC 524

  chr2_64437583_6   1072 TTTAAAA-TGTTATTA-AAAATATAGAC-TA--TTTGCATGAC-TCGAGT 1115
                          v     - v   vv -    i    i?-  -- i v i    - i i  
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_64437583_6   1116 AAGAAAA------ATTATAATAAGTAACA--AAATGCTCAAAAAACCAGT 1157
                         v  iv  ------v   -i   -- i   --   v  v   iv   v i-
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTA-GATA--TGACACCAAAAGCACAAGCAACAAA- 620

  chr2_64437583_6   1158 ATAAAATATTCATACATTAGAATACAT-GAAATTTTAAACTTTTGTTCAT 1206
                          v    v  vv   v   i  v v   -i     vv          v v 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_64437583_6   1207 TATAACATGTAATTACGAGAGTAAAAAAATAA---AC----TGAGAGAAG 1249
                         i v iv iiiv  i v  i   i    i i  ---  ----  i     i
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_64437583_6   1250 ATATTTGAAACAAA-CATAACATC-----AAGGATTAGTATTTCAAATAT 1293
                                ---    -    -i   ----- i   i v    iivi     
  L1M4_orf2#LINE/    721 ATATTTG---CAAATCATA-TATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_64437583_6   1294 ATAAAATATCTCTCTGAATT-AACATGAAAAAGACAA----CACAGTAGA 1338
                              iv -    ivv  i -  i vv          ---- v  i v? 
  L1M4_orf2#LINE/    767 ATAAAGAA-CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_64437583_6   1339 AAGAAGGGCAAAAAGTCATGAATGTA-ATTTAAT--AGGAAGAAACAAAA 1385
                           i v       iii i-     iv -    vvi-- i     v i v  
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATT-TGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_64437583_6   1386 ATGGCTAATAAACACATACAGAGA-GCATTAGCACTGGAGTCATT 1429
                              i     i     iv i   -  - i i  iii????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGC-TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (138 / 111)
Gap_init rate = 0.06 (51 / 908), avg. gap size = 1.92 (98 / 51)  


 788 28.49 7.95 6.45  chr2_64474272_64475929.rev      501  1167 (491)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_64474272_6    501 AAAACATATTATAGTACTTTGACAATTAAAACTTCATAGTACTAGCACAT 550
                              v  i  i ivi  viiii   i  i  vvii i     i   i v
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_64474272_6    551 GAATAGATAGAGAGACCAATGGAACAGT-TTAAGAAT------ATAAATA 593
                          i     i v v   i        i  v-  i   i ------     iv
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_64474272_6    594 TATACA-----GG--AATTTAGCATATGATAAAGGAAGCATTCCAA---- 632
                         i     -----  --    v viv -i  i  i  ----- v    ----
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTT-CGACAAGGG-----TGCCAAGACC 375

  chr2_64474272_6    633 ATTCAGTG-----AGAAT-------TCAATAAGTGTTGTTGAGATTCCTG 670
                              i  -----     -------    i  i  v  i  i  ivv   
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_64474272_6    671 GGTAGCCATCTTGAAAAACATTGAGCTGGAGCTATACCTCACACCATATA 720
                          i  ?   iv vv    iv  vi  i    v iv                
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_64474272_6    721 TCAGAATAAATTCCACATGGATTAAACATTTAAAGGTAAACAATAAAACC 770
                         iv i   v  i  v v      i ? v ii    v    iviv      i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_64474272_6    771 ACACAAGTACCAAGAGAAAATGTGGGAG-AAATCTTTCATAATCTTAGAG 819
                          i v  v vii ii      ii i  ? -       - i i i   i iv
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT-CGTGACCTTGGGT 574

  chr2_64474272_6    820 TGGGAAAGTCTTTCCTAATCCTGACTCACAAATCAGGAACTATAAAATAG 869
                          i  v  vvv    i  iviv    v vv   v  vi i v i    v i
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_64474272_6    870 GAAATTGATTAAGTCAACT-AATAAAAGTTGAAAAAAACTTTTTAAGCTC 918
                         i    v   v  v vi   -v  v   i  ---          --- iv 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATT---AAAAACTTTT---GTGC 668

  chr2_64474272_6    919 TTGCATGTGAAACAAACAAAAA--TCAAACCTGTATATAA---GCAAAGT 963
                           -  viv  v  v v   i  -- v   ----- v i  ---i  i i 
  L1M4_orf2#LINE/    669 TT-CAAAGGACACTATCAAGAAAGTGAAA-----AGACAACCCACAGAAT 712

  chr2_64474272_6    964 CGAAAACAAATGCAAATCTGTAAAGGATACACAAAACTCAGCAAAGGGCT 1013
                         v i i -    ----  i  i   vv   i i----  v -i  i  i  
  L1M4_orf2#LINE/    713 GGGAGA-AAAT----ATTTGCAAATCATATAT----CTGA-TAAGGGACT 752

  chr2_64474272_6   1014 AATTTCTTTAAATTATAAAGA-TACATAAACCTC--TAAAGAAAAGAC-- 1058
                         vi v  ivv  vv        -iv v  v v   --   vi       --
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_64474272_6   1059 ------CAATGAAAATACGAGCAAAGCATGTGAAAAAGTGGCTTATAGAA 1102
                         ------    v?   v i i      v  v    -----------    -
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAA-----------TAGA- 840

  chr2_64474272_6   1103 CAAT-----AATGAAAATAAATACAAATGGCTAGTAAACATATGAAAAGA 1147
                           v -----  v   i   --          i i   i  i         
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATA--TACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_64474272_6   1148 TGTTCAACCTCTTCATGATA 1167
                           i     v  v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (100 / 86)
Gap_init rate = 0.04 (29 / 677), avg. gap size = 3.31 (96 / 29)  


2624 25.75 4.11 3.33  chr2_64526141_64530269.rev     2737  3637 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_64526141_6   2737 TGGAAAGATA---CATGC-CATGGATTGAAAGATTCAATACTGTTA-TAT 2781
                                   ---    i-         i    i i    i     -v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_64526141_6   2782 GTCAAGTTTACTTAAAGTGACCTAAAGATTCAATATCATTTCAACTACAA 2831
                          v   vvi v ii   v   i   v        iiiv  ii v ii v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_64526141_6   2832 TCCTAACAGA--TTTTTGTAGAAATTGGCAGGTTAATCTTACAATTTAAA 2879
                            i i v v--      i        i  i i i   i  v    i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_64526141_6   2880 TGGAAATACAAGGGGCTTAGAATACCCAAAACAATCTAGTTGGGGGAAAA 2929
                                i      i ii      v            ---  iiii i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT---TGAAAAAGAA 197

  chr2_64526141_6   2930 CCTCAAAG--------CTCACACTAAGTGAGCTTTCTAAGTATCTGATGC 2971
                         vvv     --------        --------- i i  v -  vi ---
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACT---------TCCCAATT-TCAAA--- 234

  chr2_64526141_6   2972 TGATACTTATTATGGAGCTACTATGATCATGGTAGGGAGTTATTTAGGTC 3021
                         ----     i  iii      vi i    v ii  v v v  i vivi v
  L1M4_orf2#LINE/    235 ----ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_64526141_6   3022 AGGGTAGACAAATAGATCAATTGAACAGAACAAAGAGTCCAGAAATGGAC 3071
                            i      v          v   i    ivi             ii  
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr2_64526141_6   3072 CCATACATATATGGTTTATTGATTTTTGACAGAGGCATCAAGGATTTCCT 3121
                                 v      iv         i    ii  iii    iviv i v
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_64526141_6   3122 ATGGGGAAAGAAAATTATTTTTGACAAATGATTCTGGAATAATTGGATAA 3171
                                     v v v    ii       i v    i i  i      ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_64526141_6   3172 ATTAAACAAGATAAAATGAACTTCAATCACTAT-TCATACCACATA--AA 3218
                         -ii v iivi v i      v  vi i v   i-   i    i   --  
  L1M4_orf2#LINE/    431 -CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_64526141_6   3219 GATGTAATTCATGGTGGAACAAAGACCTATGTGTAAAAGCTAAAATTCTA 3268
                         i  -   i   vii    v  ?       vi     i        i v  
  L1M4_orf2#LINE/    480 AAT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_64526141_6   3269 AAGTT-TCAAGAGAAAACATAAAAA-ATATCTTCCTGA-----AGTAAGG 3311
                           ii - i ii          ii?i- v      v   -----i  v   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_64526141_6   3312 CAAAATTTTCTTAGGTAGAAAATTTTTATAAAATAAATAGTCATGAGAGA 3361
                            viv        i  vi v ii--- -   ii v -  iv ii i   
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACC---A-AAAGCACA-AGCAACAAAAGA 623

  chr2_64526141_6   3362 AAAAA-AGAGAAATTAGATTTCATCAAAATTAAAA---TCTGCTCATTAA 3407
                              -   v     i  i                --- i  iv v i  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_64526141_6   3408 AAGAAACCATTAAGAAAATAAGTAGGCAAGTTACAGAGTAGGA-AAAATA 3456
                          i  v  i  i      i i iv  i   vii     i i   -      
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_64526141_6   3457 TTCACAGTGCATGTAAGTGACAAATGACTTGTATGCAGAATATATTAAAA 3506
                           ii  ivv   i  vv   i  iv         v          v  i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_64526141_6   3507 ACTC--ACAA-----TAACAAAAAGACAAACAGCCAAATTTTTAAGAGAT 3549
                             --    -----   i           i i  v    ?--- i i  
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW---AAAAAT 820

  chr2_64526141_6   3550 AGGCAAAAGATTTGAGGAGACAATTCATGGAAGAAGACATATGAACAGCA 3599
                         i      i       iv     v   vivi       i   ii  ii  v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_64526141_6   3600 AATAAGCACATGAAAATGTGCTCAATATTATTAGTCAT 3637
                                         vi       i  i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (149 / 79)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.68 (67 / 25)  


 532 26.78 3.83 0.00  chr2_64565183_64570276.rev     3171  3353 (1741)    L1M4_orf2#LINE/L1        8   197 (711)  

  chr2_64565183_6   3171 ATATC--ATGTTCATGGACTGGAGGAC--AACATAGTGAAAATGTCGGTT 3216
                              --           i    i   --  i  v  v  i   v ii v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_64565183_6   3217 ATCCCTAAACTGATGTACAGGGTTAACTCAATTTCTATTAAAATCACAGA 3266
                         v    i   i    v     iv i   v    ii    i      v   v
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_64565183_6   3267 AGAATTTT--GTAGATATAGATAAAAGTATTCTAAATTTTATATGAGAAA 3314
                         v vv    -- i   v  v  i  ivvv  i     v  i     ii  v
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_64565183_6   3315 GCAAAGGAAGTAGAATAGATTAAA-AATTTTGAAAAAGGA 3353
                             i   vvi       viv   -   i         i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

Transitions / transversions = 1.04 (25 / 24)
Gap_init rate = 0.02 (4 / 190), avg. gap size = 1.75 (7 / 4)  

 985 23.30 7.52 5.10  chr2_64565183_64570276.rev     3667  4078 (1016)    L1M4_orf2#LINE/L1      244   665 (243)  

  chr2_64565183_6   3667 AAAATTA-AGTAGT--AGA-AAT-TGGTCTACTGGATTTCAAGATGTATT 3711
                            ii  -    i --   - i -    --     -iv v i   iv i-
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGT--ACTGG-CATAAGGATAGAC- 289

  chr2_64565183_6   3712 ATATAATGAT-AAT--AATCAAA---AGAACTCAAAAATAAACTTACACA 3755
                              --   -   --   vi  ---   iii  i        ii i   
  L1M4_orf2#LINE/    290 ATATA--GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_64565183_6   3756 AATATGCCCAACTGATTTTTGACAAGA-TGCAAAAGCAGTTCAGTGATGG 3804
                         vv    vi   i       i      i-   v  ii vi    i  i-  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GG 386

  chr2_64565183_6   3805 TACATATG----TTTCAATAAATAGTGCTGTAGCAATAGGACATCTGTAA 3850
                         v viv  i----      i    i      vii   iv   i ? iii v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_64565183_6   3851 GCAAACAAAACAAAACAAAA-----ACCTCAAACTAAGTTGTACGTATTA 3895
                              - i  ii  iivii -----      v  i ------------  
  L1M4_orf2#LINE/    437 GCAAA-AGAATGAAGTTGGACCCCTACCTCACACCA------------TA 473

  chr2_64565183_6   3896 TACAAAAATTAACTAAAAATTGGGTTATAGACCTAAATATAA-------A 3938
                                       v     -  i i ?          i   ------- 
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAAT-GGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_64565183_6   3939 ATTATGAAACTTTTAGAAAGAAACA--GGAAAAAATCTTCAGGACCTGGG 3986
                          i   i     i      ii     --  ?iv        iv     v  
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_64565183_6   3987 GTTAGGCAGAGAGTTCTTAGTCTTGACAACAAAAGCTTA-TCCATAAAAG 4035
                                 iv iv       viv     v       vi -v v i     
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_64565183_6   4036 TAAAAATTAATAAATTGGATTTCATCAAAATTAAAAATTTTTG 4078
                         v      vi          i                 i     
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 2.00 (62 / 31)
Gap_init rate = 0.05 (21 / 422), avg. gap size = 2.48 (52 / 21)  

1112 19.92 0.78 1.17  chr2_64565183_64570276.rev     4348  4603 (491)    L1M4_orf2#LINE/L1      654   908 (0)  

  chr2_64565183_6   4348 TAAAAATTTTTGTTCTGCAAAAGGCCCTGTTAAGAGGACAAAAAGACAAA 4397
                               i      v  v    i i v  i i    iiiii         v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_64565183_6   4398 TTATGGAGTGGGAGAAAAAAATATTTGCAAACCACATATCTGACAAAG-A 4446
                         ii ii  i          ---          i  i        i  i - 
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAA---TATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_64565183_6   4447 CTAGTATCTAGAATATATAAAGAACTCTTGAAACTCAATAGTAAAACCCC 4496
                           v     i                    iv         i     vvv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_64565183_6   4497 CAAAAATCCAATTATAAAATGAGTACAGGACATGAAGGGACATTTCGCCA 4546
                         v  v  i      ?v      i i v    iv    vi        v   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_64565183_6   4547 AAGAAGACATACAAATGGAAAATAAG-ACCTGAAAAGATGTTCAACACCG 4595
                                i          vv      -  v          i      i i
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_64565183_6   4596 TTAGCCAT 4603
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.63 (31 / 19)
Gap_init rate = 0.01 (3 / 255), avg. gap size = 1.67 (5 / 3)  


2661 25.49 6.06 2.29  chr2_65029309_65035617     4985  5859 (450)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_65029309_6   4985 TGGAAGAACATTCCATGGTCATGGATAGGAAGAATCAGTACCGTGAAAAT 5034
                              ii i  i     v        v      v i i  ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_65029309_6   5035 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5084
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_65029309_6   5085 TACCAATGACTTTCTTCACAGA--TTGGAAAAAAAC--ACTTTAAAGTTC 5130
                          v   iivi i  i  ii    --   --- v  i -- iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_65029309_6   5131 ATATGGAACCGAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAA 5180
                                 vi v  ii  v  viv  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_65029309_6   5181 GAACAAGG------------------------------------------ 5188
                               i ------------------------------------------
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_65029309_6   5189 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5238
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_65029309_6   5239 CAATGGAA-AGAAC--AGAGCCCTCAGAAGTAATACCACACATCTACAAC 5285
                                 -    i--    i  --    i   vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_65029309_6   5286 CATCTGATCTTTGACAAACCTGACAAAAACAATCAATGGGGAAAGGATTC 5335
                           vi    i  i     ivv  v   i v  v             i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_65029309_6   5336 CCTATTTAATAAATGGTGCTGGGAAAACTAGCTAGCCATATGTAGAAAGC 5385
                         i  v  i  i              v    i v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_65029309_6   5386 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5435
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_65029309_6   5436 ATTAATTTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAA 5485
                           i ?-----    i       v   v       i      vi i     
  L1M4_orf2#LINE/    496 ATCAW-----AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_65029309_6   5486 GAAAACCTAGGCA-ATACCATTCAGGACATAGGCAAGGGCAAGGACTTCA 5534
                               v    ?i- v i -   iv   v v  vvvi     v ii   v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_65029309_6   5535 TGTCTAAAACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGG 5584
                          ivv  vi            vvi         ivv     v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_65029309_6   5585 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAG 5634
                           ii v  i   v v  i i   i  ii vv    i  v    ii vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_65029309_6   5635 AGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCAT 5684
                               v  i     i                 v       vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_65029309_6   5685 CTGACAAAGGGCTAATATCCGGAATCTACAAAGAACTCAATCA-AATTTA 5733
                             i  i  i  vi     i    v  i         -- i -  i --
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--TTACAACT-- 785

  chr2_65029309_6   5734 CAAGAAAAAAAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATG 5783
                            v  v     i -    i     v  i?    i            v  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_65029309_6   5784 AACAGACACTTCTCAAAAGAAGACATGTTCATCATCACTG-GC-CATCAG 5831
                           i     i     v        i  iivv  vii  v i-  -   v i
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_65029309_6   5832 AGAAATGCAAATCAAAACCACAATGAGA 5859
                          - i    ---    v i  ????????
  L1M4_orf2#LINE/    885 A-AGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (135 / 84)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.06 (73 / 18)  


2012 20.08 8.55 0.20  chr2_65362837_65365134.rev      496   998 (1300)    L1M4_orf2#LINE/L1      120   664 (244)  

  chr2_65362837_6    496 AAAAATTGGCAAGTTTGGCCCTAAAATTTATATG-AAATGAAAAGGAACC 544
                          i      i    i - ii         i     -     v  i   v  
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCT-GATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr2_65362837_6    545 AGAATA----AAAGGATTTCGAAACAGAA----AAAGATGGAGAACTTCC 586
                               ----   vi  i i    v    ----    v     i   iv 
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_65362837_6    587 ACTACCTGAATTCAAAACTTATTATAAAGCTACAGTAATGAAGAC--TGT 634
                            v  ii v           i  i              v     --   
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_65362837_6    635 AATACTGGCATAGAGGCAGATATATCGATCAATGGAATCAAAT----AGT 680
                         ii          ii ii   i    v            vi   ----   
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_65362837_6    681 CCACAAATAAACCTTTACATT-ATGGTCAGTTGATTTTCAACAATGGTGC 729
                            v         iv      -       i         i    v     
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_65362837_6    730 TAAAACAATCCA-TGGGGAAAGGGTAATCTTTTCAATGAATGATG-TGGG 777
                         i  i  v  i  -         ii  i         ii    i  -    
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_65362837_6    778 A-----GGG-----------AAAAAAAAGAACTTTGATTCTTACCTCACA 811
                          -----  i-----------    i  v   v  v  ii i         
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_65362837_6    812 TCACACATAAAAATTGATTTAAG-TGGATCATAGACCTAAATATAAAAGC 860
                         i  i i i       i i i  i-       ?          i   i   
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_65362837_6    861 TAAAACTATAAA--TTTCAGAAGAAAA---AGAGGAAAATCTTT-TGATA 904
                                     -- i i         ---  i? v       i-   iv
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_65362837_6    905 TTAAGTTAAGCAAAGTTTGCTTAGATATGACGCTAAAATCGTGATCTATA 954
                           ii    i    v v  v            i i    v iii v v i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_65362837_6    955 AAAGAAAAAATTGATAG-TTG-ACATAATAGAAATTTAAAGCTTTT 998
                                    v    i-   -  v v  vi     v   i     
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

Transitions / transversions = 2.19 (68 / 31)
Gap_init rate = 0.03 (17 / 545), avg. gap size = 2.59 (44 / 17)  

 380 16.67 0.00 0.00  chr2_65362837_65365134.rev     1723  1806 (492)    L1M4_orf2#LINE/L1      825   908 (0)  

  chr2_65362837_6   1723 AAAATATTTGAATAGATATTTTACCAAAGAAGATTTATGAATGGCAAATA 1772
                            iv           i    iv           v  ii      v    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_65362837_6   1773 AGTACATAAAAAGATATTCATCATCATTAATCAT 1806
                           i    i       ii   v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.00 (0 / 0)  


3795 23.58 0.34 0.34  chr2_65585851_65588869.rev     1628  2522 (497)    L1M4_orf2#LINE/L1        2   896 (12)  

  chr2_65585851_6   1628 GGAAATATATTCCATGTCCATGGATTGAAAGAATCAATATTGTTAAAATG 1677
                              v    i      i         i    v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_65585851_6   1678 CCCATACTGCACAAAGCAATCTGCAGATTCAATGCAATTCCTATCAAAAT 1727
                         v v     v v    vii    i         i     i           
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_65585851_6   1728 ACCAATGGCATTCTTCACAGAAATAGAAAAAAAAATCCTAAAACTTATAT 1777
                         v   iiv  v  i  ii       v  v  ivvi         i i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_65585851_6   1778 GGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCCAAGCAAAAAGAAC 1827
                             vii   ii                 i v   iii iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_65585851_6   1828 AAAACTGGAGGAATCACA-TTACTGACTTCAAATTACACTACAGAGCTAT 1876
                            ii       v     -  v ii i      vivi      i     i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_65585851_6   1877 ATTAACCAAAACAGCATGGTACTGGCATAAAAACAGATACATAGA-CATA 1925
                          v   i   i    ii              ii i   i i     -  - 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA-A 300

  chr2_65585851_6   1926 TGGAACAGAATAGAGAACCCAGAAACAAATCCACACACCTACTGTGAACT 1975
                              i     v    ii       i   i   i   ii  iv  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_65585851_6   1976 CATTTTTAACAAAGGTGCCAAGAACATCCACTGGGGAAAAGACAGTCTCT 2025
                         v     ii    i          v   i  v        ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_65585851_6   2026 TCAATAAATGGTGCTGGAAAAACTGGATATCCATATGCAGAAGAATAAAA 2075
                             i            i v         ?   i     i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_65585851_6   2076 CTAGACCCGTATCTCTCACTACATAGAATAATCGTATCAAAATGGATTAA 2125
                         i i     v  i   v   i i   v  v   iivv           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_65585851_6   2126 AGACTTAAATCTAAGACCTCAAACTATGAAACTTCTACAAGAAAACATTA 2175
                             i     v     v  v       i     ii  v          - 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-A 549

  chr2_65585851_6   2176 GGGGAAAGTCTCCAGGACATTGGTCTGGGCAAACATTTCTTGAGTAATAC 2225
                           ? v  i   i iv   v    vi i     vvi      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_65585851_6   2226 CCTTCAAGCACAGGCAACCAAAGCAAAAATGGACAAATGGGATCCCATCA 2275
                         v ivv       i     v    v      i  i    v   iii     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_65585851_6   2276 AG-TTAAAAAGCTTCCACATGACAAAGAAAGCAATCAACAAAGTGAAGAG 2324
                          i-       -   iiiiiivv     i vi v     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_65585851_6   2325 ACAACCCACAGAATGGAAGAAAATATCTGCAAACTACCCATCAGACAGGG 2374
                                         i         i      ii ivi   v  i i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_65585851_6   2375 GATTAATAACCAGAATATACAAGGAACTCAAACAATGCTATAGGGAAAAA 2424
                           i vi  v          i  i      vv    iv v   ivi    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_65585851_6   2425 TCTAATAATACAATTTAAAAATGGGCAAAAGATTTGAATAAACATTTCTC 2474
                         v v     iv     ?             i          i         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_65585851_6   2475 AGAAGAAGAGATACAAATGGCAAACAGGCATATGAAAAGGTGCTCAGC 2522
                         vi       v           v  i i   i        i      i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

Transitions / transversions = 1.84 (134 / 73)
Gap_init rate = 0.01 (6 / 895), avg. gap size = 1.00 (6 / 6)  


1512 22.86 9.25 5.76  chr2_65659712_65661697.rev      501  1073 (913)    L1M4_orf2#LINE/L1      189   781 (127)  

  chr2_65659712_6    501 GAAAAGGAAGAACAAAGGTAGA----TTATACTATCTGATTTCAAGACTT 546
                              i           v i  ---- i i   vi ii       i    
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_65659712_6    547 TTTATAAAGCGATAGTAGAAAAGGCAGTGATGGTA--------------- 581
                         vi  i     v i    ivv   i     -     ---------------
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTG-TGGTACTGGCATAAGGATAG 287

  chr2_65659712_6    582 ---------TCA---GAACAAAACAGAAAGTCAAGAAATAAACTTATATG 619
                         ---------   ---   i i  iv  i    v          ii   ii
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_65659712_6    620 TATATGGCAAATTGATTTTT-ACAAAGATGCCAAGGCACTTCAATGAAGT 668
                          v     iv          i-    i i       i vv       ii -
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG- 386

  chr2_65659712_6    669 AAAAACTAGACATT-CAACAAATGGAGCTGGGAGAATTAAATAGGCATGG 717
                            i v   v v  -          v       v  i ii   ?v  iiv
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_65659712_6    718 GCAAAAGAA--AATCTCAATCTCTAACTCATAGTATATACAAAAAATTAA 765
                                  --  vi vi i i   v    i vi           -    
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAA 485

  chr2_65659712_6    766 AATAAATTGGATCATAAACCTACACATAAGAGATAAAACTATAAAACAAA 815
                         vvi   v       ? i     v ii      v              vvv
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_65659712_6    816 CAGTAGAAAACATAGGAGAAAATCTTAGTAGCCTTGCATTGGGCAAAGAT 865
                         i  v            ? v       v  ii     vi  i     v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_65659712_6    866 TTCTTAAAAAT------AGGGACACAA-----------AAAAATCGATGA 898
                               i v  ------ iiii     -----------      v   i 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_65659712_6    899 ATTGAACTTCATCAAAACTTAAAA-TTTTACTCTTGAAAAGATACAGTTC 947
                             i            i v    -    iiv   v   i  i  vi iv
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_65659712_6    948 AGAAACAAAACTAATAAGAAAAGACAGTTAAGGAATCAATAAGGAAAGCC 997
                              --------i --         -------------------- v  
  L1M4_orf2#LINE/    686 AGAAA--------GT--GAAAAGACA--------------------ACCC 705

  chr2_65659712_6    998 AGAGACCAGGAGAAAATATTTGCAAAACAAATATCTGGTAAAAGATCTGT 1047
                          v   vii                  v  v       i   ii  ii   
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_65659712_6   1048 GTGCACAATACTTCAAAAACTCTTGC 1073
                         i v  v    iv v  i       i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTAC 781

Transitions / transversions = 1.46 (76 / 52)
Gap_init rate = 0.03 (15 / 593), avg. gap size = 5.73 (86 / 15)  

 318 16.52 21.74 0.00  chr2_65659712_65661697.rev     1382  1496 (490)    L1M4_orf2#LINE/L1      769   908 (0)  

  chr2_65659712_6   1382 AAAAAACTCTTATAACTCTATAAGAAAAAAA------------------- 1412
                            i        i     v    v     i -------------------
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_65659712_6   1413 --GGGCAAAAAAAT-GAATACATA---CTTTATAAAAGATATACAAATGA 1456
                         --       ii v -     v i ---  ii v i              i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_65659712_6   1457 AAAATAAGCACATGCAAAGATGCTCAACATGATTATTCAA 1496
                         vv            v               v ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.02 (3 / 140), avg. gap size = 8.33 (25 / 3)  


3080 24.91 6.02 0.35  chr2_65841739_65845663     2587  3433 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_65841739_6   2587 CATGT-CACAGATTAGAAGACTCAACATAGTAAAGATGTCAATTCTCTCT 2635
                              -  ii    i       i  i  v  v      v    v   i i
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_65841739_6   2636 AAATTGATCTATAGGTATAATGTTTTTACTATTAAA---------GCCT- 2675
                                    i  i vi  i ivv iv    i   ---------    -
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_65841739_6   2676 ------------------GCT------AAAATTCACATGAAAAAGGAGAG 2701
                         ------------------   ------        i   i   v v ii 
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_65841739_6   2702 GCACTGTAATAGCCAGAATAAATTTGAGAAAGAAGAAGAAAGTGGGAGAA 2751
                          vv iiv        i  i  vi    i         v     v    i 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_65841739_6   2752 ATTATTATTTT--AATGTTAAGGTTTATTATATAGTTATAATAATCAAGG 2799
                         v i i- i  i--   v i  iii   i  i v  i  i i        i
  L1M4_orf2#LINE/    214 CTCAC-ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_65841739_6   2800 CAGTGTGGTATTTACAGAAGGATAGACACATGAATCAATGGAACAGAATA 2849
                                   i vi  v           i  ii          i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_65841739_6   2850 GGGAACTCACAAACAAATCCACACAAATATACCCAGTTAATTGCTGACAA 2899
                          i  iii  v   i   i   i   vv   ivi  i  i   vii     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_65841739_6   2900 AGGAGCCGAAGCAATTTAATCGAGGAGAAATAGCCTTTTCAGTAAATGGT 2949
                         i  v   i ii v   i   v i i ii     i       ii       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_65841739_6   2950 GCTGGGGCAATTGGATATCCACAGGCAAAAAACTGGATGTCAACCAAAAT 2999
                               i   i      ?     v      i v  i vv vi   vvv i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_65841739_6   3000 CTCACACCTTGTGCAAAA-TTGACTCAAAATGGATCATGGATTTAAATGT 3048
                                 v i i     -  i               ?i  ii       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_65841739_6   3049 GAAACCCTGAACTATACAATTTCTAGAAAAAAA--TAAGAGGAAATCCTT 3096
                         i i v ivi       v  i ii     i    --  i ? v     i i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_65841739_6   3097 GTGAACTCAGAGTAGACAAAAGGTTTATAGACTTGACACCAAAAGCATAG 3146
                             v  ii iv   i   vi v  iv    iv              i i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_65841739_6   3147 TCCATAAAATAAAATATTGATAAATTGAACCTCATTGAAATTTAAAACTT 3196
                         v v i    v    v  v         i  i    ii     v       
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_65841739_6   3197 TT-TGCTTTGCAAAAGACCATTTTAAGAGGATAAAAAGGCAAATTACAGA 3245
                           -     --    i   vv v i    iii i     i   vii     
  L1M4_orf2#LINE/    663 TTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_65841739_6   3246 CTGGGA--AAACCTTTGCAAATCATGTATCTGACAAAGGACTTGTATCTA 3293
                         v     --   iv            i       i  i           i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_65841739_6   3294 GAATATACAAAGAACTCTCAAAATTGAACATTAAAAA-ACCAACAATCTA 3342
                                i          i v  i v  i v      -  v  i  i i 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_65841739_6   3343 TTTAGAAAATGGGAAAAAGACATGAACAGACATTTTT--GAAGAGGATGT 3390
                         v  ?i        v   i  iv    i        i --i    i   i 
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_65841739_6   3391 ACAGATG----ATAAGCACATGAAAA-ATGTTCATCATCATTAGGCAT 3433
                            i   ----               -   i   v     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (138 / 69)
Gap_init rate = 0.02 (15 / 895), avg. gap size = 3.60 (54 / 15)  


2984 26.90 2.12 0.78  chr2_66027978_66034934     5571  6466 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66027978_6   5571 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATCAATATCATGACAAT 5620
                               i    i     i        v      v i     ii v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66027978_6   5621 GGCCATACTGCCCAAAATAATTTATAGATTCAATGCTATTCCCATCAAGC 5670
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66027978_6   5671 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAAAACC-ACTTTAAATTT 5718
                          v   -   v    i  -i     v v  v  i--- i- iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chr2_66027978_6   5719 CATATGGAACCAAGAAAGAG-CCCATA-TAGCCAAGACAATCCTCAGCAA 5766
                                  -- v v   i -    v -       i      i v iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_66027978_6   5767 AAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTTCA 5816
                         i          i      vv    i  v  ii i      viv    v  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_66027978_6   5817 AGGCTACAGTAACCAAAACAGCTTGGTACTGGTACCAAAACAGATACATA 5866
                          i          i   i    iv         i iv ii i   i i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_66027978_6   5867 GACCAATGGATAAGAACAGAGGCCTCAGAAATAACCCCACACATGTACAA 5916
                           i       vv    iv   ivii         v    i    v  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_66027978_6   5917 CTGTCTGATCTTTGGCAAACCTGACAAAA--AG-CAATGGGGAAAGGATT 5963
                         iiivi    i  i i   ivv  v   i -- v-            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_66027978_6   5964 CCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAA 6013
                         vi  v  i  i        i     v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_66027978_6   6014 CTGAAACTGGTTCCCTACCTTACACCTTATACAAAAAGTGACTCAAGATG 6063
                         v    ii   vi        i     v          v i      i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_66027978_6   6064 GACGAAAGATTAAAATGTAAGACCTAAAACCATAAAAACCCTAGAGGAAA 6113
                           iv ?   iiv          v       i      vi i    i    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_66027978_6   6114 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAA-ATCTTCATGAC 6161
                           v    ?i- v i -   iv   v v  vv i     -ivi   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_66027978_6   6162 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 6211
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_66027978_6   6212 TAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCGTAAGAGTG 6261
                          v  i   v v  i i   i  iiivv    i  v      ivi i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_66027978_6   6262 AACAGGCAACCTACAGAATAGGAGTAAATTTTTGCAATCTATCCACCTGA 6311
                           v  i     i       i    v    v       vii  vi i    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_66027978_6   6312 CAAAGGGCTAATATCCAGAATGTGCAAGGAACTTAAACAAATTTACAAGA 6361
                         i  i  i  vi          i ii  i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_66027978_6   6362 AAAA---------CCTTATCAAAAAGTGGGCAAAGGATATGAACAGACAC 6402
                             ---------  iv  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_66027978_6   6403 TTTTCAAAAGAAGACATTTTTGCAGCCAACTAACATATAAAAAAA-GTTC 6451
                           i  v        i  vivviii     iv i  i  i    i - i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_66027978_6   6452 ATCATCCTTGGTCAT 6466
                          v    v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.86 (26 / 14)  


 433 17.14 2.86 2.86  chr2_66044812_66046481      396   500 (1170)    L1M4_orf2#LINE/L1        1   105 (803)  

  chr2_66044812_6    396 TGGGCAGATCCATCT--TGTTCA-GTATCAGAAGACTTAATATTGTTAAG 442
                            iv    --   i--      - v  ii                    
  L1M4_orf2#LINE/      1 TGGAAAGAT--ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_66044812_6    443 ATTGTCAATTTTTCCTATATTAAACTACATATTCAATTCAATCCCAATCA 492
                           v -    vi i  i v   i v     v      iv       v    
  L1M4_orf2#LINE/     49 ATGG-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_66044812_6    493 AAATCCCA 500
                                 
  L1M4_orf2#LINE/     98 AAATCCCA 105

Transitions / transversions = 1.00 (9 / 9)
Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.50 (6 / 4)  

1463 28.61 4.57 2.80  chr2_66044812_66046481      501  1178 (492)    L1M4_orf2#LINE/L1      219   908 (0)  

  chr2_66044812_6    501 ACTGCCTGATTTCAAGACTGACCATAAAGATATACTAACGACAATGGTGT 550
                            v  ii       i   v  i i    v  i v   iv vi ii    
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_66044812_6    551 AGTATTGGCATAAGGACAGACGTGGACATTTTCAGAATATAGAACAAAAT 600
                         i   i           i    i iv v  ---  ----  i   i i   
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGAT---CA----ATGGAATAGAAT 311

  chr2_66044812_6    601 AGAGATTCTAAAAATAGATCACCACATGTGTGGTCAATTGGTTTTTTTTT 650
                         v    v  i i     i i vvi    v i          i    iv---
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG--- 358

  chr2_66044812_6    651 TTATAGAGATGTCAAGAAACTTTAACTGAAGAAAGGGAATA---TTTTTA 697
                         -- i ii i  i     vvv  i  -  ii     --    ---    i 
  L1M4_orf2#LINE/    359 --ACAAGGGTGCCAAGACCATTCAA-TGGGGAAAG--AATAGTCTTTTCA 403

  chr2_66044812_6    698 AAAAATTATGATGAAGTAATTG--TAGTT-TATCTGGAAAAATGAATATT 744
                          v    vi  v  iiii  i  --  ?ii-i  viii  i      vv v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_66044812_6    745 GACCATTGCCTCACATCACACATGAAAAGTAATTCTGTATGGACTATGGA 794
                             vi i       i  i i ii    v   i  viv     ii ?i  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_66044812_6    795 ---AGCTGAAAAATGCTAAATC-ATAAAACTTGTAAAAGAAAACA--GGA 838
                         --- iv  v  i -      v -        iv  i         --  ?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_66044812_6    839 GAAAATGTTTTTGACTTTTAATTAAGCAGCGATTTCTTATATGGGGAGAA 888
                          v    v  iv    i  vii   i   ii i       v  iv ivivv
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_66044812_6    889 AAAAGTGTAAATAAT----TTAAAAAT-GATACATTTGCATCTCATAAAA 933
                              iii  ii  i----vv      -    v   v - ii    v   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG-ACTTCATCAAA 651

  chr2_66044812_6    934 ATTAAAA-CTTCTGCTTTTTTACTAATACCATTAAATAAATAAAAAGATA 982
                                -   i  ivi  iv vvi i  i  i  iv  i i      i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_66044812_6    983 A---ATGAGATATGGCAGAAAACAGT--CAAA--ATAC-TATGATAAAGT 1024
                          --- i-   -    v      i v --    --   i- v      i v
  L1M4_orf2#LINE/    702 ACCCAC-AGA-ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_66044812_6   1025 ATGTATATATAGAATATA-AAAAAACTCTTACAATTCAATAGTAAGAGCA 1073
                          iv i   vi        -   i           i      i   i iv 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_66044812_6   1074 CGAA-AGGTAAA--GAAAAATTAGCAAAACATTTGAACAGACACTTA-CC 1119
                          i  - iviv  --?      vi     iv       i     i  v-  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_66044812_6   1120 AGAGAAGATACATGAATAACTAACATGAATATGAAAAGATACTCTACATC 1169
                          i        i ii   ii i  i v v i          i   v     
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_66044812_6   1170 ATTAGTCAT 1178
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.88 (124 / 66)
Gap_init rate = 0.04 (26 / 690), avg. gap size = 1.92 (50 / 26)  


3146 26.91 1.11 0.55  chr2_66063226_66069628.rev     5009  5911 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66063226_6   5009 TGGAACAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5058
                              vi i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66063226_6   5059 GGCCATACTGCCCAAAGCAATTTATAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v      vii  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66063226_6   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_66063226_6   5157 TATGCAACCAAAAAAGAGCGTGCATTGCCAA-----TCCTAAGCCAAAAG 5201
                             v  viiv  ii  v vv v  v     -----  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_66063226_6   5202 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACGAGAC 5251
                                i      vv   ii  v  ii i      viv      i ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_66063226_6   5252 TACAGTAACCCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5301
                                 i -  i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    249 TACAGTAATC-AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_66063226_6   5302 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATGTCTACAAC 5349
                                 i    i--    i  --        vv   i ii i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_66063226_6   5350 TATCTGATCTTGGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5399
                         i vi    i  v     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_66063226_6   5400 CCTGTTTAATACATGGTGCTGGGAAAACTGGATAGCCATATGTAGAAAGC 5449
                         i  v  i  i v            v         ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_66063226_6   5450 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5499
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_66063226_6   5500 ATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5549
                           i ?    i  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_66063226_6   5550 CCTAGGCATCACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5599
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_66063226_6   5600 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5649
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_66063226_6   5650 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5699
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_66063226_6   5700 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5749
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_66063226_6   5750 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5799
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_66063226_6   5800 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5849
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_66063226_6   5850 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACA-GAAAAAATGCTCAC 5898
                            v        i  vi viii     v  i    -     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_66063226_6   5899 CATCACTGGCCAT 5911
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


3172 27.26 0.66 0.44  chr2_66102103_66108499.rev     5000  5905 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66102103_6   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTAAAAAT 5049
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66102103_6   5050 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5099
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66102103_6   5100 TACCAATGACTTTCTTCACAGAATTGGAAAAAACGACTTTCAAGTTCATA 5149
                          v   iivi i  i  ii     v v  v  ivi  iii v  i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_66102103_6   5150 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5199
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_66102103_6   5200 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5249
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_66102103_6   5250 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5299
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_66102103_6   5300 TGGAACAGAAC--ACAGCCCTCAGAAATAATGTTGCATATCTACAACTAT 5347
                              i    i-- v  i  --        vviiii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_66102103_6   5348 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5397
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_66102103_6   5398 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5447
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_66102103_6   5448 AACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5497
                          ii    iv   v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_66102103_6   5498 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5547
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_66102103_6   5548 AGGCA-ATACCATTCAGGACAT-GGCATGGGCAAGGACTTCATGTCTAAA 5595
                            ?i- v i -   iv   v -  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_66102103_6   5596 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5645
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_66102103_6   5646 TTAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5695
                         iv  v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_66102103_6   5696 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5745
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_66102103_6   5746 GGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAAA 5795
                           i  vi          v  i  v      iv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_66102103_6   5796 AACAAACAACCCCATCAAAAAGTGGACGAAG-ACATGAACAGACACTTCT 5844
                         i     i     v  i?    i   i i   - iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_66102103_6   5845 C-AAAGTAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5893
                          -    -    i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    848 CCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_66102103_6   5894 ATCACTGGCCAT 5905
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


2442 24.17 1.67 1.67  chr2_66167956_66169663.rev      497  1216 (492)    L1M4_orf2#LINE/L1      189   908 (0)  

  chr2_66167956_6    497 GAAAGCAAAAAGAACAAATCTGTAGGCATCACATTACCCGACTTCAAACT 546
                             --  i         vi  v   vv     i v   i i      vi
  L1M4_orf2#LINE/    189 GAAA--AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_66167956_6    547 ATAATACAAGGCCAGAGTTGAGTTACCAAAACAGCATAGTGCTGGTATAA 596
                         v  v     i  i v   -- i ---   i    ii i  i    i    
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGT--AAT---CAAGACAGTGTGGTACTGGCATAA 281

  chr2_66167956_6    597 AAATAGGCACACAGACCAATGGAACAGAATAGAGAACCCAGAAATAAACC 646
                         ii    i  i i   i        i     v    ii             
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_66167956_6    647 CAAATACTTACAGCCAACTGATCTTCGACAAAGCAAACAAAAC-ATACAG 695
                           v i i   ii i   i    i        i vviv   i  -  v  i
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_66167956_6    696 TGGGGAAAGAACACCCTGTTCAACAAATGGTGCTGGGATAATTGGCAAGC 745
                                    i vi  v                    i  i   vv ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_66167956_6    746 CACGTGTAGAAGAATGAAACTGGGTCCTCATCTCTCACCCTATATAAAAA 795
                            i  i i         ii   ii  ii i   v    v    i     
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_66167956_6    796 TAAGCTCAAGATGGATCAGAGACTTAAATCTAAGATCTGAAACCATAGAA 845
                          v i     i        ?    i     v     v  i    i   i  
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_66167956_6    846 ATTCTAGAAGATAACATCGGAAAAACTCTTCCAGACATTGGCTTAGGCAA 895
                         v ii       v     v  ?iv  v     vv   v    v        
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_66167956_6    896 AGACTTCAT-GATCAAGAACCCCAAAGCAAATGCAATAAAAACAAAGATA 944
                         v ii   v -   - v  vv  v      v v    i    iv   i   
  L1M4_orf2#LINE/    582 TGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_66167956_6    945 AATAGATGGGACTT-----AAACTAAAAAGCTTCCACACAGCAAAAATAA 989
                         i   i  v      -----   i      -   iiiii vv    ii-- 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGG--A 677

  chr2_66167956_6    990 TAATAATCAGCAGAGTTAACAGACAACCCACAGAGTGGGGGAAAATATTA 1039
                         i v  -   iv i   v  v              i    i         v
  L1M4_orf2#LINE/    678 CACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_66167956_6   1040 ACAATCTATA-ATCCAACAACAGACTAATATCCAGAATCTACAAGGAACC 1088
                         i   vii   -   ii i  vi    vi          v  i  i    i
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_66167956_6   1089 CAAACAAATCAGCAAGAAAAAAACAA----CCCCATCAGAAAGTGGTCTA 1134
                          vv    v   ii  v     i    ----   v  i?i   i   v v 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_66167956_6   1135 AGGACATGAAAAGACAATTCTCAAAAGAAGATACAAAAATGGCCAGCAAG 1184
                             iv    v     v     v          i v         ii   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_66167956_6   1185 CATATGGAAAAATGCTCAAAATCACTAATTAT 1216
                           i   i   i        v    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (103 / 67)
Gap_init rate = 0.02 (12 / 720), avg. gap size = 2.00 (24 / 12)  


2300 29.21 2.97 0.50  chr2_66225693_66230470     2865  3672 (1106)    L1M4_orf2#LINE/L1        1   828 (80)  

  chr2_66225693_6   2865 TGGAAACACATTTTATGCTGATGGATGGGTAGAATCAATATTATGAAAAT 2914
                               v i  iii   i v      v  v   v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66225693_6   2915 GACCCTCCTGTCAAAGGCAATCTACAAATTCAATGCAATTCCCACCAAAA 2964
                          i vv v  vi v  ivii       i      i     i  i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66225693_6   2965 TACCACCATAATTCTTCACAGAACTAGAAAAAC-AATCCTAAAACTCATA 3013
                          v   v vvvv  i  ii     v v  v  i -i         i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_66225693_6   3014 TGGAACCAAAAAAGAGCCCACATCGCCAAAGCAACACTCATCAAAAAGAA 3063
                              viiv  ii  v  viv  v      i   ivi v vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_66225693_6   3064 CAACTCTAGAGGCATTACATTACCCGACTTCAAACTATACTACAAGGCCA 3113
                            vvi i    vv i   i v   i i      viv        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_66225693_6   3114 TAGCCACCAAAACAGCTTGGTAGTGGTATAAAAATGG-CATACAGACCAA 3162
                         i  iv i   i    iv     v   i    ii  i -    i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_66225693_6   3163 TGGAACAGAATAGAGAACCCAGAAAAGAAAAAAGCCAAATACTTACAGTC 3212
                              i     v    ii       v----   v   v i i   ii   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAAT----AAACCCATACATTTATGGTC 346

  chr2_66225693_6   3213 AACTGATCTTTGACAAAG---CAAAGAAAAA-CATGGGGGAAAGGACACC 3258
                           i    i  i     i --- v    vv v-  vv        i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_66225693_6   3259 GTAGTCGACACATGGTGCTGGGATAATTGGCAAGCCACAGGTAAAAGAAT 3308
                         v vv  i   v            i  i   vv ?     v i        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_66225693_6   3309 GAAACTGGGTCCTCATCTCTCATCCTATACCAAAATCAACTCAAGATGGA 3358
                            ii   ii  ii i   v  i v     v     i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_66225693_6   3359 TTGAAGACTTAAATCTAAGACCTGAAACCATATACGTTCTAGAAGATAAC 3408
                          ii?    i     v     v  i    i   v vv ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_66225693_6   3409 ATTGGAAAAACCCTTC------------TAGACACGGG---CTTAGAGA- 3442
                           v  ?iv  vi    ------------   i  vv  ---      v -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_66225693_6   3443 -AC-CCAAAAGCAAATGAAACAAAAACAAAGATAAATAGGTGGAACTTAA 3490
                         -  -         v v v       iv   i   i   ii v i    v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_66225693_6   3491 TTAAATTCAAAAGCTTCTGCACAGCAAAAGAAACAATCAGCAGAGTAAAC 3540
                          i   v i    i   i  ii vv    i  v  v    iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_66225693_6   3541 AGACAACCCACAGAGTGGGAGAAAATCTTCACCATCTGTACATCCAACAA 3590
                                       i           v  ii v viii  i   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_66225693_6   3591 AGAACTAATATCCAGAATCTACAAGGAACTCAAGCAAATCAGCAAGAACA 3640
                         i i   vi          v  i  i      vvi   v   ii  v  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_66225693_6   3641 AAACAAAGCATGCCATCAAAAAGTGAGCCAAG 3672
                          i     vv iv v  i?    i  i  v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.27 (130 / 102)
Gap_init rate = 0.01 (9 / 828), avg. gap size = 3.11 (28 / 9)  

 344 13.33 10.00 0.00  chr2_66225693_66230470     4197  4286 (492)    L1M4_orf2#LINE/L1      810   908 (0)  

  chr2_66225693_6   4197 AATTAAAAAA-----AAAAGA----AAAAGACAATTTTCAAAAGAAGATA 4237
                             ?     -----   i  ----  v     v  i  v          
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_66225693_6   4238 TATAAATGGCCAACAAACATATGGAAAAATGCTCAACATCACTAATCAT 4286
                           i          i  i  i   i   i             ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.02 (2 / 99), avg. gap size = 4.50 (9 / 2)  


3274 26.91 0.89 0.33  chr2_66277982_66284222.rev     4847  5749 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66277982_6   4847 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4896
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66277982_6   4897 GGCCATACTGCCCAAGGTAATTTACAGATTCATTGCCATCCCCACCAAGC 4946
                            v     v     iv i  i          vi  v     i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66277982_6   4947 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 4995
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_66277982_6   4996 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCATAAGCCAAAAGAA 5045
                              viiv  ii  v  v v  v     iv     v i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_66277982_6   5046 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5095
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_66277982_6   5096 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5145
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_66277982_6   5146 TGGAACAGAACGGAGCCCTCAGAAATAACATCGTATATCTACAACTATCT 5195
                              i    iv   vvii         vvi i  i  i  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_66277982_6   5196 GATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTAT 5245
                            i  i     ivv  vv  i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_66277982_6   5246 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5295
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_66277982_6   5296 CTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAA 5345
                         i    i    v   i     v           i  i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_66277982_6   5346 AGACTTAAACGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAACCTAG 5395
                             i    i  v   v  i    i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_66277982_6   5396 GTGTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCAAA---A 5442
                          ?  v viv   iv   v v  vv i     v ii   --- i i ---i
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC---TTAGATATG 597

  chr2_66277982_6   5443 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCGAAT 5492
                                     vvi           v     v  i    v   iivv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_66277982_6   5493 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5542
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_66277982_6   5543 GGCAACCTACAAAATGGGAGAAAATTTTTGCGATCTACTCATCTGACAAA 5592
                          i     i   i             v     i vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_66277982_6   5593 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5642
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_66277982_6   5643 AACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAAAAGACACTTCT 5688
                         i    ----   v  i?    i           iv    v     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_66277982_6   5689 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCA 5738
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_66277982_6   5739 TCACTGGCCAT 5749
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.75 (11 / 4)  


3286 27.37 0.22 0.00  chr2_66315454_66321733     4883  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66315454_6   4883 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4932
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66315454_6   4933 GACCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4982
                          i v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66315454_6   4983 TACCAGTGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5031
                          v    ivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_66315454_6   5032 TGGAACCAAAAAAGAGCCCGCACCGCCAAGTCAATCCTAAGCCAAAAGAA 5081
                              viiv  ii  v  v v iv     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_66315454_6   5082 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAATGCTA 5131
                              i      vv       v  ii i      viv        v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_66315454_6   5132 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5181
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_66315454_6   5182 TGGAACAGAACGGAGCCCTCAGAAATAATGCCGCACATCTACAACTATCT 5231
                              i    iv   vvii         vv  ii    i  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_66315454_6   5232 GATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTAT 5281
                            i  i     ivv  vv  i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_66315454_6   5282 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5331
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_66315454_6   5332 CTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAA 5381
                         i    i    v   i     v           i  i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_66315454_6   5382 AGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5431
                             i    i  v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_66315454_6   5432 GCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACA 5481
                          ?i v viv   iv   v v  vv i     v ii   v ivv  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_66315454_6   5482 CCAAAAGCAATGGCAACAAA-GCCAAAATTGACAAATGGGATCTAATTAA 5530
                                  vvi        - vv     v  i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_66315454_6   5531 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 5580
                          v v  i i   i  ii vv    i  v    i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_66315454_6   5581 AACCTCCAAAATGGGAGAGAATTTTCGCAACCTACTCATCTTACAAAGGG 5630
                             iv  i         i   v  i    vii ivi    v i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_66315454_6   5631 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 5680
                           vi          v  i  v      vv    v iv i  v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_66315454_6   5681 AAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCAA 5730
                            i     v  i?    i           iv    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_66315454_6   5731 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCA 5780
                                i  vi viii     v  i          i       v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_66315454_6   5781 CTGGCCAT 5788
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 1.00 (2 / 2)  


3157 26.83 1.33 0.67  chr2_66344613_66350913     4908  5809 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66344613_6   4908 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4957
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66344613_6   4958 GACCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5007
                          i v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66344613_6   5008 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5055
                          v    ivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_66344613_6   5056 TATGGAACCAAAAAAGAGCCCACATCAAC-AAGTCAATCCTAAGCCAAAA 5104
                                viiv  ii  -    v vi i -  iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_66344613_6   5105 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATAGTACAAGG 5154
                                 i      vv       v  ii i      viv  v     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_66344613_6   5155 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5204
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_66344613_6   5205 CAATGGAACAGAACGGAGCCCTCAGAAATCATGCCGCATATCTACGACTA 5254
                                 i    iv   vvii       v vv  ii i  i  i iii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_66344613_6   5255 TCTGATCTTTGACAAACCTGAGAAAACAAG-CAATGGGGAAAGGATTCCC 5303
                         vi    i  i     ivv  vv  i  v v-            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_66344613_6   5304 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5353
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_66344613_6   5354 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5403
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_66344613_6   5404 TAAAGACTTAAACGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAACC 5453
                         i ?    i    i  v   v  i    i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_66344613_6   5454 TAGGCATTACCATTCAGGACATGGGCATGGGCAAGGACTTCATGTCAAA- 5502
                             ?i v viv   iv   v v  vv i     v ii   --- i i -
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC---TTAGAT 594

  chr2_66344613_6   5503 --AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5550
                         --i            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_66344613_6   5551 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCGGAGTGA 5600
                         v  i   v v  i i   i  ii vv    i  v    i  vvii     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_66344613_6   5601 ATAGGCAACCTATAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5650
                          v  i     i i i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_66344613_6   5651 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5700
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_66344613_6   5701 AAA--C---CAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5745
                            -- ---i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_66344613_6   5746 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5795
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_66344613_6   5796 CCATCACTGGCCAT 5809
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


1256 27.60 8.00 5.20  chr2_66426838_66429994.rev     1340  2089 (1068)    L1M4_orf2#LINE/L1        1   771 (137)  

  chr2_66426838_6   1340 TAAAATGGTACCCTATATCTATTTGTTG----ATTCAATATTAT-AAAAT 1384
                          ii  v i  i  i  i ii  vvi   ---- i i      i -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66426838_6   1385 TTAAAT-TTCCTCAAATTAACACATAAGCTTAATGAAATTACAAAAAGAA 1433
                         vvv   -i   i      i ivi i iii i  i v   iv -----v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC-----TAT 95

  chr2_66426838_6   1434 CACAAATTATAATTCTTATTTTATTTTGGATGCAAGATTTGATAAAATAA 1483
                           -    ivi ii viiv    --------    ii v    i  iv i 
  L1M4_orf2#LINE/     96 CA-AAATCCCAGCTGCCTTTTT--------TGCAGAAATTGACAAGCTGA 136

  chr2_66426838_6   1484 ATCTAAAATTTATCTGAAAGAATAAATGAATAAAAATTCCCAGGA-AATT 1532
                         vi        i  v  i  ivii  iv  viv i   vv   ii -   i
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_66426838_6   1533 TTGTAAAAAATGTAACA-----GGAGAATATTTGTGTCATAC-----AAT 1572
                            v    i v -    -----    i i-------   i  -----   
  L1M4_orf2#LINE/    187 TTGAAAAAGAAG-AACAAAGTTGGAGGAC-------TCACACTTCCCAAT 228

  chr2_66426838_6   1573 ATTAAAA--TACTTTAATTCTAAAATAAGAAAAGT--TTTTCTACTAATA 1618
                         v i    --    vi  vv   v i   vv  iii-- v vv    iii 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_66426838_6   1619 TATGAATTGACAAACAGATTTCTGGAAGGAAATTAAGTGTTTAAAAATAA 1668
                           v i  v    v i    ivv     vii    i  v  ii i      
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_66426838_6   1669 -----------TAT------TTGA-----GA-AAAGGTAGCATTTCAAGT 1695
                         -----------   ------    -----  -  i   iv  vvv v v 
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_66426838_6   1696 GAGTAGAAAAAGAAAAATGTTTTTTGCACAAAACGGTTCTCAGATAGTAG 1745
                         v i i ii      v --  i    vv     -i   v  vi  i iiv 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATA--GTCTTTTCAACAAA-TGGTGCTGGGACAACTG 425

  chr2_66426838_6   1746 ATTAACTATTTGAAAAAAGTTCCAAAAGGAATAATAATTTGAT---TATC 1792
                         iv  ? i iv  ----------      -   i - i  v  i---  i 
  L1M4_orf2#LINE/    426 GATAKCCACATG----------CAAAAG-AATGA-AGTTGGACCCCTACC 463

  chr2_66426838_6   1793 TT------TAAAGAACAATCA-TTTAATTTGGATCACAGATATAAATGTA 1835
                          i------  v v  v   i -i i  vv       ?   iv        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_66426838_6   1836 AGAGATAAAAATTATAAAATGTTTAGAAGAAAACA--GGCATAAATCTTC 1883
                             v     -i       ivi             --  ?i         
  L1M4_orf2#LINE/    514 AGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_66426838_6   1884 ATGACCTTGGATTAGGCAATGGTTTCTTAGATATGACACCAAAAGCATAA 1933
                         i         i                                    i  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_66426838_6   1934 GCAACAAGAGAAAAAGGTAAATAAAATGCACTTCATCAAAATTTAAAATT 1983
                                i       i-  i     v  v              v    i 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_66426838_6   1984 TTCGTGTTTTAAAAGACATCATGAA-AGAGTAGGAATGCAATCCATAGCA 2032
                           i   i  i   i    ii  v  - i   iii  vi   i   i  v 
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_66426838_6   2033 TGG-AGAAAGTATTTGCAAATTACGTGTTGGATCAG--ACTTGTATTAAT 2079
                            -     i           i ii i iv   v  --        iv v
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_66426838_6   2080 GATATGTAAA 2089
                         i    i    
  L1M4_orf2#LINE/    762 AATATATAAA 771

Transitions / transversions = 1.65 (127 / 77)
Gap_init rate = 0.04 (31 / 771), avg. gap size = 3.19 (99 / 31)  

 719 16.56 0.66 1.99  chr2_66426838_66429994.rev     2524  2674 (483)    L1M4_orf2#LINE/L1      760   908 (0)  

  chr2_66426838_6   2524 AGAATATGTAAAGAACTCATTCAATTCAACAACAAAAAGGCAAGTAATCC 2573
                                i          v v   i    i  i      i   i   i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_66426838_6   2574 AATTTAAAAATGGGTAAAGAGTTTGAATAAACCTTTCTCAGAAGAATGTG 2623
                             ?         i    ii        i  v      vi     vi i
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_66426838_6   2624 TACAAATGGCCAATAAACACGTGGAA-GATGCTCAGTAAGATTAGTCATT 2672
                                         i   i  i  -        --- v  i ??????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCA---ACATCAZZZZZZ 906

  chr2_66426838_6   2673 AA 2674
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 3.00 (18 / 6)
Gap_init rate = 0.01 (2 / 149), avg. gap size = 2.00 (4 / 2)  


3067 18.34 5.62 1.04  chr2_66459333_66461000      501  1176 (492)    L1M4_orf2#LINE/L1      202   908 (0)  

  chr2_66459333_6    501 AAATTTGGAGGGCTCATACTTCCTGTTTTCAAAACTTACTACAAAGCTAG 550
                            v       i    i      iiv                       v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_66459333_6    551 AGTGATTTTTTTTTTTGTGTAGTACTCTGGCATAAGGAGAGACA-ATAAG 599
                            i  ivvvviv---    i     --          v     -   ii
  L1M4_orf2#LINE/    252 AGTAATCAAGACA---GTGTGGTACT--GGCATAAGGATAGACATATAGA 296

  chr2_66459333_6    600 GC-------CAGAATTGAGAGTCTA------------TACATCTATGGCC 630
                         v -------i             i ------------     i     i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_66459333_6    631 AATTGATTTTCAATAAGGGTGCCAAAACCATTCA-TGGGGAAATATTAGA 679
                                    i i           i        -        v v   v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_66459333_6    680 ATTTTCAACAGA--ATGCTGGGTCAGCTAAGTATCTACATGCAATAGAAT 727
                         v         i --i       v  i  iii  ? i        v     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_66459333_6    728 AAAGCACGACCCCTACCTTGCACCAAAAAAAAATTTTCACTCAAAATGGA 777
                         i   ivv           ii     v v v   vv  v            
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_66459333_6    778 TCAAAGACCTACGTACAAGAGCTAAAATGATCAAACTCTTAGAAGAAAGC 827
                            ?       vi ii           iv  v                i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_66459333_6    828 A--GAGGTAAATCTTCATGATCTTGAATTTGGCAATCGCTTCTTAGCTAC 875
                          -- i?          i   i    ii  v      v i       v  i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_66459333_6    876 AATACTTCCAAAGTA---GGAACAGAA-------TAAATAAATTGGATTT 915
                         i i  -- v    i --- v    i  -------  i          i  
  L1M4_orf2#LINE/    597 GACAC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_66459333_6    916 AATCAGAATTAAAAATTTTTTTGCATCAAAGGACATGATTCAGAAAGTGA 965
                         v    i         i    v   v          iv  iv         
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_66459333_6    966 AGACACAAGCTGTAGCATGAAAGAAAATATTTA-AAATCACATATCTGAT 1014
                          i v    v iii  v   ii           i-      i         
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_66459333_6   1015 --GATCCTAGTATCCAGAATATATAAAGAACTCTTACAACTCAATGGCAA 1062
                         -- ivv  v                                    iii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_66459333_6   1063 AAAGACAAATAGCCAAACACAGAAATGGGCAAAGGATTTGAATATTCATG 1112
                                    i  v  iv? i                      vv   v
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_66459333_6   1113 TCTGCAAAGATGATATACAAGTGACCAACAAGCATATAAAAAGATGCTCA 1162
                            v      v         i  i    i     i  i            
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_66459333_6   1163 ACATCATTAGACAT 1176
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (70 / 50)
Gap_init rate = 0.02 (13 / 707), avg. gap size = 3.46 (45 / 13)  


3277 26.32 0.44 0.44  chr2_66485919_66492309.rev     4992  5899 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66485919_6   4992 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5041
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66485919_6   5042 GGCCATACTGCCCACGGTAATTTATAGATTCAATGCCATCCCCATCAAAC 5091
                            v     v    viv i  i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66485919_6   5092 TACCAGTGACTTTCTTCACAGAA-TTGAAAAAAACT-ACTTTAAAGTTCA 5139
                          v    ivi i  i  ii     -    v  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_66485919_6   5140 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5189
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_66485919_6   5190 AACAAAGCTGGAGGCATCACGGTACCTGACTTCAAACTATACTACAAGGC 5239
                                i      vv    iv v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_66485919_6   5240 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5289
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_66485919_6   5290 AATGGAACAGAACGGAGCCCTCAGAAATAATTCCTCACATCTACAA-CAA 5338
                                i    iv   vvii         vi  vi    i  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_66485919_6   5339 TCTAATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5388
                          - i  i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_66485919_6   5389 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACTA 5438
                          v  i  i              v      v  ?   i   i i  i v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_66485919_6   5439 AAACTGGATCCCTTCGTTACACCTTATAAAAAAATAAATTCAAGATGGAT 5488
                           ii    i    v v i     v    v      v  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_66485919_6   5489 TAAAGACTTACATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAACC 5538
                         i ?    i  v    v   v  i    i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_66485919_6   5539 TAGGCA-ATACCATTCAGGACATAGGCATAGGCAAAGACTTCATGTCTAA 5587
                             ?i- v i -   iv   v v  vv       v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_66485919_6   5588 AACACCAAAACCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5637
                         i         v  vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_66485919_6   5638 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAA 5687
                          i   v v  i i   i  ii vv    i  v       vv i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_66485919_6   5688 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5737
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_66485919_6   5738 AGCGCTAATATCCAGAATCTACAAAGAACTCCAACAAATTTACAAGAAAA 5787
                         i vi  vi          v  i         iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_66485919_6   5788 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5837
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_66485919_6   5838 TCAAAAGAAGACATTTATGCAGCCAGAAAACACATGAAAAAATGCTCATC 5887
                           v        i  vi viii    iv  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_66485919_6   5888 ATCACTGGCCAT 5899
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


3310 26.87 0.44 0.44  chr2_66529414_66535681     4869  5776 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66529414_6   4869 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4918
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66529414_6   4919 GGCCATACTGCCTAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4968
                            v     v  i  iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66529414_6   4969 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5016
                          v    ivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_66529414_6   5017 TATGGAACCAAAAAAGAGCCCGCATCACTAAGTCAATCCTAAGCCAAAAG 5066
                                viiv  ii  v  v v  vi i  iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_66529414_6   5067 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATAATACAAGGC 5116
                                i      vv       v  ii i      viv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_66529414_6   5117 TACAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5166
                                 v   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_66529414_6   5167 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5214
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_66529414_6   5215 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5264
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_66529414_6   5265 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5314
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_66529414_6   5315 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5364
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_66529414_6   5365 TTAAAGACTTAAACGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAAC 5414
                          i ?    i    i  v   v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_66529414_6   5415 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5464
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_66529414_6   5465 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5514
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_66529414_6   5515 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5564
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_66529414_6   5565 AGGCAACCTACAAAATGGGAGAGAATTTTCGCAACCTACTCATTTGATAA 5614
                           i     i   i         i   v  i    vii ivi  i      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_66529414_6   5615 AGGGCTAATATCCAGAATCTACAAAGAACTCCAACAAATTTACAAGAAAA 5664
                         i  i  vi          v  i         iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_66529414_6   5665 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5714
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_66529414_6   5715 TCAAAAGAAGACATTTATGCAGCCAGAAAACACATGAAAAAATGCTCATC 5764
                           v        i  vi viii    iv  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_66529414_6   5765 ATCACTGGCCAT 5776
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3667 20.27 4.90 1.82  chr2_66544442_66546412      603  1480 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_66544442_6    603 AAAGATATGCTTTGTTCATGGTTCAGAAAACTCAGTATTGTCAAGATGTC 652
                                 v iv         v ii   i   i i      i      v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_66544442_6    653 AGTTCTCCCCAAGTTAATCTATAGATTCAACACAAATTCTAATCAAAATC 702
                          i v        i  i     i         i   vii   -        
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAAAATC 102

  chr2_66544442_6    703 TCTAAAGTTTTTTTTTTTTTGGTATACACTGACAAACTGATTGTAAAATT 752
                         i ---  i vii      --- i v v i      i     iv       
  L1M4_orf2#LINE/    103 CC---AGCTGCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_66544442_6    753 CCTGTGAGAATACAAAAGACCTAGAATAGCGAAAACAATTGTG-----GG 797
                          v i  ii   i   ii    i        v        iv  ----- i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_66544442_6    798 GGAA---AGTTGCAAGACCAACACTATCTCATTTCAAGACTTCTTATAAA 844
                         i   ---     v i   iv     vi iv       i    vi  i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_66544442_6    845 ACTACAGAAATTAAGACAATATGACAGTCATGTGTAGATAGACAAATAGA 894
                         i      v   i      i i  ii v viii ivi        v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_66544442_6    895 TCAATGAAATAAA-----GAATTCACAAATAGACCCACACATACATGGAC 939
                               i    i -----  i i  v     i     i    vi    v 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_66544442_6    940 AAGTGATTTTTGACAAGT-TACAAAGGCAACTCAATGAAGAAAGAATAAT 988
                           v       i      v- i v   i v i      ii         i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_66544442_6    989 CTTTTGAACAAATTGTGCTGGAGCAATTGAATACTCATACACAAAAAAAT 1038
                              v       v       ii   i  i   ?i  i ii     i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_66544442_6   1039 GAACTTTAACCTACACCTCCCTCCAGATGTAAAAATTAACTCAAAACAGA 1088
                            v  vi   ivi     v v   v  ii                ii  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_66544442_6   1089 TCATAAGCCTAAATGTAAGAGCTAAAACTATAAAACTCTTGGAATAAA-C 1137
                            ? ii                                 i   v   - 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_66544442_6   1138 AT----------CTTTGCAACCTTGGATTAGGCAATAGCTTCTTAACTAT 1177
                           ----------   i ii       i         i i      iv   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_66544442_6   1178 GACACTAAAA-CACAAGCACCAAAAGAAAAAAAAAGATAAATTGGATTTC 1226
                              i    -        v            v -           i   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTC 645

  chr2_66544442_6   1227 ACCAAAA--AAG----TTTGTGCTTCGAAGGACATTATCAAGATAGTGGG 1270
                          i     --  i----          i       i        v    --
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG-- 693

  chr2_66544442_6   1271 AAAAAAAAAAAACCACAGAATGGGAACAAATATTTGTAAATCATGTATCT 1320
                         --    i v  v             iv         i       i     
  L1M4_orf2#LINE/    694 --AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_66544442_6   1321 GATAAGGAATGTATATGTAGA-TATATAAAGAA-------GA---AATGG 1359
                                i iv i   vi   -           -------i ---   ii
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_66544442_6   1360 TAAAAACAACTAAAAACAAGTCAATTTAAAAATGGGCAAAAGACTTGCAT 1409
                               -i  ---   i  vi     ?             i  i   v  
  L1M4_orf2#LINE/    792 TAAAAA-GAC---AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_66544442_6   1410 AGACATTTCTTCAATAAAGATATACAATTGGTCAATAAGCACATAAGATT 1459
                                   i   vi           v   i            i i vv
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_66544442_6   1460 ATGATCAGTATCTTTAGTGAT 1480
                            v   ii   v????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (119 / 56)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 3.11 (59 / 19)  


3033 27.12 1.90 0.56  chr2_66748679_66755041.rev     4976  5871 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66748679_6   4976 TGGAAGAACATTCCATGCTCATGGATAGGAAGAGTCAATATAATGAAAAT 5025
                              ii i  i     i        v      v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66748679_6   5026 GGCCATTCTGCCCAAGGTATTTTGTAGATTCAGTGCCATCCCCATCAAGC 5075
                            v  v  v     iv iv i ii       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66748679_6   5076 TACCAATTACTTTCTTCACAGAG-TTGGAAAAAACTGCTT-TAAAGTTCA 5123
                          v   ii i i  i  ii    i-   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_66748679_6   5124 TATGGAACCAAAAAAGAGCCCACATTA-CCAAGACAATCCTAAGCAAAAA 5172
                                viiv  ii  -    v v  -    i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_66748679_6   5173 GAATAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGG 5222
                            i    i      vv       v  ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_66748679_6   5223 CTACAGTAACCAAAATAGCATGGCACTGGTACCAAAACAGACATGTAGAG 5272
                                  i   i i  ii   i     i iv ii i      i    v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_66748679_6   5273 CAATGGAACAAAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5322
                                 i i  iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_66748679_6   5323 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5372
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_66748679_6   5373 TATTTAATAAATGGTGCTGGGAAAACTGGCTAACCATATGTAGAAAGCTG 5422
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_66748679_6   5423 AAACTGGATCCCTTCCTTAGACCTTATTCAAAAATTAATTCAAGATGGAT 5472
                           ii    i    v   i v   v   v          i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_66748679_6   5473 TAAAGACTTAAATGTTAGACCTAAA-CCATAGAAACCCTAGAAGAAAACC 5521
                         i ?    i       v   v     - i   i  vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_66748679_6   5522 TAGGCA-ATACCATTCAAGACATAGGCATGGGCAA---------AGACTA 5561
                             ?i- v i -   iv   v v  vv i     ---------   -  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TA 595

  chr2_66748679_6   5562 AAACACCAAAAGCAATGGCCACAAAAGCCAAAATAGACAAATGGGATCTA 5611
                         vi            vvi  v       vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_66748679_6   5612 ACTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5661
                          ii   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_66748679_6   5662 CAGGCAACCTACAGAATGGAAGAAAATTTTTGCAATCTACCTGTCTGACA 5711
                         v  i     i         i       v       vii iv i     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_66748679_6   5712 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACG-TGAA 5760
                          i  i  vi          v  i        ivv    v iv ii- i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_66748679_6   5761 AAAACAAACAAGCCCATCAAAAAGTGGGTGAAGGATATAAACAGAGACTT 5810
                           i     i  v  v  i?    i    ii      v i  i   v i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_66748679_6   5811 CTCAAAGGAAGACATTTATGCAGCCAACAG--ACATGAAAAAATGCTCAT 5858
                            v  i     i  vi viii     i i--         i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_66748679_6   5859 CATCACTGGTCAT 5871
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (148 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


 987 26.64 4.50 0.69  chr2_66756135_66760684.rev      216   504 (4046)    L1M4_orf2#LINE/L1        1   300 (608)  

  chr2_66756135_6    216 TGGAAGAACATTCCATGCTCATGGATAAGAAGAATCAATATCATGAAAAT 265
                              ii i  i     i        vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66756135_6    266 GGCCATACTGCCCAAAGTAATTTATAGATTCGATACCATTCCCATCAAGC 315
                            v     v      v i  i  i      i ii v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66756135_6    316 TACC-GCTGACTTTCTTCACAGAATTAGAAAAAATA--CTTTAATTTCAT 362
                          v  -    v    i  -i     v v  v  iv i-- i v  v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_66756135_6    363 ATGGAACCAAAAAAGACCCCATATAGCCAAGACAATCCTAAGCAAAGAGA 412
                               viiv  ii     viv        i      i i iv  ii   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_66756135_6    413 ACAAAGCTGGAGGCATCATGCTACCTTATTC--AAACTATACTGCAAGCC 460
                               i      vv   ii  v  iv   i--     -    i   iv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_66756135_6    461 TACAGTAACCAAAACAGCAATGTACTGG--------TAGATATATGGACC 502
                                 i   i    iivv       --------    i    i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_66756135_6    503 AA 504
                           
  L1M4_orf2#LINE/    299 AA 300

Transitions / transversions = 1.75 (49 / 28)
Gap_init rate = 0.02 (6 / 300), avg. gap size = 2.50 (15 / 6)  

1599 27.52 0.92 0.92  chr2_66756135_66760684.rev     2288  2723 (1827)    L1M4_orf2#LINE/L1        1   436 (472)  

  chr2_66756135_6   2288 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2337
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66756135_6   2338 GGCCATACTGCCCAAGGTCATTTATAGATTCAATGCCATCCCCATCAAGC 2387
                            v     v     iv v  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66756135_6   2388 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAATTTCA 2435
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_66756135_6   2436 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAACCAAAAG 2485
                                viiv  ii  v  v v  v     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_66756135_6   2486 AACAAAGCTAGAGGCATCATGTTACCTGACTTCAAACTATACTACAAGGC 2535
                                i i    vv   iii v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_66756135_6   2536 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 2585
                          i      i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_66756135_6   2586 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 2633
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_66756135_6   2634 ATCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAAGGATTCC 2683
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_66756135_6   2684 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACGT 2723
                           v  i  i              v      v  ?    i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

Transitions / transversions = 1.77 (76 / 43)
Gap_init rate = 0.01 (5 / 436), avg. gap size = 1.60 (8 / 5)  

1992 27.05 0.17 0.34  chr2_66756135_66760684.rev     3475  4058 (492)    L1M4_orf2#LINE/L1      326   908 (0)  

  chr2_66756135_6   3475 TAAATACCACACATGTACAACTATCTGATCTTTGACAAACCTGACAAAAA 3524
                             i-   i    v  iiiii vi    i  i     ivv  v   i v
  L1M4_orf2#LINE/    326 TAAAC-CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_66756135_6   3525 CAAGAAATGGGGAAAGGATTCCCTATTTAACAAATGGTGCTGGGAAAACT 3574
                           vvv           i  vvi  v  i                 v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_66756135_6   3575 GGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTAT 3624
                           v  ?   i   i i  iiv    ii    i    v   i     v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_66756135_6   3625 TCAAAAATTAATTCAAGCTGGATAAACGACTTTAATGTTAGACCTAAAAC 3674
                         v          i    iv     v ?v   i v     v   v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_66756135_6   3675 CATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGC 3723
                         i      vi i           v    ?i- v i -   iv   v v  v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

  chr2_66756135_6   3724 ATGGGCAAGGACTTCATGTCTAAAACACCAAAACCAATGGCAACAAAAGC 3773
                         v i     v ii   v ivv  vi         v  vvi          v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_66756135_6   3774 CAAAATTGACAAATGGCATCTAATTAAACTAAAGAGCTTCTGCACAGCAA 3823
                         v     v  i    v v ii v  i   v v  i i   i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_66756135_6   3824 AAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATT 3873
                          i  v    i  vv i      v  i     i   i             v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_66756135_6   3874 TTTGCAATCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACGAAGA 3923
                                vii ivi      i  i  i  vi          v  ii    
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_66756135_6   3924 ACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAACAAGTGGG 3973
                             vv    v iv i  v     i     i     v  i? v  i    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_66756135_6   3974 TGAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAC 4023
                         ii      v    i     i     v        i  vi viii     i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_66756135_6   4024 AGACACATGAAAAAATGCTCATCATCACTGGCCAT 4058
                          ii          i       v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (83 / 71)
Gap_init rate = 0.01 (3 / 583), avg. gap size = 1.00 (3 / 3)  


3322 26.76 0.44 0.44  chr2_66766121_66772518.rev     4999  5906 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66766121_6   4999 TGGAAGACTATCCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5048
                              iiv         i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66766121_6   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66766121_6   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_66766121_6   5147 TATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCATAAG 5196
                                viiv  ii  v  v v  vi    iv     i i ivv v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_66766121_6   5197 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5246
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_66766121_6   5247 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5296
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_66766121_6   5297 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCGTATCTACAACT 5344
                                i    i--    i  --        vv iiiii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_66766121_6   5345 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5394
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_66766121_6   5395 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5444
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_66766121_6   5445 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5494
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_66766121_6   5495 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGATGAAAAC 5544
                          i ?    i       v   v       i      vi i    v      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_66766121_6   5545 CTAGGCATTACCATTCAGGACATAGGCATAGGCAAGGACTTCATGTCTAA 5594
                         v    ?i v viv   iv   v v  vv       v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_66766121_6   5595 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCGCATCTAA 5644
                         i            vvi          vv     v  i    i v ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_66766121_6   5645 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5694
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_66766121_6   5695 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5744
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_66766121_6   5745 AGGGCTGATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5794
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_66766121_6   5795 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5844
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_66766121_6   5845 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5894
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_66766121_6   5895 ATCACTGGCCAT 5906
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2957 26.97 4.11 0.34  chr2_66781684_66788026.rev     4977  5851 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_66781684_6   4977 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5026
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_66781684_6   5027 GGCCATACTGCCCAAGGTAATTTATAGATTCACC---ATCCCCATCAAGT 5073
                            v     v     iv i  i  i       v ---     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_66781684_6   5074 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 5121
                          v   iivi i  i  ii     -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_66781684_6   5122 TATGGAACCAAAAAAGAGCCCGTATTGCCAAGTCAATCCTAAGCCGAAAG 5171
                                viiv  ii  v  v v  v     iv     i i ivvii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_66781684_6   5172 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5221
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_66781684_6   5222 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5271
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_66781684_6   5272 AATGGAACAGA-----GCCCTCAGAAATAATGCCACATATCTACAACTAT 5316
                                i   ----- vvii         vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_66781684_6   5317 CCGATCTTTGTCAAATGTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5366
                         ii   i  i v   iv   v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_66781684_6   5367 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5416
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_66781684_6   5417 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATT-AAGATGGATT 5465
                          ii    i    v   i     v              i -  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_66781684_6   5466 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCC 5515
                          ?    i       v   v       i      vi i           vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_66781684_6   5516 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5564
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_66781684_6   5565 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAATTGGGATCTAAT 5614
                                     vvi          vv     v  i  v v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_66781684_6   5615 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5664
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_66781684_6   5665 GGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5714
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_66781684_6   5715 GGGCT--------------------AACTCAAACAAATTTACAAGAAAAA 5744
                           i  --------------------     vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_66781684_6   5745 AACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGGCACTTCT 5790
                         i    ----   v  i?    i            v    i  i  i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_66781684_6   5791 CAAAAGAAGATATTTATGCAGCCAAAAGATACATGAAAAAATGCTCATCA 5840
                          v           vi viii     v iii         i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_66781684_6   5841 TCACTGGCCAT 5851
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.90 (39 / 10)  


3913 14.15 4.85 1.44  chr2_66877187_66878909.rev      480  1242 (481)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr2_66877187_6    480 AGAAATTGAGAAGCTATGGCAAAAATTCGTACAGAAAATGCAAGAGACCC 529
                                  v     ivvv v       i  ii    -      i     
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA-TGCAAGGGACCC 168

  chr2_66877187_6    530 AGAATAGCCAAAACAATCTTGAAAAATAA---CAAAGTGAGAGGACTCAC 576
                                                   v  ---      vi          
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_66877187_6    577 ACT-----ATTGCAAAACTTGATATAAAGCTATGGAAATCAAGATTGTAT 621
                            -----   v        iv  i       ii v        iv  i 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_66877187_6    622 GGTAC---CAT-----TAGACATACAGATGAAAGGAATAGAATTGAGAGT 663
                              ---   -----        i    v  v                 
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_66877187_6    664 CTAGAAATAAGCCCATAAATGTATGGTCAATTGATTGTTGACAAGGGTGC 713
                          i        i      v  v               v i           
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_66877187_6    714 CAAGACAATTCAATGGGGAAAAAAAAAGCCTTTCAACAAGTGGCTTTGTG 763
                               v              i  v iv i         i   ivi  v 
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_66877187_6    764 ACAACTGGATATCCACATGCAAAAGAACGAAGTTGGGCCCCTACCTCATA 813
                                    ?               i        i           i 
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_66877187_6    814 CCATATAC---------CTCAAAATGGATGGACCAAAGACCTAAATATAA 854
                                 ---------            ----  ?          i   
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGAT----CAWAGACCTAAATGTAA 514

  chr2_66877187_6    855 GAGCTAAAACTATAA--CTCTTAGAAGAAAACATAGGTGTAACTCTTTAT 902
                                        --                    ?    v    ii 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_66877187_6    903 AACCTAGGATTAGACAATGGTTTCTTAGACATGTCACCAAACACACAAGC 952
                         i    v  i    i               i   v       vi       
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_66877187_6    953 AATAACAGGAAATAATAGGCAAATTAGACTTCATCGAAATTTAAAACTTT 1002
                           i  v  i   -     ii     i         i     v        
  L1M4_orf2#LINE/    615 AACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_66877187_6   1003 TGTGCATCAAAGGACGTTATCAATAAAGTGAAAAAATAAATAATCCACAG 1052
                              v         ii      v          i i  ----i      
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA----CCCACAG 709

  chr2_66877187_6   1053 AATGGGAGAAAATATTTGTGAATCATATAACTGATAAGGAACTTAGATCT 1102
                                           ii         v         i    iv   i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_66877187_6   1103 AGAAAATATAACGAATATGTACAACTAAACAGTAAAAGTACAAATAACTC 1152
                             v      v   iviv       v  i i     iv         i 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_66877187_6   1153 AATT-AACAATAGGCAAAAGATTTGAATAGACAATCCTCCAGAGAAGATA 1201
                             -  v   i      i              v i     i        
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_66877187_6   1202 TGGAAATGG--AA-------ATAAATAGATGTTATAATATCACCAACCAT 1242
                          iv      --  -------  i  v     i -i  i    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCT-CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (64 / 41)
Gap_init rate = 0.02 (14 / 789), avg. gap size = 3.43 (48 / 14)  


2142 24.68 8.42 0.57  chr2_67045951_67047643.rev      501  1201 (492)    L1M4_orf2#LINE/L1      153   908 (0)  

  chr2_67045951_6    501 GAAATACAAAAGACCTAAGATAGACCAGAA-AACTTTCAAAAAGA----T 545
                              i   ii    i ii    -   i  -  ii  v       ----i
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAG-CCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_67045951_6    546 AAAGTTGGAGGACTTACAGTACCTAACATCAAGATTGAT-------CTAA 588
                                       i   v v  i  iv    i i v i-------   v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_67045951_6    589 A--AATTAG---AGTGTGGTATTAACATCAACATGGGCAAATAGATCATT 633
                          --   i i---         i ii   v iv  i i  v        v 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_67045951_6    634 GAAACATAACTGAGA----AGAAACAGATCCATATAAATATGGTCAATTG 679
                          i  i v  i     ----     i i i     i vv            
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_67045951_6    680 ATTTTCAACAAAGGTGCAAAGACAATTAAATAGAGCAAGGACAATCTTTT 729
                               i    i     v     v   v   i i v   i i i      
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_67045951_6    730 CAACAAATGGTGTTAAAAAGATGGGCGATTCATTGGCAAAA-ACTAAACC 778
                                     i iii vi iv  vv ?i  ivv      - v i  vi
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_67045951_6    779 TCAACCAATAC---A-ACCGTATACAAAAGTTAACTCGAAATGAATTACA 824
                          vi   vv   --- -   i         i       i     i  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_67045951_6    825 GAGCTAAATGTAAAACCTGGCACTCTAAAACCTCTAG--GAAAACGAACA 872
                           v          i v  iiv   v      iii   --      -- i 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC--ATA 549

  chr2_67045951_6    873 GGAGAAAATCTTTGTGAATTTGTGTTAGGTCAAACTTTCCTAGATATAAT 922
                           ? v       i    vi   v      iv viv    i       i i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_67045951_6    923 ACCAAAA-CATGATGCA-CTAAACAAAAATTTGATAAACTGGACTTCATG 970
                                -  ii -   - v   v     v v      i          v
  L1M4_orf2#LINE/    600 ACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_67045951_6    971 AGAAGTAAGAAATTCTGCTCTTCAGAAGGCA--AT---GA---TGAAAAG 1012
                          i  v   i  v  i  iv     i i i  --  ---  ---       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_67045951_6   1013 ACAAGACATGGACCAGGAGAAAATATTTGCAAATCACATATCTGATAAAG 1062
                             vv  ii  vii                     i           i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_67045951_6   1063 AATTGAAATCTAAAATATAATGAGAAATCTCA-AATTCAA---------- 1101
                         i i viv   i i      vvi    v   i -  i    ----------
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_67045951_6   1102 ----ACATCTTAATATTTTAGTGGGCAAAATATTTGAACAGACA---CTG 1144
                         ---- i v ii   v?vvv i        iv       i     ---  v
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_67045951_6   1145 CAGCAAAGATGTATGGATGACAAA-AAGCACATGAA--GATGCTCAACAT 1191
                           ivi     i  iii   i v  -           --            
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_67045951_6   1192 TATTAGTCAT 1201
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.68 (106 / 63)
Gap_init rate = 0.03 (23 / 756), avg. gap size = 2.74 (63 / 23)  


2650 26.99 2.69 1.01  chr2_67157099_67162501     4019  4911 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_67157099_6   4019 TGGAAAAACATTTCATGCTCATGGATTGGAAGAATCAATATTGTTAAAAT 4068
                               i i  ii    i               v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_67157099_6   4069 ACCTATATTGCCCAAAGCAATTTACAGATTCAATGATATTCTTATCAAAC 4118
                         iv v   i v      vii  i           i vv  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_67157099_6   4119 TACCAATGACATTCTTCACAGAATTAGAAAAAACT-ATTTTAGAATTCAT 4167
                          v   iivi v  i  ii     v v  v  i-  -  ii  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_67157099_6   4168 ATGAAACAAAAAAAGAGCCTGAATATGCAAAGCAATATTAGGCAAAAAGA 4217
                            i  vviv  ii  v  v     vv    i    v  iiiv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_67157099_6   4218 AAATAGCTAGAGACATCACATTACCTGACTCCAAACTGTACTACAAGACT 4267
                          v v  i i   ivv     i v  ii i i    viv        ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_67157099_6   4268 ATAGTAACCAAAA-AGCATGCTACTGGTACAAAAACAGACACACATTCCA 4316
                          i     i   i -  ii  v      i i  ii i     i i vvi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_67157099_6   4317 ATGGAACTGAATAGAGAACCCAGAAATAAAGTCACCCACATACAACCATC 4366
                               iv    v    ii           vi  iv  iv  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_67157099_6   4367 TGAACTTCGACAAAGTTGACAAAAACAAGAAATGAGGGAAAGACTCCTCA 4416
                            vi        i v  v   i v  vvv    -        v vv  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCT 398

  chr2_67157099_6   4417 TT-CACTAAATGGTGCGGTGATAACTGGCTAGCCATATGCAGAAGATTGA 4465
                           -  vi         v v  i      v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_67157099_6   4466 AACTGGACTTC---CTTACACAATATGAAAAAATTAGCTCTAGACGAATT 4512
                          ii     ii ---  i    v    iv        i   v i i i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_67157099_6   4513 AAAGACTTAAATGTAAAACTGAAAACTATAAAAACTCT-GGAAAATAATC 4561
                          ?    i         i viv            -    -i   i v  iv
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr2_67157099_6   4562 TTGG---AAATAGCATTGTGAACATAGGCCCTTA--CAAAGATTTCATAA 4606
                          v  ---    -- v i    v v i  ---   --   v i    v  i
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--CTTCGTGACCTTGGG---TTAGGCAATGGTTTCTTAG 592

  chr2_67157099_6   4607 CAAAGATGCCAAAAGCAATTGTAAGAAAACAAAAATT-GATAAATTGTAC 4655
                         vv v  ii         vvv i  v    v     v -         v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_67157099_6   4656 ---AT---AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAATAGAA 4699
                         ---  ---       i -   i  ii vv    i  v        v i i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_67157099_6   4700 TAAGCAGACAACCTACAGAATAGGAGAAAATATTTGCAAGCTATGCATTT 4749
                          i iv        i       i                 iii  ii  i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_67157099_6   4750 GACAAAGGTCTAATATCCAGAATCTATATGGAACT--TA-AATTTA-CAA 4795
                           i  i  v  vi          v    vi     --  -  i i -i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_67157099_6   4796 GAAAAAATCAAACAACCCCATTAAAAAGTGGGCAAAAGACATGAACAGAT 4845
                         v     iv    i     v   ?    i        i  iv    i   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_67157099_6   4846 GATTTTCAAAAGAAGACAAGTATGCAGCCAAAAATCATATAAAAA-ATGC 4894
                         iv  i  v        i vii viii     v  v  i  i    -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_67157099_6   4895 TCAACATCACTATTAGA 4911
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.65 (33 / 20)  


2179 25.19 5.15 5.70  chr2_67166116_67168688.rev     1173  2085 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_67166116_6   1173 TGAAGAGATATACCATGTTCATAAAGCAAAAAATTAAATGTTATTATGAT 1222
                           i i      v          ii viii  i i v   i  i   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_67166116_6   1223 GCCAATTCTTCCCAAATTTATCTATAGAGTCAATGCA----CTTTCAAAT 1268
                          v    v  i        v     i   v    i   ----  v     -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr2_67166116_6   1269 GTAAACCCAGTAGTCTTTTCTGTATAAATTGA---ACTGATTTTAAATTT 1315
                         --- v     iv i     i  i v       ---i     ii    v  
  L1M4_orf2#LINE/    100 ---ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_67166116_6   1316 TATACTGAACTGGAAAGGACCTAGACTATCCAAAACAATTTTGAAAAGTA 1365
                         i   iv   v  v  i     i   v  v          i       iv 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_67166116_6   1366 A---TTTAGTTGTAGGATTTACATGACTTGATTTCAAAACTTTCTGCAAA 1412
                          ---ivv     v    i i   ivv iii            v  i    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_67166116_6   1413 ATTGCAATAATTAAAACAGTA----GCTGGCATAAGGATCAACACATAAA 1458
                         ii i  i    i  i     i----i             vi   i   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_67166116_6   1459 TAAATGGAATGGAAGAGGAAGCCCAGAA-TATGTTCACACATACCTTGTC 1507
                          v        i   vv ii  i      -  viii  i    viv v   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_67166116_6   1508 ATTTGATTTGTGACAAAG---------TTATGCAATGAGAAAAC--TAAT 1546
                          v       vi     i ---------ii  v     i i   v--  i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_67166116_6   1547 ---TCCATCAAATGATGCTGGAGTAACTAAGTATCAATATTGTTTTGAAA 1593
                         --- i  v      i      iii    iii  ? v i  ------ v  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT------GCAA 440

  chr2_67166116_6   1594 AAGGAACTTGAAAAAAAATTTTAAAAAAAGAGAAAGGAACTTCATACCTA 1643
                            i ---    i-------  -------------   v ------    
  L1M4_orf2#LINE/    441 AAGAA---TGAAG-------TT-------------GGACC------CCTA 461

  chr2_67166116_6   1644 CTTCGTGTAATACACAAAAATTAATTCAAGATGCAT-ATACATCTAAAAA 1692
                          i  iiiiv   i           i    i   v  - ? v i     vi
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_67166116_6   1693 TAAAAGCTAAACTTATAAATCTTTGGGAGTAAAGCATAGAA-TAATATCT 1741
                            i       vi      v  i vi  iv   i     i?-   -    
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCT 560

  chr2_67166116_6   1742 TCATGACTTGGAGCTACTAAAAGTTTTCATAAACA-AATAACAGAAAATA 1790
                           i    i v i i  vvv  v v    v  i i -i i v  -   ii 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA-AAAGCA 609

  chr2_67166116_6   1791 TTAATA-CAATAGAAAAAAGTAACATAA--TAGACTTTATCAAAATTAAC 1837
                         iv ii -   v        -  i-    -- i     i           v
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAA-TAG-ATAAATTGGACTTCATCAAAATTAAA 657

  chr2_67166116_6   1838 AATGTCTGTTTATCAAAAGA---TAAGAAATAAATAAATATGCAACT-AC 1883
                           iv i   viv     i  ---  vv  iv  i i  v vi    i-  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_67166116_6   1884 AGGCTGGGAGAAGAAATATTTGCAAA--ATGTATCTAAAAAATGTCCGGA 1931
                           iv        --            --  i     i v  iv v iv v
  L1M4_orf2#LINE/    708 AGAATGGGAGAA--AATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_67166116_6   1932 ATCTATGATATACAAGGAACTCTTATAACTGAATAGTAAAAAG-CAAA-- 1978
                            i vi     i  i         i    v    i       -    --
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_67166116_6   1979 ATTCAATATGATTCTTTAAATG--CAAAATATTTGAACAAGTGCTTTACA 2026
                          ii    v?i ------     --    iv       i iiiii  iv v
  L1M4_orf2#LINE/    806 ACCCAATTWAA------AAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_67166116_6   2027 AAAGATGGTATATAAATAGCCAA-AAACACATGAAAAAGTGCTTCAACTT 2075
                              v i    i    i     -  i          ii    -    v 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT-CAACAT 898

  chr2_67166116_6   2076 TATCTTTAAA 2085
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.76 (144 / 82)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.00 (99 / 33)  


3047 27.36 1.33 0.33  chr2_67207159_67209135      606  1504 (473)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_67207159_6    606 TGGAAAGACATCTCATGCTCATGAATAGGAAGTATCTATATCATTAAAAT 655
                                 i   i    i     i  v     vv iv    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_67207159_6    656 GGCTATACTGCCCAAAGCAATTAATAGATTCAATGCTACTCCTATCAAAC 705
                            v     v      vii  iv i        i  v ii         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_67207159_6    706 TAGCAAGGACATCCTTCACAGAACTATAAAAAT--ATTTTAAAATTCACA 753
                          vv  ivvi v ii  ii     v vv v  ii--  ii         i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_67207159_6    754 TGAAACCAAAAAAGAGCCCAAATAGCCAAGGCAATTTTAAGCAAAAAGAA 803
                           i  viiv  ii  v  vi         ii    i  i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_67207159_6    804 CAAAGCTGGAGGCAC-CACATTACCTGGCTTCAAACTATACTGCAAGCCT 852
                              i      -  -    i v  iiii      viv    i   iv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_67207159_6    853 GCAGTAACCAAAACAGCATGGTTCTGGTACAAAAACAGGCACTCAGATCA 902
                         i      i   i    ii    v    i i  ii i  i  ivi      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_67207159_6    903 GTGGAACAGAATAGAGAGCCCAGAAATAAGGCTGTACATCTACGATCATC 952
                         i     i     v     i          iv ii     i  i i   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_67207159_6    953 TGATCTTTAACAAGGCTGACAAAAACTAGCAATGAGGAAAAGACTTCCTA 1002
                             i  ii      v  v   i v vvv     i     ii ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_67207159_6   1003 TTCAATAAATGGTGCCTGGATAGCTGGCTAGCCATATGCAGAAAATTGAA 1052
                              i         iv   i i    v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_67207159_6   1053 GCTGGACCCCTTCTTTACACCATACACAAAAGTCAACTCAAGACAGATTA 1102
                          i         v i i        i      i i       i ii   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_67207159_6   1103 AAGACTTAAATGTAAAACCCAAAACTATAAACACCCT-GGAAGATAACTT 1151
                         ?    i         i v i           -  i  -i     v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACAT 548

  chr2_67207159_6   1152 AGGCA-ATACCATCCTGGACAAAGGAACTGGCAAAGATTTCATGGCAAAG 1200
                            ?i- v i v  v  -  vvv  iviv     v i    v i vv v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_67207159_6   1201 ACACCAGAAGCAATTGCAACAAAAGCAAAAATTGAAAAATAGGATCTAAT 1250
                               i     vvv          v      v  v    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_67207159_6   1251 TAAACTAAAGGCCTTCTGCACCGCAAAAGAAACTATCAATAGAGTAAACA 1300
                         i   v v  iiv   i  ii iv    i  v        v i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_67207159_6   1301 GACAACCTACAGCGTTGGAAAAAGTTTTTGCAAACTATGCATCTGACAAA 1350
                                i    vi v   i   i v        ii  ii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_67207159_6   1351 GGTCTAATATCCAGCATCTATAAGGAACT--TA-AATTTA-TAAGAGAAA 1396
                           v  vi       v  v     i     --  -  i i -   v i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_67207159_6   1397 AACAAACAACACCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTGT 1446
                         i     i   v v   ?    i           iv    i     i  v 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_67207159_6   1447 CAAAAGAAGACATACATGTGGCTGACAA--ACATTACAAAA-GCTTAATA 1493
                          v        i     vi    ii i  --    v v  i -   i  i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_67207159_6   1494 TCACTGATCGT 1504
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


3325 24.42 1.66 0.89  chr2_67288283_67292872     3198  4098 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_67288283_6   3198 TGGAAAAATATTCCATGTTCATGGATTGGAAGAATCATTATTGTTAAAAT 3247
                               i    i                     v i v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_67288283_6   3248 GTTCATACTACCCAAAACAATCTACAGATTCAATGCAATCGCTCTCAAAA 3297
                          viv     v      vii              i      v  v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_67288283_6   3298 TACCAATAACATTCTTCACAGAAATAGAAAAAAAAAATACTAAAATTTAT 3347
                          v   iivi v  i  ii       v  v  ivvi - v        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_67288283_6   3348 ATGGAACCACAAAAGACCCAGAATAGCCAAAGCTCTCCTAAGCAAAAAGA 3397
                               vii   ii                 i vv  i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_67288283_6   3398 ACGAAACTAGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCT 3447
                           i  ii i     v     i v  ii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_67288283_6   3448 ACAGTAACCAAAACAGCATGGTACTTGCAATAAAACAGACGCATAGACCA 3497
                                i   i    ii       v   vv ii i    ii     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_67288283_6   3498 ATGGAACAGAATAGAGAAACCAGAAACAAACCCACACACCTGCAGT-AAT 3546
                               i     v    iv       i       i   ii iii  -   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_67288283_6   3547 CTCATTTTTGACAAAAGTGCCAAAAACATACACTGGAGAAAAGGCAGTCT 3596
                         - v     i     ii       i v   v  v   i    iiii     
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_67288283_6   3597 TTTCAATAAATGGTGCTTAGAAAACTGGATATCCATTTGTAGAAGAATGA 3646
                               i          vi  v         ?   iv  i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_67288283_6   3647 AACTAGACCCTTATCTCTCACCATATACAAAAATCAA---AAAA-GGATT 3692
                          ii i     i  i   v                i  ---    -    i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_67288283_6   3693 AAAGAC--AAATCTAAAGCCTCAAACCTTGAAATTACTACAGGAAAACAT 3740
                          ?    --    v   iiv  v    iv i   i vi  v i        
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_67288283_6   3741 TGGGGAGAATTTTCAGGACACTGGTCTGGACAAAAATGTATTGAGTCAT- 3789
                         v  ? vi   i   iv   vi   vi i i   vii v v  -  vi  -
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chr2_67288283_6   3790 ACCCCACAAGCACAGGCAACCAAAGCGAAAATGGACAAATGGGATAACAT 3839
                           v   v       i     v    vi     i  i    v   ivv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_67288283_6   3840 CAAG-TTAAAAAGCTGCTGCACG-CAAAGGATACAGTCAACAAAGTAAAG 3887
                            i-       -  vi  ii v-       i  vi    v     i  i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_67288283_6   3888 AGGCAACCCACAGAATGGAAGAATATATTTGCAAACTACCCACGTGGCAA 3937
                           i               i    v           ii ivi iv  ii  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_67288283_6   3938 GGGATAAACAACCAGAATATAT---GACCTCAAACAACTATATGGGAAAA 3984
                             ivvii v           ---  v   vv      vv  iiv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_67288283_6   3985 AAA-AATCTTATAATCTGATCAAAAGATGGGCAAAA-ATTTTAATAGACA 4032
                          i -  ----    i ii  i?   i         i-    v        
  L1M4_orf2#LINE/    797 AGACAA----ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_67288283_6   4033 TCTCTACAAAGAAGACATACAAATGGCAAACAGGCATTTGGAAAGGTGCT 4082
                          i   v         i           v  i i   iv  i    i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_67288283_6   4083 CAATGTTATTGATAAT 4098
                            ii i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (137 / 79)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.53 (23 / 15)  


3325 26.79 0.44 0.33  chr2_67328844_67335250.rev     5009  5915 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_67328844_6   5009 TGGAAGAACATTCCATGTTCATGGGTAGGAAGAATCAATATCATGAAAAT 5058
                              ii i  i            i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_67328844_6   5059 GGCCATACTGCCCAATGTAATTTATAGATTCAATGGCATCCCCATCAAGC 5108
                            v     v     vv i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_67328844_6   5109 TACCAATGACTTTCTTCACAGAACTGGAAAAAACTACTTC-AAAGTTCAT 5157
                          v   iivi i  i  ii     v v  v  i-  iv i -   i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_67328844_6   5158 ATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAGA 5207
                               viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_67328844_6   5208 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5257
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_67328844_6   5258 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5307
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_67328844_6   5308 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCTTATCTACAACTA 5355
                               i    i--    i  --        vv  iivi  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_67328844_6   5356 TCTGATCTTTGACAAACATGACAAAAACAAGCAATGGGGAAAGGATTCCC 5405
                         vi    i  i     ivi  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_67328844_6   5406 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5455
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_67328844_6   5456 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5505
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_67328844_6   5506 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAACC 5555
                         i ?    i       v   v       i      v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_67328844_6   5556 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5605
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_67328844_6   5606 ACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTCAT 5655
                                     vvi          vv    iv  i    v   ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_67328844_6   5656 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5705
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_67328844_6   5706 GGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5755
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_67328844_6   5756 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5805
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_67328844_6   5806 AA-AAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCT 5854
                         i -   i     v  i?    i     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_67328844_6   5855 CAAAAGAAGACATTTATGCAGCCAAAAAACACGTGAAAAAATGCTCATCA 5904
                          v        i  vi viii     v  i   i      i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_67328844_6   5905 TCACTGCCCAT 5915
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


3086 27.61 0.55 0.66  chr2_67494348_67500797     5050  5958 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_67494348_6   5050 TGGAAGAACATTCTATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5099
                              ii i  i i   i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_67494348_6   5100 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5149
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_67494348_6   5150 TACCAA-TGACTTTCTT-CATGGAATTGGAAAAAGCT-ACTTTAAAGTTC 5196
                          v   i-  v    i  -  - i     -- v     - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_67494348_6   5197 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 5246
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_67494348_6   5247 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5296
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_67494348_6   5297 CTACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGATATAGAC 5346
                                  i   i    ii       v i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_67494348_6   5347 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5394
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_67494348_6   5395 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5444
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_67494348_6   5445 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAGC 5494
                         i  v  i  i              v      v  ?   ii  i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_67494348_6   5495 TGAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGG 5544
                             ii    i    v   i i   v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_67494348_6   5545 ATTAAAGACTTTAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5594
                           i ?    i v  ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_67494348_6   5595 CCTAGGCATTACCATTCAGGACATAGGCATGGGAAAGGACTTCATGTCTA 5644
                          v    ?i v viv   iv   v v  vv i  v  v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_67494348_6   5645 AAACACCAAAAGCAATGGCAACCCAAGCCAAAATTGACAAATGGGATCTC 5694
                         vi            vvi     vv   vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_67494348_6   5695 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5744
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_67494348_6   5745 CAGGAAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5794
                         v  iv    i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_67494348_6   5795 AATGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACGAGAAA 5844
                          iv i  vi          v  i  v      vv    -i i vv iv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAA 794

  chr2_67494348_6   5845 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACATACACT 5894
                            i     i     v  i?    i     i     iv    i v   i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_67494348_6   5895 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5944
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_67494348_6   5945 CCATCACTGGCCAT 5958
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (145 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1335 26.75 10.48 4.82  chr2_67533671_67535534.rev      535  1364 (500)    L1M4_orf2#LINE/L1       13   889 (19)  

  chr2_67533671_6    535 CTATGTTCATGGGTTGTGAGACTCAATATTGTTACAATGTCAGCTATTTC 584
                          i          i   vi     i          vi   v  i-  i i 
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA-TACTCC 61

  chr2_67533671_6    585 C-AAACTGACCTATAGATTCAACATAAATACATATGAAGG-CCCAGTGTG 632
                          -   i   i   i         ii  - v v   v  ii-     i---
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAA-TCCCTATCAAAATCCCAGC--- 107

  chr2_67533671_6    633 TGACTGTGTGTGTGTAACATGGTAAGTTTTTTCTAAAATTTATATGAAAA 682
                           v  v v -  iiv  vv  ii   i vv i        i     i   
  L1M4_orf2#LINE/    108 TGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_67533671_6    683 TGCAAGGGACCAAAAATA-TCAATAAACTCTTGAAGATCTCTCGAAGAAT 731
                                    v i    -i   v v v       i -----v      i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA-----AGAAGAAC 201

  chr2_67533671_6    732 AA---TG-AGGGTTGATATCTACCAGGTATCAAGACTTA---------TA 768
                           ---  -   ii v i ii v   iv -    i     ---------  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATT-TCAAAACTTACTACAAAGCTA 250

  chr2_67533671_6    769 TGGTAATTAAGACAGTGTTATGATGGTGTCAGGATAGACA-A-AGATGAA 816
                         ii     i          vi iv   ii v          - -    v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_67533671_6    817 AGAAACAGGAT----AGCACAGAAACAGACTTCCATATAA--ATGAACA- 859
                         v i  i  i  ----  iv      i i  --     i v--   iv  -
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAAC--CCATACATTTATGGTCAA 348

  chr2_67533671_6    860 -CGATTTAAGACAAAGGTG-----ACCCTTCTGAGCAATGGTAAAAGGA- 902
                         -i     vv     i    -----   v   -----     vi    i -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTC-----AATGGGGAAAGAAT 393

  chr2_67533671_6    903 ---CTTTTGAAATTAAATAGTGCTTGGTCTATTTGATGTTCATGTAGAAA 949
                         ---     v  --i    i     v  v v i v   i?i  ii - v  
  L1M4_orf2#LINE/    394 AGTCTTTTCAA--CAAATGGTGCTGGGACAACTGGATAKCCACAT-GCAA 440

  chr2_67533671_6    950 AAGAAAGAAACATGACCTTTACCTCAAACTTTATCCCCAAATCAGGTGCA 999
                              v   iivv    ii       v  iv   v vv    i iv -  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT-CA 489

  chr2_67533671_6   1000 TATATATTCATTATAAATTTAATTGTAGAAGATAAAA---TAACATT-TT 1045
                         v ---  vv  i ? i ii   v    ii  v     ---   v i -  
  L1M4_orf2#LINE/    490 AA---ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_67533671_6   1046 AGAAG---------GTATAAATTGTCTTCATGAC---AGA--ACGCA--- 1078
                              --------- ?i     ---    i    ---i i-- v   ---
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_67533671_6   1079 -TTT----GAAATAAAAC-AAAGGTCACCAG--------GCATAATTA-- 1112
                         -   ----  v  i v  -   i -   v  -------- v v  v  --
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGA 632

  chr2_67533671_6   1113 TAAATGTGACTACA-CAAAATTGATAATTTGAGAACTTCTGTCCATTCAA 1161
                              vv    v  -       i --------i     i   v -     
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAA--------AAACTTTTGTGC-TTCAA 673

  chr2_67533671_6   1162 AA-ACAACATTAAAGAGAAGGAAGGGCAAGGCACAAATTGGGAGAAAATA 1210
                          i-   vi  i  ii iiv i  i i   vv    i v            
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_67533671_6   1211 TTTATAAGACATAT-T----TAAGGG-CCTATATATAGGTTATATGAAGA 1254
                            ii  iv     - ----      - i i   vi  iv     i    
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_67533671_6   1255 ACTGATACAAATCACTAAGGAAATGATTGACTGTCAAAACCAAAAGTGGA 1304
                            vv     v   v   vi   v  ivi ivii v  vi?    i   i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_67533671_6   1305 TGAGACCCTTGAGCAGG-ATCTTCACAAGAGAAAATAT-TA-----TCAA 1347
                         ii iivvi    ii  i-  -   v v i    i    -i -----i   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACAT-TTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_67533671_6   1348 CAAACTTATGGAAAAAT 1364
                         i  i vi   i   i  
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGAT 889

Transitions / transversions = 1.45 (129 / 89)
Gap_init rate = 0.05 (48 / 877), avg. gap size = 2.65 (127 / 48)  


2654 23.80 8.40 2.45  chr2_67665130_67667047      577  1433 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_67665130_6    577 TAGAAAGATATGCCACACTCCTGAATTG---------------TCAAGAT 611
                          i         v   iii  v  i    --------------- i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_67665130_6    612 GTCAGTTCTTCCCAACTTTATCTGTAGATTCAATGCATTTGTAATAAAAA 661
                          v  i v  i     v  v    ii        i   v iviv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_67665130_6    662 TTTCAGC------------AAATAATTATTA--TTGATTCTAAAGTTTAT 697
                          ii    ------------ i -    ivi --i    i     i  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_67665130_6    698 AGGGAGAGGCAAAAGACCCAGA-CA--CACAACA---CTGAAGGAAAGGA 741
                          v   i v    ii        -i --  v    ---i    ii i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_67665130_6    742 ACAAAGTTGGA---CTGACA-----------------TTATTA----GGT 767
                                    ---  v   -----------------   i  ---- v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_67665130_6    768 ATAGTAATTGAGACAGTGTAGTTTTGATGAACAAACAGACAAATAGGTCA 817
                          i      ii         i  vi  iiiv vii i     v    i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_67665130_6    818 GTGGAACTGA--TGAATAACCCAGAAATA--CACATACATAAGTAGATTC 863
                         i     iv  --   i- ii         -- v       vvi i --  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATGG--TC 346

  chr2_67665130_6    864 AACTGATCTCTGACAAAGGAGCAAAGGCAAAACCATGGAGCAAAAATAGT 913
                           i    i ii     i  v  v   i v vv v    i v  i      
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_67665130_6    914 CTTTTCAACAAATGGTGTTGGAACATGGAGACTGGACATCTACATGTAAA 963
                                          i   i   -----      i ? i     i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACA-----ACTGGATAKCCACATGCAAA 441

  chr2_67665130_6    964 AAAAAAAAAAATGAACCTAGAAACATATTTTACACCATTCACAAAAATTA 1013
                          i  -------    vi i  vv v  ii i       vi          
  L1M4_orf2#LINE/    442 AGAA-------TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_67665130_6   1014 ACTCAAACTGGATCACAGACCTAAATGTAAAATTCAAAACTATAAAACTC 1063
                                v       ?              i vii               
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_67665130_6   1064 CTAGAAGGTAACACAGGAGGAAACCTGACTGACTTTGGGTATGGCAGTGA 1113
                         i      iv    i   ? v   i  vvv    i      vv    i  i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_67665130_6   1114 CTTTTTAGCTACAACAACAACAAAAGTACAAAACCCATGAAAGAAATAAT 1163
                         i  i    v  ii   - --      i    i-- v ii       v   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACA-C--CAAAAGCACAAG--CAACAAAAGAAAAAAT 629

  chr2_67665130_6   1164 TGATAAGTTGGATTTAATTAAAATTTAAAACATTTGCTCATCAAATGACA 1213
                         v     i     i  v  i      v     v    iv v     v    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_67665130_6   1214 ATACAAAGAGGATGAGAAGATAAGC-ACAGACTTGGAGAAACTATTTGCA 1262
                         v  iv    iii   i    i  v -     v v       v        
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_67665130_6   1263 AAAGATACATTTCATAAATGACTGTTATCCAAAAT-TACAAAGAAGTCTT 1311
                           vv   i  i v    iv    vv      i   -  i      v    
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_67665130_6   1312 AAAACTCAGCAATAAAA-------CAACCTGCTTAGCAAATGGGCCAAAT 1354
                          v      ii       -------i    iiv  ?iv        v  iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_67665130_6   1355 ACCTTAACAGACACCTCACCAAAGAAGATATACAAATGTCAAATAAGCAT 1404
                          ii v  i     ii  v                    v v        i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_67665130_6   1405 ATGAAAAAATTCTCCCTATGATATATCAC 1433
                                i  v   vvi  v ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (119 / 81)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.23 (93 / 22)  


2928 25.14 2.31 2.63  chr2_67675680_67680939.rev     3859  4769 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_67675680_6   3859 TGGAAAAACATTTCACACTCATGAAATGGAAGAATCAATAGTGTAGAAAT 3908
                               i i  ii  iii     i v       v i    v   vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_67675680_6   3909 GATCAGACTGCCCAAAGCAGTGTAGAGATTTAATGCAATTCTCTTCAAAA 3958
                          iiv v   v      viii v  v     i  i     i iiv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_67675680_6   3959 TAACAA-TGTCTTTTTTCACAGATAA--AACAATCT----CTAAAGTTCA 4001
                          vv  i-  i       -i    -  --i    v  ----     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGA-AATTGACAAGCTGATCCTAAAATTCA 148

  chr2_67675680_6   4002 TATGGAACCAAAGAAGAGCCTGAACAGCCAAAACAATCCTAAGCAAAAGG 4051
                                viiv iii  v  v   i             i i iv  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_67675680_6   4052 AGTAAATCTGGAGGCATCACATTACCTGACTTCAAATTATATTACAAGAC 4101
                          ii   vi      vv     i v  ii i      viv  i     ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_67675680_6   4102 TACAGTAAACAAAACAGCATGGCACTGGTATAAAAGTACCAGTGGGTACA 4151
                                 v   i    ii   i     i    iii  ------ ii i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA------GACATA 292

  chr2_67675680_6   4152 TAGACCAATGGGACAGAATAGAGACCCCAGAAATAAAGCCAAATACCTAC 4201
                             i      i i     v    vi           v   v i ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_67675680_6   4202 AATCAACTGATCTTTGACAAAACAGACAAAAACATACACCTGGGAAAGGA 4251
                         ii    i    i  i     iivv v   i v   v  viv       i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_67675680_6   4252 CATTCTATTCCATAAACGATGCTGGGAAAATTGTGTGGCCCCATGCAGAA 4301
                         i v   v   v i   i i        v  i  vi i?  v      i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_67675680_6   4302 GAATGAAACAGAATCTCTATCTTTCACCATATATAAAAATAAACTCAAAA 4351
                                iiv i i i   i  iv         i      v         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_67675680_6   4352 CGGATTAAAGACTTAAATGTAAGACCTAAAACTTTAAAAATTCTGGAAGA 4401
                         i    i ?    i           v        v     v ii i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_67675680_6   4402 AAACCTAGGAAAAATTCCTCTGAACATTGGTCTAGGCAATGAATT----- 4446
                             v    ?iv  v  i  vvi  v    vi         iv  -----
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_67675680_6   4447 -TATGACCAAAACTACAAAATCAAATGCAACAAAAACAAAAATAAATAAA 4495
                         -      ----  --     v  v v         iv       i     
  L1M4_orf2#LINE/    593 ATATGAC----AC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_67675680_6   4496 TGGGACTTAACTAAACCAAAAAACT-----ACTTCACAATGAAAGAAATA 4540
                          v      v ii   viv       -----i     -----  i  v iv
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA-----AAGGACACT 681

  chr2_67675680_6   4541 ATCAACAGAGCAAACAGACAGCCTACAGTATGGGAGAAAGTATTTACAAA 4590
                              v i  ii  v     i  i    v          i     i    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_67675680_6   4591 CTATATATTTGAAAAAGGACTAATATCCAGAATCCATAAGGAACTCAAAT 4640
                         ii      i   v  i     vi          vi    i      --- 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC---T 778

  chr2_67675680_6   4641 CAGCAAAT-AATAATTAAAAAAACAAATAATCCCATT--AAAGTAGGAAA 4687
                         i -   v -      -     i        i  v   --   i i  v  
  L1M4_orf2#LINE/    779 TA-CAACTCAATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_67675680_6   4688 ATGACATGAACAAATATTTTTCAAAAGAAGATATACAAATGGCCAACAAA 4737
                          v  iv    i i i    i  v                       i  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_67675680_6   4738 CATATTTTAAAAAGTTCAACCTCCCTAATCAT 4769
                           i  vvv  i v i     v  v????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (141 / 85)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.81 (45 / 16)  


3054 27.89 0.55 0.55  chr2_67727220_67733586     4969  5875 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_67727220_6   4969 GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCTTGAAAATG 5018
                             ii i  i     i      i v      v i     iv v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_67727220_6   5019 GCCATACTGCAAAAAGTAATTTATAGATTCAATGCCATACCCATCGAGCT 5068
                           v     v vv   v i  i  i        i  v  v  i   i iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_67727220_6   5069 ACCAATTACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAGGTTCAT 5116
                         v   ii i i  i  ii  -      -- v  i  - iii   ii     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_67727220_6   5117 ATGGAACAAAAAAAGAGTCCACATT-GCCAAGTCAATCCCAAGCAAAAAG 5165
                               - viv  i iii   v v -     iv     iii iv  i   
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_67727220_6   5166 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5215
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_67727220_6   5216 TACAATAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGACC 5265
                             i   i   i    ii       v i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_67727220_6   5266 AATGGAACAGAACAGA-AGCCTTAGGAATAACACCACACATCTACAACCA 5314
                                i    iv  -  i i-  i     vv   i    i  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC-AGAAATAAACCCATACATTTATGGTCA 347

  chr2_67727220_6   5315 TCTGATCTTTGACAAACCTGACAAAAACAAGCAACGGGGAAAGGATTCCC 5364
                         vi    i  i     ivv  v   i v  vv   i        i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_67727220_6   5365 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCTG 5414
                          v  i  i              v      v  ?i  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_67727220_6   5415 AAACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5464
                           ii    iv   v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_67727220_6   5465 TAAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5514
                         i ?    i     i v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_67727220_6   5515 TAGGCA-ATACCATCCAGGGCATAGGCATGGGCAAGGACTTCATGACTAA 5563
                             ?i- v i - i iv i v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_67727220_6   5564 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAACGGGATCTAA 5613
                         i            vvi          vv        i   iv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_67727220_6   5614 TTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTAACATCAGAGTGAAC 5663
                          i   v v  i i   i  ii vv    i  v    v  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_67727220_6   5664 AGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACCGATCTGACAA 5713
                           i     i i               v       vii ivv      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_67727220_6   5714 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5763
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_67727220_6   5764 AAACAAACAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5813
                          i     i   i v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_67727220_6   5814 TCAAAAGAAGACATTTATGCAGCCAACAGACATGAGAAAAAATGGTCACC 5863
                           v        i  vi viii     i ii  iiv     i   v   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_67727220_6   5864 ATCACTGGTCAC 5875
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (154 / 95)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 1.11 (10 / 9)  


3101 26.72 1.22 0.55  chr2_67878002_67884381.rev     4987  5888 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_67878002_6   4987 TGGAAAAACATTCCATGCTCATGGTTAAGGAGAATCAATATTGTGAAAAT 5036
                               i i  i     i      v vi i   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_67878002_6   5037 GTCCATACTGCCCAAGGTAATTTATAGATTGAATGCCATCCCCATCAAGC 5086
                          v v     v     iv i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_67878002_6   5087 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5134
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_67878002_6   5135 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTTAGCAAAAAG 5184
                                viiv  ii  v  viv  v     i      i v iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_67878002_6   5185 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5234
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_67878002_6   5235 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5284
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_67878002_6   5285 AATGGAATAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 5332
                                     i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_67878002_6   5333 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5382
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_67878002_6   5383 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5432
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_67878002_6   5433 GAAACTGGATCCCTTCCTTACACCTTATTTGAAA-TTAACTCAAGATGGA 5481
                            ii    i    v   i     v   vii   -         i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_67878002_6   5482 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAACAAAAC 5531
                          i ?    i       v   v       i      vi i     v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_67878002_6   5532 CTAGGCA-ATACCATTCAGGACATAGGCATAGAAAAAGACTTCATGACTA 5580
                         v    ?i- v i -   iv   v v  vv   iv  v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_67878002_6   5581 AAACACCAAAAGCAATGGCAACAGAAGCCTAAATAGACAAATGGGATCTA 5630
                         vi            vvi      i   vvv       i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_67878002_6   5631 ATTAAA-CTAAAGAGCTCTGCACAGTAAAAGAAACTACCATCAGAGTGAA 5679
                           i   -i    i vi i  ii vvi   i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_67878002_6   5680 CAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACCCATCTGACA 5729
                         v  i     i                vv       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_67878002_6   5730 AAGGTCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5779
                          i  v  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_67878002_6   5780 AA-ACAAA---CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTA 5825
                           -     ---   v  i?    i            v    i     i v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_67878002_6   5826 CTCAAAGGAAGACATTTATGCAGCCAACAGACACATGAATAAATGCTCAT 5875
                            v  i     i  vi viii     i ii        v i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_67878002_6   5876 CATCACTGGTCAT 5888
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


2953 26.87 0.66 0.66  chr2_67948693_67952252     2162  3069 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_67948693_6   2162 TGGAAACACATCCCATGCTCATAGATGCGTAGAATCAATACTGTGAAAAT 2211
                               v i        i    i   vv v   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_67948693_6   2212 GACCATACTGCCAAAAGCAACCTACAAATTCAAGGCAATATCCATCAAAA 2261
                          i v     v  v   vii i     i      v     vi i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_67948693_6   2262 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 2311
                          v   v vv v  i  ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_67948693_6   2312 TGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAACAAAAAGAA 2361
                              viiv  ii  v  v v         i   vvi i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_67948693_6   2362 CAAATCTGGTGGCATCACACTACCTGATTTCAAACCATACTATAAGGCCA 2411
                             vi   v  vv       v  ii        v v     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_67948693_6   2412 TAGTCACCAAAACAGCATGGTACTGGTATAGAAATAGGCATATAGACTAA 2461
                         i   v i   i    ii         i   iii    i        ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_67948693_6   2462 GGAAAGAGAATAGAGAACCCAGAAATAAACCAAATAAACCAA-AGCCAAC 2510
                         v i  v     v    ii             v -  v iiv -i i   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTATGGTCAAT 349

  chr2_67948693_6   2511 TGATCTTCAATAAAGCAAACAAAAACATAAAGTGGGGAAAGAACACCCTT 2560
                             i   i i  i vviv   i v   vv i           i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_67948693_6   2561 TTCAACAGATGGTGCTGGGATAATTGGCTAGCCACATGTAGAAGAATGAA 2610
                                i            i  i   v  ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_67948693_6   2611 ACTGGATCCTCATCTCTTAACTTATACAAAAATCAACTCCAGATGGATTA 2660
                         ii    i  ii i   vi v v           i     v i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_67948693_6   2661 AGCACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGCAGATAACATT 2710
                         ?iv  i    iv     v  i           v ii   v   v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_67948693_6   2711 GGAA-AAACCTTTCTAAACATTGGTTTAGGCAAGGATTTCATGACCAAGA 2759
                           ?i-   i   iv i v -    v        v i    v iivi v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_67948693_6   2760 ACAC-AAAAGCAAATATGCAATAAAAACCAAGAAAAATATTTGGGACCTA 2808
                         -   -       --i v    i    ivv  i v i   vv v    i v
  L1M4_orf2#LINE/    599 -CACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_67948693_6   2809 ATTAAACTAAAGAGCTTTTAAACAACAAAAGGAACAGTCAACAAAGTAAA 2858
                           i   v v  i i     ivi vv    i iv  vi    v     i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_67948693_6   2859 CAGATAACCCACAGAGTGGGAGAAAATCTTCACAATCTACACATCTGACC 2908
                         v   i          i           v  ii   vii i i      iv
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_67948693_6   2909 AAGGACTAATACCCAAAATCTACAACAAATTAAGACAAATCAGCAAGAAA 2958
                          i     vi  i   i   v  i  vi  i vvv    v   ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_67948693_6   2959 AAACCAAACAGTCCCAACC-AAAAGTGGGTGAAGGACATGAATAGACAAT 3007
                           iv    i i-     ii-    i    ii     iv          v 
  L1M4_orf2#LINE/    796 AAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_67948693_6   3008 TCTCAAAAGAGGATATACAAATAGCCAACAA--ACATGAAAAAATGCCCA 3055
                             v     i           i     i  --         i    i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_67948693_6   3056 ACATCGCTAATGAT 3069
                              i????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (140 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.20 (12 / 10)  


2918 21.51 9.44 1.55  chr2_67957154_67959447      966  1802 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_67957154_6    966 AGACATGCTATGTTCATGAAT-GAAAGACTCAAAATTATTAATGTACCAA 1014
                            i  v i         i  - i      i  v   i    vi iv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_67957154_6   1015 C-CTTCCCATATTGATGTAAGGGTTTAATACAATCCCAATCAAAATCACA 1063
                         i-  i    v      v  vi i  i  ii       v         v  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_67957154_6   1064 GCAGTCTTTTT-GTAGAAACTGGTAAGCTGATTCTAAATTTTATAGGAAA 1112
                           v i      - i     i  ii        i     v  i   v i  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_67957154_6   1113 ATG-AAATGACCCGAAATTGCTAAAATAAATTTGAAAAAGAA----AAAG 1157
                            -  iv     ii   v  i    i  vi           ----    
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_67957154_6   1158 TTAGAAAGTGTTCACTACCTGATT-CAAGACTTACTGTAAAGCTATAATA 1206
                           i  iiiiviv    v  ii   -   i       ii       i i  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_67957154_6   1207 ATTAAGTCAGTATAGTATT--TATGAGGATAAACATATAGATCAGTGGAA 1254
                           i   v    i i   i --i  i      i            i     
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_67957154_6   1255 CAAAA--GAGAGTCCAGAAATAGATC--TAC--------TCAA------- 1285
                         i i  --               i i --   --------    -------
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_67957154_6   1286 -------AGATGTCAAGGTTACTCAATGGGGAAAGA-TAGTTTTTTCCAA 1327
                         -------i i  i    iii i              -    i     -  
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC-AA 404

  chr2_67957154_6   1328 CAAATAGTGCTGGAACAATTGGATATCCATTTGGAAAAATAACAAGCCTA 1377
                              i       i    i      ?   iv  v    i-  ii ivi i
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AATGAAGTTG 453

  chr2_67957154_6   1378 GACACTAACCTTTCACACAATACATAAAAATTAACTCAAGAAGCATCACA 1427
                            v iv    --     v   i i              i v v    ? 
  L1M4_orf2#LINE/    454 GACCCCTACCT--CACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_67957154_6   1428 GGTCTAAATATAAGAGCTAAAACTATAAAACT-TCAAAAAAAAACCCGTA 1476
                          ii      i                      - i i  i     --i  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC--ATA 549

  chr2_67957154_6   1477 AGAAAAAATATTTGTGACCCTGGGTTAGGAAAATATTTCAAAAATAGGAC 1526
                         i ?iv    v  i      i         v  vvi    vv i   v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_67957154_6   1527 ACAGAGAATACAA--------AGAAAAACAT-GATAAATTAGACTTTGTC 1567
                           vi i ii    --------       -  -        i     ii  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATC 648

  chr2_67957154_6   1568 AAA-TTAAAAACTTTTGATCTTTAAAAATGACCATTAA-----TAAGAAT 1611
                            -             vv   i   iivv  i  i  ----- i i  v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_67957154_6   1612 ACAAGCCACAAAATGGGTGGGAGAAAATATCTGCAAAATTTGTATCTGAT 1661
                             v     i      ----         i      viv i        
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGG----AGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_67957154_6   1662 GAAAGACTTGAATCCAGAACATGTTAAAAAAC----ACAATTCAATAATA 1707
                         i ii      v        i  i -   i   ----    i         
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATAT-AAAGAACTCTTACAACTCAATAATA 793

  chr2_67957154_6   1708 A---GACAA----CTTGATTTTTTAGATGAGTAAAAGATTTGAA------ 1744
                          ---     ---- iii   ?vv- i   i i   i        ------
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACA 842

  chr2_67957154_6   1745 ------CAAAGAAAATATG--AATGGCAAACAAGCACATAAAAAGATGTC 1786
                         ------       i    i--      v  i        i        ii
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_67957154_6   1787 CAACGTCATTAATCAT 1802
                             i   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.67 (128 / 48)
Gap_init rate = 0.03 (30 / 903), avg. gap size = 3.07 (92 / 30)  


2814 28.20 0.33 1.09  chr2_68140674_68145531     3452  4366 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_68140674_6   3452 TGGATAAACTTTCCATCCTCATGGACAGGAAGAATCAATATCGTGAAAAT 3501
                             v i iv i    vi       iv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_68140674_6   3502 GGCCACACTGACCAAGGTAATTTATAGATTCAATGCTATTCCCATCAAAC 3551
                            v i   vv    iv i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_68140674_6   3552 TACCATTGACATTCTTCACAGAATTAGAAAAAAAAAACACTTTAAATTTT 3601
                          v   vivi v  i  ii     v v  v  ivvi v ---i    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC---CTAAAATTC 147

  chr2_68140674_6   3602 ATATG-AAAT-CAAAGAAGACCCTGTAGAGCCAAGACAATCCTAAGCAAA 3649
                              -    -   i --     v v v      i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_68140674_6   3650 AAGAACAAAGCTGGAGGCAACATGCTACCTGACTTCAAACTATACTACAA 3699
                                   i      vvv  ii  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_68140674_6   3700 GACTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAG 3749
                         ii         i   i    ii         i iv ii i          
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_68140674_6   3750 ACCAATAGGACAGAACAGAGACCTCAGAAATAACACCACACATCTACTAC 3799
                          i    i i i    iv    vii         vv   i    i  i---
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT--- 342

  chr2_68140674_6   3800 AGCCACCTGATTGTCAACAAAACTGACAAAAACAAGCAATGGCAACAGGA 3849
                         i i  vi     v  i    iiv  v   i v  vv      vi v  i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_68140674_6   3850 TCTCCTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAA 3899
                          vvi  v     i              i      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_68140674_6   3900 AGCTGAAACTGGACCCCTTCCTTACACTTTATACAAAAATTAACTTGAGA 3949
                         iiv    ii         v   i    iv                ii i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_68140674_6   3950 TAGATTAAAAACTTAAATGTAAATCCCAAAACCATTAAATCCCTAGAAGA 3999
                          i   i ? i  i         ivv i     i  v   ii i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_68140674_6   4000 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATG 4048
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_68140674_6   4049 ACAAAAACAACAAAAGCAATTGCTACAAAAGCCAGAATTTGACAAATGGG 4098
                         ivv vi   v        vvv  v       vv i   v-  i    v  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGG 640

  chr2_68140674_6   4099 ATCTAATTAAACTAAAAACCTTCTGTATAAAAAAAGAAACTATCATCAGA 4148
                          ii v  i   v v    v   i   iivvv   i  v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_68140674_6   4149 GTGAACAGGCAACCTACAGAATAGGAGAACATTTTTGCAATCTACCCATC 4198
                              v  i     i       i      v  v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_68140674_6   4199 CAACAAAGGTCTAATATCCAGAATTTACAAGGAACTTAAACAAATTTACA 4248
                         ii i  i  v  vi          v  i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_68140674_6   4249 AGAAAAACACAAACAACCCCATCAAAAAGTGAGCAAAAAACATGTGCAGA 4298
                          v     v     i     v  i?    i  i     ii iv  vii   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_68140674_6   4299 CACTTCCCAAAAGAAGACATTTACATGGCCAACAAACATATGAAAACAAG 4348
                           i   i v        i  vi v        i  i  i       v v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_68140674_6   4349 CTCAACATCACTGATCAT 4366
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (144 / 110)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3269 26.29 0.66 0.77  chr2_68202067_68208431     4965  5873 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_68202067_6   4965 TGGAAGAATATTCCATGCTCATGGATAGGAACAATCAATAATGTGAAAAT 5014
                              ii    i     i        v    v v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_68202067_6   5015 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5064
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_68202067_6   5065 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 5112
                          v   iivi i  i  ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_68202067_6   5113 TATGGAACCAAAAAAGAGCCCACGTTGCCAAGACAATCCTAAGCCAAAAG 5162
                                viiv  ii  v  vivi v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_68202067_6   5163 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5212
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_68202067_6   5213 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5262
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_68202067_6   5263 AATGGAACAGAAT--AGGGCCCCTGGAAATAATACCACACATCTACAACC 5310
                                i     --  i i  --i       vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_68202067_6   5311 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCT 5360
                          vi    i  i     ivv  vv  i v  vvv           i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_68202067_6   5361 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5410
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_68202067_6   5411 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCGAGATGGA 5460
                            ii    i    v   i     v              i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_68202067_6   5461 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAACCCCTAGAAGAAAAC 5510
                          i ?    i       v   v       i       i i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_68202067_6   5511 CTAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAAGACTTCATGACT 5558
                         v    ?i- v i -   i- i  v i  i- i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_68202067_6   5559 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5608
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_68202067_6   5609 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTATCATCAGAGTGA 5658
                         v  i   v v  i i   i  ii vv    i  v i     vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_68202067_6   5659 ACAGGCAACCTACAGAATGGGAGAAAAATTTTACAATCTACCCATCTGAC 5708
                          v  i     i                vv   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_68202067_6   5709 AAAAGGCCACTATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5758
                           ii i ivv          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_68202067_6   5759 AAAATGAAACAACCCCACCAAAAAGTGGGCAAAGGATATGAACAGACACT 5808
                            ivv   i     v ii?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_68202067_6   5809 TCTCAAAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAAATGCTC 5858
                             v        i  vi viii     i ii          i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chr2_68202067_6   5859 ATCATCACTGGCCAT 5873
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (145 / 90)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2882 24.42 2.53 2.64  chr2_68405070_68407342      907  1815 (458)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_68405070_6    907 TGGGAA--CATCCCATGCTCATGGATTGGAAGAATCAATATTGTTAAAAT 954
                            i  --i        i               v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_68405070_6    955 GGCCATATTGTCTAAAGCAGGGCAATCTACAGATTCAATGCAATTCCTAT 1004
                            v   i vi i   vii-----              i     i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG-----ATCTACAGATTCAACGCAATCCCTAT 95

  chr2_68405070_6   1005 CAAA-TACCAACTTCATTTTTCACA-AAATTAGAAAAAAAACAATTCTAA 1052
                             - v   i  v v     ii  -     i--- v  ivii  i    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAA 142

  chr2_68405070_6   1053 GATTCGTATTAACCAA---AAAAGATCCCAAATAGCCAAACTAATCCTGA 1099
                         i    i   vi --  ---  ii  i  vi          vi    i   
  L1M4_orf2#LINE/    143 AATTCATATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_68405070_6   1100 GCACAAAGAACAAAGCTGGACGCATCACATTACTGGACTTCAAATTATAC 1149
                         iv vi          i    v vv     i v ivi i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_68405070_6   1150 TACAAGGCAAGAGTAACCGAAACAGGATGGTACTAGTATAAAAACAGACA 1199
                              i  v v     i i i    vi       i i    ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_68405070_6   1200 CATAGATCAATGTAACAGTATAGAGAATTTGGAAATAAAGCCAATTACCT 1249
                         i           v  i  v  v    i iii        v   vvi ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_68405070_6   1250 ACAGCCAACTGGTCTTCAACAAGATTGACAAAAGCATATATTGGGAAAGG 1299
                          ii i   i  i i   i     iv  v   i v   vi v    i  i 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_68405070_6   1300 AACATGCTATTCAATAAATGGTGCTGGGAAAATGTGGATTGCCATATGCA 1349
                           i vv  v     i              v  i-     v?   i     
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAAC-TGGATAKCCACATGCA 439

  chr2_68405070_6   1350 ---GAATGAAACTGGACCCCTATCTCTCACCATATACAAAAATTAAT--- 1393
                         ---       ii          i   v                   i---
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_68405070_6   1394 --GTTGATTAAATACTGAAATGTAAGACCTGAAAATATAAAAATACTAGA 1441
                         --i v   i ? v  iv          v  i   v       v vi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_68405070_6   1442 AGAAAACCTAACCAAAAA-CTTTGCCAGACATTGGCCTTGGCAAAGAATT 1490
                                v  iv?iv   -   i i--   v    vi v     v iv  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGT--GACCTTGGGTTAGGCAATGGTTT 587

  chr2_68405070_6   1491 CATGACTAAGACCTCAAAAGCAAATGCTACAAAACCAAAAATAGACAAAT 1540
                          v iiv  v   vi        v v  v      vv         i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_68405070_6   1541 GGGACTTGATTAAA-TTAAAAACTTTTGCACTGCAAAATA-AGTAGCAG- 1587
                         v      v  i   -             ii  v    iv - v  v  i-
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_68405070_6   1588 --AGTGAACAGGAATCCTGAACAATGGGAGAAAAATATTTGCAAACCATG 1635
                         --      v  iv v  iiv v            -          i   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATA 736

  chr2_68405070_6   1636 CACCAGGCAAGGGACTA--ATCCAGAATCTACAAGGAACTCAAACAACTC 1683
                         i i v ii        v--         v  i  i      vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_68405070_6   1684 AACAACAACAAAAACCAAGTAACCACATTAAAAAGGGGGCAAACGACATG 1733
                           i  i  -   i  -  i     vv   ?    iv       v  iv  
  L1M4_orf2#LINE/    787 AATAATAA-AAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_68405070_6   1734 AGCAGACATTTTTCAGAAAGAGACATATAAATGGTCAGCATCACTAATCA 1783
                          ii        i  vi  ii   i   i      i  --  v vi --  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCA--ATAAGCA--CA 880

  chr2_68405070_6   1784 TCAGAGAAATGCAAATTAAAACCACAATGAGA 1815
                          v i - i    --- i  v i  ????????
  L1M4_orf2#LINE/    881 TGAAA-AGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (127 / 91)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.04 (47 / 23)  


3227 27.34 0.33 0.22  chr2_68536768_68549865      493  1399 (11699)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_68536768_6   1399 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATTGATATCATGAAAAT 1350
                              ii i  i     i        v      v  i    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_68536768_6   1349 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 1300
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_68536768_6   1299 TACCACCGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAATTTCATA 1251
                          v   v vi i  i  ii     v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr2_68536768_6   1250 TGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAAAAGAA 1201
                              viiv  ii  v  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chr2_68536768_6   1200 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTGTGCTACAAGGCTA 1151
                              i      vv       v  ii i      viv i      i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chr2_68536768_6   1150 CAGTAACCAAAACAGCATGGTACTGTTACTGAAG-CAGATATATAGACCA 1102
                               i   i    ii        vi - i i -i   i       i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATCA 299

C chr2_68536768_6   1101 ACGGAACAGAATAGAGGCCTCAGAAATAATGCCACACATCTACAACCATC 1052
                          i    i     v   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

C chr2_68536768_6   1051 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCCCTA 1002
                             i  i     ivv  v   i v  vv       i    i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

C chr2_68536768_6   1001 TTTTATAAATGGTGCTGGGCAAACTGACTAGCCATAGGCAAAAAGCTGAA 952
                           iv i             vv     iv  ?   i v      iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chr2_68536768_6    951 ACTGGATCCCTTCCTTACATCTTATACAAAAATTAACTCAAGATGGATTA 902
                         ii    i    v   i   i v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chr2_68536768_6    901 AACACTTAAACATAAGACATAAAACCATAGAAACCCTAGAAGAAAACCTA 852
                         ? v  i    ii     vv      i   i  vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

C chr2_68536768_6    851 GGCA-ATACCATTCAGGACATAGGCATGGGCTAAGACTTCATGACTAAAA 803
                           ?i- v i -   iv   v v  vv i   v v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

C chr2_68536768_6    802 CACCAAAAGCAATGGCAACAGAAGCCAAAATAGACAAATGGGATCTAATT 753
                                    vvi      i   vv        i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

C chr2_68536768_6    752 AAACTAAGGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 703
                            v v ii i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

C chr2_68536768_6    702 GCAACCTACAGATGGGGAGAAAATTTTTGCAATCTATCTATCTGACAAAG 653
                         i     i     vv          v       vii  v       i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

C chr2_68536768_6    652 GGCTAATATCCAAAATCTACAAAGAACGTAAACAAATTTACAAGAAAAAA 603
                          i  vi      i   v  i       vivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

C chr2_68536768_6    602 AACAACAACCCCATCAAAAAATGGGTGAAGGACATGAACAGACACTTCTC 553
                          vv  i     v  i?         ii     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

C chr2_68536768_6    552 AAAAGAAGACATTTATGCAGCCAACAAACTTATGAAAAAATGCGCATCAT 503
                         v        i  vi viii     i  i vi       i    v  v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

C chr2_68536768_6    502 CACTGGTTAT 493
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  

3045 26.64 1.66 0.89  chr2_68536768_68549865    11706 12606 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_68536768_6  11706 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAA 11755
                               i i  i     i        v      v i        v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr2_68536768_6  11756 TGACCATACTGCCCAAAGTAATTTATAGATTCAATGCTATGCCCATCAAG 11805
                           i v     v      v i  i  i        i  v  v  i     -
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA- 98

  chr2_68536768_6  11806 CAAATATCGACT---TTCTTCACAGAATTAGAAACACCTACTTTAAATTT 11852
                         --   vi ii  ---  i  ii     v v  v vi iv iii    v  
  L1M4_orf2#LINE/     99 --AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_68536768_6  11853 CATATGGAACCAAAAAAGAGCCTGTATAGCCAAGAGAACCCTAAGCAAAA 11902
                                  viiv  ii  v  v v        i v  i i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_68536768_6  11903 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATGCTACAAG 11952
                                  i      vv   ii  v  ii i      viv i      i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_68536768_6  11953 GCTACAGTAACCAAAACACCCTGGTACTGGTACTAAACAGATATATATAT 12002
                                   i   i   viv         i -   i--    v i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCA-TAAG--GATAGACATAT 293

  chr2_68536768_6  12003 ATACCAATGCAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACA 12052
                          v i     v  i     v   ivii         vv   i    i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_68536768_6  12053 GCCATCTGATCTTTGACAAACCTGATTAAAACAAGCAATGGGGAAACGAT 12102
                          i  vi    i  i     ivv  viv i v  vv           vi  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_68536768_6  12103 TCCCTGTTTAATAAATGGTGTTGGGAAAACTGACTAGCCATATGCAGGAA 12152
                         vvi  v  i  i        i     v     iv  ?   i     ii i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_68536768_6  12153 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGAT 12202
                         iv    ii    i    v   i     v                   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_68536768_6  12203 GGATTAAAGACTTAAACGTAAGACATAAAAACATAAAAACCCTAGAAGAA 12252
                             i ?    i    i      vv     vi      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_68536768_6  12253 AGCCTAGGCA-ATATCATTCAGGACAT------AGGCAAAGACTTCATGA 12295
                          i v    ?i- v   -   iv   v ------      v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_68536768_6  12296 CTAAAACACCAAAAGCAATGGCAACGAAAGCCAAAATAGACAAATGGGAT 12345
                         v  vi            vvi     i    vv        i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_68536768_6  12346 CTAGTTAAACTAAAGAACTTCTACACAGCAAAAGAAACTATCAACAGAGT 12395
                         i vi i   v v  i     i iii vv    i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_68536768_6  12396 GAACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCAATCTG 12445
                            v  iv    i                 v       vii  vv     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_68536768_6  12446 ACAAAGGGCTAATATCCAGAATCTACAAAGCACT--TA-AATTTGG-AAG 12491
                          i  i  i  vi          v  i    v   --  -  i iii-  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_68536768_6  12492 AAAAAACCCAACAACTTTATC-GAAAGTGGGTGAAAGATATGAAAAGACA 12540
                              iv v  i   iiv  i-i   i    ii  i   v    v     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_68536768_6  12541 CTTCTCAAAAGAAGACATTTACGTGGCCAACAAACATATGAAAAAAAGCT 12590
                         i     v        i  vi vi       i  i  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_68536768_6  12591 CATTATCACTGGTCAT 12606
                           vi    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


2875 14.93 3.54 0.20  chr2_68646433_68649723      501  1009 (2282)    L1M4_orf2#LINE/L1      171   696 (212)  

  chr2_68646433_6    501 AATTGCCAAAACAATCTTAGAAAAAAAGAAAAGAGTTGGAGGGTTCACAC 550
                            v              ii    i     v i         ii      
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_68646433_6    551 TTCTGGATTTCAAAACCTACTATGAAGCTACAGTAATCAGGACAGTC--- 597
                            ivi          i     ii               i      v---
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_68646433_6    598 --CTGGTGTAAAGAAAGACATATAGATCAAGGAAATAGAATTGAGGGTCC 645
                         --    ii   i  v               v i            i    
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_68646433_6    646 AGAAGTAAACCCCTACATTTAGGGTCAGTTGGTTTTTGACAAAGGTGTCA 695
                             i       v        v     i   i    i     i    i  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_68646433_6    696 AGACAATTAAATGGGGGAAAGAATGGTCTTTTCAACAAATGATGCTGGGA 745
                             v   v       -       i                i        
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_68646433_6    746 CAATTGAATATCCACATGCAAAAGAATGAAGTTAGTCTCCTGCTGCACAC 795
                            i  i   ?                      i v i   i iv     
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_68646433_6    796 CATATA--AAAATTAACTTACAATGGATCAGAAGTCTAAATATAAGCACT 843
                               --          i v         ? iii      i    vi  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_68646433_6    844 AAAACTACAAAACTCTTAGAAAAAAACA--GGTGTAAATCTTTGTGACCT 891
                                i             i      --  ?         i       
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_68646433_6    892 TGCATTAGGCAATG-TTT-------ATAACACCAGAAACACAAGCAAACA 933
                           vi          -   -------  i      i  i         vv 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_68646433_6    934 AAGGAAAAGTAGATAAATGGGACTTCATTACACTTAAAAG-TTCTGTGCT 982
                            i    i         v         i v v      i-  i      
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_68646433_6    983 TCTAAGGACACAGTTAAGAAAGTGAAA 1009
                           v        vi i            
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAA 696

Transitions / transversions = 2.32 (51 / 22)
Gap_init rate = 0.01 (7 / 526), avg. gap size = 2.71 (19 / 7)  

2882 26.78 1.09 0.60  chr2_68646433_68649723     1010  1838 (1453)    L1M4_orf2#LINE/L1       76   908 (0)  

  chr2_68646433_6   1010 AGATTTAGTGCCATCCCCATCAAGCTACCAATGACTTTCTTCACAGAA-T 1058
                              i ii  v     i     iv v   iivi i  i  ii     - 
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr2_68646433_6   1059 TGGAAAAAACT-ACTTTAAAGTTCATATGGAAACAAAAAAGAGCCCACAT 1107
                           -- v  i  - iii    i            iiv  ii  v  viv  
  L1M4_orf2#LINE/    126 TG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chr2_68646433_6   1108 TGCCAAGACAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACTCTAC 1157
                         v     i      i i ivv i          i      vv    v  v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr2_68646433_6   1158 CTGACTTCAAACTATACTACAAGCCTACAGTAACCAAAACAGCATGGTAC 1207
                          ii i      viv        iv         i   i    ii      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr2_68646433_6   1208 TGGTACCAAAACAGAGGTATAGACCAATGGAACAGAAC--AGAGCCCTCA 1255
                            i iv ii i   vi      i        i    i--    i  -- 
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--A 321

  chr2_68646433_6   1256 GAAATAACACCACACATCTACAACCATCTGATCTTTGACAAACCTGACAA 1305
                                vv   i    i  iiii  vi    i  i     ivv  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_68646433_6   1306 AAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAA 1355
                         i v  vvv           i  vvi  v  i  i              v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_68646433_6   1356 ACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCT 1405
                              v  ?   i   i i  iiv    ii    i    v   i     v
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_68646433_6   1406 TATACAAAAATTAATTCGAGATGGATTAAAGACTTAAATGTTAGACCTAA 1455
                                       i  i i      i ?    i       v   v    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_68646433_6   1456 AACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATA 1504
                            i      vi i           v    ?i- v i -   iv   v v
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTT 570

  chr2_68646433_6   1505 GGCATAAGCAAGGACTTAATGTCTAAAACACCAAAAGCAATGGTAACAAA 1554
                           vv  i    v ii  vv ivv  vi            vvi i      
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_68646433_6   1555 AGCCAAAATTGACAAATGGGATCTCATTAAACTAAAGAGCTTCTGCACAG 1604
                           vv     v  i    v   ii    i   v v  i i   i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_68646433_6   1605 CAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAA 1654
                             i  v    i  vv i      v  i     i               
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_68646433_6   1655 ATTTTTGCAATCTGCTCATCTGACAAAGGGCTAATATCCAGAATCTACAA 1704
                           v       viiiivi      i  i  i  vi          v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_68646433_6   1705 AGAACTCAATCAAATTTATAAGAAAAAAACAA----CCCCATCAAAAAGT 1750
                                vvv   v iv    v     i    ----   v  i?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_68646433_6   1751 GGGTGAAAGATATGAACAGACACTTCTCAAAACAAGACATTTATGCAGCC 1800
                            ii  i   v    i     i     v   v    i  vi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_68646433_6   1801 AACAGACACATGAAAAAATGCTCATCATCACTGGCCAT 1838
                           i ii          i       v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (131 / 87)
Gap_init rate = 0.01 (8 / 833), avg. gap size = 1.75 (14 / 8)  

1002 13.94 7.69 0.00  chr2_68646433_68649723     2592  2799 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_68646433_6   2592 AAGAAAGTGAAAAGACAACC-ACAGAATG--AGAAAATATTTGTAAATCA 2638
                                             -        --            i      
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_68646433_6   2639 CATAT-----AACAGACTTATATTCAGAATATCTAAAGAA-TC------C 2676
                         i    -----  vi     i   i        v       -  ------ 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_68646433_6   2677 TCAACAATGCAAAGGCAAACAACCCAATTTTAAAATGCATAACTGATTTG 2726
                             i   iv    i    i         ?v      vii  vv      
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_68646433_6   2727 AATAGACATTTTTCCAAAGAAGGTGTACAGGTGGTCAGTA-GAACATGAA 2775
                                    i          i i    ii   i  i  - v       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_68646433_6   2776 AAAATGTTCAACATCACTAGTCAC 2799
                           i   i         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (20 / 8)
Gap_init rate = 0.03 (6 / 224), avg. gap size = 2.67 (16 / 6)  


3047 26.16 1.43 1.21  chr2_68658352_68660701.rev      952  1857 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_68658352_6    952 TGGGAACATATCACATGCTTATGGATCGGTAGAATCAACATTGTGAAAAT 1001
                            i  v     v    i i      i  v   v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_68658352_6   1002 GAACATACTGCCAAAAGTAATCTACAAATTCAATGAAATTCTCATCAAAA 1051
                          ivv     v  v   v i       i      i v   i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_68658352_6   1052 TACCACCATCATTCTTCACAGGACTAGAAAAAACAATCCCAAAATTCATA 1101
                          v   v vv v  i  ii   i v v  v  ivii    i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_68658352_6   1102 TGAAAC--CAAAAGACAGCCCAAAACAAGTCTAGCCAAAGCAATACTAAG 1149
                           i  v--   ii   ---   i  ------        i    vi i i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC---CCAGAA------TAGCCAAAACAATCTTGAA 191

  chr2_68658352_6   1150 CAAAAGAAACAAATCCGGAGGCATCACATTACCCGACTTCAAACTGTACT 1199
                         v  i ii      vii     vv     i v   i i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_68658352_6   1200 ACAAGGCTACGGCCAGCAAAATAGCATGGTACTGGTATAAAAACAGGCAC 1249
                             i     i iv v   i i  ii         i    ii i  i  i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_68658352_6   1250 ATAGACCAACAGAATAGA-----GAACCCAGAAATAAAGCCAAATACTTA 1294
                              i   ii       -----  ii           v   v i i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_68658352_6   1295 CAGCCAACTGAGCTTTGACACAGCAAACAGAAATATAAAGTAGGGAAAGG 1344
                         ii i   i   vi  i    vi vviv  ii vi  vv i i       i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_68658352_6   1345 ACACCCTATTCAACAAATGGTGCTGGGATAATTTGCAAGCCACATGTAAA 1394
                          i vi  v                    i  i v vv ?       i   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_68658352_6   1395 AGAATGAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAGT 1444
                                 ii    i  ii i   v    v           i      iv
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_68658352_6   1445 ATGGATTAAAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAG 1494
                               i ?    i     v     v  i    i      v ii      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_68658352_6   1495 ATAACATCAGAAAAACCCTTCTAGAAATTGGCTTAGGAAAAGACTTCATG 1544
                          v     vi ?iv  vi    vv  vv    v     v  v ii   v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_68658352_6   1545 ACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGATGGGA 1594
                         ivi v  vv         v v    i    iv   i   i   i  v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_68658352_6   1595 CTTAATTAAACTAAAAAGCTTCTGCACG-CAAAAGAAATAATCAGCAGAG 1643
                            v  i   v v    i   i  ii v-    i  v iv    iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_68658352_6   1644 TAAACAGACAACTCACAGAGTGGGAGAAAATCTTCGCAAACTATGCATCT 1693
                          i  v       i      i           v  i     ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_68658352_6   1694 GACAAAGGACTAATATCCAGAATCTACAAGAAAAA-----ACAAATCAGC 1738
                           i  i     vi          v  i  -- i  -----    v   ii
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAA--AGAACTCTTACAACTCAAT 789

  chr2_68658352_6   1739 AAGAAAAAAGCAAATAATCCCATCAAAAAGTGGGCTAAGGACATGAATAA 1788
                           v     ii       i  v  i?    i     v     iv      i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_68658352_6   1789 ACAATTCTCACAAGAAGATATACAAATGGACAACAAACATATGAAAAAAT 1838
                            v     vv                  v   i  i  i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_68658352_6   1839 GATCAACATCACTGATTAT 1857
                          v         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.43 (24 / 7)  


1259 25.60 9.56 9.10  chr2_68678960_68681844      497  1375 (1510)    L1M4_orf2#LINE/L1       26   908 (0)  

  chr2_68678960_6    497 TTGCAAGAATCAATATTGTAAAGATAT--ATATTTCCTCAAAATCGCTCT 544
                            v    v i        v     iv--   i i  i--    i v   
  L1M4_orf2#LINE/     26 TTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC--AAATTGATCT 73

  chr2_68678960_6    545 GTAAGTTTAAAGCAGTCTTTATCAGAATCCCAATAGGGTGTATGTGCATG 594
                         ii ii  i  v   i  ii     i       -------------  -  
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCA-------------GC-TG 109

  chr2_68678960_6    595 CGTGTGTGTGTGTGTGTATGTGTGTGTATGTGTGTAAGTTGACAAACTGA 644
                          v v v -----------------------  iiv  i       i    
  L1M4_orf2#LINE/    110 CCTTTTT-----------------------TGCAGAAATTGACAAGCTGA 136

  chr2_68678960_6    645 C-------TTTATAGAGGAATAGCAAAGGACGTAGAACTCTGAATACAAT 687
                         i-------  i   vi i   -    i    vi    ivviv  v     
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_68678960_6    688 CTTCAA------GTGCAAACTTGAAAGACTTACATGACCAGATAGAAAGC 731
                            v  ------ vi    v   i i    i   ivv  vi  vvv  iv
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_68678960_6    732 CTTATTATAAAGCTACCATATATAATGCAGTTTAATATTGGTGCAAGGAT 781
                             i  i        vi  vvi  vi    v ii  i   iii      
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_68678960_6    782 AGATAAACAGTAATCAGTGCAAGAGATTAAAGAGTTCAAAACCAAACCTA 831
                            i v i  --    i  v  v   v vi     i  i  vi     i 
  L1M4_orf2#LINE/    286 AGACATATAG--ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_68678960_6    832 CATGTCTGTG---------TTTATGACAAAGGTACCACTGAAGA----TC 868
                         i ii i i  ---------   vi     i   i   ----   ----  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA----AGACCATTC 379

  chr2_68678960_6    869 TGTGGGTTAAGCATGAACTTT-CAATGAGTGGTGTTTGG-TAATTGGATA 916
                         vi    vv   v  iiv    -   ii i     i v  -i  i      
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_68678960_6    917 TTCATATG-AAAAGATAATGAATCTTAACTCCTGCCTTATACC-TATCAC 964
                         ?i  i   -      --     vi vi  i   i   i i   -   -  
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGA--ATGAAGTTGGACCCCTACCTCACACCATAT-AC 476

  chr2_68678960_6    965 AAAA--TAAATCTCA-----GAT---AGATTTT--TGTAAAACATATAAA 1002
                             --   --    -----   ---   ii v--     i vv  -   
  L1M4_orf2#LINE/    477 AAAAATTAA--CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAA 523

  chr2_68678960_6   1003 GTACAGGTAGC----AGAGGATAACATAGA---ATATATTCATGACATTG 1045
                         v  i i-- i ----   i  v       i--- v  v   i    v   
  L1M4_orf2#LINE/    524 CTATAA--AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_68678960_6   1046 GG-----CAAAGATTTCTTAAGCATGTTATAAAATG---AAGTAATCATA 1087
                           -----   v i       iii   vi iv   v ---   i  -  v 
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA-CAAA 620

  chr2_68678960_6   1088 ATCATGTTATCCAGTTGATCAGTTGGACAAAATTAAAATTAAAATTACCC 1137
                          vv vi------ i v   v i      vvv  i          --  i-
  L1M4_orf2#LINE/    621 AGAAAA------AATAGATAAATTGGACTTCATCAAAATTAAAA--ACT- 661

  chr2_68678960_6   1138 TTTATGTTATATTTAAATATAATATTAGAAGGGTGAAAAGGCAAGGCACA 1187
                            i  i vi ---  iv i v   i ii ii        i   vv    
  L1M4_orf2#LINE/    662 TTTGTGCTTCA---AAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_68678960_6   1188 AAGTAGATGAGGATATTTGTTACACATATGTC----AAAGAACTTGTATC 1233
                         i i i iv  ii       iv vv     i  ----  i i         
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_68678960_6   1234 AAAAATAAATAA------CTAGCAAC-CAATAAGAAAATGACAA----CT 1272
                         v i    v    ------  vi    -      v    v     ---- i
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_68678960_6   1273 CAGTTAAGAAAAAAAAATGAGCAAA----------AGGCACTGCACAAAA 1312
                           i  ? ------      i     ----------  i  i v v v   
  L1M4_orf2#LINE/    809 CAATTWA------AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_68678960_6   1313 GAGAACAGTGAAATGGCCAATAAGCATACAAGAAAGGTTTAATGCTTGTT 1362
                           ii i vvv                --  v    i ----     iivi
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCA--CATGAAAAG----ATGCTCAAC 896

  chr2_68678960_6   1363 AGTCATGTAGGGA 1375
                          -   ????????
  L1M4_orf2#LINE/    897 A-TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (134 / 89)
Gap_init rate = 0.05 (43 / 883), avg. gap size = 3.81 (164 / 43)  

3791 19.26 2.55 2.09  chr2_68678960_68681844     1532  2393 (492)    L1M4_orf2#LINE/L1       43   908 (0)  

  chr2_68678960_6   1532 GTGAAGATGTTCATACTATTCAAGGTGATCTACAGAATTAATGCAATCTC 1581
                           v      viv     vii   iv           v i  i      i 
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chr2_68678960_6   1582 TATCAAAATCCTAATGGTTTTTTTTGGCAGAAATAGAAAAAATTATTCTA 1631
                                    i iiv ii       -       v  v  iv v  i   
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTA 141

  chr2_68678960_6   1632 AAAT-CATGTGG----------GATCTCAAGTAGCCAAAACAATCTTGAA 1670
                             -   i   ----------  i ivi i                   
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_68678960_6   1671 ---GATGATCAAAGTTGGAGGTCTCACACTTCCTGATTTTAAAATGTATT 1717
                         ---  v  v            v           ii    i    iv  i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_68678960_6   1718 ACAAAGCCACAGTAATCCAAACAGTGTGGTACTGGCATAAAGATAGACAT 1767
                                i         v i                    i         
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_68678960_6   1768 ATAGACAAATGGAATAGACTAGAGAGCCTATAAATAAATCCTCATATATA 1817
                              iv           v v     i i v       i  vi i  v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_68678960_6   1818 TGGTTAAATAATTTTCAACAATGGTCTCAAGACAAATCAAAGAGGAAAGG 1867
                             i  v i      i    v   vi      v v    v i      i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_68678960_6   1868 ACAGATTTTTTTCAATAAAGAGTGCTCAGAAAACTGCATATTCACATGCA 1917
                          i  -- i       i   vi     vi  v     v   ?i        
  L1M4_orf2#LINE/    392 ATAG--TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_68678960_6   1918 AAAGAGTGAAGTTGGATGCTTGCCTTACACTTGTTTTCAAAATATAACTT 1967
                              i          iv i i   i    i-i v v     vv     i
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACC-ATATACAAAAATTAACTC 488

  chr2_68678960_6   1968 AAAATGGATCAAATAATCTGAACATATAAAACTATAAACATCTAAAACTA 2017
                                    ? -i i  i  -- i   i v---------         
  L1M4_orf2#LINE/    489 AAAATGGATCAWA-GACCTAAA--TGTAAGAG---------CTAAAACTA 526

  chr2_68678960_6   2018 CAAGACTCTTAGAAGAAAA--TGGGGGAGAAGCTTCATGACATTGGATTT 2065
                         i  i               -- i  ? vi  v    i    v    i  v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_68678960_6   2066 GACAAAGATTTCTTGGATATGACACCAAA-GCACAGACAACAAAAGCAAA 2114
                          i   v i      i              -     ii         v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_68678960_6   2115 AATAGAAAAATTGGACTTT-TTAAAGTTAAAAACTTCTGTACATGAAAGA 2163
                               v           i- i   i          i   i v v    i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_68678960_6   2164 ACAAAATTAACACAGAGTGAAATGACAACCTATGGAATGGGATAAAATAT 2213
                            vv  i  v --i       v       i ii        v       
  L1M4_orf2#LINE/    677 ACACTATCAAGA--AAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_68678960_6   2214 TTGCAAATTATATATCTGATAAGG-ATTAATGTCTAGAATACATAAAGAA 2262
                                 i               - i vi i  i      i        
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_68678960_6   2263 CT---ATAACTAAACAACCAAAAAACAAATTACCCAATTTGAAATTGGGG 2309
                           --- i    v  i  iv    i      v        ?i   v    v
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_68678960_6   2310 ACAGAACTTAAATAGATATTTCTCTAAAGATAATATACAAATGACCAACA 2359
                          v  i i  i      i       i     vi           i    i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_68678960_6   2360 AGCATATTAAAAGATGCTCAACATCACTAAACAT 2393
                             i  v                  ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (100 / 62)
Gap_init rate = 0.02 (15 / 866), avg. gap size = 2.67 (40 / 15)  


 412 22.92 1.04 0.00  chr2_68693098_68694854      139   234 (1523)  C L1M4_orf2#LINE/L1   (811)    97     1  

C chr2_68693098_6    234 TGGAAACACATCCCACGTTCATGGATAGGTAGAATCAATATTGTAAAAAT 185
                               v i      i          v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_68693098_6    184 GATCACACT-GTCAAAGTAATCCACAAATTCAACTCAATTCCCATCA 139
                          iiv i   -vi    v i   i   i       v    i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.01 (1 / 97), avg. gap size = 1.00 (1 / 1)  

2667 26.39 2.79 0.27  chr2_68693098_68694854      512  1265 (492)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr2_68693098_6    512 ATCCTAAAATTCATATGGAA--------------------CTAAAACAAG 541
                                             -------------------- i       v
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_68693098_6    542 ACTAAGCAAAAAGAGCAAATCTGGAGGCATCACATTACCTGATTTCAAAC 591
                         vi i iv  i    i    vi      vv     i v  ii        v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_68693098_6    592 TATGCGATAAGGCCATAGTCACCAAAACACCATGGTACTGGCATAAAGAT 641
                         iv i v i  i  i i   v i   i   vii              i   
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_68693098_6    642 AGGCACATAGACCAATGGAACAGAATAGAGAGCCCAGAAAAAAACCCCTA 691
                           i  i     i        i     v     i       v      v  
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_68693098_6    692 ATACTTACAGCCAACTGATCTTCAACAAAGATGTTTGTGTTTATAAAGTG 741
                         -i i   ii i   i    i   i    i i  -iiiv vii  vv i  
  L1M4_orf2#LINE/    336 -CATTTATGGTCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATG 383

  chr2_68693098_6    742 GGGAAAGGATACCCTATTCAACAAATGGTGCATGAATAATTGGCAAGCCA 791
                                i   vi  v               vv i i  i   vv ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_68693098_6    792 CATGTAGGAAAATGAAACTGGACCCTCATCTCTCACCTTATACAAAAATC 841
                             i ii i      ii       ii i   v    v           i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_68693098_6    842 AACTCAAGATGGATCAAGGACTTAAATCTAAGACCAGAAACTGTAAAAAT 891
                                i        ?i   i     v     v vi     i     v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_68693098_6    892 TATAGAAGACAAAACTGGAAAAACCCTTCTAGACATTGGCTTAGACAAGG 941
                         iv       v  v iv  ?iv  vi    vv   v    v    i   v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_68693098_6    942 ATTTCATAACCAAAAACCTAAAAGCAAGTGCAATAATAACAAAGATAAAT 991
                         i    v  ivi vi vv i       viv    i  v iv   i   i  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_68693098_6    992 AGCTGGGACTTAATTAAACTAAAGAGCTTTTACACAGCAAAAGCAACAGT 1041
                          iv v      v  i   v v  i i     iii vv    i vv  vi 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_68693098_6   1042 CAGCAGAGTAAACAGACAACCCACAGAGTGGGTGAAAATCTTCACAATTT 1091
                           iv i   i  v              i    v      v  ii   v i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_68693098_6   1092 GTACATCTGACAAAGGACTAATATCCAGAATCTACAATGAATTCAAACAA 1141
                         i  i      i  i     vi          v  i  v   i  vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_68693098_6   1142 ATTAGCAAGAAAAA-ACAAGCAATCCAATCAAAAAGTAGGCTAAGGACAT 1190
                         v i ii  v     -    ii  i     i?    i i   v     iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_68693098_6   1191 GAATAGACAATTTTCAAAAGAGGATATATAAATGGCCAACAAACATATGA 1240
                                  v  i  v     i      i          i  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_68693098_6   1241 AAAAATGCTCAATATCACTAGTGAT 1265
                            i        i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (118 / 77)
Gap_init rate = 0.01 (4 / 773), avg. gap size = 5.75 (23 / 4)  


4035 19.44 2.92 0.90  chr2_68740257_68743163     1526  2415 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_68740257_6   1526 TGGGAAGATATTCTGTGTTCATAGATTAGAAGACTTAATATCACCAAGAT 1575
                            i       i ii       i    i             iiii     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_68740257_6   1576 GCCAACACTTCC-AAAGGGATCTACAAATTTAATGCAATCCTTGTCAAAA 1624
                          v   i   i  -   vv        i   i  i       i i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_68740257_6   1625 TATCAATGATATTTTTTGCAGAAATAGAAAAATCCATCCTAAAAGTCATA 1674
                          vi  iiviiv              v  v  iiiv         v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_68740257_6   1675 TATTTCAATTCTCAAAGCATCTCAGA-TAGCCAAAACAATATTGAAAAAG 1723
                          iv--v   v --  i v i -    -             v         
  L1M4_orf2#LINE/    151 TGG--AAATGC--AAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_68740257_6   1724 AT---CAAGGCTGGAGGTTTCACACTTTCTGATTTCAAAACTTATTACAA 1770
                          v---   i i      vi        i ii             i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_68740257_6   1771 AGCTACGGTAATCCAAACAGTGTGGTACTGGCATAAC-ACAGACATACAG 1819
                               i      v i                    v- i       i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_68740257_6   1820 ACCAATGTAATAGACTAGAGAGCTCAGAAATAAATTATCATATAT--ATG 1867
                          i     v      v v     ii          ii--    i  --   
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATG 343

  chr2_68740257_6   1868 GTCATATAATTTTTAACAACAGTGTCAAGACAGTTCAGTGGAGAAAGAAT 1917
                             vv i     ii    vi   i      vi    i   i        
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_68740257_6   1918 AGTTTTTTCAACAAATAGTGCTGGAA-AA------------ATGCAAAAT 1954
                            i            i       i -  ------------        v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_68740257_6   1955 AATGAGGTTGGATGCCTACTTCATACCATATTCAAAAATTCACTTAAAAG 2004
                              i      iv     i   i       v        v   i    v
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_68740257_6   2005 GATTTAAAGAACCTAAACACAAAACCTGCAACTATAAAACCCTTAGCAGA 2054
                          iv i ?   -      iii  i v  iv           i     v   
  L1M4_orf2#LINE/    494 GGATCAWAGA-CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_68740257_6   2055 AAACATAAGGACAAAACTTCGTGCCATTAGATTTGGGAATAATTTCTTGA 2104
                                i ?ii   v       v v  i i  v  v   ii      ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_68740257_6   2105 ATATGACACCAAA-GCACAAGCCACCAAAGTGAAAATAGACAAATTGGAC 2153
                                      -        v  v    vi        i         
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_68740257_6   2154 TGCATCAAAATAAAAAACTTCTGTGCACGAAAGGATGTAATCAACAACAC 2203
                          v         v        i     viv      iiiv     v  vii
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_68740257_6   2204 -AAAAG-CAACCTATAGAATGGTAGAAAATATTTGCAAATATTATATCTG 2251
                         -     -     i i       v                 vv        
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_68740257_6   2252 ATAAGGGTTTAATGTTGAGAATATGTAAAGAATGCCTACAACTCAACAAC 2301
                                vi vi i iv       i       iv i          i  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_68740257_6   2302 AAAAATACAAATAACC--ATTCAAAAGTGGGCAATCGACTTGAATAAACA 2349
                              v          --   ?    i       vv  i       i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_68740257_6   2350 TTTTACTAAAGAAGATATACAAATGATCAACAAGCATATGAAAAGATGCT 2399
                            iv i                  ii   i     i             
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_68740257_6   2400 CAGAATCACTACTCAT 2415
                           iv    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (108 / 62)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.12 (34 / 16)  


2262 21.05 4.41 11.19  chr2_68746959_68749541.rev     1118  2091 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_68746959_6   1118 TGGAAAGACATTCCATGCTCATGGATTGAAAGA----ATATCATTAAAAT 1163
                                 i  i     i          i    ----    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_68746959_6   1164 GGTCCAA--CTGCACAAAGCAATCTACAGAGTCAATGCTATTCCTATCAA 1211
                           --   --  v v    vii         v    i  v  i        
  L1M4_orf2#LINE/     51 GG--CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_68746959_6   1212 ACTGCCAA-TGTTATTTTTCACAGAATTAGAAAAAACT-ATC-TAAAATT 1258
                          v v   i-  ii-     ii     v v  v  i-  -   -       
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chr2_68746959_6   1259 CATATGGAACCAAAAAAGATCCTCAATAGCCAAGATAATCCTAAACAAAA 1308
                                  viiv  ii  i  vv         i i    i i  v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_68746959_6   1309 AGAACAAAGCTGAAAGCATCACATTACCCAACTTCAAAG--TA-TATAAG 1355
                                  i  i i vv     i v     i      i--  -  i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_68746959_6   1356 GCTACAGAAACCAAAACAGCATGGTGCTGGTACAAA-ATAGCCATATAAA 1404
                                v  i   i    ii    i    i i  i-    v      i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_68746959_6   1405 CTACCAAAATATCTGGAATGCAATGAAAACAAAAGCAGTGTTAAGAGAGA 1454
                         i---   ------      ----------- i  ------  i    ---
  L1M4_orf2#LINE/    297 T---CAA------TGGAAT-----------AGAA------TTGAGAG--- 317

  chr2_68746959_6   1455 AGTTTATAGTGCTAAATGCTTACATCAAGAAGTTAGAACGATCTCAAATT 1504
                         ------------------------  v    -------------------
  L1M4_orf2#LINE/    318 ------------------------TCCAGAA------------------- 324

  chr2_68746959_6   1505 TGGAATAGAGAACCCAGTCATAAAGCTACTTACCTACAGCCATCTAATCT 1554
                         ----   ---      ----------   -- ii  ii i  vi i  i 
  L1M4_orf2#LINE/    325 ----ATA---AACCCA----------TAC--ATTTATGGTCAATTGATTT 355

  chr2_68746959_6   1555 TTGACAAAGCTGACAAAAAGAAACAATGGGAAAATGACT--TCCCATTCA 1602
                          i     i v  v   i vv vv       i   -  v --  ii-    
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTT-TTCA 403

  chr2_68746959_6   1603 ACAAATAGTGCTGGGATACCTAGCTAGCCATATGCAGAAGAATGAAACTG 1652
                               i         i v  i v  ?   i     i         ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_68746959_6   1653 GACATTTACCTTTCACCATATACAAAAATAAACTGAAGATGGATTAATGA 1702
                            vii     iv                v    v  i      i ?v  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_68746959_6   1703 TTTAAGCATAAGACCTCGAACTATAAAAATTCTAGAAGAAAACCTATG-- 1750
                         ii   iii     v  vi          v ii           v  v --
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_68746959_6   1751 -AAATACCATTCTGAACATGGGCCTTGGAAAGGAATTTATGACTAAGTCC 1799
                         -    -- v iv   v v    i- v  v  v iv  iv iiv  v v v
  L1M4_orf2#LINE/    554 TAAAT--CTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACA 600

  chr2_68746959_6   1800 TCAAAAGCAGTTGCAACAAAACAAAAAATTGACAG-TT-----------A 1837
                         i        vvv         v       v  i i-  ----------- 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_68746959_6   1838 AACTAAACAGTTTCTGTAAAGCAAAAGAAACTATCAACAGAGCAAATAGA 1887
                           i    - ii  i   ivvv    i  v        v i  ii  v   
  L1M4_orf2#LINE/    651 AATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_68746959_6   1888 CAACCTACATAATGGGAGAAAATATTTGCAAACTAT-CATCTGACAAAGG 1936
                              i   v                      ii  -i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_68746959_6   1937 ---TGGAATATCCAGAATCTATAAGGAAATTTAACAATTCAACAAGCAAA 1983
                         ---  ---          v     i   v i v    i    i  vv   
  L1M4_orf2#LINE/    750 ACTTG---TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_68746959_6   1984 AAACAAATAAAACAACCCCATTTAAAAATGTGCGAAAGACGTGAATAATC 2033
                          i        -----   v   ?       v  i  i  iv      iv 
  L1M4_orf2#LINE/    797 AGACAAATAA-----CCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_68746959_6   2034 ACTTCTC-AA--------TGCAAGTGGCCAATAAATATATTTTTAAATGC 2074
                          i     -  -------- i   i          ii i  vvvv i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_68746959_6   2075 TCATCATTACTAATCAT 2091
                            v   i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (122 / 80)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 4.34 (152 / 35)  


3219 27.64 0.22 0.22  chr2_68752684_68758187.rev     4105  5012 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_68752684_6   4105 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATCTCATGAAAAT 4154
                              ii i  i     i      i v      v i   v ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_68752684_6   4155 GGCCATACTGCCCAAGGAAATTTACAGATTCAATGCCACCCCCATCAAGC 4204
                            v     v     ivvi  i           i  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_68752684_6   4205 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 4252
                          v   iivi i  i  ii     -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_68752684_6   4253 TATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 4302
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_68752684_6   4303 AATAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4352
                           i    i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_68752684_6   4353 TACAGTAACCTAAACAGCATGGTACTGGTACCAAAACAGAGATATACATC 4402
                                 i v i    ii         i iv ii i   v     v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_68752684_6   4403 AATGGAACAGAACAGAGCGCTCAGAAATAACACCGCATATCTACAACTAT 4452
                                i    iv   v ii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_68752684_6   4453 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 4502
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_68752684_6   4503 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 4552
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_68752684_6   4553 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 4602
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_68752684_6   4603 AAAGACTTAAACGTTAGGCCTAAAACCATAAAAACCCTAGAAGAAAACCT 4652
                          ?    i    i  v  iv       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_68752684_6   4653 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 4702
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_68752684_6   4703 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTCATT 4752
                                    vvi           v     v  i    v   ii    i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_68752684_6   4753 AAACTAAAGAGCTTCTGCACAGCAAAACAAACTACCATCAGAGTGAACAG 4802
                            v v  i i   i  ii vv    iv v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_68752684_6   4803 GCTACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 4852
                         i v   i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_68752684_6   4853 GGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAA 4902
                          i  vi          v  i         vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_68752684_6   4903 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 4952
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_68752684_6   4953 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5002
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_68752684_6   5003 CACTGGCCAT 5012
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


2532 24.94 4.92 4.36  chr2_68822926_68824978      673  1566 (487)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_68822926_6    673 ATCCAATGTTTGTGGATTGGAAAACTCAGTTTTGTTATGATACTTATTCT 722
                             v     ii          i   i i v      v   iviv  v  
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_68822926_6    723 TCTCAAATT----TATAGATTTAACAAAATTCCAATTAAAATTCCAGCAA 768
                         i i      ----  i     i   iv   i  v  i     i     v-
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT- 108

  chr2_68822926_6    769 GCTCTTTTCTGTAGAAATTGACATGCTGATTCTAAGATGTATATA-AAAT 817
                           -     i  i           v      i    i  vi    i-    
  L1M4_orf2#LINE/    109 GC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_68822926_6    818 GTGAAGGATCTAGAA-----------ATTT--AAAAAGAAGAACAGAGTT 854
                          ii i   i i    -----------  i --             i    
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_68822926_6    855 GGAGGACACCTACCACTTGATTTCAAAACTTACCATAAAACTATGGTAAT 904
                                v vi  iv iii              i i   i   ii     
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_68822926_6    905 CAATATGGTGTGGTATTGGCATA-GGACAGACAACTTAATCAAAGGACCA 953
                            v ii        i       -   i     vv vi     v   vi 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_68822926_6    954 GAAACGAAGGTCCGGAATCAGACCCGCACATATACGGGCAATGAATTTTT 1003
                            vi  ii    i   vi i    ii    v  i  v    vi     i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_68822926_6   1004 GACAAAGGCACCAAAACAATTCAATGTGAAAAAGCAACTTGTGTTTGTTT 1053
                              i  ii    i  v        - ii    -  -------------
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATG-GGGAAAG-AA------------- 392

  chr2_68822926_6   1054 GTTTGTTTGTTTGTTTGTTTTTCAACAAATGGTCCTGGAACAATTGAATA 1103
                         ---------- v  i ---              v    i    i  i   
  L1M4_orf2#LINE/    393 ----------TAGTCT---TTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_68822926_6   1104 GCTAAATGGCAAGAAAA-GAACCTCAAACCTTCTTTCTATAG-ATACACC 1151
                         ? i v   -   i i  -   vi vi v  i vii  - i v-   i  v
  L1M4_orf2#LINE/    430 KCCACATG-CAAAAGAATGAAGTTGGACCCCTACCTC-ACACCATATACA 477

  chr2_68822926_6   1152 AAAATTAATTTCAGATGGCTCAAAGGTTTAAAAATATAAGCAAGAACTAA 1201
                                 i iv i    v   ?  iii    vi  vi   v i     v
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_68822926_6   1202 AGGGCTTGTAGAAGAAAACATAGGAGAGTATCTTCACAGTCTTAGG---G 1248
                          iii  iv                ? viv      iiiii   i  --- 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_68822926_6   1249 GCAGAAATAGATTTATTGGACAGAACAT-AAAAACATAAT--ATAAAATA 1295
                            ---  i -   v  i  i vi   i-    i  i  v-- i    v 
  L1M4_orf2#LINE/    578 GCA---ATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_68822926_6   1296 AAATTT-TATAGATTAGAATTCATCGAAATGAAAA--TGTTCAGCT-CAT 1341
                            vv -v   i   i  v      i    v    -- v  vv   -  -
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA- 672

  chr2_68822926_6   1342 ATGAAGACACCAGTAAGTAAATAAGTAGGCAAGCCACGAACCAGGAGGAA 1391
                         --i i     i vi   v  i i iv  i   v    ii vii    i  
  L1M4_orf2#LINE/    673 --AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_68822926_6   1392 AAATTTGTAATACGTATATCTAACAAGA-ACTTTAATCCAGAATA----A 1436
                          v     i  vv i       i i   i-    vv          ---- 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_68822926_6   1437 AGAATTACTAAAAATTAACAATGAAATGCCAA----CCCAAT--AAAAAG 1480
                             i vi  v  v i  i   i   v v   ----      --     v
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_68822926_6   1481 TAGCAAAAGCCTTGAACAGATATTTCACAAAAGAAAATGTATGAATGGCT 1530
                         vi     i vi     i   i     v v      i  i  ii      i
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_68822926_6   1531 AATTAGCACATGAAAAGTTTCTC--TCTCATTATACTA 1566
                            v             v v   --iv   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (140 / 80)
Gap_init rate = 0.03 (29 / 899), avg. gap size = 2.86 (83 / 29)  


3572 16.56 3.90 8.12  chr2_68896546_68900928     2944  3891 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_68896546_6   2944 TGGGAAGACATCCCAGGCTCCCTAGGTTGGAAGACTTAATACTAT----- 2988
                            i    i      v i  v- i i               i i -----
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCA-TGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_68896546_6   2989 ------------CCAAACCAACCTACAGATTTAATGCAATTCCTATCAAA 3026
                         ------------     iii i         i  i     i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_68896546_6   3027 ATCCCAA-TGACTTTTT-GTAGAAATAGAAAAACTCATCCTAAAGTTCAT 3074
                               i-  v      - i      v  v  i  v        i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_68896546_6   3075 ATGGAAACTCAAGGGATCCTGAATAGCAAAAAAAAAAAAAAAAAATTTTT 3124
                                iv       i  v       v    v  ----------- i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-----------TCTT 188

  chr2_68896546_6   3125 GAAAAAGAA---CATTGTTGGATAACTCACATTTCCTATTTGAATCACAT 3171
                                  ---  vv      vi       i    i ----------  
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA----------AT 228

  chr2_68896546_6   3172 AATTCAAAAATTATATGATTAGTTACAAAATTTAGAGTAAACCAAAACAG 3221
                         --       v   i---------      ii - v     -i   i    
  L1M4_orf2#LINE/    229 --TTCAAAACTTAC---------TACAAAGCT-ACAGTAA-TCAAGACAG 265

  chr2_68896546_6   3222 TGTAGTAATGGCATAAAGACAGA-A-ACAGATGAATGGAATAGAATAGAT 3269
                            i   v        i  i   - - i    v             v  v
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_68896546_6   3270 TGTCTGGAATAGAATAGATGTAGAGGTCACATACACATATATGACCTCAC 3319
                         v   ii   ----   i --------- v      ---------------
  L1M4_orf2#LINE/    316 AGTCCAGAA----ATAAA---------CCCATACA--------------- 337

  chr2_68896546_6   3320 ATATATGTGTATGGTCAAATGATTTTCAACAAGGGTGCCACGATAATTTA 3369
                         ------- v         v        i            v  iv   i 
  L1M4_orf2#LINE/    338 -------TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_68896546_6   3370 ATGGGGAAAAGATTGTCTTTTCAA-AAATGATGCTAGGAAAACTGGATAT 3418
                                  ii  v          -     i    i   v         ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_68896546_6   3419 CCACATGCAAAATAATAAAGTTAGGCCCTTACCTAATACCATATACAAAA 3468
                                     v   i     i i   i     v i             
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_68896546_6   3469 ATTAACTCAAAATGGACCTATGAACTAAATTTAAGACCCCAAACTGTAAA 3518
                                         i v?v  v      v     v iv     i    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_68896546_6   3519 ACTCTTAGAAGAAGACGTGGGGCAAAAACTTCACAACACTGAATTTGGCA 3568
                                      i  i i  ?vv   v    iii  vi  ii  v    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_68896546_6   3569 ATGATTTCTTGGCTTCAACATCAAAGGCACAGGTAACAGAAGAAAAAATA 3618
                            i      i v vii   i    i     i i    i           
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_68896546_6   3619 GTCAAATTAGACTTC-TGAAAATTTAAAAAATTACGTA--TCAAAAGATA 3665
                          vi     i      - v      -     v  vi  i--     i  i 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_68896546_6   3666 CTACCAACAGAGTAAAAA----ATCAACAGAATAGGGGAAAATATTTGCA 3711
                            i   v i   i    ---- i v       i  i             
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_68896546_6   3712 AATCATATATCTAACAAGGGATTAATATCCAGAATGTATAAAAAGCTCCT 3761
                                     i i      i vi          i      i i   i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_68896546_6   3762 A-AACTCTACAAAAAAAAACCCCACAAACAACTCAGTTCAAAAATGGGCA 3810
                          -     v i  v     i----     i   i  i  ?           
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAG----ACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_68896546_6   3811 AAGGACTCAAATAGACATTTCTCCAAAGAAGATATGCAAATGGACAATAA 3860
                              i ii                          i       v      
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_68896546_6   3861 ----ATGAAATGATGCTATCAATATTAGTAATCAT 3891
                         ----      v      --   i  i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCT--CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (100 / 53)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 4.56 (114 / 25)  


3075 24.15 1.98 2.31  chr2_69029337_69033586.rev     2848  3758 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_69029337_6   2848 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2897
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_69029337_6   2898 GACCATACTGCCAAAAGCAGTCTACAAATTCAACACAATCCCCATCCAAA 2947
                          i v     v  v   viii      i       i       i   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_69029337_6   2948 TACCACCATAATTCTTCACAGAATTAGAAAAAAACATTCTGAAATTCATA 2997
                          v   v vvvv  i  ii     v v  v  ivvv  i  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_69029337_6   2998 CGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAATACTAACCAAAAAGAA 3047
                         i    viiv  ii  v  v v         i    vi i vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_69029337_6   3048 CAAATCTGGAGGCATCACACTACCTGATTTCAAATTATACTATTAGGCCA 3097
                             vi      vv       v  ii        viv     iv i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_69029337_6   3098 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGATCAA 3147
                         i   v i   i    ii         i    ii    i  i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_69029337_6   3148 TGGAACATAATAGAGAACCCAGAAATAAACCGAAATGCTTATAGCCAACT 3197
                              i v   v    ii             v v iii    i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_69029337_6   3198 GATCCTTGACAAAGCAAACAAAAACGTAAAGTGGAGAAAGGACACCCTTT 3247
                            ii i     i vviv   i v i vv i   i     i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_69029337_6   3248 TCAACAAATAGTGCTAGGATAATTGGCTAGCCACATGTAGGAGAATGAAA 3297
                                  i     i   i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_69029337_6   3298 CTGGATCCTCATCTCTTACATTATACAAAAATCAACTGAAGACGGATTAA 3347
                         i    i  ii i   vi  vv           i    v  i i    i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_69029337_6   3348 GGACTTAAACCTAAAATCTGAAACTATAAAAATTCTAGAAGATAGCATTG 3397
                         i   i    iv   i v  i           v ii       v i   v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_69029337_6   3398 GAA-AAACCTTTCTAGACATTGGCTTAGGCAAGGATTTC------ATGAC 3440
                          ?i-   i   iv -   v    v        v i    ------     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_69029337_6   3441 --CAAGAACACAAAAGCAAGTACAATAAAAACAA-AGATAAAAAGCTGGG 3487
                         --   i i     --    ---   v i   v  -       ---- v  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAA--GCAA---CAAAAGAAAAAATAGATAAA----TTGG 640

  chr2_69029337_6   3488 ACCTAATTAATTAATTAATTAATTAATTGCTTTTGCATAGCAAAAGGAAC 3537
                           i v  i  ------      --  --i      iiivv    i iv  
  L1M4_orf2#LINE/    641 ACTTCATCAA------AATTAA--AA--ACTTTTGTGCTTCAAAGGACAC 680

  chr2_69029337_6   3538 AGTCAGCAGAGTAAATAGACAACCCACAGAGTGGGAGAAAATCTTC---- 3583
                         vi   iv i   i  v              i           v  i----
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_69029337_6   3584 ATCTATACATCTGACAAAGGATTAATATCCAGAATCTACAATGAACTCAA 3633
                            -   i      i  i   i vi          v  i  v      vv
  L1M4_orf2#LINE/    731 ATC-ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_69029337_6   3634 ACAAA-CAGTAAGAAATAAACAAACAACCCCATCGAAAAGTGGACTAAGG 3682
                             v-  i   v   v i     i     v  i?    i   i v    
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_69029337_6   3683 ACATGAATAGACTATTCTGAAAAGAAGATACACAAATGGCCAACAA--AC 3730
                          iv         vv    vv          i            i  --  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_69029337_6   3731 ATAAAAA-ATGCTCAACATCACTAATGAT 3758
                           i    -             ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (127 / 89)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.44 (39 / 16)  


2402 23.67 8.66 3.81  chr2_69077823_69080414.rev     1235  2100 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_69077823_6   1235 TGGAAAAAAATCC-ATGACCATGGATTGGAAAAATTAATATTGTTAAAAT 1283
                               i v    -   vi            i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_69077823_6   1284 GGCCATACTGCCCAAAGCAATATACAGATTCAATGCTATTCTTTTAAAAC 1333
                            v     v      vii  v           i  v  i i v v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_69077823_6   1334 TGCCAA-TGTCATTCTTCACAGAATTAGAAAAAAACT-ATTCTAAAATTC 1381
                          v   i-  i -  i  ii     v v  v  i--  -  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_69077823_6   1382 ATATGGAACAAAAAAGAGCCCA-AACAGCCAAAGCAATCCTAAGCAAACA 1430
                                 vviv  i ii    -  i       i     i i -------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------- 190

  chr2_69077823_6   1431 AAACAAAACAAATGAACAAACAAAAAACAAAGCTGAAGACATCACACTAC 1480
                         ----    -------------i  i       i  i  ivv       v 
  L1M4_orf2#LINE/    191 ----AAAA-------------GAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr2_69077823_6   1481 CAGACTTCAAACTACACTACAAAGCTACAGTAACCAAAACGGCAGGGTAC 1530
                          vi i      vivi                  i   i  i iiv     
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr2_69077823_6   1531 TGGTACAAAAACAGACACATAGACTAATGGAACAGGTTACAGAACTCAGA 1580
                            i i  ii i     i     ii       i  iv vv   iii    
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_69077823_6   1581 AATTAAGCCACACACCTACAACCATCTGATCTCCAACAAGGCTGACAAAA 1630
                            v  v   i   ii  iiii  vi    i i i      v  v   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr2_69077823_6   1631 ACAAGCAATGGGGTAAGGATTCCCTATTCAATAAATGGTGCTGGGATAAC 1680
                         v  vv        v   i  vvi  v     i              i   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_69077823_6   1681 TGGCTAGGCATATGCAGAAGATTGAAGCTGGAACC-TACCTCTCACCGTA 1729
                            v  ?v  i     i    v     i    v  -      v    i  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_69077823_6   1730 TACAAAAATTAACTCAAAATGGATCAAAGACCTCAA----AGACCTCAAA 1775
                                                   ?      v  ----   v  v   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_69077823_6   1776 CTATAAAAATCCTAGAAGATAACCTAGGAAATACAACAT--TAACCTTGG 1823
                                 v  i       v   v    ?i-  v v v -- i       
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGG 572

  chr2_69077823_6   1824 ------CAACA-----TTAGCCTTGGTA-------------------AAG 1843
                         ------   ii-----    viv  ii -------------------   
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_69077823_6   1844 AAG-----------TGGGATCT------AATTAAAGAGTTCCTGTGCAGC 1876
                           i----------- v   ii ------       i v  i-     vv 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTC 671

  chr2_69077823_6   1877 AAATGAAACTATTAACACAGTAAACAGACAACCTACAGAATAAGAGAAGA 1926
                            v  v     i  v v   i  v        i       ii     i 
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_69077823_6   1927 TATTCTCAAACTACGGATCTGACGAAGGCAAAGTATCCGTCCAGAATCTA 1976
                             iv    ii iiv      ii i  vvvv      ----     v  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCC----AGAATATA 767

  chr2_69077823_6   1977 TAGAGACCTTAAACAAATCAACAAGTGACAAACAAATAACACT-TTAAAA 2025
                           i   v  ivv    v    i  vvi v i         v v-  ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_69077823_6   2026 AATAGGCAAAAGAGATTAACTGATACTTCTTAAAAG------------TG 2063
                            i      i  vv v  iv  i i    iv    ------------  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_69077823_6   2064 GCCAACAAACATATGAAAAA----TTAGCATCACTAATAAT 2100
                              i  i  i       i---- i i     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (115 / 86)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.91 (108 / 22)  


 736 30.61 13.01 2.97  chr2_69246055_69249345     1995  2801 (490)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr2_69246055_6   1995 ATGGAGCAGTA-ACTGAGTATTGTAAAGATATCAATTGTCTTCATCTTAA 2043
                              vii v -   v i      v     iv    vv  ii  vv  i 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr2_69246055_6   2044 TATCTACT--TTTATTACAATCCAAATGAAAATTCCAAGGGGACTTTTT- 2090
                          --    v--  i vii      vv  v     i   - vv v      -
  L1M4_orf2#LINE/     71 T--CTACAGATTCAACGCAATCCCTATCAAAATCCCA-GCTGCCTTTTTT 117

  chr2_69246055_6   2091 ----AAGTTAACAAAATAATC-TGAAGTTTATGTGGAAGAATAAACACAC 2135
                         ----  i  i    iv i   - i  i  i  i     ivii  ivivv 
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_69246055_6   2136 AAGAATAGCCAA---------------GAAAAATG----TGGAA-ACTCG 2165
                         v           ---------------   i  ii----    i-    i
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_69246055_6   2166 CCCTGGCCGATTTTAAGATTTATAAAAACGCTGCAGTAATTGGAACAATG 2215
                          v  vv  i    i  i i   iv v  v   i       iiii   i  
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_69246055_6   2216 TA-TGATCACACCACAGTAGGCGAACTGAGCTTTGGAACAAA-------G 2257
                          i- iv vi  iv vii   i iv iv  v vv     i i ------- 
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_69246055_6   2258 CCCATAAACAGAACCAAACACTTA-GGTGAATTTAGTATAAAATAAGG-- 2304
                         i   v   i i v   v   i   -   v    v v v vi -i    --
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA-CAAGGGT 366

  chr2_69246055_6   2305 --CAG--CCTTTCAAATCTGTAGGGAAAGAGTGGGTTATTCAAAAAATGA 2350
                         --  i--  v     ----- i        i i vi v     v     i
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAA-----TGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_69246055_6   2351 TGTTGAGACAACTGGCCAACCACTTGGAAAAACAGTTAAGTTCATTTTTA 2400
                           i  i         vi ?    v  v    i- i v     viviiiiv
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAG-AATGAAGTTGGACCCCT 460

  chr2_69246055_6   2401 ATCTCACACCTTTCATCCAAACA--AATTCCAGATGAAGGAAAACTTTTA 2448
                          i        v --  v    v --  i  v i   i vv ? ivii v 
  L1M4_orf2#LINE/    461 ACCTCACACCAT--ATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_69246055_6   2449 ATG--GGACATGAAGCTGTAAAAATTCTAGAGGGAAACAAAA----AAAT 2492
                            --i  vv i  i  i     v ii    i i     v i----    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_69246055_6   2493 GTATATAATCTTCCAGGT--GGGAAGGATGTGTTAAACATGA----AGGA 2536
                         v vii i i   --i   --  v  v i v v   i i    ---- ii 
  L1M4_orf2#LINE/    559 CTTCGTGACCTT--GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_69246055_6   2537 GCATA--CCATGAAAGAAAAATTTGA-ATGTTTGAGTGCAT-ATTTTTAA 2582
                            i -- v ii         v v  - vi  v  v v   - vvv    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_69246055_6   2583 ATTCTCTTGT----TAAACCCTACTA-CAATAAAACAAACAAGA-AAT-- 2624
                          vv  i    ----i   vvvi    -   v   iii  -    -  i--
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA-AAGACAACCC 705

  chr2_69246055_6   2625 --AAAACTGGAAAAATAGGATATATAACAAA-CATAGGGTCAATAA---A 2668
                         -- i  iv   i   ----    v i-    -    viviii    --- 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAA----ATATTTG-CAAATCATATATCTGATAAGGGA 750

  chr2_69246055_6   2669 CTT------AG----TATAAAGACAATTCCTAAAA-TCGGTTAAAAAAAG 2707
                            ------  ----        -- i  i  v  -  ii v v      
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGA--ACTCTTACAACTCAATAATAAAAAG 798

  chr2_69246055_6   2708 GTGAATATATC---------AGTGAGTAAAAGATATGCAAAGGAAATTTT 2748
                         iii    - i --------- i  i i   i   v  -  vi  v    i
  L1M4_orf2#LINE/    799 ACAAATA-ACCCAATTWAAAAATGGGCAAAGGATTTG-AATAGACATTTC 846

  chr2_69246055_6   2749 T---AAGAAAATA-----ATGATTAATAAGCATATAGAAA-ATGTTTCAT 2789
                          ---     i   -----   iii        i  ii   -   i iv i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_69246055_6   2790 ATAACCAAGAAA 2801
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.05 (46 / 888), avg. gap size = 2.80 (129 / 46)  


 894 27.14 11.81 1.51  chr2_69451531_69453753      561   958 (1265)    L1M4_orf2#LINE/L1       13   451 (457)  

  chr2_69451531_6    561 CCACATGCATAGCCTGGAAGGCTCAACATTGTAAAACTGCCAATTCTCCC 610
                            ii v   i vi      i  i  i     v  iv  v    v     
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_69451531_6    611 CATATTCATCTATAATATTAAGGCAATTCCAATAAAAACCTCAGCAG--- 657
                           v   v     i ivv i  v     i  v  v    i i    v ---
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_69451531_6    658 ---TTGTGTAACTTGACAAGCTGCTTCTAAAATCCTTATATAAATTGAAA 704
                         ---   iiv  v           v i       i v   iv    vv  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_69451531_6    705 AGAAAAAGAATAGCCAAGATATTCTTGAAGAAAAACAGTGAGAAAAG--- 751
                         i  vvv           i i v       i  i  ----  iv    ---
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA----GAACAAAGTTG 208

  chr2_69451531_6    752 GAGGGTT-GCCCTACCAGATATCAAGACTTCTTATAAAGCTACA-TAATG 799
                             ii -i v  v  vi  v    i    vi  i         -    v
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_69451531_6    800 CAGACAGTGTTGAATTGGTACAG----AGACAAATAGCCCA-TGGAA--- 841
                         v         v v i   i i i----     v    vi  -     ---
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_69451531_6    842 ----------------ACAAACCCA--CTTATATGAACACTTGATATGAG 873
                         ---------------- i       -- v v    iv  v     v vv 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_69451531_6    874 AGGTGACGTTGCAGAGA------AATTGGGAAAGGATGGGATTTTTGATA 917
                          --ii v v   vi   ------   v       i  i vv    ii i 
  L1M4_orf2#LINE/    359 A--CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_69451531_6    918 AACA-TGCTGGGA-AATAGGATATCTTCAT-TAAAAAAA-AAAGT 958
                           ii-        -  iv     ? iv   -i    i  -i    
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

Transitions / transversions = 1.06 (55 / 52)
Gap_init rate = 0.03 (15 / 439), avg. gap size = 3.53 (53 / 15)  

 803 27.73 7.29 6.48  chr2_69451531_69453753     1238  1731 (492)    L1M4_orf2#LINE/L1      411   908 (0)  

  chr2_69451531_6   1238 GTGCTGGGATTACAGGCATGAGCCACCATGCCCGGCCAAAAAAAAAAAAA 1287
                                  iv  v  -  - ?    -    --------------    i
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGG-AT-AKCCAC-ATGC--------------AAAAG 443

  chr2_69451531_6   1288 AAAAAAGTTAAAATGAATTCCTACATCATATCAAACTTAAAA-TCCATTT 1336
                           vi     ----- i ii     v   i i  v ivi    - iv i i
  L1M4_orf2#LINE/    444 AATGAAGTT-----GGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_69451531_6   1337 CAGGTGAACTAAAAATCCAAGGATGAAAGGAAAAGCTTTAAGGGTTTTAG 1386
                         v ii  i ii ? i i i  ivi i i  vv   i  v   iiv i    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_69451531_6   1387 AAAACAATACAGGAGGATATGTTTAAGACCT------AGG-AAGGATTCC 1429
                           i v  i i   ? v v  v  iiv     ------   -  v i  i 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_69451531_6   1430 TTGAACAAGTTACATAAAAGCACAAAT--CA---GGGAAAATAAGTAATC 1474
                           ii i v vi  -i          ii--  --- ii      ii   --
  L1M4_orf2#LINE/    589 TTAGATATGACAC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAA-- 635

  chr2_69451531_6   1475 AATTTGACTACATTAAAGTTAAGAATTTCTATAC-------AATACGAAA 1517
                         -   v    v   i   i    i  i  i i i -------i i  v vv
  L1M4_orf2#LINE/    636 -ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_69451531_6   1518 AAGAGAATGAAAAGACAGGTCACA-AAGGGGAGAACATATTTGCAATACA 1566
                             i i          ivi    -  v       v          vv  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_69451531_6   1567 CA------ACAAAGAACTAGAATTCAGAATATGTAAAAAACCCCTCCAAG 1610
                         i ------ i  i i   v v  i        i    i   i i v   v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_69451531_6   1611 TTAAAAAGTAAACAATAAATCATCCAATTTTTAAAAACTGATTTTAAAAA 1660
                          i  v  vv   vi i    v i      ?--     iv ii----   i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTW--AAAAATGGGC----AAAG 828

  chr2_69451531_6   1661 GATTTGATCAGATTCATCACCAAAAAAAGCA--------GTCAATACACA 1702
                                vi   iviv  v     i  iii -------- i     vi  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_69451531_6   1703 TATGAAAAGATGCTCAA-ATCATTAATAAT 1731
                         i                -    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (87 / 46)
Gap_init rate = 0.04 (19 / 498), avg. gap size = 3.58 (68 / 19)  


 435 20.65 4.35 0.00  chr2_69747037_69750059      734   825 (2198)    L1M4_orf2#LINE/L1        6   101 (807)  

  chr2_69747037_6    734 AGACATCTTGTGTATGTGGATTGGAAGACTT---GTTGTTAGGATGTCAA 780
                            i   iii   vii               ---i      i    v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_69747037_6    781 TACTATCCAAAGCAATCTACAGGTTCAATGCCATCCCAAT-AAAAT 825
                             vi     vii        i     i  v     v  -     
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.02 (2 / 96), avg. gap size = 2.00 (4 / 2)  

 202 23.53 5.88 0.00  chr2_69747037_69750059     1448  1515 (1508)    L1M4_orf2#LINE/L1      138   209 (699)  

  chr2_69747037_6   1448 CCT-AAACCCACACGAAATCTCAAGGGACTCTGAATAACCAAAACAAATT 1496
                            -   ii  i i i  viv        i v     i         vi 
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_69747037_6   1497 AGAAAAATAA---CAAAATTGG 1515
                         v      v  ---    i    
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGG 209

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.03 (2 / 72), avg. gap size = 2.00 (4 / 2)  

3109 17.88 3.03 4.13  chr2_69747037_69750059     1805  2531 (492)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr2_69747037_6   1805 AAAAAAAAAAAAAAAATTGGAGGTCACATACCTTCTGATTTAAAAACTTA 1854
                              i  i  v   i       v v  i  i i ii    v        
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_69747037_6   1855 CTACAAAACTACAGTCATCAAAACAGTGTGGTACTGGCATAAAGACAGAT 1904
                                i       v     i                    i  i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_69747037_6   1905 ATAGAGACTAATAGAATAAAATAGAGATCCCAGAAATAAACCCTCACATA 1954
                            v   ii   i     i   v    vi              vi    v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_69747037_6   1955 TATGGTCAAATGATTTTTCAGCAAGCGTGCCAAGACCATTCAAGGGGGAA 2004
                                  v       - ii    v                 v      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_69747037_6   2005 AGGATAACCTCTTCAACAAATGGAACTGGGAAAACTGGATACCCACATGC 2054
                           i   ii  i            vi      v         ?        
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_69747037_6   2055 AAAAAAAGGA----GGACCCCTTCTTACCTCATGAC-TACACAAAAATTA 2099
                             i  v  ----        ----      iiv -  i          
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCT----ACCTCACACCATATACAAAAATTA 484

  chr2_69747037_6   2100 ACTCAAATTGGATCAAACATCTAAA-----AAGCTAAAACTACAAATTCC 2144
                                v       ? v i     -----i           i   vii 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_69747037_6   2145 TCAGAAGAAAACATATGGGAAAATCTTCATGACATTGAATTTAGCGATGA 2194
                          i             v ? v        i    v   ii  vi  i   i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_69747037_6   2195 CTTCTTGGATATGATACCAAAGGCACAGGCAACAAATGCAAAAATATGCA 2244
                         i     i       i      i     i        v v       vii 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_69747037_6   2245 AATGGAACCATAGCAAAAATTAAACACTTTTGAGTATCAAAGGACAACTA 2294
                            v i  ivi v     -     v       v iv          -   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACA-CTA 682

  chr2_69747037_6   2295 GCAAAAGAGTAGAAAGGCAATCCATGGAATGGAAGGAAATACTGTATTTA 2344
                         v   i i   ii    i   i   ii      i  i     -----   i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA-----TTTG 727

  chr2_69747037_6   2345 TAAATCATACATCTGATAAGAAGTTAACATCCAGAAAATATTAAAAATTC 2394
                         i        i          iiii vii        v    v  i  i  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_69747037_6   2395 CTAAAATTCAATAACAG------------CCCTATTAGAAAAATGAACAA 2432
                         i  v  i       i i------------   v   ?-       ii   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAA 826

  chr2_69747037_6   2433 TGGACTATTAATAGACATTTCTCCAAAGAAGATATACAAATGAGATATAC 2482
                         v   i - v                                 --------
  L1M4_orf2#LINE/    827 AGGATT-TGAATAGACATTTCTCCAAAGAAGATATACAAATG-------- 867

  chr2_69747037_6   2483 AAACAGCTAATAATAAGCACAGGAGAAGATGCTCAACATTATTAGTCAT 2531
                         -----  i     ---     v  i              i ????????
  L1M4_orf2#LINE/    868 -----GCCAATAA---GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (84 / 42)
Gap_init rate = 0.02 (13 / 719), avg. gap size = 4.00 (52 / 13)  


 545 24.77 19.16 0.47  chr2_69808810_69810720      501   714 (1197)    L1M4_orf2#LINE/L1      236   489 (419)  

  chr2_69808810_6    501 CTAATTATAAAGCTATAGTAACTAAGACAATGTGGCATGGGCACAGGGAT 550
                           v i  i       i     ii      i     i iv    i i    
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_69808810_6    551 AGACA--------ACTGG--CAGAATAGAGAGACCAGAAATTGACCTATG 590
                              -------- v   --i     v     v        vi   i  i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_69808810_6    591 GATAAATGGAGACCTGAT---------AGATGACA----TATACA-TGGG 626
                         v  vv    vv vi    ---------i i  v  ----i  v  -    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_69808810_6    627 GAA-GAGTA------------AATAGTACTGGAAAATTTGGTTATCTACG 663
                            -  i  ------------   i  i    i v vi   v  ? i  i
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_69808810_6    664 ---GAAAAAATGAAAGTGGACCCTTACCTTACATCA-ATCATAAAAATCA 709
                         ---i   i      iv       i     i   i  -  - i      i 
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTA 484

  chr2_69808810_6    710 ATTCA 714
                          i   
  L1M4_orf2#LINE/    485 ACTCA 489

Transitions / transversions = 1.89 (34 / 18)
Gap_init rate = 0.04 (10 / 254), avg. gap size = 4.20 (42 / 10)  

 516 27.03 8.14 2.89  chr2_69808810_69810720     1031  1411 (500)    L1M4_orf2#LINE/L1      466   866 (42)  

  chr2_69808810_6   1031 ATACCAT---CAATAATCAATTCAGAATGGA-------CCTAAAATGTGA 1070
                          i     ---   v   i  i   i      -------      -   - 
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA-TGT-A 513

  chr2_69808810_6   1071 AGAGC-AAATGTTTTAAATATTTAGATAATAGAAT--GAGTAGAATAGCT 1117
                              -   vv v v   ivi     vi v iv  -- ?   -   --  
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA-AAT--CT 560

  chr2_69808810_6   1118 TTATGACTTTGGGGTGGAGAAGGATTCCTTAAATAAAACACAAAAAGCAC 1167
                          ii    i     v i iv  v i  i    i   vi    v        
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_69808810_6   1168 AAACCTT----TAAAAAAT-GATAAATTTGAGACTACATTAAAATCAATA 1212
                           i vvi----v       -        --i    v   i     i  v 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATT--GGACTTCATCAAAATTAAAA 658

  chr2_69808810_6   1213 ACTTTTGT--TTATAAAAATACCATAAAATGCATAAAATGACAGGCTA-A 1259
                                 --  vv  ii i  i  v  ivivi i   v    iv i - 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_69808810_6   1260 AACTCAATCAAAATATCTGCAACTC-TAGTAACAG-TAAAG--TTTAGCA 1305
                         i v viivv       i     v  -  -  v v -   i --i  - i 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATA-TATCTGATAAGGGACTT-GTA 756

  chr2_69808810_6   1306 TCCTGAATATGTAAAGAACTCCTGTGAATCAATAAGAAACAACACAAGAG 1355
                            v      i          i iii v       v   -  v    - v
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAA-AT 804

  chr2_69808810_6   1356 AA---AA---AGCAATGCAAAAAAGACCTGTCAAGACATTTTACAGAATA 1399
                           ---  --- iv    viv   i  ii  vvv        iv vi  v 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_69808810_6   1400 AAAAATATGAAT 1411
                          i v   ii   
  L1M4_orf2#LINE/    855 AGATATACAAAT 866

Transitions / transversions = 1.12 (54 / 48)
Gap_init rate = 0.05 (22 / 401), avg. gap size = 1.91 (42 / 22)  


3701 21.33 5.13 0.00  chr2_70547264_70549120      508  1365 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_70547264_7    508 GACACCCCATGTTCATGAATTGAAAGACTTA------TTAAAATATCCAT 551
                           i i            i    i        ------    i  iv v  
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_70547264_7    552 TCTATCCAAAGCAATCTACAGATTCAATGCAATCCCTATAAAAGTCTCAA 601
                         v  vi     vii              i           v   i  i  i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_70547264_7    602 TGGCATTTTTTACATAAATAGAAAAA--AAAGTTAAAATTTATATAAAAC 649
                         iv  v      i  v    v  v  i--i vvi       i    ii  v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_70547264_7    650 TACAAAATACCCCAAATAGCCAAAACACACTTGAGAAAGAAGAACAAAGC 699
                          i   iiv    vi             vv     i              i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_70547264_7    700 TGGAGGCATCACACTTCCTGATTTCAGAA--TACTACAA-----CAAT-- 740
                               vv          ii      i  --        -----  i --
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_70547264_7    741 TTAAAACAGTCTAGTACTGG-ACAAGGATAGACATATAGAACAATGGAGC 789
                          i  i     v i       - i                 v       ii
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_70547264_7    790 AGAATAAAGAGCGCAGAAATTAATCCACACACGCATGGTCAACTGATCCT 839
                              vi    iv       v  i   i   ivi        i    ii 
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_70547264_7    840 CAACAAAGGTGCTAAAAATACAGAATGGGGAAAGGATAGTCTTTTTCATA 889
                          i    i     i  i vi ivv           i          iv i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_70547264_7    890 AATGGTGTTGGGAAAACTGGGTATCAACATGCAATAAAA--AAATTTGAT 937
                                i     v      i  ? v        v i  --  i  v  i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_70547264_7    938 TTTTATCTTACACCACACACAAAAATCAACTCAAAATAGATGAAAGACTT 987
                         iii  i  i      i i        i          i   v ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_70547264_7    988 AAATGTAAGACCTGAA-CTATAAAACTCCTATAAGAAAACATAGGAG-AA 1035
                                   v  i  -           i  v             ? -  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_70547264_7   1036 ATCTTCATG-CATTGGTCTGGGTCATGATTTTCTGGATATATCCCCAAAA 1084
                               i  - v    vi i  iv   i   ii i     iv v      
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_70547264_7   1085 GCACAGGCAACAAAGGCAAAAATAGAACAATGAGACTGCATCAAACTAAA 1134
                              i        i v         vv   vi    v       v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_70547264_7   1135 AAGCTTCTGCACATCAAAAGAAGTAATTAATAGAGTGAAAAGGCAGCCTA 1184
                           i   i  ii v     i  viiv  i  v i         i  i  i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_70547264_7   1185 TAGAATGGGAGAAAATGTTTGTAAACCATATATCAAATAAGGGGTTAATT 1234
                         i               i    i   i        vi       ii vi v
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_70547264_7   1235 TCCAAAATATATAAGGAAA----ACAGCT----------------AATAA 1264
                             i         i   v----   i  ----------------     
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_70547264_7   1265 CC-AATTTAAAAATGGGCCAAATACTTGAACAGACATTTCTCCAAAGACA 1313
                           -    ?          v  iv i     i                 vi
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_70547264_7   1314 ACACACAAATGGCCAATAGCTATATGAAAAGATGCTGAACGTCACTAGTT 1363
                          i i              ivi i             v   i   ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_70547264_7   1364 AT 1365
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.89 (117 / 62)
Gap_init rate = 0.01 (13 / 902), avg. gap size = 3.38 (44 / 13)  


3338 25.66 0.66 0.66  chr2_70568265_70570454.rev      792  1699 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_70568265_7    792 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 841
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_70568265_7    842 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 891
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_70568265_7    892 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 938
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_70568265_7    939 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 988
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_70568265_7    989 GAACAAAGCTGGAGGTATCACACTACCTGACTTCAAACTATACTACAAGG 1038
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_70568265_7   1039 CTACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATATAGAT 1088
                                  i   i    ii     i   i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_70568265_7   1089 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 1136
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_70568265_7   1137 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 1186
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_70568265_7   1187 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1236
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_70568265_7   1237 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 1286
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_70568265_7   1287 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1336
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_70568265_7   1337 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 1385
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_70568265_7   1386 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 1435
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_70568265_7   1436 AATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGA 1485
                         v  i   v v  i i   i   i vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_70568265_7   1486 ACAGGAAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 1535
                          v  iv    i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_70568265_7   1536 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1585
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_70568265_7   1586 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 1635
                            i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_70568265_7   1636 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 1685
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_70568265_7   1686 TCATCCCTGGCCAT 1699
                         v    v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1563 18.21 2.65 0.33  chr2_70571882_70575313.rev      901  1202 (2230)    L1M4_orf2#LINE/L1        1   309 (599)  

  chr2_70571882_7    901 TGAAAAAATATTCCATGTTCATGGATTGGAAGACTTAATACTGTTAAGAT 950
                           i   i    i                            i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_70571882_7    951 GGCAATACTCCCCAAATTGATCTACAAACTCAG-GCAATCCCTATCCGAA 999
                                                   i i   i-            vi  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_70571882_7   1000 TCTCAGCTGACTTCTTTGTGGAAACTAACAAGCTGATTCTAAAATTCATA 1049
                           i      v   i    ii    i i          i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_70571882_7   1050 TGGAATTGCCAGGAATCCAGAATAGCCAAA----TCTTAAAAAA--AGTA 1093
                              v   v   i i              ----    i     --  v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_70571882_7   1094 AAAAGTAAGAAGACTCACAGTTCCTGATTTCAAAACT-ACTATAAAACAA 1142
                         v     vi  i        v    ii           -    i   i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_70571882_7   1143 TGAGAATCAAAGCAGTATGAAATTGGTGCAAGAACAGACAAAACAGACCT 1192
                         iiiv      ii    i  iv i   iii   i i     -v i   i v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA-TATAGATCA 299

  chr2_70571882_7   1193 AAAAAATAGA 1202
                          vii      
  L1M4_orf2#LINE/    300 ATGGAATAGA 309

Transitions / transversions = 2.93 (41 / 14)
Gap_init rate = 0.02 (5 / 309), avg. gap size = 1.80 (9 / 5)  

2849 17.73 6.90 0.16  chr2_70571882_70575313.rev     2332  2940 (492)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr2_70571882_7   2332 AGGATAGGATAGGATAGG-ATA-GGATAGA---ATAGA---ATAGAATAG 2373
                          i  i  vi i v iv  -   -       ---     ---  i      
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_70571882_7   2374 AATAGAATGTCCAGAAATAAAATCATACCTCTGTGGCTAACCAATCTTTG 2423
                            v  iv             vi     v i i   ii  iii  i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_70571882_7   2424 ACAAAGGTACCAAGACAAGCCAATGGGGAAGGAATATTCTTTCCCAACAA 2473
                             i   i       v vi          i     v     i -     
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC-AACAA 407

  chr2_70571882_7   2474 ATGGTGCTGAGACAACTAGATAATAACATGTAAAAGGATGAAGTTGGACC 2523
                                  i       i    ?iv     i     i             
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_70571882_7   2524 CCTATCTCAAATCACATACAA-------CTCAAAATAGATAATATACCTA 2566
                             i    v i  i      -------        i   v ? v     
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_70571882_7   2567 AATATAAAAGGTAAAAATATAAAAATCTTAGAAGAAAACA--GGCATAAA 2614
                            i   i  v     v       v               --  ?i    
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_70571882_7   2615 TCTTTGTGACATTGGGTTAAGCAATGATT-CTTAAATACAACACCGAA-- 2661
                             i     v        i      i  -    i   ii     i  --
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_70571882_7   2662 --------------GAAAAAATAGATAAGTTGAATGTCATTGAAATTAAA 2697
                         --------------              i   i iv    ii        
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_70571882_7   2698 GTATTTTGTGCTCCAAGGAATACCATCAAGAAAGTGAAAAGATAATCTAC 2747
                         ivv         i   i i i  i                  i  i i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_70571882_7   2748 AGAACGGGAGAAAATATTTTCAAATTATGTATCC---AAGAGATAAGTAT 2794
                             i              v     i  i    i---   i  ivv    
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_70571882_7   2795 CTAAAATAAATAAAGAATTC--ATAACTTAACAATAAAAAGGCAAATAAC 2842
                          i i    v        i  -- i    i  i         i        
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_70571882_7   2843 CCAATTTAAAAATGGACAAAGGATTTGAATAAACATCTGTCCAAAGA--- 2889
                               ?        i               i    i v        ---
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_70571882_7   2890 TATATGAATGGTCAACAAGCATATGAAAAGATGTTCAGCATCATTAGTTA 2939
                             ii     i   i     i           i   i     ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_70571882_7   2940 A 2940
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 3.00 (78 / 26)
Gap_init rate = 0.02 (12 / 650), avg. gap size = 3.58 (43 / 12)  


 209 12.20 0.00 0.00  chr2_70737036_70739730.rev      321   361 (2334)  C L1M4_orf2#LINE/L1   (0)   908   868  

C chr2_70737036_7    361 GCCAACAGACACATGAAAAAATGCTCATCATCACTGCCCAT 321
                              i ii          i       v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.00 (4 / 1)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  

2796 23.10 6.44 2.30  chr2_70737036_70739730.rev     1334  2203 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_70737036_7   1334 GGAAGACTTCCAAT----ATGAATTGGAAGACTCAACATAGTAACAAATT 1379
                          i    iv   v  ----   i           i  i  v  v - i  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGATG 51

  chr2_70737036_7   1380 -CAATTCTCCCCAAATTGATGTACACTTTTAACACAATTCCTATCAAAAT 1428
                         -    v              v    vv  i   i    i           
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_70737036_7   1429 CTCAGCAAGATTTTT-AAAGACACAAACAACATTATTCTAAAATTTATAT 1477
                          i    vivv     -iv   v ivi    vv v  i        i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_70737036_7   1478 GGGCAGTCAAAATAACTAGAATAGCTCAAACAACTGTGAAAAAGAAGAAT 1527
                           iv vv   iiv v i        iv      iiv             i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_70737036_7   1528 AAAGTAGAAGCAGTC----TATCCAATTCCTAGACTTCTTATATAGCTAC 1573
                              v i  v v  ---- vi      i v i    vi  i v      
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_70737036_7   1574 AGTAACCAAAACAGTGTGATATTGGCA-AAGATCACAAAGGCCACAT-GA 1621
                              i   i        i  i     -   i-- i i ---  i  -  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGG--ATAGA---CATATAGA 296

  chr2_70737036_7   1622 TCAATGAAACAGAACAGAGAACCCAGAAATAGACCCACATGAATATGCCC 1671
                               i  i    iv    ii         i     i iivv    vi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_70737036_7   1672 ATCTCATTTTTGACAAAGATGC-AAAACAATTTAATACAGGAAAGA-TAG 1719
                          vi v     i     i i   -  i  v   i   i-i       -   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAG 395

  chr2_70737036_7   1720 -CTTTTCAACATTTTCAAATGGTGCTGGGACA-CTGGA------CATG-- 1759
                         -          ------               -     ------    --
  L1M4_orf2#LINE/    396 TCTTTTCAACA------AATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_70737036_7   1760 -----ATGAA------CCTCTGAGTCTCACATCTTTACACAAAAATTAAT 1798
                         -----     ------  i  i--i      i v - i           i
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTA--CCTCACACCAT-ATACAAAAATTAAC 486

  chr2_70737036_7   1799 TCAACAATGAATCATGGATTTAAATGTAAAATGTAAAACTATAAAACTTT 1848
                             -    i    ?i  ii         i vv               i 
  L1M4_orf2#LINE/    487 TCAA-AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_70737036_7   1849 TACAGAAAAAAAGCACACAAA-AAATGCTTGACATCTAGGGTTAGGCAAA 1897
                           --   i    -  i vi?i-    vi i vv i  v           v
  L1M4_orf2#LINE/    536 TA--GAAGAAAA-CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_70737036_7   1898 GAATTCTTAGATTTGATCCCAAAAGCATGGTCCATAAAAGGAAAAACTGA 1947
                          iv         v   iv         iiiv v i     i     iv  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_70737036_7   1948 TAAATTGGACTTCATCAAACTTAAAAATGTTTGTCTGGTGAAAGACCCTC 1997
                                            v       iv     vivvii  i   v  v
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_70737036_7   1998 TTAAGTGGGTGAAAAGAAAG-----GGCATTGGAGAAAATATTTTCAAAC 2042
                          i   vii         v i-----i v  v             v    i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_70737036_7   2043 CATGCATCTAACAAAGAACTAGTATTGAGAATATATAGAGAACTCTCGAT 2092
                            ii    i i  i i   v    iv          i        iivv
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_70737036_7   2093 ATTCAACAGTAAAAAAGCAAACAATCCACTTAGAAAATGGGCAAAAGAT- 2141
                          i    i i      ii    i  i   v  ?i            i   -
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_70737036_7   2142 ---ACGGA----------AAGT-GACATACAGATAGCAAAAAAGCATATG 2177
                         --- ii  ----------   v-  i     i  i  v  v     i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_70737036_7   2178 AAAAGATATTTCATATCATTAGCTAT 2203
                                ii iv i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (123 / 75)
Gap_init rate = 0.03 (28 / 906), avg. gap size = 2.71 (76 / 28)  


 606 29.13 13.59 5.70  chr2_70818130_70820106.rev      671  1494 (483)    L1M4_orf2#LINE/L1        1   889 (19)  

  chr2_70818130_7    671 TGAAGAGCTATAATTTATTCTTGG-TTAGAAAGCTTCAATAGGGTAAAGA 719
                           i i  v   vviv i   v   -  i   ii   -    vv  v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTT-AATATTGTTAAGA 49

  chr2_70818130_7    720 -GGT--TACTTCCCCAAAATTAATCAATAAAGTCAATG-GATTTCTTTCA 765
                         -  i--    i   --     i   v i i v    i -i  ii  v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCC--AAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_70818130_7    766 AAAATGGGGGAAGGTA-------TG-AGGACTTGACAAAAT-ATCCT--- 803
                            vivv----  v i-------  -  i v       iv -     ---
  L1M4_orf2#LINE/     98 AAATCCC----AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_70818130_7    804 -TCCATGTG-AAAT---------TCAGAATGGCTAGGGCAATGTTATAAA 842
                         - i   i  -    ---------i      i  i iii    v  i-   
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-AAA 192

  chr2_70818130_7    843 AAGAAAAGTAA--TTAGGAATACTAATTCCACCTCATGACAAAGTGTG-- 888
                              i ii  --  -   iv   v iv iv  iv  vv    iiv i--
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTT-GGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_70818130_7    889 ATAAAACTTTGGCAACTAA-ATGGCGTGGCACTAGCA---GAATGGATGT 934
                          i   i  vii i  ii  - ii i    i   i   --- i  i  ii 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_70818130_7    935 GCAAAACAATGCAACAGCTTAGAGAATCCAGAAATAGATCCA-AAATATA 983
                         ii i v     v  i  vv v    i          i i   - v  v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_70818130_7    984 TGAGAATTTAAC-----ACAGGAAAAGCAGGCACTTTATAAATCAGTGAG 1028
                           ivv v  i i-----   i iiviv  i -  i--  ---   i  i 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAG-ACC--AT---TCAATGGG 385

  chr2_70818130_7   1029 GGAAAGATAGACTACTTGCCA--T----CTGGGA-A---GGAAAGCTA-A 1067
                          i  ii    v  vi iiv  -- ----      - ---   v ? i - 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_70818130_7   1068 GGCAGA----TG-----------CTACTTCAT-TTATTTCAACAAGATAA 1101
                         v   i ----  -----------    i   i-ii  v --    ---  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT--ACAA---AA 480

  chr2_70818130_7   1102 ATTCCTGGTTTGTCAAAATGG----------TAAACATAAAAAGTGAACT 1141
                            vvi------         ----------    ii   i iv i  vi
  L1M4_orf2#LINE/    481 ATTAAC------TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_70818130_7   1142 CATAGGGGTATTAAAA---AACATAGACTTATGTTTTTGATGCCCTTGTG 1188
                         i   iiiv v   i  ---       i?v  vi i  i -  v     v 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGG 573

  chr2_70818130_7   1189 TTAGGGAA-GACTTATCAAGCACGGCACAAAAGGCTGCAATCTTGACAAA 1237
                              v  - ii  v i iii i i   v   i  -i   v --i     
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGC-ACAAGC--AACAAA 620

  chr2_70818130_7   1238 T--ATTAATAGATA---TGA----TATTAAACAATTCAAAACTT--GCAT 1276
                         v-- vv        ---  i----i  i   --   v       -- iii
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAA--ATTAAAAACTTTTGTGC 668

  chr2_70818130_7   1277 TTCTATAAGCCACTCCCCCACCATAAACAAGGT-AAAAGACAA-----AG 1320
                            v - i v    --------  v  v  i  -         -----  
  L1M4_orf2#LINE/    669 TTCAA-AGGACACT--------ATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_70818130_7   1321 TATGGAGGGAAATATTTTCA--CCATCTAT--GATAGTGAAAAAATTAAT 1366
                         v    ii i        v  --i   v   --    ---- iii i vi 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATA----AGGGACTTGT 755

  chr2_70818130_7   1367 ATTCTTAATTTACAAAGAGCT--TACAAATCAATGTGAAAAACAGAAACA 1414
                           i vv   v  i     i  --     v     ivv     v v   i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_70818130_7   1415 --TCAATAGAAAAATGGGCTGAGAAC----ATAAACAATTTACAAAGGAA 1458
                         --i    v?          vi  i i----   i   v  iv v  i   
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_70818130_7   1459 AATAGTTAAGTAGCCATTATATGTAATTGGAAATAT 1494
                         i   vvi  i i    --   v i vv  i   v  
  L1M4_orf2#LINE/    856 GATATACAAATGGCCA--ATAAGCACATGAAAAGAT 889

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.06 (57 / 889), avg. gap size = 2.79 (159 / 57)  


3248 26.33 1.33 0.67  chr2_70980490_70986859     4979  5878 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_70980490_7   4979 GAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATTGTGAAAATGG 5028
                            ii i  i     i     i  v      v i        v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_70980490_7   5029 CCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCACCATCAAGCTA 5078
                          v     v      v i  i  i        i  v   v i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_70980490_7   5079 CCAATGACTTTCTTCGCAGAAGTGGAAAAAACT-ACTTTAAAGTTCATGT 5127
                            iivi i  i  i      i v  v  i-  - iii    i     i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr2_70980490_7   5128 GGAACCAAAAAAAGAGCCC-GCATAGCCAAGACAATCCTAAGCCAAAGGA 5176
                             -- viv  i ii   - v        i      i i ivv i i  
  L1M4_orf2#LINE/    152 GGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_70980490_7   5177 ACAAAGCTGGAGGCATCACGCTACCTAACTTCAAACTATACTACAAGGCT 5226
                               i      vv    i  v  i  i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_70980490_7   5227 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5276
                                i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_70980490_7   5277 ATGGAACAGAGCAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 5326
                               i   iiv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_70980490_7   5327 TGATCTTTGACAAACCTAACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5376
                             i  i     ivv iv   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_70980490_7   5377 TTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 5426
                           i  i  i           v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_70980490_7   5427 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAGTA 5476
                         ii    i    v   i     v              i    i     vi 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_70980490_7   5477 AAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5526
                         ?    i           v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_70980490_7   5527 GGC---AATCCGTTTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5573
                           ?---    ---   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    550 GGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_70980490_7   5574 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 5623
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_70980490_7   5624 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5673
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_70980490_7   5674 AGGCAAATTACAGCATGGGAGAAAACTTTTGCAATCTACCCATCTAACAA 5723
                           i   vii    v           iv       vii ivi    i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_70980490_7   5724 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5773
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_70980490_7   5774 AAA------ACCCCAT-AAAAAGTGGGCAAAGGATACGAACAGACACTTC 5816
                          i ------    v  -?    i            vi   i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_70980490_7   5817 TCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTCATC 5866
                           v        i  vi viii     i ii  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_70980490_7   5867 ATCATTGGCCAT 5878
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (145 / 88)
Gap_init rate = 0.01 (8 / 906), avg. gap size = 2.25 (18 / 8)  


3154 26.03 1.78 0.78  chr2_71014199_71020624     5036  5934 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_71014199_7   5036 TGAAAGAATATTCCATGCTAATGGATAGGAAGAATCAATATCATGAAAAT 5085
                           i  ii    i     i v      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_71014199_7   5086 GGCCATACTACCCAAAGTAATTCATAGATTCAATGCCATCCCCAT-GAAG 5134
                            v     v      v i  ii i        i  v     i  -i  i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_71014199_7   5135 CTACAAATGACTTTCTT-CAGGGAATTGGAAAAAACTGCTT-TAAAGTTC 5182
                         iiv  iv  v    i  -   i-     -- v  i   v i-    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_71014199_7   5183 TTATGGAACCAAAAAAGAGCCTGCATTGACAAGACAATCCTAAGCAAAAA 5232
                         v       viiv  ii  v  v v  v v   i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_71014199_7   5233 GAACAAAGCTGGAGGCATCATGCTACCTGACTTTAAACTGCACTACAAGC 5282
                                 i      vv   ii  v  ii i  i   vivi       iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_71014199_7   5283 CTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGACATATAGAC 5332
                                  i   i    iii        i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_71014199_7   5333 CAATGGAACAGAAC--AGAGCCCTTAGAAATAACACCACACATCTACAAC 5380
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_71014199_7   5381 TATTTGATCTTTGACAAAAA---CAAGA------AATGGGGAAAGGATTC 5421
                         i v     i  i     iii---     ------           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_71014199_7   5422 CCTATTTAATAAATGGTGCTGGGAAAACAGGTTAGCCATATGTAGAAAGC 5471
                         i  v  i  i              v   v  v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_71014199_7   5472 TGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGG 5521
                             ii    i    v   i     v  i                i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_71014199_7   5522 AGTAAAGACTTAAATGTTAGACTTAAAATCATAAACACCCT-AGAAGAAA 5570
                          vi ?    i       v   vi     ii     -  i  -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAA 544

  chr2_71014199_7   5571 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGAC 5619
                           v    ?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_71014199_7   5620 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATC 5669
                           vi            vvi          vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_71014199_7   5670 TGATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5719
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_71014199_7   5720 AACAGCCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 5769
                           v  v     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_71014199_7   5770 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 5819
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_71014199_7   5820 AAAAAACAAACAATCCCATCAAAAAGTGGGCAAAGGACATGAACAGACAC 5869
                             i     i  i  v  i?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_71014199_7   5870 TTCTCAAAAGAAGACATCTATGCAACCAACAGACACATGAAAAAATGCTC 5919
                              v        i  vi viiii    i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_71014199_7   5920 GTCATCACTGGTCAT 5934
                         iv     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (144 / 86)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


2416 15.98 7.30 1.97  chr2_71106565_71111664.rev     3117  3623 (1477)    L1M4_orf2#LINE/L1        1   534 (374)  

  chr2_71106565_7   3117 TAGAAAGATACTCCCTGTCCATGGATATGGATCAGAAGATTTAATATTGC 3166
                          i        ii  v   i       -    -----   i         i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-TGGA-----AGACTTAATATTGT 44

  chr2_71106565_7   3167 TAAGATGGCAATACTCCCCGAATCAATCTACAGATTTAATGCAGTCCTCC 3216
                                            i   ii           i  i   i   iiv
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_71106565_7   3217 TCATAATTCAGGTTGGCTTCCTTTTAGAAACTGACAGGTTGATCCTAAAA 3266
                            v   i vi i  v   ii  vi     i     i i           
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_71106565_7   3267 TTCATGTGGAAATTCAAGGGATCCAGAACAGCCAAAACCATCTTGGAAAA 3316
                              i       v       i      i         v      i    
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_71106565_7   3317 G-----------TGGAAGCACATCCACTTCCCAAT--CAAAACTTATTAC 3353
                          -----------    i -  viv           --         i   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_71106565_7   3354 AAATCTACAGTAACTAAGAAAGTGTAGTAATAGCATAATAATGGACATAT 3403
                            v         ii    v     i   v i      vi  i       
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_71106565_7   3404 AGATCAATGGAATAAATTTG-GAGTCCAGAAATCA-CCTGTCACATTAAT 3451
                                       i v   -            v -  ii -     v  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTAT 342

  chr2_71106565_7   3452 GGTCAACTGATTTT---------TGCTAAGACAATTCAATGGGAGAAAGA 3492
                               i       ---------   i     v          -      
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGA 391

  chr2_71106565_7   3493 ATAGTCTCTCCAAAACATGG------GACA-CTGGAACATCCATATGCAA 3535
                                i i   v v    ------    -     -i ?   i      
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA-TAKCCACATGCAA 440

  chr2_71106565_7   3536 AAGAATGAAATTGGAACCCTGGCTCACATAATATA-AAATATTA---CAA 3581
                                  i     v    iv      iv     -   v    ---   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_71106565_7   3582 --TGGATGAAAGACTTAAATATAACAGTTAAAACCGTAAAACTC 3623
                         --     v ?    i     i   v  i      ii        
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

Transitions / transversions = 2.04 (53 / 26)
Gap_init rate = 0.03 (16 / 534), avg. gap size = 2.94 (47 / 16)  

1754 13.24 7.84 2.70  chr2_71106565_71111664.rev     4239  4608 (492)    L1M4_orf2#LINE/L1      520   908 (0)  

  chr2_71106565_7   4239 AAAACTCTAAAACTCTTAGAAAAAAACATAAGCATAAATCATTGTGACCT 4288
                               v              i        i ?i      v i       
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_71106565_7   4289 TGGATTAGGCAATAGGTTCTTAGATATGACACCATAAG------------ 4326
                            i         i v                  v   ------------
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_71106565_7   4327 ---AAAAAATAAACAA----GACATCATCAAAATTAAAT-TTTTTTTGCT 4368
                         ---        i i  ----   v              v-i    v    
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_71106565_7   4369 TTAAAGGACATCATCAAGAAAGTGAACAGACAACACACACACAGAATGAG 4418
                          i        ii              v       --- -         i 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAAC---C-CACAGAATGGG 715

  chr2_71106565_7   4419 AGAAAATATTTGCAAATCAT-----TGGTAAAGGACTGGAATTGGTATGT 4463
                                             -----  i   i     -----  -   vi
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACT-----TG-TATCC 759

  chr2_71106565_7   4464 CAAATATGTGAACAAGTCTTACAACTCAATAATAGAATGACAA----CCC 4509
                         vi     i i  v  v                  i  v     ----   
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_71106565_7   4510 AACTTTAAAATGGGCAAAGGATGTGAATAGATATTTCTCCAAAGAAGATA 4559
                           i ?v                v        i                  
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_71106565_7   4560 TACAAATGATCAATAAACATGGGAAAAGACAGCCAACATCATTCATTGT 4608
                                 ii      i  iiv       iivi        ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (30 / 17)
Gap_init rate = 0.02 (9 / 389), avg. gap size = 4.33 (39 / 9)  


2001 26.78 1.35 0.19  chr2_71331478_71338156.rev     5005  5523 (1156)    L1M4_orf2#LINE/L1        1   525 (383)  

  chr2_71331478_7   5005 TGGAAAAACATCCCATGCTCATGGATAGGAAGAATCAATATCATTAAAAT 5054
                               i i        i        v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_71331478_7   5055 GGCTATACTGCCCAAAGCAGTTTACAGATTCAATGCTATTCCTATCAAAC 5104
                            v     v      viii i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_71331478_7   5105 TACCAATGACATTCTTCACAAAACTAGAAAAAAATATTTCAAAATTTATA 5154
                          v   iivi v  i  ii  i  v v  v  ivvv  iii      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_71331478_7   5155 TGGAACCTAAAAAGTGCAC-GAATAGCCAAGGCAATCATAAGTAAAAAGA 5203
                              -v iv  i vi v -          ii     v i iv  i    
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_71331478_7   5204 ACAAAGCTGAGGGCATCACGTTACCTGACTTCAAACTATACTGCAAGTCT 5253
                               i  ii  vv    ii v  ii i      viv    i   iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_71331478_7   5254 ACAGTGACCAAAATAGCATGGTACTGGTACAAAAGCAGGCACATAAACCA 5303
                              i i   i i  ii         i i  iiii  i  i   i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_71331478_7   5304 GTGGAACAGAACAGAGACCCCAGAAATGAGACCACACATCTA----CATC 5349
                         i     i    iv    vi        i iv   i    i  ----  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_71331478_7   5350 TGATCTTTGACAAAGCTGACAAAAACAAGCACTAGGGAAAAGACTCCCTG 5399
                             i  i     i v  v   i v  vv  v i      ii ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_71331478_7   5400 TTTAATAAATGGTGCTGGGATAACCGGCTAGCCATATGCAGAAGTTTGAA 5449
                           i  i              i   i  v  ?   i     i   vv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_71331478_7   5450 GCTGGACCCCTTCCTTACACCATATACAAAAATAAACTCAAGATGGATTA 5499
                          i         v   i                 v       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_71331478_7   5500 AAGAC--AAATGTAAAACCCAAAACT 5523
                         ?    --        i v i      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACT 525

Transitions / transversions = 1.91 (90 / 47)
Gap_init rate = 0.01 (4 / 525), avg. gap size = 2.00 (8 / 4)  

1175 24.68 2.57 0.51  chr2_71331478_71338156.rev     5799  6187 (492)    L1M4_orf2#LINE/L1      512   908 (0)  

  chr2_71331478_7   5799 TAAAACCCAAAACTATAAAAACCCTGGAAGACAACCTAGGCA-ATACCAT 5847
                            i v i            vi i i     v   v    ?i- v i v 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_71331478_7   5848 CCTGGACATAGGAATGGTCAAAGATTTAATGGCGAAGACACCAAAAGCAA 5897
                          v  -  v v  iv i v   v i   vv i vv v             v
  L1M4_orf2#LINE/    562 CGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_71331478_7   5898 TTGCAACAAAAGCCAAAATTGACAAATGAGATCTAAATAAC-TTAAGAAC 5946
                         vv          vv     v  i    vi  ii v vi  v-    i   
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_71331478_7   5947 TTCTGTACAGCAAAAGAAACTATCAACAGAGTAAACAGACAACCTACAGA 5996
                           i   i vv    i  v        v i   i  v        i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_71331478_7   5997 AAGGGAGGAAATATTTGCATACTATGCATATGACAAAGGTCTGATATCAA 6046
                          v     i           v ii  ii  v   i  i  v  vi    v 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_71331478_7   6047 GCATCTATAAGGAACT--TA-AATTTAC-----AAGAGAAAAACAACCCC 6088
                          v  v     i     --  -  i i v-----  i   v   i     v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_71331478_7   6089 ATTAAAAAGTGGGCAAAGGACATGAACAGACACCTCTCAAAAGGAAGACA 6138
                            ?    i           iv    i     ii    v    -    i 
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG-AAGATA 859

  chr2_71331478_7   6139 TACATACGGCCAACAAGCATATGAAAAAAAGCTCAATATCACTGATCAT 6187
                             v i      i     i       i v      i    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (47 / 47)
Gap_init rate = 0.02 (7 / 397), avg. gap size = 1.71 (12 / 7)  


3206 27.27 0.89 0.22  chr2_71384475_71390839.rev     4972  5873 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_71384475_7   4972 TAGAAGAACATTCCATGCTCATGGATATGAAGAATCAATATCATGAAAAC 5021
                          i   ii i  i     i        vv     v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_71384475_7   5022 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCTATCCCTATCAAGC 5071
                            v     v     iv i  i  i v      i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_71384475_7   5072 TACCACTCACTTTCTTCACAGAATTGGAAAAAAGTACTTTAAAGTTCATA 5121
                          v   viii i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_71384475_7   5122 TGGAACCAGAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAAGAA 5171
                              viiv  ii  v  viv        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_71384475_7   5172 CAAGGCTGGAGGCATCACACTACCTGATTTTAAACTATACTACAAGGCTA 5221
                            i i      vv       v  ii    i   viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_71384475_7   5222 CAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 5271
                               i   ii   ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_71384475_7   5272 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5321
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_71384475_7   5322 GATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGTATTCCCTAT 5371
                            i  i     ivv  v   i v  vv            v  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_71384475_7   5372 TTAATAAATGGTGCTGGGTAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5421
                          i  i             vv      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_71384475_7   5422 CTGGATCCCTTCCTTACACCGTATACAAAAATTAACTCAAGATGGATTAA 5471
                         i    i    v   i     i                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_71384475_7   5472 AGACTTAAAGGTAAGACCTAACACCATAAAAACCCTAGAAGAAAACCTAG 5521
                             i    v      v    v  i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_71384475_7   5522 GCA-ATACCATTCAGGACATAAGCATGGGCAAAGACTTCATGACTAAAAC 5570
                          ?i- v i -   iv   v vi vv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_71384475_7   5571 ATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTA 5620
                          i        vvi          vv     v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_71384475_7   5621 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAGG 5670
                           v v  i i   i  ii vv    i  v       vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_71384475_7   5671 CAACCTACAGAATGGGAGAAAGTCTTTGCAATCTACCCATCTGACAAAGG 5720
                              i               i v       vii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_71384475_7   5721 ACTAACATCTGGAATCTACAAAGAACTTAAACAAATTTACAATTAAAA-- 5768
                            vii   ii    v  i        ivv    v iv i   v    --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_71384475_7   5769 -AAACAACCCCATCAAAAATTGGGCAAAGGATATGAACAGACACTTCTCA 5817
                         -   i     v  i?    v            v    i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_71384475_7   5818 AAAGACATTTATGCA----GCCAACAAACATATGAAATAACACTCATCAT 5863
                              - vv   i  ----     i  i  i      vi ii    v   
  L1M4_orf2#LINE/    850 AAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_71384475_7   5864 CACTGGTCAT 5873
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.00 (10 / 5)  


1281 15.35 0.41 0.83  chr2_71431598_71435033.rev     1442  1682 (1754)    L1M4_orf2#LINE/L1        2   241 (667)  

  chr2_71431598_7   1442 GGAAACATATCCCATGTTCATGAATTGGAAGAGTTAATATTATTACAATG 1491
                              v                i         v        i   vi   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_71431598_7   1492 GCAATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTTTCAAAAA 1541
                                 v      vii              i         v      -
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA- 100

  chr2_71431598_7   1542 TCCCAA-TAATGTTTTTACATAAATAGAAAAATCCATCCTAAAATTCATA 1590
                              i- iviv     i  v    v  v  iiiv               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_71431598_7   1591 TGGAATCCCAAAGGACCCTGAATAGCCAAAATAATCTTGGAAAAAGAAGA 1640
                              viv   i      v            i       -          
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-AAAAAGAAGA 199

  chr2_71431598_7   1641 ACAAAGTTGTAAGATTCACACATCCTCATTTCAAAACTTACT 1682
                                  v i  i      v   iv               
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

Transitions / transversions = 1.06 (19 / 18)
Gap_init rate = 0.01 (3 / 240), avg. gap size = 1.00 (3 / 3)  

2853 17.51 0.00 2.71  chr2_71431598_71435033.rev     1987  2540 (896)    L1M4_orf2#LINE/L1      239   777 (131)  

  chr2_71431598_7   1987 ACTACAAAGCTACAGTAATCAAAAACAGTGTGATACTGGCATAAAGATAG 2036
                                               i -       i           i     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAG 287

  chr2_71431598_7   2037 ACATGCAGATCAGTGGAATAGAACAGAGAGCTCAGAGATAAACCTTCACA 2086
                             ii      i          iv     ii    i       ivi   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_71431598_7   2087 TATATGATCAAATGATTTTCAACAAAGGTGCAAAAATCATTCACCAGGGA 2136
                          v    i    v        i    i     v  i i      vii    
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_71431598_7   2137 AAGGACAGTCTTTTCAACAAACGGTGTTGGGAAAAGTGTATATCCACATG 2186
                            i i               i    i     v  v  v   ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_71431598_7   2187 CAAAAGAATGAAATTGGACCCTTACCTTATATCATATACAAAAACTAATT 2236
                                     i        i     i i i            i   i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_71431598_7   2237 CAAAATGGGTCAAAGACCTAAACACAAAAGTGAAAACTATAAAACTCTTG 2286
                                 i   ?         iii  i  iv                 i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_71431598_7   2287 GAAGAAAATATAGGGCAAAAGCTTCATGATATTGGATTTGGCACTGACTT 2336
                                 i     ?vv   v    i   iv    i  v    v  ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_71431598_7   2337 CTTGGATATGACCCCAAAAGCACAGGCAACAAAAGAAAAAATACATAAGT 2386
                            i        v           i                  v    i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_71431598_7   2387 GAGACTTTGTCAAAATTGAAAAATTTTTGTGCATCAAAAGATAGTATTCA 2436
                         vi     ii        -     i        v     i  i v   iv 
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_71431598_7   2437 AAAGACAGTATAGGTGAGTGAAAATGCAACCCACAGAGTGGGAGAAAATA 2486
                         i  -------------        vi           i            
  L1M4_orf2#LINE/    687 GAA-------------AGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_71431598_7   2487 CCTGCAAGCAGTATATATTATAAGAAATTAATATCCAGAATATGTAAAAA 2536
                         ii     iivi     v v     ii i vi            i    i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_71431598_7   2537 ACTC 2540
                             
  L1M4_orf2#LINE/    774 ACTC 777

Transitions / transversions = 2.48 (67 / 27)
Gap_init rate = 0.01 (3 / 539), avg. gap size = 5.00 (15 / 3)  

 565 13.45 0.84 0.84  chr2_71431598_71435033.rev     2827  2945 (491)    L1M4_orf2#LINE/L1      790   908 (0)  

  chr2_71431598_7   2827 AAAAAGAAAAAAAAAAACCCAATTTTTAAAATGGGCAAAGAACTTGAATA 2876
                           v  i  i v   v       -  ?v             i i       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_71431598_7   2877 GAAATTTCTCCAAGGAAGA-ATACAGATGACCAATAAGCACATGACATGA 2925
                           v          i     -     i   i               v v  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_71431598_7   2926 TGCTCAACATCGTTAATCAT 2945
                                    i????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.14 (8 / 7)
Gap_init rate = 0.02 (2 / 119), avg. gap size = 1.00 (2 / 2)  


2395 28.34 0.94 0.53  chr2_71455946_71460670.rev     2835  3582 (1143)    L1M4_orf2#LINE/L1        1   751 (157)  

  chr2_71455946_7   2835 TGGAAACATAGCCCATCCTCATGAATGAGTAAAATCAATATTGTGAAAAT 2884
                               v   v     vi     i  vi v i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_71455946_7   2885 GACCATACTGTCAAAAGCAATCTACAAATTAAACGCAATTCCCATTTAAA 2934
                          i v     vi v   vii       i   v        i  i  iv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_71455946_7   2935 AACCACCATCATTCTTCACAGAATTAGAAAAAACAATCCTAAAATTTATA 2984
                         vv   v vv v  i  ii     v v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_71455946_7   2985 TGGAACCAAAAAGGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 3034
                              viiv  i   v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_71455946_7   3035 CAAATCTGGAGGCATCACATTATCTGATTTCAAACTATACTATAA-GCCA 3083
                             vi      vv     i vi ii        viv     i  -  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_71455946_7   3084 TAGTCATCAAAACAGCATGGTACTGGTATAAAAATAGGGATGAAGACCAA 3133
                         i   v     i    ii         i    ii    iv  iv   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_71455946_7   3134 TGGAACAGAATAGAGAATCCAGAAATAAACCCAAA----TACAGCCAACT 3179
                              i     v    i                v ----  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_71455946_7   3180 GATGTTCGACAAAGCAAACAAAAACATAAAGTCGGGAGAAGACACCCTAT 3229
                            v        i vviv   i v   vv i v    i ii i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_71455946_7   3230 TCAACAAATGGTTCTGCAATAATTGGCAAGCCACATGTAGGAGAATGAAA 3279
                                     v   vi i  i   vv ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_71455946_7   3280 CTGGATCCTCATCTCTCACCTTATACGAAAATTACCTCAAGATGGATCAA 3329
                         i    i  ii i   v    v     i       v     i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_71455946_7   3330 GGACTTAAATCTAAGACCTGAAAATATAAAAATTCTAGAAGATAGCACCA 3379
                         i   i     v     v  i   v       v ii       v i  ivi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_71455946_7   3380 GAA-AAACCTTTCTACACATTGGCTTAGGCAAAAATTCCATGACCAAGAA 3428
                          ?i-   i   iv i-  v    v        vii  i v iivi v  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_71455946_7   3429 CCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATTA 3478
                         v         v v    i    iv   i   i   iv v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_71455946_7   3479 AAGTAAAGAGCTTTTGTACGGCAAAAGGAACAGTCAGCAGAGT-AACAGG 3527
                           i v  i i       i vv    i iv  vi   iv i   -  v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_71455946_7   3528 CAACACACAGAATGGGATAAAATCTTCACAATCTATACATCTGACTGTTA 3577
                             v            v     v  ii   vii   i      --- v 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA---TAA 746

  chr2_71455946_7   3578 GGAAC 3582
                           i  
  L1M4_orf2#LINE/    747 GGGAC 751

Transitions / transversions = 1.27 (117 / 92)
Gap_init rate = 0.01 (6 / 751), avg. gap size = 1.83 (11 / 6)  

 643 19.05 2.98 0.00  chr2_71455946_71460670.rev     4066  4233 (492)    L1M4_orf2#LINE/L1      736   908 (0)  

  chr2_71455946_7   4066 ACATCTGACAAAGGACTAATATCCAGAATCTACAACGAACTCAAACAAAT 4115
                          i      i  i     vi          v  i  v      vv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_71455946_7   4116 TAGCAAGAAAAAAACAAACAATCCCATCAAAAAGTGGGCTTCAGAAATGA 4165
                         i ii  v     i     i  i  v  i?    i     vvvi  vv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_71455946_7   4166 ATAGACAATTCTC---AAAAGATATACAAATGGCCAACAA--ACATGAAA 4210
                                v     --- i                   i  --        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_71455946_7   4211 AAATGCTCAACATCACTAATGAT 4233
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (17 / 14)
Gap_init rate = 0.01 (2 / 173), avg. gap size = 2.50 (5 / 2)  


3298 26.98 0.44 0.44  chr2_71550512_71556786.rev     4876  5783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_71550512_7   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_71550512_7   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_71550512_7   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_71550512_7   5024 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_71550512_7   5074 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5123
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_71550512_7   5124 TACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATATAGATC 5173
                                 i   i    ii     i   i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_71550512_7   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5221
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_71550512_7   5222 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5271
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_71550512_7   5272 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5321
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_71550512_7   5322 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAAATGGA 5371
                            ii    i    v   i     v           i  i          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_71550512_7   5372 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5421
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_71550512_7   5422 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5471
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_71550512_7   5472 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5521
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_71550512_7   5522 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5571
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_71550512_7   5572 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5621
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_71550512_7   5622 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5671
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_71550512_7   5672 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5721
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_71550512_7   5722 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAGAAATGCTCATC 5771
                           v        i  vi viii     v ii        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_71550512_7   5772 ATCACTGGCCAT 5783
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1200 24.60 0.53 6.15  chr2_71578382_71582074        1   374 (3319)  C L1M4_orf2#LINE/L1   (555)   353     1  

C chr2_71578382_7    374 TAAAAAGATATTCCATGTTCATGGATTAGAAAAATCAGTATTGTTAAAGT 325
                          ii        i               i   i v i i         ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_71578382_7    324 GTTCATATATTGTTACAGTGTTCATGCTACCCAAAGCAATCTGCAGATCC 275
                          -------------i  ------  i  v      vii    i     i 
  L1M4_orf2#LINE/     51 G-------------GCA------ATACTCCCCAAATTGATCTACAGATTC 81

C chr2_71578382_7    274 AATGCAATCCCTATCAAAATACCAGCAACATTCTTCACAGAAATAGAAAA 225
                           i                 v     vi v  i  ii       v  v  
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

C chr2_71578382_7    224 AACAATCTTAAAATTTATACAGAACCACAACAAAAGATCCAGA-TAGGCA 176
                         ivii   i       i   ii   -- ii-   ii  i     -   v  
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAA--ATG-CAAGGGACCCAGAATAGCCA 178

C chr2_71578382_7    175 AAGCTCTCCTAAGCAAAAAGAACTAAACCAGAGGAATCACATTACCTGAC 126
                           i vv  i i iv  i      v  iiii     v     i v  ii i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

C chr2_71578382_7    125 TTCAAGTTATACTACAGAGCTATGGTAACAAAAATGGCATGGTACTGGCA 76
                              iviv       i     ii    iv  i ii ii           
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

C chr2_71578382_7     75 TAAAAACAGACACAGAGACCAGTG-AACAGAATAGAGAGCACAGAAATAA 27
                            ii i     i v   i  i  -  i     v     iv         
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

C chr2_71578382_7     26 ATCCAATAAATCTATAGTAAATTCAT 1
                          i   -  v  i   i  v    v  
  L1M4_orf2#LINE/    329 ACCCA-TACATTTATGGTCAATTGAT 353

Transitions / transversions = 2.68 (67 / 25)
Gap_init rate = 0.02 (7 / 353), avg. gap size = 3.57 (25 / 7)  

2170 26.22 8.47 4.64  chr2_71578382_71582074     2340  3201 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_71578382_7   2340 CATGTTCATGGATTGGAAGACTCAACATAATATC--GATGTTAGTTCTCC 2387
                                               i  i  -- i i--    vi i v    
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATAT--TGTTAAGATGGCAATACTCC 61

  chr2_71578382_7   2388 CTAAGTTGTTCTATTGATTTAAGGCAATTTCTACCAAA--CCAATCAAAA 2435
                          i  i   v    iv    i  v     ii   i    --  v v vivv
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_71578382_7   2436 TTTTTTGTAGGAACAGACAATCTTATTCTAAAGTTTATATGGAAAAGGAA 2485
                                i  i  iv     v  v  i     i  i         v v  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_71578382_7   2486 AGATTATGCA-AATAGCTAAAACAGTTTTGAAAAAGAAGAATAAAACTGA 2534
                         i i-- iv  -      i      i i              i   ii  i
  L1M4_orf2#LINE/    162 GGG--ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_71578382_7   2535 AGGAATC-C-CTTTCTGATG-CAAATGCTTATACTACATAGGTCCTGTAA 2581
                             v  - -   i ii  v-    -i    --     v  v v v    
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAA-ACTTA--CTACAAAGCTACAGTAA 256

  chr2_71578382_7   2582 TCAAGAGCGTGCTGTATTGGCAGAGAGAAGGAAACATACATTGATGGAAT 2631
                               vv   iv   i     v ii  vi  v i   v  ii       
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_71578382_7   2632 AGCATAGAAAACCTGGAAATAAATCTACACA-----AATCACCTAGTTAT 2676
                           v  v  i ii ii        i i i   -----ii   vi ii  v 
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_71578382_7   2677 TTACACAGAAGCAAAAGCAATTCAGCAGATGAGGAG-AGCCTTTTCAGTA 2725
                         iv   vi iv  v  ii v     iii ivi i  i-  i       ii 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_71578382_7   2726 AATTGTGCTGGAGCGATTAGACATCCATCAGCCGAA-AATGTACCTTGAT 2774
                            v       ii i i i  i ?   ivv  vi  -    v vi v  i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_71578382_7   2775 CTAAACCTCACACCTTATATTAAAACTAAAAAACTCAAAATTATATATTT 2824
                          ivv          v    iv    i   ----        ---------
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAA----CTCAAAAT--------- 493

  chr2_71578382_7   2825 AAAATTATAAAAACTGAAGGGACCTTAGGTTTAAAGGTAAAACATAACAC 2874
                         -------------------   i v?  iii    v    i vv   v  
  L1M4_orf2#LINE/    494 -------------------GGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_71578382_7   2875 TATAAAACTTACAGAAAA-----TAAGAGAAATTCTTCAGGGCCTAAGAT 2919
                                  ivi    i -----  i ? v  v     iv i   vi i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_71578382_7   2920 TGGGCAAAGAGTACTTAGACTTGACATCAAAAGCACAATTTATAAGAGGA 2969
                          i     v iv v      iv     i           viv i  i  i 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_71578382_7   2970 AAAACGGATAAATCTGATTTCATCAAGATT-------TTTGTTCT----- 3007
                             ii       iv  i        i   -------     v  -----
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_71578382_7   3008 ----------------GTGAAAAA-----TTATAGACTAATAGGAAATAT 3036
                         ----------------       i-----ii i   v iiv  i      
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_71578382_7   3037 TTGCAAATCACAAATCCAACAAAGG-CTTTTATCTAGAATACATAAAGAA 3085
                                   i v   ii i  i  -   v    i      i        
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_71578382_7   3086 GTCTCAAAAATTAACGTTTAAAA-----ATGATCCAATTAGAAAATCAGC 3130
                         v   i v  v i  iiv v    -----  i i      ?i     vi  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_71578382_7   3131 AAAAGAT----------ATTTCACTAAAGAGGATATACAGATAAACAA-- 3168
                            i   ----------     v i     i        i  iiv   --
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_71578382_7   3169 --CACCTGAAAAAAATGTCCAATATCAGTAGCTGT 3201
                         --   v      i -  ii   i    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (141 / 81)
Gap_init rate = 0.03 (24 / 895), avg. gap size = 4.71 (113 / 24)  


3278 23.35 3.53 1.94  chr2_72006143_72008008.rev      501  1378 (488)    L1M4_orf2#LINE/L1       17   908 (0)  

  chr2_72006143_7    501 GTTCATGGATGGGAAGACTCAATATTGTCAAGATGTCACTTCTTCCCAGC 550
                                   v        i        i      v  v v  i    iv
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chr2_72006143_7    551 CTTAT-TATGGGTTTAATACAATCCCAATCAAAATCCAAGACAGTTA--T 597
                         i v  -  ii i  i  ii       v          ----   i i-- 
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCC----CAGCTGCCT 112

  chr2_72006143_7    598 TTTCTG-AGTA-TCAGCAAACTGATTCTGAAGTT-ATGTGGAGAGGAAAA 644
                            i  -  v - iii   i     i  i  i  -  i    i v v  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_72006143_7    645 AAAAAAAAACCCAGAATAGTTAACACAGTATTTAAAGAGAAGAACAAAGT 694
                         ii ------          ii  v   i v  v   i             
  L1M4_orf2#LINE/    163 GGA------CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_72006143_7    695 CATAGGACTAACACTACTTGGCTTCCAGGCTTACTATAAAGCTGAAATAA 744
                         iiv      v     v iiiii   v ii       i      iv i   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_72006143_7    745 TCAAAATAGCGTGTTATTGGTGAAAGAATAAACAAACAGATCTATGGAAC 794
                             i i  i   v  i   iiv   i   i   v i     v      i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_72006143_7    795 AGAATAGAGGGCCCAGAAATAGACCCTCATAAACATCGTCAAC--ATCTC 842
                              v   i i         i    vi i vvi  v     i--  i i
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_72006143_7    843 TGACAAAGGAGCAAAGTCAATACAATGGAACAAAGGCAGTCTTTTCAATG 892
                         i     i  v  v   v v  v      iiv  iiii           ii
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_72006143_7    893 AAGGGTGCTGGAACAACTGGACATCCACATGCAGAAAAAAGTGAATCTGG 942
                           v        i         i ?         i  i  --    vi   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--TGAAGTTGG 454

  chr2_72006143_7    943 ACACGGACCTTACACCCTTCACAAACG--AACTCAAAATGGATCCCAGAC 990
                           v vv    i     v vi     vi--               v?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_72006143_7    991 CTAAATGTAAAATGC--AAACTATAAA-CTCCTAGAAAATAACATAGGAG 1037
                                   i -  --          -   i     i v        ? 
  L1M4_orf2#LINE/    505 CTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_72006143_7   1038 AAAATCTAAATAACCTTGAGTATGGTAATGACTTTTTGGATACAACACCA 1087
                         v      vvi i      i  vv  i    ii  i  i    ii      
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_72006143_7   1088 AAGGCACAAGTCATGAGAGAAATAATTGATAAGGTGGATTTCATTAAAAT 1137
                           i       iv ii i     v   v     iv    i     i     
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_72006143_7   1138 TCAAA-CCTTTGCTCTATGAAAGACACTGTCAATAAAATGAGAAGATAAG 1186
                          v   - i    iv  vii  i      i    v   i   i    i  v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_72006143_7   1187 CCTCAGCCTGGGATAGAATATTTGCAA-----------GA----GGACTG 1221
                           v   vv     v i           -----------  ----     -
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT- 752

  chr2_72006143_7   1222 TTTTGTA--CAAAATATACAAAGAAGCCTTAAAATTCAACAATAAGAAAA 1269
                         ---    --  i      i      vi    v  i    i     i  i 
  L1M4_orf2#LINE/    753 ---TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_72006143_7   1270 CAAACAACCTAATTTTAAAACGGTCAAAAGACCTCAACAGACATCTCATC 1319
                             i    i    ?v    i  v    i  ii v  i      i  vi 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_72006143_7   1320 AAAGAAGATATACAGATGGCAAATAAACATATGAAAGGATGCTCCACTAC 1369
                                       i     v     i  i      i       v  vv 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_72006143_7   1370 ATATGTCAT 1378
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.83 (130 / 71)
Gap_init rate = 0.02 (18 / 892), avg. gap size = 2.67 (48 / 18)  


2630 22.91 8.35 0.76  chr2_72057201_72058982      501  1290 (492)    L1M4_orf2#LINE/L1       59   908 (0)  

  chr2_72057201_7    501 TCCCCATATTGATCTATAGTTTCAATGAAATCCCAATAAAAATTC-AGTG 549
                               v         i  v     i v      v  v     i -  iv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_72057201_7    550 GGTTTTTTGGTAGAAATTGACATGCTAACCCTAACATTTATATGGAAAAG 599
                          vi     v i           v   i i     v   i         v 
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_72057201_7    600 CAAGAGAACTAGAATAGTCAAAATAATTTTGAAAAA------CAAAGCTG 643
                             i  v i       i     i   i        ------     i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_72057201_7    644 AAAGACTCAGACTACCTGATTTTAAGACT--------------------- 672
                         i i      v   v  ii    i  i   ---------------------
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_72057201_7    673 --------GTGGTACTGGTAAAATGATAGGTACTA-AGATCAATAGGACA 713
                         --------          i v  v     ii -  -        i i i 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACA-TATAGATCAATGGAATA 307

  chr2_72057201_7    714 CACT--AGAATCTAGAAATGGACCCTCACATATATGGCTTATTGATTTTT 761
                         v v --   i  i      ii    vi    v     iiv         i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_72057201_7    762 GACAAAGGATAAAAAACAATTCACTAGAAAAAGCATACTCTTTTCAACAA 811
                              i  vvvv  i  v     v i ii    v   v            
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_72057201_7    812 ATGGTGCTAAAGTAATTGGACATC-ACAGG-AAAAAAA--AATTTCAGTC 857
                                 iiiii  i    i ? -   v -    i  --  v  viii 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_72057201_7    858 TATACCTTACTC--TATACAAAAATTAACTACAAATGTACCATATACATT 905
                         iv     i  v --                vv     v i  ? v  v v
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_72057201_7    906 AAGGTAAATTCTAAAACTATAAAACCTGTAGAAAAATACTTTGGAAGAAA 955
                           v    ivv               iiv     i  v  v v  ?iv   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_72057201_7    956 TCTTTTTGACTTGGGGTTTGGCAA---------AGCTATGACCTAAAAAT 996
                             iv    i v     v     ---------  v      viv    v
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_72057201_7    997 CATAATTCATTCAAGAAAAAAAATTGATAAATTGGGCTTCCTTGAAAT-A 1045
                           i  viv --   i i       v          i    v ii    - 
  L1M4_orf2#LINE/    608 CACAAGCAA--CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_72057201_7   1046 AAAACTTCTGCTTTTCAAAAAACACAATTTTAAAAAACAAAAAGACA--C 1093
                                i  ivi      ii    v  iv- i   iii        -- 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCA-AGAAAGTGAAAAGACAACC 704

  chr2_72057201_7   1094 AACACATTTGGGAGAAAATATTT-TAAAACACAGATGTAATAAAGAATTT 1142
                         v   v v -              -i   v  i v  v i    i i i  
  L1M4_orf2#LINE/    705 CACAGAAT-GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_72057201_7   1143 GCATGCAAAATATA-AAAGTAACTCTTAGAACT---TAATAGGAAGACAA 1188
                          i  v  i      -    -        v    ---     ii       
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAG-AACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_72057201_7   1189 TTAGCCCAATTTAAAAATGTACAAATGATTTAAA----CACTTAACCAAA 1234
                         v  i       ?       vi    v     i  ----  i  vv     
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_72057201_7   1235 GAGGATACATGGATAGCAAATAAGCACATGAAAGGATGCTCAACACCATT 1284
                           i    i iii  i  v               i           i  ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_72057201_7   1285 AATCAT 1290
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.33 (101 / 76)
Gap_init rate = 0.02 (21 / 850), avg. gap size = 3.43 (72 / 21)  


3334 24.52 2.24 0.56  chr2_72092632_72095097.rev     1082  1974 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72092632_7   1082 TGGAGAGGCATTCCATGTTCATGAACAAAAAGACTCAATATTGTCCAGAT 1131
                             i  ii  i           i ivii      i        iv    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72092632_7   1132 GTCAGTTATTCCCAACTTGATCTATATATTCAAAGCAGTCCCAATCAAAA 1181
                          v  i vv i     v        i v      v   i    v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72092632_7   1182 TTCTAGTAAGTTATTTTGTGGGTATTGACAAACTGATTCTGAAG---ATA 1228
                          i i  ivivi v     ii iv        i     i  i  i---   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_72092632_7   1229 TGGAAAGGTAAAAGATCCAGAATAACCAGCATAATATTGAA---GAAGAA 1275
                               v i  ii  i        i   iv i   v     ---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_72092632_7   1276 CAAAATTGGGGAACTGATGCTATCCAACTTCAAGACTTACTATAAAGCTG 1325
                             i    i i   v ii  vi    i     i        i      i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_72092632_7   1326 TAGTGATCTAGA--GTGTGTTACTGG--TGAAGAAGGAAA-ATAGATCAA 1370
                         i   i   v   --     v      -- i i  vi  v -         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_72092632_7   1371 TGGAACAGAATGGAGAGCCCAGAAACAGATCCCCATAAAT--AGAGTCAA 1418
                              i     v     i       i i --      v  -- vi     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACATTTATGGTCAA 348

  chr2_72092632_7   1419 CTGATCTTTGACAAAGGAGCAAAGGCAATACAATGGAACAAAGATAGTCT 1468
                         i    i  i     i  v  v   i v  v      iiv  ii       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_72092632_7   1469 TTTTAGCAAGTGGTTCTGGAACAACTGGACATCCATATACAAAAAAATGA 1518
                            i i   i    v    i         i ?   i  i     i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_72092632_7   1519 ATCTAGACACAGAGCCTACAGCTTTCACAAAAATAAACTAAAAATGAACC 1568
                          vi i   v vv v ii   v v vi        v    v      i i 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_72092632_7   1569 TTAGACCTAAAAGTAAAATGC-AAAACTAAAATACTCCTAGAAGATAGCA 1617
                         v?         v    i -  -       v  v    i       v i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_72092632_7   1618 TAGGAGAAAACCTACATAACCTTGGGTATGGTGATGAATTTTTAGGTACA 1667
                             ? v   i  v i i         vv  ii   iv  i    i  ii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_72092632_7   1668 ACACCAAAGGTATGAACCTTAAA-GAAATAATTGATAAGCTGCACTTTAT 1716
                                 i i ii i vvi   -    v   v     ii  v    i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_72092632_7   1717 TGAAATTAGATATTTCTGCTGTATGAAAGAAAA-TGTCAAGGAAATGAGA 1765
                         ii      i v i  i  -  iv v    i v - i     i  i   i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_72092632_7   1766 AGACAAGACACAGAAT---AAAAAA-ATTTGCAAAAGACACATCTGATGA 1811
                               vv        --- i    -         vv i i       i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_72092632_7   1812 CATACTCTTACCCAAAATATGCAAAGAACTATTAAAAATCAACAATAAGA 1861
                         viv   iv  i   i     ii        v   v  v    i     i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_72092632_7   1862 AAACAAACCACCCAATTAAAAAATAGACTAAAGATCTTTAACAGAAACCT 1911
                          i     iv        ?      i i v  i   -  v  i   v ii 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGACATTT 845

  chr2_72092632_7   1912 CATGAAAGAAGATGAACAGATGGTAAATAAGCATATAAAAAGATGCTCCA 1961
                          viv         iv   i    iv        i  i           v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_72092632_7   1962 CATCATATGCTAT 1974
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (136 / 79)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


2948 26.21 1.65 1.76  chr2_72095219_72097974     1357  2264 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_72095219_7   1357 GGAAAAACATTCCATGCTCATGGATTAGAAGAACCAATGTTGTTAAAATG 1406
                              i i  i     i         i     vii   i       i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_72095219_7   1407 ACCGCACTGCCCCAAGCACTTTACAGATTCAATATTATTTCTATCAAA-- 1454
                         i vii   v   v  viiv i           iiiv  ii        --
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_72095219_7   1455 -CTA-CTGTTATTTTTCACAGAATTAGAAAAAACT--TCC-AAAACTGAC 1499
                         - i -   ii-     ii     v v  v  i-  --   -    i v i
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_72095219_7   1500 ATGAAGCCAAAAAAGAGCCCA--ATAGCCAAAGCAATCCTAAGCCAAAGC 1547
                            i iviiv  ii  -    --         i     i i i--    v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAA--AAAGA 196

  chr2_72095219_7   1548 AATCCTAATCCAAAGCCAGAGGTATCACATTACTTGACTTCAAACTATAC 1597
                          i----  --     iii    vv     i v iii i      viv   
  L1M4_orf2#LINE/    197 AG----AA--CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_72095219_7   1598 TATAAGTTTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGATA 1647
                           i  ivi        i   i    ii         i i  ii i   i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_72095219_7   1648 CATAGACCAATGGAATGGGATAGACAGCCCAGAAATAAAGCTGCACATCT 1697
                         i     i         i i  v  v  i           v iii    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_72095219_7   1698 ACAGCCATCTAATCTTCAACAAAGTTGACAAAAATAAGCAATGAAGAAAG 1747
                          ii i  vi i  i   i    i v  v   i vi vv     ii     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_72095219_7   1748 AACTCACTATTCAATAAATGGTGCTGGGATTACTGGCTAGCCATATGCAG 1797
                           ivvv  v     i              iv     v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_72095219_7   1798 AAGAATGAAAGTGGACCCCTTACCTTTCACCACACACAAAACTTAACTCA 1847
                                  iv         -    iv     i i      v        
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCA 489

  chr2_72095219_7   1848 AGGTGGATTAGAGATTTAAATGTAAGGCCTCAAACTATAAGAATTCTAGA 1897
                          ii     i ?   ii          iv  v         i v ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_72095219_7   1898 AGAAAACCTAGGAA-ACACCATTCTGGACATTGGCCTTGCGAAACAACTT 1946
                                v    ?i- v i -   vv   v    vi v - v  iiii  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG-GCAATGGTTT 587

  chr2_72095219_7   1947 ATTAC-TAAGTCCTCAAAAGCAATTGCAA-ACAAACAAAAATTGACAAGC 1994
                         v   v-  v v vi        vvv    - v  iv      v  i  ii
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_72095219_7   1995 AGGACCTAATTAAATTGAAGAGCTTCTGCACAGCAAAAGAAACCATCAAT 2044
                         v    i v  i   v v  i i   i  ii vv    i  v  i     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_72095219_7   2045 AGAGTAAACAGACAACCTACAGAACAGGAGAAAATATTTGCAAACTATGC 2094
                          i   i  v        i      ii                  ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_72095219_7   2095 ATCCAACATAGGTCTAATATCCAGAATCTATAAGGAGCTTAAACAA-TCA 2143
                            ii i vi  v  vi          v     i  i  ivv    -   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_72095219_7   2144 AAAGATGCAAAAAACAAACAACCCTATTTAGAAATGGGCAAAGGGCATGA 2193
                          v -  i-    i     i     v   ? i             iiv   
  L1M4_orf2#LINE/    788 ATA-ATA-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_72095219_7   2194 ACAGGCACTTCTCAAAAGAAGACATACAAGCAGCCAACAA--ACATGCGA 2241
                          i  i  i     v        i      iii     i  --     vi 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_72095219_7   2242 AAATGCTCAACATCACTGATCAT 2264
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (154 / 80)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 1.48 (31 / 21)  


2975 25.11 3.25 1.46  chr2_72118025_72121804     2398  3289 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72118025_7   2398 TGGAGACACATCCCATGTTCATGGAT-GGAAGAATCAATATTGTGAAAAT 2446
                             i v i                 -      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72118025_7   2447 GACCACACTGCCCAAAGCAATCTACAGATTCAATGCAATTCTTATCAAAA 2496
                          i v i   v      vii              i     i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72118025_7   2497 TACCAA-TGTCATTTTTTCACAGAATTAGAAAAAACAATCCTAAAATTTG 2545
                          v   i-  i --     ii     v v  v  ivii           ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_72118025_7   2546 TATGGAACCAAACAAGAG-CCCA-AATAACCAAAGCAATCCTAACCAAAA 2593
                                -- vi    i -    -    i     i     i i vv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_72118025_7   2594 AGAATAAATCTGGAGGGATTGTATTACCAGACTTCAAGTTATACTATAAG 2643
                             i   vi      iv iii i v  vi i     iviv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_72118025_7   2644 GCAACAGTTACCAAAACAGCACGGTACTGGTACTGGTATAAAAGCATTCA 2693
                           v     v i   i    ii------         i    iiii vv  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTG------TGGTACTGGCATAAGGATAGACA 290

  chr2_72118025_7   2694 CACAGATTAATGGAACATAATAAAGAACCCAGAAATAAAGCCAAATACTT 2743
                         i i    i       i v   vi   ii           v   v i i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_72118025_7   2744 ACAACCAACTGATCTTCAACAAAGCATAC-AAAATCATAAACTGGGGGAA 2792
                          iiii   i    i   i    i -i i -  i i   vv v     i  
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAA 389

  chr2_72118025_7   2793 AGGT-----------CAAATGATGCTGGGAAAACTAGCTAGCCACATGCA 2831
                         iii -----------      i        v    i v  ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_72118025_7   2832 GAATAATTAAATTGGATCCCTATCTCTCACCCTATACAAAATTCAAATCA 2881
                         i  v   v  i     i     i   v    v         v i  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_72118025_7   2882 AGATGGATCAAAGACTTAAATCTGAGACCTGAAACCATAAAAATTCTAGA 2931
                          i        ?    i     v i   v  i    i      v ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_72118025_7   2932 AGATAATCTTGGGAAAACTCTTCTAGTCATTGGTCTAGGCAAAGAATTTA 2981
                            v  iv v  ?iv  v     vv v v    vi       v iv  iv
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_72118025_7   2982 CGACTAAAATCCCAAA-GC-CAATGCAACAACAGCAAAAATAAATAAATG 3029
                         iiiv  vi iv     -  -   -       v  v       i      v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATT 638

  chr2_72118025_7   3030 AGACCTGATTAAA-CTAAAAAGCTTCGCACAGCAAAAGAAATAATCAGCA 3078
                         i   i v  i   -i      vi  i ii vv    i  v iv    iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_72118025_7   3079 GAGTAAACAGAGAACCCACAGAATGGAAGAAAAATATTTGCCAACTATGC 3128
                         i   i  v   v              i      -       v  ii  ii
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATAT 737

  chr2_72118025_7   3129 ATCTGACAAAGGGCTAGTATCCAGAATCTTCAAGGAACTT----AAATCA 3174
                               i  i  i  v           v vi  i     i----  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_72118025_7   3175 GCAAGAAAAA---AAAT---TCTTTCAAAAAGTGGGCCAATTACATGAAT 3218
                         ii  v     ---    ---i vv i?    i     v  vv iv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_72118025_7   3219 AGACTTTTCTCAGAAGAAGATATACAAGTGGCCAATACACATATGAAAAA 3268
                             v      vi              i         vi  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_72118025_7   3269 ATGCTCAACATCCCTAATCAC 3289
                                     v????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (134 / 86)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.33 (42 / 18)  


3260 26.65 0.55 0.55  chr2_72154981_72161245.rev     4866  5773 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72154981_7   4866 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4915
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72154981_7   4916 GGCCATAATGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4965
                            v   v v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72154981_7   4966 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5012
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_72154981_7   5013 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAA 5062
                                 viiv  ii  v  v v  v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_72154981_7   5063 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5112
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_72154981_7   5113 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATACAT 5162
                                  i   i    ii         i iv ii i   v     v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_72154981_7   5163 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAAC 5210
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_72154981_7   5211 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5260
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_72154981_7   5261 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5310
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_72154981_7   5311 CGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5360
                         i   ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_72154981_7   5361 ATTAAAGACTTAAACGTGAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5410
                           i ?    i    i  i   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_72154981_7   5411 CGTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5460
                          i    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_72154981_7   5461 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5510
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_72154981_7   5511 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5560
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_72154981_7   5561 CAGGCAACCTACAAAATGGGAGACAATTTTCGCAACCTACTCATCTGACA 5610
                         v  i     i   i         v   v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_72154981_7   5611 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5660
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_72154981_7   5661 AAAACAAACTACCCCGTCAAAAAGTGGGCGAAGGACACGAACAGACACTT 5710
                           i     iv    vi i?    i     i     ivi   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_72154981_7   5711 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5760
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_72154981_7   5761 CATCACTGGCCAT 5773
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3941 20.25 1.57 1.34  chr2_72183643_72185529.rev      502  1395 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_72183643_7    502 CTATG--CCTGGATTGGAAGATTTAATATTGTTAAGATATCAATACTAGT 549
                          i   -- v            i                iv       vvi
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_72183643_7    550 GAAAGCAATCTACAGATTTGATGCAACTCTTCTCAAAATTCTAATAACAT 599
                         v   vii           ii i    ii i v       i i iivi v 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_72183643_7    600 TTTTTGCAGAAATAGAAATATCT-ATTCTAAAATTTATATGGAATCCCAA 648
                                      v  v - v  -  i        i        viv   
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_72183643_7    649 GGGATCCTGAGTAGCCAAAACAATTTTGAAAAAGAA---CAA-GTTGAAG 694
                             i  v  i             i           ---   -    i  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_72183643_7    695 GTCTCACACTTACTGATTTCAAAACTTCTCACAAAGCTTCAGTAATAAAA 744
                          v         v ii            vii        v       v  i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_72183643_7    745 ACAGTGTGGTATTGGCATAAAGACAGACATATATACCAACAAAATAGAAC 794
                                    i        i  i         v i   iii       i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_72183643_7    795 AGAGAGCCCAGAAAAAAAAACCCTTGGATACATAGTCAAATGCTTTTCAA 844
                         v     i       v   --   v iv  vi  i     v  v     i 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAA--CCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_72183643_7    845 CAAAGA-GCCAACTCTATTCAATGGGGGAAAGGACAGTGTTTTCAACAAA 893
                            i i-     vv i           -    i i   v           
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAA 408

  chr2_72183643_7    894 TGATGCTGGGAAAACTGGATATCTTTACACAAAAATAAATGAAGATGGAT 943
                           i        v         ? ivi ii     i--       v    i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAG--AATGAAGTTGGAC 456

  chr2_72183643_7    944 TCCTATCTTACACTGTATATACCAATTAATTCAAAATAGGTTACAGACCT 993
                         i    i  i    ii    i vv      i       i i i ?      
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_72183643_7    994 AAACATTATAGTGAGAACTATAGAACTCTTAGAAAAAAAAAAAAACAGTA 1043
                            ii v v  iv i       i           i    v v i--- ?i
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG---GNG 553

  chr2_72183643_7   1044 TAAAAGCTACATGACTTTCAACTTGGCAGTGCTTGTTTGCATATGACACC 1093
                             -v  v i    i  viii v    i  v  vi  iv          
  L1M4_orf2#LINE/    554 TAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_72183643_7   1094 AAAAGCATAGACAACAAAATGAAAAATAGATAAGCTGGACTCCACCAAAA 1143
                                i ii        vi            ii      i  i     
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_72183643_7   1144 TTAAAAACTTTTATGTACGAAAGGGCATTATCAACAGAGTGAAAAGGCAA 1193
                                     i  iviv     i  i      v i         i   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_72183643_7   1194 CTCATGGAATGGGAGAAAATATTTGCAAAGCATATATCTAATAAGGAATT 1243
                          i  ii                       v         i      i i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_72183643_7   1244 AATATATAGAATATAAAAAGAATTCTTACAACTTAACAACCAACAAAAAC 1293
                         vi   vi        v      i          i  i  i-  -   i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AA-AAAGAC 800

  chr2_72183643_7   1294 AAA-AACT-GATTTAAAAACAGGCAAAGACTTT-AATAGGCATTTCTC-- 1338
                            -   i-i   ?     ii       iv   -     i        --
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_72183643_7   1339 AAAAAAATATACAAATGGCCAATAAACACATGAAAA-ATGTTCAATATTA 1387
                           i  i                   i          -   i    i  i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_72183643_7   1388 CTAATCTT 1395
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.11 (120 / 57)
Gap_init rate = 0.02 (18 / 896), avg. gap size = 1.44 (26 / 18)  


 283 32.66 17.05 2.02  chr2_72194614_72198911.rev      177   522 (3776)    L1M4_orf2#LINE/L1      309   706 (202)  

  chr2_72194614_7    177 AATAGAGAACCCAGT--CCAGCCCAGACATGTGTGG--AATTTAGGTACA 222
                            v    ii    v--iv i    v    v i   --    v vv v i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_72194614_7    223 AGAAGGAGGTGTCATG-----TCAGATCAGCAAAGA-------TGTTAAC 260
                          v    --   i  v -----   -  vi v     ------- v i   
  L1M4_orf2#LINE/    359 ACAAGG--GTGCCAAGACCATTCA-ATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_72194614_7    261 ATA----ACTAGAAAATAATGGTTATTCATATAGAAGATGACAAGATTGG 306
                          v ----i  i i v - v   v  ?i  i  iv  i vi ii ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACA-ACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_72194614_7    307 AATCCTCTTTTTTACCACATACAGAAATCAACTCAAGATAGATTGTGAAC 356
                          vi   vii ivi    i     i    i       i  i   ii?ii  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_72194614_7    357 TTACGCATTAATATCCCAAATT-TAAAACTCC-------------AGGTA 392
                         i  viii -  v v iv   i -        i-------------   ?i
  L1M4_orf2#LINE/    505 CTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_72194614_7    393 CAAA----------------------AATG-TTTTTGAAAAAAGACACAA 419
                         i   ----------------------    -   i v i v v     v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_72194614_7    420 AAAGTTTTTCTTGTAAAGGAAAAGATCAATAGATTTGTCTATATTAAAAT 469
                             ivivvvivii   i     i  vi   i   v v  vi  i     
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_72194614_7    470 TAAGAATCTTAGTTGCCT-AAAAGACA-TATAAAAGAAAGTATACAAATA 517
                            i  ii  v  -  i -   i    -   v  -      iv v i i 
  L1M4_orf2#LINE/    654 TAAAAACTTTTGT-GCTTCAAAGGACACTATCAA-GAAAGTGAAAAGACA 701

  chr2_72194614_7    518 AGCCA 522
                          v   
  L1M4_orf2#LINE/    702 ACCCA 706

Transitions / transversions = 1.44 (65 / 45)
Gap_init rate = 0.04 (17 / 398), avg. gap size = 3.88 (66 / 17)  

2755 26.81 5.18 0.69  chr2_72194614_72198911.rev     2938  3806 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72194614_7   2938 TGGAAAAACATTCCATGCTCATGGATAGGAAG------------------ 2969
                               i i  i     i        v     ------------------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72194614_7   2970 --CAGT---------------TTACAGATTCAATGGTATTCCTATCAAAC 3002
                         --  i ---------------i           i vv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72194614_7   3003 TACCAATGACATTCTTCACAGAACTAGAAAAAACTG-TTTTAAAATTCAT 3051
                          v   iivi v  i  ii     v v  v  i-   - ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_72194614_7   3052 ATGGAACCAAAAAAGAACTTGAATAGCCAAGGCAATCCTAAGCAAAACAA 3101
                               viiv  ii  v iv          ii     i i iv  i vi 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_72194614_7   3102 ACGAAGCTGGAGG-CTCACATTACCCGACTTCAAACTATACTACAGGCCA 3150
                           i   i      -      i v   i i      viv       iiv v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_72194614_7   3151 AAAGTAACCAAAATAGCATGGTACTGGTACAAAACAAGACACATAAACCA 3200
                          v     i   i i  ii         i i  iivv     i   i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_72194614_7   3201 ATGGAAAAGAATAGAGAGCCCAGAAATAAGGCAGCACACCTACAACCATC 3250
                               v     v     i          iv vii   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_72194614_7   3251 TGATCTTTGACAAACGTGACAAAAACAAGCGATGTGGAAAGGATTCTCTA 3300
                             i  i     iv   v   i v  vv i   v      i  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_72194614_7   3301 TTCGATAAATGGTGCTGTGATAACTGGCTAGCTATATGCAGAAGATTTAA 3350
                            i i           v  i      v  ? i i     i    v v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_72194614_7   3351 ACTGTACCCCTTTCTTACACCACATATAAAAATAAACTCAAGATGGATTA 3400
                         ii  v      vi  i      i   i      v       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_72194614_7   3401 AAGACTTAAATGTAAAACCCAAAACTATAAAAACTCT-GGTAAACAACCT 3449
                         ?    i         i v i            -    -i v i v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr2_72194614_7   3450 TGGAA-ACGCCATTCTGGACATAGGATCTGGTGAAGATTTCAT-GATGAA 3497
                         v  ?i- vii -   vv   v v  i iv  ii v i    v -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr2_72194614_7   3498 GACTCCAAAAGCAATCA--CAACAAGAGCAAAAATTGACAGATGGGATTT 3545
                            v         --  --      i  v      v  i i  v   i  
  L1M4_orf2#LINE/    597 GACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_72194614_7   3546 AATTAAACTAAACAGCTTCTGCACAGCAAAGGAAACTATCAACAGAGTAA 3595
                         v  i   v v  v i   i  ii vv       v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_72194614_7   3596 ACAGGCAACCTACAGGATGGGAGAAAATATTTGCAAACTATACATTTGAC 3645
                          v  i     i    i                     ii   i  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_72194614_7   3646 AAAAGTCTAATTTCCAGCATCTATATGGAAATTAAACAAATTTACAAGCA 3695
                           ii v  vi v     v  v    vi   v ivv    v iv i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_72194614_7   3696 AAACTGGAAAAACTCCATTAAAAAGTGAGCAAAGGACGTGAACAGACACT 3745
                            vvvi  v   i v   ?    i  i        iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_72194614_7   3746 TTTC---AAAAGACATACATGTGGCCAACAGGTATGTGAAAAAAAGCTCA 3792
                          i  --- i    i     vi       i i i ii      i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_72194614_7   3793 ACATCACTAATCAT 3806
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.64 (51 / 14)  


3313 26.10 0.66 0.66  chr2_72202261_72208527     4868  5775 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72202261_7   4868 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4917
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72202261_7   4918 GGCCATAATGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4967
                            v   v v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72202261_7   4968 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5014
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_72202261_7   5015 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAA 5064
                                 viiv  ii  v  v v  v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_72202261_7   5065 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5114
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_72202261_7   5115 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5164
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_72202261_7   5165 CAATGGAACAGAAC--AGAGCCCTCAAAAATAACGCCGCATATCTACAAC 5212
                                 i    i--    i  -- i      vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_72202261_7   5213 TATCTGATCTTTGACAGACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5262
                         i vi    i  i    iivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_72202261_7   5263 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5312
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_72202261_7   5313 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5362
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_72202261_7   5363 ATTAAAGACTTAAATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAA 5412
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_72202261_7   5413 CCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCC 5461
                          v    ?i- v i -   iv   viv  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_72202261_7   5462 AAAACACCAACAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5511
                          vi       v    vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_72202261_7   5512 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5561
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_72202261_7   5562 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5611
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_72202261_7   5612 AAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAA 5661
                           i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_72202261_7   5662 AAAAACAAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGACACT 5711
                            i     i     v  i?    i     i i   iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_72202261_7   5712 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5761
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_72202261_7   5762 TTATCACTGGCCAT 5775
                         vi    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2420 20.43 12.43 5.62  chr2_72210164_72212153.rev      654  1490 (500)    L1M4_orf2#LINE/L1        1   894 (14)  

  chr2_72210164_7    654 TAAAAAGATATACTGTGTTCATTAATTAGAGAACTCAATATT---AAGAT 700
                          ii        v ii       vi   i  ii   i      ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72210164_7    701 TTTAATTC-CCCCAAAT-GATCTATAGATTTTAAAACAATCCAAATAAAA 748
                         vvi   v -        -      i     i-  vi      vv  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTC-AACGCAATCCCTATCAAA 99

  chr2_72210164_7    749 ATCCCAGCAGGTTTTTTTTTTTTTTTCTAGTCAGGGGGAAAAAGGGATAG 798
                                 v vi      ----------------------------ii  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT----------------------------GCAG 121

  chr2_72210164_7    799 AAATCGACAAGCTGATTCTAAAAT------------ACAAAAGACCTAGA 836
                             i           i       ------------i   ii    i   
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_72210164_7    837 ATATCCAAAACAATTTTGTAAAA-AAGGATAAAGTTAAAAGACTTAAACT 885
                            v          i   v    -   i i      ii i    i v   
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_72210164_7    886 ATTTGATTTCA----TGACTGTAAAGCT---GTGGTCAAGACGGTGTGGA 928
                         viiii      ---- v   ii      ---  ii       i      v
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_72210164_7    929 GTTGGTGTGATGATTGATAGACACACAGATCAATAGAACAGA-------- 970
                         ii   ii i - ---        i i        i   i   --------
  L1M4_orf2#LINE/    272 ACTGGCATAA-G---GATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_72210164_7    971 ----------------------TGTGGTCTGTTGACCTTCCACAAAGGTG 998
                         ---------------------- i     vi    ii   v    i    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_72210164_7    999 CCAAGGGTGT-CAATGGGGA-----TACTCTTTTTCAATACTTAGAACTG 1042
                              ivii -         -----  v      -   i vv i vi   
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTT-CAACAAATGGTGCTG 416

  chr2_72210164_7   1043 GAACAAA-GGATATACATATGCAAAATTGTTAACCTTGATCCTCAACTCA 1091
                          i    v-     ?v  i        vvi v  vi v  i  ii v    
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_72210164_7   1092 CACCACG---AAAAATTAACATGAAATAGATCATAGACCTAAATGTAAGA 1138
                              ii---          vii    i     ?                
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_72210164_7   1139 GCTAAAACTATAATGCTTCTAAAAGAAAGCATAAAAGAAAATCCTTGTGA 1188
                                      vi  ii  i      i    ii? v     i i    
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_72210164_7   1189 CATTTGGTTAGGTA--GATTTCTTA----TGACAT-AAAAGCACA-GTG- 1229
                          v  v       i -- i       ----     i-         - ii-
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_72210164_7   1230 TAAAAGAAAAAATAT-TAAATTAGAACTCATCAAAAT-AAAAAATTTTGC 1277
                         i             v-      i  vi          -     v     i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_72210164_7   1278 TATTTGAAAGACA-TAT-ATGAAAG-----AGATATGCTATAGACTGGGA 1320
                         vv  ii  i    -   - v     -----   i vv i i   v     
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_72210164_7   1321 CAAA-TATTTGCAAGC---ATATCTG--------TTTGT--------TAT 1350
                         v   -         ii---       --------i    --------   
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_72210164_7   1351 ATAAAGAATTCTTACGCCTTAATAATAGGAAGGCAAACAACTGACTTGTT 1400
                                 i      iv  i       ii   i    i   iv v  ---
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT--- 813

  chr2_72210164_7   1401 GGGATAAAAATATGGATAAAAAGATTTGAATAAACACTTCACCAAA-AAC 1449
                         ----?      --  ii   i-          i   i   v     -  v
  L1M4_orf2#LINE/    814 ----WAAAAAT--GGGCAAAG-GATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_72210164_7   1450 ATATATGAATGACAAAAAAAAAGCACATGAAAAGATGCTCA 1490
                              ii    i v  v  ---                   
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAA---GCACATGAAAAGATGCTCA 894

Transitions / transversions = 2.09 (113 / 54)
Gap_init rate = 0.04 (36 / 894), avg. gap size = 4.19 (151 / 36)  


 705 25.87 2.99 1.00  chr2_72261629_72263979      655   855 (1496)    L1M4_orf2#LINE/L1        1   205 (703)  

  chr2_72261629_7    655 TGGAGAGACAT---ATGTCCATGGATTGAAAGACTCGACATAATGAAGAT 701
                             i   i  ---    i         i      ii i  vi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72261629_7    702 GTCATT--TCCCCAAAAATTGATTTAAAAGTTTAATGCAATTTCTATAAA 749
                          v  v --        --     i  v ii  i  i     ii    v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_72261629_7    750 AATCCTAGC-AAAGTTTTTGCCAACATATACAAGCTTTTTCTAAAATTTA 798
                              i   -ivvv       vi v  vv       vv i        i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_72261629_7    799 TATGGAAAGGCACAGGTCTTAGAATAGGTAGAATACTCTTCAGAAAGACA 848
                                 v   vi  v ii       vi i  i v    v i     vi
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_72261629_7    849 AATGAAG 855
                           ii   
  L1M4_orf2#LINE/    199 AACAAAG 205

Transitions / transversions = 1.36 (30 / 22)
Gap_init rate = 0.02 (4 / 205), avg. gap size = 2.00 (8 / 4)  

1020 22.31 2.20 21.43  chr2_72261629_72263979      942  1851 (500)    L1M4_orf2#LINE/L1      158   892 (16)  

  chr2_72261629_7    942 GCAAGA-ACCCG---TATCTAAAAAAATAAAAAATTTAAAAAAGAAGAAT 987
                              i-    i---  v i    v   ------i  i           i
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAAT------CTTGAAAAAGAAGAAC 201

  chr2_72261629_7    988 AGAGTAGAAGAAATCCCCTTACCTGATATTAAGGCTTACTATATAGAAAA 1037
                          i   v i  i v  v vi v  ii  v i  ii       i v  vv v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_72261629_7   1038 AATAATCAAGACAGTGTGGTTTTAGCAGGTGGACTGACACATTGATCAAT 1087
                          i                  vi i   viv   iv    i  v       
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_72261629_7   1088 AGAAAAGAA--GAGATGCCAGAAATAAACCCAAGCGAATATGCCCAGCCA 1135
                         i   v    --    vv               vi ivv    vi  iiii
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_72261629_7   1136 ACTTTAGAAAAAGATGCAAAAGCAATTTAGTGATGACAGA-TACCCTTGT 1184
                          i   v  v  i i   v  ii v   i i  iv  v   -  vi   v 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_72261629_7   1185 CAACAAACGGTACTGGAGCAATTGGAAATCTATAGGCAAAAACAAAAACA 1234
                                i   i    ii   i    v ? i i v      i-  vi - 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AATGA-A 449

  chr2_72261629_7   1235 GTAACAAAAAACAAAAATCCCACC-CACAATAACCTTAGACTTAAATTTC 1283
                           vi-----i  -----i  i   -    ----  v  v  vv     --
  L1M4_orf2#LINE/    450 GTTG-----GAC-----CCCTACCTCACA----CCATATACAAAAATT-- 483

  chr2_72261629_7   1284 ACGTCTCATT-TGGAAATTATAGACTTCATTATAAAAAATGAAACTATAA 1332
                         --iv    vv-    -- i ?    i v v i   i iv i         
  L1M4_orf2#LINE/    484 --AACTCAAAATGGA--TCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_72261629_7   1333 AACTTGTAGAAAAA----TAGCAAAAAATCTCCAGGATCTAGAGCTAGGC 1378
                             iv     i  ----   v?iv      i iv  i  v i i     
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_72261629_7   1379 A--GACTTCTTAAGCTTGACATGAAAAGCACAATCAATGGGGCCCGGCGT 1426
                          -- ii      iiiv     iv          -----------------
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAA----------------- 612

  chr2_72261629_7   1427 GGTGTCTCATGCCTAGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCAG 1476
                         --------------------------------------------------
  L1M4_orf2#LINE/    613 -------------------------------------------------- 612

  chr2_72261629_7   1477 ATCACCTGAGCTCAGGAGTTCAAGACCAGCCTGGGCAACATGGAGAAACC 1526
                         ----------------------------------      ----------
  L1M4_orf2#LINE/    613 ----------------------------------GCAACA---------- 618

  chr2_72261629_7   1527 CTGTCTCTAAATAAATAAATAAAAGGAAAGCAAAGCACAATAAGTAAAAG 1576
                         ---------------------    i   ---------    ------- 
  L1M4_orf2#LINE/    619 ---------------------AAAGAAAA---------AATA-------G 631

  chr2_72261629_7   1577 AAAAATTAATAACGAGGACCTCATGAAAATTAAGAAGTGTTGCTTTGTGA 1626
                          v     --------    i    v        i  v v   ivi vii 
  L1M4_orf2#LINE/    632 ATAAATT--------GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_72261629_7   1627 AAGTCTCTGTTAAGAGGATGAGAAGTCAAGCTACAGAATGGGAGGAAATA 1676
                          i v v  i i    iii   i   v   v i            i     
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_72261629_7   1677 TTTGCATGCCACATCTC--ACAAAGGACTAATTACTAGAATATGTGGAAT 1724
                               vii  i  v  -- i  i     vi vv i       i -----
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT----- 768

  chr2_72261629_7   1725 ATGCAAAGAACTCTCAAAGTTCGGCAGTGAAAA-ACAAACAATTCAATTA 1773
                         ----          i v ii  iii i i    -     i  ii     ?
  L1M4_orf2#LINE/    769 ----AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_72261629_7   1774 GAAAATGAGCAAGAGACCTGAACATCCTTATTACCCTACGG--GATTTAC 1821
                         i      i    ii  ii    i vv --   v i i vi --   v   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGAC--ATTTCTCCAAAGAAGATATAC 862

  chr2_72261629_7   1822 AGATAGCACATAAACACATAAAAAGATGTT 1851
                          i  i  vv    i     i        i 
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.62 (123 / 76)
Gap_init rate = 0.04 (26 / 735), avg. gap size = 8.27 (215 / 26)  


2898 11.50 3.54 25.06  chr2_72376938_72379559.rev      974  2130 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72376938_7    974 TGGAAATATATCTCATGCTCATGGATTGGTAGACTAAATATTGTTAAAAT 1023
                               v     i    i           v     v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72376938_7   1024 G--------CTCAAAATTGATTTATAGATTCAACACAATTCCTATTGAAA 1065
                          -------- i v        i  i         i    i     ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72376938_7   1066 TCCCCATTAACTTATTTGCAGAAATTGATAAGCTGATCTTAA------TA 1109
                             vii iv   v              i         i   ------  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_72376938_7   1110 TGGAAA--CAA-------AGAACAGTCAAAACAATCTTGAGAAAGAA--- 1147
                               --   -------    i  i              i      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_72376938_7   1148 CAAAGTTGGAAGATTCACACTTCTTGATTTCAAAATTTAGTACAAAGCTA 1197
                                   i  i         iii         i   v          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_72376938_7   1198 CAATAATCAAGATTGTGTTATACTGGCACTAAGGATAGACATGTAGCTTA 1247
                           i         iv    vi        -             i   v i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATCA 299

  chr2_72376938_7   1248 ATGGAATAGAGTTGA-AGTTGAGGAAAAACCTCTTGCATTTATGGCCAAT 1296
                                   i    -   iv  i  v  v i v i         i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_72376938_7   1297 TAACTTTTGACAAGTATGCAAAGACAATTCAGTGAGGGAAAGAATAGTCT 1346
                          i i   i      vi   v     v     i  -               
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCT 398

  chr2_72376938_7   1347 TTTCCACAAATGGTACTGTGACAACTGGATATCCACAGGTAAAGGAATGA 1396
                             v         i   v            ?     v i   i      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_72376938_7   1397 AGTTGAATCCTTTAATTATACCACA--CAAAAATTAACTCAAAGTGTATC 1444
                              i i  i vvv i i    i --                i  v   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_72376938_7   1445 AAAGACCTAAATGTAAG--CTAAAACTATAA--TCCTGAGAAAGAAACAT 1490
                          ?               --            --ii  v    ii      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_72376938_7   1491 TGAAGTAAATCTTC-TGACCTTGAGTTAGGCAACACCGTATAAACACACA 1539
                         v i?          -        i         ii--  v ---------
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG--GTTT--------- 587

  chr2_72376938_7   1540 CTCGAAAAAAGAAAAAGTAGCTTTGACTTAATCAAAATTAAAAACACGCC 1589
                           ---------------   v v    --- i     -------------
  L1M4_orf2#LINE/    588 CT---------------TAGATATGAC---ACCAAAA------------- 606

  chr2_72376938_7   1590 ACGCACAGTGGCTCACGCTCATAATCCCAGCACTTTGAGAGGCCAAGGTG 1639
                         --     i------------------------------------------
  L1M4_orf2#LINE/    607 --GCACAA------------------------------------------ 612

  chr2_72376938_7   1640 GGAAGGTTGCTTGAGCCCAGGAGTTTGAGACTAGCCTGGGCAACATGGTG 1689
                         ---------------------------------------      -----
  L1M4_orf2#LINE/    613 ---------------------------------------GCAACA----- 618

  chr2_72376938_7   1690 AAACCTCGACTCTACAAAAAATTAGCCGGGTGCAGTGGTGCACACCTGTA 1739
                            ----  -------      ----------------------------
  L1M4_orf2#LINE/    619 AAA----GA-------AAAAAT---------------------------- 629

  chr2_72376938_7   1740 GTCCCAGCTGCCCAGGAGGCTGAGGTGGGAGGATCCCCTGAGCCTGGGAG 1789
                         ----------------------  i ii----------------------
  L1M4_orf2#LINE/    630 ----------------------AGATAA---------------------- 635

  chr2_72376938_7   1790 GTTGAGGCTGCAGTGAGCTGTGATTGCTCCACTGCACTCCAGCCGGGGCA 1839
                         ----------------------    ------------------------
  L1M4_orf2#LINE/    636 ----------------------ATTG------------------------ 639

  chr2_72376938_7   1840 ACAGAGTGAGACTCTGTCTAAAAAACAAGCAAACAAAAAAACTAAAAACA 1889
                         ---------    iii  -------------------    i       v
  L1M4_orf2#LINE/    640 ---------GACTTCATC-------------------AAAATTAAAAACT 661

  chr2_72376938_7   1890 TTTGAGCTGCTAACAATACCATCAAGAAAGTGGAAAGACAAACCACAGAA 1939
                             v   v v  vi i  i            i        v        
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_72376938_7   1940 TGGGAGAAAATATTGGCAAATCATATATCTGATAAGGAACTTATATCTAG 1989
                                       v                      i    i    i  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_72376938_7   1990 AATACATAAATAATT-TCACAACTCAATAATAAAAAGA----TAGCATAA 2034
                             i     v  i - i                    ----  i vi  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_72376938_7   2035 TTTTAAAATG--CAAAAGATTTAAATGGACATTTCTCCAAAGAAAATATA 2082
                           ?v      --    i     i   i                 i     
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_72376938_7   2083 CAAATGGCCAACAATTACATGAACAAAATGCTTAGCATCATTAGTCAG 2130
                                    i  vi       -  i     i i     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (88 / 41)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 11.41 (331 / 29)  


3011 22.60 2.29 3.71  chr2_72420837_72425183     2940  3855 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_72420837_7   2940 AGTTATTTCATATTCATGGATAGGAAGAC--AATATTGTCAAGATATCAG 2987
                           v   ii   i         v       --        i     iv  i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_72420837_7   2988 TTCTTTCCAACTTGATCTATAGATTCAATGCAATCCCAATATAAACCCCA 3037
                          v  ii    v        i        i        v  vv   i    
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_72420837_7   3038 GTAAATTTTTCTATGGATGTTGATAAACTGATTCTAAAGTTTATATGAAG 3087
                          ivivi    i iii  vi    i  i     i     i  i     i i
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_72420837_7   3088 AGGCAATATATCCAGAATAGCCAACACAATATC---AAAGAAGAACTAAG 3134
                          v    viv i             v     v i---          v   
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_72420837_7   3135 TCAGA---CTTTGTTCACTCTCAGACTTCAAGACTTACTATAAAGCTATA 3181
                          ii  ---  iv---    ii vi i     i        i       i 
  L1M4_orf2#LINE/    206 TTGGAGGACTCA---CACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_72420837_7   3182 GTAATCAAGGCAGTGTGGTATTGGTGAATAAC--TAGGCAAATAGATCAA 3229
                                  i          i   i--    v--   i  v         
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGC--ATAAGGATAGACATATAGATCAA 300

  chr2_72420837_7   3230 AGCAACAAAACAGAAAGCACAGAAACAGACCCACATAAATACAGTCAGAA 3279
                         v v  i i  iv  i  iv      i i     i i vv  ii    ---
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA--- 347

  chr2_72420837_7   3280 AAAT--ATATATAAAAAAGATAGACCTCTGATGAGCAAAGGCAAAGCAAT 3327
                         --  --  v vii v  i i -------------  v   i v vv    
  L1M4_orf2#LINE/    348 --ATTGATTTTCGACAAGGGT-------------GCCAAGACCATTCAAT 382

  chr2_72420837_7   3328 GGAACAAAGATGTTCTTTTCGACAAATG-TGCTGGAAAAACTGTACAATC 3376
                           iiv  ii  iv       i       -      i v     v i ?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_72420837_7   3377 ACATGAACGAAAGAAAAGAATCTAGACACA-AACTCACAGCTTTCAAAAA 3425
                              -- i      v-   vi i   v v- v      v v vi v   
  L1M4_orf2#LINE/    433 ACATG--CAAAAGAAT-GAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_72420837_7   3426 AATAAACTACAAATGGATCACAGAAATAAATGTAAAATACAAAACTATAA 3475
                            v    vv          ?   vv         i vvi          
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_72420837_7   3476 AGCTCATAGAAGATAACATAAGAGAAAATCTAGATAACCTTGGAATTAGC 3525
                          i   v       v      i ? v      vvi i       iv vi  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_72420837_7   3526 AATGACTTCTTTTTAGATATGACTCCAAAGGCACAATCCATGAAATACAA 3575
                             ii     ---         v     i      v v ii   v v  
  L1M4_orf2#LINE/    580 AATGGTTTCTT---AGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_72420837_7   3576 TATTTATAAGCTGGACTTCATTAAAATTAAAAATTTCTGCTCTGCAAAAG 3625
                         v  vv    ii          i           i  i  iv  v    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_72420837_7   3626 ACACT--CAAAAGAATACAAAGATAAGCCACAGACTGGGAGAAAATATTT 3673
                              --   i i i iv     i  v       v               
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_72420837_7   3674 GCAAAAGACACATCTGATAAGGGACTATTATCCAAAACATACAAAGAATT 3723
                              vv i i               vv      i  i   i      i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_72420837_7   3724 TTTA-AAGTGCACAATAAAAAAACAAACAATCCAATTAAAAAATGGAGCA 3772
                         i   -  v vv i        i     i  i      ?        -   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG-GCA 825

  chr2_72420837_7   3773 AAG-ATCTTAACAGATACCTCACCGAAGAAGATAT-CA--TGGCATAAAA 3818
                            -  i v  i   i ii  v  i          -  --    v---  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC---AA 872

  chr2_72420837_7   3819 TAAGCATATTAAAAAGACGATCCACATCATATGTCCT 3855
                               i  -i      i v  v      ????????
  L1M4_orf2#LINE/    873 TAAGCACAT-GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (117 / 86)
Gap_init rate = 0.02 (22 / 903), avg. gap size = 2.50 (55 / 22)  


 474 23.08 0.96 0.00  chr2_72457488_72460217     1041  1144 (1586)    L1M4_orf2#LINE/L1       13   117 (791)  

  chr2_72457488_7   1041 CTGTGTTCGTGGATTAGAAGACTAAA-ATTGTCAAAATGTCAATTTTCCC 1089
                          ii     i      i       v  -     i  i   v    vi    
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_72457488_7   1090 CAAATTGATCTCTGAATTCAACATAATCCTAATGAAAATATCAGCAAGCT 1139
                                    viii       ii     iv  v     vi    viv  
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_72457488_7   1140 TTTTT 1144
                              
  L1M4_orf2#LINE/    113 TTTTT 117

Transitions / transversions = 1.67 (15 / 9)
Gap_init rate = 0.01 (1 / 105), avg. gap size = 1.00 (1 / 1)  

 210 17.86 0.00 8.93  chr2_72457488_72460217     1424  1479 (1251)    L1M4_orf2#LINE/L1      101   151 (757)  

  chr2_72457488_7   1424 TCCCAGCCAAGCTTTTTTTTCTTAAGAAATTGACAAATTGATTGTAAGAT 1473
                                i--  i      v ---            ii    iv   i  
  L1M4_orf2#LINE/    101 TCCCAGCT--GCCTTTTTTGC---AGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_72457488_7   1474 ATATAT 1479
                         vi    
  L1M4_orf2#LINE/    146 TCATAT 151

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.04 (2 / 51), avg. gap size = 2.50 (5 / 2)  

1698 24.86 5.57 4.35  chr2_72457488_72460217     1562  2297 (433)    L1M4_orf2#LINE/L1      164   908 (0)  

  chr2_72457488_7   1562 GGCTTAGAATAAACAAAACAACTTTGAAAAAGAAGAA-AAAGTTGGAGGA 1610
                          i ii      iv        ii              -            
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_72457488_7   1611 CTTGAACTGCTTGATTTCAAGAC--AATATAAAAGTA-AG--ATCAAGAC 1655
                           iiv   v iii       i  -- v  i   iv  -  --        
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_72457488_7   1656 A---------TAGCAAAAGGACAGACACACAGGTCAATTGAACATAATAT 1696
                          --------- i   v     i     i i  i     v   i v   - 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT-T 312

  chr2_72457488_7   1697 AGAGAATGCAGAAGGAGACCAACACATATGTGGTGAATTGATTTCTAAGA 1746
                         -    i v     iv i   v i    v i    v         iii v 
  L1M4_orf2#LINE/    313 -GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_72457488_7   1747 AAGGTATCAAGGTGCAT-CAATGGAGAAAGCATAGTCTTTTTAACAAATG 1795
                          i   ii    ii-   -      i     v          i        
  L1M4_orf2#LINE/    362 AGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_72457488_7   1796 GTGCTGGAACAACTGTACATGC-CATATAAAAATATGAACCTTGG--CCA 1842
                                i       v i ?v -   ii    iv     v-    --  v
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG-TTGGACCCC 459

  chr2_72457488_7   1843 TACTTCATATCATATTGAAAAATTAACCCAAAACATATCATCATAGACCT 1892
                            i   i i     vv          i     iiv    ?---      
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW---AGACCT 506

  chr2_72457488_7   1893 AAGTGTAAAACCTAACAGTATGAA-CTCCTAGATGAAAACATAGGAAACA 1941
                           i     i v    v v   i  -   i    v           ?i-i 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG-TA 555

  chr2_72457488_7   1942 GACCTTTGTGACCTTGGATTAGGCAAAGATTTCTTAAGATAGGACACACA 1991
                         i i   i          i        v i       -    v     vv 
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GATATGACACCAA 604

  chr2_72457488_7   1992 GAGCGTGAG--ACAT--GAAAAAAGTGACATTATAACTGTATGTCACTAA 2037
                         i   iii  --   v--       vv  i ----  i  v iv   ii  
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATA----AATTGGACTTCATCAA 650

  chr2_72457488_7   2038 AATCAGAAGAAAAAACTTAAGCTTTTTGAAAGATACTGTTAAGGAAATGG 2087
                            i ------       vv ivi  ii  i  i   i i   i  i  i
  L1M4_orf2#LINE/    651 AATTA------AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_72457488_7   2088 CCTGTTGACC---AGAACATATAAAAAACTTTCACTACTCA-ATA----A 2129
                         vvv vii   ---    iivi- i    iv  ii v v   -   ---- 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGG-AGAAAATATTTGCAAATCATATATCTGA 743

  chr2_72457488_7   2130 TAAGAA--TTATTTTTAAAACTGAATAAAATATTTGAACAAATACATTAA 2177
                             ii--  i v ii i  - iv     iv i ivv    v -  v   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAA-TATATAAAGAACTCTTACAACT-CAATAA 791

  chr2_72457488_7   2178 ACACAAAAGAAGAGATA--CAAATACATTAAACACAGAAGAAAAGAAACT 2225
                         ---i    ii v i   -- v   --- ?   v ii -- v    i vi 
  L1M4_orf2#LINE/    792 ---TAAAAAGACAAATAACCCAAT---TWAAAAATGG--GCAAAGGATTT 833

  chr2_72457488_7   2226 GAATAAAATATTT----GAACAA-ATATATTAAACACCAAATAAGCACAA 2270
                              i -i    ----i  v  -     i-   iiv v          v
  L1M4_orf2#LINE/    834 GAATAGA-CATTTCTCCAAAGAAGATATAC-AAATGGCCAATAAGCACAT 881

  chr2_72457488_7   2271 AAACAGATTCTCAGCATAATTAGTCAT 2297
                         i  v    v    i   v ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (113 / 66)
Gap_init rate = 0.05 (35 / 745), avg. gap size = 2.09 (73 / 35)  


1542 25.92 0.26 0.00  chr2_72509452_72512956     1516  1897 (1608)    L1M4_orf2#LINE/L1        1   383 (525)  

  chr2_72509452_7   1516 TGCAAAGACATTGCATGGTCATGGATTGGAAGACACAATATTGTTAAAAT 1565
                           v     i  iv    v                vi           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72509452_7   1566 GCCCATATTACCCAAAGCAATCTATAGGTTCAATGCAATTCCCATCAAAG 1615
                          v v   i v      vii     i  i     i     i  i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72509452_7   1616 TACCAA-TGACATTTTTACAGAAATAGAAAAAACAATCAGAAAATTTATA 1664
                          v   i-  v v     i       v  v  ivii   vv      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_72509452_7   1665 TGGAAACACAAAAGACCTAGAATGGCCAAAGCTATCCTGAGCAAAAAGAA 1714
                               ii   ii    i     i      i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_72509452_7   1715 CAGAACTGGAGAAATCATATTACCTAACTTCAAATCATACTACAGAGCTA 1764
                           i ii     i v   i i v  i  i      v v       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_72509452_7   1765 TAGTAATAACAACAGCATGGTACTGGCATTAAATCCGACACACAGACCAA 1814
                         i      v vi    ii            v iiviv    i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_72509452_7   1815 TGGAACAGAATAGAGAACCCAGAAAAGAATTCACATACCTATAGTAAATT 1864
                              i     v    ii       vi  ii  i i ii   i  v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_72509452_7   1865 CCTTTTAGAGAAAGGTGTCAAGAACACACACTG 1897
                         vv    v  v  i    i     v  iv  v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

Transitions / transversions = 1.68 (62 / 37)
Gap_init rate = 0.00 (1 / 383), avg. gap size = 1.00 (1 / 1)  

 735 25.63 0.00 1.01  chr2_72509452_72512956     2182  2380 (1125)    L1M4_orf2#LINE/L1      370   566 (342)  

  chr2_72509452_7   2182 AGGAACACACACTGGGAAAAAGACAGTCTCTTCAATAAATTATGGTGGGA 2231
                          i  v  iv  v    i   ii i     i     i    vi  v     
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_72509452_7   2232 AAACTAGAAATCCATATGCAAAATAATGAAACTAGACCCCTATCTCTTGC 2281
                         v    i  v ?   i        v      ii i        i   vii 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_72509452_7   2282 CATATACAAAAAGCAAATCAAAATGAATTAAAGACTTTAAAATCTAAGAC 2331
                                     vi  v        i  i ?    i --    v     v
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCT--AAATGTAAGAG 517

  chr2_72509452_7   2332 TTCAAACTATGAAAGGACTACAAGAAAACATTGAGGAAACTCTTCAGGA 2380
                         i v       i   vvvi  v          v i? v  v     iv  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

Transitions / transversions = 1.18 (26 / 22)
Gap_init rate = 0.01 (1 / 197), avg. gap size = 2.00 (2 / 1)  

1120 22.88 4.24 1.98  chr2_72509452_72512956     2662  3015 (490)    L1M4_orf2#LINE/L1      547   908 (0)  

  chr2_72509452_7   2662 ATAGGCATGAGCCACCGTG--CCTGGCCTGGGCAGACATTTCTTA-AT-T 2707
                              ?i i ii vi    -- i   vi i    ivvi       -  - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_72509452_7   2708 AATACCGCATAAGCACAGGCAACCAAAACAAAAATGGACAAATAGGATCA 2757
                         i i   -- v       i     v   iv      i  i    v   iiv
  L1M4_orf2#LINE/    597 GACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_72509452_7   2758 CAACAAG-TTAAAAAGTTTATGCACAGCAAAGGAAATAATCAACAAAGTG 2806
                           v   i-       v   -  ii vv       v iv     v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_72509452_7   2807 AAGAGACAACCCACAGAGTAGTAGAAAATATTTGCATACTATCCATCTG- 2855
                           i              i i v              v ii  vi     -
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_72509452_7   2856 ---GGAATTAATAACCCAAATATATAAGGAG-----ACAAAATACTTTAT 2897
                         ---  i i vi  v  vi         i  i-----    ----  iv  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA----CTCAAT 789

  chr2_72509452_7   2898 AGGAAAAA-ACTAATAATCCAATTTAAAAATGAGCAAAAGAATTGAATAA 2946
                          iv     -  v     i      ?       i     i  v       i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_72509452_7   2947 CTATTACTCAAAAGAACACATACAAATGGCAAACAGGTATATGAAAAGGT 2996
                         vi   v   v      v i           v  i i i i        i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_72509452_7   2997 GCTCAACATAATCGATCAT 3015
                                  v ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (47 / 32)
Gap_init rate = 0.03 (10 / 362), avg. gap size = 2.20 (22 / 10)  


3488 24.20 1.22 0.88  chr2_72522532_72525055     1128  2032 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72522532_7   1128 TGGAAAGACGTATCATGTTCATGAATTGAAGGAATTAATATTGTTAAAAT 1177
                                 ii vi          i    i i  v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72522532_7   1178 GTCCATTCTACCCAAAGTGATCTACAAACTCAATGCAATCCTTATCACAA 1227
                          v v  v  v      v         i i    i       i     v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72522532_7   1228 TACCAA-TGACTTTTTT-CAAATAATAGAATAAATAATGCTAAAGTTCGT 1275
                          v   i-  v       -  i -   v  vv iv i  v     i   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_72522532_7   1276 ATGGAACCACAAAAGACCCCAAATAGCCAAAGCAATCTTTAACAGAAATA 1325
                               vii   ii     vi          i       v  v ii  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_72522532_7   1326 ACAAAGATGGAGCTGTCACATAGTCTGATTTCAAAATCCAATACAAATCT 1375
                               v     vvv     ivvi ii         iii v      v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_72522532_7   1376 ATAGTAATCAAGACAGTATGGCACTAGTGCAAAAACTGATACACAGACCA 1425
                          i               i   i   i iii  ii iv  i i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_72522532_7   1426 ATGGAACAGAACACAGAACTCTGTAATAAACCCACACATTTATGGTCAAC 1475
                               i    ivv   iii v v          i              i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_72522532_7   1476 AAATTTTTGATAAAGATACCAATAACACACAATGGGGAAAAGAT----TC 1521
                         vi     i  i  i i i    v v  iv           ii  ---- i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_72522532_7   1522 TTCAATAAATGGTGCTGAGGAAACTAGACATCCACACGCATAAGAATGAA 1571
                              i           i iv    i  i ?     i   v         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_72522532_7   1572 ATTAGTCCCTCATCTCACATTGTAAACAAAAAATAATTCAAAATAGATTA 1621
                         i  i v   ii i      iii  v       v   i       i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_72522532_7   1622 AAGACTTAAACATAAGACCTGAAACTATGAAACTACTAGAAAAAAAAAAC 1671
                         ?    i    ii     v  i       i     vi     i    v -i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-T 548

  chr2_72522532_7   1672 AGATGAAAAAGCTCCATGACATTGATCTGTACAATGACTTTTTTTTTTGT 1721
                           i? v   -v  i i    v   ivi ivi     i-----   i  iv
  L1M4_orf2#LINE/    549 AGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGG-----TTTCTTAG 592

  chr2_72522532_7   1722 ATATAACCACAAAAGTACAGGCAACAAAAGCAAAAACAGACACACAGGAT 1771
                             i  vv      i   i          v     i   i v iv   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_72522532_7   1772 TACATCAAACTAAAAAGCTTCAGGACAGCAAAGGAAACAATCAA--AAGT 1819
                          v       v v    i   iv vi vv       v  v     --    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_72522532_7   1820 GTGAAGAGAACCTACAGAATGGGGGAATATACTTGCAAACCACACATCTG 1869
                          vi    v    i          i   v   i       i  i i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_72522532_7   1870 ATAAGGAGTTAACATCCAAACTATATAAGGAACTC--A-AACTCAATGAC 1916
                               iii vii     i v       i      -- -        i i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_72522532_7   1917 AAGAAAAGAAATAAACTGATTAAAAAATGGGCAAAGGATCTGAATAGACA 1966
                           i  i v      v ii   ?                 i          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_72522532_7   1967 TTTCTCAAGAGAAGACACATGAATAGCCAAGACGTATATGAAAACATGTA 2016
                               v i      i i ii   i     v v i i       v   iv
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_72522532_7   2017 CAACATCACTAGTCAT 2032
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (138 / 77)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


2943 25.49 0.88 1.53  chr2_72537225_72539985     1356  2269 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72537225_7   1356 TGGAAAAACATTCCATGTTCATGGACTGGAAGAATCAATATTATTAAAAT 1405
                               i i  i             i       v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72537225_7   1406 AACCATACTGCCCAAAGCAATCTACAGATTCAATGCAATTTCTATCAAAA 1455
                         ii v     v      vii              i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72537225_7   1456 TGCCAA-TGTGATTTTTCACAGTAATAGAAAAACCAATCCTAAAATTCAT 1504
                          v   i-  iv-     ii   v   v  v  i ii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_72537225_7   1505 ATGGAACCTAAAAAGAACACA-AATAGCCAAAGCAATGTTAAGTAAAAAG 1553
                               v- iv  i i  v  -          i    v  i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_72537225_7   1554 AACAAAACTGAAGGAAACACATTATCTCACTTCAAATTACACTACAAAGC 1603
                               ii  i    vv    i vi iv i      vivi          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_72537225_7   1604 TATAGTAATCAAAACAGCATGGTACTGGTATAAAAATAGCCACAAGGATC 1653
                           i         i    ii         i    ii    v  i vi    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_72537225_7   1654 AATGGAAAAGAAGAGAGAACACAGAAATAAAGTCACATATCTATAACCAA 1703
                                v    vv    iiv          vi  i i  i   iii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_72537225_7   1704 CTGATCTTCAACAAACTCAACAAAAATATACACTGTAGAAAG--TACCCC 1751
                         i    i   i    ivviiv   i vi  v  v  vi     --  vi i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_72537225_7   1752 TATTCAGTAAACAGTTTTGGGAAAATTGGATAGCCATATGCAGAATAATG 1801
                          -    ii   ii  vi     v  i      ?   i     i  v    
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_72537225_7   1802 AAACTGGACATATATCTCTCACTATATACAAACATTAACTTAAGATGGAT 1851
                           ii     viv  i   v   i         v       i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_72537225_7   1852 TAAAGACCTAAATGCAAGACCTGAAACCACAAAAATCATAAAACAAATTG 1901
                         i ?           i    v  i    i i    v  v  i  v   vii
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_72537225_7   1902 TAAGAAAAACTCTTCCAGACATTGGCCTGGGGAAACAATTTAT--GACTA 1949
                           i ?iv  v     vv   v    vi i  v  -iii   v --  -  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA-TA 595

  chr2_72537225_7   1950 AGATCTCAAAAGCAAATAGAACAAAAATGAAAATAGAGAAATAGAAAAAT 1999
                         v  ivi        v viv       --     ------      v    
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAA--GAAAA------AATAGATAAAT 637

  chr2_72537225_7   2000 GGAACTTAATTAAACTAGAAAGCATCTGCACAGTGAAAGAAATAATCAAC 2049
                         v i    v  i   v vi   i v i  ii vvii  i  v iv     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_72537225_7   2050 AGAATAAACAGACAAAATACAGAATGGGAGAAAATGTTTGCAAGCTATGC 2099
                          i i i  v      vvi                 i       iii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_72537225_7   2100 ATCTGACAAAGGACAAATATCCAGAAGCTATAAGAAAGTCAAACAAATCA 2149
                               i  i    vvi         vv     ii  v  vv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_72537225_7   2150 ACAAGAAAAAAATAAATAACCCCATTAAAAAATCGGCAAAGGACATGAGC 2199
                          i  v     i i         v   ?      v         iv   ii
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_72537225_7   2200 AGACAATTCTCAAAAAAAGACATACGCA--GCCAAAAAAAAAAAAGAAAA 2247
                              v     v   i    i    iv --     v  iv v v-     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-GAAAA 886

  chr2_72537225_7   2248 AATGCTCAACATCACTAATTAT 2269
                         i             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


3163 27.42 0.55 0.55  chr2_72542015_72548412     4999  5906 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72542015_7   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5048
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72542015_7   5049 GGCCATACTGCCCAAAGTAATTCATAGATTCAGTGCCATCCTCATCAAGC 5098
                            v     v      v i  ii i       ii  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72542015_7   5099 TACAAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5146
                          v v iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_72542015_7   5147 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCACTCCTAAGCCAAAAG 5196
                                viiv  ii  v  viv  v     iv  v  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_72542015_7   5197 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACCATACTACAAGGC 5246
                                i      vv    i  v  ii i      v v        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_72542015_7   5247 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5296
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_72542015_7   5297 AATGGAACAGAAT--AGAGCCCTCAGAAATAATGCCGCATATATACAACT 5344
                                i     --    i  --        vv  ii i  v  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_72542015_7   5345 ATCTGATGTTTGACAAACCTGACAAAAACAAGAAATGGGGGAACGACTCC 5394
                          vi    v  i     ivv  v   i v  vvv       i  vi ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_72542015_7   5395 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5444
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_72542015_7   5445 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAAGTTAAGATGGA 5494
                            ii    i    v   i     v              v i  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_72542015_7   5495 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5544
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_72542015_7   5545 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5593
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_72542015_7   5594 AAACACCAAAAGCAATGGCAGCAAAAGACAAAATTGACAAATGGGATCTC 5643
                         vi            vvi   i       v     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_72542015_7   5644 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGGAACTAACATCAGAGTGAA 5693
                           i   v v  i i   i  ii vv    i iv    v  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_72542015_7   5694 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGGCA 5743
                         v  i     i   i             v  i    vii ivi     ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_72542015_7   5744 AAGGGCTAATATTCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5793
                          i  i  vi   i      v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_72542015_7   5794 AAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTT 5843
                           i     i     v  i? v  i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_72542015_7   5844 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTTAT 5893
                            v        i  vi viii     v ii          i     i v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_72542015_7   5894 CATCACTGGCCAT 5906
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2737 25.37 3.83 1.47  chr2_72570961_72576771.rev     4433  5319 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72570961_7   4433 TGGAAACACATTCCATGCTTATGGATAAGAATATTCAGTATCATAAAAAT 4482
                               v i  i     i i      vi   v i i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72570961_7   4483 GGCCATACTGTCCCAAGTAATTTATACATTGAATGCTACTCCCATCAAGC 4532
                            v     vi  v  v i  i  i v   v  i  v ii  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72570961_7   4533 TACCA-CTGACTTTCTT-CAAAGAATTAGAAAAAACT-ACTTTAAATTTC 4579
                          v   -   v    i  -  i -    i-- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_72570961_7   4580 ATGTGGAACCAAGAAAGAG-CCCATG-TAGCCAAGACAATAT-AAACAAA 4626
                           i     -- v v   i -    vi-       i     v -i  v  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_72570961_7   4627 AAGAACAAAGCTGGAGGCATCACACTACCTGACTTTAAAGTATACTGCAA 4676
                                   i      vv       v  ii i  i   iiv    i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_72570961_7   4677 -GCTACAGTAACCAAAATAGCATGGCACTGGTACCTAA--ACAGATATA- 4722
                         -          i   i i  ii   i     i --   -- i   i   -
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATAT 293

  chr2_72570961_7   4723 AGACCAATGGAACAGAA--GAGAGGCCTCAGAAATAACACCACACATCTA 4770
                            i        i    --     v  --        vv   i    i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chr2_72570961_7   4771 CAACCATCTGTTCTGTGACAAACCTGACAAAAACAAGCAATGGGGAAAGG 4820
                         iiii  vi  v i vi     ivv  v   i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_72570961_7   4821 ATTCCCTATTTAATAAATGATGTTGGGAAAACTGGCTAGCCATGTGCAGA 4870
                           vvi  v  i  i     i  i     v      v  ?   ii    i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_72570961_7   4871 AAACTGATACTGGACCCCTTCCTTACACCTTATACAAAAGTTAACTCAAA 4920
                          i v   vii         v   i     v         i          
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_72570961_7   4921 ATGGATTAAAGACTTAAATGTAAGACATAAATC-ATAAAAACTGTAGAAG 4969
                               i ?    i           vv    v -      viiv      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_72570961_7   4970 AAAACCTAGGCAGTA--CCATTCAGCACATAGGCATGGGCAAAGACTTTA 5017
                              v    ?-   --i -   ivv  v v  vv i     v ii  iv
  L1M4_orf2#LINE/    542 AAAACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_72570961_7   5018 TGACTAAAACACCAAAAGCAATTGCAACGAAAGCCAAAATTGACAAATGG 5067
                          iiv  vi            vvv     i    vv     v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_72570961_7   5068 GATCTAATTAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTAACATCAG 5117
                           ii v  i  iv v  i i   i  ii vv    i  v    v  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_72570961_7   5118 AGTGAACAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATTTATCCGT 5167
                               v  i  i  i                 v       v i  vii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_72570961_7   5168 CTGACAAAGGGCTAATATCCAGAATCTACCAAA----TTTACAAG----- 5208
                             i  i  i  vi          v  iv  i----i      v-----
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_72570961_7   5209 ---AAAAA---AAACAACCCCATCAAAATGTGGGTGAAGGATATGAACAG 5252
                         ---     ---   i     v  i?   vi    ii      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_72570961_7   5253 ACACTTCTCAAAAGAAGACA--CTTATGCCTCCAAGAA--ACATGAAAAA 5298
                            i     v        i -- vv   v --   v  --         i
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGC--CAATAAGCACATGAAAAG 887

  chr2_72570961_7   5299 AGGCTCATCATCACTGGTCAT 5319
                          v     v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (125 / 96)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 1.88 (47 / 25)  


 558 32.33 12.67 5.19  chr2_72643146_72644991.rev      518  1346 (500)    L1M4_orf2#LINE/L1        4   894 (14)  

  chr2_72643146_7    518 AAAAATGAACCATGTTCATTGTTTGGAAGAGTTATTATTACAGTGATATC 567
                            i  ivv          v v        v   v    iiviv   iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_72643146_7    568 AGCACTTTCAAAATTGACCTATAGATTTAATTTAGTGTCAATCAAAATTT 617
                          ii   ii v       i   i     i  ivi i vi v        ii
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_72643146_7    618 CAATAGTTTTATTATAGGGAAGATGGGTACCTTACAACCTAATTATAATA 667
                           iiv ii  v  - ivi   iv  --------    v  i  iv   v 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTT-TGCAGAAATTG--------ACAAGCTGATCCTAAAA 144

  chr2_72643146_7    668 TTTCAAACTAG---TACAAAAG-CCAAGAGCAAGTGAGAGATTCCTTAAG 713
                           -  v - i --- i   ii -  v   ii ivii i v v  i v  i
  L1M4_orf2#LINE/    145 TT-CATA-TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_72643146_7    714 ACTGAGAATAATGT------------ATTTG--GATATCAAGACA-ATTG 748
                          vvi    i  v  ------------ i  v--i  v    i  v- i i
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_72643146_7    749 AAAAATCATA----TTAAGATCCTCTGATATGGTCATT-GGATAGATA-A 792
                         v   iii i ---- i    ivv v  i  iv v   v-       i - 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_72643146_7    793 TGGACC-------------------TTCA--AACAGTCTCACACATATAT 821
                          i  i ------------------- i  --  i iv i  i    v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_72643146_7    822 GGATCCTTGGGATATATATTAGGTGGCATAGGAGGTCGGTGGCATAGGAG 871
                           vivv   ------  v  ---i i  -   iv i iiviv   -----
  L1M4_orf2#LINE/    343 GGTCAATTG------ATTTT---CGACA-AGGGTGCCAAGACCAT----- 377

  chr2_72643146_7    872 GTCATTGGATAGAAGACAGACTTG--AATGAATAGCAATGGGACAGCTGA 919
                         -   v   iv i ii i  v   v--  ii   i iiv       i   i
  L1M4_orf2#LINE/    378 -TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_72643146_7    920 CT-GTCATGATGGAGGAAAATA-----------------TACACCA---- 947
                         v -?i  i-   v ii i   i-----------------i      ----
  L1M4_orf2#LINE/    427 ATAKCCAC-ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_72643146_7    948 --AAGATTGAATTTCAGGTGGATAAAATATGAAAATGTGAAAGCCAAAAC 995
                         --  i   -  i iv ii     v ? v ivv      i i   i     
  L1M4_orf2#LINE/    476 CAAAAATT-AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_72643146_7    996 CATAAATCTTTTAGAAGATAATATGAGAA-ATATCTTTATGAT-TCAGGA 1043
                         i     v  i        v  i  ii ?i- v     ii   i- ii  v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_72643146_7   1044 TATGGAAGGAGTTCTTAACTG-AAAACTAAAAGCACTATCCATAAAGGAA 1092
                           v v  v iv      iv i-i v  i        v v v i   i   
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_72643146_7   1093 AAGATTCAGACACAAAACATCAAACTACAATAAAATTATAAGA------- 1135
                           i  --   i ---  -- iii   v  vi       -  i -------
  L1M4_orf2#LINE/    625 AAAAT--AGATA---AA--TTGGACTTCATCAAAATTA-AAAACTTTTGT 666

  chr2_72643146_7   1136 -----AAAAAAC-CTCACAAAAGAGTAGGAAAATATGCCACTTAGTGAAA 1179
                         -----   ii  -  vv   i i   iii  i i vv    vv i  ii 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_72643146_7   1180 AATGGTATTTGTA-----TATAACAGC--ACGAACTA--ATTTGGAATAT 1220
                         i vii      i -----    v v v-- v i   v--  iii      
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_72643146_7   1221 ATGAAGAATTCCTACCAAATCATTACATTAAA-GATAGACATCTCAAAAG 1269
                           i     i  i   -  v   v  -  v   -  i i i v i   v--
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTAC-AACTCAATA-ATAAAAAGACAAATAACCCAAT-- 812

  chr2_72643146_7   1270 AGAAAAAATGAGCAAAAGAC------AAACAGTTTACCAAAGAAGGAATC 1313
                         -v?       i     i  i------ i   v  iv         iv  v
  L1M4_orf2#LINE/    813 -TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_72643146_7   1314 CACCTGGCTGGGAAA-ACATGTGAAAGGTGTTCA 1346
                           vv    iiiv  i-     -i    i  i   
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATG-AAAAGATGCTCA 894

Transitions / transversions = 1.64 (164 / 100)
Gap_init rate = 0.05 (43 / 891), avg. gap size = 3.44 (148 / 43)  


2113 23.48 6.74 8.04  chr2_72666060_72670379.rev     2910  3829 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72666060_7   2910 TGGAGGGACATACTGTGTTTGTGGATTGGAAGACTTAACACAGTAAAGAT 2959
                             ii  i  v ii    ii                 i iv  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72666060_7   2960 ACCAATTTTTCCTAGGTT--TTTACAAAGATTTAATGAAATTCCTAT-AA 3006
                         iv    vi i  i ii  -- i    --    i  i v   i     -  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA--GATTCAACGCAATCCCTATCAA 98

  chr2_72666060_7   3007 AGTTCCAGCAAGCTTTTT-GTAGATACAAACAAGATTATTCTAAAATTTG 3055
                          i i     viv      - i   v ivi     v v  i        ii
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_72666060_7   3056 TATTGAAAGGCAAAATAGCTAGAATAGCTAAGACAAATTTTAAAAAAAGA 3105
                            v    v    iiv v i        i  i    - i  i     -  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAA-GA 196

  chr2_72666060_7   3106 AGAATAAA-TTGGAGAAATTA-ACTCATATAATTTCAAGACTTATTATGT 3153
                             i   -      i v i -   ivi-i        i     i  iiv
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCC-CAATTTCAAAACTTACTACAA 245

  chr2_72666060_7   3154 AGCTATAGCAATCAAGATGGCATGGTATTGGCA-GAGTCTAGACTGTTAG 3202
                              i  i        ii ii     i     -i  vv     vvv   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_72666060_7   3203 ATGAGTGGGACAGAATAGAGAACCCAGGAATAGATTCACAAA-------- 3244
                           v i   i i     v    ii    i    i ii  i v --------
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_72666060_7   3245 -AAT--ATT----------------AGAC-------------AAAAATAA 3262
                         -   --   ----------------    -------------  i    i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_72666060_7   3263 T----TCAACACATAGTGTCAGAAGAATTGAACAGCCATAGACCAAAGAG 3308
                          ----      v  i   iii i v  i  i i ?   i vi -   ---
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-AAA--- 441

  chr2_72666060_7   3309 AGAGCGAGAATGAGCGTGATAGAACTTTGAGCTAACCTCCCATTTTATGC 3358
                         ------       i-  -- i  v ii ------     v  iiv   i 
  L1M4_orf2#LINE/    442 ------AGAATGAA-GT--TGGACCCCT------ACCTCACACCATATAC 476

  chr2_72666060_7   3359 AGAAATTATTATTACATTTTATACAAAATGGATTATGAACTTAAATGCAA 3408
                          i      ------- i -----          i ?ii  i      i  
  L1M4_orf2#LINE/    477 AAAAATTA-------ACT-----CAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_72666060_7   3409 AA-CTATACAAACTTCAAACCATTTAGAAAAAAA--TAGGGGAAAATCTT 3455
                         i -   ---     vi   v vi      i    --    ? v       
  L1M4_orf2#LINE/    515 GAGCTA---AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_72666060_7   3456 CAGAATCTAAGGGTAGGCA--GAGTTCTTAAATTTCCCTCTAAAAGTACT 3503
                          ivi i  vi  v      -- iv      i  v vv v i     i  v
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_72666060_7   3504 AACTTTCTTTCAGTGTAAAAGAAAAAAATTGGATAG-CTGAACCTCATCA 3552
                          i -------- ii--           -- i    i-i  i  i      
  L1M4_orf2#LINE/    612 AGC--------AAC--AAAAGAAAAAA--TAGATAAATTGGACTTCATCA 649

  chr2_72666060_7   3553 AAATTAAACACTTTTACTCTACAGAAGACTCTGCTGAGG--GT-AAAAGA 3599
                                 v      iiv  v  i i   v  iiii  i--  -      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_72666060_7   3600 TA--CAGTGGAGTGGGAGAAAATATTTGCAAATCATATATCCAGGAAATG 3647
                         i -- viii  i                             iiiv  iv 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_72666060_7   3648 AGTCCTTATGTATCTAGAATATATAAATACTTTGAAGAACTCATCAGTAA 3697
                          ---   --     i            ---------      v ------
  L1M4_orf2#LINE/    750 A---CTT--GTATCCAGAATATATAAA---------GAACTCTT------ 779

  chr2_72666060_7   3698 AACAAATAAACAAAAAACAAAAGAAACAATGCAAGTAGGAAAATGAGCAA 3747
                         -    v v  i  v   -  i v   i  iv   v ?i-      i    
  L1M4_orf2#LINE/    780 -ACAACTCAATAATAAA-AAGACAAATAACCCAATTWA-AAAATGGGCAA 826

  chr2_72666060_7   3748 AAGACATGAAGAAACAATTCACCGAGGCAGATATACTGATAGCATATAAG 3797
                          i  iv    v i   v   v  i i v        vi  i  vv     
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_72666060_7   3798 CACATGAGAAGATACTCAACATCCTTAGTTGT 3829
                                i     i         v????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (143 / 69)
Gap_init rate = 0.04 (39 / 908), avg. gap size = 3.49 (136 / 39)  


1647 23.65 4.87 3.13  chr2_72724167_72726107      519  1093 (848)    L1M4_orf2#LINE/L1      287   871 (37)  

  chr2_72724167_7    519 GACATACAGACCAA-ACAACACAATAGAGAACCCAGAAATAAAGCCACAC 567
                               i   i   -iv  i v   v    ii           v   i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_72724167_7    568 ACCTACAACCATCTGATCTTCAACA--GTCGACAAAAATAAGCAATGGGA 615
                          ii  iiii  vi    i   i   -- vi v   i vi vv       i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_72724167_7    616 AAAGGA-GTTCCTAATTCAATAAATGGTGCTGGGATAACTGTGTAGGTAT 664
                             i -iv  i --     i              i     vi  ?vi i
  L1M4_orf2#LINE/    387 AAAGAATAGTCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_72724167_7    665 ATACCAAAGAATGAAGCTGGACCCCTGTCTTTCAC-ATATACAAAAATTA 713
                           i v           i         ii  iv   -              
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_72724167_7    714 ACT-ATGATGGATTAAAGATTTCAATGGAAAACCTCAAACTATTAAAATG 762
                            - vi      i ?   ii v    v  i v  v       v   v v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_72724167_7    763 CTAGAAGAAAACCTAGG---AAATGTCATTCCAGACATCAGCCTTGGGAA 809
                         i           v    ---    -- -   vv   v ii v-  i  v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGG-TTAGGCA 580

  chr2_72724167_7    810 ATAATTTATGTCTAAGTCTA----CAAAAGCAATTGCAACAAAAACAAAA 855
                           ii   v ---  ii v i----        vvv         iv    
  L1M4_orf2#LINE/    581 ATGGTTTCT---TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_72724167_7    856 ATTGATAAATAGGACCTAATTAAACTAAAGAGCT---ACACAACAGAAGA 902
                           v       v    i v  i   v v  i i  ---iii vv  i i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_72724167_7    903 AACTATCAACAGAGAAAACAGACAACCTACATACAGAATGGGAGAAAATA 952
                         v        v i  vi  v        i   ----               
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACA----GAATGGGAGAAAATA 723

  chr2_72724167_7    953 TTTGCAAACTATGCATCTGATA-----------TCCAGAATCTATAAGGA 991
                                 ii  ii        -----------        v     i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_72724167_7    992 ACTTGAACAATTCAACAAGCAAAA-ACAAATAACCCCATTAAAAAGTCGG 1040
                            ivv    i    i  vv    -           v   ?    i v  
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_72724167_7   1041 CAAAATACATGAACAGGCACTTCTCAAAAAAAGACACACCGCAAACTTGG 1090
                             iv iv    i  i  i     v   i    i i  ---   --   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC---AAA--TGG 868

  chr2_72724167_7   1091 CCA 1093
                            
  L1M4_orf2#LINE/    869 CCA 871

Transitions / transversions = 1.38 (77 / 56)
Gap_init rate = 0.03 (18 / 585), avg. gap size = 2.56 (46 / 18)  


 861 27.20 3.35 0.42  chr2_72735854_72740321     2841  3079 (1389)    L1M4_orf2#LINE/L1        1   246 (662)  

  chr2_72735854_7   2841 TGAAGAGGTATTCCATGTTCATTAATAAGAAAACTCAATATT---AGAAT 2887
                           i i  i   i          vi  vi   i   i      --- ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72735854_7   2888 ATCAATTTCTCCCAAAT-GATCTAAAGATTCAACACAATTCCAATAGAAA 2936
                         iv    viii       -      v         i    i  v  -v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-CAAA 99

  chr2_72735854_7   2937 ATTCTAGTAAGTTATTTTGTGACTATTGACAAACTGATTCTAAAGTTTGT 2986
                           i i  ivivi v     iiivv        i     i     i  ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_72735854_7   2987 ATGGAAAGGCAAAAGACACAGAATAGCCAACATAATACTAACGAAGAGGA 3036
                                v    ii   v            v i   vi i vi    i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_72735854_7   3037 AGAAGATCAGAGGAC----AGTGTCCAACTTTAAGACTTACTATAAA 3079
                          v  ii ii      ---- v vi    i  i  i        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

Transitions / transversions = 2.25 (45 / 20)
Gap_init rate = 0.02 (4 / 246), avg. gap size = 2.25 (9 / 4)  

1271 27.40 14.55 0.68  chr2_72735854_72740321     3393  3976 (492)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr2_72735854_7   3393 AAAACTACAATAACTAAGATTGTGTGATATTGGCAAAAGAACAGAAAAAT 3442
                            i     i   ii    iv     i  i     v   i i   v v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_72735854_7   3443 AAATCAAAAGAACAGAATACTGAGTCTAGAAATGGACCCACACAAACAGA 3492
                          i     vi   i     vvv     i      ii     i   vvi vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_72735854_7   3493 GTCAACTGATCTTTGACTAGAAAATGAAGAAAATCCAATGG--AAAGGAG 3540
                              i    i  i   v  iiviiv    vv  i      --    i v
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_72735854_7   3541 AGTCATTTCAACAAATAGATGATGGAACAGCCGGAAAGCCTCATGCAATA 3590
                             v           i -  v   i   i i   v ?  v       v 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGG-TGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_72735854_7   3591 AAATGAATGTAGACACAGACCCTAACATGGTTCAAAAAACTTGACTTA-- 3638
                         i      vv i   v vv   - v   ivi vi v    v  i   i --
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACC-TCACACCATATACAAAAATTAACTCAAA 491

  chr2_72735854_7   3639 ---GACCATAGACCTAAATGTAAAACACAAAAATATAAAACTTCTGGACA 3685
                         ---  i  ?              i vvi    v         ii i  vi
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_72735854_7   3686 ATAACA--AGAGAAAATCTAGGTAACCTTGGGTTCAGTTACAACTT-TTA 3732
                          v    --i ? v      vv  i          vi iv iiii  -   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_72735854_7   3733 GATACAACACCAAAAGCATGACCTATGAAAGGAAAAAGTAATAAACTGGA 3782
                             ii            ii v v ii    i     vvi     i    
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_72735854_7   3783 ATTCATTACAATTTAAAACATCTCTGT----AAAAACAATGTTAAGAAAA 3828
                         v     i v    v     v i v  i----  ii   v i i      i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_72735854_7   3829 AGAAAC-ACAATC-ACAAACTGGG--------TT---------------- 3852
                         v    v-    i -   i v    --------  ----------------
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_72735854_7   3853 -----------------------------AGAAC------------ACAG 3861
                         -----------------------------     ------------ i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_72735854_7   3862 TAAGAAAATGAACAACCCTATTTAAAAAAAAAGGGAAAGGATTC-AACGA 3910
                            i  i ii  i     v   ?     vi--  v        i-  iii
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATG--GGCAAAGGATTTGAATAG 839

  chr2_72735854_7   3911 ATACCTCATCAAAGA---TATACAGATAGCAAATAATCACATATAAAGAT 3957
                          i ii  vi      ---      i  i  v     v     iv      
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_72735854_7   3958 GTTTAACGTCATCTGTTAT 3976
                          i i   i   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (94 / 62)
Gap_init rate = 0.02 (15 / 665), avg. gap size = 5.93 (89 / 15)  


3189 26.38 0.68 0.45  chr2_72779382_72787475     1549  2435 (5659)    L1M4_orf2#LINE/L1       20   908 (0)  

  chr2_72779382_7   1549 CATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATACTGCCCAAGGTA 1598
                              i v      v i     i  v  i     v     v     iv i
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chr2_72779382_7   1599 ATTTACAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTCAC 1648
                           i           i  v     i     iv v   iivi i  i  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chr2_72779382_7   1649 AGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAAGAGC 1696
                             -   -- v  i  - iii    i           viiv  ii  v 
  L1M4_orf2#LINE/    120 AGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_72779382_7   1697 CCGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCA 1746
                          v v  v     iv     i i ivv i          i      vv   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_72779382_7   1747 CACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCA 1796
                             v  ii i      viv        i          i   i    ii
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_72779382_7   1797 TGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGAG 1844
                                  i iv ii i   v                i    i--    
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_72779382_7   1845 CCCTCAGAAATAACGCCACATATCTACAACTATCTGATCTTTGACAGACC 1894
                         i  --        vv   i i  i  iiiii vi    i  i    iivv
  L1M4_orf2#LINE/    318 TCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_72779382_7   1895 TGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCT 1944
                           vv  i v  vv            i  vvi  v  i  i          
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_72779382_7   1945 GGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACCGGATCCCTTCCTT 1994
                             v      v  ?   i   i i  iiv    iii   i    v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_72779382_7   1995 ACACCTTATACAAAAATCAATTCAAGATGGATTAAAGACTTAAACGTTAG 2044
                              v           i  i    i      i ?    i    i  v  
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_72779382_7   2045 ACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGG 2094
                          v       i      vi i           v    ?i v viv   iv 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_72779382_7   2095 ACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAACAGCAATGGCA 2144
                           v v  vv i     v ii   v ivv  vi       v    vvi   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_72779382_7   2145 ACAAAAGACAAAATTGACAAATGGGATCTCATTAAACTAAAGAGCTTCTG 2194
                                 v     v  i    v   ii    i   v v  i i   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_72779382_7   2195 CACAGCAAAAGAAACTAACATCAGAGTGAACAGGCAACCTACAAAATGGG 2244
                         ii vv    i  v    v  vv i      v  i     i   i      
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_72779382_7   2245 AGAAAATTTTCACAACCTACTCATCTGACAAAGGGCTAATATCCAGAATC 2294
                                v  ii   vii ivi      i  i  i  vi          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_72779382_7   2295 TACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAA 2344
                           i  v      vv    v iv i  v     i     i     v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_72779382_7   2345 AAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATG 2394
                            i           iv    i     i     v        i  vi vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_72779382_7   2395 CAGCCAAAAA--ACATGAAAAAATGCTCACCATCACTGGCCAC 2435
                         ii     v  --         i       v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (135 / 95)
Gap_init rate = 0.01 (6 / 889), avg. gap size = 1.67 (10 / 6)  

3101 27.50 0.66 0.77  chr2_72779382_72787475     6694  7602 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72779382_7   6694 TGGAAGAACATTCAATGCTCATAGATAGGAAGAATCAATACCATGAAAAT 6743
                              ii i  i v   i    i   v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72779382_7   6744 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 6793
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72779382_7   6794 TACCAATGACTTTCTTCACAGAA-TTGGAAAACAA-CT-ACTTTAAAGTT 6840
                          v   iivi i  i  ii     -   ----    -  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr2_72779382_7   6841 CATATGGAACCA-AAAAAACAGCCTGCATTGCCAAGACAATCCTAAGCAA 6889
                                  vii-  iii  --  v v  v     i      i i iv  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_72779382_7   6890 AAAGAACAAAGCTGGAGGCATCATGCTACCTGACATCAAACTATACTACA 6939
                         i          i      vv   ii  v  ii iv     viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_72779382_7   6940 AGGCTACAGTAACCAAAACAGCATGGTACTAGTACCAAAACACAGAGATA 6989
                          i          i   i    ii       i i iv ii i v v v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_72779382_7   6990 GACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAA 7039
                           i        i    iv   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_72779382_7   7040 CCATCTGAGCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACGATT 7089
                         i  vi   vi  i     ivv  v   i v  vvv          vi  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_72779382_7   7090 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTATACATAGAAAG 7139
                         vi  v  i  i              v      v  ? i i iii i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_72779382_7   7140 CTGAAACTGGATCCCTTTCTTACACCTTATACAAAAATTAATTCAAGATG 7189
                         v    ii    i    vi  i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_72779382_7   7190 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAA 7239
                            i ?    i       v   v       i      v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_72779382_7   7240 ACCTAGGCA-ATACCATTCAGGACGTAGGCATGGATAAGGACTTCATGAC 7288
                           v    ?i- v i -   iv   v v  vv i ii  v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_72779382_7   7289 TAAAACACCAAAAGCACTGGCAAGAAAAACCAAAATAGACAAATGGGATC 7338
                           vi             vi    v    ivv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_72779382_7   7339 TAATTAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTACCATCAGAGTG 7388
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_72779382_7   7389 AACAGGAAACCTACAGAATGGGAGAAAAT-TTTGCAATCTATCCATCTGA 7437
                           v  iv    i                 -       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_72779382_7   7438 CAAAGGGCTAATATCCAGAATCTACAAAGTACTTAAACACATTTACAAGA 7487
                         i  i  i  vi          v  i    v   ivv   vv iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_72779382_7   7488 AAAAAGCAAATAATCCCATCAAAAAGTGGGCAAAGGATATGAACAGCCAC 7537
                             ii       i  v  i?    i            v    i  v  i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_72779382_7   7538 TTCTCAGAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 7587
                              vi       i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_72779382_7   7588 ATCATCACTGGTCAT 7602
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (151 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


1835 21.38 4.90 15.95  chr2_72799518_72801854      888  1846 (491)    L1M4_orf2#LINE/L1       56   908 (0)  

  chr2_72799518_7    888 TACTACACAAATTCAGCTACAGATTCGATGCAATTGCAATTAAAATCCCA 937
                             v v      v v          i i     iv v  i         
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_72799518_7    938 GCAGGAATTTTTATAGATAGAAACAAGCTGATTCTAGAATTTATATAGAG 987
                           v vvv     ii   v vvi          i   i    i    i  i
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_72799518_7    988 AAGCAAAGAAACCAGAATGTTAAAAACAATTATTAAAAAGAAGAATAAAG 1037
                          v    i i v       iviv        iv v           i    
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_72799518_7   1038 TGAGAGGAATTACACTATTAAATTTTAAGATTTATTTTAAAGCTACAGTA 1087
                          vi     v i     viiv     i  i i   i vi            
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_72799518_7   1088 ATCAAGACACTGTACCACTGGGAAAGGGATAGATACCAGTGATACTAATC 1137
                                  v   ivi     v v i       i -------  -  i--
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACA-------TA-TAG-- 295

  chr2_72799518_7   1138 GACATCAGTAGAACAGAACTGACATTGCAAAAATAGATTCACACTAATAT 1187
                         ---    i i   i    i   v v v  i     i ii  i  vvv   
  L1M4_orf2#LINE/    296 ---ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_72799518_7   1188 AGCCAGTTGATTTTTGACAAAACTGA-AAAACAATTCAATAGAGAAGTAA 1236
                         i i  i        i     iiv  v-  i  v       i i   iv  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_72799518_7   1237 TAGTTTATTAATTATATGGTGTTGGAACAATTGGAAAAGAAAGAAACTGG 1286
                             i v  v vi v      i   i    i    ------------ i?
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA------------TAK 430

  chr2_72799518_7   1287 GGAAAGGAAGGAGGGGAGAAAGAAAGAAGAAAGGAAAGAAGGAAGGAAGG 1336
                         vv v v v -------------------------      v    -----
  L1M4_orf2#LINE/    431 CCACATGCA-------------------------AAAGAATGAAG----- 450

  chr2_72799518_7   1337 GAGGAAAGGGAGGGGGAGGGACGGGGGAGGGAAGGAGAGAAGGGGGGAGG 1386
                         --------------------------------------------------
  L1M4_orf2#LINE/    451 -------------------------------------------------- 450

  chr2_72799518_7   1387 GGGGAAAGGAAGAGAGGAAGTTGAGGAAAGAGAGAAAGAGAAGAAACCTT 1436
                         --------------------   i---------------------   i-
  L1M4_orf2#LINE/    451 --------------------TTGG---------------------ACCC- 458

  chr2_72799518_7   1437 GAACTAAATCTTACACCTCACATGAAAATTAACTGAAAATTGCTCATAGA 1486
                         ---   --i  i     vi i ii          v     v v   ?   
  L1M4_orf2#LINE/    459 ---CTA--CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_72799518_7   1487 TCCAATTGTAAAACCTGCA-----------TTTGGAAGAAAA-------- 1517
                         i i  v     i v  iv -----------i  i        --------
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_72799518_7   1518 ----TCTTCATGTCCTAGCATAAGACAAAAAGTTCTTAGACATGACACCA 1563
                         ----     i  v   v vi v  i   viiv        i         
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_72799518_7   1564 AAATCATGATCCACTTTCTAAAAACT-GATAAATTGAACTTCATG----- 1607
                            v  ii v v  vvvvv     v -         i       v-----
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_72799518_7   1608 -------TTTTGTTCTACAAAAGACAC---------GGTTAAAAAGCAAA 1641
                         -------      v  v    i     ---------i  v    ii   v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_72799518_7   1642 CTACTGAGTGGAAAAAGATATCTGCAAATCACATATCTGGCAAAGGACTT 1691
                          i  v  i   i i  i    i         i       ii  i      
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_72799518_7   1692 GTATCCAGAATACATAAACAACTCCCACAATTCTAAAGTAAGAA-ACAAA 1740
                                     i     v     ii    i  v v i   i  -     
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_72799518_7   1741 CAATCCAATTTAAAAGTGGGAAAAATGTTTGAATAGACACTTCACCAAAG 1790
                         i  i      ?    i    v   ivi            i   v      
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_72799518_7   1791 AGTACAACTGAATGTAAAATAAATACGATGAAAAGATGCTCAAGATCCTT 1840
                          iv i vvii    vvv     ii  -                v   v??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCAC-ATGAAAAGATGCTCAACATCAZZ 902

  chr2_72799518_7   1841 AGCCAT 1846
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.24 (112 / 90)
Gap_init rate = 0.02 (17 / 853), avg. gap size = 11.76 (200 / 17)  


2826 25.90 2.04 1.92  chr2_72921907_72923719.rev      481  1314 (499)    L1M4_orf2#LINE/L1       42   876 (32)  

  chr2_72921907_7    481 TGTAAAAATGGACTAATACACTACCCAAAACAATCTACAGATTCAATGCA 530
                            v  i    --i     v --      vii              i   
  L1M4_orf2#LINE/     42 TGTTAAGATGG--CAATACTC--CCCAAATTGATCTACAGATTCAACGCA 87

  chr2_72921907_7    531 ATCCTTATCAAAGTATCAA-TGTCATTTTTCATATAAATAGAAAAAACAA 579
                             i       i vi  i-  i -     iii v    v  v  ivii 
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA 136

  chr2_72921907_7    580 TTCTGAAATTCATGTGGAACCAAAAAAGAACCTGAATAGTCAAATTGATT 629
                          i  i        i     viiv  ii  v  v      i    vii  i
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_72921907_7    630 CTGAACAAAAAGAACAAAGCAAGAGGCATCACACAGCCTGATTTTAAAAT 679
                         i    v  i          ivi    vv      vv  ii    i    i
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_72921907_7    680 ATATTACTAGGCAATAGTAACCAGAACAGCATGGTATTGGTATAAAAATA 729
                         v  i   v i  v i     i  ii    ii     i   i    ii   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_72921907_7    730 GACACATAGACCAATGGAGAAGAATTCAGAA-CCAGAAATAAATCCACCT 778
                             i     i       iv      v   i-           i   ivi
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_72921907_7    779 ACTTACAGCTAACTGATTTTTGACAAAGGCACCCAAAGCATACATTGGGG 828
                          i   ii ii  i       i     i  ii  v i v   v  v     
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_72921907_7    829 AAAGGATATCCTCTTTAATCAATAGTGCTGGGAACACTGGATATCCATGT 878
                             i   vi  i  i  iv   i         vv        ?   ii 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_72921907_7    879 GCAGAAGAATGAAACTGGACCCC---CTCAC--CGTTTACAAAAATGAAC 923
                            i         ii        ---     -- i v         v   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_72921907_7    924 TCAAGAAGGATTTAACATAAACATTAAACATAAGACCTGAAACTATAAAG 973
                             i v    ----  ? i  -i    ii     v  i          i
  L1M4_orf2#LINE/    487 TCAAAATGGAT----CAWAGAC-CTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_72921907_7    974 CAACTGGAAGAAAACATAGAGGAAACACTCCAGAACATTGGTCTAAGCAA 1023
                          vvi i             i? v  vv  i ivi  v    vi  i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_72921907_7   1024 AGATTTTATGGCTAAGATCTCAAA-GCACAGGTAACAAAACAAAAAATAG 1072
                         v i   iv i v  v  ivi    -     i i       v         
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_72921907_7   1073 ACAAATGGGAATATACTAAACTAAGAAGCTTCTGCACAGCAAAGGAAATG 1122
                          i    v   v vi ii   v v i  i   i  ii vv       v iv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_72921907_7   1123 GTCAGCA--GTGAAGAGACAGCCTGTTGAGTGGGAGAAAATATTTGCAAC 1170
                         i   iv --     i     i  iiiv  i                   v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_72921907_7   1171 TCTT-CATCCAATAAGGGA-TAATATCCAGACTATACGAAGAATCCAAAC 1218
                           v -i   ii        - vi        v    ii     ii vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_72921907_7   1219 AAC-----AGGAAAAAAATCTCCACATTTATTCTCATTAAAAAGTGGGCA 1263
                            ----- iv     i ----  v  -- vi iv   ?    i      
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGA----CAAAT--AACCCAATTWAAAAATGGGCA 825

  chr2_72921907_7   1264 AAGGACATGGATAGACATTTCTCAAAAGGAGACATAGAAATGACCAACAG 1313
                              iv  i             v    i   i   v     i    i i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_72921907_7   1314 G 1314
                          
  L1M4_orf2#LINE/    876 G 876

Transitions / transversions = 1.83 (137 / 75)
Gap_init rate = 0.02 (16 / 835), avg. gap size = 2.06 (33 / 16)  


4374 14.77 4.62 2.25  chr2_72975808_72977773.rev      593  1479 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_72975808_7    593 TGGAAAGGTATGCCATGTTCATTGATCAGAAAAGTTAATATTCTTAAGAT 642
                                i   v          v   ii   i v        v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_72975808_7    643 GGCAATACCCCACAAACTGAACTGCAGATTGAAAA-AGTCCTTATCAAAA 691
                                 i  v    i   v  i      v  vi- i   i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_72975808_7    692 CTTACTAGGTGGCTGTTTTTGTTGTTATTGTTGCAGAAATTGACAAGCTT 741
                         -- v i  ----   ii   -------  --                  v
  L1M4_orf2#LINE/    101 --TCCCAG----CTGCCTTT-------TT--TGCAGAAATTGACAAGCTG 135

  chr2_72975808_7    742 ATCCTAAAATTCTTTTGGAAATGTA-GGGACCTAGAATAGCCGAA-CAAT 789
                                     v v        i -      i         i  -    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_72975808_7    790 CTTGAAAAAGAAAAACAAAGTTGGAGGACTCACCCTTCCTAATTT-GAAA 838
                                     i                    v     i     -i   
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_72975808_7    839 CTTACTACAAAGTTACAGTAATCAAGAAAATGTTGTATTGACATAAAAGT 888
                                     i              v i   v   i  i     iii 
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_72975808_7    889 AGAAATATGGATGCCTGAAATATAATTGAGAATCCAGAAATAAACCCTTA 938
                            v    i   vvv  i    v        i               v  
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_72975808_7    939 CATTTATGATCAATTGATTTTCAACAAGAGTGACAAGATAATTCAATAGG 988
                                 i             i     i   v     iv       i  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_72975808_7    989 GAAACAATAGTCTTTTTCAGTGAATGGTATGTTGACAACTGGACATCCAC 1038
                             v           -  iii      iivvv          i ?    
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_72975808_7   1039 ATGAAAAAGAATGAATTTGGGGCCCTACCTCACAGCATTTATAAAAATTA 1088
                            v           v    iv            v   v  i        
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_72975808_7   1089 GCTTGAAATGGAT-ACAGACCT--------GAGATAATACTATAAAACTC 1129
                         i  ii        - ?      --------   v   v            
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_72975808_7   1130 TTAGATAAAAACAT-GGGATAAACATTCATTGGCTTGGGTTAGGCAATGG 1178
                              vi       -  ?i    iv   i viv                 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_72975808_7   1179 CTTCTTAGATATGATACCAAATGCATAAACAACAGAAGAAA---TAGATA 1225
                         i             i      v   i  i     i      ---      
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_72975808_7   1226 AATTTAACTT------AGCTGACA--TTTTATCCTTCTAAGACCTCTATC 1267
                             vi    ------ ii i v --    i v    v   iv v     
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_72975808_7   1268 ATGAAAGTGAAAAGACAATCTACAGAATGGGAGAAGATATTTGTAAATCA 1317
                          v                i i              i       i      
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_72975808_7   1318 CATATTTGATAAGGAATTTATATCCA-AATATATAAAGAACTCTTACAAC 1366
                         i    i        i i  i      -                       
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_72975808_7   1367 TCAACAATAATAATAACATAAAATAAGCCAATTGAAATATGGGGAAAGAA 1416
                             i     v  -i   ---     v      ?   v     v    i 
  L1M4_orf2#LINE/    785 TCAATAATAAAAA-GACA---AATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_72975808_7   1417 TCTGAATAGACATGTCTCCAAAGAAGATATACAAATGA------------ 1454
                          i           v                       i------------
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_72975808_7   1455 --AAAAGATGCTCA-CACCATTAGCTAT 1479
                         --            -  i  ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (76 / 51)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.05 (61 / 20)  


3184 15.58 6.53 0.00  chr2_73258422_73261875     1493  2089 (1365)    L1M4_orf2#LINE/L1        1   636 (272)  

  chr2_73258422_7   1493 TAGAAAGGTATTTCATGTTCATGGAACTGAAGACTTA---TTGTTAAGAT 1539
                          i     i   ii            viv         ---          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_73258422_7   1540 GGCAATACTCGCCA------------GATTCAACATATCCCCTCTCAAAA 1577
                                   v   ------------        ii vi    v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_73258422_7   1578 GTCCAACTGCTGTTTTTGCAAAAATTGGAAAGCTGATCCTGAAAAGCACA 1627
                         vi   i    iv        i      iv           i   vv  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_73258422_7   1628 TGGAAACGCTTGAGACCCAAAATAGCCAAATCAATCTTGAAAAAGAACAA 1677
                               i  vv i      i          v                v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_73258422_7   1678 CAAAG----GGCACTCACACTTTTTGATTTCAAAACTTACTACAAA---- 1719
                              ----i v          iiii                    ----
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_73258422_7   1720 ---TAA---AGACAGTGTGGTACTGGTATAAAGATAGACATATAGACCAG 1763
                         ---   ---                 i    i              i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_73258422_7   1764 TGGAATAAAAT--AGAGTCCAGAGATAAATCCTTACATTTATGACCAATT 1811
                                i   --          i     i  v          ii     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_73258422_7   1812 GATTTTCAACAGAGGTACCTAGACCATTTAATGGGGAAGGTATTGTTTTT 1861
                                i   ii   i  v        i         i v  v  i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_73258422_7   1862 TCAACAAATGGC-CTGGGACAGCTG-ATATTCACATGCAAAAGAATTAAG 1909
                                    i-        i   -   ?i               v   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_73258422_7   1910 CAGGACCCCTTTCTTACACTGCACACAAAAATTAACTCAAAATACATTAT 1959
                         iv        vi  i    iii i                   iv  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_73258422_7   1960 AGACCCAAATGTAAGAGTTAAAACTATAAAGCTCCTAGAAGAAAACATAG 2009
                              i           i            i   i               
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_73258422_7   2010 GAATAAATCTTCATGACCTTGTATGAGGCAAAACCTTCTTAGATA---CA 2056
                          ?i         i        vi v      vivi          ---  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_73258422_7   2057 CCAAA-GTACAAGCAACTGAA-AAAAAATA-ATAAA 2089
                              - i         vi  -        -     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

Transitions / transversions = 2.21 (62 / 28)
Gap_init rate = 0.02 (12 / 636), avg. gap size = 3.25 (39 / 12)  

 755 16.30 3.80 2.17  chr2_73258422_73261875     2371  2554 (900)    L1M4_orf2#LINE/L1      615   801 (107)  

  chr2_73258422_7   2371 AATAAATGAAATAAAATAAAATAAAATGGATTCCGTCTAAATTTAAAAAT 2420
                           i   v    --     i -    v    i i i  v     v    v 
  L1M4_orf2#LINE/    615 AACAAAAGAAA--AAATAGA-TAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_73258422_7   2421 TTTAGGCTTCAGAGAACACCATCGAAAAAAGTGAAAAGACACTCCACAGG 2470
                            iv      i  i    i   -  i              vi      i
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATC-AAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_73258422_7   2471 CTG----AAAGTATTTACAAATCATATATCTCATAAGGAACTAGTATCTA 2516
                         v  ----   i     i              v      i   v     i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_73258422_7   2517 GA-TGTATAAAGAACT--TATAATTCAACAATAAAAAGACA 2554
                           - i           --  i  i    i            
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.03 (6 / 187), avg. gap size = 1.83 (11 / 6)  

 451 18.97 5.17 0.00  chr2_73258422_73261875     2858  2973 (481)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr2_73258422_7   2858 AACAATAAAAAAACAA----CCCAGTTTAAAAATGGGTGCGTGATTTGAA 2903
                           i        i    ----    i  ?         iiviv        
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_73258422_7   2904 TACATAATTCTCTACA-AAGATATACAAATGGCCAACATGCATGTGAAAA 2952
                           v i v     i v -                   i v   ii      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_73258422_7   2953 GACAC-CAAAACCACTAGCCAT 2973
                           ii -   v i  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.02 (3 / 122), avg. gap size = 2.00 (6 / 3)  


1914 25.68 4.99 2.14  chr2_73487688_73489377.rev      498  1198 (492)    L1M4_orf2#LINE/L1      188   908 (0)  

  chr2_73487688_7    498 TGAAGAAAGAAAACAAGGTGGGATAACAGACATAATCAGATATCAATATT 547
                             i  ii i     i  v   vi  vv   ivvi vi  v    v i 
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_73487688_7    548 TATCATAAAACTATAGTAATTGAGGCAGGGTGGT-CTGTGTGAAAAGATA 596
                           ii i   i   i      ii  i   v     -   - iiv  i    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG-GCATAAGGATA 286

  chr2_73487688_7    597 GACAAATAAACCAATGGAGAAGAATAGAGAGTACAGAAACAGTCCCACAC 646
                             v   i i       iv     v      v      i iv    i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_73487688_7    647 ATAGGCAGATGCTCAATTAGT----GACAAAGGT----AGAAT-TTCAGA 687
                           vv----   v      ii ----     i   ----   vi-    iv
  L1M4_orf2#LINE/    337 ATTT----ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_73487688_7    688 GCAGTAGAAAACAGGCATTCTCTTCATTAAATGGTATTGGATCAATGGAA 737
                          vi - i i  i  ----   i    vi       ii   iv   iv i 
  L1M4_orf2#LINE/    383 GGGG-AAAGAATAG----TCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_73487688_7    738 TATACACACCCAAAA--ATGAAATTTGACCCC-ACCTCACACCATACCTA 784
                           ?v    iv     --     i  v      -             ivi 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_73487688_7    785 AAAATCAATTCTAGGTGGATTGCAAATCTAAATGCAAAAGGTGAAACAAC 834
                              i  i  v ii     ii? i i       i  i  v i    v i
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_73487688_7    835 AGA---TTTAGAAGAAAACATGAGACTA--TCTTCATGACCTTGAGGTAG 879
                          i ---i              ii ?v  --     i        i v   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_73487688_7    880 ACAAAACTTTCTTAAATAGGACAAAAAAAAGCACTTATTTAA-AAAGGAA 928
                         i   viv       i   v    vv    -    -- vvi  -   i   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAA-GCAC--AAGCAACAAAAGAA 624

  chr2_73487688_7    929 AAGATTAATAAACTGGATTTCATTAAGATTAGGGACTACCGTTCACCAAA 978
                           i  vi     i    i     i  i    iii   vii  v vi    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_73487688_7    979 GGATACCA-CAA-AGAGTGCAGTAGCATAAGTCACACACTGGCA-AAGAT 1025
                            i  i -   - i    v i-  - i  vi    v v   v -  i  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAA-AG-ACAACCCACAGAATGGGAGAAAAT 722

  chr2_73487688_7   1026 ATTTGCAA--CATATAACTGACAAAGGACTTACATCCAGACTGTACAAAG 1073
                                 --      v    i  i      ii       v i  i    
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_73487688_7   1074 AACTGTTAGAA-----TAA--AAAAGACAG-CAACCCAATGGAAAAATGA 1115
                             v   v  -----   --        i-i        v?       i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_73487688_7   1116 -TGAAGT-CTTGAATGGGCACTT-TACAAAAGAGATGTCCAAACATTCAA 1162
                         -ii   v-i      i i  i  - v    ii    i v    iivi   
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_73487688_7   1163 TAACCATATTTAAAAGTGCTCAACCTCATGTAAAGT 1198
                            v  i  vv   ii        v   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (113 / 63)
Gap_init rate = 0.04 (27 / 721), avg. gap size = 1.85 (50 / 27)  


3379 23.54 1.32 1.43  chr2_73541060_73545713.rev     3254  4162 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_73541060_7   3254 TAGAAAGATATTCCATGTTCACAGACTGAAATAATTAATATTGTTAAAAT 3303
                          i         i         ii  i  i  v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_73541060_7   3304 GTATGTACTATCCAAAGCAAT--ACAAAGTCAACACAATCCTTATGAAAA 3351
                          vvvi    vi     vii  --   i v     i      i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_73541060_7   3352 TGCCAATGGCATTTTTCACAAAAATAGAAAAAAAAATC-TAAAATTCATA 3400
                          v   iiv  v     ii  i    v  v  ivvi   -           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_73541060_7   3401 TAGAACCACAAAAGACTCTAAAGAGCCAAAGTAATTCTGTAAGACAAAAA 3450
                          i   vii   ii   i vi  v       ii   ii  v  i v  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_73541060_7   3451 CAAAGTTGGAGGAAGCACACTTCCTGGTTTCAAATTATATTACAAAGTTA 3500
                                      vv         iii       viv  i       i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_73541060_7   3501 TAGTAACCCAAACAGTGTGGTACTGGCATAAAAAGTAGACATGTAAACCA 3550
                         i     i v i                    ii -       i  i i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCA 299

  chr2_73541060_7   3551 ATGGAACAGAATAGAGAG-AGAAAAATAAACCCAAGCATATATGATTCGC 3599
                               i     v     -vv i           vi   v    i ivii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_73541060_7   3600 TAATTTTTGACAAGGGCACCAAGAAGACACAATAGGGAATAGAAGA-TCT 3648
                          i     i        ii      vv iv    i     -    v -   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAATAGTCT 398

  chr2_73541060_7   3649 CTTCAAATAATGGTGCTGAGAAAATTAAATTTCCTCATGCAAAAGAATGA 3698
                         i     vv          i  v  i ii  v?  v               
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_73541060_7   3699 AATTGGACCTTTATCTTACACCACCAGCAAAAATCAACTCAAAGTTGATT 3748
                          i       ii  i  i      ivvi       i        i v   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_73541060_7   3749 AAAGAACTCAACATGAAGACTTAAAACCATAAA---CCTAGAAGAAAATA 3795
                          ?   v  v  ii -    vi      i     --- i          i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_73541060_7   3796 TATGGGAAAAACTCCTTGACACTTGTCTT-GGCAATGTTGTTTTGGATAT 3844
                           v ? v   v  i v    -    vv  -       v v i  i     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_73541060_7   3845 CACAACAAAAGCTCAGGCTACAAAAGCAAAAATAAATAAATAGAACTAAA 3894
                         v   v       v  i  v       v       i      v i   vv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_73541060_7   3895 TCAAG-CTAAAGAGTTTCA--CATCTAAGTAAACAATCAACAAAATGAGA 3941
                             i-i    i v   ii-- v  v   v v  v     v   i   i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_73541060_7   3942 AGACAGTCTACTACAGATGAGAAAATATCTGCAAACCATATATCTGATAA 3991
                              ii i  viv viv          i      i              
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_73541060_7   3992 GGAGTCAGTTTCCACAATATATAAAGAACTTGTGCAACTCAGTAGAAGAA 4041
                           iiiiv  v    v               iv i       i  iv i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_73541060_7   4042 AAACAAACAACCTAATTTTAGAATGGGCAACGGACCTGAACAAACATTTC 4091
                          i     i    i    ?v i         v   ii    i i       
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_73541060_7   4092 TCCAAAACAGAAAAAAAGAAAAGAAAAATGGCCAATCAGCATATGAAAAG 4141
                               i--------    v -v v           v    i        
  L1M4_orf2#LINE/    847 TCCAAAG--------AAGATA-TACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_73541060_7   4142 ATATTCAATATTACTATCATC 4162
                           ii    i  i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (125 / 85)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.79 (25 / 14)  


1755 22.92 6.92 2.17  chr2_73551361_73553803.rev      861  1366 (1077)    L1M4_orf2#LINE/L1       14   543 (365)  

  chr2_73551361_7    861 CATGTTTATGGATTAGAAAACTCAATATTGTTAAGATGTCAAAATTATTT 910
                               i       i   i   i               v   v i --ii
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT--CC 61

  chr2_73551361_7    911 TCAAATTGATTTATAGACTCAATGAAATCTTAATAAAAAATTCCAGCAGG 960
                         i         i  i   i    i v    iiv  v    - i     v v
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCCAGCTGC 110

  chr2_73551361_7    961 CTTTTAAAATATAAATTGGGCGAGCTAATTCTAAAATTTATATAGAAATT 1010
                              vvi-i v      i- i    i  i        i    i     v
  L1M4_orf2#LINE/    111 CTTTTTTG-CAGAAATTGA-CAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_73551361_7   1011 CCAAGAATCTGAAATAATCAA-----TTTTTAAAAAGAGGAACAAAGTGG 1055
                          v i i i iii    ii   ----- i  v       i         v 
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_73551361_7   1056 GAAAAATCACACAACCTGATTTTAAGAC---------AG-TACAGTTATT 1095
                           ii v      vv  ii    i  i  ---------  -      v  i
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_73551361_7   1096 AAGA--GTGTAATATTGGCATGAGGATACATATGTAAATCAATGGAATAG 1143
                             --    ii  i      i      v i  i  i             
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_73551361_7   1144 ---TGTG----CAGAAATAGACCCACATATACAAGGTCAATTAATTTTTT 1186
                         ---  v ----        i     i i  vi v        i     iv
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_73551361_7   1187 TACAAAGATGTCATGAA-ATCCACTGGAAAAAAAGATAG---------CA 1226
                         -    i i  i  v  v-  i  v   ii   i -    ---------  
  L1M4_orf2#LINE/    359 -ACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACA 406

  chr2_73551361_7   1227 AATGGTGCTAGAATAACAATTACATATTCATATGTAAGAAAATACAGCTT 1276
                                  i i i   --- iv   ?i  i   i  i i   iv  -  
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAAC---TGGATAKCCACATGCAAAAGAATGAAG-TT 452

  chr2_73551361_7   1277 GGATGCTTCCTTCACACCATATACAAAAACCAACTCAAAATGGATCTTAG 1326
                            iv i v i                  ii               v?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_73551361_7   1327 ACATAAATGTAAAACGTAAAACTACAAAACTTCT-GAAAAA 1366
                           v         i vv        i      ii -   i  
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

Transitions / transversions = 2.35 (80 / 34)
Gap_init rate = 0.03 (17 / 530), avg. gap size = 2.71 (46 / 17)  

 912 24.37 6.35 3.55  chr2_73551361_73553803.rev     1558  1951 (492)    L1M4_orf2#LINE/L1      504   908 (0)  

  chr2_73551361_7   1558 CCAAAATGTCAATAGTGCCAAGGCTGAGAAACCCTGGTCTAGAAGAAAAC 1607
                           v      -  v  -- i  ii  ivi    i  ----           
  L1M4_orf2#LINE/    504 CCTAAATGT-AAGAG--CTAAAACTATAAAACTCT----TAGAAGAAAAC 546

  chr2_73551361_7   1608 ATAGAAGAAAAATCTCAGTGACATAGGATTAGGCCAAGATTTCTCAGATA 1657
                             i? v   -   iv     v v  i      v v i     i     
  L1M4_orf2#LINE/    547 ATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_73551361_7   1658 GTACACAAGAAATATAAACCAAAAAAGGAAAAAAAATCAATAAACAAG-T 1706
                         vv    v i  ii i  i v v     ---       vi     ivi -i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAG---AAAAAATAGATAAATTGGAC 642

  chr2_73551361_7   1707 TTCATCAAAATTAAAA-CTTCTGCCTTTCAAAGA-------CAGGAGAAT 1748
                                         -   i  ivi       i-------  i  i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_73551361_7   1749 ACAAAAACATGCCACAGACTG--------TCTCTGCAAAAGAAACAACTG 1790
                         iv   i   vv       v  -------- v i      vv v i v   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_73551361_7   1791 ATAAAGGACTTGCATCTAGAGC-TATGAAGAACTCCCAAAGCTCAA---- 1835
                             i       i   i   ii-   i        ii v i     ----
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_73551361_7   1836 AAAATGAAACAAACCAGCCA--CAAAAAATCAGGCAGAG-ATTTTAACAG 1882
                             -- i     iv v   --i?      -i    i  -    v  i  
  L1M4_orf2#LINE/    793 AAAA--AGACAAATAACCCAATTWAAAAAT-GGGCAAAGGATTTGAATAG 839

  chr2_73551361_7   1883 ATCTCTCACTGAAGAAGAAACATGGAGGGCAAATAAGCACACAAAAAGAT 1932
                          iv i  v ii       v i iii v   v          ii       
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_73551361_7   1933 GCTATATATCATTAGTCAT 1951
                            vv i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (57 / 37)
Gap_init rate = 0.04 (15 / 405), avg. gap size = 2.60 (39 / 15)  


3059 24.84 0.95 4.97  chr2_73598737_73605178     5005  5950 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_73598737_7   5005 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5054
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_73598737_7   5055 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5104
                            v     v     iv i  i  i        i  v     i     i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr2_73598737_7   5105 TACCAGTGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCGGTG 5154
                         -----------------------------     -----    i  ----
  L1M4_orf2#LINE/    100 -----------------------------ATCCC-----AGCTGCC---- 111

  chr2_73598737_7   5155 ACTTTCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCATATGGAAC 5202
                         ---  i  ii     -   -- v  i  - iii    i           v
  L1M4_orf2#LINE/    112 ---TTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_73598737_7   5203 CAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGC 5252
                         iiv  ii  v  v v  v     iv     i i ivv i          i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_73598737_7   5253 TGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAA 5302
                               vv       v  ii i      viv        i          
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_73598737_7   5303 CCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAAC 5352
                         i   i    ii         i iv ii i   v                i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_73598737_7   5353 AGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACCATCTGATC 5400
                             i--    i  --        vv   i i  i  iiii  vi    i
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_73598737_7   5401 TTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAA 5450
                           i     ivv  v   i v  vvv           i  vvi  v  i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_73598737_7   5451 TAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGG 5500
                         i              v      v  ?   i   i i  iiv    ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_73598737_7   5501 ATCCCTTCCTTACACCGTATACAAAAATTAATTCAAGATGGATTAAAGAC 5550
                          i    v   i     i              i    i      i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_73598737_7   5551 TTACATGTTAGTCCGAAAACTGTGAAAACCCTAGAAGAAAACCTAGGCA- 5599
                         i  v    v  vv v      i i   vi i           v    ?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_73598737_7   5600 ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAAAACACCA 5649
                          v i -   iv   v v  vv i     v ii   v ivv  vi      
  L1M4_orf2#LINE/    555 AAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_73598737_7   5650 AAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACT 5699
                               vvi          vv     v  i    v   ii v  i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_73598737_7   5700 AAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAGAGGAAAC 5749
                         v  i ii  i  ii vv    i  v    i  vv i      i  iv   
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_73598737_7   5750 CTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTA 5799
                          i   i             v  i    vii ivi      i  i  i  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_73598737_7   5800 ATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAA- 5848
                         i          v  i  v      vv    v iv i  v     i    -
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_73598737_7   5849 ---CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCTCAAAAG 5895
                         ---   v  i?    i    ii      v    i     i     v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_73598737_7   5896 AAGACATTTATGCAGGCAAAAAACACATGAAAAAATGCTCATCATCACTG 5945
                             i  vi viii v   v  i          i       v     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_73598737_7   5946 GACAT 5950
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 5.09 (56 / 11)  


 301 18.18 0.00 17.53  chr2_73619109_73625381.rev      347   500 (5773)    L1M4_orf2#LINE/L1      704   830 (78)  

  chr2_73619109_7    347 CTACAGGTTACAAGAAAATATTTGCAAACCTCATATCCAACAAAGGTCTT 396
                          i    iv ivi                i vi     ii i  i  v   
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_73619109_7    397 GTATCTGCTAGCCTTACATCTAACATATATACTAACATATATATACAATT 446
                              i---  ----------  i     - vv   --- v -     i 
  L1M4_orf2#LINE/    754 GTATCC---AG----------AATATATA-AAGAAC---TCT-TACAACT 785

  chr2_73619109_7    447 CACAACAGTAAAAAGGGAAAAAAAAGACAATCCAATTAAAAAATGGGCAA 496
                           -- i i       iv   -------i  i      ?            
  L1M4_orf2#LINE/    786 CA--ATAATAAAAAGACAAA-------TAACCCAATTWAAAAATGGGCAA 826

  chr2_73619109_7    497 AAGA 500
                          i  
  L1M4_orf2#LINE/    827 AGGA 830

Transitions / transversions = 2.38 (19 / 8)
Gap_init rate = 0.06 (7 / 127), avg. gap size = 3.86 (27 / 7)  

3237 26.65 0.55 0.55  chr2_73619109_73625381.rev     4874  5781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_73619109_7   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4923
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_73619109_7   4924 GGCCATACGGCCCAAGGTAACTTACAGATTCAATGCCATCCCCATCAAGC 4973
                            v    vv     iv i ii           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_73619109_7   4974 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5020
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_73619109_7   5021 ATATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAA 5070
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_73619109_7   5071 GAACAAACCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5120
                                vi      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_73619109_7   5121 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5170
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_73619109_7   5171 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCAGCATATCTACAAC 5218
                                 i    i--    i  --        vv vii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_73619109_7   5219 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5268
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_73619109_7   5269 CCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5318
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_73619109_7   5319 TGAAACTGGATCCCTTCCTTACACCGTATACAAAAATTAATTCAAGATGG 5368
                             ii    i    v   i     i              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_73619109_7   5369 ATTAAAGACTTACATGTTAGACTGAAAACCATAAAAACCCTAGAAGAAAA 5418
                           i ?    i  v    v   viv     i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_73619109_7   5419 CCTAGGCATTACCATTCAGGACATAGGTGTGGGCAAGGACTTCATGTCTA 5468
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_73619109_7   5469 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5518
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_73619109_7   5519 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5568
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_73619109_7   5569 CAGGAAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5618
                         v  iv    i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_73619109_7   5619 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5668
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_73619109_7   5669 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5718
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_73619109_7   5719 CTCAAAAGAAGACATTTATGCAGACAAAAAACACATGAAAAAATGCTCAT 5768
                            v        i  vi viii v   v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_73619109_7   5769 CATCACTGGACAT 5781
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2266 23.85 11.14 1.45  chr2_73639374_73641366.rev      676  1501 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_73639374_7    676 GAAAAATCTCACCATGTTCATGCATAGGAAGACTGAAAATTC---AAATG 722
                             i  v  -           v  v        v  v   v--- i   
  L1M4_orf2#LINE/      3 GAAAGATATC-CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_73639374_7    723 TCAAT-CTACA-AAATTGATCTACAGATTCCATACAATCCCCAAAAAAAT 770
                         v    -  v v-                  v ii       i vv     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_73639374_7    771 CCCAGT----------------AT------GCTTATTCTAAAATTTGTAT 798
                              i----------------  ------   v  i        ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_73639374_7    799 GAAAATGCAAAGGACTTGAAATAGCAAAAATAATTTTGAAAACAAA-AAC 847
                          i        i    iiii      v    i   i       vi  -   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_73639374_7    848 AAGGTTGGAGGAC--ATAA--CCTGATTTCAAGACTTACTATAAAGCTAC 893
                           i          -- i v--  ii       i        i        
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_73639374_7    894 AGTAATCAAGACATTGTGGTACTGGTGTAAAGATAAATAAAAAGAACAAA 943
                                      v           ii   i    i i v v   v   v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_73639374_7    944 GAAACAGAGTAGAAACTCTA-----AAACTTACACATATAAGGCCAACTA 988
                          i  i   i v  i v  i -----    ii i    v  v  i   i i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_73639374_7    989 ATTTT-GACCAAGGTTCCAA--CTAACTTCAATAAGGAAA---TAATCAT 1032
                              -   v i   v    -- i --      ii     ---  i  - 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCA--TTCAATGGGGAAAGAATAGTC-T 398

  chr2_73639374_7   1033 TTTTGAAAAGTGGTGCTAGAA--------TATTCCTAGGAAAGAAAATGA 1074
                            ii v  i       i i --------  ?i vi v v  i i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_73639374_7   1075 TCCTCAACTGCATAACTTACACCACAAAGGAGAATT---TGGAAACAGAT 1121
                         vvi vi  iv -  v  i      i v vi i    --- vi   ii   
  L1M4_orf2#LINE/    449 AGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_73639374_7   1122 CACAGACTTGATCACAA-AGTTAAGACCATAACATTTCTACATGAAAATA 1170
                           ?    i i viii  -  i   i  i    v i ii  v v     i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_73639374_7   1171 CAGGAGAAAACTTTTACAACACTTGA-TTAGGCAACA-TTTCTTAATCAG 1218
                         i   ? v   ii  iiii  -    i-        ii-       ivi v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_73639374_7   1219 GACACAAAAAAGTACTAATCATTAAAA--AAAAATTACCAAAGTGGAATT 1266
                              v    - i  -  v  vi    --      vivi   v    v  
  L1M4_orf2#LINE/    597 GACACCAAAA-GCAC-AAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_73639374_7   1267 CATCAAAATTAAAGCTTTCTGTTCCCCAGAG-ACACCATTAAGAAAACAA 1315
                                      ivi  i   v ii  i  -    i  i      iii 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_73639374_7   1316 AAATCACA--CCACAGACTATGAGAAAATATTCACAA----TACAC---- 1355
                            v-   --       v iv           ii   ----  i i----
  L1M4_orf2#LINE/    695 AAAG-ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_73639374_7   1356 -AGAGGATTTGTATCTGGAATATATTATAAAAATTCCTA--------TAA 1396
                         - ii   i       ii        - -  i  i  i  --------   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATAT-A-AAGAACTCTTACAACTCAATAA 791

  chr2_73639374_7   1397 TACTGAGACAAATAATCCAAT--------GGATAAAAG---TGAACAGAT 1435
                           vvi          i     --------  ii   i ---    i   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_73639374_7   1436 ACTTC-ATAAATAAAATCATGCAAATGGGCAAGAGACACA-GAAAAGATG 1483
                          i   -vi   v  i  -  i       v   v ii    -         
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGAT-ATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_73639374_7   1484 CTCAGCATCATTAGTCAT 1501
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (130 / 64)
Gap_init rate = 0.04 (38 / 906), avg. gap size = 2.74 (104 / 38)  


3451 23.80 1.09 2.39  chr2_73663810_73667999.rev     2779  3698 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_73663810_7   2779 TGGAAAAATATTCCATGTTCATGAATTAGAAGAATCAATATTGTTAAAAT 2828
                               i    i           i   i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_73663810_7   2829 GTCCATACTACCTAAAGCAGTGGGGTATTCCACTGAATCTGTATTCAAGG 2878
                          v v     v  i   ---- v i----  i  v  -------     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA----TTGA----TCTACAGA-------TTCAACG 85

  chr2_73663810_7   2879 CAATCCCTATCAAAATACTAATGACATTCTTCACAGAAATAGAAAAA--- 2925
                                         v i iivi v  i  ii       v  v  i---
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chr2_73663810_7   2926 ATCCTAAAATTTATATGGAACCACAAAAGACCCAGAATAGACAAAGCTAT 2975
                                    i        vii   ii            v    i v  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_73663810_7   2976 CTTAAGCATAAAGAACGAAACTGGAGGAATCACAATACCTAACTTCAAAT 3025
                            i iv vi      i  ii       v     v v  i  i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_73663810_7   3026 TATACTACAATACTATAATAACCAAAACATCATGGTACTGGCTTAAAAAC 3075
                         iv        vi   i i   i   i   vii          v   ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_73663810_7   3076 AGGCACATAAACCAATGAAACAGAACCAGAGAACCCAGAAACAAATCCAC 3125
                           i  i   i i     i  i    ii-    ii       i   i   i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATT-GAGAGTCCAGAAATAAACCCAT 334

  chr2_73663810_7   3126 ACACCTACAGTGAACTCATTTTCAACAAAGGTGCCAAGAACATACACTGG 3175
                            ii  ii  v  i v      i    i          v   v  v   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_73663810_7   3176 GAAAAAGACGGTCTCTTCAACAAATGGTGCTGGGAAAGCTGGTTATCTAC 3225
                          i   ii ii    i                    v i    v  ? i  
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_73663810_7   3226 ATGCAGAAGAATAAAGCTAAACCTCTATCTTTCATCATATACAGAAATCA 3275
                              i      i   i ii   i   i  iv  i        i    i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_73663810_7   3276 AATCAAAATGGATTAAAGACTTAAATCTAAGACCTCAAGCTATGAAACTA 3325
                          v           i ?    i     v     v  v  i    i     v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_73663810_7   3326 CAGGAAGAAAACACTGAGAAAACTCTCTAGGACATTAAATATTGGCAAAG 3375
                         ivi          iv i?iv  v   iiiv   v  iii - v     v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATG 583

  chr2_73663810_7   3376 ATTTCTTGAGTAATATCCCACATATACAGGCAACCAAAGCAAAAATGGAC 3425
                         i      iii  vv iv   v vii   i     v    v      i  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_73663810_7   3426 AAATGTGATCACATCAAG-TTAAAAAGATTTCACACAGCAAAGGAAAC-- 3472
                             vv  iiv      i-       v-   iiii vv       v  --
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTA 682

  chr2_73663810_7   3473 ----AACACTGAAGAGACAAACCACCGAATAGGAGGAAACATTTGCAAAC 3518
                         ----i v v    i      v    v    i    i   i         i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_73663810_7   3519 TATCCATCTGACAAGGGATTAGTAGCCATAATGTATAAAGAACTGAAACA 3568
                         i  vi      i      i v   v   v   i           vvv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_73663810_7   3569 ACTCTATAGGAAAAAAAAAATCTAATAATCCAATTTAAAAACGGGCAAAA 3618
                             v   iv     i v  ----    i      ?     i       i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAA----ATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_73663810_7   3619 GATCTGAACAAACATTTCTCAAAAGAAGACATATAAATGGCAAACAGGCT 3668
                            i    i i         v        i   i       v  i i  v
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_73663810_7   3669 TATGAAAAGGTGCTCAACATCAGTGATCAT 3698
                         i        i            ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (138 / 77)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.20 (32 / 10)  


1245 21.59 1.66 0.00  chr2_73676683_73683058      123   423 (5953)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr2_73676683_7    123 AAAAACAAAGGCAACAAAAGAAAAA-TATATATGGGAGACTTTATCAAAA 171
                             i  v i               -  v   vivvi     i       
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_73676683_7    172 TTCAAAACTTTTGTACA-CAAA--ACCCAGTCAAAAGAATGAAAAGGTGA 218
                           v           i v-    --  v vi    i i i       iii 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_73676683_7    219 CTCACAGCATAGGAGAAAATATTTGCAAATCATTTATCTGTTGAGAGATT 268
                          i     v  i                      v      v i  i  i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_73676683_7    269 AATACCTAAAATATGTAAGGAACCCTTACAACTCAACAACAATAACCCAA 318
                         vi  i i i     i   i    i            i  i  v  vv   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_73676683_7    319 ACAATCTGATTCATAAATGGGCACAGAATCTGA-TGGACATTTCTCCAAG 367
                          i  i ii   ? v         v  i  i   - i             i
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_73676683_7    368 GAAGACGTGCAAATAGCCAATAAACACCTGAAAATCTTCTCTATATCATT 417
                              ii i     i        i   v      vv v   v i    ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_73676683_7    418 AATCAT 423
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.78 (41 / 23)
Gap_init rate = 0.01 (4 / 306), avg. gap size = 1.25 (5 / 4)  

3129 27.78 0.55 0.44  chr2_73676683_73683058     4978  5884 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_73676683_7   4978 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5027
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_73676683_7   5028 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5077
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_73676683_7   5078 TACCAATGACTTTCTTCACAGAATTGGAAAAAACGACTTTTAAAGTTCAT 5127
                          v   iivi i  i  ii     v v  v  ivi  - ii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_73676683_7   5128 ATGGAACAAAAAAAGAGCCTGCATCGCCACGTCAATCCTAAGACAAAAGG 5177
                               vviv  ii  v  v v  v    viv     i i i v i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_73676683_7   5178 ACAAAGCTGGAGGCATGACGCTACCTGACTTCAAACTATACTACAAGGCT 5227
                               i      vv v  i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_73676683_7   5228 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5277
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_73676683_7   5278 ACGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAGCTA 5325
                          i    i    i--    i  --        vv  ii i  i  ii ii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_73676683_7   5326 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5375
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_73676683_7   5376 TATTTAATAAATGGTGCTGGGAAAGCTGCCTAGCCATATGTAGAAAGCTG 5425
                          v  i  i              v i   vv  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_73676683_7   5426 AAAGTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGAT 5475
                           iv    i    v   i i   v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_73676683_7   5476 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5525
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_73676683_7   5526 TAGGCA-ATACCATTCAGGACACAGGCATGGTCAAGGACTTCATGTCTAA 5574
                             ?i- v i -   iv   viv  vv i v   v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_73676683_7   5575 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5624
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_73676683_7   5625 TTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTACCATCAGAATGAAC 5674
                          i   v v  i i   i  ii vvi   i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_73676683_7   5675 AGGCAACCTACAGAATGGGAGAAAAATTTTGCTATCTACCCATCTGATAA 5724
                           i     i                vv     v vii ivi         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_73676683_7   5725 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATATACAAGAAAG 5774
                         i  i  vi          v  i  v      iv    v vv i  v   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_73676683_7   5775 AAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTTC 5824
                          i     i     v  i? v  i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_73676683_7   5825 TCAAAAGAAGACATTTATGCAGCCAACAG--ACATGAAAAAATGCTCATC 5872
                           v        i  vi viii     i i--         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_73676683_7   5873 ATCACTGGCCGT 5884
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (144 / 104)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3380 17.97 3.30 1.59  chr2_73713857_73715603.rev      501  1257 (490)    L1M4_orf2#LINE/L1      139   908 (0)  

  chr2_73713857_7    501 CTAAAATTCAT---GAAATCTCAAGGGAAACCAAACAGCCAAAATAATTT 547
                                    ---     v-       vv vi  i        i   i 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_73713857_7    548 TGAAAAA--AGAACTAAGTTACAGGTTTCACACTACCTGCTTTCAAAACT 595
                                --     v     iv   vi       v  iiv          
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_73713857_7    596 CATTTTAAATACACAGTAAATCAAAACAGTGCAGTAGTGGCATAAAGAGA 645
                         i i vi   vvi       -    i      ii   v        i  v 
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAA-TCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_73713857_7    646 GATATATAGACTAACAGAATAGA-----GAGCCCAGATAAAAACCCTCAC 690
                           i       ii  ii       -----   i     v v      vi  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_73713857_7    691 GTATATGGCTAAACGATTTTTGGCAAGAGTGCCAAGAACATTCAATGGGG 740
                         i v     ii  vi      i i    i         v            
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_73713857_7    741 AAAAAA-AGTCTTTTCAACAAACGATGTTGAGAAAACGGGATATTCACAT 789
                            i  -               i i  i  i  v   v     ?i     
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_73713857_7    790 GCAGAAGAATGAAGGTGGACCCTTATCTTACACCATACACAAAAATTAAC 839
                            i          v       i  i  i        i            
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_73713857_7    840 TCAAAATGGATCAAAGACCTAAAAGTAAAAGCTAAAATTATTAAACTCTT 889
                                      ?         v    i        i   v        
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_73713857_7    890 AAGAAGAAAAC------------TTTCACGACACTGGATTTGGCAAATAT 927
                          -         ------------i   ii   vi   i  v     vvi 
  L1M4_orf2#LINE/    537 A-GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_73713857_7    928 TTCTAAGATATGACACCAAAAGCACAAAAAACAAAA-AAAAAATAGCTAA 976
                             v                      iv       -         v   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_73713857_7    977 ATTGGACTACATCAAAATTTAAAACTTCTATATGTCAGAAGACACGGTCA 1026
                                 v          v       i i iiv   i i     vi   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_73713857_7   1027 GCAGAGTGACTGTGAAAGAGGCAACCTACAAAATGGGAGAAAATATTTGC 1076
                         iv i     -----     --     i   i                   
  L1M4_orf2#LINE/    686 AGAAAGTGA-----AAAGA--CAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_73713857_7   1077 AGATCATGTATCTAACAAGAGATCAATATCCAGAATATATAGAAAATCCC 1126
                          i     i     i i   i  iivi               i i  ii i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_73713857_7   1127 AACAACTCAAAAACCAAAAAATCAAACAGCCAGATTTAAAA-TGGCCAAA 1175
                         v         v  iv    i -    i i  vi   ?    -   v    
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_73713857_7   1176 TGACTTGAAAAGACATTTTTCAAAAGAAGATATACAAATGGTTAAATAAG 1225
                         v  i     v        i  v                   ii  -    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAG 876

  chr2_73713857_7   1226 CACATAAAAAGATGTGCAACATGAATAATCAC 1257
                              i        iv      v ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (85 / 48)
Gap_init rate = 0.02 (14 / 770), avg. gap size = 2.64 (37 / 14)  


2904 19.31 4.07 0.75  chr2_73721398_73723281.rev      510  1172 (712)    L1M4_orf2#LINE/L1      141   825 (83)  

  chr2_73721398_7    510 AGAAATCAT-TAAAAATGATAAGAAATCCTGAATAGCCAAAACAACTTTG 558
                          i  v    - ii     -i   ii i  v               ii   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_73721398_7    559 AAAGACAAGAACAATGTTGGAGTATTCACACTTCCTGATTTGAAAACATA 608
                            i v        v       v i          ii    v     v  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_73721398_7    609 TTACCAGAGGAACAGTAATCAAAATAGTGTGATATTAGTATAAAGACAAA 658
                         i   - i  vv           i i      i  i i i    i  i i 
  L1M4_orf2#LINE/    240 CTAC-AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_73721398_7    659 CAAGCAGACCAATGAAATAAGAA--AACATGCCCAGAAATAAACTCTCGC 706
                           vii   i     i    -   --i v - i            i vii 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATA-GAATTGAGA-GTCCAGAAATAAACCCATAC 336

  chr2_73721398_7    707 ATATATGTTCAAATGATTTTTGACGAGGGTGCCAAGACCACTCAGTGGGA 756
                           v    v    v       i   i               i   i    i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_73721398_7    757 AAAGGATAG-CTTT----CAAATGATGCTTGGATAACTGGATATCCACAT 801
                             i    -    ----      i    v   i         ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_73721398_7    802 GCAAAAGAATGAAATTGGACCCTTATCTTATACCATGTACAAAAATTAAC 851
                                      i        i  i  i i     i             
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_73721398_7    852 TCAAAATGGGTTAAAGACCTAAATGTAAGACCTAAACCCATATAACTCTT 901
                                  i i ?                v     v i   v       
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_73721398_7    902 ACA-GAAAA---AG--------CTTCATGACATTCAATGTGGCAATAATT 939
                          v -     ---  --------    i    v  vii vv      ii  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_73721398_7    940 TTTTGAATATTACACCAAAATCACAGGCAACGAAAGCAAAAATAGACAAA 989
                          i  ii    v         v    i     i    v         i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_73721398_7    990 CAGGACCACACTAAACTTAAAAACTT--GTACATCAGGGGACACAATCAA 1037
                         iv    iv  ii   v          --  i v   ii      v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_73721398_7   1038 CAGAGTGAAA-GACAACCTATTGAATGGGAGAAAATATTTACAAATCATG 1086
                         v i       -       i iv                  i        i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_73721398_7   1087 TATCTGAGAAGGGGTTAACATACAGAAAATATAAAGCAGTCGCAACAAC- 1135
                                v     ii vii  v     v        v v  vi -    -
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACT 785

  chr2_73721398_7   1136 -AACAACAAAAAT-CAAATA-CCTAACTAAAAGATGGGCA 1172
                         -  i  i     v-      -  i  i ?   i       
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 1.98 (83 / 42)
Gap_init rate = 0.02 (17 / 685), avg. gap size = 1.88 (32 / 17)  

 458 14.43 0.00 3.09  chr2_73721398_73723281.rev     1296  1392 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_73721398_7   1296 AAAAAAAAGTAAAAGTGGACTTGAATAGACATTTCTCTAAAGATGACATA 1345
                              vii i   ---   i                 i     v  i   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAA---GGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_73721398_7   1346 CAAATGGCCAAAAAGCATATAAAAAAATGCTCAGTATCACTAAGCAT 1392
                                    v     i  i    i       ii    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 3.00 (3 / 1)  


1063 20.59 3.59 6.54  chr2_73734168_73736697.rev      840  1145 (1385)    L1M4_orf2#LINE/L1        1   297 (611)  

  chr2_73734168_7    840 TGGTGAGACACTCACCATA--CATGGATTGGAAGTCTCAAAATTGTTAGG 887
                            vi   i -  -    i--             v  i  v       i 
  L1M4_orf2#LINE/      1 TGGAAAGATA-TC-CCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_73734168_7    888 ATGGCAATAATCCCCAAATTAATCTGTTGATTCTACACAATCTCTATCAA 937
                                  v          i    iiv     v  i     i       
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_73734168_7    938 AATTCCAGCAAGCATTTTTCAAGAAATCTACAAAATGATC-TCAACTTTA 986
                            i     viv v     vv      iv    iv     - v  v  i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_73734168_7    987 TATAGAAATGGCAAGGA--CCACAAGGGCCAAAGTTA-CTGAAAAAAAAA 1033
                            i      -     i--   v  vi      iiv -  vi     i  
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_73734168_7   1034 AAAGAAAAAAAAAAAAAAAAAAGAGGTAGAGGGCTTATATTTCCTGATTT 1083
                         i  v   ----------------- v i    i  i i i    ii    
  L1M4_orf2#LINE/    198 GAACAAA-----------------GTTGGAGGACTCACACTTCCCAATTT 230

  chr2_73734168_7   1084 CAAATCTTAT---AAAGTTACAGCAATCAAGGCATTGTGGCATTGATATA 1130
                             v    i---    i     i       i  v     i i  ii   
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_73734168_7   1131 AGGACAGA--TCTAGAT 1145
                             i   -- v     
  L1M4_orf2#LINE/    281 AGGATAGACATATAGAT 297

Transitions / transversions = 1.62 (39 / 24)
Gap_init rate = 0.03 (10 / 297), avg. gap size = 3.10 (31 / 10)  

1980 21.34 7.73 2.02  chr2_73734168_73736697.rev     1444  2038 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_73734168_7   1444 AAAGATACAGACATAT----CAATGGAACAGAATGAAAATTCCA--AATG 1487
                           i    --       ----        i     vi i v    --   i
  L1M4_orf2#LINE/    280 AAGGATA--GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_73734168_7   1488 AAGCCTTACATATGTGATCAATTAGTGTTCAACAAAAGGGCCAAAGCAAC 1537
                           v  v     v i  i      ii v   i    ii v     ii v i
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_73734168_7   1538 TAATTGGAGAAAATAATACTCTTTTGAACAAATGATGCTGGGACAATTAA 1587
                          v v   i    i-    v      v        i           i ii
  L1M4_orf2#LINE/    378 TCAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_73734168_7   1588 ATATCCCTATGCAAAGAGATGAAGTTAGACA---AC---ACACCGTACAC 1631
                            ?  vi       iii        i   v---  ---     i  i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_73734168_7   1632 AAAAAATGCACTAAAAATGGATTTCAGACCTAAACATAATAATTAAAACA 1681
                              v i-   v         iv?         ii   v ii      v
  L1M4_orf2#LINE/    477 AAAAATTA-ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_73734168_7   1682 ATAAA-CTTTTAATGAAAAACATAGGAGAATATCTCTATGACTTTGG-TT 1729
                              -  i   ivii          ? v v    iii    i    -  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_73734168_7   1730 AGGCAAACAGTTCTTGAATATAACACCCCAAGTACAATCCACAATCCATA 1779
                               vviv     ii    i     vv   i    v v    ----- 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA-----A 620

  chr2_73734168_7   1780 AAAGACAAACAGTTTAAATGGGACTTCATCA---TTA-------CTGTAT 1819
                          i i -   i  v -    v           ---   -------i   ii
  L1M4_orf2#LINE/    621 AGAAA-AAATAGAT-AAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_73734168_7   1820 T--AAA----ACCATTT-GCAATTCAAAAG-----CCACAGCCTGGGAGA 1857
                          --   ----  i  iv- v  v v     -----      vv       
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_73734168_7   1858 AGTTACTTACAAAAAATACATCTGATAAAGGACTTGTAACCAGAGTATAT 1907
                          iv  i  i    vv   i         i         v     i     
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_73734168_7   1908 AGAGAGCTCTTTCAACTCAGTAG---GAAGA----TAACCTAATTTTAAA 1950
                          i   i     v       i  i---i    ----     i    ?v   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_73734168_7   1951 ATGGGCAAAAAGATTTAAAAAGACACTTCATCAAAGAAGATGTAAGAGTG 2000
                                  i-     i  v     i   vi          i  vi i  
  L1M4_orf2#LINE/    819 ATGGGCAAAG-GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_73734168_7   2001 GCCAATAAGCACACAAAA---TGTTCAACATCATCAGTCAT 2038
                                      ii   ---  i         ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (77 / 46)
Gap_init rate = 0.03 (22 / 629), avg. gap size = 2.64 (58 / 22)  


 463 20.21 0.00 1.06  chr2_73793336_73795284.rev      244   337 (1612)    L1M4_orf2#LINE/L1      151   243 (665)  

  chr2_73793336_7    244 TAAAAATCATAAGACATCCTGAACAGCCAAAACAATTTTGAAAGAGAACA 293
                          ii    -ii   iv i  v   i            i      i    v 
  L1M4_orf2#LINE/    151 TGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_73793336_7    294 ACAATGTTGGAGGACTCACATTTCCTGATTTTAAAACATATTAC 337
                             v               i    ii    i     v  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

Transitions / transversions = 2.80 (14 / 5)
Gap_init rate = 0.01 (1 / 93), avg. gap size = 1.00 (1 / 1)  

 470 23.58 1.63 0.81  chr2_73793336_73795284.rev      501   623 (1326)    L1M4_orf2#LINE/L1      233   356 (552)  

  chr2_73793336_7    501 AAACATATTACCAAAGGTGCAATAATCAAAATAGTGTGATAGTAGCATAA 550
                             v  i   -    v i  i       i i      i  v i      
  L1M4_orf2#LINE/    233 AAACTTACTAC-AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_73793336_7    551 AGACAGACGAATAGACCAACGAAATATGATAAAGTGCCTACAAATAAACT 600
                         i  i    iv     i   i i    vi  vi  v i i v        i
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_73793336_7    601 CTCACAT--ATGGTCAAATGATTTT 623
                          vi    --        v       
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.02 (2 / 124), avg. gap size = 1.50 (3 / 2)  

2586 17.06 4.95 0.92  chr2_73793336_73795284.rev      914  1458 (491)    L1M4_orf2#LINE/L1      342   908 (0)  

  chr2_73793336_7    914 TGGCCAAAATGATTTTTGACAAGGGTGCCAAGACCACTCAATGGGAAAAG 963
                            i   v-       i                   i        i    
  L1M4_orf2#LINE/    342 TGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_73793336_7    964 AACAGATTTTTCA-CAAATGATGCTTGGAAACCTGGACATTCACATGCAA 1012
                           i  vi      -      i    v   v v     i ?i         
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_73793336_7   1013 AAGAATGAAGTTGGACTCTAGTCTTA-----TGTAAAAAAATTAACTCAA 1057
                                         i ivii  i ----- i  v              
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_73793336_7   1058 AATGGATTAAAGACCTATGTGTAAGGCCTAAAACTATCAAAGTCTTGGAA 1107
                                i ?       vi      iv          v   v    i   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_73793336_7   1108 GAAAACATAGAGGAAAGGCTTTGTGACATTGAATATGGCAGTGCTTTCTT 1157
                                   i? v  iv   i     v   ii vv    i  v      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_73793336_7   1158 GAATATGACACCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAATGGG 1207
                         ii                   i          v         i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_73793336_7   1208 AC--CACCAGGCTTAAG-----TTGTGCCTCAGGGGATGCATTCAACAGA 1250
                           --  i  iiv    i-----      i   ii   ii vv    v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_73793336_7   1251 GT-AAAAGACAACCTACGGATTGGGAGAAAATATTTGCAACTCATGAT-T 1298
                           -           i  i  v                   v    -  - 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-ATAT 739

  chr2_73793336_7   1299 CTGATA---------TA--CAGAATACACAAATAACTCTCAGAATTCAAC 1337
                               ---------  --       i i   v      i v  i    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_73793336_7   1338 AATGACAACAAAATCAATAACCTGACC-AAAAATGGGCAAAGGAATTGAA 1386
                            ---  v  i iv       ii ii-                v     
  L1M4_orf2#LINE/    790 AAT---AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_73793336_7   1387 TAGACATTTCTCCAAAGTTGATATACAAATGGCCAACAAGCATGTGAAAA 1436
                                          vv                 i     ii      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_73793336_7   1437 GATGCTCTATATCGCCAATCAT 1458
                                v i   i????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (57 / 33)
Gap_init rate = 0.02 (12 / 567), avg. gap size = 2.67 (32 / 12)  


2500 26.19 2.92 1.95  chr2_73796408_73802207.rev     1057  1877 (3923)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr2_73796408_7   1057 TGGAAAAAAATTCCATGCTTATGGATGAGAAGAATCAATATTATTGTTAA 1106
                               i v  i     i i      vi     v i      ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT---GTTAA 47

  chr2_73796408_7   1107 AATGGCCACACTTCCCAAAGCAATTTACAGATTCAATGCTATCCCTATCA 1156
                         i     v i   i      vii  i           i  v          
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_73796408_7   1157 AAAT---AGCATATCATTTTTCACAGAATTAGAAAAATGTATTCTAAAAT 1203
                             ---   - ii -     ii     v v  v  iivv  i       
  L1M4_orf2#LINE/     98 AAATCCCAGC-TGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_73796408_7   1204 TCATTTGGAACCAAACAAGA-ACCCA-AATAGTCAAAGCAATCCCAAGCA 1251
                             v     -- vi    i-     -     i    i     iii iv 
  L1M4_orf2#LINE/    146 TCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_73796408_7   1252 AAAACACCAAAGCCAAAGGCATCACATTACCCAACTT-AAAACTCCACTG 1300
                          i  v v     iiii   vv     i v     i  -      i-   i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT-ACTA 242

  chr2_73796408_7   1301 TAAGGCTACAGTAACCAAAACAGCATGGTACCGGTACAAAAACAGACAAA 1350
                         i  i          i   i    ii      i  i i  ii i     v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_73796408_7   1351 TAGACCAATGGAACAGAGTAGAGAACTCAGAAATAAACCTGCACACCTAC 1400
                             i        i   i v    iii            iii   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_73796408_7   1401 AACCATCTGACCTTCAA-AAAATTGGCAAAAATAAGCAATGAAGAAAGAA 1449
                         iii  vi   ii   i -  iiv  v   i vi vv     ii       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_73796408_7   1450 CTCTGTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAA 1499
                         ivv v v     i              i      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_73796408_7   1500 GAA----ACTGGACCCTTACCTCTCACTATATTTAAAAA--AA-TCAAGG 1542
                            ----ii       i      v   i    vi     --  -    ii
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_73796408_7   1543 TACATTAAAGATTTAAATGGAGGACCTCAAACTACAAAAATCCTAGCAGA 1592
                          iv  i ?   ii      v i  v  v      i    v  i   v   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_73796408_7   1593 AAACCTAGG---AAATACCCTTCTCAATATTGGCTTTGGAAAATAGTTTA 1639
                             v    ---    ---    vii iv    v  v  v  - i    v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA-TGGTTTC 588

  chr2_73796408_7   1640 T-GGCTAAGTCCTGAATAGCAATTGTAACAAAATAAAAAAATTGATGA-T 1687
                          -i v  v v viv  v    vvv i       -i       v   i - 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAAT 637

  chr2_73796408_7   1688 TGGTACCTAATTAAACCAAAGAGCTTCTGTACAGTAAAATAAATGATCAA 1737
                            -  i v  i   viv  i i   i   i vvi   iv v iv     
  L1M4_orf2#LINE/    638 TGG-ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_73796408_7   1738 -----TCAAGAGACAACTCACAGAATGGGAGAAAATATTAGGAAATTATG 1782
                         ----- v  i       i                     v v    i  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_73796408_7   1783 CATCCAACAAATCTCTAATGTCCAGAATCTGTAAGGAAATGTAAAAATTT 1832
                         i   ii i  ivvv  vi i        v i   i   v v v v  i i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_73796408_7   1833 AAAAAGCAAAAATCAAATAATTCCATTTGTAAAAATGGGCAAAGG 1877
                           v  vv    iv       ii v   ?--               
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGG 829

Transitions / transversions = 1.59 (130 / 82)
Gap_init rate = 0.03 (22 / 829), avg. gap size = 1.82 (40 / 22)  

 252 18.64 10.17 4.24  chr2_73796408_73802207.rev     2186  2303 (3497)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr2_73796408_7   2186 CTCAAAAAAAAAAAAAAAAAAAA--------AAAAGTAGGGGGAGCAAAG 2227
                              v  v     i v   v  --------    i i  -----     
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG-----CAAAG 828

  chr2_73796408_7   2228 AACAGGAA--GACACTTCTCAAAAGCAGATGTACAAGCAGCTGACAA--A 2273
                         i ivv   --    i     v    v    i     iii  ii i  -- 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_73796408_7   2274 CATGAAAAAATGCTCAACATCACCATTCAT 2303
                                 i             ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.03 (4 / 125), avg. gap size = 4.25 (17 / 4)  

4070 18.29 3.93 2.02  chr2_73796408_73802207.rev     4426  5316 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_73796408_7   4426 TGGGAATAGATCCCATGTTCATAGATTAGAAGTCTTAATATTTTTAAGAT 4475
                            i  v v             i    i    v         v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_73796408_7   4476 GTCAGTACTCCCCAATTCCAACTATAGATTCAATGACATCCCTACCAAGA 4525
                          v  i          v iv v   i        i vv       i   i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_73796408_7   4526 TTCATGCTGCCTTTTATTTTTTTTCAGAGACTGGCAAGCTGATCTTAAAG 4575
                          i vv          ------  v    i i  i          i    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT------TTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_73796408_7   4576 TTCACA------------GAACCCATAAATAGCTAAAGCAATTTTATAAA 4613
                             i ------------ i     -i      i   i    i  iv   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAA 193

  chr2_73796408_7   4614 AGAAAAACAAAGTTGGAGGACTCACAC------AT--CAAAATTTACCAC 4655
                             i                      ------  --     i    i  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_73796408_7   4656 AAGAACACCACAA-CAAGACGGTGTGGTGGTGGCATTTGCAGAGACATAT 4704
                           iivi  vii  -      i       iv      vv v v        
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_73796408_7   4705 GGATCAATGAAATAGAATTAAGAGTCTAGAAATAAACTCTTACATTTATG 4754
                         i        i         i      i          i v          
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_73796408_7   4755 GTCAATTAATTTTTGGCAAAGGACCCCAGACAATTTAATGGAAGAAAGAA 4804
                                i     i i   i  vv  v    v   i     i-       
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAA 392

  chr2_73796408_7   4805 TAGTCTCTGCAACAAATGGTGCGGGGTCAACTGGATATCCATATGCAAAA 4854
                               i v             v   v          ?   i        
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_73796408_7   4855 -AATGAAACTGTATCCCCTGCCTCACATTACATACAAAAATTAGCTAAAA 4903
                         -      ii  v -     i       ii i            i  v   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGA-CCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_73796408_7   4904 AATGATCATAGACCCTAATTTAAGAGCTAAAATTATAATACTCTTAGAAA 4953
                          vv     ?     iv   v            i     v          i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_73796408_7   4954 AAAGCAAAGAAGTAAACTTTTTTTGTGTGTGATGTTGGGTTAGGCAATAG 5003
                            i  v  i?     ii  i-------    iv              i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTC-------GTGACCTTGGGTTAGGCAATGG 584

  chr2_73796408_7   5004 TTT--TAAACACAACATGAAAAACACAAATGACAAAAG------TAGATA 5045
                            --  i i ii   iv    i     iii       ------      
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_73796408_7   5046 AATTGGACTTTGTCAAAACTAAAAA-TTTTGTACTGCAAATGATACCATC 5094
                                   ii      i      -      i  v    v  i  i   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_73796408_7   5095 --GAAAGTGAAAAG-CATCCCAAAGAATGGGAGACA-TGTTTTCAAATTA 5140
                         --            -  v    v           v - i   v     i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_73796408_7   5141 CATAGTGAATAAGGGACTGCTGTTCAGAATATATGGAGAACACGTCGAAC 5190
                         i   vivi          vv i i          ii     v v vv   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_73796408_7   5191 CCAATAATAAAAGAACAAAAATAAGCCAATTTAAACATGAGCATAGGATC 5240
                         i           ii     --   v      ?   v   i   v     i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAA--TAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_73796408_7   5241 TGAATAGAAATTTCTGCAAAGAAGATATTCAAATGGCTAATAGGCACTTA 5290
                                 v      v            v        i    i    v i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_73796408_7   5291 AAAAGGTGCTTCTCATTATTAGTCAT 5316
                              i    ivv   i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (97 / 62)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.12 (53 / 17)  


3105 27.28 0.55 0.66  chr2_73803529_73809909.rev     4981  5889 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_73803529_7   4981 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5030
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_73803529_7   5031 GGCCATACTGCCCAAGGTAATTTATAGATTCAATACCATCCCCATCAAGC 5080
                            v     v     iv i  i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_73803529_7   5081 TACCAACGACTTTCTTCGTAGAATTGGAAAAACCTACTTTAAAGTTCATA 5130
                          v   i vi i  i  i i    v v  v  i iv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_73803529_7   5131 TGGAATCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGAA 5180
                              viiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_73803529_7   5181 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5230
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_73803529_7   5231 CAGTAACCAAAATAGCATGGTACTGGTAACCAAAACAGAGATATAGACCA 5280
                               i   i i  ii         i -iv ii i   v       i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATCA 299

  chr2_73803529_7   5281 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACCA 5328
                               i    i--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_73803529_7   5329 TCTGACCTTTGACAAACCTGATAAAAACAAGAAATGGGGAAAGGATTCCC 5378
                         vi   ii  i     ivv  vi  i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_73803529_7   5379 TATTTAATAAATGGTACTGGGAAAACTGGCTAGACATATATAGAAAGCTG 5428
                          v  i  i       i      v      v  ?v  i  ii i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_73803529_7   5429 AAACTGGATCCCTTCCTTACAGCTTATACAAAAATTAATTCAAGATGGAT 5478
                           ii    i    v   i   v v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_73803529_7   5479 TAAAGACTTAAATGTCAGACTTACCACCATAAAAACTCT-AGAAGAAAAC 5527
                         i ?    i       v   vi  vv  i      -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr2_73803529_7   5528 CTAGGCA-ATACCATTCAGGACATGGGCATGGGCAAGGACTTCATGACTA 5576
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_73803529_7   5577 AAACACCAAAAGCAATAACAACAAAAGACAAAATAGACAAATGGGATCTA 5626
                         vi            vv i          v        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_73803529_7   5627 ATTAAACCAAAGAGCTTCTGCAGAGCAAAAGAAACCACCATCAGAGTGAA 5676
                           i   viv  i i   i  iivvv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_73803529_7   5677 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACA 5726
                         v  i     i                 v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_73803529_7   5727 AAGGGCTAATATCCAGAATCTACAACGAACGTAAACAAATTTACAAGAAA 5776
                          i  i  vi          v  i  v    vivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_73803529_7   5777 TAAATCAAACAACCCCATC-AAAACTAGGCAATGGATATGAACAGACACT 5825
                         v i -    i     v  i-    v i     v    v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_73803529_7   5826 TCCCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5875
                           i v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_73803529_7   5876 TCATCACTGCCCAT 5889
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.22 (11 / 9)  


3305 26.33 1.11 0.22  chr2_73859678_73866065     4997  5896 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_73859678_7   4997 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5046
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_73859678_7   5047 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_73859678_7   5097 TACCAATGACTTTCTTCACAGAATTGGAAAAGCT-ACTTTAAAGTTCATA 5145
                          v   iivi i  i  ii     v v  v     - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_73859678_7   5146 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5195
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_73859678_7   5196 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACCAGGCTA 5245
                              i      vv    i  v  ii i      viv      v i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_73859678_7   5246 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5295
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_73859678_7   5296 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTAT 5343
                              i    i--    i  --        vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_73859678_7   5344 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5393
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_73859678_7   5394 ATTTAATAAATGGTGCTGGGAAAACTGGCTACCCATATGTAGAAAGCTGA 5443
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_73859678_7   5444 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5493
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_73859678_7   5494 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5543
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_73859678_7   5544 AGGCATTACCATTCAGGACATAGGCATGGG-AAGGACTTCATGTCTAAAA 5592
                            ?i v viv   iv   v v  vv i  -  v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_73859678_7   5593 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCATT 5642
                                    vvi          vv     v  i    v   ii    i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_73859678_7   5643 AAACTAAAGAGCTTCTGCACAGCAAGAGAAACTACCATCAGAGTGAACAG 5692
                            v v  i i   i  ii vv   ii  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_73859678_7   5693 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5742
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_73859678_7   5743 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5792
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_73859678_7   5793 ACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACATTTCTC 5838
                             ----   v  i?    i           iv    i           
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_73859678_7   5839 AAAAGAAGACATTTATGCAGCCAAAAA--ACATGAAAAAATGCTCACCAT 5886
                         v        i  vi viii     v  --         i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_73859678_7   5887 CACTGGCCAT 5896
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


 955 19.73 2.02 15.25  chr2_74018824_74020806.rev      501   946 (1037)    L1M4_orf2#LINE/L1      278   664 (244)  

  chr2_74018824_7    501 ACAAAAACAGACACATAGATCAATGGAACAGAATAGAGAGCCCAGAAATA 550
                          i  ii i     i              i     v     i         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_74018824_7    551 AGTCCACACACCTACAAT-AATCTGATTT-CAACAAAAGCGACCAAAACA 598
                          ii   i   ii  iii -   -      - i    ii i -    i  v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAAT-TGATTTTCGACAAGGGTG-CCAAGACC 375

  chr2_74018824_7    599 AGTGATGGGGAAATGGAGAAAGGACTCCCTATTCAATAAATGGTGCTGGG 648
                          v v -------    i     i ivvi  v     i             
  L1M4_orf2#LINE/    376 ATTCA-------ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_74018824_7    649 ATAATGTTTTACTAAATACCTGGGTACTATGACCTAGCCATAACTTCCGT 698
                          i  ---------------    i  ------------------------
  L1M4_orf2#LINE/    419 ACAA---------------CTGGATA------------------------ 429

  chr2_74018824_7    699 ATCTGGTGCTAGCCATATACAGAAGATTGAAACTGGCCCCTTTCCTTACA 748
                         -----------?   i  i  i    v    ii   v   i v   i   
  L1M4_orf2#LINE/    430 -----------KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_74018824_7    749 CCATATACAAAAATCAACTCAAGAATG-ATTAAAGACTTAAATGTAAAAT 797
                                       i       -    -  i ?    i         i v
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAA-AATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_74018824_7    798 CCAAAACTACAAAACCCT-GGAAGACAACCTAGGCA-ATACCTTTCTGGA 845
                          i       i     i  -i     v   v    ?i- v i   iv  - 
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-A 566

  chr2_74018824_7    846 CAGAGAAACAGGCAAAGATTTCAT-GATGAAGATGCCAAAG--ACAATTG 892
                          vvv iivi      v i    v -   - v  ii     i--    -- 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAA--G 613

  chr2_74018824_7    893 CAACAAAAACAAAAATTGACAAATGGGATCTAA-CTAAACTAAAGAGATT 941
                                 iv      v  i    v   ii v - v   i    i ----
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA---- 659

  chr2_74018824_7    942 CTTTT 946
                              
  L1M4_orf2#LINE/    660 CTTTT 664

Transitions / transversions = 2.15 (58 / 27)
Gap_init rate = 0.05 (18 / 387), avg. gap size = 4.28 (77 / 18)  

 891 24.12 1.17 0.39  chr2_74018824_74020806.rev     1235  1491 (492)    L1M4_orf2#LINE/L1      650   908 (0)  

  chr2_74018824_7   1235 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACA--GTGAACAA 1282
                            i    i -   i  ii vv    i  v        v --     v i
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_74018824_7   1283 ACAATGTACAGAATGGGGGAAAATTTTTGCAAAGTACGCATCTGACAAAG 1332
                             ivi          i      v        vi iii      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_74018824_7   1333 GTCTAATAGCCAGCATTTATAAGGAACTTAAACAAATTTACGAGAAAAA- 1381
                          v  vi  v    v  v     i     ivv    v iv ii v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_74018824_7   1382 ACAAACGACCCCATTAAAAAGTGGGCAAAGGACGTGAACAGACACTTTTC 1431
                              ii    v   ?    i           iv    i     i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_74018824_7   1432 AAAAGAAGACATACATGCAGCCAACAAGCATATGAAAATAAACTCAACAA 1481
                         v        i     viii     i     i       v vi       v
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_74018824_7   1482 CACTGATCAT 1491
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (36 / 25)
Gap_init rate = 0.01 (3 / 259), avg. gap size = 1.33 (4 / 3)  


1478 24.42 15.02 4.64  chr2_74376054_74378354      991  1809 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_74376054_7    991 AAG-TATACTGTATTCATAAATCAGAAAAACTCAAAATTTGAAAGACGTT 1039
                            -   v ii i     ii  ii   i -  i  v   vvv    i vi
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGA-CTTAATATTGTTAAGATGGC 53

  chr2_74376054_7   1040 AATTCTTCCCAAA--------CAGAGGCAAAGATAATCCC-ATCAAAATT 1080
                            v  i      --------    vv   v -i      -        i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACG-CAATCCCTATCAAAATC 102

  chr2_74376054_7   1081 CCAACAAGTTTTCATTTTGGTGAAATT--TAAGATGATTCTAAAATTCAT 1128
                            i v- ii  --     vv      --i   v    i           
  L1M4_orf2#LINE/    103 CCAGCT-GCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_74376054_7   1129 GTGGAAATGCAAAGGGCCAAGAA----------AATATTATATAAAAAGG 1168
                         i           i  i  v    ----------   v  iv v  i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_74376054_7   1169 ACAAAAGGGGAGAGCTTGGGAGACA------AAGATATAAAGACTTAT-- 1210
                              ivv    ii  i-----   ------  -- v v  i     i--
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTC-----ACACTTCCCAA--TTTCAAAACTTACTA 242

  chr2_74376054_7   1211 --AAGCTACAGAAATGAAGAC--TGTGATACTGATATATAAATAAAC--- 1253
                         --         v   v     --    i     ii   vii   i  ---
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_74376054_7   1254 TAG-----TGAAACAGAATAAAGAACCCAGAAACAGACCCTGTCATATAG 1298
                            -----  i  i     vi   ii       i i    vvv   v  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_74376054_7   1299 GAATATTTGATATATGGCAAAGGAAGTATTGCAAAG------CAATGGAG 1342
                          ivi v     v vi i   i  ------   v   ------      i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGG------TGCCAAGACCATTCAATGGGG 386

  chr2_74376054_7   1343 AAAGAATAGTCTTT--AAAAAATA---CTGGAACAATTGA----CTATAT 1383
                                       --  v    i---    i    i  i---- i i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_74376054_7   1384 --AAAATCACAAAG---AAACACTGTCTCACAGTACACATCAGAATCAAT 1428
                         --    vv ii   ---i v v  ii      vi i i iv i   i  i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_74376054_7   1429 TCTGA-TGGATTGTAGATCTAACATGAAAGGA--AAAACAATGAAGCTTT 1475
                           vi -     ii?   i    -   v   ii--     v  i  i  i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAA-ATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_74376054_7   1476 TAGAAGGTAACATACAAGAATATCTGC-TGTCC-----------AATATT 1513
                               iv      vi? v v    v -  v  -----------   iv 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_74376054_7   1514 TGCCT-----TGA-----------------------GGAAAGTTTGATAT 1535
                          v i -----   ----------------------- i   iv v    v
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_74376054_7   1536 ATTCAATTACAATAAAACTAAGAATTTCTGTTAATCAAAAGATGCCATTA 1585
                            vi i v  vi    i   i  i  i   vvv     i  ii i  i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_74376054_7   1586 AGGATGTAAAAAGAAAAAAACAGTCACAGAGTGGGAGAAGAT-TTTGCAA 1634
                           i v  i      v  --- --i      i        i  -       
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAA---C--CCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_74376054_7   1635 CACATATAATC--ACAAAAACATTTCTACCCAGAATATATAACAAACTCT 1682
                         vv      -  -- i  iii- i  v  i             vi      
  L1M4_orf2#LINE/    731 ATCATATA-TCTGATAAGGG-ACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_74376054_7   1683 TGCAAATCAG------AAAGGCAGACAACCCAA------AATGTGCAAGA 1720
                          i   v   i------    i  i i       ------    v    ii
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_74376054_7   1721 GATTTCAACAGACACTTC--CAAA-AAGAAAGGCAATTGGGCATGTGGCC 1767
                              v  i     i   --    -    v vi   --------i     
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAA--------ATGGCC 870

  chr2_74376054_7   1768 AATAAACACAGGAATAGCTGTATTTTCAACTTCATTAGTCAT 1809
                              i    v   v  v  i----     v   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGC----TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (120 / 78)
Gap_init rate = 0.05 (42 / 904), avg. gap size = 3.83 (161 / 42)  


 347 30.58 9.28 4.81  chr2_74404262_74406355      498   788 (1306)    L1M4_orf2#LINE/L1       41   344 (564)  

  chr2_74404262_7    498 TTGT-AAGATGTCAA----CCACAAATGCATGGGTAGCTCCAAT-CTATT 541
                             -      v   ----  v     vv  vvii  v i   i- v  i
  L1M4_orf2#LINE/     41 TTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chr2_74404262_7    542 GCAACTGAAATCCCAAGGGAGGACTTTT----GGACCATGACTATCTAAT 587
                         v v iii        --- vv v     ----i  vvv    v v  i  
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCA---GCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chr2_74404262_7    588 TCTAAAGTTCCTCTAAAAAAGGTAAATGTAGG------AGAATGGTGAGG 631
                         i     i   v v ------  -     i i ------     i iv ii
  L1M4_orf2#LINE/    138 CCTAAAATTCATAT------GG-AAATGCAAGGGACCCAGAATAGCCAAA 180

  chr2_74404262_7    632 A-AAGTTCAAAAATGAAGAGAAATGGGGATGGGGCATGC---CTTAGCAC 677
                          -  vi ii    v     iv  ---i v   i v iv ---   vv  -
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAA---AGTTGGAGGACTCACACTTCCCA- 226

  chr2_74404262_7    678 ATATAGAAACTTGCGGAGAAGCTTCAGTAATTAAAGCGGTGTGATTCCAG 727
                           v vi      i vivi     v       i  ii i     i v ii 
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_74404262_7    728 GCCAGATATAGACA-AGGGATCAGTGGCACA------AGAGTCCAGAAAC 770
                         vvi iiv       - vi     i   v i ------            i
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_74404262_7    771 AGACCTGTATATCCATGG 788
                          i   ii  i  ii    
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGG 344

Transitions / transversions = 1.23 (49 / 40)
Gap_init rate = 0.05 (14 / 304), avg. gap size = 2.93 (41 / 14)  

 352 27.65 8.73 8.32  chr2_74404262_74406355     1126  1606 (488)    L1M4_orf2#LINE/L1      426   908 (0)  

  chr2_74404262_7   1126 GACAACCA-ACCTAAAAATAGAAAGTTAAATCCCTACTTTTCACCAAACA 1174
                           i ?   - ivi    iv vi     ii i      i iv     v i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_74404262_7   1175 CAATACTAAATTCTTCATAGATTAAAG-TCTAAAGATAAAAA-TAAATCT 1222
                            v v v  i  vvv  i   i ?  -i     vi   i i-    v  
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_74404262_7   1223 ATAAGCAAAAATGCAAATATACTAGAAGAGAATATAGGAGAGTATTCTTA 1272
                             ----------  v v --       i  i     ? viv  ii ii
  L1M4_orf2#LINE/    526 ATAA----------AACTCT--TAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_74404262_7   1273 TATTCTTGGAGAATATTGTGGAGAAAGACTTCCTAAACAAGGTAT-AAAA 1321
                          ivi     i-----  i-- iv  v ii   i  i i v ii i-    
  L1M4_orf2#LINE/    564 TGACCTTGGG-----TTA--GGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_74404262_7   1322 CCATAA------AGGAAAAAAATGGACAGATTTGATTGCA-CAAAACTAA 1364
                         v  i  ------ iii       i  i i   v  i v  -     i   
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_74404262_7   1365 AATAAATGAAAACTTCTATATAGTAAAATAACA-TATAAATCAAGTTCAA 1413
                           ---------    i i ii-v v   vi   -   v  vv    vv  
  L1M4_orf2#LINE/    657 AA---------ACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_74404262_7   1414 AGAAAAGTAATGTACTGAGA-AAAATATCTGCAA--CA----------AA 1450
                            v  viv iiv v  i  -       i     --  ----------  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_74404262_7   1451 GAAA---GCATC-AAAATACTAATATTTATAACAATGCTCCTTTGAATTA 1496
                          ii --- i   - i    --------     vi -i   i vii v i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATA--------TATAAAGA-ACTCTTACAACTCA 787

  chr2_74404262_7   1497 ATAAGAAATTAACCAATTAACTCAAATTATCCAATAG--AAAG------- 1537
                             v   vvi  v   -   i   v ? -vv   i --    -------
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAAT-AACCCAATTWA-AAAATGGGCAAAGGATTTGA 835

  chr2_74404262_7   1538 -TAAACAATCCT---GAGAAGAAATGAAGATGGCCAATAAACATATGAAA 1583
                         -  i   v i  ---i      v  iv i           i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_74404262_7   1584 AGATGCTCAACCTTACCAGTAAT 1606
                                    v i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (78 / 51)
Gap_init rate = 0.05 (25 / 483), avg. gap size = 3.28 (82 / 25)  


1972 17.03 2.00 26.46  chr2_74446756_74451932.rev     3488  4685 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_74446756_7   3488 AAAAAAATTTCATGTTCATGCGTAGGAAAATTCAACATTGTT-----GTC 3532
                            i v  ii          vi v    i i i  i      ----- v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_74446756_7   3533 AGTTCTCCCCAACTTGATCTATAGATGCAATATAATCCCAATAAAAATCT 3582
                          i v        v        i    v   iii      v  v      i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_74446756_7   3583 TAGCAAGTTATTTTTTTG--GATGCTGACATATTGATTCTAAAGTGTATA 3630
                         i   --- vvi       --  vii     vii    i     i vi   
  L1M4_orf2#LINE/    104 CAGC---TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_74446756_7   3631 TGGTAAGGCAAAAGACCCAGAATAGACAACATAACACTGAAAAAGTA--- 3677
                            v  v    ii            v   v i  ivi        v ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_74446756_7   3678 CAAAGTTGAAGAACTGACACTACTCAACTTCAAGACTTACTGTAAAGCTA 3727
                                 i  i   v     v i   i     i       ii       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_74446756_7   3728 CTACAATCAAG----TGTGATATTGTCAAAAGAACAGACAAATTGATCAG 3773
                          vii       ----    i  i  v  v   i i     v  v     i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_74446756_7   3774 TGGAACAGAATAAATAGCCCAGAAATGGACCCACACAAATATAATCAGCT 3823
                              i     vi v  i        ii     i   vv   ii   ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_74446756_7   3824 GATCTTTGACAAAGACACAAAGGCAATTTAATGGAAGAAGAATAATATTT 3873
                            i  i     i iii v   i v   i     iii       i v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_74446756_7   3874 TCAGCAAATGGTGATGGAATAACTGGACATTCATATGTTTAAAAAAAAAA 3923
                            i         v   i i       i ?i  i   i------    i 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC------AAAAGA 444

  chr2_74446756_7   3924 ATGAATCCAGGCCAGGTGTAATGGCTCATGCCTGTAATCCCAGCACTTTG 3973
                              ---------------------------------------------
  L1M4_orf2#LINE/    445 ATGAA--------------------------------------------- 449

  chr2_74446756_7   3974 GGAGGCCAAGGCGGGAGGATTGTTTGAGCCCAGGAGTTCAAGACCAGCCT 4023
                         ---------------------   v  v   -------------------
  L1M4_orf2#LINE/    450 ---------------------GTTGGACCCC------------------- 459

  chr2_74446756_7   4024 GGGCAACATAGAGATTTTGAGACTACTAAAAATTAAAAAAAAAAAAATAG 4073
                         --------------------------------------------------
  L1M4_orf2#LINE/    460 -------------------------------------------------- 459

  chr2_74446756_7   4074 CTGGGTGTGGTGATGCATGCCTGTGATCTCAGCTATTCTGGAGGCTGAGG 4123
                         ----------------- i   ----------------------------
  L1M4_orf2#LINE/    460 -----------------TACCT---------------------------- 464

  chr2_74446756_7   4124 TGGGAGGATTGCTTGAGCACAGGAGGTCAAAGCTTCAGTGAGCCATGATC 4173
                         -----------------    ---------------------    ----
  L1M4_orf2#LINE/    465 -----------------CACA---------------------CCAT---- 472

  chr2_74446756_7   4174 ATACCACTGCACTCCAGTCTGGATGACAGAGTAAGACTCTGTCTCAAAAA 4223
                             ----------------------------------------------
  L1M4_orf2#LINE/    473 ATAC---------------------------------------------- 476

  chr2_74446756_7   4224 AAAAAAAAATTCAGACATAGTCCTTACACCTTTCAAAAAATCATCTCAGA 4273
                         -----------------------------------      i v    i 
  L1M4_orf2#LINE/    477 -----------------------------------AAAAATTAACTCAAA 491

  chr2_74446756_7   4274 GTGGATCTTAAACCTAAATGTATAATGC-AAAACTACAAAACTTCTAGAA 4322
                         i      v? i           vi -  -       i      ii     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAA 540

  chr2_74446756_7   4323 GATAACATATGAGAAAATCTAGGTGACCTTAGGTCTGGTGATGAGTTTTT 4372
                           v      v ? v      vv        i   iv  ii   iv  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_74446756_7   4373 AGATACAACCCTAAAAGCACAATTGATGAAAAAAAAAAAATGATAAGCTG 4422
                              ii  v i          vii ii   i      v -     ii  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTG 639

  chr2_74446756_7   4423 GACTCTGTTAAAATTGAAAACTTCTGCTCTGTGAAAGACATT--TAAGAG 4470
                             iii i      i       i  iv  vii  i    i --i    i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_74446756_7   4471 AATGAAAAGAAAACCCACAGACCAGGAGAAAATATTTGCAAAAGGCATGT 4520
                          i        v          vii                  --v   i 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA--TCATAT 737

  chr2_74446756_7   4521 ATCTGATAAAAGACTTGCATCTGAAAATACCAAAAGAACTTTTAAAACTC 4570
                                  ii      i   i- i    ivv        i   v     
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCC-AGAATATATAAAGAACTCTTACAACTC 786

  chr2_74446756_7   4571 AATAA-----GGA--AACAACCCAATTTAATAATGGACAAAAGATATGAG 4613
                              -----i  --  i         ?  v     i    i   v   i
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_74446756_7   4614 CAAACACCTCATCAAAGAAGATATACAGATGGCAAATAAGCATATAAAAA 4663
                         i i   ii  vi               i     v        i  i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_74446756_7   4664 GATTCTAAATGTCATATGTCAG 4685
                            v  v  ii   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (136 / 64)
Gap_init rate = 0.02 (20 / 905), avg. gap size = 17.05 (341 / 20)  


2942 24.51 1.62 3.56  chr2_74925415_74928345.rev     1514  2439 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_74925415_7   1514 TGGAAAAACATTCCATGCTCATGGATTAGAAGACTAAATATTGTTAAAAT 1563
                               i i  i     i         i       v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_74925415_7   1564 GCCCATAGTGCCCAAAGCAATCTACAGATTCAATGATATTCCTATCAAAC 1613
                          v v   v v      vii              i vv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_74925415_7   1614 TAGCAACGTCATTTTTCACAGAATTAGAAAAAAACT-ATTCTAAAATTCA 1662
                          vv  i vv v     ii     v v  v  i--  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_74925415_7   1663 TGTGGAACTAAAAAGGAGCCCAAATAGCCAAAGCAATCCTAAGCAAAAAG 1712
                          i     v iv  i   v  vi          i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_74925415_7   1713 AACAAAGTCAGAGGCATCTAATTACTCCACTTCAAACTATACTATAAGGC 1762
                                 ii    vv  vv i v i v i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_74925415_7   1763 TATAGTAACCAAAACAACATGGTACTGGTATGAAAAGAGGACACATAAAC 1812
                           i     i   i   iii         i  i ii v  -   i   i i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG-ACATATAGAT 297

  chr2_74925415_7   1813 CAATGGAACAAAATACAGAACCCAAAAATAAAGCCACACACCTACAGCCA 1862
                                 i i   vv   ii   i       v   i   ii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_74925415_7   1863 CCTGATCTTCAACAAAGTTAACAAAAATAAGCAATGGAGAAAGCACTCCC 1912
                         vi    i   i    i v iv   i vi vv      i     v - vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGT 396

  chr2_74925415_7   1913 CCATTCAATAAATGGTGCTGGGATAACTGGCTAGTCG--TGCAGAAGAAT 1960
                          iv     i              i      v  ?i i--    i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_74925415_7   1961 AAAACTAGACCCCT--TTTGC--CGTACACAAAAATTAACACAAGATGGA 2006
                         i  ii i       --i ii -- i  i            v   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_74925415_7   2007 TTAAAGATTTAAATGTAAAAAATTAAAGATTTAAATGTAAAGATTTAAAT 2056
                          i ?   ii         ---------  vi    ------------ v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAA---------GAGCTAAA------------ACT 525

  chr2_74925415_7   2057 ATAAGAATCCTAGAAAAAAACCTAGGAG-ACACCATTATGGACTTCAGCC 2105
                             i v  i     i     v    ? - v i v ii  iv   vi --
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-- 573

  chr2_74925415_7   2106 TTAGGAAAGAATTTAT--GACTAAGTCCTCAAAAGCAATTGCAACAAAAA 2153
                              v  vii   v --  -  v v vi        vvv         i
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_74925415_7   2154 CAAAAATTGAAAGGTGGGACCTAATTAAA-TGAAAGAGCTTCTGCACAGC 2202
                         v      v  v ii v    i v  i   - v   i -   i  ii vv 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTC 671

  chr2_74925415_7   2203 AAAAGAAACTATCAACAAAGTAAACAGACAACCTACAGAATGGGAGAAAA 2252
                            i  v        v     i  v        i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_74925415_7   2253 TATCCGCAAAACTATGCATCCAACAATGGTCTAATATCCAGAATCTATAA 2302
                            ii     v -  ii   ii i  v  v  vi          v     
  L1M4_orf2#LINE/    722 TATTTGCAAATC-ATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_74925415_7   2303 GGAACTTAGACAATTCAACAAGCAAAA----AAGAACCCCATTTAAAAAG 2348
                         i     ivv    i    i  vv    ----  v     v   ?     -
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA- 819

  chr2_74925415_7   2349 TGAGCAAAAGACATGAACAGATACTTTTCAAAAGAAGACATGTAAGTGGC 2398
                           i     i  iv    i   i i  i  v        i  ii  i    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_74925415_7   2399 CAACAAACATATGAAAAAAAATGCTCAATATCACTAATCAT 2439
                            i  i  i       i --       i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (136 / 87)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.53 (48 / 19)  


2458 26.53 0.30 0.30  chr2_74935369_74937034.rev      492  1162 (504)    L1M4_orf2#LINE/L1      190   860 (48)  

  chr2_74935369_7    492 AAAAAGAACAACAGAGCTGGAGGCATCACACTACCTGACTTCAAACTATA 541
                                 v    i  i      vv       v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_74935369_7    542 CTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAG 591
                               i          i   i    ii         i iv ii i   v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_74935369_7    592 ATATAGATGCATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATA 639
                                 vv      i    i--    i  --        vv iii i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACA 337

  chr2_74935369_7    640 TCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGA 689
                          i  iiiii vi    i  i     ivv  vv  i v  vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_74935369_7    690 AAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATG 739
                            i  vvi  v  i  i              v      v  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_74935369_7    740 TAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATT 789
                         i i  iiv    ii    i    v   i     v           i  i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_74935369_7    790 CAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTA 839
                            i      i ?    i    i  v   v       i      vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_74935369_7    840 GAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTT 889
                                  v    ?i v viv   iv   v v  vv i     v ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_74935369_7    890 CATGTCTAAAACGCCAAAAGCAATGGCAACAAAAGACAAAATTGACAAAT 939
                          v ivv  vi  i         vvi           v     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_74935369_7    940 GGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATC 989
                         v   ii v  i   v v  i i   i  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_74935369_7    990 AGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTC 1039
                          i      v  i     i   i             v  i    vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_74935369_7   1040 ATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTT 1089
                               i  i  i  vi          v  i  v      vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_74935369_7   1090 ACAAGAAAAAAACAAATAACCCCATCAAAAAGTGGGCGAAGGACATGAAC 1139
                          i  v     i           v  i?    i     i     iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_74935369_7   1140 AGACACTTCTCAAAAGAAGACAT 1162
                              i     v        i  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.38 (101 / 73)
Gap_init rate = 0.00 (2 / 671), avg. gap size = 2.00 (4 / 2)  


 568 34.94 7.37 0.96  chr2_75041088_75043219.rev      502   813 (1319)    L1M4_orf2#LINE/L1        6   337 (571)  

  chr2_75041088_7    502 AGATATTCTATGCTC------TGGCA-----AATATTGTAAAAGT--CAA 538
                               i i   i  ------   v -----        v  ii --   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_75041088_7    539 T--TCTACACCTAGATCAGTACATCCATTACACCTCTAATCAAAACTTAA 586
                          --  iv  vv v    vii v  i  vii  vii iv       iiiv 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_75041088_7    587 ATTGAATTTTTT-CAGAGACTAGATAAACTTATTCTAAAATTTACATGGA 635
                         ii  vv      -    i i -  i  i  v  i        i i     
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_75041088_7    636 AGAATAAAGAGCCATGAATAGCAAAAGTCAGCTTTGAAAAAGAAGAG--- 682
                          ivii  i ii  vv       v   i-  iii             i---
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACAA 203

  chr2_75041088_7    683 ----GGGAGTCTAGCCCTGCTAGATATTAGGGCACGCTCTCAAGCCCTGG 728
                         ----  ii v  vi v  v ivi  v i iii vii  viv    ivii 
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_75041088_7    729 TAATACAAACGGTATGTTACTGGCCCAAGAACAAGCAAAACAGATCAATG 778
                             vv i  i  i  v       vi   i i ii  v -i         
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGATCAATG 302

  chr2_75041088_7    779 AGACAGAATAAAACACTCAGAAACAGACCCTTGCA 813
                         ii i     vi iviii      i i    v i  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

Transitions / transversions = 1.95 (72 / 37)
Gap_init rate = 0.03 (9 / 332), avg. gap size = 2.89 (26 / 9)  

 365 27.05 10.68 2.14  chr2_75041088_75043219.rev     1365  1645 (487)    L1M4_orf2#LINE/L1      604   908 (0)  

  chr2_75041088_7   1365 AAAGTACAAGCCATAAAGCAAAAAAAAACTGGTGGAATTA-ATTACACCA 1413
                             i      v i   --- i      iv i i-    i- i v  i  
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAA---AGAAAAAATAGATA-AATTGGACTTCATCA 649

  chr2_75041088_7   1414 AAATAAAGGATTCCTGGTCATTAAATGACACCAT-------------GGA 1450
                             v  ii i ii  vv v i   v     i  -------------i  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_75041088_7   1451 CAAC----AGGTTAGGAGAAGATACATGCACTATC-TAAAGCCAACAAGG 1495
                             ----  iv i      i   iv    v-   -  v v ii i    
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATAAGG 748

  chr2_75041088_7   1496 GACTA--ATCTAGATTAAACAAAAAACTCTAACAAATCAGGAAGGAAAA- 1542
                             v--   i   v  v i   i      v    v   iv  vi    -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_75041088_7   1543 AGAAAGAATCCTGGGTGAAAAATTAGCAGTGAATATGAAAAGGCAATT-- 1590
                          v   v  i  -iiv ?      vi   iv i  v    v  i  v  --
  L1M4_orf2#LINE/    799 ACAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_75041088_7   1591 --AAGGAAAATC--CAAAAGCTTAAGAA--ACATGAAGAGATGCTCAAGT 1634
                         --  i   i  v--    v vii  v  --       i          vv
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_75041088_7   1635 TCATAGTAATT 1645
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.21 (41 / 34)
Gap_init rate = 0.04 (13 / 305), avg. gap size = 2.77 (36 / 13)  


 992 26.91 18.39 4.33  chr2_75101659_75104259.rev     1020  1688 (913)    L1M4_orf2#LINE/L1       13   775 (133)  

  chr2_75101659_7   1020 CCATATTTATAAAATGAAAGGTTCACTATTGTAAAGATATCGTTTCTTCC 1069
                             i  i  ii v  i   ii i v      v     iv iv v  -  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT-CC 61

  chr2_75101659_7   1070 CCACAGTAATTTATAAATTCAATACAATCCCAATTAATATCTC------- 1112
                            v v i  i  i i      ii       v  i  v   i -------
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_75101659_7   1113 -TTTTTGTGGAATTTGACA----GATTCTAAAATGTACATGAAAATGCAA 1157
                         -      ii   v      ----   i       vi i   i        
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_75101659_7   1158 AGATTCAAAAATAGCAAAGATA--CTTAGAAAAAAA---CAAGGTGGGAA 1202
                         i ivi v i      v  i i --   ii    i  ---   i  v   i
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_75101659_7   1203 GAT-----CTGCTC--TCTCAGA--------TAAAGCTACCATAACTGAG 1237
                           i-----  v i -- i   i --------i        vi   iii  
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_75101659_7   1238 ACAGTATAGTACTGATGTGAGAATACCCATCAATGGAAAAGAGATACAAA 1287
                              i i      iii i  i   ---------------  v   ----
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATA---------------GACATA---- 292

  chr2_75101659_7   1288 TAGATCAATGGAAGAGAACAGAAAGGCCAGAAACAG-CC----------- 1325
                                      v    iv  i  v       i i-  -----------
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_75101659_7   1326 --TTGATTGAT----AAGAAAGGT----AG--CACT------GCAAAG-- 1355
                         -- ii      ----i v  i   ----  --  i ------ v    --
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_75101659_7   1356 CAGTG--------AGATGACGATATGGACAAGCGGATATCTAAATATGAA 1397
                         i   v-------- i   ii v i-      vi     ? i v  iii  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCAAA 441

  chr2_75101659_7   1398 GACACAAATGAGACTGGACCCCCAACCCA----ATACACAAAAATTCAAC 1443
                         ii----     iii        i v i  ----   i         -   
  L1M4_orf2#LINE/    442 AG----AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AAC 486

  chr2_75101659_7   1444 TC---------CACTG--TTA--TGAAAGA--CAAAACTATAAAGATTTT 1478
                           ---------  ?v --i  --  v    --i           iv i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_75101659_7   1479 AG-------CATATACAGAATGTCTTCATGACAATACAGTAGGGAATATT 1521
                           -------    vi?iv  -i     i    vv iviv    v   iv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_75101659_7   1522 TTCTAAAATG-AACACAAATAGCATTAGTTATAAGGAAAAAAATTGATAC 1570
                             v i  i-i    v  v    iv  iv i  iii       v    v
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_75101659_7   1571 ATTTGATTACCTTTATATTTTAA-----TGCGTATCAAAAGACAACCTTT 1615
                            v  i v v iv v   vv  -----  i iv     i    --  v 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA--CTAT 683

  chr2_75101659_7   1616 TAAGGA-GTGAAAAGGCA------------GGAAAAGATACGT-C---TC 1648
                         i   i -        i  ------------   i  i   iv - ---  
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_75101659_7   1649 ATATA-CTAA-AAAAGATTCATATCTAAAATATAACAAGCAC 1688
                              -  i -  ii  i ii    i i      vv   v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

Transitions / transversions = 1.95 (117 / 60)
Gap_init rate = 0.05 (37 / 763), avg. gap size = 4.11 (152 / 37)  


2175 26.90 13.45 0.37  chr2_75342216_75346392.rev     2883  3685 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_75342216_7   2883 TGAAACAGCATTCCATGCTCTTAGATACGAAGAATCAGTATTGCTAAAAT 2932
                           i  viii  i     i  v i   vv     v i i     i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_75342216_7   2933 GGCCAAACTACCCAAAGCAATTTACAGATTCAATGTTATTCCTAACAA-- 2980
                            v v   v      vii  i           i iv  i    v   --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_75342216_7   2981 --CCAATGACATTCTTCACAAAATTAGAAAAAC-AATTTTAAAATTCCTA 3027
                         --   iivi v  i  ii  i  v v  v  i -i  ii        v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_75342216_7   3028 TGCAATCAAAAAAGAGCCTGAATAGCCAAGGCAATTCTAAACAAAATGAA 3077
                           v  viiv  ii  v  v          ii    ii i  v  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_75342216_7   3078 CAAAGCTAGAGACATCACATATCC-AACTTCAAACTATACTACAAGGTTA 3126
                              i i   ivv     iv   -  i      viv        i i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_75342216_7   3127 CAGTAACCAAAACAGCATACTACTGGTACAAAAACAGACACATGGACCAT 3176
                               i   i    ii iv      i i  ii i     i  i  i  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_75342216_7   3177 TAGAACAG-----------CA--------CCTAT---------------- 3191
                          i   i  -----------  --------  i  ----------------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_75342216_7   3192 -------------------------------------------------- 3191
                         --------------------------------------------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_75342216_7   3192 TCAATAAATGGCGCTGGGATAACTGGCTAGCCATATGCAGAATACTGAAA 3241
                             i      i       i      v  ?   i     i  v v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_75342216_7   3242 CTGAACCACTTCCTTACACCATATCCAAAAATTAACTCAAGATGTATTAA 3291
                         i  i   v  v   i         v               i   v  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_75342216_7   3292 AGACTTAAATGTAA-------AACTATAAAAACCCTGGAAGATAACCTAG 3334
                             i         -------          vi i i     v   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_75342216_7   3335 GA-TATATCATTCTGCACATAGGCCCTGGCAAAGATTTCAT-GATAAAGA 3382
                          ?-  v   v iv  -  v v  viiv     v i    v -    v-  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATAT-GA 598

  chr2_75342216_7   3383 TGCCAAAAGCAATTGCAACACAAACAAAAATTGACAAATAGGACCTAATT 3432
                         ii         vvv      v  iv      v  i    v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_75342216_7   3433 AAACTAAAGAGCTTCTGCACAGCAAAAGAAATTATCAACAAAGCAAATGG 3482
                            v v  i i   i  ii vv    i  v i      v    ii  vi 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_75342216_7   3483 ACAACATATAGAATGGGAAAAAAATACTTGCAAACTCTGCATCTAACAAA 3532
                              vi i         i    -  i       iiv ii    i i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAG 747

  chr2_75342216_7   3533 GGTCTAATATCCAGAATCTGTGAAGAACTT----AAATTAACAAGCAAAA 3578
                           v  vi          v i i       i----  v i  i  vv    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_75342216_7   3579 AATAAACAGCCTCATTAAAAAGTAAGCGAAGGACATGAA----CACTTTT 3624
                         i i   i i  iv   ?    i ii  i     iv    ----  i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_75342216_7   3625 CAAAAGAAGACATACCCATGGCCAAGAAGCATATGAAAAATTGCTCACTA 3674
                          v        i    vv        v     i       iv      vi 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_75342216_7   3675 TCATTAATTAT 3685
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.59 (130 / 82)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 7.93 (111 / 14)  


3969 16.67 3.14 4.87  chr2_75395575_75397654.rev      665  1588 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_75395575_7    665 TAAAAAGACATTCTATGTTCATG-ATGCTCCGGAATACTTAATTTTGTTA 713
                          ii     i  i i         -  ----i    v       v      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT----TGGAAGACTTAATATTGTTA 46

  chr2_75395575_7    714 AGAGAGCAATACTTTCCAAACTGATCTATAGATTTAATGCAATCCCTATC 763
                            vi        ii     i       i     i  i            
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_75395575_7    764 AAAATTCTACATTCCTTTTTTTGGAGAAATTGACAAGGTTATTATCAAAT 813
                              i i -ii v i       v             v v  iv v    
  L1M4_orf2#LINE/     97 AAAATCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_75395575_7    814 GTATATGGGAATTCAAGGGATCCTGAACAGCCAAAACAATCTTGATAAAG 863
                         vi      i   v       i  v   i                 v    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_75395575_7    864 AAGAACAAATGAGGAGGACTCACAGTTCCCAATTTCAATACTTACTATAA 913
                                  vvv            v             v        i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_75395575_7    914 GACAACAGAAATCAAGACAATGTGGTACTGGCATAAG--TA--CAAATAG 959
                         ii v    v          i                 --  --  v    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_75395575_7    960 ATTAATGGAATAGAATTGAAAGTCCAGAAATAAAGCCATATATATGTATA 1009
                           i                i              v     i  --- -  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT---T-TA 341

  chr2_75395575_7   1010 TGGGCAATTGATCTTCAACAAGTGTGCAAAAA--ATTGTGATGGGGAAAG 1057
                            v        i   i     v    v  i --   -ii          
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAG 390

  chr2_75395575_7   1058 TATATTATTTAAAATAAATG-TGCTGGAACAACTGGATATCTACATACAA 1106
                         v   v v   vv  i     -      i           ? i    i   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_75395575_7   1107 AAGAATAAATTTGGACCCCTACCTCACACCATATACAAATGTTAATTCAA 1156
                               i  v                             vi    i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_75395575_7   1157 AATGGATCAAAGACCTAAATGCAATAACTAGATCTAGAAAACTCTCAGAA 1206
                                  ?           i  v i   i v   v        i    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_75395575_7   1207 TAAAACTTAGGTGTAAACCTTTATGAAGTTTGATCAGTCAATTGTTTCTC 1256
                         v     v    ?     i   ii   vv  v i i  v    v      i
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_75395575_7   1257 AGCTATCATACCTAAAGCACAAGAAGCCAAATAAAAAAT--------TGG 1298
                           v   v i   v          v i v   v       --------   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_75395575_7   1299 ACTCTATTGAAATTAAAAACTGTTGTACTCTCTTAAGCACTTTTTAGGGT 1348
                            ii  ii            v    i  --- i  ---------   ii
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCT---TCAA---------AGGAC 678

  chr2_75395575_7   1349 GCTCTCGAGAAAGAGAAAATATAACATACAGAGTGGGAGAAAATATTTGC 1398
                         i  v  i      v     v i   vi     i                 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_75395575_7   1399 AAATCATGTATCTAACAAGAGTCTATCCAGAATATATAAAAATCTATTCA 1448
                                i     i i   i v  ------------------ v   i  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACT------------------TGTATCCA 760

  chr2_75395575_7   1449 AAATATATAATGAACTCTTACAACCCAATCA---AAAGACAAGTAA---A 1492
                         i         v             i    v ---        i   --- 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_75395575_7   1493 ACCAAAAAA-GGGTAAGGAGAATGGTTTATATAAACTTTTCTTCAAAGA- 1540
                          ii?     -   i  i ----- i   iv   i  v     i      -
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAG-----GATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_75395575_7   1541 --TATACAAAAAGCCAATAAAAACAT---AATATGTTCAAAATTACTAGT 1585
                         --        vi        iv    ---  v   i    v  i ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_75395575_7   1586 CAT 1588
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.38 (87 / 63)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.70 (74 / 20)  


2596 24.00 5.20 2.13  chr2_75402716_75404484.rev      528  1277 (492)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr2_75402716_7    528 ATACTAAAATGTATATGGAACCAGAAAGGACCCAAAAAAGCCAAA----- 572
                           v       vi        viiv  i       i  v       -----
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_75402716_7    573 ------------GAACAAAAGTGAAGGAACTATATTACCTGACTTTAAAT 610
                         ------------       iv  i    vii i i v  ii i  i   v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_75402716_7    611 TATACTACAGAACTATAGTAACCAAATAACAG---GGTGCTGGCATAAAA 657
                         iv       i i   i     i   i--    ---   i         ii
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAG--ACAGTGTGGTACTGGCATAAGG 283

  chr2_75402716_7    658 ACAGACATATAGATCAGTGGAACAGAATTAAAATCCCAGAGATAAATCTA 707
                          i              i     i      i i vi     i     i i 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_75402716_7    708 CACATCTACAATGAACTTATTTTTGTCAAAGGTGACAAGAACATACACTG 757
                         i    i  iii v  i v     i v   i    v     v   v  v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_75402716_7    758 GGGAAAGGGCGGTCTCTTCAATAAACGGTGCTGGGAAAACTGGGTATCCA 807
                                iiii    i     i   i          v      i  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_75402716_7    808 TATGCAAAAGAATGAAACTAGACTATAGCTGCATTCTATCTTGC--CATA 855
                         i               ii i   i----------i   i  ii --    
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACC----------CCTACCTCACACCATA 473

  chr2_75402716_7    856 TGCAGAAATCAAATCAAAATGGATTAAAGACTTAA-TCAAAGACCTCAAA 904
                          i  i    i  v           i ?    i   - vv    v  v   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_75402716_7    905 CTGTGAAACCACTAAAAGAAAGCA-ATG-GTAAAACTCCCAAGGACATTA 952
                           i i    ivi  i      i  - v -     v  i --iv   v  i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC--GTGACCTTG 571

  chr2_75402716_7    953 GTCTGGGAAAATATTTTTTG--------------AGCACAGGAAACCAAA 988
                          vi i  v  vvi   i  i--------------      i v   v   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_75402716_7    989 GCAAAAATGGACAAATGGGATCACATCAAGTTAAAAAACTTCTGTACAGC 1038
                          v      i  i    v   iiv      iv v        i   i vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_75402716_7   1039 AAAGGAAACAAACAACAATGTGAAGAGACAACCCACAGAATGGGAGAAAA 1088
                               v  v v   v  v     i                         
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_75402716_7   1089 TATTTGCAAACCTCCTATCTGATAAGAGATTAATAACCAGAATATATAAG 1138
                                   i viv           i  i vi  v             i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_75402716_7   1139 TAGCTCAAACAACTCTGTTGAAAAAAAAATCTAATAATCTGATCAAAAGA 1188
                         v i   vv       vi --  v     iv v     i ii  i?   i 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAAT--AATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_75402716_7   1189 TGGGCAAAAGTTCTAAACAGACCTTTCTCAAAGGAAAACATACACATGGC 1238
                                 i v i i  i    v      v  i   i i     v     
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_75402716_7   1239 AGACAGGCGTATGAAAAGGTGCTCATCATCACTGATCAT 1277
                         vi i i  ii        i      v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (113 / 64)
Gap_init rate = 0.01 (11 / 773), avg. gap size = 5.00 (55 / 11)  


 973 27.15 7.05 1.04  chr2_75497450_75499724      118   500 (1775)  C L1M4_orf2#LINE/L1   (0)   908   503  

C chr2_75497450_7    500 ACTTAAATATAA-AGTGTAAAACTATAAAAACCCTGGAAGACAACCTAGG 452
                           i     i   -  i-             vi i i     v   v    
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

C chr2_75497450_7    451 CA-ATACCATTTAGGACATAGGCACAGGCAAAGATTTTATAACAAAGATG 403
                         ?i- v i -  iiv   v v  vvi      v i   iv  ivv v  ii
  L1M4_orf2#LINE/    552 NGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

C chr2_75497450_7    402 CCAAAGGTAATTGCAACAAAAGCAAAAATTGACA-----GATCTAATTAA 358
                              i i vvv          v      v  i -----  ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

C chr2_75497450_7    357 ACTAAAGAGCTTCTGCACAGAGCAAAAGAAATGATCAACAGAGGAAATAG 308
                          v v  i i   i  ii vv--    i  v iv     v i  vi  v  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAG 698

C chr2_75497450_7    307 ACAACCTACAGAATGGGAGAAAAATTTTGCAAACTATGCATCCAACAAAG 258
                               i                vv        ii  ii   ii i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

C chr2_75497450_7    257 GTCTAATATTCAGCATCTATAAACAAATTT-------------------- 228
                          v  vi   i   v  v      v  v i --------------------
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

C chr2_75497450_7    227 ACAAGTAACCTCATAAAAAAATGGGCAAAGGACATGAACAGACACTTTTC 178
                             i     iv  v?                iv    i     i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

C chr2_75497450_7    177 AAGAGAAGACATACATGCGGTCAACAATCATATGAAAAAAAGCTCAACAT 128
                         v i      i     vii  i   i  v  i       i v         
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

C chr2_75497450_7    127 TACTGATCAT 118
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.32 (58 / 44)
Gap_init rate = 0.02 (7 / 406), avg. gap size = 4.43 (31 / 7)  

1275 31.12 6.98 3.43  chr2_75497450_75499724      922  1795 (480)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_75497450_7    922 AAAAATATACAGCATATACTTGGACAGTAACACTCAATATTTTAAAAATA 971
                            i    v --   i v v    iv v  v   i      v v  i  i
  L1M4_orf2#LINE/      4 AAAGATATCC--CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_75497450_7    972 ACTATTGTCTCTATATTGATCCAAAGAGTTAATGAAATTCTAATGAAAGT 1021
                         i v  vv  i i v       i v   v i  i v   i iv  v   i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_75497450_7   1022 CTCAGCAGGTCTTTTATTGTTGCTGAAATTGATAAACTGTTTTGAAAATT 1071
                          i    -v i     ----    v        i  i   v iiv      
  L1M4_orf2#LINE/    102 CCCAGC-TGCCTTTT----TTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_75497450_7   1072 TAAATGGGAAT-CAGACTATCAAGAACAGCTAAGAATATCC--------A 1112
                         i v    i   -  iivv i v    i   i  i vv   i-------- 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_75497450_7   1113 ACAGCAAAGTTGGATGAC--ATATTACCTGATATCAAAACTTATTACTGT 1160
                          v i          v   -- i i v  ii  v          i   ---
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC--- 243

  chr2_75497450_7   1161 ATACACATGCAGTAATTGAGACCATGTAATATTGGTGCAAAAATAAAAAA 1210
                         -- v vv i       ii    vi   ii  i   iii  ii   i v v
  L1M4_orf2#LINE/    244 --AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_75497450_7   1211 AAGAGACCAGCAGAATGGAACAGAGAGAATAAAAAGAGATCCACATATAC 1260
                          -v   i  iii    i   iv     vvi i   v i i   i i  vi
  L1M4_orf2#LINE/    292 A-TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_75497450_7   1261 ATATTTACTCGCTCTGTGACAAAAAAGCCACTGTAG--CAG--AGCGGGA 1306
                           iv i v i v i vi     iiiv    ----  --  v-- ii   i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGG 386

  chr2_75497450_7   1307 AAATAACGGCCATTTCAATGAATTCTGTTGGGTCAATTGCCTATTTA--T 1354
                            v  ii i v      ii   vv  i    v   i  vv  ?ii -- 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_75497450_7   1355 GTAAAA--AT-AATTTAAATGT-TACTCTGCAC-------AAAAATAAAT 1393
                          i    --  -  v  ii ivi-   iiii   -------      v  i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_75497450_7   1394 T---------TCATG--TCTCAATGAGGAAGCCAAAAA-ATAAAACTGCT 1431
                          ---------   ?i--i  v    viii   i    v-        vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_75497450_7   1432 GAAAGATAACATTGGTGGAGATCTTTATAAAATTGGGATTGACAAAAATT 1481
                         ii    v     v  ? v i     ii i vv     v v i   vii  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_75497450_7   1482 TCTTAAAGAAGATA--AAACAGTGTTAAC--TTAAAGATTAAAAACTTGA 1527
                              i v v  i --   -  iiiv i --iv     --     - v  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAA-AGCACAAGCAACAAAAGA--AAAAA-TAGA 632

  chr2_75497450_7   1528 TAATTTGAACTTTGCTAAAATTAAGAATCTCTATTCAGCGAAAGACACAA 1577
                            v   i    iiii        i  ii i i v vv i  i     v 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_75497450_7   1578 TTAAAAGAGTGAAAAAAGCAAGTAATAGAGTGGGAAAAGGTATTTCCTGT 1627
                          i  i i        i -   viv i   i     i  ii     --- i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGA-CAACCCACAGAATGGGAGAAAATATTT---GC 728

  chr2_75497450_7   1628 A---CACATATTTGAC--GAAATATAT-TTCAAAAAAGATAAA-----CT 1666
                          ---  i    i   i-- ii iv i - i  i  v v     -----  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_75497450_7   1667 CATAATCATCAATAAGAAAAAAAGGCAATT---CCA--TAGAGAATCAGG 1711
                         i i  i--       v     i --   v ---   -- ?i i   -i  
  L1M4_orf2#LINE/    779 TACAAC--TCAATAATAAAAAGA--CAAATAACCCAATTWAAAAAT-GGG 823

  chr2_75497450_7   1712 CAAAATATTTAAACATAAACTTTATAAAAGTGGACATATAAATATTCTTT 1761
                             iv    i  i v v i  iviv    vi  i   i    ivi vv 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_75497450_7   1762 AAACAAATGAAAAG-TACTAATTATCATCAGATAA 1795
                           i  v        - i  v vi    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (168 / 100)
Gap_init rate = 0.04 (36 / 905), avg. gap size = 2.53 (91 / 36)  


2239 26.30 10.62 1.09  chr2_75501970_75506313.rev     3024  3852 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_75501970_7   3024 TGGAAAAACATTCCATGCTCATGGACTGGATGAACCAATATCTTTGAAAT 3073
                               i i  i     i       i    v  vii     iv  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_75501970_7   3074 GGCCATACTGCTTAAAGCAATCTACAGATTTAATGCTACTCCTATCAAGT 3123
                            v     v ii   vii           i  i  v ii        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_75501970_7   3124 TACCAACGTCATGTTTTCACAGAATTAGAAAAAATTATTTTAAAATTCAT 3173
                          v   i vv v -    ii     v v  v  iv v  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_75501970_7   3174 ATAGAACTGAAAAAGAGCCCAAATATCTCAAGCAATTCTAAGCAAAATGA 3223
                           i   v  v  ii  v  vi    v iv  i    ii i iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_75501970_7   3224 ATAAAGCTGGAGGCATTACATTACCCAATTTCAAGCTACACTATAAGGCT 3273
                          i    i      vv i   i v           ivivi    i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_75501970_7   3274 ACAGTAACCAAAACAGCATGGTACTAGTACAAAAACAGACACATAGACCA 3323
                                i   i    ii       i i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_75501970_7   3324 ATGGAACAGAATAGATAG----------GAC-----------TGG--AA- 3349
                               i     v  v  ----------i  -----------   --  -
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_75501970_7   3350 -GA--------AAGGGCTCCA----TATTCAAT----------------- 3369
                         -  --------     iv   ----i       -----------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_75501970_7   3370 ------AAATGGTGCTGAGATAGCTGGCTAACCATATGTAGAAGAATGAA 3413
                         ------           i  i i    v  ?   i   i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_75501970_7   3414 ATTGAATCCTTACCTTTCACCATAGACAAAAATTAACTCGAAATGAATTA 3463
                         i   i i  i     iv       v              i     i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_75501970_7   3464 AAGATTTAAGTGTAAGAAAGACCTCAAACTAAAAGAATCCTAGAAGAAAA 3513
                         ?   ii   i       i----  v      v  i v  i          
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAG----CTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_75501970_7   3514 CCTAAGAA-ACACCATTCTGGATATCAGCCTTGAGAAAGAATTTATCAC- 3561
                          v  i ?i- v i -   vv  iv ii v-  ii v  vii   v i v-
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGA 593

  chr2_75501970_7   3562 TAAGTCCTCAAAGGCAACTGCGACAAAACAAAAATT-GACAATTGGGACC 3610
                           v v vi    i   vvv  i      v     v -  i  v v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_75501970_7   3611 TAATTCAACTAAAGAGCTTCTGCACAGCAAAATAAACGATCAACAGAGTA 3660
                          v  iv  v v  i i   i  ii vv    iv v  v     v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_75501970_7   3661 AATAGACAACCTAAGGAATGGGAGGAAGTATTCATAAAGTGTACATCTGA 3710
                           v        i vi         i  i    iii   vii  i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_75501970_7   3711 AAAAGGTCTAACATCCAGAATCTATAA-GAA--------ACTAAACAAAC 3751
                         v  i  v  vii         v     -   --------   v  i  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_75501970_7   3752 AAAAAACAAATAACAGCA--TCAAAAATGGGCAACAGGA----------- 3788
                             i         v-  -- ?            -    -----------
  L1M4_orf2#LINE/    794 AAAAGACAAATAACC-CAATTWAAAAATGGGCAA-AGGATTTGAATAGAC 841

  chr2_75501970_7   3789 ACTTCTTAAAAGAAAATGTGCAGGCGACCAACAA--ACATGAAAA-ATGA 3835
                          i    iv      i  i i  iii i    i  --         -   v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_75501970_7   3836 TCATCATCACTAATCAT 3852
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (131 / 83)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.41 (97 / 22)  


2985 28.02 1.00 0.44  chr2_75507921_75514314.rev     5000  5902 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_75507921_7   5000 TGGAAGAACATTCCAAGCTCGTGGATAGGAAGAATCAATATTGTGAAAAT 5049
                              ii i  i   v i  i     v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_75507921_7   5050 GGCCATACTGCCCAAAGTAATTTGTAGACTCAATGCTATCCC-ATCAAAC 5098
                            v     v      v i  i ii   i    i  v     -      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_75507921_7   5099 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5145
                          v   -   v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_75507921_7   5146 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAA 5195
                                 viiv  ii  v  viv  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_75507921_7   5196 GAGCAAAGCTGGGAGCATCGTGCTACCTGACTTCAAACTACACTACAAAG 5245
                           i     i   ii vv  iii  v  ii i      vivi         
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_75507921_7   5246 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGAC 5295
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_75507921_7   5296 CAATGGAACAGAACAAAGACCTCAGAAATAACACCACACATCTACAACCA 5345
                                 i    ivi   vii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_75507921_7   5346 TCTGATCTTCAACAAACCTGACAAAAACAAGCAATAGGGAAAGGATTCTC 5395
                         vi    i   i    ivv  v   i v  vv    i       i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_75507921_7   5396 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5445
                          v  i  i        i     v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_75507921_7   5446 AAACTGGATCCCTTTTTTATACTTTATATGAAAGTTAAC--AAGATGGAT 5493
                           ii    i    vii i i  iv    ii   i     --  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_75507921_7   5494 TAAAGGCTTAAATGTAAGACCTAACACCATAAAAACCCTAGAAGAAAACC 5543
                         i ?  i i           v    v  i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_75507921_7   5544 TAGGCA-ATACCATTCGGGACATAAGCATGGCCAAAGACTTCATGACTAA 5592
                             ?i- v i -    v   v vi vv i v   v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_75507921_7   5593 AACACCAAAATCAATGGCGACAAAAGCCAAAATAGACAAAT-GGATCTAA 5641
                         i         v  vvi  i       vv        i    -   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_75507921_7   5642 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCATCATCAGAGTGAAG 5691
                          i   v v  i i   i  ii vv    i  v  i    vv i      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_75507921_7   5692 AGGCAACCTACAGGATGGGAGAACATTTTTGCAATCTATCCATGTGACAA 5741
                           i     i    i         v  v       vii  vi  v   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_75507921_7   5742 AGGGCTAATACCCAAAATCTTCAAAGAACTTAAACAAATTTACAAGAAAA 5791
                         i  i  vi  i   i   v vi        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_75507921_7   5792 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATAT-AACAGACAGTTG 5840
                          i     i     v  i?    i            v -  i     v  v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_75507921_7   5841 TCAAAAGAAGACATTTATGCAGCTAACAGACATATGCAAAAATGCACATC 5890
                           v        i  vi viii  i  i ii  i   v   i    v  v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_75507921_7   5891 ATCACTGGTCAT 5902
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (153 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.18 (13 / 11)  


3823 16.14 2.89 3.61  chr2_75658585_75660397      494  1323 (490)    L1M4_orf2#LINE/L1       85   908 (0)  

  chr2_75658585_7    494 GCAGTCCC----AAAATCTCAA-TGATGTTTTTGCAGAAATAAAAAAATC 538
                            i    ----      i  i-  viv             vi v  iii
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr2_75658585_7    539 CATACTGAAATTCATATGGAATCTCAGGGGACCCCAAACAGTCAAAACAA 588
                         v  v  i              viv  i       vi  i  i        
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_75658585_7    589 TCTTGAAAATTAA---CAAAGTTAGACATCTCACTCTTCCTGATTTCAAA 635
                                  vv  ---       i  viv     v     ii        
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_75658585_7    636 ACTTATTATAAATCTATAGTAATCAAAACAGTGTAGGCCTAGCATATAAA 685
                              i  i   v   i         i       i vv  i     -- i
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA--AG 282

  chr2_75658585_7    686 AACAGACATGTAGCTTAATGGAATAGAATAGAACATCCAAAAATAAACCC 735
                         i i      i   v i             v  ivi    i          
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_75658585_7    736 TTACATATATATATGTTCAAATTATTTTTG-CAAGGGTGCCAAGACCATT 784
                         ----   i  v    v    v v     i -                   
  L1M4_orf2#LINE/    333 ----ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_75658585_7    785 CAATGGGAAAAGACT-GCCTTTTCAGCAAACGGTGTTGGAAAAACTGGAT 833
                                i     v - i       i    i    i   i v        
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_75658585_7    834 GTCCACGTGCAAAAGGATGAAGTTGGACCCTTACCTTACACTATATA-AA 882
                         i?    i        i              i     i    i     -  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_75658585_7    883 AAATTAACTCAAAATGTGTCAAAGACCTAAATGTAACAGCTAAAAATTTT 932
                                         vi   ?              v        ---i 
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA---CT 525

  chr2_75658585_7    933 AGAAGACTGTTAGAAGAAAACA--GGGGTAAAGATTCATGACATTGGATT 980
                          v  i   v             --  ?     vv   i    v    i  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_75658585_7    981 TGACAATGATTTCTTGGATATGACACCAAAAGCACAGGCAACAAAAGTAA 1030
                         v i     i      i                    i          -- 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG--A 623

  chr2_75658585_7   1031 AAAAAAAGA-AAA--GGACTCTATGAAAATTAAAAACTTCTGTGCATCAC 1077
                              v   -   --     ii  v              i     v   v
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_75658585_7   1078 AGGGCAC----AACAGAGTAAAAAGGCAACCCACAAAATGGGAGAAAATA 1123
                            i   ----  v i   i     i         i              
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_75658585_7   1124 TTTGCAAATAATATATCTGATAAAGGGTTAATATCCAGACTGCTACCTAT 1173
                                  v             i  ii vi        v i-----   
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA-----TAT 768

  chr2_75658585_7   1174 CCTAATTCCTAATATCAGAACTCCTACAACTCAACAACTAAAA-ACAAAG 1222
                         ----------  ----       i          i  iv    -     v
  L1M4_orf2#LINE/    769 ----------AA----AGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_75658585_7   1223 AGCTCAATTTAAAAATGGGCAACAGACTTGAAGCAATATTTCTCCAAAGA 1272
                          i i     ?            vi  i     vvi i             
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_75658585_7   1273 ---TATACAAGTAGTCAATAGGCACATGAAAAGATGCTCCACATAACCAA 1319
                         ---       i i i     i                  v    v ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_75658585_7   1320 GCAT 1323
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.65 (81 / 49)
Gap_init rate = 0.02 (19 / 824), avg. gap size = 2.84 (54 / 19)  


3336 24.69 2.47 0.56  chr2_75720825_75725056     2850  3740 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_75720825_7   2850 TGGAAATACATTA-ATATCCATTGACTGGAAGAATCAATATTGTTTAAAT 2898
                               v i  iv-  i i   v  i       v i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_75720825_7   2899 ATCCGTACTACCTACAGCAATCTACAGATTCAATGCAATCCCTGTCAAAA 2948
                         iv vi    v  i v vii              i         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_75720825_7   2949 TACCAAAGACATTATTCATAGAAATAGGAAAAGTAATCCTAAAATTTTTA 2998
                          v   ivvi v  v  iii      v iv  iv i           --i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT--CA 148

  chr2_75720825_7   2999 TATGGAACCATGAAAGACCCAGAATAGCCAAAGCCATCCTGAGCAAAAAG 3048
                                viiii ii                 i v   i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_75720825_7   3049 AACAAA-CTGAAGGAATCGCATTACTGGACTTCAAATTATGCTATAGAGC 3097
                               -i  i    v  i  i v ivi i      viv i   i i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_75720825_7   3098 TAACAG------AAACAGCATAATGCTGGCATAAAAACAGACACATAGAC 3141
                           -   ------ i    ii ii i         ii i     i     i
  L1M4_orf2#LINE/    249 TA-CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_75720825_7   3142 CAATGGAACAGGACAGAAAACCCAGAAATGAATCCATACATCTGCATTGA 3191
                                 i  i iv  i ii        i  i        i iiiv v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_75720825_7   3192 ATTCATTTTTGACAAAGGTTTCAAGAACATATATTGGGAAAAAGATAATC 3241
                            v     i     i   vi     v   vi v    i   ii   i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_75720825_7   3242 TCTTCAATAAATGGTGCTAGAA-AACTGGATATCC-CATGCAGAAGAATA 3289
                          i     i          i i -         ?  -      i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_75720825_7   3290 AAACTAGACCCCTATTT--TGTCATATATAAAAATTAAATCAAAATGAAT 3337
                           ii i        ii --iii      i         v        i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_75720825_7   3338 TAAAGACTTAAATATAAGAGCTCAAACAATAAAACTGCTAAAAGAAAACA 3387
                         i ?    i     i        v    v        vi  i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_75720825_7   3388 TTGATGCAATGCTCCAGGACATTGG-TCAGGGCAATGGTTTCTTGAGTA- 3435
                          v i? i  vv  i iv   v    - i   -            iii  -
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTAGATAT 596

  chr2_75720825_7   3436 -ACACCCATAAGCACAGGCAAGCAAATCAAAAATGAACGAGTGGGATCAC 3484
                         -     v -       i    vv   vv      ii ii i v   iiv 
  L1M4_orf2#LINE/    597 GACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_75720825_7   3485 AT-AAGTCTAAACACTTCCGCACAGCAAAGAAAAC----AACAAATTGAA 3529
                           -  ivi    v    ii ii vv     i v  ----  v   v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_75720825_7   3530 GAAATAACCCACAGCATGGGAGAAAATATTTGCAAACCATCCGTCTGACA 3579
                         i i i         v                     i   vii     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_75720825_7   3580 AGGGTTTAATAACCAAAATATATAAGGAGTTA-AATAACTCTATAGAAAA 3628
                             vi vi  v   i         i  ii v-v i     v   iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_75720825_7   3629 ATGTCTAATAATCCAATT-AAAAATGGGCAAAAGATCTGAATAGACATTT 3677
                          v v v     i      -             i   i             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_75720825_7   3678 CTCAAAAGAAGACATACAAATGGCAAACAGATATGTGAAAATGTGCTCAA 3727
                            v        i           v  i iii ii      vi       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_75720825_7   3728 CATCATTGATCAT 3740
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (145 / 72)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.69 (27 / 16)  


1911 29.75 2.86 0.50  chr2_75896142_75898807     1034  1628 (1038)    L1M4_orf2#LINE/L1        1   609 (299)  

  chr2_75896142_7   1034 TGGAAAAATATTTAACGCTCATGGATTGGAAGAATCAATATCATTAAGAT 1083
                               i    iiv i i               v i     ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_75896142_7   1084 GTCCATACTGGCTAAAGCAATTTACAGATTCAGTGTTATTCCTATTAAGC 1133
                          v v     vv i   vii  i          ii iv  i     i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_75896142_7   1134 TACCAA-TGTAATTTTTCACAAAATTAGAAAAAATGATTCTAAAATTCAT 1182
                          v   i-  i-v     ii  i  v v  v  iv    i           
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_75896142_7   1183 ATGGAACCAAAAAAGAGCTTGAATATACACAGCAATTCTAAGCAAAAAGA 1232
                               viiv  ii  v iv     vv  v i    ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_75896142_7   1233 ACAAAGCCAGAGGCATCACATTACCTGACTTTAAACTATACTATAAGGCT 1282
                               iii    vv     i v  ii i  i   viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_75896142_7   1283 ACAGTAACCAAAACAGCATGGTATTGGAATAAAAACAGATACACAGACCA 1332
                                i   i    ii     i   v    ii i   i i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_75896142_7   1333 ACGGAACAGAATAAAGAACCCAGAAATGAA---------------TCATT 1367
                          i    i     vi   ii        i  ---------------   v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_75896142_7   1368 TGATTGTTGACAAAGTCAACAAAAATAAGTAATGGGGAGAGGACTCCCTA 1417
                              v i     i viiv   i vi vvi        i  i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_75896142_7   1418 TTCAAAAAAACCATGCTGGAATAACTGGCTAGTGATATGAGGGAGAATGA 1467
                              v   -ivi      i i      v  ?iv i   viii       
  L1M4_orf2#LINE/    400 TTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_75896142_7   1468 AACTGGATCCCTATTTTTCACCATATACAAAAATTAACTCAAGATGGAGT 1517
                          ii    i     ii iv                        i     vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_75896142_7   1518 AAAGATTTAAGTGTAAGACCTCAAACTACAAGAATCTTAGAAGAAAACCT 1567
                          ?   ii   i       v  v      i  i v              v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_75896142_7   1568 AGGAA-ACATCACCCTGGACGTCAGACTTGGAAAAGAATTTTTGACTAAG 1616
                            ?i- v   vi v -   v ii ii v  v  v iv  i  iiv  v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_75896142_7   1617 CCCTTAAAAGTA 1628
                         v vii     i 
  L1M4_orf2#LINE/    598 ACACCAAAAGCA 609

Transitions / transversions = 1.76 (111 / 63)
Gap_init rate = 0.01 (6 / 609), avg. gap size = 3.33 (20 / 6)  

 757 26.50 1.58 5.05  chr2_75896142_75898807     1858  2174 (492)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr2_75896142_7   1858 AAAAATGTAATTGCAACAGAAACAGAAATTGACAAGTGGAACCTAATTAA 1907
                             iiii  --      i  iv i    v  i  i v i  i v  i  
  L1M4_orf2#LINE/    603 AAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_75896142_7   1908 ACTACAGCGCTTCTGCACTCAAAAGGAT-CTATCAACAGAATAAACAGAC 1956
                          v vv ivi   i  ii  iv      i-       v i i i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_75896142_7   1957 AACCTACAGAATGAGAGAAAATATTTTCCAAGTATGCATCCAGCAAGGGA 2006
                             i        i            v v  vi  ii   iiii      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_75896142_7   2007 CTACAGCAAAGGACTAATATCCAAGATCTATTAGGAACTTAAACAATTGA 2056
                           ------------ i-      ii  v   v i     ivv    i v 
  L1M4_orf2#LINE/    751 CT------------TG-TATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_75896142_7   2057 ACAAGGCAAA---AAACAACTCTACT-GAAAATGGGCAAAAGACATGAAC 2102
                          i  viv   ---   i   i v i -i            i  iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_75896142_7   2103 AGAGAGTTCTCAAAAGGAGACATAAAAGTTGCCACAAAACATATGAAAAA 2152
                            v v     v    i   i   v  i v    vv  i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_75896142_7   2153 AATGTTCCACATCACTAGTCAA 2174
                          -  i  v      ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (53 / 31)
Gap_init rate = 0.02 (7 / 306), avg. gap size = 3.00 (21 / 7)  


2497 24.95 1.97 7.97  chr2_75961947_75967018     3615  4580 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_75961947_7   3615 TAGAAA-ACATTTTATGCTTATGGATGGGAAGAATGAATATCATTAAAAT 3663
                          i    - i  iii   i i      v      v v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_75961947_7   3664 GACTATACTGCCCAAAGCAATTTATAGATTCAATGCTATTTCTATCAAAC 3713
                          i v     v      vii  i  i        i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_75961947_7   3714 TGCCAATGATATTCCTTACATAATTAGATAAAA-AATTTAAAAATTCATA 3762
                          v   iiviiv  ii  i  v  v v  i  iv-i  iiv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_75961947_7   3763 CGAAACTAGAAAGATCCCA-AATAGCCAAGGCACTCCTGAGCGAAAAGAA 3811
                         i i  v iv  i iv    -         ii  v  i   ivi i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_75961947_7   3812 CAAAGTTGGAGGCATCACATTATCCTAATTC--AAACTATACTACAGGGT 3859
                                     vv     i -   i    i--     -       ii i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACT-TCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_75961947_7   3860 TATAGTAAACAAAAACAGCATGGTACTGGTACAATAACAGAAACATAGAC 3909
                           i     v   i -   ii         i i  vi i   v i     i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_75961947_7   3910 CAGTGGGACAGAATAGAGAGCCCAGAAGGAAGGCTGCACACCTACAACCA 3959
                           i   i i     v     i      iv  iv iii   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_75961947_7   3960 TCTCATATTTGACAAAGTTGACAAACACAAGCAATGGAGACAGGAC--TC 4007
                         vi v  v  i     i v  v   ivv  vv      i  v  i i--  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_75961947_7   4008 TTTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCGTAGGCAGAAGAC 4057
                            --    i              i      v  ?  ii v   i    v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_75961947_7   4058 TGAAACTGGACCCCTACCTAACACAACATACAAAAATCAACTCAAGATAG 4107
                             ii             v    v i          i       i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_75961947_7   4108 ATCAAATACTTAAATGTAAGCTCTAAAACTATATAAATGTAAGCTCTAAA 4157
                             ? v  i          ------------------------------
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAG------------------------------ 515

  chr2_75961947_7   4158 ACTATATAAATGTAAGCTCTAAAACTATAAAAATGTAAGCTCTAAAACTA 4207
                         -------------------------------------    --       
  L1M4_orf2#LINE/    516 -------------------------------------AGCT--AAAACTA 526

  chr2_75961947_7   4208 TAAAAATCCTGGAAGATAACCCAGGAA-ACATCCTTCTGGACATAGGACT 4256
                              v  i i     v   vi   ?i- v   -   vv   v v  ii 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTT 575

  chr2_75961947_7   4257 TGGCAAAGATTTCAT-GATAAAGACACCAAAGGCAGTTGCAACAAAAGCA 4305
                         v     v i    v -    v-         i   vvv          v 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_75961947_7   4306 AAAATTCACAAGTGGGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 4355
                              vv i  i v    i v  i   v v  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_75961947_7   4356 AGAAACTATCAATAGAGTAAA----CAATCTACAGAATAGGAGAAAATAC 4401
                         i  v        v i   i  ----   i i       i          i
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_75961947_7   4402 ATGCAAACTATGCATCTGACAAAGGTCTAATGTGCAGCATCTATAAGGAA 4451
                         v      ii  ii      i  i  v  vi i v   v  v     i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_75961947_7   4452 CTTCAACAGATTTACAA-GAAAGGAAAAACA---CA-CTAAAAAATGAAC 4496
                           iiv   iv iv i  -i   i  v   i ---  -i ?       ii 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_75961947_7   4497 AAAGGAAAGGAACAGACAATTTGCAAAAGAAGACATACATGCGGCCG-CA 4545
                               vvv   i     v  iv v        i     vii    i-i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_75961947_7   4546 ATTATGTGAAAAAACCCCTCAACATCACTGATCAT 4580
                          vi ii      i iv -         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGC-TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.57 (96 / 21)  


2967 25.78 0.86 3.74  chr2_75972531_75978690     4734  5668 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_75972531_7   4734 TGGAAGAACATTCCATGCTCATGGATAGGAAAAATCAATATCATGAAAAT 4783
                              ii i  i     i        v    i v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_75972531_7   4784 GGTCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4833
                           iv     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_75972531_7   4834 TACCATTGATTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAATTTTA 4881
                          v   viviii  i  iii    -   -- v  i  - iii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_75972531_7   4882 TACAGAACAAAAAAAGAGCCCATA-TAGCCAAGACAGTCTTAAGCAAAAA 4930
                           ii   - viv  i ii    v -       i   i    i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_75972531_7   4931 GAACAAAGCTGGAGGCATCAAACTACCTGACTTCAAACTATACTATAAGG 4980
                                 i      vv   v   v  ii i      viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_75972531_7   4981 CTATAGTAACCAAAACAGCATGGTACTGGTACCAATACAGATACGTAGAC 5030
                            i     i   i    ii         i iv iv i   i ii    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_75972531_7   5031 CAAGGGAACAGAAT--AAAGTCCTCAGAAATAACACCACACATCTACAAC 5078
                            v    i     -- i     --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_75972531_7   5079 CATCTGATCTTTGACACACCTGACCAAAACAAG-CAATGGGGAAAGGATT 5127
                           vi    i  i    vivv  -    i  v v-            i  v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_75972531_7   5128 CCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAGA 5177
                         vi  v  i  i        i     v      v  ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_75972531_7   5178 CTAAAACCGGACCCCTTCCTTACACATTATACAATTAACTCAAGGCAGAT 5227
                         v i  iii        v   i    vv       ------------ i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAA------------AAAT 482

  chr2_75972531_7   5228 TAAAGACTTAAACGTAAAACTCAAGATGGATTAAAGATTTAAACATAAGA 5277
                            ----------------     i      i ?   ii    ii     
  L1M4_orf2#LINE/    483 TAA----------------CTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_75972531_7   5278 CCTAAAACCATAAAAACCCAAGAAGAAAACCTAGGCA-ATACCATTCAGG 5326
                         v       i      vi iv          v    ?i- v i -   iv 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTG 565

  chr2_75972531_7   5327 ACATAGGCATGGGCAAAGACTTCATGACTGAAACACCAATAGCAATGGCA 5376
                           v v  vv i     v ii   v iiv ivi       v    vvi   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_75972531_7   5377 ACAAAAGTCAACATTGACAAATGGGACCTAATTAAACTAAAGAGCTCCTG 5426
                                vv  v  v  i    v    i v  i   v v  i i  ii  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_75972531_7   5427 CACAGCAAAAGAAACTATCATCAGAGTGAACAGGCAACCTACAGAATGGG 5476
                         ii vv    i  v       vv i      v  i     i          
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_75972531_7   5477 AGAAAATTTTTGCAATCTATCTATTTGACAAAGGGCTAATATCCAGAATC 5526
                                v       vii  v   i   i  i  i  vi          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_75972531_7   5527 TACAAAGAACT-TAACAAATTTACAAGAAAAAATAAAACAACCCCTTCAA 5575
                           i        - v    v iv i  v     ivv   i     vv i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_75972531_7   5576 AAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATG 5625
                            i            v    i     i     v        i  vi vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_75972531_7   5626 CAGCCAATAAACATATGAAAAAAAGCTCATCATCACTGGTCAT 5668
                         ii        i  i       i v     v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.07 (43 / 14)  


3567 24.48 0.33 1.09  chr2_76048573_76051768.rev     1790  2704 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76048573_7   1790 TGGAAAGATATTTCATGTTCGTGGATTGGAAGAATAAATATTGTTAAAAT 1839
                                    ii       i            v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76048573_7   1840 GTCCATACTACCCAACACAATGTATAAATTCAGTGCAATCCCTATCAAAA 1889
                          v v     v     vvii  v  i i     ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76048573_7   1890 TACCAATGACATTCTTCACAGAAATAGAAAAAACAATCCTGAAATCTTTA 1939
                          v   iivi v  i  ii       v  v  ivii     i    iiv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_76048573_7   1940 TGGAACCACAAAAGACCCAGAATAGCCAAAGCTGTCCTGAGCAAAAAGAA 1989
                              vii   ii                 i vi  i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_76048573_7   1990 CAAAAGTGGAAGAATGACATTACCTGACTTCAAATTATACTACAGAGCTA 2039
                             iv    i  v v   i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_76048573_7   2040 TAGTAAACCAAAGCAGCATGGTACTGGCATAAAAACAGACACACAGACCA 2089
                         i     -i   ii   ii              ii i     i i   i  
  L1M4_orf2#LINE/    251 CAGTAA-TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_76048573_7   2090 ATGGAACAGAATTGAGAACCCAGAAACAAATCTACACACCTACAATGAAC 2139
                               i          ii       i   i i i   ii  iii v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_76048573_7   2140 TCATTTTTGACAAAAGTGGCAAGGACATACACTGGAAAAAATACAGTCTC 2189
                          v     i     ii   v    iv   v  v   ii   iv i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_76048573_7   2190 TTCAATAAAAGCTGTTAGGAAAACTGCATATCCATTTGCAGAAGAATGAA 2239
                              i   v v  i i   v     v   ?   iv    i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_76048573_7   2240 ACTAGACCCCTATCTATCTATATATACAAAAATCAAATCAAAGTTGATTG 2289
                         ii i        i  vv vvi            i  v     i v   ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_76048573_7   2290 ACAACTTAAATCTAAGACCTCAAATTATGAAACTACTACAAGAAAACATT 2339
                         ?vi  i     v     v  v   i   i     vi  v          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_76048573_7   2340 GTAGAAACTCTCCAGGACATTGGTCTAAGCAAAAATTTCTTAAGTA--AT 2387
                          v? v  v   i iv   v    vi  i    vii       ii  -- i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_76048573_7   2388 ACCTGACAAGCACAGTCAACAAAAGCAAAAATGGACAAATGGGATCACAT 2437
                            -- v       iv         v      i  i    v   iiv   
  L1M4_orf2#LINE/    600 ACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_76048573_7   2438 CAA-GTTAAAAAGTCCTCTGCACAGAAAAGGAAAAAGTTCACAAAGTGAA 2486
                            -i       -- i i  ii vvv      v vvi iv v        
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_76048573_7   2487 GAGACAACCCATAGAATGGGAGAAAATACTTGCAAACTACACATCTGACA 2536
                         i          i                i       ii i i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_76048573_7   2537 AGGAATTAATAACTAGAATATATAAGGAGTTCAAGCAACTCTCTACGAAA 2586
                            i i vi  v i           i  ii  vvi      vv  vv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_76048573_7   2587 AAAAATCTAATAATCTGATTTTCTAAAAATTGGCAAAAGATTTGAATAGA 2636
                           i -- v     i ii   ---?      v      i            
  L1M4_orf2#LINE/    796 AAGA--CAAATAACCCAATT---WAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_76048573_7   2637 CATTTCTCAAAAGAAGACATACAAATGACAAATAGGCATATGAAAAGATG 2686
                                 v        i         i v    i   i           
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_76048573_7   2687 CTCAATATCATTGATATT 2704
                              i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (139 / 81)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2802 26.81 2.53 0.58  chr2_76076174_76078371.rev      826  1694 (504)    L1M4_orf2#LINE/L1        1   886 (22)  

  chr2_76076174_7    826 TGGAGAAATATTCCATGCTCATGGATTGGAAGAATCAATATTATTAAAAT 875
                             i i    i     i               v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76076174_7    876 GGCCATACTGCCAAAAGTCATCTACAGATTCAACACTATTCCTATCAAAC 925
                            v     v  v   v v               i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76076174_7    926 TACCAGCATCATTGTTCACAGAATTAGAAAAAACT-ATTCTAAAATTCTT 974
                          v     vv v  v  ii     v v  v  i-  -  i         v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_76076174_7    975 ATGGAACCAAAAATGAGCCCAAATTGCCAAAGCCATCCTAAGCAAAAAAG 1024
                               viiv  iv  v  vi   v      i v   i i i-   i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAG 198

  chr2_76076174_7   1025 AACAAAGCCAGAGG-CATACATTACCCACTT--AAAACTATAGCATAAAG 1071
                                iii    - vi   i v    v  --      -  vi i    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_76076174_7   1072 CTACAGTAACGAAAACAGCATGGTACTGATACAACAACAGATACACAGAT 1121
                                  iv  i    ii        ii i  vi i   i i i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_76076174_7   1122 GAAGGGAACAGGTTAGAGAACCCGGAAATAAACT-GCACTTCTACAACCA 1170
                         v  v    i  iv v    ii  i         i-ii  v i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_76076174_7   1171 TCTGATCTTTGACAAAGTCAACAAAAATAAGCAATGGGGAAAAGACTTCC 1220
                         vi    i  i     i viiv   i vi vv           ii ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_76076174_7   1221 TATTCAATACATGGTGCTGGGATAGCTGGCTAGCCATATGCAGAAATATG 1270
                          v     i v            i i    v  ?   i     i  iv   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_76076174_7   1271 AAAGTGGACTCCTACCTTTCACCATATACAAAAATTAATTCAAGATGGAT 1320
                           iv     i       iv                   i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_76076174_7   1321 TAAAGATTTAAATGTAAGAACTCAAACTTTAAGAATCCTAGAAGAAAACC 1370
                         i ?   ii           i  v     v   i v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_76076174_7   1371 TAGGAA-ACACCATTCTGGACATTGGCCTTGGAAAAGAATTTATGACTAA 1419
                             ?i- v i -   vv   v    vi v  v  v iv  iv iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_76076174_7   1420 GTCCTCAAAAGCAATTGCAACAAAAACAAAAATTAACAAGTGAGACCTAA 1469
                          v vi        vvv         iv      vi i  i vi   i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_76076174_7   1470 TTAAG-TGAAACAGCTTCTGCACAGCAAAAGAAACTATCAACA------- 1511
                          i  i- v   - i   i  ii vv    i  v        v -------
  L1M4_orf2#LINE/    647 TCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_76076174_7   1512 --GACAACCTACAGAATAAGAGAAAATATTCATAACCTATGCATCTGACA 1559
                         --       i       ii           iii  vii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_76076174_7   1560 ATAGACTAATATCCAAGATCTATGAAGAACCC--A-AACT-AACAAGCAA 1605
                          vi    vi      ii  v   i      i -- -    -  i  vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_76076174_7   1606 AAATCAAATAACCCCCTTAAAAAAGGAATTAAAGACATGAACAGATACAT 1655
                           iv          vv  ?     v iiiv  i  iv    i   i iv 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_76076174_7   1656 CTCAAAAGAAGACATACAAACAGCCAACAA--ACATGAGAA 1694
                            v        i       ii     i  --      i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.02 (16 / 886), avg. gap size = 1.69 (27 / 16)  


2548 26.41 4.71 0.46  chr2_76108484_76113093     3248  4118 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76108484_7   3248 TGGAAACACATCCCATGCTCATGGTTGGGTAGAATCAATATTGTGAAAGT 3297
                               v i        i      v v  v   v i        v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76108484_7   3298 GACCATACTCCC-AAA---------AG---CAACGCAATTCTCATCAAGA 3334
                          i v        -   ---------  ---         i ii     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76108484_7   3335 TACTATCATCATGCTTCACAGAACTATAAAAGC-AATCCTAAAATTCATA 3383
                          v i v vv v vi  ii     v vv v    -i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_76108484_7   3384 AGGAGCCAAAAAAGAGCTTGCATTACCAAGGCAAGACTAAGCAAAAAGAA 3433
                         v   iviiv  ii  v iv v  vi    ii   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_76108484_7   3434 CAAATTTAGAGGCATCACATTATCTGACTTCAAACTATACTACAAGGCTA 3483
                             v  i    vv     i vi ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_76108484_7   3484 TAGTTACCAAAACAGCATGGTACTAGTATGAAAAATAGGCACATAGATCA 3533
                         i   v i   i    ii       i i  -  ii    i  i        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATCA 299

  chr2_76108484_7   3534 ATGGAACAGAATAAAGAACCCAGAAATAAAGCCAAATGCTTACAGCCAAC 3583
                               i     vi   ii           v   v iii   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_76108484_7   3584 TGATACTTGACAAAGCAAACAAAAATAT-AAATCGCAGAAAGGACACCCT 3632
                             vi i     i vviv   i vi  -v   v -i     i i vi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCT 398

  chr2_76108484_7   3633 AATCAACAAATGGTGCTGGGATAATTGGCAAGCCACACGTACACAAATGA 3682
                         vv                   i  i   vv ?     i i v vi     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_76108484_7   3683 AGCTGGATTCTCATCTCTCACCTTATACAAAAATCAACTCAA----GATC 3728
                           i    ii ii i   v    v           i       ----    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_76108484_7   3729 AAAAACTTAAATCTAAGACCCGAAACCATAAAAACTACAGAATATAACAT 3778
                          ? i  i     v     v ii    i      viivi    v v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_76108484_7   3779 TGGAAAAACTCTTCTAGACATCGGCTTAGTCTAAGAGTTCATAACTAAGA 3828
                         v  ?iv  v     vv   v i  v    v v v iv   v  iv  v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_76108484_7   3829 ATCCAAAAGCAAATGCAACAAAACAAACA-TAAATAGTTGGGACCT---- 3873
                         vv         v v         v   v -  i   iv v    i ----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_76108484_7   3874 --AATTAAAAAGTTTCTGCACAGCAACAAAAATAATGAGCAGAATAAGCA 3921
                         --         v   -  ii vv   vii v iv  v iv i i i iv 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_76108484_7   3922 CACAATCCACAGAGTGGGAGAAAATATTTGCAAAGCATGCATCTAA---- 3967
                         v    i       i                    v   ii    i ----
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_76108484_7   3968 GGACTAATACCCAGAATCCACAAGGAACTCAAATAA-TCAAGAA--AAAA 4014
                              vi  i       vi i  i      vv i  -    v  --    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_76108484_7   4015 G-CAAAT--TTCA-TCAAAAAGTGGGCAAAGGACATGAATAGACAATTCT 4060
                          -     --ii  - i?    i           iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_76108484_7   4061 C---AGAAGATATACAAATGGTCAAGAA-CATATGAAAAAAATGCTCAAT 4106
                          ---                 i   v  -  i       i -       i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAAC 896

  chr2_76108484_7   4107 TTCACTAATTAT 4118
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (125 / 101)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.25 (45 / 20)  


1079 27.25 1.16 0.00  chr2_76133863_76136882.rev     1203  1547 (1473)    L1M4_orf2#LINE/L1      560   908 (0)  

  chr2_76133863_7   1203 TTCAGGACATAGGCATGGGCAAACACTTCATGACTAAAACACCAAAAGCA 1252
                            iv   v v  vv i     vvii   v iiv  vi            
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_76133863_7   1253 ATGGCAACAAAAGCCAAAATTGACAAATGAGACCTAATTAAACTAAAGAG 1302
                         vvi          vv     v  i    vi   i v  i   v v  i i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_76133863_7   1303 CTTCTGCACAGCAAAGGATACTATCATCAGAGTGAACAGGCACCCTACAG 1352
                            i  ii vv       i       vv i      v  i  v  i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_76133863_7   1353 AATAGAAGAAATTTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCC 1402
                            i i     v v       vii  vi      i  i  i  vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_76133863_7   1403 AGAATCTACAAGGAACTTAAGCAAATTTACAAGAAAAA---AAACAACCC 1449
                              v  i  i     ivvi   v iv i  v     ---   i     
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_76133863_7   1450 CATCAAAAAGTGGGCAAAGGATACGAACAGACACTTCTCAAAAGGAGACA 1499
                         v  i?    i            vi   i     i     v    i   i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_76133863_7   1500 TTTATGTGGCCAACAAACATATGAAAAAAAGC-CATCATCACTGGTCAC 1547
                          vi vi       i  i  i       i v  -  v     ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (50 / 43)
Gap_init rate = 0.01 (2 / 349), avg. gap size = 2.00 (4 / 2)  


2858 26.85 3.37 1.35  chr2_76163134_76166210     1696  2585 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76163134_7   1696 TGGAACAAATACCACATGCTCATGGAGTGGAAGAATCAATATCATTAAAA 1745
                              - i   i v    i       v       v i     ii    i 
  L1M4_orf2#LINE/      1 TGGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_76163134_7   1746 TGACCATACTGCCCAAAGCAATTTACAGATTCAATGCCATTCGTATCAAA 1795
                           i v     v      vii  i           i  v  i v       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_76163134_7   1796 ATATCAA-TGCCATTTTTTCACAGAAATAGAAAAAAAACT-ATTTTAAAA 1843
                           vi  i-    --     ii       v  v  i---  -  ii     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC--TTTTTTGCAGAAATTGACAAG---CTGATCCTAAAA 144

  chr2_76163134_7   1844 TTCATGCGAAACCAGAAAGTGTCCA-AATAGCCAAAGCAATCCTAAGCAA 1892
                              ii i  viiv  i vii   -          i     i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_76163134_7   1893 AAACAACAAAGCCAAAGGCATCATGTTATTCAACTTCAAACTATACTATA 1942
                         i  v       iiii   vv   iii vii   i      viv     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_76163134_7   1943 AGGCTATAGTAATCAAAACAGCATGGTGCTTGTGCAAAAACAGACACATA 1992
                          i    i         i    ii    i  v iii  ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_76163134_7   1993 AACCAACGGAACAGAACAGAGAACCCTGAAAAAATCCTGCACACCTACAA 2042
                         i i   i    i    iv    ii  v    v  v  iii   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_76163134_7   2043 CTATCTGATCTTTGACAAAGTTGACAAAA-------ATAAGCAAAGGACT 2085
                         ii vi    i  i     i v  v   i -------  ii v    i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_76163134_7   2086 CCCTATTTGATAAATGGTGCCAGTATAACTGGCTAGCCATATGCAAAAGA 2135
                         vi  v  ii i         ii v i      v  ?   i          
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_76163134_7   2136 ATGAAACTGGATCCTTACCTTTTACCATATACAAAAATTAACTCAAGATG 2185
                              ii    i  i     ivi                       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_76163134_7   2186 AGCTAAAGGTTTAAATGTAAGATCTAAAACTACAAAAATCCTGGAAGAAA 2235
                         iiii ?  iii           v         i    v  i i       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_76163134_7   2236 ATCTAGG---AAATACCCTTCTTGACATCTTT--TTTGGCAAAGCATTCA 2280
                          iv    ---    ---    v    --   v--  v     v vv   v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT---CTTCGTGAC--CTTGGGTTAGGCAATGGTTTCT 589

  chr2_76163134_7   2281 TGGCTAAGTTCCCAAAAGCAGTTGCAATAATAGAAAGTATTGATAAGTTG 2330
                          i v  v viv         vvv    i  v     iv  v     i   
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_76163134_7   2331 GACCTAATTAAA-TGAAAAAGCTATCACTCAGCAAAGAA-ACTATCAACA 2378
                            i v  i   - v     -  v iiiv vv     i -        v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_76163134_7   2379 GAATAAACAGACAACCTACACAATGGGAGAAAATATTTACAAATTATGCA 2428
                         i i i  v        i   v                 i     i  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_76163134_7   2429 TCCAACAAAGGTCTAATATCTGAAATTGTTAAGGAATTT----AAATCTA 2474
                           ii i  i  v  vi    iii   vvv   i   i i----  v  v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_76163134_7   2475 TAAGCAAAAAACAACT---CCATTTAAAAAGTGGGCAAAAGACATGAACA 2521
                            vv    i    v ---   v  ?    i        i  iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_76163134_7   2522 GGCACTTCTTAAAAGAAGGCATACA----GCCAGCAAACATTTAAAAA-- 2565
                          i  i    iv       ii     ----    ii  i  iv i    --
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_76163134_7   2566 TGCTCATTATCACTAAGTGT 2585
                               vi    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (156 / 80)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.33 (42 / 18)  


2832 26.80 2.59 0.45  chr2_76177670_76180204     1156  2043 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_76177670_7   1156 GGAAAAACATCCCATGCTCATGGATTGGGAGAATCAATATCATTAAAATG 1205
                              i i        i           i   v i     ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_76177670_7   1206 AATATACTGCCCAAAGCTATCTACAGATACAATGCAATTTCTATTAAC-T 1254
                         ivv     v      viv          v   i     ii    i  v- 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_76177670_7   1255 ATCAACATAATTCTTCACAGAATTAGAAAAAAAAAACCCTAGAGATAATA 1304
                         vi  i vvvv  i  ii     v v  v  ivvi -i    i iv v   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATA 150

  chr2_76177670_7   1305 TGGAACCTAAAAAGAGCCCA-AATAGCCAAAGCAATCCTAAGCAAAAAGA 1353
                              v- iv  i ii    -          i     i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_76177670_7   1354 ATAAATCTGGAGGTCTCACATTACCTGACTTCAAATTATACTATAAGGCT 1403
                          i   vi      v      i v  ii i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_76177670_7   1404 ATAATAAGCAAAACAACATGGTAGTGGTGTGAAAATTGACACATAGATTA 1453
                          i i   v   i   iii     v   ii i ii  v    i      i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_76177670_7   1454 ATACAACAGAATAGAGAACCCAGAAATAAAGCCTCATACCTAAAACTAAA 1503
                           iv  i     v    ii           v  vi i ii  viiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_76177670_7   1504 TAACCTTTGACAAAATTGATAAAAATATACACTGGGGAAAGGATAACATG 1553
                          i ii  i     iiv  vi  i vi  v  v         i   iiv v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_76177670_7   1554 TTCAATAAATGGTGCTGGTATTATTGGAGACCCATATGCAGAGGAATGAA 1603
                              i            v iv i    v ?   i     i i       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_76177670_7   1604 ACTGGACCCCTAT-TCTCACTATCTACAAAAATTAACTCTAGATGGATTA 1652
                         ii          i-  v   i  v               v i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_76177670_7   1653 AAGACTTAAATGTAAAACCTTAAACCATAAAAGTCCTAGAAGAAAATGTA 1702
                         ?    i         i v  v    i      v  i          ii  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_76177670_7   1703 TGAAAAAACCCTGAGGGACATTGGGCTAGGCAAAGAATTTATAATTAAAT 1752
                         v ?iv   i i v- v   v     i       v iv  iv  iv  viv
  L1M4_orf2#LINE/    550 GGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_76177670_7   1753 CCTCAAAAGGAAATGCAATAAAAACAAAAATAGACAAATAAGACTTAATT 1802
                          vi      v v v    i    iv         i    vi     v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_76177670_7   1803 AAA-TTAAAAA-TATTATGC---AGAGCAAAAAATTAATGGAGTAAA--- 1844
                            -       - v  i   --- i  v v vv  i  vii   i  ---
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_76177670_7   1845 -CAACCTACAGTATTGGAGAAACTGTTTGCAAAATGATGCCTCCAACAAA 1893
                         -     i    v  v       v i        - v  iiv  ii i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATAAG 747

  chr2_76177670_7   1894 GAACTAATATCCAGATTTTATAAGGAACTCATATAACTCAACAAGAGAAA 1943
                          i   vi        v v     i      v  i       i  v i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_76177670_7   1944 --------ACCCCATTAAAAAATGAACAAATAACATGAACAGACATTTTT 1985
                         --------    v   ?       ii    vi iv    i        i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_76177670_7   1986 CAAAAGAAGATATACAAACAGCCAACAA--ACATAAAAA-ATGTTTAACA 2032
                          v                ii     i  --    i    -   i i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_76177670_7   2033 TCACTAATCAT 2043
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (143 / 91)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 1.93 (27 / 14)  


3210 26.76 0.66 0.66  chr2_76229679_76233583.rev     2506  3413 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76229679_7   2506 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCGTGAAAAT 2555
                              ii i  i     i      i v      v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76229679_7   2556 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2605
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76229679_7   2606 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2653
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_76229679_7   2654 TATGGAACCAAAAGAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 2703
                                viiv   i  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_76229679_7   2704 AACAAAGCTGGAGGCATCACGGTACCTGACTTCAAACTATACTACAAGGC 2753
                                i      vv    iv v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_76229679_7   2754 TACAGTAACCAAAACAGCATGGTACT--CATACCAAAACAGAGATATAGA 2801
                                 i   i    ii       --    -- ii i   v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATATAGA 296

  chr2_76229679_7   2802 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 2849
                         i        i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_76229679_7   2850 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 2899
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_76229679_7   2900 CCCTATTTAATAAATGACGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 2949
                         vi  v  i  i     ii       v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_76229679_7   2950 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 2999
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_76229679_7   3000 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 3049
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_76229679_7   3050 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 3099
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_76229679_7   3100 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3149
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_76229679_7   3150 AATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3199
                         v  iv  v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_76229679_7   3200 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 3249
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_76229679_7   3250 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 3299
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_76229679_7   3300 AAAAACAAATAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 3349
                            i           v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_76229679_7   3350 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 3399
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_76229679_7   3400 CCATCACTGGCCAT 3413
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2991 25.57 2.30 3.06  chr2_76235068_76240843     4370  5284 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76235068_7   4370 TGGAAAAACATTCTATGCTCGTGGATTGGAAAAATCAATATTGTTAAAAT 4419
                               i i  i i   i  i          i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76235068_7   4420 GGCCATAGCCTCCAAAGCAAACTACAGATTTAATGCCATTCCTATCAA-- 4467
                            v   vi i     vii v         i  i  v  i        --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76235068_7   4468 -CCTAACAATATAATTTTTCACAGAAAT--ACAAGAAACTATAAAATTTT 4514
                         -  i i -- iiv-     ii       --     ---  i----  ii 
  L1M4_orf2#LINE/    101 TCCCAGC--TGCC-TTTTTTGCAGAAATTGACAAG---CTG----ATCCT 140

  chr2_76235068_7   4515 AAAATTCATATGGAA---CCAAAGACGTTCCCAAATGGCCAAAACAATAC 4561
                                        --- v ii   ---  vi   i           vi
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCT 187

  chr2_76235068_7   4562 TAAGCAAAAAAAACAAAGTTGGAGGCATCCCATTACTTGACTTCAAA-CT 4610
                          i iv  i  i              vv  v  i v iii i      -  
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_76235068_7   4611 ATGTTGTACTATAAGGCTACAGTAACCAAAACAGCATGGTTCTGTTACAA 4660
                         ------     i  i          i   i    ii    v   vi i  
  L1M4_orf2#LINE/    238 ------TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_76235068_7   4661 AAACAGACAAATAGACCAACGGAAGGGAATAGAGAACCCTAAAATAAAGC 4710
                         ii i     v     i   i    vi    v    ii  vi       v 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_76235068_7   4711 CACACATTTATAACTACCTGATCTTTGACAAAGTTGATAAAAATAAGCAG 4760
                           i        iiii vi    i  i     i v  vi  i vi vv  i
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_76235068_7   4761 GGGAGAAAGGATGCTCTATTCAATAAATGGTGCTGGTTTAGCTGGCTAGC 4810
                         v  i     i  iv   v     i            vvi i    v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_76235068_7   4811 CATGTGCAGAAGAATGAAACTGGACCCTTACATTTCATCATATACAAAGA 4860
                           ii    i         ii       i   v iv  i          i 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_76235068_7   4861 ATAACTCAAGAGGAATTAAATATTTAAATGTAAGACCTCAAACTGTAAGA 4910
                         v        i v i  i ? v ii           v  v     i   i 
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_76235068_7   4911 ATCTTAGAAGAAAATGTAGGAA-ACACCACTCTGGACATTGGCCTTGGCA 4959
                         v             ii    ?i- v i -i  vv   v    vi v    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chr2_76235068_7   4960 AATAATTTAT-GTCTACGTCCTCAAAAGCA---GTTGTAAGAAAACCAAA 5005
                          - ii   v -ivv  i v vi        --- ivii  i i  --   
  L1M4_orf2#LINE/    581 A-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA--AAA 627

  chr2_76235068_7   5006 ATTGACAAGTCAGGCCT------AATTAAAGAGCTTCTGCTCAGTAAAGA 5049
                           v  i  i ii i i ------       i -   i  iv vvi    i
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGG 676

  chr2_76235068_7   5050 AAACTATCAATAGCATAAAGAGATAATCTATAGAATGGGAGAAAATATTT 5099
                          v        v ivi i  i   i  i i i                   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_76235068_7   5100 TCAAACTATGCATCTAACAAATGTCTAATATACAGAATCTATAAGGGACT 5149
                         v    ii  ii    i i  iv v  vi   v      v     i i   
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_76235068_7   5150 TAAGCAATTGAAGAAGCAAAAAACTAATAACCCCCTTTAAAAATGGGCAA 5199
                         ivvi   i v  v  vv    i  v        vv  ?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_76235068_7   5200 AAGACATGAACAGACAATTCTCAGAAGAGAAAAGACATGCAAGTGGCCAA 5249
                          i  iv    i     v     vi    ----   i  i   i       
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGA----AGATATACAAATGGCCAA 872

  chr2_76235068_7   5250 GAAACATATGAAAA-ATGCTCCACATCACTAATCAT 5284
                         v  i  i       -      v      ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (149 / 81)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.45 (49 / 20)  


1131 28.76 1.58 1.32  chr2_76241391_76243534.rev      119   497 (1647)    L1M4_orf2#LINE/L1       92   471 (437)  

  chr2_76241391_7    119 CCATTAAACTACCATTGACACTCTTCACAGAATTAGAAAAAAACT-ACTT 167
                          i  i   v v   vivi vi i  ii     v v  v  i--  - iii
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCC 139

  chr2_76241391_7    168 TAAAATTTATATGGAACCGAAAAAGAGCCCATATAGCCAAGACAATCCTA 217
                                i        vi v  ii  v  viv        i      i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_76241391_7    218 AGCAAAAAGAACAAAGCTGGAGGCATCAAGCTACCAGACTTCAAACTACA 267
                          iv  i          i      vv   vi  v  vi i      vivi 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_76241391_7    268 CTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTATAAAAACAGAC 317
                               i          i   i    ii         i    ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_76241391_7    318 ACA--GACCAATGAAACAGAATAGAGAACTCAGAAATAAGACTACACATC 365
                          i --  i     i  i     v    iii         iv i i    i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_76241391_7    366 TACAATCATCTGATCTTCAAAAAACCTTACAAAAATAAGCAACAGGGAAA 415
                           iii   vi    i   i v  ivv vv   i vi vv   ii      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_76241391_7    416 TGAT--TCCATATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATA 463
                         vi  --  -- v  i  i              v      v  ?   i  i
  L1M4_orf2#LINE/    390 GAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_76241391_7    464 CAGAAAATTGAAACTGGACACCCT-CATTAAACCA 497
                           i  i v    ii     -    - v i v    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGAC-CCCTACCTCACACCA 471

Transitions / transversions = 1.77 (69 / 39)
Gap_init rate = 0.02 (7 / 380), avg. gap size = 1.57 (11 / 7)  

2268 26.30 2.81 4.55  chr2_76241391_76243534.rev      729  1652 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76241391_7    729 TAAAAATATAGACCATGTTTATGGATTGGAAGA--TGATTATGAAAAGAT 776
                          ii   v   vv       i             -- i  vv  vv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76241391_7    777 GTCAAT-TTTTCCAAATCTGATTTATAGATTTACTGTAATCCCAGTAAAA 825
                          v    -i ii      -    i  i     i vi i      vi v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_76241391_7    826 ATCTCAGCAAACTACTGTATAAATAATGGTAAAATAATTCTAAATATTT- 874
                            i    viv  vi v ii i v v  ii  iv i  i     -   i-
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA-ATTCA 148

  chr2_76241391_7    875 TATGGCATGACAAAAGAACTAGAAGAGTCAAAATATTATTGAA---GACG 921
                              v vvi   ii  v i    v  i     i v v     ---  v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_76241391_7    922 AACTAAG----AGGACCAACATTACCTGATTTCAAGACTTCATATACAGG 967
                            v   ----     iv   i v  ii       i    vv  i v  v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_76241391_7    968 TACAGTAATCAAGACAGTATAGTATTGATGAAAAAATAAGGAAATAGATC 1017
                                           i i   i  iiiv  ii   iiv v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_76241391_7   1018 AATAGAATAGACTAGAGAGAGCCCAGAAATAGATCCACACAAACATAGCC 1067
                            i       v v     --i         i i   i   vvi  i i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAG--TCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_76241391_7   1068 AATTAATATTTGACAGGGG-ACAAAGACAATTAAATGCAGAACAAATAGT 1116
                             i  v  i    i   -i v     v   v    vi   vi      
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_76241391_7   1117 CTTCTCAACAAATGTTTCTTGAATAATTGGATATCCCTATATAAAGCAAA 1166
                            i          v v  v i i  i      ?  vi  ii   --- i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA---AG 443

  chr2_76241391_7   1167 AACAAAAACAAAAAACCAAACAACAAAAAACAAAAATGTAGAAATATACC 1216
                           ii  iviii v--  vv  vv  ---------------------i   
  L1M4_orf2#LINE/    444 AATGAAGTTGGAC--CCCTACCTCA---------------------CACC 470

  chr2_76241391_7   1217 TTATGCAAAAATTAACTCAAAATGGATCATAAAAATAAATGTAAAACACA 1266
                         v   i                        ? i vv         i vvi 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_76241391_7   1267 AAACTAAAAAACTCTAAAAAAAAAAATCACAGGAGAAAATTTAAGTGACT 1316
                               v        v i  i    --  i   ? v    i vv     i
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATCTTCGTGACC 568

  chr2_76241391_7   1317 TTGAGTTGGACTATACATTGTCAGATACAACACCAAA-TCACAATTCTTG 1365
                            i   i i v  ivv  v i     ii        -v     vivvii
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_76241391_7   1366 AAAGAAAAACGAAT-GACTGGTTGGACTTCTTTAAAATTAAAAACTTTCC 1414
                                  ---  -  ivii         v i               --
  L1M4_orf2#LINE/    619 AAAGAAAAA---ATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-- 663

  chr2_76241391_7   1415 TATGC---AAATGATACTGTTAAGAGCAACAAAAAACAAGCCATAGACTG 1461
                          i   ---   v  i   i i    ivivv    i    v   i   v  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_76241391_7   1462 AAGGAAAATATTGGTGAAACACATATCTGGGAAAATAAG---CTT----C 1504
                         iii         v ii  v  i       -----     ---   ---- 
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTG-----ATAAGGGACTTGTATC 758

  chr2_76241391_7   1505 CAGAATA-GCAAAGAACTCTTAAACCTCAACAATAAGAAAACAAATGCCC 1553
                                -ii            v v     i     i  i      iv  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_76241391_7   1554 TAATTTAAAAATGGGTAAAATATCTAAAAGGATATAGCATTATAAAA-AT 1602
                         i    ?         i   iv  i i  vi  i  vv vii v i  -  
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_76241391_7   1603 ATATAGACAAAAATTAAGTATAGAAAAAGATTTGTAACATTATTTCTATT 1652
                            i i iiivv v    i i vi       vivi     i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.96 (68 / 23)  


3970 16.30 2.17 3.26  chr2_76284544_76286363      501  1328 (492)    L1M4_orf2#LINE/L1       90   908 (0)  

  chr2_76284544_7    501 CCCTATCAAA-TCCAAGCTGAATTCTTTGTAGAAAGTGACAATTTGATTT 549
                                   -   v     vv  i    i     v      vi    ii
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_76284544_7    550 CAAAATTCAAATGGAAATTCAAGGGAGCCAGAATAGCCAGAACAATCTTG 599
                         i        v        v       v            i          
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_76284544_7    600 ATAAATAAGAACAAAGTTGAAAGACTCAC--TTCCTGATTTCAAAACTTT 647
                          v   v             i i       --    ii            v
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_76284544_7    648 TCACAAAACTACAGTAAACAAAATGGTGTGGCACTGGCATAAAGCTAGAT 697
                         ii     i         v   i ii      i          i v    i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_76284544_7    698 GGATAGATCAGTGGAATAAAATTGAGAGTCTAAAATCAAACCCTCACAAT 747
                         iv        i       i           i i  vi      vi   v 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_76284544_7    748 TATAGCAGTCACCTATAGATTACAGTATGTTGATCTTTAACAAAGACACC 797
                            i ---   -----------------i     i  ii    i iii  
  L1M4_orf2#LINE/    340 TATGG---TCA-----------------ATTGATTTTCGACAAGGGTGCC 369

  chr2_76284544_7    798 AAAATCCATCAATAGGGAAA---T-GTATTTTCAATGAATGATGCTGGGA 843
                           i i vv     i      --- -  v       ii    i        
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_76284544_7    844 CAACTAGATATCCACATGCAAAAGAATGAA-TTGTGTCTCTGCCATATTC 892
                              i    ?                   -   vii i  i  vi iv 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_76284544_7    893 CACATACAAAAATGAACTCCAAATGGATAAAATAAGTAAATGTAAGAGCT 942
                           i          v     v        v ? v vv              
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_76284544_7    943 AAAACTGTAAACCTCTTATAAGAAAACATAGACGTAAATCTGCATGACAT 992
                               i    v      v            i?        v i    v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_76284544_7    993 TGGATTAGGCAAAGTTTTCTCAGATATGACACCTACAGCACAAGCAACAA 1042
                            i        v v     i            v v              
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_76284544_7   1043 AAGAAAAAATAGAAAAACTGGAAATCATCAAAATTTAAAACTTTTGAGCT 1092
                                      v   i    vv           v          v   
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_76284544_7   1093 TTAAATGGCACCCTCAAGAAAGTGAAAAGACAACTCACAACATAGGA--A 1140
                          i   v i   iv                     i    iv  i   -- 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_76284544_7   1141 GATATTTGCAAATAATGTATCTGGTAAGGGCCTTGTATCAAGAATATATA 1190
                         i            v  i      i      v        v          
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_76284544_7   1191 AAAAATTCAATAACTCTATAACTCATTAGTAAGAAGATAAA----CCAAG 1236
                           i  i  -------i  i      v  i   i    i   ----    v
  L1M4_orf2#LINE/    770 AAGAACTC-------TTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_76284544_7   1237 TGAAAAATGGGCAAAGGATCTGAATAGACAGT-CTCTAAAGA---TATAC 1282
                          ?                 i          v -   i     ---     
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_76284544_7   1283 AAATGGCTAATAAACATGTGAAAAGATATTCAACATCATTACTCAT 1328
                                i     i  ii         ii         ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (80 / 51)
Gap_init rate = 0.01 (12 / 819), avg. gap size = 3.75 (45 / 12)  


 408 28.81 9.60 0.56  chr2_76302418_76304015.rev        1   177 (1421)    L1M4_orf2#LINE/L1       25   217 (691)  

  chr2_76302418_7      1 ACTAGAAAAACTAATATTATAAAAATATC--TATTT---AAACATATCTG 45
                          i i   i vi       i v  i  iv --  i i---   ivv    i
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr2_76302418_7     46 TAGATATTAT---ATTAATGTAAAAATT---ACTGTGTTTTTGGTAGAAA 89
                         i    viv i---  ivv i v     i---i   iv     v i     
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr2_76302418_7     90 TTGATGAGTTGATTTTAAAATTTATATGGAAATACAAAGGGGCAGGAATA 139
                             ii  i    ii       i          i   i  iv vi     
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr2_76302418_7    140 GGCATGACGACTCTTGAG------GAACAAAGTTGGGGGACTTA 177
                          v  vi  i -      i------            i     i 
  L1M4_orf2#LINE/    175 GCCAAAACAA-TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

Transitions / transversions = 2.19 (35 / 16)
Gap_init rate = 0.03 (6 / 193), avg. gap size = 3.00 (18 / 6)  

 737 30.82 7.54 4.10  chr2_76302418_76304015.rev      501  1110 (488)    L1M4_orf2#LINE/L1      278   908 (0)  

  chr2_76302418_7    501 ACAGGGACAGATAAATAAATCAAAATAGCAGAATAGTGAGTCATAAAGTA 550
                          i i   i   i v   i     viv ii     v v     vvi  i  
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_76302418_7    551 GATCATTCATAGTATTCATTTATTGTCATTTCATTTGTAAGAAAGGTACT 600
                         i i ---    -----       v    v  v    vii v  i   i i
  L1M4_orf2#LINE/    328 AACC---CATA-----CATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_76302418_7    601 GTAGA--A--CAGTGAAAATAGGACAATCTTTTTATTAAATTGTGCTCCA 646
                         i-   -- --  i  iii v  i i i      i vi    v     vvi
  L1M4_orf2#LINE/    370 A-AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_76302418_7    647 TCTGCTGGATTGGAAAAAAAAAAGGAAAAAGGAAAAAAAGCTAGACCCTT 696
                         v vi      ------ ?vv v v v     --  vi   i i     i 
  L1M4_orf2#LINE/    419 ACAACTGGAT------AKCCACATGCAAAAG--AATGAAGTTGGACCCCT 460

  chr2_76302418_7    697 GTCTCATACCATACATGTAATTCAATTTCAGGTTGACTG-GGA--TAAAA 743
                         ii    i      i iiv  v i  i iv ii v  iii-i  --    -
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA- 509

  chr2_76302418_7    744 TTGCAGAAG--AAAACAATATGTTTCTAGGAAATAAA---AGGAAAATAT 788
                         -  i ii  --     v   vivi   vi   iv   ---   ?iv v  
  L1M4_orf2#LINE/    510 -TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_76302418_7    789 ATTTATACATTTTCGATGAACAAATA-TTTGTTA------ACA------G 825
                         v  ii i- ii  v i v ivv   i-   v   ------   ------ 
  L1M4_orf2#LINE/    559 CTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_76302418_7    826 CATTAACCATTAAGAAAAAGATTAATCAACTAGG----AT--ACATTAAA 869
                           iv i v iv  ii    i  vi  v  i i i----  -- v      
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_76302418_7    870 AATT-----------AAGAGC-CCATTAGGAAAATCAAAAGGCAAAACAT 907
                           i -----------   ii - i  i i    i v     i   vv  i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_76302418_7    908 CAAATGGAAGAAGATATTTGCAATACACATAGTTGACAAAAGCCTCAAA- 956
                         vi     i    i          vv  i   vi   i  ii v  iiv -
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_76302418_7    957 CCAGAATCTATAAAGAACTCCTGTAAGTTAACAAGACCAAGAAAAATAAC 1006
                                v            i ii  v i  i  v vv    v       
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_76302418_7   1007 CCAGTAGAAAAAAATGGGCAAAGAGATTTTTATTAGCAATTTTACAAAAG 1056
                            i v--?              -     vv  -  vv    iv v    
  L1M4_orf2#LINE/    808 CCAATT--WAAAAATGGGCAAAG-GATTTGAAT-AGACATTTCTCCAAAG 853

  chr2_76302418_7   1057 AAGAAATCCAAAAGACTGCTGGAGTGGA--AAAGGGTGCTCAACCTTATT 1104
                             v  v    v i iiv i-  iiv --   i i        v i ??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATA-AGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_76302418_7   1105 AGTTAT 1110
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.43 (109 / 76)
Gap_init rate = 0.04 (26 / 631), avg. gap size = 2.73 (71 / 26)  


2557 25.07 3.72 0.55  chr2_76316778_76318485.rev      491  1216 (492)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr2_76316778_7    491 AAAGGATCTA-------CAAAACAACCT-GAAAA-------CAAAGATGG 525
                           i   i i -------        i  -     -------     v   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_76316778_7    526 AGGCATCATACTACCTGACTTCAAATTATACTATAAAGCTATAATACCCA 575
                            vv   i   v  ii i      viv     i       i i  vi  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_76316778_7    576 AAACAGCATGTTACTGTCATAAAAGCAGATACATAGACCAATGGAACAGA 625
                          i    ii  v     v     iiii   i i     i        i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_76316778_7    626 ATAGAGAGCACAGAAATAAATCCATGCATTTATAGCTAACTGATTTTTGT 675
                           v     iv          i    i       i ii  i       i v
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_76316778_7    676 CAAAGATATTAAGAACATATATTTTGGAAAAGACAGTCTCTTCAATAATT 725
                            i i iii    v   vi v vv     ii i     i     i  v 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_76316778_7    726 GATGCTGGGGAAACTAGATATCCACATGAAGAAAAATGAAACTAGACCC- 774
                          i       iv    i    ?       v i  i      ii i     -
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_76316778_7    775 TATCTCTCACCTTATACAAAAAATCAACTCAAAATGAATAACAGACTTAA 824
                           i   v    v          - i           i  v ?    i   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_76316778_7    825 ATCTAAGACCCAAA-CTATAAAACTACTAGAAGAAAGCAGAGAAGAAACA 873
                           v     v i   -          vi         i  v  i? v  vv
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_76316778_7    874 CTTCATGATATTTGCTGAGGCAAGGAATTTTGGGGTAGGATCTCAAAAAA 923
                             i   iv  v v v      v iv  i vi i  v  ivi     iv
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_76316778_7    924 ACAGGCAATAAAACAAAATATGGACAAATGAGATTGCATCAAGCTAGACA 973
                            i    i    v    v  i  i    vi  i v      iv vi v 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_76316778_7    974 GCTTTTACTCAACAAAGAAAAC-ATCAACAGAGTAAAAAGACAACCCACA 1022
                         i     iiv vv     i v  -     v i   i               
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_76316778_7   1023 GAATGGAAGAAAATATTTCTGAATTATGCATTCAACCTGGGGTTAATATT 1072
                               i           vii   i  ii  iii ivv   ii vi   i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_76316778_7   1073 CGGAATATACAGAAAAATC----AATATAATAGTATAAAAACAAA--AC- 1115
                          i       i i i  v  ----  ivi    i  v   i     --  -
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_76316778_7   1116 -AATTTTGAAAAAATGGGCAAAAAACCTGAATAGACATTTCTGTAAAGGA 1164
                         -    ?---             ii ii               vi    i 
  L1M4_orf2#LINE/    809 CAATTW---AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_76316778_7   1165 GACATACAAATGGCCTATAGGTATACAAAAAC-TGCTCAACATCACTAAT 1213
                           i            v   i i i ii    v-            ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_76316778_7   1214 AAT 1216
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.87 (116 / 62)
Gap_init rate = 0.02 (12 / 749), avg. gap size = 2.58 (31 / 12)  


3066 26.36 1.44 0.89  chr2_76371192_76376357.rev     3772  4674 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76371192_7   3772 TGAAAAGATTTCCCATGTTCATGGACTGGAGGAGTAAGTATTGTTAAATC 3821
                           i      v               i    i  v v i         ivi
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76371192_7   3822 ATCCAT-TTACCCAAAGTGATGTACAGATTCAACAAAACTCCTATCAAAA 3870
                         iv v  -i v      v    v            iv  ii          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76371192_7   3871 TGCCAATGACATTTTTTCTCAGAAATAGAAGAAACACCCTTAAGATTTGT 3920
                          v   iivi v      v-       v  vi iviivi i   i   ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_76371192_7   3921 ATGTAATCACAAAAGACCCCAAAGAACCAAAACAATGTTGAGCAAAAAGG 3970
                            v  vii   ii     vi  v i          v    iv  i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_76371192_7   3971 AGAAAGCTAAAGGCATCACGCTACTTGATGTCAAAGTGTACTA-AAAGTG 4019
                          v    i ii   vv    i  v iii  v     iiv     -    iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_76371192_7   4020 ATAGTAATCAAAACAGCATAATACTGGCATAAAAAAACGGCCACACAGAC 4069
                          i         i    ii ii           ii v -- v  i i   i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA--GACATATAGAT 297

  chr2_76371192_7   4070 CAGTGAAACACAATGGAGAGCCCAGAAATAAATTCATGTATTTACAGTCA 4119
                           i  i  i v   v     i           ii   ii     ii    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_76371192_7   4120 ACTGATTTTTGACAAAGGTGCCAAAAGCAAACAAAAGAGAAAGGAAAATT 4169
                          i       i     i        i v  vv   vi i     i v i i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_76371192_7   4170 TGTTCAATAAATAATAATAGGAAAACTGTATATCCATATGCAGAAGAATA 4219
                          v     i    ii iv i   v     v   ?   i     i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_76371192_7   4220 AAATTAGACTCTTCTTTCTCGCCACATACAAAAATCAACTCAAAAAAGAT 4269
                           i  i   i i vii  v i   i          i         vi   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_76371192_7   4270 TA-AGACTTAAATATATTATCCAAAATTATAAA-CTTCTAGAAGAAAATA 4317
                         i -    i     i  vv v i    i      -  ii          i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_76371192_7   4318 TAAAGG-AAATGTTTTATGACATTGGTTTGGGCAATAATGTTTTA--TTT 4364
                           ii? -    -i  ii    v    v  i      ii v i   -- v 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_76371192_7   4365 GGCCTCAAAA-TA-AAGTCAAATGAAGCAAAAATAGACAAATGAGATTAT 4412
                          i vi     -i -   -   vvi   v         i    vi  i vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_76371192_7   4413 ATCAAACTAAAAAGCTTCGACACAGCAAAGGAAAGTAACAG---AGTGAA 4459
                               v v    i   iviii vv       v v  v  i---      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_76371192_7   4460 GAGACAACATACTGAAAGGGAGAAAGTATTTGTAAACCATACTCCTGAGA 4509
                         i       vi  v   v        i      i   i    ivi    v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_76371192_7   4510 AGG-AGTTGACTTCAAAATTTATAAGGAACTTAAACAACTCAATATCAAG 4558
                            - v   vv i  i   v     i     ivv           vi  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_76371192_7   4559 AAAACAAATAACCCTACTAAAAAAAAATGGGCAAAAGACCTAAACAGGCA 4608
                           i           v i ?     ---        i  ii i  i  i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAA---TGGGCAAAGGATTTGAATAGACA 842

  chr2_76371192_7   4609 TTTCTCAAAAGAAGACATACAATTGAGCAACAGGTATATGAAAATATACT 4658
                               v        i      v  iv   i i i i       v  i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_76371192_7   4659 AAACATCACTAATCAT 4674
                         v       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (149 / 86)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.40 (21 / 15)  


2835 26.19 3.51 0.57  chr2_76381752_76385677.rev     2553  3434 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76381752_7   2553 TGGAAAGATATTCCATGGTCATGAATTGGAAGAACTAATATTGTTAAAAT 2602
                                    i     v     i         vi            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76381752_7   2603 GACCATACTACTTAAAGCAATATAAAGATTCAATGTAACGCCTATCAAAA 2652
                          i v     v ii   vii  v  v        i i  iv          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76381752_7   2653 TACCAATGACATTCTTCACAGAAACAAAAAAA---ATCCTAAAATTTGCA 2699
                          v   iivi v  i  ii      ivi v  i---           iii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_76381752_7   2700 TGGAACCATAAAAGATTTCAAATAGTCAAAGTAATTCTTGGCACA-AACA 2748
                              viii  ii  iiivi     i    ii   -    iv v -  v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGA 199

  chr2_76381752_7   2749 ACAAAGTTCAGGGCAC-CATACTAACACA--TTCAAAATATACTATAAAT 2795
                                 vii  -  -  i   vv -  --       iv     i   v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCC-CAATTTCAAAACTTACTACAAAG 247

  chr2_76381752_7   2796 CTATAATAACTAAAACAGCATGGTACTAAGATAAAAAGAAACACAAACAC 2845
                            i i   ii  i    ii       iiv    ii v i   i v v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_76381752_7   2846 CAATGGAGCAGAATAGATAACCCAGAAATAAATCCACAGTTTTATAGCTA 2895
                                ii     v  v ii           i   i vv     i ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_76381752_7   2896 ACTCATACTTGACAAGGGTGCCAAGAACATT----GGTAAAAAGACAGTG 2941
                          i v  vi i                v    ----  vi   ii i   v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_76381752_7   2942 TTTTTAATAAATAGTGTGGAGAAAACTGGATATTCATATGCAGAAGAATA 2991
                             i  i    i   iv i  v         ?i  i     i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_76381752_7   2992 AAACCAGGCTCCTATCTCTCATCTCATACAAAAATCAACCCAAAATTGAC 3041
                           iiii i i    i   v  i vi          i   i      v  i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_76381752_7   3042 TAAAGACTGAAATGTAAGGCCAAAAACCATAAAGCAACCAGATAAAAACA 3091
                         i ?    iv         iv v     i     i vvii   vi      
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_76381752_7   3092 TAGGAG-AAATGCTTTAGGACATTGGTCTAGGCAAAGATTTTTATGACTA 3140
                             ? -    -   iiv   v    vi       v i   i vv  -  
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TA 595

  chr2_76381752_7   3141 AGGTGTCAAACTCATAGGCAAAATAACTAAAAATATATAAATGTGTCTAC 3190
                         v iiii    vv  i i    v v  vv       v      vv v  v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_76381752_7   3191 ATTAAA-CTAAAAA-------GC---AAACGAAGCAATCAAGACAGTAAA 3229
                           i   -i      -------  ---   v  vi v       v   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_76381752_7   3230 TAGAAAACCTGTAGAATGGGACAAAATATTTGCAAACTATTCATCTGATA 3279
                         v   v    iii         v              ii  vi        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_76381752_7   3280 AGATAATAATATCCAGAATATATGA-GAAATAAAACAACTCAATAATAAA 3328
                           iv v vi              i -   v vvv                
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_76381752_7   3329 AA-----AT--TCTGGTGAAAACATGGACAAAGGGTCTGAATAGACATGT 3371
                           -----  --i iii v?   v    i      i i           v 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_76381752_7   3372 CTCAAAAAAAGACATACAAATTGTCAACAAATATATGAAAGAATGCTTAA 3421
                            v   i    i        v i   i  ii i      ii     i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_76381752_7   3422 CATCACTAATCAT 3434
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (142 / 85)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


2206 25.64 9.52 1.59  chr2_76459425_76461765.rev     1031  1849 (492)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr2_76459425_7   1031 ATTGAAAGACTCAGTACTGCTAAGATATCTATTCTCCTTAAATTGATATA 1080
                             i      i i  i  i      iv v  v    ii        v  
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr2_76459425_7   1081 TAGATTCAATGCAATCACTCTCAAAACTCCAGGAGGCTTTCTTGAAGAAA 1130
                         i        i      v  v      ii    vv v    i   v     
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr2_76459425_7   1131 A-GACACACTGATTCTATAATTTATGTAAAAATTTAAGA-ATATAGGATA 1178
                         v-    vi     i   v    i  i ii    vi   i- ivi  i   
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr2_76459425_7   1179 GTCAAA-TAATCTTTAAAAAGAGAAACAAAGTTGGAGGACTCCCACTGTC 1227
                          i    -i      v       ii                  v    vi 
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr2_76459425_7   1228 TACATTCAAGATTTACTATAAAGCTATCATAATCAGGACTGTGTGGTGTT 1277
                         i vv     i i      i       ivi      i   v       ii 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr2_76459425_7   1278 GACATTAGAATAGACA-ATTG--TAA--GAATAGAATAAAGAGTCTAGAA 1322
                          i   v  i       -  v --i  --         vi      i    
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr2_76459425_7   1323 ATAGACC-------TCCTGTTCAAATGAATTTCAGCAAAGGCACCAAGTA 1365
                            i   ------- iv  v    v   v    ii   i  ii     vv
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_76459425_7   1366 AATTCAATAAGGAAAGGAAAGTCTTTTAAACAAATGGTGATTTGACAACT 1415
                         v       ii      i v        v           v vv       
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_76459425_7   1416 GAGTAAATATATAAGGGAAAAAAAACAAGTCTCAATTCCTAC-TCTCAGT 1464
                          ii  ?vi i  --- v    i  vv    - vi ii     -  v  vi
  L1M4_orf2#LINE/    425 GGATAKCCACAT---GCAAAAGAATGAAGT-TGGACCCCTACCTCACACC 470

  chr2_76459425_7   1465 ATACACAGAAAATAATTTGAGATATAATATCCATATAAACAGGAAA-CTC 1513
                            i   i   v   i ii i  iv vi ?vv iv    iivi i -  v
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_76459425_7   1514 AGACCATAAAGTTGTTAGAAGAAAACATAGTAGAACATCTTTCTGACCTT 1563
                          i  i     ii v                v? v v     iv       
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_76459425_7   1564 GGAGTAG---ATAGCTTACCTAAAGAGGATATGAAACATACTGTCCATAA 1610
                           iv   ---  i i  - i  i v v  i iv   vii  viv v i  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTT-CTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_76459425_7   1611 AA------------AAATTGGACTTCATAAAAAATTAAAATACTCT---G 1645
                           ------------              v    -      -   i --- 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAA-TTAAAA-ACTTTTGTG 667

  chr2_76459425_7   1646 CTCATCAAAATATATTGTTAAGTAAATTAATACACAAACTACAAAATGAG 1695
                           --     iv i i i i   v  i v  v v    v i   i    i 
  L1M4_orf2#LINE/    668 CT--TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_76459425_7   1696 AGACAACATTTGCA----------CT--------ACATGTAT-----ACA 1722
                            v  i       ----------  --------  v     ----- i 
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_76459425_7   1723 TATGG----CCCTGA-------------AAAAGGCAAAAAA---AAGGTG 1752
                            ii---- i  v -------------     i    v  ---  -- v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA--TT 813

  chr2_76459425_7   1753 AAAAATTAAGTGAAAGAATTGAGCAGACAGTTTTTTAAAAAGAAGATATG 1802
                         ?    v ii ii  i  v    ii     v  i ii   --        i
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA--GAAGATATA 861

  chr2_76459425_7   1803 CGAATGACCAACAAGTTCATGAAAAGATAATAAACATCACTAGTCAT 1849
                          i    i    i   iv           iv v       ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (123 / 83)
Gap_init rate = 0.03 (26 / 884), avg. gap size = 3.50 (91 / 26)  


3239 26.54 0.66 0.66  chr2_76484198_76490609.rev     5013  5920 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76484198_7   5013 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTCAAAAT 5062
                              ii i  i     i      i v      v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76484198_7   5063 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5112
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76484198_7   5113 TACCAA-TGCCTTTCT-GCACAGAATTGGAAAAAACT-ACTTTAAAGTTC 5159
                          v   i-       i -   v -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_76484198_7   5160 ATACGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAT 5209
                            i    viiv  ii  v  v v  vi    iv     i i ivv i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_76484198_7   5210 GAACAAGGCTGGAGGCATCACACTACCTGACTTCAAATTACACTACAAGG 5259
                               i i      vv       v  ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_76484198_7   5260 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5309
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_76484198_7   5310 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAAC 5357
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_76484198_7   5358 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAGGGATTC 5407
                         i vi    i  i     ivv  vv  i v  vv          i i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_76484198_7   5408 CCTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5457
                         i  v  i                 v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_76484198_7   5458 TGAAATTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5507
                             i     i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_76484198_7   5508 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAA 5557
                           i ?    i    i  v   v       i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_76484198_7   5558 CCTAGGCA-ATACCATTCAGGACATAGGCATGGTCAAGGACTTCATGTCT 5606
                          v    ?i- v i -   iv   v v  vv i v   v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_76484198_7   5607 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5656
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_76484198_7   5657 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5706
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_76484198_7   5707 ACAGGCAACCTACAAAATGGGAGAAAACTTTCGCAACCTACTCATCTGAC 5756
                          v  i     i   i            iv  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_76484198_7   5757 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5806
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_76484198_7   5807 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5856
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_76484198_7   5857 TCTCAAAAGAAGACATTTATGCAGCTGAAAGACACATGAAAAAATGGTCA 5906
                             v        i  vi viii  ii v ii          i   v   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_76484198_7   5907 CCGTCACTGGCCAT 5920
                         v i   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1826 22.31 12.51 5.31  chr2_76588778_76591581     1473  2319 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76588778_7   1473 TAGAAAAATATACTGTGTTTATTAATTGGAACACTTAATATTGCTAAAAT 1522
                          i    i    v ii    i  vi       v           i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76588778_7   1523 GTTAGTTCTTTCCATATTAACCTATAAAGTTAACAGAATCCA-ATCAAAA 1571
                          vi i v  ii   v   i i   i i v i   iv     v-       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76588778_7   1572 TCACAGAAAACTATTTTATAGATAATGACAAGCTGATTTTAAAATCTATA 1621
                           v   vviv  v    ii   v v            ii      ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_76588778_7   1622 TAAAAAGACAAA------AGAA---CTGAAATACTTTTGAACAAGAAGAC 1662
                          ii   vi   i------    --- ii   i v i     v       v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_76588778_7   1663 CAAGATCAGAAGGCTAACAATATGTAATTTCAAAACTTACTATAAAACTA 1712
                            ii ii  i i  v   v vivi                 i   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_76588778_7   1713 CAGCAATCAAAAC----TGGTA-TGTTTGAAGAAATAGTCACATAGATTA 1757
                            i      i  ----     -  vivv   i -   v  i      i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCA 299

  chr2_76588778_7   1758 ATAAAAGAGAACAGTAAGCACGGAG-TAAGACCCATATGCATTGTATG-- 1804
                           ii  v    iv vi  iv i  i-   -       --    -    --
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATA--CATT-TATGGT 345

  chr2_76588778_7   1805 -AGATAATATTTGGCAAAATTGCAAAGAT------------AAAGGATAC 1841
                         - iv i  v  i i   iiv   v    i------------    i   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_76588778_7   1842 TC----AAACAAATGGTGCTAGAACA-TT--------------AAAAGAA 1872
                           ----v             i i   -i --------------       
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_76588778_7   1873 --AAGTTGAACTTTGCCCTTTAACTTCAAACATTAAACAATAATCAACTC 1920
                         --      i  ----    ---  i   v  vv  v    v   i     
  L1M4_orf2#LINE/    446 TGAAGTTGGAC----CCCT---ACCTCACACCATATACAAAAATTAACTC 488

  chr2_76588778_7   1921 AAATTGAATCATAAATCTAAA-GTAAGATTTAAAATTATAAAACTATTGG 1969
                            v  i    ? i i     -      vi     i         v  i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_76588778_7   1970 ATAAAAACATAGAAGAAAATCT--GTGAGTCATTGTATTAGGCAAAGTTT 2017
                          vi         i? v      --    -- v   vi        v v  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGA--CCTTGGGTTAGGCAATGGTT 586

  chr2_76588778_7   2018 TCATAGATATGACACCCAAAACACATTCCATATAATCAAAAAATTAAGCA 2067
                           v             v   i    --------- v   v   -------
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACA---------AGCAACAAA------- 620

  chr2_76588778_7   2068 TGCCCCCTAAAACAAAATATTGAAAAATATAAGGTCTTCAAAACTAAGAA 2117
                         -------- i  -      --  v    vvi vv  v      i   -- 
  L1M4_orf2#LINE/    621 --------AGAA-AAAATA--GATAAATTGGACTTCATCAAAATTAA--A 657

  chr2_76588778_7   2118 AACTTCT---TTTTGAAAGATGCTGCTCAGAGAA-GAAAAACCAAGCTAC 2163
                              i ---i  ii  i  ii  iiiv   i i-     iv   v i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_76588778_7   2164 AAA----GAGAATATATATGCAAAT------TCT--------------AT 2189
                          i ----     v    v       ------   --------------  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_76588778_7   2190 C-----------AAG-----------CTAAATAATTAAAAAACAAACAGC 2217
                          -----------   -----------  v      v    i     i i 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_76588778_7   2218 T-GATTGGCAAATGGACCAATGGTTTGAACAGACACTTCACCAAAGAAGA 2266
                         i-i   ?iv      i v  v i      i     i   v          
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_76588778_7   2267 TATACAGATGGCAAACTAGCACATGAAAAGATGCTCAAATAGTCAGTAGG 2316
                               i     v  iv                     -i -   ?????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA-CA-TCAZZZZZ 905

  chr2_76588778_7   2317 AAA 2319
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.48 (111 / 75)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 4.19 (151 / 36)  


1979 22.82 5.05 4.44  chr2_76651255_76652899.rev      501  1153 (492)    L1M4_orf2#LINE/L1      252   908 (0)  

  chr2_76651255_7    501 AGTAATCAAAACAGTATGGTATTAATGAAAGAACAAATATATCAACATAA 550
                                  i     i     i iiiiv   i i i i    ------ i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT------AG 295

  chr2_76651255_7    551 AACAGAAAAAACAGAAATG-GA-TCCAAAAATACAAACAGATACA---AT 595
                          v  - vii  i    v  -  -    i     --   vv     ---  
  L1M4_orf2#LINE/    296 ATCA-ATGGAATAGAATTGAGAGTCCAGAAATA--AACCCATACATTTAT 342

  chr2_76651255_7    596 G-TCAACAGATCTTTGACAAAGGAGA-AAGGCAATTCAATGGAAAAAGGA 643
                          -    iv   i  i     i  v v-   i v         ii    i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_76651255_7    644 TTGTCTTTTCAACAAAGAGTGCTGGAATAACTGGATATTTACAAACACAA 693
                          v              vi       i i         ?ii   vi  v  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_76651255_7    694 AAATGAATGTAGACACTGACCTTACATGTTTCACAAAAACTAACTAAAAA 743
                         i      vv i   v iv    i   ivv vi       i     v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_76651255_7    744 TGGACCATTGACCTATATGTTAAATGTAAAACTATAAAACTTCCAGAAGA 793
                             i  ?v      v    v i vv               iii      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_76651255_7    794 TAACGTAGGAGAAAATATAGATGATCTTGGGTTTGGCGATGAGGTTTTAG 843
                         v   i    ? v    v vvi   i        v   i   ivv i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_76651255_7    844 ATACGACACCAAAAGCATGATCCATGAAAGAATAAATGGATGAGTTAGGC 893
                            i             ii v v ii      v    i   i i  i i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_76651255_7    894 T-CATTAAAATTTTAAAAAACAATAACAACAACAGAAAACTGCTCTATGA 942
                          -   i      ---      vv vi--------------    ii -- 
  L1M4_orf2#LINE/    643 TTCATCAAAATT---AAAAACTTTTG--------------TGCTTCA--A 673

  chr2_76651255_7    943 AAGACAGTATTAAGAGA-----AAGA-AAGCCACAGACTGGGGACAAATA 986
                          i    v   i    i -----    -  v       v    iiv     
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_76651255_7    987 TTTGCAAAAGCACATATTTGATAAAGACTTTGTATTTAAAACATA----G 1032
                                 -v  i    i      i ivi      ii i  i   ---- 
  L1M4_orf2#LINE/    724 TTTGCAAA-TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_76651255_7   1033 AACTCTTGAAACTCAACAATAAGAAAGCAA----------TTAAAGATGG 1072
                                iv       i     i  ii   ---------- ?   i    
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_76651255_7   1073 G-AAAAGATCTGAACAGACACCCTACCAAAGAAGATATACAGATGAC--- 1118
                          -   i   i    i     iiiiv                i   i ---
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_76651255_7   1119 -AAACATAGGTAAAGATGTTCAACATCAGATGGCGT 1153
                         -  i  i v v       i         ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (94 / 51)
Gap_init rate = 0.03 (19 / 657), avg. gap size = 3.26 (62 / 19)  


2641 25.50 2.21 4.53  chr2_76720770_76722667.rev      501  1406 (492)    L1M4_orf2#LINE/L1       24   908 (0)  

  chr2_76720770_7    501 GATTGGTATAATTAATATTGTACAAATGTCCACACTGCACAAAACTATCT 550
                               v v v          vv i   v v i   v v    viv    
  L1M4_orf2#LINE/     24 GATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCT 73

  chr2_76720770_7    551 ATAGGTTCAATGACAATTT-TATCAAAATTCCAATGATAATTTTTACAGA 599
                          i  i     i -    ii-         i   iiviivv     i    
  L1M4_orf2#LINE/     74 ACAGATTCAACG-CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chr2_76720770_7    600 CATAGAGAAAACAATCCTAACGT--GTACGGAATGACAAAAGAC------ 641
                         v  v  v  ivii       vi --i  i    vvi   ii   ------
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr2_76720770_7    642 --------ACAATCTTAAGAAATATGAACAAA-CTAGAGGCATTACACAT 682
                         --------        i i   v v       -i i    vv i    v 
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr2_76720770_7    683 CCTGATTTAAAAGTATATTACAAAGCTGTAGTAATCAAAACCCTATGGTA 732
                           ii    v   iiv  i         ii         i  vv i     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_76720770_7    733 TTGCCATAGAAACAGACACATTAAGCCAATGCAACAGAATATCGAGTCTG 782
                         i  v    iii i     i  - iii     v  i     vvv     ii
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATAT-AGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_76720770_7    783 GAAATAAACCTACACATGTACAGCCAACTAATTTTTGGCAAGGATGACAA 832
                                   i i    v  ii i   i i     i i     i  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_76720770_7    833 GAATACACAGTGATGAAAAGATAGTCTTTTTAATAAATGGTGCTGGAGAA 882
                           vi iv  i  iv    ii          i  i            iiv 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_76720770_7    883 ACTGAATATCCATATGCAGAAGAATAAAAGTGTGCCCTTATCTTAAACCG 932
                             i   ?   i     i      i  iv  vi   i  i  i v   i
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_76720770_7    933 TACACAAAAATTAACTCAACATAGATAAAAGACTTAAAGATAAGGCCTAA 982
                           i                v  i   v ?    i    vi    iv    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_76720770_7    983 AACAAACAAACAAAAATCCTGAAAGAAAACATAGGAGAAAATCTCCTTGA 1032
                            v -----i    v  i ii             ? v      i v   
  L1M4_orf2#LINE/    522 AACTA-----TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_76720770_7   1033 TAT-GGGTCTTGGTAGTGATGATTTTGGATATAACACCAAAATCACAGGC 1081
                         iv -    - v  i i  i v- i  i     i         v    i  
  L1M4_orf2#LINE/    567 CCTTGGGT-TAGGCAATGGTT-TCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_76720770_7   1082 AAAAATAACATAAAAAAGCAAAGCAAAACAAACAAATACACAAAAACAAG 1131
                           ------  -   i  -------    i i i    -------------
  L1M4_orf2#LINE/    615 AA------CA-AAAGAA-------AAAATAGATAAAT------------- 637

  chr2_76720770_7   1132 TGAGGCTACATCAAACTAAAAAGTTTTTACACAGAAAAAAAAAAACAGTC 1181
                           - i  v       v v    ii    iii vvv   ii v -- vi  
  L1M4_orf2#LINE/    638 TG-GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA--CTATC 684

  chr2_76720770_7   1182 AATAAAATGGAAAGGCTATCTATAAAATGGGAGAAAATATTTGCAAAGCA 1231
                           v   i  i    i v i i i i                      v  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_76720770_7   1232 TATATCTGTTAAAGGG-TTAAATCCAAAATATATAGGCATCTCATAAAAC 1280
                                 v   i  i-  iv     i        iiv v   v  v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_76720770_7   1281 TCAACAGTACACAAAACAAAGTAACCCAAATAAAAAGTAGGCAAAGAACC 1330
                             i i  v -  i     -        v ?    i i       i ii
  L1M4_orf2#LINE/    785 TCAATAATAAA-AAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_76720770_7   1331 TCATGAGACATTTTTCCATAGACGACTTAAAAATGGCGAACAGGTATACT 1380
                          v vv        i    v   v  iv  v       v  i i i i iv
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_76720770_7   1381 AAAAGGTATTCAGTATCACTAATCAT 1406
                              i ii   ii    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (143 / 84)
Gap_init rate = 0.02 (19 / 885), avg. gap size = 3.21 (61 / 19)  


3009 23.64 1.77 0.00  chr2_76733944_76735669      501  1236 (490)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr2_76733944_7    501 AAGAGACCTCAAATAGACAAAGCAATCGTGAGCAAAAAGAACAAAGCTGG 550
                            i    ivi     v    i     v   iv  i          i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_76733944_7    551 AGGAATCAAAATTTCTAACCACAAAATATGATATAAAGCTGGAGTAACCA 600
                             v   v v  i i  iiv     iv iv  i      iv     i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_76733944_7    601 AAAGAGTATGGTACTGGCCTAAG-----ACACATAGACCAATGGAAAAGA 645
                          i v   i          v    -----   i     i        v   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_76733944_7    646 ACTGAGAAACCAGAAATACATTCACACATTTATGTTCAACTAATTTTTGA 695
                          i     iv         v ii  i         v    i i     i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_76733944_7    696 CAAAGTTGCCAGGAGTGCACAATGGGAAAAAAACAATCTCTTCAACAAAT 745
                            i v     i  viiiv       i   i  i i   i          
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_76733944_7    746 GGTGTTAAAACAACTGGATATCCACATCCAGAAGAATGAACTTAAACCCT 795
                             i iii           ?      v  i         v  ii    i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_76733944_7    796 TATCTCATGCCACATACAAAACGCAACTCAAAATG-ATTAAAGGCTTAAA 844
                           i    ii   i        vvi           -  i ?  i i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_76733944_7    845 CATAAGGCCTAAA-CTGTAAAACTACTAGAAGAAAATATAGGAGAAAATC 893
                         ii    iv     -  i       vi          i     ? v     
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_76733944_7    894 TCCTTGACATTGGTCTGGGCAATGATTTTTTGAATATGAATCTGAAAGCA 943
                          i v    v    vi i       i   i  ii      vv ii      
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_76733944_7    944 CAAACAACAAAGGCAAAAATAGACAAATGGAATTACAGCAACAAGAAAAC 993
                            i       i v         i    v i i v  v   v vv    v
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_76733944_7    994 CTTCTGCACAGCAAAGAAAACCATCAACAGAGTGAAGAGGCAAAATATGG 1043
                            i  ii vv     i v  i     v i      i  i   vvi ii 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_76733944_7   1044 AATAGGAGAAAATCTTTCTAAACCATACATTTGATAAGGGGTTAGTATCC 1093
                            i         v   vi   i    i  i         ii v      
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_76733944_7   1094 AAAATATATAAAAAACTCAAACAACTCAAAAGTAAGAAAA-----AACAC 1138
                          i          i     vv         v i   i  i -----   v 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_76733944_7   1139 AATT-AGAAATCAGCAAGTGATCTAAATAGATATTTCTCACAAGAAGACA 1187
                             - i    vi    iv   i i      i       vv       i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_76733944_7   1188 TATAAATGGCCAACAGGTATAGGAAAAAATGTTCAATATAACTAATAAT 1236
                           i          i i i i v     i   i    i  v ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (112 / 59)
Gap_init rate = 0.01 (5 / 749), avg. gap size = 2.60 (13 / 5)  


2476 28.24 3.10 1.03  chr2_76757418_76763171.rev     3542  4412 (1342)    L1M4_orf2#LINE/L1        3   891 (17)  

  chr2_76757418_7   3542 GAAAAACATTCCACGCTCATGAATTAGAAGTATTAATATCTTAAAAATGA 3591
                             i i  i   i i     i   i    vv       iv v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_76757418_7   3592 CCATACTACACAAAGCAATCTACAGATTCAACACTATTTCTATCAAACTA 3641
                          v     v v    vii               i v  ii        v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_76757418_7   3642 CCATCT---TTCTTCACATAATTAGAAAGAACT-ATTCTAAAATGTATAT 3687
                            v  ---  i  ii  v  v v  v - i  -  i       vi    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATAT 151

  chr2_76757418_7   3688 GGAAC--CAAAAAACAGTTTGAATAGAAAAAGCAATCTTAAGCAAAAGGA 3735
                             v--   iii  --iiv      vv   i       i iv  i i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_76757418_7   3736 ACAAAGCCAAAGGCATCACATTACCTGACTTCAAACTATACTATAACGCT 3785
                               iiii   vv     i v  ii i      viv     i  v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_76757418_7   3786 CAAGCAACCCAGAGAGCATGGTGCTAGTACAAAAACAGTCACATAGACCA 3835
                         vv  i  i v   v  ii    i  i i i  ii i  v  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_76757418_7   3836 ATGAAACAGAATAGAAAACTCAGAGATAAAACTACAAGCCTAT---CATG 3882
                            i  i     v  i iii    i     v i i viii   ---  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_76757418_7   3883 TGAACTTCAACAAGGCCAACAAAAACAAGCAATGGGGAAAGGACTCTCCA 3932
                            vi   i      viiv   i v  vv            i ivv  iv
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_76757418_7   3933 TTCGGTAAATGATGCTGGGATAACTGGCTAGCAACATGCAGAAGATTGAA 3982
                            iii     i        i      v  ? v       i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_76757418_7   3983 GCTTGACTCCT--CTCATTCACCGTATACAAAAATTAATTAAAAATAGAT 4030
                          i v   i   --    --    i              i v     i   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCA--CACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_76757418_7   4031 CAAAGATTTGAATGTAAGACCTCAAACTA-AAAA-TCCCGGAAGACAACC 4078
                           ?   ii i         v  v      -    -  iii     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_76757418_7   4079 TAGGA--AATTATCTTCTTGGCATCAGCCCTGCCAAAGAATTATTGGCTA 4126
                             ?--  --      v  i v ii viiv v   v iv  v  i v  
  L1M4_orf2#LINE/    548 TAGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_76757418_7   4127 --ACTCCGCAAAAACAATTGCGGCAAAACCAAAAATTGACAAGTGGGACC 4174
                         --  v  iv  iv    --  ii     vv      v  i  i v    i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_76757418_7   4175 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGCAACTATCAA-----TA 4219
                          v  i   v v  i i   i  ii vv    i vv        ----- i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_76757418_7   4220 AACAGACAATTTACAGAATGGGAAAAGATATTCACAAACTATGCATCTGA 4269
                           v      iii           i  i     ii    ii  ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_76757418_7   4270 CAAAGGCTCAATATCCAGAATCTAAAGGAAACTTATATAAACCTACAAGC 4319
                         i  i  viivi          v  v iii    iv  i  vi v i  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_76757418_7   4320 AAAAACCAAATAACCACATTAAAAAATGAGCAAAGGACATGAACAGACAC 4369
                             iv         vv   ?       i        iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_76757418_7   4370 TTCTC---AAAAGACATACAAGCAGCCAACAA--ACATGAACAAATGC 4412
                              --- i    i      iii     i  --       v i    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.02 (17 / 889), avg. gap size = 2.12 (36 / 17)  

1884 23.53 3.24 4.56  chr2_76757418_76763171.rev     4585  5264 (490)    L1M4_orf2#LINE/L1      238   908 (0)  

  chr2_76757418_7   4585 TACTACAAGGCTATAGTATACAAAACAGTATGGTTTGGATATAAAAAGAG 4634
                                 i    i    vv   i     i    viv ii    ii v  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_76757418_7   4635 ACACATAGATCAACGTAAAAGAATAGAGAACCCATAAATAAAGACGCTA- 4683
                            i         i v  v     v    ii   v       vv i-  -
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TAC 336

  chr2_76757418_7   4684 ACTTACAGCCAACAAATCTTTGACAAAGCTGACAAGAACTTACAATGGGG 4733
                          i   ii i   ivi  i  i     i v  v     v v v        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_76757418_7   4734 AAAGAAAA---TATTCCATAAGTGGTGCTGAGGAAATTGTATATCCATAT 4780
                               v --- v   v i  i        i iv  i  v   ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_76757418_7   4781 GCAGAAGAATGACATTAAACCCC-ATCTCTCGCCACATACTAAAATCAAC 4829
                            i        vi  ii     - i   v i   i    v     i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_76757418_7   4830 TAAAAATGGATTA--GACTTACACATAAGACCTGAAACCATAACAATGAT 4877
                          v         i --   i  v ii     v  i    i    v v vv 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_76757418_7   4878 AGAAGAAAACCTAGGGAAAATTCTGCTGGACACTGGTATAGGCAAATAAT 4927
                                   v    ?iv  v   v vv   vi   vv       - ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGT 585

  chr2_76757418_7   4928 TTGT--GAC-TAATACCCTAAAAGCACAGGCAACAAAAAGAGAAATAGAC 4974
                           v --  i- i i   --         i         ii i       i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_76757418_7   4975 AAATGGGAATTAAAAAAAACAAAACAAAACAAAAAAAAACAAAACAGCTT 5024
                             v   v  --------  v--     iv     -----------   
  L1M4_orf2#LINE/    634 AAATTGGACTT--------CAT--CAAAATTAAAAA-----------CTT 662

  chr2_76757418_7   5025 -----CCACACAGGAAAATAATCAACAGAGTAAAGAGACAACTTGTTGAA 5069
                         ----- iv  v    v v  -    v i   i  i       iiiiv   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_76757418_7   5070 TGGGAGAAAATATTTGCTCACTATGTATCCAAGAGGGAATAAATATCCAA 5119
                                          vv ii  i    ii v i  i ivvi      i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_76757418_7   5120 AATATACAAGGAACACC-ACAAC--AGGAAAAAAAAGCCAAATAACCCCA 5166
                               i  i    v i-     -- iv  v      v          v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_76757418_7   5167 TTAAAAAGTGGGCAAAAGACAGAATATGAACAGGCAGTTCTCTAAAGA-- 5214
                           ?    i        i  ----- v    i  i  v     i     --
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGA-----TTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_76757418_7   5215 -CATACAAATGAGCAACAGAAATATGAAAA-ATGCTTAACATGACTAATC 5262
                         -i         iv   i iiv i       -     i     v ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_76757418_7   5263 AT 5264
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.34 (90 / 67)
Gap_init rate = 0.03 (19 / 671), avg. gap size = 2.79 (53 / 19)  


2096 25.57 15.27 0.89  chr2_76787028_76797212.rev     2751  3536 (6649)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_76787028_7   2751 ATTCTATATTCATGGATTAAAAGAGTCAATGTTATTAAGATGTCAGTTCT 2800
                           i i  i          ii    v i   i  i        v  i v  
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_76787028_7   2801 TCCCATCTTGATTTATATATTTAATTTAATCCCAATCAAAGTTTCAAC-A 2849
                         i    vv     i  i v   i  ivi      v      i ii  i -i
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_76787028_7   2850 AGTTATCTGTGGTTAGCAACATACTTATC-TAATGTTTATCTAGAAAGGC 2898
                         vv  v i  ii vv vii   vi  v   -   vi  i  v i    v  
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_76787028_7   2899 AAAATACCGAGAATAACTAACACAATATTATATGAGAAGAACAAAGTTGG 2948
                           iiv   v      i i  v     v  iv vi                
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_76787028_7   2949 AGGACTGACAGTATTCAACTTCAAGATTTATGATAACACTACAGTAAACA 2998
                               v   v vii   i     i i   iv i  vi         v  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_76787028_7   2999 AGGAAGTATGACACTGGT-TAAGTAATGGAGAGACAGATAAATGAAACAG 3047
                           iv   i  ii     i-    -i  i  v v i    v    i  i  
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAG-GATAGACATATAGATCAATGGAATAG 308

  chr2_76787028_7   3048 AACAGAAAGTCTAGAAATAAACCACCACCTATTTA--GTTAACTGATCTT 3095
                           iv  i    i           --  ivi     --  i  i    i  
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCAATTGATTTT 356

  chr2_76787028_7   3096 -------------------------TGGGAAAGGAA-----------ACA 3109
                         -------------------------    i  i   -----------   
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_76787028_7   3110 AA--------------CTTGACATCC------------------------ 3121
                           --------------  v  i ?  ------------------------
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_76787028_7   3122 ------TTCACA---------AAAATTTACTCAAAATGGACTGTAAACCT 3156
                         ------i     ---------      v            iii? i    
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_76787028_7   3157 AAATGTAAAAAACAAAACTTTAAAACTCCTAAAAGTTAACATAGGAGAAA 3206
                                 i ivi      v        i  i   vv        ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_76787028_7   3207 ATAAAAATGATCTTGGGTTTGGTAACAACTTTTTA-------CACCAGAA 3249
                           vvvvi   i        v  i  iiii  i   -------     i  
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_76787028_7   3250 ACGCAATCCATGAAAAAAAAAAAAGATGGATGAACTGGCCTTCATTAAAA 3299
                         i i   v ----  v    i    i  i   i  i   v      i    
  L1M4_orf2#LINE/    607 GCACAAGC----AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_76787028_7   3300 TAAAAAACT---GCTCTGCAAAAGACACTGTCAAGAGAATAAAAAGAAGA 3346
                          v       --- iv  v    i      i      i i i      vi 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_76787028_7   3347 C--AAAGACTTGGAGAAAATATTTGCAAGACATAT---------GGGA-- 3383
                          -- v   v v                 iv     ---------    --
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_76787028_7   3384 TAAATTCAAAATATACAAAGAATTCTTAAAACTCAACAAGAAAA---CCA 3430
                          iv  i  i      i      i     v       i  v    --- v 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_76787028_7   3431 ACAATCTGATTTTAAAATTGGCCAAAGATCTTAACACACACTAAATCAAA 3480
                          i  i ii   ?v     v   v  i   i v  i v   i vvvi    
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_76787028_7   3481 GAAGATATACAGATGGCCAATAAATATACATAAAGATGTTCCACATTCTT 3530
                                    i           ii i iiv       i  v    iv??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_76787028_7   3531 TGACAT 3536
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.63 (122 / 75)
Gap_init rate = 0.02 (18 / 899), avg. gap size = 7.06 (127 / 18)  

3259 27.83 0.22 0.33  chr2_76787028_76797212.rev     8785  9693 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76787028_7   8785 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 8834
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76787028_7   8835 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAAC 8884
                            v     v     iv i  i ii        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76787028_7   8885 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 8932
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_76787028_7   8933 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 8982
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_76787028_7   8983 GAACAAAGCTGGGGGCATCACACTCCCTGACTTCACACTATACTACAAGG 9032
                                 i   i  vv       i  ii i    v viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_76787028_7   9033 CTACAGTAACCAAAACAGCATGCTACTGGTACCAAAACAGAGATATAGAT 9082
                                  i   i    ii  v      i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_76787028_7   9083 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCGCATATCTACAACTA 9132
                                 i    iv   ivii         vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_76787028_7   9133 TCTGATCTTTGACAAATCTGAGGAAAACAAGCAATGGGGAAAGGATTCCC 9182
                         vi    i  i     ivv  vvi i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_76787028_7   9183 TATTTAATAAATGGTGCTGGGGAAACTGGCTAGCCATATGTAGAAAGCTG 9232
                          v  i  i             iv      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_76787028_7   9233 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 9282
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_76787028_7   9283 TAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 9332
                         i ?    i    ii v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_76787028_7   9333 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 9382
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_76787028_7   9383 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCAT 9432
                                     vvi          vv     v  i    v   ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_76787028_7   9433 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 9482
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_76787028_7   9483 AGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 9532
                         ii     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_76787028_7   9533 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 9582
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_76787028_7   9583 AACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCT 9632
                         i     i     v  i?    i    ii     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_76787028_7   9633 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAGAAAATGCTCACCA 9682
                          v        i  vi viii     v  i       i  i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_76787028_7   9683 TCACTGGCCAT 9693
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (152 / 97)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.67 (5 / 3)  


3093 26.73 2.01 0.45  chr2_76841124_76847396.rev     4888  5781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76841124_7   4888 TGGAAGAACATTCCATGCTTATGGGTGGGAAGAATCAATATCGTGAAAAT 4937
                              ii i  i     i i    i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76841124_7   4938 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4987
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76841124_7   4988 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTGTAAAGTTCA 5035
                          v   iivi i  i  ii     -   -- v  i  - iiv    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_76841124_7   5036 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5085
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_76841124_7   5086 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5135
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_76841124_7   5136 TACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGAGATATAGATC 5185
                                 i   i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_76841124_7   5186 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACTACT 5233
                                i    i--    i  --        vv iii i  i  iviii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_76841124_7   5234 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5283
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_76841124_7   5284 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5333
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_76841124_7   5334 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAAATGGA 5383
                            ii    i    v   i     v           i  i          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_76841124_7   5384 TTAAAGACTTAAACCTTAGACCTAAATCCATAAAAACCCTAGAAGAAAAC 5433
                          i ?    i    iv v   v     v i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_76841124_7   5434 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAA 5483
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_76841124_7   5484 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5533
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_76841124_7   5534 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5583
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_76841124_7   5584 AGGCAACCTACAAAATGGGAGACAATTTTCGCAACCTACTCATCTGACAA 5633
                           i     i   i         v   v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_76841124_7   5634 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5683
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_76841124_7   5684 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5729
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_76841124_7   5730 TC------ATTTATGCA----GCCAAAAAACACATGAAAAAATGCTCACC 5769
                           ------ vv   i  ----     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_76841124_7   5770 ATCACTGGCCAT 5781
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (135 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.75 (22 / 8)  


1474 27.49 8.68 1.27  chr2_76847916_76849925.rev      484  1036 (974)    L1M4_orf2#LINE/L1      177   770 (138)  

  chr2_76847916_7    484 CAAAATATTTTCCAACAAAAAGACCAAAGCTGAAGGCATCAAACTACCCA 533
                              i v i iv  v  i    v     i  i   vv   v   v    
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_76847916_7    534 ACTT-AAAACTAGACTACAAGACTACAATAACCAAAACGGCATGATACTG 582
                          i  -      -v       ii     i   i   i  i ii  i     
  L1M4_orf2#LINE/    227 ATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_76847916_7    583 GTAAGAAAACAGGCACACAGACCAATGCAACAGAATAGAGAGTCCAGAAA 632
                          i vi ii i  i  i i   i     v  i     v             
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_76847916_7    633 GAAGGCCACACACCTACAACTATATGATCTTTGACAAAGCTGACAAAAAC 682
                         v  iv   i   ii  iiiii vv    i  i     i v  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_76847916_7    683 AAGCAATGGTTTGAAAAGGACTCCCTATTTAATAAATGGTGCTGGGGTAA 732
                          vv      --- i    i ivvi  v  i  i             ii  
  L1M4_orf2#LINE/    376 ATTCAATGG---GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_76847916_7    733 GTGGCTAGCCATATGCAAAAGATTGAAATCAGACCCCTTCTTTATGCCAT 782
                         v   v  ?   i          v    i ii       v i i ii    
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_76847916_7    783 ATACAAAAA----CTCAGGATAAATTAAAG---TAAATC------CCAAA 819
                                  ----    ii  ii  i ?  ---     v------ i   
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_76847916_7    820 TACTATG------CTGGA------CATA-----AAAT------------- 839
                         -     i------i i  ------    -----    -------------
  L1M4_orf2#LINE/    523 -ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_76847916_7    840 ---TAGGTAAAGATTTCAT-GATGAAGATGCTAAAAGCAATTGCAATCAA 885
                         ---    i  v i    v -   - v  ii i       vvv    iv  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAA 620

  chr2_76847916_7    886 AACAAAAATTGACAAATGGGATCTAATTAAACTAAAAAGTTTCTGCACAG 935
                          iv      v  i    v   ii v  i   v v    ii  i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_76847916_7    936 CAGAAGAAACTATCACCAGAGTAAACAGACAACCAACAGAATGGGAGAAA 985
                           i i  v       vv i   i  v        v               
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_76847916_7    986 ATTTTTGCAAGCTTTGCATCTGACAGAATTCTAATATCCAGCATGATATG 1035
                           v       iiiv ii      i iiivv  vi       v  -    i
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT-ATATA 769

  chr2_76847916_7   1036 A 1036
                          
  L1M4_orf2#LINE/    770 A 770

Transitions / transversions = 1.73 (95 / 55)
Gap_init rate = 0.02 (14 / 594), avg. gap size = 3.93 (55 / 14)  

 500 24.54 4.29 1.23  chr2_76847916_76849925.rev     1356  1518 (492)    L1M4_orf2#LINE/L1      741   908 (0)  

  chr2_76847916_7   1356 TGAAAAGGGACTAATACATAGCATCTATAAGGAACTT----AAT---ACA 1398
                            v        vi  ivi  v  v     i     i----  i--- i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_76847916_7   1399 AGGAAAAAACAAACAACCCTTTTAAAAAGTAGACAAAGGGCATGAACAGA 1448
                          vi    i     i     vv  ?    i i i      iiv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_76847916_7   1449 CACTTCCCTAAAGAAGACATACATGAGACCAACAAGCACACATGAAAAAA 1498
                           i   i i        i     viv i    i       --      i 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA--TGAAAAGA 888

  chr2_76847916_7   1499 CTTTCAATATCACTGCTCAT 1518
                         ivi    i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (27 / 12)
Gap_init rate = 0.02 (3 / 168), avg. gap size = 3.00 (9 / 3)  


3206 27.64 0.33 0.33  chr2_76861868_76868314.rev     5048  5955 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76861868_7   5048 TGGAAGAACATTCCATGCTCATGGGTAAGAAGAATCAATATCGTGAAAAT 5097
                              ii i  i     i      i vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76861868_7   5098 GCCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5147
                          v v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76861868_7   5148 TACCAATGACTTTCTTCACAGAATTGGAAAACACT-ACTTTAAAGTTCAT 5196
                          v   iivi i  i  ii     v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_76861868_7   5197 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGA 5246
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_76861868_7   5247 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5296
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_76861868_7   5297 ACAGTGACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5346
                              i i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_76861868_7   5347 GTGGAACAGAAC--AGAGCCCTCAGAAATAGTGCCGCATATCTACAACTA 5394
                         i     i    i--    i  --       ivv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_76861868_7   5395 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGAAAAGGATTCCC 5444
                         vi    i  i     ivv  vv  i v  vv       i    i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_76861868_7   5445 TATTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5494
                          v     i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_76861868_7   5495 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5544
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_76861868_7   5545 TAAAGACTTCAACGTTAGACCTAAATCCATAAAAACCCTAGAAGAAAACC 5594
                         i ?    i v  i  v   v     v i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_76861868_7   5595 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5644
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_76861868_7   5645 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATGTAAT 5694
                                     vvi          vv     v  i    v   iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_76861868_7   5695 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5744
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_76861868_7   5745 GGCAACCTTCAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5794
                          i     iv  i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_76861868_7   5795 GGGCTAATATTCAGAATCTACAATGAACTCAAACACATTTACAAGAAAAA 5844
                           i  vi   i      v  i  v      vv   vv iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_76861868_7   5845 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5894
                         i     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_76861868_7   5895 CAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTCACCA 5944
                          v        i  vi viii     v  ii         i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_76861868_7   5945 TCACTGGCCAT 5955
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (144 / 103)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3301 26.10 0.66 0.66  chr2_76914790_76921039.rev     4851  5758 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76914790_7   4851 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4900
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76914790_7   4901 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4950
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76914790_7   4951 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4997
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_76914790_7   4998 ATATGGAACCAAAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCCAAAA 5047
                                 viiv  ii  v  v v  i     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_76914790_7   5048 GAACAAAGCTGGATGCATCACACTCCCTGACTTCAAACTATACTGCAAGG 5097
                                 i    v vv       i  ii i      viv    i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_76914790_7   5098 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5147
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_76914790_7   5148 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCGTATCTACAAC 5195
                                 i    i--    i  --        vv  iiii  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_76914790_7   5196 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5245
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_76914790_7   5246 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5295
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_76914790_7   5296 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5345
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_76914790_7   5346 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5395
                           i ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_76914790_7   5396 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5444
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_76914790_7   5445 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5494
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_76914790_7   5495 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5544
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_76914790_7   5545 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5594
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_76914790_7   5595 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5644
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_76914790_7   5645 AAAAACAAACAACCCTATCAAAAAGTGGGCAAAGGTCATGAACAGACACT 5694
                            i     i     v  i?    i          viv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_76914790_7   5695 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5744
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_76914790_7   5745 TCATCACTGGCCAT 5758
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3269 26.76 0.55 0.55  chr2_76934086_76942639     4662  5569 (2985)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76934086_7   4662 TGGAAGAACATTCCATGCTCGTGGGTAGGAAGAATCAATATCGTGAAAAT 4711
                              ii i  i     i  i   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76934086_7   4712 GGTCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCCTCAAGC 4761
                           iv     v     iv i  i           i  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_76934086_7   4762 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4808
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_76934086_7   4809 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 4858
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_76934086_7   4859 GAACAAAGCTGGAGGCATCACACTCCCTGACTTCAAACTATACTACAAGG 4908
                                 i      vv       i  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_76934086_7   4909 CGACAGTGACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 4958
                          v     i i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_76934086_7   4959 CAATGGAACAGAAC--AGAGCCCTCAGAAATAGTGCCGCATATCTACAAC 5006
                                 i    i--    i  --       ivv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_76934086_7   5007 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5056
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_76934086_7   5057 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5106
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_76934086_7   5107 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5156
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_76934086_7   5157 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5206
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_76934086_7   5207 CCTAGGCATTACCATTTAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5256
                          v    ?i v viv  iiv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_76934086_7   5257 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5306
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_76934086_7   5307 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5356
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_76934086_7   5357 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5406
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_76934086_7   5407 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5456
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_76934086_7   5457 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5506
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_76934086_7   5507 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5556
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_76934086_7   5557 CATCACTGGCCAT 5569
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

2884 24.97 5.20 2.60  chr2_76934086_76942639     7178  8062 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_76934086_7   7178 TGGAAACATATCCTGTGTTCATGGATTGGAAGAATGGAAACCGGAAAAAT 7227
                               v      ii                  v vi v ii vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_76934086_7   7228 GTCTATACTACTACAAAT---------GATTCAATGTAATCCCTATCAAC 7268
                          v v     v i-     ---------       i i            v
  L1M4_orf2#LINE/     51 GGCAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_76934086_7   7269 ATTCCAATGGCATTTTTCACATAA--TAGGAAACAGAATTGTACAATTTA 7316
                           i   iiv  v     ii  v  -- iiv  i v  - iv  v    i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCA 148

  chr2_76934086_7   7317 TATGGAACCCTAGAAGATCCCAAAGATCCAAAATA-TCTTGGTCCAAAAG 7365
                                vivi iii  i  vi  v v      i -     ivvv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_76934086_7   7366 AACAAAGCTGGAGGTATCATACTACCTGACTTCCTTCAAAGTATACTACA 7415
                                i      vv   i   v  ii i   ----   iiv       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTC----AAAACTTACTACA 244

  chr2_76934086_7   7416 AAGCTATACTAATCAAAACAGCACAATACTGGTATTAAAAACAGACACAT 7465
                               i v       i    iiiii      i  -  ii i     i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATAT 293

  chr2_76934086_7   7466 AGG--------ATAGA-----GAACTCAGAAATACATCCACATATTTACA 7502
                           i--------     -----  iii        v i   i i     ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_76934086_7   7503 GTCAATTGGTTTTTGACAAAGGGACCAAGA--ATTCACGATGGAGAAAGG 7550
                                 i    i     i  vi      --     --    i     i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAGA 391

  chr2_76934086_7   7551 ACACGCTCATCAATAAATAGTGTTGGGGCTATTGGATATTCATTTGCAGA 7600
                          i vv  iv    i    i   i    i v i      ?i  iv    i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_76934086_7   7601 AAAATGAAATTAGATTCTTTTCTTATACCATACCCAAAAATAAACTCAAA 7650
                          i      i  i  ii i vi  i i      iv       v        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_76934086_7   7651 ATTGATTGAAAACTTAAATGTAGGACCTGATACTATAAAACAAGTAGTAG 7700
                           v   ii? i  i        i  v  i v          vvv   v  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_76934086_7   7701 AAAACA-GGGGATAAG-CTCCATGAGATTGGTCTGGGTAATGATTTATTT 7748
                               -i  ?i   i-  i i   vv    vi i  i    i   ----
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT---- 587

  chr2_76934086_7   7749 TTATTTTTTGCATATGA-ACAAAAAAGTATGGGTAACTAAAGCAAAAATA 7797
                         ------i  iv      -  v    - i iii i   v    v       
  L1M4_orf2#LINE/    588 ------CTTAGATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATA 630

  chr2_76934086_7   7798 GACAAATGGTATTATATCAATCTAAAAAACTTCTGCATAGCCAGGGACA- 7846
                           i    v v i vi     vv v        i  iiivv v i     -
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_76934086_7   7847 --------GAGTGAAGGGACAATCTCCAGGATA----AAAGTATTTGCAA 7884
                         --------i      ii     i iv   i  i----   i         
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_76934086_7   7885 ACCACTTATATC--ATCAAGGGTTAATATCCAAAATATATAAGGAACTCA 7932
                          i  --      --  v i  ii vi      i         i      v
  L1M4_orf2#LINE/    731 ATCA--TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_76934086_7   7933 AACCACTCAATAGCAAAAA-ACAAATGACCTGATTTTAAAAATGGGCAAA 7981
                         v  v        ii     -      i   ii   ?-             
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAA 827

  chr2_76934086_7   7982 GAATCTGAATAGACATTTCTCAAAATAAGACAAACAAATAGCCAATTAAT 8031
                          i  i                v   v    i v      i      v ii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_76934086_7   8032 ATATGCAAAAATGCCCAACATTACTGATCAT 8062
                          i   v   i    i      i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (143 / 74)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.14 (69 / 22)  


3242 26.62 0.55 0.66  chr2_77043255_77049038     4384  5292 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_77043255_7   4384 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAGTCAATATTGTGAAAAT 4433
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77043255_7   4434 GGCCATACTGCCCAAGGTAATTGATAGATTCAATGCCATCCCCATCAAGC 4483
                            v     v     iv i  iv i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77043255_7   4484 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4530
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_77043255_7   4531 ACATGGAAGCAAAAAAGAGCCCTCATCGCCAAGTCAATCCTAAGCCAAAA 4580
                          i      iiiv  ii  v  vvv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_77043255_7   4581 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 4630
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_77043255_7   4631 CTACAGTAACCAAAACAGCATGGCACTGGCACCAAAACAGAGATATAGAT 4680
                                  i   i    ii   i       iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_77043255_7   4681 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCTTATCTACAAC 4728
                                 i    i--    i  --        vv iiivi  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_77043255_7   4729 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 4778
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_77043255_7   4779 CCTGTCTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 4828
                         i  v ii  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_77043255_7   4829 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 4878
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_77043255_7   4879 ATTAAAGACTTAAACCTTAGACCTAAATCCATAAAAACCCTAGAAGAAAA 4928
                           i ?    i    iv v   v     v i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_77043255_7   4929 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4978
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_77043255_7   4979 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTC 5028
                         vi            vvi           v     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_77043255_7   5029 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5078
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_77043255_7   5079 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATTTGACA 5128
                         v  i     i   i             v  i    vii ivi  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_77043255_7   5129 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5178
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_77043255_7   5179 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5228
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_77043255_7   5229 CTCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAAAATGCTCA 5278
                            v        i  vi viii     v  i-          i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCA 894

  chr2_77043255_7   5279 CCATCACTGACTAT 5292
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2586 27.03 3.83 1.58  chr2_77128576_77132798     2844  3731 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_77128576_7   2844 TGGAAAAACAATCCATGTTCATGGATTGGAAGAATCAATATCATTAAGAT 2893
                               i i vi                     v i     ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77128576_7   2894 GGCTATACTGCCCAAAACAACCTGTAGATTCAATGCTATTCCTATCAAAA 2943
                            v     v      vii i  ii        i  v  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77128576_7   2944 TATCGG-TGTCATTTTTTATAGAATTAGAAAAAACT-ATTCTAAAATTCA 2991
                          vi i -  i -      ii    v v  v  i-  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_77128576_7   2992 TATGGAA-TAAAAATGAACCAAGATAGCCAAAGAAATCCTGAGGAAAAAA 3040
                                - iv  iv  v   ii         iv    i   ii  i  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_77128576_7   3041 AAAAAAGCTGGGTGTATCATATTACTTGACTTCAAATTATACTATAAGGC 3090
                           v    i   iv vv   i i v iii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_77128576_7   3091 TTAAGTAACCAAAACAGCATGGTACTGGTACAAAGAGAGACACTTAAACC 3140
                          vv     i   i    ii         i i  i  v     iv  i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_77128576_7   3141 AATGAAGCACATTAGAAAACCCAGAAATAAAGCC-CACACCTACAACCAT 3189
                             i ii v v v  i ii           v  -i   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_77128576_7   3190 CTGATCTTTGAT--GAATTCAACCGAAATAAG-CAGTGGGGAAAGGACTT 3236
                         i    i  i  i-- ii ---i  i i iv v-  i         i ivv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGT---GCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_77128576_7   3237 CCTCGTCAATAACTGGTGCTTGGATACCTGGCTAATC-TGTCTGAAAGAA 3285
                         i  iv    i  v       v   i v    v  ?i -ii vii      
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_77128576_7   3286 TAAAACTGGACCCTTACCTTTCTGTGTATATAAAAAT-AACTCAAGATGG 3334
                          i  ii       i     iv vvii    i      -       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_77128576_7   3335 TCTAAATATTTAAAAGTAAGACCTCAAACTGTAAAAATCCTAGAAGAAAA 3384
                         vii ? v ii    v      v  v     i     v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_77128576_7   3385 CCTAGGAACTACCATTCAGGACATCAGCTTTTGCAAATAATTTGTTAC-T 3433
                          v    ?iiv viv   iv   v ii v  vv    - ii   v   v- 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT 594

  chr2_77128576_7   3434 AAGTCCTCAAAA--ACAATTGCAACAAAAGCAAAAATTGAGAAGTAGGGA 3481
                          v v vi     --    --          v      v  v  i -v   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAAT-TGGA 641

  chr2_77128576_7   3482 CT-------AATTAAAGGAGCTTTTG-----CACAGGATA-----AAAAA 3514
                           -------       -- i      -----  v    i -----  i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAA--AACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_77128576_7   3515 AGCTATCAGTAAACAATCAACAGAATGGAAGAAAATACTTGCAAACTATG 3564
                           --- v iv i    i v         i        i       ii  i
  L1M4_orf2#LINE/    690 AG---TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_77128576_7   3565 TATCTGACAAAGATCTAATATCTAGAATCCATAAGGAACTTAAATATCTC 3614
                                i  i iv  vi    i     vi    i     ivv i v   
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_77128576_7   3615 ATCAAGCAAAAACCAA----CCCCATTAAAAAATTGGCAATGAAAATGAA 3660
                          vi  vv    iv   ----   v   ?      v     v i vv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_77128576_7   3661 CAGACACTTCTCAAAAGAAAACATACATTTGGCTTACAAACATATGAATA 3710
                         i     i     v      i i     vv    iv i  i  i     v 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_77128576_7   3711 AATTC-CAACATTACTAATAAT 3731
                         i  v -      i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.09 (48 / 23)  


3069 24.57 3.07 1.37  chr2_77232309_77234454      768  1646 (500)    L1M4_orf2#LINE/L1        1   894 (14)  

  chr2_77232309_7    768 TGGAATGCTATCCCACATTTATGGATTTTAAAAGTTTATATTGTTAAAAT 817
                              v v       ii  i       vv  i v  v          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77232309_7    818 GTCTATAATTTCAGAAGAGATCTACAGATTCAATGCAATTTCTATCAAAA 867
                          v v   v ii vi  vv               i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77232309_7    868 TTCTAG-TATTTTTTTAG-AGAAATAGAAAAAA-AATCCTGAAATTTGTA 914
                          i i  - iii     v -      v  v  iv-i     i     ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_77232309_7    915 TGGAACCAGGAAAGACCCCACATAGCCAAAGCAATATTGAGCAAAAATAA 964
                              viivi ii     viv         i    v    iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_77232309_7    965 CAAGCAG--AGAGTA-TAACACTCCCTGATATTAAAATATATTATAATGC 1011
                            --  --i   v - v     i  ii  v i    iv  i  i  v  
  L1M4_orf2#LINE/    201 CAA--AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_77232309_7   1012 TATTGTAATAGAAATAGTATGATACAGCCATAAATATAGATACATCTACC 1061
                           iv     vi i i   i  i   v v     iv     i i  vv i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_77232309_7   1062 AGTGGAACAGGACAGAAAGCCCAGAAATAAACAAACCCAAGTATTTGTGG 1111
                          i     i  i iv  i  i            ----   vii    i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAAC----CCATACATTTATGG 344

  chr2_77232309_7   1112 TCAATTGATTTTTTACAGCATTCTCCCAAA--CACACATTGGGTCAAGGT 1159
                                     iv   -- vvv v    i--  iv  v    vv   iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACA--AGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_77232309_7   1160 TAGTCTCTTTAATAAATGGTGTTAGAAAAACTGGATATCCAGAATCAAAA 1209
                               i  i  i        i i i v         ?   v vv     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_77232309_7   1210 GAATGAAATTGGATACTTCGGTCACATCATATACAAAAATCAACTCAACA 1259
                                i     iv i vvv     i             i       v 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_77232309_7   1260 TGGGATGAAAGACTTACATGTAAGACCCCAAATTGCAAAGCTGCTAGAAG 1309
                            -  v ?    i  v        v iv   i ii   i  vi      
  L1M4_orf2#LINE/    493 TGG-ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_77232309_7   1310 AAAACA--GGGGAAAAGCTCCATGACATTGGTCTGGACAACAATTATTTA 1357
                               --  ? v   v  i i    v    vi i i   iii  vi   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_77232309_7   1358 AATGTGACCCCAAAAGCACAAGCAACAAAAGCAAAAATAGACAAACTAGA 1407
                         i  i    v                      v         i   i i  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_77232309_7   1408 TTGTACCAAC-CTAAAAGCTTCTGT-----AAAGCAAAACAATTAACAGG 1451
                         i vi i   v-i     i   i   -----    -i v  v  i  v ii
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAA 690

  chr2_77232309_7   1452 GTGAAGAGACAACC-ATAGATTGGGAGAAA-TATTTGCAAATCATAAAAC 1499
                              i        - i   v         -               v v 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_77232309_7   1500 TGATAAGAGGCTAGTATCCAAAATATGTAAGAAACTCAAACAATTAAATA 1549
                                i i  v       i     i   ii     vv    i v    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_77232309_7   1550 GCAA---------TAACCTAATTTAAAAGTGAGCAAAGGATCTGAACAGA 1590
                         ii  ---------     i    ?    i  i         i    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_77232309_7   1591 CATTTCTCAACAGAAGAGATAAAAATATCCAACAGATATATGAAAACTAA 1640
                                 v v      v   v    iv    i iii i       --i 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA--GA 888

  chr2_77232309_7   1641 TGATCA 1646
                           v   
  L1M4_orf2#LINE/    889 TGCTCA 894

Transitions / transversions = 1.47 (126 / 86)
Gap_init rate = 0.02 (18 / 894), avg. gap size = 2.17 (39 / 18)  


3105 27.05 1.22 0.78  chr2_77277039_77280164     1733  2634 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_77277039_7   1733 GAAGAACATTCCATGATTTTGGATACAAAGAATCAATATCCTGAAAATGG 1782
                            ii i  i     v iv     vvi    v i     iv v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_77277039_7   1783 CCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 1832
                          v     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_77277039_7   1833 CCAATGACTCTCTTTGCAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCATA 1880
                            iivi ii i         -   -- v     - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr2_77277039_7   1881 TGGAACCAAAAAAGGGCCCTC--ATTGCCAAGACAATCCTAAACCAAAAG 1928
                              -- viv     v  iv--  v     i      i i  vv i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_77277039_7   1929 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTAAAATGC 1978
                                i      vv   ii  v  ii i      viv     v  v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_77277039_7   1979 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAAGATATAGACC 2028
                           i     i   i    ii         i iv ii i i v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_77277039_7   2029 AGTGGAACAGAACAGAGCCTTCAGAAATAATACCACACATCTACAACCAT 2078
                          i     i    iv   vv i         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_77277039_7   2079 CTGATCTTTGACAAACCTGATAAAAACAAGGAATGGGAAAAGGAT--TCC 2126
                         i    i  i     ivv  vi  i v  vvv      i    i  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_77277039_7   2127 CTAATTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2176
                         i -- i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_77277039_7   2177 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2226
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_77277039_7   2227 TTAAAGACTTACATGTTACACCTAAAACCATAAAAACCCTAGAAGAAAAC 2276
                          i ?    i  v    v v v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_77277039_7   2277 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 2325
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_77277039_7   2326 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2375
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_77277039_7   2376 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGTGAA 2425
                           i   v v  i i   i  ii vv    i  v    i  vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_77277039_7   2426 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAAGCTACTTCTCTGACA 2475
                         v  i     i                 v       iii iv v     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_77277039_7   2476 AAGGGCTAATATCCAGAATCTGCAATGAACTCCAACAGATTTACAAGAAA 2525
                          i  i  vi          v ii  v      iv   iv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_77277039_7   2526 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGATACTT 2571
                           i    ----   v  i?    i    ii      v    i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_77277039_7   2572 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 2621
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_77277039_7   2622 CATCACTGGCCAT 2634
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.80 (18 / 10)  


3022 27.69 1.22 0.66  chr2_77300185_77306494     4916  5818 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_77300185_7   4916 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATGAATTATTGTGCAAA 4965
                              ii i  i     i        v      v v   -     vv i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT-ATTGTTAAGA 49

  chr2_77300185_7   4966 TGTCCACACTGTCCAAGATAAT-TATAGATTCAATGTCATCCCCATCAAG 5014
                           v v i   vi    iv i  -  i        i iv     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_77300185_7   5015 CTACCAATGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTAAAGTTC 5062
                         v v   iivi i  i  ii    i-   -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_77300185_7   5063 ATATGGAAGCAAAAAAGAGCCCGCATTGCCAAGACAATACTAAGCCACAA 5112
                                 iiiv  ii  v  v v  v     i     vi i ivv v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_77300185_7   5113 GAACAAAGCTGGAGGCATTATGCTACCTGACTTCAAACTATATTACAAGG 5162
                                 i      vv i ii  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_77300185_7   5163 CTACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGATATAGAC 5212
                                  i   i    ii   i     i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_77300185_7   5213 CAATGGAACAGAAT--AGAGCCCTCAGAAATAATATCACACACCTACAAC 5260
                                 i     --    i  --        vvi  i   ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_77300185_7   5261 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAATGATTC 5310
                           vi    i  i     ivv  v   i v  vv           vi  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_77300185_7   5311 CCTATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5360
                         i  v  i  i       i      v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_77300185_7   5361 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5410
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_77300185_7   5411 ATTAAAGACTTAAATGTTACACCTAAAACCATAAAAACCCTAGAAGAAAA 5460
                           i ?    i       v v v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_77300185_7   5461 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 5509
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_77300185_7   5510 AAAACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCT 5559
                          vi            vvi     i    vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_77300185_7   5560 AATTAAACTAAAGAGCTTCTACACAGCAAAGGAAACTACCATCAGAGTGA 5609
                         v  i   v v  i i   i iii vv       v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_77300185_7   5610 AGAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACGCATCTGAC 5659
                          i  i     i                 v   i   vii iii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_77300185_7   5660 AAAGGGCTAATACCCAGAACCTACAAAAAACTTAAACAAATTTACAAGAA 5709
                           i  i  vi  i      iv  i   i    ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_77300185_7   5710 AAAAACAA----CCCCATCAACAAGTGGGCAAAGGATATGAAGAGACACT 5755
                            i    ----   v  i? v  i            v    v     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_77300185_7   5756 TCTC-AAAAAAGACATTTATGCAGCTAACAGACTCATGAAAAAATGCTCA 5804
                             -   i    i  vi viii  i  i ii v        i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_77300185_7   5805 TCATCACCGGCCAT 5818
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (152 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


3224 26.40 0.66 0.77  chr2_77358051_77363904     4454  5362 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_77358051_7   4454 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4503
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77358051_7   4504 GGCCATACTGCCCAAGGTAATTGATAGATTCAATGCCATCCCTATCAAGC 4553
                            v     v     iv i  iv i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77358051_7   4554 TACCAATGACTTTCTTTACAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 4601
                          v   iivi i  i   i     -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_77358051_7   4602 TATGGAACCAAAAAAGAGCACGCATTGCCAAGACAATCCTAAGCCAAAAG 4651
                                viiv  ii  v vv v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_77358051_7   4652 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATGCTACAAGGC 4701
                                i      vv    i  v  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_77358051_7   4702 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4751
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_77358051_7   4752 AATGGAACAGAAC--AGAGCCCTCAGAAATGATGCCGCATATCTACAACT 4799
                                i    i--    i  --      i vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_77358051_7   4800 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4849
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_77358051_7   4850 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4899
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_77358051_7   4900 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4949
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_77358051_7   4950 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4999
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_77358051_7   5000 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5048
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_77358051_7   5049 AAACACCAGAAGCAATGGCAACAAAAGCCAAAAAT-GACAAATGGGATGT 5097
                         vi      i     vvi          v-      -  i    v   iv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTT 644

  chr2_77358051_7   5098 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGCGA 5147
                         v  i   v v  i i   i  ii vv    i  v    i  vv i  i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_77358051_7   5148 ACAGGCAACCTACAGAACGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5197
                          v  i     i      i          v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_77358051_7   5198 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTGCAAGAA 5247
                           i  i  vi          v  i  v      vv    v ivii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_77358051_7   5248 GAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATAAGAACAGACAT 5297
                         -   i     i     v  i?    i            vv   i      
  L1M4_orf2#LINE/    795 -AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_77358051_7   5298 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATAAAAAAATGCTC 5347
                              v        i  vi viii     v  i     i    i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_77358051_7   5348 ATCATCACTGGCGGT 5362
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2397 28.73 3.25 1.35  chr2_77373573_77376905.rev     1957  2847 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_77373573_7   1957 TGGAAAAGCATTCCATGTTCATGGATTAGAAGAATCAATGTCATTACAAT 2006
                               iii  i               i     v i   i ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77373573_7   2007 GACCATACTGCCCAAAGCAATCTACAGATTCAACACTATTCTTATCAAAT 2056
                          i v     v      vii               i v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77373573_7   2057 TACCAACATCATTTTTCACA-AAATTAGAAAAAAAAGATTCTAAAATTTA 2105
                          v   i vv v     ii  -     i-- v  ivv   i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_77373573_7   2106 TATGGAACGAAAAAGGAATTCA-AATAGCCAAAGCAATCCT---ACTTAA 2151
                                -iviv    i ii  -          i     i --- vvv  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_77373573_7   2152 AAACAAAAGTAGAGGCATCACATTACCTGACTTCAAACTGTACTATAGGG 2201
                         i      iv i    vv     i v  ii i      viv     i ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_77373573_7   2202 CAGGGATACAGTAGCAAAAACAATGTAGAACTGATACTAAAAGCAGACAC 2251
                          -----       iiv  i   i   i v    ii -   iiii     i
  L1M4_orf2#LINE/    248 C-----TACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACAT 291

  chr2_77373573_7   2252 ATAGACCAATCAAAAAGAATGAAGAACCCAGAAATAAAGCTGCACGCCTA 2301
                              i    vi  v     vi   ii           v iii  iii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_77373573_7   2302 CAGCCATCTGATCTTCAAAAAAGCAGTCAAAAATAACCAATGAGGAAAGG 2351
                         ii i  vi    i   i v  i vv i   i vi vi     i      i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_77373573_7   2352 ACTCCCTAGTCAATAAATAATGCTGGGATAGCTGGCTAGCCATATGCAGA 2401
                          ivvi  vv    i    ii        i i    v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_77373573_7   2402 AGAATGAAACTGGACCCTTACTTTTCACCATATACAGTAATTAACTCAAG 2451
                                 ii       i   i iv           iv           i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_77373573_7   2452 ATGGATTAAAAATCTAAATGTGAGAACTCCATCTATGAGAATCCCAGAAC 2501
                               i ? i i        i   i  vv v    i i v  ii    v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_77373573_7   2502 AAAACCCAAGAAACATTATTCTGGACACCAGCCTTGGAAAATCAGTTAT- 2550
                              vi i ?ivv v v   vv   - iv vv  i iv   viv  v -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTT 590

  chr2_77373573_7   2551 -GACTATGTCCTCAAACGTAATTGCAACAAAACAAAAATT-GACAG-TGG 2597
                         -  -    v vi    v i vvv         v     v -  i i- v 
  L1M4_orf2#LINE/    591 AGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_77373573_7   2598 GATCTAATTAAACTAAAGAGGTTTTGTACAGCAAAAGAAACTATCAACAG 2647
                           ii v  i   v v  i iv      i vv    i  v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_77373573_7   2648 AGT------ACC-CCCACCAGAACAG--------ATTCACAACT-ATGCA 2681
                            ------  v-     -    ii --------   ii   v -  ii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCAC-AGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_77373573_7   2682 TCAAAAAAGAATCTTG-ATTCAGAATCTGCAAGGCACTGAAACAAATTAA 2730
                           vi v   iiv    -  i      v ii  i v   vvv    v i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_77373573_7   2731 CAAGCAAAAACCAAATAACCCCATT-AAAAATGGGCATGAGAAATGAACA 2779
                         i  vv    iv          v   -           vii  vv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_77373573_7   2780 GATACTTCTCAGAAGAAGATATATGAGCAGCCAACAA--ACATGAAAAAA 2827
                           i i     vi           ii iii     i  --         i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_77373573_7   2828 TGCTCAGTGTAACTAATCAT 2847
                               iii v ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (153 / 100)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.05 (41 / 20)  


 407 27.39 0.64 3.82  chr2_77474698_77477783     1320  1476 (1610)    L1M4_orf2#LINE/L1        3   154 (754)  

  chr2_77474698_7   1320 GAAAATCATTTCATGCTCATTGTTTGGAAGAATCAAGGTCATTAAAATGT 1369
                             ivi  ii    i    v v        v i  vi ii    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_77474698_7   1370 CCATACTGTCCAAAGGAATCTCCAAATTTAACGCTATTCCTTTCAAATTA 1419
                          v     vi     vvi    v  i   i     v  i   v     v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_77474698_7   1420 TCAA-TGTCATTTTTTAACAGAATTAGAATAAAAATATTATTCTACAATT 1468
                         i  i-  i -      -i     ---- v i v  vv v  i   v    
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTT-GCAGAA----ATTGACAAGCTGATCCTAAAATT 146

  chr2_77474698_7   1469 CACATGGA 1476
                           i     
  L1M4_orf2#LINE/    147 CATATGGA 154

Transitions / transversions = 1.05 (22 / 21)
Gap_init rate = 0.03 (4 / 152), avg. gap size = 1.75 (7 / 4)  

1909 27.73 3.77 1.62  chr2_77474698_77477783     1852  2594 (492)    L1M4_orf2#LINE/L1      150   908 (0)  

  chr2_77474698_7   1852 ATGAACTAATGCA---GAGCCTGAATAGCCAAAGCAGTCCTAAGCAAAAA 1898
                            i --      ---  v  v           i  i  i i iv  i  
  L1M4_orf2#LINE/    150 ATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_77474698_7   1899 GAACAAAGTCGGAGGCATCACTTTACCTGACTTCAAACTATACTACAAGG 1948
                                  i     vv    vi v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_77474698_7   1949 C----------AAAATA---TAGTACTGGTACAAAAATAGACACATAGAC 1985
                          ----------  i i --- i       i i  ii       i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_77474698_7   1986 CAATGCAACAAAATAGAGAACCCAGAAATAAAGCTGCCA-ACAT--ACAG 2032
                              v  i i   v    ii           - --   -    -- ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAA-C--CCATACATTTATGG 344

  chr2_77474698_7   2033 CCATCTGATCTTCAACAAAGTTGACAAAACTAAGCAATGGTGAAAGGA-- 2080
                         i  vi    i   i    i v  v   i  i vv      v     i --
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_77474698_7   2081 ATCCCCATAGAATAAATAATGCTGGAATAACTGGCTAGCCATATGCAGAA 2130
                         i  ii-- vv  i    ii      i i      v  ?   i     i  
  L1M4_orf2#LINE/    395 GTCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_77474698_7   2131 GATTGAAAGTGAAACCTTTCCTTATACCAGATACAAAAATCAAATTAAGA 2180
                           v    iv  i v  i v   i i    v          i  v i  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_77474698_7   2181 TAGATAAAATACTTGAATATAA-ACCCCAAACTATACAATCCCTGGAACA 2229
                          i   v ? v  i i   i   - v iv        v  ii i i   v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_77474698_7   2230 CAACCTAGGCA-ACACCATTCTGGCCATTGACCTTGAGAAATAATATAT- 2277
                         v   v    ?i- v i v iv  i  -   iv-  ii v   ii v v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACC-TTGGG-TTAGGCAATGGTTTCTT 590

  chr2_77474698_7   2278 -GACTAAGTCCTCAAAAGCAATTGCAACAGAAGCCAAAATGGACAAATGG 2326
                         -  -  v v vi        vvv      i   vv     i  i    v 
  L1M4_orf2#LINE/    591 AGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_77474698_7   2327 CACCGTATTCAACTAAACAGCTTCTGCACAGCAAACAAAACTGTCAACAG 2376
                         v  ivi  iv  v v  v i   i  ii vv    vi v   i    v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_77474698_7   2377 AGTAAACAGACAACCTACAGAAAGGGAGAAAATAC--ATAAACTATGCAT 2424
                            i  v        i      v           i--ii   ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_77474698_7   2425 CCAATGAAGGACTAATGCTCAGAATCTATAAGAAACTTAGACAAATCCAC 2474
                          ii  i i     vi iii      v     ii    ivv    v  v i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_77474698_7   2475 AAGAAAAAT-CAAATAACCACATTAAAAACTGGGCAAAGAAGATAAACAG 2523
                           v     v-         vv   ?    v         i vv i  i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_77474698_7   2524 ACACTTTTCAAAAAAAGACACAGAAGTGGCTAACAAACATTATGAAAAAA 2573
                            i  i  v   i    i i v  i    i  i  i  i-       i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC-ATGAAAAGA 888

  chr2_77474698_7   2574 ATTCTCATCATCACTAATCAT 2594
                         - v    v     ????????
  L1M4_orf2#LINE/    889 -TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (122 / 80)
Gap_init rate = 0.03 (20 / 759), avg. gap size = 2.00 (40 / 20)  


2581 21.13 0.97 0.97  chr2_77681986_77683597      501  1120 (492)    L1M4_orf2#LINE/L1      289   908 (0)  

  chr2_77681986_7    501 CATATAGACCAATGAAATAAAATAGGAAATCCAGAAATAAACTCTCACAT 550
                                 i     i    i   v ii i             i vi    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_77681986_7    551 TTATGGTCAAATGATTTTCCATAAGGGATGCCAAGACCATTCCATGGGAA 600
                                   v        v i     -              v     i 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGA 387

  chr2_77681986_7    601 AAGGACAGTCTTTTCAAAACACGATGTTGTGA-AACTGAATATCTGTATA 649
                            i i           v v i i  i  v  -     i   ? iii  i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_77681986_7    650 CAAAAGTATGGAGTTGGGCTCTTACCTTATACCATATACAAAAAATAACT 699
                               v   i      i i i     i i              v     
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_77681986_7    700 CAAAATGAATCAAAGAACTAACTGTGAGATTGAAAACTATAAAAATCTTA 749
                                i    ?   v    v   i   viv            v     
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_77681986_7    750 CAAGAAAACATAGGGCAAAAGCTTCATGATATTGGATTTGGCAAAGATTT 799
                         v             ?vv   v    i   iv    i  v     v i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_77681986_7    800 ATTGGACATGACATCAAAAGCACAGGCAACAAAAGTAAGTAAAAGTAAAT 849
                         v  i  i      i          i          -  ---   i  i  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AA---AAAATAGAT 633

  chr2_77681986_7    850 AAGTTTCATTATATACAAATTTAAAACTTTCATACATCGAAGTGCATAAT 899
                           i  vv i vi  vv     v        ii i v  i   vi  iv  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_77681986_7    900 CAACACAGTGATAAGCCAACCCATTTA-TTGGAAAAAATATTTAAAAATT 948
                            v v     v   v       ivv - v   i         iv    i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_77681986_7    949 ATAAATTGGATAATAGGTTAACATT-AAAATATATAAGAAACACCTAAAA 997
                            v  iv     vi ii vii  i- i         ii   v i  v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_77681986_7    998 TT---TAATAACACCACAATTAATTTAATGTTAAAAATGGGCATAGGATT 1044
                         i ---      v vv    v   iii   - ?           v      
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGATT 832

  chr2_77681986_7   1045 TGAGTATAAATCTCTCCAAAGATGATATTCAAATGGTCAACAAGCACATG 1094
                            i  v v  i          v     v       i   i         
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_77681986_7   1095 AAAAGATGCTTAACATCATTAATCAA 1120
                                   i       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (72 / 55)
Gap_init rate = 0.01 (8 / 620), avg. gap size = 1.50 (12 / 8)  

 303 27.47 8.79 0.00  chr2_77681986_77683597     1510  1600 (12)    L1M4_orf2#LINE/L1        1    99 (809)  

  chr2_77681986_7   1510 TGGAAAAGCATTCTATGCTCATGAATAGGTAGAACCAATATCATCAAAAT 1559
                               iii  i i   i     i  v  v   vii     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77681986_7   1560 GGCCATACTGACCAAA-------GCA-ATTTAATGCTATTCCTATTAAA 1600
                            v     vv     -------i  -   i  i  v  i     i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.02 (2 / 99), avg. gap size = 4.00 (8 / 2)  


1222 22.15 2.35 0.00  chr2_77713941_77716230        1   298 (1992)    L1M4_orf2#LINE/L1      443   747 (161)  

  chr2_77713941_7      1 GACTGAAGTGTTAATTTTATGTTACACCATATATAAAAACTCACTCAAAG 50
                           v      vvv viii  iv i          i     i v       i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_77713941_7     51 TGGATTAAGGACATAAATAGAAGAGTTAAA-TGATGAACCTATTAAAA-- 97
                              i ?i   v     iv     i    -iv  i  v  v   i  --
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_77713941_7     98 ATATATAGGGAGAAACCTTCATGATGTTGGATTTGATAATAGATTCTTAC 147
                          v i     ?iv   i    i   iv    i  v ii   i v      v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_77713941_7    148 TTATGAAATCAAAAGCATGGGAAACAAAA---AAAACAGATATGTTGGAC 194
                         v     v i        iii v       ---    i     vi      
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_77713941_7    195 TTCATCAAAATTATCAACATTCATGTTTCAAAGGACACTATAAAGAAAGT 244
                                      vv   v  ii  i               v        
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_77713941_7    245 GAAAATA-AAGCCACAGAATGGGAGAAAATATTTGTGGATCATATATCTG 293
                              v -  v                        iii            
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_77713941_7    294 ATAAG 298
                              
  L1M4_orf2#LINE/    743 ATAAG 747

Transitions / transversions = 1.29 (36 / 28)
Gap_init rate = 0.01 (4 / 305), avg. gap size = 1.75 (7 / 4)  

2629 27.01 2.43 2.65  chr2_77713941_77716230      892  1798 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_77713941_7    892 AAAAACATTCCACGCTTCTGGATTGGAAGGATCAATATTGTTAAAATGAC 941
                            i i  i   i i iv           iv i           i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_77713941_7    942 CATATTGCCCAAAGCAATCTATAGATTCAGTGCTACTCCTAGCAAACTGC 991
                         v   i v      vii     i       ii  v ii    v    v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_77713941_7    992 CAA-TGTCATTTTTCACAGAAGT-AATAAAATCT-ATTTTAAAATTAATA 1038
                           i-  i -     ii     i -i i  i--  -  ii       v   
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chr2_77713941_7   1039 TG-AAATGAAAAACAAGCCCA-AATAACCAAAGCAATCCTAAGCAAAAAA 1086
                           -     v  iiv --    -    i     i     i i --------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGA-------- 190

  chr2_77713941_7   1087 AAAAAAAAAAAAAAAAAAAAGCCTGATGCATCGCATTACCCAACTTCAAA 1136
                         ------    i  i  v    iiv  v vv  i  i v     i      
  L1M4_orf2#LINE/    191 ------AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_77713941_7   1137 CTATACTATAAGGCCATAGTAACCAAAACAGCATTCTATTGGTACAAAAA 1186
                         viv     i  i  i i     i   i    ii vv  i   i i  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_77713941_7   1187 CAGACACA-AGACCAATGGAATGAAAT----AGCTCAGAAAAAAAGCCAT 1231
                         i     i -   i         ii   ----  ii      v   v    
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_77713941_7   1232 ACACCTAGAGTTATCAGATCTTTGACAAAGCGGACAAGAAAATGCAATGG 1281
                            ii  vi  i viv   i  i     i vv v     vv  v      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_77713941_7   1282 AAAAAAGACTTCCTATTGAATAAATGGTGCTGGGACAACTGGCTAGCCAT 1331
                         ii   ii ivvi  v  v  i                     v  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_77713941_7   1332 ATGCAGAAGATTGAAACTGGACCCCCCTCCCTCTTACCATATACAAAAAT 1381
                              i    v    ii        -- v    vi               
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCC--TACCTCACACCATATACAAAAAT 482

  chr2_77713941_7   1382 CAACTCAAGATGGATTAAAGGTTTAAATATAAGACCATAAACTTTAAGAA 1431
                         i       i      i ?  iii     i     v vv     v   i v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_77713941_7   1432 TCCCATAAAAAACCTTGGAAATA--TCATTCTGGACTTTAGTCTTGGGAA 1479
                           ii v  i   v v i i?i  --  -   vv   i  i v-  i  v 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCA 580

  chr2_77713941_7   1480 ATAATTTAT--GACTAAGTCCCCAAAAGCAATTGCAACAAAAACATAAAT 1527
                           ii   v --  -  v v v         vvv         iv v    
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_77713941_7   1528 TGACAAGTGTGACCTAATCGAACTACGGAACTTCTTTACAGCAAAAGGAA 1577
                         v  i  i vv   i v   i  v vvii     i v i vv    i iv 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_77713941_7   1578 TCCTCAGCAGTGTAAAAAGACAACCTACTGAATGGGATAAAACATTTTCA 1627
                         iiv   iv iv  i           i  v        v    i    v  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_77713941_7   1628 ACCTATGCATCTGACAAAGATTTAATATCAACAATCTGTAAGGAACTTAA 1677
                          vii  ii      i  i ivi vi    v v   v i   i     ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_77713941_7   1678 ACAAATCAACCAGAAAAATGCGAAGAACCCAATTAAAAAGTA-------- 1719
                             v    iv v     vi i  v         ?    i i--------
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_77713941_7   1720 ACCTGAACAGACATTTCTCAAAAGAAGACATACAAATGGCCAACAAATAT 1769
                          ii    i           v        i              i  ii i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_77713941_7   1770 GAGAAAAAATGCTCATCATCACTAATCAT 1798
                         iv     i       v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.02 (18 / 905), avg. gap size = 2.56 (46 / 18)  


2628 26.73 6.80 0.35  chr2_77720333_77722105.rev      429  1281 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_77720333_7    429 TGGAAATCCATCCTTTGTTAATGGGCCGGAAGAATTAATATTGGTAAAAT 478
                               vvi    iv    v    iii      v         v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77720333_7    479 ATTCTTACTATCTAAAGTGAT-------------GCATGCTTTACTGAAA 515
                         ivivv    vi i   v    -------------   vv ii  iii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77720333_7    516 T---AA-------------AAAAAT--ACAA-----TCTTAAAAGTTGTA 542
                          --- i------------- i    --    -----  i     v ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_77720333_7    543 TCACACTATTAACACCCTAAAATA-CCAAG-CAATTATGA----GCAGAA 586
                          viv v iiv iviv  i i    -    i-    iv   ---- v    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_77720333_7    587 CAAAGATAGAGGCTTCACACTTTCTGAATTCAAAGTATGTTACAAAACTA 636
                              v i    vi        i ii v      iiv ii      i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_77720333_7    637 TTTTAATTAAAACAATATGGTATGGGCATAAGAATAAGAATA-AGACTAA 685
                         ivv    i  i   i i     iv        i   iiv   -   ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_77720333_7    686 TGGAAATGAATACAGAGCCCAGAAATTAATCCACACAGTTATCTTCAACT 735
                              vv    vv    i        v  i   i   v    vv    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_77720333_7    736 GTTCTTC-AT----GTGCCATGAGCACAGAGTGGGAAAAGAATGGCCTCT 780
                          v i   - i----      v  v  ivv i    i       i i  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_77720333_7    781 TCAATATAAGGAATCAGGAAAACTTGATATTCACATGCAAGAAAATAAAA 830
                             i v v  viiii   v    v    ?i         i i   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_77720333_7    831 TTGGACCCTTACATCATGCCATATACAAAAATTAACCCAAAGTGGCTTAA 880
                                 i   v   ii                  i    i   v i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_77720333_7    881 AAATGTAAATATAAGACCTCAAACTATGAAACTGCTAGAAGAAAACATAG 930
                          i iv     i     v  v       i     vi               
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_77720333_7    931 G-GTAAATCCTTCTTGACATTGGTCTTGGCAATAGTTTTTTGGCCTTTAC 979
                          -       -   v    v    vi v      i    i  i viv v  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_77720333_7    980 ACCAAAAGTGCAGACAACAAAAGCAAAAATATACAACTGAAATTGTAT-A 1028
                                 ii  ii         v       v i  v vii i vi  - 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_77720333_7   1029 AAATTAAAACCCTCTGCATAGTGAAAGAAACATTCAACAGAGTAAGAAGG 1078
                                  v i i  iiivvii  i  v  vv    v i   i i   i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_77720333_7   1079 TAATCTACAAAATGGGAGAAAATATTTGCAAAACATATAT-----AAGGG 1123
                         i  i i   i                      v       -----     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_77720333_7   1124 GTTAATACACAAAAATGTTTAAGGGATTTATGTGGCTCAATAGCAAAAAA 1173
                         ii vi  iv  i  - i v   i i i iv iiii       ii     i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAA-TATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_77720333_7   1174 A-AATTAATCTCATTTAAAAATGTGTAAAGAACCTAAATGAACATTTCTC 1222
                          -  v   i iv   ?       v i    i ii i   ii         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_77720333_7   1223 AAAAGAAGATTTACAAATGGTACAA-AAGTACATAAAAAGATGCTCA-CA 1270
                         v         v         i-   -   i    i            -  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGC-CAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_77720333_7   1271 TCAGTAATCAT 1281
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.71 (142 / 83)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.05 (61 / 20)  


3243 26.35 0.88 0.77  chr2_77731584_77737375     4394  5300 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_77731584_7   4394 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4443
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77731584_7   4444 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4493
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77731584_7   4494 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4540
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_77731584_7   4541 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAA 4590
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_77731584_7   4591 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTATAAGG 4640
                                 i      vv       v  ii i      viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_77731584_7   4641 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 4690
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_77731584_7   4691 CAATGGGACAGAAC--AGAGCCCTCAGAAATAACGCCGCGTATCTACAAC 4738
                               i i    i--    i  --        vv  iiii  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_77731584_7   4739 TATCTGACCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 4788
                         i vi   ii  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_77731584_7   4789 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 4838
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_77731584_7   4839 TGAAACTGGATCCCTTCCTTACACCTTATATAAAAATCAATTCAAGATGG 4888
                             ii    i    v   i     v    i      i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_77731584_7   4889 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4938
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_77731584_7   4939 CCTAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTG 4986
                          v    ?-   --i -   iv   v v  vv i     v ii   v ivi
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_77731584_7   4987 TAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATC 5036
                           vi            vvi           v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_77731584_7   5037 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5086
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_77731584_7   5087 AACAGGCAACTTACAAAATGGGAGAAAATTTTTGCAACCTACCCATCTGA 5136
                           v  i    ii   i             v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_77731584_7   5137 CAAAGGGCTAATATCAAGAATCTACAATGAACTCAAACAAATTTACAAGA 5186
                         i  i  i  vi    v     v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_77731584_7   5187 AAAAAA-AAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACAC 5235
                             i -   i     v  i?    i    ii     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_77731584_7   5236 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAGAAAATGCTC 5285
                              v        i  vi viii     v ii       i  i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_77731584_7   5286 ATCATCACTGGCCAT 5300
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (145 / 90)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2806 27.79 2.23 0.89  chr2_77750888_77756631     4357  5252 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_77750888_7   4357 TGAAAAGACTTTCTATGCTTATGGATAGGAAGAATCAATATCATGAAAAT 4406
                           i     iv i i   i i      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77750888_7   4407 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTACTCCCATTAAAC 4456
                            v     v      v i  i  i        i  v ii  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77750888_7   4457 TACCATTGACATACTTCACAGAA-TTAGCAGAAACT-ATTTTAAAATTCA 4504
                          v   vivi v vi  ii     -  ii  -- i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA--AGCTGATCCTAAAATTCA 148

  chr2_77750888_7   4505 TATGGAACCACAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAG 4554
                                vii   ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_77750888_7   4555 AACAAAGCTAAAGGCAC-CACATTACCTGACTTCAAACTATAATACAAGG 4603
                                i ii   -  -    i v  ii i      viv  v     i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_77750888_7   4604 CTCCAGTAGCCAAAACAGCATGGTGCTGGTACAAAAACAGACACATAGGC 4653
                           v     ii   i    ii    i    i i  ii i     i    ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_77750888_7   4654 CAATGCAACAGAATAGAAAACTCAGAAATAAGACTGCACATCTACAAGCA 4703
                              v  i     v  i iii         iv iii    i  iiiv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_77750888_7   4704 TCTGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGGAAAGGATTTTC 4753
                         vi    i  i i   ivv  v   i v  vv            i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_77750888_7   4754 TATTTAATAAATGGTGCTGGGAGAACTGGCTAACCATATGCAAAAAAATT 4803
                          v  i  i              v      v  ?   i        i   -
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT- 446

  chr2_77750888_7   4804 GAAACTGTACCCCTTCCTTACACCTTCTACAAAAATTAACCCAAGACGGA 4853
                            ii  v      v   i     v v             i   i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_77750888_7   4854 GAAAAGGCTTAAATGTAAAATCCAAAACTATGAAAACCCTAGAAGAAAAT 4903
                         vv ?  i i         i v i        i   vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_77750888_7   4904 GTAGGCA-ATACCATTCAGGATATAGGCATGGGCAAAAATTTCATG---A 4949
                         i    ?i- v i -   iv  iv v  vv i     vii    v i--- 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_77750888_7   4950 TGAAATTGCCAGAAGCAATTTCAATGAAAGCAAAAACTGACAAATGAGTC 4999
                            v ---   i     vvvv   ii    v     iv  i    vi v 
  L1M4_orf2#LINE/    596 TGACA---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_77750888_7   5000 CTAATTAAACTAAGGAGCTTCTGTACAGCAAAATAAACTATCAACAGAGT 5049
                         i v  i   v v ii i   i   i vv    iv v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_77750888_7   5050 GGACAGGCAACCTACAGA--GGGGACAAATTTTTCCAATGTATCCACCTG 5097
                          i v  i     i     --   iiv    v   v   vvi  vi i   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_77750888_7   5098 ACAAAGGTCTAATATCCAGAATCTACAAGGAATTTAAACAAATTTACAAG 5147
                          i  i  v  vi          v  i  i   i ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_77750888_7   5148 AAAAA--------ACTCCATTAAAAAGTGAGCAAAAGACATGAACAGATA 5189
                              --------  i v   ?    i  i     i  iv    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_77750888_7   5190 TT-CTCAAAAGAAGACATTCATGTGGCCAATAA--ACATGAAAAAAACCT 5236
                           -   v        i  v  vi          --         i vv  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_77750888_7   5237 CAACATCACTGATCAT 5252
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (150 / 95)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  


2554 27.57 1.75 2.41  chr2_77775330_77777329.rev      595  1508 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_77775330_7    595 TGGAAATACATATCATGCTCATAGATCAGAAGAATTAATATTGTTAAAAT 644
                               v i  vi    i    i   ii     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77775330_7    645 GACCATACTACCTTAATAAATCTACAGATTCAGTATAATCCCTAGGAAAA 694
                          i v     v  iv   vi             iiii        vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77775330_7    695 TACCAA-TGCCATTTTTCACAGAAATAGAAATAAAAAATTCTGAAAAGTG 743
                          v   i-    -     ii       v  v - ivvi  i  i   vvii
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chr2_77775330_7    744 TATGAAACTAAAACAGAGTCCAAATAGCCAGAACAATCTTGAGCAGAAAA 793
                             i  v iv  vi  vi vi        i           i- i i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAA 197

  chr2_77775330_7    794 GAACAAAGCTAGAAGCATCACACTACCTGACTTCAAAATATATTACAAGG 843
                                 i i  i vv       v  ii i       iv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_77775330_7    844 TTGTATTCACCAAAACAACATGCTATTGGTATAAAAATAGACACCTAGAC 893
                         i ii v v i   i   iii  v  i   i    ii       iv    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_77775330_7    894 CAATGGAACAAAATAGAGAATCCAAAAATAAATACATGTATTCAGAGCTG 943
                                 i i   v    i    i       iv   ii   i vi iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_77775330_7    944 ACTGATTTTCAAAATAGGCACCAAGAACATTCATTGCAGAATAGATACCT 993
                          i        i v vi  ii      v      v  vi   -   -----
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGA----- 391

  chr2_77775330_7    994 TCTTCAGATA-TCTTCTTCAATAAATAGTGCTGAGAAAACAGAATATTCA 1042
                         -------   -    -     i    i      i  v   v i   ?i  
  L1M4_orf2#LINE/    392 -------ATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_77775330_7   1043 TATACAGAAGAAAGAAACCAGACTCTTATCTCTCAC-ATACACAAAA-TC 1090
                         i  i  i     v   iiii   i i  i   v   -   i      - i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_77775330_7   1091 AACTCAAAATGATATAAT-GATGTAAACATAAGATCTAAAACTATCCAAT 1139
                                    i-  v ?-  iv    ii     v          --  -
  L1M4_orf2#LINE/    484 AACTCAAAATGG-ATCAWAGACCTAAATGTAAGAGCTAAAACTAT--AA- 529

  chr2_77775330_7   1140 GACTACTAGAAGAAAATAGAGAAA-ACAT-TTCAGAATATTGGTCTAGGA 1187
                         i   vi          i v  i?i- v  -   ivi iv    vi    v
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_77775330_7   1188 AA--ATTTAT-GGCGAAAACATCAAA-GTACAGGCAATAAAAGCAAAAAT 1233
                           --i   v -i vv vi   i    - i   i    i     v      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_77775330_7   1234 ATACAAATGGGAATATATTAAACTAGAAAGCCTCTGCACAGCAAAACAAA 1283
                          v i    v   v vi  i   v vi   i i i  ii vv    iv v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_77775330_7   1284 CAACCAATAGAGTAAAGAGATAACCTGTTAAGTGAAAGAAAATATTTTCA 1333
                          v i   v i   i  i   i    iiivi i  ii           v  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_77775330_7   1334 AACTATATATTCATCAAGGAACTAATATCCAGAATGTACAAGGAACTCAG 1383
                           ii      iiivi    i   vi          i  i  i      vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_77775330_7   1384 AAGAACTCCACAGCAAAATAACTAATAATCCCATTAAAAAATGGGCACAA 1433
                          v-     v i ii    vi  v     i  v   ?           v i
  L1M4_orf2#LINE/    780 AC-AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_77775330_7   1434 GAC----AGAAGCATTTCTCGAAAAAAG-CATGCAAATAGCTAACATGTA 1478
                           i---- v ii        v   i   -i  i     i  i  i v i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_77775330_7   1479 TATTTAAAAATGCTCAGTATCACTAATCAT 1508
                         i  vv   i       ii    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (163 / 85)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.73 (38 / 22)  


3270 26.46 0.55 0.44  chr2_77892054_77898308     4857  5763 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_77892054_7   4857 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4906
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77892054_7   4907 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4956
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77892054_7   4957 TACCAA-TGCCTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCA 5004
                          v   i-       i  -i     v v  v  i-  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_77892054_7   5005 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5054
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_77892054_7   5055 AACAAACCTGGAGGCATCACACTACCTGACGTCGAACTATACTACAAGGC 5104
                               vi      vv       v  ii iv  i  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_77892054_7   5105 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5154
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_77892054_7   5155 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5202
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_77892054_7   5203 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5252
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_77892054_7   5253 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5302
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_77892054_7   5303 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5352
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_77892054_7   5353 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5402
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_77892054_7   5403 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5452
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_77892054_7   5453 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5502
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_77892054_7   5503 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAAC 5552
                          iv  v v  i i   i  ii vv    i  v    i ivv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_77892054_7   5553 AGGCAACCTGCA-AATGGGAGAAAATTTTCGCAACCTACTTATGTGACAA 5601
                           i     ii  -             v  i    vii iv   v   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_77892054_7   5602 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5651
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_77892054_7   5652 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGCACAGACACTTC 5701
                          i     i     v  i?    i           iv  v i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_77892054_7   5702 TCAAAAGAAGATATTTATACAGCCAAAAGACACATGAAAAAACGCTCATC 5751
                           v           vi v ii     v ii          i i     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_77892054_7   5752 ATCACTGGCCAT 5763
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


 579 31.77 12.77 2.98  chr2_77921416_77924803.rev     1770  2474 (914)    L1M4_orf2#LINE/L1        6   779 (129)  

  chr2_77921416_7   1770 AGATACACAATGCTTCTAG-TTGTTAGATGTAATGTCATAAAAATGTTGT 1818
                              iv v   i iv i -   vv   iv    i ii v  i   viiv
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_77921416_7   1819 T--TCCGCCAAAGTGACCTATAGAATCAGTGCAATTCGGATTAATATTCC 1866
                          --   -     v   i   i   v   ii     i vv  i  v  i  
  L1M4_orf2#LINE/     56 TACTCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_77921416_7   1867 AAATATATTTTTCGTAGAATTTCATAAAAATGA-AGTAAGACTTATACAG 1915
                          iv iiv     i i    v  v i  iv-   -vv   i i i   ii 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATGG 153

  chr2_77921416_7   1916 TGATATAAA--ATCTATGGATTTATCACAATTATCTTGACAAAGAAGAAT 1963
                         vi  ii  i-- i i --  v vii  v  iv       v         i
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCA--GAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_77921416_7   1964 AAATTTGGAAGACTCCATACTATCATATTTTAAGTTCTACTATACACCTA 2013
                            v     i     - i   vi vv    i  ivii     i v v   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTC-ACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_77921416_7   2014 TGATAATTAAAATAGTATGAAGTTTCTG---CAAGATTAGACAAATAGAG 2060
                         iii    i  i i   i  i--- v   ---i   iv      v     v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGG---TACTGGCATAAGGATAGACATATAGAT 297

  chr2_77921416_7   2061 CAA--------AATT--------AGATATA----CATATAT--ACAATAA 2088
                            --------    --------   v   ----    i  -- iii v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_77921416_7   2089 AT-GATTATTTATAAAGTTGCCAA-------TAAAAGCAAAGGTAATAG- 2129
                           -    v iv i  i v      -------i  vi vi  i -     -
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGT 396

  chr2_77921416_7   2130 ATATTCA-TACCTTTTGCTAGAAAAACTGAAC--CTATAGGAACAAAAAT 2176
                         v v    -i vv vv    i i v     i i-- i i v v v  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_77921416_7   2177 AAACAATGTTG-AGCTATATTTCATACCATA--CAAAGGTGA---CAGGG 2220
                         i  ----    - v iv  ii   i      --    ii v ---  ii-
  L1M4_orf2#LINE/    447 GAA----GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA- 491

  chr2_77921416_7   2221 ATG-ATTGTAAATCTAAATGTTAAAGTGAAAACTGTATAGCTTCATA-AA 2268
                            -  ii? i i        v i  iv      i  v i  - v  -  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAA 540

  chr2_77921416_7   2269 GGAAACATAGAA-TACACTAATTACTATGAT-TAAAATAAAACAACTTTT 2316
                          i        i?-  ----   iviii   i- viii v ii   ivv  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTA----AATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_77921416_7   2317 TTTCAGACAGAAC-TCACAAACACTGAAAATAAAGTAAAA--TAAACTAA 2363
                          i i   i vi  -i  v  i   viiv  i   iv    --  i iv  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_77921416_7   2364 TTGA--TTCCTC------------TTTT----------------TATCA- 2382
                            i--   v  ------------    ----------------     -
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_77921416_7   2383 GAA---GAATAGGCCAGCTTCAGATTTAGAGAAAATGTTAATAATACATA 2429
                            ---   v  i v v iv    v vi        i  vii  vv    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_77921416_7   2430 TATCTGACAAAAATCTTCATAAACGAAATACATAAAATAACTCCT 2474
                                i  iiiv   -i  vv ii    i     i-     i 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTT-GTATCCAGAATATATAAAG-AACTCTT 779

Transitions / transversions = 1.58 (136 / 86)
Gap_init rate = 0.05 (40 / 774), avg. gap size = 2.77 (111 / 40)  

 348 21.28 0.00 9.93  chr2_77921416_77924803.rev     2756  2896 (492)    L1M4_orf2#LINE/L1      782   908 (0)  

  chr2_77921416_7   2756 AACTACAACAACAAAATAACAACTCCAAATCCAATTTTTTAATAGGCAAA 2805
                             -   i  i    vi    v ---  i      ?vvv   i      
  L1M4_orf2#LINE/    782 AACT-CAATAATAAAAAGACAAAT---AACCCAATTWAAAAATGGGCAAA 827

  chr2_77921416_7   2806 GTATGAAAATAATGTTGAAGAGACATTCCACAAGATAAGATATATGAATG 2855
                          v  ----------     v       i v v i v        ii    
  L1M4_orf2#LINE/    828 GGAT----------TTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_77921416_7   2856 GTTACCAAGGATTTGAAAAGATACCCAATATCACTACTGAT 2896
                          ii vi   v iv         i i   i    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.02 (3 / 127), avg. gap size = 4.67 (14 / 3)  


2972 25.87 4.81 0.36  chr2_77963886_77965765.rev      538  1368 (512)    L1M4_orf2#LINE/L1        1   868 (40)  

  chr2_77963886_7    538 TGAAAAAAAATTCCATGTTCATGGATTGTAAGAATTAATATTGTTAAAAT 587
                           i   i v  i                v    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_77963886_7    588 GTCCATATTACCCAAAATAATGTACAGATTCAATGCAATCCCTATCAAAA 637
                          v v   i v      v i  v           i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_77963886_7    638 TTCCAATGATATTTTTCACATAAATAGAAAAAC-AACCCTAAAATTTATA 686
                          i   iiviiv     ii  v    v  v  i -i i         i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_77963886_7    687 TGAAACCATAAAAGACTCAGAATAAACAAAAGTATCCTGAGCAAAAAGAA 736
                           i  viii  ii   i       iv     vv   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_77963886_7    737 CAAATTTGGGGGAATTACATTACCTGACTTCAAATTATACCACAGTGCTA 786
                             v    i   v i   i v  ii i      viv   i   iv    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_77963886_7    787 TAGTAACCAAAACAGCATGTTACTGGCATAAAAGCAGAC-T-CAGACCAG 834
                         i     i   i    ii  v           iiii    - -i   i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_77963886_7    835 TGGAAGAGAATAGAAAACCCAGAAACAAATTCACACATCTACAGTGATCT 884
                              v     v  i ii       i   ii  i    i  ii  v vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_77963886_7    885 CATGTTTAAAAAGGGTGTCAAGAAGATATACTGGGGTAAAGACAGTCTCT 934
                         v  v  ii v       i     vv  vi v     v  ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_77963886_7    935 TGAATAAATGATGCTGAGAAAACTGTATATCCATATGCAGAAGAGTGAAA 984
                          v  i     i     i  v     v   ?   i     i    i    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_77963886_7    985 CTAGCCCCTTATCTCTTGTCATATGCAAAAATCAAATAAAACTAGATTGA 1034
                         i i v   i  i   viii     i       i  v v   v i   ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_77963886_7   1035 AGACTTAAATCTAAGACCTCAA-CCATAAAACTACTAAAGAAAAACATTG 1083
                             i     v     v  v  - i        vi  i ii       v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_77963886_7   1084 GAGAAACTCTCCAGGACATTTGACTGGGCATAGCTTTCTTGAGTAATAAC 1133
                          ? v  v   i iv   v  v ii i    vv v      iii  - i  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGAC 599

  chr2_77963886_7   1134 -CCAAAAGCATAAGCAACCAAAGTAAAAATGGACAAATGGGATCACA-CT 1181
                         -         i       v    v      i  i    v   iiv  - v
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_77963886_7   1182 AAGTTAAAAAACCTTCTGCACAACAAAGTAAACAATCAAGAAAGTGAAGA 1231
                           i       --   i  ii vv     v v  v              i 
  L1M4_orf2#LINE/    650 AAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_77963886_7   1232 GACAATCCACATAATGTGAGAAAATGTTTCCAAACTAACCATTTGACAAG 1281
                              i     v    v        i   v    ii vvi  i   i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_77963886_7   1282 AGGTTAATAACCAAAACAT--------CT--------------------- 1302
                         i ii vi  v   i  i  --------  ---------------------
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_77963886_7   1303 ----AATAATCTGATTTAAAA-TGGGCAAAAGATCTGAATAGACATTTCT 1347
                         ----     i ii   ?    -        i   i               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_77963886_7   1348 CAGAAGAAGACATGCAAACGG 1368
                          vi       i  i    i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGG 868

Transitions / transversions = 1.78 (135 / 76)
Gap_init rate = 0.01 (11 / 868), avg. gap size = 3.91 (43 / 11)  


1732 27.10 3.43 3.09  chr2_77987068_77989344      571  1153 (1124)    L1M4_orf2#LINE/L1        6   590 (318)  

  chr2_77987068_7    571 AGATATTCTATATTCATATGTAGAAAGACTGAATGTTGTCAAGATGTTAG 620
                               i i  i     ivi v i      v   i    i      vi i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_77987068_7    621 TTCTTTTCAATTTGATCTACAGAATTAATGCAATCCCAGTAAAAATACCA 670
                          v  iii   v            v i  i        vi v     v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_77987068_7    671 GTGAATTACTTTGTGGATATCAATAAACTGATTCTGAAGTTTGTAAGGAG 720
                          ivivi vi    ii  v  ii i  i     i  i  i  ii  v   i
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_77987068_7    721 AGGCAGAAGATC-AGAATAGCCAATGCAATACCT-AAGGAGAAAAACAAA 768
                          v   iii  i -           vi    - i -  ii    i      
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAACAAA 204

  chr2_77987068_7    769 GTTGGAAGACTTATACTACCCAACTTTAAGACTTACTATACAGCTATAGT 818
                               i    i i   v     i  i  i        i v     i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_77987068_7    819 AATCAAGCTAATGTGTTATTGGTAAAAGAATCATCACATAGATTAATGGA 868
                                vi i    v  i   i v   i  viv  i      i      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_77987068_7    869 CTAGAAT-AAAAATCTTCA-AAATAGATCAACA----TATAGTCAACTGA 912
                         v      -i i i  --  -     i i v i ----   i     i   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_77987068_7    913 TCTTTGACAGAGGAGT-ATGTGTAATACAATGAAGAAAAGATGGTCTTTT 961
                          i  i    ii  v i- v -iiv  v     ii    ii  i       
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_77987068_7    962 TCAATAAATGATGTTGGAACAACTGT-CATCCTACATGTAACAAAAATGA 1010
                         -   i     i  i   i       v-i ?  -     i  -  i     
  L1M4_orf2#LINE/    402 -CAACAAATGGTGCTGGGACAACTGGATAKCC-ACATGCAA-AAGAATGA 448

  chr2_77987068_7   1011 ATCTAAATAGATTTTATACTCTTCAAAAAATTTAACAACAAC-AACAAAA 1059
                          vi ii i---iii  ---- i   v vv  v  -   v  i-   vv  
  L1M4_orf2#LINE/    449 AGTTGGAC---CCCTA----CCTCACACCATATA-CAAAAATTAACTCAA 490

  chr2_77987068_7   1060 AATGGATCACAGACCTAAACATAAAACACAGACCTACCAAACTCCTGGAC 1109
                                  ?         ii   i vvi i v   iv      i i  v
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_77987068_7   1110 CATAATGTAGGAGAAAATCTT---------GGGTTTGGTGATAGCTATTT 1150
                         v v  ii    ? v       ---------     v  ii  i ---   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG---TTT 587

  chr2_77987068_7   1151 TTT 1153
                         i  
  L1M4_orf2#LINE/    588 CTT 590

Transitions / transversions = 2.23 (107 / 48)
Gap_init rate = 0.03 (19 / 585), avg. gap size = 2.00 (38 / 19)  

 919 24.92 2.46 2.46  chr2_77987068_77989344     1461  1785 (492)    L1M4_orf2#LINE/L1      584   908 (0)  

  chr2_77987068_7   1461 GCTTTTTAGATATACCACTAAAGGCTCAATCTGTTAAA--AAAAATTAAT 1508
                          i  i        iv   i   i  v   v viiv   --      vi  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_77987068_7   1509 AAATTGGACATAATTCAAATATAAAA---TTTCTGCT-CAGTGAATGACA 1554
                                  v v  iv    -     ---   v    -  ---  v    
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAAT-TAAAAACTTTTGTGCTTCA---AAGGACA 679

  chr2_77987068_7   1555 CTGTCAAAAGGACAAGAAGACAAGGCATAGCCTGGGAGAAAATAATATTT 1604
                           i    i iiiii i       vv  i  vv            ---   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA---TTT 726

  chr2_77987068_7   1605 GCGAAAGACACATCTGATAAAGG-CTGTTATTTAAAATACCCAAAGAAAA 1653
                           i  vv i i         i  -  vv   ii i    ivi      vv
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_77987068_7   1654 CTTAAAATTCAACAATTAAAAAAATGAACAACTCAGTTACAAAATGAAGC 1703
                             v  i    i   -     i ii  i   i  i  ?v      iivv
  L1M4_orf2#LINE/    777 CTTACAACTCAATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_77987068_7   1704 AAGGATCTTAACAAACACCTCATCAAAGAAGATATTTCGATGGCAAATAC 1753
                               i v  i i   ii  vi            vivi     v    v
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_77987068_7   1754 GCATATGAAAAGAT-TTCCACATCATATGACAT 1785
                            i          -i  v      ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (47 / 33)
Gap_init rate = 0.03 (9 / 325), avg. gap size = 1.78 (16 / 9)  


 679 23.86 15.82 8.31  chr2_78017685_78020361      985  1357 (1320)    L1M4_orf2#LINE/L1        1   401 (507)  

  chr2_78017685_7    985 TGTAAAGGTATACCATGCTCATAG----GAAGAGCCAACATAATAAAGCT 1030
                           v    i   v     i    i ----     vii  i  vi v   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78017685_7   1031 GTAATTTCTCTTCAAATTGATTCACAGGTTCAGTGATATTCCTATGAAAA 1080
                          vv v v   ii         ii    i    ii vv  i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78017685_7   1081 TCCCAACAAATTTTGTTGTTGTTGTTGTTGTTGTTTTGTTTCGTATTTTT 1130
                              i ------------------------  ii  -   i i v----
  L1M4_orf2#LINE/    101 TCCCAGC------------------------TGCCTT-TTTTGCAG---- 121

  chr2_78017685_7   1131 ACACTTTGACAAGCTCATTCTAAAATATTTATGCAAAGCCACAGGCCCTA 1180
                          v --          v  i       viv    v   vv  vi  v  i 
  L1M4_orf2#LINE/    122 AAA--TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_78017685_7   1181 GAATATCTAAAACAATTTTGAAAAAGAATAATA---TTG------TC--- 1218
                              v i        i           v  i ---   ------  ---
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_78017685_7   1219 -TTACCA-----------TATT-----GCTATA-TAATCATGAGAGTGTA 1250
                         -  v   -----------  i -----    i -      v  v     i
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_78017685_7   1251 GTATTGGTGGAAAAATAGGT-CATAAATCAATAGAACAGA---------C 1290
                            i   iiv  ii    ii-i   i      i   i   --------- 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_78017685_7   1291 CAGAGA---ACCTA-ACATT-A---------GACTCCTG-CAAAGGCACA 1325
                             i ---   i -     - ---------  i iii -   i  ii v
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_78017685_7   1326 AAGGCTATTCAATGCAGAAAGCATCACCTTCT 1357
                            i i        vi     v  vii   i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

Transitions / transversions = 1.70 (56 / 33)
Gap_init rate = 0.04 (18 / 401), avg. gap size = 5.00 (90 / 18)  

1360 23.31 4.05 3.85  chr2_78017685_78020361     1667  2185 (492)    L1M4_orf2#LINE/L1      389   908 (0)  

  chr2_78017685_7   1667 AGCATAG-CTTTTCAAATAAATGGTATCGCTGCAACAA---GATATCCAT 1712
                           v    -        -i       ---    vi    ---    ?   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAA-CAAATGGT---GCTGGGACAACTGGATAKCCAC 434

  chr2_78017685_7   1713 AGGCCAAAAAA-AAAGTCTTGACCTTAACCTCATGCCTTATGCAAAAGTT 1761
                          v  v   i  -i    - v    iiv      ii  v   i     i  
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_78017685_7   1762 AATATAAATAAACGTATCTTGTATTTCAACGCAAAATATAAGACTAT--- 1808
                           ivi   --- i v   v?iv ii v  i i  i vv   i     ---
  L1M4_orf2#LINE/    484 AACTCAAA---ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_78017685_7   1809 -CTTTTTGT-GAAAA-GTAGGAGAAAATCTTTGTAACCGCAG-TTAGGCA 1854
                         -  i  v v-     -i    ? v       i  i   vii -       
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_78017685_7   1855 AAGACTTCTTAGGCTTGACACCAAAAGTACAAAGCATAAAAGGAAAAAAC 1904
                          v ii       iiv            i    -   vv   i       i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAAT 629

  chr2_78017685_7   1905 AGTGATAAATTGGACTTCATCAAAATTAAAAACCCTTG--CTCCATGAAA 1952
                           --                             ii   --  i  --  i
  L1M4_orf2#LINE/    630 AG--ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAG 675

  chr2_78017685_7   1953 AGCCCTCTTAAGAGAATTGAAAAGATAACCTACAGTCTGGGAAAGAAAGA 2002
                         ii v  v i    -  v        i    i    vv     i -   v 
  L1M4_orf2#LINE/    676 GACACTATCAAGA-AAGTGAAAAGACAACCCACAGAATGGGAGA-AAATA 723

  chr2_78017685_7   2003 AATGCAAACCTCTTAT-TCAAATAAAG-ATTTTTATCTAAAATATATAAA 2050
                         vv      --  v   -  vi    i - i  v    i i          
  L1M4_orf2#LINE/    724 TTTGCAAA--TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_78017685_7   2051 CAACTCAAAAACCTCACCAGATAAAAA--TGAACAATCCAGTCAGAAAAT 2098
                         v     vv v v    vi -       --ii  i  i   i i?i     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_78017685_7   2099 GGGAAAAAATGAATTGAATATATGTTTAACCCAACAGGATATCCAGATGG 2148
                            v   i--  v       v ii   vv  v  v i     v  i    
  L1M4_orf2#LINE/    821 GGGCAAAG--GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_78017685_7   2149 CAAATAAGCA---AGAGAGATGTTGCACTTCATTAATCAC 2185
                          v        ---ii i     i vv  v   ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (66 / 51)
Gap_init rate = 0.05 (24 / 520), avg. gap size = 1.71 (41 / 24)  


3277 22.12 5.02 1.60  chr2_78072489_78074486      636  1512 (486)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_78072489_7    636 GGAAAGACACACTGTGTTCATGGATCACATGACCTACTATTC---AGATT 682
                                i iv ii           iiv v   i  v    v---    v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_78072489_7    683 GCAGTATTATTCAAAGCTG-TCTATAGTTTCAATGCAATCCCTGTCAAAA 731
                            i  i vii    -i  -    i  v     i         i      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78072489_7    732 TGAATGGGCTTTTTTGT-TTTTTTACAGAAAGGAAAAAAC-AATTATTAA 779
                          ------- iivvi  i-      i      vvi v  i -i  iv v  
  L1M4_orf2#LINE/    101 T-------CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_78072489_7    780 ATTTATATAGATTTGTAAGTTTCCCCAAATCACCAAGTCAATCTTGAAAA 829
                            i    i  vv  i   vvv   vi   vi    iv            
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_78072489_7    830 AGAA---CATTGTTGAATGAC--ACACTTCTTGATTTCAAATTTTCCTAC 874
                             ---  vv    i v   --       iii        vi  v    
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_78072489_7    875 AAATGTATAGTAATCAAAACAGTGTGGTACTAGCATTATGATAAAC---- 920
                            vv  i         i             i    v v    i  ----
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_78072489_7    921 ----CAGTAGAATAGACTTGAGAGTCCAGAAATAAATCCTCACATCTAGA 966
                         ----  i i       v                   i  vi    i  --
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-- 341

  chr2_78072489_7    967 TGGTCAATTGATTTTTGACAGGGATGCCAAGGTTAT-CAATAAGAAAATA 1015
                                        i    i  i       iii  -    ii i   v 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_78072489_7   1016 A-AGTCTCTCCAACAATTATTGCTGGGACACACCG-ATATTTACATATAA 1063
                          -     i i      v iv          -  i -   ?ii    ii  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACA-ACTGGATAKCCACATGCAA 440

  chr2_78072489_7   1064 AGAAATGAAATTGAATCCCCACCT-GCACCATTTTAAAAAGTTAACTCAA 1112
                          ii      i   i i   i    -i      v vv    i         
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_78072489_7   1113 AATGGATCAATGACCTAAATGTAAGAGCTAAAACCATATAAGTCTTAGAA 1162
                                  ?v                       i   v  v        
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_78072489_7   1163 GAAGAGATAGGTGTAAATCTTCATGGATTTGGACTTGGAAGTTAATTCTT 1212
                            i v     ?          i  ivi    ii v  v i viv     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_78072489_7   1213 AGATATAAAAACAAAAATACAGGCAGTGATACAACAAAAAAA-AAGTTAC 1261
                               i v v     ii   i   iii v v  v   v i -  i  iv
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_78072489_7   1262 ATTTCATCAAAATGAAAAACCTTTGGGCATCTAAAAATATTATCAAGAAA 1311
                          i           v      i    v  v  v  ii i i          
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_78072489_7   1312 A-GGAAAG----CCTACAGAATGAAAGAAAATACTTGTAAATTACAGATC 1356
                         i- i    ----  i        ii        i   i    i i v   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_78072489_7   1357 TCACAAGGATCTAATATGCAGAATGTCTAAAGAACTC----------ATA 1396
                          v i    iv  vi   v      i v          ----------   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_78072489_7   1397 TTGCAAATACAAACTACT-AATTAAAAAATAGGCAAACGACTTGATTAGA 1445
                         v iv   v     iv  i-    ?      i      v  i    v    
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_78072489_7   1446 CATTTCTCCAAAGA---TATACAA-TGTCTAACAAGCACATGGAAATATG 1491
                                       ---       -  v i  i         i   v   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_78072489_7   1492 CTCAACAATGTTAGTAACTAG 1512
                                --- i ????????
  L1M4_orf2#LINE/    891 CTCAACA---TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (116 / 74)
Gap_init rate = 0.03 (23 / 907), avg. gap size = 2.52 (58 / 23)  


2428 28.97 1.38 1.26  chr2_78117381_78124202     3985  4854 (1968)    L1M4_orf2#LINE/L1       38   908 (0)  

  chr2_78117381_7   3985 ATATTGTTAAAATGGTCATACATCCAAAAGCAATTTACAGATTCAATGGT 4034
                                   i    iv    vi  v   vii  i           i vv
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chr2_78117381_7   4035 ATTCCTGTCAAACTACCTATAATATTCTTCACAGACTTAGAAACAACTG- 4083
                           i   i     v v  viiviiv  i  ii    vv v  v - i   -
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGA 136

  chr2_78117381_7   4084 TTTTAAAATTCATATGAAAACAAAGAAGAGCCTAAATAGCCAAGGCAAAC 4133
                          ii             i   iiv iii  v  vi         ii   v 
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_78117381_7   4134 CTAAACAAAGAGAACAAAGCTAGAGGCATCACATTACCTGACTTCAAA-C 4182
                         i i  v  ii         i i    vv     i v  ii i      - 
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_78117381_7   4183 TAACTGCAAGGCTACAGTAACCAAAACAGCATGGTTTTGGCACAAAAACA 4232
                          v   i   i          i   i    ii    vi     i  ii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_78117381_7   4233 GACACATAGACCAACGAAGCAGAATACAGAGCTCAGAAATAATGCCACAT 4282
                             i     i   i i ii     vv    ii         vv   i i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_78117381_7   4283 ACT-ACAACCAACTGGCTTT-GACAAAGTTTTAAAAAAGAAGCAATGAGG 4330
                          i - iiii   i  ii   -     i v viv  i vv vv     i  
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_78117381_7   4331 AAAGGAATC-CCTATTCAGTAAATGGTCCTTTGCTATCTGTCTAGCCATA 4379
                             -   v-i  v    ii       v  vv vi v   vv  ?   i 
  L1M4_orf2#LINE/    387 AAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_78117381_7   4380 TGCTGAAGATTGAAACTGGTCCCTTTCCTTATAACATATACAAAAATCAA 4429
                            vi    v    ii   v   i v   i i v             i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_78117381_7   4430 CTGAAGAAGGATTTAAAGAATTAAATGTAAAACCTAAAGCTATAAAAACT 4479
                           v  i v    i- ?   vi         i v     i        -  
  L1M4_orf2#LINE/    486 CTCAAAATGGATC-AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CT 533

  chr2_78117381_7   4480 CT-GGAAGACAAATTAGGCAATATTATTCTGGACAAAAGACCTGGCAAAA 4528
                           -i     v  vv    ?ivv v v   vv   vvvi iiiv     vi
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_78117381_7   4529 ATTTC------ATGACAAAAATGCCAACAGCAATTGCAACAAAAATAAAA 4572
                         i    ------      ------    v    vvv         iv    
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_78117381_7   4573 ATTGATGAATGGGACCTAATTAAACTAAAGAGCTTCTGCACGACAAAAGA 4622
                           v   i   v    i v  i   v v  i i   i  ii vv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_78117381_7   4623 AACTACCAACAGAGTAAACAGACAAACTACCAAATGGGAGAAAATATTTG 4672
                         v    i   v i   i  v      v i  vi                  
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_78117381_7   4673 TAAACTATGCATCCAATAAAGGTCTAATGTCTAGAAGCTAGAAGGAATTT 4722
                         i   ii  ii   ii    i  v  vi i  i    vv  v  i   i i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_78117381_7   4723 AAACAAATTAACAAGCAAAAACCAAACAATTACATTAAAATGTGGACAAA 4772
                         vv    v i  i  vv    iv    i  iivv   ?   vi   i    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_78117381_7   4773 GAACATGAACAGATACTTTTCAAAAGAAGACAGACACATGCCCAACAAGC 4822
                          i iv    i   i i  i  v        i v   v   v    i    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_78117381_7   4823 ATATGAAAAAAATGCTCAAAATCACTAATCAT 4854
                          i       i -       v    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (143 / 105)
Gap_init rate = 0.01 (13 / 871), avg. gap size = 1.77 (23 / 13)  

2132 26.59 2.99 1.76  chr2_78117381_78124202     5596  6332 (490)    L1M4_orf2#LINE/L1      163   908 (0)  

  chr2_78117381_7   5596 GAACCTAAAATAAAAGTTAAAAAATATTTTAAAAA----GAATAAAGCTG 5641
                          i   i i    --- ii    v -  i  i    ----   i    i  
  L1M4_orf2#LINE/    163 GGACCCAGAATA---GCCAAAACA-ATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_78117381_7   5642 GAAGCATTATACTACCTGAATTCAAAATATACTACAAAGCTATGATTACC 5691
                           i vv i i   v  ii v       iv             iii v i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_78117381_7   5692 AAAACAACATGGTACTGGCATCCAAACAGACACATAGACCAACAGAATTG 5741
                           i   iii            vvii i     i     i   ii    v 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_78117381_7   5742 AAAGGAGAACTCAAAAATAAATTGAAATATTTACAGCCAACTCATTTTTG 5791
                           vv    iii  i       iiv v i     ii i   i v     i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_78117381_7   5792 ACAAAGTTACCAAGA--ATGTAACACTGGGTATATGATAGTGTGTTCAAT 5839
                             i v i      --  vi  ---    v v vi     v v     i
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAA---TGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_78117381_7   5840 AAATGGTGCTGG-ATAGACTAAATATCCATATGCAGAAGAATAAAACTAG 5888
                                     - i -   ii   ?   i     i      i  ii i 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACA-ACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_78117381_7   5889 ACTACTATCTCTCATCATATAAAAAAATCAAAT-AAAATCTATTAAAAAC 5937
                           iv   i   v  i      v      i  v -     vv  i ? i  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_78117381_7   5938 TTGCATGTAAGATCTGAAACCTTGAAACTACAGGAAGAAAACATTGGAG- 5986
                         i iv        v  i    iv i     vivi           v  ? -
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_78117381_7   5987 AAATGCTTCA-GAACGTGGGTCTAGACAAAGACCTATTG--TGTAACACC 6033
                             -    i-  v v     -   i   v iii v  i-- i i     
  L1M4_orf2#LINE/    555 AAAT-CTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_78117381_7   6034 TCAAAAGCACAGACAGCAAAAGTATAATTGG-TAAGTGAGATTATAT-AC 6081
                         --         ii  i      v v  v i -   i vi  i vi  - v
  L1M4_orf2#LINE/    603 --AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_78117381_7   6082 ATCTAAAAACTTGTGCACAACAAAGGAAACAATCGACAGAGTGAAGAGAG 6131
                          vi         v  ii vv       v  v   i v i      i   v
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_78117381_7   6132 AACCTATGGAATTAAAGAAAATACTTGCAAACTCTCCATCTGAGAAGGCA 6181
                             i ii    vii        i       iiv vi      v    v 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_78117381_7   6182 ATAATACCCA----ACAGAATGAA---TCAGTAACTCAATAGCAAAACCA 6224
                         v vi  i   ---- i v  v   --- i -i         ii    vv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATAAAAAGA 799

  chr2_78117381_7   6225 CAAATAATCTGATTAAAAAATGTGCAAATCATCTGAAGAGTCATTTCTCC 6274
                                i ii   ?       v     vv  i    v  v         
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_78117381_7   6275 AAAGAAGATATGTAAGTGGCTAATGGGTATATAAAAA-ATACGCAAAATA 6323
                                    ii  i    i   ii i i  i    -  i v   v  v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_78117381_7   6324 ATTAATCAT 6332
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.70 (121 / 71)
Gap_init rate = 0.03 (20 / 746), avg. gap size = 1.75 (35 / 20)  


3262 26.16 1.11 0.44  chr2_78160345_78162582.rev      845  1746 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_78160345_7    845 TGGAAAGACATCCCATGCTCATGGATTGGAAGAATCAATATTGTGAAAAT 894
                                 i        i               v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78160345_7    895 GACCATACTGCCCAAAGAAATCTACAGATTCAATGCAATACCTAACAAAA 944
                          i v     v      vvi              i     v    v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78160345_7    945 TAGCAA-TGCCATTTTCTCACAGAATTAGAAAAAATAATTCTAAAATTTT 993
                          vv  i-    --   i ii     v v  v  iv i  i        iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_78160345_7    994 TCTG-AAAGAAAAAAGAGCCTGAATAGCCAAAGAAATCCT-AAGAACAAG 1041
                          v  -   viv  ii  v  v           iv    i -  i  v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_78160345_7   1042 AACAAAGCTGTAGGCATCACATTACCTGACTTAAAAACATATTGCAAGGC 1091
                                i  v   vv     i v  ii i  v     v  i i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_78160345_7   1092 TATAGTAACCAAAACAGCATGTTATTGGTATAAAAATACACAACTAGACT 1141
                           i     i   i    ii  v  i   i    ii   v   vv    ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_78160345_7   1142 AATGGAACAGAATGGAGAACCCAGAAATAAATCTACGTGTTTACAGCTAA 1191
                                i     v    ii           i i iiii    ii ii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_78160345_7   1192 CTGATCTTTCACAAAGCCACCAAGAACATACTTTGGAAAAAGGGTACCCT 1241
                         i    i  iv    i vii      v   v vv   ii    ii  vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_78160345_7   1242 CGTTAGTAAATGGTGCTGGGAAAACTGAGTAACTGTATGTAGAAGAATGA 1291
                         iv i ii              v     ii  ? iii   i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_78160345_7   1292 AAATGGACCCCTATCTCTCACCATATGCAAAAGTCAACTAAAGAGGGATT 1341
                          iv          i   v        i     i i    v  i v    i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_78160345_7   1342 AAAGAGTTAAACATAATACTCAAAACTATAAAACTACTAGAGGAAAATGT 1391
                          ?   vi    ii   v vii              vi    i     ii 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_78160345_7   1392 -GGAGAAAATTCTTCAAGACATTAATCTTGACAAAGATTATATGGTTAAG 1440
                         -  ? v    -    iv   v  iivi v i   v i  viv i v  v 
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_78160345_7   1441 ATGTCAAAAGCACAGGCAACAAAAACAAAAATAGACAAATGGAGCTGTAT 1490
                          iii          i         iv         i    v ii  vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_78160345_7   1491 TAAACTGTAAAGCTTCTGCACAGAAACAGAAACAATCAACAGAATGAAGA 1540
                         i   v vv   i   i  ii vvv  vi  v  v     v i i    i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_78160345_7   1541 GATAACCTCTTGAATGGGAGAAATTACTTGTGAATTAC-TACTTTGACAA 1589
                           i    iviv            v  i   ii   i i-  - i   i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA-TCTGATAA 746

  chr2_78160345_7   1590 AGGACTAATATTCAGAATATGCAAGGAACTCAAACAATTCAATAATAAGT 1639
                         i     vi   i        ii  i      vv    i          iv
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_78160345_7   1640 AAATAA-TGAC---ATT-AAAAGCAGGCAAAGGACATGAATAGACATTTC 1684
                          i i  - i  ---   -    iii         iv              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_78160345_7   1685 TCAAAAGAAGACATATAAATGACCAACAAACATGTGAAAAACTGCTCAAC 1734
                           v        i   i     i    i  i  ii      iv        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_78160345_7   1735 ATCACTAATCAT 1746
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (150 / 83)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


1935 24.43 2.36 13.40  chr2_78166461_78171280     3315  4329 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_78166461_7   3315 AGATATTTCAAGTTCAAGAAT--AAAGATTCAATATAACCAAGATGTTAG 3362
                               ii  v     v i  --i    i i     viii      vi i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_78166461_7   3363 TTCATCCCATTTTAATCTATAAATTTAACTAAATTCCAACCAAAGTTTTA 3412
                          v vi    vv  i     i i   i   vv   i  v i    i iii 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_78166461_7   3413 GCAAATTATTTTGTGGATATTGGCAAACTAATTGTGAGGTTTATATGGAA 3462
                           vivi v     ii  v    i   i  i  iv i ii  i        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_78166461_7   3463 AGGGAAAAGACCCAAATTAGCCAATATAATATTGAACGAGAAGGA-AAAG 3511
                          v v  ii      i v       v i   v     vi     i -    
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_78166461_7   3512 TTAAAGGACTGACATTACCTGTCTTCAAGACTTAATATAGGACTGTAGTA 3561
                           ii      v   i v  iivi     i     v  i iii  ii    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_78166461_7   3562 GTGAAGACAGTGTGGTACTGGTGAAATAATAGACATATATATTAATAGAA 3611
                         i v                  iiv  vi           v  i   i   
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_78166461_7   3612 TGTAATAGTGAGCCCAGAAATAGACTAACGTTAATTTA--GTTAACCAAT 3659
                          iv   v v   i         i  i-- i vv     --  i  iii  
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCAATTGAT 353

  chr2_78166461_7   3660 CTTTGACAAGGA-ACAAAGGCAATGCAATGGATAAAAGGTGTTCTTCTTT 3708
                         i  i       i-i v   i v  v      iv   iii iv    i iv
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_78166461_7   3709 ACAAATGATCCTGGGACAAATCAACAACCATATGCAAAAGAAAATAAAAC 3758
                                i v         v vi i ?   i           -- i  ii
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--TGAAGT 451

  chr2_78166461_7   3759 AGAAGGGAAGAGAAGGGGAGAGGAGGGAAGGGGAGGGGAGGGGGAAGAGA 3808
                         v ------------------------------------------------
  L1M4_orf2#LINE/    452 TG------------------------------------------------ 453

  chr2_78166461_7   3809 AGAAAAGAAGGAAGGAAGGAGAGAGAAAGAAACGAGAGGAAGGAAGGAAG 3858
                         ----------------------------  vv -----------------
  L1M4_orf2#LINE/    454 ----------------------------GACCC----------------- 458

  chr2_78166461_7   3859 GAAAAAAAAAGAGGGAGAGAGAGGAAAAAAAAAACTGGACCTTACACACT 3908
                         ----------------------------------  --    i    - v
  L1M4_orf2#LINE/    459 ----------------------------------CT--ACCTCACAC-CA 471

  chr2_78166461_7   3909 TCT-CAAAAATTAACGCAAAATTAATCATAGACCTAATTCTAAAACATAA 3957
                          v -           v      vi    ?        v v   i vv   
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_78166461_7   3958 AATTTTACAAACACTT-GAAGGTAACATAGAAG--AAT------------ 3992
                           i v  -    v   -    iv       i? --   ------------
  L1M4_orf2#LINE/    522 AACTATA-AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_78166461_7   3993 GGGT-ATGCTGATGCCTTTTCAGATATAACTCCAAAACCAAAATCCATGG 4041
                             - v  -i   vi  i i      i  v      v  v  v v iii
  L1M4_orf2#LINE/    571 GGGTTAGGC-AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_78166461_7   4042 AATAAATTATCAATAAGCTGAAATTCATTAAAATTAAAATCTTCTGCTTT 4091
                           v   vv  vi    ii  i v     i          v   i  ivi 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_78166461_7   4092 GTGAAAGATACTGCCAAGGAAATGAGAAGACAAGCCACAAACTCAAAGAA 4141
                         vii  i  i   ii    i  i   i       v     i v vii    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_78166461_7   4142 AATATTTGCAAAAGATATATGTGATAAAGGATTGTTATACCAAATACATA 4191
                                     vv      v      i   i vv   v vi    i   
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_78166461_7   4192 CAGAAACTTTAAATAGCAACAATAAGAACACAAACAAATGAAT-AAAAAA 4240
                         v    vii   v vvv   i     i  v     i  viv   -?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_78166461_7   4241 TGCACAAAATACCTGAACAGACACCTCATCAGAAAATATATACAGATGGA 4290
                           vi    iv ii    i     ii  vi  i i  v       i    v
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_78166461_7   4291 AAGTAAGCATATGAAAAGATGCTCCACATCCTATGTCAT 4329
                         v i      i              v     v????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.02 (18 / 903), avg. gap size = 8.89 (160 / 18)  


2725 26.80 2.93 0.68  chr2_78192432_78195301.rev     1490  2377 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_78192432_7   1490 TGGAAACATATTCCATACTCACAGATAGGTAATATTAATATTGTAAAAAT 1539
                               v    i    ii   ii   v  v ivv          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78192432_7   1540 GACCAGCCTCACAAAAGCCATCTACAGATTCATTGCAATTTCCATCAAAA 1589
                          i v vv   v v   viv             vi     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78192432_7   1590 TACCATCATCATTCTTCACCAAACTAGAAAAAC-AATCCTAAAATTTATA 1638
                          v   v vv v  i  ii vi  v v  v  i -i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_78192432_7   1639 CTGAAACCAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 1688
                         iv    ivv  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_78192432_7   1689 CAAATCTGGAGACATCACATTACCTGACTTCAAACTGTACTACAAGGCTA 1738
                             vi     ivv     i v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_78192432_7   1739 TAGTTACCAAAACAGCATGG-A-----ATAAAAATAGGCACATAGATGAA 1782
                         i   v i   i    ii   - -----    ii    i  i      v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_78192432_7   1783 TGGAATAGAA--GAGAACCCAGAAATAAAGCCAAATACTTATGACCAACT 1830
                                   --    ii           v   v i i     ii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_78192432_7   1831 GATCTTTGACAAAGCAGATAAAAACATTAAGTGGTGGAAGATCACCCCAT 1880
                            i  i     i vv vi  i v    v i   v i    vi vi iv 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_78192432_7   1881 TCAACAAATGGTGCTGGGATAATTGGCAAACCACATGTAGAAGAATGAAA 1930
                                            i  i   vv ?       i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_78192432_7   1931 CTGGATCCTCTTCTCTCACCTTATACAAAAATCAATTCAAGATGAATCAA 1980
                         i    i  iivi   v    v           i  i    i   i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_78192432_7   1981 AGACTGAAATCTAAGACCTGAAACCATAATAACTCT------AAGACATA 2024
                             iv    v     v  i    i    -      ------  i     
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACATA 549

  chr2_78192432_7   2025 ATATCAAAAAATCTCTTCTAGACATTGCCTTAGACAAAGACTTCATAACC 2074
                         iv?vi   -----     vv   v   vv    i   v ii   v  ivi
  L1M4_orf2#LINE/    550 GGNGTAAA-----TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_78192432_7   2075 AAGAACCCAAAAGCAAATGCAACAAAA-ACAAAATAAATAGATGGGATTT 2123
                          v  vv         v v         - v      i   i  v   i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_78192432_7   2124 AATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACCGC----AGAGTAC 2169
                         v  i   v v    i   i  ii vv    i  v  iii---- i   iv
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_78192432_7   2170 ACAGACAACCCACAGAGTTGGAGAAAATTTTCACAAACTATGCATTTGAC 2219
                          v              i v         v  ii    ii  ii  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_78192432_7   2220 AAAAGGCTAATATCCAGAATCTAAAAGGACCTCGAACAAATCAGCAAGAA 2269
                           ii i  vi          v  v  i  v   vv    v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_78192432_7   2270 TAAAACAA----TCTCATCAAACAGTGGCCAAAT-ACATGAATAGACAGT 2314
                         v  i    ----i iv  i?  v i   v    v- iv          v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_78192432_7   2315 TCTCAATAGAAGATGTATAAATGGCCAAGAAACATATGAAAA-ATGCTCT 2363
                             v v       i  i          v  i  i       -      v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_78192432_7   2364 ACATCATTAATAAT 2377
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (129 / 105)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.67 (32 / 12)  


2718 25.34 5.28 1.15  chr2_78240741_78242649      547  1418 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_78240741_7    547 TGGAAAGATATTTTATGTTCATTGGTAGGAAGAC--AATATTTTTG---T 591
                                    iii        v i v       --      v  i--- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78240741_7    592 GTTAATACCACCCTAAGTAAGCTCTGGCCTCA-TGCACTCTCTATCAAAA 640
                          vi     iv   v  v i v  vii vi   -i   v  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78240741_7    641 ATTTAACAGCCATTTAGGCCTGAATGAAAAAGCTTGTCCCCGAATTCATA 690
                         viii i v   v   vv  vvi   vi v     vi   ivi        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_78240741_7    691 CGGAACTGCAAAAAACTTCAAAAACCCACAACAATTTTGAAAAAGAA-AA 739
                         i    v     iii  iivi  v v   v      i           -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_78240741_7    740 CAAAG---GAGGATTCATATTTCTCAATTTCAAAACTTTTTACAGAGCAA 786
                              ---     i   i i   i              vi    i   v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_78240741_7    787 CAGTAATCAAAGCAGTGTGAAACTGGCACAAAGATTAGAAACA-ATATAT 835
                                   ii       iv       i  i   --- i   -   v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT---AGACATATAGAT 297

  chr2_78240741_7    836 TAACTCATTAGAATTAAAAGTCTTGAAATAAACCCTCACATATACGGACA 885
                         i  ivv v       i i    iv           vi    v  i  v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_78240741_7    886 ATTGATTTTTTTTTAAAAGATAGTTATGTTT-CCCAGTGAGAAGGAGAAC 934
                                  ivvi--  i i - ii v vii-ii  i  i i i-    i
  L1M4_orf2#LINE/    348 ATTGATTTTCGAC--AAGGGT-GCCAAGACCATTCAATGGGGAA-AGAAT 393

  chr2_78240741_7    935 TATCCT--CAACAAATAATACCAAGATAACTGGATTTCCACAAGCAAAAG 982
                         vi  i --        ii i iii  i        v?     v       
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_78240741_7    983 ATTTAAGTTGAACCCC-ACTTTACACCTTTTTCAAAAATCAAC------- 1024
                          v v      i     -  i i     v v v       i   -------
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_78240741_7   1025 -------------AAATGCATGAGCTAAACCAATAAAACCCTCAGAAGAA 1061
                         -------------     i v        v v       i  i       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_78240741_7   1062 AACCTAGGCATAAAACTTTATGTCCCTGGATAAAACAATGGATTTGTTGA 1111
                            v    ?i    v   ii  v  i   i v ii      v  iv v  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_78240741_7   1112 TATATCACCAAAAA-AGAAGCAACATTAGTGAAAATAGATGAATTAAGAT 1160
                            iv        i- v        vv  vi         i    iiiv 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_78240741_7   1161 TCATGAAAATTGAAAACTTTTGTGCATCAAATAAAATTATCAAGAAAGTG 1210
                             v      i             v     vi v i             
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_78240741_7   1211 AAAATAAAACCTATTA---GGGATTTAAAATATGTATACATTGTATATTT 1257
                             v v    i ivi---    v--       v ii v  ii     i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAG--AAAATATTTGCAAATCATATATCT 741

  chr2_78240741_7   1258 TTTGAGAGCTTAATATATTGAATG----AAGTACTCTTACAGGTCAAGAA 1303
                         vv i  i vi vi   viv    i----   v         iv    v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_78240741_7   1304 CAAAATGACAAAAAAACCCAAT-GAATATTAGGCAAAGGACTTGTATAGA 1352
                         i    v      v  -      -?  v v i         i   v     
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_78240741_7   1353 CATTTTTCCATACAAGACAAACAAATGCTTAATAAGAACATGAAAA--TC 1400
                              i    v v    i v       vii      v         -- v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_78240741_7   1401 TTCAACATCTTTAGTCAT 1418
                         i        v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (121 / 97)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.67 (56 / 21)  


2505 24.92 5.86 3.49  chr2_78332456_78336656     2823  3709 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_78332456_7   2823 TGGAAGGATATTTTGTGATAATATATTGGAAGAATGAATATTGGTAAAAT 2872
                              i     iiii  v v  iv         v v       v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78332456_7   2873 GTCCATCCTAACCAAAGTGTCCTACATATTCAGTGTAATCCCTATCAAAA 2922
                          v v  v  vv     v  vi     v     ii i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78332456_7   2923 TACAAATGACATACTTCATAGAAACAGAAAAACTG-TCACAAATTTCGTA 2971
                          v v iivi v vi  iii     iv  v  i   -  vi   v   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_78332456_7   2972 TAGAGCAACAATAG-CTCA-AATAGCCAAAGCAACCTTGAGCAA-AATAA 3018
                          i  ivvi   vi - i  -          i   i     iv  -  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_78332456_7   3019 CAAAGCTGGAGACATCACACTACCTGACTTCAGAATAAACGACAA-GCTA 3067
                              i     ivv       v  ii i    i  ivv  v    -    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_78332456_7   3068 TAATAACCAAAATAAAATTGTACTACCATAAAAATAGACACATGGACAAA 3117
                         i i   i   i i ivi v     iv     ii       i  i  iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_78332456_7   3118 TGGCACAGAAATGAGAACACAGAAATAAATTTAGGCAGTTA----AAACT 3163
                            v i    v     iiv          iii vi  v   ----v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_78332456_7   3164 GATTTTTGACAAAGTTGCCAAAAACACACAATGAAGGAAAGACAGCCTTT 3213
                               i     i v      i v  iv     ii i  ii i  i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_78332456_7   3214 TCAATAAACGGT--TGGAA-ATCTGGATAGTTACATACAAAA-------- 3252
                             i   i   --   i - v       ?ii    i     --------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_78332456_7   3253 -------------------------TAAAAATCAACTCAAC-TAGATTAA 3276
                         -------------------------i      i       v- i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_78332456_7   3277 AAAGTTAAAGGTAAAACCTGGAATTATGAAACTATTAGAAGAAAACATAG 3326
                          i vi    v    i v  ii  i   i     v                
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_78332456_7   3327 GGG-AAATACTTCATGACATTAGTCTGGGCAAGAATTTTTCAGATAAGGC 3375
                          ? -    -    i    v  i vi i     vii   i i     v i 
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_78332456_7   3376 CCCCAAAGCAGAGGCAACAAAACAAAAA-CAGACAAGTGAGATTGTAT-- 3422
                         v  v      v i         v     -i   i  i vi  i vi  --
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_78332456_7   3423 -AAGTAAAAATATTTTGTACTGCGAAGGAAACAATCAACAGAGTGAAGAG 3471
                         -  v      i-      i  v i     v  v     v i      i  
  L1M4_orf2#LINE/    650 AAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_78332456_7   3472 GTAACCTACGTAATTGGAGGAAATATTTGTAAACTATGCATCTGACAAGG 3521
                         ii    i  iv   v    i         i   ii  ii      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_78332456_7   3522 GA-TTATAATGAGACTATATATATATATATATAAACCCAAACAACTCAAT 3570
                           -  i  viv   --------       v -i   i vv          
  L1M4_orf2#LINE/    749 GACTTGTATCCAGA--------ATATATAAA-GAACTCTTACAACTCAAT 789

  chr2_78332456_7   3571 AGCAAAAAAAAAAAAAAAAAAAACAAAAAAACCTGATTTTTTTTAACTGG 3620
                          ------------- v     i     v  -  ii   ?vv---  v   
  L1M4_orf2#LINE/    790 A-------------ATAAAAAGACAAATAA-CCCAATTWAA---AAATGG 822

  chr2_78332456_7   3621 GCAAAAGATGTGAATAGGCATTTCTCAAAAAAGAAAAAAATACAAATGGC 3670
                              i   v       i        v   i --- i v           
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGA---AGATATACAAATGGC 869

  chr2_78332456_7   3671 CATTAGGCATATGAAAAAATGCTCAACACCAATAATCGT 3709
                           v  i   i       i          i  ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (133 / 84)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.77 (83 / 22)  


2329 27.83 3.14 1.23  chr2_78342870_78347675     3451  4341 (465)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_78342870_7   3451 TGGAAATACATTTCATGATCATTAATTGGAAGAATCAATATTGTTAAAAT 3500
                               v i  ii    v    vi         v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78342870_7   3501 GCCCACTGTGTCCAAAGCAGTCTACACATTTAATGTTATTCCTATTAAAC 3550
                          v v ivv vi     viii      v   i  i iv  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78342870_7   3551 TACAAAC-ATTATTTTTACAGAA-TTAAAAAA--AATTCTAAAGTTCATG 3596
                          v v i -iiiv     i     -  i v  i--i  i     i     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_78342870_7   3597 TGCAA-CATAAAGATTCCA-AGTAGACAAAGCATTCTTATGCAAAAAGAA 3644
                           v  -iii  i ivi   - i   v    i  v    iviv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_78342870_7   3645 CAAATCCTGAGGCATCATATTGCCTGACATCAAATTATACTACACGGCTA 3694
                             viiv    vv   i i v  ii iv     viv       vi    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_78342870_7   3695 TAGTAAAAAAAAATTCATGAATGATACTGATACAAAAAAAGACACATAGA 3744
                         i     vv  i ---  - vi  i     ii i  ii v     i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGA---CA-GTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_78342870_7   3745 GCAATAGAACTGAATAGAGA-TCACAGAAATAAAGCCCTATAC---TATA 3790
                         v    i   iv    v    -  -          --  i    ---   i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAA--CCCATACATTTATG 343

  chr2_78342870_7   3791 CCCAACTGATATTCAATAAAGTCAATAAAAATAAACAATGTGGAATGGAT 3840
                         vi   i    v   i i  i viivi  i vi vv     v    v i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_78342870_7   3841 ATCCAATTCAATAAATGGTACTGAGAAAACTGGCTAGCCATAATGCAGAA 3890
                          vi vv     i       i   i  v      v  ?   i -    i  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAA 442

  chr2_78342870_7   3891 AACTGAAACTGGAACTCTGTCTCTCATGATATACAAAAATTAACTCGAGA 3940
                         i v    ii    v i  ii   v  iv                  i i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_78342870_7   3941 TGAATTAAAGGCCGAAGTGTAAGA-CAAGAAGCTATGAAAAATCCTAGAG 3989
                           i  i ?  i  v  i       - v i  -    -    v  i    i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTAT-AAAACTCTTAGAA 540

  chr2_78342870_7   3990 GAAAACCTAGGAAAAACTCTTCTGGACTTTAGTCTAGGCAAAAAATTAAT 4039
                               v    ?iv  v     vv   i  i vi       viiv  vv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_78342870_7   4040 -GATGAAGACTCCAAAAGCAAATGC--CAAAAAAAAAAAAAGACAAATGG 4086
                         -   - v   v         v v  --     i      v   i    v 
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_78342870_7   4087 GATTTAATAAAAGTAAAAAGCTTCTGTGCATTAAAAGAAACAATGAACAG 4136
                           i  v  v   i v    i   i     v i   i  v  v  v  v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_78342870_7   4137 AATAAACAGACAATCTACAGATT---AAAAAA-ATTTACATATTATGCCT 4182
                          i i  v      i i     v --- i    -    i  v  i  iiv 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_78342870_7   4183 CTGAGAAAAAA-TCATTTCCAGAATCTGCAAAGAACTCAAACAACTCAAC 4231
                             v  iii - ii v        v ii         vv         i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_78342870_7   4232 AAGAAATGAACAAACAGTCTCATTAAAAAGTGGACAAAGGAAAGGAACAG 4281
                           v   vii     i ii iv   ?    i   i       vvv   i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_78342870_7   4282 ATATTTCTCCAAAGAAGAAATATAAG--------AAGCACATAAAAATCT 4323
                          i                v   i  i--------        i    vv 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_78342870_7   4324 -TTCACCATTACTAATTAT 4341
                         -i   v   i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.70 (39 / 23)  


3153 26.81 0.66 0.88  chr2_78351625_78355861     2836  3745 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_78351625_7   2836 TGGAAAGATAATCCGTGTTCGTGGGTTGAAAGAATCAATATTGTTTATAT 2885
                                   vi  i     i   i   i    v i         v v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78351625_7   2886 GTCTATACTACCAAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 2935
                          v v     v  v   vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78351625_7   2936 TACCAATGATATTCTTCACAGCAATAAAAAAACTAA-CCTGAAATTTATA 2984
                          v   iiviiv  i  ii   v   vi v  i  i -   i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_78351625_7   2985 TGAAGCCGTAAAAGATTTAAAATTGCTAAAGTTACCCTCAGCAAAAAGAA 3034
                           i ivi i  ii  iii i   v  i   iiv i i v iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_78351625_7   3035 GAAAAGTAGAGCAATCATGTTACTTGACTTCAAATTATACTAGAGAGCTA 3084
                         v   iv i   v v   iii v iii i      viv     v i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_78351625_7   3085 TAGTAACTAAAATTGTATGGTACTGACATAAAAACAGACACATAGACCAA 3134
                         i     ii  i iv  i        i     ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_78351625_7   3135 TGAAACAAAAA-GAGAACCCAGAAACAAATTCATACAATTACACAGTAAA 3183
                           i  i i  v-    ii       i   ii      v   ii--  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG--GTCAA 348

  chr2_78351625_7   3184 CTCATTTTTGACAAAGGTGCCAGGAACATACATTGGGGAAAGGATAGTCT 3233
                         i v     i     i       i  v   v  v         i       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_78351625_7   3234 CTTCGATGAATGGTGGTGGGAAAACTGGATATCCATATGCAAAATAATGA 3283
                         i   i ii       v     v         ?   i        v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_78351625_7   3284 AACTTGACCACTATCTCTTGCCATATACACAAATCAAATCAAAATGGACT 3333
                          ii v    v   i   vii         v    i  v          ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_78351625_7   3334 AAAGACCTTCATCTGAGACCTCAAGCTATGAAACTACTACAAGAAAAC-T 3382
                          ?      vv  v i   v  v  i    i     vi  v        - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_78351625_7   3383 ATGGGAAACTCTCCAGGGTAT-GGTCTGGGCAAAAAAATCTTGAGTTGTA 3431
                          v ? v  v   i iv iiv -  vi i     viivv    -  v i i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chr2_78351625_7   3432 CCCCACAATCAAGGACACACAATCAAAGCAAAAATGGATACATGGGATCA 3481
                         v v -   --   v   vi   iv    v      i    v  v   iiv
  L1M4_orf2#LINE/    598 ACAC-CAA--AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_78351625_7   3482 CATTATG-TTAAAAAGCTTCTGCACTGCAAAGGAAACCATCAACAAAATG 3530
                            i vi-       -   i  ii  v       v  i     v   i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_78351625_7   3531 AACACAAAAACCCCAGAATGGGAGAAAATGCTTGCAAACTATCCATTTGA 3580
                           v v v  v  v                ii       ii  vi  i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_78351625_7   3581 CAAGAAATTAATAACCAGAATACATAAGGAACTCAAACAACTCTATAAGA 3630
                         i   ii i vi  v        i    i      vv       v    v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_78351625_7   3631 AAAAAATATGATAATATGATTAATAAGTGGGCAAAAGATCGAAATAGACA 3680
                             i i -i    ivii   ? v  i        i   ivi        
  L1M4_orf2#LINE/    794 AAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_78351625_7   3681 TTTCTCGAAA-AAGACACACAAATAGCAAACAGGCCTATAAAGAGGTGCC 3729
                               v   -    i i      i  v  i i  vi  i  i  i   i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_78351625_7   3730 CAACATCACTGATCAT 3745
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (148 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.17 (14 / 12)  


 717 25.47 10.75 6.07  chr2_78408257_78410297.rev      501   928 (1113)    L1M4_orf2#LINE/L1      163   610 (298)  

  chr2_78408257_7    501 GAATCTAGAATAGTCAAATACGCT-TTGAAAAAG--GAACAACTTTGGAA 547
                          i i i       i    -  iv -         --      vv     i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_78408257_7    548 GACTGACACTGTCTGATTTCAAGACTTA--ACAAAGTTTAAAAAAACCCA 595
                             v     vi ii       i     --      i - v iv  i v 
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT-ACAGTAATCAA 260

  chr2_78408257_7    596 --CATTTTGGTCTTATTGTAAGGATAGTCACATTGATCAATAGAACTGAA 643
                         --  v v    vi ivii         v  i  v       i   iv   
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_78408257_7    644 T-----------AGATAGGCCTATTCATATATAATCCATTGTTTTTTTTT 682
                          ----------- i   ii  i  v   v   ii  v    v    i---
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC--- 357

  chr2_78408257_7    683 TTTGACACAGATCCCAAAGATGACAAGTTAATATAACACAAGAAAAAATA 732
                         ---    vi i v    ----   v v i   i------ii    i    
  L1M4_orf2#LINE/    358 ---GACAAGGGTGCCAA----GACCATTCAATG------GGGAAAGAATA 394

  chr2_78408257_7    733 GTATTTTAAACAAATGGTAGTTGGACATAC-AGATATCCACATGGAGAAC 781
                           v    v          iv v     -  -i    ?       v i  v
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACA-ACTGGATAKCCACATGCAAAAG 443

  chr2_78408257_7    782 AA-AAAGAAAGATCA--AACTCAAATTCCAT-TAAAACAAT---CCCTAA 824
                           -i   vvi  i v-- v    v --    -  v  v   --- i v  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACA--CCATATACAAAAATTAACTCAAA 491

  chr2_78408257_7    825 ATAAATCATAAATCTTCAGGTAA----------TATATTCCTTCCATAA- 863
                           ii    ? i i  vv v    ----------    vvv  iii v  -
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_78408257_7    864 ---ACA-----ATAAATTTTGAAAAATGACTTTGGGTTAGGTAGATA-TT 904
                         ---   -----i     i  vi----    i          i -  i-  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCG----TGACCTTGGGTTAGGCA-ATGGTT 586

  chr2_78408257_7    905 TTTAAAATAGTACGCTAAAAGTAC 928
                          i v i   vv  i i     i  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCAC 610

Transitions / transversions = 1.23 (59 / 48)
Gap_init rate = 0.05 (23 / 448), avg. gap size = 3.13 (72 / 23)  

 452 25.94 4.60 2.93  chr2_78408257_78410297.rev     1303  1541 (500)    L1M4_orf2#LINE/L1      656   898 (10)  

  chr2_78408257_7   1303 AAAACTTTTGCTTTTCCAAAGTCAATAAATACTAAGCAAATAAAAGGAAA 1352
                                   ivi   v  i v  v  ----ii   v  i i   i  v 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTA----TCAAGAAAGTGAAAAGACA 701

  chr2_78408257_7   1353 ACA-AGAGATTTGCAGGTCAGAGTTGCAAAT-A-ATAGCTGAGAAAGTTC 1399
                           v- v   v v v  ivv v v        - -   v    v  i vv 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_78408257_7   1400 TTGAATATAAATATATATATAAAGGACTCTTACAATGCAATATTATAATT 1449
                            v  vi i ---          i          iv     v  v  vv
  L1M4_orf2#LINE/    752 TTGTATCCAGA---ATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_78408257_7   1450 TTAAA--AC--AATTTAAAAATGAGCACAATATATGAACAAATACATCAC 1495
                         vi   --  --    ?       i   v iv  v    i i i iv  v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_78408257_7   1496 CAAATAAGAAGTACAAATAG----TAAGTATATGAAAATATCCTCAACAT 1541
                             v    vi       i ----    i i       v  v        
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

Transitions / transversions = 0.69 (25 / 36)
Gap_init rate = 0.03 (8 / 243), avg. gap size = 2.25 (18 / 8)  


2995 28.56 1.22 0.33  chr2_78413404_78415554      760  1659 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_78413404_7    760 TGGAAGAACATTCCATGCTCATAGATAGGAAGAATCAATATCGTGAAAAT 809
                              ii i  i     i    i   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78413404_7    810 GGTCATACTGTCCAAGGTAATTTATAGATACCATGCCATCCCCATCATGC 859
                           iv     vi    iv i  i  i    v v i  v     i    viv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78413404_7    860 TACCAATGAGTTTCTTCACAGAATTGGAAAAACCTACTTTAAAGTTCATA 909
                          v   iivivi  i  ii     v v  v  i iv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_78413404_7    910 TAGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 959
                          i   viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_78413404_7    960 CAAAGCTGGAGGCATCACGATACCTGACTTCAAGCTATGCTACAAGGCTA 1009
                              i      vv    iv v  ii i     iviv i      i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_78413404_7   1010 CAGTAACCAAAATAGCCTTTTGGTACC------AAAACAGAGATATAGAC 1053
                               i   i i  --- v      i------ ii i   v       i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAG---TGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_78413404_7   1054 CAATGGAACAGAATGGACCCCTCAGAAATAACGCCGCATATCTACAACTA 1103
                                 i     v  vvvii         vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_78413404_7   1104 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 1153
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_78413404_7   1154 TATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 1203
                          v  i  i       i      v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_78413404_7   1204 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 1253
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_78413404_7   1254 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACG 1303
                         i ?    i  v    v   v       i      vi i           i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_78413404_7   1304 TAGGC-CA----TTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAAA 1348
                             ?-i ----   iv   viv  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_78413404_7   1349 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1398
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_78413404_7   1399 TAAACTAAACAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAATA 1448
                         i   v v  v i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_78413404_7   1449 GGCAACCTACAGCATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 1498
                          i     i    v            v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_78413404_7   1499 GGGCTAATATCCAGAATCTACAATGAACTCAAGCAAATTTACGAGAAAAA 1548
                           i  vi          v  i  v      vvi   v iv ii v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_78413404_7   1549 ATCAAACAACCCCATCAAAAAGTGGGCTAAGGATGTGAACAGACACTTCT 1598
                         iv    i     v  i?    i     v      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_78413404_7   1599 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 1648
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_78413404_7   1649 TCACTGGCCAT 1659
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.34 (145 / 108)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 3.50 (14 / 4)  


 517 30.18 9.10 6.59  chr2_78424758_78426365      294  1128 (480)    L1M4_orf2#LINE/L1       53   908 (0)  

  chr2_78424758_7    294 CAACTTTTTCCAAATTTATATATAAATTTCAAGCAGCTTCAATAAAGA-- 341
                            ivi ii       v  v  i i   iv v   iiii v  v  i --
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_78424758_7    342 -CA-----------TGTAAAATATT---AAGCTGATC--ACAATTATATA 374
                         -  -----------  i i  -   ---         -- v    -i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATT-CATA 150

  chr2_78424758_7    375 AAGAAGAGTACAGAAGTAGAAATAACCAAGATTATATTTTAAGAAGAAAT 424
                         vi   iv i vi i vivii    i    i iv  -i  v  i     --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAA-- 197

  chr2_78424758_7    425 ATGAGAAAAATTG----ACCTTTACTTAACAGTTACTAAGACTTATTG-- 468
                         --  iv   i   ----  iivi    vv  i  v -  i     i i--
  L1M4_orf2#LINE/    198 --GAACAAAGTTGGAGGACTCACACTTCCCAATTTC-AAAACTTACTACA 244

  chr2_78424758_7    469 AAGTTATAGACAGACATATTGAAGTTATAAAAAAAATACTGTGGAGTTGG 518
                            i  i  ------------------   vv  i i v     vii   
  L1M4_orf2#LINE/    245 AAGCTACAG------------------TAATCAAGACAGTGTGGTACTGG 276

  chr2_78424758_7    519 CAGAGTGAAAAGCTAACAGACCAATACTAAAAAATAGAGAA--CA-AAAT 565
                           v iv  v ii vv i   i    ivv v i   v    i--  -    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_78424758_7    566 AAACTGACCCAAACATTTAAGGACAATTG-----TGACAGAGAAGGAAAG 610
                             ----   v       v  v      -----i    ii iv vv   
  L1M4_orf2#LINE/    327 AAAC----CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_78424758_7    611 GGCATGACAAATCAGTGGGGATTAATTCAAGTATT--CAATAAATTGTA- 657
                         iv   ------   i      vvi v --   v  --   i    v  i-
  L1M4_orf2#LINE/    373 ACCAT------TCAATGGGGAAAGAAT--AGTCTTTTCAACAAATGGTGC 414

  chr2_78424758_7    658 TACAATAATATGATCTCCATAT----AAAAATGAAAATTATGCTGCCACC 703
                          ivi i  ivv   v?   i  ----  i      i-  ivi iv i   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAG-TTGGACCCCTACC 463

  chr2_78424758_7    704 TCATAGCATACA-AAAAAT-----CCAGATAGATTATAAAACTATTGGTA 747
                            i v    i -      ----- v i  i   i ? i v   vvv   
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_78424758_7    748 AAA-TGAAAATTTTGAAACTTTTGTAAGTATTCATAGTAGTATGTTTTCA 796
                          i -iv    i v i     i  iv   v vv     v?   vi i   i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_78424758_7    797 TGTCATCTAGAAATTGAAGCA----TTTCTCA---ACGACAC-AAAAATA 838
                           -- i  v ii-  - i   ----     i --- i     -    ii 
  L1M4_orf2#LINE/    564 TG--ACCTTGGG-TT-AGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_78424758_7    839 CAAGCCATTAA-GAAAGAA-AACTTGATCAGACT-----AAAATTTAAAA 881
                              v iv  -    i  - iv vi  ii    -----      v    
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_78424758_7    882 CGTATTATTAGTATGGCAAAATACTCTATAAGGTAAGGTTAAAAAAATGC 931
                          ---  -  -  iivv    iv  v    v i v   -- i    i iiv
  L1M4_orf2#LINE/    660 C---TT-TT-GTGCTTCAAAGGACACTATCAAGAAAG--TGAAAAGACAA 702

  chr2_78424758_7    932 CACACTG---GGGAAAATATATTTTCAATGTATATAACCAACAAAA---T 975
                          v   v ---    i  v      v   vvi     v ii i  ii--- 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_78424758_7    976 TGAATACTCAGAATTTACAGAAA---TTTAT--TTCATTTA-AAAAAGAT 1019
                           --  ii      v  i i i ---i   i--i   v v -       i
  L1M4_orf2#LINE/    753 TG--TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_78424758_7   1020 TCAACAGCCTAAATGGAGAAACGTACAAAGGATATAAACAGACAACTAAC 1069
                         -v  i i  i  - v? i   i vi        v i  i     vi vv 
  L1M4_orf2#LINE/    801 -AAATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_78424758_7   1070 AGAGGAGGAGACTA-AAATAGTCAACGTGTATGCGAAAAG-TACTTTTCA 1117
                         vi i  i  v -  -    i i   iiv i iii      - i  ivv  
  L1M4_orf2#LINE/    849 CAAAGAAGATA-TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_78424758_7   1118 CTAGGAATCAA 1128
                         ii ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.06 (49 / 856), avg. gap size = 2.67 (131 / 49)  


1006 26.61 6.05 7.86  chr2_78460245_78462240      477   972 (1024)    L1M4_orf2#LINE/L1      166   652 (256)  

  chr2_78460245_7    477 CCCAGAAC--TTAAAGTAAAATTTTAAAAAT--AGGACAAATTTTCAGGG 522
                                i--ii   -- v   i  i    v--  i     v  vv   i
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAA--ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_78460245_7    523 CTAATATTACCTGAGTTTTATCA-TTATTATAAAGTTACAGTAATCAAGA 571
                           v i i v  ii -   i vv -   i  i    i              
  L1M4_orf2#LINE/    214 CTCACACTTCCCAA-TTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_78460245_7    572 TACTAGGGCATTGCCATAAAGATAGACAAACAGACTAATGGGACAGAATA 621
                         i v iv  i i  v     i        v i   ii     i i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_78460245_7    622 GAAAATCTAGATACAGAGCCG--CATATGTGGATAACTTGACTTTTCACA 669
                           i i  i   v i i v  i--   v i   vi  -    i   iv   
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAA-TTGATTTTCGACA 361

  chr2_78460245_7    670 AAGA-ACCAAAGAAATTTGTTGGGGAAACTATAGACTTTTCAGCAAATAG 718
                          i i-i    iivv   iiv        vv    v       i     i 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_78460245_7    719 TACAGGAACAATTGAATAGC-ACAGGCAAAATACAATAAAAGTAACATTA 767
                          i v  i    i  i   ? -   v      -------------------
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAA------------------- 442

  chr2_78460245_7    768 ATAATCATAATAATAAGTAAACTTTGACCTGGACCTTATGCCATTTGAAA 817
                         --------------i i i  v  v    ivv    i ii    v iv  
  L1M4_orf2#LINE/    443 --------------GAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_78460245_7    818 ATATTATATCTCACTGGATTATA--CCTAAAAATGAAACCTGAAGCTGTA 865
                          v    vv  vv v     i ? --      vi i i v  i  i  i  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_78460245_7    866 CAACTTCTAGAAGAAAGCACAGGAGAAAATT---GTGATCACATATTTGA 912
                         v    ii         i  i   ? v    i---    i viivi  v i
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_78460245_7    913 ----GATTTCTCAG----GGCAGGTCAAAAACACAATCCATAAAAGAACA 954
                         ---- i     i  ---- i  --i     i     v v i       v 
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACA--CCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_78460245_7    955 AATG-------TG-ACTTCATCAAAA 972
                            i-------  -            
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAA 652

Transitions / transversions = 1.63 (80 / 49)
Gap_init rate = 0.03 (17 / 487), avg. gap size = 4.06 (69 / 17)  

 529 20.50 15.00 1.50  chr2_78460245_78462240     1305  1504 (492)    L1M4_orf2#LINE/L1      682   908 (0)  

  chr2_78460245_7   1305 ATTAAGA---TGAAAAGACAAGCCACAAAATAGCAGAAAATATTTTCAAG 1351
                           i    ---           v     i   i v           v   i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_78460245_7   1352 AAATATATCCCGTAA------------------ATGTAAAGAATTCTCAA 1383
                         vv       ivi   ------------------  i       i   i v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_78460245_7   1384 AACTTAATAA-------GTAAACAACTTAATACAAAATAATGG-CAAATA 1425
                             i     -------ii   i   ii   v?    --    -    vi
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAA--ATGGGCAAAGG 829

  chr2_78460245_7   1426 TTCTGAATAGGATATTTA-CCAAAGAAGGTATTCAGATGATATATAAGCA 1474
                         v i       - i    v-         i   v  i   iivv       
  L1M4_orf2#LINE/    830 ATTTGAATAG-ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_78460245_7   1475 CATGACAAAATACTCAGCATCATTAGTCAT 1504
                              v  i  i    i     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (25 / 15)
Gap_init rate = 0.03 (7 / 227), avg. gap size = 4.71 (33 / 7)  


1201 30.40 4.56 3.34  chr2_78504478_78506083.rev      458  1115 (491)    L1M4_orf2#LINE/L1      221   886 (22)  

  chr2_78504478_7    458 TTCCCAATTTCT---CTT-CTACAAAAC------AATGAAAACTAATTTC 497
                                    v---   -       i ------   v  i  - i v -
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC-AGTGT- 268

  chr2_78504478_7    498 TATTATTGGTGTGAGGATATTTATATAC-CCAGTGGAGAAAAACACAAAA 546
                         -iv  i   ii i      vvi     v-i  i    iv i  ivv i i
  L1M4_orf2#LINE/    269 -GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_78504478_7    547 TACAGAAGTAAGACCACATACTTAACAGCCAATTGTTTTTTAACAATG-T 595
                          v     i   iv   i i i   -ii i      v    ii    v - 
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTA-TGGTCAATTGATTTTCGACAAGGGT 366

  chr2_78504478_7    596 GCCTGGGTAATTAATTTGGGAAGTAGTA-TTTTTTCAACAAAAGG-GCTA 643
                            vi iiv   v v v     iv i  - i           v  -   i
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_78504478_7    644 AAA-AAT--GTTACTTATATAAAAAAAAAAGGAATAAGGTCG--ACATTA 688
                         ii -  i-- v  ?ii i  iv    i  v i i vi ii v--  v i 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_78504478_7    689 CATCGTACACAGAAA--AA-TAAAAATAGACCATAAACCTAAAGGTAAG- 734
                           i i  i   i   --  - v     i  i  ? i       v     -
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_78504478_7    735 -CCAAAACTAGAAAACTTCCAGAAGAAAACA--AGAGAATGTTTTTGTGG 781
                         - i       v      iii           --i ? v vi i  i   i
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_78504478_7    782 CATTACGATAAACATAAAGTTATCAGTTAAGACAGGGCAAAAATATCCAT 831
                          v  iv v  ii  vviiv  v i  v  v    v--     ii ivvii
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC--CAAAAGCACAAGC 614

  chr2_78504478_7    832 GATGCATTAAAAAATAAATAAAATGATCTTTTTCAAAAATAAAAGTGTTT 881
                         i iiv vv        i     v  iv   iv      v     iiv   
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_78504478_7    882 GCACTTTAAACAATACATTTAGGAAAAATAAAAGGTAATTCCCAGATATG 931
                          ii   i   vi i  vv i i    ivv     ii  ii v    -   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA-ATG 713

  chr2_78504478_7    932 A-AGACTATATTTATAATGTATGTATGTGATGAAGGATATGTATCTAGAA 980
                         i-   vv      ii  vvi  i   v    i i   iv      i    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_78504478_7    981 TGTATGAGAAAGTCTTATCATTCAATAATAA---GACAGATAACCTGATA 1027
                          i   i ii  v     iv i          ---    i      ii  v
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_78504478_7   1028 CAAAAGTGGGCAAAATGTTTGAATAGAAAGTTATGATGAGTTTTTTAAAA 1077
                         ?    i        ivi          ----i  ------  i ii   i
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGA----CAT------TTCTCCAAAG 853

  chr2_78504478_7   1078 AAGAGTAGATATGCAAATGGAAAGTAAGCCTGTTAAAA 1115
                             -----   i       vv i     vii v    
  L1M4_orf2#LINE/    854 AAGA-----TATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.72 (124 / 72)
Gap_init rate = 0.04 (24 / 666), avg. gap size = 2.17 (52 / 24)  


2960 26.95 1.89 0.78  chr2_78527363_78531604.rev     2855  3752 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_78527363_7   2855 TGAAAAGATATCTCATGATCATGGATTGGAAGAATTAATATTGTCAAAAT 2904
                           i         i    v               v          i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78527363_7   2905 GTCAATACTGCCCAAAAAACTTTACAGATTCAATGCAATTTCTATCAAAA 2954
                          v       v      vviv i           i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78527363_7   2955 TATAAATTATATTATTCACATGAATAGTAAAAGC-AATCTTAAAATTTGT 3003
                          viv ii iiv  v  ii  vi   v - v    -i   i       ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr2_78527363_7   3004 TTAGAGCCACAGAAATCCCAGAATAATGCAAGCAGTCTTAAGCAAAGAGA 3053
                         v i  ivii  iiiiv         iivv  i  i    i iv  ii   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_78527363_7   3054 ACAAAGCTAGGGGTATTATACTACCTGACTCCAAAATATGCTACAAAGCT 3103
                               i i i  vv i i   v  ii i i     iv i          
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_78527363_7   3104 GTATTAACCAAAACAGTGTGGTGCTGGCATACA-ACAGACACATAGACCA 3152
                         ii v   i   i          i        vi- i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_78527363_7   3153 ATGGAACAGAATAGAGAACTCAGAAATAAATCCACACATTCACAGGCAAC 3202
                               i     v    iii          i   i     i ii v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_78527363_7   3203 TC-TTTTTGACAAGTGTCCCAAGAGCATACATTGGGAAAAGGCCAATCTC 3251
                          v-    i      v  v      v   v  v    i    ivi i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_78527363_7   3252 --CAATAAATGATACCGGAAAAACTA-ATAACCATTCACAGAAGAATGAA 3298
                         --   i     i i i  i v    i-   ?   ivii  i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_78527363_7   3299 ACTAGACCCTTATCTTCCACCATATACAAATATCAAATTAAAGCAAATGA 3348
                         ii i     i  i  iv             v  i  v i   iiii  v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_78527363_7   3349 AAGTTTTAAATGTAAGACATGAAACTATGAAACTACTAGAAGAAAACATA 3398
                         ?  vii           vv i       i     vi              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_78527363_7   3399 GAGAAAAATGATTCAAAAAATTGGACTGGGCAAAGATTTTTTGAATAAGA 3448
                          i?iv    v-   ivi vv    ii i     v i   i  ii   v  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_78527363_7   3449 CCTCAAAAAGCACAGGCAACAAAAGCAAAAAATAGGCAAATTGAATTACA 3498
                          vi     -     i          -         ii      i i v  
  L1M4_orf2#LINE/    599 CACCAAAA-GCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCA 646

  chr2_78527363_7   3499 TCAAACTAAAAAGCTTCTGTAAAGCAAAGGAAACAATCAGTAGTGTGAAG 3548
                              v v    i   i   ivvv       v  v    iv iv     i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_78527363_7   3549 AGACAACCTATAGAACTGCAGAACACATTTTTGCAAAT----TATCTGAG 3594
                                 i i    iv v    v i    --      ----       v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTT--GCAAATCATATATCTGAT 744

  chr2_78527363_7   3595 AAGGGGTCAGTAACAAAAATACACAAGGAACTC--A-AAC---ATATTAG 3638
                              iiiv   v v i    i i  i      -- -   ---   v  i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_78527363_7   3639 AAAAATAAAGTAACCTGATTAAAACATGCACAACATATCCAAATAGACAT 3688
                            i i   -     ii   ?   v   vi   viv  iii         
  L1M4_orf2#LINE/    795 AAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_78527363_7   3689 TT-TCAAGATAAAACATACAAATGGAAAGCAGGTATACGATAAAATATTC 3737
                           -  v i v  i i          vv ii i i i i  v  i  ii  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_78527363_7   3738 AACATTGCTAATCAT 3752
                              ii????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (158 / 80)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.50 (24 / 16)  


2731 26.89 1.28 0.81  chr2_78536835_78541617     3434  4292 (491)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr2_78536835_7   3434 AAAATGGCCATACTGCCAAAAACAATCTACAAATTCAATGCAATTCCCAT 3483
                           i     v     v  v   vii       i      i     i  i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_78536835_7   3484 CAAAATACCACCATCATTCTTCACAGAACTAGACAAAGCAATCCTAAAAT 3533
                               v   v vv v  i  ii     v v     ivii          
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_78536835_7   3534 TCATATGGAACCAAAAAAGAGCCTACACATAGCCAAAGCAAGAATAAGCA 3583
                                   viiv  ii  -  i v -         i   vvv i iv 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGA-CCCAGA-ATAGCCAAAACAATCTTGAAAA 193

  chr2_78536835_7   3584 AAAACAACAAATATGGAGGCATCACATTGCCTGACTTCAAACTATACTAT 3633
                          i  v      vv      vv     i v  ii i      viv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_78536835_7   3634 AAGGCCATAGTCACCAAAACAGCATGGTACTGGTGTAAAAATAGACACAT 3683
                           i  i i   v i   i    ii         ii   ii       i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_78536835_7   3684 AGACCAATGAAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACG 3733
                            i     i  i     v    ii           v   v i i   i 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_78536835_7   3734 GCCAACTGATCATAGACAAAGCAAACAAAAACATAAATTGGGAAAAGGAC 3783
                          i   i    iv v     i vviv   i v   vv v    i    i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_78536835_7   3784 ACCCTATTCAACAAATGGTGCTGGGATAACTGGCAAGCCACTTGTAGAAG 3833
                          vi  v                    i      vv ?    v  i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_78536835_7   3834 AACGAAACTGGATTCTCATCTATGAGTTCATACAAAAATCAACTCAAGGT 3883
                           i   ii    ii ii i  vvv vivi          i       ii 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_78536835_7   3884 GGATCAAAGACTTAGATCTAAGACTTGAAACCGTAAAAATTCTAGAAGAT 3933
                               ?    i  i  v     vi i    ii     v ii       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_78536835_7   3934 AACATCGAAA-AAGCCTTTTTAGACATTGGCTTAGGCAAAGACTT----G 3978
                              v i?i-  ii   iv -   v    v        v ii  ---- 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_78536835_7   3979 ATGACCGAGAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATG 4028
                           i--i  v --         v v         iv   i   i   i  v
  L1M4_orf2#LINE/    593 ATA--TGACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_78536835_7   4029 GGACTTAATTAGACTAAAAAGCTTCTGCACAGCAAAAGA----AGTAAGG 4074
                               v  i i v v    i   i  ii vv    i  ---- vi   i
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_78536835_7   4075 A-GCAAACAGACAATGCACAGCATGGGAGAAAATCTTCACAAACTATGCA 4123
                          - ii  v      iv     v            v  ii    ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_78536835_7   4124 TTGGATGAAGGACTAATATTCAAAATCAACAAGGAATTCAAACAAATCAG 4173
                          iv   i i     vi   i  i   vv i  i   i  vv    v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_78536835_7   4174 CAAGAAAAA-AGAAACAATCCCATCAAAAAGTAGGCTAAGGACATGAATA 4222
                         i  v     - v   i  i  v  i?    i i   v     iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_78536835_7   4223 GACAATGCACAAAAGACAATATACAAATGTCCAATAAACAAATGAAACGA 4272
                             v v v v     vi           v       i  v      v  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_78536835_7   4273 TGCTCAACATCCGTCATGAT 4292
                                    v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.01 (10 / 863), avg. gap size = 1.80 (18 / 10)  


 222 29.11 2.53 1.27  chr2_78587202_78589042      511   589 (1252)    L1M4_orf2#LINE/L1        8    87 (821)  

  chr2_78587202_7    511 ATATACTAGATTCCTAGATTCAAAGGTTAATTGTTGTAAAGATGTCAGT- 559
                             v i vi   v i    vi   ii v v i    v      v  i -
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_78587202_7    560 -TCTCTAAATATCATTTATAGATTCAGTGCA 589
                         -  i i    - v  i  i       ii   
  L1M4_orf2#LINE/     58 CTCCCCAAAT-TGATCTACAGATTCAACGCA 87

Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.50 (3 / 2)  

 565 29.88 17.07 2.29  chr2_78587202_78589042      686  1341 (500)    L1M4_orf2#LINE/L1      119   871 (37)  

  chr2_78587202_7    686 CAGAA--TGGCAAGCTGAATCTGAAATGCGTACAGAAATGTAAAGGACTA 733
                              --  i        vi  i    v i  ii      i  i    iv
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr2_78587202_7    734 AGAATGTCCCAGACATTCTTGAAAATAAA----AATGTTGTGGAGATTTA 779
                              iv  v i   v         vi  ----  v    - ii  i i 
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG-GAGGACTCA 217

  chr2_78587202_7    780 TA-------------AAGCT------AAAATTACGGAAATTG---C--TG 805
                         i -------------  i  ------   ii   i v   ii--- --  
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_78587202_7    806 TGGTAAGGTTGCAAGCTTAGCTACAT-TAAAT-----GAATAAAAAAGAG 849
                              vv viii   vv   --    -  i  -----     i  vv   
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAG--ACATATAGATCAATGGAATAGAATTGAG 315

  chr2_78587202_7    850 AGCATAGAAACAGAACCATAGATATATGGACATACAATAATT----AAAA 895
                           ivi     i i v     v  v     v  --- v i   ---- v  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCA---ATTGATTTTCGACAA 362

  chr2_78587202_7    896 AGATG----G------TAGTGGAGAAGGAACAGTTTTTTCAATAAACAA- 934
                         i i  ---- ------i i   i   i   i   i       i   iii-
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_78587202_7    935 ATTGGG-CA-CTTGATGCACACGTGGATGAGAATAAAATTGGAGCCATAC 982
                         ii    -  -  v   i?v   i  v vi     i  i     v  v   
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_78587202_7    983 TTCATATCATAAATATAAAATATAGTCCAGTTGAATTATGTACATAAATA 1032
                         i   i i    v i v   v  - v  v iv  i  i ?iv  v     i
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTA-ACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_78587202_7   1033 TTAGA-TTATTACTTTAGAATT------AGATCACA-----GTAAA---- 1066
                          v   -i  vv   v  i  i ------   vv   -----     ----
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_78587202_7   1067 -GT----TTGA---AAGAAA---------AAAT----TAC---AATCACT 1092
                         -  ----   i--- i v  --------- i  ----i  ---  v   v
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_78587202_7   1093 TCCAATAAAA----AGTTTGTTAAATTAGA--TAACTAAAATAAAATCCT 1136
                         vv   i    ---- iv v v      i  -- v ii     v   vv  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_78587202_7   1137 CTAGT-CATCAAA---CACTCCATCAACAGAATATACTGATGTATCATAG 1182
                         i v  - v     ---    --     v i i iv vv  iivvi  i  
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACT--ATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_78587202_7   1183 AGTGGGAGTAGGTATTTATAACTCAGGAAATTAACAAAGGGTTT-CATTC 1231
                          i      v ii     ii  v   viv vi i i  i  ii  -i  i 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_78587202_7   1232 AGTGTAATTTTTTTAAG---TCTTA--ACTCCACA-TAAAGGG-CATACA 1274
                           vi  ---- v v   ---     --    v i -    ii -  v i 
  L1M4_orf2#LINE/    760 AGAATA----TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_78587202_7   1275 ATCCAGTAGAACAATGCACCAAAGACTTGAGTGCA-ATTTTCACGAAGTG 1323
                          i   i v?  v    vi v  i  i    i iv -    iiv i   --
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG-- 853

  chr2_78587202_7   1324 CAGAAATTCAAATGACCA 1341
                         v   v  v      i   
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCA 871

Transitions / transversions = 1.35 (111 / 82)
Gap_init rate = 0.05 (40 / 753), avg. gap size = 3.17 (127 / 40)  


2160 27.19 1.21 1.06  chr2_78595452_78598513.rev     1377  2038 (1024)    L1M4_orf2#LINE/L1        1   663 (245)  

  chr2_78595452_7   1377 TGGAAAAACATTCCATGGTCATGGATAGGAAAAATAAATATTGTTAAAAT 1426
                               i i  i     v        v    i v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78595452_7   1427 GTCCATTCTGCCTAAAGCAATTTATAGTTTCAATGCTATTCCTATTGAAC 1476
                          v v  v  v  i   vii  i  i  v     i  v  i     ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78595452_7   1477 TACCAATGAAATTCTTCACAGAACTAGAGAAAACTC-TTTTAAAATTCAT 1525
                          v   iivivv  i  ii     v v  v  i-  v- ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_78595452_7   1526 ATGGAACCATAAAAGAGACT--GAATAGCCAAGGCAATCCTAAGCAAAAA 1573
                               --  iv   i   i--          ii     i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_78595452_7   1574 CAACAAAGCTGGAGGTATCATGCTACTCAACTTCACACTATGCTACAGAG 1623
                         v       i      vv   ii  v i   i    v viv i     i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_78595452_7   1624 CTACACTAACCAAAAGAGCATGGTACTGGTACAAAAACAGACACATAGAC 1673
                              v   i   i v  ii         i i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_78595452_7   1674 CAATGGAACAGAATAGAGAACCCATAGGTAAGACCACACATCTACAA-CT 1722
                                 i     v    ii   v ii   iv   i    i  iii- v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_78595452_7   1723 ATAGGTTCTTCAACAAACCCGGCAAAGACAAGCAATGGAGAAAGGATTCC 1772
                           v i  -   i    ivvi v   iiv  vv      i     i  vvi
  L1M4_orf2#LINE/    348 ATTGATT-TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_78595452_7   1773 CTATTCAATAAATGGTACTGGAAAAACTGGCTAGCTATATGCAGAAGATT 1822
                           v     i       i    i v      v  ? i i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_78595452_7   1823 GAAACTGGACTCCTTCCTTACCCCATATACAAAAATCAACTCAAGGTAGA 1872
                            ii     i   v   i  v              i       ii i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_78595452_7   1873 TTAAAGACTTAAATGTAAAACACAAAACTATAAAAACCCTGGAAGACAAC 1922
                          i ?    i         i vvi            vi i i     v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_78595452_7   1923 CTAGT--TAATACCATTCATAACATAGGCACAAGCAGAGATTTCATGAGA 1970
                         v   v--   - i -   i i  v v  vvi i   iv i    - v   
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGA 593

  chr2_78595452_7   1971 AA-GACATTAAAAGAAATTGCAACAATAGCAAAAATTGACAAATGGGACT 2019
                         v -    ii     v vvv       v  v      v  i    v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_78595452_7   2020 TAATTAAA-CTAAAAATTCT 2038
                          v  i   -i      i i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTT 663

Transitions / transversions = 1.47 (106 / 72)
Gap_init rate = 0.02 (12 / 663), avg. gap size = 1.25 (15 / 12)  

 587 29.44 4.44 0.00  chr2_78595452_78598513.rev     2325  2572 (490)    L1M4_orf2#LINE/L1      650   908 (0)  

  chr2_78595452_7   2325 AAATAAATAGCTTCTGCACTGAAAAATGAACTATCAACAGATTAAACAGA 2374
                             v  v i   i  ii  vv   iviv        v i v i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_78595452_7   2375 CAACGTACAGAA--------AATTTTTGCAAACTCTGCATCCAACAAAGG 2416
                             vi      --------   v        iiv ii   ii i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_78595452_7   2417 TCTAATATCCAGTATCTCTAAGGAACTTAAACAAATTTACAAGAAAAAAG 2466
                         v  vi       v  v v   i     ivv    v iv i  v     ii
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_78595452_7   2467 CAAACAATCCCGTT-AAAAATAGGCAAAGAACATGAACTGAC--TTTTCA 2513
                             i  i  vi  -      i       i iv    iv   --  i  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_78595452_7   2514 GAAGCAGACAAGCATGCGGCCAACAATCATATGGAAAAAAGCTCAACATA 2563
                         i   v   i vi  vii      i  v  i   i   i v         v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_78595452_7   2564 ACTGATCAT 2572
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.28 (41 / 32)
Gap_init rate = 0.01 (3 / 259), avg. gap size = 3.67 (11 / 3)  


2418 28.08 5.06 0.58  chr2_78640675_78645398     3367  4235 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_78640675_7   3367 TGGAAAAACATTCCATGCTCATGGATATGAAGA---GACATTGTTGAAAT 3413
                               i i  i     i        vv     ---i i      i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78640675_7   3414 GGCCATACTGCCCAAAGAAATTTACAGATTTAGTGCTATTCCTATCGAAC 3463
                            v     v      vvi  i        i ii  v  i      i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78640675_7   3464 TATCAGTGACACTCTTCCCAGAATTAGA------------AAAATC---- 3497
                          vi   ivi vi i  iv     v v  ------------     i----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_78640675_7   3498 TGGGAA-G-AAGTG--CCAGAACAGCCAAGGCAATCCTAAGCAAAAAGAA 3543
                            i  - -   v --      i      ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_78640675_7   3544 CAAAGCTGGAGTCATCACATTATTCAACTTCAAAATATACTGAAAGGCAA 3593
                              i     vvv     i vii   i       iv    iv  i  v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_78640675_7   3594 CA--AATAGCAAAACAGCATGGTACTGTTGCAAAAACAAAGACATAGATC 3641
                           --   --   i    ii        viii  ii i i v i       
  L1M4_orf2#LINE/    251 CAGTAAT--CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_78640675_7   3642 AATGGAACAGAGTAGACAGTCCAGAAATAATACCACATATCTATAAACCA 3691
                                i   i v  v             vv   i i  i   iiv v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_78640675_7   3692 TCTGATCTTC-ACAAATTCAACATAAACAAGCAGTGGAGAAAGGAC---- 3736
                          -    i   -    ivviiv  vi v  vv  i   i     i i----
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_78640675_7   3737 ---TCAGTAAGTAGTGTTGGTATAACTGGCTAGCCATATGCATAAGATTG 3783
                         ---   ii  i i   i   v i      v  ?   i     v    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_78640675_7   3784 AAACTGAACCACTTCCTTACACCATACAACAAAAATCAACACAAGGTGGA 3833
                           ii  i   v  v   i        i -       i   v   ii    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATA-CAAAAATTAACTCAAAATGGA 496

  chr2_78640675_7   3834 CTAATCAC-TAAATCTGAAACCTAAAACTATAAAAACCCTGAAAGATAAC 3882
                         ii ?vv  -     v i i v              vi i ii    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_78640675_7   3883 CTAGGAAATACTATTCTGGACATATACCCT-GACAAAGATTTCATGACAA 3931
                         v    ?ivv v v   vv   v - ivvi - i   v i    v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_78640675_7   3932 AGATGCCAAAAGCAATTGCAACAAAAAGAAAAATTGACAAATGAGACCTA 3981
                         v  ii         vvv         ii      v  i    vi   i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_78640675_7   3982 ATTAAAATAGATAGCTTCTGCATAGCAAAAGAAGCTATCAACAGAGGAAA 4031
                           i     vi v i   i  iiivv    i  vi       v i  vi  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_78640675_7   4032 CAGACAACCCATAGAGTGGGAAAAAATGTTTGCAATCTATGCATGTGAGA 4081
                         v          i   i     i     i       vii  ii  v   v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_78640675_7   4082 AAGGTCTAATATTCAGAATCTAAAAGGAACTT----AAATCAACAA--GC 4125
                          i  v  vi   i      v  v  i     i----  v    i  --iv
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_78640675_7   4126 AAG-CAAA-AACCCCGTTAAAAAGTGGGCAAAGGACATGAACAGACACTT 4173
                            -    -     vi  ?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_78640675_7   4174 TTCAAAAAAAGACATACACATGATCAACAAGCAT-TTAAAAAACGTTCAT 4222
                         i  v   i    i     v   ii   i     i- v    i i i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_78640675_7   4223 CACTAATCATTAG 4235
                           ii ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.45 (49 / 20)  


1329 28.17 1.81 3.22  chr2_78674863_78677705     1161  1657 (1186)    L1M4_orf2#LINE/L1        1   490 (418)  

  chr2_78674863_7   1161 TGGAATCATATT--ATGTTCATGAATTAGAAGGTTCAACATAGCAAAAAT 1208
                              vv    i--         i   i    ii i  i  v iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78674863_7   1209 GTCAATTCTCTCCAAATCGATCTACAGAGTCAAAGCAAATCCTATAAAAA 1258
                          v    v   i      i          v    v    vi     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78674863_7   1259 TCCCAGCAAGGTTTTATAAATAGACACAGACAAGTTTATTCTGAAATATA 1308
                                vivv    v i--i   v iv      i v  i  i    vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG--CAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_78674863_7   1309 TATGGAAAGGCAAAACGGCTGTATAATAACTACAATAATTTT---AATGA 1355
                                 v    i--  vivi v    i i v  i   i  ---  v  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_78674863_7   1356 AGACCAAAGTAAAGTAGAGGACTCATACAATTCAATGTTAAGGCTTACTA 1405
                            v      ---- i         i  vvii    v i  ii       
  L1M4_orf2#LINE/    197 AGAACAAAGT----TGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_78674863_7   1406 TATAACTAT-GTAATCAATATAATGCTTTATTGGTGGAGAAAAAGGAACA 1454
                         i v i   i-        v i i  ivv  i   iiv iii v  iv i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_78674863_7   1455 TAAATCAATAGAACAGAATAAAAAGCCCAGAAATAGAACCACATAAATAT 1504
                           i      i   i     vi i  i         i v   i i vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_78674863_7   1505 GGTCAAACAAATTTTGAAAAAGA---AAAGCAACAATTAAATATAGAAAG 1551
                               vii v   i  v  i i---v   --  v   v   ivi     
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAG--ACCATTCAATGGGGAAAG 390

  chr2_78674863_7   1552 GACTGTTTTTTTCAACAAATGGTGCTGGAGCAATTGAAAAATTATGGGAA 1601
                         i iv  i    -                ii   i  i v ?ii i--- v
  L1M4_orf2#LINE/    391 AATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCAC---AT 436

  chr2_78674863_7   1602 GTAAAAGAAAGAGCCTCAACCTAAAAACCTCACACTTCGTGTAAAAATTA 1651
                          i       v  ivi vi   ivv --        ivii ii        
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTA--CCTCACACCATATACAAAAATTA 484

  chr2_78674863_7   1652 ACTCAA 1657
                               
  L1M4_orf2#LINE/    485 ACTCAA 490

Transitions / transversions = 1.53 (84 / 55)
Gap_init rate = 0.02 (11 / 490), avg. gap size = 2.27 (25 / 11)  

 930 24.56 9.52 0.75  chr2_78674863_78677705     1953  2351 (492)    L1M4_orf2#LINE/L1      475   908 (0)  

  chr2_78674863_7   1953 ATAAAAAATAACTCAAAATAGATCATGGGCTTAAAAGTGAAATGTAAAGT 2002
                          i     v           i     ?i i i    v  i i vv    ii
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_78674863_7   2003 TATAAACTTTTTAGGAAAAAA---AAGAGAAAATCTTTGT-AGCTTAGAT 2048
                               vi i    i i    --- i ? v       i  - v   i i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_78674863_7   2049 TTAGAAAAGATGTATTAGACTTAACACCAAAAGCATGATTCAAAAAAGGA 2098
                          vi v  v i v v     iv i            ii v-   v   i  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG-CAACAAAAGA 623

  chr2_78674863_7   2099 AAATGTA-ATAA-TCACA----ATTAAGATTAACACTTTTAATTCTTCAA 2142
                            vi  -    - iiv ----  i  i     v vi   vi v      
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_78674863_7   2143 AAGATTCTGTGAAGA---TGAAAA-ATAAGCTATAGAC--AGAGAAAACA 2186
                          i  iv  i v    ---      - i  v i i   v--i       i 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_78674863_7   2187 TTTGCAAATTACACTAGC-AAGAAAGCACTTG-ATTTAGAATATATGAAG 2234
                                  i i -  v -i v  i v     -  ii         i   
  L1M4_orf2#LINE/    724 TTTGCAAATCATA-TATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_78674863_7   2235 ----TTCAAAACTCAGCAATAAAAA--CA--TAATCTAATTTAAAATTAT 2276
                         ----i i v      ii        --  --   i i    ?    v iv
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_78674863_7   2277 GCAGAAGC----AGCAGACATTTCACTAA-GAAGTATAAACAGATGAC-A 2320
                            i i v---- ii         v i  -    -   v   i   i - 
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAG-ATATACAAATGGCCA 871

  chr2_78674863_7   2321 A------CATGAAAAGATGTTCAACATCATTAGCCTC 2351
                          ------            i         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (61 / 34)
Gap_init rate = 0.05 (20 / 434), avg. gap size = 2.05 (41 / 20)  


2846 23.81 2.60 2.37  chr2_78793742_78799476     4358  5243 (492)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr2_78793742_7   4358 ATGGAAAATAGGAAGAATCAATATCATGAAAATGGCCATACTGCTCAAAG 4407
                              --- v      v i     ii v  i     v     v i    v
  L1M4_orf2#LINE/     21 ATGGA---TTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr2_78793742_7   4408 TAATTTATAGAATCAATGCTATTCCCATCAAA---CCATCACTGACATTC 4454
                          i  i  i   v    i  v  i  i      ---   --i   v v  i
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA--GCTGCCTTTT 115

  chr2_78793742_7   4455 CT-CAAAGAATTAGAAAAAACT-ATT-TAAATTTCATATGGAACCAAAAA 4501
                         i -  i -    i-- v  i  -  i-    v           viiv  i
  L1M4_orf2#LINE/    116 TTGCAGA-AATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_78793742_7   4502 AG-CCCATATT--CCAAGACAATCCTAATCAAAAAGAACAAAGCTGGAAG 4548
                         i -    v v --    i      i i vv  i          i    i 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_78793742_7   4549 CATCATGCCACTGGACTTCAA--CTATGCTACAAGGCTACAGTAACCAAA 4596
                         vv   ii iv ivi i     --  - i      i          i   i
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAG 261

  chr2_78793742_7   4597 ACAGCATGGCACTGGTACCAAAACAGACATATAGACCAATGGAACAGAAC 4646
                             ii   i     i iv ii i           i        i    i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_78793742_7   4647 AGAGACCTCAGAGATAACACTACACATCTATAACCATCTGATCTTCAATA 4696
                         v    vii    i    vv i i    i   iii  vi    i   i i 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_78793742_7   4697 AACCTGACAAAA--A--CAATGGGGAAAGGATTTCCTATTCAATAAATGG 4742
                          ivv  v   i -- --            i  vvi  v     i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_78793742_7   4743 TGCTAGGAAAACTGGCTAGCTGTATGCAGAAAACTAAAACTGGACCCCTT 4792
                             i   v      v  ? iii     i  i v i  ii         v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_78793742_7   4793 CCTTACACCTTATACAAAAATTAACTCAAGATGGATTAAAGACTTAAATG 4842
                            i     v                   i      i ?    i      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_78793742_7   4843 TAAAACGCCAAA-CCATAAAAACCCTAGAAGAAAACATAGG--TAATACC 4889
                            i -  i   - i      vi i                --   - i 
  L1M4_orf2#LINE/    512 TAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATC 559

  chr2_78793742_7   4890 ATTCAGGACATAGGCAGGGGCAAAGACTTCAT-GATGAAAATGCCAAAAT 4938
                         -   iv   v v  vvvi     v ii   v -   - vi ii      v
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAG 607

  chr2_78793742_7   4939 CAATTGCATGCAACACAAGCCAAAATTGACAAATGGGATTTAATTAAACT 4988
                           ----  v      v   vv     v  i    v   i  v  i   v 
  L1M4_orf2#LINE/    608 CA----CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_78793742_7   4989 AAAGAGCTTCTGCACAGCAAAACAAACTATCATCAGAGTGAACAGACAAC 5038
                         v  i i   i  ii vv    iv v       vv i      v       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_78793742_7   5039 CTACAGAATGGGAGAAAATTTCTGCAATCTACCAATCTGACAAAGGTCTA 5088
                          i                 v i     vii ivv      i  i  v  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_78793742_7   5089 ATATCCAGAATCTATAAGGAACT--TAAAACCAAATTTACAATAAAAAGC 5136
                         i          v     i     --  v   iv   ----         v
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAAT----AATAAAAAGA 799

  chr2_78793742_7   5137 CAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTGA 5186
                             i     v  i?    i            v    i     i    vv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_78793742_7   5187 AAAGAAGACATTTACGTGACCAACAAGCA--TGAAAAAAAGCTTAACATC 5234
                                 i  vi vi  i    i     --      i v   i      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_78793742_7   5235 ACTGATCAT 5243
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.51 (125 / 83)
Gap_init rate = 0.03 (25 / 888), avg. gap size = 1.76 (44 / 25)  


 214 27.03 6.76 5.41  chr2_78804149_78808854       70   217 (4489)  C L1M4_orf2#LINE/L1   (726)   182    33  

C chr2_78804149_7    217 ACTTAACA-----AAAACGTCAGTATAACTCAAATTTATCTACGGATTTG 173
                               i -----  i i v  i  ivv i      v      i    ii
  L1M4_orf2#LINE/     33 ACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCA 82

C chr2_78804149_7    172 ATGGAATTCTAAT-AAATTCTCTGCCAACTTCTGTTGTTTTCATCAAACA 124
                          i v   i iv  -   v  ----   i  v iv  -   v  v-   iv
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATC----CCAGCTGCCTTT-TTTGCAG-AAATT 126

C chr2_78804149_7    123 GAACAAAACTCCTCCTAACAATTATATGAAGATGTAAATG--CTAGG-TA 77
                           -   i-  vv      v v i     i i   i  iv -- i  i-  
  L1M4_orf2#LINE/    127 GA-CAAG-CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

C chr2_78804149_7     76 GC-AAAAC 70
                           -     
  L1M4_orf2#LINE/    175 GCCAAAAC 182

Transitions / transversions = 1.35 (23 / 17)
Gap_init rate = 0.07 (10 / 150), avg. gap size = 1.80 (18 / 10)  

 533 24.00 3.33 0.00  chr2_78804149_78808854     3230  3379 (1327)    L1M4_orf2#LINE/L1        1   155 (753)  

  chr2_78804149_7   3230 TGGAAAG-CATTCCATGCTAATGGATAGGAAGAATCAAGATTGTTAAAAT 3278
                                -i  i     i v      v      v i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78804149_7   3279 TGCCATACTGCCCAAAGCAATTTACAAATGAAATGCTATTCCTATCAAA- 3327
                         v  v     v      vii  i    i  vv  i  v  i         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78804149_7   3328 --CTAACATCATTTTTTACAGAATTAGAAAAAA-AATTCTAAAATTCATA 3374
                         -- i i vv v      i     v v  v  iv-i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_78804149_7   3375 TAGAA 3379
                          i   
  L1M4_orf2#LINE/    151 TGGAA 155

Transitions / transversions = 1.00 (18 / 18)
Gap_init rate = 0.02 (3 / 155), avg. gap size = 1.67 (5 / 3)  

1633 26.40 3.77 3.77  chr2_78804149_78808854     3499  4267 (439)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr2_78804149_7   3499 TAAAATTCATACAGAATGAATGAAATATAGAATGCCCA-AATTGTCAAAG 3547
                                    ii   ---   v  ---i i --    -   v i    i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAA---ATGCAA---GGGA--CCCAGAATAGCCAAAA 181

  chr2_78804149_7   3548 CAATCTTAAGCAAAAAGAAAAAAGTCAGACAGA-TCACACTATCTGACTT 3596
                                i iv  i     v     ii  -i  -       vi ii i  
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGA-GGACTCACACTTCCCAATTT 230

  chr2_78804149_7   3597 CAAACTATACTGCAAGGCTACA------AAG-CAGCATGGAACTGGTACA 3639
                             viv    i   i      ------   -   ii   v     i i 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_78804149_7   3640 AAAACAGACATAGAGACCAATTAAACAAGATGGAGAACTCAGAAATAAAG 3689
                          ii i       v   i    vi  i ii  v    iii          v
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr2_78804149_7   3690 CCACACACCTACAACCACCTGATCTTCAACA--GATTAAACAATAACAAA 3737
                            i   ii  iiii  vi    i   i   -- i --iv   v v  vv
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGT--GCCAAGACCATT 378

  chr2_78804149_7   3738 GAATAGAGAAAGGA--GTCCCTATTCAATAAATGATCCTGGGATAAATGA 3785
                         v   i i     i --   -- v     i     i v      i  v  i
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_78804149_7   3786 CTTGCCACATGCAGAAGATTGAAACTGGACTGCTTCCTCTAACAATATAC 3835
                         v v?         i    v    ii     iv  v    vv  v      
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_78804149_7   3836 AAAAATTTACTGAATATGGATAAAAGACTTAAATGTTAATACCTACAACA 3885
                                v   v  v      v ?    i       -  v v   v   v
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACT 525

  chr2_78804149_7   3886 ATAAAAACTCT-AGAAGAAAGCCTATG---AAATACCATTCTGGATGCTG 3931
                               -    -        i v  v ---    -- -   vv  ivi  
  L1M4_orf2#LINE/    526 ATAAAA-CTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTG 571

  chr2_78804149_7   3932 GCTTTGGGAAAAAATTTATTAC-TAAGTCTCCAGAAGGAATTGCAAAAAA 3980
                          v  -i  v  vii   v   v-  v v v   i   v vvv    v   
  L1M4_orf2#LINE/    572 GGTT-AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_78804149_7   3981 ACCCAAAAATTCACAAGTGGCACCTAATTTAACTAGAGAGCTTCTGTCCA 4030
                          vv-      vv i  i v v  i v  iv  v vi i i   i   v v
  L1M4_orf2#LINE/    621 AGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_78804149_7   4031 GCAAAAGAAACTATCAACAAAC-----AGACAACTTACTGAATGGAAAAA 4075
                         v    i  v        v   v-----       ii  v      i i  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_78804149_7   4076 AAAATTTGCAAACTATACATGTGACAATGGTCTAATATCCAGAATCTATA 4125
                           v         ii   i  v   i  v  v  vi          v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_78804149_7   4126 AGGAAATT----AAATCAGCAAGCAAAAAACAAACAAAAAACCTCATTGA 4171
                          i   v i----  v   ii  vv    i     i  ----  iv   ? 
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAA----CCCAATTWA 815

  chr2_78804149_7   4172 AGAATGGGCAAATGACATCAACAGACACTTTTCAATGATGAAAA-ATGCC 4220
                          i          v  iv v  i     i  i  v -- v   i -  i v
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCA--AAGAAGATATACA 863

  chr2_78804149_7   4221 CATCATCAGTAATCAT-TAGAGAAATGCAAATCAAAACCACAATGAGA 4267
                         v  vii  i   v  i- ii i i    ---    v i  ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.13 (106 / 94)
Gap_init rate = 0.04 (28 / 769), avg. gap size = 2.07 (58 / 28)  


2531 27.33 3.94 1.80  chr2_78821788_78824148      981  1869 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_78821788_7    981 TGGAAACACTTCCCATGCTCACAGGTGAGTAGAATTAATATTGTGAAAAT 1030
                               v iv       i   ii i vi v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78821788_7   1031 GACCATACTGCCAAAAGCAATCAACAAACCCAATAAAACTCCCATCCAAA 1080
                          i v     v  v   vii   v   i ii   iiv  ii  i   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78821788_7   1081 TACCACCATCATTCTTCACAGAACTAAAAAAA--AATCATAATATTCATA 1128
                          v   v vv v  i  ii     v vi v  i--i   v   v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_78821788_7   1129 TGGAACCAAAAAAAGAGCCCGCATAGCAAAGACTAAGCAAAGCAAGACTA 1178
                              -- viv  i ii   ---------   v  iv    i   vvi i
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCC---------AGAATAGCCAAAACAATCTTG 189

  chr2_78821788_7   1179 AGCAAAAAGAACAAAGTTGGAGGCATCACATTACCTGACTTCAAACTATA 1228
                          iv  i                 vv     i v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_78821788_7   1229 CTATAAGGGCATAGTCATCAAAACAGCATGGTACTGGTGTAAAAATAGGC 1278
                            i  i vi i   v     i    ii         ii   ii    i 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_78821788_7   1279 ACATGGACTAATGGAACAGAATAGAGAACCCAGAAAGGAAGTCAAATACT 1328
                          i  i  ii       i     v    ii       vi  vi  v i i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_78821788_7   1329 TACAGCCAACTGATCTCTGACAAAGCAAACAAAAGCATAAAGTGGAGAAA 1378
                           ii i   i    i ii     i vviv   i v   vv i   i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_78821788_7   1379 CGATACTATATTCAACAAATGGTGCTGGGATAACTGGCAAGCCAGATATA 1428
                         vi   v v v                    i      vv ?   v  ii 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_78821788_7   1429 GAAGAATGAAACTGGATCCTCATCTCTCACCTTAAACAAAAATCAACTCA 1478
                         i         ii    i  ii i   v    v  v        i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_78821788_7   1479 AGATGAATCAAGGACTTAAATCTAAGGCCCGTAACCATAAAAATTCTAGA 1528
                          i   i    ?i   i     v    iv iiv   i      v ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_78821788_7   1529 ACATAATGTCATAAA---AACCCTTCTAGACATTGGCTTAGGCAAAGACT 1575
                          v v  ---    ii---  vi    vv   v    v        v ii 
  L1M4_orf2#LINE/    540 AGAAAA---CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_78821788_7   1576 TCATGACCAAGAACCCAAAAGCA-----AACAAAAACAAAGATGAACAGA 1620
                           v iivi v  vv         -----       iv   i  ii i i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_78821788_7   1621 TGGTACTT-----AAACTAAAAA-------GCTTC------TGCAATCA- 1651
                          v v    -----   i      -------     ------ii v    -
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_78821788_7   1652 ----GCAAACAGACAACCCACTGAGTGGGAGAAAATGTTTACAATCTATA 1697
                         ---- ii  v           v  i           i   i   vii   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_78821788_7   1698 CATCCATTAGAGGACTAGTATCCAGAATCTACAAGGAAGTCAAGTGAATC 1747
                         i   iiv  ii     v           v  i  i   v  vviii v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_78821788_7   1748 AGCAAGAAAAAAAAACAAACAAACTGATCAAAAAGTGGGCTAATAATATG 1797
                          ii  v     i --    i  v ii  i?    i     v  vi  v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_78821788_7   1798 AATAAATAATTCTCAAAAGAAGATCTACAAATGGCCAACAA--ACATGAA 1845
                             i i v     v         v             i  --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_78821788_7   1846 AATACGCTCAACATCATTAATCAT 1869
                           v i           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 4.25 (51 / 12)  


 476 23.28 2.12 11.64  chr2_78864239_78867093     1239  1427 (1428)    L1M4_orf2#LINE/L1        6   176 (732)  

  chr2_78864239_7   1239 AGATATCTTCCATGTGTATGAATTAAAATGACC-AATGTTGTTATAATAA 1287
                                --      vi   i   ii  -   i-   i      vi  ii
  L1M4_orf2#LINE/      6 AGATATC--CCATGTTCATGGATTGGAA-GACTTAATATTGTTAAGATGG 52

  chr2_78864239_7   1288 TACTTTTCCTCAAATTGATTTATAGGTCCAATACAATTTCAATCAAAATT 1337
                         i v vi   i         i  i  i i   ii    ii v        i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_78864239_7   1338 CCAATTCTAAGAGTTTTGTTTTCCTCTTTTAGAAGTGGACAGGCTGATTA 1387
                            ii ------ ii  -    v ------    i v    i      iv
  L1M4_orf2#LINE/    103 CCAGCT------GCCTT-TTTTGC------AGAAATTGACAAGCTGATCC 139

  chr2_78864239_7   1388 TGAAAGTTATAGGGAAAAAAAATTTTAAGG---CCAAAATAAC 1427
                          i   v i   v     ------ vi    ---   i    i 
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAA------TGCAAGGGACCCAGAATAGC 176

Transitions / transversions = 3.00 (33 / 11)
Gap_init rate = 0.05 (8 / 171), avg. gap size = 3.25 (26 / 8)  

1106 28.30 9.70 3.02  chr2_78864239_78867093     1721  2349 (506)    L1M4_orf2#LINE/L1      176   846 (62)  

  chr2_78864239_7   1721 CCAAAATAATTTTTGGAATCAATACTTTTTAAAATCAGGTAGGATTTGCA 1770
                               i   i  vii  vv  v vi----   i ii --    i ii  
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAAC----AAAGTTGG--AGGACTCACA 219

  chr2_78864239_7   1771 CTACCTAATTTTTAAGACTTTCTATGAACCTG-ACTA--CAATGTAGTAT 1817
                           v  i     i-  i    v   ii  v  i- v  --   vii   i 
  L1M4_orf2#LINE/    220 CTTCCCAATTTC-AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_78864239_7   1818 TGGTTCCAGGCATAA---TAGATATATTGAGT----GTATAAAATAAAGA 1860
                         -   v i-       ---    i    v  vi---- v   i   vi   
  L1M4_orf2#LINE/    269 -GGTACT-GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_78864239_7   1861 AACAAGAGAAAGAATCA-ACATTTAGTGTTACTTGATTTTTGACTAAAGT 1909
                         iv v   i v i vi  -       vv  i v        i   v ii  
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_78864239_7   1910 GCCAAAGCTATACAATGGAGAAAGAATAGTCTTTTTCAAGAACTAGGTAT 1959
                              ii i  v      i                -   v  v -   i-
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT-CAACAAAT-GGTG- 413

  chr2_78864239_7   1960 CTGTG-----TGGG--GCTGTAGG--AGAGAATC---CTTCATCTCTATC 1997
                            v -----   i--? iii v -- i     v---i vv i i   i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_78864239_7   1998 TCAGATCCTTCA-AAAAGTTAATGGGGAATAGACCATAAATATAAACGTA 2046
                            v i v vi -    i    ivvii   i  i  ? i iv    i   
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_78864239_7   2047 A-ATATAAAGTCATTAAAATTCCCA-AATAAAACACAGGAAAATATATTT 2094
                          - vv    iii  -    i  ii -  v      i   ?iv v  v  i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_78864239_7   2095 GCCACCATAAGGTAGGCAAATATTTCTTAG----GACAC----------- 2129
                          iv   v ii v       vvi        ----     -----------
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_78864239_7   2130 ------AAATAGGAAATGTGATAAATTGGACTTCATCAAAATTAAAAATT 2173
                         ------   v ii    i-                             i 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATA-GATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_78864239_7   2174 TCCACTCATGAAAAGACAGTGTTAAATAAATTAAAAAGCAAAACAAGTTA 2223
                          iiiiv v v   i    v i i  i-   v i     ----    vii 
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAAAG----ACAACCCA 706

  chr2_78864239_7   2224 CAGACTAAAAGAAA-TATTTACAATAAATGTAACGAACAAAGGACTTATC 2272
                             v iii     -     i   vvv  i  v vi i  i      i v
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_78864239_7   2273 CTCGGAATATATAAAGAACAACTACAACCCA-TA-CAAAAAGAAAAA--- 2317
                         ii i               vvi      i  -  -i       v   ---
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_78864239_7   2318 -CTAATGGTAAAATGGGC-------TCAAACAAATATTTC 2349
                         - i   v?v         ------- ii  i i i     
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

Transitions / transversions = 1.60 (107 / 67)
Gap_init rate = 0.05 (31 / 671), avg. gap size = 2.58 (80 / 31)  


1865 22.53 4.67 12.77  chr2_78885244_78887654.rev      949  1911 (500)    L1M4_orf2#LINE/L1        1   885 (23)  

  chr2_78885244_7    949 TGGAGAGATACACCATGTTCATGGGTTGGAAAA-TTAATATTACTAAGAC 997
                             i     iv            i      i -        ii     i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_78885244_7    998 ATCCAT--TCTCTAGAT-GATCTATAGATTTATCACAATTTCAGTGAATA 1044
                         iv v  --  i i i  -      i     i v i    ii vi v  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_78885244_7   1045 TCCTAGAACTG---TTTTCCTAGAAATAACCAAGGTGAATCTAAAATTTG 1091
                            i  --   ---    ivi      viv    v   vi        ii
  L1M4_orf2#LINE/    101 TCCCAG--CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_78885244_7   1092 TGTAGAAAAGCAAATGAATAAAAACAATCAAAATGATTTTGAAAAACAAT 1141
                          i i    v    iv  viv i  i ii     ii  i        v  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_78885244_7   1142 TACAAAGATGGAAGAATCAC--TATCTAAATTTAAGATTAACTCTAAA-C 1188
                         v      v    i  v    -- vi i  v  i  i i v   vi   - 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_78885244_7   1189 TACAATTATGAAGAAACTG--GTATTAACTAAAGAAAAGATACATAGATC 1236
                             i v  v    v v  --   i ii vv   i v   i i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_78885244_7   1237 AATGAAACACAAT----ACTCTAGAAATGTACCCACACATAGGTGGTTAA 1282
                             i  i v   ---- v  i      iv     i    vvi    i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_78885244_7   1283 TTGATTTGCAGCATGGGTACAAAGGAAATTCAATGAGGGGAAAAGCAGTT 1332
                                v ii  v    i v   ivv        -   i  i ii   i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTC 397

  chr2_78885244_7   1333 TTCGTAACAAATGGTTATGAAATAATTGGATACCCATTTTTTTCTTTAGT 1382
                           ivi          vv  ii i  i      ?   i-------------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC------------- 434

  chr2_78885244_7   1383 TTTGAGAAATCTCCGTAATGCTTTCTTGGGTTCAGTAGAAGCCTAAACCC 1432
                         -----------------    --------------- i   ----  ---
  L1M4_orf2#LINE/    435 -----------------ATGC---------------AAAAG----AA--- 445

  chr2_78885244_7   1433 CTGCATTATGCAATATATCCTTGTAACAAACCTGCACGTGGACCTCCTGA 1482
                         --------  v i ------------------------      i ----
  L1M4_orf2#LINE/    446 --------TGAAGT------------------------TGGACCCC---- 459

  chr2_78885244_7   1483 ATCTAAAATTTAAAAATAAATAAATAAATACCTTGC--CTTATATAAAAA 1530
                         ----------------------------     ii -- v    i     
  L1M4_orf2#LINE/    460 ----------------------------TACCTCACACCATATACAAAAA 481

  chr2_78885244_7   1531 TCA-TTCAAAATGGATCATAGACCTAAA---AAAAATCATAAAATATAAA 1576
                          i -i             ?         ---  i iii -   v      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAA 530

  chr2_78885244_7   1577 ACTTCTATGAGAAA-CA---GGGCAAA--------ATCTTGAGTTAGTTA 1614
                            ii  vi     -  --- ? i   -------- i    i     vi 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_78885244_7   1615 AACATTTCATATATATAACATCAAAAACACAATGCA-TAACAGAAAAACA 1663
                          vvi    v  v    i   i     i     -   -i  v       - 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAA-GCAACAAAAGAAAAA-A 628

  chr2_78885244_7   1664 TAGG-AAATTGGGCTTCATAAAAATTATAAATTGCTGTTACTT-AAAAGA 1711
                            i-       i      v       v   i vi   -i   -   i  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT-GCTTCAAAGGA 677

  chr2_78885244_7   1712 TAATATTAAGAGAATGAAGAGACAAGATATGAAGTGTGAAAAGATATTTA 1761
                         i v   i    i i    i      vvi iii i  v  i  i      i
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_78885244_7   1762 CAGTGTTTATAAGTGGTAAAGGATTTGTAGCAAGAAAATATTAAAAACTC 1811
                           ivviv    vv  i   i   i     v v    v    v  i     
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_78885244_7   1812 TCAAAACTCAATAG-AAATATTCAAA----CCAAT---AAAACGAGCAAA 1853
                          i v         i-   v vv    ----     ---    i i     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_78885244_7   1854 ATATTTGAGGAAACACTTCAGCAAGGAAGATATTCAGGTGGTAAATAAGC 1903
                         iv      iv i   i   vv   i        v  ii   iv       
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_78885244_7   1904 ACATGAAA 1911
                                 
  L1M4_orf2#LINE/    878 ACATGAAA 885

Transitions / transversions = 1.64 (133 / 81)
Gap_init rate = 0.04 (32 / 885), avg. gap size = 5.25 (168 / 32)  


1764 25.17 8.89 4.62  chr2_79110603_79112516      558  1423 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_79110603_7    558 AAATACACCATGTTCATGAACTGACAGACTTATTATTGTTAAGATTTCAA 607
                          i   iv           i i  iv       v            vv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_79110603_7    608 TTCTCCCCAAATTGATTCACATATTCAACAAAATCCCAGTCAAAAATCTC 657
                          v              ii   v       iv      vi      -  i 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCC 104

  chr2_79110603_7    658 AGAAGG--TTTGTGTAAACAATGATGAGCT------AAAATGTATATAAA 699
                           vv v--   v  i i v v   ii    ------     vi    ii 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_79110603_7    700 AATGAAAATGACCTAAAATAGGTAAAGCAATTTTGGAAAAGA-GAACAAA 748
                             v  iv    i i     vi   i    i   i      -       
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_79110603_7    749 ATTGGAGGACTCACACTAGCTAATTTCAAAACTTACCATAATGCTACAGA 798
                         i                vv i               i i  v       v
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_79110603_7    799 AGTCAAGAC-------TACCTGAATATAGGTATATGTATAGA-------A 834
                          i       -------   iv v   vi i  v ii      ------- 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_79110603_7    835 ATTGAACTGG------------------ACACAT--ATAGTCAA--GA-- 860
                           v   i  i------------------ i    --  i     --  --
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_79110603_7    861 ------AAGGCATCCCAAAAT--TTCAATTGATAAATGATAATCTTCTAA 902
                         ------    -i v    i i--      v iv   vi   i    i v 
  L1M4_orf2#LINE/    355 TTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_79110603_7    903 TCAACTGTTGCT-------CT--ATAAACTTA-GAGAAAAAGTAAACTCT 942
                         v   v  v    -------  --   ?v vi - vi   i i i  v iv
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_79110603_7    943 GATTCTTACCTTATACCATACACAAAATCTACCTCAAAATAGATTATAGT 992
                           ii i     i i      i      vi  v        i   i ?  v
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_79110603_7    993 GCTATTTCTAAGAGCTCAAAAAATAAAAAGTAAAAAAAAAAAATACATAG 1042
                         v   vv v        v   vv      vvivv i  i    ---     
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA---CATAG 550

  chr2_79110603_7   1043 AAGAAAGTATCCATCAACTTAGTATAGGGAAATACTTGTTAGACCTCACA 1092
                         i? v  i v i i v v   i vv    v  vvii  v     iv v   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_79110603_7   1093 C-AAAAG-ACAAACAAACAAACAGGAATCATTTAAAAAATATTGA-AAAT 1139
                          -     -    i   -    -  ---------        --  -    
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAA-CAAA-AG---------AAAAAATA--GATAAAT 637

  chr2_79110603_7   1140 TCCAAGTTCATAAGAGCTAAAAAAGTTTTTTCCTTAGACAAAACCATTAA 1189
                          v-i v     v i ii      vv   v v i i i vi v  i  i  
  L1M4_orf2#LINE/    638 TG-GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_79110603_7   1190 GAA-GTAGGTAAGACAG------AAATTGGGCAAAACATTTGCT--TTAC 1230
                            -  - iv      i------i   v  iv    i      v-- i i
  L1M4_orf2#LINE/    687 GAAAGT-GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_79110603_7   1231 ATCTCTGACAAGGAACCTACAGCTTCTTTGACAATACAAAAGAATAGACA 1280
                           v     i    i  i ii ---  i-------------      v i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTA---TCC-------------AGAATATATA 769

  chr2_79110603_7   1281 GGAAGTTAGTTCAACTTTACAATGAGAAGATACATAACCCAGAATTAAGA 1330
                         iii ii vv v     iv i   i i    i v        --   ? i 
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA--ATTWAAA 817

  chr2_79110603_7   1331 AATAGACAAAACATATTAACAGACATTCCATCAAAAAAAAGATAAGCAAA 1380
                            i i    iv  v v  i       i vi    i  i v   --    
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA--CAAA 865

  chr2_79110603_7   1381 TGACTATTAAGAACATGAAAAAATGCTCAACTTCCTTAATTAC 1423
                           i i v    v         i         v  v????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (118 / 96)
Gap_init rate = 0.04 (32 / 903), avg. gap size = 3.66 (117 / 32)  


3483 22.37 2.77 2.99  chr2_79113451_79115824.rev      981  1883 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_79113451_7    981 ACATTCCATGTTCATGGACTGAAAGACT-AATATTGGTAAATTGTGAATA 1029
                          i  i             i  i      -       v   iv  vv    
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_79113451_7   1030 CCACATGAA--GACCTACAGATTCA-TATAATCTCTATAGAAATCTTGAT 1076
                          iv vii  --  i           -iii    i    vi     iiiii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_79113451_7   1077 GACTTTTCTTTCAGAAATAGAAAAATCCATCCTAAAATTCATATAGAATT 1126
                         vi i   i  v       v  v  iiiv                i   v 
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_79113451_7   1127 TCAAGGAACCCTGAATAGCCAAAACAATCTTGGAAAAAAA-AATGAAGTT 1175
                         v     i    v                    i    i  -  ii     
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_79113451_7   1176 GGATATCTTATACTTCCTGCTTTCAAA-CTTACTATAAGGCTATGGTAAT 1224
                            viv  i i      iiv       -       i  i    ii     
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_79113451_7   1225 CAGAACACCGTGGTACTGATATAAAAGCAGACACATAAGCCAGTGAAATA 1274
                           ii   vi         ii    iiii     i   iii  i  i    
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_79113451_7   1275 GAATACAGA-TCCAGAAATATACCCTTGCATATATAGTCAAGTGATTTTC 1323
                             vv   -          v    v i   v   i     v        
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_79113451_7   1324 AACAAGACTGCCAAAAATAT--GATGAAGAAAGTGTAGTCTTTTTCTGCA 1371
                         i     iv      i vi  --i   ii     vi         ----  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT----CA 403

  chr2_79113451_7   1372 ACAAATGGCATCAGAAAATCTAGATATTCACACATAAAA-----AAGTTG 1416
                                 iiiii i v v  i    ?i    iii    -----      
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_79113451_7   1417 GATTTTTACCTTACACCATATGCACAAATTAACTCACAATGGAAGGAAGG 1466
                           iiii     i         i  v           v      vvi?  i
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_79113451_7   1467 CCCATATACAAAACCCAAAACTATTAAATTCTTAAAAGAAGACATAAGGT 1516
                           i v  ii  i v i        v   i     i     i     i ?v
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_79113451_7   1517 AAAAACTTTATAACATTTTATTTGGCAATGACATCTTGGATGTGATATCA 1566
                         v   v   ii i  v  vvi  v       iiv    i   i   i i  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_79113451_7   1567 AAAGCACAGGCAACAAAATAAAAAAAATAGGTAAGTTGGAT------AAA 1610
                                 i         --i         i   i     i------   
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAA--GAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_79113451_7   1611 ATTGAAATATTCTGTGCATCAAAGGACACTCAAACTGAGTGAAAAGGCAA 1660
                            i   vv  i     v            ------- vii i  i ii 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACT-------ATCAAGAAAGTGA 694

  chr2_79113451_7   1661 CCCAAAGACAATCCACGGAATGGGAGAAAATATTTGTCAATCATATATCT 1710
                         ---        i    i                   iv            
  L1M4_orf2#LINE/    695 ---AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_79113451_7   1711 GACAAGGAATTGATATCCAGAATATATAAAGGACTCCTACAACTCAACAA 1760
                           i    i i vi                  i    i          i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_79113451_7   1761 CTCAACAACAAAAAGCTCAGACAAACCAACTTAAAATACGGGCAAATGAT 1810
                         i--------      v-  i i  v    i ?    - i       v   
  L1M4_orf2#LINE/    792 T--------AAAAAGA-CAAATAACCCAATTWAAAA-ATGGGCAAAGGAT 831

  chr2_79113451_7   1811 CTGAATGTATATTTTTCTAAAAAATATACACAAAATAGCCAATAA----- 1855
                         i     iv i    i  i   i  v   i     - i        -----
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACA 880

  chr2_79113451_7   1856 TGAAAAGATGCTAAACACCTGAAATGCA 1883
                                     v    i v????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.41 (140 / 58)
Gap_init rate = 0.02 (18 / 901), avg. gap size = 2.89 (52 / 18)  


 898 23.51 8.42 3.51  chr2_79181266_79183375.rev      501   785 (1325)    L1M4_orf2#LINE/L1       58   356 (552)  

  chr2_79181266_7    501 CTCCTAAATTTGATTTATAGATTCAATGTTATCCTTTTAAAAATCCCAGT 550
                             iv  v     i  i        i iv    i v v          i
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_79181266_7    551 AAACTTTT-------------------GATTTGAAAATTTATATCAAAAT 581
                         viv     -------------------   iiv      i    vi    
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_79181266_7    582 -CAAATGAGCTGAAATAGCCAAAACAATTTTGGAAAACAAGAACAAAGTA 630
                         -   iv  v iii               i   i    v           -
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT- 206

  chr2_79181266_7    631 ACAAATTTGGCAAAAC--ATATTACCCAATTTCAAAGCTTCTTATAAAGC 678
                         -------   - ii  -- i i v            i   vi  i     
  L1M4_orf2#LINE/    207 -------TGG-AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_79181266_7    679 TACTGTAAGTAAGGCAGTATGGTACTGATGAAAGGATAGACATGTAGCTC 728
                            v    vi   i    i        iiiv            i   v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_79181266_7    729 AATG-AACAGAACAAACAAGGCTAGTCACAGACCTACAAAAT-AGAGTCA 776
                             -  i    ivi -i  v i  vv i i   i i v v - vi    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_79181266_7    777 ATTGATTTT 785
                                  
  L1M4_orf2#LINE/    348 ATTGATTTT 356

Transitions / transversions = 1.68 (42 / 25)
Gap_init rate = 0.03 (8 / 299), avg. gap size = 4.25 (34 / 8)  

1423 28.07 5.39 0.37  chr2_79181266_79183375.rev     1081  1618 (492)    L1M4_orf2#LINE/L1      344   908 (0)  

  chr2_79181266_7   1081 GTCAACTGATTTTTGACAAAGGTGTCAAA-----------GGCAATGAAT 1119
                              i       i     i    i   i-----------  v  v    
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_79181266_7   1120 AGTCTCCTCAAGAAACAGTGCTGGAGCAATTCGATGTCCATATGCAAAAT 1169
                              ii    v   ii       ii   i v   i?   i        -
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA- 442

  chr2_79181266_7   1170 AAATGAAACTTGATATAGATTTCACAACTTATACAAAAATTAACTCAGAA 1219
                         i      ii v  ivivv ii     v v                  i  
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_79181266_7   1220 TGGATAGTAGCTCGAAATATAA-ATATAAAACTATAATACTTGAAAAAGA 1268
                              vi?  vi v    i   - vv           v   ivv i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_79181266_7   1269 AACTATAAAAATAA-TCCTAGTAGCTTTGAGTTAAGCAAAAAAAAAATAA 1317
                           vi   ii?i   -  i v  ii i   i    i    viivvvvv  i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_79181266_7   1318 GTATG-TAC--AAAGCACA--CAA-----GAAAATGTTATTAAGTTGGAC 1357
                         i    -i  --        --   -----     vi viv   i      
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_79181266_7   1358 CCAATGAAAACAAAAATATTTTGCTCTTCCTGAGAAATTGTTAAGAATAT 1407
                         iiv  v    iv    vv     iv    vvii  v i i i     vi 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_79181266_7   1408 AAAAAAGCAAGTCATAAACTGGGAGAAAATGTTTCTAAAACATAT-TTTG 1456
                         i    ii   vi  i i v           i   vi   v     - i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_79181266_7   1457 GTCAAAATAAATCTATCTAAAATATTTAAAGACCTCTTGCATCTCAATAA 1506
                         i -  iiv vv v    i i     v      v     i  v        
  L1M4_orf2#LINE/    743 AT-AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_79181266_7   1507 TAATAAGACAA----CCCGAT-ACAAAATGGACAAAAGATTTAAAGAGAC 1551
                            v       ----   i  -?v       i    i     i  v    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_79181266_7   1552 ATTTCACTGGAAAAGATCTATACATGTTAACTTGGCACATGAACAATTTA 1601
                              v iii i     v  i v   viv v vi         v iv vv
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_79181266_7   1602 TCAATATCATTCACTAT 1618
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (83 / 64)
Gap_init rate = 0.02 (12 / 565), avg. gap size = 2.58 (31 / 12)  


2897 27.76 0.77 1.53  chr2_79216773_79222628.rev     4451  5365 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_79216773_7   4451 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4500
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_79216773_7   4501 GGCCATAACGCCCAAAGTAATTTATAGATTCAATGCTATTCCCACTAAGC 4550
                            v   viv      v i  i  i        i  v  i  i ii  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_79216773_7   4551 TTCC-TTTGACTTTCTT-CAAAGAATTAGAAAAAACT-ACTTTAAATTTC 4597
                          i  -vi  v    i  -  i -    i-- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_79216773_7   4598 ATATGGAACAACAACAACAACAAAAAGCCTGTATAGCCAAGACAATCCTA 4647
                                 vvi   --------iii v  v v        i      i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAA--------GGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_79216773_7   4648 AGTAAAAAGAACAAAGCTGGAGGCATCAGACTACCTGACTTCAAACTATA 4697
                          iv  i          i      vv   v   v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_79216773_7   4698 CTACAAGGTTACAGTAACAAAAATAACATGGTATTGGTACCAAAACAGAT 4747
                               i i        iv  i i iii     i   i iv ii i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_79216773_7   4748 ATATAGACTAATGGAACAGAACAGAGGCCTCAGAAATAAACCTGCATGTC 4797
                                ii       i    iv   ivii            iii ii i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_79216773_7   4798 TACAACCATCTGATCTTTGATAAACCTGACAAAAACAAGCAATGTGGAAA 4847
                           iiii  vi    i  i  i  ivv  v   i v  vv     v     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_79216773_7   4848 GGATTCTCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCAATACACA 4897
                          i  vv   v  i  i        i     v      v  ? v i ii  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_79216773_7   4898 GAAAACAGAAACTGGACTCCTTCCTTACACCTTATACATAAATTAACTCA 4947
                         i  i vv   ii     i   v   i     v      v           
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_79216773_7   4948 AGATAGACTAAAGACTTAAACATGAGACCTAAAACCATAAAAAAACTAGA 4997
                          i  i  ii ?    i    ii i   v       i      vvvi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_79216773_7   4998 AGAAAACCTAGG--TAATACCATTCAGGACATAGGCATGAGCAAAGACTT 5045
                                v    --   - i -   iv   v v  vv ii    v ii  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_79216773_7   5046 CATGACTAAAACACCAAAAGCAATTGCAACAAAAGACAAAATTGACAAAT 5095
                          v iiv  vi            vvv           v     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_79216773_7   5096 GGGATCTAATTAAACTAAAGAGTTTCTGCACAGCAGAAGAAACTATCATC 5145
                         v   ii v  i   v v  i ii  i  ii vv  i i  v       vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_79216773_7   5146 AGAGTGAAAATGCAACCTACAGAACGGAAGAAAATTTTTGCAATCTATCC 5195
                          i        vi     i      i  i       v       vii  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_79216773_7   5196 ATCTGACAAAAGGCTAATATCCAGAATTTACAAGGAACTTAAACAAATTT 5245
                               i  ii i  vi          v  i  i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_79216773_7   5246 ACAAGAAAAAAACAAACAACCCCATCAAAAATTGGGTGAAGGAATATGAA 5295
                          i  v     i     i     v  i?    v    ii     v -    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT-TGAA 836

  chr2_79216773_7   5296 CAGAGACTTCTCAAAAGAACACATTTATGGGGCCAACAA--ACATGAAAA 5343
                         i   v i     v      v i  vi viv      i  --         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_79216773_7   5344 AAGGCTCATCATCGTGGGTCAT 5365
                         i v     v    i????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (153 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.91 (21 / 11)  


3263 25.91 0.88 0.77  chr2_79244727_79250977.rev     4853  5759 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_79244727_7   4853 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4902
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_79244727_7   4903 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4952
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_79244727_7   4953 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4999
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_79244727_7   5000 ATATGAATCAA---AAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAA 5046
                              i --  ---  ii  v  v v  v     iv     i i ivv i
  L1M4_orf2#LINE/    148 ATATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_79244727_7   5047 AAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAA 5096
                                   i      vv    i  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_79244727_7   5097 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 5146
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_79244727_7   5147 ATCAATGGAGCAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACA 5194
                                  ii    i--    i  --        vv  ii i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr2_79244727_7   5195 ACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT 5244
                         iii vi    i  i     ivv  vv  i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_79244727_7   5245 TCCCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5294
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_79244727_7   5295 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGAT 5344
                         iv    ii    i    v   i     v           i  i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_79244727_7   5345 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5394
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_79244727_7   5395 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5444
                            v    ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_79244727_7   5445 TAAAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATC 5494
                           vi            vvi     v    vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_79244727_7   5495 TAATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5544
                          v  iv  v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_79244727_7   5545 AACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 5594
                           v  i     i   i             v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_79244727_7   5595 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5644
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_79244727_7   5645 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATCAACAGACAC 5694
                             i     i     v  i?    i           iv v  i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_79244727_7   5695 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAATATGATC 5744
                              v        i  vi viii     v  i          v   v  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_79244727_7   5745 ACCATCACTGGCCAT 5759
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (134 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2666 26.99 2.51 3.50  chr2_79282263_79286061.rev     2393  3307 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_79282263_7   2393 GAAACTTATCCCATGTTCATAGACTGGATAAGTTAATATTGTTAAAGTCT 2442
                             vv              i  i    vi v             ii vv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_79282263_7   2443 TCATACTACCCAAAGCAATCTACAGTTTCAATGCAATTCCTGTTGAATTT 2492
                         iv     v      vii        v     i     i   i ii  v i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_79282263_7   2493 CTAATAACATTTTTCACAAAAGTAGGAAAAATAATCTTAAAATTGAGATA 2542
                          i iivi v     ii  i  i v iv  iv i   i       v v  i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_79282263_7   2543 GACCCACAAAAGACCCCAGATATTCACAGCAATCTTGAGCCAAAAGAATA 2592
                           vvii   ii     vii   vi  v i         ivv i     i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_79282263_7   2593 ATGCTGGAAACATCATACAACCTGATTTCAAAATATACTACAAAACTATA 2642
                          v i    iivv   i  vv  ii         iv         i   i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_79282263_7   2643 TTAATCAAGACAGCATTGTAGTAGCATAAAAACAAATCCATAGACCAATG 2692
                         v            ii v   v i      ii i i ivi     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_79282263_7   2693 GAGCAAAAT----AGCCCAGAAATAAATTCACATATTTACAGTCAATGGA 2738
                           ii i   ----  i           ii  i i     ii      v  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_79282263_7   2739 GTTTT--TAAAGATGCCAAGAATAGATAATGTTGATA-AACAGTTTCTTC 2785
                         v   i--i  i i        vi vvi    vv  v -  i   i i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_79282263_7   2786 AATAAATGGTGTTGTGAAAGCTTAACGTGCATACATAAAATAATAAAATT 2835
                           i        i  v  v i  vi ii?v  i iii    v   i  i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_79282263_7   2836 AGACGCTTATCTCATACTGTACAGAAAAATAAACTCAAAATGGGT-AAAG 2884
                         i   v i  i    i  ii  i v      v            i - ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_79282263_7   2885 ACTTGAACATAAGACTGGGAACTCTAAAACTACTACAAGAAAACTTAGGG 2934
                           i i  ii     vivii    v       vi  v        v    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_79282263_7   2935 GGAAATGT-CACAACATTGTCCATGTTATGACTGTATGACAAAATCAACT 2983
                          v    v - iii  v   v----    --------- i   ------- 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGG----GTTA---------GGCAA-------T 582

  chr2_79282263_7   2984 GGAAAATCATTTTTTGGTTATAATAGAAAAAACGCAAGGGTAA-AAAAGC 3032
                           -------   i  i v   i i vv    i i    --i  -     v
  L1M4_orf2#LINE/    583 GG-------TTTCTTAGATATGACACCAAAAGCACAAG--CAACAAAAGA 623

  chr2_79282263_7   3033 AGAAAGAGACAAATGAGATTGTATCAAAAT-AAAAACTTCTGCACAGGAA 3081
                          i   v   i    vi  i vi        -        i  ii vvv  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_79282263_7   3082 AGGGAACAAATATTAGAGTGAAGGGACTACCTACAGAATGGGAGAAAATA 3131
                            iv  v vi vv i      ii   v   i                  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_79282263_7   3132 TTTACAAAGCATACATATGATAAGGGGTTAATATTCAAACTGTATGAGGA 3181
                            i    v    i  v         ii vi   i  i v i   i i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_79282263_7   3182 ACT-TAATAACT----GGCAAAAA----AATACCCCAATTTAAAAAATGG 3222
                            - v i    ----iii     ----    v       ?     -   
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGG 822

  chr2_79282263_7   3223 TCAAAGGACCTGAACAAACTTTTCTCCAAAGAAGATA--CAAATATCTAG 3270
                         v       ii    i i  v                 --     iv i i
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_79282263_7   3271 -AGGTATATGAGGAAAACGGCTTAACATCAGTTATCAC 3307
                         - i i i    --   ivv   i       ????????
  L1M4_orf2#LINE/    873 TAAGCACATGA--AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (155 / 88)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 2.89 (55 / 19)  


2840 27.18 2.46 0.89  chr2_79288143_79293102.rev     3575  4468 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_79288143_7   3575 TGAAAAAACATTCCAGGCTCATTGATAGGAAAAATCAATATTGTTAAAAT 3624
                           i   i i  i   v i    v   v    i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_79288143_7   3625 GGCCATACTGCCCAAGGCAATTTATAGATTTAATGTTATTCATAAGAAAC 3674
                            v     v     ivii  i  i     i  i iv  i v  vv   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_79288143_7   3675 TACCGGAAACTTTCTTCACAGAATTAGAAAAACT-ATTTTAAACTTTATA 3723
                          v  i vvi i  i  ii     v v  v  i  -  ii    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_79288143_7   3724 TGGAA---CAAAAAAGCCCGAATAGTCAAGGCATTCCTAAGCAAAAAGGA 3770
                              ---   iii v  v      i   ii  v  i i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_79288143_7   3771 CAAAGCTGAAGGCATCACATTGCCCAACTTCAAATTATACTAGAAGGCTA 3820
                              i  i   vv     i v     i      viv     v  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_79288143_7   3821 CAGTAACCCAAACTGCATGGTACTAGTACAAAAAGAGACAGATAGACCAA 3870
                               i v i  v ii       i i i  ii v     v     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_79288143_7   3871 AGGAACAGAATAGAAATCCCAGAAATAATGCTACATACCTACAAACATCT 3920
                         v    i     v  i vi          vv i i i ii  iiiv  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_79288143_7   3921 GATCTTCAACAAAGTTGACAAAAATAAGCAGTGGGAAAAGGACTTCCTAT 3970
                            i   i    i v  v   i vi vv  i    i    i ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_79288143_7   3971 TCAATAAATGGTGCTGGGATAACTGGATAGTCATATGTAGATGATTGAAA 4020
                             i              i         ?i  i   i i v  v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_79288143_7   4021 CTGGACCCCTTCTTTATACTATTTTAAAAGGTAAACTCAAGATGGATTAA 4070
                         i         v i i i  i  v vv   ii v       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_79288143_7   4071 AGAGTCAAATGTAA-------AACTATAAAA-TCCTGGAAGATAACCTAG 4112
                            vii        -------          -  i i     v   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_79288143_7   4113 G---AAATGCCCTTCTGGACATAGGATCTTGCAAAGATTTCAT-GATGAA 4158
                          ---    ---    vv   v v  i ivv    v i    v -   - v
  L1M4_orf2#LINE/    551 GNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr2_79288143_7   4159 GATGCCAAAAGCAATTGCAACAAAAACAAAAATTGACAAATGGGATCTAA 4208
                           ii         vvv         iv      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_79288143_7   4209 TTAAAGAAAAGAGCTTCTAAACAACAAAAGAAATTATCAAAAGAGTAAAC 4258
                          i   ivv  i i   i ivi vv    i  v i      i i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_79288143_7   4259 AGACAACCTACAGAATGGGAGAAAACATTTGCAAACTATGCATCTGACAT 4308
                                 i                i         ii  ii      i -
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA- 745

  chr2_79288143_7   4309 AGTTTGGTCTAATATCCAGAATCTACAAAAA--TCTTA-AATT-AGCAAG 4354
                           ---  v  vi          v  i   i --     -  i - ii  v
  L1M4_orf2#LINE/    746 AG---GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_79288143_7   4355 CAAAAACTGAACAACTGCATTAAAACGTGTGCAAAGGACATGAACAGACA 4404
                         v    ivii  i   ivv   ?   vi  v        iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_79288143_7   4405 CTTTTCGAAAGAAGATATACACACAGCCAAGAAGCATAT--AAATATGCT 4452
                         i  i  v              v ii     v     i  --   v     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_79288143_7   4453 CAAAATCACTAATCAT 4468
                            v    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


3231 26.21 0.77 0.77  chr2_79421290_79427552.rev     4864  5771 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_79421290_7   4864 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4913
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_79421290_7   4914 GGCCATACTGCCCAAGGTAATTTACTGATTCAATGCCATCCCCATCAAGC 4963
                            v     v     iv i  i   v       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_79421290_7   4964 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5010
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_79421290_7   5011 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5060
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_79421290_7   5061 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5110
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_79421290_7   5111 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5160
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_79421290_7   5161 CAATGGAGCAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5208
                                ii    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_79421290_7   5209 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATAGGGAAAGGATTC 5258
                         i vi    i  i     ivv  vv  i v  vv    i       i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_79421290_7   5259 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5308
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_79421290_7   5309 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5358
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_79421290_7   5359 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5408
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_79421290_7   5409 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5458
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_79421290_7   5459 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5508
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_79421290_7   5509 ATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5558
                           iv  v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_79421290_7   5559 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5608
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_79421290_7   5609 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACTAGATA 5658
                          i  i  vi          v  i  v      vv    -i i v  -   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATA-ATA 793

  chr2_79421290_7   5659 GAAA--CAAACAACCCCATCAAAAAGTGGGCAAAGGACATCAACAGACAC 5706
                         i   --    i     v  i?    i           iv v  i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_79421290_7   5707 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5756
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_79421290_7   5757 ATCATCACTGGCCAT 5771
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2529 20.50 6.26 2.82  chr2_79632201_79634664      772  1410 (1054)    L1M4_orf2#LINE/L1        5   665 (243)  

  chr2_79632201_7    772 AAGATATCTCATGTTCATGGA-------AC------------AGATAACA 802
                                 i            -------  ------------    ii  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_79632201_7    803 -----TCCCAAACTTATCTGCAGATTCAAATCAAATCCTTTAAAAATTCC 847
                         -----i      i v    i         vv   vi   v v     -  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT-CC 103

  chr2_79632201_7    848 CAGCTGCCCTATTTTTTTTTTTTTTCAGAAATTGACGAACCAATCCTAAA 897
                                 ----------      v           i i ii        
  L1M4_orf2#LINE/    104 CAGCTGCC----------TTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_79632201_7    898 ATTTATGTGGAAATGCAGGGGATCTAGAATAGCAAAATCAGTCTTGAAAA 947
                            i  i          i    i i        v   v  i         
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_79632201_7    948 AGGAAACATGAATTTGGAAGACTCACGTTTCTGGATTTAAAAACATACTG 997
                           i i - ii  v     i       ii   ivi    v     v    i
  L1M4_orf2#LINE/    194 AGAAGA-ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_79632201_7    998 CAA-GCTACAGTAATCAAGACAGTGTAGTACTGGTATAAAAATAGACATG 1046
                            -                      i       i    ii        i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_79632201_7   1047 TAGATCTATGGATTACAGTAGAGACCCGGGAAGTAAAACTGCACATTAGT 1096
                               v     v  v i v    vi vi   i    v iii     vi 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_79632201_7   1097 GACCAATTGATTTTCCATGAAAGTGTCGAGAAAATTCAGTACA-AAAGA- 1144
                          ii            v ii ii   i i   vv     i ivi-     -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_79632201_7   1145 ---TTTTTTCAACAAATGTTACTAGAAACAA-TGCATATCCACATGCCAA 1190
                         --- i             v i  i i -   -  v   ?        v  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGA-CAACTGGATAKCCACATGCAAA 441

  chr2_79632201_7   1191 AGAAAGAATTTGTACTCTTTGTTTGCAC--TGTACAAAAATTAAGTCAAA 1238
                             v   v   v  i i vvi ii   -- i            v     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_79632201_7   1239 ATGGATTATAGATATATATGGAATAGCTAAAATTATAAAGTTATTAGACA 1288
                               i ?   iv  v   v  v        i      ii v     vi
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_79632201_7   1289 AAAACATTCGTATAAATCTTTGTGACCTTGGATTGAGCAATAATGTCTTA 1338
                                vv ?i        i          i  ii     ii v     
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_79632201_7   1339 GAGACAACATTAAAAGCACAAGTGACAAGACCAAAAAAAAACCAGA---A 1385
                           v ii   ii           ii    ----  i      i-   --- 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAA----AAGAAAAAAT-AGATAAA 636

  chr2_79632201_7   1386 TT----TTTTTCAAAATTAAAAACTTTTG 1410
                           ----  iv                   
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.84 (83 / 45)
Gap_init rate = 0.02 (16 / 661), avg. gap size = 3.62 (58 / 16)  

1005 18.53 5.94 1.05  chr2_79632201_79634664     1687  1972 (492)    L1M4_orf2#LINE/L1      609   908 (0)  

  chr2_79632201_7   1687 ACAA--AACAAAACAAAAAACAAACAAA--------CAAAAAAAC-AACA 1725
                             --       v      i i i   --------  vv    i-  v 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_79632201_7   1726 ACTTTTGCGCTGCAAATGACACCAT--AGAAGG--AAAAGACAACCCACA 1771
                                i   v    v     i  --    i --               
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_79632201_7   1772 GAATGGAATAAAGTATTTTACAAATTTTGTATCTGATACAGAA-TTATAT 1820
                               i v   i     -i     iv i         vi i -  i   
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTT-GCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_79632201_7   1821 ACAGAATATATAAA-AACATTTACACCTCAATAATATAAATTTGAATAAT 1869
                         v             -   vi     v          v   vvii     i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_79632201_7   1870 GTAATTTTTAAATGGACAGAAGATCTGAATAAATGTATTTTTAAAGAAGA 1919
                         vi    ?vv      i  i i   i      i ii v i ii        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_79632201_7   1920 TATACAAATGGCAAATAAGCACACATGAAAAGATGCTTATCATCATCCAT 1969
                                     v          --            i v     ?????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACA--TGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_79632201_7   1970 TAG 1972
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.48 (31 / 21)
Gap_init rate = 0.03 (9 / 300), avg. gap size = 2.22 (20 / 9)  


4152 15.19 3.45 5.60  chr2_79664594_79666555      543  1470 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_79664594_7    543 TGGAAATATATGT-ATGTTCACAAATGGGAAGACTTAGTATTGTTAATAA 591
                               v    vi-       iii  v          i         v v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_79664594_7    592 GGCAA----------ATTGATTTAGAGATTCAATGCTATTGCTGTGAAAA 631
                              ----------      i  v        i  v  iv  i v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_79664594_7    632 TCCTAGCTTCCTTTTTTTTTTGCAGAAATTGCTATGCTCATTCTAAAATT 681
                            i    v        ----          vi v   v  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT----GCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_79664594_7    682 CATTTGTAAAATA----------AGAATAGTCTGAAACAATCTTAAAAAA 721
                            v  -i    i----------       i -i          i     
  L1M4_orf2#LINE/    147 CATATG-GAAATGCAAGGGACCCAGAATAGCC-AAAACAATCTTGAAAAA 194

  chr2_79664594_7    722 GGTGAACAAAGTTGGAAGAC--ACACTTCTTAATTTCAAAACTAACCGCA 769
                          iv             i   --       ii            v  ii  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_79664594_7    770 AAAGTATAATAATCGAGACTAAATGGTATTGACATCAGCATAGGCATTTA 819
                           iv  i i     i    vivi     i  i   v  v    i   v  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_79664594_7    820 TTTTACTGGAATAGAATTGAGCATTCCGAAATAAACCCATATATTTATGG 869
                         vv i v               vi i v              i        
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_79664594_7    870 TTAATTGATTTTTCAACAAGGGTGACAAGACAATTTAATGGGGGAAAGAA 919
                          i          - i         v      v   i       -      
  L1M4_orf2#LINE/    345 TCAATTGATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAA 392

  chr2_79664594_7    920 TAGTTATTTAAACAAATGGTGCTGAGACAACTGAATAAACATTTACATGG 969
                             iv   v              i        i   ----?ii     v
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA----KCCACATGC 438

  chr2_79664594_7    970 AAAAGA-TGAATTTGGACCGCTTTCTCCTCCCATATACAAAAATTAATGA 1018
                               -    v       v  vi   viv                 i--
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC-- 486

  chr2_79664594_7   1019 TAGACTTCAATATGCATTATAGACCTAAATATGAGAGCTAA--CTATGAA 1066
                         ------    v   v  i ?          i i        --    i  
  L1M4_orf2#LINE/    487 ------TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_79664594_7   1067 ACTCTTGGAAGAAAACATAGGTGTAAATCTTAGTGACCTTGGATTAGGCA 1116
                               i              ?         v          i       
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_79664594_7   1117 TTGGTTTCTTGTATTAGGCAGTAGATTTTTAGATATGACACCCAAAGCTC 1166
                         v         --------------------            v     v 
  L1M4_orf2#LINE/    581 ATGGTTTCTT--------------------AGATATGACACCAAAAGCAC 610

  chr2_79664594_7   1167 AAGCAATAGAAGAAAAATAATGTAAATTTGACTTTATCAAAATTAAAAAC 1216
                               i i        vv vi      v     i               
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_79664594_7   1217 TTTTATGCATCAAAGGACAGCATCAGGAAAGTGAAAAGACAACCCACAGA 1266
                             i   v          vi    i                        
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_79664594_7   1267 ATGGGAGAACATATTTACAAATCATAT---CAGTAAGAATCTATTCTTCC 1313
                                  v      i          ---iii    iiv  --------
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT-------- 752

  chr2_79664594_7   1314 AAATTTATAAAGAACCATATAAAGAATGATTACAGCTTAATAGTAAAAAG 1363
                         --- v   vv    i-          ivv     i  i    i       
  L1M4_orf2#LINE/    753 ---TGTATCCAGAAT-ATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_79664594_7   1364 A---ATACCTAAATTTAAAAATGGACAAAGGACTAGAATAGACATTTCTC 1410
                          ---   v iv    ?        i       i v               
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_79664594_7   1411 CAAAGAAGATATACAAATGGCAAATAAGCACACGAAGAGATGCTCAGCAT 1460
                                              v          i   i         i   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_79664594_7   1461 CATCAAGTGA 1470
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.28 (77 / 60)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.67 (84 / 18)  


2731 17.17 9.45 2.05  chr2_79699992_79701618.rev      501  1135 (492)    L1M4_orf2#LINE/L1      227   908 (0)  

  chr2_79699992_7    501 ATTTCAAAATTTACCACAAAGCTACTGTAATCAAAACAGTCTAATAATGA 550
                                  i    i          v        i     v ii  v  i
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_79699992_7    551 TATAAGGATAGACACACAGACATTTTGATTAATAGAATAGAATTAAGATT 600
                         i             i i   -------- i   i          i   v 
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGA--------TCAATGGAATAGAATTGAGAGT 318

  chr2_79699992_7    601 CCCCAAATAA-CCCTTACATTTCTA-TCAATGGATCTTTGA--------- 639
                           vv      -   v       v i-     v   i  i  ---------
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_79699992_7    640 -------------------------------------AGATAGTGTTGAA 652
                         ------------------------------------- i  i   i  ii
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_79699992_7    653 ACAATTGGCTATCCACATACAAAAGAATGTAGTTGGATGCCTACC----- 697
                             i   v  ?      i          v       iv      -----
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_79699992_7    698 --ATATATGAAAATTAACTAAAAATTGATCAAAAATCTATAAATATAGAA 745
                         --     ii          v     v     ? i i   --   i  ii 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA--AATGTAAGA 516

  chr2_79699992_7    746 GTAAAAACTAGAAAACTCTCAGAAGAAAATACAGGCATAAATATGTGTGC 795
                          iv       v        i         i i   ?i     v vi   v
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_79699992_7    796 TTTTGGATTAGGCAATCATTTCTTAGATATGACACCAGAAGAGCAAGAAA 845
                         ii    i         vi                   i   vi    v  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_79699992_7    846 CCAAAATAAAAACAAATACATTTGACTTCCTCAAAATTAAAAACTTTTGT 895
                          v   iv     i i   v   v      v                    
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_79699992_7    896 GCTTCAAAGCACACCATCAAAAAACTGAAAAGACATTTCACAGAATGGAA 945
                                  v    i     i   v          vii          i 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_79699992_7    946 GAAAATTTTTTCAAATCATATATCTAGTAAGACTCTAATATCCAGAATAT 995
                               v   v              ii    ivv  vi            
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_79699992_7    996 ATAAAAAACTATTATAACTCAATAATAAAAAGACAAATG---CAAATAGC 1042
                              i    v   i                       i---   v ?i-
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA- 815

  chr2_79699992_7   1043 CCAAGATGGGCAAAG-ATCTGAATAGATATTTCTCCAAAGAAGCTATATG 1091
                         --  i          -  i        i               v    ii
  L1M4_orf2#LINE/    816 --AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_79699992_7   1092 AG-GGCCACCAAGTACATGAAAAGATGCTCAACATCATGAGTCAT 1135
                          i-     vi   i                       ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (66 / 39)
Gap_init rate = 0.01 (10 / 682), avg. gap size = 7.30 (73 / 10)  


2677 24.18 1.77 0.54  chr2_79736842_79738568.rev      501  1236 (491)    L1M4_orf2#LINE/L1      164   908 (0)  

  chr2_79736842_7    501 GATCCAGAAGAGCCAACTCATTATTGAAGGAGAAGAATAAAGTCAGAGAA 550
                           i      v      vv  v v     ii       i     ii   i 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_79736842_7    551 TTGACACTACCCAACTTCAAGACTTACTATAAATCTACAGTAATGAAGAC 600
                         i v     v     i     i        i   v          v     
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_79736842_7    601 AGTGTGGTATTAGTAAAAGGAGAGACAAATAGATGAATAGAACAGGACGG 650
                                  i i i v     v     v      v   i   i  i iv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_79736842_7    651 AGATCCCAGACATAGGCCCACATAAATACAGTGAACTGACCTTTCACAAA 700
                            vi     v   ii    i i vv  ii  v  i   ii  iv    i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_79736842_7    701 AGAGAGAAGGCAACAGAATGGAGCAAAGATACTCTTTTCAAAAAGTGGTG 750
                         i v vv   i v ivv     i v  ii   v         v  i     
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_79736842_7    751 TTGGAAAAACTGGATATTCACAT-TAAAAAAA-GCGGTCTAGATATAGAC 798
                         i   i v         ?i     -i    i  - vi  - i  ivivv  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT-TGGACCCCTAC 462

  chr2_79736842_7    799 CTTACACCTT-CATAAAAATCAAATCAAAATGGATCACAGATGTAAACAT 847
                           i     v -i i      i  v             ?   iv    ii 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_79736842_7    848 AAAATGC-AAAACTATAAAACTTCTAAAAGATAACATAAGAGAAAGCCTA 896
                           i -  -              ii  i    v      i ? v  ii  v
  L1M4_orf2#LINE/    513 AAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_79736842_7    897 GATGACCTTGAGCATGACAATGATATTTTAGATA---CATCAAAGGCATG 943
                         vi        i ivv i     i v i       ---  i    i   ii
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_79736842_7    944 ATCCATGAAAGAAATAATTGATAAACTAGACTT-ATTAAAATTTAAAA-- 990
                          v v ii       v   v      i i     -  i      v    --
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_79736842_7    991 TGTCTGCTCCAAAAAAGATAATGTCAAGAGAATGAGAAGACAATACACAC 1040
                          v v    i    i--  i v i      i i   i       iv    v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAG--GACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_79736842_7   1041 ACTGGGAGAAAATATATGCAAAAGATACATCTGATAAAGAACTGTTATCC 1090
                          v             v      vv   i         i i   vv     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_79736842_7   1091 AAAATATCCAAAGAATTCTTAAAACTCAACAAGAAAATGG---ATAACCT 1137
                          i     vi      i     v       i  v    v i---      i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_79736842_7   1138 AATTTAAAAATTGGCCAAAGACCTTAAAAGATATCTCACCAAATTAGATA 1187
                             ?      v   v  i  ii v  v   i  i  v     vv     
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_79736842_7   1188 TACAGATGACAAATAAGCATATGAAAAGATGCTCCACATCGTATGTCAT 1236
                             i   i v        i              v     i????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (101 / 73)
Gap_init rate = 0.01 (11 / 745), avg. gap size = 1.55 (17 / 11)  


2540 24.23 6.55 1.61  chr2_79745200_79749460     2961  3769 (492)    L1M4_orf2#LINE/L1       60   908 (0)  

  chr2_79745200_7   2961 CTTCAAATTGAT-TATA-------TGCAATCTCAATCAAAATTCCAGTAA 3002
                          ii         -  i -------i      i v        i    ivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_79745200_7   3003 GATTTTTGGCAAAAATTGACAAGCTCATTTGATAATTTACATGGAAATTC 3052
                         vv     v   i             v  iiv v    i i        v 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_79745200_7   3053 CAAGGATCCGGGAAT-GCAAAAATAACTTCGGAAAGGTATAAGTATGTTG 3101
                         v i   i  i -   -  v    i  ii i i   i v v  vv v    
  L1M4_orf2#LINE/    160 AAGGGACCCAG-AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_79745200_7   3102 GAGGACTAACAGTATGTGACT-CAAGACTTACTATAAAGGTACAGTAATT 3150
                                v   v vivii i -   i        i    v         i
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_79745200_7   3151 TTGCCAATGTGGTGTTGACATCAAGCTAGACAAATAGACCA-T--AAGAA 3197
                         vv v  i      ii  i   v i v      v     i  - --  v i
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_79745200_7   3198 AATAGAAAGTCCAGGAATAGACCAGCATGCAT--ATGGATAACTGATCTT 3245
                            v  i       i    i   --   i   --    vi  i    i  
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCAATTGATTTT 356

  chr2_79745200_7   3246 TGAGAAAGGTGCAAAGGCAGTTCTTTGCAGGATGCATACATAGTCTTTTC 3295
                         i  v  i     v   i vi   vv  -i   --- viv           
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATG-GGGA---AAGAATAGTCTTTTC 402

  chr2_79745200_7   3296 CACAAATGGTGCCGGAACAGTTGTATATCCATATGCCAAAAAAATGATCT 3345
                         v           i  i   ii  v   ?   i    -    i     vv 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGC-AAAAGAATGAAGT 451

  chr2_79745200_7   3346 TCAATCCATAACTTACATCATATAACAAAATTAAATACAAATGGA--ATG 3393
                          vi i  v  v  i   i      vv        v vv       -- ?i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_79745200_7   3394 GATTCTGACGATACAATCGAAAACTCTAAAACTTCTAGAAGGAGACATAG 3443
                           i-  i vvi  vi v v      v       ii      i i      
  L1M4_orf2#LINE/    502 GAC-CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_79745200_7   3444 GAGAAAATGTTTGTGACTTTAGAT---ACACTG----------------- 3473
                          ? v    v  i     i  i i ---i  v  -----------------
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_79745200_7   3474 -CAAAAGCATAATCCATGAAACAAA---TCAATAAATTGAGCTTCATCAA 3519
                         -        i  v v ii   v   --- vi        ii         
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_79745200_7   3520 AAGTAAAATCTTTCGTTTTTTTGAAGGACATTGTTATAAGAAGGAAAAGA 3569
                           v     v    i  vi  i-i       i i i vi i iv       
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTC-AAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_79745200_7   3570 TCAGCCATAGACTGGAAGAACATCTTTGCAAAGTATATATCTGATAAAGA 3619
                         iv v   i   v   i    v  v        vi             i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_79745200_7   3620 ACTTATGTCCAGAATGTATAAGGAACTCTTAAAA-TCAATAAGAAAACAA 3668
                             i i        i     i         v  -       v    -- 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA--A 797

  chr2_79745200_7   3669 AACAGTGTAAC---ATT------TGGAGAAATAATTTAAATAG-CATCTA 3708
                         i   i-i    ---   ------   iv   vi    i     -   i v
  L1M4_orf2#LINE/    798 GACAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_79745200_7   3709 TC-AAAGAAGATATAAATATGGCAAATAAGCACGTGAAAATAATTTCAGC 3757
                           -            v v     v         i      v vvi   i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_79745200_7   3758 ATCATTGGTCAC 3769
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (109 / 84)
Gap_init rate = 0.03 (25 / 849), avg. gap size = 2.64 (66 / 25)  


 255 29.55 19.17 2.72  chr2_79972786_79974360.rev      461  1086 (489)    L1M4_orf2#LINE/L1      180   908 (0)  

  chr2_79972786_7    461 AAGAATTTTTAAAAAGGGGTAATAAAG------------CATTGCCCTGA 498
                           v   i  v      ii -  i    ------------  i v   ---
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAG-AACAAAGTTGGAGGACTCACACTTCCC--- 225

  chr2_79972786_7    499 TAGATATCAATATTTATTAATAAGCTATGGTAACTAAATCAAAGTGGTAT 548
                         --i  v    v i   i  vv      ii    ii  iv  iv      i
  L1M4_orf2#LINE/    226 --AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr2_79972786_7    549 --------------ACATATAGA--AATTGACCTATAGAGTAGATAGCCT 582
                         --------------         --   v  ---     i v  v  i i
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGA---ATAGAATTGAGAGTCC 320

  chr2_79972786_7    583 GCAAACAG-CTCAACTTACATATATG--CAAATG-----TGACA--TATG 622
                         iv   i i- i  ---     v    --   v  -----i    --vi  
  L1M4_orf2#LINE/    321 AGAAATAAACCCA---TACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_79972786_7    623 ACAA---------ATAGGGGTGGA-TGGACTGTTTAATAAACAGTGCTAA 662
                         v   ---------  i   ivi  - i v  v  i  i   ii     ii
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_79972786_7    663 -ATA-TTGACTAAGAATAGGAAAATTAATAAAACTAGACTT-TAATTCAA 709
                         - i -i  iv  ?vv i v v   vv   i  ii i   ii-  vi   v
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_79972786_7    710 AGAGTA---AAAAGT-----CAAA---GAT-AAAGACTTAAATGTAAAAG 747
                          vvi  ---    i -----    ---   - ?    i         i  
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_79972786_7    748 C-AACATTTTTAAACATTTAGCAAAATATTTAGAGATA--TATTTATGAT 794
                          -  v i v v    vi    v i  v iv   i?i  -- v  ii   i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_79972786_7    795 ATTGGGTTAGAAAAAAATTTCTTAAATAGGACAC-------ATATACAAT 837
                         v         iv  vii       i   v     ------- i vi   i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_79972786_7    838 AAAGATCAATGCAACTAA-TTGTATTT--TTAAGA--AAAA---TTTATA 879
                            iivv  vii iv   -   v i  -- i  i --    ---   i i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_79972786_7    880 CAACAATAGGCAT----AAGCAAAATGAAAATATTAGTCATGCACTGGGG 925
                          vv   vi i  i----   -   i      v iv vi  iiv v    i
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAG-AAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_79972786_7    926 GTA--TATTTGCAAAAAATAGTACATAAAATACAAAGTTTGAATAT-GAA 972
                          v --          --- vi  i  vvi   viiiii   v  vi-   
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAA---TCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_79972786_7    973 AATGTAA-GAA-TCATGC--TT------TAAGATGACAATCAACCCAATG 1012
                         v  i   -   -  v i --i ------   i v     vi        v
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_79972786_7   1013 AAAAAGGAGACAAAGAA----AATAG---------CAAA-------CCCA 1042
                         ?    ivi i     i ----     ---------    -------iv  
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_79972786_7   1043 AATGACTAATAAAGATATGAAAAGCATAC-CAAC-TGAAGAAATAA 1086
                             i i     iv i        -  i -    - v ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (108 / 73)
Gap_init rate = 0.06 (42 / 729), avg. gap size = 3.26 (137 / 42)  


2799 26.60 2.69 0.79  chr2_80016867_80021606.rev     3358  4248 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_80016867_8   3358 TGGAAAAACATTCCAACCTCATGGATAGGAAGAATCAGCATTGTGAAAAT 3407
                               i i  i   vvi        v      v i ii     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_80016867_8   3408 GGCCATACTGCCCAGAGTAATTTATAGAATAAATGCTACTTCCATCAAAC 3457
                            v     v    i v i  i  i   v v  i  v iii i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_80016867_8   3458 TACCATTGACATTCTTCACAGAATTAGAAAAAGAAACT-ACTTTAAATTT 3506
                          v   vivi v  i  ii     v v  v  i----  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chr2_80016867_8   3507 CATATGGAATTAAAGAAGACCCCGTATAGCCAAGACAATCCTAAGCAAAA 3556
                                  v iv iii     v v        i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_80016867_8   3557 AGAACAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTAAACTACAAG 3606
                                  i i    vv   ii  v  ii i      vivv       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_80016867_8   3607 GCTACAGTAACCAAAACAGCATGGTACTGGTCCCAAAACAGACA----GA 3652
                                   i   i    ii         iviv ii i     ----  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_80016867_8   3653 CCAACGGAACAGAAGAGAGACCTCAGAAATAACACCACACATCTACAACC 3702
                         i   i    i    vv    vii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_80016867_8   3703 ATCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAATAATCTC 3752
                          vi    i  i     ivv  v   i v  vv           v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_80016867_8   3753 CTATTAAATAAATAGTGCTGGAA-AACTGGCTAGTCATAGGCAGAAAACT 3801
                           v  v  i    i       i -      v  ?i  i v   i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_80016867_8   3802 AAAACTGGACCCCTTCCTTACACCTTATGCAAAAACTAACTCAAGATGTA 3851
                         i  ii         v   i     v   i      i        i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_80016867_8   3852 TTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAAC 3901
                          i ?    i         i v i     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_80016867_8   3902 CTAGGCA-ATACCATTCAGGAAATAGGCATGGGCAAAGACTTCAT-GATG 3949
                         v    ?i- v i -   iv  vv v  vv i     v ii   v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr2_80016867_8   3950 AAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGTATCT 3999
                          vi            vvv          vv     v  i    v v ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_80016867_8   4000 AACCAAACTAAAGAGCTTCTGCACAGCAAAAGA-ATCATCAG---AGTGA 4045
                         v i    v v  i i   i  ii vv    i  - ii    i---     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_80016867_8   4046 ACAGGCAATCTACGGAATGGGAGAAAATTTTTACAA-TCGACTCATCTGA 4094
                          v  i   i i  i              v   i   -  - ivi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGA 743

  chr2_80016867_8   4095 CAAAAGTCTAATATTCAGAATTTACAAGGAACT--TA-AATT------TA 4135
                         i  ii v  vi   i      v  i  i     --  -  i ------  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_80016867_8   4136 CAAAAACAAACAACCCCATCCAAAAGTGGAGAAAGGATATGAACAGACAC 4185
                         v   i     i     v  i?    i   iv       v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_80016867_8   4186 TTCTCAAAAGAAGATGTTTACATGGCCAACAA--ACATGAAAAAAAGCTC 4233
                              v         i vi v        i  --         i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_80016867_8   4234 AACATCACTCATCAT 4248
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.94 (31 / 16)  


3142 27.86 0.44 0.44  chr2_80232040_80238438.rev     5000  5907 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_80232040_8   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5049
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_80232040_8   5050 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5099
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_80232040_8   5100 TACCAATGACTTGCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 5148
                          v   iivi i vi  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_80232040_8   5149 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAGGA 5198
                               viiv  ii  v  v v  v     iv     i i ivv i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_80232040_8   5199 ACAAAGCTGGAGGCATCATGCTACCTGACTTTAAACTATACTATAAGGCC 5248
                               i      vv   ii  v  ii i  i   viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_80232040_8   5249 ACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGACCA 5298
                           i    i   i    ii         i iv ii i   v v     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_80232040_8   5299 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTA 5346
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_80232040_8   5347 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5396
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_80232040_8   5397 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5446
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_80232040_8   5447 AAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGAT 5496
                           ii    i    v   i i   v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_80232040_8   5497 TAAAGACTTACATGTTAGACTTAAAACCATAAAAACCCTACAAGAAAACC 5546
                         i ?    i  v    v   vi      i      vi i  v        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_80232040_8   5547 TAGGCA-ATACCATTCAGAACATAGGCATGGGCAAGGACTTCATGTCTAA 5595
                             ?i- v i -   ivi  v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_80232040_8   5596 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAAAAATGGGATCTAA 5645
                         i            vvi          vv     v  v    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_80232040_8   5646 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5695
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_80232040_8   5696 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5745
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_80232040_8   5746 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5795
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_80232040_8   5796 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATCAACAGACACTTC 5845
                          i     i     v  i?    i    ii      v v  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_80232040_8   5846 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5895
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_80232040_8   5896 ATCACTGGCCAT 5907
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


3241 26.65 0.77 0.88  chr2_80349250_80355661.rev     5013  5920 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_80349250_8   5013 GGAAGAACATTCCACGCTTATGGGTAGGAAGAATCAATATTGTGAAAATG 5062
                             ii i  i   i i i    i v      v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_80349250_8   5063 GCCATACTTCTCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 5112
                           v     i i   iv i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_80349250_8   5113 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTCA 5160
                         v   iivi i  i  ii     -   --- v  i  - iii    i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCA 148

  chr2_80349250_8   5161 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTCAGCCAAAAG 5210
                                viiv  ii  v  viv  v     i      i v ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_80349250_8   5211 AACAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5260
                                i i    vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_80349250_8   5261 TACAGTAACCAAAATAGCATGGTCCTGGTACCAAAACAGAAATATAGACC 5310
                                 i   i i  ii    v    i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_80349250_8   5311 AATGGAACAGAAT--AGAGCCCTCATAAATAATACTACACATCTACAACC 5358
                                i     --    i  -- v      vv i i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_80349250_8   5359 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5408
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_80349250_8   5409 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 5458
                           v  i  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_80349250_8   5459 GAAACTGGATCCCTTTCTTATACCTTATACAAAAATTAACTCAAGATGGA 5508
                            ii    i    vi  i i   v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_80349250_8   5509 TTAAAGACTTAAATATTAGACCTAAAACCATAGAAAGCCTAAAAGAAAAC 5558
                          i ?    i     i v   v       i   i  vv i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_80349250_8   5559 CTAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGACT 5606
                         v    ?i- v i -   i- i  v i  i- i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_80349250_8   5607 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAGTAGACAAATGGGATAT 5656
                          vi            vvi          vv   i    i    v   iv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_80349250_8   5657 -ATTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATTAGAGTG 5705
                         -  iv   i    i -   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_80349250_8   5706 AACAGGCAACCTACACAATGGGAGAAAATTCTTGCAATCTACCCATCTGA 5755
                           v  i     i   v             vi      vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_80349250_8   5756 CAAGGGGCTAATATCCAGAATCTACAAAGAACTTCAACAAATTTACAAGA 5805
                         i     i  vi          v  i        iiv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_80349250_8   5806 AAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5855
                             iv    i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_80349250_8   5856 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGTTC 5905
                              v        i  vi viii     i ii          i   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_80349250_8   5906 ATCATCACTGGCCAT 5920
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (151 / 87)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 1.36 (15 / 11)  


1117 28.53 0.92 0.61  chr2_80732529_80734894.rev      100   425 (1941)    L1M4_orf2#LINE/L1        1   327 (581)  

  chr2_80732529_8    100 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATACTGTGACAAT 149
                               i i  i     i        v      v i    i   v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_80732529_8    150 GGCCACACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 199
                            v i   v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_80732529_8    200 TTCCATTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTCA 248
                          i   vivi i  i  ii     v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_80732529_8    249 TGTG-AAACA-AAAAAAGCCTGTATAGCCAAGACGATCCTAAGCAAAAAG 296
                          i  -   ii-  iii v  v v        i  i   i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_80732529_8    297 GACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTAAACTACAAAGC 346
                         i      i      vv   ii  v  ii i      vivv          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_80732529_8    347 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACACACATATACACC 396
                                 i   i    ii         i iv ii i v       v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_80732529_8    397 AACAGAACATAACAGAGACCTCAGAAATA 425
                           ii   i v  iv    vii        
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATA 327

Transitions / transversions = 2.00 (62 / 31)
Gap_init rate = 0.01 (4 / 327), avg. gap size = 1.25 (5 / 4)  

3460 18.97 3.84 4.28  chr2_80732529_80734894.rev      965  1876 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_80732529_8    965 TGGAAAGTCATTCAATAAATGTGGATTGGAAGACTTAATATT---AAGAT 1011
                                vi  i v  ivvii                     ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_80732529_8   1012 GTCAATACTACTGAAAGAGATCTACAGATTCACTGTAATCCCTATCAAAA 1061
                          v       v iv   vv              vi i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_80732529_8   1062 CCCAAA--GGCATTTTGGCCAAAATTTAAAAATCCATCCTAAAATTCACA 1109
                         i  v i-- v v    v  vi     v v  iiiv             i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_80732529_8   1110 TGGACTCTCAAGGCAACACA-AATAGCCAAAGCAATCTTGAAAA----GA 1154
                             vviv     -i  v  -          i            ----  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_80732529_8   1155 ACAAAAATTGGAGACCTCACAATTTTTGATTTTAAAACTTACTA------ 1198
                              i-      iv      v  iiii    i           ------
  L1M4_orf2#LINE/    200 ACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_80732529_8   1199 -----TAATCAAAATAGTGTCATACTGGCATACAGACAGACATAGAGACC 1243
                         -----       i i     vi          vi  i       v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_80732529_8   1244 AATGGAATAGAAT--GGAGTTCAGAAATAGATCCTTATATATATATATAA 1291
                                      --i    i        i i  ----   i  v   --
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCC----ATACATTTAT-- 342

  chr2_80732529_8   1292 GGTCAAATGATTTTCCACAAAGGTACTAAGATTTTTGCTAAGATTTGGGT 1341
                               v        v    i   i i    iiv  --i  ----    -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT--CAA----TGGG- 385

  chr2_80732529_8   1342 CTTGGAAAAGGGCAGTGTTTTCAATAAATGGTGCTGGTAAAACTGGATTA 1391
                         -----i    iii   v       i            v v        - 
  L1M4_orf2#LINE/    386 -----GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT-A 429

  chr2_80732529_8   1392 TCTACATGCAAAAGCA-GCAGCAG--TCCTCATGTTATACCTCATTTAAA 1438
                         ? i           v - v  iv --i  ii iv i i   vi  vi   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_80732529_8   1439 AATTAACTAAAAATGGATGAAAGACCTAACCATAAGAACTAAAG-TATAA 1487
                                 v         v ?        vii     i     i-     
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_80732529_8   1488 AACTCAAAGAAGAAAACACAGGAGAAAA-CTTCATGACATTGGATTTGGT 1536
                              vv           i   ? v   -    i    v    i  v  i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_80732529_8   1537 AATAATTTCTTGCATATGACACCAAAAGTATAAGCAACAAAAGAAAAAA- 1585
                            ii      iv               i i                  -
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_80732529_8   1586 AAAGATGTTGAACTTCA---AGATTAAAAACTTGTGTGTGTCAAAGAACA 1632
                          i v vi   i      --- i           v    iv      i   
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_80732529_8   1633 CTATCAACAAATAGTGAAAAAGAAACCAATAAAATGAGAGAAAATAGTAA 1682
                                v   --       iiv    v i i    i         ----
  L1M4_orf2#LINE/    680 CTATCAAGAAA--GTGAAAAGACAACCCACAGAATGGGAGAAAATA---- 723

  chr2_80732529_8   1683 TTCTTTATCAGGAATTTGTAATTCCTGATAAGAAATTAATATCCGGAATA 1732
                         ---   ---- v  v ii  - vi        ii i vi     i     
  L1M4_orf2#LINE/    724 ---TTT----GCAAATCATA-TATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_80732529_8   1733 TACCAAGGACTCCTACAACTCAACAACAAAAAAGCAAACAAACAACCCAA 1782
                           iv   i    i          i  i     i----     i       
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAG----ACAAATAACCCAA 811

  chr2_80732529_8   1783 CTAAAAAATGGGCAAAAGACTTGGATAGACATTGTTCCAAAGGAGATATA 1832
                         i ?             i  i   i         vi       i       
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_80732529_8   1833 CAA-TG-CCAATAAGCATA-GGAAAGTTGTTCAACATAATTAATCAT 1876
                            -  -          i - i    v  i       v ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (105 / 64)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.64 (74 / 28)  


2001 25.85 0.90 1.80  chr2_80870513_80873476     1242  1798 (1166)    L1M4_orf2#LINE/L1        2   553 (355)  

  chr2_80870513_8   1242 GGAAAAATATTCCATATTCATGGATTGAA----TCAATATTGTTAAAATG 1287
                              i    i    i           i ---- i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_80870513_8   1288 TTCACACTACCCAAAGAAATCTGCAGTTTCAATGCAATACCTATGAAAAT 1337
                         viv i   v      vvi    i   v     i     v     v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_80870513_8   1338 ACCAATGAACCAGTGACATTCTTCACAGAAATAGAAAAAATTATCTTAAA 1387
                         -  -------   ivi v  i  ii       v  v  iv v   i    
  L1M4_orf2#LINE/    102 -CC-------CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_80870513_8   1388 ATGTATACAGACCCACAAGAGACCTATAATAGCCCAAGCTATACTAATCA 1437
                           vi   ii  vvii    i    i v       v  i v  vi i vv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_80870513_8   1438 AGAAGAACAAAATTGGAGGAATTACATTACATGACTTCCAATTACACTAC 1487
                                    i        v i   i v vii i   v  vivi     
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_80870513_8   1488 AGAACTACAATAAGCAAAAATACATGGTACAGGGATAAAAACAGACACAT 1537
                          i i     i   v   i vviii      v  v    ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_80870513_8   1538 AGACCAACAGAACAAAATAGATAACCCAGAAATAAATCTAAACATCTACA 1587
                            i   ii   i i   v  v ii           i i v    i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_80870513_8   1588 GTGAACTCATTTTTGACAAAGTTTGTAAGAAC-TTAACACTGAGGAAAAG 1636
                           v  i v     i     i v vvi    v -  --  v  i     ii
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATT--CAATGGGGAAAGA 391

  chr2_80870513_8   1637 GTAGTCTCTTCAATAAATGGTGCTAAGAAAACTGGATATTCATATGCAGA 1686
                         i      i     i          ii  v         ?i  i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_80870513_8   1687 AGAATGAAACTAGACCCCTCTCTGTCACTATATACAAAAATCAAATCAAA 1736
                                 ii i       vi  vv   i            i  v     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_80870513_8   1737 ATGGATTAAAGATTTAAATCTAAGATCTCAAACCATAAAACTACTATAAG 1786
                               i ?   ii     v     v  v    i        vi  v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_80870513_8   1787 AAAACTTTGGGG 1798
                              v v  ? 
  L1M4_orf2#LINE/    542 AAAACATAGGNG 553

Transitions / transversions = 1.52 (85 / 56)
Gap_init rate = 0.01 (5 / 552), avg. gap size = 3.00 (15 / 5)  

1100 26.32 2.77 0.55  chr2_80870513_80873476     2112  2472 (492)    L1M4_orf2#LINE/L1      540   908 (0)  

  chr2_80870513_8   2112 AAAAAACATTGGGGAAGCTCTCCAGGACGTTGGTCTGTGCAAAAATTTCT 2161
                          i       v  ? v iv   i iv   v    vi iv    vii     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_80870513_8   2162 GGAGCAATACCCCACCAGC-CAGGCCACCAAAACAAAAATGGAAAAATGG 2210
                         viiii vv  v   vv   -  i  v  v   iv      i  v    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_80870513_8   2211 GATCACATC-TAGTTAAAAAGCTTCTGCACAGCAAAGGAAATAATCAA-- 2257
                           iiv    -v i       -   i  ii vv       v iv     --
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_80870513_8   2258 -AGTGAAGAGACAACCCACAGAATGGAAGAAAATATTTGCAAACTGCCCA 2306
                         -      i                  i                iiiivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_80870513_8   2307 TCTAAGAAGAAGTTAACAACCAGAATATATAAGGAACTCAAACAACTCTA 2356
                            i v   iiii vii v             i      vv       v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_80870513_8   2357 TAGGAAAAAAATCTAACAGTCTGATCAAGAAATGGGCAAAATTTTTGAAT 2406
                           iv     i - v  i ii ii  i? i           ivv       
  L1M4_orf2#LINE/    789 TAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_80870513_8   2407 AGACATTTCGCAAAAGA-----CACAAATGGCAAACACACATAGGAAAAG 2451
                                  v v     -----i         v  i vi  i v      
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_80870513_8   2452 GTGCTCAACATCATGAGTCAT 2472
                         i            ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (52 / 41)
Gap_init rate = 0.02 (6 / 369), avg. gap size = 2.00 (12 / 6)  


1691 26.86 6.33 5.55  chr2_80888323_80892588.rev     2874  3774 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_80888323_8   2874 TGAAAAGAGATACTATGTTAACGGATTGAAAAA---AA----ATCAAGCC 2916
                           i     v  v i     v i      i  i ---  ----i i   vi
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_80888323_8   2917 AGTAAATATATTCCCCCCAAAA--GATATACTGTCAAGACT-GACACAAT 2963
                         i i  ---  i     ---   --   v   -----   i -i  i    
  L1M4_orf2#LINE/     51 GGCAA---TACTCCCC---AAATTGATCTAC-----AGATTCAACGCAAT 89

  chr2_80888323_8   2964 TATTATCAAAATACTAGCAAGATTATTT-TAGACATAAATCAGGTTATCC 3012
                         ivi         v i   vivv  v   -i   v  vi iv  v v    
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_80888323_8   3013 TGAAATGTATACAGAAAGACCGTAGAACTAAAGTAGATTAAACAATTTTA 3062
                          i    vi   ii    vi vivi  v i i i   viv       i  i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_80888323_8   3063 TATTTAAAAAGTATAAAAAAG----AAAAATCAGGCTATTTAATTT-AAT 3107
                         -----      v v  v    ---- ii v   vi  viii     -  v
  L1M4_orf2#LINE/    190 -----AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_80888323_8   3108 ACTTACTCTACAACTACGATAATCAGTAGCATGTGGTATTGTCAGAGAGA 3157
                                vi v i    ii      iv vvi       i  v  v ii  
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_80888323_8   3158 CAGACACACAAATTGATG-AACA-AGTAGAGATCTCATAAATAGACTCAT 3205
                         i     i i i  ii   -  i - i v    vii  v     i  i   
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_80888323_8   3206 ACCAGATT---GTTCAACTGATGTTCACATCACAAAGGTGCAAAAGCAAA 3252
                           ---   --- v    i    v   i----    i     v  ii v v
  L1M4_orf2#LINE/    335 AC---ATTTATGGTCAATTGATTTTCG----ACAAGGGTGCCAAGACCAT 377

  chr2_80888323_8   3253 TCAATGGAGGAAAGATAGCCTTTCTAACAAATGGTGCTGAAGCAACTGGA 3302
                                i i  ii    i    ii              iii        
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_80888323_8   3303 CATCCA--TGGCCTCCCCTCAAAAAATATGTAATTTGACC--TA----A- 3343
                         i ?   --  ---------     i -   v i  v    --  ---- -
  L1M4_orf2#LINE/    428 TAKCCACATG---------CAAAAGA-ATGAAGTTGGACCCCTACCTCAC 467

  chr2_80888323_8   3344 ---ATTCATAAAAATTAAC--AAAATGAATCATGGACTTAAATATAAAAG 3388
                         ---  vi i          --      i    ?i   i     i   i  
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_80888323_8   3389 TCAAAGCCATGTAACTTTTAGGAAAAGAAACCA--GG---AAATCTTCAA 3433
                         ii   i i  iv    i    ---      v  --  ---        iv
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAG---AAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_80888323_8   3434 GATACATGG-TTAAAGAAT------TTACATACTTAGCAC-AAAAGCATG 3475
                           i- v   -   iiv   ------   v   -- ii   -       ii
  L1M4_orf2#LINE/    565 GAC-CTTGGGTTAGGCAATGGTTTCTTAGATA--TGACACCAAAAGCACA 611

  chr2_80888323_8   3476 ATCCATAAAAAGAAAAGTTAATCAAATGATCTTCATTAGCTCATTTCCTT 3525
                          v v i    ii    i vi  v  v  iv      i iv--   -----
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA--ATT----- 654

  chr2_80888323_8   3526 CATTACTTTTGTGGTGAGGAAAAGATCCTGTTAAGC---TGAAAAAGACA 3572
                         v vv         v vv--   i  iv  i i   v---      -    
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTC--AAAGGACACTATCAAGAAAGTGAAAA-GACA 701

  chr2_80888323_8   3573 AGCTAATGAGTGAGAGAAACTATTTACAAACCACCTAGCCACCAAAGGAA 3622
                          v i vv  i  i      v     i    i  iv  v iivi  i   v
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_80888323_8   3623 GAATAGCAAGAATATATAA------CTCAAATCACAACAGTAAAAAAGCA 3666
                         vvi  v v           ------  i v v v   i i      ii  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_80888323_8   3667 AACAATCTGATTACACAATTGAGCAGAAGACGTGAAGATACATTCCACCC 3716
                           i  i ii   ?v v   - i   i i  iv    v v     i v  v
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAAT-GGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_80888323_8   3717 AACAGGATTTACAGATGGTGAATAAGTACGTGAAAATATGTTCATCATCA 3766
                           v i   v    i    iv      i  i      v   i   v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_80888323_8   3767 TTAACCAC 3774
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.04 (38 / 908), avg. gap size = 2.82 (107 / 38)  


1307 25.60 23.46 1.88  chr2_80894829_80896667.rev      615  1360 (479)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_80894829_8    615 GGAAAAACA-CTCACTGCTCATGGGTAGGAAGAATCA-TATTGTTAAAAT 662
                              i i - i  -  i      i v      v i -         i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCA-TGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_80894829_8    663 GGCCATAGTGCCCA--TTGCAATTTATAGATTCAAAGCCATTTCTATTAA 710
                            v   v v    --   --  i  i        v  v  ii    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_80894829_8    711 ACTACCAACTTTTTTTTTCACAGAATTAGAAAAA--AACTTCTAAAATTC 758
                          v v   i  vii     ii     v v  v  i--i - i         
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTC 147

  chr2_80894829_8    759 ATACGGAACCAAAAAATAGCCAGTATAGCAAAAGCAATCCTAAGCAAAAA 808
                            i    viiv  iiv v    v     v   i     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_80894829_8    809 GAACAAAGTGGGGGGCATTATACTACCTGACTT-AAAACTATACCACAAA 857
                                  v  i  vv i i   v  ii i  -      -   i     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr2_80894829_8    858 ACTGCAGTAACCTAAA---TGTGGTACTACTACAGAAACAGACACTTTGA 904
                         i  i      i v i ---         ivi i iii i     iv v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_80894829_8    905 CCAATGGAACAGAACATAGACCACAGAAATAAAGCTGCACACCTATAATC 954
                         i        i    ivv   viv          v iii   ii   ii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_80894829_8    955 A------------------------------------------------T 956
                          ------------------------------------------------ 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_80894829_8    957 CTT--------AT------------------------------------- 961
                            --------  -------------------------------------
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_80894829_8    962 ---------------CTTC---------------------------TGGA 969
                         --------------- i  ---------------------------    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_80894829_8    970 TTAAAGACTTAAGTGT------TAAAACTA-AAAA-TCCTAGAAGAATAC 1011
                          i ?    i   i   ------        -    -  i        v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_80894829_8   1012 CTAGG---AAATACCATTCTGGACACAGGCTCTAGATAA-GATTTCAT-G 1056
                         v    ---    -- -   vv   viv  v -   ii  - i    v - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAG 592

  chr2_80894829_8   1057 ATGATAACTCCAAAAGCTATTGCAACAAAACAAAAATT-GACAAGTGGAA 1105
                           -  i  v        vvvv         v     v -  i  i v i 
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_80894829_8   1106 CCTAATTAAACTAAAGAGCTTCTGTAGAGTGAAAGAA-GCTATTAACAGA 1154
                          i v  i   v v  i i   i   - vv v    i -i    i  v i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGT-GCTTCAAAGGACACTATCAAGAAA 690

  chr2_80894829_8   1155 ATAAAAAAACAACT-ACAGAGTGAGGGATAAGATATTTGTAAACTATGCA 1203
                         i i    i     i-     i  --   v  i       i   ii  ii 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATG--GGAGAAAATATTTGCAAATCATATA 738

  chr2_80894829_8   1204 ACTGACACAGGTCTAATACCCATAATCTGTAAG---------TAACTTAA 1244
                         v    i vi  v  vi  i   v   v i   i---------i    i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_80894829_8   1245 CAA-GCAAAGGCAA----CCCCATTAAAAAATTGATGAGGAATATGAACA 1289
                         i  -iv    i   ----   v   ?      v iii i i  v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_80894829_8   1290 GACACTTCTCAAAAGAACACATACACATGGCCAACAAGCATATGAAAAAA 1339
                             i     v      v i     v        i     i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_80894829_8   1340 AGGCTTAACACTAATCGTTAG 1360
                         -v   i    ii ????????
  L1M4_orf2#LINE/    889 -TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (118 / 71)
Gap_init rate = 0.04 (33 / 907), avg. gap size = 5.73 (189 / 33)  


1716 27.79 9.98 2.49  chr2_80902340_80906387     2715  3556 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_80902340_8   2715 AAAGGCATAATATGTTCATGGATATAAAGATTTGAAACTGTGAAAATGTT 2764
                             ii  vvi            vvi    i  i v i   v  i   vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_80902340_8   2765 AG-ACTTTTT---CTAATCTGTAGATTCAGCACAACCCCTATTAAAACTC 2810
                          i-   iiii---i i    ii       i i   i      i    ii 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_80902340_8   2811 CAA--------TTCATAGATACTGG-AATATTATTCTAAAATGTGTACAG 2851
                           i--------  iii   v i  i-  vv v  i       vii  ii 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_80902340_8   2852 AAA---AGACGATCTAAAATAAGCAAAATAATCTCCACTCAGGTGAAAGA 2898
                            --- iiv  i i i    iv     i     iv vvv  iv   vi 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_80902340_8   2899 AGT---ATGACACCATACTT---AGTTCCAAGACTAACTATAATGCTATG 2942
                            --- v   -i  i    --- i  i   i   v    i  v    ii
  L1M4_orf2#LINE/    204 AGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_80902340_8   2943 CTAATCAAAACTGTGTGCAATTG---T-----TAGACATGTAGATCAATG 2984
                         v       i  v     vv i  --- -----       i          
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_80902340_8   2985 AAGCAAAC---AGAATCCAAGAAGAAGGATCAAACTTATATTGCCAGTTG 3031
                         i ii i v---   i    ii  v  iv-i  v  v v   v i  i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTTATGGTCAATTG 351

  chr2_80902340_8   3032 ATTTCTAATAAATGTGCCAAG-TTATTTAAATGGCAAAAAA--------- 3071
                             iii i  iv        -ii   i  vv  v   i  ---------
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_80902340_8   3072 --------GGTG---GAACATCTGG-CACTCACAGG-AAAAAAATAAAAA 3108
                         --------    --- i   v    -i ?i    v -    i   -----
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT----- 446

  chr2_80902340_8   3109 CAGAGAGAAACTTAACACTTACCTTGCCCCA-ATAACAAAATTGACTTGA 3157
                         ------   ii vi  v i     ii v   -   vv      i   ii 
  L1M4_orf2#LINE/    447 ------GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_80902340_8   3158 AATAGATCATAGAGCTAAGTGCAAAAACTAAATCTATACAATCTCTATAA 3207
                            i     ?   v    i  i  i i     v     v  iiii  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_80902340_8   3208 GTAGATCTAGTTGAAATTCTTTGCAACCTTGGCATAGGCAACGGTTTCTT 3257
                          v i iv   v? v  v    i ii       vv       i        
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_80902340_8   3258 AG----GACACAAAAAGCACTAACAAAGAAACAAAAGAATAGATGA--TG 3301
                           ----     v        v i   vi   v    -       i --  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTG 639

  chr2_80902340_8   3302 --CTTGTCATTTAAA--AAAAAGTTCTGCTCATTAA-GAATATGGTGAAG 3346
                         --   --   iv   --     v  i  iv v i  - i i ivi v   
  L1M4_orf2#LINE/    640 GACTT--CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_80902340_8   3347 AAAAATAAAACAATGAAACCCA--GACTGGAAGAAAAAATT-GCATTTTA 3393
                            i- i   vi i--      --  v   i      v   -   vv i 
  L1M4_orf2#LINE/    688 AAAG-TGAAAAGAC--AACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_80902340_8   3394 GATGTAATTGGCAAGAGA-TTCTATTTTGAATACA-----AACGCTTACA 3437
                         v  i --i  ii   i  -  v   iiv     i -----   v      
  L1M4_orf2#LINE/    735 TATAT--CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_80902340_8   3438 TTGCAACTCCGAGA-GACAAA----CCA--TTACAAATTGGCAAAAGATT 3480
                         viv   ivvii i -      ----   -- ? v    v      i    
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_80902340_8   3481 TTAATAGACATTTTACAAAACAACATATAAAAAAGGCCAATGTGCACAAG 3530
                          v           iv v   v  v     v   v       iv     v 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_80902340_8   3531 AAAAGCTATTCAACATCATTATCATC 3556
                              v ii         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.04 (36 / 905), avg. gap size = 2.92 (105 / 36)  


2973 26.29 1.10 1.64  chr2_80945341_80951166      823  1735 (4091)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_80945341_8    823 TGCAAAGACATCCCATGCTCAGGGGTTGGAATAATTAATATTGTTA-GAT 871
                           v     i        i   v  i      v v            -   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_80945341_8    872 G--AACATGCCAATCAAAGCAATCTACAGATTCAATTCAATCCCTATCAA 919
                          --  i iv  --i    vii              iv             
  L1M4_orf2#LINE/     51 GGCAATACTCC--CCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_80945341_8    920 AATACCAACACTATTTTTCACATAAATAGAAAAAAACAATTCTAACACTC 969
                            v   i vviv     ii  v    v  v  iv-ii  i    v i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTC 147

  chr2_80945341_8    970 ATATGGAACTGAAAAGGAGCCCAAATAGCCAAAGAAGTACTGAGTAAAAA 1019
                                 v  v  i   v  vi          iv i vi   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_80945341_8   1020 GAACAAAGCTGGAGACATCATACTATCTGACTTCAAAATATACTACAAGT 1069
                                 i     ivv   i   vi ii i       iv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_80945341_8   1070 CTGTACTAACCAA-ACAGCAAGGTATTGGTATAAAAATAAACACATAGAT 1118
                           ii v   i   -    iiv    i   i    ii   i   i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_80945341_8   1119 CAATAAAACAAAACAGAGAACCAAGAAATAAATTTGCAAATGTACAGCCG 1168
                             ii  i i  iv    ii v         iiiii v  v  ii i -
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC- 346

  chr2_80945341_8   1169 CATATTTGATCTTTGACAAAGCAATCAAGAACATACATTTGGGAGAGGAA 1218
                         --- v     i  i     i vvii     v   v  v v    i  i v
  L1M4_orf2#LINE/    347 ---AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_80945341_8   1219 ATCCTCTTCAATAAATGGTACTGAGAAAATTGGATAACCACATGTAGAAG 1268
                          vi  i     i       i   i  v  i      ?       i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_80945341_8   1269 AATGAAACCGGACCCCAGTCTCTCACCAAATGCAAACATCAACCCAGAAT 1318
                               iii       vii   v     v  i    v  i   i  i   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_80945341_8   1319 GGATTAATGACTTACAGACAAGACCTGAATCTATAAAACTGTTAGAATAA 1368
                             i ?v   i  v vii    v  i  v          v      v  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_80945341_8   1369 AACATAGGGAAAACTCATCAAGACATTGGTCTAGGCAAATACTTTATGGC 1418
                                 ?iv  v  v  iv   v    vi       vvii  iv i v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_80945341_8   1419 TAAGACCTCAAAATCACAGGCAACAAAAACAAAAATAAACAAACTGGGAC 1468
                           v   vi     v    i         iv       i i   i   -  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG-AC 642

  chr2_80945341_8   1469 TATAATGAACTAAAAAGCCCCTGAACAGTAAAAGAAACAATCAATAGATT 1518
                          vi vii  v v    i iii  vi vvi   i  v  v     v i v 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_80945341_8   1519 TAAGAGACAACTTGCTGAATGGAAGGAAATATTTGCAAATGATTCATCTA 1568
                         v  i       iii v      i  i              v  vi    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_80945341_8   1569 ACAAGGGACAAACATCCAGAATACTCAAGGAACTC----AACTTAAGAGT 1614
                          i       vvii          ivi  i      ----    i  ----
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA---- 788

  chr2_80945341_8   1615 TAAAAAAAAACCCACAAATAATCCTATTAAAAATAGGACAAAGGATATGA 1664
                            v     i---        i  v   ?    vv  i        v   
  L1M4_orf2#LINE/    789 TAATAAAAAG---ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_80945341_8   1665 ATAGACGTTTCTCAAAAGATGACATACAAATGCCCAACAGGTGTATAAAA 1714
                               i      v     v  i         v    i i iii  i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_80945341_8   1715 AG--GTTCAACATCGCTAATTAT 1735
                           -- i        i????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.27 (25 / 11)  

2863 27.06 4.47 0.34  chr2_80945341_80951166     4463  5334 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_80945341_8   4463 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATAGTGAAAAT 4512
                              ii i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_80945341_8   4513 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 4562
                            v     v     iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_80945341_8   4563 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4610
                          v   iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_80945341_8   4611 TATGGAACCGAAAAAGAGCCCACATTGCTAAGACAATCCTAAGCCAAAAG 4660
                                vi v  ii  v  viv  v  i  i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_80945341_8   4661 AACACAGCCGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4710
                             v  ii     vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_80945341_8   4711 TACAGTAACCAAAACAGCATGGTGCTGGTACCA----AAACA-------- 4748
                                 i   i    ii    i    i iv ---- i   --------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_80945341_8   4749 --------------GAGGCTTCAGAAATAATACCACACATCAACAACCAT 4784
                         --------------   iv i         vv   i    iv iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_80945341_8   4785 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 4834
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_80945341_8   4835 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACTGA 4884
                         v  i  i              v      v  ?   i   i i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_80945341_8   4885 A-----ACCCTT-CCTTACACCTTATACAAAAATTAATTCAAGATGGATT 4928
                          -----    i -   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_80945341_8   4929 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGCAGGAAACCT 4978
                          ?    i  v    v   v       i      vi i   v  i    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_80945341_8   4979 AGGCA-ATACCATTCAGGACATAGGCATGGGCACAGACTTCATGACTAAA 5027
                            ?i- v i -   iv   v v  vv i    vv ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_80945341_8   5028 ACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAAT 5077
                                     vvi          vv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_80945341_8   5078 TAAACTAAAGAGCTTCTGCATGGCAAAAGAAACCACCATCAGAGTGAACA 5127
                         i   v v  i i   i  iiivv    i  v  i i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_80945341_8   5128 GACAACCTACAGAATGGGAGAAAATTTTTGCA--TTATCCATCTGACAAA 5175
                                i                 v      -- i  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_80945341_8   5176 GGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGGAAAA 5225
                           i  vi          v  i  i     ivv    v iv i  vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_80945341_8   5226 AACAAAAACCTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5275
                         i     v v i v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_80945341_8   5276 CAAAATAAGACATTTATGCAGCCAACAGACACATGAAAAA--GCTCATCA 5323
                          v   v    i  vi viii     i ii          i--     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_80945341_8   5324 TCACTGGTCAT 5334
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.82 (42 / 11)  


2792 28.08 1.55 0.78  chr2_80953078_80959820     5351  6251 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_80953078_8   5351 TGGAAAAACATTCCATGCTCATGGACAGGAAGAATCTT--TATTGTGAAA 5398
                               i i  i     i       iv      --   --      v  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA--CTTAATATTGTTAAG 48

  chr2_80953078_8   5399 ATGGCCATACTTCCCAAAGTAATGTATAGATTCAATGCTCTTTCCATTAA 5448
                              v     i      v i  v  i        i  vv ii i  i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_80953078_8   5449 ACTACCATTGACTTTCTTCACAGAATTAGAAAAATT-ACTTTAAATTTCA 5497
                          v v   vivi i  i  ii     v v  v  ii - iii    v    
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_80953078_8   5498 TATGGAACCAAAAAAGAGCCTGTATAGCACAGACAATCCTAAGTAAAAAG 5547
                                viiv  ii  v  v v     vv i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_80953078_8   5548 AACAAAGCTGGAGGCATCATGGTACTTGATTTCAAACTATACTACAAGGC 5597
                                i      vv   iiv v iii        viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_80953078_8   5598 TATGGTAAACAAAACAGCATGGTACTGGTACCAAAACACATATATAGACC 5647
                           ii    v   i    ii         i iv ii i v i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_80953078_8   5648 AAGGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAT 5697
                           v    i    iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_80953078_8   5698 CTGATCTTTGACAAACCTGACAAACACAAGAAATGGGGAAAGATTCCATA 5747
                         i    i  i     ivv  v   ivv  vvv            ----   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA----ATA 394

  chr2_80953078_8   5748 -----TTTAATAAATGATGCCAGGAAAACTGGCTAGCTATATGCAGAAAA 5792
                         -----  i  i     i   ii   v      v  ? i i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_80953078_8   5793 CTAGAACTGGCCTCCT-TCTTACACCTTATACAAAAATTAACTCAAGATG 5841
                         v ii ii   v i   -i  i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_80953078_8   5842 GACTAAAGACTTAAACAAGAAACCCAAAACCATAAAAACCCTAGAAGAAA 5891
                           ii ?    i    iivi i v i     i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_80953078_8   5892 ACCTAGGCA-ATACCATTCGGGACAAAGGCATGGGCAAAGCCTTCATGAT 5940
                           v    ?i- v i -    v   vvv  vv i     v vi   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_80953078_8   5941 TAAAACACCAAAAGCA-ATGCAACAAAAACCAAAATTGACAAATGGGATA 5989
                           vi            - v         ivv     v  i    v   iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_80953078_8   5990 TAATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTAGCATCAGAGGG 6039
                          v  i   v v  i     i  ii vv    i  v    v  vv i  v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_80953078_8   6040 AACAGGCAACCTACAGAATGGGAGGAAATTTTTGCAATCTAGCCATCTGA 6089
                           v  i     i            i    v       vii vvi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_80953078_8   6090 AAGAGGTCTAATATCCAGAATCTACAAGAAACATAAATAAGTTTACAAGA 6139
                         v ii  v  vi          v  i  ii   vivv i  v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_80953078_8   6140 AAAAAA-AAATGACCCCATCAAAAAGTGGACAAAGTATATGAACAGACAC 6188
                             i -    i    v  i?    i   i     v  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_80953078_8   6189 TTCTCAAAAGAAGACATTTATGTGGCCAACAA--ACATGAAAAAAAGCTC 6236
                              v        i  vi vi       i  --         i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_80953078_8   6237 ATCGTCATGATCATT 6251
                          v i   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (143 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.91 (21 / 11)  


2801 24.13 7.42 2.09  chr2_81053233_81057746.rev     3161  4022 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81053233_8   3161 TGGAAAGATATTTTATGTTTATGGATTGAAAAAAATTAATATTGTTAAAA 3210
                                    iii     i        i  i v-             i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chr2_81053233_8   3211 TTTTCACACTCCCCAAAGCAATCTACAGATTCAATGCAATCTCTATCAAA 3260
                          vviv i          vii              i      i        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_81053233_8   3261 ATACCAGTGATATTCTTCACAGAAATATAAAAAAAAATCCCAAAATTTAT 3310
                           v    iviiv  i  ii       vv v  ivvi    i      i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_81053233_8   3311 ATGGAATCACAAAAGACTCAGAATAGCTGAAGCCATTCT----AAG---- 3352
                               vii   ii   i         ii  i v  ii ----   ----
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_81053233_8   3353 -------------------------------CAAAA--------AGAGCT 3363
                         -------------------------------     -------- i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_81053233_8   3364 ATAGTAACCAA-ACAGCACATTACTGGCATAAAAACATATTCATAGACCA 3412
                          i     i   -    iiiiv           ii i v ivi     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_81053233_8   3413 GTCGAATAGAATAGAGAACCCAGAAACAAATGCACACACCTATAGTGGGC 3462
                         i v         v    ii       i   iv  i   ii   i  viii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_81053233_8   3463 TCATTTTTGACCATAGTGTCAAGAACATACACTGGGAGAAAGATAGT--T 3510
                          v     i   v vi   i     v   v  v    ii  ii     -- 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_81053233_8   3511 TTCAATGAATGGTACTGGGAAAACTGGACATCCATTTGCAGAAGAATGAC 3560
                              ii      i      v       i ?   iv    i        v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_81053233_8   3561 ACTAGACCCGTATCTCTCACCCAAAGTCAT-TATAAAAATTTAAATCAAA 3609
                         ii i     v  i   v    -------  -  i       -  v     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACC-------ATATACAAAAATT-AACTCAAA 491

  chr2_81053233_8   3610 ATGGATTAAAGACGTAAATCTAAGGCCTCAAACTATGCAGTTACTGAAAG 3659
                               i ?    v     v    iv  v       iv ii vi ii   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_81053233_8   3660 AAAATATTGGGGAAACTCCTAGACATGGTCTTG--TCAA--AAT--TTTC 3703
                             i  v  ? v  v  i --- i  ii    -- i i--   --    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTT---CGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_81053233_8   3704 TTGAGTCATATC-CC-----CACAGGCAACCAAAGCAAACATAAGACAGA 3747
                           -  vi  iv -  -----    i     v    v   v   -  i i 
  L1M4_orf2#LINE/    589 TT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAA 636

  chr2_81053233_8   3748 TGGGATCATATCAAG-TTAAAAAGCTTCTGCACAGCAAAAGAAATAATCA 3796
                          v   iivi     i-       -   i  ii vv    i  v iv    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_81053233_8   3797 ACAAAGTGAAAAGACAACCCACAGAATTGTAGAAAATATTTGCAAACTAC 3846
                          v                         v v                ii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_81053233_8   3847 CCATCAGACAAGAGATTAATAACCAGAATGTACAGGGAGCTCAAACAACT 3896
                         vi   v  i   i  i vi  v       i  i ii  i   vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_81053233_8   3897 TTATAAGGAAAAAACCCTAATAATTTGATTAAAAAAATGGTCAAAAGATA 3946
                         iv    vi    i  v--     iiii   ?     -   v    i   v
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACA--AATAACCCAATTWAAAAA-TGGGCAAAGGATT 832

  chr2_81053233_8   3947 TGAATAGGCATTTCTCAAAAGAAGACATAAAAATGGCAAGCAAGCCTATG 3996
                                i        v        i   v       v ii    vi   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_81053233_8   3997 AAAAGGTGCTCAACATCATTGATCAT 4022
                              i            ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (132 / 72)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.90 (82 / 21)  


3228 20.54 2.92 8.24  chr2_81071138_81075124     2537  3495 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81071138_8   2537 TGCAAAGACATCTCATGTTCATGCATTGGAGGAGTTAATATTGTTAAGAT 2586
                           v     i   i          v      i  v                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81071138_8   2587 GCCATTACTAACCAAAGTGATCTACAGATACAATTCAACTCATATCAAAA 2636
                          v  v    vv     v            v   iv   ii v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81071138_8   2637 TTCCAATGACCCTTTTTGCAGAAATGAAAAAGCATATCCTCAAGTTCATG 2686
                          i   iivi  i             vi v    vv     v  i     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_81071138_8   2687 TGGAAATACAAAGGCCCCTAAATATGTAAAACAATGTTTTAAAAGAATTA 2736
                                i   i  v   vi    vvi        v  vv       vv 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_81071138_8   2737 CAAA---------CTCATGCTTCCTGATTTCAAAACTTACTACAATGCTA 2777
                             ---------    ii     ii                   v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_81071138_8   2778 CAGTAACCAAAATAGTGCAGTAGTGGCATAGAG-TAGACATATAAACTAA 2826
                               i   i i    ii   v       ii -          i ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_81071138_8   2827 TGGAATGGAATTAAGAGTCGACACGCAAAACCATACGAATATGGTCAATT 2876
                               i     i      v v vii   v      ivv           
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_81071138_8   2877 GATTTTGAACAAGAAGGCCAAGACGATTCAGT-----AAGAGTGCCAAGA 2921
                               vi     iiv        v     i -----    i ----  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT----AGT 396

  chr2_81071138_8   2922 CTCTTTAACAACTGGCACTGGGACAATTGCATATTTACCTGCAAAAGAAT 2971
                           i  i     v   ii         i  v   ?ii  v           
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_81071138_8   2972 ACGGTTTTACTTTTACCTTACAACAAATACAAATATGAAATAAAAATAGG 3021
                         ivi   vv  iii     i   v  v       v  v  v v     i i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_81071138_8   3022 TCCATGACTTAAA-----GAGCTAAAACCACAGATCCCCTAAAAGAAAAT 3066
                           v?v   i    -----          i i i v i i  i       i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_81071138_8   3067 GTAAGAGTAAATCTCAATACACTCGAATTTGGAAATGGACTTTTGG-TAT 3115
                         i  i ?        ivi ivv  i ii  v  v     vi i  i -   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_81071138_8   3116 AATGCCAAAAGTATGAGCAAAAAAATATTATATGTATATATTATATATAT 3165
                         i ii       i ii     v    -------------------------
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAA------------------------- 621

  chr2_81071138_8   3166 ATTATATATATACATGCACAAGCACACGTATACATATATATGTATGTGTA 3215
                         --------------- v v  --------   v   v  -----------
  L1M4_orf2#LINE/    622 ---------------GAAAAA--------ATAGATAAAT----------- 637

  chr2_81071138_8   3216 TGTGTGTATATATATATGACTTCATCAAAATTAAAA--TTTTGTGCATTA 3263
                         ----  -----------                   --        v i 
  L1M4_orf2#LINE/    638 ----TG-----------GACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_81071138_8   3264 G-GGAAACCATCAAGACAGTAAAAAGAGTATGCACAGAATGGGGAAAAAT 3312
                         i-   v  i       v   i      vv iv           ii     
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_81071138_8   3313 ATTTGAAGGTTGTGTTTCTGACAATGGTCTGCCATCCAGAATATATAAAA 3362
                              v ii ii i v     i  v  v  vvi                i
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_81071138_8   3363 AATACCTACAAGTCAACAACAAAAAGACAAGCAGCCCAATTTTAAAAATG 3412
                           iv i     v    i  i          ii i       ?-       
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATG 821

  chr2_81071138_8   3413 GGTAAAAAACTTGAATACACATTTCTCTAAAAA---TATACAAATGGCCA 3459
                           i   ii i       v         i   i ---              
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_81071138_8   3460 GTG-GCACATGAAAAGATGGTCAACATTATTTGTCAC 3495
                         i i-               v       i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (113 / 80)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 7.13 (107 / 15)  


2304 29.83 2.20 1.27  chr2_81107526_81112461     3588  4452 (484)    L1M4_orf2#LINE/L1        1   873 (35)  

  chr2_81107526_8   3588 TGGAAAAACATTTTATGCTCATTGATTGGAAGAATCAGTATTGTTAAAAT 3637
                               i i  iii   i    v          v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81107526_8   3638 GGCCGTACTGCCTAAAGCAATA-AAAGATTCAATCCTATTGTTATCAAAA 3686
                            vi    v  i   vii  v- v        iv v  ivi        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81107526_8   3687 TACCAACATCATTTTTCACAGAATTAGAAAAA-TACTCTTCTAAAATTCA 3735
                          v   i vv v     ii     v v  v  i- iv  --          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC--CTAAAATTCA 148

  chr2_81107526_8   3736 TTTGGAACCAAAAAAAGAGCAAAATAGT-AAGGCAATTCTAAGCAAAAAG 3784
                          v     viiv  iiiivv  i     i-  ii    ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_81107526_8   3785 AACAAAGCTGAAGTCATCACATTATCTGACTTCAA--CTATACTACAAAC 3832
                                i  i  vvv     i vi ii i     --  -         v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_81107526_8   3833 CTACAATAACCCAAACAGCATGGTCCTGGTATAAAGACAGACACACAGAC 3882
                              i   i v i    ii    v    i    i  i     i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_81107526_8   3883 AAGTGGAAAAGAGTAGAGAATCCAGAAATAAAGCCACACACCTACAGCCA 3932
                         v i     v   i v    i            v   i   ii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_81107526_8   3933 TCTGATCTTCAATAAAGTCAACAAATATGTGCAATGAGGAAAGGATTTTG 3982
                         vi    i   i i  i viiv   ivvii v     i      i  vv v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_81107526_8   3983 TATTCAATAAATGGTGCTATGATAGCTCACTAACGATATGCAGAAGAATA 4032
                          v     i          iv  i i  viv  ? v i     i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_81107526_8   4033 AAATTTAACCCCAACCTTTCCCCATATATAAAA-TTAATTAAAGATGAAT 4081
                           i  vi     v    iv v       i    -    i v  i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_81107526_8   4082 TAAATATTTAAACATAAGTCATCAATATATAAGAATCCTGGAAGAAAACC 4131
                         i ? v ii    ii    vvv v  vv     i v  i i         v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_81107526_8   4132 TAGG----AATCGTCATCTGGATTTTGGCCTTTGAAAAGAATTTAT--GA 4175
                             ----    v  i ---  ii    v-  v iv  vii   v --  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGT---GACCTTGGG-TTAGGCAATGGTTTCTTAGA 593

  chr2_81107526_8   4176 CTAAGTCCTCAAAAGCAATTGCAACAGAAACAAAAATTGAAAAGTGGGAC 4225
                         -  v v vi        vvv      i  iv      v  v  i v    
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_81107526_8   4226 CTAATTATACTACAGAGCTTCTGCACAGCAAAAGAAACTGTTAACAGAGT 4275
                         i v  i v v vv i i   i  ii vv    i  v   i i  v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_81107526_8   4276 AAACGGCTATCTGACA-AATGGAAGAAAATATTCACAAACTGTGCATCCA 4324
                         i  vi vi v iv   -     i          ii    iii ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_81107526_8   4325 ACAAAGTTCTAATATCCAGAATCTATAG-GAACTTAAACAATTCAACAAG 4373
                          i  i vv  vi          v    i-     ivv    i    i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_81107526_8   4374 CAGAAAACAAATAACCCCACTAAAAAGTGGGCCAAGGACATGAGCAGGC- 4422
                         v i  i           v i ?    i     v     iv   ii  i -
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_81107526_8   4423 ----TCAAAAGAAGACATATACACAGTGGCTCAT 4452
                         ----  v        --      - i    iv  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGA--TATACA-AATGGCCAAT 873

Transitions / transversions = 1.43 (150 / 105)
Gap_init rate = 0.02 (17 / 873), avg. gap size = 1.76 (30 / 17)  


2631 22.58 3.94 7.24  chr2_81127013_81130932     2490  3428 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81127013_8   2490 TGGAAAAAG--TCTATGTTCATGGATCAGAAGAATCAATGTTGTTAAAAC 2537
                               i v--i i            ii     v i   i       i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81127013_8   2538 GTCCATATTACCCAA--TGCATTATACAGATTCAGTGCAATTTCTATCAA 2585
                          v v   i v     --  -  i-          ii     ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG-ATC-TACAGATTCAACGCAATCCCTATCAA 98

  chr2_81127013_8   2586 AATTACAATGATATTCTTCACAGAAATAGAAAAATCTATCCTAAAATGTA 2635
                            iv  iiviiv  i  ii       v  v  iiiv          vi 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_81127013_8   2636 TATGGAACCACAGAAGACCCAGAATAGCCAAAGCTATCCTGAGAAA-AAT 2684
                                vii  iii                 i v   i   i   -  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_81127013_8   2685 AACAAAACTGGACGAATCACATTACCTGTATTT--AAATTATACTACAGA 2732
                               ii    v  v     i v  ii-    --   i -       i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACT-TACTACAAA 246

  chr2_81127013_8   2733 GCCATAGTGACCAAAACAGC------TTGGCATTAAAAAAGATATGTAGA 2776
                           i i   i i   i    i------i      v ii v   i  i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_81127013_8   2777 TCAATGCAACAGAGTGAAAAAAAAAAACAGAAATAAA----TACATCTAC 2822
                               v  i   i vi i ivv----          ----     i  i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC----CAGAAATAAACCCATACATTTAT 342

  chr2_81127013_8   2823 AGTGAACTCATTTTCAACAAAGGTGCCAAGAACATATATTGAGGAAACAG 2872
                         i  v  i v      i    i          v   vi v  i     v i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_81127013_8   2873 CAGTCTCTTCAGTAAATGGTGCTGAATAAACTGTATATCCATATGCAGAA 2922
                         i     i    ii           i-------------------------
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGG------------------------- 417

  chr2_81127013_8   2923 TAATGACATTAGATTCCTATCTCTCACTATAAACTGTATATCCATATGCA 2972
                         ----    ------------------------    v   ?   i     
  L1M4_orf2#LINE/    418 ----GACA------------------------ACTGGATAKCCACATGCA 439

  chr2_81127013_8   2973 GAAAAATGAAATTAGATTCCTATCTCTCACTATATACAAAAATCAAATCA 3022
                         i  i      i  i  ii    i   v   i            i  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_81127013_8   3023 AAAT-----AAAGACTTAAACCGAGGGCCTCAAACTATGAAGCTGCTAAA 3067
                             ----- ?    i    ivv i iv  v       i  i  vi  i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_81127013_8   3068 AGAAAACAATAGAAA-AACTTTCCAGGACATCAGACTCGGCAAATATTTC 3116
                                 -   i?i-  v i i iv   v ii ii v     vvi    
  L1M4_orf2#LINE/    540 AGAAAACA-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_81127013_8   3117 TGAAATAATGTC-CCAAAAGCACAGGAAACCAAAGCAAAAATGGACAAAT 3165
                          v i   -  v -           i v   v    v      i  i    
  L1M4_orf2#LINE/    589 TTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_81127013_8   3166 GAAATCACATCAAA-TTAAAAAGCTTCTGCCCAGCAAATGAAACAATCAA 3214
                         vii iiv       -       -   i  iv vv    v  v  v     
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_81127013_8   3215 G----TGAAGAGACAACCTGCAGAATAGAAAAAAAAAATTTGCAAAC--- 3257
                          ----    i        ii      i i i    v -        i---
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA-TTTGCAAATCAT 735

  chr2_81127013_8   3258 -TATCTGACAAGAGATTAATAACCAAAATATATTAGGATCTCAAACAACT 3306
                         -       i   i  i vi  v   i       v i  v   vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_81127013_8   3307 C--TA-TAAAATATCTAATAATCTGATT-AAAAATGGGGAAAAGATCTGA 3352
                          --  -     viv v     i ii   -         v   i   i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_81127013_8   3353 ATAGTACGTATTTCTCAAAAGAAAACATACAGATGGCAAACTGGGACATA 3402
                             -  --       v      i i     i     v  ivi v    i
  L1M4_orf2#LINE/    836 ATAG-AC--ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_81127013_8   3403 AAAAGGTGCTCAAAATCATATCATTA 3428
                              i       v    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (136 / 73)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.75 (105 / 28)  


3051 25.59 3.38 1.01  chr2_81138030_81140027.rev      620  1506 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81138030_8    620 TGAAAGAATATTCCATGTTTGTGGATTCCAAGAATCATTATTGTTAAAAT 669
                           i  ii    i       ii      vv    v i v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81138030_8    670 GTTCATACTATTCAAAACCATCTGAAGATTTAATGTATTCCCTATCAAAA 719
                          viv     vii    viv    iv     i  i i v            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81138030_8    720 TATCAATGACATTCTTCACATAAATAGAAAAAAACAATTCTAAAAT---- 765
                          vi  iivi v  i  ii  v    v  v  iv-ii  i       ----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_81138030_8    766 ATGGAACCACAAAAAACCCAGGGCAGCCAAAACTACCCTGAGCAAAAA-A 814
                               vii   iii      iii         v i i   iv  i  - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_81138030_8    815 ACAAAACTGGAGGAATCACATTACCTGAATTTAAATTATAATACAGAGTC 864
                              ii       v     i v  ii v  i   viv  v    i  ii
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_81138030_8    865 ACAGTAACCAAAGCAGCATGGTTTTGGAATAAAAATAGACATGTAGACCA 914
                                i   ii   ii    vi   v    ii        i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_81138030_8    915 TTGAAATAGAATGGAGAACCGAGAATCAAATCAAATCCCTACATCTACAG 964
                         v  i        v    ii v    ----  -   i  v     i  ii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAA----AT-AAACCCATACATTTATGG 344

  chr2_81138030_8    965 TGAACTCATTTTTGACAAAAGTGCCAAGAACATACACTGAGGAAAGGACG 1014
                          v  i v     i     ii         v   v  v  i      i ii
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_81138030_8   1015 GTCTCTTCAATAAATGGTGCTGGGTAAACTGGATATCCATATGCAGAAGA 1064
                             i     i             vv         ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_81138030_8   1065 ATGGGACTAGACCCCTATTTCTTGCCATACAGAAAAATCAA------ATG 1108
                            iiii i        ii  vii     i v      i  ------   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_81138030_8   1109 -------------AATG--AAAACTCAAACTATGAAACTATTACAAGAAA 1143
                         -------------    -- i i  v       i     v   v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_81138030_8   1144 ACATTTTGGAAACTCTTAAAAGACATCAATTTGGGCAAAGATTTCTTGAG 1193
                             vvv? v  v    viv-   v iiiv  i     v i      iii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_81138030_8   1194 TAATATTCCATAAGCACAGGCAACCAAAGGAAAAGTGGAGAAATGGGACC 1243
                           vv iv   v       i     v    i    i i  v    v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_81138030_8   1244 ACGTCAAG-TTAAAAACTTTCTGCACAGCAAAGGAAACACTCAAAAAAGT 1292
                         v i    i-           -  ii vv       v  vv    i     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_81138030_8   1293 AAAGAGACAACCCACAAAATGAGAGAAGATATTTGCAAACTATCTATCTT 1342
                         i  i            i    i     i           ii  v     v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_81138030_8   1343 ACAAAGGATTAATAACCAGAATATACAAGGAGCTCAAACAACTCTACAGG 1392
                          i  i   i vi  v          i  i  i   vv       v i iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_81138030_8   1393 AAAAAATTCTAACGATTCTATTAAAAAGTGAGCAAAA-ATTTAAATAGAC 1441
                              iv- v  ii ii v   ?    i  i     i-    i       
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_81138030_8   1442 ATTTCTCAAAAGAAGACACACAAATGGCAAA-ATG-ACATGAAGAGGTGC 1489
                                v        i i         v  - v -       i  i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_81138030_8   1490 TTAACATCATTGATCAT 1506
                          i       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (142 / 82)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.60 (39 / 15)  


2796 26.81 2.31 2.53  chr2_81158979_81163155.rev     2776  3685 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81158979_8   2776 TGGAAACACATTCAGTGCTTATGGATGGGTAGAATCAATATTGTGAAATT 2825
                               v i  i vi  i i      v  v   v i        v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81158979_8   2826 GACTGTACTGCCCAAAGCAATCAACACAGTCAATGCAATTTCTATCAAAA 2875
                          i vi    v      vii   v   v v    i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81158979_8   2876 TACCATCATCATTCTTCACAAAACTAGAAAAAAGAATCCTAAAATTCATA 2925
                          v   v vv v  i  ii  i  v v  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_81158979_8   2926 TAGAACCAAAAAAGAGCCCACATAGCCAAAGCAATACTCAGTAAAAACAA 2975
                          i   viiv  ii  v  viv         i    vi v iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_81158979_8   2976 CAAATCTGGAGGCATCACATTACCTGACTTCAAAGTATACTGTAAGGCCA 3025
                             vi      vv     i v  ii i      iiv    ii  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_81158979_8   3026 TAGCCACCAAAAAGGCATAGTATTGGTATAAAAATAGTCACATAGACCAG 3075
                         i  iv i   i vi ii i   i   i    ii    v  i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_81158979_8   3076 TAGAGCAGGATAGAGAATCAAGAAATAAAGCCAGATATTTACAGCCAACT 3125
                          i  ii  i  v    i  v         v   v i     ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_81158979_8   3126 GATTTTTGACAAAGCATACAAAAAT-------TGGGAAAAGGATACCCTA 3168
                               i     i -i i v  i i-------    i    i   vi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_81158979_8   3169 TTCAATAAACAAATGGTGCTTGGATAACAGACAAGCCACATGTAGAAGAA 3218
                              ----           v   i   v ivv ?       i i     
  L1M4_orf2#LINE/    400 TTCAA----CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_81158979_8   3219 TAAAACTGGATCCTCATTTCTCACCTTATACAAAATTCAACTCAAGTTGG 3268
                          i  ii    i  ii ii  v    v         v i       iv   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_81158979_8   3269 ATCAAAAACTTAAATCTAAGACCTGAAACTATAA--------GAAGATAA 3310
                             ? i  i     v     v  i         --------     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_81158979_8   3311 CATAAAAA-AACTCTTTGAGACATTGGGCTAGGAAAAGATTTCATGACTA 3359
                             ii?i-  v    i v   v     i    v  v i    v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_81158979_8   3360 AGACCCCAAAAACAAATGCAGCAAAACCAAAAATAAATAAATGGGACATA 3409
                         v   v      i  v v   i     vv       i      v    v v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_81158979_8   3410 ATTAAACTAAAAAGCTAAAAACTAAAATTTCTTTTTCATAGCAAAAGAAA 3459
                           i   v -------        ----   v vi    -----  i  v 
  L1M4_orf2#LINE/    646 ATCAAAAT-------TAAAAACT----TTTGTGCTTCA-----AAGGACA 679

  chr2_81158979_8   3460 TTAATCAGCAGAGTAAACAAACAACACACAGAGTGAGAGAAAATATTCAC 3509
                         i  -   iv i   i  v i     v      i  i           ii 
  L1M4_orf2#LINE/    680 CTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_81158979_8   3510 AAACTATGCATTTGACAAAAGACTAATATCCAGAATCTGCAAGGAATTCA 3559
                            ii  ii  i   i  ii    vi          v ii  i   i  v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_81158979_8   3560 AACAGAT---TGGCAAGAAAACAAAATAATCTCATC--AAAATGGGCAAA 3604
                         v   iv --- iii  i  i     -   i iv  i--            
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAA 827

  chr2_81158979_8   3605 TGACATGAATGGGCATTGCTCAAAAGAGCATATACAAACAGCCAACAAAC 3654
                         v  iv     i i    v   v     iv         ii     i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_81158979_8   3655 ATATGAAAAAATGTTCAATATCACTAATTAT 3685
                          i       i   i    i    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.67 (44 / 12)  


2807 23.50 4.63 2.03  chr2_81193650_81197858.rev     2834  3718 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81193650_8   2834 TAGAATGATACCCAACATTTATGAATTTGAATAATTCATATTGTTAA--- 2880
                          i   v    i  v ii  i   i   v   v v  v          ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81193650_8   2881 ---AATATTCAT-AAACACTTAATCTACA-ATTCAACAGAATTCCTATAA 2925
                         ---    i  vi-   ---  i       -       iv   i     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA---TTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_81193650_8   2926 TAATTTCAA-TGTCATTCTTCATATAAATAGAAAAA--AATACTAAAATG 2972
                         v   ii  i-  i -  i  iii v    v  v  i--i  v       v
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_81193650_8   2973 TATACAGAACCACAAAAGGACCCA-AATAGTCAAATCAATCTTGACAAAA 3021
                         i   ii   vii   i-       -     i    v         v   i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_81193650_8   3022 AAGAACAAAGTTGGAG-ACATTTCAACCAATCTGCATACCAAATTTCAAA 3070
                                         -  ---   --  v i------  v         
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGAC---TCA--CACTT------CCCAATTTCAAA 234

  chr2_81193650_8   3071 ATGTGTTTCAAAGCTATAGTAATTAAAAGATCATGGTACTGGCATAAA-A 3119
                          iv ii v        i      i  i v vii              i- 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_81193650_8   3120 CAGACACACCAACCAGTGGAATAGAATAGAGTGCCCAGAAGTAAACCC-C 3168
                         i     i ivi i  i           v   v i      i       -i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_81193650_8   3169 ACATCTATAGTCAATTGATTTTTTATCAAAGTGCCAACAACACACAATAG 3218
                             i   i             iv iv ii       v v  iv    i 
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_81193650_8   3219 G---AGAACAGTCTCTTCAATAAATTGTGTTGCGAAAACTGGATATACAC 3265
                          ---    i     i     i    v   i  v  v         ?v   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_81193650_8   3266 ATACAGAATAATAAAAATGGACCCTTTCCTCAC--CAATTATACAAGAAT 3313
                           i  i  v   i  iv       i v      --  --       i   
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA--TATACAAAAAT 482

  chr2_81193650_8   3314 AAACTCAAAATGGATGACATACTTAAAAAGAAGACCTGAAAATATAAAAC 3363
                         v              v ? v  i    viv    v  i   v        
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_81193650_8   3364 TAATGGAAGAAAACATTGGA-TAAAACTCCAAGTCATTGGTCTGGGTAGA 3412
                          vv i           v  ?-    v  i iv v v    vi i  i iv
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_81193650_8   3413 GATTTCTTGAATATGAC-TCAAAAGCACACGTAATGAAAGCAAAAATAGA 3461
                          i      ii       -i          v i  ii    v         
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_81193650_8   3462 CAAATAAAACTGCAT-GAAACCAAAAGCTTCTGCACAGCAAAGAAAAC-- 3508
                         i    vii   v   -i   ii    i   i  ii vv     i v  --
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_81193650_8   3509 --AGTAGAGTAAGGAGACAACCCTCAT--TGGGAGGAA-TATTTGCAAAT 3553
                         -- iv i   i ii         v  v--      i  -           
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_81193650_8   3554 TATGCATCAGATGAAAGGTTCATATCCAAAACATACAA-GAA-------A 3595
                         i  ii   v   i ii ii ii      i  i   i  -   ------- 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_81193650_8   3596 ATT-AATAATAAGAC-ACAAATAGCCATATT-GTAAATGGGCAAACAACT 3642
                          i -        i v-       i  vv   -iv           vi i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_81193650_8   3643 TGAATAGATATTTCTCAAAGGCAGACATACAAATGACCAACAGATATATA 3692
                                 i       v  i v   i         i    i iii i  i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_81193650_8   3693 AAAACATGTTCAACATCTTTAATAAT 3718
                             v   i        v????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (130 / 75)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.03 (59 / 29)  


1537 27.31 2.20 1.32  chr2_81218157_81221150     1293  1746 (1248)    L1M4_orf2#LINE/L1        8   465 (443)  

  chr2_81218157_8   1293 ATATTTCGTGTTTATGAACCGGACAAATTAATATTGTGAAAACGACCAAA 1342
                             ii i    i   i ii   vi v          v  i i i v v 
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_81218157_8   1343 ATATAAAGAACAATCTACAGAGTCAATGCAATCCCTATCAAAATATCAAT 1392
                         v vivv i vii         v    i                 vi  ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_81218157_8   1393 GATACTATTCACAGAAAT-AAAAAAT--ATCTTAAAATTCATATGGCACT 1439
                         viivi v  ii       -i v  ii--   i              v v 
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_81218157_8   1440 ACAGAAGTCCCTAAATCACCAAAGCAATCCTGAACAAAAAGAACAAAGCT 1489
                         i  iii v   vi   vi     i     i    v  i          i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_81218157_8   1490 GAAGTCATCACATTACCTGACTTCAAAATATATTCTAAAGCTATAGTAAC 1539
                          i  vvv     i v  ii i       iv  i vi       i     i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_81218157_8   1540 AAAAACAGCATGTCACTGGCATAAAAAACTA-ACACATAGACCAATGAAA 1588
                         v  i    ii  vi          ii --  -   i     i     i  
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGA--TAGACATATAGATCAATGGAA 305

  chr2_81218157_8   1589 CAGAATCAAGAATCCAGAAACAAATCCGTATATTTATGGCCAACTGATTT 1638
                         i     ii   i        i   i  i  i        i   i      
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_81218157_8   1639 TTGATAAAGGCAGTAAGAATATTCACTGGAAAAAGAAGTGAATGCTCTTC 1688
                          i  i  i  iivi    vi     v   ii      - - i -  i   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-T-AGT-CTTTTC 402

  chr2_81218157_8   1689 CATAAATGCTGCTGAAAAAATTAGATATCCATATGCAGAAAAAATGAA-- 1736
                         v i     v     ii v  i i    ?   i     -   i      --
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAATGAAGT 451

  chr2_81218157_8   1737 ----CCTCTATCTC 1746
                         ----  i   i   
  L1M4_orf2#LINE/    452 TGGACCCCTACCTC 465

Transitions / transversions = 2.42 (87 / 36)
Gap_init rate = 0.02 (9 / 458), avg. gap size = 1.78 (16 / 9)  

1328 24.33 6.19 2.27  chr2_81218157_81221150     2018  2502 (492)    L1M4_orf2#LINE/L1      405   908 (0)  

  chr2_81218157_8   2018 CAAA--GTGCTGGGATTACAGGCATGAGCCAC-CGC-----------GCC 2053
                             --         iv  v  -  - ?    -i  ----------- ii
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGG-AT-AKCCACATGCAAAAGAATGAAGTT 452

  chr2_81218157_8   2054 AGACCTCTGTTTCTCATCATATACAAAAATAAAATGAAAATGGATTAAAG 2103
                         i    i  iii  v  i             v  v v         i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_81218157_8   2104 GCTTAAACGTAATACCTGAAACTATGAATGTACTAGAAGAAAACATTGGG 2153
                         i i    i    v v  i       i  vv vi             v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_81218157_8   2154 GAAACACTTCAGGACATTGGTCTGGGCAAAGATATTTTTGATAAGACCTC 2203
                          v  vv    iv   v    vi i     v i v i  v    v   vi 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_81218157_8   2204 AAAAGCACACTGTTACACAAACATAAATAGACAAACGGGATTATATCAAG 2253
                                  v- iv   v  iv v       i   iv   i vi     i
  L1M4_orf2#LINE/    603 AAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_81218157_8   2254 -CTAAAAA-----GTACAAGAAAGGAAACAAGTAACAGAGTGATGAGGCA 2297
                         -i      -----  i vvv      v  v vi  v i     vi  i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_81218157_8   2298 ACCTAT----TTGCA---AATATTTGCAAACTATTCATCTGACAACTGAT 2340
                            i i---- v v ---            ii  vi      i  vv  i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_81218157_8   2341 TAATAACCAGAATATAAAAGAAACTAAAACAACTCAAAAAGCAAAAGCAA 2390
                          vi  v          v  ii    vvv         v  v-------- 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT--------A 793

  chr2_81218157_8   2391 AAAAAAAAAAAAAACTGATTAAAAAGTGGGCAAATGATCTGAATAGACAT 2440
                             i v   v  v ii   ?    i        v   i           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_81218157_8   2441 TTCTCAAAAGGAGACATACAAATGGCCAACAGGCATATGAAAAACTGC-- 2488
                              v    i   i              i i   i       iv   --
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_81218157_8   2489 -ACATCACTAATCAC 2502
                         -      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (57 / 57)
Gap_init rate = 0.02 (12 / 504), avg. gap size = 3.42 (41 / 12)  


2065 24.62 3.21 6.41  chr2_81276308_81278066      488  1267 (492)    L1M4_orf2#LINE/L1      154   908 (0)  

  chr2_81276308_8    488 AAATACTGGGGA----AAATTGCCAAAGCAATCCTAAGCAGAAAAAACAA 533
                             i vi    ----i   v      i     i i iv ii  i     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_81276308_8    534 ATCTAGAGGCATCACATTGCTGAACTTCAAATAATACTACCAGGCTATAA 583
                          vi i    vv     i v iv  i      vvv      v i    i i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_81276308_8    584 TTGTCAAAACAGTATGGTATTAATATAAAAGTAGGTACACAGACCAGTGG 633
                          vi    i     i     i iii    iii   ii i i   i  i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_81276308_8    634 AGAAGAATTGAGAACCCAGAAATAAAGCAAAATACTTTTAACCAACTGAT 683
                          iv          ii           v v v i i  v iii   i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_81276308_8    684 CTTCAACAAAGTATTCAAAAACAT--ATTGGGGAAAAGAT-GTGCTATTT 730
                         i   i    i vvvi   i v   -- v        ii  -  -  v  i
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT-CTTTTC 402

  chr2_81276308_8    731 AATAAATGGTGCTGGGAAACCTGGCTAGCGACATGTAGAAGAATGAAAC- 779
                           i              v v    v  ? v     i i         ii-
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_81276308_8    780 AGATCCCTAGGTCTCACCTTATACAAAAATCAACTCAAGAAGGATCAAAG 829
                         i  i     vv  v    v           i       i v      ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_81276308_8    830 ACTTAAATCTAAGATCT-------------TCT--GAAGATAACATTGGG 864
                           i     v     v  -------------   --     v     v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_81276308_8    865 AAAAATCTTCCGGATATTAGCCTAGGCAAAGAATTCATAACTAAAACCCG 914
                         iv        vv  iv  i vi       v iv   v  iv  vi  v v
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_81276308_8    915 AAAAGCAAATGCAACAAAAAAATAAAAAAGTTAATGGGACCTGATTAAAC 964
                                v v         i  v   v ii v   v    i v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_81276308_8    965 TAAAAAGCTTCCAAACAGCAAATAATAATAATAATAATAATAATGAGCAA 1014
                          v    i   iiivi vv    vi i v  vi  ----------  --- 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAA----------GA---A 689

  chr2_81276308_8   1015 AGTAAGGAGACAACCCACAGAATGA-AGAGAATATTTGCAAACTATGCAT 1063
                            i ii                 i-   i            ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_81276308_8   1064 CCAACAAGGATATATCCAGATATAGATTCTGGATGTATATTTGGTGCATG 1113
                          ii i    ---------------  i --------------------  
  L1M4_orf2#LINE/    740 CTGATAAGG---------------GACT--------------------TG 754

  chr2_81276308_8   1114 TATCCAGAATCTACAAGGAACTCAAACAAATCAACAAGAAAAAAATAA-T 1162
                                   v  i  i      vv    v    i  v     i i  - 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_81276308_8   1163 AATCTCATCAAAGAGTGGGCAAATAATATTAATAGACATTTCTCAAAAGA 1212
                           i iv  i?  i i        vi  v v              v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_81276308_8   1213 AGATATATAAATGGACAAGAAACATATGAAAAAAAGATTCAACTTCACTC 1262
                                i      v   v  i  i       i v -i     v   ???
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATG-CTCAACATCAZZZ 903

  chr2_81276308_8   1263 ATCAT 1267
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.41 (110 / 78)
Gap_init rate = 0.02 (14 / 755), avg. gap size = 5.36 (75 / 14)  


3031 18.34 9.69 4.96  chr2_81410643_81415065     3065  3931 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81410643_8   3065 TGAAAACAAATCCCATGATCATGAATTAGAA---TTAATGTTGTTAACAT 3111
                           i   v v        v     i   i   ---     i       v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81410643_8   3112 GTCAGTGCCACCCAAAATGATCTACAGATTTAGTGCAATTCCTATCAAAA 3161
                          v  i i iv      v             i ii     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81410643_8   3162 TTCCA-CTGTTTTTTTTTCTTTTTTTTTTTTTTTGCAGAAATAGAGAGCC 3210
                          i   -   ii      -----------------        v  v iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-----------------GCAGAAATTGACAAGC 133

  chr2_81410643_8   3211 TTTTCCTACAAGTCTTATGGAAATTCAAGGGACCCCAAATAACTGAAGCA 3260
                          vv     v  v  v         v          vi    i ii  i  
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr2_81410643_8   3261 ATCTTAAAAACAAAGAACAAAGCTGGAGGA----------------TCAA 3294
                              i    vi          i       ----------------    
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_81410643_8   3295 AA-------------------------GAT--TGTGGTACTGGAATAAAT 3317
                           -------------------------  i--           v    iv
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_81410643_8   3318 ATAGCCATTTAGA-CAA----ACAAAA------GCCTTGAAATAAACCCT 3356
                             v   v    -   ---- i i  ------ i iv           v
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_81410643_8   3357 CACATATATAGTCAAATGATTTTTTTAGAAGAGTGTCAAAATCACTCAAA 3406
                         i    v   i     v       iv- v   i   i   i i  i    v
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAAT 382

  chr2_81410643_8   3407 GGGGGAAGTACAATCTTTTCAACAAATGATGCTGGAATCTCTG------- 3449
                             i   v i i               i      i ivv   -------
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_81410643_8   3450 -CATGAAAAAAAATGAAGTTGGACCCTTACATAATACAATACACAAAAA- 3497
                         -    v    i               i   v v i  v   i       -
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_81410643_8   3498 --ATT---AATGGATCGAAGAC-TAAGTGTAAGACCTAAAGCTGTAAAAC 3541
                         -- i ---        i?    -   i       v     i  i      
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_81410643_8   3542 TTTTAGGAGAAAACAT-GGGGTAAAAGCTTCATGACACTGAATT-TGTGA 3589
                          i    i         -  ?     -v    i    vi  ii  -v ii 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_81410643_8   3590 TGATTTCTTGGATACAACACCAAAGGCATAGGCAACAGCAGCAACAACAA 3639
                           i      i    ii        i   i ---------        ---
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACA---------AGCAACAA--- 619

  chr2_81410643_8   3640 CAACAGCAACAACAAAAATAGAAAAATCGGACT-CATGAATATTTTTAAA 3688
                         -------  v  --        v    i     -   v  v   ---   
  L1M4_orf2#LINE/    620 -------AAGAA--AAAATAGATAAATTGGACTTCATCAAAATT---AAA 657

  chr2_81410643_8   3689 A---TATGTACTTCAAAAGAGAATATTAACAGAGT-AAAGGGCAACCCAC 3734
                          --- v   i       i  v v   i  v i   -   i i        
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_81410643_8   3735 AGAATAGAAGAAAATATTTGTAGAT--TTTGTCTGATAAGGAATTAATAT 3782
                              i i            i i  -- v i          i i vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_81410643_8   3783 TCAGACTATGTTGAGAACTTTCAAAAGTCAACAATTAAAAAA-AAA-AAC 3830
                         i    v   i vi      i i v  v    i   v    i -   -   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_81410643_8   3831 TTGATTCAAAAATGGACAAAAGACTTCAATAGACATTTCTTCAAAGAAGA 3880
                         iii   ?        i    i  i  v             i         
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_81410643_8   3881 TAGACAAATGGCCAAAAAGCACATAAAAAGATTCTCAATATCACTAATTA 3930
                           v            v        i       v     i    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_81410643_8   3931 T 3931
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.64 (97 / 59)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 4.70 (127 / 27)  


2575 26.65 0.28 0.28  chr2_81485951_81491734.rev      502  1214 (4570)    L1M4_orf2#LINE/L1      196   908 (0)  

  chr2_81485951_8    502 AAGAACAAAGCTGGAGGCATCAAACTACCTGACTTCAAACTATACTACAA 551
                                   i      vv   v   v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_81485951_8    552 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 601
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_81485951_8    602 ATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACA 649
                                   i    i--    i  --        vv  ii i ii  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr2_81485951_8    650 ACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT 699
                         iii vi    i  i     ivv  vv  i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_81485951_8    700 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 749
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_81485951_8    750 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGAT 799
                         iv    ii    i    v   i     v           i  i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_81485951_8    800 GGATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 849
                             i ?   ii    i  v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_81485951_8    850 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 899
                            v    ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_81485951_8    900 CAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 949
                         i vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_81485951_8    950 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 999
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_81485951_8   1000 AACAGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGA 1049
                           v  i     i   iv            v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_81485951_8   1050 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 1099
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_81485951_8   1100 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGACAC 1149
                             i     i     v  i?    i     i i   iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_81485951_8   1150 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 1199
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_81485951_8   1200 GTCATCACTGGCCAT 1214
                         iv     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (109 / 77)
Gap_init rate = 0.00 (2 / 713), avg. gap size = 2.00 (4 / 2)  

3029 25.66 1.43 1.43  chr2_81485951_81491734.rev     1933  2840 (2944)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_81485951_8   2840 TGGAAAAATATTCCATGCTCATGAATATAAATAATCAATATTAT-AAAAT 2792
                               i    i     i     i  vvi  v v i      i -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_81485951_8   2791 GGCCATATTGCCCAAAGTAATTTATAGATTCAATGCTATTCTCATTAAAC 2742
                            v   i v      v i  i  i        i  v  i ii  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_81485951_8   2741 TACCATTGACATACTTCACA-AAATTAGAAAAAAACT-ATTTTAAAATTC 2694
                          v   vivi v vi  ii  -     i--- v  i  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

C chr2_81485951_8   2693 ATGTGGAACCAAAATAAAAAAG-TCCA-AATAGCCAAGGCAATATTAAGC 2646
                           i     -----  iv  ii -i   -         ii    v  i iv
  L1M4_orf2#LINE/    148 ATATGGAA-----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

C chr2_81485951_8   2645 AAGAAGAA-AAAGCTGGAGTCATTACACTACCTGACTTCAAACAATACTA 2597
                                 -    i     vvv i     v  ii i      vvv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

C chr2_81485951_8   2596 TAGGGTTACAGTAAACAAAACATCATGGTACTGGCACAAGAACAGACACA 2547
                         i ii i        v   i   vii           i   i i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

C chr2_81485951_8   2546 TAGACCAATGGAACAGAATAGGGAATCCAGAAATAAGGCTGCACACCGAC 2497
                             i        i     v i  i           iv iii   iiv i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

C chr2_81485951_8   2496 AACCATCTGATCTGTGACAAACCTGACAAAAAC---CAATGGGGAAAGGA 2450
                         iii  vi    i vi     ivv  v   i v ---            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

C chr2_81485951_8   2449 T--TCCATATTTAGTAAACAGTGCTGGGAGAACTGGCTAGCCATATGCAG 2402
                          --  -- v  i ii   ii         v      v  ?   i     i
  L1M4_orf2#LINE/    393 TAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

C chr2_81485951_8   2401 AAGATTGAAACTGCACCCCTTCCTTACACCATATACAAAAATTAACTCAA 2352
                             v    ii  v      v   i                         
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

C chr2_81485951_8   2351 AATGGATTAAGGGCTTAAATGTAAATCCAAAAACTATAAAAACCCTAGAA 2302
                                i ?i i i         ivv v            vi i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

C chr2_81485951_8   2301 GAAAATCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTCA 2253
                              iv    ?i- v i -   iv   v v  vv i     v i    v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

C chr2_81485951_8   2252 T-GATGAAGATACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATG 2204
                          -   - v  i          vvv          v      v  i    v
  L1M4_orf2#LINE/    590 TAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

C chr2_81485951_8   2203 GTATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACA 2154
                          v ii v  i   v v  i i   i  ii vv    i  v        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

C chr2_81485951_8   2153 GGATAAACAGACAACCTACAAAATGGGAGAAAATTTTTGCAGTCTATGCA 2104
                         iii i  v        i   i             v      ivii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

C chr2_81485951_8   2103 TCTGAAAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTA 2054
                              v  i  v  vi       v  v     i     ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

C chr2_81485951_8   2053 CAAGAAAAGAACAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACA 2004
                         i  v    ii     i     v   ?    i           iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

C chr2_81485951_8   2003 GATACTTCACAAAAGAAGACATACATCCTGTCAACAAACATATGAGAAAA 1954
                           i i   v v        i     vviv i   i  i  i    -   i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAG 887

C chr2_81485951_8   1953 AAGCCCAACATCACTAATCAT 1933
                          v  i        ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.62 (26 / 16)  


3150 27.34 0.77 0.66  chr2_81495998_81502380.rev     4985  5891 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81495998_8   4985 TGGAAGAACATTCCATGCTCATGGGTAGGAAGCATCAATATCGTGAAAAT 5034
                              ii i  i     i      i v     vv i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81495998_8   5035 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5084
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81495998_8   5085 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5132
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_81495998_8   5133 TATGGAACCAAAAAAGAGCCCACATTGCCGAGAAAATCCTAAGCCAAAAG 5182
                                viiv  ii  v  viv  v   i i v    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_81495998_8   5183 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATATGACAAGGC 5232
                                i      vv       v  ii i      viv  iv    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_81495998_8   5233 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5282
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_81495998_8   5283 AATGGAACAGAATGGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5332
                                i     v   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_81495998_8   5333 CTGATCTTTGACAAACCTGACAAGAACAAGAAATGGGGAAAGGATTCCCT 5382
                         i    i  i     ivv  v     v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_81495998_8   5383 ATTTAATAAATGGTGCTCGGAAAACTGGCTACCTATATGTAGAAAGCTGA 5432
                         v  i  i          v   v      v  ? i i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_81495998_8   5433 AACTGCATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5482
                          ii  v i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_81495998_8   5483 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5532
                          ?    i           v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_81495998_8   5533 AGGCA-ATATCATTCGGGACATAGGCATGGGCAAGGACTTCGTAACTAAA 5581
                            ?i- v   -    v   v v  vv i     v ii   v  iv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_81495998_8   5582 ACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGTGATCTAAT 5631
                                     vvi          vv        i    vv  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_81495998_8   5632 TAAACCAAAGAGCTTCTGCACAGCAAAAGAATCTACCATCAAG----TGA 5677
                         i   viv  i i   i  ii vv    i  ---i  i      ----   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGA---CACTATCAAGAAAGTGA 694

  chr2_81495998_8   5678 ATAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGAC 5727
                          v  i     i                 v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_81495998_8   5728 AAAAGGCTAATATCCAGATTCTACAAAGAACTTAAACAAATTTACAAGAA 5777
                           ii i  vi        v v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_81495998_8   5778 AAAATCAATCAACCCCATCAAAAAGTGGGCAAAGGGTATGAACAGACACT 5827
                            iv   vi     v  i?    i          i v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_81495998_8   5828 TCTGAAAAGAAGACCTTTATGGAGCCAACAGATACTTGAAAAAATCCTCA 5877
                            vv        iv vi vivi     i iii  v      i  v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_81495998_8   5878 TCATTACTGGTCAT 5891
                         v   i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


1371 32.03 3.74 0.36  chr2_81614693_81616633      501  1062 (879)    L1M4_orf2#LINE/L1      251   831 (77)  

  chr2_81614693_8    501 CAGTAACCTAAACAGCACAGTACTGGTACCA----AAACACACAGGCCAA 546
                               i v i    iiii       i iv ---- i   i i  ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_81614693_8    547 TAGAACAGAATAGAGAACCCAGAAGTAATGCTGCATGCCTACAATTATCT 596
                          i   i     v    ii      i   vv iii iiii  iii i vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_81614693_8    597 GATCTTTGACAAAGTCGATGAAAACAG-CAATGTGGAAAGGACACTCTAT 645
                            i  i     i vi vii i v  v-     v      i i v   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_81614693_8    646 TCAATAAATGGTGCCGGGATAACTGGCTAGCCATATGCAGAAGGTCAAAA 695
                             i         i    i      v  ?   i     i   ivii  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_81614693_8    696 CTGGATTATTTCATTACACCAAGTACAAAAATGCACTCAAGATGGATTAA 745
                         i    iivi v v i      vi         vv      i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_81614693_8    746 AGACTTACATGTAAAAGTAAAAATAATAGAAATCCTGTAACATAACTTAG 795
                             i  v      i  iv    iv   i  v  i iv  v v   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_81614693_8    796 G---AAATATTCTGGACATAAGAC----CAAAGATTTCAT-GACAAGCAT 837
                          ---    v   vv   v vi ii----   v i    v -  i v - i
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG-AC 599

  chr2_81614693_8    838 GCCAAAAGCAATTGCAACGAAAACAAAAA-AGACAAATCAGACCTAATTA 886
                         i         vvv     i   iv     -   i    ii   i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_81614693_8    887 AACTAAATATCTTCTGCATAGCAAAAGACACTACCAATAGAG----AAAA 932
                           v v  v v   i  iiivv    i       i   v i  ----  i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_81614693_8    933 CAGTCTACAGAATAAGAGAAAATATTTGCAAACTCTGCATCCAACAAAGG 982
                           ii i       ii                 iiv ii   ii i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_81614693_8    983 TTTAATAGCTAGATTCTATAAGGAACTTGATCAAATTTACAAGCAAAAAA 1032
                         vi vi  v i   v v     i     ivvv   v iv i  vv    i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_81614693_8   1033 TAAA---CCCCATTAAACGCAGGAGCAGAAAAT 1062
                         i   ---   v   ?  vi- v i   i ii  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAA-ATGGGCAAAGGAT 831

Transitions / transversions = 1.72 (112 / 65)
Gap_init rate = 0.02 (10 / 581), avg. gap size = 2.30 (23 / 10)  

 374 21.85 0.00 2.52  chr2_81614693_81616633     1331  1449 (492)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr2_81614693_8   1331 AAAAAGAAAATTAACAACAACAACAAAAAGTGGACAAAAGACATGAACTG 1380
                                v  v    v-   i--i?    i   i    i  iv    iv 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACC-CAAT--TWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_81614693_8   1381 ACACTTTTCAAAAGAAGTCATACATTTGGCCAACAGGCACTTGGAAAAAT 1430
                            i  i  v       vi     vv       i i    v  i   i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_81614693_8   1431 ACTCAACATCACTAATCAC 1449
                         i          ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.50 (3 / 2)  


1736 27.20 8.34 4.57  chr2_81693577_81696405     1465  2339 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81693577_8   1465 TGGAACTATATTTTATATTCA--GATAGGAGGACTCGGAAATTGTCAAGA 1512
                              vv    iii  i    --   v   i    ii- v     i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTA-ATATTGTTAAGA 49

  chr2_81693577_8   1513 TACTGGTTCTTCTCAACTTGACCTATAAATAAACTAAGGTATTAATACAT 1562
                          iviii v  i i   v    i   i i  ----------- i  ii  -
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGAT-----------TCAACGCA- 87

  chr2_81693577_8   1563 TAAATACAATTAAATCCCAATAAAAATCCTA-CAGAGTTATTTTGTAGAT 1611
                         -------------     v  v       i - v vv  -     i   v
  L1M4_orf2#LINE/     88 -------------ATCCCTATCAAAATCCCAGCTGCCTT-TTTTGCAGAA 123

  chr2_81693577_8   1612 AATGATAAACTGATCCTCAAGTTTATATATGGAGA--AAAAGGACCCAGA 1659
                          v   i  i        v  i  i    --   i --v  i         
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATAT--GGAAATGCAAGGGACCCAGA 171

  chr2_81693577_8   1660 AAAATCAACACAAGATTGAA---GTAGAACAAAGTTGAAGAACTGATGGT 1706
                          v ii   v    vv     --- v            i  i   v iiv 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_81693577_8   1707 ATCTGACTTCAAAACAGACTTTACAGCTGTAGTAATCCAGATAATATAGT 1756
                         vi ii i        vv   vi v    ii       v   i i i i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_81693577_8   1757 TTTAGTGAAAGTGTAGACA----GATAAATGGAACAGAACAGAATTTTCA 1802
                         vi i iiv   vi      ----   v       i    iv  ivv i  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_81693577_8   1803 GATATAGACCCACAGACATATAGACAACTGATTTTTGACAAAGATGGAAA 1852
                           v   i     i v iv   i v   i       i     i i  vv  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_81693577_8   1853 GGTAATACAAGGGAAATAAGATAAATCTT--CAACAAACAATGCTGCAAC 1900
                          iiv  v   v  ii -    vv i    --       iii     vi  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGA-AAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_81693577_8   1901 AACTGGCATGTACATACACACACACACAAAAATGAATCTAGACACAGACC 1950
                               -------   ?v    ii  v  i      vi i   v vv   
  L1M4_orf2#LINE/    421 AACTGG-------ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_81693577_8   1951 TTCCACCCTTCGTAAAAATAAACACAAAATGGAGTGCAGATCTAAATTT- 1999
                          iv    v viii      v   v         vii?   i      v -
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_81693577_8   2000 ----TTATA--TATACAAT------ATGTAAATATA----TATATTTACA 2033
                         ----i  v --    v  i------ v v   i   ----  v  i v i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_81693577_8   2034 TG-------------CAA-----------------CACCAATCGTAAAAT 2053
                           -------------   -----------------      vv i v  v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_81693577_8   2054 CTATAAAG-----AATTGGTAAGCTGGTGATCATTAACATTTCTAAAATA 2098
                          v i   i-----   v i   ii   vvv    i  v   v--    iv
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA--AAAACT 661

  chr2_81693577_8   2099 TCTGCTCTTTGAAATAAACTGTCAAGAGAATAAAAACACAAGACAAAGAC 2148
                          i  iv   ii  iv v   i      i i i    v    vv  v   v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_81693577_8   2149 AGGGAGAAAATATTTGTAAAAAACATATCATATAAAGGACTGCTATCCAA 2198
                         v               i   vv i     vv    i     vv      i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_81693577_8   2199 AAGATACAAAAAAATTGTTAAAACTCAACAATAAAGACACAAA----CCA 2244
                           v   i   i  v i-   v       i      i v     ----   
  L1M4_orf2#LINE/    762 AATATATAAAGAACTC-TTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_81693577_8   2245 ATTCTATAATGGGCGAAAACTTTTGACAGACACCTCACCAAA-AAGACAT 2293
                            ?v v       i  iiv   vi i     ii  v     -    i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_81693577_8   2294 ACAGAT--CCAATTATCATATGAAAAGGCACTCCACATTGTTTGTCTT 2339
                            i  --     v v  i        iii   v    ii????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (129 / 106)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 4.52 (113 / 25)  

1369 27.14 0.50 0.25  chr2_81693577_81696405     2430  2827 (2)  C L1M4_orf2#LINE/L1   (144)   764   366  

C chr2_81693577_8   2827 TGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAACAAATGGTGCT 2778
                           v   i v  vvv           i  vvi  v  i             
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

C chr2_81693577_8   2777 GGGAAAACTGGCTAGACATATGTAGAAAGCTGAAGCTGGATCCCTTCCTT 2728
                             v      v  ?v  i   i i  iiv     i    i    v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

C chr2_81693577_8   2727 ATACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTACATGTTAG 2678
                          i   v              i    i      i ?    i  v    v  
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

C chr2_81693577_8   2677 ACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAG 2629
                          v       i      vi i           v    ?i- v i -   iv
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGT 564

C chr2_81693577_8   2628 GACATAGGCATGGTCAAGGACTTCATGTCTAAAACACAAAAAGCAATGGC 2579
                            v v  vv i v   v ii   v ivv  vi    v       vvi  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

C chr2_81693577_8   2578 AACAAAGCCAAAATTCG-CAAATGGGATCTAATTAAACTAAACAGCTTCT 2530
                               ivv    v v -i    v   ii v  i   v v  v i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

C chr2_81693577_8   2529 GCACAGCAAAAGAAACTACCACCGGAGTGAACAGGCAACCTACAGAATGG 2480
                          ii vv    i  v    i  vvii      v  i     i         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

C chr2_81693577_8   2479 GAGAAAATTTTTGCAATCTACTCATCTGACAAAGGGCTAATATCCAGAAT 2430
                                 v       vii ivi      i  i  i  vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

Transitions / transversions = 0.98 (52 / 53)
Gap_init rate = 0.01 (3 / 399), avg. gap size = 1.00 (3 / 3)  


2804 24.21 5.43 2.71  chr2_81702920_81705641     1347  2230 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81702920_8   1347 TGGGAAGACATCCTGTGTACGTGGATTGGAAGACTTAATATTGGTAAAAT 1396
                            i    i    ii   v i                      v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81702920_8   1397 ATCTATGCTACCCAAAGGGATCTACAGATTCAATGGAGTCCCTGTCAAA- 1445
                         iv v  i  v      vv               i v i     i     -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81702920_8   1446 TCTCAATGGCATATTTTATAGAAAT-GA-AAGC-AATTCTACAATTCGTA 1492
                           i  iiv  v v    ii      -  -    -i  i   v     i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_81702920_8   1493 TGAAACCTTGAAGAATTATGACTATCCAAATCAATCTTTAGAAAGAAAAA 1542
                           i  vivii i i iivv  v  v     v       v i      i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_81702920_8   1543 GAAAGCTGAAGGCATCACACTTCCTAATTTCAAAATATATTACAATGCTA 1592
                         v    i  i   vv          i          iv  i     v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_81702920_8   1593 CAATAACCAAAATTGTATGGTACTTTCATAAAAACAGATATATAGACCAA 1642
                           i   i   i iv  i       vv     ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_81702920_8   1643 TAGAACAGAAT--A-----CAGA----------------TATAGTCAACT 1669
                          i   i     -- -----    ----------------   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_81702920_8   1670 GATCTTCAACAAGGAAGTTAATAATAT---ATGATCAAAAAATTACGTTT 1716
                            i   i      iv ii  v vi  ---   ivv   i   - -  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT-A-GTCT 398

  chr2_81702920_8   1717 TTTCAATAAATTCTGGTGGGAAAATTGGATATTCACATGAAGAAGAA-AA 1765
                               i    vv  v     v  i      ?i      v i     -i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_81702920_8   1766 AGTGAGATCCTCATCTTACACCATATAAAAAAATCAAATAGAAATGAATT 1815
                            vi  i  ii i  i          v      i  v vi     i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_81702920_8   1816 AAATATTTAAATGTAAAATCTGAAATTTTAAAACTCCTAGGAGGAAATAT 1865
                          ? v ii         i v  i   i v        i   i  i   i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_81702920_8   1866 ATGGA-AAATGCTTCAGAATACTTGT-TTCGAAAATTATTTTATGCATAT 1913
                          v ?i-    -    ivi i-    v-  v iv   vi   iv iv    
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_81702920_8   1914 GACACTAAAAGCATAGGCAACAAAAACAAAATTAAACAAGTAGAACTACA 1963
                              i       i i         iv    v  i i  i v i   v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_81702920_8   1964 TCAAACTGAGAAGCTTCTGCAC---AAAG---------AAGAAAATAACA 2001
                              v v i  i   i  ii ---    ---------      i i --
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA-- 694

  chr2_81702920_8   2002 GAGGATAAAGGTCTAAATAATGGAATAAAATATTTTTGAAATGCATATTT 2051
                         i i  i  ---i i v v     i v         vii  viii    i 
  L1M4_orf2#LINE/    695 AAAGACAA---CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_81702920_8   2052 GATAAGTAATCAGTTTCCAAAATGTATAAGAAACTCCTACAACTCAATAC 2101
                               vi iiv  v    i   i     ii     i            -
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA- 790

  chr2_81702920_8   2102 AAAAAACAAAGCAAAACAGAACTAATAACCCAATTTACAAATGGGCAAAG 2151
                         ----- i   --  i   -----            ? v            
  L1M4_orf2#LINE/    791 -----ATAAA--AAGACA-----AATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_81702920_8   2152 AACTTAAATAGATATTTCTCCAAAGA---CATACAAATAGCCAACAGGTT 2198
                         i i  i      i             ---i        i     i i iv
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_81702920_8   2199 TATTAAAACAAATGCTCAATGCCACCAATCAT 2230
                         i  v    --i        iii  ????????
  L1M4_orf2#LINE/    879 CATGAAAA--GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (140 / 70)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.00 (72 / 24)  


1482 24.40 1.98 3.08  chr2_81776216_81778853       41   495 (2143)  C L1M4_orf2#LINE/L1   (286)   622   173  

C chr2_81776216_8    495 TAGCCAAAACAATCCTAAGCAAAAAGAACAAAGCTGGAGACATCACGCTA 446
                                       i i iv  i          i     ivv    i  v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

C chr2_81776216_8    445 CCTGGCTTCAAACTATACTAAAAGGCTACAGTAACCAAAACAGGATGGTA 396
                           iiii      viv     v  i          i   i    vi     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

C chr2_81776216_8    395 CTGGTACCAAAACATATATATAGACCAGTGGAACAGAGCAGA-AGTCTCA 347
                             i iv ii i v i       i  i     i   iiv  -    -  
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC-CA 321

C chr2_81776216_8    346 GAAATAACACCACACATCTG----CAACTGTCTTATCTTTGACAAACCTG 301
                                vv   i    i i----   i  ----  i  i     ivv  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTG----ATTTTCGACAAGGGTG 367

C chr2_81776216_8    300 ACAAAAATAAGCAATGGGGAAAGGATTCTGTATTTAATAAATGGTGTTGG 251
                         v   i vi vv            i  vv v v  i  i        i   
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

C chr2_81776216_8    250 GAAAACTGGCTAGCCACATGCAGAAAACTGAAACTGGACCCCCTTCCTTA 201
                           v      v  ?         i  i v    ii        - v   i 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC-TACCTCA 466

C chr2_81776216_8    200 CACCTTATACAAAACTTAACTCAAGATGGACTAAAGACTTAAACATAAGA 151
                             v         v         i     ii ?    i    ii     
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

C chr2_81776216_8    150 CCTAAAACCATAAAAAAAAAACCCTAGAAGAAAACCTAGGCA-ATACCAT 102
                         v       i      v-----i i           v    ?i- v i - 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAAC-----TCTTAGAAGAAAACATAGGNGTAAATC-T 560

C chr2_81776216_8    101 TCAGGACACAGGCGTGGGGAAACACTTCATGAATAAAACACCAAAT---C 55
                           iv   viv  vv i  v  vvii   v ii   vi        v--- 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

C chr2_81776216_8     54 AATGGCAACAAAAG 41
                           --          
  L1M4_orf2#LINE/    611 AA--GCAACAAAAG 622

Transitions / transversions = 1.45 (64 / 44)
Gap_init rate = 0.02 (10 / 450), avg. gap size = 2.30 (23 / 10)  

2738 26.43 4.58 0.80  chr2_81776216_81778853     1273  2146 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_81776216_8   1273 GAAAAAACATTCCATGCTTATGGAT-AGAAAA-TCAATAT-G--AAAAAG 1317
                          i   i i  i     i i      -i   i - i     - --  i v 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_81776216_8   1318 GCCATACTGTCCAAAGTATTTTGTAGACTCAATGCTATCCCCATCAAGCT 1367
                           v     vi     v iv i ii   i    i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_81776216_8   1368 ACTATTGGCTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTCAT 1416
                         v i viv  i  i  ii     v v  v  i--  - iii    v     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCAT 149

  chr2_81776216_8   1417 ATGGAACCAAGAAAGGG-CCC-GTATAGCCAATACAAGCCTAAGCAAAAA 1464
                               -- v v     -   - v        v    v i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_81776216_8   1465 GAACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTAAAAGG 1514
                                 i     ivv   ii  v  ii i      viv     v  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_81776216_8   1515 GTACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGATATATAGAC 1564
                         v        i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_81776216_8   1565 CAATGTAACAGAATAGAGGCCTCAGAAATAACACCACACATCTGTAACTA 1614
                              v  i     v   ivii         vv   i    i i iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_81776216_8   1615 TCTTATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 1664
                         vi v  i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_81776216_8   1665 TATTTAATAAATGGTGTTGGGAAAACTGG---CCCACATGAAGAAAACTG 1711
                          v  i  i        i     v      ---?       v i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_81776216_8   1712 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAAATGGGT 1761
                           ii    i    v   i     v                        i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_81776216_8   1762 TAAAGACTTAAACATAAGAGCTAAAACCATAAAAACCCTAGAAGAAAACC 1811
                         i ?    i    ii             i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_81776216_8   1812 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 1860
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_81776216_8   1861 AACACCAAAAGCAACTGCAACAAAAGCCAAAATTGCCAAATGCGA----- 1905
                         i            vvv          vv     v vi    vv  -----
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_81776216_8   1906 TCAA--TTAAAGAGCTTCTGCACAGCAATAGAAACTATCATCAGAGTGAA 1953
                             --     i -   i  ii vv   vi  v       vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_81776216_8   1954 CAGGCAACCTACACAATGGGAGAAAATTTTTGCAATCTCTTCATATGGCA 2003
                         v  i     i   v             v       viiv vi  v  ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_81776216_8   2004 AAGGGCTAATATCCAGAATCTACAAAGAGCTTAAACAAATTTACAAGAAA 2053
                          i  i  vi          v  i     i  ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_81776216_8   2054 AAG---------------------TGGGCAAAGGATATGAACAGACTCTT 2082
                            ---------------------            v    i    vi  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_81776216_8   2083 CCCAAAAGAAGACATTTATGCAACCAACAAACATATGAAAAAAATGCTCA 2132
                          i v        i  vi viiii    i  i  i       i -      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCA 894

  chr2_81776216_8   2133 TCATCACTGGTCAT 2146
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (132 / 96)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 2.76 (47 / 17)  


2810 23.00 3.66 3.78  chr2_81818484_81820349      501  1374 (492)    L1M4_orf2#LINE/L1       36   908 (0)  

  chr2_81818484_8    501 TAATAAT-TTATAATGCCCATACTACCAAAATTAATCTACAGATTAAATA 549
                              v -   vi   v v     v  v     i           v  ii
  L1M4_orf2#LINE/     36 TAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACG 85

  chr2_81818484_8    550 TGATACCTGTTGAAATCCCAGTGGTATTTTTTTAACAAAT--ACAAA--- 594
                         ii  v   i ii         iv iv      vv v    --    i---
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chr2_81818484_8    595 -----AAAATTTATGTGGATCC-CAAAAGACCCCAAATAGCCAAATCAAT 638
                         -----      i  i    vvi-   ii     vi          v    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_81818484_8    639 CTTAAAAAAGAA---CTAATATGGAGGCCTCATACTTCT-GATTTCAAAA 684
                            i        --- v  vv      v    i     i-i         
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_81818484_8    685 TATATTACAAAGCTACAGTAATGAAAACAGTATAGGACTGGCATAAAGAT 734
                         iv  i                 v  i     i i v          i   
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_81818484_8    735 ATGATAAGTAGAACGATCAAACAGAAT--AGAGCTCAGAAATAACTTCAG 782
                          -  i vi    v i  vi  i     --    ii         vii  v
  L1M4_orf2#LINE/    286 A-GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_81818484_8    783 GAATATATGATCAACTGATCTTCAACAAGGGAGCCAGGAATATATGATAG 832
                         iv  v    i    i    i   i       v    i  vi  vii  i 
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_81818484_8    833 AGAAAGGATAGACTCTTCCAGAAATGTTTATGAGAAAACTGGATATCCAC 882
                         i     i    v  i   v v     v vv  i  v         ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_81818484_8    883 ATGAAAAAAGAATGAAATTGGATTCTT-TCTTATATCACTCA-AAAAATT 930
                            v    -       i     ii i -i  i i i  ivi -       
  L1M4_orf2#LINE/    435 ATGCAAAA-GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_81818484_8    931 AACTCAAAATAGAGTGAAGACTTAAGTGTAAGACCTAAGACCATATAAAA 980
                                   i  vii?    i   i       v    i  --       
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC--TATAAAA 531

  chr2_81818484_8    981 CTTTCAGAAGACAACATAGAAGGAAAGACTCATGACACTGTTCTTGACAG 1030
                           i i      v       i? v   vvi  i    vi  vvi v i  i
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_81818484_8   1031 TGTTTTCCTGAATATGACACTGAAAGCACAGGGAACAAAAGCAAAAATAG 1080
                           v    i ii         ii        i v        v        
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_81818484_8   1081 ACAAGTCAGGCTACCTCAAA-TTAAAAAAGCTTCTGCATAGCAATGGAAA 1129
                          i  i ii i  v v     -       --   i  iiivv   v   v 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACA 679

  chr2_81818484_8   1130 --A--AAGTCACAGTGAAAACAAAACCTATAGAGTAAGAGAAAATATTTG 1175
                         -- --   -- v        v v    i i   i ii             
  L1M4_orf2#LINE/    680 CTATCAAG--AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_81818484_8   1176 CAAGCCATATATGTGATAAATG----GT-TCTAAAATATATAGA-AACTC 1219
                            ii       v      iv ----  -  i i        i -     
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_81818484_8   1220 AAACC-CTCAATACTAAAACAGAAAACCCAAAACATTAAAATAAAACCTT 1268
                         vv  v-       v     -   -----    ------------------
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAA-AGA-----CAAA------------------ 803

  chr2_81818484_8   1269 ATAATCTAATTTTAAAATGGGTTAAAGACTTAAACAGGCATATTTCTAAA 1318
                         -   i i    ?v        iv  i  i  i  i  i   v i  i   
  L1M4_orf2#LINE/    804 -TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_81818484_8   1319 GAAGACATACAAATTGCCAATAGGTATTTGAAAAGATATTTAATGTCACT 1368
                              i        v       i i iv         ii i  ii   ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_81818484_8   1369 AATCAT 1374
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.59 (121 / 76)
Gap_init rate = 0.03 (24 / 873), avg. gap size = 2.71 (65 / 24)  


3154 26.59 1.56 0.56  chr2_81863365_81865323      569  1467 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81863365_8    569 TGGAAGAACATTCCATGTTCATGGATAGGAAGAATCAATATTGTGAAAAT 618
                              ii i  i              v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81863365_8    619 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATTCCCATCAAGC 668
                            v     v     iv i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81863365_8    669 TACCAATGACTTTTCTTCACAGAATTAGAAAAAACT-ACCTTAGAGTTCA 717
                          v   iivi i   i  -i     v v  v  i-  - i i  i i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_81863365_8    718 CATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAAGCCTAAGCAAAAAG 767
                         i      viiv  ii  v  v v  v     i    v i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_81863365_8    768 AACAAAGCTGGAGACATCACGCT----GACTTCAAACTATACTACAAGGC 813
                                i     ivv    i  ----i i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_81863365_8    814 TACAGTAACCATAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 863
                                 i  vi    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_81863365_8    864 AATGGAACAGAACGGAGCCCTCAGAAATAACACCACACATCTACAACCAT 913
                                i    iv   vvii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_81863365_8    914 CTGATCTTTGACAAACCTGACAAAAAAACAAGAAACGGGGAAAGGATTCC 963
                         i    i  i     ivv  v   i v--  vvv  i        i  vvi
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGAC--CATTCAATGGGGAAAGAATAGT 396

  chr2_81863365_8    964 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1013
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_81863365_8   1014 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1063
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_81863365_8   1064 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1113
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_81863365_8   1114 CTAGGCA-ATACCATTTAGGCCATAGGCATGGGCAAGGACTTCATAACTA 1162
                         v    ?i- v i v ivv i  v i  i- i     v ii   v  iv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr2_81863365_8   1163 AAACACCAAAATCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 1212
                         vi         v  vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_81863365_8   1213 AGTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1262
                          vi   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_81863365_8   1263 CAGGCAACCTACAAAATGGGAGAACATTTTTGCAATCTACCCATCTGACA 1312
                         v  i     i   i          v  v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_81863365_8   1313 AATGGCTAATATCCACAATCTACAAAGAACTC----AAATTTACAAGAAA 1358
                          iv i  vi      v   v  i         ----  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_81863365_8   1359 AAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1404
                           i    ----   v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_81863365_8   1405 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 1454
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_81863365_8   1455 CATCACTGGTCAT 1467
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


2152 26.59 3.50 4.16  chr2_81882776_81888131      493  1406 (3950)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_81882776_8   1406 TGGAAATTCATTTTCTGCTCACATATTAGAAGAATCAATATTGTTAAAAT 1357
                               vvi  iiiv  i   iiv   i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_81882776_8   1356 GACCATGGTGCTCTAAGCAATCTATAGATTCAACACAATTCCTATCAAAT 1307
                          i v  iv v i v  vii     i         i    i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_81882776_8   1306 TACCAACATCGTTTTTCACAGTATCATTAA-AA----ATTCTAAAATTCA 1262
                          v   i vv v     ii   v --   i -  ----  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

C chr2_81882776_8   1261 TACAGAACCAAAGAAGAGCCAGAATTGCTAAAGCATTCCCAAGCAAAAGG 1212
                           ii   viiv iii  v       v  i   i  v  iii iv  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr2_81882776_8   1211 AACAGAGCAGGAAGCATCACATTACCCGACTTCAAACTATACTACAAGCC 1162
                             i  iv   i vv     i v   i i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr2_81882776_8   1161 TGTGGTAACCAAAACAGCATGGTACTGGTATAAACATAGGAACGCAAGTC 1112
                          iii    i   i    ii         i    iv    iv iii ii  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr2_81882776_8   1111 AATGTAATAGAATAGAGAACCCAGAAATCAAACCAAACATCAAACACCTA 1062
                             v        v    ii        -     ---   ---   ii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAAT-AAACC---CAT---ACATTTA 341

C chr2_81882776_8   1061 ----CAACCAATATTCAACAAATTCAACACAGATAAA-CAATGGGGAAAG 1017
                         ----   iii  v   i    ivviiv  -   iv v-            
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAG 390

C chr2_81882776_8   1016 GACATTCTATTAAATAAATGGTGCTGGGAAAACTGGCTAGCCACATTCAG 967
                         i i v   v  v  i              v      v  ?      v  i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

C chr2_81882776_8    966 CAGAAGGTAACCAGACCCTTATATTTCAACATATACAAAAATTAAATCAA 917
                         v    v v iiii     i  iv iv  v                v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

C chr2_81882776_8    916 GATAGACTAAAGACTTAAGTGTAAGACTTTAAACTACAAAAACCCTA--A 869
                         i  i  ii ?    i   i       vi v      i    vi i  -- 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

C chr2_81882776_8    868 GAAAACTCATAGGAA-AACTCTTCTGGACATTGACCTACGCAAAGAATGC 820
                               --     ?i-  v     vv   v   ivi  v    v iv v 
  L1M4_orf2#LINE/    541 GAAAAC--ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

C chr2_81882776_8    819 ATGAGTAAGACTTAGAAAGCAAATGCAA-----ACAAAAATAGACAAATG 775
                         v iii  v   vivi      v v    -----iv         i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

C chr2_81882776_8    774 TGACTT------AGTTAAAGAATTTTTGCATAGCATAAGAAACAATCAAC 731
                         v     ------ i     -  i     iiivv  v i  v  v     v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAG 687

C chr2_81882776_8    730 AGAGTAAAGAGATAACTTACAGAATGGGAGAATATATTTGCAAATC-TAT 682
                          i   i  i   i   ii              v             -   
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

C chr2_81882776_8    681 AAGGAATTTAATCAATAAGACAAAACAACATTAAAAATCTATAAGGAATT 632
                          ----- i i  -  -ii   ----ivii  iv i   v     i   i 
  L1M4_orf2#LINE/    738 A-----TCTGAT-AA-GGGAC----TTGTATCCAGAATATATAAAGAACT 776

C chr2_81882776_8    631 T----AA-TCAATAAGACAAAACAACATTAAAAATCTATAAGGAATTTAA 587
                         i----  -       --i    vi   --  v  i i ------   ?  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAA--TAAAAAGACA--AATAACCCA------ATTWAA 816

C chr2_81882776_8    586 TCAATAAGACAAAACAACATTAAACAGACAATTCTCAAAAGACAACATAC 537
                         -v   ii -    i-i i-  i  i     v     v     vi i    
  L1M4_orf2#LINE/    817 -AAATGGG-CAAAG-GAT-TTGAATAGACATTTCTCCAAAGAAGATATAC 862

C chr2_81882776_8    536 AAGTCGTAAAGAA--ACATGAAAATATGCTCAGAATCACTAATCAT 493
                           i v iv  v  --         v       iv    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.33 (70 / 30)  

2606 19.84 12.43 0.66  chr2_81882776_81888131     4114  4869 (487)    L1M4_orf2#LINE/L1       64   908 (0)  

  chr2_81882776_8   4114 AAATTAATGTATGCATTCAGTTCAATCCC-ATCAAAATCCTAACTGCCTT 4162
                              i  v  iiv     iiv       -          i i       
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_81882776_8   4163 TTTTGTAGAAATTTGCAAGCTG-----------------------CAA-- 4187
                              i       vi       -----------------------   --
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_81882776_8   4188 -ATCTA-------------AATTTTGTAGAA---------ATTTGCAAG- 4213
                         - i i -------------   i   v i  --------- v   v i -
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_81882776_8   4214 CTGATCCTTTTCAATTTTAAGACTTACCTCGAAACTACTCTTTTCAAAAC 4263
                           v iv   ii      i  i      iv i  i    vv vv    i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_81882776_8   4264 AGTGTGGTAGTGACATAAAGATAGACATATAGACCAAAAAGAATAGAATC 4313
                                  v  i     i              i   vi-         i
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG-GAATAGAATT 312

  chr2_81882776_8   4314 GAAAGTCCAGAAATAAACTCA-A-GTTTTTCGTAAATTTATTTTCAAAAA 4361
                           i               i  - -i   v v  v    v      i v  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_81882776_8   4362 GTTTTCCAAGACAAGTAAATGGGAAAGGAACCCTCTTTTTTAGCAAATAA 4411
                          vv v       v v v      i  i   ivv      i- i     ii
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC-AACAAATGG 411

  chr2_81882776_8   4412 TGCTGGGACAACTGGATATCCAAATGCAAAATCAT-----------CCTA 4450
                                           ?   v        vv  -----------    
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_81882776_8   4451 CCTCACAACACGCACAAAATTTAACTCAGAATTGATCAAAGAACTGCATT 4500
                                v  iii      v        i   v     ?   v  iv  v
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_81882776_8   4501 TAAGAGCTAAAATAATAATACTCTTAGAACA---TATAGATATAAATCTT 4547
                                     iv    v          v ---i    i?i        
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_81882776_8   4548 ----AACATGGATTATGTAATTATTTCCTAGAT-TGACAC---ACACACA 4589
                         ---- v v   i   v i   vi    i     -      --- vi    
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_81882776_8   4590 AA-AACACCAAAGAAAAA---GATAAATTTGACTTTATCAGGAT-AAAAA 4634
                          i-    --         ---        v     i    ii  -     
  L1M4_orf2#LINE/    612 AGCAACA--AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_81882776_8   4635 -TTTTGTTCTTCAAAG-ACACTATTAA-AAAGTGAAAATGTAAGTCCGAG 4681
                         -      v        -       i  -          vii  vi vv  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_81882776_8   4682 AATAGTAGGAA-TATTTACAAATAATTTACCCAATAAGAATCTAATATCT 4730
                            i v  i  -     i     v  v  i ii     iiv  vi    i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_81882776_8   4731 ACAGTATATTAAAGAACTC--ACAACTCAACAATAAAAAAACAAACAACC 4778
                          v i     -         --         i        i     i    
  L1M4_orf2#LINE/    760 AGAATATAT-AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_81882776_8   4779 TAATTTAAAA-TGGATA-----T---AATAGATATTTCTATAAAGAAGAT 4819
                         i    ?    -   ii ----- ---      i      vi         
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_81882776_8   4820 ATACAGATGGCCAATAAGCTCATAAAAAGATGCCCAATGTTATTAATCAA 4869
                              i             v   i         i   ii i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (86 / 60)
Gap_init rate = 0.03 (28 / 845), avg. gap size = 3.54 (99 / 28)  


2698 28.89 1.90 0.22  chr2_81894539_81899463     3541  4433 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81894539_8   3541 TGGAAACACATCCCATGTTCATGG-------GA-TCAATGTAGTGAAAAT 3582
                               v i               -------  - i   i v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81894539_8   3583 GACCATACTGCCAAAAGCAATCTACAAATTCATTGCAATTCCCAGCAAAA 3632
                          i v     v  v   vii       i     vi     i  i v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81894539_8   3633 TACCACCATTATTCTTCACAGAACTGGAAAAGGCAATCCTAAAATTCATA 3682
                          v   v vviv  i  ii     v v  v   vii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_81894539_8   3683 TGGAACTAAAAAAGATCCTGCATAGGGAAAGCAAGACTTAAGCAAAAGGA 3732
                              v iv  ii  i  v v    vv   i   v-   i iv  i i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGA 199

  chr2_81894539_8   3733 ACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATACTGTAAGTCC 3782
                              vi      vv     i v  ii i      viv    ii  iv i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_81894539_8   3783 ATAGTCACAAAAACATCTTGGTACTGGTATCAAAATAGGCACATAGACAA 3832
                          i   v iv  i   viv         i  v ii    i  i     iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_81894539_8   3833 ATGGAACAGAATAGAGAACACATAAATAAAGCCAAATACTTACAGCCACT 3882
                               i     v    iiv  v       v   v i i   ii i  v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_81894539_8   3883 TGATCTTTTACAAAGCAAACAAAAACAT-AAGTGGTGAAAGGACACCCTA 3931
                             i  iv    i vviv   i v   -v i   v     i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_81894539_8   3932 TTCAGCAAATTATGCTGGGATAGTTGACAAGTCATATGTAGAAGGATGAA 3981
                             i     vi        i ii  ivv ?i  i   i i   i     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_81894539_8   3982 ACTGAATCCTCATTTCTCACCTTATACAAAAATCAACTCAAGATGAATCA 4031
                         ii  i i  ii ii  v    v           i       i   i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_81894539_8   4032 AAGACTTAAATATAAGACCTGAAACCACAAAAATTCTAGAAGGTAACATC 4081
                         ?    i     i     v  i    i i    v ii      iv     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_81894539_8   4082 AGAA-AAACCCTTGTAGACATTGGCTTAGGCAAAGACTTCATGACTAAGA 4130
                         i ?i-   i i i  -   v    v        v ii   v iiv  v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_81894539_8   4131 ACCCAAAAGCAAATGCAACAAAAACAATGATAAATAGGTGGGACTTAATT 4180
                         vv         v v         iv  vi   i   ii v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_81894539_8   4181 TAACTAAAAAGTTCATGCACAGCAAAAGAAACAATCAGCAGAGTAAACAG 4230
                         v  v v    ii iv  ii vv    i  v  v    iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_81894539_8   4231 AAAAACCATAGAGCAGGAGAACATCTTCACAA-TC-TACATTTGACAAAG 4278
                          v  v   i   iii      v  v  ii   -  -  i  i   i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_81894539_8   4279 -ACTAATATCCACAATCTGCAAGGAACTTACACAAATTAGTGAGAATAAA 4327
                         -   vi      v   v ii  i     ivi    v i i i v  v  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_81894539_8   4328 ACAA----TGCCATCAAAATATGGGCTAAGGACATTACTAGACAATTCTT 4373
                             ----iv v  i?   v      v     iv v v      v    i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_81894539_8   4374 AAAAGAAGATATCCAAATGGCCAACAAACATATGAAAGAATGCTCAACAT 4423
                         v           v           i  i  i      ii           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_81894539_8   4424 CACTAATGAT 4433
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.35 (146 / 108)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


1729 23.37 14.46 5.06  chr2_81909938_81914239.rev     2983  3812 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81909938_8   2983 TGGACAGTTATTCCATATTCTTGGATAGGAAGACT--ATATT---AAGAT 3027
                             v  v   i    i   v     v        --     ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81909938_8   3028 GATAATTCTTCCCAGCTTGAGCTACACATTTAACACAATCCCAATAAAAA 3077
                          ii   v  i    iv    v     v   i   i       v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81909938_8   3078 TCTCAGCAATTTAGTTTATGGATATCAACAAACCGATTCTAAAGTGTGCA 3127
                           i    viii vv   iii  v  ii    i i   i     i viii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_81909938_8   3128 AGAAAAGATAAG--ACGTAGCAAAGCCAAG--------------GAGG-- 3159
                         v i   vii   --  vi  v v      i--------------  i --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_81909938_8   3160 CAATATTG--------ACAT-----GACTTCAAGATTTTCTATAAATCTA 3196
                            vi   --------   i-----i i     i i  v   i   v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_81909938_8   3197 TGGTGATCAAGATAGTATGTCAAT--CATGAA-ATAAATACATA----AA 3239
                         ii  i       i   i  vi v --   i i-   i i i   ----  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_81909938_8   3240 TGGAACAGAATAGAGAGCCCAGAAATAGACCTATACATATATAGTCAACT 3289
                              i     v     i         i   i      v   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_81909938_8   3290 GATTTTTGACAAAGG---CAA-----TTCTATGGAGAAAAAACAGTCATT 3331
                               i     i  ---   -----   v    i    i  i    v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_81909938_8   3332 TTAACAAATG-TG--GAAACAAGTGAACATCCGCATTGTGTGCGTGTGTG 3378
                          i        -  -- ii    v  i i ?  i   -----  i------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-----GCA------ 439

  chr2_81909938_8   3379 TGTGTGTGTGTGTGTTTGTGTGTGGAGAGAGAGAGA--GAAA----ACCT 3422
                         ------------------------- i   iv  ii-- i v----    
  L1M4_orf2#LINE/    440 -------------------------AAAGAATGAAGTTGGACCCCTACCT 464

  chr2_81909938_8   3423 T---CCATA-AAAGAAATTAACTCAAAATGAATCACAGATCTAACTTTAA 3468
                         i---     - v i                i    ?   i    v v   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_81909938_8   3469 AA-TTCAAACTGTTCAATTTCTAGAAGA-----TAGGAAGAAATCTAGCT 3512
                         i -i v     i vv  i ii       -----    ?iv      vvv 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_81909938_8   3513 GACATTAGATTGGACAATGACTTTTTAGATACAA----AAAAACATAATT 3558
                            v  i i  i i     ii  i       ii ----    i  i  vi
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_81909938_8   3559 TATCAGAGAAAACAT-GATGTAATAG--TTCATTAAAAAGTTACA--CTT 3603
                         v iv i      v  -   iv v i --     i    --   v --   
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA--TTAAAAACTT 662

  chr2_81909938_8   3604 TT-----CAAAAGAACAG-AT---GAAAGTAAAAAGAATTGCAACAGACA 3644
                           -----iv    i   v-  ---      i      ----    vv   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA----CAACCCACA 708

  chr2_81909938_8   3645 GA------GAATAT-TTTTCAAAT-A-ACATCTGATAA----CTGGTATT 3681
                           ------   v  -   v     - - i         ----  v    i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_81909938_8   3682 ---ATTAT-TAAGGG--TCTTAATACT------TAAGAAAACAAA----- 3714
                         --- v   -   i i--     vv   ------   i  i     -----
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_81909938_8   3715 CAGTAAACAAATGGGCAATAGATCTGAACAGACAC--CTCTAAGGAAGAC 3762
                           i v? v          vi   i    i     i--   i  i     i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_81909938_8   3763 ATACACGTGGAAAGCAAGCACAGAAAAAGATGCTCAGCATTGTATGTCAA 3812
                              vi   vv ii       vi            i   ii????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (123 / 67)
Gap_init rate = 0.05 (42 / 908), avg. gap size = 3.86 (162 / 42)  


2624 25.33 9.39 1.43  chr2_81941833_81945717.rev     2553  3393 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81941833_8   2553 TGGAAAGATACTCTGTGTTCATGAATTGGAACACATAATACTGTTAAAAC 2602
                                   ii ii        i       v  v     i      i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81941833_8   2603 AGCCATACTACCTAATGCAGTCAGTACATTCGGTGCAATCCCTATACAAA 2652
                         i  v     v  i  vviii  vii v    iii           vv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81941833_8   2653 TTCTAATGGCATGTTTCACAGAAATAGAAAAAT--ATTCTAAAACCTATA 2700
                          i i iiv  v v   ii       v  v  ii--  i      iii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_81941833_8   2701 TTGAACTATACACACATAAAAC--AAATAGCCAAATCAATGTTGAGAAAC 2748
                          v   --  i  --- vii v --i          v    v    i   v
  L1M4_orf2#LINE/    151 TGGAA--ATGCA---AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_81941833_8   2749 ACGAACATAGCTTAGGGCATCACATTACATTGTTTCAAAATATACTG--- 2795
                          v     v  i vii  vv     i v vivi        iv    i---
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_81941833_8   2796 AGTTATAGTAATGAAAGCAACATTGTACTGACATAAAAACAAATGTATAG 2845
                           i  i      v  ii  iii v      i     ii i i ii     
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_81941833_8   2846 GTCACTGGAACAGAATAGGCAGCCAAGAAGTAAATATACACAGTTATTGT 2895
                         i   v     i     v iv  i v    i    ivi i   v    v  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_81941833_8   2896 CAATTGATATTTGACAAAGTTGCCAAGGCCTTTGAATGAGGAAAGAAAGA 2945
                                 v  i     i v       i  v  v    i        -v 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TA 394

  chr2_81941833_8   2946 GTCTCTTCAATAAATGGTGTTGGGAAAACTGAGTGTCTATGTATAGAAGA 2995
                             i     i        i     v     ii i? i ii ii i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_81941833_8   2996 ATGACAATGGAC-------------------------------------- 3007
                             viv     --------------------------------------
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_81941833_8   3008 --------ACTTAACTGTTACACCTGAAACTGTAGAAGTCGTAGAAGAAA 3049
                         --------  i   v   v v v  i     i  i  v  v         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_81941833_8   3050 A-----GGGAAAAGCTTCTTGACATTTGTCTTGGAAATGATTTTTTGAAC 3094
                          ----- ? v   v    v    v  v vi v  v    i   i  ii i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_81941833_8   3095 ATGACCTCAAAAGCACAGGCAACAAAAGCAACAATGGACAA--TGAAATT 3142
                              vi          i          v  v   i  i  --  i v  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_81941833_8   3143 GTATCAAA-TTAAATAACTAACTTCTGCACAGCAAA---------CAACA 3182
                         -i      -     -----     i  ii vv    ---------   v 
  L1M4_orf2#LINE/    645 -CATCAAAATTAAA-----AACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_81941833_8   3183 GAGTAAAAAG----CCTATGGAATGTGAGAAAATATTTGTAAACCTTACT 3228
                         i   i     ----  i ii     v             i   i v  iv
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_81941833_8   3229 TCTGATAAGGCATTAATTTCCAAAATAAATAACAAACTCACACATCTCAA 3278
                                   v i vi v    i    v    vi     vi   v     
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_81941833_8   3279 TGTCAAGAAAACAA----CCCAATT-AAAAATGGGGAAAAGACTTGAACA 3323
                          ivi  i  i    ----       -         v   i  i     i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_81941833_8   3324 GATATTTTCCAAAAGAAAACATACAAATGGCCAACAAGTATATGAAAAAA 3373
                           i    ii v      i i              i   i i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_81941833_8   3374 TGCTCAACATCACTAATCAT 3393
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (130 / 81)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 5.69 (91 / 16)  


1819 24.11 7.68 2.14  chr2_81969309_81974190     3227  3786 (1096)    L1M4_orf2#LINE/L1        1   591 (317)  

  chr2_81969309_8   3227 TGAAAAGACATCCCATGTTCATGGATTGGAAAAAAATAATATTGTAAAGA 3276
                           i     i                      i vv-         v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACT-TAATATTGTTAAGA 49

  chr2_81969309_8   3277 TGATCATACTATAATACCCAAAGTAAAGAACAGATTTAATGCAATTC-TA 3325
                           iiv     v-----      v i vvv       i  i     i -  
  L1M4_orf2#LINE/     50 TGGCAATACTC-----CCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_81969309_8   3326 T-AAAATGACTAATGTCATTCTTCACAGAAAT-GAAAAA---ATCCTAAA 3370
                          -     vv viv  i -  i  ii       -  v  i---        
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_81969309_8   3371 ATCTGTATGGAACTACAAAAGACTCTGAATAGTCAAACCAATCTTAGCCA 3420
                           iii       v i   ii   i v      i    v       iivv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_81969309_8   3421 AAAAGAACAAAGCTGAAGACATCGTACTAGTAAATTTCAAAATATATTAC 3470
                          i          i  i  ivv  ii   vviv          iv  i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_81969309_8   3471 AAAGCTA---TAATCAAAATAGCAATGGTACTGGCATAA----AGACACA 3513
                                ---       i i  ii-              ----     i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTG-TGGTACTGGCATAAGGATAGACATA 292

  chr2_81969309_8   3514 TTGACTAACCAAATAGAGTT-----CCCAGAAACATGCTTATACATCTAT 3558
                          v  ii  ivi      i  -----i       i vi ii      i   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_81969309_8   3559 GGCTTAACTGATTTTTGACAAG----CCAAGA--------------AAAC 3590
                           - i  i       i      ----      --------------  iv
  L1M4_orf2#LINE/    343 GG-TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_81969309_8   3591 ACAATCTCTTCAATAAATGGTATTGGGAAAACTGGATATCCACACACAGG 3640
                          i i   i     i       ii     v         ?     ii  ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_81969309_8   3641 -GAGTGAAAATGGATTCTTACC-----CTTTATATATGAATCAATT-AAA 3683
                         -  i    iv    ii i    ----- iv    i vi   i  i -   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_81969309_8   3684 ATGAATTAAAGTTATAAATGTAAGATCTGAGACTGTAAAACTACTAGAAG 3733
                            i  i ?  viv           v  i i   i       vi      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_81969309_8   3734 AAAACATACCATGCAAAACTCCATGACATTGGTTTGGGTAGTAATATTTT 3783
                                 v-i? i   v  i i    v    v  i  i i ii --  i
  L1M4_orf2#LINE/    542 AAAACATAG-GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT--TTC 588

  chr2_81969309_8   3784 TTA 3786
                            
  L1M4_orf2#LINE/    589 TTA 591

Transitions / transversions = 2.22 (91 / 41)
Gap_init rate = 0.03 (19 / 591), avg. gap size = 2.89 (55 / 19)  

 642 28.75 3.51 2.56  chr2_81969309_81974190     4079  4391 (491)    L1M4_orf2#LINE/L1      593   908 (0)  

  chr2_81969309_8   4079 ACATGACCCCTAAAACACAGACAACCACAGCAAAAACAGACAAATGAGAG 4128
                          i     v  v   i    ii    v v  v     i   i    vi  v
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_81969309_8   4129 TGCATCAAACTAGAGAACTTTCTCACAGTAGAGGAAAT----AACTGAGT 4174
                          v       v vi i      ivii vvi i    v i----  vvi   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_81969309_8   4175 GAAGAGATACTTAAAACCTACAGA-TGGTAGAAAATAATTTTAGAAATCA 4223
                            i   i ------   i     -   v        --   iv      
  L1M4_orf2#LINE/    693 GAAAAGACA------ACCCACAGAATGGGAGAAAATA--TTTGCAAATCA 734

  chr2_81969309_8   4224 TACCTTGAATAAGAGACTAATATTCAAAAGATACAAGACACTCAAGTTAC 4273
                           iv ivi     i    vi   i  i  v   i  iiv    vviiv  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_81969309_8   4274 TCAATAAAAAGTAAACAAATAGCT--ATTTAAAT-TGAGTAAAGACATTG 4320
                                v  iv i       i i--   ?   v-  i i    ivv   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_81969309_8   4321 AATAGAC---CCTCAGAAGATGACATACAAATAACCAACAGATAAATGAA 4367
                                ---i   vi    v  i        ii    i iii v     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_81969309_8   4368 AAAACAGCAAACATCTCTAGTCAG 4391
                           i iiviv      v????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (52 / 37)
Gap_init rate = 0.02 (7 / 316), avg. gap size = 2.71 (19 / 7)  


3174 26.21 1.10 1.10  chr2_81979075_81984607     4134  5041 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_81979075_8   4134 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4183
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_81979075_8   4184 GGCCATACTTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4233
                            v     i     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_81979075_8   4234 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT---CCTTTAAAGTT 4279
                          v   iivi i  i  ii     -   -- v  i  ---   --   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCT--AAAATT 146

  chr2_81979075_8   4280 CATATGGAATCAAAAAAGAGCCTGCATTACCAAGTCAATCCTAAGCCAAA 4329
                                  viiv  ii  v  v v  vi    iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_81979075_8   4330 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 4379
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_81979075_8   4380 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 4429
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_81979075_8   4430 CCAATGGAAGAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 4477
                         i        v    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_81979075_8   4478 CCATCTGATCTTAGACAAACTTGACAAAAACAAGAAATGGGGAAAGGA-- 4525
                         i  vi    i  v     ivv  v   i v  vvv           i --
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_81979075_8   4526 GTCCCTATTTAATAAATGGTGCTGGTAAAACTTGCTAGTCATATGTAGAA 4575
                            -- v  i  i            v v    v v  ?i  i   i i  
  L1M4_orf2#LINE/    395 GTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_81979075_8   4576 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 4625
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_81979075_8   4626 TGGATTAAAGACTTACATGTTATACCTAAAACCATAAAAACCCTAGAAGA 4675
                              i ?    i  v    v v v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_81979075_8   4676 AAACCTA--CGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 4723
                             v  --? i  - i -   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_81979075_8   4724 GTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 4773
                         ivv  vi            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_81979075_8   4774 ATATAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 4823
                          iv v  i   v v  i i   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_81979075_8   4824 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATC 4873
                              v  i     i                 v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_81979075_8   4874 TGACAAAGGTCTAATATCCAGAATCTACAATGAACTCAAACAAATCTACA 4923
                            i  i  v  vi          v  i  v      vv    v  v i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_81979075_8   4924 AGAGAAAAACAAACAGCCCCATCAAAAAGTGGGTGAAGGATATGAACAGA 4973
                          v i   i     i i   v  i?    i    ii      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_81979075_8   4974 CATTTCTCAAAAGAAGACATTTATGCAGCCAGCAGACACATGAAAAAATG 5023
                                 v        i  vi viii    ii ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_81979075_8   5024 CTCATCATCACTGGCCAT 5041
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


2926 27.75 0.99 0.99  chr2_82055656_82060818.rev     3764  4671 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_82055656_8   3764 TGGAAGAACATTCCATGGTCATGGATAGGAAGAATCAATATCACAAAAAT 3813
                              ii i  i     v        v      v i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_82055656_8   3814 GGCCATAATGCCCAGGGTAATTTATAGACTCAGTGCCATCCCCATCAAGC 3863
                            v   v v    iiv i  i  i   i   ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_82055656_8   3864 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAACT---CCTTTAAAGTT 3909
                          v   iivi i  i  ii     -   -- v  i  ---   --   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCT--AAAATT 146

  chr2_82055656_8   3910 CATATGGAACCAAAAAAGAGCCCGCATTGGCAAGTCAATCCTAAGCCAAA 3959
                                  viiv  ii  v  v v  v v   iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_82055656_8   3960 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 4009
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_82055656_8   4010 GCTACGGTAACCAAAACAGCATGGTACTGATACCAAAGCAGAGATGTAGA 4059
                              i    i   i    ii        ii iv iiii   v  i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_82055656_8   4060 CCAATGGAACAGAA--AAGAGCCCTCAGAAATAATACCACACATCTACAA 4107
                         i        i    --i    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_82055656_8   4108 CCATCTGATCTTTGATAAACCTGACCAAAACAAG-AAATGAGGAAAGGAT 4156
                         i  vi    i  i  i  ivv  -    i  v v-v    i      i  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_82055656_8   4157 TCCCTGTTTAGTAAATGGTGCTGGGAAAACTGGCTGGCCATATGTAGAAA 4206
                         vvi  v  i ii              v      v i?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_82055656_8   4207 GCTGAAACTGTATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 4256
                         iv    ii  v i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_82055656_8   4257 GGATTAAAGACTTAAATATTAGACCTAAAACCTTAAAAACTCT-AGAAGA 4305
                             i ?    i     i v   v       iv     -    -      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGA 542

  chr2_82055656_8   4306 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGACAAGGATTTCATT 4354
                             v    ?i- v i -   iv   v v  vv i i   v i    v v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_82055656_8   4355 TCTAAAACAACAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGA 4404
                         vv  vi   v        vvi          vv        i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_82055656_8   4405 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAACAAAACTACCATCAGAG 4454
                         ii v  i   v v  i i   i  ii vv    vi v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_82055656_8   4455 TGAACAGGCAACCTACAGAATGGGAAAAAATTTTTGCAATCTACTCATCT 4504
                             v  i     i           i     v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_82055656_8   4505 GACAAAGGGCTAATATCCAGAATCTACAAACAACTCAAGCAAATTTACAT 4554
                           i  i  i  vi          v  i   v     vvi   v iv i v
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_82055656_8   4555 GAAAAAAAGAAACAACCCCATCAAAAAGTGCCTGAAGGATATGAACAGAC 4604
                         v     i v   i     v  i?    i  vvii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_82055656_8   4605 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGC 4654
                          i     v        i  vi viii     v ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_82055656_8   4655 TCATCATCACTGGTCAT 4671
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


2954 28.16 1.22 0.55  chr2_82084222_82090944.rev     5330  6231 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_82084222_8   5330 TGGAAAAACATTCTATGCTCTTGGATATGAAGAATCAATATTGTGAAAAT 5379
                               i i  i i   i  v     vv     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_82084222_8   5380 GGCCATACTGTCCAAAGTAATTTATAGATTCAGTGCTATGCCCATCAAGC 5429
                            v     vi     v i  i  i       ii  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_82084222_8   5430 TACCA-TTGACTTTCTT-CACAGATTTGGAAAAAACT-ATTTTAGACTTC 5476
                          v   -i  v    i  -  v i   ---i v  i  -  ii  i v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chr2_82084222_8   5477 ATGTGGAACCAAAAAAGAGCCCACATAGCCAAGATAATCCTAAGCAAAAA 5526
                           i     viiv  ii  v  viv        i i    i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_82084222_8   5527 GAACAAAGCTGGAGACTTCACGCTACCTGTCTTCAAACTATACTACAAGG 5576
                                 i     ivi    i  v  iivi      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_82084222_8   5577 GTACAGTAACTGAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5626
                         v        iii i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_82084222_8   5627 CAATGGAACGGAACAGAGGCCTCAGAAATAAGTCTACACATCTACAACCA 5676
                                 ii   iv   ivii         ii i i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_82084222_8   5677 TCTGATCTTTTACAAACTCAACAAAAATAAGCAATGGGGAAAGGGTTCCC 5726
                         vi    i  iv    ivviiv   i vi vv            ii vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_82084222_8   5727 TATTTAATAAATGGTGTTAGGAAAACTGGCTAGCAATATGCAGAAAACTG 5776
                          v  i  i        i i   v      v  ? v i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_82084222_8   5777 AAACTGGATCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGAAT 5826
                           ii    i    v   i i   v                   i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_82084222_8   5827 TAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5876
                         i ?    i           v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_82084222_8   5877 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5925
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_82084222_8   5926 AACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGAGATTTAA 5975
                         i            vvi         ivv     v  i    vi  i  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_82084222_8   5976 TTGAAATAGAAAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 6025
                          ii    vi   i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_82084222_8   6026 AGGCACCCTATAGAATGGGAGAAAAATTTTGCAATCTATCCATCTGACAA 6075
                           i  v  i i              vv       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_82084222_8   6076 AGAGCTAATATCCAGAATCTGCAAGGAACTTAAACAAATTTACAA-GAAA 6124
                         i ii  vi          v ii  i     ivv    v iv i  -i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_82084222_8   6125 AGAAAAA-AAC---ATTCAAAAAGTGGGTGAAGGATATGAACAGA-ACTT 6169
                            v   -   ---   ?     -    ii      v    i   - i  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTT 845

  chr2_82084222_8   6170 CTCACAAGAAGACATTTATGCGGCCAAAAAACATATTTAAAAA-GCTCAT 6218
                            vv       i  vi vii      v  i  i  vv   i -     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_82084222_8   6219 CATCACTCGTCAT 6231
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (154 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


2184 28.70 3.03 1.05  chr2_82157279_82160047     1421  2277 (492)    L1M4_orf2#LINE/L1       35   908 (0)  

  chr2_82157279_8   1421 TTAACATAATTAAAATCTCAATTCTACTCAAAACAATTTACAGATTCAAT 1470
                             i  vi    i  vv    v  v i    vii  i           i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr2_82157279_8   1471 GCAATCACTATAAAAA-CACAATTGACATTATTTCAAAAATAGAAAAA-- 1517
                               v    v    - v  ii  v v  v  v  i    v  v  i--
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr2_82157279_8   1518 AAGTCTAAAATTTGTATGGAACCATAAAAAAACCTGAATAGCCAAAGCAA 1567
                         i vi        ii       viii  iii v  v           i   
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_82157279_8   1568 TCCTGAGGGGGGAGGGGGAAATCTGGAGGCATCATACTAGCTGACTTCAG 1617
                           i   iiii i  iivi  i -      vv   i   vv ii i    i
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_82157279_8   1618 AATATACAAGAAATCCATAGTAACCAAAACAATATGATTCTACCAGTAAA 1667
                           iv   v v   v i i     i   i   i i  i v  iv  -   i
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA-TAAG 282

  chr2_82157279_8   1668 AA--GACACATTGACCAATGGAACATAATAGAGAGTACAGAAATAAATTC 1715
                         i --    i  v  i        i v   v      v          ii 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_82157279_8   1716 ACGTATTTACAGCCAACTCATTTTTAACACG--TG--AAGAACATACG-T 1760
                          iii     ii i   i v     ii   v --  --    v   v i- 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_82157279_8   1761 TGAGAAAGGAGAGTTTCCTCAGTAAATTCTTCCGGGAAAACTGGATAACC 1810
                         v i     i v   i ii   ii    vv v i    v         ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_82157279_8   1811 AAATGCAGAAGGATTAAGCTAGAGCCATAAATCTCATTATATACAACAAT 1860
                          v     i   i  v   i i  v  v  vv  v  ii        v   
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_82157279_8   1861 TAAATCAAAATGTAT--------TAAATGTAAGACATGAGACTTTAAA-C 1901
                            v        v  --------           vv i i   v    - 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_82157279_8   1902 TGCTAAAATACAGTATTAGGG-AAATGCTTCAGGATACTGGTTTGCATGA 1950
                          vi  i  v v ii  vi ? -    -    iv  ivi   v  iviii 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAA 581

  chr2_82157279_8   1951 AGATTTTTGGGGTAAGAACAC-AAAAGTTCAGGCAATAAAAATACAAATA 1999
                         v i   i vi i  v  -   -     iv  i    i    iv v     
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_82157279_8   2000 GACAAATGGGATCATATTAAGCTAAAAAGCT---GCAAAGCAAAGGAAAC 2046
                           i    v   iivi  i  iv v    i  --- iivvv       v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_82157279_8   2047 CATCAACAAAGTGAAGAGAGAATCTCCAGAATGGGAGAAAATATTTGAAA 2096
                         i     v        i   v  i iv                     v  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_82157279_8   2097 ACTATTCACCCTAAAAGGGCTTAATAACCGCAATACAGGAGGATCTCAAA 2146
                          ii  vi i iv v     vi vi  v  iv    i vi i  v   vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_82157279_8   2147 AAACTCAATAGCAAAAAACAAAACAAATAATCTGAACTGTTAAA-GGATA 2195
                         v         ii     i----        i i-  i ?vv   -  ii 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAG----ACAAATAACCC-AATTWAAAAATGGGCA 825

  chr2_82157279_8   2196 AAATATCTCAATAGACATTTCTC-AAAGAAGACATACAAATGGCCAAGAA 2244
                           iv  i v              -        i              v  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_82157279_8   2245 GTACATTTTAAAAAGTTCAAAATCACTAATCAT 2277
                          i    vvv  i v i    v    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (138 / 105)
Gap_init rate = 0.02 (19 / 874), avg. gap size = 1.84 (35 / 19)  


1479 25.61 3.09 2.43  chr2_82184417_82186359       87   539 (1404)    L1M4_orf2#LINE/L1        1   456 (452)  

  chr2_82184417_8     87 TGGTAAGATAACTCTTGCTCATAAATTACAAGAATTACAGTTGTTAAAAT 136
                            v      v i v  i    ii   iv    v   vvi       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_82184417_8    137 GTTCAGACTACCCAAAATGATCTACAGATTCAATGTATTCGCTATGAATA 186
                          viv v   v      v                i i v  v    -----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT----- 95

  chr2_82184417_8    187 TAAAA----AG--GCATTTTTCACAGAAATAGAAAAA---ATTCTAGAAT 227
                         i    ----  --  v     ii       v  v  i---  i   i   
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_82184417_8    228 TCATATGAAATCACAAATTTCTCTGAATAGCCAAAACAATGGTGATTAAA 277
                                i  vii   ivvv i v                vv   vv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_82184417_8    278 AAGAACAAAGTTGTGG---TCATGTCATTATCTGGCTTCAAAGTATACCA 324
                                      vi ---   ---  i vi iiii      iiv   i 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCA---CACTTCCCAATTTCAAAACTTACTA 242

  chr2_82184417_8    325 CAAAGCTATAGTAATCAAAACAGCATGATACTGGTATAAAAACAGACTCA 374
                                 i         i    ii  i      i    ii i    vi 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_82184417_8    375 TAGTCCAGTGGAATACACTAGGGAGCCCAGAAATAAATCCACACATTTAC 424
                            vi  i       v v v i   i           i   i       i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_82184417_8    425 AGTCAACTGATTTTTGTCAAAGGTTTCAAGAACATATATGGGGGGAAAAG 474
                         i     i       i v   i   vi     v   vi -iv       ii
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAGA 391

  chr2_82184417_8    475 ATACTGCCTTCAATAAATGTTGTCTAGAA-AACTGGACA-CCACCACTCA 522
                            v vii     i     v  -  i i -       i -    - iv  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTG-CTGGGACAACTGGATAKCCAC-ATGCA 439

  chr2_82184417_8    523 AGGAAATAAGAGAGGAC 539
                          iii   i iivv    
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGAC 456

Transitions / transversions = 1.58 (71 / 45)
Gap_init rate = 0.02 (11 / 456), avg. gap size = 2.27 (25 / 11)  

2560 28.26 1.66 1.43  chr2_82184417_82186359      549  1454 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_82184417_8    549 TGGAAAAAGATTCCATCCTCATCGATAGGAATAATCAATATCATGAAAAT 598
                               i v  i    vi    v   v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_82184417_8    599 GGCTATACTGCCCAAAGTAATTTATAAATTTAATGCTATTCAATTCAAAA 648
                            v     v      v i  i  i i   i  i  v  i vvv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_82184417_8    649 TACCATTGACATTCTTCACA-AAATTAGAAAAAAAACT-ACTTTAAATTT 696
                          v   vivi v  i  ii  -     i---- v  i  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr2_82184417_8    697 TATATGGAACAAAAAAAAGAGTCTTCATAGCCAAGAAAATCCTAAGCAAA 746
                         i        - viv  ii  vi vvv        i v    i i iv  i
  L1M4_orf2#LINE/    147 CATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_82184417_8    747 GAGAACAGAGCTGGAGGCCTCACACTACCTGACTTCAAACTATACTACAA 796
                         i      i  i      v        v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_82184417_8    797 GGCTACAGTAACCAAAACATCATGGTACTGGTACCGAAACAGACATATAG 846
                         i          i   i   vii         i iviii i          
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_82184417_8    847 ACTGATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAAC 896
                          iii      i    iv    vii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_82184417_8    897 CATCTGATCTTCCACAAACCTGACAAAA--AAGAAATGGGGAAACGATTC 944
                           vi    i   v    ivv  v   i -- vvv          vi  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_82184417_8    945 CCTATTTAATAAATGGTGCTGCAAAAACTGGTTAGCCATATGCAGAAAAC 994
                         i  v  i  i           vi v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_82184417_8    995 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATAG 1044
                             ii    i    v   i     v                   i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_82184417_8   1045 ATTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACTCT-AGAGGAAA 1093
                           i ?    i         i v i     i      -    -   i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr2_82184417_8   1094 ACCTAGGCAATAATAATTCAGTATAT--AGTCATAGGCAAAGACTTCAT- 1140
                           v    ?ivv   v-   ivv iv --i  --       v ii   v -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGT--TAGGCAATGGTTTCTTA 591

  chr2_82184417_8   1141 GATGAAAACACCAAAAGCAATTGCAACAAAAGCTAGAATC-ACAAAT-GG 1188
                            - vi            vvv          vv i   v- i    -  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_82184417_8   1189 ATCTAATTAAA-CTAAAGAGTTCTGCACAGCAAAAGAAACTAGCATCAGA 1237
                          ii v  i   -i    i v  i  ii vv    i  v    v  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_82184417_8   1238 ATGAACAGATGACCTACAGAATGGGAGACAATTTTTGCAATCTACCCATT 1287
                         i    v   ii   i             v   v       vii ivi  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_82184417_8   1288 TGACGAAGGTCTAATATCCAGAATCTACAGGGCACTTAAATAAATTTACA 1337
                            ii i  v  vi          v  i ii v   ivv i  v ---  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CA 787

  chr2_82184417_8   1338 AGAAAAAAAAAGCCAACAACCCTATCAAACAGTGGGCAAAGAAC----AT 1383
                          v  v     ii v  i     v  i?  v i         i i----  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_82184417_8   1384 AAACAGTTATCAAGAGAAGGCATTTCTGTGGCCAATAAACATACAAAAAA 1433
                          i   v  v  v i     ii  vivvi          i  i ii    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_82184417_8   1434 AAGCTCATCACTAATCATTAG 1454
                          v     v  ii ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (146 / 106)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.65 (28 / 17)  


2766 23.12 2.86 6.57  chr2_82209881_82212081.rev      768  1710 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_82209881_8    768 TGGAAAGACATCCCATGCTCATGGATTAGAAGAATTAATATTGTTAAAAT 817
                                 i        i         i     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_82209881_8    818 GACCATACGACCCAAAGCAATCTACAGATTTAATGCAATTCTTGTTGAAA 867
                          i v    vv      vii           i  i     i i i ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_82209881_8    868 CACCAATGACATTCTT--CAGACATAGAAAAAA-AATCATAAAATTTTTA 914
                         iv   iivi v  i  --    v  v  v  iv-i   v       iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_82209881_8    915 TGAAATCACGTAAGT--TCCTGAATAGCCAAAACAATCCTGAACAAAAAA 962
                           i  -- i i   v--i  v                 i    -   i  
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAA 197

  chr2_82209881_8    963 AAATAAGGGAGCTTGAAGCA-TCACACT--ACGATATTCTAAACATCTTA 1009
                         i  i  i ----   i  v -       --v i  -   v    v vi  
  L1M4_orf2#LINE/    198 GAACAAAG----TTGGAGGACTCACACTTCCCAAT-TTCAAAACTTACTA 242

  chr2_82209881_8   1010 CAAAGCTATAGTAACCAGAAGAGCATGGTGTTGACATAAAAACAAACACA 1059
                                 i     i  ii v  ii    ii  i     ii i i   i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_82209881_8   1060 GAGACCAATGGAACTATAGAGAATAGAAAATCAAGAAATGAATCCATATA 1109
                         v   i        i-----     v  i i  v      i  i     i 
  L1M4_orf2#LINE/    293 TAGATCAATGGAAT-----AGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_82209881_8   1110 CCTACAGCCAACTGATTTTTGACAAAGGTGCCACAAACACTCACTGGGGA 1159
                         ii  ii i   i       i     i       vi v  i   v      
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_82209881_8   1160 AAGAACAATAAATATATAGCAATATAAAGCAATATATCATTATGTAACAT 1209
                              -----------   -----------------  v  ---------
  L1M4_orf2#LINE/    388 AAGAA-----------TAG-----------------TCTTT--------- 400

  chr2_82209881_8   1210 ATAAAGTAATAAATCATTCTTGGAAAACTGGATATCCACAGTCAGAAGA- 1258
                         - ----i  i    vi v  v   v         ?     vv  i    -
  L1M4_orf2#LINE/    401 -T----CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_82209881_8   1259 --------GACCTCTACCTCTCACCCTATACAAAAATCAAGTCAAAATGA 1300
                         --------    i       v    v           i  v        i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_82209881_8   1301 ATCAAACACCTAAATGTAATACTTGAAACTATAAAATTACTAAAAGAAAA 1350
                             ? v            v vi i           i vi  i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_82209881_8   1351 TATAGGGG-AAATGCTTCAGGACATTGG-TCAGGAAAAGATTGTAGGGAT 1398
                         i     ? -    -    iv   v    - i   v  v i  vivvi   
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_82209881_8   1399 AAGACTTCAAAAGCAGAGGCAACAAAATCAAAAATAAACAAATTAAATTA 1448
                          v   vi        v i         vv       i i     ii i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_82209881_8   1449 TATCAAACTATGAAGCTTCTGCACAGCAAAAGCAAGAAAACAACCAACAG 1498
                         i      v vvi  i   i  ii vv    i ----- v  v i   v i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGG-----ACACTATCAAGAA 689

  chr2_82209881_8   1499 AGTAAAATGACAGCTTACCAAATGGGAGGAAATATTTGCAGACTACTCAT 1548
                            i   v    i ii  vi        i           i ii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_82209881_8   1549 TTGAGAGCAGATTAATATCCAGAATATACAAAGAATTCAAACATCTCAAC 1598
                         i   v ivi  i vi             i      i  vv   v     i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_82209881_8   1599 AG-----AAACAAA--ATCTGATTTAAAAAATGAGCAAATGGTCTGAA-A 1640
                          i----- i     -- i ii   ?     -  i     v i i    - 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATA 838

  chr2_82209881_8   1641 AACATTTCTCAAAAGAATACATAAAAATGGCCAACAAATATATCTAAAAA 1690
                         i         v      v i   v          i  ii i  vv   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_82209881_8   1691 TGCTTAGCATCGCTAATCAT 1710
                             i i    i????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (136 / 78)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.87 (89 / 23)  


3402 22.95 3.20 0.80  chr2_82331983_82333848      499  1374 (492)    L1M4_orf2#LINE/L1       12   908 (0)  

  chr2_82331983_8    499 CTCATGCTTAAAAATTAGAGGACTTAGAATTGTTAAAATGTCTATACTAC 548
                          i    i i vii   i  i      iv        i   v v     v 
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chr2_82331983_8    549 CCAAAGCAACCCACAGATTCAATGCAATTCCTATCAAAATTCCAGAGATG 598
                              vii i i          i     i           i    vviiv
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_82331983_8    599 GTTTTTCTAGAAATAGGAAAA--AGTTCTAAAATTTATAATATAATTTAA 646
                         v     vi      v iv  i--ii i        i   vviv   vi  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_82331983_8    647 AAATAACTCA-AAT-GCAAAAATAATCTTGAAAAAGAAGAGAAAATTTGA 694
                         iii--  i  -   -  v    i                 iv   v   i
  L1M4_orf2#LINE/    162 GGG--ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_82331983_8    695 AAGCCTCACACTTTCTGATTTCAAAACATACTTTAAAGTAATAGTAATCA 744
                          i v         i ii          v    vi    iv i        
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_82331983_8    745 AGACAGTATGATGTTGGCATAAAGACAGACATATAGACCAATGGAACAGA 794
                                i  i ii        i  i           i        i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_82331983_8    795 AGAGAGAAGTCAGATATAAAACCTTGCATATGTGGCCAAATGGTTTTCAA 844
                          vv    ivi    v     v  v i   v i   i   v  i     i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_82331983_8    845 CAAGGGTGTTAAAGGCTACATCATGGGGAAAGAACAGTGTCTTCAGCAAA 894
                                 ii  - i i iviv            i   v i    i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_82331983_8    895 TGGTACTGGGAAAACTGGATATCCATGTATAATAGAATGAACTTGGACTC 944
                             i      v         ?   ii ii  v        v      i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_82331983_8    945 CTACCCTACATTATATA---AAAGTAATATAAAATGAATTGTAGACTTAA 991
                              ii   ii     ---   v   ivi      i  ii?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_82331983_8    992 ACCTAAGAACTAAA-CTATAAAACTTCTAGATAAAATCCTAGAAG-AAAT 1039
                          iv     i     -          ii    vi   v v   i? -    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_82331983_8   1040 AATTCAAGACACTGGATTTGCCAATGATTTCTTTAATATGGCACCAAAA- 1088
                         v-   iv   vi   i  v v     i      vi     i        -
  L1M4_orf2#LINE/    559 C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_82331983_8   1089 -ACAGGCAACAAAAGAAAACATAAACAAACGGGAC---ATCAAACTCAAA 1134
                         -   i              v   i i   iv    ---      v i   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_82331983_8   1135 AACT---GTGTATCAAAAGAAATAATCAGCAAAGTAAAAAAGCAACTTAT 1181
                             ---   iv     i  v iv    iv     i    ii    ii i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_82331983_8   1182 AGAATGCAAGAAAATATTTGCAACTCATATATCTGATAAGGGGTCACTAT 1231
                               vi               v                  iiivv   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_82331983_8   1232 TCATAATATATAAGGGA--------ACTCTATAACAAAAA--CAACAAAA 1271
                         i  v         i i --------    v    i     --   vv  v
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_82331983_8   1272 CCAATTTTTAAAAAATGGGCAGAGGACTTCAGTAG-CAATTCTCCAAAGA 1320
                               ?---           i    i  v i   -  v           
  L1M4_orf2#LINE/    808 CCAATTW---AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_82331983_8   1321 AGATATACCAATGGCCAACAAGAATATATAACAATGTTGAACATCACTAA 1370
                                 v         i   v i  iv  vi   i v       ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_82331983_8   1371 TCAT 1374
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.70 (124 / 73)
Gap_init rate = 0.02 (16 / 897), avg. gap size = 2.19 (35 / 16)  


2606 28.68 1.34 0.78  chr2_82348080_82352363.rev     2897  3792 (492)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_82348080_8   2897 ACATCCCATGCTCATGGATAGGTAGAATCAATATTACGAAAAAGACCAGA 2946
                          i        i        v  v   v i      iiv  i v i v v 
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_82348080_8   2947 CTGCCAAAAGCGATCTACAAATTCAATGCAATCCCCATCAAAAATACCAC 2996
                           v  v   vi        i      i        i       - v   v
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCCAG 106

  chr2_82348080_8   2997 CATCATTCTTTACAGAACTAGAAAAA--AATTATAAAATTCATATAGAAC 3044
                          vv v  i   i     v v  v  i--i  iv            i   -
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA- 155

  chr2_82348080_8   3045 CAAAAAAGAGACC--ACATAGCCAAAGTAAGATTAAGCAAAAAGCACAAA 3092
                         - viv   i    --iv         ii  vv  i iv  i   v     
  L1M4_orf2#LINE/    156 -ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_82348080_8   3093 TCTGGTGGGATCACATTACCTGACTTCAAACTATACTACAGGGCCATAGT 3142
                         vi   v  iv     i v  ii i      viv       ii  i i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_82348080_8   3143 CACCAAAACAGCATAGTATTGGTATAAAAATTGGTACACAGACCAATGGA 3192
                         v i   i    ii i   i   i    ii  v ii i i   i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_82348080_8   3193 ACAGAATAGAAAACCCAAAAATAAAGTCAAATACTTACAGCTGACAGAAC 3242
                          i     v  i ii   i       vi  v i i   ii iii iv  vi
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_82348080_8   3243 TTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACAACCTACTCAA 3292
                            i    i vviv   i v   vv i         i i ii  vi    
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_82348080_8   3293 GAAATGGTACTGGGATAATTGGCAATTCACATGTGGAAGAATGAAACTTG 3342
                         v       i      i  i   vv ?i      iii         ii v 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_82348080_8   3343 ATCTTTATCTCTCACTTTATACAAAAATCAAC-CAAGATGGATCAAAGAC 3391
                          i ii  i   v   iv           i   -   i        ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_82348080_8   3392 TTAAATCTATGACCTGAAACCACAAAAATTCTAGAAGATAACATCAGAA- 3440
                         i     v  v  v  i    i i    v ii       v     vi ?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_82348080_8   3441 AAACATTTTAGACATTGACTGAGGCA--GACTTCATGACCAGGAACCCAA 3488
                            iv  ivv   v   iv v     -- ii   v iivi v  vv    
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_82348080_8   3489 AAGCAAATGCAGCAAAGACAAAGATAAGTTGATGGGACTTAATTAAACTA 3538
                              v v   i    iiv   i   ii vi  v      v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_82348080_8   3539 AAACACTTTTGCACAGCAAAAGAGATAATCAGCAGAGTTAACAGACAACA 3588
                            v       ii vv    i  v iv    iv i   v  v       v
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_82348080_8   3589 CAGAGAATAGGAGAACATCTTTGAAAACTATGCATCCAACAAAGGACTAA 3638
                           v     i      v  v    v   ii  ii   ii i  i     --
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT-- 752

  chr2_82348080_8   3639 TAAATATTTAGAAACTACACAGAACTC----AAATCAGCAAGAACAAAAC 3684
                          i--   ii    vv  i v       ----  v   ii  v  v  i  
  L1M4_orf2#LINE/    753 TG--TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_82348080_8   3685 CAATAATCCCATCAAAAACTGGGCTGAGGACATGAATACACGATTCTCAA 3734
                         v     i  v  i?    v     vi    iv      v  iv     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_82348080_8   3735 AAGAAGATATACAAATAACCAACAAGAAAACGAAAAAATGCTCAACATCA 3784
                                         ii    i   v v i     i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_82348080_8   3785 CTAATGAT 3792
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.39 (147 / 106)
Gap_init rate = 0.01 (10 / 901), avg. gap size = 1.90 (19 / 10)  


2428 26.83 3.29 3.83  chr2_82390222_82396132.rev     4507  5419 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_82390222_8   4507 TGGAAAAGCATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4556
                               iii  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_82390222_8   4557 GGCCACACTGCCCAAAGTAATTTATGGATTCAGTGTTATTCCCATTAAAC 4606
                            v i   v      v i  i  ii      ii iv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_82390222_8   4607 TACCA-CTGATATTTTT-CATATAATTAGAATAAAGT-ATTTTAAAATTC 4653
                          v   -   viv     -  v -    i-- i  iv -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_82390222_8   4654 ATATGGAATCACAAAAGAGCCCGTATAGTGAAAA---TCCTAAGCAAAAA 4700
                                 vii   ii  v  v v    iv    ---  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_82390222_8   4701 GAACAAAGCTGGAGGCATCATGCTGCCTGACCTCAAGCCATACTACAAAG 4750
                                 i      vv   ii  v  ii ii    iv v          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_82390222_8   4751 CTATGGTAACCAAAACAGCATGGTACTGGTAAAAACAAAACAAAACAAAC 4800
                            ii    i   i    ii         i v  i---------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAG--------------- 282

  chr2_82390222_8   4801 AAACAAACAAAACACATAAACCAATCGACTAGAGTAGAAAACTCAGAAAT 4850
                         -i i i   -----i   i i    v  v    i v  i iii       
  L1M4_orf2#LINE/    283 -GATAGACA-----TATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_82390222_8   4851 AACAACATACACCTACAACCATCTGGTCTTTGACAAACTGGACAAAAGAA 4900
                           vvv      ii  iiii  vi  i i  i     ivvv v   i vv 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_82390222_8   4901 AGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAGAACTGG 4950
                         vv            i  vvi  v  i  i              v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_82390222_8   4951 CTAGCCTTTTGCAGAAAATTGAAACTGGACCCCTTTCTTAGACCTTATA- 4999
                         v  ?  viv    i  i v    ii         vi  i v   v    -
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_82390222_8   5000 -AAAATAAACTCAAGACAGATTAAAGACATAAATGTAAATACTTAA-CTT 5047
                         -     v       i ii   i ?    v         ivi  v  -  v
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_82390222_8   5048 TAAAACCCT-GGAAGAAAACCTAGGCAATACTATTCAGGACAC--AGTCA 5094
                               i  -i         v    ?ivv v v   iv   vi--i  i 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_82390222_8   5095 TGAGCAAAGATTTTAT-GATGGAAACACCAAAAGCAATTGCAACAAAAAC 5143
                         --i    v i   iv -   ivi -           vvv         iv
  L1M4_orf2#LINE/    577 --GGCAATGGTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAGA 623

  chr2_82390222_8   5144 AAAAATTGACAAATGGGATTTAATTAAACCTAAGAG-----GT-CTGCAA 5187
                               v  i    v   i  v  i   vi   i i-----  -  v   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_82390222_8   5188 AGCAGAAGAAACTATAATCAGCATGAACAGACAACCTACAGAATGGGAG- 5236
                           -----  v     v vv ivi    v        i            -
  L1M4_orf2#LINE/    674 AG-----GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_82390222_8   5237 ---------CAATCTATCCATCTGACAAAGGTCTAACATCT-GAGTCCAC 5276
                         ---------   vii  vi      i  i  v  vii   i-  i vi i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_82390222_8   5277 AAGAAACTTAAACAAATTTAGAAGAAAAAATGAACAAAGAACCAGATTAA 5326
                           ii    ivv    v iv v  v     i---     v    vi   ? 
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAG---ACAAATAACCCAATTWA 815

  chr2_82390222_8   5327 AAAGTGAGAAAAGGACATGAACAGACACTTTTCAAAAGAAGACATACATG 5376
                            i  i v      iv    i     i  i  v        i     vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_82390222_8   5377 GGGCCAACAAACATATGAAAAAAAGCTCAACATTACTGATGAT 5419
                         v      i  i  i       i v         i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.10 (65 / 21)  


1920 27.99 5.92 2.96  chr2_82494970_82498334.rev     1995  2873 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_82494970_8   1995 AGAGATAGTCCTA-GCTCATCTGTCAGATGAGTCA---TTATTAAGGTAT 2040
                          i     -   i - i    vvi ii  v  v i ---  i     i iv
  L1M4_orf2#LINE/      4 AAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_82494970_8   2041 CAATTCTTTCCAACTTGATCTCTTGAGTAAACAAAATCCCTATCAA--TC 2088
                             v  ii    v       viv  v v   iv            --  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_82494970_8   2089 CCACAAATATGTTTTATAGATATTTAAAAAATGGTTTTTAAAATTTATAC 2138
                            vvviiv v    ii   v   v v  iv  i ii -      i   i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAATTCATAT 151

  chr2_82494970_8   2139 AAAAATGCAAAG-ATGCAAAATAGTCAACACA-----GACAAAGGGAGAT 2182
                         ii        i - iv  i     i   v   -----  v    iiii i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_82494970_8   2183 AAATTTGGAGTACTAATATTACAAGGCTTCAAGA-TTACTATAAAGCTAG 2231
                            v      v   v i i v vviii     i -      i       v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_82494970_8   2232 AGTGATAAAAACAGCATTGTGTTAGTG-AAAAATAACCATAGAGATCAGT 2280
                            i  v  i    ii v  ii i ii-  ii   iv    v      i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_82494970_8   2281 AAGCCAGGAT--AGATTTCTCAGAGTTAGAAC-ATCACGAATATAGTCAA 2327
                         iiivi  i  --   v i --   iv  i v -  -  ivv   i     
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCC--AGAAATAAACCCAT-ACATTTATGGTCAA 348

  chr2_82494970_8   2328 CTCATCTTTGACACAGGAGCAAAGATAATTCAAATAAAGAAAGAATAGTT 2377
                         i v  i  i    vi  v  v    iv      - iii           i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTC 397

  chr2_82494970_8   2378 CTTTTTTTCTAGCACGTTGTTCTAGAA-ACCTAGATATCCACATACCAAA 2426
                         ----     - i  vi v  v  i i - v  i    ?      i ----
  L1M4_orf2#LINE/    398 ----TTTTC-AACAAATGGTGCTGGGACAACTGGATAKCCACATGC---- 438

  chr2_82494970_8   2427 AAAAAAAAAAAAAAAAAATCTAGACACTGGCCTTACACCTTTCACAAGAA 2476
                         ------    i  vi  i - i   v ivi   i     v vi    i  
  L1M4_orf2#LINE/    439 ------AAAAGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_82494970_8   2477 TGAACTCAAAAGGAATCATAGACCTAAATGTGAAATTCAAAACTATAAAA 2526
                          v         v i    ?            i i vii            
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_82494970_8   2527 CTCCTAGAAAAATAACA---------------GTGATATTGGGTTTGGCT 2561
                            i     i  -    ---------------    iv       v   v
  L1M4_orf2#LINE/    532 CTCTTAGAAGAA-AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_82494970_8   2562 ATGAGTTTGTATATACATCATCAAAAGCATAATCCATGAAAGAAATAGAA 2611
                            iv  iv  v   iiv  i        i  v v ii       v iv 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_82494970_8   2612 TATAAGTTGGATTTTATTAAAATGAAAAA----TGTACTTACAAA--ACA 2655
                         v    i     i  i  i     v     ----   i   -    --   
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT-CAAAGGACA 679

  chr2_82494970_8   2656 ATGGGTTAAGAGAATGAAGAGGATAGCTACA-AATTGGAGAAA-TGTTTA 2703
                         v i-- i    i i    i  ivv v i   -   v       - i   i
  L1M4_orf2#LINE/    680 CTA--TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_82494970_8   2704 CAATACAGACATAT--TGAAATATTTATATTTA-AATATGGAAATAGCTC 2750
                            vv  v i  v -- i iiv i  i   ii -     iv   v i   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_82494970_8   2751 TTAAAATGTAACAACTAAAA-ACA------CCAAATAAAAGA-GGCCAAA 2792
                            v  ivi  i  iv    -   ------    v ?   i -  v    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_82494970_8   2793 AGATGTGAATGCACACTTTGCCAAAGAAGACATACAGATAAAAAATATAC 2842
                         i   v     iv   i  iv          i     i  iivv    vi 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_82494970_8   2843 ATATAAAAATCTGCTCAGCATCATCATCATT 2873
                          i  i    vv      i     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.04 (32 / 905), avg. gap size = 2.44 (78 / 32)  


 900 25.94 0.75 1.50  chr2_82498673_82500882.rev      609   874 (1336)    L1M4_orf2#LINE/L1        1   264 (644)  

  chr2_82498673_8    609 TAGAAGGAAAGCATGTGTTCATTATTTGAAACAATTAATATTGTTAAACT 658
                          i   i  v v vii       viv   i  v v             iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_82498673_8    659 GTCCATACTATCCAAAGTGATCTACAGAATCAATGCAATCCTTATGAAAA 708
                          v v     vi     v           v    i       i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_82498673_8    709 TCCAAATAGCATTACCTACAGAAATTTAAAAAA-AATCCTAAAATTCACA 757
                            v iiv  v  vii i        v v  iv-i             i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_82498673_8    758 TGGAACACCAAAAGATCCGTAATAGCCAAAGCAATCTTGAGCAATGAGAA 807
                              vvv   ii  i  iv          i         iv  vi    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_82498673_8    808 CAAAGCTGGAGGGAGGCATCAATCTTCCTGATTTCAAAATATTTTATAAA 857
                              i      ---i -   vv     ii         iv vi  i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG---AC-TCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_82498673_8    858 -TTGCAGTCACTAAAACA 874
                         -i i    v ii  i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACA 264

Transitions / transversions = 1.16 (37 / 32)
Gap_init rate = 0.02 (4 / 264), avg. gap size = 1.50 (6 / 4)  

1940 25.45 3.14 0.83  chr2_82498673_82500882.rev     1114  1718 (492)    L1M4_orf2#LINE/L1      290   908 (0)  

  chr2_82498673_8   1114 ATATAGATCAATGAAACAGAAAAGTGA-TCTAGACATAAATTCATGCATA 1162
                                      i  i    vv v  -  i   v     ii   i   v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_82498673_8   1163 TACAGTCAATTGATCTTTGCCAAGGAAGCCAAGCACACACAATGGAGAAA 1212
                           ii          i  i v     iv      vv  iv      i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_82498673_8   1213 ATATAGTTTCTTCAATAAATGGTG---AAAAAACTGGATATCCACATGCA 1259
                         iv     i i     i        ---ii v         ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_82498673_8   1260 GAAGAATGAAATTATACCTATATATCGCATTATATGCAAAAATCAAGTAA 1309
                         i         i  iv   iv  iv  i  ii    i       i  v v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_82498673_8   1310 CAATGAATTGAAGACTTAAACATAAGACATTAAAC-GTAAAAGCAATAGA 1358
                         v    i  ii?    i    ii     vv v    -i     vivv    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_82498673_8   1359 AGAGAATATAGAAAAAGGGCCTCTTGACATCGATGAT--GGCAAAAATTA 1406
                            i  i    i?iv iiv i  v    v i -- i --     vii  -
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTG--GGTTAGGCAATGGTT- 586

  chr2_82498673_8   1407 TTTTGGATATGACCCCAAAAAGTATA-GCAATAAAAGAGAAAATAGACAA 1455
                          i  i        v      - i i -    i      i        i  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_82498673_8   1456 GTGGGATTGCATCAAACTAAAAAGCTTCTGCACAACAAAGGAAAC----A 1501
                         i v   i v       v v    i   i  ii vv       v  ---- 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_82498673_8   1502 ACTGAGTGAAAAGGCAATCTATGGAATGGGAGAAAATATTTGAAAACCAC 1551
                          vvi         i   i i ii                   v   i  i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_82498673_8   1552 ACATCTCATAAGGGGTTCATATTCAAAATACATTAAAGAGCTAAAACAAT 1601
                          i    v       ii ii   i  i    i  -     i  vvv    i
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATAT-AAAGAACTCTTACAAC 784

  chr2_82498673_8   1602 TAAATGACAAA----TAAATAAC--AACTAAAATATGGACTAAG-ACATA 1644
                          v   i i   ----i       --  i ?   v    i v   - iv i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_82498673_8   1645 AAAAGACATGTTTTAAAAGATGACATACAAATGGCCAATGGGTAAATGAA 1694
                           v      v i iv     v  i               ii i v     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_82498673_8   1695 AACATGGTCACTGTCACTAATCAT 1718
                           v   v   vii   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (94 / 56)
Gap_init rate = 0.02 (13 / 619), avg. gap size = 1.85 (24 / 13)  


 821 24.52 4.21 0.77  chr2_82532344_82533968.rev       19   279 (1346)    L1M4_orf2#LINE/L1        5   274 (634)  

  chr2_82532344_8     19 AAGATATCT-GTGTTCATAAATTAGAAGAGTTAATAGTGTTAAAATACCC 67
                                 i-i       ii   i     v      v      i  iv v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_82532344_8     68 ATACAACCCAGAGTGATCTACAGATTCAATGTAATTACTATAAAAATTCT 117
                             vv    i v                i i   iv    v     i i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_82532344_8    118 AA-TGACGTTTTCACAGAAATAGAAAAAC-AATCCTAATATTCA-ATGTA 164
                          i-  v v    ii       v  v  i -i       v     -   v 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_82532344_8    165 AACACGAAG-ATCCTGAATAGTTAAAACAAACTTAAGCAAAAAAGTGCAA 213
                           ii i i - i  v      ii       v   i i-   i   vi   
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAACAA 203

  chr2_82532344_8    214 AGCATAAAGTA-TCACACTGCCTATTTTTAAAACCTACTA--AACTTATA 260
                           i- ii  v -       v  i v   i     i     --  vi  i 
  L1M4_orf2#LINE/    204 AGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_82532344_8    261 CTAATCTAAACA---TGATATT 279
                         v     v i   ---  i  i 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACT 274

Transitions / transversions = 1.67 (40 / 24)
Gap_init rate = 0.04 (10 / 270), avg. gap size = 1.30 (13 / 10)  

2156 24.28 3.19 1.44  chr2_82532344_82533968.rev      508  1133 (492)    L1M4_orf2#LINE/L1      272   908 (0)  

  chr2_82532344_8    508 ACTGGCATAAACATAGATACATAGACCAAAGGAGCAAAATACAAAGTCCA 557
                                   iv     i i     i   v   ii i   vv i      
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_82532344_8    558 GAAATAAAACCAACCATTTATAGTCAGTTGATTTTTGACAAAAGTAGTAA 607
                                 v   vv       i    i        i     ii  ivi  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_82532344_8    608 TAACA--CAATGAGGCAAGAACAGTCTCTTCAACAAATTTTGTTGAGACC 655
                         v v  --     i  v     i     i          vv  i  i   v
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_82532344_8    656 A--GGATATTTACATTCAGAAGAATGAAATTAAAACTGTATCTCACACCA 703
                          --     ?ii    v  i         i  ii v iv  i         
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_82532344_8    704 TATACAAAAACGATCAGCTCAAAATGAACTTAACACTTAAATGTAAGAAC 753
                                   --- i i         i iiv? v  i           i 
  L1M4_orf2#LINE/    472 TATACAAAAA---TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_82532344_8    754 TGAAACTGTAAAACTTCTGGAAGAAAGCAATAGGGGGCAAGCTCCAGGTC 803
                          i     i       ii i       i  -    ? vv  v  i iv v 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACA-TAGGNGTAAATCTTCGTGAC 567

  chr2_82532344_8    804 ACTGGTGTGTGAAATTCTTTTTCTGATATGACCCTGCAAAACACAGGCAA 853
                         vi   vv iv v   vv   i iv        v ii-   i    i    
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA-AAAGCACAAGCAA 616

  chr2_82532344_8    854 CAAAACCAGAAATAGACAAAT-GGCTTTACAGTAAACTAAAAAATTTCTG 902
                              vv i       i    -  vi  -  vi   v v     i  i  
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTT-CATCAAAATTAAAAACTTTTG 665

  chr2_82532344_8    903 TGC---AAGAGAAACAGTCAACAGAGTGAAAAGAC--TTCATAAATGAGG 947
                            ---  ii  v  vi    v i           --ii  i i -- v 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA--ATG 713

  chr2_82532344_8    948 GGAGAAA-TATTGATAATTTATACATTTCATAAGAAGTTAAATATCCAAA 996
                                -    vii  v i   i  i v     iiii vi-      i 
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG-TATCCAGA 762

  chr2_82532344_8    997 ATATATAA-GAA--------ACTCAACAGCAAGAAAACAAATAACCCAAT 1037
                                 -   --------      i ii  i  i              
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_82532344_8   1038 TCAAATAGGGGCAAAGAAACTGAATACACATTTCTCAAAAAAAGACACAC 1087
                          ?   v v        i vi      v         v   i    i i  
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_82532344_8   1088 AAATGACCAACAGGTATATGAAAATGTGTGCAATATCACTAATCAT 1133
                              i    i i i i       vi  iv   i    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (94 / 54)
Gap_init rate = 0.02 (14 / 637), avg. gap size = 2.07 (29 / 14)  


2474 24.32 3.38 4.36  chr2_82712701_82714732.rev      626  1542 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_82712701_8    626 TGGAGAGATAGTCCATGCTCAGGGATAGGAAGACTCAATGTTGCCGAGAC 675
                             i     vi     i   v    v        i   i   iii   i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_82712701_8    676 ATCAGTTCTTCCTAATGTGATCTGCAGATTTAATGCAATCCCAATCAACA 725
                         iv  i v  i  i  vv      i      i  i        v     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_82712701_8    726 TCT-AGCAATTTATTTTGT-GATATTAACAA----ATTCTAAAGTTTATA 769
                           i-   viii v     i-  v   i    ----  i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_82712701_8    770 TGGAGAGGGAAAATAGCCAGCATAGCCAGCATAATATTGAAAGAGATAAA 819
                             i v v  iiv v    v       iv i   v      i   vi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_82712701_8    820 ---AGCTGGATGACTGACAAT-ACCATCTTCAAGAATTACTATAAATGC- 864
                         ---  i    v    v   v -v   vi     i v      i   -  -
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-GCT 249

  chr2_82712701_8    865 ACAGTAATTGAGAGAATGTGGTGTTAATTTTTAAAATAAACAAATAGTCC 914
                                 ii   v i      ii iiiv v- ii   i   v    vi 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATA-AGGATAGACATATAGATC 298

  chr2_82712701_8    915 AATGAAACAGATTCAAGAACCCCGAAACAGACCCA--CATTAATTTGGCT 962
                             i  i   v ii   ii  v    i i     --    v  --  ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT--GGTC 346

  chr2_82712701_8    963 AATTGATCTTTGACCAAAGAATAA-AAGAA-ATACAATGGAGCAAGA-TA 1009
                                i  i   --   ii iv-    v-  v      i v    -  
  L1M4_orf2#LINE/    347 AATTGATTTTCGAC--AAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_82712701_8   1010 AACTCTCCAACAAACAGTGCTGGAACAACTAGACATCAAATTGCAAA-GA 1058
                         iv  i i       ii       i      i  i ? v vv      -  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_82712701_8   1059 ATAATAATAATATTTTTTTAAAAATCTAGACACAGATCTTAAATACAATC 1108
                           i - i viv iiii ------ i  ---    ----ii v      vv
  L1M4_orf2#LINE/    445 ATGA-AGTTGGACCCCT------ACCT---CACA----CCATATACAAAA 480

  chr2_82712701_8   1109 AC-AACTCAAAATGGACCACAAACCTAAGAT-TAAAATATAAAACTATAA 1156
                          i-             i  ? i      -  -   i vv           
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAA-ATGTAAGAGCTAAAACTATAA 529

  chr2_82712701_8   1157 AACTCTTAGAACATAATATAGAATAAAATTTAGATGATCAAACAAATTTA 1206
                                    v v  i    i?vv    i vvi   i --------  i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC--------TTG 571

  chr2_82712701_8   1207 TATGACCGGTTTGGAAATGACTT-TTAAATATGACATCAAAGGCACAATC 1255
                         -------    v  v    ii  -   i        i    i      v 
  L1M4_orf2#LINE/    572 -------GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_82712701_8   1256 CATAACGTAAATAGTTGATAGATTGGACTTCACTAAAATTAAAA--TGGT 1303
                         v i  viv   v i v    i           ii          -- vv 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_82712701_8   1304 GTACTCTGTGAAAGACATTGTCAAGGGAATAAAAACACAAGCCACTGACT 1353
                           i  iii--  i    i i     ii i i    v    v    v  v 
  L1M4_orf2#LINE/    665 GTGCTTCA--AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_82712701_8   1354 GGAATAAAATATTTGCAAAAGACCTATTTGATAAGGAAATACTAACTGTA 1403
                           i v              vv iv   i        i v vv  v iiv 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_82712701_8   1404 ATATACAAAGAACTCT-AAAACTCAACAATAAGAA---AAAAAAACAAAT 1449
                              i          - v       i     i  ---   v  v v   
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_82712701_8   1450 TGAGTAAAATG--TAA--GACCTTAATAGACACCTCACCAAAGAAGATAT 1495
                          ? --      --i  --  ii v        ii  v             
  L1M4_orf2#LINE/    813 TWA--AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_82712701_8   1496 ACAGATGGA-AATAAGAATATGATAAGATGCTCTACATGATATGTTTT 1542
                            i    v-      v i    v         v    v ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (130 / 89)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 2.15 (71 / 33)  


 997 29.07 11.84 3.83  chr2_82754569_82757011     1117  1952 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_82754569_8   1117 AGAAATTACAAGT-CATAAATTGAGAGATAAACTGCATTAAT-TTGAGTA 1164
                            v  iv  v  -   ii    ii   i--------     -   -- v
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGAC--------TTAATATTG--TT 45

  chr2_82754569_8   1165 AAGACATGCCTATTCTTTCCAAATTG--CTATCCATTCTCTCCAATATGG 1212
                             --  v v  v  ii        --   ivv    vviv    vi--
  L1M4_orf2#LINE/     46 AAGA--TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC-- 91

  chr2_82754569_8   1213 TCTA-CAAAATTACAGCAGATTTTTTT-----AAGTGACAAG-------- 1248
                         -   -      iv    v vi      -----  v       --------
  L1M4_orf2#LINE/     92 -CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_82754569_8   1249 -----------GGAACTACAAAGGACCTAGAAGAGCCAACACAATATTGA 1287
                         -----------    v i   i     i    v      v     v    
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_82754569_8   1288 TAAAGAAA----------------TCATATTGTCTGATGTTAAAGACTTC 1321
                         v      i----------------   i i vi ii  v i   -    v
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-ACTTA 239

  chr2_82754569_8   1322 TTATATATCTGCAATAGTTAAGACAGTGAAGCGCTGTCATTAACAACAGA 1371
                         i  i v v  i  i  i i         vi ii   v   -  vi i   
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGA 288

  chr2_82754569_8   1372 CAAGTA-ATCATTTAAACAGTCTACAAAGTAAAACAAAAGACACATGTTT 1420
                           vi  -    v vi  i  vv vv i   vv iv  v i  v   iiv 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_82754569_8   1421 ATATAATAAACTTATCTTTG----------CAAAATATTTAAATGGAAAA 1460
                         v   ii v  i v  i  i ----------   i ivv  v     ii  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_82754569_8   1461 AGAAAA----CTTCCACAAATTGCACTGGAATAACTAGACATTCATATGG 1506
                             v ----i   v      v ii    i i    i  i ?i  i   v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_82754569_8   1507 AAAAGGGTAAA-----AGCCCTCAGTCATACTTCAAATAGTGCAAAAATT 1551
                              ii i  ----- v    vvv   i  --  v   ---        
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACAC--CATATA---CAAAAATT 483

  chr2_82754569_8   1552 ATTCTGAAATGGATTTTAGACATAAACATAAAATATTTTACTACAACGCT 1601
                          viiii        iv?    v    ii   i vv vvv    i  vi  
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_82754569_8   1602 TCTAGAAAGAAGCA---GCAAAACATCTTCATAACTTTGAGGTAAACAAA 1648
                         ii     ii  i  --- ?iv  -      i i  i   i v  ii   v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_82754569_8   1649 AATTTATTAGAAAGGCCATTAAAGGCACTAACTCTCAAAAGAAAAA-TAG 1697
                         ii   v     v v v  ii   i    v i vv-           -   
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAA-CAAAAGAAAAAATAG 631

  chr2_82754569_8   1698 -CAAATTTTGTTCCAACAAC-TTAAAAGCTTT---GCTCATAAATAACTT 1742
                         -i     vvii i  v   v-      i    ---   i-i   vi  vi
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT-CAAAGGACAC 680

  chr2_82754569_8   1743 CATTTGGAAAATGAAAGAAACAAAGAACAGACTTAGAGAAATTGTT---- 1788
                         i  ivi    i     - i    vvv     v vi      v i  ----
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAA-AGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_82754569_8   1789 -ATACATACAGTTAGAAAAGGAATTGTTCCCATGATAACCAAATAATTTA 1837
                         -  -    i vi iiv  i   v    vi   vi   vvi   v  i iv
  L1M4_orf2#LINE/    730 AAT-CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_82754569_8   1838 CGCAGTTAAATACTAT---GTCATAAATA---TAAT--AAAAATGAACCA 1879
                         ii  ii v    v  v--- -- i     ---i   --       ii v 
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAG--ACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_82754569_8   1880 GGAATT------GACA---CTACAAA--AGATATCGTACAAATAGTCAAT 1918
                         i i   ------    ---  v    --      ---      i i    
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATAT---ACAAATGGCCAAT 873

  chr2_82754569_8   1919 AAACACATGTAAATATTCTGCACAT-ACTAGTCAT 1952
                           i      v   v  v  vv    - ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (131 / 109)
Gap_init rate = 0.04 (39 / 903), avg. gap size = 3.36 (131 / 39)  


1296 29.78 6.34 3.51  chr2_82768360_82770516      795  1677 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_82768360_8    795 TGGAGAGACACAACAGTTTAATGAATTGGAATTCTCAAGTTTGTAAAAAA 844
                             i   i ivv  vv  v   i       vv  i  vv    v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_82768360_8    845 TTCATTTTTCCTACAAATTCATATATGGATTCAATTTAATC----TCAAA 890
                         vv  v vi   i-      v  v  ii       ivi    ----     
  L1M4_orf2#LINE/     51 GGCAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_82768360_8    891 ATCTCATCAGAGTTTTGTATGTGTGTAGAATTTGACAAGATAACTTTAAA 940
                            i  v v vv    ----- -  i    v        v i iii    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTT-----T-TGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_82768360_8    941 ATAT-TGTGAAAATAAAAGG--CCAAGAAAAATGAAGACAGTCCTAAGAA 987
                           vi- i  i    iv    --  v    v iiv  i   i  i i i  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_82768360_8    988 GGAAGAATATATTTGGAGGAATTATCCTTTCAGAATTCAAGACTTACTCT 1037
                         i      i v v        v i iv   i vi v     i       --
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT-- 241

  chr2_82768360_8   1038 ATTAAAGAACTTAAGAAATGAAGGCAGTGTGGTGTTGCAACAA----AAA 1083
                         --- v i i  vv  v   v   i         ii  vv i  ---- i 
  L1M4_orf2#LINE/    242 ---ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_82768360_8   1084 CA-ATAAAACAATACAACCAAATGCTAAGTCTAAAAACAGACCAAGTACA 1132
                           -   i v    iv  ivi   vvvi    i i   i i   v -    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACA 337

  chr2_82768360_8   1133 T--ATTATCACCTGGCTTTTGACAAAGTTTTTACTGCTATACAGTGAGGA 1180
                          --  vi   vi  ii   i     i v vii vvi i  v  i  i   
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_82768360_8   1181 GAAAATAAACAAACAAACAAACAAAAAGAGGCTGGC-CTATCAGATGTCT 1229
                         i i    iv vvviv      i----- iv     v- v iii   i? i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAAT-----GGTGCTGGGACAACTGGATAKCC 432

  chr2_82768360_8   1230 GTATG-GAGATAATGAATCTTGATTCCTACCTATCACTCTATACAGAAAT 1278
                         ii   -i i v      vi v  ii       vv   iv      i    
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_82768360_8   1279 TAATACCTGCTGGATTATAGATATAAATGAGATAGCTAAAAGTG-ATACC 1327
                            iv vviv     i ?   iv      vi v        v i- v v 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_82768360_8   1328 TCTT-GAAGAAAAGAAAAAGAATAA--CATCATAACTATGGAGTAGGCAA 1374
                             -        v v i- ?i   -- v  i i  iv   iv       
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAG-GNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_82768360_8   1375 -GGTGTTCTTAAAAATAATAACCTCACCATAATTCATA----------T- 1412
                         -   -      i v  i i v vvv v  i  viv i ---------- -
  L1M4_orf2#LINE/    582 TGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_82768360_8   1413 GATTAATTGTACTTCCTTAAAGT-AAGAGCTTCTGTTTACTGAAAGAGAG 1461
                            v     v     v i   i -  i i   i   viviii  i  v v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_82768360_8   1462 TATCAAGAGGGTGAAAAGATAA------------GAGAAGACATTTGTAA 1499
                                 ii         i  ------------     i i     i  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_82768360_8   1500 TGAATAAACCTGAGAAAGGCTTCATA-CCATCAATACATAAATAACTA-- 1546
                         vvv   v i    v  i  vi ii  -   v-    i     v    v--
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAG-AATATATAAAGAACTCTT 779

  chr2_82768360_8   1547 AAAACCTTTAATCTTACAGATGACCAAACTATACACCAA---AAAAATGG 1593
                          v   -- i   vv  v i -   -   -  -  -    ---        
  L1M4_orf2#LINE/    780 ACAAC--TCAATAATAAAAA-GAC-AAA-TA-AC-CCAATTWAAAAATGG 822

  chr2_82768360_8   1594 GCAGAATTCTTGAATGCTCACTTC-CCAAAAAAG-TATTTAAAT---CAA 1638
                            i ivvi      ivv  i   -     i   -   vi    ---   
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_82768360_8   1639 TACAGAAAATGTGAAAATGTGTCGAATACTAGTCAGCAT 1677
                           -  v v   vi  i   i-  -  i ii ????????
  L1M4_orf2#LINE/    873 TA-AGCACATGAAAAGATGC-TC-AACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (139 / 121)
Gap_init rate = 0.04 (40 / 908), avg. gap size = 2.17 (87 / 40)  


 858 28.10 1.81 3.93  chr2_82780567_82786856     4494  4824 (1466)    L1M4_orf2#LINE/L1        1   324 (584)  

  chr2_82780567_8   4494 TGGAAAAGAAAATTCCATGCTCATTCATAGAAAGAATAAATATCATGAAA 4543
                               i-- v  i     i    vv  v i    v v     ii v  i
  L1M4_orf2#LINE/      1 TGGAAAG--ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_82780567_8   4544 ATGGCCATAATTCCCAAAGTAATTTATAAGTTCAATGCTATTCCTATTAA 4593
                              v   v i      v i  i  i ii     i  v  i     i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_82780567_8   4594 ACTACCATTGACATTCTTCACA-AAATTATAATAGAAGAAACTG-TTTTA 4641
                          v v   vivi v  i  ii  -     i------- v  i   - ii  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG-------ACAAGCTGATCCTA 141

  chr2_82780567_8   4642 AAATCCATATGGAACCAAT-CAATAG-TCCA-AATATCAAAGACTGTCCT 4688
                             i         ---  -   vi -i   -    v v  i  vi  i 
  L1M4_orf2#LINE/    142 AAATTCATATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr2_82780567_8   4689 AATCAAAAACAGCAAACCTGGAGGCATCATGCTCCTTGACTTCAAACTAT 4738
                         i vv  i  v i    vi      vv   ii  i iii i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_82780567_8   4739 ACTACAAGGCTACAGTAACCATAACAGCATGGTACTGATACACAAACAGA 4788
                                i          i  vi    ii        ii i vii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_82780567_8   4789 CACACAGACCCAATGGAACAAAATAGAGAA-CTAGAA 4824
                           i i   i -       i i   v    i- i    
  L1M4_orf2#LINE/    289 CATATAGATC-AATGGAATAGAATTGAGAGTCCAGAA 324

Transitions / transversions = 1.91 (61 / 32)
Gap_init rate = 0.03 (10 / 324), avg. gap size = 1.90 (19 / 10)  

1638 26.71 1.00 1.67  chr2_82780567_82786856     5207  5805 (485)    L1M4_orf2#LINE/L1      314   908 (0)  

  chr2_82780567_8   5207 AGAG-CCAGACCATATCAACC-ACACACCTAGAACCATCTGATTATTGAC 5254
                             -     v-   --    - i   ii  viii  vi     v i   
  L1M4_orf2#LINE/    314 AGAGTCCAGAA-ATA--AACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_82780567_8   5255 AAACCTGAAAGAAACAAGCAATGGGGAAATAAT--TCCATATTTATTAAA 5302
                           ivv  vv ii v  vv           v   --  -- v  i vi   
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC--TTTTCAACAAA 408

  chr2_82780567_8   5303 TGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAATTGAAACTGGACTG 5352
                                    v      v  ?   i     i  i v    ii     iv
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_82780567_8   5353 CTTCCTTACACCTTATACAAAAATTAACAAAAGATGGATTAAAGACTTAA 5402
                           v   i     v               vv  i      i ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_82780567_8   5403 ATGTAAAACCCAAAAGTATAAAAACCATAGAAGAAAATCTAGGCAATACT 5452
                               i v i    v       vi v          iv    ?ivv v 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_82780567_8   5453 ATTCAGGATATAGGCACAGGCAGAGATTTCATTACAAA-AACTCCAAAAG 5501
                         v   iv  iv v  vvi     iv i    -   v v -i  v       
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGACACCAAAAG 607

  chr2_82780567_8   5502 CAATAGCAAGGAAACAAAAAACTTGACAAATGGGATCTAATTAAACTAAA 5551
                           vv     vi   v      - v  i    v   ii v  i   v v  
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_82780567_8   5552 GAGCTTTTGCACAGCAAAAGAAACTATCATCAGAGTGAACAGACAACCTA 5601
                         i i      ii vv    i  v       vv i      v        i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_82780567_8   5602 CAAAATGGAAGAAAA-ATTTTCCAATCTATTCACCTGACAAAGGCCTAAT 5650
                           i     i      -    v v    -  vi i    i  i  v  vi 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGGGACTTGT 755

  chr2_82780567_8   5651 ATCCAGAGTCTACAATGAACTTAAAGAAATTTACAAAAAAAAACCCCACA 5700
                                i v  i  v     ivv v  v iv i  v     iv vv i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_82780567_8   5701 ACTCCATTCAAAAGTGGGCAAATGACATGAACAGATGCTTCTCAAAAGAA 5750
                           i v   ?    i        v  iv    i   iii     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_82780567_8   5751 GACATATATGCATCCAACAAACATATGGAAAAAAAAGCTCGACCTCACTA 5800
                           i   i viiiv    i  i  i   --    i v    i  v   ???
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATG--AAAAGATGCTCAACATCAZZZ 903

  chr2_82780567_8   5801 ATCAT 5805
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 0.97 (77 / 79)
Gap_init rate = 0.02 (12 / 595), avg. gap size = 1.33 (16 / 12)  


2323 25.68 0.45 1.05  chr2_82860394_82862051.rev      500  1165 (492)    L1M4_orf2#LINE/L1      247   908 (0)  

  chr2_82860394_8    500 GCTATAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGATACAGA 549
                             i     i   i    ii           iv ii i   v   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_82860394_8    550 CCAATGGAACAGAAT--AGAGCCCTTAGAAATAATACCACACATCTACAA 597
                         i        i     --    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_82860394_8    598 CCATCTGATCTTTGACAAATCTGACAAAAACAAGAAATGGGGAAACAATT 647
                         i  vi    i  i     ivv  v   i v  vvv          v   v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_82860394_8    648 CCCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 697
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_82860394_8    698 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 747
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_82860394_8    748 GATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAGA 797
                            i ?    i  v    v   v       i      vi i       i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_82860394_8    798 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGAC 846
                           v    ?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_82860394_8    847 TAAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATC 896
                           vi            vvi          vv i   v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_82860394_8    897 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 946
                          v  i   v v  i i   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_82860394_8    947 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 996
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_82860394_8    997 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 1046
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_82860394_8   1047 AAAAAACAAACAACACCATCAAAAAGTTTATATCGAAGGATATAAACAGA 1096
                             i     i   v v  i?    i vvii ---      v i  i   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCA---AAGGATTTGAATAGA 840

  chr2_82860394_8   1097 CACTTCTCAAACGAAGACATTTATGCAGCCAAAAAAACACATGAAAAAAT 1146
                           i     v  v     i  vi viii     v  i-          i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGAT 889

  chr2_82860394_8   1147 GCTCATCATCACTGGCCAT 1165
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (95 / 72)
Gap_init rate = 0.01 (6 / 662), avg. gap size = 1.67 (10 / 6)  


2608 27.02 0.76 1.85  chr2_82910238_82915187     3541  4458 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_82910238_8   3541 TGGAAACACATCCCAAGCTCATGAATAGGTAGAATGAATATTGTGAAAAT 3590
                               v i      v i     i  v  v   v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_82910238_8   3591 GACCATACTGCCAAAATCAATTTACAAATTCAACACAATTCCCACTGAAA 3640
                          i v     v  v    ii  i    i       i    i  i iii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_82910238_8   3641 TACCATCATCATTCTTCACAAAAGTAGAAAAAC-AATTCTAAAATTCATA 3689
                          v   v vv v  i  ii  i  i v  v  i -i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_82910238_8   3690 TTGAACCGGAAAAGAGCCCTCATAGCCAAAAAAAAGACTAAGCAAAAAGC 3739
                          v   vi v  ii  v  vvv          v  -vvi i iv  i   v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGA 199

  chr2_82910238_8   3740 ACACATCTGGAGGCATCTTATTACCCAATTTCAAATTATATTGCAAGGAT 3789
                            v vi      vv  vi i v            viv  i i   i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_82910238_8   3790 ATAGTTAAACAAAACAGTATTGTACCCATATAAAAATAGGCACAGAGATC 3839
                          i   -  v   i     i v    ivii    ii    i  i v     
  L1M4_orf2#LINE/    250 ACAGT-AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_82910238_8   3840 AATGGAAAAGAATAGAAAACCCAGAAAAAAAATCA-ATACTTACAG-CAT 3887
                                v     v  i ii       v   vi  - i i   ii -  -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA- 347

  chr2_82910238_8   3888 ACTGATCTTTAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGATATCC 3937
                          i    i  ii    i vviv   i v   vv i         i   vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_82910238_8   3938 TTTTCAACAAATTATACTAGGATAATTGGCAAGCCAGATGTAGAAGAATA 3987
                                     vi i  i   i  i   vv ?   v   i i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_82910238_8   3988 AAGCTGGATCCTCATCTTTCACCTTAATCAAAAAATCAACTCATGATAGA 4037
                            i    i  ii i  iv    v  - vv      i      vi  i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATA-TACAAAAATTAACTCAAAATGGA 496

  chr2_82910238_8   4038 TCAAAGACTTAAGTCTAAGACCTGAAATCATAAAAATTCTAGAAGATAAC 4087
                            ?    i   i v     v  i   ii      v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_82910238_8   4088 ATCAGAAAAACTCTTATAGACATTGTCTTAGGCAAAGAATTTAT-GATCA 4136
                           vi ?iv  v    vvv   v   vv        v iv  iv -   vv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_82910238_8   4137 AAAATCCAAAAGCAAGTGCAACAAAA--ACAGATAAATAGATGGGACCTA 4184
                         i v -         viv         -- v i   i   i  v    i v
  L1M4_orf2#LINE/    597 GACA-CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_82910238_8   4185 AATAAACTAAAAATCTTCTGCACAGAAAAATAAATAACCAGCAGAGTAAA 4234
                          vi   v v    v   i  ii vvv   iv v iv i  iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_82910238_8   4235 AAG-CAACCCACAGAATGGGACAAAATATTCACAAACTATGAATAATATT 4283
                            -                 v        ii    ii  -----    i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-----ATATC 740

  chr2_82910238_8   4284 CAGAATCCAGGACTAATATCCAGAATCTACAAGGGACTCAAACAAATCAA 4333
                         ii--  vvi     vi          v  i  i i    vv    v    
  L1M4_orf2#LINE/    741 TG--ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_82910238_8   4334 CAAGAAAAAAACAAATAATCCCATCAAAATGTGGGCAAAGGACATGACAC 4383
                         i  v     i        i  v  i?   vi           iv   ---
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA--- 835

  chr2_82910238_8   4384 GAATAGATAATTCTCAAAAGAAGATATACATATGGCCAACAAACACATGA 4433
                         --     i v     v              v        i  i       
  L1M4_orf2#LINE/    836 --ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_82910238_8   4434 AAAAATGCTCAATATCATTAATTAT 4458
                            i        i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (132 / 112)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.71 (24 / 14)  


1963 25.39 7.57 1.26  chr2_82974866_82976488.rev      498  1131 (492)    L1M4_orf2#LINE/L1      235   908 (0)  

  chr2_82974866_8    498 ACTTACTACAAACCTACAATAATGTAAAGAGTATGATAGCG-TATAAAAA 546
                                     v     i    vv i v   i  i  vi -i    ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_82974866_8    547 CAGATACATAGACCAGTGGAATAGAATAGAGAATCCAGAAATTAATCCAC 596
                         i   i i     i  i           v    i         v  i   i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_82974866_8    597 ATATCTACAGCCAACTGATTTTTGACAAAGGTGGCAAAAACACTGACTGG 646
                          i  i  ii i   i       i     i    v   i v  i v v   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_82974866_8    647 AGAA------GTCTCTCTGATACATGATGCTGCTGAAAAAACTGGATATC 690
                         i   ------    i iii i v   i     ---ii v         ? 
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTG---GGACAACTGGATAKC 431

  chr2_82974866_8    691 CATATGCGGAAGAATAAAACTAGACACCCACTTCTCTCCCTATATAAAAA 740
                           i    ii      i  ii i   v  i  i  v v  v    i     
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_82974866_8    741 TCAACTCAGAATGAATCAATCATCTAAATATAAGACCCAAAACTATAAAA 790
                          i      i    i    ?vv i      i     v i            
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_82974866_8    791 CTACTAGAATAAAACATAA-CGAAACACTTCAGGATGTTGGTCTGGAAAA 839
                           vi     v        i-? v  vv    iv  iv    vi i iv  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_82974866_8    840 AGATTTTATGAATAAGATCTTAAAAGCACAGGCATCAAAAACAAACATAA 889
                         v i   iv ii   v  ivii         i   v     iv   v   i
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_82974866_8    890 ACAAAT-GGA----------ATTA-------------------------T 903
                          i    -   ----------    ------------------------- 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_82974866_8    904 ATCCACAAAGTGAAAAGACAAGCTACAGAATGGAAGAAAATATTTGCAAA 953
                            v v               v i         i                
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_82974866_8    954 CCATTCATTGGACAGGATAATAATATTCAGAAAATGCAAGGAACTCAAGC 1003
                         i   vi  iv  i i iv v vi   i     v  ii  i      vvi 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_82974866_8   1004 ATCTCAACTGCAGAAGAAAAAATG---TGATT-AAAATTGGGCAAATGAA 1049
                          v     ivii i  ii v    i---ii   -    v        v  v
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_82974866_8   1050 CTGAACAGACATTTCTTAAAGGAAGACTTACAGTCAGTCTGGCCAAGAAG 1099
                         i    i          iv  i     iv    --- i --      v   
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACA---AAT--GGCCAATAAG 876

  chr2_82974866_8   1100 TAAATGAAAAAATTCTCAACATCACTAATCAT 1131
                         i v       i  v          ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (100 / 58)
Gap_init rate = 0.02 (11 / 674), avg. gap size = 5.09 (56 / 11)  


2879 27.73 1.22 0.99  chr2_83009551_83014315.rev     3369  4273 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_83009551_8   3369 GGAACACATATCCCATGCTCATGGATTGGAATAATCAATATCATGAAAAT 3418
                             - v          i             v v i     ii v  i  
  L1M4_orf2#LINE/      2 GGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83009551_8   3419 GACCATACTGCCCAAAGTAATCTACAGATTCAACACAGTTCTTATTAAAA 3468
                          i v     v      v i               i  i i i   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83009551_8   3469 TACCAACATCATTTTTCACAGAATTAGAAATATTAATCCTGAAATTCATA 3518
                          v   i vv v     ii     v v  v vii i     i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_83009551_8   3519 TGGAACTAACAAG--ACCCTGAATAGCCAATGCAATTCCAAGCAAAAAGA 3566
                              v i-    --    v          vi    iiii iv  i    
  L1M4_orf2#LINE/    151 TGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_83009551_8   3567 GCAAATCTGGAGGGGTCACATTACTGGACTTCAAAGTATACTGTTAGGCT 3616
                         i    vi      iv     i v ivi i      iiv    iiv i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_83009551_8   3617 ATAGTTACCAAAGCAGCACGGTGCTGGTATAAAAGTAGATACTTAGACCA 3666
                          i   v i   ii   iii   i    i    iii    i iv    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_83009551_8   3667 ACGGAACAGAA--GACAGACAAACCCAGACAAAAAGCCAAATATTTAGAA 3714
                          i    i    --  v  -----i     v v   v   v i     vii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAG-----TCCAGAAATAAACCCATACATTTATGG 344

  chr2_83009551_8   3715 CCAACTGATATTCTACAAGGCATATGAAAAT-ATAAATTGGGGAAAATAC 3763
                         i   i    v   v      -i iiv  i i-  vv v        iv i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_83009551_8   3764 ACCCTATTTAATAAGTAGCTCTGGGATAACTGGATAGCCACATGTGGAAG 3813
                          vi  v  i  i  i i iv      i         ?       iii   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_83009551_8   3814 AGTCAGACTGGATCCCTATCTCTCACCTTATACAGAAATCAATTCAAGGT 3863
                          i v iii    i     i   v    v      i    i  i    ii 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_83009551_8   3864 GGATCAAAGACTTAAATCGAAGACCTGATACCATGGTAATTCT-AGAAGA 3912
                               ?    i     vv    v  i v  i  ii-  i   -      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGA 542

  chr2_83009551_8   3913 CAATATTGGAAAAACTCTTCTGGATATTGGCCTGGGCAAAGAATTCATGG 3962
                         v  i  v  ?iv  v     vv  iv    vi i     v iv   v i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_83009551_8   3963 CTAAGACCCCCAAAGCAAATGGAATTAAAACGAAAATAAATAAATGAGAT 4012
                         v  v   v  v      v v v  iv   ivi      i      vi  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_83009551_8   4013 CTAATTAAACTAAAAAGTTTCAGAACAGTAAAAGAAATAATAATTAGAGT 4062
                         i v  i   v v    ii  iv vi vvi   i  v iv  v vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_83009551_8   4063 AAA----CAATCCACAGAATGGGATAAAATATTTGTAAACCATGCAACTG 4108
                         i  ----   i             v          i   i   ii v   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_83009551_8   4109 ATGAAGAACAAATATCCAGAATCTACAAGGAAACCAAACAAATCAGCAAG 4158
                           i i i  vvi          v  i  i   vi vv    v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_83009551_8   4159 AAATATTATAATAATCCCATT-AAAAGTGGGCAAATGACATGAATAGAAA 4207
                            v vvvv     i  v   -    i        v  iv        v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_83009551_8   4208 TTTCTCAAAAGAAGATATACAAATGGCTAAGAAATATATTAAAAAATGCT 4257
                               v                    i  v  ii i  v    i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_83009551_8   4258 CAGCATCACTAATCAT 4273
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (143 / 105)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 1.82 (20 / 11)  


2613 29.01 0.55 0.77  chr2_83014920_83020453     4133  5042 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83014920_8   4133 TGGAAACACTTTCCATGCTCATGGACAGGAAGAATCCATACTGTAAAAAT 4182
                               v iv i     i       iv      v iv   i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83014920_8   4183 GGATGTATTGCCCAAGGTAATTTATAGATTCAATGCTATTCCCATTAAAC 4232
                           vvi  i v     iv i  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83014920_8   4233 TAACATTGACGTTCTTCACACAATTAGAAAAAAAAAACATGTTAAAATTC 4282
                          vv  vivi v  i  ii  v  v v  v  ivvi v ---i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC---CTAAAATTC 147

  chr2_83014920_8   4283 ATACGTAATCAAAAAAGAACCTGTATAGCCAAGACAATCCTAAGCAAAAA 4332
                            i v  viiv  ii  v  v v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_83014920_8   4333 GAACAAAGCTGGAGACATCACGCTACACAACTTCAAACTATACTACTAGG 4382
                                 i     ivv    i  v v   i      viv      v i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_83014920_8   4383 CTACAGTAAACAAAACAGCATTGTACTGGTAGAAAAACAGACAAATAGAC 4432
                                  v   i    ii v       i v  ii i     v     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_83014920_8   4433 GAATCGAACATAATAGATAACTCAGAAATAAGACTGAACACCTACACCCA 4482
                         v   v   i v   v  v iii         iv iiv   ii  iivi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_83014920_8   4483 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCTC 4532
                         vi    i  i     ivv  v   i v  vv       i    i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_83014920_8   4533 TATTTAATAAATGGGTCTAGGAGAACTGACTAGCCATATGCAGAAAATTG 4582
                          v  i  i      vv  i   v     iv  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_83014920_8   4583 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 4632
                           ii         v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_83014920_8   4633 TAAAGATTTCAATGTAAAACCCCAAACCATAAAAACCCTAGAAGAAAACC 4682
                         i ?   ii v       i v iv    i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_83014920_8   4683 TAAGCAGCACCATTTAGGACATAAGCACAGCCAAAGATTTTGT-GACAAA 4731
                           i ?ivv viv  iiv   v vi vvi  v   v i   iv -  i vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_83014920_8   4732 ACACCAAAAGCAATTGCAACAAAAGCAAAGATTGACAAATGAGATCTAAT 4781
                                     vvv          v   i  v  i    vi  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_83014920_8   4782 TAAACTAAAGAGCTTCTTCACAGCACAAAAAACTACCATCAGAGTAAAAA 4831
                         i   v v  i i   i vii vv  v ii v    i  vv i   i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_83014920_8   4832 AACAACCTACAGAATGGGAGAAAATTTTTTCAATCTAACCATCTGACAAA 4881
                         i      i                 v   v   vii vvi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_83014920_8   4882 GGCCTAGTATCCAGAATCTACAAGGAACTTAAAGAAATTTACCA-GAAAA 4930
                           v  v           v  i  i     ivv v  v iv iv -i    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_83014920_8   4931 GAAAAAAAA---AATTAAAAAGTGGGTAAAGGACATGAACAGGCAGACAC 4977
                           v   v  ---    ?    i    i      iv    i  ----   i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG----ACAT 843

  chr2_83014920_8   4978 TTCTCAAAAGAAGACATTCATATGGCCAACAAACACATCAGAAAAAGCTC 5027
                              v        i  v  v        i  i     v i  i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_83014920_8   5028 AACATCACTGATAAT 5042
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (137 / 123)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.40 (12 / 5)  


3079 24.75 1.76 1.87  chr2_83050974_83053350      978  1886 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83050974_8    978 TGAAAAGATTTTCCATGTTCATGAATTGGAAGAATAGATACTGTTAAAAT 1027
                           i      v i           i         v vi   i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83050974_8   1028 GTCCATACTACCCAAAGCAATACATAGATTCAATGCAATCCCTTTCAAAA 1077
                          v v     v      vii  vi i        i         v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83050974_8   1078 TACAAAGGACATTCTTCACAGAAATAGAAAATATAGCCCTAAAATTTATA 1127
                          v v ivvi v  i  ii       v  v  vv iii         i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_83050974_8   1128 TGAAACCACAAAAGACCCAGACTAGCCAAAGCCATCTTGAACAAAAAGAA 1177
                           i  vii   ii        v        i v        v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_83050974_8   1178 CAAAACTGGAGGTATCACGTTACCTGACCTCAAATTATATTACATAGCTA 1227
                             ii      vv    ii v  ii ii     viv  i    v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_83050974_8   1228 TAGTAGCCCAAACAGCACAGTACTGGCATGAAAACAGAAACATAGACCAA 1277
                         i    ii v i    iiii          i ii i   v i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_83050974_8   1278 TGGAACAGAAGAGAAAACCCAGGGATAAATCCATACATCTACAGTGAGAT 1327
                              i    vv  i ii    ii     i        i  ii  v iv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_83050974_8   1328 CATTTTCAATAAAATTGCCAAGAACATACATTGGATTAAAGACAGTTTCT 1377
                         v      i i  iiv        v   v  v   ivv  ii i   i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_83050974_8   1378 TCAATAAATGTT-CTGGAAAAACTGGATATCTAAATGCAGAAAAAAATGA 1426
                             i     v -    i v         ? i v     --   i     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA--AAAGAATGA 448

  chr2_83050974_8   1427 CAATAAACCCATATCTCA-AT-ATATGCAAAAATCAAATAAAAATACATT 1474
                         viv ii    v  i    - i-    i       i  v v     iv  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_83050974_8   1475 AAAGACTTAAATTTATGATTTAAAACCATGAAACTACTTA-AAGAAATTT 1523
                          ?    i     v  v  vi      i  i     -    -      viv
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACA 547

  chr2_83050974_8   1524 TTTGAGAAACTCTCCAGGACATTTTTG---TGGGCAAAGATTTCTTGAGT 1570
                          vv ? v  v   i iv   ---i   --- i     v i      -  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGAC---CTTGGGTTAGGCAATGGTTTCTT-AGA 593

  chr2_83050974_8   1571 CAT-ACCTCAAAAGCACAGGCAGCGTAAGCAAAAATGAACAAATAGGATA 1619
                         i  -  vi          i   i iv   v      ii i    v   iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_83050974_8   1620 ACATAGGATCACATAAAGTTAAGTAACTTTTGCAAAGCAAAGGAAAGAAT 1669
                         v   ---------i   i    i-        iivvv       v vv  
  L1M4_orf2#LINE/    644 TCAT---------CAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_83050974_8   1670 CAACAAAGTGAAGAGACAATTCAC-GAATGGGAGAAAATATCTGCAAACT 1718
                            v        i      ii   -                i      ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_83050974_8   1719 ACCCATCTGACTAGGGGTTAACAAACAGAATATATAAGGAACTTATATAA 1768
                          ivi      iv    ii vii vv            i     iv  i  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_83050974_8   1769 CTCATTAA--AAAAATCTAATAATCCAATT--AAAATGGGCAAAA-ATCT 1813
                             v   --    iv v     i      --            i-  i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_83050974_8   1814 GAATAGACATTTCTCAAAGGAAGACATACAA-TGGTTAACAGGTATATGA 1862
                                        v  i     i      -   ii  i i i i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_83050974_8   1863 AAAGATGCTCAACAT-AGTTAATCA 1886
                                        - ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (137 / 85)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.83 (33 / 18)  


 930 22.79 1.36 1.36  chr2_83083294_83090260.rev      175   468 (6499)    L1M4_orf2#LINE/L1      615   908 (0)  

  chr2_83083294_8    175 AACAAATGCAAAACTAGATTAATGGGGTTACATCAAACTATAAAGCTTCT 224
                               v v    v     v   v  ii v       v vv   i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_83083294_8    225 GCCCAAAAAAGGACATAATCAACAGAGAAAAAAGATAACCCACAGAATAG 274
                          iv vvv        iv     v i  vi      i            i 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_83083294_8    275 GAGAAAATGTTTACAAAATATATATCTAACAAAGGGTTAATATCCTAAAA 324
                                 i   i    vi        i i  i  ii vi     - i  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC-AGAA 763

  chr2_83083294_8    325 GA-ATAAAGAACTCATGCAACTCAATAGCAAAAATACCCAAATAACTCAA 373
                         v -           v i          ii     v  --       i   
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGAC--AAATAACCCAA 811

  chr2_83083294_8    374 TT-AAAATTATGCAAAGAATTTAAATTGACATTTCTC-AAAAAAGTACAT 421
                           -    v iv      i    i   v          -   i   - i  
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG-ATAT 860

  chr2_83083294_8    422 ACCAATTGTAAGTAGGTATGTGAAAATGTACTGAAC-TTACTAATCTT 468
                           v   v iv i  i i ii      vi i  v   - i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (38 / 29)
Gap_init rate = 0.02 (7 / 294), avg. gap size = 1.14 (8 / 7)  

2807 27.65 1.86 2.62  chr2_83083294_83090260.rev     5561  6475 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83083294_8   5561 TGGAAAAACATTCCATGCTCATGGATAGGAATAATCAGTATCATGAAAAT 5610
                               i i  i     i        v    v v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83083294_8   5611 GGCCATACTGCTCAAAGTAAT-TATAGATTCTATGCTATTCTCATCAAGC 5659
                            v     v i    v i  -  i      v i  v  i ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83083294_8   5660 TACCA-TTGACTTTCTC-CACATAATTAGAAAAAACT-ACTTTAAGTTTC 5706
                          v   -i  v    i i-  v -    i-- v  i  - iii   iv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_83083294_8   5707 ACATGGAACCAAAAAAGAGCCAGTACAGCTAAGACAATCCTAAGCAAAAA 5756
                          i      viiv  ii  v    v i   i  i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_83083294_8   5757 GAACAAAGCTGGAGGTATCATGCTACCTGACTTCAAACTATACTACAGTA 5806
                                 i      vv   ii  v  ii i      viv       ---
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA--- 244

  chr2_83083294_8   5807 TAGTTTGAGGCTATAGCAACCAAAACAGCACGGTGCTGGTACCAAAACAG 5856
                         ------- i    i  i  i   i    iii   i    i iv ii i  
  L1M4_orf2#LINE/    245 -------AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_83083294_8   5857 ATATATAGACCAATGGAACAGAACTGAGGCCTCAGAAATAACACCACACA 5906
                          i       i        i    i    ivii         vv   i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_83083294_8   5907 TCTACAACCGTTTGATCTTTGACAAACCTGATAAAAACAAGCAATGGGGA 5956
                          i  iiii iv     i  i     ivv  vi  i v  vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_83083294_8   5957 AAGGACTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATG 6006
                            i ivvi  v  i  i              v      v  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_83083294_8   6007 TAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAACT 6056
                         i i  iiv    ii    i    v   i     v i              
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_83083294_8   6057 CAAGATGGAGTAAAGATTTAAATGTTAGACCTAGAACCATAAAACCATAA 6106
                            i     vi ?   ii       v   v   i   i       -----
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC----- 532

  chr2_83083294_8   6107 AAATCCTAGAAGAATATCTAGGCA-ATACCATTTAGGATATAGGCATGTG 6155
                         ---  i        v iv    ?i- v i -  iiv  iv v  vv iv 
  L1M4_orf2#LINE/    533 ---TCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGG 578

  chr2_83083294_8   6156 CAAAGACTTTATGACTAAAACACCAAAAGCAATTGCAACAAAAGCCAAAA 6205
                            v ii  iv iiv  vi            vvv          vv    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_83083294_8   6206 TTGACAAATGGGGTCTAATTAAA-TTAAAGAGCTTCTGCACAGCAAAAGA 6254
                          v  i    v  iii v  i   -     i -   i  ii vv    i  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

  chr2_83083294_8   6255 AACTGTCATCAGAGTGAA-------CCTACAGAATGGGAGAAAATTTTTG 6297
                         v   i   vv i      -------  i                 v    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_83083294_8   6298 CAATCTATCCATCTGGCAAAGGGCTAATATCCAGAATCTACAAGAAACTT 6347
                            vii  vi     ii  i  i  vi          v  i  ii    i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_83083294_8   6348 AAACAAATTTCACAGGAAAAAAACAA----CCTCATCAAAAAGTGGGCAA 6393
                         vv    -i iv i iv     i    ----  iv  i?    i       
  L1M4_orf2#LINE/    778 TTACAA-CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_83083294_8   6394 AAGATATGAACAGATACTTTTCAAAAGAAGATATTTATGAGGCCAAGTAA 6443
                          i   v    i   i i  i  v           vi viv      vv i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_83083294_8   6444 CATATGAAAAAAAGATCATCATCACTGGTCAT 6475
                           i       i v v   v     ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (156 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.73 (41 / 15)  


2060 25.37 5.22 1.49  chr2_83102620_83104301.rev      520  1189 (492)    L1M4_orf2#LINE/L1      214   908 (0)  

  chr2_83102620_8    520 CTGACATTACCTGACTTTGAATTATGCTACAAGGATATAGTAACCAAAAT 569
                           v   i v  ii i  ii  viv i      i v  i     i   i i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_83102620_8    570 AGCATGGTGCTGATATAAAAATAGATACACAGATATATGAAACAGAATAG 619
                           ii    i   ii    ii     i i i    vv   i  i     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_83102620_8    620 AGAACCCAGAAATAAAGCCGCATACCTGCAACCAACTGATTTTTGAAAAA 669
                            ii           v  ii i ii iiiii   i       i  v  i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_83102620_8    670 GTCAACAAATGGGGTGCA---AATAGGGAAATGACACCCTATTTAATCAG 716
                          viiv   ---- ii-  ---   i      vi i vi  v  i  iv i
  L1M4_orf2#LINE/    364 GGTGCCAA----GAC-CATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_83102620_8    717 TTTTGCTGGGAAAATTGTATAGTCATAAGTGAAAGGATGAAACTGGATCC 766
                          vv        v  i  v   ?i  i v ii    i     ii    i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_83102620_8    767 ATATCTCTTACCATATAAAAAAATTAACTCAAA-TGGATTAAGGACCTAA 815
                         v  i   vi        v               -     i ?i       
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_83102620_8    816 ACCTAAGACCTGAAACTAAAACATTCCTAGAAGAAAACCTAGG-GCAAAT 864
                          iv     v  i      v  v i  i           v    - i    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_83102620_8    865 CTTTGTTGGACGTTGGCCTAGGCAAATAATTT-------ATGACT----A 903
                            i  --   v    vi       - ii   -------     v---- 
  L1M4_orf2#LINE/    559 CTTCGT--GACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAA 605

  chr2_83102620_8    904 AGCAAATAAAACCAAAACAAAAATAGACAAACAGGACTT-----AAACTA 948
                             v viv   v   iv         i   iv      -----   i  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_83102620_8    949 AAAAGCTTCTGCACAGGAAAAGAAACGATCAACAGAGTGAAGAGACAGCC 998
                             -   i  ii vvv   i  v  v     v i      i     i  
  L1M4_orf2#LINE/    656 AAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_83102620_8    999 CACACAATGGGAACAAATATTTGCAAACTATGCATCTGATAAAGGGCTAA 1048
                             v       iv             ii  ii         i  i  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_83102620_8   1049 TATCTAGAATCTACAAGGAATTC----AAC--GAGAA-AAAAAAACAAAC 1091
                             i     v  i  i   i  ----   --i v  -     i     i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_83102620_8   1092 AGTCCTATT-AAAAATGAGCAAACGACATGAACAGACATATTTCAAAAGA 1140
                          ii  v   -       i     v  iv    i      v i  v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_83102620_8   1141 A-ATATG---GTAGCCAAGAA--ATGTGAAGAAAATGCTTAACATCACTA 1184
                          -    i---i i     v  -- ii    -  i     i       ???
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAA-AAGATGCTCAACATCAZZZ 903

  chr2_83102620_8   1185 ATCAT 1189
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.05 (113 / 55)
Gap_init rate = 0.03 (19 / 695), avg. gap size = 2.37 (45 / 19)  


 271 27.92 5.84 3.25  chr2_83142910_83146707.rev       22   175 (3623)    L1M4_orf2#LINE/L1      376   533 (375)  

  chr2_83142910_8     22 ATTAAATAGGCAAAGTACTGCTTTTTGAAAAAATTTGATGCTAGAAAAGT 71
                            v   i  v    v iv ii    v  v    -- i    i i v ii
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT--GGTGCTGGGACAAC 423

  chr2_83142910_8     72 TGGGTATCAGCATTGACAAAAG--TAACTGTTAG-CCAGTATTCCACCAC 118
                            i  ? vi   --i      -- i v-   i -  vv  iii   vv 
  L1M4_orf2#LINE/    424 TGGATAKCCACAT--GCAAAAGAATGAA-GTTGGACCCCTACCTCACACC 470

  chr2_83142910_8    119 AAACACAAAAACGAACTCAAAGTGTATCAGAG---TAT-TACAAGA--TA 162
                          v i       iv        i  v    ?  ---  v- ii    --  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_83142910_8    163 ATACTATAAACCT 175
                          v        v  
  L1M4_orf2#LINE/    521 AAACTATAAAACT 533

Transitions / transversions = 1.16 (22 / 19)
Gap_init rate = 0.05 (8 / 158), avg. gap size = 1.75 (14 / 8)  

1977 28.56 3.56 4.22  chr2_83142910_83146707.rev     2399  3298 (500)    L1M4_orf2#LINE/L1        1   894 (14)  

  chr2_83142910_8   2399 TAGAAACATATTCCATGTTCATGAATTAGAAGACTCAACAGTAGTCAGAT 2448
                          i    v    i           i   i       i  i v iv v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83142910_8   2449 GTCAATTTCTTTTTTCCAAGTTGATCTATAGATTCAAGGTAATACTAAAC 2498
                          v    vi---- ii    i        i        v i   v iv v 
  L1M4_orf2#LINE/     51 GGCAATAC----TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_83142910_8   2499 AAAGTCCCAGAAATTTATTCTGTGAATGTAAATAAAATGATTCTAAAATT 2548
                            i      vviii v  i  iii vi vi i  iv    i        
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_83142910_8   2549 TATTTAAAGATACATAAATCTCTGAAATATCAACACAAT---------AA 2589
                         i  v ii i  i  viiiv i v   vvii   v     ---------i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_83142910_8   2590 AGATCAAAGTTGGAGGACTGACACT-ACCACCTTCAAAATTTA--A-AAA 2635
                            v               v     -v   vi       i   -- -   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_83142910_8   2636 GACACTGTAATTAAGACAGCTTAACATTGGCAAAAGAATATATACTGGGA 2685
                          vi  v     i       iv iii i     v   i   v i ivvi  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_83142910_8   2686 TTAACAGGAATA-AATAGAAAGCCTGGGAATAGACCCACAAAAATAAAGT 2734
                          i  i-      -   v  i  i ii i    i     i v vv  vi  
  L1M4_orf2#LINE/    297 TCAAT-GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_83142910_8   2735 TAATTGATTTTTGAC-------TCAAGACACACACACTAGTAAAGAGGTT 2777
                         i          i   -------i      -  iv  v i vi  iiii v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATA 394

  chr2_83142910_8   2778 GTTGCTTTTAAAAAAATGAAGCTGGAACAGTTGGAAACACATGTGCAGGA 2827
                           --     v  v     iv     i   ii    v ?v  ii    ---
  L1M4_orf2#LINE/    395 GT--CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA--- 439

  chr2_83142910_8   2828 AAAAAATGAAATTAGACACAAATCTCACACTTTTCACAAAAGTAAACTCA 2877
                            i      i  i   v vv i       iv vi      i v      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_83142910_8   2878 AA-TGAATCATATAACTAAATATATAATACGGTACTCTAAAATTTTTAGA 2926
                           -  i    ? v v      i  vi vviiiv   v     i i     
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_83142910_8   2927 ATAAAGCACAGGAGAAAATGTATGTGAACT-GGGTTTGGCAGTGAGATTT 2975
                          v   i  i   ? v    v vi    v  -     v    i  ivv i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_83142910_8   2976 TAGA-ACAACACCAAAATCACAATCAATGAAATAAAATATTTAAGAATTT 3024
                             - ii         v     v   ii   v    -------------
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA------------- 626

  chr2_83142910_8   3025 AGACTTTGTTAATAAACATTTAATTAAGGTTTAATTAACATTAAAACCTT 3074
                         ----------    i i ---    i- ii  v  i  v       v   
  L1M4_orf2#LINE/    627 ----------AATAGATA---AATTG-GACTTCATCAAAATTAAAAACTT 662

  chr2_83142910_8   3075 CTGTTTTGAGAAAGACACTGTTAGGAGAATCAAAAGACAAGCTATATACT 3124
                         i   vi vvi  i      i i i  i i v         v i i v v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_83142910_8   3125 GAAAGAAAATCTTTGCAAAACACATATCTAACAAAGAATTTGTTTCTTAA 3174
                          ii       v        v  i      i i  i i i    v  ivi 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_83142910_8   3175 ACACACAAAAATCTCTTAAAAGCCAAGAATAAAAAACAAAACAATTTAAC 3224
                          i i i   i v      v  vi   v        ivv   i  iii  i
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_83142910_8   3225 T-AATAATGAGTAGAAGATTAGAAGAGGGAACTCACTATATA-TATATAT 3272
                          -  v    i i i i    v   v  iv vi  v i v v -v     i
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_83142910_8   3273 ATATGTACAA-AA--ATATGAAA---TGCTCA 3298
                          v   vv   -  -- i      ---      
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.44 (150 / 104)
Gap_init rate = 0.02 (22 / 894), avg. gap size = 3.18 (70 / 22)  


 428 32.87 0.00 1.40  chr2_83151004_83152674       45   187 (1484)    L1M4_orf2#LINE/L1      114   254 (654)  

  chr2_83151004_8     45 TCTTGTGGATATTACCAAATTGATTCTGAAGTTTGAATGAAGAGTCTAAA 94
                          i   ii  v   iv   ii    i  i  i  iiv   i i vv v ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_83151004_8     95 AACATGGAACAACCATCACAATATTGAAGGAGAAGAAGAAAGTTGGAGGA 144
                         i  vii   i i   vv     v     ii       v            
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_83151004_8    145 CTGACACAACCTGACTCTAAGACTTACTATAGCCAGTTGTAGT 187
                           v    vv  ii i ii  i        i i--  i ii   
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAA--AGCTACAGT 254

Transitions / transversions = 2.36 (33 / 14)
Gap_init rate = 0.01 (1 / 141), avg. gap size = 2.00 (2 / 1)  

1766 23.71 6.63 6.92  chr2_83151004_83152674      501  1179 (492)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_83151004_8    501 AAAGCTTACTATAAAGCTACAGTAATCAAAAC--TGTAGTATTGTTTTTT 548
                            i       i                 i  --   i   i  viv --
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-- 279

  chr2_83151004_8    549 TTTTTAAAAAAAAAAAAAAAAGACAAATAAAAAAATCAAAAGAACAGAAT 598
                         --------------  ii v     v   i ----    vi   i     
  L1M4_orf2#LINE/    280 --------------AAGGATAGACATATAGA----TCAATGGAATAGAAT 311

  chr2_83151004_8    599 AGCGGGCCCAGAAATTGACCCACATACATCTA--GTCAACTGATCATTGA 646
                         v v i i        vi     --     i  --     i    iv i  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAATTGATTTTCGA 359

  chr2_83151004_8    647 TGAAAGAGCTAAGACAATACAATGTAGCAAAGGCAGTCTTTTTCAACAAA 696
                         ii ii v  i     v  v     vi v  iiii        -       
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT-CAACAAA 408

  chr2_83151004_8    697 TGCTGCTGGAACAGCATCCATATGCCAGAAGTACTTATGTACATCCATAG 746
                           v      i   i ----------------------  v i ?   i v
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAAC----------------------TGGATAKCCACAT 436

  chr2_83151004_8    747 GCAAAACAATGAATCTTGACACAGACCTCACATCCTTTGCAAAAATTAAC 796
                               v      vi v   v vv        i v v i           
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_83151004_8    797 TTAAAATGCATCATACACTTGAGTGTTAAATGTGAAACTATGCAACT--- 843
                          i      v    ? v  i i i   v i vv i       iv    ---
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_83151004_8    844 GGAAGATCAAACAGAGGA--AAACCTAGATGACTTCGGGTATGTCAGTGA 891
                         i     --     v   ?--   i  vvi    i i    vv v  i  i
  L1M4_orf2#LINE/    537 AGAAGA--AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_83151004_8    892 TTTGATAGATATAACATCAAGGGCATGATCCATTAAAGTAATGATTAATA 941
                            vv       i   i   ii   ii v v iv    v  vi  vi   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_83151004_8    942 AGCTGAACTTTA------------------GTAC---------------C 958
                          ii  i    i ------------------  i --------------- 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_83151004_8    959 AAGAGAATAACAGGACAAATAACAGACTTGGAGAAA-TATTCGTAAAAGA 1007
                             i i i v i     viv     v v       -    i i   vv 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_83151004_8   1008 TACATTTGATAAACAACTGTTATTCAAAATATACAAAGAACATTTAAAAC 1057
                           i  i      ivi   vv   i  i      i       vi   v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_83151004_8   1058 --AACAATAAGAAAACAAACAACCCAGTTAAAAAATAGGCCAAAGACTTT 1105
                         --  i     i  i     i      i  ?      i   v  i  i  v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_83151004_8   1106 AACAGACATATCAGCAAAGAAGATATATAGGTGGCAAATAAGCCTATGAA 1155
                           i      v  vv             i ii    v       vi     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_83151004_8   1156 AAGATGCTTCACATCATATGTCAT 1179
                                 iv      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (92 / 65)
Gap_init rate = 0.02 (14 / 677), avg. gap size = 6.57 (92 / 14)  


3357 26.54 0.44 0.44  chr2_83227087_83233364     4879  5786 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83227087_8   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4928
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83227087_8   4929 GGCCATACTGCCCAAGGTAATTTCTAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83227087_8   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_83227087_8   5027 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_83227087_8   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_83227087_8   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_83227087_8   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_83227087_8   5225 ATCTGATCTTTGACAGACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i    iivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_83227087_8   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_83227087_8   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_83227087_8   5375 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_83227087_8   5425 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_83227087_8   5475 AACACCAAAAGCAATGGCAACAAAAGAAAAAATTGACAAATGGGATCTAA 5524
                         i            vvi                 v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_83227087_8   5525 TTAAAATAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5574
                          i     v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_83227087_8   5575 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5624
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_83227087_8   5625 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_83227087_8   5675 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_83227087_8   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5774
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_83227087_8   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2519 26.95 2.36 1.30  chr2_83322054_83324149      751  1596 (500)    L1M4_orf2#LINE/L1       36   890 (18)  

  chr2_83322054_8    751 TAATATTATTAAAATGTCCATACTACTCAAAACAATCTACAGATTCAATG 800
                                i    i   v v     v i    vii              i 
  L1M4_orf2#LINE/     36 TAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACG 85

  chr2_83322054_8    801 TGATCTCTGCCAAAAGTCCAATGGCATTTTGTTACAGAAATAGAAACAGC 850
                         ii   i  ii     vi   iiv  v    -  i       v  v -   
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTT-TTGCAGAAATTGACA-AGC 133

  chr2_83322054_8    851 -AATTAGAAACTAAATATGAAACTACAAAAATCCTCAAATAATCAGAACA 899
                         -i  ivv   v vv     i  v i   iiiv  ivi    ii  i    
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr2_83322054_8    900 ATCTTGATCGATAAGAACAAAGATGGAGACATCAAACTTCCTAACTTCAA 949
                                vvi v          v     ivv   v      i  i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_83322054_8    950 A--TTATTTTACAAAGGTATAGTAATCAAAACACTATGGTACTAGCATAA 997
                          --   i --      v  i         i   v i       i      
  L1M4_orf2#LINE/    234 AACTTACT--ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_83322054_8    998 AAACACACATATAGACCAATGGAACAGAATAGAGAGCCCAGAAATAAGCC 1047
                         ii i v         i        i     v     i          i  
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_83322054_8   1048 CATGTGAATAAAAATCAACTAATCTTTGACAAGGGCACCAAGATTACAAA 1097
                            ii- v v vii    i i  i  i        ii      ii ivv 
  L1M4_orf2#LINE/    332 CATAC-ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_83322054_8   1098 ATAGGAAACAAATAAACCCTTCAATAAATG-CGTTAGAAAAACTTCATAT 1146
                           i  i  vi    iv ii     i     -i i i i v    vv   ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_83322054_8   1147 TCATAAGCAAAAGAATGAAAGTATAACCTTACTTTACT---TACACAAAA 1193
                         i  i v             iv iv v  i   i i  v---  i      
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_83322054_8   1194 AACAATTCAAAGTAGACTGAAGATTTAAATATAA-ACCTGAAAATGTAAA 1242
                          vi  i     i i  iii?   ii     i   - v  i   v i    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_83322054_8   1243 ATCTCCTAGAAAAAAAAAAGCAGAGCAGAAAAACTCCTTGGCATTGGTCT 1292
                          -   i     i    ----  v  v? v   v  i v  i v    vi 
  L1M4_orf2#LINE/    531 A-CTCTTAGAAGAAAA----CATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_83322054_8   1293 TGGCAATGATTTTTTGGACATGACACCAAAA-CACAGGCAATAAAGGCAA 1341
                         v       i   i  i  i            -    i    i   i v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_83322054_8   1342 AAATAAACAAGTAGGACTATATCAAACTAAAAAATTTTTGTAGAGCACAA 1391
                              i i  i v     vi      v v     i      ivvv  v i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_83322054_8   1392 GAAACAATCAGCAGAATGAAAGGGCAACATACAGAAACATTAAAAAATGT 1441
                           v  v    iv i i     i i    vi      -iivv i     i 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAA-TGGGAGAAAATAT 724

  chr2_83322054_8   1442 T--CAAACCACATATCTAACAAGGAGTTAATATTCATAACATATAAGGAA 1489
                          --    i  i      i i    iii vi   i  v  i      i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_83322054_8   1490 TTCATACAACTGTATATTAAA--------TAACCAAAT-AAAAAATGAGG 1530
                         i  v       vv   v    --------     v   -?       i v
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_83322054_8   1531 AAAGGACATAAATAAATACTTCTAAACAGAAGAAATTAAAATGGCCAAAA 1580
                               iv i    i i i    vv v      v  vv          v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_83322054_8   1581 GATATATGAAAAGGTG 1596
                         iii i        i  
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATG 890

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.02 (16 / 855), avg. gap size = 1.94 (31 / 16)  


2467 23.25 2.15 7.00  chr2_83390846_83392857      592  1520 (492)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr2_83390846_8    592 ATTTAAAGATTTAATATTGTTAAAATGTCCTCATTACCCAAAGCAATCTA 641
                            vi    i             i   v vvi i v      vii     
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr2_83390846_8    642 TACATTCAGTGAAATGCCTATCAACATTCCAATAACATTTTTCACAGAAA 691
                         i v     ii v   v        v  i   iivi v     ii      
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr2_83390846_8    692 T-AAAAAAAGAATCCTAAAGTTTAAATGGAACAACAACAAAAAAACCCCA 740
                          -i v  ivvi        i  i v      vvi   ----iii    vi
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA----GGGACCCAG 170

  chr2_83390846_8    741 TATA-CCAACATGATCTT----AAGAAGAA---AGTTGGAGGCATTACAC 782
                         v   -    v ii     ----        ---         vv i    
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_83390846_8    783 TTCCTGCTTTCAAAA--TATTACAAAGCTATGATAATTAAAACAGCATGG 830
                             iiv        --  i          iii    i  i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_83390846_8    831 TACTGACATTAAGACAGACATATAGACCTATGAGACAGCATACAGA-TCC 879
                              i   v i  i           i v   ii i  v  vv   -   
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_83390846_8    880 AGAAATAAACTCTCACATACATTGTCAGTTGATCTTTGAGAAGCATTCCA 929
                                   i vi    vi  v    i     i  i  v   vi v   
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_83390846_8    930 AGAACACACAATTGAGAAAAAATATTTTCTTCAACAACTGGTATTGAAAA 979
                            v  iv    v i    i    v i i        v    ii  ii v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_83390846_8    980 AATGAAACATCCACATGCAAAAGAATAAAATTAGACAGTTATCTTACACC 1029
                           ivii i ?                i  i  i   vvi  i  i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_83390846_8   1030 ACACACAAAAATAAACTCAAAATA-AT----GACATAAACATAAGACCTA 1074
                          i i        v          i-  ----   v    ii     v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_83390846_8   1075 AAACTATAAAACCACAAAACTCCTAGGGGGAAAAAAAAAGAAACTCGGGG 1124
                                     --------  i   ----------  ii    ------
  L1M4_orf2#LINE/    521 AAACTATAAAAC--------TCTTAG----------AAGAAAAC------ 546

  chr2_83390846_8   1125 GAAAAAAAAGAATCTCAGGGGAAAAAGCTTCTTGACATTGGCCTTGGTAA 1174
                         -----------  ---   ? v   -v    v    v    vi v  i  
  L1M4_orf2#LINE/    547 -----------AT---AGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_83390846_8   1175 TGATTT-TTGGATATGACATTAAAAACACAGGGGAAAAAAAGCAAAAAAT 1223
                           i   -  i         ii    i    i v-  v     -       
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGC-AACAAAAG-AAAAAAT 629

  chr2_83390846_8   1224 -TATAAGAAAGACTACATCAAACTAAAGATCTTGTGCACAGCAAAAGAAA 1272
                         -v    ivvi    v       v v  i v   v  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_83390846_8   1273 CAATCAATGGAATAAAAAAGACAACCTATGAAACAGGAGAAAATATTTTC 1322
                          v     - i  vvi           i iii  ii             v 
  L1M4_orf2#LINE/    680 CTATCAA-GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_83390846_8   1323 AAACCATTCATCTGATAAGGAGTTAATATCCAAAATACAAAAAAAAATCA 1372
                            i   vi           iii vi      i    i v   i  v  -
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC- 777

  chr2_83390846_8   1373 CCTACTTCTCCATAGCAAAACGAAACAAAATACAAGTAACCCAATTTTTA 1422
                         -i   vv   v   ii    -- i     -------          ?-- 
  L1M4_orf2#LINE/    778 -TTACAACTCAATAATAAAA--AGACAAA-------TAACCCAATTW--A 815

  chr2_83390846_8   1423 GAAA-GGACAAAAGACTTCAATAAGCATTTCTGGAAAGAAGAAAGACAAA 1471
                         i   -  i    i  i  v    ii       vv        v v     
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_83390846_8   1472 TGGCCACTTGATTTAGGTTTAGGAAAAAGTGTTAATCATCAGGGAAATG 1520
                               ----  -- i ivi v     ii  i v v     ????????
  L1M4_orf2#LINE/    866 TGGCCA----AT--AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (127 / 86)
Gap_init rate = 0.03 (26 / 884), avg. gap size = 3.27 (85 / 26)  


2536 29.41 2.11 1.33  chr2_83397437_83399585      757  1657 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83397437_8    757 TGGAAAAACATTACATGCGCATGGATAAGAAGAATCAATATAGTTAAAAT 806
                               i i  iv    iv       vi     v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83397437_8    807 GGCCATACTGCCCAAAGCAACTTACAGGTTCAATGGTATTCCTATCAAAC 856
                            v     v      vii ii     i     i vv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83397437_8    857 TACCAAAGACATTCTTCATAGAATTAGAAAATAACT-ATTTAAAAATGCA 905
                          v   ivvi v  i  iii    v v  v  --i  -  iiv     v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr2_83397437_8    906 CATAGAACCAAAAAAGAGCCTGAATAGCCAAGGGAAATCTAAGCAAAAAG 955
                         i  i   viiv  ii  v  v          iiv  vii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_83397437_8    956 AACAAAGCAGGGAGCATAGTATTATCTGACTTCAAACTATGTTACAAAGG 1005
                                iv  ii vv vii i vi ii i      viv ii       v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_83397437_8   1006 TACAGTAACCAAAACAGCTTGATACAGGTACAGAAACAGACACATAAGCC 1055
                                 i   i    iv  i   v  i i iii i     i   iii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_83397437_8   1056 AATGGAATACAATAAGTAAATAGCCCAGAAATAATGCAACACACTTACAG 1105
                                  v   --- i i-  i          vv v i   i   ii 
  L1M4_orf2#LINE/    299 AATGGAATAGAAT---TGAG-AGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_83397437_8   1106 CCATCTGATCTTCAACAAAGCAAACAAAACAAG-CAATAGGAACAGGACA 1154
                         i  vi    i   i    i vviv   i  v v-    i  i v  i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_83397437_8   1155 CCCTATTCAACAAATGGTGCTGGGGTAACTGGCTAGCCATGTGCAGAAGA 1204
                         vi  v                   ii      v  ?   ii    i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_83397437_8   1205 TTGAAACTGCACCCCTTTCTTAAACCATATGCAAAAATCAACTCAGGATG 1254
                         v    ii  v      vi  i v       i       i      ii   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_83397437_8   1255 GATTAAAGACTTAAATGTAAAACCGAAAACTATAAAAACCCTGGAAGATA 1304
                            i ?    i         i v v            vi i i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_83397437_8   1305 ACCCAGGCAATATTATTCTGGACATTACAGTGGACAAAGACTTC------ 1348
                           vi   ?ivv v v   vv   v  iviv i i   v ii   ------
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_83397437_8   1349 ATGACAAACCTGCCAAAAGCAATTGCAATAAAAGCAAAAATTGACAAATG 1398
                               ------         vvv    i     v      v  i    v
  L1M4_orf2#LINE/    595 ATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_83397437_8   1399 TGATCTAATTAAA-CTAAAGAGCTCTGCACAGCAAAAGAAACTACCAACA 1447
                         v  ii v  i   -i    i vi i  ii vv    i  v    i   v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_83397437_8   1448 GGGGAAACAGACAACCTACTGGATGGGAGAAAATTCTCGCTAACTATGCA 1497
                         ii vi  v        i  v i            vi i  v  ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_83397437_8   1498 TCTGACAAAGGTCTAATATCCAGGATCTAAAGGAAACTTT---AATTTA- 1543
                              i  i  v  vi       i  v  v iii    i ---  i i -
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_83397437_8   1544 CAAGGAAAAAACAAACAACTCCATTAAAAAGTGGGCAAAAGAT----ATG 1589
                         i  vi    i     i   i v   ?    i        i   ----  i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_83397437_8   1590 GAAACTTTTCAGAAGAATATATACATGTTGCCAACAATTA--TGAATAAA 1637
                           v i  i  vi     v       vi v     i  vi --    v i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_83397437_8   1638 AGCTCAACATTACTGATTAT 1657
                         v         i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (159 / 102)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


1830 26.23 17.96 1.03  chr2_83476076_83477994      654  1427 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_83476076_8    654 AGAGATATTCTATGTTCACTGATAAGAAGACATGATAATGTCAAGATTTC 703
                          i      i i       iv   vi      v i   v   i     vv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_83476076_8    704 AGTTTTTCTCAACTTTATCTAGAGACTCAATGCAATCCCAAACAAAGTTC 753
                          i vi i i   v  v     v   i    i        v v    i i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_83476076_8    754 T-GCAAGTTATTTTGTGAATATTTACAAAC-AATTCTAAAATGTATAAAG 801
                         i-  vivi v     iii v   v    i -i  i       vi   vi 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_83476076_8    802 AGAGATAAAAGGCCAAGAATAGCCAACACAATTTTGAAAGAGAAGAACAA 851
                          i vii  ii i  v           v     i      i          
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_83476076_8    852 AATTGGAGAACTGACAGTACTCGACTTCAAGACTTACTGTAAAAC-GCAG 900
                          i      i   v   v v i i i     i       ii   i -i   
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_83476076_8    901 TAATCAAGATGGAGTGGTTTTGAC----GCATAGAAAAGTATGTCAACGA 946
                                  ii v     vi  i ---- v     v vi  vi    i i
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_83476076_8    947 AACAGAATAAAAAG-CCAGGCAATAGACTCACACAAATATAGTCAACTGA 995
                           i     vi i  -    i-    i  i  i   vv   i     i   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGA-AATAAACCCATACATTTATGGTCAATTGA 352

  chr2_83476076_8    996 TCTTCAGCAAGGAAACAAAG-CAATGCCATGGAGAAAAGACAGTGTTTTC 1044
                          i   ii     ivi v   - v  v v    i    ii i   v     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_83476076_8   1045 -------------------------------------------------- 1044
                         --------------------------------------------------
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_83476076_8   1045 -------------------------------------------------- 1044
                         --------------------------------------------------
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_83476076_8   1045 ----------------------TATAAAACTAATAGAAATAAACATAGAG 1072
                         ----------------------         vv     iv        i?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_83476076_8   1073 G-AAATGCTTTCTGAAATTGGACTCGGCAAAAAGATCTTGAGATG-GACT 1120
                          -    -   iv   vv    ii v     viivv    -    i-   v
  L1M4_orf2#LINE/    553 GTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACA 600

  chr2_83476076_8   1121 TCAAAAGCATAGGAAACAAAAGCAAAAACAGACAAATGGGGTTACATTAA 1170
                         i        i i v        v     i   i    v  ii v   i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_83476076_8   1171 ACTAAAAAGTTTCTGAACAGCAAA--ATA--ATCAATAAAGTGAAGAGAA 1216
                          v v    ii  i  vi vv    -- i --     v        i   v
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_83476076_8   1217 CACCTACAGAATGGGAGAAAGTATTTA-AAATCTATGAATCAGATAAGGG 1265
                         v   i               i     i-     -  iv   v        
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGGG 749

  chr2_83476076_8   1266 GTTAAATTCTAAAATATAAAAGGGACTCAAACCACTCAATAGCAAAAAGA 1315
                         ii vivv  i i      v  i i    vv  v        ii       
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_83476076_8   1316 AAACCAAATAATGTAATTTAAAAACGGGCAAAAGGCCTACATAGACATTT 1365
                         ----       ivi    ?     i       i iii iv          
  L1M4_orf2#LINE/    800 ----CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_83476076_8   1366 CTTAAAAGAGGACATGCAAATATCCAACAGATACACGAAAA-ATGTTCAA 1414
                           iv     i  i  i     iv    i iii   i     -   i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_83476076_8   1415 TATCAATAATCAT 1427
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (125 / 76)
Gap_init rate = 0.02 (18 / 905), avg. gap size = 8.17 (147 / 18)  


3181 27.10 0.88 0.44  chr2_83485757_83492027     4876  5779 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83485757_8   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 4925
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83485757_8   4926 GGCCATACTGCCCAAGGTAACTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i ii           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83485757_8   4976 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 5024
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_83485757_8   5025 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTGAGCCAAAAGA 5074
                               viiv  ii  v  v v  v     iv     i   ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_83485757_8   5075 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5124
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_83485757_8   5125 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGATCA 5174
                                i   i    ii         i iv ii ii  v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_83485757_8   5175 ATGGAACGGAAC--AGAGCCCTCAGAAATAACGCCGCCTATCTACAACTA 5222
                               ii   i--    i  --        vv  iivi  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_83485757_8   5223 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5272
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_83485757_8   5273 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5322
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_83485757_8   5323 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5372
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_83485757_8   5373 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAAC 5421
                         i ?    i    i  v   v       i      -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr2_83485757_8   5422 CTAGGCATCACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5471
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_83485757_8   5472 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5521
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_83485757_8   5522 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCCTCAGAGTGAAC 5571
                          i   v i  i i   i  ii vv    i  v    i vvv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_83485757_8   5572 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5621
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_83485757_8   5622 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACCAGAAAA 5671
                         i  i  vi          v  i  v      vv    v iv iv v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_83485757_8   5672 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5717
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_83485757_8   5718 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5767
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_83485757_8   5768 AACACTGGCCAT 5779
                          v  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2319 26.28 1.78 6.70  chr2_83556404_83561450     3601  4555 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83556404_8   3601 TGGAAA-ACATTTCATGCTTATGAATTGGAAGAATCAATATTACTGAACT 3649
                               - i  ii    i i   i         v i      ii i iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83556404_8   3650 GACCATAATGCCCAAAGCAATCTATAGAGTGAATAGAGTTCCTATGAAAT 3699
                          i v   v v      vii     i   v v  iiv i i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83556404_8   3700 TACCAA-TGTCATTTTT-CGGATAACTAGAAAACAAAATCCTAAAGTTTA 3747
                          v   i-  i v     - i  -  i iiv  i vi -       i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGA-TCCTAAAATTCA 148

  chr2_83556404_8   3748 TATGGAACCAAAAAAGAGCCCAAAA-AGCAAAAGCAATGCTAAGCAAAAC 3796
                                viiv  ii  -    i  -   v   i    vi i --    v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGA--AAAAG 195

  chr2_83556404_8   3797 AAAAACAAAAACAAACAAACAACAACAACAACAACAAACCAGAGATAGGA 3846
                           i      iviii -ii  ------------------i  ---------
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGA-GGAC------------------TCA--------- 217

  chr2_83556404_8   3847 CATTGCTTGACTTTAAATTATACTATATGATTATTGTAACCAA-AGAGTG 3895
                           i v iii i  i   viv     i viii  iv    i   - v    
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_83556404_8   3896 TGGTACTGGTACAAATATAGACACGTTAATCAATGGAACAGAATAGAGAA 3945
                                  i i  iv       ii vi          i     v    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_83556404_8   3946 CCCGGAAATAAAGCTACAGACCTACAACCAATTGATCTTCAACAAAGTCA 3995
                         i  i        v i i v ii  iiii        i   i    i ---
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG--- 364

  chr2_83556404_8   3996 GTGCGAAAATGAA-CAATGGGGAAAGGACAACTTATTCAATAAATTGTGG 4044
                             v  i iv v-            i i iii v     i    v   v
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_83556404_8   4045 GAGGAATATTGGATAGCCGTATGCAGAAGAATAAAACTAGATCTCTATCT 4094
                         vi   vv i      ?  ii     i      i  ii i  i i   i  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_83556404_8   4095 CTTACTATATGCAAAAATTCACTCAAAATGGATTAAAAAATTAAATATGA 4144
                          vi  i    i        v             i ? i vi     i i 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_83556404_8   4145 GACCTGAAACTATAAAAATTCTAGAAGAAAACCTAAGAAAAACTCTTCTT 4194
                           v  i           v ii           v  i ?iv  v     v 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_83556404_8   4195 GACATTGGGGTAGGCAAAGAATGTACTATTAAACC---CAC-AAAAGCAA 4240
                            v     v       v ---  -i v   i iv---   -       v
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATG---GT-TTCTTAGATATGACACCAAAAGCAC 610

  chr2_83556404_8   4241 ATAAAACAAAAACAACAA-AACCAAATAGGACTTAAT--AAATTAATGAT 4287
                          viv       iv  v  - ivi    v      v  --       vi -
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA- 659

  chr2_83556404_8   4288 CTTCTGCACAGCAAACAAACAAACAAACAAACAAACAAAAAAACTATCCA 4337
                            i  ii vv    -----------------ii   ------     v 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAA-----------------GGACA------CTATCAA 686

  chr2_83556404_8   4338 CAAATTACACAGACAACCTAGAGAATGGGAGGAAATATTTGCAAGTTATG 4387
                         v   v iv v        i v          i            i i  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_83556404_8   4388 CTTCTGACAAATGAGCAATTTCTAGAATCTACAAGGAACTCAAACTGCTC 4437
                         iv     i  iv  vivi v  i     v  i  i      vv  vi   
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_83556404_8   4438 AACCAGAAAAATTCCAACACCACCATTAAAAAGTGGGCAAAGAAC----A 4483
                           iv v     vv v  i v v v   ?    i         i i---- 
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_83556404_8   4484 CAGATATTTCTCAAAAGAAGATATACAAGCAACCCACAAGCATATGAAAA 4533
                         i   i       v               iiii  v i     i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_83556404_8   4534 ATTACTCAACATCACTATTTAT 4555
                         iv i          ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (155 / 92)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.38 (81 / 24)  


2986 27.17 0.66 0.77  chr2_83691029_83697086.rev     4658  5566 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83691029_8   4658 TGGAAAAACATTCCATGCTCATGAATAGAAAGAATCAATATTGTGAAAAT 4707
                               i i  i     i     i  v i    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83691029_8   4708 GGCCATACTGCCCAAAGTAATTTATATATTCAATGCTCTTCCCATCAAAC 4757
                            v     v      v i  i  i v      i  vv i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83691029_8   4758 TACCATTGACATTCTTCACAGATTTAGAAAAAA-AATACTTTAAAATTTA 4806
                          v   vivi v  i  ii    vv v  v  iv-i  v  --      i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chr2_83691029_8   4807 TATGGAACCAAAAAAGAGCTCTCATAGCCAAGACAATCCCAAGCAAAAAG 4856
                                viiv  ii  v ivvv        i      iii iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_83691029_8   4857 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTGTAAGCC 4906
                                i      vv   ii  v  ii i      viv    ii  iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_83691029_8   4907 TACAGTAACCAAAACAGCATGGTACTGGTAACAAAACAGAAATATAGACC 4956
                                 i   i    ii         i vv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_83691029_8   4957 AATGGAACAAAATAGAGACATCAGAAATAACACCACACATCTACAATCAT 5006
                                i i   v    vvi         vv   i    i  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_83691029_8   5007 CTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCCCT 5056
                         i    i   i    ivv  v   i v  vv       i    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_83691029_8   5057 ATTTAATAAGTGGTTTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5106
                         v  i  i  i    vi     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_83691029_8   5107 AACTGGACCCCTCCCTCACATCTTATACAAAAATTAATTCAAGGTGGGCT 5156
                          ii         v       i v              i    ii   iii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_83691029_8   5157 TAAGACTTAAATGTAAAAGCCAAAACCATAAAAGCCCTAGAAGAAAACCT 5206
                         v?    i         i   i     i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_83691029_8   5207 AGGCA-ATACCATTCAGAACAT--AGTTATGGGCAAAGATTTTAT-GATA 5252
                            ?i- v i -   ivi  v --i    --     v i   iv -    
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATA 595

  chr2_83691029_8   5253 AAATCACCAAAAGCAATGGAAACAAAAGCTAAAATTGACAAATGGGATCT 5302
                         vi -           vvi v        vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_83691029_8   5303 AATTAAACTAAAGAGCTTCTGGACAGCAAAAGAAACTATCATCAGAGTGA 5352
                         v  i   v v  i i   i  vi vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_83691029_8   5353 GCAGGCAATGTACAGAATTGGAGAAAATTTTTGCAATCTATCCATCTGAC 5402
                         iv  i   ivi       v         v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_83691029_8   5403 AAAGGTCTAATATTCAGAATTTACAAGAAACATAAACAAACTTACAAGAA 5452
                           i  v  vi   i      v  i  ii   vivv    -  i vv iv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chr2_83691029_8   5453 AAAAAACAAACAACTCCATCAAAAAGTGGGTAAAG-ATATGAACAGACAC 5501
                             i     i   i v  i?    i    i    -  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_83691029_8   5502 TTCTCAAAAGAAGACATTCATGTGGCCAAAAAGCATATGAAAATAAGCTC 5551
                              v        i  v  vi       v     i       v v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_83691029_8   5552 GACATCACTGATCAT 5566
                         i      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (138 / 105)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3230 22.16 5.21 0.83  chr2_83728702_83733513     3469  4312 (500)    L1M4_orf2#LINE/L1       18   898 (10)  

  chr2_83728702_8   3469 TTCATGAATTGGAAGATTTA------TCAAGATGACACTACACCTCTAAT 3512
                               i         i   ------ i      i  v   v  i v   
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr2_83728702_8   3513 TGATTTTTACCTTCAATACAACCCCTATCGCAATCCCTATTTCAATCTT- 3561
                             i vi vv     ii   i       iv      vii v vv i  -
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr2_83728702_8   3562 ------ATTACAAAGCTGATTCTTATATTCATATGTAATTTCAAGAGATC 3605
                         ------   ivv        i  v v         v  v v    i  i 
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_83728702_8   3606 CCAAATATTCAAAACATCCCTAATAAAAAT---CAAAGTTACAAAATACA 3652
                          vi    vi       vi i i v   i v---       iv ii iv  
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_83728702_8   3653 CACTTCCCAATATCAAAACATATTATCTGGCTATAATAATCAAAACAATG 3702
                                    v       v  i  ivvi    i i       i   i  
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_83728702_8   3703 TTGTACTGACACAGAGTTAGATATATACATCAATGGAATAGAATTGAGAG 3752
                          v      i  i ii v    i     v                      
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_83728702_8   3753 TGCAGATTTAAACATATATATGGATAGTCAATAGATTTTTGAAAAGAACT 3802
                          v    vv     vi   i  vv  i      v      i  v   ii- 
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG-T 366

  chr2_83728702_8   3803 TTCAAGACCATTAAATGAGAAAAGAATAGTCTCTTTGACAAATAATGCAG 3852
                         vi          v    i i            i  ii      ii   v 
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_83728702_8   3853 GGGCAACTGGATAGCCACAGGCAAAAACAATGAGTTTAGATCTTTATCTG 3902
                           i          ?     v      i-     iv  i  i ii  i  v
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAG-AATGAAGTTGGACCCCTACCTC 465

  chr2_83728702_8   3903 ACACCATATACAAACATTAACTCTAAATGGATCA-AAATCTAAGTATATG 3951
                                       v        v          - i i    i i  v 
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_83728702_8   3952 TGCTAAACCTATAAAACTAT---AAGAAAACATAGGAGTAAATTTTTATA 3998
                         v      v          v ---             ?      i  ii i
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_83728702_8   3999 ATCTTGGATTTGGCCAGGGGTTCATAGATA-----------GCACAAGCC 4037
                          i     i  v   v v  v   v      -----------        v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_83728702_8   4038 TCAAAA----ACATACATA--CTGGACTTCTTCAATATTCAGAACTTTTG 4081
                         v     ---- v   v   --i        v    v   v i        
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_83728702_8   4082 TGCATCAAAGAACACTTTCAATAGTGTAAAAA----ACCTGAAGAATGTG 4127
                            v      i     v    v iv  i    ----   iiv      v 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_83728702_8   4128 ACAAAATATTTTCAAATCAACATATCACATAAGAGGATAGTATCTAGAAT 4177
                          v         v       -i     vv     i iv v     i     
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCA-TATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_83728702_8   4178 ATATTTTTAAAACCTCTTATACCTAAA-AATAAA--GACAAAATAATCCA 4224
                             v---  i v      i v  v  -      --      -   i   
  L1M4_orf2#LINE/    765 ATATA---AAGAACTCTTACAACTCAATAATAAAAAGACAAA-TAACCCA 810

  chr2_83728702_8   4225 ACTAGAAAATTGGCAAAGAACTCCAAGGGACATTTATCCAAAGAAGATAT 4274
                          i ?i     v       i i iv  vi       v              
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_83728702_8   4275 ACAAGGGGCAAACAAGCACATGAGGAGCTGCTCAATAT 4312
                             iv   v  i          ii  v       i  
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

Transitions / transversions = 1.11 (97 / 87)
Gap_init rate = 0.02 (16 / 881), avg. gap size = 3.19 (51 / 16)  


2223 27.13 5.33 2.27  chr2_83742301_83747210     3539  4419 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83742301_8   3539 TGGAAAGATATTCCATGCTCATGGATCAGAAGAATCAATATTGTTAAAAT 3588
                                    i     i        ii     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83742301_8   3589 GATCATACTGCCCAAGACAATCTATAAATTCAATGCAATTCCCATTAAAT 3638
                          iiv     v     ivii     i i      i     i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83742301_8   3639 TACCAACATAATTTTTCACAGAATTAGAAAAA--AATTCTAAAATTTGTA 3686
                          v   i vvvv     ii     v v  v  i--i  i        ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_83742301_8   3687 TG-AAATGAAAAAAAGCCTGAATAGCCAGAACAATCCTAAGCAAAAAAAA 3735
                           -     v  iii v  v         i       i i ---    i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAA 197

  chr2_83742301_8   3736 TAATAAAGCTCAATGAATCACATTACCTGACTTCAAATTACACTACAAGG 3785
                         v  i    i vi v  v     i v  ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_83742301_8   3786 CTATAGTAAACAAAATAGCAGTTGATGGTAAAAAAATAAATAAATAAATA 3835
                            i     v   i i  ----  -     vviiv    i------i   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAG----TG-TGGTACTGGCATAAG------GATA 286

  chr2_83742301_8   3836 CACACATAGATTCATGGAACAGCATAGACAACCCAGAAATACAGCCA--C 3883
                         v   i      iv      i  v  v  v ii         v v   -- 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_83742301_8   3884 ATTCCTACAACCAATTGATCCTTGACAAAGTCAACAAAAAAGTACACCAG 3933
                            --  iiii        ii i     i viiv   i vvi v  vii 
  L1M4_orf2#LINE/    337 ATT--TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_83742301_8   3934 GTAAAGAGCTCCCTATTCAATAAATGGTGCTAGGAAAATTAAATAGCCAT 3983
                          v     iivvi  v     i          i   v  i ii   ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_83742301_8   3984 ATCCAGAAGAATAAAACTGGACCCAGATATCTCACCATCTACAAAAATTA 4033
                           v  i      i  ii       vv iv  v      v           
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_83742301_8   4034 GCTCATGATAGATTAAACACTTAAA--------------CTATAAAAATC 4069
                         i    vi  i   i ? v  i    --------------        v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_83742301_8   4070 CTAGAAGAAAACCTAGGGAAAATTATTCTGGACATTGGCTTAGGCAAATA 4119
                         i           v    ?iv  v v   vv   v    v        - i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TG 583

  chr2_83742301_8   4120 ATTTAT--GACTAAGTCCTCAAATGCAAATACAACAAAGGAGACAAAAG- 4166
                         i   v --  -  v v vi    v   v vi       i  i v  v  -
  L1M4_orf2#LINE/    584 GTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_83742301_8   4167 ------GAATTT------AATTAAA-----CTGTACAGCAAAAGAAATGA 4199
                         ------ i i  ------       -----i   i vv    i  v iv 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_83742301_8   4200 ACAATGGAGTACATAGACAACCTCAATAATGGGAGAAAATATTTTCAAAT 4249
                         v   vii   iv v        ivv v                 v     
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_83742301_8   4250 AATGCATCTGACAAAGAAATAGTATCCAGAATTTGCAA-GAAC-CTCAAA 4297
                         v  ii      i  i i v v           v ii  -    -  i v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_83742301_8   4298 ACACTCAACAA----GAGA-AAACAATCCCATCAAAAAGAGGGCAAAGGG 4342
                           --    i  ----i   -   i  i  v  i?    iv         i
  L1M4_orf2#LINE/    783 AC--TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_83742301_8   4343 CATGAACAGACATTTTTCAAAATTAGTCGTATAAGCAGCCGACAAAAATT 4392
                         iv    i        i  v   vv  vii  i  iii   i i  iv iv
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_83742301_8   4393 TTAAAAAGC-CTCAACATCCAGAATCAT 4419
                          v    iii-         v????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.19 (67 / 21)  


1069 30.27 8.74 2.02  chr2_83768237_83772030.rev       15   460 (3334)  C L1M4_orf2#LINE/L1   (321)   587   112  

C chr2_83768237_8    460 TTTTTCACAGAACTAGA-AAGAAAATATTCTTAAATTTATATG-AAACAA 413
                              ii     v v  -   vvi  --i  v     i     -   iiv
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGAT--CCTAAAATTCATATGGAAATGC 159

C chr2_83768237_8    412 AAAGAAGTCAGAATAATCAAAGCAATCCTAAGCAAAAAGGACAAAGCCAG 363
                           i i vi       ii    i     i i iv  i   i      iii 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

C chr2_83768237_8    362 AGGCATCATATTATCTGACTTCAAAAAATACTACAAGACCACAGTAGCCA 313
                            vv   i i vi ii i       vv        ii i      ii  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

C chr2_83768237_8    312 AAACAGTATGATGCTGGTACAGAAGCAGACACAGAGACCAATGGAATAGA 263
                          i     i  i i    i i iiiii     i v   i            
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

C chr2_83768237_8    262 ATAGAGAACCAACAAATAAAGCCCCACATTGACAGCCATCTGATCTTCAA 213
                           v    ii v v       v  vi     v ii i  vi    i   i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

C chr2_83768237_8    212 TAAAATCAGTG--GAAATAAG-CAAGAGTTAAAGGAT---CCCTTACGCA 169
                         i  ii---   --i i iv v-   vi vv    i  --- ii  ---  
  L1M4_orf2#LINE/    360 CAAGG---GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT---CA 403

C chr2_83768237_8    168 ATAAATGATGCTGGGATGACTGGCTTTTCATTGGTAGAAGAATGAA---- 123
                          i     i        ii     v v?i  ivv i i         ----
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

C chr2_83768237_8    122 ---------------------------ATCAACTCAAGATTAATTAAGGA 100
                         ---------------------------  i       i  vi  i ?i  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

C chr2_83768237_8     99 CTTAAGTGTAAGACCTCAAACTATAAAAATCCTCGCAGAAAACTTAGAAA 50
                          i   i       v  v           v  i v v       v   i?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

C chr2_83768237_8     49 ATAATTTTCTTAACATCAGCCTTGGCAAATAATTT 15
                         vv   i   v i  v ii vi v     - ii   
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTT 587

Transitions / transversions = 2.07 (89 / 43)
Gap_init rate = 0.02 (10 / 476), avg. gap size = 4.80 (48 / 10)  

2513 25.81 3.01 5.38  chr2_83768237_83772030.rev     2373  3302 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83768237_8   2373 TGGAAAGTTATCCCATGAGTATGAATT---------AATATTGGTACAAT 2413
                                v         vvi   i   ---------       v  vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83768237_8   2414 TCCCATACTATCTAAAACAAA--GCAGATTCAAAACAATGCCTATGAAAA 2461
                         vv v     vi i   vii v--i         vi    v     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83768237_8   2462 TTCCAA-TGTCCTGTC-ATATAAATAGAAAAAATAAGCCTAAAACTCACA 2509
                          i   i-  i i v i-ii v    v  v  iv i v       i   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_83768237_8   2510 TGGAAGCACAAAAAA---ATAACAACCAAGGCAATTATGAGCAAAAAGAA 2556
                              iii   iii --- v  i i    ii    iv   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_83768237_8   2557 CAAAACTTAAGGATTATTTATTTTCTTCCTATAGGGTTGAAACAAAACAA 2606
                             ii vi    i -----------------------------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACT----------------------------------- 215

  chr2_83768237_8   2607 AATCACACTAACTGATTTCAAATACT-GCTACAAATCAGTAGTAATTAAA 2655
                         ---      vv ii        -   -i       v vii      i  i
  L1M4_orf2#LINE/    216 ---CACACTTCCCAATTTCAAA-ACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_83768237_8   2656 ACAGCATGGTACTGGCAAAAAAAAAAAAATGACTCATTGACCAATGAAAC 2705
                             ii           v  ii v i v  -----  v  i     i  i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACAT-----ATAGATCAATGGAAT 306

  chr2_83768237_8   2706 AGAATAGAGAGCCCAGTCATGAATTCATGCATGTGTACAGTCAAATGATT 2755
                              v     i    vv  i  ii   i   - -  ii     v     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACAT-T-TATGGTCAATTGATT 354

  chr2_83768237_8   2756 TTCAACAAAGGTGTCAAA--CATGCACGCTAAGAAAAGGAGAGTTTCTTC 2803
                            i    i    i   i--   v  v-- ii i    i v   i i   
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTCTTTTC 402

  chr2_83768237_8   2804 AATAAATAGTGTTAGGAACATTGAATATTTCTAGGCAAAACAATGAAAGT 2853
                           i    i   i i   vv i  i   ?iivi v      v      iv 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_83768237_8   2854 TGACCGTTCTTTTACACCCAATACAAAAATCAACTAAAAATGGATTCAGG 2903
                         v    vi vii i     vv          i    v         iv?i 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_83768237_8   2904 ACTTAAACATAAGACCTGAAACTGTAAAACTATAAGGAGCAAACATAGGG 2953
                           i    ii     v  i     i       v v  i  v         ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_83768237_8   2954 AAAAA-CTACACAACATTGGTTTGAGCAATAATTTTTAAAATTTGACCCC 3002
                         iv   -  v iii  v    v  ii     ii   i v i  v    v  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_83768237_8   3003 ACAAGTGCAGGCAATTAAA---AAAATAGACAAATGGGATTACATTGAAA 3049
                          v   ii  i    iv   ---        i    v   i v   ii   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_83768237_8   3050 TAAAAAGATTCTGCACAACAAAAGAAAATAATAACAGAGTGAAA-GATAA 3098
                          v    iv  i  ii vv    i  v v  vi  v i       -  i  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_83768237_8   3099 CCTATGAATTGGGAGAAAATATTTGCAAGCCTTACATCTGATAATGGGTT 3148
                           i iii v                   ii v  i         v  ii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_83768237_8   3149 AACATCCAAAATATATAAAGAACTC----AACTCTATAGAAAGAAAATAA 3194
                         vii     i                ----     v   iv  i  i i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_83768237_8   3195 ATAATCCAACTTAAAAAAGTAAGTAAAGGACTTGAGGAGACATTCCTCAA 3244
                             i    i ?     -- ii i      i    iv       i   v 
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_83768237_8   3245 ATGTAGATATAGAAATGGACAACAGATATATGAAAAAATGTTCAACATCA 3294
                          v v       v      v   i iii i       i   i         
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_83768237_8   3295 CTAATCAT 3302
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.71 (149 / 87)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.33 (78 / 18)  


 948 23.02 2.38 2.78  chr2_83797768_83799417.rev       36   287 (1363)    L1M4_orf2#LINE/L1        1   251 (657)  

  chr2_83797768_8     36 TAGAAAGGTTTCCCATGTTCTTGTTCCAGAAAACTCAGTGTTTTTAAAGT 85
                          i     i v          v  vviii   i   i i i  v    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83797768_8     86 GGCAATATTCCCCAAATTAATCCACAGATTCTATAAAATATGTATTCATA 135
                                i          i   i        v iiv   viv   iv v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83797768_8    136 CCATAGCTAGAGGTTTTTTTTTCCAGAAGTTGACAACCCTATTCTAAAAT 185
                         i vi    i-----ii      v     i       v iv  i       
  L1M4_orf2#LINE/    101 TCCCAGCTG-----CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_83797768_8    186 TAATATGGAAATGCAAGAGACTCAAAATAACTTTAAAA-AATCT-GCAAA 233
                          v               i   i  i    i i--    -     - v   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCC--AAAACAATCTTGAAAA 193

  chr2_83797768_8    234 AATAG--CA--GTTAGAAAGCTCACAATTTCCAATTTCAAATTTTACTAC 279
                          iv  --  --   i  iii      v  i           vi       
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_83797768_8    280 AAAGCTAC 287
                                 
  L1M4_orf2#LINE/    244 AAAGCTAC 251

Transitions / transversions = 1.90 (38 / 20)
Gap_init rate = 0.02 (6 / 251), avg. gap size = 2.17 (13 / 6)  

2528 20.36 3.34 2.28  chr2_83797768_83799417.rev      501  1158 (492)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr2_83797768_8    501 AAAGCTACCATAATCAAGACAATTTGCT-CTGACCTAGAGATATATGTAG 549
                                 vi           i v  v -   i v  ii    v ii  v
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_83797768_8    550 AGATTGATTGAATAGAATTCAATGTCTAGAAATAAGCCTGTACATTTAGG 599
                             ii  v          v iv   i        i  ii        v 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_83797768_8    600 GTCAATTAGTTTTT-ACAGTGCTGTCACGACAATTCAATGGGGAAAGAAT 648
                                ii    i-   iv v  i  v   v                  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_83797768_8    649 AGTCACTTCAACAAATGGTGCTGAGACAACTGGATATACATGTGAAAAAT 698
                             vi                 i            ?v  ii  v    -
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA- 442

  chr2_83797768_8    699 ATATAAAT-AAGTAAATGTGAACTCCTTCCTCATGCCACGCTTAAAATTT 747
                         ----i   -    -----  i  i   v     ii   iiivi    v  
  L1M4_orf2#LINE/    443 ----GAATGAAGT-----TGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_83797768_8    748 AACTCGAAATGGATCATAAACCAAATTGTAACAGTTAATACTATAAAACT 797
                              i          ? i   v  v     v  i   v           
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_83797768_8    798 TTTAGAAAAAAATTCTATGAGAAAATCTTTGTCACCTTGGATTAGGCAAC 847
                         i      i    i-v  v ? v       i  v       i        i
  L1M4_orf2#LINE/    534 CTTAGAAGAAAAC-ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_83797768_8    848 ACGTTTTTTTGATATTACACCAAAAGCACATAAAGCAAAATAAAAATTAC 897
                         i-    i  v     v              viv i     v     v  v
  L1M4_orf2#LINE/    583 G-GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_83797768_8    898 A-------GA--TCATCAAAACTGAAATGTTTTTGT-CATTAAATGATAG 937
                          -------  --         i i   -ii      - v i   v  i v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACAC 680

  chr2_83797768_8    938 CATCAAGAAAGTGAAATGTCAGTCCACAGAATGAAAGAATATATTTGCAA 987
                         i               v v  ii          ii    v          
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_83797768_8    988 ATCATATATCTGAAAATTGACCCATATATAGAATACATAAATA-TTCATA 1036
                                      v  vv   iii   vi      i     v -i  v  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_83797768_8   1037 CATTTCAATAATAAAGTGTATAAA------AAGT--AAAATGGGCATGGG 1078
                           vi           iv - i   ------  v --          vi  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_83797768_8   1079 ATTTGAATAGACGTTTTGCTAAAAAAGATAAACAAATTGCTAATTAAAAA 1128
                                     i   iv i   i      v      v  i   -  iv 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCA 878

  chr2_83797768_8   1129 TATTAAAATATGTTCAACATCATTAGTCAT 1158
                         i  v    v   i         ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (74 / 57)
Gap_init rate = 0.02 (16 / 665), avg. gap size = 2.31 (37 / 16)  


1948 25.76 15.53 0.88  chr2_83845254_83848311.rev     1780  2571 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83845254_8   1780 TAAAAAAAAATTCCATGCTCATGGATAGGAAATATCAATATTGTTAAAAT 1829
                          ii   i v  i     i        v    ivv i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83845254_8   1830 GGCCATACTGGGCAAAGTGATTTATAGATTCAATGCTATTTCTAT-AAAA 1878
                            v     vvv    v    i  i        i  v  ii    -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83845254_8   1879 ------CTACC-----------AAT-GACA------TTCT-----TCA-- 1897
                         ------  i  -----------   -    ------ i  -----   --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_83845254_8   1898 -----------------CAGAA-------------CTAGAAAAA------ 1911
                         -----------------     -------------  v      ------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_83845254_8   1912 -----------------------------TCAAACTATACTACAGGGCTA 1932
                         -----------------------------     viv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_83845254_8   1933 CAGTAACCAA-ACAGCATGGTACTGGTACAAAAAAACAGACACACAGACC 1981
                               i   -    ii         --  v  ii i     i i   i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGG--CATAAGGATAGACATATAGATC 298

  chr2_83845254_8   1982 A---GAATAGA-----GAACCCAGAAATAAGGCCACACTACTATAAAGAT 2023
                          ---       -----  ii          iv   i  vvi   --- i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT---GGT 345

  chr2_83845254_8   2024 C---TGATCTTCAACAAAGCTGACAAAAACAAGCAATGGGGAAAGGACTA 2070
                          ---    i   i    i v  v   i v  vv            i ivi
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_83845254_8   2071 CCTATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATCCAGAAGAT 2120
                         i  v  i  i              i      v  ?   i  v  i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_83845254_8   2121 CGAGACTGGACCCCTTCCTTAAACCATATGCAAAAATTGACTCAAGGTGG 2170
                         i  iii         v   i v       i        i      ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_83845254_8   2171 ATTAAATACTTAAACGTAAAATCCAAAGGTATAGAAACCCTGGAAGACAA 2220
                           i ? v  i    i    i v i   iv    i  vi i i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_83845254_8   2221 CCTAGGCA-ATACCATTCTGTACATAGGAATAGGCAAAGATTTCAT-GAT 2268
                          v    ?i- v i v iv  -  v v  iv       v i    v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_83845254_8   2269 GAAGATCTGAAAAGCAATTACAACAATAGAAAGAATTGGCAAATGAGATC 2318
                         - v  iviv       vvvi      v     i   v ii    vi  ii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_83845254_8   2319 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAACAGAATA 2368
                          v  i   v v  i i   i  ii vv    i  v    i   v i i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_83845254_8   2369 CACAGACAACCTACAGAATGGCAGAAAAACTTTGCAAAC--TGCATTTGA 2416
                         v v        i         v      vv        i-- ii  i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_83845254_8   2417 TAAAGGTCTAATATCCAGCAACTATAAGGAACTTAAACAATTTTACAAGA 2466
                            i  v  vi       v vv     i     ivv    i iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_83845254_8   2467 AAAAAACAA----CTCCATTCAAAAGTAGGCAAAGAAC----ATTAACAC 2508
                             i    ---- i v   ?    i i       i i----  vi   i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_83845254_8   2509 TT-TCAAAAGGAGACATATGTGCAACCAACAAGCATATGAATAAAAGCTC 2557
                           -  v    i   i   iiviiii    i     i     v i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_83845254_8   2558 AA-ATCACTGATCTT 2571
                           -    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (121 / 79)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 5.42 (130 / 24)  


3294 26.87 0.44 0.44  chr2_83906585_83912864     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_83906585_8   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83906585_8   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83906585_8   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_83906585_8   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_83906585_8   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_83906585_8   5129 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i  v ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_83906585_8   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5226
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_83906585_8   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_83906585_8   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_83906585_8   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_83906585_8   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_83906585_8   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_83906585_8   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_83906585_8   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_83906585_8   5577 AGGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5626
                           i     i   iv            v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_83906585_8   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_83906585_8   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_83906585_8   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5776
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_83906585_8   5777 ATCACTGGTCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2902 23.79 1.82 6.11  chr2_83914957_83918195.rev     1815  2747 (492)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_83914957_8   1815 TGTTTACTGCTTGGAAGAATTAATATTGTTAAAATGTCTATAAAATTAAA 1864
                             i iv v        v             i   v ----------- 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC-----------A 54

  chr2_83914957_8   1865 GTAATCTGTAGATTACCAAGTAATCTATAGATTCAATGTAATCCTTATTA 1914
                         i  v  ivi i   i-------     i        i i     i   i 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTG-------ATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_83914957_8   1915 CAATTTAAA-TGGTATTTTTATAGAAACAAAAAAGCTTAC------ATTT 1957
                         v   iiv i-  viv     ii     ivi v     v i------   i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_83914957_8   1958 ATTAGGATCCACAACAGTTCCCAAATAGCCAAAGCAGTCTTGAGAAAAAA 2007
                           vv   vvii   vi vi  vi          i  i      i   i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_83914957_8   2008 GAACAAAGCTGGAGGCATTGCACTTCCTGCTTTCAAAATGTATTACAAAG 2057
                                 i      vv ii       iiv        iv  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_83914957_8   2058 GTAGTGTAGTCAAAATGGTATGATACTAGCATAAAG-CAGACACATAGGC 2106
                         v  vv   i    i ii  i  i    i      i -i     i    ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_83914957_8   2107 CAATGAAACAGAATGAAGTGTCTATAAAAAAACCCATACATATGCAGTAC 2156
                              i  i     vi  v   i v   v            v iii  vv
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_83914957_8   2157 ACTAATATTTGATAAGGGTACTAAGAATATACAAAAGAGAAAGAAAAAGC 2206
                          i i  v  i  i      i i    vi  v   vi i       v iv 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_83914957_8   2207 TCTTAAATAAATGGTGGTAGAAAACCTGGATATCCACATGCAAAAGAATA 2256
                          i  v  i        v i i v v       ?                i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_83914957_8   2257 TAATTAAACTCCTATCTTGCATTATTCACAAAAATTACCTTAAAATGAAT 2306
                         v i  ii  i    i  ii  ii  vi          v  i      i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_83914957_8   2307 CAAAGATGTAAATGTAAGATCTGAACCT-TAAAACTTCTTAAAA---ATT 2352
                           ?   iv           v  i  v  -       -    i  --- vi
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAAC 546

  chr2_83914957_8   2353 ATAGAA-TAAAAACCTCTTCG--ACATTGGTATTGGTAATTACTTTTTGG 2399
                             i?-    ----      --  v    vv v  i   vii  i  i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAA----TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_83914957_8   2400 GAATGATACCAAAAGTACAGTCAACAAAAACAAAAATAAATATGT-GGGC 2448
                         iv    i        i   iv        iv       i   vi -  i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_83914957_8   2449 TAGCATCAAAGTAAAAAGAGTCTGCATAGCAAAAGAAACAACCAACAAAG 2498
                          -v       i v    ivv i  iiivv    i  v  v i   v    
  L1M4_orf2#LINE/    643 T-TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_83914957_8   2499 TAAAAACACAACCCACGGCATGGAAGAAAGTATTTTAAAACCATATACCT 2548
                          i    v         i v    i     i     vv   i      i  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_83914957_8   2549 AATAAAGAATTAATATCCAGAACATATAAGGA-CTCATAAAACTCAATAG 2597
                         i    i i i vi         i      i  -   v  v         -
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA- 790

  chr2_83914957_8   2598 CAAAAGGAACAACAGCAACCAAAACAACAAAAACAAAAAAACAAATAATC 2647
                         -------------------------------- i     i        i 
  L1M4_orf2#LINE/    791 --------------------------------ATAAAAAGACAAATAACC 808

  chr2_83914957_8   2648 TGATTAAAAAATTGGCAAAGGACTTGAATAGACATTTTTCCAAAGAAGAA 2697
                         ii   ?      v         i              i           v
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_83914957_8   2698 ATACAAATGTCCAACAGGTACAAGAAAAAAGGCTCAAGGTCACGAATCGT 2747
                                  v    i i i   v     i v      vi   ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (136 / 82)
Gap_init rate = 0.02 (15 / 893), avg. gap size = 4.93 (74 / 15)  


3930 18.76 3.60 1.69  chr2_83936072_83938873.rev     1421  2310 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_83936072_8   1421 GGAAAAACATTGTGTGTTCATGGGTTGGAAGATCTAATATGACGATTAAG 1470
                              i i  ivii         i        ii      ------ i--
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT------TG-- 43

  chr2_83936072_8   1471 ACTTAAGATGGTAATACTCCCCAAATAGATCTACAGATTCAATGCAATCC 1520
                         --         i              v               i       
  L1M4_orf2#LINE/     44 --TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chr2_83936072_8   1521 CTATAAAAATTTCA----TTTTTTTTCCAGGAATGAGCAAGTTAATACTA 1566
                             v     ii  ----ii      v   i   vii    i i  v   
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr2_83936072_8   1567 AAGTTTATATGAAATTACAGGGGACCCCAAATAATAGAAACAGTCTT-AA 1615
                           i  i     i  v i  i       vi    iivi     i    -  
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_83936072_8   1616 AACGAAGATCAAATTTTGAGGACTCGCACTGACCAAATTAAAAA-TTATG 1664
                           v     v    v  v        i    vv    v  v    -   iv
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_83936072_8   1665 ACCAAAGGACAGTAATTAAGGCAGCATGGTTCTGGCATAAAAATATTCAT 1714
                           v  ivv        i   i   ii    v         ii   vv   
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_83936072_8   1715 ATAGATAAATGGAGT-----TGAACATCCAGAAATAAACCTATACATCTA 1759
                               v      i -----   ivi              i      i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_83936072_8   1760 CAGTCAGTTGATCTTCAACAAGGGTACCAAGACCATTTGATAGAGA--GA 1807
                         ii    i     i   i        i           ii  i i  --  
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_83936072_8   1808 ATAATCTCTTCCACAAAAGGTGCTAACACAACTGGAAAACCACATGCAAA 1857
                            i   i   v     v      iiv         v ?           
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_83936072_8   1858 AGAATGAAGTTGAAGCCTTACCTCATGCCATATACAAAA--TACACTCAA 1905
                                     i v  i       ii            --  -      
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA-ACTCAA 490

  chr2_83936072_8   1906 AATTAATTAAATACCTAAACATAAGGGCCAAAACAACAGAACTCTTTGGG 1955
                            vi  i ? v       ii    i  i     v i i       v ii
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_83936072_8   1956 GAAAACCTAGGGGCAAATCTTCATAAACTTGGTTTTGTCAGTTAAATCTT 2005
                               v    ? i        i i v     v  v v  i vivv    
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_83936072_8   2006 AGATAAGACA---GAAACACAAA-AACAAAACAAAAAA--GACAAATAGG 2049
                              v    ---i  i     i-       v      --  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_83936072_8   2050 ACTTCATCAAAATTAACAACTTTTGTGCATCAAAGGGCATTATCAGGAAA 2099
                                         v           v       i  i     i    
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_83936072_8   2100 ACAAAAAGACAGCCCACAGAG-GGGA-----TATTTGCAAATTATATATC 2143
                         iii        i        i-    -----           i       
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_83936072_8   2144 TGACAAGGGAGTAGTATTTAGAATCTATAAA-AACTATTACAACTCAATT 2192
                            i      v v    ii     v      -    v            v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_83936072_8   2193 TACAAAAGTACAAAAAACCCAACGGAAAAATAATGGACAAAG-ACTTGAA 2241
                         - i    iv     v       iv?      ---  i     - i     
  L1M4_orf2#LINE/    791 -ATAAAAAGACAAATAACCCAATTWAAAAAT---GGGCAAAGGATTTGAA 836

  chr2_83936072_8   2242 TAGATATGTTTCCCAA--AGATGTACAAATGGCTAATAAGCACA-GCAAA 2288
                             i  v i   v  --    i          i          - v   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_83936072_8   2289 GATGCTCAATACCATTAGTCAT 2310
                                  i i  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (104 / 59)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 2.35 (47 / 20)  


3676 18.45 1.39 0.69  chr2_83992811_83995076      603  1323 (943)    L1M4_orf2#LINE/L1        1   726 (182)  

  chr2_83992811_8    603 TGGAAA-ATATTTCATGTTCATGGAGCAGAAAAC--AATATTGCTAAGAG 649
                               -    ii            vii   i  --       i     v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_83992811_8    650 AAGTAGACACCTTGGATTGAGCTACAGATTCAATACAGTCTCTTTCAGAA 699
                         iivv v  v  iiii     v            ii  i  i  v   i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_83992811_8    700 CTGCAGATGACTTCTTTATAGAAATTGACAAGCTTATTCTAAAATCCATA 749
                         iiv   v  v   i   ii               v  i       i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_83992811_8    750 TGTAATTGCAAGCTGTCAATAATAGTCAATACAATCTTGTAAAGAAAGAA 799
                           v  v      vvii v v     i   v         v   ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_83992811_8    800 CAAAGTAGGAGAACTCACACTTCCTTATTTCAAAATTTACCACAAAGCTA 849
                               v    i            iv         i    i         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_83992811_8    850 TGTTAATTAAAACAATGTGCTATTGACATAAATATAGACTCATAGACCAA 899
                         iiv    i  i   i    v  i  i     iv      vi     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_83992811_8    900 AGAAACAGCATTGAGAGTTCAGAAATAAACTCATATATCTATGATCAATT 949
                         v i  i  v         i           i    i  i    i      
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_83992811_8    950 GTTTTGTGACAAGAGTATCAAGACCATTCAATAGC-AAAGAATAGTCTCT 998
                          v   vi      i  ii              i v-            i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_83992811_8    999 TCAACAAATGGTGCTGGGATACCTGGATAGCCACATGCAAAAAAACAGAA 1048
                                            i v       ?            i  i----
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT---- 446

  chr2_83992811_8   1049 GAAGT-GGACCCCTACCTCATACCATACACAAAAACTAACTCAAAATGGA 1097
                              -              i      i       i              
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_83992811_8   1098 TCAATTACCTAAATATAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAT 1147
                            ?vv        i                                  i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_83992811_8   1148 ATAAGAATAAATCTTTGTGACTTTAGATTTGACAACAGTTTCTTAAATAG 1197
                            i ?i        i     i  i i  v i   ii        i   v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_83992811_8   1198 GA-ATCAAAAGTGTAAGTAACAGTGATAAAAATAGATAAATTGTACTTCA 1246
                           - i      iii   i    iviiv                v      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_83992811_8   1247 TCAGAATTAAAATATTTTTGTA--TCAAAGAACACTATCCAGAAAGTGAA 1294
                            i        - i      i--      i        v          
  L1M4_orf2#LINE/    647 TCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_83992811_8   1295 AAGACAAATCACAAGATGGGA--AAATATTT 1323
                                vi    ii      --        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTT 726

Transitions / transversions = 2.17 (89 / 41)
Gap_init rate = 0.01 (9 / 726), avg. gap size = 1.67 (15 / 9)  

 555 20.00 7.22 3.89  chr2_83992811_83995076     1595  1774 (492)    L1M4_orf2#LINE/L1      723   908 (0)  

  chr2_83992811_8   1595 ATTTTCAAATAATATATCTGATGTGGATCTAGTTTCCAGAATGTATAAAG 1644
                             v     v           iv  iv  v  v        i       
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_83992811_8   1645 AACTGTAATAATTCAATGAGCAAAT----AATAATACAATTTTAAAATGG 1690
                             v v i  i     i vv   v----     iv     ?v       
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_83992811_8   1691 GCAAAGGACTC---------TTTATTCAAAGATATACAAATGAATATAAA 1731
                                 i i---------   v i      ----- i  --   i   
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGA-----AGAT--ATACAAA 865

  chr2_83992811_8   1732 TGGACAACAAGCACGAAGAAAGATGCATGACATCACTGGTCAT 1774
                            v   i      ivii        vii      ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.06 (18 / 17)
Gap_init rate = 0.02 (4 / 186), avg. gap size = 5.00 (20 / 4)  


3157 26.88 1.00 0.55  chr2_84114683_84121074     4997  5900 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84114683_8   4997 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5046
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84114683_8   5047 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84114683_8   5097 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5144
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_84114683_8   5145 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5194
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_84114683_8   5195 AACGAAGCTGGAGGCATCACGCTACATGATTTCAAACTATACTACAAGGC 5244
                            i   i      vv    i  v vii        viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_84114683_8   5245 TACAGGAACCAAAACAGCATGGTAATGGTTCCAAAACAGAGATATAGACC 5294
                              v  i   i    ii     v   iviv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_84114683_8   5295 AATGGAATAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5342
                                     i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_84114683_8   5343 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5392
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_84114683_8   5393 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAATCT 5442
                           v  i  i              v      v  ?   i   i i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_84114683_8   5443 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5492
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_84114683_8   5493 TTAAAGACTTACATGTTAGACCTAAAACCAGAAAAACCCTAGAAGAAAAC 5542
                          i ?    i  v    v   v       i v    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_84114683_8   5543 CTAGGCA-ATACCATTCAGGGCATAGGCATGGGCAAGGACTTCATGTCTA 5591
                         v    ?i- v i -   iv i v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_84114683_8   5592 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5641
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_84114683_8   5642 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 5691
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_84114683_8   5692 TAGGCAACCTACTGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5741
                         v  i     i  v              v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_84114683_8   5742 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5791
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_84114683_8   5792 ----CAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5837
                         ----    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_84114683_8   5838 CTCAAAAGAAGACATTTATGGAGCCAAAAAACACATGAAAAAATGCTCAT 5887
                            v        i  vi vivi     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_84114683_8   5888 CATCACTGGCCAT 5900
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (137 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


 251 15.38 5.77 0.00  chr2_84126276_84128973.rev      980  1031 (1667)    L1M4_orf2#LINE/L1        1    55 (853)  

  chr2_84126276_8    980 TGGGAAGACATCCTGTGTT-ATGAATTGGAAGAC--AATTTTCTTAAGAT 1026
                            i    i    ii    -   i          --   v  v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84126276_8   1027 GTCAA 1031
                          v   
  L1M4_orf2#LINE/     51 GGCAA 55

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.50 (3 / 2)  

3321 20.02 5.19 0.49  chr2_84126276_84128973.rev     1398  2206 (492)    L1M4_orf2#LINE/L1       62   908 (0)  

  chr2_84126276_8   1398 CCAAAGTGATCTTCAGATTCAATCTAATCCCTATACAAATTCTAGCAGAC 1447
                              v      v         ivi         vv    i i   v v 
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_84126276_8   1448 TTCTTTGCAGAAACAGAAATGCTGATTCTCAAATAGTTGTGGAATTGCCA 1497
                           i          iv  v v      i  v    vvv i     v   v 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_84126276_8   1498 GGGATACTGAAGAGCCAAAATCAAGTTGAAAAATAA---CAAATTTGGAG 1544
                             iv v   v        iv vv        v  ---    v      
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_84126276_8   1545 GACTTATATTTCCTACTAT---AACTTACTATAAACCAATATTAATCAAA 1591
                             i i i    i v v ---         i   v v i v       i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_84126276_8   1592 ACAGTATGGTACTGGCATAAGGACAGACATATAAACCAGTGGAATACAAC 1641
                              i                 i         i i  i       v  i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_84126276_8   1642 TGAGAGTATAGAAATAAATCCTTATGCTTATGGCCAATTGATTT-CAACA 1690
                                vi         i  v  iii      i          - i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_84126276_8   1691 AGGATGCCAA-ACCATTCAAAAGATAAGGAATACTCTTATCAAAAAATTG 1739
                            i      -         vi iv  i     v    v    v    v 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_84126276_8   1740 TG-TGGGACATCTGGATATCCATATGGAAAAAAAATGAAATTGAAACCCT 1788
                           -       v       ?   i   v    i  -    i   i v    
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCT 460

  chr2_84126276_8   1789 ACCTTACACCACAT-TAAAGTAATTAACTCAAAATTGATCAATGACCGAC 1837
                             i      i  -i   --              v     ?v    v v
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAA--AATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_84126276_8   1838 AAATAAAAGCAAAAACCAT----------GAAGGAAA----------AAT 1867
                          vi   i   v     i  ----------    i   ----------   
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_84126276_8   1868 TTT-ATGGTCTAGTATTTGGCAGTGGTTTCT-AGATATGATGTCAAAAAC 1915
                         i  -i  ii  v vi  v    i        -        iii     i 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_84126276_8   1916 ATGGGCAACAGA-GAAAAATTAGGTAAATTGGACTTAATCAAAATTTTAA 1964
                          iii      i -      v   i            v         vv  
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_84126276_8   1965 ACTTTTGTATATCAAAAAAACTTATT--GATAGAGAAAAAAT--CCTACA 2010
                                 iiv     ii vvi   i--  v  v     i i--  i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_84126276_8   2011 AAATGGGA-AAAATATTTGCAAATTATATATTTGGTAGGGTTCTATTATC 2059
                         i       -               i      i  i  i  vv  vv    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_84126276_8   2060 CAGAACATATAAAGAACACTCACAACTCAACAACAATATGACAAACAATT 2109
                              i           v  i         i  i  v v      i  ii
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_84126276_8   2110 CTATTTAAAAA-GGGCAGAAAACTTGAGTAGACATTTCTGCAAAGA---T 2155
                          v   ?     -     i ii i    i           v      --- 
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_84126276_8   2156 AAACAAATAGCCAACAAGCCCCTTGAAAAGATGCTCAACATCATTAATCA 2205
                          v      i     i    v v -                   ???????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACAT-GAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_84126276_8   2206 T 2206
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.24 (88 / 71)
Gap_init rate = 0.02 (19 / 847), avg. gap size = 2.42 (46 / 19)  


3365 25.33 1.11 0.22  chr2_84146473_84149064     1201  2100 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84146473_8   1201 TGAAAAAACATCCAATGTTCATGGATCAGAAGAATTAGCATTGTTAAAAT 1250
                           i   i i    v            ii     v   ii        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84146473_8   1251 GAT--TGCTACCCAAAACAATCTACAGATTCAATGCAATCTTTATCAAAA 1298
                          ii-- i  v      vii              i      ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84146473_8   1299 TAGCAA-TGACATCCACACAGAAATAGAATAAAAAATCCTAAAATCTGTA 1347
                          vv  i-  v v iivii       v  vv ivvi          iii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_84146473_8   1348 TGGACCCTCCAAGGACACTGAATAACCAGAGCAATTCTGAGCAAAAAGAA 1397
                             vviv v i    v v     i   i i    ii   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_84146473_8   1398 CAAAGCTAACATCATCAAAATACCAGACTTCAAAATATACTACAAAGCTG 1447
                              i iivivvv   v v v  vi i       iv            i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_84146473_8   1448 TGGTAACCAAAGCTGCATGGTACTGGCATAAAAACAAA-A-ACAGACCAC 1495
                         ii    i   ii v ii              ii i i - - i   i  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_84146473_8   1496 TGGAACAGAATAGAGAACCCAGAAATTAATCCATGTAACTACAGCCAACT 1545
                              i     v    ii        v  i    ii vi  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_84146473_8   1546 GATTTTTGACAAGGGCACCAAGAACATAGATTAGGGAAAGGACA-TCTCT 1594
                               i        ii      v   vv v i       i i -   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_84146473_8   1595 TTGATAAATGCTACTGGGAAAACTGGATGTCTATATGCTGAAGAATGAAA 1644
                          ii i     v i      v        i? i i    vi         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_84146473_8   1645 CTAAACCCCCACCCCTCTCTCTATACAAAAATCAACTCAAAATGAATCAA 1694
                         i ii     i   i v v iv           i           i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_84146473_8   1695 AGACCTAAATTTAAGACCTAAAACTATAAAACTACTAGAAGCAAACAAAG 1744
                                   v     v                vi      v     v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_84146473_8   1745 GGA-AAATGCTTCAAGACATTGATCTGGGAAAAGATGTTATGAATAAGAC 1793
                          ?i-    -    iv   v   ivi i  v  v i v iv ii   v   
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_84146473_8   1794 CTCAAAAGTACAGGCAATAAGAGCAAAAATAAACAAATGGGATTATATCA 1843
                         vi      i   i    i  i  v       i i    v   i vi    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_84146473_8   1844 AACTGAAAAGGTTCTATACGGCAAAGGAAACAATCAACAAAGTGGA--GA 1891
                           v v    iv  i i i vv       v  v     v      i --  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_84146473_8   1892 CAACCTACAGAATGGGAGAAAATATTTGTAAATTACCCATCTGACAGAGG 1941
                              i                      i    i ivi      i ii  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_84146473_8   1942 ATTAATATCCAGACTATACAAGCATCTCAGACATCTCAACAGCAAAAAG- 1990
                          i vi        v    i  iv v   vv   v     i ii      -
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_84146473_8   1991 CAAACAATCCAATTTTAAAATAGGCAAATGATCTGAACAAACATTTCTCA 2040
                             i  i      ?v     i      v   i    i i         v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_84146473_8   2041 AAGGAAGACATGCAAATGGCCAATACATACATGAAAAAAATGCTCAACAT 2090
                           i     i  i             vii         i -          
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACAT 898

  chr2_84146473_8   2091 CACTAATCAT 2100
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.73 (142 / 82)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.20 (12 / 10)  


2441 24.53 4.86 4.50  chr2_84150388_84152223      501  1344 (492)    L1M4_orf2#LINE/L1       62   908 (0)  

  chr2_84150388_8    501 CCAACTTTATCTATACATTCACTGCAACCCCAATCAAAA-----GTTA-- 543
                             v  v     i v     vi    i   v       ----- i i--
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_84150388_8    544 --TTTTGTGGCTACTGATAA-CTAATTCTAAAGTTTACCTGGAGAGACAA 590
                         --     ii vv i   i  -  i  i     i  i iv    i vi   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_84150388_8    591 AAGACCCTGAATAGCCAACACAATAT------ATAAGAATAAAGTT---- 630
                         ii     v          v     v ------ v     i      ----
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_84150388_8    631 --CTGACACTACCTGACTT-AAGACTTACTATAAGCCTACAGTAATCAAG 677
                         --  v     v  ii i  -  i        i  iv              
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_84150388_8    678 ACAATGTATCATTGGCA-AAGTGTAGACA----GATCAACATAACAGAAT 722
                            i   ivi i     -   vi      ----      iiv  i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_84150388_8    723 AGAGAGCCCAGAAATAGACCCAAATAAATATAGTTAACTGAGCTTTGACA 772
                         v     i         i     v i vv   i  i  i   vi  i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_84150388_8    773 AAGGTGCAAATGCAATATACTGGAGCAAAGATTGTCTTTTGAACAAATGG 822
                          i     v  vi v  vi v   i v  ii  v       v         
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_84150388_8    823 TGTTAGAAAAACTGGACATCTATATGCAACAACCACAAAAACAACAAAAG 872
                           i i i v       i ? i i      -------  i  i------- 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAA-------AAGAAT-------G 447

  chr2_84150388_8    873 AATCTAGACACACATCTCACACCTTTCACAAAAATCAACTCAAAATGTAA 922
                           vi i   v vi i        v vi        i           v v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_84150388_8    923 CATAGATCTAAGTGTAAAATGTATAACTACAAAAGTTTTAGAAGATAACA 972
                           ?   i    i     i vv  v     i    v i        v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_84150388_8    973 TATGA-TAAACTCTATGGGTATGGTTTGGTATAACAACCTTGAGTATAAA 1021
                           v ?-    -   ------------ v  i-----      i  -  ii
  L1M4_orf2#LINE/    548 TAGGNGTAAA-TCT------------TCGTG-----ACCTTGGGT-TAGG 578

  chr2_84150388_8   1022 -AATGTCATTTTAGATAGGATACCATAGGTATGATCCCTTAAAGAAATAA 1070
                         -    viv i       v  i    v i i ii v vviv       v  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_84150388_8   1071 TTGATAAGCTAGACTTTGTTAAAATTAGAAACTTCTACTCTGTAAAAGAC 1120
                          v     ii i     ii i       i      i iiv  vi   i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_84150388_8   1121 AATGTCATGGAAATGAGAAGATAAACCACAAACTAAAAAAAGATATTTGC 1170
                          v i   v i  i   i    i  v     i v iii i  i        
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_84150388_8   1171 AAAAGTCACAT--TTGATAAAGAACTGTTATCTAAAATACGCAAA---CT 1215
                            --   i  --i      i i   vv    i i    iii   ---  
  L1M4_orf2#LINE/    729 AAA--TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_84150388_8   1216 CCCAAAAAATCAACAATAAAAAAA-----AACTAAATT-AAAATTAGGTG 1259
                          ii v  v-    i        i -----   iv    -    v i  ii
  L1M4_orf2#LINE/    777 CTTACAAC-TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_84150388_8   1260 AACGACCTGCATAGATACCTTTTCAAAGAAGATATACAGATGGCAAATAA 1309
                           v  ii  v     i ii i i               i     v     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_84150388_8   1310 ACATATATAAAAAGATGTTTAACATTATACAGCAT 1344
                         i  i  i--        i i     i ????????
  L1M4_orf2#LINE/    876 GCACATG--AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (132 / 72)
Gap_init rate = 0.03 (23 / 847), avg. gap size = 3.43 (79 / 23)  


2164 24.19 4.16 0.92  chr2_84234865_84236504      501  1149 (491)    L1M4_orf2#LINE/L1      239   908 (0)  

  chr2_84234865_8    501 ACTACAAAGTTATAGCAAATAAAAAA---TGGTACTGGCATCAAAACAGA 547
                                  i  i  i  vi  i v ---            v ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_84234865_8    548 CACATGGACCAATGGAACAGGATAGAGAGCCCAGAAATAAATCCACACAT 597
                           i  i  i        i  i  v     i           i   i    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_84234865_8    598 TTA--GTCAATTGATTTTCAACAAAGATGTTGAGCATACACAATGGGGAA 645
                            --              i    i i  iii  vvi iv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_84234865_8    646 AAAGCAGTCTCTTCAATGAGTGGTGGTGGAAAAAT---ATTTCCTTCATG 692
                          i ii     i     ii i     v   i v  i---  v?  v-    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA-CATG 437

  chr2_84234865_8    693 CAAAAAAAATATAATTATACCATTACCTTACATCATATACAAAAATCAAC 742
                              i  - iv i  iv   vi     i   i             i   
  L1M4_orf2#LINE/    438 CAAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_84234865_8    743 TCAAAATGGATGAAATATTTAAACATAAGACCTGAAACTGTAAA-CTACT 791
                                    v ? v ii    ii     v  i     i    -  vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_84234865_8    792 AAAAGAAAACA--GGGGGAAA-CTCCATGATAGCAGTCTGGGCAATGATT 838
                          i         --  ? v   -  i i   ivvii vi i       i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_84234865_8    839 TGTTTAATATAATCCCAAAAGCACATGCAACAAAAACAAAAATACACAAA 888
                          v  vi    i iv           v         iv       v i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_84234865_8    889 TGAAATTACATTAAA-TTAAAAACCTACACACAGCAAAGGGAACAATGAA 937
                          vii i v   i   -        i viiii vv      iv  v  v  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_84234865_8    938 TAAAG-----AGACAATCTTTGGAATA--AAAAAAT---TGCAAACCATA 977
                         v    -----      i ivii    i-- i     ---      i    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_84234865_8    978 CATCTAATAAGGGGGTACTATCAAAAATACATTAAAAA---TTAAACCAA 1024
                         i    i       iv vv    v i    i  v  i  ---   ---   
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA---CAA 783

  chr2_84234865_8   1025 CTGAATAACAACAAAACAAATAACCTCATTGACAAATGAGCAAAGAATCT 1074
                           v     i  v  i          iv   ? v     i      i  i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_84234865_8   1075 AAATTAACACTTTTCAAAAGAAGAAACTCAAATGGCCAACAGACATGTTG 1124
                         i   vi   i  i  v        v iv           i ii  ii - 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-G 882

  chr2_84234865_8   1125 AAAAAATGCTCAACAT-AGTCATAAG 1149
                             i           - ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (102 / 51)
Gap_init rate = 0.02 (16 / 670), avg. gap size = 2.06 (33 / 16)  


3189 26.43 1.10 1.10  chr2_84242940_84248725     4387  5294 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84242940_8   4387 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4436
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84242940_8   4437 GGCCATACTGCCCCAGGTAATCTATAGATTCAATGCCATCCCCATCAAGC 4486
                            v     v   v iv i     i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84242940_8   4487 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4534
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_84242940_8   4535 TCTGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 4584
                          v     viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_84242940_8   4585 AACAAAGCTGGAGGCATCACGCTACCTGACTTCCAACTATACTACAAGGC 4634
                                i      vv    i  v  ii i   v  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_84242940_8   4635 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4684
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_84242940_8   4685 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCGTATCTACAACT 4732
                                i    i--    i  --        vv  iiii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_84242940_8   4733 ATCTGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCC 4782
                          vi    i  i i   ivv  v   i v  vv       i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_84242940_8   4783 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4832
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_84242940_8   4833 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCCAGATGGA 4882
                            ii    i    v   i     v              i  v i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_84242940_8   4883 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4932
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_84242940_8   4933 CTAGGCA-ATACCATTGAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4981
                         v    ?i- v i v i v iv v i  i- i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr2_84242940_8   4982 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGTTCTA 5031
                         vi            vvi          vv     v  i    v  vii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_84242940_8   5032 ATTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5080
                           i   -     i -   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_84242940_8   5081 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5130
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_84242940_8   5131 AAAGGGCTAATATCCACAATCTACAATGAACTCAAACAAATTTACAAGAA 5180
                           i  i  vi      v   v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_84242940_8   5181 AAAAACAAACAACCCCATCAACAAGTGGGTGAAGGATGTGAACAGACACT 5230
                            i     i     v  i? v  i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_84242940_8   5231 TCTCAAAAGAAGACTTTTATGCA----GCCAACAGACACATGAAAAAATG 5276
                             v        ----   i  ----     i ii          i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_84242940_8   5277 CTCATCATCACTGGCCAT 5294
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


1922 15.87 2.69 0.00  chr2_84293701_84297020.rev     1522  1855 (1465)    L1M4_orf2#LINE/L1       11   353 (555)  

  chr2_84293701_8   1522 TCTTATGTTCATGGATCA-AACACTTAATATTGTTAAGATAGCAATCCTC 1570
                           ii            ii-  v                  i     v   
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chr2_84293701_8   1571 CCTAAATTGATCCACAGATTCAATACAATCCCTATCAAAGTCCTAGCTAT 1620
                           i         i          ii              i   i    ii
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr2_84293701_8   1621 CATTTTTGCAGAAATTAATGAGCTGATTATAAAATTTATATGGAA---TA 1667
                          v              i ii       iv       i        ---i 
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_84293701_8   1668 AGGGACCTAGAATAGCCAAAGCAATGTTGAAAAAGAAGTATGAAGTTGGA 1717
                                i            i    v            v ii        
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_84293701_8   1718 AGACTAACATTTTCCAATTTCAAAACTTACTACAAAGCTATAGTAATAAA 1767
                         i    v   i  i                           i      v  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_84293701_8   1768 GACAGTGTGGGATTGACATAAAAATAGACAGGGAGATCAATAGAGTAAAA 1817
                                   v i  i     ii       viv        i  i  i  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_84293701_8   1818 CTGAGAATCCAGGAGTAAACTCCTACAA--ATGG---ATTGAT 1855
                         i     i     i i     i v    v--    ---      
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

Transitions / transversions = 3.08 (40 / 13)
Gap_init rate = 0.01 (4 / 343), avg. gap size = 2.25 (9 / 4)  

2371 17.86 7.54 0.60  chr2_84293701_84297020.rev     2317  2820 (500)    L1M4_orf2#LINE/L1      354   892 (16)  

  chr2_84293701_8   2317 TTTCGACAAAGTTGCCAAAACAATTAACTGGAGAAAGAATATTTTTTTTC 2366
                                  i v      i  v   v v   i         v i    - 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT-C 402

  chr2_84293701_8   2367 AACAGATGAGGCTAGGACAACCAACTATTCACATGTAAAAGAATGAAGTT 2416
                             i   iv   i       iiiv  ?i      i              
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_84293701_8   2417 GGACCCCTTCTTCACTCTATACTCAAAACTTAACTCAAAATGAATCAAAG 2466
                                 v i    v i   iv     v             i    ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_84293701_8   2467 ACCTAAATGTAAGAGCTAAAATTATAAAAATCTTAGAAGAAAATAT---- 2512
                                              i       v             i  ----
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_84293701_8   2513 ------CTTCATG--CTCAGGTTTGGCAAAGCCTTCTTA--TATGACACC 2552
                         ------    i  --  ii    v     v vi      --         
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_84293701_8   2553 AAAATTACAACTGACCAAACAAAGAAAATAGATGGATTAGACTTCCTCAA 2602
                             vi    vii  v   v   --        ii   i      v    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAA--AAATAGATAAATTGGACTTCATCAA 650

  chr2_84293701_8   2603 AATTAGAAACTTTTATGCTTCCAAGGACACCATCAATAAAGTTCAAACAT 2652
                              i        i      v        i     v     vv   v i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_84293701_8   2653 AATCCACAAAATGGGAAAAAAT-TTT-CAAATCATATAT--------GGT 2692
                           i     i       i     -   -            --------  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_84293701_8   2693 CTAGTATTTAAATTATGTGAAGAATTTTTA--------------GAAGAT 2728
                           v    ii i v   i i     i i   --------------i    i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_84293701_8   2729 GAATAACTCAATTAAAAAATGGGTAGGACATTTGAGTAGATATTTCTCCA 2778
                         i      i     ?         i iiiv      i    i         
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_84293701_8   2779 AAGAAGGTTTACAAATGGTCAATAGACACATGAAAAGATGTT 2820
                               i v         i     ii              i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.90 (57 / 30)
Gap_init rate = 0.02 (9 / 539), avg. gap size = 4.56 (41 / 9)  


3201 26.88 0.88 0.44  chr2_84363021_84369442     5027  5930 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84363021_8   5027 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5076
                               i i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84363021_8   5077 GGCCACACTGCCTAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5126
                            v i   v  i  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84363021_8   5127 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 5171
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_84363021_8   5172 TGGATCCAAAAAAGAGCCGGCATCACCAAGTCAATCCTAAGCCAAAAGAA 5221
                             vviiv  ii  v  i v  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_84363021_8   5222 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5271
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_84363021_8   5272 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5321
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_84363021_8   5322 TGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCACATATCT-CAACTAT 5368
                              i    i--    i  --    i   vv   i i  i -iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_84363021_8   5369 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5418
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_84363021_8   5419 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTGA 5468
                         v  i  i              v      v  ?   i   v i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_84363021_8   5469 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5518
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_84363021_8   5519 AAAGACTTAAATATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5568
                          ?    i     --  v   v       i      vi i          i
  L1M4_orf2#LINE/    499 AWAGACCTAAAT--GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_84363021_8   5569 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5618
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_84363021_8   5619 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5668
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_84363021_8   5669 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5718
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_84363021_8   5719 AGGCAACCTACAAAATGGGAGAAAATTTTCCCAACCTACTCATCTGACAA 5768
                           i     i   i             v  iv   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_84363021_8   5769 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5818
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_84363021_8   5819 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5868
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_84363021_8   5869 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5918
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_84363021_8   5919 ATCACTGGCCAT 5930
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3149 27.53 0.44 0.44  chr2_84400662_84407037     4977  5884 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84400662_8   4977 TGGAAGAACATTCAATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5026
                              ii i  i v   i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84400662_8   5027 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5076
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84400662_8   5077 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 5124
                          v   ivvi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_84400662_8   5125 TATGGAACCAAAAAAGAGCCCGCTTTGCCAAGTCAATCCTAAGCCAAAAG 5174
                                viiv  ii  v  v vv v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_84400662_8   5175 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5224
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_84400662_8   5225 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5274
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_84400662_8   5275 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACT 5322
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_84400662_8   5323 ATCCAATCTTTGACAAACCTGACAAAAGCAAGAAATGGGGAAAGGATTCC 5372
                          viii  i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_84400662_8   5373 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5422
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_84400662_8   5423 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5472
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_84400662_8   5473 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5522
                          i ?    i       v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_84400662_8   5523 CTAGGCAATAACATTCAGGACATAGGCATGGGCAAGGACTTCATGCCTAA 5572
                         v    ?ivv  iv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_84400662_8   5573 CACAACAAAAGCAATGGAAACAGAAGCCAAAATTGACAAATGGGATCTAA 5622
                         v   v        vvi v    i   vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_84400662_8   5623 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 5672
                          i   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_84400662_8   5673 AGGCAACCTACAGAATGGGAGAAAATTTTTGCCATCTACTCATCTGACAA 5722
                           i     i                 v     v vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_84400662_8   5723 ATGGCTAATATCCGGAATCTACAAATAACTCAAACAAATTTACAAGAAAA 5772
                         iv i  vi     i    v  i   v     vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_84400662_8   5773 AAACAAACGACCCCATCAACAAGTGGGTGAAGGATGTGAACAGACACTTC 5822
                          i     ii    v  i? v  i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_84400662_8   5823 TCAAAAGAAGACACTTATGCAGCCAACAGACACATGAGAAAATGCTCATC 5872
                           v        i ivi viii     i ii       i  i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_84400662_8   5873 ATCACTGGCCAT 5884
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (142 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2709 26.02 2.52 2.85  chr2_84480731_84486852.rev     4720  5630 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84480731_8   4720 TGGAAAATCACTTCATGCTCATGGATAGGAAAA-TCAGTATCATGAAAAT 4768
                               ivi iii    i        v    i - i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84480731_8   4769 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATTCCCATCAAAC 4818
                            v     v     iv i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84480731_8   4819 TACCATTGACATTCTTCACATAATTAGAAAAATTCTAATTCTTTAAATTA 4868
                          v   vivi v  i  ii  v  v v  v  i--  i  i  --------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCT-------- 140

  chr2_84480731_8   4869 GAAAAACTTTAAATTTCATATGGAA-T-CAAAGAAGACCCTGTATAGATG 4916
                         --    --------           - -   i --     v v    vii
  L1M4_orf2#LINE/    141 --AAAA--------TTCATATGGAAATGCAAGG--GACCCAGAATAGCCA 178

  chr2_84480731_8   4917 AGACAATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCACACTACCTGAC 4966
                          i      i i iv  i          i      vv       v  ii i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr2_84480731_8   4967 TTCAAACTATAC-ACAAGGCTACAATAACCAAAACAGCATGATACTGGTA 5015
                               viv   -    i      i   i   i    ii  i      i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_84480731_8   5016 CCAAAATAGACATATAGACCAATGGAACAGAACAGAGACCTCAGAAATAA 5065
                         iv ii             i        i    iv    vii         
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_84480731_8   5066 CACCACACATCTACAACCATCTGATCTTTGACAAACCTGAGAAAAACAAG 5115
                         vv   i    i  iiii  vi    i  i     ivv  vv  i v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_84480731_8   5116 CAATGGGTTAAGGATC-TCTATTCAATAAATGGTGCTGGGAAAACGAGCT 5164
                                vv   i  v-   v     i              v   vi v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_84480731_8   5165 AGCCATATGCAGAAAACTGAAACTGG-CCCCTGTCTTTATACCTTATACA 5213
                          ?   i     i  i v    ii   -     ii  i- i   v      
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC-ACACCATATACA 477

  chr2_84480731_8   5214 AAAATTATCTTGAGATGGATTAAAGAGTTAAATGTAAAACCACAAACCGT 5263
                                v  ii i      i ?   vi         i v vv    ii 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_84480731_8   5264 AAAAACCCTAGAAGAAAACCTATGC---AATCCCATTCAGGACATTGGCA 5310
                             vi i           v  v ?---    ---   iv   v    vv
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC---TTCGTGACCTTGGGT 574

  chr2_84480731_8   5311 TGGGCCAAGACTTCATGAAAAAAATGCCAAAAGAAATTGCAACTAAAACC 5360
                          i   v v ii   v ii v vi ii       v vvv     v   ivv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_84480731_8   5361 AAAATTGACAAAT--GATTT-ATTAAA-CTAAAGAGCTCTGCACAGCAAA 5406
                              v  i    --  i  -  i   -i    i vi i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_84480731_8   5407 AGAAACTATCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTT 5456
                         i  v       vv i      v  i     i                 v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_84480731_8   5457 TTTCAATCTACCCATCTGACAAAGGCCTAATATCCACAATTTACAAGGAA 5506
                           v   vii ivi      i  i  v  vi      v   v  i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_84480731_8   5507 CATGAACAAATTTACAAGAAAAA-------AACCCCATCACAAAGTGGGC 5549
                          vivv    v iv i  v     -------     v  i?v   i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_84480731_8   5550 AAAGGATGTGAACAGACATTTTTCAAAAGAAGACATTTACATAGCCAACA 5599
                                v    i        i  v        i  vi v  i     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_84480731_8   5600 A--ACATGAAAAAA-GCTTAACATCACTGATCAT 5630
                          --         i -   i       ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (134 / 99)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.58 (49 / 19)  


2530 25.71 5.44 2.60  chr2_84504314_84506996     1309  2191 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84504314_8   1309 TGGAAAAACATTCCATGCTCATGAATAGGAAGAATCAAT--CATTAAAAT 1356
                               i i  i     i     i  v      v i   --ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84504314_8   1357 TGCTATACCACCTAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 1406
                         v  v    iv  i   vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84504314_8   1407 TGCCAATGACGTTCTTCACAGAACTAGAACAAAAAAACTATTTAAAAAAT 1456
                          v   iivi v  i  ii     v v  -   i----  iv ivv     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAG----CTGATCCTAAAAT 145

  chr2_84504314_8   1457 TT-TATGAAACCAAAAAAGAGCCAAAATAGCCAAGGCAATCCTAAGCAAA 1505
                          i-    i  viiv  ii  v   i         ii     i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_84504314_8   1506 AAGAACAAA-----------CAC-----CCAGTCT--ACACTTAC---AG 1534
                                  -----------   -----   i i -- v      --- i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_84504314_8   1535 GACTTCAGTCACCAAAACAGGATGGTATTTACTGGTACAAAAACAGACAC 1584
                         ii  v    v i   i    vi     ----    i i  ii i     i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTA----CTGGCATAAGGATAGACAT 291

  chr2_84504314_8   1585 ACAGACCAACGGAACAGAATAGAGAGCCCAGAAATAATGCCACACACCTA 1634
                          i   i   i    i     v     i          vv   i   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_84504314_8   1635 CAACCATCTGATATTCAACAAAGCTGACAAGAAACAAGCAATAGGGAAAG 1684
                         iiii  vi    v   i    i v  v     v-  vv    i       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAG 390

  chr2_84504314_8   1685 GACTCCCTATTCAATAAATGGTGTTGGGATAACTGGCTAACCATATGCAG 1734
                         i ivvi  v     i        i     i      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_84504314_8   1735 AAAATTGAAACTGGACCCCTTCCTTA-----TATAAAAAAATCAACATGA 1779
                           i v    ii         v   i -----    v      i   vii 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_84504314_8   1780 GATGGATTAAAGACTTAAATGTAAAAACCAAAACTATAAAAAGCCTAGAA 1829
                         i      i ?    i         i i i            vv i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_84504314_8   1830 GACAATCTAAGCA-ATACCATTCTGGACATAGGAACAGGCAAAGATTTCA 1878
                           v  iv  i ?i- v i -   vv   v v  ivi      v i    v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_84504314_8   1879 TGACAAAAACACCAAAAGCAATCA--TAACAAAAGCAAAAATTGACAAAC 1926
                          iivv vi            --  --i        v      v  i   i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_84504314_8   1927 GAGATCTAATTAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTATCAAC 1976
                         vi  ii v  i   v    i i   i  ii vv    i  v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_84504314_8   1977 AGAGTAAAGAAACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGT 2026
                          i   i  i i      i                          ii  i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_84504314_8   2027 ATCTGACAAAAGTCTAAAAAGTCCAATATTCAACATCTATAAGGAACTT- 2075
                               i  ii v  ------ ---i   i  iv  v     i     i-
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACT------T---GTATCCAGAATATATAAAGAACTCT 778

  chr2_84504314_8   2076 ---AAATTAACAAGAAAAAAACA------CCA-TTAAAAAGTAGGCAAAG 2115
                         ---  v i  i  v     i   ------   -  ?    i i       
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_84504314_8   2116 AACATGAATA-----TTCTGCAAAAGAAGACATATATGCAGCCCACAAGC 2160
                         i iv      -----    v    -     i   i viii   v i    
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGC 877

  chr2_84504314_8   2161 ATATAAAAGAAAGCTCAATATCACTAATCAT 2191
                          i  i   ii v      i    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (147 / 76)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.23 (71 / 22)  


2763 25.66 2.75 2.75  chr2_84517995_84520277      884  1791 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84517995_8    884 TGGAAAAATATTCCATGCTCATAAATAGGAAGAATCATTATTGTTAAAAT 933
                               i    i     i    ii  v      v i v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84517995_8    934 GGCCATATTGCCAAAACCAATCTGCAGATTCAATGCTATTTGTATTAAAC 983
                            v   i v  v   iii    i         i  v  iiv   i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84517995_8    984 TACCAACATAATTTTTCACAAAATTAGAGAAAAAATTCTAAAATTCCCAT 1033
                          v   i vvvv     ii  i  v v  v  i-----  i ---   i -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGA---TCCTA- 141

  chr2_84517995_8   1034 GGAGCCAAATTCATATGGAACCA-AAAAGAGCCTGAATAGGCAAACCAAT 1082
                         ------              vii-  ii  v  v      v    v    
  L1M4_orf2#LINE/    142 ------AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_84517995_8   1083 CCTAAGCAAAAAGAACAAAGCTGGAGGCAC-CACATTACCTGACTTTAAA 1131
                          i i iv  i          i      -  -    i v  ii i  i   
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAA 234

  chr2_84517995_8   1132 CCATACTATAAGGCTACAGTAACCCAAACACCATGGTACTGACATAAAAA 1181
                         v v     i  i          i v i   vii        i     ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_84517995_8   1182 CAGACACACAGACCAATGGAACAGAATAGAAAGCCCAGAAATAAAGCTGC 1231
                         i     i i   i        i     v  i  i           v iii
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_84517995_8   1232 GCACCTATAGCCATCTGATCTTAGACAAGGCCAACAAAAATAAGCGAATG 1281
                         i  ii   i i  vi    i  v       viiv   i vi vv -    
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC-AATG 383

  chr2_84517995_8   1282 GGAAAGGACTC-CCTTTTCAATAAATAGTGCTGGGATAGCTGGCTAGCTA 1330
                           i  i  v v-i        i    i         i i    v  ? i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_84517995_8   1331 TATACAGAAGAATGAAAGTGGACCCCTACCCTCCACCAAATAAAAAAAAT 1380
                         i  i  i         iv            iiv     v   v     - 
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-T 482

  chr2_84517995_8   1381 TATCTCAGA-TGGATTAAAAGTTTAAACGTTAGACCTCAAACTATAAAAA 1429
                           v    i -     i ? iiii    i  v   v  v           v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_84517995_8   1430 TCCTAGAAGAAAACTTAGGAAACACTATTCTGGAAATTGGCCTTGGA--A 1477
                           i           v    ?ivv v v   -- ----  i      i-- 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTC--G----TGACCTTGGGTTA 576

  chr2_84517995_8   1478 AAGAATGTATGATTAAGTCT-----CAAATGCAACCGTAACAAACACAAA 1522
                         iiv    vv vv   ii v -----    v   vvv i      viv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_84517995_8   1523 AACTGACAAATGGGACCCAAT---AACTAAAGAGCTTT----TCCACAGC 1565
                           iv  i    v    iiv  ---  i    i vi   ---- i  v  v
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_84517995_8   1566 AAGCAATCAACAGAGT-AACAGACAACCTACAGAATGGGAGAAAATATTC 1614
                          vi v     v i   -  v        i                    i
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_84517995_8   1615 ACAAAC--TGCATTTGACAAAGGTCTAATATCCAGAATCTATAAGGAACT 1662
                         i    i-- ii  i   i  i  v  vi          v     i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_84517995_8   1663 T----AAATTAACAAGCAAAAAACAAGCAATCCCATTAAAAAGTGGACCA 1708
                         i----  v i  i  vv    i    ii  i  v   ?    i   i v 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_84517995_8   1709 AGGACAGGGACTGACACTTTTCAAAAGAAGACATAAAAGTGACCAATAAA 1758
                             ivv i iv    i  i  v        i   v  i  i       i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_84517995_8   1759 CATATGAAAAAAATGTTCAACATCACTAATAAT 1791
                           i       i -  i         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.50 (50 / 20)  


2956 27.59 1.78 0.78  chr2_84536573_84541552     3590  4488 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84536573_8   3590 TGGAAAAACATTCCATGTTCATGGATAGGAAGAACAAATATTGTGAAAAT 3639
                               i i  i              v      viv        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84536573_8   3640 GGCCATATTGCTCAAAGTAATTTATAGATCCAGTGCTATCCCCATCAAGT 3689
                            v   i v i    v i  i  i    i  ii  v     i     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-- 98

  chr2_84536573_8   3690 GAA---CATTGACTTTCTTCACAGAACTGGAAAAATCTACTTTAAATTTC 3736
                         -  ---  vivi i  i  ii     v v  v  iiiv iii    v   
  L1M4_orf2#LINE/     99 -AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_84536573_8   3737 GTATGGAACCAAAAAAGATCCAGCATAGCCAAGACAATCCTAAGCCAAAA 3786
                         i       viiv  ii  i    v        i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_84536573_8   3787 GAAAAAAGCTGGAGGCATTACACTACCTGACTTCAAACTGTACTACAAGG 3836
                            v    i      vv i     v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_84536573_8   3837 CCATAGTAACAAAAACAGCATGGTACTGGTAACAAAACAGATATATGGAC 3886
                          i i     iv  i    ii         i vv ii i   i    i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_84536573_8   3887 CAACGGAACAGAA--GAAAGGCCTCAGAAATAACACCACACATCTACAAC 3934
                            i    i    --  i  v  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_84536573_8   3935 CATCTGATCTTTAACAAACGTGACAAAAACAAGCAATGGGGAAAGGATTC 3984
                           vi    i  ii    iv   v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_84536573_8   3985 CCTATTTAATAAACAGTGTTGGAAAAACTTGATGGTCATATGCAGAAAGC 4034
                         i  v  i  i   ii   i   i v    v   i?i  i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_84536573_8   4035 TGAAACTGGATCCCTTCCTTACATCTTATACCAAAATTAACTAAAGATGG 4084
                             ii    i    v   i   i v     v          v  i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_84536573_8   4085 ATTAAAGACTTAAACAGAAGACCTAAAACCATAAAATCCCCAGAAGAAAA 4134
                           i ?    i    iiv    v       i      ii ii         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_84536573_8   4135 CCTAGGCA-ATACCATTCAGGACATAGGCATTGGCAAAGACTTCATGACT 4183
                          v    ?i- v i -   iv   v v  vv v     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_84536573_8   4184 AAAACACCAAAAGCAATGGCAACAAAAGCCAAATT-GACAAATGGGATCT 4232
                          vi            vvi          vv   v -  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_84536573_8   4233 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAG---AGTGA 4279
                         v  i   v v  i i   i  ii vv    i  v       i---     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_84536573_8   4280 ACAGGCAACCTACAGAATGAGAGAAAAATTTTGCAATCTATCCATCTGAC 4329
                          v  i     i        i       vv       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_84536573_8   4330 AAAGGGCTAATATCCGGAATCTACAAGGA--TCTAAACAAATTTACAAGA 4377
                           i  i  vi     i    v  i  i  --   v -   v iv i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATA 793

  chr2_84536573_8   4378 AAAA---AAACAACCCCATCAAAAAGTGAGCAAAGGATATAAACAGACAC 4424
                             ---   i     v  i?    i  i         v i  i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_84536573_8   4425 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAA-GCTC 4473
                              v        i  vi viii     i ii  i       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_84536573_8   4474 ATCATCACTGTTCAT 4488
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (153 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


 471 25.93 0.74 0.74  chr2_84550183_84551835        3   137 (1516)    L1M4_orf2#LINE/L1       77   211 (697)  

  chr2_84550183_8      3 GATTCAATGTAATCCCTATTAAAATTCCAATGACATTTTTCACATTAATA 52
                                i i         i     i   iivi v     ii  vv   v
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

  chr2_84550183_8     53 GAAAAAC-AATCCTTAAAATGTGTATGAAACTAAAAAGGACCCCTAATAA 101
                           v  i -i     -     vii    i  v iv  i      vv    i
  L1M4_orf2#LINE/    127 GACAAGCTGATCCT-AAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr2_84550183_8    102 CCAAAGCAATATTGAGCAAAAAGAACTAAGATGGAG 137
                              i    v    iv  i      v   v     
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

Transitions / transversions = 1.33 (20 / 15)
Gap_init rate = 0.01 (2 / 135), avg. gap size = 1.00 (2 / 2)  

 296 22.89 7.23 0.00  chr2_84550183_84551835      431   513 (1140)    L1M4_orf2#LINE/L1      189   277 (631)  

  chr2_84550183_8    431 GAAAAAG--GAACTAAGATGGAGGCATCACACT----GATTTCAAACTAT 474
                                --    v   v      vv       ----i        viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_84550183_8    475 ATTACAAAGGTATATTTATCATAACAGCATGATACTAGC 513
                          i       v  i v v    vi    ii  i    i  
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

Transitions / transversions = 0.90 (9 / 10)
Gap_init rate = 0.02 (2 / 89), avg. gap size = 3.00 (6 / 2)  

2243 24.07 6.83 0.93  chr2_84550183_84551835      518  1161 (492)    L1M4_orf2#LINE/L1      227   908 (0)  

  chr2_84550183_8    518 ATTTCAAACTATACTACAAAGGTATAGTTACCAAAACAGCATAGCACTGG 567
                                 viv          v  i   v i   i    ii i i     
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_84550183_8    568 CATAAAAATAGACATATAGACTAATGGAACAGAATAG-GAGCCCAGAAAT 616
                              ii             ii       i     v -   i        
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_84550183_8    617 TTATCCTCTCATATACAGTCAACTAATCCT-GA-AAGTCT-TCAGAAGTA 663
                         vv i  viv   v  ii     i i  ii -  -   vv -i  ii vi 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_84550183_8    664 CACAATAGGGAAAGAATAGTGTCTTCAATAAATGATGTTAGGAAATCTGG 713
                         iv    i             v i     i     i  i i   v v    
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_84550183_8    714 ATAGCCACATGCAAAAGAATGAAATTGGACCCTTATATTACA-------- 755
                            ?                   i        i  iv i   --------
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_84550183_8    756 ----------TCAAAATGCATTAAAGTTTCT---TTTAGGAGTT----TT 788
                         ----------        v  i ?  vi-  --- v  i   i ----i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGAC-CTAAATGTAAGAGCTAAAACT 525

  chr2_84550183_8    789 ACAGTTGCCCCTAAAGGAAAA--TGGG---AAAACTCCTTCACATTGGTC 833
                          i iv-i i i  i i     -- i  ---   v  i v v  v    vi
  L1M4_orf2#LINE/    526 ATAAA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_84550183_8    834 TTGGCAATGATTATTTAGACATGACACTAAAAGCATA-----CAGAAGCA 878
                          v       i  vi     i       i       i -----  i   v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_84550183_8    879 AAAATAAACAAGTGGGACTACACCAAACTAAAAAGTTTCTGCACAGCAAA 928
                               i i  i v     v  i    v v    ii  i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_84550183_8    929 GAAAACAAT---GAAAATGAAAGGGCAACCTACAAAATGGGAGAAAGCAT 975
                          i v  v  ---    i     i i     i   i           ii  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_84550183_8    976 TTTCAAACCGTGTGTATGACAAAGGTTTGATTAAAATCCAAAATATATAA 1025
                           v    i i i i v   i  i  vi vi ----     i         
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGT----ATCCAGAATATATAA 770

  chr2_84550183_8   1026 GGTACTCACACAATTCAATAGCAAAAAT-CAAATAGCCCAATTAAAAAAT 1074
                         i v    vi    i      ii     v-      i       ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_84550183_8   1075 GGG-AAAAAACCTGAATAGACAATTTTTCAAACAAGACATACAAGTAGCC 1123
                            -   ii ii          v  i i    v    i      i i   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_84550183_8   1124 AACAGGTATATGGAAAGGTGCTCAACATCACTCTACAG 1161
                           i i i i   i    i            ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.23 (105 / 47)
Gap_init rate = 0.02 (16 / 682), avg. gap size = 3.12 (50 / 16)  


3520 23.37 1.88 1.33  chr2_84638069_84642286.rev     2825  3727 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84638069_8   2825 TGGAAAAATATTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 2874
                               i    i                     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84638069_8   2875 ATCTATACTACCTAAAGTAAGCTACAGTTTCAATGGAATCCCTATCAAAT 2924
                         iv v     v  i   v i v      v     i v             v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84638069_8   2925 TATCAATGACATTCTTCACAGAAATAGAAAAGACAATCCTAAAATTTATC 2974
                          vi  iivi v  i  ii       v  v   vii           i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_84638069_8   2975 TGGAACCATA-AAAAGACCCAGAGTAGCCAAAGCTATCCTGAGCAAAAAG 3023
                              --  i-  ii        i        i v   i   iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_84638069_8   3024 AGCAAAACTTGAGGAATCACATTACCTGACTTCAGTTTATACTACAGAGC 3073
                          i    ii v     v     i v  ii i    ivviv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_84638069_8   3074 TATAGTAACCATAACAGCATGGTACTGGCATAAAAACAAACACATAGA-C 3122
                           i     i  vi    ii              ii i i   i     - 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_84638069_8   3123 GATGGAACAGAATAGAGAACCCAGAAACAAATCCACACACCTATAGTGAA 3172
                         i      i     v    ii       i   i   i   ii   i  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_84638069_8   3173 CTCATTTTGGACAAAGATGCCAAGAACATACACTGGGGAAAGA-CAATCT 3221
                         i v     v     i i        v   v  v          -i i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_84638069_8   3222 CTTCAATAAATGATGCTGGAAAAACTGGATATTCATATGCAGAATAATGA 3271
                         i     i     i      i v         ?i  i     i  v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_84638069_8   3272 GACTAGACCCCCATCTCTCACCATATACAAAAATCAAATAAAAATGGATT 3321
                         iii i      i i   v                i  v v         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_84638069_8   3322 AGAGAGCTACATCTAAGACTTCAGACTATGAAACTGCTATGAGAAAGCAT 3371
                          ?   v   v  v     vi v i     i     vi  vi     i   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_84638069_8   3372 TGGGGAAAATCTCCAGGACATTGGTCTCGGAAAAAACATTTCTTGAGCAA 3421
                         v  ? v      i iv   v    vi v  v  vii--      iiii v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG--TTTCTTAGATAT 596

  chr2_84638069_8   3422 TACCCCACAAGCGCAGGCAACCAAAGCAAACATGGACAAATGGGATCACA 3471
                         v  v   v    i  i     v    v   v  i  i    v   iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_84638069_8   3472 TCAAG-TTAAAAAGCTTCTGCACAGCAAAGGGTACGAT-AACAAAGTGAA 3519
                             i-       -   i  ii vv      ii  v  -  v        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_84638069_8   3520 GAGACAACTCACAGAATGG----------TTGCAAACTACCCATTTGACA 3559
                         i       i          ----------       ii ivi  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_84638069_8   3560 AG--ATTACTAACCGGAATATATAAGGAACTAAAACAACTCTATTGGAAA 3607
                           -- i vv  v  i          i     vvv       v  ------
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT------ 789

  chr2_84638069_8   3608 AAAAAAAAAACTAATAACCTGATCAAAAAAATGGGCAAAAGGTTTGAATA 3657
                           v     i  v       ii  i?     -        i i        
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATA 838

  chr2_84638069_8   3658 GACATTTCTCAAAAGAAGATGCACAAATGTCAAACAGGCATATGAAAAGG 3707
                                   v         ii       v v  i i   i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_84638069_8   3708 TGTTCCACATCCTTGATCAT 3727
                           i  v     v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (127 / 80)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  


3095 26.71 0.99 0.77  chr2_84644600_84650982.rev     4986  5891 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84644600_8   4986 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5035
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84644600_8   5036 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5085
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84644600_8   5086 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5133
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_84644600_8   5134 TATGGAACCAAAAAAGAGCCTGCAGTGCCAAGTCAACCCTAAGCCA-AAG 5182
                                viiv  ii  v  v v vv     iv   i i i ivv -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_84644600_8   5183 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAAGGC 5232
                                i      vv    i  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_84644600_8   5233 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5282
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_84644600_8   5283 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5330
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_84644600_8   5331 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5380
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_84644600_8   5381 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5430
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_84644600_8   5431 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG- 5479
                            ii    i    v   i     v              i    i    -
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_84644600_8   5480 TTAAAGACTTACATGTTAAA-CTAAAGCCATAAAAACTCT-AGAAGAAAA 5527
                          i ?    i  v    v i -     i i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr2_84644600_8   5528 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 5576
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_84644600_8   5577 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCT 5626
                          vi            vvi          vv     v  i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_84644600_8   5627 AAGTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGA 5676
                         v vi   v v  i i   i  ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_84644600_8   5677 ACAGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTACTCGTCTGAC 5726
                          v  i     i       i         v       vii ivii     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_84644600_8   5727 ATAGGGCTAATATACAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5776
                          vi  i  vi   v      v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_84644600_8   5777 AAAAACAAACAACCCCATCAAAAAAGTGGGCAAAGGATATGAACAGATAC 5826
                            i     i     v  i?     -            v    i   i i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACAT 843

  chr2_84644600_8   5827 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACACGAAAAAATGCTC 5876
                              v        i  vi viii     v  i    i     i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_84644600_8   5877 ACCATCACTGGCCAT 5891
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.23 (16 / 13)  


3007 25.91 1.43 1.32  chr2_84659507_84663947.rev     3043  3949 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84659507_8   3043 TGAAAAAACATTCCATGCTCTCCGTG-ATAGGAAGAATCAGTATCATTAC 3091
                           i   i i  i     i  ---i  -  v      v i i   ii   v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTC---ATGGATTGGAAGACTTAATATTGTTAA 47

  chr2_84659507_8   3092 AATCGCCATACTGTGCAAAGCAATTTACAGATATAAGGCTATTCCTATCA 3141
                         i  v  v     viv    vii  i       vi  v  v  i       
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_84659507_8   3142 AA--CACAAATGACATTCTTCACAGAACTAGAAAAAACT-ATCTTAAAAT 3188
                           -- v  iv  v -  i  ii     v v  v  i-  -   i      
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAAT 145

  chr2_84659507_8   3189 TCATATGGAACCAAAAAGGAGGCTGAATAGCCAAGGCAATCCCAAGCATA 3238
                                   viiv  i   vv v          ii     iii i--- 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA---A 192

  chr2_84659507_8   3239 AAGAAGAACA---CTGGAGGCATCATGTTACCTGACTTCAAACTATACTA 3285
                                   ---i      vv   iii v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_84659507_8   3286 CAGGGCTACAGTAACCAAAACAACATGGTACTGGTACAAAAACAGACATG 3335
                           ii          i   i   iii         i i  ii i      i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_84659507_8   3336 TAGACCAACAGAACAGAATAAAGAGCCCAAAAATAAGGCCGCACATGTAC 3385
                             i   ii   i     vi    i   i      iv  ii    v  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_84659507_8   3386 AACCATGTCATCTTTGACAAAGCTGACAAAAACAAGCAATAGAGAAAGGA 3435
                         iii  vv v  i  i     i v  v   i v  vv    i i     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_84659507_8   3436 CTCCCTATTCAATAAATGGTACTGGGATAACTGGCTACCCATATGCAGAA 3485
                         ivvi  v     i       i      i      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_84659507_8   3486 GATTAAAAATGGACCCTTTCCTTACACCATATACAAAAATTAACTCAAGA 3535
                           v i  iv       i v   i                         i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_84659507_8   3536 TGGATTAAAGACATAAATGTAAAACCCCAAACTATAAAACCCCTGGAAGA 3585
                              i ?    v         i v iv            i i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_84659507_8   3586 CAACGTAGGCA-ATACCATTCTGAACGTAGGAATT-GGCAAAGATTTCAT 3633
                         v   i    ?i- v i v iv   v v i  --  -     v i    v 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTT 590

  chr2_84659507_8   3634 GACAAAGATACCAAAAGCAATTGCAACAAAATCAAAAATTGACAAATGGG 3683
                         iivv v  i          vvv         vv      v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_84659507_8   3684 ATCTAATTAAACTTAAGAACTTCTGCATAGCTAAAGAAACTATCAACAGA 3733
                          ii v  i   v    i     i  iiivv v  i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_84659507_8   3734 GTGAAAAAACAACCTACAGAATGGAAGAAAATATTTGTAAGCTATGCATC 3783
                                i      i         i            i  iii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_84659507_8   3784 TT-TGAAGGTCTAATATCCAGAATCTACAAGAAACAA--ACAAATCTACA 3830
                          v- i i  v  vi          v  i  ii   vv--    v  v i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_84659507_8   3831 A-AAAAACCCACAAACAAACCCATTAAAAAGTGGGCAAAGGACATGAACA 3879
                          -     v--     i  v  v   ?    i           iv    i 
  L1M4_orf2#LINE/    791 ATAAAAAG--ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_84659507_8   3880 GACACTTTTCAAAAAAAGACATAGACATAGCGAACAAGCATATGAAAAAA 3929
                             i  i  v   i    i   v v  i  v  i     i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_84659507_8   3930 AGCTCAATATCACTGGTCAT 3949
                         v      i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (141 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


2289 26.29 0.30 0.76  chr2_84699440_84701085      497  1154 (492)    L1M4_orf2#LINE/L1      254   908 (0)  

  chr2_84699440_8    497 TAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGG 546
                            i   i    ii         i iv ii i   v              
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_84699440_8    547 AACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTTCAACTATCTG 594
                           i    i--    i  --        vv  ii i  i viiiii vi  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_84699440_8    595 ATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATT 644
                           i  i     ivv  vv  i v  vv            i  vvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_84699440_8    645 TAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCTGAAAC 694
                         i  i              v      v  ?   i     i  iiv    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_84699440_8    695 TGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAA 744
                             i    v   i     v              i    i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_84699440_8    745 AACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGG 794
                         i  i    i  v   v       i      vi i           v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_84699440_8    795 CATTACCATTCAAGACATAGGCATGGGCAAAGGACTTCATGTCTAAAACA 844
                         ?i v viv   iv   v v  vv i     v  -i   v ivv  vi   
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGACA 600

  chr2_84699440_8    845 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACAGGATCTAATTAA 894
                                  vvi          vv     v  i   iv   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_84699440_8    895 ACTAAAGAGCTTCTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 944
                          v v  i i   i v   vi--    i  v    i  vv i      v  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_84699440_8    945 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTGCTCATCTGACAAAG 994
                         i     i   i             v  ii   viiiivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_84699440_8    995 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 1044
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_84699440_8   1045 ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACATTTCTC 1094
                              i     v  i?    i            v    i           
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_84699440_8   1095 AAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTGATCAT 1144
                         v        i  vi viii     v ii          i     v v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_84699440_8   1145 CACTGGCCAT 1154
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.35 (97 / 72)
Gap_init rate = 0.01 (4 / 655), avg. gap size = 1.75 (7 / 4)  


2382 27.00 6.72 1.51  chr2_84701781_84704880.rev     1754  2616 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84701781_8   1754 TGGAAAAAGATTCCATGCTCGTGGACTGGAAGAATCATTATTGTTAAAAT 1803
                               i v  i     i  i    i       v i v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84701781_8   1804 GGCCATAATGCCCAAAGCAATTTACAGATTCAATGCAATTCCTATCAAAC 1853
                            v   v v      vii  i           i     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84701781_8   1854 TATTTA--TATCTTTTTTCACAGAATTAGAAAAAACT-ATTCTAAAATTC 1900
                          -iii -- ii       -i     v v  v  i-  -  i         
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr2_84701781_8   1901 ATATGGAACCAAAAAAGAGCCA-ACTAGCCAAAGCAATTCTAACCAAAAA 1949
                                 viiv  ii  v   - v        i    ii i vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_84701781_8   1950 CAACAAAGGTAAAGGCAGCACATTACCTGGGCTTCAAACTATGCTACAAG 1999
                         v       v ii   vvv    i v  iiivi iv     - i      i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr2_84701781_8   2000 GCTACAGTAACCAAAACAGCAAGGTATTGGTACAAAAACAGACACATAGA 2049
                                   i   i    iiv    i   i i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_84701781_8   2050 CCAAGAGAACAGAACAGAAAACCCAGAAATAAAGCTGCACACCCACAACC 2099
                         i   vi   i    iv  i ii           v iii   iii iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_84701781_8   2100 ATCTAATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAAGATTCC 2149
                          vi i  i  i     i v  v   i v  vv           ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_84701781_8   2150 CTATTCAATAAATGGTGCTGGAATAACTCACTAGCCATATGCAGAAGAAA 2199
                           v     i            i i    viv  ?   i     i     v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_84701781_8   2200 GAAACTGCACCTCTACCTTTCCTAATATACAAAAATTAACTCAAGATGGA 2249
                            ii  v   i      iv viv                    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_84701781_8   2250 TTAAAGATTTAAATGTACAATCTCAAACTATAAAATTCCTAGAAAACAAG 2299
                          i ?   ii        vi v  v           i  i     ----- 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA-----G 541

  chr2_84701781_8   2300 AAAACCTAGAAAATAACCTTTTCGACACAGGCTT-GGCAAAGAATTGTTG 2348
                              v   i?ivv  i   ivi   viv  v  -     v iv  v  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_84701781_8   2349 GTTGTTTG----CAAAA--ACAATTGGAACAAAAACAAAAATTGACAAGT 2392
                          v i -- ----     --    -- v       iv      v  i  i 
  L1M4_orf2#LINE/    592 GATAT--GACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAAT 637

  chr2_84701781_8   2393 GGCACCAAATTAAACTAAAGAGCACCTGCACAGCAAAAGAAATTTTCAA- 2441
                         v v  ivv  i   v v  i i vii  ii vv    i  v i v    -
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_84701781_8   2442 ----TAAACACACAACCTACATAATGGGAGAAAATATTCACAAACCGCAT 2487
                         ---- i  v v      i   v                ii    i ii  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_84701781_8   2488 --TTGACAACGGTCTAATATCCAGAATCTATTAAAAACTT----AAATCA 2531
                         --i   i  v  v  vi          v   v  i    i----  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_84701781_8   2532 ACAAGCAAAAAACAA----CCTCATCAAAAAATGG-CAAA---------- 2566
                          i  vv    i    ----  iv  i?        -    ----------
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_84701781_8   2567 ---------------------ATACAAGCAGCCAGCAAACATATGAAAAA 2595
                         ---------------------      iii    ii  i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_84701781_8   2596 ATGCTAATTATAACTAATCAT 2616
                              v vi  v ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (141 / 88)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.74 (71 / 19)  


3578 21.95 3.47 1.79  chr2_84729466_84731638      789  1681 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84729466_8    789 TAGAAAGATATCCCATGTTCATTGATTAAAAGACTTAATATTGTTAAAAT 838
                          i                    v    ii                  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84729466_8    839 ACCTGTACTACCCAAAGTGACTTATACATTCAATGCAATCCTTACCAATT 888
                         iv vi    v      v   ii  i v      i       i  i   vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84729466_8    889 TCCCAATGACATTTTCTAAAGAAATATTAAAAACAAATTCTAAAATTTAT 938
                              iivi v    i iv      - v v  i vi  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_84729466_8    939 AGGGAACCACAGAGGACCTCGAGTACCCAACACAATCTTGAGAAATAGGA 988
                          v    vii  ii     iv  i  v    v          i   v i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_84729466_8    989 AAAAAGCTAAAGGTCTCACACTTCCTAATCTAAAAACATATTACAAAGCT 1038
                          v    i ii   v           i   i v     v  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_84729466_8   1039 ATAGTAATTAAAATAGTATGGTACTAGCAT--GCATTCAGACATATAGAC 1086
                          i      i  i i   i       i    -- v  --           i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT--AGACATATAGAT 297

  chr2_84729466_8   1087 CAATGAAACAGAATGGAAAACCGCAAAACAA---CAAA----TATGGTCA 1129
                              i  i     v  i ii vvi   i  ---  v ----        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_84729466_8   1130 ACGCATCTATGGCAAAGGTGCCAAAAATACACAACAGGGAGAGGATAGTC 1179
                          ivv  i vi i   i        i vi iv   ii    i  i      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_84729466_8   1180 TCTTCAACAAACGGTGTTAAGG-AACTGGATATTCATATGCAAAAGAATG 1228
                          i         i    i ii i-         ?i  i             
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_84729466_8   1229 AAGCTGAACCCTTAC------------ACAAAAATCAGTTCAAAATGAAT 1266
                            i  i    i   ------------        i ii        i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_84729466_8   1267 GGGTTAAAGACTCAAA----AGAACTAAAACTATAAAATTCCTAGAGGAA 1312
                         ----i ?    ii   ----   i              i  i    i   
  L1M4_orf2#LINE/    498 ----CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_84729466_8   1313 AAGGTAGGAG-AAATCTTCATGACATTGGCCTTGGCTATGATTTCTTGGA 1361
                           vi    ? -        i    v    vi v   v   i      i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_84729466_8   1362 TGTGACACCAAAAAC-CAATGTAACAAAAACAGAAATAGACAAGTGGAAC 1410
                          i           i -   - i       iv i       i  i v i  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_84729466_8   1411 TACATCAAACTAAACAGCTTCTGCAAAGCAAAGGAAACAATCAACAGAGT 1460
                          v       v v  v i   i  iivvv       v  v     v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_84729466_8   1461 AAAAAGGCAACATACAGAATGAGGGAAAAAATTTGCAAATTATATACTTG 1510
                         i     i    vi        i i     v          i     ii  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_84729466_8   1511 ATAAGAGGTTATTATCTAAACTCCTTATAGATAAGGAACTCCTACAACAC 1560
                              i ii vv    i i ------   v    i      i      v 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGA------ATATATAAAGAACTCTTACAACTC 786

  chr2_84729466_8   1561 AATAGCCAAAA---AAAAAACCCAAATTTTTAAAATGGACAAAGGACTTG 1607
                             iiv    ---   v       --  ?v       i       i   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAA--TTWAAAAATGGGCAAAGGATTTG 834

  chr2_84729466_8   1608 AATGAACATTTCTCTAAAGAAGACATACAAATGGTCAACAGGCATGTGAA 1657
                            ii         i        i          i   i i   ii    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_84729466_8   1658 AAGACACCCAACATCAATAATCAT 1681
                             ii i        ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.20 (132 / 60)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.13 (47 / 15)  


2390 23.76 2.18 5.82  chr2_84737362_84739178.rev      501  1325 (492)    L1M4_orf2#LINE/L1      114   908 (0)  

  chr2_84737362_8    501 TTTTATAGATATTGAGAAGCTAAATATAAAATAGATATGGAAAGGCAAAG 550
                             ii   v     v     i viv      vv         v    i 
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_84737362_8    551 GAATTAGAATAGACAAAATAATTGTAAAAAGGAAGAACAAAATTGGAGGA 600
                           vii       v     i   iv i    i          i        
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_84737362_8    601 TTAAGACTACTTGATTTCAACACTTACTA----GCTATCGTAATTAAGAA 646
                         i v v   v iii       v        ----    iv     i    v
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_84737362_8    647 AGTGTAGTATTGATGAAAGAATAGGCTTATAGAACAATGAAACAGAAC-- 694
                              i   i  iiiv   i    i v      v     i  i    i--
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_84737362_8    695 AGAGTCCAGAAATAGACTAAAAAAT--ATAGTCAATTGACTTTTGGCAAA 742
                                       i  iv v v  --  i         i   i i   i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_84737362_8    743 TGTGCAAAGGTGAGTCAATGGAGAAGAGTGCCTGGGGAGGATAGTCATTT 792
                         v    v   iiv v       i   ------------  i      -   
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAA------------AGAATAGTC-TTT 400

  chr2_84737362_8    793 CCAAATAATGACTGAAGAAAAAATAATCATTTCAAATAATGCTGTTCCTT 842
                         i   ----------------------------     ii     vvv --
  L1M4_orf2#LINE/    401 TCAA----------------------------CAAATGGTGCTGGGAC-- 420

  chr2_84737362_8    843 TAATTGGATATA-ATATGTACAAAAGTACACCTTGA----TACCTCATAT 887
                         -  i      ?v- i   i v  i i iv vi v  ----       i i
  L1M4_orf2#LINE/    421 -AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_84737362_8    888 T-TATGAAAAAATTAACTCAAAATAGATCATATACCTAAACATAGAAAAC 936
                         i-   iv                 i     ? v       ii  ii ivi
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_84737362_8    937 AAAACCTTTAAACTTCTAACAGAAGAAACATAGAGA-AAATATGTGTGAC 985
                              iv v     ii  iv    --       i?i-    v vi     
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAA--AACATAGGNGTAAATCTTCGTGAC 567

  chr2_84737362_8    986 CTTAAGTTTGAAAAAAAAGTGT-TTGGATACTATACTAAAAGCTTGATTC 1034
                            ii   -- iiv  vi  v -  i    iv i  i      vii viv
  L1M4_orf2#LINE/    568 CTTGGGTT--AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_84737362_8   1035 ATAAAAGAAAAAAATTATAAATTAGAGTTTATTGAAATTAAAACTTTTTG 1084
                          i           vvv       i  v  i  ii         vi     
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_84737362_8   1085 CTCTGTGAAAATCACTGTACAGGAACTGAAAAGACAAGCAACTGACTGGA 1134
                         iv  vii  iiv    i vv  i  v           v v  v  v   i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_84737362_8   1135 AGAAAATATTTTCAAGTTACATATCTGAAAAAAAACTTTTATGCAGAATA 1184
                                    v   i i i        v  iii    v   v       
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_84737362_8   1185 TATGAATAACTCTTAAAACTCAATTATAACCAAGCAAACAACCCAATT-A 1233
                            i  v        v        v    vv ii    i         - 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_84737362_8   1234 AAAATGGGCAAAAGATCTGAACAGACATTTAATCAAAGAATATAGATGGA 1283
                                     i   i    i        vvi       v   v iii 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_84737362_8   1284 TGGCAAATA-GCATATAAGAAGATGTTCAACATTATCAGTATT 1325
                             v    -   i  i i      i       i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (115 / 78)
Gap_init rate = 0.02 (16 / 795), avg. gap size = 4.12 (66 / 16)  


2903 24.26 2.40 3.17  chr2_84753061_84755253.rev      787  1701 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84753061_8    787 TGGAAACACATCCTATGTTCATGAATGGGTAGAATCAATATTGTGAAAAT 836
                               v i    i         i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84753061_8    837 GACCATACTGCCATAAGCAATCTATAAACTCAATGCAATTGTCATAAAAA 886
                          i v     v  vv  vii     i i i    i     ivii  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84753061_8    887 TAACACCATAATTCTTCACAGAGTTAGAAAAATATAATTCTAAATTTCAT 936
                          vv  v vvvv  i  ii    iv v  v  ii- i  i     v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_84753061_8    937 ATGGAACCAAAAAAAGAGCCCACA-TAGCCAAAGCATGACTAAGCAAAAA 985
                               -- viv  i ii    v -        i  vvvi i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_84753061_8    986 GAACAAATCTGGAGGCATCACATTACCTGACTTTAAACTATACTACAAGG 1035
                                vi      vv     i v  ii i  i   viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_84753061_8   1036 CCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCATATAGAC 1085
                          i i   v i   i    ii         i    ii    i        i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_84753061_8   1086 CAATGGAACAGAATAGAGAACCTGGAAATAAAGCAAAATACTTATAGCCA 1135
                                 i     v    ii ii        v v v i i    i i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_84753061_8   1136 ACTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGAAAAGGATACCC 1185
                          i    i  i     i vviv   i v   vv i    i    i   vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_84753061_8   1186 TATTCAACAAATGGTGCTGGGATAACTGGCAAGCCACATGTAGAAGAATG 1235
                          v                    i      vv ?       i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_84753061_8   1236 AAACTGGATCCTCATCTCTCACC-----TAAAAATCAAATCAAGATAGAT 1280
                           ii    i  ii i   v    -----i      i  v    i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_84753061_8   1281 CAAAGACTTAAATCTAAGACCTGAAACCATAACAATTCT-GGAAGATAAT 1329
                           ?    i     v     v  i    i    -  i   -i     v  i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAAC 546

  chr2_84753061_8   1330 ATTGGAAAAACACCTCTTGACATTGGCTTACGCAAGAACTTCATGACCAA 1379
                           v  ?iv  vv i  v    v    v   v    viii   v ------
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT------ 590

  chr2_84753061_8   1380 AACCCAAAGGCAAATGCGACCAAAACTCAAAAGCAAATGCAACAAAAGAA 1429
                         ----------- i  ii   ----  -        v v            
  L1M4_orf2#LINE/    591 -----------AGATATGAC----AC-CAAAAGCACAAGCAACAAAAGAA 624

  chr2_84753061_8   1430 AGA-TAAATAGATGGGACTT----AAACTTAAAAGCTTCTGCACAGCAAA 1474
                          i -  i   i  v      ----   v      i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_84753061_8   1475 AGAAAC-AGCAAGCAGAGTAAACAGACAACTCACAGAGTGGGAAAAAATC 1523
                         i  v  - v    - i   i  v       i      i     i     v
  L1M4_orf2#LINE/    675 GGACACTATCAAG-AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_84753061_8   1524 TT--CAGAATCTGTACATCTGGCAAAGGACTAATAGCCAGAATCTGCAAG 1571
                           --  -    -i  i     ii  i     vi  v       v ii  i
  L1M4_orf2#LINE/    724 TTTGCA-AATC-ATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_84753061_8   1572 GAACTC----AAATCAGCAAGAAAAAAACAAACAATCCCTTCAAAAAGTG 1617
                               ----  v   ii  v     i     i  i  vv i?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_84753061_8   1618 AGCTAAGGACATGAATAGACAATTCTCAAAAGAAGGTATACAAATGGGCT 1667
                         i  v     iv          v     v       i           v v
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_84753061_8   1668 ATAA--ACATGAAAA-ATGCTCAACATCACTAATGAT 1701
                             --         -             ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (129 / 89)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.68 (51 / 19)  


3413 21.39 1.90 6.22  chr2_84794821_84797154.rev      898  1846 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84794821_8    898 TGGAGAGAAATACCACATTCATGGATAGGAAGACTAAATAGTCTTAAGAT 947
                             i   v  v   ii         v        v    v v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84794821_8    948 GTCAAT-TTCTCTGATGTTATCTATAAATTCAACACAATCTCAGTTAAAA 996
                          v    -i  i ii vv v     i i       i     i vi i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84794821_8    997 TTCCAGCAAGTTACTTTGTGGATTAATTGACAAACTGATTCTAAAGTTTA 1046
                          i     vivi vi    ii  --         i     i     i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA--AATTGACAAGCTGATCCTAAAATTCA 148

  chr2_84794821_8   1047 TATGGAAAGGCAAAAAACCCAGAATAACCAACACAAC------AAAAAAG 1090
                                 v    iii          i    v    i------   i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_84794821_8   1091 AACAAAGTTGAAAAACTGACACTACCCAACTTCAAGACTTACTATACAGC 1140
                                   i ii   v     v     i     i        i v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_84794821_8   1141 TGCAGTAATCAAGACAGTGGGTTATTGTTGAAAGAATGGACAAGTAGATC 1190
                          i                 v v  i  viiv   i  i    vi      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_84794821_8   1191 AATGGAACAGAATGGAGAGCACAGAAATAGACCTGCATAAGTACAGTCAA 1240
                                i     v     iv        i   iii i vv  ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_84794821_8   1241 TTGATTTTTAACGAAAAAGCAAAGGCAATCTGATGGAGAAAGGACAGTCT 1290
                                 ii  i iiiv  v   i v  iii    i     i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_84794821_8   1291 TTTCAAAAAATGGTGCTGGAACAACTGGATATACACATGCAAAAAAACAA 1340
                               v            i           ?v           i  ii 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_84794821_8   1341 ATCTAGACACAGACCTTATACCCTTCCTAAAAATTAACTGAAAATGGATT 1390
                          vi i   v vv    i i   v vivi           v         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_84794821_8   1391 A------TAAATGTAA-AGCAAAAAATATACAGTTTTTAGAAGATAACA- 1432
                          ------         -   v    v    v ii i        v    -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_84794821_8   1433 -GGAGAAAATCTACATGACTTTGGGCTTGGTGATGACTTTTTAGGTATGA 1481
                         -  ? v      v i    i     i v  ii   ii  i    i     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_84794821_8   1482 CACCAAAGGCACCATCCATGAGGGAAAAAACTGGTAAGTTGAATTTCATT 1531
                                i    v v v ii ii       iv i   i   i i     i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_84794821_8   1532 AAAATTAACTTCTACTCTGTGAAACACACTGTTAAGAGAATAGAAGATGA 1581
                                 ----------------------------------------- 
  L1M4_orf2#LINE/    649 AAAATTAA-----------------------------------------A 657

  chr2_84794821_8   1582 AATATTTATACAATCTGAAGAGAAACCGGAGTATTGTTAAGAAAATAAAA 1631
                           iv   i i -- iii   -  v  -------- i i      i i   
  L1M4_orf2#LINE/    658 AACTTTTGTGC--TTCAAAG-GACAC--------TATCAAGAAAGTGAAA 696

  chr2_84794821_8   1632 AGACAAGCCATAGACTAGGAGAAAATATTTGCAAAAGATATAATCTGATA 1681
                               v   i   v i                  vv     -       
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA-TCTGATA 745

  chr2_84794821_8   1682 AAGAA-TTGAATTCAAAATATATAAAGAACTCTTAAAATTCAACAATAAG 1730
                          i i -   v  i  i                   v  i    i     i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_84794821_8   1731 AAAACAAACAACCCAATTTCAAAATGGGCCAAAGACCTTCCTTAATAGGC 1780
                           i     i         ?v         v  i  --  -- v     i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGA--TT--TGAATAGAC 841

  chr2_84794821_8   1781 ACCTCATGAAATACGATACATAGATAGCAAACAAACATATGAAAAGATGC 1830
                          ii  viv   v v    i i i  i  v  i  i  i            
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_84794821_8   1831 TCAA-ACCATTTGTCAT 1846
                             - i  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (132 / 68)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 5.13 (77 / 15)  


 799 25.08 6.27 2.64  chr2_84800426_84806794       16   318 (6051)    L1M4_orf2#LINE/L1        1   314 (594)  

  chr2_84800426_8     16 TGGAGAGATATACTATGTTCATGGATTG--AGA--TACTATTATTAAGTT 61
                             i      v i              --   --  v    i     v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84800426_8     62 ATCAGTTCTTTCCAAAATATTTTGAAGATTTTAGGCAACTTCAATCCCAA 111
                         iv  i v  ii     v iv i iv     iv v    iii v   --  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC--AA 98

  chr2_84800426_8    112 AATCCCAACAGA-TTTTTTCCATGAAATCTGACAATCTCATTCTAAAATT 160
                                i v v-      v  -     -      v  v  i        
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCA-GAAAT-TGACAAGCTGATCCTAAAATT 146

  chr2_84800426_8    161 TATATAAAAATGTAAAAGATCTA---TAACTGAGATAATCTTGAA---GG 204
                         i    ii     i  ii  i i ---  i ii i i         --- i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_84800426_8    205 AACACACATTTGGAGGACTTA-ACTACATGACTTGAATAATTCAAGACAA 253
                          iv   v v          i -   v vii i  v  -  i i --- v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA-AACTTA---CTA 242

  chr2_84800426_8    254 TAAAACAGCAGCAATTCAGA--GTGTGGCATTGGTGAAAGGATAT-CAAA 300
                         i   i vi   i   iv   --      i i   iiv       v-  v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_84800426_8    301 TAGA-CAA---ACTAGTATTGA 318
                             -   --- v   v     
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGA 314

Transitions / transversions = 1.53 (46 / 30)
Gap_init rate = 0.05 (15 / 314), avg. gap size = 1.80 (27 / 15)  

3157 26.62 0.77 0.88  chr2_84800426_84806794     4969  5877 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84800426_8   4969 TGGAAGAACATTCCATGCTCATGGATAGGAATAATCAATATTGTGAAAAT 5018
                              ii i  i     i        v    v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84800426_8   5019 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5068
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84800426_8   5069 TACCAATGACTTTCTTCACAGAAGTGGAAGAAACT-ACTTTAAAGTTCAT 5117
                          v   iivi i  i  ii     i v  v-  i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr2_84800426_8   5118 ATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAGGA 5167
                               viiv  ii  v  viv  v     i      i i ivv i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_84800426_8   5168 ACAAAGCTGGAGGCAC-CATGCTACCTGACTTCAAACTATACTACAAGGC 5216
                               i      -  -  ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_84800426_8   5217 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGACC 5266
                                 i   i    ii  i      i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_84800426_8   5267 AACGGAACCGAAC--AGAGCCCTCAGAAATAATACCACACTTCTACAACC 5314
                           i    iv   i--    i  --        vv   i  v i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_84800426_8   5315 ATCTGATCTTTGACAAACCTG--AAAAACAAGAAATGGGGAAACAATTCC 5362
                          vi    i  i     ivv  --  i v  vvv          v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_84800426_8   5363 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5412
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_84800426_8   5413 GAAATTGGATCCCTTCCTTACACCTTATACAAAAATTAATTTCAAGATGG 5462
                            i     i    v   i     v              i -   i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT-CAAAATGG 495

  chr2_84800426_8   5463 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5512
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_84800426_8   5513 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5561
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_84800426_8   5562 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5611
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_84800426_8   5612 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGTGTGA 5661
                         v  i   v v  i i   i  ii vv    i  v    i  vv iv    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_84800426_8   5662 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGAC 5711
                          v  i     i                 v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_84800426_8   5712 AAAGGGCTAATATCCAGAATCTATAAAAAACTTAAACAAATTTACAAGAA 5761
                           i  i  vi          v      i    ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_84800426_8   5762 AAAAAATCAAACAACCACATCAAAAAGTGGGCGAAGGATGTGAACAGATA 5811
                            i --    i    vv  i?    i     i      v    i   i 
  L1M4_orf2#LINE/    795 AAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_84800426_8   5812 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGGT 5861
                         i     v        i  vi viii     i ii          i   v 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_84800426_8   5862 CATCATCACTGGCCAT 5877
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2785 23.54 6.99 1.17  chr2_84873928_84878937.rev     3663  4520 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84873928_8   3663 TGGAAAAACATCCCACACTTATGGGTTGGAAGAATCAATATCATTAAAAT 3712
                               i i      iii i    i        v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84873928_8   3713 GACTATGCTATCCGAAGCAATCTACAGATTTAATGCTATTCCTATCAAAT 3762
                          i v  i  vi  i  vii           i  i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84873928_8   3763 TACCAA-TGTCATTTTCCATAGAATTAGAAAAAACT-ATTCTAAAATTCA 3810
                          v   i-  i -    iiii    v v  v  i-  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_84873928_8   3811 TA-GGAAA--CAAAAAATATGCCCA-AACAGCCAAGGCAATCCTAGTAAA 3856
                           -     --   iii ----    -  i      ii     i iiv   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_84873928_8   3857 AAAGGACAAAGCCAGAGGCAC-CATGTTATTCAACATGTAAATATACTAC 3905
                         i   i      iii    -  -  iii vii   iv vv   iv      
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_84873928_8   3906 AAGACTACAGTAACCAAACCAACATGGTACTGGTACAAAAGTAGACACAT 3955
                           ii         i   iv  iii         i i  iii      i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_84873928_8   3956 --------GGAACAGAATAGAGACCCCTGAAATAAAGCCACACACCTACA 3997
                         --------    i     v    vi  v        v   i   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_84873928_8   3998 ACCAACTGATCTTTGACAAAGTGAATAAAA--AT--AATGTGGAAAGAAT 4043
                         ii   i    i  i     i vvivi  i --  --    v         
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_84873928_8   4044 ACTCTATTCAATAAATGA-GCTGGGAAAACTGGCTAACCATATGCAGAAG 4092
                          v   v     i     i-       v      v  ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_84873928_8   4093 AATGAAACTGGACCCCCTACTTCTTACCATATATAAAAATTAACTCAAGG 4142
                               ii        -   i  vi        i              ii
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_84873928_8   4143 TTGA----AGA---------AAAACCTCAAACTATGAAAATCCTAGAAGA 4179
                          v  ----   ---------  i v  v       i   v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_84873928_8   4180 AAACTTAGGAAATACTCTTCTAGACATTGGCCTAGGCAA-AGTATTTATG 4228
                             v    ?ivv v     vv   v    vi       -i  v i vv 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_84873928_8   4229 ATGAAGAGTCCAAAAGCAAATGCAACAAAATAAAAAATAGACAAATGGGA 4278
                           - v  vv         v v         v          i    v   
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_84873928_8   4279 TTT-----AAACTAAAGAGCTTCTGCATAGCAAAATAAAATATCAACTGA 4323
                         i  -----   i    i -   i  iiivv    iv v v      vvi 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_84873928_8   4324 GTGAACAGACAATGTACATAATGGGAGAATATATTTGCAAACTATGCATC 4373
                              v      ivi   v          v           ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_84873928_8   4374 TTACAAAGAACTAATATTCAGAATCTATAAAGAACTT----AAATCAATA 4419
                          v i  i i   vi   i      v           i----  v      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_84873928_8   4420 A----AATGTAAATAAGCCCATTAAAAAGTGGGCAAAGAACATGAATAGA 4465
                          ----  vii      v  v   ?    i         i iv        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_84873928_8   4466 CACTTCTCTAAAGAAGACATAC----------TAA---CATGAAAAAATG 4502
                           i     i        i    ----------   ---        i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_84873928_8   4503 CTCAACATGACTAATCAT 4520
                                 v ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (127 / 72)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.80 (70 / 25)  


2528 18.86 0.44 0.00  chr2_84891423_84895487.rev     1774  2229 (1836)    L1M4_orf2#LINE/L1        1   458 (450)  

  chr2_84891423_8   1774 TGGAAAAACACCACATGTTCATAGATCAGATGACTTAATGTTGTTAAGAG 1823
                               i i i v         i   ii  v        i         v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84891423_8   1824 GTAAATATTCCCCAAATTGATCTTCAGGTTCAATGCCATTCTTATCAAAA 1873
                          vv    i               v   i     i  v  i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84891423_8   1874 TCTTAGCTGGCTTCTTTTCAGGAACTGACAAGCTCATTGTAAAACTCATG 1923
                           ii     v   i   v   i  i         v  iv     i    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_84891423_8   1924 TGAAAGTTCAAGGGACCTGGAATAGCCAAAACGATCTTGAAAAAGGAAAA 1973
                           i  i v         ii             i            i i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_84891423_8   1974 CAAAGTTGGAGGAGTCATGCTACTGGATTGTAAAACTTACTTCAAAGCTG 2023
                                      v   ii  v ivi   vi          v       i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_84891423_8   2024 CAGTAATCAAGATGGTGTGACATTGGAATAAGGATAGACATATAGGCTAA 2073
                                     ii     ii i   v                  iii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_84891423_8   2074 TGGAATAAAATTGAAAATTCAGAAAAAAACTCTCACAATTGTAGTCAACT 2123
                                i      i i i      v    i vi   v  i i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_84891423_8   2124 GATTTTCAGCAAGGCTGCCAGAATCATTCAATGGGTAAGGAGTAGTCTTT 2173
                                ii     v     ii i           v  i  i        
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_84891423_8   2174 -CAACAAATGATGCTGTGACAACTGG-TAGCAACATGCAAAAGAATGAAG 2221
                         -         i     v         -  ? v                  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_84891423_8   2222 TTGGGGCC 2229
                             iv  
  L1M4_orf2#LINE/    451 TTGGACCC 458

Transitions / transversions = 2.27 (59 / 26)
Gap_init rate = 0.00 (2 / 458), avg. gap size = 1.00 (2 / 2)  

 251  8.33 0.00 13.33  chr2_84891423_84895487.rev     2525  2584 (1481)    L1M4_orf2#LINE/L1      439   490 (418)  

  chr2_84891423_8   2525 AAAAAAAAGAATGTTGGACTCTTACTTCACACTTGACATCATATACAAAA 2574
                             i  v   -       i i   i      -------           
  L1M4_orf2#LINE/    439 AAAAGAATGAA-GTTGGACCCCTACCTCACAC-------CATATACAAAA 480

  chr2_84891423_8   2575 ATTAACTCAA 2584
                                   
  L1M4_orf2#LINE/    481 ATTAACTCAA 490

Transitions / transversions = 4.00 (4 / 1)
Gap_init rate = 0.04 (2 / 52), avg. gap size = 4.00 (8 / 2)  

 320  9.62 0.00 0.00  chr2_84891423_84895487.rev     2874  2925 (1140)    L1M4_orf2#LINE/L1      477   528 (380)  

  chr2_84891423_8   2874 AAAAATTAACTCAAAATGTATCAAAGATCTAAATGTAAGAGCCAAAACTG 2923
                                           v    ?   i              i      i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_84891423_8   2924 TA 2925
                           
  L1M4_orf2#LINE/    527 TA 528

Transitions / transversions = 3.00 (3 / 1)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.00 (0 / 0)  

1984 12.67 4.31 1.89  chr2_84891423_84895487.rev     3203  3573 (492)    L1M4_orf2#LINE/L1      529   908 (0)  

  chr2_84891423_8   3203 AAATTCTCAGAAGAAAACATAGGTGTAAATATTTATGACCTTGGATTAGG 3252
                            i   i               ?      v  ii         i     
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_84891423_8   3253 CAATGGTTTCTTAGTTGTGACATTAAAAGCACAAGCAACAGAAGAAAAAA 3302
                                       v i     ii                i         
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_84891423_8   3303 AAATAGATAAACTGGACATCATCAAAATTAAAAGCTTTTGTGCTTCAAAA 3352
                         ---        i     v               i               -
  L1M4_orf2#LINE/    629 ---TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA- 674

  chr2_84891423_8   3353 GGACACTACCAAGAAAGCGAAAAGACAGCCCATAGGATGAGAGAACATTC 3402
                                 i        i         i    i  i   i     v  vi
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_84891423_8   3403 TTGCAAATCATATATCTGATAAGAAACTTGTAGCTAGGATAT-TAAAAAA 3451
                                                ii       v i  i    -    i  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_84891423_8   3452 AACCTTTTACAACTGCATGATAAAAAGACAAATAATCCAGTTTAAAA-TG 3500
                         ---  i        vv  i                i   i  ?    -  
  L1M4_orf2#LINE/    775 ---CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_84891423_8   3501 G-TAAAGAATCTGAATAGACAGTTC-------------CACAAATAGCCA 3536
                          -i    i  i          v   -------------i      i    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_84891423_8   3537 AAAAGCACAAGAAAAGATGCTCATTATCATTAGGGAA 3573
                          v       v             vi    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.75 (33 / 12)
Gap_init rate = 0.02 (7 / 380), avg. gap size = 3.29 (23 / 7)  


2896 24.55 1.80 5.71  chr2_84896656_84899848     1757  2701 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84896656_8   1757 TGGAAAAACATCTGATGCCCATGGATAAGAAGAATTACTATCAATAAAAT 1806
                               i i   iv   ii       vi     v   v   iiv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84896656_8   1807 GACCATACTGTCCAGAGCAATCCACAGATTCAATGTAAACCCTA-AAAAA 1855
                          i v     vi   i vii   i          i i  v     -v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84896656_8   1856 TACCAACATCACTTTTCACAGAATTAGAAAAAGCAATCCTAAAATT-ATG 1904
                          v   i vv vi    ii     v v  v  ivii           -  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_84896656_8   1905 TGGAACCAAAAAAGACCCCAAATAGCCAATGCAATCCTAAGAAAAAAGAA 1954
                              viiv  ii     vi         vi     i i i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_84896656_8   1955 AAAAGCTGGAAGCATCACATTATCTGACATCAATTATATTACAAGGCTAT 2004
                         v    i    i vv     i -  i-----     ---------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACT-TCC-----CAATT--------------- 229

  chr2_84896656_8   2005 AGTAGCCTTGTAATAAATGAAGTGCTGACATCAAATTATATTACAAGGCT 2054
                         ------------------------------     viv  i     i   
  L1M4_orf2#LINE/    230 ------------------------------TCAAAACTTACTACAAAGCT 249

  chr2_84896656_8   2055 ATAGTAATGAAAACAGCATGGCACTGTTATAAAAATAAATACATAGATCA 2104
                          i      v  i    ii   i    vi    ii   i i i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_84896656_8   2105 ATGGAACAGAATAGAAAACCCAGAAATAAAGCCACATATTTGCAGCCAAC 2154
                               i     v  i ii           v   i i    iii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_84896656_8   2155 CAGTCTTTGGCAAAGTCAACAAGAACATACAATAGGAAAAAGACACCTCT 2204
                         iii i  i i   i viiv     v   v    i  i   ii i viii 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_84896656_8   2205 TTCAGTAAATGGTGGTGGGAAAATTGGATTGCCATTTGCAGAAGAATGAA 2254
                             ii        v     v  i     v?   iv    i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_84896656_8   2255 ACTGGATCCCTATCTCTCACTATATACAAAAACCAACTAAAGATGAACTA 2304
                         ii    i     i   v   i           ii    v  i   i ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_84896656_8   2305 AAGACTTAAAAGTAAGACCTGAAACTATAAAAATACTAGAAGAAAAC-CA 2353
                         ?    i    v      v  i           v vi           -i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_84896656_8   2354 AGGGAAACTCTTCTTGACATTGGTCTAGGCAAAGAATTAATGACTAAGAC 2403
                         i ? v  v     v    v    vi       v iv  vv iiv  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_84896656_8   2404 CTCAAAAGCACAGGCAACAAAA-----AATAGGCAAATGGGACTTAATTA 2448
                         vi          i         -----     ii    v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_84896656_8   2449 T--CTAAGAAGCTTCTGCTCGGCAAAAGAAATAATCAGCAGAATAAATGA 2496
                         v--i   i  -   i  iv vv    i  v iv    iv i i i  vii
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_84896656_8   2497 ATAATCTGCAGAATGGGAGAAAATACTTGCAAACTATGCATCTGACAGGG 2546
                          i  i ii                 i       ii  ii      i i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_84896656_8   2547 GACTAATATCCACAATACACAAGGAACTCA-ACAAC--AATAACAAAGAA 2593
                             vi      v    i i  i      v-     --     i   -  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AA 797

  chr2_84896656_8   2594 AAGAGATAATCCAATTAAAAAACAGGCAAAGGGACATAAATAGACATTTT 2643
                         i v i    i      ?     ii        - iv i           i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGG-ATTTGAATAGACATTTC 846

  chr2_84896656_8   2644 TC---AAAAGACATACAAATGGCTAACAGGTATATGAAAA-ATACTCAAC 2689
                           --- i    i           i  i i i i       -  i      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_84896656_8   2690 ATCACTAATCAT 2701
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (155 / 73)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.73 (71 / 15)  


2776 26.84 4.84 0.23  chr2_84912121_84915268.rev     1789  2656 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_84912121_8   1789 TGGAAAAACATTCTATGCTAATTCACTTGAAGAATCAATACTGTTAAAAT 1838
                               i i  i i   i v  vv i v     v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_84912121_8   1839 GACCATACTTCCCAAAGCAATATACAAATTTAATGCTATTCCTATCAAAC 1888
                          i v     i      vii  v    i   i  i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_84912121_8   1889 TACCCA--TATCACT---GCAAAA---------CT-ATTCTAAAATTCAT 1923
                          -    -- ii vi ---   i  ---------  -  i           
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_84912121_8   1924 ATATAACCAAAAAAGAATCTGAATGGCCAAAGCAATCCCGTGTAAAAAGA 1973
                           iv  viiv  ii  vi v    i      i     ii viv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_84912121_8   1974 ACAAAGCTGGGGCATT-ATATTACCCAACTCCAAACTGTACTATAAGGCT 2022
                               i   i v i - i i v     i i    viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_84912121_8   2023 ACAGTAACCAAAGCAGCATGGTACTGGTACAAAAATAGACACACAGACCA 2072
                                i   ii   ii         i i  ii       i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_84912121_8   2073 ATAGAATAGAATAGAGACCCCAGAAATAAAGCTGCACACCTACAGTCATC 2122
                           i         v    vi           v iii   ii  ii    vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_84912121_8   2123 TCATCTTTGACAAAGTTGACACTAATAAACAATGGGGAAAAGATTTTCTG 2172
                          v  i  i     i v  v  vv vi vv           ii  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_84912121_8   2173 TTTAATAAATGGTGTTAGGATAGCTGACTAGCTATATGCAGAAGAATGAA 2222
                           i  i        i i   i i   iv  ? i i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_84912121_8   2223 ACTGGACTCTTATGTTTCACTATATACCAAAATTAACTCCAGATGGATTA 2272
                         ii     i i  iv iv   i      v           v i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_84912121_8   2273 AAGATTTAAATGTAAGACCTCAAACTATAAAAATCTTAGAAGATAACCTA 2322
                         ?   ii           v  v           v          v   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_84912121_8   2323 GGAA-ACACCATTTTAGACATCAGCCTTGGAAAAGAATTTATGATTAAGT 2371
                           ?i- v i v iv -   v ii vi v  v  v iv  iv iiv  v v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_84912121_8   2372 CCTCCAAAGCAATTGCAACAAAACCAAAAATTGATATATGGGACCAAATT 2421
                          vi v      vvv         vv      v    v  v    ivv  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_84912121_8   2422 AAGTGGAAGACCTTTTGTGCAGAAAAAGAAACTATCAACAGGGT--AAAC 2469
                           ivvv  i v         vvv   i  v        v ii  --   v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_84912121_8   2470 ACAACCTACAGAATGGGAGAAAATAT-----------GTATCTGA-AAAA 2507
                               i                   -----------i       -  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_84912121_8   2508 GTCTAATTTTCAGAATCTATAAGAAAGTT----AATTCAACAAGCAAAAA 2553
                          v  vi v i      v     ii  v i----  i    i  vv    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_84912121_8   2554 ACAA----CTCCATTAAAAAGTGGACAAAAGATATGAATAGACACTTCTC 2599
                             ---- i v   ?    i   i    i   v          i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_84912121_8   2600 AAAAGAAGACATACAGGCGTCCAA-AAACATATAAAAA--TTCTCAACAT 2646
                         v        i     iii v    -  i  i  i    -- v        
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_84912121_8   2647 CACTAATCAT 2656
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.93 (44 / 15)  


2899 16.14 5.82 1.16  chr2_84928340_84929925      501  1101 (485)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_84928340_8    501 AAGAATTGGCTTATAAATCAATGGAACAGAGTTGAGAATCCAAAAATGA- 549
                            i  v i v    i          i   i      i    i    i -
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_84928340_8    550 CCTTTATATTTATGACCA-CTGATTTTCAACAAAGGTGCCAAGGCAATTC 598
                           iv  i       ii  -i        i    i         i v    
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_84928340_8    599 AATGGGGGAAGGATAGTCTTTTCAACACATGATGCTGGGACAATTGGGTG 648
                                i   i               v   i           i   i i
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_84928340_8    649 TCCATATACAAAAGGATAAATTTGGACCCTTAT-----ACCATACACAAA 693
                         ?   i  i      i  i  v        i  i-----      i     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_84928340_8    694 AATTAATTCAAAATGGGTGACAGACCTACAAT-TAACAGATAAA--TGTA 740
                               i         i v ?       -   -   v  v    -- i  
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTA-AATGTAAGAGCTAAAACTATA 528

  chr2_84928340_8    741 AATCTCTTAGAAGAAAGCTTTGGAGTGAATT---GTGATTTGGGGTTAGT 787
                           v             i v v  ?  i   i---    ii v       v
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_84928340_8    788 CACTGACTTCCGAGATATGACAC-AAAA-------------AAGAAAAAA 823
                           v  ii   iv           -    -------------         
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_84928340_8    824 TA----AATTGGACTTCATCAACATCTAAAACTTTTACACTTCAACACAC 869
                           ----                v  iv         iii      viv  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_84928340_8    870 ACCATCAAGAAAGTGAAAAGGCAAGACACAGACTGAAAGAAAATATTTGC 919
                           i                 i   vv      v  ii             
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_84928340_8    920 AAATCATATATCTGATAAGGG-CTTGTATCCAAAGTATATAAAGACCTCT 968
                                              -          i i          v    
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_84928340_8    969 TACAACTCAACAATAAGAA---AAATAACTCAATATTAAAATGGTTGAAG 1015
                                   i     i  ---       i    v?v       vii   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_84928340_8   1016 ATTTTATTTGAATAGACATTTCACCAAAGAAGACATACAAATGCCCAGTA 1065
                         i----                 v          i         v   i  
  L1M4_orf2#LINE/    829 G----ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_84928340_8   1066 AACACATGTCAAGATGCTCAATTTGTCATGAGGGAA 1101
                          i      vv           i--i   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAAC--ATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (62 / 31)
Gap_init rate = 0.02 (14 / 629), avg. gap size = 3.00 (42 / 14)  


 499 31.29 8.33 8.84  chr2_85162240_85164623.rev      623  1210 (1174)    L1M4_orf2#LINE/L1       10   594 (314)  

  chr2_85162240_8    623 ATACCAACTTCATGGACTGGAAGGTTCA----TAATAAAATGTCAACA-- 666
                           v   vv        i      ii i ---- iv   i   v   i --
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_85162240_8    667 ---------GATTTGTGGATTCAATACAATTAATAACCAAAATTTAAAAA 707
                         ---------   i iii       ii    ivv  -i      iiv ivv
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAAAATCCCAGCT 108

  chr2_85162240_8    708 GAATTTTTTTGTGGGGCATGGTAAGCTGA--CTCAAATGTTGATGCAAGT 755
                          v-i       ii iivv  ii       --  v    vivv   v  i 
  L1M4_orf2#LINE/    109 GC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_85162240_8    756 TACAAAAAGGGCCAAGGAGAGTCAAGATGCTCCC----AAGAAAAATGAG 801
                         -i   i--  i  v  i v  i   i iiv  ii----     i  ii i
  L1M4_orf2#LINE/    158 -GCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_85162240_8    802 ATAGAGGGACTTGTTTTATATATCAAGAGCTAAACTAATAAATAATAAGT 851
                         i v ii     i----- i iv  ---------- i   ---------- 
  L1M4_orf2#LINE/    205 GTTGGAGGACTC-----ACACTTC----------CCAAT----------T 229

  chr2_85162240_8    852 AACACCATAACAAATAATAAACCTATAATAACTACAGTAAGATGG-AATG 900
                         ----i  v   vv iv i   v   i i   ii viii ivi   - v  
  L1M4_orf2#LINE/    230 ----TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_85162240_8    901 GCACCAGGGTAGAGACAAACTGGCCCATGGAATAGAACGGAAAGACCAGA 950
                            iv   i    v i v -- ii v           iv  i  v     
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATA--GATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_85162240_8    951 AA------CAGATGTTGA-----AATCTGTTTTACAACAGCAAGGTCACT 989
                           ------  v ii  v -----   -  v   v i   -- i   -i i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAAT-TGATTTTCGACA--AGGGT-GCC 369

  chr2_85162240_8    990 AAAGAGCACT----GAGAAAAAAAGGGAATGGACAATAAATGGTGCTGA- 1034
                           -  v  i ---- i i   i  vi vv vvv   i           i-
  L1M4_orf2#LINE/    370 AA-GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_85162240_8   1035 ACAGGTGATTATCTGCATGTGGGGAAAACAGAATTGGATCTCT-CCCCAT 1083
                            iv  iv  ? ii    iiii- i  iii i     i i  -  i  i
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAA-AGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_85162240_8   1084 ATCCTATACACACAAAAAATCAATTCCACATGGTTTAAAGAC--GGATTC 1131
                          i v      -----     i  i  v v    v i ?    --ii  vi
  L1M4_orf2#LINE/    468 ACCATATACA-----AAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_85162240_8   1132 AAAAG----AACAATGAAAAATATCTCT-AGAAGACAATATAGA---ATA 1173
                           i  ----   v  i   -----    -      v  i    i--- v 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAA-----CTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_85162240_8   1174 TTTTTATGAGTCTAAAGTAGAAAACAATTTCTTAAAT 1210
                          i  ii   vii iiiv   iv  iii       i  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

Transitions / transversions = 1.98 (121 / 61)
Gap_init rate = 0.05 (30 / 585), avg. gap size = 3.37 (101 / 30)  

 426 24.32 5.41 3.78  chr2_85162240_85164623.rev     1708  1892 (492)    L1M4_orf2#LINE/L1      721   908 (0)  

  chr2_85162240_8   1708 ATATGTACAA--CATACATGACAGACAAAAGTTTGGTATTCAGAATGCAT 1755
                             v i   --    i  -- v  i  ii vi v    i      ii  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATAT--CTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_85162240_8   1756 TATGAACTCTTACATATCAGTAAGTAAATGATGAATG-CTTAGTAGAAAA 1804
                         v v           vv   i   vv   v  ii   i- ii i v?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_85162240_8   1805 ATGGAGAAA---CCTGTCAAAGGGCACT----CAAAGAACAACAAACATA 1847
                             iv   ---ii  --  vi i  i ----       -i i v   --
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTG--AATAGACATTTCTCCAAAGAA-GATATACA-- 863

  chr2_85162240_8   1848 AATGGCCAGTAAACATATGAAAAGATGCTCAATCTCATTAGTCAT 1892
                                 i   i  i                iv   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (28 / 16)
Gap_init rate = 0.04 (8 / 188), avg. gap size = 2.12 (17 / 8)  


3214 11.21 2.09 26.11  chr2_85168381_85172376.rev     2312  3506 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_85168381_8   2312 TGGAAGCATATCCCATGTTCATGTATCAGCAGATTTAATATTATTAAGAT 2361
                              iv                v  ii v   i        i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_85168381_8   2362 GGCAATACTCTCCAAACTAATCTACCGATTCGACATAATTCCATTCAAAA 2411
                                   i     i i      v     i  ii   i  vv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_85168381_8   2412 TCCTAGTTGGCTTCTTTGCAGAAACTGACAAGCTGAATCTAAAATACA-- 2459
                            i  i  v   i          i           vi       v  --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_85168381_8   2460 --GAAATGAAACGGACACAGAATACCCAAAATAATATTGAAAAAGAA--- 2504
                         --      v  v    v       v      i   v           ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_85168381_8   2505 CAAAGTTGGAAGACTCACTCTTCTTGATTTCAAAGCTTACTATGAAGCTA 2554
                                   i       v    iii        i       ii      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_85168381_8   2555 CAGAAATCAAGACAGTGTAGTACTGGCATAAAGACAGACATGTAGGCTTG 2604
                            v              i            i  i      ---------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT--------- 291

  chr2_85168381_8   2605 GCATGGTGGCTCACGCCTGCAATCTCAGCACTTTGGGAGGCTGAGGCAGG 2654
                         --------------------------------------------------
  L1M4_orf2#LINE/    292 -------------------------------------------------- 291

  chr2_85168381_8   2655 CAGATCACTTTGAGCTCAGGAGTTTGATACCAGTTTGGGCAATGTGGAAA 2704
                         --------------------------------------------------
  L1M4_orf2#LINE/    292 -------------------------------------------------- 291

  chr2_85168381_8   2705 AACCCCATCTCCACAAAAAATTTAAAAATCAGCTAGGCGTGGTGGCTTCC 2754
                         --------------------------------------------------
  L1M4_orf2#LINE/    292 -------------------------------------------------- 291

  chr2_85168381_8   2755 ACCTGTGATCCCAATTACTTGGAAGGCTGAGGGTGGAGGATTGCTTGAGC 2804
                         --------------------------------------------------
  L1M4_orf2#LINE/    292 -------------------------------------------------- 291

  chr2_85168381_8   2805 CTGGGAAGCGGAGGCTGCAGTGAGCCAAGATCGCACCACTGCACTCCAGC 2854
                         --------------------------------------------------
  L1M4_orf2#LINE/    292 -------------------------------------------------- 291

  chr2_85168381_8   2855 CTGGGTGAAAGTGAGACTCTGTGTCAAAAAACAAACAAAAACACCAGGCA 2904
                         --------------------------------------------------
  L1M4_orf2#LINE/    292 -------------------------------------------------- 291

  chr2_85168381_8   2905 TATAGATCAATGTGAATAGA-CTGAGAGTCTAGAAATAAACCC-T-CATT 2951
                         -           -       -i        i            - -    
  L1M4_orf2#LINE/    292 -ATAGATCAATG-GAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_85168381_8   2952 TATAGTCAACCTATTTTTAACAAGAGTGCCAAGACAATGCATTGGGTAAA 3001
                            i     iiv     ii     i          v  v  v    v   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_85168381_8   3002 GAATAGTCTTTCCAACAAAAGATACTGGGACAACTGAATACTCACATGCA 3051
                                    i       v i i            i   ?i        
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_85168381_8   3052 AAAGAATAAAGTTGGCCCTTTACCTCATTCCACATATAAAAATTAATTCT 3101
                                i       v  ii       iv   i   i         i  v
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_85168381_8   3102 AAATGGGTCAAATATCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 3151
                               i   ? v i                                   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_85168381_8   3152 AGAACACACAAGTTTAAATCTTCGTGACTTTGAATTAGGCAGTGATTTTC 3201
                             v   i i ?v              i   ii       i  i   ii
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_85168381_8   3202 TAGATACAGCATCAAATGCACAA----CAAATGAAAAAATACATAAACGG 3247
                               iii  i    v      ----    v         v     iv 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_85168381_8   3248 GACATTATCAGAATTAGAAG-TTTTGTGCTTCAAAGCACACCACCAAGAA 3296
                            v i    i     i  i-               v    i i      
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_85168381_8   3297 AGTGAAAACACAACCCACAGAATGGGAGAAAATTTTTGCAAATCATCTAT 3346
                                 v                        v            v   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_85168381_8   3347 CAGATAAAAAAACTTACATA-AGGA---ATAAAAAACTATTACAATTCAA 3392
                          v     iii -   ii  v-  i ---     i    v      i    
  L1M4_orf2#LINE/    740 CTGATAAGGGA-CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_85168381_8   3393 TAACAAA--GACACATTATCCAATTAAAAAATGGGCAAAGGATC--AA-- 3436
                            i   --    v  v i      ?                 i--  --
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_85168381_8   3437 GGTATTTCTTCAAAGTAGATATACAAATGGCCCATAAGCACAAGAAAAGA 3486
                          ii      i     v                v         v       
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_85168381_8   3487 TGCTCAACATAATTTATATT 3506
                                   v ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (84 / 46)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 22.47 (337 / 15)  


 362 25.95 0.00 8.23  chr2_85256429_85265509.rev     6246  6403 (2678)    L1M4_orf2#LINE/L1        8   152 (756)  

  chr2_85256429_8   6246 ATATTCTGTTTTCATCAACTGGAATATTTAATATTATAAAAATGTTAATT 6295
                             i ii v     vi i     v i        i v  i   vi   v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_85256429_8   6296 CTATTCAAATTGATGAATAGATTCAATATAAACCCAATTAAAAAACCGTG 6345
                           vii         vv i        iii  v   v  i    vv  i--
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA-- 105

  chr2_85256429_8   6346 TGTGTGTGTGTGTGTGTTTGTGTGTATAAACTGACAAGCTGATTCTACAA 6395
                         --------- i-  iv   v -  i v   i            i   v  
  L1M4_orf2#LINE/    106 ---------GC-TGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_85256429_8   6396 TAGATATG 6403
                          vv     
  L1M4_orf2#LINE/    145 TTCATATG 152

Transitions / transversions = 1.16 (22 / 19)
Gap_init rate = 0.02 (3 / 145), avg. gap size = 4.33 (13 / 3)  

 623 31.27 13.70 0.26  chr2_85256429_85265509.rev     7372  7758 (1323)    L1M4_orf2#LINE/L1      227   665 (243)  

  chr2_85256429_8   7372 ATTTTAAGACTTGTTAGAAATGTACAGTGCCC----CTTCTTGGTGCTAG 7417
                             i  i    ii  v   vv      ivi ---- vviv    i  i 
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_85256429_8   7418 TCTA------GACAATTAGACTAACGGAA---------AAATCTTGACAC 7452
                         iv  ------    vv    ii  i    ---------i i  iv  v i
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_85256429_8   7453 AGATCCACACTTACATGAT-ACCTGATTTATGATAAAGTTGTCATG---- 7497
                          i i   i  v vi   i - vi      vi  i  i v  i  v ----
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_85256429_8   7498 -TCAGTG---AAAGAG-AG-------AAAGGATGGGATTAG--CAACC-- 7531
                         -   i  ---     i-  -------  vii    vii i --    i--
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_85256429_8   7532 --ATCCATATG-GAGGGAA-AAACCTTGATCTCTAATTCAGGGCATACAC 7577
                         -- ?   i   -i ii   -i  vi v  i i   vi   viv    i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_85256429_8   7578 AAAAATACAATTCAGA-TGGATTGTAGATCTACACTTAA-AG-TAAAACA 7624
                               -i  i   i -     ii?   i   v iv   -  -      v
  L1M4_orf2#LINE/    477 AAAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_85256429_8   7625 ACAAAGCTCCTAGGACACAATAT-GGAGAATATCTTCACAACCTTGATGT 7673
                          i   i   i   i v v  i  -  ? v v      iii      ivv 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_85256429_8   7674 GAGCAAAGATTTCTTCAATAGGAC-CCACAAGTACTAACTATAAAGGTAA 7722
                         ii    v i      vi   v   -   v   i  v i v i   i v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_85256429_8   7723 AG-T-GA-AAACTGGACTATATTAAACTTAAGA-CTTTTG 7758
                          i- -  -   i      vi  i   v    i -      
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.74 (75 / 43)
Gap_init rate = 0.05 (22 / 439), avg. gap size = 2.45 (54 / 22)  

 660 31.15 0.77 0.38  chr2_85256429_85265509.rev     8332  8591 (490)    L1M4_orf2#LINE/L1      648   908 (0)  

  chr2_85256429_8   8332 CAAAATAAAGAATTTTGATTTCTTAAATAACATCATTATTAGAGTAAAAT 8381
                               v  i  i   vi vii i   vi   ii  i vv i   i   v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_85256429_8   8382 GGCAAGCCACAGACAAGATGAAAATATTTGCTTTACACATATCTGACCAG 8431
                          i   v       vvi iv            vvvv  i        iv  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_85256429_8   8432 AGACTC--ATTCGGAATATATGAATAACTTACACAAGCCCATAAGGAAAA 8479
                         i    i--  i i        i  v    ivi    vi v    vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_85256429_8   8480 AACCAGACAACCCAAGAAGAAAATAGACAAGATACTTCACTGGATACTTC 8529
                         i  - i i       vv?i     i i   iiv i  v v i  i i   
  L1M4_orf2#LINE/    798 GAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_85256429_8   8530 ATCAAAAAGTATATCCAGATAACCAAGAAGCATATGAAAAGGTAGTCAAC 8579
                         vi    i iv    v  i  ii    v     i        i iv     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_85256429_8   8580 GTAATTAATGCC 8591
                         i v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (48 / 32)
Gap_init rate = 0.01 (2 / 261), avg. gap size = 1.50 (3 / 2)  


4361 18.50 3.29 0.23  chr2_85963715_85966392.rev     1306  2186 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_85963715_8   1306 TGGAAAGACATCCCATGTTTATAGATTGAAAAACTTAACATTATTAAGAT 1355
                                 i          i  i     i  i      i   i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_85963715_8   1356 AGCAATACTCCC-AGATT---C--CAAATTCAATGCAATCCCTATCAAAA 1399
                         i           - i   --- --  i      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_85963715_8   1400 TTTC----GACTT-----CAGCAATGGACAAGTTGCTTTTAAAATGCATA 1440
                          ii ---- v   -----   v   v      i  v ii      v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_85963715_8   1441 TGAAAATGCAAGAAAACACAAATAGCTAAAGAAATCTTGAAAAAG----- 1485
                           i         ii v vvi      i   iv             -----
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_85963715_8   1486 -----TTGGATAATTTATGCTACCCAATTTTAAAACCTGCTATAAAATGA 1530
                         -----     vi i i ii  v        i     i i   i   iiv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_85963715_8   1531 CAGTAATCAAAACAGTGTGGTATGGGCATAAGGACAGATCTATACATCAA 1580
                                   i           iv          i   iv    v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_85963715_8   1581 CAGAATGGAACTGAGAGCCCAGAAATTAACCCACATATCTATGGCCAGTT 1630
                         ii    i   i      i        v      i i  i     i  i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_85963715_8   1631 GATTTTGAGCAAGAGTGCCAACTTCTTTCAATGGAAAAAGAATAGTCCCC 1680
                               vii    i       vvi v        ii           iii
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_85963715_8   1681 TCAGCAAATGATGTGGGGACACCTGAATTTCCACATGCAAAAGAATGAAG 1730
                            i      i  iv      v   i  v?                    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_85963715_8   1731 TTGGATCCATATTTCACACTGTATAAAAAAACTAACTCAAAATGGATCAA 1780
                              i  v  ii      ii    v     i                 ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_85963715_8   1781 TGACCTATAAAGAAGAACTAAAATCATAAAAGTCACAGAAGAAAACATAG 1830
                         v      v viv    i      ii      v  vi              
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_85963715_8   1831 TGATAAATCCTTATGACCCTGGATTTGGCACTGCATTCTTAGAT-TGACA 1879
                         v?i      i ii     i   i  v    v  vv         -     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_85963715_8   1880 CCAAAAGCATGAGCAACTAAAGAAAAAAACAGATAAACCAG---CCATCA 1926
                                  ii      v          -i       iii ---i     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCA 649

  chr2_85963715_8   1927 GAATAAAAAACTTTGGGGCTTCAAAAGACACTATCAAAACAGTGAAAAGA 1976
                         i   v         v v        i           i v          
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_85963715_8   1977 CAACCCAAAGAATGGGAAAAAATTGTTTGCAAACTATAAACATAATAAGT 2026
                                v         i     -i        ii   v iv i     v
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAAT-ATTTGCAAATCATATATCTGATAAGG 748

  chr2_85963715_8   2027 TGCTTGTATCTAGAATATATAAAGAACAATTACAACTCAAGAATAAAAAG 2076
                         vi        i                vv           v         
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_85963715_8   2077 ACAAATAGCCCAATTCAAAAATAAGCAAAGGATCTGAATAGATATTTCTT 2126
                                i       ?      ii         i        i      i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_85963715_8   2127 TAAAAAAGATATACAAATGGCCAATAAGCACATAAAGAGGTCCTGAATAT 2176
                         i   i                            i  i  i v  v  i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_85963715_8   2177 TATTAGCCAT 2186
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.12 (108 / 51)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.10 (31 / 10)  


2894 22.91 5.15 1.29  chr2_85971674_85975791     2850  3626 (492)    L1M4_orf2#LINE/L1      102   908 (0)  

  chr2_85971674_8   2850 CCCGATGACATTCTTCACAGAAATAGAAAAAATAATTCCAAAATTTACAT 2899
                            iiivi v  i  ii       v  v  iv i  i i      i i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_85971674_8   2900 GGAACCACAAAAGACCCCAAATAGCCAAAGCAATCCTGAGCAAAAAGAAC 2949
                             vii   ii     vi          i     i   iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_85971674_8   2950 AAAGCTATAGGAATCACACTACCTGACTTCAAAATATACTACAAAGCTAT 2999
                             i iv    v       v  ii i       iv             i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_85971674_8   3000 AGTAACCAAAACATCATGGTACTGGCAT--GCAAAGACAT-CAGACCAAT 3046
                              i   i   vii            -- v v      -i   i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_85971674_8   3047 GGAACAGAATAGAGAACCCAGACCCAGATATAAATCCATGCGTTTATAGC 3096
                             i     v    ii     ----- -     i    i i     i i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGA-----A-ATAAACCCATACATTTATGGT 345

  chr2_85971674_8   3097 CAACTCATTTTTGACAAAGGCACCAAGAACATACAATGGGGAAAGGAGAG 3146
                            i v     i     i  ii      v   v            i v  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_85971674_8   3147 AGTCTCTTCAATAAATGATGCTGGGAAAACTGGATAGTTATATGCAAAAG 3196
                         --   i     i     i        v         ?ii i         
  L1M4_orf2#LINE/    396 --TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_85971674_8   3197 AATAAAACTGAACCTCTATCTCTCACCATATACAAAAACCAAAGCAAA-T 3245
                            i  ii  i   i   i   v               ii  vv    - 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_85971674_8   3246 GGATTAAAGATTTAAATCTAAGACCTAAAACTATGAAAC----------- 3284
                             i ?   ii     v     v          i    -----------
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_85971674_8   3285 -------------A-CTCCAGGACATTGGTCTGGGCAAAAATATTTTGTG 3320
                         ------------- -  i iv   v    vi i     vii v i  ivi
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_85971674_8   3321 TAAGAGCTCAAAAGCACAGGCAACCAAAGCAAAAACAGACAAATAGAATT 3370
                           v  vvi          i     v    v     i   i    v i i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_85971674_8   3371 ACATCAA-GCTAAAAACATTCTGTGCAGTAAAGGAAACAATCAACAA-GT 3418
                         v      -ii       -  i     vvi      v  v     v  -  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_85971674_8   3419 CAAGAGACAATCCATGGAATGGGAGAAGATACTTGTGAACTATCCATCTG 3468
                         v  i      i   ii           i   i   ii  ii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_85971674_8   3469 ACAAGGGGTTAATAACCAAAATATATAAAGAGTTCAAACAACTCAAAAGT 3518
                          i     ii vi  v   i            ii  vv         v i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_85971674_8   3519 AAAAA-ACAAA----CTGATTTTAAAATGGGCAAAAGATCTAAAGAGACA 3563
                              -     ---- ii   ?v            i   i i  v     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_85971674_8   3564 TTTCTCAAAAAAAGA----CAGAGGGCCAAGAGGTATATGAAAAAAATGC 3609
                               v   i    ----  i v      v i i i       i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chr2_85971674_8   3610 TTAATATTACTAATCAT 3626
                          i  i  i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (119 / 56)
Gap_init rate = 0.02 (15 / 807), avg. gap size = 3.33 (50 / 15)  


4151 13.85 2.88 0.55  chr2_86077673_86079393      501  1229 (492)    L1M4_orf2#LINE/L1      163   908 (0)  

  chr2_86077673_8    501 GGATCCAGTGTAGCCGAAACAATGTTGAGATAAAAGAACAAGGTTGGAGG 550
                            i    vi     i       v    i v i        i        
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_86077673_8    551 --TCACAATTCTCAATTTCAAAACTTACTAAAAAGCTACAGTAACCAAGT 598
                         --     v   i                  v             i    v
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_86077673_8    599 CAGGGTGGTACTGGCATAAGGACAGACATA--GATCAATGGAACAGAATT 646
                            v                  i       --           i      
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_86077673_8    647 GACAATCCAGAAACAAATCTTCGTATTTATAATCAATTGATTTTCAACAA 696
                           v i        i   i iviii      ii             i    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_86077673_8    697 GGGTGTCAAAACAATTCAATGAGGAAAATAATAGTATTTTCAGCAAATGG 746
                              i   i  v        i     i-      v      i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAAATGG 411

  chr2_86077673_8    747 TACTGGAACAACTGCATATCCACATGCAAGAGAATGAAGTTGGACCTCTG 796
                          i    i       v   ?          i                i  i
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_86077673_8    797 TCTTATACCATATACAAAAATTAACTCAAAATGGATCAAAAGCCTAAATG 846
                         i  i i                                ? ii        
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_86077673_8    847 TCAGAGCTAAAAAATTATAAAGCTATTAGAAGAAAACATAGGCATACATC 896
                          v          --i      i  v                 ?i  v   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAA--CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_86077673_8    897 TTCATGACCTTGGATTA-------------TA--TATGACACTAAAAACA 931
                            i         i   -------------  --        i    i  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_86077673_8    932 T--GTGACAAAAGAAAAAAAGAAACAAATTAGACTTACTCAAAATTTAAA 979
                         i-- ii             -v i i     i     vv        v   
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_86077673_8    980 CTCTTTGTACCTCAAAGAACATAATCAAGAAAGTGAAAAGACAACCCACA 1029
                         vii     i i      i   iv                           
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_86077673_8   1030 GAATGGGAGGAAATTTTCACAAATCATATGTTTGATAAAGGTCTTGTACC 1079
                                  i    v  ii          i i      i  v      i 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_86077673_8   1080 TAGACTATATAAAGAACTCCTACAACTCAATGATAAAAAGATAAATAACC 1129
                         i   v              i           i         i        
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_86077673_8   1130 TAATTTTAAAATGAACAAAGAATATTAATAGACATTTCTCCAAAGAAGAT 1179
                         i    ?v      ii     i  v v                        
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_86077673_8   1180 ATACAAATGGCCAATAAGCACATGAAAAGATACTCAACATCATTAGCCAT 1229
                                                        i          ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.59 (70 / 27)
Gap_init rate = 0.01 (8 / 746), avg. gap size = 3.12 (25 / 8)  

 763 25.08 14.33 0.98  chr2_86077673_86079393     1305  1611 (110)    L1M4_orf2#LINE/L1      383   730 (178)  

  chr2_86077673_8   1305 GGGGCAAAGATGGTCTTTTGAA------------GGGCAATTGAATAGTC 1342
                             v  ii  i       v  ------------  i   i  i   ?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_86077673_8   1343 AAATGGACAA-AATAAA-TTGTGACCCCTACTTCACATATTGTTCATAAA 1390
                          v   v v  -   i  -   -         i     ivv i v  v   
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTG-GACCCCTACCTCACACCATATACAAAAA 481

  chr2_86077673_8   1391 --AATTCCAGATGGATTGTAGGTCTAAATGTGGAAGGTTTAAAA--ATAA 1436
                         --  i  v i      ii?  ii        --   ivi     --    
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGT--AAGAGCTAAAACTATAA 529

  chr2_86077673_8   1437 ATCTTTTAGAAGAAAAC----------------------TTGGGGTAGGC 1464
                          v  i            ----------------------     v     
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_86077673_8   1465 AAATGTTTCTTACA-ACGACATAAAAATAACTTATTATAAAGGAAAAAA- 1512
                           vv        v - i    iv    vv  vviiv i   i       -
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_86077673_8   1513 AGAAAAATTGGACTACATTAAGATCAAGAACTGCTGTCCATCAAAAGACA 1562
                            v          v   i  i  i  i    vi   v v     i    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_86077673_8   1563 TCATTTAAACTG-GGAAAGATAAGC-ATAGACTGGGAGAAGGCATTTACA 1610
                         ii  iv i vv - i     i  v - i   v        iii    i  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_86077673_8   1611 A 1611
                          
  L1M4_orf2#LINE/    730 A 730

Transitions / transversions = 1.34 (43 / 32)
Gap_init rate = 0.03 (12 / 348), avg. gap size = 3.92 (47 / 12)  


3355 26.21 0.55 0.55  chr2_86102078_86108479     5003  5910 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_86102078_8   5003 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5052
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_86102078_8   5053 GGCCATACTGCCCAAGGTAATTTATAGATTCAACACCATCCCCATCAAGC 5102
                            v     v     iv i  i  i         i v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_86102078_8   5103 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5150
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_86102078_8   5151 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCTTAAGCCAAAAG 5200
                                viiv  ii  v  viv  v     iv       i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_86102078_8   5201 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5250
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_86102078_8   5251 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5300
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_86102078_8   5301 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTATAACT 5348
                                i    i--    i  --        vv  ii i  i   iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_86102078_8   5349 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5398
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_86102078_8   5399 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5448
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_86102078_8   5449 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5498
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_86102078_8   5499 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5548
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_86102078_8   5549 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCGA 5597
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_86102078_8   5598 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTC 5647
                         vi            vvi          vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_86102078_8   5648 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 5697
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_86102078_8   5698 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5747
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_86102078_8   5748 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5797
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_86102078_8   5798 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5847
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_86102078_8   5848 CTCAGAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5897
                            vi       i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_86102078_8   5898 CATCACTGGCCAT 5910
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1915 24.50 8.91 8.02  chr2_86198278_86200340      675  1572 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_86198278_8    675 GAAGGACATACTATGTTCATAATTTAGATGACTCAATAGTGTAAATACGT 724
                            i  i  v i        iiv  i  v    i    v   v  v i v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_86198278_8    725 TGATTCTCCCTAAAGTGACCTACAGAGGCAATGCAATCCCAATGAAAAAT 774
                         ii  v     i   v   i       vv   i        v  v    - 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-T 101

  chr2_86198278_8    775 TCTAGCAGGTATTTGTGTGCACAGTGTGAAAGTTTACAAGCTGACTTTAA 824
                         i i   v viv   v  ----   -----  i  v         iii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTG----CAG-----AAATTGACAAGCTGATCCTAA 142

  chr2_86198278_8    825 AATTTATATGGAAATACAAACACCCCAAAATAGTTGA--CAGTCTTTTTT 872
                             i          i   iviv    i     iii --  i    ----
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT---- 188

  chr2_86198278_8    873 TTTTAAAGGTATATTGAGATGTAATTAAAGCCTATCAAGGCAGTCTTGAA 922
                         ----i  -------------------    ------------------  
  L1M4_orf2#LINE/    189 ----GAA-------------------AAAG------------------AA 197

  chr2_86198278_8    923 GAACAAAGCTGTAG-ACTTTTACTATCAGAAGTCAAGATTTAGTATAAAC 971
                                 i  v  -   ivi   vi vi vv    i i   v  i   v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_86198278_8    972 CCACAGTAATTAAGACAGTGTGCTGTTGGTG------------------- 1002
                          i        i           v ii   ii-------------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_86198278_8   1003 CAATGGAAACAAAC--AGGGTCCAGAAACATACCCACTCATATATTACTA 1050
                                 vvi  i--  i         i v     iv   v   viii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_86198278_8   1051 CTTGGTTTGTGACACAGGAGTACTAG-------CAGTAGAGCAG---TGG 1090
                         v   i   vi    -   -  i i i-------  i i i v i--- i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACA-AGG-GTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_86198278_8   1091 ACTTTTCAACAAATGATGTTGCATTCACTGGCTAGGAAATCCATATGGGA 1140
                         v              i  i  viviv     v  ?-----   i   vi 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAK-----CCACATGCAA 440

  chr2_86198278_8   1141 AAATATGACTCTTGACCCCTACCTCACTTCATGCACATCCACAAAAATCA 1190
                           iv    vvi v              vi   ----  --        i 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCAT----AT--ACAAAAATTA 484

  chr2_86198278_8   1191 TCCCTAGGCAGATAGCAGACCCAAGTGTGAAAGGTAAAACAATATAGCTA 1240
                         v i v iiii   vi?     i  i   i i  v      v   v i  v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_86198278_8   1241 CTAGACGATAACAGAGGGGAATACCTACAAGACCTCAGGGCAGGCAA--- 1287
                         i    v  v    v   ? v v i  v iv     ii  vi      ---
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_86198278_8   1288 ------AGA----GCTCCTACAGGACTAGTCACAAAA--------AGCCA 1319
                         ------   ----i v  v v  v  v  iv      --------  vi 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_86198278_8   1320 AGATTGG-CT--AT--AAATTAGAAACTTCTGATCATTAGAAAACAGTAT 1364
                          -     -  --  --      i      i  vv v i i ii   v   
  L1M4_orf2#LINE/    635 A-ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_86198278_8   1365 TAGG----TGAAAAGGCTAGCCACCAAGT---AGAAGGTATTTGCAATGT 1407
                         i i ----       i v v    vi i ---    ii         vvi
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_86198278_8   1408 ATATATCTGCTAATGGACTTATA-CCAAATTATAGTTTAAAAACCTCTCA 1456
                                  v   v      i  -   i v    ---    i v    i 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATA---TAAAGAACTCTTA 780

  chr2_86198278_8   1457 TCTGTCAATAAGAAAATGACA------------TAGAAATAGGCAAAAGA 1494
                         ivvv       v    v    ------------? i    i      i  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_86198278_8   1495 TTTGAAAAGGCACATCACAAAAGATGATATCCAAATGGCCAATAAGCATA 1544
                               v  i  iv  v v     v     v                 i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_86198278_8   1545 TGAAGAGGTGCTCAACCTCTCTTGTCAT 1572
                             i  i        v  v????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (119 / 97)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 5.24 (152 / 29)  


2933 25.00 8.02 0.94  chr2_86233918_86236409     1153  2000 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_86233918_8   1153 TGGAAAAACATCCCATACTTATAGATCAGAATAATTAATATTGTTAAAAT 1202
                               i i       ii i  i   ii   v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_86233918_8   1203 TACTACACTACCCAAAGCAATTTACAGATTCAGTACAATCCCTATCAAAA 1252
                         vi v i   v      vii  i          iii               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_86233918_8   1253 TACCAATGACATTCTTTGCAGAAACAGAAAAAAAAAAATTGTAACATTTG 1302
                          v   iivi v  i          iv  v  ivvi -- iv   v   ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chr2_86233918_8   1303 TATAGAACCATAAAAGACCCTGAATGGCCAAAGCAATCTTGAGTAAAAAG 1352
                            i   viii  ii     v    i      i         iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_86233918_8   1353 AACAAAGCTGGAGGCATCACACTACCAGAATTCAAAATATACTACAAAGC 1402
                                i      vv       v  vi v       iv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_86233918_8   1403 TGTAGTAACCAAAACAGTAGGATACTGGCATGAAAACAGAAACAAAGGCC 1452
                          ii     i   i     iv i         i ii i   v i v  ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_86233918_8   1453 AATGAAA----ACAGGGAACCCAAAAATTAATCTGCATATCTACAGCCAA 1498
                             i  ---- iv i  ii   i    v  i iii i  i  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_86233918_8   1499 CTGATTTTTGCAAAAGGTGCCAAGAACATACACTGGGGAAAAGGACAGTG 1548
                         i       i vv  i          v   v  v        - i i   v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTC 397

  chr2_86233918_8   1549 CCTTTAATAAATGATGCTGGGAAAACTAGATATCCATATGCAGAAGAATG 1598
                         ii  i  i     i        v    i    ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_86233918_8   1599 AAACTAGATCTCCACTGCTCCCC-TCTACAAAAGTCAACTCAAAATTGAT 1647
                           ii i  i i i  iv v v  - v       i i          v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_86233918_8   1648 CAATGACCTAAATATAAGGTCTGGAA-------------------AAATA 1678
                           ?v         i    iv  ii  -------------------   i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_86233918_8   1679 T-----------TTTATGA------ATCAGAC------------------ 1693
                          -----------  ii   ------i i  i ------------------
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_86233918_8   1694 ---CTCAAAGCACAGGCAACAAAAGCCAAAATAAACAAATGAGATTTTAT 1740
                         --- iv        i          vv      i i    vi  i  i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_86233918_8   1741 CAAACT---AAGCTTCTGCACAACAAAGTAGTCAGTCAACAGAGTGAAAA 1787
                             v ---  i   i  ii vv     v vv vi    v i        
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_86233918_8   1788 GACAACCTACGGAATAGGAGAAAATATTTGCAAACTATTCATCTTAGGGA 1837
                                i  i    i                  ii  vi    ----  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT----GA 743

  chr2_86233918_8   1838 CAGAGGCTTAATATCCAGAATATGTAAGGAACTCAAACATCTCAACAGCA 1887
                         i ii  vi vi            i   i      vv   v     i ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_86233918_8   1888 AAAATCCCAAACAATTCGATTAAAAAATGGGCAAATGATCTGAACAAACA 1937
                             vv -   i  ii i   ?             v   i    i i   
  L1M4_orf2#LINE/    794 AAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_86233918_8   1938 TTTCTC---AAAACACATACAAATGGCCAACAAATATATGAAAAAATGTT 1984
                               --- i  v i              i  ii i       i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_86233918_8   1985 CAACATCACTAGTCAT 2000
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.22 (144 / 65)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 6.33 (76 / 12)  


1092 28.36 13.69 4.16  chr2_86427145_86429147.rev      694  1511 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_86427145_8    694 CCATGTTCACAAAGAGGAA-ACTTGAAACCATAAAGATGGTGATTCTTCT 742
                                  iii vv    -    i v iii v       ii  v  i i
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_86427145_8    743 AGTAAATT---TTATGAATACAGTGAAATTCCAATCAAAATCTAAATAAG 789
                         --i     ---i  iii  v  ii v   i  v         iv iiviv
  L1M4_orf2#LINE/     63 --CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr2_86427145_8    790 GTTTTATGTGGGACTTGACAAACT-ATCATGAAATTTATATAGAAAAACA 838
                         v    v  ii i v       i  -   v i     i    i    vi  
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_86427145_8    839 AAGGGTCAAGAATAGCCAAGATTCTACATTGAAATTTCTAATAAAAAAAA 888
                          i  ii v           i -- v iv      -----  v  i  v  
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAA--CAATCTTGAAA-----AAGAAGAACAA 203

  chr2_86427145_8    889 AGAATGGCCAAGAC--AATTTTAAGAATATCAGGATTCATTATAAAGTCA 936
                           v-   -- i   -- vvi  vvv   v   ii i i i  i    i--
  L1M4_orf2#LINE/    204 AGT-TGG--AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC-- 248

  chr2_86427145_8    937 TGGTTGTTAATATTATGGTTATTATAAAGACACCGTGGTATAGGTGCATG 986
                         -------------  ii  v  i ---     vi      iv  iii v 
  L1M4_orf2#LINE/    249 -------------TACAGTAATCA---AGACAGTGTGGTACTGGCATAAG 282

  chr2_86427145_8    987 GTTAGACA-GTAGATCAGTCAAATAGA---GAG---CTGAAAATAATACC 1029
                          v      -i       i vi      ---   --- iii      -   
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA-ACC 331

  chr2_86427145_8   1030 TATGCCTAT-TGGAAACTTTATGTATGAC--GGGTAGCACTGCAAATCAG 1076
                         i  i v v -   vv v  v  v vi   --    iv  vvi v v   i
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_86427145_8   1077 TGGGA----------------------------TGGGACAATTGGG-ATC 1097
                             i----------------------------        i   i- ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_86427145_8   1098 CATATAGAAAAGAATAAAATTGAATTCCTAACTCACATCATACATAAAGA 1147
                           i  iv        i  i   i ii    v      i    i i   i 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_86427145_8   1148 TCAATTCCAAATGAATGA-AAATCTAGTATTGAAAAAGC-AAAAGTTTAA 1195
                          i  i  v     i  v - i i   -- v  v  i   -    v v   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTA--AATGTAAGAGCTAAAACTATAA 529

  chr2_86427145_8   1196 AACTCTTGTAAGAAAATATA------------CGTGACC-------AGG- 1225
                                iv       i   ------------       -------   -
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_86427145_8   1226 -AT--TTTCTCA-ACAAGATAGAAAAAATCTG----------GAAAAGAC 1261
                         -  --     i - i v  i vv    iivii----------     i i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_86427145_8   1262 TGATATATTTGTCTATAT-AAAATTTAAAGCTAGAAAGCAAGAAAATGCA 1310
                         v    v   v v  vi  -      v   i  vvviv  vvv   ivi  
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_86427145_8   1311 CCACAAACCAAGTTAAGAGA--GCTTATAT--TGAGGAAAAACATTTGTA 1356
                          i iv  vv    v  i   --i ii i v--  i ii    i     i 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_86427145_8   1357 ATGCATATGTCCGAGAAAGGATTTATACCCAAAATTCACAAAGAATTCCT 1406
                          vv     i  i  v  i   i  i  i   i   vi i      i  i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_86427145_8   1407 AAAAATCACTAAGAACAAGATAAA----CTAAT--------GG---AGGG 1441
                          v  v   v   v  v    i   ---- i   --------  --- i  
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_86427145_8   1442 ATATAAACAGGGTAGTT-----AAGCAGCC---CAAATGGCCAA-AAG-G 1481
                           v i  i  i-i v  -----   v  vi---           -   -i
  L1M4_orf2#LINE/    830 ATTTGAATAGA-CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_86427145_8   1482 CATAAAAAGTTGCTTGACTTCACCTGCCAC 1511
                            i     v    ii  v   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (137 / 94)
Gap_init rate = 0.04 (39 / 896), avg. gap size = 3.74 (146 / 39)  


1470 28.20 7.29 3.44  chr2_86461602_86463684      865  1591 (492)    L1M4_orf2#LINE/L1      154   908 (0)  

  chr2_86461602_8    865 AAAGGCTGGGGACCACTGCA---CTAAGGCACTCTTTAA---GGAGAACA 908
                            v  vi      - v v --- i  ii  v    v  --- i      
  L1M4_orf2#LINE/    154 AAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_86461602_8    909 AGGT-GGGGAACTTGCCACG-CCAGACATCAAGACTTTTCATAAAGTTCT 956
                          i  -  i i   ii -  v-  vi iv    i    vii i    i vi
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_86461602_8    957 GGTACT-AACACAGCGTGGCACTGTGGCAGGCAGACGAAC-TAT---TCA 1001
                         i   v -  v    i    i    --   vivi  iii  -   ---   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTG--GCATAAGGATAGACATATAGATCA 299

  chr2_86461602_8   1002 ATGGTACAGAATGAAGGGCCCAGAAACAGGCCTGCACATT-ATAG-AAAC 1049
                             v i     vi  i i       i ii  iii     -  i -v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_86461602_8   1050 TCACTTTATGACAGGGCAGGGCACTGCAGGTC--TGAA--GAGAAAGCAT 1095
                          v i   -i    ----    ii ii-  ii -- v  -- i     v  
  L1M4_orf2#LINE/    350 TGATTTT-CGACA----AGGGTGCCA-AGACCATTCAATGGGGAAAGAAT 393

  chr2_86461602_8   1096 AAACTTTTGAATAAATAGAGCCAGGAAAACTGGCTTTTCATGTGAAGAAA 1145
                          iv     v  i    i v  ii   v      v v?i  ii  v i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_86461602_8   1146 AAAGAAAAAAAGAAAAAAAATTAGACTGCTGCTTCACATCATATATAAAA 1195
                           v   i-------------  i   iv  i i     i      i    
  L1M4_orf2#LINE/    444 AATGAAG-------------TTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_86461602_8   1196 ATCAACTCAAGGTAGAGTAAGAAATTAAATGTGAACAGA-AAAACTAGAA 1244
                           i       ii i  vi ?ii vi       -  v  v-       v  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAA 529

  chr2_86461602_8   1245 AACTGCTAGGAGCAA-TATGGAAGAATAATTTCACAATTTT--------- 1284
                             vi   i  v  -i  i i? v v vi   iii ii  ---------
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_86461602_8   1285 -AT--TTTCCTAG----GACACAAAAAGCAAAAACTATAAACGAAAAAAA 1327
                         -  --    i   ----     v       v  i v i   v       v
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_86461602_8   1328 AAATGCTGTCTATTGCATTAATATTAAGAACTTCTGATTATCAATGTAGA 1377
                          i  ivvv vv i v   i  v     i     i  vviv    v v v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_86461602_8   1378 CTAT--AAAAAATGATAAAATAAATCACAGACTGGGAGAAGACATTTGTA 1425
                             -- i   i   v  i i  vi      v        i i     i 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_86461602_8   1426 A--CACATAAATGACAGAAGTTTAGCATCCAGAAGAGTTAAAGAACTCCT 1473
                          --  i   vv   i iii vi v i        v vv          i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_86461602_8   1474 ACAAATCAATAAGATAAGGACAAG-AG--------AAAAACTGGCAA--G 1512
                             v       v v  i     i- i--------     iv     -- 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_86461602_8   1513 ACTTGAGCAGGCGCTTCACAGAAGAGAGA-ACATGAATGGCCAATAAACA 1561
                          i    ii  i ii   v vi    -   - i ii            i  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCA 878

  chr2_86461602_8   1562 TATGAAAAGATGCTCAGTCTCATGAGTGTT 1591
                         i               iiv   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (127 / 75)
Gap_init rate = 0.04 (31 / 755), avg. gap size = 2.52 (78 / 31)  

 300 32.92 3.73 3.73  chr2_86461602_86463684     1747  1907 (176)    L1M4_orf2#LINE/L1      195   355 (553)  

  chr2_86461602_8   1747 GAAGAACAAA--TGGTGGA---GCACTTGCCAAGCCGGACATCAAGAATT 1791
                                   --   v   ---i     v    vi------    i v  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATT------TCAAAACTT 238

  chr2_86461602_8   1792 TTCATCACGCCAC-GTAATTACAACAGTGTGGTGTTGGTGCAGGGTCAGT 1840
                         vii iv v  i  -     i vi          ii   iii i  vi  v
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_86461602_8   1841 CAAAGTGATCAATGACACAGGATAAAAAGCCCCAGGATAGGCCCCCTTTT 1890
                           v vv        iv i  i  vi i  i  viii   ii   viviv 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_86461602_8   1891 CTATGGAAACTTAATTT 1907
                         i     vv v  i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTT 355

Transitions / transversions = 1.41 (31 / 22)
Gap_init rate = 0.02 (4 / 161), avg. gap size = 3.00 (12 / 4)  


2762 24.48 4.56 0.78  chr2_86514791_86520398.rev     3905  4672 (936)    L1M4_orf2#LINE/L1        1   797 (111)  

  chr2_86514791_8   3905 TGGAAAGACATACTATGTTCAGAGGTTGTAAGAAATAATATTATTAAAAT 3954
                                 i  v i       vi i   v    vv       i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_86514791_8   3955 GTCCACACTACCCAAAGTGATCTACAGATTCAATGCAATTCTTATTAAAA 4004
                          v v i   v      v                i     i i   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_86514791_8   4005 TACCAGTGACATTCTTCACAGAAATAGAAAAAACAATCCAAAAATGTGTA 4054
                          v    ivi v  i  ii       v  v  ivii    v     vii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_86514791_8   4055 TGGAACCACAAGGAGCCT-GAATAGCCAAAGACA-TCATGAGCAAAAAGA 4102
                              vii     ii  i-           -   -  v   iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGA 199

  chr2_86514791_8   4103 ACAAAGCTGGAGGCATCACTCTACCTGACTTCAGAATATTCTACAAGGCT 4152
                               i      vv    v  v  ii i    i  iv v      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_86514791_8   4153 AC----------------------TAGCATAAAAACAGGCACATAGACCA 4180
                           ---------------------- i      ii i  i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_86514791_8   4181 ATGAAACAGAATAGAGAACCCAGAAATAAATTCACCGATTT---GCTACC 4227
                            i  i     v    ii           ii  ivv    --- ii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_86514791_8   4228 TGATTTTCAACAAAAGTGCCAAGAACATATATTAGGGAAAGGACAGTCTT 4277
                                 i    ii         v   vi v i       i i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_86514791_8   4278 TTCAATAAATGGTGCTGGGACAATTGAAGAAT-ACTTG--GAAGAATAAA 4324
                              i                 i  i v ?i-  v  --i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_86514791_8   4325 ACTAGACCACTATCTCTCACCATATACAAAAACCAATTCAAGATAGAGTA 4374
                         ii i    v   i   v               ii  i    i  i  vi 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_86514791_8   4375 AAGAGTTAAAT-TAAAGACGAGAAACAATGAAACTACTAGAAGAAAACA- 4422
                         ?   vi     -   iii v -    v  i     vi            -
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_86514791_8   4423 -GGAG-AAATGTGTTAGGATGTTAGTCTGGGCAAAGATTTTTATGGATAA 4470
                         -  ? -    v - iiv  iv  i vi i     v i   i - i    v
  L1M4_orf2#LINE/    549 AGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCT-TAGATAT 596

  chr2_86514791_8   4471 GACCTCGAAAGCACAGGCAACAAAAACAAAAACAGACAAATGGGATTATA 4520
                            vi i        i         iv     i   i    v   i vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_86514791_8   4521 T-AAAATTTTTAAAACTTCTGCGCAGCAAAGGAGCCAATCAACAGAGTGA 4569
                          -      v--       i  i  vv       vv v     v i     
  L1M4_orf2#LINE/    647 TCAAAATTA--AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_86514791_8   4570 AGAGACAACATACAAAGTAGGAGAAAATATTTGCAAATTATCTATCCAAC 4619
                          i       vi   i i i                   i  v    ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_86514791_8   4620 AAAGGATTAATATCCTGGATATAGAGGGAACTCAAACAACTCAACAGCAA 4669
                           i   i vi     v i     v ii      vv         i ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_86514791_8   4670 AAA 4672
                            
  L1M4_orf2#LINE/    795 AAA 797

Transitions / transversions = 1.80 (119 / 66)
Gap_init rate = 0.02 (15 / 797), avg. gap size = 2.73 (41 / 15)  

 537 19.51 0.00 0.81  chr2_86514791_86520398.rev     4994  5116 (492)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr2_86514791_8   4994 AATAATAATAATAGTAATAATTTGGTTTAAAAATGGGCAAATGATCTGAA 5043
                                 v  v vv     iiiii  ?             v   i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_86514791_8   5044 AAGACATTTCTCAAAAGAAGACATACAAATGGCTGACAGGTATGTGAAAA 5093
                         v           v        i           ii i i i ii      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_86514791_8   5094 AAATGCTCAACACCACTAATTGT 5116
                         i -         i  ????????
  L1M4_orf2#LINE/    887 GA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 1.00 (1 / 1)  


1105 27.64 0.00 0.36  chr2_86525874_86530117.rev     2211  2485 (1759)    L1M4_orf2#LINE/L1        1   274 (634)  

  chr2_86525874_8   2211 TGGAAGAGATATTTCATGTTCATGGATAGGAAGACTCAATATTTTCAAGA 2260
                              -      ii             v        i      v i    
  L1M4_orf2#LINE/      1 TGGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_86525874_8   2261 TGTCAGCTCTTTTCAATTTTACCTATGCATTCAATGCAATCCAACTCAAA 2310
                           v  iiv  iii   v  v i   iiv      i       vvv     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_86525874_8   2311 ATCTTAGTAAATTATTTTGTGGATATCTATAGACCAATTCTAAAGTTCAT 2360
                            ii  ivivi v     ii  v  iv i ii ii  i     i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_86525874_8   2361 ATGGAGAGGCAAAAGACTCAGAATAACCAACTCAATATTGAAGGAGAGGA 2410
                              i v    ii   i       i    vv    v     ii   i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_86525874_8   2411 AGAAAATCAGAAGAGTGACACTACCTGGCTTCAAAAGTTATTACAGAGCT 2460
                          v   i ii  i  v v     v  iiii       v   i    i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_86525874_8   2461 ATGGTAATAAAGACAGTGTAACACT 2485
                          ii     v          iii   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACT 274

Transitions / transversions = 2.04 (51 / 25)
Gap_init rate = 0.00 (1 / 274), avg. gap size = 1.00 (1 / 1)  

1905 26.99 3.09 0.81  chr2_86525874_86530117.rev     3138  3752 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_86525874_8   3138 AAAAAAAGACAAATTGGGCAATGGAACAGAATAGAATAGAAAGCCCAGAA 3187
                           ii v     v  v iv        -----      v  i  i      
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAA-----TAGAATTGAGAGTCCAGAA 324

  chr2_86525874_8   3188 ATAGACCCACATAAATAT----AATT-ATCTTTGGCAAAGGAGCAAGGGT 3232
                            i     i i vv   ----    -  i  i i   i  v  v i ii
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_86525874_8   3233 AATACAGTGGAACAAAGATGGTTATTTGAACAAATGATGTTGGAACAACT 3282
                         v  v  i   iiv  ii  i  iv   v        i  i   i      
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_86525874_8   3283 AGACATCCACATAAAAAAAAATTCATCTAGACACAGACCTTATGCCCTTC 3332
                         i  i ?      iv    i   vv vi i   v vv    i ii  v vi
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_86525874_8   3333 ACAGGAATGAACTAAAAATGGATTATAGATCTGAACATAATACACAAAAC 3382
                            ii   v    v         i ?   i  i  ii   v vvi     
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_86525874_8   3383 TGTAAG-CTCCTAGAAGATAACATAGGAGAAAATCTAGGTGACCTTGGCC 3431
                          i   i-   i       v        ? v      vv          vi
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_86525874_8   3432 TTGGCAATGACTTTTTCAATACAACAACAAAGACA-GATCTATGAGAGAA 3480
                          v       ii  i  vi   ii   v    ii  -i v v ii i    
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_86525874_8   3481 AGAATTGATAAGAGGGACCTCATTAAGATTAAAAAATTCTGCTCTGTGAA 3530
                          i   v     ivv    i    i  i        v  i  iv  vii  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_86525874_8   3531 AAACAATGTCAAAAGAACAAGAAGATAAGCCACAGTTTGGGAGAAAATAT 3580
                         ii   v i    i i iii i    i  v      vv             
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_86525874_8   3581 TTGCAAAAGACACATCTGATAAAAGACTATCATCCAAAATATACAAAGAA 3630
                                vv i i         ii    vvi     i      i      
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_86525874_8   3631 GTCT-------CAACAATAAGAAAATGAACAACCCAATTAAAAAATGGG- 3672
                         v   -------   i     i  i ii  i         ?         -
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_86525874_8   3673 AAAATACCTGAATAAACACCACACCAAAAAATATATACAAATAG----TA 3718
                            iv ii      i   iiv v     i  v          i ----  
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_86525874_8   3719 TGCATACAAAAAGAAGTTCAACATCATATGTCAT 3752
                         v   i ii      v i         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (103 / 59)
Gap_init rate = 0.01 (8 / 629), avg. gap size = 3.00 (24 / 8)  


1504 17.26 4.47 25.94  chr2_86640447_86642532      501  1595 (491)    L1M4_orf2#LINE/L1       49   908 (0)  

  chr2_86640447_8    501 ATGTCAGTTTTTGCCAACTTGACCTGTGGATTCAATGCAATCCCAATCAA 550
                            v  i vi iv    v    i  iii       i        v     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_86640447_8    551 AA-CCCAGCAAAGTATTTTGTGGATCCTGACAAACTGGTTCTAAAGTTTA 599
                           -      vivv v     ii  vvi      i   i i     i  i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_86640447_8    600 CATGGAAAGGCAAAAGACCCAGAATAGCTGGCACAATATTGAAAGAGAAA 649
                         i       v    ii             iiiv     v      i    i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_86640447_8    650 AA---GGTCAGAAGACTGATATTACCCAACTTTAAGACTCACTATAAAGC 696
                           ---i  ii  i    v i i v     i  i  i   i    i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_86640447_8    697 TACAGTAATTAAGATAGGGTGGTAATGGTGAAAAAATAGACATA---ATC 743
                                  i    i  v      v   iiv  ii         ---   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_86640447_8    744 ACTGGAAACAAATAGGGAGCCCAGAAATAGCCCCACACAAATATAGTCAA 793
                          v     vvi   v i   i         iv    i   vv   i     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_86640447_8    794 CTGATCTTTGACAAGGAAGCAAACGCAATACAATGGAGAAAAGACAGTCT 843
                         i    i  i       iv  v  vi v  v      i    ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_86640447_8    844 TGGCTGGGGCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAA 893
                          -------------------------------------------------
  L1M4_orf2#LINE/    399 T------------------------------------------------- 399

  chr2_86640447_8    894 AGAGGAAGGATCACTTAAGTCCAGGAGTTCGAGACCAGCCTGGGCAATAT 943
                         ---------------------------   --------------------
  L1M4_orf2#LINE/    400 ---------------------------TTC-------------------- 402

  chr2_86640447_8    944 AGTGAAACCTCATCTCTACAAAAACACCTTTAAAATTTAGCTGAGCATGA 993
                         ----------------------    ------------------------
  L1M4_orf2#LINE/    403 ----------------------AACA------------------------ 406

  chr2_86640447_8    994 TGGCATGCACCAGGGGAAGGATCACTTGAGCCCAGGAAGCAGAGGTTGCA 1043
                         --------------------------------------------------
  L1M4_orf2#LINE/    407 -------------------------------------------------- 406

  chr2_86640447_8   1044 GTAAGCCAAAATGGCATCACTCCACTCCAGCATGGGTCGACAGAGTGAGA 1093
                         ---------     -------------------------------  ---
  L1M4_orf2#LINE/    407 ---------AATGG-------------------------------TG--- 413

  chr2_86640447_8   1094 CCCTGTCTCAAAAGAAGTATTTTCAACATCAACAAATGGTGAACAACTGG 1143
                         --   ----------------------------------- i        
  L1M4_orf2#LINE/    414 --CTG-----------------------------------GGACAACTGG 426

  chr2_86640447_8   1144 ACATGCACATGCAAAAAAAAAAAAAGAAATCAATCTAGACACAGACTTTA 1193
                          i ?v           i  v-----   i ----- i   v vv  i i 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAAT-----GAAGT-----TGGACCCCTACCTCA 466

  chr2_86640447_8   1194 ACACCCT-CACAAAAATTAACTCAAAGTAGATCACAGACCTAAATGTAA- 1241
                         -    v -i                 i i     ?              -
  L1M4_orf2#LINE/    467 -CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_86640447_8   1242 ------AAC-ACAAAATTCCTGGAAGATAACA--GGAGAAAATCTAGATG 1282
                         ------   - i    i  i i     v    --  ? v      vvi  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_86640447_8   1283 GCTGTGGGTTTGGTGATGATTTTTTAAAATACAACACTAAAGGCACAATC 1332
                         i iv      v  ii   i   i   i -  ii    i   i      v 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGC 614

  chr2_86640447_8   1333 CATGAAA---AACACAGATAAGCTGGATTTCAATAAAAATAAAAACTTCT 1379
                         v ii   ---  v i      ii    i    vi    v         i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_86640447_8   1380 GCTTTGTGAAAGCCACTGTCAAGATAATGAGAAGACAAACCACAGACTGG 1429
                          ivi vii  i v    i      v i   i       v       v   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_86640447_8   1430 GATAAAATATTTGCAAAAGGCACATCTGATAAAGGACTGTTAGCCAAAAT 1479
                           v              vvii i         i     vv  v   i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_86640447_8   1480 AGACAA----CACTTAAAATTCAATAATCAGAA-----ATA-CCCAATTA 1519
                          v i  ---- v    v  i        v i  -----   -       ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_86640447_8   1520 AACAACAGGCAAAAGACCTGAAAAGACAACTTACCAA-GAAG-------- 1560
                           v  ii      i  ii    v     vi iv    -    --------
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_86640447_8   1561 --------CAAGCATATGAAAAGATGTTCAACAT-ATGTCATGA 1595
                         --------i     i           i       - ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (117 / 68)
Gap_init rate = 0.03 (24 / 860), avg. gap size = 13.88 (333 / 24)  


2517 13.70 1.93 25.63  chr2_86669204_86674253.rev     3369  4558 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_86669204_8   3369 TGGAAAGACATCACATTTTCATGTATTGGGAGATTAGATATTGTTAAGAT 3418
                                 i   v   v      v     i   i vi             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_86669204_8   3419 GTCAGTAGTACCCCAAAGCAATCTTATACATTCAAAGTGCAATCCTTATC 3468
                          v  i  v -       vii    - i v      --i       i    
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCT-ACAGATTCAA--CGCAATCCCTATC 96

  chr2_86669204_8   3469 AAAATCCCAATGACATTTTTTGTAGAAATAGAGATATCTG-TCCTAAAAT 3517
                                  iivi v       i      v  v - v   -         
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAAT 145

  chr2_86669204_8   3518 TCTTATAGAATCTTAAGAGACCCTAAATAATCAAAATAGTCTTAAAAAA- 3566
                           v   i   vivi   i     vi    ii     i i    i     -
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_86669204_8   3567 -AGAA---AGTTTAACAACTCAC--TTCCTGGTTTCAAAACTTGCCACAA 3610
                         -    ---    vi vi      --    iii           i i    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_86669204_8   3611 AGCTACAGAGATAAAATCAATGTAGTACTGACATAA----AGACATATAA 3656
                                 vi  v  iv  i   i      i     ----         i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_86669204_8   3657 ACGAATGGAATAGAAATAGGTATCCAGAAA--AACT-ATGTGTCTGTTGT 3703
                          iv            v ii vi        --   i-  iii i i v  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_86669204_8   3704 CAACTGATTTTTGACAAGGGTAGCAAGACCATTCAGTGGAGGAAAGGACA 3753
                            i       i         iv            i   -      i i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATA 394

  chr2_86669204_8   3754 GT--TTTCAGCAAATGGTGCTGGGAAAACTGGATATCCATATGCAAAAGA 3801
                           --     i               v         ?   i          
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_86669204_8   3802 ATTCAGTTGGACCTTTACCTAACAATGTATACAGAAACTAACCCCAAATG 3851
                           vv         ii     v   vii      i   i    i v     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_86669204_8   3852 GATCAAAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAAAAA 3901
                              ?                                        i   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_86669204_8   3902 ACACAG-AGTAAAACTTCACAACTTGAAGAACAAACTGCTGGGCGTGGTG 3950
                            i  -?     v    iii  i --------------    ivv  ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCT--------------TGGGTTAGGCA 580

  chr2_86669204_8   3951 ATGTGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAAGACCAG 4000
                            -  vi  ----------------------------- i  -------
  L1M4_orf2#LINE/    581 ATG-GTTTCT-----------------------------TAGA------- 593

  chr2_86669204_8   4001 TTGAGGCCAGGAGTATGAAGCTGTAATGTGCTATAATCATGCCTGTGAAT 4050
                         -------------     -------------------  --  ----  v
  L1M4_orf2#LINE/    594 -------------TATGA-------------------CA--CC----AAA 605

  chr2_86669204_8   4051 AGCCACTGCACTACACCCTGAGCAACATAGATCCATCTCCAAAAAATAAA 4100
                            ---------   -----       ----------------   v   
  L1M4_orf2#LINE/    606 AGC---------ACA-----AGCAACA----------------AAAGAAA 625

  chr2_86669204_8   4101 AAAGAGTAGACAAACTGGACTTCATGAAAATCAAAAATTTTTGTGCATCT 4150
                            ---    i   i          v     i     i        v  -
  L1M4_orf2#LINE/    626 AAA---TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC- 671

  chr2_86669204_8   4151 TAAAAAGATTACCTGGCAGGGCACAGTGGTTCACACCTGTAATTCCAGCA 4200
                         --   i  ----------------------------------------  
  L1M4_orf2#LINE/    672 --AAAGGA----------------------------------------CA 679

  chr2_86669204_8   4201 CTTTGGGAGGCTGTGGTGGGTAGATTGCTTGAGCCCAGGTGTTTGAGACC 4250
                           ------------------------------------------------
  L1M4_orf2#LINE/    680 CT------------------------------------------------ 681

  chr2_86669204_8   4251 AGCCTGGGCAACGTGGCGAAACCCCATCTCTACAAAAAAAGAAAAAGAAA 4300
                         --------------------------------------------------
  L1M4_orf2#LINE/    682 -------------------------------------------------- 681

  chr2_86669204_8   4301 AATTGTACATTAAAAAAATAAAAAGATGTTACCAACGGAGGAAAAGGCAA 4350
                         --------  i  i   i i      ---------------------   
  L1M4_orf2#LINE/    682 --------ATCAAGAAAGTGAAAAGA---------------------CAA 702

  chr2_86669204_8   4351 CTCATAGAATGGGAGAAAGCATTTGCAAATCATTTATCTGATGAGAGG-T 4399
                          i  i             ii             v        i  i i- 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_86669204_8   4400 TGTATTCAGAGTATATACAGAACACCTAAAATGCCACAACAATAAAACGA 4449
                              i    i      v     v i  v  iv v i  i  v  i  i 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_86669204_8   4450 ----CTTAATTCAAAAATGGGCAAAAGACTTCAATAGACTTTTGGAATTT 4495
                         ---- ii    ?             i  i  v       -------    
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC-------ATTT 845

  chr2_86669204_8   4496 CTCCAAATAAGCTGTACAAATTGTCAGTAAGTACATGAAAAGATGTTTAA 4545
                                v   v i       v i  i    i             i i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_86669204_8   4546 CATCACTAATTAT 4558
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (107 / 52)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 10.25 (328 / 32)  


 365 27.00 0.00 2.00  chr2_86720011_86723007      402   501 (2496)    L1M4_orf2#LINE/L1        1    98 (810)  

  chr2_86720011_8    402 TGGAGACACATACTATGTTAATAGACTGGAAAATGCAATGTAGTAAAGAT 451
                             i v i  v i     v  i  i     i ivi   i v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_86720011_8    452 GTCAATTCTCCCCACATTGGCATATATAGGTTTAACATAATTTCTACCAA 501
                          v    v       v    --  v  i  i  i   ii   ii   i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAA 98

Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.01 (1 / 98), avg. gap size = 2.00 (2 / 1)  

 716 24.49 15.91 6.06  chr2_86720011_86723007      725  1120 (1877)    L1M4_orf2#LINE/L1        1   435 (473)  

  chr2_86720011_8    725 TGGAGAAATATACCACGT------ATTGGAAGACTCAATATTGTAAAGAT 768
                             i i    v   i  ------           i        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_86720011_8    769 AACAATTCACCCCAAAAGTGATCTACAGATTTAATGCAATCCA-GTTAAA 817
                         ii    v v       -v             i  i       v-i i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_86720011_8    818 ATCACAGAAGTGCTTTTGGTAGTGAGTTTTGATAAGCTAATTCACAAATT 867
                            v   vv ivi    v i  vi ---    i     i  i -i   v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAA---TTGACAAGCTGATCC-TAAAAT 145

  chr2_86720011_8    868 TTATGTGGAAATGCAA---------AATA-----------CT-------- 889
                          i  i           ---------    -----------  --------
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_86720011_8    890 ------AAAGTCAGAAGATTCATGCTACCTGATATGAATGGTATTTTTAA 933
                         ------     ii  i  i   ii  v  ii  -----------  iv  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAAT-----------TTCAAA 234

  chr2_86720011_8    934 ATT--CTG-AAAACTAAAAT--TCAA--TAGTGTTGT---GAAATTATTA 973
                          i --  i-   i   v i --    --i     v  --- iv  v vv 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_86720011_8    974 TAGA------GAACAATGGAACAGAATAGAGAATCGAGTAGCACAAAGAT 1017
                             ------  v        i     v    i  v  ------   v v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG------AAATAA 328

  chr2_86720011_8   1018 ACATAAACACT----GTCAGTTGATTTACAACAAA--TGCTACCACAATT 1061
                           vi v   i ----    i       v i    i--   i vv  v   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_86720011_8   1062 TAGCGGAAGACGTGATATTCTTTCCATTAAGTTTTGTTAGGTCTATTTAG 1111
                         i ii  iii v -i   v     i  vi  i vv  i i  v v i -i 
  L1M4_orf2#LINE/    379 CAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACT-GG 426

  chr2_86720011_8   1112 ATATCCACA 1120
                            ?     
  L1M4_orf2#LINE/    427 ATAKCCACA 435

Transitions / transversions = 1.46 (57 / 39)
Gap_init rate = 0.05 (20 / 435), avg. gap size = 4.35 (87 / 20)  

 247 23.88 4.48 0.00  chr2_86720011_86723007     1429  1495 (1502)    L1M4_orf2#LINE/L1      426   495 (413)  

  chr2_86720011_8   1429 GATATCCACAAGAAAAAG--TGAACATAAATCTCTACCTCACACCACACA 1476
                             ?     v v     --    vv ii i i             i i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_86720011_8   1477 CAAAA-TTAATCTGAGATGG 1495
                              -    iiii i    
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGG 495

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.50 (3 / 2)  

 411 31.10 6.22 0.48  chr2_86720011_86723007     1786  1994 (1003)    L1M4_orf2#LINE/L1      477   697 (211)  

  chr2_86720011_8   1786 AAAATTTAATCTGAGATGGATTG-AAACTGAAATAAGACAGGTAAACAGA 1834
                             v    iiii i      ii- i  iv    ivi v  v    vvv 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_86720011_8   1835 CAAAGCATCC------AAAACA--GGAAAATATTTTCATAACTTTGAGGT 1876
                         i   i -  i------      --  ?iv v  i   i i  i   i v 
  L1M4_orf2#LINE/    527 TAAAAC-TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_86720011_8   1877 AGGCAAAGGTGACTTAAACAGAACAC--AAATTTTAATTAGCTA--TAAA 1922
                               v   vv    i i vi    --   vivi  vi i v --v   
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_86720011_8   1923 AAATTGCTAAATTGGATTTCTTAAACATTAAGAACTTCTGTTCATTAAAA 1972
                             v v         i   v v  v     i     i   v v i   i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_86720011_8   1973 GACGCCATTAAGAGAGTAAAAA 1994
                            i i  i    i   i    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAA 697

Transitions / transversions = 1.37 (37 / 27)
Gap_init rate = 0.03 (6 / 221), avg. gap size = 2.33 (14 / 6)  

 368 25.31 9.88 1.23  chr2_86720011_86723007     2344  2505 (492)    L1M4_orf2#LINE/L1      733   908 (0)  

  chr2_86720011_8   2344 CATATTTTCAACAGAATACTCATATCAAGAATACA----GAACTCTTGCA 2389
                              v iii i iiiv   ii    v      i ----        i  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_86720011_8   2390 AATTAATAAC-----------TCATCATAATTTTTAAATGAGCAAAGTAC 2428
                          v i     i----------- v i -i    ?vv     i      v i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACC-CAATTWAAAAATGGGCAAAGGAT 831

  chr2_86720011_8   2429 TTAAATAGGCACTTCACAAAATAAGATATTAAAAGTGCCAATAA-CAGTA 2477
                           i     i  i   v v   v       vv   vv        -  -i 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA-CA 880

  chr2_86720011_8   2478 TGAAAGGATGATTAATATCATATTCATC 2505
                              i    v i  i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (24 / 16)
Gap_init rate = 0.03 (5 / 176), avg. gap size = 3.60 (18 / 5)  


 557 23.57 0.00 2.14  chr2_86790225_86793373     1128  1267 (1882)    L1M4_orf2#LINE/L1        4   140 (768)  

  chr2_86790225_8   1128 AGAGATATACTGTGTTGATGGGTCAGAAGACTCAATATTGTTAAGATGTT 1177
                          i      v ii    v    i ii       i               vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_86790225_8   1178 ATTTCTCCTAAAATTGGTCTATAGGTTTAATGCAATCTTAATAAAAATCA 1227
                          v v    iv      i    i  i  i  i      iiv  v      v
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_86790225_8   1228 AAGCAAGTTTTTTAATGATAAAAATTGACAAGCTGATTCT 1267
                         v   vivi     --  -i i                i  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTT--TG-CAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 1.75 (21 / 12)
Gap_init rate = 0.01 (2 / 137), avg. gap size = 1.50 (3 / 2)  

2180 23.21 3.73 3.57  chr2_86790225_86793373     1556  2171 (978)    L1M4_orf2#LINE/L1      126   742 (166)  

  chr2_86790225_8   1556 TGACAAGCTGATTCTAAAATTCATATGGAAATACAAAGGATCTGAAATAG 1605
                                     i                   i   i   i iii     
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr2_86790225_8   1606 TTAAAACA--TTTGAAAAAGTAGGACAAAGTTAGAGAACTAACACTACCT 1653
                         ii      --i         v  i        i   i   v     v  i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_86790225_8   1654 GATTTCAAAAATTATTATAAAACTATAGTAATCAGGACAGTGTAGTATTG 1703
                         i         v   i  i   i   i        i        i   i  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_86790225_8   1704 GCACAAAATCTGAAAAATAGATTAGTAAAACAGAATAGAGATACTAGCAA 1753
                            i  iiviv  v v      i i ii  i     v    vv i  v  
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_86790225_8   1754 TAAACCCAGGCATATATGGACAACTGATTTTTTACAAAGGTAC--AGGCA 1801
                                 vi   v     v   i       iv    i   i --  i v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_86790225_8   1802 ATTTAGTGGAGAAAGGAAAGTCTTGTCATCGAATGGTGCTAAAACAATTG 1851
                            i i   i     i v      v   v i         iii    i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_86790225_8   1852 GAGATATTCACATGCAAAAACAAAACAAAACAAAAACCACTTCAATCCAT 1901
                           --  ?i           i--------  ii  i-----  vi i  v 
  L1M4_orf2#LINE/    426 GA--TAKCCACATGCAAAAG--------AATGAAG-----TTGGACCCCT 460

  chr2_86790225_8   1902 ACCT-GTATCATATATAAAAATTTACTCAAAAT-------AGACTTAGAT 1943
                             -ii i      i       v         -------    i  i  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_86790225_8   1944 -------CTAAAACTATAAAATTTCCAGAAAAAAACAAAGTAGATAATCT 1986
                         -------              i iii    i      v  v? vv     
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_86790225_8   1987 TTGTGATCTTGGCTTATATAAACATTTCTTAGGTATATTATCAAAAGTAG 2036
                          i    i     v   vii  vvi        i   ivi i      i v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_86790225_8   2037 AATTCATTTTTTTAAAAAACCCAAATTAATAAATTGGACTT----AAAAT 2082
                           viv i------    i vv-    vi             ----     
  L1M4_orf2#LINE/    611 AAGCAAC------AAAAGAAA-AAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_86790225_8   2083 TAAACACTTCTACTCTTTGGAAGACAATGTTGAGAGAATGAAAAGAGAAG 2132
                             v    i iiv   iii i    v i ii   i i        v  v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_86790225_8   2133 CTACAGATCGAGAGAAAATATTTTAAAATCATGTATCTG 2171
                          i     vi i            vv       i      
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

Transitions / transversions = 2.07 (95 / 46)
Gap_init rate = 0.02 (11 / 617), avg. gap size = 4.09 (45 / 11)  

 454 26.67 1.67 1.67  chr2_86790225_86793373     2478  2657 (492)    L1M4_orf2#LINE/L1      729   908 (0)  

  chr2_86790225_8   2478 AAAT-ATATGTCTGATATAAAAAGTTGTGGATCCAGAATGTATAAA-ATC 2525
                             -    i       - iii v    --         i      - v 
  L1M4_orf2#LINE/    729 AAATCATATATCTGATA-AGGGACTTGT--ATCCAGAATATATAAAGAAC 775

  chr2_86790225_8   2526 TTTCAAAACTCAGTAATAAGCAAACCAACAACCCA-TGTAAAAGTCAGAA 2574
                          i i v      i      iv i  v  i      - v?    i vi v 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_86790225_8   2575 AACTATTTTAATAGACCCTTAGTTAAAGAAGACACATGGTGGGCAAATAT 2624
                           vv    v       vi  vvii        i i iiivv   v    v
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_86790225_8   2625 ACATCTAATAAGGTTTTCAACATCATTAGCCAT 2657
                         i  iv i v   i vi         ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (26 / 21)
Gap_init rate = 0.03 (5 / 180), avg. gap size = 1.20 (6 / 5)  


3306 26.98 0.44 0.44  chr2_86794271_86800549.rev     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_86794271_8   4880 TGGAAGAACATTCCATGCTCGTGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i  i   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_86794271_8   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_86794271_8   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_86794271_8   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_86794271_8   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_86794271_8   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_86794271_8   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_86794271_8   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_86794271_8   5276 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_86794271_8   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_86794271_8   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_86794271_8   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_86794271_8   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_86794271_8   5526 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_86794271_8   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_86794271_8   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_86794271_8   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_86794271_8   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_86794271_8   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3093 27.21 1.11 0.66  chr2_86801973_86808380     5013  5916 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_86801973_8   5013 TGGAAGAACATTCCATGCTCATGGATATAAAGAATCAATATCGTGAAAAT 5062
                              ii i  i     i        vvi    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_86801973_8   5063 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5112
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_86801973_8   5113 TACCAATGACTTTCTTCACAGGA-TTGGAAAAAACT-ACTTTAAAGTTCG 5160
                          v   iivi i  i  ii   i -   -- v  i  - iii    i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_86801973_8   5161 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAG 5210
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_86801973_8   5211 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGA 5260
                                i      vv   ii  v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_86801973_8   5261 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGACC 5310
                                 i   i    ii         i iv ii i   v v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_86801973_8   5311 AATGCAACAGAACAGAG-GTCTAAGCAATAACACCACACATCTACAACCA 5359
                             v  i    iv   -   i - v     vv   i    i  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATGGTCA 347

  chr2_86801973_8   5360 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATACCC 5409
                         vi    i  i     ivv  v   i v  vvv           i   vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_86801973_8   5410 TATTTAATAAATTGTGCTGGGAAAACTGGGTAGCCATATGTAGAAAGCTG 5459
                          v  i  i    v         v      i  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_86801973_8   5460 AAACTGGATCCCTTCCTTACACATTATACAAAAATTAATTCAAGATGGAT 5509
                           ii    i    v   i    vv              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_86801973_8   5510 TGAAGACTTAAATGTTCGATCTACAACCATAAAAACCCTAGAAGAAAACC 5559
                         ii?    i       vv  v   v   i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_86801973_8   5560 TAGGCA-ATACCATTCAGGACACAGGCATGGGAAAGGACTTCATGACTAA 5608
                             ?i- v i -   iv   viv  vv i  v  v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_86801973_8   5609 AACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5658
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_86801973_8   5659 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5708
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_86801973_8   5709 AGGCAACCTACAGAATGGTAGAAAAATTTTGCAATCTACCCATCTGACAA 5758
                           i     i         v      vv       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_86801973_8   5759 AGGGCTAATATCCAGAATCTACAAAGAAGT--TAATCAAATTTACAAGAA 5806
                         i  i  vi          v  i      v --  --   v iv i  v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAA 794

  chr2_86801973_8   5807 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5852
                            i    ----   v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_86801973_8   5853 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5902
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_86801973_8   5903 TCGTCACTGGTCAT 5916
                         v i   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2673 20.93 5.14 5.39  chr2_86829370_86834057     2974  3771 (917)    L1M4_orf2#LINE/L1        1   796 (112)  

  chr2_86829370_8   2974 TGGAGAAACACACTTTGTTCATGGATTGGAAGACTCAACATT---AAGAT 3020
                             i i i iv iv                    i  i   ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_86829370_8   3021 GTCAACTGTCCCCAAATTGATTTATATATTCAATGCAATCCCAATTAAAA 3070
                          v   ivv             i  i v      i        v  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_86829370_8   3071 TCTCAATAGGCTTTTT-GTAAAAATTGACAAATTGATTATTAAATTCAAA 3119
                           i  iiv v      - i i          ii    iv v       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_86829370_8   3120 TGGAAATACAAAGTACCTAGAATAGCCAAAACAACTTTTACAAAAGAAGA 3169
                                i   i v   i                - i  iv         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGA 199

  chr2_86829370_8   3170 ACAAAATTAAAGAACTTTCATTACATGATTCCAAGGC--ACTATAAAACT 3217
                              i  ii  i   iv  i v vii   i   ii --    i   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_86829370_8   3218 ACAGTAATCGAGACAGTATGGAATTGGCATTAAGACAGACAAATAGATAA 3267
                                  i       i   v i      v i  i     v      v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_86829370_8   3268 ATGGAA-AGA--TGGTGGATCCCAGAAATAAACCCACATATATGTAAACA 3314
                               -   --  i--  vi               i i  v i iiv  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGA--GAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_86829370_8   3315 ACTGATGTTTTCATAAACTT-TAAAGGCAATTC-------------TATT 3350
                          i    -   iv i  ivv -iv   i v    -------------  v 
  L1M4_orf2#LINE/    348 ATTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_86829370_8   3351 TTTTTCAACAAATTTTACTGGAACAATTGGATAGCCATATCCCCCCCCAA 3400
                         i            vv i    i    i      ?   i  v --------
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-------- 438

  chr2_86829370_8   3401 AAAAAAAGAAAAAAAGAAAATGAACTTTGATCCATACCACACAGTACACA 3450
                         -----------       --    v  v  i  v    v    vi i i 
  L1M4_orf2#LINE/    439 -----------AAAAGAA--TGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_86829370_8   3451 AAAAAATTAATTCAAACTGGATCACAAACCTAAATGTAAAATCTAAAAGT 3500
                         v         i     v       ? i            i v      v 
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_86829370_8   3501 ATAAATGTTCTAGAAGAAAACACAGGAGAAAGTCTTTGTGACCCTGGTTT 3550
                              vv ii            i   ? v  i    i      i   v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_86829370_8   3551 GGTCAATGGTTTCTTAGAAACAATACCAAAATCACAATC--CA------- 3591
                         i v               v ii i       v     v --  -------
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_86829370_8   3592 ---TCTATAATTTTTTTTTACTTTATCCAAATGAAGAACTTCTGCTCTTT 3638
                         --- vv    v  vv----    i   v    v  i     i  iv   i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGG----ACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_86829370_8   3639 GAAAAACACTGTTAAGAGAATGAAAAGACAAGAGACA-AGTGTTGGA-AA 3686
                         i  ii     i i    i i           vvv   - i  --   -  
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG--GGAGAA 719

  chr2_86829370_8   3687 AATATTTGTAAATCACATATCTGATAAAGAACT-GTGTCCTTTAATGTGC 3735
                                 i      i           i i   -  i   ----------
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC---------- 759

  chr2_86829370_8   3736 AAAGAATATATATA---TTTTCAAAACTAACTAATAAAA 3771
                         --          v ---i i i v    v v        
  L1M4_orf2#LINE/    760 --AGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

Transitions / transversions = 1.52 (99 / 65)
Gap_init rate = 0.03 (21 / 796), avg. gap size = 4.00 (84 / 21)  

 281 17.09 7.69 3.42  chr2_86829370_86834057     4087  4203 (485)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr2_86829370_8   4087 AAGAAAAAAAAAACATTAACAACCCAACACAAAAATGGGCAAAATA---- 4132
                           v  v     i   --  i       iv?             iv ----
  L1M4_orf2#LINE/    787 AATAATAAAAAGACA--AATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_86829370_8   4133 ---AGAC--TTCATCAAAGAAGATACACAGACGGCAAATAAGAAAATGAA 4177
                         ---    --   vi           i   i i   v      v v     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_86829370_8   4178 GAGATGTTCAAAAAATCATTAGCCAT 4203
                         i     i    v --   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACA--TCAZZZZZZZZ 908

Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.03 (4 / 122), avg. gap size = 3.25 (13 / 4)  


2679 25.14 6.11 1.38  chr2_87018106_87020996     1533  2399 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_87018106_8   1533 TGGTAACACATCCCATGATCATGGATTTGAAGAATCCATATTGTGAAAAT 1582
                            v  v i        v         v     v iv       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_87018106_8   1583 GATCATCCCGCCAAAAGCAATCTATACATTTCACCATAATTCTCATCAAA 1632
                          iiv  v iv  v   vii     i v   -  v ii   i ii      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT-CAACGCAATCCCTATCAAA 99

  chr2_87018106_8   1633 ATACGATCT-TTTTTTTAATAGAGTTGGAAAAAACAATTCTAAAATTCAT 1681
                           v v v  -ii     vii   iv v  v  ivii  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_87018106_8   1682 ATGGAACCAAAAGAG-CCCAAAATAGCCAAAACAATCCTAAGCAAAAAGA 1730
                               viiv   i -    i                i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_87018106_8   1731 ACAA-GTATGTAG------------CCA---TCACA-TATACTGCAAGGC 1763
                             -  -  v  ------------   ---   v -iv    i   i  
  L1M4_orf2#LINE/    200 ACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_87018106_8   1764 TATAATTACCAAAACAGCATGGTACTGGTATAAAAGTAGGCACATAGACC 1813
                           i i v i   i    ii         i    iii   i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_87018106_8   1814 AATGGAACAGAATAGAGAAACCAGAAATAAAGCCAAATACTTGTAATCAA 1863
                                i     v    iv           v   v i i  i ii    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_87018106_8   1864 GTATTTGATCTTTGACAAACAAGCATACAAAAACATAAATTGGGGGAAGG 1913
                         ----     i  i     iviv  ---   i v   vv v     i   i
  L1M4_orf2#LINE/    349 ----TTGATTTTCGACAAGGGTGC---CAAGACCATTCAATGGGGAAAGA 391

  chr2_87018106_8   1914 ACA-TCTTATTTAGTAAATGGTGCTGGGAAAACTG-ATA-CCTTTTTTAG 1960
                          i -    -  i ii              v     -   -  viv vi i
  L1M4_orf2#LINE/    392 ATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_87018106_8   1961 AAGAATGAAATTGGATTTTTTTATCTCTCACCTTATACAAAAGTCAGTTC 2010
                                  i     iiii -- i   v    v         i i ii  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCT--ACCTCACACCATATACAAAAATTAACTC 488

  chr2_87018106_8   2011 AAGAGGGATCAAAGGCTT-----TAAGCCCTGAAACCATAAAAATTCCAG 2055
                           i v      ?  i i -----    vv  i    i      v iii  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_87018106_8   2056 AAGATAACCTTGGAAAAACTCTTCTGGACATTGGCCTAGGCGAAGAATTT 2105
                             v   v v  ?iv  v     vv   v    vi     i v iv  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_87018106_8   2106 ATGACTAAAACAACAGAAGCAAATGCAACAAAA---ACAATAAATAAATG 2152
                         v iiv  vi   v  i     v v         --- v    i      v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_87018106_8   2153 GGACCTGATTAAAATAAAAAGCTTCTGCACAGCAGAAGAAA-TGTCA-GA 2200
                             i v  i     v    i   i  ii vv  i i  v - i   -  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_87018106_8   2201 A--TAGACAGATAGTTCACACAGTGGGAGAAAATATTTGCAAACTGTGCA 2248
                          -- ii v   i iii    v i                    iii ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_87018106_8   2249 TCCAACAAAGCACTAGTATCCAGAATATATAAGGAACTC----AGATCAG 2294
                           ii i  i v   v                 i      ---- iv   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_87018106_8   2295 CAA------GACAGA-AGCTCAA----AAAGTGGGTAAAGGACATGAGTA 2333
                         i  ------    i - i i   ----   i    i      iv   i  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_87018106_8   2334 GACAGTTCTCAAAAGAAGATATACAAATGGCCAACAA--ACATGAAAC-- 2379
                             v     v                       i  --        v--
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_87018106_8   2380 TGCTCAATATCACTAATCAT 2399
                                i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (134 / 82)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.50 (65 / 26)  


 819 32.61 8.33 1.99  chr2_87455227_87457517.rev      587  1138 (1153)    L1M4_orf2#LINE/L1        1   587 (321)  

  chr2_87455227_8    587 TGGAGAGAGATATTGTGTTCATGGATTATATAATTTAATAGTGT------ 630
                             i   v  viii            iv vi i      v   ------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_87455227_8    631 ---AAT----------TTGATCTATATATTCAGTGCAATTCTTGTCAAAT 667
                         ---   ----------        i v     ii     i i i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_87455227_8    668 TCCTAA-TAATTTTTTTAAAAATAGAACCTGAAAAAATGATTCTAAACTT 716
                            i i- ivi      i----i    vi   v  iv    i     v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG----CAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_87455227_8    717 -ATGTGAAAGCATAAAAGACCAAAAATAG----GATGTTTCTGAAAAGGT 761
                         -  i  i  iiii  ii    v i     ----i iiv ii      i v
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_87455227_8    762 AG--TGA--TCAGGGGTTTC-C-CTTATTGATGTCTGGACTT-TTATGAG 804
                           --ii -- ii i  vi  - -   viii  v  vii    -i  ii i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_87455227_8    805 GCTGGAGCAATTAAAACCCTGTAGTTTTGGTGCAGAGACAGAAAAACAGA 854
                            iv  i   i  i  vv   i  vi   iii ii  i   v v i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_87455227_8    855 CCA-TGGGGTATGAAT-AAGATCCCAGAAAAAGATGGATGCAAATAAAG- 901
                         i  -   ii  -    -i   vi       v i ivv  i  vv  vi -
  L1M4_orf2#LINE/    297 TCAATGGAATA-GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_87455227_8    902 -AATGTTGGTTTATTACAGAGGATAC-AGGA--GGTCAGTGAGGAGAGGA 947
                         -   --  i   viv   -   i i - i  --iv   i  i   i  i 
  L1M4_orf2#LINE/    346 CAAT--TGATTTTCGACA-AGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_87455227_8    948 --GGCTGATAAACAAATGGAGGTGGAAAAAAGTAGTTATTCATATGGGAA 995
                         -- v  vv v         v v   i v  v- i v  ?i  i   vi  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAAC-TGGATAKCCACATGCAAA 441

  chr2_87455227_8    996 AAAATGAACTTGAATATCTCTCTCAAACTATATCCGAAAAATAACCCTAG 1045
                          i      v   i ivi  vi    v  i    v i    v    i v i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_87455227_8   1046 ATAGATTCAGGAATTAAATGTCAAAAAAGAAACTTTATAATTTATAG--T 1093
                           i   iv?i  vi       v i ivvi     v  v  i iv   --v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_87455227_8   1094 AAAATACAGG--TAACTATTTTAT-ACCTTGGAGTAGTGATATGGTTT 1138
                             i i   --   v -i  ii -       iv   vv -       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCA-ATGGTTT 587

Transitions / transversions = 1.74 (113 / 65)
Gap_init rate = 0.04 (26 / 587), avg. gap size = 2.19 (57 / 26)  

 522 25.37 4.10 2.99  chr2_87455227_87457517.rev     1528  1795 (496)    L1M4_orf2#LINE/L1      625   895 (13)  

  chr2_87455227_8   1528 AAAAT-GATAAATTTAACTATGTCAAAATAAAGAACATTTGTTCACCAAG 1576
                              -        vi   vii       v  i   v     v vi   i
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_87455227_8   1577 AGATACCTTTAA-AAAGTAAAAAGACAAAGTAAAAACTGGGACAAGATAT 1625
                         i  i  iv i  -     i         vvi v i v     v  i    
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_87455227_8   1626 TCATAATATCA---ACC--ACAAAGGTTTAGTACCAAGAATATATGTAGA 1670
                          iii  -    --- i -- i  i  vi v   i v         iv   
  L1M4_orf2#LINE/    725 TTGCAA-ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_87455227_8   1671 ACTGCTACAAATCAATTTTGTTAACAAAGCACAAATAACC-AGTATAATA 1719
                            vi     v     ---iv   -    -          - i v?  v 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAAT---AATAA-AAAG-ACAAATAACCCAATTWAAAA 818

  chr2_87455227_8   1720 ATGGGGAAAAAAAGCACCAATGG-CATTTCACAGAAGAGGAAACATATAT 1768
                              v   ii vvii--   i -      v vi    i  v i i v  
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTG--AATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_87455227_8   1769 GCCCAATAAACTTATGAAAAGAT--TCAA 1795
                          v       i vi          --    
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.23 (37 / 30)
Gap_init rate = 0.04 (12 / 271), avg. gap size = 1.58 (19 / 12)  


1832 23.91 5.10 6.71  chr2_87831647_87833321      499  1184 (491)    L1M4_orf2#LINE/L1      234   908 (0)  

  chr2_87831647_8    499 AGCTTATCGTAAAGCAACTGTAATCA-------GTAGGATTGGTGTCAAG 541
                          i    iiii     v  v       -------  i v i   ii v i 
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_87831647_8    542 ATGGGTACACAGATGGGTAGAAAAGAATTGAGAATCCAGAAATAGACTCA 591
                           i ii i i    vii i   v          i          i  i  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_87831647_8    592 TATTTACATGGTCAATTTATTTTTGACAAAGGCACCAAAGAAATTTAGCA 641
                           iv vi          v     i     i  ii    iivv   i iii
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_87831647_8    642 TAGAAAGTATAATCTT--CATCAAATGATGCTGGAAAAATTGAGTAACTA 689
                         vi     v   i    --  v      i      i v  i  ii  ? i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_87831647_8    690 TATGCAAAAAAGAAAGAAAAGAAAGAAAAAAGTGAAAACCTCCACCTCCG 739
                         i        ---------------   vi    vii -------- i  -
  L1M4_orf2#LINE/    434 CATGCAAAA---------------GAATGAAGTTGGA--------CCCC- 459

  chr2_87831647_8    740 TCATTACTTCATACCATATA-AAAAATTAACTCAGAATAGATCATAGACA 788
                         ----   i   i        -             i   i     ?    v
  L1M4_orf2#LINE/    460 ----TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_87831647_8    789 TAAATGTAATAGCTAAAACTATAAAACTCCTAAAAGAAAACAGGAGAAAA 838
                                  v                   i  i         --------
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-------- 547

  chr2_87831647_8    839 TAGAGA-AAACCTTGGTGATCTTGGTTTTGGCAGTGATCTGTTAAAT--- 884
                            i?i-   i   v    i     v  v    i  i i v   i  ---
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_87831647_8    885 ---TCAATAG-ATAAAACACAAATTAGAAATAAGGTATTGACTGAACCTC 930
                         ---i   v  - i  ivv     --     v  viv  vi i  i  i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAA--AGAAAAAATAGATAAATTGGACTTC 645

  chr2_87831647_8    931 ATAAAAATAAAACATAAACTTTTGTTCTTCAAAAGACATT--TAGGAAAA 978
                           v     v   ----         v       i    i --i i    i
  L1M4_orf2#LINE/    646 ATCAAAATTAAA----AACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_87831647_8    979 TGAAAAGGAAAGCCCCAGACTGAGGTAAAATATTTGCAAAACATATATAT 1028
                                iv  v  v    v  i iv              v       v 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_87831647_8   1029 AATAAAGGTTTTGTATCCAGAATGTATAAAGAAGT--------------- 1063
                         i    i  vi             i         v ---------------
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_87831647_8   1064 TAAGAAGAAAAGCAACATACTTTTTTTTTAGTTGACAAAAGATCTGAAAA 1113
                            i    v  ii   vi v  ?vvv--- i v i    i   i    v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAA---AATGGGCAAAGGATTTGAATA 838

  chr2_87831647_8   1114 AGACATCTCACCAAGTCGTTTGTAGGACTGGCAAATAAGTAAACAAGAAG 1163
                         -     i  v    ivvivv i  vi v    v      i v ii i   
  L1M4_orf2#LINE/    839 -GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_87831647_8   1164 AGGCCCAACACCTTTAGTCAT 1184
                          v  i     i v????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (99 / 61)
Gap_init rate = 0.02 (16 / 675), avg. gap size = 5.06 (81 / 16)  


2832 26.08 2.55 1.78  chr2_88012264_88017744.rev     4089  4989 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_88012264_8   4089 TGGAAAAATATTTCATGCCCATAGATAGAAATAATCAATATCGTAAAAAT 4138
                               i    ii    ii   i   v i  v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_88012264_8   4139 GGCCATACTGCCTTAAGTAATTTATAGAGTCAATGCTATTCCCATTAAAC 4188
                            v     v  iv  v i  i  i   v    i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_88012264_8   4189 TACCA-CTGACATTCTTCACAGAACTAGAAAAAACT-ATTTCAAAATGCC 4236
                          v   -   v -  i  ii     v v  v  i-  -  iii     v v
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_88012264_8   4237 TATGGAACCAAAAAAGACCCTGAATAACCATGACAATCCTAAGAAAAACA 4286
                                viiv  ii     v     i   vi      i i i   i vi
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_88012264_8   4287 AACAAAGCTGGAGGCATCATATTACCTGACTTCAAATTACACTACACTTC 4336
                                i      vv   i i v  ii i      vivi      ----
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA---- 244

  chr2_88012264_8   4337 AAATTAAACTGCAGTAAACCAAACAGCATGGTACTGGTACAAGAACAGAC 4386
                         -----  i  i      v v i    ii         i i   i i    
  L1M4_orf2#LINE/    245 -----AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_88012264_8   4387 ACATAGACCAGTGGAACAGAATAGAAAACTAAGAAATAAGACCACACACC 4436
                          i     i  i     i     v  i iiiv        iv   i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_88012264_8   4437 TACGGCCAAGTGATCTTCAACAAATCTGACAAAAACAAACAATGGGGAAA 4486
                           i  i   v    i   i    ivv  v   i v  vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_88012264_8   4487 GGATTTCCTATTTAATAAATGGTGCTGGGAGAACTGGCAAACCATATGCA 4536
                          i  vvi  v  i  i              v      vv ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_88012264_8   4537 GAAAATTGAAATTGGACCCCTTCCTTACACTATATACAAAAATTAACTCA 4586
                         i  i v    i          v   i    i                   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_88012264_8   4587 ACATGGATTAAAGGCTTAAATGTAAAACCCAAAACTATAAAAACCCTAGA 4636
                          v      i ?  i i         i v i            vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_88012264_8   4637 AGAAAATCTAGGCA-ATACCATTTAGGACATAGGCATGGGCAAAGACTTC 4685
                               iv    ?i- v i -  iiv   v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_88012264_8   4686 AT---CATGAAAATGCCAAAAGCAATTGGAACAAAAGCAAAAATTAACAA 4732
                         v ---i    v ---         vvv v        v      vi i  
  L1M4_orf2#LINE/    589 TTAGATATGACA---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_88012264_8   4733 GTGGTATCTAATTAAA-TTAAAGAGCTTCTGCACAGGAAAATAAACTATT 4781
                         i v v ii v  i   -     i -   i  ii vvv   iv v     i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chr2_88012264_8   4782 ATCAGAGTGAACAGACAACCTAGAGAATGGGGGAAATTTTTTGCAAGGTA 4831
                          vv i      v        i v        i    v v       ivi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_88012264_8   4832 TCCATCTAACAAAGGTCTAGTATCCAGGGTCTAGGGGAAACTTAAATAAA 4881
                          vi    i i  i  v  v        ii v  viiii    ivv i  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_88012264_8   4882 TTTACAAGAAAAA---AAA-AACC----------ATAGGCAAAGGACATG 4917
                          iv i  v     ---   -    ----------  i         iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_88012264_8   4918 AACAGACACTTCTCAAAAGAAGACATTCATATGGCCAACAA--ACATGAA 4965
                           i     i     v        i  v  v        i  --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_88012264_8   4966 AAAAAGCTCAACATCATTGATCAT 4989
                           i v           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (135 / 97)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.60 (39 / 15)  


2428 25.87 4.33 6.06  chr2_88067081_88072613.rev     4118  5041 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_88067081_8   4118 TGGAAAAATATTCCATGCTCATAGATAGGAGGAATCAATATCATTAAAAT 4167
                               i    i     i    i   v   i  v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_88067081_8   4168 GACCATACCATCCAAAGCAATTTATAGATTTAATGACATTCTTGTTAAAC 4217
                          i v    ivi     vii  i  i     i  i vv  i i i i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_88067081_8   4218 AGCCATTCATATTCTTCACAGAACTGGAGAAAACT-ATTTTAAATTTCAT 4266
                         vv   viiiiv  i  ii     v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_88067081_8   4267 ATGGAACTGAAAAGGAGCCTGAATAGCCAAAGAAGTCCTAAGCAAAACAC 4316
                               v  v  i   v  v           iv i  i i --    ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAA--- 194

  chr2_88067081_8   4317 ACACACACACACACACACACACACACACATACACACACACAAAAAAAACA 4366
                         ------------------------------------------i  i    
  L1M4_orf2#LINE/    195 ------------------------------------------GAAGAACA 202

  chr2_88067081_8   4367 AAGCTGGAGGCATCACACTACCCAACTTCAAACAAC--ACTACAGAGCTA 4414
                            i      vv       v     i      --  --      i     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAGCTA 250

  chr2_88067081_8   4415 CAGTAACCAAAACAGCACAATACTTGTACAAAAACAGGCAAATAGATCAA 4464
                               i   i    iiiii    v i i  ii i  i  v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_88067081_8   4465 AGGAACAGAATAGAGAACCCAGAAATAAGACCACACACCCACAGCTATCT 4514
                         v    i     v    ii          iv   i   iii ii ii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_88067081_8   4515 GATCTTTGACAAACTTGACAAAAACAAGCAATGGGGAAAGGATTGT---- 4560
                            i  i     ivv  v   i v  vv            i  v  ----
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_88067081_8   4561 ----------GTGT--------------------ATGCAGAAGACTAAAA 4580
                         ----------   i--------------------     i    v i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_88067081_8   4581 CTGGACCCCTTTCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 4630
                         i         vi  i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_88067081_8   4631 AGACTGAAATGTAAAACCCAAAACTATAAAAAAAACCCTGGAAGACAACT 4680
                             iv        i v i            v---i i i     v   v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAAC---TCTTAGAAGAAAACA 547

  chr2_88067081_8   4681 TAGGCA-ATATCATTCAGGATATAGGCATGGGCAAAGATTTCATGAGGAA 4729
                             ?i- v   -   iv  iv v  vv i     v i    v iiiv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_88067081_8   4730 GATGCCAAAACCTATTGCAACAAAAGCAAAAATTGACAAATGGAATCTAA 4779
                           ii      v vvvv          v      v  i    v i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_88067081_8   4780 TTAAAATTAAGAGCTTCTCCACAGCCAAGGATACTGTCAATAGAGTAACC 4829
                          i        i i   i vii vv v     i   i    v i   i vv
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_88067081_8   4830 CGACAACCTACAGAATGGGAGAAAATATCTGCAAACTATTCGTCTAGCAA 4879
                         v       i                   i      ii  vii   iii  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_88067081_8   4880 AGGTCTAATATCCTGAATCTATAAGAAAGT-TAATAAATTTACAAGAAAA 4928
                         i  v  vi     v    v     ii  v - v i  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_88067081_8   4929 AAA-AACCCACCTCATTAAAAAGTGGGTGATGGACATGAACAGACACTTC 4977
                          i -  viv   iv   ?    i    ii v   iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_88067081_8   4978 TCAAAAGAAGACATACATGTGACCCACACAATCCTATGAAAAGAAGTTCA 5027
                           v        i     vi  i  - - i  v vi         v i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCC-A-ATAAGCACATGAAAAGATGCTCA 894

  chr2_88067081_8   5028 ACATCACTGATCAT 5041
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 6.40 (96 / 15)  


1624 25.66 5.46 7.08  chr2_88081635_88083304.rev      501  1178 (492)    L1M4_orf2#LINE/L1      242   908 (0)  

  chr2_88081635_8    501 ACAAAGCTATAGTAGACAAAACACCATGAAATTCGTATTGAAACAGAAAA 550
                                  i    iv   i   vii  iv i v i  viii i   v -
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA- 290

  chr2_88081635_8    551 CATAGACCAATTGAATAAAACAGAGAACCCAGAAATAAATCCATGTATTT 600
                         i     i    v     i  iv    ii           i    ii    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_88081635_8    601 GAAGCCAACTAACTTTTGG--AGGAGGCTTCAAGATTATATATTAGAAAA 648
                         ivi i   i i i   i i--   iv  --     ii  vi v i ii  
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGC--CAAGACCATTCAATGGGGAA 388

  chr2_88081635_8    649 AGAACAACTTACTCAACCAACGATGATGGGAAAACTGGATACTCATATGC 698
                             i iii vi     v  i i  v     v         ?i  i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_88081635_8    699 AGAAGAATGAA---------------CACA-----------AATCAACTC 722
                          i         ---------------    -----------   i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_88081635_8    723 AAAATACATAAAATACTTTAATGTAAGACCTGAAACTGTAAAACTACTAG 772
                              iv  v ? v  i v         v  i     i       vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_88081635_8    773 AAGAAAACATAGAGGGAAAGCTCCACGACATTATTGTAGGCAAAGATGCT 822
                                     i? v   v  i ii   v  ivvv       v i vii
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_88081635_8    823 ATAGGAAAGACTTCAAAAGCTTGGGCAACACAAACAAAAATAGACAAATG 872
                         v   iv v   vi       viii      v  iv         i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_88081635_8    873 AGGCTACATTAAGCTAAAAAGCTTCTGCACAGCAAAAGAAACAATCAACA 922
                         i i  v   i  iv v    i   i  ii vv    i  v  v     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_88081635_8    923 GAGTAAAGAGACAATCTGAAGAATGAGGGACTATATTTACAAACTATATA 972
                         i   i  i      i iiv      i i  vv      i    ii     
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_88081635_8    973 TCCAGCAAGGAACTGATATCCAGAGTATACAAGGAACTC----AACTCAA 1018
                           iiii    i   vi        i    i  i      ----       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_88081635_8   1019 AAGCAAAACAAACAAACAAACAAAAAACAAAACACAACATTATGGAACAA 1068
                         v ii    --------- i     v   ----------------------
  L1M4_orf2#LINE/    789 TAATAAAA---------AGACAAATAAC---------------------- 807

  chr2_88081635_8   1069 AATAAAACAAAATTCTCATTACAAAATAGGCAAAGAGTCTGAATAGATAT 1118
                         -------------- iv   ?v     i       ii i        i  
  L1M4_orf2#LINE/    808 --------------CCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_88081635_8   1119 TTTTC-AAAAAA---ATACAAGTGGCCAA-AGGTATATGAAAAAATGTAC 1163
                           i  -   i  ---      i       - i i i       i   iv 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_88081635_8   1164 AGCAGCACTAATCAT 1178
                          i  v  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (114 / 56)
Gap_init rate = 0.02 (11 / 667), avg. gap size = 7.73 (85 / 11)  


4215 14.98 6.62 0.62  chr2_88305338_88307101.rev      471  1271 (492)    L1M4_orf2#LINE/L1       60   908 (0)  

  chr2_88305338_8    471 CCCCAAATTG----------TCAAGCAAAACCTGACTGGCATAATTCCAA 510
                                   ----------    - iv  i i--  iv  v   i   i
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAA-CGCAATCC--CTATCAAAATCCCAG 106

  chr2_88305338_8    511 CTGCCTTCTTTGCAGAAAT---------GATCCTAAAATTCATTTAGAGG 551
                                i           ---------               v i  ii
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_88305338_8    552 TGCAAGGAACCCAGAGTAGCCAATATAATCT------------------- 582
                                i       i       v i     -------------------
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_88305338_8    583 -GGAGGACTTACACTTCCTAATTTTAAATCCTAGTACAAATCTAT-GTAA 630
                         -        i        i     i   v i  v      v   i-    
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_88305338_8    631 ATCAAGATGGCCTGGTACTGGCATAGGGATAGAAAAACAGATCAATGGGA 680
                         -      ii iv             i       v v i          i 
  L1M4_orf2#LINE/    257 -TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_88305338_8    681 TAGAATTAAGAATCTAGAAATAAATCCATACCCATACGATCAATTGATTT 730
                                i   i  i         i      viv  i i           
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_88305338_8    731 TTGACAAGGATGTCAAGACTATTCAATGGGGAACGAATAATCTT--AAAT 778
                          i       i  i      i             v     i    --v  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_88305338_8    779 AAATTATAACTGG-ACAACTGGACATCCATACACAAATAAGTGAGTTTGG 827
                             vi i-    -         i ?   i ii    vi i   iv    
  L1M4_orf2#LINE/    406 AAATGGTG-CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_88305338_8    828 ACCCCTACCTCACACCATATGCAGAAATTAGCTCAAAATGGATCAAAGAC 877
                                             i  i      i              ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_88305338_8    878 CTAAGTATAAGAACTAAAACTATAAACCTCTTAGAATTAAACATAGGTTT 927
                             i i     i             v         vv         ?v 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_88305338_8    928 AAATCATCGTGACCTTGGGTGAGGCAACAGTTTCCTAAATATGACACCAA 977
                              v              v      ii     i  i            
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_88305338_8    978 AAGCACATGCAACAAAAGAGAAAACAGATAAATTGAACTTCATCGATATT 1027
                                v           i    i          i        i v   
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_88305338_8   1028 AAAA-CTTTTGTGCATCAAAGGAC--TATTAAGAAAGTGAAAAGACAACC 1074
                             -         v         --   i                    
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_88305338_8   1075 TACAAAGTGGGAGAAAATAGTTGCAAATCATATACCTGATAAGAATCTAG 1124
                         i   i i            v              i        iiv  v 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_88305338_8   1125 TATCCAGAATATATAGAAAGCTCTTACAACTCAATAATAAAAATATC--T 1172
                                        i i i                       v iv-- 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_88305338_8   1173 AAGTC--TT---AAATGGGCAAAGAACATAAATGGACATTTCTCTGAAGA 1217
                           vi --  ---            i iv i   i          ii    
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_88305338_8   1218 AGATAGACAAATGGCCAATAGGCACATCAAAAGATGTTTAACATCATTCA 1267
                              v              i      v        i i       ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_88305338_8   1268 TCAT 1271
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.25 (81 / 36)
Gap_init rate = 0.02 (15 / 849), avg. gap size = 3.87 (58 / 15)  


1248 27.01 8.29 1.90  chr2_88540450_88543271      862  1283 (1539)    L1M4_orf2#LINE/L1        6   454 (454)  

  chr2_88540450_8    862 AGATATACCATGTTCATTAGTTTGAAGACTAACCATA-----AAAGTGTC 906
                               v          vii  v       v --   -----  ii  v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTA--ATATTGTTAAGATGGC 53

  chr2_88540450_8    907 AATTATGTCCAAACTAATCTA--------------------TCAAAGCCT 936
                            vv vi     i i     --------------------     ii i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_88540450_8    937 CAACAGGATTCTTTGTAGATACAAACAAGCTGA--CTGAAATTTATACAG 984
                           i v vv  i    i   v ivi         --  i     i   ii 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_88540450_8    985 GGAAGCAAAGGAACTAGAATAGCTAAAACAATTTTGAAAAAGAA---TAA 1031
                         ii v    i   v i        i        i           ---i  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_88540450_8   1032 AATGGGAGGAATCAAATTACCTGATTTTAAGACTTACTTATTATATGGTA 1081
                          i v      v   v i v  ii    i  i       ---- i vi iv
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT----ACAAAGCT 249

  chr2_88540450_8   1082 ACAGAAATTAAGACAGTGTGGTGTTGGCAGAGGAACAGACACTTGTGATC 1131
                             v   i             ii     v i i i     iv i-    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA-GATC 298

  chr2_88540450_8   1132 ACTGGAACAGAGC--AGAGTACAAAAATTGGCCAATATATTCAC---CAA 1176
                          v     i   ii--     v  i    vii  v   i   i i---   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_88540450_8   1177 CAGATTTTTGACAAAGGTGCAAAAGTGATTCAATGGAGGAAGGATAACCT 1226
                         iv      i     i     v  iiiv         i i   i   ii  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_88540450_8   1227 TTATAATAAATAGTCTTGAAACAATTGGATATTTATAGATTAAAAAAAGA 1276
                           vi  i    i  vi  ii    i      ?ii i viiv   i  v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_88540450_8   1277 ACATTGG 1283
                          -i    
  L1M4_orf2#LINE/    449 A-GTTGG 454

Transitions / transversions = 2.14 (77 / 36)
Gap_init rate = 0.02 (10 / 449), avg. gap size = 4.30 (43 / 10)  

1212 25.30 6.62 0.95  chr2_88540450_88543271     1908  2330 (492)    L1M4_orf2#LINE/L1      462   908 (0)  

  chr2_88540450_8   1908 CCTCACACTTCGTGCAAAAATTATCTCAAAATGGATCATATTCCCAAATG 1957
                                 ivii i         v              ? vv  i     
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_88540450_8   1958 CCAAACAAAAAACCATAGAGCTCTTAGAA-------TA-----AAATCTT 1995
                         iv i vvv     i   i i         -------  -----       
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_88540450_8   1996 CATAGCCTAGGATTAGGTGAAGAGTTCTCAGACATGATAACAAAGACATG 2045
                          i ii   v  i     ii v iv    i   i    i v    ii  ii
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_88540450_8   2046 ATTTACAAGACAAAAAAAAATCAATAAATTGCTCTTCATCAAAATTAAAA 2095
                          ---i   v v  i       vi        vv                 
  L1M4_orf2#LINE/    612 A---GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_88540450_8   2096 ACTTT-GCTCTGTGAAAGATTCTGTTAAGAGAATAAAAAGACAAACAACA 2144
                              - iv  vii  i  iv  i i    i i i         v v   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_88540450_8   2145 GACTGTAATAAAAGGTCTGCAAATCACACATCCAACAAAGAACTTGTATG 2194
                           v  vi v    vi i         i i   ii i  i i        v
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_88540450_8   2195 CAGAATGTATAAAGAACTCTCTA-AATTCAACAG--AAAAGAAAAATC-T 2240
                               i             -  -  i    i i--      v    v-i
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCT-TACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_88540450_8   2241 CCAATCAGAAAACAG--AAAAAA-------AAACACTTTACCAAGGAGTA 2281
                              i?i    ii --   ii ------- i   i  iv    i  iv 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_88540450_8   2282 TATATGTATGGCAAACATGCAGATAAAAAAA-ATTCA-CATCATTAGTCA 2329
                             iiv     v  i v   v  i    i -ii   -     ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_88540450_8   2330 T 2330
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.00 (70 / 35)
Gap_init rate = 0.03 (12 / 447), avg. gap size = 2.67 (32 / 12)  


3295 26.98 0.44 0.44  chr2_88867993_88871269     1878  2785 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_88867993_8   1878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_88867993_8   1928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_88867993_8   1978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2025
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_88867993_8   2026 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 2075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_88867993_8   2076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2125
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_88867993_8   2126 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2175
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_88867993_8   2176 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 2223
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_88867993_8   2224 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2273
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_88867993_8   2274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_88867993_8   2324 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 2373
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_88867993_8   2374 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 2423
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_88867993_8   2424 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 2473
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_88867993_8   2474 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 2523
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_88867993_8   2524 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2573
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_88867993_8   2574 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 2623
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_88867993_8   2624 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2673
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_88867993_8   2674 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 2723
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_88867993_8   2724 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 2773
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_88867993_8   2774 ATCACTGGCCAT 2785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2971 25.08 2.60 0.79  chr2_88880093_88884592.rev     3124  4008 (492)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_88880093_8   3124 ACATCCCATGCTCATGGATGGGTAGAATCAGTATTGTGAAAATGACCATA 3173
                          i        i        v  v   v i i      v  i   i v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_88880093_8   3174 TACTGCCAAACGCATTCTACAAATGCAATGCCATTCCCATCGAAATACC- 3222
                         iv i-     ivv  -     i  v   i  v  i  i   i    v  -
  L1M4_orf2#LINE/     58 CTCC-CCAAATTGAT-CTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_88880093_8   3223 GCCATCATTCTTCACAGAACTAGAAAAAA-AATCCTAAAATTCATATGGA 3271
                           iii -  i  ii     v v  v  iv-i                   
  L1M4_orf2#LINE/    106 GCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_88880093_8   3272 AAAGCAAAGAGCCCACA-TAGCCAAAGCAAGACTAAGCAAAAAGAACAAA 3320
                           v    i ii    v -        i   vvi i iv  i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_88880093_8   3321 TCTGGCAGCAGT-ACATTACCTGACTTCAAACTACACTATAAGGTCATGG 3369
                         vi   -  v v -   i v  ii i      vivi    i  i ii ii 
  L1M4_orf2#LINE/    205 GTTGG-AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_88880093_8   3370 TCACCAA-ACAGCATGGTACTGGTATAAAAACAGGCATATAGACCAATGG 3418
                          v i   -    ii         i    ii i  i        i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_88880093_8   3419 AATAGAATAGAGAAGCCAGAAATAAAGCCAAATACTTACAGCCAACTGAT 3468
                                 v    iv           v   v i i   ii i   i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_88880093_8   3469 CTTCAACAAAGCAAACAAAAATAT-CAAGGGGGAAAGGACACCCTATTCA 3517
                         i   i    i vviv   i vi  -   v        i i vi  v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_88880093_8   3518 ACAAATGGTGCTGGGATAACTGACAAGCCACATATAGAAGAATGAAACTG 3567
                                         i     ivv ?      ii i         ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_88880093_8   3568 GATTCTCATCTC---TTATACA-AAAAATCAAATCAAGATGGATCAAAGA 3613
                           ii ii i   ---ii   i -      i  v    i        ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_88880093_8   3614 CTTAAATTGAAGACTTGAAACTATAAAAACTCT-AGAGGACAACACTGAA 3662
                          i     vv    vi i           -    -   i  v    iv i?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGN 552

  chr2_88880093_8   3663 --AAATCCCTTCTAGACACTGGCTTAGGCAAAGATTTCATGACGAAGAAC 3710
                         --     --   vv   vi   v        v i    v iivv v  vv
  L1M4_orf2#LINE/    553 GTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_88880093_8   3711 CCAAAAGCAAATGGAACAAAAACAAAGATAAGTAGGTGGAACTTAATTAA 3760
                                  v v v       iv   i   ii  ii v i    v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_88880093_8   3761 AATAGAGAGCTTCTGCACAACAAAAGGAACAGTCAGCAGAGTAAACAGTC 3810
                            vi i i   i  ii vv    i iv  vi   iv i   i  v  v 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_88880093_8   3811 AACCCACAGAGTGGGAGAAAATCTCCACAATCTATACAACTGAAAAAGGA 3860
                                   i           v iii   vii   i v    v  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_88880093_8   3861 CTAATATCTAGAATATATAAGGAACTC----AAATTAGCAAGAAAAA--- 3903
                           vi    i           i      ----  v i ii  v     ---
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_88880093_8   3904 AAAT--CCCA-TCAAAAAGTGGGCCAAGGACATGAATAGACAATTCTCAA 3950
                             --    - i?    i     v     iv          v     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_88880093_8   3951 AAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCA 4000
                                               i  i  i       i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_88880093_8   4001 CTAATGAT 4008
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.66 (136 / 82)
Gap_init rate = 0.02 (20 / 901), avg. gap size = 1.50 (30 / 20)  


1969 24.10 2.30 1.48  chr2_88936602_88938201.rev      500  1109 (490)    L1M4_orf2#LINE/L1      294   908 (0)  

  chr2_88936602_8    500 AAATTAATAAAATTCAATAGACAGTCCAGAAATAGATA-ACACATATGCA 548
                          i  i   ii   vv   v  v            i iv- i    v iii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_88936602_8    549 ACCAGCCTATGACTGACAAAGGCAGGATGGCAATGCAGTGGAGAAAGGAC 598
                         ii  iiiv  vvii     i  iivv v i v  v  i   i     i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_88936602_8    599 AGCCTTTTCAACATGTGGTGCTGGAACAATTGGCTGTCCATATCCAAAA- 647
                           i          vi         i    i   v i?   i  v     -
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_88936602_8    648 AGTGAACATGAATCCATACCTCACCTCACTCCATATACAAAAGGAAACTC 697
                          i    vv  i i  v        ---  --           ivv     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCAC---AC--CATATACAAAAATTAACTC 488

  chr2_88936602_8    698 AAAATGGAGCACAGATTTAAATGTAAGATCCAAATCTGTAAAATTTCTAG 747
                                 v  ?   ii           v i   v  i     i ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_88936602_8    748 AACAAA-CATAGGAA-AAATCTTTGTGACCTTGTGCTAAGCAAACATTTT 795
                           v   -      ?i-       i         v i  i    vvi   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_88936602_8    796 TTACATATGACACAAAATGCATAATCTGTAAT-TCAACAAT---TAAATT 841
                            v         v   v   i  v vii  v-vv  v   ---      
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_88936602_8    842 GGACTTCATTACGATTAAAATCTTCTGCTCTTCAAAAGATACTACAAAGC 891
                                  i vi       v   i  iv       i  i    iv   v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_88936602_8    892 AAGTGAAAAGTCAACCCA-AAAACTGGAGAAAATGCCCTTGTAAAAAA-G 939
                                   v       - i  iv         ii--   i   vv -i
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT--TTGCAAATCATA 736

  chr2_88936602_8    940 TAGCTAA-AAAGTAATAGTATCCA-AATACATACAGAATTATTAAAACTC 987
                           v  i -  i v v v       -    i   v    i v   v     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_88936602_8    988 AACAAGTAAGAAAACAT-CAACCTACTTTTTTAAATGG-CAAAAGATTTG 1035
                           i  -   i  i   v-i    i v  ?vv-      -    i      
  L1M4_orf2#LINE/    787 AATAA-TAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTG 834

  chr2_88936602_8   1036 AAAAGACAGTTCAACAAAGAAGATGTACAGATGGCAAATAAACACATGGA 1085
                           v     v   vv          i    i     v     i      i 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_88936602_8   1086 AAGATGCTCAACATTTTAGTCATT 1109
                                       iv????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (79 / 64)
Gap_init rate = 0.03 (17 / 615), avg. gap size = 1.35 (23 / 17)  


 746 27.98 10.70 0.41  chr2_89043272_89047055.rev      501   743 (3041)    L1M4_orf2#LINE/L1      239   506 (402)  

  chr2_89043272_8    501 ACTATAAA-CTACAGTTTCCAGGACAAGATGGTGCTGGCACAAAAATGAA 549
                             i   -       vvi  i    ivi    i      i  ii  ii 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_89043272_8    550 CTTATAGATCAGTAGGATGGAATTGAGAATCTAGAAATAAACCTTTACAT 599
                          v         i i i  i         i  i           iv     
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_89043272_8    600 TTTTGGTAAGTT-ATTTTTTAAAATAATGCCTAGGAAATTAAATGGGAGG 648
                           v    v i  -     iv v  vii    v  ivv   v      - i
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GA 387

  chr2_89043272_8    649 AAGGATAGATTTT-------------------CAATTGG-TATCTATAGG 678
                            i    vi   -------------------   i   -  ? i i v 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_89043272_8    679 TGAAAAGACGAATTTAGGCCCTGATCTCTTGCCATGCACA----CTAGAT 724
                         ii   ii i   v  i i   iv i   vii    ii   ----i  iv 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_89043272_8    725 CAAAATAGATCAGAGATCT 743
                               i     ?   i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCT 506

Transitions / transversions = 2.30 (46 / 20)
Gap_init rate = 0.02 (6 / 268), avg. gap size = 4.50 (27 / 6)  

2955 27.21 0.77 1.53  chr2_89043272_89047055.rev     1501  2415 (1369)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_89043272_8   2415 TGGAAAAACATTCCATATTCACTGATAGGAGTAATCAGTAACATTAAATG 2366
                               i i  i    i    iv   v   iv v i i  vii    -- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA--G 48

C chr2_89043272_8   2365 GTGGCTATACTGTCCAAAGCAATTTATAGATTCAATGCTATTCCCATTAA 2316
                         i    v     vi     vii  i  i        i  v  i  i  i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

C chr2_89043272_8   2315 AGTACCA-CTGACATTCTTCATAAAACTAGAAAAAAACAATTTTAAAGTT 2267
                          i v   -   v -  i  iii i  v v  v  iv-ii  ii    i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATT 146

C chr2_89043272_8   2266 CATACGGAACAACAACAACAAAAAAGTCCTGAATAACCAAGGCAATCGTA 2217
                             i    ----- ii-   iii -i  v     i    ii     v i
  L1M4_orf2#LINE/    147 CATATGGAA-----ATG-CAAGGGA-CCCAGAATAGCCAAAACAATCTTG 189

C chr2_89043272_8   2216 AGCAAAAAGAACAAAGCTGGAGGCATCACACTACCCAATTTCAAATTATG 2167
                          iv  i          i      vv       v            viv i
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

C chr2_89043272_8   2166 CTACAGGGCTACAGTTATCAAAACCACATGGTACTGGTACAAGAACAGAC 2117
                              ii        v     i  viii         i i   i i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

C chr2_89043272_8   2116 ACATAGACCAATGGAATAGAATAGAGAGCCCAGAAATATGTCCTCACACC 2067
                          i     i              v     i         vii  vi   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

C chr2_89043272_8   2066 TATAACCATCTGATCTGTAATAAAGTTAACAAAAACAAAAAATGGGGAAA 2017
                            iii  vi    i vii i  i v iv   i v  vvv          
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

C chr2_89043272_8   2016 GGACTTCCTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATGTGCA 1967
                          i ivvi  v     i              i      v  ?   ii    
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

C chr2_89043272_8   1966 GAAGATTGAAACTGGACGCCTTTCCTTAAGCCAGATACAAAAATCAACTC 1917
                         i    v    ii     -  i v   i vi   v          i     
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTC 488

C chr2_89043272_8   1916 AAGATGGAT-AAAGTATTTAAATTTAAAACCCAAAACTATAAAAACCCTG 1868
                           i      - ?  - ii     v   i v i            vi i i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAG-ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

C chr2_89043272_8   1867 AAAGACAACCTAGGCA-ATACCATTCAGGACACAGGCACAGGCAAAGATT 1819
                         i    v   v    ?i- v i -   iv   viv  vvi      v i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

C chr2_89043272_8   1818 TCATGACGAAGATGCCAAAAGCAATTGCAACCAAAGCAAAAATTGACAAA 1769
                           v iivv v  ii         vvv     v    v      v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

C chr2_89043272_8   1768 TGGGATCTAATTAAACTAAAGAGCTTCTGCACACCAAAAGAACCTATCAA 1719
                          v   ii v  i   v v  i i   i  ii vi    i  vv       
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

C chr2_89043272_8   1718 CAGAATGAATAGATC-CCTACAGAATGAGAGAAAAATTTTTCAAGCTATG 1670
                         v i i    v   iv-  i        i       vv   v   iii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

C chr2_89043272_8   1669 CATCTGACAAAGGTCTAATATGCAGCATCTATAAGGAACTTAAACAAAT- 1621
                         i      i  i  v  vi   v   v  v     i     ivv    v -
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

C chr2_89043272_8   1620 --TTACAAGAAAACAATCAACCCCATTAAAAAGTGGGCAAAGGATGTGAA 1573
                         -- v i  i  i    vi     v   ?    i            v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

C chr2_89043272_8   1572 CAGACACTTCTCAAAAGAAGACATACAAGCAGTCAATAGTCATATGAAAA 1523
                         i     i     v        i      iii i     iv  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

C chr2_89043272_8   1522 AAAGCTCAACATCACTGATCAT 1501
                         i v           ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  

1001 26.11 10.28 0.00  chr2_89043272_89047055.rev     2933  3292 (492)    L1M4_orf2#LINE/L1      512   908 (0)  

  chr2_89043272_8   2933 TAAAATCTGAAATTATAAAAACTTTAGGTTAAAAC-T---------TTTC 2972
                            i v  i   i       vii    ivv     - --------- i i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_89043272_8   2973 CAT--TTCTGGGTTCACCAAATATTTCTTAGTTACAACATCAAAAGCTCA 3020
                          i --iii      viv   vvi        v  ii   i       v  
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_89043272_8   3021 ACTTATGAAAGAAAATGCTAATATATTAGGTTTCATTAATGTTCAAAACA 3070
                          viv ii        viivi   v   i ii     i  vi  v     v
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_89043272_8   3071 TTTGCATTTCAAAGGATACCATTAAGAAAATGAAAAGACAAACCACAGAC 3120
                             iii         i  i  i      i           v       v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_89043272_8   3121 CAG-AGAAATTATTTATAAACCATTTATCTGATACACGCCATATTTCCAG 3169
                         ii -     v     ii   i   v         viv v v i v     
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_89043272_8   3170 AATATATAAG-------------TCA-TAA------GACAA----CCCAA 3195
                                  i-------------   -   ------     ----     
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_89043272_8   3196 TTTAAAAATGAACAAAATATTTTAGTATAGATGTTATGGAAGAAGATATA 3245
                           ?       ii    iv    v i  v v  v ivivi           
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_89043272_8   3246 TGAACAGACAGTAATCACATGAAAAGGTGCTCAACATTATTAGTCAT 3292
                         ii  ii v  i   v           i          i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (57 / 36)
Gap_init rate = 0.02 (8 / 397), avg. gap size = 4.62 (37 / 8)  


2962 27.94 1.33 0.67  chr2_89256621_89261935     3922  4823 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_89256621_8   3922 TGGAAAAACATTCCATGTTCATAGACAGGAAGAATGAATTTCGTTATAAT 3971
                               i i  i          i  iv      v v   v i    vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_89256621_8   3972 GACCATATTGCCAAAAGCAATTTATATATTCAATGCTATTATCATTAAAG 4021
                          i v   i v  v   vii  i  i v      i  v  ivii  i   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_89256621_8   4022 TACCA-TTGTGATTATCTACA-AACTAGAAAAAAACTG-TTTTAAAATTT 4068
                          v   -i  ivv  - i i  -  v v  v  i--   - ii       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_89256621_8   4069 ATATGGAACCAAAAAAGAGCCCAAATAGTCAAAGCAATTGTAAACAAAAA 4118
                                 viiv  ii  v  vi     i    i    iv i  v  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_89256621_8   4119 GCACAAAGCTGGAGGCATTACACTGCCTGACTTCAGACTATACTACAAGG 4168
                          v      i      vv i     v  ii i    i viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_89256621_8   4169 CTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGATACATAGAT 4218
                                  i   i    ii         i i  ii i   i i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_89256621_8   4219 CAATGGAACAGAATAGAGAACCTGCAAATAAGACTGCATACCTACAACTA 4268
                                 i     v    ii iiv      iv iii i ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_89256621_8   4269 TCTGATCTTTGACAAATTTGACAAAAGCAAGCAATGGAGAAAGGATTCCC 4318
                         vi    i  i     ivv  v   i v  vv      i     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_89256621_8   4319 TATTCAAGAAATTGTGCTGGGATAACTGGGTAGCCATATGCAGAAGATTG 4368
                          v     v    v         i      i  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_89256621_8   4369 AAACTGGACCCCTTCCTTACACCATATACAAAAATTAACTAACGATGGAT 4418
                           ii         v   i                      v vi      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_89256621_8   4419 TACAGACTTAAATGTAAAACCCAAAAACTCTAAAAATCCTGGAAGACAAC 4468
                         i ?    i         i v i    -  v     v  i i     v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAAC 546

  chr2_89256621_8   4469 CTAGGCA-ATACCATTCAGGACATAGACATGGGCAAATATTTCATCACAA 4517
                         v    ?i- v i -   iv   v v ivv i     vvi    - i v v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGAT 594

  chr2_89256621_8   4518 A-GACACCAAAAGCTATTGCAACAAAAGCAAAGATTGACAAAAGGGGTTT 4566
                          -            vvvv          v   i  v  i   vv  ii  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_89256621_8   4567 AATTAAACTAAAGAGCTTCTGCACAGCCAAAGATACTATCAGCAGAATAA 4616
                         v  i   v v  i i   i  ii vv v  i  i       iv i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_89256621_8   4617 ACAGACAACCTATAGAAAGGGAGAAAATGTTTGCAAACTCTGCATCTGAC 4666
                          v        i i    v          i        iiv ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_89256621_8   4667 AACAGTTTAATATCCAGCATCTATAAAGAACTTAAACAAATTTACAAGAA 4716
                           vi vi vi       v  v           ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_89256621_8   4717 AAA----AATAGCCCCATTAAAAAGTGGGCAGAGGACATGAACAGATACT 4762
                            ----    i   v   ?    i      i    iv    i   i i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_89256621_8   4763 TTTC---AAAAGACTTACAAGTGGCCAACACTTATATGGAAAAAAGTTCA 4809
                          i  --- i    iv     i       i vvi i   i   i v i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_89256621_8   4810 ATATCACTGATTGT 4823
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


2656 27.15 2.32 2.10  chr2_89270105_89272594     1093  1998 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_89270105_8   1093 TGGAAAAATATTTCATGCTCATGGATGGAAAGAATCAATATTCTTAAAAT 1142
                               i    ii    i        v i    v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_89270105_8   1143 GATCACATAGCCCAAAGCAATTTACAGATTCAATGCTATTTATATCAAAC 1192
                          iiv i ivv      vii  i           i  v  iiv       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_89270105_8   1193 TATCAACAAAATTTTTCACAGAAGTAGAAAAACT-ATTCTAAAATTCATA 1241
                          vi  i vivv     ii     i v  v  i  -  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_89270105_8   1242 TGGAACCACAAAAGAGCCCGAATAGACAAAGCCGTCCTAAGCAAATATGA 1291
                              vii   ii  v  v      v    i vi  i i i-   v v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chr2_89270105_8   1292 ACAAAACCAGAGGCATTGCACTACCCGACTTCAAACTATATACTACAAGG 1341
                              iiii    vv ii    v   i i      -- iv        i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAG 247

  chr2_89270105_8   1342 CTACGGTAACCAAAATTGCATGGTTCTGGTACAAAAATAGGCACATAAAT 1391
                             i    i   i iv ii    v    i i  ii    i  i   i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_89270105_8   1392 CAATGTAACAGGTTAGAGAACCCAGACTTAAAGCTGTACATT-ATAACCA 1440
                              v  i  iv v    ii     vv    v ii      -  iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_89270105_8   1441 TCTGATCTT-GACAATGTTGACAAAAGGTAGCAATAGAGAAAAGGCTCCC 1489
                         vi    i  -     v v  v   i vvvvv    i i    iiiivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_89270105_8   1490 TATTTGATAAATGGTGCTAGCATAACTGGCCAGCCATATATAGAAGATTG 1539
                          v  ii i          i v i      vi ?   i  ii i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_89270105_8   1540 AAACTGGACCCCTTCCTTTCACCATATACAAAAATCTACTCAACATGGAT 1589
                           ii         v   iv                iv      v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_89270105_8   1590 TAAAGACTTAAATGTAAAACCTAAAACTTCAAAAACTCT-AGAAGAAAAT 1638
                         i ?    i         i v        vi    -    -         i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr2_89270105_8   1639 CTAAG---AAATACCATTCTAGACAAAGGCCGT--AGTAAAAATTTC--- 1680
                         v  i ---    -- -   vv   vvv  --  --i i  vii    ---
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGG--GTTAGGCAATGGTTTCTTA 591

  chr2_89270105_8   1681 ---ATGACAAAAACTCCAAAAGCAACTGCAACAAAAACAAAAATTGATAA 1727
                         ---      ------         vvv         iv      v     
  L1M4_orf2#LINE/    592 GATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_89270105_8   1728 ATGGGACCTAATTAAAGTAAAGAGCTTCTGCACAAGTTAAAGAA-ACTAT 1776
                           v    i v  i   i v  i i   i  ii --v i    i -     
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGC--TTCAAAGGACACTAT 683

  chr2_89270105_8   1777 AAACAGCGTCAACAGACAGCCTACAGATTGAGGGAAAATATTTGTAAACT 1826
                         v  v iv  v  v     i  i     v  i i           i   ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_89270105_8   1827 ATGCATCCGACAAAGACCCAATAACCAGAATCTGTAATGAAC----GTAA 1872
                           ii   i  i  i iv ivi  v       v i   v    ----ii  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_89270105_8   1873 ATTAACAAGCAACAAACAAAAACAACCCCATTAAAAAGTGGCCAAATGAC 1922
                         v i  i  vv  v i     --i     v   ?    i   v    v  i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAA--TAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_89270105_8   1923 ATGAACAGACTCTTCTTAAAACAAAACATGCACATAGTCAACAAGCATAT 1972
                         v    i    vi    iv   v  i i  i  v  i i   i     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_89270105_8   1973 GAAAA-ATTCTCAACACCACTAATCAT 1998
                              -  v       i  ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.11 (40 / 19)  


2172 25.15 4.01 0.46  chr2_89296445_89298084.rev      501  1148 (492)    L1M4_orf2#LINE/L1      238   908 (0)  

  chr2_89296445_8    501 TATTTCAAGGCTATGGTTACCAAAACAGCATGGTTCTAGTATAAAAATAG 550
                           i v   i    ii  v i   i    ii    v  i i    ii    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_89296445_8    551 GCACATAGATCAATGGAACACAATAGAGAACACAGAAATAAACCCAAATG 600
                         i  i              i v   v    iiv              v ii
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_89296445_8    601 CTTATAACCAACTGATCTTCAACAAAGCATAC-AATAACAAACAGTGGGG 649
                         i    iii   i    i   i    i -i i -  v v  vv  i     
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGG 386

  chr2_89296445_8    650 AAAGGACACCCTATTCAATAATTGGTACTGGAAAAACTGGCAAGCCACAG 699
                             i i vi  v     i  v    i    i v      vv ?     v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_89296445_8    700 GTAGAAGAATAAAACTGGATCTTCATATCTCACCTTATACGAAAATCAGC 749
                          i i      i  ii    i iii iv  v    v     i     i i 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_89296445_8    750 TCAAGATGAATCAAAGGCTTAAATCTAAGAACTGAAACCATATAAATTCT 799
                             i   i    ?  i i     v     i  i    i   -   i   
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCT 535

  chr2_89296445_8    800 -AGAAGATAACATTGGAAAAACTCCTCTAGACCTTGGCTTAGTGAAAGAA 848
                         -      v     v  ?iv  v  i  vv        v    vv  v iv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_89296445_8    849 TTCATGACTAAGACCCCAAAAGGAAATGCCACAAAAACAAAAAATAAATA 898
                            v iiv  v   v       v v v  v      i-        i   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATA 634

  chr2_89296445_8    899 AATGGAACCTAA-CTAAGCTAAAAA-------GCTTC------TAC-AT- 932
                            v i  i v - v  ii      -------     ------i  -  -
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_89296445_8    933 -----AGCAAACAGACAACCCACAAAGTGGGAGAAAATATTCACAAACTG 977
                         -----  ii  v            i i              ii    iii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_89296445_8    978 TGCATCTGTTGAAGGA---ATAACCATAATCTATGAGGAACTCAAACAAA 1024
                          ii     v i i   ---i  v   v   v   i i      vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_89296445_8   1025 TCAGTAAGAAAAAAACAAATAATCCCACCAAAAAGTGGGCAAAGAATATG 1074
                            i   v     i        i  v ii?    i         i  v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_89296445_8   1075 AACAGACAATTCTCAAAAGAAGATATACAAACAGCCAACAAATACATAGA 1124
                           i     v     v                ii     i  ii    ii 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_89296445_8   1125 AAAATGCTCCACATCACTAATTAT 1148
                           i      v      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (101 / 58)
Gap_init rate = 0.02 (11 / 671), avg. gap size = 2.64 (29 / 11)  


2187 25.00 4.01 0.46  chr2_89756860_89758490      492  1139 (492)    L1M4_orf2#LINE/L1      238   908 (0)  

  chr2_89756860_8    492 TATTTCAAGGCTATGGTTACCAAAACAGCATGGTTCTAGTATAAAAATAG 541
                           i v   i    ii  v i   i    ii    v  i i    ii    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_89756860_8    542 GCACATAGATCAATGGAACACAATAGAGAACACAGAAATAAACCCAAATG 591
                         i  i              i v   v    iiv              v ii
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_89756860_8    592 CTTATAACCAACTGATCTTCAACAAAGCATAC-AATAACAAACAGTGGGG 640
                         i    iii   i    i   i    i -i i -  v v  vv  i     
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGG 386

  chr2_89756860_8    641 AAAGGACACCCTATTCAATAATTGGTACTGGAAAAACTGGCAAGCCACAG 690
                             i i vi  v     i  v    i    i v      vv ?     v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_89756860_8    691 GTAGAAGAATAAAACTGGATCTTCATATCTCACCTTATACGAAAATCAGC 740
                          i i      i  ii    i iii iv  v    v     i     i i 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_89756860_8    741 TCAAGATGAATCAAAGGCTTAAATCTAAGAACTGAAACCATATAAATTCT 790
                             i   i    ?  i i     v     i  i    i   -   i   
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCT 535

  chr2_89756860_8    791 -AGAAGATAACATTGGAAAAACTCCTCTAGACCTTGGCTTAGTGAAAGAA 839
                         -      v     v  ?iv  v  i  vv        v    vv  v iv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_89756860_8    840 TTCATGACTAAGACCCCAAAAGGAAATGCCACAAAAACAAAAAATAAATA 889
                            v iiv  v   v       v v v  v      i-        i   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATA 634

  chr2_89756860_8    890 AATGGAACCTAA-CTAAGCTAAAAA-------GCTTC------TAC-AT- 923
                            v i  i v - v  ii      -------     ------i  -  -
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_89756860_8    924 -----AGCAAACAGACAACCCACAAAGTGGGAGAAAATATTCACAAACTG 968
                         -----  ii  v            i i              ii    iii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_89756860_8    969 TGCATCTGTTGAAGGA---ATAACCAGAATCTATGAGGAACTCAAACAAA 1015
                          ii     v i i   ---i  v       v   i i      vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_89756860_8   1016 TCAGTAAGAAAAAAACAAATAATCCCACCAAAAAGTGGGCAAAGAATATG 1065
                            i   v     i        i  v ii?    i         i  v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_89756860_8   1066 AACAGACAATTCTCAAAAGAAGATATACAAACCGCCAACAAATACATAGA 1115
                           i     v     v                iv     i  ii    ii 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_89756860_8   1116 AAAATGCTCCACATCACTAATTAT 1139
                           i      v      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (100 / 58)
Gap_init rate = 0.02 (11 / 671), avg. gap size = 2.64 (29 / 11)  


2573 28.15 2.10 1.88  chr2_89782498_89784987.rev     1093  1998 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_89782498_8   1093 TGGAAAAATACTTCATGCTCATGGATGGAAAGAATCAATATTCTTAAAAT 1142
                               i   iii    i        v i    v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_89782498_8   1143 GATCACATAGCCCAAAGCAATTTACAGATTCAATGCTATTTATATCAAAC 1192
                          iiv i ivv      vii  i           i  v  iiv       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_89782498_8   1193 TATCAACAAAATTTTTCACAGAAGTAGAAAAACT-ATTCTAAAATTCATA 1241
                          vi  i vivv     ii     i v  v  i  -  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_89782498_8   1242 TGGAACCACAAAAGAGCCCAAATAGACAAAGCCGTCCTAAGCAAAAATGA 1291
                              vii   ii  v  vi     v    i vi  i i iv  i  -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GA 199

  chr2_89782498_8   1292 ACAAAACCAGAGGCATTGCACTACCTGACTTCAAACTATATACTACAAGG 1341
                              iiii    vv ii    v  ii i      -- iv        i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAG 247

  chr2_89782498_8   1342 CTACGGTAACCAAAATTGCATGGTTCTGGTACAAAAATAGGCACATAAAT 1391
                             i    i   i iv ii    v    i i  ii    i  i   i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_89782498_8   1392 CAATGTAACAGTTTAGAGAACCCAGACTTAAAGCTGTACATT-ATAACCA 1440
                              v  i  vv v    ii     vv    v ii      -  iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_89782498_8   1441 TCTGATCTT-GACAATGTTGACAAAAGGTAGCAATAGAGAAAAGGCTCCC 1489
                         vi    i  -     v v  v   i vvvvv    i i    iiiivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_89782498_8   1490 TATTTGATAAATGGTGCTAGCATAACTGGCCAGCCATATATAGAAGATTG 1539
                          v  ii i          i v i      vi ?   i  ii i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_89782498_8   1540 AAACTGGACCCCTTCCTTTCACCATATACAAAAATCTACTCAATATGGAT 1589
                           ii         v   iv                iv      v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_89782498_8   1590 TAAAGACTTAAATGTAAAACCTAAAACTTCAAAAACACTAGAAGAAAATC 1639
                         i ?    i         i v        vi    vivi          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_89782498_8   1640 TAAG---AAATACCATTCTAGACAA-AGGCCATAGTAAAAATTTC----- 1680
                           i ---    -- -   vv   vv-i  ii -i i  vii    -----
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGA 593

  chr2_89782498_8   1681 -ATGACAAAAACTCCAAAAGCAACTGCAACAAAAACAAAAATTGATAAAT 1729
                         -      ------         vvv         iv      v       
  L1M4_orf2#LINE/    594 TATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_89782498_8   1730 GGGACCTAATTAAAGTAAAGAGCTTCTACACAAGTTAAAGAA-ACTATAA 1778
                         v    i v  i   i v  i i   i iii --v i    i -     v 
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGC--TTCAAAGGACACTATCA 685

  chr2_89782498_8   1779 ACAGCGTCAACAGACAGCCTACAGAATGAGAGAAAATATTTGTAAACTAT 1828
                          v iv  v  v     i  i        i             i   ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_89782498_8   1829 GCACCCGACAAAGACCCAATAACCAGAATCTGTAATGAAC----GTAAAT 1874
                         ii i i  i  i iv ivi  v       v i   v    ----ii  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_89782498_8   1875 TAACAAGCAACAAACAAAAACAACCCCATTAAAAAGTGGCCAAATGTCAT 1924
                         i  i  vv  v i     --i     v   ?    i   v    v viv 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAA--TAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_89782498_8   1925 GAACAGACTCTTCTTAAAACAAAACATGCACATAGTCAACAAGCATATGA 1974
                            i    vi    iv   v  i i  i  v  i i   i     i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_89782498_8   1975 AAA-ATGCTCAACACCACTAATCAT 1998
                            -          i  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (156 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


3002 27.72 1.33 0.67  chr2_89793174_89799157.rev     4591  5492 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_89793174_8   4591 TGGAAAAACATTCCATGTTCATAGACAGGAAGAATGAATTTCGTTATAAT 4640
                               i i  i          i  iv      v v   v i    vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_89793174_8   4641 GACCATATTGCCAAAAGCAATTTATATATTCAATGCTATTATCATTAAAG 4690
                          i v   i v  v   vii  i  i v      i  v  ivii  i   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_89793174_8   4691 TACCA-TTGTGATTATCTACA-AACTAGAAAAAAACTG-TTTTAAAATTT 4737
                          v   -i  ivv  - i i  -  v v  v  i--   - ii       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_89793174_8   4738 ATATGGAACCAAAAAAGAGCCCAAATAGTCAAAGCAATTGTAAACAAAAA 4787
                                 viiv  ii  v  vi     i    i    iv i  v  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_89793174_8   4788 GCACAAAGCTGGAGGCATTACACTGCCTGACTTCAGACTATACTACAAGG 4837
                          v      i      vv i     v  ii i    i viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_89793174_8   4838 CTACAGTAACCAAGACAGCATGGTACTGGTACAAAAACAGATACATAGAT 4887
                                  i        ii         i i  ii i   i i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_89793174_8   4888 CAATGGAACAGAATAGAGAACCTGCAAATAAGACTGCATACCTACAACTA 4937
                                 i     v    ii iiv      iv iii i ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_89793174_8   4938 TCTGATCTTTGACAAATTTGACAAAAGCAAGCAATGGAGAAAGGATTCCC 4987
                         vi    i  i     ivv  v   i v  vv      i     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_89793174_8   4988 TATTCAAGAAATTGTGCTGGGATAACTGGGTAGCCATATGCAGAAGATTG 5037
                          v     v    v         i      i  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_89793174_8   5038 AAACTGGACCCCTTCCTTACACCATATACAAAAATTAACTAACGATGGAT 5087
                           ii         v   i                      v vi      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_89793174_8   5088 TACAGACTTAAATGTAAAACCCAAAAACTCTAAAAATCCTGGAAGACAAC 5137
                         i ?    i         i v i    -  v     v  i i     v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAAC 546

  chr2_89793174_8   5138 CTAGGCA-ATACCATTCAGGACATAGACATGGGCAAATATTTCATTACAA 5186
                         v    ?i- v i -   iv   v v ivv i     vvi    -   v v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGAT 594

  chr2_89793174_8   5187 A-GACACCAAAAGCTATTGCAACAGAAGCAAAGATTGACAAATGGGATTT 5235
                          -            vvvv      i   v   i  v  i    v   i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_89793174_8   5236 AATTAAACTAAAGATCTTCTGCACAGCCAAAGATACTATCAGCAGAATAA 5285
                         v  i   v v  i v   i  ii vv v  i  i       iv i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_89793174_8   5286 ACAGACAACCTATAGAAAGGGAGAAAATGTTTGCAAACTCTGCATCTGAC 5335
                          v        i i    v          i        iiv ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_89793174_8   5336 AACAGTTTAATATCCAGCATCTATAAAGAACTTAAACAAATTTACAAGAA 5385
                           vi vi vi       v  v           ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_89793174_8   5386 AAA----AATAGCTCCATTAAAAAGTGGGCAGAGGACATGAACAGATACT 5431
                            ----    i i v   ?    i      i    iv    i   i i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_89793174_8   5432 TTTC---AAAAGACTTACAAGTGGCCAACACTTATATGGAAAAAAGTTCA 5478
                          i  --- i    iv     i       i vvi i   i   i v i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_89793174_8   5479 ATATCACTGATTGT 5492
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


2956 23.48 6.10 2.19  chr2_91045199_91047943     1385  2253 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_91045199_9   1385 AAATATCTTACAGCCATGAATTGGAAGATTTAATATTGT---------AG 1425
                          i     ii iivi    i         i          --------- i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_91045199_9   1426 TACTTTC-AAGTTGAACTACAGATTTGACGTAATCCCTG-CAAGTATCCC 1473
                             ii -  i    v         ii   i       i-   i-     
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA-ATCCC 104

  chr2_91045199_9   1474 AACAGACTTCTGTCTAGAAACTGACAAGCTGATTCTAAAATACACATGGG 1523
                          i v v   i v vi     i            i       v  i    i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_91045199_9   1524 AATGTAAGGGACTCAAAATAGCCAAAATAGTCTTGAAAAAAGAAAACATA 1573
                             i       i  i           i i          ii i    v 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_91045199_9   1574 TTAGGATAATTCACACCCCCGTGCTCCAAACCTTACGGCAAGGCATCAGT 1623
                         v v   vi i      ii  vvii i    v     vi   i  vv    
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_91045199_9   1624 AATCAAGACAACACAATACTGACGAAAGAA-AAATATATAGATTGATGGA 1672
                                   iiiiii     i iv   i - i i        ii     
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_91045199_9   1673 AGAGAATTGAGAGTCCATATATAAAACTATGTGTGTATAGTCAATGGATT 1722
                          v               v v     v i  iii v   i      v    
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_91045199_9   1723 CTT-ACAGTGGTGCCATGTGCAATTCAATGAGGAAGGGACAGTCTTTG-A 1770
                         i i-   iv       v -i v        i    i i i       v- 
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_91045199_9   1771 ACAAA-----CTGGGTCAACAGCGTACACTTGGATCGCCACTTGCAAAAT 1815
                              -----     v    ----------     v?    v       v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAAC----------TGGATAKCCACATGCAAAAG 443

  chr2_91045199_9   1816 AATAAATTGGAACCCTTACCCCAAAGCATACAAAAATATTAACTCAAA-T 1864
                            i  v v i    i    i  v v    i v   v           - 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_91045199_9   1865 GAATTAAAGACATACATGCAAGAGCTA-----------------GAATAA 1897
                          i  i ?    v  v   i        -----------------   v  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_91045199_9   1898 AGCATATGGGAAAATCTTCAGGATTTTGGATCTAGCAAAGA---AATAGC 1944
                          i    v ? v        iv  ii    i ivi    v i---vv   v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_91045199_9   1945 TGTAACACCAAAAACATGAGCAACAAAATAAAAATTAGATATTTAAAATT 1994
                          i i         i  ii          v     v      vv vii i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_91045199_9   1995 TCTTAAAAATTAAAGACATTGGTGTTTCAAAGGACA--ACCAAGCAAGTC 2042
                           v v         i  v  v   i           -- i    v    v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_91045199_9   2043 AAAAGGCAGCTCAAAAATTGTGAGAAAATATTTGAAAAACACATATCT-A 2091
                              i  i i  v i v  v             v   v  i      - 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_91045199_9   2092 TATGTCTGCATATATATGTATCTTGAATATAGAAA-AATTGTTTTAACTC 2140
                           v -------iv iv      iv       v   -  i v  vi     
  L1M4_orf2#LINE/    744 TAAG-------GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_91045199_9   2141 AGTAA--------CAAATATCCCAACTCAAAACTGA-TAAACGATAGGAA 2181
                          i   --------      v     i ?    v  i-i   v   vv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_91045199_9   2182 TAGATGTGTTTTCCAAGAAGATACACGAACGGTCAATAATCCCATAAAAA 2231
                             ii v i i v         i  i  i  i      v v   i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_91045199_9   2232 GATACTCAACAGCATCACTCAT 2253
                            i       v  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (118 / 82)
Gap_init rate = 0.02 (19 / 903), avg. gap size = 3.79 (72 / 19)  


2902 29.30 0.89 0.11  chr2_91061933_91067088     3764  4664 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_91061933_9   3764 TGGAAGAACATTCCATGCTCATGGGTTGGAAGAATCAATATCGTGAAAAT 3813
                              ii i  i     i      i        v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_91061933_9   3814 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATACCCATCAACC 3863
                            v     v     iv i  i  i        i  v  v  i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_91061933_9   3864 TACCAATGACTTTCTTCACAGAATTTGAAAAAACGTCTTTAAAGTACATG 3913
                          v   iivi i  i  ii     v    v  ivi viii    i v   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_91061933_9   3914 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAGGAA 3963
                              viiv  ii  v  v v  v     iv     i i ivv i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_91061933_9   3964 CAAAGC---A----TCACGCTACCCGATTTCAAACTATACTACAAGGCTA 4006
                              i--- ----    i  v   i        viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_91061933_9   4007 CAGTAACCAAAACAGCATGTTACTGGTACAAAAACACAGACATAGATCAA 4056
                               i   i    ii  v      i i  ii i v v i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_91061933_9   4057 TGGAACAGAACGGAGCCCTCAGAAATAATGCCGCATAACTACAACTGTCT 4106
                              i    iv   vvii         vv  ii i vi  iiiiiivi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_91061933_9   4107 GATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCTAT 4156
                            i  i     ivv  vv  i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_91061933_9   4157 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 4206
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_91061933_9   4207 CTGGATCCCTTCCTTACACCTTATGCAAAAATTAATTCAAGTTGGATAAA 4256
                         i    i    v   i     v   i          i    iv     v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_91061933_9   4257 AGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGACAACCTAG 4306
                             i  v    v   v       i      vi i       v   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_91061933_9   4307 GCA-ATACCGTTCAGGACATAGGCGTGAGCAAGGACTTCATGTCTAAAAC 4355
                          ?i- v i -   iv   v v  vv ii    v ii   v ivv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_91061933_9   4356 ACCAAAAGCAATGGGAACAAAAGCCAAAATTGACAAATGGGATCTAATTA 4405
                                   vvi v        vv     v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_91061933_9   4406 AACTAAAGAGCTTCTGCACAGTAAAAGAAATTACCATCAGAGTGAACAGG 4455
                           v v  i i   i  ii vvi   i  v i  i  vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_91061933_9   4456 CAACCTACAAAATGGGAGAAAATTTTTGCAACTTACTCATCTGACAAAGG 4505
                              i   i             v       v i ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_91061933_9   4506 GCTAATAACCAGAATCCACAATGAACTCAAACAAATTTACAAGTAAAAAA 4555
                         i  vi  v       vi i  v      vv    v iv i  vv    i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_91061933_9   4556 CAAACAACCCCATCAAAAAGTGGGTGAAGAACACGAACAGACACTTCTCA 4605
                             i     v  i?    i    ii   i ivi   i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_91061933_9   4606 AAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGTTCATAATC 4655
                                 i  vi viii     v  i          i   i   vv   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_91061933_9   4656 ACTGGCCAT 4664
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.36 (150 / 110)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.25 (9 / 4)  


3280 22.73 2.99 2.66  chr2_91297688_91300337     1257  2158 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_91297688_9   1257 AATGATATCCCCAAGTTTGTGGATTGGAAGA----ATATTGTTAAAATGT 1302
                           v        - v   ii            ----          i   v
  L1M4_orf2#LINE/      4 AAAGATATCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_91297688_9   1303 CCATACTATCCAAAGTGATCTACAGATTCAATGCAATCCCTATCAAATTT 1352
                          v     vi     v                i               v i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_91297688_9   1353 CCAAAGGCATTTTTCACAAAAATAGAAAACACAATTCTAAAATTTGTATT 1402
                            ivv  v     ii  i    v  v  vvii  i        ii   v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_91297688_9   1403 AAATCATAAAAGACCCTGAATAGCCAAAAGAATCTTGAGAAAGAAAAACA 1452
                         i  viii  ii     v            v        i      i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_91297688_9   1453 AAGTAGAAGGTATCACACTACCTGATTTCAA--CTTATATTACAAAGTGA 1500
                             v i   vv       v  ii       --    i--       iv 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGCTA 250

  chr2_91297688_9   1501 TAGTTATCAAAAC-GTATGGTACTGGCATAAAAGCAGACACATGGATCAA 1549
                         i   v     i  -  i              iiii     i  i      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_91297688_9   1550 TGGAACTGAATACAGAGCCCAAAAATAAACCCAAACATATATTATGAGCT 1599
                              iv    vv    i   i           v    v   vi v ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_91297688_9   1600 AATTTTTGACAAG--T-CCAATAAGATACAATAGGGAAAAGATGGTGTCT 1646
                         i     i      -- -    v vv  v    i      ii  i  v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_91297688_9   1647 TCAATAAGTAGTGGTAAGAAAACTAGATATCTATATGCAAAAGAATGAAA 1696
                             i  i i   v ii  v    i    ? i i               i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_91297688_9   1697 CTGGACCTGATGCCTATCTTACACATCATACATAAAAAGCAACTCAAA-T 1745
                         i      -----    i  i    --    i i     vi        - 
  L1M4_orf2#LINE/    451 TTGGACC-----CCTACCTCACAC--CATATACAAAAATTAACTCAAAAT 493

  chr2_91297688_9   1746 AGATTAAATACCTAAC------ACCTGAAACCATAAAACTCCTAGAAGGA 1789
                         i   i ? v      v------ v  i    i         i      i 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_91297688_9   1790 AATATAGGAGAAAAACTCCTTAATATCCTC---CTTGACAATGATTTTTT 1836
                           i     ? v   v  i v i ---   i---i v i     i   i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGA---CCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_91297688_9   1837 GGATATCACACCAAAAGCTCAGGCAGCAAAAGCAAAAATAAGCAAGTGGG 1886
                         i     v           v  i   i      v       iii  i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_91297688_9   1887 ACTACATCAAGCAAAT---AAGCTTCTGCATAGCAATAAAAAAAAACAAA 1933
                            v      ---   ---  i   i  iiivv   vii v vv v   i
  L1M4_orf2#LINE/    641 ACTTCATCAA---AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_91297688_9   1934 ATGGGGTAAAAAGGTAGCACAGGGATTAGGGGAAAATATTGGCAAACCAC 1983
                          --ii  i     ii i v  vi  v i  i         v     i  i
  L1M4_orf2#LINE/    688 A--AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_91297688_9   1984 ACATCTGATAAGGGGTTAAAATCCAAAACATATAAGGAACTCACACAACT 2033
                          i            ii viv     i  i      i      vi      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_91297688_9   2034 CAGTAGCAAAAAAAAAACCCCAAATAACTGGATTTTAAAATAGGCAA-GG 2082
                           i  ii     i ------        ivi   ?v     i     -  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA------CAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_91297688_9   2083 ACCTGAATAGCCATTTTTCCAAAGT---CACACAAATGGTCAAATGGTAT 2129
                          ii       v     i       v---i i        i   vvi i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_91297688_9   2130 ATGAAAAGATGCTCAATATCATAATCATG 2158
                                         i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (130 / 71)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 2.68 (51 / 19)  


3209 25.22 2.34 1.00  chr2_91437619_91439887.rev      882  1777 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_91437619_9    882 TGAAAAGACATTC-ACACTCATGGATCAGAAATATGAATGTTGTTAAAGT 930
                           i     i  i - iii        ii   ivv v   i       ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_91437619_9    931 GACAGTACTACTCAAAAGCAACCTACAGATTCCATGCAATCTCTATCAAA 980
                          i  i    v i    -vii i          v i      i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_91437619_9    981 ATACCTA--TGAATATTCTTCACA-AAATTAAAAAA--AATCCAAAGAGA 1025
                           -  i --  --iv  i  ii  -     i v  i--i    v  i --
  L1M4_orf2#LINE/    100 AT-CCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-- 144

  chr2_91437619_9   1026 TTT-TATGGAATCAAAAAATATCCTGAATAGCCAAAGCCATCCTAAGCAA 1074
                           i-       viiv  iiv i  v           i v   i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_91437619_9   1075 AAAGAACAAAGCTGGATGTATCATGCTGCCAGACCTCAGAATATACTACA 1124
                         i          i    v vv   ii  v  vi ii   i  iv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_91437619_9   1125 AAACTGTAGTAACCAAAACATCATGGTATTGGCATAAAAACAGACACATA 1174
                           i  ii     i   i   vii     i        ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_91437619_9   1175 GACCTATGGAATAGAATAAAGAACCCAGAAA---ATCCACATATCT-CAG 1220
                           i v            vi   ii       --- i   i i  i -ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_91437619_9   1221 CCAACGGATTTTTTACAAAGGCGCCAAGAACACTCATTGGGGAAAGGATA 1270
                         i   iv      iv    i  i       v  i   v         i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_91437619_9   1271 GTCTCTTCGATAAATGGTGCTGGAAAAACTGGATATCCATATGCAGAAGA 1320
                             i   i i            i v         ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_91437619_9   1321 ATGAAACTAGACCTCTGCCTCTCACCCTATACAAAGATCAACTCAAAGTA 1370
                              ii i    i  i    v    v        i  i        i i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_91437619_9   1371 TCTCAAATACCCAAATATAAGACCCAAAATGGTAAAGCTACTAGAAGAAA 1420
                         vv   ? v   i    i     v i    ivi    i  vi         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_91437619_9   1421 ACATAGGGG-AGATCCTTCAGGACATTGCTCTGGGAAAATATTTTATGAA 1469
                                ? - i   -   iv   v   vvi i  v  vvi   iv ii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_91437619_9   1470 TAAGGCATCAAAAGCACAGGCAGCAAAAGAAAAAATAAACAAATGGGATC 1519
                           v i  i          i   i              i i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_91437619_9   1520 ACATCAAGCTAAAAATCTTCTGCACAGCAAAGGAAATAATAAAGTGAGTG 1569
                         v      iv v    v   i  ii vv       v iv  v   vi    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_91437619_9   1570 AAAAGGCAATCTACAGAATGGGAGAAAATAT----AAACTCAT----CTG 1611
                              i   i i                   ----   -    ----   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTG 742

  chr2_91437619_9   1612 GCAGGAAATTAATATCAAGAATATACAAGGAATTCAAACATATCAACAGC 1661
                         ii i ii i vi    v        i  i   i  vv   vv    i ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_91437619_9   1662 AAAGAAGCACAACAATCTAATT-AAATATAAACAAATGCTCTGAACAGAC 1710
                            i ii  -  i  i i    -   v  iii    v v i    i    
  L1M4_orf2#LINE/    793 AAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_91437619_9   1711 ATTTCTCAAAAGAAGACATACAAATGACCAACAAGTATATGAAAAAATGT 1760
                                v        i         i    i   i i       i   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_91437619_9   1761 TCAACACCACTAATCAG 1777
                               i  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (156 / 67)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.67 (30 / 18)  


3006 28.74 0.33 0.33  chr2_91510762_91517141     4981  5888 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_91510762_9   4981 TGGAGGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5030
                             iii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_91510762_9   5031 GGCCATACAGCCAAAGGTAATTTATAAATTCAATGTCATCCCCATCAAGC 5080
                            v    vv  v  iv i  i  i i      i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_91510762_9   5081 TACCAATGGCTTTCTTCACAGAATTGGAAAAAACAACTTTAAAGATCATA 5130
                          v   iiv  i  i  ii     v v  v  ivii iii    iv     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_91510762_9   5131 TGGAACCAAAAAAGAACCTGCATTGCCAAGTCAATCCTAAGCAAAAAGAA 5180
                              viiv  ii  v  v v  v     iv     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_91510762_9   5181 CAAACCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGCTA 5230
                             vi      vv       v  ii i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_91510762_9   5231 CAGTAACCAAAACAGCATGGTACTGGTGCCAAAACAGAGATACAGACCAA 5280
                               i   i    ii         iiiv ii i   v   i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_91510762_9   5281 TGAAACAGAAT--AGAGCCCTCGGAAATAATACCACACATCTACAACCAT 5328
                           i  i     --    i  --i       vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_91510762_9   5329 CTGATCTTTGACAAACCTGACATAAACAAGAAACGGGGAAAGGATTCCCT 5378
                         i    i  i     ivv  v  vi v  vvv  i        i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_91510762_9   5379 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAGCTGA 5428
                         v  i  i              v      v  ?   i   iii  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_91510762_9   5429 AACTGGATCCCTTCCTTACACCTTATATAAAAAGTAATTCAAGATGGATT 5478
                          ii    i    v   i     v    i     v   i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_91510762_9   5479 AAAGACTTAAATATCAGACCTAAAACCATAAAAACCCTAGAAGAATACCT 5528
                          ?    i     i v   v       i      vi i        v  v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_91510762_9   5529 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGAATTCATGACTAAA 5577
                            ?i- v i -   iv   v v  vv i     v iv   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_91510762_9   5578 ACACCAATAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCGAAT 5627
                                v    vvi          vv     v  i    vi  iivv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_91510762_9   5628 TAAATTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5677
                         i   v i  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_91510762_9   5678 GACAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCCTCTGACAAA 5727
                                i                 v   i   vii iviv     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_91510762_9   5728 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTATATGAAAAA 5777
                           i  vi          v  i        ivv    v iv   vv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_91510762_9   5778 ATCAAACTACCCCATCAAAAAGTGGGCAAAGGGTATGAACAGTGACTTCT 5827
                         iv    iv    v  i?    i          i v    i  vv i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_91510762_9   5828 CAAAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5877
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_91510762_9   5878 TCACTGGCCAT 5888
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (150 / 107)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3152 26.65 0.88 0.88  chr2_91530574_91536853     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_91530574_9   4881 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_91530574_9   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_91530574_9   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_91530574_9   5029 TATGGAACCAAAAAAAGAGCCC-GTATTGCCAAGTCAATCCTAAGCCAAA 5077
                                -- viv  i ii   - v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_91530574_9   5078 AGAATAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAA- 5126
                             i    i      vv       v  ii i      viv        -
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_91530574_9   5127 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5176
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_91530574_9   5177 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCG--CATTCCTAC 5222
                                  i    i--    i  --        vv  i--    --  i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATT--TAT 342

  chr2_91530574_9   5223 AACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGA 5272
                         iiii vi    i  i     ivv  vv  i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_91530574_9   5273 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGA 5322
                          vvi  v  i  i              v      v  ?   i   i ii 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_91530574_9   5323 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGA 5372
                         iiv    ii    i    v   i     v           i  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_91530574_9   5373 TGAATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGA 5422
                           i  i ?   ii    i  v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_91530574_9   5423 CAACCTAGGTATTACCATTCAGGACATAGGCATGGGCAAAGAATTCATGT 5472
                         v   v    ?i v viv   iv   v v  vv i     v iv   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_91530574_9   5473 CCAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5522
                         vi vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_91530574_9   5523 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5572
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_91530574_9   5573 GAACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTG 5622
                            v  i     i   iv            v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_91530574_9   5623 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 5672
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_91530574_9   5673 AAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACA 5722
                              i     i     v  i?    i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_91530574_9   5723 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGACAAAATGTT 5772
                         i     v        i  vi viii     v  i       v  i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_91530574_9   5773 CATCATCACTGGCCAT 5788
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2479 27.18 1.17 0.78  chr2_91536961_91538748      528  1296 (492)    L1M4_orf2#LINE/L1      137   908 (0)  

  chr2_91536961_9    528 TCCTAAAATTCATGTGGAACTCAAAAATAGCCCGCATAACGAAAGCAAGA 577
                                      i     v vv  iiv v  v v   i v   i   vv
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_91536961_9    578 CTAAGCAAAAAGAACAAATGTGGATGCATCACATTGCTTGACTTCAAGCT 627
                         i i iv  i         vv    v vv     i v iii i     ivi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_91536961_9    628 GTACTATAAGTCTATAGTCACCAAAGCAGCATAATACTGCTATAAAAATA 677
                         v     i  iv   i   v i   ii   ii ii     vi    ii   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_91536961_9    678 GGCACGTAGACTAATGGAATCGAATAGAGAACTGAGAAATAAAGCCAAAT 727
                          i  ii    ii        v    v    iiiv         v   v i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_91536961_9    728 ACTTA-AGCCAACTGATCTTTAACAAAGGAAACAAAAACATAAAGTTGGG 776
                          i   -i i   i    i  ii    i  viv   i v   vv i v   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_91536961_9    777 AAAGGACACCATATTCAACAAATGGTGCTGGGTTAATTGGCAAGCCATAT 826
                             i i viv v                   vi  i   vv ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_91536961_9    827 GTAGAAGAATGAAACTGCATCCTCATCTCTCACCTTATACAAAAATCAAC 876
                          i i         ii  v i  ii i   v    v           i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_91536961_9    877 TCAAGATGGATCAAAGACTTAAATCTAACACCTAAAACTATAAAAATTCT 926
                             i        ?    i     v   v v              v ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_91536961_9    927 AGAAGGTAACATTGG---AAATACCCTTCTAGACATTTGCTTAGGCAAAG 973
                              iv     v  ---    ---    vv   v  v v        v 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_91536961_9    974 ACTTCATGACCAAGAACCCAAAAGCAAAGGCAACAAAAGCAAAGATAAGT 1023
                         ii   v iivi v  vv         v i          v   i   ii 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_91536961_9   1024 AGATGGGACTTAATTAAACTAAGAAGCTTCTACACAGCAAAAGA-ATTAA 1072
                          i  v      v  i   v v i  i   i iii vv    i  - i  -
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA- 682

  chr2_91536961_9   1073 TCAGCAGAGTAAAAAGACAACCTATATAGAGTGGGAGAAAATCTTTACAA 1122
                            iv i   i           i i --  i           v   i   
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACA--GAATGGGAGAAAATATTTGCAA 730

  chr2_91536961_9   1123 ACTATGCATCCAACAAAGTGCTAATATGTAGAATCCATAAGGAACACAAA 1172
                          ii  ii   ii i  i vi  vi   vi     vi    i    v vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_91536961_9   1173 CAAATCAGCAAGAAAAAAACAAACTACCCTATCAAAAAGTGTGTTAAGGA 1222
                            v   ii  v     i     iv    v  i?    i  v iv     
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_91536961_9   1223 CATGAATAGACACTTCCCAAAAGAAGATATA--AATGGCCAAGAA--ACA 1268
                         iv          i   i v            --         v  --   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_91536961_9   1269 TGAAAAAATCCTCAATATCACTAATTAT 1296
                               i  v     i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (120 / 86)
Gap_init rate = 0.01 (8 / 772), avg. gap size = 1.88 (15 / 8)  


2411 19.97 6.87 1.15  chr2_94890449_94892046      501  1111 (487)    L1M4_orf2#LINE/L1      263   908 (0)  

  chr2_94890449_9    501 CAATTTGGCCTTGGCATAAGAATAGATATA------AACAAACTAAGAAT 544
                           i v   ivi         i     i   ------  iii v  -    
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA-GAAT 311

  chr2_94890449_9    545 TGATAATCTACAAATAAACCTGCACATTTACAGTCAATTGATTTTATACA 594
                            v i  i v         iii       ii             vv   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_94890449_9    595 AGGTTAACAAAAGAACAGAATGGGAAAAGAATAGTCTTTTCAACAAATGG 644
                            v iv   i vv ivv      i                         
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_94890449_9    645 TGCTGGGACAACTGGATATCCACATGCAAAAAATAAATAAAGTTGGACCA 694
                                           ?            i ---  i          v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGA---ATGAAGTTGGACCC 458

  chr2_94890449_9    695 --A----ATATCTTATTTAAAAATTACCTCAAAATAAAACAGTGAACT-- 736
                         -- ---- i i v   vi        v        ii v  ?v  v  --
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_94890449_9    737 --GTAACAGCTAAACCTATAAAACCCTCAGAAGAAAACCCTGGCATAAAT 784
                         --    v       v         i  i          viv  ?i     
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_94890449_9    785 CTTTGTGAC--TGCATTTGGCAGTATTTTCTTAGCTATAACTCCAAAGG- 831
                            i     --  vi  v    i iv        v   i  v     i -
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_94890449_9    832 ---------------AAAAATGGATTCAATGGACTTCA---AAATTGAAA 863
                         ---------------      i   vv v         ---     i   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_94890449_9    864 ACTGCTGTGCCTGAGAAGACAGTATCAAGAA-GTGAAAAGGTAAGACACT 912
                            vi     i v i i    v         -        ii  vv   v
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_94890449_9    913 GACTAGAAGAAAGTATTTGAAAAGCATGTATCTGATAAGGGACTTACATA 962
                           v i i     i      v   v   i                 i--  
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG--TA 756

  chr2_94890449_9    963 TGTAGGATACATAAAGAACCTTTGCAATTCATAAATAACAAGA----TAA 1008
                          vi  i   i         ii  i   i   vv     v    ----   
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_94890449_9   1009 CCCAATTTAAAAAATGGGCAAAGATTTTGAATAGATATATTTGCAAAGAA 1058
                                ?     -         iv          i  v i v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_94890449_9   1059 GATTTAAAGATGGGTAATAAGCACATTAACAGATGCTTAATGTAATTAGT 1108
                            v  v i    vi           v  v       i  ii v ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_94890449_9   1109 CAT 1111
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.19 (64 / 54)
Gap_init rate = 0.02 (13 / 646), avg. gap size = 3.77 (49 / 13)  


1472 23.22 11.61 5.03  chr2_95168724_95170389.rev      464  1178 (488)    L1M4_orf2#LINE/L1      147   908 (0)  

  chr2_95168724_9    464 CATCTGGAAAATCCAAATATTTGGAAACTA-AATGACACCTAAATAACCA 512
                            v      - v   ------  i v i -   ii -- v   i  i v
  L1M4_orf2#LINE/    147 CATATGGAAA-TGCAA------GGGACCCAGAATAGC--CAAAACAATCT 187

  chr2_95168724_9    513 TGAGAAAGAACAAAAATAAAAAGGGGGAAATTAGCATTTTG-AACT---G 558
                            i      ---i  i   ivv  i i v i -  i  iv-  i ---i
  L1M4_orf2#LINE/    188 TGAAAAAGAA---GAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAA 233

  chr2_95168724_9    559 AACAGACTA--AAGCTACAGTCATT--TACCTTGTGGTACCAG--TGAAG 602
                            vv    --          v  i--v  vv        ii -- i i 
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_95168724_9    603 ATAGACACA--GATCAATGGAAGAAAAT--AGAATATAGAAATACACCC- 647
                                i --           v i   --   i vi       v    -
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_95168724_9    648 TCCAAATGTGGTCAGTTGAGTTTTGACAAAGATGCAAAGGAAATTTAGTG 697
                          v  vv i      i    v   i     i i   v   ivv   i i  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_95168724_9    698 AAGAAAAGATAGGAGAATAG-------GAGAAAGATAGGAGTGGTGGAAT 740
                         ii    --------      -------i v   -- i ---  v   i i
  L1M4_orf2#LINE/    384 GGGAAA--------GAATAGTCTTTTCAACAAA--TGG---TGCTGGGAC 420

  chr2_95168724_9    741 AGATGGATATCCATATGCAAAATA-TGAGCTTTGAACCATATATCACACT 789
                          iv      ?   i        v -   iv  v  v  v  iv      i
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_95168724_9    790 ATATACAAAAACTAAC-CAGTGATGTTTCACA--CCTACATTTACAACCC 836
                                    i    -  i-i   vv   ? --    v  v  vi v i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAA-AATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_95168724_9    837 AAAACTA--AAACTGCTA----AAAACCTAGACGCAA-TCTTTGTGACCT 879
                                --     vi  ----     v   i? i  -    i       
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_95168724_9    880 -----------AT--------AGCTACAATATCAAAGGCACAATCTGTAT 910
                         -----------  --------  v  ii i i    i      v vii v
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_95168724_9    911 G--------TTGATAAATTGAACTTTATCAAAATTCAGAATTTCTTCTCT 952
                         i-------- v         i    i         v i  i  i viv  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_95168724_9    953 TGAAAAGATAGT-TTGAAAAAGTCTTCCACAGACTGGGTGAGTCACACA- 1000
                          v   i  i v - ii i     --------  vvi iii vi    v -
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGT--------GAAAAGACAACCCACAGAA 711

  chr2_95168724_9   1001 TGGAAGAAAATGTTTGCCAG--ACATATCTAATAAAGGACCTGTATTCAG 1048
                            i       i     v i-- i      i    i    i     i   
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_95168724_9   1049 GATACATAAA----TCTCAAAACTCG-TAATTAGAA----AATAAC--AA 1087
                         i   i     ----   i v     i-    v i  ----      --  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_95168724_9   1088 T--AAAAATGGGCAAAATATTTG----GACACTTA-CCAAAGAAGATACA 1130
                          --             iv     ----    i  v-            i 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_95168724_9   1131 GATATGGCAAATAAGTCCATGAAAAGGTGCTTATCAGTCATTAGAGAA 1178
                         v v     v      iv         i    i v  -   ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (97 / 66)
Gap_init rate = 0.05 (40 / 762), avg. gap size = 2.98 (119 / 40)  


3199 26.86 0.44 1.31  chr2_95179869_95186229     4954  5869 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_95179869_9   4954 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCGTGAAAAT 5003
                              ii i  i     i        v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_95179869_9   5004 GGCCATGCTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5053
                            v  i  v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_95179869_9   5054 TACCAATGACTTTCTTCACAGAATTGGAAAACACT-ACTTTAAAGTGCAT 5102
                          v   iivi i  i  ii     v v  v  -i  - iii    i v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_95179869_9   5103 ATGGAGCATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAA 5152
                              i---   ----   ii--  v  v v  v     i      i i 
  L1M4_orf2#LINE/    150 ATGGAA---ATG----CAAGG--GACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_95179869_9   5153 GCCAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATAC 5202
                         ivv i          i      vv   ii  v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_95179869_9   5203 TACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGA 5252
                              i          i   i    ii         i iv ii i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_95179869_9   5253 TATAGACCAATGGAATCGAACAGAGGCCTCAGAAACAACACCACACATCT 5302
                               i         v   iv   ivii      i  vv   i    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_95179869_9   5303 ACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAG 5352
                          iiii  vi    i  i     ivv  v   i v  vvv           
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_95179869_9   5353 GATTCCCTATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAG 5402
                         i  vvi  v  i  i       i      v      v  ?   i   i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_95179869_9   5403 AA-AGTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAA 5451
                           - i    ii    i    v   i     v              i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_95179869_9   5452 GATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAA 5501
                         i      i ?    i       v   v       i      vi i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_95179869_9   5502 GAAAACCAAGGCA-ATACCATTCA-GGTCATAGGCATGGGCAAGGACTTC 5549
                               vv   ?i- v i -   i- ii v i  i- i     v ii   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTC 588

  chr2_95179869_9   5550 ATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATG 5599
                         v iiv  vi            vvi          vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_95179869_9   5600 GGATCTAATTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCA 5649
                            ii v  i   v v  i i   i  iiivv    i  v    i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_95179869_9   5650 GAGTGAACAGGCAACCTACCGAATGGGAGAAAATTTTTATAATCTACCCA 5699
                         i      v  i     i  v              v   ii  vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_95179869_9   5700 TCTGACAAAAGGCTAATATCCAGCATCTACAAAGAACTCAAACAAATTTA 5749
                              i  ii i  vi       v  v  i         vv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_95179869_9   5750 CAAGAAAAAATCAAACTACCCCATCAAAAAGTGGGCAAAGGATATGAACA 5799
                         i  v     iv    iv    v  i?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_95179869_9   5800 GACACTTTTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAA 5849
                             i  i  v        i  vi viii     i ii          i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_95179869_9   5850 TGCTCATCATCACTGGTTTT 5869
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3055 26.15 2.47 0.56  chr2_95328277_95335874     6216  7106 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_95328277_9   6216 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATAAAAAT 6265
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_95328277_9   6266 GGCCATACTGCCCAAAGTAATTTATAGATTGAATGGCATTCCCATTAAAC 6315
                            v     v      v i  i  i     v  i vv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_95328277_9   6316 TACCATCAACATTCTTTACAGAATTAGAAAAAAACT-ATTTTAAAATTCA 6364
                          v   v vi v  i   i     v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_95328277_9   6365 TATGGAACCAAAACAGAGCCCAAATAGCCAAGACAATCCTAAGCAAAAAG 6414
                                viiv  vi  v  vi         i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_95328277_9   6415 CACAAAGCTGGAAGCATCACACTACCCAACTTCAAACTATACTACTAGGC 6464
                         v      i    i vv       v     i      viv      v i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_95328277_9   6465 TGCAGTAACCAAAACAGTATGATACTGGTACAAAAACAGACACATAGACC 6514
                          i      i   i     i  i      i i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_95328277_9   6515 AATGGAACAGAATAGAGAACCCAGACATAAAGTTGCATACCTACAGCCAT 6564
                                i     v    ii     v     viiii i ii  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_95328277_9   6565 CTGAGCTTCAACAAAGTTGACAAAAATAAGCAATGGGGAAAGGACTCCCT 6614
                         i   vi   i    i v  v   i vi vv            i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_95328277_9   6615 ATTCAATAAACAGTGCTGGAATAGCCAGCAAGCCATATGCAGAAAATTGA 6664
                         v     i   ii       i i i ii vv ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_95328277_9   6665 AACTGGACCCCTACCTTTCACTATATACAAATATTAACTCAAGATGGATT 6714
                          ii             iv   i         v          i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_95328277_9   6715 AAAGATGTACATGTAAGACCTCAAAGTATAAGAATCCTAGAAGAAAACCT 6764
                          ?   iv  v        v  v   v     i v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_95328277_9   6765 AGAAG-ACACCATTCTGGACATTGGCCTCAGGAAAGAATATAT--GATTA 6811
                           i? - v i -   vv   v    vi -   v  vii v v --   - 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTT-AGGCAATGGTTTCTTAGAT-A 595

  chr2_95328277_9   6812 AGTTCTTAAAAGCAATTGTGCCAAAAGCAAAACTTGACAAGTGGGACCTA 6861
                         v vivii       vvv iiv      v    v v  i  i v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_95328277_9   6862 ATTAAACTAAAGAGCTTATGCATAGCAAAAGAGACCATCAACAGAGTAAA 6911
                           i   v v  i i   v  iiivv    i  v  i     v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_95328277_9   6912 CAGACAACCCACAGAATGGGAGAAAATATTAACAAACTATGCATCTGACA 6961
                         v                             vi    ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_95328277_9   6962 AAGGTCTAATATTTATAATCTATAAGGAACT--TA------AACAATTAA 7003
                          i  v  vi   ii v   v     i     --  ------  i   v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_95328277_9   7004 AA-----ACAACCCCATTAAAAAGTGGGCAAAAGA-----ACAGACACTT 7043
                           ----- i     v   ?    i        i  ----- i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_95328277_9   7044 CTCAAAAAAAGACATACAAGTGGCCAACAAACATATGAAAAAATGCCCAA 7093
                            v   i    i      i       i  i  i       i    i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_95328277_9   7094 CATCAGTAATCAT 7106
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (137 / 92)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.45 (27 / 11)  


3097 27.18 1.10 0.77  chr2_95339960_95346332.rev     4978  5882 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_95339960_9   4978 TGGAAGAACATTCCATGTTCATGGGCAGGAAGAATCAATATTGTGAAAAT 5027
                              ii i  i            iiv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_95339960_9   5028 GCCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5077
                          v v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_95339960_9   5078 TACCAATGACTTTTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTGCA 5125
                          v   iivi i     ii     -   -- v  i  - iii    i v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_95339960_9   5126 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5175
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_95339960_9   5176 GACAAAGATGGAGGCATCTCGCGACCTGACTTCAAACTATACTACAAGGC 5225
                         i      v      vv  v i vv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_95339960_9   5226 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5275
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_95339960_9   5276 AATGGAACAGAAC--AGAACCCTCAGAAATAATGCCACATATCTACAACT 5323
                                i    i--   ii  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_95339960_9   5324 ATCTGATCTTTGACAAACCTGACAGAAACAAGAAATGGGGAAAGGAT--T 5371
                          vi    i  i     ivv  v  ii v  vvv           i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_95339960_9   5372 CCTTATTTAATAAATGGTGCTGGAAAAACTGGCTAGTCATATGTAGAAAG 5421
                          i  -- i  i            i v      v  ?i  i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_95339960_9   5422 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5471
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_95339960_9   5472 GATTAAAGAC-TAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5520
                            i ?    -       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_95339960_9   5521 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5569
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_95339960_9   5570 TAAAACACCAA--GCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATC 5617
                           vi       --   vvi          vv   i v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_95339960_9   5618 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5667
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_95339960_9   5668 AACAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5717
                           v  i     i i               v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_95339960_9   5718 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5767
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_95339960_9   5768 AAAAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAGCAGACAC 5817
                             i     i     v  i? v  i     i      v   ii     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_95339960_9   5818 TTCTCAAAAGGAAACATTTACACAGCCAAAAGACACATGAAAAAATGCTC 5867
                              v    i i i  vi v ii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_95339960_9   5868 ATCATCTCTGGCCAT 5882
                          v    v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


1052 31.10 3.51 3.67  chr2_95790341_95791959.rev      501  1127 (492)    L1M4_orf2#LINE/L1      283   908 (0)  

  chr2_95790341_9    501 GATAGAGAAATTATCCAGTGGAA-AGGATCACAGAACCCAGAAATAGATC 549
                               v v  vivi  i     -  i  ii-   ii         i i 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTG-AGAGTCCAGAAATAAACC 331

  chr2_95790341_9    550 CATATATGTATGAACACCACTTCATAT-AAACACAACTGACAGTGCAGGT 598
                             i  v    i---i  v  v  v -vi   viiv  v  ivi viv 
  L1M4_orf2#LINE/    332 CATACATTTATGG---TCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_95790341_9    599 CAACAAGGAAAGAACAGACTATTCAACAAATCTCCCTGCAACAACTATTT 648
                            iii        i  v  v          vviv   vi      ivv 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_95790341_9    649 AACCATA--CAAACCAACTAAATTGGAATTCTACTTCACAGCATACACAA 696
                          ?   i --    vv  iv  i     vii    i     v    i    
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_95790341_9    697 AA-TCAATTCTAGGTGGCTTAATAACTTAAATATGTAGGGTAAAATT-TA 744
                           - i  i  v ii   v i ?vi  i     i ivii v     i -  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_95790341_9    745 AAACT-TTAGAAGACAATATGAGGGAATATCTT--TGACTTTAAGATAGG 791
                              -        v  i  ii ? v v     --    i  ii v    
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_95790341_9    792 AAATACTTTTGCTTTAAAACACAATATAAAAAATAAAACTCATAAA-GAA 840
                         v   iv   --   -- i i ii i iv    ii v  viv i   -   
  L1M4_orf2#LINE/    579 CAATGGTTT--CTT--AGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_95790341_9    841 AAGATTGTTAACTTTGACTATGTTGAAATCAAGAATGTGGGTTCATCAAA 890
                           i  v v   v  v    vii ii    i  i  iv vv  v v     
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_95790341_9    891 ATACACTAT--AAAAATCGAAAAGACTAGGCACAATCTGGGAGAAAATAT 938
                         iv       -- i   vi        v vv    ivv             
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_95790341_9    939 TTGTGACACATATA----ATCAACCACAGGTTTTCAGGACA------GAA 978
                            ii vv      ----  v ivv  vv  v i   i i ------   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_95790341_9    979 TTTCTGCAAATCAGTAAGGAAAAGGCAAACAGCTTAACAACAACAACAAC 1028
                         i ii i   v   i   vi     i    i i ii  i------------
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT------------ 812

  chr2_95790341_9   1029 AGAAAAAAAAGTCAAAAAAATCATGAATAATCATTTTACAGAAGAGGAAA 1078
                         -v?     vi v    ii v --      iv     iv vi    i  v 
  L1M4_orf2#LINE/    813 -TWAAAAATGGGCAAAGGATT--TGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_95790341_9   1079 CACAAGTTTCCAATAAACATACAAAAATCCTTTCAACCTCACCAGTAAT 1127
                         i    i vv       i  i ii    vvivi     v   ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (107 / 84)
Gap_init rate = 0.03 (17 / 626), avg. gap size = 2.65 (45 / 17)  


2083 25.54 3.93 1.61  chr2_95833831_95838853      974  1533 (3490)    L1M4_orf2#LINE/L1        1   573 (335)  

  chr2_95833831_9    974 TGGAATGACATTCCAGGATCATGGATTGAAAGAATCAGTATTGTTAAAAT 1023
                              v  i  i   v v          i    v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_95833831_9   1024 GTCCATAATATTCAAAGCAACCTATAGATTCAATGCAATCCCTATCAAAA 1073
                          v v   v vii    vii i   i        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_95833831_9   1074 TACCAATGACATTGTTCACATAAATAGAAAAAA-AATCCTAAAATTTATA 1122
                          v   iivi v  v  ii  v    v  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_95833831_9   1123 TGGAACCCCAAAAGACCCAGTATAGCCAAAGCTATCCTAAGCCAAAAGAA 1172
                              viv   ii       v         i v   i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_95833831_9   1173 CAAAACTGGAGGAATCACATTACTTGACTTCAAATTATACTACAGAGCTA 1222
                             ii       v     i v iii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_95833831_9   1223 TAGTAACTAAAGCAGCATGGTACTGGCATAATGATGGACACATAGACCCA 1272
                         i     ii  ii   ii              v   i    i     i - 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC-A 299

  chr2_95833831_9   1273 GTGGAACAGAATAGAGAACCTAGAAACAAATCCACACACCTACAGTGAAC 1322
                         i     i     v    ii i     i   i   i   ii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_95833831_9   1323 TCATTTTCAACAAAGGTGCCAAGAACACACACTGGGGAAAAGATAGTCTC 1372
                          v      i    i          v  iv  v        ii       i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_95833831_9   1373 TTCAGTATATGGTGCTGAGAAAACTAGATTTCCATATGCAGAAGAATGAA 1422
                             ii v         i  v    i   v?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_95833831_9   1423 ACTAAATCCTAGACTTCTGTATCTTGCCATATGTAAAA-TCAAATCAAAA 1471
                         ii ii i  -------  iiv  vii      ii    - i  v      
  L1M4_orf2#LINE/    450 GTTGGACCC-------CTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_95833831_9   1472 GTG---------------TTTAAAGGCT-----TATGAAATTACTATAAG 1501
                         -  --------------- v   ii   -----   i   i vi  v   
  L1M4_orf2#LINE/    493 -TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_95833831_9   1502 GAATCATTGGGGAAAATCTCCAGGACATTGGG 1533
                         i  v   v  ? v      i iv   v     
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

Transitions / transversions = 1.94 (93 / 48)
Gap_init rate = 0.01 (7 / 573), avg. gap size = 4.43 (31 / 7)  

1087 23.26 1.21 1.51  chr2_95833831_95838853     1891  2221 (2802)    L1M4_orf2#LINE/L1      579   908 (0)  

  chr2_95833831_9   1891 CAAAAATTTATTTAGCAAT-ACCCCACAAACAGAGGCAGCCAAAGCAAAA 1939
                            vii   -i    vv  -  v   v  i  v i   i v    v    
  L1M4_orf2#LINE/    579 CAATGGTTT-CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_95833831_9   1940 TTGGACTAATGGTAGCACATCAAG-TTAAAAAGTTTC-TACATAGCAAAG 1987
                         v i  iv   v v viv      i-       v   i- i v --     
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAG 675

  chr2_95833831_9   1988 GAAACAATCAACAAACTGAAGAGACAGCCCACCAAATGGTGGAAAATATT 2037
                           v  v     v   v    i     i     vi     vi         
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_95833831_9   2038 TGCAAACTACCCATCTGACAAGAAACTAATAACCAGAATATATGAGTAGC 2087
                               ii ivi      i   ii   vi  v           i iv i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_95833831_9   2088 TAA-ACGACTCTATAAGGAAAAAAATATAATAATCCTATCAAAAACTGGG 2136
                          vv-  i    v    v-     i i -     i  v  i?    v    
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAAT-AAAAAGACA-AATAACCCAATTWAAAAATGGG 823

  chr2_95833831_9   2137 CAAAAGATTTGAATGGACATTTCTCTGAAGAAGACATACAAATGGCAAAC 2186
                             i         i          ii       i           v  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_95833831_9   2187 AGGCATATAAAAAGGTGCTCAACGTCATTGATCAT 2221
                          i   i  i     i        i   ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (43 / 33)
Gap_init rate = 0.02 (8 / 330), avg. gap size = 1.12 (9 / 8)  

1987 27.39 2.11 3.65  chr2_95833831_95838853     3282  3993 (1030)    L1M4_orf2#LINE/L1        1   701 (207)  

  chr2_95833831_9   3282 TGGACAGATACTCCTTGTTCATGCACAGGAAGACTCA-TATTGTCAAGAT 3330
                             v     ii  v        v iv        i -      i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_95833831_9   3331 GTCAGTTCTTCC-AATTTCATCTATGCATCAAATATAATCCCAATCAAAA 3379
                          v  i v  i  -  v  v     iiv  iv  iii      v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_95833831_9   3380 TCTTAGCAAGGTATTTTCTG--GATATTGA-AAACTAACTTTAAAGTTTA 3426
                           ii   --v iv    i  --  v     -  i  i iii    i  i 
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_95833831_9   3427 TTCAAAGAGGCAGAAGAGCCACAATAGTCAACACCATATTGAAGGAGAAG 3476
                          viii i v   iii  v   v     i   v  v  v     ii     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_95833831_9   3477 AACAAAGTTGGAGGGCTGATGCTACCTGGCTTCAAGACTTGCTATAAAAC 3526
                                       i  v ii  v  iiii     i    i   i   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_95833831_9   3527 GATCATAATCATGACAGTGTGG-ATTGGTGAAAGAATAGACAAGTAGATA 3575
                         v ivi      v          - i   iiv   i       vi     v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_95833831_9   3576 AATGGAACAGA-----GAGCCTAGAAATAGATCCCCATAAAAT-ACAGTC 3619
                                i   -----   i i       i --      v v - ii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACATTTATGGTC 346

  chr2_95833831_9   3620 AGCTCATCTTTGTGAAAGGATCAAAGGCAAAACTGTAGAGCAAAATCAAT 3669
                          ii v  i  i vv  i  vv v   i v vv vi i i v  i vi i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_95833831_9   3670 CTTTTCAACAAAAGGTGCTGGAACAAATAGACATAGACACACAAACGCAA 3719
                                     v        i    v i  --  ?v    i----    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGA--TAKCCACAT----GCAA 440

  chr2_95833831_9   3720 AAAAAAAATAGAAGAAGAAGAATCTAGACA-AACACCATATACCCCTCAT 3768
                           i  --- ----    vv i i ivv  v-v           -------
  L1M4_orf2#LINE/    441 AAGAA---T----GAAGTTGGACCCCTACCTCACACCATATAC------- 476

  chr2_95833831_9   3769 AGAAATTTACTCAAAATGGATTAAAAACCTAAATGCAAAATGC-AAAACT 3817
                          i     v             i ? i         i  i -  -      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACT 525

  chr2_95833831_9   3818 ATAAAAGTTCTACAAGATAACATAGGAGAAAATCTAGATTATCATGGGAC 3867
                               v ii  v    v        ? v      vvi v i v    vi
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_95833831_9   3868 AG-TGATGACTTTTAAAATACATCATCAACGGTGCAATTCATGAATGAAA 3916
                           -ii   ii  i v i   iiv  i   vi ii   viv ii  v    
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_95833831_9   3917 ATATTTGATAAGCTGGACTTCATTAAAGTTAAAGACTTCTGCTCTGTGGA 3966
                          v  v-     ii          i   i     i    i  iv  viii 
  L1M4_orf2#LINE/    626 AAATA-GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_95833831_9   3967 ACACACTTCCAAGAGAATAAGAAGACA 3993
                         iv     vi     i i i i      
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACA 701

Transitions / transversions = 1.59 (118 / 74)
Gap_init rate = 0.03 (19 / 701), avg. gap size = 2.16 (41 / 19)  

 781 16.05 0.62 0.00  chr2_95833831_95838853     4370  4531 (492)    L1M4_orf2#LINE/L1      746   908 (0)  

  chr2_95833831_9   4370 AAGGACTGTTATCTAAAATGTATAAAGAACTCTTTAAACTCAACAATAAG 4419
                          i     vv    i i   i              vv       i     i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_95833831_9   4420 CAAATGAATAACCCAATT-AAAAATGGGCAAAAGACCAGAATAGACAACT 4468
                         v i ii            -             i  iiv         vi 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_95833831_9   4469 CACCAATGAAGACATACAAATGGCAAAGAAGCATATGAAAAGATGCTCAA 4518
                          v    v     i           v  v     i                
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_95833831_9   4519 CATCATATGCTAT 4531
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (15 / 11)
Gap_init rate = 0.01 (1 / 163), avg. gap size = 1.00 (1 / 1)  


 242 22.00 0.00 0.00  chr2_95865601_95871988        1    50 (6338)  C L1M4_orf2#LINE/L1   (29)   879   830  

C chr2_95865601_9     50 ATATGAGGAAATAGTTCTCCAAAAAAGATACACAGATGGTCAATGAGCAC 1
                           v   iv i i v         i      i   i    i    i     
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.00 (0 / 0)  

 258 30.48 15.67 1.71  chr2_95865601_95871988       76   426 (5962)  C L1M4_orf2#LINE/L1   (0)   908   509  

C chr2_95865601_9    426 ATG-AATAGCCAGA-TTATAACA-TGTTAGAAAACAAAACACACAGGGGA 380
                            -  v   i i -i     v - v      i --     i -i ? v 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA--AAACATA-GGNGTA 555

C chr2_95865601_9    379 ACTTACCAAAA----GGAGTAG--AA-GATTTCTTAGACAAAATTTCAAA 337
                          v ivi ivi ----  iv   --  - i         i vi ivi    
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

C chr2_95865601_9    336 -GCAGAAACCATAAGGCAGAAAAAGTGGAGG----GGATTTCAT-GATGT 293
                         -   v  i v i  i--       i i  vi----   i     -i vi 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAA--AGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

C chr2_95865601_9    292 TACAA-----------TCAAATAGAT-CTGTT--GCAAGTGACA---CA- 261
                           v  -----------     -i  i-  i i-- v      v ---  -
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAAAGACAA 702

C chr2_95865601_9    260 -TGGCAAAATGAGAGAAGTTATGTGCAG-TC-TAAAACTGACAAGAGATT 214
                         -ivi  i    i     iv   v    i-  -  v v    i   i  i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

C chr2_95865601_9    213 AGTGGCCTCAATATACGAGGAGCTC------CTGAAAATTAACAAGAAAA 170
                         v  iv  vv      ii i  i   ------  v  v v   v    v  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

C chr2_95865601_9    169 ATAA------------ATAGACAAAGGACACGAGCAGGCAGTTTTTGGGA 132
                             ------------  i i       ivi  ii  i  v  i ivii 
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

C chr2_95865601_9    131 GAGGAAACCCCAAAAGCCAGGAAGCATATGAGGAAGTGGCTAAGATCATT 82
                           i  v iv v  vi    iv     i    ii ii  vii  v    ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

C chr2_95865601_9     81 AGTACA 76
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.59 (65 / 41)
Gap_init rate = 0.06 (22 / 400), avg. gap size = 2.77 (61 / 22)  

3245 26.93 0.66 0.44  chr2_95865601_95871988     4991  5896 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_95865601_9   4991 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5040
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_95865601_9   5041 GGCCATAATGCCCAAGGTAATTTATAGATTCAATGCCCTCCCCATCAAGC 5090
                            v   v v     iv i  i  i        i  vv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_95865601_9   5091 TACCAATGACTTTCTTCACAGGA-TTGGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii   i -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_95865601_9   5139 TATGGAACCAAAAAAGAGCCCACACAGCCAAGACAATCCTAAGCAAAAAG 5188
                                viiv  ii  v  viv i      i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_95865601_9   5189 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5238
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_95865601_9   5239 TACAGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGACACATAGACC 5288
                                 i   i    ii     v   i iv ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_95865601_9   5289 AATGGAACAGAATGGAGGCCTCAGAAATAA--CCACACATCTAAAACCAT 5336
                                i     v   ivii         --   i    i  viii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_95865601_9   5337 CTGATCTTTGACAAACTTGACAAATACAAGAAATGAGGAAAGGATTCCCT 5386
                         i    i  i     ivv  v   ivv  vvv    i      i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_95865601_9   5387 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5436
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_95865601_9   5437 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAGT 5486
                          ii    i    v   i     v                   i     vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_95865601_9   5487 GAAGACTTAAATGTAAGACCTAAAACCATTAAAACCCT-AGAAGAATACC 5535
                         i?    i           v       i  -     i  -       v  v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chr2_95865601_9   5536 TAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5584
                             ?i- v   -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_95865601_9   5585 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5634
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_95865601_9   5635 TTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGAAC 5684
                          i   v v  i i   i  ii vv    iv v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_95865601_9   5685 AGGCAACCTACAAAATGAGAAAAAATTTTTACAATCTACCCATCTGACAA 5734
                           i     i   i    i  i     v   i   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_95865601_9   5735 AGGGCTGATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAG 5784
                         i  i  vi          v  i        ivv    v iv i  v   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_95865601_9   5785 AAACGAACAACCCCACCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 5834
                          i  i  i     v ii?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_95865601_9   5835 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5884
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_95865601_9   5885 ATCACTGGTCAT 5896
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (148 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


1792 23.82 3.43 2.12  chr2_95953066_95954662      495  1107 (490)    L1M4_orf2#LINE/L1      288   908 (0)  

  chr2_95953066_9    495 ACCTGCAAATTAATAAAATTCAACAGACAGTCCAGAAATAGATAACACAT 544
                           v ii i  i   ii   vv  iv  v            ---   v   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA---AACCCAT 334

  chr2_95953066_9    545 AAGCAACCA-GCTTA--TGACT---GACAAAGGCAGGATGGCAATGCAGT 588
                          --  vii - v i --   i ---     i  iivv v i v  v  i 
  L1M4_orf2#LINE/    335 A--CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_95953066_9    589 GGAGAAAGGATAGCCTTTTCAACATGTGGTGTTGGAACAATTGGCTGTCC 638
                           i     i    i          vi     i   i    i   v i?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_95953066_9    639 ATATCCAAAA-AGTGAACTTGAATCCATACCTCACCTCACTCCATAGACA 687
                          i  v     - i    v   i i  v        ---  --    v   
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC---AC--CATATACA 477

  chr2_95953066_9    688 AAAGGAAACTCAAAATGGAGCACAGATTTAAATGGAAGATCCAAATCTAT 737
                            ivv             v  ?   ii      v    v i   v    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_95953066_9    738 AAAATTTCTAGAACAAA-CACAGGAA-AAATCTTTGTGACCTTGTGCTAG 785
                             i ii     v   -  i   ?i-       i         v i   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_95953066_9    786 GCAAACATTT-TTACATATGACACAAAATGCAAAATCTGTAAT-TCAACA 833
                             vvi   -   v         v   v   v  v vii  v-vv  v 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_95953066_9    834 AT---TAAATTGGATTTCATTACGATTAAAATCTTCTGCTCTTCAAAAGA 880
                           ---         i     i vi       v   i  iv       i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_95953066_9    881 TACTACAAAGCAAGTGAAAAGTCAACCCAAAAACTGGCA-AAAATACCCT 929
                         i    iv   v          v       v i v   v -      i-- 
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT--T 725

  chr2_95953066_9    930 TGTAAAAAA-GTAGCTAA-AAGTAA-TAGTATCCA-AATACATACAGAAT 975
                           i   vv -i  v  i -   vi - v       -    i   v    i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_95953066_9    976 TATTAAAATTCAACACGTAAGAAAACAT-CAACCTACTTTTTTA-TATGC 1023
                          v   v  i    i -i   i  i   v-i    i v  ?vvv - iv  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_95953066_9   1024 AGAAGATGTGAAAAGACAGTTCAACAAAGAAGATGTACAGATGGCAAATA 1073
                          i i   v    v     v   vv          i    i     v    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_95953066_9   1074 AACACATGGAAAGATGCTCAACATTTTAGTCATT 1107
                          i      i               iv????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.06 (73 / 69)
Gap_init rate = 0.04 (22 / 621), avg. gap size = 1.55 (34 / 22)  


3235 26.98 0.44 0.44  chr2_95956652_95963063     5013  5920 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_95956652_9   5013 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAGTATGGTTAAAAT 5062
                               i i  i     i      i v      v i i   v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_95956652_9   5063 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCACCATCAAGC 5112
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_95956652_9   5113 TCCCAAAGACTTTCTTCACTGAA-TTGGAAAAAACTGCT-TTAAAGTTCA 5160
                              ivvi i  i  ii v   -   -- v  i   v -i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_95956652_9   5161 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTTAGCCAAAAG 5210
                                viiv  ii  v  v v  vi    iv     i v ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_95956652_9   5211 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5260
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_95956652_9   5261 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5310
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_95956652_9   5311 AATGGAACAGAAT--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5358
                                i     --    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_95956652_9   5359 ATCTGATCTTTGACAACCCTGAGAAAAACAAGCAACGGGGAAAGGATTCC 5408
                          vi    i  i     vvv  vv  i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_95956652_9   5409 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5458
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_95956652_9   5459 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5508
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_95956652_9   5509 TTAAAGGCTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5558
                          i ?  i i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_95956652_9   5559 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5608
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_95956652_9   5609 AACACCAACAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATCTAA 5658
                         i       v    vvi          vv     v  i i  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_95956652_9   5659 TTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5708
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_95956652_9   5709 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACGA 5758
                           i     i   i             v       vii ivi      ii 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_95956652_9   5759 AGGACTAATATCCAGAATCTACAATGAACCCAAACAAATTTACAAGAAAA 5808
                         i     vi          v  i  v    i vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_95956652_9   5809 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATCAACAGACACTTC 5858
                          i     i     v  i?    i            v v  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_95956652_9   5859 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAACAATGCTCACC 5908
                           v        i  vi viii     v  i         vi       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_95956652_9   5909 ATCACTAGCCAT 5920
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (138 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3080 26.90 0.88 0.77  chr2_96062221_96064162      544  1450 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_96062221_9    544 TGGAAGAACATTCCATTCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 593
                              ii i  i    vi      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_96062221_9    594 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCC-AGCAACC 642
                            v     v     iv i  i  i        i  v     - v   vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_96062221_9    643 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 690
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_96062221_9    691 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 740
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_96062221_9    741 AATAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 790
                           i    i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_96062221_9    791 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 840
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_96062221_9    841 AATGGAACAGAAC--AGAGCCATCAGAAATAATGCTGCATGTCTACAA-C 887
                                i    i--    i --         vv iii ii i  iii- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTC 346

  chr2_96062221_9    888 TATCGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 937
                         v  i   i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_96062221_9    938 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 987
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_96062221_9    988 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 1037
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_96062221_9   1038 TTAAAGACTTACACGTTAGACCTAAAACCATAAAAACCCTAAAAGAAAAC 1087
                          i ?    i  v i  v   v       i      vi i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_96062221_9   1088 CTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTA 1136
                         v    ?i- v i -   iv   viv  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_96062221_9   1137 AAACACCAAAAGCAACGGCAACAAAAGCCAAA-TATGACACATGGGATCT 1185
                         vi            vvi          vv   -  -  i v  v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTT 644

  chr2_96062221_9   1186 AATTAAACGAAAGAGCTTCTGCCCATCAAAAGAAACTACCATCAGAGTGA 1235
                         v  i   vvv  i i   i  iv v     i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_96062221_9   1236 ACAGGCAACCTACAGAATGAGAGAAAATTTTTGCAACTTACTCATCTGAC 1285
                          v  i     i        i        v       v i ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_96062221_9   1286 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1335
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_96062221_9   1336 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 1385
                            i     i     v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_96062221_9   1386 TCTCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAAAATGCTC 1435
                             v        i  vi viii     v  i-          i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTC 893

  chr2_96062221_9   1436 ATCATCACTGGCCAT 1450
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


 242 22.00 0.00 0.00  chr2_96127837_96134224.rev        1    50 (6338)  C L1M4_orf2#LINE/L1   (29)   879   830  

C chr2_96127837_9     50 ATATGAGGAAATAGTTCTCCAAAAAAGATACACAGATGGTCAATGAGCAC 1
                           v   iv i i v         i      i   i    i    i     
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.00 (0 / 0)  

 270 30.20 15.67 1.71  chr2_96127837_96134224.rev       76   426 (5962)  C L1M4_orf2#LINE/L1   (0)   908   509  

C chr2_96127837_9    426 ATG-AATAGCCAGA-TTATAACA-TGTTAGAAAACAAAACACACAGGGGA 380
                            -  v   i i -i     v - v      i --     i -i ? v 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA--AAACATA-GGNGTA 555

C chr2_96127837_9    379 ACTTACCAAAA----GGAGTAG--AA-GATTTCTTAGACAAAATTTCAAA 337
                          v ivi ivi ----  iv   --  - i         i vi ivi    
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

C chr2_96127837_9    336 -GCAGAAACCATAAGGCAGAAAAAGTGGAGG----GGATTTCAT-GATGT 293
                         -   v  i v i  i--       i i  vi----   i     -i vi 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAA--AGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

C chr2_96127837_9    292 TACAA-----------TCAAATAGAT-CTGTT--GCAAGTGACA---CA- 261
                           v  -----------     -i  i-  i i-- v      v ---  -
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAAAGACAA 702

C chr2_96127837_9    260 -TGGCAAAATGAGAGAAGTTATGTGCAG-TC-TAAAACTGACAAGAGATT 214
                         -ivi  i    i     iv   v    i-  -  v v    i   i  i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

C chr2_96127837_9    213 AGTGGCCTCAATATACGAGGAACTC------CTGAAAATTAACAAGAAAA 170
                         v  iv  vv      ii i      ------  v  v v   v    v  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

C chr2_96127837_9    169 ATAA------------ATAGACAAAGGACACGAGCAGGCAGTTTTTGGGA 132
                             ------------  i i       ivi  ii  i  v  i ivii 
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

C chr2_96127837_9    131 GAGGAAACCCCAAAAGCCAGGAAGCATATGAGGAAGTGGCTAAGATCATT 82
                           i  v iv v  vi    iv     i    ii ii  vii  v    ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

C chr2_96127837_9     81 AGTACA 76
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.56 (64 / 41)
Gap_init rate = 0.06 (22 / 400), avg. gap size = 2.77 (61 / 22)  

3245 26.93 0.66 0.44  chr2_96127837_96134224.rev     4991  5896 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_96127837_9   4991 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5040
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_96127837_9   5041 GGCCATAATGCCCAAGGTAATTTATAGATTCAATGCCCTCCCCATCAAGC 5090
                            v   v v     iv i  i  i        i  vv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_96127837_9   5091 TACCAATGACTTTCTTCACAGGA-TTGGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii   i -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_96127837_9   5139 TATGGAACCAAAAAAGAGCCCACACAGCCAAGACAATCCTAAGCAAAAAG 5188
                                viiv  ii  v  viv i      i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_96127837_9   5189 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5238
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_96127837_9   5239 TACAGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGACACATAGACC 5288
                                 i   i    ii     v   i iv ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_96127837_9   5289 AATGGAACAGAATGGAGGCCTCAGAAATAA--CCACACATCTAAAACCAT 5336
                                i     v   ivii         --   i    i  viii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_96127837_9   5337 CTGATCTTTGACAAACTTGACAAATACAAGAAATGAGGAAAGGATTCCCT 5386
                         i    i  i     ivv  v   ivv  vvv    i      i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_96127837_9   5387 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5436
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_96127837_9   5437 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAGT 5486
                          ii    i    v   i     v                   i     vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_96127837_9   5487 GAAGACTTAAATGTAAGACCTAAAACCATTAAAACCCT-AGAAGAATACC 5535
                         i?    i           v       i  -     i  -       v  v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chr2_96127837_9   5536 TAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5584
                             ?i- v   -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_96127837_9   5585 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5634
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_96127837_9   5635 TTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGAAC 5684
                          i   v v  i i   i  ii vv    iv v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_96127837_9   5685 AGGCAACCTACAAAATGAGAAAAAATTTTTACAATCTACCCATCTGACAA 5734
                           i     i   i    i  i     v   i   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_96127837_9   5735 AGGGCTGATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAG 5784
                         i  i  vi          v  i        ivv    v iv i  v   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_96127837_9   5785 AAACGAACAACCCCACCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 5834
                          i  i  i     v ii?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_96127837_9   5835 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5884
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_96127837_9   5885 ATCACTGGTCAT 5896
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (148 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


4463 13.82 4.24 5.44  chr2_96173574_96175622      646  1564 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_96173574_9    646 TGAAAAGATACCCTGTGTTAATCAATTAGAAGACTTAATATTATGAAGAT 695
                           i       i  ii    v  vi   i              i v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_96173574_9    696 GAAAATACTCCCCAAATTGATCTACAAACTTAATGTAATCCCTATCAAAA 745
                          iv                       i i i  i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_96173574_9    746 TTC-ATCCAGCTTCTCCCAAAAAAATGACAAGCTGATCACAAAATTCATA 794
                          i - v iiv   i iivv i   v             vi          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_96173574_9    795 CAGAAATCTAAGGAACCCAGAGTAGACAAAACAATATTGAA---GAAAAT 841
                         ii     vi    i       i   v         v     ---   i v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_96173574_9    842 CAAAGTTGGAGGA-------TTTCCAATTTTAAAATTTACTACTGCTAAC 884
                                      -------  i       i    i       v---  v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA---AAG 247

  chr2_96173574_9    885 CTACATTGATTAAGAC--TGTGGCACTGACATAAGGATACACATTCCAAT 932
                              v i  i     --     i    i          v    vivi  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_96173574_9    933 CAATGGAACAGAATTGAGAATCCAGGAATCAACTCTTGTATTTATGGTCA 982
                                 i          i     i   v   i v ii           
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_96173574_9    983 AATTGATTTTCAGCAAAGGTGCCAAGACAGTTCAATGAAGGGAAGACTAG 1032
                          -         ii   i           vi       i-  i    v   
  L1M4_orf2#LINE/    348 A-TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAG 395

  chr2_96173574_9   1033 TCTTTTCAAGAAATGGTA-TGGGGCCACTGGATAGCCACATGCAAAAGAA 1081
                                  v       i-    i v        ?               
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_96173574_9   1082 TGAATTTGGTTCCCTGCCTCACACCATATATAAAA-----CTCAAAATGA 1126
                             v    vi    i              i    -----         i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_96173574_9   1127 ATCACAGATTTAAATGTAAGAGCTAAAACTATAAAACTCTTACAAGAAAG 1176
                             ?   ii                                v      i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_96173574_9   1177 CATAAATGTAAATCTTCATGATATTAGATTAGGCAATGGTTTCTTAACTA 1226
                             ii?          i   iv  i i                  iv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_96173574_9   1227 TGACATTAAAAGCACAAACAACCAAA---AAATTAGATGAATTGGACTTC 1273
                              ii          i    v   ---   v     i           
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_96173574_9   1274 A---AAATTAAAA-CTTTTGTGCTTCAAAGGA------------AGTGAA 1307
                          ---         -                  ------------      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_96173574_9   1308 ATGACAACCCACTGTATGCGAGAAAATATTTGCAAATCGTATATCTGATA 1357
                          v          v v   v                   i           
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_96173574_9   1358 AGGGACAGATATGTAAGATCTGGGACTTATCAGATAAGGGACAGATCTGA 1407
                               --------------------  i --------------   i--
  L1M4_orf2#LINE/    746 AGGGAC--------------------TTGT--------------ATCC-- 759

  chr2_96173574_9   1408 TAAGGGACTAGAATAGATAAAGAACTCTTCCAACTCAATAATGAAAAGAC 1457
                         ---------      v             v            i       
  L1M4_orf2#LINE/    760 ---------AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_96173574_9   1458 AAATGGTCCAATTTAAAAATGGGCAAAGTATCTGAAAAGACATTTCTCCA 1507
                             iii      ?              v  i    v             
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_96173574_9   1508 AAGAAGATATACAAATGGCCAGTAAGCACATAAAAAGATGTTAGAC-TTA 1556
                                              i         i        i vi  - i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_96173574_9   1557 ATTAGTCA 1564
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.93 (81 / 42)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 5.24 (89 / 17)  


3403 14.78 0.47 2.20  chr2_96181242_96182869      501  1136 (492)    L1M4_orf2#LINE/L1      284   908 (0)  

  chr2_96181242_9    501 ATAGACATATAGACTAGTGGAGTAGAATTGAGAGTCCAGAAATAAACCCA 550
                                      ii i    i                            
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_96181242_9    551 ATATGTCTATAGTCCATTGATTTTCAACAAGAGCAGCCCGAACATTCAAT 600
                         -  ii i   i   v          i     i iiv vv  v        
  L1M4_orf2#LINE/    334 -TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_96181242_9    601 GAGAAAAGAATAGTCTTTTTGATAAATGGTACTGGGAAAACTGGATATCC 650
                          i i               ii i       i      v         ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_96181242_9    651 ACATGCTAAATAATGAAAATGAAGCCCAACTTCACACCATCTATAAGAAT 700
                               v   v      iv  i v   v  i         v  i  i   
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_96181242_9    701 TAACTCAAAATGGATCAGAGATCTTACATTTAGTAAGTGCTTAAACTATA 750
                                          ?   i  - v  ---     v   v        
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCT-AAAT---GTAAGAGCTAAAACTATA 528

  chr2_96181242_9    751 AAACCCTTGGAAGAAAATATAGGGGTAAATATTCATGACCTTGGATTTGG 800
                             i   i        i     ?      v   i         i  v  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_96181242_9    801 TGATGAATTCTCAGCTATGACACCAAAAGTGTAAGCAACAAAAGAAAAAA 850
                         ii   iv    i  v              iii                  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_96181242_9    851 TAGGTAA-TTAGAATTCATCATAACTAAAAACTT--GTTCCTCAAAGAAT 897
                            i   -  i  v       v  i         --  v i      i i
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_96181242_9    898 ACCATCAAGAAAGTCAAAAGACAACCTACAGAATGGGAGAAAGTATTTGA 947
                           i           v           i               i      v
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_96181242_9    948 AAATCAAATACTTACACACCTGATAAGGATCTAGTATCCAGAATACATAA 997
                               v   i--------         iv  v            i    
  L1M4_orf2#LINE/    729 AAATCATATAT--------CTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_96181242_9    998 AGAACTCTTTCAACTCAATAACAAAAAGACAAAGAACCCAACTGAAAAAC 1047
                                  v           i           v       i ?     -
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA- 819

  chr2_96181242_9   1048 TGGGCAAAGGACCTGAATAGGCATTTCTCCAAAGACAATATATGAATGGC 1097
                                    ii       i              vi     ii      
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_96181242_9   1098 CAAACAGCACATGAAAAGATGTTTAACATCACTGTTTGT 1136
                            vv                i i       ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (58 / 32)
Gap_init rate = 0.01 (7 / 625), avg. gap size = 2.43 (17 / 7)  


 632 31.63 11.70 3.66  chr2_96214616_96217718.rev     1310  1856 (1247)    L1M4_orf2#LINE/L1      124   714 (194)  

  chr2_96214616_9   1310 ATTGACAGGGTGATTATAAAGTTTTTATATGAGAATATGAAAGGTCAATA 1359
                                i v    iv    i  i--     ii   iii ii ii v v 
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTC--ATATGGAAATGCAAGGGACCCAGA 171

  chr2_96214616_9   1360 ATAGCCAAGACATCCCTGAAG--GAAAAACTAAA----AAGACTTGTCCT 1403
                                 i   vi i    i--   i   v  i---- i    iiiv  
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_96214616_9   1404 AGCAGATGTTAGTCATCTAGTTCATGAAACGTCTTTACATAAAT------ 1447
                         vv vi  v i i-v ii  v v  --  i -----    vv   ------
  L1M4_orf2#LINE/    222 TCCCAATTTCAA-AACTTACTACA--AAGC-----TACAGTAATCAAGAC 263

  chr2_96214616_9   1448 -GCATAGCACTGGAGCAAGGCTAGACA-ATTGCCCGCTGGAACAGAATCA 1495
                         - ii i i     vii    v      -  v vi iv     i     ii
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_96214616_9   1496 AA--TTTAGAAACAGATTC---CATTCAGAAGCA---GAGCCTTGATGAA 1537
                          i-- ii     i i ii ---    i viiv  ---  vii i  ii i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_96214616_9   1538 GG-GCCATTGATGGTCACT--ATGG---AAGGACAGTTAAGTTACTTAGT 1581
                           -    --- - ii  i --    ---   i i   ivvv i viv i 
  L1M4_orf2#LINE/    364 GGTGCCA---A-GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_96214616_9   1582 TGTCTTAGAGCCATTTAGCATCTA--TTTAAAA------------ATCCC 1617
                         v  vi i ii v i viii ? i -- vi    ------------ i   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_96214616_9   1618 TAACTCATATCATGCGCAAA---TAACTCTGGATGCATGAAAGAC--ACA 1662
                           v    i i   iii    ---      vii   v  v ?    -- v 
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_96214616_9   1663 TGTAATA---AAAACTTTAACATGTTTAGAAAAAAA-ATATATAGTAAGA 1708
                              v ---      v   v ivi      i    -   vi?-    i-
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN-GTAAA- 557

  chr2_96214616_9   1709 TCTCTTCATGACCTTGGGATAGGGAAGGATCACTTAAATGAGATAC---- 1754
                         --     i          v    v  v i iv    i  iv  i  ----
  L1M4_orf2#LINE/    558 --TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_96214616_9   1755 AGCACTAATTGTAAAACTAGAAAGATTCATAAATTCAACTACATTAA--T 1802
                              v iivii    --ii   i  vv       vi   v   i  -- 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAA--GAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_96214616_9   1803 TATAA--CTTTGT---CCAAAGG-CACCAAAAAGAAAGTGAAAATACAGG 1846
                           v  --i     ---i      -   i vv             v   iv
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_96214616_9   1847 TTACA-AATAG 1856
                         ii   -   i 
  L1M4_orf2#LINE/    704 CCACAGAATGG 714

Transitions / transversions = 1.83 (110 / 60)
Gap_init rate = 0.05 (31 / 591), avg. gap size = 2.71 (84 / 31)  


2832 20.38 7.05 5.71  chr2_96313882_96316750.rev     1488  2380 (489)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_96313882_9   1488 AGAGATATGCTATGTTCATGAATTGGGAAGACTCCATATTGCTAAGACAT 1537
                          i      v i         i     -      iv      i     iiv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGG-AAGACTTAATATTGTTAAGATGG 52

  chr2_96313882_9   1538 CAATTCTCCCCAAATTAA-----AGATTCAATGCAGTCCCAATCAAAATC 1582
                             v           i -----        i   i    v         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_96313882_9   1583 TGATCAG--GCATTTTTTTGGGGTAGAAATTGACAAGGTGACTCTAAAAT 1630
                         i---   --  v      ---- i             v   ii       
  L1M4_orf2#LINE/    103 C---CAGCTGCCTTTTTT----GCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_96313882_9   1631 GTATATGGGAACACAAGGGACTCAGAACAGGCAAAA-AACGTTGCAAAAC 1679
                         vi      i  ii        i     i  v     -  iv   v    -
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA- 194

  chr2_96313882_9   1680 AAAAAACCAGGTTGGAGGACTTATATTTAATTGATTTCAGTACTTACTTT 1729
                         i  i   v i           i i i  v-iii      iv       --
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTC-CCAATTTCAAAACTTACT-- 241

  chr2_96313882_9   1730 ATAGCTACACTAATTACTTTATTAGCTACACTAATCAAGATAGGGTGAAA 1779
                         ------   --  -----------      v         i  v   iv 
  L1M4_orf2#LINE/    242 ------ACA--AA-----------GCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_96313882_9   1780 CTGGCATAAGGA----CATATAGATCAATGAAACAGA-------GTCTAG 1818
                                     ----              i  i   -------   i  
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_96313882_9   1819 AAGTAGGCCCACACATATATGGTGAACTGGGTTTCAACACAG-TGCAAAG 1867
                           i  ii    i    v      v  i  iv    i   vi -   v   
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_96313882_9   1868 GCCTTTAGAATGGGGAGAAAAAGATAATCTTTTCAACAAATTATGTTACA 1917
                         i  v  v-        i i  ---  i              vi  i ivi
  L1M4_orf2#LINE/    373 ACCATTC-AATGGGGAAAGAA---TAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_96313882_9   1918 GCAACGTGATATCTATATGGGGAAAAAATGAACCCCTATCCTTACCTGAT 1967
                         i    vv    ? i i   vi-   i      viivv i  i     v i
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCA-AAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_96313882_9   1968 ATCATATATAAAAATTAGCTCAATATGTATCATTGATATAAGTGTAAAAA 2017
                          i      i        i     v   v    ?v  iv   i     i i
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_96313882_9   2018 TGAAAACCATAACATTTCTAAAGGAAAACATAG------ACCTCTGTTAT 2061
                         iv     i    v i ii  i i          ------ i  ii  v i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_96313882_9   2062 GTTTGGATAAGCAAAGATTTCTTAGATAGGACAC--AAACCATTA----- 2104
                         v  v  v  i    v i           v     --   v  iv -----
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_96313882_9   2105 --------AAATTTTTTTTTTGATGCACTGAACATCATCAAAATCAAATA 2146
                         --------    v--------   iv i  i  v          i   v 
  L1M4_orf2#LINE/    618 AAAAGAAAAAATA--------GATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_96313882_9   2147 TTTGTATTCTTCA---GACACAAGTAAGACAATGAAAAGGCAAGCC-TGG 2192
                         i  v i v     ---     v vi    v i       i   v  -ii 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_96313882_9   2193 AACTGGAGAAAATATTTTCAAA--ACATATCTGAATAAAGGGCTTGTATC 2240
                           iv             v    -- i        -   i  i        
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGA-TAAGGGACTTGTATC 758

  chr2_96313882_9   2241 CAGAATATATAAACAATT--TA------AATAATAAAAA-----ATAATT 2277
                                      v  i --  ------           -----    ii
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_96313882_9   2278 TTTTTTAAATTTAAAAACGGGCAAAATATTTCAAAAAACAAGTC---ATA 2324
                         i------    ?     i       iv    v  v i   vv  --- v 
  L1M4_orf2#LINE/    809 C------AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_96313882_9   2325 AAAGAGAAACAAATGGTCAATAAGCACATGAAAAAATGCTTAACAAGACT 2374
                         i    v v        i                 i     i    vv ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_96313882_9   2375 ACTCAA 2380
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.56 (109 / 70)
Gap_init rate = 0.03 (30 / 905), avg. gap size = 3.80 (114 / 30)  


3254 27.31 0.33 0.33  chr2_96466094_96472491     4999  5906 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_96466094_9   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5048
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_96466094_9   5049 GGCCATACTGCCCAAGGTATTTTACACATTCGATGCCATCCCCATCAAGC 5098
                            v     v     iv iv i    v    i i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_96466094_9   5099 TACCAATGACTTTCTTCACAGAATTGGAAAAAACGACTTTAAAGTTCATA 5148
                          v   iivi i  i  ii     v v  v  ivi  iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_96466094_9   5149 TGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAGAA 5198
                              viiv  ii  v  viv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_96466094_9   5199 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5248
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_96466094_9   5249 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGATCAA 5298
                               i   i    ii         i iv ii i   v i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_96466094_9   5299 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5346
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_96466094_9   5347 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5396
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_96466094_9   5397 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5446
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_96466094_9   5447 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCCAGATGGATT 5496
                          ii    i    v   i     v              i  v i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_96466094_9   5497 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5546
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_96466094_9   5547 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5596
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_96466094_9   5597 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5646
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_96466094_9   5647 AAA-TGAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAATGAATC 5695
                            - v   i -   i  ii vv    i  v       vv i i    vv
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_96466094_9   5696 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5745
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_96466094_9   5746 GGGTTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5795
                           ii vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_96466094_9   5796 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5845
                         i     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_96466094_9   5846 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCA 5895
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_96466094_9   5896 TCACTGGCCAT 5906
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3165 27.02 1.00 0.44  chr2_96528280_96533965     4292  5194 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_96528280_9   4292 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4341
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_96528280_9   4342 GGCCATACTGCCCAAGGTAATTTACACGTTCGATGCCATCCCCATCAAGC 4391
                            v     v     iv i  i    vi   i i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_96528280_9   4392 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4439
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_96528280_9   4440 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4489
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_96528280_9   4490 AACAAAGCTGGCGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4539
                                i   v  vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_96528280_9   4540 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAAGATATACATC 4589
                                 i   i    ii         i iv ii i i v     v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_96528280_9   4590 AATAGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 4637
                            i   i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_96528280_9   4638 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4687
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_96528280_9   4688 CTATTTAATAAATGGTGCTGGGAAACCTGGCTAGCCATAGGTAGAAAGCT 4737
                           v  i  i              v v    v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_96528280_9   4738 GAAACTGGATCCCTTCATTACACCTTATACAAAAATTAATTCAAGATGGA 4787
                            ii    i    v v i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_96528280_9   4788 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4837
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_96528280_9   4838 CTAGGCTTTGCCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAA 4887
                         v    ?v viviv   iv   v v  vv i i   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_96528280_9   4888 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 4937
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_96528280_9   4938 TTAAA-CTAAAGAGTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4986
                          i   -i    i v  i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_96528280_9   4987 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5036
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_96528280_9   5037 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5086
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_96528280_9   5087 AAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5132
                          i    ----   v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_96528280_9   5133 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5182
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_96528280_9   5183 ATCACTGGCCAT 5194
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3011 27.20 1.10 1.10  chr2_96541535_96548230     5297  6204 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_96541535_9   5297 TGGAAAAGCATTCCATGCTCATGGATAGGAAGAATCAATATGA--AAAAT 5344
                               iii  i     i        v      v i     vi--  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_96541535_9   5345 GGTCATGCTTCCCAAAGTAATTTATAGATTCAGTGTTATTCCCATCAAGC 5394
                           iv  i  i      v i  i  i       ii iv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_96541535_9   5395 TGTCATTGACTTTCTTCCCAGAACTTGAAGAAAAACT-ACTTTAAATTGC 5443
                          vi  vivi i  i  iv     v    v---  i  - iii    v v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC---AAGCTGATCCTAAAATTC 147

  chr2_96541535_9   5444 ATATGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATACTAAGCAAAAA 5493
                                 viiv  ii  v  v v        i     vi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_96541535_9   5494 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5543
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_96541535_9   5544 CTACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGATATATAGAC 5593
                                  i   i    ii   i     i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_96541535_9   5594 CAATGGAGCAGAAC--AGAGTCCTCAGAAATAGCACCACACATCTACAAC 5641
                                ii    i--       --       ivv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_96541535_9   5642 CATCTGATCTTCAACAAACCTGACAAAAACAAGCAATCAGGAAAGGATTC 5691
                           vi    i   i    ivv  v   i v  vv    vi      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_96541535_9   5692 TCTATTTAATAAATGGTGCTGGGAAAACTGACTAGTCATATGCAGAAAAC 5741
                            v  i  i              v     iv  ?i  i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_96541535_9   5742 AGAAACTAGACCCCTTCCTTACATCTCATACAAAAATTAACTCAAGATGG 5791
                         v   ii i       v   i   i vi                  i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_96541535_9   5792 GTTAAAGACTTAAATGTAAAATGTAAAACCATGAAAACCCTAGAAGAAAA 5841
                         i i ?    i         i vv      i  i   vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_96541535_9   5842 CCTAGGCCATAACATGCAGGACAT---ATTCATGGGCAAAGACTTCGTGA 5888
                          v    ?vvv  iv v iv   v ---i  ---i     v ii   v ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTT---AGGCAATGGTTTCTTAG 592

  chr2_96541535_9   5889 ATAAAACAC-AAAAAC-CAATTGCAACAAAAGCCAAAATTGACAAATGGG 5936
                            vi    -    i -   --          vv     v  i    v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_96541535_9   5937 ACTTAATTAAACAAAAGAGCTTCTGCTCAGCAAAAGAAACTATCATCAGA 5986
                             v  i   vvv  i i   i  iv vv    i  v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_96541535_9   5987 GTGAACAGGCAACCTACAGAATGGCAGAAAATTTTTGCAATCTATCCATC 6036
                              v  i     i         v       v       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_96541535_9   6037 TGACAAAGGTGTAATAACCAGAATCTACAAGGAACTTAAACAAATTTACA 6086
                            i  i  vv vi  v       v  i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_96541535_9   6087 AGAAAAAAGCAAACAACCCCATCAAAAAGTGGGCAAAGTGTATGAACAGA 6136
                          v     ii    i     v  i?    i         vi v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_96541535_9   6137 CACTTCTCAAAAGAAGACATTCATGTGGCCAACAAACTTATGAAGAAAAG 6186
                           i     v        i  v  vi       i  i vi     i i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_96541535_9   6187 CTCATCATCACTGGTCAT 6204
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2591 21.13 8.76 0.31  chr2_96577158_96578795.rev      508  1146 (492)    L1M4_orf2#LINE/L1      216   908 (0)  

  chr2_96577158_9    508 CACACTTTCTGATTTTGAATTATACTACAAAGCTATAGTAATCAATACAG 557
                                i ii    ii  viv             i         v    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_96577158_9    558 TATGGTACTGGCATAAAAACAGAAAAATAGATCCATAAAACAGAAT-AAG 606
                          i              ii i   v v       v  ii  i     -i  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_96577158_9    607 GATCCTAGAAATAAACCCATGCATATATGATCAACTTATCTTCAACAAAG 656
                         ii   -              i   v    i    i v  i   i    i 
  L1M4_orf2#LINE/    316 AGTCC-AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_96577158_9    657 -CACCAAGAATACAGAATAGGGAAGCGACAGTCTCTTCAATCAATGGTAT 705
                         -ii      vi ivv   i     ivi i     i     iv      ii
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_96577158_9    706 GGAGAAAACTGGATAGCCACATGAAAAAGGATAAAATTGGACCC-TATCT 754
                         v i  v         ?       v     i  i  i        -  i  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_96577158_9    755 TACACTATGCACAAAAGTCTACTGAAAATGGATTA--GACTTAAATGTAA 802
                         i    i  ii      i iv   v         i --   i         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_96577158_9    803 GACCTGAAACCGTAAAACTCCTAGAAGAA--------------------- 831
                           v  i    ii        i        ---------------------
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_96577158_9    832 -----------------TGATTTTTTGGATATGACATCTAAAGCATGAGT 864
                         -----------------  i   i  i         i v      ii  i
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_96577158_9    865 AACAAAAGCAAAAACA----AGTGGGACTGCATCAAACTAAAAAGCTTCT 910
                                 v     i ---- i v     v       v v    i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_96577158_9    911 GCATAGCAAAGGAAACAATCAACAAACTGAAAAGGC----CACAG--T-- 952
                          iiivv       v  v     v   v       i ----     -- --
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_96577158_9    953 -AGAAAATATTTGCAATATTTTGTATACAATAAGGGGTTAATATCCAAAA 1001
                         -               -  iv i   vii       ii vi      i  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAA-ATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_96577158_9   1002 TATATAAGGGACTCATATGACTCAATATTAGAAAAACAAATAACCTGATT 1051
                                i i    v  ii        v  i   i          ii   
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_96577158_9   1052 TAAAACTGGGCAAAAGACCTGAATAGACATTTCTCCAAAGAAGACATAAC 1101
                         ?    v        i  ii                         i   vv
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_96577158_9   1102 AATGGCCAATACGTATATTAAAAGGTGTTCAATATCACTAATCAT 1146
                                    v i i  v     i  i    i    ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (92 / 41)
Gap_init rate = 0.02 (11 / 693), avg. gap size = 5.27 (58 / 11)  


2691 12.36 3.39 26.50  chr2_96810405_96815451.rev     3374  4554 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_96810405_9   3374 TGGAAAGATGTTCTATGG-CATGGATTGGAAGACTTGGTATTGTTAAGAT 3422
                                  i i i   v-                 ii            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_96810405_9   3423 AGCAGTACTCCCCACATTGCTCTAT---------GCAGTCCCTACCTCTC 3463
                         i   i         v    v    i---------   i      ----  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA----TC 96

  chr2_96810405_9   3464 AAAAACTTAGCTGGCTTCTTGGCAAAAATTCACAAGCTGATCTTAACATC 3513
                             v ii     v   i  v   i     v           i   v  i
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_96810405_9   3514 CATATGGAAATTCAAGGGACTCAGAATAACCAAAATAATCTTGACAAACA 3563
                                    v        i       i      i        v   v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_96810405_9   3564 G---TGAAGTTGGAATGCTCACACTTCCTGATTTCAAAACTTACTACAAA 3610
                         i---ii        ivi           ii                    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_96810405_9   3611 GCTACAATAATAAAGACAGTGTGCTACTGGCATCTGGGTAGACATACAGA 3660
                               i    v           v         vv  i        i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_96810405_9   3661 TCAATGGAATAGAACTGAGAGTCTGGAAATAAAACGTCACATTTA--ATC 3708
                                       i        ii        v vvi       --i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_96810405_9   3709 AATTAATTTTCTTTTTCTTTCTTTTTTTTTTTTGAGACAGAGTCTCGCTC 3758
                             i      ------------------------    -----------
  L1M4_orf2#LINE/    347 AATTGATTTTC------------------------GACA----------- 361

  chr2_96810405_9   3759 TGTCTCCCAGGCTGGAGTGCAGTGGCACGATCTCGGCTCACTGCAAGCTC 3808
                         --------   -----    -----------------------    ---
  L1M4_orf2#LINE/    362 --------AGG-----GTGC-----------------------CAAG--- 372

  chr2_96810405_9   3809 TGCCTCCTGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGG 3858
                         ----------------i      ---------------------------
  L1M4_orf2#LINE/    373 ----------------ACCATTC--------------------------- 379

  chr2_96810405_9   3859 GACTACAGGTGCCTGCCACCACGCCTGGCTATTTTTTTTTTTAATATATA 3908
                         --------------------------------------------------
  L1M4_orf2#LINE/    380 -------------------------------------------------- 379

  chr2_96810405_9   3909 TGTTTTTAGTAGAGATGGGGTTTCACCATATTAGCCAGGATGGTCTCGAT 3958
                         -------------i      ------------ i--  i  i    ----
  L1M4_orf2#LINE/    380 -------------AATGGGG------------AA--AGAATAGTCT---- 398

  chr2_96810405_9   3959 CTCCTGATCTCGTGATCCACCCGCGTCGGCCTCCCAGTGTGCTGGGATTA 4008
                         --------------------------------------------------
  L1M4_orf2#LINE/    399 -------------------------------------------------- 398

  chr2_96810405_9   4009 CAGGCGTGAGCCACCGTGCCCGGTCTAATCAATTAATTTTCCACAAGATA 4058
                         -------------------------------------    v    -  i
  L1M4_orf2#LINE/    399 -------------------------------------TTTCAACAA-ATG 410

  chr2_96810405_9   4059 ATTCAATGGGGAAAGAATCATCTTTTCAACAACTAGTTATCCACGTGTAA 4108
                         i v --    ------------------      i v  ?    i  i  
  L1M4_orf2#LINE/    411 GTGC--TGGG------------------ACAACTGGATAKCCACATGCAA 440

  chr2_96810405_9   4109 AATAATGAAGTTAT-TCCCTATTTCACACCACACAGAAAATTTAACTCGA 4157
                           v         iv-i     ii        i i v    v       i 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_96810405_9   4158 AATGGATGAAAGATCTAAATGTAAAAATTAAAACTATAAAACTTTTAGAA 4207
                                v ?   i          i ii               i      
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_96810405_9   4208 AAAAAAAATATCGGATTGATTCTTCTTGACTTTGGATCAGGCAGTTGTT- 4256
                         i    ---i  v  ?v i v     v    i    i i     i v   -
  L1M4_orf2#LINE/    541 GAAAA---CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_96810405_9   4257 ---AGATGTGACACCAAAAGAAAAAGCAACGAAAGAAAAG---GATAAAT 4300
                         ---    i            v v       i        i---       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_96810405_9   4301 TGAACTTCATCAAAATTGAAACCTTACGTGTTTCATAGGACATCATCAAG 4350
                           i              i   v   vi   i    v      ii      
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_96810405_9   4351 GAAATGTAAAGA--ACCTACAGAATGGGAAAAGATATATGCAAATCATAT 4398
                         i  i  v     --   i           i  i    v            
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_96810405_9   4399 --CTTATTAGAGATTTGTTT---GAA-ACGTAAAGAACTATTACAACTCA 4442
                         --  v  v  i  i    v ---   - ii         v          
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_96810405_9   4443 ATAGTAA---GACAA----CCAAATTAGAAAATGGGCAAAAGATCTTAAT 4485
                            i   ---     ----  v    ?i            i   i v   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_96810405_9   4486 AGGTATTTCTCTAGAAGAGATATACAAGTGGCCAAGAAGCT--TGAAAAG 4533
                           ii       i i ii          i       v    v--       
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_96810405_9   4534 AGGCTGAGCATCATCAGCCAT 4554
                          v   v i     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (93 / 49)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 12.61 (353 / 28)  


3123 27.40 0.77 0.44  chr2_97216335_97218274.rev      544  1448 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_97216335_9    544 TGGAAGAACATTCCAGGCTCATAGGTAGGAAGTATCAATACTGTCAAAAT 593
                              ii i  i   v i    i i v     vv i    i   i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97216335_9    594 GGCTGTACTGCCCAAGGTAATTTATAGATCCAATGCCATCCCCATCAAGC 643
                            vi    v     iv i  i  i    i   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97216335_9    644 TAACAATGACTTTCTTCACAGAACTGGAAAAAACT-ATTTTAAAGTTCAT 692
                          vv  iivi i  i  ii     v v  v  i-  -  ii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_97216335_9    693 ATGGAACGAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 742
                               vviv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_97216335_9    743 ATAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 792
                          i    i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_97216335_9    793 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACCA 842
                                i   i    ii         i iv ii i   v   i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_97216335_9    843 ATGGAACAGAAC--AGAGCCCTCAAAAATAATGCCGCATGTCTACAA-CT 889
                               i    i--    i  -- i      vv  ii ii i  iii- v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_97216335_9    890 ATTGATCTTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCCC 939
                               i  i     ivv  v   i vv vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_97216335_9    940 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 989
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_97216335_9    990 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 1039
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_97216335_9   1040 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTACAAGAAAACC 1089
                         i ?    i    i  v   v       i      vi i  v        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_97216335_9   1090 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCACGTCTAA 1138
                             ?i- v i -   iv   v v  vv i     v ii   viivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_97216335_9   1139 AACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAA 1188
                         i            vvi      i   vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_97216335_9   1189 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTACCATCAGAGTGAAC 1238
                          i   v v  i i   i  ii vv    i  v i  i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_97216335_9   1239 AGACAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 1288
                                 i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_97216335_9   1289 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 1338
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_97216335_9   1339 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 1388
                          i     i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_97216335_9   1389 TCTAAAGAAGACATTTATTCAGCCAAAAA--ACATGAAAAAATGCTCATC 1436
                           i        i  vi vvii     v  --         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_97216335_9   1437 ACCACTGGCCAT 1448
                          i  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3197 27.42 0.44 0.44  chr2_97313485_97319888.rev     5005  5912 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_97313485_9   5005 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATGGTTAAAAT 5054
                              ii i  i     i      i v      v i i   v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97313485_9   5055 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCACCATCAAGC 5104
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97313485_9   5105 TCCCAAAGACTTTCTTCACTGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5152
                              ivvi i  i  ii v   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_97313485_9   5153 TATGGAACCAAAAAAGAGCCCGCATCACTAAGTCAATCCTTAGCCAAAAG 5202
                                viiv  ii  v  v v  vi i  iv     i v ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_97313485_9   5203 AACAAGGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5252
                              i i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_97313485_9   5253 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5302
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_97313485_9   5303 AATGGAACAGAAC--AGAGCCATCAGAAATAACGCCGCATATCTACAACT 5350
                                i    i--    i --         vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTC 346

  chr2_97313485_9   5351 ATCTGATCTTTGACAACCCTGAGAAAAACAAGCAACGGGGAAAGGATTCC 5400
                          vi    i  i     vvv  vv  i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_97313485_9   5401 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5450
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_97313485_9   5451 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5500
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_97313485_9   5501 TTAAAGGCTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5550
                          i ?  i i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_97313485_9   5551 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5600
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_97313485_9   5601 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATCTAA 5650
                         i            vvi          vv     v  i i  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_97313485_9   5651 TTAAACTGAAGAGATTTTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5700
                          i   v v  i iv     ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_97313485_9   5701 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5750
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_97313485_9   5751 AGGGCTAATATCCAGAATCTACAATGAACCCAAACAAATTTACAAGAAAA 5800
                         i  i  vi          v  i  v    i vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_97313485_9   5801 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATCAACAGACACTTC 5850
                          i     i     v  i?    i            v v  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_97313485_9   5851 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5900
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_97313485_9   5901 ATCACTGGCCAT 5912
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1763 23.89 3.46 2.14  chr2_97321880_97323476.rev      501  1107 (490)    L1M4_orf2#LINE/L1      294   908 (0)  

  chr2_97321880_9    501 AAATTAATAAAATTCAACAGACAGTCCAGAAATAGATAACACATAAGCAA 550
                          i  i   ii   vv  iv  v            ---   v    --  v
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATA---AACCCATA--CAT 338

  chr2_97321880_9    551 CCA-GCTTA--TGACT---GACAAAGGCAGGATGGCAATGCAGTGGAGAA 594
                         ii - v i --   i ---     i  iivv v i v  v  i   i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_97321880_9    595 AGGATAGCCTTTTCAACATGCGGTGTTGGAACAATTGGCTGTCCATATCC 644
                           i    i          vii    i   i    i   v i?   i  v 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_97321880_9    645 AAAA-AGTGAACTTGAATCCATACCTCACCTCACTCCATAGACAAAAGGA 693
                             - i    v   i i  v        ---  --    v      ivv
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCAC---AC--CATATACAAAAATT 483

  chr2_97321880_9    694 AACTCAAGATGGAGCACAGATTTAAATGGAAGATCCAAATCTATAAAATT 743
                                i     v  ?   ii      v    v i   v        i 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_97321880_9    744 TCTAGAACAAA-CACAGGAACAA-TCTTTGTGACCTTGTGCTAGGCAAAC 791
                         ii     v   -  i   ?ii  -    i         v i       vv
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_97321880_9    792 ATTT-TTACATATGACACAAAATGCAAAATCTGTAAT-TCAACAAT---T 836
                         i   -   v         v   v   v  v vii  v-vv  v   --- 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_97321880_9    837 AAATTGGATTTCATTACGATTAAAATCTTCTGCTCTTCAAAAGATACTAC 886
                                 i     i vi       v   i  iv       i  i    i
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_97321880_9    887 AAAGCAAGTGAAAAGTCAACCCAAAAACTGGCA-AAAATACCCTTGTAAA 935
                         v   v          v       v i v   v -      i--   i   
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT--TTGCAAA 731

  chr2_97321880_9    936 AAA-GTAGCTAA-AAGTAA-TAGTATCCA-AATACATACAGAATTATTAA 981
                         vv -i  v  i -   vi - v       -    i   v    i v   v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_97321880_9    982 AATTCAACACGTAAGAAAACAT-CAACCTACTTTTTTA-TATGCAAAAGA 1029
                           i    i -i   i  i   v-i    i v  ?vvv - iv     i  
  L1M4_orf2#LINE/    782 AACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_97321880_9   1030 TGTGAAAAGACAGTTCAACAAAGAAGATGTACAGATGGCAAATAAACACA 1079
                          v    v     v   vv          i    i     v     i    
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_97321880_9   1080 TGGAAAGATGCTCAACATTTTAGTCATT 1107
                           i               iv????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.07 (73 / 68)
Gap_init rate = 0.04 (22 / 615), avg. gap size = 1.55 (34 / 22)  


2373 29.40 1.04 0.52  chr2_97420990_97425140     2450  3221 (930)    L1M4_orf2#LINE/L1        1   776 (132)  

  chr2_97420990_9   2450 TGGAAAAACATTCCATGCTCATGTATAGGAAGAATCAATATTATGAAAAC 2499
                               i i  i     i     v  v      v i      i v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97420990_9   2500 GGCCATACTGCCCAAAATAATTTATTGATCCAATGCTATTCCCATTAAAC 2549
                            v     v      v i  i  iv   i   i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97420990_9   2550 TACCATGGAAGTTCTTCACAGAAATAGAAAAAAAAATATTTTAAAATTCA 2599
                          v   vvvivv  i  ii       v  v  ivvi  --ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT--CCTAAAATTCA 148

  chr2_97420990_9   2600 TGTGGAACCCAAAGAGAGCCTGAAGAGCCAAGGCAATTCTCAGCAAAAAG 2649
                          i     vivv   i  v  v   v      ii    ii v iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_97420990_9   2650 AA-AAATCTGGAGGCATCATGCTCTTCAACTTCAAACTATACTACAGGTC 2698
                           -   vi      vv   ii  iii   i      viv       iiv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_97420990_9   2699 TACAGTAACCAAAGCAGCATGGCACTGGTGCAAGAAAAGACACATAGACC 2748
                                 i   ii   ii   i     iii   i v     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_97420990_9   2749 AATGGAACAGAATAGAGAACCCAGAAATAAGACTACACCCCTACAG-CAA 2797
                                i     v    ii          iv i i  vii  ii -   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_97420990_9   2798 TCTGATATTTCACAAACCCGACAAAAACAAGCAATGGAGAAAGGAT--TC 2845
                          -    v  iv    ivvi v   i v  vv      i     i  --  
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_97420990_9   2846 TCT--AATAAATGGTGCTGGGAAAGCTGGCTAGCCATATGTGCAA-ATTG 2892
                          i --  i              v i    v  ?   i   iiv  - v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_97420990_9   2893 AAACTGGACTCCAGCCCCACACCTTATATAAAAATCAGCTCAAGATGAAT 2942
                           ii     i  vi  i      v    i      i i     i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_97420990_9   2943 TAAAGACCTAAATGTAAAACCCCAGACTATAAAAATCCTAGAAGAAAGCC 2992
                         i ?              i v iv i         v  i         i v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_97420990_9   2993 TAGGCA-ATACCACTCGGAACATAGACATGGGCAAAGATTTCATGACAAA 3041
                             ?i- v i -i   vi  v v ivv i     v i    v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_97420990_9   3042 GATGCCAAAAGCAATTGCAACGAAAGCCAAAATTGACAAATGGGATCCAA 3091
                           ii         vvv     i    vv     v  i    v   iiiv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_97420990_9   3092 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAACAGCAGAGTAAAC 3141
                          i   v v  i i   i  ii vv    i  v    v  iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_97420990_9   3142 GGACAACCTAAAGAATGAGAGAAAAGTTTTGCAAACTATGCATCTAACAA 3191
                         i       i v      i       vv        ii  ii    i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_97420990_9   3192 AGGTCTAATATCTAGCATCTGTAAGAAACT 3221
                         i  v  vi    i  v  v i   ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.49 (134 / 90)
Gap_init rate = 0.01 (9 / 776), avg. gap size = 1.33 (12 / 9)  

 277 19.05 0.00 0.00  chr2_97420990_97425140     3582  3644 (507)    L1M4_orf2#LINE/L1      801   863 (45)  

  chr2_97420990_9   3582 AAACAACCCCACTAAAAAGTGGGCAAAGGACATGAAAAGACACTTTTCAA 3631
                            i     v i ?    i           iv    v     i  i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_97420990_9   3632 AAGAAGACATACA 3644
                                i     
  L1M4_orf2#LINE/    851 AAGAAGATATACA 863

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.00 (0 / 0)  


2373 29.40 1.04 0.52  chr2_97530584_97534742.rev     2458  3229 (930)    L1M4_orf2#LINE/L1        1   776 (132)  

  chr2_97530584_9   2458 TGGAAAAACATTCCATGCTCATGTATAGGAAGAATCAATATTATGAAAAC 2507
                               i i  i     i     v  v      v i      i v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97530584_9   2508 GGCCATACTGCCCAAAATAATTTATTGATCCAATGCTATTCCCATTAAAC 2557
                            v     v      v i  i  iv   i   i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97530584_9   2558 TACCATGGAAGTTCTTCACAGAAATAGAAAAAAAAATATTTTAAAATTCA 2607
                          v   vvvivv  i  ii       v  v  ivvi  --ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT--CCTAAAATTCA 148

  chr2_97530584_9   2608 TGTGGAACCCAAAGAGAGCCTGAAGAGCCAAGGCAATTCTCAGCAAAAAG 2657
                          i     vivv   i  v  v   v      ii    ii v iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_97530584_9   2658 AA-AAATCTGGAGGCATCATGCTCTTCAACTTCAAACTATACTACAGGTC 2706
                           -   vi      vv   ii  iii   i      viv       iiv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_97530584_9   2707 TACAGTAACCAAAGCAGCATGGCACTGGTGCAAGAAAAGACACATAGACC 2756
                                 i   ii   ii   i     iii   i v     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_97530584_9   2757 AATGGAACAGAATAGAGAACCCAGAAATAAGACTACACCCCTACAG-CAA 2805
                                i     v    ii          iv i i  vii  ii -   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_97530584_9   2806 TCTGATATTTCACAAACCCGACAAAAACAAGCAATGGAGAAAGGAT--TC 2853
                          -    v  iv    ivvi v   i v  vv      i     i  --  
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_97530584_9   2854 TCT--AATAAATGGTGCTGGGAAAGCTGGCTAGCCATATGTGCAA-ATTG 2900
                          i --  i              v i    v  ?   i   iiv  - v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_97530584_9   2901 AAACTGGACTCCAGCCCCACACCTTATATAAAAATCAGCTCAAGATGAAT 2950
                           ii     i  vi  i      v    i      i i     i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_97530584_9   2951 TAAAGACCTAAATGTAAAACCCCAGACTATAAAAATCCTAGAAGAAAGCC 3000
                         i ?              i v iv i         v  i         i v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_97530584_9   3001 TAGGCA-ATACCACTCGGAACATAGACATGGGCAAAGATTTCATGACAAA 3049
                             ?i- v i -i   vi  v v ivv i     v i    v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_97530584_9   3050 GATGCCAAAAGCAATTGCAACGAAAGCCAAAATTGACAAATGGGATCCAA 3099
                           ii         vvv     i    vv     v  i    v   iiiv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_97530584_9   3100 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAACAGCAGAGTAAAC 3149
                          i   v v  i i   i  ii vv    i  v    v  iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_97530584_9   3150 GGACAACCTAAAGAATGAGAGAAAAGTTTTGCAAACTATGCATCTAACAA 3199
                         i       i v      i       vv        ii  ii    i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_97530584_9   3200 AGGTCTAATATCTAGCATCTGTAAGAAACT 3229
                         i  v  vi    i  v  v i   ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.49 (134 / 90)
Gap_init rate = 0.01 (9 / 776), avg. gap size = 1.33 (12 / 9)  

 277 19.05 0.00 0.00  chr2_97530584_97534742.rev     3590  3652 (507)    L1M4_orf2#LINE/L1      801   863 (45)  

  chr2_97530584_9   3590 AAACAACCCCACTAAAAAGTGGGCAAAGGACATGAAAAGACACTTTTCAA 3639
                            i     v i ?    i           iv    v     i  i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_97530584_9   3640 AAGAAGACATACA 3652
                                i     
  L1M4_orf2#LINE/    851 AAGAAGATATACA 863

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.00 (0 / 0)  


2048 26.48 12.32 0.74  chr2_97567429_97569261      532  1343 (490)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_97567429_9    532 GAGATATGTACCGTATTCATAAGT----AGATTCAATGCTATTAAGATGT 577
                           i v  i v  i i     iii ----   i i   ii i        v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_97567429_9    578 CAGTTCTTTCCAA--TG---TATAGATTCAATGCAATTCTACTCTAAAT- 621
                           i v  ii    --  ---  i        i     i ivv  v    -
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_97567429_9    622 ------------------GAAAATG-----------------TTTATATG 636
                         ------------------    v  -----------------  i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_97567429_9    637 GAGAGGCAAAAGACCTTGAATAGCTAACACCATATTGAAGGAGAAGAACA 686
                           i v    ii    iv       i  v  v  v     ii         
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_97567429_9    687 AACTTGGAGGACAGACACTACTCAATTTCAAGACTTACCCTAAAGCTACA 736
                           v         vv     v i         i      ivi         
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_97567429_9    737 GTAATGGAGACAGTGTGGTATTAGTGAAAGAACAAACGGATAAA---ATG 783
                              vi             i i iiv   i i i  iv   i ---   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_97567429_9    784 AGATAGA-----GAGTTCACAAATAGAA--ACACATTAATACATTCGATT 826
                         ii     -----    i  v     i v-- i     --  iiv  i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAATT 350

  chr2_97567429_9    827 AATTTTTGACAAAAAAGTAAAGGC-ATT--ATGATGATGAAACAGTTTTT 873
                         i     i     iiiv iv   i -   --   iv  vii  i   i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_97567429_9    874 TCAGGAAGGGCTGCTGGAATACCTGGATATCCACATGCAAAAAAAAAATA 923
                            iv  iv v      i i v       ?            i  vi --
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA-- 448

  chr2_97567429_9    924 AATTG----CAGACCTTACACCCC-CACCAAAATTAACTCAAAATGGATC 968
                          i   ---- vv    i     vi-i  v                     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_97567429_9    969 AGCAACATAAATATACAA---AAAACTATAAAATTTATAGAAGATAATAT 1015
                          ?vi  v     i  vi ---            i iv       v  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_97567429_9   1016 AGAAGGAAATACAGATTATCTTGGGTTTAATGATGACCT-TTAGAAAAAA 1064
                           i? v    vivvi v i        viiii   iii -     v vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_97567429_9   1065 CACCAAA-GTTGAAGTCAATAGAAGAAAGAATTGACAAGCTGGACTTGAT 1113
                                - ivv   -   i i      i   v  i  ii       v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_97567429_9   1114 GAAAATGTAACATTTTTACACCATTAAAGACACT-----GAAAG--AAAA 1156
                         v     vv  v i    iii iviv  i      -----     --    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_97567429_9   1157 GAGAAACCACAGA-TGGAAAAAAAT--TTGCCAAA--ACGTATCTGATTA 1201
                           v  v       -   i i     --    -   -- ii        v 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGC-AAATCATATATCTGATAA 746

  chr2_97567429_9   1202 AGAACTATTATTCAAAACATATTA-GTATTCTTAAAGCTGAGCAGTAAAA 1250
                         i i   vv   i  i  i    v - v i     v i  v ii i     
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_97567429_9   1251 -GACA------------------TGAGCTAAAGACCTTAACAAGTACCTC 1281
                         -    ------------------  i  v  i  ii v  i iii ii  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_97567429_9   1282 ACCAAGTAAATTATACAAATGGAAAATAAGCATATGTAATGAGGCTACAC 1331
                         v    iv  iv           vv        i   v  v  v   vv  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_97567429_9   1332 ATAATATTTCCT 1343
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (130 / 82)
Gap_init rate = 0.03 (27 / 906), avg. gap size = 3.93 (106 / 27)  


1788 23.33 3.59 2.28  chr2_97596310_97597906      495  1107 (490)    L1M4_orf2#LINE/L1      288   908 (0)  

  chr2_97596310_9    495 ACCTGCAAATTAATAAAATTCAACAGACAGTCCAGAAATAGATAACACAT 544
                           v ii i  i   ii   vv  iv  v            ---   v   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA---AACCCAT 334

  chr2_97596310_9    545 AAGCAACCA-GCTTA--TGACT---GACAAAGGCAGGATGGCAATGCAGT 588
                          --  vii - v i --   i ---     i  iivv v i v  v  i 
  L1M4_orf2#LINE/    335 A--CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_97596310_9    589 GGAGAAAGGATAGCCTTTTCAACATGCGGTGTTGGAACAACTGGCTGTCC 638
                           i     i    i          vii    i   i        v i?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_97596310_9    639 ATATCCATAAAG--TGAACTTGAATCCATACCTCACCTCACTCCATAGAC 686
                          i  v  -    --    v   i i  v        ---  --    v  
  L1M4_orf2#LINE/    433 ACATGCA-AAAGAATGAAGTTGGACCCCTACCTCAC---AC--CATATAC 476

  chr2_97596310_9    687 AAAAGGAAACTCAAAATGGAGCACAGATTTAAATGGAAGATCCAAATCTA 736
                             ivv             v  ?   ii      v    v i   v   
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_97596310_9    737 TAAAATTTCTAGAACAAA-CACAGGAA-AAATCTTTGTGACCTTGTGCTA 784
                              i ii     v   -  i   ?i-       i         v i  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_97596310_9    785 GGCAAACATTT-TTACATATGACACAAAATGCAAAATCTGTAAT-TCAAC 832
                              vvi   -   v         v   v   v  v vii  v-vv  v
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_97596310_9    833 AAT---TAAATTGGATTTCATTACAATTAAAATCTTCTGCTCTTCAAAAG 879
                            ---         i     i v        v   i  iv       i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_97596310_9    880 ATACTACAAAGCAAGTGAAAAGTCAACCCAAAAACTGGCA-AAAATACCC 928
                          i    iv   v          v       v i v   v -      i--
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT-- 724

  chr2_97596310_9    929 TTGTAAAAAA-GTAGCTAA-AAGTAA-TAGTATCCA-AATACATACAGAA 974
                            i   vv -i  v  i -   vi - v       -    i   v    
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_97596310_9    975 TTATTAAAATTCAACACGTAAGAAAACAT-CAACCTACTTTTTTA-TATG 1022
                         i v   v  i    i -i   i  i   v-i    i v  ?vvv - iv 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_97596310_9   1023 CAAAAGATGTGAAAAGACAGTTCAACAAAGAAGATGTACAGATGGCAAAT 1072
                             i   v    v     v   vv          i    i     v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_97596310_9   1073 AAACACATGGAAAGATGCTCAACATTTTAGTCATT 1107
                           i      i               iv????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.01 (70 / 69)
Gap_init rate = 0.04 (23 / 621), avg. gap size = 1.57 (36 / 23)  


3215 27.31 0.44 0.44  chr2_97599902_97606298     4998  5905 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_97599902_9   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTTAAAAT 5047
                              ii i  i     i      i v      v i i   i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97599902_9   5048 GGCCATACTGCCCGAGGTAATTTATAGAATCAGTGCCATCCCCATCAAGC 5097
                            v     v   i iv i  i  i   v   ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97599902_9   5098 TCCCAATGACTTTCTTCACTGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                              iivi i  i  ii v   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_97599902_9   5146 TATGGAACCAAAAAAGAGCCCGCATCACCACATCAATCCTAAGCCAAAAG 5195
                                viiv  ii  v  v v  vi   v v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_97599902_9   5196 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_97599902_9   5246 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5295
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_97599902_9   5296 AATGGAACAGAAC--AGAGCCATCAGAAATAATGCCACATATCTACAACT 5343
                                i    i--    i --         vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTC 346

  chr2_97599902_9   5344 ATCTGATCTTTGACAACCCTGAGAAAAACAAGCAACGGGGAAAGGATTCC 5393
                          vi    i  i     vvv  vv  i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_97599902_9   5394 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAACGCT 5443
                           v  i  i              v      v  ?   i   i i  viv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_97599902_9   5444 GCAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5493
                          v ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_97599902_9   5494 TTAAAGGCTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5543
                          i ?  i i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_97599902_9   5544 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5593
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_97599902_9   5594 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATCTAA 5643
                         i            vvi          vv     v  i i  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_97599902_9   5644 TTAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5693
                          i  iv v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_97599902_9   5694 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5743
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_97599902_9   5744 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5793
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_97599902_9   5794 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATCAACAGACACTTC 5843
                          i     i     v  i?    i            v v  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_97599902_9   5844 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5893
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_97599902_9   5894 ATCACTGGCCAT 5905
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3236 27.01 0.66 0.55  chr2_97647840_97649781      544  1450 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_97647840_9    544 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 593
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97647840_9    594 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 643
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97647840_9    644 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 691
                          vi  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_97647840_9    692 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 741
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_97647840_9    742 AATAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 791
                           i    i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_97647840_9    792 TAGAGTAACCAAAACAGCATGGTACTGGTACCGAAATGGAGATATAGACC 841
                           v     i   i    ii         i iviii  i  v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_97647840_9    842 AATGGAACAGAAC--AGAGCCATCAGAAATAATGCTGCATGTCTACAA-C 888
                                i    i--    i --         vv iii ii i  iii- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTC 346

  chr2_97647840_9    889 TATCGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 938
                         v  i   i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_97647840_9    939 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 988
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_97647840_9    989 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 1038
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_97647840_9   1039 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAAAAGAAAAC 1088
                          i ?    i  v    v   v       i      vi i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_97647840_9   1089 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1137
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_97647840_9   1138 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACACATGGGATCTA 1187
                         vi            vvi          vv     v  i v  v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_97647840_9   1188 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1237
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_97647840_9   1238 CAGGCAACCTACGGAATGGGAGAAAATTTTTGCAACTTACTCATCTGACA 1287
                         v  i     i  i              v       v i ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_97647840_9   1288 AAGGGCTAATATCCAGAATCTACAAAGAGCTCAAACAAATTTACAAGAAA 1337
                          i  i  vi          v  i     i   vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_97647840_9   1338 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1387
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_97647840_9   1388 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1437
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_97647840_9   1438 CATCACTGGCCAT 1450
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


 242 22.00 0.00 0.00  chr2_97671263_97677677.rev        1    50 (6365)  C L1M4_orf2#LINE/L1   (29)   879   830  

C chr2_97671263_9     50 ATATGAGGAAATAGTTCTCCAAAAAAGATACACAGATGGTCAATGAGCAC 1
                           v   iv i i v         i      i   i    i    i     
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.00 (0 / 0)  

 308 30.31 15.68 1.05  chr2_97671263_97677677.rev       76   362 (6053)  C L1M4_orf2#LINE/L1   (0)   908   580  

C chr2_97671263_9    362 AAAGATTTCTTAGACAAAATTTCAAA-GCAGAAACCATAAGGCAGAAAAA 314
                           v i         i vi ivi    -   v  i v i  i--       
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA--AGAAAAA 627

C chr2_97671263_9    313 GTGGAGG----GGATTTCAT-GATGTTACAA-----------TCAAATAG 280
                         i i  vi----   i     -i vi   v  -----------     -i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA-GG 676

C chr2_97671263_9    279 AT-CTGTT--GCAAGTGACA---CA--TGGCAAAATGAGAGAAGTTATGT 238
                          i-  i i-- v      v ---  --ivi  i    i     iv   v 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

C chr2_97671263_9    237 GCAG-TC-TAAAACTGACAAGAGATTAGCAGCCTCAATATACGAGGAACT 190
                            i-  -  v v    i   i  i v i v  vv      ii i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

C chr2_97671263_9    189 C------CTGAAAATTAACAAGAAAAATAA------------ATAGACAA 158
                          ------  v  v v   v    v      ------------  i i   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

C chr2_97671263_9    157 AGGACACGAGCAGGCAGTTTTTGGGAGAGGAAACCCCAAAAGCCAGGAAG 108
                             ivi  ii  i  v  i ivii   i  v iv v  vi    iv   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

C chr2_97671263_9    107 CATATGAGGAAGTGGCTAAGATCATTAGTACA 76
                           i    ii ii  vii  v    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (53 / 34)
Gap_init rate = 0.04 (14 / 329), avg. gap size = 3.43 (48 / 14)  

3210 27.42 0.55 0.55  chr2_97671263_97677677.rev     5016  5923 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_97671263_9   5016 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5065
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97671263_9   5066 GGCCATACTACCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5115
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97671263_9   5116 TACCAATGACTTTCTTCACAGGA-TTGGAAAAAACT-ACTTTAAAGTTCA 5163
                          v   iivi i  i  ii   i -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_97671263_9   5164 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAGGCCAAAAG 5213
                                viiv  ii  v  v v  v     iv     i iiivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_97671263_9   5214 AACAAAGCTGGAAGTGTCACACTACCTGACTTCAAACTATACTACAAGGC 5263
                                i    i vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_97671263_9   5264 TACAGTAACCAAAACACCATAGTACTGGTATCAAAACAGAGATATAGACC 5313
                                 i   i   vii i       i  v ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_97671263_9   5314 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGTCACACATCTAAAACC 5361
                                i    i--    i  --        vvi  i    i  viii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_97671263_9   5362 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5411
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_97671263_9   5412 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5461
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_97671263_9   5462 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5511
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_97671263_9   5512 TTAAAGATTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5561
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_97671263_9   5562 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5610
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_97671263_9   5611 AAACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGGGATCTA 5660
                         vi            vvi         ivv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_97671263_9   5661 ATTAAACTAGAGAGCTTCTGCATAGCAAAAGAAACTGCCATCAGAGTCAA 5710
                           i   v vi i i   i  iiivv    i  v   ii  vv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_97671263_9   5711 CAGGCAACCTGTAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACA 5760
                         v  i     iii               v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_97671263_9   5761 AAGGGCTAATATCCAGAATCTACAAAGAATTTAAACAATTTCACAAGAAA 5810
                          i  i  vi          v  i      i ivv    i iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_97671263_9   5811 AAATCAAACAACCCCACAAAAAAGTGGGCGAAGGATATGAACAGACATTT 5860
                           iv    i     v iv?    i     i      v    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_97671263_9   5861 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5910
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_97671263_9   5911 CATCACTGGCCAT 5923
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2079 26.42 3.45 1.55  chr2_97703219_97708244.rev      974  1552 (3474)    L1M4_orf2#LINE/L1        1   590 (318)  

  chr2_97703219_9    974 TGGAATGACATTCCAGGATCATGGATTGGAAGAATCAGTATTGTTAAAAT 1023
                              v  i  i   v v               v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97703219_9   1024 GTCCATAATATTCAAAGCAACCTACAGATTCAATGCAATCCCTATCAAAA 1073
                          v v   v vii    vii i            i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97703219_9   1074 TACCAATGACATTTTTCACATAAATAGAAAAAAAAAATCCTAAAATTTAT 1123
                          v   iivi v     ii  v    v  v  ivvi -          i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_97703219_9   1124 ATGGAACCCCAAAAGACCCAGTATAGCCAAAGCTATGCTAAGCCAAAAGA 1173
                               viv   ii       v         i v  vi i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_97703219_9   1174 ACAAAACTGGAGGAATCACATTACTTGACTTCAAATTATACTACAGAGCT 1223
                              ii       v     i v iii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_97703219_9   1224 ATAGTAACTAAAGCAGCATGGTACTGGCATAATGATGGACACATAGACCC 1273
                          i     ii  ii   ii              v   i    i     i -
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC- 298

  chr2_97703219_9   1274 AATGGAACAGAATAGAGAACCTAGAAACAAATCCACACACCTACAGTGAA 1323
                                i     v    ii i     i   i   i   ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_97703219_9   1324 CTCATTTTCAACAAAGGTGCCAAGAACACACACTGGGGAAAAGACAGTCT 1373
                         i v      i    i          v  iv  v        ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_97703219_9   1374 CTTCAATATATGGTGCTGAGAAAACGAGATTTCCATATGCAGAAGAATGA 1423
                         i     i v         i  v   vi   v?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_97703219_9   1424 AACTAAATCCTAGACTTCTGTATCTTGCCATATGTAAAA-TCAAATCAAA 1472
                          ii ii i  -------  iiv  vii      ii    - i  v     
  L1M4_orf2#LINE/    449 AGTTGGACCC-------CTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_97703219_9   1473 AGTGTTTAAAGACTTA-----------TGAAATTAC--------TACAAG 1503
                          vv v i ?    i  ----------- i   i  i--------  v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_97703219_9   1504 GAATCATTGGGGAAAATCTCCAGTACATTAGTCTGGGCAAAAATTCCTT 1552
                         i  v   v  ? v      i ivv  v  i vi i     vii  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.78 (96 / 54)
Gap_init rate = 0.01 (6 / 590), avg. gap size = 4.83 (29 / 6)  

1075 23.56 1.21 1.51  chr2_97703219_97708244.rev     1886  2216 (2810)    L1M4_orf2#LINE/L1      579   908 (0)  

  chr2_97703219_9   1886 CAAAAATTTATTTAGCAAT-ACCCCACAAACAGAGGCAGCCAAAGCAAAA 1934
                            vii   -i    vv  -  v   v  i  v i   i v    v    
  L1M4_orf2#LINE/    579 CAATGGTTT-CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_97703219_9   1935 TTGGACTAATGGTAGCACATCAAG-TTAAAAAGTTTC-TACATAGCAAAG 1982
                         v i  iv   v v viv      i-       v   i- i v --     
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAG 675

  chr2_97703219_9   1983 GAAACAATCAACAAACTGAAGAGACAGCCCACCAAATGGTGGAAAATATT 2032
                           v  v     v   v    i     i     vi     vi         
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_97703219_9   2033 TGCAAACTACCCATCTGACAAGAAATTAATAACCAGAATATATGAGTAGC 2082
                               ii ivi      i   ii i vi  v           i iv i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_97703219_9   2083 TAA-ACAACTCTATAAGGAAAAAAATATAATAATCCTATCAAAAACTGGG 2131
                          vv-       v    v-     i i -     i  v  i?    v    
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAAT-AAAAAGACA-AATAACCCAATTWAAAAATGGG 823

  chr2_97703219_9   2132 CAAAAGATTTGAATGGACATTTCTCTGAAGAAGACATACAAATGGCAAAC 2181
                             i         i          ii       i           v  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_97703219_9   2182 AGGCATATAAAAAGGTGCTCAATGTCATTGATCAT 2216
                          i   i  i     i       ii   ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (44 / 33)
Gap_init rate = 0.02 (8 / 330), avg. gap size = 1.12 (9 / 8)  

2065 27.21 1.82 3.51  chr2_97703219_97708244.rev     3284  3996 (1030)    L1M4_orf2#LINE/L1        1   701 (207)  

  chr2_97703219_9   3284 TGGACAGATAATCCTTGTTCATGCACAGGAAGACTCA-TATTGTCAAGAT 3332
                             v     vi  v        v iv        i -      i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97703219_9   3333 GTCAGTTCTTCC-AATTTCATCTATGCATCAAATATAATCCCAATCAAAA 3381
                          v  i v  i  -  v  v     iiv  iv  iii      v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97703219_9   3382 TCTTAGCAAGGTATTTTTTG--GATATTGACAAACTAACTTTAAAGTTTA 3429
                           ii   --v iv       --  v        i  i iii    i  i 
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_97703219_9   3430 TTCAAAGAGGCAGAAGAGCCACAATAGTCAACACCATATTGAAGGAGAAG 3479
                          viii i v   iii  v   v     i   v  v  v     ii     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_97703219_9   3480 AACAAAGTTGGAGGGCTGATGCTACCTGGCTTCAAGACTTGCTATAAAAC 3529
                                       i  v ii  v  iiii     i    i   i   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_97703219_9   3530 GATCATAATCATGACAGTGTGG-ATTGGTGAAAGAATAGACAAGTAGATA 3578
                         v ivi      v          - i   iiv   i       vi     v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_97703219_9   3579 AATGGAACAGA-----GAGCCTAGAAATAGATCCCCATAAAAT-ACAGTC 3622
                                i   -----   i i       i --      v v - ii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACATTTATGGTC 346

  chr2_97703219_9   3623 AGCTCATCTTTGTGAAAGGATCAAAGGCAAAACTGTAGAGCAAAATCAAT 3672
                          ii v  i  i vv  i  vv v   i v vv vi i i v  i vi i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_97703219_9   3673 CTTTTCAACAAAAGGTGCTGGAACAAATAGACATAGACACACAAACGCAA 3722
                                     v        i    v i  --  ?v    i----    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGA--TAKCCACAT----GCAA 440

  chr2_97703219_9   3723 AAAAAAATAGAAGAAGAAGAATCTAGACA-CACACCATATACCCCTCATA 3771
                           i  -- ----    vv i i ivv  v-            ------- 
  L1M4_orf2#LINE/    441 AAGAA--T----GAAGTTGGACCCCTACCTCACACCATATAC-------A 477

  chr2_97703219_9   3772 GAAATTTACTCAAAATGGATTAAAAACCTAAATGCAAAATGC-AAAACTA 3820
                         i     v             i ? i         i  i -  -       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTA 526

  chr2_97703219_9   3821 TAAAAGTTCTACAAGATAACATAGGAGAAAATCTAGATTATCATGGGTAC 3870
                              v ii  v    v        ? v      vvi v i v     vv
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_97703219_9   3871 AGTGATGACTTTTAAAATACATCATCAACGGTGAAATTCGTGAATGAAAA 3920
                         i ii   ii  i v i   iiv  i   vi iiv  viviii  v     
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_97703219_9   3921 TATTTGATAAGCTGGACTTCATTAAAATTAAAGACTTCTGCTCTGTGGAA 3970
                         v  v-     ii          i         i    i  iv  viii i
  L1M4_orf2#LINE/    627 AATA-GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_97703219_9   3971 CACACTGCCAAGAAAATAAGAAGACA 3996
                         v     ii       i i i      
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACA 701

Transitions / transversions = 1.55 (116 / 75)
Gap_init rate = 0.02 (17 / 701), avg. gap size = 2.24 (38 / 17)  

 781 16.05 0.62 0.00  chr2_97703219_97708244.rev     4373  4534 (492)    L1M4_orf2#LINE/L1      746   908 (0)  

  chr2_97703219_9   4373 AAGGACTGTTATCTAAAATGTATAAAGAACTCTTTAAACTCAACAATAAG 4422
                          i     vv    i i   i              vv       i     i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_97703219_9   4423 CAAATGAATAACCCAATT-AAAAATGGGCAAAAGACCAGAATAGACAACT 4471
                         v i ii            -             i  iiv         vi 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_97703219_9   4472 CACCAATGAAGACATACAAATGGCAAAGAAGCATATGAAAAGATGCTCAA 4521
                          v    v     i           v  v     i                
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_97703219_9   4522 CATCATATGCTAT 4534
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (15 / 11)
Gap_init rate = 0.01 (1 / 163), avg. gap size = 1.00 (1 / 1)  


 297 27.96 6.45 0.00  chr2_97922395_97924545      134   226 (1925)    L1M4_orf2#LINE/L1        5   103 (805)  

  chr2_97922395_9    134 AAAATATT--GTGTTCATGGGTTAGAAGACTCAATATT----AGATGTTA 177
                           i    i--i         i  i       i      ----     vi 
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_97922395_9    178 GTTCTCCTGAAATGGATTTATATATCTAATGCAAGTGGAACCAAAATTC 226
                         i v    iv    v   i  i v  ii  i    vivvv i      i 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.02 (2 / 99), avg. gap size = 3.00 (6 / 2)  

1321 26.50 0.89 4.90  chr2_97922395_97924545      485   933 (1218)    L1M4_orf2#LINE/L1       97   527 (381)  

  chr2_97922395_9    485 AAAAACTCAGCAGTATTTTTTTTTAAAGAAACTGACACGCTGATTCTAAA 534
                             v i    v i---i      iv     i     v      i     
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGC---CTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_97922395_9    535 ATTTAGATGATAAAGAAAGGAAATAAGGAAAGCCAAAGCAATTCTGAAAG 584
                            i v   iv  v v    i viv  i v       i    ii     i
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_97922395_9    585 AGAAAATCAAAATTGGAGGATTCATAGTATCTAATTCTAAGAATTAATAT 634
                             i v    i        i   i v vi i    ii  i v   v  i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_97922395_9    635 AAAGCCACAGTTATCAAAACAGTATGG-GCTGGTGAAAGGACAGGTATTT 683
                              i     v     i     i   -i    iiv     i  ii  --
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT-- 291

  chr2_97922395_9    684 CAGAGTCTATTAGATACGTATTAGAACATAGTGAAGAGTCCAAAACCAGA 733
                         --------  -    ---i v i   i v i vi        i  vi i 
  L1M4_orf2#LINE/    292 --------AT-AGAT---CAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_97922395_9    734 CTCACACATACAAGGTCAACTGACTTTCAACAAAAGTACAGTGGGAT--T 781
                          i  i    vi v      i   i    i    ii  i --iii  i-- 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC--CAAGACCAT 377

  chr2_97922395_9    782 TCAATGAA-AAAGAATAGTTGTTTTCAACCAACAGTCCAGGAACCAATGA 830
                               ii-          i-        v  ii  v v  i  v v  i
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTC-TTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_97922395_9    831 ATATCCACACACAAAACAAAACAATCCTCAATCCATATCTTATACCATAA 880
                            ?     ii     v  viv i -- vi i  v  i  i i      v
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGT--TGGACCCCTACCTCACACCATAT 474

  chr2_97922395_9    881 ACAAACAGTAGCTAAAAATGGACTGTAGATCTAAATATAAAATCTAAAAC 930
                              v v  i  v        iii?   i      i   i v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_97922395_9    931 TAT 933
                            
  L1M4_orf2#LINE/    525 TAT 527

Transitions / transversions = 2.00 (78 / 39)
Gap_init rate = 0.02 (10 / 431), avg. gap size = 2.60 (26 / 10)  

1316 23.16 3.54 0.54  chr2_97922395_97924545     1293  1659 (492)    L1M4_orf2#LINE/L1      531   908 (0)  

  chr2_97922395_9   1293 ACTTCTAGGAAAAAAAA-AGGAGAAAATCTTTGTGACTTTGGATTAGGCA 1341
                            ii   i i    v -   ? v       i     i    i       
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_97922395_9   1342 AAGATTTCCTAGCTACAACTCCCAAAGCATGACCCATAAAAGAACAATTT 1391
                          v i    i   v  ii  v  v      ii v v i       v  v v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_97922395_9   1392 GATAAACTGGACACCATGAAAATTATAAACTTCTGCTCTTTCAAATATTA 1441
                               i     vi   v       v      i  iv   iv  iv ivv
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_97922395_9   1442 TATAAAAAGAATGAAAAGGTATGACACAAACTGGAAGAAAAGACTTGCAA 1491
                            v  i i i       ii vvv    i v   i      v i      
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_97922395_9   1492 ATCACATATCTCAAGAAAGACTTGTATCCTGAACACATAAGGAACTCTCA 1541
                             i      v vi ii           v   i i    i       i 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_97922395_9   1542 CGAACTCAATGAGAAAA---CAAACAACTCAACTTAAAAAACAGGCAAAG 1588
                          -        i v    ---    i   i   -  ?     ii       
  L1M4_orf2#LINE/    781 C-AACTCAATAATAAAAAGACAAATAACCCAA-TTWAAAAATGGGCAAAG 828

  chr2_97922395_9   1589 AACT-GAACAGACACTTCACCAAAGAAAACATATGGATGGCAAATAA--- 1634
                         i i -   i     i   v        i i   iii     v     ---
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_97922395_9   1635 -----AAAGATGCTCAAAATCAATTTTCAC 1659
                         -----            v    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (51 / 32)
Gap_init rate = 0.02 (6 / 378), avg. gap size = 2.50 (15 / 6)  


2950 27.08 1.55 0.78  chr2_97946957_97953592     5244  6144 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_97946957_9   5244 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5293
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97946957_9   5294 GGCCATACTGCCCAAAGTAATTTATAGATTCACTGCTATCCCCAACAAGC 5343
                            v     v      v i  i  i       vi  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97946957_9   5344 TACCA-CTAACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAACTTC 5390
                          v   -  iv    i  -ii    -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_97946957_9   5391 ATATGGAACCAAAAAAGAACCCGTATTGCCAAGACAATCCTGGGCAAGAA 5440
                                 viiv  ii  v  v v  v     i      i  iiv     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_97946957_9   5441 GAACAAAGCTAAAGGCATCACACTATGTGACTTCAAACTATGCTACAAGG 5490
                                 i ii   vv       vivii i      viv i      i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_97946957_9   5491 CTACAGTAACGAAAACAGTATGGTACTGGTACCAAAACAGATATATAGAC 5540
                                  iv  i     i         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_97946957_9   5541 CAACGGAACAGAA--GAAAGGCCTCAGAAACAACACCACACATCTACAAC 5588
                            i    i    --  i  v  --     i  vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_97946957_9   5589 CATCTGATGTTTGACAAACCTGACACAAACAAGCAATGCAGAAAAGATTC 5638
                           vi    v  i     ivv  v  vi v  vv     vi    ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_97946957_9   5639 CCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 5688
                         i  v  i  i        i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_97946957_9   5689 TGAAACTGGACCGCTTCCTTGTACCTTATACAAAAATAAACTCAAGATGG 5738
                             ii      v  v   iii   v           v       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_97946957_9   5739 ATCAAAGACTTAAACATATGACCTAGGACCATAAAAATCCTAGAAGAAAA 5788
                             ?    i    ii  v  v   ii  i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_97946957_9   5789 CCT-GGGGAATACCAATCAGGACATAGGCATGGGCAAAGACTTCATGACT 5837
                          v -  ? v v i v-  iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_97946957_9   5838 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACACATGGGATCT 5887
                          vi            vvi          vv     v  i v  v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_97946957_9   5888 AATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5937
                         v  i   viv  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_97946957_9   5938 ACAGGCAGCCTACAGAATGGGAGAAAAGTTTTGCAATCTATCCATCTGAC 5987
                          v  i  i  i                vv       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_97946957_9   5988 AAAGGGCTAACATCCAGAATCTACAAGGAACTTAAACAAAT---TTACAA 6034
                           i  i  vii         v  i  i     ivv    v --- v i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_97946957_9   6035 GAAAATAAG--ATCCCATTAAAAAGTGGGCAAAGGATAGGAACAGACA-- 6080
                         i  i i  i-- i  v   ?    i            vv   i     --
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_97946957_9   6081 -CTTCAAGAGAAGACATTTATGCAGCCAACAAACATATGAAAAAATGCTC 6129
                         -  i   -      i  vi viii     i  i  i       i      
  L1M4_orf2#LINE/    845 TCTCCAA-AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_97946957_9   6130 ATCATCACTGGTCAT 6144
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


 653 26.43 6.43 5.00  chr2_97966616_97973553.rev     1595  1874 (5064)    L1M4_orf2#LINE/L1        3   286 (622)  

  chr2_97966616_9   1595 GAAAGAT--TCCGCGTTCATGGATTAGAAGACT-------GTGAAGATGA 1635
                                --i  ii           i       -------  v      i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_97966616_9   1636 TAATTCTCCCCAGATCAGTTT-TAGATT-AA-GCAATTCCAATAGAAATT 1682
                         i   v       i  iii i -i     -  -     i  v  vi    i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_97966616_9   1683 TCAACAGACAATTTTTTTTTTTAGAAATTGATAAGCTGCTTTTCAAGATT 1732
                         i  i v v -----      vi         i      v ii v  iv i
  L1M4_orf2#LINE/    103 CCAGCTGCC-----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_97966616_9   1733 AGATGGAAAACGTTAAGCATCTAGAATAGACCAAACAAGTTTTAAAAAGA 1782
                          v       -i iv i v i i       v v      vi  v       
  L1M4_orf2#LINE/    148 ATATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_97966616_9   1783 AAAACA---TCAGAAGATTTAAACTACATGTTTTGAAGATCAAGTTTAAA 1829
                          i    --- ii  i  i i v   v viiv   v  i iiv v vi   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_97966616_9   1830 ACTTC--TTGTCCAGAT-GTGTCAAGGTAATTCAATGGCACAAGAATA 1874
                         i  v -- vi  v   i-    ---    --- --     i   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGT---GGTA---C--TGGCATAAGGATA 286

Transitions / transversions = 1.64 (46 / 28)
Gap_init rate = 0.05 (13 / 284), avg. gap size = 2.46 (32 / 13)  

2997 26.34 2.34 1.00  chr2_97966616_97973553.rev     4043  4938 (2000)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_97966616_9   4043 TGGAAAAACTTTCCATGCTTATGGATAGGAAGAATCAATATCGTGAAAAT 4092
                               i iv i     i i      v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_97966616_9   4093 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTGTCCCCATCAAGC 4142
                            v     v      v i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_97966616_9   4143 TACTA-TTGACTTTTCTTCACAGAATTGAAAAAAACT-ACTTTAAACTTC 4190
                          v i -i  v     i v  v -      v  i--  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAG--CTGATCCTAAAATTC 147

  chr2_97966616_9   4191 ATATGGAACGAAAAAAGAACCCACG-TAGCCAAGACAACTCTAAGCAAAA 4239
                                 -iviv  i i     vi-       i    iii i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_97966616_9   4240 AGAACAAGGCTAGAGGCATCATGCTACCTGACTTCAAA--TTATTCTGCA 4287
                                i i i    vv   ii  v  ii i      --   --  i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACA 244

  chr2_97966616_9   4288 AGGCTGCAGTAACCACAACAGCATGGTACTGGTACCAAAACAGATACATA 4337
                          i   i      i  vi    ii         i iv ii i   i i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_97966616_9   4338 AACCAATAGAACAGAAGTGAGGCCTCAGAAATAACACCACACATCTACAG 4387
                         i i    i   i    v    ivii         vv   i    i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_97966616_9   4388 CCATCTGATCTTTTGACAAACCTGACAAAAACAAGCAATGCAGAAAGGAT 4437
                         i  vi    -   i     ivv  v   i v  vv     vi     i  
  L1M4_orf2#LINE/    345 TCAATTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_97966616_9   4438 TCCCTATTTAATAAATGATGTTGGGAAAACTGGCTAGCCATATGCAGAAA 4487
                         vvi  v  i  i     i  i     v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_97966616_9   4488 ACTGAAACTGGACCCTTTCGTTATACCTTATACAAAAATTATCTCAAGAT 4537
                          v    ii       i v v i i   v             v     i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_97966616_9   4538 GGATTAAAGACTTAAAACGTAAAACCTAAAACCATAAAAATCCTAGAAGA 4587
                             i ?    i    -i    i v       i      v  i       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_97966616_9   4588 AAACCTAGGCA-ATACCATTCAGGACGTAGGCATGGGCAAAGACTTCATA 4636
                             v    ?i- v i -   iv   v v  vv i     v ii   v  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_97966616_9   4637 TCTAAAACACCAGAAGCAATGGCAGCAAAAGCCAAAATTGACACATGGGA 4686
                         vv  vi      i     vvi   i      vv     v  i v  v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_97966616_9   4687 TCTAATTAAACTAAAGAGTTTCTGCACAGCAAAAGGCACTATCATCAGAG 4736
                         ii v  i   v v  i ii  i  ii vv    i i        vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_97966616_9   4737 TGAACAGGCAGCCTACAGAATGGGAGAAAATTCTTGCAA-TC---TATCT 4782
                             v  i  i  i                 vi      -  ---     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_97966616_9   4783 GACAAAGAGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTA-CAA 4828
                           i  i ii  vi          v  i        --  -  i i -i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_97966616_9   4829 GAAAAAAA-----AACC--ATCAAAAAGTGGGTGAAGGATATGAACAGAC 4871
                         v     i -----    --  i?    i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_97966616_9   4872 ACTTCTCAAAAGAAGACATTTATGCGGCCAACAAACATATTTAAAAAAGC 4921
                          i     v        i  vi vii      i  i  i  vv   i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_97966616_9   4922 TCATCATCACTGGTCAT 4938
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (145 / 87)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.58 (30 / 19)  

 432 26.83 6.50 7.72  chr2_97966616_97973553.rev     5663  5908 (1030)    L1M4_orf2#LINE/L1      387   629 (279)  

  chr2_97966616_9   5663 AAAAAAAAGTCTTTTTCAACAAATGATAGTAGGCCTACTGGATATTTACA 5712
                            i  v        -         i iv i  v v        ?ii   
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_97966616_9   5713 -GAGAAAGAAAAAGTGAACTTTAATCTTTAACTCACACCAT-CGCCACAA 5760
                         - vi      ----    v  vi i ii  v          -ii v v  
  L1M4_orf2#LINE/    436 TGCAAAAGAA----TGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_97966616_9   5761 TTAACTTAAAACAGACAATAATAAATAGGCTCATGTCTAAAAGTTAAAGG 5810
                               i    ii  iv ? ------- i ii vi v   i  i    iv
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWA-------GACCTAAATGTAAGAGCTAAAAC 524

  chr2_97966616_9   5811 TTTAAAATTTTTAGGATAAAAC-CAAGCTTTTCATAGAAATATTTGCAAA 5859
                          v     i i    i v     -i i ?v -------    v  i ii v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGT-------AAATCTTCGTGAC 567

  chr2_97966616_9   5860 CT-GGACAAAGC--------TTTAAA----ATACCAAAAACACATACCAT 5896
                           -  iiv i  --------i   i ---- i       i    vi v i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_97966616_9   5897 AAAAGAAAAAAT 5908
                                     
  L1M4_orf2#LINE/    618 AAAAGAAAAAAT 629

Transitions / transversions = 1.86 (41 / 22)
Gap_init rate = 0.04 (10 / 243), avg. gap size = 3.50 (35 / 10)  

 530 22.09 20.08 1.61  chr2_97966616_97973553.rev     6198  6446 (492)    L1M4_orf2#LINE/L1      614   908 (0)  

  chr2_97966616_9   6198 CAA-AAAAGAAAAAATGATCATCATTTCGACCTCATCAGAATTTAAAACT 6246
                            -            ii--  v v  v   i      i    v      
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAG--ATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_97966616_9   6247 TAGGCTCTTCAAAAGACACCATTAATAAAAGGAAAAGGTAAACCA--GGA 6294
                          vv iv       i     i  i  v   iv      ii  v   -- i 
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_97966616_9   6295 CCAGGGTAAAAATATTTGCA------------------GCAC--GTA--- 6321
                         i--   vi            ------------------ v  --   ---
  L1M4_orf2#LINE/    712 T--GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_97966616_9   6322 -------ACAGAGAACTCTTACAACTGAATAATAA---GACAGACATTCC 6361
                         ------- i i               v        ---    i i vi  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_97966616_9   6362 AGTTAAAAAAC----------TTTCCACAGACGTTT----ACAAAAGATA 6397
                          i  ?     i----------   vv i    i   ---- v i      
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_97966616_9   6398 CCTAATTGTACACCAAGTAAATGGAAAGATGGTCAACATTATTCATCAT 6446
                         ivi  v  vv  vi   i v   i       v       i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (30 / 24)
Gap_init rate = 0.03 (10 / 295), avg. gap size = 5.40 (54 / 10)  


1437 24.69 5.19 11.20  chr2_97994807_97997292     1035  1998 (488)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_97994807_9   1035 GAAAAATATAC--TGTCTCA--GACTGTCAGACTGAATACTGAAAATTCT 1080
                             i    v --   -   --  i  vv     v    i  ----  --
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGT-TCATGGATTGGAAGACTTAATATTG----TT-- 45

  chr2_97994807_9   1081 GAAAGATTTTTAATTCTTGCCAAATTGATCTTCAGATTCTGAGTGACGCT 1130
                         --     vvi-   v  iv            v       viv ii iv i
  L1M4_orf2#LINE/     46 --AAGATGGC-AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chr2_97994807_9   1131 AATAAAAAATCCCGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 1180
                         v  v    -    iiv  iv v v -------------  iivivi -  
  L1M4_orf2#LINE/     93 TATCAAAA-TCCCAGCTGCCTTTTT-------------TGCAGAAAT-TG 127

  chr2_97994807_9   1181 TAAAGCTAATTGAAAAGATACATATGGAAG-GCAAAGAACTGAGAATAAC 1229
                         vv     i  ivv   -  v         i-    i i  iv      i 
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAA-ATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr2_97994807_9   1230 CAAGACATTACTGAGAA-GAATAACAAAGTGTCAGGATTTGTTCTACCAA 1278
                            i   v vi   i  -   v        vvv    i iiiv  v  v 
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_97994807_9   1279 ATATCAAAACTT--TA-AAAACTATAGTCATTAAAACGGTG--ACCCTGG 1323
                           v         --  -   i   i   v  i  i  i   --iiv    
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_97994807_9   1324 TATTAGGATAGACAAATAAGCCAAAGAAATCCAATACAGTGCCCAGAAAC 1373
                         i  v          v   iii   v i   vv   vv  v i       i
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_97994807_9   1374 AGGCTCACACATATATGGACACTTGATTTATGAATAAGGTGTCACTGACA 1423
                          ii i  i    v     v  v       vi  vv i    i  v-   v
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACC 375

  chr2_97994807_9   1424 AAT-ACTAGGGAAAGAAAA--CATTGGGAAATAGTCAATAAAGGATGCTG 1470
                          v - v i         v -- v  ---------    i   v i     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTT---------TCAACAAATGGTGCTG 416

  chr2_97994807_9   1471 AGACAAT--------CAAATACAAGA-AATAAAAT-----CTTGATCTCA 1506
                         i     i--------  v  i   i -   i  i ----- iiv i    
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_97994807_9   1507 CATCA-ATAACAAAAATTTATTCCAGACAGAATTT---GAGCTAACTGTG 1552
                           i  -   -        v i  v i ii  -- i---  v    v   i
  L1M4_orf2#LINE/    467 CACCATATA-CAAAAATTAACTCAAAATGGA--TCAWAGACCTAAATGTA 513

  chr2_97994807_9   1553 AAAGGCAAAACAGTAAAATTCT------AGAATACGGGAGAATATCTTCA 1596
                          i  vi     vi     i   ------ i  i ii  ? v v      i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_97994807_9   1597 CGACCTTGGGATAGAAAAACATT----GAACAAGACACAAAATAAAAAAG 1642
                         i         v   iv  vvi  ----ii i v     v   ------  
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA------AG 607

  chr2_97994807_9   1643 TATTAACCATAATGGAAAATACTGACAGACTGAACTTCATTAAAATTAAG 1692
                         i iv i v i  vi     v iv  i i i  i       i        i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_97994807_9   1693 AATTCCTGTTCACTAAAAGTCACCATTACATAAGCCAAAAGGGCAATCCA 1742
                           i ii   v vii   i v   i  i viv   iv     i-   i   
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA-CAACCCA 706

  chr2_97994807_9   1743 TCCAGTGAGAGAAGCTATTTTCAATATATGTAACCAATAAAGAACTCATG 1792
                         ivv i  i     ---------     v  i  ---  --------   i
  L1M4_orf2#LINE/    707 CAGAATGGGAGAA---------AATATTTGCAA---AT--------CATA 736

  chr2_97994807_9   1793 TAATGGAACTGATTTTTGTTACTGCTGTGAGGTTACGGCTCCAGGAAAGA 1842
                           ------------ i  v  ---------------------   i ---
  L1M4_orf2#LINE/    737 TA------------TCTGATA---------------------AGGGA--- 750

  chr2_97994807_9   1843 TCTTGTATTCAGAACTTATAAAGAACCTCTACAA---AACAATGGGAAAA 1889
                         -       i     iv          iii     ---  i   ----   
  L1M4_orf2#LINE/    751 -CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT----AAA 795

  chr2_97994807_9   1890 AAGACATGCAAACCAACAGCAAAATGGGTAAAAGACTT-AACGGA--TGT 1936
                               vii  v    iv?v        i   i  i  -  ii  -- v 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_97994807_9   1937 CACAAAGGAAGATATCCAAATGGTCAAGTAA--ACATGAAAAGTTGCTCA 1984
                          v v  i        v       i   -   --          v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGATGCTCA 894

  chr2_97994807_9   1985 GCTTTATGAGAAAT 1998
                         i v i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (135 / 101)
Gap_init rate = 0.05 (42 / 906), avg. gap size = 3.76 (158 / 42)  


3213 26.98 0.55 0.55  chr2_98012283_98017217     3536  4443 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_98012283_9   3536 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 3585
                              ii i  i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_98012283_9   3586 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3635
                            v     v      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_98012283_9   3636 TACCAATGACTTTCTTCACAGGATTGGAAAATACT-ACTTTAAAGTTCAT 3684
                          v   iivi i  i  ii   i v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_98012283_9   3685 ATGGAACCAAAAAAGAACCCACATTGCCAAGACAATCCTAAGCCAAAAGA 3734
                               viiv  ii  v  viv  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_98012283_9   3735 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 3784
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_98012283_9   3785 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 3834
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_98012283_9   3835 ATGAAACAGAAC--AGAGCCCTCAGAAATAATACAACACATCTACAACCA 3882
                            i  i    i--    i  --        vv v i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_98012283_9   3883 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 3932
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_98012283_9   3933 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 3982
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_98012283_9   3983 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 4032
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_98012283_9   4033 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4082
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_98012283_9   4083 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAACGACTTCATGACTAA 4131
                             ?i- v i -   iv   v v  vv i     i ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_98012283_9   4132 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATCTAA 4181
                         i            vvi          vv     v  i i  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_98012283_9   4182 TTAAA-TGAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4230
                          i   - v   i -   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_98012283_9   4231 CAGGCAACCTACAGAATGGGAGAAAATTTTTACCATCTACCTATCTGACA 4280
                         v  i     i                 v   i v vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_98012283_9   4281 AAGGGCTAATATCCAGAATCGACAAAGAACTTAAACGAATTTACAAGGAA 4330
                          i  i  vi          vv i        ivv  i v iv i  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_98012283_9   4331 AAATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGGCACTT 4380
                           iv    i     v  i?    i     i      v    i  i  i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_98012283_9   4381 CTCAAAAGAAGACACTTATGCAGCCAACAGATACATGAAAAAATACTCAT 4430
                            v        i ivi viii     i iii         i  i    v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_98012283_9   4431 CATCACTGGCCAT 4443
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


1115 19.32 10.23 0.76  chr2_98017950_98020208      562   825 (1434)    L1M4_orf2#LINE/L1        1   289 (619)  

  chr2_98017950_9    562 TAGAAAGATATCTGGTATTCATAAGCTAGAATACTTAATAATGTTAAAAT 611
                          i          ivi i     iiii i   v        v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_98017950_9    612 GGTAATATTC---------------AGATCCAACGCAATC-TTGTCAAAA 645
                           i    i  ---------------    i          -i i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_98017950_9    646 TCTCACCTTGCTCTTTTGCA--AATCGACAAGTGGCTCCTGAAGTTCATA 693
                           i  v  vv  i       --   i      iv v    i  i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_98017950_9    694 AGAATATTCAAG--------AATAGCCAAAACAGTTTTGAAAAAGAAAGA 735
                         v i v  v    --------             i i           ii 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_98017950_9    736 CACAAT-GGAGGACTCAAAACTTCCCGATTTCAAAACTTAACTACAAAGG 784
                           v i -          -v       i             -        v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTA-CTACAAAGC 248

  chr2_98017950_9    785 TATATTAATCAAGACAGAACAGTACTGGAATAAAGATAAAC 825
                           i v            viii       v    i    i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

Transitions / transversions = 2.00 (34 / 17)
Gap_init rate = 0.02 (7 / 289), avg. gap size = 4.14 (29 / 7)  

2568 18.70 3.33 3.65  chr2_98017950_98020208     1137  1767 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_98017950_9   1137 AAAGATAAACCTAATCAAATAGATCAAACAGAATAGAACTGACAGTCCAG 1186
                           i    i  ---  ---         -ii        i   v       
  L1M4_orf2#LINE/    280 AAGGATAGAC---AT---ATAGATCAA-TGGAATAGAATTGAGAGTCCAG 322

  chr2_98017950_9   1187 AAACAAACCCTCGCATTTATGGCCAATTGATTTCGGCACTCAATTGATGA 1236
                            i      vii         i          ------  i i-- v i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTT------TCGAC--AAGG 364

  chr2_98017950_9   1237 ATGCCAAGATAACTCAGAGGAGAAAAGAACAATCTTCTCAACAACTGGCA 1286
                         i        iv i   - v i i      i i    i       v   ii
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCA-ATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_98017950_9   1287 CTGGAATAACTAGGTATCTGCTTGGAAAAGAATGAGGACGGACCC-TGCC 1335
                             i i    i i  ? ii v  v          i vi      - i  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_98017950_9   1336 TAACAACATATGCAAAAATTAAATCCAGAAGGAACAAAGACCTCAGTGTA 1385
                          v   v     i          v  v i v   v  ?      v i    
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_98017950_9   1386 AGAGATAAAGCTATAAAACTTTT-GAAGATAACATAGATGTAAATCTTCA 1434
                             v    i          i  -     v       i?          i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_98017950_9   1435 TAACCTCTGATGAGGCAATGGTTTCTTA--------ACTAGAA---TAGG 1473
                          i    iv i v                --------  i i  ---i i 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_98017950_9   1474 TAAGCAAAGACAACACAGATAAATTAGACTTTATCAAAATTAAAACAGTT 1523
                         i  vv     v  v i         i     i             vvv  
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_98017950_9   1524 TGTGCTTCAAAGGGCACTATCAATAAAGTGAAAAGACAACCCACAGGATG 1573
                                      i         v                      i   
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_98017950_9   1574 GGAGAAAATTTCTGCAAATGATGTATCTGATAAGAGATACATACAGAGAA 1623
                                  v i       v  i           i  ivii  ivv    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_98017950_9   1624 TATAAAAAGAACTCTTGCAA-TGAATAA----AAGACAAACCTCCCAATC 1668
                             v           i   - v     ----        ivv      i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_98017950_9   1669 AAAAAATGGACAAGGAAACTGACTAGACATTTCTCCAAAGA---TACATA 1715
                         ?        i   i i vi   v                  ---  i i 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_98017950_9   1716 AACGGACAATAATACATACATACACGAAAAGACGCTCAAAACCAGTCCTT 1765
                           i  v      -------ii   i       i      v i  ??????
  L1M4_orf2#LINE/    864 AATGGCCAATAA-------GCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_98017950_9   1766 AG 1767
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.78 (73 / 41)
Gap_init rate = 0.02 (14 / 629), avg. gap size = 3.14 (44 / 14)  


2914 21.29 4.88 4.43  chr2_98020724_98023946     1831  2732 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_98020724_9   1831 GAAAGATATACCATGTTCATGCATCAAAAGAACCAATATTGTTA---CAG 1877
                                  v           v  iii    vii          ---ii 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_98020724_9   1878 CAATTTTCCCCAAATTGATCTAGACAGTCAATACAATTCCAATCAA---- 1923
                             vi                v v v    ii    i  v     ----
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_98020724_9   1924 ------GTTTTTTGTTGTAAAAATTTACAAGATGATTCTAAAAGTTATAC 1967
                         ------ ii    -   i i     v     v    i      v i   i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_98020724_9   1968 AGAAAAGCAAAGGACCCAAAATAGTAAAAAGAATTTTGAAAAAGAAGAAC 2017
                         i    v    i       i     iv    v   i               
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_98020724_9   2018 AAGATTGGAGGACTCAACATTGCCTGATTT-AAGACTTA-----AAATCA 2061
                           ii            -  i v  ii    -  i     -----  iii 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_98020724_9   2062 TAGTAATCAAGATGGTATAAAACTGACACA--GATA-----ACAGATGTG 2104
                         i           ii  i iiv    i  i --    ----- i    vvi
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_98020724_9   2105 TGAAATAGAACAGAGACTCCAAAAGTAGACCCCCACATATATGGTCAACT 2154
                           i       iv    v    i  i  i    vi    v         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_98020724_9   2155 GATTG-CAACA-GGGTGCCAAGGCAATTCAATTGGGGAAAAGTAATCTTT 2202
                             v- i   -          i v       v   i  i i  i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_98020724_9   2203 TCAATAAGTCATGCTGGTACAAATGAATAGCCACATGGGAAAGAAAAACA 2252
                             i  i vi      v    v  i   ?       vi      ---ii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA---TG 447

  chr2_98020724_9   2253 AAAGAGAATCTGGATGCTC-CAAAATTTACAAAAATCAACTTGAAATGAA 2301
                           ivv i i ivv i-   -  vv  v         i    ii     i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTAC-CTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_98020724_9   2302 TAACAGAATTTA-TGTAAGAGCTAAAATTCTAAAGTTCCTAGAAATCAAC 2350
                          v ?   vi v -              i v    ii  i     ivv   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_98020724_9   2351 ACGGGA--AAATTTTAGTGATCTTGAGTTTGGCAAAGATATTCTTAAGTA 2398
                          ii  ?--    i  v    i    i   v     v i -      ii  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATA 595

  chr2_98020724_9   2399 GGATACAAAAAAGAAAAAAATCTTGAACTATAAAAGAAAAAA-AGATGAA 2447
                         v  i  v    iv v  iv --------- i           -    i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCA---------ACAAAAGAAAAAATAGATAAA 636

  chr2_98020724_9   2448 TTGAGAGGT-----GGATTAAAAATTTTTTTTTTAGCTTTTACTCCTCAA 2492
                            -  vv -----ii        i    v ----    --------   
  L1M4_orf2#LINE/    637 TTG-GACTTCATCAAAATTAAAAACTTTTGT----GCTT--------CAA 673

  chr2_98020724_9   2493 AAGACACTGTTACAAAAGTAAAAATACAAGCCACAGACTGGAA-ATAATA 2541
                          i      i i vi     i    v    v       v   i - v    
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_98020724_9   2542 TTTGCAAAATGCTTATCTGACAAAGGACTTGTATCCAGAATATGTAAATA 2591
                                 viiiv       i  i                   i    v 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_98020724_9   2592 ACTGTTACAACTAAATAAGAAAA---CAAACAGCTCAATTTAAAAAAATG 2638
                            v        v     v    ---    i i i     ?     viv 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_98020724_9   2639 CAAAAAAGATGTGAACAGACATTTAAGCAAAGACAACATG--AATAGCAC 2686
                             i--   v    i        vvv      vi i  i--   i  - 
  L1M4_orf2#LINE/    824 CAAAG--GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC-C 870

  chr2_98020724_9   2687 ATGAAATAAGAGGGCACATGAAAAGATGCTCAAAATCCTTAGTCAT 2732
                          ----     ----                   v   v????????
  L1M4_orf2#LINE/    871 A----ATAAG----CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (115 / 73)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 2.90 (84 / 29)  


3138 21.46 3.76 3.76  chr2_98049645_98052901     1862  2765 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_98049645_9   1862 AAAATATCCC-TGTTCATGTGTCAGAAAACTAAATACTGTTAAGAAGTCA 1910
                           i       -        vi ii   i   v    i        v v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_98049645_9   1911 GTTCCCCCCACAAATTCATCTATAGATTCAACACAGTCCCAATCAATACC 1960
                         i v i     --    v     i         i  i    v     v i 
  L1M4_orf2#LINE/     55 ATACTCCCCA--AATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_98049645_9   1961 CAAGAAGGCTCTGTTGTACAAATTGATAAGCTGATTCTAAAATTCATAAT 2010
                          v  vv v  i v   i v       i        i            vv
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_98049645_9   2011 GAAATGTGAAGGATCTTGAATAGGCAAAAC--TCT-GAAACAGAA---CA 2054
                               ii i   i iv      v      --   -    v    ---  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_98049645_9   2055 AAGTTGGTGAACTGACACT-----GTTTCGGTAACTATAATACA--GCTG 2097
                                v i   v     -----i    ii-    -  v    --   i
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAA-AACT-TACTACAAAGCTA 250

  chr2_98049645_9   2098 CAGT---CAAGACAGTGTGGTACTGGCATCAAGGCAGAAAAATAGATTAA 2144
                             ---                      v i ii   v v      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_98049645_9   2145 CAGAACAAAA--GAGAGACAGACAACCAGAAATAAACTCACACATGTACA 2192
                         ii   i i  --     v -------           i  i    v  ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-------CAGAAATAAACCCATACATTTATG 343

  chr2_98049645_9   2193 TGCAATTGCTTTTCAACAAG--TAC-AAGCACAATACAGTGGGAAAAGGG 2239
                         vv      v     i     -- i -   -  v  v  i    i    --
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAG-- 390

  chr2_98049645_9   2240 TAGTAGTCTTTTTAATTGACTTTTTAATAGACACTAGAAGAACTGGTTAT 2289
                         - i         i  i-- ------   i -ii  i i v      v  ?
  L1M4_orf2#LINE/    391 -AATAGTCTTTTCAAC--A------AATGG-TGCTGGGACAACTGGATAK 430

  chr2_98049645_9   2290 TTATATGCAAAAAAAAAAAAAAAAAAGAACTTGGGTACAAAACTCATATC 2339
                         ii i        i  v----------   v    iiv vv v    i i 
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAAT----------GAAGTTGGACCCCTACCTCACACC 470

  chr2_98049645_9   2340 ATATGTAAAA-TGAACTCAAAATCAATCACAGATCTAAATGAAAGACCTA 2388
                             ii    - v          vi    ?   i       v    v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_98049645_9   2389 CCACTATAAAACTTCCAGAAAAGAATACAGGAGAAAATCTTTGTGACCTT 2438
                         vv           iii    i i  i i   ? v       i        
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_98049645_9   2439 GCATTAGGCAGAGATTTCTTAGATACGATACCAAAAACATGATCTATAAA 2488
                          vi       iv i           i  i       i  ii v v i   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_98049645_9   2489 AGAGCAAATTGGTAAAGTTGATTCAATCAA--TTAAAAACTTCTGCTCTT 2536
                            iv    v i    v v  i iv     --          i  iv   
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_98049645_9   2537 CAAAAGAC--TGTTATGAGAATAAAAACACAAACCTCAGACTTGGAAGGA 2584
                             i   -- i i v  i i i    v    v  v    v v   iii 
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_98049645_9   2585 ATCCTTGTAAAT-ATGTATCTC-CAGAATACTGGTACCCAGAACATATAA 2632
                           vi   i    -  i     v-i iiiv   v   i      i      
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_98049645_9   2633 AGAACTCTCAAATCTCAAAAATAAGAA----AATAGCCTAAT-AAAACAT 2677
                                 i v v     v     i  ----    i  i   -?   v  
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_98049645_9   2678 GGGCAAAAGATGTGAAAAGACACTTTACCAAATGAGATATATGGATGGCA 2727
                                i   v    v     i  iv     vi       iii     v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_98049645_9   2728 AATAAGCACATGAAAAGATGCTCAACATCATTATTCAC 2765
                                                       ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (114 / 76)
Gap_init rate = 0.03 (27 / 904), avg. gap size = 2.52 (68 / 27)  


3870 19.09 6.29 0.58  chr2_98062198_98064163      616  1474 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_98062198_9    616 TGGAAAGACATCCCAAGTTTATGGGTTAAAA-------TACTGTTAAGAT 658
                                 i      v   i    i  ii  -------  i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_98062198_9    659 ATCAATACTACCCAATGTGATCTATAGGTTCAACACAATCACTATCAAAA 708
                         iv       v     vv       i  i      i     v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_98062198_9    709 TCCCAAAATCC-------CAAGGCAAGTAGAAAAGTGCATCCTAAAATTC 751
                              ivvv  -------  i---  i v  v   ivv            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG---AAATTGACAAGCTGATCCTAAAATTC 147

  chr2_98062198_9    752 ATACAGAATCTCAAGGGACCCCAAATAGCCAAAATAATCTTGAAAAGGAA 801
                            ii   viv          vi           i           i   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_98062198_9    802 GAAGACAGTTAGAGGTCTCACATTTCCTTATTTCAAAACATATTACAAAG 851
                            v v    i    v      i    iv          v  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_98062198_9    852 CTATAGTATTCAAAATAGTCTGGTACTGGCATAAAGACAGACACACAGAG 901
                            i    v    i i   v              i  i     i i   v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_98062198_9    902 CAGTTAAACAGAATAAAGTGTCCAGAAATAAACCCTTGCATATATAGCCA 951
                           i vi  i     vi  v                v i   v   i i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_98062198_9    952 ATTAATTTTCATACAAGGACACAAAGACTACTCAGTGAAGAAAGGACAGC 1001
                            i      i-      iii v     i i   i  ii     i i  i
  L1M4_orf2#LINE/    348 ATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_98062198_9   1002 CTCTTCAACAAATGGAACTGGAGAAACTGGATATCCACATGCAAAAGAAT 1051
                           i            vi    iiv         ?                
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_98062198_9   1052 AGAGTTATACCCTTTATCTTACACCATAAATAAAAGTTAACTCAAAATGG 1101
                         ii    iv    i - i  i        v i    i              
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_98062198_9   1102 GTTAAAGACCGAAACATAAGACCCAAAACTATAAAATGCCTAGGAGAAAG 1151
                         i i ?     v   ii     v i            iv i   i     i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_98062198_9   1152 CATAGGGAAAAAG-TTCATGACATTGGATTTGGCAATGATATCTTGGATA 1200
                               ?iv   v-   i    v    i  v       i v    i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_98062198_9   1201 TGACACCAAAAGCAAAAGTAAC-----------TA--------------T 1225
                                       v   i   -----------  --------------i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_98062198_9   1226 ATCAAA--CAAAAACTTTTGT---TCAAAGAATATGATCAACAGAGTGAA 1270
                               --i            ---      i i iv     v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_98062198_9   1271 AAGGCAACCTGCCAAATGGGAGAACATAGTTGCAAATCAT----CTGATA 1316
                            i     ii vi          v   v           ----      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_98062198_9   1317 AGGGG-TAATATCCAGAATATATAAGGAACTCCTATAACTCAACAACAAC 1365
                             i- vi                i      i  i       i  i  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_98062198_9   1366 AA--CAAA--ACCTGAATATAACGTGGGCAAAGGACGTGAATAGACATTT 1411
                           --    --   ii v ?v  vi           iv             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_98062198_9   1412 CTCCAAAGGAGATATACAAATGCCCAAGAAGGATATGAAAAGACGCTCAA 1461
                                 i             v    v   v i         i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_98062198_9   1462 TATCATTAATCAT 1474
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (103 / 57)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.21 (59 / 14)  


 206 26.87 1.49 0.00  chr2_98186132_98187862.rev      503   569 (1162)    L1M4_orf2#LINE/L1      227   294 (614)  

  chr2_98186132_9    503 ACTTCAAACTATTCTACAAGGATACAGTAACCAACACAGCATGGTACTGG 552
                          i      viv v      i v        i   v    ii         
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_98186132_9    553 TA-AAACACACACACACA 569
                         i -  iv i v   i i 
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATA 294

Transitions / transversions = 1.57 (11 / 7)
Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1)  

1717 23.50 3.94 5.36  chr2_98186132_98187862.rev      606  1239 (492)    L1M4_orf2#LINE/L1      284   908 (0)  

  chr2_98186132_9    606 ACAGACATATAGAACAATGGAACAGAATACAGAA-CCAAAAATAAAGCCA 654
                          i           v        i     vv   i-   i       v   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_98186132_9    655 CACAACTACAGTCATATGATCTTCAA-AAAGTTGACAAAAATAAGCAATG 703
                         i   vi  ii    vv    i   i -  i v  v   i vi vv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_98186132_9    704 AGGAAAGGACTCCCTATTCAATAAATGACTCTGAAATAGCTGGCTAGCTA 753
                         i      i ivvi  v     i     iiv   ii i i    v  ? i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_98186132_9    754 CATGCAGAAGAATGAAACTGGACCCCTACCTTTCACTATATAAAAAAATT 803
                               i         ii             iv   i     v       
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_98186132_9    804 AATTGAAGATGGATTAAAAATTTAAACATAAGATC-----CTAGGGAA-T 847
                           i v  i      i ? i ii    ii     v -----   vii  - 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_98186132_9    848 CCTAGAAGAAAACCTAAG---AAATATT----ATTCTGGGCACAGGCCTT 890
                          i           v  i ---    v  ---- iii    i-i    ---
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGC--- 579

  chr2_98186132_9    891 GGCAAATAATTTAT-AACTAAGTCCTCAACAGCAATTGCAACAAAAACAA 939
                         ----   ii   v - iv  v v vi   v    vvv         iv  
  L1M4_orf2#LINE/    580 ----AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_98186132_9    940 AAATTGATAAGTAGAACCTAATTAAA-TTAAAGAGCTTCTGCTCAGCAAA 988
                             v     i v i  i v  i   -     i -   i  iv vv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAA 674

  chr2_98186132_9    989 AGAAACTATCAACAGAGTAAGCAGACAACTTATAAAGTAAAAGAAAATAT 1038
                         i  v        v i   i iv       ii i i i iii         
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_98186132_9   1039 TTGCAAATATTTATTGAAAATATTTGCAAACTGTGCATCCAATAAAGA-- 1086
                                 ---i  -----    i  ---------------    i i--
  L1M4_orf2#LINE/    725 TTGCAAAT---CAT-----ATATCTG---------------ATAAGGGAC 751

  chr2_98186132_9   1087 TTGAATATCCAGAATCTATAAGGAAGTTAAACTATTCAGCAAGCAAAA-- 1134
                            --          v     i   v ivv  v i   ii  vv    --
  L1M4_orf2#LINE/    752 TTG--TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_98186132_9   1135 --AATAACCCCATTTAAAAATGGGCAAAAGACATGAATAGACACTTCTCA 1182
                         --        v   ?             i  iv          i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_98186132_9   1183 AAAGAAGACACATAAGTGGATAAGAA--ACAAGAGAAAATGCTCAACATC 1230
                                 i i i  i   vi  v  --   v  i  i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_98186132_9   1231 ACTAATCAT 1239
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.61 (90 / 56)
Gap_init rate = 0.03 (18 / 625), avg. gap size = 3.28 (59 / 18)  


1723 28.36 11.16 0.60  chr2_98274591_98276841.rev      629  1291 (960)    L1M4_orf2#LINE/L1       42   774 (134)  

  chr2_98274591_9    629 TGTTA-GACGTCAATTCTCTTGAATCTGATCTATAGACTTAAGGGAATCT 677
                              -  i v    v   iiv  vi       i   i i  v v    i
  L1M4_orf2#LINE/     42 TGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chr2_98274591_9    678 TAATCAAAATCCTAG-TGTACTGTTTTGTAGATTTCAACAA-CTGATTCT 725
                         iv          i  -  i-  v     i   vv ii    -     i  
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_98274591_9    726 GAAATGTACAAGGCAGGTCAAAGGAACTATATAACAGCCAAAAAAATTTG 775
                         i    vi i v  v ivv   i   v i v -- i        v   i v
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGA--ATAGCCAAAACAATCTT 188

  chr2_98274591_9    776 GAAG--GAAATACAAAGCTAGAGGATTCAGGTTGGCTGATTTCAAGACTC 823
                            i--   iv      i i     i   vii vv ii       i   i
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_98274591_9    824 AGTGTAAAGTCACAATAATAAAGACAATGTGATGTTGGTGAAAGAACAGA 873
                          v ii    ii   i    v      i    i ii   iiv   i i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_98274591_9    874 CACCTA--TTAATAG--TTCAAT-GAAA---CAAAAATAGACCCACACGG 915
                           iv  -- i   i -- vv   -  i ---  i     i     i  iv
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_98274591_9    916 ATATAGTCAAATGATTTTTGACAAGAA-GCAATAGTAATTCCACGGAGAG 964
                         v   i     v       i      ii-  v viiiv    v i  i  i
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_98274591_9    965 AGGAATAGTTACTTAGACAAACAGTGCTGG---------AT--------- 996
                           -      ivi  vi     ii       ---------  ---------
  L1M4_orf2#LINE/    389 AG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_98274591_9    997 --------------------CCTGCCTCACACCTTATACAAAAATGAACT 1026
                         --------------------   i         v           v    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_98274591_9   1027 CAAAATGAACCCTATTCTTAAACACAGAATGTAAAACCATTACATTTGAG 1076
                                i i v? vv i    iii ii vv      i  v v i ivvi
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_98274591_9   1077 GATGAAAACAT--GAGAAAACCTGCATGACT---------GCAATG--TG 1113
                           v        -- ? v   i  v i    i---------      -- v
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_98274591_9   1114 TTTAGCTATGGGTCTAAAAGCACAATCCGTAAAG--AAAACTTGGCAACT 1161
                         i    v    ivv i          v vii   i--    v v ii  v 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_98274591_9   1162 TCGACTTTATCAAAATTAAAAACTTATACACAGTGAAAAACCCTATTAAG 1211
                          v     i                 v iii vvii  ii  v    i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_98274591_9   1212 GGAATGAAAAG-----CCATAGATTGGGAGAAAATACTTGCAAATTGTAA 1256
                         ii i       -----   i   v            i        ii  v
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_98274591_9   1257 GTCTGATAAAG--TTTATGTGCAGAATACATGAAGAA 1291
                         i        i --i  i i v       i  i     
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

Transitions / transversions = 1.70 (117 / 69)
Gap_init rate = 0.03 (20 / 733), avg. gap size = 3.90 (78 / 20)  

 478 16.22 1.80 3.60  chr2_98274591_98276841.rev     1641  1751 (500)    L1M4_orf2#LINE/L1      782   890 (18)  

  chr2_98274591_9   1641 AACTCAATCTTAAGAAAACAAACAACTCAATTAAAAAATGGGCAAAATAT 1690
                                 vv   i  i     i   i     ?             iv  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_98274591_9   1691 CTGAACAGATATTTCACCAAAGAAGACATACATACAGATGCCTAATAAGC 1740
                         i    i   i     v          i     ----i   v i       
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACA----AATGGCCAATAAGC 877

  chr2_98274591_9   1741 A--TGAAAAGACG 1751
                          --        i 
  L1M4_orf2#LINE/    878 ACATGAAAAGATG 890

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.02 (2 / 109), avg. gap size = 3.00 (6 / 2)  


2959 28.64 1.90 0.34  chr2_98299337_98302312     1592  2485 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_98299337_9   1592 TGGAAAGATATGTCCTGTTCACGGATTGAACGACTTAACAT-ATTAGAGA 1640
                                    vi v      i      i v       i  -i   -   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGA 49

  chr2_98299337_9   1641 CGTCAGTTCTCCCCAGCTTGATCTATAGGTTTATCAAAATTTCTATAAAA 1690
                         i v  i v       iv        i  i  i v iv   ii    v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_98299337_9   1691 ACCCCAGAAAAGTTTTTTACAGACATAGTTAAGCCTATC-TGAAATTTAT 1739
                          i     vvivv      i    v  v vi    iv   - i     i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_98299337_9   1740 ATGACAAGTCACAGGCTCTAAAAATGTTTAAACAATCTTGAAAAAGAAAA 1789
                            iv  vv  vi  vi i i  vv iiv                   i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_98299337_9   1790 ATAAAATGGGAAGAATCATTATACCTAGTATTAAGGCTTACTATGTAGCT 1839
                          i   i v   i  v   ivv v  i i v i  ii       iiv    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_98299337_9   1840 GCATTCATCAAGATGTATTTGCT-CTGGTGGAGAAACAGACACGTAGACC 1888
                         i  v v       ii-i v  v -    iiv iii i     ii    i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACA-GTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_98299337_9   1889 AATGGAACAG--TTA------TAGAAATACACCCACACAAC-ATGCTCGA 1929
                                i  --  i------i       v     i   vi-   v  i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_98299337_9   1930 CTGATTTTTGACAAAGATGCAAAAGCAATCCAGCGGAGGAAGGATAGCCA 1979
                         i       i     i i   v  ii v  i  ii  i i   i    i v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_98299337_9   1980 TCTCAATAAATGGT--TGGAGCAATTGGATATCCAAAGGCAAAATAATAA 2027
                          i    i       --   ii   i      ?   v v      v   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_98299337_9   2028 ACCCCAACCTAAACCTCATACCTCATGGACATCTTAACTCAAAATGGAGT 2077
                          viivi   ivv      i   vi  iv v vv               vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_98299337_9   2078 GTGGACTTAAATCTAAAACATAAAACTGTAAAACTTCTAGAAAGAAATGT 2127
                         i?i   i     v   i vv       i       ii     ii   ii 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_98299337_9   2128 GGGAA-AAATTATGGGGATGTTGGGCTAC-CAAAGGATTTTTAGTCTTGA 2175
                         i  ?i-    iv v v  iv     i  v-   v  v  i    viv   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_98299337_9   2176 TTCCAAAAGCATTATCCATAAAAGGAAGGATTAATAGATTGGACCTCATC 2225
                         iv         iv v v i     i  ii  vi   i       i     
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_98299337_9   2226 AAAATTAAAAGCTTTCACTCTGTGGGAGACCCTGTTAAGAACATAAAAAG 2275
                                   i    iiiv  viiiii   v  i i     vi i     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_98299337_9   2276 ATGAGCTGCAGACTTAGAGAAAGTATCTGCAAATGACATGTCAGACAAAG 2325
                          ii v ii    v vi      i   i       v i  i  v  i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_98299337_9   2326 GTCTTAGTATCTAGAATATATGAAGAACTCTTAAAACTTAACAGTAGAAA 2375
                          v   -     i         i           v    i  i i  i   
  L1M4_orf2#LINE/    749 GACTT-GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_98299337_9   2376 -ACAAACCATCTAATCAGAAAATAGGCAAAATGTATGCACAGACATTTCA 2424
                         -     iv i i   i?i     i      ivi v  v i         v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_98299337_9   2425 CTGAAGAGAATCTACAGATGGCAAAGAAGCACATGAAAAGAGGGTCAACA 2474
                          ii    ii  v    i     v  v               v v      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_98299337_9   2475 TCGTAAAATTC 2485
                           i????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.68 (158 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


 340 16.13 3.23 0.00  chr2_98332113_98340408.rev      442   503 (7793)    L1M4_orf2#LINE/L1        4    67 (841)  

  chr2_98332113_9    442 AAAGACATTTTGTGTTCATGGATTGAAAGACTTAAT--TGTTAAAATGTC 489
                              i  iiii             i          --      i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_98332113_9    490 CATACTACCCAAAT 503
                         v     v       
  L1M4_orf2#LINE/     54 AATACTCCCCAAAT 67

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.02 (1 / 64), avg. gap size = 2.00 (2 / 1)  

3816 19.59 2.82 3.04  chr2_98332113_98340408.rev     2501  3388 (4908)    L1M4_orf2#LINE/L1        4   889 (19)  

  chr2_98332113_9   2501 AAAGACATTTTGTGTTCATGGATTGAAAGACTTAAT--TGTTAAAATGTC 2548
                              i  iiii             i          --      i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_98332113_9   2549 CATACTACCTAAAGTGATGTACA-ATTCTATGCAATCCCTATCAAAATCC 2597
                         v     v  i   v    v    -    v i                   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_98332113_9   2598 CAATGGTATTTTTTGTATAAGT--ACAAAAAGATCCTAAAATTTATATGG 2645
                           iiv iv       i v  i --    ivv            i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_98332113_9   2646 AATTTCAACAGATCCTGAATAGCCAAAACAATCTTGAGAAAGAAGAACAG 2695
                           v v   vi  i  v                     i           i
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_98332113_9   2696 AGTTGGAGGCCTCATACTTCCAGATATCAAAACACATTACAAAGCTACAA 2745
                                  v    i      vi  v       vi i            i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_98332113_9   2746 TAATCAAAACACTGTAGTGTAATCAAAGCAGTGGTACTGGCCTAAAGACA 2795
                                i   -----    ------------         v   i  i 
  L1M4_orf2#LINE/    254 TAATCAAGACA-----GTGT------------GGTACTGGCATAAGGATA 286

  chr2_98332113_9   2796 GACATATTGAATACTGGAACAGAATAAAGAGTCCATAAATAAGCTCTCAT 2845
                                v  vi v     i     vi        v      i i vi i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_98332113_9   2846 GTGATCTTGTCAAGTGATTTTTGACAAGGGTGCCAAGACTACACAAAGGA 2895
                         i v- v v     v       i                 i iv   v  i
  L1M4_orf2#LINE/    337 ATT-TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_98332113_9   2896 AAAACGACAGTCTCTCCAAGAAGTGATTCTGGGGAAACTGGTTATCCATA 2945
                         i   vi i     i i   v  i  i v     iv      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_98332113_9   2946 TGCAAAAGAATGAAGTTGGACTCTTGGTTTAAAACATATATAAAAACTAA 2995
                                              i i ivi i v v      i     i   
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_98332113_9   2996 CTCAAA-CAGAT--------TAAATAT-----CCAAGCCTATACAACTCC 3031
                               -ii   --------     i ----- i  iv     v     i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_98332113_9   3032 TAGAAGAAAACA--GGGATAAAGCTTCATTATACTGAATTTGGCAA-GCT 3078
                                     --  ?i    v    i v ivi  ii  v     - v 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_98332113_9   3079 TTTTTGGATATGACACCAAAAGTGTAGGCAGCAAAAGCAAAAATAGACAA 3128
                           i  i                iii i   i      v         i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_98332113_9   3129 ATGGGACTATATTATACTTAAAAACTTTTGTGCATCAAAGAAAATAGCTG 3178
                           v     vi  i v v                v      i --------
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-------- 677

  chr2_98332113_9   3179 CAC-ATCAACAGAGTGAAACAGCAACCTAAAAAATGGGAGAAAGTGTATG 3227
                            -     v i       vii     i v i           i i v  
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_98332113_9   3228 CAAATCATAAACCTGAGAATGGGTTAATGTCCAGAATATATAAACAACTC 3277
                                  v i    v  v  ii vi i               v     
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_98332113_9   3278 CTACAACTCAACAATAACAA--CAACATAACCCAGTTTCAAAATGGATAA 3325
                         i          i     v  --   -        i  ?v       ii  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAA-ATAACCCAATTWAAAAATGGGCAA 826

  chr2_98332113_9   3326 AGGGCTTGACTAGACATTTCTCCAAAGAAGATATACAAATGTCCAGGAAT 3375
                            ii    v                               v   iv  v
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_98332113_9   3376 CATGTAAAAAAAT 3388
                           ii i    i  
  L1M4_orf2#LINE/    877 CACATGAAAAGAT 889

Transitions / transversions = 1.51 (103 / 68)
Gap_init rate = 0.02 (15 / 886), avg. gap size = 3.47 (52 / 15)  

4288 16.86 3.76 0.34  chr2_98332113_98340408.rev     6927  7804 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_98332113_9   6927 TGGAAAGACATTCTATGTTCATTGATTGGAAAAC--AATATTGTTAAAAT 6974
                                 i  i i        v        i  --           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_98332113_9   6975 GGTAATACTCTTCAAAGCAATCTTTAGATTAAATATAATCCCTACAAAAA 7024
                           i       ii    vii    vi     v  iii        iv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_98332113_9   7025 TTCCAATT---TTTTTTTCAGAAATAGAAAAGCCAATCCTCAAATGTATA 7071
                          i   ii ---      v       v  v    ii     v    vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_98332113_9   7072 CAAAACTTCAAGGGGCCCTGAATAGCCCAAACAATTTTGAAATAGAAGAA 7121
                         iii  v v      i   v        v       i      v       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_98332113_9   7122 CAAAGTTGAAGGACTCATATTTCCTAATTTCAAAACTGAATACAAATCTA 7171
                                 i        i i    i            v v      v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_98332113_9   7172 CAATAATTAAAACAGTGTCA-ACTTGCATAAATATAGTCATATATAGACC 7220
                           i    i  i       vi-   v      iv    -- i       i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG--ACATATAGATC 298

  chr2_98332113_9   7221 AGTGGAATAGAATAGAGAGTCCAGAAATAAACCCAAACATTTATGGTCAG 7270
                          i           v                     v             i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_98332113_9   7271 ATGATTTTTGACAAGGGTGCCAAGACCATTCAA-AGGGAAAGAATAGTCT 7319
                         v       i                        -i               
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_98332113_9   7320 CTTAAACAAATAGTGCTGGATAAACTGGATATTTACATGAAAAAGAATGA 7369
                         i  v       i       ivv         ?ii     v          
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_98332113_9   7370 AGTTGGAACCCTACTTCACACCAGATACAAAAAGTCCCTCAAAAATGGAT 7419
                                v      i        v         v vv       -     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGAT 497

  chr2_98332113_9   7420 CAAAAGTCCAAATGTAAGACCTAAAACTGTAAACATATTAGAAGAAAACA 7469
                           ? iii i          v        i    vv v             
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_98332113_9   7470 AAAGGATAAATGCTCATGATTTTGTATTTGGCAATGGATTCTTAGATTTG 7519
                         v i ?i     vi  i   ii   vi  v        v         v  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_98332113_9   7520 ACACCAAAAACACAAACAA-AAGAAAAAAAA-AGAAGAATTC-ACTTCCT 7566
                                  i     i   -  i i      -   vi    v-     v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_98332113_9   7567 AAAACTTAAAAACTTTTGGACCTCCAAGGACATTATGAAGAATACGAAAA 7616
                         v   v             vi i  v       i   v     vii     
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_98332113_9   7617 GATAACCCATAGCATGGGAGAAAATACTGACAAATCAGATATCTGATAAT 7666
                           i      i  v             i vi       v           v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_98332113_9   7667 G-ACTTA-ATCC--------TCA-GAAGTTATACAAC--------AAAAA 7697
                          -    i-    -------- v -   v iv      --------     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_98332113_9   7698 CACAA----CCCAATTGGAAAATGGACAAAGAACTTGAATAAACATTTCT 7743
                         v    ----       ?i       i     i i       i        
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_98332113_9   7744 CCAAAGAAGATATACAAATGGACAACAAGCACATGAAAAGATGTTTAACA 7793
                                              v   i                 i i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_98332113_9   7794 TCATTGGTCAT 7804
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (83 / 61)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.40 (36 / 15)  


2546 25.03 3.93 2.58  chr2_98402691_98405049      990  1880 (479)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_98402691_9    990 AGATAAATCAAGTTCATAGATTGGGGGGAAAAGA-TCAACATTATTAAGA 1038
                              vvi  v      i      ------    - i  i   i      
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGG------AAGACTTAATATTGTTAAGA 49

  chr2_98402691_9   1039 TGTCAATTCTCCCCCAAACC--TCTATAAATTCAATGATATTCCACACAT 1086
                           v    v      -   ii--    i i      i vv  i  vvv  v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_98402691_9   1087 AGTTCCAGCAGGTTTGTTGACAGAAACTAGGAATCTTATTCTAAAATACA 1136
                          i i     v vi  v  vi      i iiv  v  v  i       v  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_98402691_9   1137 TGTAGAAATATAAAGGAACTAAAATTTCCAAATCATTCTTAATAAAATAC 1186
                          i i     ii  i   v i i   vv     v  v    i v   iv v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_98402691_9   1187 CATGAAGTTGGGGGATTTAACCTACCTCATCTCAAGGCCTACTTTAAAGC 1236
                         v ii       i   i i vv  v  iv  i    ii i    vi     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_98402691_9   1237 TACATTAAACAATAAGGTGTGGTTTTGGTGAAAGGATTGCCATATAGATC 1286
                             v   v   v vi       vi   iiv      v v          
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_98402691_9   1287 AACTGAATGAAA--AATAGTCCAAAAAAGGACCCACACACATATATGGTC 1334
                           iv    ii  --i v      i   vii     i   -- v       
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA--TTTATGGTC 346

  chr2_98402691_9   1335 AACTGATTTTCAACAAAAGTCCCAAGGCAATTTGATGGGGCAGAGAA-AG 1383
                           i        i    ii  v     i v   ii      - i    -  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAG 395

  chr2_98402691_9   1384 TCTTTTCAACAAATGATAATTAGAAAAACTGGATATTCATATGGGGAAAA 1433
                                        i i-i i i v         ?i  i   vi-   i
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTG-CTGGGACAACTGGATAKCCACATGCA-AAAG 443

  chr2_98402691_9   1434 AATGACCATAAACAA-TAAATCACACCATAAATAAAAATTCACAGGAAAT 1482
                              vvv ii  vv-  vv          v i       v  vvi    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_98402691_9   1483 AGATTAGATCATAGACATAAATGTAAAAGCTAAAACTACAAAATATCT-- 1530
                         i   -----  ?    v         i           i    i-   --
  L1M4_orf2#LINE/    494 GGAT-----CAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTA 537

  chr2_98402691_9   1531 ----AAAACTTAGGAAGAAATATTTGTGACCATGGAGGTAGGCTAATG-T 1575
                         ----     v    ?iv    v  i      v   - v     -    - 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGC-AATGGT 585

  chr2_98402691_9   1576 TTATTTGTCAAGTTACAAAAATCACTAAACA-TAAACGAAAAAATTGATG 1624
                           v  v vi v vi  v    v   -  i  -i   v        v   i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCAC-AAGCAACAAAAGAAAAAATAGATA 634

  chr2_98402691_9   1625 --TTTGTCTCCATTAAAATTCGAAACTTCTACTCAAAAAAAGATACTAAC 1672
                         --  v v  i   i      vi      i iiv vvv   i  i    v 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_98402691_9   1673 AAGGAAACAAATAAGCAAACCACAGACGGAGAGAAAATATTTGCAATACG 1722
                            i  iii  v ii   v       vv i                vv i
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_98402691_9   1723 TATTATTTGATAAAGGACTGGTTTCTAGGATATA-AAATAACTCTTACAA 1771
                            -  i      i     v  v  i  i     -   v           
  L1M4_orf2#LINE/    735 TAT-ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_98402691_9   1772 CTCAGTAGTAAAAAGGCAAACAACCCTTTTTTTTTAATGGGCAA--GAT- 1818
                             i  i       i    i     vv  ?vvv-         --   -
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATT 832

  chr2_98402691_9   1819 -------------CTTAAAAGTGGATCTATGACTGGCCA-TAAGTACATG 1854
                         -------------  iv    vi   v  ii v      -    i     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_98402691_9   1855 AAGAGTAGATCTCCATCATTAGCCAT 1880
                           i  vv v  vv     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.07 (113 / 106)
Gap_init rate = 0.03 (26 / 903), avg. gap size = 2.23 (58 / 26)  


2711 27.49 1.46 1.09  chr2_98436573_98439046.rev      764  1585 (889)    L1M4_orf2#LINE/L1        1   825 (83)  

  chr2_98436573_9    764 TGGAAAAGCATTCCATGCTCATGGATGGAAAAAAATCATTATCATGAAAA 813
                               iii  i     i        v i  i v- i v   ii v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chr2_98436573_9    814 TGGCCATACTTCCCGAAGTAATTTATAGATTCAATGCTATTCCCATTAAA 863
                             v     i   i  v i  i  i        i  v  i  i  i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_98436573_9    864 CTACCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAAATTCA 912
                         v v   vivi v  i  ii     v v  v  i-  - iii         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_98436573_9    913 TATGGAAACCAAAAAGAGCTTGTATAGCCAAGACAATCCTAAACAAAAAG 962
                                 ivv  ii  v iv v        i      i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_98436573_9    963 AACAAAGCTGGAGGCATCATGGTACCCAACTTCAAACTATGCTATAAGAC 1012
                                i      vv   iiv v     i      viv i   i  ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_98436573_9   1013 TATAGTAACCAAAACAGCATGGTACTGATACAAAAATAGGGATATAGACC 1062
                           i     i   i    ii        ii i  ii    iv       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_98436573_9   1063 AATGGAACAGACTAGAAAACTCAGAAATAAGACCACACATCTACAACCAT 1112
                                i   v v  i iii         iv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_98436573_9   1113 CTGATCTTTAACAAATCTGACCAAAGCAAGT-AATGGGGAAAGGATTCCC 1161
                         i    i  ii    ivv  -    ii v v -           i  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_98436573_9   1162 TATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAATTG 1211
                          v  i  i              v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_98436573_9   1212 AAACTGGACCCCTTCCTTACACCTTTTACAAAAATTAACTCAAGATGGAT 1261
                           ii         v   i     v v                 i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_98436573_9   1262 TAGAGACTTAAATGTAAAACCCCAAACTGTAAAAACCCTAGAAGAAAATA 1311
                         i ?    i         i v iv     i     vi i          i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_98436573_9   1312 TA--CGCAATACCATTCAAGAC---AGGCACGGGCAAAGGCTTCATGACA 1356
                           --? i  - i -   iv   ---i  i-ii     v  i   v iivv
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_98436573_9   1357 AAAACATCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAACAGGATCT 1406
                          vi   i        vvv          v      v  i   iv   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_98436573_9   1407 AATTAAT-TTCAGGTGTGCTTCTGCACAGCAAAAGAAACTATCATCAGAG 1455
                         v  i  v-  v ii---i   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAA---ACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_98436573_9   1456 TGAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCT 1505
                             v        i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_98436573_9   1506 GGCAAAGGTCTAACATCCAGCATCTATAAGGAACTTAAATGAATTTGCAA 1555
                          ii  i  v  vii      v  v     i     ivv ii v ivii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_98436573_9   1556 GAAAAAAA-AAACAAC---ATTAAAAAGTGGGCA 1585
                         v     i -   i   ---   ?    i      
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 1.74 (141 / 81)
Gap_init rate = 0.02 (14 / 825), avg. gap size = 1.50 (21 / 14)  

 384 19.05 9.52 0.00  chr2_98436573_98439046.rev     1857  1982 (492)    L1M4_orf2#LINE/L1      771   908 (0)  

  chr2_98436573_9   1857 AAAACTCT-GC--CTCAAAAAAAAAAAAAAAAA-AA--------AAAAGT 1894
                          i      -i --     v  v     i v   -  --------    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_98436573_9   1895 GGGCAAAGGACATGAAAAGACACTTCTCAAAAGAAGACATTTATGTGGCT 1944
                                   iv    v     i     v        i  vi vi    i
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_98436573_9   1945 AATAAACATATGAAAAAAAGCTTAACGTCACTGATCAT 1982
                              i  i       i v   i   i   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (15 / 9)
Gap_init rate = 0.03 (4 / 138), avg. gap size = 3.00 (12 / 4)  


4121 18.11 4.10 0.68  chr2_98497712_98502228     3154  4031 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_98497712_9   3154 TGGAAAGACATCT-ATGTTTATGGATTAGAAGACCTAGTATTTTTAAGAT 3202
                                 i   i-     i       i      i  i    v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_98497712_9   3203 GACAATATTCCCTGGACTTATTTA--GACTCAACACATTTCCTAACAAAA 3250
                          i     i    iii i v  i  --  i     i  v i    v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_98497712_9   3251 TTCTACCTGGCTTCTTTGCAGAAATTATTAAGCTGATGCTAAATTTCATT 3300
                          i i v   v   i            ivi        v     v     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_98497712_9   3301 TGGAAATTCTAGGGACCCAGAAGAACCAAAGCAATCTTGAAAAATAA--- 3347
                                v v            v i     i             v  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_98497712_9   3348 CAAAGTGAGAGGATTCACACTTCCTGATTTCAAATTTTACTACAAAGCTA 3397
                               vi     i          ii        vi              
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_98497712_9   3398 --GTAATCAAGATAGTGTGATACTAGAATAAGAAAAAATGTACAGATCAT 3445
                         --          i      i    i v     i v i ii  i      v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_98497712_9   3446 TGGAATACAATTGGGAATTTAGAAATAAGTCCTCATATTTACAGTCAGTT 3495
                                v     i  i ii        ii  vi i     ii    i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_98497712_9   3496 GATTTTTGGCAAGAGTGTCACTGGA--ATTCAATGGAAGAAAGAATAGTC 3543
                               i i    i   i  --i  --         i-            
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCA--AGACCATTCAATGGG-GAAAGAATAGTC 397

  chr2_98497712_9   3544 TGTTAAACAAACAATGCTGGAACAGCTGGCTATCTAGAAG-ACAAGTATG 3592
                          v  v      iii      i   i    v  ? i v v - v   v   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_98497712_9   3593 AAGTTGTACTCTTACCTCACACCATATTCAAAAATTAGCTCAAAATAGAT 3642
                               v  i i               v         i        i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_98497712_9   3643 CATATATCTCA-TGTAA---------CTATAAAATTCTTAGAAGAAAACA 3682
                           ? v i  v -     ---------        i               
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_98497712_9   3683 TTGGCATATATCTTTTTGACCTTCGAATAGGCAGTGGCTTTTTAGATATG 3732
                          v  ?i  v     iv       v iv      i   i  i         
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_98497712_9   3733 ACACAAAAAGCACAACCAACAAAATAAAAAATAGACAATTTAGACACTAT 3782
                             v          v        v          i  v  i   vii  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_98497712_9   3783 TAAA-TTAAAAACTTTTGTTTTTCAAAAGATGC-ATCAAAAAATTACAAA 3830
                         i   -              vi      i  ii -     i   v iv   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_98497712_9   3831 G-CACCCCAGAGAATGGGAGAAAA-ATTTGTAAATCATATATCTGAGAAG 3878
                          -  v    v              -     i               v   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_98497712_9   3879 GGATTTGTATCCAGAATATCTAAAGAACAC--ATAACTCAATAATA---- 3922
                            i               v        v -- i            ----
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_98497712_9   3923 --CAAATAATACAATTTAAAAACAGGCAAAAAATCTGAATAGCTATTTCT 3970
                         --       iv     ?     ii      ii  i       vi      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_98497712_9   3971 CAAAAAAAGAGATATACAAATACCCCAAATTCATAT---AAGATGCTCAA 4017
                          v   i    --         iv  v v vv  i  ---           
  L1M4_orf2#LINE/    848 CCAAAGAAGA--TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_98497712_9   4018 TTATTATTTTCTGC 4031
                         i-  i ????????
  L1M4_orf2#LINE/    896 C-ATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (97 / 58)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.21 (42 / 19)  

1920 15.01 5.10 0.85  chr2_98497712_98502228     4017  4369 (148)  C L1M4_orf2#LINE/L1   (512)   396    29 *

C chr2_98497712_9   4369 GAAGACTATATATT-TTAAGATGGCAATATTTCCCCCAACTTGATCTA-A 4322
                                vv     -              i --      v        - 
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACT--CCCCAAATTGATCTACA 76

C chr2_98497712_9   4321 AATTCAAAGCAATCCGTATTAAAATCCCAGCTGGTTTCTTTGTAGAAATT 4272
                         i      v       v   i             vi  i    i       
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

C chr2_98497712_9   4271 GGCAAGCTGATC-TAAAATTTATATGGAAATGCAAGAGACCCAGAATAAC 4223
                          i          -       i               i           i 
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

C chr2_98497712_9   4222 CAAAACAATCTTGAAAAAGAA---TAAAGTTAGAGGACTTACGCTTCCCA 4176
                                              ---i      i       i  i       
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

C chr2_98497712_9   4175 GTTTCAAA--T----------CTACAGTAGTCAAGACAGTATGTCACTGA 4138
                         i       -- ----------        i          i  vi    i
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

C chr2_98497712_9   4137 TGTAAGAATAGAAATGACGATCAGTGGAATAGAATTGAGGGTCCGGAAAT 4088
                         ii    i     v  ivv     i               i    i     
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

C chr2_98497712_9   4087 AAGCCCTCACTTTTATAGTCAGTTGATTTTTGATGGGGATGCCAAGACAA 4038
                           i   vi  v     i    i        i  iii  i         v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

C chr2_98497712_9   4037 TTCAACGCAGAAAATAATAAT 4017
                              i vi    i-    i 
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAG-AATAGT 396

Transitions / transversions = 2.79 (39 / 14)
Gap_init rate = 0.02 (8 / 368), avg. gap size = 2.62 (21 / 8)  


3445 17.23 5.85 7.48  chr2_98670731_98672791      650  1572 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_98670731_9    650 TGGAAAGACATCTTGCGCACATGGATTGAAAGACCTAATATTGTTAAGAT 699
                                 i   iiii iv         i     i               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_98670731_9    700 GACAGTACTATCAAAAGTGAGCTACAGATTCAATGTACCCCCCCCCCATC 749
                          i  i    vi v   v   v            i i vi   i----   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT----ATC 96

  chr2_98670731_9    750 AAATTCCCAACTGATTTTTTTGTGTGTGGAAATAGAAAAATCCATCCTAA 799
                            v     i   vi       ii----     v  v  iiiv       
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCA----GAAATTGACAAGCTGATCCTAA 142

  chr2_98670731_9    800 GATTTACATCGAATCTCAAGGAACCCCAGGTAGCCAAAACAATCTTGAAA 849
                         i   i i  v   viv     i    viii                    
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_98670731_9    850 AAGAA---CAAAGCTGGAGGTCGCATACTTCCTGATTTCAAAGCTTATTA 896
                              ---     i      v v  i      ii        i    i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_98670731_9    897 TTACAGAGCTACAGTAATCAAAATAATGTGGCACTGGCATAAATATGTAC 946
                         ---  i               i i i     i          iv  iv  
  L1M4_orf2#LINE/    243 ---CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_98670731_9    947 AGACAGA--AGTGCAGAATAGAATAGCATGCCCAGAAATAAACCCTGGCA 994
                          v i   -- i  --         v viv i              vvi  
  L1M4_orf2#LINE/    290 ATATAGATCAATG--GAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_98670731_9    995 TATATGGTCAAATGATTTTCCACA-GGATGCCAAGACCATTCAATGGGGA 1043
                          v         v        v   -  i                      
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_98670731_9   1044 AAGAACA-TCTTTTCAACAAATGGTGTTGGGAAAACCAGCTATCCTTAGG 1092
                              i -                  i     v   ii v  ?  vi v 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_98670731_9   1093 CAAAA-----AAGCTGGAC----AC-TCACACCATATACAAAAGTTAACT 1132
                              -----   i     ----  -                 i      
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_98670731_9   1133 CAAAATAGATCAAAGACATAA-TTTAAAAGCTAAAACTCTAA--CTCCTA 1179
                               i     ?    v   - v   i          v   --   i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_98670731_9   1180 GAAGAAAACACAGGAG-AAA-CTTCAT-----TGG---AGTCAGCGGTGA 1219
                                   i   ? -   -    i -----   ---  v  ii   vv
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_98670731_9   1220 CTTGGGTATGACACCAAAAGCACAGGCAACAAAAGTAAAAACA----AAC 1265
                            i i                  i          v     i ----  i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_98670731_9   1266 TAGACTACACCAAAATGCAAAACCCCTGTGCATTTAAAAAA-------AA 1308
                          i    v  i      vv     iii     -  i   ii -------  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAA 686

  chr2_98670731_9   1309 AAAA----AAAGGCAGCCTACAGAATGGGAGAAAATATTTGCAAATCATG 1354
                         i   ----    i  i  i                              i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_98670731_9   1355 CATCTGATAAGAGGTTAACATCTAGAATATACAAGGAACT--------TC 1396
                         i          i ii vii   i        i  i     --------  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_98670731_9   1397 AACAATAAAAGAGCAAACAACCTATTTTTTTAATACCCATCTACCACCTT 1446
                           i       iii    i    i v  ?vvv   ivv  -----------
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA----------- 825

  chr2_98670731_9   1447 AACCATTTTAAGGGATTTAACCCATTTGAATGATTTAACTCATTCAAAAT 1496
                         ---------    ----------        -------------------
  L1M4_orf2#LINE/    826 ---------AAGG----------ATTTGAAT------------------- 837

  chr2_98670731_9   1497 GACTTGAGACATCTCTCCAAAGA-GATATACAAATGGCCAACAAGTACAT 1545
                         ------      i          -                 i   i    
  L1M4_orf2#LINE/    838 ------AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_98670731_9   1546 GAAATTATGTTCACCACTAATCATTAG 1572
                             vv   i   v  ii ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (103 / 52)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 4.73 (123 / 26)  


2872 23.93 2.99 6.52  chr2_98734528_98736648      697  1632 (489)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_98734528_9    697 AGATATCTT-TGCTCATGGATTGGAAGAATTAATATCATTTAAATGTCCA 745
                                ii-  i               v       ii  v i   v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_98734528_9    746 TATTACCCAAAGTGATCTACAGATTCAATGTAATCCCTATCAAAAAATTT 795
                           i v      v                i i              v-iii
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT-CCC 104

  chr2_98734528_9    796 AATGACATTTTTCTCAGAAATGGGAAAAA-AATCCTAAAATTCATATATA 844
                          iivi v     iv       v iv  iv-i                iv 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_98734528_9    845 ACCACACACACACACACACACGCACGCGCACACACACACACACACACACA 894
                          ------------------ i   v v ----------------------
  L1M4_orf2#LINE/    155 A------------------ATGCAAGGG---------------------- 164

  chr2_98734528_9    895 CACACACACACACACACAACAAATAGCCAAGGTAATCATGAGGAAAAACA 944
                         -------------  v  i--         iii    v   ii  i  v 
  L1M4_orf2#LINE/    165 -------------ACCCAG--AATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_98734528_9    945 ATAAAGCTGGAGGCAACACACTTTATTATTTCAAACTATACTATGAAGCT 994
                          i    i      vvv       iviv        viv     ii     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_98734528_9    995 ATAATAATGTAAACAGTATGGTATTGATTTTTAAAAAACAGACACACTGG 1044
                          i i    vv i     i     i  iiv ---  ii i     i iv i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCAT---AAGGATAGACATATAGA 296

  chr2_98734528_9   1045 CCAATGGAACAGAATATAGAGCCTAGAAATGAACTCATGTATGTATGGTC 1094
                         i        i     vv    i i      i   i   ii  v       
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_98734528_9   1095 AATTGATTTTCAGCAAAGGTGCCAAGAACACTCAATGAAAAAAG-----T 1139
                                    ii   i          v  i      iii    ----- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_98734528_9   1140 TTCTTTAGTAAATGGTGCTGAGAAAACTGGATATCCACATACAGATGAAT 1189
                         i i  i ii           i  v         ?      i  i v    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_98734528_9   1190 GAAAGTGGAACTTCAACTCACGTGAAATATACAAATAAACTCAAAATGGA 1239
                            iv    v iii v     iiv v   i v    v             
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_98734528_9   1240 TTGAAAAC--------AAAAG--AAGACTCTAAAACTACCAGAAGAAAAC 1279
                          ii? i  --------  i  --  i   v       vii          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_98734528_9   1280 ATAAGGGAAAAACTACACGACATTGGCCTGGGCAATGGTTTTTTGGATAT 1329
                            i ? v   v  v ii   v    vi i           i  i     
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_98734528_9   1330 GACCCCAAAAGCTCAGGCAACAAGAACAAAAATAGACAAATAGGATCACA 1379
                            v        v  i       i iv         i    v   iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_98734528_9   1380 TCTAACT--AAAACTCTTCTACATGGCAAAGGAAATAATTAACAGCATGC 1427
                           v  v --      i  v i v --       v iv  i  v ivi  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGA 694

  chr2_98734528_9   1428 CT-GACAACCTATGGGTTAGGAGAAAATATCTGCATGCTGCACATCTGAT 1476
                         vv-       i ii iv i           i    viiiii i       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_98734528_9   1477 AAACAGTTAATATCCAAAATATATAAGGAACTCAAACAGCTCAAGAGTAA 1526
                           iviii vi      i         i      vv   i     v i   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_98734528_9   1527 GAAAA-----AACAC--TGAAAAAATAGGCAAAGGACCTGAACAGACATT 1569
                         i  i -----   v -- v?      i         ii    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_98734528_9   1570 TCCCAAAAGATGACATACAAATGGCCAACAGATATACGAAAA-ATCCTCA 1618
                           i v     v  i              i iii i i     -  v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_98734528_9   1619 ACACTGCTAATCAT 1632
                            iii????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (142 / 78)
Gap_init rate = 0.02 (16 / 903), avg. gap size = 5.56 (89 / 16)  


2872 21.58 6.33 1.03  chr2_98917630_98919396.rev      503  1276 (491)    L1M4_orf2#LINE/L1       94   908 (0)  

  chr2_98917630_9    503 ATCAAAATCCCAGCAAAACTTTTTGCAGATATTGGCAAGCTGACTTGAAA 552
                                       vivvi          v    i        iiiv   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_98917630_9    553 ATGTATGTGAAGAAGCAAAGAACT-AGAATAGGTAAAACAATTTTGAAAA 601
                           vi  i  i i v    i i  i-       vi        i       
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_98917630_9    602 AACA---TAAAGTTGAAAGCTTCATACTACCTGTTTTTAAGACTTACTAT 648
                          iv ---i       i i vi   i   v  iiv   i  i        i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_98917630_9    649 AAAGCTGCAGTAATCAAGACAGTATGGTATTGGCAAAAGGATAGATACAC 698
                               i                i     i     v         i i i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_98917630_9    699 AGA--GACAGAAGGGAGT--AGAGTTCAAAAACAGACCCATACAAATATG 744
                            --i ii   vi  i --     i  i   i i         vv    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_98917630_9    745 GTTAATTAATTTT-GACAAAATTGCAAAATCAATTCATTGGATAAAAGAT 793
                           i    i     -     iiv   v  iv v     v   iv   ii  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_98917630_9    794 AATATTC-CAACAAATGGTGCTGTAACAATTGGACATTCATATGCAAA-- 840
                          i v  i-               vi    i    i ?i  i       --
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_98917630_9    841 --TA------------TACCTCACAGATTATACAAAAATTAACTCAAAAT 876
                         -- i------------         vvv                      
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_98917630_9    877 GTGTCATAAACCTAAATGTAA-------AACTCTAACGCCTTTAAAAGAA 919
                          vi   ? i            -------    v   vi ii   i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_98917630_9    920 AGCATAGCAGAAGATAGTTATGACCAAGGATTAGGCAAGGGTT-CTTAGA 968
                          i     v? v i  vv ii     vv  i        v    -      
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_98917630_9    969 TATAATACCTGAATC-----CATAAAAGGAAAAAATGTATAAATTGGACT 1013
                            i i   vi  v -----  vv   i        iv            
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_98917630_9   1014 TCATCAAAACTTTAAAA--TATGGT-CTGTGAAAGACACTTTTAAGAAAA 1060
                                  --      -- v v  -  vii  i      v i      i
  L1M4_orf2#LINE/    644 TCATCAAAA--TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_98917630_9   1061 TGAAAAGACAAGTCACAGACTAGAAGAAAATATTTATAAATCACAC--TT 1108
                                    vi      v i i           ii      i i--i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_98917630_9   1109 GATATAGGACTTACATCCAGCATATATTTAGAACTCTCAAAATTCAAAAA 1158
                             vi      ii      v      vv        i v  i    v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_98917630_9   1159 TAAGAAAACAAATAACTCAGTTACAAAATGGGGAGCAAAT--TTTAAAT- 1205
                            i  i         i  i  ?v        ---    v--   i   -
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGG---CAAAGGATTTGAATA 838

  chr2_98917630_9   1206 --CATGCTTTACCTAAGAAGATGTACAAAATGGCAAAGAAGCATATGAAG 1253
                         --   --  iv  v        i      -    v  v     i     i
  L1M4_orf2#LINE/    839 GACAT--TTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACATGAAA 885

  chr2_98917630_9   1254 AAATGCTCAATATCTATAATCAT 1276
                          i        i   v????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (102 / 61)
Gap_init rate = 0.02 (20 / 815), avg. gap size = 2.85 (57 / 20)  


3791 16.95 6.53 3.89  chr2_98932219_98936516     2926  3798 (500)    L1M4_orf2#LINE/L1        1   896 (12)  

  chr2_98932219_9   2926 TGGAAAGATATCCTGTGTTCATAAATCAGAAGAC--AATATTATTAA-AT 2972
                                      ii       ii  ii      --      i    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_98932219_9   2973 GGCAGTATTCCCCAAACTGATTTACAGAATCAATGCAACCTTTATCAAAA 3022
                             i  i        i    i      v    i    i ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_98932219_9   3023 TCTCAGCTGGATTTTGGGCAGAAAGTAACAAGCTGATCTGAAAATTTATG 3072
                           i      vv    vv       v i           iv      i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_98932219_9   3073 TGGAAATGCAAGGGACCTTGCAAAGTCAAAATAATCTTGAAAAATAA--- 3119
                                          iv v v  i     i            v  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_98932219_9   3120 CAAAGATGGAGCATTCACACTTTCCATTTTCAAAACTTACTACAAAGCTA 3169
                              v     v i        i   v                       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_98932219_9   3170 CAGTAATCAGGACTGTACTGTACTGGCATATTGGTAGACATATAGTTCAA 3219
                                  i   v  iiv           vv i           v    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_98932219_9   3220 -------------------CAGAAATAAACACATACTCTTATGGCCAATT 3250
                         -------------------           v     vi      i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_98932219_9   3251 GATTTTCAATGAGGGTGTCAAGACAACTCAATGGAG---GGATATCATCT 3297
                                i ii      i      v i       i --- i   --i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA--GTCT 398

  chr2_98932219_9   3298 TTTCAACAAACCGGGCTGGAACAAGTAGACATCGACATGCAAAA-AATAA 3346
                                   iv v     i    v i  i ? v          -   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_98932219_9   3347 TGT-GTACTCTTACCTCACACTGGTTACATAAAAATTACCCCAAAATGGC 3395
                         v  - v  i i          ii--  i i        v i        v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCA--TATACAAAAATTAACTCAAAATGGA 496

  chr2_98932219_9   3396 TCATAGATCTAAATTGTAAGTGCTAAAACTATAAAGCTCTTAGAGGAAAA 3445
                            ?   i      -     v              i        i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_98932219_9   3446 CA--GGAGTAAGCCT--GTCATTTTAGGTTAGGCAATAATTACTCAGATG 3491
                           --  ?    ii  --  v ii  i           ii  v  i    i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_98932219_9   3492 TGACATCAAATGCAT------CAAAAGAGAAGATAGGTAAGTTTGACTTC 3535
                              i    v   i------       i  i    i   i  v      
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_98932219_9   3536 AACA---TTATAAGATTTTA--ATTCAAAGGACTCT--CAAGAAACTGTA 3578
                          v  ---   v  iv    i--v          v  --       v  v 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_98932219_9   3579 AAGACAAC----AGACTAGG-GAAAATACTTGTATATCATCTATCTGATA 3623
                                 ----   v i  -       i   i v     v         
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_98932219_9   3624 CAGGATTGGTATGCAGAACATGGAAAGAATTCTTATAACTCAATAATAAA 3673
                         vi   i v    v     i  iv      i     i              
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_98932219_9   3674 AAGA----TATCCCA-TTTAAAAACAGACAAAGGATTTGAACATAACTTG 3718
                             ----  v    -  ?     ii i             i -i  ---
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA-GAC--- 841

  chr2_98932219_9   3719 CACAAAGAAGGCAAACTTACACAAAGAAGGCATAAAGTAGGCAAATGAAT 3768
                         -------------- i  viv        ii   -------      ---
  L1M4_orf2#LINE/    842 --------------ATTTCTCCAAAGAAGATATA-------CAAATG--- 867

  chr2_98932219_9   3769 GGCTAATAAGTGCATGAAAAGATGCTCAAC 3798
                         -  i      ii                  
  L1M4_orf2#LINE/    868 -GCCAATAAGCACATGAAAAGATGCTCAAC 896

Transitions / transversions = 1.77 (92 / 52)
Gap_init rate = 0.03 (24 / 896), avg. gap size = 3.79 (91 / 24)  


3186 20.00 4.93 1.87  chr2_99028387_99031921      501  1250 (2285)    L1M4_orf2#LINE/L1       30   802 (106)  

  chr2_99028387_9    501 AAAACTTAATGTTGTTAAGAGCATAATACATTCCAAGTTGATTTACAGAT 550
                           i       i         vvii     vii    i     i       
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGAT 79

  chr2_99028387_9    551 TTAATATAATGCCTATCAAAAACCCAGCTCACTTTTTTTTTGCAGCAATT 600
                          i  iii   v          v       -i i      --    v    
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCT-GCCTTTTTT--GCAGAAATT 126

  chr2_99028387_9    601 CATAAGCTCTTCCTAAAATTCATAAGGAAATACAAGAAACCCAGAGTAGC 650
                         v i     vv              v      i    ii       i    
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr2_99028387_9    651 CAAAACAACAATCTTGAAAAATAA---CAAAGATAGCGGACTTATACTTT 697
                                 ---          v  ---     v i v     i i    i
  L1M4_orf2#LINE/    177 CAAAACAA---TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr2_99028387_9    698 CCAGTTCCAAAG-TTATTGTAAAGCTACAGAAACCAAGACGATTTGGTAC 746
                            i  i    i-   i ii          v  i      ii v      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr2_99028387_9    747 TGGTACA-GGATAGACATATATATCAAGGGAACAGAATTGCTAATATGTA 795
                            i i -             v     v    i       vv i viiv 
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_99028387_9    796 AATAAACCCTTACATTTATGGTTAATTAATGTTTGACAACAACGTCAAGA 845
                                  v            i    i  v  i     viii i     
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr2_99028387_9    846 TAATTCAATAGGGGAAGGAATAGTCTTTTCAATAAACGTTCCTGGAACAA 895
                         iv       -      i               i   i v v    i    
  L1M4_orf2#LINE/    374 CCATTCAAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_99028387_9    896 CTGGAAATCTGCATGCCAAAGAAGGAATGAGGATCCTTTCCTCACATCAC 945
                              v ? ii     v      v   vvv   i  i v       i  i
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_99028387_9    946 ACACACACACAAAAT-AATCTACAGTGGATTGTAGACATATATGTGAGAG 994
                          i   -----     -  iii v i     ii?    v  v    i    
  L1M4_orf2#LINE/    473 ATACA-----AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_99028387_9    995 ATAAAACTATAAAACTCTTAGACAAAAGCATAGGAATAAATAGTTTTGAC 1044
                         v                     vi   i      ?i     vv iv    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_99028387_9   1045 -TTCGGTTAGGCATTGATTTTTTATGTTTGATGCCAAAGGTGCAAGTGAT 1093
                         -  v         v  i   i   vi v   ii     i ii    ii i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_99028387_9   1094 AGAAGTCAACATTTGTAAA--------CATCA----TAAA---TTTTGTG 1128
                          i   vv  v  vvi    --------     ----    ---       
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_99028387_9   1129 TTTCAAAGTACACCATCAAAAAAGTTTTAAAA---AACCCA--------- 1166
                         i       v    i     i     v--    ---      ---------
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTG--AAAAGACAACCCACAGAATGGG 715

  chr2_99028387_9   1167 ---AAATATTTGTAAATTTTATATTTTATAAGGAACTTGTATCCAGAATA 1213
                         ---         i    iv     i v      i                
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_99028387_9   1214 TGTAAAGAACTCTTGCAATTCTATAATAAAAAGACAA 1250
                          i            i   i  v               
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

Transitions / transversions = 1.62 (91 / 56)
Gap_init rate = 0.02 (16 / 773), avg. gap size = 3.19 (51 / 16)  

 419 21.05 7.02 0.00  chr2_99028387_99031921     1540  1653 (1882)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr2_99028387_9   1540 AACAATAAAAAGACAA-----CCATATTAAAAGTGGGCAAAAGAGTCCAA 1584
                           i             -----   vv ?    i        i  v iv  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_99028387_9   1585 CATGCATATCTCCAAAGA---CATATGAATGGCTAATAAATATGTTAAAG 1631
                         i vi   v          ---i   ii      i     ii ii v   i
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_99028387_9   1632 GATGCTCCACATCATTAGTTAT 1653
                                v      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.02 (2 / 122), avg. gap size = 4.00 (8 / 2)  

1178 31.43 5.36 2.50  chr2_99028387_99031921     1867  2426 (1109)    L1M4_orf2#LINE/L1       15   590 (318)  

  chr2_99028387_9   1867 ATGTTCAGGGACTGGAAGATTCCATATCATGGAGATGTTCATTCCCCTCA 1916
                                v   i       i iv    ii vi     viv  v i  i  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_99028387_9   1917 AATGGATCTGTAGATTTGATATGGTACC-ATAAAAATCTTAATAAG---T 1962
                            v     ii     ii iiiii v  -  v      ii iiviv--- 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr2_99028387_9   1963 TTCACAAGGAATTTTGCTAAG-TGATTTTCAAAT-CATATGGAAATGCAA 2010
                           ii  - i    -- vi   -    ii v    -               
  L1M4_orf2#LINE/    115 TTTGCA-GAAATT--GACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_99028387_9   2011 AAG--CAAAAATGGCCAAGATACTTTTGAACAATAACA-TAATATGAAAA 2057
                         ii -- v i   i     i i v i     v  v  v -i  vi vii i
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_99028387_9   2058 GACTTGTGCTAAAGGATATCAAGACTTTATTGTAAAGATATACTAATTAA 2107
                             iiii  vvvvi  v    i    - i ii    v  i v    i  
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTT-ACTACAAAGCTACAGTAATCAA 260

  chr2_99028387_9   2108 AGCAATGAGGTATTTGTCA----GACAGACAAACAGACCAATAGAATAGT 2153
                         ii  i  v    i v -  ----  i     v i   i    i      v
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGG-CATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_99028387_9   2154 ATAGAATGCCCAGAAACAAACCCACACAT--------AATTCATCCTTGA 2195
                           v  iv i       i       i    --------    v  ii i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_99028387_9   2196 TAGGACAAGATAGTAAAGCACAG-CAGCAGGGTAAGAG-GGTCTTTTCAA 2243
                         i ---- i i ivi  ii -  v-  iii   v    i-i          
  L1M4_orf2#LINE/    360 CA----AGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_99028387_9   2244 TAAATGATGCTGAGTTAACTCAAAATCTA--TGTAGAATATTTAAAATTT 2291
                         i     i     i vi    vi v ? i --  i i  v v v  i--  
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG--TT 452

  chr2_99028387_9   2292 CCACATCTGTCACAAACCATATATAAAAATCAATTCCAGATGAACTGTAG 2341
                         vv  vi  ii v  v        i      i  i  v i   i iii?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_99028387_9   2342 CTCTAAAATTCACAAGC-AAAACAATAAAGTTTATAAAAGACAATATGAG 2390
                         vi     - vi vi   -     v     ii iv  i    v  i  -  
  L1M4_orf2#LINE/    503 ACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AG 550

  chr2_99028387_9   2391 ATATAG----TTATGACCTTAAGGTAGGGAAAGATTTCTT 2426
                         i?i  i---- ii       ii v    v  v i      
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.98 (115 / 58)
Gap_init rate = 0.04 (22 / 576), avg. gap size = 2.00 (44 / 22)  

 739 25.16 4.97 1.86  chr2_99028387_99031921     2726  3047 (488)    L1M4_orf2#LINE/L1      577   908 (0)  

  chr2_99028387_9   2726 GGCCAAGGTTTCTTAGA-AGGACAGAAAAAATCCACATCCTTAAAGGAAA 2774
                            v v           - v    vv    iiv  - v vvi   i    
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACA-AGCAACAAAAGAAA 625

  chr2_99028387_9   2775 TTATTAATAAATTGGACATTATTAAAATTAAAAACTTCTGTTTATTAAAA 2824
                         vv  vi           v i  i              i   viv i   i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_99028387_9   2825 GACAACATTAAATGAGTGAAAAAGCAAGCCACA--ATGGAAGAT--TATT 2870
                             vi  i  ivi        ii   v     --    i   v--    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_99028387_9   2871 TGCAACACATGCTACC-AACAACAAGCTTGTATCCATAATACTACCTAAA 2919
                              vv   i-  i -i i  viii          v    -  --    
  L1M4_orf2#LINE/    726 TGCAAATCATA-TATCTGATAAGGGACTTGTATCCAGAATA-TA--TAAA 771

  chr2_99028387_9   2920 AAACT---ATAATTTAA--GTAAAA-GAGAAA--ACCCAGTAGAAAACTA 2961
                         i    --- i  i i  --i     -  v   --     i v?    v i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_99028387_9   2962 GGTAAAAAACATGAATAGGAACTTCAC--AAATACATATACCGATTGGGA 3009
                           i   ii iv       iv i   v --  iv v      vi  -  vv
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT-GGCC 870

  chr2_99028387_9   3010 AATAAGCACCTAAAAAGGTGCTCAGCTCCATTAGTTAT 3047
                                  v i     i      i vi  ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (44 / 36)
Gap_init rate = 0.04 (14 / 332), avg. gap size = 1.57 (22 / 14)  


 581 26.97 0.66 0.00  chr2_99036609_99042298.rev     3997  4148 (1542)    L1M4_orf2#LINE/L1        3   155 (753)  

  chr2_99036609_9   3997 GAAAATCATTCCATGCTCATGGATAGGAAGAATCAATATCATTAAAACTG 4046
                             ivi  i     i        v      v i     ii    i iv 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_99036609_9   4047 CCATACTGCCCAAAGCAATTTACAGATTCAATGCTGTTCCTGTCAAACTA 4096
                          v     v      vii  i           i  vi i   i     v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_99036609_9   4097 CCAACGACATTGTTCACAGAACTAGAAAAACT-ATTTTTAAATTTATATG 4145
                            i vi v  v  ii     v v  v  i  -  ii v     i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_99036609_9   4146 GAA 4148
                            
  L1M4_orf2#LINE/    153 GAA 155

Transitions / transversions = 1.41 (24 / 17)
Gap_init rate = 0.01 (1 / 153), avg. gap size = 1.00 (1 / 1)  

2451 26.25 2.23 1.44  chr2_99036609_99042298.rev     4443  5204 (486)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr2_99036609_9   4443 AAAATT-ATATGGAACTTAAAAAAGGCCCA-AATAGTCAAGGCAATCCTA 4490
                               -        v -iv  ii i    -     i   ii     i i
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_99036609_9   4491 AGCAAAATGAAAA-AAAGCAGGAGATAGCACACTACCAGACTTCAAACTA 4539
                          --    vi i  -    iv    ivvv      v  vi i      viv
  L1M4_orf2#LINE/    190 A--AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_99036609_9   4540 TACTACAGGGCTACAGTAACCAAAACAGCATAGGAGTGGTTCAAAAACAG 4589
                                ii          i   i    ii i v v   ivi  ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_99036609_9   4590 ATGCATAGACCAATGGAACAGAATAGAGAGCCCAGAAGTAAGGCTGCACA 4639
                          iii     i        i     v     i      i   iv iii   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_99036609_9   4640 CCTACAACCATCTGATCTTTGACACAGCTGACAAAAACAAGCTATGGGGA 4689
                         ii  iiii  vi    i  i    vi v  v   i v  vv v       
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_99036609_9   4690 AAGGACTGTCTATTCAATAAATGGTGCTGGGATAACTGGGTAGCCATATG 4739
                            i iv    v     i              i      i  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_99036609_9   4740 CAGAAAATTGAAACTGCACCCGTTCCTTACACCATATGCAAAAATCAGCT 4789
                           i  i v    ii  v    v v   i         i       i i  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_99036609_9   4790 CAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACCATGAAACCCCTG 4839
                            i      i ?    i         i v i     i  i    i i i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_99036609_9   4840 AAAGACAACCTAGGC---AATGCCATTCTGAACATAGGAATGGGCAAAGA 4886
                         i    v   v    ?---   -- -   vvi  v v  iv i     v i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_99036609_9   4887 TTTCATGATTAAGATGGCAAAAGCAATTGCAACAAAAGCAAAAATTGACA 4936
                             v iiv  v  iiv        vvv          v      v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_99036609_9   4937 AATGGGA-----TCTAAA----GAGCTTCTGCACACCAAAAGAAACCATC 4977
                            v   -----  v   ----i i   i  ii vi    i  v  i   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_99036609_9   4978 AACAGAGTAAACAGACAACCTACAAAATGGGCAAAAGTATTTGCAAACTA 5027
                           v i   i  v        i   i      vi   i          ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_99036609_9   5028 TGCATCTGATAAAGGTCTAATATCCAGCATTCATAAGGAACTTAAACAAA 5077
                          ii         i  v  vi       v  vi    i     ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_99036609_9   5078 TTTGCAATAGACAAACCCAT--CCCCATTAAAAAGTGGGCAAAGGACATG 5125
                          ivii    i v i  vv  --   v   ?    i           iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_99036609_9   5126 AACAAACACTTTTCAAAAGAAGACATACATGCAGCCAATAAGAATATGAA 5175
                           i i   i  i  v        i     viii         v i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_99036609_9   5176 AAGAAATGCAAATCAAAACCACAATGAGA 5204
                             --   ---    v i  ????????
  L1M4_orf2#LINE/    885 AAGA--TGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (124 / 72)
Gap_init rate = 0.02 (13 / 768), avg. gap size = 2.15 (28 / 13)  


3227 26.43 0.77 0.77  chr2_99052317_99058750     5035  5942 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_99052317_9   5035 TGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5084
                           i  ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_99052317_9   5085 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5134
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_99052317_9   5135 TACCAATGACTTTCTTCACAGGA-TTGGAAAAAACT-ACTTTAAAGTTCA 5182
                          v   iivi i  i  ii   i -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_99052317_9   5183 TATGGAA-TGAAAAAAGAGCCCACATT-GCCAAGGCAATCCTAAGCCAAA 5230
                                -  v  i-- ii    v v -     ii     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_99052317_9   5231 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5280
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_99052317_9   5281 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5330
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_99052317_9   5331 CCAATGGAACAGAA--GAGAGCCCTCAGAAATAATGCCACATATCTACAA 5378
                         i        i    --     i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_99052317_9   5379 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATT 5428
                         ii vi    i  i     ivv  vv  i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_99052317_9   5429 CCCTATTTAATAAATGGTGCTGCAAAAACTGGCTAGCCATATGTAGAAAG 5478
                         vi  v  i  i           vi v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_99052317_9   5479 GTGAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATG 5528
                         i    ii    i    v   i    iv              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_99052317_9   5529 GGTTAAAGACTTACATGTTTGACCTAAAACCATAAAAACCTTAGAAGAAA 5578
                          i i ?    i  v    vv  v       i      vi           
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_99052317_9   5579 ACCTAGGCA-ATACCGTTCAGGACATAGGCATGGGCAAAGACTTCATGTC 5627
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_99052317_9   5628 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5677
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_99052317_9   5678 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5727
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_99052317_9   5728 AACAGGCAACCAACAGAATGGGAGAATATTTTTGCAATCTACTCATCTGA 5777
                           v  i     v              v  v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_99052317_9   5778 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACGAATTTACAAGA 5827
                         i  i  i  vi          v  i  v      vv  i v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_99052317_9   5828 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 5877
                             i     i     v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_99052317_9   5878 TTCTCAAAAGAAGAGATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5927
                              v        v  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_99052317_9   5928 ACCATCACTGGCCAT 5942
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


 915 28.10 13.55 1.16  chr2_99082332_99083931      504  1108 (492)    L1M4_orf2#LINE/L1      229   908 (0)  

  chr2_99082332_9    504 TTAAAAA--TACCACATAGCCTCTATAATTAA-ATAGTGTGGGACTG-CA 549
                           v    --   i   v   iv vi    i  - i       v    -  
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_99082332_9    550 CATGAATAGGCA----GATCAATGGAATAGAAATAGAAAGTCCAAAAAGA 595
                         i v i    i  ----                v -  i      i   v 
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATT-GAGAGTCCAGAAATA 327

  chr2_99082332_9    596 GATC----------TG---AAT--------GAC----------------- 607
                         i i ----------  ---   --------   -----------------
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_99082332_9    608 ----TGGGACAAAGA---GTCTTTTAAATCAATGATCTTG---CAACTTG 647
                         ----    i-     ---       v  iv    i vi  ---     v 
  L1M4_orf2#LINE/    378 TCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_99082332_9    648 ATAGTCAGTTGGAAAAAGATAAAATTAGATCCATTTCTCAAACCATACAT 697
                            ?i  vv  v    ii  i  i  i  i  v vi    v      i i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_99082332_9    698 AAAA-TAAACTCCAAATGAATCAGATATCTAAATGCAAAAAGTAAAAATA 746
                             - v     v     i    ? v i       i  i iv     v  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_99082332_9    747 TACAAGTACTAAAAGAAAACAT---------TCCTCTACTATCTGGGGAG 787
                           v  v vi  i          ---------  i  -iiv i  v   vv
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGGGTT 575

  chr2_99082332_9    788 AGAGAAAGATTTGCTAACTGTGA-ATAGAAATCCAGATGCATTAAAGGAA 836
                           iv  v i   vi  iv i   - ivi   v - v v   vi   i   
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGC-ACAAGCAACAAAAGAA 624

  chr2_99082332_9    837 AAGCTTTA-AAATCTGACTACA-CAAAAATAAAAACTTT-ATAGAGAAAA 883
                           iv vv -    iv    v  -     v          -i ivvvv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_99082332_9    884 AGGCAATA-CAGTAAGATTAAAAGACAAATGACAAAAAAGTGAGAAAATA 932
                         i i  v  -  iv  ii v         viv   i  vi -         
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG-GAGAAAATA 723

  chr2_99082332_9    933 TTGGTAG--CATATATCACCAATAAAGAGATAATTTCTGAAATGTACTAA 980
                           v i i--        --ii    i iiv vi v  iii   i  iv  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATC--TGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_99082332_9    981 AAATTTTTTTAAC--------AAAAAGATCTAAAGTCCATTAGAAAAATA 1022
                         i  i i  vi   --------       ivv v ii   v v?      i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_99082332_9   1023 GACGAAGAAAT-GAATAGCTAATTCCCAAAAAGAGATATAATAATAGCCC 1071
                          i i   i v -      vi v   i v   ii       vv   i   v
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_99082332_9   1072 TTAAACCTATGAAAAGATATTCAACTTCACTCACAAT 1108
                         v   i vi          ii     v   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (91 / 76)
Gap_init rate = 0.04 (26 / 680), avg. gap size = 3.42 (89 / 26)  


3651 17.54 5.13 1.35  chr2_99097404_99101700.rev     2688  3428 (869)    L1M4_orf2#LINE/L1        1   769 (139)  

  chr2_99097404_9   2688 TGGAAACACATCCCATGTTCATGGGCCAGAACACTTATCATTGTTAAGAT 2737
                               v i               iiii   v     vi           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_99097404_9   2738 GGCATTACTCCCAAAACTGATCCACAAATTTAATGCAATGCTTATCAGAA 2787
                             v       v   i     i   i   i  i     v i     i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_99097404_9   2788 TCCCAGGTGTCTT----GTAGAAATTGTCAAACTGATC-TAAAATTCATA 2832
                               v  i   ---- i        v   i      -           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_99097404_9   2833 TGGAAGTGCAAGTGA------ATAGCCAAAACAATCTTGAAAAAGAAAAA 2876
                              i      v  ------                          i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_99097404_9   2877 GAAAGTTGGAGAA-TCACACTTCCCTGATTTCAAAACTGGCTGCAAAACT 2925
                         v          i -           -i           vi  i    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCC-AATTTCAAAACTTACTACAAAGCT 249

  chr2_99097404_9   2926 GAAGTAATCAAGACAATGTGGTACTAGCATAAGGAAAGACATAGAGGTTG 2975
                         iv             i         i         v       v  i ii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_99097404_9   2976 ATGGAACAGAATTCAGAGTCCAGAAATGG-TTTATACATTTGTGCCCAAA 3024
                               i      v             ii-iii        i  vi   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_99097404_9   3025 TGATTTTTCAAAATACAGGTGCTAGGACAATTCAATGAGGAAAGAATAGT 3074
                                i---i i vi     i i   v        i            
  L1M4_orf2#LINE/    350 TGATTTTC---GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_99097404_9   3075 ATTTTTAGCAAATGGCGTTGGGACAACCTAATATCTATGTGGAAAAGAAT 3124
                         v    i i       i i         ivi   ? i ii  v        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_99097404_9   3125 GAAGTTGGA--------TCACA-----TGCAAAGATTAACTGAAAATGAA 3161
                                  --------     ----- i    i       v      i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_99097404_9   3162 TCATAGGGCTATATGTAACAGCCAAAACTGTA-----TTAAGAAGAAAAC 3206
                            ?  iv   v      v   i      i  -----i v          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_99097404_9   3207 ACAGAAGTAAATCTTTGTGACCTTGGGTTAGGCAGCACTTTCTTAAATAC 3256
                          i  i?         i                  iiiv       i   i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_99097404_9   3257 -ACATCAAAAACACAAACAA------AAAAAATAGATTAAGTAGACTTGA 3299
                         -   i     i     i   ------           v  v i     v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_99097404_9   3300 TCAAAATAAAAAAAAAAACCTTCTGTGCTGCAAATGATATCATCAAGAAA 3349
                                v     ------   i      v    v  i ii         
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA------CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_99097404_9   3350 GTGGCAAGACGATGCACAAGATGTGAGAAAACATTTGCAAACCATATATC 3399
                            iv     i iv    ii   v       i         i        
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_99097404_9   3400 TGATAAGAGATTCATATTCAAAATATGTA 3428
                                i  i ii   i  i     i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATA 769

Transitions / transversions = 2.43 (90 / 37)
Gap_init rate = 0.02 (13 / 769), avg. gap size = 3.69 (48 / 13)  

 561 13.39 0.00 1.57  chr2_99097404_99101700.rev     3679  3805 (492)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr2_99097404_9   3679 CTCAAAAAACAAAAAACTTAATAACCCAACTAAAAAATTAGGCAAAGGAT 3728
                              v  vv    i  v-          i ?      -i          
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACA-AATAACCCAATTWAAAAAT-GGGCAAAGGAT 831

  chr2_99097404_9   3729 ATTAATAGACATTTCTCTACATAAGATACATAAATGGCCAATAAACACAT 3778
                         v v              i v v      i i             i     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_99097404_9   3779 GAAAAGATGCTGAACATCATTAATAGA 3805
                                    v       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.78 (7 / 9)
Gap_init rate = 0.02 (2 / 125), avg. gap size = 1.00 (2 / 2)  


3044 27.43 0.55 1.31  chr2_99119699_99124472     3368  4282 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_99119699_9   3368 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3417
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_99119699_9   3418 GGCCATACTGCCCAAAGGGATTTATAGATTCAATGCTATCCCCATCAAGC 3467
                            v     v      vv   i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_99119699_9   3468 TACCATTGACTTTCTTCACAGAATCAGAAAAAAGCT-ACTTTAAACTTCA 3516
                          v   vivi i  i  ii     -- vvi v     - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr2_99119699_9   3517 TATAGAACCAAAAAAGAGCCCATACAGCCAAGACAATCCTAAGGAAAAAG 3566
                            i   viiv  ii  v  viv i      i      i i ii  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_99119699_9   3567 AACAAAGCTGGAGGGATCATGCTACTGGACTTCAAACTATACCACAAGGC 3616
                                i      iv   ii  v ivi i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_99119699_9   3617 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACATATATATATACA 3666
                                 i   i    ii         --------    viv   v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGG--------CATAAGGATAGACA 290

  chr2_99119699_9   3667 CACACACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCT 3716
                         i i v i        i    iv   ivii         vv   i    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_99119699_9   3717 ACAACTATCTGCTCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAG 3766
                          iiiii vi  v i  i     ivv  v   i v  vvv           
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_99119699_9   3767 GATTCCCTATTTCATAAATGGTGTTGGAAAAACTGGCTAGCCATATGCAG 3816
                         i  vvi  v  iv i        i   i v      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_99119699_9   3817 AAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAA 3866
                           i v    ii         v   i     v                   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_99119699_9   3867 GATGGATTAAAGACTTAAACGTAAGATCTAAAGCCATAAAAATCCTAGAA 3916
                         i      i ?    i    i      v     i i      v  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_99119699_9   3917 GAAAACCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCA 3965
                               v    ?i- v i -   iv   viv  vv i     v ii   v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_99119699_9   3966 TGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGG 4015
                          iiv  vi            vvi          vv     v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_99119699_9   4016 GATCTAATTAAA-CTAAAGAGCTCTGCACAGCAAAAGAAACTGTCATCAG 4064
                           ii v  i   -i    i vi i  ii vv    i  v   i   vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_99119699_9   4065 TATGAACAGGCAACCTAAAGAATGGGGGAAAATTTTTGCAATCTATTCAT 4114
                         vi    v  i     i v        i      v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_99119699_9   4115 CTGACAAAGGGCTAATATCCAGAGTCTACAAAGAACTTAAACAAATTTAG 4164
                             i  i  i  vi        i v  i        ivv    -i i i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAA 788

  chr2_99119699_9   4165 AAGAAAAAAAACAGACGACCCCACCAAAAAGTGGGCAAAGGATATGAACA 4214
                         v iv     i   i ii    v ii?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_99119699_9   4215 GGCACTTCTCAAAAGAAGACACTTATGCAGCCAACAA--ACATGAAAAAA 4262
                          i  i     v        i ivi viii     i  --         i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_99119699_9   4263 AGCTCATCATCACTGGTCAT 4282
                         v     v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


2669 24.94 8.11 0.48  chr2_99133710_99136774     1736  2573 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_99133710_9   1736 GATACACCATGTTTATGGATTGGAAGACTCAATATTGTTAAAATCTCAAC 1785
                             iv       i               i           i  vv   i
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_99133710_9   1786 TCTTCCCATACTGAACTGTATATTCAAAATAATGCTAATCAAACCCCAAG 1835
                         v  i    v i   v  ii v      vii   v iv      vi  v  
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_99133710_9   1836 TAGGTTTTTTTTCTGTAGAAAATGATATGCTCATTCTAAA-TTTATGTGG 1884
                         iv vi      --- i     v   i v   v  i     -  i  i   
  L1M4_orf2#LINE/    107 CTGCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_99133710_9   1885 AAATGCAGAGGACCCATAGTAGCCAAA-CA--TTTGAGGAA--AGAACAC 1929
                                ii       v i        -  --i    ii  --      v
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_99133710_9   1930 ATTTGGAGGATTTA-ACTAACTCATTTCAAGATCTACCATAAAGATATAT 1978
                          v        i i -   vv iv       i ii   i i    v  i v
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_99133710_9   1979 TAATCAAGTCACTGGGTTACTGGC-TAAGGATAGATGTATA--CC----- 2020
                                 v  v  v v       -          ii    --i -----
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_99133710_9   2021 --CAGAA--GAGAGTATAGAAACAGATCCACACATATATGATCATTTGAT 2066
                         --i    --      vi     i i i   i    v    i   v     
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_99133710_9   2067 TTTTGTGAAAAATTTGTAGATAATTCAATGATGAAATAA--GTCTTTTCA 2114
                            i vv  iii vivv   iv        iv    v  --         
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_99133710_9   2115 ATAAGTGGTGCTGG-ATACCTTCATATCTGTATGAGAAAAAATGAACCTT 2163
                          i  i         - i v  vv   ? iii   vi   i      vi v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_99133710_9   2164 GACCCTTATCTTACATCATACACAAGTATTAATTCAAT-TGTAGCATAGA 2212
                              i  i  i   i    i    iv     i    v-  v v  ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_99133710_9   2213 TCTAAATATAAAATCTAAAAATATAAAATTCCTAAAAGAAAGTCTATGC- 2261
                         i      i   i v      v       i  i  i      iiv  v ?-
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_99133710_9   2262 ------------ACCTTGGTGCATGCAAAGATTTATCAG----GACAT-A 2294
                         ------------       vvi v    v i   v i  ----    i- 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_99133710_9   2295 GAAGTACAAAGTATAAAA-AGAAAATTGGTAAACTGGACTTCATCAAAAA 2343
                         i   i    ivv i    - i     v i    i               v
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_99133710_9   2344 TGTAAAACTTCTGCTCTTAGAATGATTTTATTAAGAAAACAGAAAGGCAA 2393
                          i-       i  iv   vi  v  ivi   i      iiii    i   
  L1M4_orf2#LINE/    654 TA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_99133710_9   2394 GCCAATGACTGGGAGAAAATATC--CAAA------ATCTAA--AG----- 2428
                         v   vv  v             i--    ------    i --  -----
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_99133710_9   2429 --TGTTCAAAAAATAT---------CTACAATTTAATAACAAGAAGATAA 2467
                         -- i i  i  v    ---------i     i i     i  i    i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_99133710_9   2468 ACATGCCAATAAAAAGATGGGCAATAGATTTGAACAGCTACTTCACAAAA 2517
                          i vv     v?   i        vi        i  vi i   v v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_99133710_9   2518 GAAGATAGACTCATGACCAGTAAGCATGTGAAAATCTGTTCAACATCATT 2567
                                v  vv   i   i      ii      vv  i         ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_99133710_9   2568 AGTCGT 2573
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.44 (121 / 84)
Gap_init rate = 0.03 (23 / 902), avg. gap size = 3.13 (72 / 23)  


2977 26.96 0.66 0.33  chr2_99165075_99170143     3673  4577 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_99165075_9   3673 TGGAAACATGTCCCGTGCTCATGGATGAGTACAATCAAAAATGTGAAAAT 3722
                               v  i    i  i        vi v v v i  v v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_99165075_9   3723 GAACCTACTGCCAAAAGCAATATACAAATTCAATGCAATTCCCATCAAAA 3772
                          ivvv    v  v   vii  v    i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_99165075_9   3773 TAACACCATCTTTCTTCACAGAACTAGAAAAGACAATCCCAAAATTCATA 3822
                          vv  v vv i  i  ii     v v  v   vii    i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_99165075_9   3823 TGGAACCAAAAAAGAGCCCACATAGCCAAGGCAAGACTAAGCAAAAAGAA 3872
                              viiv  ii  v  viv        ii   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_99165075_9   3873 CAAACCTGGAGGCACT-GCATTATCCAACTTCAAACTATACTACAAAGCT 3921
                             vi      -   -i  i vi    i      viv            
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_99165075_9   3922 ACAGTTATCAAAAAAGCATGGTACTGATATAAAAATAGGCACTTAGACGA 3971
                              v     i v  ii        ii    ii    i  iv    iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_99165075_9   3972 ATGCAACAGAAT-AAGAACGCAGAAATAAGGCCAAATGCTTAAAGCCAAC 4020
                            v  i     -i   iiv         iv   v iii   vi i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_99165075_9   4021 TGATCTTCGACAAAGCAAACAAAAATATGAAGTAGGGGAAAGGACACCTT 4070
                             i        i vviv   i vi  vv i -        i i vii 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCT 398

  chr2_99165075_9   4071 ATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGAAGAATGA 4120
                         v                    i  i   vv ?       i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_99165075_9   4121 AACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATC 4170
                          ii    i  ii i   v    v           i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_99165075_9   4171 AAGCACTTAAATCTAAGACCTGAAACCATAAAAATTATAGAAGATAACAT 4220
                          ?iv  i     v     v  i    i      v iv       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_99165075_9   4221 TGAAAAAACCCTTCTAGACATTGGCTTAGGCAGTGACTTTACGACCAAGA 4270
                         v i?iv  vi    vv   v    v       i  ii  iviiivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_99165075_9   4271 ACCCAAAAGCAAATGGAACAAAAACAATAAGTAGGTA----GGACTTAAT 4316
                         vv         v v v       iv  -  i   i  ----      v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCAT 647

  chr2_99165075_9   4317 TAAACTAAAAAGTTTCTGCACAGCAAAAGAAACACTCAGCAGAGTAAACA 4366
                         i   v v    ii  i  ii vv    i  v  vv   iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_99165075_9   4367 GAAAACACAAACAGTGGGAGAAAATCTTCACAATCCATATATCTGACAAA 4416
                           v   v  v v i           v  ii   vi           i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_99165075_9   4417 GGACTAATATCCAGAATCTACACGGAACTCAAACAAATTAGCAATAAAAA 4466
                              vi          v  i vi      vv    v i ii        
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_99165075_9   4467 AACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGATAATTTT 4516
                         i     i  i  v  i?    i     v     iv        i v  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_99165075_9   4517 CAAAAGAAGATATACAAATGGCCAACAAACAAATTAAAAAATGCTCAACA 4566
                          v                       i  i  v  v    i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_99165075_9   4567 TCACTAATGAT 4577
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.22 (132 / 108)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2993 26.00 2.32 1.88  chr2_99204861_99210858.rev     4605  5508 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_99204861_9   4605 TGGAAAAACATTCCATGCTCATGGATCAGAAGAATCAATATTGTGAAAAT 4654
                               i i  i     i        ii     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_99204861_9   4655 GGCCATACTGCCCACAGTATTTTATAGATTCAATGCTGTCCCCATC---- 4700
                            v     v    v v iv i  i        i  vi    i   ----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_99204861_9   4701 -------TACTTTCTTCACA-AAATTAGAAAAAACT--TCCTTAAATTTC 4740
                         ------- i i  i  ii  -     i-- v  i  --    v     - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT-C 147

  chr2_99204861_9   4741 ACATGGAACCAAAAAAGACCCCATATAGCCAAGACAATCCTAAGCAAAAA 4790
                          i      viiv  ii     viv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_99204861_9   4791 GAACGAAGCTGGAGGGATCATGCTACCTGACTTCAAACTATACTACAAGG 4840
                             i   i      iv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_99204861_9   4841 CTACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGATATATACCA 4890
                                      i    ii         i iv ii i   i     --i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA--G 295

  chr2_99204861_9   4891 ATATATATATACCAATGGAACAGAACAGAGGCCTCAGAAACAACGCCACA 4940
                           ----------        i    iv   ivii      i  vv   i 
  L1M4_orf2#LINE/    296 AT----------CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_99204861_9   4941 CATCTACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGG 4990
                            i  iiii  vi    i  i     ivv  v   i v  vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_99204861_9   4991 GAAAGGATTCTCTACTTCATAAATGATGTTGGGAAAACTGGCTAGCCATA 5040
                              i  vv   vi iv i     i  i     v      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_99204861_9   5041 TGCAGAAAACTGAAACTAGACCCCTTCCTTACACCTTATACAAAAATTAA 5090
                             i  i v    ii i       v   i     v              
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_99204861_9   5091 CTCAAGATGTATTAAAGACTTAAACATAAAACATAAGACCATAACAACTC 5140
                              i   v  i ?    i    ii   i vv   i  i    -     
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTC 534

  chr2_99204861_9   5141 T-AGAAGAAAACCTAGGCA-ATACCATTTAGGACATAGGCATGGGCAAAG 5188
                          -          v    ?i- v i -  iiv   v v  vv i     v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chr2_99204861_9   5189 ACTTCATGACTAAAACACCAAAAGCAATGGCAAGAAAAGCCAAAATTGAC 5238
                         ii   v iiv  vi            vvi    v     vv     v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_99204861_9   5239 AAAT-GGATCTAATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTAT 5287
                             -   ii v  i   v v  i i   i   i vv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_99204861_9   5288 CATCAGAGTGAACAGGAAAC--ACAGAATGGGAGAAAATATTTGCAATCT 5335
                           vv i      v  iv   --                         vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_99204861_9   5336 ACCCATCTGACAAAAGGTTAATATCTAGAATCTATAAGGAACTTAAACAA 5385
                          ivi      i  ii ii vi    i     v     i     ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_99204861_9   5386 ATTTACAAGAAAAAAACAGACGACCCCATCAAAAAGTGGGCAAAGGATAT 5435
                         v iv i  v     i   i ii    v  i?    i            v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_99204861_9   5436 GAACAGACACTTCTCAAAAGAAGACATTTATGCAGCGAACAA--ACATGA 5483
                            i     i     v        i  vi viii  v  i  --      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_99204861_9   5484 AAAAAAGCTCATCATTGGTCATTAG 5508
                            i v     v   ii????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (144 / 87)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.71 (38 / 14)  


2957 25.97 4.35 0.46  chr2_99304239_99308712     3109  3982 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_99304239_9   3109 TGGAAAAACATCC-ATGCTTTTGGATTGGAAGAATCAATATTGTTAAA-- 3155
                               i i    -   i iv            v i           i--
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_99304239_9   3156 -GCAGT---------------CTACAGATTTAACACTATTCCTATCAAAC 3189
                         -   i ---------------         i   i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_99304239_9   3190 TACCAACATCATTTTTCACATAATTAGGGAAA--AA----AAAACT---A 3230
                          v   i vv v     ii  v  v v iv  i--i ----    i --- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_99304239_9   3231 TTGTAACCCAAATGGAGGCTGAATAGCCAAAGTAATCCTAAGCCAAAAGA 3280
                          v v  iv   i-   vv v           ii    i i ivv i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_99304239_9   3281 ACAAAGCCAGAGGCATCACTTTACCTGATTTCAAACTATATTACAAGGCT 3330
                               iii    vv    vi v  ii        viv  i     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_99304239_9   3331 ACAGTAATCAAAACAACATGGTACTGGTATTAAAACAGATACATAGACCA 3380
                                    i   iii         i  v ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_99304239_9   3381 ATAGAACAGAACAGAGAACCTAGAAATAAAGCCACACATCTGCAATCATC 3430
                           i   i    iv    ii i         v   i    i iiii   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_99304239_9   3431 TGATCTTTGACA--GGTGACAAAAATAAGCAATGGGGAAAGGACTCCCTA 3478
                             i  i    --    v   i vi vv            i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_99304239_9   3479 TTCAATAATTGGTGCTGGGATAAATGGCTAGCC-TATGCAGAAGAATGAA 3527
                              i  v           i  v   v  ?  -i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_99304239_9   3528 ACTGGACCCCTACATTTCACCATATACAAAAATGAACTCAAGATGAACTA 3577
                         ii           v iv                v       i   i ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_99304239_9   3578 AGAACTTAAATGTAAGACCTCAAACTATAGAACTCCTATAAGAAAACCTG 3627
                         ?ii  i           v  v        i     i  v        v i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_99304239_9   3628 GG---AAATACCCTTCTTGATGATGGCTTTGGGAAAGAATTTATGGTTAA 3674
                           ---    ---    v   ivv   v  v  v  v iv  iv i v  v
  L1M4_orf2#LINE/    550 GGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_99304239_9   3675 GTCCTCAAAAGCAATTACAACAAAAACAAAACTCGGCAAATGGGACCTAA 3724
                          v vi        vvvi        iv    v v ii    v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_99304239_9   3725 TTAAACTAAAGAGCTTCTGCACAGCGAAAGAAACTATTAACAGAGTAAAC 3774
                          i   v v  i i   i  ii vv i  i  v     i  v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_99304239_9   3775 AGACAAC----AGAATGGGAGAAAGTATTCACAAACTGTGCATCTGGCAA 3820
                                ----             i    ii    iii ii     ii  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_99304239_9   3821 AGGTCTAATATCCAGGATCTATAAGGAAGTTAAGCAAACCAACAAATAAA 3870
                         i  v  vi       i  v     i   v ivvi   vi   i  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_99304239_9   3871 ACACAAATAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTC 3920
                          v           v   ?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_99304239_9   3921 TCAAAAGAAGATTTACAAGCAACTAACAAACATATGAAAAAATGCTCATC 3970
                           v         v     iiii i  i  i  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_99304239_9   3971 ATCACTAATCAT 3982
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (134 / 90)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.50 (42 / 12)  


 931 23.99 7.48 3.12  chr2_99428794_99431076.rev      656   976 (1307)    L1M4_orf2#LINE/L1        1   335 (573)  

  chr2_99428794_9    656 TGAAGAGACATGCCATGTTCATGGGCTATAAGACTCAACACAGTAAAGAT 705
                           i i   i  v            ii iv      i  i iv  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_99428794_9    706 GACAATCAGCCCTAAAATGATATACAGGTTTAATGCAATTCCAATAAAAA 755
                          i    vvv   i   v    v     i  i  i     i  v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_99428794_9    756 TCTCAGCAAGATTTTTAGGACATAACCAATAGAGACAAGGTTATTCTAAT 805
                           i    vivv     v --  v  ---  v  --    v v  i    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG--CAGAA---ATTGA--CAAGCTGATCCTAAA 143

  chr2_99428794_9    806 ATTTATATGAAAAGGCAAAGAAACTAGAATAGCTAAACCAATTTTGAAAA 855
                            i     i   v    i i v i        i   v    i       
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_99428794_9    856 A--AGACTAAAATGTGAGGAATCATACTACCAGATTTCAAGACTTAA-GC 902
                          --   vi   i vv     v   i   v  vi       i     v-i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_99428794_9    903 AAAGCTCT----------------TGGTACTGGCAAAGGAATAGACACA- 935
                               vi----------------           v i i       i -
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_99428794_9    936 -GATCAAGACGAGAAGAGA---GAGAACCCAAAAACAGTCCCACA 976
                         -      vi---   v   ---    ii   i   i iv    i 
  L1M4_orf2#LINE/    294 AGATCAATG---GAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

Transitions / transversions = 1.20 (42 / 35)
Gap_init rate = 0.03 (9 / 335), avg. gap size = 3.78 (34 / 9)  

1048 24.55 15.69 2.41  chr2_99428794_99431076.rev     1307  1803 (480)    L1M4_orf2#LINE/L1      346   908 (0)  

  chr2_99428794_9   1307 CAATTAATTTTTGACAAAGGTGCAAAAGC------------AGAGGGTAG 1344
                              i     i     i     v  ii ------------ i  ii   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_99428794_9   1345 CCTCTTTAACAAACAGTGCTACAGCAAATGGACACCTATCACACAAAA-- 1392
                         i  i  i      ii     ivii   v    i ? i -  ii     --
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA-CATGCAAAAGA 444

  chr2_99428794_9   1393 ATGAA------CCTCACCCTCAGTCCTTATCCAAGAGTGAACCCAAGATA 1436
                              ------  i vv     vv  v   v   i i v   i   i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_99428794_9   1437 TATGATGTACTTAAAAA-AATAAATAAAAGCATAAA-CTTTTAG--GAAA 1482
                         v  v ?iv  i    vi-  v iv     vi     -  i    --    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_99428794_9   1483 A-----GAGTAAAATATCTTTCAGATCTAGCACTAAGCAAAGAGTTAAGA 1527
                          ----- ?     ---    ivv  i  v vii  i    v iv  ----
  L1M4_orf2#LINE/    545 ACATAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTT---- 587

  chr2_99428794_9   1528 GTTAAGACTTGAAACTAAAAGCACAATC--CAAAAGAAG----------- 1564
                         -i v   iv   v  i          v --        i-----------
  L1M4_orf2#LINE/    588 -CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_99428794_9   1565 -TGGAACTCATCAAAA------ACTTTTG--CTGTGAAAGACTATGTGAA 1605
                         -    vi         ------       --  vii  i   vv i v  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_99428794_9   1606 GGGAATGAAGA-ACAAGCTACAAAATGGGAAAAAATATTTCCAAATCACA 1654
                          ii i    i -    v i   i       i         v       i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_99428794_9   1655 ----------AGGATTAACAACTAGAATATACCCAAAACTCTCAAAACTC 1694
                         ----------i   i vii v i        ivv i      i v     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_99428794_9   1695 AACAGTAAAATAAATCCAAACAATCCAATTAAAAAATGGGCAAAAGGCAT 1744
                           i i     - i --    i  i      ?             i iiv 
  L1M4_orf2#LINE/    787 AATAATAAAA-AGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_99428794_9   1745 AAAAAGACATT---CCACTGAAGATATACACATGGCAAATAA-------- 1783
                         i  v       ---   vv           v     v     --------
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_99428794_9   1784 ----ATGTTCA-CATCATTAGCTAT 1803
                         ----   i   -     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (73 / 45)
Gap_init rate = 0.04 (21 / 563), avg. gap size = 4.29 (90 / 21)  


1712 25.17 16.55 1.67  chr2_99441150_99442849      501  1219 (481)    L1M4_orf2#LINE/L1       68   893 (15)  

  chr2_99441150_9    501 TAATCTGTAGATTCAGTTCAATCCCAGTCAAAATCACAGCATGG-TATTT 549
                          i    ii       iiv       vi        v    -  v- v   
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCTTTTT 116

  chr2_99441150_9    550 TGTAGCTATCTGTCAA-CTAGTTCTAAAATGGATATGAAGAGACCAGAGA 598
                           i  vv  -  v   -  ii i       vv     i i vi v  i  
  L1M4_orf2#LINE/    117 TGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_99441150_9    599 GTTAGAATGGCCAAAATATGTTTGAAAAAGGAGAACAAACTTAGA----- 643
                         vii     i       i vvi         i        v  i  -----
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_99441150_9    644 -ATAC---CTGATTTCAAGACTTAGTATAAAGCTATAGGAATTAATACAG 689
                         - i  --- ii       i     v  i       i  v   i  v    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_99441150_9    690 TGTGATATTGCCAGAAAGATAGACAAACAGAT-----AAATAG------- 727
                             i  i  v  v  i        v i    -----i     -------
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_99441150_9    728 --------------TCTATACAT----GGTTAGT---------ATATAGG 750
                         --------------i i      ----   i i --------- i vi  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_99441150_9    751 TGA-AAGGTAATTCAGTGGATAAAATACAGTATTTGTAGCAAGTGGTACT 799
                           v-   iiv     i   iv   iv i   v   vi i   i    i  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_99441150_9    800 AGAACAATTGGACATCTGTATGCAGAAAAACCCAAAACCAG--TTTTAAT 847
                         i i    i    i ? iii     i  i  i--i  iiii --iii  vi
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAAT--GAAGTTGGACCCCTACC 463

  chr2_99441150_9    848 TCCCACTGTATA--AAAATTGACCCAAA-TGGGTATCATA--TGTAAATG 892
                           v   ii    --      i  i    -   --    ? --iv      
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGG--ATCAWAGACCTAAATG 511

  chr2_99441150_9    893 TAAAATATACAA---TAATACTTTCAGAGGAAAACATAGGAGGATATCTT 939
                            i vv  v  ---   v   i i   i           ? v v     
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_99441150_9    940 -GTG--------TTAGGCA--GAGTGCTTAGATAGGACTCTAAA------ 972
                         -   --------       -- iv v        v   v i   ------
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_99441150_9    973 --CCATAAAAGGAAAAA-AGATACATT----TTGAGAAAGACCAGTTCAG 1015
                         -- v i     i     -     v   ----  v vv  i ----  v i
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA----TTAAA 657

  chr2_99441150_9   1016 AACTTTTCT-CTGCAAAAGACACTGTCAAGAGAAT----------TCCA- 1053
                                v -  v    i      i      i i ----------i   -
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_99441150_9   1054 --------AGACAGTACCTCCAAGTCAGATATCTGAGAAAGAATTAACAT 1095
                         --------   v i  ii v   i   v        v  i i i vii  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_99441150_9   1096 CCAAAATATATAAAGACCTCTCAAAATTCAACTATAAGAAAACCAATAAG 1145
                            i            v    i v  i    iv    i  i  v     v
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_99441150_9   1146 TTCATTTAAAAATGGGCAAAAGGTATCAACAGACACTTTCACCAGA-AAG 1194
                         iiv   ?             i i v v  i     -    v   i -   
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACA-TTTCTCCAAAGAAG 856

  chr2_99441150_9   1195 CTATAC-------------GCATCTGAAAAGAATGTTC 1219
                         v     -------------   iv        -  i  
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

Transitions / transversions = 1.68 (111 / 66)
Gap_init rate = 0.04 (32 / 826), avg. gap size = 4.09 (131 / 32)  


1664 24.51 7.41 1.76  chr2_99460729_99464353.rev     1580  2146 (1479)    L1M4_orf2#LINE/L1        6   604 (304)  

  chr2_99460729_9   1580 AGAGATACCATGCTCACTGATCAAAAGATGCAATATTGCTAAAAGAGCCA 1629
                            v  v     i   iv   iii    ivi       i   i vi  - 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC-A 54

  chr2_99460729_9   1630 ATTCTCTCAAAATTTATCTACAGATTGAAACGCAATCCCAATCAAAATCC 1679
                           v   i v     v           v  -         v          
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAAATCC 103

  chr2_99460729_9   1680 TAAAAGGCTTTTT-GTGGAAACGAACAAGCTGA-CTGAAAACTTTATATT 1727
                         i ivv v      - ii    ivi         - iv    -  i    v
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCATATG 152

  chr2_99460729_9   1728 GAAATCCAAGG-ACCTAAAATAGCCAAAACAATAT----AAAGAA-AACT 1771
                              v     -   i i               v ----      -   v
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_99460729_9   1772 AAGTTGAAGGATTTACCACTACCAGCTTTCAAAACTTTACTATGAAGCTA 1821
                               i    i i  -   v  viv           -    ii      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTT-ACTACAAAGCTA 250

  chr2_99460729_9   1822 TAATGA----GACAGGGTAGTAGTGGCATAGGAATG--TATATAGAGCAA 1865
                         i i i ----     v  i   v       i i  i--i       v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_99460729_9   1866 TGGAACAAAAGATAAATTCTAGGAA------CAGACATATATGGTCAATT 1909
                              i i  vvv i v  i  i  ------  v    v           
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_99460729_9   1910 AATTATTGACAAAGATTCCAAACTAATTCCATGGGGAAAAAAATAATTTT 1959
                         i   v i     i i v    iviv    v         i  -  i i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTT 399

  chr2_99460729_9   1960 TTCAGCAAAGAGTCTTTAAATAACAAAATATTTCTATGGAAAAAAA---- 2005
                             i    vi  vi vii i   vii   ?iivi   v    i  ----
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_99460729_9   2006 GT-AAACCCTGACCTCACACTATATAAAAAAA------------AGATCA 2042
                           -ii    iv         i     v     ------------i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_99460729_9   2043 CTGATCTCAATGTAAAAAAAGCTCCAACTATTAAACATCT-----GGAAA 2087
                         ?v  i  v       i ---   vv      v    -   ----- i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA---GCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chr2_99460729_9   2088 CACCAGAGAAAAATTTAATGAACTTGGGATAGGAAAAGATTACTTACATA 2137
                           ivi ? v   vi  vi   v      v    v  v i  v    v   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_99460729_9   2138 GAACACAAA 2146
                         vi    v  
  L1M4_orf2#LINE/    596 TGACACCAA 604

Transitions / transversions = 1.23 (75 / 61)
Gap_init rate = 0.03 (20 / 599), avg. gap size = 2.60 (52 / 20)  

 236 24.42 9.30 0.00  chr2_99460729_99464353.rev     2443  2528 (1097)    L1M4_orf2#LINE/L1      601   694 (214)  

  chr2_99460729_9   2443 CCAAAAATA-----AATAAAATATAAAA---ATTAGTTGGATTTCACCAA 2484
                               ii -----  i    v v    ---  v i     i    i   
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_99460729_9   2485 AATCAGAAATTTCTTCTCTTCAAAACACACTATTAAGAAAAGGA 2528
                            i i   i  i viv       iv       i      iv  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 4.00 (8 / 2)  

 435 20.18 8.33 10.09  chr2_99460729_99464353.rev     2918  3145 (480)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_99460729_9   2918 AAGAAAATGAAAAACCAAGTCCCAGACCATAAGAATACATCAGCAGTACA 2967
                               i      iv   vi v    viivi    v i  iv   ivv  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_99460729_9   2968 TACAAGTGAAAAAGGAATTATATACATAGAACCAGAA-GTATAAAGAACT 3016
                           i vv   v  i   v  i   --------      -i           
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTAT--------CCAGAATATATAAAGAACT 776

  chr2_99460729_9   3017 CTTAAAACTCAACAATAAAA------------CAATCTAATAAAGAACAA 3054
                             v       i       ------------    i?  v  v ii   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_99460729_9   3055 AGGATTT---TGAACATATTTTTCAAAGAA---ACAGATATGGTCATCTC 3098
                                --- ii    -  i i       --- i v v    i  ----
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACAT-TTCTCCAAAGAAGATATACAAATGGCCA---- 871

  chr2_99460729_9   3099 TCTAAGCATAAGTACATGAAAAGATGCATAAAGCCATTAGTCACTGT 3145
                         -------     i              vi  ---   i ????????
  L1M4_orf2#LINE/    872 -------ATAAGCACATGAAAAGATGCTCAA---CATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (26 / 19)
Gap_init rate = 0.04 (8 / 224), avg. gap size = 5.25 (42 / 8)  


3816 17.73 0.68 1.08  chr2_99611823_99613548      497  1235 (491)    L1M4_orf2#LINE/L1      173   908 (0)  

  chr2_99611823_9    497 TAGCCCAAAATAATCTTGCAAAAGAAGAACAAAGTTGGAAGACTCACA-T 545
                              -    i       v                    i        - 
  L1M4_orf2#LINE/    173 TAGCC-AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_99611823_9    546 TCCTGATTTCAGATATTACTACAAAGTTACAGTAATCAAGATGGTGTGGT 595
                            ii      i vv           i              ii       
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_99611823_9    596 GCTGCCATAAGGATGGATATAGAGGTTATTGGAATGGGAATGAGAGTCCA 645
                         i   v         i  i   v  i i v      i i v          
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_99611823_9    646 GAAATAAGCCCTCGTGTGTGCAGCCAATTCATTTTGGACAAGGGTGCCAA 695
                                i   viiii v iii i     v     v              
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_99611823_9    696 GAAAATTCAATGGGGGGTGGGGAGAGAATACTCTTTTTAATAAATGGTGC 745
                           vv           ------- i      v      i  i         
  L1M4_orf2#LINE/    372 GACCATTCAATGGGG-------AAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_99611823_9    746 TGAGATAGCTGGATATCCACATGCAAAAGAATGAAGCTGCACCCCTACCT 795
                           i  i i       ?                    i  v          
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_99611823_9    796 CACACCATACACAAAAAGTAACTTAAAATGAATCACAGATCTAAATACTA 845
                                  i       v     i      i    ?   i      iiv 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_99611823_9    846 CAGCTAAAACTTTGAAAGTCCTTGAAGAGGATATAAGAGCAAATCTTCAT 895
                         v          v i   v  i v     ii i   i ? i        i 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_99611823_9    896 GACCTTGAGTTGAACAAAGCCTTCTTATATATGACAT-GAAAGCCTGAG- 943
                                i   iii   v vi      v        i-i     vii  -
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_99611823_9    944 -ACAAAATTTCAAATGGATACATTAAACTTCATCACAATGAGAAACTTTT 992
                         -      vvvv    i    v   ii         v   v i        
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_99611823_9    993 GCACAACCAAAGGCAGTATCAAGAAGGTGAAGAGAAAACTCACAGAATTT 1042
                          ii vv v  i i  v         i     i   v   i        vv
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_99611823_9   1043 GAGAAAATATTTGCAAATCATATATCTGATAGGGATCTAGCATTCAGAAC 1092
                                                        i  iv  v i  i     i
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_99611823_9   1093 ATATAAAAACCCCTTACAACTTAACAATAAAAAGACAAATAACCTAATTT 1142
                                i v i         i  i                   i    ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_99611823_9   1143 TAAAATGGGCAAAGGATTTGCATAAACATTTCTCCAAGGAAGATATA-AA 1191
                         v                   v   i            i         -  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_99611823_9   1192 ATGGCCAATAACTATATAAAAGGATGCTCAACATCCTTAGTATT 1235
                                    vi i  i   i             v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (81 / 46)
Gap_init rate = 0.01 (6 / 736), avg. gap size = 2.17 (13 / 6)  


3005 26.90 2.34 1.00  chr2_99701808_99704699.rev     1505  2400 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_99701808_9   1505 TGAATAAACATTTTATGCTTTTGGATAGGAAGAATCAATGTCATGAAAAT 1554
                           i v i i  iii   i iv     v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_99701808_9   1555 GGCCATACTGCCCAAAGAAATTTACAGATTCAGTGTTATTCCCATTAAAC 1604
                            v     v      vvi  i          ii iv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_99701808_9   1605 TACCA-TTGACATTCTT-CAAAGAATTAGAAATAAACT-ATTTTAAAGTT 1651
                          v   -i  v v  i  -  i -    i--- i  i  -  ii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAGCTGATCCTAAAATT 146

  chr2_99701808_9   1652 CATATGAAACCAAAAAAGAGCCCTAGTAGCCAAGGCAATCCTAAGCAAAA 1701
                               i  viiv  ii  v  vv i       ii     i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_99701808_9   1702 AGAACAAAAAGCTGGAGGCATCGTACTACCCAACTTCAAACTATACTACA 1751
                                 -- i      vv  ii   v     i      viv       
  L1M4_orf2#LINE/    197 AGAACAAA--GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_99701808_9   1752 GGGCTATGGTAACCAAAACAACATGGGTACTGGTACAAAAACAGACACAT 1801
                         ii    ii    i   i   iii   -      i i  ii i     i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGG-TACTGGCATAAGGATAGACATAT 293

  chr2_99701808_9   1802 AGACCAATGGAACAGAATAGAGAGCCCAGAAAAAAGGCCATACACCTATA 1851
                            i        i     v     i       v  iv       ii   i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_99701808_9   1852 ACCATCTGATCTTTGACAAAAG----AAG------CAATGGGGAAAGGAT 1891
                         ii  vi    i  i     ii ----   ------            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_99701808_9   1892 TCCCTATTTAATAAATAATGCTGGGAAAACTGGGTAGCCATATGCAGAAG 1941
                         vvi  v  i  i    ii        v      i  ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_99701808_9   1942 ATTGAAATTGGACCCCTTCCTTATACCATTTACAAAAATCAACTCGAGAT 1991
                          v    i          v   i i     v         i     i i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_99701808_9   1992 AGATTAAAGACTTAAGTATAAAACCCCAAAACTATAAAAACCCTGGAAGA 2041
                         i   i ?    i   i i   i v i-            vi i i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGA 542

  chr2_99701808_9   2042 CAACGTAGGC---AATATTC-TGGTCATATGAATGGGCAAAGATTTCATG 2087
                         v   i    ?---   v   -  ii v i- iv i     v i    v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTG-GGTTAGGCAATGGTTTCTTA 591

  chr2_99701808_9   2088 ACAAAGATGCCAAAAGCAATTGCAATAAAAGCAAAAATTGACACATGGGA 2137
                         ivv v  ii         vvv    i     v      v  i v  v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_99701808_9   2138 TCCAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCATCAACAGAG 2187
                         iiiv  i   v v  i i   i  ii vv    i  v  i     v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_99701808_9   2188 TAAACAGACAACCTTCATAATGGGAGAACATTTTTGCAAACTATGCATCT 2237
                          i  v        iv  v          v  v        ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_99701808_9   2238 GACAAAGCTCTAATATCCAGCATTTCTAAGGAACTTAAACAAATTTACAA 2287
                           i  i vv  vi       v  v v   i     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_99701808_9   2288 GAAAAAAACAA----CCCTATTAAAAAGTAGGCAAAGGACATGGTCAGAC 2333
                         v     i    ----   v   ?    i i         iv  ivi    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_99701808_9   2334 ACTTTACAAAAGAAGACATACATGCGGCCAACAAGCATATGAAAAAAAGC 2383
                          i  iv v        i     vii      i     i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_99701808_9   2384 TCAACATCACTGATCAT 2400
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (153 / 84)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


2471 25.39 9.67 1.57  chr2_99791970_99795016.rev     1737  2563 (484)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_99791970_9   1737 ACGTTCATGAATTGGAAAACTTGATAGTGTTGACATCTCGATTTTTCTCA 1786
                          i       i       i    i   v    i v  vv i  vi i i  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_99791970_9   1787 TCTTGATCTATAGATTCAACACAATCTTGATCAAAAGACCTGCAGGACAT 1836
                         vv        i         i     iiv       vv  v  -v v v 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCTT 113

  chr2_99791970_9   1837 TTTTATAGAAAATGGTTTTACA----GATTCTAAAATCTTTATAGAAAAC 1882
                             ii     v  -----   ----   i       iiv   i    vv
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTG-----ACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_99791970_9   1883 CAAAAGA-----GGTAGCCAAAACAGTCTTTAA---GAACAACAGAGTTA 1924
                            ii  -----ii           i    v  ---   v    i    i
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_99791970_9   1925 GAGGCCTTACAGTACCTGACTTCAAGACTTACTGTAAAACTAAAGTAATT 1974
                             v  i   v v  ii i     i       ii   i   v      i
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_99791970_9   1975 TAAGACAGTGTGGCACTGATATAAGGGCAGACAAATAAATCAATAGAA-A 2023
                         -            i    ii      ii     v   i      i   - 
  L1M4_orf2#LINE/    259 -AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_99791970_9   2024 AAAT----AGTCTAGAAGTGGATCCATATGGATATGGTCATTTGATTTTC 2069
                         i   ----    i    i ii i     iivv        v         
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_99791970_9   2070 CTCAGAGACACCAAAGCAGTCCAGTGGGGAAAGCCGGGTCTTTTCAACAA 2119
                         vv  ii iii    ii vi i  i         vvvi             
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_99791970_9   2120 ATGATGCCAGAGCAACT------TCTCAGGGGAAA-AATGAA-------- 2154
                            i   ii ii     ------i v  v vi   -      --------
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_99791970_9   2155 ----TCTCATACCACACACAA--------TTGAGAGGGAGCACAGATCTC 2192
                         ----i    i    i i    -------- ii i v   v  ?   i  v
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_99791970_9   2193 AATATAAACGCTAAAACAACAAAGTTTCTAGAGGAAAACAGAAGACAGTA 2242
                            i   iv        v i   ii ii    i       v i ?--   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN--GTA 555

  chr2_99791970_9   2243 --TCTTTACAAC-TAGGAACAGACAGAGATGTCTTACAGAGGTCAC-AAA 2288
                         --    iiii  - v  ivi  i  iv i v     v v v v   -   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_99791970_9   2289 ACCACA--CAACATGAAAGAAAGTTCTAATGGATTGGACTTCATCAAAAT 2336
                          v    --     --       ivvivi  ii                  
  L1M4_orf2#LINE/    606 AGCACAAGCAACA--AAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_99791970_9   2337 T----------------TAAAGATAACTGCTCATCAAAATGAAAAGTCAA 2370
                          ----------------i    ivv   i-   vv   i       v   
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAA 702

  chr2_99791970_9   2371 GCTGCGAACCGGGAGAATATATTCGCAATACGTGTATCTGACAAATAATT 2420
                         v ii ii vi       v     i    vv i i       i  ivi i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_99791970_9   2421 TGTGTCTAGAATATATAAGATATTCTGACAATTCAATGACAAAATTATAA 2470
                            i  i           iiv i   v    i     i i    vv i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_99791970_9   2471 AT--TTC--TT---AAATGGACAAAAGCTTTGAACAGACA-------AAA 2506
                           --ii --  ---      i    i v      i     -------   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_99791970_9   2507 GAAGATACACAAATTGGCCAATAAGCAGATGAAAAGGTGCTTTTCACTAA 2556
                                i      -            v        i    ivv  ii ?
  L1M4_orf2#LINE/    853 GAAGATATACAAAT-GGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_99791970_9   2557 TAACGTT 2563
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.81 (134 / 74)
Gap_init rate = 0.03 (25 / 894), avg. gap size = 3.72 (93 / 25)  


2341 26.32 8.19 1.99  chr2_99873956_99875807      508  1362 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_99873956_9    508 TAGAGAGACATACCATGTTCATGATTTGGAAGAATCGATATTGTTAAGAT 557
                          i  i   i  v           iv        v ii             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_99873956_9    558 GCCAATTCTTTCTAAATTCATTTGTAGATTCAATGCAATCATAATAAAAA 607
                          v    v  ii i     v  i ii        i      viv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_99873956_9    608 TCCTAATAGGCTTTTTATTTGTGTGGAAATTGACAAGTTGGTTCTAAAAT 657
                            i iiv v      -----  ii            i  i i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-----TGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_99873956_9    658 TTACACAGAAA-----AGGTGTTAAAATAACCAAAATAA-CTTGAAAAAC 701
                          i i ii    -----i  vvii i    i      i  -         v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_99873956_9    702 AAGAATAAAATCGAAAGATT-ATACT-----ATTTGATAGAAAATCA-TA 744
                              i   i i i i  i - i   -----    v ---   v i -  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA---AAACTTACTA 242

  chr2_99873956_9    745 CA--GCTATAGTGACCAAGACAGTGTGATACCAGTGTAAGGACTGACA-- 790
                           --    i   i i            i   ii ii      iv    --
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_99873956_9    791 ---------AGAACCAAACAGAGAATCCAGAAATACACC-ACATATCTAC 830
                         ---------i   ivi  iv    i          v   - i i  i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_99873956_9    831 AAACAACTGATTTTCAGCAAAAGTGCAAAGGCAATTAAGTGGAGAAAGGA 880
                         iiv   i        ii   ii    v   i v   v i   i     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_99873956_9    881 CAGTATTT-CAACAAATGGTACTGGAATAACTGGATACTCATGTGCAAAA 929
                         i   v   -           i    i i         ?i  ii       
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_99873956_9    930 G-------TTGAATTTCCATC-CACACT----------------TCACAA 955
                          -------   i iii i i -     i----------------   v  
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_99873956_9    956 TGAATCTTAAACCCAAATGTAAAGTCTAAAACTGCAAAGTGTTCTGAACC 1005
                           i   v? i   i        iiv        ii   iivi iv   vv
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_99873956_9   1006 TAACATAGAAAAAAATCCATTGTGACTTTAGATTATACCAAGATTTCTTA 1055
                         v       i?iv     i- i     i  i i   vi v v i       
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_99873956_9   1056 GCCACAACTCCAAAAACAAGAACCATAAATTAAAAAATGTA-AAACAGAA 1104
                          vi ii  v      i  vi i v i   vv       iv -   iv i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_99873956_9   1105 CTTCATAGAAATTAA---TTTTTTAACAAAGTTTGAAAGACATGTCTTTA 1151
                               vi       ---i    vvi ----  ii  i    i- v iv 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGC----TTCAAAGGACAC-TATCAA 686

  chr2_99873956_9   1152 CAATCTCTAAAGACAAGCCCCATACTTAGAGAAGATATTTGCAAAGTATG 1201
                         v  vv vv        v  v  v v vi     i           vi  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_99873956_9   1202 TA---AATAA----CTTGAATGTAGAACATATAAAAAAGACTTTTCAAAA 1244
                           ---i    ----    v  vi    i       i  --  i  - v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA--CTCTT-ACAA 783

  chr2_99873956_9   1245 ATCAACAATGAGAACA-AAACAACCTAGT--AAAAAAGGCCAAAGTTTTT 1291
                         v    i   i i  v -   i    i i --     v  v     vv   
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_99873956_9   1292 ---TGAACACATCACCACAGAAGATACATGGATGGAAAATAAGTGTATGA 1338
                         --- ii   iv  v   v        i iii    vv      iii    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_99873956_9   1339 AAAGATGCTCAATA-CAACCAATCA 1362
                                     i -  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (147 / 75)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.22 (87 / 27)  


 950 22.90 5.98 13.98  chr2_99994162_99997450     1812  2798 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_99994162_9   1812 TGGAGGGATATACCATGCATGCATGAATTGGAAGACTCAACAGTGCTCAG 1861
                             ii     v     -- v    i           i  i v  i v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATG--TTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_99994162_9   1862 ATGTCAATTCTTCCCAAATTGATCTAAAGATTCAATACCATCCAAGTCAA 1911
                            v    v  i              v        ii v    vvi    
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_99994162_9   1912 AATCTCAGCAAAGTTTTCT-CAAAA---GA-AAACACATA--AAAATACA 1954
                             i    vivv    i -  i  ---  -  i vv  v--     v  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_99994162_9   1955 ACTTGAAACAGTCACAGACCTAAACATCAAAGCTAAAA-ATTGTTATCAG 2003
                         vv v    i- iv vi    i i -  ---   i    - v v  ---- 
  L1M4_orf2#LINE/    149 TATGGAAAT-GCAAGGGACCCAGA-AT---AGCCAAAACAATCTT----G 189

  chr2_99994162_9   2004 AAACAATGAGAATGCCAACTCTGTAACATTCATTCTTTCTA-T-----AA 2047
                            -  vi    ---   vvi  v iv i   iv   i i - -----  
  L1M4_orf2#LINE/    190 AAA-AAGAAGAA---CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_99994162_9   2048 CTCAC-----AATTGCAGTCTCATCATGAAAA----GAATTT-CA----G 2083
                           i  ----- ii i    v--    v  v i---- v i v-  ---- 
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTA--ATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_99994162_9   2084 ATAAACACATA--TTGATGGTTATTCTACAAAATTCTTAGAGTAGTCTTC 2131
                            i   i   -- ii    -- ---- i i    ----   -    -- 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGG--A----ATAGAATT----GAG-AGTC--C 320

  chr2_99994162_9   2132 AAAAGTGTCAAGGCTATAAA-----AGACAAGGGA----AGACTGAGGAA 2172
                          i  i ---  iv i   v -----i v   vv  ----v   vii  vi
  L1M4_orf2#LINE/    321 AGAAAT---AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_99994162_9   2173 CTACAACAGATTG---GAGGAAACTGAGGAGTTATCACAACCAAATGCAA 2219
                          i vi  v-   v--- i     --  iv   iv iv    -     --i
  L1M4_orf2#LINE/    368 CCAAGACC-ATTCAATGGGGAAA--GAATAGTCTTTTCAAC-AAATG--G 411

  chr2_99994162_9   2220 TG-TAGTATCCCAGATTGGATCCTGGAATGAAACAGGACATTATGGGGAA 2268
                           - i v ---  - i     v?iviv   v  v  i i--------   
  L1M4_orf2#LINE/    412 TGCTGGGA---CA-ACTGGATAKCCACATGCAAAAGAAT--------GAA 449

  chr2_99994162_9   2269 AATTGTTGAAATCCAAACAAAGTCTGTAGTTTACTTAATCTACTGTAAT- 2317
                         ----    i vi  ------------  vi i  viv  v   viv   -
  L1M4_orf2#LINE/    450 ----GTTGGACCCC------------TACCTCACACCATATACAAAAATT 483

  chr2_99994162_9   2318 -GTTCATTTCTTGGTTTTAATAACTGTACCATGGTC----ATGTAAAATG 2362
                         -ii   ---------------  v  v i  ?i v ----      i - 
  L1M4_orf2#LINE/    484 AACTCA---------------AAATGGATCAWAGACCTAAATGTAAGA-G 517

  chr2_99994162_9   2363 TTAA---CATCAAGCGTAGCT--GAAGGAAGTGTACGTAGGCACTCAATG 2407
                         i   ---i  v  i - --  --    i  ----  i    ?------- 
  L1M4_orf2#LINE/    518 CTAAAACTATAAAAC-T--CTTAGAAGAAA----ACATAGGN-------G 553

  chr2_99994162_9   2408 TACTATCTTTGCAACTTCCTATAATTTTGA-AATTATTTCAAAATAAAAA 2456
                           v-     i ii  i ---- iiv  v i-   vi    ----------
  L1M4_orf2#LINE/    554 TAA-ATCTTCGTGACCT----TGGGTTAGGCAATGGTTTC---------- 588

  chr2_99994162_9   2457 GCTTTAAAAAGAGTTATTAGAATGAAAGAGACACTTCTTGTAACACAGAA 2506
                         ---   i ------   v v vii    v-   v----- i    ---  
  L1M4_orf2#LINE/    589 ---TTAGA------TATGACACCAAAAGC-ACAA-----GCAACA---AA 620

  chr2_99994162_9   2507 AGGAATAAATGTGAAAGAAAAATTGGACTTCATCACAATTAAAAATATCT 2556
                           i  -    -----   v                v         iv i 
  L1M4_orf2#LINE/    621 AGAAA-AAAT-----AGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_99994162_9   2557 GTTCATCAAAGAGTACCATCAAAAGAATAAACAAGTAAGCCACGAAATGA 2606
                           v v      iii  i     i i i i  v iii  v    ii    i
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_99994162_9   2607 GAGAAAATATTTGCAATACATATATCTGACAAATGACTTGGATCCAGAAT 2656
                                         vv           i  iv      v         
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_99994162_9   2657 ATAAAAACCACTCTGGTA-CTCAATAATAAAAATTAGCAA-CAACACTAT 2704
                            v   vv     vii -              --ii   -i   v v  
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAA--GACAAATAACCCAAT 812

  chr2_99994162_9   2705 -AAAAGATAGGCAAAAGATTTGAAGAAACCCTTCACAAATGAAGATA-GC 2752
                         -?   i  i      i        v i  vi   v v  v       -i 
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_99994162_9   2753 ACATGGCCAATAAGCACATGAAAAAGTATTCAACATCTTTCCTATG 2798
                          v                      ii ii        v????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (123 / 99)
Gap_init rate = 0.07 (64 / 908), avg. gap size = 3.08 (197 / 64)  


2901 25.75 0.52 6.23  chr2_100226840_100233277.rev     4984  5946 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_100226840_   4984 TGGAAGAACATTCCATGCTTGTGGGTAGGAAGAATCAATATCGTGAAAAT 5033
                              ii i  i     i ii   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_100226840_   5034 GGCCATACTGCCCAAGGTAATTTATAGATTTAATGCCATCCCCATCAAGC 5083
                            v     v     iv i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_100226840_   5084 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5131
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_100226840_   5132 TATGGAACCAAAAAAGTGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5181
                                viiv  ii vv  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_100226840_   5182 AACAAAGCTGTAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5231
                                i  v   vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_100226840_   5232 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5281
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_100226840_   5282 AATGGAACAGAAC--AGAGCCCTCGGAAATAATGCTGCATATCTACAACT 5329
                                i    i--    i  --i       vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_100226840_   5330 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACAATTCT 5379
                          vi    i  i     ivv  v   i v  vvv          v   vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_100226840_   5380 CTATTTAATAAATAGTGCTGGAAAAACTGGCTAGCCATATGTAGAAAGCT 5429
                           v  i  i    i       i v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_100226840_   5430 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5479
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_100226840_   5480 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5529
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_100226840_   5530 CTAGGCA-ATACCATTAAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5578
                         v    ?i- v i -  viv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_100226840_   5579 AAACACCAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGGGATCTA 5628
                         vi            vvi          iv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_100226840_   5629 ATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5678
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_100226840_   5679 CAGGCAACAGGCAACAGAACAGGAGAGGAGAGAACAGAACAGGAGAGGAG 5728
                         v  i    ------------------------------------------
  L1M4_orf2#LINE/    696 AAGACAAC------------------------------------------ 703

  chr2_100226840_   5729 AGAACAGAACAGGCGACAGAATGGGAGAAAATTTTTTCAATCTACTCATC 5778
                         ------------- v                 v   v   vii ivi   
  L1M4_orf2#LINE/    704 -------------CCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_100226840_   5779 TGACAAAGGACTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACA 5828
                            i  i     vi          v  i         vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_100226840_   5829 AGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGA 5878
                          v     i     i     v  i?    i     i     iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_100226840_   5879 CATTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATG 5928
                                 v        i  vi viii     v ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_100226840_   5929 CTCGCCATCACTGACCAT 5946
                            iv     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 8.12 (65 / 8)  


 412 25.62 5.79 0.83  chr2_100245027_100248359     1829  1949 (1384)    L1M4_orf2#LINE/L1       91   217 (691)  

  chr2_100245027_   1829 CCTATAAAAATCTCA-------TTTCTCCTCAAATTGACCTATTGATTCA 1871
                              v      i  -------   i v vv        vvii    i v
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_100245027_   1872 GTAAGTTTATATGGGAATGCAAAGGGCCAAGAAGAGTCAAGACAACCTTG 1921
                         i-  i  i      i       i  i  v    v  i   i    i    
  L1M4_orf2#LINE/    141 A-AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_100245027_   1922 AAGAATAAGAAGAAAGATGAAGATCTTA 1949
                           i  v     v    v  i  iv  i 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCA 217

Transitions / transversions = 1.38 (18 / 13)
Gap_init rate = 0.02 (2 / 127), avg. gap size = 4.00 (8 / 2)  

1169 29.55 8.57 1.57  chr2_100245027_100248359     2270  2841 (492)    L1M4_orf2#LINE/L1      297   908 (0)  

  chr2_100245027_   2270 TCTATGGAA-ACAATGGAGAGTCCAGAAACAGACTGGCATGTACATT--- 2315
                           v      - v   v             i i  i--   --     ---
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CAT--ACATTTAT 342

  chr2_100245027_   2316 -GTCA-CTGATTTATGACAAGGGTGACACTGCAGCACAGTGGGG---GCA 2360
                         -    -i      vi          v  vvi viiv  i     --- v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_100245027_   2361 T--TTTTTCCAA-AGGCAGTGCTGGGCCAATTGGATACCCATAAGGGACA 2407
                          -- i   i   - iiii        v   i      ?   i v vi - 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA-A 441

  chr2_100245027_   2408 AAAAT----CTTGACATCTGCGTCACACCATA--CAAAGTTACCAATTCC 2451
                          i   ----i v   vi  i v          --    i-- ii  i  v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA--ATTAACTCA 489

  chr2_100245027_   2452 AGGTGACTTGCAAATCTACCTGTGAAGGGTAAA-CCATAAAACTTCCAGA 2500
                          ii  iv ii? i i   vv   i ii v    - i        iii   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_100245027_   2501 AGAAAACATTGGAGAATATCTTTGTGACACAGGGTTAAGCAAAGATTTAT 2550
                                  v  ? v v     i     viv      i    v i   v 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_100245027_   2551 TAAATAGGATACAAAAAGCATTGACTATGAGGGAAAA--TTGATAAATTA 2598
                           i   v  i  v       ivii v ii ii     -- v        i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_100245027_   2599 GACTATGTTAAAATTAAGAATTTCTGTTCCTCAAAAGAATAGAATGCTAG 2648
                             vii i        i  i  i   v i     i  -i vv  - v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-CACTAT-CAAG 687

  chr2_100245027_   2649 GGAGTTAAGGTGCAAATCATTGAATAGATCAAAGTATTTGCAATTCATAT 2698
                         ii   v  iivi   vi  iv    i ivv   i         v      
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_100245027_   2699 --CTAACAGAGAATTTG------------ATAAAGAAATTATACCAATAA 2734
                         --  i i ii i i   ------------        v iv   v v v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_100245027_   2735 ATGAAGAAAATGCAGACAAACC--TT-------GGACAAGACATGCAAGC 2775
                           i vi    vi  i i  v  --  -------  i   iiv  vii ii
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_100245027_   2776 AGCTATATCACAAAGGGA---AGACAAATGTTCAATATTAATATGAAAG- 2821
                           vi  v  v v  i i --- v       vi     vvv i      i-
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_100245027_   2822 -CGTTTCACATCATGAGACAT 2841
                         -i i iv      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (101 / 65)
Gap_init rate = 0.04 (22 / 612), avg. gap size = 2.64 (58 / 22)  


3585 17.19 5.40 0.00  chr2_100502929_100507101     2377  3080 (1092)    L1M4_orf2#LINE/L1        1   742 (166)  

  chr2_100502929_   2377 TGTAAATGCATCCCATGTTCATATATCAGAGGACTTAATACTGTTAAGAT 2426
                           v   vii             iv  ii  i         i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_100502929_   2427 ----ATACTCTCCATATTGATCTACAACTTTATTGCAATCCTCATCAAAA 2472
                         ----      i   v           iv  i vi       ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_100502929_   2473 TTCCGGCTGGCTTCTTGGTAGAAATAGCCAATCTGAAGCTAAAATTCACA 2522
                          i  i    v   i  v i      v v   v    vv          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_100502929_   2523 TGAAAATGTAAGACACTCAGAGTGGCCAAAACAATCTTCAAAAGGAAGAT 2572
                           i     i   iv  i    i i              v    i     v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_100502929_   2573 CAAAGTCTGAGGAATCACACTTCCTGATCTTAAAATATACTACAAAGCCA 2622
                               iv     v          ii  i i    iv           i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_100502929_   2623 CAGTAATCAAGACAGTGTGGTAACAGCATAAGAACAGATATATAAATCAG 2672
                                               vii       i i   i     i    i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_100502929_   2673 TGGAATAGAATTGAGAGTCCAGAAATAAGCC-----ATTTATGGCCAATT 2717
                                                     i  -----        i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_100502929_   2718 GGTTTCCAACAGGAGTGCTAAGACAATAAAATAAAAAAGGAATAGCTTTT 2767
                          i   i i   i i    i     v  vv   iiii  i      ii   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_100502929_   2768 TCAATAGATGGTACTGAGACAACTGGATATCCACATGCAAAAGAATGAAT 2817
                             i i     i   i            ?                   v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_100502929_   2818 TTAGATGCCTCTCTCACACT-TACACAAAAATTAACTCAAAATGGACCAT 2866
                           i  iv   vi       i-  i                      i  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_100502929_   2867 AGACTTAA---CAAGAGCTAAAACTA-AAAA-TCT-AGTA-AAAACACAG 2909
                             i   ---i              -    -   -  v -      i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_100502929_   2910 GCATAAATCTT-ATAACCTTGGGTGAGACAGTATCTTCTTAGATATGCCA 2958
                          ?i        -i i         v  i  i ivi            v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_100502929_   2959 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT------------ 2996
                                                               ------------
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_100502929_   2997 --TTAAAAAATTT-GTCCTTCAAAGGATACTATCAGGAAAATGAAGAGAA 3043
                         --       v   -  v          i       i    i    i   v
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_100502929_   3044 AATCCACAGAATTTTT-----TTTTTGCAAATCATATATATG 3080
                           i         vvvv----- v                v  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

Transitions / transversions = 2.03 (79 / 39)
Gap_init rate = 0.02 (12 / 742), avg. gap size = 3.17 (38 / 12)  

 906 17.95 1.54 1.03  chr2_100502929_100507101     3487  3681 (491)    L1M4_orf2#LINE/L1      713   908 (0)  

  chr2_100502929_   3487 GGGGACAAACATC--CAAACTATAGCAATATGGTAAAGGACTAACATCTA 3534
                            iiv   i  i--    ii   v--  v  i   i     vii   i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATAT--ATCTGATAAGGGACTTGTATCCA 760

  chr2_100502929_   3535 GAATATCTACAGAATTCTTACAGTGTAATAATAAAAAGACAAATAGCCCA 3584
                               v  v    i       iivi                   i    
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_100502929_   3585 ATTTAAATATGGGTAAAGGGTCTGCATAGACATTT-TCCAAAGAAGATAT 3633
                            ?   v     i     i i  v          -              
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_100502929_   3634 ACACATGGCTGATAAGCACATGTAAAGCTGCTGAACATCATTCATAAG 3681
                            v     ii           v    v    v       ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (21 / 13)
Gap_init rate = 0.02 (3 / 196), avg. gap size = 1.67 (5 / 3)  


1160 29.11 7.28 0.27  chr2_100517403_100521366.rev     1580  1950 (2014)    L1M4_orf2#LINE/L1        6   402 (506)  

  chr2_100517403_   1580 AGACACACCATGTTCAAGAGTTAAAAGACTCAGCATAGTAAAGATGTCAA 1629
                            i iv         v ii  ii      i ii  v  v      v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_100517403_   1630 TTCTCCTCAAATTGAT----------------------ATCAAAGTTCCA 1657
                          v    i         ----------------------      i i   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_100517403_   1658 GCAAGAATTTTTGTATA----GACAAGTTTATACTAAAATTTATATGGCA 1703
                           vivvv      i v ----      i v  v        i      v 
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_100517403_   1704 ATGTAAAGAAACTAGAACAGCTAAAATGACTTTGATAAAGAAGAATAAAG 1753
                            i  i i v i    i   i    ii ii    v         i    
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_100517403_   1754 CAGGAAGACTGCAT-CTAACCAATCTCTAGACTTCTTATTTAGCTTTGGC 1802
                         iv   i    -  i-  vv     i  v i    vi  ivv    vii i
  L1M4_orf2#LINE/    206 TTGGAGGACT-CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_100517403_   1803 AATCTAGAATGTGTGGCATCAGCAGAGAGATAAACACAGAGGTCAAGGAA 1852
                             v   vv      i iii   v ii    i   i v  i    v i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_100517403_   1853 ACAGAATAGAGAATCCAGAAAGAGGTCTACATAAATATGCCCAACTATTT 1902
                          i     v    i        v iii i i i vv    vi   i iv  
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_100517403_   1903 TTTGACAAAGATGCAAAAGCAATTCTATGGAGGAAAGATGGCCTTTTC 1950
                           i     i i   v  ii v    v    i i  ii  i i      
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

Transitions / transversions = 1.77 (69 / 39)
Gap_init rate = 0.01 (4 / 397), avg. gap size = 7.00 (28 / 4)  

1106 29.10 0.79 1.85  chr2_100517403_100521366.rev     2621  2998 (966)    L1M4_orf2#LINE/L1      387   760 (148)  

  chr2_100517403_   2621 AAAAAATAGCCTTTTCAACAAAGGATGCTGAAGCAATTGAATATCCATAG 2670
                            i     i            v i     iii   i  i   ?   i v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_100517403_   2671 GCAAAAAAGTGACCATCAG---TCTAAGTCTCATTCCTTACCCAAAAGCG 2717
                               i i   v-i ii ---i   --i    iv  v  iv     iiv
  L1M4_orf2#LINE/    437 GCAAAAGAATGAA-GTTGGACCCCTA--CCTCACACCATATACAAAAATT 483

  chr2_100517403_   2718 AACTCAAATCAGGTCCTGGATCTAAATGTAAAATGTAAACCTATAAAACA 2767
                                 vii i  v?i  i          i vv    v         v
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_100517403_   2768 TTTAGAAGAAAGAAATCAGAGAAAATATTCAAGGGCTAAAGCTAGGCAAA 2817
                         i          - v  vi ? v    v   iv iv  vii i       v
  L1M4_orf2#LINE/    534 CTTAGAAGAAA-ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_100517403_   2818 GAATTCTTATACTTGAAACTGAAACCATGAGTCCTAAAAAGAAAAACTGA 2867
                          iv      v iv   v  ii   v  ii  ivvi    ii     iv  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_100517403_   2868 TAAAACTGGATTTCATCAAAAGTAAAGACTTTTGCTCTACTAAACACCTT 2917
                             -i    i          v    i       iv  v v  iv  vi 
  L1M4_orf2#LINE/    633 TAAA-TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_100517403_   2918 GCAAAGAGAATAAAAAGGCAAGTTAACAGACTAGAGGAAAATATTTGTAA 2967
                         iiv    i i i     i   vii -    v i ii           i  
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCA-CAGAATGGGAGAAAATATTTGCAA 730

  chr2_100517403_   2968 ACCGCATATCTGATACAGGACTGTTAGTCCA 2998
                          i ii          vi     vv  -    
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTA-TCCA 760

Transitions / transversions = 1.61 (66 / 41)
Gap_init rate = 0.02 (7 / 374), avg. gap size = 1.43 (10 / 7)  

 345 17.33 22.00 1.33  chr2_100517403_100521366.rev     3335  3484 (480)    L1M4_orf2#LINE/L1      728   908 (0)  

  chr2_100517403_   3335 CAAACCATAT--C-----AAGGACTAATATCTAGAATATATAAAGAACTC 3377
                             i     -- ----- i     vi    i                  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_100517403_   3378 TCAAAACCCAATAATAAA----CAAAAATTTCAATTAGAACATGAGAAAA 3423
                          i v   i          ----    v vii     ?i  v   i v   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_100517403_   3424 AG----GAAAAGAC----------------TACTACAGATG-CCAATTAA 3452
                         i ----   v    ----------------  -    i   -     -  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATA-TACAAATGGCCAAT-AA 875

  chr2_100517403_   3453 GCACATAAAAAG-TATTGGATATCATTAGCCAT 3484
                               i     - ii vi i    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (17 / 8)
Gap_init rate = 0.05 (9 / 181), avg. gap size = 3.89 (35 / 9)  


2786 28.08 1.11 0.33  chr2_100577507_100579462      565  1465 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_100577507_    565 TGGAAATACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAGAT 614
                               v i        i        v  v   v i        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_100577507_    615 GACCATACTGTCAAAAGCAATCTACAGACTGAATACAATTCCCATCAAAA 664
                          i v     vi v   vii         i v  ii    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_100577507_    665 TACTATCGTCATTCTTCACAGAACTAGAAAAAAAAACTCTAAAATTCATA 714
                          v i v vv v  i  ii     v v  v  ivvi ii            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_100577507_    715 TAGAACCAAAAAAGAGAACCTGCATAGCCAAAGCAAGACTAAGCAAAAAG 764
                          i   -- viv   i  v  v v         i   vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_100577507_    765 AACAAATCTGGAGGTAGCACATTACCTGACTTCAAACTATACTACAAAAC 814
                               vi      vvv    i v  ii i      viv         i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_100577507_    815 TATAGTTACCAATAAAATG-GGCAT--GTATAAAAATGGGCATGTAGACG 861
                           i   v i   v v i  -  i i-- i    ii  i i   i    iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_100577507_    862 AATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATATGTACAGCCAA 911
                                i     v    ii           v   v i  v  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_100577507_    912 CTGATATTTGACAAAGCAAACAAAAACATGAAGTGAGGAAA-AACACCCC 960
                         i    v  i     i vviv   i v   vv i  i     -  i vi i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_100577507_    961 ATTCAACAAATGGTACTGGGATAATTTGCAAGCCACAAGTAGAAGAATAA 1010
                         v             i      i  i v vv ?     v i i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_100577507_   1011 AACTGGATCCTTAATTCTCGTTTTATACAAAAATAAGCTCAAGATGGATT 1060
                          ii    i  i  vi  v iiiv           v i     i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_100577507_   1061 AAAGAATTAAATCTGAGACCTGAAACCATAAAAATTCTAGAT---AACAT 1107
                          ?   vi     v i   v  i    i      v ii    v---     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_100577507_   1108 TGGAAAACCTCTTCTAAACATTGGCTTGGGCGAAGAGTTCATGACCAAGA 1157
                         v  ?iv vv     vvi  v    v  i   i v iv   v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_100577507_   1158 ATCCAAAAGCAAATACAACAAAAACAAAAATAAATAGATGCGGTCTAATT 1207
                         vv         v vi        iv       i   i  vv iii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_100577507_   1208 AAACTGAAAAGCTTCTGCACAGCAAAATAAATAATCAGCAGAATAAACAG 1257
                            v v    i   i  ii vv    iv v iv    iv i i i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_100577507_   1258 ACAATCCA--GAGTGGG-GAAAATATTCACAAACTATGCATCCAACAAAG 1304
                             i   --  i    -         ii    ii  ii   ii i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_100577507_   1305 GATTAATATCCAGAATCTACAAGAAACTCAAACAAATCAGCAAGAAAAAA 1354
                           i vi          v  i  ii     vv    v   ii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_100577507_   1355 AACAAATAATCCCATCAAAAAGTGGGCAAAGGTCATGAATAGACAATTCT 1404
                          -       i  v  i?    i          viv          v    
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_100577507_   1405 CAAAGGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACA 1454
                          v  i                    i  i  i       i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_100577507_   1455 TCCCCAATTAC 1465
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.33 (142 / 107)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3312 25.41 1.33 0.99  chr2_100708899_100712178.rev     1887  2791 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_100708899_   1887 TGGAGAGGCATACTTACTGTGTTCTCAGATTGGAAAACTCAACATAATAA 1936
                             i  --   -- v ii     vii        i   i  i  vi v 
  L1M4_orf2#LINE/      1 TGGAAAG--ATA--TCCCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chr2_100708899_   1937 ATATGTCAATTTTCCCTAAATTGATCTATAGGTTTAAAGCAATTGCTACC 1986
                          v   v    vi    i           i  i  i  v     iv   i 
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_100708899_   1987 TAAATCCCAGGAAAGTTTTCTGTAGATATTGACAAACTTAGTCTAAAGTA 2036
                         v         vvivv    i  i   v        i  v vi     i v
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_100708899_   2037 TGTATGGTAAAGTACAGGCTCTAGAATAGTTAAAACGATTCTGACAAATA 2086
                         ii     v  v i vi  vi i       ii     i  ii   v   v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_100708899_   2087 AAAATAAAGTGAGAGGACTCATTCTGCCCATTATTAAGACCT-CTATGTA 2135
                          i  i     vi         iv  v    v v i  i  i -   iiv 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_100708899_   2136 ACTATAGTAATCAAGATAGCATTGTATTA-CAGAGGGATGGAC-CATAGA 2183
                         i   i           i  ii v   i i-  v i    i   -i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_100708899_   2184 TCAATGGAATA--AT---AAACTCAAAAACAAACCCACACAAATACATGC 2228
                                    --  ---i iii  i   i       i   -- vi   v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA--TTTATGG 344

  chr2_100708899_   2229 CCATCTGATTTTTAACAAGG-TACAAAGGCAATTCAATAAAGGATGAATT 2277
                         i  vi       ii      - i v   i v       iii i v    v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_100708899_   2278 GCCTTTTCAATAGATAATGCTGGAGCAATGGGACTCTTGTAGGCCAAACA 2327
                          i        i i  ii      ii   iv   iv?iiii v  v   v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_100708899_   2328 AGTGAATTACGACCTAAACTTCACACTTTATACAAAA-TTAACTCAATTT 2376
                          -    v vv    ivv  i      iv         -         vv 
  L1M4_orf2#LINE/    445 A-TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_100708899_   2377 GGATCATAGACTTAAATGTAAAATGTAAAACTATAAAACTGTTAGAAAAA 2426
                               ?    i         i vv               v      i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_100708899_   2427 CATATGGGCGAAAGTCTTTAAAAAGTAGGACTATGCAAAAAGTTCTTAGA 2476
                         v i  i  ? v  i    iivi vv v  ii  v    viiv        
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_100708899_   2477 CTTGACACCAAAAGCATGATCTATAAAAGGAAAAAATTGACGAATTGGAC 2526
                         iv              ii v v i     -       v  ii        
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGAC 642

  chr2_100708899_   2527 CTCACCAAAGCTAAAAACTTTTGCTCTGTGAAAGCTCA-TGTTAAGAGGA 2575
                         i   i    ii            iv  - v    vv  - i i    iii
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAAG 691

  chr2_100708899_   2576 TGAAAAGACAAGCTATAGACTGGGAGAAAATATTTGCAAACCATATATTC 2625
                                    v i i   v                    i       ii
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_100708899_   2626 AACAAAGGACTAGTATCTAGAATATAAAAAGAATGCTCAAAACTCAACAG 2675
                         i i  i     v     i        v      iv  i v       i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_100708899_   2676 TAAATAC-CAAACAATCCCATTTAAAAATGGGCAAAAGATATACACAGAC 2724
                             v v-    i  i  v   ?             i   v iv i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_100708899_   2725 ATTTCACCAAAGAAGATATACAGATGGCAAATAAGCACGTGGAAAGATAT 2774
                              v                i     v         i  i      ii
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_100708899_   2775 TCAACACTGTTAGCCGT 2791
                               iii????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (141 / 85)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.40 (21 / 15)  


2115 24.62 15.64 1.03  chr2_100762616_100764492.rev      607  1386 (491)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_100762616_    607 ATGTTCATGGATTGGAAAGTTCAAGATTATTGAGATGTCATTTCTCCCTA 656
                                          iii i  v   i  i     v  v v     i 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_100762616_    657 A-----CCCA----------GCAATTTTT----------TGGTTTTGTTT 681
                          -----i i ----------     iii ----------ii i -- ii 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT--GCCT 112

  chr2_100762616_    682 TTGTTTGGTAGAAATTGATGAACCAAGTCTATAATTCATATGGAAATCAA 731
                           -    -i         ii i ii vi   v               vv 
  L1M4_orf2#LINE/    113 TT-TTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_100762616_    732 AAGGACCTAAAATAGGGAGAACAATTTTAAAAAT--------AAGTTGGA 773
                          i     i i     vv i      i  i    v--------        
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_100762616_    774 GGGTATATACTACTTGATTTGAAGACTTACTATAAAGCTACAG-AATTGA 822
                           iivi i   v iii    v  i        i          -   ii 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_100762616_    823 AATGGTATGATAGTAACATATAAATTGACAAATAGACAAATGAAGCAAAA 872
                         i ii  i  i  v ii    vii  v    v     iv    i ii i  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_100762616_    873 T--ATAATCCAGATATAGACAAACGCATGTATGGTCAACTGATTTTTAAC 920
                          -- v i      v   i  vv ii   v         i       ii  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_100762616_    921 AACAG---AAAAGCAATGTAATAGGGAAAGGA-AGTTTTTT-ATTAAATG 965
                           vi ---v  ii v  vi   i       i -   i    - vi     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_100762616_    966 GTGCTAA---AACTGAACATTTATGTG-GTGGGGAT-AAGCTGGATCCCT 1010
                              ii---     i i ?ii ii  -ivii i  -   i    i    
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_100762616_   1011 ACTACACATCATATACAAAACCTA-TTAAAAGTGGATTGCAGATCTGAAT 1059
                           iv    i           vi  -i v   i     ii?   i  i   
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_100762616_   1060 ATAAGTGATAAAACTATAAGACTTCTAGAATAAAGCATAGAA--AAATAT 1107
                         i    v v           i   ii     v   i     i?--    v 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_100762616_   1108 -CACGACCTGGGGGTAGGCAA---------AGATATG------------- 1134
                         - ii     v   v       ---------       -------------
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_100762616_   1135 ------------------TTGA--AATTGAACGTCATCAAAACAAAAAAC 1164
                         ------------------ v  --     i  v         iv      
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_100762616_   1165 TTCTG--CTCCAAA-------------------AAAAG-CA--CCATAGA 1190
                           i  --  i    -------------------     -  --   i   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_100762616_   1191 CTGGAA-AAAATAGTCCCAATCCATATATCTGACAAAAGTACT-GTTTCT 1238
                         v   i -      v iv   vi           i  ii -   -  v  i
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG-ACTTGTATCC 759

  chr2_100762616_   1239 AGTATATATAAAGAACTCCTATGACTCAATATTAAAAAAACAAAC--TCC 1286
                           v               i  ii        v      i     i--i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_100762616_   1287 ATTTTTTTAAAAGAAGCAAAAGTCTTGAACAGATACTT-TACAAAGAAAG 1335
                          v  ?v--    vii     i vi     i   i i  - v       - 
  L1M4_orf2#LINE/    810 AATTWA--AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-G 856

  chr2_100762616_   1336 ATATACAGATGGTCAATAAACATGTGAAAAC-TGTTCAACATCTTTAGTC 1384
                                i    i      i  ii      v-  i        v??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_100762616_   1385 AT 1386
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.36 (132 / 56)
Gap_init rate = 0.04 (33 / 894), avg. gap size = 3.94 (130 / 33)  


2249 26.46 2.79 4.37  chr2_100812820_100815178      642  1465 (894)    L1M4_orf2#LINE/L1        9   819 (89)  

  chr2_100812820_    642 TATACCACATAAATGGGAAAAAAGACTTAATATTATTAAGATGGCAATTC 691
                            v   ii vv    ivvii             i             v 
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr2_100812820_    692 TCTTCAAATGAATCTATAGTCTCAATACAATCCTAATCAAGTTCTTAACA 741
                           ii     vi     i  vi    ii      iv     iv  ii i v
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_100812820_    742 GGCTTCTTTTATAAATATT----AGATAATTCTCAAATGTGTATGGAAAT 787
                          v   -    ii i v   ----  v i  i  v    vii         
  L1M4_orf2#LINE/    109 GCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_100812820_    788 GCAAAGAACCTAGAATATCCCAAGATATTCCTTTGAAAAGGAAGA-CAAA 836
                             i i   i      v  -  i i v  --       i     -    
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCC-AAAACAATC--TTGAAAAAGAAGAACAAA 204

  chr2_100812820_    837 CATTAGAGTCTTCGCATTGCCTGATTTAAAGACTCACTG-AAACCTACAG 885
                         -i  i   vvi  i  i v  ii    v  i   i   i-   v      
  L1M4_orf2#LINE/    205 -GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_100812820_    886 TGATGAAGACAATGTGAGACCAACAGAACATTAAAAAATGCCAAATGTGG 935
                          i  v      i    iv  iii  v  viv  i ------  -- i i 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGA------CA--TATAG 295

  chr2_100812820_    936 ACCCACACATTA--ATTGATTTTTAACACAGGGATGTGGATCCACACATT 983
                          i v iiv v  --     v---- iiv   ii  i--i i   i     
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAG----AGTCCAGAAATA--AACCCATACATT 339

  chr2_100812820_    984 -------AATTGATTTTTAACACAGGGGCTAAGATAATTGAACAGGAAAA 1026
                         -------          ii   vi  v  i    iv   v  ii  i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_100812820_   1027 AGAGAGTCCTTTGAACATATGGTGCTAGAACAACTGTGTATTCATACTGA 1076
                         ii v    i   v    v        i i       vi  ?i  i i---
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT--- 436

  chr2_100812820_   1077 GGGAAGAAAATGAAGCTCGGTGCC-GTCTCAG--CATAAACAAAGAACAC 1123
                         - v  i i       i v iiv  -ii    v--    v     i ----
  L1M4_orf2#LINE/    437 -GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA---- 481

  chr2_100812820_   1124 TCAGAGTAAAACTCAAAGTGGATCACAGACCTAAATGTAAAAGCTAAAAT 1173
                          i -------       i       ?              i        i
  L1M4_orf2#LINE/    482 TTA-------ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_100812820_   1174 CGTATATATTTTAGAAGGAAACATAGGAGACTATCTTACTGATTTGGGAT 1223
                         ii  v vv i       i         ? vvv     vv   ii v  i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_100812820_   1224 TAGACAACAATTTCATAGACAGGACACAGAGAGCAATAACC--CAAAAGG 1271
                            i   iii    v    i v     vi i    -i  v --      i
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCA-CAAGCAACAAAAGA 623

  chr2_100812820_   1272 AAAAATTGATATATTACCCTTAATCGAAATTTAAAA-TTCTGCCCATCAA 1320
                               v    v   ivv   v   i     v    -  i  iv v    
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_100812820_   1321 AAGACACCACTAAGAAAATGAAGAGGAAAACTACAGATTGTGATAAAATG 1370
                          i     i ii      i    i  iv  v i     v  v  v     i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_100812820_   1371 TTAGCAAAAACAT-TATCTGACAAAGGGCTTATATCCAAAAGAAATAAAA 1419
                           v     v-   -       i  i  i   i      i  v v     i
  L1M4_orf2#LINE/    724 TTTGCAAAT-CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_100812820_   1420 AGCTTCTGTAACTCAGAAATAAAATAA-AAAGAACTCAATTTTAAAA 1465
                          i  ii ii      iv       vi -   v   i     ?v    
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

Transitions / transversions = 1.68 (134 / 80)
Gap_init rate = 0.03 (24 / 811), avg. gap size = 2.46 (59 / 24)  

 313 20.18 3.51 1.75  chr2_100812820_100815178     1755  1868 (491)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr2_100812820_   1755 AAAAAAATAAAAAAATAAA---AGAGATGAGAGCAAAAGATATGAACACA 1801
                              i i   v  viv  --- i i   i --    i   v    i v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGG--CAAAGGATTTGAATAGA 840

  chr2_100812820_   1802 CACTTTGCAGAAAAAGATATACAAATGGCAAATAAGCTTGTGAAAAGATG 1851
                           i  iv vi  i                v       vii          
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_100812820_   1852 CTCAACAT-ATTAATAAT 1868
                                 - ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.03 (3 / 116), avg. gap size = 2.00 (6 / 3)  


 609 13.04 2.17 7.25  chr2_100885649_100887588.rev      468   605 (1335)    L1M4_orf2#LINE/L1      272   402 (506)  

  chr2_100885649_    468 ATTGGCATA-GGACATGGATGACAAGTGTAAAACATTAAGGTAATAGAAT 516
                          i       -   i -----    -- i  i --- i  v v        
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATA-----GACA--TATAGA---TCAATGGAATAGAAT 311

  chr2_100885649_    517 -GAGAGCACAGAAATACACCCTTACATTTATGGTCAATTGATTTT-GACA 564
                         -     iv        v    v                       -    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_100885649_    565 AAAGTACCAAGACAATTCAATGGGGAAGGAGTAGTCTTGTC 605
                          ii  i       v             i  i       v  
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

Transitions / transversions = 1.57 (11 / 7)
Gap_init rate = 0.05 (6 / 131), avg. gap size = 2.17 (13 / 6)  

2197 16.16 4.37 5.32  chr2_100885649_100887588.rev      923  1448 (492)    L1M4_orf2#LINE/L1      388   908 (0)  

  chr2_100885649_    923 AAGAGTAGTCTTTCTAACAAACAAATAGTCCTGGGAC---TGGATATCAA 969
                             i        ii      ---- i  v       ---      ? v 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAA----TGGTGCTGGGACAACTGGATAKCCA 433

  chr2_100885649_    970 GACACAAA----TGAAGTTGGATCTCTACCTTGCATCATGTTCAAAAATT 1015
                         v ii    ----          i i      ii  i   i v        
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_100885649_   1016 AACTCAAA-TGGATCAACTGCATAAATATAAGAGTTAAAATGATAAAATC 1064
                                 -       ?vvi v     i      i     iv      - 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-C 532

  chr2_100885649_   1065 GCCAGGAAGAAAATGTAGGTGGTAAAGCATCATGACCTTGAATTTGGCAA 1114
                         v ivi        ii    ? -    v v  i        ii  v     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_100885649_   1115 AGGATTCTAAAATTGGCAAAGGACTCTTGTATAACACCAAAAGCACAAGC 1164
                         v  v    v i  -----------------  i                 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGAT-----------------ATGACACCAAAAGCACAAGC 614

  chr2_100885649_   1165 AACCAAAGAAAAA---GATACATTAGACTTCATCAGAAGTGACAACTT-- 1209
                            v         ---    v   i          i  v i v     --
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_100885649_   1210 GTGAT------GATACTATCTAGAAAGTGAAAAGACAACCCATAAAGTGG 1253
                            v ------  i      v                     i i i   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_100885649_   1254 GAGAAAATATTTGCAAAGCATGTATCCGATAAGGGACTTGTATCTGCAAT 1303
                                          v   i    i                 iiv   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_100885649_   1304 -TATAAA--ACTCTTATAACTCAGTAATGAAA-GACAAATAATCTAATTT 1349
                         -      --       i      i    i   -         i i    ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_100885649_   1350 TAAAATAGGCAAAAGATCTGAATAGACTTATCTATAGTGTATAGAAAGTA 1399
                         v     i      i   i         v v   vi i-----    ii  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA-----AGAAGATA 859

  chr2_100885649_   1400 TACACTTGGCCAAAAAGCACATGGAAAGATGCTCAACATTATGAGTCAT 1448
                             vv       v         i               i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (50 / 31)
Gap_init rate = 0.03 (14 / 521), avg. gap size = 3.64 (51 / 14)  


1415 27.72 6.46 4.25  chr2_100974228_100975825      472  1106 (492)    L1M4_orf2#LINE/L1      260   908 (0)  

  chr2_100974228_    472 AGACATCCTGATTCTGTCCTGCAGAATTGAGACACATAGGATAAATGAAG 521
                              viv  i v   v v i-  i  --     i    -  v    i i
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATA-AGGAT--AGACATATAG-ATCAATGGAA 305

  chr2_100974228_    522 CTAAAT--ATAGTCCATAAATAA-----TGCATATAAGATCACACACTAT 564
                         ivi   -- v      v      ----- i   v  v i   vviiv v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_100974228_    565 TTGATGAAAGTGCTAATGCAATTCAACAGGGAAATAAATGCCTTTTAAAC 614
                          i  ii ii    i  vi v      ii      v  vv i     v   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_100974228_    615 AAACTATTCTGGAG-----GGATGTCCATATTGGGGGCGTGGTGGGGGTG 659
                            ivi v    ii-----    i?   i  -----  ivii--------
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACAT-----GCAAAA-------- 442

  chr2_100974228_    660 GTGGTGAATAATGTCCGAGCCCTATCCAACACTACACATAAAATTTAAGT 709
                         -----    i v  iv  v     i iv    i i i i    v    v 
  L1M4_orf2#LINE/    443 -----GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_100974228_    710 TGCAATGGACTGTGGATCAAAATGTGAAAGCTAAG-TGATGAAGCTTCTA 758
                         iiv      iii?i  i v      i i      i-iv  i  i  ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_100974228_    759 GAGGAAAACATAGGA-TAATTCTTCACGACATTGAGGT-GGCAAATATAT 806
                           i           ?-   v     ii   v   i v -     vvi v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_100974228_    807 TTTAGA----ATACAAAAATCGCTAACCATAAAATAAAAGGTTGATAAAT 852
                         i     ---- i  v    v i v i v i    v    ii v       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_100974228_    853 TAGACTTTATCAAAATTTAAAACT-----GCTCATCAGAAGACACCATCC 897
                          i     i         v      -----   --   i i     i   v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTATCA 685

  chr2_100974228_    898 AAAAAGCACCAAGGCCACCCACAGACTGGGAGAAAATGTTCACCATTCAT 947
                          i    iivv   i v         v           i  ii v v    
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_100974228_    948 ATTTTCTGACAAAGTACTTGTACCTGGTAGAGATAAA---CTTCTATGA- 993
                           v -    i  i v       i ii v v v     ---  ii  ii -
  L1M4_orf2#LINE/    736 ATAT-CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_100974228_    994 TCAGTATGATGAAGACTAACAGTCCAATTTTTTTAAGCAGGCAAAAGAAT 1043
                            i  vv vi     v  i ii      ?vv--  iii      i  v 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAA--AAATGGGCAAAGGATT 832

  chr2_100974228_   1044 T----AGACATCTTACAAAAGAAGATATCTAAATAGCCAGT--------G 1081
                          ----      i iv v           vi    i    i -------- 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_100974228_   1082 AAAAG-TGCTCTGCATCATTAGTCAT 1106
                              -     vi     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (103 / 69)
Gap_init rate = 0.03 (21 / 649), avg. gap size = 3.24 (68 / 21)  


2758 26.99 0.43 3.93  chr2_101172871_101176788     2486  3426 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_101172871_   2486 TGGAAAAACATTTCATCCTCATGGATAGGAAGAATCAATATTGTGAAAAT 2535
                               i i  ii   vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_101172871_   2536 GGCCATACTGCTCCAAGAAATTCATAGATTCAATGCTATTCCCATCAAAC 2585
                            v     v i v  vvi  ii i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_101172871_   2586 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTCAT 2634
                          v   vivi v  i  ii     v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_101172871_   2635 ATGGAA-T-CAAAGAAGACCCCATATAGCCAAGACAATCCTAAACAAAAA 2682
                               - -   i --     viv        i      i i  v  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_101172871_   2683 GAACAAAGCTGAAAATACTACTAAAAATTTATTTATTTTTAGTACACACT 2732
                                 i  i ii----   ----------------------      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG----ACT----------------------CACACT 221

  chr2_101172871_   2733 ACCTGATCTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGT 2782
                         v  ii  i     viv        i          i   i    ii    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_101172871_   2783 ACTGGTACCAAAACAGGCACACAGACCAATGCAGCAGAACAGAGACCTCA 2832
                              i iv ii i  i  i i   i     v ii    iv    vii  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_101172871_   2833 GAAATAACACCACACGTCTACAACCATCTGATCTTCAACAAACCTGACAA 2882
                                vv   i  i i  iiii  vi    i   i    ivv  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_101172871_   2883 AAATAAGCAATCGGGAAAGGATCTCCTACTCAGTAAATGGTACTGGGAAA 2932
                         i vi vv    v       i  vvi  vi   ii       i      v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_101172871_   2933 ACTGGCTAGCCACATGCAGAAAACTGAAACTGGACCCCTTCCTTACACCT 2982
                              v  ?         i  i v    ii         v   i     v
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_101172871_   2983 TATAGAAAAATTAACTATTAACTCAAGGTGGATTAAAGACTAAAATGTAA 3032
                             v           -------   ii     i ?    iv        
  L1M4_orf2#LINE/    472 TATACAAAAATTAACT-------CAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_101172871_   3033 AACCCAAAACCATAAAAACCCTACAAGAAAACCTAGGCA-ATACCATCCA 3081
                         i v i     i      vi i  v        v    ?i- v i - i i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCG 563

  chr2_101172871_   3082 GGACATAGACATGAGCACAGACTTCATGACTAAAACACCAAAAGCAACTG 3131
                         v   v v ivv ii   vv ii   v iiv  vi            vvv 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_101172871_   3132 CAACAAAAGCCAAAATTGACAGATGTGATCTAATTAAACTAAAGATCTTC 3181
                                  vv     v  i i  vv  ii v  i   v v  i v   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_101172871_   3182 TGCACAGCAAAAGAAATTAGTATCAGAGTGAAGAGGCAACCTACAGAATG 3231
                           ii vv    i  v i  vi vv i      i  i     i        
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_101172871_   3232 GGAGAAAATTTTTGCAATCTACTCATCTGACAAAGATCTAATATCCAGAA 3281
                                  v       vii ivi      i  i iv  vi         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_101172871_   3282 GTTACAAGGAACTTAAACATATTTACAAGAAAAAGCTAAATAACTCCATC 3331
                         vv  i  i     ivv   vv iv i  v      vi       i v  i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_101172871_   3332 AAAAACTGGGTAAAGGATATAAACAGATACTTCTCAAAAGAAGATATTTA 3381
                         ?    v    i       v i  i   i i     v           vi 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_101172871_   3382 CGCAGCCAACAAACGTATGAAAAAAAGCTCAACATCACTAATCAT 3426
                         viii     i  i ii       i v           ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (147 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 4.10 (41 / 10)  


1952 21.06 9.45 0.98  chr2_101177371_101180859     1838  2345 (1144)    L1M4_orf2#LINE/L1        1   551 (357)  

  chr2_101177371_   1838 TAGATAGATATTCCACATTCATGGTTTAGAAGATTTAATACTGTTAAGAT 1887
                          i  v      i   ii       v  i     i      i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_101177371_   1888 G-TAATTCCTCCCAATTTTATCTACAGATTCAACGCAATCCCAATAAAAA 1936
                          -i   v ii     v  v                       v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_101177371_   1937 TCCCA--CACACTATTTTGTAAATATTGACAA-CTGATTCTAAAGTTGAT 1983
                              --ii -  v     i i v        -     i     i  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_101177371_   1984 ATAAAAATGTCAAGATAT--AGAGAAGCCAACACAATACTGGAGAAGAAG 2031
                           ii     -    iv i--   iv      v     vi  i i      
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_101177371_   2032 AACAAAGTTGGAGGACTCACACTACGCAATTTCAAGACTTGCTACAAAGT 2081
                                                v v         i    i        i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_101177371_   2082 TACAGTAATCAAGACAGTGTGGTGGTACTGGTAATAGATTAGATATGTAA 2131
                                                ---     i vv  iv    i  i  i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGT---ACTGGCATAAGGATAGACATATAG 295

  chr2_101177371_   2132 GTCAAT--------ACTTAG----------TAAA----TAC--TTATCGT 2157
                         i     -------- i v  ----------    ----   --    v  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_101177371_   2158 TGACTAA--------AAAG---CAAAGGTAGTTCAGTGGAGAAGGA-CAG 2195
                         ii i i --------  i --- v   iivi    i   i   i  -i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_101177371_   2196 TCTTTTCAACAAACGGTGCTAAATCA-CTAGACATCCGTATGCAAAGAAA 2244
                                      i      iiiv  -  i  i ?  ii       ii  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_101177371_   2245 TGAACCCAGACACAGACCTTACATCTTTCACAAAAAGTAATTCAAAATGG 2294
                             viii   v vv    i   i v vi       v   i         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_101177371_   2295 CTCATAAACCTACGTGTAAAACAGAAAACTATAAAACTTCTACAA----- 2339
                         v   ? i     vi     i vvv              ii  v  -----
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_101177371_   2340 CATAGG 2345
                               
  L1M4_orf2#LINE/    546 CATAGG 551

Transitions / transversions = 1.84 (68 / 37)
Gap_init rate = 0.03 (16 / 551), avg. gap size = 3.31 (53 / 16)  

1244 23.55 6.09 0.55  chr2_101177371_101180859     2651  3011 (478)    L1M4_orf2#LINE/L1      528   908 (0)  

  chr2_101177371_   2651 AAAACTTCTACAACATAACACAGGAGAAGGCCTAGATGAC--TAAGTGTG 2698
                               ii  v  v v    i   ? v iii  vvi    -- ii  vv 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_101177371_   2699 GTGATGACTCTGTAGAGATAACACCAGAAGCATGATCCATGGG-GAAAAA 2747
                          ii   ii iiv    v  i      i     ii v v iiii-      
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_101177371_   2748 ATTGATG--TTAGACTTTAT-----TTTAAAATTTTTGCTCTGCAAAGGA 2790
                           v   i--  i     i  -----  v    i     iv  v       
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_101177371_   2791 CACC-T-----GAGTACCAAAAGACAAGCCACTGACTGAGAGAAAGTACT 2834
                            i- -----i   i--         v    v  v  i      i  i 
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTG--AAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_101177371_   2835 TGCAAA--ACACGTCTGATAAAGGACTTATATCCAAAATATACAAAGAAT 2882
                               -- i ii        i      i      i      i      i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_101177371_   2883 TCTTAAAACTCAACAATAAGAAAACAAATGACCCAATT-AAAAATAGGCA 2931
                              v       i     i  i      i        -      i    
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_101177371_   2932 AAAAATCTGAATAGATATCTCACCACAGAAGATATACAGATGACAAATAA 2981
                           ii  i        i  i  v   v            i   i v     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_101177371_   2982 -CATATGAAGTGTTTTGCAAC--CACCCTGGTC 3011
                         -  i     iv v viv    --  ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (57 / 27)
Gap_init rate = 0.03 (11 / 381), avg. gap size = 2.18 (24 / 11)  


1119 15.09 1.72 6.03  chr2_101257052_101260358.rev      629   860 (2447)    L1M4_orf2#LINE/L1        3   224 (684)  

  chr2_101257052_    629 GAAAAACATACATATGATCATAGATTATAAGAGTTAATATTATTAAAATG 678
                             i i  v -i   v    i    iv    v        i    i   
  L1M4_orf2#LINE/      3 GAAAGATATCC-CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_101257052_    679 GCAATATTATTCAAAGTGATCTACAGATTCAGTGCAATTCCTATCAAAAT 728
                               i vii    v               ii     i           
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_101257052_    729 CCTACCTGGCTTTTTTTTTTTTTTTTTAATGGAAATTGACAAGCTGATC- 777
                           i v   v       ------------iii                  -
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT------------GCAGAAATTGACAAGCTGATCC 139

  chr2_101257052_    778 TCAAATTCCTGTGGAAATGCAAGAAACTGAGAGTAGCGAAAACAATCTTG 827
                          v      v i            ii  iv   i    v            
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_101257052_    828 AAAAAGAA---TAAAGTTGGAGGACTCACACATTCC 860
                                 ---i                   -    
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACAC-TTCC 224

Transitions / transversions = 1.92 (23 / 12)
Gap_init rate = 0.02 (5 / 222), avg. gap size = 3.60 (18 / 5)  

2401 17.48 4.51 2.44  chr2_101257052_101260358.rev     1153  1684 (1623)    L1M4_orf2#LINE/L1      211   753 (155)  

  chr2_101257052_   1153 GGACTCACATTTTCTAATTTCAAAAC--AA-ACATAGCTACAATAATCAA 1199
                                  i  i i           -- v-   v       i       
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_101257052_   1200 GACTATGTAATACTGACATAGGCGTAGACATGTAGATCAATGGAATAGAC 1249
                            vi   ii     i    i vi       i                 v
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_101257052_   1250 TTGAAAATCCAGAAATAAATGTTTACATT-ATAGTCAATTGATTTTCAGC 1298
                             i i            iviv      -  i              ii 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_101257052_   1299 AAATGTCCCAAGACAATTTAATGGGAAAA---TAATCTTTTTAACATGTC 1345
                           iv  v       v   i      i   ---  i      i    ----
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA---- 406

  chr2_101257052_   1346 ACATTGGTTGTGGGACAATTGGATATTTACACGTAAAAGAATGACATTGA 1395
                         -- v    vv        i      ?ii   i i          vi   i
  L1M4_orf2#LINE/    407 --AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_101257052_   1396 ACCCCTACCTCA-ACCACATG-AAAAATTAACTCAAAATGGAAAAAAAAA 1443
                                     -    i  i-                    vv ? i -
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA- 503

  chr2_101257052_   1444 ACCCATAAATTTAAAAGTTAAAACTATAAA-TTCTTAGAAGCATACATAA 1492
                         --  -     v   i  i            -i         v v     i
  L1M4_orf2#LINE/    504 --CC-TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_101257052_   1493 GTGTACATCTTCATGACTTTAGGTT-----------TCTTACATATGGCA 1531
                          ?   v      i    i  i    -----------     v     i  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_101257052_   1532 CCAAAAGTACAAACAACAACAAAAGAAAAAATAGGTAAACTGAACATTAC 1581
                                i    i      ---            i    i  i  v i i
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAA---AAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_101257052_   1582 AAAAATTAAAAACATTTGCTCTTCAAAAGACAGCATCAAGAAAGCGAAAA 1631
                         v            v    iv       i    vi          i     
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_101257052_   1632 GACAATCCACG---TGGGAAGCAATTTTTCGAAATCATATATCCAATAAG 1678
                              i    i---     iiv   v   vv            ii     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_101257052_   1679 AGATTT 1684
                         i  i  
  L1M4_orf2#LINE/    748 GGACTT 753

Transitions / transversions = 2.00 (60 / 30)
Gap_init rate = 0.02 (13 / 543), avg. gap size = 2.85 (37 / 13)  

 851 12.18 2.56 0.00  chr2_101257052_101260358.rev     2660  2815 (492)    L1M4_orf2#LINE/L1      749   908 (0)  

  chr2_101257052_   2660 GACTTGTATCTAGAATATGTAAAGAACTATTACAGCTCAATAATAAAATG 2709
                                   i       i         v     i             v 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_101257052_   2710 A---A-AACCCATTTTAAAAATGGGTAAAGGATCTGAATAGACAGTGCTT 2755
                          --- -      v  ?         i       i          v v  i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_101257052_   2756 CAAAGAAGATCTACCAATGACTAATAAACACTTGAAAAGATGCTCAACAA 2805
                                   v   v    i i     i   v                 v
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_101257052_   2806 CATTAGCTAT 2815
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.00 (9 / 9)
Gap_init rate = 0.01 (2 / 160), avg. gap size = 2.00 (4 / 2)  


2769 21.01 2.28 12.29  chr2_101283918_101287227.rev     1810  2818 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_101283918_   1810 TGGAAAG----CCCATGCTCATGGGTTGAAAGA----ATATTGTTAAACT 1851
                                ----      i      i   i    ----          iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_101283918_   1852 GTCCATGGTACCCATGGTGTCCATGCAATCTACAGATTCAATATGCTCCC 1901
                          v v  iv v    viv  --------              iiiiv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG--------ATCTACAGATTCAACGCAATCCC 92

  chr2_101283918_   1902 TGTCAAAATACCAA-TGCCATTCTTCACAGAAATAAAAAATAAAATCCCA 1950
                          i       v   i-    -  i  ii       vi v  vvvi    i 
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr2_101283918_   1951 AAATTTTTATGGAACCACAAAAGACACCAAATAGCCAAAGCAATCCTGAG 2000
                              iv       vii   ii   v vi          i     i   -
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA- 190

  chr2_101283918_   2001 CAAAAAGGATTGCCGTCCCTTGGGCCTGCTGTCCCTTGGGCTTGTGTGCC 2050
                         --     i -----------------------------------------
  L1M4_orf2#LINE/    191 --AAAAGAA----------------------------------------- 197

  chr2_101283918_   2051 TCTTCCTTCTGCTTCCCTCTATGTTCTTTCTCTGCAGTAACCCATAACCA 2100
                         -------------------------------------------------i
  L1M4_orf2#LINE/    198 -------------------------------------------------G 198

  chr2_101283918_   2101 AACAAAGCTGAAGGCATCAGACTCCCTGACTTCAAAATATACTACAATGC 2150
                                i  i   vv   v   i  ii i       iv        v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_101283918_   2151 TATAATAACCAAAACAGTATGGC-TTGTGTATAAAACCATGACACATAAC 2199
                           i i   i   i     i   i-i  - i    iivi -    i   iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTG-GCATAAGGATA-GACATATAGA 296

  chr2_101283918_   2200 CAAATGGAATAGAATAGAGAACCCAGAACTAAATTCACACATTTACAGCC 2249
                         iv             v    ii      v    ii  i       ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_101283918_   2250 AACTCATTTTTGACAAAGGCTCTGAGAACATATACTTGGGAAAGAAGAGT 2299
                           i v     i     i  iv ii   v   vi v v         v   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_101283918_   2300 ATCTTCAATAAACGATGCTGGAAAAACTGAATATCCATATGCAGAAGAAT 2349
                         v i     i   i i      i v     i   ?   i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_101283918_   2350 AAAATTAGACCCCCCTCTCTCTCACCATGTACAAAAATCAAATCAAAATG 2399
                         i  i  i      -- vi   v      i         i  v        
  L1M4_orf2#LINE/    447 GAAGTTGGACCCC--TACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_101283918_   2400 GATTAAAGACTGATATGTAAGACTTGAAACTATAAAACCACTAAAAAAAC 2449
                            i ?    iv v        vi i            ivi  i  i  v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_101283918_   2450 ACCGTAGAGG-AACCACCTTAG-GACATTAATCTGAGCAAAGATTTTATG 2497
                           -i   i? -  -- i   v -   v  iivi ii    v i   iv i
  L1M4_orf2#LINE/    545 AC-ATAGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_101283918_   2498 GAGAAGAACTCGAAAGCACAGGCAACCAAAGCGAAAATAGATCAATGGGA 2547
                           v v  vvi i        i     v    vi         v   v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_101283918_   2548 TTACATCAAGCTAAAAAGCTTCTGCACAGCAAAGAAAATAATCAACAGAG 2597
                         i v      iv v    i   i  ii vv     i v iv     v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_101283918_   2598 TGAAAAGACAACTTACAGAAAGGGAGAAAATGTTTGCAAACTATGCATCT 2647
                                     ii      v          i        ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_101283918_   2648 AACAAGGGGTTATGCAAACCATTGTTATATGCCAGAATATATAAGGAACT 2697
                         i i     ---------  -----  i   -             i     
  L1M4_orf2#LINE/    742 GATAAGGG---------AC-----TTGTAT-CCAGAATATATAAAGAACT 776

  chr2_101283918_   2698 CAAATAACTCAATGGCAAAAGGTCAAATAATTGGATTTAAAAGT------ 2741
                          vv i        iii    i v       iivi   ?    i ------
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_101283918_   2742 -----TTGAATAGACATTTATCAAAAGAAGATATACAAATGGCCAACAGG 2786
                         -----              v  v                       i i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_101283918_   2787 TATATGAAAAAATGCTCAACATCACTAATTAT 2818
                         i i       i             ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (135 / 73)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 7.74 (147 / 19)  


3106 26.86 1.55 0.78  chr2_101391995_101396229     2843  3743 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_101391995_   2843 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATTTCGTGAAAAT 2892
                              ii i  i     i        v      v i   v i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_101391995_   2893 GGCCATGCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2942
                            v  i  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_101391995_   2943 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 2991
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_101391995_   2992 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGA 3041
                               viiv  ii  v  v v  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_101391995_   3042 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 3091
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_101391995_   3092 ACAGTAACCAAAACAGCATAGTACT--CATACCAAAACAGAGATATAGAC 3139
                                i   i    ii i     --    -- ii i   v       i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATATAGAT 297

  chr2_101391995_   3140 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAAC 3187
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_101391995_   3188 CATCTGGTCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 3237
                           vi  i i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_101391995_   3238 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAGC 3287
                         i  v  i  i              v      v  ?   ii  i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_101391995_   3288 TGAAACCGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 3337
                             iii   i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_101391995_   3338 ATTAAAGACTTAAATGCTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3387
                           i ?    i      iv   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_101391995_   3388 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 3436
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_101391995_   3437 GAAACACCAAAAGCAATGGCAACAAAAGCCAAAATGG--------GATCT 3478
                         ivi            vvi          vv     i --------  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_101391995_   3479 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGA 3528
                         v  i   v v  i i   i  ii vv    i  v    i ivv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_101391995_   3529 ACAGGCAACCTACACAATGGGAGAAAATTTTTACAATCTACCCATCTGAC 3578
                          v  i     i   v             v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_101391995_   3579 AAAGGGCTAATATCCAGAATCCACAGAGAACTTAAACAAATTTGCAAGAA 3628
                           i  i  vi          vi i i      ivv    v ivii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_101391995_   3629 AAAAATCAAACAACCCCATCAGAAAGTGGGCAAAGGATATGAACAGACAC 3678
                            i -    i     v  i?i   i            v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_101391995_   3679 TTCTCAAAAGAAGACATTTATGCAGCAAACAGACACATGAAAAAATGCTC 3728
                              v        i  vi viii  v  i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_101391995_   3729 ATCATCACTGGCCAT 3743
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (148 / 90)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


2744 24.57 5.35 2.28  chr2_101422073_101424301.rev      880  1758 (470)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_101422073_    880 GAGAGATA--CCATGTTCTTGGATTGGAAGATACAA-ACAGTAAAGATAT 926
                           i     --        v            ivi  - iv  v     iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_101422073_    927 CAGTTCTCCCCATCTCCATCTCTAGGTTTAATGCAATTCCTATCAAAATC 976
                           i v       vv iv    vi  i  i  i     i            
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_101422073_    977 TCAACAAGGA---TTTTGTAGACCTATACAAGCTTATTTTAAAAGTTACA 1023
                         i  i --v v---     i   vv vv       v  ii     v i i 
  L1M4_orf2#LINE/    103 CCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_101422073_   1024 TGGAAAGGCACAGGCATTGAAATAGCTAAAACAGTCTTGTAAAAGCAGAA 1073
                               v   vi  vviiii      i      i     v     v    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_101422073_   1074 TAAGGTAGGAGAAATCATTCTATTTAATAT--AGAGTTATGATGTAGCTA 1121
                         i  i  v    i v   iv  viii   v -- i v   iv iiv     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_101422073_   1122 CAGTATTCAAGA-AGTGTGGTATTTGGTGGAGGCATAGAAACACA--TTG 1168
                              v      -         i -  iiv i v     v i i -- ii
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACT-GGCATAAGGATAGACATATAGATCA 299

  chr2_101422073_   1169 ATGGAACAGAATAGGGAATCTAGAAATAGGCCCACACAAATATGCTCAAC 1218
                               i     v i  i  i       ii    i   vv    v    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_101422073_   1219 TGATTTTCTTTTACAAAAGTAC-AAAACTAATTCAACAG----AGGATAG 1263
                                 v---    ii  i -  i  i -     ii ----  i    
  L1M4_orf2#LINE/    350 TGATTTTCG---ACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAG 395

  chr2_101422073_   1264 CCTTTTCAATAAGTG----TGGAGTAAGTGGACATCCATAGGAAAATAAA 1309
                         i        i  i  ----   iii  v    i ?   i v v   - i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-AGA 444

  chr2_101422073_   1310 ATGAACCTTGGACTAA-ACTTCATACCTTATGCAAAAATTAACTCA---- 1354
                              v-      ivv-  i   i   v   i              ----
  L1M4_orf2#LINE/    445 ATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_101422073_   1355 -GATCATATCTGTAAAAATAAAATGTAAAACTATAAAACTAT------AG 1397
                         -     ? vviv    vi   i vv               v ------ i
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_101422073_   1398 GATATAGA---AAATCTTTTGGAACTAGGGCTAAGCAAAGGGTTGTTAGA 1444
                         i i    i---       ivv  v  v   i  i    v  v  v     
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_101422073_   1445 CTTGATACCAAAAGCACAATTCATAAAAGAAAATTT-GATAAATTAAACT 1493
                         iv   i             viv i         vv -        ii   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_101422073_   1494 TCATCAGAATTTAAAACATTTGTTCTGCAAAAGACCATGTTAAAAGGCCG 1543
                               i    v     v     v  v    i   vv i i  i iivi 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_101422073_   1544 AGAAGACAGGCCACATACTGGGAGAAAATATTTCCAAACCACATATCCAA 1593
                          i      iv     v v               v    i  i     ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_101422073_   1594 CAAAAGATTAGTATCTAGAATATATAAAGAACTGTCAAAACTCAACAGCT 1643
                         i  ii  i v     i                 v i v       i iiv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_101422073_   1644 AAAAAAT------TCTAATTAGAAAATGGAGCACA-----TGAACAGACA 1682
                             i i------i i    ?i       -   v -----    i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGG-GCAAAGGATTTGAATAGACA 842

  chr2_101422073_   1683 TTTCACTGCAGAGGATATAAAAATGGCAAATAAGCGCATGAAAAGACATG 1732
                             v iiv   i      v       v       ----------     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGC----------ACATG 882

  chr2_101422073_   1733 AAAAGACAGTCAACAGCACTAGTCAC 1758
                               iiv      v  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (124 / 89)
Gap_init rate = 0.03 (24 / 906), avg. gap size = 2.79 (67 / 24)  


2212 26.13 0.36 0.36  chr2_101529128_101535856.rev     5012  5562 (1167)    L1M4_orf2#LINE/L1        1   551 (357)  

  chr2_101529128_   5012 TGGAAGAACGTTCTATGCTCATAGATAGGAAGAATCAATATCGTGAAAAT 5061
                              ii ii i i   i    i   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_101529128_   5062 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5111
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_101529128_   5112 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5159
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_101529128_   5160 TATGGAACCATAAAGGAGCCTGCATAGCCAAGATAATCCTAGGCCAAAAG 5209
                                viii  i   v  v v        i i    i iiivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_101529128_   5210 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5259
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_101529128_   5260 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5309
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_101529128_   5310 AATGGACCAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5359
                               vi    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_101529128_   5360 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGCATTCCCT 5409
                         i    i  i     ivv  v   i v  vv            v  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_101529128_   5410 ATTTAATAAATGTTGCTATGAAAACTGGCTAACCATATGTAGAAAGCTGA 5459
                         v  i  i     v    iv  v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_101529128_   5460 AGCTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 5509
                           i    i    v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_101529128_   5510 AAAGACTTATATGTAAGACCTAAAACGATAAAAACCATAGAAGAAAACCT 5559
                          ?    i  v        v       v      vi v           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_101529128_   5560 AGG 5562
                            
  L1M4_orf2#LINE/    549 AGG 551

Transitions / transversions = 1.68 (89 / 53)
Gap_init rate = 0.01 (3 / 551), avg. gap size = 1.33 (4 / 3)  

1162 27.69 0.27 0.27  chr2_101529128_101535856.rev     5866  6237 (492)    L1M4_orf2#LINE/L1      537   908 (0)  

  chr2_101529128_   5866 AAAAGAAAACCTAGGCA-ATACCACTCAGGACATAGGCATGGGCAAAGAC 5914
                          i        v    ?i- v i -i  iv   v v  vv i     v ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_101529128_   5915 TTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAA 5964
                            v iiv  vi            vvi          vv     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_101529128_   5965 ATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCA 6014
                           v   ii v  i   v v  i i   i  ii vv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_101529128_   6015 TCAGAGTGAACAAGCAATCTACAGAATGGGAGAAAATTTTTACAATCTAC 6064
                         vv i      v ii   i i                 v   i   vii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_101529128_   6065 CCATCTGACAAAGGGCTAATATCCAGAATCTACAAATAACTTAAACAAAT 6114
                         vi      i  i  i  vi          v  i   v    ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_101529128_   6115 TTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGTAAAGGGTATGA 6164
                         iv i  v     i     i     v  i?    i    i     i v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_101529128_   6165 ACAGACTCTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAA 6214
                          i    vi     v        i  vi viii     i ii         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_101529128_   6215 AAATGCTCATCATCACTGGTTAT 6237
                          i       v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (57 / 44)
Gap_init rate = 0.01 (2 / 372), avg. gap size = 1.00 (2 / 2)  


 875 30.79 9.55 1.67  chr2_101611221_101613310.rev      424   842 (1248)    L1M4_orf2#LINE/L1      141   592 (316)  

  chr2_101611221_    424 AAAATT-ATATTGTAA-GTTAAAAACTGAGAATAGATAAGATGCTGT--- 468
                               -    v v  - iv iii  iv       vi  i iiv v ---
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_101611221_    469 ----GAAGAA----GTTAG-TAACTCTTGTTTCTCCAGACATTAAAACTT 509
                         ----      ----   i -vi    viii   -   - iv i       
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTC-CCA-ATTTCAAAACTT 238

  chr2_101611221_    510 GTTATAAAGCTATAGTCATTAAGACAGTATGGAACT--CTCAGGGATAGA 557
                         ii  i       i   v  i        i   v   -- vi i       
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_101611221_    558 CAGACAGACTGATGGAACAAAA--GAAA-CCTAGAAATAAAGCCATGCAT 604
                           v i   iii      i i  --  i -i i         v    i   
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_101611221_    605 GTATGG--AA------------AAGAATGGCACTGTAGA----TCGATGA 636
                         v     --  ------------   ii  v  ----   ----  i   i
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCA----AGACCATTCAATGG 384

  chr2_101611221_    637 --AAAAGATAGACTTCCCAGTAAATGACACTGGAACAATTGGTTATCCAT 684
                         --   ii    v   ii  ii     iii    i    i   v  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_101611221_    685 AAGGTAAAAGAACAGAACTGGATCACTGCCTTACTCCATATACAACAATC 734
                          -v i       iii ii    i v  i   i  v          v   i
  L1M4_orf2#LINE/    435 A-TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_101611221_    735 AATTTCAGGTAGATTAAATGCTTAAATAACAAAGCTGAC-CTTTATAACT 783
                           i iv ii i   i ? vi i     ivv i    i v-  v  v    
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_101611221_    784 CTAAGAGAAAAATATAAAAGAATATTTTTATAATGCCAGCATAAAGAAAG 833
                           v   ii    i   ii? v v  i  ii i iviii vv  iiv  v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_101611221_    834 TTTTCTTGG 842
                         v      i 
  L1M4_orf2#LINE/    584 GTTTCTTAG 592

Transitions / transversions = 2.23 (87 / 39)
Gap_init rate = 0.04 (17 / 452), avg. gap size = 2.76 (47 / 17)  

 766 25.78 5.59 2.17  chr2_101611221_101613310.rev     1277  1598 (492)    L1M4_orf2#LINE/L1      576   908 (0)  

  chr2_101611221_   1277 AGGAAAT--TTTCTTA------ACACCCAAAGTGGTAACCAGAAAAGCAA 1318
                            v   --       ------     v    iivv i v v     v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_101611221_   1319 ATGACTGATACATTTGACAACATTAAAATTAAGACTGTTTCTTCCTCAAA 1368
                          -i iv    v   v   vv   i        i viv   v v i     
  L1M4_orf2#LINE/    626 A-AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_101611221_   1369 AGATATCAT--AAAAAATGAAAAGGCAGGCCACAAACTAAAAGTCAATAT 1416
                         i  i ii  -- i   i       i  iv     i v iii  vv     
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_101611221_   1417 TTTCAA--CATATGTAACCAACAAAGGGTTAGTAACAAGAATATATGAAG 1464
                           v   --     i -- ii i  i  ii v   v v         i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATAT--CTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_101611221_   1465 AGTTCTTACAAATCTATAAGAAAAAAGACAAA---CCCAATAGAAAAATA 1511
                          ii        v  v    v     -      ---      v?      i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAA-GACAAATAACCCAATTWAAAAATG 821

  chr2_101611221_   1512 AACAGATGACCGGAACAG---TCTCTTCACAGAAAAGGAGCTGAAAGTGG 1558
                         ii  i v  iiv   i  --- i   i  v    ---  vv iv  i   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAA---GATATACAAATGG 868

  chr2_101611221_   1559 CCAATACTTATATGAAAAGATGATCAATATCATTAATAAT 1598
                               vvi i           v    i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (45 / 37)
Gap_init rate = 0.03 (10 / 333), avg. gap size = 2.50 (25 / 10)  


3324 21.83 2.29 3.17  chr2_101615612_101617957.rev      939  1854 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_101615612_    939 TGGAGAGATATCCCAAGTGCACATGGATT-------TCAATATTATCATG 981
                             i          --  iv        ------- i      i i v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCA--TGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_101615612_    982 ATGGCAGTTCTCCCCCAAATTGATTTATTAACCTAACACAATCCCTATCA 1031
                               i v      -        i  ivi iii   i            
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_101615612_   1032 AACACCCAGGAAGCTTTTTTTGTGAGAATTGATAACCTAATTTAAAAATA 1081
                           vv     vv-  i       iiii      i  v  i  iiv     -
  L1M4_orf2#LINE/     98 AAATCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT- 145

  chr2_101615612_   1082 TCTATATAAAAATGCAAAGGATCTGGAGTAGCCAAA-CAATTTTTTAAAA 1130
                           -    ii        i   i ii  i        -    i  vv    
  L1M4_orf2#LINE/    146 TC-ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_101615612_   1131 GA-GAACAAA-TTAG-GGACTGACATTACTCAATAT-GAAACTTACTCTA 1176
                           -       -  i -     v   i v i    v -i         vi 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_101615612_   1177 AAACTACACTTTTTAAGACTATATGGTATTAGCACAAGGATAGATATATA 1226
                           i     v vv i     vi i     i i   i         i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_101615612_   1227 GATCAGTGGAGTGGAATTATAAGTCTAGAAACAAACCCTCACATTTACAA 1276
                              i    i i     ivi    i     i      vi       iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_101615612_   1277 CCAACTGATTTTCTAAAAAGATTCCAGAAAACTCAGTTCAATGATGAAAG 1326
                         i   i        v v  i i v   -- i  -  -       iv     
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCA--AGAC-CA-TTCAATGGGGAAAG 390

  chr2_101615612_   1327 GGTTATCTTTTCAAAAAACATTGCTGGGACAATTTAATAACCACGTGCCA 1376
                         ii vi         v   iiv           i vi   ?    i   --
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-- 438

  chr2_101615612_   1377 AAAAAAAAAAAAGAGAAAGAACTTAGGCTCTCATTTCACAGCATAAACAG 1426
                         ----------  i    v   v  i i i ii ii     v    v   -
  L1M4_orf2#LINE/    439 ----------AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA- 477

  chr2_101615612_   1427 AAAAATTAATCCACAATGGATCATAGACATAAATGTAAGAGATAAAATTA 1476
                         -        ii  v         ?    v            v     i  
  L1M4_orf2#LINE/    478 -AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_101615612_   1477 TTCAACTTGTAGAAGAAAACATAGAAGACAATTTTTTCTGACCTTAGATT 1526
                          vv    iv               i? -i  v i  iv       i i  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTT 575

  chr2_101615612_   1527 AGGCTATATATTTTTATGA-GTGACACCAAAAGTAAGATCCATACAAGAA 1575
                             v  ivv  i   -  -i            i vi v v i v     
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTA-GATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_101615612_   1576 AAAAATTTATAAATTAGACCCCATCAAAATTGAAAACATTCATGCTTTAA 1625
                             - vv       i   ii          i     v  ii     i  
  L1M4_orf2#LINE/    625 AAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_101615612_   1626 AAAATACCACTAAGAAAATAAAAAGATAAGCCAAATACTCAGAGAAAATG 1675
                          ii i  i ii      i i      i  v   v v v vi        i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_101615612_   1676 TTTGCAAATC-------TGATAAAGGACTTATATACAAATTATATAAAGA 1718
                                   -------      i      i   v  i v          
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_101615612_   1719 GTTCTCCAAACATATATTGATAAGAAAACAAATAACCGAATATAAAAATG 1768
                         ii   ivv   vi -  -i    i  i          v   v?       
  L1M4_orf2#LINE/    774 ACTCTTACAACTCA-AT-AATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_101615612_   1769 GTCAAAAGAATTGAATAGACATTTCACCAAAAAAT-TATACAAATGGCTA 1817
                          v    i  v               v     i  v-            i 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_101615612_   1818 AAAAGCTCTTGAAAAGATGTTCAACAACATTAGTTAC 1854
                          v    v v          i      v  ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (124 / 72)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.08 (50 / 24)  


3326 23.06 4.57 0.91  chr2_101659036_101664628.rev     4226  5101 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_101659036_   4226 TGGAAAGACATCTTATGTTCACAAATTGGAAGAATTAATATTGTGAA-AT 4274
                                 i   ii       iii         v          v  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_101659036_   4275 GATA-TACTACCCAAAGCAATCTATAGATTCAATGCAATTCCTATCAAAA 4323
                          ii -    v      vii     i        i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_101659036_   4324 TACCAATTATATTCTTCACAGAATTAGA-AAACAAATTCTATAATTTCAG 4372
                          v   ii iiv  i  ii     v v  -  i vi  i   v    ivvi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_101659036_   4373 TGAAACCACAAAAGAGCCCAAGTAGCCAAAGCAATCCTGAGCAAAAAGAA 4422
                           i  vii   ii  v  vi i        i     i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_101659036_   4423 CAAAGCTGGAGGTAC-CACATTACCTGGCTACAATATATACTACAAAGCT 4471
                              i      -  -    i v  iiii v   v iv            
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_101659036_   4472 ATAGTAACCAAAACAGTATGGTACTGGCATAAACGCAGACACATAGACCA 4521
                          i     i   i     i              ivii     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_101659036_   4522 GTGGAACAGAATAGAGAACCCAGAAATAAATCCACATATTTATAGCT--- 4568
                         i     i     v    ii           i   i i      i ii---
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_101659036_   4569 --------GACAA------------CATTCAATGGAGAAAGGACAGTGTC 4598
                         --------     ------------          i     i i   v i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_101659036_   4599 TTCAACAAATAGTTCTGGGAAAACTGAATATCTATATTTAGAAAAATGGA 4648
                                   i  v      v     i   ? i i  vi i  i    i 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_101659036_   4649 ATGAGACTACTATTTCTTATCACATACAAAAATTAACTCAAAATAGATTA 4698
                         i vi   iv   ii  vi i  i                     i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_101659036_   4699 AAGACTTAAGTGTAGGACCTGAAACTATGAAACAACTGGAAGACAACTTT 4748
                         ?    i   i    i  v  i       i    vvi i     v   v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_101659036_   4749 GGGG-AAATGCTTCAGGAGATTGACCTGGGCAA-AATTTCTTTTTGGGTA 4796
                           ? -    -    iv  vv   ivi i     -ii      ---i i  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT---AGATA 595

  chr2_101659036_   4797 AGAACTTAGAAGCACAGGAAA-AAAAGCAAAAATAGACAAATGGGATTAT 4845
                         v  vvii i       i v  -     v         i    v   i vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_101659036_   4846 ATCAAG-TTAAAAAGTATGTGCACTGCAAAGGCAACAATCAACAGAGTAA 4894
                              i-       v - v  ii  v      vv  v     v i   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_101659036_   4895 AGAGACAACCTACAGAATGGGAAAACAATATTTGCAAACTATGCATCTAA 4944
                          i        i           i  -            ii  ii    i 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCATATATCTGA 743

  chr2_101659036_   4945 TAAGGGATTAGTAACCAGCATATATAAGGGATGCAAAGAACTCAATAGCA 4994
                                i v   v    v        i i iv vv v         ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_101659036_   4995 AACAAACAAACAAAC------AAAA---GGCCAATGATCTGAATAGACAT 5035
                           v i     i  v ------    ---   v  v   i           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_101659036_   5036 TTATCAAAAGAAGACATACAAATGGCCAACAGGCATATGAAAAAAATGCT 5085
                           v  v        i              i i   i       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr2_101659036_   5086 CAACATCAGTTATCAT 5101
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (133 / 66)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.67 (48 / 18)  


 269 26.06 1.41 9.15  chr2_101664725_101671476      822   963 (5789)    L1M4_orf2#LINE/L1        1   131 (777)  

  chr2_101664725_    822 TAAAAATGATATGC-ATGTTCATGCAATTACCA-ATTCAATATTGTCAAG 869
                          ii   -     v -         -i   ivv - i i        i   
  L1M4_orf2#LINE/      1 TGGAAA-GATATCCCATGTTCATG-GATTGGAAGACTTAATATTGTTAAG 48

  chr2_101664725_    870 TTGCCAATGCTCCTTCTAGACTGGTGTCCAGAGGCAAAACAATTACAATT 919
                         v  v    i    -- i i i  i v v    vv   vi    iv v  i
  L1M4_orf2#LINE/     49 ATGGCAATACTCC--CCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_101664725_    920 AAAATTTCTACAGGTATTTTTTGATTATATAAAAAAACTGACAA 963
                              ii ---  v iii    --  ii ----i   i      
  L1M4_orf2#LINE/     97 AAAATCCC---AGCTGCCTTTT--TTGCA----GAAATTGACAA 131

Transitions / transversions = 1.85 (24 / 13)
Gap_init rate = 0.06 (8 / 131), avg. gap size = 1.88 (15 / 8)  

 537 25.40 8.82 10.43  chr2_101664725_101671476     4846  5219 (1533)    L1M4_orf2#LINE/L1      117   484 (424)  

  chr2_101664725_   4846 TGCAGTGA--AACAAGATGTGCCTAA----C-TACGGATGTGAAAAGGTC 4888
                              vi --i     v  vv     ---- -  i   vi  v  i  v 
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr2_101664725_   4889 ATTAAAGAGTCAAGACGCTTTTGAAGAGGAA-AACCAAGTAAGAAAAACT 4937
                         vivi  v  i   i  iv i     i i   -   v    vi  ii -  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA-CT 215

  chr2_101664725_   4938 TGC-TTTACCAATTATTTGCAAATATAATGCAAATAATTATGCAAATAAT 4986
                         ii -i  v      -------------------------- -    - v 
  L1M4_orf2#LINE/    216 CACACTTCCCAATT--------------------------T-CAAA-ACT 237

  chr2_101664725_   4987 TATTGCCTTATAAAGGTGCAATAATTCAAACAGTGTAGCATTAGCATAAG 5036
                           i ----- i    v i  i    iv i       i i i i       
  L1M4_orf2#LINE/    238 TACT-----ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_101664725_   5037 CCTCGA------GATGAATGGAACAGAATACAGAATGCAAAACCAGACTC 5080
                         vv v  ------   v       i     vv   i v  i  vi i  i 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_101664725_   5081 GTGCATATATGGACA---------TGACAAATTGGCACTGCAGAGAGTA- 5120
                         i i   v     v  ---------i     i--  ---   vi   vi -
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAG--GG---TGCCAAGACCAT 377

  chr2_101664725_   5121 --AGTG----AACCAGAGTATTTTAAACAGATTATGCTGGAAAAATTGAA 5164
                         -- i  ----  vv v   v    v    i  vi      i v  i  i 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_101664725_   5165 TACCCATGTGGAAAAAAATGAAACTTGGCCACTACCTCACTCCATATA-- 5212
                           ?   ii  v    i      ii v i  v         v       --
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_101664725_   5213 AAAATCA 5219
                              i 
  L1M4_orf2#LINE/    478 AAAATTA 484

Transitions / transversions = 1.35 (54 / 40)
Gap_init rate = 0.05 (17 / 368), avg. gap size = 4.24 (72 / 17)  

 379 30.38 17.69 0.00  chr2_101664725_101671476     6001  6260 (492)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr2_101664725_   6001 AAAAGCACTTGC--CAAAGGAAAAGACCGATGATCAGGATTACGTGAAGA 6048
                                 vv  --    i     i iv   i viv   i v i v  i 
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_101664725_   6049 CTAAGAACTTCTGTTTATCAAAAGATGCCACTAA-ACAGTGAAAAGTCAA 6097
                         i   i     i   viv     i  ii i ii  - v         v   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_101664725_   6098 TGCATGTTATGGACGATGATATTTGCAACTCGTGTAACC--------ACT 6139
                         iv  iivv    iv  vi          v  i i  v i--------   
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_101664725_   6140 ------------------GGAACTTCTAAAATTCAAGAA-GAAAAGATAG 6170
                         ------------------i     ii  v  i    v  -i      i i
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_101664725_   6171 ACAACTCAA--AAGACAGGGACAAGAGCTT------AACA-------AAA 6205
                          i   i   --? i v v  i   ii v  ------i   -------   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_101664725_   6206 GAGGATATCCTG-TGGCCCAGAAACATATGCGATGAGGCTGTACCTCATG 6254
                           i     v vi-     v v  i  i   vi v  v   vv  v   ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_101664725_   6255 AGTAAT 6260
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.36 (45 / 33)
Gap_init rate = 0.03 (9 / 306), avg. gap size = 5.11 (46 / 9)  


2567 19.38 1.38 18.00  chr2_101679931_101682027      517  1605 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_101679931_    517 TGAAAAGATATGCCGTGTCCATGGATTAGAA---TTAATATTGCAAAAAT 563
                           i        v  i   i        i   ---         iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_101679931_    564 GACCATACTACCCAAACATATCCACAGATTTAATGCACTCCCTATCAAAA 613
                          i v     v      ivv   i       i  i   v            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_101679931_    614 TACTAAAGACATTCTTCACAGAAATAGAAAAAAAAAATCCTAAAATTCAT 663
                          v i ivvi v  i  ii       v  v  ivvi -             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_101679931_    664 ATGGAACCACAAAAGACCCCAAAAGGCCAAAGCAATTCTGAGCAAAATCA 713
                               vii   ii     vi  vi      i    ii   iv  i vv 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_101679931_    714 ACAAAGTTGGAGACATCACACTACCTGATTTCAAAATATACTATAAAGCT 763
                                     ivv       v  ii         iv     i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_101679931_    764 GTAGTAACCAGAACAACATGGTACTGGCATAAAAACAAACACATAAAACA 813
                         ii     i  ii   iii              ii i i   i   i v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_101679931_    814 ATGGAATAGA-----GAGCCTAGAAATAAATTCAGGCACCTACAGCCACC 858
                                   -----   i i         ii  vi  ii  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_101679931_    859 TGTTCTGACAACAGCCACCTGTTTTTGACAATGATACCAAGAACACACAT 908
                           ------------------i    i     v i i      v  iv  v
  L1M4_orf2#LINE/    350 TG------------------ATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_101679931_    909 TGGGGAAAAGATTGTCCCTTTAATAAATTGAATATCCTAGGGAGGCTGAG 958
                                 ii  v   ii  i  i    ----------------------
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAAT---------------------- 409

  chr2_101679931_    959 GCAGGAGAATAACTTGAACCCAGGAGGTAGAGTTTGCAGTGAGCCGAGAT 1008
                         -------------------------------------i   ---------
  L1M4_orf2#LINE/    410 -------------------------------------GGTG--------- 413

  chr2_101679931_   1009 TGTGACACTGCACTCCAGCCTGGGCAACAGAGTGAGACCCTGTCTCAAAA 1058
                         -------------------     --------------------------
  L1M4_orf2#LINE/    414 -------------------CTGGG-------------------------- 418

  chr2_101679931_   1059 ATAACATAAAATAAAATAAATTGAATATCCACATGCGAA-GAATAAAATT 1107
                          i   ----------------  i   ?        i  -    i  i  
  L1M4_orf2#LINE/    419 ACAAC----------------TGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_101679931_   1108 AGACCCCTATCTCTCACCGTGTATGAAAATCAACTCAAAATGGATAGAAG 1157
                         i        i   v    i i  ii     i              vi?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_101679931_   1158 GCTTAAAAGTAAAATCTGAAACTATAAAACTACTAGAAGAAAACA--GGG 1205
                         i i    v    i v  i             vi            --  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_101679931_   1206 GAAAGACTTCACAACACTAAGCTAGGCAGGGATTTTTTAAATAGGAAGTC 1255
                          v  iv    iii  vi ii i      iv i   i   i   v  vii 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_101679931_   1256 AGAGGCACAGGTATCAAAAGCAAAAATAGACAAATGGGACTACATGAAAT 1305
                          i i     i i v      v         i    v     v   -----
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT----- 647

  chr2_101679931_   1306 CAAAAGCAAAAACAGACAAATGGGACTACATGAAATTAAAAAGCTTTTGC 1355
                         ------     ------------------------       -      i
  L1M4_orf2#LINE/    648 ------CAAAA------------------------TTAAAAA-CTTTTGT 666

  chr2_101679931_   1356 ATAACAAAGGAAACAATTAACAAAGTGACGAGAAAACCTACACTGTCTTA 1405
                         iivv       v  v  i  v       vi   v    i   --------
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA-------- 708

  chr2_101679931_   1406 TAGGTTTGGAAGAAAATATTTGCAAAC----TATCTAACAAGGGGTTATT 1451
                         --- vv   i                i----     i i     ii vv 
  L1M4_orf2#LINE/    709 ---GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_101679931_   1452 ATCCAGAAATATATAAGGAACTTAAACAACTCAACAGCAATAAACCAAAT 1501
                                 -       i     ivv         i ii  v  iv     
  L1M4_orf2#LINE/    756 ATCCAGAA-TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_101679931_   1502 AACCCGATTAAAAAATGGCCAAAAAACCTTAATAGACATTTCTTAAAAGA 1551
                              i   ?        v    ii ii v             iv     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_101679931_   1552 AGACATACAAATGGACAACAGATACATGAAGAAATGCTCAACATCACTAA 1601
                            i          v   i iii       i i             ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_101679931_   1602 ATGT 1605
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.09 (140 / 67)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 13.19 (211 / 16)  


1157 24.29 6.94 0.63  chr2_101954434_101957309.rev     1209  1525 (1351)    L1M4_orf2#LINE/L1        1   337 (571)  

  chr2_101954434_   1209 TGGAGAGAGATTTCCATGTTAATGGAC-AGAACAGTCAATACTGTCAAGA 1257
                             i   v  i-       v     i-i   v v i    i   i    
  L1M4_orf2#LINE/      1 TGGAAAGATATC-CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_101954434_   1258 CATCAGTACTTTCCAACTTGATCCACAGAGTCAATGCAATTCTAATCAAA 1307
                         iiv  i    ii    v      i     v    i     i iv      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_101954434_   1308 ATCCCAAGT---TATTTTGTACATATCAATAAGCTGACTCTAGAG----- 1349
                               iv --- v     i v v  ii i       ii   i i-----
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_101954434_   1350 --------GCAAAAGACCCAACACAGTCCACATAACATTAAAAAAGAA-- 1389
                         --------    ii      iv i  i v v i  iv  i        --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_101954434_   1390 -CAAAGTTGAAAGACTGACAGTACCTGACTTCAAGATTTACTATAAATCT 1438
                         -        i i    v   v v  ii i     i i      i   v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_101954434_   1439 ACAGTAATCAAAACAGTGTGGTTATTAGCACAAAAAGAGACAAATAGATA 1488
                                    i          - i i   i  ii v     v      v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGT-ACTGGCATAAGGATAGACATATAGATC 298

  chr2_101954434_   1489 AATGGGAAAAAAT--AGAGCCCAGAAATAGAACTATACA 1525
                              i v i   --    i         i v i     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

Transitions / transversions = 2.08 (52 / 25)
Gap_init rate = 0.02 (7 / 337), avg. gap size = 3.43 (24 / 7)  

1702 24.52 4.73 1.75  chr2_101954434_101957309.rev     1814  2384 (492)    L1M4_orf2#LINE/L1      321   908 (0)  

  chr2_101954434_   1814 AAAAATAGAACTATACAAATATAG-CAGT-AATCT---ACAAAGGAGCAC 1858
                          i     i v i     vv   i -  i -i  i ---    i  v  - 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC-C 369

  chr2_101954434_   1859 AAG-CAATTCAATGGAGAAAGGTTAGTCTTTTTAATGAATGCTGCTGCAA 1907
                            - v         i     iv         i  ii    v     vi 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_101954434_   1908 CAACTAGATATCCATAGGCAAAAGAAAATAAATCT--ACACAAACTTTGA 1955
                              i    ?   i v         -- i  vi --  v vv  i iiv
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAA--TGAAGTTGGACCCCTACCTCAC 467

  chr2_101954434_   1956 AACTTTCACAAATATCAATTCAAAATGGATTGTGGACCTAAATGTGAAAC 2005
                          v v vi     v  i  i           ii?i           i i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_101954434_   2006 ACAAAGCTGTAAAGCAGATTCTAGAAGGTAACAGAAGA--AAATCCAAGT 2053
                         vi   i  i    i --- ii      iv    v i ?--     ivv  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAAC---TCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_101954434_   2054 GACTCTGGATTTGGCAATGACTTTTTAGATACAATACCAGAAGCACAATT 2103
                            ii   i  v       ii  i       ii i    i        vi
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_101954434_   2104 CATGAAAGAAAAAACTAG-TAAGTTGGACTTCACTAAAAT-AAAAACTTC 2151
                         v ii          -   -   i          ii     -        i
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_101954434_   2152 TCTTCTGCAAAAGACATCATTCCACAGCATGAACAAACAAGCCACAAACT 2201
                          v v  v    i    ii  - v v ivi    v i    v     i v 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTAT-CAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_101954434_   2202 GGCAGAAAATATCCGCAAAACACATATCTCATCAGAAACTTAGATCCAAA 2251
                           v         ii     v  i      v  v  ii    iv     i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_101954434_   2252 ATACACGAAGAACTCTTAAAACTCAACAATAAGCAAGCAA-CAATCCAAT 2300
                            i ii           v       i     iv ii   -i  i     
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_101954434_   2301 TACAAAATGGATTAAAGATA-GAAGAAATACTTCACCA--GAAGATATAC 2347
                          ?v       iiv  i   v-   v i i i   v   --          
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_101954434_   2348 AAA-----------CATAAGAAAAGATGTACCATACATCATTAGGAAA 2384
                            -----------  i v         i-i  -      ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGC-TCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (87 / 49)
Gap_init rate = 0.03 (19 / 588), avg. gap size = 1.95 (37 / 19)  


2674 26.68 3.81 2.02  chr2_101991750_101993860      728  1619 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_101991750_    728 TGGAGAGGTGTACCATGTTCATGAGCTAGAGGGCATCAACATAGTAAAGA 777
                             i  i i v           iii i  i i - i  i  v  v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chr2_101991750_    778 TGCCCATTTCCCCTGAATTTGCACATAAGTTTAATGCAA-CTGTATCAAA 826
                           v v  vii   ii    viivi i ii  i  i    - iv       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_101991750_    827 ATGCCAGGAAGATG---TTTTTGTAGATATAGACAAGCTTATTATAAAAT 873
                           v    v----  ---      i   v  v        v  iv      
  L1M4_orf2#LINE/    100 ATCCCAGC----TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_101991750_    874 GAACATGGAAAGGCAAAGGAGCTGGAACTGCTAAAATAATTATAGAAAA- 922
                         vv i       v    i   v ii   iv  i    i   iv ii    -
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_101991750_    923 AAGTATAAAGT------AC-CA-ATTTATCTGATTTTAAGACTTTCCATA 964
                            v i     ------  -  - i  -i ii    i  i    v i i 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACA 244

  chr2_101991750_    965 TAGCTATAGTCATCAAGACAGTGTGTTGTTGACATAGAAATTGACACA-- 1012
                         v     i   v              v ii  i    iii  v    i --
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_101991750_   1013 GATCAATGGGACAGGATAGACAACCTAGAAATCAAGTCACACAATTATAA 1062
                                  i i  i  v  v ii i      v  vi  i   v    --
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT-- 342

  chr2_101991750_   1063 CTGCCCAACCTATTTTTGACAAATGTACTAAAAACTGTGCAATAATGGAA 1112
                         -- vi   iiv     i     iv  i i  i - ii v    iiv i  
  L1M4_orf2#LINE/    343 --GGTCAATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAA 389

  chr2_101991750_   1113 ACATACCCTTTTTCAACAAATGGTGCTAGAAAAACTGGACATCCATAGGC 1162
                         iv   vi     -              i i v       i ?   i v  
  L1M4_orf2#LINE/    390 GAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_101991750_   1163 CAAGAAAAAAAAATT---CTCAAACAACCACACTGCTTATACAAAG-TTA 1208
                         -  i i  vi  i  --- i --- v   v   vv v        i-   
  L1M4_orf2#LINE/    439 -AAAAGAATGAAGTTGGACCC---CTACCTCACACCATATACAAAAATTA 484

  chr2_101991750_   1209 ACTCAAAATGTATTGTGAATGTGTACATAAAACATAATATAACAATACTT 1258
                                   v  ii?ii iv iv ii   i vv   v iv i  v   i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_101991750_   1259 TTAGAAGAAAATATAGGAGAAAACCTTTGAGATCTGGGGCTAGATGAAGT 1308
                                    i     ? v   i   i v  i  v   i   iii v v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_101991750_   1309 GTTCTTAAACATGACACCAAA-GCAGGATCCATGAAAGAAAAAATTGATA 1357
                         v      i i           -   vi v v ii           v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_101991750_   1358 AACTGAACTTCATCAATAT-AAAAACT---GCTCTTTGAGAGACCTTCTT 1403
                           i  i          v  -       --- iv   ii ii   vi v i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_101991750_   1404 AAGAAAG--AGAATACAAACTTCAGAATGGGAGATAATATTTGTAAACCA 1451
                                -- i  v    v iv            v        i   i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_101991750_   1452 TATATTAGGCACAGAATGCATATCTAAAATACATAAAGAACTCT------ 1495
                              iv ii vi i ivii    i i    i            ------
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_101991750_   1496 -CAACAGTAAAAA-ACACCTAACATCCAGTTAGAAAATGGGCAAAAGACA 1543
                         -   i i      -   vv    --   i  ?i            i  iv
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAAC--CCAATTWAAAAATGGGCAAAGGATT 832

  chr2_101991750_   1544 TGAAGAATCATTTAACCAAAGAAGATATACACATGGCAAATAAGCACATG 1593
                             v iv     vv                v     v            
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_101991750_   1594 AAATAAGGTTTAATATTATCAGCCAC 1619
                            vi v i i  i  i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (147 / 87)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.17 (52 / 24)  


3010 25.31 2.45 1.23  chr2_102113770_102116865.rev     1708  2604 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_102113770_   1708 TGGAAAAACATTCTATGCTCATGGATAAGAAGAATCAATATCATTAAAAT 1757
                               i i  i i   i        vi     v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_102113770_   1758 GGCCAAACTGTCCAATGCAATTTATAGATTCAATGCTATGCCTATTAAAC 1807
                            v v   vi    vvii  i  i        i  v  v     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_102113770_   1808 TGCCATTGACATTATTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 1856
                          v   vivi v  v  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_102113770_   1857 ATGGAA-TCCAAAAAAAGCCTGAATAGCCAAAACAATCCTAAGCAAAAAG 1905
                               - v   iii v-  v                 i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_102113770_   1906 AACGAAGCTGGAGGCATCACACTTCCCAACTTTGAACTATACTACAGGGC 1955
                            i   i      vv             i  ii  viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_102113770_   1956 TACAACAACCAAAAC-GCATGGTACTGGTACAAAAACAGACACATAGATC 2004
                             ii  i   i  - ii         i i  ii i     i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_102113770_   2005 AATTGAATAGAATAGAGCACCCAGAAATAAGACCATACACCTACAACTAT 2054
                            v         v   vii          iv       ii  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_102113770_   2055 TTGATCTTCAACAAACCTGACAAAAACAAGCAATGGAGAAAGGAC--TCC 2102
                              i   i    ivv  v   i v  vv      i     i i--  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_102113770_   2103 TTATTCAATAAATGGTGATGGAATAA-TGGCTAGCCATATGCAAAT---T 2148
                           --    i        v   i i  -   v  ?   i       v--- 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_102113770_   2149 AAAACTGGACCCCTTCCTTACACCATATACAAAAATTAACTCAAAATGGT 2198
                         i  ii         v   i                              v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_102113770_   2199 TTAAAGAGTTAAATGTAAACCCCAAAACTACAAAAACCCTGGAAGACAAC 2248
                          i ?   vi         ivv i       i    vi i i     v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_102113770_   2249 CTAGGCA-ATATCATTCAGGATATAGGCATGGGAAAACATTT------TA 2291
                         v    ?i- v   -   iv  iv v  vv i  v  vvi   ------  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_102113770_   2292 TGACAAAGATGCTAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATTG 2341
                              ------ i       vvv          v      v  i      
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_102113770_   2342 AATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAG 2391
                         i ii v  i   v v  i i   i  ii vv    i  v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_102113770_   2392 AGTAAACACACAATCTATAGAATGGGGGAAAAATTTTGAAAACTATGCAT 2441
                            i  v v    i i i        i     vv    v   ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_102113770_   2442 CTGACAGAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTAC 2491
                             i ii  v  vi       v  v     i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_102113770_   2492 AAGAAAAAACCAA----CCCCAT-AAAAAGTGGACAAAGGACATGAAAAG 2536
                           v     iv   ----   v  -?    i   i       iv    v  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_102113770_   2537 ACACTTTTCAAAAGAAGATATACATGCAGTCAACAATCATATGAAAAAA- 2585
                            i  i  v              viii i   i  v  i       i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_102113770_   2586 GCTCAACATCACTGACTAT 2604
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (133 / 90)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.06 (33 / 16)  


3981 19.98 2.93 0.68  chr2_102152199_102155964     2389  3274 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_102152199_   2389 GAAAGACATCCCATGTTCATGAATCAGAAGACTTAACTTTTTTAAAGATG 2438
                               i              i  ii          iv  v    -    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA-GATG 51

  chr2_102152199_   2439 GCAGTACTCCCCAAATGTATCC-CAGATTTATCACAATCCTTATGAATAT 2487
                            i            vv   i-      i v i      i   v  v  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_102152199_   2488 CCAAATTGCCTTTATTGCAGAAATTGAGAAACTGCTCATAAAATACACAA 2537
                           v ii       v             v  i   v  v      v  i v
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_102152199_   2538 GGAAATGCAAAGGATGGAGAATATCCAAAACAATCTTGAAAAATAA---C 2584
                                   i   ivv      v                   v  --- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_102152199_   2585 AAAGTCA-ATGACTTACACTCCC--ATTTTAAAACTTACTACAAAGCAAC 2631
                              ii- v    i     i  --    i                 v  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_102152199_   2632 GGTATCCAAGACAGTAGGATGTTCTCA-GAGTATAAATATAAAAATCAAT 2680
                         i   vi         iv i ii vv  -i  v   i i   v i      
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_102152199_   2681 AAAAATAGAATTAAGAATTCAGAAATATGCCCTTACGTTTATGGTCAATT 2730
                         ii  -       i   i i        vi   v   i             
  L1M4_orf2#LINE/    302 GGAA-TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_102152199_   2731 GGTTC-CAAGAAAGATGCCAG--CAATTCAGTGGGGGAAAGAATAATCTT 2777
                          i  i- i v  i i     i-- v     i     -        i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTT 399

  chr2_102152199_   2778 CTTAATAAAAGGTGATGGGACATCTGGATATCCACATGTGAA-GAAAAAA 2826
                         i i  i   v    v       v       ?       ii  -   vi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_102152199_   2827 TTTGCATCTCTATCTCATACTGTACACAAAAATTTACTCAAAAAGCAATC 2876
                         v   v i i   i    i  ii  i         v        v -i   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG-GATC 498

  chr2_102152199_   2877 ATAGAACTAAACGTATGATCTAGAACTGCAAAACTCTTAGAAGGAAATAT 2926
                          ?   v     i   v  v   i    ii              i   i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_102152199_   2927 AAATATAAATCTTTGTGACCTTGAATTGGGCAATGCTTCCTTAAGTAT-A 2975
                          ii?i        i         ii  i       v  i    ii   - 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_102152199_   2976 CAGCGCCAGAGCACAAGCAACAACA----AAATAGATAA-TTGCACTTCA 3020
                           v i-- i              v ----          -   v      
  L1M4_orf2#LINE/    599 CACCA--AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_102152199_   3021 CCAAAATTAAATCCTTTCATGTTTTAAAGTACTCTCTTAAGAAAGTGAAA 3070
                         i          vv    ii  i  i    v  v  v i            
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_102152199_   3071 ATATAGCTCATGGAGTGGGATAAAATATTGGCAAAT----TATCTGATAA 3116
                          v i i i  ii  i     v        v      ----          
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_102152199_   3117 TGAACTTGTATCCATAATATGCACAAATCTCTGATAAATTAACAATAAAA 3166
                         v i           v     ii v i v    v i  v i  i       
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_102152199_   3167 AGACAA----CCCAATTAAAAAGTGAGCAAAAGATTTGAATGGACATTTC 3212
                               ----       ?    i  i     i         i        
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_102152199_   3213 GCTGAAGAAGATAGATAAAGGGTTGCTAAGCACATTAAAAGATGCTCGAC 3262
                         v ii         v i   v  iiiv         v           i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_102152199_   3263 ATTACTGGTCAT 3274
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (109 / 64)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 1.78 (32 / 18)  


1806 30.25 5.66 2.31  chr2_102159465_102161669.rev      852  1717 (488)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_102159465_    852 CATGTTCAATAATTGAAAGATTTGATGTTGTAAAGTTGTCAGTTATTCCC 901
                                 vvi    i    i  i  i    v   v  v  i vv i   
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_102159465_    902 AAATTGATTTATAAATTAATTGCAATCCCAATCAAAATCGCTGTTGG-TA 950
                                 i  i i   v vi        v         v v i  v- v
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_102159465_    951 TTTTGTGGGAATTGACAGG-TGATTTTAAAATTCATATGAAAATATTAAA 999
                              ii i        i -    ii             i    iiv ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_102159465_   1000 TGCAAATAATAGCTATGGCAATCTTGAG---GAATAGTAAAG-------A 1039
                         vi vv v      i vii         i---   v ii    ------- 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_102159465_   1040 CTTACCCTACTAGAT---AGCATTTTATATCAGGGCTATAGTAATTAGGA 1086
                           i  v  v ivi  --- iv i  vv  -  ii    i      i i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTA-CAAAGCTACAGTAATCAAGA 262

  chr2_102159465_   1087 CAGCATTTCAGTGA---AAATTTATACAAACTGGCCAATGCAATAGAATG 1133
                            ii vvi v  i---  ivv  v   v iv ii     v        v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_102159465_   1134 AATAGTCCAGAAAAAGACTCATACACACCTACATAGTTACCTGATTTATG 1183
                         i v          v i  i      ---- vi  i  i vi      vi 
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACA----TTTATGGTCAATTGATTTTCG 358

  chr2_102159465_   1184 CCCAACACGCCACTGA--ACTGAAGAGAGAAAAGAGTATTCATTTCTCTA 1231
                         v v ivii    v-  -- i v  vi i    -  i  v  v    vvi 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAA-GACCATTCAATGGGGAAA-GAATAGTCTTTTCAACA 406

  chr2_102159465_   1232 AATGGCACTGAATCATTTGGATAGTCAAATGGAGAAATGAAAATTGAACC 1281
                              ii   iiv  vi      ?i  v   v i  --   ---    v-
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAA--GAA---TGAAG- 450

  chr2_102159465_   1282 TTGAGCCACTGCTTAATACCATATCCAAATCTTAATT---GTTGGTCTGC 1328
                            ii  v  i i v i       v    vv    i ---iv   viii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_102159465_   1329 AGATCTGAATGTGAAAAGTAAAACAATAAAGCCTTTA-AAGAAATGCACA 1377
                            i  i     i i iv      v     i ii   -      -i  i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA-ACATA 549

  chr2_102159465_   1378 GGAGAAAATTTTTATGACTTTGGAGTAGGCAAATAGTTG-TAAAACA-GA 1425
                           ? v    i  ii    i    iv       - i   v- v i i -  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGA 598

  chr2_102159465_   1426 CACAAAATATTCTAATAATCAAAGAAAGACTATTGATAAAT--------- 1466
                            v   viiv v ii  iv       i v  --       ---------
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTCA 646

  chr2_102159465_   1467 -CAAGGTG---------TGTTCATCCAAAGACACCATTAGGGAAATGAAA 1506
                         -   ii v---------   v v  v  i     i  i i i  i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_102159465_   1507 TG-CAATCCACAGAGTTGAAGCAGGTATTTGGAA--TAGATACTGCTGAC 1553
                         v -   i       i v i  v ii      v  --i v   i--    i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT--CTGAT 744

  chr2_102159465_   1554 AAAGTGTTCTTACCCAGAATGCATTAAAAACCACTGCAAATCAGTAAGAA 1603
                           i vii iv  i       ii  v  i   ivi i   v   i   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_102159465_   1604 AAATCTAGGTAACCCAATAGAAATACAAACAAAAGGTT-GAACTGATCCT 1652
                            vvi ii         v?   v iiii    i i  -   iv  ivi 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_102159465_   1653 TAACAAAAGAAAATATTTAAATGGCCAAAAAATAATTTGAAAAAGTGTTC 1702
                          vv v      i    vi          v  ii -iv      ii  i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCA-CATGAAAAGATGCTC 893

  chr2_102159465_   1703 AACTGCATTAGCCAT 1717
                            vv  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (153 / 105)
Gap_init rate = 0.03 (28 / 895), avg. gap size = 2.46 (69 / 28)  


1637 27.40 10.17 1.41  chr2_102398850_102406728.rev      502  1209 (6670)    L1M4_orf2#LINE/L1      139   908 (0)  

  chr2_102398850_    502 CTAAAGTCTGCATGGCAAAT-TAAAGTCCTGGGAATACCCAAGACATGGT 550
                              i iiii    -    -i  i vv ivi     v    i   vvv 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGG-AAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_102398850_    551 TAAAGAAAAAGAACAAAGTCAGAGAACTTACACAACCTGACCTTAAGACT 600
                          i  i  i           ii   i   i    vv  ii ii i  i   
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_102398850_    601 TAATATAAAAGCTACCATAGTGAAAACAGTGTGGTATGGGCATAAAGACA 650
                           v  i   -     vi  i v  i           iv       i  i 
  L1M4_orf2#LINE/    238 TACTACAAA-GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_102398850_    651 GACATGTTGATCAA------AGAAGAGAGAGTCCAGAAGTAGACTCAAAA 694
                              i v      ------    vv            i  i  i  v v
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_102398850_    695 ATATATAGTAAATTGATGTTTGATTAAAGTGCCAACATAAGTTTATTGTG 744
                           v   i  v       v  i  iv ii       v iv -  i v  v 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGG 385

  chr2_102398850_    745 AAAAACACTGCCTT--CGACACATAATGATAGAAAAATTGACTCTCTATG 792
                         i   iv iv i   -- i   v  ii  v i i v  i  iv v? i ii
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_102398850_    793 TGAAAAAG-------------CTCTACCTCATATTATACAGAAAAATGAA 829
                           v     ------------- i        i ii   i v      v  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_102398850_    830 ATAAAAATGGAT------------TGTA----------TTACATAAC--- 854
                         v v         ------------    ----------i  i v   ---
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_102398850_    855 ------AGAACAT----------CTT---AAACCTGAAGTAGGAACATA- 884
                         ------ i     ----------   ---i v i  iiv    v -  i-
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGG 584

  chr2_102398850_    885 TTTTTTAAATG-GATACAAAAATCACTAATCATGAAAGAAAAA-TAAATC 932
                            i   i  i-  i  v    v   v iiv ii         -  i  -
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT- 633

  chr2_102398850_    933 ATAGCTGGGACTTTATTAAAATTAGAAACTTTTCTTCTTCAAAG-ACATC 981
                         -- iv v      i  i       i        v v        -   ii
  L1M4_orf2#LINE/    634 --AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_102398850_    982 ATTA-GAATTTGAATAGACTAAGCCACAGTCCAG-ACAAAATACTCATAA 1029
                           i -   vv    v    -  v      vvii - v      i iii  
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGAC-AACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_102398850_   1030 TTTGCATATCAGATGAAAGACTTGTATCTATACTTCATAAATAACTCTTA 1079
                         v iii     v   i ii          i v v vi     v        
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_102398850_   1080 CAAGTTCATATGAAAAAGATAAAATAGCCCAATTTTTAAAATGAGGAAAA 1129
                            v iv   vv       i   -  i       ?v-      i v   i
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAA-TAACCCAATTWA-AAAATGGGCAAAG 828

  chr2_102398850_   1130 GACTTGTACTGATATTTCACAAAAGAAAATATATCAATGTTCAATAAGCA 1179
                           i   v iv  i     v v      i     iv    vi         
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_102398850_   1180 CAGGACAAAGTGCACAAAGTTACTAGTTAT 1209
                           v  v  ii   v   vi i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (113 / 79)
Gap_init rate = 0.03 (23 / 770), avg. gap size = 3.57 (82 / 23)  

3149 27.56 0.66 0.55  chr2_102398850_102406728.rev     1993  2899 (4980)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_102398850_   2899 TGGAAGAACATTCCATGCTCATAGGTAGGAAGACTCAATATCATGAAAAT 2850
                              ii i  i     i    i i v        i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_102398850_   2849 GGCCATACTGCCCAAGTTAATTTATAGATTCAATGCCATCCCCATCAAGC 2800
                            v     v     i  i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_102398850_   2799 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2752
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chr2_102398850_   2751 CACAGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGTCAAAAG 2702
                         i ii   viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr2_102398850_   2701 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 2652
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr2_102398850_   2651 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 2602
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr2_102398850_   2601 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATGTCTACAAGT 2554
                                i    i--    i  --        vv iii ii i  iiivi
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chr2_102398850_   2553 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 2504
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chr2_102398850_   2503 CTATTTAACAAAGGGTGCTGGGATATCTGGCTAGCCATATGTAGAAAGCT 2454
                           v  i      v          i v    v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chr2_102398850_   2453 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2404
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chr2_102398850_   2403 TTAAAGACTGAAATTTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2354
                          i ?    iv    v v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chr2_102398850_   2353 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 2305
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chr2_102398850_   2304 AAACACCAAAAGCAATGGCAACAAAAGACAAAGTTGACAAATGGGATCTA 2255
                         vi            vvi           v   i v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chr2_102398850_   2254 ATTAAACTAAAGAGCTTCTGCACAGTGAAAGAAACTACCATCAGAGTGAA 2205
                           i   v v  i i   i  ii vvii  i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chr2_102398850_   2204 CAGGCAACTTACAGAATGGGAGAAAATTTTTGCAATCTACTTATCTGACA 2155
                         v  i    ii                 v       vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chr2_102398850_   2154 AAGG-CTAATATCCAGAATCTACAATTAACTCAAACAAATTTACAAGAAA 2106
                          i  -  vi          v  i  vv     vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chr2_102398850_   2105 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 2056
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chr2_102398850_   2055 CTCAAAATAAGACATTTATGCAGCCAAAAGACACGTGAAAAATTGCTCAT 2006
                            v   v    i  vi viii     v ii   i      iv      v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chr2_102398850_   2005 CATCACTGGCCAT 1993
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


 490 24.87 0.52 8.81  chr2_102427991_102430803.rev     1105  1297 (1516)    L1M4_orf2#LINE/L1        7   183 (725)  

  chr2_102427991_   1105 GATATACCACGTTTACGGATTGGAAGACTTAAGACATCTATTCTCCACAC 1154
                              v   i   i i                ------    v iv v i
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAA------TATTGTTAAGAT 50

  chr2_102427991_   1155 TGTATATTTTTAGACTCTATATATTACAGAATCTATATATTTAATACAAT 1204
                         v i -  ------    ivi v   i----     i v   i  ii    
  L1M4_orf2#LINE/     51 GGCA-AT------ACTCCCCAAATTG----ATCTACAGATTCAACGCAAT 89

  chr2_102427991_   1205 TCA-ATCCAAATCCCAGGAAAATTTTTCAAAGAAATTAAGAAGCTGTTTC 1253
                         i v-   v         vvivv     iiv       i v      v i 
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_102427991_   1254 TAAAATTCATATGAAAATGCAAATAATCTAGGATTGTCCGGACA 1297
                                      i        ivi i i  i  v i vii   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

Transitions / transversions = 1.40 (28 / 20)
Gap_init rate = 0.03 (5 / 177), avg. gap size = 3.60 (18 / 5)  

1567 24.08 6.70 7.25  chr2_102427991_102430803.rev     1591  2321 (492)    L1M4_orf2#LINE/L1      182   908 (0)  

  chr2_102427991_   1591 CAATCTTGACAAAGATGAACAAAGTTGAGAGACTTATACT----GACTTG 1636
                                  v     v           iii    i i   ----i i  v
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_102427991_   1637 AGGATTTATAATAAGGCAATAGTAATTATGGCAATGTGATATTCACAGAA 1686
                          ii i   iv i  i  v i      i v i  i    i  i vi  v  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_102427991_   1687 ACATACAAACATA---CAA---AATAGAA-----AGT--AGACTAATAGA 1723
                         iv   v v i   ---   ---       -----   --   --    i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA--AATAAA 329

  chr2_102427991_   1724 TCCACACATATCTAGTCAATTGATTTTTTTAACAAAG-CACCATGTCAAT 1772
                         i   i    v v i             i--i    i -ii   v v v  
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTC--GACAAGGGTGCCAAGACCAT 377

  chr2_102427991_   1773 TCAGTGGGGAAAAAACAGTCTTTC--ACAAACATTGCTGGAACAGCTGGG 1820
                            i        i  i       i--     iiv      i   i    i
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_102427991_   1821 TACCTCTACAGAAGAAGCAGCAGCAGAAAAAAGAACTTTG-TCCTTGCCT 1869
                           --? i   v-----------   i  i  v   v  v -i  i i   
  L1M4_orf2#LINE/    428 TA--KCCACAT-----------GCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_102427991_   1870 TGTTCTATATACAAGTATCAATTCACAATAGACCATGGACCTAAACATAA 1919
                         iiiv i        iv  i  i   v   i  i  ?i        ii   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_102427991_   1920 AAGCTAGAACCGTAAATATTTCATAAAAATACAGAGAAGACCCTTGAACA 1969
                         i     i   ii    vv i i v  i  v   v  i? -----------
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG----------- 553

  chr2_102427991_   1970 GGCAAAAAATAAATAAATAAATCATGCTCTTGGAC-AGGCAAAAAAAAAA 2018
                         ---------     v-- ---  i  vi     ii-      viiv----
  L1M4_orf2#LINE/    554 ---------TAAATC--T---TCGTGACCTTGGGTTAGGCAATGGT---- 585

  chr2_102427991_   2019 AATTCTTAGCTAGGACACAAAAAA---AAATAGCCATTTGGGACACATTG 2065
                         --       v  v     v    i---  ii i v v--i i v v  v 
  L1M4_orf2#LINE/    586 --TTCTTAGATATGACACCAAAAGCACAAGCAACAAA--AGAAAAAATAG 631

  chr2_102427991_   2066 ATTAATTGGACATCACCAAAATTAAAAA--TGTCTACTAAACAAAGACAT 2113
                           v        v   i            -- v v i  vv -  i    i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACAC 680

  chr2_102427991_   2114 CACTTAAAAA-TGAATAGATAACCC------TGG----AAATATTCTCAC 2152
                         i iiv i   -    v   i     ------   ----       iv  v
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_102427991_   2153 TTTACATCTATCTGGCAAAGAACTTGCATCCACAATACATAAATAATTCC 2202
                         v --   v      ii  i i     i     v    i     v  i  i
  L1M4_orf2#LINE/    731 AT--CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_102427991_   2203 TACACATCAACAATATAAAAAGAAATA---CAATTTAAATA-AGGCAAAA 2248
                             vv    i    v   i v     ---     ?   v -i      i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_102427991_   2249 TATTT---T-GCC--TTCACTAAAAAATATATACGAATGGCCAATGAAAA 2292
                         v    --- - v --   v i   i  v      i          i iv 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_102427991_   2293 CATGAAAAGG-GCTCATCATCATGAGTCGG 2321
                                  i-     v     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (106 / 66)
Gap_init rate = 0.04 (31 / 727), avg. gap size = 3.29 (102 / 31)  


3170 24.35 3.96 1.36  chr2_102501947_102506040.rev     2720  3602 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_102501947_   2720 GAAAG-TATTCTGTGTCCATGGATTGGAAGAATTAATATTGAGAAAATGT 2768
                              -   i ii   i              v         vv  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_102501947_   2769 CCTTACTACTCAAAGTGATCTACACATTCAATGCAAACCCTATCAAAATG 2818
                          vv    v i    v         v      i    v            v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_102501947_   2819 TC-GTTG--TTTTTTACAGAAATACAAAAAACT-ACCCTTAAATTCATAT 2864
                         i - i  --      i       -ii v  i  - i   v          
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATAT 151

  chr2_102501947_   2865 GGAACCACAAAAGACCCCAAATAACCAAAACAATCTTGAGCAAAAAGAAC 2914
                             vii   ii     vi    i               iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_102501947_   2915 AAAGCTAGATGGTTCATACTCCGTGATTTCAAAATATATTGTTAAGCCAT 2964
                             i i  v ii   i   i vii         iv  i iiv    i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_102501947_   2965 TTAAATCAAAACAGCATGGTACTGGCATAAAAACAGACACATGAACAAAT 3014
                         vvv      i    ii              ii i     i  ii iv   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_102501947_   3015 GGAATATGACAGAAAGCCCAGAAAGAAACCCACACATTTATGGTCAATAA 3064
                               vi iv  i  i       v       i               vi
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_102501947_   3065 ATTAAAAAAAAAAAAAAAGATGCCAAGAACACACAATGGGGAAAGGATTA 3114
                            vvvi v  i------ i        v  iv            i  vi
  L1M4_orf2#LINE/    352 ATTTTCGACAAG------GGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_102501947_   3115 TCTCTCCAATAAATGGTGTTAGGAAAACCGGCTATCTACAGGGAGAAGAA 3164
                            i i   i        i i   v   i  v  ? i   v v i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_102501947_   3165 TGAAATTG------TATCTCATAGCACATACAACCCATCAATTCAAAATG 3208
                             i   ------  i    i v  i      vv-  i  i        
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATG 494

  chr2_102501947_   3209 GGTTAAAGAATGAAATAGAAGACCTAAAGTTGTAAAACTTCTAAAAGAAA 3258
                          i i ?   viv    iv    v     ii i       ii  i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_102501947_   3259 ACATAGAGGGAAAGCTCTACAGCACTG--TTATGGGCAAATATTCTTTTG 3306
                               i? v   v  iiiiii vi  --   --     - iv i i  i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTA--GGCAA-TGGTTTCTTA 591

  chr2_102501947_   3307 AATATGACCCTGAAAGCACAGGCAACAAAAACAAAAATAGAAAAATGATA 3356
                         i       v ii        i         iv         v    viv 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_102501947_   3357 TAGCAT-AAAACTAAAAAGCTTCTGTGTAGCAAAGGA------------- 3392
                         ivv   -    i      -   i    ivv       -------------
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_102501947_   3393 -------AACAACCCACCAAATGGG-GAAAATATTTACAAGCTATATATC 3434
                         -------i         vi      -          i   iii       
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_102501947_   3435 TGATAAGGAGTTAATGTGAAGAATATATAAGGAACTCAAACACTGCATTA 3484
                                 iii vi i vv           i      vv   viv  v  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_102501947_   3485 GCAAGAAAACAAATAGCCCATTTTAAAAATAGGCAAGAGACCTGAAAAGA 3534
                         ii  i  i       i    v  ?      i     ii  ii    v   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_102501947_   3535 TATTTCTCAAAAGAAAGGATGCAAATGGCCAACAACTATATGAAAAAATG 3584
                         i       v      iiv  i           i  vi i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_102501947_   3585 CTGAGTATCACTAATCAT 3602
                           v ii    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (137 / 74)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 3.13 (47 / 15)  


2477 25.53 7.18 1.88  chr2_102531621_102536137     3176  4025 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_102531621_   3176 CATGTTTGGTGATACAAAGATTCAACATATTGTCAAATCAACAATCCCCT 3225
                               iivv   vvi    i i  --      i  iviii    v i i
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAA--TATTGTTAAGATGGCAATACTCC 61

  chr2_102531621_   3226 TTACATTGATTAAGAGGTTTAACGCAATTCCAACTGATATTCCAGCAGAA 3275
                         ii v      iv v  i  i        i  v iii v  i     v vv
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_102531621_   3276 TTTTTTGTAGATTATAGGCAAACTAATTCTAAAATATATGTGGGAAAGCG 3325
                                i   v-  v i   i  i  i       vi  i   i  v  i
  L1M4_orf2#LINE/    112 TTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_102531621_   3326 AATAAACTAGAAAAACCAAAGCTAT-TTGGAAAAGAA-AATAAAGTTGGA 3373
                          ivi v i    v i     i v  -   i       -  i         
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_102531621_   3374 GGAGTCATGCTAGACGATTTTATGAATCAATAAAAAGTTACAGCAACCAA 3423
                            v   ii  vvv i    i vi v i v  v    i     i  i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_102531621_   3424 AATGGTGTGATATTAACA-AAG------CA-ATAGATCAATGGAACTGAG 3465
                         i ii     i  i ii  -   ------  -              iv  i
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_102531621_   3466 TAGAAAGTCTAGAAATACATCCACACAAATATGGCCTATTGATTTT-GAC 3514
                          v  i    i       v i   i   vv     i v         -   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_102531621_   3515 AAATTTTCAAAGGCAATTCAAT----AAAGAATAGAGTTTTAAACAAATG 3560
                           ivv v v   i v       ----         vv    v        
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_102531621_   3561 GTTTTGCATCAATTGGACATACATATGCAATAAGATGAAG---------- 3600
                           vi  viv   i    i ?v  i      v ii      ----------
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_102531621_   3601 --CTCACAGCTTATACAAAA-TTAACTTGTAATAGGCCATAGATCTCAAT 3647
                         --      v v         -      iiv   i ii  ?   i  v   
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_102531621_   3648 GTAAAGCCTAAATCTATAAAACTGTTAGAAGAAAACAT------------ 3685
                             iiv     v          v              ------------
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_102531621_   3686 ----GACCTAGGATTAGAAAAAGAGTTCTTAGATGTAACACCAAAAGCAT 3731
                         ----     v  i    iv  v iv         i i            i
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_102531621_   3732 GATCCGTAGAGAAAAAAA-----AAGTTGGAGTTTAACAAAGTTAAAACC 3776
                         i v vii i ii      -----  i     v  i v    i      --
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA-- 658

  chr2_102531621_   3777 ACTTTT-----TCCGAGAAAACCACTGCTAAAAGGATGAAAAAAAAAAAC 3821
                               -----  vi  i ---    iii  i iii      i ----- 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGA---CACTATCAAGAAAGTGAAAAGA-----C 700

  chr2_102531621_   3822 AAGCTTTAAATTGACAAAAATTATTTCAAAATCACAAGTCCAATAAAGGA 3871
                           v ivi i v  iv i   v     vv      i vi  ii    i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_102531621_   3872 CTTGTGCTGAGAGTTTATAAAGATTTCTCTA-AACTCAATAATAA----- 3915
                              iiiv   i v        vi   -  -             -----
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCT-TACAACTCAATAATAAAAAGA 799

  chr2_102531621_   3916 CAAGTAGCTACCAATTAAAAAAGGAGCAAAA-ACTTGAATAGACATTTTG 3964
                            i  i --      ?     v i     i- i              iv
  L1M4_orf2#LINE/    800 CAAATAAC--CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_102531621_   3965 CTAAAGAGGACAGACAGATGGCAAACAGGCACATAAAAAGATGTGCAACA 4014
                          i     i  i v   i     v  i i      i        iv     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_102531621_   4015 GCACCATCCAC 4025
                         v  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.61 (132 / 82)
Gap_init rate = 0.02 (22 / 895), avg. gap size = 3.50 (77 / 22)  


2068 25.58 4.41 5.29  chr2_102569732_102571759      631  1537 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_102569732_    631 ATGTCATATTCATTAAT-GGAAGAGTAAACATTTTTAAGGAATCAGTTTT 679
                           vi   i     vi  -      v v  i   v     iviv  i vi 
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_102569732_    680 CTCCTATTTGATCTATAGATTCAATAAGAGCCC-ATCAAAATCCCAGAAA 728
                          i  v v        i        iivi v   -             vvi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_102569732_    729 ACATTTTAGTAGAAACTGACAAAGCTGATTCTAAAAATCTGTTTGGAAAT 778
                         v v    v i     i      -      i      v  -i v       
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTC-ATATGGAAAT 157

  chr2_102569732_    779 GTGAATGACCTAGATTACATGAAGCAATGTCTAAAACTAAAGAACAAAGC 828
                          ii iv    i   v  vvii  i    v - i   vvi          i
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCT-TGAAAAAGAAGAACAAAGT 206

  chr2_102569732_    829 TGAAAGACTTA----------TTTGATGACTTACTATAATGCCACGATAA 868
                           i i    i ----------   v vi        i  v  i  ii   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_102569732_    869 TTATAATAATTCTACACAAATGACAATATTAATTAAAGAATAGAGATATA 918
                          i vi i i vivii  ---  i  --------   i  -    v     
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTAC---TGGCA--------TAAGGA-TAGACATATA 294

  chr2_102569732_    919 GA-CTATGAAAGAGACTGGAGAGTTTAGAAATAGACTTACATATACATGG 967
                           - v   i  v   v v      ii       i  ii i i  vi    
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_102569732_    968 CCAATTAATTTTTGGCAAAAGAACTAAGGCAATTCAATGG--AAGGCAAA 1015
                         i     i     i i   ii vi i   i v         --  i v v 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_102569732_   1016 GTCTGTTCAACAAATGGTACTGAAA-AACTCTGGTATCCATGTGGAAAAC 1064
                             v             i   ii -    v- i  ?   ii  v    v
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTG-GATAKCCACATGCAAAAG 443

  chr2_102569732_   1065 A-TGAAAATC-ACCCCTAACCTCAAGCCATATTTAAAAATTAACACAACA 1112
                          -    iv v-       -     vi      vi          v   v 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_102569732_   1113 TGTATCATAGATG-AAATGGAAAAGGTATAATTATAAATCTCCTGGAAGA 1161
                           v    ?   iv-     v  i  v  v  i      v   i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_102569732_   1162 AAACATGGAAGTAAAATCTTTATGACTATAG---AAACAAAGACTTTTTG 1208
                               i i?     -    ii    iv i --- ii   v ii  ----
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTT---- 587

  chr2_102569732_   1209 ACCTTGGAGTAGTCAAAAGACAGGAAAAGCACAAATCAAAACACACACAA 1258
                         --   i  -  - -----    vv          ii---    -------
  L1M4_orf2#LINE/    588 --CTTAGA-TA-T-----GACACCAAAAGCACAAGC---AACA------- 618

  chr2_102569732_   1259 AAAAGAAAAAGCA-ATGAATTGGATTTTATCAAAAGAAAAAAAAT--GCT 1305
                         -         ii -  i       i  i       vv     vv -- iv
  L1M4_orf2#LINE/    619 -AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_102569732_   1306 CTTCAAAATGCACAGTCAAAAAAG--------CAAGCTACATA-TGAAAG 1346
                                ivi   vi    i    --------   v i   v -  ii  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_102569732_   1347 AAAACCTTCACTATACATGCATTTCACAAAAGAC----ATAGAGAATATG 1392
                             iv  ii v vv   ii  i v i  ii   ----  vv       i
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_102569732_   1393 GAAATAATTTTAAATAATTTTAGTTCTCAATAAGGGTATAAACAGCTCAA 1442
                         v   v  i i v -i  i i- i ----     iiiv i   i i i   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTA-CAACTC-AAT----AATAAAAAGACAAATAACCCAA 811

  chr2_102569732_   1443 TT-GAAAATAAGAAAAAGATTTGAACAGATACACCATAAAAGATGATATA 1491
                           -i     ii v   i        i   i ivi viv     v      
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_102569732_   1492 CTCATGGTCAGTAAGCACATGAAAATATGCGCAACAT-AGTAATCAG 1537
                          vv    i  i              v    v      - ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.04 (35 / 899), avg. gap size = 2.51 (88 / 35)  


3303 26.87 0.44 0.44  chr2_102641584_102647862.rev     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_102641584_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_102641584_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_102641584_   4980 TACCAATGGCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iiv  i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_102641584_   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_102641584_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_102641584_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_102641584_   5178 AATGGAACAGAACAGAGCTCTCAGAAATAATGCCACATATCTACAACTAT 5227
                                i    iv   vvii         vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_102641584_   5228 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5277
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_102641584_   5278 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5327
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_102641584_   5328 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5377
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_102641584_   5378 AAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5427
                          ?   ii    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_102641584_   5428 AGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAA 5477
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_102641584_   5478 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5527
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_102641584_   5528 AAACTAAAGAGCTTCTGCACAGTGAAAGAAACTACCATCAGAGTGAACAG 5577
                            v v  i i   i  ii vvii  i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_102641584_   5578 GCAACCTACAACATGGGAGAAAATTTTCGCA--TCCTACTCATCTGACAA 5625
                         i     i   iv            v  i   --  v  i--      i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGATAA 746

  chr2_102641584_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_102641584_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_102641584_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_102641584_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2955 25.87 5.08 0.23  chr2_102648582_102651587.rev     1649  2514 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_102648582_   1649 TGCAAAGATATCCCATGTTCATGGATTAGAAGA----ATATTTTTA---- 1690
                           v                        i     ----     v   ----
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_102648582_   1691 --TAATAT---CCATAGGGATCTACTGATTCAATGCAATTGTTATAAAAA 1735
                         --i    i---   v vv       v       i     ivi   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_102648582_   1736 TACCAAAGACATTCTTCACAGAAACAGAGAAAAAAACCTTAAGATTTATA 1785
                          v   ivvi v  i  ii      iv  v  ivvi i i   i   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_102648582_   1786 TGGAACCACAAAAGACTCCAAATGACCAAAGCAATTTTGAGCA-GAAAAG 1834
                              vii   ii   i vi   ii     i    i    iv -   i i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_102648582_   1835 CAAAGTTGGAAATATCACTTTACCTGACTTCAAAATATACTACAAAGCTA 1884
                                   iivv    vi v  ii i       iv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_102648582_   1885 TAGTAACCAAAACCGCATAGTACTGGCATAAAAACATACACACAGACCAA 1934
                         i     i   i  v ii i            ii i v   i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_102648582_   1935 TGGAACAGAATAGATAACCCAGAAATAAATTCACATATTTATAGCCAACT 1984
                              i     v  v ii           ii  i i      i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_102648582_   1985 GATTT-CAACCAAGGCATCAGGAATGTAAAGTGGGGAAAGGACAGTCTCT 2033
                              - i  v i  iii  i  vii vv i         i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_102648582_   2034 TCAATAAATAGTGATGGGAAAACTGGATATACACATAAAGAAGAACAAAA 2083
                             i    i   v     v         ?v     iv i     ii  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_102648582_   2084 CTAGACCCATATCTCTCACCATATAAAAAAATCAATTCAAAATGGACTTA 2133
                         i i     v  i   v         v      i  i          iiv?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_102648582_   2134 AGACTTAAATGTAAG-GCTGAAACCTATGAAGCTTCTAGAAAAGAACATA 2182
                             i          -   i    -   i  i  ii     i i      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAAC-TATAAAACTCTTAGAAGAAAACATA 549

  chr2_102648582_   2183 GGAG-AAATACTTCAGAATATTGATTTGGGCAAAGAATTTTTGGATAATA 2231
                           ? -    -    ivi iv   iv  i     v iv  i  i    vv 
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_102648582_   2232 CCTCAAAGGCATAGGAAATGAAAGCAAAAATAGGCAAACAGGATTATATC 2281
                          vi    i   i i v  ii    v        ii   iv   i vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_102648582_   2282 AAACTAAAAACCTTCTGCACAGCAAAGGAAA--A--AACAGAATGAAGAG 2327
                            v v    v   i  ii vv       v -- --  v i i    i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_102648582_   2328 ACAATCTA---AATGGGAGAAAATATTTTCAAATTATCCACCTAA-AAGT 2373
                             i i ---                 v     i  vi i  i -   v
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_102648582_   2374 GATTAACCTCCAGAATACATAAGAAACTCAAACAACCCAACAACAAAAAA 2423
                           i viiv         i    ii     vv     i   i  i     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_102648582_   2424 GCAAAAAATTCTAATTAAAAATGGGCAAATAATCTGAATAGA-------- 2465
                         i    v  ii v v ?             vi  i        --------
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_102648582_   2466 -----------TACAAATGTCCAGTATGTATATGAAAAAATACTGAGCTT 2504
                         -----------        v   i  v i i       i  i  v i v 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_102648582_   2505 CACTAATTAT 2514
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.97 (146 / 74)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.29 (46 / 14)  


2665 26.93 0.64 0.52  chr2_102700548_102702311      497  1272 (492)    L1M4_orf2#LINE/L1      132   908 (0)  

  chr2_102700548_    497 GCT-ACTTTAAAGTTCATATGGAACCAAAAAAGAACCCACATTGCCAAGT 545
                            - iii    i           viiv  ii  v  viv  v     iv
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr2_102700548_    546 CAATCCTAAACCAAAGGAACAAAGCTGGAGGCATCACGCTACCTGACTTC 595
                              i i  vv i i        i      vv    i  v  ii i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_102700548_    596 AAACTATACTGCAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCA 645
                            viv    i   i          i   i    ii         i iv 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_102700548_    646 AAACAGACATATAGACCAATGGAGCAGAAC--ACAGCCCTCAGAAATAAT 693
                         ii i           i       ii    i-- v  i  --        v
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAA 329

  chr2_102700548_    694 ACCACATATCTACAACTATCTGATCTTTGACAAACCTGACAAAAACAAGA 743
                         v   i i  i  iiiii vi    i  i     ivv  v   i v  vvv
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_102700548_    744 AATGGGGAAAGGATTCCCTATTTAACAAATGGTGCTGGGAAAACTGGCTA 793
                                    i  vvi  v  i                 v      v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_102700548_    794 GCCATATTTAGAAAGCCAAAGCTGGATCCCTTCCTTACACCTTATACAAA 843
                         ?   i  vi i  iivii   i    i    v   i     v        
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_102700548_    844 AATTAATTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAA 893
                               i    i      i ?    i       v   v       i    
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_102700548_    894 AAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGG 942
                           vi i           v    ?i- v i -   iv   v v  vv i  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGG 578

  chr2_102700548_    943 CAAGGACTTCATGTCTAAAACACCGAAAGCAATGGCAACAAAAGCCAAAA 992
                            v ii   v ivv  vi     i      vvi          vv    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_102700548_    993 TTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAATGA 1042
                          v  i    v   ii v  i   v v  i i   i  ii vv    i-  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GA 677

  chr2_102700548_   1043 -ACTACCATCAGAGTGAACAGGCAACCTACAGAGTGGGAGAAAATTTTTG 1091
                         -    i  vv i      v  i     i     i           v    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_102700548_   1092 CAATCTGCTCATCTGAAAAAGGGCTAATATCCAGAATCTACAAAGAACTC 1141
                            viiiivi      v  i  i  vi          v  i         
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_102700548_   1142 AAACAAATTTACAAGAAAAAAACATACAACCCCATCAACAAGTGGGCGAA 1191
                         vv    v iv i  v     i   v i     v  i? v  i     i  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_102700548_   1192 GGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGACAACAGAC 1241
                             v    i     i     v        i  vi viii v   i ii 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_102700548_   1242 ACATGAAAAAATGCTCATCATCACTGGCCAT 1272
                                  i       v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (121 / 84)
Gap_init rate = 0.01 (7 / 777), avg. gap size = 1.29 (9 / 7)  


3061 25.42 2.58 0.90  chr2_102719346_102725208     4479  5371 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_102719346_   4479 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4528
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_102719346_   4529 GTCTATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4578
                          v v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_102719346_   4579 TACCA-TTGACTTTCTT-CAGAGAACTGAAAAAGACT-ACTTTAAATTTC 4625
                          v   -i  v    i  -    -  i   v  i--  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAG--CTGATCCTAAAATTC 147

  chr2_102719346_   4626 ATATGGAAA--CAAAAAA---AGA-----CAAGACAATCCTAAGCAAAAA 4665
                                  --   iii ---   -----   i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_102719346_   4666 GAACAAAGCTGGAGGCATTATGCTACCTGACTTCAAACTATACTACAAGG 4715
                                 i      vv i ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_102719346_   4716 CTACAGTGACCAAAACAGCATGGTACTGATACCAAAATAGGTATATAAAC 4765
                                i i   i    ii        ii iv ii    ii     i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_102719346_   4766 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 4815
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_102719346_   4816 TCTGATCTTCGACAACCCTGACAAAAACAAGTAATGGGGAAATGATTCCC 4865
                         vi    i        vvv  v   i v  vvi          vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_102719346_   4866 TATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACTG 4915
                          v  i  i   i          v      v  ?   i   i i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_102719346_   4916 AAACTGGACCCCTTTCTTACACCTTATATAAAAATTAACTCAAGATGGAT 4965
                           ii         vi  i     v    i              i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_102719346_   4966 TAAAGGCTTAAGTGTAAAACCTAAAACCATAAAAACTCT-AGAAGAAAAC 5014
                         i ?  i i   i     i v       i      -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr2_102719346_   5015 CGAGGCA-ATACCATTCAGGACATAGGCATGGGCA---GAACCTTAATGA 5060
                         vv   ?i- v i -   iv   v v  vv i    --- vvi    --  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA--GA 593

  chr2_102719346_   5061 CTAAAACACCAAAAGCAATTGTAACAAAAGCCAAAATTGACAAATGGAAT 5110
                         -  vi            vvv i        vv     v  i    v i i
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_102719346_   5111 CTAATTAAACCAAAGAGCTTCTGCACAGCAAAA---ATTATCATCAGAGT 5157
                         i v  i   viv  i i   i  ii vv    i--- i     vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_102719346_   5158 GAAGAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTCTCCATCTG 5207
                            i  i     i                 v      iviiv vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_102719346_   5208 ACAAAGGTCTATTATCCAGAATCTATAAGGAACTTAAACAAATTTACAAG 5257
                          i  i  v  vv          v     i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_102719346_   5258 AAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATCAACAGATG 5307
                              i     i     v  i?    i            v v  i   ii
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_102719346_   5308 CTTCTCAAAAGAAGACATTTATGTGGCCAACAA--ACATGAAAAAAAGCT 5355
                         i     v        i  vi vi       i  --         i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_102719346_   5356 CATCATCACTAGTCAT 5371
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.82 (31 / 17)  


2263 25.55 4.28 1.82  chr2_102851377_102853045.rev      407  1177 (492)    L1M4_orf2#LINE/L1      119   908 (0)  

  chr2_102851377_    407 CAGAAATTTCTAGAACTAATAAGTAAATTCAGCATATTTGCAGGAAA-GC 455
                                 vvi - i  i  vvvv       ---   -----     -  
  L1M4_orf2#LINE/    119 CAGAAATTGACA-AGCTGATCCTAAAATTCA---TAT-----GGAAATGC 159

  chr2_102851377_    456 AAG----CTA-AACATTTAAAA--ATCTATCGTAGTAGAAAAAC------ 492
                            ---- i -  i vii    --    --i v iv    i   ------
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCT--TGAAAAAGAAGAACAAAGTT 207

  chr2_102851377_    493 -GAAGACTGACACAATCCACCTTCAATACTTACTATCAAGCTAGAATAAC 541
                         -  i    v    vvi   vi     v        iv      v i   i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_102851377_    542 AAAGGAATTGTAGTATTGGTAAAAGAATAAA----TAGATCAATGGAACA 587
                         v   iv v   i   i   i v   i   i ----             i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_102851377_    588 GAAAAGAGAGCCCAGAAAGAGACCTACACAAATATAATCAACTAATCT-- 635
                            vv     i       v i   i i   vv   ii    i i  i --
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_102851377_    636 GACAAAAAGGCGAAGGAAATTCAATGGAGAAAG--TCGTTTTTTCCATAA 683
                              iiiv  v   ivv         i     -- v  i     v i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_102851377_    684 ATGGTGCTGACACAATTGAAAATCCATACGCAAAATAATGAACCTAGACA 733
                                  iv    i  i v ?   i i      v      vi i   v
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_102851377_    734 CAGATCTTACACCTTTCACAAAATTTGACTCAAAATAAATCATAGATCTA 783
                          vv i  i     v vi      v  i         ii    ?   i   
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_102851377_    784 AATGTAAAATGCTAAA-CCATAAAACTCCTTGAAAA-----TAAGGGAAA 827
                                i -      - i         i v   i -----  i ? v  
  L1M4_orf2#LINE/    508 AATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_102851377_    828 CTCTAGGGAATCTTGGGTTGGGTAATGACTTTTTATATACAATACGAAAA 877
                         v   vv vi i        i  i    ii  i   v   ii i  v    
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_102851377_    878 GCATCACCCAAGAAAAAAAACAGAGACAAATTGGACTTTATTAAAATTTA 927
                            iv v v vi   i    v v   i           i  i      v 
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_102851377_    928 AAATTTCTGCTCTGTGAACGACACTGTTAAGAAAATGTAAAGAAAAGCCA 977
                            i  i  iv  vii  v      i i      i  v     v  v   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_102851377_    978 CAAACTGGGATAATTTTTTTTTTAAAAACATGTATCCAATAAAGGACTGG 1027
                           i v     v  vv v   vi--   v   i    ii    i     v 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGC--AAATCATATATCTGATAAGGGACTTG 754

  chr2_102851377_   1028 TACTGAAAATACGCAAAGAAATCTTAAAATTCAAGAATAAAAAACCAAAC 1077
                           iiv i    iii      v     v  i    v        iv    i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_102851377_   1078 AATCCAATTAGAAACTGAG---AGAATTT-AACAGAAGCCTCACAAAAGA 1123
                           i      ?i   v  i ---  i    -  i   viii  v v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_102851377_   1124 AGAAATACAGATAGTAAATAAGCATGAGAAAAGATGTTCAACATCATATG 1173
                            v     i  i iv        iiv         i         ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_102851377_   1174 TCAT 1177
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.35 (111 / 82)
Gap_init rate = 0.02 (18 / 790), avg. gap size = 2.61 (47 / 18)  


3103 27.86 0.44 0.44  chr2_102949250_102955651.rev     5002  5909 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_102949250_   5002 TGGAAGAACATTCCATGCTCATGGCTAGGAAGAATCAATATGGTGAAAAT 5051
                              ii i  i     i      v v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_102949250_   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCATCAAGC 5101
                            v     v     iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_102949250_   5102 TAGCAATGACTTTCTTCACAGAA-TCGGAAAAAACT-ACTTTAAAGTTCA 5149
                          vv  iivi i  i  ii     - i -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_102949250_   5150 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_102949250_   5200 AACAAAGTCATAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5249
                                 iiv   vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_102949250_   5250 TATAGTCAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5299
                           i   v v   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_102949250_   5300 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 5347
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_102949250_   5348 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5397
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_102949250_   5398 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5447
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_102949250_   5448 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5497
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_102949250_   5498 TTAAAGACTTCCATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5547
                          i ?    i vv    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_102949250_   5548 CTAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAA 5597
                         v    ?i v viv   iv   v v  vv i i   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_102949250_   5598 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5647
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_102949250_   5648 TCAAACTAAAGAGCTTCTGCAGAGCAAAAGAAACTACCATCAGAGTGAAC 5697
                              v v  i i   i  iivvv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_102949250_   5698 AGGCCACCTACAGAATGGGAGAAAATTTTCGTAACCTACTCATCTGACAA 5747
                           i v   i                 v  i i  vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_102949250_   5748 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5797
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_102949250_   5798 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5847
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_102949250_   5848 TCAAAAGAATACATTTATGCAGCCAAAAGAGACATGAAAAAATGCTCATC 5897
                           v      v i  vi viii     v iiv         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_102949250_   5898 ATCACTGGCCAT 5909
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (142 / 107)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2300 24.85 3.20 9.59  chr2_103108068_103112391.rev     2863  3832 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103108068_   2863 TGGAAAGATAGCCTATGTTCACAGATCAAAAGAATTAATATTTTTAAAAT 2912
                                   v  i       ii   iii    v        v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103108068_   2913 GTT--CACTACCCAAAGCAATTTACAGATTCAATGTAATCTCTATCAAGA 2960
                          vi--i   v      vii  i           i i    i       i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103108068_   2961 TTCCAATAGCATTTTTCAAAAAAACTTTTTAAAAA----ATTCTAAAATT 3006
                          i   iiv  v     iiv i   ----  i v  ----  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA----TTGACAAGCTGATCCTAAAATT 146

  chr2_103108068_   3007 CATATGGAACCAGAAAAGACACAGAATCACCAAAGTCATCTTCGGCAAAA 3056
                                  viiv  ii   v      vi     iiv     viiv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_103108068_   3057 AGAGCAAAGTTGGAGGTATCACATAACCTGATTTCAATATATAATATAAA 3106
                            i            vv     ivv  ii       v iv  v  i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_103108068_   3107 GCTATAGTATTTAAAATAGTATGATACCAGCAT--GAACAGACATACAGA 3154
                             i    v i  i i   i  i   ii    -- i i       i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_103108068_   3155 ACAATGGAACAGACTAGAGAACTCAAAAATAAGCACATGCTTTTGTGGTC 3204
                         v        i   v v    iii  i      i v   i v   i     
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_103108068_   3205 CACTGATCATTGGCAAAAATACCAATAACACACA-TGGGGAAAGGATTAT 3253
                         v i    iv i i   iii i    v v  iv  -         i  vi 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_103108068_   3254 CT---CAATAAACTGTGGTGGG-CAAATGAGTGTTGGGAAAGCTTAAAAG 3299
                           ---   i   iv   v    -   v  ii i?iviv v-  --     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-GC--AAAAG 443

  chr2_103108068_   3300 AATGAAATCGAACTCTTATTTCATACCATACACAAAAATCAACTCAAAAT 3349
                               i i i  i i  ii   i      i        i          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_103108068_   3350 AGATTTAAGACTTAAATATAAGATCTTTAGCTGCAAAACTACTAGAAGAA 3399
                         i   iv?    i     i     v  vv i  ii      vi        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_103108068_   3400 AACTTTTGAAAAAAGCTTCTTAATATTGGTCTGGGCAATGATTTTTTTTT 3449
                            v vv ?iv   v    v i iv    vi i       i   i  ---
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--- 590

  chr2_103108068_   3450 CTTTTTTTTATTTTTATACTTTAAGTTCTAGGGTACATGGATGAAGCTGG 3499
                         --------- v----   --- i vvi v ii i   -------   viv
  L1M4_orf2#LINE/    591 ---------AG----ATA---TGACACCAAAAGCACA-------AGCAAC 617

  chr2_103108068_   3500 AAACCATCATTCTCAGCAAACTATCGCAATGGGCAATGATTTTTTTTTTT 3549
                            -----------  v   -------   i ii  --------------
  L1M4_orf2#LINE/    618 AAA-----------AGAAAA-------AATAGATAA-------------- 635

  chr2_103108068_   3550 GGATTAGATCTCCAAAGCATTGGCAACAAAGCAAAACTGGACAAATGAGA 3599
                         --   i  ii  ------  -----------     i --------- i 
  L1M4_orf2#LINE/    636 --ATTGGACTTC------AT-----------CAAAATT---------AAA 657

  chr2_103108068_   3600 AGCTTCTGCACTACAAAGGAAACAATCAGTAGAGTGAAGGGA-------- 3641
                          i   i  ii  v       v  v    iv i      ii  --------
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_103108068_   3642 ---ATGGG-TAAAATATGTATAAACTATACATCTCACAAGGGTTTAATAT 3687
                         ---     -v       v ii   ii   i    v i     vi vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_103108068_   3688 CCAAAATATAGAAGGGACTC----AGCTCAATAACAAGGAAACAAAGAAC 3733
                            i      v  i i    ---- i        i  ii i     v   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_103108068_   3734 TCAATTAAAAAACAGGCATAGGACATGAATATAAATTGTCTAAAAGAAGA 3783
                         i     ?     ii    v    iv      v v   viiiv        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_103108068_   3784 CATACAAATGGGCGGAAAGTA--TGACAAAGTGCTCAATGTCACTAATCA 3831
                         i          v iiv   i --   v  ii       ii   ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_103108068_   3832 C 3832
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.89 (155 / 82)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 5.39 (124 / 23)  


3175 24.92 1.54 1.76  chr2_103124698_103128918.rev     2823  3729 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_103124698_   2823 AAAAAT---CCATGTTTATGGATTGGAAGAAGCAATACTGTTAAAATTTC 2869
                            i  ---       i             vvi    i      i  vv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_103124698_   2870 CATACTACTCAAAGCAATCTACAGATTCATTGCAATTGCTACCAAAACAC 2919
                         v     v i    vii             vi     iv   i     iv 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_103124698_   2920 TAGTGACATTCTTCACAGAAATAGAAATAAC-AATTCTAAAATTTATGTG 2968
                         i  ivi v  i  ii       v  v - i -i  i        i  i  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATATG 152

  chr2_103124698_   2969 GAACCACAAT--ATTCTGAATATTCAAAGCTATCATGAGCAAAAAGAAAA 3016
                            vii   v-- ii v     vi    i v   v   ---       i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAAGA 199

  chr2_103124698_   3017 A-AAAATTGGAGGATTCACATTACCTGACTTCAAATAATACTACAGAGCT 3065
                          -   i        i     i v  ii i      vvv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_103124698_   3066 GTAGGAACAAAAACAGCATGGTACAGGCATAAAAAATAGACACACAGACC 3115
                         ii  v  iv  i    ii      v       ii -      i i   i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATC 298

  chr2_103124698_   3116 AGTAGAACAGAATAGAGAACCCAGAAATAAATCCAAACATCTACACTGAA 3165
                          i i   i     v    ii           i   v    i  iiv v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_103124698_   3166 CTTCTTTTTGGCAAATGTGCAAAGAACATACACTGGG-AAAGGACAATCT 3214
                         i vv    i i   iv    v    v   v  v    -    i i i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_103124698_   3215 CTTCAATAAATGGCGCTGAGAAAACTGAATATCCATGTGCAGAAGAATGA 3264
                         i     i      i    i  v     i   ?   ii    i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_103124698_   3265 AACTAGACTGCTATCTCTTGCCATATACAAAGAAAGAAATCAAACCAAAA 3314
                          ii i   iv   i   vii           ------   i  vi     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAA------AATTAACTCAAAA 492

  chr2_103124698_   3315 TGGACTAGAGACTAAAATGTAAGACCTCAAACTATGAAACAACCATACGA 3364
                             ii ?    iv          v  v       i    vvii v v  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_103124698_   3365 AAACATTGGGAAAACTTTCCAGGACATTGGAGTAGGCAAAGATTTCTTCG 3414
                               v  ?iv  v i i iv   v    iv       v i      v 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_103124698_   3415 GTATTATCACACAAGCACAGGCAACCAAAGCAAAAATGGATGCGTGGGAT 3464
                         i   v ivv  v       i     v    v      i   ivi v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_103124698_   3465 CACATCAAG-TTAAAAAGCTGCTGCACAGCAAAGGAAATGATCAACAAAG 3513
                         iv      i-       -  vi  ii vv       v iv     v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_103124698_   3514 TGATGAGATCGCCCACAGAATTGAAGAAAATATTTGCAAACTATCCATCT 3563
                            vi   ivi          v i                ii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_103124698_   3564 GACAAGAAATTAGTAACCAGAATATATAAGGAGCTCTAACACTTCTATAG 3613
                           i   ii i v   v             i  i    v   vi  v   i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_103124698_   3614 GAAAATATTAAATAATCTGATC-AAAAATAGGCAAAATACTTGAATAGAC 3662
                         v    vivi      i ii  i-      i      iv i          
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_103124698_   3663 ATTTCTCAATAGAAGACATACAAATGGCAAACTGGCAAGCAACTG----G 3708
                                v v      i           v  i----     vv  ---- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAAT----AAGCACATGAAAAG 887

  chr2_103124698_   3709 ATGCTCAACACCACTGATCAT 3729
                                   i  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (133 / 90)
Gap_init rate = 0.02 (14 / 905), avg. gap size = 2.14 (30 / 14)  


2565 27.70 2.67 1.67  chr2_103164270_103166724.rev     1085  1983 (472)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103164270_   1085 TGGAAAAACTTTCCATACTAATGGATAGAAAGAATCAATATTATCTAAAT 1134
                               i iv i    ii v      v i    v i      i iv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103164270_   1135 AGCCCTGCTGCTCAAAGCAATTTATAGATTCAACACTATTTTTATCAAAC 1184
                         i  vv i  v i    vii  i  i         i v  iii       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103164270_   1185 TACCAATGAGATTCTTCACAGAACTAGAAAAAAGCT-ATTTTAGAATTCA 1233
                          v   iivivv  i  ii     v v  v  --   -  ii  i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr2_103164270_   1234 TATGGAATCAAAAAAGAGCCCAAATAGCCAAGGCAACCT-AAGGAAAAAG 1282
                                viiv  ii  v  vi         ii   i  -i ii  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_103164270_   1283 AACAAAGCTGGAGGCATCATGCAACCCAACTTCA-----TACTATGTTTA 1327
                                i      vv   ii vv     i    -----     i---- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC----A 244

  chr2_103164270_   1328 TGGCTACAGTAACCAAAACA---TGATACTGG-ACAAAAGCAGACACGTA 1373
                         vi          i   i   ---  i      - i  iiii     ii  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_103164270_   1374 GACCAAGTGAATAGAATAGAGAGCCCAGAAATAAGACCACACACCTACCA 1423
                           i   vv         v     i          iv   i   ii  ivi
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_103164270_   1424 CCAACTGATCTTCAACAAAGTTGACAAAAACAAGCAATGGGGAAAGGACT 1473
                         i   i    i   i    i v  v   i v  vv            i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_103164270_   1474 CCCTATTCAATAAATGGTGCTGGGTTAACTGCCTAGCTATATGCAGAAGA 1523
                         vi  v     i             vi     vv  ? i i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_103164270_   1524 TTGATACTGGACCCCTTCCTTACACAATACACAAAAATCAACTCAAGATT 1573
                         v   vii         v   i    v   i        i       i  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_103164270_   1574 AATTAAAGACT--AATATAAAACCCCAAATTTTAAAAATCCT-GAAGACA 1620
                         i  i ?    i--   i   i v iv   i v     v  i -     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_103164270_   1621 ACCTAGGCA-AGACCATTCTGGACATAGGAACTGGCAAAGATTTCATAAC 1669
                           v    ?i- i i -   vv   v v  iviv     v i    v  iv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_103164270_   1670 AAAGATGCCAAAAGTGATTGCAACCAAAGCCAAAATTGACAAAT--GACA 1717
                         v v  ii       iivvv     v    vv     v  i    --   v
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_103164270_   1718 TCTACTTAAACTTAAGAGTTTATTTACAGCAAAAGAAACTATCAATGGAG 1767
                           - - i   v    i ii  v v i vv    i  v        vii  
  L1M4_orf2#LINE/    644 TC-A-TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_103164270_   1768 TGAACACAAAACCTAGAGAATGGGAGGAAATTTTTGGAAACTATTAAACT 1817
                             v v v    i v          i    v    v   ii  vv v  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_103164270_   1818 GACAAAGAGGTCTAATATCCAGCATCTATAAGGAATTTAAACAAATTAAC 1867
                           i  i -- v  vi       v  v     i   i ivv    v i  i
  L1M4_orf2#LINE/    742 GATAAGG--GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_103164270_   1868 AAGCAAAAATCAAACAACCCCATTAAAAAGTGGGTAAAG----TACATGA 1913
                           vv    iv    i     v   ?    i    i    ---- iv  ii
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_103164270_   1914 ACACTTTTCAAAAGAAGATATACATGTGGCCAAAAAGCATATTTTTAAAA 1963
                            i  i  v              vi       v     i  ----i   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT----GAAA 885

  chr2_103164270_   1964 AG---CTTAGTATCACTGATCTT 1983
                           ---  i ii    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.17 (39 / 18)  


1611 23.99 23.46 1.74  chr2_103181513_103183460.rev      711  1456 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103181513_    711 TGGAAGAGATATTTCATGTTCATGGATT---------------------- 738
                              -      ii              ----------------------
  L1M4_orf2#LINE/      1 TGGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_103181513_    739 ---CAATTCTTTCTAAATT-ATCTACA------ATGGAATCTCGACAAAA 778
                         ---    v  ii i     -       ------ i v    i v iv   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_103181513_    779 ATCGTAGCT--TTTTTTTA---AATTTGACAACCTGAATTTAATATGTGT 823
                            vi    --i      i---  v       v    vii   v  vii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_103181513_    824 ATGGAAAGGCAAAGGTACCAGAATAACCAAAAAAGCCT---AAAGGAAAA 870
                                v    i  vv        i      v ii  ---   i   i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_103181513_    871 GCAAAAATTATAGAACTCATATAACCCAATTTCAAGACTTACTGTAAA-C 919
                         i    i-  iv  i     i ivv           i       ii   - 
  L1M4_orf2#LINE/    200 ACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_103181513_    920 TACAGTTATGGAGTAGGCATGGTATTGGCCAAAGAAGAGATACATAGGTA 969
                               v  vi  vvi ii     i    vv   i v   i i    i v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_103181513_    970 AATTGAACAGA-------GCCCAGAAATAGACCAACACA----------- 1001
                            v   i   ------- i         i   v i   -----------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_103181513_   1002 --GAT-----ACA-----GCCAA-----CTTA-----------------T 1017
                         --   -----   -----     -----i i ----------------- 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_103181513_   1018 TTCTGACAAACGATGCTGGAATAATTGGACGTTCATGTG-----AAATGG 1062
                           iii     i i      i i  i    ii?i  ii  -----i    i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_103181513_   1063 TGCTGA---CATAATTCATTACC-----CAAAA-TGAGCCCAAAATGGAT 1103
                         v i  i--- v  vi   i-   -----     - v i i          
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCAC-ACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_103181513_   1104 TGTAGACCTAAGTGTAAATAAAACACAAAACTATAAAACTACCAGAGGAT 1153
                         ii?        i     i--- i -i              vii   i  v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAG---AGC-TAAAACTATAAAACTCTTAGAAGAA 543

  chr2_103181513_   1154 AACACAGGAG-AAA-CT--GAAACCTTGGGCTTTGTGATAAGTT-TTGGC 1198
                             i   ? -   -  -- vi        i vv ii  iiv  -  i v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_103181513_   1199 TA------CAAAACCA---GCAATTCTTGAAGGAAAAAA---ATAAGTTT 1236
                           ------     v  ---    i----i  i       ---    i  v
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAAC----AAAAGAAAAAATAGATAAATTG 639

  chr2_103181513_   1237 AACTTTCTTAAAAGAAAAAAAAATTATGTG-----AAAGACACT------ 1275
                         i    iv i    vv     v--  v    -----  i      ------
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAAC--TTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_103181513_   1276 ---GTAAAGAGGC--------------------------------CACAT 1290
                         ---  i  i  i --------------------------------  i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_103181513_   1291 TTCTGATAAAGGACTCATATCCAGAGTATATAAGGAGCTCTCAAAACTCA 1340
                         v        i     ii        i       i  i    i v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_103181513_   1341 ACAGTAAGAA----AATAACTCAATTAAAAAATGGGGAAAATATCTGAAC 1386
                          i i   i  ----      i     ?         v   iv  i    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_103181513_   1387 AGGTAAATCATCAAAGAAGATATGGAGATAGCAAATGAACATATGCAAAG 1436
                           ii vv  vi            iv i  i  v   i i  i   v    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_103181513_   1437 ATGTTTA-CATCACTTGTCAC 1456
                            i i -     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.18 (120 / 55)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 5.22 (188 / 36)  


 904 31.69 5.19 1.09  chr2_103258365_103261983     1480  1845 (1774)    L1M4_orf2#LINE/L1        1   381 (527)  

  chr2_103258365_   1480 TGAAGAGGCATACAGTGTTTATTACATGGAAAATTCAG-GTAGAAAAGGT 1528
                           i i  ii  v vi    i  vivv     i i i i-i v vv   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103258365_   1529 GTCAGTTCTCCCCACATTGAGCTCTCAATTTAATGCAATTCCTACCAAAA 1578
                          v  i v       v     v  vivi   i  i     i    i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103258365_   1579 TCCCA-CCAAGGTTTCTGTACACATAGATAAGCTCATTCAAAAGTTTCTG 1627
                              - iivvv   i  i v v  v  i     v  i v   i  iv i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_103258365_   1628 TGGAA-------GGGCACA----AGCTAAAACAATCTTTAAAAAATAATA 1666
                              -------  i v  ----   i           v     i---- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG----A 196

  chr2_103258365_   1667 ATAATAAAATGGGAAGGCTCACTCT-ACAGATATTAAGGGCTACTCTATA 1715
                          v  i   i v   i i     v  -v vi  v i  iivi    vi v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_103258365_   1716 GCTACAGTAGCCAAAGCTATGTGGTATTATCAGAAGGATAAATAAAAAGA 1765
                                  ii   ii vi       i iv  v       i i v v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_103258365_   1766 TTAATAAGACAGAA-----AACCCAGAGACAGTCACACATAAATATGGCC 1810
                          i   iii i    ----- ii     i i iv v  i i vv     i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_103258365_   1811 AACTGACTTTTGACAAATGTGCAAAACCTATTCAA 1845
                           i   i   i     iv    v  iv i      
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

Transitions / transversions = 1.52 (70 / 46)
Gap_init rate = 0.02 (7 / 381), avg. gap size = 3.29 (23 / 7)  

1658 24.81 3.89 1.67  chr2_103258365_103261983     2580  3119 (500)    L1M4_orf2#LINE/L1      306   857 (51)  

  chr2_103258365_   2580 TGGAGTCCAGAGTTCAGAAATAAAGCCACACACTTACAACCATCTGATCT 2629
                          i  i iv     i          v   i   i   iiii  vi    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_103258365_   2630 TTGACAAAATCAACAAAAAACAAGACA-TGGGGAAAGGACTCCCTATCTA 2678
                          i     iiviiv   i -- v vv  -         i ivvi  v ii 
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGA--CCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_103258365_   2679 ATAAATGGTGCTGGGATAACTAGCTTGCCATATGCACAAGACTGAAACTG 2728
                          i              i    i v v?   i     v    v    ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_103258365_   2729 GACCACTTGCACACACCATATACAAAAATCAACTTAAGGCAGACTAAATA 2778
                             v  vv v                  i    i  iiii  ii ? v 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_103258365_   2779 CTGAAATGTATAACCTAAAACTAGCAAAACTCT-AGAAGAAAACCTAGGA 2827
                          iv       vi v         -i        -          v    ?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTA-TAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_103258365_   2828 AGTAG--CATTGTGGACATAAGACCTGGCAAAGATTTCAT-GATGAGGAC 2874
                         -   i-- v i   -  v vi iiiv     v i    v -   - v   
  L1M4_orf2#LINE/    553 -GTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGAC 599

  chr2_103258365_   2875 ACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGAATCTAAT-A 2923
                                   vvv          v      v  i    v i ii v  - 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_103258365_   2924 AAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCAAAAGAATAAACAG 2973
                            i    -     i  ii vv    i  v        i i i i  v  
  L1M4_orf2#LINE/    650 AAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_103258365_   2974 ACAACCTATGGAATGGGAGAAAAATTTTTTGTAAACTATGCATCTGATAA 3023
                               i ii             -- v    i   ii  ii         
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAA--TATTTGCAAATCATATATCTGATAA 746

  chr2_103258365_   3024 AGGTCTAATATCCAGCATCTTGAAAGAACT--TA-AATTTA-CAAGAAAA 3069
                         i  v  vi       v  v vv        --  -  i i -i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_103258365_   3070 AAA----------AATTTAAAAATGGAGAAAGGACATGAAT-GACACTTT 3108
                          i ----------    ?        iv      iv     -    i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_103258365_   3109 TCCAAAGAAGA 3119
                                    
  L1M4_orf2#LINE/    847 TCCAAAGAAGA 857

Transitions / transversions = 1.50 (78 / 52)
Gap_init rate = 0.03 (17 / 552), avg. gap size = 1.76 (30 / 17)  


2712 27.44 3.51 0.57  chr2_103265460_103271129     4297  5178 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103265460_   4297 TGGGAAAATATTCAATGTTCACATATAGGAAGAATCAATATCATTAAAAA 4346
                            i  i    i v       iiv  v      v i     ii    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103265460_   4347 GGCCATGCTGCCCAAAGCAATTTACAG--TCAATGCTATTAGTATTAAAC 4394
                            v  i  v      vii  i     --    i  v  ivv   i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103265460_   4395 TACCAATGACATTCTTCACAGAGGTAGAAAAAACT-ATTTTAAAATTCAA 4443
                          v   iivi v  i  ii    ii v  v  i-  -  ii         v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_103265460_   4444 ATGGAACAAAAAAGAGCCCCA--ATAGCCAAGGCAAACCAAAGCAAAAAG 4491
                               - viv   i v    --        ii   v ivi iv  i   
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_103265460_   4492 AACAAAGCTGGAGCA-TCATGCTACCCGACTTCAAACTATACTACAAGGC 4540
                                i     v -   ii  v   i i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_103265460_   4541 TATAGT------GACAGCATAGTACTGATACAAAAACAGACACATAGAGC 4584
                           i   ------     ii i      ii i  ii i     i     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_103265460_   4585 AGTGGAAATGAATAACGAGCCCAGAAATAAGGCTGCACACCTACAGCTAT 4634
                          i     vv    viv   i          iv iii   ii  ii ii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_103265460_   4635 CTGATATTTGACAAGC-TCCACAAAAACAAGCAATGGGGAAAGGATTCCC 4683
                         i    v  i      v- v -   i v  vv            i  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_103265460_   4684 TATCCAATAAATGGTGCTGGGTTAACTGGCTAGCCATATGCAGAAGATTG 4733
                          v i   i             vi      v  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_103265460_   4734 AAACTGGACCCCTTCCTTACACCATATACAAAAATTAACTCAAGATGGAC 4783
                           ii         v   i                         i     i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_103265460_   4784 TAAAGACTTAAATGTAAATCCCAAAACTATAAAAACCCTGGAAGGCAAT- 4832
                         i ?    i         ivv i            vi i i    iv  i-
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_103265460_   4833 TAGGCAATAGCATTCTGAACATAGGACTGGGCAAAAATTTCATGACAAAG 4882
                             ?ivv iiv   vvi  v v  ii i     vii    v iivv v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_103265460_   4883 ACACCAAAAGCA--ATTTGAACAAAAACAAAAATTGACAGATAGGACCTA 4930
                                     -- vi--       iv      v  i i  v    i v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGC--AACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_103265460_   4931 AGTAAACTAAAAAGCTCCTGCACAGCAAAAGAAACTATTAACAGAGTAAA 4980
                          vi   v v    i  ii  ii vv    i  v     i  v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_103265460_   4981 CAGACAAGCAACAGAATGGGAGAAAAGTTTTGCAAACTATGCCTCTGACA 5030
                         v      v v                vv        ii  iiv     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_103265460_   5031 AAGGTCTAATATCCAGCATCTATAAGGAACTTAAACGAATTTACAAGAAA 5080
                          i  v  vi       v  v     i     ivv  i v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_103265460_   5081 AA------------AATTTAAAAATGGGCAAAGGACATGAACAGACACTT 5118
                           ------------    ?                iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_103265460_   5119 TTC---AAAAGACATACATGCAGCCAACAAGCATACAAATTAAAGCTCAA 5165
                         i  --- i    i     viii     i     i ii  vvi v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_103265460_   5166 CATCACTGATTAT 5178
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.57 (36 / 14)  


3211 27.07 0.77 0.44  chr2_103275042_103281422     4985  5889 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103275042_   4985 TGGAAGAACATTCCATGCTCTTGGGTAGGAAGAATCAATATCGTGAAAAT 5034
                              ii i  i     i  v   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103275042_   5035 GGCCATAATGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5084
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103275042_   5085 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5132
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_103275042_   5133 TATGGAACCAAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCTAAAAG 5182
                                viiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_103275042_   5183 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAA--CTA-TACAAGTC 5229
                                i      vv    i  v  ii i      --i  -     iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_103275042_   5230 TACACTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5279
                             v   i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_103275042_   5280 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCATATATCTACAGCT 5327
                                i    i--    i  --        vv     i  i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_103275042_   5328 ATCTGATCTTTGACAAACCTGACAAAAACAAGCTATGGGGAAAGGATTCC 5377
                          vi    i  i     ivv  v   i v  vv v          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_103275042_   5378 CTATTTAATAAATGGTGCTGGGGAAACTGGCTGGCCATATGTAGAAAGCT 5427
                           v  i  i             iv      v i?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_103275042_   5428 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5477
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_103275042_   5478 TTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5527
                          i ?    i     i v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_103275042_   5528 CTAGGTATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5577
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_103275042_   5578 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5627
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_103275042_   5628 TTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTATCATCAGAGTGAAC 5677
                          i   v v  i i   i  ii vv v  i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_103275042_   5678 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5727
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_103275042_   5728 AGGGCTAATATCCAGGATCTACAATGAACTCAAACAAATTTACAAGAAAA 5777
                         i  i  vi       i  v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_103275042_   5778 AAACAAACAACCCCATCAAAAATTGGGTGAAGGATATGAACAGACACTTC 5827
                          i     i     v  i?    v    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_103275042_   5828 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCGCC 5877
                           v        i  vi viii     v ii          i      iv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_103275042_   5878 ATCACTGACCAT 5889
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


 354 28.97 0.00 0.00  chr2_103351978_103355270     1625  1731 (1562)    L1M4_orf2#LINE/L1        1   107 (801)  

  chr2_103351978_   1625 TAGAGATATACACCATGTTCATAGACTGGAAGACTCGTTATAATTAAGTT 1674
                          i  i v   iv          i  i         iiv   vi     v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103351978_   1675 GTTGATTCACAGAAATTTGATCAATAGATTCCATGCAATCCCTTTGAAAA 1724
                          vii  v v vvv  v      v i      v i         v v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103351978_   1725 ACTCAAC 1731
                         v i  i 
  L1M4_orf2#LINE/    101 TCCCAGC 107

Transitions / transversions = 0.82 (14 / 17)
Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.00 (0 / 0)  

1855 29.64 5.80 1.05  chr2_103351978_103355270     2043  2801 (492)    L1M4_orf2#LINE/L1      114   908 (0)  

  chr2_103351978_   2043 TTTTGTAGCTTTTTAGAAGTTAATTTTAACATT-ATATGGAGAGTCAGGT 2091
                              i  vvv  v v   i i  ii   v   -       i vv  i v
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_103351978_   2092 GACTTACAATATGAAAAAACAACTCTGAAAAAGAA---TACAGTTGAAGG 2138
                            ii v    - vv       iii          ---i v     i   
  L1M4_orf2#LINE/    164 GACCCAGAATA-GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_103351978_   2139 ACTCAAACCATCTAATTTTAAGATGTACTATAAAAATATTGTAATCATTA 2188
                              v  ivi i     i  i iv     i   iv  iv       vv 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_103351978_   2189 CAGTAAAATATTGATGAAATGATGAATACATAAACTGATGGA-TGAAATA 2237
                             ivii  i  iiiv  v   ii i i   i iii     - ii   v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_103351978_   2238 GAGGACCCCAAAATAGACCCATACTAATACAATTTATTGGTTTTTGATAA 2287
                            iii  vi     i        vvv  iii iv    i    i  i  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_103351978_   2288 AAGTGCAAAGACAATTCAATGAAGAAATAATA---TTTTCATCAAAAAGT 2334
                         ii    v     v        ii    v    ---      v    vi  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_103351978_   2335 ATTGGAACAAATTAGTATACATATGTGGAA-AGTAAATTTCAAAAGATAC 2383
                         ii   i    v vii  ?v  i   iii  - i i  v  vi vvvv   
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_103351978_   2384 ATTACACTTTTTATAAAAATTAACTCAAAATGGATCATAGGCTTAAACAT 2433
                         v i    iv v  i                       ?  i i    ii 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_103351978_   2434 AA--------AC-ATA-------TAGTAG----CATAGGAGAAAATCTCT 2463
                           --------  -   -------   v  ----      ? v      ii
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_103351978_   2464 CTAATTTGGCATTTGGCAATGATTTGAGGAATATCACAGTAAAAGCACAA 2513
                         v i ii v vi  v       i   vvvii    v   vi          
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_103351978_   2514 ACTAGAAAAGGAAAACCAAAATTTGATAAATTACACTTGCCCCAGATTAA 2563
                         i v v     i    vi ------        iv    vvi v i     
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATA------GATAAATTGGACTTCATCAAAATTAA 656

  chr2_103351978_   2564 ---CTTTTATTCTGTGAAAGATACTGTTAAGATAATAAAATGATGATTCA 2610
                         ---     i v  vii  i  i   i i    v i i   v  ii ii  
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_103351978_   2611 CAGGCTATTACAAAATATTTACAAATCACTTATCTGATAAAGAA-TTGAG 2659
                            iv ivv v         i       iv          i i -   vi
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_103351978_   2660 TTCATAATATAGTAACAGTCCTTAAAGCTCAACCCTTTGAAG-------- 2701
                          i  v      vv  v iii    v i     ivv vvi   --------
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_103351978_   2702 --CAGT-AAAAAGTGAGAAAAAAATTCTGAACAGGCATTTTACCAAAGAA 2748
                         --  i -?    i  i v   ii   -    i  i     iv        
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATT-TGAATAGACATTTCTCCAAAGAA 855

  chr2_103351978_   2749 GATATATGGAGGGCATGTAAGCATATGAAAAGATGTTCAACATCATAAGT 2798
                               iii v   vvi      i           i         ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_103351978_   2799 CAT 2801
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.02 (16 / 795), avg. gap size = 3.25 (52 / 16)  


2157 25.07 1.47 2.64  chr2_103392460_103394133.rev      501  1182 (492)    L1M4_orf2#LINE/L1      235   908 (0)  

  chr2_103392460_    501 ACTATACTACAGGGCAACAGTAAACAAAACAGCATGGTAATGTTACAAAA 550
                            -       ii  v       v   i    ii     v  vi i  ii
  L1M4_orf2#LINE/    235 ACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_103392460_    551 ATAGACACATAGACCAATGGAACAGAATAGAGAACCCAGAGATAAGGCTG 600
                                i     i        i     v    ii     i    iv ii
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_103392460_    601 TACAACTGCAACCATCTGGTTTTCGA-AAAAAT-CCACAAAAAAAAAAAA 648
                             vi iiiii  vi  i       -  iii -   ----------- i
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA-----------AG 372

  chr2_103392460_    649 AAAAACCAATGGGGAAAGACTC-CCTATTCAATAAATGGTGCTGGGACAA 697
                          vv vi             v v-i  v     i                 
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_103392460_    698 CTGTCTAGCCATATGCAGAAGGTTTAAACTGGACCCACT-CCTTATACTA 746
                            vv  ?   i     i   iv v  ii       -  -   i i  i 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC-CTACCTCACACCA 471

  chr2_103392460_    747 TATGCAAAAATCAACTCAAGATGGATTAAAAACTTAAATCTAAAATCAAA 796
                            i       i       i      i ? i  i     v   i v v  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_103392460_    797 AGCTACAAAAAACCCAGAAGACAACCTAGG--TAATATCATTCTTGTTAC 844
                          i   i    vv ii      v   v    --   -   -   v  vivi
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATC-TTCGTGACCT 569

  chr2_103392460_    845 AGGACCTGGCAAAGATTTTTATGAAAAAGACACCAAAAGCAATTGCAACA 894
                         v  iiiv     v i   i - ii v v             vvv      
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCT-TAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_103392460_    895 AAAACAAAAACTGACAAATGGGACCTAATTAAACCAAAGAGATTCTGCAC 944
                            iv     iv  i    v    i v  i   viv  i iv  i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_103392460_    945 AGCCAAAGAGTCTCTCAGTAGAGTAAACAGACAACCTAGACAATGGGAGA 994
                         vv v  i  vv  v   iv i   i  v        i v v         
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_103392460_    995 AAGTATTTGCAAAC--TGCATCTGACAAAGGTCTAATATCCAG--CATAT 1040
                           i          i-- ii      i  i  v  vi       --i    
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_103392460_   1041 AAAGAACTTCAATAATTTAACCAGCAAAAAAACAAACAACCCCATTAAAA 1090
                                 iiv i  i i  i- ii     i     i     v   ?   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAAT-AATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_103392460_   1091 AGTGGGCAAGGGACATTTAACAGACACTTTTCAAAAGAAAACATACACAC 1140
                          i       i   i-  v  i     i  i  v      i i     v i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGAT-TTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_103392460_   1141 TGCCAACAAGCATATGAAAAAATGCTCAACATCACTAATCAT 1182
                         v     i     i       i             ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (107 / 61)
Gap_init rate = 0.02 (15 / 674), avg. gap size = 1.87 (28 / 15)  


2117 23.79 3.66 7.06  chr2_103450354_103452103.rev      494  1258 (492)    L1M4_orf2#LINE/L1      170   908 (0)  

  chr2_103450354_    494 GAAAAAGCAAAGCCATTCTGAGGAAAAAAAAAAACAAAGCTTGAGGCATC 543
                            v iv    i v  ii   ---    i  i       i v    vv  
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGA---AAAAGAAGAACAAAGTTGGAGGACTC 216

  chr2_103450354_    544 ACATTTTCTGATTTTAAATTATATTACAAAGCTATAGTAATCAAAACAGT 593
                            i  i ii    i   viv  i          i         i     
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_103450354_    594 ATGATACAGGCATAAA-----ACATAAATAGGCTAATGGAACAGAGTAGA 638
                         i  i   v       i-----     --   iii       i   i v  
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATA--TAGATCAATGGAATAGAATTGA 314

  chr2_103450354_    639 AATGCCAGAAATAAACCCGTACGTATAAGGTCAACTAACCTCTGACAAAG 688
                         i vv              i   i v  v      i i ii ii     i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_103450354_    689 TCATAAAGAATACACAATGAAGAAAGGACAGTCTCTCCAATAAATGGTTT 738
                         viiiv    vi iv     ii     i i     i i   i       vi
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_103450354_    739 TGGGAAAACTGGATATCCACA--CAGAAACAATGAAATTGGATCCTTATC 786
                              v         ?     --  -   v      i     i  i  i 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCA-AAAGAATGAAGTTGGACCCCTACC 463

  chr2_103450354_    787 TTACACCATACACACACACACACACAATAAAACAAACAAAA--AACTCAA 834
                          i        i   -----------------------    --       
  L1M4_orf2#LINE/    464 TCACACCATATACA-----------------------AAAATTAACTCAA 490

  chr2_103450354_    835 AATAGGTTAAAAACTTAAACATAAGACTTGACGCTGTAAAACTCCTAAAA 884
                            i i i ? i  i    ii     vi i vi  i        i  i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_103450354_    885 TAAAACATGAGGG-AAAGCTCTACTGGTCTTGG------CAATGAGTTTT 927
                         v       ii ? -   v  iii-  ii     ------     iv  i 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_103450354_    928 TGGACAT---ACCTAAAAAACAGATAACAAATGCAAAAAGAGACAAGTGG 974
                          i  i  ---   v   iv   iii      v v     v   i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_103450354_    975 AACT-----AAAA--AGAAATTCTTA--CAGCAATGAAAATAATCAACAC 1015
                         i   -----    -- i   i i  i-- vv   v i v iv     v v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_103450354_   1016 TATGAAAATGCAACCTATAGAATGGGAGGACATATTTGCAATCCCTTATA 1065
                         vi      vi     i i          i v          vi v -   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-ATA 738

  chr2_103450354_   1066 TTTGATAAGGGATTAATAACCAAAAAATACAAGGACCTCATACAACTCAA 1115
                          i          i vi  v   i  v   i  i  v   v          
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_103450354_   1116 TAGCAAAACAAAACATAACAAAACAAAACAAATAGCAGGATTAATAAATG 1165
                           ii    ----------------- i       i vvi   ? v     
  L1M4_orf2#LINE/    789 TAATAAAA-----------------AGACAAATAACCCAATTWAAAAATG 821

  chr2_103450354_   1166 GGAAAAACACACAAATAGACATTTTTCCAAAGAAGATATATATTAATAGA 1215
                           v   iv ivii           i               i --   i -
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA--AATGG- 868

  chr2_103450354_   1216 TGTCCAAAGAGTTTTTGAAAGGGTGCTCAATATCATTAATCGT 1258
                         ---    vi  iviv     i i       i    ????????
  L1M4_orf2#LINE/    869 ---CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (120 / 58)
Gap_init rate = 0.02 (18 / 739), avg. gap size = 4.56 (82 / 18)  


3313 17.07 3.14 8.06  chr2_103531682_103533941      820  1774 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103531682_    820 TGGAAAGACATTACTCGTTGATAGATTTGAAGGCTCAGGATTGTTTAAAT 869
                                 i  iv vi   v  i    v    i  i iv      v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103531682_    870 AGCAATACCCACCTACTCCAAATTGAT-TAGAGAT----------CTCTT 908
                         i       i ------i          -  v    ---------- i  v
  L1M4_orf2#LINE/     51 GGCAATACTC------CCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_103531682_    909 TTAAAATCTCAGCCTCCTTTTTATCAGAAATTGATAAGCTGATTTAAAAA 958
                          i      i    iv       vv          i        iiv    
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_103531682_    959 TCCATATGAAAATGCAAATGACTCATAATGCTCAAAACAATCTAGTAAGA 1008
                          i      i        iv   i  v   ivi           v -  i 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-AAAA 193

  chr2_103531682_   1009 AGGAAAACAAAATTGGAGAACTCACATTTTCTGACTTCAAA-CTTACTCC 1057
                           i i      i      i       i  i ii i      -      v 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_103531682_   1058 AAAGCTACAGTAATCAAGACAGTGTGGTAATGGCTTAAAGATAGTCATAT 1107
                                                      v    v   i     v     
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_103531682_   1108 AGATCAATGGAATATAATTTAGAGGCCAAATTAAAAACAACAATAACAAC 1157
                                       v    v    v   i -----------     --  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGA-----------AATAA--AC 330

  chr2_103531682_   1158 CAAAGCACTTACAGTTACAGTCAATTTATTTT-GATAAGGGAGTTAAGGA 1206
                          ----  --    v   ii       v     -  i     v ii   iv
  L1M4_orf2#LINE/    331 C----CA--TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_103531682_   1207 AATTTAAGAGAGAAAGAATAATCTTTTCAACCAATGATG-TGTGGCAACT 1255
                         v   i  vi i         i          v    i  -  v i     
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_103531682_   1256 GGATGTCTTTATGAAAAATAGAACAAACAATTAAGTTATACTTGTAATTC 1305
                             i? ivi   v    --   ------- v     iv  iiv  vi  
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAA--GAA-------TGAAGTTGGACCCCTACCTC 465

  chr2_103531682_   1306 ACA--ATAAACAATTAAGTTATACTTATAATTCACATATTCACAAAATGT 1353
                            --   v    --  i   -   -----------------       -
  L1M4_orf2#LINE/    466 ACACCATATACAA--AAATTA-ACT-----------------CAAAATG- 494

  chr2_103531682_   1354 GCAAAAAAAACCTTAAAATGAATACCTAAATATAAATGCTAAAACTAAAA 1403
                         --------i -- i ? i-----        i   iv          v  
  L1M4_orf2#LINE/    495 --------GA--TCAWAG-----ACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_103531682_   1404 AACTCTTAGAAGAAAACA--AGTATCACTCTTGATAATCTTAAATTAGAA 1451
                                           --i ?i v v    vi i i   iii    iv
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_103531682_   1452 AATAGTTTCTTAGATATGACACCAAAAGCACAAGGAACAAAAGAAAAA-T 1500
                            i                              v             - 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_103531682_   1501 ACATAAATTT-ACTTCATAAAAAT-GGAAACTTCGGTGCTGCAAAAGACA 1548
                          v       v-       v     -ii      iv     v    i    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_103531682_   1549 TTATCAAGAAATTCAACAGACAACCCAAATAATGTAATACAATATTTTAA 1598
                         i          v v  v          v v    vi v v       -iv
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GC 728

  chr2_103531682_   1599 AAATCATATATTTGATAAGT--CTAGTGTCTAGAATATATGATGCATACA 1646
                                    i       v--  v  i  i         i v - -  v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG-A-ACT 776

  chr2_103531682_   1647 CTTAC----CCAT--TAAAAAGACAAATAACCCAATTTAAAAATGGACAA 1690
                              ---- v  --                      ?        i   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_103531682_   1691 AAGATTTGAACAGACCTATTTCCAGAAGAGATATACGAATGGCTAATAAG 1740
                          i        i    v v i    i ii        i      i      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_103531682_   1741 GACAGGAAAA-ATGCTCAACAAAGTCATTAAAGAA 1774
                         v   v     -          ---   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACA---TCAZZZZZZZZ 908

Transitions / transversions = 1.34 (91 / 68)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 3.34 (107 / 32)  


3217 25.82 0.65 1.74  chr2_103545898_103551718.rev     4412  5329 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103545898_   4412 TGGAAGAACGTTCCATGCTCATGGATAGGAAAAATCAACATAGTGAAAAT 4461
                              ii ii i     i        v    i v i  i  v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103545898_   4462 GGCTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4511
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103545898_   4512 TACCAATTACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4559
                          v   ii i i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_103545898_   4560 TATGGAGCCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAG 4609
                               iviiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_103545898_   4610 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACCACAAGGC 4659
                                i      vv       v  ii i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_103545898_   4660 TACAGTAACCAAGACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4709
                                 i        ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_103545898_   4710 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCATACATCTACAACC 4757
                                i    i--    i  --        vv        i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_103545898_   4758 ACCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 4807
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_103545898_   4808 CTCTTTAATAAATGGTTCTGGGAAAACTGGCTAGCCATATATAGAAAGCT 4857
                           i  i  i       v      v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_103545898_   4858 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGTA 4907
                            ii    i    v   i     v                   i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_103545898_   4908 TTAAAGACTGAAATGTCAGACCTAAAACGAAAAAAACCCTAGAAGAAGAC 4957
                          i ?    iv      v   v       v v    vi i        i  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_103545898_   4958 CTAGCCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5006
                         v   v?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_103545898_   5007 AAACACCAAAAGCAATGGCACCAAAAGCCAAAATAAACAAATGGGATCTC 5056
                         vi            vvi   v      vv      i i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_103545898_   5057 ATTAAACTGAAGAGCTTCTGCACTGCAAAATAAACTACCATCAGAGCGAA 5106
                           i   v v  i i   i  ii  v    iv v    i  vv i  i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_103545898_   5107 CAGGTAACCTACAGAATGGGAGAAAAGTTTTGCAATCTACCCATC-TGTC 5155
                         v  ii    i                vv       -------   - i -
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAA-------ATCATAT- 737

  chr2_103545898_   5156 AAAATCTGACAAAGAGCTAATATCCAGAATCTATAGAGAACTCAAACAAA 5205
                         ---      i  i ii  vi          v    i       vv    v
  L1M4_orf2#LINE/    738 ---ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_103545898_   5206 TTTACAAGAAAAAATCAAACAACCCCATCAACAAGTGGGCAAAGAATATG 5255
                          iv i  v     iv    i     v  i? v  i         i  v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_103545898_   5256 AACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAA 5305
                           i     i     v        i  vi viii     v ii        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_103545898_   5306 AAAATGCTCATCATCACTGGCCAT 5329
                           i       v     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.20 (22 / 10)  


2178 26.86 9.47 0.60  chr2_103583701_103586084.rev     1059  1892 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103583701_   1059 TAGAGACACATCCCATGCTCATGGATTAGTAGAATCAGTATTGTGAAAAT 1108
                          i  i v i        i         i v   v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103583701_   1109 TACCATACTTTCAAAAACAATCTACAAATTCAATGCAATTCCCATAAAAA 1158
                         vi v     ii v   vii       i      i     i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103583701_   1159 TACCACCATCGTTCTTCACAAAACAAGAAAAAAAAATCCTGAAATTCATA 1208
                          v   v vv v  i  ii  i  vvv  v  ivvi     i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_103583701_   1209 TAGAACCAAAAAAGAACCCACATAGCCAAAGCAAGACAAAACAAAAAGAA 1258
                          i   viiv  ii  v  viv         i   vvivi  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_103583701_   1259 AAAATCCGGAGGCATCACATTACCCGACTTCAAACTAGACTGCAAGACTA 1308
                         v   vii     vv     i v   i i      vivv   i   ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_103583701_   1309 GAGTTACCAAAACAGCATGGCAGTGGTATA-GAACAGTCACATAAACCAA 1357
                         v   v i   i    ii   i v   i   - i i  v  i   i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_103583701_   1358 TGAAACAGAA--GAGAACCCAGAAATAAACCCAAATACTTACAGACAACT 1405
                           i  i    --    ii               v i i   ii v   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_103583701_   1406 GATCTTTGACAAAGCAAACAAAA-CATAAAATGGGGAAAGTACACCCTAT 1454
                            i  i     i vviv   i -   vv           v i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_103583701_   1455 TCAACAAATGGTGCTGGGA------------------------------- 1473
                                            -------------------------------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_103583701_   1474 ------------------------------------------TGGATCAG 1481
                         ------------------------------------------       ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_103583701_   1482 AGAATTAAATCTAAGACCTGAAACCATAAAAATCCTGTAAGTTAACATCA 1531
                            vi     v     v  i    i      v  i iv   vv     - 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-A 549

  chr2_103583701_   1532 GAAAAAAACACTTCTAGATATTGGCTTAGGCAAAGACTTCATGACTAAGA 1581
                          i?iv   i-    vv  iv    v        v ii   v iiv  v  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_103583701_   1582 -ACCGAAAAGTAAATACAACAAAAACAAAGATAAATAGATGGGACTTAAT 1630
                         -   -     i v vi        iv   i   i   i  v      v  
  L1M4_orf2#LINE/    599 CACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_103583701_   1631 TAAACTAAAAAGCTTCTGCACAGCAATGGAAATAATCAGCAGAGTAAACA 1680
                         i   v v    i   i  ii vv   v   v iv    iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_103583701_   1681 CACAACCCACAGAGTGGGAGAAAATCTTCCCAAACCATGCATCTGACAAA 1730
                         v            i           v  iv    i   ii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_103583701_   1731 AGACTAATATCCAGAATATACAA-GAACTCAAGCAAATCAGCAAGAAAAA 1779
                         i    vi             i  -      vvi   v   ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_103583701_   1780 TAAATAAATAATCCCATCAAAAAGTGGGCTAAGAACATGAATTGACAATT 1829
                         --i i      i  v  i?    i     v   i iv     v    v  
  L1M4_orf2#LINE/    798 --GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_103583701_   1830 CTCAATAGAAGATACAGAAATGGCCAACAAATACATGCAAAAATGCTCAA 1879
                            v v        i v          i  ii     v   i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_103583701_   1880 CATCACTAATTAT 1892
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (123 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 8.40 (84 / 10)  


2288 25.69 2.76 3.34  chr2_103607427_103610093.rev     1308  2175 (492)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr2_103607427_   1308 AAAATGACCTTACTGCCCAAAGTAATCAACAGACTAAATGCAATTGCTAT 1357
                           i   i vv    v      v i   v     i v  i     iv    
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_103607427_   1358 CCAAATACCAA-TGTCATTTCTCACAGAATTAGAAAAAGTAATCCTGAAA 1406
                          v    v   i-  i -   i ii     v v  v  iv i     i   
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_103607427_   1407 TTCACATGGAA---CAAGAAAAGTCCA-AATAGCCCAAACAATCCTAAGT 1452
                             i      ---    ii --i   -       v        i i iv
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_103607427_   1453 AAAAAGAACAAA-TCAGAAACCATCACATCATCTAACTTCAAATCATAAG 1501
                           i         - ii  iiv -     iivi i  i      v v  vv
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACT 241

  chr2_103607427_   1502 ACAAGGCTATATTAACCAAAACAGCATGGTACTAGTATAAAAGTTAGACC 1551
                             i    i v   i   i    ii       i i    i- v     v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACA 290

  chr2_103607427_   1552 TATAGACCAATGGAAAAGAATAGAGAGCCCAGAAATAAAGCTGAATTCTG 1601
                               i        v     v     i           v iiv ivi v
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_103607427_   1602 AAAACCAACTGATCTCCAACAAAGCAGGCAA--CTA--CACTGGGGAAAA 1647
                          viii   i    i i i    i vv v   -- i --  v        i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_103607427_   1648 GACACCCTATTCAATAAATGATCCTGGGAAAATTGGATGGCCATATTTAG 1697
                         i i vi  v     i     i v      v  i     i?   i  vi i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_103607427_   1698 AAGAATAAAACTATCTTCTAATATCACTTCTGATATCACTATCACTCATC 1747
                               i  ii i------------------  i-- v   i v v  i 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTG------------------GAC--CCCTACCTCACACC 470

  chr2_103607427_   1748 ATATACAAAAAATTAACTCAAGATGGATTAAAGACTTAAATTTAAAACCT 1797
                                    -         i      i ?    i     v   i v  
  L1M4_orf2#LINE/    471 ATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_103607427_   1798 GAAACCATCAAAATTCT-AGAAGAAACTCTAGGGATAACTCTTCTGGGCA 1846
                         i    i  -    i   -        viv    ?i   v     vv i v
  L1M4_orf2#LINE/    520 AAAACTAT-AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_103607427_   1847 TT---CTAGTGAAGAATTTAT--GACTAAGACTCCAAA-GCAAAGGCAAC 1890
                           ---i   vv  vii   v --  -  v   v     -   v i     
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAAC 617

  chr2_103607427_   1891 AAAAACAAAAATAAATAAATGAGATCTAATTAAACTGGAAAGTTTCTGCA 1940
                             iv       i      vi  ii v  i   v vi   ii  i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_103607427_   1941 GAGAAAAAGAAATGATCACCATAGTAAA----CAATCTAGAGAATCAGAG 1986
                         vvvv   i  v iv    vv v   i  ----   i i v     vi   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_103607427_   1987 AAAATATTTGCAAACTATCCATCCAAAAAAGGACTAATATCCAGAATCTA 2036
                                       ii  vi   ii v  i     vi          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_103607427_   2037 CAAGGTACTCAAAGAAATCAGCAAAAACAAAACAAATAATCCCAATAAAA 2086
                         i  i v    vv v  v   ii  v  v  i        i  v v ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_103607427_   2087 AGTGGACAAATGATATAAAT-GACATTTCTTAAAAGAAGATATACAAATG 2135
                          i   i    v   v i   -         iv                  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_103607427_   2136 GGCAAAAA--AAATGAAAAAAAAGCTCAAGGTCACTAATCTT 2175
                          v   v  -- v       i v-      vi   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (124 / 95)
Gap_init rate = 0.03 (23 / 863), avg. gap size = 2.30 (53 / 23)  


1979 29.25 2.99 1.09  chr2_103611512_103613238.rev      503  1237 (490)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr2_103611512_    503 AAAGGAGCCTGAATAGCCAAAGCAATGTTAAGCAAAAAGAACAAAGCCAG 552
                           i   v  v           i    v  i iv  i          iii 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_103611512_    553 AGACATCACATTGCTCAACTTGAAATTATACTATAAGGCTATAGTATTGA 602
                           ivv     i v i   i  v   viv     i  i    i    v v 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_103611512_    603 AAATAGCATAATAGTGGTACAAAAACAGACACACAGACCAGTGGAACAGT 652
                          i i  ii ii  v   i i  ii i     i i   i  i     i  v
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_103611512_    653 ATAGAGAAGGCAGATGTAAACATGCACAACTACAACCATCTGATCATTAA 702
                           v    ivv    vi     viii   vi  iiii  vi    iv ii 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_103611512_    703 CAAAATCAACAAAAATAAGCAATAGGGAAAAGACTCTCTATTCAATAAAT 752
                            iiviiv   i vi vv    i      ii ivv   v     i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_103611512_    753 GGTGTTGGGATAACTGGCTAGCTGTATGTGGAAGAATGAAACTGGACCCC 802
                             i     i      v  ? iii   iii         ii        
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_103611512_    803 TACCTCTTACCATATATGAAAATGAACTCCAGATGGATTACAGAGTTAAA 852
                               vi        ii     v     v i      i ?   vi    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_103611512_    853 TGTAAGCCCTCAAATTATAAAAATTTTAGAGTAAATCCTAGG---AAATA 899
                               vv  v   i       v i     iv   v v    ---    -
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT- 558

  chr2_103611512_    900 CCCTTTTCAACATATGATTTGGCAAAGAATTTATGGTGAAGTCCCCAAAA 949
                         --   ivii  v vv i  v     v iv  iv i vv v v v      
  L1M4_orf2#LINE/    559 --CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_103611512_    950 GCA---ATGGCAAAAAAACCCTAAAATTAACAAGTGGGACCTAATTAAAA 996
                            ---iiii     i  ----     vi i  i v    i v  i    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAA----AAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_103611512_    997 TAAAAAGCATCTACTCAGCAAAAGAAACTACCAACAGAGTAAA----CAG 1042
                          v    i v i iiv vv    i  v    i   v i   i  ----  i
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_103611512_   1043 CCTACAGAATGGAAGAAAATCTTTACAAAGTATACATCTGACAAAGGTCT 1092
                           i         i       v   i    vi   i      i  i  v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_103611512_   1093 AATGTCCAGAAACTACAAGGAACTTAAACAAATGAACAAATAATAAAGTA 1142
                         vi i       vv  i  i     ivv    v v  i  -   v  iii 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAGACA 801

  chr2_103611512_   1143 A-TAATTAAATT-AAAAATAGGCAAAGGGCATGAACAG-CA-------AA 1182
                          -   iiv    -      i        iiv    i  -  -------  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_103611512_   1183 GGAATACATAAAAGCAGTCAACAA--ACATGAAAATATGCTCAACATAAC 1230
                         i   v i   v  iii i   i  --         v           v ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_103611512_   1231 TAATCAT 1237
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.60 (131 / 82)
Gap_init rate = 0.01 (11 / 749), avg. gap size = 2.73 (30 / 11)  


3434 21.87 3.95 1.58  chr2_103641834_103644078      881  1767 (478)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103641834_    881 TGGAAAGGCATCTCATGTTTATGGTTAGGAAAACGTAAT-TT-TTAGAAA 928
                                ii   i      i    v v    i  v    -  -   --- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA---A 47

  chr2_103641834_    929 TATATAAATACTACCCACAGTAATCTAAAG-TTCAGTGCAACGTCTACCC 977
                         v  ivv      v    v v i     v  -    ii    ivi   i v
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_103641834_    978 AAATTCTAAA-GCTTGCTGAGGAGAAATGAAAAATCTGATCCTCAAATTC 1026
                             i i iv-  i vi vv v      vi v  v        v      
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_103641834_   1027 AT-------------GAGTCCTGAATATGTAAAACAGACATGAAAAAGAA 1063
                           ------------- iii  v     vvi      iv v          
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_103641834_   1064 GAACAAAATTGGATGTCTCACATTTTTCCATTTTAAAACCTATGACAAAG 1113
                                i     v v      i  ii v    i     i  iv      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_103641834_   1114 -TACAGTAATCAAAAGAGTGTGGTACTTTCATAAGAAGGTACATATAGAC 1162
                         -            i v           vv      i viv         i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_103641834_   1163 CAATGAGTTAGAATTGAGAATCCAGAAATAACCCCAGACACATGTGGCTA 1212
                              iiv           i           v    v   iv i   ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_103641834_   1213 ATTGATTTTTGGCAAGGGTGCCAAATTCATTCAATAGGGAAAGTGTGTTT 1262
                                  i i            ivi        i       vi iv i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_103641834_   1263 TTTTTTCAAAAAGTAATGCTGGGGAAAGTGTATTTCAACACATAAAACAA 1312
                             --   v  i ii       iv  v  v  v? v   iii    v  
  L1M4_orf2#LINE/    398 TTTT--CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_103641834_   1313 TGATGTTGGAGCTCTACCTCACCTCATAAACAAAAATTCATTCAAAATGG 1362
                            v      v i         vi    v         v i         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_103641834_   1363 ATCAATGACATAAACATAAAAGTTAAAAACATAACACGTTTAGAAAAAAA 1412
                             ?v   v    ii   i  i     vi    v  vi      i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_103641834_   1413 CATAGAATTAAGTCTTCATAACCTTGGATTTGGCAAT--------AAATA 1454
                              i?v   i     i i       i  v      -------- i   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_103641834_   1455 TGAAACCAAGAACAGGAACAACAAAAGAAAAAGTAGATACAC-GCAATTC 1503
                            v     i i  vi i              i      v i- v v   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_103641834_   1504 ATCAAAATTAAAACTTTTTGTGCATCAAATGACATTTTTAAGGAAGTAAA 1553
                                      vi        v     v    i v i   i    i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_103641834_   1554 AAGAAAACATACAGAATAG------ATGTTTGCAAATTATATGTCTTATA 1597
                             v   vi       i ------  i         i    i   v   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_103641834_   1598 AGGGTCTAGTGTTCAGAATATACAAAGAACTTTTACAACTCAACAGCAGA 1647
                             v  v  i i         i        i           i ii i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_103641834_   1648 AAAACAAAAAACCCAATTGAAAAAAAAAAAACTGGGTAAAAGACA-GAAT 1696
                           i     v         ?     --------    i   i  iv-    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAA--------TGGGCAAAGGATTTGAAT 837

  chr2_103641834_   1697 AGGTAGTTCCCCAAAGAAGATATACAAATGGACAACAAACACATAAAAAT 1746
                           ii v   i                     v   i  i     i    -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA- 886

  chr2_103641834_   1747 AATG-TGAATGTTATTAATCAT 1767
                         i   - v  ii i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (110 / 80)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.27 (49 / 15)  


2722 18.04 1.72 7.16  chr2_103651848_103653593.rev      501  1254 (492)    L1M4_orf2#LINE/L1      196   908 (0)  

  chr2_103651848_    501 AAGAACAGAGTTACAGGACTCCCATTTCCTGATTTCAAAACTAACTACGC 550
                                i    iv       v  i    ii           v     iv
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_103651848_    551 AGCTACAACAATCAAGACAATATATGGTACAGGCATACAGATAAAAGTAT 600
                                ii          i i --     v      vi    i vi   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGT--GGTACTGGCATAAGGATAGACATAT 293

  chr2_103651848_    601 AGAT-AA---AATAGAATTGAGAGTACAGAAAAAAAAAAAACACCTTACA 646
                             -  ---               v      v   ----- -  v    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-----C-CCATACA 337

  chr2_103651848_    647 CGTTTGGTTCAGGTTATTTTGAGACAAGTGTTTAAAGACAATTCAACATG 696
                         iv v    -  iv v     v-      v  viv     v      iiv 
  L1M4_orf2#LINE/    338 TTTATGGT-CAATTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_103651848_    697 AAAA-AATATTGTTTTCAACAAATAATGCTGAGATAACTGGATACTCACA 745
                         i   -    v v            ii     i  i         ?i    
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_103651848_    746 TGAAAAAGA-TGAAGTTGGAACTCTTACATAACAC--TGTACAAAAAGTA 792
                           v      -          - i i   v v    -- i        v  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGA-CCCCTACCTCACACCATATACAAAAATTA 484

  chr2_103651848_    793 ACACAAAACACCTTTAAGATGAACATGTCAGAGATAAAAATACAAAATTC 842
                           v     iivv iv?   ivv v    v    v     v  i    i  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_103651848_    843 TTAGAAGAAAACAAAGGTAAGATGTACATGTCAGAGACAAAAGTATAAAA 892
                                      -------------------------------------
  L1M4_orf2#LINE/    535 TTAGAAGAAAACA------------------------------------- 547

  chr2_103651848_    893 TTCTCAGGAGGAAACCTTCATTATCTTTTGTTAGACAATGTTTTCTAAAA 942
                         ----i   ? v   i    i v i   vv     i     v     v i 
  L1M4_orf2#LINE/    548 ----TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_103651848_    943 TATAGAACCAAAAGTATAAGTAAAAAGAGAAAAAA--AATAAATTGGATT 990
                            iiv        i i   i  v  i        --i          i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_103651848_    991 T-ACTAAAATTTAAAACTTTTATGCTGTAAATTACACTATTAGCAGAGTG 1039
                          - ii      v         i    vi   vv       i iv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_103651848_   1040 AAAAGACAACCCACAAAATAGCAGAAAATATTTAAGAATCATATGTCTGA 1089
                                        i   i v           ivi        i     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_103651848_   1090 TAAGGGAATGGTATTGGCAGTA-ACGGAAAGAACTCTTACAACTCAAAGA 1138
                                v v    i--   v - iiv                    vi 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATC--CAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_103651848_   1139 TAAAAAGACAAATAACC-AATTTAAAAATGGGCAAACGATTTGCATAAGC 1187
                                          -    ?             v      v   ii 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_103651848_   1188 ATTCCTTCGAAGAAGATATGCAAATGGACAATAAACATGTGAAAAGATGC 1237
                            i  i i          i       v      i  ii           
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_103651848_   1238 TCAACATTACAAGTCAT 1254
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (73 / 59)
Gap_init rate = 0.02 (17 / 713), avg. gap size = 3.94 (67 / 17)  


2258 23.14 1.26 13.36  chr2_103667691_103674983     5769  6801 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103667691_   5769 TGGAAAAAACTTCCATTCTCATTGATAGGAAGAATTAATATACTTCAAAT 5818
                               i vv i    vi    v   v      v       vv  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103667691_   5819 GGCCATATTCTCAAAAGCAATTTACAGATTCAATGCTATTCCTACCAAAC 5868
                            v   i  i v   vii  i           i  v  i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103667691_   5869 TACCAATGACATTCTTAACAGAAA--GATAAAAAATATTTAAAAATACAT 5916
                          v   iivi v  i  vi      --  i  ivvi-  iiv     v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chr2_103667691_   5917 ATGGAATCAAAAAAGAGCCAGAATCACCAAAGCAATCCTAAGCAA-AAGA 5965
                               viiv  ii  v       vi     i     i i iv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_103667691_   5966 ATAAAGCTGGAGGCATCATAGTACTCAGTCTCAAACAGTGAAAATGCCCT 6015
                          i    i      ---------     --------  -------------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG---------ACTCA--------CA------------- 219

  chr2_103667691_   6016 CTAGATCATCCAGATCAAAAGGAGCAGGTATCAATCATGCCCAAATGCAG 6065
                           ------   --------------------    i--------------
  L1M4_orf2#LINE/    220 CT------TCC--------------------CAATT-------------- 229

  chr2_103667691_   6066 CTCAAAACACTTTTCTCAACCACACCCCCATGGGAAACAGCTGTGATAAA 6115
                         -       ----  ----  i   --------------------------
  L1M4_orf2#LINE/    230 -TCAAAAC----TT----ACTACA-------------------------- 244

  chr2_103667691_   6116 TCTTTAGGCTACAGTAATCAAAATAGCACAGTATTGGTACAAAAACAGAC 6165
                         ----- i              i i  iiii   i   i i  ii i    
  L1M4_orf2#LINE/    245 -----AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_103667691_   6166 ACATAGACCAGTGGAACAGAACAGAGAATGCAGAAATAAAGCCACACACC 6215
                          i     i  i     i    iv    i v          v   i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_103667691_   6216 TACAACCACCTGATCTTTGACAAAGTTGTCAATAACAAACAGTGGGGAGA 6265
                           iiii  vi    i  i     i v  i   v v  vv  i      i 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_103667691_   6266 GGATTCTCTATTCAATAA-TCGTGCTGGGATAATTGGCTAGCCATATGCA 6314
                          i  vv   v     i  - v         i  i   v  ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_103667691_   6315 AAAGACTGAAACTGGAGCCCTTCTTTTCACCATACACAAAAATCAACTCA 6364
                              v    ii    v    v i iv       i        i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_103667691_   6365 ACATGGATTAAAGACTCAAATGTAAGACCTGAAACAATACAATCCATAGA 6414
                          v      i ?    ii          v  i    v   v  ii v    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_103667691_   6415 AGAAAACCTAGGAAATACTGTTCTGAAAATCGGCCTTAACAAAGATTTGT 6464
                                v    ?ivv v v   vvi vv i  vi vii   v i   v 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_103667691_   6465 --GATAAGTTGTGAAAAGCAATTGCAACTCCTCCAATTGCCAATTTGTTG 6512
                         --    v viiiv       vvv     ------  -----  ------ 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAAC------AA-----AA------G 622

  chr2_103667691_   6513 ATTTTGTTAACAAAAATTGATGAGTGGTATTTAACTAAACTATAGAGCTT 6562
                          ----------      v   i i v v i  v ii   v vv i i   
  L1M4_orf2#LINE/    623 A----------AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_103667691_   6563 CTGCAC---AAGAGAAACTATCAATAAAGTGAACAGACAACCTACAAAAT 6609
                         i  ii ---  ii  v        v        v        i   i   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_103667691_   6610 GGGAGAAAATGTCTGCAAAGTACACATTTAACAAAGGTGTAATATCCAGA 6659
                                   i i      vi i i  i i i  i  vv vi        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_103667691_   6660 TTCCATAAGGAACTT----AAATCAGTAACCAAAGACCAAATAACCCCAT 6705
                         v vi    i     i----  v   i   iv   iiv          v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_103667691_   6706 TAAAGAATGGGTGAAGAACATGAACAGACACTTTTCAAAAGAAAACATAC 6755
                          ?  i      ii   i iv    i     i  i  v      i i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_103667691_   6756 ACATGGCCAACAAGTATATGAAGAAATGCTAAACACCACTAATCAT 6801
                          v        i   i i     i i     v    i  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 7.55 (151 / 20)  


 469 30.74 7.04 2.22  chr2_103683650_103686197      906  1175 (1373)    L1M4_orf2#LINE/L1       21   303 (605)  

  chr2_103683650_    906 ATTGATTGACAGATTCA---TTATTAAGATAACATTTGTTCCAGAATTCA 952
                           v     iv   i i ---  i       ii  v vv i  vi    v 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr2_103683650_    953 CCTATGGATTCAAAGCTATCACTTTCAAAATACCA-CTATTTATTTTATA 1001
                         i   ii       v  v   v  v       v   -  iii v    ii 
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr2_103683650_   1002 GAAATTAGCAAAGATATTCTAAAAAGTTT-TATGATAATGTTAATGATCC 1050
                               ii   ivvv  i      --  i-    iv    iv iv  i  
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAA--TTCATATGGAAATGCAAGGGACCC 168

  chr2_103683650_   1051 AGAATAGATAAATTA---TTAAAA--------TAAGTTTGGAAGAGTTAA 1089
                                vi   vi ---  i   --------i  iv     i  v i v
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_103683650_   1090 AAATGACCTGATTTCAAGAAT-AGTATAAGGTTAGTGCAATTAAGCGAGT 1138
                          vv --  ii       i v - v  i  i i  vv i   i   vv   
  L1M4_orf2#LINE/    219 ACTT--CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_103683650_   1139 GAGAT--TTGTATGTTAAAATAGGCATATAGAGCGCTGG 1175
                          v i -- v i  i-- ii    i        v iv   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATA--AGGATAGACATATAGATCAATGG 303

Transitions / transversions = 1.31 (47 / 36)
Gap_init rate = 0.04 (10 / 283), avg. gap size = 2.50 (25 / 10)  

1312 26.67 7.50 2.67  chr2_103683650_103686197     1465  2064 (484)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_103683650_   1465 AAAAATTAGCATATAGATTAATGAAACAGAAGAGGGATTTCAGAAAAAGA 1514
                           ii  vii         i    i  i    vv i  v i      --v 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA--TA 327

  chr2_103683650_   1515 AACTCTTATAT--ATGGTCAATTAACTTTTGACAAAGATTTTGAGGAAAT 1562
                            i v  i  --          i i   i     i i viii  ivv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_103683650_   1563 TCAGTGGTAAAAGGAAAGTCTTTTTAACAAATTGTGTTGGAACAATTAAA 1612
                            i   vi    i v        i       v   i   i    i ii 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_103683650_   1613 TATACATATAGAAAA-AGTAAATTTTGACTCCTATCAAACAAAACGCATA 1661
                           ?v  i  iv    - i i  v  v   i    i vv   vv iii i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_103683650_   1662 AATATCAACTCAAAACTCTATTAAGTAGAGATCTAAATGTGAAGGTTAAA 1711
                           v  i         ----- vi vi ?   i        i ii i    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAA-----TGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_103683650_   1712 ATAATAAAACTTTTAATAGAAGAGAA-ATCAG---AAATCTTTACTAACT 1757
                          iv        i   ---     i  -  vi ---       iiiv v  
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTA---GAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_103683650_   1758 CAGAGTATGAAAAGATTTCTTAG-TA---CATAAAAAGTATGAATTA-AA 1802
                         ii iv  v v  v i        -  ---  iv     i ii iiv -  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_103683650_   1803 AAGAA--------TCCACTTAATTTTGTTGAAATCAAATATTTTT-TGCT 1843
                              -------- vv i vi i  ii ii    i   v i    -    
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_103683650_   1844 CTTAAAAGAGCA-TAT---AAAAGAGGAAAGGCAAGCTATGAAATGGGAT 1889
                         - i   i  -  -   ---i    v i    i   v i iii       v
  L1M4_orf2#LINE/    670 -TCAAAGGA-CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_103683650_   1890 AAGATATTTGCAATGACAAATTTCAAACAACAAACTTTTATCCAGTATAT 1939
                           i          -iv  v  v  vi i  vii    v       v    
  L1M4_orf2#LINE/    718 AAAATATTTGCAA-ATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_103683650_   1940 ATAAATAGTCCTTATAACTCAATAATAGAAGATTAAAAACAACCTA--TA 1987
                              v iii    i            i  ii-- v   i    i -- ?
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAG--ACAAATAACCCAATTW 814

  chr2_103683650_   1988 ATAAAATGGGAGAAAGATTT-------CA-----CAAAAGAAGATACACA 2025
                          -        vi  i     -------  ----- v          i   
  L1M4_orf2#LINE/    815 A-AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_103683650_   2026 AATGTCCACTTAACACATGAAAA------CAGCATTAGGAATCAG 2064
                             v   v v i          ------  i   i ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (103 / 54)
Gap_init rate = 0.04 (23 / 629), avg. gap size = 2.65 (61 / 23)  


1871 20.91 2.01 19.27  chr2_103697092_103702943     3058  4152 (1700)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_103697092_   3058 GAAAAAAATCCCATGTTCATGTACTGAAAGAATTAGTAGTGTTAAAATGT 3107
                             i v              v i  i    v   i  v      i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_103697092_   3108 ATATATTACCCAAAGTGATTTAAAGAGTCAATGCAATCCCTATCAAAATT 3157
                         vv   i v      v    i  v   v    i                 i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_103697092_   3158 GCA--TGGCATTTTTCAAGAAATAGGGAAAACGATGTTTAAAGTTGTATG 3205
                         v  --  v v     vv      v iv  ivi   vi v   v ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_103697092_   3206 AAACTATGAAATAATGTGAATAGCCAAAACAACCTTGAACAAAAAGAACA 3255
                         i  v iii iiv vivv               i      v  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_103697092_   3256 AGGTTAAAGGCATTGCACTTCATGACTTCAAAAGTTATTA---------- 3295
                          i   ii   vv ii      vii i       v   i  ----------
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_103697092_   3296 -TAATTAAAACAGCATGCTACTGGCATAAAAACAGAGACATCAATGAATG 3344
                         -    i  i    ii  v           ii i   v i  vi  v    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_103697092_   3345 AAGCAGGAA-GAAAGCTCAGAAACAAACCAACACATTTATGGTCAATTGA 3393
                         i ii  i v-  i  ii      i     v i                  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_103697092_   3394 TTTTGGACAAGTATGTCAAGAATACTCAATGGGAAAAAGAGAGTGTCTTC 3443
                             v      vi  i     vi i        i   -------------
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA------------- 389

  chr2_103697092_   3444 AATAAATTATATTGACACTACTCAACTTTAAACTATACCATAAGGCTACA 3493
                         --------------------------------------------------
  L1M4_orf2#LINE/    390 -------------------------------------------------- 389

  chr2_103697092_   3494 GTAATAAAAACAGCATGGTACTAGTATAAAAACCTACACATAGACCAATG 3543
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    390 -------------------------------------------------G 390

  chr2_103697092_   3544 AAACATAATATAAAGCACAGTAAAAAGATACACACCTACAACTGTCTAAT 3593
                           --------------------------------------------  i 
  L1M4_orf2#LINE/    391 AA--------------------------------------------TAGT 396

  chr2_103697092_   3594 CTTTGACAAAAGTCACAAAAACAGGCAACGGTGAAGTAATTCTCAATTCA 3643
                             -------------------------------------------   
  L1M4_orf2#LINE/    397 CTTT-------------------------------------------TCA 403

  chr2_103697092_   3644 ATAAATGGAGCTGGGATATCTGACTACCCATATGCAGAAGAATGAAATTA 3693
                          i      v       i v   iv  ?   i     i         i  i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_103697092_   3694 GACCCTTACCTTTCACCACATACAAAAATTAAAT-AAGATGTATTAAAGA 3742
                              i     iv     i             v -  i   v  i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_103697092_   3743 TTTAAATGTAAGAGTTCTAACTATAAAAATCTTAAAAGAAAACCTAGGAA 3792
                         ii            i vv          v     i        v    ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_103697092_   3793 ATACTCTTCTCAATATTGGTCTTGGCAAAGAATTTGTGGCTAAGTTTTGA 3842
                         vv v     vii iv    vi v     v iv  iv i v  v viviv 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_103697092_   3843 AAAGCAATTGCAATAAAACCAAAAATTGATAAGTGGGATATAGTTAAACT 3892
                               vvv    i    vv      v     i v   iv vi i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_103697092_   3893 AAAGAGCTACAGTACAGCAAAAGAAACTATCAACAGAGTAAACAGGCAAC 3942
                         v  i i  viv  i vv    i  v        v i   i  v  i    
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_103697092_   3943 ATATCAAATGGGAGAAAATATTTGCAAACTATGCATCCAACAAAGGTCTA 3992
                         vi ivi                      ii  ii   ii i  i  v  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_103697092_   3993 ATGTCCAGAATCTATAAGGGACTTGAACAAATCAACAAGCAAAAAAAAAA 4042
                         i i        v     i i   ivv    v    i  v-----------
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT----------- 792

  chr2_103697092_   4043 AAAAAAAAAAAAAAACCA--TTAGAAATGGGCAATGGATATGAAGAGACG 4090
                              i v   v  v   -- ? i          v    v    v    i
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_103697092_   4091 CTTCTC-AAAAAAGACAT-CAAACAGCCAAAAAG-ACATAGAAATA-GC- 4135
                         i     -   i    i  -    ii     v   -    ii   v -  -
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_103697092_   4136 CAACAGACATTTTAAAA 4152
                              v-  ????????
  L1M4_orf2#LINE/    893 CAACAT-CAZZZZZZZZ 908

Transitions / transversions = 1.21 (123 / 102)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 15.53 (233 / 15)  

1396 25.43 8.97 0.64  chr2_103697092_103702943     4893  5360 (492)    L1M4_orf2#LINE/L1      402   908 (0)  

  chr2_103697092_   4893 CAAAAAATTGTGTAGGGAAAACCGGTTTGCCACATGCAGAAGGATAAGAT 4942
                            v    v   iv    v   i  v v?         i   i  i ii 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_103697092_   4943 TGGACCCGTATATTATACCATACACAAATATCAACTCAAAATGGAAGA-A 4991
                                v  iv i i      i     v  i             vv - 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_103697092_   4992 GGCCTAAATATAAAACCTGAAACTGTTAAACTACTAGAAAAAAATAT-GG 5040
                          i       i   i v  i     i v     vi     i    i  -  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_103697092_   5041 GACAA--CTTATACAACATTAG-TTGGGCAATGACTT-TTGCATATAACC 5086
                         ?ii  --   -iiii  v  i -  i       ii  -  iv    i  v
  L1M4_orf2#LINE/    552 NGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_103697092_   5087 TCA---------------------------------TGGGGTTGCATCAA 5103
                         i  --------------------------------- v  ii v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_103697092_   5104 ACTAAAATGCTTCTGCACAACAAAGAAAACAATTAACAAAGTGCAGAAGC 5153
                          v v   vi   i  ii vv     i v  v  i  v      v i ii 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_103697092_   5154 AACCTACAGAGTGGATTAAAATATTTCCAAACTACTCATCTGATTAGGAG 5203
                             i     i   ivv         v    ii ivi       v   ii
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_103697092_   5204 TTAATATCCAAAATATATAA-GAACTCAAACAACTCAATAGCAAAAA--C 5250
                         i vi      i         -      vv           ii     -- 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_103697092_   5251 AAACAACCTGATTAAAAAAGTAGGCAAATGATCTAAAAAAACATTTCTCA 5300
                            i    ii   ?     - i      v   i i  v i         v
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_103697092_   5301 AAAGAAGACATCCAAACGACTAAGAGGTACATAAAAAAGATTCTCAGTAT 5350
                                 i  v    i i i  v i i    i    -   v    ii  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAACAT 898

  chr2_103697092_   5351 CACTAACCAT 5360
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.76 (74 / 42)
Gap_init rate = 0.02 (11 / 507), avg. gap size = 4.09 (45 / 11)  


1747 26.42 10.86 2.77  chr2_103708895_103710715.rev      501  1329 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_103708895_    501 CCATGTTCATTGGCTGAAATTATCTAATAATATTAAAATGTCAATTCTT- 549
                                   v ii  i  v- ii     v i    i   v    v  i-
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGATGGCAATACTCC 61

  chr2_103708895_    550 -----TTAACTTTACAGATT-AAT-TAAACTCAATCAAAATTCCAAA-GA 591
                         -----  i - i        -  i-i  v i v        i   iv- v
  L1M4_orf2#LINE/     62 CCAAATTGA-TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr2_103708895_    592 AGTATTTGTAGATATCAACAAACT------------TATATGAAAAGGCC 629
                         vv v    i   v  ii    i  ------------i     i   v  v
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_103708895_    630 AAAGACCTAGGAGAGCCAAAGAAATACTAAAGAAAAAGAAAAACATTATA 679
                          ii    i  i v       iv   vi ---         i    -- - 
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTT---GAAAAAGAAGAACA--A-A 204

  chr2_103708895_    680 GCTGAAGAACTGATGGCACT---CAACATGAAGACTGACCATAAAGTTAA 726
                          i  i  i   v ---    ---   iv v  i   v  i i    i  v
  L1M4_orf2#LINE/    205 GTTGGAGGACTCA---CACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_103708895_    727 AGTAA--AAAA--GTATCGTACTGGTGAAAGAATGGAAACA-AAACCTAT 771
                              --  i --  i v       iiv   i  i  v i - i i v  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_103708895_    772 GCAACAAAAT-ACAAGCCTAGAGATTAAACTCACACAAGTGTAGCCAATT 820
                          v  i i   -ivi  i i   i  -    i  i   vv i i i     
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAAT-AAACCCATACATTTATGGTCAATT 350

  chr2_103708895_    821 GCATTTTGACATAGGAGCAAAGGTTATTAAATAGAGTAAAAATAAAAATT 870
                          vv   i    vi  v  v   iii   v   i i v  i    ivvv  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_103708895_    871 TCAACATGTGCTGCTGGAATGTTTGGATGTCTAGATGCAAAAAATAATAA 920
                               vi  v      i iivi     i? i v        i --  i 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA--ATGA 448

  chr2_103708895_    921 AAATGCTCATAGAAACAGACCTTATACCTAACACAAATATTAACTCAAAA 970
                          iv  ------  vv vv    i i   vv i     v            
  L1M4_orf2#LINE/    449 AGTTG------GACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_103708895_    971 TGAAACATAGACTTAAATGTAAAATGAAAAGCTACAAAATTCCTAGAAGA 1020
                           i v  ?    i         i vvv   i   i    i  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_103708895_   1021 AAATACA------------TGTGACCCTGGGTATGATGACAGATTTTTAG 1058
                            i i ------------i      i     vv iii ii v  i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_103708895_   1059 ATACAACACTAAAATCATAATGAATGAATAAAAAATTTCATAAGTTGGAC 1108
                            ii    i    v  i  vv  ii  vi     v vv    i      
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_103708895_   1109 TTTATTAAAATTAAAA-CTTTGGCTCTTTTAAAGACAC----AAAAAATG 1153
                           i  i          -    v iv   iv  i     ----  i   - 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA-G 691

  chr2_103708895_   1154 TTAAAAGACAG--------------GAAAATATGTGCAAAATATATATCT 1189
                          v        i--------------        v      vi        
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_103708895_   1190 AATATCAAA-TCGTA----------ACAGAGAATTCTTACAACTCAA-AA 1227
                         i   vvii - i   ---------- i i    i             -  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_103708895_   1228 TATGAATACAAACAATGCAATTTTTAAAAA--GGC-------CTAAAT-- 1266
                           vi  v     i  iv     ?--     --   -------i i   --
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAG 839

  chr2_103708895_   1267 -TA-----CCAAAGAAGGTGTTAAGATGGCAAACAAACATATGGAAGGAT 1310
                         -i -----         i i vv i     v  i  i  i   i  i   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_103708895_   1311 GCTCGACATTATTTGTCAT 1329
                             i    i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (135 / 81)
Gap_init rate = 0.04 (32 / 896), avg. gap size = 3.53 (113 / 32)  


 366 23.27 4.46 6.93  chr2_103775177_103777007      194   395 (1436)    L1M4_orf2#LINE/L1      439   635 (273)  

  chr2_103775177_    194 AAAAGTACAATAAAGT-GAATCTTTGCA-CAGACCATACAACTTTCTAAA 241
                              ---   i    - i i ii i v-  v      i ------i   
  L1M4_orf2#LINE/    439 AAAAG---AATGAAGTTGGACCCCTACCTCACACCATATA------CAAA 479

  chr2_103775177_    242 AATTAACTCAAAATGGATCACAGACCTAAA-AT----GCAAAACCTCTAA 286
                                             ?         -i ----  v   v  v   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_103775177_    287 AACTTCT-GAAGATAACATTGGAAACAAATCTAGTTGACCTTCTTTTTCA 335
                             ii -     v     v  ?i-i      vvv       vvv  vvi
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_103775177_    336 TAATGGTT-CTTCATTTCAATACCAAAAGAAAAGTCCGTAAGAGGAAAAA 384
                         i       -   viv vii i        v v i--- i  v i-  i  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAA---GCAACAA-AAGAA 624

  chr2_103775177_    385 AAAAAAGATAA 395
                             v      
  L1M4_orf2#LINE/    625 AAAATAGATAA 635

Transitions / transversions = 1.05 (23 / 22)
Gap_init rate = 0.06 (11 / 197), avg. gap size = 2.09 (23 / 11)  

 362 24.27 3.88 0.97  chr2_103775177_103777007      403   505 (1326)  C L1M4_orf2#LINE/L1   (691)   217   112 *

C chr2_103775177_    505 TCTTTTGCAGAACATGACAAGCTAATCAGAAAAATGTGTATGCCAATAGA 456
                          i          vv         i   vv    - vii    vv   iv 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCATATGGAAATGCA 160

C chr2_103775177_    455 AAACACCCAGAATAGCCA-CATAATTTTGAAAAAGAA---TGAGGTTGAA 410
                          iiv              -v i   i           ---ii i    i 
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

C chr2_103775177_    409 GAACTTA 403
                          i   i 
  L1M4_orf2#LINE/    211 GGACTCA 217

Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.03 (3 / 106), avg. gap size = 1.67 (5 / 3)  

1743 26.12 8.82 2.35  chr2_103775177_103777007      501  1350 (481)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_103775177_    501 AAAGATATATCATGTTCATGGATTGGAAAACTCAAAATTGTTAAGGTGTC 550
                                 vi                  i   i  v         i  v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_103775177_    551 AATTCTCTCCAGTTTGATCTATGCATTCAATTCAATTC--ATCAAAATGT 598
                            v   i   iv        iiv      iv    i --        vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_103775177_    599 CAGGGAGCTTATTTGTAAATGCTAACAAGCAGTTTCTAAAATTTATATCA 648
                            vviv   v    i i vii i      v v i        i    vi
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_103775177_    649 AAAGGAAAAAGAACTAAAAGGGTTATACATTTTTTTAAAAAACAAAAA-A 697
                            v v  ii  v i i  vi ii - v ivv i  i     v  i  - 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCA-AAACAATCTTGAAAAAGAAGAACA 202

  chr2_103775177_    698 GAGT-G------TTACACTAGGCAATTTTAAGACTTATTAAAAAGCTATC 740
                         i   - ------ i     vvv      i  i     i  v       iv
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_103775177_    741 ATAATCAA-ACAAGGTGTTATCAGTGAAAAAA-ATACACATAAATCAATG 788
                         i       -   iv   v  iii iiv  ii - v   i   i       
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_103775177_    789 AAACAGAATAAAGA-CCCATAAAAAGATCCATAAAAATATAGTCAATAAG 837
                         i  i     vi   -i   v   v i i     v vv   i      vii
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_103775177_    838 TTTTT--TAAG--TGCAAAGGCAACTCAATGAGGAAAACATAGACTT--C 881
                             i--i   --   v   i v i      i     iv    v   -- 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_103775177_    882 AA-AATTGATACTGGAACATTTCCAAGTCCATATGCAAAATAAATTAATT 930
                           -  v  i i    i   vi vv vi?   i        -i   v  v 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAAGT 451

  chr2_103775177_    931 TCAACCTATACCCCGCATATTATACCCCGCATATTGAACT-AAAATGGAA 979
                          vi   iv    i i  ivv     ---iv v   -    -        v
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATAC---AAAAATT-AACTCAAAATGGAT 497

  chr2_103775177_    980 CATAGATCCAGATATAAAGAGTAAAAAACTG-AAAATACTTATAAGGAAA 1028
                           ?   i i i  i   -   iv    -  i-    iv    v   i   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAA-GAGCTAAAA-CTATAAAACTCTTAGAAGAAAA 545

  chr2_103775177_   1029 CATAAAAGAAAATTTGCACAGTTTT----TAAGTATTATGTTGAGTTTC- 1073
                             ii? v    i v iiiiii  ----  i i --   ----     -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA--ATG----GTTTCT 589

  chr2_103775177_   1074 -AGATATGACAACAAAAGCAGAATCTATA---GAAAATTATACTATAA-- 1117
                         -          v        v  v v i ---     v-   v-    --
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAG-ATAAAT 637

  chr2_103775177_   1118 TG----TTATCAAAAT-AAAAACGTTTTCTCTGTGAAAGTTATTGTTAAA 1162
                           ---- i        -      v   viv  vii  i vi i i i  -
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA- 686

  chr2_103775177_   1163 GGAAGGGAAAGTAAGCAAATAAC----TGAGAGAAA-TATATGTAAATCA 1207
                          i   v    -- ii   viv  ----  i      -   v  i      
  L1M4_orf2#LINE/    687 GAAAGTGAAA--AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_103775177_   1208 TATATCTGATAA-----------------TACGTAAAGAACTCTTA-AAC 1239
                                     -----------------  ii             -   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_103775177_   1240 TCAACAAGGGAAAAA-ATGTAATTTAA---AAAAATGGACAAAA-AGCTG 1284
                             i  vii   i - vi   iii  ---        i    i- vi  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_103775177_   1285 AACAGACACTTCACCAATGAACATATA----TGGACATCAAG-----GAA 1325
                           i     i   v    v   v     ----   v  vi   -----   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_103775177_   1326 GCATATACTTATCATTAGGGAAATA 1350
                         i- v  i  i v   i ????????
  L1M4_orf2#LINE/    885 A-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (131 / 88)
Gap_init rate = 0.05 (41 / 905), avg. gap size = 2.32 (95 / 41)  


2627 26.27 1.38 5.19  chr2_103787895_103791234.rev     1911  2854 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103787895_   1911 TGGGAAGACATTCCATGCTCATGAGTCAGAATAATTAATATTGTTAAGA- 1959
                            i    i  i     i     ii ii   v v               -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103787895_   1960 GACCATGCTGCCTAAAGCAATCTATGGATTCAATGTAATCTGTACCAAAA 2009
                          i v  i  v  i   vii     ii       i i    iv  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103787895_   2010 TACCAA-TGTCATGTTTAACAGAAATAGGAAAGAGCGTCCTAAAATATGC 2058
                          v   i-  i v v   i-       v iv   vvvi         viii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_103787895_   2059 ATTAAACAAAAAAAACAAAAGAGCCTCGATAGTGAAAACAATCCTAAGCA 2108
                           ------ii   vi   ii  v  vvi    iv         i i iv 
  L1M4_orf2#LINE/    150 AT------GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_103787895_   2109 AAAAGAACAAAGCTAGAGGCATCACACTATCTAACTTCAAAATATATTGC 2158
                          i          i i    vv       vi i  i       iv  i i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_103787895_   2159 AAGACCATAGTAACCCAAGCAACATGGTATTGGTATAAATATAGCCACAT 2208
                           ii i i     i v ii  iii     i   i    iv    v  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_103787895_   2209 AGATCAATGAAAAAGAATAGACCACTCAGACAGAAATCCACATATTTATA 2258
                                  i  v     v  vviii    v v   i   i i      i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_103787895_   2259 GCCAACTGATTTTTGACAGAGGTGTGAGGAACACAGATTGGAGGAAATGA 2308
                          i   i       i    ii    iv i  v  ivv v   -     vi 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAA 392

  chr2_103787895_   2309 CACCCACTTCAATAAATGGTGCTGAGATAATTGGATATCCATATGCAGAA 2358
                         i vi vi     i           i  i  i      ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_103787895_   2359 GAATGAAACTAGATCCTTATCTCTCATCATATTAAAAAAGTCAACTGAAA 2408
                                ii i  i  i  i   v  i     - v    i i    v   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAA 491

  chr2_103787895_   2409 ATGAATTAAAGACTTAAATGCAAGAACTGAAACTATAAAACTACTTAGAA 2458
                            i  i ?    i      i    i  i             -       
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAA 540

  chr2_103787895_   2459 GAAAACATAGAGGAAGCACTTGAATATATTAGCCTAGGCAAAGATTTTAT 2508
                                   i? v ivv   vivv iv  i vi       v i   iv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_103787895_   2509 GACTAGGAACTCAAAAGCATGAACAACAAAACGAAAA-TAGATAAACGGG 2557
                         iiv  v  vvi        ii i        vi    -        iv  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_103787895_   2558 TGTATATTAAACTAAAAAGCCTCTATAAAGCAAAAAGAAAAAAAACAAGA 2607
                         vv vi  i   v v    i i i i ivvv    -- i v vv v     
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA--GGACACTATCAAGA 688

  chr2_103787895_   2608 AAAGAAAAAAAAAATAAAACACAATAAACAGGGTACAGAGACAACCTGTT 2657
                           i----------- i   -------------------        iiiv
  L1M4_orf2#LINE/    689 AAG-----------TGAAA-------------------AGACAACCCACA 708

  chr2_103787895_   2658 GAATGGGAGAAAATATTCGCAAACTATTAATTCAAGAAGAAACTAATATC 2707
                                          i     ii  vv  iii v   ii   vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_103787895_   2708 CACAATATACAAGAAACTCAAATGACTCAACAGTTTAAATTAAAAAAAAT 2757
                           v      i  ii     vv ii      i i --   --  i v    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAAT--AAA--AAGACAAAT 804

  chr2_103787895_   2758 ATC---ATTTAAAGA-GGGCAAAGGCCATGAATAGCTATTCCTCAAGAGA 2803
                          v ---   ?   i -         viv       vi   i   v i   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_103787895_   2804 GAGAAGCATACAAATGGCCAACAGGCATATGAAAAAA------ACATCAC 2847
                         -   --i              i i   i       i ------      ?
  L1M4_orf2#LINE/    855 -AGA--TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_103787895_   2848 GCATCAT 2854
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.80 (157 / 87)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.44 (62 / 18)  


2452 27.92 4.31 1.25  chr2_103792378_103797458     3715  4595 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103792378_   3715 TAGAGAAACATCCCATGTTCACTGATAGGAAAAAATCAATATCATTAAAA 3764
                          i  i i i            iv   v    i v- i     ii    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chr2_103792378_   3765 TGCCA-TACTGCCCAAAGCAATTTACAGATGTAATACTGTTTCTAGCAAA 3813
                           v  -    v      vii  i       vi  ii vi ii   v    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_103792378_   3814 TTACCAATGACATTCTTCATGGAATTTGAAAAAAACT-ATTTTAAAATTC 3862
                         v v   iivi v  i  iiii   v    v  i--  -  ii        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_103792378_   3863 ATGTGAAA---CCAGAGAGGCCAAATAGCCAAAGAAATCCTGAGCAAAAA 3909
                           i  i  --- v  i  vv vi          iv    i   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_103792378_   3910 GAATAGAGTTGGAGGCCTCATGTTACCTGACTTCAAACTATACTACAGGG 3959
                            i i         v    iii v  ii i      viv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_103792378_   3960 CTACAGTAACCAAAAGAGCATGGTAATGGTACAAAAAGAGGCATATAGAC 4009
                                  i   i v  ii     v   i i  ii v  i        i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_103792378_   4010 CAATGGAACAGAACAGTGAGCCCAGGAATAAGGGCACACACCTA-AGCCA 4058
                                 i    iv v   i    i     ivv  i   ii  -i i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_103792378_   4059 TCTGGTCTTTCACAAAGCTGACAAAAGCAAGCAATGGAGAGAG----GTC 4104
                         vi  i i  iv    i v  v   i v  vv      i  i  ----   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_103792378_   4105 TCCCTATTCGATTAATGGTGGTAAGATACCTGGCTAGCCATATGCAGAAA 4154
                          i----   i iv       v ii  i v    v  ?   i     i  i
  L1M4_orf2#LINE/    398 TT----TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_103792378_   4155 ATTAAAACTGGGCCTCTTCATTACACCATATACAAAGAT--------GGT 4196
                          v i  ii   i  i  v v i              i  --------ii 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_103792378_   4197 GTAACA---ACCTTGATGTAAACCCCAAGAGTATAAAAACTATGGAAGAC 4243
                          v v  ---    vi      ivv i  i v       viiv i     v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_103792378_   4244 AACCTAGGTG-ATACCATTCTGGACATAGGAATTGGCAAAGATTTCAT-G 4291
                            v    ? - v i -   vv   v v  iv v     v i    v - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_103792378_   4292 ACGAAT-ACATCAAAAGCAACTTCAACAAAATCAAAAATTGACAAACGAG 4340
                          i--  -   i        vvvv        vv      v  i   ivi 
  L1M4_orf2#LINE/    593 AT--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_103792378_   4341 GTCTAGTTAAGTTTAAGAACTTCTGCCCAGAAAAAGAAATTTTCAACAGA 4390
                         iii vi i  iv    i     i  iv vvv   i  v i v    v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_103792378_   4391 GTAAACAGACAACCTACACAGTGGGAGAAAATATTTGCAAATTATGTATC 4440
                           i  v        i   v i                     i  i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_103792378_   4441 TGATAAAGGTCTAACATCCAGGATCAT-TAAGGAACT--TA-AATTTA-T 4485
                               i  v  vii      i  -  -   i     --  -  i i - 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAAT-ATATAAAGAACTCTTACAACTCAAT 789

  chr2_103792378_   4486 AAGAAAAA-ACAAA---CTCA-TTAAAAACTGGGCAAAGAAC----ATTA 4526
                           v     -     --- i  -  ?    v         i i----  vi
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_103792378_   4527 ACACTTTTCAAAAGAAGACATACATGTGGCCAAAAAGCATATTTTAAAAA 4576
                            i  i  v        i     vi       v     i  vvv  i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_103792378_   4577 GCTCAATAAGACTGACCAT 4595
                               i vv ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.04 (49 / 24)  


2169 30.31 1.42 2.08  chr2_103800477_103803089.rev     1211  2124 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103800477_   1211 TGAAAAAACATCTGATGCTCATG-ATAGGAAGAAAAGATATTGTTAAAAT 1259
                           i   i i   iv   i     -  v      vvvi          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103800477_   1260 GGCCATACGGCCTAAAGCAATTTATTAATACAGTGGTATTCCTATCAAAA 1309
                            v    vv  i   vii  i  ivi  v  ii vv  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103800477_   1310 TACCAAAAACTATTTTCATAGAATTAGAAAAACACTATCCTAAAATTTAC 1359
                          v   ivvi iv    iii    v v  v  i -iv           i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_103800477_   1360 ATCCCATTTCTTTTAGTTCTTTCTTGGGAACTCCCGAATAGCCAAAGCAA 1409
                           vvv v v ---- i----------  i  -  v           i   
  L1M4_orf2#LINE/    150 ATGGAAATGC----AA----------GGGAC-CCAGAATAGCCAAAACAA 184

  chr2_103800477_   1410 TCCTACGTGAAAAGAACAAAGCCAGAGGCATCACATTACCTGACTTCAAA 1459
                           i ivivi i          iii    vv     i v  ii i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_103800477_   1460 CTACACAAGAAGGCTACAGTAACCAAGACAGCATGATAGTGATACAAA-A 1508
                         vivi  v v  i          i        ii  i  v  ii i  i- 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_103800477_   1509 GAGACTCATAGACCAAGGGAACGGAATACAGAACCCAGAAATAATGTTGA 1558
                         v    vi     i   v    ii    vv   ii          vviiiv
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_103800477_   1559 ACACCTTCAACCATCTGATCTTTGACAAAATCAACATAAACAGGAAAAAG 1608
                            ii viiii  vi    i  i     iiviiv  vi v  vvv  vi 
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_103800477_   1609 GCAAAAGGACACCCTATTCAATAAATGGTCCTGGGATAACTGGCTAGCCA 1658
                          -i    i i vi  v     i       v      i      v  ?   
  L1M4_orf2#LINE/    385 G-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_103800477_   1659 TACACAGAAGATTGAA-----ACTTTT---TTTCACTATACATGAAAATA 1700
                         i ii  i    v    -----  iii --- iv   i   i ii     v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_103800477_   1701 AAATCAACATGGATTAAAGACTTAAATGTGAAGCCCAAAACAATAAAAGC 1750
                           v    v      i ?    i       i iiv i     v      vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_103800477_   1751 CATAGAGGAAAACCTAGGAAATACTGTTC-TGAAAATAAGCCTTGGCAAA 1799
                          v    i      v    ?ivv v v   -   vvv ii i- v     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAAT 582

  chr2_103800477_   1800 GGATTTATGACTAAGTTCTGAAAAGCAATTGAAACAAAACCAAAAATTGA 1849
                           v  iv iiv  v viviv       vvv v       vv      v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_103800477_   1850 CAAGTGAGACCTAATTAAACTAAAGGGCTTCTGTACAACAAGAGAAACTA 1899
                         i  i vi   i v  i   v v  iii   i   i vv   ii  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_103800477_   1900 TCAACAGAATAAATAGACCACCTACAGAATGGGAGAAAATATTTGCAAAC 1949
                             v i i i  v    v   i                          i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_103800477_   1950 TATGCATTCAACAAAGGTCTAATATGCAGAATATATAATGAACTTAAACA 1999
                         i  ii  iii i  i  v  vi   v            v     ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_103800477_   2000 AATTAACAAGGAAAAT-CAAACAACCTCATTAAAAATTGGGAAAAAGACA 2048
                          v i  i  vi    v-    i    iv   ?    v    v   i  iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_103800477_   2049 TGAACAGATACTTCTCAAAAGAAGACAT-CACACAGCCAACAAGCATATG 2097
                             i   i i     v        i  -  v ii     i     i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_103800477_   2098 AAAAAAATGCTCAACAGGACCACTCAT 2124
                             i -         vv ????????
  L1M4_orf2#LINE/    883 AAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (154 / 119)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.29 (32 / 14)  


3028 26.36 2.22 1.22  chr2_103900457_103905410.rev     3564  4462 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_103900457_   3564 TGGAAA--TACTTTATGGCCATAGATTGGAAGAACCAATATTGTTAAATC 3611
                               --  iiii   vi   i          vii           ivi
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_103900457_   3612 AGCCATATTGCCCAAAGCAGTTTACAGATTCAATGCTATCCCTATCAAGA 3661
                         i  v   i v      viii i           i  v           i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_103900457_   3662 TATCAA-TGTTATTTTTCACAGAATTAGGAAAATTGATTCTAAAATTTAT 3710
                          vi  i-  ii-     ii     v v iv  ii    i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_103900457_   3711 ATGGAATCAAAAAAGAGGCC--AAATAGCCAAAGCAACCCTAAGCAAAAA 3758
                               -- viv   i i  --i          i   i i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_103900457_   3759 GAACAAAGCTG----ACATCACAGTACTCAACTTCAAACTATACTGTAAG 3804
                                 i  ----  -     v v i   i      viv    ii  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_103900457_   3805 GCTATGGCAACCAAAACAGCATGGTACTGGTATAGAAACATACATACAGA 3854
                             ii i  i   i    ii         i   iii i v     i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_103900457_   3855 TCAATGGAACCGAATAGAGAACCAAGAAATAAATCTATCCACTTACAATC 3904
                                  iv    v    ii v         i i  v  i   iii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_103900457_   3905 ATCTGATCCTTGACAAAATTGATAAAAATAAGTGATGGGGAAAGGACTCC 3954
                          vi    ii i     iiv  vi  i vi vvii          i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_103900457_   3955 CTATTCAGTAAATGGTGCTGGGGTAACTGGCCAGCCATATGCAGA-GAAT 4003
                           v    ii             ii      vi ?   i     i -    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_103900457_   4004 GAAACTAGACAATTACCTCTTACTACACATAAAAATTAACTCAAGATGGA 4053
                            ii i   vvi      vi  i i i i              i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_103900457_   4054 TTAAAAATTTAAATGTAAGAGCTCAAACTATAAAAATCCTAGAAAAAATT 4103
                          i ? i ii              v           v  i     i   vi
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_103900457_   4104 GTAGG---AAATACCCTTCTCGACATTGGCTCTGGCAAAAGGTTAT-GGT 4149
                         i    ---    ---    vi   v    v iv     vi v  v -i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_103900457_   4150 TAAGTCCCCAAAA--ACAATTACAACAAAAACAAAAAATTGATAAGTGGG 4197
                           v v v      --    --i        i-       v     i v  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAA--GCAACAAAAG-AAAAAATAGATAAATTGG 640

  chr2_103900457_   4198 ACCTAATTGAACTAAAGAGCTTCTGCACAGGAAAGGAAGTTACCAACAGG 4247
                           i v  ii  v v  i i   i  ii vvv      vii  i   v ii
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_103900457_   4248 GTAAACAGACAGCCTACACAAAGGGAGAGAATATTCACAAAATATGCATT 4297
                           i  v     i  i   v  v      i      ii    vi  ii  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_103900457_   4298 TGACAAAGACCTAATATCCAGAATCTACAAGGTACCTAAACAAATCAACA 4347
                            i  i iv  vi          v  i  i v  iivv    v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_103900457_   4348 AGCACAAAACAAATAATCCA-TTTAAAAATGGGAAAAGGACAT-AACAGA 4395
                          vv v  i        i   -  ?         v      iv -  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_103900457_   4396 CACTTTTCAAAAGAAGATGTGCAAGTGGTCAAAAA--ACATGAAAAGAGT 4443
                           i  i  v         i i   i   i   v  --           - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-T 889

  chr2_103900457_   4444 GCTCAACATCACTAATCAT 4462
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (156 / 78)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.72 (31 / 18)  


2913 28.17 1.68 0.22  chr2_103983371_103985930.rev     1180  2070 (490)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_103983371_   1180 AAGATATTCTGTATTCATAGATAGGAAGACTCAATATTGTCAAGATTTTT 1229
                                i ii i     i   v        i        i     vviv
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_103983371_   1230 GTTCTTCTCAAGTAAATGTGTAGATTGCATGCAATCCCAGCTGAAGTCAC 1279
                         i v  i i   i vi  v ii     vv i        viiii  i  v 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_103983371_   1280 TGCAAATTATTTTGTGGGTATCAATACACTGATCTGATACATTACAAGGA 1329
                         v  vivi v     ii iv  ii i vi      iv v vv i i v   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_103983371_   1330 GAGGCAAATGACCAAGACTAGCCAACACAGTATTGAAGAAAATGGAAAAA 1379
                         i v    iv    v   v       v   i v     i  i v i v   
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_103983371_   1380 GTTGGAGAACTAATACTACCCAACTTCAAAACTCATTATAAAGTGACAGT 1429
                                i   v i   v     i         i i  i    iv     
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_103983371_   1430 GATAAAAACAGTGTGTTATTGGTAAAATAATAGAAA-ATGTATCAATGGA 1478
                         i  v  i        v  i   i v  vi     v -  iv         
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_103983371_   1479 ACAAAATAGAGAGCCCAGATATAGGCCCACATAAGCAAAGTTATCTGATC 1528
                          i i   v     i     v   ii    i i vvi vi  i vi    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_103983371_   1529 TTGGAGAAAGGAGCAAAGACAGTACAATGGAGCCAAGATACTTTTTTCAA 1578
                           v  v  i  v  v     vi v      i vv ii   v i       
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_103983371_   1579 CAAATGATGGTAGGTCAGCTGGACATTCACATGCAAAA---TACA--TAG 1623
                               i  v i  v  i     i ?i           --- iv -- i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_103983371_   1624 ATGCAGACCTTACACTCTTCAGAAAAATAAACTGAAAATGAGCCATAAAC 1673
                          iv vv    i    iv vi v      v    v      iii  ? i  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_103983371_   1674 CTTAATGCAAACAC-AAAATTATAAAATTTGTAGAAGATAACATAAGAGA 1722
                           v    i  ivi -    i       i iv       v      i ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_103983371_   1723 AAACCTGTATGACCTTCA--TATGATGATGACTT-TTAGATACAACCCCA 1769
                            i  vii       vi--  - iii   ii  -       ii  v   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATATGACACCA 603

  chr2_103983371_   1770 ATGGCACAATACATGGAAGAAATAATTGACAAACTTGACTGCATCAAAAT 1819
                          vi      vvv iii      v   v  i   i v    v         
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_103983371_   1820 TAAAAACGTCTGCTCTGTCAAAG-ACAATGTCAAGAGAATGAGAAGACCA 1868
                                v i  iv  -      -   v i      i i   i     v 
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_103983371_   1869 GCCACAGAGTGGGAGAAAATATTTGCAAAAGACACATCTGATGAAAGACT 1918
                         v       i                    vv i i       i ii    
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_103983371_   1919 GTTATCTGAAATACACAAACAACCCCTAAAAATCAACAATAAGAAAACAC 1968
                         vv    iii    i i   v   i i  v  v    i     i  i   v
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_103983371_   1969 ----TCCACTTTACAAATGGGCCAAAGATCTTAATGGACACCTCATCAGA 2014
                         ----i   v  ? v        v  i   i v   i    ii  vi  i 
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_103983371_   2015 GAAGATATACAGATTGAAAATAAGCATATGAAAAGATGGTCCACATTCTA 2064
                                    i  v vv        i           v  v    iv??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_103983371_   2065 TGTCAG 2070
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.35 (142 / 105)
Gap_init rate = 0.01 (10 / 904), avg. gap size = 1.70 (17 / 10)  


1790 26.99 9.34 4.73  chr2_104018472_104020411      582  1448 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_104018472_    582 GGAGAGGCATACTATATTCATGGATTTGAAGACTGAACATAGTAAAGATG 631
                            i  ii  v i  i          v       v  i  v  v      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_104018472_    632 TTAGTTCTCCCCAGAACGATACATCATTTTGATACAGTTCCT-TCAA--- 677
                         vi i v       i vi   vi iviv  ii ii  i i   -    ---
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_104018472_    678 -------GCC------------------AAGCAGATTATAAAATTTATGA 702
                         -------   ------------------    v   iv       i  - 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT-A 150

  chr2_104018472_    703 TGGAAAAGCAAATAAACTAGAATAATCAATACAATTTCAAAACAGAAGGA 752
                               v    ivi v i      ii   v     i ii   v     i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_104018472_    753 CAAAGTGGGAGGAACTTG-ACTACATGACTTCAGGACTTATTACATAGCT 801
                               v      -  ii-   v vii i    ii     i    v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGA-CTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_104018472_    802 ACAATTATTGAAACTGTGTGGTATTAGCAGAGTGATAGTCAGACAGATAA 851
                            i v  ii i  v        i i   v iv     v  v i    v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_104018472_    852 AAGGAAAGGAGCAGAGAATCCAGAAATTGGCTCATACAATTATGCTCACA 901
                          v    vi  iiv    i         vii i      v     v   --
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA-- 347

  chr2_104018472_    902 CAGTTATACTTTTGACAAATATGACAGAGATTCCAAAATAATTCAGTGAG 951
                         --i  i- i   i     ivi  ---------    i iv     i  i 
  L1M4_orf2#LINE/    348 --ATTG-ATTTTCGACAAGGGTG---------CCAAGACCATTCAATGGG 385

  chr2_104018472_    952 GAAATGATAGCATTTTTTAACAAATGGTCCTGAAACAATTGAATATCCAC 1001
                             vi    i-i    i          v   ii    i  i   ?    
  L1M4_orf2#LINE/    386 GAAAGAATAGT-CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_104018472_   1002 AAGGGTAAAAAAAAAATTAACTTATATTTTAGTCTCCTACTTTATA-AAA 1050
                          v v-----    i   v  v  iv iiiivii   vi  iv    -   
  L1M4_orf2#LINE/    435 ATGC-----AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_104018472_   1051 CTTTAATTCAAGATATTTTAAAGGCTTAAATGTAA-----AAAA------ 1089
                         vv    i    i  ivv i ?  i i         -----    ------
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_104018472_   1090 ------TAGGAGAAA-------TGT----TTTGGTA---TAGCATTGGAA 1119
                         ------   i     -------?  ----i  v  i--- v vi  i iv
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_104018472_   1120 AAAAGTATTCTTTGATTTCACACCAAAAGCACAATCTACAAAAGGAAAAA 1169
                           vi  -     v   v v               v v       i     
  L1M4_orf2#LINE/    580 AATGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_104018472_   1170 TTGATAAACTAGATCTCATCAAAACCAG---TTTCTCTGAAAAAAAAAAA 1216
                          v      i i  ii         ii i---i  i v  vv---------
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT--------- 669

  chr2_104018472_   1217 GAATAAAAAAATCCCTGTTAAAAGGAAT-AAAAGAAAAGCTATAGATTGG 1265
                         --- v   ii - v  i i  i i- i -      v  v i i   v   
  L1M4_orf2#LINE/    670 ---TCAAAGGA-CACTATCAAGAA-AGTGAAAAGACAACCCACAGAATGG 714

  chr2_104018472_   1266 AACAACATATTTGTGAGCCACATATCTGACAAAGGACTCGTATCTACACT 1315
                         i v  v       ii ii  i        i  i     i     i v v 
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_104018472_   1316 ATATTAAGAACTCTAAAAACTTACTCCGGAGTAAAAGAACAA-----TCA 1360
                             v         v v    i v ---- i     ii    -----i  
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAAT----AATAAAAAGACAAATAACCCA 810

  chr2_104018472_   1361 G---AAAAA-GAACAAAGG---CACAAAGACAGATTTCACATAAAAATGT 1403
                         i---     - ii      ---iiv v     vv i  vv vi  i  i 
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_104018472_   1404 AGAA--GGCAACTAAGTACAC-AAAAGATATTTACCATCACTAGTAAT 1448
                          v  --   v v    i   i-       ii i v     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (142 / 89)
Gap_init rate = 0.03 (30 / 907), avg. gap size = 4.07 (122 / 30)  


1946 26.30 5.88 5.77  chr2_104043200_104045186.rev      595  1495 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_104043200_    595 GATATACTGCATGTTCATGCATTGAAAAACTCAATAATATGTCAAAAATC 644
                              v --          v    i  i   i    v i ----------
  L1M4_orf2#LINE/      7 GATATCC--CATGTTCATGGATTGGAAGACTTAATATTGT---------- 44

  chr2_104043200_    645 AATAATATGGTGATACATCAGTCCTCCCCAACTTGATCTGCGGATTCAAT 694
                         --   v    ii    --------       v       i i       i
  L1M4_orf2#LINE/     45 --TAAGATGGCAATAC--------TCCCCAAATTGATCTACAGATTCAAC 84

  chr2_104043200_    695 ACTGTCTCAATCAACATCCCAGCAGGCTATTTTATGGTTATCAACAAACC 744
                         i vi  i v     v        v v  v    iii vv  ii    i i
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr2_104043200_    745 GATTGTACACTTTATGTAAAAAAGCCCAAAGATTTGGAACAGCCAATGTA 794
                            iv  v v  i  i ii   v  v- ii  iiii   i      vii 
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCA-AGGGACCCAGAATAGCCAAAACA 183

  chr2_104043200_    795 ATACTGAA---GAATAACAGAGTAAGAGGACTCACAATAATCAATTTGAA 841
                           vi    ---   v    i   vi           v vvi      v  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_104043200_    842 GACATAATTAAAAGCTACAATAGTTAAGACAGTATGGTATTTGCAGAAAA 891
                         i  v  v vv         i  i i        i     i v   v  ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_104043200_    892 ACAGATACATAAACCAATGTGAA-AGAACAGAAAGCCCA-AAACGGACCC 939
                          i   i i   i i     -   -    iv  i  i   -   iii    
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATG-GAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_104043200_    940 ATGCAAATATTACC---TGAACTTTGACAA----------AC-------- 968
                           i  vv   vii ---   vi  i     ----------  --------
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_104043200_    969 -GAGAAAAAACATTTATTTTCATTAAATGTTGCTGAAACTTTTGGACGTT 1017
                         - i    i  i v i-      vi     v     ii  vvi    ii?i
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTC-TTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_104043200_   1018 TATGGTTAAAAAAAAGAAACTAGACACAGACTTTACACTTTTCACAAAG- 1066
                         i iivvi    i  v   ii i   v vv  i i    iv vi     i-
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_104043200_   1067 TTAATTCAAAATGAA-CATATACTTAAATGGAAAATGC-AAAATTATGAA 1114
                             i        i -  ? v  i      v  i -  -    i   i  
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAA 530

  chr2_104043200_   1115 ACTTCTAGAAGAAAATATAGGAGAAAAATCTATGTGACCTTGGGTTTAAT 1164
                            ii          i     ? v   -   vi             viii
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGC 579

  chr2_104043200_   1165 AGTGATATTTTACATACAACAC-------ACAA--AACAAAATTCATGAA 1205
                          i  i v i   v   ii    -------    --       ---ivi  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA---GAAAA 626

  chr2_104043200_   1206 AATAAAT---TTGGTTTGACTACTTTATTAAAATTGAAAACCTGTATTCT 1252
                             i  ---    -------    i  i      i     i v i v  
  L1M4_orf2#LINE/    627 AATAGATAAATTGG-------ACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_104043200_   1253 GTGAAAGACAGTGTTAAAAGAATCAA--GACAAGCAATCAGC-TTTAAAA 1299
                         vii  i    v i i  i i i v  --     v v -   v- vvi i 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA-CAGAATGGGAGA 718

  chr2_104043200_   1300 TAATATTTTCAAAACATATATCTTATAAAGAACTTGAATGTTCTTTATGT 1349
                         v       v    v         v    i i     ------------- 
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTG-------------T 755

  chr2_104043200_   1350 ATATATAACATACAAGGAAATGT-AAGACTCAATATCTAAAATCACCAA- 1397
                           vi v  i   i  i   v v - vi        -v     vv  v  -
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAAAAGACAAAT 804

  chr2_104043200_   1398 -ACCAATTTTAAAAATAGGTAAGAGATCCGAGCAGACATCTTACCAAAGA 1446
                         -   v v  ?      i  i  ii   ii  ii      i iv       
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_104043200_   1447 ---TATA-AGATAGTAAATATACATATGTGA-TATGCTCAATATCAATGG 1491
                         ---    - i  i iv    vi  i   vi -v        i    ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_104043200_   1492 TACT 1495
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.65 (145 / 88)
Gap_init rate = 0.04 (32 / 902), avg. gap size = 3.28 (105 / 32)  


2020 27.73 1.87 3.20  chr2_104062105_104064582.rev      484  1233 (1245)    L1M4_orf2#LINE/L1       82   821 (87)  

  chr2_104062105_    484 AATGTCATGCTTATTTAAAAATCCCAGCATAGTTTTATGTAGACATAGAC 533
                           i iv  v i   i--           vvvv    v  i   v  v   
  L1M4_orf2#LINE/     82 AACGCAATCCCTATC--AAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chr2_104062105_    534 AAGCTTATTCTAAAATTTATATGGGAAAGGACTGGCCCAAGAATAGCTAA 583
                              v  i        i      i  v v vv  v  v        i  
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_104062105_    584 AATGACTTTGACAAATGAGCATAAAGTACAAGAAATCCCTCTAGCTTATA 633
                           ii ii    v   vi  v i     vvi  i v  v v  vv iv  v
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_104062105_    634 TCAAGGTAGATACAAGCTACCTTATTAGGTAGCTACAGTAATCAAG---- 679
                             ---------  -----    i  viv                ----
  L1M4_orf2#LINE/    230 TCAA---------AA-----CTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_104062105_    680 TGTAATA-TAGCACAGGGATAGACACATAGATTAGTGTAATCCAATAGAC 728
                            ii  - i   i i         i      i i  v   vv   v  v
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_104062105_    729 AA-CTAGAAAATGACCCACGCAAACATGTTCAACTGATTTTTTTGAGAAA 777
                          i- i     vvi     ii  vvi   v    i       i----  v 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC----GACA 361

  chr2_104062105_    778 ACAATGCAAAAAAGAATTCAGTGGAGGAAGGAAAACTTGATTTCAACAAG 827
                          vii   v  i vv -    i   i i   i v iii --         i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCT--TTTCAACAAA 408

  chr2_104062105_    828 -GGTGCTGGATCAATTAGATGTCCATA-GCAAAAAAATAAGCTTTGAGTT 875
                         -        iv   i i   i?   i -      i   i iv  v  vii
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_104062105_    876 GAACCTCATATCTGATCTAAAAATGAACTCAAAATGGAACATGGAT-TAA 924
                         vv      i i vv  vi      v             v  ?i  i-   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_104062105_    925 AAGTGAATG-TAAAACTGTAAAACTTTTAGGCAAAAACATAGAAGTAAAT 973
                          v  i iv -       i       i    ivi         i?      
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_104062105_    974 CTTTGAGATCTGGCACTTGGCAAAGCATTCTTGGACTTGACATCAAAAAC 1023
                            i v  i  v vii v     v vv     i  iv     i     i 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_104062105_   1024 ACAATCCATGAAAGCAGCAAGTTATGAATTGAGTCTCATCAAAATTAAAT 1073
                             v v ii    v iv  vvv  i     iiii              v
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_104062105_   1074 GATTTTGCTGTGTCAAAGGCC-CTGTGAAGAGGATGGAAAGGCAACCTAC 1122
                         iv     -  iv       v -  i v    iii  i    i     i  
  L1M4_orf2#LINE/    659 ACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_104062105_   1123 AAACTGGGAGAAAATATT-GCACACCACGTAGCTGACATAAGACTTGTAT 1171
                          i v              -   v i  ii  v    i vii         
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_104062105_   1172 CTAGAAAATATAAGACATTATAAAAAGTCAACAG-AAAAAAA-AAGCAGT 1219
                          i    v      iiv i v v v  v    i i-     i -  ii ii
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_104062105_   1220 CCTATTAGAAAATG 1233
                           v   ?i      
  L1M4_orf2#LINE/    808 CCAATTWAAAAATG 821

Transitions / transversions = 1.24 (113 / 91)
Gap_init rate = 0.02 (18 / 740), avg. gap size = 2.11 (38 / 18)  

 297 22.36 4.97 6.21  chr2_104062105_104064582.rev     1833  1993 (485)    L1M4_orf2#LINE/L1      750   908 (0)  

  chr2_104062105_   1833 ACATGTATCCTAAA-ACTTAAAGCA---TAATAAT--AATAATAATAATA 1876
                           v       vi  - iv     v --- v i  i--        v  v 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_104062105_   1877 ATAATAAT--AATTAAAAAAAAGAAAATGACCAAAGGGCATGAAGAGACA 1924
                         vv     i--    ?     -------  iv      iiv    v     
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAA-------TGGGCAAAGGATTTGAATAGACA 842

  chr2_104062105_   1925 TTTCACTAAGAGGAGGACAAACAAATGACAAGTAAGCGCATGAAAGGATG 1974
                             v i  i--  i  i v       i v i     i       i    
  L1M4_orf2#LINE/    843 TTTCTCCAAA--GAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_104062105_   1975 CCCAGGAATTAGCCATCAC 1993
                          i  iv - i ????????
  L1M4_orf2#LINE/    891 CTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.19 (19 / 16)
Gap_init rate = 0.04 (7 / 159), avg. gap size = 2.57 (18 / 7)  


1148 30.28 6.50 5.34  chr2_104084753_104089207.rev     3112  3973 (482)    L1M4_orf2#LINE/L1       37   908 (0)  

  chr2_104084753_   3112 AATATTATAAAGATGTTAATTCTCTCTATAGTCACTTT-----TTAAATA 3156
                               i v      vi   v   i i - i iiv i -----  v  ii
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCA-AATTGATCTACAGATTCAACG 85

  chr2_104084753_   3157 CAATACCAATAAAAACTCTAGCAAGTGTATTTACAGTAGTTTAATTTTTT 3206
                             v  v  v    ii i   viviv v   i   v i  ---------
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT--------- 126

  chr2_104084753_   3207 CGAACACTTCTAAAGATGACCCTAACATTTATATTGAAATGTATATGGTC 3256
                         --i   -------  v   i     v   i    v      i viv ii 
  L1M4_orf2#LINE/    127 --GACA-------AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_104084753_   3257 AAAAGTAACTAAGGCAATCATGAA------GGACA---TTTCATGAATTT 3297
                         v i i  i i  ii     v    ------ i   ---  vv v  v iv
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_104084753_   3298 CATTTCCAGAT---AAAA------ATAAA----TGATATTTAAGATAACT 3334
                           i    vi  ---    ------ i   ----iii  v i    i iiv
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_104084753_   3335 TAATATTAGCTTAAGTGTATACAAAAAGACCAATGGAATAGAATAAGGAG 3384
                          ii  i i  v    vi  v   v v   i              vii   
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_104084753_   3385 TCCAGAAATATATTCCTAAATATATATGGCCAATTAATTTATCACAAAAT 3434
                                   v --  i v i  v     i     i    viv    iiv
  L1M4_orf2#LINE/    318 TCCAGAAATAAA--CCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_104084753_   3435 TGACACTGCAGTGTAGTGGGCAAAGCTTTGATAGTTTTCTTAATGGGTGT 3484
                           v  vvi vi vi i    v    ----i     i  i i  iiii  v
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAG----AATAGTCTTTTCAACAAATGG 411

  chr2_104084753_   3485 TACTAGGTCAATTTGATATTCTTATGGGAAA-AATAAATCTTGAACC--T 3531
                          i  i  v   i v    ?i vi   vi   -   i  v-   i   -- 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG-TTGGACCCCT 460

  chr2_104084753_   3532 GACTCATACCATACACAAA--TTAACTCTGGTTAAAT-ACAGATTTAATT 3578
                         iv    i      i     --       viiv ii  - ?   ii   --
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA-- 508

  chr2_104084753_   3579 ATGCAAGTG--AATAATCATAAAACTTCTTGAAAATACCATAGGAAAATA 3626
                            i   v --  -  ii        ii v   i v v      ?iv v 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAA-AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_104084753_   3627 TCTTCAAAGTCTTGAGGATATACAACTATTTTTTA-ATAAGATAC--ACA 3673
                              iviii    -  v  vi   ivi   i   -   v  i  -- v 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_104084753_   3674 TCCCATTGATCATAATGAAGAGTTTGGTAAACAAGGTTGTATTAGAATTA 3723
                         v v  vvv v  v  -   i iv v i    ivi ii vi  i i     
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_104084753_   3724 ATAAATTCAATTCATCAAAAGACACCAATAAGAGATTTTAAAAAC----T 3769
                          v  v  ivi v v     i     i vi    i v vv   i  ----i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_104084753_   3770 AGAGAGTGATTGAAAATATTAGCAACAGAAATATATATACATAACAAAAA 3819
                          v   i  ivv         v    -----  -i     iv i i  ii-
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAA-----AT-CATATATCTGATAAGG- 748

  chr2_104084753_   3820 AGACTTGCATCCAGAACATATAA----CTCT--CAATTATTGACAAGGAA 3863
                         -      i        i      ----    --   i --ii i  vi  
  L1M4_orf2#LINE/    749 -GACTTGTATCCAGAATATATAAAGAACTCTTACAACT--CAATAATAAA 795

  chr2_104084753_   3864 TAGTCAGGTCAGATAATTTTTTTTAAAGATG----AAATACTTAAGTTGG 3909
                         ----- i v  i    iiivv  ?   i   ----  iv i  i i v i
  L1M4_orf2#LINE/    796 -----AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_104084753_   3910 CATTTC-ATAAAGATGATATCAAAATGACTAATAAACATATGAATAG--- 3955
                               -vi     v     vv     i i     i  i     v  ---
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_104084753_   3956 CCCCACCTCATTCATGTT 3973
                          i v  v   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (152 / 105)
Gap_init rate = 0.04 (34 / 872), avg. gap size = 3.00 (102 / 34)  


3291 20.09 8.75 1.42  chr2_104137264_104139283      683  1528 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_104137264_    683 TGAAAAGACATCT--TGTTCATGGATTAGAATACATAATCTTACCAAGAT 730
                           i     i   i--            i   v  v    v  iii     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_104137264_    731 GACCTCACTACCCAAAGCAATTTACAGATTCAATGCAATAGCTATCAAAA 780
                          i vvi   v      vii  i           i     vv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_104137264_    781 ATACCAAGGATTTTCTTTTTGCAGGAATAGAAAAATTCATCCTAATGTTT 830
                         - v   -- v viii         i   v  v  ii v       vi  i
  L1M4_orf2#LINE/    101 -TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_104137264_    831 ATATG-AAATCTCAAGCACCTTCAAGAGCCAAAGTCATCTTGAAAAATAA 879
                              -    viv i v   ivv  v       iiv           v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_104137264_    880 GAACAAAGATGGAGGAATTACACTTCCCAATTTCAAAAGGCACTGCAAAG 929
                                 v       v i                   vvi   i     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_104137264_    930 ACCTA-----------ACAGTGTGGTGCTGGCTTAAGGACAGACATATAG 968
                         --   -----------          i     v      i          
  L1M4_orf2#LINE/    248 --CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_104137264_    969 GCCAATGCAATAGATATAGAGCCTCCG--AATAAACCTTTACATATAAAG 1016
                         ii     v      -  v   vv   i--        iv     v  vi 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGA-ATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_104137264_   1017 TCAATTGATTTTTAGCAAGGGTGCCAAGACCATTTAATGAAGGAAAGGAC 1066
                                     iii                   i    i-      i i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAAT 393

  chr2_104137264_   1067 ATTCCTTTCAACAAA--GTGAACTTAAGAAAACTGGATATTCACAGGCAA 1114
                          v  i          --   ---i ii  v         ?i    v    
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTG---CTGGGACAACTGGATAKCCACATGCAA 440

  chr2_104137264_   1115 AAGAATCATGTAAAACTTGTACCACATGCCACTTACAAAAACTTACTCAA 1164
                               v v  vii  iiv    v  ii   iv        i v      
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_104137264_   1165 AATGGATCAAAGACCTAAACTTAGAAGGTAAAATTCCAAAACTCTTACAA 1214
                                  ?         iv  ii  v     i vi          v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_104137264_   1215 AAAA---TAG--------CTTGTATGACATTGGATTTGGCAGAGATTGCT 1253
                         i   ---   --------   -ii    v    i  v    iv i  v  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_104137264_   1254 TGCATATGATATCAAAAGCAGAGGCAATAAAAGAAATAGTAAGTAAATTG 1303
                          iv      i i        v i    i        v i  ii       
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_104137264_   1304 GACTTCATCAAAATGTAAAA--TGTTGTACATCAAAGGATGCTATCAAG- 1350
                                       -     -- v    i v        ii        -
  L1M4_orf2#LINE/    640 GACTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_104137264_   1351 ---TGAAAA------------------------TATTTGTAAGTCATATA 1373
                         ---      ------------------------      i  i       
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_104137264_   1374 CCTGATAAGTGATTAATATCCAGAATGCATAAATAACTTCTAAAACTTAA 1423
                         i        v  i vi          ii     v    ii  v    i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_104137264_   1424 CAAGAAAAA--CAAACAA-------------TGGTTAAAGGACTTGAATA 1458
                         i  v     --    i  -------------   vi      i       
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_104137264_   1459 AACATGTCTCCAAGGAAGATACACAAATGGGCAACACGCAGTTGAAAAAA 1508
                         i    v       i       i        v   i v   vv      i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_104137264_   1509 TGCTCAGCATCACTCATCAT 1528
                               i     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (98 / 70)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.30 (86 / 20)  


3075 21.97 4.71 2.91  chr2_104139340_104141826     1104  1995 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_104139340_   1104 TGGAGAGACCTTCCATATGTTTGAATTGAAAAA-TTAATCCTTTTATGAT 1152
                             i   iv i    i viv  i    i  i -     vi v   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_104139340_   1153 GTCAATTCTCCCCTAAATTGATTTATAAATTTAACACACACCCTATCAAA 1202
                          v    v      -        i  i i   i   i  vv          
  L1M4_orf2#LINE/     51 GGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_104139340_   1203 ATCTCAGTAGGTTGGGGTTTTTGTTGTTGTTGTTTGCAAAAATGGACAAG 1252
                            i   i----  ---ii   ----------      i    v      
  L1M4_orf2#LINE/    100 ATCCCAGC----TG---CCTTT----------TTTGCAGAAATTGACAAG 132

  chr2_104139340_   1253 CTGATTCTAAAATTTATAAAAAATTACAAAACACCTAGAACAGCCAGAAT 1302
                              i        i   vii  v i   iiv   i    i     i  i
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_104139340_   1303 AACTTTGAAAAAGAA---TAAAGTTGAAGGACTTAGACTTCTATAATTCA 1349
                           ii           ---i       i      i v     ivv v    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_104139340_   1350 AAA-TTACTATAAGTCCACACTAAGCAAGATAGAATGCTGCCAGTGTGAG 1398
                            -      i  iv i   v   v     i  vi  v i ii ii i  
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_104139340_   1399 GATAAACATATAGATCAGTGGTACAGAATTGAGAATCCTGAAATAAAC-- 1446
                             i            i   v i          i   v         --
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_104139340_   1447 --ACATTTGTGGTCAAATAATTTGAAA-AAAGGTGTCAAGGCAATTCAGT 1493
                         --      i       v i    vvi -  i    i    i v     i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_104139340_   1494 GAGGAAAAAAATAGCCTTT-CATATAAACAATACAGGGACAACTGAATGT 1542
                          i     i  -   i    -  - i   iii i v          i  i?
  L1M4_orf2#LINE/    383 GGGGAAAGAA-TAGTCTTTTCA-ACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_104139340_   1543 CCACATGTCAAAAGACTGATGT-AGACCTGTATGTCCCATCGTA--CAA- 1588
                                -       v   v  -i    iv  iv  v  i i  --   -
  L1M4_orf2#LINE/    431 CCACATG-CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_104139340_   1589 ---CAACTCAAAAATGTCTCAGAGACCTCA-TATAAAAGTCAAACTCATA 1634
                         ---i         -  vv   ?      v - i   i  ii   vii   
  L1M4_orf2#LINE/    480 AATTAACTCAAAA-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_104139340_   1635 AAACATCCACAAGAAAATATATGAGAAAATATTTGTTAACTT----TAAG 1680
                             viii v       i   v ? v    v  i  v v   ----  i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_104139340_   1681 -------------GA---GACACCAAAAGTGCAACTCATAACAACAAAAA 1714
                         -------------  ---           ii   viv i  v iv     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_104139340_   1715 AAGATAAATTGAAATTCATCCTAATTAACAA-TTTTAAGCTTTGAAAGAT 1763
                         v          i v      vv      v  -    iv    ii  i  i
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_104139340_   1764 ATCATGAA-AAAGTTAAAAGACAAGACATAAAGTGGAAGAAAATACTTGC 1812
                          ii  v  -     v         vv  i i i   i        i    
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_104139340_   1813 AAATCATATATAGGATAAATGACTAGTTACGAGACTTTATCTAGAACTGT 1862
                                    vv     iv    v  vv v   v v   vv      v 
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_104139340_   1863 TACAATTCAATAATAAAAAAACAATCGAACAACCCAATTTAAAAATGGGT 1912
                              i             i    ---- i         ?         i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAA----ATAACCCAATTWAAAAATGGGC 824

  chr2_104139340_   1913 AAAATATTTGGATAGACATTTCACCAAAGAAGATATATGAATGGCTAATA 1962
                            iv     i           v              ii      i    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_104139340_   1963 ATCACATGAAAAGGTGC-AAACATTATTAGTAAT 1995
                          v           i   -v     i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (116 / 76)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.72 (68 / 25)  


3252 20.79 4.85 1.96  chr2_104162141_104164642.rev     1145  2010 (492)    L1M4_orf2#LINE/L1       18   908 (0)  

  chr2_104162141_   1145 TTCATGGATCAGAAGACTTAAAATTTTTAATAGGGTAATATTCCC-AAGT 1193
                                  ii          v   v    v v  i    i    -  i 
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr2_104162141_   1194 TAATCTACAGATTCAGTAAAATCACTGTCATAAACCCAGATGGCTTTT-- 1241
                          i             iiiv    v  i   v  v     v  v     --
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr2_104162141_   1242 GCTGAAATTGATA-GCGTATCTGAAAATTTATATGAAAATACAAAGGTTT 1290
                           v        i -  vv   iv      i     i    i   i  vii
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_104162141_   1291 T-GAAAAAACAAAA-AATCTT----AAGAGGAATAA-------------- 1320
                         i-   v iv     -      ----    i   i  --------------
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_104162141_   1321 --CTTTCTGATTCTGAGGCTTACCACAAAGCT-CAGTAAACAAGATACTG 1367
                         --   i ii   iii ii     i        -      v     i v  
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_104162141_   1368 TG-TAATGGCACAAGGAGAGATGTATATGTTAATGGGATGGATCTGAAAG 1416
                           -  v     i     v   ii    vi i     i  i  vi   i  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_104162141_   1417 TCTAGAA-TAAACTCTT-CATT-ATAGCCAATTGGTTTTTGAAGAAAGTG 1463
                           i    -     i v -    -  i i      i    i  vi ii   
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_104162141_   1464 CCAAGATGATTTAATGGGGGAGAAATATAGAATAGTCATTTCAAAAAATA 1513
                               iv   i       i -------         v      v    i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAA-------AGAATAGTCTTTTCAACAAATG 410

  chr2_104162141_   1514 GCATTGGGACAACTGGATATTCACATGCAAAAAAAGAAAAGAAATCTAGA 1563
                          iii               ?i           i  v----   i - i  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT----GAAGT-TGGA 455

  chr2_104162141_   1564 TTTCTGCCTCACATCATATGTAAAATTC--TTCAAAATAAATTGTTGACC 1611
                         iii  i       i     ii    v i--i       ii  ii?v    
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_104162141_   1612 AAAATGTAAGCTCTAAAATGACAAACTTATCAGAAGAAAACATAAGAGTA 1661
                         v         vv      iv i   vi v i             i ?   
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_104162141_   1662 AACATTCATGACCTGGGGTTAGGCAATG-TTACATTAGACACGACAACAA 1710
                           iv   i      v             -  v -     i i    v   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGACACCAA 604

  chr2_104162141_   1711 A-TCAGATGCA-CAAAA-AGAAAATAAATAATTATTGAACTCCACCAAAA 1757
                          -v  v v   -     - i      i    --    i   i  i     
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAA--ATTGGACTTCATCAAAA 652

  chr2_104162141_   1758 TTAAAAACTTTTGTTCTTCAAAT-ATACTATAAAGACAATAAAAGAGATA 1806
                                       v       v- i     v    v i i   -   i 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA-AGACA 701

  chr2_104162141_   1807 AGCTATAGCCTGGGAGAAAAAATTTGCAAATCATATAACTAATAAGGGAC 1856
                          v i i  vv          v                v  i         
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_104162141_   1857 TTGAACCCA-AATATATAAAGAACACTTGCAATTCAATAATAAAAATGAT 1905
                            v i   -              v   i   i             -  i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA-GAC 800

  chr2_104162141_   1906 AAATAGTCCAATTTAAAACTAGACAAAT-ATTTGAATAGAAAATTCTT-- 1952
                              ii      ?    v i i    v-           v v    i--
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_104162141_   1953 AAGAAGATACGCAAATCATCAATAAACACATAGAGTGATAATTAACATCA 2002
                                  ii     vii      i     ii iv   iv i       
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_104162141_   2003 TTAGTCAT 2010
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.84 (114 / 62)
Gap_init rate = 0.03 (28 / 891), avg. gap size = 2.11 (59 / 28)  


2431 25.28 2.41 1.14  chr2_104176565_104178259      502  1205 (490)    L1M4_orf2#LINE/L1      196   908 (0)  

  chr2_104176565_    502 AAGAACATAGCTGGAGGTATTACATTATCTAATTACAAGCTATACTACAA 551
                                v  i      vv i   i vi i    v   iviv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_104176565_    552 AGCTATAGTAATTAAAAC-GCATGGTGTTGGCAAAAA---AGATATGTAA 597
                              i      i  i  - ii    ii     v  i---   i  i  i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_104176565_    598 ACCAATGGAATAGAA-----AACCCAGAAATTAACCCATAC--CTACAGA 640
                          i             ----- ii        v         --i  ii v
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_104176565_    641 CAAATGATTTTCTATAAAGCTGCCAAGAATACACAATGGGAAAAATACAG 690
                            v        v i  i v        vi iv       i   iv i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_104176565_    691 TCTCTTCAATAAATGGTGTTGGGAAAACTGCATTTCCACATGCAGAAGAA 740
                            i     i        i     v     v  v?         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_104176565_    741 TAAAATTGGACCTACCT--CTCACACTATACACAAAAACTA-CCCAAAAT 787
                          i  i       --   --       i   i       i  - i      
  L1M4_orf2#LINE/    446 TGAAGTTGGACC--CCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_104176565_    788 GGATTAAGGATTTAAACATAAAATCAGAAACTCTTAAACTACTAGAAGAA 837
                             i ?i  ii    ii   i v vi     v v     vi        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_104176565_    838 AACAGAGGGGGAAAAACTATATGACATTGGTCTGGGCAATGATTTTTTTG 887
                             v   ? v   v-  vii    v    vi i       i   i  -i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-A 591

  chr2_104176565_    888 GATTTGACTCCAAAAGCACAGGCAGCAAGTCCAAAAGCAGACAAACAAGA 937
                            v    v           i   i   ivvv    ii   i   ivi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_104176565_    938 TTACATCAGACTAGAAAGCTTCTGCACATCAAAGAAAACAATTAACAGTT 987
                         i v     i v vi   i   i  ii v      i v  v  i  v ivv
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_104176565_    988 TGCAAAAACAACCTAAGGGTTGGGAGAAAATATTAGCAAA-CGCATATCT 1036
                           v   i      i vi iv              v     - ii      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_104176565_   1037 GATAAAG-AGTTATAACCAAAGTACATAAGGAGCTCCAAGAACTCAATAG 1085
                              i - v  i  v   i i  i    i  i   iv v         i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_104176565_   1086 CAGAAAACAAAACAAAACAAAAAATTAAAAAATGGGCAAGAAGTCTGACT 1135
                         i i   ivv   i  vv   ----  ?            iiii i   v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAA----TTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_104176565_   1136 AGATAGTTATCAAAAAAAGACATGCAAATGGCCAGCAGATGCATGGAAAA 1185
                            i v  v  v   i    i  i          ii iiii    i   i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_104176565_   1186 ATGTTCAACA-CGGCTAATCA 1205
                            i      - i????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (113 / 61)
Gap_init rate = 0.02 (13 / 713), avg. gap size = 1.92 (25 / 13)  


1793 12.46 0.98 28.52  chr2_104179970_104181855      480  1394 (492)    L1M4_orf2#LINE/L1      246   908 (0)  

  chr2_104179970_    480 AGGTAGAGTAATTTTTTAAAA-AGTGTGGTAGCTGCCACAAGGGAAGATA 528
                           v  v      i----  i -         -   v  i    iv   i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATC----AAGACAGTGTGGTA-CTGGCATAAGGATAGACA 290

  chr2_104179970_    529 TATAGATCAATAGTATAGAATAAAGAACTTAGAAATAAACCTTCACATAT 578
                                    i v       vi   iiii           ivi    v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_104179970_    579 ATGCTCAAAAGATTTTCAACAAGGATGCCAAGAGTATTAAGTAGGGGAAA 628
                            v    vv       i      i        vi   v i -       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAA 389

  chr2_104179970_    629 GGACAGTCTT--CAACAAATAATGTTTGGA-AACTGAATAGCCACATGCA 675
                          i i      --        ii  i v   -     i   ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_104179970_    676 AAGAAATGAAGTTGTACCCCTCCCTTGCACCATGTACAAAAATTAACTCA 725
                           ii          v      v   ii      i                
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_104179970_    726 AAATAGATGAAAGACCTAAATGTAAGATCTAAAACTATAGAATTCTTACT 775
                             i   v ?                v           i  i     --
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA-- 537

  chr2_104179970_    776 CGAGACCAGCCTGGCCAACATGGTGGAACCCCGTCTCTACTAAAAATACA 825
                         -------------------------   -------------i    i i 
  L1M4_orf2#LINE/    538 -------------------------GAA-------------GAAAACATA 549

  chr2_104179970_    826 AAAATTAGCCAGGCATGGTGGTGCACACCTGTAATCCTAGCTACTCGGGA 875
                         -------------------  ? i -------    i ------------
  L1M4_orf2#LINE/    550 -------------------GGNGTA-------AATCTT------------ 561

  chr2_104179970_    876 GGCTGAGGCACGAAAATCGCCTGAACCTGGG--AGGCAGTGGTTGCAGTG 923
                         -----------------  --   v i    --     i     ------
  L1M4_orf2#LINE/    562 -----------------CG--TGACCTTGGGTTAGGCAATGGTT------ 586

  chr2_104179970_    924 AGCCGAGATTGCACCACTGCACTCCAGCCTGGGTGACAGAGTGAGACTCT 973
                         --------------------------------------------------
  L1M4_orf2#LINE/    587 -------------------------------------------------- 586

  chr2_104179970_    974 GTCTTGAAAAAATAAATAAATATAAATAAATAGATAAAACTATAGAACTC 1023
                         -    ---------------------------------------------
  L1M4_orf2#LINE/    587 -TCTT--------------------------------------------- 590

  chr2_104179970_   1024 TAAGAATGAAACATAGATAAAAATATTAAAAACATTAAATTTGTCAGTAA 1073
                         --------------     -------------------------------
  L1M4_orf2#LINE/    591 --------------AGATA------------------------------- 595

  chr2_104179970_   1074 TTTTTTGAATGTGATACCAAAAGTAGAGGCAACAAAAAATCAAATAGATA 1123
                         -----------   i        i v i         i vv         
  L1M4_orf2#LINE/    596 -----------TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_104179970_   1124 AAATGGACTTAATGAAAATTAAAAACTTGTGTA--TCAAAAGAAACTATT 1171
                           v       v  v              v   i--     i  v     i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_104179970_   1172 AAGAGAATAAAAAAGCAACCCATATATTGGGAGAAGATATTTGCAAGTCA 1221
                             i i i    ii       i v v        i          i   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_104179970_   1222 CATAACTGATAAAGGATTAATATCCAGAATATATGAAGAACTCCTAAAAC 1271
                         i   v       i   i vi              i        i  v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_104179970_   1272 TCTACAACAATGGAACAAATAACCCAATTCAAAAATAGTCAAAG-ACTCA 1320
                           v i  i  viii               ?      i v     - i ii
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_104179970_   1321 AATAGACATTTCTCCAATAAAGATGTACAAACGGACAATAAGCACATGAA 1370
                                          vi     i      i  v               
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_104179970_   1371 AAGATATTCAACATCAGGAATTGC 1394
                              ii         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (73 / 37)
Gap_init rate = 0.03 (18 / 663), avg. gap size = 15.00 (270 / 18)  


1127 27.07 3.68 6.81  chr2_104203215_104207589     2674  3216 (1159)    L1M4_orf2#LINE/L1        1   526 (382)  

  chr2_104203215_   2674 TGGAAAAACTTAATGTGTTCATGGATTGGAAGAC--AGCATGGTAAAGTT 2721
                               i iv vvii                   -- ii  v  v   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_104203215_   2722 GTCAATTCTTCTCAAATTGATGCACAGGCTTA-TGCAATTCTGATCAAAA 2770
                          v    v  i i         vi    ii i -i     i iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_104203215_   2771 TCCCAGGAAGATATTTTTATAGATATAGAAAAG---ATCT--AAACTCTC 2815
                               vvivv -     ii   v  v  v   ---   i--   i  vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_104203215_   2816 ATGGAAATACAAAATAATTAGAATGGCTAAAGCAACTTTAAATAATAAAT 2865
                                 i   iiv vii     i  i   i   ii  i  v  v  iv
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_104203215_   2866 ATAAAAT-AAAGGCATTATTGTACTTGTTGTCAAGACTTACTATATAATT 2914
                          i   i -ii   vv i ivv v iiiv v    i        i v ii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_104203215_   2915 ATAGTCATCAAGATCGTGTTGTATTGGCA-----ATCTACAGGTAGATCT 2959
                          i   v       iv    v   i     -----  vv   vi      v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_104203215_   2960 ATGTAACAGAATAGAAAATCCAGAAATTGTCAAAAAATAATATTGTACTA 3009
                            v  i     v  i i         -------   i--------- i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAAT-------AAAC---------CCA 333

  chr2_104203215_   3010 TTATAAATCATATTTATCAT--ATTG-TATTGGTCTAAGATACAAAAGCA 3056
                          -------- i      vi --    - v  v v v i i i v  ii v
  L1M4_orf2#LINE/    334 T--------ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_104203215_   3057 ATTCAATGCAAAAA-AATAGT-TTATCAACAAATAATGCTAGAGCAATTA 3104
                                 vii   -      -  v         ii    i ii   i i
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_104203215_   3105 GATACACATAAGCAAAAAAGAAAAAGGAAACAAGATTTTAAATCTAAAAC 3154
                             ?v  i v      i ----- v   i-------  ii i ivv v 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGA-----ATGAAG-------TTGGACCCCTACC 463

  chr2_104203215_   3155 TCACACTTTATCCAAAG-CTAACTCAATATGGATCATATACTTAAATGTA 3203
                               iv   v    i-i        v        ? v  i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_104203215_   3204 AAACATGAAACTA 3216
                          i vv i      
  L1M4_orf2#LINE/    514 AGAGCTAAAACTA 526

Transitions / transversions = 1.38 (84 / 61)
Gap_init rate = 0.03 (17 / 526), avg. gap size = 3.35 (57 / 17)  

1123 26.85 4.63 1.62  chr2_104203215_104207589     3461  3892 (483)    L1M4_orf2#LINE/L1      464   908 (0)  

  chr2_104203215_   3461 TCACACCATGCCCCACAAAT--ATGTAAAATTAGT-ATATGCCAATTAAA 3507
                                  iiv v -    -- ivi     vii - ? vi  ---    
  L1M4_orf2#LINE/    464 TCACACCATATACAA-AAATTAACTCAAAATGGATCAWAGACC---TAAA 509

  chr2_104203215_   3508 AATAGTAA-TAAAAGCAAAAAATGTTTAGGAAAAAACAATAGGTA-AAAT 3555
                         vi  iv i-     vi v    ivi    i i      -    ?i-    
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-TAGGNGTAAAT 558

  chr2_104203215_   3556 GTTCAGGTTCTAATTTTTGGTAAAGAGTTCTTGGATATGCCACCAAAAGC 3605
                         v   iv vi  vivv  v  i  v iv     i      v          
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_104203215_   3606 ACAA-------AAGAACAATT-GATAAATTAGAACTTCATCAAAATTAAA 3647
                             -------     v  v -        i  -                
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGA-CTTCATCAAAATTAAA 657

  chr2_104203215_   3648 ACCATTTGCTCTTTGGAAGACCCTGTTAAGAGAAAT-AGAAGAAGAGCTG 3696
                          v v    iv   iii i   v  i i    -  i - i    vi v ii
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGA-AAGTGAAAAGACAACCCA 706

  chr2_104203215_   3697 CAATCTTGGAGAAAATATTTGCAAACCACATTTCTGACAGAGAACTCATA 3746
                           ivv v                  i  i  v     i ii i   ii  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_104203215_   3747 TCTAAAATATATAAAGAACTCTCAAAACTCAGTGGCTAAGAAACAG---- 3792
                           i i                 i v      i iiiv  i i   i----
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_104203215_   3793 -CCAGTAAGAAAATGGGCAAAAGACATGAAGAAATGTTTCATGAAAGTGG 3841
                         -   i v?i            i  iv    v i ii    viv    vi 
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_104203215_   3842 AGCTATGAATGACAAATATGCACATGAAAAGATGTGTAA-ATCACTAGCT 3890
                          vv  ii    i v    v               ivi  -    ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_104203215_   3891 AT 3892
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.51 (68 / 45)
Gap_init rate = 0.03 (14 / 445), avg. gap size = 1.93 (27 / 14)  


3100 25.72 2.21 1.99  chr2_104315461_104320286     3429  4334 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_104315461_   3429 TAAAAAGACAAACCATTTTTATGGATTGGAAGAATTCAAATTGTTTAAAT 3478
                          ii     i vv    v  i             v  v v      v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_104315461_   3479 ATTAATACTACCCAAAGTGATCTATAGATTCAACACAATTCCCATCAAAA 3528
                         ivi      v      v       i         i    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_104315461_   3529 TATTAATGACATTCTTCACAGAAATAGA------GA-----AAATTTATA 3567
                          vii iivi v  i  ii       v  ------  -----     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_104315461_   3568 CAAAACCTTAAAAGACTCCAAATAGCCTAAGAAATCCTGAGCAAAAAGAA 3617
                         iii  vivi  ii   i vi       v  iv    i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_104315461_   3618 CAAAGTGGGAGACAACACACTATCTGATTTTAAACCATACTACAAAGCTA 3667
                               v    ivvv      vi ii    i   v v             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_104315461_   3668 TTGTAACTAAAACAGCATGGTACTGATATACAAGCAGACACATAGGCCAA 3717
                         iv    ii  i    ii        ii   viiii     i    ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_104315461_   3718 TGAAATAGAATAAAGAACCCAGAAATGAATATATTTATTTACAGTCAACT 3767
                           i        vi   ii        i  ivi  vi     ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_104315461_   3768 GATTTTTGACAAGG-CACCAAGAACATACATTAAGGAAAGAACAACCTCT 3816
                               i       -ii      v   v  v ii        i ii  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_104315461_   3817 TCAGTAAATGATGCTGAGTAACCTGGATATCTATATACAGAGGAATAAAA 3866
                            ii     i     i vv v       ? i i  i  i i    i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_104315461_   3867 CTAGTGTCTTATCTCTCACCATATAAAAAACTCAACTCAAA-TAAATTAA 3915
                         i i vvi i  i   v         v    v i        - ii  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_104315461_   3916 ACACTTAAATATGAGAACCTAAACTATAAAACTAATTTAAAAAA-----T 3960
                          v  i     i i   i iv             --i   i  i ----- 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACT--CTTAGAAGAAAACAT 548

  chr2_104315461_   3961 AGGAG-AAATGCCTGAGT-ACATTGGTCTAGACAAAAATTTTATGGATAA 4008
                            ? -    --  vv  -  v    vi   i   vii   iv i    v
  L1M4_orf2#LINE/    549 AGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_104315461_   4009 GACTCCAAAAACACAGGTGAGAAAAGCAAAAATAGGCAAATGGAATAATA 4058
                            v      i    i ii v     v        ii    v i ivvi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_104315461_   4059 TCAAACCAAAAACCTCCTGCACAGCAAAAAGAAGCAATCAAAAGAGTGTA 4108
                              viv    v  ii  ii vv    i-  vi v     i i    v 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGAA 695

  chr2_104315461_   4109 GAGACAACTGACAGAATGGGAGAAAATATTTGCAAACTATTCATCTGACA 4158
                         i       iv                          ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_104315461_   4159 AGGGATTAATATCCAGAATACACAAGGAACTCAAACAACTCAATAGTAAA 4208
                              i vi           i i  i      vv           i    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_104315461_   4209 AATGATTAATAATAATAATAATGGTCCAGTTAAAAAATTGACAAAGGGTT 4258
                           -  iv     i------------   i  ?      v i      i  
  L1M4_orf2#LINE/    796 AA-GACAAATAAC------------CCAATTWAAAAATGGGCAAAGGATT 832

  chr2_104315461_   4259 TGAATAGACATTACTGTTAAGAATTCATGCAAATGGTCAATGGGCATATG 4308
                                     v  viv     vvi  i       i    ii   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_104315461_   4309 AAAAAACGCTCAACATCACTAATTGT 4334
                             i i           ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (151 / 78)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.17 (38 / 12)  


3447 24.75 0.88 1.42  chr2_104330161_104334551     2987  3899 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_104330161_   2987 TGGAGAAATATTCCATGTTTATTGATTGGAAGAATCAATATTGTTAAAAT 3036
                             i i    i       i  v          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_104330161_   3037 GCCCATATTACCCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 3086
                          v v   i v      vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_104330161_   3087 TATCAA-TGTTATTCTTCACAGAAATAGAAAAAA-AATCATAAAATTTAT 3134
                          vi  i-  ii-  i  ii       v  v  iv-i   v       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_104330161_   3135 ATGCAACCACAAAAGGCCCAGAAGAGCTTATCCTAAGCAA-----AAAAA 3179
                            v  vii   ii i       v   ----- v  i   -----     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGC-----CAAAACAATCTTGAAAAA 194

  chr2_104330161_   3180 AAAGAAAAAAGAAAACTGGAAGAATCGTGTTACATGACTTTAAATTATAC 3229
                         i     v    ----i    i  v  iiii v vii i  i   viv   
  L1M4_orf2#LINE/    195 GAAGAACAAAG----TTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_104330161_   3230 TGCAGAGCTATAGTAACCAAAGCAGCATGGTACTGCTATAAACAGAGACA 3279
                          i  i     i     i   ii   ii        vi    iv v     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_104330161_   3280 TATAAACCAATGGAACATAATAGAGAACCTAGAAACAAATCCACACACCT 3329
                             i i        i v   v    ii i     i   i   i   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_104330161_   3330 ATAGTGAACTCATTTTCAACACAAGTGCCAAGAACATACACCAGAGAAAA 3379
                           i  v  i v      i   vii         v   v  vii i    i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_104330161_   3380 GACAGTCTCTTCAATAAATGGTGCTGGGAAAACTGAATATCCACATGCAG 3429
                         i i     i     i              v     i   ?         i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_104330161_   3430 AGGAGTGAAATTAGACACCTATCTCTCACCACATACAAAAATCAAATAAA 3479
                          i  i    i  i   v    i   v     i          i  v v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_104330161_   3480 AATAAATCAAAGACTTAAATCTAACATTTCAAACTATGAAACTGCTACAA 3529
                            ii    ?    i     v   v vi v       i     vi  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_104330161_   3530 GAAAACATTGGGGAAATTCTCCCAGACATTGGTCTGAACAAAAGTTTCTT 3579
                                 v  ? v  v   i vv   v    vi iii   vi       
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_104330161_   3580 GAGCAGTACCTCACAAGCACAGGCAACCAAAGCAAAAATGGACAAATGGG 3629
                         iiii vv  vi  v       i     v    v      i  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_104330161_   3630 ATCACATCAAG-TTAAAAAGCTTCTGCATGGCAAAGGAAACAATTGAAAA 3678
                          iiv      i-       -   i  iiivv       v  v  ii i  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_104330161_   3679 GGTGAAGACATAACGCACAGAATGGGAGAAAATATTTATAAACTACCCAT 3728
                         i     i v i   v                      ii   ii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_104330161_   3729 CTAACAAGAGATTAATAACCAGAACATATAAGGAGTGCAAACAACTCTAT 3778
                           i i   i  i vi  v      i      i  iiv vv       v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_104330161_   3779 TGGAAAAAAAATCTAATAATCCAATCAAAAGGTGGGCAAAATGTTTGAAT 3828
                         viv     i -- v     i     i?   ii        ivi       
  L1M4_orf2#LINE/    790 AATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_104330161_   3829 AGACATTTCTCAAAAGAAGACATACAAGTGGCAAACAGGCATATGAAAAT 3878
                                    v        i      i    v  i i   i       v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_104330161_   3879 GTGCTCAACATCACTGATCAT 3899
                         i            ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (143 / 79)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.33 (21 / 9)  


1946 23.40 19.95 3.84  chr2_104338219_104342600     3109  3890 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_104338219_   3109 TGAAAAGATATAC-ATGTTCATGGGTTAGAAGAATTAATGTTGTTAAAAT 3157
                           i        v -          i  i     v     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_104338219_   3158 ATCCGTATGATACAAACAGATATAACTGGTTTAATCCAATCCCTATCAAA 3207
                         iv vi  ivviv    iv   v  - v i  i  iv              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTA-CAGATTCAACGCAATCCCTATCAAA 99

  chr2_104338219_   3208 ATTCCA----------------AAAT----------ACTCTAAAATTCAT 3231
                           i   ----------------    ---------- ii           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_104338219_   3232 ATAGAACTACAAAAGATCCCAATTAGCCTAAACAATCTTAAGTAAGAAAA 3281
                           i   v i   ii  i  vi v     v          i iv     i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_104338219_   3282 ATACTTACTTAAGATTGCATTAACTATTGTGGCATTGCACTGCCTGATTT 3331
                          i -------   -   v -----------  vv ii    v  ii    
  L1M4_orf2#LINE/    200 ACA-------AAG-TTGGA-----------GGACTCACACTTCCCAATTT 230

  chr2_104338219_   3332 CAAATTATGTTATACAGCTACAATAATTAAAACAGAATGATGCTGGCATG 3381
                             viv ii  i v       i    i  i    vi  i i       i
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_104338219_   3382 AATACAAATATCTAGACT----GAATAAA-----GAGCCTAG-------- 3414
                          iv i i i  v    ii----     i -----   i i  --------
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr2_104338219_   3415 CCA---------GGT--ATT---CTTCAACAAGGGCACCAAGA--ATACA 3448
                            ---------   --   ---i   i       ii      --  v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_104338219_   3449 TGTGGGGAAAGGAAATTCTCTTCAACAAACAGTGTTGGGAAAACTAGACA 3498
                         -i         i v v   i         ii   i     v    i  i 
  L1M4_orf2#LINE/    381 -ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_104338219_   3499 TTCACATGCAGAAAACATGAAATTGGACCCTTGT-----ACCATACACAC 3543
                         ?i        i  i -     i        i ii-----      i   v
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGA-ATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_104338219_   3544 ATATCAACTCAAAGTAGATTAAAGATCTAAAAGTAAGACTTGATGCCTTA 3593
                          v  i        i i   i ?   i     v      vi i vi iv  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_104338219_   3594 AAACTCCTCAAATAAAATGTAGGGGTAAATCTCCTTGACAATGGCCTTGG 3643
                               i vi  v    ii    ?        i v    vv   vi v  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_104338219_   3644 CCATGATTTTTGAGGTATTACACCAAAAGT-------------------- 3673
                          v   i   i v  i   v          i--------------------
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_104338219_   3674 --------TTGA-----------------------TATGC---------- 3682
                         --------   i----------------------- i   ----------
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_104338219_   3683 -----------------------------AGAATAAGAGAAAATATTTGC 3703
                         -----------------------------     ii              
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_104338219_   3704 AACT-ATACATCTGATAAAGGGTTAATATTAATATCCAGAATATACAAGG 3752
                           v -   i         i  ------ i vi             i  i 
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGG------ACTTGTATCCAGAATATATAAAG 772

  chr2_104338219_   3753 AACCTACACCACTCAATAGCAAGAAAATAAATAACCAAACTAAAAAATGG 3802
                            iivi  v        ii  i  i i        v  i ?        
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_104338219_   3803 AAAAATGACCTGAATAGAAATTTTTCCAAATCACACATAAAAAAATAACC 3852
                         iv   v  ii        v    i      --iv v   v v    ii  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAA--GAAGATATACAAATGGCC 870

  chr2_104338219_   3853 AATAGACATATTAAAAGGTGTTCAACATCACTAATCAT 3890
                             ii  i  v     i  i         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (120 / 59)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 8.09 (186 / 23)  


2173 25.22 14.29 1.49  chr2_104531697_104535499.rev     2507  3311 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_104531697_   2507 TAAAAATACACACAATGTTAATGAATCAGAAGACCCAACATAATAAAGGT 2556
                          ii   v i iv v     v   i  ii      ii  i  vi v   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_104531697_   2557 GTTAATTATCCCCAAATAGATAGATCTATGAGCTTAGTGCAATTTCTATC 2606
                          vi   vv         --- -      iiiii i ii     ii     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT---T-GATCTACAGATTCAACGCAATCCCTATC 96

  chr2_104531697_   2607 AAACTTC-AGCAATGGTTTTTGTAGACATAAACAAGTT-----TAA--TT 2648
                            v i -   viivv      i   v  vi     i -----   --  
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_104531697_   2649 TAAGTGGAAAAGCACAGCTCATAAAATAGCTAAAAACAATTTTGAA---G 2695
                         i vi      v   vi vv vi i      i    -    i     --- 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAG 195

  chr2_104531697_   2696 AAGAATAAAGTAAGAAGAT------------ATT--AAAGCTCACTACA- 2730
                              i     vi  i  i------------   --   i  i      -
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_104531697_   2731 -----TAATAATTGAAGACAGTGAAGTACTGGCAGAGGGATAGACA---A 2772
                         -----i i    i-         vi         v i         --- 
  L1M4_orf2#LINE/    246 AGCTACAGTAATC-AAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_104531697_   2773 GGAAGAGAGAAAAGAATAGAGAACTCAAAAATAGTC---TACACTAATAT 2819
                          ivvi vi   v     v    iii  i     iv ---    i --   
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TAT 342

  chr2_104531697_   2820 ACCCAACTAATTTTTGACTAAGGTGCAAAAGCAATTCAGTAGGTAAAGGA 2869
                         ivi   i i     i   v i     v  ii v     i i  v    i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_104531697_   2870 TAGCCTTTTCAATAAACTGTATTGGAGAAATTGGGCATCCATATAAAAAA 2919
                            i        i   iv  ii   iiv  i   ii ?   i  iv    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_104531697_   2920 AAATGATCCTCCACCTAAATCTCCCACCTTCTACAAAAATTAACTCAAAA 2969
                         i     vvi vv   ivv i   v    v v                   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_104531697_   2970 TGGATCACAAGTTTAAATGT----GGTAAAA-TATCAAACTTTTATTAAA 3014
                                ? iiii       ---- v     -   v     i   vv i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_104531697_   3015 AAGCACAGGAG-AAATCTTTCAGGAATTAGGGCTAGACAAATAGTT-CTT 3062
                           i  i   ? -       - iv  vi v   i   i   - i   -   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAA-TGGTTTCTT 590

  chr2_104531697_   3063 AGACATGACATTAAAAGCACAATCCATAAAGAGAGAGACTGATAAATTGA 3112
                            i      ii          v v i   iii i i iv         i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_104531697_   3113 ACTTCATCAAAAATAAAA-CTTTTG--CTCTGAATAAACCTTGTTAAGAA 3159
                                     v     -      --  iii  -ii  vi i i     
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAA 689

  chr2_104531697_   3160 GATGAAAAGACATGCCACAGACTGGTCGAAAATATTTGCAAA-------- 3201
                         ii          vv       v   vv               --------
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_104531697_   3202 -------------------------------------------------- 3201
                         --------------------------------------------------
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_104531697_   3202 ----------CAAACAATCCAATTAGAAAATGGGCAAAAGATATGAACAG 3241
                         ----------    i  i      ?i            i   v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_104531697_   3242 ACATTTTACTGCAGAAGATACGCAGATGGCAAATAAAGCACATGAAACAA 3291
                               iv iiv        ii  i     v     -          vi 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAA-GCACATGAAAAGA 888

  chr2_104531697_   3292 TGTTCAACATCATTAGCCTT 3311
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (130 / 69)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 5.08 (127 / 25)  


2979 27.05 0.88 1.42  chr2_104698994_104705080.rev     4723  5635 (452)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_104698994_   4723 TGGAAAAACATTCCATGCTCATGGATAGGAATAATCAATATCATGAAAAT 4772
                               i i  i     i        v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_104698994_   4773 GGCCATTCTGCCCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 4822
                            v  v  v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_104698994_   4823 TACCATTGATTTTCTTCATAGAATTAGAAAGAACT-ACTTTAAATTTCAT 4871
                          v   viviii  i  iii    v v  v - i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr2_104698994_   4872 ATGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTGGGCAAGAAGA 4921
                               viiv  ii  v  v v        i      i  iiv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_104698994_   4922 ACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATGCTACAGGACT 4971
                               i      vv   vi  v  ii i      viv i     iii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_104698994_   4972 GCAGTAACCAAAACAGCATGGTACTTGTACCAAAGCAGATATATAGACCA 5021
                         i      i   i    ii       v i iv iiii   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_104698994_   5022 ATGGAACAGAACAGGGGCCCCAGAAATAATACCACACATCTACAACCATC 5071
                               i    iv i ivi          vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_104698994_   5072 CGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATTCCCTA 5121
                         i   i  i     ivv  v   i v  vv      i     i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_104698994_   5122 TTTAATAAATGGTTTTGGGAAAATTGGCTAGCCATATGCAGAAAAATGAA 5171
                           i  i       vi     v  i   v  ?   i     i  i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_104698994_   5172 ACTAGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 5221
                         ii i       v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_104698994_   5222 AAGACTTAAACCTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACTTA 5271
                         ?    i    iv     v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_104698994_   5272 GG--TAATACCATTCAAGACATAGGCATGGGCAAAGACTTCATGACTAAA 5319
                           --   - i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    550 GGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_104698994_   5320 ACACCAAAAGCAATTGCAACAAAACCCAAAACAGACAAATGGGATCTAAT 5369
                                     vvv         vvv    i   i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_104698994_   5370 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 5419
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_104698994_   5420 GGCAACCTACAGAATGGGAGAC----TTTTTTAATCTATCCATCTGACAA 5465
                          i     i             v----   viv    -  vi      i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAA 746

  chr2_104698994_   5466 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5515
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_104698994_   5516 AAACAAACAACCCCATC-AAAATTGGGTGAAGGATATGAACAGACACCTC 5564
                          i     i     v  i-    v    ii      v    i     ii  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_104698994_   5565 TCAAAAGGAGACATTTATGTGGCTCATCATCACTGGTCATTAGAGAAATG 5614
                           v    i   i  vi vi    iv  v v   -----  v i - i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCAC-----ATGAAA-AGATG 890

  chr2_104698994_   5615 CAAATCAAAACCACAGTGAGA 5635
                          ---    v i  ????????
  L1M4_orf2#LINE/    891 C---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.91 (21 / 11)  


1090 23.28 11.34 3.88  chr2_105026593_105028625      497   831 (1202)    L1M4_orf2#LINE/L1      165   524 (384)  

  chr2_105026593_    497 ACTTAAAATAGACAAAACAATTTTGAA---GAAGAACAAAATTGGGTGAC 543
                           ii i     v         i     ---          i    iv   
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_105026593_    544 TTACACTAACTGATTTCCATATTTGTTATAAAGATGCAATAATCAAGAC- 592
                          i     vv ii     v v i  ii  i    v i  i          -
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_105026593_    593 -TGTGATACTGGTGTAATGATGGACATATAGGTCAGTGGAACAAAATAAA 641
                         -    i      ii   v   i         i   i     i i   vi 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_105026593_    642 GAGTCCAGAAATAAACTCATACAAATGTGATCAACTAATTTTCAATGAAA 691
                                         i      vv i  i    i i      i ii ii
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_105026593_    692 GTGTCAGTGTGATTCAATGGCAGAAATTATAG------------------ 723
                            i  iviiv         -i    vv    ------------------
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_105026593_    724 ------------AATATCGGCATGCAAAAAAAAAAAACCTCCAATAAACC 761
                         ------------i   ? vi         i  ------------ i  vi
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAA------------TGAAGT 451

  chr2_105026593_    762 TCGATCCTTACCTCACA---TGCATAAAAATAAACATGAGATGGAACATA 808
                          v  i  i         --- ii i      v   vii i     v  ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_105026593_    809 GACCTAAATATAAGAACAAAAAC 831
                                  i     i v     
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAAC 524

Transitions / transversions = 2.45 (54 / 22)
Gap_init rate = 0.02 (6 / 360), avg. gap size = 8.50 (51 / 6)  

 974 22.29 3.10 4.64  chr2_105026593_105028625     1219  1541 (492)    L1M4_orf2#LINE/L1      591   908 (0)  

  chr2_105026593_   1219 AAATATATCACTGAA-GCATGATCCATAATAGAAAAAATTGATAAATTGT 1267
                          i    iv   ii  -   ii v v i  v         v         v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_105026593_   1268 ATTTCATCAAAATTAAAAATGTTCCT-TTTCAAAAGACAC----AAGAAA 1312
                          i                 iv  iv -i      i     ----      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_105026593_   1313 ATGAAAAGGTCAGCCATTGGTCAGGAGAAAATATTTGCAAAACATATGTC 1362
                         i       iiv v   iv ivii                  v     i  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_105026593_   1363 TGACCAACAATTCGTATCCAGAATATATAACTAACCCTTATAATTCAA-- 1410
                            iv ivi i i                 vv   i    i  i    --
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_105026593_   1411 ATATAAGCGCTCTTTCAAATCAATAATAGAACAAAAAGAGAGGGGTGGTG 1460
                            v  ---------- i iv     ivv  iv?   i vi  -----ii
  L1M4_orf2#LINE/    791 ATAAAA----------AGACAAATAACCCAATTWAAAAATGGG-----CA 825

  chr2_105026593_   1461 GAAGATTTGGATAGACATTTG-CTGAAGAAGATATGCAAATGGAAAATAA 1509
                         i i      i          v- ii          i       vv     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_105026593_   1510 GTACATAAAAAGATGATCA-CATCATTAGTCAT 1541
                          i    i        v   -     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (44 / 27)
Gap_init rate = 0.03 (8 / 318), avg. gap size = 3.12 (25 / 8)  


3387 22.40 2.23 0.50  chr2_105028833_105039149.rev     3396  4203 (6114)    L1M4_orf2#LINE/L1       87   908 (0)  

  chr2_105028833_   3396 AATCCCTACCTAAATCCCAATGGCACTTTTTGCAGAAA-CAAAAAAAAAA 3444
                                 i v        iiv  vi            -ii v  ivvi 
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr2_105028833_   3445 TCCTGAAATTTGAATGGAATTGCAAAACACCCTGAATAGCCATAATAATC 3494
                             i     iiv      v     iiv    v         v  i    
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_105028833_   3495 TTGAGAAAGAAGAACAAAGCTGGAGGCTTCATACATACTGTTTTCAAAAC 3544
                             i              i      vi   i  v v iiv         
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_105028833_   3545 ATATTACAAAGTTACACCAATCAAAAGAGTATGGTACTGGCATAAAGACA 3594
                         v  i       i    vi      i v   i              i  i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_105028833_   3595 GACATATAGACCAATATAACAGAATAGAGAGCCCAGAAATGTTCCCTTCA 3644
                                   i    iv  i     v     i        ivv   v - 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-A 335

  chr2_105028833_   3645 CATCTATGGTCAAATGATCCTTGACAAAGATACCAAGACTACACAATGGG 3694
                            i         v    ii i     i i i       i iv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_105028833_   3695 GAATGGATAATTTCTCTAACAAATTTGGTTAGGAAAATT-------CATA 3737
                            v i   i i i ii       vvv i i   v  i -------  i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_105028833_   3738 TGTAAAAGGAAAAAGTTAGGCCCTTTTCTTATACCATACACAAAAATTAA 3787
                           i     i vi     i i   i vi  i i      i           
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_105028833_   3788 CTTGAAATTAATTAAAAACCTAGAGATAAGACCTGAAACTATAAAATTCT 3837
                           ii    vi  i ? i     i vi     v  i           i   
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_105028833_   3838 TAGAAGAAAACATAGGAGGAAACCTTCATGACACTGGATTTGGCAATGAT 3887
                                         ? v   i    i    vi   i  v       i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_105028833_   3888 TTCATGAATATGACATCAAAAACACAGGCAACAGAAGCAAAAATA----A 3933
                            v ii        i     i    i      i   v       ---- 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_105028833_   3934 ATGGGACTACATCAAACTTTAAAATTTCTGCTCAACAAAGGAAAAAATCC 3983
                           v     v       v  v    i  i  iv vv       v vv   v
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_105028833_   3984 GCAGCATGAAAAGTCATCCTGCA-AATGGGAGGAAATATTTGCCAACCAC 4032
                         iv ivi       v  v  ii  -        i          v  i  i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_105028833_   4033 ATATCTGAAAAGGGGATAATAATTGGAATATATTTTAAAAACTCTGACAA 4082
                                 v     iv vi  viii        --v  i      v    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATAT--AAAGAACTCTTACAA 783

  chr2_105028833_   4083 CCCAATAACAA----CCAAA-AACTTGATTTAAAAATGGGCAAACAACCT 4127
                          i      i  ----v    -   iii   ?             vi ii 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_105028833_   4128 AAATGGGCATTTCTCCAAAGAAGATATACAAATGGCCAAGAAGCATATGG 4177
                         i   i i                                v     i   i
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_105028833_   4178 AAGACATGTTCAACATCATTAATTAA 4203
                           - v   i         ????????
  L1M4_orf2#LINE/    884 AA-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (112 / 66)
Gap_init rate = 0.01 (9 / 822), avg. gap size = 2.44 (22 / 9)  

3062 28.02 0.78 0.22  chr2_105028833_105039149.rev     8923  9825 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_105028833_   8923 TGGGAGAACATTCCATGCTCACGGATAGGAAGAATCAATATCATGAAAAT 8972
                            i ii i  i     i   i    v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_105028833_   8973 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAATC 9022
                            v     v     iv i  i  i        i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_105028833_   9023 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTACATA 9067
                          v   iivi i  i  ii     v v  v  i--- --     i v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_105028833_   9068 TGGAACAAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAGAA 9117
                              vviv  ii  v  v v  v     i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_105028833_   9118 CAAAGCTGGAGGCAGCATGCTACCTGACATCAAGCTATACTACAAGGCTA 9167
                              i      vvv  ii  v  ii iv    iviv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_105028833_   9168 CAGTAACAAAAACAGCATGGTACTGGTGCCAAAACAGATATATAGACCAA 9217
                               iv  i    ii         iiiv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_105028833_   9218 TGGAACAGAACAGAGGCCTCAAAAATAACACCACACATCTACAACCATTT 9267
                              i    iv   ivii  i      vv   i    i  iiii  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_105028833_   9268 GATCTTTGACTAACCTGACAAAAACAAGAAATGGGGAAAGGATCCCCTAT 9317
                            i  i   v ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_105028833_   9318 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 9367
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_105028833_   9368 CTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGACGGATTAG 9417
                         i    i    v   i     v  i           i    i i    i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_105028833_   9418 AGACTTAAATGTTAGACCTGGAACCATTAAAACCCT-AGAAGAAAACCTA 9466
                             i       v   v  ii   i  -     i  -          v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATA 549

  chr2_105028833_   9467 GGCA-ATACCATTCAGGACATAGGCATGGGAAAGGACTTCATGACTAAAA 9515
                           ?i- v i -   iv   v v  vv i  v  v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_105028833_   9516 CACCAAAAGCAATGGCAACAAATGCCAAAATAGACAAATGGGATCTAATT 9565
                                    vvi        v vv        i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_105028833_   9566 AAACTAAAGAGCTTCGGCACAGCAAAAGAAACTACCATCAGAGTGAACAA 9615
                            v v  i i   iv ii vv    i  v    i  vv i      v i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_105028833_   9616 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAG 9665
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_105028833_   9666 GGCCAATATCCAGAGTCTACAAAAAACTTAAACAAATTTACAAGAAAAAA 9715
                          i ivi        i v  i   i    ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_105028833_   9716 ATAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 9765
                          i   i     v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_105028833_   9766 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 9815
                         v        i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_105028833_   9816 CACTGGCCAT 9825
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (150 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


1898 19.85 2.28 19.58  chr2_105081894_105085823     2351  3448 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_105081894_   2351 TGAAAAAATATATCTTGCTCATAGAT---AAGAGTTAATATAGTTAAAAT 2397
                           i   i    vi v  i    i   ---    v       v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_105081894_   2398 AT--AGAGTCTTCAAACTGGTATGCAAAATCAATGAAATTCCAGTCAAAA 2445
                         iv-- v v  ii    i  i v i  i v    i v   i  vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_105081894_   2446 TTC-AACTGCCTTTTTTTATAGAAATTGAAAAAGCTCATTTTAAACTTTA 2494
                          i - i           -ii         v  -   v  ii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr2_105081894_   2495 TATGGAGGTGCATGGGACCTAGAAGAATCAAAATGATGCTGAAAAAGAAT 2544
                               ii    v      i    v ii     ii  vi          v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_105081894_   2545 AACAAAGATGAATAACTCAAATATCTGTGTGT-AAGCTTTACAATAAAGC 2593
                                v  i vi     v iv  ivvi v -  ivi    v i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_105081894_   2594 TACAATAATCAAAACAGTGTGGTATTGGTGTAAAACTGGACAAACTGATC 2643
                             i       i           i   ii   iiv i    v iv    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_105081894_   2644 AATGGGATAGA-TT------CTAGAATATAGACTAACATATGTATGGTAA 2686
                              i     -  ------ i    -   i  iv i i  v      v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAA-ATAAACCCATACATTTATGGTCA 347

  chr2_105081894_   2687 ATTTATTTTCAACAATAGTGCTAAGTTAATTCAGCAGGAAAAGGATAATC 2736
                            v      i    vi    i   viv     iii  i    i   i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_105081894_   2737 TATTCACCAAATAGTTGTTAGAACAATTGGATAGCCATATACAAAA-AAT 2785
                          v    v     i  - i i i    i      ?   i  i     -   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGT-GCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_105081894_   2786 AACCATA-ACCTTTCCTTCACATTTCCATCATATAAAAAATTAGCTTTAT 2834
                         i vvv i-   ii v i     ---    -   i     -----------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACA---CCAT-ATACAAAAA----------- 481

  chr2_105081894_   2835 TCTGCTGAGCAGTCAAGGGAGGAAAAGAATTAACTTGAAATGGATCATAT 2884
                         -----------------------------      ii          ? v
  L1M4_orf2#LINE/    482 -----------------------------TTAACTCAAAATGGATCAWAG 502

  chr2_105081894_   2885 ATGTAAATATAAGAGCAAAAACT-TAAAAATATCCAGAATAGAATACAAA 2933
                          iv     i       v      -     v v i-    v i  i i ii
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTT-AGAAGAAAACATAGG 551

  chr2_105081894_   2934 ACAAAACCATAGTAACCTTGGATTCAGCAAAGAGTTATTTTTGTTGCTGT 2983
                         ?vv   i v v  i       i  vi    -----------------  -
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAA-----------------TG- 583

  chr2_105081894_   2984 GTTTCCTTTCTTTCTTTTTTTAGATATGGGGTCTTGCTGTGTTCTGTAGG 3033
                              --------------         ----------------------
  L1M4_orf2#LINE/    584 GTTTC--------------TTAGATATG---------------------- 597

  chr2_105081894_   3034 CTGGGCTTGAACTCCTGGCCTCAAGTGATCCTCCCCACTCGGCCTCCCAA 3083
                         --------------------------------------------------
  L1M4_orf2#LINE/    598 -------------------------------------------------- 597

  chr2_105081894_   3084 GTAGCTGCAGACTACAGGCACATGTCACCATACCCAGCTAGAATTTGTAA 3133
                         --------------------------------------------------
  L1M4_orf2#LINE/    598 -------------------------------------------------- 597

  chr2_105081894_   3134 ATATGACACAAAATGTATAAACTATAAAAAGAAAAATGAGAACAAGTGGA 3183
                         -----    v   v i i  i v i    ii      -   vv  v    
  L1M4_orf2#LINE/    598 -----ACACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAATTGGA 641

  chr2_105081894_   3184 TTTCATCAAAATTTAAAACTTTTGCCCTACAAAAGACAATGTTAAGAAAA 3233
                         i            v          iv  v    i    v i i      i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_105081894_   3234 TTAAAAGGCAAGCCACATACTAGAAGAAATTATTTGAAAA--AAGTGTCT 3281
                          v     i   v     v v i i     v      v   -- vi i   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_105081894_   3282 TACAAAGAACTTCTATATGGAATACATAAAAAGCT--TATGATTCAAAAA 3329
                         v i  i i    v   vii     i     i i  --  ii i    v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_105081894_   3330 TAAGAAGACAAA----CCATGTTTTTAATGGGCAAAAGATTTAAACAGAT 3375
                            i        ----   vv ?vvv          i     i  i   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_105081894_   3376 ACTTAGCCAAATAAGGTATACAGATGGTAAATAAGCACATGAAAGGATGT 3425
                          i  vv     v   i      i    iv               i    i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_105081894_   3426 TCAACCTAGTTATCAGGGAATTA 3448
                              ------    ????????
  L1M4_orf2#LINE/    892 TCAAC------ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (130 / 84)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 9.23 (240 / 26)  


3103 25.97 1.33 0.55  chr2_105086628_105091271.rev     3252  4152 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_105086628_   3252 TGGAAACACATCTCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3301
                               v i   i    i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_105086628_   3302 GACCATACTGCCAAAAGAAATCTACAAATTCAATGCAATTCCCATCAAAA 3351
                          i v     v  v   vvi       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_105086628_   3352 TTCCA-CCGTCATTCTTCACAGAGCTGGAAAAAC-AATCCTAAAATTGAT 3399
                          i   - i i -  i  ii    iv v  v  i -i           v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_105086628_   3400 ATGGAACCAAAAAAGAGCCCACAG-AGCCAGAGCAAAACTAACCAAAAGG 3448
                               viiv  ii  -    v i-     i i   vvi i vv  i i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_105086628_   3449 AAAAAATCTGGAGGCATCACATTACCTGATTTCAAACTATACCATAAGGC 3498
                           v   vi      vv     i v  ii        viv   i i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_105086628_   3499 CATAGTCACCAAAACATCATGGTACTGGTATAAAAATAGGCACACAGACC 3548
                         i i   v i   i   vii         i    ii    i  i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_105086628_   3549 AATGGAACAGAATAGAGAATCCAGAAATAAACCCAAATATACTTACAGCC 3598
                                i     v    i                --  i i   ii i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTC 346

  chr2_105086628_   3599 AACTGATCTTCGACAAAGCAAGCAAAAACATAAAGTGGGAAAGGGACACC 3648
                           i    i        i vviv   i v   vv i    i  i i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_105086628_   3649 CTATTCAACAAATAGTGCTGAGATAATTGGCAAACCACATATAGAAGAAT 3698
                           v          i      i  i  i   vv ?      ii i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_105086628_   3699 GAAAATGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGGTGGA 3748
                            iv    i  ii i   v    v           i       ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_105086628_   3749 TTAAGGACTTAAATCTAAGACCGGGAACTGTAAAAATTCTAGAAGATAAC 3798
                          i ?i   i     v     v vii    i     v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_105086628_   3799 ATCGAAAAAAACCTTCTAGATGTTGACTTAGGCAAGGATTTCATGACCAA 3848
                           v i?iv   i    vv  iv   iv        v i    v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_105086628_   3849 GAACCCAAAAGCAAATGAAATAAAAACAAAGTTAAATAGCTAGGACTTAA 3898
                           vv         v v v  i    iv   iv  i   iv v      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_105086628_   3899 T--AAACTAAAAAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAA 3946
                          --   i      -      ii vv    i iv  vi   iv i   i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_105086628_   3947 CAGACAACCCACAGAGTGGGAGAAAATCTTCACAAACTATACATCTAACA 3996
                         v              i           v  ii    ii   i    i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_105086628_   3997 AAGGACTAATATCCAGAATCTACAATGAATTCAAACAAATTAGCAAGAAA 4046
                          i     vi          v  i  v   i  vv    v i ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_105086628_   4047 AAAA--AATCAC---ATCAAAATGCATGCTAAGGACATGAATAGACAATT 4091
                           i --   v  ---  i?   viiiv  v     iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_105086628_   4092 CTCAAAAGAAGATATACAAGTGGCAAACAA--ACATGAAAAGATGCTCAA 4139
                            v               i    v  i  --                  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_105086628_   4140 CATCACTAATGAT 4152
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


2852 17.88 1.12 0.19  chr2_105206159_105208811      839  1375 (1278)    L1M4_orf2#LINE/L1        1   542 (366)  

  chr2_105206159_    839 TGAAAAGACATCCCGTGTTC-TAGATGGAAAGACTTAATATTGTTAAGAT 887
                           i     i     i     - i   v i                     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_105206159_    888 AATAACACTACCCAAAGCAATCTAGAGATTTAACACCATCCTTGTTCAAA 937
                         iii  i   v      vii     v     i   i v    i i iv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_105206159_    938 TTCCAACAGTGTTCTTTGCAGAACTGGGAAAGCCAACCCTCAAATTTATA 987
                          i   i v iv  i         v v iv    ii i   v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_105206159_    988 TGTAATTGCAAGGGACCCCAAATAGCCA-CACAATCTTGGAAAAAATGAA 1036
                           v  v            vi        -v         i    i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_105206159_   1037 CAAAGGTGGAAGACCCACATCTCCTGATTTCAAAACTTACTATAAAGCTA 1086
                              v    i   i    ii   ii                i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_105206159_   1087 AAGTAATCAAAGCAATATGGTACTGGCATAAAGATAGACACACTGACCAA 1136
                         v         ii  i i              i        i iv  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_105206159_   1137 TGGAATAGAATTGAGAGTCCAGAAATTAATC-ATACATGTGTGGCCAATT 1185
                                                   v  i -      v i   i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_105206159_   1186 GATTTTTGATAAGG-TGCCAACTCTG-TCAATGGGGAAAGAATAGTCTCT 1233
                               i  i    -      vv ii-                     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_105206159_   1234 CCAACAAATGGTGCTGGGACAACTGGATTTCCACATTCAAAAGAATGAAG 1283
                         i                           v?      v             
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_105206159_   1284 TTAGACCCCCTACCTCACA-TATAAATAAAACTTAGCTCAAAAAAGATCA 1332
                           i      -         -i   v i    v   i       vi     
  L1M4_orf2#LINE/    451 TTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_105206159_   1333 ATGATCTAAATATAAGAAAGAAACCTATAAAAATCTTAGAAGA 1375
                         ?v  i      i     ivv   v        v          
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

Transitions / transversions = 1.76 (60 / 34)
Gap_init rate = 0.01 (7 / 542), avg. gap size = 1.00 (7 / 7)  

 379 18.46 0.00 0.00  chr2_105206159_105208811     1671  1735 (918)    L1M4_orf2#LINE/L1      528   592 (316)  

  chr2_105206159_   1671 AAAAATCTTAGAAGAAAACATAGGGGTGAGTCTTCATAACCTTGGATTGG 1720
                             v                   ?  i i     i i       i  i 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_105206159_   1721 GCACTGGGCTTTTAG 1735
                            v   vi i    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAG 592

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.00 (0 / 0)  

1400 16.23 2.60 0.97  chr2_105206159_105208811     1855  2162 (491)    L1M4_orf2#LINE/L1      596   908 (0)  

  chr2_105206159_   1855 TGACTGACCAAAAGCATAAGTGACAAATGAAAAAATA----AATTGGACT 1900
                             --          i   ii     v         ----         
  L1M4_orf2#LINE/    596 TGAC--ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_105206159_   1901 TCATCAAACTGTACAACTTTT-TCCATCTAAGGATGATTGTTAAGAGGGT 1949
                                 v vv v       - v v  v     i- i i i    ii  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC-ACTATCAAGAAAGT 692

  chr2_105206159_   1950 AAAAAAACAGCCTATGGAATAGAAGAAAATATTTGGAAATTATTTATCTG 1999
                         i    i   i  i ii    i i            v    i  v      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_105206159_   2000 ATGAGG-ATTAATATCCTGAATATATAAAGAACTCTTAACACTCAACAAT 2048
                           i   - i vi     v                    vv      i   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_105206159_   2049 AAAAAGACAAACAACACAATTAAAAAACAG-CAAAGGACTTGAATAGACA 2097
                                    i   v     ?     ii -       i           
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_105206159_   2098 TTTCTCCAAAGAA-ATATATATATGGCCAATAAGCACATGAAAATATACC 2146
                                      -     i v                      v  i i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_105206159_   2147 TAATATCTTAAGTCAT 2162
                         i  i   v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (31 / 18)
Gap_init rate = 0.02 (7 / 313), avg. gap size = 1.57 (11 / 7)  


2602 25.45 4.46 3.12  chr2_105232636_105237006     2994  3889 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_105232636_   2994 TGGAGAAACATGCAATGTTCATGGATTGGAATACTCAACATAATGAAGAT 3043
                             i i i  v v                 v   i  i  vi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_105232636_   3044 GGCAATTCTATTCAAATTGATGTGCATGTTTAATGCAATTTCTATCAAAA 3093
                               v  vii         v i  vi  i  i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_105232636_   3094 TCCCAGGAAGATTTTTTTGTCTATATAAACAGGATTGTCCTAAAATTTAT 3143
                               vv- vi       ivv v  vi   i v vi          i  
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_105232636_   3144 TTTAAAAGGTAAAGGAACTAGAAAAGCTAAAGTAATTTTGTTTTTTAAAA 3193
                         v vi   v i  i   v i    v   i   ii   i   -------   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-------AAA 192

  chr2_105232636_   3194 AAGATAAAATGGAATTAATTAATCTACAC-----AATTTCAAGTCTTATT 3238
                             - i  iii i  iivvi iii    -----        iv    i 
  L1M4_orf2#LINE/    193 AAGA-AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_105232636_   3239 ATATAGCTGCAGTATTAAAGCCTGCATGGTCTTGGTGGAAG-ATAAACAC 3287
                          i v    i     v v   v v ii    vi   iiv   -   i   i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_105232636_   3288 TTGGATCAATGGAACGAAACAGAGAACCCATATAGAAACCCACACAAGTT 3337
                         v i           iii  iv    ii   v v v       i   vv v
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_105232636_   3338 CGG-CAACTGATTCCAAAATCAAACACAAAAGCGCAAAAACAATTCAATG 3386
                         i  -   i     i-----  i ---   ii i  v  i  v        
  L1M4_orf2#LINE/    342 TGGTCAATTGATTT-----TCGA---CAAGGGTGCCAAGACCATTCAATG 383

  chr2_105232636_   3387 G---AAGGATCATCTTTCCAACAAATGGTGCTGGAGCAATTGGACATCCA 3433
                          ---   i  vi     i                ii   i    i ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_105232636_   3434 CAGGGAAAAAAATCAAGGTTTAAATA---ACCTTTCACTTTATACAAATG 3480
                           v v    i   v   --  ii iv---    iv   iv        vi
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAG--TTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_105232636_   3481 TTAAT-----ATGAATCATAAATTACAATATAA-AGCATAACACTGTAAA 3524
                             i-----   i    ? i iivv   i   -   -   v   i    
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAA 530

  chr2_105232636_   3525 ACTTTTAGAAGAAAACATAG---TAGGGCTTGGTG---------TAGA-- 3560
                            i                ---  iiv   v   ---------   i--
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_105232636_   3561 ---GTT-CTCAGAGATGACACTTGGAAGCACAATCCATAAAAGAAAAAAC 3606
                         ---   -  i   v       i-ii        v v i           i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACC-AAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_105232636_   3607 TCAAAAATTAGACTTCATCAAAATTTAAACTATTTGTTCTGTAAAAGACT 3656
                         vv v     i               v   viv     v  vi   i   v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_105232636_   3657 TTGTTAAAAAGACTAACAGACAAGCGATAGGCTGGGAGAAAATACTTGCA 3706
                         i i i  i  iiiv  v      v v i  iv            i     
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_105232636_   3707 ACCTACATGTCTGACAAAGGATTCTTATCTAGAATATATCAAGAACTCTC 3756
                          vii i  i     i  i   i iv    i         v         i
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_105232636_   3757 -CAACGTCAACAGTAAAAAAA-AAA-AATCTAATATTAAAATGGGCTACA 3803
                         -    -    i i      i -   -  i i   v?v         v vi
  L1M4_orf2#LINE/    780 ACAAC-TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_105232636_   3804 TACATGAAGAGCCATGTCAGTGAAAAGGATATATGGAGGGCAAATAAGCA 3853
                         v iv    v  v   v  vvii  i i      iii v   v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_105232636_   3854 GATGAAAAGATAGCATCATCAACCATCAGGGAAATG 3889
                         v          -  ----     -    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGAT-GC----TCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.62 (68 / 26)  


1971 27.08 5.06 4.72  chr2_105555043_105559573     3150  4039 (492)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_105555043_   3150 TGTTCTTGAATTGGAAGACACAATATTATTATGATGACAGTTCTCTCAAA 3199
                              v  i          vi      i   v    i  i v   i v  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_105555043_   3200 ATTCATCTATAAATGTATTTTGTAATCTCATAT-AAAATACTAACAGA-T 3247
                            v     i i  vi vi-- i    i -   -     v i i v v- 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAAC--GCAATCCC-TATCAAAATCCCAGCTGCCT 112

  chr2_105555043_   3248 TCTTTGTTGAAACCTGACAAGGTGATTTTAAGTTCTATGTGGAATTGCAA 3297
                          i    iv    i-       v    ii   iv ii  i     v     
  L1M4_orf2#LINE/    113 TTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_105555043_   3298 AGGGCCAAGAAGAGCTGAGACAATTTTGAAACGCACACACACAATGCAGA 3347
                         i  i  v    v   ii i     i      -----------  - v   
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAA-----------AA-GAAGA 199

  chr2_105555043_   3348 AAATAGTCAGAGG--TC----TTCCTGATATTAAGATTTCTTATAAAGCT 3391
                          v v   ii    --  ----    ii  v i  i i  vi  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_105555043_   3392 ATAGTAATTAAAATAGCATGCTATTGGTACAAGGCTAGAGAAATAAATCA 3441
                          i      i  i i  ii  v  i   i i    v    v v   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_105555043_   3442 ATAGAGTAGAA---AAAGTTCAGAAACATACCCACACAAA-AGGGCCACC 3487
                           i  i     --- i   i      i v     i   vv- v  i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_105555043_   3488 TGATGTACCATAAAGGTGC---AAC--TTTAATGTTGTAAGGGAAATGAG 3532
                             v v v i  i     ---i  --  i    ------      vi v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATG------GGGAAAGAAT 393

  chr2_105555043_   3533 AGCCTTTTCAATAAATGGGGCTGGGTCAACTGGCTA--CTTATGAAAAAA 3580
                           i        i      v      v       v  -- vi   v    i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_105555043_   3581 CATGAGTCTTGACCTCTATCTCACACCACAGACAAAAAAATAAAAATCAG 3630
                         v    ivi v    i   i         i v       -------- i i
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAA--------TTAA 485

  chr2_105555043_   3631 TTGCAGATGGATTGTGAGCCGGAATGAAAAGGGTGAAACAGTAGTTTCTT 3680
                         i vv i      ii?iii  vi    v  ii v i    vi  ivviii 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_105555043_   3681 TA----AAAATGTAG-AGTA--TCTTTATGACCCTTGAGTTAGGCAAAGA 3723
                           ----    ii   -?   --    ii     -   i         v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGG 584

  chr2_105555043_   3724 GTTCTCAAAC-TGTACATGCAAACCACTAACCACAAA-TAAAAGTTTGAA 3771
                         v    i i i-  -   ivv   v   v i v     -v    iv v  v
  L1M4_orf2#LINE/    585 TTTCTTAGATATG-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_105555043_   3772 AAACTGTTTTTCACTAAAATGAACAATT-----------AAGGGCACCAT 3810
                            i  vvi    ii     v  v  i -----------    i   i  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_105555043_   3811 TTAGAGACTGAAACATCAAGCCACAGACTAGAATAGA-TATTTGCAG-CC 3858
                         iv   i v     viv   v       v i i v i -        i-i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_105555043_   3859 ATATA-CTAAAGACAAAGATGAATATTAAGCAGATATTTTTAAAAACTTC 3907
                              -  ---  i  i --  v vv  vv    -  v v    i vi  
  L1M4_orf2#LINE/    734 ATATATCT---GATAAGG--GACTTGTATCCAGA-ATATATAAAGAACTC 777

  chr2_105555043_   3908 TT-TAAGTAAATAAGAAAAAGGCAGACAAATCAGTTTTTAAGCCTGGG-- 3954
                           -i  v v     v      i  i i  vi  i  ?--  ivv    --
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTW--AAAAATGGGCA 825

  chr2_105555043_   3955 AAGGAGTTGAACGGGCACTTTACAAAAAGAGGATAACCAAAATGCCAAAA 4004
                              v     ii i  i  iv v   -  i    vv    vv     v 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAA-GAAGATATACAAATGGCCAATA 874

  chr2_105555043_   4005 TCCTTATGAAAAAACAGTTCAATGTCATTAGGCCA 4039
                         vv vi       i i- i    ii   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.04 (35 / 893), avg. gap size = 2.49 (87 / 35)  

 279 21.15 0.00 0.00  chr2_105555043_105559573     4380  4431 (100)    L1M4_orf2#LINE/L1      375   426 (482)  

  chr2_105555043_   4380 CATGTAACAGGAAAAGAAAAGCCCTTTCAATAAATGGTGCTGGGTCAACT 4429
                            vi  ii  i      v  i i      i             v     
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_105555043_   4430 AG 4431
                         i 
  L1M4_orf2#LINE/    425 GG 426

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.00 (0 / 0)  


3561 20.13 1.06 0.79  chr2_105731870_105734881     1228  1982 (1030)    L1M4_orf2#LINE/L1        1   757 (151)  

  chr2_105731870_   1228 TGGAAAGACAGCTCATGTTCATGTATTGGAAGATTTAACATTGTTAAGAT 1277
                                 i v i          v         i    i           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_105731870_   1278 GTTAATACTGCCCAAAGTGA---A-AAATGAAGTGCAATACCTGTCCAAA 1323
                          vi      v      v   --- - i  vv ii     v   i  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_105731870_   1324 TCCTAA-TACCATTTTTTCAGAAATAGAAAAATCCATCCTAAGATTCATA 1372
                            i i- i  v     v       v  v  iiiv       i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_105731870_   1373 TGGAATCTCAAGGGACTCTAAGTAGTCGAAACAATCTTGGGAAAGAAAAA 1422
                              viv        i vi i   i i           ii      i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_105731870_   1423 TAAAGTTAGAGGTCTCACACTTTCTGTTTTCAAAACTAATTATAAAGCTA 1472
                         i      i    v         i iiv          v i  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_105731870_   1473 GAATAATCAAAGCAGTGCAGTACTAGCATAAAGACAGACATGTGGACCAA 1522
                         v i       ii     ii     i      i  i      i i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_105731870_   1523 TTGAATAGAATAGAGAGCCCAGAAGTAAACCCTGATGTACATGACCAAAT 1572
                          v         v     i      i       vv ii vi   ii   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_105731870_   1573 GATTCTTGACAAGGGTGCCAAAACCATTCAATAGGTAAAGGACATTATTT 1622
                             i i              i          i  v    i i v v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_105731870_   1623 TCAACAAATAGTGCAGGAAAAATGGAATATCCACATACAGAAAAATGAAG 1672
                                  i    v  i v  iv i   ?      i  i  i       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_105731870_   1673 CTGAACCCTTACTCCACACCATATACAAA--TTAACTCAAAATGGATTAA 1720
                         i  i    i   ii               --                i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_105731870_   1721 ATACCTAAATGTAACAACTACAACTATAAAACTCTTAGAAGCCCACATAG 1770
                          v            v i   v                    vvv      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_105731870_   1771 GGGGAAAACTTCACAACATTGGATTTGGCAACAACTTCTTCGATATGACA 1820
                          ? v   v    iii  v    i  v     iiii     v         
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_105731870_   1821 CCAAAAGCACAAGCAATAACAAAAAAAAGATAGATGAAATGCACTACATC 1870
                                         i  --  i    i      i  v  v   v    
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAA--AAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_105731870_   1871 AAAATTTAAAACATTTGTACATTTAAAGAACACAATGAATAGAGTGTAAA 1920
                               v     v     i -  i    i    v  v  v i    v   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_105731870_   1921 GGCAGACTACAGAATGGAAGAAAAATATTTGAAAACCAGATGTCTGTTAA 1970
                          i  iv i         i      -      v   i  v  i    v   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAA 746

  chr2_105731870_   1971 GGG-CTTAAGTAT 1982
                            -   --    
  L1M4_orf2#LINE/    747 GGGACTT--GTAT 757

Transitions / transversions = 1.61 (92 / 57)
Gap_init rate = 0.01 (9 / 757), avg. gap size = 1.56 (14 / 9)  

 625 13.84 0.00 5.03  chr2_105731870_105734881     2362  2520 (492)    L1M4_orf2#LINE/L1      758   908 (0)  

  chr2_105731870_   2362 CCAGAATATACAAAGAACTCCTATAACTCAACATCGTCATCAACAACAAA 2411
                                   i         i  i       i -----  v  -  -i v
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATA-----ATAAA-AA-GAC 800

  chr2_105731870_   2412 AAATAACCCAATTTTAAAAATTGGCAAAGTACTTGAAGAGACATTTCTCC 2461
                                      ?-      v       v i     v            
  L1M4_orf2#LINE/    801 AAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_105731870_   2462 AAAGAAATTATACAAATAAACAATACACATATGAAAAGATGTTCATCATC 2511
                               iv         iiv     vi  i           i   v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_105731870_   2512 ACTAATCAT 2520
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.33 (12 / 9)
Gap_init rate = 0.03 (4 / 151), avg. gap size = 2.00 (8 / 4)  


2111 20.94 9.80 10.69  chr2_105735427_105739310.rev     2487  3384 (500)    L1M4_orf2#LINE/L1        1   890 (18)  

  chr2_105735427_   2487 TGAAGAGATATTCCATGTTTATTATTTGGAAGTCTCATTACTGATGAGAT 2536
                           i i      i       i  viv       v  i v  i  v i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_105735427_   2537 GTCATT----------TTGATCTATA-ATTCAACTCAATCTCAATCAAAA 2575
                          v  v ----------        i -       v     i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_105735427_   2576 TTCCACAGAACTTATT--CTAAAATTTACAAGTTAATTCTAGGCTT---- 2619
                          i   vvviv   v  -- vi     v     i i  i   iiv  ----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_105735427_   2620 ----------AGGGATT-AGACTGGCCAAAT---TCTTGAAAAAAAA--A 2653
                         ----------     ii-   v i      v---          i  -- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_105735427_   2654 CAA---TGGAAGACTCATGCTATCTGATTCCAAGATAAAGCTACATAAAT 2700
                            ---    i      ii  vi ii   i   -------------  v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAA-------------AACT 237

  chr2_105735427_   2701 TATGTAGCTTGTACTCTGGGTAAAGCTACATTAATTAAGATGGTGTGATA 2750
                           i--------   -------         v    i    ii     i  
  L1M4_orf2#LINE/    238 TAC--------TAC-------AAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_105735427_   2751 CTGGCATAAGGACAGACAAAGAAGTCAGTG-------------AGCCCAG 2787
                                     i     v v ii   i  -------------  i    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_105735427_   2788 AATTAGAC----ACACTTATGTAGTCAATTGATTTTTGACAAATGTGCCA 2833
                           v  i  ----   i     --             i     iv      
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATG--GTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_105735427_   2834 AAACAATTTAATGAGGAAACAATAGCCTATTTAAAAAATGATGCTGCAAC 2883
                          i  v   i    i     v     i  v  i  v     i     vi  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_105735427_   2884 AACTGGATAAATGTGTATGTTATGTACATGTAGGGGGTGAGGGAGGAACA 2933
                                  ---------?ii ii i  --- ii ii   i vv   ---
  L1M4_orf2#LINE/    421 AACTGGATA---------KCCACATGCA---AAAGAATGAAGTTGGA--- 455

  chr2_105735427_   2934 AGACTCCCACCTCATACCACGCTCAGAAGTTAACTTAAGAAAAATAGATC 2983
                         --- i  i      i    iiiv  i  i      i  ----   i    
  L1M4_orf2#LINE/    456 ---CCCCTACCTCACACCATATACAAAAATTAACTCAA----AATGGATC 498

  chr2_105735427_   2984 A-AG-CCTAAA------ATCTGTAGCTCTAAAGCTTCTAGAACAAAACAT 3025
                          -  -      ------ v  iv i  v    i  ii     v       
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_105735427_   3026 AAG---ATGTCTTCATGACCTTGATGTAGGTAAACATTTTTTAGAAAGGT 3072
                          i --- vi     i        ivv    i  vvi   i     v v v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_105735427_   3073 CACTAACAGAACTAACCACAAAAGAAATATTA--T---TTTAATTTCATA 3117
                            i  v  v  v i v          v v  -- ---  vi i     v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_105735427_   3118 AAAATTAAAGACCT--GCTCTTTACAAGATCACTA---AAAAAATAAAAA 3162
                                  i  i -- iv   i v i  -     --- i   i i    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGA-CACTATCAAGAAAGTGAAAA 697

  chr2_105735427_   3163 TGCGAGCCACAGACTGGGAGAAGATATTTAGTATATATATATATATATAT 3212
                         vi i v       v        i      - i v  --------------
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTT-GCAAAT-------------- 732

  chr2_105735427_   3213 ATATATATATATATATATATATATATATATTTGACAAAGGATTT------ 3256
                         -----------------------i      i   i  i   i  ------
  L1M4_orf2#LINE/    733 -----------------------CATATATCTGATAAGGGACTTGTATCC 759

  chr2_105735427_   3257 ---ATATGTAAAGAACTCCTCCAAATCAATTTTTTTAAAAAAGAC---TA 3300
                         ---    i          i v   v     vv ----        ---  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAAT----AAAAAGACAAATA 805

  chr2_105735427_   3301 AC--AATTAAAAAAATGAGCAAAAGATTTGAACAGATACTTCACCAAAGA 3348
                           --    ?     -  i     i        i   i i   v       
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_105735427_   3349 AGATGCATGAATGGACAGGAAGTCCATGGAAAGGTG 3384
                             ii ii     v  iv   iv    i    i  
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

Transitions / transversions = 1.74 (118 / 68)
Gap_init rate = 0.04 (34 / 890), avg. gap size = 5.41 (184 / 34)  


3028 24.42 2.86 2.97  chr2_105776979_105781231     2853  3761 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_105776979_   2853 TGAAAAGGTATTCCATGCTCATGGATTGGAAGAATTAATATCAATAAAAT 2902
                           i    i   i     i               v       iiv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_105776979_   2903 GACCATACTACCCAAAGCAATGTACAGATTTAATATGATCTCTATTAAAA 2952
                          i v     v      vii  v        i  iiii   i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_105776979_   2953 TATCAATTATATTCCTCACAGAAATAGAAAAAACAATCCTAAAATTTGTG 3002
                          vi  ii iiv  ii ii       v  v  ivii           ii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_105776979_   3003 TGGAACCTCAAAAGACCTTGAATAGCCAAAGCAATCCTGAGCCAAAAACA 3052
                              viv   ii    iv           i     i   ---    i--
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAG-- 195

  chr2_105776979_   3053 AAACAAAGCAAAAAAACAAATAACAAAGCTGAAGGCATCACACTACCTGA 3102
                         -----   -------------       i  i   vv       v  ii 
  L1M4_orf2#LINE/    196 -----AAG-------------AACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_105776979_   3103 CTTCAAAATGTACCACAAAGTTATAGTAACCAAAACAGCATGGTATTGAT 3152
                         i       iv   i      i  i     i   i    ii     i  ii
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_105776979_   3153 ATAAAATCAGACACATAGACTAATGGAAAAGAATAGAGAACCCAGAAA-A 3201
                             iivi     i     ii       v     v    ii       - 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_105776979_   3202 GAGCCACATATTTACAGCCAACTTATTTTTGACAAAAGTGCCATGAACAT 3251
                         i v   i i     ii i   i v     i     ii      v  v   
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_105776979_   3252 T----GGGAAAAGGACAGCCTCTTCAATAAATGGAGTAGGGA-AACCTGA 3296
                          ----   i    i i  i  i     i      v iv    -   iv  
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_105776979_   3297 TATTCA--TGGAGAAACCTGATATTC-ATTCCTATTTCTCACCATATTAA 3343
                           ?i  --  v i  ivv   vi  v- ii    ii  v        - v
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT-AC 476

  chr2_105776979_   3344 AAAAATCAACTCAAAATACATTAAAGACATAAACATAAGACCTCAAACTA 3393
                               i          iv  i ?    v    ii     v  v      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_105776979_   3394 TAAAACTACTAGAAAAAAATATGGG---AAATGCTTCAGGAC-TTGGTCT 3439
                                vi     i    i  i  ---    -    iv   -    vi 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTT 575

  chr2_105776979_   3440 AGGCAAAGATTTCATAGCTAGGACCTCAAAAGCACAGGCAACAAAAACAA 3489
                               v i    v   v  v   vi          i         iv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_105776979_   3490 AAGTAAATAAATGAGACTGTAT--AAACTAAGCCACTTCTGCATAGCAAA 3537
                           i  i      vi    vi  --   i   iv-    i  iiivv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAA 674

  chr2_105776979_   3538 GGAAACACTCAGCA--GTGAGAAGACAGCCCGTAATATAGGAGAAAATAA 3585
                            v  vv   iv --    i      i   ii iv  i          v
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_105776979_   3586 TTACAAACTATTCATCTGACAAGAAATGAATATCTAGAATATTCAAGGAA 3635
                           i    ii  vi      i   ii ivvi    i       vi  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_105776979_   3636 CTC----AATTCAGCACCAGAAAAGAAAAAT--CCCA-TTAAAAAGTAGG 3678
                            ----  i   ii vi -      v    --    -  ?    i i  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATA-AAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_105776979_   3679 CAAAAGTTTTGAATAGAAATTTCTCACAAGAAGAC-TACAATTGACCAAC 3727
                             i v          v       vv       i-     v  i    i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_105776979_   3728 AGGCATATAAAAA-ATATTCCACATCACTGATCAT 3761
                          i   i  i    -  ii  v      ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (148 / 71)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.52 (53 / 21)  


2915 26.07 1.75 2.30  chr2_105972325_105977157.rev     3429  4341 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_105972325_   3429 TGGAAAAAAAATTCATGCTCCTGGATAGGAAGAATCAATATTGTTAAAAT 3478
                               i v vii    i  v     v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_105972325_   3479 GGCCATACTGCCCAAAGCAATTTATAGATTCAGTGTTGTTCCTATTAAAC 3528
                            v     v      vii  i  i       ii ivi i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_105972325_   3529 TGCCATTGACATTATTTACGGAACTATAAAAAAAC--ATTTTAAAATTTA 3576
                          v   vivi v  v   i i   --  vi v  i --  ii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr2_105972325_   3577 TATGGAACCAAAAAAGAGCTGAAATAGCCAAGGCAATCCTAAGCAAAAAG 3626
                                viiv  ii  v iii         ii     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_105972325_   3627 AAGAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAGGGC 3676
                           v    i      vv   ii  v  ii i      viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_105972325_   3677 TACAGTAACCAAAACAGCATGGTACTGGTAAAAAAAAAAACCAGACATAT 3726
                                 i   i    ii         i v  ii -----i        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-----TAGACATAT 293

  chr2_105972325_   3727 AGACCAATGGAGGAACAGAATAGAGAGCCAAAGAATAAGGCCACTACACA 3776
                            i       --- i     v     i v ii     iv   -    iv
  L1M4_orf2#LINE/    294 AGATCAATGGA---ATAGAATTGAGAGTCCAGAAATAAACCCA-TACATT 339

  chr2_105972325_   3777 TGCAACCATCTGATTTTTGACCAAGTTGACAAATGACAAG-CAATGGGGA 3825
                          iiiii  vi       i   v i v  v   --   v v-         
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAA--GACCATTCAATGGGGA 387

  chr2_105972325_   3826 AAGGAC--TCCTTATTCAATAAATGCTGCTGGGATAACCGGCTGGCTG-G 3872
                            i i--  i  --    i     v        i   i  v i? ii-i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_105972325_   3873 TGAAGAAGATTGAAACTGGATCCCTTCCTTACACCATATACAAAAATCAA 3922
                           v i    v    ii    i    v   i                 i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_105972325_   3923 CTCAAGATGGATTAAAGACTTAACATGTGAAACCCAAAATTATAAAAACT 3972
                              i      i ?    i   -    i i v i    i       -  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAA-ATGTAAGAGCTAAAACTATAAAA-CT 533

  chr2_105972325_   3973 CT-GGAAGACAACCTAGGC---AATACCACTCTG-GACATAGGAACAGGC 4017
                           -i     v   v    ?---   ----  ii -   v v  ivi    
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGC 579

  chr2_105972325_   4018 AAGGATTTCATGACAAAGATACCAAAAGCAATTGCAACTAAAGCAAAAGT 4067
                           v i    v iivv v  i          vvv     v    v    i 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_105972325_   4068 TGACAAATGAGATCTAAATAAACTAAAGAGCTTCTGCACAGCAAAAGAAA 4117
                         v  i    vi  ii v vi   v v  i i   i  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_105972325_   4118 CTATCCACAGAGTAAACAGACAACCTACAGAATGGCAGAACATTTTCGCA 4167
                              v v i   i  v        i         v    v  v  i   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_105972325_   4168 AATTCTGCATCTGACAAAGGTCTAATATTCAGTATCTATAAGGAACTTAA 4217
                            iv ii      i  i  v  vi   i   v  v     i     ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_105972325_   4218 ACAAATTTACAAGAAAAAAACCCAC--CTCAAT-AAAAAGTGGGCAAAAG 4264
                             v iv i  v     i  vv i-- i    -?    i        i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_105972325_   4265 ACATGAACAGACACTTTTCAAAATAAGACATACATGTGGCCAACAA--AC 4312
                          iv    i     i  i  v   v    i     vi       i  --  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_105972325_   4313 ATGAAAAAAAGCTCAGCATCACTGGTCAT 4341
                                i v     i     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (143 / 91)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.95 (37 / 19)  


3275 27.09 0.44 0.44  chr2_106205367_106211647     4882  5789 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_106205367_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_106205367_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_106205367_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_106205367_   5030 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_106205367_   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_106205367_   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_106205367_   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5227
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_106205367_   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_106205367_   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_106205367_   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_106205367_   5378 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_106205367_   5428 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_106205367_   5478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5527
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_106205367_   5528 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_106205367_   5578 AGGCAACTTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5627
                           i    ii   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_106205367_   5628 AGGGCTAATATCCAGAATCTACAGTGAACTCAAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i iv      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_106205367_   5678 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_106205367_   5728 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5777
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_106205367_   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3456 23.35 1.76 1.76  chr2_106320400_106322538      740  1647 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_106320400_    740 TGAAAAGACATTCCATGTTCATGGGTTGGAAGAATTAATATTGTTAAAAT 789
                           i     i  i            i        v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_106320400_    790 GACCACACTATTCCAAAT-GATCTACAGATTAAGTGCAATCTCTATCAAA 838
                          i v i   -ii      -            v ii      i        
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_106320400_    839 ATATCAATGATATTCTTTGCAGAAAT--AAAAAC-AATCCTAAAATTCAT 885
                           vi  iiviiv  i           -- v  i -i              
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_106320400_    886 ATGGAACCACAAAAGACTTGGACTAGCCAAAGCAAACCTGAGAAA-AAGA 934
                               vii   ii   iii  v        i   v i   i   -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_106320400_    935 ACCAAGCTGGAGGCATCACACTACCTGACCTCAAAATATAGTACAAG--- 981
                           v   i      vv       v  ii ii      iv  v     i---
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_106320400_    982 ATAGTAACCAGAAAAGCACAGTACTGGCATAAAAACAGGTACATAGACTA 1031
                          i     i  ii v  iiii            ii i  ii i     ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_106320400_   1032 CTGAAACAGAATAGAGAACCCAGAAATAAATACATGTATCTACAGCCAAC 1081
                         v  i  i     v    ii           iv   ii  i  ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_106320400_   1082 TGATTTTCAACAAAGACATCAAGAATATACATTGGCAAAAGGACAGCCTC 1131
                                 i    i iiii     vi  v  v   vi    i i  i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_106320400_   1132 TTCAATAAGTGGTAATGAGAAAACTGGATATCCATATGCAGAAGAATAAA 1181
                              i  i    iv  i  v         ?   i     i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_106320400_   1182 ACTAGACCCCTATCTCTCACCATATACAAAAATAAACTCAAA-TGGATTA 1230
                         ii i        i   v                v        -     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_106320400_   1231 CAGACTTAAATGCAAGACCCAAAACTATAAAACTACCAGAAGAAAACATA 1280
                         ?    i      i    v i              vii             
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_106320400_   1281 AGGA-AAATGCTTAG-GTCATTGATCTAGGCAAATATTTTATGGATGAGA 1328
                         i ?i-    -   v - v v   ivi       vvi   iv i   - vi
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr2_106320400_   1329 ACAC-AAAAGCACAGGCAACAAC-GAAAAAATAGACAAATGGGATTATAT 1376
                             -         i       v-           i    v   i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_106320400_   1377 CAAACTCAAAAGCCTCTGCACAGCAAAGGAAACAATCAACAGAGTAAAGA 1426
                             v i    i i i  ii vv       v  v     v i   i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_106320400_   1427 GTCAACTTGCAGAATGGAAGAAACTATTTACAAACTACTCATTTGACAAG 1476
                          v    iii        i     v     i    ii ivi  i   i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_106320400_   1477 GGATTAACATCCAGAATAAACAAAGAACTCAAATAACTCAACAGCAAATA 1526
                            i vii          v i         vv i       i ii   - 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-A 796

  chr2_106320400_   1527 AAACACAACAAAAAATAACCCTGTTTTTTTTAAATGGGCAAATGATCTAA 1576
                          i   --------        vi  ?vv---           v   i i 
  L1M4_orf2#LINE/    797 AGACA--------AATAACCCAATTWAA---AAATGGGCAAAGGATTTGA 835

  chr2_106320400_   1577 GTAGGCATTTTTC---AAAAGATCTACAAATGGCCAACAAGTATAAGAAA 1623
                         i   i     i  --- i     v             i   i i v    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_106320400_   1624 AAAATGCTTAATATCACTAACCAT 1647
                          i -    i  i    ????????
  L1M4_orf2#LINE/    886 AGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.47 (148 / 60)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.78 (32 / 18)  


 929 23.97 3.31 2.07  chr2_106382591_106384695.rev      501   742 (1363)    L1M4_orf2#LINE/L1        4   248 (660)  

  chr2_106382591_    501 AGAAATACATTGTGTTCATGGATTGGAAGATTCAATATTATTAAAATGTC 550
                          i i   iviii                  i i      i    i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_106382591_    551 AATTCTTCCCAAATTAGTCTATAGGTTCAACACAGTCCCAGTCAATCTTC 600
                            v  i        ii    i  i      i  i    vi    vv i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_106382591_    601 CAGCAGGCTGTTTTACAGATATAAATAACCTGATTCTAAAATATACAT-- 648
                             v v  v    i    v  vi i  v     i       vi i  --
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_106382591_    649 -AAGGCAAA-----TAAAATAGCCAGAAACAATTTTTTGAAAAGGAGAAA 692
                         -  v    i-----i i        -       i  --     i  ii  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCA-AAACAATCTT--GAAAAAGAAGAA 200

  chr2_106382591_    693 CAAATGATCAGAGGACTCACCCTACACGATTCCAAGATTTACTCTAAAGC 742
                             --i ii          v  v v i   i   i i     vi     
  L1M4_orf2#LINE/    201 CAAA--GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

Transitions / transversions = 2.22 (40 / 18)
Gap_init rate = 0.02 (5 / 245), avg. gap size = 2.60 (13 / 5)  

1984 26.77 5.23 1.23  chr2_106382591_106384695.rev      967  1616 (489)    L1M4_orf2#LINE/L1      233   908 (0)  

  chr2_106382591_    967 AAGTTTGCTGTAAAGCTTCAGCAGTCAAGACAGTGTGGCATTGGTGAAAG 1016
                           ii  i  ii      v   i i              i i   iiv   
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_106382591_   1017 GACAGACA----AATCAACAGAACACAACAGAG-GTGCACACA-AAA--- 1057
                           i     ----i     ii   i v  iv   -  v  v v -   ---
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_106382591_   1058 --------GTAGACAAATGATTTGTGACAAGGCTGGAAAAGGCAATTCCA 1099
                         --------i i v   v      vi       v  vv  - i v    v 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAA 381

  chr2_106382591_   1100 TGGAGAAATGACAGTCTTTTCAATAAATGACACTGGAATAATTGAACAAT 1149
                            i    vi i           i     iii    i i  i  i i ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_106382591_   1150 CCTATACAAAAACATAAATCTCAATCCATACTTCACACCTTATGCATAAA 1199
                          vi  i     iv  i  vi vi i  v   i       v   i  v   
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_106382591_   1200 TTAACTCAAAACAGACTGGAAA---AAAAAT----GCTAAAACTATAAAC 1242
                                    ii  iii? i ---   vi ----              v
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_106382591_   1243 CTTCTATAAGAAAGCATAGTAGAAAATTTTCATGACCTTGATTTAGGTGA 1292
                           ii  v      i     v? v    i   i        iv     ii 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_106382591_   1293 AGAGTTTTTATATGCAACTTCAAAC-TATGACTCATAAAAGAAAACACTG 1341
                         v iv  i   v  iii  vi    v-i ii viv i         v iv 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_106382591_   1342 ATAAATTAGACTTTATTAAAATGTGAAACTTTTGCTCTGCGAAAGATACA 1391
                                i     i  i     vvi         iv  v i  i  i  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_106382591_   1392 AT--AGAGAATGAAA---CAAGACACAAACTAAAAGAAAATATTTTCAAA 1436
                           --   i i     ---   vv    i v iii           v    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_106382591_   1437 TCACATTTCTGACAGAGGACTTTCATCCACTAAGACTATATAAAGAGTTC 1486
                            i  v     i ii      vi     ----  v          ii  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCA----GAATATATAAAGAACTC 777

  chr2_106382591_   1487 CTAAAATTCAGCAATAAGAAATAAAATAATTCAGTTTTTAAAAATTGGGC 1536
                         i  v  i   ii     i  ivv      ii  i  ?--      -    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTW--AAAAAT-GGGC 824

  chr2_106382591_   1537 AAAAAATGTGAATAGACTCTTTAACGAAGAAGATATACAGGTGAC----A 1582
                            ii  v         vi  ivv i             ii  i ---- 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_106382591_   1583 AGCATATGAAAACATCCTCAACAGTATTAGTCAT 1616
                             i       v  v       vi ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (110 / 60)
Gap_init rate = 0.02 (14 / 676), avg. gap size = 3.00 (42 / 14)  


3962 17.88 0.87 6.98  chr2_106674432_106676340.rev      501  1417 (492)    L1M4_orf2#LINE/L1       48   908 (0)  

  chr2_106674432_    501 GATGCCAGTACTTCCCAAATTGATCTACAGACTCAAGGCAATAACTATTA 550
                             v  i    i                  i    v     vv    i 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_106674432_    551 GAGTCCTAGGGAGCTTCTTTATAGAAATTAACAAGCCAGTGTTAAAATTC 600
                         i i   i  vviv   i   ii       i      iii vi        
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_106674432_    601 ATGTGGAATTTCATGGGTGGGTCCCAGAATGGCAAAAACACTCTTGCAAA 650
                           i     ----   viv   v        i  v      v     v   
  L1M4_orf2#LINE/    148 ATATGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_106674432_    651 AGAAGAACAAAATAGAACAATGTATACTTCTCAATTCCAAAACTTAGAAT 700
                                    i v i vi ivi i     i     i         vv i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_106674432_    701 AAAGCAACAGTAATCAAGACAGTGTAGTATTAGCATGATAATAGACATGT 750
                              v                   i   i i    i vi        i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_106674432_    751 AGATCAGTGAAATAGAATTCAGAGTCTAGAA-TAAACCCATACACCTATG 799
                               i  i         v      i    -            ii    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_106674432_    800 GTTAACCGATTTTTGATGAGGGTGCCAAGGCCATTCAATTGGGAAGCAAT 849
                           i  ii      i  ii           i         v     iv   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_106674432_    850 AGTCTTTTCAACAAATG-CACTGAGTCATTTGTATAGCCACCTGCA---G 895
                                          -ii   i v  vi  v   ?    v    --- 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_106674432_    896 AACAAACTTGGAGATTTACTTTATATAATATGCAAAACGTAACTTAAAAT 945
                           ii  v     vvii   i i i iv    i     vv     i     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_106674432_    946 GGCTCAAAGACCTAAATGTAAGAGCCAAACCTATAAAACTCTTAAAAGAA 995
                           v   ?                  i   v              i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_106674432_    996 AA--TAGGGAAAAATCTTCATGACATTGAATTTGGCAATAATTTTTTGGA 1043
                           --    ?iv        i    v   ii  v      ii   i  i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_106674432_   1044 TATGACTCTACAAGCACAGGCAACAAAATATAAAATAGATAAATTGGACT 1093
                               v i v       i         v v                   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_106674432_   1094 TCATCAAAATGGAAAACTTAT-TACCTGAAAGGATACCATCAAAAAAATA 1142
                                   vi       v - i i v      i  i     i   i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_106674432_   1143 AAAAGACAATTCACAAAATGAGAGAAAATATTTCCAAACCATATATCTGA 1192
                                  ii    i    i            v    i           
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_106674432_   1193 TCAGGGAATTGTATCTGGAGTATATACAGGATTCAAAAGAACAACTCAAC 1242
                          v     v       ii  i      v  i i  ----vv         i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTC----TTACAACTCAAT 789

  chr2_106674432_   1243 AATAAAAATATTATTAAATAATCTAAGATATACTCATATAAATACTTTTA 1292
                                 v i----      i i  --------------------  ? 
  L1M4_orf2#LINE/    790 AATAAAAAGAC----AAATAACCCAA--------------------TTWA 815

  chr2_106674432_   1293 AAAATCTATAATAAAAAGAAAAAAACAGATTTAAAATGGGCAAAGGACCT 1342
                              --------------------------------          ii 
  L1M4_orf2#LINE/    816 AAAAT--------------------------------GGGCAAAGGATTT 833

  chr2_106674432_   1343 GGATATACATTTCTTCAAGGAAGATGCACAAATAGCCAATAAGCATATAA 1392
                          i   v        i   i      ii      i           i  i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_106674432_   1393 AAAGATGTTCAACATCATTAGTCAT 1417
                                i         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (106 / 54)
Gap_init rate = 0.01 (10 / 861), avg. gap size = 7.20 (72 / 10)  


2702 24.36 6.84 1.74  chr2_106691098_106693010.rev      560  1421 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_106691098_    560 GAGAAATATTCCATGTTCACGGAT-AGAAGACTCAATATCATCAAGATAT 608
                           i i    i         i    -i       i     ii i     iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_106691098_    609 TAGTTCTTCCCAATGTAATATATAGATTCAATACAAACCCAATCAAAATC 658
                         i i v  i     vv i  v  i        ii   v   v         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_106691098_    659 CCAAC-AAGTTACTTGTGGATATGAACAAACTGATCTCAAAGTTTACATG 707
                            i -ivv  vi   ii  v  vi    i      ii   i  i i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_106691098_    708 GAGAGGGAAAAGTCCCAGAATAGCCAAAACAACGTTCAGAAAAGAAGTGC 757
                           i v v  ii v                   iv  v -        vi 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAGAAC 201

  chr2_106691098_    758 CA-GTCAGAGGACTGGCA--TCAC----------CTCACT---------- 784
                         v -  ii       vi  --  v ----------  i   ----------
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_106691098_    785 -----TCAAAACAGTGTGGTATTA-TAAAAGAATAGACAAATTGGTCAAT 828
                         -----    i           i i-i v   i       v  v i     
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_106691098_    829 AAACCAGAATAGAGAGCGCTTAAATAGACCCACATAAATGTAGCCAGCTG 878
                         ii vi     v     iv vv     i     i i vv i i i  ii  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_106691098_    879 ATCTTTGGCAAAGGAGCAAAGGTAATAAAATGGAGAAAATATAGTCTTTT 928
                           i  i i   i  v  v   iiv  vv     i    iv          
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_106691098_    929 CAAAAGATAGTGCTGGAACAACTGTACATCCACATGCAAAAAGTAAATAA 978
                            v i  i       i       v i ?            i------- 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-------A 444

  chr2_106691098_    979 ATAAATCTAGACATTGATCTTATGCTTTTCACAAAAATTAACTCAAAAAT 1028
                           i  vi i   viiv i  i ii iv vi                  vv
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_106691098_   1029 AATCATATACCTAAACGTAAAATACAAAACTATAAAATTTCTGGAAGGTT 1078
                         i    ? v       i    i vvi            i ii i    ivv
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_106691098_   1079 GTATTTGGGAGATAAAA--TAGTTAACATTGTGTTTGGCG-TGA---CTT 1122
                         ii  --i  ? -    v-- v  -i  v   v   v   i-  i---   
  L1M4_orf2#LINE/    545 ACAT--AGGNG-TAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_106691098_   1123 AGATACAACATCAAAAGCACAATTAATGAAATAAAATATTGATAAATTGG 1172
                              ii   i           vi  ii   v    v  v          
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_106691098_   1173 AC---AT---AATTAAAA-CTTCTCTGT---GGAAGACACTGTTAAGAGA 1212
                           ---  ---        -   i v  i---ii i      i i    i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_106691098_   1213 ATGAAAAGACAACCCACCGTCTGGGAGAAAATACTTGCAAAACACGTATC 1262
                         i                v vv            i       v  ii    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_106691098_   1263 TGATAAAAGACTGTTATCTAAAATATAAAAAGAACTCTTAAAATTCAACA 1312
                               ii    vv    i i      v            v  i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_106691098_   1313 ACAAGAAAACAA----CCCAATTAAACAAGTGGCCAAAAAAATGTGAA-- 1356
                          i  i  i    ----       ?  -  i   v    ii - v    --
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGA-TTTGAATA 838

  chr2_106691098_   1357 GCCATG-----AAAGAAGATAATACAGTTGAC-AATCAGCATACGAGAAG 1400
                          v   v-----          -    iv  i -   v    i i  i   
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATA-TACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_106691098_   1401 ATGCTCAACAGCATCTTAGGA 1421
                                   v  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (130 / 76)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 2.85 (74 / 26)  


2521 19.41 1.65 1.28  chr2_106740587_106742696.rev      492  1037 (1073)    L1M4_orf2#LINE/L1      151   698 (210)  

  chr2_106740587_    492 TGGAATCATAAAGATCCACTGAGTATAGCCAAA-CAATCTTAAAAATGAA 540
                              viii  i i---  iv  v         -       i    v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG---ACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_106740587_    541 GAACAAATTTGGAGGACTCAAACTTGCCAACTTCAAACCTTACTACAAAG 590
                                v            v    v    i      v            
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_106740587_    591 CTACAGTAATCAAGACAGTGTGGCACCAGCATAAGGATAAACACATAAAG 640
                                                i  ii           i   i   -- 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA--G 295

  chr2_106740587_    641 ATCAACAGAATAGAGTGGAAAATTCAGAAATAAACCTTTACATTTATGGT 690
                              ii       i v  i i i            iv            
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_106740587_    691 CAATGGATTTTGGACAAGGTTGACACAAAAATCCAAGGGAGAAA---TGG 737
                             v      v       v  v  vi vv  i   v  i    --- i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_106740587_    738 TCTT--CAACAAATGGTAGTGCGGCAGGTGGATATCTACATGCAAAAAGA 785
                             --           iv  v i  iv      ? i          -  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GA 444

  chr2_106740587_    786 ATAAATTTAGACTCCTACCTCACACCATATG-AAAAAGTAACTCAAAATA 834
                           i  v  i   i                 i-     v           i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_106740587_    835 TGCCATGGACCTAAACTTATGAGTGAAAATTATAAAACTTGTAGAACTAA 884
                         vii  ?i        iv  v   iv    i         iv     vv  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_106740587_    885 TCGTAAGAGTCAACCTTTATCACCCTGGTTTAGGTAATGATTTCTTAAAT 934
                         v i  i ?  v  i   ii v   i   v     i    i       i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_106740587_    935 TTAATACCAGAAGTCCAAGAGAGAAAAGAAAAAAACAGATA--TTGTACA 982
                         v i i    i   iv    vi v           -i     --   v  v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACT 643

  chr2_106740587_    983 TCATTAAAACTGAAAATATTTTTGCTTCAAAGGATACCATCAAGAAAGTG 1032
                             i    i i    iv   v            i  i            
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_106740587_   1033 AAAAG 1037
                              
  L1M4_orf2#LINE/    694 AAAAG 698

Transitions / transversions = 1.45 (61 / 42)
Gap_init rate = 0.02 (9 / 548), avg. gap size = 1.78 (16 / 9)  

 932 14.02 7.01 2.80  chr2_106740587_106742696.rev     1405  1618 (492)    L1M4_orf2#LINE/L1      686   908 (0)  

  chr2_106740587_   1405 AGGGAGGGAAAAGGCAACCCACAGAATGACAAAAAA-ATTTTCAAACTGT 1453
                           ii  v      i              iv i    -    v    iii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_106740587_   1454 AACTTATCATCTGATAAG------ATGTCCAAAATATA------ACTCTT 1491
                          ------i          ------i i    i      ------      
  L1M4_orf2#LINE/    736 A------TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_106740587_   1492 ATAACTCAACAATAAAAATACAAATAATC-AATTTAAACATGAGCCAAGG 1540
                          i       i        v        i -    ?   v   i  v    
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_106740587_   1541 AATTGGTTAAACATTTCTCCAAGGAAGATATACAAATGGCCATTAAGCAC 1590
                          v   iv  i            i                   v       
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_106740587_   1591 ATGAAAAGATG-TCAAAATCACCAGCTAT 1618
                                    -    v    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.03 (6 / 223), avg. gap size = 3.50 (21 / 6)  


 379 27.62 0.00 1.90  chr2_106748697_106751296.rev      738   842 (1758)    L1M4_orf2#LINE/L1        1   103 (805)  

  chr2_106748697_    738 TGGAAAAACACTTCATGCTCATAGATAGGAAAAATCCACATCATGAAAAT 787
                               i i iii    i    i   v    i v iv i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_106748697_    788 GGCCATACTGCCCAAAGTAATGTAAAGATTCAGTGCTATTCCCATTAAAC 837
                            v     v      v i  v  v       ii  v  i  i  i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr2_106748697_    838 TATCC 842
                         -    
  L1M4_orf2#LINE/    100 -ATCC 103

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.01 (1 / 103), avg. gap size = 2.00 (2 / 1)  

2305 28.37 1.31 0.78  chr2_106748697_106751296.rev     1344  2108 (492)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr2_106748697_   1344 TAAAATTCATATGAAACCA-AAAAGAGTCTGTGTAACCAAGACAATCCTA 1392
                                      i  vii-  ii  vi v vi  i    i      i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_106748697_   1393 AGCAAAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATA 1442
                          iv  i          i      vv    i  v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_106748697_   1443 CTACAAGTCTACAGTAACCAAAACAACGT--TATTGATACCAAAACAGAC 1490
                               iv         i   i   ii  --  i  ii iv ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_106748697_   1491 ACATAGACCTATAGAACAGAATAGAGATTTCAGAAATAAGACCACACATC 1540
                          i     i v  i   i     v    v i         iv   i    i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_106748697_   1541 TACAACCGTCTGATCTCTGACAAGCCTGACAAAAGCA----ATGGGGAAA 1586
                           iiii ivi    i ii      vv  v   i v  ----         
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_106748697_   1587 GGATTCCCTATTAAATAAGTGGTGCTAGGAAAACTGGCTAGCCTTATGCA 1636
                          i  vvi  v  v  i  i       i   v      v  ?  vi     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_106748697_   1637 GAAAACTAAAACTGGGCCTTTTCCTTACATCTTATGCAAAAATTAACTCA 1686
                         i  i v i  ii   i  ii v   i   i v   i              
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_106748697_   1687 AGGTGGATTAAAGACTTAAATGTAAAACCCACAACCATAAAAACCCTAGA 1736
                          ii     i ?    i         i v i v   i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_106748697_   1737 AGAAAATCTAGGCA-ATACCATTGAGGACATAGGCATGGGCAAAGACTTC 1785
                               iv    ?i- v i v i v iv v i  i- i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTC 588

  chr2_106748697_   1786 AT-GATGAAATCACCAAAAGCAATTGTAACAAAAGCAAAAATTGACAAAT 1834
                         v -   ivi -           vvv i        v      v  i    
  L1M4_orf2#LINE/    589 TTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_106748697_   1835 GGCATACAATTAAACTAAAGAGCTTCTGCACAGGAAGAGAAACTATCATC 1884
                         v v iviv  i   v v  i i   i  ii vvv  ii  v       vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_106748697_   1885 AGAGCTAACAGGCAACCTACAGAATGCGAGAAAATTTTTGCAATCTACTC 1934
                          i  iv  v  i     i        v        v       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_106748697_   1935 ATCTGCCAAAGGTCTAATATCCAGAATCTACAAGGAATGTAAACACATTT 1984
                              vi  i  v  vi          v  i  i   ivivv   - i -
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACT- 785

  chr2_106748697_   1985 ACAAGAAAAAAAAAACAAACAACCCCATCAAAAAGTGGG-AAAGCAACAT 2033
                         -   v  v     i     i     v  i?    i    -    -i iv 
  L1M4_orf2#LINE/    786 -CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG-GATTT 833

  chr2_106748697_   2034 GAACAGACACTTCTCAAAAGAAGATATTTATGCAGCCAACAAACATATGA 2083
                            i     i     v           vi viii     i  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_106748697_   2084 AAAAAATCTCAACATCACTGATCAG 2108
                            i vv          ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (131 / 82)
Gap_init rate = 0.01 (11 / 769), avg. gap size = 1.45 (16 / 11)  


2286 27.34 5.68 2.60  chr2_106757212_106759450.rev      895  1739 (500)    L1M4_orf2#LINE/L1        4   874 (34)  

  chr2_106757212_    895 AAAGACATGTCATATTTGTGGACTAGAA-ATTTAATATAGTAAGGATGTC 943
                              i  vi   i  ii    i i   - i       v  v i    v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_106757212_    944 AACTCTCCCTAAATTTATATACATGTATAATGCAATTCCTATCAGAAGCT 993
                           iv     i     v  v    vi vi  i     i       i  v i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_106757212_    994 CAGCAAGACTTTCCGTAGACATAGATAAAATTGTTCTAAAATTTATACAG 1043
                             vivvi   ii i   v  v  i  iv vi i        i   ii 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_106757212_   1044 AAGGGCAAAGAAACTAGAAGCTAGATCAATAGCTAAATCAATTTTGAAAA 1093
                           iv    i i v i    ----------    i   v    i       
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAA----------TAGCCAAAACAATCTTGAAAA 193

  chr2_106757212_   1094 AATAAAGAAGAAAGTGGAAGAAATTATTTTTCTCAACTTCAAGACA-ACT 1142
                          i--     v     v i  i v i ivi   i   i     i  v-   
  L1M4_orf2#LINE/    194 AG--AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_106757212_   1143 ACAAGAC-ATAGTAATCAAGATTGTGTGATATTGGCAGAGGGAACAGACA 1191
                             ii - i           iv     i  i     v i   -i     
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACA 290

  chr2_106757212_   1192 CATAGATTAATGGTACATAATAGAGAATTCAGAAACAACCCAATACA--- 1238
                         i      i     v i v   v    i i      i  v  v     ---
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_106757212_   1239 AGAGTGCCAACTGATCTGATTTTTTGACAAATGTGCAAACACAACTCAAC 1288
                          vi  --   i    ------   i     iv    v  v  v i    i
  L1M4_orf2#LINE/    341 ATGGT--CAATTGAT------TTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_106757212_   1289 AGAGGAAGAATAGTCATTTCAACAA-TCACGCCAAAGAAACTGCATATTC 1337
                         i i i          v         - vii  iiiiiv     v   ?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_106757212_   1338 ACAGGCACAAAAATGAACCTCAGCATAAATCTTATACCTTTTACAAAAAT 1387
                            v   v  i      vi vii vivv i  i i   v v         
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_106757212_   1388 TAACTCAAAATGGATCATAGATTTAAACGTAAAACACTAAA-TTATAAAA 1436
                                          ?   ii    i    i -i     -i       
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAA 531

  chr2_106757212_   1437 CTTCTATATGATAACACAGGAG-ATATCTTCAGGACCTAGGGCTTGCTGA 1485
                           ii  v v  v    i   ? - v      iv     v   i v vii 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_106757212_   1486 AGAGTTCTTAAACCTAGTACAAAAAGCATGAATTATTGAA--AAAAATTG 1533
                         v iv      i iv iii  v       ii iiv ivi  --      v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_106757212_   1534 -TGAATTAATATTCATCAAAATTATA--TTTTTGCTCTGTAAGAAACTTT 1580
                         - i    iivv             v --i     iv  vi  iii  vi 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_106757212_   1581 GTTAATAAAATGAAAATACAA------------GGCAAAATATCTGCAAG 1618
                         i i  v   i      v    ------------ iv       i     i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_106757212_   1619 CCCCATATCTGACAAAGGGCTTATATATATAATATGTAAAGAAGTCTAGA 1668
                         i vi        i  i  i   i   vi v     i       v   viv
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_106757212_   1669 AATTCAACA-------GA----------AATT--AGAATGTGCAAAAGAT 1699
                           i    i -------  ----------    -- i    v     i   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_106757212_   1700 CTAAAGAGACATTTCACCAAGCA---CATAGAAATGTTCAATA 1739
                         i i  v         v    iv ---i   v     vi     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.65 (142 / 86)
Gap_init rate = 0.02 (21 / 871), avg. gap size = 3.33 (70 / 21)  


2532 19.94 3.03 6.74  chr2_106794663_106796376.rev      501  1227 (487)    L1M4_orf2#LINE/L1      209   908 (0)  

  chr2_106794663_    501 GAGGACTAACAATACCCAACTTTAAGACTTACTATGAAGCTATCACAGTC 550
                                v   v v     i  i  i        ii      ivii i  
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_106794663_    551 CAGACAGTGAGGTATTGACCAAAGAATAGACACATAGATCAATGGAATGG 600
                         v        v    i  i vv   i       i               i 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_106794663_    601 AATAAAGAGCCCAGAAATAGACCCATACAAATATTGTCCACTGATCTTTG 650
                            vi    i         i         vv   v   v i    i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_106794663_    651 GCAAAAGAGCAAAGGCAATACAATGGAGAAAAGAGCATCTTTTCAACAAA 700
                         i   ii v  v   i v  v      i    ii vvi             
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_106794663_    701 TGGTGCTGGAACAATCAGATATTCGCATGCAAAAAAAAAAAAAAAAAAAT 750
                                  i    iii    ?i i         i  vi  i------- 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG-------T 451

  chr2_106794663_    751 CTAACACATGCCTTACAGCTTTCATGAGAACTAACTCTAAATGGGTCATA 800
                         ivi  v v i   i   v v vi ii i  i      v      i   ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_106794663_    801 GACCTAAATGTAAAATGC-AAAATTATAAAACTCCTATGAGAGAAT-CAG 848
                                      i -  -    i          i  vi   i  i-i  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_106794663_    849 G------------TGACCTTGAGTTTGGCAGTGACTTTTGAGTTACAATA 886
                          ------------        i   v    i  ii  i v  v  ii i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_106794663_    887 CAATCCATGAAACACACACACACACACACACACACACACAAGCACAATCC 936
                          ----  -i  i    vi  ---------------   v   --------
  L1M4_orf2#LINE/    601 C----CA-AAAGCACAAGCA---------------ACAAAAG-------- 622

  chr2_106794663_    937 ATGTAAAAAA-GGATAAGTTATATTTCATGAAAATGAAAAACTTATTCT- 984
                         ----      -i     i  iv i     v     v        -  v -
  L1M4_orf2#LINE/    623 ----AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT-TTGTG 667

  chr2_106794663_    985 CTACAAAAGGCATTA---AGAGAATGAAAAAACAAGCCACAGTCTGGGAG 1031
                           v    i i  i  ---   i i      i    v      vv      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_106794663_   1032 AAAATATTTGCAAAACATATATCTGATAAAGTACTTGCACCCAAAATATA 1081
                                       v              i v     i i   i      
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_106794663_   1082 GAAAGAACTCTTAAAACTCAACAATAAGAAAAAAAA-AGC--AATTTAAA 1128
                         v            v       i     i  i v   - i --    ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_106794663_   1129 AATGGGCAGAAGATTTAAACAGACATCTCACCAAAGAAGATACACAGATG 1178
                                 i i     i  i      i  v            i   i   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_106794663_   1179 GCACAGATGGCAAGTAGCATATGAAAAGATGCTCAAACTCATATGTTAT 1227
                           --------   vv    i                vv   ????????
  L1M4_orf2#LINE/    868 GC--------CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (91 / 51)
Gap_init rate = 0.02 (16 / 700), avg. gap size = 4.44 (71 / 16)  


3409 17.27 11.56 1.70  chr2_106812868_106814810.rev      630  1451 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_106812868_    630 AGACATCC-ATGTTCATGGATCAAAAGACTTAAGATTATTAAGATGATGA 678
                            i    -            iii         v   i        iii 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_106812868_    679 TACTACTCAAAGTGTTCTACAGATTCAATTCAATCTCTATTAAAATTCCA 728
                             v i    v  v             iv     i    i     i   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_106812868_    729 A-TGTTTATTTTTGCAGAAATGGAAAAGCCAATTCTCAAATTCATAAATT 777
                         i-  ii -             v  v    ii  i  v         ----
  L1M4_orf2#LINE/    106 GCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA---- 150

  chr2_106812868_    778 CATAAAGAATTACAAGGAACCCAGAATAACCAAAACAATCTTGAAAATGA 827
                         -- i--   v i     i          i                  v  
  L1M4_orf2#LINE/    151 --TG--GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_106812868_    828 A----AAAGTTGAAAA------------CAATTTCAAAACTAACTACCT- 860
                          ----       i ii------------             v     vv-
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_106812868_    861 GTTACAGTGATAAAAAGAGTATGGTACTGGTATAAAGATAGACATATAGA 910
                          i      i  v  i v   i         i    i              
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_106812868_    911 CCAATGAAATAGAATTGAGACTACAGAAATAAACCCATAAACCTATGGCT 960
                         i     i             v v                v ii     ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_106812868_    961 AATTGATTTTTAATAAGGATGCCAAGACAATTTAATGGGGAA-GACT-GT 1008
                                   ii i    i         v   i         -  v -  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_106812868_   1009 CTCTTCAACAAGTAGAGCTGT-ATAACTGCATATCCACA---AAA----- 1049
                           i        i i v    v- i     v   ?     ---   -----
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_106812868_   1050 -------------------------TATA------TTAAT---------- 1058
                         -------------------------    ------    i----------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_106812868_   1059 -----GATCTACCTGTAAGTGATAAAAACCAAAAAGCCCTTAGGAGAAAA 1103
                         -----  i   vv      v v     - i v   i i     i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAA 545

  chr2_106812868_   1104 CATAGTAGTGAATTTTCATAACCTGAGATTTGGCAATGAATTCTTAAATG 1153
                              v?  i   i   i i    vi i  v       iv      i  i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_106812868_   1154 TAGCACCAAAAGCAAGTGCAACAAAA-----AATAGATAAGTTGGACTTC 1198
                          ii           viv         -----         i         
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_106812868_   1199 ATCAAAATTAAAAACTTTTGTTTACCAAGGTACATTAGCAAACAAGTTAA 1248
                                              vivi   i v   i  v   iv    v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_106812868_   1249 AAGACAATCTACAGAATGGGAGAAAATATTTGTAAAC-----ATCTGCTA 1293
                                i i                      i   i-----     v  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_106812868_   1294 AGGGTCTATCTAGTATCCAGAATGTATAAAGAACTCTTACAACTCAGCAG 1343
                             v  --- -           i                      ii i
  L1M4_orf2#LINE/    746 AGGGACT---T-GTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_106812868_   1344 --AAAAGA--AGTATCCCAATTAGAAAATGGGCAAAGAATTTGGACAAAC 1389
                         --      -- i  v       ?i             i     i i i  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_106812868_   1390 ATCT-TGCAATGA---TACGCAAGTACCCAA-AAACACATGAGAAGATAC 1434
                           i - v   v  ---  ii   i iv    -  i       i     i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_106812868_   1435 TCAACATCATTAACCAT 1451
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (93 / 46)
Gap_init rate = 0.03 (25 / 903), avg. gap size = 4.36 (109 / 25)  


2068 25.75 10.42 1.68  chr2_106977524_106980432.rev     1585  2419 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_106977524_   1585 TGGAGAGGCATACCAAATTTATGGATTAGAAGACTCAATAGAGTCAAGAA 1634
                             i  ii  v   vi  i       i       i    vv  i    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_106977524_   1635 GTCAATTTCCTCCAAATTGACAAATGCATTTAACAAAATTCCTATCAAAA 1684
                          v    vii i         ivv iiv   i   iv   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_106977524_   1685 TCCCAGGAATAATTTCTGTAGATATAGACACCATTATTTTAAAACTTATG 1734
                               vviivv   i  i   v  v    vvv v  ii     i i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_106977524_   1735 TGGAAAGACAAAGAAACTAGATAAAATAACTAAAACAATTCTGAAAA--- 1781
                               vi   i i v i   ----   i i        ii      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGA----ATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_106977524_   1782 ----TAAAGTGGGAGGAATCAT--TTAACCCAATTTTAAAACTTAG---A 1822
                         ----i     v      v   i--  --        i        v--- 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTT--CCCAATTTCAAAACTTACTACA 244

  chr2_106977524_   1823 AAGCTACAGTAATCAAGACTGTGTAGGACTGGGGTAGTAAT-GACACAGA 1871
                                            v    i v     vi  ivi  -    i v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_106977524_   1872 GATCCATGGTTCAGA-TTAAAGACCTACAAATAGCTCTATGCAATTATGA 1920
                             v    vvi   -  i iiii i v     ivi i  i  v     i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_106977524_   1921 CCAACTAAT----AACAAAGGCAT--AAACGCATTTATATGAAGGAAGGC 1964
                         i   i i  ----i    i  iii-- i  -    i -   ii i   iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCA-ATGGGGAAAGAA 392

  chr2_106977524_   1965 TAGTCTTTCTAACAATCGGTGCTAGAGCGATTGGCTATCTATTGGCAAAA 2014
                                 ii     vi      i ii i i   v  ? i ivv      
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_106977524_   2015 GC-TGAACCTAGACCTAAGCCTCAAACC------------TGACTCAA-- 2049
                          v-    vi i    ivvi     v   ------------ i      --
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_106977524_   2050 TG-----TAGATTTAAATGGTAAACATAAAACAATTAAACTTTTTAGAAG 2094
                           -----?   ii      vv i vv      v  v     i  -     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT-AGAAG 541

  chr2_106977524_   2095 ACAG--TAGA--TAACATCTTTGGGACCT-GGGTCTTGGTGAATAGTT-C 2138
                          v i--   i--   -     i v     -    - v  i-   i   - 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAA-ATCTTCGTGACCTTGGGT-TAGGC-AATGGTTTC 588

  chr2_106977524_   2139 TAAGATATAACACTAAAAACATAATTTATAACAGAAAAATATTGACACAG 2188
                          v      i    i    i  i  viv i  v       -  v  i v v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAAT 637

  chr2_106977524_   2189 TGGACTACAACAATATTTCAAACTTTTGCTCTGCAAAAGACCCTGTTAAA 2238
                               v  v   v   vv         iv  v    i   v  i i  i
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_106977524_   2239 A---TGAAAAGACAA-------AGT-------AATATTTGTAAATTTCAT 2271
                          ---           ------- i -------        i    ivi  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_106977524_   2272 ATTTAACAAAAGTCTA--ATCTATACTGTATAAAAAAACTCTCAGAAATC 2319
                           i i i  ii v  v--   i v v i      i  -    i v  v  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTC 786

  chr2_106977524_   2320 GACATTAAAAA--CA--TAATCCAATTAAAAAATG---------TCT-AA 2355
                         i i v      --  --   i      ?       --------- i -  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_106977524_   2356 CA-ACAT------GAAGA-GATATATGAATGGCAAATACTCACATGAGCA 2397
                         i -    ------i    -      ii      v    vv       iv 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_106977524_   2398 GATGTTCAACGTAAGTAACCAT 2419
                             i     i v ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (128 / 84)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 2.81 (101 / 36)  


1796 27.48 0.95 0.95  chr2_107024555_107026606.rev      506  1029 (1023)    L1M4_orf2#LINE/L1      253   776 (132)  

  chr2_107024555_    506 GTAACTAAAACATCATGCTATTGGTATTTAAAAA-AAACACATAGACCAA 554
                             ii  i   vii  v  i   i  --  ii - i   i     i   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGATCAA 300

  chr2_107024555_    555 TGGAACAGAATAGAGAAACTAGAAATAAGTCTACATATTTATAGCCCACT 604
                              i     v    iv i        ii i i i      i i v i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_107024555_    605 GAGTTTGGACAAAGGTATCAAGAACATATGTTGGGGAAAGGATACCCTCT 654
                           v   v     i   ii     v   viiv         i   vi  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_107024555_    655 TCCATAAATGATGCTGGGAAAATTGGATAGCCATGGGCAGAAGAATGAAA 704
                           v i     i        v  i      ?   iiv   i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_107024555_    705 TTGGACTGCTATTTCTCACATTGTACACAAATCAACTTATAATGGATTAA 754
                               iv   ii  v   vv i    v    i    i v       i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_107024555_    755 AGACTTTAAATGCAAGACCTGAAACTATAGAACCACTAGAAGAAAACTTA 804
                             i -     i    v  i        i   ivi           v  
  L1M4_orf2#LINE/    501 AGACCT-AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_107024555_    805 GGGGGAATACTTCAGGACATTGGTCTAGGCAAAGATTT--TAGCACTATG 852
                           ? v  vv    iv   v    vi       v i   --   - -    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-A-TATG 597

  chr2_107024555_    853 ACCTTAAAAGTACAGTCAACAAAAACAAAAATAGAAAAATGAGACTATAG 902
                           vii     i   iv        iv         v    vi    vi v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_107024555_    903 TAAACTAAAAAGCTTCTTCATAGCAAATGAAAGAATCAACAGAGTGAAGA 952
                         i   v v    i   i viiivv    v  v vv     v i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_107024555_    953 AATGATCTGCCAAATGGGAGAAAAT--TCACAAACTATTCATCCAACAAG 1000
                         i ii i ii vi             -- ii    ii  vi   ii i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_107024555_   1001 GAACCAATATTGAGAATATACAAGGAACT 1029
                          i  ivi   iv        i  i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.76 (90 / 51)
Gap_init rate = 0.01 (7 / 524), avg. gap size = 1.43 (10 / 7)  

 404 16.85 4.49 0.00  chr2_107024555_107026606.rev     1472  1560 (492)    L1M4_orf2#LINE/L1      816   908 (0)  

  chr2_107024555_   1472 AAAGCGGGTAAAGGACATGAATAGACATTCCTC---AAAAGACATACAAA 1518
                            ii   i      iv            i   --- i    i       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_107024555_   1519 TTGCCAATAGGTATCTAAAAA-ATGCTCAACATTACTAATCAT 1560
                          v       i i iv i    -           i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.02 (2 / 93), avg. gap size = 2.00 (4 / 2)  


2864 26.53 2.00 1.22  chr2_107112973_107117877     3519  4419 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_107112973_   3519 TGGAAAAACATCCCAAGCTCATAAGTACGAAGAACCAATATCATTACAAT 3568
                               i i      v i    iii vv     vii     ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_107112973_   3569 GGCTATACTGACCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 3618
                            v     vv     vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_107112973_   3619 TACCAAC---ATTTTTCACAGAATTAGAAAAAAACTAATT-TAAATTTCA 3664
                          v   i ---v     ii     v v  v  i--  i  i-    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_107112973_   3665 TATGGAACCAAAAAAAGAGCCCA-AACAGCCAAGGCAATCCTAGGCAAAA 3713
                                -- viv  i ii    -  i      ii     i iiiv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_107112973_   3714 AGAATAAAACTGAAGGCATCACATTACCTGACTTCAAACTATACTACAAG 3763
                             i   ii  i   vv     i v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_107112973_   3764 GCTACAGTAACTAAAACAGCATGGTACTGGTACAAAAACAGGCATATAGA 3813
                                   ii  i    ii         i i  ii i  i        
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_107112973_   3814 CCAAAGGAACAGAATGGAGATCCCCAGAAATAAGGCTACACATCTATGAC 3863
                         i   v    i     v    vi  -        iv i i    i    ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC-AGAAATAAACCCATACATTTATGGT 345

  chr2_107112973_   3864 CATCTGATTTTTGACAAAGCTTGCAAAAATAAGCAATGAGGAAA--ATAC 3911
                           vi       i     i v vv   i vi vv     i     --   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_107112973_   3912 TCCATGTTCAATAAATGGTGCTGGGATAACTGGGTCACCATACGCAAAAG 3961
                           -- v     i              i      i v?   i i       
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_107112973_   3962 ATTAAAGCTGAACCCTTTCCTTACGCCACATCCAAAAATCAACTCAAGAT 4011
                          v i   i  i    i v   i  i   i  v       i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_107112973_   4012 GAATTCAAGACTTAAATGTAAAACCTAAAACTAGTAAAAACTCT-GGAAG 4060
                          i  iv?    i         i v         -     -    -i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTA-TAAAA-CTCTTAGAAG 541

  chr2_107112973_   4061 ACAACTTAGGCATTACTATCCTGGACGTATAAATGAAAAAA-GATATCAT 4109
                          v   v    ?i v v v i vv   v - iii v iiv  - i v  v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTT 590

  chr2_107112973_   4110 GACAAAGACATCAAAACCAACCACAACAAAAGCAAAAATTGACAAGTGGG 4159
                         iivv v    i     v  vvvi         v      v  i  i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_107112973_   4160 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTATCAACACA 4209
                          ii v  i   v v  i i   i  ii vv    i  v i      v v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_107112973_   4210 C-----AGACAACCTACAGAATGGGAGAAAATTTTTGCAAACTATGCATC 4254
                         v-----        i                 v        ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_107112973_   4255 TGACAAAGATCTAATATCCAACATTTATAAGGAACT--TA-AATTTA-CA 4300
                            i  i iv  vi      iv  v     i     --  -  i i -i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_107112973_   4301 AGAGAAAAATCAAACAATCCCATGAAAAAGTGGGCAAGGGACATGAACAG 4350
                          v i   i -    i  i  v  v?    i       i   iv    i  
  L1M4_orf2#LINE/    791 ATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_107112973_   4351 ACACTTGTCAAAAGAAGACATACATGCAGCCAACAAGCATTTGAGAAAAA 4400
                            i  v  v        i     viii     i     iv   i  i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_107112973_   4401 GCTCAATATTACAGAACAC 4419
                               i  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (146 / 89)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.61 (29 / 18)  


1332 27.68 8.64 3.84  chr2_107159059_107163004     2277  2901 (1045)    L1M4_orf2#LINE/L1        8   662 (246)  

  chr2_107159059_   2277 ATATATCACATTTATGAATCAGAGGG-TCAATATTAT-AAAACAATAATG 2324
                             vi  ii  i   i  ii  i i- i      i -  i iiii   i
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_107159059_   2325 ACCTCCATGTTGATCTATAGATTAAATGCAATTCCAATATAAATCTCAGA 2374
                         vi i   vi        i     v  i     i  v  vv     i   -
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG- 106

  chr2_107159059_   2375 ATAATTTATTTATTTGTTTTGTAGAAATC-ACAAGCTCATTCTAAAATTT 2423
                         ---------i iii v     i      i-       v  i        i
  L1M4_orf2#LINE/    107 ---------CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_107159059_   2424 GTACTGAAATGCCAAAGGG--TAAGAATAGAACCAA--CAACC---ACAA 2466
                         i  iv       --     --iv       --    --   i --- v  
  L1M4_orf2#LINE/    148 ATATGGAAATGC--AAGGGACCCAGAATAG--CCAAAACAATCTTGAAAA 193

  chr2_107159059_   2467 AGAAG-------TGGGAGGACTTAT--TTCATCAGATATGAAGACTTATT 2507
                              ------- v        i i--   -i  -  v v  i     i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTC-CCA-ATTTCAAAACTTACT 241

  chr2_107159059_   2508 GTAAAGCCACAGTAATTAATCCAACGTCCTTTTGGCTCAAGGGTATATAT 2557
                         ii     i        i  vv  ii  vv vi    vi    i  v i  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_107159059_   2558 TTA--CCAATAGA-TA-AATATATAGCCCAGAAACAGACCCTTGTATGCA 2603
                         v  --i    i  -  -   vv v  i       i i    v ii  vi 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_107159059_   2604 TGAAC--TTGATTTATAGCAAAGG----AAGCACTGTAGTGCAGTGGGTA 2647
                           iv --       viii   i  ----   -  ii -- -  i    v 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAG-ACCAT--T-CAATGGGGA 387

  chr2_107159059_   2648 ATAAA-GGTCTTTTCAAAATACTGATGCTGAGTCAATTGGTTATTCGGAG 2696
                          vi  -i          v - v  i     i v   i   v  ?i iv v
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACA-AATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_107159059_   2697 AGAAGAAAATAAATCTTGACCCCTACTTCTCATCATACACAAAAACCAAT 2746
                         iv  i i   i  vi v         i  v  i    i       ii  -
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA- 485

  chr2_107159059_   2747 CTCAAG-TAAATCATAGATCTAAATATAAATGGTAAAGCAGTATAGCTTC 2795
                              i- ii    ?   i      i   iv v    i vi  v i  ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_107159059_   2796 TAGGAAACAATATAGGA--AAATAGCTTCATAACCTTGAAGTAGAGGATA 2843
                            i i v  i     ?--    --    i i      iiv   ivi  i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_107159059_   2844 ------TA-ACAGGACATAAAAAATGCTAATTATAAAA--------AGAT 2878
                         ------  - i v    iv    iii v iiv i    --------    
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_107159059_   2879 AAACCGTAC------AACATTAAAAACTT 2901
                            ii v  ------  v           
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTT 662

Transitions / transversions = 2.09 (115 / 55)
Gap_init rate = 0.05 (31 / 655), avg. gap size = 2.52 (78 / 31)  

 536 25.51 8.50 2.83  chr2_107159059_107163004     3208  3454 (492)    L1M4_orf2#LINE/L1      648   908 (0)  

  chr2_107159059_   3208 CAAAACAAAAAAACCTTACGTCCATCTAAATACCCCATTAAGAAAGT--- 3254
                              iv     --   vi  v v  v  iv  v i  i        ---
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_107159059_   3255 -AGACAGACCATGTTAGTTAGGGAGGCAGCATCTGCAAACTATATAAATA 3303
                         -     iv   i---  vvv     iv ii  i      ii     vv i
  L1M4_orf2#LINE/    696 AAGACAACCCAC---AGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_107159059_   3304 ACAAAGACCTTATATGCAAAATATAAAAAGAGTTATTTCACATCAATAAG 3353
                          i  i iv   i   v  i      v     ii v  v  vv       v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_107159059_   3354 AAAAGAAGACACACAACTCAATAGAAAA----GCA-------------GT 3386
                             --     v i   i    v?    ----   ------------- v
  L1M4_orf2#LINE/    793 AAAA--AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_107159059_   3387 CACTTCATAAGATAAGATATGCAAATGGCCCACAATTATATGAAAAGGTG 3436
                           i   viv i v       i         v i  vi i        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_107159059_   3437 CTCAACATTATTGTTTTT 3454
                                 i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.07 (32 / 30)
Gap_init rate = 0.02 (6 / 261), avg. gap size = 4.67 (28 / 6)  


1140 27.39 16.52 2.90  chr2_107193863_107196579.rev      741  1430 (1287)    L1M4_orf2#LINE/L1        4   787 (121)  

  chr2_107193863_    741 AAAAACATACAATGTTCATGAATATGGAAGACCCAGTGT-GCCA-GATA- 787
                            i i  v v         i  -        ii i i - ii -   i-
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGAT-TGGAAGACTTAATATTGTTAAGATGG 52

  chr2_107193863_    788 CATTATTTCTTCAAGTGATGT-CAATTTC--------CCTTATCAAGA-- 826
                           v  i i iiv  v    v -  iv   --------  i      i --
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_107193863_    827 --ATTTGTGTT------AGAAAATTGACAAGCTAATTCTACATTTCATAT 868
                         -- vi  iv  ------     -          i  i   v v       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_107193863_    869 GG---TG-----GACTTAGATTAAC------------------------- 885
                           ---  -----   ii   v  i -------------------------
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_107193863_    886 -AGGT--------------------------AGACTTATTA--AAGCCAC 906
                         - i  -------------------------- i     i  --    i  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_107193863_    907 AGCAATCAAGAAAGTGTGAAATTAGTGCAAAGACAGATAAATCGACAGAT 956
                           i        v      iv i i iii  i  i   i v  v  ivi  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_107193863_    957 TGAACAAAATAAAAAATGCAGAAAAAGACAAACATACAAGTA--GTTACT 1004
                         v   i i   vi i i v      v i  v--      vv  --  i v 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCAAT 349

  chr2_107193863_   1005 TGGTTTATAACAAAGGTTCTAATGCAGTACAGTGAGGAAAGGATGATCTT 1054
                           i   vii    i   v i  vi vi v  i  i      i  ii    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_107193863_   1055 TTAAATAAATAATACTGAATCAATTGGATAGGAATATGGAGAA-AATAAA 1103
                           v  i    ii i   iiv   i      ?vv i   v i  -   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_107193863_   1104 TTTTTACCTCTACCTCACACTAGGTG--------AACT------GTAT-- 1137
                         v  vv   i           i vi i--------    ------ v  --
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_107193863_   1138 ---ACCTAA---TAAAAGGTAAAAACAATAAAATTTCCAGAAGGTAATGT 1181
                         ---      ---   i  v     - v      i iii     iv  ii 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACAT 548

  chr2_107193863_   1182 AGAATGACATCTGTATGATATCTTCATGGCCTTAGTGTAGTCAAATATGT 1231
                           ---------- ?i i -      i  i    i vv   v   vvi v 
  L1M4_orf2#LINE/    549 AG----------GNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_107193863_   1232 CTTAAATAAAATTTAAAAATAAGAATTAACACATAAAAAATTTAGACAGA 1281
                             i   vi iviv    vv v  vi    v vi     v -   i i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAA 636

  chr2_107193863_   1282 TTGGACTTTTATAAAAATTATGACCTTTT-TG--TCAAAAGATACCATTA 1328
                                 i-  v       vi v     -  --     i  i  i  i 
  L1M4_orf2#LINE/    637 TTGGACTTC-ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_107193863_   1329 AGAACATGAAAAATTAATTCAGAGAATGGGAGACAGTATTTGCTACACAT 1378
                             vi      ivi  ii  v           v i       v vv   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_107193863_   1379 ATACAAGATAAAAAGCTTATA--CAGTAATATATAAAGAAATATTAAAAA 1426
                            ivv     iiii   i  --   -             v v   v  -
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAG-AATATATAAAGAACTCTTACAA- 783

  chr2_107193863_   1427 CTCA 1430
                             
  L1M4_orf2#LINE/    784 CTCA 787

Transitions / transversions = 1.53 (113 / 74)
Gap_init rate = 0.04 (31 / 784), avg. gap size = 4.32 (134 / 31)  

 351 24.06 6.02 0.75  chr2_107193863_107196579.rev     2093  2225 (492)    L1M4_orf2#LINE/L1      769   908 (0)  

  chr2_107193863_   2093 AAAGAAATTCTCAAAA-TCAGTAATTAAAAGATAATCAATTTAATTTTTA 2141
                             -  i   i v  -   i    v      i  vi  iii    ?vv 
  L1M4_orf2#LINE/    769 AAAG-AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_107193863_   2142 AGTGGGTGAAGTACTT----AGACACTTCTTTAAGGGAGATAT-CAAAGT 2186
                          i    ii   v i  ----     i    ii  i i      -    vv
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_107193863_   2187 GCCAATAA--AAATTAAAATGTGCTTAACCTCATGAGTAAT 2225
                                 -- v  v    vi    i   v   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (19 / 12)
Gap_init rate = 0.04 (5 / 140), avg. gap size = 1.80 (9 / 5)  


3205 26.90 0.66 0.55  chr2_107214493_107220874.rev     4984  5890 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_107214493_   4984 TGGAAGAACATACCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5033
                              ii i  v     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_107214493_   5034 GGCCA-ACTGCTCAGGGTAATTTATAGATTCAATGCCAACCCCATCAAGC 5082
                            v -   v i  iiv i  i  i        i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_107214493_   5083 TACCAATGACTTTCTTCACAGGA-TTGGAAAAAACT-ACTTTAAAGTTCA 5130
                          v   iivi i  i  ii   i -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_107214493_   5131 TATGGAACCAAAAAAGGGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5180
                                viiv  ii iv  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_107214493_   5181 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5230
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_107214493_   5231 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5280
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_107214493_   5281 AACGGAACAGAAC--AGAGCCCTCAGAAATAATATCACACATCTACAACC 5328
                           i    i    i--    i  --        vvi  i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_107214493_   5329 ATCTGATCTTTGACAAACATGACAAAAACAAGAAATGGGGAAAGGATTCC 5378
                          vi    i  i     ivi  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_107214493_   5379 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 5428
                           v  i  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_107214493_   5429 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5478
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_107214493_   5479 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5528
                          i ?    i  v    v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_107214493_   5529 CTAGGCA-ATACCATTCAGGACATAGGCATCGGCAAGGACTTCATTCCTA 5577
                         v    ?i- v i -   iv   v v  vv v     v ii   v vvv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_107214493_   5578 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5627
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_107214493_   5628 ATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5677
                           i   v v  i ii  i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_107214493_   5678 CAGACAACCTACAGAATGGGAGAAAATTTTTACCATCTACCCATCTGACA 5727
                         v        i                 v   i v vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_107214493_   5728 AAGGGCTAATATCCAGAATCTACAAAGAACCTAAACAAATTTACAGGAAA 5777
                          i  i  vi          v  i       iivv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_107214493_   5778 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5827
                           iv    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_107214493_   5828 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5877
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_107214493_   5878 CATCACTGGCCAT 5890
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3203 23.36 2.30 1.96  chr2_107314073_107315939      507  1375 (492)    L1M4_orf2#LINE/L1       37   908 (0)  

  chr2_107314073_    507 AATATTGTTAATATGCCAACACTACCCACAGTGATGTACAGATGCTGTGT 556
                                    v   v   i   v    v v    v       v vii i
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chr2_107314073_    557 AATCCCTAGGAAAAAAATGACT-TTTTTTTTGCAGAAATAAAAAGAAAGA 605
                                 vv    vvviii  -ii              vi v iivv  
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr2_107314073_    606 AC--AAAATTCATATGGAGACTTAAGGGATTCTAAATAGCCAAAACAATT 653
                         v --              i ivi      ii vi               i
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_107314073_    654 TTGGGAAAAAAAAAAACTAAGTT------CTTATACTTAGTGATTTCAAT 697
                            --     i  i   v     ------  i i    vvii       v
  L1M4_orf2#LINE/    187 TTG--AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_107314073_    698 ATATATTGCAAAGCTACAGTAGTCAAAACAGTGTGCTACTGGCATAAAGA 747
                          iv  i i             i    i        v           i  
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_107314073_    748 CAGACA-GTAGACCAATGGAATAGAATAGACTGCCCA-AAATAATCCCTT 795
                         i     -i    i              v  vv i   -      v   v 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_107314073_    796 ATGTGTCTGATTAAGTAATCTTAGATAAGGGTATCAAAAGCACCTAATGG 845
                          ii v v  i i  v i  i  v  i      ii   i v  iii     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_107314073_    846 GGAATGA-TAGTCTCTATAACAAATTGGGGGTGGGAAAACTGGATATCGA 894
                             v  -      i vi       -  v v     v         ? v 
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAAT-GGTGCTGGGACAACTGGATAKCCA 433

  chr2_107314073_    895 CATGCAAA-GAATGAAGTTGGGCCTATATATTTCTCCTTACAAAAAGATT 943
                                 -            i  iv  iv iv v  v  i v   i   
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_107314073_    944 AACTCAAAATGAATTAAACACATAAACATAAGAACCAAAACAATAAAATT 993
                                    i  i ? v  v    ii     i i     v      i 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_107314073_    994 CCTAGAAGCAAACGTAAGGGAAAAGCGTCATAACATTGGACATGGCAATC 1043
                          i      v    i  i ? v   v v  i i  v    iivv      v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_107314073_   1044 AATTCTTGAAGATGACACTCAAAGCATAGGCAATAAAAGCAAAAATAAAC 1093
                         iv     ii v       iv      i i    i     v       i i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_107314073_   1094 AAATGAGACTACATTAAATGTTTAAATTTCTGTGCATCAAAAGGCACAGT 1143
                             vi    v   i   vv vv   i  i     v     i i   vi 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_107314073_   1144 CAATAGAGTGAAAAGATAACTTACATAATGGGA-AAAACATTTGCAAACT 1192
                            v i          i   ii   v       -    i         ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_107314073_   1193 ATATATCTGATAAAGGGTTAGAGTAATATCCAGGACATGTGAAGAATTTC 1242
                                      i  ii v -----       i i  i i     i ii
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTG-----TATCCAGAATATATAAAGAACTCT 778

  chr2_107314073_   1243 TACAACTCGACTGTTGACAACAAAAAC---CAACCCAATTTAAAAATGGG 1289
                                 i ---- i i  -   i  ---i         ?         
  L1M4_orf2#LINE/    779 TACAACTCAA----TAATAA-AAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_107314073_   1290 CAAATGACTTAAATAGATATATATTTCTCCAGTGA---CATGGAAATGAT 1336
                             v  i  i      i  ----       iv  ---i  iv     ii
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACAT----TTCTCCAAAGAAGATATACAAATGGC 869

  chr2_107314073_   1337 AAACAAGCATGGGAAAAGATGTTCAACATCACCAGCCAT 1375
                         v  i     iiv         i         ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (120 / 79)
Gap_init rate = 0.02 (16 / 872), avg. gap size = 2.31 (37 / 16)  


3315 24.45 1.88 1.44  chr2_107325354_107328766.rev     2048  2951 (462)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_107325354_   2048 TGGAGAGGTAGTCCATGCTCATGGATAGTAAGACTCAATACTTTCAAGAT 2097
                             i  i  vi     i        v v      i    i v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_107325354_   2098 GTCAG-ATTTCACAACTAGATCTATAGATTCAGTGCAATTCCAATCAAAA 2146
                          v  i- i i v   v v      i       ii     i  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_107325354_   2147 TCCCAGCAAGTTATTTTATAACTATTGAAAAAATGACTCTAAAGTTTATG 2196
                                vivi v    ii ivv     v  iv   ii     i  i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_107325354_   2197 AGGAGAGGCAAAAAACCCAGGATAGTCAACATGATATTGAAGGA-AAGAA 2245
                         v   i v    iii      i    i   v ii  v     ii -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_107325354_   2246 CAAAGTTGAAGGACTGCCACCACCTGACTTTAAGACTTACTATAAAGTTA 2295
                                 i      vv   iv  ii i  i  i        i    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_107325354_   2296 CAGTAATCA-GACAGTGTGATATTGGCAAAAGAATAGACACATATATCAA 2344
                                  -         i  i     v   i       i   v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_107325354_   2345 TGGAACAGAATAGAGAGCCCATAAATAAACCCACATAAATATAGTCAACT 2394
                              i     v     i   v           i i vv   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_107325354_   2395 GATCTTTGACAAAGAAGCTAAGACAATACAATTGAGCCAAGATAGTTTTT 2444
                            i  i     i iv  i     v  v    v i vv ii     i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_107325354_   2445 TCAACAAATGGTGCTGGAACAACTAGATGTTCACATGCAAAAAAAATAAA 2494
                                          i      i   i?i           i  - i  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAA 449

  chr2_107325354_   2495 --TAAATCCAGACAAAGGTGGTCTTATCATG----AAAATTTGCTCAGAA 2538
                         -- ii i  vv  v-------  vi i   i----      vi    i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACC-------TCACACCATATACAAAAATTAACTCAAAA 492

  chr2_107325354_   2539 TGAATCACAGACCTAAATGTAAAACAAAAAACTATGGAACTCCTGGAAGA 2588
                           i    ?              i vvv        ii     i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_107325354_   2589 TAACACAAGGAAAAAATCTAGATGACCCTGGGTATGACAATGATTTCATA 2638
                         v    i -  ?iv      vvi     i     vv i     i    v  
  L1M4_orf2#LINE/    543 AAACATA-GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_107325354_   2639 G---TTACAGTGGAGAAGCACTATCCATGAAAGAAAAATTTGGTAATCTG 2685
                          --- v   vi-- i      v v v ii         v v i   vi  
  L1M4_orf2#LINE/    592 GATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_107325354_   2686 GACTTCATTAAAATTAAAAACTTCTACTCTGCAAAAGAGAATGTCAAAGG 2735
                                 i              i iiv  v    i  v v i    iii
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_107325354_   2736 AATAAGAAGACAAGCCACAGACTGAGAGGAAATATTTTCAAAAGACACAT 2785
                          i i i       v       v  i   i        v    vv i i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_107325354_   2786 CTAATAGAGGATTGCCATCCAGAAAACACACAGAACTCTTAAAACCCAAC 2835
                           i   ii   i vvi        v i i v          v   i   i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_107325354_   2836 AACAAGAAAATAAACAACCAAGTTAAAAAGTGGACCAAGGACCTTG--CA 2883
                           i  i  i i   i    v i  ?    i   i v     i-   --i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATA 838

  chr2_107325354_   2884 AACATCTCACTAAAGAAGATATACAGAATG-CAAATAAGCATTTTTAAAA 2932
                         i    i  v i              -    - v        iv vv   i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACA-AATGGCCAATAAGCACATGAAAAG 887

  chr2_107325354_   2933 --GTTCCACATTAGATATTAC 2951
                         -- i  v    i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (137 / 80)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.00 (30 / 15)  


3173 26.59 0.88 1.10  chr2_107369050_107375444.rev     4994  5903 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_107369050_   4994 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5043
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_107369050_   5044 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5093
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_107369050_   5094 TACCAATGACTTTCTTCACAGGATTTGAAAAAAACTGCTT-TAAGGTTCA 5142
                          v   iivi i  i  ii   i v    v  i--   v i-   ii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_107369050_   5143 TATGGAACCTCAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5192
                                viv   ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_107369050_   5193 AACAAAGCTGGAGTAATCACCCTATCTGACTTCAAACTATACTTCAAGGC 5242
                                i     v v    v  vi ii i      viv    v   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_107369050_   5243 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5292
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_107369050_   5293 AATGGAACAGAAC--AGAGCCCTCACAGATAATGCCACATATCTACAACC 5340
                                i    i--    i  -- v i    vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_107369050_   5341 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCT 5390
                          vi    i  i     ivv  v   i v  vv            i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_107369050_   5391 CTATTTAATAAATGGTGCTGGGAAAATGCTACTGGCTAGCCATATGTAGA 5440
                           v  i  i              v  -----    v  ?   i   i i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAA-----CTGGATAKCCACATGCAAA 441

  chr2_107369050_   5441 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAG 5490
                          iiv    ii    i    v   i     v              i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_107369050_   5491 ATGGATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAG 5540
                               i ?    i  v    v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_107369050_   5541 AAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 5589
                              v    ?i- v i -   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_107369050_   5590 GACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 5639
                         iiv  vi            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_107369050_   5640 ATCTTATTAAACTAAAGAACTTCTGCATAGCGAAAGAAACCACCATCAGA 5689
                          ii i  i   v v  i     i  iiivv i  i  v  i i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_107369050_   5690 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATC 5739
                              v  i     i                 v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_107369050_   5740 TGAGAAAGGGCTAATATCCACAATCTACAATGAACTCAAACAAATTTACA 5789
                            v  i  i  vi      v   v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_107369050_   5790 AGAAAAA---AAA-AACCCCATCAAAAAGTGGGCAAAGGAAATGAACAGA 5835
                          v     ---   -     v  i?    i           vv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_107369050_   5836 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAGAACACGTGAATAAATG 5885
                           i     v        i  vi viii     vi i   i    v i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_107369050_   5886 CTCATCATCACTGGCCAT 5903
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


2835 28.73 1.22 0.88  chr2_107405530_107407529      606  1510 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_107405530_    606 TGGGAAAACATTCCATGCTCATGGATTGAAAGAATCAGTATTGTTAAAAT 655
                            i  i i  i     i          i    v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_107405530_    656 GGCCATGATACCCAAAGCAATTTATAGAGTAAATGCTATTCCTGTCAAAG 705
                            v  iv v      vii  i  i   v v  i  v  i   i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_107405530_    706 GGCTAACATCGTTTTTTACAGAATTAGAAAAAAAG-TTCTAAAATTCATA 754
                         vv i i vv v      i     v v  v  ivv - i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_107405530_    755 TGGAACCAAAAAAAAAGAGACTTA--ATAGCCAAAGCAATCCTCAGCAAA 802
                              ----- viv   i   ii --         i     i v iv  i
  L1M4_orf2#LINE/    151 TGGAA-----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_107405530_    803 AAGAACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATACTATAA 852
                                  vi      vv     i v  ii i      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_107405530_    853 GGCTACAGCAACCAAAACAGCATAGTACTGATACAAAAACAGACACATAG 902
                         i       i  i   i    ii i      ii i  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_107405530_    903 ACCAATGGAACAGGATGGAGAACCCAGAAATAAAGCCACACTCCTACAAC 952
                          i        i  i  v    ii           v   i  vii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_107405530_    953 CACTCAATCTTTGACAAAGTTGACAAAAATAAGCAATGAGAAAAAACT-- 1000
                           v ii  i  i     i v  v   i vi vv     i i   i v --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_107405530_   1001 TCCTATTCAATAAATGATGCTGGGATAACTGGCTAGCCACATGCAGA-GA 1049
                           i -     i     i        i      v  ?         i -  
  L1M4_orf2#LINE/    396 TCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_107405530_   1050 TTGAAACTGAACCCCTACCTATAACCATATATAAAGATTAACTCAACCTA 1099
                         v    ii  i          vvv        i   i          vv i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_107405530_   1100 GATTAAAGACTTGAATATAAGACCTTAAACTATACAA-TCCTAGAAGAAA 1148
                            i ?    i i   i     v  v        v  -  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_107405530_   1149 ACCTAGGAAATACTTCTCTTAATATCAGCCATGGCAAAGGATTTATGGCG 1198
                           v    ?ivv v ii  v i iv ii vivv     v  v  iv i vv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_107405530_   1199 AGGCCCTCAAAGGTAATTCCAGCAAACACAAAAATTGACAAGTGGGTTCT 1248
                          v v vi    i i vvvv  i    viv      v  i  i v  vii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_107405530_   1249 AATCAATCTAAACATCTTCTGCACAGGAAAAGAAACTATCAAGGGAGTAA 1298
                         v     vv v  v v   i  ii vvv   i  v         ii   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_107405530_   1299 ACAGAAAACCTACAGAATGGAAGAAAATATTTGCAAACTATGCATCCGTC 1348
                          v   v    i         i                ii  ii   i vi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_107405530_   1349 AAAGGTTTAATATCCCAAATCTACGAGGAATTT----AAATCAACAAGCA 1394
                           i  vi vi     vi   v  ii i   i i----  v    i  -i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TA 793

  chr2_107405530_   1395 AAGAAACCAAGTAACCTCATCAAAAAGTGTGCAAAGAACATGAACAGACA 1444
                           i i  -  i     iv  i?    i  v      i iv    i     
  L1M4_orf2#LINE/    794 AAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_107405530_   1445 CTTCTAAAGAGAAAACATACAAGTGGCCAAGAAACATATGAAAAAAGGTT 1494
                         i    vv i    i i      i       v  i  i       i v i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_107405530_   1495 CATGATTGCTAGTCAT 1510
                           vv  ii????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (155 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


2570 24.03 3.33 6.22  chr2_107581477_107583599.rev      700  1631 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_107581477_    700 AGAAATATTCTACATATATGGAAAGGGTAATTCAATACTGTTAAGATCTC 749
                          i i    i i ii vi     vv  ivi i i    i         vv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_107581477_    750 ATTTTTTCCCAACTTGCTCTATAGATTCAATGCAATCCCAATCAAAATCT 799
                          v vi i     v   v    i        i        v         i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_107581477_    800 CAGCAAGTTACTTTGTGGATATCAACAAACTGATTCTAAAGTTTATATGG 849
                             vivi vi    ii  v  ii    i     i     i  i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_107581477_    850 AGAGGCGAAAGACCCAGAAAAGCCAATACAAGATGGAAAAA--AGATCAA 897
                          i v  i ii         v      v    vv v      --   v   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_107581477_    898 AGTCAGAGTACTGAAATTCACCAAAATAAAAACTTCCTATAAAGCTATAG 947
                            ii   v   v v i iv    vv v       v   i       i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_107581477_    948 TAATCAAAACAATGTGGTATTTGTGAAACAACAGACAGATAGATCAATAC 997
                                i   i       i v iiv  vi i     v          iv
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_107581477_    998 AACAGACAGATAGATCAATATAACAGACAGATAGATCAACACAACAGAAC 1047
                           i   -----------  - i v  ---------  -------     -
  L1M4_orf2#LINE/    304 AATAGA-----------AT-TGAGAG---------TC-------CAGAA- 324

  chr2_107581477_   1048 AGAGAGCCCACATATAGTCCACCAAATATAACCAACAGATCTTGGATGAA 1097
                          v i -    i i  -- --------   iii   iv   i  v  ii i
  L1M4_orf2#LINE/    325 ATAAA-CCCATACAT--T--------TATGGTCAATTGATTTTCGACAAG 363

  chr2_107581477_   1098 AGAGGAAAGGCAATTCAATG------------TCTTTCTAACAGAGGGTG 1135
                         i v vv   i v        ------------     ii    i v    
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_107581477_   1136 CTGAAACAACTGGATATCCACAAGCAAAAATATAAATCTAAACACAGACC 1185
                            ii           ?     v      iv  i  vi ii  v vv   
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_107581477_   1186 TTTCAC-------AAACATCAACTCAAAGTAGGTAATAGACACCAATGTA 1228
                          iv   -------   v  i        i i i v ?    viv      
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_107581477_   1229 AAATATAAAACTATGAAACTGCTAGAAGATAA--TAGA---AAATATAGA 1273
                          i vv         i     vi       v  --   i---    v vvi
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_107581477_   1274 TGACCTTGAGTTTGAAAATGACTTTTAAGATACCACACTGAGAAAGCAGG 1323
                                 i   v iv    ii  i v     iv    ii --     vi
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA--AAGCACA 611

  chr2_107581477_   1324 ATCTATGAAATAGAAAATGGATAAATTGGACCTCATTAAATTTTTTTTTT 1373
                          v v ii   v i     i            i    i   v  -------
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT------- 654

  chr2_107581477_   1374 AAAAATCCTTCT-CTGCAAAATGCACT--TAAGAGAATAAAAAGACAATT 1420
                              iii  v -  v    ivi    --i    i i i         ii
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_107581477_   1421 CACAGAACAGGAGAAAATATTTGCAAAAGACTTCTCTGATAAAAACAAAC 1470
                                ii                  vv iv v        iii---  
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG---AC 751

  chr2_107581477_   1471 CCAAATTCAGAATATACAAAGAACTCTTAAAGCTCAACAGTACAAAAGCA 1520
                         iiiv  i         i            v i     i i  v   ii  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_107581477_   1521 AACAACCCAATT-AAAAATTGGCAAAAAAAAAAAATCTGAAAAGACACTT 1569
                           i         -      v      ii ------ i    v     i  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGA------TTTGAATAGACATTT 845

  chr2_107581477_   1570 CATCAAATAAAGTATACAGGTGGCAAA-AAGCATATGAAAAGATGCTCAA 1618
                          vi    v  ii      ii    v  -     i                
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_107581477_   1619 CAACATATGCTAT 1631
                           v  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (135 / 87)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 4.24 (89 / 21)  


1802 28.11 5.27 1.76  chr2_107591598_107595187.rev     2294  3090 (500)    L1M4_orf2#LINE/L1       66   890 (18)  

  chr2_107591598_   2294 ATAGATAGATAGATTTAATATTATCTTCATCAAAATCCTGGAAGCCTTTT 2343
                           v   vv i     i  iiiv   iii          ii vv       
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_107591598_   2344 CTGTTGAAAATGACAAGGTGATCCTTACATTTATTTAAGCAATGCAAATA 2393
                         i  iv    v       v       v v   i  v i- v       ivi
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG-GAAATGCAAGGG 164

  chr2_107591598_   2394 ATGTAGAATTACCAAACTATTTTTGACAAAGAATAACAAATACAGAGAAC 2443
                          ivi     vi     vi v i    v      v      vvii   i  
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_107591598_   2444 CTAGAGTATCTGATTTTAAGATTTATTTCAAGACTACAATAATCAAGACA 2493
                         ii v v vi ii    i  i i   i v   ii     i           
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_107591598_   2494 GTATGG------CATAAAGATGGAAATATAAGCCAAAAAAACAGGTTAGA 2537
                           i   ------     i   i  v     iii   vii  i  iv v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_107591598_   2538 CAGTGCATAAATAGACCTACA-ATGTGTG--CAATTGATTTCTGGCCAAG 2584
                         v   v  v     i   i i -  v i  --          ii i v i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_107591598_   2585 GAACTGAGGAAACTAAATGAGGAGAGAATAATATTTATATCAAACTGTAC 2634
                          vi ii  ivv i v    i   i      i v   vi v    iv  i 
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_107591598_   2635 TGGAACTACTGGATAGTCCTATGCAAAAGAACTGA-----GACTT-TATC 2678
                            i  v        ?i vi           -   -----   ii-  i 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCTACC 463

  chr2_107591598_   2679 TCATACAATAT-TAAAAA---ACTCAAATTGAATCATAGAGCTACATGGG 2724
                            i  v    -i     ---       v  i    ?   v   v   vi
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_107591598_   2725 AAAGTTAAAACTATATAAGTTCAAGAAGAAACCA-AGAGGTCA-TTTTAG 2772
                          i  i          v  v iiv        v  -  i?  v - i  v 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_107591598_   2773 TAATCTTGGCTCTGACAAAGATTTCTTAAA-GTGGGACCCG--GCAC--G 2817
                          i i     v iv i   v i       i -i  iv   vi--    -- 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_107591598_   2818 CT-TAAAATATATAAAAAATAATTTGGACTTCATTAAATTTTAAA-CATT 2865
                          v-i    v v v  v i    v           i   v  v   - v  
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_107591598_   2866 TGTCCTTCAATATACATATTTAAGAAAACCAAAAGGAAAGCTATGAATTG 2915
                            v      viv   ivv i      iiv     iv  v i iii v  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_107591598_   2916 GAAGAAAACATTTACAAAACACATGCATGAAAAGACAAAGTTCTTGTATC 2965
                          i      i    i    v  i  iiv   v   iv -----        
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGA-----CTTGTATC 758

  chr2_107591598_   2966 ----ATATATA--TAACATATATAATACTGACAAAAATAAGAAAAATAAA 3009
                         ----       --v   viv  i  iv -i i  v  v    v      v
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTC-AATAATAAAAAGACAAATAAC 807

  chr2_107591598_   3010 TCAGT--AAAAATGGA-AAAATATTT-AACAGAAATATCACATGCAAAAA 3055
                         i  i --        i-   iv    -  i   v  v  v ---    i 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC---CAAAGA 854

  chr2_107591598_   3056 A--TATACAGATG--CAAAAATATCACATGCAGAAAATG 3090
                          --      i   --   v  v--      - i  i   
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAG--CACATG-AAAAGATG 890

Transitions / transversions = 1.28 (124 / 97)
Gap_init rate = 0.03 (28 / 825), avg. gap size = 2.00 (56 / 28)  


1428 27.06 10.37 4.89  chr2_107596435_107598446.rev      674  1512 (500)    L1M4_orf2#LINE/L1        1   885 (23)  

  chr2_107596435_    674 TGAAGAGGTATCTTATGTTCATGATTTGAAAGAATCAATACAGTAAAATT 723
                           i i  i    ii         iv   i    v i    iv  v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_107596435_    724 ATCAACTCTGGCTATATAAAACTATTGAATTGATCCTATGCGT-TCGG-- 770
                         iv   iv  vv i v  vi v   iv  v ii iv v  v v -  ii--
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_107596435_    771 --CCAGATG-----TTTATAGAAATTGACATGCTGTTGTTAG--TCTACA 811
                         --    v  -----   ii           v    v vi  i-- ii i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_107596435_    812 AGAATATGCAAATAAATTAGTATTTCTAATACATGTATTCTAGATAAAAC 861
                         v i v      ivi vii  v  vv i  v   ---  -  v  v   iv
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACA---AT-CTTGAAAAAGA 196

  chr2_107596435_    862 AGAACAAAGTTGGAGGTTCTTATACT----GACTTCAAAACTTAATATAA 907
                                         v-  i i   ----i i           v  i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGA-CTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_107596435_    908 AGCTACATTAATCAAGGCAATATGATTCAGGCATGAGGATTAACAAATAA 957
                                v        i  i i  i v v     i     vi   v   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_107596435_    958 GTGAATAGCACAGTATATAAAGCCCCCAAATA----------------GT 991
                         i v   i v i  v  vv i  i  vv     ----------------  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_107596435_    992 CATTTGATTTTTCAACCAATGTGCCAAAGCAATCCAAGGAAGAGAGAA-A 1040
                           v        - i  v iv       ii v  i   v ii  i    - 
  L1M4_orf2#LINE/    346 CAATTGATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_107596435_   1041 GCCTGTTTAA-AAATAATG-TAGT----TTGGATATCCATAAGAAAAAAG 1084
                          i  v  i  -    ii  - i v----i      ?   i v v    - 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-G 443

  chr2_107596435_   1085 AAAAACAGTAAGTGTTTAAGCCTTGACTCCCAGCTCAC--CATTTACCTA 1132
                           vi -   ---  ----------   i  i v     --   v   -- 
  L1M4_orf2#LINE/    444 AATGA-AGT---TG----------GACCCCTACCTCACACCATATAC--A 477

  chr2_107596435_   1133 AATATTAATTTGAGGTTGATTATACAACCTAAACATAAAAATTAACATTA 1182
                           v     i ii ii v   i ? -i       ii   i ii   v i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWA-GACCTAAATGTAAGAGCTAAAACTA 526

  chr2_107596435_   1183 TGAAGTCTTTATAAGGCAAGTTACCTTTTGAGAGAAAATGTCTTTATTAT 1232
                          i  iiii   v   iv  vv  -------i ? v    --   ii v i
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATA-------GGNGTAAAT--CTTCGTGAC 567

  chr2_107596435_   1233 ATGAAGGAAAGCAACAGTTTCTTAGCTAGGACACGGGAAGCA--ATCAAC 1280
                         v vii vv i    ii         v  v     vii     -- v    
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_107596435_   1281 ATTGAAGAAAAAA--GTTGAACTGTATGTTACCAAAAT------------ 1316
                          --i         -- v i  i  v iv i i      ------------
  L1M4_orf2#LINE/    618 A--AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_107596435_   1317 -GCT-CATTAAGAACACTGGC------GTGT-----CA--TTACTAA--- 1348
                         -   -  --   i     iv ------   v-----  --ii  vi ---
  L1M4_orf2#LINE/    666 TGCTTCA--AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_107596435_   1349 GGAAAAAATATTTTCAATAAACATACGTAGCTGATGAAGGACTGTTACCT 1398
                            i         v   -- v    --  v     i i     vv  i i
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAA--ATCATA--TATCTGATAAGGGACTTGTATCC 759

  chr2_107596435_   1399 AGGATATATAAAGGGTTCCAATAACTCAGTAATAAAAAGACAAACAAAC- 1447
                           i          iii  iv i      i               i  v -
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_107596435_   1448 -----AAAAATTTTTAA-TGATTTCTACAGACA-----CAAAAGAAGATA 1486
                         -----      vvvi  -v     vv i     ----- v          
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_107596435_   1487 TACAAATGTCCAATATGCATATGAAA 1512
                                 v      v   i      
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAA 885

Transitions / transversions = 1.29 (126 / 98)
Gap_init rate = 0.04 (38 / 885), avg. gap size = 3.37 (128 / 38)  


2206 25.09 9.16 1.55  chr2_107623622_107625961     1008  1848 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_107623622_   1008 AGAGATACAATATTTTTATATATTGAAAGA---AAG--TGTTAAAATGTC 1052
                          i     ivvi  v  i  iv    i    ---  v--      i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_107623622_   1053 AGTTCTTCCCAAACTGATTTATAAATTAAACATAGTTCCAATCAAAATTT 1102
                          i v  i      i    i  i i   v   ii i i  v        ii
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_107623622_   1103 CAGAAGCTTTTTT---AGAAATTATCAAACTACTTCTAAAATTTATGTGA 1149
                            vv  i     ---       iv   i  iv i        i  i  i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_107623622_   1150 AAAATAAAAATGACCACAAGTAGCAAAAATCATTTTGAACAAAGAAGA-- 1197
                            - iv  iv    vvi i    v    iv  i     -        --
  L1M4_orf2#LINE/    154 AAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAAC 201

  chr2_107623622_   1198 -----TGGAGAATTCACACT------------AGCTGACTTCAA-GCCAT 1229
                         -----     i i       ------------ i  v   v   -  i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_107623622_   1230 A----TGAAG-CAGCTATGGTATCGGTGTAAGGATAAATAT-TAGATTCC 1273
                          ---- v   -   - i     ii  ii        i i  -     ivv
  L1M4_orf2#LINE/    252 AGTAATCAAGACAG-TGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_107623622_   1274 TGGAACAGAAT--AGAGTCCAAAAATGAACCCACATTTTTATGTTCAACT 1321
                              i     --        i    i      i iv      v    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_107623622_   1322 GCGTCTCAGAAAGGGGGCCAAGGTTATTCAAGGAAGAAAGTATTACCTTT 1371
                          vv i  iiv     v      iii      v ii     v  vii    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_107623622_   1372 TCAACAAAAGATCCTGGGACTACTG--TATTTTCATGCTTATAATAAATA 1419
                                 v i v       v    --  ?iiv     -- v  -i   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC--AAAA-GAATG 447

  chr2_107623622_   1420 AGA--AAATATTGACTTCATACCACATACCAAAATTAACTCAAAATGCAT 1467
                          ii--ii iviiv  i   i    i    v                 v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_107623622_   1468 TATACACCTAAGCATAATCATTATAA-TATAATAAATAT-AGAAGAAAAT 1515
                         i ? v      iii   vvii  v  -     -  v v -         i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAAC 546

  chr2_107623622_   1516 AT--GAACAAGTCTTTGCAGCTTTGGGGCATGTAAAAACTTCATAAACAG 1563
                           -- ?ii  i    i iii i     vi v i  viii   v  i i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_107623622_   1564 GACACAAAAATCATGAGTCACAAAAGAAAAA-TA---AAATTATTCTT-A 1608
                              v    v  ii  iv            -  ---     ivv   - 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_107623622_   1609 TCAAAATTAAAA-CTTTTACTGTTTGAAAA-ACACTGTATTTTAAAAATG 1656
                                     -     i-  i  v   i-     --  ivvi   i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACT--ATCAAGAAAGTG 693

  chr2_107623622_   1657 AAAGG-CAAGCTACAAACTGAGAGAAAATATC------------ATCTCA 1693
                            i -   v i   i v  i          i------------    v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_107623622_   1694 TAAAGAATTTGTATTGAGGATATATTAACAAACTCTCCCAACTCAATAAT 1743
                            i i i      iv  i      -  vi      iv            
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATAT-AAAGAACTCTTACAACTCAATAAT 792

  chr2_107623622_   1744 AAAAACAGAAATAACTC---CCAAAAATGGGCAAAAGATATGAAC----- 1785
                              v v       i ---i?             i   v    i-----
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_107623622_   1786 ---CTTGAAAGAC-ATATTATAAGTA-CCAGATAAACTCATAAATATATG 1830
                         ---  iv     v-    - i  i i-   -    i v   i  v v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATAT-ACAAATGGCCA-ATAAGCACATGAAAAGATG 890

  chr2_107623622_   1831 TTCAACATCATTAATCAT 1848
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (132 / 75)
Gap_init rate = 0.04 (37 / 905), avg. gap size = 2.43 (90 / 37)  


 670 28.57 3.30 3.66  chr2_107714684_107718134.rev     1739  2011 (1440)    L1M4_orf2#LINE/L1        5   276 (632)  

  chr2_107714684_   1739 AAAATATTTTATGCTCATAGATTGGAATACATGCTGGTGTTAAAATGTCC 1788
                           i    iii   i    i        v  v iv iv      i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_107714684_   1789 ATCCTACTTAAAGATATCTACAAAC-CATAAGTGAGGCATATCAACAACT 1837
                           v  v ii   vvv       i i-  - v ii vv v      v v i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCA-ACGCAATCCCTATCAAAATCC 103

  chr2_107714684_   1838 CAATGGTAGGTTGTTTTTTTTTTTAAGAAATAGAAAAA--AATGTTAAAA 1885
                           ------- i  ii      vi--      v  v  i--i  vi     
  L1M4_orf2#LINE/    104 CA-------GCTGCCTTTTTTGC--AGAAATTGACAAGCTGATCCTAAAA 144

  chr2_107714684_   1886 TGTATATGGAACCACAAAAGCCTCTAAATAGCCAATGAAATTTTGAAAAA 1935
                          vi        vii   ii v i vi         viv   i        
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_107714684_   1936 GAA---CAAAGCTGGAGACATCATAGTTATTGTTTTCAAAGAT-ATTGCA 1981
                            ---     i     ivv   i v  viiiv       iv - i i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_107714684_   1982 AAGCTATAGTAATTAAAACAGTATGG--CTGG 2011
                               i      i  i     i   --    
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

Transitions / transversions = 1.36 (45 / 33)
Gap_init rate = 0.03 (8 / 272), avg. gap size = 2.38 (19 / 8)  

2352 24.35 1.23 1.68  chr2_107714684_107718134.rev     2309  2961 (490)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr2_107714684_   2309 AAAAAAATATGAGACTAACATTAAAACAGACTTACAAACCA-TGGAACAG 2357
                           i v i i  iv   ii   v ii i    v  i i i  -     i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_107714684_   2358 AGTAGGGATCCCAAAAATAAACTCAAACATAGATGGTTAA--GGTATTTG 2405
                          i v i  vi   i        i  v    vv     i  -- i v  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_107714684_   2406 ACAAGGGTGCCAAGAATACACAATGAGAAAATGACAGTCTCTTCAACAAG 2455
                                        vi iv     i i   vi i     i        -
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA- 407

  chr2_107714684_   2456 TATGGT--TGAGA-AATTAAATTTCCACATGCAAGAGAATGAAATTGCAA 2502
                         -     --  i  -  i ii  v?          i        i   v v
  L1M4_orf2#LINE/    408 -ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_107714684_   2503 CTTTATTTTACACCACAGAGAAAAGTCAACTTAAAATGGGTTGAAGATTT 2552
                          ii  ii i      i v v    i i    i       i ii?   ii 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_107714684_   2553 TAACATAAGACCTGAAACTGTAGAACTCCTAGAAGAAA-CGTATGGGAAA 2601
                         v  ii     v  i     i  i     i         - i  v ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_107714684_   2602 AGTCTCATGGCATTGGGCTTGCTAATAATTTCTTAGATATGACACCAAAA 2651
                          vii  i  i v     i v vi   ii                      
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_107714684_   2652 GCACAATGAACAAAAGCAATATTACATAAATGGGACTACAGCAAACTAAA 2701
                               vv        v  v v  v      v     v  v    v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_107714684_   2702 AGGCTTCTGCACAGCAAAGAAAACAATCAACAGAGTGAAGAGACAATGAA 2751
                          ii   i  ii vv     i v  v     v i      i      ivv 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_107714684_   2752 CAGAATAGGAGAAAATATTGGCAAACCAGATATCTGATAAAAGGTTAATA 2801
                               i            v     i  v           ii ii vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_107714684_   2802 TTCAACATATGTAAGGAACTCATACCACTAAAAGACAAACAAAACCAAAC 2851
                          i  iv    i   i      v   v   v  vi i   -  i  -   i
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGAC-AAAT 804

  chr2_107714684_   2852 AATCCAACT-AAAAATGGGCAAAGAATCTAATTAGACATTTTCTTCTTCC 2900
                           i    i -              i  i i v         i-----   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC-----TCC 849

  chr2_107714684_   2901 AAAGAAGACATACAAATGCCCAGCAAGTATATGAAAAAAAATGTTCAACA 2950
                                 i         v   ii   i i       i --  i      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAACA 897

  chr2_107714684_   2951 TTGCTAATTGT 2961
                          ii????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.89 (102 / 54)
Gap_init rate = 0.02 (11 / 650), avg. gap size = 1.73 (19 / 11)  


1904 25.91 1.15 1.15  chr2_107735835_107738726      501  1021 (1871)    L1M4_orf2#LINE/L1       87   607 (301)  

  chr2_107735835_    501 AATTTCAATCAAAACTTCAGCAAGTTGTTTTCCACATATTGACAAACTGA 550
                            ii v       iii    vivi v    v  v v        i    
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr2_107735835_    551 TGCTAAATTTTCTATGCTGAGGCAAAAGATTCAGAATAGCCAACACAAAC 600
                          v     v  iv    vvi v    ii  ii            v    v 
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_107735835_    601 TTAAAGGAGAAGAACAAAGTCAAAAGTCTGACACTACCCAATTTCAAGAC 650
                           i  ii             iii i v  v     v           i  
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_107735835_    651 TTATTATAAAGCTATAGTAATTCAGGCAGTGTAGTATTA-CAGAAGGAAT 699
                            i  i       i      iv  i      i   i i-  v     - 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-T 285

  chr2_107735835_    700 AAACAAATAGTTCAATGGAAGGGAATAGAAAGTCTAGAAATAGAC--AGA 747
                          i   v    v         vi    v  i    i       i  -- v 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_107735835_    748 CATAAATAGTAACAATTGATCTTTGACAAAAG-ATCATGGGCAATACAAT 796
                            vv  i  --        i  i     ii -ii  -i i v  v    
  L1M4_orf2#LINE/    336 CATTTATGGT--CAATTGATTTTCGACAAGGGTGCCA-AGACCATTCAAT 382

  chr2_107735835_    797 GGAGAAAATATAATCTCTTCAATAAGTGGTGCTGGAACAACTGAAGTTTC 846
                           i    iv   i   i     i  i         i       i vv?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_107735835_    847 ACATGCAAATATATTTTTCTAGACACAGACCTCACATCTTTTACAAAAAT 896
                                  viv  vvvvi i   v vv        i v v         
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_107735835_    897 TAGCTCGAATTAGATCATTGACTCAAATGTAAA--CTGCAAATCTACAAA 944
                           i   i  v i     ?v   ii        i--  --   v   i   
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT--AAAACTATAAA 530

  chr2_107735835_    945 ACTCTTAGAAGATAATATAGGAGAAAATCTGGATAATCTTGGGTATGGTG 994
                                     v  i     ? v      vvi i i       vv  ii
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_107735835_    995 ATGTCTTTCTATACACATCACCAAAGG 1021
                            vi  ii  v i iiv       i 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAG 607

Transitions / transversions = 1.40 (77 / 55)
Gap_init rate = 0.02 (8 / 521), avg. gap size = 1.50 (12 / 8)  

1021 21.20 4.24 2.12  chr2_107735835_107738726     2118  2400 (492)    L1M4_orf2#LINE/L1      620   908 (0)  

  chr2_107735835_   2118 AAGAATTAACTGATAAGCTAAACTTCATTAACATTAAAAATTTCTGCTCT 2167
                              vv  iv     ii ii       i  v        i  i  iv  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_107735835_   2168 TGAAAAGATACTGCCAAGAAAATGAGGAAAGAAGACAGTCTAC----TGA 2213
                          v   i  i   ii       i   i-----      ii i  ----  i
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAA-----AAGACAACCCACAGAATGG 714

  chr2_107735835_   2214 AAAAAAAT---TGCAAAACACATATCTGATAAAGGACTATTTTCCAAAAT 2260
                         i i     ---      v  i           i     vv v    i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_107735835_   2261 ATACAAAGACCTCTT-TAACTCAATGATAAGAAAGA-GAACAATCTAACT 2308
                            i     v     -i        i    -     -i  i  i i  i 
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAA-AAAGACAAATAACCCAATT 813

  chr2_107735835_   2309 TAAACACTGGCAAAGGACCTTAACAGACACCTCACC---GAAGATCTACA 2355
                         ?   v iv         ii v  i     ii  v  ---      v    
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_107735835_   2356 CATGGCAAATAAGCATATGAAAAGATACTTAACATCATAGGTCAT 2400
                         v     v        i          i  i       ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.28 (41 / 18)
Gap_init rate = 0.02 (7 / 289), avg. gap size = 2.57 (18 / 7)  


2003 26.45 1.98 0.83  chr2_107742138_107743742      501  1105 (500)    L1M4_orf2#LINE/L1      244   855 (53)  

  chr2_107742138_    501 AAGGCTACAGTTACCAAAGCAGCACAGCACTGGTACAAAAACAGACACAT 550
                           i        v i   ii   iiii i     i i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_107742138_    551 AAACCAATGGAAGAGATTAGAGAACTCAGAAATAAGACTGCACACCTACA 600
                          i i        v   v v    iii         iv iii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_107742138_    601 GCCATCTGACCTTCGA-AAACCTGACACAAATAAGCCATGGAGAAAGGAT 649
                          i  vi   ii     -  ivv  v  vi vi vv v    i     i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_107742138_    650 TCCCTATGTAATAAATGGTGCTGGAAGAACTGGCTAGCAATATGCAGAAA 699
                         vvi  v vi  i            i v      v  ? v i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_107742138_    700 AATGAAATTGGACCCCTTCTTCACACCTTATACAAAAATTAACTCAAGAT 749
                               i          v i       v                   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_107742138_    750 GGATTAAAGACTTAAATGTAAAACCCCAAACCATAAAAACCCTAGAAGAA 799
                             i ?    i         i v iv    i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_107742138_    800 AATCTAGGCA-ATACCATTCACAACATAGGCATGAGCAAAGATTTCAT-G 847
                           iv    ?i- v i -   iii  v v  vv ii    v i    v - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_107742138_    848 ATGAAAATGCCAAAAGCAACTGCAACAAAAGCAAAAATTAACAAATGGGA 897
                           - vi ii         vvv          v      vi i    v   
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_107742138_    898 TCTAATTAAACTAAAGAGCTTCTG-----CAAAAGAAACTATCATCAAAG 942
                         ii v  i   v v  i i   i  -----    i  v       vv    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_107742138_    943 TGAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCATCT 992
                             v        i                 v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_107742138_    993 GGCAAAGGTCTAATATCCAGAGTCTACAAGGAACT--TA-AATTTA-CAA 1038
                          ii  i  v  vi        i v  i  i     --  -  i i -i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_107742138_   1039 GATAAAAACAAATAGCCCCATTAAAAAGTGAGCAAAGGACACGAACAGAC 1088
                         v v   i       i   v   ?    i  i        ivi   i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_107742138_   1089 ACTTCTCAAGTCAAGAA 1105
                          i     v ---     
  L1M4_orf2#LINE/    842 ATTTCTCCA---AAGAA 855

Transitions / transversions = 1.64 (97 / 59)
Gap_init rate = 0.02 (10 / 612), avg. gap size = 1.70 (17 / 10)  


 322 30.56 7.78 0.00  chr2_107802511_107805079      900  1079 (1490)    L1M4_orf2#LINE/L1       18   211 (697)  

  chr2_107802511_    900 TTCAAGTATTGAAAAATTCAACATAGTAAAGAAGTCAGTTCTCCCCAAAT 949
                             v v    i  i i i  i  v  v    v v  i v          
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr2_107802511_    950 TGA----CATAT-------AATTCTCATGAAAATCTCAAAAAGATTTTT- 987
                            ----  v  -------   i ii  v      i  ivvivv     -
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr2_107802511_    988 ATAGACATATAAAAGATTAGTCTAAATTTTACATGGAAAAGCAAAGAAAC 1037
                         ii   v  vv v   v v vi     v  i i       v    i i v 
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_107802511_   1038 TAAAATAGTTAATATAATTTCAAAAAA--AGAATAAAATAGAAG 1079
                         i i     ii  v i   i ii     --    i   i v i  
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

Transitions / transversions = 1.20 (30 / 25)
Gap_init rate = 0.02 (4 / 194), avg. gap size = 3.50 (14 / 4)  

1391 25.14 4.19 7.08  chr2_107802511_107805079     1386  2077 (492)    L1M4_orf2#LINE/L1      237   908 (0)  

  chr2_107802511_   1386 TTACTGTATGGCTACAATGAAAAAAATTCTGTGGAATTGTCAGAGGTACA 1435
                              ii vi      i i vv  i ivv     v i  v  v i v i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_107802511_   1436 GACACAGAGATCAATGAAACAGTACAGAGTATCCAGAAATAGACCCACAG 1485
                             i v         i  i  v iv   vi          i     i v
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_107802511_   1486 AAATTTAC--TCAAAAGATTCTTGAAAAAAGAAAGGTGCAAAAGCAACTT 1533
                          --    i--    vv    i i  v  i-----     v  ii v i i
  L1M4_orf2#LINE/    337 A--TTTATGGTCAATTGATTTTCGACAAG-----GGTGCCAAGACCATTC 379

  chr2_107802511_   1534 AAAAAGGAATATAGACTATTCGACAGTTCAACAAATGGTGCTGGAGCAAT 1583
                           vii    ---   v  v  v---v                  ii   i
  L1M4_orf2#LINE/    380 AATGGGGAA---AGAATAGTCT---TTTCAACAAATGGTGCTGGGACAAC 423

  chr2_107802511_   1584 TGGACATCTAT-TGGCACAAAAGAGATCAAAAAAGGACCCCGATCT-A-- 1629
                             i ? i i-  ---       -  -i  ivv       v i  - --
  L1M4_orf2#LINE/    424 TGGATAKCCACATG---CAAAAGA-AT-GAAGTTGGACCCCTACCTCACA 468

  chr2_107802511_   1630 --AGATGCAAAATTCATCCAATTAATCTGAAATGAATACATGGATCATGG 1677
                         -- v  i     --------     -  v   -------        ?i 
  L1M4_orf2#LINE/    469 CCATATACAAAA--------ATTAA-CTCAAA-------ATGGATCAWAG 502

  chr2_107802511_   1678 ACTTAA-TGTGAAA-CAGACATTATAAAACTTTTAGAAGACAACATAGGA 1725
                           i   -   i i - vi v i         i        v        ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_107802511_   1726 AAAAACATTC-T-ATCTCAGGAAAGATGAAATA--TTGTTAGACTTGACA 1771
                         iv   iv   - - i  ii  vv  -- v   i--  v     iv     
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAG--GCAATGGTTTCTTAGATATGACA 600

  chr2_107802511_   1772 TCAAAAGTACCATCAATCAAACAAAAATTTGATAAAATGGACCTTATCAA 1821
                         i      i  v v   iv   v     v v      v     i i     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_107802511_   1822 AATTAAAAA---TTATGCTCTGTGAAAACTACACT-----GAAGATAAAG 1863
                                  ---  i    ii----   vv     -----   ii i  i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTC----AAAGGACACTATCAAGAAAGTGAAA 696

  chr2_107802511_   1864 ATAAAAGCTACAGAGTGGAAGAAAATATTTGCAAACCACATATCCAACAA 1913
                          v v  v i     i   i                i  i     ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_107802511_   1914 AGAAATAGAATTTATAATATATTTTTTAAAAACTCACAAAACCTAACAGT 1963
                         i i v v v  ii v       v----  i     vi v   ii  i i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATA----AAGAACTCTTACAACTCAATAAT 792

  chr2_107802511_   1964 CAAGAAAAAAAACAATTAAC----TTGGGACACAAACAACAGACATGAAG 2009
                         -----     i    v    ----  ?ii v iiii   vi  iv    v
  L1M4_orf2#LINE/    793 -----AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_107802511_   2010 AAACACTTCACTGAAAAGGCTATATGGATGACACATAAGCCCATGAAA-- 2057
                          i   i   v ii  i i v    iii   i vv      v       --
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_107802511_   2058 -TGTTTAACATCACTCGCCAC 2077
                         -  i i       ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (102 / 68)
Gap_init rate = 0.04 (27 / 672), avg. gap size = 2.89 (78 / 27)  


3672 20.27 3.23 2.12  chr2_107864254_107867689     2047  2944 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_107864254_   2047 TGAAAATACATGCCCTGTT-ATAGGCTAGAAGACTTAATATTATTGAAAT 2095
                           i   v i  v  v    -  i ii i              i  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_107864254_   2096 GTCAGTATTATCCAAAGCAATCTACAGATGTAATGCAATCTCTATCAATA 2145
                          v  i  i vi     vii          vi  i      i       v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_107864254_   2146 TTCCAACAGCAGTTTTTGCAAAAATAGAAAAATCTG-CCCTAAGATTTGT 2194
                          i   i v  vv        i    v  v  i-   -i     i   ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_107864254_   2195 ATGGAATCCCAAGGGACCCTAAATAGCCAAAACTATCTTTAAAAATGAAA 2244
                               viv          vi            v     v     -   -
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA-GAA- 197

  chr2_107864254_   2245 GGAACTAAGTTGGAGGTTTCACATTTCCTGATTTCAAAACTTATTATGAA 2294
                         -    v          vi     i    ii             i  ii  
  L1M4_orf2#LINE/    198 -GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_107864254_   2295 GGTATGGTCGTCAAAACAGTATGGTGCTGGCA-GAGG-----CACATA-A 2337
                          v  ii  vi    i     i    i      -i   -----  i   - 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_107864254_   2338 TTA------TACACATAA------AGAAATACACCCTCACATATATAGCC 2375
                          i ------  v vv i ------       v    vi    v   i i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_107864254_   2376 AAATGATTTGCAACAGGTTTGCCAAGACCATCCTGCTGAGAAAGGACAGT 2425
                           v      v i   i vv            i viiv i     i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_107864254_   2426 GCCTTTAAGAAATGGGGTTGGGAAGACTGGATATCCACA----AAAGAAT 2471
                         vii  i  v      v i     vi        ?     ----       
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_107864254_   2472 GAAGGTGAATTTCTCCTACCTTATACCACACTATATCATATACACAAATT 2521
                             v  i --- i       -----     -----        v     
  L1M4_orf2#LINE/    447 GAAGTTGGA---CCCCTACCT-----CACAC-----CATATACAAAAATT 483

  chr2_107864254_   2522 AACTCAAAATGGATCAAAGGCCTAAATTAAAGACCCAAAACTGTAAAACT 2571
                                         ?  i       vv    v i      i       
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_107864254_   2572 CCTAAAAGAAAACATAGGGGAAAAGCTGTATGACATTGTACATTA--CAA 2619
                          i  i             ? v   v  vii    v   vi--   --   
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAA 581

  chr2_107864254_   2620 TAATTTATCGTATATGACACCAAAAGAACAGAGAACAAAAGTAAAAATAG 2669
                          ii   v iiv               v   iiv        v        
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_107864254_   2670 AAAAATTGGACTACATCAAAATTAATAACTTCAGTGCAGCAAAGGAAATA 2719
                          v          v            v     iv    vv       v iv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_107864254_   2720 ATCAACAGAGTGAAGAGGCAACCTACAAAATGGGAGAAAATATTTGCAAA 2769
                              v i      i  i     i   i                      
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_107864254_   2770 T-ATATATTTGACAAGGGATTAATATCCAGAATATATTAATAACTACTAC 2818
                          -      i   i      i vi              v  v    vi   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_107864254_   2819 AATTCAACAACAACAAAACAAATAATCTTATTTTAAAATGAGCAAAAAAC 2868
                           i    i  i  v  i        i iv   ?v      i     ii i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_107864254_   2869 TTGAATAGATATTACTACAAAGAGAATATATTA-TGGCCAATAAGCATGT 2917
                                  i   v  v      ii     iv -             ii 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_107864254_   2918 AAAAAGATGCTCAATATCACTGATCAT 2944
                         i             i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (106 / 72)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.67 (48 / 18)  


1657 29.26 7.38 1.34  chr2_107868181_107869916      500  1244 (492)    L1M4_orf2#LINE/L1      119   908 (0)  

  chr2_107868181_    500 CAGAGAGTGAAAAACAGTTCTTAAAAAATTACATAGAAAGGCACAGGCTT 549
                             i v   v  i v v  i     v- i i  i    v   vi  vii
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAAT-TCATATGGAAATGCAAGGGACC 167

  chr2_107868181_    550 TAGAATAGCCAGAACAATCTT-AAAAGTAAGAGTAAAATGAAAGGAATCA 598
                         i          i         -    iv    ii   i vii    v   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_107868181_    599 CTCTCCTCAATACTAATGTCTATTATGTAGTTATCATAAACAAAACAATG 648
                          v  i i    vii  viii  i  iiv  i  ivi   v   i   i  
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_107868181_    649 TGGTATTAGTGGACACGTAGACACATAAATCAATGGAACAGAGTAGAAAG 698
                              i i iiv vivi      i   i          i   i v  i  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_107868181_    699 CTAAGAAGTACACCCACAAAAATATGCCCAGCTCTTT--TTTTTGACAAA 746
                         iiv    i  v     i v vv    vi  i----  --    i     i
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAA----TTGATTTTCGACAAG 363

  chr2_107868181_    747 AGTACTAAAACAGTCCCAAGCGTAAGGA---------------------G 775
                         i  i i  i  vi i v v v v  i  --------------------- 
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_107868181_    776 CTAGAATAATTGGACATCCATAAGCAGGAAAAAATAA---TGAAACTCAA 822
                           i i i  i    i ?   i v   --   i   i ---  i v i v 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCA--AAAGAATGAAGTTGGACCCCTA 461

  chr2_107868181_    823 CC-AAAACTTTATACAAATA--AACTTTATACAAAT---AAACTTTACAT 866
                           -v v  iv        v --    iv v iii  --- i  i - v  
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT-AAAT 510

  chr2_107868181_    867 CTTA----TAAAA--ATAAAAATTTTC-------ATATATATGAAAATCC 903
                         v v ----     --      v i  v------- i   vi? v     i
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_107868181_    904 TTGGGAGCTAGGGCAAGACAAAGAGTTGATAAACTTGGCACTAAAAGCAC 953
                          i v  v  v   iv  i   v iv  vv  i iv  i   i        
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_107868181_    954 AGTCCTTAATAGAAAATATTAATAAATTGAACCTTATCAAAAGTTAAAAC 1003
                          iv vvi  v      v  vi        i  i i       v v     
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_107868181_   1004 TTT-GCTCTGCAAAG---ACTGTGGGGAAGATGAAAAGACAAGCTACAGA 1049
                            - iv  v     ---   i vii   ii           v i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_107868181_   1050 TGTAGGGGAAA-TATTTATAGACCACATATTTGAGAAAG-ACTTGTATGG 1097
                         -i i  i    -     ii i i  i    i   v  i -        vv
  L1M4_orf2#LINE/    711 -ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_107868181_   1098 AGATTATCTAACAAACAC--ACAAACTCAGCAACAATAA-ACAAACAATA 1144
                            v   v   vi   v --    -    ii  i  v  -     i  iv
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAA-CTCAATAATAAAAAGACAAATAACC 808

  chr2_107868181_   1145 TGATTAGAAAATGGGCAAAAGACATGGGTACGCATTTCACCAAAGAAGAT 1194
                         ii   ?i            i  iv  ii  vi      v           
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_107868181_   1195 ATGCAGAGGGTACATAAGTACAAGAAAAAATGTTCAACATCACTGGCCAC 1244
                           i  i v  ivv     i   v     i   i         ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (130 / 85)
Gap_init rate = 0.03 (22 / 790), avg. gap size = 2.95 (65 / 22)  


3383 23.56 2.21 1.77  chr2_107987947_107990077      736  1639 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_107987947_    736 TGAAAAGACATTCCATGTTCATGGGTTGGAAGAATTAATATTGTTAAAAT 785
                           i     i  i            i        v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_107987947_    786 GACCACACTATTCCAAAT-GATCTACAGATTAAGTACAATCTCTATCAAA 834
                          i v i   -ii      -            v iii     i        
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_107987947_    835 ATATCAATGATATTCTTTGCAGAAAT--AAAAAC-AATCCTAAAATTCAT 881
                           vi  iiviiv  i           -- v  i -i              
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_107987947_    882 ATGGAACCACAAAAGACTTGGACTAGCCAAAGCAAACCTGAGAAA-AAGA 930
                               vii   ii   iii  v        i   v i   i   -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_107987947_    931 ACCAAGCTGGAGGCATCACACTACCTGACCTCAAAATATAGTGCAAG--- 977
                           v   i      vv       v  ii ii      iv  v i   i---
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_107987947_    978 ATAGTAACCAGAAAAGCACAGTACTGGCATAAAAACAGGTACATAGACTA 1027
                          i     i  ii v  iiii            ii i  ii i     ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_107987947_   1028 CTGAAACAGAATAGAGAACCCAGAAATAAATACATGTATCTACAGCCAAC 1077
                         v  i  i     v    ii           iv   ii  i  ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_107987947_   1078 TGATTTTCAACAAAGACATCAAGAATATACATTGGCAAAAGGACAGCCTC 1127
                                 i    i iiii     vi  v  v   vi    i i  i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_107987947_   1128 TTCAATAAGTGGTAATGAGAAAACTGGATATCCATATGCAGAAGAATAAA 1177
                              i  i    iv  i  v         ?   i     i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_107987947_   1178 ACTAGACCCCTATCTCTCACCATATACAAAAATAAACTCAAA-TGGATTA 1226
                         ii i        i   v                v        -     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_107987947_   1227 CAGACTTAAATGCAAGACCCAAAACTATAAAACTACCAGAAGAAAACATA 1276
                         ?    i      i    v i              vii             
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_107987947_   1277 AGGA-AAATGCTTAG-GTCATTGATCTAGGCAAATATTTTATGGATGAGA 1324
                         i ?i-    -   v - v v   ivi       vvi   iv i   - vi
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr2_107987947_   1325 ACAC-AAAAGCACAGGCAACAAC-GAAAAAATAGACAAATGGGATTATAT 1372
                             -         i       v-           i    v   i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_107987947_   1373 CAAACTCAAAAGCCTCTGCACAGCAAAGGAAAC----AACAGAGTAAAGA 1418
                             v i    i i i  ii vv       v  ----  v i   i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_107987947_   1419 GTCAACTTGCAGAATGGAAGAAACTGTTTACAAACTACTCATTTGACAAG 1468
                          v    iii        i     v i   i    ii ivi  i   i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_107987947_   1469 GGATTAACATCCAGAATAAACAAAGAACTCAAATAACTCAACAGCAAATA 1518
                            i vii          v i         vv i       i ii   - 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-A 796

  chr2_107987947_   1519 AAACACAACAAAAAATAACCCTATTTTTTTTAAATGGGCAAATGATCTAA 1568
                          i   --------        v   ?vv---           v   i i 
  L1M4_orf2#LINE/    797 AGACA--------AATAACCCAATTWAA---AAATGGGCAAAGGATTTGA 835

  chr2_107987947_   1569 GTAGGCATTTTTC---AAAAGATCTACAAATGGCCAACAAGTATAAGAAA 1615
                         i   i     i  --- i     v             i   i i v    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_107987947_   1616 AAAATGCTTAATATCACTAACCAT 1639
                          i -    i  i    ????????
  L1M4_orf2#LINE/    886 AGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.54 (150 / 59)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.89 (36 / 19)  


2891 22.97 7.66 2.32  chr2_108030799_108032814      663  1524 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_108030799_    663 TGGAGAGATGTTCTGTGTTTATGCATTAGAACACTTAAGGTATTCC--AG 710
                             i    i i ii    i   v   i   v      --    vi--  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAA--TATTGTTAAG 48

  chr2_108030799_    711 ATGCCAATTCTTTTTGATTTGAACTATTGATTAAATACAGTCTTTATCAA 760
                            v    v  iiiii v    v   iv    v  ii  i  ii      
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_108030799_    761 ------------------TACTGAAGCTGGCA-------TTTGAACTTTT 785
                         ------------------ i v   ii  i  -------ii i  v  iv
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_108030799_    786 TTTGGTAGTGCAAG---CCCTGAATAGCAAAAGCAA-CTTTTAAGAGAAG 831
                          v   v i      ---   v       v   i   -   vv  i     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_108030799_    832 AACAATGTTCAAATACACATACTACACAACATTAAAAC-----ATAAAGG 876
                              v   vi iv  v  i   v v   iv i     ----- i    v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_108030799_    877 TACAATAATCTACACGGTGTGATACTGGCATAAGAGCAGGCATATAGATC 926
                             i     v v  i     i            iii  i          
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_108030799_    927 AATGGAATTGGCCTGAGAGTCCAGAAACAAATCCTTACATTTCTGGTCAC 976
                                 v ivi              i   i  v       v      v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_108030799_    977 CTAATTTCTAACAAATCTCCCATTATAAGTCAATGGGGAAAGGATAGTCT 1026
                         i i    iii    ivv v   vv iv v             i       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_108030799_   1027 TTTCAACAAATGGTTCTGGGTCAAATGAATTTTCACAAGCAAAATAATGA 1076
                                       v     v   v  i  v?i    v      v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_108030799_   1077 ATGTAAGTTTC-ACCTCACACCACACGCAAAAATTAATGCAAA-TGAATC 1124
                          vv iiiiii -           i ii          iv    -  i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_108030799_   1125 ATAGACCTAAACGTAAAAGTGAAAACTGTAAATCTTCTAGAA-AAAAGAT 1173
                          ?         i    i  iv      i    v  ii     -    v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_108030799_   1174 AGAAG-ACATTTTTGCATCCTCGGGTTAAACAA---------AGATATGA 1213
                           i? - v  i  i iiv   i      ii   ---------        
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_108030799_   1214 CACCAAAAGCACAATTCATAACAGAAAGAAAT-GATACACTGGACTTCAT 1262
                                       viv i  v     -    -    v i          
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCAT 647

  chr2_108030799_   1263 CAAAATTAAAAAGAGATAAAAAGTCCTCT---CTTTAAAAAAAA--AAGA 1307
                                     ------------ i i ---   i   ii v -- vv 
  L1M4_orf2#LINE/    648 CAAAATTAAAAA------------CTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_108030799_   1308 AAAAAA-GAAAAGACAAGGCATAGACTGAAGGAAAATATTTGCAAACCAT 1356
                          i   i-          vv  i   v  iii               i   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_108030799_   1357 ATGTCTGTTTAAAGACTTGTATCCAGAATATGCAAATAACTCTTGCAATT 1406
                           i    v v ii                  ii   v       i   i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_108030799_   1407 CAATAATAA---GACAAAGAGCAGCTTAAA-AAAAAACATGCAAAAGAGT 1452
                                  ---      ---i i ii  v-?     iiv     i  --
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAA---TAACCCAATTWAAAAATGGGCAAAGGA-- 830

  chr2_108030799_   1453 TCTG------CTCTTGACCAAAGAAGGTATAGAAATGACAGATAGACACA 1496
                          i  ------ vi  vv         i    v     i vi   ii    
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_108030799_   1497 TGAAAAGATTCTCAGCATCATTAGTCAT 1524
                                  v    i     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (119 / 75)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.74 (86 / 23)  


3534 25.39 0.67 0.11  chr2_108164925_108166724.rev      407  1308 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_108164925_    407 GGAAAAA-ATGTTGTGTTCATTGATTAGAAGAGTCAATATTGTTAAGATG 455
                              i -  viii       v    i     v i               
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_108164925_    456 TCCACACTACCCAAAGTGATCTACAGATTCAATATAGTCCCTATCAAAAT 505
                         v v i   v      v                iii i             
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_108164925_    506 ACCAATAACATTCTTCACAGAAATAGAAAAAACAATCATAAAATTTATAT 555
                         v   iivi v  i  ii       v  v  ivii   v       i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_108164925_    556 GGAACCACAAAAGACCAGGGATAGCCAAAGCCATCCTAAAGAAACAGAAC 605
                             vii   ii    vi i         i v   i i  i  iv     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_108164925_    606 AAAGCTAGAGGAATCACATTACCTGATTTCAAATTATACTACAGAGCTAT 655
                             i i     v     i v  ii        viv       i     i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_108164925_    656 ACTCACCAAAATATCATGGTACTGGCATAAAATCAGACATATAGACCAAT 705
                          v v i   i i vii              iivi           i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_108164925_    706 GGAACAGAATATAGAACCCAGAAACAAATCCACATACTTATAATGAATTC 755
                             i     vv   ii       i   i   i i i    ii v    v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_108164925_    756 ATTTTCAACAAATGTGTCAAGAACGTACACTGGGGAAAAGACAATCTCTT 805
                               i    iv   i     v i v  v        ii i i   i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_108164925_    806 CAATAAATGGCTCAGGGAAAACTGGATATCCATATGCAGAAGAATGAAAC 855
                            i      iv v    v         ?   i     i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_108164925_    856 TAAACCCCTATCTCTCATGATGTACAATAATCAAATCAAA-TTGATTGAA 904
                          ii       i   v  iv  i     v   i  v     - v   ii? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_108164925_    905 GACTTAAATCTAAGATCTCAACCCATGAAATTACTAAAAGAAAACGTTGG 954
                            i     v     v  v  v i  i   i vi  i        i v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_108164925_    955 GGAAAATCTCCAACACATTGGTCTGGGCAAAAATTTCTTGAGTAATACCC 1004
                         ? v      i ivv  v    vi i     vii      iii  vv  v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_108164925_   1005 CACAAGTACAGGCAACCAAAGCAAAAATGGACAAATGGGATCACATTAAG 1054
                           v   i   i     v    v      i  i    v   iiv   i  i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_108164925_   1055 -TTAAAAAGCTTCTACAGAGCAAAGGAAACAATCAACAATGTAAACAGAC 1103
                         -       -   i iiivvv       v  v     v  v  i  v    
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_108164925_   1104 AATCCACAGAATGGGAGAAAGTATTTGCAAACTAC---TTCAACAAGGGA 1150
                           i                 i          ii i--- iii i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_108164925_   1151 TTCATAACCTGAATATATAAGGAATTCAAACAACTCTATATTTAAAAAGC 1200
                         i ii  v  v          i   i  vv       v   v v    ii 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_108164925_   1201 TGATAATCTTATCAAAAAATGGGCAAAGGATTTGACTATACCTTTCTCAA 1250
                         vi    i iv  i?                     v  v  v      v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_108164925_   1251 AAGAAGACATACACATGGCAAACAGGCATATAAACACATATTCAACATCA 1300
                                i     v     v  i i   i  i  v v  ii         
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_108164925_   1301 TTGATCAT 1308
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.59 (138 / 87)
Gap_init rate = 0.01 (5 / 907), avg. gap size = 1.40 (7 / 5)  


2972 22.20 8.83 0.48  chr2_108169958_108173515     2231  3068 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_108169958_   2231 TAGTAAGTTATATGATGGTCATGTTTTAGAAGACTTTATGTGGT-AAGAT 2279
                          i v   v   viv   v     vv  i        v  i v  -     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108169958_   2280 CACAAAACTACCCTAGGTGATCTAAAGATTTAAC-----------CAAAA 2318
                         vi   v   v   v iv       v     i   -----------     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_108169958_   2319 TTCCAACAACATTT---GTAGAAAC-AAAAAGCCCATCTGCAAATTTCTA 2364
                          i   i vi v   --- i     i-i v    iv   ivv     iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_108169958_   2365 GAGAATGGCAAAGATACCCA-AAGAGACAAAATAATCTTGAAAAAGAA-- 2411
                         vi   vv    i i-     -  v  v     i               --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_108169958_   2412 -CTAAG--ACAAAATTTACACTTCCTAATTTTAAAATGTACCATAAAGCA 2458
                         - v   --iv ii i i        i     i    iv   i i     v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_108169958_   2459 ATGGCAATTG---C--TTTGTTACTGGTA---GGA-AGATATATAGACAA 2499
                          ii i   ii--- -- v  v      i ---   -   i       iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_108169958_   2500 AGGAAATATAATTGAGAGTCCAAAAACAAACCTATAACCCATCTATGACC 2549
                          v i    v             i   i     i   ---   i    ii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA---CATTTATGGTC 346

  chr2_108169958_   2550 AAATGATTTTAGACAAGGATGCCGAGACCATTCAATGGGAACATCAAAGT 2599
                           v       v       i    i               i v vv v   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_108169958_   2600 CTT--CAACAAATGGTGCTGGGACAACTTGAGAGCCACATGCAATGGGAT 2647
                            --                       v  v ?          vi i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_108169958_   2648 CAATTTGTACCCTTAACTTATACTGTATATATAAATGAACTAAAAATGGA 2697
                         v  v   v    i  v  i i  ii    i v    v    v        
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_108169958_   2698 TCAATGCCCCAAATGCAAGAGCTAAAACTACAAAACTCTTAGAAGAAAGT 2747
                            ?v v  i     i              i                 ii
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_108169958_   2748 ATA--AATAGATCTTCAAGACCCTTGACT-GTCCATGGATTTTT---CAT 2791
                            --?i  i      iv    i v ii - v v    v  i  ---i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_108169958_   2792 GACCCCAAAGACAAGAGC--CAAAAAAAAGAA-----AAATTGAACTTTA 2834
                            v     ii  vi   --     i   i  -----      i    i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_108169958_   2835 TCAACATTAAATATTTTTGTTCATCAAAGGAAATTATCAAGAAAGTGAAA 2884
                             v      v i      v v        v i                
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_108169958_   2885 -TACACTCTGCAAAATGAGAGAAAATATTTTCAAATCATCTATTTGATAA 2933
                         -v   vi ii  i    i            v        v   i      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_108169958_   2934 GGGTTTAGTATATAGAACATATGAAGAATTCTTACAAC------------ 2971
                            vi v    vi    i    i     i         ------------
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_108169958_   2972 -AACAAA-------------AAATCAGCCATGTATTTGAATAGACATTTC 3007
                         -i     -------------    vi  v v v                 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_108169958_   3008 TCTAAAGC-GATGTGTAAATAGCTATCAGGCACTTGAAAAGATATTGAAC 3056
                           i    v-   i ii    i  i vi i    v         ii v   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_108169958_   3057 ATAATTAATCAT 3068
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (101 / 82)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.39 (78 / 23)  


 584 28.11 1.38 3.69  chr2_108215575_108218635     1340  1556 (1505)    L1M4_orf2#LINE/L1        1   212 (696)  

  chr2_108215575_   1340 TGGAAAAACATTCCATGCCCAGGAATAGTAAGAATCAATATTGTTAA-AT 1388
                               i i  i     ii  v i  v v    v i           -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108215575_   1389 GGCCATACTGACCAAA-CAATTTATAGATTGAATGCTATTCTTCTTAAAC 1437
                            v     vv     -ii  i  i     v  i  v  i i v i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_108215575_   1438 TATCAACAGCATTCTTTACAGAACTAGAAAAAACTATTTTAAAATTCATA 1487
                          vi  i v  v  i   i     v v  v  iviv  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_108215575_   1488 TGCAACCAAAAAAAAAAAAAAAGCCCA-AATAGCCAGGACAATCCTAAGC 1536
                           --------i   viv  iiii    -        ii      i i iv
  L1M4_orf2#LINE/    151 TG--------GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_108215575_   1537 AAAAATAACAAAACTAGAGG 1556
                           i  v      ii i    
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGG 212

Transitions / transversions = 1.65 (38 / 23)
Gap_init rate = 0.02 (4 / 212), avg. gap size = 2.75 (11 / 4)  

2011 25.95 2.57 3.78  chr2_108215575_108218635     1821  2560 (501)    L1M4_orf2#LINE/L1      158   888 (20)  

  chr2_108215575_   1821 GCAATGGAGTGAGACTCCGCCAAAAAAA-----AAAAAAAAAAA-AAAGC 1864
                             v   viv   v v-       v  -----     i  i  -    i
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATA-GCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_108215575_   1865 TGGAGGCATCATGCTACCAGACTTCAAACTGTACTGCAGGGCTACAGTAA 1914
                               vv   ii  v  vi i      viv    i  ii          
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_108215575_   1915 CAAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCAATGGAAC 1964
                         iv  i    ii         i i  ii i     i     i        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_108215575_   1965 AGAATAGAGAACTCATAAATAAGACTGATA--TCTACAACTATTTGATCT 2012
                              v    iii  v      -  iv   -- i  iiiii v     i 
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCAATTGATTT 355

  chr2_108215575_   2013 TCTACAAACCTGACACATACAAGCAATGGGGAAAGGACTCTCTATTCAAT 2062
                           v    ivv  v  vivv  vv            i ivv   v     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_108215575_   2063 AAATGGTGCTAGGGTAACTGGTTAGCCACATGCAGAAGATTGAAACTATA 2112
                                   i  ii      v  ?         i    v    ii iv 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_108215575_   2113 CCCTTTCCTTTCACCATATACAAAAATTAACTCAAGGTGAATTAAACACT 2162
                            i v   iv                        ii  i  i ? v  i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_108215575_   2163 TAAAATGTAAAACCAAAGTTAAAA--AAAAAACTCT-GGAAGACAACCTA 2209
                             -     i ----- i     -- v        -i     v   v  
  L1M4_orf2#LINE/    506 TAAA-TGTAAGA-----GCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_108215575_   2210 AGCA-ATACCATTCTGGACACAGGAACTGGCAAAGATTTCGT-GATGAAG 2257
                         i ?i- v i -   vv   viv  iviv     v i    v -   - v 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr2_108215575_   2258 ACATGAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATAGGATCTAAT 2307
                            iv       vvv          v      v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_108215575_   2308 TACACTACAGTGCTTCTGCATAGCAAAATAAACTATCAACAGAGTGAACA 2357
                         i v v vv ivi   i  iiivv    iv v        v i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_108215575_   2358 GACAACCTACTGAGTAGTGGGGAATTTTTTTTTTTTTTTTTTTTTTTGCA 2407
                                i  v  i i vi ii   v   ------------------   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTT------------------GCA 729

  chr2_108215575_   2408 AACCATGCATCTGACAAAGGCCTAATACCCAGCATCCGTAAAGAACTTAG 2457
                           i   ii      i  i  v  vi  i    v  vii         ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_108215575_   2458 ACAAGTTTACAAGAAAAAAA-AAA-AACC--ATTAAAAAGTGGGCAAAGG 2503
                             v iv i  v     i -   -    --   ?    i          
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_108215575_   2504 GCATGAAGAGACACTT-TCCAAAGAAGACATACATGCAGCCAACAAGCAT 2552
                         iiv    v     i  -           i     viii     i     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_108215575_   2553 AT-AAAAGA 2560
                           -      
  L1M4_orf2#LINE/    880 ATGAAAAGA 888

Transitions / transversions = 1.29 (106 / 82)
Gap_init rate = 0.03 (19 / 731), avg. gap size = 2.47 (47 / 19)  


1122 29.79 10.47 2.13  chr2_108266715_108268309      501  1111 (484)    L1M4_orf2#LINE/L1      247   908 (0)  

  chr2_108266715_    501 GTTATAGTAATTAAGGTTGTGTGCTGTGGGCAGTAGCAGAGACAAATAAA 550
                          i  i      i   iiv     v iiv    vv  v v     v   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_108266715_    551 CCAAAGGAACTAAACAGAAAATCTAGAAACACATCCCCACACTTTATTAT 600
                         i   v    ivi  iv  i i  i     i v --    i  v  --   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACATT--TAT 342

  chr2_108266715_    601 GGTGGAGGTAAATTGT-------AGTGCAAAGA-----------GAAAAG 632
                            vi -- vi   v -------i    v    ----------- i    
  L1M4_orf2#LINE/    343 GGTCAA--TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_108266715_    633 AAACGTCTCTTCAAATAATAGTTCTGGGTCAATTACACCTTCACATG--- 679
                           vv    i     vv   i  v     v   i iv iv?i      ---
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_108266715_    680 AAAAATGTCAACATTGATTCCTACTTCACAGTTGAT-TAAAAAGTAGACT 728
                           i    --  vv v  ii     i     vivv  -i     v  -   
  L1M4_orf2#LINE/    441 AAGAATG--AAGTTGGACCCCTACCTCACACCATATACAAAAATTA-ACT 487

  chr2_108266715_    729 CCAGATAGACTGGAGATCTGAGTATGAATAG-TAGAACAATTAAACTACC 777
                          v i  i  iii?   i  i i i -  v  -  i   v  v     vii
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTT 536

  chr2_108266715_    778 AGAAGAAAACATAAGAGAACATCCTTGTGACCTTGGAATGAGCGAAGATT 827
                                      i ? v v   i i          iv ii  i v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_108266715_    828 TCTCAAGCACAACAA-AAGAGCTGCAGTTACTAAGAAAAACATTGATAGA 876
                            i iii ii   v-  i   vvv  iv  v  ii    v  v    i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_108266715_    877 CTGGAC------AATAATCGA-----TTTGTCTCTCAAAAGGTACAATTA 915
                         i     ------  -   ii -----     vii     i ii  v  i 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAA-AATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_108266715_    916 AAAGAGTGAAATGTCAGGTCTATGCATTGGGAGAAGATATTTG-AAATAA 964
                          i i       v v  i-i i iiv v        i       -    v 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_108266715_    965 TCACAATTCACAATGGACAAACACCCAGAATATGTAAGTAACTTCTACAA 1014
                          - i vi v i  v    vvii i         i   iv    ii     
  L1M4_orf2#LINE/    735 T-ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_108266715_   1015 GTCAAAAAGAAGAAAACA----------TT---------GTAGAAAACT- 1044
                         v    v  v  i  i   ----------  --------- i i ii i -
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_108266715_   1045 --------GTTTCACAAAAGAAAATATCCAAATGGCCACTCAACATATAA 1086
                         --------i    v v      i    v          v v i  i  i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_108266715_   1087 AAAGATGCTTGAGGCCGAGAGCAGT 1111
                                  ii vii i????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (108 / 71)
Gap_init rate = 0.03 (21 / 662), avg. gap size = 3.67 (77 / 21)  


3125 27.34 0.66 0.55  chr2_108271268_108273674     1009  1915 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_108271268_   1009 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCACTATCATGAAAAT 1058
                              ii i  i     i      i v      v i v   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108271268_   1059 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCAACCCCATCAAGC 1108
                            v   i v     iv i  i  i        i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_108271268_   1109 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 1156
                          v   iivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_108271268_   1157 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1206
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_108271268_   1207 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1256
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_108271268_   1257 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATA 1306
                                 i   i    ii         i iv ii i   v        v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_108271268_   1307 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTAAAACT 1354
                                i    i--    i  --        vv iii i  i  viiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_108271268_   1355 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGAGAAAGGATTCC 1404
                          vi    i  i     ivv  v   i v  vvv     i     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_108271268_   1405 CTATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1454
                           v  i  i     i        v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_108271268_   1455 GAAACTGGATCCCTTCCTCACACCTTATACAAAAATTAATTCAAGATGGA 1504
                            ii    i    v         v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_108271268_   1505 TTAAAGACTTACATGTTAGACCTAAA-CCATAAAAACCCTAGAAGAAAAC 1553
                          i ?    i  v    v   v     - i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_108271268_   1554 CTAGGCA-ATACCATTCAGGACATAGGTATGGGCAAGGACTTCATGTCTA 1602
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_108271268_   1603 AAACACCAAAAGTAATGGCAACAAAAGCCAACATTGACAAATGGGATCTA 1652
                         vi          i vvi          vv  v  v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_108271268_   1653 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGTGAA 1702
                           i   v i  i i   i  ii vv    i  v    i  vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_108271268_   1703 CAGGCAATCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 1752
                         v  i   i i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_108271268_   1753 AAGGGCTAATAACCAGAATCTACAACGAACTCAAACAAATTTACAAGAAA 1802
                          i  i  vi  v       v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_108271268_   1803 AAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACACTT 1852
                           i     i     v  i? v  i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_108271268_   1853 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1902
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_108271268_   1903 CATCACTGGCAAT 1915
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2831 26.36 3.62 1.13  chr2_108278366_108288831.rev     2837  3720 (6746)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_108278366_   2837 GAAAGATTTTCTGTGTTAATGTATTGAAAGA----ATATTTTTAAAATAT 2882
                                v i ii    v   v    i    ----     v    i  iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_108278366_   2883 CTGTACTACCCAAAGCCATTCATAGACTCTATGCAATCTCAATCAAAGTC 2932
                          vi    v      viv  ii i   i  v i      i v      i  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_108278366_   2933 TCAAGGTCATTCTTCACAGAAATAGA-AAGAGAAGTTATAAAATTCACAT 2981
                         i  ivvv v  i  ii       v  -   vvi - iv         i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATAT 151

  chr2_108278366_   2982 GAAACCACAAAAGGCC----AC-GCCAAAGCCATCTTGAGCAAAAAGAAC 3026
                          i  vii   ii i  ---- i-      i v       iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_108278366_   3027 AAAGCTAGAGGCATCACACCACCAGATTCCAAAACACTTTACAAAGCTAT 3076
                             i i    vv      iv  vi   i      vivi          i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_108278366_   3077 AGTCGTCAAAACAGCATGGTGCTGGCATAAA-ACAGATACATCATCCAAT 3125
                            vi    i    ii    i         i- i   i i  vivi    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_108278366_   3126 GAACTAGGATAGAGAGTTCAGAAATAAACACCCACAATTACAGTCTATTA 3175
                          i v   i  v      i           v vi   v   ii   v   i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_108278366_   3176 ATTTTTGAAAAAAGTGCCAGTAACACACAATGGGAAAAGAACAGTCTCTT 3225
                              i  v  ii      iv v  iv       i      i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_108278366_   3226 CAATAAATGGTGTTGGGAAAATTGGATATCCACATGCAGAAGAATAAAAG 3275
                            i        i     v  i      ?         i      i  iv
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_108278366_   3276 TAAACGATTTTCTTACCCCTTATACAGGAATCAACTCAAAATGGGCTAAA 3325
                          ii  vvi vi  i  v  v      ii   i            iii ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_108278366_   3326 GACTTAAAATATATGAGCTGAAACTGTAAAACTACTAGAGGAGAACATAA 3375
                            i    - i  v     i     i       vi    i  ------  
  L1M4_orf2#LINE/    502 GACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGA------AA 544

  chr2_108278366_   3376 ACATAGTGGTAAAGCTCCATGGC-----ATAAGTC--TGG------AGCT 3412
                               v?     v  i i  i -----i v  v --   ------  v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_108278366_   3413 ATG----TGAAATCACT-GTGATGGAC--AAAAACAGACAAATGTCACTG 3455
                            ----ii   v   v- ii iii v--     i   i    vvv   v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_108278366_   3456 CATTGAT-CTGAAAGCTTTCTAAACATCAAAGGAAACAATTAACAGAATG 3504
                            ii v-i i   i    - ivi v        v  v  i  v i i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_108278366_   3505 AAAAGACAACCCACAACCTGGGAGAAAACATTTGCAAATCATAGATTGGA 3554
                                        ivv          i              v  iv  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_108278366_   3555 TTAGAGGCTAATATTTAAAATACACAAGGAACTCATACAACTGAATAACA 3604
                          v  i i  vi   ii i    i i  i      v       v     i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_108278366_   3605 AAAAAAAGAAATAACCCTAATTAAAAATGGACAAAGGTTCTAAATAGTAA 3654
                             i v-         v v ?        i      v i i     vv 
  L1M4_orf2#LINE/    794 AAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_108278366_   3655 TTTCTCAAAAGAATACATAGAAATGGACTACAGATATAGGAAAAAGTGCT 3704
                               v      v i   v      v v i iii i v     ii    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_108278366_   3705 GAACCTCTCCAATCAT 3720
                         v   v  v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 2.47 (42 / 17)  

3012 26.83 1.66 1.00  chr2_108278366_108288831.rev     9073  9974 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_108278366_   9073 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 9122
                               i i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108278366_   9123 GGCCATACTTCCCAAGGTTAGTTTATAGATTCAATGCCATCCC-ATCAAG 9171
                            v     i     i-  ii i  i        i  v     -     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_108278366_   9172 CTACCAATAACTTTGTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 9219
                         v v   iivi i  v  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_108278366_   9220 ATATGGCGCCAAA---AAAGAGCCCACA-TCGCCAAGTCAATCCTAAGCC 9265
                               ----   ---  i ii    v - v     iv     i i ivv
  L1M4_orf2#LINE/    148 ATATGG----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_108278366_   9266 AAAAGAACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTAC 9315
                          i          i      vv   vi  v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_108278366_   9316 AAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAT 9365
                           i          i   i    ii         i iv ii i   v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_108278366_   9366 AGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCCA 9413
                            i        i    i--    i  --        vv iii i  ii 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chr2_108278366_   9414 CAACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGAGAAAGG 9463
                         iiiii vi    i  i     ivv  v   i v  vvv     i     i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_108278366_   9464 ATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAAATGTAGA 9513
                           vvi  v  i  i              v      v  ?   v   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_108278366_   9514 AAGCTGAAACTGCATCCCTTCCTTACACCTTATACAAAAATTAATTCAAG 9563
                          iiv    ii  v i    v   i     v              i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_108278366_   9564 ATGGATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAG 9613
                               i ?    i  v    v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_108278366_   9614 AAAACCTAGGGATTACCATTCAGGACAAAGGCATGGGAAAGGACTTCATG 9663
                              v    ?i v viv   iv   vvv  vv i  v  v ii   v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_108278366_   9664 TCTAAAACACCAGAAGCACTGGCAACAAAAGCCAACATTGACAAATCGGA 9713
                         vv  vi      i      vi          vv  v  v  i    i   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_108278366_   9714 TCTAATTAAACTAAAGAGCTCCTG-----CAAAAGAAACTACCATCAGAG 9758
                         ii v  i   v v  i i  ii  -----    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_108278366_   9759 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCT 9808
                             v  i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_108278366_   9809 GACAAAGGGCTAATATCCAGAATTGACAATGAACTCAAACAAATTTACAA 9858
                           i  i  i  vi          vv i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_108278366_   9859 GAAAAAAACAAACAACCCA-CCAAAAAGTGGGAGAAAGACCTGAACAGAC 9907
                         v     i     i      -ii?    i    vi  i  ii    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_108278366_   9908 ACTTCTTAAAAAAAGACATTTATACAGCCAAAAAACACATGAAAAAATGC 9957
                          i    iv   i    i  vi v ii     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_108278366_   9958 TCATCATCACTGGCAAT 9974
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.00 (24 / 12)  


1782 28.49 0.59 0.59  chr2_108503627_108510540     5205  5713 (1201)    L1M4_orf2#LINE/L1        1   509 (399)  

  chr2_108503627_   5205 TGAGAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5254
                           ii  i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108503627_   5255 CGCCATACTGCCCAAAGTAATTTATGGATTCAATGCTATCCCCGTCAAGC 5304
                         v  v     v      v i  i  ii       i  v     ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_108503627_   5305 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 5352
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_108503627_   5353 TATGGAACCAAAAGAGAGCCCACATAGCTAAGACAATCCTAAGCAAAAAG 5402
                                viiv   i  v  viv     i  i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_108503627_   5403 AGCAAAGCTAGAGGCATCAAGCTACCTGACCTCAAACTATACTACAAGGC 5452
                          i     i i    vv   vi  v  ii ii     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_108503627_   5453 TACAGTAACCAAAACAGCATGGTACTTGTGCCAAATCAGATATATAGACC 5502
                                 i   i    ii       v iiiv iivi   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_108503627_   5503 AATGCAACAGAACAAAGGCCTCAGAAATGACACCACACATCTACAA-CAA 5551
                             v  i    ivi  ivii       i vv   i    i  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_108503627_   5552 TCTGAACTTTGACAAACCTGACACAAACAAACAATGGGAAAAGGATTCCC 5601
                          -   vi  i     ivv  v  vi v  vv       i    i  vvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_108503627_   5602 TATTTAATAAATGGTGTTGAGAAAACTGGCTAGCCACATGCAGAAAACTG 5651
                          v  i  i        i  i  v      v  ?         i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_108503627_   5652 AAACTGGACCCCTTCCTTACACCTTATAAAAAAATCAACTCAAGATGGAT 5701
                           ii         v   i     v    v      i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_108503627_   5702 TAAAGACTTAAA 5713
                         i ?    i    
  L1M4_orf2#LINE/    498 CAWAGACCTAAA 509

Transitions / transversions = 1.80 (92 / 51)
Gap_init rate = 0.01 (5 / 509), avg. gap size = 1.20 (6 / 5)  

1206 27.04 0.47 1.86  chr2_108503627_108510540     5995  6423 (491)    L1M4_orf2#LINE/L1      486   908 (0)  

  chr2_108503627_   5995 CTCAAAAAAAA-AAAAGACTTTAACATAAGACCTAAAACCATAAAAACCC 6043
                                vii -v ?    i v  ii     v       i      vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_108503627_   6044 TAGAAGGAAACCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAAGA 6092
                               i    v    ?i- v   -   iv   v v  vv i     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_108503627_   6093 CTTCATGACTAAAACACCAAAAGTGATGGCAACAAAAGCCAAAACTGAAA 6142
                         i   v iiv  vi          iivvi          vv    iv  v 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_108503627_   6143 AATGGGATCTAAGTAAACTAAAGAGCATCTGCACACCAAAAGAAACTATC 6192
                            v   ii v vi   v v  i i v i  ii vi    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_108503627_   6193 ATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAGTCTA 6242
                          vv i      v  i     i                vv      ivii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_108503627_   6243 TCCATCTGACAAATGGCTAATATCCAGAATCTACAAAGAACTTAAACAAA 6292
                          vi      i  iv i  vi          v  i        ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_108503627_   6293 TTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGTAGTCT 6342
                          iv i  v     i     i     v  i?    i         v ----
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA---- 830

  chr2_108503627_   6343 GTTTGAACAGACACTTCCCCCAAAAAAAGACATTTATGCAGCCAACAAGC 6392
                         -      i     i   i  --   i    i  vi viii     i    
  L1M4_orf2#LINE/    831 -TTTGAATAGACATTTCTCC--AAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_108503627_   6393 ATATGAAAAAATGCTCATCATCGCTGGTCAT 6423
                          i       i       v    i????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (63 / 50)
Gap_init rate = 0.01 (5 / 423), avg. gap size = 2.00 (10 / 5)  


1624 29.55 3.73 1.87  chr2_108530922_108535853.rev     3259  3901 (1031)    L1M4_orf2#LINE/L1        3   657 (251)  

  chr2_108530922_   3259 GGAAGACATTTCATGCTCACAAA------------ATATTGTTGAAATGA 3296
                          i    i  ii    i   iii ------------        i i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_108530922_   3297 TCATACTATCCAAACTAATGTACAG-TTCAATGAAATCCCTATTAAAATA 3345
                         iv     vi     i i  v     -     i v         i     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_108530922_   3346 CCAACACCATTTTTCAAAGAAACAGAAAAAAGAATCCTAATGTTTTCATG 3395
                            i vv v     iiv     iv  v  ivvi       vi  ivi   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_108530922_   3396 AAACCAAAAAAAAAGCCAGAAAAGCTAAAGAAATTCTGAGTTAAAA-AAT 3444
                         i  viiv  iii v-      v   i   iv   ii   ivv i  -  i
  L1M4_orf2#LINE/    153 GAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_108530922_   3445 AAAGC-GGCGGCATCATTCTACTTGACTTCAAAACATATTACGAGGCTAT 3493
                             i-  v  vv   iv  v iii i        v  i   i i    i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_108530922_   3494 AGAAACCAAAGCAACAAAGTATTGGTATATAAACAAGCATACAGACCAAT 3543
                           v  i   ii  iiivi   i   i   vii i ii    i   i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_108530922_   3544 GGAACAAAATAGAGAACCCAAAAATAAATCCTCATATTTATACACAACCG 3593
                             i i   v    ii   i       i  vi i      ivv   ii 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_108530922_   3594 ATCTTCGACAATGCCATTAAGAACACACACTGGGCAAACGACACCCTCTT 3643
                           i        v viiii    v  iv  v    v   vi i vi  i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_108530922_   3644 -AACAAACGGTGCCAGGAAATCCAGGTAACTATATGCAGAAGAATGAAAG 3692
                         -      i     ii   v v ii i  ? i i     i         iv
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_108530922_   3693 TGAGTCCCTATCTCTCACCATTTAGTTGATACAAATATCAAC-AAAAATA 3741
                           iii     i   v      -------       v  i   -v     i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCAT-------ATACAAAAATTAACTCAAAATG 494

  chr2_108530922_   3742 GATTAAAGACTTATATTATATAAGACCCAAAAGTGTAAAACTAAAAGAAG 3791
                            i ?    i  - --  i     v i    v i       vvv     
  L1M4_orf2#LINE/    495 GATCAWAGACCTA-A--ATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_108530922_   3792 AAAACACAGG-GCAAATGCATCAAGACATTGGTCTAGGCAAAGATTTTAT 3840
                               i   - i    - v  iv   v    vi       v i   iv 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_108530922_   3841 GGCTAAGATCTCAAAAGCCCAGGCAACAAAA------ACAGACAAATAGG 3884
                         i v  v  ivi       v  i         ------ i   i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_108530922_   3885 ACTACATTAAACTGAAA 3901
                            v   i   v v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAA 657

Transitions / transversions = 1.76 (120 / 68)
Gap_init rate = 0.02 (13 / 655), avg. gap size = 2.77 (36 / 13)  

 840 23.48 3.24 0.40  chr2_108530922_108535853.rev     4194  4440 (492)    L1M4_orf2#LINE/L1      655   908 (0)  

  chr2_108530922_   4194 AAAAGCTTCTGCATAGCAAAAGAAACAATCAACAGCATGAAGAAGACAAC 4243
                             i   i  iiivv    i  v  v     v ivi    -        
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA-AAGACAAC 703

  chr2_108530922_   4244 CTCTTAAATGGGACAAAATATTTGCAATCTACTCATCCAATATGGGACTA 4293
                          ivivi       v             vii ivi   ii   v      v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_108530922_   4294 ATACCCAGAGTATACAAGGAACTCAAACAACACAACATTAAAAA-----A 4338
                         i  i     i    i  i      vv     v   i v      ----- 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_108530922_   4339 TAACCCCATTAAAAAATAGGCAAGGGACATGAATAGACATTTCTT---AA 4385
                               v   ?      i     i   iv               i--- i
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_108530922_   4386 AAGACAAAGAAATGGCCAAGAAGTATATGATAAAATACTCAATATCACTA 4435
                             i v v          v   i i    v  i  i     i    ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_108530922_   4436 ATCAT 4440
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.48 (34 / 23)
Gap_init rate = 0.01 (3 / 254), avg. gap size = 3.00 (9 / 3)  


 482 25.19 5.19 0.74  chr2_108674258_108679647.rev     2723  2857 (2533)    L1M4_orf2#LINE/L1        1   141 (767)  

  chr2_108674258_   2723 TGGAAAGACATTCCATG------GGTTGAAAGAATCAATATTGTTAATAT 2766
                                 i  i     ------ i   i    v i           v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108674258_   2767 GTCCATACTACTCAAAGCAATTTATAGATTCAATAAAATCCTTATCAAAA 2816
                          v v     v i    vii  i  i        iiv     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_108674258_   2817 TACCAATGACATTCTTCACAGAAATAGAATAAAC-AATTCTA 2857
                          v   iivi v  i  ii       v  -i  i -i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTA 141

Transitions / transversions = 2.09 (23 / 11)
Gap_init rate = 0.02 (3 / 141), avg. gap size = 2.67 (8 / 3)  

2028 25.28 0.74 0.74  chr2_108674258_108679647.rev     3783  4320 (1070)    L1M4_orf2#LINE/L1      128   665 (243)  

  chr2_108674258_   3783 ACGAAC-AATTCTAAAATTTATGTGGATTCACAAAACAGCT-GAATAGCC 3830
                           i i -i  i        i  i    vvii   iiv v i-        
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_108674258_   3831 AAAGCTATCTTAAGCAAAAAGAACAAAACTGGGGGAATCACATTACTGGA 3880
                            i v     i iv  i         ii   i   v     i v ivi 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_108674258_   3881 TTTCCAATTATACTGGAGAGCTATAGTAACCAAAACAGCATGGTATTGGC 3930
                             v  viv    iv i     i     i   i    ii     i    
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_108674258_   3931 ATAAAAACACACATATAGACCAATGGAACGGAATAGAGAACCCAGAAACA 3980
                             ii i v         i        ii    v    ii       i 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_108674258_   3981 AAATCCACACACCTACAGTGAAGTCATTTTCCATAAAGGTGCCAAGAACG 4030
                           -i   i   ii  ii  v  v v      v i  i          v i
  L1M4_orf2#LINE/    328 AA-CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_108674258_   4031 TACACTGAGGAAAAGACAGTCTCTTCAACAAATGGTGCTGGGAAAACTGA 4080
                          v  v  i     ii i     i                    v     i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_108674258_   4081 ATATCCATAATGCAGAAGAATGAAACTAGACCCCTACCTCTCACCATAAA 4130
                            ?   i -    i         ii i            v       v 
  L1M4_orf2#LINE/    427 ATAKCCACA-TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_108674258_   4131 CAAAAATCAAATCAAAATGAATTAAAGACTTAAATCTAAGATCTTAAACT 4180
                                i  v        i  i ?    i     v     v  v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_108674258_   4181 ATGAAACTAGTATAAGGAAATGTCTG-GCAAACTCTCAAAGATATTGGTC 4229
                           i     vv  v   i   ii vv - i   -   iviv  iv    vi
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGT 574

  chr2_108674258_   4230 TGGGCAAAAATTTATTGAATAATACCCCACAAGCACAGGCAACCAAAGCA 4279
                          i     vii   v  ii   vv  v   v       i     v    v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_108674258_   4280 AAAATGCACAAATGGGATCACATTAAG-TTAAAAAGCTTCTG 4320
                              iv i    v   iiv   i  i-       -   i  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTG 665

Transitions / transversions = 1.73 (85 / 49)
Gap_init rate = 0.01 (8 / 538), avg. gap size = 1.00 (8 / 8)  

 930 21.79 0.39 2.72  chr2_108674258_108679647.rev     4648  4904 (486)    L1M4_orf2#LINE/L1      658   908 (0)  

  chr2_108674258_   4648 AGCTTCTGTACAGCAAAGGAAAACAGTCAACAAAGAGAAAAGACAACC-A 4696
                          i   i   i vv      - v  vi    v    v            - 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGG-ACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_108674258_   4697 CAGAATGGGAGAAGATATCTGCAAACTAACCATCTGACAAGGGGTTAATA 4746
                                      i    i      ii vvi      i     ii vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_108674258_   4747 ACCAGAATATATAAGGGGCTTAAACAACTCTATAGTAAAAAAATCAAATA 4796
                         v             i ii  ivv       v   i      i -      
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATA 805

  chr2_108674258_   4797 TAATAATCTGATCAGAAAATGGGCAAAATATATGAAAAGATATTTCTCAA 4846
                         ----- i ii  i?i            iv  v    v   i       v 
  L1M4_orf2#LINE/    806 -----ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_108674258_   4847 AAGAAAACGTACAAATGGCAAACAGGCCTATGAAAAGGTACTCAATACCA 4896
                              i ii          v  i i  vi        i i     i i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_108674258_   4897 CTGATCAT 4904
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.89 (36 / 19)
Gap_init rate = 0.02 (4 / 251), avg. gap size = 2.00 (8 / 4)  


2809 26.31 2.18 3.06  chr2_108717681_108724710     5623  6538 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_108717681_   5623 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATCAATTTTG------- 5665
                               i    i     i        v      v i   v   -------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108717681_   5666 GGCTATACTGCCCAAAGTAATTTATAGATTCAATGCTGTCCCCATCAAGC 5715
                            v     v      v i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_108717681_   5716 TACTATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAATTTCA 5763
                          v i vivi i  i  ii     -   -- v  i  - iii i  v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_108717681_   5764 CATGGAACCAAAAAAGAGCCTGCATAGCCAAGACATTCCTAACCAAAAAG 5813
                         i      viiv  ii  v  v v        i   v  i i vv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_108717681_   5814 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAAGTATACTACAAGTC 5863
                                i      vv    i  v  ii i      iiv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_108717681_   5864 TACTTTGTTACTACAAGGCTGTTTTGTTACTACAAAAACAGCATGGTACT 5913
                            ------------  ----------  -- iv  i    ii       
  L1M4_orf2#LINE/    249 TAC------------AG----------TA--ATCAAGACAGTGTGGTACT 274

  chr2_108717681_   5914 TATACCAAAACAGATATATAAACCAATGGAACAGAACAGA-AGCCTCAGA 5962
                         vii iv ii i   i     i i        i    iv  -  i -    
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC-CAGA 323

  chr2_108717681_   5963 AATAACGCCACACATCTACAACCATCTGATCTTTGACAAACCTGACAAAA 6012
                              vv   i    i  iiii  vi    i  i     ivv  v   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr2_108717681_   6013 ACAAGCAATGGGGAAAGGTTTCCCTATTTAATAAATGGTGTTGGGAAAAC 6062
                         v  vv            iv vvi  v  i  i        i     v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_108717681_   6063 TGGCTAGCCATATGCAGAAAGCTGAAACTAGATCCCTTCCTTACACCTTA 6112
                            v  ?   i     i  iiv    ii i  i    v   i     v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_108717681_   6113 TACAAAAATTAACTGAAGATGGATTAAAGATTTAAATGTAAGACATAAAA 6162
                                       v  i      i ?   ii           vv     
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_108717681_   6163 CCATGAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGG 6211
                          i  i   vi i           v    ?i- v i -   iv   v v  
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGG 572

  chr2_108717681_   6212 CATGGGCAAGGACTTCATGTCTAAAACACCAACAGCAATGGCAGCAAAAG 6261
                         vv i     v ii   v ivv  vi       v    vvi   i      
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_108717681_   6262 CCAAAACTGACAAACAGGATCTGACTAAACTAAAGAGCTTCTGCATAGCA 6311
                         vv    iv  i   iv   ii v ii   v v  i i   i  iiivv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_108717681_   6312 GAAGAAACAATCATCAGAGTGAACAGACAACCTACAGAATGGGAGAAAAT 6361
                         i i  v  v    vv i      v        i                 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_108717681_   6362 TTTTGCAATCTACTCATCTGACAAAGGGCTAATATCCAGAATCTATAAAG 6411
                         v       vii ivi      i  i  i  vi          v       
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_108717681_   6412 AACTAAAACAAATTTACAAGAAAAA-------AACCCCATCAAAAAGTGG 6454
                             vvv    v iv i  v     -------     v  i?    i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_108717681_   6455 GCAAAGGATATGAACAGACACTTCTCAAAAGAAGATATTTATGCAGCCAA 6504
                                  v    i     i     v           vi viii     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_108717681_   6505 CAG--ACATGAAAAACAGCTCATCATCACTGATCAT 6538
                         i i--         ivv     v     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (137 / 100)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.69 (48 / 13)  


2694 25.77 7.33 0.83  chr2_108883085_108886572.rev     2151  2996 (492)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_108883085_   2151 ACATTTCATGTTCATGGACTGGAACAATTAATACTGTCAAAATAAC---- 2196
                          i  ii            i     v v      i   i  i  ii ----
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_108883085_   2197 -----CAAAGTCATCTACAGATTCAACATAATGTTTATTAAAATACCAAC 2241
                         -----    v v               ii   vii   i     v   i 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_108883085_   2242 AACATCCTTCACAGAAATAGAAAAA--AATTCTAAACTGTGTATGAAATC 2289
                         vi v ii  ii       v  v  i--i  i     v vii    i  vi
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_108883085_   2290 ATGAAAGACCCCAAATAAGCGAAAGCGATCCTGTGCGAAAACAACAAAAC 2339
                         iii ii     vi    -  v   i i   i  vivi i  v      ii
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATA-GCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_108883085_   2340 TGGAGGCATTACACTACCTAAACTCAAAATATACTACAAAACTGTAGTAA 2389
                               vv i     v  i  vi      iv         i  ii     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_108883085_   2390 CCAGAACAGCATAGTATTGGCATAAAAACAGACACATAGACTAATGGAAC 2439
                         i  ii    ii i   i        ii i     i     ii       i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_108883085_   2440 AGCATAGAGAACTCAGAAATAAATCCACACATTTACAGCCAACTGATTTT 2489
                           v  v    iii          i   i       ii i   i       
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_108883085_   2490 CTACAAAGGTGCCAACAACATT-AATAAGGGAGATGACAGTCTCCTCAAC 2538
                          v    i        v v    -   i-    i vi i     ii     
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTTCAAC 405

  chr2_108883085_   2539 AAATCATGCAGG---AAATGGATATCCATATGCCTAAGAATAAAACTAGA 2585
                             vi   v  ---  v      ?   i    vv      i  ii i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_108883085_   2586 CCCCCATCTCCCATCACAGACAAAAATCAACCCAAAATGGATTAAAGACT 2635
                             i i   v  i  i v        i   i          i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_108883085_   2636 TTGAAATATAAGACCCAAAACTATGCAACTACTAGAGGAAAAAATGGG-- 2683
                          --    i     v i        iv    vi    i     v  i  --
  L1M4_orf2#LINE/    506 T--AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_108883085_   2684 -AAATAGTTCACGACAATCGCCTGGGCAAAGATACTATGGATAAGACCTC 2732
                         -    v-   ii   vv v vi i     v i viiv i    v   vi 
  L1M4_orf2#LINE/    554 TAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_108883085_   2733 AAAAGCACAAGCAACAAAAGCAAAAACAGACAAATGAGATT--------- 2773
                                             v     i   i    vi  i ---------
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_108883085_   2774 ----------------------GGAAACAATAAAAAGAATAATGATACAA 2801
                         ----------------------   v  v  v  i i i i vi v    
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_108883085_   2802 CCTGCAGAATAGGAGAAAATATATGCAAACTATTCATCCAACTAGGG--- 2848
                           ii      i           v      ii  vi   ii iv    ---
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_108883085_   2849 TGAAAATCCAGACAATACAAGGAACTC---------AACAGCAAAAAAAT 2889
                           v --      vv   i  i      ---------  i ii     i i
  L1M4_orf2#LINE/    753 TGTA--TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_108883085_   2890 AA-TAATCCAAATAAAAAATGGGTAAATAATCTGACTAGACATTTCTCAA 2938
                           -   i    v ?         i   vi  i   v            v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_108883085_   2939 ACAAAGGCATACAAACAGCCAACAGGTATATGAAAAAATGCTCAATATCA 2988
                          vi   ii       ii     i i i i       i        i    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_108883085_   2989 CTAATCAT 2996
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.16 (147 / 68)
Gap_init rate = 0.02 (14 / 901), avg. gap size = 4.93 (69 / 14)  


3977 18.52 3.48 1.57  chr2_108900480_108902546.rev      685  1575 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_108900480_    685 TGGAAAGACATCT--TGTTCATGGATTAGCAGAC--AATGTTGTTAAGAT 730
                                 i   i--            i v    --   i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108900480_    731 GCCAAGACTTCTCAAATTAATCCACAGATTCAATGCAGTCCTTAATCAAA 780
                          v   v   i i      i   i          i   i   i  -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAAA 99

  chr2_108900480_    781 ATCCCAGCTGGTTTCTTTGCAGAAATTGAAAGGCTGCCCCTGAAATTCAT 830
                                   vi  i              v i    vi   i        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_108900480_    831 ATGAAAATGCCATTGACCCAGAACAT-----ATA----TGGAAAAGAAGG 871
                            i      v vv         i v----- i ----  i        i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_108900480_    872 ACAAAGTTGGAAGATTCACACTTTGT--TTTCAAAATTTACTACAAAGCT 919
                                    i  i        ivi--        i             
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_108900480_    920 ACAGTAATGAATCGAGTGTGACACCGGCATAAGGATAGACAAATAGAACA 969
                                 v  vvv      ii  i                v     v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_108900480_    970 ATGGAATGGAACTGAGAATCCAGATATGGACCCTCTTATTTACACTGTAT 1019
                                i   i     i      v  ii    vivi     iiv vv  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_108900480_   1020 TTATTTTCAACA-TGGTACCGAAACAATTCAATAGGGAAGGAATAGATTT 1068
                          v      i   -v   i  i i  v       i     i      vi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_108900480_   1069 TTCAACTAATGATGCTGAAACAAATGGGTATCTACAGGTAAAA-AATGAG 1117
                               v    i     ii    v   i  ? i   v i    -     i
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_108900480_   1118 GTTACACTCCT--CCAACACTATATATGAAAACTAACTCAAAATGCATCA 1165
                            iv  i   -- iv    i     ii    i            v    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_108900480_   1166 AAGGCCTAAACATGTTAAGAGGTAAAGGTATTAAACTCTTGAAAGAAAAC 1215
                         ?  i      --   -     v    iv   v        ii        
  L1M4_orf2#LINE/    500 WAGACCTAAA--TGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_108900480_   1216 ATACAGATAAATCTTTGTGGATCTGGATTTGGCAAAGTTTTCTTAAACAT 1265
                            vi?i        i   ivii   i  v     v v       i i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_108900480_   1266 GATGCAAAACATACAAGCAA----AGAAAAAA-GCATAAATTGGACTTTA 1310
                           ii v   vii        ----        -iv             i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_108900480_   1311 TAAAAATTTAAAACCTTTATGCTTCAAAGGATACTATCCAGAAAGTCAAC 1360
                          v      v     i   i            i      v       v  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_108900480_   1361 AGACAACT-ACTGAATGG-AGAAAATATTTTCAAATCACATATTGGATAA 1408
                                i-  v      -           v       i    iv     
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_108900480_   1409 GGTACATCCATCTTGAATATTTAAAAACAAAACCTCCTACAAAAAACTCA 1458
                           v  v vi   iv      v    i ----  -  i     ----    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGA----AC-TCTTACAA----CTCA 787

  chr2_108900480_   1459 GTAATAAAAA---AGATAACTCAATT-AAAAATGCTCAATGGATTTAAGT 1504
                         i         --- i     i     -       vv   v      i i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_108900480_   1505 AGACACTTA-CCAATAAAAGATATCCAAACGGCCAACAAGCACATGAAAT 1553
                              i  v-    - i       v    i      i            v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAA-AGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_108900480_   1554 GATGTTCAACATTAGTCATCAG 1575
                             i       i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (99 / 63)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.05 (45 / 22)  


 384 31.18 9.58 4.90  chr2_108902826_108904869       53   501 (1543)    L1M4_orf2#LINE/L1      213   682 (226)  

  chr2_108902826_     53 ATTCCCA-TTCCCATATGTAAACATATATTA--AAACCACAGTGATTAGA 99
                          i  v  -      -  v v  v iv  i  --  i i     i  i ii
  L1M4_orf2#LINE/    213 ACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_108902826_    100 ACATTGTGGTAGTAGTATAGG---AG-CACACAAATTGATGGAACAGAAC 145
                            v       v i i   i ---  -  i i i  ii      i    i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_108902826_    146 -GTGACCACAAAAACAGATCCAAAC-TT----GTAAATAGATTTCACATA 189
                         - v  viv  i   i i i   v  -  ----  v   v     i-----
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT----- 356

  chr2_108902826_    190 TGATAAAGGTAGCATGTTAAATCAATGGAGGAA-AATAGGAATTATTTCA 238
                         i  i  i   iv  v viv v       i i  -     --- iv     
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG---TCTTTTCA 403

  chr2_108902826_    239 -TAAATG-TATCAAAACTACTGGTTTACCAT---TAAAAAAAAGAAGGTG 283
                         -i     - iiiiii  v     v v?   i---i    i  v    v  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_108902826_    284 GTTCTATACCATACTTC-----------TTAACACCAAAATATATTGTAG 322
                          vi iv    vi  vi -----------     -i      iv  ii?  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAAC-TCAAAATGGATCAWAG 502

  chr2_108902826_    323 A--TAAATATTTGGAG-GTTATCGTGAAACCATAGAAAACCC------AA 363
                          --     i ---i  - i  -----    i   --    i ------i 
  L1M4_orf2#LINE/    503 ACCTAAATGT---AAGAGCTA-----AAACTATA--AAACTCTTAGAAGA 542

  chr2_108902826_    364 AAATATAACATTAAATATTTATCAAATACGAGAACAAGGAA-GGTTTTTA 412
                            i   iv?v     v  ii --i ivivi ivi i v  -     i v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGT--GACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_108902826_    413 ATGT-TTACACAAATGGTAAAAATAACAAAATGAAGACTA--TAGATTTA 459
                          vi - v    v  vi i v  ii       vi  i v  --  i   vi
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_108902826_    460 ATGACGTAAAAACATAAAACTTTTATATGTCAAAGAATACTA 501
                          ivv i v    ivv         i iiv      i i    
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

Transitions / transversions = 1.69 (86 / 51)
Gap_init rate = 0.06 (26 / 470), avg. gap size = 2.50 (65 / 26)  

1726 12.84 3.62 29.78  chr2_108902826_108904869      502  1552 (492)    L1M4_orf2#LINE/L1      133   908 (0)  

  chr2_108902826_    502 CTTATCCTAAAATTGATATGGAATCTG-AAGGCACAATGAAAAGCCAAAA 550
                           v           v        -v  -    v  vvv   v        
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAA 181

  chr2_108902826_    551 CAACCATAAAAA----GAACAAAGTTAGAGAGAGCTCTCATACTTTCTGA 596
                            i v i    ----          i   -  ---    i    i ii 
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAG-GA---CTCACACTTCCCAA 227

  chr2_108902826_    597 TTTCAAAACTTAGTACAAAGCTATAGTAATCTAAAC--TGTGATACTGAC 644
                                     v          i       v i  --    i     i 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_108902826_    645 ATAAG-----ACATGTAGACCAATGGGATAGAATGGAGAGCCCA-ATATA 688
                              -----    i    i      i       v     i   - v   
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_108902826_    689 AGCCCTCACAT--ATAGTCCAATGATTTTTGACAAGCGTACGGAGACCAC 736
                          i   vi    --  i   v v       i      v  i vi      i
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_108902826_    737 TCAGTGGAGGAAGGACAGTCTTTTCAACAAATGGTGTTGAAA-AACTGGA 785
                            i   i i   i i                    i  ii -       
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_108902826_    786 TACCCTCATGCAACAAAATGAGTATGAGCCTTACCTTATACGATATGTAA 835
                           ?  v       v i     -----------------------------
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGA----------------------------- 448

  chr2_108902826_    836 AATTTAACTCGGCTGGGCGTGGTGGTTCACATTTGTAATTCCAGCACTTT 885
                         --------------------------------------------------
  L1M4_orf2#LINE/    449 -------------------------------------------------- 448

  chr2_108902826_    886 GGGAGGCTGAGGTGGACAGATCACCAGGTCAGGAGTTCGAGACCAGCCTG 935
                         ---------  v     ---------------------------------
  L1M4_orf2#LINE/    449 ---------AGTTGGAC--------------------------------- 456

  chr2_108902826_    936 GCCAACATAGTGAAACCCTATCTGTACTAAAAATACCAAAAATTAGCCAG 985
                         ---------------     i  ---------------------------
  L1M4_orf2#LINE/    457 ---------------CCCTACCT--------------------------- 464

  chr2_108902826_    986 TCATGGTGGCAGGCACCTGTAATCCCAGGTACTCGAGATGCTGAGGCAGG 1035
                         --------------------------------------------------
  L1M4_orf2#LINE/    465 -------------------------------------------------- 464

  chr2_108902826_   1036 AGAATTGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCGAGATCACGC 1085
                         ---------------------------------------------   i 
  L1M4_orf2#LINE/    465 ---------------------------------------------CACAC 469

  chr2_108902826_   1086 CATTGCACTCCAGCCCAGGTGACAGTGTGAGACTCCCTCTCAAAAAGAAA 1135
                            ------------------ i ----------------      ----
  L1M4_orf2#LINE/    470 CAT------------------ATA----------------CAAAAA---- 481

  chr2_108902826_   1136 AAAATTTAACTCAAAATGGGTCAAAGGCTTAAATGTAAGAATTAAAACTA 1185
                         -----              i   ?  i i           ii        
  L1M4_orf2#LINE/    482 -----TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_108902826_   1186 TAAAACTCTTAGAAGAAGACACAGGA--AAATCTTCATGATATTAGATTT 1233
                                          i   i   ?--        i   iv  i i  v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_108902826_   1234 GGCAGTGATTATATGGCTAAGACATCAAAAGCACAAGCAATAAAAGCAAA 1283
                             i  i  viv i v  v    i               i     v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_108902826_   1284 AATA----AACTGAACTTCATCAAAATTAAAAATGTTTGTGC-------- 1321
                             ----  i  i                   iv       --------
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_108902826_   1322 -----ATCAACAGATTGAAATGGTAATCTCCAGAATGGGAGGAAATATTA 1366
                         -----     v i v     v ii  i iv           i       v
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_108902826_   1367 GCAAATTGTGTATCTGACAAGCGATTGCTACCCACAATATATAAGGAACT 1416
                               ii i       i   v  i vv  i   v         i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_108902826_   1417 CCTTCAACTCAGCAAAAAACAAAACCAAAAAGACCCTATTTTTAAAAAAG 1466
                          i v       ii  v   -  i  --   vi    v   ?----    i
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAA-AAGAC--AAATAACCCAATTW----AAAAA 819

  chr2_108902826_   1467 CAAGCAAAGAACCTAAATAGCTATTTCTCCAAAGA---TAAAGAAATGGC 1513
                         iii      i ii i     vi             ---  v v       
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_108902826_   1514 CCCTAAGCTCATAAAAAGATGCTTAACATCACTACTCTC 1552
                          vv     v   i          i       ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (83 / 48)
Gap_init rate = 0.03 (23 / 776), avg. gap size = 15.26 (351 / 23)  


2223 24.19 14.64 1.99  chr2_108933628_108937652.rev     2728  3533 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_108933628_   2728 TGGAAAAACATTCCATGCTCAAGGATTGGAAGAATTAAGATCATTTAAAT 2777
                               i i  i     i   v           v    v  ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108933628_   2778 GGTTATATTGCCTAAAGCAATCTATGGATTCAACACAATTCCTATCAAAT 2827
                           iv   i v  i   vii     ii        i    i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_108933628_   2828 TACCAACATTATTCTTCACAGAATTAGAAAAAAAAAAAATTGA-----AA 2872
                          v   i vviv  i  ii     v v  v  i-------i   -----  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-------CTGATCCTAAA 143

  chr2_108933628_   2873 ATTCATATGGAAC--CAAGAATGAGCCCA-AACAGCCAAAACAAACTTAA 2919
                                     v--    --- ii    -  i           v   i 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAG---GGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_108933628_   2920 GTAAAAAGAACAAAGCTGGAAGCATCATGTTATCTGACTTCAAACTATAC 2969
                         iv  i          i    i vv   iii vi ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_108933628_   2970 TACAAGGCTATAGTAACCAA-ACACCATGGTACTGGTATATAAAAAGACA 3018
                              i    i     i   -   vii         i   vii v     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_108933628_   3019 CACAGACCAATGGAACAGAATAGAGAAACT-GAAATAAAACCACATACCT 3067
                         i i   i        i     v    iv i-        v   i i ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_108933628_   3068 ACAACCAACTGATTTTCAACAAAG-------------------------- 3091
                          iiii   i        i    i --------------------------
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_108933628_   3092 ------------------------------------------------AA 3093
                         ------------------------------------------------  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_108933628_   3094 AA---------------------TCACA--ATATACAAAAATTAACTCAA 3120
                           ---------------------     --                    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_108933628_   3121 GATGGAACAAAGACTTAAATGAAAGATGTCAAATTATAAAAATCCTAGAA 3170
                         i     v  ?    i      v    vv v   i       v  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_108933628_   3171 GAAAATCTAGGAAATACTCTTCTGGACATTGGCCTAGGCAAAAAATT--- 3217
                              iv    ?ivv v     vv   v    vi       viiv  ---
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_108933628_   3218 ---TATGACAAACTCATCAAAAGCAAATGCAATAAAAATAAAAATTGACA 3264
                         ---       ------i        v v    i    iv      v  i 
  L1M4_orf2#LINE/    591 AGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_108933628_   3265 ACTGGGACCTACTTAAACTAAAGAGCTTCAGCATAGCAAAAGAAACTATC 3314
                          v v    i vv i   v v  i i   iv iiivv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_108933628_   3315 AACAGAGTAAACAGACAACCTATAGAATGGGAGAAAATATCTGCAAATTC 3364
                           v i   i  v        i i                 i       iv
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_108933628_   3365 TGCATCCAACAAAGGACTAATATCCAGAATCTACAAGGAGCTCAAACAAA 3414
                          ii   ii i  i     vi          v  i  i  i   vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_108933628_   3415 TCAATGAGAAAAAG-----CAACCCCGTTAAAAAGTAGGCAAAGGACATG 3459
                              i v      -----i     vi  ?    i i         iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_108933628_   3460 AACAGATACTTCTCAAAAGAAGACATACAAGTAGCCAACAAATATATTTA 3509
                           i   i i     v        i      i i     i  ii i  vv 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_108933628_   3510 AAAATGCTCAACATCACTAATCAT 3533
                           i             ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (119 / 73)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 10.31 (134 / 13)  


2318 25.56 4.94 2.59  chr2_108960809_108965287.rev     2792  3601 (878)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr2_108960809_   2792 TGGAAAAAGGTCCCATGCTCATGGATAAGAGAAATTAGTATCATTAAAAT 2841
                               i vi       i        vi  ii v   i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108960809_   2842 AACCACGTTGCCCAAAGCAATCTACAGATTCAATGCAATCCCCATCAAAA 2891
                         ii v iii v      vii              i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_108960809_   2892 TACCAACATCACTTTTCACAGAATCAAAAAAGC-AATCCTAAAATTCATA 2940
                          v   i vv vi    ii     vivi v    -i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_108960809_   2941 TGGAAA--CA---GA---AAAAGAGCTCAAAGTCATCCTGAACGAAAAGA 2982
                               --  ---  --- i  v   -    iiv   i    vi i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGC-CAAAACAATCTTGAAAAAGAAGA 199

  chr2_108960809_   2983 CAAAAGCTGTAGGCATCACAATGACTCACTTCAAAACATATTACAAGGAT 3032
                         vv    i  v   vv     v vv iv i        v  i     i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_108960809_   3033 ATAGTAACCAAAACAGCATGGTACTGTTATAAAAACGGACACGTAGACCA 3082
                          i     i   i    ii        vi    ii ii    ii    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_108960809_   3083 ATGGAACAAAATAAAGAAACCAGAAATAAGACACATA--TTTATGGCCAA 3130
                               i i   vi   iv          -  v    --       i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCAA 348

  chr2_108960809_   3131 GTGATCTTTGACAAAG---CCAAAAAGAACTAAACACTGTGGAAAGTTCA 3177
                         v    i  i     i ---    i ---- i vv  v  v      vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGA----CCATTCAATGGGGAAAGAATA 394

  chr2_108960809_   3178 CCCTCTTCAATAAATGGTACTGAGAAAATTGGTTAACCAGATGCAGAGGA 3227
                         vi  i     i       i   i  v  i   v  ?   v     i i  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_108960809_   3228 ATGAAAATGGACCCCTATCTCTCATCATATACAAAAATAAACTAAAAATA 3277
                              iv          i   v  i             v    v     i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_108960809_   3278 GATTAGAGATTTACACATAGGACATGAAACTATAAAAAAC--AGCATAAG 3325
                            i ?   ii  v ii  i  vv i           vv --  ---   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG---AAG 541

  chr2_108960809_   3326 AAAGCCTAGGGAAAACTCTC--------------AGGGAAAGAATTTATG 3361
                            i v    ?iv  v   i--------------   v  v iv  iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_108960809_   3362 ACTGAGACCTCAAAAGCACAGGCAACAAAACAAAAA-TAGACAAATAGGA 3410
                         iv iv   vi          i         v     -    i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_108960809_   3411 TT--ATAATAAACTAAAAATACTTGACACAGAAAAGGAAATGATCAACAG 3458
                         i --  v -   i      ivi   -ii vvv      v iv     v i
  L1M4_orf2#LINE/    642 CTTCATCA-AAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAA 689

  chr2_108960809_   3459 AGTGAAGAGACAACCTAATGAATAGTAGAAAATATCTGCAAACTATTCAT 3508
                               i        i vv    i v         i      ii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_108960809_   3509 CCAACAGGGGACTAATTTTCTGAATACACAAGGAACTCAAACAGCTCCAC 3558
                          ii i i      vi v i v     i i  i      vv   i   v i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_108960809_   3559 AGT-------TAAATTTTTTTTTTAAATCCCATTAAAAAGTGGGCAAAGG 3601
                          i -------i    ----------  i  v   ?    i          
  L1M4_orf2#LINE/    790 AATAAAAAGACAAAT----------AACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.48 (121 / 82)
Gap_init rate = 0.02 (18 / 829), avg. gap size = 3.39 (61 / 18)  

 399 18.10 10.48 0.00  chr2_108960809_108965287.rev     3883  3987 (492)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr2_108960809_   3883 AAAAAAATAAATAA-----------AGTGGGCAAAGGACATGAATAGACA 3921
                              i i      ----------- i           iv          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_108960809_   3922 TTGTTCAAAAGAAGACATACAGGTAACCAACAGATACATGAAAAAATGCC 3971
                           vi  v        i     ii ii    i iii         i    i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_108960809_   3972 CAACATCAGAATGAAA 3987
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 5.33 (16 / 3)
Gap_init rate = 0.01 (1 / 116), avg. gap size = 11.00 (11 / 1)  


2240 24.54 1.42 9.33  chr2_108974686_108979699     3543  4528 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_108974686_   3543 TGAAGAGATATACCATGCCCATGGCTCAGAAGACTCGACATAATAAAGAT 3592
                           i i      v     ii     v ii       ii i  vi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_108974686_   3593 GTCAAATCTTCCCAGATTGATATACAGTTTTGTTGCAACTC--ATTAAAA 3640
                          v   vv  i    i      v     v  iivi    ii --  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_108974686_   3641 TCCCAGCAAGGCATTTTGTACATATA--GGGAAGATTATTATAAAACTTA 3688
                                --v  v    v i  v v -- iv   v v  iv     i i 
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_108974686_   3689 TATGGAAAGGCAAAGGAACTAGAATAGCTAAAAGATTTTTGAAAAAAAAA 3738
                                 v    i   v i        i    v v i        i  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_108974686_   3739 TAAAGGAAAATGGGAGCAGTC-CATTT---GATTTCAGGACTTATATGTT 3784
                         --- iv   i v    v v  -  i  ---i      ii     i-----
  L1M4_orf2#LINE/    199 ---AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC----- 240

  chr2_108974686_   3785 ATTACATAATTTATACAAGAATCAAGACCTTGTGGTATTATCAGAGGGAC 3834
                         --    v ii ---   iv         vv       i iv  v i   i
  L1M4_orf2#LINE/    241 --TACAAAGCT---ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_108974686_   3835 AGACATGTAGATAAATGCAACAGAACAGCAACCCCAGAAAATAGACCTAT 3884
                               i     v    v  i    iv vi vi       -  i   i  
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCAT 334

  chr2_108974686_   3885 ACAAATATGCCAAACTGATTTTTGACAAAGTTTGAAAAGCAATTCAATGG 3934
                            vv    viv  i       i     i v vvv  ii v         
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_108974686_   3935 AGGAAAGATAATTTTTCAAAAAAATGGTGCTGGAGCAATTGGACATCCAT 3984
                         i i  ii   i i   iv  v            ii   i    i ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_108974686_   3985 AGACAAAAAAATGAACTTTGACCCAAGTTTCATATCTTCTATAAAAATCA 4034
                          vi     i      v  v     vviii   i i v v  i      i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_108974686_   4035 ACTCAAACTTAAATGCAAAATATAAAACTATGTGAACTTAAATGTAAAAC 4084
                                -----   ---i  -i ? i--------  i         i v
  L1M4_orf2#LINE/    485 ACTCAAA-----ATG---GAT-CAWAG--------ACCTAAATGTAAGAG 517

  chr2_108974686_   4085 ATAAAAACTATGTGGACTTAGAATGTAAAACATTAAGCTATAAAACTTCT 4134
                         v     -------------------------------          ii 
  L1M4_orf2#LINE/    518 CTAAAA-------------------------------CTATAAAACTCTT 536

  chr2_108974686_   4135 AGAAAAAATTGTGGGAGCAAATCTCTGGGATCTAGGACTAGGCAAGAGAG 4184
                             i   vii i  ? i      ii v  i  v  ii       vi vv
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_108974686_   4185 ATCTTAGATTTGACAC-AAAAGCATCATCCATAAAAAGAAAACTTTATAA 4233
                         -        v      -       iv v v i    ii    ----   i
  L1M4_orf2#LINE/    587 -TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA----ATAG 631

  chr2_108974686_   4234 TTAGTTTCATAAATTTGACT-CATAAAAATTTAAAACATC-ATTCTATGA 4281
                         --------       v    -   v      v     v i-i v  vii 
  L1M4_orf2#LINE/    632 --------ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_108974686_   4282 AAGACCCTGTTAAGAGACTGAAAAGATAAGCTAAACTATAGAATGG-AGA 4330
                          i   v  i i    i v        i  - ---- i i       -   
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAA-C----CCACAGAATGGGAGA 718

  chr2_108974686_   4331 AAACATTTATAAAACCACATATCCATCATAGGACTAGTGTCTAGAATATA 4380
                            i    ii   -i  i     iivi vi     v  i  i        
  L1M4_orf2#LINE/    719 AAATATTTGCAAA-TCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_108974686_   4381 TTTTTAAAAACCCTCAAAACTCAACAGCAAAAAAATCATACGATACCATT 4430
                          v---  i   i  i v       i ii     i -  v ii iv v   
  L1M4_orf2#LINE/    768 TA---AAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATT 813

  chr2_108974686_   4431 GAAAAATGGGCAAAAGACATGAAGAAACATTCATTTTACTGAAGAGGACA 4480
                         ?             i  iv    v i     --- i - ii    i  i 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATT---TCT-CCAAAGAAGATA 859

  chr2_108974686_   4481 CACAGATGA--AAAAAACACAAGAAAACATATTTAAACAATAGGAACATG 4528
                         i   i   i--  v  i    v     v  ii i  -  vi ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (148 / 90)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 3.53 (106 / 30)  


3143 21.69 1.64 8.32  chr2_109149531_109153195     2201  3173 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_109149531_   2201 TGGAACGATATCTCATCTTAATTAATTGGAAGAATTAATATTGTGTAAAC 2250
                              v      i   v  v  vi         v          vv i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_109149531_   2251 ACTTATACTGCCCAAAGTGACCTACATGTTGAATGCAATCCCTATCAAAA 2300
                         iviv     v      v   i     vi  v  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_109149531_   2301 TTCTAAGGGCATTTTTCTCAGAAATAGGAAAAC-AATTCTGAAATTTATA 2349
                          i i ivv  v     iv       v iv  i -i  i  i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_109149531_   2350 TGGTACCACAAAAGATCCTGAATAGCTAAGGCAATCTGGAGAAAGAAGAA 2399
                            v vii   ii  i  v       i  ii      v  i         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_109149531_   2400 GAAAGTTAGAGTCATTGCACTCCCTGATTTCAAATGATACTGCAAAGCCA 2449
                         v      i   vvv ii    i  ii        vvv    i      i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_109149531_   2450 TACTAATCAAAACTCAATGGTATTGGCATAAAAACAGACACAGAAACCAA 2499
                         i v       i  vvvi     i        ii i     i v i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_109149531_   2500 TGGAACAAAAT----AGCCCCAAAATAAGCTCACGAAAATATGGCTAACT 2545
                              i i   ----  i  vi      i i  iiv vv     ii  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_109149531_   2546 AATTTTCAACAAGGACCCCAAGAATACACAATGGGGAAAGA-TAGTCT-- 2592
                         i      i      iiv      vi iv             -      --
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_109149531_   2593 -AAATAAATGGTTTTGGAAAAACTGGATATCCACATGCAAAAGAATAAAA 2641
                         -v  i       vi   i v         ?                i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_109149531_   2642 GTAGGACTTTATCTCACACCATATACAAAAGTCAGCTCAAAATGGATTAA 2691
                         v i iv ii  i                  i i i            i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_109149531_   2692 AAACTTAAATGTAAGACCTTAAACCATAAAACTCCTACACGGAAACATAG 2741
                          i  i           v  v    i         i  v v i        
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_109149531_   2742 AGAAAAATCTCCTTGAAGAAGATTCAAGGATGAATGTTTTTTGATAAAGA 2791
                         i?iv      i --------------------------------------
  L1M4_orf2#LINE/    551 GNGTAAATCTTC-------------------------------------- 562

  chr2_109149531_   2792 TTTTTATGATGATCTGCTTCCACTTAATGAATAAAGTCCACTTAATGTCT 2841
                         --------i   i  ------------  ii ----------  ------
  L1M4_orf2#LINE/    563 --------GTGACCT------------TGGGT----------TA------ 576

  chr2_109149531_   2842 TGGCAATGATTTTTTTGGATATAACACCAAATGCACAAGCAACAAATGCA 2891
                         -       i   i  -i     i        v              v v 
  L1M4_orf2#LINE/    577 -GGCAATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_109149531_   2892 AAAATAAACAAGTGGGACTAGATTAAA-CTAGAAGCTTCTGCACAGGAAA 2940
                               i i  i v     vv  i   -i  i  i   i  ii vvv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_109149531_   2941 GGAATGAATCAATGAAATGAAAAAGCAACCAACAGAATGGGAGAAAATA- 2989
                            vvvv     vi  i      ii     v                  -
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_109149531_   2990 ---CAACCCATATATCTGATAAGGGTGTTAGTATACAAAATATATTAGGT 3036
                         ---   vi                 vv  -    v  i       v i v
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTT-GTATCCAGAATATATAAAGA 773

  chr2_109149531_   3037 ACACATATAACTCTATAGCAAAA-GATGAATAACCTGATT-AAAAATGGG 3084
                           v v  i     v   ii    -  ii       ii   -         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_109149531_   3085 CAAAGGACTTGAATAGATAGTTTTCGAAAGAGGACATACATACAAATGTC 3134
                                i         i v  i  v     i  i     ----    v 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA----AATGGC 869

  chr2_109149531_   3135 CAATAGGTATATGAAAAAGTACCCAACATCACTATCATC 3173
                              i i i       ii i i        ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (129 / 79)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 6.47 (97 / 15)  


3233 27.20 0.44 0.44  chr2_109186858_109193259.rev     5003  5910 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_109186858_   5003 TGGAAGAACATTCCATGCTCATGGATAGAAAGAATCAATATCGTGAAAAT 5052
                              ii i  i     i        v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_109186858_   5053 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5102
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_109186858_   5103 TACCAATGACTTTCTTCACAGAA-TCGGAAAAAACT-ACTTTAAAGTTCA 5150
                          v   iivi i  i  ii     - i -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_109186858_   5151 CATGGAACCAAAAAAGGGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5200
                         i      viiv  ii iv  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_109186858_   5201 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5250
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_109186858_   5251 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5300
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_109186858_   5301 AGTGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACC 5348
                          i     i    i--    i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_109186858_   5349 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5398
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_109186858_   5399 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5448
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_109186858_   5449 GAAATTGGATCCCTTCCTTACACCTTTTACAAAAATTAATTCAAGATGGA 5498
                            i     i    v   i     v v            i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_109186858_   5499 TTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5548
                          i ?    i     i v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_109186858_   5549 CTAAGCATTACCACTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5598
                         v  i ?i v vivi  iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_109186858_   5599 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5648
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_109186858_   5649 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5698
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_109186858_   5699 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5748
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_109186858_   5749 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5798
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_109186858_   5799 AAACAAACAACCCCATCAAAAAGTGGGCAAACGATGTGAACAGACACTTC 5848
                          i     i     v  i?    i        v   v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_109186858_   5849 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5898
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_109186858_   5899 ATCACTGGCCAT 5910
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


4492 18.49 2.00 0.89  chr2_109293890_109296152      874  1771 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_109293890_    874 TGGAAATGCATCTCTTGTTCATGGATTGGAAGACTTAATATTGTTGAGAT 923
                               vii   i v                              i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_109293890_    924 GACACTACTACTCAAAGTGATCTACAGATTCAGGGCAATCTCTATCAAAA 973
                          i  v    v i    v               iv      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_109293890_    974 CCCCAATGGCGTTTTTTAGAGAAATAGTAAAAAAGC--ACTCTAAAATTT 1021
                         i    iiv  v      iv      v --- v    -- ii        i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_109293890_   1022 ATATGGAATCTCAAGGGACCCCAAATAACCAAAACAATCTTGAAAAGGAG 1071
                                 viv          vi    i                  i  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_109293890_   1072 GAGCAAAGTTGGAAGACTCACACTTCCTGATTTCAAAATGTACTATAA-G 1120
                           i          i             ii         iv     i  - 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_109293890_   1121 CAATAGTAATCAAAAC--TATGTTATTAGCATAAGGGATAGATATATAAA 1168
                          v i         i  -- i  v  i i        -     i     i 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAGACATATAGA 296

  chr2_109293890_   1169 CCAATGGAATACAACAGAGATCCCAGAAACAAACTGTCACATGTATGGTC 1218
                         i          v  iv    vi       i    ivvi    v       
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_109293890_   1219 CATTGGTTTTTCAACAAAGAAGCCAAGATCAGTCAATGAGGAATGGGCAG 1268
                         v    i    - i    i iv       i  v      i    v iii  
  L1M4_orf2#LINE/    347 AATTGATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_109293890_   1269 CCTTTTTAACAAATGGTGCTGGGAAAACTGGATATTCTTATGCAAAACAA 1318
                         i     i                 v         ?i vi        v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_109293890_   1319 TGAAGTCAGACCTTTATCTAACATGGTCTA-GAAAATTAACTCAAAATGG 1367
                               ii    ii  i  v   ivi v  -i                  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_109293890_   1368 GTTAAAGATCTCAACATAAGAGCTAAAATTATAAAACTGTTATAAGAATA 1417
                         i i ?   i  v  ii            i         v   v     v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_109293890_   1418 CACAGGTAAAAACCTTCATGGCCTGGAATTAGGCAATGATTTCTTGAGTG 1467
                           i   ?iv   i    i  i   v ii          i      iii i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_109293890_   1468 TGACACCAAAAGCACAGGCAATACAAGAAAAAAATACATAATTTGGATTT 1517
                                         i    i v         -  v    v     i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTT 644

  chr2_109293890_   1518 CATCAAAACGCAAAAGTTTTGTGCTTCAAAGGATACCATCAAGAGAGTGA 1567
                                 ivv    v                 i  i       i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_109293890_   1568 AAAGATAACCTAAAGAATGGGAGAAAATATTTGCAAATCAT-TGTTTAGT 1616
                              i    i v                            - i i ii 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_109293890_   1617 AAATAATGAATATCTGGAATATATAAAGAACTTCTATAACTCAATAATTT 1666
                           ivi ivvi    ii                ii  i           --
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-- 792

  chr2_109293890_   1667 AAAAA--------ACCCAATTCAAAAATGGGTCAAGGTTTTCAGTAAACA 1708
                              --------        ?         iv    v   v i  i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_109293890_   1709 TTTTCCCAAAGA---TATACAAATGGCCAGTAAGCACATGAAAAGATGCT 1755
                            ii       ---              i                    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_109293890_   1756 TCATGTCATTTGTTAC 1771
                         iv ii   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (109 / 53)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.17 (26 / 12)  


3115 24.20 2.85 1.54  chr2_109433047_109434990.rev      602  1444 (500)    L1M4_orf2#LINE/L1        6   859 (49)  

  chr2_109433047_    602 AGATATTTCATGTTCATGGATAGGAAGACTCAATATTGTCAAGATGTCAG 651
                               ii             v        i        i      v  i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_109433047_    652 TTCTTTTCAACTTGTTGTATAGATTTAACACAATCTCAATCAAAGTATCA 701
                          v  iii   v   v v  i     i   i     i v      i vi  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_109433047_    702 GCAAGTTCTTTTGTGAATATTGACCAACTGATTCTAAAGTTTATATGGAG 751
                           vivi i     iii v      v i     i     i  i       i
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_109433047_    752 AGGCAAGAGACCTAGAAGAGCCAACA-AATATTGAAGGAGAAGAACAA-- 798
                          v     i    i    v      v -   v     ii          --
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_109433047_    799 -----GGGCCAACACTACATGACTTCGAGACTGAAAATAAAGTTACAATA 843
                         -----  i iv     v vii i   i i   v vv i    i    i  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_109433047_    844 ATGAAGACAGTCTGTCATTGGCA-ATGCAATAGACAACTAGATCAATGGA 892
                           v        v  vi i     - v -i       vv            
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATATAGATCAATGGA 304

  chr2_109433047_    893 ATGGAA--GAGAGCACCCAGAAATAAACCCACATAAATACAGTCAGCTGA 940
                           i   --     i--               i i vv  ii    ii   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGT--CCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_109433047_    941 TCTTTGACAAAGGAACAAAGACAATACAATGGAGAAAAGATAGTTTTTAA 990
                          i  i     i  vi v     v  v      i    ii     i   vv
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_109433047_    991 AATAAACAGTGGTAGGAAAACTAGACATCCACATGCAAAA-AATCTAGAA 1039
                           i   ii   v i   v    i  i ?            -   ---   
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT---GAA 449

  chr2_109433047_   1040 AT-AAACATTCCACCCCTCAC-------AAAAATGAACTCAATATAGATC 1081
                         i -ii  -ii i   i v   -------      v       v  i    
  L1M4_orf2#LINE/    450 GTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_109433047_   1082 ACAGACCTAAATGTAAAATATAAAACTACAAAACTCCTAGAAGATAATGT 1131
                          ?              i vv        i       i       v  ii 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_109433047_   1132 AGGAGAAAATCTAGATGATCTTGGGTTTGGCAATGACTTTTTGGATATAG 1181
                            ? v      vvi   i        v       ii  i  i     ii
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_109433047_   1182 CACCAAAAGCATGATCCACAAAAGAAAGAATTGATAAGTTAGACTTCATT 1231
                                    ii v v          i   v     i  i        i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_109433047_   1232 AAAATTAGTAATTTGTACTCTGCAAAAGATACTGTCAAGGTAATGAGAAG 1281
                                iv  i  v iiv  v    i  i   i     iv i   i   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_109433047_   1282 ACACGCTACAGACTGGGAGAAAATATTATCAAAAGACAACTATGATAAAG 1331
                            vv i     v              vv    vv i vv v      i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_109433047_   1332 GATTATTATGCAAAATACACAAAAAACTCTTAAAACTCAACAACAAGAAA 1381
                           i vv   v  i    i i   i        v       i  i  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_109433047_   1382 ACAG----TCTGATTGAATGGTGAGTCAAAGACCTTCACCAAAGAAGACA 1427
                            i----i ii   ?  vii  i -     ivi  -----i iv     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGG-CAAAGGATTT-----GAATAGACA 842

  chr2_109433047_   1428 CTTCACCAAAGAAGACA 1444
                         i   v          i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATA 859

Transitions / transversions = 1.70 (126 / 74)
Gap_init rate = 0.02 (14 / 854), avg. gap size = 2.64 (37 / 14)  


 350 17.58 0.00 10.99  chr2_109696179_109698849     1004  1094 (1577)    L1M4_orf2#LINE/L1       15    95 (813)  

  chr2_109696179_   1004 ATGCTCATGGAATCAATATAGTTGGAAGAATCAATATAGTTAAAACGGCC 1053
                            i       ----------        v i     v     i i   v
  L1M4_orf2#LINE/     15 ATGTTCATGGA----------TTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_109696179_   1054 ATACTACCCAAAGCAATCTACAGACTCAACGCTATTGCTGT 1094
                              v      vii         i       v  iv  i 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

Transitions / transversions = 1.29 (9 / 7)
Gap_init rate = 0.01 (1 / 81), avg. gap size = 10.00 (10 / 1)  

2339 25.03 6.48 1.14  chr2_109696179_109698849     1395  2181 (490)    L1M4_orf2#LINE/L1       80   908 (0)  

  chr2_109696179_   1395 TCAATGCTATTTCTATCAAACTACCAA-TGTCATTTTTCACAGAATTAGA 1443
                             i  v  ii        v v   i-  i -     ii     v v  
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGA 128

  chr2_109696179_   1444 AAAAACT-ATTCTAAAATTCATAAAGAAACAAAAAAGAGACTGAATAGCC 1492
                         v  i-  -  i            vi    iiv  ii  vv v        
  L1M4_orf2#LINE/    129 CAAG-CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_109696179_   1493 AAAGCAATACTAAGCAA-AAGAACAAAGCCTGAGGAATCACATTACCTGA 1541
                            i    vi i iv  -          iiv     v     i v  ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_109696179_   1542 CTTCAAACTATACTATAAGGCTACAGTAACCAAGACAGCATGGTTGTGGT 1591
                         i      viv     i  i          i        ii    vv   i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_109696179_   1592 ATAAAAACAGACAAATAGACCAATGGAATAGAACAGAGAACCTAGAAATA 1641
                             ii i     v     i             iv    ii i       
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_109696179_   1642 AAGCCGCACACCTACAGGCATCTGATCTTCAACAAAGCTGACAAAAATAA 1691
                           v  ii   ii  ii v  vi    i   i    i v  v   i vi v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_109696179_   1692 GCAATGGGGAAAGGACTCTCTATTCAATAAATGGTGCTAGGATAACTGGC 1741
                         v            i ivv   v     i          i   i      v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_109696179_   1742 TAGCCATATGCAGAAGAATGAAACTGGACCCCTATGTTTTACCATAAACA 1791
                           ?   i     i         ii          iv ivi      v   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_109696179_   1792 AAAATTAACTCAAGATGGATTAAAGACTGAAATGTAAGACCTCAAA-TAA 1840
                                      i      i ?    iv          v  v   -  v
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_109696179_   1841 AAGAATCCTGGAAGAAAACCTAG----AAAGCACCATGCTGCACATTGGC 1886
                           i v  i i         v   ----   v vi i  ----  v    v
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG----ACCTTGGG 573

  chr2_109696179_   1887 CTTGGAAAAGAATT--TACGAT-TAAGTCCTGAAAAGCAAATGCAACAAA 1933
                         i v  v  v iv  --  -   - i vv  --       v v        
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTA-GATATGACACC--AAAAGCACAAGCAACAAA 620

  chr2_109696179_   1934 AACAAAAATTGCCAA-----------TTAAACTAAAGAGCTTCTACATAG 1972
                          iv      v vi  ----------- i   v v  i i   i iiiivv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_109696179_   1973 CAAAACAAACCATCATCAGAGTAAACAGACAACCTACAGAATGGGAGAAA 2022
                             iv v  i    vv i   i  v        i               
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_109696179_   2023 ATTTTTACAAACTATGCATCCAACAATAGTCTAGCAGCCAGAATCTGTAA 2072
                           v   i    ii  ii   ii i  vi v  v i v       v i   
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_109696179_   2073 GAAACTA--ACAACTAAACAAGGAAAAAACAA----CCCCATTAAAAAGT 2116
                         ii    v--      v  i  vi    i    ----   v   ?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_109696179_   2117 GGCCAAA----------AGACAT-----------GGACATACAAGCAGCC 2145
                           v    ----------      -----------i  i      iii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_109696179_   2146 AACAA--ACATGACAAAACGCTCAACATAACTCATCAT 2181
                           i  --      v  i i         v ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (114 / 80)
Gap_init rate = 0.02 (18 / 829), avg. gap size = 3.33 (60 / 18)  


1315 29.38 8.15 3.54  chr2_109783359_109785009      502  1151 (500)    L1M4_orf2#LINE/L1      182   861 (47)  

  chr2_109783359_    502 CATTCATGAATGGGAAGGATAAAGCTGGAGTTATCATACTACTTGACTTC 551
                           v  v    vii    i i    i     vvv   i   v iii i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_109783359_    552 AAAATGTACTAGGAAGCTGCAGTAACCAAATCTGCATGACCATGTCCTGA 601
                             iv     vi     i      i   iv v ii  iivv  v v i 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_109783359_    602 AAACAGACAAATAGATCAATGAAAGGGAATAGAGGACCCAGATATACATG 651
                         ii i     v           i  vi    v   iii     v   v iv
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_109783359_    652 CACAGATTTACAGCTAACTCATCTTTGACAAAGACACCAAGAAAATACAT 701
                           i v     ii ii  i v  i  i     i iii      v----   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC----CAT 377

  chr2_109783359_    702 ACAATGGGGAAA-------C-------------GT--------------- 716
                         v           ------- -------------  ---------------
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_109783359_    717 ------CATGCACAAGAAGGAGACTAGACTCCTATCTCTCCTCATACATG 760
                         ------      v     v  iii i   i    i   v vi    i ii
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_109783359_    761 AAAATAAAATCAAA-TGGATTAAACACTTA--TGCTGAAGACCAGAAACC 807
                              v  v     -     i ? v  i  --  i--    v vi    i
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGT--AAGAGCTAAAACT 525

  chr2_109783359_    808 ATGAAACTACTAGAATAAAAACATTGTGGAAACACTCCAAGACACTGGTC 857
                           i     vi     -i       v v? v  vv  i iv   vi   vi
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAA-GAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_109783359_    858 TAGGCAAAAGTTTTTGGTTTAAGACTTCAAAATCACAGGCGACCAAAGCA 907
                                vi    i vivv  v   vi     v    i  i  v    v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_109783359_    908 AAAACAAACAAATGAAATTCTGTCATCCTAAAAAGCTTTCAGCACAGCAA 957
                             i i i    vii i iii   vvv v    i    i- ii vv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT-GTGCTTCAA 673

  chr2_109783359_    958 AAGAAACAACAAAGAAAG----GAGACGACACACAG---GAGAAACAATA 1000
                          i  v  v iv       ----i    i  v     --- i  i v    
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_109783359_   1001 TTTTCAAACTCCCCACCCCTGA--AGGGATTCATAACCAGAATATATAAT 1048
                            v    i-- vi ivi    --     i ii  v             v
  L1M4_orf2#LINE/    724 TTTGCAAAT--CATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_109783359_   1049 AAGCTCAAACAACTCAATACCAAAAAACCTCCAGAAAACCAAAAAGAATC 1098
                         i i   vv           vi     i----------  ---   v  i 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAG----------AC---AAATAACC 808

  chr2_109783359_   1099 TGATTTAAAAATGAACAGAAGATCTGAATAAATATTTTTTGAGAGAAGAC 1148
                         ii   ?       ii  i i   i      i i    i iv i      i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_109783359_   1149 ACA 1151
                          i 
  L1M4_orf2#LINE/    859 ATA 861

Transitions / transversions = 1.54 (114 / 74)
Gap_init rate = 0.02 (15 / 680), avg. gap size = 5.07 (76 / 15)  


1803 28.62 7.62 1.12  chr2_109899255_109901247      702  1501 (492)    L1M4_orf2#LINE/L1       57   908 (0)  

  chr2_109899255_    702 ATTCCTCCAAACTTGATCTATAGACCCAGTGCAATTCCAATCAAAATCCC 751
                          i   -     -        i   ii  ii     i  v           
  L1M4_orf2#LINE/     57 ACTCC-CCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_109899255_    752 AGC----------AAAGACACCAATAAAATGTTTCTAAA----------- 780
                            ----------iv   v iii i  iv  v i     -----------
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_109899255_    781 -----------CCTAAAATAGACAATATAAGACTGAG---GAGGAACAAA 816
                         -----------  i i     v   v i  vvi   i---  i       
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_109899255_    817 GATGAAGAATTCACACATCCAGATTCCAAGACTTAT---AAATCT-CTG- 861
                          v  i  i i      v   vi   i   i     i---   v  - v -
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_109899255_    862 ----AAGAGAGTGTAACATTGGGGAAGAAATGGTCACACAGACAAATGGA 907
                         ----    v     iii i   viv iii  i v  i i   iv      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_109899255_    908 ACAATACAGAGAGCCCCTAAATAGACCAACATAAATATAGCCAACTGATT 957
                          i iv iv     i  vv     i   v i i vv   i i   i     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_109899255_    958 CT-GTCAAAGA-GCAAAG-CTGCTCAGTGGAGAAA--AGAGTCTTTTCCA 1002
                         i - v   i i-  v   - iii   i   i    -- v         v 
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_109899255_   1003 TAAATGGTGATGAAACAGCCAGATTACCTTGTGGGATAAAACGAA--TGT 1050
                         i        v  ii   i ii   v?  vii  vi v i  i   --  v
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_109899255_   1051 ACAAACAAACTTTACAACGTACACAAAAATACATACAAAATTATTCATAG 1100
                           v-- vv  i i   v i  i        vv iv      viv   ?  
  L1M4_orf2#LINE/    455 ACC--CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_109899255_   1101 ACTTATAATTTAAAGTAG--AAAACTGTAAAAATTCTAGGATAGAACATA 1148
                           i  -   v   i--  --      i     v ii   i v i      
  L1M4_orf2#LINE/    503 ACCTA-AATGTAAG--AGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_109899255_   1149 GAAGAAAATCTACCTGACCTTGCATTTGGTGATGAGGTTTTATACACAGC 1198
                          i? v      v v        vi  v  ii   ivv i   v i iii 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_109899255_   1199 ACCAAAAGC-CAATCCAGGAAAGGAAAACAT-GATAATGTAGACCTTATT 1246
                                  -   v v vi    i    -  -     vv i   i i  i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATC 648

  chr2_109899255_   1247 AAAACTGAAAATGTCTACTCCATAAAAGACCCCATTAGGAGAATGAAAAG 1296
                             i i    iv i iiv ivi   i   v i  i i  i i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_109899255_   1297 GCAAGGCACATACTGGGAGAAAATATTTGGAAAACATCTA-CTAAAAAAG 1345
                         i   vv    v v                v   v   v  -  i v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_109899255_   1346 GACTGTTATTCAAAGTATACCAAGAAAG--TAAAACTCAACCAGAAGGAA 1393
                             vv   i  i i    iv     vv--  v       iv v  ii i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_109899255_   1394 ACAAACCATCCAAGT-AAAAATGGGTGA-TGATCTGAACAGACACCTCAC 1441
                              iv i    v -         ii -v   i    i     ii  v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_109899255_   1442 CAA-GAATATATAAAGATGGCAAATAAGCATTACCAAAAGCAGCTCAATA 1490
                            -   v     v i     v        i- iv     vv      i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCAC-ATGAAAAGATGCTCAACA 897

  chr2_109899255_   1491 GCATATGTCAT 1501
                         v  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.03 (26 / 852), avg. gap size = 2.69 (70 / 26)  


3162 24.56 1.64 2.08  chr2_109996896_110001306.rev     3008  3919 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_109996896_   3008 TAGAAAGATATCCCATGCTCATTGGTC---AGATTTAATATCATTAAAAT 3054
                          i               i    v i i---   i       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_109996896_   3055 GATCATACTGCCCAATGCAATCTACATATTCAATGGGATCTCTATCAAAA 3104
                          iiv     v     vvii       v      i vi   i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_109996896_   3105 TACCAA-TGTCATTTTT-CAAAGAATTAGAAAAAAC--ATGCTAAAATTA 3150
                          v   i-  i v     -  i -    i-- v  i --  v        v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_109996896_   3151 ACATGTAACCAAAAAAGAGCCGGAATAGCCAAAGCATTATAAAACAACAA 3200
                          i   v  viiv  ii  v  i           i  v v vi  v  v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_109996896_   3201 CAACAAAGCTAAAGCTGTCACATTACCAGACTTCAAATTATAATACAAGG 3250
                         v       i ii  vvv     i v  vi i      viv  v     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_109996896_   3251 CTGTAGTAACCAAAACAGTATGATACTGGTACAAAAATAGACACATAGAT 3300
                           ii     i   i     i  i      i i  ii       i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_109996896_   3301 CAATAGAATAGAAAAGAGAATCCAGAAATAAAGCCACATATT-ACAGCCA 3349
                             i        vv    i            v   i i   - ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_109996896_   3350 ACTGATATTTGACAAAATCAACAAGAACATACAGTGGAGAAAGGACACCC 3399
                          i    v  i     iiviiv     v   v  i   i     i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_109996896_   3400 TTTTCAATAAATGATGCTGGGATAATTGGATTGGCATCTGCAGACGAATG 3449
                                i     i        i  i     v?v  iv    i v     
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_109996896_   3450 AAACTGGACCACCATCTTTTACCATATAAAAAAATCAACTCAAGATGAAT 3499
                           ii      v i i  ivi        v      i       i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_109996896_   3500 TAAAGATTTAAATGTAAGACCCGAAACTACAAAAACACTAGAAGAAAATC 3549
                         i ?   ii           v ii      i    vivi          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_109996896_   3550 TGGGGAAAACTCTTCCGGACATTGATCTAGGCAAAAAATT----GATGAC 3595
                          i  ?iv  v     vv   v   ivi       viiv  ----   ---
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--- 594

  chr2_109996896_   3596 AAAGACCTCAAAAGCACAGACAACAAAAACAAAAATAGGCAAATGGGACT 3645
                         - v   vi          ii        iv        ii    v     
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_109996896_   3646 TAATTAAACTAAAAGGCTTCTGCACAGCAAAAGAAATAATCATCAGAGTG 3695
                          v  i   v v   ii   i  ii vv    i  v iv    vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_109996896_   3696 AACAGACAACCTGCAGAATGGGAGAAAATATTTACAAACTATGTAT--GA 3743
                           v        ii                    i    ii  i   --  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_109996896_   3744 CAGGGGACTAATGTCCAGAATTTACAAGGAACTCAAACAATGCAACAACA 3793
                         i i      vi i        v  i  i      vv    iv   i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_109996896_   3794 ACAACAACAACAAAATAGAAAACAATCCCATTAAACAATAGGCAAAGGAC 3843
                          v  ----i     --------i  i  v   ?  v   i         i
  L1M4_orf2#LINE/    794 AAAA----GACAAA--------TAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_109996896_   3844 ATGAATAGACACTTTTG-AAAGAAGACATACAAATGGCCAAGAGGCATAT 3892
                         v          i  i v-        i              v i   i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_109996896_   3893 GAAAAAATGCTTAACATCACAAATCAC 3919
                              i     i       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (137 / 83)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.62 (34 / 13)  


2102 24.11 0.56 0.75  chr2_110006826_110008942.rev      511  1041 (1076)    L1M4_orf2#LINE/L1      136   665 (243)  

  chr2_110006826_    511 ATTCTAAAATTTATGTGGAGTCACAAAACACCC-GAATAGCCAAAGCTAT 559
                           i        i  i    ivii   iiv    -           i v  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_110006826_    560 CTTAAGCAAAAAGAACAAAACTGGGGGAATCACATTACCGGATTTCCAAT 609
                            i iv  i         ii   i   v     i v  vi     v  v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_110006826_    610 TATACTGGAGAGCTATAGTAACCAAAACAGCATGGTATTGGCATAAAAAC 659
                         iv    iv i     i     i   i    ii     i        ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_110006826_    660 ACACATATAGACCAATGGAACAGAATAGAGAACCCAGAAACAAAATCCAC 709
                          v         i        i     v    ii       i   -i   i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCAT 334

  chr2_110006826_    710 ACACCTACAGTGAAGTCATTTTCCACAAAGGTGCCAAGAACGTACACTGA 759
                            ii  ii  v  v v      v    i          v i v  v  i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_110006826_    760 GGAAAAGACAGTCTCTTCAATAAATGGTGCTGGGAAAACTGAATATCCAT 809
                              ii i     i     i              v     i   ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_110006826_    810 AATGCAGAAGAATGAAACTAGACCCCTACCTCTCACCATAAACAAAAATC 859
                          -    i         ii i            v       v        i
  L1M4_orf2#LINE/    435 A-TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_110006826_    860 AAATCAAAATGAATTAAAGACTTAAATCTAAGATCTTAAACTATGAAACT 909
                           v        i  i ?    i     v     v  v       i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_110006826_    910 AGTACAAGGAAATGTCTG-GCAAACTCTCAAAGACATTGGTCTGGGCAAA 958
                         vv  v   i   ii vv - i   -   iviv   v    vi i     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_110006826_    959 AATTTATTGAATAATACCCCACAAGCACAGGCAACCAAAGCAAAAATGCA 1008
                         ii   v  ii   vv  v   v       i     v    v      iv 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_110006826_   1009 CAAATGGGATCACATTAAG-TTAAAAAGCTTCTG 1041
                         i    v   iiv   i  i-       -   i  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA-CTTTTG 665

Transitions / transversions = 1.68 (79 / 47)
Gap_init rate = 0.01 (7 / 530), avg. gap size = 1.00 (7 / 7)  

 961 21.40 0.39 2.72  chr2_110006826_110008942.rev     1369  1625 (492)    L1M4_orf2#LINE/L1      658   908 (0)  

  chr2_110006826_   1369 AGCTTCTGTACAGCAAAGGAAAACAGTCAACAAAGTGAAAAGACAACC-A 1417
                          i   i   i vv      - v  vi    v                 - 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGG-ACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_110006826_   1418 CAGAATGGGAGAAGATATCTGCAAACTAACCATCTGACAAGGGGTTAATA 1467
                                      i    i      ii vvi      i     ii vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_110006826_   1468 ACCAGAATATATAAGGGGCTTAAACAACTCTATAGTAAAAAAATCAAATA 1517
                         v             i ii  ivv       v   i      i -      
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATA 805

  chr2_110006826_   1518 TAATAATCTGATCAGAAAATGGGCAAAATATATGAAAAGATATTTCTCAA 1567
                         ----- i ii  i?i            iv  v    v   i       v 
  L1M4_orf2#LINE/    806 -----ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_110006826_   1568 AAGAAAACGTACAAATGGCAAACAGGCCTATGAAAAGGTACTCAATACCA 1617
                              i ii          v  i i  vi        i i     i i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_110006826_   1618 CTGATCAT 1625
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.00 (36 / 18)
Gap_init rate = 0.02 (4 / 251), avg. gap size = 2.00 (8 / 4)  


1917 28.04 1.18 0.20  chr2_110055319_110059871     2830  3339 (1214)    L1M4_orf2#LINE/L1        1   515 (393)  

  chr2_110055319_   2830 TGGAAGCACATTCCATGCTCATGGATGGGTAGACTCGATACTGTGAAAAT 2879
                              iv i  i     i        v  v     ii   i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_110055319_   2880 GATCATGGTGCCAAAAGCAGTCTATGGATTCGATGCAATTCCCATCAAAA 2929
                          iiv  iv v  v   viii    ii     i i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_110055319_   2930 TACCATCAGCATTTTTCATGGAGCTTTAAAAAGC-AATCCTAAAATTCAA 2978
                          v   v v  v     iiii  iv-  i v    -i             v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCAT 149

  chr2_110055319_   2979 ATGGAACCAAAAAAGACCCTACATAGCCAAAGCAAGACTAAGCAAAAAGA 3028
                               viiv  ii     viv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_110055319_   3029 ACACATCTGGAGGCATCACATCACCTGACTTTA-----TACTACAAGGCT 3073
                            v vi      vv     iiv  ii i  i -----        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_110055319_   3074 GTAGTTACCAAAACAGTATGGTACTGGTATGAAAACAGGCAAGTAGACCA 3123
                         ii   v i   i     i         i  i ii i  i  vi    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_110055319_   3124 ATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAGTTAAC 3173
                               i     v    ii           v   v i i   ii  i  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_110055319_   3174 TGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTA 3223
                             i  i     i vviv   i v   vv i         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_110055319_   3224 TTCAACAAATGGTGCAGGGATAACTGGGAAGCCACATGTAGAAGGGTAAA 3273
                                        v    i      iv ?       i i   ii i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_110055319_   3274 ACTGAATCCTCATCTCTCAACTTATACAAAAATCAACTCAAGATGGATCA 3323
                         ii  i i  ii i   v  v v           i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_110055319_   3324 AAGACTTAAATCTAGG 3339
                         ?    i     v  i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAG 515

Transitions / transversions = 2.00 (94 / 47)
Gap_init rate = 0.01 (3 / 515), avg. gap size = 2.33 (7 / 3)  

1347 22.71 0.97 1.93  chr2_110055319_110059871     3648  4061 (492)    L1M4_orf2#LINE/L1      499   908 (0)  

  chr2_110055319_   3648 AAAGACTTAAAATCTAAGACCCAAAATCATAAACATTCC-AGAAGATAAC 3696
                          ?    i    - v     v i    ii     - i  i-      v   
  L1M4_orf2#LINE/    499 AWAGACCTAAA-TGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chr2_110055319_   3697 ATC--AGTAAAACTACCCTAGACATTGGTTTAGGCAAAGAGTTCGTTAAC 3744
                           v--?     v  -i v -   v    v        v iv   -   iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCT-TCGT-GACCTTGGGTTAGGCAATGGTTTC-TTAGA 593

  chr2_110055319_   3745 TACCAAGAACCCAAAAGCAAATGCAACAAAAACAAAAATAAATACATTGG 3794
                           i---  vv         v v         iv       i   v     
  L1M4_orf2#LINE/    594 TAT---GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_110055319_   3795 ACCTAATTAAG-TTACAAGTTTCTGCATAGCAAAAGAAATAATCAGCAGA 3843
                           i v  i  i-   v  ii  i  iiivv    i  v iv    iv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_110055319_   3844 GTAAACAGACAACCCACAGAGAGGGAGAAAATATTCTCAAACTATGCATC 3893
                           i  v              iv             iv    ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_110055319_   3894 TCACAAAGGACTAATATTTAGAATCTACAAGGAACTCAAACAAATCAGCA 3943
                          v i  i     vi   ii     v  i  i      vv    v   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_110055319_   3944 AGAAAAAAACAAATAATCCCATCAAAAAGTGGGCAAAGGAAATTAATAGA 3993
                          v     i        i  v  i?    i           vv v      
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_110055319_   3994 CAATTCTCAAAAGAAGATGTACAAATGGCCAACACACACATGAAAAAATG 4043
                           v     v         i             i vi          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_110055319_   4044 CTCAGCATCACTATCAGG 4061
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (50 / 41)
Gap_init rate = 0.02 (9 / 410), avg. gap size = 1.33 (12 / 9)  


3247 27.75 0.22 0.22  chr2_110067415_110073811     4998  5905 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_110067415_   4998 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATCAATATTGTGAAAAT 5047
                              ii i  i     i       iv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_110067415_   5048 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5097
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_110067415_   5098 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 5146
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_110067415_   5147 ATGGAACCAAAAAAGAGCCCTCATTGCCAAGACAATCCCAAGCAAAAAGA 5196
                               viiv  ii  v  vvv  v     i      iii iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_110067415_   5197 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5246
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_110067415_   5247 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5296
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_110067415_   5297 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 5346
                               i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_110067415_   5347 TGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTA 5396
                             i  i     ivv  vv  i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_110067415_   5397 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGAAAGCTGAA 5446
                           i  i              v      v  ?  ii   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_110067415_   5447 ACTGGATCCCTTCCTTATGCCTTATACAAAAATTAATTCAAGGTGGATTA 5496
                         ii    i    v   i ii  v              i    ii     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_110067415_   5497 AAGGCTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5546
                         ?  i i       v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_110067415_   5547 GGCA-ATACCATTCAGGACATAGACATGGGCAAGGACTTCATGACTAAAA 5595
                           ?i- v i -   iv   v v ivv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_110067415_   5596 CACCAAAAGCAATGGCAACAAAAGCCGAAAGAGACAAATGGGATCTAATT 5645
                                    vvi          vvi   v   i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_110067415_   5646 AAACTAAAGAGTTTCTGCACAACAAAAGAAAATGCCATCAGAGTGAAAAG 5695
                            v v  i ii  i  ii vv    i  v v ii  vv i         
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_110067415_   5696 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTAGCCATCTGACAAAG 5745
                         i     i                 v       vii vvi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_110067415_   5746 AGCTAATGTCCAGAATCTACAAATAACTTAAACAAATTTACAAGAAAAAA 5795
                         ii  vi i        v  i   v    ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_110067415_   5796 TCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 5845
                         v    i     v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_110067415_   5846 AAAAGAAGACATTTATGCAACCAACAGACACATGAAAAAATGCTCATCAT 5895
                         v        i  vi viiii    i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_110067415_   5896 CACTGGTCGT 5905
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.58 (152 / 96)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.00 (4 / 4)  


1607 19.10 1.86 4.24  chr2_110179630_110182399.rev      667  1043 (1727)    L1M4_orf2#LINE/L1        1   368 (540)  

  chr2_110179630_    667 TAGAAAGGAATCC-ATGGTTATGGATTGGAAAACCTAATATT---AAGAA 712
                          i     iv    -   v i           i  i       ---    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_110179630_    713 TGCTATATTTCTCAAATTTATCTACAGAGG-AATGCAATCCCTAGCAAA- 760
                         v  v   i i i      v         vv-  i          v    -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_110179630_    761 CCCCAATGGGAAATGGCAATTTTGGAGAAATTCACGACCTGACCCTAAAA 810
                         i    ii------  v vv     v       v  i v    i       
  L1M4_orf2#LINE/    101 TCCCAGC------TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_110179630_    811 TTCAAGTGGACATGCAAAGGACCCAGAATGGCCCAAATGATTTAGATCTT 860
                             vi    v      i           i   v   ii  ------   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT------CTT 188

  chr2_110179630_    861 GAAAAAGAAGGACAAAAGTAGAGAGCTCACATTTCCTACTTTCAAAACTT 910
                                   i     iv i   ii      i    i v           
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_110179630_    911 AGTACAAAGCTACAGTAATCAATACAGTAAAAGTGGTATTAGCAAAAGTG 960
                          v                    v     ----      i i   v   vi
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGT----GTGGTACTGGCATAAGGA 284

  chr2_110179630_    961 TAGACAT-CACAACAACAGAATATAATTAAGAGTCCAGAAACAACTCGCC 1009
                                -i v v   ii     v    i            i  vi vvi
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_110179630_   1010 ATATTCACAGTCAATTGATTTTTGACAAGGATGC 1043
                          i   i ii             i       i   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

Transitions / transversions = 1.40 (42 / 30)
Gap_init rate = 0.02 (8 / 368), avg. gap size = 2.88 (23 / 8)  

2183 15.77 2.87 9.32  chr2_110179630_110182399.rev     1725  2282 (488)    L1M4_orf2#LINE/L1      387   908 (0)  

  chr2_110179630_   1725 AAAGAATAGTGTTTTCAGCAAATGGTGCTGGAACAACTGGATATCCACAA 1774
                                   v      i             i           ?     v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_110179630_   1775 GCAAAAGAATGAAGGTGGACCCCTACTTCACTCCATATACAAAAACTAAC 1824
                                       v           i    v             i    
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_110179630_   1825 TCAAAATGTATAAAAGACATAAAACGTAAGAGTTAAAACCACTAAACTCT 1874
                                 v  v ?    v    -i       i      i iv       
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_110179630_   1875 TAGAAGAAAACACAGGAGTAAATGTCCATGATCTTGGATTAGGCGGAGGT 1924
                                     i   ?      v i i   i     i      iiv   
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_110179630_   1925 TTCTTAGGTGTAATGCCAAAAGTATCAGCAACAGAAGAAAAAA---ATAA 1971
                                i i i ii       i iv       i         ---    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_110179630_   1972 ATTGGACCTTGCCTTAAAACACAGATGGCAGAGAAGAAAAAATATACTTC 2021
                                ----------------------------------------   
  L1M4_orf2#LINE/    636 ATTGGAC----------------------------------------TTC 645

  chr2_110179630_   2022 ATCAAAATTAAAAACTTTTTTGCTTCAA-TGAGATCATCAAGAAAAGTGA 2070
                                            v        -v  v ii         -    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA-GTGA 694

  chr2_110179630_   2071 AATGATAACCCATAAAATGG-AGAAAA-----GCA-----CGTATCTGAT 2109
                           v  i      i i     -      -----   -----ii        
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_110179630_   2110 GAGGGATTTGTATCTAGAATACAGAAAGAACTCTTACAACTCAATAATAA 2159
                         i     i       i      i v                          
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_110179630_   2160 AAAGACAAA-AATTCCATTAAAAAGTAGATGAAGGTTCTGAATGGTGAAT 2208
                                  -  ii v   ?    i i iii    v i     i -----
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG----- 839

  chr2_110179630_   2209 GTATATATATGTATATATATACACACACAAATAGCCAAGAGCCACATTCA 2258
                         ---- i  v v vi v v - v i i      i     v iv     vv 
  L1M4_orf2#LINE/    840 ----ACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_110179630_   2259 AAAATATTGAACTTTGTTTGCCAG 2282
                           i  ii v   v ii????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (54 / 30)
Gap_init rate = 0.02 (11 / 522), avg. gap size = 6.18 (68 / 11)  


3350 26.11 0.55 0.22  chr2_110222938_110227945     3613  4516 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_110222938_   3613 GGAAACACATCTCATGCTCATGGATGGGTAGAATCAATGTTGTGAAAATA 3662
                              v i   i    i        v  v   v i   i    v  i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_110222938_   3663 ACCATATTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATCAGAAT 3712
                         i v   i v  v   vii       i      i        i    i   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_110222938_   3713 ACCACCATCATTCTTCACAGAATTAGAAAAAAAAATTCTAAAATTCATAT 3762
                         v   v vv v  i  ii     v v  v  ivvi  i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_110222938_   3763 GGAACAAAAAAGAGCCCA-CATAACCAAAGCAAGACTAAGCAAAAAGAAC 3811
                             vviv  i ii    -v   i     i   vvi i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_110222938_   3812 AAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGCCAT 3861
                            vi      vv       v  ii        viv     i  i  i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_110222938_   3862 AGTCACCAAAACAGCATGATACTGGTATAAAAATAGGCACATAGACCAAC 3911
                            v i   i    ii  i      i    ii    i  i     i   i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_110222938_   3912 GGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAACTG 3961
                             i     v    ii               v i i   ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_110222938_   3962 ATCTTTGACAAAGCAAACAAAAACAT--AATGTGGGGAAAGGACATCCTT 4009
                           i  i     i vviv   i v   --    --       i i vi   
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATG--GGGAAAGAATAGTCTT 399

  chr2_110222938_   4010 TTGAATAAATGGTGCTGGGATAATTGGCTACCCACATGTAGGGGATTGAA 4059
                           v  i              i  i   v  ?       i iii  v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_110222938_   4060 ACTGGATCCTCATCTCTCACCTTATACAAAAACCAACTCAAGATGGATTA 4109
                         ii    i  ii i   v    v          ii       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_110222938_   4110 AGGACTTAAACTTAAGACCTGAAATTACAAAAATTCTAGAAGATAACATT 4159
                         ?i   i    iv     v  i   i  i    v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_110222938_   4160 GGCAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAA 4209
                           ?iv  vi    vv   v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_110222938_   4210 CCCAAGAGCAAATGCAATGAAAGCAAAGATAAATAGCTGGGACCTAATTA 4259
                         v    i    v v    ii    v   i   i   iv v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_110222938_   4260 AACTACAGAGCTTTTGCACAGCAAAAGGAACAGACAGCAGAGTAAACAGA 4309
                           v vv i i      ii vv    i iv  viv  iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_110222938_   4310 TAACCCACAGAGTGGGAGAAAATCTTCGCAATCTGTACATCTGACAAAGG 4359
                         i          i           v  i    viii  i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_110222938_   4360 TCTAATATTCAGAATCTACAAGGAAGTCAAACAAATCAGTAAGAAAAAAA 4409
                         v  vi   i      v  i  i   v  vv    v   i   v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_110222938_   4410 CAAACAATCCCATCAAAAAGTGGGCCAAGGACATGAATAGACAATTCTCA 4459
                             i  i  v  i?    i     v     iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_110222938_   4460 AAAGAAGATATACAAATGGCCAACAA--ACATGAAAAAATGCTCAACATC 4507
                                                i  --         i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_110222938_   4508 ACTAATGAT 4516
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.00 (4 / 907), avg. gap size = 1.75 (7 / 4)  


2185 25.63 3.73 1.94  chr2_110301324_110311868     2154  2824 (7721)    L1M4_orf2#LINE/L1        1   683 (225)  

  chr2_110301324_   2154 TGGAGAAACATTCCATGCTTGTGGATAGGAAGAATCA-TATCGTGAAAAT 2202
                             i i i  i     i ii     v      v i -   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_110301324_   2203 GGACATACTGCCCCAAAT-AATGTATAGATTCAATGCTATTCCCATCAAA 2251
                           vv     -        -i  v  i        i  v  i  i      
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_110301324_   2252 CTTCCATTGACATTCTTCACAGAATTAGAAAAAGCT-ATTTTAAAATTTA 2300
                         v i   vivi v  i  ii     v v  v  -   -  ii       i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr2_110301324_   2301 TATGGAA---CAAA------AGAAGAGCCCAAATAAGC------AAAAAG 2335
                                ---   i------    v    v   i  v ------  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_110301324_   2336 AACAAAGCTGGAGGCATCACACCACCTAACTTCAAACTATATTACAAGGC 2385
                                i      vv      iv  i  i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_110301324_   2386 TACAGTAACTAAAACAGCATGGTACTGGTAAAAGAACAGACACATAGGCC 2435
                                 ii  i    ii         i v   i i     i    ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_110301324_   2436 AATGGAACAGAATAGAGAACTCAGAAATAAGACTTGCACACCTACAACCA 2485
                                i     v    iii         -  iiii   ii  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCA 347

  chr2_110301324_   2486 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGCGGAAAGGGCCCCC 2535
                         vi    i  i     ivv  v   i v  vv     v      iiivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_110301324_   2536 TATTTAATAAATGATGCTGGAAGAGCTGGCTAGCTATACGCAGAAAATTG 2585
                          v  i  i     i      i v i    v  ? i i i   i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_110301324_   2586 AAACTAGAACCCCTTCCATACACCATATACAAAAATTAATTCAAGATAGA 2635
                           ii i  -     v  vi                    i    i  i  
  L1M4_orf2#LINE/    448 AAGTTGGA-CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_110301324_   2636 TTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACTCT-AGAAGAAAA 2684
                          i ?    i         i v i            -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr2_110301324_   2685 TCCAAGCAATAGCATTCAGGACATAGGCACAGGCAAATATTTC------A 2728
                         ivi i ?ivv iiv   iv   v v  vvi      vvi    ------ 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_110301324_   2729 TGACAACAAAAAGCCAAAAGCAATTGCAACAAAAGCAAAACTTGACAAAT 2778
                              --------         vvv          v    v v  i    
  L1M4_orf2#LINE/    596 TGACA--------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_110301324_   2779 AGGATCTCATCAAACTAAAGAACTTTTGCACAGCAAAAGAAACTAT 2824
                         v   ii        v v  i        ii vv    i  v     
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

Transitions / transversions = 1.64 (105 / 64)
Gap_init rate = 0.02 (14 / 683), avg. gap size = 2.71 (38 / 14)  

 547 23.81 5.95 0.60  chr2_110301324_110311868     4385  4552 (5993)    L1M4_orf2#LINE/L1      678   854 (54)  

  chr2_110301324_   4385 CACTATCATCAGAATGAACAGACAACCTACAGAATGGGGGAAAATGTTTA 4434
                                 vv i i    v        i          i      i   i
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_110301324_   4435 CAATCTATCCATCTGATGAATGTCTAATATCCAGAGTCTAAAAATAA--- 4481
                            vii  vi       i iv v  vi        i v  v   v  ---
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_110301324_   4482 --GCAAATTTATAAGAAAAAAA-----AACCCCATTAAAAAGTGAGCAAA 4524
                         --i   v iv    v     i -----     v   ?    i  i     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_110301324_   4525 AGGACATGAAGTGACACTTCTCAAAAGA 4552
                         -   iv    vv    i     v     
  L1M4_orf2#LINE/    828 -GGATTTGAATAGACATTTCTCCAAAGA 854

Transitions / transversions = 1.05 (20 / 19)
Gap_init rate = 0.02 (3 / 177), avg. gap size = 3.67 (11 / 3)  

3208 26.79 0.66 0.55  chr2_110301324_110311868     9147 10053 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_110301324_   9147 TGGAAGAACATTCCATGCTCATGGGTAGGAAGTATCAATATCGTGAAAAT 9196
                              ii i  i     i      i v     vv i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_110301324_   9197 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 9246
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_110301324_   9247 TACCAATGACTTTCTTTACAGAA-TTGGAAAAAACTA--CTTTAAGTTCA 9293
                          v   iivi i  i   i     -   -- v  i  i-- i v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_110301324_   9294 TATGGAACCAAAAAAGAGCCCACATTA-CCAAGTCAATCCTAAGCCAAAA 9342
                                viiv  ii  -    v v  -    iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_110301324_   9343 GAACAAAGCTGGAGGCATCACGCTACCTAACTTCAAACTGTACTACAAGG 9392
                                 i      vv    i  v  i  i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_110301324_   9393 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 9442
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_110301324_   9443 CTATGGAATAGAAC--AGAGCCCTCAGAAATAATGCCATATATCTGCAAC 9490
                          v           i--    i  --        vv     i  i iiiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_110301324_   9491 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATTC 9540
                         i vi    i  i     ivv  v   i v  vvv          vi  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_110301324_   9541 CCTATTTAATAAATGGTGCTGGGAAAACCGGCTAGCCATATGTAGAAAGT 9590
                         i  v  i  i              v   i  v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_110301324_   9591 TGAAACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 9640
                             ii    iv   v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_110301324_   9641 ATTAAAGACTTAAATGTTGGACCTAAAACCATAAAAACCCTAGAAGAAAA 9690
                           i ?    i       vi  v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_110301324_   9691 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACGTCATGTCTA 9740
                          v    ?i v viv   iv   v v  vv i     v iiv  v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_110301324_   9741 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 9790
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_110301324_   9791 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 9840
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_110301324_   9841 CAGGCAACCTACAGAATGGGAGAAAATTGTTGCAATCTACTCATCTGACA 9890
                         v  i     i                 vv      vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_110301324_   9891 AAGGGCTAATATACAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 9940
                          i  i  vi   v      v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_110301324_   9941 AAAACAAACGACGCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 9990
                           i     ii  v v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_110301324_   9991 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 10040
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_110301324_  10041 CATCACTGGCCAT 10053
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (137 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3364 26.43 0.44 0.44  chr2_110543831_110546538.rev     1310  2217 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_110543831_   1310 TGGAAGAACATTCCATGTTCATGGGTAGGAAGAACCAATATTGTGAAAAT 1359
                              ii i  i            i v      vii        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_110543831_   1360 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCACCCCCATCAAGC 1409
                            v     v     iv i  i  i        i  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_110543831_   1410 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 1457
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_110543831_   1458 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 1507
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_110543831_   1508 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1557
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_110543831_   1558 TACAGTAACCAAATCAGTATGGTACTGGTACCAAAACAGAGACATAGATC 1607
                                 i   iv    i         i iv ii i   v i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_110543831_   1608 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 1655
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_110543831_   1656 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1705
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_110543831_   1706 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1755
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_110543831_   1756 GAAACTGGATCCCTTCCTTACACATTATACAAAAATTAATTCAAGATGGA 1805
                            ii    i    v   i    vv              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_110543831_   1806 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1855
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_110543831_   1856 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1905
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_110543831_   1906 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1955
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_110543831_   1956 TTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTACCATGAGAGTGAAC 2005
                          i   v v  i i      ii vv    i  v    i  v  i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_110543831_   2006 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 2055
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_110543831_   2056 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 2105
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_110543831_   2106 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 2155
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_110543831_   2156 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 2205
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_110543831_   2206 ATCGCTGGCCAT 2217
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3237 27.86 0.22 0.22  chr2_110604830_110611226.rev     4998  5905 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_110604830_   4998 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATCAATATTGTGAAAAT 5047
                              ii i  i     i       iv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_110604830_   5048 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5097
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_110604830_   5098 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 5146
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_110604830_   5147 ATGGAACCAAAAAAGAGCCCTCATTGCCAAGACAATCCCAAGCAAAAAGA 5196
                               viiv  ii  v  vvv  v     i      iii iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_110604830_   5197 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5246
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_110604830_   5247 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5296
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_110604830_   5297 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 5346
                               i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_110604830_   5347 TGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTA 5396
                             i  i     ivv  vv  i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_110604830_   5397 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGAAAGCTGAA 5446
                           i  i              v      v  ?  ii   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_110604830_   5447 ACTGGATCCCTTCCTTATGCCTTATACAAAAATTAATTCAAGGTGGATTA 5496
                         ii    i    v   i ii  v              i    ii     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_110604830_   5497 AAGGCTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5546
                         ?  i i       v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_110604830_   5547 GGCA-ATACCATTCAGGACATAGACATGGGCAAGGACTTCATGACTAAAA 5595
                           ?i- v i -   iv   v v ivv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_110604830_   5596 CACCAAAAGCAATGGCAACAAAAGCCGAAAGAGACAAATGGGATCTAATT 5645
                                    vvi          vvi   v   i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_110604830_   5646 AAACTAAAGAGTTTCTGCACAACAAAAGAAAATGCCATCAGAGTGAAAAG 5695
                            v v  i ii  i  ii vv    i  v v ii  vv i         
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_110604830_   5696 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTAGCCATCTGACAAAG 5745
                         i     i                 v       vii vvi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_110604830_   5746 AGCTAATGTCCAGAATCTACAAATAACTTAAACAAATTTACAAGAAAAAA 5795
                         ii  vi i        v  i   v    ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_110604830_   5796 TCAAACAACCCCATCAAAAGGTGGGCAAAGGATATGAACAGACACTTCTC 5845
                         v    i     v  i?   ii            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_110604830_   5846 AAAAGAAGACATTTATGCAACCAACAGACACATGAAAAAATGCTCATCAT 5895
                         v        i  vi viiii    i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_110604830_   5896 CACTGGTCGT 5905
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.59 (153 / 96)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.00 (4 / 4)  


1917 28.04 1.18 0.20  chr2_110618786_110623341.rev     2834  3343 (1213)    L1M4_orf2#LINE/L1        1   515 (393)  

  chr2_110618786_   2834 TGGAAGCACATTCCATGCTCATGGATGGGTAGACTCGATACTGTGAAAAT 2883
                              iv i  i     i        v  v     ii   i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_110618786_   2884 GATCATGGTGCCAAAAGCAGTCTATGGATTCGATGCAATTCCCATCAAAA 2933
                          iiv  iv v  v   viii    ii     i i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_110618786_   2934 TACCATCAGCATTTTTCATGGAGCTTTAAAAAGC-AATCCTAAAATTCAA 2982
                          v   v v  v     iiii  iv-  i v    -i             v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCAT 149

  chr2_110618786_   2983 ATGGAACCAAAAAAGACCCTACATAGCCAAAGCAAGACTAAGCAAAAAGA 3032
                               viiv  ii     viv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_110618786_   3033 ACACATCTGGAGGCATCACATCACCTGACTTTA-----TACTACAAGGCT 3077
                            v vi      vv     iiv  ii i  i -----        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_110618786_   3078 GTAGTTACCAAAACAGTATGGTACTGGTATGAAAACAGGCAAGTAGACCA 3127
                         ii   v i   i     i         i  i ii i  i  vi    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_110618786_   3128 ATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAGTTAAC 3177
                               i     v    ii           v   v i i   ii  i  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_110618786_   3178 TGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTA 3227
                             i  i     i vviv   i v   vv i         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_110618786_   3228 TTCAACAAATGGTGCAGGGATAACTGGGAAGCCACATGTAGAAGGGTAAA 3277
                                        v    i      iv ?       i i   ii i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_110618786_   3278 ACTGAATCCTCATCTCTCAACTTATACAAAAATCAACTCAAGATGGATCA 3327
                         ii  i i  ii i   v  v v           i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_110618786_   3328 AAGACTTAAATCTAGG 3343
                         ?    i     v  i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAG 515

Transitions / transversions = 2.00 (94 / 47)
Gap_init rate = 0.01 (3 / 515), avg. gap size = 2.33 (7 / 3)  

1340 22.95 0.97 1.93  chr2_110618786_110623341.rev     3651  4064 (492)    L1M4_orf2#LINE/L1      499   908 (0)  

  chr2_110618786_   3651 AAAGACTTAAAATCTAAGACCCAAAATCATAAACATTCC-AGAAGATAAC 3699
                          ?    i    - v     v i    ii     - i  i-      v   
  L1M4_orf2#LINE/    499 AWAGACCTAAA-TGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chr2_110618786_   3700 ATC--AGTAAAACTACCCTAGACATTGGTTTAGGCAAAGAGTTCGTTAAC 3747
                           v--?     v  -i v -   v    v        v iv   -   iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCT-TCGT-GACCTTGGGTTAGGCAATGGTTTC-TTAGA 593

  chr2_110618786_   3748 TACCAAGAACCCAAAAGCAAATGCAACAAAAACAAAAATAAATACATTGG 3797
                           i---  vv         v v         iv       i   v     
  L1M4_orf2#LINE/    594 TAT---GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_110618786_   3798 ACCTAATTAAG-TTACAAGTTTCTGCATAGCAAAAGAAATAATCAGCAGA 3846
                           i v  i  i-   v  ii  i  iiivv    i  v iv    iv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_110618786_   3847 GTAAACAGACAACCCACAGAGAGGGAGAAAATATTCTCAAACTATGCATC 3896
                           i  v              iv             iv    ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_110618786_   3897 TCACAAAGGACTAATATTTAGAATCTACAAGGAACTCAAACAAATCAGCA 3946
                          v i  i     vi   ii     v  i  i      vv    v   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_110618786_   3947 AGAAAAAAACAAATAATCCCATCAAAAAGTGGGCAAAGGAAATTAATAGA 3996
                          v     i        i  v  i?    i           vv v      
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_110618786_   3997 CAATTCTCAAAAGAAGATGTGCAAATGGCCAACACACACATGAAAAAATG 4046
                           v     v         i i           i vi          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_110618786_   4047 CTCAGCATCACTATCAGG 4064
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (51 / 41)
Gap_init rate = 0.02 (9 / 410), avg. gap size = 1.33 (12 / 9)  


2102 24.11 0.56 0.75  chr2_110669717_110671833      511  1041 (1076)    L1M4_orf2#LINE/L1      136   665 (243)  

  chr2_110669717_    511 ATTCTAAAATTTATGTGGAGTCACAAAACACCC-GAATAGCCAAAGCTAT 559
                           i        i  i    ivii   iiv    -           i v  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_110669717_    560 CTTAAGCAAAAAGAACAAAACTGGGGGAATCACATTACCGGATTTCCAAT 609
                            i iv  i         ii   i   v     i v  vi     v  v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_110669717_    610 TATACTGGAGAGCTATAGTAACCAAAACAGCATGGTATTGGCATAAAAAC 659
                         iv    iv i     i     i   i    ii     i        ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_110669717_    660 ACACATATAGACCAATGGAACAGAATAGAGAACCCAGAAACAAAATCCAC 709
                          v         i        i     v    ii       i   -i   i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCAT 334

  chr2_110669717_    710 ACACCTACAGTGAAGTCATTTTCCACAAAGGTGCCAAGAACGTACACTGA 759
                            ii  ii  v  v v      v    i          v i v  v  i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_110669717_    760 GGAAAAGACAGTCTCTTCAATAAATGGTGCTGGGAAAACTGAATATCCAT 809
                              ii i     i     i              v     i   ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_110669717_    810 AATGCAGAAGAATGAAACTAGACCCCTACCTCTCACCATAAACAAAAATC 859
                          -    i         ii i            v       v        i
  L1M4_orf2#LINE/    435 A-TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_110669717_    860 AAATCAAAATGAATTAAAGACTTAAATCTAAGATCTTAAACTATGAAACT 909
                           v        i  i ?    i     v     v  v       i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_110669717_    910 AGTACAAGGAAATGTCTG-GCAAACTCTCAAAGACATTGGTCTGGGCAAA 958
                         vv  v   i   ii vv - i   -   iviv   v    vi i     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_110669717_    959 AATTTATTGAATAATACCCCACAAGCACAGGCAACCAAAGCAAAAATGCA 1008
                         ii   v  ii   vv  v   v       i     v    v      iv 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_110669717_   1009 CAAATGGGATCACATTAAG-TTAAAAAGCTTCTG 1041
                         i    v   iiv   i  i-       -   i  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA-CTTTTG 665

Transitions / transversions = 1.68 (79 / 47)
Gap_init rate = 0.01 (7 / 530), avg. gap size = 1.00 (7 / 7)  

 961 21.40 0.39 2.72  chr2_110669717_110671833     1369  1625 (492)    L1M4_orf2#LINE/L1      658   908 (0)  

  chr2_110669717_   1369 AGCTTCTGTACAGCAAAGGAAAACAGTCAACAAAGTGAAAAGACAACC-A 1417
                          i   i   i vv      - v  vi    v                 - 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGG-ACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_110669717_   1418 CAGAATGGGAGAAGATATCTGCAAACTAACCATCTGACAAGGGGTTAATA 1467
                                      i    i      ii vvi      i     ii vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_110669717_   1468 ACCAGAATATATAAGGGGCTTAAACAACTCTATAGTAAAAAAATCAAATA 1517
                         v             i ii  ivv       v   i      i -      
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATA 805

  chr2_110669717_   1518 TAATAATCTGATCAGAAAATGGGCAAAATATATGAAAAGATATTTCTCAA 1567
                         ----- i ii  i?i            iv  v    v   i       v 
  L1M4_orf2#LINE/    806 -----ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_110669717_   1568 AAGAAAACGTACAAATGGCAAACAGGCCTATGAAAAGGTACTCAATACCA 1617
                              i ii          v  i i  vi        i i     i i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_110669717_   1618 CTGATCAT 1625
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.00 (36 / 18)
Gap_init rate = 0.02 (4 / 251), avg. gap size = 2.00 (8 / 4)  


3162 24.56 1.64 2.08  chr2_110678276_110681763     2085  2996 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_110678276_   2085 TAGAAAGATATCCCATGCTCATTGGTC---AGATTTAATATCATTAAAAT 2131
                          i               i    v i i---   i       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_110678276_   2132 GATCATACTGCCCAATGCAATCTACATATTCAATGGGATCTCTATCAAAA 2181
                          iiv     v     vvii       v      i vi   i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_110678276_   2182 TACCAA-TGTCATTTTT-CAAAGAATTAGAAAAAAC--ATGCTAAAATTA 2227
                          v   i-  i v     -  i -    i-- v  i --  v        v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_110678276_   2228 ACATGTAACCAAAAAAGAGCCGGAATAGCCAAAGCATTATAAAACAACAA 2277
                          i   v  viiv  ii  v  i           i  v v vi  v  v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_110678276_   2278 CAACAAAGCTAAAGCTGTCACATTACCAGACTTCAAATTATAATACAAGG 2327
                         v       i ii  vvv     i v  vi i      viv  v     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_110678276_   2328 CTGTAGTAACCAAAACAGTATGATACTGGTACAAAAATAGACACATAGAT 2377
                           ii     i   i     i  i      i i  ii       i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_110678276_   2378 CAATAGAATAGAAAAGAGAATCCAGAAATAAAGCCACATATT-ACAGCCA 2426
                             i        vv    i            v   i i   - ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_110678276_   2427 ACTGATATTTGACAAAATCAACAAGAACATACAGTGGAGAAAGGACACCC 2476
                          i    v  i     iiviiv     v   v  i   i     i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_110678276_   2477 TTTTCAATAAATGATGCTGGGATAATTGGATTGGCATCTGCAGACGAATG 2526
                                i     i        i  i     v?v  iv    i v     
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_110678276_   2527 AAACTGGACCACCATCTTTTACCATATAAAAAAATCAACTCAAGATGAAT 2576
                           ii      v i i  ivi        v      i       i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_110678276_   2577 TAAAGATTTAAATGTAAGACCCGAAACTACAAAAACACTAGAAGAAAATC 2626
                         i ?   ii           v ii      i    vivi          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_110678276_   2627 TGGGGAAAACTCTTCCGGACATTGATCTAGGCAAAAAATT----GATGAC 2672
                          i  ?iv  v     vv   v   ivi       viiv  ----   ---
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--- 594

  chr2_110678276_   2673 AAAGACCTCAAAAGCACAGACAACAAAAACAAAAATAGGCAAATGGGACT 2722
                         - v   vi          ii        iv        ii    v     
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_110678276_   2723 TAATTAAACTAAAAGGCTTCTGCACAGCAAAAGAAATAATCATCAGAGTG 2772
                          v  i   v v   ii   i  ii vv    i  v iv    vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_110678276_   2773 AACAGACAACCTGCAGAATGGGAGAAAATATTTACAAACTATGTAT--GA 2820
                           v        ii                    i    ii  i   --  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_110678276_   2821 CAGGGGACTAATGTCCAGAATTTACAAGGAACTCAAACAATGCAACAACA 2870
                         i i      vi i        v  i  i      vv    iv   i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_110678276_   2871 ACAACAACAACAAAATAGAAAACAATCCCATTAAACAATAGGCAAAGGAC 2920
                          v  ----i     --------i  i  v   ?  v   i         i
  L1M4_orf2#LINE/    794 AAAA----GACAAA--------TAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_110678276_   2921 ATGAATAGACACTTTTG-AAAGAAGACATACAAATGGCCAAGAGGCATAT 2969
                         v          i  i v-        i              v i   i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_110678276_   2970 GAAAAAATGCTTAACATCACAAATCAC 2996
                              i     i       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (137 / 83)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.62 (34 / 13)  


1803 28.62 7.62 1.12  chr2_110777706_110779698.rev      702  1501 (492)    L1M4_orf2#LINE/L1       57   908 (0)  

  chr2_110777706_    702 ATTCCTCCAAACTTGATCTATAGACCCAGTGCAATTCCAATCAAAATCCC 751
                          i   -     -        i   ii  ii     i  v           
  L1M4_orf2#LINE/     57 ACTCC-CCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_110777706_    752 AGC----------AAAGACACCAATAAAATGTTTCTAAA----------- 780
                            ----------iv   v iii i  iv  v i     -----------
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_110777706_    781 -----------CCTAAAATAGACAATATAAGACTGAG---GAGGAACAAA 816
                         -----------  i i     v   v i  vvi   i---  i       
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_110777706_    817 GATGAAGAATTCACACATCCAGATTCCAAGACTTAT---AAATCT-CTG- 861
                          v  i  i i      v   vi   i   i     i---   v  - v -
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_110777706_    862 ----AAGAGAGTGTAACATTGGGGAAGAAATGGTCACACAGACAAATGGA 907
                         ----    v     iii i   viv iii  i v  i i   iv      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_110777706_    908 ACAATACAGAGAGCCCCTAAATAGACCAACATAAATATAGCCAACTGATT 957
                          i iv iv     i  vv     i   v i i vv   i i   i     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_110777706_    958 CT-GTCAAAGA-GCAAAG-CTGCTCAGTGGAGAAA--AGAGTCTTTTCCA 1002
                         i - v   i i-  v   - iii   i   i    -- v         v 
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_110777706_   1003 TAAATGGTGATGAAACAGCCAGATTACCTTGTGGGATAAAACGAA--TGT 1050
                         i        v  ii   i ii   v?  vii  vi v i  i   --  v
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_110777706_   1051 ACAAACAAACTTTACAACGTACACAAAAATACATACAAAATTATTCATAG 1100
                           v-- vv  i i   v i  i        vv iv      viv   ?  
  L1M4_orf2#LINE/    455 ACC--CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_110777706_   1101 ACTTATAATTTAAAGTAG--AAAACTGTAAAAATTCTAGGATAGAACATA 1148
                           i  -   v   i--  --      i     v ii   i v i      
  L1M4_orf2#LINE/    503 ACCTA-AATGTAAG--AGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_110777706_   1149 GAAGAAAATCTACCTGACCTTGCATTTGGTGATGAGGTTTTATACACAGC 1198
                          i? v      v v        vi  v  ii   ivv i   v i iii 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_110777706_   1199 ACCAAAAGC-CAATCCAGGAAAGGAAAACAT-GATAATGTAGACCTTATT 1246
                                  -   v v vi    i    -  -     vv i   i i  i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATC 648

  chr2_110777706_   1247 AAAACTGAAAATGTCTACTCCATAAAAGACCCCATTAGGAGAATGAAAAG 1296
                             i i    iv i iiv ivi   i   v i  i i  i i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_110777706_   1297 GCAAGGCACATACTGGGAGAAAATATTTGGAAAACATCTA-CTAAAAAAG 1345
                         i   vv    v v                v   v   v  -  i v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_110777706_   1346 GACTGTTATTCAAAGTATACCAAGAAAG--TAAAACTCAACCAGAAGGAA 1393
                             vv   i  i i    iv     vv--  v       iv v  ii i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_110777706_   1394 ACAAACCATCCAAGT-AAAAATGGGTGA-TGATCTGAACAGACACCTCAC 1441
                              iv i    v -         ii -v   i    i     ii  v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_110777706_   1442 CAA-GAATATATAAAGATGGCAAATAAGCATTACCAAAAGCAGCTCAATA 1490
                            -   v     v i     v        i- iv     vv      i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCAC-ATGAAAAGATGCTCAACA 897

  chr2_110777706_   1491 GCATATGTCAT 1501
                         v  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.03 (26 / 852), avg. gap size = 2.69 (70 / 26)  


1803 28.62 7.62 1.12  chr2_111059001_111060993.rev      702  1501 (492)    L1M4_orf2#LINE/L1       57   908 (0)  

  chr2_111059001_    702 ATTCCTCCAAACTTGATCTATAGACCCAGTGCAATTCCAATCAAAATCCC 751
                          i   -     -        i   ii  ii     i  v           
  L1M4_orf2#LINE/     57 ACTCC-CCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_111059001_    752 AGC----------AAAGACACCAATAAAATGTTTCTAAA----------- 780
                            ----------iv   v iii i  iv  v i     -----------
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_111059001_    781 -----------CCTAAAATAGACAATATAAGACTGAG---GAGGAACAAA 816
                         -----------  i i     v   v i  vvi   i---  i       
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_111059001_    817 GATGAAGAATTCACACATCCAGATTCCAAGACTTAT---AAATCT-CTG- 861
                          v  i  i i      v   vi   i   i     i---   v  - v -
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_111059001_    862 ----AAGAGAGTGTAACATTGGGGAAGAAATGGTCACACAGACAAATGGA 907
                         ----    v     iii i   viv iii  i v  i i   iv      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_111059001_    908 ACAATACAGAGAGCCCCTAAATAGACCAACATAAATATAGCCAACTGATT 957
                          i iv iv     i  vv     i   v i i vv   i i   i     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_111059001_    958 CT-GTCAAAGA-GCAAAG-CTGCTCAGTGGAGAAA--AGAGTCTTTTCCA 1002
                         i - v   i i-  v   - iii   i   i    -- v         v 
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_111059001_   1003 TAAATGGTGATGAAACAGCCAGATTACCTTGTGGGATAAAACGAA--TGT 1050
                         i        v  ii   i ii   v?  vii  vi v i  i   --  v
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_111059001_   1051 ACAAACAAACTTTACAACGTACACAAAAATACATACAAAATTATTCATAG 1100
                           v-- vv  i i   v i  i        vv iv      viv   ?  
  L1M4_orf2#LINE/    455 ACC--CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_111059001_   1101 ACTTATAATTTAAAGTAG--AAAACTGTAAAAATTCTAGGATAGAACATA 1148
                           i  -   v   i--  --      i     v ii   i v i      
  L1M4_orf2#LINE/    503 ACCTA-AATGTAAG--AGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_111059001_   1149 GAAGAAAATCTACCTGACCTTGCATTTGGTGATGAGGTTTTATACACAGC 1198
                          i? v      v v        vi  v  ii   ivv i   v i iii 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_111059001_   1199 ACCAAAAGC-CAATCCAGGAAAGGAAAACAT-GATAATGTAGACCTTATT 1246
                                  -   v v vi    i    -  -     vv i   i i  i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATC 648

  chr2_111059001_   1247 AAAACTGAAAATGTCTACTCCATAAAAGACCCCATTAGGAGAATGAAAAG 1296
                             i i    iv i iiv ivi   i   v i  i i  i i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_111059001_   1297 GCAAGGCACATACTGGGAGAAAATATTTGGAAAACATCTA-CTAAAAAAG 1345
                         i   vv    v v                v   v   v  -  i v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_111059001_   1346 GACTGTTATTCAAAGTATACCAAGAAAG--TAAAACTCAACCAGAAGGAA 1393
                             vv   i  i i    iv     vv--  v       iv v  ii i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_111059001_   1394 ACAAACCATCCAAGT-AAAAATGGGTGA-TGATCTGAACAGACACCTCAC 1441
                              iv i    v -         ii -v   i    i     ii  v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_111059001_   1442 CAA-GAATATATAAAGATGGCAAATAAGCATTACCAAAAGCAGCTCAATA 1490
                            -   v     v i     v        i- iv     vv      i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCAC-ATGAAAAGATGCTCAACA 897

  chr2_111059001_   1491 GCATATGTCAT 1501
                         v  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.03 (26 / 852), avg. gap size = 2.69 (70 / 26)  


4205 15.68 5.81 0.58  chr2_111179551_111181674.rev      772  1632 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_111179551_    772 GAAACAAATCCTGTGCTACTAATTTGGAAGGCTTAATATTGTTACGATGG 821
                             v v    ii  i vv iiv       i             v     
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_111179551_    822 CAATATTCCTCAAATTGATATACACATTTAATGCAATCACTACTAAAATT 871
                              i   i         v    v   i  i      v   ii     i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_111179551_    872 ATGGCAGCATTTTTTTTTTTGCAGAAATGGACAAGCTGATCC-AAAATTC 920
                         vii  v  -----i              v             -       
  L1M4_orf2#LINE/    103 CCAGCTGC-----CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_111179551_    921 ATATGGAATTGCAAGGGAACAAGAATAGCTAAAATAATATTGAAAAAGAA 970
                                 v         v v        i    i   v           
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_111179551_    971 ---CAAAGTTAAAGGACTCAC--TTCCTGATTTCAAAACTTCCTATAAA- 1014
                         ---       ii         --    ii            v   i   -
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_111179551_   1015 CAAC--TAATCAAAACAGTGTGGTATTGGCATAACGATAGACATATAGAT 1062
                          v  --       i           i        v               
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_111179551_   1063 CAATGGGATGCAATTGAGAGTCCAGAAATAAACCCACATATTTATAGTCA 1112
                               i  iv                         i i      i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_111179551_   1113 ATTGATTGTTGACACAG-----AAAATTA--AAGTGAGAAAAGT-TCATC 1154
                                v i    vi -----  i ii --v i  i i    v- vi  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_111179551_   1155 TTTT-AACAAATAGTACTGGGATAATTGGATAACCACATACCAGAGAATG 1203
                             -       i  i      i  i      ?      i v i      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_111179551_   1204 GAGTTGAACCCTTAATTCATGCCATATACAAAAATTAACTCAAAATAGAT 1253
                         i     i    i  vi   ii                         i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_111179551_   1254 CAAAGACCTAAA------------AATTATAAAGCTCCTGGAAGAAAACA 1291
                           ?         ------------  i      i   i i          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_111179551_   1292 TAGGC-TAAATCTTCATTAACTTGGATGTGGCAATGGATTCTTAGAAATG 1340
                             ?-         i v v     i vv        v        v   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_111179551_   1341 ACACCGAAAGTATGAGCAACAAAAGAAAAAA---ATAAATTGGACTTTAT 1387
                              i    i ii                 ---             i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_111179551_   1388 CAATATTAAAA-CTTTT-TACAGCAAAAGACATTATCAAGAAAGTGAAAC 1435
                            v       -     - i vv    i    i                v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_111179551_   1436 -ACAGCCCAAGGAATGGGAGAAAATATTTGTAAATCATATATATC-TAA- 1482
                         -   i    vi                   i           v v-   -
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_111179551_   1483 --AC----ATTCACAATATATAAAATACTCTTACGATTCAATAACAAAA- 1525
                         --  ----  i  v          iv        i i       i    -
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_111179551_   1526 GACAAACAACTTGATTGATTAATGGGCAAAGGACTTGAATAGACATTTCT 1575
                               i   iii   ? vv             i                
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_111179551_   1576 CCAAAGTAGATA----AATGGACACTAAGAACATGAAAGGAGCCTCAACA 1621
                               v     ----     v  v    v        i  vv       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_111179551_   1622 TTATTAGCCAT 1632
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.62 (81 / 50)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 2.62 (55 / 21)  


2961 26.13 4.64 1.92  chr2_111236351_111238262      537  1420 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_111236351_    537 TGGTGGGATATTCTATGTTCATGGAGAGGAA-ACTTAATGTTGTTAAGAT 585
                            vii     i i           vv    -       i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_111236351_    586 -----TA------------------------AACGTCATCTCAATCAAAA 606
                         -----  ------------------------    iv   i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_111236351_    607 TCTTGGCAAGTTATTTCATGGATATCAACAAACTGATTTTAAAGCCTATA 656
                           iii  vivi v   iiii  v  ii    i     ii    iiii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_111236351_    657 AGGAGAGACAAAAGACTCACAATAGCCAATACAAAATTGAAGGAGAAGAA 706
                         v   i vi   ii   i  v         v    vv     ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_111236351_    707 CAAAGTTGGAGGACAGCCACT-ACTGGCTTCATGACTTACTACAAATCTA 755
                                       vvv    -v iiii    vi            v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_111236351_    756 CAGTAATTAAAAATGTATAGTGGTGGTGAAAGAACAGACAAATGGATCAA 805
                                i  i vv  i i  iv   iiv   i i     v  i      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_111236351_    806 TGAAACAGAATAGAAAGTCCAGAAATGGACTCACATAAATATAGTCAACT 855
                           i  i     v  i           ii  i  i i vv   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_111236351_    856 GATCTTTGACAAAGGAGCAAAAACAATAAAATGGAGAAAAGATAGCTTTT 905
                            i  i     i  v  v  i  v  vv     i    ii    ii   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_111236351_    906 TCTACCAATGATGCTGTGACAACTGGACGTCAACATACAACCCCCACCCC 955
                           v  v    i     v          ii? v    i   ----- v---
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA-----AA--- 442

  chr2_111236351_    956 CACATAAATCTATACATAGACCTTACACCCTTCACAGAAAGTAACTCAAA 1005
                         -iv  i  vi iv  vivv    i     v vi   i   v         
  L1M4_orf2#LINE/    443 -GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_111236351_   1006 ATGGATCACAGGCCTAAATGTAAAATGTAAAACCATAAAATTCCTAGGAG 1055
                                 ?  i           i vv      i      i  i   i  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_111236351_   1056 A---TCTAGAAGAAAGTCCATATGACTTTGCATTTGGTGATGACTTTTTA 1102
                          ---iv   i? v  i  ivii    i   vi  v  ii   ii  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_111236351_   1103 GATACAACACCAAAGGCATGGTCTATGAAAGAAAGAATTGGTAAATTGAA 1152
                             ii        i   iiiv v ii       i   v i       i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_111236351_   1153 TTTTATTAAAAGGAAAACTTTCTGCTCTGTGAA------TGTCAAAAGGA 1196
                         i  i  i    vv    vi  i  iv  vii  ------ i    i iii
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_111236351_   1197 TGAAAAGGCAAGCCATGGATTGGGAGAAAATATTTGCAACAGACACATAG 1246
                                i   v   ii  v                   --iv  i   -
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA--ATCATATA- 738

  chr2_111236351_   1247 ACACGTCTAATATAAGACTGTTATTCAGAATATACAAAGAACATTTCAAA 1296
                         -----   i   vii    vv   i         i       vi  vv  
  L1M4_orf2#LINE/    739 -----TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_111236351_   1297 CTCAACAATAAGAAAACAAACAACCCCATCAAAAAATGGGCCAAAGACCT 1346
                              i     i  i     i     v  i?          v  i  ii 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_111236351_   1347 TAACAGACACCTCACCAAAGAAGATATATAGCAGGCAAATGAGCATATTA 1396
                         v  i     ii  v              i ivv   v   i    i  v 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_111236351_   1397 AAA-ATGCTCAACATCATATGTCAT 1420
                            -             ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (147 / 80)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 5.27 (58 / 11)  


4059 16.10 1.33 8.41  chr2_111247674_111249960      821  1795 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_111247674_    821 GAAAGGCATCCTATGTTCATGAATTGGAAGACCTCATATTGTTAAAATGT 870
                              ii    i         i          i v          i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_111247674_    871 CAATACTACT-AAAGCAATCCACAGTTTCAGTGCAATTCCTATCAAAATC 919
                                v i-   vii   i    v    ii     i            
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_111247674_    920 CCAAAGATGA--TTTTTGCGGAAATAGAAAAACTCATCCTAAAATTCACA 967
                            -- v  v--       i     v  v  i  v             i 
  L1M4_orf2#LINE/    103 CCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_111247674_    968 TGGAATCTCAAGGGACTCTGAATAGCCAAAGCAATCTTGGAAAAGAAGAA 1017
                              viv        i v           i        i          
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_111247674_   1018 TAAAGTTGGAGGCCTCTCACTTCCTGATTTCAAAATTTACTGCAAAGCTA 1067
                         i           v   v       ii         i     i        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_111247674_   1068 CTATAATCAAAAC--TGTGGAACTGGCATAAAGACAGGCGTAGAGACCAA 1115
                          vi       i  --     v          i  i  i i  v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_111247674_   1116 TGGAATGGAATAAAGAGCCCCTAGAAATAAAACCTCACATAGGTGGTCAA 1165
                               i    vi    i  --         v  vi    vvi       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_111247674_   1166 T-GATTTCTGGCAAGGGTGCCAAGACCATTCAGTGAGGAAAGAGCAATCT 1214
                          -     ii i                     i  i       ii i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_111247674_   1215 TCTCAACAAATGATGCTGGGATAACTGGATATCTACAAGCCAA-GTATGA 1263
                          i          i        i         ? i   v  v  - v    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_111247674_   1264 CGTTGGAAGCTTACCTTACAGCATATCCAAAATTTAACTCAAAATGGATT 1313
                         v      vv i     i   v     v     v                i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_111247674_   1314 AAAGACCTAAATGTAAGAGCAAAAACTAATAAAAAATTCA-AAGAAAGCA 1362
                          ?                  v       -     vvi i -      i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTA-TAAAACTCTTAGAAGAAAACA 547

  chr2_111247674_   1363 TAAAGAAAGGGCTTCTTAACATTGGATTTGACAATGATTTCTTGGATAGA 1412
                           ii?iv iiv    v i  v    i  v i     i      i    vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_111247674_   1413 ACACCAAAAACACAGGCTTTTGAAAAACGTAGATACATTTTTGGAATAAA 1462
                                  i    i  ---------------------------------
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGC--------------------------------- 614

  chr2_111247674_   1463 AATGATCTAATTATTAAAAACAATTTTAAAAAGCATTTAAGTAAAAATTT 1512
                         ------------------     ---------------   v      --
  L1M4_orf2#LINE/    615 ------------------AACAA---------------AAGAAAAAAT-- 629

  chr2_111247674_   1513 ATATAAAAATAAACTGGACTACATCAACATCAAAATCTTTTGTGCATCAA 1562
                         ------ i     i      v      v  i    v         v    
  L1M4_orf2#LINE/    630 ------AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_111247674_   1563 GGGACACTATCAACAGAGTGAAAAGGCAACACATGGAATGGGAGAAAATA 1612
                         i            v i         i    v  ii               
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_111247674_   1613 TTTGCATGTTATATGTCTGATAAGGGATTGATATCCCCAGAATAGATAAA 1662
                               vi i    i            i vi     --      v     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCC--AGAATATATAAA 771

  chr2_111247674_   1663 -AACTCCTACAACTCAACAAGAAAAAAACCAAACAACTAGATTAAAAAAT 1711
                         -     i          i  v     i  -   i   ivi   ?      
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAAT 820

  chr2_111247674_   1712 GGTCAAAG-AGTTGAAGATATAGTTCTTCAAAGA---TAAACAAATGGCC 1757
                           v     - v     v v i v    i      ---  v          
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_111247674_   1758 AATAAACACATAGAAAGATGCCCAACGTCACTAATCAT 1795
                              i     ii        i    i   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (94 / 59)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 5.59 (95 / 17)  


2057 23.75 7.87 4.59  chr2_111252771_111254519      501  1262 (487)    L1M4_orf2#LINE/L1      122   908 (0)  

  chr2_111252771_    501 AAATTTACAGGTTGCTTC-AAAACATATATGGAAATGCAAAAGACCTAGA 549
                              v   i i  v i -    ivi              ii    i   
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_111252771_    550 AGAGTTAAAACAATTCTAAAAAAGGA---CAAAGTTAGAAGACTCAC--T 594
                          v  ii        ii i      i ---       i  i       -- 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_111252771_    595 ACATGACTTCAGCCCTTATATTATAAAGCTGC-----TCAAGGTCATGGG 639
                         v vii i    ivv    i--  i      i -----     iivi  v 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTAC--TACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_111252771_    640 GTATTGGCATAAGGAAAGACA-ATGAGATCAATGGAATGGAATGGCAGGT 688
                            i           v     -  -             i    v vii  
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATAT-AGATCAATGGAATAGAATTGAGAGT 318

  chr2_111252771_    689 TCTGAAAGAAACTCACACATATATGACCAATTGA-----------GTTGC 727
                         i v    v    i  i    v    ii       ----------- v   
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_111252771_    728 CAAGGCAATTCAATGGGAAAAGCAAT-GTCTTGGCAGTAAACGATGCTGG 776
                             i v          i    -   -     vv  ii   i i      
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_111252771_    777 AACAACTAGATAAGCATATGGGAAGAAAGTTAACTTTCATCCCTACCTCA 826
                         i      i    ?v  i   vi  ii  - v  v  vv i          
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCA 466

  chr2_111252771_    827 TGCTACACACAAAA-CTAATTTGAGACACATTAGATGCCTAAAC---AGA 872
                         ii i i i      -i   i ii i iiv  i ? vi      i---   
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_111252771_    873 GACTCAAAAATTACTACATTTGTAGAATAA----TAGAGGAGAATGTCC- 917
                          -  --    i  iv v i iv     v  ----   i? vi   v i -
  L1M4_orf2#LINE/    517 G-CT--AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_111252771_    918 TA---TTAGGATAGGCAGGGGTT-CTTAGAGGAGACTCAAAAATCACTTG 963
                          i---  i  v      iv    -      viv   v v    v   --i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC--A 611

  chr2_111252771_    964 AACATATAAACGAAAATATACTAATGAACTGGTCTACAATAAAATTAAGA 1013
                          i  - i   v     v   --i  i  i   v  v  vi        i 
  L1M4_orf2#LINE/    612 AGCA-ACAAAAGAAAAAATA--GATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_111252771_   1014 ACTGCTGTTCATTAAAAGACATCATTAAGAGAATAAAAAGGCAATGTACA 1063
                            vi   v v i   i    ii  i    i i i     i   ivi   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_111252771_   1064 AAGTAGGAAAAAAT--CTGTAATGCATATATCTGACAAAA-ACTTGTGTC 1110
                         i i i   i     --i  i  vv           i  ii-      i  
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_111252771_   1111 CAGATATAAAGGATTTGTTCCCATACTATATAAAAATCCCTAGAACTTGA 1160
                             ------------------   -    -  i  ii i  v    ii 
  L1M4_orf2#LINE/    759 CAGA------------------ATA-TATA-AAGAACTCTTACAACTCAA 788

  chr2_111252771_   1161 CAATAAAAAGACAAACAGCCCAATTTTAAAAATGTGGCCAAAGACTTGAA 1210
                         i              i i       ?-       -   v  i  i     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTW-AAAAATG-GGCAAAGGATTTGAA 836

  chr2_111252771_   1211 ----CACTT---------------ACAAATGGCCATTAAGCATATGCAAA 1241
                         ----  i  ---------------           v      i   v   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_111252771_   1242 TGTGCTCA-TATCTCTAGTCAT 1262
                         vi      -i   v????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (119 / 58)
Gap_init rate = 0.04 (32 / 787), avg. gap size = 2.97 (95 / 32)  


3966 14.32 3.35 0.94  chr2_111276492_111278229      501  1247 (491)    L1M4_orf2#LINE/L1      144   908 (0)  

  chr2_111276492_    501 ATTCATATGGAAATGCAGGAAACTTAGAATAGCCAAAACAATCTTGATAA 550
                                          i ii  ii                      v  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_111276492_    551 AGAAGAACAAAGTAGGAGGACTCATACCT-GTGATTTGAAAACTTACTAC 599
                                      v          i  i -vii    v            
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_111276492_    600 AAAG------TAATCAAGACAGTGTGGTATTTGAATAAGGATAGATATAT 643
                             ------                   i v v           i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_111276492_    644 GTA-CAATGGAATAGAATGAAGAATCTAGAAATAAATCCTTACAGTTACA 692
                         iv -              vi   i  i         i  v    v   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_111276492_    693 ATCAATTAATATTCCACTGCAGAGCCAAGACAATTCAATGGGGAAAGAAT 742
                         i      i  v   v  vivi v        v                  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_111276492_    743 AGTCTTTTTGACAAATGGTGCTGGGACAAACTAGATAGCCACATGCAAAA 792
                                 ii                   -  i    ?            
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAA 442

  chr2_111276492_    793 GCATGAAGTTGGACCTTTACTGCCTACCATATACAAAAATCAACTCAAAA 842
                          v             ii   iv vi               i         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_111276492_    843 TGGATCACAGACCTAAATGTAAGAGCTAAAACTACACAAATCTTAGAAGA 892
                                ?                          i v  v          
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_111276492_    893 AAACACAGGTGTGAATTTTTGTGACCTGGGTTTAAGCA---GTCTATTAG 939
                              i   ?  i   i  i       v  v   i   ---  i v    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_111276492_    940 ACGTGGCACCAAAAGCACAACTAACCAAAGAAAAAATAGATAAATTGGAC 989
                          ii  i              vi   v                        
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_111276492_    990 TTCATCGAAGTTATAAAAAACTTTT-TGCATCAAAGAACACTATGAATAA 1038
                               i  i   ---         -   v      i       v  v  
  L1M4_orf2#LINE/    643 TTCATCAAAATTA---AAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_111276492_   1039 AGTGAAAA-----CCTACAGAGTGGGAGAAAATATTTGTAAGTCATATAT 1083
                                 -----  i     i                i  i        
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_111276492_   1084 ATTAATATAAGGGTATAGTATCCACAATATAGAAATAACTATTACAGCTC 1133
                         -i i   --    vv v       v      v   v    v     i   
  L1M4_orf2#LINE/    740 -CTGATA--AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_111276492_   1134 AAGAATAAAAAGACAA----CCCAATTTTAAAATGAGCAAA-AATCTGAA 1178
                           v             ----       ?v      i     -i  i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_111276492_   1179 TAGACATTTCACTAAAGA---TTTACAAATGACTGCTAAGCATATGAAAA 1225
                                   v i     --- v        i iiv      i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_111276492_   1226 GATGCTCAATGTCGTTGCCATT 1247
                                  ii  i????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (62 / 41)
Gap_init rate = 0.02 (13 / 765), avg. gap size = 2.46 (32 / 13)  


2154 23.52 17.87 1.16  chr2_111297025_111298811.rev      518  1295 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_111297025_    518 TGAAAAGGTATTCCATATCAATGAATTAGAGGATTCGAGGTTGTTAAGGT 567
                           i    i   i    i iv   i   i  i  i ii vi        i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_111297025_    568 GTCA---CTTT----ATGG-------GACCCTAACAGAATCCCAATCAAG 603
                          v  ---  ii----  v -------  ii -   iv      v     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTC-AACGCAATCCCTATCAAA 99

  chr2_111297025_    604 TTCCCACCAAGTTATTTTCTAGATATTGGCAAACTGGTTCTAAAATTTAT 653
                         v     v vivi v    vi   v    i   i   i i        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_111297025_    654 TTAAAAATGCAAAAGACCTAGAAAAGCCAAAACAATATTGAA---GTAGG 700
                         v ii        ii    i    v            v     --- v  i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_111297025_    701 ACAAAGTTGAAGGATTCACATT----------AGA--TTATTTCAAGATG 738
                                  i    i     i ---------- i --   i v   iiiv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_111297025_    739 ATAGTAATCAAGACAGCAAGGCATTGGAGAAAGAATAGACACCTAAGTCA 788
                          i              iiv  i i   viv   i       iv  ii   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_111297025_    789 ATGAAACAGAAGAGAGAATTCAGAAATATCCCCACATAAATATAATCAAC 838
                            i  i    vv    i i        vv    i i vv   ii    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_111297025_    839 TGAGTT----------------GACTAT---AT----------------- 852
                            v  ----------------   i  ---  -----------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_111297025_    853 -----------------------TTGTATA-------------------- 859
                         -----------------------i  v   --------------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_111297025_    860 --TAGACACAGACCTTACACCTTAAACAAAA-TTCCCTTAAATTGG-TCA 905
                         -- i   v vv    i     v  v      -  vv  i   v   -   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_111297025_    906 AGAACCTAAATGTAAAATGC-AAAACCATAAAAC---------AAAGGAT 945
                         ?ii            i -  -     i       ---------   iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_111297025_    946 A-----AAATCTATATGGCCTTGGGTT-TGTGATGAATTTTTAGATATAG 989
                          -----      vii  i         -v ii   iv  i        ii
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_111297025_    990 CACCAAAAGCACAATCCATGAAAGAAAAAACAAACAAATTAGACTTTATT 1039
                                       v v ii          i i i     i     i  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_111297025_   1040 AAAATTAAAAACTTCTGCCCT----ATGACACTGTTAAGACAATAAAAAG 1085
                                       i  iv  ---- v      i i    v i i     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_111297025_   1086 -----CCAGAGATTGGAAGAAAATCTCTGCAAAACACATACCTAACAAAG 1130
                         -----   v   v   i       v i      v  i   i  i i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_111297025_   1131 GACTGATATCCAAAACATACAAATAACTCTTAAAACT-AACAATAAGAAA 1179
                             vi      i  i   i   v        v    -  i     i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_111297025_   1180 ACAAGCAACTCAACTGAAAATAAAAATGGGCAAAAAGATCTGAACAGATA 1229
                             ii   i   i -----?             i-   i    i   i 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATT-----WAAAAATGGGCAAAG-GATTTGAATAGACA 842

  chr2_111297025_   1230 CTTG-CCAAAAATATATATTCAGAGGGCAAACATGCACATGAAATGATGC 1278
                         i  v-     i - v    v  i v   v  i v          v     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_111297025_   1279 TCAACATCATTTGTCAT 1295
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (119 / 62)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 5.92 (148 / 25)  


1798 24.33 6.90 1.53  chr2_111304221_111307146     1054  1575 (1351)    L1M4_orf2#LINE/L1        1   550 (358)  

  chr2_111304221_   1054 TGGAGACACGTACCATGTTTATACATTGGAAGACTCCACATGATAAAGTT 1103
                             i v ii v       i  iv           iv i  vi v   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_111304221_   1104 GTCAATTCTCCTCA------------GATTTAATGCAATTCCTATCAAAA 1141
                          v    v    i  ------------    i  i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_111304221_   1142 TCTCAGCAAGGTTTTATGTAAATATATCCAGGGTTATTCTAAAATTTATA 1191
                           i    vivv    v  i i v  vvv  i v v  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_111304221_   1192 TGGGAGGGCAAA------AGAATAGATAAA-CAATTCTGAAAAAGAAGAA 1234
                            i iv    i------       vi   -    ii             
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_111304221_   1235 TAAAGTAGGTAGAATCAGTCTACCCAATTTCAAGA-----TATATAGCTA 1279
                         i     v  vi  v   vv  v           i -----  i v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_111304221_   1280 CAGAAATCAAGACTGTGTGGTACTGGCAGGAAGATCTACAAGTAGATCAA 1329
                            v         v              vi i   vv   vi        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_111304221_   1330 TGGAGCAGA-TTAGGCATCCCAGAAATAGAACCAAACCAATT----GCCC 1374
                             ii   -  ii vi   -       i v   v  --   ---- i v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC-AGAAATAAACCCATAC--ATTTATGGTCA 347

  chr2_111304221_   1375 GTTGATTCTTTACAAAGGTGG-AAGAGTGATTCAATGGAGGAAAGATGGC 1423
                         i      i iv    i    v-    vi-         i i  ii  i i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACC-ATTCAATGGGGAAAGAATAGT 396

  chr2_111304221_   1424 CTTTTCCACAAACAGTGCTGGAGTAATTGAACATCCACACATGAAAAAAC 1473
                               v     ii       iii  i  i i ?     iiii   i  i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_111304221_   1474 AA-----GCCTTATACAAGTCTTACACCTTATATAAAAAT-GACTCAAAA 1517
                         i ----- v iiv   ----  i     v    i      -i        
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTAC----CTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_111304221_   1518 GGGGTCACAGACTTAAATGTAAAATTTAAAACCATAAAACTTTTAGAAAA 1567
                         v  i   ?    i         i vi      i        i      i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_111304221_   1568 AAAAATAG 1575
                            v    
  L1M4_orf2#LINE/    543 AAACATAG 550

Transitions / transversions = 1.60 (77 / 48)
Gap_init rate = 0.02 (13 / 550), avg. gap size = 3.38 (44 / 13)  

1079 21.67 3.00 1.00  chr2_111304221_111307146     2135  2434 (492)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr2_111304221_   2135 AAAAAAAAAAAAAAAAAAAGAACAAACTAG-TAAGTTGGACTTCATCAAA 2183
                             iv v  iv  v       v   -   -   i               
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAA 651

  chr2_111304221_   2184 AT-----ACTCTT-TCCCTCTGTGAATACCTTGTTACAAGGATGAAATGA 2227
                           -----   i  - v i  viv i i  -- i i vi iii     v  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACAC--TATCAAGAAAGTGAAAAGA 699

  chr2_111304221_   2228 CAAGT-GCAGACTGGGAGAAAATATTTACAAATCACATATCTGACAAAGG 2276
                            vi-i    v               i       i        i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_111304221_   2277 ACTAGTATGTAGAATATGTTAAGAGCTCTCAAAACTCAACAATAAAA-GC 2325
                            v    vi       i v    i    i v       i       - v
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_111304221_   2326 TGAACAATCCAATTATAAAATGGGTAAAAGAGATTAAGAGCTATTTATCT 2375
                         ii  i  i      ?v        i   i  vv v  v  vi    v  i
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_111304221_   2376 GAAAAAGACATACAGATGGCAAATAAGCACATGAAAAGATGTTTAACATC 2425
                         i  i    i     i     v                    i i      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_111304221_   2426 ACTAGCTAT 2434
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.56 (39 / 25)
Gap_init rate = 0.02 (7 / 306), avg. gap size = 1.71 (12 / 7)  


 401 27.10 0.00 0.00  chr2_111322678_111324830      501   607 (1546)    L1M4_orf2#LINE/L1       64   170 (738)  

  chr2_111322678_    501 AAATTGATCAGGAGATTCAACACAGCTCAAATTAAAATCCCAGTAAGATT 550
                                  viv         i  iii vv  i          ivivv  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_111322678_    551 TTGTGTAGAAATTGGCAAGATAATTCAAAAAATTTTATGGAAAGGCAAAA 600
                           v  i        i    v i  i v    v iv        v    ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_111322678_    601 GACCTAG 607
                             i  
  L1M4_orf2#LINE/    164 GACCCAG 170

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.00 (0 / 0)  

2310 24.83 3.07 3.07  chr2_111322678_111324830      913  1661 (492)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr2_111322678_    913 AACAGAACTAGACCAGCCAAG-CAATTTTGAAAAAGAA---CAGAGCTGG 958
                           vi  v i   vi      i-    i           ---  i  i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_111322678_    959 AAGACTTCCAGTACCTCATTTTCAGAA-TCGCTGTAAAGCTGCAGTAATC 1007
                          i    iv  v v  -  v     i  - ii  ii      i        
  L1M4_orf2#LINE/    210 AGGACTCACACTTCC-CAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_111322678_   1008 AAGAGCAGACTATAGGACATGTAGGCAAAAGGACAGACTTGTAGTCCAAT 1057
                             -   -- i i v  -  ---   v     i    v i   vi    
  L1M4_orf2#LINE/    259 AAGA-CAG--TGTGGTAC-TG---GCATAAGGATAGACATATAGATCAAT 301

  chr2_111322678_   1058 GGGACATAGGA---AGAAGTCAGGAGCAGACCC-CACATGAATGATCAAT 1103
                           i --   i ---   ivi   i ii i    -i    vv   i     
  L1M4_orf2#LINE/    302 GGAA--TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_111322678_   1104 GGATTTTCAACAAAGGCGCCAAAATGATTCAGTGGAGAAAGGATAATCTT 1153
                         v       i    i  i     i iv     i   i     i   i    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_111322678_   1154 TTAAATAAATGGAGC------AATTGGACATCCATATAAAAATTCAAAAA 1197
                           v  i      v  ------  i    i ?   i  iv   ---- i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA----AGAA 445

  chr2_111322678_   1198 CCAAGAAAAACCCATACCACATACCTTGTAGCATGTACAAGCAAC-AAAG 1246
                         iv   vvii    v    v  i   v i  -  --- v  vi   -v  i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATA-CA---AAAATTAACTCAAA 491

  chr2_111322678_   1247 ATGGATCATGAACCTAAATGTAAAGCCTAAAACCGTAAACCTTCTGGAAG 1296
                                 ?ii            iiv       ii    v  ii i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_111322678_   1297 AAAACATAGAAGAAAATCTTTGTGGTCTTGGCTTAGAGAAAACTTTCTTC 1346
                                  i? v       i   ii     v    iv  viv      v
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_111322678_   1347 A----GACACAGAAAGTATGAACTGTCAAGGAAAAAGTTGGCAAAAATGG 1392
                         i----     vi    i ii i viiv  i      i v ii   v-   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT-TGG 640

  chr2_111322678_   1393 ATTTTATCAAAATTAAAAACAGCTGCTCTTTGAAAAACACTG-CAAAGAA 1441
                          i  i               vvi  iv   ii  ii     i-   ii  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_111322678_   1442 ATAAAAAGACAAGCCACACATGGGGACAAAATATTTGTAAAACACATATC 1491
                         i i         v     v vv    v          i   v  i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_111322678_   1492 TGATAAAGAAGTTGTATCCAGAGTATGTA--GAACTCTTACAGCCCCTTC 1539
                               i i v           i   i  --           i i vv v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_111322678_   1540 ACAAGAAAATGAAACAACTCAATGTAATAAATGGGCAAAAAATACTCGAA 1589
                          i  i  i i-   i   i    v?  -           ii  -- i   
  L1M4_orf2#LINE/    791 ATAAAAAGAC-AAATAACCCAATTWAA-AAATGGGCAAAGGAT--TTGAA 836

  chr2_111322678_   1590 CTGATTATTCACCAAACAAGATGCATAGATGGCAAATAAGACCATGAAGG 1639
                         iv  ivv   v     v     ii i i     v      vv      ii
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_111322678_   1640 GATGCTCACCCTCATTAGTCAT 1661
                                 v v   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (117 / 65)
Gap_init rate = 0.03 (23 / 749), avg. gap size = 2.00 (46 / 23)  


4329 16.40 3.03 3.26  chr2_111363366_111365549.rev      805  1694 (490)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr2_111363366_    805 ATAAATGGAAAGAC---ATTTTATGAAAATGGCAATACTTCCCAAACTGA 851
                           ii  v i     ---  v  i v  i           i      i   
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr2_111363366_    852 GCTGCAAGTTCAATGTAATCTCCATCAGAATCCAAGTTTCCTCATTTTTC 901
                         v  i  ii     i i    i i    i     v  i v   i-    v 
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT-TTTTGC 119

  chr2_111363366_    902 AGATATCAACAAGATG-TACCGAAATTCACATGGGAATTAGAAGGGGCCC 950
                            v  ii     v  - v ii       i    i   -iv     i   
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT-GCAAGGGACCC 168

  chr2_111363366_    951 AGGAGAGCCAGAGCAATCTTGAAAAAAAAGAATAATGTTGAAAGACTCAC 1000
                           i v     i i             i     i  v    i i       
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_111363366_   1001 ACTTCTCAATTGGAAAACTTGATACACAGCTACAGTAATTGAGAAAAGGT 1050
                              i     vv       iv    v            ii   v iv  
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_111363366_   1051 GATACTGGCATA-GGATAGACATATAGATCAATGGAATAGAATTGAGAGT 1099
                          i          -                                     
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_111363366_   1100 CTAGAAATATATCCTTATATTTATT-TCCATTGATTTTTCCTCAAGAGTG 1148
                          i       v i  v  i      v-  v         - vv    i   
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTT-CGACAAGGGTG 367

  chr2_111363366_   1149 CCAAGATAAACAAATGGTGAAAGAATAGTCTTTTCAATGAATAGTACTGA 1198
                               iv viv     v                   ii   i  i   i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_111363366_   1199 AATAACTGGATATTCACATGAAAAAGAAAGAAGTTTGAGCCCTTCCTCAC 1248
                         i i         ?i      v       v      v  v    v      
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_111363366_   1249 ACCATACACAAAA-TTAACTCAAAATGGATCACAGACCTAA-TGCAGGAG 1296
                               i      -                  ?        -  i i   
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_111363366_   1297 TTAAAACTATAACACTCTTAGAAGATAGCATAGCAGCAAATCCTCATGAC 1346
                         i           v            v i     v? i     i  i    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_111363366_   1347 CTTGGATTAGGCAATGGTTCCTTAGGTATGATACCAAAAGCA-------- 1388
                              i             i     i     i          --------
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_111363366_   1389 --AAGA---------TAAGCTGGACTTCATTAAAATTAAAAACTTCTGTG 1427
                         --    ---------   ii          i              i    
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_111363366_   1428 CTTCCAAGGATGTCGTCATCAAGAAAGTTAAAGAAAATCATCAAGAAAGT 1477
                             v     i------------------------- ii           
  L1M4_orf2#LINE/    668 CTTCAAAGGAC-------------------------ACTATCAAGAAAGT 692

  chr2_111363366_   1478 GAAAAGACAATCTACAGAATGGGAGAAGATATTTGCAAATCATATCTCTC 1527
                                   i i              i                 v   v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_111363366_   1528 ATCATGGAATGATATCTGGAATATATAAAGAACTCATCCAACTCACTAAT 1577
                           v v   v vi    ii                 v v       v    
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_111363366_   1578 AAAAAGATCAATAACAAAATTTTAAACATGGATAAAGAATCTGAACAGAC 1627
                                iv      vv    ?-   v    ii    i  i    i    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_111363366_   1628 CTTTCTCCAGAGAAGGTATACAAATGGCTAATAAGCACATAAAAAGATGT 1677
                         v        i     i            i           i        i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_111363366_   1678 TCAATATAATTAGTCAT 1694
                             i  v ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (89 / 53)
Gap_init rate = 0.01 (13 / 888), avg. gap size = 4.31 (56 / 13)  


 868 22.05 6.83 2.48  chr2_111384363_111387326      139   460 (2504)  C L1M4_orf2#LINE/L1   (0)   908   573  

C chr2_111384363_    460 GTTATAGCAATG---TCTTAGAAAAGACACAGAAAGCAATAATCATAAAA 414
                             -i      ---       v v     vi      vv iiv i    
  L1M4_orf2#LINE/    573 GTTA-GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

C chr2_111384363_    413 CAAGAAAAGGATAAATTAGACTTAAGCAGTATTAAAA--TTTTCTGCTCC 366
                         v  i   vi        i     v v  iv       --    v    i 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

C chr2_111384363_    365 CCCAAATAACATTATTAAGAAAATAAAAAGGCAAAATCCACAC--TGACC 318
                         ---   vi   i   i      i i     i   --i     v--  ivv
  L1M4_orf2#LINE/    672 ---AAAGGACACTATCAAGAAAGTGAAAAGACAA--CCCACAGAATGGGA 716

C chr2_111384363_    317 AAAAATATTT--AAA--ATA-----AGTAAGTG-CTTGTTTTTGTTATAA 278
                         i         --   --   -----ii    v -     v iiivv   v
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

C chr2_111384363_    277 ATAAA---CTCTTATAAGTCAATAACAATAAGATAAACAAGTCAATTTAG 231
                              ---      i  v       i  v    i   i  vi     ? -
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA- 815

C chr2_111384363_    230 AAAAATATGCAAGAGATTTAAATAGATCTTTC-ACAGAGAAGATATACAA 182
                         -     iv    ii     i      iv    -v  i             
  L1M4_orf2#LINE/    816 -AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

C chr2_111384363_    181 -TGGCCAATGTGCACATGAAAAAGTACTCAATGTCGACAGCCAC 139
                         -        iv           ii i     ii  i????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (42 / 28)
Gap_init rate = 0.04 (14 / 336), avg. gap size = 2.14 (30 / 14)  

4362 17.12 2.83 1.47  chr2_111384363_111387326     1591  2472 (492)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_111384363_   1591 ATGTTCATGGATCAGAAGATGTAATGTTGTTAAGGTGACTATACTCCCTA 1640
                                     ii     iv    i        i  i v        i 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_111384363_   1641 AATTAATCTGTAGATATAAAGCAGTCTCTATCAAAATCCCAGAAACCTGA 1690
                             i    ii    vi  v   i  i               vvi   --
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT-- 112

  chr2_111384363_   1691 TCTTTTTAGAAATTGACAAGCTGATCCTAAAATT--TATGGAAATATAAA 1738
                          i   vi                           --         ii  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_111384363_   1739 GGAACCAGTATAGCCACAACAATCTTGAGAAAGAGTAACAAAGTTGGAAG 1788
                            v    v       v           i     iv            i 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_111384363_   1789 GCTCACATTTCTCAATTCAGAAACTTAATATGAAGCTGCAGTAATCAAGA 1838
                         i      i   i     ivi       v  ii     i            
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_111384363_   1839 CAGTGTGGTACTGGCATT-GGATAGATACACAGGTCAACAGAATTAAATC 1887
                                          v-       i i i  i    ii    vi   i
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_111384363_   1888 AAGAG-ACAGAAACACATCCCTAAATTTATGGCCAGTTTATTTTTTACAA 1936
                         i    -v      i v i  v  v        i  i  v     iv    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_111384363_   1937 AGATGCTAAGACAATTCAATGAAAGAAAGAATACTCTTTTCAATAAATGG 1986
                         i i   i     v        ii-         v         i      
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_111384363_   1987 TGCTAGGACAACTGGATATTGATATGCAAAA-AATGAAGTTGGACCCCTA 2035
                             i             ?iv i        -                  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_111384363_   2036 ------------TACAGCAGTTAACTTAAAATGGAGCATAAGCCTAAATT 2073
                         ------------    iv i      i        v  ? ii       v
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_111384363_   2074 TAAGACCTAAAACAATAAATCTCTTAGAGGAAAACA--GGAGCAAATCTT 2121
                              v       v     v        i       --  ? i       
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_111384363_   2122 TGCAACTGTAGGTTAGGCAGTGGTTTCTTAGATAGAATACCAAAAGCACA 2171
                         i ii  iv i         i              vi i            
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_111384363_   2172 ATTA-CAAAAGAAAAAAGTGTATACATTGGACTTCATAAGAGGTAAAAGA 2220
                          vi -            - iv   v            v i iv     i-
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAA- 659

  chr2_111384363_   2221 TTTTTTGTGCTTAAAAAGTCACCATCAAGAAAGTGAAA-GACAATCCACA 2269
                         -i          v   i v   i               -     i     
  L1M4_orf2#LINE/    660 -CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_111384363_   2270 GAATAGGAGAAAGTATTTTCAAATTATATATCTGGTATATACATCTGGAC 2319
                             i       i     v     i         i  vi-------    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG-------GGAC 751

  chr2_111384363_   2320 TTGTATCTAGAACATACAT-GAATTCTTTCAATTCAACAATAAAATGACA 2368
                                i    i   i v-   i    v   i    i       v    
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_111384363_   2369 AATAATCCAATTGAAAAATGGGCAAAG-ATCCAAA--GACTTTCCTCCAA 2415
                              i      ?              -  iii  --   v  i      
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_111384363_   2416 AGAAGATGTACAAATAACCAATAAGCACATGAAAAAGTTCTAAAAGTCAT 2465
                                i       ii                  ii v  v  vi   ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_111384363_   2466 TATTTGT 2472
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.06 (99 / 48)
Gap_init rate = 0.02 (16 / 894), avg. gap size = 2.38 (38 / 16)  


2367 30.43 2.17 0.92  chr2_111485854_111489670     2444  3317 (500)    L1M4_orf2#LINE/L1        1   885 (23)  

  chr2_111485854_   2444 TGGAGTAGTATGCTGTGCTTGTGTATGGGAAAACTCCACATTGCCATAAT 2493
                             ivii   v ii  i ii  v  v    i   iv i    ii vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_111485854_   2494 GTTCATCCTCCTGAAATTAGCCTATAGATTCAGCACCATTTCAAGCAAAA 2543
                          viv  v    iv     iii   i       i i v  ii v v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_111485854_   2544 TCTTGGCAGGAATGTTTGTAGAAACTCATAAGCTGATTTGACAAT-CACA 2592
                           iii  v vvv v    i     i v i        iiv v   -  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_111485854_   2593 TGGAAATGTGAATGGCCTAAAATAGCCCAAACAA-CTTCAAAAAACATTG 2641
                                 ii iv i  i i       v      -   v     iv -- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA--G 198

  chr2_111485854_   2642 AAGAAATGTAGAGGGATTGTACTACCTGATTTCAAAGCTTGTGCTAATGC 2691
                           v   vv i    iv iii   v  ii        i   iivvi  v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_111485854_   2692 TTCAATAATACAGACA---TGGTACTGGCATCAGAATAAGCAGAGAGATC 2738
                          v  i    vv     ---            v  i   ii  v v     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_111485854_   2739 AATGGAACACTAC--AGAGTCCAGAAATTGACCCACATGTATATGTTCAC 2786
                                i vv i--             vi     i ii v    v   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_111485854_   2787 TTGATTTTTTGACAAAGGTATGAAGGAAATTCAATGATGAAAAGAAT--- 2833
                                 i-     i   iiv   ivv        i- i       ---
  L1M4_orf2#LINE/    349 TTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGT 396

  chr2_111485854_   2834 -TTTTTAATA----GTGCAGGAAACATCTAGATATCTGAAGGAAAATAAA 2878
                         -    i  i ----    v  i -  v  i    ? iiv v v   vi  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGA-CAACTGGATAKCCACATGCAAAAGAA 445

  chr2_111485854_   2879 TTAACTGTGACCTTCTTTTCTGCATAATACACAAAGGTTAATTTGAGATT 2928
                          v  v vv    iiivii  -i  iv   i     ii    i ii i  v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTC-ACACCATATACAAAAATTAACTCAAAATG 494

  chr2_111485854_   2929 GATCATAGACTTCAATGTAAAAGGGAAAAACTATAAACTTCTCAAAAGAA 2978
                              ?    i v       i  vv    -       vi   i i     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAA 543

  chr2_111485854_   2979 AACATAGGAGAATATCTTTGGGAAGTTGGCATAAACTGAGATTTCTCAAA 3028
                                 ? v v     i v  vv    vv  ii viv i     i i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_111485854_   3029 AA-GACACAAAAAGTACTAATTGGTAAATTAAATCTTGATAAATTGAATC 3077
                         v -     v     i  v iivivv   vv   vv v         i - 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA-C 642

  chr2_111485854_   3078 TTTTCCAAAAGTGAACATTTTTCTTCTCTAAAAGATATCATTAAGAACAT 3127
                           ivi     v i  v i    v v  ii   i  i ii  i     vi 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_111485854_   3128 ACAAAGACAAACCATAGCCTTGGAGAAATTATTTGCAATACCTGTATCTG 3177
                         iv        v   i  vv v       v         vv v i      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_111485854_   3178 GCAAAACACTTCTATCCAGAATATATAAAGAATACCTACAATGCAATAAT 3227
                         ii  iiv    v                    iv i     iv       
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_111485854_   3228 GTATAGATA--CAACCCAGG-AAGAATTGCACAAAAAGCTTTAAAAGATA 3274
                         iv v   i --i      iv-? i  v  vi    iiii  v  v   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_111485854_   3275 TCTCATAAAAGAATATAAAAGAATGGTTAATGAGCACATGCAA 3317
                          i  viv      v   v vi     ii   i        v  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

Transitions / transversions = 1.24 (145 / 117)
Gap_init rate = 0.02 (16 / 885), avg. gap size = 1.69 (27 / 16)  


2546 23.25 7.95 4.27  chr2_111498875_111502949.rev     2733  3575 (500)    L1M4_orf2#LINE/L1       16   889 (19)  

  chr2_111498875_   2733 TGTTCATAGGTCAGAGAACTCGATATTGCTAAGATGTCACTTCTCCCCAT 2782
                                i i ii  ii   ii      i       v  v v       v
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_111498875_   2783 ATTGATCTATAGATGCAACACAATGCCAATCAAAATGAATGCCAGCAGAC 2832
                                  i    v    i    v  v        v----     v - 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATC----CCAGCTG-C 110

  chr2_111498875_   2833 CTTATTTTGTGTGAGTATGGTAGAACCAT--ACAAGCTAATTAGAAAATT 2880
                            -     i-----------    --  --       i  ivv      
  L1M4_orf2#LINE/    111 CTT-TTTTGC-----------AGAA--ATTGACAAGCTGATCCTAAAATT 146

  chr2_111498875_   2881 TGTAAAAGAATACAGAGGACCTAGAAAAGTCAAAACCATTTTGAGAAAAG 2930
                         ii  viii   i  ii     i    v  i      v  i    -     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAG 195

  chr2_111498875_   2931 AAG--CA---TTGGAGGATTCACACTGCCTCATTTTAAGGCTTCCTATAA 2975
                            --  ---        i       v  iv    i  ii   v   i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_111498875_   2976 AGCTATAGTAAACGCAACAGTACGGTATTGGGGTAAGGATAGAAACATGA 3025
                              i     v ivi     ii    i   vi          v i  ii
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_111498875_   3026 GTGAATAGAACACAGTAGAGAGTTCAGAAACAGAGCCACATATGTATATG 3075
                         i v   i   i v i v      i      i i v   i i  - -    
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-T-TATG 343

  chr2_111498875_   3076 GTCTACTGATTTTCTACAAAGGTACCAAGGTAATTGAATGAGGGGAAAAC 3125
                            v i        v    i   i     iiv   v    i  ii i  i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_111498875_   3126 AAT-TTTTCAACAAATGGCACTAAAACAATTGAACATCCACATGAAAAAA 3174
                          i -              ii  iii    i  i i ?       v    i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_111498875_   3175 CAAAGAAATAAATGAACCTTATCCTTTACTTCATACCATATACAAAAGCT 3224
                         -  v   i ---  i   ----   --  i   i             ii 
  L1M4_orf2#LINE/    444 -AATGAAGT---TGGACC----CCT--ACCTCACACCATATACAAAAATT 483

  chr2_111498875_   3225 AGCCCAAAGAGAATCATAGACCTAAATGTAAACACTAAATCTACAAAGTT 3274
                          i i    iv i    ?              ivi     v   i   ii 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_111498875_   3275 TCTAGATGAAAACCTAACAGAAAATCTTAGTGACCTTGGTTTAGAT---- 3320
                         ii    v      v  iv? v       v          v    ii----
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_111498875_   3321 -TTTGTGAGATAAGACAC------------------------AAAT---T 3342
                         -   v v     v     ------------------------    --- 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_111498875_   3343 ---TTGAATGTTTTCAAAATTTAAA--T---------------ACACTGT 3372
                         ---   i iv iv        v   -- ---------------     i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_111498875_   3373 GAAGCAAATGAAAAGGCAGGTAATGGATGAGGCAAAAATCTATGCAATCT 3422
                         v   v  i       i  iviv ii  vvi  vi     v v     -v 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA-AT 732

  chr2_111498875_   3423 CATATA----ATAAAGGATTTCTGTACAGAATTTGTAAAGACATCT-ACA 3467
                               ----    i   i  v i v      v i      vv   -   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_111498875_   3468 GCTCAGTCACAGGAAAACAAA--ACCCAGTTTAACAGATGGACAGAAAAT 3515
                         i    i v i ii  i     --     i  ?  - i    i  i ii  
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGAT 831

  chr2_111498875_   3516 CTGAACACACACTTCACCAAAGAAGACAAAATGAATAGCAAATAAACACA 3565
                         i    i v   i   v          i v -ii   i  v     i    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATA-CAAATGGCCAATAAGCACA 880

  chr2_111498875_   3566 TGAAGAAGAT 3575
                             -     
  L1M4_orf2#LINE/    881 TGAA-AAGAT 889

Transitions / transversions = 1.91 (126 / 66)
Gap_init rate = 0.03 (29 / 874), avg. gap size = 3.55 (103 / 29)  


2583 26.51 2.86 2.97  chr2_111535280_111540079     3400  4308 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_111535280_   3400 TGGAGAGATATACCATATTCATCAATTGGAAGATTCAGCATAGTAAAGAT 3449
                             i      v    i     vi         i i ii  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_111535280_   3450 ATTATTTATCCCCATATCGA-ATACAGGTTTAACCTAATTTTTATCAAAA 3498
                         ivi v vv      v  i  -v     i  i   vi   iii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_111535280_   3499 TTTCAGCAAGATTTTTTTATTGCTATAGACAAACTTATACTGAAATTTAT 3548
                          ii    v- vi      iiv vv  v     i  v  v  i     i  
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_111535280_   3549 ATGGAAAGGCAAAGGAACTAGAATAGCTAAAACAATTTTGAAAAAGAA-- 3596
                                v    i   v i        i        i           --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_111535280_   3597 -TAAAGTGGGAGGAATCAGTCTATCCAATTTTAAGACATAT-----AACT 3640
                         -i     v      v   vv  vi       i  i  v  i----- i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_111535280_   3641 ATAGTAATGAAGACTGTATGGTATTGGCAGGTGAATACACACATAGAACA 3690
                          i      v     v  i     i     viv i   v   i     v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_111535280_   3691 ATGGATAAAAATAGGGAGTGCAGAAATAGACCCATACCAACATGCCCAAC 3740
                              vv i   v i    v        i        vvvi   vi   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_111535280_   3741 TGATTTTTTTATGAAA-TGGCATGAGCAACTCCAGTGAAGTAAGA-TAGC 3788
                                iv- ii ii-  v  v  v  -- i  i  ii v    -   i
  L1M4_orf2#LINE/    350 TGATTTTCG-ACAAGGGTGCCAAGACCA--TTCAATGGGGAAAGAATAGT 396

  chr2_111535280_   3789 CTTTTCAACAGATGGTTCTGGAATACTTGAACATCCATAGGCAAAATAAG 3838
                                   i     v    i i vi  i i ?   i v      v  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_111535280_   3839 AAAAATTAAAGAACCTTAATCTAAGTTCCACATTTTATATGAAATTTAAC 3888
                         i  i-  --- i   iiv i  ------    iiv    ii   v     
  L1M4_orf2#LINE/    447 GAAG-TT---GGACCCCTACCT------CACACCATATACAAAAATTAAC 486

  chr2_111535280_   3889 TCAAAATAGATCATGGACTTAAATGTACATAAAATGTAACACTGCAAAAA 3938
                                i     ?i   i        --- i ii-   v   ii    v
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTA---AGAGC-TAAAACTATAAAAC 532

  chr2_111535280_   3939 CTTTAGAAGTAAACATATAGAAGAAAACCTTTGGCAACTATGGTTAGACG 3988
                         ii       v       -- i? v   i   i vv v  vv      i i
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATA--GGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_111535280_   3989 GTGAGCTCTTAGGGTTCACACCCAAAGCGTGATTCATAAAAGGAAAAACT 4038
                         i  ivi      ivv v     v     iii viv i     i     iv
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_111535280_   4039 GATAAACAGGACATCATCAAAATTAAAAGCATTTGTTCTGTGAAAGACTA 4088
                               iv    v               i v     v  vii  i   vv
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_111535280_   4089 TGTTCAGAGTCTGAAAAGACAAGCTACAGTCTGGGATA---TGTTTGCAA 4135
                          i iv   ivv           v i    vv     v --- i       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_111535280_   4136 AGCACATATCACACACTAAGGCA-TAGTACCTACAATATACAAGGAAC-- 4182
                          v  i     vv ---     v - v   i i v      i  i    --
  L1M4_orf2#LINE/    731 ATCATATATCTGA---TAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_111535280_   4183 ----AA-TCAAATGTAAACAGGTTTTTAAA-AATCCAGTTAGGAAAAGGG 4226
                         ----  -    vvi    v  ii----   -  i   i  ?ii   v   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGAC----AAATAACCCAATTWAAAAATGGG 823

  chr2_111535280_   4227 CAAAAGATAAAAACAGGCGTTTCACTCATGAGGCTAGA--GACGGCAAAT 4274
                             i   vvi  i  i i    v iv v  i v  v --i i   v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_111535280_   4275 AA-CGCATGAAAAGACATTCAACATCATTAACCAT 4308
                           - i          iii         ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (134 / 103)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.30 (53 / 23)  


2588 27.01 2.03 1.69  chr2_111546319_111550919.rev     3225  4109 (492)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr2_111546319_   3225 ATGGATCGGAAGAGTCAACATAGTACATTTGTTAATTCTTCCCAAACTGA 3274
                               i      v i  i  v  vv vv  vi   v  i      i   
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr2_111546319_   3275 TCCATAGATTTTTTATAATTCCAATCAAAATCACCAA-TGAATTTTCTGT 3323
                           i i     ivviii   i  v         -   i-  vv    i  i
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATC-CCAGCTGCCTTTTTTGC 119

  chr2_111546319_   3324 AGATAGAGACAAAATGATTCTAAAATTTGCATGTAAAAGAAAAGAAACTA 3373
                            v vv     iv    i        iii   v   v v  i i v i 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_111546319_   3374 GAATCACTAAAACAAT-TTGCCAAAGATGAATAAAGTCAGAGGAATTATC 3422
                             vi i        -   vv     v   i     ii     v i iv
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_111546319_   3423 TTATTTGATTTTAAGGCTTAGTATAAAGTTATACTAATGAAGATAGTGTG 3472
                         i viiii    i  ii    v  i    i  i v    v    i      
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_111546319_   3473 GT--TG----AGAAATATACACGTAGGTCAATGGGAACAAAATATAAAAA 3516
                           --  ---- iii   v   ii   i       -  i i   - i i i
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGG-AATAGAAT-TGAGAG 317

  chr2_111546319_   3517 TCCAGAAATAATTCTACACAAATATGTCCAAATATTTTTTCACAAAGATG 3566
                                    vi i i   vv    vi   v iv    iv    i i  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_111546319_   3567 CAAAAGGAATTGAATGAAGAAAGGATAGTATTTTCAACAGATATCACAAT 3616
                          v  iivv   v    ii     i     v         i  ivii vi-
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG- 416

  chr2_111546319_   3617 AGTCAATTTGATATC-ACAATAGTCAAAAGA-TAAGCATATCTTGACCTA 3664
                         i v   i v    ? -   - i--       - i ---- vi v    iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACA-TG--CAAAAGAATGA----AGTTGGACCCC 459

  chr2_111546319_   3665 AACTTCACATCTTACAGACAAATCAGGTCAAAATGAATTATAAATCTAAA 3714
                         v  i     i v  i v v    i iv        i  i ? i i     
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_111546319_   3715 TGTAAAACAAAAAAACTCTTAAACTTTTAGAAAAATA-ATGAGATAAAAC 3763
                              i -ivv      v v     i      i  v -  ii ?vv   i
  L1M4_orf2#LINE/    510 TGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_111546319_   3764 CTTCATGACTTGAGGTTTAACGAAGAGTTCTTAGGTTTGGCATCAAAAGC 3813
                             i    i vi    vii i v iv       i v  i  i       
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_111546319_   3814 ATAACTCATGAAAGAGAAAAATGGATAAATTGGATTTCATCAAAATAAAA 3863
                          i  viv ii     -      i           i           v   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_111546319_   3864 AACTTTTCT-CTGCAAAAGGCACTGATAAGGAAATGAAAATACATACTAT 3912
                                v -  v    i i    ivi   i  i      v   vv i i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_111546319_   3913 ACAATGGGAGAAGATATTTGCAAAAGTCACATATCCAAAAGAGAATTTGT 3962
                          v          i           --   i     ii v ii i i    
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAA--TCATATATCTGATAAGGGACTTGT 755

  chr2_111546319_   3963 ATTTAGAATCTATAAATAACTCTCAAAGCTCAACAGTAGGAAAACAAATT 4012
                           ii     v      v      i v i     i i  ii  i      v
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_111546319_   4013 ATCCAATT-AAAAATGGGAAAATGATTTTATCAG---TTTCACTAAAGGG 4058
                          i      -         v   v     v vi  ---    v i    ii
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_111546319_   4059 GATA--CATATGGCAAACAAGCACATCGAAAGATTTTCAACAGCATCAGC 4106
                             --  v     v  i        vi      vi      v  ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_111546319_   4107 TAC 4109
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.02 (21 / 888), avg. gap size = 1.57 (33 / 21)  


3100 24.92 3.35 1.90  chr2_111557987_111562361     2989  3883 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_111557987_   2989 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGATAAAAT 3038
                               i i  i     i        v      v i       v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_111557987_   3039 GGCCATCCTGACCAAAAC-ATTTACAGATTTAATGCTATTCCTATCAAAC 3087
                            v  v  vv     vi-  i        i  i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_111557987_   3088 TATCAATGACATTCTTCACAGAAGTAGGGAAAGCTG-TTTTAAAATTCAT 3136
                          vi  iivi v  i  ii     i -v iv      - ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_111557987_   3137 ATAGAACCAAAAAAGAGTCCAAATAGCCAAGGCAATCCTAAGCAAAAGGA 3186
                           i   viiv  ii  vi vi         ii     i i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_111557987_   3187 ACAAAGTTGGAGGCATCATATTACTCAACTTCAAACTGTATTACAGA--T 3234
                                      vv   i i v i   i      viv  i    i -- 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_111557987_   3235 ACAGTAACCAAAATAGCATAGTACTGGTACAAAAACAGACACATAGACCA 3284
                                i   i i  ii i       i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_111557987_   3285 ATGGTACAGAATAGAGAGCCCAGAAATAATGCTGCACACCTACAATGCAG 3334
                             v i     v     i          vv iii   ii  iii ----
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT---- 345

  chr2_111557987_   3335 CACACCATCTGATCTTTGACAAAGCTAACAAAAACAAGCAATGAGGAGGG 3384
                         -----  vi    i  i     i v iv   i v  vv     i   ii 
  L1M4_orf2#LINE/    346 -----CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_111557987_   3385 GACTCCCTATTCAATAAATGGTGCTGGGATAACTGACTAGCCATATGCTA 3434
                         i ivvi  v     i              i     iv  ?   i    v 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_111557987_   3435 AAGACTGAAACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAA 3484
                             v    ii         v   i                 i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_111557987_   3485 GATGGATTAAAGACTTAAATGTGAAATCTAAACCTATGATAACC--TGGG 3532
                         i      i ?    i       i i v     v    i -   i-- i i
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGA 539

  chr2_111557987_   3533 AAATACCATTCCAGACGTAG--------GAACT-------GGCAAAGATT 3567
                          i v v   ---  i?   i--------  v  -------     v i  
  L1M4_orf2#LINE/    540 AGAAAACAT---AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_111557987_   3568 TCATGACAAAGATGCCAAAAGCAATTAA--AACAGAAGCAAAAATTAACA 3615
                           v iivv v  ii         --i  --    i   v      vi i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATA 634

  chr2_111557987_   3616 AATGGGATCTAATTAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATC 3665
                            v   ii v  i   v v  i i   i  iv vv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_111557987_   3666 AACAGGGTGAACAACCAACTTACAGAATGGGAGAAAATATTTGCAAACTA 3715
                           v ii     v iv    ii                          ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_111557987_   3716 TACATCTGACAAAGGTCTAATATCCAGCATCTCTAAGGAACT--TA-AAT 3762
                           i      i  i  v  vi       v  v v   i     --  -  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_111557987_   3763 TTA-TAAGACAAAAACAAACAACCCCATTGAAGAGTAGGCAAAGAACATG 3811
                          i -   v v   i     i     v   ?  i i i       i iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_111557987_   3812 AACAGACA---CTTCAGAAGAAGACATACATGTGGCCAAAAAGCATATGA 3858
                           i     ---  i  -       i     vi       v     i    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCA-AAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_111557987_   3859 AAAAATGCTCAATATCACTAATCAT 3883
                            i        i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (143 / 76)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.76 (47 / 17)  


2736 25.64 4.01 2.79  chr2_111577897_111580118.rev      834  1730 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_111577897_    834 TAGAGAGACATACCATATTCAGAGACTGGAAGATTCAGCACAGT-AAGAT 882
                          i  i   i  v    i    vi  i       i i ii iv  -     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_111577897_    883 GAAATTTCTCCTCAAATTAACTTACAGGTTTAATGCAATACCTATCAAAA 932
                          iv v v    i      i ii     i  i  i     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_111577897_    933 TCCCAGAAAGATTTGTTGTAAATATAGGCAAGATTATCCTAAAATTTCTA 982
                               vvivv   v   i i v  v i    v v           iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_111577897_    983 TAAAAAGGCAAAGGAATTAGAATAGCTAAAGTGATTTTGTAAAATAATAA 1032
                          ii   v    i   vii        i   iii  i   v    v  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_111577897_   1033 -AGAGGTGGAA---TCAAACTACCATATTTTAAGACTTA-TGTAA--CTA 1075
                         - i  v    i---   v   v  vv    i  i     - ii  --   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_111577897_   1076 TATTAATTAAGACCATGTGGTATTGGTGAAGGGATAGACACACAGATGCA 1125
                         i v    i     vi       i   iiv i         i i    vv 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_111577897_   1126 TAGA-TAAAGTAGGAAAATGCAGAAATAGAACCATACAAATACGACCAAC 1174
                          i  -  i i -v  i i v        i v       vv  i ii   i
  L1M4_orf2#LINE/    301 TGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_111577897_   1175 TAATTTTT---AAAGGTGTTAAGGCAATTTAACATGGGAAATATAGCCTT 1221
                          i     i---  i    ii   i v   i  iiv  i  iv    i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_111577897_   1222 TTCAACTACTAGTATTGGAGCAATTGGACATTGGTACACAAAAAAACCAA 1271
                               v v i  ii   ii   i    i ?ivii ii     i  i---
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT--- 446

  chr2_111577897_   1272 CAAGCAAAAAG--GAATCTCAACCTAAGTTTCCTACCTTATATAAAAAGT 1319
                         -------i   -- i i i v    ------ vi   v    i     v 
  L1M4_orf2#LINE/    447 -------GAAGTTGGACCCCTACCT------CACACCATATACAAAAATT 483

  chr2_111577897_   1320 AACTAAAAATGGATCATGG--CTCAATGAAAAATGTAAAAGTATAAAATT 1367
                             v           ?i --  v    v  i vv     v       i 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_111577897_   1368 TTTAGATAAAGCCCATAGGA-TAATACCTTCAGGATCTAGGAATAGGTGA 1416
                         i     - i ivv      ?-   - i    iv  i  v  iv    ii 
  L1M4_orf2#LINE/    534 CTTAGA-AGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_111577897_   1417 AAAGTTTTTAGACTTGACAGTAAAAGTACATTACAGTCCATAAAAGGAAA 1466
                         viiv  i     iv     vi     i   ----  - v i     i   
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACA----AG-CAACAAAAGAAAA 626

  chr2_111577897_   1467 AATGGATAAATTAGACTTTATTAAA-TTAAAAACTTTTGCTCTATTGAAG 1515
                            i        i     i  i   -             iv  - ii   
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAG 675

  chr2_111577897_   1516 ACCA-TATTAAAAGAGTAAGAAGGCAAGCTATAAATTAGGAGAAAATATT 1564
                         iv  -   i  i i   i i   i   v i i i v i            
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_111577897_   1565 TGCAAGCTACATATCTGACAAAGGACTAGTATCTAGAACATATAAA---- 1610
                              iii i        i  i     v     i    i       ----
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_111577897_   1611 -----CAGTT------TAAAAAAATAA-CAATCCAATT-AGAAATGGGCA 1647
                         -----  ii ------      i i  -i  i      - i         
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_111577897_   1648 AATGAAGTGAACAAACTTTTCAACAAAGAGAACATACAGATGGCAAATAA 1697
                           v  vv    i i  v    vv      ii i     i     v     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_111577897_   1698 GCATATGAAAAGATACTCAACATCATTAGCCAT 1730
                            i          i          ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (152 / 75)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.54 (61 / 24)  


3228 22.17 4.03 2.46  chr2_111683566_111688464.rev     3515  4407 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_111683566_   3515 GGAGAGATATACTTTGTTTAAAGGTCAGAAGTCTCAGTATTGCTAAAATG 3564
                            i      v iv    i vi i ii    v  i i     i   i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_111683566_   3565 AGAACTCTTCCCAA------------------TGCAGTGCTAATCAAATT 3596
                         iv  iv  i     ------------------i   i v iv      v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_111683566_   3597 TCTAGCAGGCTTTTT-GTAGAAATTGAAAAGCAGATT-TGAAATTCATAT 3644
                         i i   v v      - i         v    v   i- i          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_111683566_   3645 GGAAGTGCGAACAAAACCAAAAGAGCCAATATAACTTTAAAAAAGA-GAA 3693
                             i   -  vii v   i  v      v i  ii  i       -   
  L1M4_orf2#LINE/    152 GGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_111683566_   3694 --AAGATGAAGTTCTAAAACTATCTGCTTTCAAGATTTATTATAAAGCTA 3741
                         --   v  i  vv  v v   vi iiv      i i   i  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_111683566_   3742 CAAGTGATCAAAATATTCTAGTACTAGCAGCAAGATAGAGGAAAAGATCA 3791
                           -  i     i i v v i     i   vv i      viv v      
  L1M4_orf2#LINE/    251 CA-GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_111683566_   3792 ATGAACCA-AATAGAAAGTCCAGAAATAGACACACTCAAAAATATGGACA 3840
                            i vi -   v  i            i  v  iv  vv--     v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCA 347

  chr2_111683566_   3841 ACTGATTTTGGACAATATTGCAAAAGCAATTCAATGAAGAAAGGATAGCC 3890
                          i       v     viv   v  ii v        ii     i    i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_111683566_   3891 TTTTCAACAAACAGTACTGGAAGAGTTAGATTCCTGTATGCAGAAACAGA 3940
                                    ii  i    i v ii i   v? iii     --------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-------- 439

  chr2_111683566_   3941 CAAAAACAATGAACTTGGATGCAAACGT-GCATTATATAAAAAGAAGTGA 3989
                         ---   v      v     iv vv  v -i  ii     v   -  v i 
  L1M4_orf2#LINE/    440 ---AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA-AATTAA 485

  chr2_111683566_   3990 TTCAAA-TGGATTGCAGATCTCAATGTAAAATCTAAAACTATAAACCT-T 4037
                         i     -     ii?   i  v       i v             v  - 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_111683566_   4038 TAGAAGAAAACATAAAAGAAAATCTTCATGACCTTGGGTTAGGCA--GAG 4085
                                       ii? v        i                 -- iv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_111683566_   4086 TTTTTAGGTATGACACCAAACACACAGTCCATAAAA-AATAAATTGATAA 4134
                           i    i            vi    iv v i    -  v    v     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_111683566_   4135 ATTAGACTTTATCAAAATTTAAAATTTTCATTCTTTGAAAGATACTCTGA 4184
                            i     i         v    i   ii v   ii  i  i   v v 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_111683566_   4185 AGAGATTGAAAAAATAAGCCACAGATTGGGAGAAAATGTTTGCCAAGAAT 4234
                            i v      i i  v       v           i     -- i vi
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC--AAATC 733

  chr2_111683566_   4235 ACACATCTGATAATGCACTTATATCCAGAATATATGAAGAATTCTTAAAA 4284
                          i i         v v    i              i     i     v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_111683566_   4285 CTCAATAATAAGAA----AATAGCCCCATTAAAAATAAAATAGGCAAAGG 4330
                                    i  ----    i   v   ?    ----  i        
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAA----ATGGGCAAAGG 829

  chr2_111683566_   4331 ATTTCAACAGACATTTCCCCAAAGAAGATATATGGATGGT-AATAAGCAC 4379
                             v  i         i              iii    i-         
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_111683566_   4380 ATGAGAAGATG-TCAGCATCATTAGGGAA 4407
                             i      -   i     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (118 / 76)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 2.76 (58 / 21)  


2121 24.25 8.74 4.71  chr2_111702048_111705640     2232  3101 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_111702048_   2232 AGAGACACCCATCACATTCATGGATTGAAAGAC--AA------------- 2266
                          i   i i  --  ii           i     --  -------------
  L1M4_orf2#LINE/      4 AAAGATATCC--CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_111702048_   2267 -CAATTCTCCT-ATATTCATATACAGTTTTAACAAAATTTGCATTAAAAT 2314
                         -    v    i- v   v  v     v  i   iv   iivi  i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_111702048_   2315 ACCAGCAATGTTTTCTGTAGA------TAAGATTATTCGAAAATTTATA- 2357
                         v     viiv    i  i   ------i   v v  i v      i   -
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_111702048_   2358 AGAAAGGTCACAAAAACTAAACTAGCCTAAGCAATTCTAAAAAAGAAGAA 2407
                         i    v -  viii v i i v     v  i    ii i           
  L1M4_orf2#LINE/    152 GGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_111702048_   2408 TAAA--TGGACAAGAACCAGTCTACTCAAGGCTAAGGCTTTCTACTTAGC 2455
                         i   --    --i  vi  vv  v i   vvii  ii   v    vv   
  L1M4_orf2#LINE/    201 CAAAGTTGGA--GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_111702048_   2456 AACAGTGATCAAGACAGTGTGATATTGGCAGAGGATTAGACACACAGATC 2505
                         v     i              i  i     v i iv      i i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_111702048_   2506 AGTGGAACAGA-CAAAGAATCCAAAAAGAGACCCAGAAAAATATGGCCAA 2554
                          i     i   -ivi   i    i   v i     v v vv     i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_111702048_   2555 ATGATTTTTGATGAAGAT-CCAA--------AATGGATAAAGAATGGGCT 2595
                         v       i  ii i i -    --------     iv       i v  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_111702048_   2596 TTTCAACAAATAGTGCTTGAGTAACTAGGGAAGTGTGGGCTTACAGAAAA 2645
                                    i     v iii    --   -- i?vvi v i  i  i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACT--GGA--TAKCCACATGCAAAAGA 444

  chr2_111702048_   2646 AGGTACTTTG-----TACCTAACACATTATAAAAAAAAAAAAGAGCAAAA 2690
                          v v v  v -----     --    ii   v ------------     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCT--CACACCATATA------------CAAAA 480

  chr2_111702048_   2691 CAAAACTCAAAATAGATCACAGCCTTAAATGTAAAATGTAAAACTATAAA 2740
                         vvv          i     ?  v i         i vv            
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_111702048_   2741 GCTTTCAGGAAAAAACA--GGACAAAATTTCCAGGAGCTCCT--AGTT-G 2785
                         i  i i  i i      --  ?vv    i i iv  ---   --i   - 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA---CCTTGGGTTAG 577

  chr2_111702048_   2786 GC----------TAGACTTGGCACCAAAA---CATGTTGTATAAACTGAA 2822
                           ----------    iv  i        ---  v ivii -   vvi  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA-AAAGAAAA 626

  chr2_111702048_   2823 AATTGATAAATTGGACTTCATAAAAATTAAAGACATTTGC----CAGTAA 2868
                            v                 v         i  v    i----  i- i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA-AG 675

  chr2_111702048_   2869 AATATCAT-AAGAGAATGCAAAGACAAGGTGCAGATTAGGAGAAAGTATT 2917
                         i i ii  -    i i  v        vvii    v i       i    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_111702048_   2918 TCTAAATAATTCTGATATCTGATCGTCAATAAAGGACTCATATCTAGAAT 2967
                          vi    v  ----         -------  i     ii    i     
  L1M4_orf2#LINE/    726 TGCAAATCAT----ATATCTGAT-------AAGGGACTTGTATCCAGAAT 764

  chr2_111702048_   2968 TTATTTAAAGAACTGTTAAATCTTATCAATAACAA-ATAAACAGTCTAAT 3016
                         v   --        v   v v  i vi     v  - i   i ii i   
  L1M4_orf2#LINE/    765 ATAT--AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_111702048_   3017 TAGATATTGGGCAAAAGGCATGAAGAGCCATTTTACCAAAGA-------- 3058
                          ?i v v        i iiv    v  v     iv       --------
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_111702048_   3059 ---TGGAAAATAAGCATATGAAAAGATGCTCAACACCACTGCCCAC 3101
                         ---   vv        i                  i  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (122 / 85)
Gap_init rate = 0.04 (32 / 905), avg. gap size = 3.66 (117 / 32)  


2688 24.41 4.63 3.50  chr2_111717638_111719919      906  1790 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_111717638_    906 CATGTTTGCAGATTGGAAGACTCAATGTTGTTGAGATGTCAGTTCTCCAC 955
                               iiii            i   i     i     v  i v    v 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_111717638_    956 AAATTGATCTGTAGAGTTATTGCAATCCCAGTAATAATGCTAGCAGGAAT 1005
                                   ii   v i vi        vi v v   v i   -v vv 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCT 112

  chr2_111717638_   1006 CTGTTGTAGAAATTTACAAATTGATTCTAAAATTTATATAGACATGCAAA 1055
                         i v   i       v    ii    i        i    i  v      i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_111717638_   1056 GAATCTAGCGTATCTATAACAATCTTGAATTAGGAAAATAAATCTGGAGT 1105
                          i i i  vi  v i v            vv  i i  i   vi     v
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_111717638_   1106 GCTCAAACTACATGACTTTAAAAC--ATTATAATACCGACATTGTTGGTT 1153
                         i    v   v vii i  i     -- i  i  - v v   ---------
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAA-AGCTACA--------- 252

  chr2_111717638_   1154 TTATAATTAAGACAGTATGTTACTGGCATAGGGACTGACAAATAGATCAG 1203
                         --i    i        i  v          i   iv    v        i
  L1M4_orf2#LINE/    253 --GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_111717638_   1204 TGGATCTGAGAA--GAGAG-CTGGAAACAGGCCCATG-ATTACATGGTCA 1249
                             vi--    --     - ii    i ii     i-   -i       
  L1M4_orf2#LINE/    301 TGGAAT--AGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGGTCA 347

  chr2_111717638_   1250 TTTG---TTTGCCAAAGGTACCAAAGCAATCAATCCATGGGGAAAGAAAA 1296
                         v   ---  i v   i   i    i--- i  v  v            v 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAG---ACCATTCAATGGGGAAAGAATA 394

  chr2_111717638_   1297 GTCTTTTCAA-AAATGGTGCTGTATTAACTAGATGTTCAGAAGTAAACAC 1345
                                   -           vivi    i   i?i  v v i   ---
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA--- 441

  chr2_111717638_   1346 ACAAAGAAAACTTTAACTTATTTCTCACGTCACAAACAAAAATTAATTCT 1395
                          v  v   i--  vi  iiv vi     ii  i v           i  v
  L1M4_orf2#LINE/    442 AGAATGAAG--TTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_111717638_   1396 AAATT-ATTGTAGGGCTAAATATAA-------AATCATAAAACTTTTAGA 1437
                             v-  ii?  iv      i   -------  ii        i     
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_111717638_   1438 -GAAAATATAGGAGAGCATCTTCATAACCTGGAGACAGGCAAATGTTTAT 1486
                         -     i     ? viv      i i    v i vi      vv    v 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_111717638_   1487 -AGACA-AACAGGCCACAGA---AAGCAATAAACGTAACAGAAAATGAAT 1531
                         -   i -i   --   v ii---      i   v ---- i     ii  
  L1M4_orf2#LINE/    590 TAGATATGACA--CCAAAAGCACAAGCAACAAAAG----AAAAAATAGAT 633

  chr2_111717638_   1532 AAATGTGTCCCTGTCAAAATTAAAAGCTTCTGCTGAT--AAGTGATACCA 1579
                             vv v iiii            i   i  -  v --  iv  i  i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTA 682

  chr2_111717638_   1580 TTAAGAAAAT----AGGCAAGCCATAGATTAGGAGAAAATATTTGCAAA- 1624
                          i      i ----  i   v   i   v i                  -
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_111717638_   1625 ---ACATCTGAAAAAAGATTGAAATCCTGGGTTTATGAAGAACTCTTTCA 1671
                         --- i      v  ii  i viv    v ii v   i          v  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_111717638_   1672 ACTCAATAATAAAAAGATAA-----TCAATC-AGAAATGGATGAAACAGT 1715
                                          i  -----i    i- i      iii  iv v 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_111717638_   1716 TGAAGAGACAGTTC-ACAAAAAAGATACACAAATAGCCATTCGGTATATG 1764
                             v     v   -v    i      i      i    v vi i i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_111717638_   1765 AAGAGACACTTATCATTACTCATTTG 1790
                           i   ii  i v   i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (134 / 79)
Gap_init rate = 0.03 (29 / 895), avg. gap size = 2.48 (72 / 29)  


1806 24.20 5.10 6.71  chr2_111730181_111731857.rev      501  1186 (491)    L1M4_orf2#LINE/L1      234   908 (0)  

  chr2_111730181_    501 AGCTTATCGTAAAGCAACTGTAATCA-------GTAGGATTGGTGTCAAG 543
                          i    iiii     v  v       -------  i v i   ii v i 
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_111730181_    544 ATGGGTACACAGATGGGTAGAAAAGAATTGAGAATCCAGAAATGGACTCA 593
                           i ii i i    vii i   v          i         ii  i  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_111730181_    594 TATTTACATGGTCAATTTATTTTTGACAAAGGCACCAAAGAAATTTAGCA 643
                           iv vi          v     i     i  ii    iivv   i iii
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_111730181_    644 TAGAAAGTATAATCTT--CATCAAATGATGCTGGAAAAATTGAGTAACTA 691
                         vi     v   i    --  v      i      i v  i  ii  ? i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_111730181_    692 TATGCAAAAAAGAAAGAAAAGAAAGAAAAAAGTGAAAACCTCCACCTCCG 741
                         i        ---------------   vi    vii -------- i  -
  L1M4_orf2#LINE/    434 CATGCAAAA---------------GAATGAAGTTGGA--------CCCC- 459

  chr2_111730181_    742 TCATTACTTCATACCATATA-AAAAATTAACTCAGAATAGATCATAGACA 790
                         ----   i   i        -             i   i     ?    v
  L1M4_orf2#LINE/    460 ----TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_111730181_    791 TAAATGTAATAACTAAAACTATAAAACTCCTAAAAGAAAACAGGAGAAAA 840
                                  v i                 i  i         --------
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-------- 547

  chr2_111730181_    841 TAGAGA-AAACCTTGGTGATCTTGGTTTTGGCAGTGATCTGTTAAAT--- 886
                            i?i-   i   v    i     v  v    i  i i v   i  ---
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_111730181_    887 ---TCAATAG-ATAAAACACAAATTAGAAATAAGGTATTGACTGAACCTC 932
                         ---i   v  - i  ivv     --     v  viv  vi i  i  i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAA--AGAAAAAATAGATAAATTGGACTTC 645

  chr2_111730181_    933 ATAAAAATAAAACATAAACTTTTGTTCTTCAAAAGACATT--TAGGAAAA 980
                           v     v   ----         v       i    i --i i    i
  L1M4_orf2#LINE/    646 ATCAAAATTAAA----AACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_111730181_    981 TGAAAAGGAAAGCCCCAGACTGAGGTAAAATATTTGCAAAACATATATAT 1030
                                iv  v  v    v  i iv              v       v 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_111730181_   1031 AATAAAGGTTTTGTATCCAGAATGTATAAAGAAGT--------------- 1065
                         i    i  vi             i         v ---------------
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_111730181_   1066 TAAGAAGAAAAGCAACATACTTTTTTTTTAGTTGACAAAAGATCTGAAAA 1115
                            i    v  ii   vi v  ?vvv--- i v i    i   i    v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAA---AATGGGCAAAGGATTTGAATA 838

  chr2_111730181_   1116 AGACATCTCACCAAGTCGTTTGTAGGACTGGCAAATAAGTAAACAAGAAG 1165
                         -     i  v    ivvivv i  vi v    v      i v ii i   
  L1M4_orf2#LINE/    839 -GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_111730181_   1166 AGGCCCAACACCTTTAGTCAT 1186
                          v  i     i v????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (101 / 61)
Gap_init rate = 0.02 (16 / 675), avg. gap size = 5.06 (81 / 16)  


2992 24.22 3.60 1.44  chr2_111859808_111863525.rev     2366  3199 (519)    L1M4_orf2#LINE/L1        1   852 (56)  

  chr2_111859808_   2366 TGGCAAGATAGTCCCTGCTTATCTGTTGGAAGACTTGGTATTGTTAAGAT 2415
                            v      vi  v  i i  vvi           ii            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_111859808_   2416 GTGAAGTATTTAT-AACTTGATC---AGA------GCAGTCCAATTCAAA 2455
                          - v i  i ivi-  v      ---   ------   i   vvv     
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_111859808_   2456 ATCCCAGCAGGTTATTTTTTAGATATTGATAAACTGATTCTAAAATTAAT 2505
                                 v vi v    vi   v     i  i     i        v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_111859808_   2506 ATAAACAAGCAGAAGGCCTAGAATAGCTAACACAATACT---AAAGAAGA 2552
                           ii v v   iii i  i        i  v     vi ---        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_111859808_   2553 TCAAAGTTGGAGTACTCAGAGTCCTTCATTTCAAGAATTACTATAAAGCT 2602
                         v           v     v v i iiv       i v      i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_111859808_   2603 ATAATAATCAAGATGGTGTGGTATTGGCAAAAAAA-GGACACATAAATCA 2651
                          i i         ii        i     v  ii -i    i   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_111859808_   2652 ACA------AATGGAGATGCCAGAAATAGACCCCCCCACACAAT-ATAAT 2694
                          ii------   v    vv         i    ---- i   v -  ii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCC----ATACATTTATGGT 345

  chr2_111859808_   2695 AACCTGACTTTTGACAGAGGCGCAAAGGCAACTCAATGGAGCAAGTGAAG 2744
                         v vi   i   i    ii  i  v   i v i       i v   viv  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_111859808_   2745 TCTTTTCACCAAGTGGTGCTGGAACAATTGGATGTTCATAGGCTAAA--- 2791
                                 v   i         i    i     i?i  i v  v   ---
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_111859808_   2792 TGAATCTGGACACAGAACTTGCAACTTACACAAAAAATAACTCTAAATGG 2841
                             vi     v vv v  ii  v v  i       v      v      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_111859808_   2842 ATCATAAACCTAAATTTAAAATGC-AAATTTATAAAACTTTTAGAAGAAA 2890
                             ? i        v   i -  -   vi         i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_111859808_   2891 ACATAAGAAAAAAATTTATGTGACCTTGGGTTTGGTGAGGAATTTTTAGA 2940
                              i ?iv   vi  -i             v  ii v iv  i     
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_111859808_   2941 TACACGACCAAAAGCATGAACCATGAAAGAAAAAAAAAATAGAGAAGTTG 2990
                           iivv          ii i v ii          ----    v  i   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAA----TAGATAAATTG 639

  chr2_111859808_   2991 GACTTTATTAAAATTAAAAACTTCTGCTCTATGAACGATTCTGTTAAGAT 3040
                              i  i              i  iv  vii  v  iv  i i    v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_111859808_   3041 AATGAAAACACAAGCTGCAGACTGAAAAGAAATATTTGCAAAACATGAAC 3090
                          i      v    v ii    v  ii ii             v   iv i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_111859808_   3091 CTGATAAGAAACTTGTATCCAAAATATTTTAAGAAATCTTAAAAGTCAAC 3140
                                 ii           i     v v     v     v  v    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_111859808_   3141 AAAAAGACCATAAGTAATCCAATTGAAAAAATGAATAAA---TCTGAACA 3187
                           v  i vv i  i   i      -?       iii   --- i    i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAATA 838

  chr2_111859808_   3188 GACAC--CTCCAAA 3199
                             i--       
  L1M4_orf2#LINE/    839 GACATTTCTCCAAA 852

Transitions / transversions = 1.48 (118 / 80)
Gap_init rate = 0.02 (17 / 852), avg. gap size = 2.47 (42 / 17)  


 821 32.43 8.33 1.99  chr2_112016691_112018981      587  1138 (1153)    L1M4_orf2#LINE/L1        1   587 (321)  

  chr2_112016691_    587 TGGAGAGAGATATTGTGTTCATGGATTATATAATTTAATAGTGT------ 630
                             i   v  viii            iv vi i      v   ------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_112016691_    631 ---AAT----------TTGATCTATATATTCAGTGCAATTCTTGTCAAAT 667
                         ---   ----------        i v     ii     i i i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_112016691_    668 TCCTAATAATATTTTTAAAAATAGAACCTGAAAAAATGATTCTAAACTT- 716
                            i iiviiv     vi---i    vi   v  iv    i     v  -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG---CAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_112016691_    717 ATGTGAAAGCATAAAAGACCAAAAATAG----GATGTTTCTGAAAAGGTA 762
                           i  i  iiii  ii    v i     ----i iiv ii      i v 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_112016691_    763 G--TGA--TCAGGGGTTTC-C-CTTATTGATGTCTGGACTT-TTATGAAG 805
                          --ii -- ii i  vi  - -   viii  v  vii    -i  ii   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_112016691_    806 CTGGAGCAATTAAAACCCTGTAGTTTTGGTGCAGAGACAGAAAAACAGAC 855
                           iv  i   i  i  vv   i  vi   iii ii  i   v v i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_112016691_    856 CA-TGGGGTATGAAT-AAGATCCCAGAAAAAGATGGATGCAAATAAAG-- 901
                           -   ii  -    -i   vi       v i ivv  i  vv  vi --
  L1M4_orf2#LINE/    298 CAATGGAATA-GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_112016691_    902 AATGTTGGTTTATTACAGAGGATAC-AGGA--GGTCAGTGAGGAGAGGA- 947
                            --  i   viv   -   i i - i  --iv   i  i   i  i -
  L1M4_orf2#LINE/    347 AAT--TGATTTTCGACA-AGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_112016691_    948 -GGCTGATAAACAAATGGAGGTGGAAAAAAGTAGTTATTCATATGGGAAA 996
                         - v  vv v         v v   i v  v- i v  ?i  i   vi   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAAC-TGGATAKCCACATGCAAAA 442

  chr2_112016691_    997 AAATGAACTTGAATATCTCCCTCAAACTACATCCGAAAAATAACCCTAGA 1046
                         i      v   i ivi  v     v  i i  v i    v    i v i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_112016691_   1047 TAGATTCAGGAATTAAATGTCAAAAAAGAAACTTTATAATTTATAG--TA 1094
                          i   iv?i  vi       v i ivvi     v  v  i iv   --v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_112016691_   1095 AAATACAGG--TAACTATTTTC-T-ACCTTGGAGTAGTGATATGGTTT 1138
                            i i   --   --  i   - -       iv   vv -       
  L1M4_orf2#LINE/    543 AAACATAGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCA-ATGGTTT 587

Transitions / transversions = 1.68 (111 / 66)
Gap_init rate = 0.04 (26 / 587), avg. gap size = 2.19 (57 / 26)  

 483 26.12 4.10 2.99  chr2_112016691_112018981     1528  1795 (496)    L1M4_orf2#LINE/L1      625   895 (13)  

  chr2_112016691_   1528 AAAAT-GATAAATTTAACTATGTCAAAATAAAGAACATTTGTTCACCAAG 1576
                              -        vi   vii       v  i   v     v vi   i
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_112016691_   1577 AGATACCTTTAA-AAAGTAAAAAGACAAAGTAAAAACTGGGACAAGAGAT 1625
                         i  i  iv i  -     i         vvi v i v     v  i v  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_112016691_   1626 TCATAATATCA---ACC--ACAAAGGTTTAGTACCAAGAATATATGTAGA 1670
                          iii  -    --- i -- i  i  vi v   i v         iv   
  L1M4_orf2#LINE/    725 TTGCAA-ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_112016691_   1671 ACTGCTACAAATCAATTTTGTTAACAAAGCACAAATAACC-AGTATAATA 1719
                            vi     v     ---iv   -    -          - i v?  v 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAAT---AATAA-AAAG-ACAAATAACCCAATTWAAAA 818

  chr2_112016691_   1720 ATGAGGAAAAAAAGCACCAATGG-CATTTCACAGAAGAGGAAACATATAT 1768
                            i v   ii vvii--   i -      v vi    i  v i i v  
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTG--AATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_112016691_   1769 GCCCAATAAACTTATGAAAAGAT--TCAA 1795
                          v       i vi          --    
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.23 (38 / 31)
Gap_init rate = 0.04 (12 / 271), avg. gap size = 1.58 (19 / 12)  


2021 25.84 4.86 6.70  chr2_112124400_112126326      511  1435 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_112124400_    511 TGGAAGGATGAACTATGTTCATGGATCAGAAGATTTTGTGATTCTGTATT 560
                              i   ivv i            ii     i  ---i  -----   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTT---AAT-----ATT 42

  chr2_112124400_    561 GTAAAAGTATTGATTCTCCCCTAATC-ATCTATAACTGCAATGCCATTCT 609
                           v  ii ivii  v      v   i-     i iv v   i  v  i i
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chr2_112124400_    610 AATCAAAATCTCAGCATGGTGGTGGTGTGTGTGTGTGTGTGTGTGTGTGT 659
                         v         i    ----------------------------  iv v 
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGC----------------------------TGCCTTT 114

  chr2_112124400_    660 GTGTGTGTGTAATGTGACAAGCTGATTCTAAAAT--ATTTAGAAACACAC 707
                         v -  ii- v   -            i       --  v i    ii  v
  L1M4_orf2#LINE/    115 TT-TGCA-GAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_112124400_    708 AGCTCCAAGAATAGCCAAGATAATCTTGCA---GGGGAACAAGGTTGGAG 754
                         i vv  v           i i       v --- ii      i       
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_112124400_    755 GATTTATAC--CGCAG--------------ATAAA-CTACAGTAGTTAAG 787
                           i i i  -- v  i-------------- i   -        i i   
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_112124400_    788 ACAGTGTGGTTTCTCATAAAAGAGTCAACAAATAGATATATTGTACAGAA 837
                                   v-  vii v   ii vi   v      vv  v v i    
  L1M4_orf2#LINE/    262 ACAGTGTGGTA-CTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_112124400_    838 CAAGGAGTACAGAAACAGACCTTCACATATAAGTCCACTTGATTTACAGC 887
                         ivii    v      i i   ivi    v  v vi  v       v ii 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_112124400_    888 AATGGTTCTATAGCAATATCC--TAGACAAAGGATAAAAGTACATTATTT 935
                           v   v i -  - vi  i -- i iv    i   i---------- i 
  L1M4_orf2#LINE/    361 AAGGGTGCCA-AG-ACCATTCAATGGGGAAAGAATAG----------TCT 398

  chr2_112124400_    936 TTTCAATAAATGGTTTTGGTTCAATTGGATATATGAACGGAAAA-AACAA 984
                               i       vi   vv   i      ?viiv i v    -  ii 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_112124400_    985 AGCTTGATGCCTACCTCATACCATATACAAAAATCAATTTCCGTAGT--A 1032
                           i v  iv         i               i  i -- iv i -- 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACT--CAAAATGGA 496

  chr2_112124400_   1033 CCATAAATCTAAATGTGAAAGGCAAATCAATAAAGTTTCTCTAACATTAC 1082
                         i  ? i i        i i  vi   v v     ii ii vv  v vv  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_112124400_   1083 ATAGGA--AAATAATTTTATAGCCTTGAGCTAGGCAAAGATTTCTCAAAT 1130
                              ?--    --i  ii ii     i i       v i     i i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_112124400_   1131 AGGACAC-AAAATCGC---CAACGAGTAAGTGAAAAATTGCTAAATTTCA 1176
                          v     -    v i ---    i --   -i      v v      vv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAA--AAG-AAAAAATAGATAAATTGGA 641

  chr2_112124400_   1177 CTTCATTAAAATTAAGAA-TATTGAGA--AAAAAGACACTATTCAGAAAG 1223
                               i        i  - v   v v--v   i        iv      
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_112124400_   1224 CAAAAAAGCAAATAATCTAGTAGGACAAAGTAACTGTAG--CATAGGTAT 1271
                         ii    ii   viv ivv i i   v   i  vi  i i--    --   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA--TAT 739

  chr2_112124400_   1272 CCAACAAGGGACTCATATACAGGATATATAAAGAACATCT-----CTAAA 1316
                          ii i        ii   v   i             -   -----  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAAC-TCTTACAACTCAA 788

  chr2_112124400_   1317 TCAGACAAGCTCTGATAACCCAATTTAAAATTGAGCAAATAATGTAAACA 1366
                          v v v  ivv vi           ?    v  i     vi  v i  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_112124400_   1367 GGCCCTTCAAAAAAGGAGATATCCAAATGGCAAA-AAAAATATGAAAAGG 1415
                          i vi   vvv    i      v        v  -  iv i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_112124400_   1416 TACAGGACATTATTAATCAT 1435
                          i vvi    i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.24 (107 / 33)  


2671 25.58 5.99 1.38  chr2_112343778_112346664.rev     1528  2395 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_112343778_   1528 TGGTAACACATCCCATGATCATGGATTTGAAGAATCCATATTGTGAAAAT 1577
                            v  v i        v         v     v iv       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_112343778_   1578 GATCATCCTGCCAAAAGCAATCTATAGATTTCACCATAATTCTCATCAAA 1627
                          iiv  v  v  v   vii     i     -  v ii   i ii      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT-CAACGCAATCCCTATCAAA 99

  chr2_112343778_   1628 ATAAGATCT-TTTTTTTTATAGAGTTAGAAAAAACAATTCTAAAATTCAT 1676
                           vvv v  -ii      ii   iv v  v  ivii  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_112343778_   1677 GTGGAACCAAAAGAG-CCCAAAATAGCCAAAACAATCCTAAGCAAAAAGA 1725
                         i     viiv   i -    i                i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_112343778_   1726 ACAA-GTATGTAGCCATCACAT------ATT----------CTACAAGGT 1758
                             -  -  v  vvv     i------   ----------      i i
  L1M4_orf2#LINE/    200 ACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_112343778_   1759 TATAATTAGCAAAACAGCATGGTACTGGTATAAAAGTAGGCACATAGACC 1808
                           i i v v   i    ii         i    iii   i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_112343778_   1809 AATGGAACAGAATAGGGAAACCAGAAATAAAGCCAAATACTTGTAATCAA 1858
                                i     v i  iv           v   v i i  i ii    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_112343778_   1859 GTATTTGATCTTTGACAAACAAGCTTACAAAAACATAAATTGGGGGAAAG 1908
                         ----     i  i     iviv  ---   i v   vv v     i  ii
  L1M4_orf2#LINE/    349 ----TTGATTTTCGACAAGGGTGC---CAAGACCATTCAATGGGGAAAGA 391

  chr2_112343778_   1909 GCATCCTATTTAGTAAATGGTGCTGGGAAAACTG-ATA-CCTTTTTTAGA 1956
                         ii vi  v  i ii              v     -   -  viv vi i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_112343778_   1957 AGAATGAAATTGGGTTTTTTTTATCTCTCACCTTATACAAAAGTCAGTTC 2006
                                 i    iiiii --- i   v    v         i i ii  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCT---ACCTCACACCATATACAAAAATTAACTC 488

  chr2_112343778_   2007 AAGAGGGATGAAAGGCTT-----TAAGCCCTGAAACCATAAAAATTCTAG 2051
                           i v    v ?  i i -----    vv  i    i      v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_112343778_   2052 AAGATCACCTTGGAAAAACTCTTCTGGACATTGGCCTAGGCAAGGAATTT 2101
                             vv  v v  ?iv  v     vv   v    vi       v iv  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_112343778_   2102 ATGACTAAAACACCAGAAGCAAATGCAACAAAA---ACAATAAATAAATG 2148
                         v iiv  vi      i     v v         --- v    i      v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_112343778_   2149 GGACCTAATTAAAATAAAAAGCTTCTGCACAGCAAAAGAAA-TGTCA-GA 2196
                             i v  i     v    i   i  ii vv    i  v - i   -  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_112343778_   2197 A--TAGACAGATAGTTCACACAGTGGGAGAAAATATTTGCAAACTATGCA 2244
                          -- ii v   i iii    v i                    ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_112343778_   2245 TCCAACAAAGCACTAGTATCCAGAATATATAAGGAACTC----AGATCAG 2290
                           ii i  i v   v                 i      ---- iv   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_112343778_   2291 CAA------GACAGA-AGCTCAA----AAAGTGGGTAAAGGACATGAATA 2329
                         i  ------    i - i i   ----   i    i      iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_112343778_   2330 GACAGTTCTCAAAAGAAGATACACAAATGGCCAACAA--ACATGAAAC-- 2375
                             v     v          i            i  --        v--
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_112343778_   2376 TGCTCAATATCACTAATGAT 2395
                                i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (134 / 86)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.78 (64 / 23)  


2305 26.58 4.43 1.65  chr2_112488739_112490504.rev      485  1274 (492)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr2_112488739_    485 AAGATTACAGCAGAACTTTTGCCAGACACAGATAAGCTGATTCTAAAGTT 534
                           i  iv    v vvi    vv    v iv  i        i     i  
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_112488739_    535 TCAGTGGAAGGGCAATGAAACCAGAATAGTTAAAACAATTCTGAAAAAGT 584
                         ivvi     iv    v i v         ii        ii        v
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_112488739_    585 AGAACAAAGTAGGAAGAATCACACTGGGTGATTTTAAGATTTATAACAA- 633
                                   v   i  v       vvvii    i  i i   iv    -
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_112488739_    634 GCTTCAGTAATCAAGACAATGTGATAGGGGCA-AAGGATGGGCACAGAGT 682
                            v              i    i  vv    -      i i  i v  v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_112488739_    683 TTAATGAAACAGAACAGAGGACTCAGAAATG------TACA------ACC 720
                          i    i  i    iv   iiii       i------    ------ii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_112488739_    721 AACTGCTTTTAGACAAAGGTAC-AAGAGCAACTCAATGGATTAAGGACAG 769
                           i  v    v     i   i -    v  -i       ivv   i i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAG 395

  chr2_112488739_    770 TCTTTTCATGGATTAAGATAGTCTTTTG-CTATTGGTCATCTATACGCAA 818
                                 --- i-- i  i  vi vv - v i   vi ? i i i    
  L1M4_orf2#LINE/    396 TCTTTTCA---AC--AAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_112488739_    819 AAAAAGCAAACCTTAAACTAA-ATCTCAAACCCTATACAAAAAATAACTC 867
                           i  vv  i--  ii  ivv- i    v   v          v      
  L1M4_orf2#LINE/    441 AAGAATGAAG--TTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_112488739_    868 AGAATTGGTCATATACTTAAATGTAAAATGTAAAAGAACATAATCTTTAG 917
                          i   v i   ? v  i         i vv     vv i v  iii    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_112488739_    918 AAAAGAA-ATAGGAGAAAATCTTTTT-ACTAGGGGTTAGGCAAAGAGTTC 965
                           i i  -     ? v       iv -  ivv           v iv   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_112488739_    966 TTAGACATGAGAGCAAAAGCATGACTCATTAAAAAAAAACT-GATAAATT 1014
                              i    v v        ii viv iv   i     v -        
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_112488739_   1015 GGGCTTTATCAAAATTAAAATATTTTTGCCC------G-----TGTTAAG 1053
                           i   i             - i     iv ------ ----- i i   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_112488739_   1054 AGAATGCAATGACAAGCTACAAACTTGGAAAACAGTCTCTGGAAACCACA 1103
                          i i  v  v     v i   i v v   i  - i v i  v   i  i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCATA 736

  chr2_112488739_   1104 TATCCAACAAAAGAACTATATTTAGAACATATAAAGAACTCTCAAAAT-- 1151
                             ii i  ii  vi i   ii    i              i v  i--
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_112488739_   1152 -ATGACGAGAAAATCAACAACTCAATTAAAAAATAAACAAAATACTTGAA 1200
                         -  i ii i  i iv  i   i     ?      iii    iv i     
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_112488739_   1201 CAACAGACACT-CATCAAAGCGGATGTAAGGATGGCAAATAAGCACATGG 1249
                         i ---    i - vi     vi   i  vii     v            i
  L1M4_orf2#LINE/    837 TA---GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_112488739_   1250 CAAGATGCTCAACATCATTAGTCAT 1274
                         v                ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (127 / 79)
Gap_init rate = 0.03 (21 / 812), avg. gap size = 2.29 (48 / 21)  


3197 25.61 1.55 1.66  chr2_112543232_112549037.rev     4409  5314 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_112543232_   4409 AAAGATGTTCCATGCTCATGGATATGAAGAATTAATACTGTTAAAATGGC 4458
                               i i     i        vv     v      i      i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_112543232_   4459 CCTGCTGCCCAAAGCAACTTACAGATTCAATGCTATTCCTATCAAACTAC 4508
                         vv i  v      vii ii           i  v  i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_112543232_   4509 CAATGACATTCTTCACAAAACTAGAAAAAACT-ATTTTAAAATTCATATG 4557
                           iivi v  i  ii  i  v v  v  i-  -  ii             
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATG 152

  chr2_112543232_   4558 GAACCAGAAGAGAGCCCGAATAGCCAAGGCAATCCTAACCAAAAGGAACA 4607
                            viiv   i  v  v          ii     i i vv  i i     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_112543232_   4608 AAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACCACAGGGCTATA 4657
                            i      vv   ii  v  ii i      viv   i   ii    i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_112543232_   4658 GTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCAGTG 4707
                             i   i    ii         i i  ii i     i     i  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_112543232_   4708 GAACAGAATAGAGAGCCCAGAAATATCGGAGC----ACACGTATAATAAT 4753
                            i     v     i         ---- i ----   iv   ii v v
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATA----AACCCATACATTTATGGTCAA 348

  chr2_112543232_   4754 TTGGTCTTTAATAAAGTTGACAAAAACAAACAATGGGGAAAAGACTCCCT 4803
                            i i  ii i  i v  v   i v  vv           ii ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_112543232_   4804 ATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGACTGA 4853
                         v     i              i      v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_112543232_   4854 AACTGGACCCTTTGCTTACATTATATACAAAAATCAACTCAAGATGGATT 4903
                          ii       i vv  i   ii            i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_112543232_   4904 AAAGAGTTAAATGTAAAACTTAAAACTATGAAAACCCTATGAAGACAACC 4953
                          ?   vi         i vi         -     i  vv     v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chr2_112543232_   4954 TAGAC-CATACCATTCTGGACATAGGACAGGTGACGATTTC------ATG 4996
                            i?-i v i v iv  iv v i  vi   ii i i    ------   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_112543232_   4997 ACAAAGTTGCCAAAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATAG 5046
                            ------      ivi   --          v      v  i    v 
  L1M4_orf2#LINE/    598 ACA------CCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_112543232_   5047 GATCTAATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTATCAACAG 5096
                           ii v  i   v v  i ii  i  ii vv    i  v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_112543232_   5097 AATAAAAAGATAACCTACAGAATGAGAGAAAATATTTGCAAGCTATGCAT 5146
                          i i      i    i        i                iii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_112543232_   5147 CTGACAAAGGTCTAATGTCCAGTGTCTATAAGGAACTTAAACAAATTTAC 5196
                             i  i  v  vi i     vi v     i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_112543232_   5197 AAGAAAAAAAACAAAAAAA--AATTAAAAAGAGGGCAAAGGACATGACTA 5244
                           v     i -    v  v--    ?    iv          iv   v  
  L1M4_orf2#LINE/    790 AATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_112543232_   5245 GACATTTTTCAAAGGAAGACATGCATATGGCCAACAAGCATATTTTAAAA 5294
                                i  v  i     i  i  v        i     i  vvv  i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_112543232_   5295 AGCTCAATATCACTGATCAT 5314
                         v      i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (143 / 85)
Gap_init rate = 0.01 (11 / 905), avg. gap size = 2.64 (29 / 11)  


 449 27.27 4.81 3.74  chr2_112575093_112578782     2026  2212 (1478)    L1M4_orf2#LINE/L1        1   189 (719)  

  chr2_112575093_   2026 TGTAGAGATAGAACCTGTGTC--TGAATTGGAACTCTCAGTATT---AAG 2070
                           v i     v--  ii   i--  i       vv  i i    ---   
  L1M4_orf2#LINE/      1 TGGAAAGATAT--CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_112575093_   2071 CTCTCAGT--TTCCCAGTCTGATAAATAGATTCAGTGCAATCCCAATTAT 2118
                         v vv  i -- i    ivi    vv i       ii        v  i v
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_112575093_   2119 AATTCTAGCTGACTTAA--AAAAAAATACAGTGGTTAAGTTGATTCTAAA 2166
                            i i     v   vv--iv i    ----  ii-   i    i     
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAAT----TGAC-AAGCTGATCCTAAA 143

  chr2_112575093_   2167 ATGTATATGGAAAAGCAAAAGACGTAGAAGATCCTTAACATTCTTG 2212
                           vi         v    ii   vi    v v  vv    v     
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

Transitions / transversions = 1.12 (27 / 24)
Gap_init rate = 0.04 (7 / 189), avg. gap size = 2.29 (16 / 7)  

2136 22.60 7.98 2.81  chr2_112575093_112578782     2524  3200 (490)    L1M4_orf2#LINE/L1      197   908 (0)  

  chr2_112575093_   2524 AAAATAAAATTAGTGGATTTATACT----GATTTCAAGACATAATTATTT 2569
                          i  i   i  i v   i i i   ----i       i  ----   i v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC----TTACTA 242

  chr2_112575093_   2570 CAGA-TTACAGCAATCCAGACAGTGTGGTATTGGCATAAGGATAGAGAAA 2618
                           i -i     i    v             i               v v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_112575093_   2619 TCCATCAAGGTAGTAAAAT--AGAGTCCAGGAATAAACCCATGCATGTGT 2666
                          vv     v v i  i   --         i           i   v i 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_112575093_   2667 GGTCAGTTGATTTTTGACAAAGGCACCAAGGC--TTACATGAAGAGAGGA 2714
                              i        i     i  ii     i --  vv   ii  i  i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_112575093_   2715 TAGTCTTTTTAATAAATGGTACTGGAACAACTGGATAA--ATGTGTAGGA 2762
                                  i  i       i    i           ?-- ii  i ii 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_112575093_   2763 AAAAAAATCATTAGACTTTTGTTGCACATCTCACA-----ATCAATTCAA 2807
                         i  vi  --i  i   iii iiiv    i vi i -----  i  i    
  L1M4_orf2#LINE/    443 GAATGAA--GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_112575093_   2808 GATGGATCACAGACCTAA-TGGAAAAGCTTCAACTGTTATTCTTCTAGAA 2856
                         i        ?        -  v  i    vv    i v vv  ii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_112575093_   2857 GAAAA-A-AGGAAAATATTTTAATGACGTTGGATGGGGTAAT---TTCTT 2901
                              - -   ?iv v  i  vi    v    i vi  i   ---     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_112575093_   2902 AG----GACATGAAAAACAGTAACCATTAAATTAAAAAAT-GA------- 2939
                           ----    iv    i  -i  v  vi   vv       -  -------
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_112575093_   2940 GACTTTATCAAAATTTAAAA--TCTATGCTCATCAGGAAGAAT----TTA 2983
                              i         v    -- i i    --   --   i i---- i 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCT--TCA--AAGGACACTATCA 685

  chr2_112575093_   2984 AGAAAATAAGAAGGCTAGCTACAG--TGGGAGATAAAATATTCTCAGTAC 3031
                              i i i   i v v i    --       --       i--- i v
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGA--AAATATTT---GCAA 730

  chr2_112575093_   3032 AT-ATATATCTGACAAAGGGCTTATATCCAGAATATAAGTAGAATTCCTG 3080
                           -          i  i  i   i             viv    i  i i
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_112575093_   3081 TAAATCAATAA----ATGA----TAACCTATGTTGCAAAAAATGAGCAGA 3122
                         i  v       ---- v  ----     i -i  --?       i   i 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCA-ATT--WAAAAATGGGCAAA 827

  chr2_112575093_   3123 AGACTAGTGTAGACA---CTTCAAAGAAGACATAGGAATGGCCAATAAAC 3169
                         i  i v vi      ---  i         i   vi            i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_112575093_   3170 CCGTTAAAAGGTGCTCAATATAATCAGTCAT 3200
                         v i v     i       i  v ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (104 / 45)
Gap_init rate = 0.04 (29 / 712), avg. gap size = 2.52 (73 / 29)  


4802 13.44 3.30 0.91  chr2_112599052_112602875     2461  3338 (486)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_112599052_   2461 ATTCCATGTTCACAGA-----AGACTTAACATTGTTAAGATAGCAGTCTT 2505
                           i         ii  -----        i           i   i vi 
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_112599052_   2506 CCCCAAATTGACCTA--GATTCTGATAATGCAATCCTTACCAGAATCCCT 2553
                                    i   --     ----  i       i  i  i      v
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTC----AACGCAATCCCTATCAAAATCCCA 105

  chr2_112599052_   2554 GCCAACTTCTTTGTAGAAATTGAGAAGCTGATTTTAAAATTCATATGCAA 2603
                           iiv   i    i         v        ii             v  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_112599052_   2604 TTTCAAGGGACCCAGAATAGCCAAAATAATGTTGAA---TAAGAACTAAG 2650
                         v v                       i   v     ---v      v   
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_112599052_   2651 A-GGAGGACTCACAC------ATCTCAAAACTTACTTTAAAGCAACTATA 2693
                         v-             ------  i            vi     v  vi  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_112599052_   2694 ATCAAGACAGTTAAGTAACTG-CAAAAGGATAG-TATATAGATCAATGGA 2741
                                    vvi   -   -  v        -i               
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTA-CTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_112599052_   2742 ATAGAATTCAGAGTCTAGAAATAAACCCATACATCTATGGTCAGATGACT 2791
                                 v      i                  i        iv   i 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_112599052_   2792 TTCAGCAAGAGTGCCAAGACCATTCAATGGAGAAAGAACAGTCTCTTTAA 2841
                            ii    i                    i       i     i  i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_112599052_   2842 CAAATAGTGCTGGGACAACTGCATAGCCACATGCAAAAGAATGAAGTTGG 2891
                              i               v   ?                        
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_112599052_   2892 ACTCCTACCTGAGAATATATACAAAAATTAACTCAAAATGGACCAAAGAC 2941
                           i       v v vi                          i  ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_112599052_   2942 ATAAATTTAAGAGCTAGATCCATAAATCTCTAAGAAGAAAACATACGGCT 2991
                         v     v         i v i     v    v             v ?v 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_112599052_   2992 AAATCTTCATGACCTTATATTTGACAAACTA--TTTTTAGAGTTCACGCC 3039
                                 i       ivi  v i   -- i--  i     vv v  i  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAA--TGGTTTCTTAGATATGACACC 602

  chr2_112599052_   3040 AAAAGCGTAAGCAACAAAAGAAAGAAACAGATAGATTGGACTTCATCAAA 3089
                               ii               -   i     i                
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAA 651

  chr2_112599052_   3090 ATTAAGAACTTTTGTGCTTCAGAGGACACTATCAAAAAA-TGAAAAT-CA 3137
                              i               i             i   -      v-  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_112599052_   3138 ACCCACAGAATGGGAGAAACTATTTGCAAGTCATATATCTGATCAGGGAC 3187
                                            v         i             v      
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_112599052_   3188 TTGTATCTAGACTGTATAAAGAACTCCTTCAACTCAATAATAAAAGGACA 3237
                                i   v i            i v                i    
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_112599052_   3238 AATAATCCAACCAAAACATGG-CAAAGGTTCTGAATACACATTTT----A 3282
                              i    ii?   v    -      v i      v      i---- 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_112599052_   3283 GGAAGATATACGACAGGCCAATAAGCACATAAAAAGATGCTCTA-ATCAT 3331
                         i          i vv               i           v -    ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_112599052_   3332 TACTAAT 3338
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.48 (68 / 46)
Gap_init rate = 0.02 (17 / 899), avg. gap size = 2.18 (37 / 17)  


2144 13.29 6.21 26.84  chr2_112699420_112703266     2218  3361 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_112699420_   2218 TGGAGAGACATTCCATGCTCACAGATCAGAATTCT--ATGT--------- 2256
                             i   i  i     i   ii   ii   vv  --  i ---------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_112699420_   2257 -GCAATTTTCC------------ACAGATGCAATGCAATCCCTATCAAAA 2293
                         -     vi   ------------      v   i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_112699420_   2294 TCTCAGCATGGGTTTTTTGCAGAA--TGTACAAGCTGATCTTAAAACTTA 2341
                           i    -  vv            --  -           i     i i 
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCA 148

  chr2_112699420_   2342 TATGGAAAAGCAAAAGATCCAGAGTAGCCAAAACAATCTTTGAAAAGTAG 2391
                                 v    ii  i     i                vi     v  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_112699420_   2392 AACAAAGCTAGACAGCTTACGCTTCCTTATTTCAAAACTTAGAACAAAGC 2441
                                i i  vii  i  i     iv             vv       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_112699420_   2442 TATAGTAATCAAGACACTGTGATAGTG-TATAAGGACACACATATAGAGG 2490
                           i             v    i  v  -i       i v         --
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA-- 296

  chr2_112699420_   2491 TCAATGGAACACAACTAAG--TACAGAAATAAATCCATACATTTATAGTC 2538
                                  i v  i i  -- v          i            i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_112699420_   2539 AGCTGATTTTTGACAAAGGCATGAAGGCAAGTCAGGGGGAAGGGGCAGTC 2588
                          ii       i     i  -------------------------------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGG------------------------------- 365

  chr2_112699420_   2589 TTTTTTTAAAATGGTGCTGGTGGCCAGGCACAGTGGCTCACCTTTGTAAT 2638
                         --------------   ---------------------------------
  L1M4_orf2#LINE/    366 --------------TGC--------------------------------- 368

  chr2_112699420_   2639 CCCAGAATTTGGGAGGCCAAGGTGGGCAGATCACCTGAGGTCAGGAGTTC 2688
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    369 -------------------------------------------------C 369

  chr2_112699420_   2689 AAGACCAACCTGGCCAACATAGTGAAAGCCTGTCTCTACTAAAAATAACA 2738
                                -------------------------------------------
  L1M4_orf2#LINE/    370 AAGACCA------------------------------------------- 376

  chr2_112699420_   2739 AAAATTAGGAGGCATGGTGGTACACACCTACAGTTCCAGCTACTCGGGAT 2788
                         ---------------------------------   v ------------
  L1M4_orf2#LINE/    377 ---------------------------------TTCAA------------ 381

  chr2_112699420_   2789 GCTGAGGCATGAGAATCACTTGAACCTGGGAGGCAGAGGTTGCAGTGAGC 2838
                         --  i  v --     ----------------------------------
  L1M4_orf2#LINE/    382 --TGGGGAA--AGAAT---------------------------------- 393

  chr2_112699420_   2839 CGAGACTGCACCACTGCACTCCAGTCTGGCAACAGAGTGAGACTCTGTCT 2888
                         ----------------------     -------------------- i 
  L1M4_orf2#LINE/    394 ----------------------AGTCT--------------------TTT 401

  chr2_112699420_   2889 CAAAAAAAAAAAAAAAAGTGCTGGGACAATTGGACATCTACATGTAAAAA 2938
                            v   vi--------            i    i ? i     i    i
  L1M4_orf2#LINE/    402 CAACAAATG--------GTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_112699420_   2939 AA---AGTTTTGCCCTTAACTCACACAATTCCTAAAAATTAACTCAAAAT 2985
                           ---    vvi   i  v       v  vivi                 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_112699420_   2986 GAATCATAGACATAAACACAAGAGCTAAAACTAGAAAATTTTTAGAAGAA 3035
                          i    ?    v    iii              v    i i         
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_112699420_   3036 AACATAAGAGCACATCTT-GTGACTTTGTGTTAGGCAATAAATTCTTAGA 3084
                               i ? i v     -     i   v          iiv        
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_112699420_   3085 TACAACACGGAAAGCATGATCCATAGAAGAGAAAACTGATAAACTGTACG 3134
                           ii    vi      ii v v i i    i    iv      i  v  v
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_112699420_   3135 ACATCAAAAT-GAAAACTTTGATGCTTCAAAAGATACCATTAATAAAAT- 3182
                         v         -i        vi         i  i  i  i  v   i -
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_112699420_   3183 --AAGACAAGCCACAGATTGGGA-----TATTTGCAAATCATGTATCTAA 3225
                         --       v       v     -----              i     i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_112699420_   3226 TAAAGGATCTGTATCCAACATACGTAAAGAACTCCTAAAACTCAATAA-- 3273
                            i   ii        iv   ii          i  v          --
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_112699420_   3274 ----GA-AAACAATCTAATTTTAAAATGGGCAGAG-ATCTAAACTGAC-- 3315
                         ----  -   i  i i    ?v          i  -  i i  iv   --
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_112699420_   3316 --------------TA-----ATGGCCAATAAGCACATGAAAAGATGTTC 3346
                         --------------  -----                          i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_112699420_   3347 ATAGTCATTTGAGAA 3361
                          vvi   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (98 / 50)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 14.00 (378 / 27)  

 359 25.50 8.50 7.00  chr2_112699420_112703266     3444  3643 (204)    L1M4_orf2#LINE/L1      247   449 (459)  

  chr2_112699420_   3444 GCTACGGTAATTAAGATAGTATA-TACTGG---AGAAAAAGACA------ 3483
                              i     i    i   i i-      --- iii v     ------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_112699420_   3484 --AATGGAGAAGAACTGACATCCCAGAAACAGACCTTCAGATCTTCACTT 3531
                         --      iv    i   v vi       i i   --  v ----  i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATA----CATTT 340

  chr2_112699420_   3532 GATGGAAACTTGACATATACCAAAAGGGGTATTACAGG----TTAGTGGG 3577
                         -    vv v    iv ---i i v i    iii -  i---- i i    
  L1M4_orf2#LINE/    341 -ATGGTCAATTGATTT---TCGACAAGGGTGCCA-AGACCATTCAATGGG 385

  chr2_112699420_   3578 GGAAAGAGCAGTCTTTTTAATTAAATAATGCTTGGGA-GATTGGTTATCC 3626
                          -     ii        i  i-    ii    -    -i i   v  ?  
  L1M4_orf2#LINE/    386 G-AAAGAATAGTCTTTTCAAC-AAATGGTGCT-GGGACAACTGGATAKCC 432

  chr2_112699420_   3627 ATGTGGGAAAAAGGGAA 3643
                          ii  vi   i iv   
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAA 449

Transitions / transversions = 2.85 (37 / 13)
Gap_init rate = 0.06 (13 / 203), avg. gap size = 2.38 (31 / 13)  


3151 23.96 1.98 2.20  chr2_112914213_112918618     3005  3914 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_112914213_   3005 TAGAAAGATATCCCATGCTCATTGGTC---AGATTTAATATCATTAAAAT 3051
                          i               i    v i i---   i       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_112914213_   3052 GATCATACTGCCCCA---TGCAATCTACATATTCAATGGGATCTCTATCA 3098
                          iiv     -     ---  --       v      i vi   i      
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_112914213_   3099 AAATACCAA-TGTCATTTTT-CAAAGAATTAGAAAAAAC--ATGCTAAAA 3144
                             v   i-  i v     -  i -    i-- v  i --  v      
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAA 144

  chr2_112914213_   3145 TTAACATGTAACCAAAAAAGAGCCGGAATAGCCAAAGCAATTATAAAACA 3194
                           v i   v  viiv  ii  v  i           i    iv i   - 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-A 193

  chr2_112914213_   3195 ACAACAACAAAGCTAAAGCTGTCACATTACCAGACTTCAAATTATAATAC 3244
                          v  v       i ii  vvv     i v  vi i      viv  v   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_112914213_   3245 AAGGCTGTAGTAACCAAAACAGTATGATACTCGTACAAAAATAGACACAT 3294
                           i   ii     i   i     i  i    v i i  ii       i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_112914213_   3295 AGATCAATGGAATAGAAAAGAGAATCCAGAAATAAAGCCACATATT-ACA 3343
                                          vv    i            v   i i   - ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_112914213_   3344 GCCAACTGATATTTGACAAAATCAACAAGAACATACAGTGGAGAAAGGAC 3393
                          i   i    v  i     iiviiv     v   v  i   i     i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_112914213_   3394 ACCCTTTTCAATAAATGATGCTGGGATAATTGGATTGGCATCTGCAGACG 3443
                          vi        i     i        i  i     v?v  iv    i v 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_112914213_   3444 AAAGAAACTGGACCACCATCTTTTACCATATAAAAAAATCAACTCAAGAT 3493
                           v   ii      v i i  ivi        v      i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_112914213_   3494 GGATTAAAGATTTAAATGTAAGATCCGAAACTACAAAAACACTAGAAGAA 3543
                             i ?   ii           v ii      i    vivi        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_112914213_   3544 AATCTGGGGAAAACTCTTCTGGACATTGATCTAGGCAAAAAATT----GA 3589
                           iv i  ?iv  v     vv   v   ivi       viiv  ----  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_112914213_   3590 TGACAAAGACCTCAAAAGCACAGACAACAAAAACAAAAATAGGCAAATGG 3639
                          ---- v   vi          ii        iv        ii    v 
  L1M4_orf2#LINE/    594 T----ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_112914213_   3640 GACTTAATTAAACTAAAAGGCTTCTGCACAGCAAAAGAAATAATCATCAG 3689
                              v  i   v v   ii   i  ii vv    i  v iv    vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_112914213_   3690 AGTGAACAGACAACCTGGAGAATGGGAGAAAATATTTACAAACTATGTAT 3739
                               v        iiv                   i    ii  i   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_112914213_   3740 --GACAGGGGACTAATGTCCAGAATTTACAAGGAACTCAAACAATGCAAC 3787
                         --  i i      vi i        v  i  i      vv    iv   i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_112914213_   3788 AACAACAACAACAAAATAGAAAACAATCCCATTAAACAATAGGCAAAGGA 3837
                           i  v  -i     --------i  i  v   ?  v   i         
  L1M4_orf2#LINE/    790 AATAAAAA-GACAAA--------TAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_112914213_   3838 CATGAATAGACACTTTTG-AAAGAAGACATACAAATGGCCAAGAGGCATA 3886
                         iv          i  i v-        i              v i   i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_112914213_   3887 TGAAAAAATGCTTAACATCACAAATCAC 3914
                               i     i       ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (134 / 80)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  


3410 24.80 2.23 0.78  chr2_112940614_112943784     1785  2679 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_112940614_   1785 TGGCAGAATATTCCA-ATCCATGGATTGGAAGAATTAATCATGTTAAAAT 1833
                            v ii    i   -i i              v     vv      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_112940614_   1834 GATAATTCTATTCAAGGCAATGTATAGATTTAGTGCAATCCCTATCAAGA 1883
                          ii   v  vii   ivii  v  i     i ii              i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_112940614_   1884 TACCAATTACATTCTCCACAGAAAT--AAAAACAAATCCTAAAATTTATA 1931
                          v   ii i v  i iii       -- v  i vi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_112940614_   1932 TGGGACCACAGAAGACACCAAACAGCCAAAGCAATCCTGAGCAAAAAGAA 1981
                            i vii  iii   v vi  i       i     i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_112940614_   1982 CAAAGCTAAAGGCATCACACT----GACTTCAAAATATACAACAAAGCTA 2027
                              i ii   vv       ----i i       iv   v         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_112940614_   2028 TAGTATCCAAATCAGCATGGTACTGGCATAAAAACAGACACATAGACCAA 2077
                         i    vi   iv   ii              ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_112940614_   2078 CCAATGGAATAGAATAGAGAACCAAGAAACAAATTCACACATTTGCAGCC 2127
                         ----           v    ii v     i   ii  i      iii i 
  L1M4_orf2#LINE/    301 ----TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_112940614_   2128 AACTCATTTTTGATAAAGGCACCAAGAACATATAATAGGGAAAGGACACT 2177
                           i v     i  i  i  ii      v   vi   i       i i v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_112940614_   2178 TTCCTCAATAAACCGTGCTGGGAAAACTGGATATTCACATGCAGAAGAAT 2227
                         i ii    i   iv         v         ?i        i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_112940614_   2228 GAAGCTAGACCCCTATCTTTCACCATACAGAAAACTCAAGTCAAAATGGA 2277
                             i i        i  iv       i v    v i  v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_112940614_   2278 TTAAAGACTTAAATCTAAGACTGGAAACTATGAAACTACTAGAAGAAGAC 2327
                          i ?    i     v     vivi       i     vi        i  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_112940614_   2328 ATTGGA-CAAACACTTCAGGACATTGGTCTGGTCAAAGATTTTTTGTGTA 2376
                           v  ?-i   i-    iv   v    vi i v   v i   i  ivi  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_112940614_   2377 AGACTTCAAAAGTACAGGCAAAATAAAGTAAAAATAGGCAAATGGGATTA 2426
                         v   vi      i   i    v -    v        ii    v   i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAATTGGACTT 644

  chr2_112940614_   2427 CGCCAAGCTACAAAGCTTCTGCACAGCAAAGGAAACCATCAA-AAAGTGG 2475
                          ii   iv vv   i   i  ii vv       v  i     -      i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_112940614_   2476 ACAGACAATCCACAGAATGGGAGAACATATTTGCAAACTATTCATCTGAC 2525
                          v      i                v           ii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_112940614_   2526 AAGGGACTAACAACCAGAATACACAAGGAGCTCAAACAATTCAATAACAA 2575
                                 vii v        i i  i  i   vv    i       i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_112940614_   2576 AAAAGAGAAATAATCCGACTTAAAAATGGGCAAAATATCTGAACAGAGTT 2625
                            -  v      i  i i ?             iv  i    i   vv 
  L1M4_orf2#LINE/    795 AAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_112940614_   2626 TTC-----ATAAAATAC------GGCCAACAGGTAAATGAAAACGTATTC 2664
                            ----- v  i   i------      i i i v       vi ii  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_112940614_   2665 AACATCACTAATCAT 2679
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (147 / 71)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.45 (27 / 11)  


3287 26.98 0.44 0.44  chr2_112977873_112984153.rev     4882  5789 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_112977873_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_112977873_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_112977873_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_112977873_   5030 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_112977873_   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_112977873_   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_112977873_   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5227
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_112977873_   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_112977873_   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_112977873_   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_112977873_   5378 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_112977873_   5428 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_112977873_   5478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5527
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_112977873_   5528 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_112977873_   5578 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5627
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_112977873_   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_112977873_   5678 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGAGACTTC 5727
                          i     i     v  i?    i     i     iv    i   v i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_112977873_   5728 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5777
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_112977873_   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3109 27.13 1.11 0.55  chr2_112997854_113002544.rev     3297  4199 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_112997854_   3297 TGGAAGACCATTCCATGCTCATGGATAGGAAGAATCAATGTTGTGAAAAT 3346
                              iivi  i     i        v      v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_112997854_   3347 GGCCATACTACCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3396
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_112997854_   3397 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3444
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_112997854_   3445 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 3494
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_112997854_   3495 AACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGGC 3544
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_112997854_   3545 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3594
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_112997854_   3595 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGTCACACATCTACAACC 3642
                                i    i--    i  --        vvi  i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_112997854_   3643 ACCTGATGTTTGACAAACCTGATAAAAACAAGAAATGAGGAAAGGATTCC 3692
                          vi    v  i     ivv  vi  i v  vvv    i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_112997854_   3693 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACATAGAAAGCT 3742
                           v  i  i              v      v  ?   i iii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_112997854_   3743 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAGGACGCA 3792
                            ii    i    v   i     v              i   ii i v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_112997854_   3793 TTAATGACTTAAATGTTAGATGTAAAACCATAAAAACCCTAGAAGAAAAC 3842
                          i ?v   i       v   vv      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_112997854_   3843 CTAGGCA-ATACCATTCAGGACATAGGCATGGGAAAGGACTTCATGTCTA 3891
                         v    ?i- v i -   iv   v v  vv i  v  v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_112997854_   3892 AAACACCAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGGATCTA 3941
                         vi            vvi          v      v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_112997854_   3942 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCA--GCAAA 3989
                           i   v v  i i   i  ii vv    i  v    i  vv -- ii  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_112997854_   3990 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACA 4039
                         v  i     i                 v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_112997854_   4040 AAGGGCTGATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 4089
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_112997854_   4090 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACGCTT 4139
                           iv    i     v  i?    i            v    i    ii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_112997854_   4140 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA- 4188
                            v        i  vi viii     v ii          i       -
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_112997854_   4189 --TCACTGGCCAT 4199
                         --   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3226 26.82 0.66 0.44  chr2_113082763_113089660.rev     5501  6406 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_113082763_   5501 TGGGAAAACATTCCATGCTCATGGATGGGAAGAATCAATATCGTGAAAAT 5550
                            i  i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_113082763_   5551 GGCCATACTTCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5600
                            v     i      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_113082763_   5601 TACCACAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5648
                          v   vvvi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_113082763_   5649 TATAGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTGGGCAAGAAG 5698
                            i   viiv  ii  v  v v        i      i  iiv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_113082763_   5699 AACAAAACTGGAAGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5748
                               ii    i vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_113082763_   5749 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5798
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_113082763_   5799 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACAGCTACAACCAT 5848
                                i    iv   ivii         vv   i   vi  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_113082763_   5849 CTGATCTTTGACAAACCTGACACACACAAGCAATAGGAAAAAGATTCCCT 5898
                         i    i  i     ivv  v  vivv  vv    i  i   ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_113082763_   5899 ATTTAATAAATGGTGTTGGGAGAACTGGCTAGCCATATGCAGAAAACTGA 5948
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_113082763_   5949 AACTGGACCTCTTCCTTACACCTTTTACAAAAATCAATTCAAGATGGATC 5998
                          ii      i  v   i     v v         i  i    i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_113082763_   5999 AAAGACTTAAATGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAACCT 6048
                          ?    i           v   ii  i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_113082763_   6049 --GAGCAATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGCCTAA 6096
                         -- ? i  - i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_113082763_   6097 AACACCAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGTGATCTAA 6146
                         i            vvi          iv     v  i    vv  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_113082763_   6147 TTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 6196
                          i   viv  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_113082763_   6197 AGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTATCTATCTGACAA 6246
                           i     i                vv       vii  v       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_113082763_   6247 AGGGCTAATATCCAGAATCTACAAAAAACTTAAACAAATTTACAAGAAAA 6296
                         i  i  vi          v  i   i    ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_113082763_   6297 AAGCAAACAACCCCATCAAAAAATGGGCAAAGGGTATGAACAGACACTTC 6346
                          ii    i     v  i?               i v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_113082763_   6347 TAAAAAGAAGACATTTATGCAGCCAACAG--ACATGAAAAAATGCTCATC 6394
                          vv        i  vi viii     i i--         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_113082763_   6395 GTCACTGGTCAT 6406
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2318 27.26 6.19 2.41  chr2_113368730_113371040.rev      947  1819 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_113368730_    947 GAGAGAGATGCTATGTTCATAGATTAGAAGAATCAAC--TGAATAAAGAC 994
                           i   v  v i        i    i     v i  i--  -- v    i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTG--TTAAGAT 50

  chr2_113368730_    995 ATCAGTTCTTTTTAAATTAATGTATAGGCATAATGCAATTCTTATCAAAA 1044
                         iv  i v  iiii     i  v  i  iivi  i     i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_113368730_   1045 TCTTCATAAGGCTTTCGGTTAGACATAGACAAAGTTATTTTAAAATTTAT 1094
                           i-  vvv v    ivvvi   v  v     iv v  ii       i  
  L1M4_orf2#LINE/    101 TCC-CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_113368730_   1095 ATG------TAAAGGCCCTAGAATATCCAAAAATTTTTTGAAAAAGAA-- 1136
                            ------i  i  v  i      v      vvv i           --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_113368730_   1137 -TAAAGCAGGAAAAA-CACTTTTCCTAATGCTAAGGCTTACTATATAACT 1184
                         -i    iv   ii v-   vi    i   vii  ii       i v i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_113368730_   1185 GCAATAATCAAGACAATGAGGTATTGGTGGAGGAACTGATGCATTTTTTA 1234
                         i  i           i  v    i   iiv i i iv  iii  vvv i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_113368730_   1235 AAAGTAACATGATAAAGAGCCCAGAAATAGACTCACACAAATATGTCCAA 1284
                          vi -  i vi  vi    i         i  i  i   vv    vi   
  L1M4_orf2#LINE/    300 ATGG-AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_113368730_   1285 TTAATTTCTGACAAAGG---CAA-----TTCAATGGAGGAAGGATACCCT 1326
                           i    ii     i  ---   -----        i i   i   vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_113368730_   1327 TTTCAATGAAAGGGAACTGGAGCAATTAAA----CATATGTAATTTTTTT 1372
                               i-   v  vi    ii   i ii ----  i   i  -------
  L1M4_orf2#LINE/    399 TTTCAAC-AAATGGTGCTGGGACAACTGGATAKCCACATGCAA------- 440

  chr2_113368730_   1373 TTAAAAAACCCTAAACCTAAACATCTACCT------ATATACAAAAATTA 1416
                         ---  i  --- i  vi ii  vi      ------              
  L1M4_orf2#LINE/    441 ---AAGAA---TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_113368730_   1417 ATTAACAATGGATCATGGACTCCAATGTAAAACATGAAACTCTAAA-CTT 1465
                          i v v         ?i   iiv       i vv i     v    -  i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_113368730_   1466 CTAGAAAAAAA-ACTGGAGAAAACCTTTGGTACCTATGACAAGGCA-CAG 1513
                         i     i    - iv  ? v   i   i vv    vv iiv     -ii 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_113368730_   1514 TTT-TTAGACTTAACACTAGAAGTGTGAACTATACAAGAAAAAATTAATA 1562
                            -     iv i    i i   iiii i v i v          vi   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_113368730_   1563 ATTTGAACCTTATGAAAATCAAA--TTATTTGCTCTCCAAAAGACCCTGT 1610
                          v   i  i i  v     i   --i -    iv  i    i   v  i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACT-TTTGTGCTTCAAAGGACACTAT 683

  chr2_113368730_   1611 TAAGAGGATGAAAAC-TAAATTACAGATTGAGAGAAAATATTTGTAAATC 1659
                         i    iii      v-i  vii     v  i             i     
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_113368730_   1660 ACATATTTGACAATGGACTTGTATCTAAAATATCTAAAGAACTCTCAAAA 1709
                          i    i   i  v           i i     v           i v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_113368730_   1710 CTCAACATTAAAAA---AAATA-TCTAATTAGAAAATGAG---------T 1746
                              i v      ---     -i i    ?i      i --------- 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_113368730_   1747 GAA----CATTTTACGAAAGGGGCCTTATAGATTAGCAAATAAAACACTT 1792
                            ----     iv v    ii viv  i i  -i  v     i-   v 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAAT-GGCCAATAAG-CACAT 881

  chr2_113368730_   1793 GAAAAGATACTCAGCATCACTAGCCAT 1819
                                 i    i     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (155 / 80)
Gap_init rate = 0.03 (27 / 906), avg. gap size = 2.78 (75 / 27)  


2615 24.21 3.60 1.30  chr2_113417840_113419496.rev      474  1167 (490)    L1M4_orf2#LINE/L1      199   908 (0)  

  chr2_113417840_    474 AGCAGATTTCAAAGACCTAGTACATGCCCTGATTTCAAGCTATATTACAA 523
                          i  i v  vi i   ii ---  ivi  ii       iviv  i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCA---CACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_113417840_    524 AGCTGTGGTAATCAAAACAGTATGGCATTGGGAAAAAAATAGACACATTG 573
                             iii        i     i   i i   v v  ii       i  v 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_113417840_    574 GTCAATGTGACAGAATAGAGAGCCCAGAAATAAACCCGTGCATGTATAGT 623
                         i      vi i     v     i              i i   v   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_113417840_    624 CAACTAATCTTTGACAAGAGTACCAAGAATACACAATGGGGAAAG----- 668
                            i i  i  i      i  i      vi iv            -----
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_113417840_    669 TCTCTTCAATAAGTGGTGTTGGGAAAACTAGATATCCACATGCAAAAGAA 718
                            i     i  i     i     v    i    ?               
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_113417840_    719 AGAAATTAGACCCTTGTATTACACAAAAT-CTAAAATTAATTCAAAATAG 767
                         v   i  i     i iiv i    v v  - v        i       i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_113417840_    768 A-AAAAGACTTACATGTAAGATCTAAAACCATAAAACTCCTAGAAGAAAA 816
                          -v ?    i  v        v       i         i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_113417840_    817 CATAGGGAAAGAGCTCCTTGACACTGGCATTAG-CAGTAATTTTTCAGAT 865
                               ?iv i v  i v    vi   -i    -  i ii   i i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGAT 594

  chr2_113417840_    866 ATAACATCAAAAGTACAGGCAATGAAAGCAAAAACAAGTGA----GAGTA 911
                           i   i      i   i    ii    v     i ii i ----  v v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_113417840_    912 TATCAAACTAAAAAGTTTCTGCACAGCATAA-ACA--ATCAACAGAGTAA 958
                         i      v v    ii  i  ii vv  v i-   --     v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_113417840_    959 AGACATGACGTATGGAATGAGAGAAAATATTGACA---------TCTGAC 999
                          i v ii  vi ii     i           vi  ---------     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_113417840_   1000 AAAGGGTTAATATCCAAAATATATAAGTAATTCACACAACTCAGTAACAA 1049
                           i  ii vi      i         iv  i  vi        i   i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_113417840_   1050 AA-GCCAAATAACCTGACTTTTTTTTAAAATGGGCAAAGTACCTGAATAG 1098
                           - v         ii -----  ?v             v ii       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAA-----TTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_113417840_   1099 GTATTCCTCAAAAGAAGACATACAAATGGCCAAGAGATGTATGAAAAGCT 1148
                         ii   i   v        i              v iiiii        v 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_113417840_   1149 GCTTAACATAACTAATCAT 1167
                            i     v ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.42 (116 / 48)
Gap_init rate = 0.02 (12 / 710), avg. gap size = 2.83 (34 / 12)  


 580 25.66 7.92 4.53  chr2_113516338_113518277.rev      358   622 (1318)    L1M4_orf2#LINE/L1        3   276 (632)  

  chr2_113516338_    358 GAACGATATGCCTTCCTCAAGGGTCAGAGGATTCAATATTATTAAAAAGT 407
                            v     v  v vi   v  i ii  i  i i      i    i v v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_113516338_    408 GAATTTTCCCCAACTTGACCTGTAGATCCAATACAATCCCAGTCAAAATC 457
                         v   vi       v    i  ii    i   ii       vi        
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_113516338_    458 CTAGCAGGCTTTTATTAAAGAAATTGACATGCTGATT-----ATTACATG 502
                          i   v v     -  iv           v      i-----   -   i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATT-CATA 150

  chr2_113516338_    503 TGGCATTGGCAAA------AAGATAGACAAATAGGTC--AATGAAAAAGG 544
                            v v  -   i------ ii    v    vvii  --i vi  i   i
  L1M4_orf2#LINE/    151 TGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_113516338_    545 ATAGAGTCCAGAAATAGACTTACACAT----ATATGAACAACTGATTTTC 590
                          i i   i-- i i--    i    v ----  v v  -    v i ---
  L1M4_orf2#LINE/    200 ACAAAGTT--GGAG--GACTCACACTTCCCAATTTCAA-AACTTACT--- 241

  chr2_113516338_    591 AACAAACATACA--AATACAACCAGTGTGG--CTGG 622
                         -     vv    --   vv iv        --    
  L1M4_orf2#LINE/    242 -ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

Transitions / transversions = 1.27 (38 / 30)
Gap_init rate = 0.05 (13 / 274), avg. gap size = 2.54 (33 / 13)  

1225 27.41 2.41 3.52  chr2_113516338_113518277.rev      911  1450 (490)    L1M4_orf2#LINE/L1      375   908 (0)  

  chr2_113516338_    911 CAATCAGTGGAGAAAAAAATACCATGTTCAACAAATGGTGACAAATCAAT 960
                           v   i   i    i  -  viv v              viiiiv   i
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAA-TAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_113516338_    961 GAGATATTCATATAATGACAACAAAAAGGTGAATTATGATCCATTTCTTG 1010
                         vi    ?i  i  i-------     iii    v vv  i  v vi  ii
  L1M4_orf2#LINE/    424 TGGATAKCCACATG-------CAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_113516338_   1011 CAGCATATGGAAAAAT-AATTCAAAATTGATCATAAATCAAAATGGAAAA 1059
                           v     iv      -  i       v     ? i i v     v  i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_113516338_   1060 CATAAT-CTACAATGCT-TCATAATTAAACATAGAAG-AAACCTTTTTCA 1106
                         vv   v-   i  vi  - i v  vv        i? -   i   iv v 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_113516338_   1107 TTCTA--TTAAGCAAAGATTTCTTAGATA---CAGTGAGAAATTATGGTA 1151
                         iii i--   i    v i           ---  vii i ivvi v vv 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_113516338_   1152 CGTATGATTTTTTAAATTGCTAAATTTGACTTTATTAAAAACAAAAATTT 1201
                          iv v  vv----    v v      v     i  i    vi     i  
  L1M4_orf2#LINE/    617 CAAAAGAAA----AAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_113516338_   1202 CT---TTTTGAAAGATTCTATTCAGAGAATGAAAAGAGAAGTCACTGACT 1248
                         i ---i  ii  i  iv    iv   i i        v  vi   v  v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_113516338_   1249 GGGA-AAAATACTTGTAATGTATATATCTGAGAAAGGACTTGTATCCACA 1297
                             -      i   i  vvi          v  i             v 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_113516338_   1298 GTATATAAAGAACTCTCAAAACTTAATAAAAAGGAAACAAAAAAGACAAT 1347
                         i               i v    i     v  ii i     v  vv    
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_113516338_   1348 TTTTAAAATGGGCAAAAACTTAGAACAGATATTTGTATCAAATAATATAT 1397
                          ?v-            iiv  v   i   i    v -i    v  v    
  L1M4_orf2#LINE/    813 TWA-AAAATGGGCAAAGGATTTGAATAGACATTTCT-CCAAAGAAGATAT 860

  chr2_113516338_   1398 ACAGATGACCAAAACAAAAAGCCTACAAAAAGATGTTCAATATAATTAGT 1447
                            i   i    v -----   vi ii        i    i  v ?????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATA-----AGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_113516338_   1448 CAT 1450
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.22 (79 / 65)
Gap_init rate = 0.03 (14 / 534), avg. gap size = 2.29 (32 / 14)  


2234 26.31 0.60 1.20  chr2_113568493_113570153.rev      501  1169 (492)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr2_113568493_    501 AAGGCCATAGTCACCAAAACAGCATAGTACTGGTATAAAAATCAGCATAT 550
                           i  i i   v i   i    ii i       i    ii  vii     
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_113568493_    551 AGACCAATGGAACAGAATAGAGGACCCAGAAATAAAGCCAAATACTTACA 600
                            i        i     v   iii           v   v i i   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_113568493_    601 GTCAACTGATCTTTGACAAAGCAAACAAAAACGTAAAGTGGGAAAAGGAC 650
                              i    i  i     i vviv   i v i vv i    i    i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_113568493_    651 ACCCTATTCAACAAATGGTGCTGAGATAATTGGGAAGCCACATGTAGAAA 700
                          vi  v                 i  i  i   iv ?       i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_113568493_    701 AATGAAACTGGATCCTCATCTCTCATCTTATACAAAAATCAACTCAAGAT 750
                               ii    i  ii i   v  i v           i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_113568493_    751 GGATCAAGAACTTAAATCTAAGACCAAAAACCATAAAAATTCTAGAAAAC 800
                               ?ii  i     v     v v     i      v ii     i -
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA- 542

  chr2_113568493_    801 CCTTCTAGACATTGGGA-AACCCTTCTAGACATTGGCTTAGGCAAAGTCT 849
                         ------ i    v  ?i-  vi    vv   v    v        v vi 
  L1M4_orf2#LINE/    543 ------AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_113568493_    850 TCATTACCAAGAACGC-AAAAGCAAACACAACAAAAATAAAGACAAATAA 898
                           -   vvv vi  i -       v vi        iv   i i i    
  L1M4_orf2#LINE/    587 TC-TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_113568493_    899 ACGGCACTTAATTAAAATAAAAAGCTTCTGCACAACAAAAGAAATAATCA 948
                          iv v    v  i     v    i   i  ii vv    i  v iv    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_113568493_    949 ACAGAGTAAACCGACAACCCATAGAGTGAGAGCAAATCTTCACAATCTAT 998
                          v i   i  vv         i   i  i   v    v  ii   vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_113568493_    999 ACATCCAAAAAAGGACTAATATCCAGAATCTACAAGAAACTCAAACAAAT 1048
                          i   ii v  i     vi          v  i  ii     vv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_113568493_   1049 CAGCAAGAAAAAAA--AACAAACCCATCAAAAAGTGGGCTAAGGACATGA 1096
                           ii  v     i --  i  v  v  i?    i     v     iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_113568493_   1097 ATAGACAATTCTCAAAAGAAGATATAGGAATGGCCAACAAACTTATGGAA 1146
                                v     v            vi         i  i vi   i  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_113568493_   1147 AAATGTTCAATATCACTATCAGG 1169
                          i   i    i    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (108 / 64)
Gap_init rate = 0.01 (5 / 665), avg. gap size = 2.40 (12 / 5)  


1037 30.61 4.33 4.01  chr2_113818685_113820300.rev      501  1124 (492)    L1M4_orf2#LINE/L1      283   908 (0)  

  chr2_113818685_    501 GATAGAGAAATTATCCAGTGGAA-AGGATCACAGAACCCAGAAATAGATC 549
                               v v  vivi  i     -  i  ii-   ii         i i 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTG-AGAGTCCAGAAATAAACC 331

  chr2_113818685_    550 CACATATATATGAACACCACTTAATATAAACACAACTGACAGTGCAGCTC 599
                           i i  v    iv  -- i v v v vi   viiv  v  ivi vii  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCA--ATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_113818685_    600 AACAAGGAAAGAACAGACTATTCAACAAATCTCACTGCAACAACTATTTA 649
                           iii        i  v  v          vvii   vi      ivv  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_113818685_    650 ACCATA--CAAACCACCTAAATTGGAATTCTACTTCACAGCGTACATAAA 697
                         ?   i --    vv viv  i     vii    i     v i  i i   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_113818685_    698 A-TCAATTCTAGGTGGCTTAATAACTTAAATATGTAGGGTAAAATT-TAA 745
                          - i  i  v ii   v i ?vi  i     i ivii v     i -   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_113818685_    746 AACT-TTAGAAGACAATATGAGGGAATATCTT--TGACTTTAAGATAGGA 792
                             -        v  i  ii ? v v     --    i  ii v    v
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_113818685_    793 AATACTTTTGTTTTAAA----ACACCATATAAAAATAAAACTCATAAA-G 837
                            iv   i---   i ----      ----   ii v  viv i   - 
  L1M4_orf2#LINE/    580 AATGGTTTC---TTAGATATGACACCA----AAAGCACAAGCAACAAAAG 622

  chr2_113818685_    838 AAAAGAT---TAACTTTGACTATGTTGAAATCAAGAATGTGGGTTCATCA 884
                             i  ---   v  v    vii ii    i  i  iv vv  v v   
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_113818685_    885 AAATACACTAT-AAAAAATTGAAAAGACTAGGCACAATCTGGGAGAAAAT 933
                           iv       -  i   v         v vv    ivv           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_113818685_    934 ATTTGCAACACATATA----ATCAACCACAGGTTTTCAGGACA------G 973
                                 vv      ----  v ivv  vv  v i   i i ------ 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_113818685_    974 AGTTTCTGCAAATCAGTAAGAAAAAGGCAAACAGCTTAACAACGACAACA 1023
                          ii ii i   v   i   v      i    i i ii  i----------
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT---------- 812

  chr2_113818685_   1024 ACAACAACAAATGTCAAAAAAATCATGAATAATCGTTTTACAGAAGAGGA 1073
                         ----i? v     vvv   ii  i-      iv i   iv vi    i  
  L1M4_orf2#LINE/    813 ----TWAAAAATGGGCAAAGGATT-TGAATAGACATTTCTCCAAAGAAGA 857

  chr2_113818685_   1074 AACACAAGTTTCCAATAAGCATACAAAAATCCATTCAACCTCACCAGTAA 1123
                         v i    i vv          i ii    vviii     v   ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_113818685_   1124 G 1124
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.34 (107 / 80)
Gap_init rate = 0.03 (18 / 626), avg. gap size = 2.89 (52 / 18)  


3189 27.39 0.44 0.55  chr2_113945542_113951852.rev     4911  5819 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_113945542_   4911 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4960
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_113945542_   4961 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5010
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_113945542_   5011 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5058
                          v    ivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_113945542_   5059 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5108
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_113945542_   5109 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5158
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_113945542_   5159 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATT 5208
                                 i   i    ii         i iv ii i   v        i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_113945542_   5209 CATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5256
                         v      i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_113945542_   5257 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAGTGGGGAAAGGATTCC 5306
                          vi    i  i     ivv  vv  i v  vv  i         i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_113945542_   5307 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5356
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_113945542_   5357 GAAACCGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAACATGGA 5406
                            iii   i    v   i     v           i  i    v     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_113945542_   5407 TTAAAGACTTAAACGTTCAACCTAAAACCATAAAAACCCTAGAAGAAGAC 5456
                          i ?    i    i  vvi v       i      vi i        i  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_113945542_   5457 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5506
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_113945542_   5507 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATCTAA 5556
                         i            vvi          vv     v  i i  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_113945542_   5557 TTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5606
                          i   v v  v i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_113945542_   5607 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5656
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_113945542_   5657 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5706
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_113945542_   5707 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5756
                          i -    i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_113945542_   5757 CTCAAAAGAAGACATTTATGCAGCCAAAGAACACATGAAAAAATGCTCAC 5806
                            v        i  vi viii     vi i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_113945542_   5807 CATCACTGGCCAT 5819
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3199 26.58 1.11 0.55  chr2_114132205_114136758     3160  4062 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_114132205_   3160 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATCATGAAAAT 3209
                              ii i  i     i i    i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_114132205_   3210 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3259
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_114132205_   3260 TACCAATTACTTTCTTCACA-AGATTGGAAAAAACT-ACTTTAAAGTTCA 3307
                          v   ii i i  i  ii  - i    -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_114132205_   3308 TATGGAACCAAAAAAGAGTCCGCATCACCAAGTCAATCCTAAGCCAAAAG 3357
                                viiv  ii  vi v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_114132205_   3358 AACAAAGCTGGAGACATCACCCTACCTGACTTCAAACTATACTACAAGGC 3407
                                i     ivv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_114132205_   3408 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3457
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_114132205_   3458 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 3505
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_114132205_   3506 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGAAAAGGATTCC 3555
                          vi    i  i     ivv  v   i v  vvv      i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_114132205_   3556 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3605
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_114132205_   3606 GAAACTGGATCACTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3655
                            ii    i v  v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_114132205_   3656 TTAAAAACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3705
                          i ? i  i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_114132205_   3706 CTAGGCA-ATACCATTCAGTACATAGGCATGGGCAAGGACTTCATGTCTA 3754
                         v    ?i- v i -   ivv  v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_114132205_   3755 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3804
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_114132205_   3805 ATTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGAA 3854
                           i   v v  i i   i  ii vv v  i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_114132205_   3855 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 3904
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_114132205_   3905 AAGGACTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 3954
                          i     vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_114132205_   3955 AA-----ACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 3999
                           ----- i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_114132205_   4000 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 4049
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_114132205_   4050 CATCACTGGTCAT 4062
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


1647 24.82 2.95 0.98  chr2_114158758_114166674     5510  5916 (2001)    L1M4_orf2#LINE/L1        1   415 (493)  

  chr2_114158758_   5510 TGGAGAAATATGTTATGTTCCTGGGTCAGAAAACTCAGTATTGTTCAGAT 5559
                             i i    vii      v   i ii   i   i i       v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_114158758_   5560 GGCAATTCTACCCAAATTTACCTACAAATTCAAATGCAATCCCTACCAAA 5609
                               v  v        v i     i      -i          i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAA 99

  chr2_114158758_   5610 ACTCCAGTTAGGATTTT-GTAGAAATTAGCAAGTTGATTCCAAAATATAT 5658
                          ii    i ivvv    - i       ii    i    i i     vi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_114158758_   5659 ATTAAGATGCAAAGGATGTAGACTAGCCAATGTAAGTTTGAAAAAAAACC 5708
                           vi i      i   ivi   v       vii  vi        i  vv
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_114158758_   5709 CACAA----------TTCATATTACTTCACTTCAAAATTTACTGTAAAAC 5748
                         -    ----------i   i i v iiv i       i     ii   i 
  L1M4_orf2#LINE/    200 -ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_114158758_   5749 TAGAGTAATCAACTCAGGGCGGTATTGGCATACAGACAGACATGTTGGTC 5798
                           v         vv   v i    i       vi  i      i v i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_114158758_   5799 AATGGAACAGAATAGAGAGTACAAAAATAAACCTTTACATTTATGGACAA 5848
                                i     v      v  i         iv           v   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_114158758_   5849 TTGATTTTTGACAGTGGTGCAAAGGCAATCCC-CGTAGAAAAGACAGCTT 5897
                                 i    iv     v   i v  i v-i vi    ii i  -- 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG--T 396

  chr2_114158758_   5898 TTTTTCAACAGATAATGTT 5916
                         i         i  ii  i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCT 415

Transitions / transversions = 1.97 (67 / 34)
Gap_init rate = 0.01 (6 / 415), avg. gap size = 2.67 (16 / 6)  

1484 21.40 4.59 3.71  chr2_114158758_114166674     6975  7432 (485)    L1M4_orf2#LINE/L1      447   908 (0)  

  chr2_114158758_   6975 GAGGTTGTACTAATTTACATTCCCACCAGCAGATATACACAAAAATTAAT 7024
                           i    v  i--ii   -i  v     -------  i           i
  L1M4_orf2#LINE/    447 GAAGTTGGACC--CCTAC-CTCACACCA-------TATACAAAAATTAAC 486

  chr2_114158758_   7025 TTAAA-TGGACCATAAGCTTCCATGTAAGAACTAAAACTATAAAACTTCT 7073
                          i   -    i  ? ii i vv        i                i--
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC-- 534

  chr2_114158758_   7074 TTAAAAGA-----TAGAAGAAAAATCTTTGTGGCCTTGAATTAGGTAAAA 7118
                            i    -----   i? v   -    i   i     ii     i  vi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_114158758_   7119 AAAAGATTTTTAGATTTGACATCAAAAATATGATTCATAAAAGAAAATAT 7168
                         ---- v  i      v     i     ii ii viv i         v  
  L1M4_orf2#LINE/    584 ----GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_114158758_   7169 TGATAAATTATACTTCAACAAAATTTAAAACTTTTCTTCTTCAAAAGACA 7218
                         v        iv      v       v         v v       i    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_114158758_   7219 GCATTAAGAAAGTAAACAGATAAACTATACACTTGGAGAAAATATTTGCA 7268
                         vi  i        i  v   i  v i i v v v                
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_114158758_   7269 AATGGTTTATTTGATCAAGGATTTATATACAGATAATGCAAAGAATTTGA 7318
                            vi v   i    v i   i  i   v    vv  ii      i ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_114158758_   7319 ACAGCTCAATAGTTAGAAG---------CTAATT-AAAAATGTGTAAAGG 7358
                            i       i v i   --------- i    -       v i     
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_114158758_   7359 ATTTTAGTAGACATATCACCTAAGAAGATATATAAATGGCTAA----CAC 7404
                             v i       v  v  v           i       i  ----   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_114158758_   7405 ATGAAAA-ATGTTCCAAATAATTAATCAT 7432
                                -   i  v v  v ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (56 / 40)
Gap_init rate = 0.03 (12 / 462), avg. gap size = 3.17 (38 / 12)  


2290 21.81 1.24 3.19  chr2_114251848_114254421      523  1086 (1488)    L1M4_orf2#LINE/L1        1   553 (355)  

  chr2_114251848_    523 TGGAAATACATCCTCTGTTCATGGATTAGGAGAATTAATACAGTTAAAAT 572
                               v i    iv            i i   v      iv     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_114251848_    573 CTCCATGC-CACTAAACATGAACTACATATTCAATGCAATTCCCATGAAA 621
                         vv v  i - v i   i-   v     v      i     i  i  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_114251848_    622 ATTCCAATAACATTCTTCACAGAAATAGAAAAA--AGTCCTAAAATTCAT 669
                           i   iivi v  i  ii       v  v  i--ii             
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_114251848_    670 ATGGAACCACAAAAAACCCCAAATAGCCAAAGCAATGTTGAACAAAAAGA 719
                               vii   iii    vi          i    v     v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_114251848_    720 ACAAAGCTGGAGGCATCATACTATCTGGTTTCAAAATATACTACAAAGAT 769
                               i      vv   i   vi iii        iv          v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_114251848_    770 ACAGTAATGAAAATGGCATGGTACTGGCAAAACAAACAAACAAAAAAACT 819
                                 v  i ii ii           v  -ii i i   --------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAA-GGATAGACA-------- 290

  chr2_114251848_    820 GGATGCATAGACCAATGGAAGAGAATAGAGAGCCCAGAAATAAATCCACT 869
                         -----i     i        v     v     i           i   - 
  L1M4_orf2#LINE/    291 -----TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-T 334

  chr2_114251848_    870 TCATTTATAGTTAATTGATTTTCAACAAAGGTGCCAGGAACACACAATGA 919
                         v       i  i           i    i       i  v  iv     i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_114251848_    920 GGAAAGGAGAATCTCTTCAGTAAATGATGTTAGGACA-CTCGATATCCAC 968
                               i v i   i    ii     i  i i     -  v    ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_114251848_    969 ATACA---GAATGAAATTAGACCCTTATCTCTCATGTCATATTAAAAAAT 1015
                           i  ---       i  i     i  i   v  i--     vv      
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC--CATATACAAAAAT 482

  chr2_114251848_   1016 CAACTCAAAGTGGATTAAAGACTAAAATGTAAGACCTGAAACTATAAAAG 1065
                         i        i     i ?    iv          v  i           v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_114251848_   1066 TATTAGAAAAAAATAGAGAGG 1086
                          v      i    i v  i? 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNG 553

Transitions / transversions = 1.93 (79 / 41)
Gap_init rate = 0.02 (9 / 553), avg. gap size = 2.78 (25 / 9)  

1009 25.44 1.41 0.00  chr2_114251848_114254421     1378  1660 (914)    L1M4_orf2#LINE/L1      539   825 (83)  

  chr2_114251848_   1378 AAAAAAAC-CAGGGGGAGAGCTCCCTGACAGTGGTCTGGGCAATGTTTTT 1426
                           i     -i   ? v i v  i v    vv   vi i       v   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_114251848_   1427 TTGGATGGAAACCCAAAAGCACAGCCAACAAACCAAAAA-TAGACAAAGA 1475
                           i   ivi vv           iv       vv     -    i   vv
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_114251848_   1476 GGGTTATATCAAA-CTAAAAACTTCTGCACAGCCAAGGAAATAATGAACA 1524
                           ii vi      -i         i  ii vv v     v iv  v  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_114251848_   1525 GAGTGAAGAGACAACCTGTAGAATGGGAGAAAATATTTGTAAACCATTTA 1574
                         i      i        iii                    i   i   v  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_114251848_   1575 TTTATGAAGGGGCT-ATATGCAAAATATATAAGGAATTCAAGCAACTCAA 1623
                          i ivv     i  -i   v  i         i   i  vvi        
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_114251848_   1624 TAGTAAGAAAACAAGTAACCTAATTAAAAAATGGTCA 1660
                           i   i  i    i     i    ?        v  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 1.33 (40 / 30)
Gap_init rate = 0.01 (4 / 287), avg. gap size = 1.00 (4 / 4)  

 281 21.83 7.04 1.41  chr2_114251848_114254421     1941  2082 (492)    L1M4_orf2#LINE/L1      759   908 (0)  

  chr2_114251848_   1941 CAAAATAAATAAATAA-----ATAAATAAA-AATAAAAATA-AAATAAAT 1983
                           i    v     v  ----- i  v v  -        v -      vi
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_114251848_   1984 AAAT-AAAAAATGGGCAAAGTGCCTGAATGG-CATTTCTCAAAAGAAAAC 2031
                         v   -?              viii     i -        v      i i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_114251848_   2032 ACACAAATGCTCAGCAGGTATATTTTTTAAG-TGTTCAACATCATTAATC 2080
                          i       vi  ii i i i  vvv--   -  i         ??????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAA--AAGATGCTCAACATCAZZZZZZ 906

  chr2_114251848_   2081 AT 2082
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.31 (17 / 13)
Gap_init rate = 0.05 (7 / 150), avg. gap size = 1.71 (12 / 7)  


3851 16.08 6.23 0.50  chr2_114379551_114381340.rev      501  1302 (488)    L1M4_orf2#LINE/L1       61   908 (0)  

  chr2_114379551_    501 CCCAAATCGATCCACAGATTCAA-GCATTTCCCATCAAAATCCTAA-TAA 548
                                i    i          -   v i  i          i i- iv
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr2_114379551_    549 CATTTTTGCAGAAATAGAAAAATCCATCCTAACATTCATATGGATCT-CA 597
                          v             v  v  iiiv       v           vv -  
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_114379551_    598 AAGGATCCTGAATAGCCAAAATAATCCTGAAAAAGAA---CAAAGTTGGA 644
                          i   i  v            i    i          ---          
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_114379551_    645 GATCTCACACTTCCTCATTTTAAAAGTTACTACAAAGCTATAGTGACCAA 694
                          iv           iv    i    v              i   i i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_114379551_    695 AACAGTATGGTACTGGCATAAGAACTAACA-----------------GAA 727
                         i     i               i ivi   -----------------   
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_114379551_    728 TCAGGAGCCCAGAAATAAACTCTCACATATATAATTAAATGATTTTTAAC 777
                          iii   i            i vi    v   ii i  v       ii  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_114379551_    778 AAGGATGCCATAACTACTAAGATGAAGAAAGGACAGTCTTTTGAACAAAT 827
                             i     vi  i i v -   ii     i i        v       
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCA-ATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_114379551_    828 GGTGCTGGAA-AACTGGATATCCACATGCAAAAGAATGAAGTTGTACCTT 876
                                 i -         ?                       v   ii
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_114379551_    877 TACCTTACACCATACACAAAAGTTAACTCAAAGTTGATCACAGACCTAAA 926
                              i        i      i          i v     ?         
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_114379551_    927 CACAAGAGCTAAAACTATAGAACTCTTAGAAAAAAAACATAAGGTGAAAA 976
                         iii                i           i    -    -  ? v   
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATA-GGNGTAAA 557

  chr2_114379551_    977 GCTTCATGATACTAAATTTGGCTATGATCTCTTGGCTATGACACCAAAAG 1026
                         v    i   ivi iii  v   v   i i    i v              
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_114379551_   1027 CACAAGTAACAAAAGAAAAAA-AGAGAAA---AACTTCATCAAAATTAAA 1072
                               i              -   v   ---i                 
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_114379551_   1073 AACTT--GTGTATCAAAGGACACTATCAA--CAGTGGAAAGGCAATCCAC 1118
                              --   iv                 --v    i    i   i    
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_114379551_   1119 AGAATGGGAGAAAATATTTGCAAATCAC-TATCTG-TAAGGGATTAATAT 1166
                                                    i-      -       i vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_114379551_   1167 CCAGAATA----AAGAAC------AACACAACAATCAAAAAA-----AGC 1201
                                 ----      ------   v   i   v    i ----- i 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_114379551_   1202 CCAACTGAAAAATCAGCAATCAACCTGTAAT-GACATTTCTCCAAAGAAA 1250
                             i ?      vi    vvi ii  -   -                 i
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTG-AATAGACATTTCTCCAAAGAAG 856

  chr2_114379551_   1251 ATATACAAATGGCCAATAAACACAAGAAAAGATGTTCAACCTTACTAATA 1300
                                            i    v         i     v i ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_114379551_   1301 AT 1302
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.21 (86 / 39)
Gap_init rate = 0.02 (20 / 848), avg. gap size = 2.70 (54 / 20)  


3126 27.89 0.55 0.44  chr2_114487034_114493433.rev     5002  5908 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_114487034_   5002 TGGAAGAACATTCCATGCTCATTGATAGGAAGAATCAATATTGTGAAAAT 5051
                              ii i  i     i    v   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_114487034_   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_114487034_   5102 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_114487034_   5150 TATGAAACCAAAAAGGAGCCTGCATTGCCAAGTCAATCCTGGGCCAAAAG 5199
                             i  viiv  i   v  v v  v     iv     i  iivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_114487034_   5200 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5249
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_114487034_   5250 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5299
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_114487034_   5300 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGTTGCATATCTACAACT 5347
                                i    i--    i  --        vviiii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_114487034_   5348 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAATGGATTCC 5397
                          vi    i  i     ivv  vv  i v  vv          v i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_114487034_   5398 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5447
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_114487034_   5448 GAAACTGAATCCCCTCTTTACACCTTACACAAAAATTAATTCAAGATGGA 5497
                            ii  i i   iv i i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_114487034_   5498 TTAAAGACTTAAATGTTAGA-CTAAAACGTTAAAAACCGTAGAAGAAAAC 5546
                          i ?    i       v   -       vv     vi v           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_114487034_   5547 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5596
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_114487034_   5597 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAACAGGATCTAA 5646
                         i            vvi          vv    iv  i   iv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_114487034_   5647 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5696
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_114487034_   5697 AGGCAACCTACAAAATGGGAGAAAATTTCCACAACCTACTCATCTGAGAA 5746
                           i     i   i             v iii   vii ivi      v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_114487034_   5747 AGGGCTAATATCGAGAATCTACAATGAACTCAAACAAATTTACAAGAGAA 5796
                         i  i  vi    v     v  i  v      vv    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_114487034_   5797 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5846
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_114487034_   5847 TCAAATGAAGGCATTTATGCAGCCAAAAAACACATGAGAAAATGCTCACC 5896
                           v  v    ii  vi viii     v  i       i  i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_114487034_   5897 ATCACTTGCCAT 5908
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3446 13.33 1.98 20.18  chr2_114564819_114566952.rev      535  1644 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_114564819_    535 TAGAAACATATCCCATATTCATGGAGTAGAAGAC--AATATTGTCAAGAT 582
                          i    v         i        v i      --        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_114564819_    583 AGCAATACTTTCCAATTTGATGTGAAAATTGAGCATTACCCCTATCAAAC 632
                         i        ii    v     v iv i   v i iiv i          v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_114564819_    633 TCCCAGCTGC-TTTTTCGAAGAAATTGACAAGTTGATCTTAAAACTCATA 681
                                   -     i v             i     i     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_114564819_    682 TAGGAATACTATGGATTTAAAATGGCCAAAACAACCTGGAAAAAGAA--- 728
                          i i   i v v   iii i   i          i  v         ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_114564819_    729 CAAATTTGAAGAGCTCACACTTCCCAAGTTGAAAACTTAATACAA----- 773
                             v   i  ii              v  v        v     -----
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_114564819_    774 ---TAATCAAGACTGCTTAACACTG-CATAATGACAGACACATA--TTAA 817
                         ---          v iv iii    -     v  i     i   -- i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_114564819_    818 TAGAATAGAATTCATAATCCAGAAATAAATGCATATATTTATGGTCAATT 867
                          i          v v i            iv    i              
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_114564819_    868 GATTTTCAAGAAGGGAACCAAGAA-ATTCAATGGAGAAAAAATAGTCTTT 916
                                i v     vi      v-         i    i          
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_114564819_    917 TTAACAAATAGGGCTGGGACTTCTGAATATCAAAATATCCACTTTCAAAA 966
                          i       i v        vv   i   ? --------   v v     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKC--------CACATGCAAAA 442

  chr2_114564819_    967 AAATTAAGTTGGACCCTTATTTTATACCATACACAAAAATTAACTCGAAA 1016
                         i   v           i  ii i i      i              i   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_114564819_   1017 TGGATGAATGATCTAAATGTAAGTACTAAAACTGTAAAACACTTAGAAGA 1066
                              v ?v  i           vi        i      v         
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_114564819_   1067 AAACATAGGAGTGAGTCTTTGTGACCTTGGATTAGACAGTG-TTTTTTGG 1115
                                  ?  i i    i          i    i  i  -   i  i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_114564819_   1116 ATATGACACCAAAGGCACAAGCAACAAAAGAAAAAATAGATAAATTG-AT 1164
                                      i                                 - i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_114564819_   1165 GTGATTAAAATTAAAAACATTTGTGTTT-AAAGAACACTATAAAGAAAAC 1213
                         v v  i            v      i  -    i       ---------
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT--------- 683

  chr2_114564819_   1214 ATGGTGAAAGCCGGTCTCTACTAAAAATACAAAAATTAGCCAAATGTGGT 1263
                         --------------------------------------------------
  L1M4_orf2#LINE/    684 -------------------------------------------------- 683

  chr2_114564819_   1264 GGTGTGCACCTGTAGTCCCAGCTAGTCGGGAGGCTGAGGCAGGAGAATCA 1313
                         --------------------------------------------------
  L1M4_orf2#LINE/    684 -------------------------------------------------- 683

  chr2_114564819_   1314 CTTGAACCCAAGAGGCGGAGTTTGCAGTGAGCTGATATCACACCACTGCA 1363
                         --------     -------------------------------------
  L1M4_orf2#LINE/    684 --------CAAGA------------------------------------- 688

  chr2_114564819_   1364 CTCCAGCCTGGCAACAAAGTGAGACTCCGTCTCAAAAAAAAAAAAAAGGA 1413
                         --------------------------------------------------
  L1M4_orf2#LINE/    689 -------------------------------------------------- 688

  chr2_114564819_   1414 AACGAAAAAAGAAAATGAAAACACAACCCACAAAAAAGAAGGAAATATTT 1463
                         ------------  i      v          i  vi i  i        
  L1M4_orf2#LINE/    689 ------------AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_114564819_   1464 GTAAGTCACATATCTGATAAGAATCAAATACCCAGAATATATAAAGTACT 1513
                          i  i   i            iiv vvi  i               v   
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_114564819_   1514 GTTATGATTCAACAATAAAAAGTCAAATAACCCAATTAAAAACTGGGTAA 1563
                         v   ii i    i         v              ?    v    i  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_114564819_   1564 AGAATTC-AATAGACATTTCTCCAAAGAAGATGTGTAAATGGCCAATAAG 1612
                           i   i-                        i ii              
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_114564819_   1613 CTCATGAAAAGATATTCAACATGATTAGTAAC 1644
                          v           ii       v ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (95 / 49)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 17.57 (246 / 14)  


3238 27.23 0.55 0.44  chr2_114570354_114576712.rev     4961  5867 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_114570354_   4961 TGGAAGAATATTCCACGCTCATGGGTAGGAAGAATCAATAGCGTGAAAAT 5010
                              ii    i   i i      i v      v i    vi  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_114570354_   5011 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5060
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_114570354_   5061 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 5108
                          v   iivi i  i  ii     -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_114570354_   5109 TATGGAGCCAAAAAAGAGCCCGCGTCGCCAAGTCAATCCTAAGCCAAAAG 5158
                               iviiv  ii  v  v vi v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_114570354_   5159 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5208
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_114570354_   5209 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5258
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_114570354_   5259 TGTGGAACAGAAC--AGAGCCCTCAGATATAACGCCACATATCTACAACT 5306
                         vi     i    i--    i  --   v    vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_114570354_   5307 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5356
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_114570354_   5357 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 5406
                           v  i  i              v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_114570354_   5407 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5456
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_114570354_   5457 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5506
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_114570354_   5507 CTAGGCATTACCATTCAGGACATAGGCATGGGCAATGACTTCATGTCTA- 5555
                         v    ?i v viv   iv   v v  vv i       ii   v ivv  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_114570354_   5556 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5605
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_114570354_   5606 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGCAAAC 5655
                          i   v v  i i   i  ii vv    i  v    i  vv i  ii  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_114570354_   5656 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5705
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_114570354_   5706 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAGATTTACAAGAAAA 5755
                         i  i  vi          v  i  v      vv   iv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_114570354_   5756 AAACAAAGAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5805
                          i     v     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_114570354_   5806 TCAAAAGAAGACATTTATGCAGCCAACAAACACATGAAAAAATGCTCATC 5855
                           v        i  vi viii     i  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_114570354_   5856 ATCACTGGCCAT 5867
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3159 22.60 5.59 1.94  chr2_114579501_114581505.rev      640  1515 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_114579501_    640 TGGGAAGACATCCCATGTTCATAAATCGAAA----TAATAATGTTAAAAT 685
                            i    i             ii  i i  ----     v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_114579501_    686 GTACATACTACCCCAAGTGATCTACAGATGTAATGCAATCCCTGTTAAAA 735
                          vvv     v   v  v            vi  i         i i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_114579501_    736 TTCCAA-TGTTATTCTTCACATAAATAGAACAAA--AACTCTAAAGTTTA 782
                          i   i-  ii-  i  ii  v    v  -   i--i ii     i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chr2_114579501_    783 TATAAAACCATA-AAAAAACCCA--ATTGCCAAAGCAATCTTGAATGAAC 829
                            ii  --  i-  iii     --  v      i          vi iv
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_114579501_    830 AGTACAAAGCTTGAAGCATCACACTACCCAACTTCAAAA--TATT----- 872
                           v      i v  i vv       v     i       --  i -----
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_114579501_    873 ----------------------GGGATT----TAAAAACAGACACATTAG 896
                         ----------------------  v i ----   ii i     i  vii
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_114579501_    897 TCAACGGAATCAGATAGAGAACCCAGAAATAAATTAACATAATTAACATC 946
                             i     vii  v    ii           ii--    -----   i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATA-----CATT 339

  chr2_114579501_    947 TGTGGTTAAGGAATTTTTAATAAAAGTGCCAAGAACACACAATGGAGAAA 996
                          i    i  vvi     ii i  ii         v  iv      i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_114579501_    997 GGACAGTCTCTCTAATAAATGGTGTTAGAAAAACTGGTTATCTACATTCA 1046
                          i i     i ii  i        i i i v      v  ? i    v  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_114579501_   1047 GAAGAATGAAATTGGACCCATATCTCAC--CATTTATATAAGAATCAACT 1094
                         i         i        v  i     --   --   i  i   i    
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCAT--ATACAAAAATTAACT 487

  chr2_114579501_   1095 CATTATAGATTAAAGACTTAAATATAAGACCTAAAACTATAAAACTACTA 1144
                           vv  i   i ?    i     i     v                vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_114579501_   1145 GAAGAAAACATAAGGAGGTAG--TTACATGACATTGGCTTGGGCAGTGAT 1192
                                     i ?--   i--i v i    v    v  i    i  i 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGN--GTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_114579501_   1193 TTCTTGCATATGACCCCAAAATCACAAGCAACAAAAGCAAAGA--GACAA 1240
                              iv       v      v               v   i --  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_114579501_   1241 ACTGGATTGCATCAATCTAAAAAGCTACTGCATAGCAAAGGAAACAATTG 1290
                          i    i v      vv v    i  vi  iiivv       v  v  ii
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_114579501_   1291 ACAGAATGAAAAGACAACCCTCAAATTAGGAGAAAATATTTGCAAATCAT 1340
                          v i i              v  i v i                      
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_114579501_   1341 ACATGAGCTAAGGGGCTCATATCCAAAATACATAGGCAACTCAAACTACT 1390
                          i  vv v      i  ii      i    i   iiv     vv  v   
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_114579501_   1391 CAATAACAAGAAAGCAAATAACCCTATTTTAAAAATGGGCAAAGGACCTG 1440
                               i  i  ii          v   ?-                ii  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTG 834

  chr2_114579501_   1441 AATAGACATTTCTCAAAAGAATACATACAAAAAGCCAACAAATATATGAA 1490
                                       v      v i       vi     i  ii i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_114579501_   1491 AAAAATATTCAACATAACTCATCAT 1515
                           i - ii       v ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (129 / 65)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.30 (66 / 20)  


1622 25.86 2.53 3.62  chr2_114670950_114672975.rev      501  1053 (973)    L1M4_orf2#LINE/L1      192   738 (170)  

  chr2_114670950_    501 AGAAAGGAATAAAGTTGAAGAGAAAATGATATTT---GATTTCAAAATTT 547
                          i i i   i       i  i--- v v i i  ---i         i  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGG---ACTCACACTTCCCAATTTCAAAACTT 238

  chr2_114670950_    548 ATTACAAAGCTTCAAAAATAAAAAT--TATGAGATTGGCATAAGGATTTG 595
                          i         v  iv   v  i i-- i  iv i            ---
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT--- 285

  chr2_114670950_    596 TCTATGGCTTTTTCCATGGCTCAGTGGAATAGAAT----AGCCCAGAATT 641
                         --- - i v -----  i v   i           ----  i      v 
  L1M4_orf2#LINE/    286 ---A-GACAT-----ATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_114670950_    642 ATATCTACATGTATATGGACAACTGATTTT-GACAAACACGAAAAGACAA 690
                          v i i i ii v     v   i       -     ivii vv     v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_114670950_    691 GTTAATAGCAAAAGAATAGCCTACTCAGCAAACGGTGGTAGAACAATTAG 740
                         v i   i vi         i  vi   i    i    v i i    i i 
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_114670950_    741 ATGGCCATGTACAAAAAAA---AATTATGATCGATACCTTGCACCATATA 787
                           i?   ii i     i  --- i  i-  i vv     ii         
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTG-GACCCCTACCTCACACCATATA 475

  chr2_114670950_    788 TAAAAATTAATTTGAAATAAATTGTGGACCTAACTGTAATACTTAAAATC 837
                         i         i ii    ii  ii?i       v     v vi     ii
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_114670950_    838 ACAGTACTTCTAGAATAAAATATAAAAGAAATTATTTGTGGCTTTGGGTT 887
                          i iv   ii     v    i   ii? v  v v  i   i i       
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_114670950_    888 AGGCAAAGTTTTCTTAGATAAATCAACAAAAGCATAAAAAAAATCCATAA 937
                               v v           viv  v        i  iv  --- v v i
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA---CAAAAG 622

  chr2_114670950_    938 AAAAAATTTATAAATTTGACTTCACCAAAATTTCAAACTTCTCT-TTTCA 986
                                vv       v       i       vv      i v -i    
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_114670950_    987 AAGGATTCTGTTAACATAATCAAAAAAACAAACCATAGACTGAGAGAAAA 1036
                              iv  i i  v v i -i    i    v   i   v  i       
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGT-GAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_114670950_   1037 TACTTAAAAATCATATA 1053
                           i  iv          
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATA 738

Transitions / transversions = 1.80 (90 / 50)
Gap_init rate = 0.02 (13 / 547), avg. gap size = 2.62 (34 / 13)  

 521 26.37 1.10 2.20  chr2_114670950_114672975.rev     1353  1534 (492)    L1M4_orf2#LINE/L1      729   908 (0)  

  chr2_114670950_   1353 AAATCATATCTGTGATAAACAGCTTGAATCCAGAACATAAAAAAAAAACT 1402
                                  v v      ivii    v        i   v   i  --  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA--CT 776

  chr2_114670950_   1403 TTCAAAACTCATTTATAAGGAATGAAACAATCCATTTTTTTTTAATGGAC 1452
                         i i v      v v    ii ivv   i  i   v  --?vvv     i 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATT--WAAAAATGGGC 824

  chr2_114670950_   1453 AAAAAGTTTAGGCAGACATTTTACTGAAAAAGATATATGGATGGCAAATA 1502
                            iii   iiii        iv ii  i        iii     v    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_114670950_   1503 A--ATATGACAAGACGCTCAACATTATAGTCACA 1534
                          -- i    v    i         i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (30 / 17)
Gap_init rate = 0.02 (3 / 180), avg. gap size = 2.00 (6 / 3)  


 284 22.03 0.00 0.00  chr2_114703695_114707159.rev     1535  1593 (1872)    L1M4_orf2#LINE/L1        1    59 (849)  

  chr2_114703695_   1535 TGGAAACACATCCCATATTCGTGGATGGGTAGAATCAATACTGTGAAAAT 1584
                               v i       i   i     v  v   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_114703695_   1585 GACCATACT 1593
                          i v     
  L1M4_orf2#LINE/     51 GGCAATACT 59

Transitions / transversions = 1.17 (7 / 6)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  

2252 26.65 0.00 7.87  chr2_114703695_114707159.rev     2047  2973 (492)    L1M4_orf2#LINE/L1       55   908 (0)  

  chr2_114703695_   2047 ACACTGCCAAAAGCAATCTATAAATTCAGTGCAATTCCCATCAAAACATC 2096
                          i   v  v   vii     i i     ii     i  i       ivi 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_114703695_   2097 ATCATCATTTTTCACAGAACTAGAAAAAAACAATACTAATAGTCATATGA 2146
                          v vv v     ii     v v  v  iv-ii  v    v v       i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATGG 153

  chr2_114703695_   2147 AACCAAAAAAGAGCCCGCATAGCCAAAGCAAGAGTAAGCAAAAAGAACAA 2196
                           viiv  ii  v  v v         i   vvv i iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_114703695_   2197 ACCTGGAGGCATCTCATTACCTGACTTCAAACTATACTATAAGGTCAAAG 2246
                          vi      vv  v  i v  ii i      viv     i  i ii v  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_114703695_   2247 GTACCAAAACAGCGTGGTACTTTTATAAATGTGGGCATGTAAAATAATGG 2296
                         vv i   i    i        vvi    ivi i i   i  i vi     
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_114703695_   2297 AACACAGTAAAAAACCCAGAAATTAAGCCAAATACTTACAGCCAACTGAT 2346
                           i v i vi i ii        v  v   v i i   ii i   i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_114703695_   2347 CTTCAACAAAGCAAACAAAAACATAAAGTGGGCAAAGGACACCCTATTCA 2396
                         i   i    i vviv   i v   vv i    v    i i vi  v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_114703695_   2397 ACAAATGGTGCTGAAATAATTGGCAAGTCACATATAGAAGAATGAAACTG 2446
                                      ii i  i   vv ?i     ii i         ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_114703695_   2447 GATCCTCAACTCTCATCTTGTACAAAATTTAACTCAACGTGGATCTGAGA 2496
                           i  ii v   v  i v i       v         vi      v?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_114703695_   2497 TTTAAATTTAAGACCTGAAACCATACAAATTAGCTCCACACACCTATAGT 2546
                         ii     v     v  i    i   -   ---------------------
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATA-AAA--------------------- 531

  chr2_114703695_   2547 TCTCCACTCTACCAACTGAGCTATTGAAGGACATGTGAAACCATATAAAT 2596
                         ------    ----------------------------------------
  L1M4_orf2#LINE/    532 ------CTCT---------------------------------------- 535

  chr2_114703695_   2597 TCTAGAAGATAACATTGGAGAAACTCTTCTAGACATTGACTTAGGCAAAG 2646
                         --       v     v  ? v  v     vv   v   iv        v 
  L1M4_orf2#LINE/    536 --TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_114703695_   2647 AGTTCATGACCAAAAACCCCAAGGCAAATGCAACAAAAACAAAGATAAAT 2696
                         iv   v iivi vi vv  v  i   v v         iv   i   i  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_114703695_   2697 AGATGGGACTTAATTAAAATAAAAAGCTTCTGCACAGCAAAAGAAAAAAT 2746
                          i  v      v  i     v    i   i  ii vv    i  v vv  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_114703695_   2747 CAGCAGAGTAAACAGACAACCCACAGACTGGGAAAAAAGTACTCACAAAC 2796
                           iv i   i  v              v     i    -  i ii    i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAAT 732

  chr2_114703695_   2797 TATGCGCCCAACAAAGGACTAATATCCAGAATGTACAAGGAACTCAAACA 2846
                         i  iiii ii i  i     vi          i  i  i      vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_114703695_   2847 AATCAGCAAGGAAACAACAAACAATTCCATAAAAAAAGTGGGCTAAGGAC 2896
                          v   ii  vi   vi     i  ii v  v?     -     v     i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGAT 831

  chr2_114703695_   2897 ATGAATAGACAGTTCTCAAAAGAAGATATACAAATGGCCAACAAACATAT 2946
                         v          v     v                       i  i  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_114703695_   2947 GGACAAATGCTCAACATCACTAATTAC 2973
                          i v i             ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (138 / 105)
Gap_init rate = 0.01 (6 / 854), avg. gap size = 12.17 (73 / 6)  


 876 27.19 0.00 0.00  chr2_114778220_114780790.rev      251   467 (2104)    L1M4_orf2#LINE/L1        1   217 (691)  

  chr2_114778220_    251 TAGAAAGATATTCCATGTTCATAAATTGGAAGAATCAATATTGTTAAAGT 300
                          i         i          ii         v i           ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_114778220_    301 GTCCATACTACCCGAAGCAATGTGCAGATTCAATGCAATCCCTATCAAAA 350
                          v v     v   i  vii  v i         i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_114778220_    351 TACCAATGACATTTCTCACTGAAATGGGGAAAAAAATCCTAAAACTTATA 400
                          v   iivi v   i ii v     v iv  ivvi         i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_114778220_    401 TAGAACCACAAAAGACCCAAAGTAACCACAGCTATCCTAAGCAAAATGAA 450
                          i   vii   ii      i i  i   v i v   i i iv  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_114778220_    451 CAAAACTGGGGGAATCA 467
                             ii   i   v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCA 217

Transitions / transversions = 1.95 (39 / 20)
Gap_init rate = 0.00 (0 / 217), avg. gap size = 0.00 (0 / 0)  

2226 25.54 3.80 6.52  chr2_114778220_114780790.rev     1160  2079 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_114778220_   1160 CATGTTTATGGATTGAAAGCCTCAACAAACTAAAGATGTCAGTTCTCCAC 1209
                               i        i   v  i  i vvv v      v  i v    v 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_114778220_   1210 AAATTGATTTACAGGCTTAACACAATTCTTGTCAAAATCCCAA-TA---T 1255
                                 i     ii i   i    i i i           i- i--- 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_114778220_   1256 TTTTATAGACATAAACAAGATTATTCCAAAATTTATATGAAATGGCAAAA 1305
                             ii   v  vi     v v  i i      i     i  vv    ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_114778220_   1306 AAACTAGATTAGCTTAAAAACAATTTTGAAAGCAAAAAAAATAGCATGGC 1355
                         i v i   v    i--        i      --  i  i  i ivi v v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCC--AAAACAATCTTGAAA--AAGAAGAACAAAGTTGG 209

  chr2_114778220_   1356 AATAGTC-TACTT---GATTGCAAG--TTACCATATATAGTTCTAGTAAT 1399
                          iv v  -i    ---i   v   i--    --  i v  i vi      
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGCTACAGTAAT 257

  chr2_114778220_   1400 CAATAGCATATGGTATTGATGAAGGAATAGACACACATATCGATAGAACA 1449
                            v vvi i     i  iiiv i i       i i v   i  i   i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_114778220_   1450 GAATAGAGAGCTCAGAAATAGATCCACACAAATATGCCCAACTGATTTTT 1499
                             v     ii        i i   i   vv    vi   i       i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_114778220_   1500 GAAAATGGT-CCAAAAGCAATTTAATGGAGGAAAGATAGATTTTTAAACA 1548
                           v  v   -    i v  -  i     i i  ii    vi    v    
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_114778220_   1549 AAC--TGCTAAAATAATTAGAGATCCAAAACAAAACCAAACAACAACAAC 1596
                           i--    iii i  i i  v ?   ---------  vi   -------
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCA---------CATGCAA------- 440

  chr2_114778220_   1597 AAAGAAAACAAAGAGAGAGCCTCAACTTAAGCCTCAAATCTTGTATAAAA 1646
                         -     --ii   vvi  v  ii -------     v i v i  i    
  L1M4_orf2#LINE/    441 -AAGAA--TGAAGTTGGACCCCTA-------CCTCACACCATATACAAAA 480

  chr2_114778220_   1647 ACTAATTCAAAAGGAATCATGAACTTAAATATAAAATGC-AAAACTATAA 1695
                          i   i      v i    ?ii  i     i   i -  -          
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAA 529

  chr2_114778220_   1696 AACTTGTTTTAAAACATGTAAGAAAAACTTCAG----AATCTTTGGGATC 1741
                             i---   i  --------i     v vi ----      i v  i 
  L1M4_orf2#LINE/    530 AACTC---TTAGAA--------GAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_114778220_   1742 TAGGGCTAG--------TTATTAGACTTGACACCAAAGGGACAATCCATA 1783
                          v   i   --------  v     iv          i v    v v i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_114778220_   1784 AAAGAAAGGCTTGATAAATTAGACTTCAGAAAAAGGAAAAAAGAAAAAAA 1833
                                iiv v        i       vv    vv     ---------
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA--------- 659

  chr2_114778220_   1834 AAAAACTTTTGCTCTGTGAAATATCCTGTCCAGAGGACGAAAAGAAAAAC 1883
                         -----      iv  vii  iv iv  i  v   iiii       v  v 
  L1M4_orf2#LINE/    660 -----CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_114778220_   1884 TA--GAGTGGGAGAAAATGCTTCCAAACCACGTACCTGACAAACGA---- 1927
                         i --  i           ii  v    i  ii  i    i  iv  ----
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_114778220_   1928 -ATC--GAATATATAAAGTATTCTCAACACTTGACAAAAAAAAAAGAAAA 1974
                         -   --            v i   i vv   ii i  v     i v   -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA- 803

  chr2_114778220_   1975 CAATTCTGTTAGAAAATGGGCTAAAGTTATAAAGAGGCATCTCAACACAC 2024
                         i  ii vi  ?i         v  i v v i  v  i   i  vv  v v
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_114778220_   2025 AGGATATACAGATGGAAAATAAGCACATGATAACACGTTCAACATCATTA 2074
                          i        i    vv             v  v i i         ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_114778220_   2075 GCCAT 2079
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.64 (144 / 88)
Gap_init rate = 0.03 (26 / 895), avg. gap size = 3.65 (95 / 26)  


2077 23.20 4.86 12.87  chr2_114952367_114955635      580  1566 (1703)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_114952367_    580 TAGAAATATATTCCATGTTCATGGATTGAGAAGCTCAAAATAGGGAAGAT 629
                          i    v    i                ii ii  i  v  v vv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_114952367_    630 GTCAATTATTCCCAAGTT--TCT---GTTT-------------------- 654
                          v    vv i     i  --   --- v  --------------------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_114952367_    655 -------TGTTTTGTTTTTACACATAGACAAGCTTATTCTCAAATTTATA 697
                         -------  ii  v   vi v v  v        v  i  v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_114952367_    698 TAGAAAGGCA-TAAATCTTGAATTAGCTAAAACCATCTTGAAAAAGAAAA 746
                          i    v   -vii i iv    -   i     v              i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAAT-AGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_114952367_    747 ATGAAATATGAGGAATCATTCTACCTG-TTTTAAGGCTTACTGTATAACT 795
                          ii  i vv     v   iv  v  ii-   i  ii      ii v i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_114952367_    796 ACAAAAATAAAATTATTGTGGTATTGATAGAGAGATACATAGATCAATGA 845
                            iv   v  ivi v       i  i----------    ---------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGG----------CATA--------- 280

  chr2_114952367_    846 AAAAATGAAAAAAAAACAGAACTATTCAAATATGCCAAACTGATTGTTGA 895
                         --------------------------------------------------
  L1M4_orf2#LINE/    281 -------------------------------------------------- 280

  chr2_114952367_    896 TAAAGGTGCAAATGTAGTTCAATGTAGAAAAGATAGCCTTTTCAACAAAT 945
                         ----------------------------- i     --------   ---
  L1M4_orf2#LINE/    281 -----------------------------AGGATAG--------ACA--- 290

  chr2_114952367_    946 GGTTTTGCAGAGATATAGACCAATGGATCAGAAC--AGAGCCCTCAGAAA 993
                         -------------      i       vi    i--    i  --     
  L1M4_orf2#LINE/    291 -------------TATAGATCAATGGAATAGAATTGAGAGTCC--AGAAA 325

  chr2_114952367_    994 TAATGCCGCATATCTACAACTATCTGATCTTTGACACACCTGACAAAAAC 1043
                            vv  ii i  i  iiiii vi    i  i    vivv  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_114952367_   1044 AAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTG 1093
                          vv            i  vvi  v  i  i              v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_114952367_   1094 GCTAGCCATATATAGAAAGCTGAAACTGAACCCCTTCCTTACACCTTATA 1143
                          v  ?   i  ii i  iiv    ii  i      v   i     v    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_114952367_   1144 CAAAAGTTAATTCAAGATGG-TTAAAGACTTAAATGTTAGACCCAAAACC 1192
                              i    i    i    - i ?    i       v   v i     i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_114952367_   1193 ATCAAAACCCT-AGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGC 1240
                           -     i  -          v    ?i- v i -   iv   v v  v
  L1M4_orf2#LINE/    526 AT-AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

  chr2_114952367_   1241 ATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGC 1290
                         v i     v ii   v ivv  vi            vvi          v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_114952367_   1291 CAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTATGCACAGCAA 1340
                         v     v  i    v   ii v  i   v v  i i   v  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_114952367_   1341 AAGAAACCACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATT 1390
                          i  v  i i  vv i      v  i     i                 v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_114952367_   1391 TTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGA 1440
                                vii ivi      i  i  i  vi          v  i  v  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_114952367_   1441 ACTCAAACAAATTTACAAGAAAAAAACAA----CTCCATCAAAAAGTGGG 1486
                             vv    v iv i  v     i    ---- i v  i?    i    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_114952367_   1487 CGAAGGATATGAACAGACATTTCTC-----AAGACATTTATGCAGCCAAA 1531
                          i      v    i           -----    i  vi viii     v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_114952367_   1532 ACACAAATGAAAGAATGCTCATCATCACTGGCCAT 1566
                          vi  v      ii       v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (127 / 98)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 9.21 (175 / 19)  

 672 26.30 17.69 2.95  chr2_114952367_114955635     2337  2777 (492)    L1M4_orf2#LINE/L1      403   908 (0)  

  chr2_114952367_   2337 AACAAAAAGTTTTGCAGCAAGTGGACATCTATAGACAAAAAA--GGAG-- 2382
                               vi  vi  vii   v    i ? i i vi     i -- i  --
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_114952367_   2383 ---CCTCTACTTAAACTTCTTACTGTTTATAAAAATCAACTTAAAATGAA 2429
                         ---  i    i v ------i  ii v  i      i    i      i 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCA------CACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_114952367_   2430 TAATGAACTTACATATAA-------AACATATAAAGCAGTTAGGGGAAAA 2472
                          v ?ii  i  v  i   -------   -      i vv    ---  i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAAC-TATAAAACTCTTAG---AAGA 542

  chr2_114952367_   2473 AAAAACAGGAGAAAATCTTCAAGATTTACCATGAGACAAATGGTTT-TTA 2521
                            v i   ? v        iv  ii vvvi v  i   -      -   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA 591

  chr2_114952367_   2522 GATTTGACACCGAAAGCATGATCCAAAAAAGGAACAAAT-GAGAAAT-GT 2569
                            v       i      ii v v v     i  -    -  v    - v
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGG 640

  chr2_114952367_   2570 ACTACATCAAACTAAAAAA----------------------------AAA 2591
                            v       v v     ----------------------------   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_114952367_   2592 GT-----------------AGTAGAAG----TATTTGCAAACTACGTATT 2620
                           ----------------- i i i  ----          ii ii   i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_114952367_   2621 CAATGAAGGACTAGTGTCTAGTATATACATAGAGCTCTCTA-ACCTCAA- 2668
                         ii  i i     v  i  i  v     i v   i    -  - v     -
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAACTCAAT 789

  chr2_114952367_   2669 AGGAAAAAGAAAACT---TCAA-------ATGAACAGAAGACATAAAGAA 2708
                          iv       v  v ---i   -------   ii  i i  iv i  v i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_114952367_   2709 ATATTTCACCCAGGACTATATACAGATAACAAATAAATAAATGAAAAAAT 2758
                          i     v  v i  vv       i  ii v     ii v       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_114952367_   2759 CTTTAACATCATTAGCTAT 2777
                         vi i       ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (70 / 43)
Gap_init rate = 0.04 (19 / 506), avg. gap size = 4.79 (91 / 19)  


2749 28.65 0.77 1.10  chr2_115163137_115168169.rev     3631  4541 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_115163137_   3631 TGGAGAAACATTCCATGCTCGTAGATAGGAAGAATCAATACTGTGAAAAT 3680
                             i i i  i     i  i i   v      v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_115163137_   3681 GGACATACTACCCAAAGTAATTTATAGATTTAATGCTTTTCCCATTAAAC 3730
                           vv     v      v i  i  i     i  i  vv i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_115163137_   3731 TACCATTTACATTCTTCACAGAATTAGAAAAAATATTTGTATA-TTCACA 3779
                          v   vi i v  i  ii     v v  v  iv iv iv  v -    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_115163137_   3780 TGGAACCA-AAAAGATCCCAAATAGCCAAGACAATCCTAAGCAA-AAGAA 3827
                              vii-  ii  i  vi         i      i i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_115163137_   3828 CAAAGCTGGAGGCATCATGCTACCTGGCTTCAAACTATATTATTACAAGG 3877
                              i      vv   ii  v  iiii      -- i-   i     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--AC-TTACTACAAAG 247

  chr2_115163137_   3878 CTACTGTAACCAAAACAGCATGGTACGGGTACAAGAACAGACACACAGAA 3927
                             v    i   i    ii      v  i i   i i     i i   v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_115163137_   3928 CAATGGAACAGAATGAAGAACTCAGAAATAAGACTGCACACCTACACCCA 3977
                                 i     vi   iii         iv iii   ii  iivi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_115163137_   3978 TCTGATATTTGACAAAATTAATAAAAATAAGCAATGGGGAAAGGACTCCC 4027
                         vi    v  i     iiv ivi  i vi vv            i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_115163137_   4028 CATTTAATCAATGGTGCTGGGAGTGCTGGCTAGCGATATGCAGAAAACTG 4077
                         iv  i  iv             vvi    v  ? v i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_115163137_   4078 AAACTAAACCAGTTCCTTACACAGAATACAAAAATTAACTCAAGACATAC 4127
                           ii ii   vv v   i    viv                  i iiv i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_115163137_   4128 AAAAGACTTAAATGTAAAACTCAAAACTATAAAAACCCTAGAAGAAAGTC 4177
                         v ?    i         i vii            vi i         iiv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_115163137_   4178 TAGGCA-ATACCATTCAGTATATAGGCATGGGCAAAGATTTTATAATGAT 4226
                             ?i- v i -   ivv iv v  vv i     v i   iv  --   
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA--GAT 594

  chr2_115163137_   4227 AT--CAACAAAAGCAATTGCAACAAAAACAAAAATTGACAAATGGGATCT 4274
                           --  v        vvv         iv      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_115163137_   4275 AATTAAACTAAAGAGCATCTTCACAGCAAAAGAAACTGTCATCAGAGTGA 4324
                         v  i   v v  i i v i vii vv    i  v   i   vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_115163137_   4325 ACAGACAACCTAAAGAATGGGAGAAAAT-TTTGCAATCTATCCATCTAAC 4373
                          v        i v               -       vii  vi    i i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_115163137_   4374 AAAGGACTAATATCCAGAGTCTACAAGGTACTTACACAAATTTACAAGAA 4423
                           i     vi        i v  i  i v   ivi    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_115163137_   4424 ATAAACAAACAACCCCATTAAAAAAAGTGGGCAAAGGACATGAACAGACA 4473
                          v i     i     v   ?     --           iv    i     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATAGACA 842

  chr2_115163137_   4474 CTTCTCAAAAGAAGACATACACGCGGCCAACCAACATATGAAAAAAAAAG 4523
                         i     v        i     vii      iv i  i       i v-- 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT--G 890

  chr2_115163137_   4524 CTCAGCATCACTGATCAT 4541
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (155 / 102)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


2787 26.61 3.38 1.01  chr2_115387331_115392518     3810  4696 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_115387331_   3810 TGGAAAAACATTCCATGCTCATGGATAGGAG---TCAATATAGTTAAAAT 3856
                               i i  i     i        v   i--- i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_115387331_   3857 TGTCATACTTCCAACAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 3906
                         v iv     i  v v vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_115387331_   3907 TACCAA-TGTCATTTTTGACAAAATTAGAAAAAAGCT-ATTCTAAAACTG 3954
                          v   i-  i v      vvi     i--- v     -  i      i v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_115387331_   3955 AAACCAAAA---AAGGAGCCT-GAATAGCCAAAGCAATCCTCAGCACAAA 4000
                          v ivi   ---    ii  i-           i     i v iv vi  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_115387331_   4001 AAA-AAAGCTGGAGGCATCAC-----CTGACTTCAAACTATACTACAAGG 4044
                         i  -    i      vv    ----- ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_115387331_   4045 CTACAGTAAGCAAAACAGCATGGTATTTGTGTAAAAACAGACACATAGAC 4094
                                  v   i    ii     i v ii   ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_115387331_   4095 CAATAGAACAGGTCAGAGAACCC-TAAATAAATCTACACACCTGCAACCA 4143
                             i   i  iviv    ii  -v       i i i   ii iiiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_115387331_   4144 TCAGATCTTTCACAAAGCTGACAAAAACAAGCAATGGGGAAAGGACTCCC 4193
                         viv   i  iv    i v  v   i v  vv            i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_115387331_   4194 TATTAAATAAACGGTGCTGGTATAACTGGCTAGCCACATGCAGAAGACTG 4243
                          v  v  i   i        v i      v  ?         i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_115387331_   4244 AAACTGGGCCTCTTCCTTTCCCCACATACAAAAATCAACTCAAGATGGAT 4293
                           ii   i  i  v   iv v   i          i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_115387331_   4294 TAAAGACTTAAACATAAAACCTAAAAGTATAAAAATTCCTAGGAGAAAAC 4343
                         i ?    i    ii   i v      v       -i  i   i       
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr2_115387331_   4344 CTAGGAAATACTATTCCAGACATAGGCCTTGGTAAAGATTTC------AT 4387
                         v    ?ivv v v   vv   v v  vi v  i  v i    ------  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_115387331_   4388 GACAAAGACCCCAAAGCAATGGCAACAAAAACAAAAATTGACAAATGGAA 4437
                             -----  v      vvi         iv      v  i    v i 
  L1M4_orf2#LINE/    597 GACA-----CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_115387331_   4438 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACA--- 4484
                         ii v  i   v v  i i   i  ii vv    i  v        v ---
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_115387331_   4485 -GCATAAACAATCTACAGAATGGGAGAAAATATTCTCAAACTATGCATCC 4533
                         - v v i    i i                    iv    ii  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_115387331_   4534 AA-AAAGGTCTAATATCAAG--TCTATAGAGAACTTAAACAAATCAACAA 4580
                         i -  i  v  vi    v  -- v    i      ivv    v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_115387331_   4581 GCAAAAACCAAACAATCTCATTAAAGAA-GGGCAAAGGACATGAATAGAC 4629
                         vv    iv    i  i iv   ?  i  -          iv         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_115387331_   4630 ACTTCCCAAAAGACGACATGCATGTGGCCAACAAGCATAGGAAAAAATGT 4679
                          i   i v     v  i  i  vi       i     i v     i   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_115387331_   4680 TCAATATCACTCATTAG 4696
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.44 (39 / 16)  


1659 25.36 5.65 4.04  chr2_115418190_115419800      501  1119 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_115418190_    501 AAGAATAGACATA-AG-TTGCTAGAACAAAAC----AGCTTAGAAATAGA 544
                            i         -  - iiv i   i i  i----  iii       i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_115418190_    545 TCCACACAAGTATAATCAACTGCTCTTTGAAAAAGGAGCAAAGAT-GTTG 593
                         i   i   vv   ii    i  v i  i  v  i  v  v    i-i  -
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT- 378

  chr2_115418190_    594 CTGCAATGGAGAAAAGGTTAGTCTCTTCAACAAATGATATTGG-AGAACT 642
                         ---      i    - iv      i           i ii   - v    
  L1M4_orf2#LINE/    379 ---CAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_115418190_    643 TGAGTGTCCATATGCAAAAACCAGAACAAAAGCATAAA-----ACAAAAC 687
                         v  - i?   i        ----   ii  iv-- ii -----  vvv  
  L1M4_orf2#LINE/    425 GGA-TAKCCACATGCAAAA----GAATGAAGT--TGGACCCCTACCTCAC 467

  chr2_115418190_    688 ACC-TAGACA----CCAATTCAAAATAAATTGTATACCTACAGGTTACAC 732
                            -  v   ----ii  i       ii  ii? v     ------ - i
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA------A-AT 510

  chr2_115418190_    733 GTAAAATGC-AAAACCAAAAAATTCCTAGAA--AAGCGTGAAGCAGAAAA 779
                             i -  -     i v    i  i     --  i i --  v? v   
  L1M4_orf2#LINE/    511 GTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACAT--AGGNGTAAA 557

  chr2_115418190_    780 TCTATGTAAATTTGTGTTTGGTGGTGATATTTTAGATACAATACTAAAAG 829
                            vi  i vi   v   v  iii  i v i       ii i  i     
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_115418190_    830 CATAATCTGTAACAAA--------TTGATACGTTGCATTTTATTAAAAGT 871
                           i  --- i      -------- v    vi   v i  i  i    v 
  L1M4_orf2#LINE/    608 CACAA---GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_115418190_    872 AAAAGCTTCTGCTCTCTGGAAGATAATGTTAAGAGAACGACTAGACAAGC 921
                             i   i  iv  iiii i  i v i i    i ii  vv      v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_115418190_    922 TACAGACTGGAAGAAAATATTTGTAAAGTATGTATCTGATAAGGGA-TTG 970
                         i     v   i            i   vi  i              -   
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_115418190_    971 TATGCAAAATATACAAAGAAATCCTACAATTCAACAATAAGGAAACAATC 1020
                            v  i      i      v  i     i    i     ii i    vi
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_115418190_   1021 AATTTTTTT---AAATGGGCAAAAGATCTGAACAGACATCTCACCAATGA 1067
                           iiivv  ---           i   i    i      i  v    v  
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_115418190_   1068 AAGTACACAGAGGGCAGGTAAGCATATGAA--GACTCTCAACATCATTTT 1115
                          ii  i   i v   vii      i     --  iv          ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_115418190_   1116 ATTG 1119
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.42 (109 / 45)
Gap_init rate = 0.04 (24 / 629), avg. gap size = 2.50 (60 / 24)  


3072 24.29 3.32 0.71  chr2_115427320_115431608     2949  3792 (497)    L1M4_orf2#LINE/L1        1   866 (42)  

  chr2_115427320_   2949 TGGAAAGATATCCCATGTTCATGGATTGAAAAAGTTTATATATTTTAAAT 2998
                                                     i  i v  v    vv  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_115427320_   2999 ATCCATCCTACCCAAAGTGATCTACACATTCAATGCAGTCTGTATGAAAA 3048
                         iv v  v  v      v         v      i   i  iv   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_115427320_   3049 TCAAAA-TGTCATTTTTCATGGAAAGAAAAAAG-TG-TCCTAAAATTTAT 3095
                           vv i-  i -     iiii    vvi v   -  -          i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_115427320_   3096 TTGAAACCATAAAAGACCCCAAATGGTAAAAGCAATTGTAAGCAAAAAGA 3145
                         v  i  viii  ii     vi   i iv   i    iv i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_115427320_   3146 AGAATCCTGGAGGTATCATGCTACCTGACTTTAATACCTATTGCAAATTT 3195
                          v  vvi      vv   ii  v  ii i  i  v  i  i i    vi 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_115427320_   3196 ATAGTAATTGAAACAGAATAATACTGGCATAAAAACAGACACATTGACAA 3245
                          i      ii i    vi ii           ii i     i  v  iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_115427320_   3246 ATGGAACAGTATGGAGAGCCCAGAAATTAACCTGTGCATTTATGGTCTAT 3295
                               i  v  v     i        v    ii i           v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_115427320_   3296 TGATTTTTGGCAAAGATAACAAGAATATGCAATGGAGAAAAGACAGTCTC 3345
                                i i   i i iv     vi  v      i    ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_115427320_   3346 TTCAATAACTGGTGTTTGGAAAGCTGGAGA------TG----AAAATGAA 3385
                              i  v     i v   v i     v ------  ---- i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_115427320_   3386 GTTAGACCCTTTTCTCACACCATATAAAAAATATCAACTCAAAATGAACT 3435
                            i     i vi             v    -  i           i ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATGGATC 498

  chr2_115427320_   3436 AAAGACTTACATGTAAGACCTAAAACTCTAAAACTATTCAAAAAAAAAAA 3485
                          ?    i  v        v        v       v  -- i  i    v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT--AGAAGAAAAC 546

  chr2_115427320_   3486 AAAAGAGAAAA-CTGCATGATATTGATCTGAGCAAAGGTTTCTTGGATAT 3534
                          v i ? v   -  v i   iv   ivi ii    v        i     
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_115427320_   3535 TAGCAA-AAAAACACAGGCAACAAAA-------TAAACAAATAAGAATAC 3576
                         v -  v-    i    i         -------  i i    vi  v v 
  L1M4_orf2#LINE/    597 GA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_115427320_   3577 GTGAAAATAAAAAGCTTCTGCATGGCAAAGGAAAT----AATAGAGTGAA 3622
                         i v     v    i   i  iiivv       v i----  v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_115427320_   3623 AAAACAACCCAGGAATTGGGAGAAAATATTTGCAAACCACACATCTAATA 3672
                           i        vii v                    i  i i    i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_115427320_   3673 AGGGGCTAATATCCTAAATATTTAAGGAGCTCAAACAACTCAATAACAAG 3722
                             i  vi     vi     v   i  i   vv            i  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_115427320_   3723 AAAATAAATAACCCA-TTGAAAAATGGGCAAGGGATCTGAACAGACATTT 3771
                           i i          -  ?            i    i    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_115427320_   3772 -TCCAAGAGAAGACATATATAT 3792
                         -     -      i   i v  
  L1M4_orf2#LINE/    846 CTCCAA-AGAAGATATACAAAT 866

Transitions / transversions = 1.59 (124 / 78)
Gap_init rate = 0.02 (16 / 866), avg. gap size = 2.12 (34 / 16)  


2951 26.65 1.01 1.23  chr2_115486856_115491062     2815  3707 (500)    L1M4_orf2#LINE/L1        1   891 (17)  

  chr2_115486856_   2815 TGGAACAACATTCCATGCTCATGGATAGGAAGGGCCAATATTGTGAACAT 2864
                              vi i  i     i        v     ivii        v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_115486856_   2865 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGTTATTCCCATCAAGC 2914
                            v     v      v i  i  i        i iv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_115486856_   2915 TACCA-TTGACTTATTTCATAGAATTAGAAAAAACTACTC--AAAATTTC 2961
                          v   -i  v   -   iii    v v  v  i-  iv  --      - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAG-CTGATCCTAAAATT-C 147

  chr2_115486856_   2962 ATATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAA 3011
                                 viiv  ii  v  viv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_115486856_   3012 GAACAAGGCTGGAAGCATCACGCTTCCTGACTTCAAACTATACTACAAGG 3061
                               i i    i vv    i     ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_115486856_   3062 CTAAAGTAACCAAAACAGCATGGGATTGGTACCAAAACAGATATATAGAC 3111
                            v     i   i    ii   v i   i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_115486856_   3112 CAATGGAACAGAACAGAACAGAGGCCTCAGAAATAATGCCACATATCTAC 3161
                                 i    iv  ---   v  --        vv   i i  i  i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGA---GAGTCC--AGAAATAAACCCATACATTTAT 342

  chr2_115486856_   3162 AACCATCTGATCTTTGACCAGCCTGACGAAAACAAGCAATGGGGAAAGGA 3211
                         iii  vi    i  i   v  vv  v i i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_115486856_   3212 TTCCCTATTTAATAAATGGTTTTTGGAAAACTGGCTAGCCATATGCAGAA 3261
                          vvi  v  i  i       vi v   v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_115486856_   3262 GACTGAAACTGGAACCCTTCCTTACACCTCATACATAAATTAACTCAAGA 3311
                           v    ii    v    v   i     vi     v            i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_115486856_   3312 TGGAATAAAGAC-TAAACATAAGACCTAAAACCATGAAAACCCTAGAAGA 3360
                             vi ?    -    ii     v       i  i   vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_115486856_   3361 AAACCTAGGCA-ATACCATTCAGGATATAGGCATGGGCGAAGACTTCATG 3409
                             v    ?i- v i -   iv  iv v  vv i   i v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_115486856_   3410 ACAAAAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGA 3459
                         ivv vi            vvii         vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_115486856_   3460 GCTAACTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTATCATCAGAG 3509
                         vi v ii   v v  i i   i   i vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_115486856_   3510 TGAACAGGCAACCTACAGAATGGGGGAAAATTTTTGCAA--TATACTCAT 3557
                             v  i     i          i      v       --i   i--  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--AT 739

  chr2_115486856_   3558 CTGACAAAGGGCTAATATCCAGAATCTTCAAGGAACTCAAACAAATTTAC 3607
                             i  i  i  vi          v vi  i      vv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_115486856_   3608 AAGAAAAAAA-AAACAACCCA-TCAACAAGTGGGCAAAGGATATGAACAG 3655
                           v     i -   i      - i? v  i            v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_115486856_   3656 ACATTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACACGAAAAAAT 3705
                                  v        i  vi viii     i ii    i     i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_115486856_   3706 GC 3707
                           
  L1M4_orf2#LINE/    890 GC 891

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.02 (14 / 891), avg. gap size = 1.43 (20 / 14)  


2996 26.37 2.12 0.89  chr2_115492779_115497710     3546  4440 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_115492779_   3546 GAAACACATCCCATGCTCATG-ATGAGGAGAGTCAATATTGTGAAAATGA 3594
                             v i        i     -  vi i   v i        v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_115492779_   3595 CCATACTGCCAAAAGCAATCTATAGATTGAATGTAATTTCCATCAAAATA 3644
                          v     v  v   vii     i     v  i i   ii i        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_115492779_   3645 CCACCATCGTTCTCCACAGAACTAGAAAAAACAACCCTAAAATTCATATG 3694
                            v vv v  i iii     v v  v  ivii i               
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_115492779_   3695 GAACCAAAAAAGAGCCCACATAACCAAAGCAGGACTAAGCAAAAAGAACA 3744
                            viiv  ii  v  viv   i     i  ivvi i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_115492779_   3745 AATCTGGAGGGATCACATTACCTGACTTCAAACTATACTATAAGGCCATA 3794
                           vi      iv     i v  ii i      viv     i  i  i i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_115492779_   3795 GTCATCAAAACAGCATGGTACTTGTATGAAAA-AGGGACAGAGACTAATG 3843
                           v     i    ii       v i  i ii -  iv i v   ii    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_115492779_   3844 GAACAAAATAGATAACCCAGAAATAAAGCCAAATACTTACAGCCAATTGC 3893
                            i i   v  v ii           v   v i i   ii i      v
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_115492779_   3894 TCTTCAACAAAGCAAACAAAAGCATGTAGTGGGGAAAGGACACTCCATTC 3943
                          i   i    i vviv   i v   vi i         i i v  iv   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_115492779_   3944 AACAAATCGTGCTGAGATAATTGGCAAGCCACATGCAGAAGAATGAAACT 3993
                                v      i  i  i   vv ?         i         ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_115492779_   3994 GGATCCTCACCTTTCACCTTATACAAAAATCAACTCAAGATAGATCAAAG 4043
                            i  ii    iv    v           i       i  i     ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_115492779_   4044 ACTTAAATCCAAGATCTGAAACCAGAAAGATTCTAGAAGATAACATCGGA 4093
                           i     vi    v  i    i v   iv ii       v     v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_115492779_   4094 A-AAACCCTTGTAGACATTGACTTAGACAAAGACTTC------ATGACCG 4136
                         i-   i i i  -   v   iv    i   v ii   ------     --
  L1M4_orf2#LINE/    553 GTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC-- 599

  chr2_115492779_   4137 GGAACTCAAAAGCAAATACAACAAAAACAAAGATAAACAGATGGGACTTA 4186
                         ---  -        v vi        iv   i   i i i  v      v
  L1M4_orf2#LINE/    600 ---AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_115492779_   4187 ATTGA--CTAAAAACCTTCTGCACAGCAAAAGAAATAATCAGCAAAGTAA 4234
                           ii --i       i  -  ii vv    i  v iv    iv     i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_115492779_   4235 ACCGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATATATCCAAC 4284
                          vv             i           v  ii   vii       ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_115492779_   4285 AAAG-ACTAATATCCAGAATCTACAAAAAACTC----AAATCATCAA-GA 4328
                           i -   vi          v  i   i     ----  v   vi  -i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_115492779_   4329 AAAGA--AACAATCCCATCTAAGAGTGGGCTAAGGACATGAACAGACAAT 4376
                              --  i  i  v  i?  i i     v     iv    i     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_115492779_   4377 TCTCTAAAAAAGATATACAAATGGCCGACAAGCATATGGAAAAATGCTCA 4426
                             i   i                 i i     i   i   i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_115492779_   4427 ATATCACTAATCAT 4440
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (149 / 83)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 2.08 (27 / 13)  


 586 22.46 0.00 3.62  chr2_115499061_115501691.rev      918  1055 (1576)    L1M4_orf2#LINE/L1        4   136 (772)  

  chr2_115499061_    918 AAAAATATTCCAAGCTCATGGATTGGAAGACTGAATATTGCTAAAATTAC 967
                            i    i   v i                 v       i   i  vi 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_115499061_    968 AATACTACTCAAAGCAATTTACAGATTTAATGTAATCTCTATCAAAATAC 1017
                               v i    vii  i        i  i i    i          v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_115499061_   1018 CAAGGATATTCTTCACAGAAATAGAAAAAACAGGCTGA 1055
                           ivviiv  i  ii       v  -----  i     
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGA-----CAAGCTGA 136

Transitions / transversions = 2.10 (21 / 10)
Gap_init rate = 0.01 (1 / 133), avg. gap size = 5.00 (5 / 1)  

2317 23.10 3.74 4.90  chr2_115499061_115501691.rev     1365  2139 (492)    L1M4_orf2#LINE/L1      143   908 (0)  

  chr2_115499061_   1365 AATT-ATATGGAACCGCAAAAGACCCAGAATAGTCAAAGCAATCCTGAAC 1413
                             -        vi    ii            i    i     i    v
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_115499061_   1414 AAAAAGAACAAAGCTGCAGGCATCATACTACCTAACTTTAAAATATACAA 1463
                           i          i  v   vv   i   v  i  i  i    iv   v 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_115499061_   1464 GACAGCTATAGTTAATCT-----GTATGGTACTGGCATAAAAACAGATAC 1508
                         v v     i   -    v-----  i              ii i   i i
  L1M4_orf2#LINE/    243 CAAAGCTACAGT-AATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_115499061_   1509 ATAGACCAATGGAACAGAATAAGGAAACTGGATATAAATCCATACATTTA 1558
                              i        i     vii  iv ii  v     i           
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_115499061_   1559 TACCCAACT---------CAATGGTACCTAGAACATACAATAAGGAAAAG 1599
                          ivi   i ---------   v   i  v   v   v    ii     ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_115499061_   1600 ACAGTCTCTTCAAAAAATGGTGCTTCAAAAGCTGAATAACCATAAGCAGA 1649
                          i     i     v          vvi v i   i   ?   i v   i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_115499061_   1650 AAAATGGAATTAGATCCCTATCTCTCACCACATA-AAAAAT-----CAAA 1693
                          i    i i  i  i     i   v     i   -      -----    
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_115499061_   1694 ATGTATTAAAAATCATATCTAAGTTTTAAATCTAA-ACCTGAAACTATGA 1742
                            v  i ? i i ------------     v   - v  i       i 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACC------------TAAATGTAAGAGCTAAAACTATAA 529

  chr2_115499061_   1743 AACTACTAAAAGAAAACGTTAGGG-AAATGTTCTAGTATATTTTT--CTG 1789
                             vi  i        i vi ? -    v   --  i- ii  v--i i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTC--GTG-ACCTTGGGTTA 576

  chr2_115499061_   1790 GACAAAGATATTTTGTGTAAAATCTCAAAAGCACAGGCAACAAAAGCAAA 1839
                          i   v i v i  ivi  vi ivi          i          v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_115499061_   1840 AATAAACAAATGGGATCACATCAAGCTAAAAAGCTTCTATACACCAAAGG 1889
                             i i    v   iiv      iv v    i   i i i vi      
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_115499061_   1890 AAAAAATCAACAAAGTGAAGAACCAACCCACAGAATAGGAGAAGATATTT 1939
                          v vv     v        i iv             i      i      
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_115499061_   1940 ACAGAGTAACCACCTGACAAGGGATGAATAACCAGAACACACAAGGAGCT 1989
                         i  i vi vvi i    i      ivvi  v      i i i  i  i  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_115499061_   1990 CAGAAAACTCAATAGCAAACAAACAAACACCCAAAAAGACCCCACAAAAT 2039
                          vv v         ii   v i     i ---------    -----   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATA---------ACCC-----AAT 812

  chr2_115499061_   2040 ATCTTATTAAAAATGGGCAAAAAATCTAAA---ACATTTCTC-AAAGAAG 2085
                         ------ ?             ii  i i  ---         -       
  L1M4_orf2#LINE/    813 ------TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_115499061_   2086 ACATACAAATGACCAAGAGGTATATATAAAAAAAAGCTCAACATCACTGA 2135
                          i         i    v i i i  i--    i v           ????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATG--AAAAGATGCTCAACATCAZZZZ 904

  chr2_115499061_   2136 TCAT 2139
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.92 (115 / 60)
Gap_init rate = 0.02 (18 / 766), avg. gap size = 3.72 (67 / 18)  


3171 22.78 3.99 0.91  chr2_115541643_115543809.rev      814  1691 (476)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_115541643_    814 AAAAAAATCT-ATGTTTATATATTGGAAGAATCTATATTGTTAAAAATTC 862
                            i v   i-     i  iv         v iv          i vvv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_115541643_    863 AAAAC-----AAAT------ACAGAATCAATGCAAGCCCCATAAAAATCC 901
                           v  -----    ------     v    i    v   i  v       
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_115541643_    902 -AATGGTATTATTTACAGAAATACAAAAGA-AATCCTAAAG--CATATGA 947
                         - iiv iv  v   i       vv v   v-i        i--      i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_115541643_    948 AACCACAAAAGTTCCA-AACAGTCAAAAGTAATCCTGACAA----GAACA 992
                           vii   ii vi   -  i  i     -i    i   v  ----     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACA 202

  chr2_115541643_    993 ATGATGAAGGCATCATACTACCAGATGTTGAAATATACTACAAAGCTATA 1042
                          v v  i   vv   i   v  vi  v ii   iv             i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_115541643_   1043 GTAATAAAAACAACATGATACTGGCATAAAAATAGACATACAGCCCAATG 1092
                              v  i   iii  i           ii         i  vi     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_115541643_   1093 GAATTGTATAGAGAGCCCAGAAATAAATCCACACATTTATTGTCAACAGA 1142
                             v v  v     i           i   i        v     iv  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_115541643_   1143 TCTTCGACAAAGATGACAAGAACATGCAATGGGGAAAG-----TCTTTTC 1187
                          i        i i  v     v   v            -----       
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_115541643_   1188 AATAAA-GATGTTGGGAAAACTGCTTATCTAAATGCAGAAGAATGAAATT 1236
                           i   - i  i     v     vv  ? i v     i         i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_115541643_   1237 GTACCCTTATCTCACACTGTCTACATAAATCAACCCAAAATAGATTAAAG 1286
                          v    i  i       ii v    v    i   i      i   i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_115541643_   1287 ACTTCAATGTAACATCTGAAACTATAAAATTATTGAAAGACAACATAGGA 1336
                           i v       v v  i           i v  ii    v        ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_115541643_   1337 AAAAACCCCTTTTGACATTGGTCTGGGCAAATAATTT-TTGGATATGATC 1385
                         iv   i i- iv    v    vi i     - ii   -  i       iv
  L1M4_orf2#LINE/    553 GTAAATCT-TCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACA 600

  chr2_115541643_   1386 CCCAAAGCAAAGGCAACAAAATCAAAAATAGACAAATGGGATTGCATCAA 1435
                           v      v i         vv         i    v   i v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_115541643_   1436 --CTAAAAAGCTTCTGTATAACAAAGGAAATAATTAGCATAATGAAGAGG 1483
                         --i      -   i   iivv       v iv  i iv v i    i  i
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_115541643_   1484 CAACCTACA---TGGGAGAAATTGTTTGCAAGCCATATATACAATGAGAG 1530
                              i   ---         v i       ii       vii  i  i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_115541643_   1531 ATTAATATCCAAAACATATAAGGAATTCAAAGATCTCAACAGCAAAAA-- 1578
                          i vi      i  i      i   i  vv v v     i ii     --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_115541643_   1579 CAAATAACCTAATTAAAAAATGGGCAAAGGATCGGAAGAGACAGTTCTCA 1628
                                  i    ?                 iv   v     v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_115541643_   1629 AAAGAAGACATATAAGTGGCCAATAGGTACATGAAAAAAAAAAAGCTGAA 1678
                                 i   i  i         i i         i v----   v  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT----GCTCAA 895

  chr2_115541643_   1679 CATTACTAATCAT 1691
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (115 / 81)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 2.26 (43 / 19)  


2429 22.52 4.76 9.09  chr2_115702435_115704758.rev      887  1832 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_115702435_    887 AAAGATATTCCGTGTTCATGGGCTCGAAGAATCAATATTGTTAAAATGTC 936
                                 i  i         ii v     v i           i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_115702435_    937 CACACTACTCAAAGGAATCTGGAGATTCAGTGCAATTCCTATCAAAATAC 986
                         v i   v i    vvi    iv       ii     i           v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_115702435_    987 GAA-TGCCATTCTTCACAGAAATAGGAAATACAATCCTAAAATTTACGTG 1035
                         v i-    -  i  ii       v iv  vvii           i ii  
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_115702435_   1036 GAATCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAGCCAAAAAAAAA 1085
                            vii   ii                 i v   i i ------------
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------------ 190

  chr2_115702435_   1086 AAAGAAAGAAAAGAAAAGAAAAAATGGAGAAATTACATTACCAGACTTCA 1135
                         --------       i iv   iv     i v i   i v  vi i    
  L1M4_orf2#LINE/    191 --------AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_115702435_   1136 AATTATACTTCAGAGCTATAGTGAACAA-ACAACATGCTACTGGCATAAA 1184
                           viv    v  i     i   i v   -   iii  v           i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_115702435_   1185 AAGAAACATA--GACCAATAGAATAGAATAGAATAGAATAGAATAGAATA 1232
                         i v i     --  i    i         ---------------------
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAAT--------------------- 311

  chr2_115702435_   1233 GAATAGAATAGAATAGAATAGAATAGAATAGGAGAACTCAGAAACAAATT 1282
                         ---------------------------- --    iii      i   ii
  L1M4_orf2#LINE/    312 ----------------------------T--GAGAGTCCAGAAATAAACC 331

  chr2_115702435_   1283 TATACATATACAGTGAATTCATTTTCGACAAAGGTCCTAAGA-------- 1324
                         i      v  ii  v    v           i   v i    --------
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_115702435_   1325 ----------ACAATCTCTTCAATAAATGATGATGGAGAAACTGGATATC 1364
                         ---------- i i   i     i     i  v   iiv         ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_115702435_   1365 CACATGCA---GAATAAGACTAGATCT------------GTATATAAAAA 1399
                                 ---    i iii i  i i------------i    i     
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_115702435_   1400 TCAAATAAACATGGATAAAAGACTAAAATCTAAGACCTCAAACTATGAAA 1449
                          i  v v  v      v ?    iv    v     v  v       i   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_115702435_   1450 CTACTGTACAAAAACA-AGAAACAAAAACCACTGAGGAATCAGGACATTG 1498
                           vi iv vi      -  i?ii   v----  ------  iv   v   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAAT----CT------TCGTGACCTTG 571

  chr2_115702435_   1499 TAGTT-GGCAAAGATTTCTTGAGTAATA-ATCAACAAGCATGCGCAACGA 1546
                         -i   -     v i      iii  vv - i   -     iiv     i 
  L1M4_orf2#LINE/    572 -GGTTAGGCAATGGTTTCTTAGATATGACACCAA-AAGCACAAGCAACAA 619

  chr2_115702435_   1547 AAGCAAAGATGGACAAATGGAATCATATCAAG-TTAAAAAGCTTCTGCAC 1595
                            v   i  i  i    v i iivi     i-       -   i  ii 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGC 668

  chr2_115702435_   1596 AGCAAAGGAAACAATCAACAAAGTGAAGAGACAACCTACAGAATGGGGGA 1645
                         vv       v  v     v        i        i          i  
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_115702435_   1646 ACAGATTTTCAGACTATCCATCTGATAAGAGATTAATAACCAGATTACAT 1695
                          v v    v  i ii  vi          i  i vi  v     v  i  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_115702435_   1696 AAGGAGCTCAAACAACTATATAGGGAAAAAGTCTAATAATGCAATT-AAA 1744
                           i  i   vv      vv   iv-      v v     iv     -   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAAT-AAAAAGACAAATAACCCAATTWAAA 817

  chr2_115702435_   1745 AATGGGCGAAG-ATCT-AATAGACACCTCTTAAAAGAAGAC-TACAAATG 1791
                                i   -  i -        ii   iv        i-        
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_115702435_   1792 GCAAACAGGTGTATGAATAGATGCTCAACATCACTGATCAT 1832
                           v  i i iii     v               ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (133 / 77)
Gap_init rate = 0.03 (24 / 905), avg. gap size = 5.46 (131 / 24)  


3000 22.72 7.03 0.70  chr2_115791034_115793956.rev     1582  2435 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_115791034_   1582 TGAAAAGACATTCCATATTTATGAGTTGGAACACT-AATATTTCTAAGAT 1630
                           i     i  i    i  i   ii      v   -      vi      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_115791034_   1631 GGTAATATTACCTAAAGCAA-ATACAGACTCAATGCAATTACTATTAAAA 1679
                           i    i v  i   vii -v      i    i     iv    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_115791034_   1680 TCCCAACTGGCTTTCTTGCAGAAATAAAAAAGCTAATTCTCAAATTTATA 1729
                              i   v    i          vi v     i  i  v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_115791034_   1730 TGGAACTGTGATGGGCTCTTCATAGC-AAAGCAATAT----ATATATTTT 1774
                              v  ii v  i i vvv     -   i    v ---- v v vvvv
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_115791034_   1775 TAAAGT-GTAATAGTCACACTTCCAGATTTCAAACATT-CCACAAAGGTG 1822
                         i     - v iv v          vi        vv  - i      v i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_115791034_   1823 CAGTAATCCAAACAATGCAGTACCAGCATGAGGACAGATATAGAGATGAA 1872
                                 v i   i  ii    ii    i    i   i   v    v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_115791034_   1873 TGAAGTAAAATTATAAGCCCAGAAATAA-CTCATATATCTATAACCAAGG 1921
                           i i  i    ivi  i          - i    i  i   iii   vv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_115791034_   1922 AAGGTTC-ACA-------CAATA--AT--AATTGGGAAAGAATGGTCTCT 1959
                         i vv   -   -------   v --  --   v          i    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_115791034_   1960 TCAATAAATGGTGCTGGGTGAAATGGTTATTCACATGCAAAA-ATTAAAG 2008
                             i             vv  v   v  ?i           - v i   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_115791034_   2009 CTAGACTCCCTAACTCACACCATA-AAAAAAATTAACTCAAAATGAATCA 2057
                         i i   -     v           - v                  i    
  L1M4_orf2#LINE/    451 TTGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_115791034_   2058 ATGACCCA--TGTAGATAAACTAAAACCATAAA-CTCATTTAAAAAAAAC 2104
                         ?v    i --    ii-- i       i     -   -  vi  i     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAG--AGCTAAAACTATAAAACTC-TTAGAAGAAAAC 546

  chr2_115791034_   2105 A-AAAGACAGATCTTTGTGACCTTGGATTCAGCAGTGTATTCTTAAATAA 2153
                          - ii?ii i     i          i  vi   i  vv      i   v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_115791034_   2154 GACATCAGAAGCACAAGCAATGAAAGAA----CAGGTGAAT--GA----- 2192
                             i  i            ii      ----i  i i   --  -----
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_115791034_   2193 ---------AGAACTTT-GTGCACCAAATGAAACTATTATGAAAGTAAAG 2232
                         --------- i      -    vi    v  v     i v      i  i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_115791034_   2233 AGACAACCTACATTATAGAAGAAAGTATATGAAAAT-ATGTTTCTGACAA 2281
                                 i   vv  i i     i   v  v    -  i v     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_115791034_   2282 GAGATTAATATCCGGAATA----AAGAACTCCTACAACTCACTATCAGTA 2327
                          i  i vi     i     ----        i         v  vi iv 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_115791034_   2328 AAACCAGCAAGTCCC--TT--AAAATGGGCAACAGGCTTAAATAGATCTA 2373
                          i  v ii  --   --  --           vi ii  i      iv v
  L1M4_orf2#LINE/    797 AGACAAATAA--CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_115791034_   2374 TCTTTAAAGAAGATATATAAATGGCCAATAGACACATAAGAAGATACTCA 2423
                            ii            i            ii     i i     i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_115791034_   2424 G--TCAACATAGTT 2435
                         i--   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (122 / 69)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.28 (66 / 29)  


3199 26.37 1.79 0.34  chr2_115803495_115808228.rev     3348  4242 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_115803495_   3348 TGGAAGAACGTTCCATGCCCATGGATAGGAAGAATCAATATCGTGAAAAT 3397
                              ii ii i     ii       v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_115803495_   3398 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 3447
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_115803495_   3448 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTAAAGTTCA 3495
                          v   iivi i  i  ii     -   -- v  i  - i i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_115803495_   3496 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 3545
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_115803495_   3546 AACAAAGCTGGAGGCATCATGCTACCAGACTTCAAACTATACTACAAGGC 3595
                                i      vv   ii  v  vi i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_115803495_   3596 TACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGATATAGACC 3645
                                 i   i    ii       v i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_115803495_   3646 AATGGAACAGAA---------CAGAAATAGTACCACACATCTACAACTAT 3686
                                i    ---------        ivv   i    i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_115803495_   3687 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 3736
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_115803495_   3737 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3786
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_115803495_   3787 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3836
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_115803495_   3837 AAAGACTTAAATGTTAGAGTTAAAACCATAAAAACCCTAGAAGAAAACCT 3886
                          ?    i       v    i      i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_115803495_   3887 AGGCA-ATACCATTCAGTACATAGGCATGGGCAAGGACTTCATGTCTAAA 3935
                            ?i- v i -   ivv  v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_115803495_   3936 ACACCAAAAGCAATGGCAACAAAAGCCACAATTGACAAATGGGATCTAAT 3985
                                     vvi          vv v   v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_115803495_   3986 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 4035
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_115803495_   4036 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 4085
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_115803495_   4086 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 4135
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_115803495_   4136 AACAAA---CCCAAC-AAAAAGTGGGCAAAAGATATGAACAGACACTTCT 4181
                         i     ---     i-?    i        i   v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_115803495_   4182 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 4231
                          v        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_115803495_   4232 TCACTGGCCAT 4242
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  


3275 26.65 0.66 0.66  chr2_115850609_115856879.rev     4872  5779 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_115850609_   4872 TGGAAGGACATTCCATGCTCATGGGTAGGAAGAATCAATAGCGTGAAAAT 4921
                              i  i  i     i      i v      v i    vi  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_115850609_   4922 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4971
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_115850609_   4972 TACCAATTACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5019
                          v   ii i i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_115850609_   5020 TATGGAAC--CAAAAAACAGCCCGCATCGCCAAGTCAATCCTAAGCCAAA 5067
                                v--   iii  --  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_115850609_   5068 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5117
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_115850609_   5118 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5167
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_115850609_   5168 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTGCAA 5215
                         i        i    i--    i  --        vv   i i  i iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_115850609_   5216 CTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5265
                         ii vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_115850609_   5266 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5315
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_115850609_   5316 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5365
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_115850609_   5366 GATTAAAGACTTAAACGATAAACCTAAAACCATAAAAACCCTAGAAGAAA 5415
                            i ?    i    i vv i v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_115850609_   5416 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5465
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_115850609_   5466 AAAATACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5515
                          vi i          vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_115850609_   5516 AATTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACTACCATCAGAGTGA 5565
                         v  i   v v  i i   i vii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_115850609_   5566 ACAGGCAACCTACAGAATGGGAGGAAATTTTTGCAATCTACTCATCTGAC 5615
                          v  i     i            i    v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_115850609_   5616 AAAGGGTTAATATCCAGAATGTACAATGAACTTAAACAAATTTACAAGAA 5665
                           i  ii vi          i  i  v     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_115850609_   5666 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACT 5715
                            i     i     v  i?    i    ii     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_115850609_   5716 TCTCAAAACAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5765
                             v   v    i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_115850609_   5766 CCATCACTGGCCAT 5779
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


 902 22.06 0.00 2.94  chr2_115926758_115931900     2220  2423 (2720)    L1M4_orf2#LINE/L1        1   198 (710)  

  chr2_115926758_   2220 TGGAGAGACATTCCATGTTCATGAATTGTAAGTCTCCATACTGTGAAGAT 2269
                             i   i  i           i    v   v  iv   i   v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_115926758_   2270 GGCAATTCTCCCAAAATTGATCTATACATTGAATGCAATTTCTATCAAAA 2319
                               v     v           i v   v  i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_115926758_   2320 TTCTAAGTAGGCTTTTTTTGGAGGTAGAAATTGATGAGCTGGTTTAGAAA 2369
                          i i iv --  i       ----i         ii     i iivi   
  L1M4_orf2#LINE/    101 TCCCAGCT--GCCTTTTTTG----CAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_115926758_   2370 TTTATGTGAAAATGTTAAGGACCTAAAACAGCCATGACAATATTTAAAAA 2419
                           i  i  i     iv i     i i  i     vi     v  v     
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_115926758_   2420 TAAG 2423
                         v   
  L1M4_orf2#LINE/    195 GAAG 198

Transitions / transversions = 2.00 (30 / 15)
Gap_init rate = 0.01 (2 / 198), avg. gap size = 3.00 (6 / 2)  

2776 27.60 1.52 0.58  chr2_115926758_115931900     2424  3278 (1865)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr2_115926758_   2424 AAAATGGCCATACTGCCCAAATTGATTTATAGATTCAATCCTACCCCAAT 2473
                           i     v     v           i  i        iv v i   v  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_115926758_   2474 CAAACTACT-GTTGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAA 2520
                             v v i- i  v    i  -i     -   -- v  i  -  ii   
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAA 142

  chr2_115926758_   2521 ATTTCATATGGAACCAAAAAAGAGCTCACATAGCCAAGACAATCCTAAGC 2570
                          v           viiv  ii  v iviv        i      i i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_115926758_   2571 AAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTTAAACTACACCG 2620
                           i          i      vv   ii  v  ii i  i   vivi  ii
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_115926758_   2621 CAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATA 2670
                            i          i   i    ii         i iv ii i   i   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_115926758_   2671 TAGACCAATGGAACAAAACAGAGGCCTCAGAGACAACACCACACATCTAC 2720
                             i        i i  iv   ivii    i i  vv   i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_115926758_   2721 AACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGAA 2770
                         iii  vi    i  i     ivv  v   i v  vv              
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_115926758_   2771 TTCCCTATTTAATAAATGGTGTTGGGAAAACTGTCTAGCCATATGTAGAA 2820
                          vvi  v  i  i        i     v     vv  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_115926758_   2821 AGCTGAAAGTGGATCACTTCCTTTCACCTTATACAAAAATTAACTCAAGA 2870
                         iiv    iv    i v  v   iv    v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_115926758_   2871 TGGATTAAAGACTTAAACATAAGACTAAAAACCATAAAAACCCTAGAAGA 2920
                              i ?    i    ii     viv     i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_115926758_   2921 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATG 2969
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_115926758_   2970 ACTAAAACACTAAAAGCAATGGCAACAAAAGCCACAATTGACAAATGGGA 3019
                         iv  vi    i       vvi          vv v   v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_115926758_   3020 TCTAACTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAG 3069
                         ii v ii   v v  i ii  i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_115926758_   3070 TGAACAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 3119
                             v  i  i  i                 v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_115926758_   3120 GACAAAGGGCTAATATCCAAAATCTACAAAGAACT--TA-AATTTA-CAA 3165
                           i  i  i  vi      i   v  i        --  -  i i -i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_115926758_   3166 GAAAAAAACAA----CCCCATCAAAAAGTGGGTGAAGAAAATGAACAGAC 3211
                         v     i    ----   v  i?    i    ii   i vv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_115926758_   3212 TCTTCTCAAAAGAAGATCAT-TATGTACCCATCAAACATATGAAAAAAAG 3260
                         vi     v         -  -i vi iv   vi  i  i       i v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGAT-ATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_115926758_   3261 CTCATCATCACTTTTCAT 3278
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (141 / 91)
Gap_init rate = 0.02 (13 / 863), avg. gap size = 1.38 (18 / 13)  

1720 23.85 14.37 0.76  chr2_115926758_115931900     3998  4651 (492)    L1M4_orf2#LINE/L1      166   908 (0)  

  chr2_115926758_   3998 CCCAGAAC--TTAAAGTATAATAATAAAAACAAAAAAGAAA-TTGGAGGA 4044
                                i--ii   -- i   vv i    vi  i  v   -        
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAA--ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_115926758_   4045 ATTGCCATACCCGATTTCAAAACTTACTATAATGTTACAGTAGCCAAGAA 4094
                         v ii vv v   i                i  v i       ii     v
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_115926758_   4095 AATGTGGTACTATCATAATGACAAAAATATAAATCAGTGAAATAGAATTG 4144
                          i         iv     v  i i v     i    i  i          
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_115926758_   4145 AAAGTCAAGAAATAAGCCCTTAGGTTTATGGCCAATTAATTT---AAAAA 4191
                          i    v        i   v  vi       i     i    --- v  i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_115926758_   4192 AATAGCAAGGCAATTCAATGAAGGAAAGAATAGTATTTTCAACAAATGGT 4241
                         ii iv    i v        i-            v               
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_115926758_   4242 GATAGGAAAATTATATATCCACTTGAAAAAAAATGAATTTAGACCCTGAT 4291
                          v i   v  i iv   ?    v  v    i      v  i     iv i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_115926758_   4292 ACCACA--ATAGA-AAAAA--AATTCAGAAT--ATAGAAGACCTTAATGT 4334
                         vi    --   v -     --  i   i   --  vi?      v     
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_115926758_   4335 TAGCACTAACACTATAAAACTTTTTAGAAAAAGAC-TACCAGATAATCTT 4383
                         v  vi    v           i  -    i  i  -  vv? vv      
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTT-AGAAGAAAACATAGGNGTAAATCTT 561

  chr2_115926758_   4384 --TTACCTTGATTTAGACAA--ATATTCTTAAATGTGATATCAAGAGCAT 4429
                         -- v      iv    i   --i -      i  i   i i   i    i
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATATGACACCAAAAGCAC 610

  chr2_115926758_   4430 CATTCATAAAAGTGAAAATTAATAAACTTGACTT-------ATT------ 4466
                         v viv i     vi     vi     i v     -------   ------
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_115926758_   4467 ------GCT---------------AAGAGAATGAAAAGTCA--------- 4486
                         ------   ---------------    i i       v  ---------
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_115926758_   4487 --GGGAGAATGAATTTGCAAACCTTATATTTTATGAAGATCTTATATCTA 4534
                         --       viv         i v     i v  i i iv   i    i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_115926758_   4535 AAATGTAT--------TTTAAAA------AATCAAAA--CAAAT----CA 4564
                         i   i   --------i   v  ------   v    --     ----  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_115926758_   4565 -----------GGCGAGAGATTTTAACAAATTTTTTACCAAAGAATTCAT 4603
                         -----------   i ii     v  i i iv   iv        vvi  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_115926758_   4604 GTGATTGGGTAATACATACATGGAAAGGTGCTCACCATCATTATCTTT 4651
                         iii v   vi    vii     i    i      v     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (90 / 63)
Gap_init rate = 0.03 (23 / 743), avg. gap size = 4.30 (99 / 23)  


1053 21.32 2.94 1.47  chr2_115950061_115953118     1262  1533 (1525)    L1M4_orf2#LINE/L1        1   276 (632)  

  chr2_115950061_   1262 TGAAAAGCTATTCCACATACATGGATTGAGAGAC--AGTATTGTTAAGAT 1309
                           i    v   i   ii v         ii    -- i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_115950061_   1310 GCCAATAATGTCCAAAACAATATACACAGATT-AATGTAGTCCTTATAAA 1358
                          v     v vi     vii  v    --    -  i i i   i   v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA--GATTCAACGCAATCCCTATCAA 98

  chr2_115950061_   1359 AATCCCAA-TGA-TTTTTTGCATAAATAGACAAACCCTTCCTAAAACTTA 1406
                                i-  v-         v    v     i ivv        i i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_115950061_   1407 TATGGAATCTTAAGGTATCCA-ACTAATCAGTACAATCCTCAATATAGAA 1455
                                vivi    v i   - v  ii  iv      i v  v -    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA-AGAA 197

  chr2_115950061_   1456 TAACAAAGCATTGAG--CTCATACTTCATGATTTCAAAATTTACTGCAAA 1503
                         v       i- v   --    i     vii         i     i    
  L1M4_orf2#LINE/    198 GAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_115950061_   1504 GCCACAGTAATCAAAACAGTGTGGTAATGG 1533
                           i           i           v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGG 276

Transitions / transversions = 1.42 (34 / 24)
Gap_init rate = 0.03 (9 / 276), avg. gap size = 1.33 (12 / 9)  

2253 24.80 2.86 1.43  chr2_115950061_115953118     1938  2566 (492)    L1M4_orf2#LINE/L1      271   908 (0)  

  chr2_115950061_   1938 TATTGGCATAACAACAGACATATAGACCAATGGAATAGAATAGAGGGCCC 1987
                           i        vi i           i              v   i i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_115950061_   1988 AGAAATAAATTCTCAAATATGTGGTTAACTTATTTTCAACAAGGGTATTG 2037
                                  ii vi v  v i    i  i v      i        iiii
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_115950061_   2038 AGACC--TCAGTGAGGAAAAGACAGTACTTTCAACAAATGTCATTGGGAA 2085
                              --   i  i     ii i   vi            viii     v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_115950061_   2086 AATTGTTTATCTACATGCAACAGAATGGAATGGGATTGTTAACTAAAATG 2135
                           i  vv  ? i        v      i i v   iivi  v  v v iv
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_115950061_   2136 ATGTTTAAAAACTAGTTCTAAGTGAATCTATCACTTAAGTGTTAAACCTA 2185
                           i vi     i  ii  v  i  i   v?vv  i   i   v i v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_115950061_   2186 AAACTATAAAACATTTAGAAGAAAGCA--GGACAAAAGCCTCAAGAT-TT 2232
                                     vi          i  --  ?vv   v i  iv  i-  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_115950061_   2233 GGGTTTGGCAGTAATATTTCTTGGAAATGACATCAAATGCACAGACAGCG 2282
                              v    i ii --     i  v      i    v     ii  i i
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGT--TTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_115950061_   2283 CAAGAAAATATACACAAATTGGACTT-AT--AAATT-----TTTTTAAGT 2324
                         v       v   v i           -  --     -----i    ----
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT---- 664

  chr2_115950061_   2325 GTGCATCAAAAGACATCATCCACAGAGCCATAAGGTAATCCATAGATTGG 2374
                             v     i    ii   v v i  iv v   ii  i   i   v   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_115950061_   2375 GAAGAAATATTTGCAAGTCATATCTATGGTAAGGGATTAATATCCAGAAC 2424
                           ii            i      v v  i       i vi         i
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_115950061_   2425 ATATAGAAAATGCCTACAACTCAACAAGAATTACAAAACAAACAGCATAA 2474
                              i i  iv i          i  v  -- -  i     i i vi  
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAA--A-AAGACAAATAACCCAA 811

  chr2_115950061_   2475 TT----GATAGACAAAGGAGTTACATGAATATTTTTCCAAA-AAGATATG 2519
                           ----i  i i       v  iv  ii i    i      -       i
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_115950061_   2520 CAAATATCCAATAATCATGAAAAAAGATGCTCAATGTCACTAATCAT 2566
                              iv       v  iivi             ii   ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (100 / 53)
Gap_init rate = 0.02 (12 / 638), avg. gap size = 2.25 (27 / 12)  


2843 21.77 9.57 1.32  chr2_115983263_115985327.rev      738  1573 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_115983263_    738 AAAGACATTGTATGTCTACAGATCAGAA--CCT-----TGTTAGTGTAGC 780
                              i  ivi    ii ii   ii   -- i -----     ivi i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_115983263_    781 ACTATTTTTCAAATTGATCTACATAAGCAATATAATCACCATCAAAAGTC 830
                          v  i iii              v vv   iii    v i       -  
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TC 102

  chr2_115983263_    831 TTAGCTTCTTTTGACTTTGTTTGCA-AATTTTACGAGTTGATCTTAAAAT 879
                         ii    v i   -------      -  v  v  i  i     i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTT-------TTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_115983263_    880 TCATATGGAAATGTAAGGGACACAGAA--ATC----CAATTTTGAAAAAG 923
                                      i       v     --ii ----    i         
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_115983263_    924 AG---CAAAGTTCAAGGGCTCACACATCTTGATTACAAGTCTCACCACAT 970
                          i---       vi   i       v  iii   v   iv  i  i   v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_115983263_    971 AGCTACAACAGTCAAGAC--TGAACTTCTGGCCTAAGGATAAACATATAG 1018
                                ii i       --  viv v     v        i        
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_115983263_   1019 ATTAATAGAATACA-----GAGTCCCAAGACAAAATCATATATTTGTGGT 1063
                           i   i     v -----      vi i i   vi    i    i    
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_115983263_   1064 CAGCTGACATTTGAGAAGGGTGCCAAAATTATTCAACAGAAAAAAAA--A 1111
                           ii   iv  i  v           i ii      ii ii   i  --i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_115983263_   1112 TCTTTTCAA-AAATGTTACATGGATAATTGTATTTCCACATGCAAAAGAA 1160
                                  -     v i vv   i  i  v  v?               
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_115983263_   1161 TAAATGTGGACCTCTTTCCTCACATCATATTAAAAAATCCACTCAAAATG 1210
                          i  vv      i  v-       i     vv      iv          
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_115983263_   1211 TATCATAGAACTAAACATAGAAATAAAAATCTATTATGTTCTCA----AA 1256
                         v    ?   v     ii  ii iiv    -    v vii   i ----  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAA 543

  chr2_115983263_   1257 CACACAA----AAA-------GA-----AGTTAG---------TCT-AAA 1280
                         v   i i----   -------  -----i     ---------   - i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_115983263_   1281 T-TAACA----ATGTATAGAAAACTAAAGAAAAAATAGAT---TTG-ACT 1321
                          - i   ---- v i i iiv   v               ---   -   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_115983263_   1322 TTATCAACATTTAAA--TCTGGTGCATCAAAAGACACCAATCAGAAAGTG 1369
                          i     v   v   -- i v    v     i     i viv        
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_115983263_   1370 AAA-GACAACATACC---TGGGAGAAAACATTTGAAACTTATGTATCTGA 1415
                            -      vi  v---          i     v  v i  i       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_115983263_   1416 CAAGGAATTTG-ATTTATAATATATGAAAAAATCTTACAATTCAGCAATT 1464
                         i    i i   -  ii v       i  i  v        i   ii   -
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT- 792

  chr2_115983263_   1465 GAAAAGA------GCTCAAT-AAAAAATGGGCAAAGAATTTGAACAGACA 1507
                         i      ------i i    -?              i       i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_115983263_   1508 TTTCTCCAACAAAGATATACAAATGATCAATAAGCACAAGAAAAGATCCT 1557
                                  vi              ii           v        v  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_115983263_   1558 CAATATCATCAATAAA 1573
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (119 / 60)
Gap_init rate = 0.03 (31 / 905), avg. gap size = 2.94 (91 / 31)  


1395 20.31 12.25 9.46  chr2_116000442_116002078      501  1145 (492)    L1M4_orf2#LINE/L1      246   908 (0)  

  chr2_116000442_    501 AGCTATTGTAATGAAGAC----TGGAACTGGCAGTAGGACAAACACATAG 546
                              iv     v     ----   v       vv    i i   i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_116000442_    547 ATCAATGAAAGAGAAGAGAGAACCCAGAAATAGACCCTCACAACTATGCC 596
                                i  v    vv    ii         i    vi   vi    vi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_116000442_    597 TAATAGATTGTTGGCAAAGGTGCACAAG-CAATTTAATGG----AGGACA 641
                         i   v    v i i   i     -    - v   i     ----  i i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATA 394

  chr2_116000442_    642 GTCTTTTCAACAACTAGTGCCAGAACAATCAGATATCCATAGGCAAAA-A 690
                                      v i    ii i    iii    ?   i v      - 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_116000442_    691 ATAAAAACAAAAAGCCCACAAAAAACAAAAACATCATATTGG---CTTAA 737
                           i  i--------------------------------    --- i  -
  L1M4_orf2#LINE/    445 ATGAAG--------------------------------TTGGACCCCTA- 461

  chr2_116000442_    738 GCCACACACCTTATACAAA------CTCAGAATGGATCATGCTTTTAAAT 781
                         -  v      v        ------    i         ?ivvii     
  L1M4_orf2#LINE/    462 -CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_116000442_    782 GTAA-AGTATAAATCTATAAAACTTTTAGAAAAAAA------------TG 818
                             -  i-    v          i      i    ------------ v
  L1M4_orf2#LINE/    511 GTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_116000442_    819 TTTGGGATTTAAGGCTAGGGAAAAATTTCTTAAAC-TGTATACCAAAAGC 867
                           i v  ii vi  i    v  vii       i i-  - i         
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG-ACACCAAAAGC 608

  chr2_116000442_    868 ACAGTC--CAAAGGAG------GATAAACTATTG--TTCCATGA----TA 903
                            iv --    i  i------      ---   --i i   v ----  
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAA---TTGGACTTCATCAAAATTA 655

  chr2_116000442_    904 GACCCTGTT----TTCA--GG---CTA-----------AAAATACAAGTT 933
                         i vv  v  ----    --  ---   -----------    v    vii
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_116000442_    934 ACAGTCTAGAAGAAAATATTTGAAATTCCCATGTGTGACAAAGGATCAAC 983
                             vv i i            v  v  vi  i v   i  i   iivii
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_116000442_    984 ATTCA---TATATAAAGAATTCTTAAAAATGAACGGTTAAAAACAACAAC 1030
                           i  ---           i     ---------------------    
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTA---------------------CAAC 784

  chr2_116000442_   1031 T--ATAACAAAAACACAACTA-TACAATCAGAAAGTGGGCCCAG-ACATG 1076
                          --    i     v    v  -iv    i?i   i     vv  - iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_116000442_   1077 AAGAGACATTTCACT---GAAGATTTACAGATGGC-AATAAGTACATGAA 1122
                           v         v i---      v    i     -      i       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_116000442_   1123 AATAT-TTTAACATTACTAGCCAA 1145
                           v  -i i     i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (78 / 50)
Gap_init rate = 0.05 (31 / 663), avg. gap size = 4.52 (140 / 31)  


3243 26.43 0.66 0.66  chr2_116008169_116010349.rev      782  1689 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116008169_    782 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 831
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116008169_    832 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 881
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116008169_    882 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 928
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_116008169_    929 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 978
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_116008169_    979 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 1028
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_116008169_   1029 CTACAGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGAGATATAGAT 1078
                                  i   i    ii     v   i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_116008169_   1079 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTGCAAC 1126
                                 i    i--    i  --        vv   i i  i iiiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_116008169_   1127 TATCTGATCTTTGAGAAATCTGAGAAAAACAAGCAATGGGGAAAGGATTC 1176
                         i vi    i  i  v  ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_116008169_   1177 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1226
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_116008169_   1227 TGAAACTGGATCCCTTCCTTACACCTTATAAAAAAATCAATTCAAGATGG 1276
                             ii    i    v   i     v    v      i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_116008169_   1277 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1326
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_116008169_   1327 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCGAGGACTTCATGTCT 1375
                          v    ?i- v i -   iv   v v  vv i   i v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_116008169_   1376 AAAACACCAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGGGATCT 1425
                          vi            vvi          iv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_116008169_   1426 AATTAAAGTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 1475
                         v  i   i v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_116008169_   1476 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 1525
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_116008169_   1526 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1575
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_116008169_   1576 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 1625
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_116008169_   1626 TCTCAAAAGAAGACATTTATGCAGTCAAAAAACACATGAAAAAACGCTCA 1675
                             v        i  vi viii i   v  i          i i     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_116008169_   1676 CCATCACTGGCCAT 1689
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1903 28.06 4.17 1.15  chr2_116140412_116142102.rev      505  1199 (492)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr2_116140412_    505 AAAAAGAACAAAGCTGTAGGCATCATATTACCCAACTTTAAACTACACTG 554
                           i          i  v   vv   i i v     i  i   vivi   i
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_116140412_    555 TAAGGCTGCAGTAACCAAAATGGCATGGGACTGGTACAGAAACAGACACA 604
                         i  i   i      i   i ii ii   v     i i iii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_116140412_    605 TAGACCAATGGAACACGTAAAA--GAAAA--CAAAAATAAAGCTGCACAA 650
                             i        ----  i  --  i i--  i       v iii   v
  L1M4_orf2#LINE/    293 TAGATCAATGGAA----TAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_116140412_    651 CTATAATC--TTG-----TGACAAAGTCAACAAAAACAAGCAATGGGGAA 693
                         i   ii  --   -----i     i viiv   i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_116140412_    694 AGGACTCCCTTTTTAATAAATGGTGCTGGGATAAGTGGCAAGACATTTGG 743
                           i ivvi     i  i              i  v   vv ?v  iv  v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_116140412_    744 AGAAGAATGAAACTGTACCCTTTCTTTAC--CACATACAAAAACCAACTC 791
                          i         ii  v    i v i i  --  i         ii     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_116140412_    792 AAGATGGATTAAAGAGTTAAATGAAAACCCTGAAACTATAAAAATCCTGG 841
                           i      i ?   vi      v  ivv  i           v  i i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_116140412_    842 AAAATAACCTAGGAAATACTATTCTGGACATAGAAACTGGAAAAGATT-- 889
                           i v   v    ?ivv v v   vv   v v iiviv  v  v i  --
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_116140412_    890 ----GTATGAAAATACCAAAAGCAATTGCAACAAAAATGAAAATTGACAA 935
                         ----i     ---i          vvv         ivi     v  i  
  L1M4_orf2#LINE/    589 TTAGATATGA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_116140412_    936 GTGAGATTTAATTAAACTGAAGAGTTTCTGCACAGTGAAAGAAACTATTC 985
                         i vi  i  v  i   v v  i ii  i  ii vvii  i  v     iv
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_116140412_    986 ACACAC-----AAACAACCTACAGACTGG-AGAAAGTATTTATAATTTAT 1029
                          v v v----- i      i     v   -     i     ii  v i  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_116140412_   1030 GCATCTGACAAAGTTCTAATATCCAGAATCTATAAGGAACTTAAACAAAT 1079
                         ii      i  i vv  vi          v     i     ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_116140412_   1080 CAACAAGTAAAAA--CAAATAACCATATTAAAAATTAAGCAAAGGACATG 1127
                            i  -      --         vv   ?    v ii        iv  
  L1M4_orf2#LINE/    786 CAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_116140412_   1128 AACAAACACTTTTTGAAAGAAAAAACACAAATGGCTAACAA--ACATGAA 1175
                           i i   i  i iv      i v i         i  i  --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_116140412_   1176 AATACGCTCAACATCACTAATCAT 1199
                           v i           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (116 / 75)
Gap_init rate = 0.02 (13 / 716), avg. gap size = 2.85 (37 / 13)  


2800 19.76 5.44 7.10  chr2_116170516_116176160     4245  5145 (500)    L1M4_orf2#LINE/L1        1   886 (22)  

  chr2_116170516_   4245 TGTAAAGGCATACCATGTTCATGAATTGGAAGATGTAATCTTGTTATGAT 4294
                           v    ii  v           i         iv    v      v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116170516_   4295 GTCAATA-TGCCCAACACAATCTACAGATTCAATTCAATCCCTATCAAAA 4343
                          v     - v     vvii              iv               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116170516_   4344 TCCAAATAATGTCTTTTTTGCAGATATAGAAAAGCCTATCCTAGAATTCG 4393
                            v ii--  i            v  v  v    iv      i     i
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_116170516_   4394 TATGAAATTTCATAGGGCTTCA-AGTATCCGAAACATTTGTAAAAAAGAA 4442
                             i  v v  -    vii  - i  v  i     v iv i        
  L1M4_orf2#LINE/    149 TATGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_116170516_   4443 GAA---AGTTGGAGAACTCACACTACTGA--TTCAAAACTTACTACAATG 4487
                            ---        i         v iv --                 v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_116170516_   4488 -TATAGAATTCAAAATAGTGTGACATAAATTAACTGTGCTGGTACAAAGA 4536
                         -  i  v v    i i      -------------  i    i i  i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTG-------------GTACTGGCATAAGGA 284

  chr2_116170516_   4537 CAGTAATATAGACCAATGGAAAAGAAGAGAGAGTCCAAAAATAAACTTTC 4586
                         i  vv       i        v    vv         i        iivi
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_116170516_   4587 GCATTTATGATCAAATGA----------AGGTGCCAA-ATCATTGAATCA 4625
                         i        i    v   ----------i        - i    v   vi
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_116170516_   4626 GGAAAGGACTATCTTTTTTAAACAACTGATACTGGAAAAACTGGATATCC 4675
                               i ivi      i--     v  i i    i v         ?  
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTC--AACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_116170516_   4676 ACATACACAAAAAATAAA------CTCTTACCTAATATCACATTCAAAAC 4719
                             i  -   i   i  ------ i i     v i i  i  v     v
  L1M4_orf2#LINE/    433 ACATGCA-AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_116170516_   4720 TTAACTCAGATTGGATCAAATATCTCAGCATAAGCTCTAAAACTATAAAA 4769
                                 i v       ? v i  v iii    vv              
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_116170516_   4770 CTTTTAGAAGAAAATATAAGTCAGAAGTTTGAAGATATTGGAAGGAATAA 4819
                           i           i   i ?-----  ---- i  v  v ---------
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGN-----GT----AAATCTTCG--------- 563

  chr2_116170516_   4820 ATGAA-TTGAATCATTTTGCAGTGCTTTCTTGGATATGACACAAAAGACA 4868
                         -   v-   ii i v---   i  v      i          v   ii  
  L1M4_orf2#LINE/    564 -TGACCTTGGGTTAG---GCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_116170516_   4869 CATG-----AAATTAAAAATTGACAAATTAGATTTTATCAAAACTTAAAA 4913
                           v -----   vv      v  i     i  i  i       i v    
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_116170516_   4914 CTTTTGTGCATCAA-GAACACTATCATTGGAGTAAAAAGGCAACATGTGG 4962
                                  v    - i         vvii   i     i    viiii 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_116170516_   4963 AAT---AGAAAATATTTCCAAATCACTTATCTAAGAAGAGGTTAATATAG 5009
                            ---           v       iv     i v   i ii vi   vv
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_116170516_   5010 AGGAATAAAGTATACAGGAGTTCTTATATAGAGGGATTCTAAAACGTAAT 5059
                           -    ---    - i  ii     i ------- i  ---  --    
  L1M4_orf2#LINE/    760 AG-AATA---TATA-AAGAACTCTTACA-------ACTC---AA--TAAT 792

  chr2_116170516_   5060 AAAAAGA-AAGCAACCTGATTAATTCCAAAATGGGCAA------TGAACC 5102
                                -  ii    ii   ? ----           ------    --
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWA----AAAATGGGCAAAGGATTTGAA-- 836

  chr2_116170516_   5103 TAGATAT-----CAAAAAA--TATGTAAATGGCCAATAAGTTCATCAAAA 5145
                             i  -----    i  --   ii              iv   v    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.52 (105 / 69)
Gap_init rate = 0.04 (33 / 886), avg. gap size = 3.42 (113 / 33)  


1702 27.56 11.95 1.46  chr2_116230450_116233580     1822  2641 (490)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_116230450_   1822 GGAAGCTATTCCATGTTTTTAAATAGAAAAAATTAATATTGTTAAGATAT 1871
                          i   v   i       iv ii  v i  i v                iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_116230450_   1872 TAATTCTACCCAAATTTAACCATAATTTTAATATAATACCAATTAAAGTC 1921
                         i   v  v        v v i i iv  i  iii   v  v  i   i  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_116230450_   1922 CCTTCTGATTTTTTTTGTAGAAACAGACAAGCTGTTTTTAAAATTAATAT 1971
                           vv   -ii       i     iv         v ii       v    
  L1M4_orf2#LINE/    103 CCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_116230450_   1972 GGAAACAAAAAATACCTGAACAAGTCAAAGTAATCCTGTAAAAGAA---T 2018
                              iiv  iiv   iii vv  i    ii    i  v       ---i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_116230450_   2019 AAAATTGAAGGAGTTAGCCCTACCTGATTTCAAGAATAAATAAAAAGCTA 2068
                            i   i    v i - v  v  ii       i v v v  v       
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_116230450_   2069 CAAAAACCTGGAGA-TGCTAGTGGAGGCATAAGGACC-ACAAATAGGTCA 2116
                           iv  i vi  v -  - i  ivv          iv-   v    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTG-TGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_116230450_   2117 ACTAAATTGAAT--GGTTTGCAGAGAACAGACCCACATTTATATGATTGA 2164
                          ivi   v    --i vv v    -  i i     i iv v    i ii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGA-AATAAACCCATACATTTATGGTCAA 348

  chr2_116230450_   2165 TTGATTTTCTACACAGGTGCTAAAGCAGTTCAATGGAGAAA--------- 2205
                                  v   vi     i  ii vi        i    ---------
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_116230450_   2206 --------AATGGTGCTGAAAAAATTGG-CATCCCGATTGGATAAAAAAA 2246
                         --------          ii v  i   -i ?  vv  ---ii    i  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT---GCAAAAGAA 445

  chr2_116230450_   2247 ATTGATGTTTGAC----AACTCATATCATATTCTAAAATCAATTTGGGAT 2292
                         --   v   v   ---- v    i i     v v     i  i iiii  
  L1M4_orf2#LINE/    446 --TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_116230450_   2293 AAATCATAGCCCTAAATTTAAGAGCTAATACTGTCAGTGTTCTAGGGGAA 2342
                         ii    ?  v       v          v   i v ivv ii   ii   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_116230450_   2343 AATAT-GAAATAAA--------ACCTTA--CTATAC----------TGAA 2371
                           i  - i?i    --------     i--i  vi ---------- ii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_116230450_   2372 TAAG---CCAAAA----AATCATTAATTATGAAACAATA----AATTGGA 2410
                           v ---      ----  v  vi  -- v    v    ----       
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAA--AAGAAAAAATAGATAAATTGGA 641

  chr2_116230450_   2411 CATCAATAAAATTAGAAACTTCT---CATCAAAG-ACACCATTAGGGAAA 2456
                          v   vi       i      i --- v      -    i  i i i  i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_116230450_   2457 AGGATATGCAAACTACAGTCTGGAAGAAAATATTTTGCCAAATGGGTATC 2506
                         v i v vi   v i    vv   i           -  v  viivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATC 740

  chr2_116230450_   2507 AGACAAAA-AC-----------ACATATAAAGAAATTCTATAACTCAATA 2544
                         v  i  ii-  ----------- i          v ii  i         
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_116230450_   2545 ATAAAAACACAA----CCTCATAAAAACAT---CAAAACATGTGAACAGT 2587
                                v    ----  iv  v?   v  ---    iv  v    i  v
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_116230450_   2588 TACTTAT--AAGGAAAA-----GAATG-------AACATATGAAAAAGTA 2623
                         i i  v --  i   i -----i    ------- i  i       ii i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_116230450_   2624 CTCAACATTTGGTCAGGT 2641
                                 iv????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (133 / 89)
Gap_init rate = 0.03 (31 / 906), avg. gap size = 3.55 (110 / 31)  


3235 27.12 0.55 0.44  chr2_116273492_116279879.rev     4990  5896 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116273492_   4990 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5039
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116273492_   5040 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATTCCCATCAAGC 5089
                            v     v     iv i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116273492_   5090 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5137
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_116273492_   5138 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5187
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_116273492_   5188 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5237
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_116273492_   5238 TACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGATATAGACC 5287
                                 i   i    ii       v i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_116273492_   5288 AATGGAACAGAAC--AGAGCCTCAGAAATAATGCCGTATATCTACAACTA 5335
                                i    i--    i -         vv  i  i  i  iiiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chr2_116273492_   5336 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5385
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_116273492_   5386 TATTTAACAAATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5435
                          v  i        i        v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_116273492_   5436 AAACTGGATCCCTCCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5485
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_116273492_   5486 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5535
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_116273492_   5536 TAGGCA-ACACCATTCAGGACAAAGGCATGGGCAAGGACTTCATGTCTAA 5584
                             ?i- v i -   iv   vvv  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_116273492_   5585 AATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGTGATCTAA 5634
                         i i          vvi          vv     v  i    vv  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_116273492_   5635 TTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACTGTCAGAGTGAAC 5684
                          i   v v  i ii  i  ii vv    i  v    iiivv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_116273492_   5685 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5734
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_116273492_   5735 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5784
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_116273492_   5785 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5834
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_116273492_   5835 TCAAAAAAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5884
                           v   i    i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_116273492_   5885 ATCACTGGCCAT 5896
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


2756 27.69 1.54 1.76  chr2_116327813_116332185.rev     2972  3881 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116327813_   2972 TGGAAAAACGACTCTTGGTCATGGACTGGAATAACTAATATTGTTAAAAT 3021
                               i iiv i v  v       i     v vi            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116327813_   3022 AGCCATACTACCCAAAGAAACCTATAGATTCAATGCAATCTGTAT-AAAA 3070
                         i  v     v      vvi i   i        i      iv   -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116327813_   3071 TACCAATGATATTATTCATATAAACAGAAAAAAAAATCATAAAGTTAGTA 3120
                          v   iiviiv  v  iii v   iv  v  ivvi   v    i  vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_116327813_   3121 TGAAAACACAAAACAGCCCAAATAGCCAAAGCAATACT----AAGCAAAC 3166
                           i   ii   iiv v  vi          i    vi ----   v i v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_116327813_   3167 CAAAGCTGAAGGCATCACACTATCTGACTTTAAAACATACTACAG----- 3211
                              i  i   vv       vi ii i  i     v       i-----
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_116327813_   3212 TAGTAACCAAAACAGCATGGTATTGGCATAAAAACAGATACATAGACTAA 3261
                         i     i   i    ii     i        ii i   i i     ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_116327813_   3262 TAGAGCACAATAGAAAATGCAGAAACAAATCCATGTATTTTCAGGCAACT 3311
                          i  ii v   v  i i v      i   i    ii    vii v   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_116327813_   3312 AATATTTGACAAAGGCACAAAGAACACATGTTGAGAAAATAACATTTTCT 3361
                         i  v  i     i  ii v    v  iviiv  i i   v  i v i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_116327813_   3362 TCAATAAGTGGTTCTGAGACAATGGAATATTCATATGCAGAAGAGTGATA 3411
                             i  i    v   i     iv i   ?i  i     i    i   vi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_116327813_   3412 CTAGAACCCAATCTTTCACCATATATAAAAGTCAACTCAAAATTCACTGG 3461
                         i i  v   v i  iv         i    i i          vv iii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_116327813_   3462 AAACTTAAATGTAAGACCTGAAACTATAAAACTGTTGGAAGAAAAGA-AG 3510
                          i  i           v  i             v  i        v -  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_116327813_   3511 GAG-AAGTGCTTCAGAAAATTAGTCTAGGCA-TAGATTTTAAGGCTAAGT 3558
                          ? -  i -    ivi vv  i vi      - i v  i v  i-  v v
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGA 598

  chr2_116327813_   3559 CTTCAAAAGTGCAGGCAACAAAAAACAAAAACATAGACCAATAAAATTGC 3608
                          vi      ii  i         i -     --    iv   vii i v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGA-AAAAA--TAGATAAATTGGACTTC 645

  chr2_116327813_   3609 ATTGAACTAAAAAGCTTCTGCACAGCAAAGGAAATAATCAGCAGAGTGAA 3658
                           ii  v v    i   i  ii vv       v iv    iv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_116327813_   3659 AAGACAACTTATAGAATGGGAGAAAGTATTTACAAACTATTCATTCAACA 3708
                                 ii i             i     i    ii  vi  iii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_116327813_   3709 AGGTACTCATATCCAGAATATACAAGGAACTCAAAACAACTCAACAGAAA 3758
                            v   ii             i  i      vv -        i ----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATA---- 790

  chr2_116327813_   3759 AGAAAAAAAAGAACCATATAATCTAATTTCAAAAATGGGCAAATGAGCTA 3808
                         --- v       --  v    i i    ?-             v  vi i
  L1M4_orf2#LINE/    791 ---ATAAAAAGA--CAAATAACCCAATTW-AAAAATGGGCAAAGGATTTG 834

  chr2_116327813_   3809 AATAGGCTTTTTTCAGAAGAAGAAATACAAAACACCAACAGGTATATGAA 3858
                              i v   i  vi       v       vvi    i i i i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_116327813_   3859 AA-ATACTCAGCACCACTAATCAT 3881
                           -  i    i  i  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (162 / 86)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.00 (30 / 15)  


2845 25.55 2.75 2.75  chr2_116363150_116369844.rev     5296  6203 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116363150_   5296 TGGGAAAACATTCCATGCTTGTGGATAGGAAGAATCAATATTGTGAAAAT 5345
                            i  i i  i     i ii     v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116363150_   5346 GACCATATGGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5395
                          i v   ivv      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116363150_   5396 TACTATTGACTTTCTTCACAGAAGTAGAAAAACTAATT-TAAATTTCATA 5444
                          v i vivi i  i  ii     i v  v  i  i  i-    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_116363150_   5445 TGGAAAAACAACAACAACAAAGAGCTCATA-TAACAAAGACATCCATAAG 5493
                               vi   ---------i ii i  v -  i v  i   vi v i -
  L1M4_orf2#LINE/    151 TGGAAATGCAA---------GGGACCCAGAATAGCCAAAACAATCTTGA- 190

  chr2_116363150_   5494 CAAAAAAAAAAAAAAAAAAAAAAGCTGGAGGCATCATGCTTCCTGACTTC 5543
                         ---------    i  i  v    i      vv   ii     ii i   
  L1M4_orf2#LINE/    191 ---------AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_116363150_   5544 AAACCATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCA 5593
                            v v        i          i   i    ii         i iv 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_116363150_   5594 AAACGGATATATAGACCAATGGAACAGAACAGAG-GTCTCAGAAAAAAAG 5642
                         ii ii  i       i        i    iv   -   -      v   v
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAAC 330

  chr2_116363150_   5643 TGCAGCACAACTGCAACCATCTGATCTTTGACAAACCTGACAAAAGCA-- 5690
                         i-  -i   vi iiiii  vi    i  i     ivv  v   i v  --
  L1M4_orf2#LINE/    331 C-CA-TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_116363150_   5691 --ATGAGGAAAAGATTCCCTACTTAATAAACGG-GTTGGGAAAACTGGCT 5737
                         --   i     ii  vvi  vi i  i   i  - i     v      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_116363150_   5738 AGCCATATGCAGAAAACTGAAATTGGGCCCCTTCCTTACACCTTATAGGA 5787
                          ?   i     i  i v    i    i     v   i     v    vi 
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_116363150_   5788 AAATTAAC--AAGATGTATTAAAAACTTAAATGTAAGACCTAAAAACCAT 5835
                                 --  i   v  i ? i  i           v      - i  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTAT 527

  chr2_116363150_   5836 GAAAACCCTAGAGGAAAATGTAGGCAGTA--CCATTCAGGACACAGGCAC 5883
                         i   vi i    i     ii    ?-   --i -   iv   viv  vvi
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGN-GTAAATC-TTCGTGACCTTGGGTT 575

  chr2_116363150_   5884 TGGCAAAGACTTCATGACTAAAACACCAAAAGCAATGGCAACAGAAGCCA 5933
                         v     v ii   v iiv  vi            vvi      i   vv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_116363150_   5934 AAATAGACAAATGGGATCTAATTAAA-CTAAAGA-------GCTT-AAAG 5974
                                i    v   ii v  i   -i    i -------    -    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_116363150_   5975 AA-ACTATCATCAGAGTGAAAAGGCAACCTACAGAATGGGAGAAAATTTC 6023
                         i -       vv i         i     i                 v i
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_116363150_   6024 TGCAATCTATCTGTCTGTCAAAGGGCTAATATCCAGAATCTACAAAGAAC 6073
                              vii  v i    vi  i  i  vi          v  i       
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_116363150_   6074 TAA-ACAAATTTACAAGAAAAAAACAAACAACCTCATCAGAAAGTGGGCA 6122
                          vv-    v iv i  v     i     i    iv  i?i   i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_116363150_   6123 AAGGATGTGAATAGACACTTCTCAGAAAAAGACATTTATATGGCCAACAA 6172
                               v          i     vi  i    i  vi v        i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_116363150_   6173 --ACATGAAAAAAAGCTCATCATCACTGTTCAT 6203
                         --         i v     v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (145 / 83)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.38 (50 / 21)  


2362 26.37 2.68 2.14  chr2_116398201_116403196.rev      648  1394 (3602)    L1M4_orf2#LINE/L1        8   758 (150)  

  chr2_116398201_    648 ATATTTCACTTTCATTTATAGGAAGACTCAATATTGTCAAGATGTTGGTT 697
                             ii  iv     vv  v        i        i      viii v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_116398201_    698 CATCCCAACTTGTTCTGTAGATTCATTGCCATACCAATCAAAATCCTAGC 747
                          vi     v   v   ii       vi  v  v  v          i   
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_116398201_    748 AAGTTACTTTACAGATA-----AACTTTATTCTAAAGTTTATATAGAAGG 792
                         vivi vi   i    v -----  vi v  i     i  i    i   iv
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_116398201_    793 ACAAAAGACCCAGATTAGCCAACACAATAATGGA---GAAGAACCAAGTT 839
                         i   ii        v       v     vv  i ---       v     
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_116398201_    840 GGAGGATTAATACTACCCAAATTCAAGACTTACTATAATGCTACAGTAAT 889
                               i v i   v     v     i        i  v           
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_116398201_    890 CAAAACAGTGTGCTTTTAGCAAAATGATATTAAAAATGGATCAATAGAGC 939
                            i        v vi i   v  v    v- v v  i       i  ii
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAG-ACATATAGATCAATGGAAT 306

  chr2_116398201_    940 AGAATAAAGGGCCTAGAAATATGCCCATATAAATGTAATCAACTAATCTT 989
                              vi  i i i       vi      i vv i ii    i i  i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_116398201_    990 TGACAAAGGAGCAAAGGCAGTACAATGGAGGAAAGACAGTCATTTCAACA 1039
                         i     i  v  v   i vi v      i i  ii i    v        
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_116398201_   1040 AATCGTACTGGAACAATCAAATATCCACATATAAAAATAATAATAATAAT 1089
                            v  i    i    iiii   ?      ii    i-   i - i viv
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AATGA-AGTTGG 454

  chr2_116398201_   1090 ATCTCTACACAGACCTAACATCCTTCATACAAATTGGCTCAAAATATCCC 1139
                          i i    ------  v   i v vi i v     ii        ivvi 
  L1M4_orf2#LINE/    455 ACCCCTAC------CTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_116398201_   1140 ACGGGCCTAAATGTAAAACACAAAACTATAAAATTTCTATAAGATAACAT 1189
                          ?i i           i vvi            i ii  v    v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_116398201_   1190 AGGAGAAAATCTAGATGACAT--GGTTTGGTGATAGCTTTTCAGATATGT 1237
                            ? v      vvi    v --    v  ii  i i  i i       v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_116398201_   1238 CACCAAAA-CTTGACCCAGGAAAGAAAGAATTGTTCAACTGGACATTATT 1286
                                 - vii v v vi       i   v v v  i     v i  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_116398201_   1287 AAAATTTTTAGAAAATCTACTCTGTGT---AAA--ACTCTGTCAAGAAAA 1331
                               -----    v  -- i    i---   --  v  i        i
  L1M4_orf2#LINE/    649 AAAATT-----AAAAACT--TTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_116398201_   1332 GGAAAAAATGAG--ACAGACTAGGGGATA-TATTTTCAAAAGACATATCT 1378
                         v     i ii v--     v i  i  v -     v    vv i      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_116398201_   1379 GATAAAGGACT-GTGTC 1394
                              i     -  i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATC 758

Transitions / transversions = 1.40 (113 / 81)
Gap_init rate = 0.02 (15 / 751), avg. gap size = 2.40 (36 / 15)  

 436 23.35 2.99 3.59  chr2_116398201_116403196.rev     1676  1842 (3154)    L1M4_orf2#LINE/L1      743   908 (0)  

  chr2_116398201_   1676 ATAGCAGACTGTTATCCAAAATGTATGAAGAACACTTAGAACTCCACAAT 1725
                            ivi    vv      i   i   i      v    v     v i   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_116398201_   1726 AAGAAAACCGACTAACTGAATTTAAAAAAAAAATGGACCTAAAACTTTAA 1775
                           i  i  -i v    iv    ?     -----   i vv ii i  v  
  L1M4_orf2#LINE/    793 AAAAAGAC-AAATAACCCAATTWAAAAA-----TGGGCAAAGGATTTGAA 836

  chr2_116398201_   1776 TAGACA-----CCAAAAAATACAAAGCAATGACAAATAAGCACATAAAAT 1820
                               -----     i  v i v vv    i v           i   v
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_116398201_   1821 AATGCTCCATATCATATTTAAT 1842
                         i      v i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (20 / 18)
Gap_init rate = 0.02 (3 / 166), avg. gap size = 3.67 (11 / 3)  

 226 24.53 0.00 0.00  chr2_116398201_116403196.rev     3259  3311 (1685)    L1M4_orf2#LINE/L1        1    53 (855)  

  chr2_116398201_   3259 TGGAAACACATCCAATGCTTATGGATGGGTAGAATCAATATCATGAAGAT 3308
                               v i    v   i i      v  v   v i     ii v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116398201_   3309 GAC 3311
                          i 
  L1M4_orf2#LINE/     51 GGC 53

Transitions / transversions = 1.17 (7 / 6)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.00 (0 / 0)  

2098 28.96 3.10 0.72  chr2_116398201_116403196.rev     3667  4505 (491)    L1M4_orf2#LINE/L1       50   908 (0)  

  chr2_116398201_   3667 TGACCATACTGCCAAAAACAATCTACAAATTCAATGCAATTCCCATCAAA 3716
                           i v     v  v   vii       i      i     i  i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_116398201_   3717 ATACCACCATCATTCTTCACAGAATTAGAAAAAC-AATCCTAAAATTCAT 3765
                           v   v vv v  i  ii     v v  v  i -i              
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_116398201_   3766 ATGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAGGCAAAAAGA 3815
                               viiv  ii  v  viv         i   vvi iiiv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_116398201_   3816 ACAAATTTGGAGGCAAAACATTATCAGACTTCAAACTATACTATAAGGCC 3865
                              v       vvvv   i vi vi i      viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_116398201_   3866 ATAATCAGCAAAACAACATTGTACTGGTATAAAATCAG-CTCATAGACCA 3914
                          i i v v   i   iii v       i    iivi  - vi     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_116398201_   3915 ATGGAACAGAATAGAGAACCCAGAAATAGAGCAAAATACTTACAGCCAGC 3964
                               i     v    ii         i v v v i i   ii i  ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_116398201_   3965 TAATCTTCAACAAAG----CAA-ACAA--AAGTGGGTACAGGACACTCTA 4007
                          i  i   i    i ----   -  v --v i    v v  i i v   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_116398201_   4008 TTACACTAACGGTGCTATGATAATTGGCAAGCCACATGTAGAAGAAAAAA 4057
                           vv  v  i      iv  i  i   vv ?       i i     vi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_116398201_   4058 ACTGGTTCCTCATTTCCCAACTTATATAAAAACATTGACTCAAGATGGGT 4107
                         ii   vi  ii ii  v  v v    i     --  i      i    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAATGGAT 497

  chr2_116398201_   4108 CAAAGACTTAAACCTAAAACCTGAAACCATAAAGATTCTAGAAGATAACA 4157
                           ?    i    iv   i v  i    i     iv ii       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_116398201_   4158 TTGCAAACAACCTTCTGGACATTGGCTTAGGCAAAGATTTCATGACCAAG 4207
                          v v?ivv  i    vv   v    v        v i    v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_116398201_   4208 AACTCAAAAACAAATACAACAAAAACAAACACAAA-AGATGAGACTT--- 4253
                          vvi     i  v vi        iv   v i i - i  vi     ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_116398201_   4254 --AAACTAAAGAGTTTCTGGACAGCAAAAGAAATAATCAGCAGAGTTAAC 4301
                         --   i    i v   -  vi vv    i  v iv    iv i   v  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_116398201_   4302 AAACAACCCACAGAATGGGAGAAAATCTTCACAATCTGTACATCTGACAA 4351
                          i                        v  ii   viii  i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_116398201_   4352 AGGACTAATAACCAGAATCAACAAAGAAATC----AGC-CAA----AAAC 4392
                         i     vi  v       vv i      v  ---- i -   ----   v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_116398201_   4393 CCCCACAAAATCCTATCAAAAAATGGTCTAAAGACATGTATAGACAATAC 4442
                         vvv  v v  i  v  i?        v v  i  iv  v       v v 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_116398201_   4443 TCAAAATAAGATATACAAATGGCCAACA-GTATATGGAAAAAAAAT-CTT 4490
                           v   v                   i - i i   ---    i  -  i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATG---AAAAGATGCTC 893

  chr2_116398201_   4491 AACATCGCTAATTTA 4505
                               i????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (130 / 109)
Gap_init rate = 0.02 (15 / 859), avg. gap size = 2.13 (32 / 15)  


 516 26.22 3.05 1.83  chr2_116420989_116422682.rev       81   244 (1450)    L1M4_orf2#LINE/L1        1   166 (742)  

  chr2_116420989_     81 TGGAAAACCATTCCACGCTCATGGATAGGAAGAATCAGTATCGTGAAAAT 130
                               ivi  i   i i        v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116420989_    131 GGCCATGCTGCCCAAAGTAATTCAAAGATTCAATGCTATTCCCATCAAGC 180
                            v  i  v      v i  ii v        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116420989_    181 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTC 227
                          v   -   v    i  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_116420989_    228 AT--GGAACCAAAAAAGAC 244
                           --    viiv  ii   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC 166

Transitions / transversions = 1.69 (27 / 16)
Gap_init rate = 0.04 (6 / 166), avg. gap size = 1.33 (8 / 6)  

2524 25.35 1.82 0.84  chr2_116420989_116422682.rev      471  1184 (510)    L1M4_orf2#LINE/L1      140   860 (48)  

  chr2_116420989_    471 TAGAATGAATATGGGAATAGCATTGAATCTA---TAGCCAAGACACTCCT 517
                           i   vv      i   -   vv i i i ---       i   v  i 
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr2_116420989_    518 AAGCAAAAACAACAAAGCTGAAGGCATCATGCT----GACTTCAAACTAT 563
                         i iv  i  v       i  i   vv   ii  ----i i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_116420989_    564 ACTACAAGGCTACACTAACCAAAACAGCATGGTACTGGTACCAAAACAGA 613
                                i      v   i   i    ii         i iv ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_116420989_    614 TATATAGATCAGTGGAAAAGAATGGAGGCTTCAGAAATAACACCACACAT 663
                         i          i     v     v   iv i         vv   i    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_116420989_    664 CTACAACCATCTGATCTTTGGCAAACCTGACAAAAACAAGCAATGAGGAA 713
                         i  iiii  vi    i  i i   ivv  v   i v  vv     i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_116420989_    714 AGGATTCCCTATTTAATAAATGGTGTTAGGAAAACTGGCTAGCCATATGC 763
                           i  vvi  v  i  i        i i   v      v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_116420989_    764 AGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTC 813
                          i  i v    ii         v   i     v                 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_116420989_    814 AAGATGGATTAAAGACTTAAATGTAAGACCTAAAACCATACAAACCCT-A 862
                           i      i ?    i           v       i   -    i  - 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTA 537

  chr2_116420989_    863 GAAGAAAATGTAGGC---AATGCCATTCAGGACATCGGCATGGGCAAAGA 909
                                 ii    ?---   -- -   iv   v i  vv i     v i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_116420989_    910 CTTCATGACTAAAACACCAAAAGCAATGAAAACAAAAGCCAAAATTGACA 959
                         i   v iiv  vi            vviiv        vv     v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_116420989_    960 AATGGGGTCTAATTAAA-TTAAAGAGCTTCTGCGCAACAAAAGGAACTAT 1008
                            v  iii v  i   -     i -   i  i  vv    i iv     
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chr2_116420989_   1009 CATCAGAGTGAACAGGAAACCTACAGAATGGGAGAAAATTTTTACAATCT 1058
                           vv i      v  iv    i                 v   i   vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_116420989_   1059 ATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAA 1108
                           vi      i  i  i  vi          v  i  i     ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_116420989_   1109 ATTTACAAGAAAAA-ACAAACAACCCCATCAAAAAGTAGGCAAAGGATAT 1157
                         v iv i  v     -     i     v  i?    i i          v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_116420989_   1158 GAACAGACACTTCTCATAGGAAGATAT 1184
                            i     i     vv i        
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.49 (106 / 71)
Gap_init rate = 0.02 (11 / 721), avg. gap size = 1.73 (19 / 11)  


2675 27.36 2.89 1.89  chr2_116432392_116440455.rev     4972  5870 (2194)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116432392_   4972 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5021
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116432392_   5022 TGCCATACTGCCCAAGGTAATTTACAGATTCAGTGCCATCCCCATCAAGT 5071
                         v  v     v     iv i  i          ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116432392_   5072 TACCAATGACTTTCTTTACATTA-TTGGAAAAAAACT-ACCTTTAAGTTC 5119
                          v   iivi i  i   i  vv -   --- v  i  - i i v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_116432392_   5120 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCAAAAA 5169
                                 viiv  ii  v  viv  v     iv     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_116432392_   5170 GA-CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACAACAAGG 5218
                           -     i      vv   ii  v  ii i      viv   v    i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_116432392_   5219 CTACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATACAGAC 5268
                                  i   i    ii        vi iv ii i   v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_116432392_   5269 CAATGGAACAGAAC--AGAGCCCTCAGAAATAA-----TAC--------- 5302
                                 i    i--    i  --        -----   ---------
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_116432392_   5303 CATCTGATCTTTGACAAAACTGACAAAAACAAGAAATGAGGAAAGGACAC 5352
                           vi    i  i     iiv  v   i v  vvv    i      i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_116432392_   5353 CCTATTCAATAAATG-CGCTGGGGAAACTGGCTAGCCATATGCAGAAAGC 5401
                         i  v     i     -i      iv      v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_116432392_   5402 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAACTAATTCAAGATGG 5451
                             ii    i    v   i     v          i   i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_116432392_   5452 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5501
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_116432392_   5502 CCTAGGCAATACTATTCAGGACATAAGCATGGGCAAGAACTTCATGACTA 5551
                          v    ?ivv v v   iv   v vi vv i     viii   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_116432392_   5552 AAGCACTAAAAGCAATGGCAAAAAAAAAAAAAAAAAAGCCAAAGTAGACA 5601
                         vii   i       ----   iv  v    i      -------    i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCA----CAAGCAACAAAAGAAAAAA-------TAGATA 634

  chr2_116432392_   5602 AATGGCACCTAATTAATCTAAAGAGCTTCTGCACAGCAAAAGAAACTACC 5651
                            v v  i v  i  vv v  i i   i  ii vv    i  v    i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_116432392_   5652 ATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAGATTTTTGCAATCTA 5701
                          vv i      v  i     i              i  v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_116432392_   5702 CCCATCTGACAGAGGGCTAATAGCCAGAATTTACAAAGAACTTAAACAAA 5751
                         ivi      i ii  i  vi  v       v  i        ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_116432392_   5752 TTTACAAGAAAAA-----ACAACCCCATCAAAAAGTGGGCCAAGTTTATG 5796
                          iv i  v     ----- i     v  i?    i     v   vv v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_116432392_   5797 AACAGACACTTCTC-AAAAAAGACATTTATGCCGCCAACAGATACATAAA 5845
                           i     i     -   i    i  vi viiv     i iii    i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_116432392_   5846 AAAAATGCTCATGATCACTGGTCAT 5870
                           i -      vv    ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.07 (43 / 14)  

2625 26.80 4.79 1.25  chr2_116432392_116440455.rev     6696  7572 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116432392_   6696 TAGAAGGATCTTTCTTGTTCATAATTAGGAAGACTCAATATTGTCATGAT 6745
                          i   i   v ii v       iiv v        i        i v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116432392_   6746 GTCAGCTATTTCCTAT-TTAATGTATAAATTCAATGTAATTCCAATAAAA 6794
                          v  i-  i i  i v-  i  v  i i      i i   i  v  v   
  L1M4_orf2#LINE/     51 GGCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_116432392_   6795 ATCCTAACAGC-TGTTTTGTGGCCATCAGCAAAGTGACTTTAAAGTTTAT 6843
                             i i v  - v     ii vv  iii   iv   iii    i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_116432392_   6844 ATGGAGAGGCAAAAAAGAAACCCCACGTAATAACCAACCAAATATTGAA- 6892
                              i v    iii -----    - -    i    vvv   v     -
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-----CCCA-G-AATAGCCAAAACAATCTTGAAA 192

  chr2_116432392_   6893 --GAAGAACAAAGTCCGAGAATGTACAATATCCAACTTTAAGACTTTATA 6940
                         --            iv   i ivi   v vi    i  i  i    vv  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_116432392_   6941 TAAAGCTGCAGTAATCCAGACAGTGTGGAACTGGTGAAATAATAGGCAAA 6990
                         i      i        v           v     iiv  vi    i  v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_116432392_   6991 TAAATCAGTGGAACAGAATAGGGACCCCAGAAATAGATTGATA------T 7034
                           i    i     i     v i  vi         i iiv   ------ 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_116432392_   7035 GGTCAACTGATATTTGACAATGGAGCAAAAACAACACAATGGAGCAAGGA 7084
                               i    v  i     v  v  v  i  v iv      i v   i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_116432392_   7085 --GTGTTTTCAAAAAATGGTAATAAAATAACCTCACATCGACAT---AAA 7129
                         --  v       v       iv iii i   ivv i ? v    ---   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_116432392_   7130 AAAT----CTAAATACAAACTTTACACCCTTGACAAAAACTGACTCAAAG 7175
                         i   ----i ii iv vv  i i     v vv       i i       i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_116432392_   7176 TATATCTCAGAACTAAATTGTAAAACACAAAACTATAAAATTCCTAGAAG 7225
                          iv   v?   v      -    i vvi            i  i      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_116432392_   7226 ATAATATGGAAGAAAATCTAGAAGGCCTTGGGTTTGACAATGATTTTTCA 7275
                          v  i  i i? v      vviv i         v i     i   i i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_116432392_   7276 GATATGACACTAAAGAT--------CAAAATATTGAATTATTAAGCTGGA 7317
                                   i   iii--------     v vvi   viv   ii    
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_116432392_   7318 CTTAATCAAAATTACAAATTTTGACTCTCTGTAAAAAGTCTA--AGGAGA 7365
                            v          v   i   viiv  iii-  ii vv   -- i  i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGAAA 690

  chr2_116432392_   7366 ATGAAAAGACAAGTCACAGAGTGGG-GAAAATGTTTGCAAAAGACATAAC 7414
                         i           vi      i    -      i        vv i   -i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA-T 739

  chr2_116432392_   7415 CT--TAAAGGACTGTTATTCCAAATATGCCA-GAACTCCTAAAACTCAAC 7461
                           --   i     vv   i vi     iiv -      i  v       i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_116432392_   7462 AATAAGAA-------AACTTAATTTAAAAATTGCTAACAACCTTGA-CAG 7503
                              i  -------   ii    ?      v vi  viivi    -i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_116432392_   7504 ACATCTCACCAAAGAAGATACACAAATGGCAAATAAGCACATAAGGAGAT 7553
                             i  v            i         v           i ii    
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_116432392_   7554 GTTCCACAACATATTTCAT 7572
                          i  v   v  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (140 / 91)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.52 (53 / 21)  


2026 24.21 1.49 0.74  chr2_116444188_116446381.rev      492  1028 (1166)    L1M4_orf2#LINE/L1       22   562 (346)  

  chr2_116444188_    492 TGAACAGGAAA--TTAATATTGTGAAAATTTCCACACTACCCAAAGCAAT 539
                           i iv    i--          v  i  vv v i   v      vii  
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGAT 71

  chr2_116444188_    540 ATGCAGATTCAATATATTCTCTATCAAAATTGCAA-TGGCAATTTTG-AG 587
                         v i         iii v  i          iv  i-  v vv     -  
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAG 121

  chr2_116444188_    588 AAATTGAAAAAACAATACTAAAATCCATATGGAACCACAAAAGACCCCAA 637
                                v  ivii  v       i         vii   ii     vi 
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_116444188_    638 GTAGCCAAAGCAATCTTGTAAAAGAAAAACAAAGTTGAACGCATCACTCT 687
                         i        i        v       i          i v vv    v  
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_116444188_    688 GTCTCATTTCAAA--TTACATCATAAAGTTACAGTAATCAAAACAGCATA 735
                         vi iv        --    --i i    i            i    ii i
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTAC--TACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_116444188_    736 GTACCGACATAAA-ACAGACAGATAAACGAGTGGAACAAAATAGAGAGCC 784
                             i i     i- i     v   i iv i     i i   v     i 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_116444188_    785 CCAGAAATAAAACCAAGCATATATGGTCAACTAATTTTTGAAAACGGTAC 834
                          -         v   vi   v         i i     i  v  v   i 
  L1M4_orf2#LINE/    320 C-AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_116444188_    835 CAAAAACATACAAAAGAGAAAGAATAGTCTTCTTCAATAAATGATGCTGG 884
                            i v   v   vi i              -     i     i      
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGG 417

  chr2_116444188_    885 GAAAACTGTCTAACCACATGCAAAAGTGTAAGACTGGATCATTACCTTAC 934
                           v     vv  ?             vi i iii    i vi     i  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_116444188_    935 ACCATACACAAAATTCAACTCAAAATGCATTAAAGATTTACATGTAAGAC 984
                               i      v i           v  i ?   ii  v        v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_116444188_    985 TTGAAACCA-AAATCTCCTAGAGGAAAATAAACGGGGAGAGCCTC 1028
                         i i    i -   v   i    i     i v v ? v i v i  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

Transitions / transversions = 1.54 (77 / 50)
Gap_init rate = 0.02 (9 / 541), avg. gap size = 1.33 (12 / 9)  

1095 23.93 2.56 1.71  chr2_116444188_116446381.rev     1352  1702 (492)    L1M4_orf2#LINE/L1      555   908 (0)  

  chr2_116444188_   1352 AAAGCTTCTTGATGTTGGTCTACACAGTGAGATTTTGGATAGGATAACAA 1401
                            v    v   iv    vi  vi  i  ivv i  i    v  i v   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_116444188_   1402 A-GCACAGGAAACAAAAGAAAAGGTAAAAAAGTAGGTCTACATCAAAGT- 1449
                          -     i v            ii  i v  i v  v  v       i -
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_116444188_   1450 AAAAAGTTT----CCACAAACAGGAAGTAGATAATTAATAAAATGAAAGG 1495
                              v   ---- iv    --   v---- iv  i  v   i     i 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAA--GGAC----ACTATCAAGAAAGTGAAAAG 698

  chr2_116444188_   1496 GCAGCATATAGATTGCGAGAAAATATTTGCAAACCATTTATCAAAAAAGG 1545
                         i  i vi i   v  v                 i   v    vi v    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_116444188_   1546 AGTTAATATTAGAAATATATAAGGAACTCACAGAATTCAATAGCAAAAA- 1594
                         iii vi   ivii         i      vi v  i      ii     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_116444188_   1595 ATGAATAATCCAGTTAAAATATGGGCAAAGAACCTGAATAGACAA--CTC 1642
                          ii     i   i  ?   v          i ii          v--   
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_116444188_   1643 TAAAGAAGATATAAAAATGACCAATAAGTATATGAAAAGGTGTTCACCAT 1692
                         i            v     i        i i        i  i   v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_116444188_   1693 CACTAATGAT 1702
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (50 / 33)
Gap_init rate = 0.02 (7 / 354), avg. gap size = 2.14 (15 / 7)  


2846 24.58 2.44 1.88  chr2_116452311_116456648.rev     2944  3846 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116452311_   2944 TGAAAACATATCCCATGCTCATGGGTTAGAAGAATCAATACTGTGAAAAT 2993
                           i   v          i      i  i     v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116452311_   2994 GACCATACTGCCCAAAGCAATCTACAGATTCAATGCAATTCCCATAAAAA 3043
                          i v     v      vii              i     i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116452311_   3044 TATCAGCATCATTTTTCACAGAATTAGAAAAAAAAATCCTAAAATTCATA 3093
                          vi    vv v     ii     v v  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_116452311_   3094 TGCAACTGAAAAACAGCCCA--AGAGCCAAAGCAATTCCAAGTAAAAAGA 3141
                           v  v  v  iiv -    -- v       i    iiii iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_116452311_   3142 ACAAATCTAGAGGCATCACATTACCAGACTTCAAG--TTACGCTACAAGG 3189
                              vi i    vv     i v  vi i     i--    --     i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAG 247

  chr2_116452311_   3190 CTATAGTTACCCAAACAGCATGGTACCAGCATAAAAGTAGGCACATAGAC 3239
                            i   v i v i    ii      ii      iii   i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_116452311_   3240 CAATGGAATAGCATAGCAAACCAAGAAATAAATCCAAATACTTACAGCCA 3289
                                    v  v vi ii v         i   v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_116452311_   3290 ACTGATCTTTAGCATAGGATAC-AAAAC-ATAAATTGGGGAAAGGACACT 3337
                          i    i  iii  -   i i -  i  -  vv v         i i v 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACA-AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_116452311_   3338 CTATTTAATAAATGTTACTGGGAATGCTGGCTAGCCAACATGCAGAAGAA 3387
                           v  i  i     v i      vvi    v  ?   -      i     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA-CATGCAAAAGAA 445

  chr2_116452311_   3388 CGCAACTGGATCCCGATCTCTCACCCTACAGAAAAATAAACTCAAGATGG 3437
                         i v ii    i   v i   v    v  i v      v       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_116452311_   3438 ATCAGAG--TTAAATCTAAGACTTGAAACCATAACAATTCT-AGAAAATA 3484
                             ?  --i     v     vi i    i    -  i   -    i v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAA 544

  chr2_116452311_   3485 ACCTTTGAAAAATTCTTTTAGATGATGGCCTAGGCAAAAAAA----AAAT 3530
                           v vv ?iv  v    ivv  ivv   vi       viivv---- i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_116452311_   3531 ATGACTAAAACCCCAAAATCTAATGCAGCAAAAACAAAAATAAATA--TT 3578
                              ----   --    v vv v   i     iv       i   --  
  L1M4_orf2#LINE/    595 ATGAC----ACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_116452311_   3579 CAAGACCTGATTAAACTAAAAAGCTTCTGCA-TGCAAAAGAAATAATCTT 3627
                         --i   i v  i   v v    i   i  ii- v    i  v iv   --
  L1M4_orf2#LINE/    639 --GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC-- 684

  chr2_116452311_   3628 CAAGA--GTGGACAGACAACCCACAGAATGGGAGAAAATATTTGCAAACT 3675
                         -    --   i v                                   ii
  L1M4_orf2#LINE/    685 -AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_116452311_   3676 GTGAATTCAATAAAGGACTAGTATCTGGAATCTACAAGGATCTCAAACAT 3725
                         i iv  iii    i     v     ii    v  i  i  v   vv   v
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_116452311_   3726 ATCAGCAAGAAAAA-ACAAATAATCTCATCAAAAATTGGGCAAATGATAT 3774
                         v   ii  v     -        i iv  i?    v        v   v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_116452311_   3775 GAATATACTTTTCTCAGAAGAAGATACACAAATGGCCAACAA--ACATAA 3822
                              v  v      vi         i            i  --    i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_116452311_   3823 AAA-ATGCTCAACATCAATAATCAA 3846
                            -             ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (125 / 93)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.77 (39 / 22)  


2877 26.00 1.29 3.34  chr2_116463484_116466135.rev     1234  2160 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116463484_   1234 TGGGGAGATAGTCCCTTTTTATGGATTGGAAGAATCAA-ATTGTTAAAAT 1282
                            ii     vi  v v  i             v i  -        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116463484_   1283 ATCCATAAGCCC-AAAGCAATCTACAGATTCAATGCAATCTCTATCAAAA 1331
                         iv v   vv   -   vii              i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116463484_   1332 TACCAATGACATTCTTCATGGAAATATAAAAAAAAAAAACTTAAAATTTA 1381
                          v   iivi v  i  iiii     - i v  ivvi v- i       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGAT-CCTAAAATTCA 148

  chr2_116463484_   1382 TATGAAGCCACAAAAGACCCAGAAATGCCGAAGGCATCCTGCACAAAAAG 1431
                             i ivii   ii         vv   i  ivv   i  v v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_116463484_   1432 AACAAAACTGGAAGAATCACATTACCTGACTTCGAATTGTACTAAATAGC 1481
                               ii    i  v     i v  ii i   i  viv     v v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_116463484_   1482 TATTGAGACCAAAACAGCATGGTACTGGCATAAAAACAGATGCATAGATC 1531
                           iv vi i   i    ii              ii i   iii       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_116463484_   1532 AATGCAACAGTATAGTGAACACAGAAACAAATCCATGTACATATAATAAA 1581
                             v  i  v  v v  iiv      i   i    ii iv   ii v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_116463484_   1582 CTTGTTTTCAACAAAGGTGTCAAGAACATGTA-TAGAGAAAAGACAGTCT 1630
                         i vi     i    i    i     v   vi - i i    ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_116463484_   1631 CTTCAATAAATGTTTCTGTGAAAACTGGATATCCATGTTCAAAAGAGTGA 1680
                         i     i     v v   v  v         ?   ii v       i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_116463484_   1681 AACTAGACCCTTATCACTTGCCATACACAAAAATCAAGTCAAA-TGTATT 1729
                          ii i     i  i v vii     i        i  v     -  v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_116463484_   1730 AGAGACTTAATTCTAAGACCTCAAACTATGAAACTACTAAAAGAAAACTT 1779
                          ?    i   v v     v  v       i     vi  i        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_116463484_   1780 TGGGGAAATTCTCTAAGACAGAGAATCTCCATCCTAGAATTCTCTAGGAC 1829
                         v  ? --------   --------    i i ----  ----i  v  ii
  L1M4_orf2#LINE/    549 AGGNG--------TAA--------ATCTTCGT----GA----CCTTGGGT 574

  chr2_116463484_   1830 TGGTCAATGATTTCTTGAGTAATACCCCACAAGCACAGACAACCAAAACA 1879
                          i v     i      iii  vv  v   v       ii    -    v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-AAAAGA 623

  chr2_116463484_   1880 AAAAAT-GACAAATGGGATTACATCAAG-TTAAAAAGCTTCTGCACAACA 1927
                               -  i    v   i v      i-       -   i  ii vv  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCA 672

  chr2_116463484_   1928 AAAATAACAATCAACAATGTGAGGATACAACTCACAGAATGGGAGAATAC 1977
                           iivv  v     v  v    ii v     i               v i
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_116463484_   1978 ATTTGCAAACTACCCATCTGACAGAGG-CTAATAACCAGAATATATAAGG 2026
                                  ii ivi      i ii  -  vi  v             i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_116463484_   2027 AATTCAAACAACACTATAGGAAAAAAAATCTAATAATTTGATT----AAT 2072
                           i  vv     v v   iv     i -- v     iiii   ----   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAAT 820

  chr2_116463484_   2073 TAGCAAAAAATCTGAATAAACATTTCTCAAAGGGAGACATA-AAACTGTC 2121
                         vi     ii  i      i         v  i i   i   -   iv i 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_116463484_   2122 ATACAGGTATATGAAAAGGTGTTCAACATCATTGATCAT 2160
                          - i i i i        i  i         ????????
  L1M4_orf2#LINE/    871 A-ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (151 / 87)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.26 (43 / 19)  


1904 27.26 3.20 4.17  chr2_116517845_116519554      501  1219 (491)    L1M4_orf2#LINE/L1      197   908 (0)  

  chr2_116517845_    501 AGAATAAAGCTGGAGGCATCCCATTACTCAACTTCAAAGCATAGTAACTG 550
                             i    i      vv  v  i v i   i      i v  v  - --
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA-C-- 243

  chr2_116517845_    551 AAAGTTAGTATAGTCAGTATAGTTACGGCAGTGACCGAAACAGCATGGTA 600
                             i  ---------------------    i i i i    ii     
  L1M4_orf2#LINE/    244 AAAGCTA---------------------CAGTAATCAAGACAGTGTGGTA 272

  chr2_116517845_    601 CTGGTACGAAAACAGACACATAGACCAATGAAACAGAATAGAGAGCCCAG 650
                             i ii ii i     i     i     i  i     v     i    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_116517845_    651 AAATAAGGCTGCACACCTACAGCTGTATGATTTTTGACAAAACTGACAAA 700
                               iv iii   ii  ii iiivv       i     iiv  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_116517845_    701 AACAAGCGATGAAGAAAGGACTCCCTATTCAATAAATGGTACTAGGATAA 750
                          v  vv i   ii     i ivvi  v     i       i  i   i  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_116517845_    751 CTGGCTAGCCATATACAGAAGATTGAAACTGGGGCCCTTTCCTTCCACCA 800
                             v  ?   i  i  i    v    ii   i-   i v   iv     
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGA-CCCCTACCTCACACCA 471

  chr2_116517845_    801 TATACAAAAATCAACACAAGATGAATTAAAGACTTAAATGTAAAACCTAA 850
                                    i   v   i   i  i ?    i         i v    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_116517845_    851 AAATATAAAAACCCTGGAAGATAACGTAGGCAATACTGTTCTAAACATAG 900
                           v       vi i i     v   i    ?ivv v v   vvi  v v 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_116517845_    901 GAACGAACAAAAATTTCATGACGAAGATACCGAAAGCAATTGCAACAAAA 950
                          iviiii   vii    v iivv v  i   i      vvv         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_116517845_    951 TCAAAAATTGACAAATGGGATGT------AATTAAAGAGTTTCTGCACAG 994
                         vv      v  i    v   iv ------       i v   -  ii vv
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTT 670

  chr2_116517845_    995 CAAAA-ACAACAACAAGGGAGTGGTAATCAGATAACCTACAGAATGGGAG 1043
                             i-   vi v    ii    i-  --   i    i            
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGA-AA--AGACAACCCACAGAATGGGAG 717

  chr2_116517845_   1044 ACAATATTTGTAAACTATGCATCCATCAAAGGTCTAATATCCAGAATCAA 1093
                          v        i   ii  ii   iivi  i  v  vi          vv 
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_116517845_   1094 TAAGAAACT------------TAAGCAAAAC-CAAACAACCCCACTAAAA 1130
                            ii    ------------   vv    v-    i     v i ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_116517845_   1131 AATGGGCAAAGGAAATGAGTAGATGCTTTTCAAAAGAGACATATGTGAA- 1179
                                      vv   i    iii  i  v     - v    iii  -
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA-AGATATACAAAT 866

  chr2_116517845_   1180 -ACCAACGAGTATGTAAGAA-ATGCTCAGCATCTTATTAGAG 1219
                         -i    ii  i ii i i  -       i    v????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (123 / 69)
Gap_init rate = 0.02 (14 / 712), avg. gap size = 3.79 (53 / 14)  


 399 30.77 0.77 0.00  chr2_116523000_116529273.rev      362   491 (5783)    L1M4_orf2#LINE/L1        1   131 (777)  

  chr2_116523000_    362 TAGAAAAGCATTCCATGTTCATGGAAAGGT-GAGTCAATATAGTTAAAAT 410
                          i    iii  i             vv  v-  v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116523000_    411 GGCCAAACTGCCCAAAGCAATTTATAGAGTCAATGTTATTTCCATCAAAC 460
                            v v   v      vii  i  i   v    i iv  ii i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116523000_    461 TACCAATAATATTCTTTACAGAACTAGAAAA 491
                          v   iiviiv  i   i     v v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

Transitions / transversions = 1.22 (22 / 18)
Gap_init rate = 0.01 (1 / 131), avg. gap size = 1.00 (1 / 1)  

3285 26.76 0.44 0.44  chr2_116523000_116529273.rev     4875  5782 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116523000_   4875 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4924
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116523000_   4925 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4974
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116523000_   4975 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5022
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_116523000_   5023 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5072
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_116523000_   5073 AACAAAGCTGGAGGAATCACACTACCTGACTTCAAACTATACTACAAGGC 5122
                                i       v       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_116523000_   5123 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5172
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_116523000_   5173 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATAACTACAACT 5220
                                i    i--    i  --        vv  ii i vi  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_116523000_   5221 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5270
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_116523000_   5271 CTATTTAATAAATGGAGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 5320
                           v  i  i      v       v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_116523000_   5321 GAAACTGGATCCCTCCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5370
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_116523000_   5371 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5420
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_116523000_   5421 CTAGGCATTACCATTCAGGACATAGGCATGGCCAAGGACTTCATGTCTAA 5470
                         v    ?i v viv   iv   v v  vv i v   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_116523000_   5471 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5520
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_116523000_   5521 TTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5570
                          i   v v  i ii  i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_116523000_   5571 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5620
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_116523000_   5621 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATGTACAAGAGAA 5670
                         i  i  vi          v  i  v      vv    v vv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_116523000_   5671 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5720
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_116523000_   5721 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5770
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_116523000_   5771 ATCACTGGCCAT 5782
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2794 26.59 1.75 2.41  chr2_116547795_116550153.rev      980  1893 (466)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116547795_    980 TGGAAAAACATTTCATGCTCATGGCTCATGAATAAGAAGAATCAATATTA 1029
                               i i  ii    i      -------  vi     v i      i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGG-------ATTGGAAGACTTAATATTG 43

  chr2_116547795_   1030 TGAAACTGGCATTACTGCTCAAAACAATTTACAGATTCAATGCTATTCCT 1079
                          v  iv     v    v i    vii  i           i  v  i   
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr2_116547795_   1080 ATTAAACTACCATTGACTTTCTTCACAGAATTGGAAAAAAAAAAAAGGCT 1129
                           i   v v   vivi i  i  ii     v v  v  ---------   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA---------GCT 134

  chr2_116547795_   1130 -ATTTTAAAATTCACATGGAACCAAAAAAGAGCTTGTATAGCCAGGACAA 1178
                         -  ii         i      viiv  ii  v iv v       ii    
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_116547795_   1179 TTACAGACAAAAAGAACAAAGCTGGAGGCATCATGTTACTTGACTTCAAA 1228
                          iviii v  i          i      vv   iii v iii i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_116547795_   1229 CTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAA 1278
                         viv        i          i   i    ii         i i  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_116547795_   1279 CAGGCACATAGACCA-TGAAACAGAATAGCTAACTCAGAAATAAAACCAC 1327
                         i  i  i     i  -  i  i     v vv iii          v   i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_116547795_   1328 ACCTCAACAACCATCTGATTTTTGACAAACCTGACAAAAACAAGCAATGG 1377
                           v iv iiii  vi       i     ivv  v   i v  vv      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_116547795_   1378 AGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCTT 1427
                         i     i  vvi  v  i  i              v      v  ?  vi
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_116547795_   1428 ATGCAGAAAATAGAAACTGGACCCTTTCCTTACACCTTATACAAAAATTA 1477
                              i  i vv   ii       i v   i     v             
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_116547795_   1478 ACTCAAGATGGATTAAAGATTTAAATGCAAAACCCAAAACTATTAAAATC 1527
                               i      i ?   ii      i  i v i        v   v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_116547795_   1528 CTAGAAGAATATCTAGGCA-ATACCATTCTGGAAATAGGCATGGGCAAAA 1576
                         i        v iv    ?i- v i -   vv  vv v  vv i     vi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chr2_116547795_   1577 GATTTTATGATGAAATCACCAAAAGCAATTGCAACAAAAGCAAAAATTGA 1626
                          v  i vv   ivi -           vvv          v      v  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_116547795_   1627 AAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAGCAGGA-ACT 1675
                         v    v   ii v  i   v v  i i   i  ii vv  i-    -   
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACT 681

  chr2_116547795_   1676 ATCATCAGAGCGAACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAAT 1725
                             vv i  i   v  i     i                vv       v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_116547795_   1726 CTATCCATCTGACAAAGGTCTAATATCTGGAATCTACAAAGAACT--TA- 1772
                         ii  vi      i  i  v  vi    ii    v  i        --  -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_116547795_   1773 AATTTA-TAAGAGACAAAAACAAACAACTCCATTGAAAAGTAGGCAAAGG 1821
                           i i -   v i --  i     i   i v   ?    i i        
  L1M4_orf2#LINE/    782 AACTCAATAATAAA--AAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_116547795_   1822 ACATGAACAGACACTTCCCAAAAGAAGACATACA--TG--CAATATACCA 1867
                          iv    i     i   i v        i     --  --     - v  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA-AGCA 878

  chr2_116547795_   1868 CAT----AGACATACAACAGTGTAACTAAC 1893
                            ----   iiiv     vii????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  


 896 30.48 3.17 0.63  chr2_116562788_116566465.rev     1604  1918 (1760)    L1M4_orf2#LINE/L1        1   323 (585)  

  chr2_116562788_   1604 TAGAAAAACATCCCATGTTCATGGATCAGCATAGTTAATATTATTGAAAG 1653
                          i    i i                 ii v v v        i  i i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr2_116562788_   1654 TGACTATACTACCCAA-----TCTATAGATTCAATGGAATTCCTGTCAAG 1698
                           i v     v     -----    i        i v   i   i    i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_116562788_   1699 CTATTTACATCCTTTTTCACAGAAATAGAAAAAA-AATTCTGAAAGCTAA 1747
                         v viivi vv       ii       v  v  iv-i  i  i   -i v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCA 148

  chr2_116562788_   1748 TATGGAACCAAAATTGAGCCCAAATACCCAAAGCAATACTGA----GCAA 1793
                                viiv  vv  v  vi    v     i    vi   ---- v i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_116562788_   1794 AACAAAGTAAGAACAATTATACTACCTGACTTCAAAGTATATTACAAGGC 1843
                                 vi  iv v i i   v  ii i      iiv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_116562788_   1844 TATAGTAAAGAAAATAGCATGGCATTGTTATGAAAACAGATATATAGGCT 1893
                           i     vv  i i  ii   i i  vi  i ii i   i      iii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_116562788_   1894 AAAGGAACAGAATAAAGAACTCAGA 1918
                           v    i     vi   iii    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGA 323

Transitions / transversions = 1.82 (62 / 34)
Gap_init rate = 0.02 (5 / 323), avg. gap size = 2.40 (12 / 5)  

1269 28.01 1.31 0.52  chr2_116562788_116566465.rev     2265  2646 (1032)    L1M4_orf2#LINE/L1      331   715 (193)  

  chr2_116562788_   2265 CCACATATTTAAAGCCAATTGATTTTTGACAAGG-CACCTAGAATATACA 2313
                            i i     vi i           i       -ii  v   vi  v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_116562788_   2314 TTGGAGAAAGGATACACCCTTCAATAAATAATGCTGGGAAAACTGGATTT 2363
                         v   i     i   vv ii     i    ii        v        v?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_116562788_   2364 CCTTATGCAAAAGAATGAAACTCAACCCCCATCTCTTTTCATAAACAAAA 2413
                           vi               ii vi     i i   vivi    v      
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_116562788_   2414 ATCAATTCAAGATGGATTAAAGACGTCA-CATATGACCCAAAACTATAAA 2462
                           i  i    i      i ?    v v -ii  v  v i           
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_116562788_   2463 GGTGCTGGGAGAAAACATAGGAG--AATCATTTCAGCACATTGGTCTAGG 2510
                         iv vi i i            ? --    --   ivv  v    vi    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGG 578

  chr2_116562788_   2511 CAA-AATTTTATGGTTAAGACTTAAAAAGCACAGGAAAGAAAAACAAAAA 2559
                            -ii   iv i v  v   viv         i v  v    iv     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_116562788_   2560 TAGACAAATGGGACTATGTTAAACTTAAAGGCTTCTGCACAGCAAAGAAA 2609
                             i    v     vii i   v     ii   i  ii vv     i v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_116562788_   2610 ATAATCAACAGAGTTAAGAGAAAACCTGTAGGCCGGG 2646
                          iv     v i   v  i   v    iii  ivi   
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

Transitions / transversions = 1.42 (61 / 43)
Gap_init rate = 0.01 (5 / 385), avg. gap size = 1.40 (7 / 5)  

 621 19.35 0.81 10.48  chr2_116562788_116566465.rev     2939  3186 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_116562788_   2939 AAAAAAAAAAAGAGAAAACCTGTAGAATGAATGGGGGAAAATATTTGCAA 2988
                           i   ivi  i   v    iii      ----  i              
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATG----GGAGAAAATATTTGCAA 730

  chr2_116562788_   2989 ACTATTCATCAGACAAGGGACTAATATGCAGAATATACAAGGAACTCATT 3038
                          ii  vi   v  i        vi   v         i  i      -  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC-TT 779

  chr2_116562788_   3039 TCAATACTAAAAAAAAAAACAAAAACAAAAAAAGGAAACCCAAAAGAATT 3088
                         v   --  v  v  v    --- i     v  ------     -------
  L1M4_orf2#LINE/    780 ACAA--CTCAATAATAAAA---AGACAAATAA------CCCAA------- 811

  chr2_116562788_   3089 GCATTAAAATGTGGGCAAACGACATAAACA--CATTTCTCGAAAAAAGAC 3136
                         ---  ?   vi        v  iv i  i --        v   i    i
  L1M4_orf2#LINE/    812 ---TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_116562788_   3137 TTACAAATGGCCAACAGGTATATAAACCAATGTTCAACATCACTCAGGAT 3186
                         v             i i i i  i  vvi   i         ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (29 / 18)
Gap_init rate = 0.03 (7 / 224), avg. gap size = 4.00 (28 / 7)  


2975 26.59 1.78 0.78  chr2_116575746_116577943.rev      808  1706 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116575746_    808 TGGAAAAACATTCCATGCTCGTGGATAAGAAGAATCAATATCGTGAAAAT 857
                               i i  i     i  i     vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116575746_    858 GGCCAAACTGCCCCAAGTAATTTAGATATTCAATGCTATCCCCATCAAGC 907
                            v v   v   v  v i  i  v v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116575746_    908 TACCA-TTGACTTTCTT-CATATAATTAGAAAAAACT-ACTCTAAATTTC 954
                          v   -i  v    i  -  v -    i-- v  i  - ii     v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_116575746_    955 ATATGGAA-TGAAAAAAGAGCCCATA-TAGCCAAGATAATCCTAAGCAAA 1002
                                 -  v  i-- ii    v -       i i    i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_116575746_   1003 AAGAACAAAGCTGGAGGCATGACGCTACCTGACTTCAAATTATACGACAA 1052
                                   i      vv v  i  v  ii i      viv   v    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_116575746_   1053 TGCTACAGTAACCAAAACAGCATGATACCGGTACCAAAACAGATATATAG 1102
                         v          i   i    ii  i   i  i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_116575746_   1103 ATCAATGGAACAGAACAGAGGCCTCAGAAACAATGTCACGCATCTACAAC 1152
                                   i    iv   ivii      i  vvi  ii   i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_116575746_   1153 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGACTC 1202
                           vi    i  i     ivv  v   i v  vv            i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_116575746_   1203 CCGATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 1252
                         i vv  i  i        i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_116575746_   1253 CGAAACTGGACCCCTTCCTTATACCTTACACAAAAATTAATTCAAGATGG 1302
                         i   ii         v   i i   v  i           i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_116575746_   1303 ATTAAAGACTTAAACATAAGACCTAAAATCATAAAAATTCTAGAAGAAAA 1352
                           i ?    i    ii     v      ii      v ii          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_116575746_   1353 CCTAGGCA-ATACCATTCAGGATATAGGCATGGGCAAAGATTTCATGACT 1401
                          v    ?i- v i -   iv  iv v  vv i     v i    v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_116575746_   1402 AAAACACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGACCT 1451
                          vi    i       vvi          vv     v  i    v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_116575746_   1452 -----AAACTAAAGATCTTCTGCACAGCAAAATAAGCTATCATCAGAGTG 1496
                         -----   i    i -   i  ii vv    iv vi      vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_116575746_   1497 AATAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCAATCTCA 1546
                           v  i     i                 v       vii  vv    v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_116575746_   1547 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 1596
                         i  i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_116575746_   1597 AAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGAAAA 1642
                             i    ----   v  i?    i    ii      v    i   v v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_116575746_   1643 TTTTC-AAATAATACATTTATGTGGCCAAAAAACATATGAAAAAAAGCTC 1691
                           i  -   v  v i  vi vi       v  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_116575746_   1692 ATCATCACTGGTCAT 1706
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


1571 25.81 9.16 9.05  chr2_116671454_116675134.rev     2287  3181 (500)    L1M4_orf2#LINE/L1        1   896 (12)  

  chr2_116671454_   2287 TGGAGAACTATTCCATGTTAATGGATAGGAAAAATCAACACTGTCAAGTT 2336
                             i iv   i       v      v    i v i  i i   i   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116671454_   2337 GCCAGTTCTTCCCAATTTGACCTATAGATTCAATGCAATCCCAGGCAAAA 2386
                          v  i v  i     v    i   i        i        viv     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116671454_   2387 TCACAGAAAGTTATTTTGTCAGTA-TTGACAAAC--ATC---------GT 2424
                           v   vvivi v     -   v -       i --   ---------i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_116671454_   2425 ATAGAAGGGAAGAAGACCCACAATTGCCAACAAAACA--CT-------AA 2465
                           i   iv v iii      v   v     ---    --  -------i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAA---AACAATCTTGAAAAAGA 196

  chr2_116671454_   2466 AGAACAAAATTGGAGTACTGATACTACCTGGTTTTAAACCTTCCTATAAA 2515
                                 i      v   v i   v  iii   i   v   v   i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_116671454_   2516 GCTATAATAATAAAGACAGGGTGTTATCGATGAAAGATTAGACAAATAGA 2565
                             i i    v       v   v  ii iiiv   iv      v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_116671454_   2566 TCAATGGGGCAGAATAAAGAGCCCCAAAACAGATCTACATAAATAAAGTC 2615
                                iii     vi    i  vi   i i i i i i vv  vi   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_116671454_   2616 AACTGATCTTTTCGA--AGGA-GAAAAGGCAATACAATAGAAAAATGATA 2662
                           i    --      --   i- vv   i v  v    i ii   vi   
  L1M4_orf2#LINE/    347 AATTGAT--TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_116671454_   2663 ATCTACTCAAAATACGGTGTGAGGAAAACTAGACATC-ACATGTAAATGT 2711
                         i   vi    v v i    ivi   v    i  i ? -     i   v v
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_116671454_   2712 GTGTGTGTGTGTGTGTATACACACACATTTGCATGTGATGTCTAGTATAC 2761
                         i  --------------------- - v   -----  ivi   ------
  L1M4_orf2#LINE/    445 ATG---------------------A-AGTTG-----GACCCCTA------ 461

  chr2_116671454_   2762 AACACATAACACAAATTTTATGTACATATATTTATAGACCTTATACCCTT 2811
                         ---- v v    ------------      --------------------
  L1M4_orf2#LINE/    462 ----CCTCACAC------------CATATA-------------------- 475

  chr2_116671454_   2812 CCAAAATTTAACTCAGA-TAAATTATAGATATAAGTGTAAAATGC-AAAA 2859
                         -     v        i - ii  i ?   iv   i     i -  -    
  L1M4_orf2#LINE/    476 -CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAA 523

  chr2_116671454_   2860 TGATATAACTCCTGGAAGCTAATATAGGAGGAAATGTAGATGATACTGGG 2909
                         iv   v     i i    vv  i     ? v    v vvi   ivi    
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_116671454_   2910 TACAGTGCTGACTTTGTATATACAACATCAAAGGTACAATCAATGAAAGA 2959
                          vvi iiv  ii  iv  v   ii   i    i i    v   ii     
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_116671454_   2960 AATAATTAATAAACTGAACTTCATTAGAATAAAAAACTGCTGTTGCTCGA 3009
                           v   vi     i  i       i i   v       vi   -   iv 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT-GCTTCA 672

  chr2_116671454_   3010 TGAAAGATAACGTCAGGAATACAGGAAGGAAAGCCACGAACTGTGAGGAA 3059
                         --  i  i vii   i   viiiii   iv  v    ii v  v   -  
  L1M4_orf2#LINE/    673 --AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG-AA 719

  chr2_116671454_   3060 AATATTTGCCAA-CACG----------------------CAAAATA---- 3082
                                  v  -  ii----------------------  i    ----
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_116671454_   3083 -AGAACTCTTA------------------------AACCTGATTAAAAAT 3107
                         -          ------------------------    ii   ?    v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_116671454_   3108 TGAGCCAAAGACT--AACAGAC-TCGTTACCAAGGAGATATGCAGAAGAA 3154
                           i  v  i  i --  i    - ivi v v   i      i  i v iv
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_116671454_   3155 AAACACGCATAAGAAAAGAGGCTCAGC 3181
                         v  i v   i v       v     i 
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAAC 896

Transitions / transversions = 1.47 (135 / 92)
Gap_init rate = 0.03 (29 / 896), avg. gap size = 5.62 (163 / 29)  


3460 19.69 4.50 2.59  chr2_116693813_116697704     2512  3400 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_116693813_   2512 GAAAAATACATTCTGTGTTCATAAATTGAAATAGTTAATATTATTAAAAT 2561
                             i   -- i ii       ii    i  v v        i    i  
  L1M4_orf2#LINE/      3 GAAAGATA--TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116693813_   2562 AGCTAGACTTCCCAG--TGATCTACCAATTTA-TGCAGGCCCTATGAAAA 2608
                         i  v v   i    i--        vi   i -i   iv      v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116693813_   2609 TCACAATGGCCTTTTTCCTCCCAAAAGGGG-AAGTTAATGTTCACATTCA 2657
                           v  iiv        -- v vi   vv i-   i i  vi v v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT--TGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_116693813_   2658 TATGAAGTCGCAAAGTCTCCCAAATAGCTAAAAACATGTCTTGAAAAA-- 2705
                             i ivi    i vvi  vi      i    -  -i          --
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CA-ATCTTGAAAAAGA 196

  chr2_116693813_   2706 AGAACAAATTTGAAGAACTTACATTATTTT--TTTCAAAACTTACCAAAA 2753
                                 v   i  i   i   i - iii--             i v  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACT-TCCCAATTTCAAAACTTACTACAA 245

  chr2_116693813_   2754 AGCTACTGTAATCAAAAGATTGTGGTACTGGCATAAAGATGGACATAAA- 2802
                               v        i v v                i   i      v -
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_116693813_   2803 --CA-TGGAATCAAATTGAGTGTCCAGAAAAAAAAAATCATA--TTTATG 2847
                         --  -      vi       v         v   v--i    --      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC--CCATACATTTATG 343

  chr2_116693813_   2848 GTCATTTAATATTTGGCAAAGTTGCCAAGACTATTCACGGAGAGACAGAA 2897
                             v  i  v  i i   i v         i     vv i -  v    
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAA 392

  chr2_116693813_   2898 TGGTCTTCTCAGAAAATGGTATTGTGACAACTGGGTATCCAACATGTAAA 2947
                          i     i   iv       ii  v         i  ?   -    i   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA-CATGCAAA 441

  chr2_116693813_   2948 ATAATGATGTCGGAC---TACATCACACCATATGTAAAAGTTA-CGCAAC 2993
                          v     v  i    ---   v           ii    i   - v   v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_116693813_   2994 ATGGATTAATCACCTAGATATAATATCTCAAAGTAAAACTATTAAAGTCT 3043
                               i ?vv     i  i   v v  ------        v   v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCT------AAAACTATAAAACTCT 535

  chr2_116693813_   3044 TAGA-TAAAACACAGGAGTCA--CTTCATGACCTTGGATTTGGCAATGAT 3090
                             -v      i   ?  v --    i         i  v       i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_116693813_   3091 T-CTTATATGTGAAACCAAAAGCCTGGGCAACAAAAGGAAAA-----TAA 3134
                          -    v  i   v         viii          i    -----   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_116693813_   3135 ATTATACTTCCTCCAAATT-----TTTTTTAATGTGCATCAAAGAACATT 3179
                            iv     v  v     -----i    ----    v      i   i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTT----GTGCTTCAAAGGACACT 681

  chr2_116693813_   3180 ATCACGAAAGTAAAAAGATAACTTACAAAATAG----AAATATTTTCAAA 3225
                             v      i      i   ii   i   i ----        v    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_116693813_   3226 TCTTACATCTGATAAGGGTCTAATATCTAGGACATATAAAGAACTCCTAT 3275
                           v  i            v  vi    i  i i             i  i
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_116693813_   3276 AACTAAATAATACAAAGACAAAAAATTCTATT-AAAAGTGGGAAAAGGGA 3324
                             v       v         v  ii v   -    i    v     iv
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_116693813_   3325 TTGAACAGCTATGTCTCCAAAGAAGATATATAAATGG---ACAAGCACAT 3371
                              i  vi  v                 i      --- i        
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_116693813_   3372 AAGCAAAGATACTCAACATCATTAGTTAT 3400
                         i --      i          ????????
  L1M4_orf2#LINE/    882 GA--AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (100 / 72)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 2.17 (63 / 29)  


 436 21.43 6.25 1.79  chr2_116699753_116701975.rev      542   653 (1570)    L1M4_orf2#LINE/L1        1   117 (791)  

  chr2_116699753_    542 TAGAAAGCCATTCTGTGTTTATAGATTAGAAGACTTTATATTGTTAAAAT 591
                          i     vi  i ii    i  i    i        v          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116699753_    592 GTCTGTACTACCTA-GTT-ATCTACAGAT-----GCAATTGCTATCAAAA 634
                          v vi    v  i -i  -          -----     iv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116699753_    635 TCTCAATGGCAATTTTTTT 653
                           i  iiv  --i      
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CTTTTTT 117

Transitions / transversions = 2.43 (17 / 7)
Gap_init rate = 0.03 (4 / 117), avg. gap size = 2.25 (9 / 4)  

2744 23.26 2.86 2.74  chr2_116699753_116701975.rev      928  1731 (492)    L1M4_orf2#LINE/L1      104   908 (0)  

  chr2_116699753_    928 CAGCTGGCAATTTTTTTTAAGAAATAGA-AAGTAGCACC-AACACTTACA 975
                               v ---      vv      v  -   iv vv  -  v i i i 
  L1M4_orf2#LINE/    104 CAGCTGCC---TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_116699753_    976 -GGAAATTTCAATTTTAAGAGATCCCACATAGCCAAAATAGTACTAAAAA 1024
                         -      vi-------   i  i  viv          i i vi i    
  L1M4_orf2#LINE/    151 TGGAAATGC-------AAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_116699753_   1025 ATACGGAC----TT------CTTACATTTCCTAATTTCAAAACATACTAT 1064
                          v v i  ----  ------  i   i    i           v     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_116699753_   1065 AA-GCAATGGATCTCAAGATAGTGTGTCACTGGCATATAGACCAATATAG 1113
                           -  v ii vvv      i      vi         vi  ivi i   v
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_116699753_   1114 AGGTCAATGGAACAAAACAGAGCACCTAGAAATAAACCCTTACATATATA 1163
                           i         i i  iv   vii i            v     v   i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_116699753_   1164 GCCAAAGGATCTTTGACAAGGG-ACCAAGACTACATAATGGGGAACTGTC 1212
                          i   vv   i  i        -i       i ivi         vvivi
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_116699753_   1213 AGTATTTCTGTGAAAAAAATGGTTTTGAGAAAATTGGATCTCCATATGAA 1262
                            v   ii----  v       vi  i  v  i     v?   i   v 
  L1M4_orf2#LINE/    394 AGTCTTTTC----AACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_116699753_   1263 AAAGAATAAATTTAGACCCTTACCTAACACCATATACAAAAATTAACTGA 1312
                                i  v  i     i     v                      v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_116699753_   1313 AAATGAATTAAAAACCTAAACTTAAGACCAAAAACTATCAAACTCCTAGG 1362
                              i  i ? i       iv     v v        v      i   i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_116699753_   1363 AGAAAACATAGGGGAAAA-CATCA-GACTGTTAGATTTGGCAATGATTTC 1410
                                     ? v   - v  i-   i-  i i  v       i    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTC 588

  chr2_116699753_   1411 TTGGGTAGGGTATGAAAAGCACAGGCAGCCAAAACAAAAGTAGACAAATA 1460
                           i i  v ii iv         i   i v   iv    i    i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_116699753_   1461 AGACTACATCAAACTTAAAAA-TTCTAT----CACACGA-AGTAGTAAAT 1504
                         i    v       v       -  i i ----  v v  - v  vi  i-
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG- 687

  chr2_116699753_   1505 AAAGTGAAAAGGCAATCTATGGAATGGGAGAAAATATTTGCAAATCCTGT 1554
                                    i   i i ii                         v i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_116699753_   1555 GTATGATAAAGGATCAATATTAAGAGTATGTGAGTAGCTTCTACAACTCA 1604
                         i v      i   iivi   iv   i   i i iv i  ii         
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_116699753_   1605 ACAGCAGCAACAACAACAAAAATAACCCAATTAAAAAATGATGAAAAGAC 1654
                          i ------ i  v  v v             ?       ivv   i  i
  L1M4_orf2#LINE/    788 ATA------ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_116699753_   1655 TTCAATACACAGTTGCCCAATGAAGATATACATATGACCAACAAGCATAT 1704
                           v    v   v  vi    v           v   i    i     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_116699753_   1705 GAAAAAATGTTCAACATCACTCATCAT 1731
                              i   i         ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (107 / 76)
Gap_init rate = 0.02 (18 / 805), avg. gap size = 2.50 (45 / 18)  


 347 28.83 2.70 0.00  chr2_116704930_116706684      109   219 (1536)    L1M4_orf2#LINE/L1       50   163 (745)  

  chr2_116704930_    109 TGGCCATAGTGCCAAAAACAATTTACAGATTTAATGCTATTCCTATCAAA 158
                             v   v v  v   vii  i        i  i  v  i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_116704930_    159 TGACCAATGGCATTTTTCATAGAATTAGAAAAAAAGATTCTGAAATTCAT 208
                         vvv   iiv  v     iii    v v  v  ivv   i  i        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_116704930_    209 ATAG---TGCTAGG 219
                           i ---   v   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG 163

Transitions / transversions = 0.88 (15 / 17)
Gap_init rate = 0.01 (1 / 114), avg. gap size = 3.00 (3 / 1)  

1900 27.32 2.45 4.38  chr2_116704930_116706684      488  1263 (492)    L1M4_orf2#LINE/L1      148   908 (0)  

  chr2_116704930_    488 ATATAGAAATAAATCACGTGAAACCAAAACAGCCAAAGTAATACTAAGCA 537
                             i     i---  v - i v   i  i       ii   vi i iv 
  L1M4_orf2#LINE/    148 ATATGGAAATG---CAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_116704930_    538 AAGAGGACAAAGCCAGAATCATCAAGCTACTCAACTTCAAACTATACTAC 587
                          ii  i      iii  ivvv   vi  v i   i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_116704930_    588 AAGGCTACCATAACCCAAACAGCATGGTACTGGTACAAAAACAGACACAT 637
                           i     vi   i v i    ii         i i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_116704930_    638 AGACGAATGGAACAGGTTAGGGAACCCAGAAATAAAGCTACACACTTACA 687
                            iv       i  iv v i  ii           v i i   i   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_116704930_    688 ACCCTCTGATATTTGACAAAGTCAACAAAGTCAAGCAATGGGAAAATGAC 737
                         ii vvi    v  i     i viiv   iii  vv       i   vi i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_116704930_    738 --TCCATATTCAATATATGTTGCTGGGATTACTGGCTAGCCAAATATATA 785
                         --  -- v     i v   v        iv     v  ?   ----i  i
  L1M4_orf2#LINE/    394 AGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA----CATG 437

  chr2_116704930_    786 CAGGAAATTCAAACTGGACCCCTTTCTTTCACCATATACAAAAATCAACT 835
                           ii i v v  ii         vi  iv                i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_116704930_    836 TATGATAGGTTAAAGACTTAAATGCAAAACTGAAAACTATGAAAACCCTA 885
                         i vi  i i i ?    i      i  i viv        i   vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_116704930_    886 GAGGAAAACTTAGA---AAATACTATTGTGCACATAGGTCCCTGACAAAG 932
                           i      v   i---    -  - i   vv v i   iv-- i   v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT-CT-TCGTGACCTTGGGTTA--GGCAATG 583

  chr2_116704930_    933 ATTTCAT-GATGAAGACTCCAAAAGCAATTGCAATAAAAACAAAAATTGA 981
                         i    v -   - v   v         vvv    i    iv      v  
  L1M4_orf2#LINE/    584 GTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_116704930_    982 TAAATGGGACCT------AATTAAAGAGCTTCTGCACAGTGATATACATC 1025
                              v    i ------       i -   i  ii vvii viv   ii
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT 681

  chr2_116704930_   1026 ATCAG---AGTAAACAGACAATCTACAGAATGGGAAGAAAAAATTCACAA 1072
                             i---   i  v      i i           -     v   ii   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA-GAAAATATTTGCAA 730

  chr2_116704930_   1073 ACTATACATCAAACAAAAGTCTGATATCCAGAATCTATTAGAAACAA--A 1120
                          ii   i   vi i  ii v  vi          v   v ii   vv-- 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_116704930_   1121 CAAATTAACAAGCAAAAC-CAAACAACCCCATTAAAAAATGGGCAAAAGG 1169
                            v i  i  vv    v-    i     v   ?             i i
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_116704930_   1170 TCATGAACATACACCTCTC-AAAGATGACATACATCTTTTATTACATACA 1218
                          i-    i v   ii    -     v  i     ------------- - 
  L1M4_orf2#LINE/    831 TT-TGAATAGACATTTCTCCAAAGAAGATATACA-------------A-A 865

  chr2_116704930_   1219 TGCAGCCAGCTAGCATGTGAAAAAACATTCCACATCACTCATTAC 1263
                           --    iiv    ii      i iii  v      ????????
  L1M4_orf2#LINE/    866 TG--GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (134 / 75)
Gap_init rate = 0.03 (22 / 761), avg. gap size = 2.41 (53 / 22)  


2872 24.59 6.29 0.47  chr2_116749685_116752850.rev     1817  2674 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116749685_   1817 TAAAAAGATATCCTATGTTTATGGATTAAGATAAATAATATTGTTAAAAT 1866
                          ii          i     i       iii v vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116749685_   1867 GTCCATATTACCTAAAGCAATCTACAGATTCAGTGCAATCCATATCAAAA 1916
                          v v   i v  i   vii             ii       v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116749685_   1917 TCCCAATGGCAGTCTTGGCAGAAATAGGACAAAC--ATCCAAAAATTTAT 1964
                              iiv  vv i  v        -v     i --    v      i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_116749685_   1965 ATGGAATCCTTGGGAACTTTACATAGCAGTAAGAATCTTGAGAAAGAG-- 2012
                               vivivi  i  iiviv     viv  v        i     i--
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_116749685_   2013 -CAAAGCTTCAGGCCCCACACTGCC-AGGTTTAAAACATATTGCAAAGTA 2060
                         -     i vv   v i      v  - iv  i     v  i i     iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_116749685_   2061 ATAGCCATCATAACAGTATGATGCTGGTATAA----AGAC-CATCCATCA 2105
                          i  iv    vi     i  i i    i    ----    -i  vv    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_116749685_   2106 ATGGAATGGGTTAGAGAGCCCAAAACTTAACCTTCACTCATATAGTCAAA 2155
                                i iv v     i   i  v v    ivi  viv   i     v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_116749685_   2156 TGATTTTTGACAAAGGTGCTACAATGATGCAATGAGGAAAGGATAGTCTC 2205
                                i     i     i vi iv  v     i      i       i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_116749685_   2206 TTCAACAAATGGTGTTAAGAAAACTTGATATACACAATGGAAAAGAATGA 2255
                                       i ii  v    v    ?v    -  v          
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGAATGA 448

  chr2_116749685_   2256 AGATGTACCTTTATCTTACTCTGTTTATACAAATTAA----AAATAAATT 2301
                           v  v   ii  i  i  v ii v  i v       ----    ii  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_116749685_   2302 AAAGGCCTAACTGTAAGACCTGGA-CTATAAAACTCCTAAAAGAAAACA- 2349
                          ?  i     v       v  ii -           i  i         -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_116749685_   2350 AAGTGAAAATTAATTATGACATTAGAAT-GGTGAT--TTTTTTGGATATG 2396
                          i ? v    iv- ii    v  i iv -  ii  --   i  i      
  L1M4_orf2#LINE/    549 AGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_116749685_   2397 ATACCAAAAGCATAAACAACAAAAGCAAAAATAGACAAATGTGATTGTAT 2446
                          i          i  i         v         i    vv  i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_116749685_   2447 CAAATTTTAAAACTTCTGCACAGCAA--GATA--AACAAGAGAGTTAAAA 2492
                             v  v       i  ii vv   --  i -- v     i   v    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_116749685_   2493 GGGCAATC-ATGAAACAGAAGAAAATATTTGCAAACCATATATCAGATAA 2541
                          i-   i - iii  ii i                i        v     
  L1M4_orf2#LINE/    698 GA-CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_116749685_   2542 AGAGTTAATATCTATTATATATAAGAAACACCCACAAATCAATAACAAAA 2591
                         i iii vi    i vv        ii   v ii    v       i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_116749685_   2592 A-------AACTCAA-----AAAT----------T---ACTAGACATTTA 2616
                          -------   i   -----    ---------- --- v         v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_116749685_   2617 CTTAAAGAAGATAAACA----GTCAACAGGCACATAAAAAGATGTGCAAA 2662
                         iii          v   ---- i   i i      i        iv   v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_116749685_   2663 ATCACTAATCAT 2674
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (128 / 80)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.64 (58 / 22)  


2162 30.17 1.74 2.83  chr2_116762921_116764969      640  1557 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116762921_    640 TGGAAAAATTTTCCACGTTCATCAATTGGAAAAACTAATATCTTGAAAAT 689
                               i  v i   i      vi       i vi      iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116762921_    690 TGCCACACTGCCCAAAGCAATCTACAAATTCAGCACTGTTTCTATCAAAC 739
                         v  v i   v      vii       i     i i vi ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116762921_    740 TATCAATTTTATTTTTTAATAGAA-TTACAAAAAAAATTCTAAAATTAAT 788
                          vi  ii viv      i-i    -  ivv  ivvi  i        v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_116762921_    789 ATGGGACTATAAAAAGCCCA-AATGACAAGAGGAATCCTAAGCAAAGAGA 837
                             i v ii  iiii    -   ii v i iv    i i iv  ii   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_116762921_    838 AGAAAGCCAGAGGCATCACATTACCCAACTTCAAACTACACTGTAAGTCT 887
                          v    iii    vv     i v     i      vivi   ii  iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_116762921_    888 ATGGTAACCGAAACAGTATAGTACTGGTATATAAACAGACACATAAACTA 937
                          ii    i i i     i i       i   vii i     i   i ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_116762921_    938 ACAGAACAGAATAAAGAACCCAGAAAAAAAGGTGCACATCTACAGCCATC 987
                          ii   i     vi   ii       v   vviii    i  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_116762921_    988 TGAGTTTTAGCCTTTGAGCTAAACTCAACAACAACAAAAAAAG-CAATGG 1036
                            -    ------i  --------   viiiiv   i vv v-      
  L1M4_orf2#LINE/    350 TGA-TTTT------CGA--------CAAGGGTGCCAAGACCATTCAATGG 384

  chr2_116762921_   1037 AGAAAAGACTGCCTATCCAATACGTTGCTCTGGGATGGCAGGCTAGATAT 1086
                         i    ii iv i  v i   i vi v iv      iii v  v  ?vi i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_116762921_   1087 ATGCAAAAGTATGACACTGGATGTCTACCTTTCACCATATACAAAAATTA 1136
                                  v    vii    ivi      iv                  
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_116762921_   1137 AATAAAGATGGATTAAAGATTTAAATGTAAGACCTCAATCTATAAGAATC 1186
                          v v  i      i ?   ii           v  v  v      i v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_116762921_   1187 CTAGAAGAAAATGTAGGAG-ACACCACTGTGGACATAAGTCTTGAAAAAG 1235
                         i          ii    ? - v i vii   iv v ii  - v iv  v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATG 583

  chr2_116762921_   1236 AATTAATAACTAAGTCTTCAAAA--ACTATTGCAACAAAAACAAAAATTG 1283
                         iv  vv  iv  v v vi     --  v --         iv      v 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAG 631

  chr2_116762921_   1284 ACAAGGGGGATCTAATTAAACTAAAGAGCTTCTGTGCAGCCAAAAAAAAC 1333
                          i  ivv   ii v  i   v v  i i   i     -vi    ii v  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACAC 680

  chr2_116762921_   1334 TACCAACAGAGTAAACAGGCCTCTTAGAGAATGGGAGAAAACATTTGCAA 1383
                           i   v i   i  v  i vv ii v              i        
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_116762921_   1384 ACTAAGAATCCAACAAAGGTCT-ATATCTATAATCTATAAGAAATTC--- 1429
                          ii viv   ii i  i  v  -i    i v   v     ii  i  ---
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_116762921_   1430 -AAATCAACAAGCAAAAATTAAAACGAATATCCCCAAT--AAAAATAGAC 1476
                         -  v    i  -i     ----i  i    -v      --      i i 
  L1M4_orf2#LINE/    781 CAACTCAATAA-TAAAAA----GACAAATA-ACCCAATTWAAAAATGGGC 824

  chr2_116762921_   1477 AAAAGGCAT-AACAGATACTTCTCAAAAGAAGACACACAAGTGGCTGACA 1525
                            i iiv -  i   i i     v        i i    i    ii i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_116762921_   1526 A--ACATGAAAATATCCTCTACATCACAAATCAT 1557
                          --         v  v   v      ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (174 / 100)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.10 (42 / 20)  


2251 25.92 9.34 0.74  chr2_116771650_116776139     3185  3998 (492)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr2_116771650_   3185 ATTGGAAAAATTAATAATGTTAAAATGAAAATATTATTCAAAGCAATTTA 3234
                                i v      v      i   iv    i vii    vii  i  
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr2_116771650_   3235 CATATTCAATGACATCTCTATCAAAATACCAA-TGACATTCTTCCGGGAA 3283
                           v      i vv   i          v   i-  v v  i  v i i  
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr2_116771650_   3284 ATAGGAAAAAAAAATGCCTAACACTTACGTGGATCCACAAAAGACTTCGA 3333
                         v --  v  ivvi  -     v i i ii    vvii   ii   iiv  
  L1M4_orf2#LINE/    125 TT--GACAAGCTGAT-CCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_116771650_   3334 ATAGCCAAAGCAATCCTGAACATAAGGGACAAAAGCAGAAGTGTTACAAT 3383
                                  i     i    v vi i i     ivii  i vv i   v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_116771650_   3384 ACCTGATTTCAAAATATCTCACAAGGCTATAGTAA-CAAAATCAGCATGC 3432
                         v  ii         iv vii    i    i     -   i -   ii  v
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGG 270

  chr2_116771650_   3433 TACTGGGGTAAAAACAGAAACATAGAGCACTGGAACGTAATAGAGAACCC 3482
                               vi   ii i   v i     v  v     iiv   v    ii  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_116771650_   3483 AGATATAAATCCACACAGTTACAGCCAATTCAGTTTTGACAAAGGCACCA 3532
                            v     i   i   v   ii i     v v   i     i  ii   
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_116771650_   3533 AGAACATACAATGGGGAAC-AACAGCCTTTTAAATAAATACTGGTAGGGA 3581
                            v   v          v-  i  i     v  i    iv  v i  iv
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_116771650_   3582 AACTTGATAACCATATGCAGAAGAATGAAACTATATCCCT-CTTCTCACC 3630
                             v    ?   i     i         ii iv i    - i  v    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_116771650_   3631 ATATACAAAAATAAAATCAAAACAGATTAAACATTTAAATCTAAGGCCTG 3680
                                     v  v      ii   i ? v ii     v    iv  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_116771650_   3681 AAATTATGAAATTAATACAAGAAAGC-------TAAA------------- 3710
                            i   i   i vv  v      i -------    -------------
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_116771650_   3711 ------GGCAA--------------------CAAAAG------------- 3721
                         ------     --------------------      -------------
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_116771650_   3722 -AAAAAAATAGACAAATGAGATTACATCAAAAGAAAAAGTTTCTGCACAG 3770
                         -i          i    vi  i v        vv    ii  i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_116771650_   3771 CTAA--ATA-TAT----AAAGTAAAGAGACAACCTACAGAATAAAATAAC 3813
                          v  -- i -   ----     i  i        i       iii v  v
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_116771650_   3814 CTATTTGCAAACTCTCCATC----AAGGGATTAATAACCAGAATATAAAA 3859
                         v          iiv vi   ----      i vi  v          v  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_116771650_   3860 GGAGCTCAAACAACTCAATAGCAAAAAACACCAAATAATTTTATTTAAAC 3909
                         i  i   vv           ii     i-  -      iiiv   ?   v
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAG-AC-AAATAACCCAATTWAAAA 818

  chr2_116771650_   3910 ATGAGCTAAAG-TCTAAAAAGACATTTCTCAAAATAAGACATACAAATGG 3958
                            i  v  i - i i  v           v   v    i          
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_116771650_   3959 CCAATAGGTATATGAAAAAATGCTCAACATCATTAATCAT 3998
                               i i i       i             ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (127 / 81)
Gap_init rate = 0.02 (18 / 884), avg. gap size = 4.56 (82 / 18)  


2990 25.57 3.62 0.90  chr2_116805852_116811671.rev     4445  5328 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116805852_   4445 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAA 4494
                              ii i  i     i        v      v i     i  v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr2_116805852_   4495 TAGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAG 4544
                          i  v     v     iv i  i  i        i  v     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_116805852_   4545 CTACCAATGACTTTCTTCACAGTATTGGAAAAA---A--CTAAAGTTCAT 4589
                         v v   iivi i  i  ii   v v v  v  i--- --     i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_116805852_   4590 ATTGAACCAAAAAAGAGCCTGCATTGCCAAGAAAATCCTAAGCAAAAAGA 4639
                           v   viiv  ii  v  v v  v     i v    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_116805852_   4640 ACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTACAAGGCT 4689
                               i     ivv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_116805852_   4690 ACAGTAACCAAAACAGCATGGTACTCATGGCA-AA--ACAGAGACATAGA 4736
                                i   i    ii       ---    -  -- i   v i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACT---GGCATAAGGATAGACATATAGA 296

  chr2_116805852_   4737 CCAATGGAACAGAACAGAGGCCTCAGAAAAAATACCAGACATCTACAACC 4786
                         i        i    iv   ivii      v  vv   v    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_116805852_   4787 ATCTGATCTTTGACAAACCTGACCAAGA------AATGGGGAAAGGATAC 4830
                          vi    i  i     ivv  -      ------           i   v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_116805852_   4831 CCTGTTTAATAAATGTTGCTGGGGAAACTGGCTAGCCATATGCAGAAAGC 4880
                         i  v  i  i     v       iv      v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_116805852_   4881 TGAAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATAG 4930
                             ii    i    v   i     v i            i    i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_116805852_   4931 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAACCCT-AGAAGAAAA 4979
                           i ?    i       v   v       i       i  -         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_116805852_   4980 CCTAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGAC 5027
                          v    ?i- v i -   i- i  v i  i- i     v ii   v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGA 593

  chr2_116805852_   5028 TAAAACACCAAAAGCAATGGCAAAAAAAGCCAAATGAGAT--------CT 5069
                           vi            vvi    v     vv   vv    --------  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_116805852_   5070 -------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5112
                         -------       i -   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_116805852_   5113 GAACAGGCAACCTACATAATGGGAGAGAATCTTTGCAATCTACCCATCTG 5162
                            v  i     i   v         i   v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_116805852_   5163 ACAAAGGGCTAGTATCCAGAATCTACAAAGCACTCAAACAAATTTACAAG 5212
                          i  i  i  v           v  i    v    vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_116805852_   5213 AAAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 5262
                              iv    i     v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_116805852_   5263 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATTAAAAAATGCT 5312
                         i     v        i  vi viii     i ii     v    i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_116805852_   5313 TATCATCAGTAGCCAT 5328
                         i v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (134 / 88)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.50 (40 / 16)  


 703 29.72 2.81 0.40  chr2_116831981_116837549        1   249 (5320)    L1M4_orf2#LINE/L1      370   624 (284)  

  chr2_116831981_      1 AAGACCAT-----GGAACAAAGGTAGTACTTTCAACAAATAATACTGGAA 45
                                 -----  iiv  iii    vi           ii i    i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_116831981_     46 CAACTGTATATACACATACCAGAAAATAAATCTAGACAGAGACTATAAGC 95
                               v   ?v     i v i i   i  vi i   vvvv  ivi vi 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_116831981_     96 TGTGCATAAAAAGTAACTCAAAATG-ATCACAGGCCTAAATGTAAAATGC 144
                         ii ii i     v            -    ?  i           i -  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GC 518

  chr2_116831981_    145 -AAAACCATAAAACTACTAGAAGATAACACAAGAGAAAATGTAGGTAATC 193
                         -     i        vi       v    i i ? v    v vv  i i 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_116831981_    194 TTGTGTTTGATGATTACATTTTAAACATGAAATCAAAGGCACAATCCCTG 243
                            v   v iii  viiv i   i i    v i    i      v vvii
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_116831981_    244 AAAGAA 249
                               
  L1M4_orf2#LINE/    619 AAAGAA 624

Transitions / transversions = 1.63 (44 / 27)
Gap_init rate = 0.02 (4 / 255), avg. gap size = 2.00 (8 / 4)  

2823 25.99 3.95 1.47  chr2_116831981_116837549     4193  5077 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_116831981_   4193 GGAAAAACATTCCATGCCCATGGATAGGAAGAACCAATATCGTCAAAATG 4242
                              i i  i     ii       v      vii     i  i  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_116831981_   4243 GCCATACTGCCCAAAGTAATTTATAGACTTAATGCTATCCCCATCAAGCT 4292
                           v     v      v i  i  i   i i  i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_116831981_   4293 ACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTGTAAATTTCAAA 4341
                         v   vivi i  i  ii     v v  v  i-  - iiv    v    v 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr2_116831981_   4342 TGGAACCAAAAAAGAGACC--ATATAGCCAAGACAATCCTAAGCAAAAAA 4389
                              -- viv   i    --iv        i      i i ------- 
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-------A 191

  chr2_116831981_   4390 AAAAAAAAACAAAGCTGGAGGCATCCCGCTACCTGACTTCAAACTATACT 4439
                            i  i       i      vv  v i  v  ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_116831981_   4440 ACAAGTCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACACATAT 4489
                             iv         i   i    ii         i iv ii i v i  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_116831981_   4490 GTAGACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTA 4539
                         i    i        i    iv   ivii         vv   i    i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_116831981_   4540 CAACCATCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAGG 4589
                         iiii  vi    i  i     ivv  v   i vi vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_116831981_   4590 ATCCCCTATTTAATAAATGGTGTTAGGAAAACTAGCTAGCCACATGCAGA 4639
                           vvi  v  i  i        i i   v    i v  ?         i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_116831981_   4640 AAACTGAAACTGGACCCCTCCCTTAAACCTTAAGCAAAAATTAACTCAAG 4689
                          i v    ii         v   i v   v  vi               i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_116831981_   4690 ATGGATTAAAGACTTAAGTGTAAGACCTAAAACCATAAAAACCCTAGAAG 4739
                               i ?    i   i       v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_116831981_   4740 AAAACCTAGGCAGTA--CCATTCAGGACA--GAGGCATGGCAAAGACTTC 4785
                              v    ?-   --i -   iv   v-- i vi -     v ii   
  L1M4_orf2#LINE/    542 AAAACATAGGN-GTAAATC-TTCGTGACCTTGGGTTA-GGCAATGGTTTC 588

  chr2_116831981_   4786 ATGACTAAAACACCAAAAGCGATGGCAACAAAAGCCAAATTTGACAAATG 4835
                         v iiv  vi           ivvi          vv   v v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_116831981_   4836 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCA 4885
                            ii v  i   v v  i i   i  ii vv    i  v    i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_116831981_   4886 GAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTATCCA 4935
                         i      v  i     i                 v      ivii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_116831981_   4936 TCTGACAAAGGGCTAATATCAAGAATCTACAA-GAACTTAAACAAATTTA 4984
                              i  i  i  vi    v     v  i  -     ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_116831981_   4985 CAAGAAAAA---------CCCATTCAAAAAGTGGGCAAAGGATATAAACA 5025
                         i  v     ---------    v i?    i            v i  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_116831981_   5026 GACACTTCTCAAAAGAAGACAT-----T------------TATGAAAAAA 5058
                             i     v        i  ----- ------------i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_116831981_   5059 -GCTCATCATCACTGGTCAT 5077
                         -     v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 3.20 (48 / 15)  


1490 28.16 1.43 1.43  chr2_116933590_116936047      736  1225 (1233)    L1M4_orf2#LINE/L1        1   490 (418)  

  chr2_116933590_    736 TGTAAAAACATCCCATGATCATGAATCGAAAGAATTGCTATTGTTAAAAT 785
                           v   i i        v     i  i i    v  iv         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116933590_    786 GACACTATTACCCCAAA-CAATCTACTGATATAATGCAATTTCTATTAAC 834
                          i  v  i -       -ii      v   vi  i     ii    i  v
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_116933590_    835 ATACTAATGACATTCCTCACATAATTGGAAAAAC-AATTTTAAAATTTGT 883
                           v i iivi v  ii ii  v  v v  v  i -i  ii       ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_116933590_    884 ATGGAATCACAAAGGACCTCAAACAACCCAAAGCAATTTTGAACAAACAC 933
                               vii   i     ivi  i i  -   i    i     v  iv v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCC-AAAACAATCTTGAAAAAGAAG 198

  chr2_116933590_    934 AACTAAGCTGGTCACATCACACTACCAGACTTCAAAATATACCACAAAAC 983
                            v   i   vvivv       v  vi i       iv   i     i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_116933590_    984 TGTAGTAACCA-GACTAGCACTGTACTCACATAAAAACAGAAACAAAGAC 1032
                          ii     i  -   -  iiiv     vi     ii i   v i v   i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGAC-AGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_116933590_   1033 CAACAGAACAGAATGGAGAATGCAGAAAT----CCATATATCTACAGCCA 1078
                            ii   i     v    i v       ----     i  i  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_116933590_   1079 ATAGATTTTTGACAAAGGTGTCAAAAAACATACATTAAGGAAAAGAAAAT 1128
                           v      i     i    i   i -v   v  v ii     ii v i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAGT 396

  chr2_116933590_   1129 CTCTTCAATAAATGGTGCTAGAAAAACTGGATATCCATATGCAGAAGTAT 1178
                           i     i          i i v         ?   i     i   v  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_116933590_   1179 GAAACTAGATTTCCCACCTATCACCTGATTTAAAAAAAAAAAATCAA 1225
                            ii i  -ii  i    vv    --  v  v     vv  v    
  L1M4_orf2#LINE/    447 GAAGTTGGA-CCCCTACCTCACACC--ATATACAAAAATTAACTCAA 490

Transitions / transversions = 1.85 (89 / 48)
Gap_init rate = 0.02 (10 / 490), avg. gap size = 1.40 (14 / 10)  

1243 26.51 1.86 0.93  chr2_116933590_116936047     1537  1966 (492)    L1M4_orf2#LINE/L1      475   908 (0)  

  chr2_116933590_   1537 ATAAAAATCAACTCGGCATGGGTCAAAGGCCTAAATGTAAGACTTGAAGC 1586
                          i      i     iiv    i   ?  i             vi i  i 
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_116933590_   1587 TATAAAACTATTACATGAAAACTTAGGGGAAATTCTTCAGGACATTGATC 1636
                                  v   v v      v    ? v  v     iv   v   ivi
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_116933590_   1637 TGGGAAATGATTTTATGAATGGGACCTGAAAAGCACAGGAAACAAAAGCA 1686
                          i  v    i   iv ii  iv   viv         i v        v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_116933590_   1687 AAAGTAAATAAATGAAATTGTATCAACCTAAAAAAGCTTCTGCAC-ACAA 1735
                            i  i      vii i vi     vv v     -   i  ii -v   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chr2_116933590_   1736 AGGAAAAAAAATGAATGGAGTGAAAAGACCATCTAAAGAATAAGAGAAAA 1785
                             --v vv  v  vii           v i i v     ii       
  L1M4_orf2#LINE/    674 AGGA--CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_116933590_   1786 TATCTGCAAACCATTCGTCTAACAAGGGTCATATAT-----ATATATCTA 1830
                            i      i   vii   i i     v v i   -----      v- 
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA-A 770

  chr2_116933590_   1831 GGAACTCAAACATCACAACA-TCAAACACCAAAGAATCCTATTACAAAAT 1879
                         i      vv   v v   i - v   viv    v  i  v   ?v     
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_116933590_   1880 GGACAAATGATCTGATCACACATGTATCAGAAGAAAAC-TACAAATATCC 1928
                           i    v   i   vi v    v v  vi     i i-       iv  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_116933590_   1929 AATAAATATATGAAATAATGTTCAACATCACTAATCAT 1966
                              ii i      vi   i         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (58 / 53)
Gap_init rate = 0.02 (7 / 434), avg. gap size = 1.71 (12 / 7)  


2499 29.06 2.10 1.77  chr2_116978282_116983871.rev     4194  5098 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116978282_   4194 TGTAAAAACATTCTATGCTCATAGATCGGAAGAATCAATGTTGTTAAAAT 4243
                           v   i i  i i   i    i   i      v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116978282_   4244 GGCCATACTGTCCAAAGCAATCTACAAATTCAATGCTATTTCTATCAAGC 4293
                            v     vi     vii       i      i  v  ii       iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116978282_   4294 TACCAACGTCATTTTTCACAGATCTAGCAAAAACT-ATCCTAAAATTTGT 4342
                          v   i vv v     ii    vv v - v  i  -           ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr2_116978282_   4343 ATGGAACCAAAAAAGAGCCTGAATTGCCAAAGCAATCCTAAGCAAAAGGA 4392
                               viiv  ii  v  v    v      i     i i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_116978282_   4393 ACAAAGCTTGAAGCATCATGTTACCCACCTTCAAATTATACCATAAGGCT 4442
                               i v  i vv   iii v    vi      viv   i i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_116978282_   4443 ACAGGAACCAAAATAGCATCATACCAGTACAAAAACAAACACATGTACTA 4492
                             v  i   i i  ii vi   ii i i  ii i i   i  iv ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_116978282_   4493 GTGGAACAGAATAGAGAAGCCAGAAATAAAGGTGCATGC--CTACAACCA 4540
                         i     i     v    iv           --iv   i --i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACATTTATGGTCA 347

  chr2_116978282_   4541 TCTGATCTTTGA-AAAACTCAGTTAAAAAAAG-CAAAGAGGAAAGGAATC 4588
                         vi    i  i  -  iiv -- ii  i vv v-   v i      -   v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGT--GCCAAGACCATTCAATGGGGAAAG-AATA 394

  chr2_116978282_   4589 -CCTATTCAATAAATGGTGCTGCGATAGCTGGCTAGCCATATGCAGAAGA 4637
                         -i  v     i           v  i i    v  ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_116978282_   4638 ATGAAACTAGGTGTCTCCTTTCTACCATAGACAAAAATTATCTTAAGATG 4687
                              ii i iivi  v i ivi      v          v  i  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_116978282_   4688 GATTAATTATTTAAATGGAAAACCTCAAACCATAAGAATTCTAGAAGAAA 4737
                            i ?vv ii      v  i v  v    i    i v ii         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_116978282_   4738 ACCTAGGAA-ACACCATTCTGGACATTAGCCCTGGAAAAAAATTTGTGAC 4786
                           v    ?i- v i -   vv   v  i viiv  v  viiv  iv iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_116978282_   4787 TAAGTTCTCAAAAGCAATTGCAACGAAAACAAAAATTGAAAAGTGGGACC 4836
                           v vivi        vvv     i   iv      v  v  i v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_116978282_   4837 TAATTAAACTAAATAGCATCTGATTTAGTTTGATTAAAA------TATCA 4880
                          v  i   v v  v i v i  --------  v  v   ------     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTG--------TGCTTCAAAGGACACTATCA 685

  chr2_116978282_   4881 ACAGAGTAAACATACAACCTACAGAATGGGAGAAA-TATTCAGAAATCAT 4929
                          v i   i  v v      i               -    iiv       
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_116978282_   4930 GCATTTGACAGAGGTTTACTATCTAGAATCTATAAAGAGCTGAAACAATT 4979
                         ii  i   i ii  vi vv    i     v        i  vvv    i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_116978282_   4980 CAACAAGCAAAAAACAAATAACTCCATT-AAAAACAGGCAAAAGATATGA 5028
                            i  vv    i         i v   -     ii      i   v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_116978282_   5029 ACAGACACTTCTCAGAAGAAGACACACAAGCAGC----AAACGTATTAAA 5074
                          i     i     vi       i i    iii  ----  i ii  v   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_116978282_   5075 TAAATACTCAACATCACTAATCAT 5098
                         - i  i          ????????
  L1M4_orf2#LINE/    886 -AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (159 / 101)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.06 (35 / 17)  


2712 27.81 1.31 2.29  chr2_116995484_116998184.rev     1311  2227 (474)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_116995484_   1311 TAGAAAAACATTCCATGCACATGGATAGGAAGAATCAATATCGTTAAAAT 1360
                          i    i i  i     iv       v      v i     i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_116995484_   1361 GGCCACACTGCCCAAAGCAATTTACAGATTCAATGTTATTTCTATCAAAC 1410
                            v i   v      vii  i           i iv  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_116995484_   1411 TACCAATAACATTCTTCACAGACCAAG-AAAAAACT-ATTTTAAAATTCA 1458
                          v   iivi v  i  ii    --  v-i v  i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA--AATTGACAAGCTGATCCTAAAATTCA 148

  chr2_116995484_   1459 TATGAAACCAAGAAGGAGCCCGAATAGCCAAGGCAATCCTAAGCAGAAAG 1508
                             i  viivi i   v  v          ii     i i iv ii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_116995484_   1509 AGCAAAGCTAGAGGCATCACGCT-ACTGATTTTGAACTATAATACAGGGC 1557
                          i     i i    vv    i  -v ii    ii  viv  v    ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_116995484_   1558 TGCAATAAACAAAACAGCATGGTACCAGTACAGAAACAGACACATAGACC 1607
                          i  i   v   i    ii      ii i i iii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_116995484_   1608 AATGGAACAGAATACAGAGCCTAGAAATAAGGCTGCACACCTACA-TCAA 1656
                                i     vv    i i        iv iii   ii  ii-    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_116995484_   1657 TTGATTTTTGATGAAGCTGACGAAAAAAAAAAAAGCAATGAGGAAAGGGC 1706
                                 i  ii i v  v -----  i vv vv     i      iii
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCC-----AAGACCATTCAATGGGGAAAGAAT 393

  chr2_116995484_   1707 ACCCTATGCAAAAAATCGTACTGGGATAACTGGATAACTATATGCAGAAG 1756
                          vi  v v   v    v  i      i         ? i i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_116995484_   1757 ATTGAAATTGGACCCCTTATTTACACCATACACAAAA-TTATCTCAAGAT 1805
                          v    i          vvi i        i      -   v     i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_116995484_   1806 GCATTAAAGACTTAAATATAAAATGTAAAACCGAAAACTGTAAAAACCCT 1855
                          v  i ?    i     -------    i v v      i     vi i 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAAT-------GTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_116995484_   1856 GGAAGATAACCTAGGCAACAACATTCTGGACATAGAAACTAGCAAATATA 1905
                         i     v   v    ?ivv  iv   vv   v v iivivi    vvi v
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_116995484_   1906 TCAT-GATGAAGATGCCAAAAGCAATTTCAACAAAAGCAAAAATTGACAA 1954
                           v -   - v  ii         vvvv         v      v  i  
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_116995484_   1955 ACTGAATCTAATTTAA-CTAAAAACTTTCACATAGCAAAATAAACTATCA 2003
                          i  i ii v  iv  -i          iiiiivv    iv v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_116995484_   2004 ATAGAGTAAACAGGCAACCTACAGAATGGGAGAAAATATTTGCAAACTAT 2053
                          v i   i  v  i     i                          ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_116995484_   2054 GCAGCTGACAAAGGGCTAATATCCAGCATCTATAAGGAGCTGAAAGAAAT 2103
                         ii v    i  i  i  vi       v  v     i  i  vvv v  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_116995484_   2104 TTACAAGGAAAAAGCAATT--CC---TTAAAAAGTGGGCAAAGTACATGA 2148
                         iv i  vi    ii   v --  ---  ?    i         v iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_116995484_   2149 ACAGAAACTTTTCAAAAGAAGACATATATGTGGCCAATAAGCACTTGAAA 2198
                          i   v i  i  v        i   i vi              v     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_116995484_   2199 AAAAAGAAAAGCTCAATATTGCTGATAAT 2227
                          i v------      i  ii????????
  L1M4_orf2#LINE/    886 AGAT------GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (155 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.36 (33 / 14)  


3016 25.64 2.13 0.67  chr2_117040786_117044926.rev     2757  3649 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_117040786_   2757 GAAAAATATTCTATGTTCATGGATTGGAAGAATCAAAACTGTTAAAATGT 2806
                             i    i i                   v i  v i      i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_117040786_   2807 CCATACTACC-AAAGCAATCTACAGATTCGATGAAATCCTTATCAAAATA 2855
                          v     v  -   vii            i i v     i         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_117040786_   2856 CAAATGACATTCTTCACAGAAATAGAAAAAAAGATCTTAAAACTTATATG 2905
                          v iivi v  i  ii       v  v  ivv    i     i i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_117040786_   2906 GAACCACAAAAGACCCAGAATAGCCAAAGCTATTCCAAGCTAAAAGAACA 2955
                            vii   ii                 i v  iiii ivv i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_117040786_   2956 TAATTGGAGGAATTAC-----CTGGCTTCAGATTATACTACAGAACTTTT 3000
                         v i        v i  ----- iiii    i viv       i i  viv
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_117040786_   3001 GTAACCAAAACAGCATGGCACTGGCATAAACACAGACAGATAGAACAATG 3050
                             i   i    ii   i          iv i     v     v     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_117040786_   3051 AAACAGAATGGAGAACCCATAAAACAGTCCCCACACCTACAGT-AACTTA 3099
                         i  i     v    ii   v   vv ii  vi   ii  ii  -  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_117040786_   3100 TTTTAGACAAAGGTGCCA-GAACATAACAGTAAGGAAAGGAAAGTCCCTT 3148
                             v     i       -  v   v-  i ii      i v    ii  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAGTCTTTT 401

  chr2_117040786_   3149 CAATAAATTGTGCTAGGACAACTGGGTGTCTATATGCAAATGAATGAAAC 3198
                            i    v     i          i i? i i       v       ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_117040786_   3199 TGTACCCCTATTTCTCACCATATACAAAAATAAAATAAAAATGAATTAAA 3248
                           v       ii  v                v  v v      i  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_117040786_   3249 GAATTACAT-CAACACCTCAAACCATGAAACTACTATAAGAAAACATTGA 3297
                           vi  v  -i  v v  v    i  i     vi  v          v i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_117040786_   3298 GGAAAATACTTAG-GACATTGGTCTGGGCAAGAATTT----GA-GTGATA 3341
                         ? v    -   v -   v    vi i     vii   ----  -i   i 
  L1M4_orf2#LINE/    552 NGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_117040786_   3342 CCCTGTAAGCACAGACAACCAAAGAAAAAATGAGCAAATGGTA--TCATG 3389
                           --iv       ii    v           iiii    v v --    -
  L1M4_orf2#LINE/    601 CC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT- 647

  chr2_117040786_   3390 TCAAGTTAAAAAGCTTCTGCACACCAAAGCATACAATCAACAAAGTGAAG 3439
                         iv  i       -   i  ii vi     v i  v     v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_117040786_   3440 AAACAGCC-ACAGAATGGGAGAAAATATTTGCAAACTACCTATCTGACAA 3488
                          i   i  -                          ii iv       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_117040786_   3489 GGGATTAATAACCACACTATATTAAGATCTCAAACA-TTCTATAGGAAAA 3537
                             i vi  v   v v     v    v   vv   -i  v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_117040786_   3538 CATCTAATAATTTGATCAAAAGATGGGCAAAATATTTGAAGAGAACTTTC 3587
                         viv v     iiii  i?   i         iv       v   vv    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_117040786_   3588 TCAAAATAGGAGATACAAATAACAAACAGGGATATGAAAAGGAGCTCAAA 3637
                           v   v i  v        ii v  i i v i        iv      v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_117040786_   3638 ATCATTATCAGA 3649
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (133 / 92)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 1.56 (25 / 16)  


2942 24.15 3.85 0.91  chr2_117091649_117096837     2004  2885 (2304)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117091649_   2004 TGGAAAGATACACCATTTCCATTGCTTGGAAGAATGAATATTTTTTGAAA 2053
                                   iv    v i   v v        v v      v  -i i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAGA 49

  chr2_117091649_   2054 TGCCCACACTACCAAAAGCGATCTACAGATTCAGCACAATCTCAATCAAA 2103
                           v v i   v  v   vi              i i     i v      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_117091649_   2104 ATTCTAATAGTATTTGTAACAGATACAGAAAAAATG---TTAAAATTCAC 2150
                           i i iiv iv   v vi    v iv  v  iv  ---i         i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_117091649_   2151 ATGGAACCACAAAAGACCCATAATAGCTAAAGCAATCTTAAGAAACAAGA 2200
                               vii   ii      v      i   i       i i   v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_117091649_   2201 ACAAAGCTGG------CATAATATCTGATCTCAAATTATGTTTCAAAGGT 2244
                               i   ------  i v vi ii  i     viv ii v     v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_117091649_   2245 ATAGTAATGAAAACAGTATGGTACTGGCATTAAAAACAGACACCTAGACC 2294
                          i      v  i     i            -  ii i     iv    i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATC 298

  chr2_117091649_   2295 AATAAGACAGAAA-GAGAATCTAGAAATAAGCCCATATATATATATTCAA 2343
                            iii i    v-    i  i        i      i  v   iv    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_117091649_   2344 CTAATCTCCATCAAAGGTGCCAGGA--ATACA-CGAGGAGAAAATAGCCT 2390
                         i i  i i iv   i       i  --  v  -i i   i i     i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_117091649_   2391 CTTCATATAAATGGTGTTGTGA-AACTGGATATGGACATGCAAAATAAAA 2439
                         i    - i        i  v  -         ?vv          -i  v
  L1M4_orf2#LINE/    399 TTTCA-ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAAT 446

  chr2_117091649_   2440 AAAATTGAACTC--ATCTTTTACCA-A---AAAAATTAACTCAAAGTAAA 2483
                         i  i   i  i -- i  ivi    - ---               i ii 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_117091649_   2484 TTAAAGAATTGAGTATA-GACCTAAAATTGTAAAACTCCTAGAGGAAAAC 2532
                          i ?   vi i i i  -  v      i i        i    i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_117091649_   2533 ATAGGTGAAAACCTTTTAGACATTATCTT-GGCAATGACTTTTTTGGCTA 2581
                              ? v   i   ivv   v  ivv  -       i-   i  i v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATA 595

  chr2_117091649_   2582 TGACACCAAAAGCACAGGCAACAAA-GCAAAAATTAATAT-TTGTGACTA 2629
                                         i        - v      vi   v-   -    v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG-GACTT 644

  chr2_117091649_   2630 TATCAAG-TTAAAA--TTTTCTGCACAGAAAAATA--AACAACAAAATGA 2674
                         i     i-      --    v   vivi  ii i -- v   v   i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_117091649_   2675 AATG-CAACCCATAAAATGAAATAAAATATCTGCAAACCATATATCTCAT 2723
                           v -       i i    ii v       i      i         v  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_117091649_   2724 AAGAAGCTATTATCCAAAATATATTAAAAATTCATACAACTCAATATTAT 2773
                            iii  vv      i       v  i  i  v            v  v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_117091649_   2774 AAAGAGGTATTGCCTGATTAAAAAGTGAGAAGTGAGGAA--GAATAGACA 2821
                              viv  vi  ii   ?    i  i v i--    v--         
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAA--AGGATTTGAATAGACA 842

  chr2_117091649_   2822 TTT-TCCAAGAAAGATATTGAAGTGAGCAATAGGCATATGAAAAG-TGCT 2869
                            -     ii       vv  i  iv     i   i        -    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_117091649_   2870 CAATACCTCTAGTCAC 2885
                            i i v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (131 / 78)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 1.56 (42 / 27)  

3837 18.88 2.92 1.24  chr2_117091649_117096837     3809  4698 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_117091649_   3809 AAAGGCAACCTACATTCTTGGATTG--AGACTTAATATTGTTCAGATGTC 3856
                             ii v  i ii   v       --               v     v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_117091649_   3857 AATACTACCCAGAGAAATCTACAGATTCAGTGCAATCCCTAT-AGAATCC 3905
                               v    i vvi             ii           - i     
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_117091649_   3906 CAACAGCCTTGTTTGCAAAAAT-GATAAAAGC-AATTCTCACATTTATAT 3953
                           i v     v      i    -  i  --  -i  i  v v   i    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCATAT 151

  chr2_117091649_   3954 GAAATTTCAAGGGACTCA--ATAGCCAAAATAATCTTACAAAAGAAAAA- 4000
                          i  v v        i  --          i      iv       i  -
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_117091649_   4001 -AAACTGAATGGCTCATGCTTCCTGATTTCAAACCCTATTACAAAGCAAC 4049
                         -  ii  i v i    ii     ii        v i  i        v  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_117091649_   4050 AA-ATTCAAAACAGTGTGATACCAGAATAA---TACATATATAGATTAAT 4095
                          i- v    i        i   ii v    ---  v i        i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_117091649_   4096 GGAATAGAACTGAGAGTCCAGAAGTAAACC-ATGAATCTATTGCCAATTA 4144
                                  i             i      -  iv  i   v i     i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_117091649_   4145 ATTTTTGGCAAGGGTGTCGAGATCAT-CACTGGA-AAAGAATGGACTTTT 4192
                              i i        i i   i   -  v   i-       i v     
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_117091649_   4193 TAACAAATTGTGCTGGAATATCTGGATATCCACAGGCAAAATAATAAATT 4242
                         i       v       i i v       ?     v      v   i  v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_117091649_   4243 TTGAGACCTGCC--ACAC-ATACATAAAAAGTACCTCAAAATAGTTCA-- 4287
                          v  vv   i  --    -   i i     v  v        i v   --
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_117091649_   4288 -ATCTAAATACAAGTGCTAAAACCATAAAACTAATGGTGAAGAAAACTTA 4336
                         - i      ii   v        i        vv i --        v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG--AAGAAAACATA 549

  chr2_117091649_   4337 GTAGTATATATTCATGACAAATCTATTGGATTTGTCAATGGATTCTTAGA 4386
                          v?   v  v   i    ----  --   i  v v      v        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGAC----CT--TGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_117091649_   4387 TATGACACCCAAAGCATGAGAAACAAAATAATAAAATAGATAAATTACAC 4436
                                  v      ii  v       v  -              iv  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAA-AAAATAGATAAATTGGAC 642

  chr2_117091649_   4437 CTCAT-AAAATTAAAACATTTTTTGCATCAAAGGACATTATAAATAAAAT 4485
                         i    -          vv    v   v          i   v  v   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_117091649_   4486 GAAAAGACAATT-GCAGAATGGGAGAAAATATTTGCAATTCATCCATATT 4534
                                   ii-i                        v    vi  v v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_117091649_   4535 ATAAGGGTCTAGTAAAGAGAGTATAAAAAGAACT--TATAATGCAATTGC 4582
                                v  v   vvv   i    v        --  i  iv    vii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_117091649_   4583 AAAAGGACAAACAACCTGATTAAAATATAAGCAGAGGACTTAAATAGACA 4632
                             i      i    ii   ?   v  ii   i    i  i        
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_117091649_   4633 TTTCTCCAAAGAAAATATACAAATGGCCAACACATACATGAAAAGATGCT 4682
                                      i                i vii               
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_117091649_   4683 CAATATCTTTAGTCAT 4698
                            i   v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (95 / 70)
Gap_init rate = 0.02 (22 / 905), avg. gap size = 1.68 (37 / 22)  


2105 26.58 11.87 0.74  chr2_117110327_117113201     1575  2383 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_117110327_   1575 ATCCCATGTTCATAAATAGGAAGA----ATATTTTGAAAATGAGCCTACT 1620
                                      ii  v      ----     v v  i   ivvv    
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_117110327_   1621 ACCAAAAGCAATCTAAAAGTTTAATACAATTCTTAACAAAATACCAATTA 1670
                         v  v   vii     v ii  i  ii    i i  v      v   ii i
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_117110327_   1671 TATTCTCTACAGAACTAGAAAAAGCAATCCTAAAATTTGTATGGAACCAG 1720
                         iv  i i i     v v  v  ivii           ii       viiv
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_117110327_   1721 GAGAGATCCTGAATAGCCAAAGCAAACCTAAGTAAAAAGAACCAAGCTGG 1770
                         i  i  i  v           i   v i i iv  i      v   i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_117110327_   1771 AAGCATCACATTTCAAAAGTTCAAAATATACT-CAAAGCTGTAGTAACTA 1819
                          i vv     i   vv  v       iv    -       ii     ii 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_117110327_   1820 AAAGAACATGGCACTG-CATAAAAACAGACCCATAAGCCAATGTAACAGA 1868
                          i v iii   i    -     ii i    vi   iii     v  i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_117110327_   1869 ATAGAGTATCCAGAAACAAATCCACAAGTTTAAAGCCAACTGCTTTTCAA 1918
                           v   vi        i   i   i vi    vi i   i  v     i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_117110327_   1919 CAAAGGTGCCAAGAACATTTACTGGGGTAGGGACAATCTCTTTAATAAAT 1968
                            i          v    i v     v i i i i   i  i  i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_117110327_   1969 GATACTGGAA-AACCAGATATTTATATGCAGAAAAATAAAATTAGACCCC 2017
                          i i    i -   ii    ?ii i     i  i   i  i  i      
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_117110327_   2018 TATATCTTACCATATACAAAAATCAACTCAAAATCTATTAAAGACTTAAC 2067
                           iv  vi               i          vv  i ?    i   v
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_117110327_   2068 TGTAAGACCTAATGCTATTTAACTACTAGAATAAAACTCAGGG--AAATG 2115
                                v    vi    vv    vi     v     vi   ?--    -
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT- 558

  chr2_117110327_   2116 CTTGAAGACATTGGTCTAGGCAAAGATTTTATGGAAAAGAACTCAAAAGC 2165
                            viv   v    vi       v i   iv i  v v  vvi       
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_117110327_   2166 ATAGAAAACAAAAGCAAAC-TAGATTAATGTAATTTCAT-AAAACTAAAC 2213
                          i iiv        v   v-     v   vvi i     -    i    v
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_117110327_   2214 A-------GCTTC--------------------TG-----------CACA 2225
                          -------     --------------------  -----------    
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_117110327_   2226 G------------------CAAA-----------ATAAA-------TACC 2239
                          ------------------    -----------    i-------  i 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_117110327_   2240 TAGAATATACAATAAACTAAAACAATTCAATAAAAAAACCAGA-AATTAG 2288
                         i        i  vi    vvv    i       v    --   -  v  i
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAA--AGACAAATAA 806

  chr2_117110327_   2289 TTT--TTTAAA---GGACACATGGGCTGAATAGATATGTCTCAAAAGAA- 2332
                         iii--  ?   ---  i  v v ivi        i  v    v      -
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_117110327_   2333 --ATACAAGTAGTTAACAGGTGTATTTTTAAAA--TGCTCAACATCACTA 2378
                         --      i i ii  i i iii  v---    --            ???
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATG---AAAAGATGCTCAACATCAZZZ 903

  chr2_117110327_   2379 ATCAT 2383
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.60 (130 / 81)
Gap_init rate = 0.02 (21 / 899), avg. gap size = 4.86 (102 / 21)  


 557 16.67 1.85 0.00  chr2_117301221_117303444.rev      576   683 (1541)    L1M4_orf2#LINE/L1        1   110 (798)  

  chr2_117301221_    576 TGGAAAGACATCCCATGTTCATGGATTTGAAGAATTCATATTGT-ACTAT 624
                                 i                  v     v  v       - vv  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117301221_    625 GTCTAC-CTATCCAAAATGATCTACAGATTGAATGCAATCTCTATCAAAA 673
                          v v i-  vi     v             v  i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117301221_    674 TTCCAGTGGC 683
                          i    iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGC 110

Transitions / transversions = 0.64 (7 / 11)
Gap_init rate = 0.02 (2 / 110), avg. gap size = 1.00 (2 / 2)  

2401 24.87 7.03 1.56  chr2_117301221_117303444.rev      968  1735 (489)    L1M4_orf2#LINE/L1       99   908 (0)  

  chr2_117301221_    968 AATTCCAATGGCATTCTTTACAGAACTAGGAAAAATTAAAACCTAAAATT 1017
                            i   iiv  v  i   i     v -v  v  ii i v-         
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGAT-CCTAAAATT 146

  chr2_117301221_   1018 AATATAGAAGTATAAGACACCCCAGATGGCCACAACCATCTTGAGCAAGA 1067
                         v    i   i ii   iv    vii  i    v   v       iv    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_117301221_   1068 AGACCCATTCTGGATGCATCACATTTCCTAATTTGAAAATATATTACAAA 1117
                            v v vvi    v vv     i    i     v    iv  i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_117301221_   1118 GCTACAGTAATCAAAATAGTTTGGTACTGGCATAAAAGACAGCCACAGAG 1167
                                       i i   v              i-  i  v  i v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATATAG 295

  chr2_117301221_   1168 TAAAATAAAAGAGAATAGATGGCCCAGGAGTAAATTTATTCATTTACAGT 1217
                         vvv   ii  v     v  vi i    i i    iii  v      ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_117301221_   1218 CAACTAATCTTCGACAAGGTTACCAATA--ACTCA--------------- 1250
                            i i  i          v i    v -- i   ---------------
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_117301221_   1251 ------------------------CAATGGGATATCCACAGGCAAAATAA 1276
                         ------------------------   iv     ?     v      v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_117301221_   1277 TAAAATTAAACCCTTATATCACACCATATA--AAAATAAAATTAAAGTCA 1324
                          i  i  ii    i  iv            --     v  v i   i vi
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_117301221_   1325 ATTA-AGACATAGATGTAAGACCTATAAATGTAAACCTATTATTACTTGA 1373
                           i -    v  i        v   v  v i    v  v   ------  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA------GA 539

  chr2_117301221_   1374 AGAAAAGATAGGAA-AAAGCTTTTTGAC-TTGGTCTGGGTAATGCATGTT 1421
                               v     ?i-   v   iv    -    vi i  i    -i v i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTC 588

  chr2_117301221_   1422 TTGGGTATGACACCAAAAGTGCAAGCAA-AAAAGTTAAAATGCACACATG 1470
                           i i              ii       -     vv     iv i v  v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_117301221_   1471 GAATTACATCTAACA--AAAAGCTTATGCAC---AAAAGATAACTACCAA 1515
                          i i v    -  v --    i   v  ii ---   i  i -   i   
  L1M4_orf2#LINE/    639 GGACTTCATC-AAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAA 686

  chr2_117301221_   1516 CAGAATAAAAAGAAAGCATATGGAGTGGGAGAAAATATTTGCAAACTTTA 1565
                         v i i i      v i vi ii  i                    iiv  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_117301221_   1566 CACCTGATAAGGGATTAATATTCCAATTGTATGAGAAATTTATGCAACTC 1615
                         i i           i vi   i vi v i   i ii  i iv i      
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_117301221_   1616 AATAGCAAAAAC-CAAAAAATCCAATT-AGAAATTGGCAAAGGATCTGAA 1663
                             ii     v-    v  i      - i    v          i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_117301221_   1664 TAAACATATCTCTAAAGAAGACATGCAAATGGCCAACAGGTATATGAAAA 1713
                           i    v    i        i  i           i i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_117301221_   1714 GATGTTTAATAATATCATTAAT 1735
                             i i  i vi ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (117 / 72)
Gap_init rate = 0.02 (18 / 810), avg. gap size = 3.67 (66 / 18)  


 900 31.28 11.47 2.66  chr2_117319913_117322483     1262  2089 (482)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_117319913_   1262 ATATACTTTACTCAT--ATTTAGAAAGATCCATTATTGTTAAGAAATAAA 1309
                             v iv ii    --   -- i    iii v           vivv  
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATT--GGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_117319913_   1310 TTATTTTCAAATTCACCTATAGATTCAATATAATTCCAAGCAAAAAACCG 1359
                          vv iii      v i   i        iii   i  v v     vv  i
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_117319913_   1360 GCAAGCTTTTTTGTGTGTGTGGAAAC--ATAAAAT-ACTTTAAAAGTCAT 1406
                           v-  i     -----  ii    i-- i  iv - iii     v    
  L1M4_orf2#LINE/    106 GCT-GCCTTTTT-----TGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_117319913_   1407 ATAGAAAATTGAAGGACCTGCCATATCCAAGATAAACTTCTAGAAAAGGA 1456
                           i    vvii i     iivv   v    i i  v   vv i  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_117319913_   1457 A--ATGTCACAG-----ATACTATCCAACTGTGG--CTCATTACAGAATT 1497
                          -- v  iiv  ----- i   vi    i viii--  i i    i ii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_117319913_   1498 AAAGTAATTAGGATGATAGGGTGTTTGTGCAATGATATGA-ATA---AT- 1542
                          v      i i  iii iv   ii v iii  v    -  -   ---  -
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGATC 298

  chr2_117319913_   1543 ACTGGAACAGAACAGA-AGTCCAAAAATAGACTCTGAAATAAA---ATG- 1587
                          v     i    iv  -      i     i  i ----   v ---   -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCC----ATACATTTATGG 344

  chr2_117319913_   1588 TCCTTTAACTTATAACAAA------AACATCA--CAGT--------AAT- 1620
                           vv  i i  vii    i------  v i  --  i --------   -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_117319913_   1621 ---TTTTCAAGAAACGATGTTGTGGCAATTAAACATTAAT-TTTAAAA-- 1664
                         ---       v   i i  i  v i   i ii i ?iv i- vi    --
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_117319913_   1665 ATGAACCTTG-CCTGTGTATTGTAACACTCATCTA-----ATTAATTTGA 1708
                              vi v -  iv iiv i---    -   v  -----     i ii 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTC---ACAC-CATATACAAAAATTAACTCAA 490

  chr2_117319913_   1709 TTTAGATCACAGGCCCAAATACAAAAGGCAAAGCAACTAGTATTCT-AGA 1757
                         vv i     ?  i  i    ii  i  vi   i v -  iv i   -   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA-TAAAACTCTTAGA 539

  chr2_117319913_   1758 AGAAAGCATAGAAACATATCTTCATGACTTAGTGTAGAAAAATTGT--AC 1805
                              i     i?ii v      i    i v v  viiiv   v  --vi
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_117319913_   1806 TAAATTTGACAC--AAAGCATTAATCATCAAAT-----AATTTATAAATT 1848
                           i  v      --      i-  v  v    v-----   vv       
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCAC-AAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_117319913_   1849 GGATTTTAATAGGATTAAAA-CTTTTAAA--TCAAATG-TATAATTAAAG 1894
                            i  i vi ii       -     ivi--     v -i iv  i  ii
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_117319913_   1895 GAGTGAAA-GACAACTCACACACTGAGAAAAGGCCTTCATAATACATAAT 1943
                         i       -      i    v v  i  i  iiiv  iii  vv    - 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA-T 737

  chr2_117319913_   1944 GTCTGATACGA-ACTTGTA---------------GAAATCT---AATTCA 1974
                         i       v i-       ---------------   v   ---  i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_117319913_   1975 ATAA-ATATGAATATATATTTCATATATATATATGAAAGATAAGACTAGA 2023
                             - v vii i v   vii  -  v? v v   iivi - i  i v  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCAA-AGGATTTGA 835

  chr2_117319913_   2024 GCAGATATTTTATAAAAGTAGATATCCAAAT-------AAGCATATGGGA 2066
                         ii   i    iviv    v      v     -------     i   ii 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_117319913_   2067 AAATGATGCATATTGCCAAGAAA 2089
                          i   v vv i  ii????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (162 / 93)
Gap_init rate = 0.05 (45 / 901), avg. gap size = 2.60 (117 / 45)  


1704 27.13 7.16 1.98  chr2_117332271_117333925      500  1155 (500)    L1M4_orf2#LINE/L1      189   878 (30)  

  chr2_117332271_    500 GGAAATGAAGAACAAAGTTGAAGGAATTAT-----CTGATTCTAAGACTT 544
                          i   v              i    v i i----- ii   ii  i    
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_117332271_    545 ACTCTGAACTTCCAGTAATCAAGATAGTGT------------AAGACAAA 582
                            vii  vi v            i     ------------ i  i i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_117332271_    583 ---ATAGATCAAGTGAAATAA---TG-GTGTCCAGACATAGATTCACACA 625
                         ---         -  i    i---  - v       v   i ii  i   
  L1M4_orf2#LINE/    289 CATATAGATCAA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_117332271_    626 TAACAAATGA--AATTAGTTTTT-ATAATGAGATCAAATCAATTTAATGG 672
                          vv---   i--    ii    i- i  v ivii   iv v   i     
  L1M4_orf2#LINE/    338 TTT---ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_117332271_    673 AGGAAATAAACAGTCTT--CAAAGAATAGTGCTTGAGCAACTGGAAATCT 720
                         -     -i  i      --   vi   i     v ii        v ? i
  L1M4_orf2#LINE/    385 -GGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_117332271_    721 GTATTTTGTAAAA-AATGACCTTCAGTTCTTACTTCATACCCTACATAAA 769
                         ii  --- i    -     vv  viiii i   i   i   v  i i   
  L1M4_orf2#LINE/    433 ACAT---GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_117332271_    770 ATTTAATGTGAGATGAAAAACAGACCTAAATGCACATGTTAGTACTATAA 819
                          v    ivii i   i vv ?           i viv i  iv       
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_117332271_    820 AGCTTGTAGAAGAAAACATTAAAGAATGTCTCCATGACTTTGGGGGAGGC 869
                          i  iv             vii? v vi   i i    i     vv    
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_117332271_    870 AAATG--TTCTTAAAAGCACACATTGAAAGCACTAACCATAGGGAATAAA 917
                           -  --      i viii-   iii       v i v i iiii v   
  L1M4_orf2#LINE/    580 AA-TGGTTTCTTAGATATG-ACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_117332271_    918 AT-GATAAACTG-ACTTCAT-AAAATTAAAAATGTCGGCATATCAAATGG 964
                           -      i  -       -           iv iv iiiv     v i
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_117332271_    965 TATCATTAAAAAA-TAAATAGGCAAGTCA-AGACTGAGA-AAAATATCT- 1010
                         i ii  i  i   - i  v  i   vi  -   v  i  -       i -
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_117332271_   1011 -AAATTACATATATTTGACAAAATATCTTTATTTGGAATATATAAAGAAT 1059
                         -    --       i   i  iiv ii v   iii              i
  L1M4_orf2#LINE/    728 CAAAT--CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_117332271_   1060 TTCTACAACTGAATAATATAAAGACAA----TCCAAC---AATATGGACA 1102
                          ii       v       v        ----i    i---  v    i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_117332271_   1103 AAAGGCTCTAATAGACATTTCACAAGAGAAGGTACGTAAATGACCAATAA 1152
                           i ii iv            v v i     i  iii     i       
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_117332271_   1153 GCA 1155
                            
  L1M4_orf2#LINE/    876 GCA 878

Transitions / transversions = 2.37 (123 / 52)
Gap_init rate = 0.04 (27 / 690), avg. gap size = 2.22 (60 / 27)  


2741 26.86 2.11 1.33  chr2_117341374_117345906.rev     3142  4042 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117341374_   3142 TGGAAAAACAATCCATCCTCACAGATAGGAAAAAACAATATCATGAAAAT 3191
                               i i vi    vi   ii   v    i vvi     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117341374_   3192 GGACATACTGCTGAAAGTAACTTATAGATTCAATGCTATTCCCATAAAAC 3241
                           vv     v iv   v i ii  i        i  v  i  i  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117341374_   3242 TACCATTGACAGTCTTTACAGAA-TTGGAAAAAACTACTTC-AAATTTAA 3289
                          v   vivi vv i   i     -   -- v  i  iv i -   v  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_117341374_   3290 TTTGGAA-T-CAAAGAAGACCTTGTATGGCCAAGACAATTCTGAACAAAG 3337
                          v     - -   i --    iv v  i     i     ii    v  ii
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_117341374_   3338 AGAACAAAGCTGGAGGCATCACGTTACATGACTTCAAACTATACTACATG 3387
                                  i      vv    ii v vii i      viv       vi
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_117341374_   3388 GCTACAGTAACCAAAACAGCATGGTACTTGTATCAAAACAGGCATATAGA 3437
                                   i   i    ii       v i  v ii i  i        
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_117341374_   3438 CCAATGGAACAGATCAGAGACCTCAGAAATAATGCCACACATCTGCAGCC 3487
                         i        i   viv    vii         vv   i    i iii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_117341374_   3488 ATCTGATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATCTC 3537
                          vi    i        ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_117341374_   3538 CTTTTCCACAAAAGGTGCTGGGAAAACTGGCTAGCCACATGCAGAAAACA 3587
                               v     v          v      v  ?         i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_117341374_   3588 GAAACTGGACCCCTTCCTTATACCTTATACAGAAATTACCTCAAGATGGA 3637
                            ii         v   i i   v      i      v     i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_117341374_   3638 TTGAAAACTTAAATGTAAAACCCCAAACTGTAAAAATTCTAGAAGAAAAC 3687
                          ii? i  i         i v iv     i     v ii           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_117341374_   3688 CTAGGC--AATTCCATTCAGGGCATAGACATGGGCAAAGACTTCATGACA 3735
                         v    ?--  v  --   iv i v v ivv i     v ii   v iivv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_117341374_   3736 AAAACGCCAAAAGCAATTGCAACAAAAGGCAAAGTTGACAAATGGGATTT 3785
                          vi  i         vvv          iv   i v  i    v   i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_117341374_   3786 AATTAAA-TTAAAGTGCTTCTGCACAGCAAAAGAAACTATCTTCAGAGTG 3834
                         v  i   -     i-i   i  ii vv    i  v      vvv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_117341374_   3835 AACAAGCAATCTACAGAATGGGAAAAAAAATTTTACAATCTACCCATCTG 3884
                           v ii   i i           i    v    -i   vii ivi     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTG 742

  chr2_117341374_   3885 ACAAAGGTCTAATATGCAAAATTTACAAGGAACT--TA------AATTAC 3926
                          i  i  v  vi   v  i   v  i  i     --  ------   v i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_117341374_   3927 AAAAAAACCAAACAACTCCATCAAAAAGTGGGCAAAGGGTATGAACAGAC 3976
                              i  -   i   i v  i?    i          i v    i    
  L1M4_orf2#LINE/    793 AAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_117341374_   3977 ACTTCTCAAAAGAAGACATTTACAAGT--CCACCAA--ACATGAAAAAAA 4022
                          i     v        i  --    i --   vi  --         i v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_117341374_   4023 AGCTCAACATCTCTGATCAT 4042
                         -          v????????
  L1M4_orf2#LINE/    890 -GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.72 (31 / 18)  


 446 30.71 0.00 1.43  chr2_117358569_117360357      191   330 (1459)  C L1M4_orf2#LINE/L1   (765)   143     6  

C chr2_117358569_    330 AAATATTCCATGCTCATGGATAGGAAGAATCAGTATAATGAAAATGATGA 281
                          i    i     i        v      v i i   vi v  i   iii 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

C chr2_117358569_    280 TACTTCCCAAAGTAATTTTTAGATTCAGTGGTATTCTCATCAAGCTACCA 231
                             i      v i  i vi       ii vv  i ii     iv v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

C chr2_117358569_    230 TTGACTTTCTTTGCAGAATTAGAAACGCCATATTTCTAAA 191
                         vivi i  i         v v  v v  -- iv i     
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAA 143

Transitions / transversions = 1.53 (26 / 17)
Gap_init rate = 0.01 (1 / 138), avg. gap size = 2.00 (2 / 1)  

1923 24.66 3.45 9.62  chr2_117358569_117360357      489  1299 (490)    L1M4_orf2#LINE/L1      148   908 (0)  

  chr2_117358569_    489 ATATAGGAATGCATGGAACCAAAAAAGAGCCTGTATAGAAAAGACAATCC 538
                             i i      v  i   v i  -v    ---------  i      i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAA-TAGCC---------AAAACAATCT 187

  chr2_117358569_    539 T--AAGCGGAGGACAAAGCTGTAAG---CA----TCCTGACTTCAAGCTG 579
                          --  iv i  i      i  v i ---  ----   ii i     iviv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_117358569_    580 TACTACAAGGCTACAGTAACCAAAACAGCATGGTACAGGCACCAAAACAG 629
                                 i          i   i    ii      v    iv ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_117358569_    630 ATATATATGTGTGTGTATATATATATATATATATATATATCTCGATAGTT 679
                          i     -------------------------------------------
  L1M4_orf2#LINE/    288 ACATATA------------------------------------------- 294

  chr2_117358569_    680 AGATACAGATATATATAATTATCAATGGAAAATAACAGAGACCTCAGAAA 729
                         -------   ------------        v v  iv    vii      
  L1M4_orf2#LINE/    295 -------GAT------------CAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_117358569_    730 TAACACCACTCATCTACAACCATCTGATCTTTGACAAACCTGACAAAAAC 779
                            vv   iv   i  iiii  vi    i  i     ivv  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_117358569_    780 AAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTG 829
                          vv            i  vvi  v  i  i              v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_117358569_    830 GCTAGCCATATGCAGAAAACAGAAACTGGATCCCTTCCTTATACTGTGTA 879
                          v  ?   i     i  i vv   ii    i    v   i i  ii i  
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_117358569_    880 TGAAAATTAACTCAAGATGGATTAAAGACGTAAATGTAAAACTCAAAACC 929
                         ii             i      i ?    v         i vii     i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_117358569_    930 ATAAAAACCCCAGGTGAAAACCTAGGCA-ATACCATTCAGGAC-TTAGGT 977
                               vi ii  iv      v    ?i- v i -   iv   -  i   
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT 574

  chr2_117358569_    978 ATGGGCAAAGACTTCGTGACTAAAACACCAAAAGC--------CAAAA-- 1017
                         - i     v ii   v iiv  vi           --------     --
  L1M4_orf2#LINE/    575 -TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_117358569_   1018 -----TTGACAAGTGGGATCTAATTAAA-CTAAGAGCTTCTGCATAGCAA 1061
                         ----- v  i  i v   ii v  i   -i   i i   i  iiivv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_117358569_   1062 AAGAAACTAGCATCAGAGTGAGCAGGCAACCTACAGAATAGGAGAAAATT 1111
                          i  v    v  vv i     iv  i     i       i         v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_117358569_   1112 TTTGTAATCTATCCATTTGATAAAGGTCTAATATCTAGAATCTACAAAGA 1161
                             i  vii  vi  i      i  v  vi    i     v  i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_117358569_   1162 ACTTAAATATAC-CAAAAAAAAAAACCCCACAAACAACCCCATCAAAAAG 1210
                            ivv i -  -   v  v     v---     i     v  i?    i
  L1M4_orf2#LINE/    774 ACTCTTACA-ACTCAATAATAAAAAG---ACAAATAACCCAATTWAAAAA 819

  chr2_117358569_   1211 TGGGCAAAGCATATGAACAGATACTTCTCAAAAAAAGACATTTATGTGGC 1260
                                  v  v    i   i i     v   i    i  vi vi    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_117358569_   1261 CAACAAATGTATGAACAAAAGCTCATCATTGGTCATTAG 1299
                            i  iiii     v i v     v   ii????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (124 / 72)
Gap_init rate = 0.02 (17 / 761), avg. gap size = 6.24 (106 / 17)  


 262 25.32 3.80 0.00  chr2_117362731_117365199.rev     1084  1162 (1307)    L1M4_orf2#LINE/L1       15    96 (812)  

  chr2_117362731_   1084 ATATTCACGGATTAGAAGAAAAAATATT--TAAGATATCCATTCTGCTCA 1131
                           i    i     i     vvv      --      iv v  v  v i  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_117362731_   1132 AAGTGAACTACAAATTTCGTGCAATCT-TATC 1162
                           v   v     i   ivii      i-    
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATC 96

Transitions / transversions = 1.00 (10 / 10)
Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.50 (3 / 2)  

2434 27.43 5.22 1.58  chr2_117362731_117365199.rev     1164  1987 (482)    L1M4_orf2#LINE/L1       55   908 (0)  

  chr2_117362731_   1164 ATTCTGCTCAAAGTGAACTACAAATTTCATGCAATCTCTATCAAAATTTT 1213
                           v  v i    v   v     i   iv i      i          iii
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_117362731_   1214 AA-TGTCATTTTTCACAGAAATAGA--AACAAAGCTTAAAATCTGTACGG 1260
                          i-  i -     ii       v  -- i vi v i      iii  i  
  L1M4_orf2#LINE/    105 AGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_117362731_   1261 AAACACAAAAGACCTCAAAGAGCCACAACAACTTTGAGCAAAAACAACAA 1310
                            ii   ii    ivi  v     v     ii    ---    v  ---
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAA--- 197

  chr2_117362731_   1311 TAAATAAAGCTGGAAGTATCACACTCCCCGATTTTAAAA-----TATAAA 1355
                         -i  i    i    i vv       i   i    i    -----  i   
  L1M4_orf2#LINE/    198 -GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_117362731_   1356 GTTATGGTAATCAAAACAGCATGGTACTGGCATAAAAATAGGCACATTGA 1405
                          i  ii        i    ii              ii    i  i  v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_117362731_   1406 AAAATGAAACAGGACAAAACATGCAGAAATAAACCCATGTATATATGATC 1455
                         vv    i  i  i ivi ivi v               ii  v    i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_117362731_   1456 A-TTGATCTTTCACAAATATACCA-------------GAAAAAAAGTCAT 1491
                          -     i  iv    ivi i   ------------- ii   i i vi 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_117362731_   1492 TTTCTTCAATAAATGGTGTTGAATAAACAAGATATCCATATGCTGATGGA 1541
                         i  -     i        i  iivv   vi    ?   i    vi v i 
  L1M4_orf2#LINE/    397 CTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_117362731_   1542 TGAAACTGTATCCTTGTCTTACATCATATTCATAATTTCACTAAAAAAAT 1591
                             ii  v i  i ii  i   i     v  v  v  v   v    -- 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA--T 493

  chr2_117362731_   1592 GGATAAAAAACACAAGCATAAGCCCTGAGATTGTAAAACATCTAGAAAAA 1641
                             v ? i  vi  iii    vv  i i i i      vii     i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_117362731_   1642 AACCTGGGTG-AAATGCTCCACAACACTGGTCTGAGCAAAGATTTCTTGA 1690
                            v i  ? -    -  i iii  vi   vi ii    v i      ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_117362731_   1691 ATATGACCCTGAAAACACAGCCAGCAAAACCAAAATTCAATAAATAGGAT 1740
                                v ii   i    iv  i     vv    v vi      v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_117362731_   1741 TCAATCAAA-CGAAAAACTTTCTATACAGCAAAGAGAACAATTAACAGAG 1789
                          iv      -iv         - i i vv     iiv  v  i  v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_117362731_   1790 TGAAG-GAAATCCTATGGAATGGGAGAAAATATTTTCAAACCACAAATCT 1838
                             i-  v v  i ii                  v    i  i v    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_117362731_   1839 GATGTGAGGCCAATATCCAAAATATATGAGAAACTC----AACTTGATAT 1884
                            iv i i ivi      i       i ii     ----    ii   v
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_117362731_   1885 CAAGAAAACAAAGAACCCAATT-AGAAATGGACAAAGGACCTAAATAGAC 1933
                         i  i  i     v         - i      i       ii i       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_117362731_   1934 ATTTATTGGCATAAGTCATACAAATGGCTAACA------------GAT-C 1970
                             v iviv v   vi           i  i ------------   - 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_117362731_   1971 TCATCATCACGAATTAT 1987
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (151 / 72)
Gap_init rate = 0.02 (19 / 854), avg. gap size = 2.95 (56 / 19)  


2329 28.38 2.86 2.97  chr2_117445959_117449444.rev     2086  2994 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117445959_   2086 TGAAAAACCATTCTATGCTCATGAATAGGAAAA-TCAATACTCCTAAAAT 2134
                           i   ivi  i i   i     i  v    i - i    i vi   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117445959_   2135 GGCCATACTGCCCAAAACTCAATTTACAGATTGAGTGCTACTCCTGTCAA 2184
                            v     v      -- ii  i        v ii  v ii   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_117445959_   2185 ACTACCAATGACATTTTTCACA-AAATTAGAAAAAAACTG-TTCTAAAAT 2232
                          v v   iivi v     ii  -     i--- v  i   - i       
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAAT 145

  chr2_117445959_   2233 TCACATGGAACCAAAAAAGTGCCTGAATAGCCAAAACAATCCTAAGCAAA 2282
                            i      viiv  ii vv  v                 i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_117445959_   2283 AAGAACAAAGCCAGAGGTATCACATTATCGTATTTCAAACTACAAGGTTA 2332
                                   iii    vv     i vi vv        --  ----   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--AC----TTA 239

  chr2_117445959_   2333 CTACTTTGATTACAAGTAGACTTGTAACCAAAACAGCATGATCTTGATAC 2382
                             ------- v iv  v ---    i   i    ii  i vi  ii i
  L1M4_orf2#LINE/    240 CTAC-------AAAGCTACA---GTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_117445959_   2383 AAAAACAGACACATAGACCAGTGAAACAAAATAGAGAG-CCAGAACTAAA 2431
                           ii i     i     i  i  i  i i   v     -      v    
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_117445959_   2432 ACCACGTATCTACAACCATCTGATCTTCAACAAAACTGACAAAAACGAAC 2481
                         v   iii  i  iiii  vi    i   i    iiv  v   i v ivv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_117445959_   2482 AAAGGGGAAAAGACAACCTATTCAATAAATGGTGCTAGGATAACTGGCTA 2531
                           v       ii i ii  v     i          i   i      v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_117445959_   2532 GCCATATGCAAAAGATTGAAACTGGATCCCTTTTTTTTCACCGTATACAA 2581
                         ?   i          v    ii    i    vii iv-    i       
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA-CACCATATACAA 478

  chr2_117445959_   2582 CAATCAACTCAAGATGAATTAAAGATGTAAAGGTAAAACTTAAAATTATA 2631
                         v   i       i   i  i ?   iv    v    i vi     i    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_117445959_   2632 AAAACACTAGAAGATGACCTAGGAAGTA--CCATTCTGGACATAGGCCCT 2679
                            vivi       vi  v    ?-   --i -   vv   v v  viiv
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGN-GTAAATC-TTCGTGACCTTGGGTTA 576

  chr2_117445959_   2680 GGGAAAGATTTCATGACAAAGATGTCAAAACCAATTGCAACAAAAACAAA 2729
                           v  v i    v iivv v  iii     v  vvv         iv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_117445959_   2730 AATTGACAG-----------TTAAACTAAAGAGCTTCTGCACAGTGAAAG 2768
                            v  i i----------- i   v v  i i   i  ii vvii  i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_117445959_   2769 AAACCAGCAACAGAGTAAA----CAACCTACAGAATTGCAGAAAATATTT 2814
                          v  i v   v i   i  ----     i       v v           
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_117445959_   2815 GCAAACTATGCATCCAGCAAAGGTCTAATATCCAGAATCTGTAAGGAACT 2864
                              ii  ii   iiii  i  v  vi          v i   i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_117445959_   2865 T----AACTGACCAAACCAAAAAAAATAAACAATCCCATTAAAAAGTGGG 2910
                         i----    v vi  v---     i i   i  i  v   ?    i    
  L1M4_orf2#LINE/    777 CTTACAACTCAATAAT---AAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_117445959_   2911 CAAATTATAAGAACAGACACTTTACAAAAGAAGATATGTGTACTCACAAC 2960
                             vv  vv   i     i  iv v           iiiv ivvv   i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_117445959_   2961 AAGAATACAAAAA-ATGCTCAACATTATTAATCAT 2994
                            v i ii    -           i ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (159 / 95)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.79 (53 / 19)  


 328 17.33 0.00 1.33  chr2_117474459_117480836        1    75 (6303)    L1M4_orf2#LINE/L1      748   821 (87)  

  chr2_117474459_      1 GGATTGTTATCAAAAATATACAAAGAACTCTTATGACTCAACAATAAAAA 50
                            i vv    v i      i            ii      i        
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_117474459_     51 AAACCAACAACCCAATTTAAAAATG 75
                         i - v  i         ?       
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATG 821

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1)  

3128 26.68 0.88 0.77  chr2_117474459_117480836     4980  5886 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117474459_   4980 TAGAAGAACATTCCACACTCATGGATAGGAAGAATCAATATCGTGAAAAT 5029
                          i   ii i  i   iii        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117474459_   5030 GGCCATACCGCCCAAGATAATTTATAGATTAAATGCCATCCCCATCAAGC 5079
                            v    iv     iv i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117474459_   5080 TACCAGTGACGTTCTTCACAGAATTGGAAAACACT-ACTCTAAAGTTCAT 5128
                          v    ivi v  i  ii     v v  v  -i  - ii     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_117474459_   5129 GCGGAACCAAAAAACAACCCATATT-GCCAAGACAACCCTAAGCCAAAAG 5177
                         ii    viiv  ii-i     v v -     i    i i i ivv i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_117474459_   5178 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGGC 5227
                                i      vv   ii  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_117474459_   5228 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5277
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_117474459_   5278 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5325
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_117474459_   5326 GTCTGATCTTTGACAATCCTGACAAAAACAAGAAATGGGGAAAG--TATT 5373
                         ivi    i  i     vvv  v   i v  vvv           --  v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_117474459_   5374 CCTTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5423
                          i  -- i                 v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_117474459_   5424 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5473
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_117474459_   5474 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCT-AGAAGAAA 5522
                            i ?    i       v   v       i      vi  -        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_117474459_   5523 ACCTAGGCA-ATACCATTCATGTCATAAGCATGGGCAAGGACTTCATGAC 5571
                           v    ?i- v i -   i  v v vi vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_117474459_   5572 TAAAACACCAAAAGCAACGGCAACAAAAGCCAAAATAGACAAATGGGATC 5621
                           vi            vvi          vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_117474459_   5622 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5671
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_117474459_   5672 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCACCTGA 5721
                           v  i     i                 v       vii ivi i    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_117474459_   5722 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 5771
                         i  i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_117474459_   5772 AATAATCAAACAACCCCATCAAAAAGTGGGAGAAGGATATGAACGGACAC 5821
                           v iv    i     v  i?    i    vi      v    ii    i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_117474459_   5822 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 5871
                              v        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_117474459_   5872 ATCATCACTGGCCAT 5886
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (146 / 92)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


1376 27.76 8.64 4.61  chr2_117483738_117486042.rev      946  1813 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_117483738_    946 AGATATGCCATGTTTAGGAATCAGAAGATTCAATAATGCTACGGTATCTG 995
                               v       i v i  ii     i i    v  i  v i iv vi
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_117483738_    996 TTCTCATCAAATTGATAAACAGCTTCAGTGAAATTCAAATCAAAATGCCA 1045
                          v   vi         vv    v    ii v   i vv        v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_117483738_   1046 ATTGACTTTA--GCATAAAATTATCACTATAAT--TAAATATGTTATATT 1091
                         ii  v    v--   -i     iv  vvv i  --    -  - i    v
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCA-GAAATTGACAAGCTGATCCTAAA-AT-TCATATG 152

  chr2_117483738_   1092 GA----CAAGAGGAATTAAAACAGCCAAAAGGGTTTTGCTAAAGAATAAC 1137
                           ----    -   vii i  i        vii i   vv      v   
  L1M4_orf2#LINE/    153 GAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_117483738_   1138 AAAACTTGAATATTTGAACTATTTGATTCCAAGACTGACT------CTAG 1181
                            ii v  iv i iiv   viiii   i   i   v   ------   v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_117483738_   1182 GGAAAT----------------TTGCATAGG--------------TCAAT 1201
                         i v   ---------------- v     i --------------     
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_117483738_   1202 GAAACAGAA--GAGAATCTAGAAATGGACCCACAGTGTATATGGTCCACT 1249
                          i  i    --    i  i      ii     i -ii v       v i 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGTCAATT 350

  chr2_117483738_   1250 AACATTCTTACGAACACTACCATGATGTGTCAATGGGAAAATATATGTGT 1299
                         i iv   v-  -  viv i   v  ivvv        i   v -  i-  
  L1M4_orf2#LINE/    351 GATTTTCG-AC-AAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATA-GT 396

  chr2_117483738_   1300 CGTATTTTTTCAATACCAAAAAATTAGATGCAGAG-CAACAAGACATA-A 1347
                          -----       i ------   -- i   v i -    vi  i ?v- 
  L1M4_orf2#LINE/    397 C-----TTTTCAACA------AAT--GGTGCTGGGACAACTGGATAKCCA 433

  chr2_117483738_   1348 CTTAGCAAAC--ATGAACTTGAACCTTTATCTTACG-----TACAACAAT 1390
                          v -     v--     v   i   ii  i  i  i-----     -  -
  L1M4_orf2#LINE/    434 CAT-GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA-AA- 480

  chr2_117483738_   1391 ATCAACTTAAAATGTGGCGTATAAACGTAAATCTAAAAAAACTAAAGTTA 1440
                           i    i      -- vvi ? i  v     v   i i--     ii  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATG--GATCAWAGACCTAAATGTAAGAG--CTAAAACTA 526

  chr2_117483738_   1441 TAATATTTCTTGAAGAAAACAT-GGGGAAAATTTTTGCAATTTGGGGATA 1489
                            v i ii v           -  ? v    i  i ii ii v   v  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_117483738_   1490 AACAAATATTT-TTAGTAAAAACAGAAAAAGCATGAGCCATGTAAGAAAA 1538
                         ii   vvi   -    vv vi   vv       ii   v iiv       
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_117483738_   1539 AGTA-ATAAATTGTGTTTTATTGAA-TCAAAAACCTATGTTGTTTAAAA- 1585
                          i  -        vii  i  ii  - i      i v   vv  i   i-
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_117483738_   1586 ATATTATTAAGAAAAT-ATATTACAAGCCACAAAGTGGAAAAAACCCCGC 1634
                          i i   i      i - v vv    v     i i   i i   viv---
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA--- 723

  chr2_117483738_   1635 TGTGAAACATGATACATATATCTGAAAAACAGCTTTTATTTAGAATATAT 1684
                          v  v  ----  -           v  ivii   v   ii         
  L1M4_orf2#LINE/    724 TTTGCAA----AT-CATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_117483738_   1685 AAACA---TTCACAATTAAATTACGAAAAGGTACTCGGCTCCCCAAATAG 1731
                            v ---i i    i v   v ii     ii vviii ---    v ?i
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC---CCAATTWA 815

  chr2_117483738_   1732 GAAA-AAACAACGGA---------ATATTTC-ACATGGAAGATATAAAAA 1770
                         i   -iii   v   --------- i     -v  vi         v   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_117483738_   1771 TGACCGATAACCAAATGAAAAGATGTGAAACATCATGAGTTGC 1813
                           i  i    v  v           ivv       ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.05 (42 / 903), avg. gap size = 2.74 (115 / 42)  


2460 28.42 4.22 0.57  chr2_117507992_117511586     2228  3103 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117507992_   2228 TGGAAAAACATTCCATGCTCATAGATGGTAAGAATCAATATTGCAAAAGT 2277
                               i i  i     i    i   v v    v i       iv  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117507992_   2278 GGCCATACTTCCCAAAGCAATTCATAGATTTAATGCTACTCCCATTAAAC 2327
                            v     i      vii  ii i     i  i  v ii  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117507992_   2328 TACCATTGACACTCTTCACAGAACTAGAAAAAAAAATCTTAAAATTCATA 2377
                          v   vivi vi i  ii     v v  v  ivvi   i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_117507992_   2378 CGGAACCAAAAAAGAGTAAGAATAGCCAAGACAAACCTAAACAAAAAG-- 2425
                         i    viiv  ii  viv           i    v i i  v  i   --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_117507992_   2426 -------GAAGCA-TCACACTACCTGCCTTCAAACTATACTAAAAGACTA 2467
                         ------- i  v -       v  iivi      viv     v  ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_117507992_   2468 CAGTAGCCAAAACACCGTGGTACTGGTAAAAGAACAGACACA--GACCAA 2515
                              ii   i   vi          i v   i i     i --  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_117507992_   2516 TTGAACAGAATAGAGAACCCAGAAATAAGACTGTACACCTACAACCATCT 2565
                          v   i     v    ii          iv ii    ii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_117507992_   2566 GATCTATGAAAAACCTGGCAAAAACAAGCAATGGGGAAAGGATTCCCTAT 2615
                            i vi  v  ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_117507992_   2616 TTAATAAATGATGCTGAGAGAACTGGCTAGCAATATGCAGAAAATTGAAA 2665
                          i  i     i     i  v      v  ? v i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_117507992_   2666 ATGGACCCCTTCCTTACACCACATACAAAAAAGAACTCAAGATGGATTAA 2715
                         v         v   i      i         vv       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_117507992_   2716 ATATTTAAATGTAAAACCCAAAACTATAAAAAAACCCT--GGATACAACC 2763
                          v ii         i v i            --- i  -- i v v   v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA---CTCTTAGAAGAAAACA 547

  chr2_117507992_   2764 TAGGCAATAAGT-TTCAGGACACAGGCACAGACAAACATTTTTT-GATGA 2811
                             ?i-   i -   iv   viv  vvi  i   vvi   i  -   - 
  L1M4_orf2#LINE/    548 TAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr2_117507992_   2812 AGACCCCAAAAGTAATTGCAACAA--GCAAAAATTAACAAGTGGGACCTA 2859
                         v   v       i vvv       -- v      vi i  i v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_117507992_   2860 ATTAAACTGAGGAGCTTCTGCACAGCAAAAGAAATTACCAG---AGTAAA 2906
                           i   v v ii i   i  ii vv    i  v i  i  i---   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_117507992_   2907 CAGACAGCCTATGGTATGAGAGAAAATCTTTGCAATCCATGCATTAGACT 2956
                         v     i  i ii v   i        v       vi   ii  iv  iv
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_117507992_   2957 AAGGTCTAATATCCAGTATCTATAAGCAACATTTACAA---------GAA 2997
                          i  v  vi       v  v     iv   vi      ---------i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_117507992_   2998 AAAA-AAA-AACCC--TTAAAAAGGGGGCAAAGGACATGAACAGACACTT 3043
                           i -   -     --  ?    iv          iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_117507992_   3044 CTCAAAAGAAGACACATGG-CAGCCAACAATCAC--GAAAAAAAGTTCAA 3090
                            v        i i iii-ii     i  v   --     i v i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_117507992_   3091 CATCACTTGTTAC 3103
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.47 (42 / 17)  


2218 28.30 4.43 3.07  chr2_117512197_117514298      740  1619 (483)    L1M4_orf2#LINE/L1       17   908 (0)  

  chr2_117512197_    740 GTTTATTGCATTTGAAGACT----------AAGATG-CTAT-TTACCCCA 777
                            i  v -   v       ----------      - v  -i v   v 
  L1M4_orf2#LINE/     17 GTTCATGG-ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_117512197_    778 TTTGATACATAGGTTTGACATGACTTCTGTCAAAATCCCAGC-------- 819
                         v     vi i  i  ii  iii iii  i             --------
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_117512197_    820 ---AAAAAATTTTT--GCTAATG-TAAAATTTAAACAGAAAGGCAAAGGA 863
                         ---v i     vvi--   i  v-       i v ii    v    i   
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_117512197_    864 ACTAAAATAGCAATAACAATTTTGTATGAGAAAAATGAAGTGGGAAAA-- 911
                         v i i      v v      i   v vi    i  ii    v   ii --
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_117512197_    912 -AAGTGTATCTGATTTTAAAACTTATTGTATAACTATAGTAATCAAAGCT 960
                         - viiv -i ii    i        i ii v i   i         ii v
  L1M4_orf2#LINE/    216 CACACTT-CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_117512197_    961 GTATGGTATTGACAAAGGGGTAGACACATAGATTAATGTAA--GAATAAA 1008
                           i     i  i  v i  i      i      i    v  --    vi 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_117512197_   1009 TAATTGAGAAATAGACCCATCCGTATATACCCAACTGATTTTTGACAAAA 1058
                         v i iv       i      v i v   ivi   i       i     ii
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_117512197_   1059 GT-TTAAAATTAATACAAGGAAGCAAAGATAGACTTTTCAACAAATGGTT 1107
                           -ii  i ii v -   v ii v  ii    v                v
  L1M4_orf2#LINE/    365 GTGCCAAGACCATT-CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_117512197_   1108 CTGGGGCCACTGAACATTTGTAGGCAAAA-AATAAGCTTCTACCTAAGCT 1156
                              i v    i i ?iiii v      -   i iv  vv   ivvi i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_117512197_   1157 TCATTCCTTTTACAAATATTAACTCAAAATGGATCACA--CTTAAGTATA 1204
                            iv  v v      v                   ? -- i   i i  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_117512197_   1205 ACCATACAAATCTATAAAACTTTTAGTGAAAAAGCACAGAGGAAAATCTT 1254
                          vvii-i   v          i    -i i   i  i  i? v       
  L1M4_orf2#LINE/    514 AGAGC-TAAAACTATAAAACTCTTAG-AAGAAAACATAGGNGTAAATCTT 561

  chr2_117512197_   1255 TAGAATCTCAGGGTAGGTAAAAAGTTCTTAGACTTGTCACCAAAAGCATA 1304
                         iivi i  ii  v    i  viiv        iv  v           i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_117512197_   1305 ATTCATAAACAGAAGAATTGATTAATTTGAATTCATCATAAAACAAAATA 1354
                          viv i   vii  i   v   v    v  v       ------   v  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA------AAATTA 655

  chr2_117512197_   1355 AAACAAAACAGAAAGCATTTGTTCAACAAAATACCCAGTTAAAAGGATGA 1404
                            -----------i v     v vv    iv  v vi i  i iii   
  L1M4_orf2#LINE/    656 AAA-----------ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_117512197_   1405 AAAGACAAGTTATATACCGGGAGAAAATATTTGTAAATCACACACCTAAC 1454
                                 vii i v vi               i      i i i  i i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_117512197_   1455 AAAGCACTAGTACTTAGAATACATAAAGAACTGTGAAAACTCAACTGCAA 1504
                           i v   v   iii      i          v v v       ivii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_117512197_   1505 AAGCA-AAATAGCAATTCAATTAGAAAATTGACAGAAGATGTTTAGTAG- 1552
                           iv -     --- ii     ?i     v i  i i   -  v i   -
  L1M4_orf2#LINE/    795 AAAGACAAATA---ACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGA 840

  chr2_117512197_   1553 CATTTCGTTGAAGAGAATATATACATAACAAATAAGCATATGGAATAGAT 1602
                               viii    ii     i v  ii v        i   i  -    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGAT 889

  chr2_117512197_   1603 --TCAAAGCCATTTGCCAT 1619
                         --    vii  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (157 / 88)
Gap_init rate = 0.03 (24 / 892), avg. gap size = 2.75 (66 / 24)  


2239 27.07 4.94 2.10  chr2_117576430_117582993.rev     4922  5730 (834)    L1M4_orf2#LINE/L1        1   832 (76)  

  chr2_117576430_   4922 TGAAAAAACAACCTATGTTCACAGATAGAAAAAATCAATATCATTAAAAT 4971
                           i   i i v  i       ii   v i  i v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117576430_   4972 GGCTCTTCTCCTCAAAGCAATTTATAGATTCAATGCTATTCCTATCAAAC 5021
                            vv v    i    vii  i  i        i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117576430_   5022 TACCAATGACATTCTTCACAGAACTAGAAAAAAACT-ATTTTAAAACTCA 5070
                          v   iivi v  i  ii     v v  v  i--  -  ii     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_117576430_   5071 TATGGAACCAAAAAAGAAATGGAATAGCCAAGGCTGTTCTAAGCAAAAAG 5120
                                viiv  ii  vvii          ii vi ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_117576430_   5121 AAGAAAGCTGTAGGCATCATGCTTG--------------TACTA---AAC 5153
                           v    i  v   vv   ii   v--------------     --- i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_117576430_   5154 TA-----ACCAAAACAGCATGACACTGATATAAAAACAGACACATACACC 5198
                           ----- i   i    ii  ii    ii    ii i     i   v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_117576430_   5199 AGTGGAACAGCA--GAGAGCTCAGAAATAAGGCCAAACACCTACCACCGT 5246
                          i     i  v --     ii         iv   v   ii  ivii iv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_117576430_   5247 CTGATCTTCAATAAAGCTGACAAAAACAAGCAATGTGGAAACGAGTCG-C 5295
                         i    i   i i  i v  v   i v  vv     v     -  i v - 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTC 397

  chr2_117576430_   5296 TATTCAACAAATGGCGCAGGGATAGCTGGCTAGCCATATCCAGAAGATTG 5345
                          v            i  v    i i    v  ?   i  v  i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_117576430_   5346 AAACTGGACCTCTTTCTGGCACCATATACAAAAATTAACTCAAGATTGAT 5395
                           ii      i  vi  vi                        i  v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_117576430_   5396 TAAAGACTTAAAGGTAAAACCTGAAAGTATAAAAACCCTGAAAGACAACC 5445
                         i ?    i    v    i v  i   v       vi i ii    v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_117576430_   5446 TAGGC---AATACCACTCTG-GACTTGGGAATGGGCAATGATTTCATGGC 5491
                             ?---   ----  ii -   i v  iv i       i    v i -
  L1M4_orf2#LINE/    548 TAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG- 592

  chr2_117576430_   5492 ACA-GACACCAAAAGCAACCAA---ACAAAAGCAAAAACTGACAAATGGG 5537
                          i -             --   ---       v     iv  i    v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_117576430_   5538 ATCTAGATCTAG-TTAACAGCTTCTGTACTGCAAGAGAAACTATCAACAG 5586
                          -  vv   v i-    v i   i   i  v   ii  v        v i
  L1M4_orf2#LINE/    641 A-CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_117576430_   5587 AGTATACAGACAA---A-AGAATAAAAGAAAA-ATTTAGCAAACTATGCA 5631
                            iv v      --- -     iii      -    -     ii  ii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATA 738

  chr2_117576430_   5632 TCTAACAAAGGTCTAATATCCAGCATCCATAAGGAACTTAAACAAATTTA 5681
                            i i  i  v  vi       v  vi    i     ivv    v ---
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--- 785

  chr2_117576430_   5682 CAAAAAATTAAAAATCCAAACAATCTTATTAAAAAGTGAGGAAAGGACT 5730
                            v  --      vv    i  i iv   ?    i  i v      i 
  L1M4_orf2#LINE/    786 CAATAA--TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

Transitions / transversions = 1.69 (135 / 80)
Gap_init rate = 0.03 (23 / 832), avg. gap size = 2.48 (57 / 23)  

 253 25.30 1.20 0.00  chr2_117576430_117582993.rev     6009  6091 (473)    L1M4_orf2#LINE/L1      825   908 (0)  

  chr2_117576430_   6009 AAAGAACATGAACAAACACTTTT-CAAAGAAGACATACATGTGGCCAGCA 6057
                             i iv    i i   i  i -         i     vi      ii 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_117576430_   6058 AGCATATTTTATAAACCTCAATATCACTGATAAT 6091
                             i  vvv vi vv     i    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1)  


3128 27.31 0.55 0.55  chr2_117629341_117635607     4868  5775 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117629341_   4868 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4917
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117629341_   4918 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4967
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117629341_   4968 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5014
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_117629341_   5015 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5064
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_117629341_   5065 GAACAAAGCTGGAGGCATCACACCACCTGACTTCAAACTATACTACAAGG 5114
                                 i      vv      iv  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_117629341_   5115 CTACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGAC 5164
                                  i   i    ii    i    i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_117629341_   5165 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5212
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_117629341_   5213 TATCTGATCTTTGACAAACCTGAGAAAGACAAGCAATGGGGAAAGGATTC 5262
                         i vi    i  i     ivv  vv  iiv  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_117629341_   5263 CCTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5312
                         i  v  i  i   i          v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_117629341_   5313 TGAAACTGGATCCGTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5362
                             ii    i  v v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_117629341_   5363 ATTAAAGACTTAAAGGTTAGACCTAAAACCATAAAAACCCTACAAGAAAA 5412
                           i ?    i    v  v   v       i      vi i  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_117629341_   5413 CCTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5462
                          v    ?v v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_117629341_   5463 AAACACCAACAGCAATGGGAACAAAAGACAAAATTGACAAATGGGATCTA 5512
                         vi       v    vvi v         v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_117629341_   5513 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5562
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_117629341_   5563 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5612
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_117629341_   5613 ATGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5662
                          v  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_117629341_   5663 AAAACAAACAACCCCATCAAACAGTGGGCAAAGGACATGAACAGACACTT 5712
                           i     i     v  i?  v i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_117629341_   5713 CTCAATAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGTTCAT 5762
                            v v      i  vi viii     v  i          i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_117629341_   5763 CGTCACTGGCCAT 5775
                          i   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 275 29.11 0.00 0.00  chr2_117697972_117699887.rev      425   503 (1413)    L1M4_orf2#LINE/L1        1    79 (829)  

  chr2_117697972_    425 TAGAAATGTATCACATGATCATGGATGGGGAGAATTAGTATCGTAAAAAT 474
                          i    vi    v    v        v  i   v   i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117697972_    475 GACCATATTGCCCAAGGAAATCTATGAAT 503
                          i v   i v     ivvi     iii  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGAT 79

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.00 (0 / 0)  

2571 26.69 1.85 2.94  chr2_117697972_117699887.rev      507  1424 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117697972_    507 TAGAAACATATCTCATGATCATGGATGGGGAGAATTAATATTGTAAAAAT 556
                          i    v     i    v        v  i   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117697972_    557 GACCATATTGCCCAAAGAAATCTACAGATTCAATGCAATTTCCATAAAAG 606
                          i v   i v      vvi              i     ii i  v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117697972_    607 TAGCAGTATTATTTTTCACAGAACTAGAAAAAAAAAATCCTAATATTCTT 656
                          vv   ivviv     ii     v v  v  ivvi -      v    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_117697972_    657 GTGGAACCAAAAAAGAACCCAAACAGCCAAAGCAATCCTAATGAAAG--G 704
                         i     viiv  ii  v  vi  i       i     i i -i    -- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAG 198

  chr2_117697972_    705 AATCAAATCTGGAGGCATCACATTACCACACTTCAA---TTATAACGCAA 751
                           -    vi      vv     i v  vv i     ---   iv  --  
  L1M4_orf2#LINE/    199 AA-CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC--AA 245

  chr2_117697972_    752 GGCTATAGTTAACAAAACAGCATGGTACTGGTTTTAAAATAGGTACTTAG 801
                         i    i   v v   i    ii         iv v ii    ii iv   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_117697972_    802 ACCAATGGAACAGAATAAAGAACTCAGAAATAAAGTCAAATACTCATAAC 851
                          i        i     vi   iii          vi  v i i i  iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_117697972_    852 CAACTCATCTTTGACAAAGCATACAAAAAC-ATAAATTGGGGAAAGGATA 900
                            i v  i  i     i -i i v  i  -  vv v         i   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_117697972_    901 CTCTATTCAAGAAACAGTGCTGGGAAAACTGGCAAACCACATGTAGAACA 950
                         v   v     v   ii         v      vv ?       i i  v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_117697972_    951 ATGAAACTGG-TCCCTCTCTCTCACCTTATACAAAAATCAACTCAACATG 999
                              ii   -i    vi   v    v           i       v   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_117697972_   1000 -ATCAAAGACTTAAATATAAGACCTGAAACCATAAAAATTCTAGAAGACA 1048
                         -    ?    i     i     v  i    i      v ii       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_117697972_   1049 ATGTTGGAAAAACTCTTCTAGACATCAGCCCTAAGCGAAGAATTAATGAC 1098
                          ii v  ?iv  v     vv   v ii vi-  i  i v iv  vv iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGA 593

  chr2_117697972_   1099 TAAGACCCCAAAAGCAAATACAACAAAAACAAAAAGAAATAAATGAGACC 1148
                           v   v         v vi        iv     v i      vi   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_117697972_   1149 TAATTAAACTAAAAAGCTTCTGAGCACAGCAAAATAAATAAGCGGCAGAG 1198
                          v  i   v v    i   i  v  vi--    iv v iv v iiv i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAG 691

  chr2_117697972_   1199 TAAATAGGTAACCCACAGAATGGAAGAAAATATTTTCAATCTATGTATCC 1248
                          i  v  ii              i           v   vii  i    i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_117697972_   1249 GACAAATAACTAGCATCCAGAATCTACAAGGAACTCAAACAAATCAC--- 1295
                           i  ivi   v i         v  i  i      vv    v   v---
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_117697972_   1296 -----AGCCTCCCCCTTCTGCCCCCTAAAATAATTCCATCAAAATGTGGA 1340
                         -----  v ------------------      ii v  i?   vi   i
  L1M4_orf2#LINE/    792 TAAAAAGAC------------------AAATAACCCAATTWAAAAATGGG 823

  chr2_117697972_   1341 CAAGGGATATAAATAGATGTTTCTCAAAAGAAAATATATAAATGGCCAAG 1390
                            i    v i      ii      v      i     i          v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_117697972_   1391 AAGCATACAAAAAAATG-TAAGCATCACTAATTAT 1424
                              i ii    i   - v i     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (135 / 106)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.93 (44 / 15)  


3285 26.33 0.77 0.33  chr2_117706979_117713989     1309  2212 (4799)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117706979_   1309 TGGAAAAACATTCCATGCTCATGGATAAGAAGAATCAACATTGTGAAAAT 1358
                               i i  i     i        vi     v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117706979_   1359 GGCCATATTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGA 1408
                            v   i v      v i  i  i        i  v     i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117706979_   1409 TACCTTAG--ACTTTCTTCACAGAATTGAAAAAACT-ACTTTAAATTTCA 1455
                          v  --  --i i  i  ii     v vi v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCC--AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_117706979_   1456 TATGGAACCAAAAAAGAGCCTGCATAGCCAAAACCGTCCTAAGCAA-AAG 1504
                                viiv  ii  v  v v           vi  i i iv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_117706979_   1505 AACAATGCTGGAGGCATTATGCTACCTGACTTCAAACTATACTACAAGGC 1554
                              v i      vv i ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_117706979_   1555 TGCAGAAATCAAAACAGTAGGGTACTGGTACCAAAACAGATATATAGACC 1604
                          i   v      i     iv        i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_117706979_   1605 AATGGAACAGAACAGAGATCTCAGAAATAATGTCACACATCTACAATCAT 1654
                                i    iv    vii         vvi  i    i  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_117706979_   1655 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGGAAGGATTCCCT 1704
                         i    i  i     ivv  v   i v  vv        i   i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_117706979_   1705 ATTTAATAAATGGTGCTGGGAAAACTAGCTAGCCATATGCAGAAAGCTGA 1754
                         v  i  i              v    i v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_117706979_   1755 AACTGGATCCCTTCCTGACACCTTATAAAAAAATTAACTCAAGATGGATT 1804
                          ii    i    v   v     v    v              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_117706979_   1805 AAAGACTCAAAAGTAAGACCTAAAATCATAAAAACCCTAGAAGAAAACCT 1854
                          ?    ii   v      v      ii      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_117706979_   1855 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 1903
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_117706979_   1904 ACACTAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTAAT 1953
                             i       vvi     i    vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_117706979_   1954 TAAACTAAAGAGCTTCTGCACAGCAAAAGTAACTATCATCAGAGTGAATA 2003
                         i   v v  i i   i  ii vv    i vv       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_117706979_   2004 GGCAACCTACAGAATGGGAGAAAATTTTTGCACTCTATCTATCTGACAAA 2053
                          i     i                 v      vvii  v       i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_117706979_   2054 GAACTAGTATCCAGAATCTACAAA--ACTTAAACAAATTTACAAGAAAGA 2101
                          i   v           v  i   --   ivv    v iv i  v   i 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_117706979_   2102 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 2151
                         i     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_117706979_   2152 CAAAAGAAGACATTTATGTGGCCAACAATCATATGAATAAAAGCTCATCA 2201
                          v        i  vi vi       i  v  i     v i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_117706979_   2202 TCACTGGTCAT 2212
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (135 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

2545 29.03 0.99 1.53  chr2_117706979_117713989     5614  6526 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117706979_   5614 TGAAAAACCATTCCATGCTTACAGATTGGAAGAATTA-TATCATTAAAAT 5662
                           i   ivi  i     i i ii          v   -   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117706979_   5663 GGCCATACTGCTCAAAGAAATCTACAGATTCAATGCTATTCCTATCAAAC 5712
                            v     v i    vvi              i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117706979_   5713 TACCAATATCATTTTTTCAAAAAATTGTAAAAAACT-ATTTTAA--TTTA 5759
                          v   iivv v      vv i      -- v  i  -  ii   --  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_117706979_   5760 TATGGAACCAAAAAGGAGCCAAATATTAGTCAAAGCATTTCTAAGCAAAA 5809
                                viiv  i   v   i -  -  i    i  v ii i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGA-AT-AGCCAAAACAATCTTGAAAAAGA 196

  chr2_117706979_   5810 AGAACAAAGCAAGAAGCATCAAAAGAACCAGCTTCAAAA--TACTCTTAA 5857
                                  ivi  i vv   v vvvv   ii       --    vi-  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC-AA 245

  chr2_117706979_   5858 AGCTACAGTAATCAAAAGAGTATAGTACTAGTACAAAGACAGACACAAAT 5907
                                        i v   i i     i i i  i  i     i -- 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA--T 293

  chr2_117706979_   5908 ACTGCCCAATGGAACAGAATAGAGAACACAGAAACTAAGCAACATACCTA 5957
                          -- vi        i     v    iiv      iv  v v i i ii  
  L1M4_orf2#LINE/    294 A--GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_117706979_   5958 CAACTATCTGATCTTCAACAATGTCAACAAAAATAAGCAATGTGAAAAGA 6007
                         iiiii vi    i   i    v viiv   i vi vv     v i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_117706979_   6008 ACTCCCTATTCAATAAATGGTACTAGGGTCATTAGGTAGCCATATGCAGA 6057
                          ivvi  v     i       i  i  iiv i i i  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_117706979_   6058 AGAATGAAAGTGGACCCCTGACATT-TACTATATACAAAAATTAACTCGA 6106
                                 iv         -  v i-i  i                  i 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_117706979_   6107 GATGTATTAAAGATTTAAATTTCAGGCCCCAAACCATAAACATCTTAGAG 6156
                         i   v  i ?   ii     v v  iv iv    i     vv       i
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_117706979_   6157 GAAAACGTAGGAATTACTTTTCTGGACATCAGCCCTGGCAAAGAATTTAT 6206
                               i    ?i v v i   vv   v ii viiv     v iv  iv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_117706979_   6207 GACTAAGTCCTCAAAA--ACAATTTCAACTAAAACAAAAATTGACAAGTG 6254
                         iiv  v v vi     --    v--    v   iv      v  i  i v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAG--CAACAAAAGAAAAAATAGATAAATT 638

  chr2_117706979_   6255 GTACCCAATGAAACTAAAGAGCTTTTGCACAGCAAAGGAAACTATCAGTA 6304
                          v  iiv  v   v v  i i      ii vv       v       iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_117706979_   6305 GACTAAACAGGCAACCTACAGAATGAGAAAAAAATATTTGCAAACTACGC 6354
                         i v i  v  i     i        i  i    -          ii iii
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATAT 737

  chr2_117706979_   6355 ATTGGACAAAGTTCAAATATCCAGAATCTATAAGGAACTTGAACACGTCA 6404
                           iv  i  i vv vvi          v     i     ivv   vv   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_117706979_   6405 ACAAACAATAAGCAAATAACCTCGTTAAAAAGTGGGCAAAGAACATGAAC 6454
                          i  vv  v ii         ivi  ?    i         i iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_117706979_   6455 AGACATTTCTCAAAAAAGGATATACTAGCAGTCAACAAGCATATGAAAAA 6504
                                    v   i i       v iii i   i     i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_117706979_   6505 AATGTTCCATACTAATTATTAA 6526
                          -  i  v i ii ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (156 / 105)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.44 (23 / 16)  


3110 26.66 0.88 0.44  chr2_117775872_117780032     2766  3669 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117775872_   2766 TGAAAATATATTCCGTCCTCACGGATTGAAGGAATCAATATCATTAAAAT 2815
                           i   v    i  i vi   i      i i  v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117775872_   2816 GTCCATACTACCCAAAGCAATCTACAGATGCAATGAAATCCCTCTCAGAA 2865
                          v v     v      vii          v   i v       v   i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117775872_   2866 TACCAGTAACATTCTTCACAAAAATAAAAATAAAAAATTCTAAAATTTAT 2915
                          v    ivi v  i  ii  i    vi v - ivvi  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr2_117775872_   2916 ATGGTACTACAAAAGACCCAGAATAGCCAAAGTTATCCAAAGCAACAAGA 2965
                             v v i   ii                 iiv   ivi iv  v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_117775872_   2966 ACAAAATGGAAGGAATCACATTACCTGACTTCTAATTATACTACAGAGTT 3015
                              i v i    v     i v  ii i   v  viv       i  i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_117775872_   3016 ACAGTAACCAAAGCAGCATGATACTGGCATAAAAACAGATACACATACCA 3065
                                i   ii   ii  i           ii i   i i i v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_117775872_   3066 ATGGAACAGAATAGAGAACCAAGAAACAAATCCACACTCCTACAGTAAAC 3115
                               i     v    ii v     i   i   i  vii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_117775872_   3116 TCATTTTTAACAAAGTTGCCAATAATATACACTGGGGCAAGT-CAGTCTC 3164
                          v     ii    i v      v vi  v  v     v   v-i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_117775872_   3165 TTCAATAAATGATGCTAGAAAAGCTGAATAGCCACATGAAGAAAGATAAA 3214
                              i     i    i i v i   i   ?       v i  ii  i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_117775872_   3215 ATTAGACTC-TATCTCTTGCCATTTACAAAAATCAA-TCAAAGTAGATTA 3262
                         i  i   i -  i   vii    v         i  -     i i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_117775872_   3263 AGGACTTAAATCTAATACCTCAAACTATGAAACTACTACAATAAAACAT- 3311
                         ?i   i     v   v v  v       i     vi  v  v       -
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_117775872_   3312 TGAGAAAATGCTCCACGACATCAGCCTGGCCAAAGATTTCTTGAGTAATA 3361
                         v ? v    -  i ii   v ii vi i v   v i      iii  vv 
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_117775872_   3362 CCCCACAAGCACAGGAAATCAAAGAAAAAAATGGACAAATTGGA--TCAC 3409
                          v   v       i v  -    ii       i  i        --   i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAA-CAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_117775872_   3410 TACAAGTTAAAAA--TCTGCACAGCAGAGGAAACAATGAACAAAGAGCAC 3457
                         i -  i       -- i  ii vv  i    v  v  v  v    v v v
  L1M4_orf2#LINE/    648 CA-AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_117775872_   3458 AGACAACTAACAGAATGGGAGAAAATATCTGCAAACTATCCATCTGACAA 3507
                                iv                   i      ii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_117775872_   3508 GGGATTAATAATCAAAATACATAAGGAGCTTAAGCAACTGATTAGGAAAA 3557
                             i vi  vi  i    i    i  i  ivvi     v v  iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_117775872_   3558 TATCTAATAATCCAATTTAAGAATGGGTAAATTGTTTGAATAGACATTTT 3607
                         viv v     i      ?  i      i   vvi               i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_117775872_   3608 TCAAAAGAAGACATACAAATGGCAAATGAACATATGAAAAGTTGGTCAAC 3657
                           v        i           v   i i  i        v  v     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_117775872_   3658 ATCATTAAGAAA 3669
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (146 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.20 (12 / 10)  


 359 27.50 5.83 0.00  chr2_117816978_117819112      501   620 (1515)    L1M4_orf2#LINE/L1      177   303 (605)  

  chr2_117816978_    501 CAAAACAATTTTTAAA--GGAAAATAAGGCTGAAGGATGCACACTACCTG 548
                                  i  v   -- i i  i  i i  i    iv      v  ii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_117816978_    549 ATTGTAACAGTTACTATGGTGGTGCATTAAACAGGACAGCGTGGAATTGG 598
                            vi  v v      iiiv v i  v   v  i     i    v i   
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_117816978_    599 CATGGGG-TA--TATATTGAT--ATGG 620
                            ii  -  --i    v   --    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGG 303

Transitions / transversions = 1.75 (21 / 12)
Gap_init rate = 0.03 (4 / 127), avg. gap size = 1.75 (7 / 4)  

1209 26.80 3.92 5.72  chr2_117816978_117819112     1024  1635 (500)    L1M4_orf2#LINE/L1      286   886 (22)  

  chr2_117816978_   1024 AGACATATACGAAGGCTGGTGGTATAGAATACATAGACCAGATACCCAAA 1073
                                  ---- iiiii   v       vv v  v     v i--   
  L1M4_orf2#LINE/    286 AGACATATA----GATCAATGGAATAGAATTGAGAGTCCAGAAAT--AAA 329

  chr2_117816978_   1074 TGTAGACATAAACAGAAAGTCAATTGATTTTTGACAAAGGTTCTAAAGTA 1123
                         ivi v    vv ii ----            i     i   v i  iiiv
  L1M4_orf2#LINE/    330 CCCATACATTTATGG----TCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_117816978_   1124 ATCCAATGGGAAAAGATTAGTATATTCATTTAAATG-TGCTAG-ACAGTT 1171
                           i       i     v    v v    vi-     -    i -   ii 
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAAC-AAATGGTGCTGGGACAACT 424

  chr2_117816978_   1172 GGACATATATAAGAAAAAACAAAACAAAAC-AAACCACCTCCTCAAAAAA 1220
                            i ?vi i v v    i---  ii  ii-ii   ----   -------
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAG---AATGAAGTTGGACC----CCT------- 460

  chr2_117816978_   1221 CACTTTATGCCACATATAAAAATTAATTCAAAATGTACCATAGACCTAAA 1270
                         -  i i ii   i   i         i        v i  ?         
  L1M4_orf2#LINE/    461 -ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_117816978_   1271 GTTAAGAGCTGAAATTTTAAAAATCAAAAAAAAAGAAACCACAGGAGAAA 1320
                         vv        i   i v     v  vv i  ---    v  i   ? v  
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAA---GAAAACATAGGNGTAA 556

  chr2_117816978_   1321 AATCCT-GTGACCCTGCATTGCACAAAAATTCCTTA----TCACAGGAAG 1365
                          -  i -      i  vi  ivi   vii  i    ---- v   vv  -
  L1M4_orf2#LINE/    557 A-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA- 604

  chr2_117816978_   1366 AAGCA--AACCATAAAAAGACAACT-GATAAATTGAACTTTCTTTATAAT 1412
                              -- i v i    ii v  v -         i    - v i v   
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATCAAAAT 653

  chr2_117816978_   1413 GGCGAACTTTTCT-CTTCAAAAAAGACTGCCAAAAATGTGAAATT----T 1457
                         vivi       v -       ii v   ii   i  v      vv----i
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_117816978_   1458 CTACAAGTTTGGAGAATATATTTACATAACGTATGTCTGATAAAA-ATTT 1506
                          i   iiv v      v      i  v v i   i        ii- i  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_117816978_   1507 GTATCCGGCATATGCAAAGATATCTTAAAACT------TAAGAAGAAATA 1550
                               i v    ii     vv     v    ------   i    v v 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_117816978_   1551 TAATTTGATTTAAAAATAGTGAGCAAAATATTT-AATAGATACTTCAACA 1599
                            iiii   ?      i ---     iv    -      i i   vv  
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGG---GCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_117816978_   1600 AAAATGTCAAAGGAACGGCAAGTGAACACATTAAAA 1635
                           i v vi v vi  i   v i i i     v    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.42 (94 / 66)
Gap_init rate = 0.04 (24 / 601), avg. gap size = 2.46 (59 / 24)  


3345 19.41 1.07 1.34  chr2_117830848_117832586.rev      501  1247 (492)    L1M4_orf2#LINE/L1      164   908 (0)  

  chr2_117830848_    501 GACTCTGAATAGCCGAAACAACTTTGATAAAGAA---CAAAGCTGAAAGA 547
                            i v        i      ii    v      ---     i  i i  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_117830848_    548 CTCATACTTCCTGACTTTAAGACTTACTACAAAGCTACAGTAATCAGAAA 597
                             i      ii i  i  i                         ii v
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_117830848_    598 AGCATGGTACTGGCATAAAGATAGACAAGTAAACCAAAGAAACCAAATAG 647
                           ii              i        vi  i i   v i  ivi   v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_117830848_    648 AGAGCCTAGAAATTAACCCTAACATGTATGGTCAAATAATTTGTGGCAAC 697
                             i i      v     vv    v         v i    vi i   v
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_117830848_    698 GGTGCTAACACAATTTAATGGGGAAAAAACAGTCTTTTCAAAAAATGATG 747
                              i  v  v   i          i  i           v     i  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_117830848_    748 CTGAGAAAACTGGATATCCACATGCAAAATAATTATTGAATTCAGCCCTT 797
                            i  v         ?            v   v --- i  vii   i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGA---AGTTGGACCCCT 460

  chr2_117830848_    798 ACTTAATAGCATATTCAAAAATTAACTCAAAATC-ATCA-AGACCTAAAT 845
                           i v i v     v                  v-    -          
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_117830848_    846 GTAAGATCTAAAACAATAAAACTATTAAAAGTAAA---AAGGGTAAATAT 892
                               v       v        v   i   v   --- i ?      -i
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-C 559

  chr2_117830848_    893 TTCATGACATTGGATTTGACAATGATTTCTTAGATATCACACTAAAGGCA 942
                            i    v    i  v i     i            v    i   i   
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_117830848_    943 GAGGCAACAAAAGAAAACATAGACAACTTGGACTTCACAAAAATGTAGAA 992
                         v i              v     i  v          iv     vv i  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_117830848_    993 GTTTTGTGCTTCAAAAGACACTAACAACAGAGTAAAATGGTGAATCACAG 1042
                         v              i       v   v i   i   v iii vi     
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_117830848_   1043 AGTGGGAGAAAATATTTGGAAGTCATAAATCTGATAAGGGATTAATATTC 1092
                          i                v  i     v             i vi   i 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_117830848_   1093 AGAGTATACTGAGTACTCCTAAGACAACAACAACAACAACAACAAACCAG 1142
                            i    ivi  v    i  ---    v-   i  i  -  - i  v i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTA---CAACT-CAATAATAA-AA-AGACAAA 803

  chr2_117830848_   1143 TAACTCTATCCATAAATGGGTAAAAGACTTCAATAGATATTTCTGTAAAG 1192
                             i v  i? v       i   i  i  v      i      vi    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_117830848_   1193 AAGATAAGCAAATGTTCAATAAGCTCATGAAAACATGCTCAACATTACTA 1242
                               vi      vi        v        v           i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_117830848_   1243 AACCT 1247
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.45 (84 / 58)
Gap_init rate = 0.01 (10 / 745), avg. gap size = 1.80 (18 / 10)  


1700 27.75 2.33 4.96  chr2_117849730_117852182.rev      742  1386 (1067)    L1M4_orf2#LINE/L1        1   628 (280)  

  chr2_117849730_    742 TGGAAAGATATATTGTGTTCATGGACTGGAAGATGCAATATATTTAAGAT 791
                                    viii          i       ivi     vv       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117849730_    792 GTCAGT--TCCCAAAAATTGATCTACGGATTCAATGCAATCTCAATTAAA 839
                          v  i --    v   -         i       i      i v  i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_117849730_    840 ATTCCATAAGAATTTTTTATAGATATCCATAGGCTAGTCTCAAATTTTAC 889
                           i   vvv vv      ii   v  iv i i   ii  ii   v  i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_117849730_    890 ATGAAAAGGGCAAGAG-CCCAGTATAGCCAAAATAACTTTGAAA--TAAG 936
                            i   v -    i -     v          i  ii      --v   
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_117849730_    937 AATAAAGTTAGAGGACTTACATTGCCTAATTTTAATACATACTATGAATC 986
                           i      i       i   i v  i     i  v  v     ii  --
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-- 246

  chr2_117849730_    987 TTAACTATAATATAACCTAACTATAACAATCAAGGCAGGGTAG-ACTGGA 1035
                         -------------------i   i ii       i   v  i -     v
  L1M4_orf2#LINE/    247 -------------------GCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_117849730_   1036 GAAAAGATGCATAGATAGATAAATGAGACAGAGCAGAAAGTTCAGAAATA 1085
                         iv  i   iv i v      v    ii i   iiv  i   i        
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_117849730_   1086 GGCGTGCAGAAATATGGCCAATTGATTTTTGACAATAGTGTGAAGGAAAT 1135
                         ii viii v vv     i           i     vi   iv   ivv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_117849730_   1136 TCAGTGGAGGAAGAACAAATTTTTATAATAAATTGTGGTGGAAAAATTTA 1185
                            i   i i     i ivi    -i  i    v   v   i v  i vi
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGG 426

  chr2_117849730_   1186 ACGTTTGCATATATATGTATG-----GAACTTCAATCTATATTCTTTATG 1230
                          ii?iii   ii v v v   ----- i  ii v i  -i iv iv   i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT-CACACCATATA 475

  chr2_117849730_   1231 TGAAAA---ATTCAAAATGAATTATAAGTCTAATTTTAAAATATGAAACT 1277
                         ii    --- i        i  i ? iii    v v   i vv i     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_117849730_   1278 ATAAAGATTTTA-AATAAAACATAAGAGAAAAAATTTTATGCCCTTAGGT 1326
                              iv i   -  v        i ? v   v-i  ii  v    i   
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGT 574

  chr2_117849730_   1327 TAGGCAAAGAGATCTTAGATAAGAACAACACACCAAAACTATGATCTATA 1376
                                v ivv         v  ------        vi ii v v i 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGA------CACCAAAAGCACAAGCAACA 618

  chr2_117849730_   1377 AAAAAGAAAA 1386
                            i i    
  L1M4_orf2#LINE/    619 AAAGAAAAAA 628

Transitions / transversions = 1.79 (113 / 63)
Gap_init rate = 0.02 (14 / 628), avg. gap size = 3.36 (47 / 14)  

 843 23.93 9.64 0.36  chr2_117849730_117852182.rev     1682  1961 (492)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr2_117849730_   1682 AAAAAAAAAAGAAA-AAGAAAGAAAACTGATAAATTTGACTTCTTCAAAA 1730
                             iv v   v  -  i i i    iv        v      v      
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_117849730_   1731 TAAAATATTTTTGCTTTGCAAAAATCATTTGTTAAGAGAATGAGAAGACA 1780
                          v   v i     ivi v    iiv  i -i i    i i   i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGAAAGTGAAAAGACA 701

  chr2_117849730_   1781 AGTCACAGACTGGCAGAAAATATCTGCATATCATACATCTGACAA----- 1825
                          vi      v   v         i    v      i      i  -----
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_117849730_   1826 -------------------AGAACTCTCAAAACATAATGATACGGAAACA 1856
                         -------------------        i v   vi   i   vii i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_117849730_   1857 AACAACCCAAT-AGAAAATGGGCAGAAGATCTGAGCAAACACTTTACCAA 1905
                           i        -?i          i i   i   ii i   i  iv    
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_117849730_   1906 AGAAGGTATATGGACAGAAAATAAGCACATTAAAAGATG-TCAATCTCAT 1954
                              i    iii ii vv           v        -    iv   ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_117849730_   1955 TAGTCAT 1961
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.87 (43 / 23)
Gap_init rate = 0.02 (5 / 306), avg. gap size = 5.60 (28 / 5)  


2235 25.84 7.78 3.83  chr2_117857241_117861926.rev     3003  3838 (848)    L1M4_orf2#LINE/L1        1   869 (39)  

  chr2_117857241_   3003 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATTAGTATTGGGAAAAT 3052
                               i i  i     i               v   i     vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117857241_   3053 GACAATACT------AT------ACGGA--CATAGAAAATTCTA---AAA 3085
                          i       ------  ------  i  --  vv v  vii   ---   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117857241_   3086 T------------TTGTATAGAA--------------CCAAAAA-----A 3104
                          ------------  v ii    --------------  v    ----- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_117857241_   3105 AAAAAAAAAAAAAGACCTTCAATAGCCAAAACAATCCTGAGAAAAAAGAA 3154
                         vii   viv  ii    ivv                i   i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_117857241_   3155 CAAAGCTGGAGGCATCATACTACTTGACTTCATAATATATTCTAAGAGC- 3203
                              i      vv   i   v iii i    v  iv  i vi  -   -
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA-AGCT 249

  chr2_117857241_   3204 ATAGCAACCA--------TGGTGTTGGTATAAAAACAAACACATAGACCA 3245
                          i  i  i  --------    ii   i    ii i i   i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_117857241_   3246 ATGGAATGGAATAGAGAACCCGGAAATAAAACTATGTATTTA----CACC 3291
                                i    v    ii  i        v i  ii     ----  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_117857241_   3292 TGATTTCTGACAAAGGATCCAGTAACATTTACTGGTAAAAGGACATCCTT 3341
                               ii     i  vv   iv v    i v   vi    i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_117857241_   3342 TTTTAATAAACAGTGCTAGAAATATTGGATATCCATATGCAGAATAATAA 3391
                           i-  i   ii     i i vv i      ?   i     i  v   i 
  L1M4_orf2#LINE/    400 TTC-AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_117857241_   3392 AACTAGATCACTATCTCTCACCATATACAAAAATCAACTCAGAATAGATT 3441
                          ii i  i v   i   v                i      i   i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_117857241_   3442 AAAGACTTAAACATAAACCCTGAAACTA---GATTACTAGAAGAAAACGT 3488
                          ?    i    ii   ivv  i      ---i i vi           i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_117857241_   3489 AGGGAAAACACTTTAGGACATTGGTCTTGGCAAAGATTTTACACGGCTGA 3538
                            ?iv  vv   iiv   v    vi v     v i   ivi -- v iv
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA--GATAT 596

  chr2_117857241_   3539 GACCTCCAAAACACTGGCAACAAAACCAAAAATAGACAAATGGGACTATA 3588
                            vi v   i   vi         vv         i    v     vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_117857241_   3589 TTAAA-TTAAAAAGCTTCTACACAGCCAATGAAACAATAAACACAGTGAG 3637
                          i   -       -   i iii vv v  v  v  v  v  v v     i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_117857241_   3638 AAGACAGCCTGTTGAATTATAGAAAATATTTGCAAATTATCCATCTAACA 3687
                               i  iiiv    viv                 i  vi    i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_117857241_   3688 AGGGACTAACATCCAGAATATATGAGCAACGCAAACAACTCAACAGCAAA 3737
                                vii             i iv   v vv         i ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_117857241_   3738 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAATAATCCCATTAAAAC 3787
                           i v   ---------------------------   i  v   ?   v
  L1M4_orf2#LINE/    796 AAGACAAA---------------------------TAACCCAATTWAAAA 818

  chr2_117857241_   3788 ATGGTCAAGGGACATGAATAGAAATTTCTCAAAAGAAGACATGCAGGGGG 3837
                             v   i   iv        v       v        i  i  iiv  
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_117857241_   3838 C 3838
                          
  L1M4_orf2#LINE/    869 C 869

Transitions / transversions = 1.59 (130 / 82)
Gap_init rate = 0.02 (17 / 869), avg. gap size = 5.71 (97 / 17)  

 249 18.64 0.00 0.00  chr2_117857241_117861926.rev     4136  4194 (492)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr2_117857241_   4136 AAAGAAGATATGCAAATAGCCAAGAGATATATAAAAAAATACTTAACATC 4185
                                    i     i     v iii i  i    i  i  i      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_117857241_   4186 AATAAGCAT 4194
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 10.00 (10 / 1)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


2782 27.26 2.79 1.34  chr2_117887843_117890831.rev     1604  2498 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117887843_   1604 TGAAAACACACCTCATGCTCGTGGATGGGTATAATCAATATTGTGAAAAT 1653
                           i   v i i i    i  i     v  v v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117887843_   1654 GACCATACTGTCAAAAGCAATCTGCAAATTTAATGCAATTCCTATCAAAA 1703
                          i v     vi v   vii    i  i   i  i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117887843_   1704 TGCCACCATCATTCTTCACAGAACTAGAAAAGATAATCCTAAAATTCATA 1753
                          v   v vv v  i  ii     v v  v   v i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_117887843_   1754 TGGAA-----------CCA----AGCCAAAACAAGACTAAGCAAAAAGAA 1788
                              -----------   ----           vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_117887843_   1789 CAAATCTGAAGGCATCACATTACCTGACTTCAAACTATACTATAAGGTCA 1838
                             vi  i   vv     i v  ii i      viv     i  i ii 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_117887843_   1839 TAGTCATCAAAACAGCATGGTTCTGGTAAAAAAAAAAAAAAAAAAAAGGC 1888
                         i   v     i    ii    v    i v  ii v i ----------- 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA-----------C 289

  chr2_117887843_   1889 ACATAGACCAATGTAACAGAACAGAGAATGCAGAAATAAAGCCAGATACT 1938
                          i     i     v  i    iv    i v          v   v i i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_117887843_   1939 TACAGCCAACTGATCTTTGACAAAGCAAACAAAAACATAAAGTGTGGAAA 1988
                           ii i   i    i  i     i vviv   i v   vv i  v     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_117887843_   1989 GGACACCCTATTCAACAAATGGTGCTGGGATAATTGGCAGGCCACATGTA 2038
                          i i vi  v                    i  i   vvi?       i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_117887843_   2039 GTAAAATGAAACTAAGTCCTCATCTCTCACCTTATATAAAAATCAACTCA 2088
                         iv i      ii iiii  ii i   v    v    i      i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_117887843_   2089 AGATGGATAAAGGACTTAAATCTAAGACCTAAAGTCATAAAATTTCTAGA 2138
                          i      v ?i   i     v     v     iii      i ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_117887843_   2139 AGATAATGTCAGAAAGACCCTTCTGGATATTGGCTTAGGCAAAGAGCTTG 2188
                            v  ii vi ?ivi vi    vv  iv    v        v ivi iv
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_117887843_   2189 TGACCAAGAACCCAAAAGCAAATGCAACAAAAATGATAATAAATAGGTGG 2238
                          iivi v  vv         v v         ivi v    i   ii v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_117887843_   2239 GACTT-----AAACTAAAAAGTTTCTGCACAGCAAAAGAAAGAATCAGCA 2283
                              -----   i      v   -  ii vv    i  v vv    iv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGA 688

  chr2_117887843_   2284 GAGTAAACAGACAACCTACAGAGTGGGAGAAAATCTTCACAATCTAAACA 2333
                         i   i  v        i     i           v  ii   vii v i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_117887843_   2334 TCTGAAAAATAACTAATATCCAGAATCTACAAGGAACTCAAACAAATTAA 2383
                              v  ivi   vi          v  i  i      vv    v i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_117887843_   2384 TGAGAAAAA-ACAAACAATCCTATCACAAAATGGGCTAAGGACACGAGTA 2432
                          i v     -     i  i  v  i?v         v     ivi  i  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_117887843_   2433 GATGATTCTCAAAAGAAGATATACAAATGGCCA-CAA--ACGTGAAAAAA 2479
                           iiv     v                      -i  --  i      i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_117887843_   2480 TGCTCAGCAT-AGCTAATGA 2498
                               i   - ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 4.11 (37 / 9)  


3270 26.76 0.44 0.44  chr2_117931339_117938771.rev     4214  5121 (2312)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_117931339_   4214 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4263
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117931339_   4264 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4313
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117931339_   4314 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4361
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_117931339_   4362 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4411
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_117931339_   4412 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4461
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_117931339_   4462 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4511
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_117931339_   4512 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCGGCATATCTACAACT 4559
                                i    i--    i  --        vv vii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_117931339_   4560 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4609
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_117931339_   4610 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4659
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_117931339_   4660 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4709
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_117931339_   4710 TTAAAGAGTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4759
                          i ?   vi    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_117931339_   4760 CTAGGCATTACCATTCAGGACATAGGCATAGGCAAGGACTTCATGTCTAA 4809
                         v    ?i v viv   iv   v v  vv       v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_117931339_   4810 AACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTCA 4859
                         i            vvi     v    vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_117931339_   4860 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4909
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_117931339_   4910 AGGCAACCTACAAAATGGAAGAAAATTTTTGCCACCTACTCATCTGACAA 4959
                           i     i   i     i       v     v vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_117931339_   4960 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5009
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_117931339_   5010 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5059
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_117931339_   5060 TCAAAAGAACACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5109
                           v      v i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_117931339_   5110 ATCACTGGCCAT 5121
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

2809 28.20 1.13 0.57  chr2_117931339_117938771.rev     6051  6933 (500)    L1M4_orf2#LINE/L1        1   888 (20)  

  chr2_117931339_   6051 TGGAAACACACCCCATGCTCATGGATGGGTAGAACCAGTATTGTGAAAAG 6100
                               v i i      i        v  v   vii i      v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_117931339_   6101 GAACATACTGTCAAAAATAATCTATAAATTCACTGCAGTTCCCATCAAAA 6150
                          ivv     vi v   v i     i i     vi   i i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_117931339_   6151 TACCACCATTATTCTTCACAGAACTGAAAAAAAAAATCCTAAAATTTATA 6200
                          v   v vviv  i  ii     v vi v  ivvi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_117931339_   6201 TGGAACCAAAAAAGAGCCCGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 6250
                              viiv  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_117931339_   6251 CAAACCCGGAGCTATCACATTACCTGACTTCAAACTGTACTATAAGGCCA 6300
                             vii    vvv     i v  ii i      viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_117931339_   6301 TAGTCACCAAAACAGCATGGTATTGGTATAAAACTAGGCACATAGACCAA 6350
                         i   v i   i    ii     i   i    iiv   i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_117931339_   6351 TGGAACAGATTAGAGAACCCAGAAATTAACCCAAATACCTACAGCCGACT 6400
                              i   v v    ii        v      v i ii  ii i i i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_117931339_   6401 TATTTTTGACAAAGCAAACAAAAACATAAAGTGTGGAAAGGACAATCTTT 6450
                         v     i     i vviv   i v   vv i  v      i i i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_117931339_   6451 TTAACAAATGGTGCTGGGATAATTGGCAAGCAACATGTAGAAAAACGAAA 6500
                          i                 i  i   vv ? v     i i  i  i   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_117931339_   6501 CTGGATTCTCATCTCTTACCTTATACAAAAATCAACTCAAGACAGATCAA 6550
                         i    ii ii i   vi   v           i       i ii     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_117931339_   6551 AGACTTAAATGTGAGATCTGAAACTACATCAATTCT-AGAGGAAGACAAC 6599
                             i       i   v  i      i -v  i   -   i   i   --
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACA-- 547

  chr2_117931339_   6600 CTAGGAAAAAACACTTCTGGATATTGACCTGGGCAAAGATTGACTAAA-- 6647
                         -    ?iv   i-    vv  iv   ivi i     v i  vvi  i --
  L1M4_orf2#LINE/    548 -TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_117931339_   6648 --ACCCCAAAAGCAAATGCAACAAAAACAAAATTAAATAAATGAGATATA 6695
                         --  v         v v         iv    v  i      vi  iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_117931339_   6696 ATTAAACTAAAAAGCTTCTGTAGAACAAAAGAAATAATCATCTCAGTAAA 6745
                           i   v v    i   i   ivvv    i  v iv    vvvv   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_117931339_   6746 AAGACAACTCACAGACTGGGAGTAAATATTTGCAAAGTATGCATCTGACA 6795
                                 i      v      v             vi  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_117931339_   6796 AAGGACTAATAACCAGAATCTACAAGGAACTCAAACAAGTTTGCAATAAA 6845
                          i     vi  v       v  i  i      vv    v ivii      
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_117931339_   6846 A-GACAAGTAATCCCACCAAAAAGTGGGAAAATTACATTAATAGATACTT 6894
                          -     i   i  v ii?    i    v   vv iv v      i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_117931339_   6895 CTC-AAAAAA---ATACAAATGGCCAATAAACTCATGAAAAAA 6933
                            -   i  ---                 i v        i 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (8 / 888), avg. gap size = 1.88 (15 / 8)  


2754 27.09 1.08 2.82  chr2_117946383_117952328     4532  5454 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_117946383_   4532 GGAAAAAAAAATCATGCTCATGGAT----AGAATCAATATCGTGAAAGTG 4577
                              i v vvi    i        ----   v i     i  v  ii  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_117946383_   4578 GCCATACTGCCTAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGCT 4627
                           v     v  i   v i  i  i        i  v  i  i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_117946383_   4628 ATCATTGACTTTCTTCACAGAACTAGAAAAAACT-ATTTTAAATTTCATA 4676
                         vi  vivi i  i  ii     v v  v  i-  -  ii    v      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr2_117946383_   4677 TGGAACCTAAAAGGAGCACGTATAGCCAAGACAAGCCTAAGCAAAAAGAA 4726
                              vivv  i   v vv v        i    v i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_117946383_   4727 CAAACTTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGGCTA 4776
                             v       vv   ii  v  ii i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_117946383_   4777 CAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGGTATATAGAACAA 4826
                               v   i    ii         i iv ii i  ii       v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_117946383_   4827 TGGAACAGAGCAGAGGCCTCAGAAATAACACCACACATATACAACCATCT 4876
                              i   iiv   ivii         vv   i    v  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_117946383_   4877 GTTCTTCCACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTGT 4926
                          v i   v    ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_117946383_   4927 TTAATAAATGGTGCTCAGAAAACTGGCTAGCCATATGCAGAAAACTGGCT 4976
                          i  i          ---------  -------------  v      v 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCT---------GG-------------GACAACTGGAT 428

  chr2_117946383_   4977 AGCCATATGCAGAAAACTGAAACTGGACCCCTTCCTCTACACCTCATACA 5026
                          ?   i     i  i v    ii         v    -     vi     
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC-ACACCATATACA 477

  chr2_117946383_   5027 AAAATTAACTCAAGATGAATGAAATACTTAAACATAGAACCTAAAACCAT 5076
                                      i   i  v ? v  i    ii  ii v       i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_117946383_   5077 GAAAAGCCTAGAAGACAACCTAGGCA-ATACCATTCAGGACATAGGCATG 5125
                         i   vv i       v   v    ?i- v i -   iv   v v  vv i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTA 576

  chr2_117946383_   5126 GGCAAAGACTTCATGACTAAAACACAAAAACCATG-GCAACAAAAGCCAA 5174
                              v ii   v iiv  vi    v    v  ii-          vv  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_117946383_   5175 AATTGGCAAATGGGCTCTAATTAAACTAAAGAGCTTCTGCTCAGCAAAAG 5224
                            v ii    v  vii v  i   v v  i i   i  iv vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_117946383_   5225 AAAGTATCATGAGAGTGAATAGGCAACCTACAGAAATGGGAGAAAATTTT 5274
                          v v     v  i      v  i     i      -           v  
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAA-TGGGAGAAAATATT 725

  chr2_117946383_   5275 TGCAATCTATCCATCTGACAAAGGTCTAGTATCCAGAATCTACAAGGAAC 5324
                              vii  vi      i  i  v  v           v  i  i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_117946383_   5325 TTAAACATATTTACAAGAAAAGAACAAACAATCCCAT-AAAAAGTGGGCA 5373
                          ivv   vv iv i  v    ii     i  i  v  -?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_117946383_   5374 AAGGATATGAACAGATGCTTCTCAAAAGAAGACATTTATGCAGCCAACAA 5423
                               v    i   iii     v        i  vi viii     i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_117946383_   5424 --ACATGAAAAACAGCTCATCATCACTGGTCAT 5454
                         --         ivv     v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (135 / 111)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 3.00 (36 / 12)  


1215 26.37 1.61 0.00  chr2_117960800_117962863.rev      537   847 (1217)    L1M4_orf2#LINE/L1      140   455 (453)  

  chr2_117960800_    537 TAAAATTCCTATGGACCCACAAAAGACCCTGAATAGCCAAAGTAATCTTG 586
                                 v      vvii   ii     v           ii       
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_117960800_    587 GGAAAGAGGAACAAATCTGGAATCATCAAACTTTTGGATTTCAAACAGTA 636
                         ii     i       vi    ivvv   v    iivi        vvv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_117960800_    637 TTACAAAGCTACAGTAATAAAAATAGTACGGTAACAGCATGAAAACAGAC 686
                         i                 v  i i   ii    vii    i ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_117960800_    687 ATGCAAACCAATGGAATAGAATAAAGAGCCCATATATAAACCTATAGATA 736
                           ii i i              vi    i   v v       i   v  v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_117960800_    737 TATGGTCAACT-----TTGGCAAGAGCACAAAGAATACACAATGGGAAAA 781
                                  i ----- i i    i ii v    vi iv       i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_117960800_    782 GAAAAATCTTTTTAATAAATGGTATAGAGAAAGCTGAATATTCACATGCA 831
                            v i      i  i       iiv i  v i   i   ?i        
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_117960800_    832 GAAAAATAAAATTTGA 847
                         i  i   i  i  v  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGA 455

Transitions / transversions = 2.00 (54 / 27)
Gap_init rate = 0.00 (1 / 316), avg. gap size = 5.00 (5 / 1)  

1632 21.41 3.00 4.07  chr2_117960800_117962863.rev     1101  1567 (497)    L1M4_orf2#LINE/L1      405   866 (42)  

  chr2_117960800_   1101 CAAA--GTGCTGGGATTACAGGCATTGAGCCACCACGCCCA--------G 1140
                             --         iv  v  -  -- ?    - i  vv -------- 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGG-AT--AKCCAC-ATGCAAAAGAATGAAG 450

  chr2_117960800_   1141 CCAGATTCTTGTCTTATACCATATTCAAAAATTAACTCATAATTAATTAA 1190
                         iii  ii i ii  i i       v              v   vi  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_117960800_   1191 AGACTTAGATGTAAGACCTAAAACTATAGAACTCCTAGAAGAAAACATAA 1240
                             i  i        v           i     i              i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_117960800_   1241 GAAAAAAACCTCCTTGACATTAGTCTTGGCAATGAGTT-TTGGCTCTGCC 1289
                          ?iv   -i  i v    v  i vi v       iv  -  i v v  v 
  L1M4_orf2#LINE/    551 GNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_117960800_   1290 ACCAAAAGCACAGAAGATACAAGCAAAAATAAATGTGTGGGACTACATCA 1339
                                     iivi i v   v       i  ivi v     v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_117960800_   1340 AACTAAAAGAATTTTGCACAGCAAAGAAAACAATCAGCAAAATAAAAAGA 1389
                           v v   i v     ii vv     i v  v    iv   i i      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_117960800_   1390 CAACCTAGGGAATGAGGGAATATATTTGCAAACCATATATCTGATGAGGG 1439
                              i vi     i i   v           i            i    
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_117960800_   1440 -CTTATTAGCTAAAACATATAAAGAGTGC--ACAAACTCAATAGTAAAAC 1486
                         -   i - v i i  i         iiv --    -       i     -
  L1M4_orf2#LINE/    750 ACTTGT-ATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAAA- 796

  chr2_117960800_   1487 AAAACCAAAAACCACAAATAACCTAATTAAAAAATGGGCAAAGGAACTGA 1536
                         -------- i  ---        i    ?                vi   
  L1M4_orf2#LINE/    797 --------AGAC---AAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_117960800_   1537 AGAGACATTTTCCCAAAGAAGATATACATAT 1567
                          v        ii                v  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAAT 866

Transitions / transversions = 1.53 (58 / 38)
Gap_init rate = 0.03 (13 / 462), avg. gap size = 2.54 (33 / 13)  


2097 25.46 1.23 2.47  chr2_118039448_118041078      484  1131 (500)    L1M4_orf2#LINE/L1      232   871 (37)  

  chr2_118039448_    484 AAAACATACCGAAATGTAAGCCTGCAGTAACCACAACAGCATGGTACTGG 533
                              v   ----- ii  iv  i      i  vi    ii         
  L1M4_orf2#LINE/    232 AAAACTTAC-----TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_118039448_    534 TACCAAAACAGAGATACAGACCAATGGAACAGAC---AGAGGCCTCAGAA 580
                         i iv ii i   v   i   i        i   v---    v  --    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAA 324

  chr2_118039448_    581 ATAACACCACACATCTACAACTATCTGATCTTTGACACACCTGACAAAAA 630
                             vv   i    i  iiiii vi    i  i    vivv  v   i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_118039448_    631 CAAGCATTGGGGAAAGGAT--TCCATATTTAATAAATGGTGTTGGGAAAA 678
                           vv  v         i  --  -- v  i  i        i     v  
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAA 422

  chr2_118039448_    679 CTGGCTAGCCATATGCAGAAAACTGAAACTGGACCTCTTCCTTACACCTT 728
                             v  ?   i     i  i v    ii      i  v   i     v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_118039448_    729 ACACAAAAATTAACTTAAGATAGATTAAAGACTTAAACATAAGACCTAAA 778
                          i             i  i  i   i ?    i    ii     v     
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_118039448_    779 ACCATAAAAGCCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAG 827
                           i      vi i           v    ?i- v i -   iv   v v 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chr2_118039448_    828 GCATGGGCAAGGACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAA 877
                          vv i     v ii   v iiv  vi            vvi         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_118039448_    878 GCCAAAATAGACAAATGGGATCTAATTAAACTTAAAGAGCTTCTACATGG 927
                          vv        i    v   ii v  i   v     i -   i iiiivv
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTT 670

  chr2_118039448_    928 CAAAAGAAACTACCAACAGAGTGAACAGACAACCTACAGAATGGGAAAAA 977
                             i  v    i   v i      v        i           i   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_118039448_    978 AAAAAATTGCAATCTACTCATCTGACAAAGGGCTAATATCCAGAATCTAC 1027
                          v v--      vii ivi      i  i  i  vi          v  i
  L1M4_orf2#LINE/    721 ATAT--TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_118039448_   1028 AAAGAACTTAAGCAAATTTACAAGGAAAAAAAAACAAGCAACCCTATCAA 1077
                                 ivvi   v ---   vi v     i    ii     v  i? 
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACT---CAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_118039448_   1078 AAAGTGGGGGAAGGATATGAACAGACACTTCTCCAAAGAAGACATCTA-- 1125
                            i    vi      v    i     i              i  vi --
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_118039448_   1126 TGGCCA 1131
                               
  L1M4_orf2#LINE/    866 TGGCCA 871

Transitions / transversions = 1.52 (97 / 64)
Gap_init rate = 0.02 (11 / 640), avg. gap size = 2.18 (24 / 11)  

 274 22.81 0.00 0.00  chr2_118039448_118041078     1124  1180 (451)  C L1M4_orf2#LINE/L1   (851)    57     1 *

C chr2_118039448_   1180 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 1131
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_118039448_   1130 GGCCATA 1124
                            v   
  L1M4_orf2#LINE/     51 GGCAATA 57

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.00 (0 / 0)  


1470 27.53 0.78 0.26  chr2_118058122_118061617        5   389 (3107)    L1M4_orf2#LINE/L1      130   516 (392)  

  chr2_118058122_      5 AAACT-ACTTTAAAGTTCATATGGAACCAAAAGAGAGCCTGCATTGCCAA 53
                           i  - iii    i           viiv   i  v  v v  v     
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_118058122_     54 GACAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCATGCTATCTGACT 103
                         i      i i ivv i          i      vv   ii  vi ii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_118058122_    104 TCAGACTATACTACAAGGCTACAGTCACCAAAACAGCATAGTACTGGTAC 153
                            i viv        i        v i   i    ii i       i i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_118058122_    154 CAAAACAGA--TATAGACCAATGGAACAGAAGAGAGGATTCAGAAATAGC 201
                         v ii i   --      i        i    vv   ii i        iv
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_118058122_    202 ACCACACATCTATAACCATCTGATCTTTGACAAACCTGACAAAAACAAGA 251
                         v   i    i   iii  vi    i  i     ivv  v   i v  vvv
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_118058122_    252 AATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGGAAACTGGCTA 301
                                    i  vvi  v  i  i             iv      v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_118058122_    302 GCCATATGTATAATGCTGAAACTGGATCCCTTCCTTATACCTTATACAAA 351
                         ?   i   i v  viv    ii    i    v   i i   v        
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_118058122_    352 AAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGA 389
                           -    i    i      i ?    i       v   
  L1M4_orf2#LINE/    480 AA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

Transitions / transversions = 1.74 (66 / 38)
Gap_init rate = 0.01 (3 / 387), avg. gap size = 1.33 (4 / 3)  

 445 23.81 1.90 0.00  chr2_118058122_118061617     1847  1951 (1545)    L1M4_orf2#LINE/L1        3   109 (799)  

  chr2_118058122_   1847 GAAATGTATCCCATGTTTATGGATTAGAAAAATCAAAATCTTGAAAATGT 1896
                             vi           i       i   i v i  v  iv v  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_118058122_   1897 CCATACTTCCCAAAGCAAACCACAG--TCAATGCAATTGCTATCAAAATT 1944
                          v     i      vii v i    --    i     iv          i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_118058122_   1945 CCAGGTG 1951
                             v  
  L1M4_orf2#LINE/    103 CCAGCTG 109

Transitions / transversions = 1.27 (14 / 11)
Gap_init rate = 0.01 (1 / 107), avg. gap size = 2.00 (2 / 1)  

2241 25.90 4.98 3.86  chr2_118058122_118061617     2202  3004 (492)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr2_118058122_   2202 AAGATTCCAA-TGTCATTTTTCACAGAAA---ACAAAATATATTCTGAAA 2247
                           i  i   i-  i -     ii      ---    iv i-  i  i   
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAA 144

  chr2_118058122_   2248 TTTATATGAAACAAAAAAAAACCCTGAATAACCAAA-----CTTAACAAA 2292
                           i     i  vviv  iii    v     i     -----   i v   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_118058122_   2293 -AATAACAAAAATGGAGGCATCACA-TCCTTAGTTTTCAAGTCATATTAT 2340
                         -  v      iv      vv     - i ii i   -   iv v  i  i
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT-CAAAACTTACTAC 243

  chr2_118058122_   2341 AAAGTGAATATAATCAAAACATCATTGTACTGGCATTTAAAAAGACACAT 2390
                             iv vvi       i   vii v          vvii v     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_118058122_   2391 AGACCAACAGAACAAGATAGAAATCCCAGAAATAAACACATGCATTTGTA 2440
                            i   ii   i ii  v  i vi            v   i     i i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_118058122_   2441 GTCAATTCACTTTTTATAAAATTGCCGAGAACACACAATGGGACAAGGAC 2490
                                v i   iv i  iiv    i   v  iv       iv   i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_118058122_   2491 GGTCTCTTCAATAAACAACGTTGGGAAAACTGAATATCCACATGCAGAAG 2540
                         i    i     i   iiii i     v     i   ?         i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_118058122_   2541 AATAATATTGGACATTTGTCTCACATTATATTTTAAAA--AACTCAAAAG 2588
                            i vi      vii ii      ii    viv    --         v
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_118058122_   2589 AGATTAAAAACTTAAATATAAAACCTGAAACTA-------CTAGAAAAAA 2631
                         i   i ? i  i     i   i v  i      -------  vii  i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_118058122_   2632 AACATAGGGGAAAAT-TTCACAACAGTAGTTTGGGCAACAACTTTTTAAA 2680
                                 ? v    -   iii  vv i v  i     iiii  i   i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_118058122_   2681 CATAATTCCAAAACCACAAGCAACAAAAGTAAAAATAGACAAATAGGATG 2730
                         i  i iv      v               v         i    v   iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_118058122_   2731 ACATCAAACTAAAAAGCATCTACATAGCAGAGGAAACAATCAACAACTCC 2780
                         v       v v    i v i iiiivv  i    v  v     v  ----
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA---- 689

  chr2_118058122_   2781 CATTCTTCCATTTCTTCACTTTGTTGTGAAGCAATAACCCACAGAATGGG 2830
                         ----------------- -------     ivi i               
  L1M4_orf2#LINE/    690 -----------------A-------GTGAAAAGACAACCCACAGAATGGG 715

  chr2_118058122_   2831 AGAA------TGGAA-------------TAAGGAATTAATAACCAATGTA 2861
                             ------  v  -------------     i i vi  v   ivi  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_118058122_   2862 TATAAGAAACTTATGTAACTCAATAGCAAGAAAACAAATAACCCAAGTAA 2911
                              ii    iv ii         ii  i  i             v ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_118058122_   2912 AAAATGGACAACCGACCTAAACAGATATTTCTCACAAGAAGACATACAAA 2961
                                i   vv  ii i  i   i       vv       i       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_118058122_   2962 TGGCCAGGAGGTACATGAAAACATACTCAGCATCACTAATCAT 3004
                               iv i i         v  i    i     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (136 / 68)
Gap_init rate = 0.02 (15 / 812), avg. gap size = 4.73 (71 / 15)  


1557 27.23 0.67 0.67  chr2_118063501_118067668.rev        1   448 (3720)    L1M4_orf2#LINE/L1      183   630 (278)  

  chr2_118063501_      1 AATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCA 50
                             i i ivv i          i      vv       v  ii i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_118063501_     51 AACTATACTACAAGCCTACAGTAACCAAAACAGCATGGTACTGGTACCAA 100
                           viv        iv         i   i    ii         i iv i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_118063501_    101 AACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAACATCA 148
                         i i   v                i    i--    i  --     i vvv
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAAC 330

  chr2_118063501_    149 CCGCATATCTACAACTATCTGATCTTTGAGAAACCTGAGAAAAACAAGCA 198
                           ii i  i  iiiii vi    i  i  v  ivv  vv  i v  vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_118063501_    199 ATGGGGAAAGGATTCCCTACTTAATAAATGGTGCTGGGAAAACTGGCTAG 248
                                   i  vvi  vi i  i              v      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_118063501_    249 CCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAA 298
                            i   i i  iiv    ii    i    v   i     v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_118063501_    299 ATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCCTAAA 348
                              i    i      i ?    i    i  v   v       iv    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_118063501_    349 AACCGTAGAAGAAAACCTAGGCATTA-TCATTCAGGACATAGGCATGGGC 397
                          vi v           v    ?i v -  -   iv   v v  vv i   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGC 579

  chr2_118063501_    398 AAGGACTTCATGTCTGAAACACCAAAAGCAATGGCAACAAAAGCCAAAAC 447
                           v ii   v ivv ivi            vvi          vv    i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_118063501_    448 A 448
                          
  L1M4_orf2#LINE/    630 A 630

Transitions / transversions = 1.33 (68 / 51)
Gap_init rate = 0.01 (4 / 448), avg. gap size = 1.50 (6 / 4)  

2627 26.67 4.09 1.02  chr2_118063501_118067668.rev     2796  3676 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118063501_   2796 TAGGAACACATCCCATGCTCATGGAAGGGTAGAATCAATATTGTGAAAAT 2845
                          i i  v i        i       vv  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118063501_   2846 GACCATGCTGCCAAAAGCAATCTGCAA--TCAATGTGATTCCCATCAAAA 2893
                          i v  i  v  v   vii    i  i--    i ii  i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118063501_   2894 TACCACCATAATTCTTCACAGAACTAGAAAATACAGTTCTAAAATTCATA 2943
                          v   v vvvv  i  ii     v v  v  vviii i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_118063501_   2944 TGGAACCATAAAAGAGCCTGCATAGCCAAAGCAAAGCTAAGCAAAAAGAA 2993
                              viii  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_118063501_   2994 CAAATCTGGAGGCATCATATTACCTAACTTCAAACTTTACTATAAGGCCA 3043
                             vi      vv   i i v  i  i      vi      i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_118063501_   3044 TAGTCACCAAAATAACATGA-ACTGGCACA------------TAGACCAA 3080
                         i   v i   i i iii  i-       i ------------    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_118063501_   3081 GAGAATAAAAATAGAGAACCCAGAAATAAACTGCAGTAC--TTATAGCCA 3128
                         vi     i  v -    ii            i-  -   --    i i  
  L1M4_orf2#LINE/    301 TGGAATAGAATT-GAGAGTCCAGAAATAAACC-CA-TACATTTATGGTCA 347

  chr2_118063501_   3129 ACTAATCTTTGATAAAGCAAACAAAAACATAAAGTGGG-AAAGAACATCC 3177
                          i i  i  i  i  i vviv   i v   vv i    -      i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_118063501_   3178 TATTCAACAAATGGTGC-GGGATAATCAGCAAGCCAAACGTAGAAGAATG 3226
                          v               -    i  iii vv ?   v i i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_118063501_   3227 AAACTGGATTCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGAT 3276
                           ii    ii ii i   v    v           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_118063501_   3277 CAAAGAGTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACA 3326
                           ?   vi     v     v  i    i      v ii       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_118063501_   3327 T---CGTAAAAGCCCTTGTAGACATTTGCTTATGCAAAGACTTCAT-GAC 3372
                          ---?     --i i i  -   v  v v   v    v ii   v -  i
  L1M4_orf2#LINE/    548 TAGGNGTAAA--TCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_118063501_   3373 CAATAAC-CCAAAAGAAAATGCAACAAAAACAATGATAAATAGGTGGGAC 3421
                         --  i  -       v v v         iv  vi   i   ii v    
  L1M4_orf2#LINE/    595 --ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_118063501_   3422 TTAATTAAACGAAAAAGTTTCTGCACAGCAAGGGAAACAATCAGCAGAGT 3471
                           v  i   vvv    ii  i  ii vv   i   v  v    iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_118063501_   3472 AGACAGATAATCCACAGAGTCGGAGAAAAT-TTT--------CATATCCA 3512
                         ii v   i  i       i v         -   --------i     ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_118063501_   3513 GCAAAGGACTAATATCCAGAATCCGTGAGGAACTCAAACAAATTAGCAAT 3562
                         ii  i     vi          vii i i      vv    v i ii   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_118063501_   3563 AAAAAAACAAACAATCACA--TCAAAAATGA-CTAAGGACATGAATAGAA 3609
                              i     i  i -  -- ?       i- v     iv        v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_118063501_   3610 AATTCTCAGAAGAAGTTATACAAATGGCCAACAAACATATGGAAAAATGC 3659
                          v     vi      v               i  i  i   i   i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_118063501_   3660 TCAACATCACTAATGAT 3676
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (143 / 88)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.25 (45 / 20)  


3228 25.63 0.88 0.99  chr2_118098899_118102834     2536  3444 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118098899_   2536 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAGT 2585
                              ii i  i     i      i v      v i     i  v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118098899_   2586 GGCCATACTGCCCAAGGTAATTTACAGTTTCAATGCCATCCCCATCAAGA 2635
                            v     v     iv i  i     v     i  v     i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118098899_   2636 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2682
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_118098899_   2683 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 2732
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_118098899_   2733 GAACAAAGCTGGAGCCATCACACTACCTGACTTCAAACTATACTACAAGC 2782
                                 i     vvv       v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_118098899_   2783 CTACAGTAACCAAAACAGCATGGTACT--CATACCAAAACAGAGATAATA 2830
                                  i   i    ii       --    -- ii i   v   -  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATA-TA 294

  chr2_118098899_   2831 GATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTAC 2878
                                    i    i--    i  --        vv  ii i  i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chr2_118098899_   2879 AACTATCTGATATTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGA 2928
                         iiii vi    v  i     ivv  vv  i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_118098899_   2929 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 2978
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_118098899_   2979 AGCTGAAACTGGATCCCTTCCTTACAACTTATACAAAAATCAATTCAAGA 3028
                         iiv    ii    i    v   i   v v           i  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_118098899_   3029 TGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGA 3078
                              i ?    i    i  v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_118098899_   3079 AAACCTAGGCA-ATACCATTCAGGGCATAGGCATGGGCAAGGACTTCATG 3127
                             v    ?i- v i -   iv i v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_118098899_   3128 TCTAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGA 3177
                         vv  vi            vvi           v     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_118098899_   3178 TCTCATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 3227
                         ii    i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_118098899_   3228 TGAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCT 3277
                             v  i     i   i             v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_118098899_   3278 GACAAAGAGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 3327
                           i  i ii  vi          v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_118098899_   3328 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGAC 3377
                         v     i     i     v  i?    i     i i   iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_118098899_   3378 ACTTCTCAAAAGAAGACATTTATGTAGCCAAAAAACACATGAAAAAATGC 3427
                          i     v        i  vi vi i     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_118098899_   3428 TCATCATCACTGGCCAT 3444
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


3350 25.88 0.55 0.55  chr2_118122491_118128766     4877  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118122491_   4877 TGGAAGAACATTCCATGCTAATGGATAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i v      v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118122491_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118122491_   4977 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5023
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_118122491_   5024 ATATGGAACCAAAAGAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5073
                                 viiv   i  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_118122491_   5074 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGC 5123
                                 i      vv       v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_118122491_   5124 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGAT 5173
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_118122491_   5174 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAAC 5221
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_118122491_   5222 CATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5271
                           vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_118122491_   5272 CCTATTTAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5321
                         i  v  i ii              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_118122491_   5322 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5371
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_118122491_   5372 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5421
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_118122491_   5422 CCTAGGTATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5471
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_118122491_   5472 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTC 5521
                         vi            vvi          vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_118122491_   5522 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5571
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_118122491_   5572 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5621
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_118122491_   5622 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAGGAAA 5671
                          i  i  vi          v  i  v      vv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_118122491_   5672 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5721
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_118122491_   5722 CTCAAAAGAAGACATTTATGCAGCCAAGAAACACATGAAAAAATGCTCAT 5771
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_118122491_   5772 CATCACTGGCCAT 5784
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3153 27.97 0.44 0.44  chr2_118251485_118257877     4994  5901 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118251485_   4994 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5043
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118251485_   5044 GGCCATATTGCCCAAGGTAATTTATAGATACAATGCCATCCCCATCAAGC 5093
                            v   i v     iv i  i  i    v   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118251485_   5094 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5141
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_118251485_   5142 TATGGAACCAAAAAAGAGCCTACATCACCAAGTCAATCCTAAGCCAAAAG 5191
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_118251485_   5192 GACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAAGGC 5241
                         i      i      vv    i  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_118251485_   5242 TACAGTAAGCAAAACAGCATGGTACTAGTACCAAAACAGAGATATAGATC 5291
                                 v   i    ii       i i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_118251485_   5292 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5339
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_118251485_   5340 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCCATGGGGAAAGGATACC 5389
                          vi    i  i     ivv  vv  i v  vv v          i   vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_118251485_   5390 CTATTTAATAAATGGTGCCTGGAAAACCAGCTAGCCATATGTAGAAAGCT 5439
                           v  i  i         iv   v   ii v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_118251485_   5440 GAAACTGGATTCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5489
                            ii    ii   v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_118251485_   5490 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5539
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_118251485_   5540 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5589
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_118251485_   5590 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTCA 5639
                         i            vvi           v     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_118251485_   5640 TTAAACTAAAGAGCTTCTGCACAGCAGAAGAAACTACCATCAGAGTGAAC 5689
                          i   v v  i i   i  ii vv  i i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_118251485_   5690 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCTTCTGACAA 5739
                           i     i   i             v       vii iviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_118251485_   5740 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5789
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_118251485_   5790 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5839
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_118251485_   5840 TCAAAGGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5889
                           v  i     i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_118251485_   5890 ATCACTGGCCAT 5901
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (153 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3232 27.50 0.33 0.44  chr2_118280719_118283368     1250  2158 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118280719_   1250 TGGAAGAACATTCCATGCTCTTGGGTAGGAAGAATCAATATCGTGAAAAT 1299
                              ii i  i     i  v   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118280719_   1300 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1349
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118280719_   1350 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1397
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_118280719_   1398 TATGGAACCAAAAAAAGAGTCC-GCATTGCCAAGTCAATCCTAAGCCAAA 1446
                                -- viv  i iii  - v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_118280719_   1447 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 1496
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_118280719_   1497 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 1546
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_118280719_   1547 TCAATGGAACAGAACAGAGCCCCCAGAAATAACGCCGCATATCTACAACT 1596
                                  i    iv   vvi          vv  ii i  i  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_118280719_   1597 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1646
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_118280719_   1647 CTATTTAATAAATGGTGCCTGGAAAACCAGCTAGTCATATGTAGAAAGCT 1696
                           v  i  i         iv   v   ii v  ?i  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_118280719_   1697 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1746
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_118280719_   1747 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1796
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_118280719_   1797 CTAGGCATTACCATTCAGGATATAGGCATGGGCAAGGACTTCATGTCTAA 1846
                         v    ?i v viv   iv  iv v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_118280719_   1847 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 1896
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_118280719_   1897 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1946
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_118280719_   1947 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 1996
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_118280719_   1997 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTGCAAGAAAA 2046
                         i  i  vi          v  i  v      vv    v ivii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_118280719_   2047 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 2096
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_118280719_   2097 TCAAAGGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 2146
                           v  i     i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_118280719_   2147 ATCACTGGCCAT 2158
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


4111 17.23 2.85 3.18  chr2_118315737_118318539.rev     1412  2322 (481)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118315737_   1412 TGAAAAGACATGCCATATTCATACATTGAAAGACAACATTA-TATTATTA 1460
                           i     i  v    i     iv    i     ----   -    i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC----TTAATATTGTTA 46

  chr2_118315737_   1461 AGGTATCATTACTTCTCAAAGCAATCTATAGATTTAATGCAATCCATATC 1510
                           i iv  v    i i    vii     i     i  i       v    
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_118315737_   1511 AAAATCACAACAGCCTTTTTTTTTCAGAAATAGA-AAACTCAGTCCTAAA 1559
                               v  i v         v--       v  -  i  v -       
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTG--CAGAAATTGACAAGCTGA-TCCTAAA 143

  chr2_118315737_   1560 ATTTATATGGAATCTCAAGA-ACCTGGAATAGCCAAAACAATTTTGAGAA 1608
                            i        viv    i-   ii                i    i  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_118315737_   1609 A--AGAATAAAGTTGAATGACTCATAATTCACAGGATCAAAACTGACTGC 1656
                          --    i       i v      i v   v  ivv        v   i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_118315737_   1657 AAAGCTACAGTAATCAAAAAAGTGTGGTTCTGGCATCAGGATACACATAT 1706
                                          i v        v       v      v      
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_118315737_   1707 ACACCAATGGAACAGAATTGAGAGTTCATAAATAAATTCATATATCAATG 1756
                          v i        i            i  v       ii    i  iv   
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_118315737_   1757 GTCAATTGATTTTTGA--ACAGTGCCAAGACCATTCTATGGGAAAAGGAA 1804
                                      i  -- vi               v     i    -  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AA 392

  chr2_118315737_   1805 CACTCTCTTCAACAAATTGTTCTGGAACA--------TCCGCATGTAAAA 1846
                         i v   i          v  v    i   --------?  i    i    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_118315737_   1847 GAAAGATGTTGAATCCTTATCTCATACCTAATGCAAACATTAACTCAAAA 1896
                            v  v    i i  i  i    i   vv  i    v            
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_118315737_   1897 TCTATCAAAGACTGAAAGTTAAGAGCTAAAAATATAAAACTCTTAGGAGA 1946
                          vv    ?    iv   vv            v              i   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_118315737_   1947 CAACATAGAGGAAACTCTTCAGAGCAGTAGCTTGTGCACTGGTTTCTTAA 1996
                         v       i? v  v     ivii vv i v  iv   v          i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_118315737_   1997 CTATGACACCGAAGGCACAAGCAACAAAAGAAAACAATGGATAAATTGGG 2046
                         v         i  i                    -   i          i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGA 641

  chr2_118315737_   2047 CTT-GTCAAAATTTGAAACTT--GTGCATCAAAGGACAAGTTGACAAGTT 2093
                            -i        vi      --    v          ------------
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA------------ 679

  chr2_118315737_   2094 GTGCACTACTAAGAAAGTGAA--GACAACCCACAGAATGGGAGAAAATAT 2141
                         -----   ii           --                           
  L1M4_orf2#LINE/    680 -----CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_118315737_   2142 TTGCAAATTATATATTTGATAAGAGTCTAGTATCCAACATATGTGAAGAA 2191
                                 i      i       i v  v       iv    i i     
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_118315737_   2192 CTTTTTCAACTCAGCAATT------TAAATTTCCCAATTTTTAAAAGGGC 2235
                           i  v       ii   v------i    vv       ?vv   v    
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_118315737_   2236 AAAGGATCTGAAAAGATATTTCTCTAAAGAAGATATACAAATGGCCAACA 2285
                                i    v   i       i                       i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_118315737_   2286 AACACCTAAAAAGATGCTAAGTGATATGAGTCATTAG 2322
                          i   v i          v --- i  v ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCA---ACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (85 / 68)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.24 (55 / 17)  


3384 24.38 1.19 2.82  chr2_118340428_118344977.rev     3136  4058 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118340428_   3136 TGGAAAGGTATTCCATGTTCATTGATTGGAAGAATAAATCTTATTAAAAT 3185
                                i   i          v          v v   v  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118340428_   3186 GTTCACACTACCTAAAGCAATCTACAGATTCAATGCAAGCCCTATGAAAA 3235
                          viv i   v  i   vii              i    v      v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118340428_   3236 TACCAATAACATTCTTCACAGAAATAGAAAAAACAATCCTAAAATTTATA 3285
                          v   iivi v  i  ii       v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_118340428_   3286 TAAAAACACAAAAGACCCAGAGTAGCCTAAGCTGTCCTAAGCAAAAACAA 3335
                          ii   ii   ii        i     v  i vi  i i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_118340428_   3336 CAAAACTGGAGGAATTATATTACCGGACTTCAAACTGTGCTACAAAGCTA 3385
                             ii       v i i i v  vi i      viv i           
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_118340428_   3386 TAGTAACCCAAACAGCATGGAACTGTCATAAA-ACAGACACAAAGACCAA 3434
                         i     i v i    ii   v    v     i- i     i v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_118340428_   3435 TAGAACAAAATAGAGAACCCAGAAAAAAATCCATACATCTACAGCAAACT 3484
                          i   i i   v    ii       v   i        i  ii iv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_118340428_   3485 CATTTTTGACAAAGGTTCAAAGAACATACACTGGGGAAAGGACAGTCTCT 3534
                         v     i     i   v v    v   v  v         i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_118340428_   3535 TCAATAAATGGTGCTAGGAAAACTGAATATCTGTATGCAGAAGAATGAAA 3584
                             i          i   v     i   ? iii     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_118340428_   3585 CTAGACACCTGCTTCTTGTCACATGTAAAAATCAATTAAACATGGATTAA 3634
                         i i   v   i i  viii  i  ii      i  i v  v      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_118340428_   3635 AGACTTAAATCTAAGACCTCAAACTATGAAACTCCTACAAGAAAATATTG 3684
                             i     v     v  v       i      i  v       i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_118340428_   3685 GGGAAGCTCTTTAGAACACTGGATTTGGCAAAGGTTTCTTAAGTAATACC 3734
                          ? v iv    iivi  vi   i  v     v         ii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_118340428_   3735 CCACAAGTACAGGCAACCAAAGCAAAAATGGACAAGTAGGATCACATCAA 3784
                            v   i   i     v    v      i  i  i v   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_118340428_   3785 G-TTAAAAAGATTCTGCACAGCAAAGGAAACAATCAACAAAG-----AGA 3828
                         i-       v-  i  ii vv       v  v     v    -----   
  L1M4_orf2#LINE/    651 AATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_118340428_   3829 CAACCCATAGAATGGAAGAAAATATTTGTGAACCATCCATCTGTCAAGGG 3878
                                i       i            ii  i   vi     vi     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_118340428_   3879 ATTAATAACCAGAATATATAAGGGATTCAATAACCAGAATATATAAGGGA 3928
                          i vi  v             i i i  ----------- -  i  ----
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTC-----------T-TACAA---- 783

  chr2_118340428_   3929 TTCAAATAATTCTATATGAAAAAATCAAATAATTTGATTAAAAAGTGAGT 3978
                         i    -    --------     iv       iiii   ?    i  i i
  L1M4_orf2#LINE/    784 CTCAA-TAAT--------AAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_118340428_   3979 AAAAGATTTGAATAGACACTTCTCAAAAAAAGA----CAAATAGCAAACA 4024
                            i              i     v   i    ----     i  v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_118340428_   4025 GGTGTACTAAAATGTGCTCAACATCACTGCTCAT 4058
                         i iii iv    vi            ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (144 / 77)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.70 (37 / 10)  


3248 27.06 0.33 0.44  chr2_118345369_118349683.rev     2915  3823 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118345369_   2915 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2964
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118345369_   2965 GGCCATAACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAG 3014
                            v   -  v     iv i  i  i        i  v     i     i
  L1M4_orf2#LINE/     51 GGCAATA-CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_118345369_   3015 CTATCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTC 3062
                         v vi  iivi i  i  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_118345369_   3063 ATATGGAACCAAAAAAGAGCCTGCATCGCCAAGTTAATCCTAAGCCAAAA 3112
                                 viiv  ii  v  v v  v     ivi    i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_118345369_   3113 GAACAAAGCCGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 3162
                                 ii     vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_118345369_   3163 CTACAGTAACCAATACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 3212
                                  i   v    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_118345369_   3213 CAATGGAACAGAACGGAGCCCTCAGAAATAATGCCACATATCTACAACCA 3262
                                 i    iv   vvii         vv   i i  i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_118345369_   3263 TCTGATCTTTGAGAAACCTGACAAAAACAAGAAATGGGGAAAGGTTTCCC 3312
                         vi    i  i  v  ivv  v   i v  vvv           iv vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_118345369_   3313 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTTG 3362
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_118345369_   3363 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 3412
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_118345369_   3413 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 3462
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_118345369_   3463 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAA 3511
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_118345369_   3512 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 3561
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_118345369_   3562 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3611
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_118345369_   3612 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3661
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_118345369_   3662 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3711
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_118345369_   3712 AAACAAACAACCCCACCAAAAAGTGGGCAAAGGATATGGACAGACACTTC 3761
                          i     i     v ii?    i            v  i i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_118345369_   3762 TCAAAAGAATACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 3811
                           v      v i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_118345369_   3812 ATCACTGGCCAT 3823
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


2476 22.62 1.04 4.91  chr2_118354349_118356010.rev      499  1170 (492)    L1M4_orf2#LINE/L1      263   908 (0)  

  chr2_118354349_    499 CAGCATGGCACTGGCATAAAAAACAGACACTTTGGCCAATGAAACAGGAT 548
                            ii   i          ii -i     iv v ii     i  i  i  
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAAT 311

  chr2_118354349_    549 AGAGAGTCCAGAAATAAATCAATGTATCTGTGGTCAGTTGATTTTCTATA 598
                         v                 i v  ii  i i      i         v i 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_118354349_    599 AATATGCCAAGAACACACAATAGGAAAA-AACAGTCTCTTCAATAAATAG 647
                          ivi        v  iv    i  i   -  i     i     i    i 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_118354349_    648 TAGATATAAAATGAAACTAAAACTAGGTATTTTTTAATAAAAACTAGATA 697
                          i--------------------  i  ------------ v    i    
  L1M4_orf2#LINE/    412 TG--------------------CTGGG------------ACAACTGGATA 429

  chr2_118354349_    698 TCCACATAAAAAAGAACAAAATTGGGCCCTTATCTTACCTCTTACACAAA 747
                         ?      iv       ii  i    i   i  i  i  vi v  i     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_118354349_    748 AATCAACTCAAAATATATTAATGACTTAAATGAAAGACCTGAAACTATAA 797
                            i          iv  i ?v   i      v    v  i         
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_118354349_    798 GACTACTAGAAGAAAACATAGGGGAAAAGCTCCTTGACATTGGGTTAGAT 847
                         i   vi                ? v   v  i v    v         ii
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_118354349_    848 AATGATTTTTGGGATATGATCCTTAAAGCACAGGCAACAAAAGCAAAAGT 897
                             i   i vi       iv iv        i          v    i 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_118354349_    898 AGACAAGTGAGATTACATCAAACCAAAAAGCTTCTACACAGCAAAAGAAA 947
                            i  i vi  i v       viv    i   i iii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_118354349_    948 C----AACAGTGTGAAGAGACAACTCACAGAATGAGAGGAAATATTTGAA 993
                          ----  v iv     i       i         i   i         v 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_118354349_    994 AACCATATATCTAATATGGGGCTAATATTTAAAATATATAAGGAATTTGA 1043
                           i         i   v   i  vi   ii i         i   i ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_118354349_   1044 AAAACTCAACAGCAAGAAAACAAATAACCTGATT-AAAAGTGGACAAAAG 1092
                          v       i ii  i  i          ii   -    i   i    i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_118354349_   1093 ACTTCAATAGATATTTCTCAAAAGAAGATATACAAATGGGCGAGAGGTTT 1142
                          i  v      i       v                   v i v i ivi
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_118354349_   1143 ATGGAAAAA-AATCAACATCACTAATCAG 1170
                            i   i -iv         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (103 / 46)
Gap_init rate = 0.01 (7 / 646), avg. gap size = 5.71 (40 / 7)  


2964 26.01 2.80 1.23  chr2_118366238_118370742.rev     3122  4013 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_118366238_   3122 GAGAGATATTCT-TGTTCATGGATGGGAAGACTCAATCAGGTCAAGATGT 3170
                           i      i i-           v        i   vvv  i      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_118366238_   3171 GAGTTCTTTCCAACTTGAT--------TCAATGCAGTTCTGATCAAAACT 3212
                         v i v  ii    v     --------    i   i i iv       ii
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_118366238_   3213 CCAGGAAGTTATTTTGTGGATATTGACAAACTAATTCTAAAGTTTATATG 3262
                             vvivi v     ii  v        i  i  i     i  i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_118366238_   3263 GAGAAGCAAAAGACCTAGAATAGCCAACATAATATTGAAGGAAAAGAAT- 3311
                           i v    ii    i           v i   v     ii i     i-
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_118366238_   3312 --TTTGGAGGATTATAACTACTTGACTTGAGGACACACTATAAAGCTTCA 3359
                         --v        i vvv   v iii i  v ii  vi    i      v  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_118366238_   3360 GTAAATAAGACAGAG--GCATTGGTGAAAAAATAGTGACA-ATAGATCAA 3406
                             vi       v -- i i   iiv  ii    --   -         
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAG--ACATATAGATCAA 300

  chr2_118366238_   3407 TGGAACAGAAAGGAGAGCCCAGAAATAAACCCACATAAATACAGTCAACT 3456
                              i    vv     i               i i vv  ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_118366238_   3457 GACCTTTGATGAAGGAGGAAAGGCAAT-AAACAGAGAAAAGACAGTCTAC 3505
                           ii  i  ii i  v vv   i v  -v  ii i    ii i     vi
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_118366238_   3506 TCAACAAATAGTGCTTTAACAACTAGATATTCAT-TGGAAAAGAAAAATT 3554
                                  i     vvi      i    ?i  i-  v       --- v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA---TG 447

  chr2_118366238_   3555 AATCTAGAACTAGACCTTACACCCTTCACAAAAATTAACTGCAAATGGAT 3604
                           vi i  v ivv    i     v vi             vv        
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_118366238_   3605 CACAGGC-TAAATGTAAAATGC-AAAACTATGAAACTCCTAAAAGATAGC 3652
                           ?  i -         i -  -        i      i  i    v i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_118366238_   3653 ATAGGAAAAAAAATTAGATGACCTTGGGTTTGGTGATGACTTCTCAGATG 3702
                              ?iv   vv  v -            v  ii   ii    i    i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_118366238_   3703 CAATACTAAAGGCACAATCCAGTAAAGAAAGAATTGACATGCTAGACTTC 3752
                         ii i  i   i      v v vv       i   v  i vii i      
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_118366238_   3753 ATCAAAAACAACAACAAAAATCTGCTCTGTAAAAGACACTGACAAGATGA 3802
                                vi  v   v---- i  iv  vi   i      iv     vii
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACT----TTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_118366238_   3803 TCGAAAGATAAGCCGCAGTCTGGGAGAAAATATTTGCAAAAGACTTATCA 3852
                          vi     i  v  i   vv                    vv iv    v
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_118366238_   3853 GATAAAATACTGTTATCCAAAATACACAAAGAACTCTTAAAATTCAATGA 3902
                              iiv   vv      i    i i            v  i     i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_118366238_   3903 ---GAGCATGAACAACCCATTTAAAAAATGGGCCAGAAACGTTAATAGAC 3949
                         ---i iv ii  i      v  ?          v iii iv v       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_118366238_   3950 A---CCTCAAAGAAGATATACAGATGGCATATCAACATTTGAAAAGATGG 3996
                          --- ii               i     vv  v i  iv          v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_118366238_   3997 TCCACAGCATATGTCAT 4013
                           v   v  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 2.25 (36 / 16)  


3155 27.88 0.77 0.33  chr2_118371629_118375682     2659  3562 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118371629_   2659 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2708
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118371629_   2709 GGCCATACTGCCCAAGGTAATTTGTAGATTCAGTGCCATCCCCATCAAGC 2758
                            v     v     iv i  i ii       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118371629_   2759 TACCAATGACTTTCTTCACAGAATTGGAAAAATCTACTTTAAAGTTCATA 2808
                          v   iivi i  i  ii     v v  v  iiiv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_118371629_   2809 TGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCTTAAGCCAAAAGAA 2858
                              viiv  ii  v  v v  vi    iv       i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_118371629_   2859 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 2908
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_118371629_   2909 CAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 2958
                                   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_118371629_   2959 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAA-CAA 3005
                              i    i--    i  --        vv   i i  i  iii-   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_118371629_   3006 TCTGATCTTTGACAAACTTGAGAAAAATAAGCAATGGTGAAAGGATTCCC 3055
                          -    i  i     ivv  vv  i vi vv      v     i  vvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_118371629_   3056 TATTTAATAAATGGTGCTGGGAAAACCGGCTAGCCATATGTAGAAAGCTG 3105
                          v  i  i              v   i  v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_118371629_   3106 AAACTGGATTCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 3155
                           ii    ii   v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_118371629_   3156 TAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 3205
                         i ?   ii    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_118371629_   3206 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTCAA 3255
                             ?i v viv   iv   v v  vv i     v ii   v ivv vvi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_118371629_   3256 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCAT 3305
                                     vvi          vv     v  i    v   ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_118371629_   3306 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGCGAACA 3355
                         i   v v  i i   i  ii vv    i  v    i  vv i  i   v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_118371629_   3356 GGAAATCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAG 3405
                          iv  i i   i             v  ii   vii ivi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_118371629_   3406 GGGCTAATATCCATAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 3455
                           i  vi      v   v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_118371629_   3456 AGCAA----CCCCATCAAAAAGTGTGCGAAGGACATGAACAGACACTTCT 3501
                         ii   ----   v  i?    i  v  i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_118371629_   3502 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCA 3551
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_118371629_   3552 TCACTGGCCAT 3562
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.00 (10 / 5)  


3077 26.79 1.10 0.99  chr2_118396436_118402827     4994  5900 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118396436_   4994 TGGAAGAACATTCCATTCTTATGGGTAGGAAGAATCAATATCGTGAAAAT 5043
                              ii i  i    vi i    i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118396436_   5044 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5093
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118396436_   5094 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5141
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_118396436_   5142 TATGGAAC--CAAAAAACAGCCCCCAAT-GCCAAGTCAATCCTAAGCCAA 5188
                                v--   iii  ---  vv   -     iv     i i ivv i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_118396436_   5189 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAA 5238
                                   i      vv   ii  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_118396436_   5239 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 5288
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_118396436_   5289 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCACATCTACA 5336
                          i        i    i--    i  --        vv  ii    i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr2_118396436_   5337 ACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT 5386
                         ii  vi    i  i     ivv  v   i v  vvv           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_118396436_   5387 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATTATGTAGAA 5436
                         vvi  v  i  i              v      v  ?   i-   i i  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC-ATGCAAAA 442

  chr2_118396436_   5437 AGCTGAAACTGGATCCCTTCGTTACACCTTATACAAAAATTAATTCAAGA 5486
                         iiv    ii    i    v v i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_118396436_   5487 CGGATTAAAGACTTAAATGTGAGACCTAAAACCATAAAAACCCTAGAAGA 5536
                         i    i ?    i       i   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_118396436_   5537 AAACCTAGGCA-ACACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 5585
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_118396436_   5586 TCTAACACACCAACAGCAATGGCAACAAAAGCCAAAATTGACAAGTGGGA 5635
                         vv  vv       v    vvi          vv     v  i  i v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_118396436_   5636 TCTCATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTACCATAGGAG 5685
                         ii    i   v v  i i   i  ii vv    iv v    i  viii  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_118396436_   5686 TGAACAGGCAACCTAAAGAATGGGAGAAAATTTTTGCAATCTACTCATCT 5735
                             v  i     i v               v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_118396436_   5736 GACAAAGGGCTAATATCCAGAATCTACAATGAACTC--AAAACAAATTCA 5783
                           i  i  i  vi          v  i  v      -- v   vv v v 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_118396436_   5784 CAAGAAAAAAAACAACCCCATCAAAAAGGGGGCAAAGGACATGAACAGAC 5833
                         i  i  i v   i     v  i?    iv          iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_118396436_   5834 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAGTGC 5883
                          i     v        i  vi viii     v ii          ii   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_118396436_   5884 TCATCATCACTGGCCAT 5900
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


3284 27.53 0.22 0.22  chr2_118611051_118617326.rev     4877  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118611051_   4877 TGGAAGAACATTCCATGTTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i            i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118611051_   4927 GGCCCTACTGCCCAAGGTAATTTGTAGATTCATTGCCATCCCCATCAAGC 4976
                            vv    v     iv i  i ii       vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118611051_   4977 TACCAATGACTTTCTTCACAGAATTGGAAAAATCTACTTTAAAGTTCATA 5026
                          v   iivi i  i  ii     v v  v  iiiv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_118611051_   5027 TGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAGAA 5076
                              viiv  ii  v  v v  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_118611051_   5077 AAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5126
                         v    i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_118611051_   5127 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5176
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_118611051_   5177 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5224
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_118611051_   5225 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5274
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_118611051_   5275 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5324
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_118611051_   5325 AACTGGATCCCTTCCTTACACTTTATACAAAAATCAATTCAAGATGGATT 5374
                          ii    i    v   i    iv           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_118611051_   5375 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5424
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_118611051_   5425 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGGCTTCATGTCTAAAA 5474
                            ?i v viv   iv   v v  vv i     v  i   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_118611051_   5475 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5524
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_118611051_   5525 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACGATCAGAGTGAACAG 5574
                            v v  i i   i  ii vv    i  v    iv vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_118611051_   5575 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 5624
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_118611051_   5625 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5674
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_118611051_   5675 ACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTC 5724
                              i     v  i?    i     i      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_118611051_   5725 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 5774
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_118611051_   5775 CACTGGCCAT 5784
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


1815 24.64 3.83 3.65  chr2_118685856_118690688     2810  3357 (1476)    L1M4_orf2#LINE/L1        3   551 (357)  

  chr2_118685856_   2810 GAGAGACGTACTATGTTCATGGATTGGGAGATTCATCATACTA--AAAGT 2857
                           i   ii v i               i   i i --   i i--  ii 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTA--ATATTGTTAAGAT 50

  chr2_118685856_   2858 GTCAGTTCTCCCTAAATTGATATACAGGTTTTATGCAATTCCTAT-AAAA 2906
                          v  i v     i        v     i  iv i     i     -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118685856_   2907 TCCTAGCAAGGATTTTTTTTTTTTTGTATATATAGACAAAATTATTCTAA 2956
                            i   -------- vii       i v v  v     iv v  i    
  L1M4_orf2#LINE/    101 TCCCAGC--------TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr2_118685856_   2957 AATTTAGCTGGAAGGGCAAAGGAACTAGAATGACTAAGACAATCTTGGAA 3006
                             i vv     iv    i   v i     ii i  i         i  
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_118685856_   3007 AAGAA-AATAAAGTTGGAGAAATCAGTCTATGTAATTTCAAGACTTATTA 3055
                              -  i          i v   vv  vivi        i     i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_118685856_   3056 TATAAGAATTCTACAGATTTCAAGGCTGTGTAGTATTGATGGAGGGGCAG 3105
                         i -   ----      vvv     i v    i   i  iiiv i  ii  
  L1M4_orf2#LINE/    243 CA-AAG----CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_118685856_   3106 ACATATTGATCAATGGGACGGAATAAAGAACTCAAAAATCAGATCCA--- 3152
                               v         i ii    vi   iii  i    - i i   ---
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT-AAACCCATAC 336

  chr2_118685856_   3153 AT--ATGCTCATCTGATATTTGAGAAGGATGCAAAGGTAATTCAATGGAA 3200
                           --   v   vi    v  i  v    i   v   iiv         ii
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_118685856_   3201 GAAGAATAGCCACTTCAATAAGCAGTGCTGGAACAA-TGGA----CACA- 3244
                         i        i vi     i  iii       i    -    ----    -
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_118685856_   3245 ------AAATTAACTTTGACCTATGTCTTACACCTTATGCAAAAATTAAC 3288
                         ------i   v  v  v    iv ii  i     v   i           
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_118685856_   3289 TCAAAATTAATTATGGACTCACATGTAAAACATAAAACCATAAAACTTTT 3338
                                vi  i ?i   ii v      i vv      i        i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_118685856_   3339 GTTTGAAAAACAGGATAGG 3357
                         i---   i  - iv     
  L1M4_orf2#LINE/    537 A---GAAGAA-AACATAGG 551

Transitions / transversions = 2.05 (90 / 44)
Gap_init rate = 0.03 (15 / 549), avg. gap size = 2.73 (41 / 15)  

1046 24.57 7.23 0.58  chr2_118685856_118690688     3996  4341 (492)    L1M4_orf2#LINE/L1      540   908 (0)  

  chr2_118685856_   3996 AAAAAACA---GGATAGTTTTTCTGGATCTAGGGCTAGGTGAAATA--CT 4040
                          i      --- ?i  iv i   vv  i  v   i    i--   i--i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC--AATGGTTT 587

  chr2_118685856_   4041 CTTAGACTTGACACCAAAAACTTAATTCATAAAATAAAAAATA----AAT 4086
                               iv           i vi  viv i    v        ----   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_118685856_   4087 TGTGGTTCA---AAATTAAAAACTTCTGTTCTGT----GACTCTGTTAAT 4129
                           viv    ---             i   v  vi----   v  i i  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_118685856_   4130 AAGAAAAAAAGACAAGTTACAGAGTGAAAGAAAATATTTACAAGTCACAC 4179
                           iivi         vii     i  ii           i   i   i i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_118685856_   4180 ATCTGACAGAGGGCTAATATGTAGAATGTATAAA-AACTCTCAAAACTCA 4228
                               i ii  i  vi   vi     i      -      i v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_118685856_   4229 ACAA-----GGA--AATGACCCAATTAGAAAATGAACAAAAGACATAAAA 4271
                          i  -----i  --   i        ?i      ii    i  iv i  v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_118685856_   4272 AAACATTTCACCAGAGAAGTTATACCGATGGCAAAAAAGAACATTAAAGG 4321
                          i       v   i     v     vi     v  v   v    v   i 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_118685856_   4322 -TGTTCAACTTCATTAGCCAT 4341
                         -  i     v   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (53 / 30)
Gap_init rate = 0.03 (10 / 369), avg. gap size = 2.70 (27 / 10)  


3559 18.91 5.01 4.00  chr2_118831093_118835813.rev     3331  4229 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118831093_   3331 TGGAAAAGCCTCCTATGTTT-TACAATGAAAGACTTAATATTGTCAAGAG 3379
                               iiiv   i     i- iv v  i               i    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118831093_   3380 AAAAATAATACC-AAAGTGATCTACAGATTTAATGTTGTCTCTGTCAAAA 3428
                         iiv    v v  -   v             i  i ivi  i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118831093_   3429 ATCACCGTGTGTTATATACGATTTTTTTT-----TTAA-------ATTCT 3466
                         -  v v i-  ii--------      vi-----  i -------  i  
  L1M4_orf2#LINE/    101 -TCCCAGC-TGCC--------TTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_118831093_   3467 AAAATCTACATGGATCC-CAATGGACCCTGAATAGCTGGCGCAATCTTGA 3515
                              ii i     vvi-   v      v       iiivi         
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_118831093_   3516 AAAAGAA---CAAAGTTGGAGGACTTACACTTTCTAATTTCAAAACTTAG 3562
                                ---               i      i i              v
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_118831093_   3563 TACAAAGTTACAATAATCAAAACAGTGTGGTACTGGCAGAAAGACAGACA 3612
                                i    i       i                 v  i  i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_118831093_   3613 TATAAACTAATAGGATAGAATAGAAAAACAAGAAATAAATTCTTCCATAT 3662
                             i ii   i i       v  i iv v         ii v v   v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_118831093_   3663 ATACTCAAATGATTTTTGACAAGGGTGCCATTACCATCCAATGGGGAAAG 3712
                           iv    v       i             vv     i            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_118831093_   3713 A-CAGGTTTTTTTTATTTTTTGGTTTTTTTTTTAAGAAATAATGTTGAGA 3761
                          -i  --------------------- i    i  v    ii  i  i  
  L1M4_orf2#LINE/    391 AATAG---------------------TCTTTTCAACAAATGGTGCTGGGA 419

  chr2_118831093_   3762 AAACTGGATATCCACATGAAAAACAATAAAGTTGCAGCCTTACTTTATAC 3811
                         v         ?       v    v   i      v v  i   i i i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_118831093_   3812 CACATACAAAAATTAACTCAAAATGGATCAAAGACAGAAATGTAAGAGTC 3861
                           i                           ?    vv           ii
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_118831093_   3862 AAAACTATAAAACACTTAGAAGAAAATGTAGGGGAAAAAATTCATAGCTT 3911
                                      v            ii    ? v   vv   i ii i 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_118831093_   3912 TGCATTTGACAATAATTTTTTGGACATGACACCAAAAGCATAGGCAATAA 3961
                           vi  v i    ii   i  i  i               i i    i  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_118831093_   3962 AAGAAAAAAGAGATAAATTTGACA-CATTAAAATT--------------- 3995
                                  v         v   v-   i      ---------------
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_118831093_   3996 --------CACTATCCACAGAGTGAAA-GAGAACTCACAGAGCTAGAAAA 4036
                         --------       v v i       -  v   i      i- i i i 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA-TGGGAGA 718

  chr2_118831093_   4037 ACACATTTTAAAATTATATATCTAATCAGAGATTAATATCCAAAATATAT 4086
                          v i    vv    i        i  v  i  i vi      i       
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_118831093_   4087 AAAGAACTATTACAATTCAACAACAACAAAAACAACAACTTACCCAATT- 4135
                                 v      i    i  i  -   i    -- - v        -
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAA-AAAGACAA--A-TAACCCAATTW 814

  chr2_118831093_   4136 AAATATTGGCAAAGGACATGAATAGACAGTTTTCCAAAGAAGATATACAA 4185
                            v  v         iv          v  i                  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_118831093_   4186 ATAACCATTAAGCACATAAAAAGATCTTCAACATCACTCATCAT 4229
                           ii   v         i       vi         ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (105 / 62)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 4.26 (81 / 19)  


3531 23.23 1.11 1.00  chr2_118873250_118876552.rev     1910  2813 (490)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_118873250_   1910 AAAAAAGTTCCATGTTCATGGATTTGAAGAATTAATGTTGTTAAAATGTT 1959
                            i vi i               v     v     i       i   vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_118873250_   1960 CATACTACCCAAAGCAATCTACAGATTGACTGCAGTCCCTATCAAAATAC 2009
                         v     v      vii           v vi   i             v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_118873250_   2010 CAATGATATTCTTCACAGAAATAGAAAAAGCAATTCTGAAATGTATATGT 2059
                           iiviiv  i  ii       v  v  ivii  i  i    vi     v
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_118873250_   2060 AACTACAAACAACCCAGAATAG--AAAACGATTATCCTAAGCAAAAAAAG 2107
                           v i   ivi           --     i  --- i i --    i   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAAT---CTTGA--AAAAGAAG 198

  chr2_118873250_   2108 AA--AAGT-AGAGGAATCACATTACCTGAATTCAAATTATACTACAGAGC 2154
                           --    -i     v     i v  ii v      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_118873250_   2155 TATAGTAACCAAAACATCATGGTACTATCATAAAAACAGGCATA--GACC 2202
                           i     i   i   vii       iv     ii i  i    --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_118873250_   2203 AATGAAACAGAATAGAGAACCTAGAAACAAATCCACACACCAA-AGTGAA 2251
                             i  i     v    ii i     i   i   i   iiv -i  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_118873250_   2252 CTCATTTTTTACAAAGGTGCCATGAACATGCACTGGGGGAAAGACAGTCT 2301
                         i v     iv    i       v  v   v  v     i  ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_118873250_   2302 CTTCAATAAATGGTGCTGGGAAAACTGGATAACCACATGCAGAAGAATGA 2351
                         i     i              v         ?         i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_118873250_   2352 AACTAGACCCCTCTCTCCCACCATATACAAAAATCAAATAAAAATGGGTT 2401
                          ii i       vi   v                i  v v       i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_118873250_   2402 ACAGACTTAAATCTAAGACCTTAAACCATGAAACTACTATAAAAAAACAT 2451
                          ?    i     v     v  v    i  i     vi  v  i       
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_118873250_   2452 TGGGGAAAATCTCCAGGACATTGGTCTAGGCAAAAATTTCTTGAACAATA 2501
                         v  ? v      i iv   v    vi       vii      ii i vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_118873250_   2502 CCCCACAAGCACAGAAAACCAAAGCAAAAATGGACAAATAGGATCACATC 2551
                          v   v       iiv   v    v      i  i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_118873250_   2552 AAG-TTAAAAAAACATTTTGCACAGCAAAGAATACAATGAAAAAAGTGAA 2600
                           i-       -- -     ii vv     i i  v  v  i        
  L1M4_orf2#LINE/    649 AAAATTAAAAA--C-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_118873250_   2601 GTGGCAACCCACAGAATGGGAGAAAAATATTTGCAAACTACCCATCTGAC 2650
                         iv i                      -          ii ivi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGAT 744

  chr2_118873250_   2651 AAGGGATTAATAACCAGAATACATAAGGAGCTCAAACAACTCTATAGGAA 2700
                               i vi  v        i    i  i   vv       v   iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_118873250_   2701 AAATATAA-TAATCCAGTCAAAAGATGGGCAAAAAGTTTGAATACACATT 2749
                            v i  -   i   i i?   i         iii        v     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_118873250_   2750 TCTCAAAAGAAGACCTACAAATTGCAAACAGGCACATGAAAATGTGCTCA 2799
                             v        iv       v  v  i i           vi      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_118873250_   2800 ACATTGTTGATCAT 2813
                             ii????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (127 / 79)
Gap_init rate = 0.01 (12 / 905), avg. gap size = 1.58 (19 / 12)  


3285 26.27 0.77 0.55  chr2_118882587_118889278     5295  6200 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118882587_   5295 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5344
                              ii    i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118882587_   5345 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5394
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118882587_   5395 TACCAA-TGACTCTTC-GCAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5440
                          v   i-  v  i  i-      -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_118882587_   5441 TATGGA--TCCAAGAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAA 5488
                               -- v    i--  v  v v  v     i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_118882587_   5489 GGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAAGTATACTACAAG 5538
                         i        i      vv       v  ii i      iiv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_118882587_   5539 CCTACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGA 5588
                         v         i   i i  ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_118882587_   5589 CCAATGGAATGGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACC 5638
                         i         i   iv   ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_118882587_   5639 ATCTGATCTTTGACAACCCTGACAAAAACAAGAAATGGGGAAAAGATTCC 5688
                          vi    i  i     vvv  v   i v  vvv          ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_118882587_   5689 CTATTTAATAAATGGTGCTCAGAAAACTGGCTAGCCATATGTAGAAAACT 5738
                           v  i  i          vi  v      v  ?   i   i i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_118882587_   5739 GAAACTAGATCCCTTCCTCACACCTTATACAAAAATTAATTCAAGATGGA 5788
                            ii i  i    v         v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_118882587_   5789 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTGGAAGAAAAC 5838
                          i ?    i       v   v       i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_118882587_   5839 CTAGACA-ATACCATTTAGGTCATAGGCATGGGCAAGGACTTCATGTCTA 5887
                         v   i?i- v i v ivv ii v i  i- i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr2_118882587_   5888 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGCATCTA 5937
                         vi            vvi          vv     v  i    v v ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_118882587_   5938 ATTAAACCAATGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAGTGAA 5987
                           i   viv vi i   i  iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_118882587_   5988 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 6037
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_118882587_   6038 AAGGGCTAATATCCAGAATCTTTGAAGAACTCAAACAAATTTATAAGAAA 6087
                          i  i  vi          v v i        vv    v iv    v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_118882587_   6088 AAAACAAAGAACCCCATCAAAAAGTGGGCAAAAGATATGAACAGACACTT 6137
                           i     v     v  i?    i        i   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_118882587_   6138 CTTAAAAGAAGACATCTGTGCAGCCAACAGACACATGAAAAAATGCTCAT 6187
                           iv        i  viiviii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_118882587_   6188 CATCACTGGCCAT 6200
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3245 27.26 0.44 0.22  chr2_118925362_118932045.rev     5287  6192 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_118925362_   5287 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5336
                              ii    i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_118925362_   5337 GTCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5386
                          v v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_118925362_   5387 TACCATTGACTTTCTTCACAGAATTAGAAAAACT-ACTTTAAATTTCATA 5435
                          v   vivi i  i  ii     v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_118925362_   5436 TGGAATCAAAAAAGAGCCTGTATAGCCAAGACAATTCTAAGCAAAAAGAA 5485
                              viiv  ii  v  v v        i     ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_118925362_   5486 CAAAGCTGGGGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5535
                              i   i  vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_118925362_   5536 CAGTAATCAAAATAGCATGGTACTGGTATCAAAACAGATATATAGACCAA 5585
                                   i i  ii         i  v ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_118925362_   5586 TGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCATCT 5635
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_118925362_   5636 GGTCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGATTC-CCTAT 5684
                          i i  i     ivv  v   i v  vvv            v v-i  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_118925362_   5685 TTAATAAACACTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAA 5734
                          i  i   iiv  i     v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_118925362_   5735 CTGGACCCCTTCTTTACACCTTATACAAAAATTAACTCAAGATGGATTAA 5784
                         i         v i i     v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_118925362_   5785 AGACTTAAATGTAAAGCCTAAGACCATAAAAACCCTAGAAGAAAACCTAG 5834
                             i         iiv    i  i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_118925362_   5835 GCA-ATATCATTCAGGACATAGGCATGGGCAAATACTTCA-AGACTAAAA 5882
                          ?i- v   -   iv   v v  vv i     vvii   v-   -  vi 
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGA 598

  chr2_118925362_   5883 CATCAAAAGCAATGACAACAAAAGCCAAAATTGACATATGGGATCTGATT 5932
                           i        vvii         vv     v  i v  v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_118925362_   5933 AAACTAAAGAGCTTCTGCACAGCTAAAGAAACTACCATCAGAGTGAACAG 5982
                            v v  i i   i  ii vv v  i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_118925362_   5983 GCAACCTACAGAATGGGAGAAAATTTTTGTAGTCCATCCATCTGACAAAG 6032
                         i     i                 v    i ivi   vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_118925362_   6033 GGCTAATATCCAGAATATACAAGGAACTTAAACAAATATACAAGAAAAAA 6082
                          i  vi             i  i     ivv    v vv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_118925362_   6083 ACAAACAACCCCATCAAAAAGTAGGTGAAGGCTATGAACAGACACTTCTC 6132
                              i     v  i?    i i  ii    v v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_118925362_   6133 AAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCATCAT 6182
                         v        i  vi viii     i  i  i       i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_118925362_   6183 CACTTGTCAT 6192
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.00 (6 / 6)  


 207 17.31 0.00 3.85  chr2_119110584_119112294      456   507 (1204)  C L1M4_orf2#LINE/L1   (0)   908   859 *

C chr2_119110584_    507 ATGTGAATGCAGCCAACAAACATATGAAAAAAGTCTCAACATCACTGATT 458
                           iii    --     i  i  i       i vv          ??????
  L1M4_orf2#LINE/    859 ATACAAATG--GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

C chr2_119110584_    457 AG 456
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 2.00 (2 / 1)  

2337 26.69 0.84 0.98  chr2_119110584_119112294      500  1211 (500)    L1M4_orf2#LINE/L1      144   854 (54)  

  chr2_119110584_    500 ATTCACATGGAG-T-CAAAGAAGACCCC-ATTAGCCATGACAATCCTAAG 546
                              i     i- -   i --     v- v      vi      i i i
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_119110584_    547 CAAAAGGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACT 596
                         v  i i        i      vv    i  v  ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_119110584_    597 ACAAGGCTACAGTAACCAAAACAGCATGGTACTTGTACTAAAACAGACAT 646
                             i          i   i    ii       v i iv ii i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_119110584_    647 CTAGACCAATGGAACAGAACAGAGACCTCAGAAA-AAACACCACACATCT 695
                         v    i        i    iv    vii      -    -   i    i 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTT 340

  chr2_119110584_    696 ACAACCATCTAATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAG 745
                          iiii  vi i  i  i     ivv  v   i v  vv            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_119110584_    746 GATCTCCTATTCAATAAATGGTGCTGGAAAAACTGGCTAGCCATATGCAG 795
                         i  vvi  v     i            i v      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_119110584_    796 AAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAG 845
                           i v    ii         v   i     v                  i
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_119110584_    846 GATGGATTAAAGACTTAAACGTAAAACCCAAA-CCATAAAAACCCTAGAA 894
                         i      i ?    i    i    i v i   - i      vi i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_119110584_    895 CAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGGAAAGACTTTA 943
                         v     v    ?i- v i -   iv   v v  vv i  v  v ii  iv
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_119110584_    944 TGACGAAAACTCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGG 993
                          iivv vi  v         vvv          vv     v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_119110584_    994 GACCTAATTAGGGGCTAAAGAGCTTCTGTGCAGCAAAATAACCTATCATC 1043
                            i v  i iii-i    i -   i     vv    iv vv      vv
  L1M4_orf2#LINE/    640 GACTTCATCAAAA-TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_119110584_   1044 AGACTGAACTGGCAACTTACAGAATGGGAGAAAATTTTTGTAATCTACCC 1093
                          i v    vv i    ii                 v    i  vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_119110584_   1094 ATCTGACAAAGGTCTCATATCCAGAATTTACAAGGAACTTAAACAAATTT 1143
                               i  i  v  ii          v  i  i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_119110584_   1144 ACAAGAAAAAGAACAAGCAATCCCATCAAAAAGTGGGCAAAGGGTATAAA 1193
                          i  v       -   ii  i  v  i?    i          i v i  
  L1M4_orf2#LINE/    788 ATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_119110584_   1194 CAGACACTTCTCAAAAGA 1211
                         i     i     v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGA 854

Transitions / transversions = 1.42 (109 / 77)
Gap_init rate = 0.02 (12 / 711), avg. gap size = 1.08 (13 / 12)  


3222 27.01 0.55 0.44  chr2_119369820_119373628.rev     2411  3317 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_119369820_   2411 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2460
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_119369820_   2461 GGCCATACTGCCCAAGGTAAT-TATAGATTCAATGCCATCCCCATCAAGC 2509
                            v     v     iv i  -  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_119369820_   2510 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2557
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_119369820_   2558 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 2607
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_119369820_   2608 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2657
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_119369820_   2658 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2707
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_119369820_   2708 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 2755
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_119369820_   2756 ATCTGATCTTTGACAACCCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2805
                          vi    i  i     vvv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_119369820_   2806 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2855
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_119369820_   2856 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 2905
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_119369820_   2906 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2955
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_119369820_   2956 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 3005
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_119369820_   3006 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3055
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_119369820_   3056 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3105
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_119369820_   3106 AGGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 3155
                           i     i   iv            v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_119369820_   3156 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3205
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_119369820_   3206 AAACAAAGAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 3255
                          i     v     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_119369820_   3256 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 3305
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_119369820_   3306 ATCACTGGCCAT 3317
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2153 22.18 1.13 17.11  chr2_119420221_119422389.rev      614  1677 (492)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_119420221_    614 ATGTGCATGGATTGTAAGTCTGCAATAATA--AAGATATCAATTCTCTCT 661
                             v         v   v  -i    v i--     iv    v   i i
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACT-TAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_119420221_    662 ACATTTATCTATAGGTGTAACACAATGCCTATCAAAATTTCAGCAAGATC 711
                          v   v     i  i vi   i    v           ii    v- vii
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT-GCCT 112

  chr2_119420221_    712 TTTTTGTAACCGTAGACAAGCTGACACTTAAATTTATATGGAAAGGCAAA 761
                               i ivvi v          iv  v     i         v    i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_119420221_    762 AACCCTAGAATAGCTAAAGCAGTTTTGAAAA-GAAGACTAAAATTTGAGG 810
                         iiv  i        i   i  i i       -     vi   i  v    
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_119420221_    811 AATAACTCTATTTGATAATAACGCTTACAATATAACTATAGTAATCAAAG 860
                          v v  v  viiii  vvi  vi     v i v i   i         ii
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_119420221_    861 CACTGTGGTATTGGTAGAGGGATAGTCACATAGATCACTGGAATAGAATA 910
                           v       i   i v i      v  i        v           v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_119420221_    911 AAGAATGCAGAATGAGATGCACACAAATTTAC--CCAAGTTG-TTTTTGA 957
                         i   i v     vv i iv  i   --    i--i   -   -    i  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACA--TTTATGGTCAA-TTGATTTTCGA 359

  chr2_119420221_    958 CAAAGGTGTAAAAGCAATTCAACAGGGAAAGGATAGCCTTT-CAACAAAT 1006
                            i    iv  ii v      ii       i    i    -        
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_119420221_   1007 GGTGCTGGAATGACTATGTATCCATGGTCAACAAAATGAAACATATGAAA 1056
                                 i ii   ivi  ?   iivv   v i      ii---  i -
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT---TGGA- 455

  chr2_119420221_   1057 ACCTTGGCCTACACATTATACGTTATACGAGAATCAATTCAAAATGGATC 1106
                         -  iivi   -    ii   -----   i i   i  i            
  L1M4_orf2#LINE/    456 -CCCCTACCT-CACACCATA-----TACAAAAATTAACTCAAAATGGATC 498

  chr2_119420221_   1107 ACGGGCAGGCATGGTGGTATGAGCCTCTAGTCCCAGCTACTTGGGAGGCT 1156
                          -------------------------------------------------
  L1M4_orf2#LINE/    499 A------------------------------------------------- 499

  chr2_119420221_   1157 GAAGTGGGAAGATCACATGAGCCCATGAGTTTGAGGCTGCAATGCACTAT 1206
                         --------?   i ------------------------------------
  L1M4_orf2#LINE/    500 --------WAGACC------------------------------------ 505

  chr2_119420221_   1207 GATCACACCTGTGAATAGCCACTGCACACTCCAACTTGGGCAACATAGTG 1256
                         --------------------------------------------------
  L1M4_orf2#LINE/    506 -------------------------------------------------- 505

  chr2_119420221_   1257 AGATCTTGTCTCTAACATATAAAAATAAAAATAATGTAAAACTACAAAAA 1306
                         ------------   -  i   i ii----------        i    v
  L1M4_orf2#LINE/    506 ------------TAA-ATGTAAGAGC----------TAAAACTATAAAAC 532

  chr2_119420221_   1307 TTTTAGAATAAGATAGAGAAGAAAATCTTCACCAACAAGGGCTAAAGAAC 1356
                          i      v  i i v  i? v        iiv v vv   i  iiv  i
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_119420221_   1357 ----TCTTAGACTTGACACCGAAAGCATAATACATACATGGAAAAATTGT 1402
                         ----       iv       i      i  vvv i v v i      v v
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_119420221_   1403 TAGGTTGGACCTTGTCAGAATTAAAAACTTTTGCATTGTAAAAGATGCTG 1452
                           ii      i ii   i               iii vi   i  ii  i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_119420221_   1453 ATATGAACATAACAATGCAAGTTACAGACTCGGAGAAAATATGTGCAAAC 1502
                         vi v   vi i v  vi   vii     v v           v      i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_119420221_   1503 CACATATCTAGCAAAGGACTTATATATAGAATATATAAAGAACTCTTAAA 1552
                           i      iii  i      i   vi                     v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_119420221_   1553 ACCAAACCATAAAAA-ATAAAAGATCCAATTAAAACATGGGCAAAAGACA 1601
                           iv  iv       - i   vi i      ?   v         i  iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_119420221_   1602 CAAAGAGACATTTCACTGAAGAGGCTATACATATGGTATTTAAGCACATG 1651
                         ii  v         v ii    i v      v    ivvv          
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_119420221_   1652 AGAAGATAGTCAACATTACTGGCCAT 1677
                          i     iv       i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (144 / 88)
Gap_init rate = 0.02 (19 / 894), avg. gap size = 10.21 (194 / 19)  


2986 26.16 3.06 0.23  chr2_119428708_119433700     3619  4501 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_119428708_   3619 TGGAAACACATCCCATGCTCATGGATGGGTAGAAACAATAATGTGAAAAT 3668
                               v i        i        v  v   vvi    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_119428708_   3669 AATCGTACTGCCAAAAGCAATCTACAAATTCGATGCAATCCCCATCAAAA 3718
                         iiivi    v  v   vii       i    i i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_119428708_   3719 TACCACCATCATTCTTCACAGAGTTAGAAAAAACAATTCTAAAATTCATA 3768
                          v   v vv v  i  ii    iv v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_119428708_   3769 TGGAACCAAAAAAGAGAAGGCATAGCCAAAACAAGACTAAGCAAAAAGAA 3818
                              viiv  ii  vvvi v             vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_119428708_   3819 CAAATTTGGAGGCATCACACTATCTGATTTCAAACTATACTATAAGGCCA 3868
                             v       vv       vi ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_119428708_   3869 CAGTCACCAAAACAGTGTGGTACCAGTATAAAAAATAG-CACATAGACCA 3917
                             v i   i            ii i    ii -   -  i     i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCA 299

  chr2_119428708_   3918 ATGGAAAAGAACAGAGAACCCAGAAATAAACCCAAATACTTAAAG-CAA- 3965
                               v    iv    ii               v i i   vi -   -
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_119428708_   3966 ---------ACAAAAATATAAAG---------TGGGGAAAGGACACCCTT 3997
                         ---------    iii iiv   ---------         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_119428708_   3998 TTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATATAGGAGAATGAA 4047
                                             i  i   v  ?      ii ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_119428708_   4048 ACTTGATCCTCCTCTCTCACCTTGTACAAAAATCAACTCAAGATGGATTA 4097
                         ii v  i  iivi   v    v i         i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_119428708_   4098 AGGACTTAAACCAAAGACCTGAAACTGTAAACATTATAGAAGATAACATT 4147
                         ?i   i    ivv    v  i     i    vv iv       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_119428708_   4148 GGGAAAACCCTTCTAGACATTGGCTTAAGCAAAGATTTCATGACCAAGAA 4197
                           ?iv  vi    vv   v    v   i    v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_119428708_   4198 CCCAAAAGTAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTAATTA 4247
                         v       i v v    i    iv   i   i   iv v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_119428708_   4248 AACTAAAGAGCTTTTGCACGGCAAAAGGAACAGTCAGCAGAGTAAACAGA 4297
                           v v  i i      ii vv    i iv  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_119428708_   4298 CAACCCACAGAGTGGGAGAAAATCTTCACAAATCTATACATCGGACAAAG 4347
                                    i           v  ii      -   i   v  i  i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGG 748

  chr2_119428708_   4348 GATTAATGTCCAGAATCTACAACAAACTCAAACAAATCAGTAAGAAAAA- 4396
                           i vi i        v  i  vi     vv    v   i   v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_119428708_   4397 --AAAT--TCCA-TCAAAAAGTGGGCTAAGGATATGAAAAAACAATTCTC 4441
                         --    --i   - i?    i     v      v    v i   v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_119428708_   4442 AAAAGAAGATGTACAAATGGCCAAGTGACATGTGAAAAAATGCTCAACAT 4491
                         v         i             vvii  ii      i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_119428708_   4492 CACTAATGAT 4501
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.34 (130 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.22 (29 / 9)  


3057 23.49 2.48 4.63  chr2_119516474_119518708.rev      816  1743 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_119516474_    816 TGGAAAGATATCCTGTGTTCATGAATTGGAAGAAATAATATTGTTAAACT 865
                                      ii        i         vv            iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_119516474_    866 ATTCATACAACCCATAGGAATATACAGATTTAACACAACTGCTATCAAAA 915
                         iviv    vv    v vvi  v        i   i   iiv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_119516474_    916 TACCAATAGCATTCTTCACAGAAATAGAAAAAACAATTCTAAAATCCACA 965
                          v   iiv  v  i  ii       v  v  ivii  i       i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_119516474_    966 GGGAAACACACACACACACACACACACACACACACACACACACACACACC 1015
                         v     ii  --------------------------------- viv   
  L1M4_orf2#LINE/    151 TGGAAATGCA---------------------------------AGGGACC 167

  chr2_119516474_   1016 CTGAATAGCCCAAGCAATCCTGGACA-GAAAAA-AAAGTTCGAGGCAACT 1063
                          v        v  i     i  i v -   i  -      v    --   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG--ACT 215

  chr2_119516474_   1064 CA-ATTTCT-AATTTAAAATTTTGTTACAAAGTTATAGTAATCAAAACAG 1111
                           - i   i-     v   vi  ii       i  i         i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_119516474_   1112 TATGGTACCAGTATAAAAATAGATATATAAACCAATAGAACATTTTAGAG 1161
                          i      ii i    ii     i     i i    i   i vvv v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_119516474_   1162 AGCCCAGAAATAAATTCACACATATATGGACAACTATATTTTGACAAGGA 1211
                           i           ii  i    v     v   i ivv   i       i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_119516474_   1212 CATCAAAATAACACAATGGGAAAAGAATAGTCTCTCCAATAGACAGCGCT 1261
                         iii   i iv iv       i            i i   i i ii i   
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_119516474_   1262 ---ACA---GAACTTTCCACAATTTCATGCAAACAAATGAAATTGGACCC 1305
                         ---   --- i - v?     ------      vi      i        
  L1M4_orf2#LINE/    416 GGGACAACTGGA-TAKCCACA------TGCAAAAGAATGAAGTTGGACCC 458

  chr2_119516474_   1306 TTACT-----CTGTAAACAAAAATTAACTTAAAATGAATAAAAGATTTAA 1350
                         i   i----- ii  v             i      i  v ?   ii   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_119516474_   1351 ATGTAAGATATGAAACCATAAAACT---AGAAGAGAACCTAAGGGAAAAG 1397
                                 vv i    i        ---      i   v  i ? v   v
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_119516474_   1398 CTATTTCACATTGGTCTTGGCAATATTTATTTTGGATATCACACCAAAAG 1447
                           viv v  v    vi v      iv  - i  i     v          
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAGATATGACACCAAAAG 607

  chr2_119516474_   1448 CACAGGCTACAAAAACAGAAATAAATAAATAGAACAGCATTAAACTAAAA 1497
                             i  v      iv i     i      v i  vv   i   v v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_119516474_   1498 AGCCTCTGTACAGCAAAGTAAACAACTGACAAA----AAAG-CAACCTAT 1542
                          i i i   i vv     v v  v iii v   ----    -     i i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_119516474_   1543 GGACTGCGAAAAAATAATTGCAAACCACATATCTGTTAAGAGGTTAAGAT 1592
                         i  v  v  i      v       i  i       v    i ii viv  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_119516474_   1593 CTAAAATTTATAAAGAACTCTTGCAACTCAATAGCAGAAAAGCAGATAAA 1642
                          i i   v              i          ii i   ii  i    v
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_119516474_   1643 CCAATTGAAAAGTGAGCAAAAGACCTGAACAGACATTTCTCCAAAGAAGG 1692
                               ?    i  i     i  ii    i                   i
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_119516474_   1693 CATAAGAATGGCCAATAGGTATATACAAAGGTGCTCAATATCACTAATCA 1742
                         i   vi           i i i  iv    i       i    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_119516474_   1743 T 1743
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.78 (137 / 77)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.40 (66 / 15)  


2933 26.94 2.02 0.11  chr2_119518733_119522973.rev     2860  3750 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_119518733_   2860 TGGAAACACCTCTTATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2909
                               v iv  ii   i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_119518733_   2910 GACCACAC--AGCAAA---ATCTACAAATTCAGTGCAATCCCCATCAAAA 2954
                          i v i  --vv    ---       i     ii        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_119518733_   2955 TGCCA-CGATCATTCTT-CAGAGTTATAAAAAAC-AATTATAACATTAAT 3001
                          v   - vii v  i  -    iv - i v  i -i  iv   v   v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_119518733_   3002 ACAGAACCAAAAAAGAGCCCACTTATCCAAAGCAAGACTAAGCAAAAAGA 3051
                          ii   viiv  ii  v  vivv  v     i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_119518733_   3052 AAAAATCTGGAGGCATCACACTACCTGATTTCAAACTAAACTATAAGGCC 3101
                          v   vi      vv       v  ii        vivv    i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_119518733_   3102 ATAGCCACCACAACAGTATGGTACTGGTATAAAAATAGGCACATAGGCCA 3151
                          i  iv i  vi     i         i    ii    i  i    ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_119518733_   3152 GTGTAGTGGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCCAC 3201
                         i  v i i    v    ii               v i i   ii i v i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_119518733_   3202 -GATCTTTG-CAAAGCAAACAAAAACATAAAGTGGG--AAGAACACCCTT 3247
                         -   i  i -   i vviv   i v   vv i    --     i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_119518733_   3248 TTCAACAAATGGTGCTGGGATAATTGGCTAGCCACACGTAGGGGAATGAA 3297
                                             i  i   v  ?     i i iii       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_119518733_   3298 ACTGGATCCTCATCTCTCATCTTATACAAAAATCAACTGAAGATGGATTA 3347
                         ii    i  ii i   v  i v           i    v  i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_119518733_   3348 AGGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATT 3397
                         ?i   i    iv     v  i           v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_119518733_   3398 GGAAAAACCCTTCTAGACATTGGCTTAGACAAGGATTTCATGACCAAGAA 3447
                           ?iv  vi    vv   v    v    i   v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_119518733_   3448 CCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATGA 3497
                         v         v v    i    iv   i   i   iv v      v  v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_119518733_   3498 AACTAAAGAGCTTTTGCACGGCAAGGGGAACAGTCAGCAAAGTAAACAGA 3547
                           v v  i i      ii vv   i  iv  vi   iv     i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_119518733_   3548 CAACCCATAGAGAGGGAGAAAATCTTCACAATCTATACATCTGACAAAGA 3597
                                i   iv          v  ii   vii   i      i  i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_119518733_   3598 ACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGTAAGGGAAAAA 3647
                            vi          v  i  v      vv    v   i   vii   i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_119518733_   3648 -AAAT--CCCA-CCAAAAAGTGGGCCAAGGACATGAATAGACAGTTCTCA 3693
                         -    --    -ii?    i     v     iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_119518733_   3694 AAAGAAGATATACAAATAGCCAACAA--ACATGAAAAAATGCTCAACATC 3741
                                          i     i  --         i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_119518733_   3742 TCTAATGAT 3750
                         v????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


2149 27.12 5.14 3.23  chr2_119564767_119568010.rev     1908  2744 (500)    L1M4_orf2#LINE/L1        1   853 (55)  

  chr2_119564767_   1908 TAAAAAGATATTCTGGTATTCATGGATCAGAAGAATCAACGTTATTAAGA 1957
                          ii        i ii- i         ii     v i  ii  i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCA-TGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_119564767_   1958 TGTCAGTTCTCCTCAAACTGATGTATAAATTCAAAGCTATCCA-ATCAAA 2006
                           v  i v    i    i    v  i i      v  v    v-      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_119564767_   2007 TTGTCAGAAAATTTTCTTGTAGAAGTTGACAGATTGATTCAAAAATTTAA 2056
                         v vi   vvivi   i   i    i      iii    i v      i v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_119564767_   2057 AAGGAAATGTAAAGAACCAACTATAGTGAAAATAATCTTGAAAAA----- 2101
                          v       i  i i   v vv    iv    i            -----
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_119564767_   2102 --AAAACTGGAAGGCTTATATTAATTGATCTCAAGACTTACTGTAAAACT 2149
                         --   ii    i i  i i i vviii  i    i       ii   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_119564767_   2150 ATATTA-TTGAGACAATATACTCTTGGCATTGGGCTATACTAAGACCAGG 2198
                          i v  - ii     i i iv vi      vi  --   ----   - vi
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGG--ATA----GAC-ATA 292

  chr2_119564767_   2199 AAAATCAATGAAAGAAAA--GAGAATC-------AGACCCATGTATATAT 2239
                         v i       i  v i  --    i  ------- i      ii  v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_119564767_   2240 GACCAGTTGATTTTCTAGAAAGGCACTGACGCAAATCAGTGGGTGGAAAA 2289
                          ii  i         v v  i  ii ii vi v v   i    --    i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG--GAAAG 390

  chr2_119564767_   2290 GAAAGTCTTTTGGGCAAAAAGTGCTAGGG----TTGAGGGACAAATATAA 2335
                         i v        vii    vi     i  i---- v  vi?v  v  ii  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_119564767_   2336 AATATAGAAAAAAATCCCTGACCCTCTCTACTTCACAC-ATAACACAAAA 2384
                           ----   vi  i iv--     ---    i      -   -i      
  L1M4_orf2#LINE/    441 AA----GAATGAAGTTG--GACCC---CTACCTCACACCATA-TACAAAA 480

  chr2_119564767_   2385 AGTAAGTTGAGGTGGATCACAGACCAAAAC--AAAAGCTAAG--TAAAAA 2430
                          v   v ii ii       ?     v   i--  i      i--  v   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_119564767_   2431 GTTTCTAAGCAAAAAAAACATTTTTGAAAAATTTTTGACACCTGGAGGTA 2480
                         ii ii  i---  i       vvv? v   - i  i vv    v i v  
  L1M4_orf2#LINE/    531 ACTCTTAG---AAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTA 576

  chr2_119564767_   2481 GGCAGAGATTTCTTAGAGAGGACACAAGAAGCTCTATCCATAGAAGAAAA 2530
                             iv i         v v     v i    v v v v i i       
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_119564767_   2531 AGTTGATACATTAGATTTCATCAAAATTAATAA--TTTCTGCTGAGCAAA 2578
                          i v    v   i  i              v  --   v    v--    
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAA 674

  chr2_119564767_   2579 AGACACTATTAAGAAGATGTAGAACACA--TTACAGGCTGGGAGAA---- 2622
                         i        i     ii  - i  v   --ii    iv        ----
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTG-AAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_119564767_   2623 ----CAATCTATATACCTGACACATGTCTTGAATCTAGAATATGGAAATA 2668
                         ----   vii     i    i viv v    v   i       iv   v 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_119564767_   2669 ATTCTTATACATCAACAGTAAAAACACAAACACTCCAAT--AAAAATGA- 2715
                          i     i vv    i i      v     i vi     --       i-
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_119564767_   2716 -AAAATATTTTGATAGCCACTTCACTAAAG 2744
                         -   iv    vi    v  i   v i    
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAG 853

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.03 (27 / 853), avg. gap size = 2.59 (70 / 27)  


3150 25.92 2.11 1.11  chr2_119569068_119575410     4953  5851 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_119569068_   4953 TGGAAGAACATTCCATGCTCATTGATAGGAAGAATCAACATTGTGAAAAT 5002
                              ii i  i     i    v   v      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_119569068_   5003 GGCTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5052
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_119569068_   5053 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5100
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_119569068_   5101 TATGGTACGAAA---AAAGAGCCCACATT-GCCAAGACAATCCTAAGCCA 5146
                              ----   ---  i ii    v v -     i      i i ivv 
  L1M4_orf2#LINE/    149 TATGG----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_119569068_   5147 AAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACA 5196
                         i          i      vv       v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_119569068_   5197 AGGCTACAGTAACCAAAACAGTATGGTACTGGTAGCAAAACAGAGATATA 5246
                          i          i   i     i         i vv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_119569068_   5247 GACCAATGGAACAGAAT--AGAGCCCTCGGAAAT---------CATCTAC 5285
                           i        i     --    i  --i     ---------   i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chr2_119569068_   5286 AACCATCTGATCTTTGACAAATCTAATGAAAACAAGAAATGGGGAAAGGA 5335
                         iii  vi    i  i     ivv ivii i v  vvv           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_119569068_   5336 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 5385
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_119569068_   5386 AGCTGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGA 5435
                         iiv    ii    i    v   i     v  i           i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_119569068_   5436 TGGATTAAAGACTTAAATGTTAGACCTAAA-CCATAAAAACCCTAGAAGG 5484
                              i ?    i       v   v     - i      vi i      i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_119569068_   5485 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 5533
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_119569068_   5534 ACTAAAACACCAAAAGCAAAGGCAACAGAAGCCAAAATTGACAAATGGGA 5583
                         iv  vi            v i      i   vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_119569068_   5584 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5633
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_119569068_   5634 TGAACTGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCT 5683
                             vv i     i                 v   i   vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_119569068_   5684 GGCAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAA 5733
                          ii  i  i  vi          v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_119569068_   5734 GAAAAAAAACAAACAAACCCATCAAAAAGTGGGTAAAGGATATGAAAAGA 5783
                         v     i -    i  v  v  i?    i    i       v    v   
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_119569068_   5784 CACTTCTTAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATG 5833
                           i    iv        i  vi viii     i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_119569068_   5834 CTCATCATCACTGGCCAT 5851
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (142 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.23 (29 / 13)  


2806 23.05 4.83 5.16  chr2_119799119_119803832.rev     3312  4222 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_119799119_   3312 TGGAGAGGTATACTGTGTTCATGGATCAGAAAACTCAAAACTGTTAAGAT 3361
                             i  i   v ii           ii   i   i  v i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_119799119_   3362 GTCA-TGTGTCCTCAAACTGTGGTATTGATTC----CAGTTCTAATCAAA 3406
                          v  - ii-   i    i  vvv  iv     ----  i i iv      
  L1M4_orf2#LINE/     51 GGCAATAC-TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_119799119_   3407 ATTCTGGCAGGCTTTTTTTTTTCCTTTCAGATAATACCAAACTTATTCTA 3456
                           i ii  v v       v--------    v v iv   i  v  i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTG--------CAGAAATTGACAAGCTGATCCTA 141

  chr2_119799119_   3457 AAATTTGTAAGGAAAGGCAAAAGACCTAAAATCGTCATAAC--TCACAAA 3504
                              ii  v     v    ii    i i   v i  v   --  vii  
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_119799119_   3505 AAGAAGGAAAAAAGTTGAAGAAATTACACTACCTTATTTCATGACTTACT 3554
                           ii i   v       i  i v i     v  iv      vi       
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_119799119_   3555 GCTATAAAACTATAGTAATCAAGTACTGCATATGTGATACTGGTGTGTAG 3604
                         --- i   i   i          -  v ----    i      ii ivi 
  L1M4_orf2#LINE/    242 ---ACAAAGCTACAGTAATCAAG-ACAG----TGTGGTACTGGCATAAGG 283

  chr2_119799119_   3605 ATAAACATATACGTTAATGGAAGCG------GAGTCCAGAGACAGACACA 3648
                            i       vi i       vv ------         i i i  v  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_119799119_   3649 CAGAT--GTGTTAAATTGATTTTTGCTCAAGGTATT-------TT---TG 3686
                         i v  --i  v v          i viv i   iii-------  ---  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_119799119_   3687 AGGAGAGTGTAATTTTCCCAAGCAA--GGTATTAGGACAATTGGATAGCC 3734
                         i   i  vi  i i  ii   -   --   ii i      i      ?  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAA-CAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_119799119_   3735 ATATGCAAATAAATGAACCTCAATGCTTACCTCCTACCATATACAAAAAT 3784
                          i       vi      vi vi iv i      vi               
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_119799119_   3785 -AACTCAAAATTGGCCA-AGAACTAAATGTAAAAGGTAAAACTATAAAAC 3832
                         -          v ii  -   v          i  v              
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_119799119_   3833 ATCTAGAAGAAAACA--GCAACAAACCTTAGAGACTTTGATTTTGGTAAA 3880
                         vii            -- v?ii   i   v v   i   iv  v  i  v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_119799119_   3881 AGTTTCTTAAATACAGCACAATAAGCATAAACTATAAAAGCAAAAATC-- 3928
                         i        i   iii   v v     i  i v i     v      v--
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_119799119_   3929 --AATTGGGCTTTAGCAAAATTAAAAACTTTTCCTTTTCAAAATATACTA 3976
                         --      i   i v                 vivi      iv i    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_119799119_   3977 ---AAAAAATGAAAAACCAAACCACAGA-TGTGGAGAAGATATTTGTAAA 4022
                         --- i   i      iv   v       -  -      i       i   
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATG-GGAGAAAATATTTGCAAA 731

  chr2_119799119_   4023 ACATACATCCAACAAGGAACTATTAGGAACTATTATCTAGAATA-ATAAG 4071
                         v    i   ii i    i   --------- i -   i      -    -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACT---------TGT-ATCCAGAATATATAA- 770

  chr2_119799119_   4072 AATTAAAACCAAAACCAAAACCTCTTATAACTCAATAATAA---GACACA 4118
                         ---------------- i   -     i             ---    v 
  L1M4_orf2#LINE/    771 ----------------AGAAC-TCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_119799119_   4119 CAACACAATT-AAAAGTGGGCAAAATATTTGAACGGACACTTCACTAAAG 4167
                         i   v     -    i        iv       ii    i   v i    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_119799119_   4168 AAGACGTATGTATGGCAGATAAGCACATTAATTAATACTCATCATTAGTC 4217
                             ii  iiv     vi          v  vvi  i    v   i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_119799119_   4218 TTTAG 4222
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.81 (134 / 74)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.25 (91 / 28)  


 917 29.64 7.19 0.00  chr2_119977278_119979254      507   840 (1137)    L1M4_orf2#LINE/L1      196   553 (355)  

  chr2_119977278_    507 AAGAA--AAGTGGAAAGAATCGGTTTACCTGATTTTAAGATGTATTATAC 554
                              --    v i i  v  ivvi v  ii    i  i iv  i  i v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_119977278_    555 AGGTACAGTAATCAA-ACAGGATATCAATGG---AAGAATAGAAAAGTAG 600
                           v            -    vi ivi v   ---   i     v vi   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_119977278_    601 ATCAATGGA-CACAATAGAAAACCTAGAAATAGACCTACGTAAATATGCA 649
                                  -i v   v  i ii i       i   i iii vv    vv
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_119977278_    650 CAACCAATTACTGACAAAGGTACAAAGGG-ATTCAATG---AAAGGATCA 695
                            iii   vii     i   i v   iv-        ---    i  vi
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_119977278_    696 TCTTTTCAACAAATGGTGTTGAAGCAACCGAACATCTGTAGACAATAAAA 745
                                           i  iii    i i i ? iii vi   v i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_119977278_    746 TGAACCTTGAGCTCAGTCTCACACTTTACACAAAAATTAA-----AATGG 790
                             vi v  v i vii       iv  i           -----     
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_119977278_    791 ATCACGGGCTTAAATTCAAG--------CTATGAAACTTTTATTTAAAAG 832
                             ?i i i     vi   --------    i     i   vvvi   i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_119977278_    833 CATAGGAG 840
                               ? 
  L1M4_orf2#LINE/    546 CATAGGNG 553

Transitions / transversions = 1.82 (62 / 34)
Gap_init rate = 0.02 (8 / 358), avg. gap size = 3.00 (24 / 8)  

 826 30.33 3.60 0.26  chr2_119977278_119979254     1121  1509 (468)    L1M4_orf2#LINE/L1      507   908 (0)  

  chr2_119977278_   1121 AAAAATAAAAATTAAAAATAAATAAATAAATAAATAAAAGCATAGGAGAA 1170
                            vi   i ii     v  v -   ivvv  i vi   i      ? v 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_119977278_   1171 AATCTTCA-AATCTAAAGCT--GCATAGAGTTCTTATGCTTGGCACCAAA 1217
                                i-i i  vii i --   vv iv      viiv  i       
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_119977278_   1218 AGCATGATCCATATAAGAAAAGATTGACAAATTAGACACAATAAAAATTA 1267
                             ii v v i v       i  v  i     i   viv  v       
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_119977278_   1268 AAACCTTTGCTCCTTGAAAAACCA-TGTTAAGAAGATGAAGAGACAAGCT 1316
                            v    vv v   v   iiv  - i i     ii    i      v i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_119977278_   1317 ATGGAATCGGAGAAAATGTTTACAAACTACATATTCAAGGAAGGAATAAT 1366
                          ii    v         i   i    ii i    iii vi i   v vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_119977278_   1367 ATCTAAAATATACAAAGAATGCTTGAAACTCAACAGTAAAGAAGCAAAAA 1416
                            i i      i      iv   iv       i i    i ii    v 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_119977278_   1417 TTCTAATTAGATCATAAGCAAAAGACATGAAGAGATAGTTTAC---AGAA 1463
                         vi i    ?i vv  ii     i  iv    v   i v  iv ---    
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_119977278_   1464 GATATACAGATGGC--ACAGAGAAATGCAAA-----TCAAAACCACAATG 1506
                                 i     -- i iiv v   v   -----    v i  ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_119977278_   1507 AGA 1509
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.52 (70 / 46)
Gap_init rate = 0.02 (7 / 402), avg. gap size = 2.14 (15 / 7)  


3443 25.60 0.33 0.55  chr2_120091601_120098587     5586  6495 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_120091601_   5586 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5635
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_120091601_   5636 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 5685
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_120091601_   5686 TGCCATTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTCA 5734
                          v   vivi i  i  ii     v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_120091601_   5735 TTTGGAACCAAAAAAGAGCCAGTATCGCCAAGACAATCCTAAGCAAAAAG 5784
                          v     viiv  ii  v    v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_120091601_   5785 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5834
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_120091601_   5835 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACACATATATAAACC 5884
                                 i   i    ii         i iv ii i v i     i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_120091601_   5885 AATGGAACAGAACAGA-AGCCTCAGAAATTATGCCACACATCTACAACCA 5933
                                i    iv  -  i -       v vv   i    i  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chr2_120091601_   5934 TCTGATATTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCTC 5983
                         vi    v  i     ivv  v   i v  vv            i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_120091601_   5984 TATTTAATAAATGGTGTTGGGAAAACTGGGTAGCCATATGCAGAAAACTG 6033
                          v  i  i        i     v      i  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_120091601_   6034 AAACTGGACCCCTTCCTTAACACTTTATACAAAAATTAACTCAAGATGGA 6083
                           ii         v   i -   iv                   i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_120091601_   6084 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTGGAAGAAAAC 6133
                          i ?    i       v   v       i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_120091601_   6134 CTAGGCA-ATACCATTCAGGACCTAGGCACAGGCAAAGACTTCATGACTA 6182
                         v    ?i- v i -   iv     v  vvi      v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_120091601_   6183 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGACCTA 6232
                         vi            vvi           v     v  i    v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_120091601_   6233 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 6282
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_120091601_   6283 CAGGCAACCTATAGAATGGGAGAAGATTTTTGCAATCTATCCATTTGACA 6332
                         v  i     i i            i  v       vii  vi  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_120091601_   6333 AAAGGCTAATATCCAGAATATACAAGGAACTCAAACAAATTTATAAGAAC 6382
                          ii i  vi             i  i      vv    v iv    v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_120091601_   6383 AAAACAAACAACCCCATCAAAAAATGGGTGAAGTATATGAACGGACACTT 6432
                           i     i     v  i?         ii   v  v    ii    i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_120091601_   6433 CTCAAAAGAAGATGTTTATGTGGCCAACAAACATATGAAAAACAGCTCAT 6482
                            v         i vi vi       i  i  i       ivv     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_120091601_   6483 CATCACTGGTCAT 6495
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


 555 22.35 1.76 5.88  chr2_120273650_120278380.rev     3025  3194 (1537)    L1M4_orf2#LINE/L1        1   163 (745)  

  chr2_120273650_   3025 TGGAGAGACATAACTATGTTCACGGACTGGAACATTCAAACTAGTAAACA 3074
                             i   i  v- i       i   i     v i i  vv v  v  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATC-CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_120273650_   3075 CGTCAATTCTCTCCAAATAGGCATACAGGTTTAATGTAATTTCTATCAAA 3124
                         i v    v   i      v iiv     i  i  i i   ii        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_120273650_   3125 ATCCCAG-TAC-TTTTTTGTAGATAATTTTATTTTAGATAATTTTATTCT 3172
                                - i -       i   -    --------  i  vi v  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGA-AATT--------GACAAGCTGATCCT 140

  chr2_120273650_   3173 AAAATTAATATGGAAG-GCCAGG 3194
                               v        i-  v   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGG 163

Transitions / transversions = 1.53 (23 / 15)
Gap_init rate = 0.04 (6 / 163), avg. gap size = 2.17 (13 / 6)  

1833 22.13 8.30 7.11  chr2_120273650_120278380.rev     3486  4244 (487)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr2_120273650_   3486 AAAATTAATATGGAAAGGCAAAGGAATCATTGTAGCAAAAACAATTTTGA 3535
                               v         v    i   vi  vvi    v        i    
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_120273650_   3536 AAAAGAC---TAAAGTGGGAGTAACTATACTCCCACTCCCAAAGAAAAAT 3582
                               v---i     v    v ------   v    i  v  -------
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGA------CTCACACTTCCCAA------- 227

  chr2_120273650_   3583 AAACTGGGAATCCCTCTCCCAGATTTTATGATTATGTACCTACATTTATC 3632
                         ---------------i i v i i  ---- i  iiv v     v v   
  L1M4_orf2#LINE/    228 ---------------TTTCAAAACTT----ACTACAAAGCTACAGTAATC 258

  chr2_120273650_   3633 AAGACTGT-TGGTAACGACAGAAGTAGAGACACCGAGATCACTGGAACAA 3681
                              v  -     vi i  v   v v     ivv      v     i i
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_120273650_   3682 AAT---------AGAATTA---CCACACAAGTACAGCCAACTGATTTTTA 3719
                            ---------    v  ---   i   vv  ii i   i       ii
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_120273650_   3720 ACAAAGGTACAAAAACAATTCAACAGAGAAAGGATGGCCTTTTCAACAAA 3769
                             i   i v  i  v      ii i     i  i i            
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_120273650_   3770 CAGTGCTGAACCAATCAGAAATCCATACACAAAATGAAAAATGAACCTCA 3819
                         ii      iiv   iii  v ?   i ii     ----i      vi vi
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAA----GAATGAAGTTGG 454

  chr2_120273650_   3820 ACCTAAACCTCACACCTTATGCAAAAAATTACTCAC--TGACTCA--GAT 3865
                            ivv          v   i      v v     v--  iv   --  i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_120273650_   3866 TTAAATGTAAAACCTAAAACACTAA--CTTTTAGAAGAAAACATACTAGA 3913
                         i         i v       vv   --  i               vv? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_120273650_   3914 AAATCTTAGGGACCT-AGGTATGGTGAAGTGTTCTTAGATGTGACATCAA 3962
                                v v     -i   vv  ii v vv         i     i   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_120273650_   3963 AAGCATGATTCATAAAAACAACAACAAAAA-AGACAAATTAGCTATATCA 4011
                              -----  - iv     v iv     -   i     i -- iv   
  L1M4_orf2#LINE/    605 AAGCA-----CA-AGCAACAAAAGAAAAAATAGATAAATTGG--ACTTCA 646

  chr2_120273650_   4012 TCAAAATTTAAAACTT---------ACAG---ACTGTAAAAAAAA--AAA 4047
                                 v       --------- v  ---   i v  i   i--   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_120273650_   4048 AG----CC---------------------TGCAAAACATTTATCTGACAA 4072
                           ----  ---------------------      v   v       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_120273650_   4073 TAGACTAGTACTCAGAATATGTAATAAACTCTCAGAACTCAACAGTAAAA 4122
                         vi    v   ii        i   vi      i v       i i     
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_120273650_   4123 AAAAAAAAAAATCAAATAATCCCATTAGAAAATGGGCAAAAAAACATAAA 4172
                          i ---------       i  v   ?i            ii vi- i  
  L1M4_orf2#LINE/    797 AGA---------CAAATAACCCAATTWAAAAATGGGCAAAGGATT-TGAA 836

  chr2_120273650_   4173 AAGACATTTTACCGAATGGGATATTCAGATGGCCATTAAGCACATGAAAG 4222
                         v        iv  i  vii     v  i       v             i
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_120273650_   4223 GATGCTCAATCTGAGCCATTTG 4244
                                  iv v ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (90 / 75)
Gap_init rate = 0.03 (23 / 768), avg. gap size = 5.09 (117 / 23)  


 520 32.03 0.00 0.00  chr2_120378457_120382610     2514  2666 (1488)    L1M4_orf2#LINE/L1        1   153 (755)  

  chr2_120378457_   2514 TAGAAAAACATCTCATACTCATGAATTAGAAAAATTAGTACTGTGAAAAT 2563
                          i    i i   i   ii     i   i   i v   i  i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_120378457_   2564 GACCACACTACCCAAAGCATTCTACAGATTCAATGCAACATCTGTCAAAA 2613
                          i v i   v      viiv             i    ivi  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_120378457_   2614 TATCAATGACATTCTTCACAGGCATAGAAAAAGCAGTTTCAAAATTCATA 2663
                          vi  iivi v  i  ii   iv  v  v  iviii iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_120378457_   2664 TGG 2666
                            
  L1M4_orf2#LINE/    151 TGG 153

Transitions / transversions = 2.50 (35 / 14)
Gap_init rate = 0.00 (0 / 153), avg. gap size = 0.00 (0 / 0)  

2145 26.23 7.39 1.30  chr2_120378457_120382610     2969  3658 (496)    L1M4_orf2#LINE/L1      141   872 (36)  

  chr2_120378457_   2969 AAAATATTGTATGGAACCCTAAAAGATCCTGAATAGCCAAAACAATACTG 3018
                              - ii       vivi  ii  i  v                vi  
  L1M4_orf2#LINE/    141 AAAAT-TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_120378457_   3019 AGTCAAGAGGACAAAGATGGAAGACATCA--------AATTATC------ 3054
                          ivv ii  i      v    i   -   --------    -  ------
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAATT-TCAAAACT 237

  chr2_120378457_   3055 --CTGTGAAGCTACAGTATTCACAACAGCATGGTACTGGTATTAAAATAG 3102
                         --  iii           v   vi    ii         i  v ii    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_120378457_   3103 ACACATAGACCCAACAGAACAGAATAGAGAACATAGAAATAAATCCACGT 3152
                            i     i -  ii   i     v    iivi         i   iii
  L1M4_orf2#LINE/    288 ACATATAGATC-AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_120378457_   3153 ATTTACAGCCAACTGAATTTTGACAAAGGCACCTAGAACATAGAGTAGGG 3202
                              ii i   i   v   i     i  ii  v   v   vv i i   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_120378457_   3203 AACAGACACCCTTTTCCATAAATGGTACTGAGAAAACTGGGTATCTAT-T 3251
                           vii i vi      v i       i   i  v      i  ? i i- 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_120378457_   3252 GCAGAAGAATGGAACCAGACCCTTATCTCAG--TATATA-AAAAATCAGC 3298
                            i       i iiii     i  i    v--i     -      i i 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_120378457_   3299 TCCAAATGGATTAGAGAGTTACACGTAAGACCTGAAACTATAAAACTGCT 3348
                           v        i ?   vi  v i      v  i             vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_120378457_   3349 AAATGAA--CATAGAGG-AAATGCTTCAGAATACTGATCTAGGCAAAGAT 3395
                          i v   --     i? -    -    ivi ivi  ivi       v i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_120378457_   3396 TTTATGGGTAGGTCTTTAAAAGTACAGGCAACAGAAAGAAAAATAGTCAA 3445
                           iv i i  v v vii     i   i      i  ii        vi  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_120378457_   3446 ATGGGACT--ATCAAACTAAAACGCTTTTACATAGCAAAGGAAACAATCG 3493
                           v     --      v v   vi     iiiivv       v  v   i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_120378457_   3494 ACAGAGTATAGAGACAACCTATAGAACTGGAGAAAATATTTGCAAATTGT 3543
                          v i   iv i        i i    iv                   ii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_120378457_   3544 ACATCCAACAAGGGCCTGGTATCCAGAATA-ACAAGGAACTG-------- 3584
                          i   ii i     v  v            - i  i     v--------
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_120378457_   3585 -AACAGCAAAAGCCAGCCCAATAATTCATTTT----------------TT 3617
                         -  i ii    ---  v v     ii  v  ?----------------  
  L1M4_orf2#LINE/    786 CAATAATAAAA---AGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_120378457_   3618 AAAATTGACATTTCTCAGAAAAAAGACATGCAAATGGTCAA 3658
                         vi   v          v-   i    i  i       i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCC-AAAGAAGATATACAAATGGCCAA 872

Transitions / transversions = 2.11 (120 / 57)
Gap_init rate = 0.02 (18 / 732), avg. gap size = 3.33 (60 / 18)  


3742 19.48 5.35 2.16  chr2_120444734_120446730.rev      628  1505 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_120444734_    628 GAAAGACCATCCTGTGTTCATGCTTTGCAAGATGTGATATCACTATTATG 677
                               i-    ii        vv   v    iv i    iii  vv   
  L1M4_orf2#LINE/      3 GAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_120444734_    678 ACAATACTTCCCAATTTGATCTAGAGATTCAACCCAATCCCTATGAACAT 727
                         i       i     v        v         v          v  v  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_120444734_    728 TCTGGTTGCTGGTTTTTTTTTTATTTTTTCAGAAAG-AATAAACTTATTC 776
                         i ii i   i------      i------      v-i i  i  v  i 
  L1M4_orf2#LINE/    102 CCCAGCTGCC------TTTTTTG------CAGAAATTGACAAGCTGATCC 139

  chr2_120444734_    777 -AAAATTCATATGAAAATGCAAGGGGCATAGAATAGCTAAATCAAGCTGG 825
                         -            i           i vi        i   v   v  v 
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_120444734_    826 AAAATGAAAAA--GAGTTAC-GGATTTACATTTCCTGATTTTAAATTTTA 872
                             v   i  --i    iv-   i i   i    ii    i   vi   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_120444734_    873 CAACAAAGCTACAGTAATGATGACAGTGTAGTACTAGCATAGGAACAGAG 922
                          v                v v        i     i     i i i   v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_120444734_    923 ATACAAATCAATGGAATAGAATTGGAAGTCTAGAAATAAACTCTTATATT 972
                            i i                  ii    i          i v  i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_120444734_    973 TGTGCTCAACTGATTTTTGACAAGAGCCCTGAGACAATTCAATGGG-AAA 1021
                          i  v    i       i      i iv ii    v          -   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_120444734_   1022 GAACAGTCATTTTAACAAATGGTGCTGGGACAAGTGGGTAACCACATGCA 1071
                            i    v   i                    v   i  ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_120444734_   1072 AAAGAGTTAAGTTGGAACCCTACCTCAAACCACACACAATAATTAGCTCA 1121
                              i v        v          v    i i    v     i    
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_120444734_   1122 AAATGGATCAATG--CTAAATGCAAGAGCTAAAACTATAAAACTTGTAGA 1169
                                   ?v --       i                     iv    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_120444734_   1170 --------------------CTCAT--TTATGGGTTAGGTAATAATTTCT 1197
                         --------------------i  i --iiv         i   ii     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_120444734_   1198 CATCTATGATACCAAAAGCATAAGTGATAAAGGAAAAA-CAGATAAACTA 1246
                         i vv     i          i   ii i   i      -i       i i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_120444734_   1247 GACTTCACCAAA-TTCAAAACTTCTGTGCATCAACTACTATAATCAAGAA 1295
                                i    -  v       i     v    vvivi iv        
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_120444734_   1296 AACAGAAAGAGAA-------AATGGAAGCAAATATTTGCAAACCACAGAT 1338
                          iiii     v  -------     i  v             i  i v  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_120444734_   1339 CTGATCAGAAACTTTTATCCAGAAAACATAAAAAAAATACTTACAACTCG 1388
                              v  ii    v         v i     i  --iv          i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAA--CTCTTACAACTCA 787

  chr2_120444734_   1389 CCAATAAAATGGCGG----CCAAATTCAAAAACAGGCAAAAGATTTGAAC 1434
                         vi       v i ii----  v    ?     ii      i        i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_120444734_   1435 AG----TTCTCCAAAAAATATATACAAATAAATAGCTAATTATCACATGT 1480
                           ----         i  v          i----  i   v v      v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATG----GCCAATAAGCACATGA 883

  chr2_120444734_   1481 AAAGATGCTTAACATCATTAGTGAT 1505
                                  i       ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (109 / 59)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 3.67 (66 / 18)  


 645 23.71 7.76 5.17  chr2_120462541_120465424      904  1135 (1749)    L1M4_orf2#LINE/L1        1   238 (670)  

  chr2_120462541_    904 TGGAAATGTATCCCATATTCATGGATTGGAAAA------ATGGTTAAAAT 947
                               vi        i              i ------  v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_120462541_    948 GCCTGTGTACTATCCAGA---AT--ACAGATTCAACACAATTTCTATGAA 992
                          v vi --   vi   i ---  --           i    ii    v  
  L1M4_orf2#LINE/     51 GGCAAT--ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_120462541_    993 AATTCCAAAGGCATCATTCATAGAAATAGAAAAA---ATTCTAAAATGTG 1039
                            i   ivv  v iv  iii      v  v  i---  i       vii
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_120462541_   1040 TATGGAACCAAGAAAGACCCTAAATAACCAACACAGTCTTAAGAAAGAA- 1088
                                viivi ii     vi    i    v   i    i i      -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_120462541_   1089 --CAATGTTGGGCCAGACACGGTGGCTCACACTTGT-AATCCCAGCACTT 1135
                         --   v     ---  ------- i         vi-   ii  iv    
  L1M4_orf2#LINE/    199 AACAAAGTTGG---AG-------GACTCACACTTCCCAATTTCAAAACTT 238

Transitions / transversions = 1.75 (35 / 20)
Gap_init rate = 0.04 (9 / 238), avg. gap size = 3.33 (30 / 9)  

1735 23.05 8.79 0.98  chr2_120462541_120465424     1386  1897 (987)    L1M4_orf2#LINE/L1      190   741 (167)  

  chr2_120462541_   1386 AAAAAAAAGAACAATGTTG-AGGCATCATTCTTCCTGATTTCAA--CTTA 1432
                              i        v    -   vv   iv     ii       --    
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_120462541_   1433 TATTATAAGGCT---GTCATCAAAATATTACGGTACTGATGTGAAAACAG 1479
                         i--  i  i   ---  v     i i v ii       iii i ii i  
  L1M4_orf2#LINE/    240 C--TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_120462541_   1480 ACACATAGAACAATGGAGCAGAAT--AGACTCCAAAAATAAACC--TTCA 1525
                            i     v       ii     --   v    i         -- v  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_120462541_   1526 CTGATATGGTTAAATGGTTTTTGGTAAGGATGCCAAGACCAT-------- 1567
                         i --      i  v  i    i ii    i            --------
  L1M4_orf2#LINE/    338 TT--TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_120462541_   1568 -----------CTTTTCAACAAATTAAGCTGGGAAAACTGAAAATCCACA 1606
                         -----------             viv       v     i v ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_120462541_   1607 TGCAAAACAATGAAATTAGACCCTT-CC----ACTATGCACAAAAATCAA 1651
                                v      i  i     i -  ----  i  ii        i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_120462541_   1652 TTCAAAATTGAATGAATACTTAAACATAAGACCTGGAACTGTAAAAATCC 1701
                         i       v  vii? v  i    ii     v  ii    i     v  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_120462541_   1702 TAGAAGAAAACATAGG---AAAACTTCCTGACATTGGCCTTAACAATAAT 1748
                                         ---   v    v    v    vi vii    ii 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_120462541_   1749 GTTTTTGGATACCACACCAAAAGGTCTGGCAACAAAAGCAAAAACA---- 1794
                         -  i  i    iv          vv vi          v     i ----
  L1M4_orf2#LINE/    586 -TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_120462541_   1795 AGTGGGATCACATCAAACTAATAAGCTTCTGAATAGCAAAGGAAACAATT 1844
                          i v   iiv       v v v  i   i  viivv       v  v  i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_120462541_   1845 AACGAAATTAAAAGGTAACCCACACT-TGGGACA---TATTTGCAAACCA 1890
                           vi  i v     ii        vv-     v ---          i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_120462541_   1891 TATATCT 1897
                                
  L1M4_orf2#LINE/    735 TATATCT 741

Transitions / transversions = 1.58 (71 / 45)
Gap_init rate = 0.03 (15 / 552), avg. gap size = 3.33 (50 / 15)  

 824 13.99 3.11 7.77  chr2_120462541_120465424     2200  2392 (492)    L1M4_orf2#LINE/L1      725   908 (0)  

  chr2_120462541_   2200 TTGCAAACCATATATCTGATAAGGGGTTAATATCCAAAATATATAAAGAA 2249
                                i                 ii vi      i             
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_120462541_   2250 CTC--ACAACTAAATAGCAAAAATAAATAGCCCAATGGCATAAATAACCC 2297
                            --      v    ------     v  --------- i         
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATA------ATAAAAAG---------ACAAATAACCC 809

  chr2_120462541_   2298 AGTTATTAAATGGGCAAAGGACCTGAA----CATTTTTCCAAAGAAGGCA 2343
                          i  ?vv              ii    ----     i          ii 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_120462541_   2344 TAAAAATGGCCAACAGGTATGTGAAAAGGTGCCCAATATCACTAATCGT 2392
                           v          i i i ii       i   i   i    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.33 (20 / 6)
Gap_init rate = 0.02 (4 / 184), avg. gap size = 5.25 (21 / 4)  


3398 14.48 3.94 14.68  chr2_120510212_120512587      870  1884 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_120510212_    870 GGAAGATATCCCACGTTCAAGAATTTGGAGACTTAATCTTGTTAAGAAGA 919
                          i           i     v i   v i         v         v i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_120510212_    920 CAGTACTACCCAAAGTGATCCATAGATTAAATGCAATTCCTATCAAAATC 969
                           i    v      v     i i     v  i     i            
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_120510212_    970 CAAACGATGTTATTTGCAGAAATAGAAAAACCCATTCTAAAATCCATATG 1019
                          v i viiv  v           v  v  i iv  i       i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_120510212_   1020 GAATCTG-AAGGGA---------GCCAAAACAATCTTGAAAA-GAAGAAG 1058
                            -v  -      ---------                   -      v
  L1M4_orf2#LINE/    153 GAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_120510212_   1059 AAAGTTAGAGGACTCACAGTTCCTGATTTATTTCAAAAGTTACTACGAAA 1108
                               i           v    ii    ----     v       i  i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTT----CAAAACTTACTACAAAG 247

  chr2_120510212_   1109 CTACAGAATCAAAAACTGTGGGGCTGCGTGTGATGGCTCACACCTGTAAT 1158
                               ----------------------------------------    
  L1M4_orf2#LINE/    248 CTACAG----------------------------------------TAAT 257

  chr2_120510212_   1159 TCCAGTGCTTTGGGTGGCTAAGGCAGGAGGATTGCTTGAGACCAGGAGTT 1208
                         --------------------------------------------------
  L1M4_orf2#LINE/    258 -------------------------------------------------- 257

  chr2_120510212_   1209 CAAGACCAGGCTGAGCAACATAGCCAGACCCCATCTCTACAAAAGAAAAA 1258
                               --------------------------------------------
  L1M4_orf2#LINE/    258 CAAGAC-------------------------------------------- 263

  chr2_120510212_   1259 AAAAAGCAGTGTGTTACTGGCAATACAGACAGACAT-T-GACCAATGGAA 1306
                         -------      v        -  vi  i      - -  i        
  L1M4_orf2#LINE/    264 -------AGTGTGGTACTGGCA-TAAGGATAGACATATAGATCAATGGAA 305

  chr2_120510212_   1307 TAGAATAGAGAGACTAGAAACAAACCCTTGTAAATATGGTAAAATGATTT 1356
                               v     v i     i      v ii vv      v  v      
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_120510212_   1357 TTGACAAGGGTGCCAAAACCACTCAGTGGAGAAAAGACAGTCTTTTCAAC 1406
                          i              i    i   i   i    ii i            
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_120510212_   1407 AAATGGTGATGAGAAAACTGGATACCCACATGGAAAAGAAAGAAGTCAGA 1456
                                 v  i  v         ?       v       v     ii  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_120510212_   1457 CCTTTTCCTTATACCATATACAAAAATTAATGTAAAGATGGCTCAAAGAC 1506
                           ii v   i i                  ivi   -    v   ?    
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAA-ATGGATCAWAGAC 504

  chr2_120510212_   1507 ATAGA-----GACCTAAAACTATAAAATTCATAGAAGAAAACA-GGGAAA 1550
                         v  i -----  v              i  v            -i  ?iv
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_120510212_   1551 AAATCTTCATGACATTAGATATGGCAGTGATTTTGTAGGATATGATAACA 1600
                                 i    v  i i vv    i  i   iv   -      i v  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-ATATGACACCA 603

  chr2_120510212_   1601 AAAGCACAGGCAGCACAACAAA-------TAAGTTGGACTTCATCAAAG- 1642
                                 i   i  v  v   -------   i               i-
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_120510212_   1643 ------CTTTTGTGTATTAAAGGACACTGCCAAGAGAGTAAAAAGACAAC 1686
                         ------        iv i          ii     i   i          
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_120510212_   1687 CCACAGAATGTGAGAAAATGTTTGCGAACCAGATATATGATAAGAGATTA 1736
                                   v        i     i  i  v    v       i  i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_120510212_   1737 ATATCCAGAATATATAAAGAACTCCTACAACTCAGCAACAACAAC-CAAA 1785
                         i                       i         ii  i  v  v-    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_120510212_   1786 --AGCCAATTCGAAAATAGGCAAAGAACTT----ACACATTTCTCCAAAG 1829
                         -- v      ?i     i       i i  ---- v              
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_120510212_   1830 AACATATATAAATGGCTAATAAGCACATTAAAATATTTTCAGCATCACTA 1879
                           v     i       i           v    v  vi   i     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_120510212_   1880 ATCAG 1884
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.47 (85 / 58)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 9.45 (189 / 20)  


3108 26.89 0.66 0.99  chr2_120519714_120526128.rev     5013  5923 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_120519714_   5013 TGGAGGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5062
                             iii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_120519714_   5063 AGCCATACTGCCCAAGGCAATTTATAGATTCAATGCCGTCCCCATCAAGC 5112
                         i  v     v     ivii  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_120519714_   5113 TAACAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5160
                          vv  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_120519714_   5161 TACGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAG 5210
                           i    viiv  ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_120519714_   5211 AACAAAGCTGAAGGCATCATGCTACCTGACTTCATACCATACTACAAGGC 5260
                                i  i   vv   ii  v  ii i    v v v        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_120519714_   5261 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGACC 5310
                                 i   i    ii         i iv ii i   v i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_120519714_   5311 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5358
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_120519714_   5359 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATAGGGAAAGGATTCC 5408
                          vi    i  i     ivv  vv  i v  vvv   i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_120519714_   5409 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5458
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_120519714_   5459 AAAATTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5508
                         i  i     i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_120519714_   5509 TTAAAGACTTAAATGTTAGACCTAAAAACCATAAAAACCCTAGAAGAAAA 5558
                          i ?    i       v   v      - i      vi i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAA 545

  chr2_120519714_   5559 CCTAGGCA-ATACCATTCAGGATATAGGCATGGGCAAGGACTTCATGTCT 5607
                          v    ?i- v i -   iv  iv v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_120519714_   5608 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGGCAAATGAGATCT 5657
                          vi            vvi          vv     v ii    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_120519714_   5658 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5707
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_120519714_   5708 ACAGGCAACCTACAGAATGGGAGAACATTTTTGCAATCCACCCATCTGAC 5757
                          v  i     i              v  v       vi  ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_120519714_   5758 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 5807
                           i  i  vi          v  i         vv    v ---   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAA 791

  chr2_120519714_   5808 -AAAAAAAAAAACAACCCCATCAAAAAGTGGGCGAAAGGTATGAACAGAC 5856
                         -     i v   i     v  i?    i     i  i i v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_120519714_   5857 ACTTCTCAAAAGAACACATTTATGCAGCCAACAGACACATGAAAAAATGC 5906
                          i     v      v i  vi viii     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_120519714_   5907 TCATCATCACTGGCCAT 5923
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2357 22.89 5.28 7.17  chr2_120532102_120534322      532  1326 (895)    L1M4_orf2#LINE/L1        1   780 (128)  

  chr2_120532102_    532 TGGAAAGACATTCTA----CATTGAATGGAAGACTCAACA-----AAGAT 572
                                 i  i i ----   v  v         i  i -----     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_120532102_    573 ACCAGTTCTCCCCAAATTGATATACAGGTTTAATGCAGTTTTTCTCAAAA 622
                         iv  i v              v     i  i  i   i iii v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_120532102_    623 TTCCAGTAAGATCTTTTGTAGATATAGGTAAGATTATTCTAAAATTTATA 672
                          i    ivivv i     i   v  v ii   v v  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_120532102_    673 TGGAAAGACAGAGGACTACTAGAATGGCTAAAGTAATTTTAAAAAAGGGG 722
                               vi  ii    -- i     i  i   ii   i  i      ii 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_120532102_    723 AATAAAATGGGAGGAATCATGCTACCCAATTTCAAGACTTACTATATAGC 772
                           i   i v      v   ii  v           i        i v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_120532102_    773 TTTCATAATCAAGACTTTGTGGTATTGGCA-AAGCGACAGACATGTAGAT 821
                          vivi          vv       i     -   -  i      i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATATAGAT 297

  chr2_120532102_    822 CAATGGAA---------------AGAAATAG--CCATACACAAATATGAC 854
                                 ---------------       i--       iv--    ii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGT 345

  chr2_120532102_    855 CT-CTGATTTTTGTCAAAGGTGCCAAAGTAATTCAGTGG---AAGAATAG 900
                          v-i       i v   i        iiiv     i   ---        
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_120532102_    901 TCTTAATAATGGTGCTGGATTAGAACCTGTGGAAGAAGGAAAAACAAACA 950
                             ---------------  ----- ---------------      ii
  L1M4_orf2#LINE/    396 TCTT---------------TT-----C---------------AACAAATG 410

  chr2_120532102_    951 AACTAAAAAAAGTGCTGGAGCAGCTGGATATCTGTAAG--ACAGAA-AAA 997
                         -----------       ii  i       ? iii v -- v    -i  
  L1M4_orf2#LINE/    411 -----------GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_120532102_    998 CCTTGACCTAAACCTTATACC-TATACAAAAATTAACTCAAAATGGATAA 1046
                         vi v    ivv    i i   -                          v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_120532102_   1047 TGAGCCTGAATATAAAATATAAAACTATGAAACTTAGAGACAAATAAACA 1096
                         ?iii   i   i   i vv         i     ivv   vi  v v i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_120532102_   1097 GGAGAAAATCTGTGGGACCTAGAGTTTAGAGAAGAGTTACTAGTAAACAT 1146
                           ? v      vi v     v i   -  iv  vi   v  --  i i  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTT-AGGCAATGGTTTCT--TAGATAT 596

  chr2_120532102_   1147 GATACCAAAAGGATGATTTTTAAAAAAAA-----GATAAAATGGACTTCA 1191
                           i        v ii vivvi    i   -----      v         
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_120532102_   1192 TAAAAAATTAAAAACTTTTG--CTTTGGGAAAGACTCTGTTAATAGAACG 1239
                          v    -             --   ii--  i   v  i i  v i ii 
  L1M4_orf2#LINE/    647 TCAAAA-TTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAAAGTG 693

  chr2_120532102_   1240 AGAAGCTAAGCTACAGACTGGGAGAAAGTATTCGTATATCACACATCTGA 1289
                          i   vi  v i     v         i    i i v    i i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_120532102_   1290 CCAGGAACTCGTGTCTAGCATATATACACAATGCCTA 1326
                         iv   i   i  i  i  v       v v  iv i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

Transitions / transversions = 1.80 (115 / 64)
Gap_init rate = 0.03 (23 / 780), avg. gap size = 4.30 (99 / 23)  

 431 23.57 3.57 3.57  chr2_120532102_120534322     1603  1742 (479)    L1M4_orf2#LINE/L1      769   908 (0)  

  chr2_120532102_   1603 AACAAGCTCCT-CAGCTCAACAATTAGAAAGCAAACAGTCTAATTCAAAA 1651
                           vi i   i -  i     i   v i  ii    i ii i    ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_120532102_   1652 ATGAACAAAAGACATGAAGAGACATTTCACCTGAGAGGATATACAGATGA 1701
                            ii    i  iv    v         v  vi   i        i   i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_120532102_   1702 C----AAATTCATGAAAAGATGTTAGACTAGCCATCAGGGAAGTG 1742
                          ----  iiv            i vi  -----    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAAC-----ATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (24 / 8)
Gap_init rate = 0.02 (3 / 140), avg. gap size = 3.33 (10 / 3)  


2507 27.21 7.09 1.51  chr2_120541915_120546501     3236  4095 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_120541915_   3236 TGGAAAAACATTTCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 3285
                               i i  ii    i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_120541915_   3286 GGCCATACTGCTCAAAGTAATTTATAGATTCAGTGGTATCCCCATCAA-- 3333
                            v     v i    v i  i  i       ii vv     i     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_120541915_   3334 -----GCTACCT--------GAAA-------------------------- 3344
                         -----   i   --------    --------------------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_120541915_   3345 ---------AAGAG-CCC-GTATAGCCAAGACATTCCTAAGCAAAAAGAA 3383
                         ---------   i -   - v        i   v  i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_120541915_   3384 CGAAGCCGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 3433
                          i   ii     vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_120541915_   3434 CAGTAACCAAAACAACATGGTGCTGCTACTGAAACAGATATATAGACCTA 3483
                               i   i   iii    i   vi iviii i   i       i v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_120541915_   3484 TGGAACAGAACAGAGGCGTCAGAATTAACAACACACATCCACAACCATCT 3533
                              i    iv   ivvi     v   vvv  i    ii iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_120541915_   3534 TATCTTTGATAAACCTGACAAAAACAAGCAATAGGGAAAGGATTCCCTAT 3583
                         v  i  i  i  ivv  v   i v  vv    i       i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_120541915_   3584 TTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAC 3633
                          i  i        i     v      v  ?   i     i  i v    v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_120541915_   3634 CTGGACCCTT-CCTTACACCTTATACAGAAATTAACTCAAGATGGATTAA 3682
                         i       i -   i     v      i            i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_120541915_   3683 AGACTTAAACGTGTAAAACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3732
                             i    --     i v       i      vi i           v 
  L1M4_orf2#LINE/    501 AGACCTAAA--TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_120541915_   3733 AGGCAGTA--CCATGCAGGACATAGGCATGGGCAAAAACTTC--AAACTA 3778
                            ?-   --i - v iv   v v  vv i     viii   -- i -  
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TA 595

  chr2_120541915_   3779 AAACACCAAAAGCAGTGGCCACAAAAGCCAGAATTGACAAATGGGATCTA 3828
                         vi            vvi  v       vv i   v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_120541915_   3829 ATTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTATCATCAGAGCGAA 3878
                           i   v v  i i   i  ii vvi   i  v       vv i  i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_120541915_   3879 CAGGCAATGTACAAAATGTACAATGTACAGAAAATTTTTGCAATGTATCC 3928
                         v  i   ivi   i    vi--------       v       vvi  vi
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGG--------AGAAAATATTTGCAAATCATAT 737

  chr2_120541915_   3929 ATCTGGCAAAGAGCTAATATCCAGAATGTATAAGAAACTTAAACAAATTT 3978
                              ii  i ii  vi          i     ii    ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_120541915_   3979 TCCAGAAAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAAC 4024
                         viv v     i    ----   v  i?    i    ii      v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_120541915_   4025 AGACACTTCTCAAAAGCAGACATTTATATGGCCAGCAAACACATGAAAAA 4074
                              i     v    v   i  vi v       ii  i          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_120541915_   4075 AAGCGCATCATCACTGGTTAT 4095
                          v  v  v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 5.29 (74 / 14)  


3141 26.62 0.77 0.88  chr2_120554164_120559933.rev     4370  5278 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_120554164_   4370 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4419
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_120554164_   4420 AGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4469
                         i  v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_120554164_   4470 TAACAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4517
                          vv  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_120554164_   4518 TACGGAACCAAAAAAGAGCCCATATAGCCAAAACAATCCTAAGCAAAAAG 4567
                           i    viiv  ii  v  viv               i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_120554164_   4568 AACAAAGCTGAAGGCATTACGCTACCTGACTTCAAACTATATTACAAGGC 4617
                                i  i   vv i  i  v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_120554164_   4618 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4667
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_120554164_   4668 AATGGAACAGAAC--AGAGCCCTCGGAAATAATACCACACATCTACAACC 4715
                                i    i--    i  --i       vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_120554164_   4716 ATCCAATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4765
                          viii  i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_120554164_   4766 CTATTTAATAAATGGTGCCGGGAAAACTGGCTAGCCGTATGTAGAAAGCT 4815
                           v  i  i         i    v      v  ?  ii   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_120554164_   4816 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4865
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_120554164_   4866 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4915
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_120554164_   4916 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTA 4964
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_120554164_   4965 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5014
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_120554164_   5015 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA-CATCAGAGTGAA 5063
                           i   v v  i i   i  ii vv    i  v    -  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_120554164_   5064 CAGGCAACCTACAGAATGAGAGAAAAGTTTTGCAATCTACCCATCTGACA 5113
                         v  i     i        i       vv       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_120554164_   5114 AAGTGCTAATATCTAGAATCTACAAAGAACTCAAACAAATTTACAAGAA- 5162
                          i vi  vi    i     v  i         vv    v ---   v  -
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAAT 792

  chr2_120554164_   5163 AAAAAAACAAACAACCCCACCAAAAAGTGGGCAAAGGATATGAACAGACA 5212
                              i     i     v ii?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_120554164_   5213 TTTCGCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCT 5262
                             v v        i  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_120554164_   5263 CATCATCACTGGCCAT 5278
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (147 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3720 23.89 1.00 0.33  chr2_120609690_120613895     2815  3714 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_120609690_   2815 GAAAGATATTCCATGTTCATGGATTAGAAGACTCAGTATTGATTCAATGT 2864
                                  i               i       i i     v vvi   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_120609690_   2865 CCATACTTCCCAAAGCAGTTTGCCAATTCAATTTAATCCCTATCAAAATA 2914
                          v     i      viii i i vi      ivi               v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_120609690_   2915 CCAATGATATTCTTCAAAGAAATAGAAAAAAATAAT-CTAAAATTTATAT 2963
                            iiviiv  i  iiv      v  v  -iv i  -        i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATAT 151

  chr2_120609690_   2964 GGAACCACAAAAGACTCAGAATAGCCAAAGCCGTCCTGAGAAGAAAAAAC 3013
                             vii   ii   i             i vi  i   i  ii  i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_120609690_   3014 GAAACTTTAGAACTCATAGTACCTGACTTCAAATTATACTACAGAGCTAT 3063
                         i  ii vv  i     i v v  ii i      viv       i     i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_120609690_   3064 AGTAACCAAAAC-TCATGGTATTAGCATAAAAACAGACACATAGACCAAT 3112
                              i   i  -vii     i i      ii i     i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_120609690_   3113 GTAACAGAATAGAGAAGCCAGAAATAAATCCATACATCTGCAGTGAGCTT 3162
                          v  i     v    iv           i        i iii  v ii v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_120609690_   3163 ACTTTTGACAAAGGTGCCAAGAACATACACTGGGGAAAGGACAGTCTCTT 3212
                          i   i     i          v   v  v         i i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_120609690_   3213 CAATAAATGGTGCTAGGAAAACTGGATTTCCATATGCAGAAGAATGAA-- 3260
                            i          i   v        v?   i     i         --
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_120609690_   3261 ---ACTTCTATCTC-TGCCATATACAAAAATCAAATGAAAATGGATTAAA 3306
                         ---  ii   i   -ii              i  v v         i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_120609690_   3307 GACTTAAATCTAAGGTCTCAAACTATGAAACCACTAAAAGAAAATATTGG 3356
                            i     v    iv  v       i    ivi  i       i  v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_120609690_   3357 AGCAACTCTCTAAAACATCAGTCTATGCAAAGATTTCTTGAATAATATCC 3406
                         ? i  v   iiivi  v ii vi  v    v i      ii   vv iv 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_120609690_   3407 CAAAAGCATAGGCAACCAAAGCAAAAATAGACAAATGAGATCACATCAA- 3455
                                 i i     v    v         i    vi  iiv      -
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_120609690_   3456 GTTAAAAAGTTCCTGCACAGCAAAGGAAACAATCAACAAAGTGAAGAGAT 3505
                         i       v  -i  ii vv       v  v     v        i   i
  L1M4_orf2#LINE/    652 ATTAAAAACTT-TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_120609690_   3506 GACCCACAGAATGGTAGAAAATATCTGCAAATTACCCATCTGACAATGGA 3555
                         i             v         i       i ivi      i  v   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_120609690_   3556 CTAATAACCAGAATATATAAAGAGCTCAGACAACTCAATAGGAAAAAAAT 3605
                           vi  v                i   vv           iv     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA- 799

  chr2_120609690_   3606 CTGATAATCTGATTTTAAAATGGGCAAAAAATCTGAATAGACATTTCCCA 3655
                          vi    i ii   ?v            ii  i              i v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_120609690_   3656 AAAGAAGACATACAAATGGCAAACAAGTTTATGAAAAGGTGCTCAACATC 3705
                                 i           v  i   ivi        i           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_120609690_   3706 ACTGATCAT 3714
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.89 (138 / 73)
Gap_init rate = 0.01 (8 / 906), avg. gap size = 1.50 (12 / 8)  


3243 15.31 6.95 8.36  chr2_120669507_120674050     3133  4053 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_120669507_   3133 TGGAAAGACATCATATGGTCATAG----GAAGATTTGATATTGTT----- 3173
                                 i   vi   v    i ----     i  i        -----
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_120669507_   3174 GTCAGTACTACCCAA--TGCTATCTACAGAGTCAATGCAATCC-TACTCA 3220
                          v  i    v     --  --         v    i       -  iiv 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_120669507_   3221 AATACCAACAGCGTTTTT-GCAGAAATAGAAAAACTGATCCTCAAATTCA 3269
                            v   i v  v     -        v  v  i        v       
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_120669507_   3270 TTAAAAAAAAAAAATCCCCGCAAGGCATTAAAACACACACACACACACAC 3319
                          ------ vii    ----      ------i  v  -------------
  L1M4_orf2#LINE/    149 T------ATGGAAAT----GCAAGG------GACCCA------------- 169

  chr2_120669507_   3320 ACACACACACACACAAACTTGAAGTTGCCAAAACAATCT-GTAAAGGCAG 3368
                         --------------------   - v             - v   i v  
  L1M4_orf2#LINE/    170 --------------------GAA-TAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_120669507_   3369 CACAAAGTCGGA---CTCACACTTCCCAATGTCAGAACTTACTACAAAGC 3415
                         v       i   ---               v   i               
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_120669507_   3416 TACAATAATCAAAACAG-GT----TTGGCATAAGGATA----TATGGTCC 3456
                             i       i    -  ----i             ----   i vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_120669507_   3457 AATGGAAC-----TGAGAGTCCAGAAATAAGCTCATATGTCTATG----A 3497
                                i-----                 i i    ii i    ---- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_120669507_   3498 CTGATTTTTGACATGAGTGCCAA---------ATGGTGAAAGAACTATCT 3538
                         i       i    v i       ---------    v       ivi   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_120669507_   3539 TTTCAACAAGTGGTACTGTGACAACTGGATTTCCACTTGAAAAAGAATGA 3588
                                  i    i   v           v?    v  v          
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_120669507_   3589 GGTTGGCCTCTCCCCTACATGGTTCATAAAATCATGTAAATAAAATATTC 3638
                         i     v ----      ----i   i ---i   i  --i    -   -
  L1M4_orf2#LINE/    449 AGTTGGAC----CCCTAC----CTCACA---CCATATA--CAAAA-ATT- 483

  chr2_120669507_   3639 ATAGAATTATTGATCAATGGATCAACAATCTAAATATAAGAACTAAA-CT 3687
                         ----  i --ii --         ?vi i      i     i     -  
  L1M4_orf2#LINE/    484 ----AACT--CAA--AATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_120669507_   3688 -TGAAACACCTGGAAGAAAGCATAGGGGTAAATC---AGGTCCTTGGAGC 3733
                         - i    v i i       i      ?       ---iv v      ivi
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_120669507_   3734 TGGCAATGGGTTCCTACATATGACACCAAAAGCATGAGCAACACCAACAA 3783
                         v        v   i  v                 ii       v-  v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA-AAGAA 624

  chr2_120669507_   3784 AGAA-----AAATTGGGCTTTATCAAAATTAAAAACTTTTGTACATGAAC 3828
                          i  -----       i   i                     i v v  v
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_120669507_   3829 GGACATTACCAAGAAAAGTTAAAAGACAAAGTACAGA-TGGGATAAAATA 3877
                              i  i       -  v         vvi     -     v      
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAA-GTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_120669507_   3878 T--GCAAAATATATAATTGATAAGAGATGAATCTCCAAAATACATAAAGA 3925
                          --     vi     vi       i  ivvi v    i    i       
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_120669507_   3926 ACA---ACG-CTCAACAA-AAAAAGATAAACAATCCAATTAAAACACAGG 3970
                           v---  i-     i  -       i   i  i      ?   v ii  
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_120669507_   3971 CAAAGGTCTTGAATAGACATTTCTCTAAAGAAGATATGCAAATGGCCAAT 4020
                               vi                 i           i            
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_120669507_   4021 AAGCACAT-AAAAGATG-TCAATATCCTTAATCAT 4053
                                 -        -    i   v????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (83 / 54)
Gap_init rate = 0.04 (40 / 908), avg. gap size = 3.52 (141 / 40)  


2583 14.57 3.95 24.23  chr2_120843398_120845901.rev      874  2012 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_120843398_    874 TAGAAATACATCCTATGTTCATGGAT-------------------GAGAT 904
                          i    v i    i            -------------------i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_120843398_    905 GACAATACTCCCCAGATTGTTCTGCACATTCAATGTAATCTCCATTAAAA 954
                          i            i    v   i  v      i i    i i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_120843398_    955 TTCCAGCTGGCATCTTTGCAAAAAGTAATAGGCTAATCCTGAAATTCACA 1004
                          i       v v i      i   v i i i   i     i       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_120843398_   1005 CAGATATTTAAAGACTCTAGAATAACCAAAACAA---------------- 1038
                         ii  v  vi  i ivi i      i         ----------------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_120843398_   1039 ---AATTAGAGGGTTCACAATTCCTGATTTCAAAACTTACTACAAAACTA 1085
                         --- i  i    ii     v    ii                    i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_120843398_   1086 CAGCAATTAAGAGAGTTTGTTACCAGCACAAGGATAGATATATAGAGCAA 1135
                            i   i    v   v  v   ii   i         i       v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_120843398_   1136 TGGAATA-AGTTGAAAGTTCAGAAATAAACCTTCGCATTTCCAGTCAACT 1184
                                - i    i   i            ivii     vii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_120843398_   1185 AATTTTTTTAAACTGTGCCAAGATAATTCAATGGAGAAAGAATTGTCTTT 1234
                         i     ivvv  vv         iv         i        v      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_120843398_   1235 TGAACAAATGGTACTGGGGCAAGTGACTATCCACATGCAAAAGAATGAAG 1284
                          v          i     i   v  iv  ?                    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_120843398_   1285 CTGGATAGGAAAATCAAGCCAAAGACCTAAATGTGAGAACTAAACTATAA 1334
                         i    ---------------------------------------------
  L1M4_orf2#LINE/    451 TTGGA--------------------------------------------- 455

  chr2_120843398_   1335 AACTCTTATAAGAAAACACATATAGGCCTGGCGCAGTGGCTCACACC-TG 1383
                         -- i i  i------------------------------        - i
  L1M4_orf2#LINE/    456 --CCCCTAC------------------------------CTCACACCATA 473

  chr2_120843398_   1384 TAATCCCAGCACTTTAGGAGGCCAAGGTGGGTGGATCCCAAGGTCAGGAG 1433
                           ------------------------------------   ------- i
  L1M4_orf2#LINE/    474 TA------------------------------------CAA-------AA 480

  chr2_120843398_   1434 ATTGAGACCATCCTGGCTACCACGGTGAAGCCCCATCTCTATTAAAAACA 1483
                            -------------------------------------------   v
  L1M4_orf2#LINE/    481 ATT-------------------------------------------AACT 487

  chr2_120843398_   1484 CAAAAAATTAGCCGGGCGTGGTGGCACCTGCCTCTCGGGAGGCTGAGGCA 1533
                              ----------------   --------------------------
  L1M4_orf2#LINE/    488 CAAAA----------------TGG-------------------------- 495

  chr2_120843398_   1534 GGAAAATCGCTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCAACATTGC 1583
                         -----   i--?ii    ------- i ---  i i-    i  v i ii
  L1M4_orf2#LINE/    496 -----ATCA--WAGACCT-------AAA---TGTAA-GAGCTAAAACTAT 527

  chr2_120843398_   1584 ATCACTGCACTCCAGCCTGGGTGACAGAGCGAGACTCCATCTCAAAAAAA 1633
                          ------------------------------ i    ---- i i  ---
  L1M4_orf2#LINE/    528 A------------------------------AAACTC----TTAGAA--- 540

  chr2_120843398_   1634 AAGAAAAAAGAAAACATACATATAAATATTCATGACTTTGGATTAGGCAA 1683
                         ---------         vi?i     v   i    i    i        
  L1M4_orf2#LINE/    541 ---------GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_120843398_   1684 TGGGTTCTTAGATATGACACCAGTAGCACAAGCAACAAAAGAACAAAAGA 1733
                            v                  iv                   ------ 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA------A 625

  chr2_120843398_   1734 AAACAGATAAATTGCATTTTA-CACAAATTTAAAACATTCATGCATCAAA 1782
                            i          v i  i -  -     v     v  ii   v     
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCA-AAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_120843398_   1783 GAACATTATCAAAAAAGCAGGAAAAAAA---GCAGAAGGGGAGAAAGCAT 1829
                          i   i      i    iiii  i v  ---i     v        ii  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_120843398_   1830 TTGCAAATTATACCTCTGATAAGGGACTTGTCATCAGACTATATAAAGAC 1879
                                 i   iv                 vvi    v          v
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_120843398_   1880 CTCTTACATCTTGGTAATAAAAAGACAAATAATCTAACTTAAAAATGGGC 1929
                                 v  iii                  i i  i ?          
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_120843398_   1930 AAATGATCTGAATAGACATTTCTCCAAAGAAAATATACAAGTGGCCAAGA 1979
                            v   i                       i        i       v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_120843398_   1980 AGCACAGGAAGA-ATGAACAACATCGCCAGCCTC 2012
                               v   i -   vv       i????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (113 / 49)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 13.96 (321 / 23)  


2779 22.97 6.06 2.29  chr2_121228668_121230900.rev      876  1750 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_121228668_    876 TGGAAGGACATACCTCGTTCATGAGCCAGATTACTCAATATTATTAAGAT 925
                              i  i  v  vi       iiiii  vv   i      i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_121228668_    926 GTCAATTCTCTCCAAATACATCTACA--TTTACCACAATCTCAATCAAAA 973
                          v    v   i      vv       --  i v i     i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_121228668_    974 TCTTAAAAGCAGGGTTTTTGGAGAGATTGCCAAGATGATTCCAAAATTCA 1023
                           ii ivv  vv--      v   i    v    v    i i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT--TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_121228668_   1024 TATGAAAATGCAAAGGACCTAGAAT-GC--AAAC--TCT-GAAAAAGAAA 1067
                             i        i     i     -  --    --   -         i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_121228668_   1068 AAGAATACTTAGAGAGCTAA-GCTACCTGACTTCAAGACTTGTTATAAAG 1116
                           v  - v  i   ii  v -i  v  ii i     i    ii  i    
  L1M4_orf2#LINE/    199 AACAA-AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_121228668_   1117 CTACAATAACCAAGAAAGTGTGCTGTCACTGTCA--ATG-TACACAAATA 1163
                              i   i     v      --  -    v  -- v -  v   v   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTG--GT-ACTGGCATAAGGATAGACATATA 294

  chr2_121228668_   1164 GATCAAAAGAATAGAACAGAAAGTCCAGAA-TAGGCCCACACATATATGG 1212
                               vi        iv  i         -  ii    i    v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_121228668_   1213 GAAGCAGATTTTTTTACAAAGGTGCAAAGGCAAGTTGATGCGGACAGAAT 1262
                         vv iiv      iv-    i     v   i v v ii   v   v     
  L1M4_orf2#LINE/    345 TCAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_121228668_   1263 AATCTTTTCAACGAATGGGGCTGGAACAATT---T-------TTTAAAAG 1302
                          i          i     v     i    i --- ------- vi     
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_121228668_   1303 AAC----TTTGATACATACTTTGTATTATATACAAATATTAGCTTAATTT 1348
                           i----  v  iv v   i iii ii         v    i  i  ---
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA--- 490

  chr2_121228668_   1349 AATATATATCATATAT-TAAATTTAAAACCTAAAACTTTAATACTTCTTA 1397
                            iv  --  ? v i-     v   i v        v   v   -    
  L1M4_orf2#LINE/    491 AATGGAT--CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTA 537

  chr2_121228668_   1398 AAAGAAAACATAAGAGAAAATCCTTGTGACTTCAATTTAGGCAAATATTT 1447
                         i           i ? v     i i     i iiiv        vvi   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_121228668_   1448 CTTAGATGAAATTCCAAATGCATGATATATACAAGAAAAATTTGACAAAC 1497
                                ivi iv     v   ii vvv i v        v v  i   i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_121228668_   1498 TGGAGTTCATCAAAACTAAAATCCTTTAGTCTACAAAAGACACTGTTAGG 1547
                             v          i     v i   ivv  v    i      i i i 
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_121228668_   1548 AAAATGAAAAGATAAGCCACAGGCTGGGA-----TATCTGCAAA------ 1586
                            i        i  v      iv     -----   i      ------
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_121228668_   1587 ----------AGACTTCTATCCAAAATATATAAAGAATTCTCAAAACTAA 1626
                         ----------i     v      i             i   i v    v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_121228668_   1627 GCAATAAGGAAACCACCAACCCATGTTAAAAAAAAAATTGAGCAAAAGAT 1676
                         ii     ii i  v vi      -i  ?     -----  i     i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCA-ATTWAAAAA-----TGGGCAAAGGAT 831

  chr2_121228668_   1677 TTTCTTAGACTTTTCACTAGAGACAATATACAGGTGGC-AATAAAGCACA 1725
                           vvv     v    v i i   vi       ii    -     -     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA-GCACA 880

  chr2_121228668_   1726 CCAAAAGA--ATCA-CATCACTAGTCAT 1750
                         iv      --v   -     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (115 / 83)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.52 (73 / 29)  


 815 30.40 9.40 3.96  chr2_121310292_121312821.rev      900  1580 (950)    L1M4_orf2#LINE/L1       13   730 (178)  

  chr2_121310292_    900 CCGTGATCATGGGCGGGAAAACTCAAAATGACAAAGATGGCAATCTTCTC 949
                           i  v      iiv    i   i  v  viiv           vi  i 
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_121310292_    950 CAAATTCATTCACAAAT--AACTCAATTATAATCAAAACCCCAACAGGGA 997
                               v  ii   i  --   v    iviv       i    i v vvv
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_121310292_    998 TTTT--CAGGACTCTAACAAGTTGATCCTAAAGTTCTCACGGTAGAACAA 1045
                             --   i v - i     i          i   vi i  v ivi   
  L1M4_orf2#LINE/    113 TTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_121310292_   1046 GGG---CAGAAAAAGAGCCAAGACCAT-TTGAAAGAG--GAACACA-TGA 1088
                            ---     ---v      i  v  -      i  --     v - vi
  L1M4_orf2#LINE/    162 GGGACCCAGAA---TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_121310292_   1089 GGGGATT-----TTCCC---TGCCATGCTTAACAGAAAGCTGTAAGACCT 1130
                          i   i -----     --- v v vi    vi v      ii iv vii
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_121310292_   1131 AAGACAATGTGAGA-TGGCACCAGAAGAAACTAATAGACCAAAGGAACAA 1179
                               i    iv -     iv  i v i  vv     i   v    i i
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_121310292_   1180 AGTAGGGAGCCCGGAAACAGAGCTACATATGCAAGGAAAATTGACATGTG 1229
                          i v i   i  i    i i v i i i  vi v  vv      iv vi 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_121310292_   1230 ACA---GTTTTTGCATTTAAAAAAATCATTAAA-AATTAAGAAATAG--- 1272
                            ---  ----  v------  i i    v  -iivv  ii     ---
  L1M4_orf2#LINE/    359 ACAAGGGT----GCC------AAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_121310292_   1273 ----AATAATTGCTACTGAGACGATT----ATTCACATAGATAAAGTAAA 1314
                         ----  i  v  v i   i   i i ---- ?i     iv -    --  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAG--AA 445

  chr2_121310292_   1315 ACAAATTTGATCTCTACATAATGTCAAAGACAAAACAGT--CTCAGC-TA 1361
                         vv  i  v  i i    v v iii  v v      - v --    iv- i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATG 494

  chr2_121310292_   1362 AATTTAAAAGCTACATGTAAATGC-ACAATTTTTTAAATTTTAGAA---- 1406
                         i  iv? i v   v      iv  - v  i v vv  v i      ----
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_121310292_   1407 ---TAGGAGAATAGCCGTATGACCTCAAGGACAGA-AAGAACCTCCTAAA 1452
                         ---    ? v v v ivii      ii-  vi  i-  viiii  i  i 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGA 593

  chr2_121310292_   1453 ----ATAC---AAACACAAGCCACAGAGGAAAAGAATC-ATACACTCGAC 1494
                         ---- i  ---  i       v   i i     -   v-   v i v   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGAC 642

  chr2_121310292_   1495 TGTGTTAAAATGTACAACCGTTGT--CTCAATAAACCATGCCA------T 1536
                          vii i     vv v   iv    --i    vii  vv ii  ------ 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_121310292_   1537 ACCCAAAGATAATGGCCAACAGAA-GACTGAGAAATTATTTATAA 1580
                         iv--     i  ---  v      - i--      v     ii  
  L1M4_orf2#LINE/    693 GA--AAAGACAA---CCCACAGAATGG--GAGAAAATATTTGCAA 730

Transitions / transversions = 1.29 (115 / 89)
Gap_init rate = 0.05 (36 / 718), avg. gap size = 2.53 (91 / 36)  


1631 18.35 2.14 0.61  chr2_121453696_121455813.rev      499   825 (1293)    L1M4_orf2#LINE/L1      157   488 (420)  

  chr2_121453696_    499 TGCAATGAACCCTGAAGAGCCAGAACCATCTTGCAAAAGGAGGACAAATT 548
                              v i    v   v     i   v      v     i  i     v 
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_121453696_    549 TGGAGAACTCATATGCCCCAATTT----ACTTCCTACAAATTGACAGTAA 594
                              i     i ivi        ----    v       viv       
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_121453696_    595 TAAAGACTGCATGTGGTACTGACATAAAGAGAGACATAGAGATCCAGGCA 644
                          v     v --          i     i  v       v     v v v 
  L1M4_orf2#LINE/    257 TCAAGACAG--TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_121453696_    645 ATATAACTGGCAGTTCAGAAAGAAACCCAGACACTTAAGGTCAATTGATT 694
                            v  i  iv   i      v       v   i   v            
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_121453696_    695 TTTGACAAGGATACCAAGACCATTCAA-ATGGAAAGAACAAT-TTTTCAG 742
                           i       i i              -iv        i i -      i
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_121453696_    743 CAAATGG-ACTCAGACAACTGCGTAATCACATGCAAAAGAGTAAGTTTGG 791
                                -i  vi        vi  ?i             i i iv    
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_121453696_    792 ATCCCTACCTCATACCATGTACAAAGATTAACTC 825
                          i          i     i      i        
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTC 488

Transitions / transversions = 1.27 (33 / 26)
Gap_init rate = 0.02 (5 / 332), avg. gap size = 1.80 (9 / 5)  

 327 10.34 1.72 0.00  chr2_121453696_121455813.rev     1119  1176 (942)    L1M4_orf2#LINE/L1      477   535 (373)  

  chr2_121453696_   1119 AAAAATTAACTCCAAATGGATCAAAGACCTCAATGGAAGAGCTA-TATTA 1167
                                     v          ?      v    v        -v i  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_121453696_   1168 TAAAACTCT 1176
                                  
  L1M4_orf2#LINE/    527 TAAAACTCT 535

Transitions / transversions = 0.25 (1 / 4)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1)  

1896 14.58 5.99 1.04  chr2_121453696_121455813.rev     1243  1626 (492)    L1M4_orf2#LINE/L1      506   908 (0)  

  chr2_121453696_   1243 TAAAT--AAAAGTCTATATAAACTATAAAACTCTTAGAAGAAAACATAGA 1290
                              --  i  -   ---                              i
  L1M4_orf2#LINE/    506 TAAATGTAAGAG-CTA---AAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_121453696_   1291 GGTAAATTTTTGTGACCTTGGATTAGGCAATGGTTCCTTAGCTATGACGC 1340
                         ?      i  i          i             i     v      i 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_121453696_   1341 TAAAAGCACAAGCAATTAAA------------AAATTGTACAGCCTCAAA 1378
                         i              iv   ------------      v  vv v     
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_121453696_   1379 ATTAAGAACTTT-GTGCTCTAAAAGAAAGTATCAAGGAAATGAAAAGAAA 1427
                              i      -     ii   i  v v       i  i        v 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_121453696_   1428 ATCCAGAGAATGGGAGAAT-TATTTGCAAATCATATATCTGACAAGGGTC 1476
                          i   v            v-                      i     v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_121453696_   1477 TAGTAACCAGA-TATATGAAAAATTCTTACAATTTAACAGCAAAAAGACA 1525
                          v   v     -     i  i  i        i i  i ii         
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_121453696_   1526 A----CCAGGTTTCAAAATGGGCAA--TATTTGGGTAGACAGTTCTCCAG 1569
                          ----  vii  ?v           --v     ii      v       i
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_121453696_   1570 AGAAGATACGCAAATGGCCAATAAGCACCTGAAAAGATGTTTAACATTAT 1619
                                 ii                  v          i i     i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_121453696_   1620 TAATCAC 1626
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.84 (35 / 19)
Gap_init rate = 0.02 (9 / 403), avg. gap size = 3.00 (27 / 9)  


3012 16.02 8.55 0.62  chr2_121487206_121489295      501  1143 (947)    L1M4_orf2#LINE/L1      120   813 (95)  

  chr2_121487206_    501 AAAAATAGAAAAGCTAATCCTATCACTCATATGAAATTGCAAGGCACCCT 550
                          i    v  v     i      vv i       i  v       v    -
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC- 168

  chr2_121487206_    551 CAAATAGCTAAAACAATCTTGAAAAAGAAAAACAAGGT-GGAGGACTCAT 599
                         vi      i                    i     i  -          i
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_121487206_    600 ATTTTCTGATT-CAAAACGTATTACAAAGCTACAGTCATCAAAACAGTGT 648
                          i  i ii   -      v  i              v     i       
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_121487206_    649 AGTACTGTAATAAAAATAAGCATATAGATCAATGGGATAGAAGTAAG-GT 697
                         i      vv    ii   ii               i      v i  -  
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_121487206_    698 CCAGAAATAAAC----------------AA---ATTTTCAACAAGGGTGC 728
                                     ----------------  ---      i          
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_121487206_    729 CAAGAGCATCAGATGGGGAAAGAATAGAGTCTTCAACA------------ 766
                              v   ivi               vv i       ------------
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_121487206_    767 -------------TACAT--AAAACAATCAAGTTGGACCTCTACTTCACA 801
                         -------------i    --    v   v          i    i     
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_121487206_    802 CCATACACAAAACTTAATACTAATGAATCAATCAAAGACCTGAATGGAAG 851
                              i      v    iv -  --   vi    ?      i    v   
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTC-AA--AATGGATCAWAGACCTAAATGTAAG 515

  chr2_121487206_    852 AGCAAAAACTATAAAACTCTTAGAAGAAAACATAGCGGTGAATCTTCATA 901
                            v                               v?  i       i i
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_121487206_    902 ACCTTGGATTTGCCACTGGACCCTTAGATATGACACCTAAAGCATACACA 951
                                i  v v  v   vii               v      i vi  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_121487206_    952 ACCAAAGAAAAAA---ATAAATTAAGCGTTATCAAAATTTAAAAAGTTTG 998
                           v          ---       iii v i         v    vv    
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_121487206_    999 TGCTTCAAGGGATACCATTAAAAAAGTGAAAAGACAACCTACAGAATGGG 1048
                                 i   i  i  i  i                 i          
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_121487206_   1049 A---AATATCTGCAAATCATATATCTGATAATATTCTATTATCCAGAATA 1095
                          ---     i                     vivv  vv           
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_121487206_   1096 CATGAAGAACTCTTACAACTGAACAACAAAAAGACAAGCAACTCAATT 1143
                         i  i                v  i  i          ii   i     
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

Transitions / transversions = 1.46 (60 / 41)
Gap_init rate = 0.02 (12 / 694), avg. gap size = 4.92 (59 / 12)  

 520 16.82 0.00 0.93  chr2_121487206_121489295     1492  1598 (492)    L1M4_orf2#LINE/L1      803   908 (0)  

  chr2_121487206_   1492 ACAGCCCAATTTTTTAAATGGGTAAATAACTTGAATAGATATTTACCCAA 1541
                          i i     -  ?vv       i   vi i         i    vi    
  L1M4_orf2#LINE/    803 ATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_121487206_   1542 AGAAGATATACAAATAGTCAACAAGCACATGAAAAGATGTTCAAAGTCAT 1591
                                        i i   i                 i    vi   ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_121487206_   1592 TAGTCAT 1598
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.01 (1 / 106), avg. gap size = 1.00 (1 / 1)  


 573  9.92 4.13 0.83  chr2_121618229_121622050      493   613 (3209)  C L1M4_orf2#LINE/L1   (0)   908   784  

C chr2_121618229_    613 CTCAA-AA-AACAAAACAAAACAAAACAA--AAAAACTGGGCAAAGGACT 568
                              -  -  v  i     -i  vv   --?    v           i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATT 832

C chr2_121618229_    567 TGAATACACATTTCTCCAA-GAAGATATACAGATGGCCAGTAAGCACATG 519
                               v            -           i       i          
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

C chr2_121618229_    518 AAAAGATGCTCGACATCACTAGTCAT 493
                                    i      ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (6 / 5)
Gap_init rate = 0.04 (5 / 125), avg. gap size = 1.20 (6 / 5)  

3224 17.35 2.28 0.91  chr2_121618229_121622050      891  1547 (2275)  C L1M4_orf2#LINE/L1   (79)   829   164  

C chr2_121618229_   1547 GACTCTAGATAGCCAAAACAAAAGTGAAAAAAGAAGAACAAAGTTGAAGG 1498
                            i vii             vvv       -              i   
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAA-GAAGAACAAAGTTGGAGG 212

C chr2_121618229_   1497 TCTCATACTTCTTGAT-----AATTTGCTACAAAGCTACAGTAATCAAAA 1453
                         v    i     iii  -----  i  i                     i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

C chr2_121618229_   1452 CAGTATGGTACTGGCATAAAGACAGACATATA-CTCAAATGCGATCCAAT 1404
                             i              i  i         -v  -    vi  vv   
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATC-AATGGAATAGAAT 311

C chr2_121618229_   1403 ACAGGGCCCAGAAATAAACCCTCACAT----GGTCAAATGATTTCCAACA 1358
                         vv  i i              vi    ----      v      i i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

C chr2_121618229_   1357 ATGATGCCAAGACTACTCAATGGGGAAAAAACAGT--TTTCCACAAATGG 1310
                          v i         i i            i  i   --    v        
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

C chr2_121618229_   1309 TGTTGAGAAAACAGGATATCCACATGAAAAAAAAATTGTAGGTGAAGCCT 1260
                           i  i  v   v     ?       v    i  --  v  v  i v  i
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAA--TGAAGTTGGACCCC 459

C chr2_121618229_   1259 TGCCTTATACCACATACAATATTTAATTGAAAATAGACCAAAGACCTAAA 1210
                          i   i i    i      v v    i v     i  i  ?         
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

C chr2_121618229_   1209 CTTAAGAGTTGAAACTATAAAACTCTTAGAAGAAAACATAGG-GTAAAAC 1161
                         iv      i i                               -     v 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

C chr2_121618229_   1160 TTCATGACATTAGATTTGCCAATGATTTCTTGGATATGACACCAAAAGCA 1111
                            i    v  i i  v v     i      i                  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

C chr2_121618229_   1110 CAGGTAA-GAAAGGAAAAATAGATTAATTAGACTTCGTCAACATTAAAAT 1062
                           i i  -i    i          v    i      i    v       v
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

C chr2_121618229_   1061 GCTTTGTACATTGAAGGACACAATCAGCAGAGTGAAAAGGCAACCCACAG 1012
                         vi     i v ii        v    iv i         i          
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

C chr2_121618229_   1011 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAACGATTAATATCC 962
                                                              iv  i vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

C chr2_121618229_    961 AGAATATATTTTTAAAATTC-TACAACTCAACAACAAAAAAACAAACAAC 913
                                  --vv i  i  -          i  i     i     i   
  L1M4_orf2#LINE/    760 AGAATATAT--AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

C chr2_121618229_    912 TTAATTAAAAACTGGGCAAAAG 891
                         ii    ?    v        i 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.71 (70 / 41)
Gap_init rate = 0.02 (11 / 666), avg. gap size = 1.91 (21 / 11)  

 373 25.35 5.63 3.52  chr2_121618229_121622050     1856  1997 (1825)    L1M4_orf2#LINE/L1       45   189 (719)  

  chr2_121618229_   1856 TAAGAATGTCAGT-TTCCCCAAATT-ATTTATAGTTTTAAAGCAAAT--- 1900
                              -  v  i -i          -  i  i  v  i  v    vi---
  L1M4_orf2#LINE/     45 TAAGA-TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr2_121618229_   1901 -TCAATATTCCTCCCAA--GATTTTTTTGTAACTATAGACAAGCTTCTTC 1947
                         -    v  ----    i-- vi       i ivv  v        vv i 
  L1M4_orf2#LINE/     94 ATCAAAAT----CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_121618229_   1948 TAAAATTTATATGGAAAGATAAAAGAATTAGAATGACCAAAACTGTTTTG 1997
                                i         vii  ii  vii     ii       vi i   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

Transitions / transversions = 1.57 (22 / 14)
Gap_init rate = 0.04 (6 / 145), avg. gap size = 2.17 (13 / 6)  

1397 26.86 6.80 4.69  chr2_121618229_121622050     2287  2904 (918)    L1M4_orf2#LINE/L1      176   806 (102)  

  chr2_121618229_   2287 CTAAAACCATATTTGGGAAAAAGAAAAGGATAAAGTGGAAGAAATCCCTC 2336
                          i     v  v  ---         i -- i     v i  i v  v v 
  L1M4_orf2#LINE/    176 CCAAAACAATCTT---GAAAAAGAAGA--ACAAAGTTGGAGGACTCACAC 220

  chr2_121618229_   2337 TACCTAATTTTAAGGCTTACTACATAGCAGTGCTAATCAAGGTAGTGTGC 2386
                          v  i     i  ii         v   viiiv        ii      v
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_121618229_   2387 TATTGGCAGAGGGACAGATACAAAGACCAGTGGCGCAGGGCAGAGAATCT 2436
                           i     v i   i   i i v   i  i   vii  iiiv    i  i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_121618229_   2437 AGAAATAGACCCACACAAGCACAGCCAACTG--TTTTGACAAAGTTGTAA 2484
                                i     i   vvi ii i   i  --   i     i v  iv 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_121618229_   2485 AAGTC---CAACAGCGA-----TAATCTTTCCAACAAATGGCACTACAGC 2526
                          iii ---   ii v  -----  i     i          ii  ivii 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_121618229_   2527 AACTGGA------CATG-GAAAGTATGAAACTTGACCCAAATCTCACACC 2569
                                ------    -i    v     ii v     vv i        
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_121618229_   2570 CTAGACAATAATCAA----AAAGGGAC-----ACTGAACTG-AAGTG-TA 2608
                         v  v    v   i  ----   v   i-----  iv  v  -   v -  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_121618229_   2609 AAACTGTAAAACTTCTAAAAGAAAA--TAGGAGGAAATCTTTGAGACTTC 2656
                              i       ii  i       --    ? v       i v   i i
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_121618229_   2657 AGGCTGGCCAAGGACCTCCTAGATAT-ACA--AAAAGCATGATCCATAAA 2703
                         i  i i v   v iii  i       -   --       ii v v i   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_121618229_   2704 AGAAAAAAATTGACAAATTGGACCTTATGTTTTTAAAGTAAAAACCCTTG 2753
                                 - v  i         i i  ----iv   v       ii   
  L1M4_orf2#LINE/    621 AGAAAAAA-TAGATAAATTGGACTTCAT----CAAAATTAAAAACTTTTG 665

  chr2_121618229_   2754 TTCTGCTGGCAATGCTACCACTACTATTAGCCCCTTTTCTGCCAGAACAA 2803
                          v  v viivi ii   i  vv -- --  ---------  vv ii    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGA--A--AG---------TGAAAAGACAA 702

  chr2_121618229_   2804 ACCCCTGGAGCACATTTTAAGGAATATA-ATGAATCACATACCCAA---- 2848
                         -   vii  ----  vvv iii     v-iii     i   i ii ----
  L1M4_orf2#LINE/    703 -CCCACAGA----ATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_121618229_   2849 ---CTTGTATCCAGAATACATAAAGGACTCTCTA-GACTCAGCTGTAAGA 2894
                         ---               i      i     -  -i     iivi   i 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCT-TACAACTCAATAATAAAA 796

  chr2_121618229_   2895 AACCAAAGAA 2904
                          iv    v  
  L1M4_orf2#LINE/    797 AGACAAATAA 806

Transitions / transversions = 1.89 (108 / 57)
Gap_init rate = 0.04 (25 / 631), avg. gap size = 2.84 (71 / 25)  

 400 19.83 2.59 2.59  chr2_121618229_121622050     3215  3330 (492)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr2_121618229_   3215 AAAAAGAAACCAAATAATCCAATTGGAAAATGGGCAAAAGACACGAAAAG 3264
                                ---       i      ?i            i  ivi   v  
  L1M4_orf2#LINE/    793 AAAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_121618229_   3265 ATGCTTCACCAAATA---CACACAAATGGCAAGAAAACATATGAAAAGAT 3311
                          iii   v     v ---i i         v iv  i  i          
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_121618229_   3312 GTTCAGTATCACTAACCAT 3330
                          i   ii    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.67 (16 / 6)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 3.00 (6 / 2)  


 448 21.21 2.02 1.01  chr2_121636478_121640274.rev     1234  1332 (2465)    L1M4_orf2#LINE/L1        8   107 (801)  

  chr2_121636478_   1234 ATAACTCAT--TCATTGATTGGAAAGCTCTGTATTGTTATGATGCCAATT 1281
                            v i   --    v        ii  ivi        v    v    v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_121636478_   1282 CTCCTGCAAATTGATTTATGAATTCAATGCAGTCCCAATCAAAACCTCAG 1331
                             i-         i  iii      i   i    v       i i   
  L1M4_orf2#LINE/     58 CTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_121636478_   1332 C 1332
                          
  L1M4_orf2#LINE/    107 C 107

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.50 (3 / 2)  

 825 18.79 1.82 0.61  chr2_121636478_121640274.rev     1642  1806 (1991)    L1M4_orf2#LINE/L1       97   263 (645)  

  chr2_121636478_   1642 AAAAACCCAGCAGACTATTTTTGTAGAAATTGGCAGGCTGGTTCTAAAAT 1691
                             v      v v  -      i        i  i    i i       
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_121636478_   1692 TCATACGAAAATGCTAAGGACCCAGAATAGCCAAAATAACTTTGGAAAAT 1741
                              i i      v i                   i  ii   i    v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_121636478_   1742 AAGAATAAATTTAGAGTACTAACACTATCAGATTTCAAGACTTA---TAA 1788
                              i   v  i   v   v     vi vi       i     ---i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_121636478_   1789 AGCCGTAGTAATCAAGAC 1806
                            iii            
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGAC 263

Transitions / transversions = 2.10 (21 / 10)
Gap_init rate = 0.01 (2 / 167), avg. gap size = 2.00 (4 / 2)  

 788 25.34 5.88 0.00  chr2_121636478_121640274.rev     2288  2508 (1289)    L1M4_orf2#LINE/L1      254   487 (421)  

  chr2_121636478_   2288 TGATCAAGACAATGTGGTATTGTTATCAGGACAGACAAATAGATGAATGG 2337
                          i         i       i  vi  v    i     v      v     
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_121636478_   2338 AACAGCAAAGAAGGTACATAAATGTACCTACACAT--ATGGAAAATGGAT 2385
                           i  v vv  ii  v  v    iv   i i    --    vv   v   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_121636478_   2386 TTTTGACAATTATGTAAAGGCAATTCAGTGCAGAAAGGATAGT-TTTTCA 2434
                            i     vvi  iv   i v     i  vi     i     -      
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_121636478_   2435 TCAAATGGC---------ACTAGATAGTTGTATGTCAAGAAATAAGCTTT 2475
                         v       i---------   i    ?iiii   iv  ii   i iv  v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_121636478_   2476 GACCCATACCTTACACTATATA-AGAAATTAACT 2508
                              v     i    i     - i         
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACT 487

Transitions / transversions = 1.39 (32 / 23)
Gap_init rate = 0.02 (4 / 234), avg. gap size = 3.25 (13 / 4)  

1396 19.91 2.16 8.66  chr2_121636478_121640274.rev     2851  3312 (485)    L1M4_orf2#LINE/L1      477   908 (0)  

  chr2_121636478_   2851 AAAAAGGAACTCATGATGGATTATAGACCAAAATATGAAACTATTAAAAC 2900
                              vv      vi      i ?     v    i i i --ii      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA--GCTAAAAC 524

  chr2_121636478_   2901 TATAGAAGTTCTAGAAGAAGCCACAAGAGAAAAATCTTTGTGACATTGGG 2950
                             i  v ii        iv  i i ? v   -    i     v     
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGG 573

  chr2_121636478_   2951 TTAAACAATA-TTTTTT-GATATCACACCAGAAGTATAATTCATTGAAAA 2998
                            ii    i-   i  -     v      i   i i  viv ivi  i 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_121636478_   2999 AAAAATTAATATATTGGACTCAGCCCAAATTGAAAGCTGTGGTGAGATGG 3048
                               vi   v        ivii v     i   i  v v   ------
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG------ 667

  chr2_121636478_   3049 GCCCTGAGAGCTGGAAGTTCTGCTCTTCATAAGACACTGTTCAGAGAGTT 3098
                         ------------------------     v i      i iv   i   v
  L1M4_orf2#LINE/    668 ------------------------CTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_121636478_   3099 AAAAGATAAGCCACAGAGTAGGAGAAAATCTTTGCAAAAACATGTATCTG 3148
                               i  v       i i         v        v-   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT-CATATATCTG 742

  chr2_121636478_   3149 -TGAAGAACTTGTACCCAGAATATAAAAAGAACTGTTGAAACTCAGTAAT 3197
                         - i i i       i          v        v  iv      i    
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_121636478_   3198 AAGAAAACAG----CCCAATTTTAAAAGATGAGCAAAAGATTTGAACAGA 3243
                           i  i   i----       ?--   i   i     i        i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_121636478_   3244 GACTTCATTCCAAAAAATATATA---ATGGCAGAAAAATCACATGAAAAG 3290
                         v i   --      i  v     ---     v-  v  v           
  L1M4_orf2#LINE/    841 CATTTC--TCCAAAGAAGATATACAAATGGCC-AATAAGCACATGAAAAG 887

  chr2_121636478_   3291 ATTCTCATTAGTCATTAGGGAA 3312
                           v    vi -   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.62 (55 / 34)
Gap_init rate = 0.03 (13 / 432), avg. gap size = 3.85 (50 / 13)  


2903 23.24 7.42 1.24  chr2_121966364_121968164      501  1309 (492)    L1M4_orf2#LINE/L1       50   908 (0)  

  chr2_121966364_    501 TGTCCATACTACTCAAAGCAATCTATAGATCCAACATAATCCCTATCAAA 550
                           v v     v i    vii     i    i    ii             
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_121966364_    551 -TGCCAATGACATTCTTTACAGAAATAAAAAAG-TAATCCCAAAATTTAT 598
                         - v   iivi v  i   i       vi v   - i    i      i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_121966364_    599 ACGGAACCACAAAAGACTCAGAATAGCCAAAGTCATCCTAAGCAAAAAGA 648
                          i    vii   ii   i             iiv   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_121966364_    649 ACAAAACTAGAAGAATCACATTATCTGACTTCAAATTATACTACTACCAT 698
                              ii i  i  v     i vi ii i      viv      - vvii
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC-AAAGC 248

  chr2_121966364_    699 TGCTGTTTTTGTGGCAGCATGGTACTGGAAAAAAAACAGACACACAGACC 748
                          i v  vv iiv i   ii         v v  ii i     i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_121966364_    749 AATGGAACAGAATAGAGATCCCAGAAATAAATCCACACATCTACAGTGAA 798
                                i     v    vi           i   i    i  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_121966364_    799 CTCATTTTTGACAACAGTGCCGAAAAGAACACACACTGGGGAAAGGACAG 848
                         i v     i     vi     ---    v  iv  v         i i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCC---AAGACCATTCAATGGGGAAAGAATAG 395

  chr2_121966364_    849 TCTCTTCAATAAATGGTGCTGGAAAAACTGAATATCCATATGCAGAAGAA 898
                            i     i            i v     i   ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_121966364_    899 TAAAACTGGACCCCCATATCTCTCACCA----CAAAAATCAAATCAAAAT 944
                          i  ii        --  i   v     ----       i  v       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCC--TACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_121966364_    945 GAATTAAAGAGTTAAACCTAAGACCTCAAACTATAAAACTACTAAAAGAA 994
                          i  i ?   vi    iv     v  v             vi  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_121966364_    995 AACATGGGGGAAACTCTCCAGGACATTGGTCTGGGCAAAGATTTTTTCAG 1044
                              i  ? v  v   i iv   v    vi i     v i   i  vii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_121966364_   1045 TA--ACACCC----CACAAGTA----------------------TGGGC- 1065
                           --     v----      i ----------------------   i -
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_121966364_   1066 --------------AAC----------CAAAGCAAACAATCAACAAAGTG 1091
                         --------------   ----------     v v  v     v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_121966364_   1092 TAA-GACAACCCACAAAATGCAAGAAAATATTTGCAAACTACCCATCTGA 1140
                         v  -           i    vi                ii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_121966364_   1141 CAAGGGATTAATAACCAGAATATATGAGGAGCTCAAACAACTCAATAGAA 1190
                         i      i vi  v           i i  i   vv           iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_121966364_   1191 AAAAAAAATCAAATAATTCAATTTAAAAGTAAGCAAAAGATCTGAATAGA 1240
                             i ---       ii     ?    i ii     i   i        
  L1M4_orf2#LINE/    794 AAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_121966364_   1241 CATTTTTCGAAAGAAGACACACAAATGGCAAACAGGCATATTAAAAAAGT 1290
                              i  v        i i         v  i i   i  v    i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-T 889

  chr2_121966364_   1291 GCTCAACATCATTGATTAT 1309
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (121 / 63)
Gap_init rate = 0.02 (14 / 859), avg. gap size = 5.00 (70 / 14)  


1321 27.71 11.08 4.13  chr2_122011094_122014174     1747  2594 (487)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_122011094_   1747 GGAAAGATA----AAACT-ATAGGCTGGAATACTCAGTACTGTGAAATTT 1791
                                  ---- vii -  i ii     v   i i  i   v  iv v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_122011094_   1792 TCAGTTCTCCC-AAATTGATCTAAACATTCAATAACATTCCACTA--AAA 1838
                         v  i v     -           v v      ii-  v   -   --   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACG-CAATCC-CTATCAAA 99

  chr2_122011094_   1839 ACCCTAATAAACACAAACATATATTTTTTTAAGAACTAAATAAGTTGATT 1888
                          i  i ii----------- iiv      vv    v vi i   i    i
  L1M4_orf2#LINE/    100 ATCCCAGC-----------TGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chr2_122011094_   1889 CCAAAATACGTGTGATAATAC----------GAATGGC-AAGGCACTCTT 1927
                          i     v i i  iv   i ----------    i  -  ii  v    
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr2_122011094_   1928 TTG-----GTTAAACAAGGTGATAAAACTTGC--TCCCCGTGGATATCAA 1970
                         -- ----- vvi     i  viv ii   ii -- i   i---  v    
  L1M4_orf2#LINE/    189 --GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA---ATTTCAA 233

  chr2_122011094_   1971 GATTTATTACAATATCACAGGAATTAAGACAATGTGCTATCAGT-T---G 2016
                         i i   i     viii    v   i      i    v  iii i- --- 
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_122011094_   2017 ATGGACAGACACACCAACAGA-CAGGATAAAGAA-ACAGATTCGGGCCTA 2064
                           i    v i v i   ii  -i  i  vi   i-v    vviiii  i 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_122011094_   2065 TG-----AGGGT------ATTTTATGACAAAG----CAGG--CATTACAG 2097
                          i----- v   ------     -i     i ----  i --    -  i
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTT-CGACAAGGGTGCCAAGACCATT-CAA 381

  chr2_122011094_   2098 AGCAGTGACAATACGGCTACTTTTTAA--ATTGATGCCCCTGGATCAACT 2145
                         v vi vi v    -- i--     i  -- v  i   ---   iv     
  L1M4_orf2#LINE/    382 TGGGGAAAGAATA--GT--CTTTTCAACAAATGGTGC---TGGGACAACT 424

  chr2_122011094_   2146 GAATATCTACATGGATTTAAAAA--GAAGTTG-ACTCCTATCTCACACCC 2192
                          i   ? i     v ---   i --       -  i    i        v
  L1M4_orf2#LINE/    425 GGATAKCCACATGCA---AAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_122011094_   2193 TGCACAAAAATGAATTC----CTGATAATAGA--TAAACGTGCAGAAAGC 2236
                          ii        v  i  ----iv   v ?   --    i  i--- i   
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA---AGAGC 518

  chr2_122011094_   2237 -AAAGCAATAAACCTTTTAGAAAATAACATAATAG-----CTTCAAGATC 2280
                         -   i v     v  i      i v      iv? -----    iv  i 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_122011094_   2281 CCAGGATAGAGGAAAATATC--AG----GACACAATAAACACAAACCATA 2324
                         iii  v   ivi vii v  --  ----     v v  i     i v i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_122011094_   2325 AAGGACAAGATTGATGAACTGGACCAAATTAGAATTAAGAACTTTGGCAT 2374
                           i  v  i  v   i  i     ivv  i i      i      v iii
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_122011094_   2375 ATCAAAAC-CACT--TAAGAAAGTGAAA-GTCAAGTCACGC--TAGAAGA 2418
                         v     iv-    --i            - v   vi   iv-- i i   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_122011094_   2419 AGATATT-ACAAAACAAATAAGCAACAACAGGCTTGTTTCTAGAATATAT 2467
                          i     -i    v  v   vvii i  vi i     v  i         
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_122011094_   2468 AAAGGTGCTCT-ACAAAGCAACTGATA----GGCAAG----CCAGTAGAA 2508
                             i-i    -    vv   - i   ---- i   i----   i v?  
  L1M4_orf2#LINE/    769 AAAGA-ACTCTTACAACTCAA-TAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_122011094_   2509 AAACAGGCAAAATATGTGAAGAGGCA---CTTCACAGAAGATA--CCAAT 2553
                            ii      iv  v    v  i  ---  i  v        -- v   
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_122011094_   2554 GGTCAACATTC-TAAGAAAAGTTGTTCAATTTCTACTAGTCA 2594
                           i   i vv -i v      v  i    iv  v????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (145 / 86)
Gap_init rate = 0.06 (50 / 907), avg. gap size = 2.58 (129 / 50)  


3044 26.22 1.78 0.89  chr2_122021457_122026910     4063  4962 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122021457_   4063 TGGAAAAATATCCCATGCCCATGGATAGGAAGAATCAGTATCATTAA-AT 4111
                               i          ii       v      v i i   ii    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122021457_   4112 GGCCATACTACCCAAAGCAATTTACAGATTCAGTGCTATTCCTATCAAAA 4161
                            v     v      vii  i          ii  v  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122021457_   4162 CTACCACTGACATTCTTCAAAGAACTAGAAAAAAATATTTTAAAATTCAT 4211
                         iiv vi   v -  i  iiv    v v  v  ivvv  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_122021457_   4212 ATGGAACCAGAAAAAAAGCCCA-AATAGTCAAGGCAATCCTATGCAAAAA 4260
                               viiv  iii --    -     i   ii     i iviv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_122021457_   4261 GAACAAGGCTGAAGGCATCACATTACCTGAGTTCAAA-----CTATA--- 4302
                               i i  i   vv     i v  ii v      -----   i ---
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_122021457_   4303 CTACAGTAACCAAAACAGCATGCTACTCATACAAAAACAGGCACATAGAC 4352
                                  i   i    ii  v    vii i  ii i  i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_122021457_   4353 CAATGGAATAGAATAGAAAGCCCAGAAATAGGCT-GCACACCTATGACCA 4401
                                       v  i  i         ii i-ii   ii    ii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_122021457_   4402 TCTGATCTTCAACAAGC-TGACAGAAACAAGCAATGGGGAAAAAACTTCC 4450
                         vi    i   i     v-  v  ii v  vv           i  ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_122021457_   4451 TATTCAATAAATGGTGCTGAGATAACTGGCTAGCCATCTGCAGAAGATTA 4500
                          v     i           i  i      v  ?   iv    i    v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_122021457_   4501 AAGCTGGAACCGTGCCTTACACCATACATAAAAATCAAGTCATGATGAAT 4550
                            i    v  v i   i        i i      i  v   vi   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_122021457_   4551 TAAAGACTTAAATGTCAAACCCAAAACTATAAAAACCCTGGAAGACAACC 4600
                         i ?    i       v i v i            vi i i     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_122021457_   4601 TAAGCA-ATACCATCCTGGACACAGGAATGGGCAAAGTTTTCATGACAAA 4649
                           i ?i- v i v  v  -  viv  iv i     v v    v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_122021457_   4650 GACACCAAAAGCAATCGCAACAAAAGCAAAAATTTACAAATGGGATCGAA 4699
                                      vvv          v      vv i    v   iivv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_122021457_   4700 TTAAACTTAAGAGCTTCTGCACAGCAAAAGAAATTATCAACAGAGTAAAT 4749
                          i   v    i i   i  ii vv    i  v i      v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_122021457_   4750 AGACAACCTACAGAATGGGAGAAAATATTTGCAAACCACGCATCTGACAA 4799
                                 i                          i  iii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_122021457_   4800 AGGTCTAATATCCAGCATCTATAAGAAACTTTAACAAATTTACAAGAGAA 4849
                         i  v  vi       v  v     ii    i v    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_122021457_   4850 A---AAACAACCCCATTAAAATACAGGCAAAGGACATGAACAGACACTTT 4896
                          ---   i     v   ?   v ii         iv    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_122021457_   4897 TCAAAAGAAGACATACATGCAGCCAACATGTAGGCATATGAAAAAAAGCT 4946
                           v        i     viii     ----  i   i       i v   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAA----TAAGCACATGAAAAGATGCT 892

  chr2_122021457_   4947 CAACATCACTGATCAT 4962
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (143 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.00 (24 / 12)  


 608 13.27 8.16 0.00  chr2_122093960_122097217.rev     1172  1269 (1989)    L1M4_orf2#LINE/L1        1   106 (802)  

  chr2_122093960_   1172 TGGAAAGATACTCTATGTTCAGGGATTGGAAGACTTAATATTGTTATGAT 1221
                                   ii i       v                        v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122093960_   1222 GGTAATATTCCCCA--------TATAGATTTAGCACAATCCCTATTAAAA 1263
                           i    i      --------  i     i i i          i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122093960_   1264 TTCCAG 1269
                          i    
  L1M4_orf2#LINE/    101 TCCCAG 106

Transitions / transversions = 5.50 (11 / 2)
Gap_init rate = 0.01 (1 / 106), avg. gap size = 8.00 (8 / 1)  

2127 14.22 7.84 0.49  chr2_122093960_122097217.rev     1570  1977 (1281)    L1M4_orf2#LINE/L1       97   534 (374)  

  chr2_122093960_   1570 AAAAACCCAGTTGCCTAGTTTGCAGAAATTGACAAGCTGATCTTAAAACT 1619
                             v     i     vv                        i     i 
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_122093960_   1620 CATGTAGAAATGCAAGGGACCCAGAATTGCCAAAACAATCTTGAAAAA-- 1667
                            i i                     v                    --
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_122093960_   1668 ------AAGTTGGAGGACT-------------TTCATAACTTACTACAAA 1698
                         ------             -------------    v             
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_122093960_   1699 GTTACAATAATTGAGACAATCTGATACTGGCATAAAGATAGACATATAGA 1748
                          i    i    ii     i v  i           i              
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_122093960_   1749 TCAATGGCATAGAAT-GAGAATCCAGAACTAAACCCTTCTGTTTATGGTC 1797
                                v       -    i       v       v vii         
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_122093960_   1798 AATTGATTTTCAACAAAG-TGCAAGGACAATTAGGTGGAGAAAGAATAAT 1846
                                    i    i -   v i   v   vii   i         i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_122093960_   1847 CTTTTTCAACAAATGATGGTGGTACA---GG---TCCACACAACAAAAAA 1890
                              -         i  v   v   ---  ---?     ii-     i 
  L1M4_orf2#LINE/    397 CTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGA 444

  chr2_122093960_   1891 AGGAATTTGGACCCTTACCTCAC-TTATATATATATA--AATTCAGAATT 1937
                          v   v        i        -ii     i v v --  i   i   v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_122093960_   1938 CATCATAGACCTAAATGTAAGATCTGAAACAATAAAACTC 1977
                         v    ?                v  i    v         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

Transitions / transversions = 1.43 (33 / 23)
Gap_init rate = 0.02 (10 / 438), avg. gap size = 3.40 (34 / 10)  

 355 16.39 0.00 0.00  chr2_122093960_122097217.rev     2113  2173 (1085)    L1M4_orf2#LINE/L1      530   590 (318)  

  chr2_122093960_   2113 AACTCTTAGAAGAAAACATGGTTGTAAATCTTCATGCCCTTGTATTACAG 2162
                                            i v?          i  v     vi   viv
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_122093960_   2163 AATGGTTTCTT 2173
                                    
  L1M4_orf2#LINE/    580 AATGGTTTCTT 590

Transitions / transversions = 0.80 (4 / 5)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.00 (0 / 0)  

1274 20.57 4.11 0.63  chr2_122093960_122097217.rev     2462  2777 (481)    L1M4_orf2#LINE/L1      582   908 (0)  

  chr2_122093960_   2462 TGGCTTCTTCAGTATGACACCTAAAACATAGGCACTGAAAGAAAAA-CAG 2510
                            i     vii         v   i  i i   vii         -i  
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_122093960_   2511 GTAAATTGATATTAATTGAAACAGAAAACCTTTTT--TTCAAATGGCACC 2558
                         i       ivv  v  ii   ivi     i   v --      v i   i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_122093960_   2559 ATCAAGAAAATGAA--GACATCCCA--GAATGAGAAAAAATATTTG---- 2600
                                  i    --    v    --     i  i          ----
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_122093960_   2601 TCATATATCTGATAAAGGACTTTTATCCAAAATATATTTTAGAAATTCTT 2650
                                        i      v      i       v-- ii  i    
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATA--AAGAACTCTT 779

  chr2_122093960_   2651 AAAA-TCAACAGTAAAAAGACACATAACCCAGTTAACAAATGAGCAAAGG 2699
                          v  -    i i          v        i  ? v     i       
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_122093960_   2700 ATTTGATCAGATACTTCTTCAAAGATGCTGTCCAAATGGCCAGTACATCC 2749
                               vi   i i    i      v v i v          i  viiv 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_122093960_   2750 ATGAAAAGAAG-TCAAGGCCGGGCGTGGT 2777
                                  v -    vii i????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (41 / 23)
Gap_init rate = 0.02 (8 / 327), avg. gap size = 1.88 (15 / 8)  


2021 27.33 0.44 4.22  chr2_122145196_122152080     4825  5512 (1373)    L1M4_orf2#LINE/L1        1   662 (246)  

  chr2_122145196_   4825 TGGGAACACATCTCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 4874
                            i  v i   i    i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122145196_   4875 GACCATACAGTCAAAAGCAATCTACAAATTCAGTGCAATTCCTGTCAAAA 4924
                          i v    vvi v   vii       i     ii     i   i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122145196_   4925 TACCATCATTATTTTTCACAGAACTATAAAAATAAAATCCTAAAATTAAT 4974
                          v   v vviv     ii     v - i v  vvvi           v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_122145196_   4975 ATGGAACCAAAAAAGAGCCCACATAGCCAAAGCGAGACTAAGTGAGAAGA 5024
                               viiv  ii  v  viv         i i vvi i ivi      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_122145196_   5025 ACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAAGGCT 5074
                              vi      vv     i v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_122145196_   5075 ATAGTTACCAAAACAGCATGGTACTGGTATAAAAATAGGCGTGTACATCA 5124
                          i   v i   i    ii         i    ii    i i i  v    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_122145196_   5125 ATGCAACAGAATAGAGTACCCAGAAATAAAGCCAAATATTTAAAGCCAAC 5174
                            v  i     v   vii           v   v i     vi i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_122145196_   5175 TGATCTTCGACAAAGCAAACAAAAACATAAAGTGGAGAAGGA-CACCCTG 5223
                             i        i vviv   i v   vv i   i   i  -i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_122145196_   5224 TTCAACAAAGGCTGCACCCTAACCACAAATGGTCAAATGGTGCTGGGATT 5273
                                  ----------------------------           iv
  L1M4_orf2#LINE/    400 TTCAACAAA----------------------------TGGTGCTGGGACA 421

  chr2_122145196_   5274 GTTGGCAAGTCACATGTAGAAGAATGAAACTTAATCCTCATGTCTCACCC 5323
                         ii   vv ?i      i i         ii vi i  ii iv  v    v
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_122145196_   5324 TATACAAAAATCAACTCAAAATGGATCAAAGACTTGAATCTAAGACCTGA 5373
                                    i                ?    i i   v     v  i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_122145196_   5374 AACCATAAAAATTCTAGAATATAATATTGGAAAAACTCTTCTAGACATTG 5423
                            i      v ii     v v  i  v  ?iv  v     vv   v   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_122145196_   5424 GCTAAGGTA--GAGTTAATGACTAAGAACCCAAAAGCAAATACAACAAAA 5471
                          v v   i -- iv  vv iiv  v  vv         v vi        
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_122145196_   5472 ACAAAAATAAATAGATGAGACCGAATTAAACTAAAAAGCTT 5512
                         iv       i   i  vi   ivv  i   v v    i   
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

Transitions / transversions = 1.15 (99 / 86)
Gap_init rate = 0.01 (4 / 662), avg. gap size = 8.00 (32 / 4)  

 768 21.72 3.17 0.45  chr2_122145196_122152080     6173  6393 (492)    L1M4_orf2#LINE/L1      682   908 (0)  

  chr2_122145196_   6173 ATCAGCAGAGTAAACAGAGAACCCCCAGAGTGGGAGAAAATTTTCACAGA 6222
                             iv i   i  v   v     v    i           v  ii  i 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_122145196_   6223 CTATTCATCCAACAAAGGACTAATACCCAGAATCTACCAGGAACTCAAAC 6272
                         ii  vi   ii i  i     vi  i       v  iv i      vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_122145196_   6273 AAATCAGCAAAAAAAAAA-----AATCCCATCAAAAAGTGGGCTAAGGAC 6317
                           v   ii  v     i -----  i  v  i?    i     v     i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_122145196_   6318 ATGAATACACAATTCTCAAAAGAAGATATACAAATGTCCAACAA--ACAT 6365
                         v      v   v     v                  v    i  --    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_122145196_   6366 GAAAAAAATGCTCAACATCACTAATTAT 6393
                              i -            ????????
  L1M4_orf2#LINE/    882 GAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (27 / 20)
Gap_init rate = 0.01 (3 / 227), avg. gap size = 2.67 (8 / 3)  


2808 26.61 1.31 2.29  chr2_122426941_122429085.rev      737  1653 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122426941_    737 TGGAAAAATATTCCATGTTCATGGATAGGAAGAATCAATATCATGAAAAT 786
                               i    i              v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122426941_    787 GGCCATGCTGCCCAAAGCAATTTATAGATTCAATGCTATTCCCATTAAAC 836
                            v  i  v      vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122426941_    837 TACCATTGACATTCTTCACAGAAGA-GA-AAACT-ACCTTAAAATTCATA 883
                          v   vivi v  i  ii     iv-  -  i  - i i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_122426941_    884 TGGATAACTAAAAAAGAGACC--AAATAGCCAAGGCAATCCTCAGCAAAA 931
                             -  i---iv   i    --i         ii     i v iv  i 
  L1M4_orf2#LINE/    151 TGGA-AAT---GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_122426941_    932 AGTACAAAGCTGGAGCCATCATGCTACCCAACTTTGAACTATACTACTGG 981
                           v      i     vvv   ii  v     i  ii  viv      vii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_122426941_    982 GCTACAGTAACCAAAACAGCATGGTACTGGCACAGAAAGAGACAAAATAG 1031
                                   i   i    ii           i iii v     v -   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAG 295

  chr2_122426941_   1032 ACTAATGCAACAGAACAGAGAACACAACAGTAAGGCCACACACCTACACT 1081
                          ii    v  i    iv    iiv  iv i   iv   i   ii  iiv 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_122426941_   1082 -ATCTGACCTTCCACAAAGCTGACAAAAACAAGCAATGGGAAAATGATTC 1130
                         - vi   ii   v    i v  v   i v  vv       i   vi  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_122426941_   1131 CCTATTCAATAAATGTTACTGGGATAATTAACTAGCCATATGCAGAAGAT 1180
                         i  v     i     v i      i  i iiv  ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_122426941_   1181 TGAAACGAGACCTCTTCCTTACACGACATACAAAAATTAACTCAAGATAG 1230
                             iivi    i  v   i    v i                  i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_122426941_   1231 ATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAAACCTGGAAGACAA 1280
                           i ?    i         i v i            vv i i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_122426941_   1281 CCTAGGCA-ATACCATTCAAGACGTAGGCACGGGCAAAGATTTCATAATG 1329
                          v    ?i- v i -   iv   v v  vvii     v i    v  ivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_122426941_   1330 AAGACACATAATGAAGCAAAAGCAATTGCAACAAAAGCAAAAATTGAGAA 1379
                          v     ---------        vvv          v      v  v  
  L1M4_orf2#LINE/    595 ATGACAC---------CAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_122426941_   1380 ATGGGATCTAATTAAACTAAAGAACTTCTACACAGCAAAAGAAACTATCA 1429
                           v   ii v  i   v v  i     i iii vv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_122426941_   1430 ACAGAGTAAACAGACAACCTACAGAACAGAAGAAAATTTTTGCAAACTAG 1479
                          v i   i  v        i      ii i       v        ii v
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_122426941_   1480 GCACCTGACAACGGTCTAATATCCAGCATCTATAAAGAATTTAAACAA-- 1527
                         ii i    i  v  v  vi       v  v         i ivv    --
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_122426941_   1528 -GATTGCAAGAAGA-AAACAACCCCATTAAAAGGTGGGCAAAGGACATGA 1575
                         -i  vii  i    -   i     v   ?   ii           iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_122426941_   1576 ACAGACACAGACACTTCTCAAAAGAAAACATACATGCAACCAACAAGCAT 1625
                          i     i------     v      i i     viiii    i     i
  L1M4_orf2#LINE/    836 ATAGACAT------TTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_122426941_   1626 ATGAAGAAA-GCTCAATATCACTTATCAC 1653
                              i i -      i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


2050 22.86 6.43 1.61  chr2_122451640_122456501.rev     3091  3650 (1211)    L1M4_orf2#LINE/L1        1   587 (321)  

  chr2_122451640_   3091 TGGAAAGACATACAGTGTTCATGGATTGGAAGACTCAGTGTAGTAAAGAT 3140
                                 i  v vi                    i i i v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122451640_   3141 GTCAATTCTTCCCAAATT-ATCTATTGATTTAATGCAATTTCTGTAAAAC 3189
                          v    v  i        -     iv    i  i     ii  i v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122451640_   3190 TCCAAGC--CCGATATTTTATA-ATACAGACAACCTGATTCTAAAATTTA 3236
                            v   --  -- v    ii - v iv     v     i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_122451640_   3237 TATGAAAAGCCAAAGAAACTAGAATAGCCAGAATAATTTTGAAAAAAAA- 3285
                             i   vv   i i v i          i  i   i        i  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_122451640_   3286 -ATAAACTTTCAAGACTCAAACTCCCCAATTTCATAACCTATTATAAAAC 3334
                         - i   v  vv i      v   i          v   i  i  i   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_122451640_   3335 TACAATAATCAAGACAGCATGGTATTAGTGAAGAAATAAACACATGGGTC 3384
                             i            ii     i i iiv iii   i   i  i i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_122451640_   3385 AATGAAACAAAATGAAGAGTTCAGAAACAGACCCACACAAATATGGTAAA 3434
                             i  i i   vi     i      i i     i   vv      v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_122451640_   3435 TTGA-------CAATGGTGCAAAGACAATTCATTGGAGGAAGAAAGGATA 3477
                             -------   v     v     v     v   i i     ----  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA----TA 394

  chr2_122451640_   3478 ATTTTTTTAACAAATAATATTGGAACGAGTGGACATTCATATGCAAATGA 3527
                         i i    i       ii ii   i  i v    i ?i  i       v  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_122451640_   3528 ACG---TTG-ACTTGAACTTCACACCCTACATAAAAATTAACTAAAAATA 3573
                          i ---   -  iivv  i       v  i i           v     i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_122451640_   3574 GATTA------TAAATATAA--------ACTATAAAACTTTAAATAAACA 3609
                            i ------     i   --------           i ---  i vi
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT---TAGAAG 541

  chr2_122451640_   3610 CACACACAGAAGAAAATCTTCATGACCT--GGTAAT---ATGGTTT 3650
                         v v   i  i? v        i      --   v v---       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

Transitions / transversions = 1.93 (83 / 43)
Gap_init rate = 0.02 (14 / 587), avg. gap size = 3.21 (45 / 14)  

1210 24.70 3.31 0.00  chr2_122451640_122456501.rev     4038  4369 (492)    L1M4_orf2#LINE/L1      566   908 (0)  

  chr2_122451640_   4038 ACCTGGGATTAGGCAAAGAATTCTGAGACATGACACCAAAAGTACTGTTC 4087
                             v  i        v iv    v   i             i  viviv
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_122451640_   4088 ATAAAAGAAGTGTTTGATAAATTGAATTTCATCAAAACTAAGAACTTCTA 4137
                          i       iviv v         i i          i   i     i i
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_122451640_   4138 TTCTTTGAAAAACATTGTTAAAAGAACAAAAAAAAAAGCCAAAAACTGAG 4187
                          v   ii  ii   i i i  i i iii    i v  v   v i v  i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_122451640_   4188 GGAAAATATTTGCAATGCATGTAGCTGATAAAGGACTTGTATCCAGAATA 4237
                         i              vv   i  v       i                  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_122451640_   4238 CATAAAGAGCTCTCAAATCTGAATAAGAAAA---CAAACCAGCCA----- 4279
                         i       i    i v v  v     v    ---    iv v   -----
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_122451640_   4280 CAAATGGGCAAAAGATTTATACAGTCA---CTTTAGCCAAGATGTACCAG 4326
                         v           i     iv i  v  ---  ii ivv     i   v i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_122451640_   4327 TGGAAAATAAGCACATAAAAATATGCCCATTATCATTCATCCT 4369
                            vv           i    v    i  vi    ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (48 / 34)
Gap_init rate = 0.01 (3 / 343), avg. gap size = 3.67 (11 / 3)  


3212 27.39 0.44 0.55  chr2_122486729_122493014.rev     4886  5794 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122486729_   4886 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4935
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122486729_   4936 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCAGCCCCATCAAGC 4985
                            v     v     iv i  i           i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122486729_   4986 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5033
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_122486729_   5034 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5083
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_122486729_   5084 AACAAAGCTGGAGGAATCACACTACCTGACTTCAAACTATACTACAAGGC 5133
                                i       v       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_122486729_   5134 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5183
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_122486729_   5184 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5231
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_122486729_   5232 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5281
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_122486729_   5282 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGGAAGCT 5331
                           v  i  i              v      v  ?  ii   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_122486729_   5332 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5381
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_122486729_   5382 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAAACCCTAGAAGAAAA 5431
                          i ?   ii    i  v   v       i      v-i i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chr2_122486729_   5432 CCTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCCA 5481
                          v    ?i v viv   iv   viv  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_122486729_   5482 AAACACCAAAAGCAATGGCAACAGAAGACAAAATTGACAAATGGGATCTA 5531
                         vi            vvi      i    v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_122486729_   5532 ATTAAACTAAGGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5581
                           i   v v ii i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_122486729_   5582 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5631
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_122486729_   5632 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5681
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_122486729_   5682 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5731
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_122486729_   5732 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5781
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_122486729_   5782 CATCACTGGCCAT 5794
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3340 26.76 0.44 0.44  chr2_122520256_122526555.rev     4901  5808 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122520256_   4901 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4950
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122520256_   4951 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5000
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122520256_   5001 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5048
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_122520256_   5049 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5098
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_122520256_   5099 AACAAAGCTGGAGGAATCACACTACCTGACTTCAGACTATACTACAAGGC 5148
                                i       v       v  ii i    i viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_122520256_   5149 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5198
                           i     i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_122520256_   5199 AATGGAACAGAAC--AGAGCCCTCTGAAATAACGCCGCATATCTACAACT 5246
                                i    i--    i  v--       vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCA--GAAATAAACCCATACATTTATGGTC 346

  chr2_122520256_   5247 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5296
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_122520256_   5297 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5346
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_122520256_   5347 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5396
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_122520256_   5397 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5446
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_122520256_   5447 CTAGGTATTACCATTCAGGACATAGGCAGGGGCAAGGACTTCATGTCTAA 5496
                         v    ?i v viv   iv   v v  vvvi     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_122520256_   5497 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5546
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_122520256_   5547 TTAAACTAAGGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5596
                          i   v v ii i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_122520256_   5597 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5646
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_122520256_   5647 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5696
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_122520256_   5697 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5746
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_122520256_   5747 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5796
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_122520256_   5797 ATCACTGGCCAT 5808
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3266 27.04 0.33 0.11  chr2_122559998_122564351.rev     2956  3861 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122559998_   2956 TGGAAACACATCCCATGCTCATGGATGGGTAGCATCAGTATTACAAAAAT 3005
                               v i        i        v  v  vv i i    iiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122559998_   3006 GGCCATACTTCCCAAAGCAATCTAAAGAGTCAGTGCAATTCCCATCAAAA 3055
                            v     i      vii     v   v   ii     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122559998_   3056 TACCA-TTATTATTCTTCACAGAACTAGAAAAACCAATCCTAAAATTCAT 3104
                          v   -i iii-  i  ii     v v  v  i ii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_122559998_   3105 ATGGAACCAAAAAAGAGCCTGCCTAGCTAAAGCAAGACTAAGCAAAAAGA 3154
                               viiv  ii  v  v vv    i   i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_122559998_   3155 ACAAATCTGGAGGCATCATGTTACCCAACTTCTAATTATACTACAAGGCT 3204
                              vi      vv   iii v     i   v  viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_122559998_   3205 ATAGTTACCAAAACAGCATGATACTCGTATAAAAATGGGCATGTAGACCA 3254
                          i   v i   i    ii  i    v i    ii  i i   i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_122559998_   3255 ATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTGTAGCCAAC 3304
                               i     v    ii           v   v i i  i i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_122559998_   3305 TGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTA 3354
                             i  i     i vviv   i v   vv i         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_122559998_   3355 TTCAATAAATGGTGCTGGGAAAACTGGCAAGCCACATGTAGAAGAATGAA 3404
                              i              v      vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_122559998_   3405 ACTGGATCCTCATCTCTTACCTTATAGAAAAATCAACTCAAGATGGATCA 3454
                         ii    i  ii i   vi   v    v      i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_122559998_   3455 AAGACTTAAATCTAAGACCTGAAACCCTAAAAATTCTAGAAGATAACATC 3504
                         ?    i     v     v  i    iv     v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_122559998_   3505 GGAAAAACTCTTTTGGACATTGGCTTAGGCAAAGAATTCATGACTAACAC 3554
                           ?iv  v    ivv   v    v        v iv   v iiv  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_122559998_   3555 CCCAAAAGGAAATGTAACAAGAACAAAAATAAATAAATGGGACCTAATTA 3604
                         v       v v v i     i iv       i      v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_122559998_   3605 AA-CTAAAAATCTCTGCATGGCAAAAGAAATAATCAGCAGAGTAAACAGA 3653
                           -i      ii i  iiivv    i  v iv    iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_122559998_   3654 CAACCCATAGAGTGGAAGGAAATAATTGTAAGTTATGCATCCAACAAAGA 3703
                                i   i   i  i     v   i  i i  ii   ii i  i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_122559998_   3704 ACTAATATCCAAAATCTACGAGGAACTCAAACAAAGCAAGAAAAAAAAAA 3753
                            vi      i   v  ii i      vv    vv   v  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_122559998_   3754 CAAATAATCCCATCAAAAAGTAGGCAAAGGACATGAATAGACAATTCTCA 3803
                                i  v  i?    i i         iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_122559998_   3804 AAAGAATATATACAAACAGCCA-CAAACATATGAAAAAATGTTCAGTGTC 3852
                               v         ii    -i  i  i       i   i   iii  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_122559998_   3853 ACTTACTAT 3861
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.00 (4 / 4)  


3231 26.95 1.45 0.33  chr2_122590671_122599907.rev     5538  6435 (2802)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122590671_   5538 TGAAAAAACATTCCATGCCCATGGATAGGAAGAATCAATATCGTGAAAGT 5587
                           i   i i  i     ii       v      v i     i  v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122590671_   5588 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCAATCCCCATCAAGC 5637
                            v     v      v i  i  i       ii        i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122590671_   5638 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGGTCA 5685
                          v   iivi i  i  ii     -   -- v  i  - iii    iv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_122590671_   5686 TATAGAACAAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAAAAG 5735
                            i   vviv  ii  v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_122590671_   5736 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5785
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_122590671_   5786 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5835
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_122590671_   5836 AATGGAACAGAACAGGGGCCTCAGAAATAACACCACACATCTACAACCAT 5885
                                i    iv i ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_122590671_   5886 CTGATCTTTGACAAACCTGTCAAAAACATGCAATGGGGAAAGGATTCCCT 5935
                         i    i  i     ivv  i   i v   v            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_122590671_   5936 ATTTAATAGATGGTGTTGGAAAAACTGGCTAGCTATATGCAGAAACCTGA 5985
                         v  i  i i      i   i v      v  ? i i     i  ivv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_122590671_   5986 AACTAGATCCCTTCCTTACACCTTACACAAAAATCAACTCAAGATGGTTT 6035
                          ii i  i    v   i     v  i        i       i    v i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_122590671_   6036 AAAGACTTAAATGTAAGACCTAAAACCATAAAAATCCTAGAAGAAAACCT 6085
                          ?    i           v       i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_122590671_   6086 AGGCAATACCTTTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAAAA 6135
                            ?ivv vii   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_122590671_   6136 CACCAAAAGCAATGGCAATGAAAGCCAAAATTGACAAATGGGATCTAATT 6185
                                    vvi    ii    vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_122590671_   6186 AAA-TTAAAGAACTCCTGCACAGCAAAAGAAACTATCATCAGAGTGAATA 6234
                            -     -    ii  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    649 AAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_122590671_   6235 GGCAACCCACTGAATGGGAGAAAATCTTTGCAATCTACCCATCTGACAAA 6284
                          i        v              v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_122590671_   6285 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 6334
                           i  vi          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_122590671_   6335 AACA----------TCAAAAAGTGGGCAAAAGATATAAATAGACACTTCT 6374
                         i   ---------- i?    i        i   v i        i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_122590671_   6375 CAAAAGAAGACATTTATGCAGCCAACAACCATATGAAAAACAGCTCATCA 6424
                          v        i  vi viii     i  v  i       ivv     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_122590671_   6425 TCACTGCTCAT 6435
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.62 (147 / 91)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.67 (16 / 6)  

2970 23.72 0.82 7.60  chr2_122590671_122599907.rev     7772  8745 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122590671_   7772 TAGAAAAACATGCCATACTTATGCATCAGAAGAACTAATATTGTTAAAAT 7821
                          i    i i  v    ii i   v  ii     vi            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122590671_   7822 GGCTATATTGCCCAAAGCAATCTACAGATTCAACGCACTCCTTATCAAAA 7871
                            v   i v      vii                  v   i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122590671_   7872 TATCAA-TGTCACTCTTCACAGAC-TTACCAAAAAATTTCTAAAATTTAT 7919
                          vi  i-  i -i i  ii    v-  iv   ivviv i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_122590671_   7920 ACAGAACCAAAAAAAAGCCTGAATAGCCAAAGCAATCCTGAGCATTAAGA 7969
                          ii   viiv  iii v  v           i     i   iv vv    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_122590671_   7970 ACAAAGCTGGAGGCATAACATTATCTGACTTCTAAATATATGATAATGCT 8019
                               i      vv v   i vi ii i   v   iv  iv i  v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_122590671_   8020 ATAGTAACCAAAACAGCACAGTATTGATATAAAAA-AGACACACAGACCA 8068
                          i     i   i    iiii   i  ii    ii -     i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_122590671_   8069 ATGGAACAGAATCCAGAATCCAGAAATAAAGCCACATATTTATAGCCATT 8118
                               i     iv   i            v   i i      i i  v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_122590671_   8119 TGATTTTCAACAAAGCCAACAAGAACTTACATTGGGGAAAGGATGCCCTC 8168
                                 i    i viiv     v v v  v         i  ivi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_122590671_   8169 TTCAGCAAATGATGCCAGGAAAATTGGATAGCCATATGCAGAATAATGAA 8218
                             i      i   ii   v  i      ?   i     i  v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_122590671_   8219 GCTGGATTCCTACCTTTCAGCATATACAAAAATCAATTCAAAATGGATTA 8268
                          i    ii       iv  v             i  i           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_122590671_   8269 AATATTTAAGCGTATGACCCAAAACTATAAAAATACCAGGAGAAAACCTA 8318
                         ? v ii   ii   v  v i            v vii  i       v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_122590671_   8319 GAGAAAACTCTCCTGGACATCAGACTAGACACAAAATTTAT--GACTAAG 8366
                          i?iv  v   i vv   v ii ii   i  - vii   v --  -  v 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAGA-TATG 597

  chr2_122590671_   8367 ACCTAAAAAGCATAGGCAACAAAAGCAAAAATAGACCAATGGGACTTAAT 8416
                           viv       i i          v         iv   v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_122590671_   8417 -GAAATTAAAATGCTCCTGTATACCAAAAGAAATAATCAAAAGAGCGAAG 8465
                         -i         -i  ii   iivi    i  v iv     i i  i   i
  L1M4_orf2#LINE/    648 CAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_122590671_   8466 AGACAATCTGTTGAATGGGAGAAAATATTATTTAATAATATTTAATAATA 8515
                               i iiiv                 ---------------------
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATT--------------------- 725

  chr2_122590671_   8516 TTTAATATTAATATTAATAATATTTAATAATATTATTAAATAATATTTTT 8565
                         --------------------------------- ii-    v    ----
  L1M4_orf2#LINE/    726 ---------------------------------TGC-AAATCATAT---- 737

  chr2_122590671_   8566 AAGCTATTCATCTGAAAGAGGACTAATATCCAGAATATATAA-GAACTCA 8614
                         ---------      v ii     vi                -      v
  L1M4_orf2#LINE/    738 ---------ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_122590671_   8615 AACAAC-CAACAGGAAAAAGAAGCAAATAATCCCATTAAAAAGTGGGCAA 8663
                         v     -   i iv       --       i  v   ?    i       
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_122590671_   8664 AAGACATGAATGGACATTTCTCGAAAGAAGACCTACAAACAGCCAATAGG 8713
                          i  iv     i          v        iv      ii       i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_122590671_   8714 TGTATGAAAAAATACTCAATGTCACTAATCAC 8745
                         iii       i  i     ii   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.99 (151 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 5.47 (82 / 15)  


2868 26.07 3.39 0.90  chr2_122774899_122780239     3964  4849 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122774899_   3964 TGGGAAAACATTCCATACTCATGGTTAGGAAGAATCAGTGTTTTTAAAAC 4013
                            i  i i  i    ii      v v      v i i i  v    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122774899_   4014 GGCCATACTACTCAAAGCAATTTATACATTCAAAGCTATTTCTATCAAAC 4063
                            v     v i    vii  i  i v      v  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122774899_   4064 TACCAATGACATTTCTCACAGAATTAGAAAAAACT-ATTCTAAAATTCAT 4112
                          v   iivi v   i ii     v v  v  i-  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_122774899_   4113 ATGGAACAAAAAAGAGCCCA-AAGAGCCAAGGCAATCCTAAGCCAAAAGA 4161
                               vviv  i ii    -  v      ii     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_122774899_   4162 ACAGAGCTGGAGGCATCATAGTACCCTACTTCAAAGTATTCTACAAGGCT 4211
                            i  i      vv   i v v   v i      iiv v      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_122774899_   4212 ACAGTAATCAAAACAACATGGTACTGGTACAAAAATAGATACATA--CTA 4259
                                    i   iii         i i  ii     i i   --ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_122774899_   4260 ATGGAATAGAATATAGAGCTCCCAAGTAAAGCTGCACACCTACAGCCATC 4309
                                     vv    ii vv  i    v iii   ii  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_122774899_   4310 TGATCTTTAATAAAATTGACAAAAACAAGCAATGAAGAAA--AGAGTCCC 4357
                             i  ii i  iiv  v   i v  vv     ii    -- v    --
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-- 397

  chr2_122774899_   4358 TATTCAATAAATAGTGCTAGGATAACTGGCTAGCCATATGCAGAAGACTG 4407
                          v     i    i     i   i      v  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_122774899_   4408 AAGTTGGATCCCTTCCTTACACCATATACAAAAATTAACTCAAGAGGGAT 4457
                                 i    v   i                         i v    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_122774899_   4458 TAAATATTTAAATGAAAAACCTACAATTATAAAAACCCTT-GAGGAAAAC 4506
                         i ? v ii      v  i v   v  i       - i   -  i      
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr2_122774899_   4507 CTAGG---AAATACCTTTCTAGACATAGGCCCTGGCAAAAATTTTAT-GA 4552
                         v    ---    --   iv -   v v  viiv     vii   iv -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--CTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_122774899_   4553 TAAAGATGCCAAAAGCA------ACAAAACAAAAATT-GACAAATGGGAC 4595
                           v-  ii         ------      v     v -  i    v    
  L1M4_orf2#LINE/    594 TAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_122774899_   4596 CTAATTAAACTAAAGAGCTTCTGCATATCAAAAGAAACTATCAACAGAGT 4645
                         i v  i   v v  i i   i  iiiv     i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_122774899_   4646 AAATAGACAACCCATAGAATGAGA-AAAATATTTACAAACTATGCGTCTG 4694
                         i  v          i      i  -         i    ii  iii    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_122774899_   4695 GCAAAGGCCTAATATACAGAATCTATAAGAAACTT----AAATTAACAAG 4740
                         ii  i  v  vi   v      v     ii    i----  v i  i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_122774899_   4741 CAAAAAACAAACA--CCA-CTAAAAAATAT-CAAAGGACATGAACAGATA 4786
                         v    i     i --   -i ?      iv-       iv    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_122774899_   4787 CTTTTC---AAAAGACATATGCATGTCCAACAAGCTTATGAAAAAATGTT 4833
                         i  i  --- i    i   iiv   v    i    vi       i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_122774899_   4834 CAACATCACTGATCAT 4849
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (146 / 82)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.81 (38 / 21)  


3284 26.21 0.66 0.66  chr2_122820026_122826620.rev     5196  6103 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122820026_   5196 TGGAAGAACACTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5245
                              ii i ii     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122820026_   5246 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5295
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122820026_   5296 TACCCA--TGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 5341
                          -    --  v    i  -i     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chr2_122820026_   5342 CATATGGAACCAAAAAAGAGCCCGCATCACCAAGGCAATCCTAAGCCAAA 5391
                                  viiv  ii  v  v v  vi    ii     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_122820026_   5392 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAA 5441
                                  i      vv    i  v  ii i      viv         
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_122820026_   5442 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5491
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_122820026_   5492 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 5539
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_122820026_   5540 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCCATGGGGAAAGGATT 5589
                         ii vi    i  i     ivv  vv  i v  vv v          i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_122820026_   5590 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5639
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_122820026_   5640 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5689
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_122820026_   5690 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5739
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_122820026_   5740 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5789
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_122820026_   5790 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5839
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_122820026_   5840 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTGA 5889
                         v  i   v v  i i   i  ii vv    i  v    ii vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_122820026_   5890 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5939
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_122820026_   5940 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5989
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_122820026_   5990 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 6039
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_122820026_   6040 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 6089
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_122820026_   6090 TCATCACTGGCCAT 6103
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


1640 30.16 6.96 1.62  chr2_122911310_122915298     2636  3497 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122911310_   2636 TGTAGGGATATACCATGTTCATGAACTGAAGGATTAAATA--GTTAAATA 2683
                           v ii     v           i i  i i  i v    --     i- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-A 49

  chr2_122911310_   2684 TGTCAATTTTTCCTAAATTAATCTATAAATTCAG---AACCCTAATTAAT 2730
                           v    vi i  i     i     i i     i---  i  iv  i  v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_122911310_   2731 ATCCTAGCAGGTGTTTTGGTGGAAATTAATAAGCTAATTCTAAAATTCAT 2780
                             i   v viv    v ii      i i     i  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_122911310_   2781 ACAGGACTATACCTGACCAAAAATACATAAGACAATCTT---AAAGAAGA 2827
                          ii i v ii vvv    v i    vvi  i        ---        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_122911310_   2828 A-AAAGTT-----AC-CAT------CAGTTATCAAGTTTTATTCTAAATC 2864
                          -      -----  -  i------  i  -    ivi   i vi   v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATT-TCAAAACTTACTACAAAGC 248

  chr2_122911310_   2865 TAAAATA-------CAGTATAATATTAATGAAGAGACAGACAAACACATT 2907
                           v i  -------    i ii  i iiiiv ii  i     v i v  i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_122911310_   2908 AATTAAACAGTATAGAGAATCCAGAAACAGAGCCACACACATA-AGCAAA 2956
                            vi  i  v  v    i        i i v   i   iv  -i iv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_122911310_   2957 CTAATTTTGATGATAAAAGTGGTGCTATAGAGTA----GTGGAGAATGA- 3001
                         i i     --i  i  i---     i -   vi ----i   i   v  -
  L1M4_orf2#LINE/    349 TTGATTTT--CGACAAG---GGTGCCA-AGACCATTCAATGGGGAAAGAA 392

  chr2_122911310_   3002 TAGACTT--CAATAAATAATGC-AGGATAAGTTGATTAATTATATACTTA 3048
                            v   --   i    ii   -i   i  v v   - ?ii i  i v- 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCA-A 440

  chr2_122911310_   3049 AAAAATGAACATTCACTTCTACCTAACACTTTACAGAAAAG------CAA 3092
                           i      vv vv  ii      v    iv  i v    i------   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_122911310_   3093 AAGTTTTATTGCAGCTCTACATTTAAAAGATAAAA-TATAAAACTTCTAA 3141
                           -- vv  ii?  vi   v  v   i  v     -         ii  i
  L1M4_orf2#LINE/    491 AA--TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_122911310_   3142 AATA---CAT-----TA--TCTTTATGACAGTAAGTTAGGAAAATATTTC 3181
                           v ---   -----  --    ii    vv ii      v  vvi    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_122911310_   3182 TTAAATAGGATGTTAATTTTCCGA-CAATAGGAAAACATTTAAAAAAATC 3230
                            i   v  iiii  vvviv i -   i ii i  v vv  i v    i
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_122911310_   3231 C-ACTATGTTAATGTAAAAAACTTGTTTTTTTCAAAAGATACTATTTAAA 3279
                         v-   vii i  vi v        v v vi      i  i     iv i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_122911310_   3280 GAGTAAAGAAGCAAGCAGTACAGTGGAAAAAAGTAATTTTCAACACATAT 3329
                         i   i  i ii   v vii v i   i i   i  -   v   vv     
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATA-TTTGCAAATCATAT 737

  chr2_122911310_   3330 AACTGACAAAGAAGTCCT-TTCAGAGTATATAAAAA---CCTATAAATCA 3375
                          v    i  i i v iv - i    i        i --- i  i  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_122911310_   3376 ATAAGAAAAGAATAGAAAATCTAATTTTAAAACTGGACAAACGTCTTGAA 3425
                             v    ii i i v  i i    ?-    v   i    v vi     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAA 836

  chr2_122911310_   3426 AAGGCACTTGACAAAAGAAGACATCCAAATGGCTCACATATATCCAAAAT 3475
                         v  i  i  vv v        i  v        iv i vii ivii   v
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_122911310_   3476 GATGCTCAACTTCATTGGTCAT 3497
                                   v   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (159 / 98)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 2.31 (74 / 32)  


3226 22.02 6.26 1.04  chr2_122917921_122920806.rev     1532  2394 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122917921_   1532 TGGAAAGATATCCCATGTTCAAAAATTGGAAGAACTGATATTGTTAAAAT 1581
                                              vii         vi i          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122917921_   1582 GTCCATACAACCCAAACTAATAAACAGATTCAATGCAATATCTATCAAAA 1631
                          v v    vv      i i  vv          i     vi         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122917921_   1632 TTCCAA-TGTCATTTTTCACAGATTTAGAAAAAATACTCCTTCAATTCAT 1680
                          i   i-  i -     ii    vv v  v  iv iv    vv       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_122917921_   1681 AT-------------ACCATGAATAGC-AAAACAATCTTGAACAAAAAGA 1716
                           -------------   vv       -              v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_122917921_   1717 ACAAAGCAGGAGGCATCACACTCCCTGATTTCAAAATACATCATAAAGTG 1766
                               iv     vv       i  ii         ivi ii i    iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_122917921_   1767 ATTGTAATTATAACAGGGTGGTACTGGCATAAAAACAGACACATTGA-CA 1815
                          iv     i vi    v               ii i     i  v  -  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_122917921_   1816 ATGGAATG----TG---GT-------------------TTTATGGTTAGT 1839
                                i----  ---  -------------------        i i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_122917921_   1840 TGATTTTTGACAAAGGTACCAAGAACACACACTGGGAAAGGGGCAGTCTC 1889
                                i     i   i      v  iv  v    i  i iii     -
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT- 398

  chr2_122917921_   1890 TTTCAAGAAATGGTTTTTGGGAAAATTAGTTACCCGCATGCAAAAGAAGG 1939
                               v       vi -    v  i i v  ?  i            v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_122917921_   1940 A---TAGACCTTGGTTTCACAACATACACAAAAATCAACTCAAAATGAAT 1986
                          --- i    iiviii     v    i        i           i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_122917921_   1987 TAAAGATTTAAATATAAGATCTCAATGTGGAAAACTATTCAAAGAAAACA 2036
                         i ?   ii     i     v  v  vv iv      v  vi         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_122917921_   2037 CAGAAGAAAAGCTCCATGAAATTTGTCTGGGCAAAAAATTTTTTTTAATA 2086
                         i  i? v   v  i i   vv  v vi i     vii--   i  vi   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG--TTTCTTAGATA 595

  chr2_122917921_   2087 TGAC-CCAGAAAGCACAGGCAACAAATGCAAAAATAGCCAAATAGGATGG 2135
                             -   -        i        v v        vi    v   ivv
  L1M4_orf2#LINE/    596 TGACACCA-AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_122917921_   2136 CATCAAA-CTAAAAACCTTCGCACAGCAAAGGAAACAATTAACAAACTGA 2184
                                -i       i  i ii vv       v  v  i  v   v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_122917921_   2185 AGAGACAACCCACAGAATGGGAGAAAATATTTGTAAGTGATACATCTGAT 2234
                          i                               i  i v   i       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_122917921_   2235 AAGGGGTTAATATTAGAAATATATAAGGAACTCAGTTA--ACTCAATAAC 2282
                              ii vi   ivii         i      --   --         i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCAATAAT 792

  chr2_122917921_   2283 AATAAGACAA----TTCAATTAAAAAA-AGGTAAAGAGCCTAAATAGACA 2327
                           v       ----ii     ?     -i  i    iiii i        
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_122917921_   2328 TTTCTCAAAAGCAATACATACAAATAGCCAATGGGTACATGAAAAACTGT 2377
                               v    -  v i        i      ii i         iv  i
  L1M4_orf2#LINE/    843 TTTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_122917921_   2378 TCAGCATCACTAGTCAT 2394
                            i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (113 / 73)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.15 (63 / 20)  


1384 22.06 1.66 18.29  chr2_122925507_122928209      797  1698 (1005)    L1M4_orf2#LINE/L1        1   752 (156)  

  chr2_122925507_    797 TGAAAAAATATTCCATGCTCATCGATTAGAAGAATCAATACAGTTATTAT 846
                           i   i    i     i    v    i     v i    ---  i   -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA---TTGTTA- 46

  chr2_122925507_    847 AAAATAATCATACTTTCCAAAGCAATCTATAAACTTAATGCTATCGCTGT 896
                         - i  iiiv     ii     vii     i i i i  i  v   v  i 
  L1M4_orf2#LINE/     47 -AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_122925507_    897 CAAAATACCAA-TGCCATTTTTCACAGAATTAGAAAAAATCT-ATTTTAA 944
                               v   i-    -     ii     v v  v  i--  -  ii   
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAA 142

  chr2_122925507_    945 AATTTATTTGGAAC--CAAAGAAGAGCCCA-AATAGTTAAAGAAATCCTA 991
                             i  v     v--   i i ---    -     ii   iv    i i
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTG 189

  chr2_122925507_    992 AATAACAACAACAACAAAAAAGAAAGCTGGAGGAATCACATTGGCTGACT 1041
                           ----------  vi  i  v    i       v     --------  
  L1M4_orf2#LINE/    190 AA----------AAAGAAGAACAAAGTTGGAGGACTCACA--------CT 221

  chr2_122925507_   1042 TCCAAGTTTATTCTAAAGCTATTAAAATAAGCTCTAAAGCTACTAAAGAA 1091
                            v i   ----i   i  --------------------     -----
  L1M4_orf2#LINE/    222 TCCCAATTT----CAAAACT--------------------TACTA----- 242

  chr2_122925507_   1092 AGCTGGAGGCATCACATTGGCTGACTTCTAAGTTTATTCTAAAGCTACTA 1141
                         ---------------------------------------i        --
  L1M4_orf2#LINE/    243 ---------------------------------------CAAAGCTAC-- 251

  chr2_122925507_   1142 AGATAAGCTTCTAAAAGTAAAGTAAGCTACTAAAACTACTAAAGTAAGCT 1191
                         --------------------------------------------------
  L1M4_orf2#LINE/    252 -------------------------------------------------- 251

  chr2_122925507_   1192 TCTAAAGTAATCAAAATAGCATGATA---GCATTACAAACAATATACACA 1238
                         -----         i i  ii  i  ---    ----  vi   v   i 
  L1M4_orf2#LINE/    252 -----AGTAATCAAGACAGTGTGGTACTGGCAT----AAGGATAGACATA 292

  chr2_122925507_   1239 TAGATCAATGGAACAGAATAGAGAACCTAGAAATAAACCCACATACCTAC 1288
                                      i     v    ii i             i i ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_122925507_   1289 AACCATCTGATCTTCAACAAAATCAACAAAAATAAGCACTGGAGAAAGGA 1338
                         iii  vi    i   i    iiviiv   i vi vv  v   i     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_122925507_   1339 CTCCCTATTTAACAAATGGTACTGGGATAACTGGTGAACCACAGGCAGAA 1388
                         ivvi  v  i          i      i      vv ?     v   i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_122925507_   1389 GAATAAAACTGGAAACTTACATCTCACCATATACAAAAATTAATTCAAGA 1438
                             i  ii    vv i   v  v                   i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_122925507_   1439 TAGATTAAAGATTTAAATCTAAGATCTCAAACTA-AAAA-TGATAGAAGA 1486
                          i   i ?   ii     v     v  v      -    - vv       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_122925507_   1487 AAATCTAGG---AAATACCCTTCTAGACATAGACTTTTGCAAACAACTTA 1533
                            iv    ---    ---    vv   v v iv  vv    vvivi iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_122925507_   1534 TGGCTAACTCATCAAAAGCAATGACAACAAAAGCTAAAATTGACAAGTGG 1583
                          i v  vvv  i        vvii         vv     v  i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_122925507_   1584 GACCAAATTAAACTATAGAGCTTCTTCTGCACAGTGAAAGAA-ATTAACA 1632
                            ivv  i   v vv i i   -  v   ---v v    i - i  v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTT-TTGTGC---TTCAAAGGACACTATCA 685

  chr2_122925507_   1633 ACAGAGTAAACAGACAGGTTGCAGAATGGGAGAAAATATC-ACAAACTGT 1681
                          v i   i  v     iviii                  i-i    iii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_122925507_   1682 GCATCTGACAAAAGACT 1698
                         ii      i  ii    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACT 752

Transitions / transversions = 1.59 (121 / 76)
Gap_init rate = 0.03 (25 / 752), avg. gap size = 7.20 (180 / 25)  

 467 20.36 8.98 0.60  chr2_122925507_122928209     2047  2213 (490)    L1M4_orf2#LINE/L1      728   908 (0)  

  chr2_122925507_   2047 CAAATCATAT--C--------AACTAATATCTAGAATCTGTTAGCAAATT 2086
                                   -- --------i   vi    i     v i v iv  v i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_122925507_   2087 AAACAAATCAACAAGTAAAAA--CTAAAAATCCAGTT-AAAAATGGGCAA 2133
                         vv    v    i  -      -- v  v  i   i  -            
  L1M4_orf2#LINE/    778 TTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_122925507_   2134 AGGACATGAACAGACCCTTCTTAAAAGAAGTCACACAAGTGGCCAATAA- 2182
                             iv    i    vi    iv       vi i    i          -
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_122925507_   2183 -ACATGCAAAAATGTTCAACATGACTAATCAT 2213
                         -     v   i   i       v ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (18 / 16)
Gap_init rate = 0.03 (6 / 181), avg. gap size = 2.67 (16 / 6)  


2752 26.41 3.84 1.35  chr2_122928318_122931631     1937  2822 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_122928318_   1937 TGGAAAAGCATTCCATGCTCATGAAATGGAAGAATCAGTATAGTTAAAAT 1986
                               iii  i     i     i v       v i i   v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_122928318_   1987 GTCCATATTTCCCAAAGCAAGTTACAGATTCAAT-CTATTCTTATCAAAT 2035
                          v v   i i      vii vi           i- v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_122928318_   2036 GAGTAACGTCATTTTTCACAG-------CA------TTCTAAATTTCATT 2072
                         vvvi i vv v     ii   -------  ------ i     v     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_122928318_   2073 TGGAAC--CAAAGAAAAGCCCAGA-TA-CCAAAGGCAATCCTAAACAAAA 2118
                              v--   i i ---      -  -     i-     i i  v  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAA-CAATCTTGAAAAAGA 196

  chr2_122928318_   2119 AGAATGAAGCTGGAGGCATCACATTGGCTGATTTCTAAGTTTATTATAAG 2168
                             ii   i      vv     i vv ii     v  ii   i  i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_122928318_   2169 GCTACAATAATCAAAATAACATGGTACGAGTACAAAAAATAGATTCATAG 2218
                               i       i i iii      vi i i  ii -    ivi    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAG 295

  chr2_122928318_   2219 GCCAGTGGAACAGAATAGAGAACCTAGAAATAAACCCACACACCT--GAT 2266
                         ii  i     i     v    ii i             i   ii -- i 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_122928318_   2267 C---TGATCTTCAACAAAATCTACAAAAATAAGCAATAGGGAAAGGAC-- 2311
                          ---    i   i    iivivv   i vi vv    i       i i--
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_122928318_   2312 TCCATATTTAATAAATGGTACTGGGATAACTGGTGAGCCACAGGCAGAAG 2361
                           -- v  i  i       i      i      vv ?     v   i   
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_122928318_   2362 AATGAAACTGGACCCCTACCTCTCACCATATACAAAAATTAACTCAAGAT 2411
                               ii              v                        i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_122928318_   2412 GAATTAAAGATTTTAATGTAAGACATGAAACTATAAAAATTCTACAAGTA 2461
                          i  i ?   ii v         vv i           v ii  v   v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_122928318_   2462 GATCTAGG---AAATCCTCTTCTAGACATTGGCTTAGGCAAATAATTTAT 2508
                         i iv    ---     i  v ---   v    v        - ii   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGT---GACCTTGGGTTAGGCAA-TGGTTTCT 589

  chr2_122928318_   2509 --GACTAAGTCCTCAAAAGCAAATTCGACCAAAATAAAAGTTGATAATTG 2556
                         --  -  v v vi        v vv i  v   iv    i v     v v
  L1M4_orf2#LINE/    590 TAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_122928318_   2557 GGACCTAATTAAACTGAAGAGCTTCTACACAACAAAACAAACTATCAGCA 2606
                             i v  i   v v  i i   i iii vv    iv v       iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_122928318_   2607 GAGTCAACAGATAGCCTGAAGAATGGAAGAAAATATTTGCAAACTATGCA 2656
                         i   v  v   i i  iiv       i                ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_122928318_   2657 TCTGAAAAAGTACTAATATCCAGAATTTGTAAGGAACTTAAATGAGTCAA 2706
                              v  i v   vi          v i   i     ivv ii v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_122928318_   2707 -GACAAAAA--CAAATAATCCCATTAAAAGGTAGGTAAATGTTATAAACA 2753
                         -i i     --       i  v   ?   ii i  i   v v v i  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_122928318_   2754 GACACTCCTCAAAAGAACACATACAAGCAGACAACAAACATATAAAAA-A 2802
                             i i   v      v i      iii v   i  i  i  i    - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_122928318_   2803 TGCTAAAGATTATCAATTAT 2822
                             v  v  i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (144 / 87)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.19 (46 / 21)  

 986 28.57 1.27 1.59  chr2_122928318_122931631     2996  3310 (4)  C L1M4_orf2#LINE/L1   (473)   435   122  

C chr2_122928318_   3310 AAATTAGAAAAATCTATTCTAAAATTCATTTGGAACAAAAAAGAGCACA- 3262
                              -  v  iiiv  i           v     vviv  i ii v  -
  L1M4_orf2#LINE/    122 AAATT-GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

C chr2_122928318_   3261 AATAGCCAAAGCAATCCTAAACAAAAAGCACAAAGCTGGAGGCATCACAT 3212
                                   i     i i  v  i   v      i      vv     i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

C chr2_122928318_   3211 TGGCTGACTTCTAAGTTTATTATAAGGCTATGGTAATCAAAATAACGTGA 3162
                          vv ii i   v  ii   i  i  i    ii        i i ii   i
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

C chr2_122928318_   3161 TACCATTACCAAAAATAGACACATGGACCAGTGGAACTGAATAGAGAACC 3112
                            iivi i-  ii       i  i  i  i     iv    v    ii 
  L1M4_orf2#LINE/    271 TACTGGCAT-AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

C chr2_122928318_   3111 CAGAAATAAACCCATATACCTAAAACCATCTGATCCTCAACAAAATTAAT 3062
                                         i ii  viii  vi    ii  i    iiv ivi
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

C chr2_122928318_   3061 AAAAATAAGCAATGGAGAAAGGA--GTCCCTGTTCAATAAATGGTGCTGG 3014
                           i vi vv      i     i --   -- v     i            
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGG 417

C chr2_122928318_   3013 -ATAACTGAGAAATCCCCA 2996
                         - i     -  v ?  v  
  L1M4_orf2#LINE/    418 GACAACTG-GATAKCCACA 435

Transitions / transversions = 2.30 (62 / 27)
Gap_init rate = 0.02 (7 / 314), avg. gap size = 1.29 (9 / 7)  


3174 26.66 1.22 0.77  chr2_123024052_123030377     4931  5834 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_123024052_   4931 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4980
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_123024052_   4981 GGCCATACTGCCCAAGGTAATTTGTAGATTCATTGCCATCCC-ATCAAGC 5029
                            v     v     iv i  i ii       vi  v     -     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-- 98

  chr2_123024052_   5030 AA--CCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGT 5075
                           --   iivi i  i  ii     -   --- v  i  - iii    i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAAT 145

  chr2_123024052_   5076 TCATATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAA 5125
                                   viiv  ii  v  viv  v     iv     i i ivv i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_123024052_   5126 AAGAACAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATACTACAA 5175
                                   i      vv   ii  v  ii        viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_123024052_   5176 TGCTACAGTAACCCAAACAGCATGGTAGTGGTATCAAAACAGAGATATAG 5225
                         v          i v i    ii     v   i  v ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_123024052_   5226 ACAAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACA 5273
                          iv       i    i--    i  --        vv   i    i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr2_123024052_   5274 ACTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAATGAT 5323
                         iii vi    i  i     ivv  v   i v  vv           vi  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_123024052_   5324 TCCCTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGAAA 5373
                         vvi  v  i                 v      v  ?  ii   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_123024052_   5374 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 5423
                         iv    ii    i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_123024052_   5424 GGATTAAAGACTTAAACGTTATACCTAAAACCATAAAAACCCTAGAAGAA 5473
                             i ?    i    i  v v v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_123024052_   5474 AACCTAGGCAATACCCTTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5523
                            v    ?ivv vi    iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_123024052_   5524 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5573
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_123024052_   5574 TCATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5623
                             i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_123024052_   5624 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5673
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_123024052_   5674 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 5723
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_123024052_   5724 AAAAAACAA----CCCCCTCAACAAGTGGGCGAAGGATATGAATAGACAC 5769
                             i    ----   vv i? v  i     i      v          i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_123024052_   5770 TTCTTAAAAGAAGACATCTATGCAGCCAACAGACACGTGAAAAAATGCTT 5819
                             iv        i  vi viii     i ii   i      i     i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_123024052_   5820 ATCATCACTGGCCAT 5834
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


2614 24.70 6.20 1.46  chr2_123156826_123158663.rev      517  1338 (500)    L1M4_orf2#LINE/L1        1   861 (47)  

  chr2_123156826_    517 TAAAAAGACATTCTCCACTCATGGATCAAAAGAATTAATGTTGTTATAAT 566
                          ii     i  i iviii        iii    v     i      vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_123156826_    567 GCCCATACTACCCAAAGTGATCTACAGATTCAATGCAATTCCTTCCAAAA 616
                          v v     v      v                i     i   vi     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_123156826_    617 TCTCAGTGATATTCATTACAGAGATAAAAAAA---AT--TAAAATTCATT 661
                           i   iviiv  iv  i    i  vi v  i---  --          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_123156826_    662 TGGAACCACAAAAGACCACAAATACCCATAGCAATATTGAGCAAGAAGGA 711
                              vii   ii    vvi    v   v i    v    iv      i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_123156826_    712 TAAAGCTGAAGGCATCACATTT-------TCAAAATGTATTGTAAAGCGA 754
                         i    i  i   vv     i  -------      iv  i ii     v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_123156826_    755 TAGTAATAAAAACACTATGGTACTAACATAGAACCAGTCATATGGACCAA 804
                         i      v  i   v i       ii    iiivi  v     i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_123156826_    805 TGGAACAGAATAGAGAGCTTAGAAATA--TTCACACGCTGATAGTCAACT 852
                              i     v     iii       --ii  i  ii v  i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_123156826_    853 GATTTTTGACAAAAATACCAAGAACACACAACAGTGAAAAGATAATCTCT 902
                               i     iii i      v  iv   ii v    ii   i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_123156826_    903 TCAATAAATGATGCTGGCAAAACTGGCAATCCA-ATGCAAAAAAAATAAA 951
                             i     i      v v      vv ?   -        i  - i  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAA 449

  chr2_123156826_    952 ATTTGACCTTTCTCTCACATCATAT-TAAAAAC-------AAATATA--- 990
                         i  v    ii vi      i     -i     i-------    iv ---
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_123156826_    991 -AGAC---AATG---------AAACTGTACAACTACTAGAAGAAAATATA 1027
                         -    ---    ---------     i  v    vi          i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_123156826_   1028 TCTGAAAAAGCTTCTTGATATTGGTCTTGGCAAAAAATATTTTGTT---T 1074
                         vv? v   -v    v   iv    vi v     ---- iv   v  --- 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA----TGGTTTCTTAGAT 594

  chr2_123156826_   1075 ATGACACCAAAAGCACAGGCAACACAAGCAAAAATA----AACTGAGATT 1120
                                          i      v   v       ----  i  -  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG-GACT 643

  chr2_123156826_   1121 GCATCAAA-CTAAAAATATTCTGCACAGCAAAAGAAACAATCAACAGACT 1169
                         v       -i      i-  i  ii vv    i  v  v     v i v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_123156826_   1170 GTAAAG-CAATCTACATAATGAGCAAAAATATTTGCAAACCATATATCTG 1218
                          v    -   i i   v    i vi              i          
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_123156826_   1219 ATAAGGGGTTAATACCCAAAATATATAAGAAACTGATGCAACTCAGTAGC 1268
                                ii vi  i   i         ii    vv i       i  --
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-- 790

  chr2_123156826_   1269 ACAACAAAACAAAATAA---AATACTGAAATGGATAAAGGACCTGATTAG 1315
                          i  v  i     -   ---   v?vi      ii      ii   v   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_123156826_   1316 GCATTTCTTAAAAAGAAGACATA 1338
                         i       iv   -     i   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAA-GAAGATATA 861

Transitions / transversions = 1.74 (127 / 73)
Gap_init rate = 0.03 (23 / 861), avg. gap size = 2.74 (63 / 23)  


2438 28.51 2.56 1.45  chr2_123189809_123192182     1002  1899 (475)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_123189809_   1002 TAGAAACACATCCCATGCTCATGGATATGAAGTAATAATATCATTAAAAT 1051
                          i    v i        i        vv    vvv      ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_123189809_   1052 GGCCATACTGCCAAAAGCAATTTACAGATTAAATGATATTCCTATCAAAC 1101
                            v     v  v   vii  i        v  i vv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_123189809_   1102 TACTGATGAAATTCTTCACAGACTTAGAAAAAACT-ATTTTAAAATCCAC 1150
                          v iiiivivv  i  ii    vv v  v  i-  -  ii      i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_123189809_   1151 A-GATCCTAAAAAGAGCTCA-AATAGCCAAG-CAATCCCGAGCAAAAAGA 1197
                          - ivvv iv  i ii i  -         i-     ii  iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_123189809_   1198 AAAAAGCTGGAGGCATAATGTTACCCAAATTCAATCTATGCTATAGGGGT 1247
                          v    i      vv v iii v     v     vviv i   i ii v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_123189809_   1248 ACAGTAGCCAAAACAGCATGATACTGCTGTTACAGAAACAGGCACATAGA 1297
                               ii   i    ii  i     -- i- i iii i  i  i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTG--GC-ATAAGGATAGACATATAGA 296

  chr2_123189809_   1298 CTAAGGGAACAGAATACAGAGCCCCCAAATTAAGGCCACACACCTGTGAC 1347
                         ii  v    i     vv    i  vv    -  iv   i   ii i  ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAAT-AAACCCATACATTTATGGT 345

  chr2_123189809_   1348 CATCTGATCTTTGACAGAGATGACAAAA--AATAAGGATTGGGGAAAAGA 1395
                           vi    i  i    ii i  v   i -- v v i---        ii 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA---TGGGGAAAGAA 392

  chr2_123189809_   1396 CTCCCTATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATACAGAA 1445
                         ivvi  v  i  i              i      v  ?   i  i  i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_123189809_   1446 GATTGAAGCTGAACCCCTTCCTTAAACCATATGCAAAAATCGACTCAAGG 1495
                           v     i  i      v   i v       i       ii      ii
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_123189809_   1496 TGGATTAAAGACCTCAATGTAAAACTCCAAACTGTAAAAATCCTAAAAGA 1545
                              i ?      v       i viiv     i     v  i  i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_123189809_   1546 CAACCTAGCCA-ACACCATCATGGACACAGAAATGGGCAAAGATTTCATG 1594
                         v   v   v?i- v i v  i  -  viv iiv i     v i    v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_123189809_   1595 ACAAGGACACCAAAAGCAATTGCAACAAAAGCAGAAATTGACAAATGAGA 1644
                         ivv v             vvv          v i    v  i    vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_123189809_   1645 TCGAATTAAGCTTAAGAACTTCTGCACAGCAAAAGAAACTATCAACAATA 1694
                         iivv  i  iv    i     i  ii vv    i  v        v  vi
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_123189809_   1695 TAAACAGATAGTCTACAGAATGGGA-AAAATATTTGCAAACTATGCATCT 1743
                          i  v   i ii i           -              ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_123189809_   1744 GACAAAGGTCTAATACCCAGAATCTATAATG------TACA--TAAACAA 1785
                           i  i  v  vi  i       v     v ------    -- v  i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_123189809_   1786 ATTTACAAAAGAAAAA-AACACA-TTAAAAAGTGAGCAAAGGACATGAAC 1833
                         ---  -      v   -   v  -  ?    i  i        iv    i
  L1M4_orf2#LINE/    792 ---TA-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_123189809_   1834 AGACACTTTTCAAAAGAAGACATACATGCAGCCAGCAA--ACAGGAAAA- 1880
                              i  i  v        i     viii    ii  --   v     -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_123189809_   1881 -T-TTCAGTATTACTGATTGT 1899
                         - -i   ii  i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (155 / 97)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.64 (36 / 22)  


2446 26.85 3.07 1.82  chr2_123239169_123241311      773  1651 (492)    L1M4_orf2#LINE/L1       19   908 (0)  

  chr2_123239169_    773 TCATAGAT-----GAC--GATATCATTAAAATATCTACACTGCCCAA--- 812
                             i   -----   --i    ii    i  iv v i   v     ---
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chr2_123239169_    813 --TCTATACTTTCAATGTTATATGTACCAAATTACCAA-TGTTATTTTTT 859
                         --    i vv     i iv  viv  i    v v   i-  ii-      
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTT 117

  chr2_123239169_    860 AAAAAAGAATTAGAAAAAAGC--ATTCTAAAATTTATATGGACTCCCAAA 907
                         iv i  --   i--- v    --  i        i       vviv   i
  L1M4_orf2#LINE/    118 GCAGAA--ATTG---ACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_123239169_    908 AGAGCCTGAATAAGAAAAGCAATCCTTAGCAAAAAAAAAACAAAGCTGAA 957
                         i  v  v     ivv   i     i -- v    i  i       i  i 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTT--GAAAAAGAAGAACAAAGTTGGA 210

  chr2_123239169_    958 GGCATCACATTGCCCAACTTCAAAATATACTATAAGGCCATAGTAATCAA 1007
                           vv     i v     i       iv     i  i  i i         
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_123239169_   1008 AACAGCATGGTACTGTTAATAAACTAGACACATAGACCAATGAAACAGAA 1057
                         i    ii        vi vv iiv      i     i     i  i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_123239169_   1058 TAGAGAATTCAGAAATAAAGCAGCACACCTAGAACCAACTGACCTGTGAC 1107
                          v    i i          v vii   ii  viii   i   ii vi   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_123239169_   1108 AAAATGGGCAAAAATAAGCAATGAGGAAATGACTCCCTATTCAATAAATG 1157
                           iivv v   i vi vv     i     vi ivvi  v     i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_123239169_   1158 ATGCTGGGAAAACTGGCTAACCATTTGTGGAAGAATGAAACTAGACCACT 1207
                         i        v      v  ?   iv  iii         ii i    v  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_123239169_   1208 CCCTCTCACTATATACAAAAAATAACTCAAGATATATTAAAGACTTAAAT 1257
                         v    v   i           v        i  iv  i ?    i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_123239169_   1258 ATAAGACCTCAAACTATAACAATTATT-GAAGAACACCTACA---AAATA 1303
                         i     v  v         -  i v  -      v  v  vi---    v
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_123239169_   1304 CTC----TCTCAAGTATCAGCATAGGCAAAGAGTTTATGACTAAGTCCTC 1349
                         i  ----i  iii  -------       v iv  iv iiv  v v vi 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGT-------TAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_123239169_   1350 AAAAGCAATAGCAACCAAAACAAAAACTGATAATTGGGACCTAGTTAAAC 1399
                                vv      v   iv     iv     v v    i vi i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_123239169_   1400 TAAAGAGCTTCTGAACAGCAAAAGAAACTATCAACAGAGTAAAAAGGCAC 1449
                          v  i i   i  vi vv    i  v        v i   i     i  v
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_123239169_   1450 CCTACAGAATGGGACAACATATTTGCAAACTATGAATGT-ATAAAGGACT 1498
                           i           v  v           ii  iv  v -    i     
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_123239169_   1499 AATATGCAGAATCTATAAAGAACTTAAATAAATCAACAAGAGAAAAAGAA 1548
                         vi   v      v           ivv i  v    i  v i   i v  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_123239169_   1549 AGTACACCATTAAAAAGTGGGCAAAAAGTATAAAAAG-TATT-CTCAAAA 1596
                          vv  v v   ?    i        iii v i  v  -i   -   v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_123239169_   1597 GAAGACATAAAAGTGGCCAACAGACATATAAAAA-ATGCTCAACATCACT 1645
                              i   v  i       i ii  i  i    -             ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_123239169_   1646 AATTAG 1651
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.31 (132 / 101)
Gap_init rate = 0.02 (18 / 890), avg. gap size = 2.39 (43 / 18)  


2752 27.49 2.23 0.78  chr2_123245951_123251773     4437  5331 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_123245951_   4437 TGGAAAAAAAGTTCCATGCTTATGTGTAGGAAGAATCAATATTGTGAAAA 4486
                               i v - i     i i   vi v      v i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_123245951_   4487 -----GTAT------AAGTAATTTATAGGTTCAATGTTATTCCCATCAAG 4525
                         -----i  i------  v i  i  i  i     i iv  i  i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_123245951_   4526 CTACCA-TTGATTTTCTTGACAGAACTAGAAAAATCTACTTCAAATTTCA 4574
                         v v   -i  vi   i   -     v v  v  iiiv iiii   v    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_123245951_   4575 TATGGAACCAAATAAGAG-CCCATA-TAGCCAAGAAAATCCTAAGCAAAA 4622
                                -- vii   i -    v -       i v    i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_123245951_   4623 ATAACAA-GCTGGAGGCATCACGCTACCTGATTTTAAACTATACTACAAG 4671
                          v     - i      vv    i  v  ii    i   viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_123245951_   4672 GCTACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGA 4721
                                   i   i    ii  i      i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_123245951_   4722 CCAATGGAACAGAATAGAGGCCTCAGAAATAACACCAGACATCTACAACC 4771
                         i        i     v   ivii         vv   v    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_123245951_   4772 ATCTGATCTTTGACAAACCTAACAAAAACAAGGAATGGGGAAAGGATTCT 4821
                          vi    i  i     ivv iv   i v  vvv           i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_123245951_   4822 CTATTTAATAAGTCATTCTAGGAAAACTGGCTAGCCATATGCAGAAACCA 4871
                           v  i  i  i vi v  i   v      v  ?   i     i  ivvv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_123245951_   4872 GAAACTGGACCCTTTCCTTATACCTTATACAAAAATTAACTCAAGATGGA 4921
                            ii       i v   i i   v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_123245951_   4922 TTAAAGACTTAAATGTAAAACCTAACACTATAAAAACCCTAGAAGAAAAC 4971
                          i ?    i         i v    v         vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_123245951_   4972 CTAGGCA-ATACCATTCAGGACATAGGCACGGACAAAGACTTCATGAACA 5020
                         v    ?i- v i -   iv   v v  vvii i   v ii   v ii i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_123245951_   5021 AAACACCAAAAGCAATTGCAACAAAATCCAAAATTGACAAATGTGATTTA 5070
                         vi            vvv         vvv     v  i    vv  i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_123245951_   5071 ATTAAA-TTAAAGAGCTTTGCTCAGCAAAAGAAACTATGATCAGAGTGAA 5119
                           i   -     i vi    iv vv    i  v     v vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_123245951_   5120 GAGGCAACCTACAGAATGAAAGAAAATTTTTGCAATCTATCCCTCTGACA 5169
                         i  i     i        ii       v       vii  viv     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_123245951_   5170 AAGGTCTAATATCCTGAATCTACAAGGAACTAAAACAAATTTACAAGAAA 5219
                          i  v  vi     v    v  i  i     vvv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_123245951_   5220 AAAACAAACAAGCCCATCAAAAAGTGAGCAAAGTATATGAACAGACACTT 5269
                           i     i  v  v  i?    i  i      v  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_123245951_   5270 CTCAAAGAAAGACATTTATATGGCCAA---GCAAACATGAAAAAAAGCTC 5316
                            v  ii    i  vi v        ---   --        i v    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCA--CATGAAAAGATGCTC 893

  chr2_123245951_   5317 ACCATCACTGGTCGT 5331
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (136 / 106)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.93 (27 / 14)  


2978 27.20 2.60 0.11  chr2_123283215_123288361     3776  4661 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_123283215_   3776 TAGAAACACATCCCGTGCTCATAGATTTGTAGAAGCAGTATTTTGAAAAT 3825
                          i    v i     i  i    i    v v   vvi i    v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_123283215_   3826 GACCATACTGCCAAAAGCAATCTACAAATTAAATGGAATGCCCATCAAAA 3875
                          i v     v  v   vii       i   v  i v   v  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_123283215_   3876 TACCACCATCATTCTTCACAGAATTAGAATAAAC-AATTCTAAAATTCAT 3924
                          v   v vv v  i  ii     v v  -i  i -i  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr2_123283215_   3925 ATGAAACCAAAAAAGAGCCCAAATAGCCAAAGCAAGACTAAGCAAAAAGC 3974
                            i  viiv  ii  v  vi          i   vvi i iv  i   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_123283215_   3975 ACAAATCTGGAGGCATCACACTACCTGATTTCAAATTCTACTATAAGGCC 4024
                              vi      vv       v  ii        vii     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_123283215_   4025 GTAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCA 4074
                         ii   v i   i    ii         i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_123283215_   4075 ATGGAACAGAATAGAGAACCCAGAAATAAATCCAAATACTTACTGCCAAC 4124
                               i     v    ii           i   v i i   iv i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_123283215_   4125 TGAATTTTGACAAAGCAAACAAAAATATAAAGTAGGGAAAGGACACCCTT 4174
                            v   i     i vviv   i vi  vv i i       i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_123283215_   4175 TTCAACAAATGATGCTGGGATAATTGGCAAGCCACAGGTAGGAGAATGAA 4224
                                    i        i  i   vv ?     v i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_123283215_   4225 TCTGGATTCTCATCTCTCACCTTATACAAAAAGCAACTCAAGATGGATTA 4274
                         vi    ii ii i   v    v          vi       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_123283215_   4275 AGGACTTAAATCTAAGACATGAAACTATAAAAATT-----AGAAACCA-- 4317
                         ?i   i     v     vv i           v i-----     v  --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_123283215_   4318 -----AACCCTTTA-GACATTGGCTTAGGCAAGGATTTCATGACCAAGAA 4361
                         -----  vi   ii-   v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_123283215_   4362 CCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTAATTA 4411
                         v         v v    i    iv   i   i   iv v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_123283215_   4412 CA-CTAAAGAGTTTTTCATGGCAAAAGGAACAGTCAGCAGAGTAAACACA 4460
                         v -i    i v    viiivv    i iv  vi   iv i   i  v v 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_123283215_   4461 CAACCCACAGAGTGGGAGAAAATCTTCACAGTCTATACACCTGACAAAGG 4510
                                    i           v  ii  ivii   i i    i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_123283215_   4511 ACTAATATCCAGAATCTACAACAAACTC----AAATCAGTAAGAAAAAAA 4556
                            vi          v  i  vi     ----  v   i   v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_123283215_   4557 CAA----TCCCATCAAAAAGTGGGCTAAGGACACGAATAGACAATTCCCA 4602
                            ----i  v  i?    i     v     ivi         v   i v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_123283215_   4603 AAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGTTCAATGTC 4652
                                                i  i  i       i   i    ii  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_123283215_   4653 ACCAATGAT 4661
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.00 (24 / 8)  


2440 27.12 4.41 1.81  chr2_123449528_123453588     2685  3569 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_123449528_   2685 TGGAGAGATATTTCACATTCACAGAAAGTAGGACTCAACATTGTAAAGAT 2734
                             i      ii  ii    ii  vv v i    i  i     v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_123449528_   2735 GTTAGTTCTTTCCTACTTGATCTATACATTTGATGCAATACCAATCAAAA 2784
                          vi i v  ii  v v        i v   ii i     v  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_123449528_   2785 TCCCAGCGAGTTATTTTGTGGATATAAACAAAATGATTCTAAAGTTTATA 2834
                                vivi v     ii  v  vi    iv    i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_123449528_   2835 TGCAAAGTCAAAAAACCCAGAATAGGCAAAA-AATATTGAA---GGAGGA 2880
                           v   vv   iii           v     -   v     --- i  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_123449528_   2881 CAAAATTGAAG-ACAGACACTATCTGGATT--AACACTTACTATAAAA-T 2926
                             i   i  -  vv     -  ivi   --  v        i   i- 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACT-TCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_123449528_   2927 ACAATAATTAAGACAGTATGTATTGTATTGGT-----GAAAGA---ATAG 2968
                            i    i        i  ----   i   i-----  v   ---    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTG----GTACTGGCATAAGGATAGACATATAG 295

  chr2_123449528_   2969 ATCAATGAAATATACTAGAGAGCCAAGAAATAGGCCTGTGTAAACATCAT 3018
                                i    v v v     i v       ii  ii ii vvi  vi 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_123449528_   3019 CAACTAACCTCTGACAAAGTAGTCAAGGCAATAGAATCTAGACAAAGCCA 3068
                            i i ii ii     i vv i    i v  vv   vvi  v i ii- 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT-A 394

  chr2_123449528_   3069 GTCTT----GCAAATGGTG-TAGCACACATGGAGAGCCACATGCAAAAAA 3113
                              ----i         - i v   vv    v ?            i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_123449528_   3114 CAAAACAAAGAATGTAGACATAGACCTTAACATTTT-TACAAAAATTGAC 3162
                         ---- ii   -- - i   vivv    i -  iiv -          i  
  L1M4_orf2#LINE/    445 ----ATGAAG--T-TGGACCCCTACCTCA-CACCATATACAAAAATTAAC 486

  chr2_123449528_   3163 TCAAAATAGATTATATACCTAAA-GTAAAATGTAAAACTGTAAAGCTCCT 3211
                                i   i ? v       -    i vv       i    i   i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_123449528_   3212 AGAAGATAATGAAAGAGAAAGCCTACATGATCTTGAGGATGGCAATAG-- 3259
                               v  iiv i ? v  ii  v i   i    i vvv      i --
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_123449528_   3260 -----GGCACAATACTGAAGGCACAATCCATGAAGGAATTAATTGATAAG 3304
                         ----- ii ii i  ii  i      v v ii  i   vv   v     i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_123449528_   3305 CTGTATTTCATTAAAATTTTAAAATTCTGCCTCACAAAAGTCAC-----A 3349
                         i  v i     i      vv   v  i  iviiv    i v   ----- 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_123449528_   3350 GAA--TGAAGAGACAAGCCACAGACTTTGGGAACATATT-GCAAAAAACA 3396
                            --    i      v       v vv i   v     -     vv i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_123449528_   3397 CATCTGATAATGGGCTGTTATTCAAAATATGCAAATAACTCTTACAAGTC 3446
                         i         v  i  vv   i  i     ii   v           v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_123449528_   3447 AACCATAAGAAAACAAACAAGCTGATTTTAAAACTGGGCCAAAGGCCTTC 3496
                           iv    i  i     i  v ii   ?-    v     -     vi  v
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGC-AAAGGATTTG 834

  chr2_123449528_   3497 A-CAGACACCTCACCAAAGAAGACGTTCATACGATAAATACACAAATGAA 3545
                          -i     ii  v          ii v  v i iiv    vi  v     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_123449528_   3546 AAGATGTTACAGATCATCTGTCAT 3569
                               i vv v    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.20 (55 / 25)  


3009 25.27 0.98 1.86  chr2_123480530_123484810     2878  3791 (490)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_123480530_   2878 GAAAGACATCTCATACACATGGATCAGAAGAATTAATAATGTTAAAAATA 2927
                               i   i   iiv       ii     v      v      i vvi
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_123480530_   2928 CAGCACTACTCAAAACAATCAAGGGATTTGATGCAATTCCTAACAGAATA 2977
                           ii   v i    vii   v vi    ii i     i    v  i   v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_123480530_   2978 CCAGTGGCATTCTTCACAAAAACAGAAATAGC-AATTCTAAAATTGTTAA 3026
                             iv  v  i  ii  i   iv  v -   -i  i        vv  v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATAT 151

  chr2_123480530_   3027 AGCAATTCTAAAATCTCGAAAGACCCTTAGTAGCCAAAGCAATATTGAGC 3076
                         i --------    v- i ii     vv i        i    v    iv
  L1M4_orf2#LINE/    152 GG--------AAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_123480530_   3077 AAAAAGAGCAAAGTTGGGAGCATCACACTGCCTAATTTCAAAATATACTA 3126
                           i    i         ii vv       v  i          iv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_123480530_   3127 CAAAGATACAGTAACCAAAGCAGTGTGGTATTG-TACAAAAATAGACACA 3175
                              v        i   ii          i  -i i  ii       i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_123480530_   3176 CAGACCAATGAAACAGAATAGAAAG-CCAGACATAAATTAATGTATTTAT 3224
                         i   i     i  i     v  i  -     v     iiv  ii      
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_123480530_   3225 TGCCAATTAGTTTTCTACAAATGCACCAAGAACATACATTGGGCTAAATA 3274
                         v i     ii     v    iv ii      v   v  v    vv  iv 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_123480530_   3275 TA-TCTTCTTCAATAAATAGTGCTGGAAAAACTGGATATCCATATGCAAA 3323
                           -    -     i    i       i v         ?   i       
  L1M4_orf2#LINE/    393 TAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_123480530_   3324 ATAATGAAACTAGATCCCTATCTCTCACTCTATACAAAGATCAAGTAAGA 3373
                          v      ii i  i     i   v   iv        i  i  v v i 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_123480530_   3374 GTGGATTAAATACTTAAATATAAGACCTGCAACTATAAAACTACTAGAAG 3423
                         i     i ? v  i     i     v  iv            vi      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_123480530_   3424 AAAACATAAGGG-AAATACTTCAAGGCATTGGTCTAGGCAATGGTTTTAT 3472
                                 i ? -    -    iv i v    vi             iv 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_123480530_   3473 GGTTAATACTTTAAAGCTTCAGGCAACAGAAACCAAAAAGAGACAAATGA 3522
                         i v  vv  vii   iviv  i      -   vv     v   i    vi
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAATTG 639

  chr2_123480530_   3523 GAGTGTATTAAACTAAAAAAAAATCCTGCATGGCAAAGAAAACAATCAGC 3572
                           v vi  i   v v     vvv iv   v --     i v  v    iv
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAG 687

  chr2_123480530_   3573 AAAATGAAAAGACAACCTGCAGAATGGGAAAAAATGTTTGCAAGCTATTC 3622
                            i             ii          i     i       iii  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_123480530_   3623 ATCTGACAATAGACAGATATAGAGAAGATACAAGAAACTCAAATAATTTG 3672
                               i  vi   vvi   vv    v   i  ii     vv i  i ii
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_123480530_   3673 ATACCAAAAAT-CAACT---CCATATAAAAAAGTGGGCAAAGGATGTGAA 3718
                            vi     v-   v ---   -  v?    i            v    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_123480530_   3719 CTAGACATTTCTGAAAAGAAGACATACAAACCATCAACAGGTATATGAAA 3768
                         -           vv        i       ivii   i i i i      
  L1M4_orf2#LINE/    837 -TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_123480530_   3769 AAATGGTCAACATGACTAATCAT 3791
                          i   v       v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 1.62 (26 / 16)  


1772 22.18 5.45 1.32  chr2_123504553_123506483      500  1031 (900)    L1M4_orf2#LINE/L1      277   830 (78)  

  chr2_123504553_    500 CATAAAGACAGA--TATAGATACAATGCAATAAAACAGAAAGCTCAGAAA 547
                              i  i   --       -     v    i  iv  i  ii      
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGAT-CAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_123504553_    548 TAAA---ATATTTTATATATGGTGAAATAATTTCAGACGTGAGTGCCAAG 594
                             ---   iv  ---      v  v i    iv   iv i        
  L1M4_orf2#LINE/    326 TAAACCCATACATT---TATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_123504553_    595 ACTATTTAATGG--AAAGATCACAGTCTTTTGAGAAAGTGGCATTGGGAA 642
                           i   i     --     -- i        v iv  i   iii     v
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGA--ATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_123504553_    643 AGGTTGTTATTCACATACAAGAGAATGAAGTTGAACCCTT----TATAC- 687
                          iv v v  ?i     i   i            i    i ----i i  -
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_123504553_    688 ATATATAAAA-TTGACTAAAGCTGGATAAAAGAGCTAAACATAACAGCTA 736
                              i    -  i   v  iv     v ?   v     ii   v     
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_123504553_    737 GAGCTATGGAACTC--AGAAGAAAACAAAGAAGAAAAACCTTTGAGAAAC 784
                         i i    ii     --           v  i? v   -i   i v  vvi
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCT 569

  chr2_123504553_    785 TGGATTTTGCAATGATTAGTTGAATATGACAACAAAAGCACAGGCAA--- 831
                            i  vv      i  vv  ii        v          i    ---
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_123504553_    832 ----AAACATC-ATAAATTGAAA---ATCAAATTTAAAA-CTTTTCTACA 872
                         ----   v  v-        i v---      v      -     v i v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_123504553_    873 TCAAAGGGCACTACCAACAAAGTAAAATGGCAACTCATGAAGTGGAA--A 920
                                i     i   v     i   v i    i  iii i   i -- 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_123504553_    921 AATATTTGCAAATTATATATCTAATAAGTGATTAATATAAAGAATATGTA 970
                                      i        i     v  i vi   vv       i  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_123504553_    971 AATAACTTTTACAACTCAATAACTAAAAACCAAAAATACTAATTAAAAAA 1020
                           v    i              iv    iv    v vv i    ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_123504553_   1021 TGGGAAAAGGA 1031
                             v      
  L1M4_orf2#LINE/    820 TGGGCAAAGGA 830

Transitions / transversions = 1.43 (67 / 47)
Gap_init rate = 0.03 (16 / 554), avg. gap size = 2.25 (36 / 16)  

 383 16.67 14.17 1.67  chr2_123504553_123506483     1333  1452 (479)    L1M4_orf2#LINE/L1      774   908 (0)  

  chr2_123504553_   1333 ACTCT---GACTCAAAAAAAAAAAAAAAAAT---------TAAAAATGGG 1370
                              ---i      v  v     i v    ---------?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_123504553_   1371 CAAAGGACTTGGAAAGACATTTCTCAAAAGGCAATGTCCAATTGGCCAAT 1420
                                i   i v           v    ivi  i v   v        
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_123504553_   1421 AGGCTCATGAAGGG-----CAAAGCATCACTAACCAT 1452
                          i  v      ii -----   --     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAA--CATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.03 (4 / 135), avg. gap size = 4.75 (19 / 4)  


1903 29.89 2.25 3.60  chr2_123553305_123555189.rev      501  1390 (495)    L1M4_orf2#LINE/L1       31   908 (0)  

  chr2_123553305_    501 AAAATCAATGTTGTTAAAATGGCCATATTGCCCAAATAAATTTACAGATT 550
                          i v i   i       i     v   i v       vi  i        
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chr2_123553305_    551 CAATGTTATTTCTATCCAGCTGTTAACATCATTTTTCAAAAAAAAAAAAA 600
                            i iv  ii     v iv vii i vv v     iiv i   vvi --
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA-- 128

  chr2_123553305_    601 ACTAAACTAAAAAAAACCATTTTAAAATT-ATATGGAACCAAAAAACAGC 649
                         --i  i  i --------- ii       -        -- viv  vi v
  L1M4_orf2#LINE/    129 --CAAGCTGA---------TCCTAAAATTCATATGGAA--ATGCAAGGGA 165

  chr2_123553305_    650 CCTAAAAT--CCAAAGCAATCCTATGCAA-AAGAACAAAGCCAGAGACAT 696
                           i i   --     i     i iviv  -          iii   ivv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_123553305_    697 CACGCTGCCCAACTTCAAACTATATTTGTAAGGCTACAGTGACCAAAACA 746
                            i  v     i      viv  i -ii  i        i i   i   
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACT-ACAAAGCTACAGTAATCAAGACA 264

  chr2_123553305_    747 GCATGGTGACAGTACAGAAACAGATCTATACATAAATAGAACACAATGGA 796
                          ii    ivii i i iii i   iv    v  v   i   i v   v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_123553305_    797 GAACACAGAAGTAAAGCCTCATACCTACATCCATTCAAACTTTGACGAAG 846
                           iiv     i    v  vi i ii  iivi  v ii vi  i   i i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_123553305_    847 TTCACAAAAATAAGCAAAGGGGAAATGACTCA-CTATTTAATCAGTGGTG 895
                         v vv   i vi vv   v       -  v vi-  v  i  iv i     
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTG 413

  chr2_123553305_    896 CTTAGATAACTGAAAAGCCATATGCAAAAGAATGAAACTGGGCTCTTACC 945
                           vi  i     i v ?   i               ii   i i i    
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_123553305_    946 TTTCCCTTTCGTTACATACAAAAATTACCTCAAG-TAGGTTAAAG-TTTA 993
                          iv v i------ i            v     i- i i i ?  -ii  
  L1M4_orf2#LINE/    464 TCACACC------ATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_123553305_    994 AATGAAAGCCCTCAAACTATTACAAACTTAGAAGGAAATGTAGA---AAA 1040
                             v   vv  v       v v vv        i   ii   i---   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_123553305_   1041 ----CACAATTCTGGGCATCAAACTTGGGAAATAATTTAT--GATTAAGT 1084
                         ---- iii iii    --------  i  v   ii   v --   - v v
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGG--------TTAGGCAATGGTTTCTTAGAT-ATGA 598

  chr2_123553305_   1085 TCTCAAAAGAAGTTGCAACAAAAACAAAAACTATCAAGTAGAATTTAATT 1134
                         ivi      v vvv         iv     ivivi  i v i i  v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_123553305_   1135 AAACTAAAGAGCTTCTGTACAT-AAAAGA-AGTATAAACAGAGTAAACAG 1182
                            v v  i i   i   i v -   i  - v   v  v i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_123553305_   1183 ACAACCCACATTACGGGTGAAAATATTCACCAACTATGCATA-GACAAAT 1231
                                   vv i   v         ii v  ii  ii  v-  i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_123553305_   1232 GTCTAATATCCAGGATCTATAAAGAACTTAAAGAAATCAACAAGAAAAAA 1281
                          v  vi       i  v           ivv v  v    i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_123553305_   1282 ACATATAATCTTATTAAAATGTGGGCAAAATACATCAACAGGCACTTCTC 1331
                            v    i iv   ?   vi        iv iv v  i  i  i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_123553305_   1332 AAAAGAAGACATACAATTGGCCAA-AAAAACATGAAAAAATACTCCATAT 1380
                         v        i      v       -  iv         i  i   v i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_123553305_   1381 CACCAATCAT 1390
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (157 / 106)
Gap_init rate = 0.02 (21 / 878), avg. gap size = 2.48 (52 / 21)  


1220 28.06 4.25 8.08  chr2_123582400_123584376      545  1485 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_123582400_    545 AGAAATATACCATATTTGTGGATAGAAAAATATAAGATTATTAAAATGTC 594
                          i i    v    i  ii     v i  i iv   v   i    i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_123582400_    595 AATTATCTCCAATTTGATCCAGGGGATTAATGAAATCCTGTTCAAAATT- 643
                            vv  i    v      i vi iv i  i v     ivv       i-
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_123582400_    644 --GCTGCAATATTTTTGATGGTATGAATAA-CTAATTCTATAGTATATAT 690
                         --     --iv      vv iv  vi i  -  i  i   v i vi    
  L1M4_orf2#LINE/    104 CAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_123582400_    691 CTGGGAAGGTAAAGAAACTAAAATAGCAAAAATAATTCTACCAAAAAAAT 740
                         --  i  v i  i i v i i      v    i   ii iv-    i  v
  L1M4_orf2#LINE/    152 --GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAG 198

  chr2_123582400_    741 AAT----TTTCAGGACACTCACTGTCCTTCTGCAGGTCTTCATATAAAGT 786
                           i----  vv     v v    vi  vvi v  iiv   vv  i    i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_123582400_    787 TCCTATAGTTAAATC--TATGGCACTGGTGAATGGATAGATCTATAAATC 834
                          v vi  i i  iv -- i   i     iiv v       iv    i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_123582400_    835 AAAAGGAACTAAAATAAAGACCCCAGAAACAAACCCAAGCACATATAGTG 884
                           v-    -  i   vi   vi       i       vi  iv   i  v
  L1M4_orf2#LINE/    299 AAT-GGAA-TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_123582400_    885 AACATATTTATGACAAAGATGCAAAGACAATTTAACAAAGAAGAAATGGA 934
                           ivv    vi     i i   v     v   ---   v ii    --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAA--GA 391

  chr2_123582400_    935 ATAA-CTTTACTCAAATTCAGACAGTTATGTG-CAA-TAAATAAGAAAAT 981
                            i-    --    ---  i ii  vv  v -   - ii   ?vv v  
  L1M4_orf2#LINE/    392 ATAGTCTTT--TCAA---CAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_123582400_    982 ATAAAACAAAAAAACAAACATCCTTAACTTATACCTCACAGTTTATAC-- 1029
                         i-----     i  ii  -i -- vi  iiv         viv     --
  L1M4_orf2#LINE/    437 G-----CAAAAGAATGAA-GT--TGGACCCCTACCTCACACCATATACAA 478

  chr2_123582400_   1030 ---TGAACTCAAAATTGATCACAAACATAAGTATAAAATATACAACTATA 1076
                         --- v          v     ? i  v   i i   i vv  v       
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_123582400_   1077 AAAATTGTATAACAAGTTATAAGAAATGGTCTGTATGATATTGAATTTGA 1126
                            v iv  v  v  ivi   i ?ivvii   vii   iv   ii  v i
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_123582400_   1127 CAA--GTT--------ATTACTTCAAAAACATTATCCATAAGGAAAAAAA 1166
                            --   --------  v  vi     i  iv v v i  iii      
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_123582400_   1167 ATGTTTTCTAGTTTAAGAGCTTTTGCTGTATAAAATA-ATTTTATCAAAT 1215
                         --------   ------------------     v i- i  i      v
  L1M4_orf2#LINE/    629 --------TAG------------------ATAAATTGGACTTCATCAAAA 652

  chr2_123582400_   1216 TTAAAACCTTAAATTTTAGTGCTC------ATGCTCTTTAAAAGAAAGTG 1259
                               ------ i   v     i------ ii  v i---         
  L1M4_orf2#LINE/    653 TTAAAA------ACTTTTGTGCTTCAAAGGACACTATC---AAGAAAGTG 693

  chr2_123582400_   1260 TTACATTTAAAAAGAGTCTATACACTGGGA-AAAATATTTGCAAATTATA 1308
                         ---- ---   i v ii i i v v     -               i   
  L1M4_orf2#LINE/    694 ----A---AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_123582400_   1309 TGTCTTATAAAACAC--ATATCTAGACTAT-TAAGAAAAACAAAACTCAA 1355
                          i   v    iiv  --i    i   v   -   ------- i     vv
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAA-------AGAACTCTT 779

  chr2_123582400_   1356 ACAAACCCCAACAATAACAAAACAA-CAAGCCAAATAATAAATGAATAGA 1404
                             -- i   i     v  i    -i  v    v ? v     iii i 
  L1M4_orf2#LINE/    780 ACAA--CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_123582400_   1405 CTATCTGAAGAGACATTTCATCAACAATGATGTTTATGTAGAAAATAAAT 1454
                         vv  i    v         vi   vi v   i vi vi i vv     ii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_123582400_   1455 ATTGGAAATTATGCTCAGCATCATTAGTCAT 1485
                          ivv    vv       i     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (145 / 115)
Gap_init rate = 0.04 (36 / 905), avg. gap size = 3.22 (116 / 36)  


2246 28.05 4.30 2.60  chr2_123590170_123596011      493  1376 (4466)  C L1M4_orf2#LINE/L1   (0)   908    10  

C chr2_123590170_   1376 ATTCCATGCTCATGGATAAGAAGAATCAATATTGTTAAAATTACCATACT 1327
                           i     i        vi     v i           i  vi v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

C chr2_123590170_   1326 GCCCGAAGCAATTTACACATTCAATACTACTCCTATCAAACTAACAATGA 1277
                         v   i  vii  i    v      ii v ii         v vv  iivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

C chr2_123590170_   1276 CATTCTTCATCAAGTTAGAAA---AAAAACT-ATCTTAAAACTTATATGG 1231
                          v  i  iii------     --- v  i  -   i     i i      
  L1M4_orf2#LINE/    110 CCTTTTTTGC------AGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

C chr2_123590170_   1230 AACCAAAAAAGAACTTGAATATCCAAGGGCATCTTAAGCAAAAGGAACAA 1181
                           viiv  ii  v iv     v    iivv     i iv  i i      
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

C chr2_123590170_   1180 ACCTTGGGGCATCGTGTAAATGACTTCAAACTATACTGCAAGGCT----A 1135
                          vi v i  vv  ii-------     --- i - i v   ii  ---- 
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCAC-------ACTTC---CCA-ATTTCAAAACTTACTA 242

C chr2_123590170_   1134 CAAGGCTATAGTAACCAAATCAGCATGGTACTGGCACAAAAACAGAAACA 1085
                            i    i     i   iv   ii           i  ii i   v i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

C chr2_123590170_   1084 CAGACTAGTGAAAAAGAACAGACAGACTCAAAATAGTGCCACACATCTAA 1035
                         i   ii i  i  v    iv  v  v ivi     ivv   i    i  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

C chr2_123590170_   1034 AACCATCTGAGATTTGACAAAGTTGACAAAAACAAGTAATGGGGAAAGAA 985
                         iii  vi   vv  i     i v  v   i v  vvi             
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

C chr2_123590170_    984 CACCCTATTTAATAAGTAATGCTGGGATA-TTGAA--------------- 951
                         i vi  v  i  i  i ii        i -i  i ---------------
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

C chr2_123590170_    950 -AATGAA------CCCCTTCCTTACACTCTATACAAAAATCAATTCAAGG 908
                         -      ------     v   i    iv           i  i    ii
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

C chr2_123590170_    907 TAAATTAAAGACTTATATGTAA-AGCTAAAACTATGAAAACATTGCAAAA 859
                          ii  i ?    i  v      -            i   viv  iv  i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

C chr2_123590170_    858 TATCCTAAG---AAATACCATTCTGGACATAGGTGCTCG-CAAAGACTTC 813
                         v v v  i ---    -- -   vv   v v  - i v -   v ii   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT--C-TTCGTGACCTTGG-GTTAGGCAATGGTTTC 588

C chr2_123590170_    812 AT-GATGAAGATGCCAAAAGTAGGTGCAACAAAAACAAAAATTGACAAAT 764
                         v -   - v  ii       i viv         iv      v  i    
  L1M4_orf2#LINE/    589 TTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

C chr2_123590170_    763 GGGACCTAATTATACTAAAGAGTTTCTGCACAGCAAAAGAAACTGTCAAC 714
                         v    i v  i v v v  i ii  i  ii vv    i  v   i    v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

C chr2_123590170_    713 ATAGTAAACAGACAACCTACAGAATGGGAGAAAGTATTTGCTAATCATTC 664
                          v   i  v        i               i       v      vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

C chr2_123590170_    663 ATCCAACGAAGATCTAATATCCAGAATCTATAAGAAACTTAAATAAATTG 614
                            ii ii i iv  vi          v     ii    ivv i  v i-
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC- 786

C chr2_123590170_    613 AAGAGTAATAA-ACAAACAACCCTATTAAAAATTATGCAAAGGACATAAA 565
                           v i   v  -     i     v   ?    v iv        iv i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

C chr2_123590170_    564 CAGACACTTCTAAAAAGAAGACGTATACTTGGCTAGTAAGCATATGAAAA 515
                         i     i    vv        ii  i vv    i i      i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

C chr2_123590170_    514 AATACTCAACATCACTGATCAT 493
                         i  i          ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.02 (20 / 899), avg. gap size = 3.05 (61 / 20)  

 450 27.45 1.31 2.61  chr2_123590170_123596011     4083  4235 (1607)    L1M4_orf2#LINE/L1        1   151 (757)  

  chr2_123590170_   4083 TAGAAAAGTATTCTATGAGCATGAATTGGAAGAAACAACATCGTTAAAAT 4132
                          i    ii   i i   vv    i         vvi  i  i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_123590170_   4133 GACCATACTACCTAAAGCAATCTACAGATTTAACGTTTTTCCTAACAAAC 4182
                          i v     v  i   vii           i    ivv i    v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_123590170_   4183 TACTAA-TGCCATTTTCCACAGAATTAGAAAAAAATCTG-TTCTAAATTC 4230
                          v i i-    -    iii     v v  v  i---   - i     v i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chr2_123590170_   4231 TATAT 4235
                         i    
  L1M4_orf2#LINE/    147 CATAT 151

Transitions / transversions = 1.62 (26 / 16)
Gap_init rate = 0.03 (4 / 151), avg. gap size = 1.50 (6 / 4)  

1383 28.48 2.58 7.22  chr2_123590170_123596011     4575  5350 (492)    L1M4_orf2#LINE/L1      169   908 (0)  

  chr2_123590170_   4575 AAAAAAACCAACAACAAC---AACAACAAAAGAATATAGAACTAGAAAGA 4621
                          i  v i    -     i---i v  - i     i v  --- v i i  
  L1M4_orf2#LINE/    169 AGAATAGCCAA-AACAATCTTGAAAA-AGAAGAACAAAG---TTGGAGGA 213

  chr2_123590170_   4622 GCC-CAGTTTC-AGTTTCAGAGTATACCAGAAAGTTACAGTAACCAATAC 4669
                         vi -  v  i - i     i iiv   i v    i        i   v  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_123590170_   4670 AGCATGATTGATACTGGTAAAATAAATAAAATAAAATAATAAAATATAAA 4719
                           --  --  i      i -------------------------------
  L1M4_orf2#LINE/    264 AG--TG--TGGTACTGGCA------------------------------- 278

  chr2_123590170_   4720 AGCTAAATTTAAAAACAGACAAATCGACAAATGGAACAGAAAAGAAAACC 4769
                         ---------   ii i     v  v  iv       i    vv  i ii 
  L1M4_orf2#LINE/    279 ---------TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_123590170_   4770 CAGAAATAAAGCTCGACACTTACAACCT-CTGTCCTTCAA-AAAAGTCAA 4817
                                   v ivv   i   iiii v-i  vii   i -  ii  --i
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT--G 367

  chr2_123590170_   4818 CAAAAATCAG-CAATGGGGAAAGCAAT--------TAATAAATGGTGCTG 4858
                          v  i i  v-            -   --------i  i           
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_123590170_   4859 AGACAACTGGCTAGTCATATAGAGAAGAATGAAACCAGACCCCCGCCTTT 4908
                         i         v  ?i  i  iv i         iiii      ii   iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_123590170_   4909 TACCATATATAAAAAATAAACGCAAGGTGCATTAAAGATTTAAATGTAAG 4958
                         i        i     v   - v   ii  v  i ?   ii          
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAA-CTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_123590170_   4959 ACCTAAAACTATAAAATTACTAGAAGAAAACCTGGGAAATAACATTCTGG 5008
                          v              i vi           v i  ?ivv  iv   vv 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_123590170_   5009 ATATCACCCTTCTCAAAGAATTTATGACTAAGTCCTCAAAAGCAATTGCA 5058
                          iv iivvi vvv   v iv  iv iiv  v v vi        vvv   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_123590170_   5059 ACAAAAAGAAAAATCCGCAAGTAGGTCCTAA-CTAAACTAAGAGCTACTG 5107
                               ii      vvii  i v  v i v - v   i   i i  vi  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_123590170_   5108 CACAGCAAAATAAATAATCAACGGAGTAAACAAACAATATACAGAACGGG 5157
                         ii vv    iv v iv     vii   i  v i    ivi      i   
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_123590170_   5158 AGGATATATTTACAAACTATGTGTCTGATAAGGGTCTCATATTCATAATC 5207
                           i v      i    ii  i i           v  ii   i  v   v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_123590170_   5208 TACAAAGAACTTAAACAATTGTAGGAGGAAAAAACAAATAGCCCCATTAA 5257
                           i        ivv    i vv vi vi    i       i   v   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_123590170_   5258 AAAAGTAGGGGAGGCACACATACAGACACTTTTCCAAAGA---TTTACAA 5304
                             - i  vi i v iviiv i     i  i        --- v     
  L1M4_orf2#LINE/    816 AAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_123590170_   5305 GCAGCCAACAAAGATCTGAAAAAAAAAGTTCATCATCACTAATCAT 5350
                         iii     i  iv iv      i v-- i   v     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (131 / 86)
Gap_init rate = 0.03 (20 / 740), avg. gap size = 3.80 (76 / 20)  


2711 26.53 4.04 0.69  chr2_123675592_123679432.rev     2483  3349 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_123675592_   2483 CCATGTTTATGCTATGAAAAA----ATACTGTTAAACTGTCCATACTACA 2528
                                i   vvv  i  i ----   i      iv  v v     v v
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_123675592_   2529 CAAAGCAATCTGTAGATTCAATGCAATCCCTAAGAACATACCAATGACAT 2578
                             vii    ii        i          vv  v  v   iivi v 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_123675592_   2579 GTTTCACAGAAATAGA-AA----------AAATTTATACGAAACCACCAA 2617
                         v   ii       v  -  ----------     i   i i  vii v i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_123675592_   2618 AGACCCAGAATAGCCAAAGCTCTCCTAAGCAAAAATAACTAAACTGGAGG 2667
                         i                 i vv  i i iv  i  v   v  ii      
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_123675592_   2668 AATCACATTACCTTACTTCAAATTATACTAAAGAGCTATATTAATCAAAA 2717
                          v     i v  iv i      viv     v i     i v       i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_123675592_   2718 CAGTGTGGTACTGCCATAAAAAACAGACACATAAAAGAATGGGAGAGGAT 2767
                                      v     ii -i     i   i vv     i v  i  
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAAT 311

  chr2_123675592_   2768 AGAGAACTCAAAAACAAATTCACACACCTACAGTGAACTCACTTTTGATA 2817
                         v    iii  i   i   ii  i   ii  ii  v  i v i   i  i 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_123675592_   2818 AACATGCCAAGAACATACGCTGGAGAAAGGACAGTCTT--CAATAAATGG 2865
                          ivi        v   v iv   i     i i      --   i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_123675592_   2866 TGCTGGGGAAACTGGATATCCATATGCACACAAAATAAAACTAGACCAGT 2915
                                iv         ?   i     v - i   i  ii i    vv 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAA-AGAATGAAGTTGGACCCCT 460

  chr2_123675592_   2916 ATCTCTCCCCATGTACAAGAATCAAGTCAAA-T---------ACTTAAAT 2955
                          i   v v    i     i   i  v     - ---------  i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_123675592_   2956 CTAAGACCTCATACTATGAAACTACTAAAAGAAAATGTTTGGGAATCTCT 3005
                         v     v  v v     i     vi  i       ii vv ? v vv   
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_123675592_   3006 TCAGGATATTGGACTGGGCAAAGATTTTCTGAATAATAC-CCAACAAGTA 3054
                           iv  iv    ii i     v i   ii ii   vv  -    -   i 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA-AAGCA 609

  chr2_123675592_   3055 CAAGAGAACAAA-GCAAAAATGAATAG-TGAGATTACATCAAG-TTAAAA 3101
                             v-      - v      ii   i- vi  i v      i-      
  L1M4_orf2#LINE/    610 CAAGC-AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_123675592_   3102 AGTCTCTGCACAGCAAAGGAAACAGTCAACAAACTGAAGAGACAACCCAC 3151
                          v i -  ii vv       v  vi    v   v    i           
  L1M4_orf2#LINE/    659 ACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_123675592_   3152 AGAATGAGAACAAATATTTGCAAACTATCCATATGACAAGAGATTAGT-- 3199
                               i  iv             ii  vi  v   i   i  i v  --
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_123675592_   3200 TCAGAATAAATAAGGAGCTCAAACAACTTTGTGGGTAAAAT--CTAATAA 3247
                         i       v    i  i   vv      ivi ii-     v-- v     
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAA 806

  chr2_123675592_   3248 TCTGGTTTTAAAATGGGCAAAACACCTCAATAGACATTCCTCAAAAGAAC 3297
                         i iii  ?v            iv ii v          i   v      v
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_123675592_   3298 ACATACTAATGGCAAACAGGTATATAGAAAGATGCTCAACATCATTGATC 3347
                          i    v      v  i i i i  ii                 ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_123675592_   3348 AT 3349
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.47 (135 / 92)
Gap_init rate = 0.02 (18 / 896), avg. gap size = 2.28 (41 / 18)  


3098 27.82 0.45 0.45  chr2_123729890_123732155.rev      877  1771 (495)    L1M4_orf2#LINE/L1        1   895 (13)  

  chr2_123729890_    877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_123729890_    927 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 976
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_123729890_    977 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 1025
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_123729890_   1026 ATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGA 1075
                               viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_123729890_   1076 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 1125
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_123729890_   1126 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 1175
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_123729890_   1176 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTA 1223
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_123729890_   1224 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGAAAAGGATTCCC 1273
                         vi    i  i     ivv  vv  i v  vv       i    i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_123729890_   1274 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 1323
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_123729890_   1324 AAACTGGATCCCTTCCTTACACCTTATACAAAAATAAATTCAAGATGGAT 1373
                           ii    i    v   i     v           v  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_123729890_   1374 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1423
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_123729890_   1424 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 1473
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_123729890_   1474 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1523
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_123729890_   1524 TAAACTAAAGAGCTTCTGCACAGCAAAAGGAACTACCATCAGAATGAACA 1573
                         i   v v  i i   i  ii vv    i iv    i  vv i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_123729890_   1574 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 1623
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_123729890_   1624 GGGCTAATATCCAGAATCTACAATGAACACAAACAAATTTACAAGAAAAA 1673
                           i  vi          v  i  v    v vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_123729890_   1674 AACAAACAACCCCATCAAAAAGTGGGTGAAGTACATGAACAGACACTTCT 1723
                         i     i     v  i?    i    ii   v iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_123729890_   1724 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGATAAAAAT-CTTAA 1771
                          v        i  vi viii     v  i       -   i  -  i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTCAA 895

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (6 / 895), avg. gap size = 1.33 (8 / 6)  


 815 28.30 6.60 4.01  chr2_123745122_123747237.rev       66   489 (1627)    L1M4_orf2#LINE/L1        2   436 (472)  

  chr2_123745122_     66 GAGAGGCTATATTATGCTTATAAATTGAAAGGCT--GTGTTGCTAAGATG 113
                          ii i v   vii   i i  ii    i   i  --i i   i       
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_123745122_    114 TCAGC-CATCTTAAATTGCCTTATATATTCAATGCAAT----A-CAAAGA 157
                         v  ii- vi ii      vii  i v      i     ---- -    --
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA-- 99

  chr2_123745122_    158 TATTCTAGA-ATTTTTTTT----AAAT-GACAAGAAAA-CTTAAAATCTA 200
                         -  i i  v-iii      ----    -      vvi - i      ii 
  L1M4_orf2#LINE/    100 -ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_123745122_    201 TTTGGAAATTCAAAGTATATGGAAGAATCAAA-TAGTTGTGAAAAAGAAG 249
                          v       v   i v ivii   v ii    -i i iv           
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_123745122_    250 AAAACAATTGCTTGCCT-ATACTACCTATTATGAGAAT--------AAAC 290
                           v v i   vvv v  - i   v  i v v v i  i--------  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_123745122_    291 TATAGTAATCAAGAAAGCATAGTTATAACAGATGGAAAAATAATTAGAAC 340
                           i           v  ii i  vv ii  v v   v i i vv    v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_123745122_    341 TATTGGACAGAATAGGAAGTCTAGAAATAGACTTAGATTGTAAAATAGAC 390
                         v  v i i     v ii    i       i  ii ----------  -- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCA----------TA--C 336

  chr2_123745122_    391 ATATATGGTCAAATGATTTTTGACAAATTTG--AAGGAATAATTAAAAGG 438
                           v         v       i     ivv  --   -- iv   v  v  
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG--ACCATTCAATGG 384

  chr2_123745122_    439 AGAATGTATAGTCATTTCAA-AAATGGTGCTGGAAAAACTGGACATCTAT 487
                         i   v v      v      -            i v       i ? i i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_123745122_    488 AT 489
                           
  L1M4_orf2#LINE/    435 AT 436

Transitions / transversions = 1.48 (71 / 48)
Gap_init rate = 0.04 (17 / 435), avg. gap size = 2.65 (45 / 17)  

 249 33.33 7.25 2.42  chr2_123745122_123747237.rev      501   707 (1409)    L1M4_orf2#LINE/L1      230   446 (462)  

  chr2_123745122_    501 TCAATACCTATTTTGAAGC---AATAATTAAGACTTTATGG-ATTAGCAT 546
                             v  i  i vii    --- i    i     vv i   - i i    
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_123745122_    547 ATGAATTGACAAATGTAGTAATATAAAAGAATCAAT--TCCAGAAATTTA 594
                          v i  v    v  iv vi   iv  v     ii v--         vv 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_123745122_    595 CATCTACATATAATACTAACTGATTTATGAAACATGTGACAAGGCTATAC 644
                          viv     v  vviii  i      vi  v viv   v    i i  v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_123745122_    645 AGCAG-------ATATGTATTTTTTCAATAAA-GGT-TTAAATCAATTAA 685
                          iii -------   ---i i       i   -   -i iiiv   i ii
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATA---GTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_123745122_    686 GTTTCCATATAAACAAAAAAAT 707
                         i v?   i  i--     i   
  L1M4_orf2#LINE/    427 ATAKCCACATG--CAAAAGAAT 446

Transitions / transversions = 1.52 (41 / 27)
Gap_init rate = 0.04 (8 / 217), avg. gap size = 2.50 (20 / 8)  

 542 27.30 8.40 2.89  chr2_123745122_123747237.rev     1244  1624 (492)    L1M4_orf2#LINE/L1      507   908 (0)  

  chr2_123745122_   1244 AAATGTGAAGGGTAAAATAATAAAGCTTTTATAGCAAAACAAAGGA--AA 1291
                               i ii v     iv     i  i   v iv      v   ?--  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_123745122_   1292 ATACCTGATGCCATTGGAAGAGGCTCATATTATCTTAAATCTGACATTAA 1341
                           - i vi  v v    ivv    -v  iv v     i  v     ii  
  L1M4_orf2#LINE/    557 AT-CTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTAGATATGACACCAA 604

  chr2_123745122_   1342 CATCTACTACCT-CTAAAGAAAAAA-------ATTGG--TGTATCTTAAA 1381
                         v v -  v v v- v          -------     -- vi   ---  
  L1M4_orf2#LINE/    605 AAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC---AA 650

  chr2_123745122_   1382 AATTATAA-TATTTGTTCATTGGAAGACACAATTTAGA--GTAAAATTCT 1428
                              v  -iv     v v iii i     v  iv   --  i   vvvi
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_123745122_   1429 AATC-ACAGA----GAGAAAAGTATTGATA---CATACAGCTAACAAAAG 1470
                           i -     ----       -    vii ---    i v  i i  ii 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGG 749

  chr2_123745122_   1471 ATTTGCATCTCAAACTTACAAAAAATTCATAAAA-TCAATAATCAATCAA 1519
                          i   i   ivi  iv  i   i  i  v  v  -        v  --  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA--AA 797

  chr2_123745122_   1520 AACAGATAAATACAGT--AAATGTAAGCAAA--ATTTGGAATAGGC---T 1562
                         i   i    vi-  i --   vi ii     --     -     i --- 
  L1M4_orf2#LINE/    798 GACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTG-AATAGACATTT 845

  chr2_123745122_   1563 TTAAAAGGCAGCTACTTGAATGACCATCAAGCCTAT-AAAAGATATTCAA 1611
                         i vv  i v  v  ivii    i   vi    vi  -       ii    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_123745122_   1612 CATCATTAGTCCT 1624
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (57 / 46)
Gap_init rate = 0.05 (22 / 402), avg. gap size = 1.95 (43 / 22)  


2098 25.25 9.09 3.03  chr2_123799499_123802441     1151  1942 (1001)    L1M4_orf2#LINE/L1        4   843 (65)  

  chr2_123799499_   1151 AAAGACATTGCATATTCATAAACTGGAAGCCTTAAAATTGTTAAAATGTC 1200
                              i  iv   i     ii i      v     v        i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_123799499_   1201 CATA-TACCAAGAGTGATCTACAGATTCAGTGCAATCCCTATCAAAATCA 1249
                         v   - v  v i v               ii                  v
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_123799499_   1250 TAATGGCATATTTTATAGAAATAGAAAAAAGGCAG-TTCTAAAATTCATA 1298
                         i iiv  v v    ii      v  v  ---  v - i            
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAA---GCTGATCCTAAAATTCATA 150

  chr2_123799499_   1299 TGGCTACACAAAGGATGCTGACAAGCCAAAAGAGTTTCGTG---GAAAAA 1345
                            vv ii   i   iv v  vv        v i i i vi---   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_123799499_   1346 CAAAGCTGGAAGCCTCAAATTTCTTGATTT-AAAATATATTACAAAGCTA 1394
                              i    i v    v i   iii    -    iv  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_123799499_   1395 AAATAATCAAAACAGTGTGGTAGTGTCATAAAAGTGG---------CCAA 1435
                         v i       i           v  v     iii i ---------i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_123799499_   1436 TGGAACAGAATAAAAAGCCCCAAAATGAACCCACATATATATACTTTTAG 1485
                              i     vi i  i  vi    i      i i  v   iv i-- i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC--AA 348

  chr2_123799499_   1486 CCTTGTTTTTC-ACAACGGTGCCAAGAATACACAATGGGGATGGGATTAT 1534
                         --   v     -    v          vi iv         vi i  vi 
  L1M4_orf2#LINE/    349 --TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_123799499_   1535 CTCTTCAA---ATGGTGTTAGAAAAACTGAATATTCACAAATGAAAGAAT 1581
                           i     ---      i i i v     i   ?i    viii       
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_123799499_   1582 AAAAATGGACCC-----------------------------------AGA 1596
                         i  iv       -----------------------------------i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_123799499_   1597 TC------TTAAATGTAACACCTGAAA-TATGAAATTTCTAGATCAAAAC 1639
                           ------i         v v  i   -   i   i ii    vv     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_123799499_   1640 A--GGTGAAAAGTTTCATGGCATTAATCTTGGTAATT-TTTTTTA--TAT 1684
                          --  ? v   vi   i  i v  iivi v  i   v-   i   --   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_123799499_   1685 GACAATGAAAATTCAGGCAACAAATACAAGAATACACAAGTGGAGCTGCA 1734
                             vii   iiv  i        viv  i    v i  i v ii  v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_123799499_   1735 TCAAACTAAAAAGCTTCTACAGAGCAAAGAAAAAAAATCAACAGATTAAA 1784
                              v v    i   i iiivvv     i v vv -    v i v i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAA 695

  chr2_123799499_   1785 AATGCAACATACAGAATAGG-GAAAATATTTGCAAACCATGTATCTAATA 1833
                           vi    vi       i  -               i   i     i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_123799499_   1834 AGGGGTTAGTATTCAATATATATAAAGAACT---ACAACTCAATAGCCAA 1880
                             ii v    i  iv              ---           -----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA----- 790

  chr2_123799499_   1881 AAATAAAAATAAAATAAAACAAAAAAC--AAATAAAAACCAAGCAAAGAA 1928
                         --       --------i     v   --  v ?    viii      i 
  L1M4_orf2#LINE/    791 --ATAAAAA--------GACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_123799499_   1929 ATATAAGCAAACAT 1942
                         v - i ii i    
  L1M4_orf2#LINE/    831 TT-TGAATAGACAT 843

Transitions / transversions = 1.56 (120 / 77)
Gap_init rate = 0.03 (23 / 840), avg. gap size = 4.17 (96 / 23)  

 341 22.89 0.00 0.00  chr2_123799499_123802441     2369  2451 (492)    L1M4_orf2#LINE/L1      826   908 (0)  

  chr2_123799499_   2369 AGGGATGTGTATGGACATTTATTTAACAGAGACATATAAATGACCAATAG 2418
                          i    v  v  i       v ii  vii   i   i     i      i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_123799499_   2419 GTATATGAAAAGATGATTAGCATCATTAATTGT 2451
                          i i           v i i     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.80 (14 / 5)
Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.00 (0 / 0)  


1833 29.06 5.19 0.00  chr2_123809768_123813036     2162  2777 (492)    L1M4_orf2#LINE/L1      261   908 (0)  

  chr2_123809768_   2162 GGCAGCATGGCACTGGTCCAAAAACAGACACCTAGACCAATGGAACAGAA 2211
                          i   ii   i     ivi  ii i     iv    i        i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_123809768_   2212 CAGAAAACCCAGAAATAAGACTACACACCTATAACTATCTGATCTTCAGC 2261
                         iv  i ii          iv i i   ii   iiii vi    i   ii 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_123809768_   2262 ACACCTGGCAAAAATGAGCAATGGGGAAATGATTTCCTATTCAATATAGG 2311
                          vivv  v   i viivv           vi  vvi  v     i v v 
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_123809768_   2312 GTGCTTGGATAACTGGCTAACCATAAGCAAAAGATTGAAGCTGGACTCTT 2361
                              v   i      v  ?   i v        v     i     i i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_123809768_   2362 TTCTTATGCCATATACAAAAATTAACTTAAGATG---TAAAGCCC----- 2403
                         vi  i ii                   i  i   ---i ?  v  -----
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_123809768_   2404 ---------AAAACTATAAAACCCCTGGAAAAAAACCTAGGCA-ATACCA 2443
                         ---------             i i i   i     v    ?i- v i v
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_123809768_   2444 TTTAGACTTAGGCACTGGCAAAGATTTTATGACAAAGACACCAAAAGCAA 2493
                          ivv   i v  vviv     v i   iv iivv v             v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_123809768_   2494 TTGCAACAAAAGCAAAAATAGACAAGTTGGATCTAATTAAACTAAAGAGC 2543
                         vv          v         i  i     ii v  i   v v  i i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_123809768_   2544 TTCTGCACAGCAATAGAAACTGTCAACAGAATAAACAGACAACCTACAGA 2593
                           i  ii vv   vi  v   i    v i i i  v        i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_123809768_   2594 ATGGGAGAAAAATTTTGCAAACTATGCATTCAACAAAGGTCTAATATCTA 2643
                                    vv        ii  ii  iii i  i  v  vi    i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_123809768_   2644 GCATCTATGAGGAACTTAAACAAATTTACAAGAAAAAAATAAACAGCCCC 2693
                          v  v   i i     ivv    v iv i  v     i i   i i   v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_123809768_   2694 ATAACAAAGTGGGCAAAGGACATGAACAGACACTTTTCTAAAGAAG---- 2739
                           v?v   i           iv    i     i  i  i       ----
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_123809768_   2740 --------CCAACA-GT-CATGAAAGAAAGCTCAATATCATTGATCAT 2777
                         --------    i - i-       ii v      i    ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (108 / 67)
Gap_init rate = 0.01 (6 / 648), avg. gap size = 5.33 (32 / 6)  

 557 27.39 4.35 2.61  chr2_123809768_123813036     3037  3266 (3)    L1M4_orf2#LINE/L1      112   345 (563)  

  chr2_123809768_   3037 TTTTTTGGAATATATGGTTGGGTTGATTCTAAAGTTGTTATGGATATCCA 3086
                                v iv -  v viii i    i     i  vv      v  v  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_123809768_   3087 AATGAC--AGAATAACCAG--CTATCCTGAAAAAGATGGGGAAGGTTGGG 3132
                          iv   --      i   i-- v   i         v iiv  i     i
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_123809768_   3133 ATATTTACTCTGTTTGACTTTTAAGGTATAAAATAAA-CTACAGTAATCA 3181
                         iv i i  v  - iiv v   i  iiiv  vv i   -            
  L1M4_orf2#LINE/    211 GGACTCACACT-TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_123809768_   3182 ACACAGTATAATATAGGTGATA-GGATAAACAAGTAAATCAACAGAATAG 3230
                          v     i ii  iv  i-   -     i   vi  i     ii      
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGC-ATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_123809768_   3231 AGT--AGAG--CAGAAGTAAATCTACACATAAATTTTGGT 3266
                          i --    --     i    i i i    ---  v    
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACAT---TTATGGT 345

Transitions / transversions = 1.74 (40 / 23)
Gap_init rate = 0.04 (10 / 234), avg. gap size = 1.60 (16 / 10)  


1721 28.60 5.36 3.91  chr2_123826310_123828173.rev      478  1372 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_123826310_    478 TGGAAAGATATTTCATGTACATTGATAGGCAGAATCAATACTGTTAAGAT 527
                                    ii     v   v   v  v   v i    i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_123826310_    528 GTCATTCTTTCTGATTTTTTTCTATAGATTTATTGCAATCTCAGATAAAT 577
                          v  v vi i iv vv  vv    i     i vi      i vivi   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_123826310_    578 TTATTGCAATTTATTTTGAATATATGAGCAAAGTGTTGCTAAGGTTTATG 627
                          iviv  viii v     v v v  vii   iv  v v    ii  i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_123826310_    628 TGAAAAGGCAAAAGACACAGAATAACCAACATAATACTAAAAAACAAGAA 677
                           i   v    ii   v       i    v i   vi i     ------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA------ 194

  chr2_123826310_    678 AATGGAGGAAAAAGAGAAAAACAGGAAAAGAAGAGTCAT--TATTCAGCT 725
                         ---------------   i    iiivvi  i  v   i-- vii  ii 
  L1M4_orf2#LINE/    195 ---------------GAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_123826310_    726 TCGAGACTTACTAAAAACCTACAATTATCAAGGCAA------A-----AT 764
                           i i        v   v     i v      i  i------ -----  
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_123826310_    765 AAA---AGACAAGTA-ATCAATGAAGCAAAATGGAGAGCCCAGAAATAA- 809
                           i---     vi  -       i ii i   v     i          -
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_123826310_    810 -TCAACTACAGTTGCATAATGACAATCAACTGGTATTTGACAAAGGAGCC 858
                         -i  --    v  -----   i---    i  i v  i     i  v   
  L1M4_orf2#LINE/    330 CCCA--TACATTT-----ATGG---TCAATTGATTTTCGACAAGGGTGCC 369

  chr2_123826310_    859 GAGGCAATTAAATATAGAAAGAGTAAACTTTTCTACAAATGATGCTGGAA 908
                         i  i v   v   ivi      i  iv      v       i      i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_123826310_    909 CAACTGG-CATCAACAATGAAAAAAAATGAATCCAGATATAAACTTTACA 957
                                -i ? v   -  v    i      viii  ivivv  i i   
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACA-TGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_123826310_    958 TCTTTCACAAAA-TTAATGCATAATGAATTATTGACCTAAAT-TAAAATT 1005
                         i v vi      -    iv  v    i  i ?v         -   i vi
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_123826310_   1006 CAAAATGATAAAACATCTATAGTGTAACATAAATGAAAATCTT-AT--TT 1052
                         i    iv       vii  v iviv      ii? v       -i --ii
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_123826310_   1053 TTTATTTTGATGATGAGTTTTTAGGCA--ATGCTGAAAGCACAATCTATA 1100
                           viv  v iii   iv  i    ii -- ii ii         v v i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_123826310_   1101 AAAAAACAA-----CAAGTTAGATTT-ATTATAATTAAAGTAGTTTTGTG 1144
                            i  v  -----i  i  i  i  -  i v       i- v       
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTG 667

  chr2_123826310_   1145 ----AAAGCA-ACTG--AAGAGAATGAAAA--TAATCAA-AGACTAA-AG 1183
                         ----    v -   i--    i i      --i  i v -   v ii-  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_123826310_   1184 AAAATATGT-TAAAACATCTACATAATAAAGCACTATTACCAAAAATATA 1232
                                v -i   v   v  iv i    i v   vv  i v i      
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_123826310_   1233 CAAATAACTCTTAAATCTTCACAATAAGAAAATTAACAACTAAATTTGTT 1282
                         i   v        v v  iv i     i  i iv  i   iv    ?iv-
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA- 816

  chr2_123826310_   1283 TAAATAAGCAAAAGATCTGAATAAG--TTTC-ACACTAAAAATATACCAT 1329
                         -    ii     i   i      ii--    -v  vvi  i      v v
  L1M4_orf2#LINE/    817 -AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_123826310_   1330 TGGCAAATTGGCATATGAAAAGACGCTTAGCATCATGTATCAT 1372
                             v   vi   i         i   i i     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (151 / 101)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.77 (83 / 30)  


 223 25.24 4.85 1.94  chr2_123830641_123832280.rev       64   166 (1474)    L1M4_orf2#LINE/L1      458   563 (345)  

  chr2_123830641_     64 CCTAAGCCTTATACCATATA--AAATTTAAGTAAAAATAAGTTATGCACT 111
                             --   i i        --   v    v v     iii i ?iv  i
  L1M4_orf2#LINE/    458 CCTA--CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_123830641_    112 TAAATGTAAAATGTAAAACTATAATAATTTTATT-GAAACTAT--GAGAA 158
                                  i vv           v v i   vv-    vi  -- ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_123830641_    159 AATCTTTG 166
                               i 
  L1M4_orf2#LINE/    556 AATCTTCG 563

Transitions / transversions = 1.00 (12 / 12)
Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.75 (7 / 4)  

 568 30.42 7.44 3.88  chr2_123830641_123832280.rev      169   477 (1163)    L1M4_orf2#LINE/L1       57   376 (532)  

  chr2_123830641_    169 ACCTCCCATATTGGTCAATAGGTTAAAGAGAATTTCTATCAAAGCCTCAA 218
                           ii    v    i  v i  i  v  viv   ii        ii i  i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_123830641_    219 AAAGGGTTTTTTTGC-----TT-------T--TTTT----TTTGTACGGT 250
                         v--v vi        -----  ------- -- ii ----  ii  i  v
  L1M4_orf2#LINE/    107 C--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_123830641_    251 AAGGTTAAGGCCTTAGAATAGCTAAAACAATATTAACAAATAAAAATAAA 300
                           v iv i  v ii        i        v  i v   v  i  i   
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_123830641_    301 GTAGAAAGA---ATAGTTTCGTTAGGATAAAAACTCATTTTATGGCAAGA 347
                           v i i  --- i v  i --i ivv v      i i vi vi  v v 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCC--CAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_123830641_    348 AAAATTAAGACAGTATGGTATTGGTGGAAGAGTAGACATATAGATCAATA 397
                         iv   i        i     i   iiv   ii                 i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_123830641_    398 GAACAGAAT--AGAGGCCAAAGAGCACAGGAAGTTCTACACACCTATGCT 445
                            i     --    v   i i ---i --  --i i i   ii    v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAA---TA--AA--CCCATACATTTATGGT 345

  chr2_123830641_    446 GAAGTAATTTTTCAGAAAAGAACAAAAGATCA 477
                         v  v i     iv v  ii vi v  -  i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAA-GACCA 376

Transitions / transversions = 1.76 (60 / 34)
Gap_init rate = 0.04 (12 / 320), avg. gap size = 2.92 (35 / 12)  

1024 28.05 6.94 4.83  chr2_123830641_123832280.rev      486  1148 (492)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_123830641_    486 AAAACACATTTTATGGCAACAAAAATTAAGACAGTATAGTATTGGTGGAA 535
                              vi i vi vi  v   iv   i        i i   i   iiv  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_123830641_    536 GGGTAAACATATAGATCAATAGAGTAGAATAGAGGGTCAAAGAGCACAGG 585
                           i  i              i  i      v   i   v ii ii ----
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA---- 327

  chr2_123830641_    586 AAGTTCTACACATGTATGCTGAAGTAATTTTTCAGAAAAGAACAAAAGAA 635
                           --i i i    v    v v  v i     iv v  ii vi v  iivv
  L1M4_orf2#LINE/    328 AA--CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_123830641_    636 ATTCA--GGAAAGAAAATAGAAACTGTTTAACTAATGATGCTGTAGTAAT 683
                              --  ii i i     v--  v  i   v    i     viii  i
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGT--CTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_123830641_    684 TGGAATTCCAGAGGCATAAACATCAA------CCTCAACCTAAGACT-TA 726
                             vv?   v v   v  iv  v  ------  i v    v v  i-  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_123830641_    727 TACTGCATAAAAACCAAGTCAAAATAAATTATGCACTTAAATGTAAAACA 776
                            -----     ii  v       ii  i ?iv  i         i vv
  L1M4_orf2#LINE/    474 TAC-----AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_123830641_    777 TAAAACTATAATACTTTTGTTAAAAAATAT--GAGAAAAGCTTGGAGATC 824
                                    v   i  ivv i    i  -- ? v   v   v v  i 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_123830641_    825 -----------AATGGTT----AGATAAAACTTGGCACTAAAAGAAAAAT 859
                         -----------       ----     -----  i   i     v v  v
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATA-----TGACACCAAAAGCACAAG 613

  chr2_123830641_    860 CCAT----TAAAAAATAGAAAACTTCAACCTCAATATATAAAA--AAAAA 903
                          v i----v          v  v  vi  i   --- -i    --     
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCA---T-CAAAATTAAAAA 659

  chr2_123830641_    904 CTT--ATTCTGCAAAAGCCGATTTGAAAAGGATTAAAAG-CAAT-----G 945
                            --i v  v    i v iv v v  i iii v     -   i----- 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_123830641_    946 ACTGGGA-AGTGTATTTTCAATCTACATTTTCTACAAAGATACA-ATATC 993
                          v     - ivi     v   vii i  v iiv i  i i-  v-i    
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG-ACTTGTATC 758

  chr2_123830641_    994 TGTAATATA-AAAAATTTCCCAAAACTCAATATTAAAAAAAAAAAAGAAA 1042
                         iiv      -   i vi  ii v         v      i v   -----
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA----- 803

  chr2_123830641_   1043 ACAGCAATCCAATTGGAAATTGAGAAAATGACAAGATTACACATTTCCCT 1092
                         ----i  i      ?i   v  i v   v  ivv  v  v       i i
  L1M4_orf2#LINE/    804 ----TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_123830641_   1093 ---GAAGATATACACAGAGCATGCAAGCACAGAAAAAGATGCTAAACATC 1139
                         ---           v vi  vvii       vi          v      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_123830641_   1140 ATCAGCTAT 1148
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.19 (99 / 83)
Gap_init rate = 0.04 (24 / 677), avg. gap size = 3.25 (78 / 24)  


1449 25.71 8.68 9.23  chr2_123887799_123890087      898  1807 (482)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_123887799_    898 AAAAGTATACCATGTTTATAGACTG-AAGATTCAACATAGAAAATATGTT 946
                            ii   v       i  i  i  -    i i  i  --------    
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT--------TGTT 45

  chr2_123887799_    947 AACTTGGCA--------CAAAT------ACATTTTAAAC-CACTTT-TAC 980
                           vv     --------     ------   vv  v   -  v ii-  i
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_123887799_    981 CAAAATTCCGACAATAATTTTTGTGGACATAGGCAAGTTTATTCTAAAAC 1030
                               i  ii viivv      ii  v  v i    i v  i      i
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_123887799_   1031 TAACATAAAAAAGCACAAATCCTAGAATAATTCAAACAATCTT----ATG 1076
                          v i  ii   v   viiiv  i      iiiv          ---- v 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_123887799_   1077 AAGAATCAAGTAGGAAGTCTCATTTTACCCACTATTAAAGTTTACTATCT 1126
                              iv    v   i v    ivi v    v v i   ii      ivv
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_123887799_   1127 AGCTACAGTCATCAACATATTGTTGAATTACAGG---AAGGAGAGACACA 1173
                                  v     v i v   v ---   v  ---     v     i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGG---TACTGGCATAAGGATAGACATA 292

  chr2_123887799_   1174 --GATCAATTAAACAGAATAGAGGACCTAGAAATAAAACTGTACCTACAT 1221
                         --       vi  i     v   iii i         ------  i ---
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA------CCCA--- 333

  chr2_123887799_   1222 TTATATATATACATATATGGATATACATGTTCTCAGTTGATATTTGATGA 1271
                         ---------     v     ------------   i     v  i  ii 
  L1M4_orf2#LINE/    334 ---------TACATTTATGG------------TCAATTGATTTTCGACAA 362

  chr2_123887799_   1272 AAAAGAAAAAGCAATTTGATGGCGGAAAAATGGGCTTT-CAACAAATGG- 1319
                         iiiv vv  ii v   ii    v i  i   i v    -          -
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_123887799_   1320 -----AACAATTAGAAATTCATA------------------GATC---AC 1343
                         -----i    i i  v ?i  i ------------------  i ---  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_123887799_   1344 ---ACACACACACACAAAAACATTCAACCAAAACCCCAGATAGCTCATGC 1390
                         ---    -  i i       --  -------   i v i  i v   ?iv
  L1M4_orf2#LINE/    463 CTCACAC-CATATACAAAAA--TT-------AACTCAAAATGGATCAWAG 502

  chr2_123887799_   1391 ACTTAAAAGTAAAATATAAAAGTATAAT-CTTTTAGAAAAAAATA---AA 1436
                           i    v    i vv     v     v-  i      i    i ---i?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_123887799_   1437 ATAAATTTTTAGAATCTAGGGCTAGGGAAAGAGTTCTTGAACTTGATACC 1486
                         i     i  iivi i  v   i    v  v iv     ii iv   i   
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_123887799_   1487 AAA--CATAATCCTTAAAAGGGAATATAGGTAAATTGGAACTAATCCAAA 1534
                            --  i  v vvi     ii  v    i         vi v   v   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_123887799_   1535 TTAAAAGGGAAAAAGCAAAAAAATCTCTG-GC--CATGGGAAAGCCTGTG 1581
                               ---------------- ii i  -  --  ----  i v vv i
  L1M4_orf2#LINE/    653 TTAAAA----------------ACTTTTGTGCTTCA----AAGGACACTA 682

  chr2_123887799_   1582 TGAAGAGGCTGAAAAGATAATTCTAGACTGTAGAGATTGGAAGAAAATAT 1631
                          v    iiv        i  ii ---  -----   v   i         
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCC---AC-----AGAATGGGAGAAAATAT 724

  chr2_123887799_   1632 TTGCAAATCAAATTTCTAACAAAGCATTTTTACC-----TATATTAAGAG 1676
                                   v  v   i i  i v i  v  i -----     v    i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_123887799_   1677 CCCTTA--ACACGACAGTAATAAAACCA----TCCAGTAAGAAAGTGAGC 1720
                          i    --  v i i i   v  i  v ----i   i v?i   i  i  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_123887799_   1721 AAAATATGTAAACAAATCTTTCACTGAAAAGAACTTACAAATGTCAAATA 1770
                            iv  v i  i i iv    v ii  i ii iv        v v    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_123887799_   1771 GACACA--AGAAGTTGTTCAATTAGACATCAAGCCACAA 1807
                         ii    -- i   v  i    -----     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAA-----CATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (141 / 89)
Gap_init rate = 0.04 (35 / 905), avg. gap size = 4.66 (163 / 35)  


2514 29.08 3.99 0.46  chr2_123933237_123935344.rev      740  1616 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_123933237_    740 TGGACAGATATTCTATGTTTATTTATTGGAAGA--TAATTTTGTTAAAAT 787
                             v      i i     i  vv         --    v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_123933237_    788 GCCAGTTCTTCATAACTTTATCTAAAGATCCAGCACA-TCCTTATCATAC 836
                          v  i v  i vi  v  v     v    i  i i  -   i     v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_123933237_    837 TCTCAGCAAGCTTATTTGTAGATATTGACAAAGTGGGCCTTCAATTGATA 886
                           i    viv   v    i   v        iv  iv   vv    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_123933237_    887 TGGAAAGGCAAAAGACCTAGAACAACCAACACAATTCTGCAATGGATGT- 935
                               v    ii    i    i i    v     ii  v  vi  v v-
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_123933237_    936 CAATATTAGAATACTCATATGATCTGATTTTAGGACTTACTATAAAGC-- 983
                            vi  i  iv     i ivvi ii    i ii        i     --
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_123933237_    984 CAGCTTCATCGAGATTTCATGGTGTTGTCAAAAGTATAAACTTGTTGGTT 1033
                            -- v   i   ivvii    ii  v  v   v   i  v i v i i
  L1M4_orf2#LINE/    251 CAG--TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_123933237_   1034 ACTGGAATGGAATAGAAAACCCAGAAACAGACTCCTACCAATATAATATA 1083
                          v      i    v  i ii       i i  i v   vvv   ii vv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_123933237_   1084 CTAATTTTTGACAAAGGCACAAAGGCAAATCAATGAAAAAACAACTATGT 1133
                         i i     i     i  ii v   i v v      iii   v  ivi v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_123933237_   1134 -----ACATATGATGCTGGAAAAATTGGCCATCCATATGCAAAAAAACAT 1178
                         -----   v   i      i v  i   vi ?   i        i  iiv
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_123933237_   1179 AACTAGAGAGAAACTTTATG--ATTTACAAAAAGAAAACTAAAATGGATC 1226
                          ii i  vvvvv  i i ii--  v        vv  vii          
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_123933237_   1227 ATAGACTTAA-TGTA-----------TATAATATTTCTATAGGGAAACAT 1264
                          ?    i   -    -----------     v i ii  v i i      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_123933237_   1265 ACAAGAAAATTCGTGCGACTTTGGGTTTGCTAATAAATTTTTGCTTATAA 1314
                          vi? v    iivi i   i       v vi   iiv  i  ivv   i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_123933237_   1315 TATTGAAAGCA-AATCAATGAAAGAAAAATTTGGTAAGTTGGCCTTTATT 1363
                         i iii      -  v   ii         v v i   i    v   i  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_123933237_   1364 AAAACTAAATA-TTTTGTTCTACAAAAGGTTCTGTTAAGAGAATAAAAAA 1412
                             i    v -      v  v    i iiv  i i    i i i    i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_123933237_   1413 AAAACCTATACACTTGGAAAAAATATTTGCCAGTTACATACCTGATAAAG 1462
                          v    i i v v v   i           v i i i   i       i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_123933237_   1463 GATTTGTAGCTAGAAAATACAATGCATTCTTTAAATTCAACTATAAGAA- 1511
                           i     v i    v   i  v v i    vv  i    iv    i  -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_123933237_   1512 ---AATAACACAATT-AAAAATGGGCAAAAAGTCTGGGAGAACATCTCAC 1557
                         ---      v     -             iii i  iivii    i  v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_123933237_   1558 ACAAAAAAAATA--CAGATGGCAAGTAAGCATATAAAAAAGATGCTCAA- 1604
                         -    i  i   --  i     v i      i  i    -         -
  L1M4_orf2#LINE/    849 -CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAAC 896

  chr2_123933237_   1605 ATCATATTTCAT 1616
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (152 / 100)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.29 (39 / 17)  


1256 29.77 7.73 5.23  chr2_123983087_123985056      599  1478 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_123983087_    599 GAAATCCATTATGTTCAGGGATTGTAAGACCCAAAGTTGTTCAT-TGCCC 647
                           v    --i       v      v     ii  vi     v v-  v v
  L1M4_orf2#LINE/      7 GATATCC--CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_123983087_    648 AT--TCTCTACATTTATTTAAAGGTTTAATGGAATTTCTACCAAATTTCC 695
                           --  i i v   v  i  v  i  i  i v   ii   i    v i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_123983087_    696 AACAGGCTTTTC-------ATTTA-AAATAAATTCTAAAATTTATTTGGA 737
                          i v v     i-------   v -  iivi  i        i  v    
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_123983087_    738 AAGGTTAAGTTTGTTAATCAG--CAG--AAAAAAATCTTGAAAACAATGA 783
                           v iv i --- -- vi   --i  --    v           vi v  
  L1M4_orf2#LINE/    155 AATGCAAGG---G--ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_123983087_    784 ACTAAGTTGGAAGAC--GTATTACTTGATTTTAAGATTTACTCGAAAGCT 831
                           v        i   --ii i v iii    i  i i     vv      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_123983087_    832 ATACTAAACAATCATTGATTAAAGGCTGCATAAATATTTCTGTGTAACAA 881
                          i v   ----   --------  i v ii ii-  i v-- ii   vi 
  L1M4_orf2#LINE/    250 ACAGTAA----TCA--------AGACAGTGTGG-TACTG--GCATAAGGA 284

  chr2_123983087_    882 TAGAAAGTCATATGTGATATATATGATGTGTGTGTGTGTGTGTGTGTGTG 931
                             ----     i-   vv  ivi  i----- vi -  v v  viivi
  L1M4_orf2#LINE/    285 TAGA----CATATA-GATCAATGGAATA-----GAAT-TGAGAGTCCAGA 323

  chr2_123983087_    932 TGTGTGTCTGTGTGTGTGTGTAGGCAGTTTATTTTCAACAAATATACCA- 980
                         vi ivii ii iii v i  -- v  i  v      i    ivi i   -
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATG--GTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_123983087_    981 GAGCAATTAATGAGAAAAAAATTTACAAGTGTTTTCA-CAAAAACTGTT- 1028
                           v  v i    i i   i   -----   v      -    viv  i -
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAAT-----AGTCTTTTCAACAAATGGTGCTG 416

  chr2_123983087_   1029 ------TTGTGTTTTCATATG---AACATTGAC-----ACTTTTCCTTC- 1063
                         ------i  vi v?i  i   ---  v v   v-----  iii v i  -
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_123983087_   1064 --TCAGACACAAGGAGTATTCTGAAATGGATCATAGGCCTACACATGAAA 1111
                         --i  v i    ii v  viiii          ?  i    v ii i i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_123983087_   1112 TTCAGAATCATAAGGCTTCTAGAG---ACTGTAATAGAAAATTT--ATAA 1156
                         vii i  ii    ii  ii    i--- vii  iv? v    i --i i 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_123983087_   1157 TTTTGTGGTAAGTACAGATTTCATGGACAGGATAAAATAAGCACAAACCA 1206
                         ii   v v  i i vv i    v i  i v  i vv v        i v 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_123983087_   1207 TAAAA----AAGTCTA-AAATTGGATTTTATCAAAATTAAAAATTTT--- 1248
                         i    ----  i vv -        i  i              i   ---
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_123983087_   1249 ACTTATCAAATGACAAGATTAAGGACACAAATAGGCAAGCTACTCTCTAG 1298
                         i   --    v    vv  i   i viii  v  i   v i  vvvv i 
  L1M4_orf2#LINE/    667 GCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_123983087_   1299 GA-AAAATAGTTGCAG--CA-ATATATGAAAAAGGAACTCTACCCAGAAT 1344
                           -      v     i--  -    v   v  i   vi v  i       
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_123983087_   1345 ACATAAAGAATATTTATAAATCAATATTTAA----CAATATAAT--AATT 1388
                          i        ivi   i  v      v v  ----   -    i--    
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA-ATAACCCAATT 813

  chr2_123983087_   1389 ----ACTAGGTAACATAATTGAATAGAC---TCTTTAAAAAATGAGACAT 1431
                         ---- v i  i  viv v          ---   ii   i  ---  i  
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA---GATAT 860

  chr2_123983087_   1432 ACAAATGGTCTGTAAG-GCATGAAAAGATATTCGGCATCACTATTAGT 1478
                                 i vi    -i           ii  ii     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (158 / 101)
Gap_init rate = 0.05 (42 / 902), avg. gap size = 2.71 (114 / 42)  


3156 27.39 0.55 0.66  chr2_124009142_124011043.rev      502  1410 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124009142_    502 TGGAAGAACATTCCATGTTCATGGGTAAGAAGAATCAACATCGTGAAAAT 551
                              ii i  i            i vi     v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124009142_    552 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 601
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124009142_    602 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 649
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_124009142_    650 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCTTAAGCCAAAAG 699
                                viiv  ii  v  v v  vi    iv       i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_124009142_    700 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAAGTATACTACAAGGC 749
                                i      vv    i  v  ii i      iiv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_124009142_    750 TACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATATAGATC 799
                                 i   i    ii     i   i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_124009142_    800 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 847
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_124009142_    848 ATCTGATCTTTGACAAACCTGAGAAAAATAAGCAATGGGGAAAGGATTCC 897
                          vi    i  i     ivv  vv  i vi vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_124009142_    898 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCCTATGTAGAAAGCG 947
                           v  i  i              v      v  ?  vi   i i  iivv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_124009142_    948 GAAACTGGATCCCTTCCTTACACCTTATATACAAAAATGAATTCAAGATG 997
                            ii    i    v   i     --            v  i    i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACC--ATATACAAAAATTAACTCAAAATG 494

  chr2_124009142_    998 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 1047
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_124009142_   1048 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 1097
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_124009142_   1098 AAAACACCAAAAGCAATGGCAACAAA-GCCAAAGTTAACAAATGGGATCT 1146
                          vi            vvi        - vv   i vi i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_124009142_   1147 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTGA 1196
                         v  i   v v  i i   i  ii vv    i  v    ii vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_124009142_   1197 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 1246
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_124009142_   1247 AAAGAACTAATATCAAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1296
                           i i   vi    v     v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_124009142_   1297 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 1346
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_124009142_   1347 TCTCAAAAGAAAACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 1396
                             v      i i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_124009142_   1397 TCATCACTGGCCCT 1410
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


2510 27.46 2.90 1.56  chr2_124013397_124015599.rev      816  1711 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124013397_    816 TGGAAAAA-ATTCTATGCTCATGGATTGGAAAAATCAATATAATTAATCT 864
                               i -  i i   i             i v i     vi    vv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124013397_    865 GTTAATATTACCCAAAGCAATCTAGAGATTCAGCAAAAT-----TCAAAT 909
                          vi    i v      vii     v       i iv   -----     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124013397_    910 TACCAA-TGTCATTTTT-CATGGAACTAAAAAAA-AATTCTAAAATTTAT 956
                          v   i-  i v     -  - i  i i v  iv-i  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_124013397_    957 AGAGGGCCAAA---AATGAGTCCAGA-TAGCCAAAGCA-TCCTAAGCAAA 1001
                          vi ----   ---  v iii     -        i  -  i i iv  i
  L1M4_orf2#LINE/    150 ATGG----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_124013397_   1002 AATAACAAAGTCGGAGTAATAACATTATCTGACTTCAAACTATACTATTA 1051
                           v        i    v v v   i vi ii i      viv     ---
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA--- 242

  chr2_124013397_   1052 TACCAGGCTACAGTAACCAAAACAGCCTGGTACTGGCACAAAAATTAGA- 1100
                         -- v i          i   i    iv           i  ii  -   -
  L1M4_orf2#LINE/    243 --CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGAC 289

  chr2_124013397_   1101 -TATAAACCAATAAGACAAAATAGAGAG-CCAGAATTAAAGCTAGACACT 1148
                         -    i i    iii i i   v     -      v    v i v   i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_124013397_   1149 TATAACTAAACAATCTTCCAGAAAGTTGACAAAA--A--CAATGAGGAAA 1194
                            iiii  vii  i   v v  i v  v   i -- --     i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_124013397_   1195 AGACATGCTATTCGAAAAACGGTGCTGGAAAAACTGACTAATCATATGCA 1244
                         ii i vv  v   i v   i        i v     iv  ?i  i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_124013397_   1245 GAAGAATGAAAGTAAATCCATACCTCTCACCATATGCACAACTTAACTTA 1294
                         i         iv ii i  v      v        i  v  v      i 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_124013397_   1295 TGATGGATTAGACACTTAAATGCAAGACCTAATGTTATAAAAATTCTAGA 1344
                         vi      i ? v  i      i    v    vii       v ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_124013397_   1345 AGAAAACTTGGGAAATACTTTTCTGGACATTGGCCTAGGGAAATGATTTA 1394
                                v i  ?ivv v i   vv   v    vi    v  -  i   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTC 588

  chr2_124013397_   1395 T--GACTAAGGCCTTACAAGCAAATGAAACAAAAACAAAAATGGTCAAGC 1442
                          --  -  v i vii v     v v v       iv      i vi  ii
  L1M4_orf2#LINE/    589 TTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_124013397_   1443 GGGAGCTGATTAAACTAAAGAGCTTGGGCGCAGCAAAAGAAACTATCGGC 1492
                         v   vi v  i   v v  i i   vv i  vv    i  v      iiv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_124013397_   1493 AGAGTACACAGACAACCTATAGAATTGGAGAAAATATTTGCAAACTATGC 1542
                          i   iv v        i i     v                  ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_124013397_   1543 ATCTGACAAAAGACTAACAATCAGATTCTATAAAGAACTTGGATAAATCA 1592
                               i  ii    vii vi    v v           ivv i  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_124013397_   1593 ACAAGAAAAAAACAACT---TCATTTTAAAAACTAGGCAAAACATATGGA 1639
                          i  v     i    v ---i  v  ?     - i      iv  v  i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chr2_124013397_   1640 CAGATACTTCTCAAAAGAAGGCATACAAGCAGCTAACACAAATATGAAAA 1689
                         i   i i     v       ii      iii  i  i viv i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_124013397_   1690 AATGCTCAACATCACTAATAAT 1711
                         i             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.90 (40 / 21)  


2330 26.08 5.06 1.14  chr2_124031861_124035738.rev      808  1597 (2281)    L1M4_orf2#LINE/L1       88   908 (0)  

  chr2_124031861_    808 ATTCCCATTAAACTACCATTGAGATTTTTCACA-AAATTAGAAAAAAAAC 856
                           i  i  i   v v   vivivv     ii  -     i---- v  i 
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGC 133

  chr2_124031861_    857 T-ATTTTAAAATTCATATGTAACCAAAAAAGAGCTCATATAGCCAAAACA 905
                          -  ii             v  viiv  ii  v iviv            
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr2_124031861_    906 ATACTTAGCAAA-AAGAACAAAGATGGAGGCATCATGCTACCAGACTTCA 954
                           -   iiv   -          v      vv   ii  v  vi i    
  L1M4_orf2#LINE/    184 AT-CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_124031861_    955 AGCTATACTATAAGGCTACAATAACCAAAGCAGCATTGTACCGGTGCAAA 1004
                          iviv     i  i      i   i   ii   ii v    i  iii  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_124031861_   1005 AAGAGACACATACACCAATGGAAGAGAATAGAGAACTCAGAAACAAGACT 1054
                         i v     i   v i        v     v    iii      i  iv i
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_124031861_   1055 GCACATTGACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAAT 1104
                         ii     v iiii  vi    i  i     ivv  v   i v  vv    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_124031861_   1105 GGGGAAAGGATTCCCTGTTTCATCAA-TGGTGCTGGGAGAACAGGATATC 1153
                                 i  vvi  -     v   -           v   v     ? 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCT-TTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_124031861_   1154 AGTATGCAGAAAATTGAAACTGGAACCCTTCCTCACACCTTATGCAAAAA 1203
                         vii     i  i v    ii    v    v         v   i      
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_124031861_   1204 TTAACTCAACATAGATTAAAGATTTAAATGTAAAACCCACAACTATAAAA 1253
                                  v  i   i ?   ii         i v i v          
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_124031861_   1254 ATCCTAGAAGAAAATCTAGGC---AAT-------ACCAT---TTA--CAA 1288
                         v  i          iv    ?---   -------   v ---   --   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_124031861_   1289 ------CATAATTATAAAATCACCAAAAGAAATTGCAACAAAAGCAAAAC 1332
                         ------ v  iv   i ---         v vvv          v    v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGA---CACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_124031861_   1333 TTGACAAATGGGACTTAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAA 1382
                          v  i    v      v  i   v v  i i   i  iiivv    i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_124031861_   1383 ACTATCATCAGAGCAAACAGATAACCTACAGAGTGGGAGAAAAGTTTTGC 1432
                                vv i  ii  v   i    i     i          vv     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_124031861_   1433 AA-TC---TCTCTGACGAAGGTCTAATATCCAGAATCTACCAGGAACTCA 1478
                           -  --- v     ii i  v  vi          v  iv i      v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_124031861_   1479 AACAACTTTACAAGAAAAAAACA-----------TTAAAAATGAGCAAAG 1517
                         v      iv i  v     i   ----------- ?       i      
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_124031861_   1518 GACATGAACAGAGACTTCTCAAAAGTAGACATTCATGCAGCCAACAAACA 1567
                           iv    i   v i     v    v   i  v  viii     i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_124031861_   1568 TATGGAAAAAAGCTCAACATCACTGATCAT 1597
                         i   i   i v           ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (114 / 88)
Gap_init rate = 0.02 (16 / 821), avg. gap size = 3.06 (49 / 16)  

2238 25.06 5.70 4.14  chr2_124031861_124035738.rev     2516  3409 (469)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124031861_   2516 TAGAAA-ACATTCCATGTTCATGGAGAGGAAGAATCAGTATCATTAAAAT 2564
                          i    - i  i             vv      v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124031861_   2565 GGCCTTACTCCCCAAAGCAATGTATAGATTCAATGCTATTCCTATTAAAC 2614
                            vv           vii  v  i        i  v  i     i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr2_124031861_   2615 TATCTTTGAGA--TTCTTCACAGATCTAGAGAAAACT-ATTTTAAAATTC 2661
                         -   iiv vvi--  i  ii    vv v  v  i-  -  ii        
  L1M4_orf2#LINE/    100 -ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr2_124031861_   2662 ATACAGATCCAAAAGAAAGAGACT--GAATAGCCAAGGCAATACTAAGCA 2709
                            ii  ----  v v   i   i--          ii    vi -----
  L1M4_orf2#LINE/    148 ATATGGA----AATGCAAGGGACCCAGAATAGCCAAAACAATCTT----- 188

  chr2_124031861_   2710 GAAAACAAAACAAAACAAACAATAAAAGCTGGAGGCATCACTCTACCTGA 2759
                              - i  --i      -------- i      vv    v  v  ii 
  L1M4_orf2#LINE/    189 GAAAA-AGAA--GAACAAA--------GTTGGAGGACTCACACTTCCCAA 227

  chr2_124031861_   2760 CTTCAAACTATGCAACAGGGATACAGTAACCAAAACAGCATGGTACTGGT 2809
                         i      viv i v   ii v        i   i    ii         i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_124031861_   2810 ACAAAAACAGACACATAGACCAATGAAACAGAATAGAGAACCCAGAAATA 2859
                          i  ii i     i     i     i  i     v    ii         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_124031861_   2860 AGAC--TACATTCCTACAACTATCTACTCTTCAACAAACCTGACAAAAAA 2907
                          iv --      --  iiiii vi iv i   i    ivv  v   i vv
  L1M4_orf2#LINE/    328 AACCCATACATT--TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_124031861_   2908 AAAGCAATTAG-AAAGGATTCCCTATTCAGCAATTGTTGCTGGGATAACT 2956
                          v-v    vi -    i  vvi  v    i   v  v        i    
  L1M4_orf2#LINE/    376 AT-TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_124031861_   2957 GGCTAGCCATATGCAGAAGATTAAAACTGGACACTTTCCTTACATCAAGT 3006
                           v  ?   i     i    v i  ii     v i v   i   i  vi 
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_124031861_   3007 A-AAAAATTAACTCAAGATGGATTAAAGACTTAAATATAAAACCCAATGC 3055
                          -              i      i ?    i     i   i v i  vi 
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_124031861_   3056 TATAAAAACTCT-GGAAGGCAGCCTAGAC---AAT----GCCATTCAGGA 3097
                                -    -i    iv i v   i?---   ---- iv iiiv  i
  L1M4_orf2#LINE/    525 TATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_124031861_   3098 TACACGCA---------TAAAGATG---TCAAAAGCAATTGCAACAAAGG 3135
                          -i v   ---------  i v   ---i        vvv        i 
  L1M4_orf2#LINE/    574 T-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_124031861_   3136 CAAAAATTGACAAACAGGATCTAATTAAACTAAAGAGGTTCTGCACAGCA 3185
                         v      v  i   iv   ii v  i   v v  i iv  i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_124031861_   3186 AAAGAAACTATCAACAGAGT-AACAGACAACCTACAGAATGGGAGACAAA 3234
                           i  v        v i   -  v        i             -   
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA-AAA 721

  chr2_124031861_   3235 TTTTTGCACACTATGCGTCTGACAAAGGGCTGCTAATATCCAGCATCTAT 3284
                          v      v ii  iii     i  i  i  -- i-       v  v   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACT--TG-TATCCAGAATATAT 768

  chr2_124031861_   3285 ---------TTACAA---------GAAAAAACTAAACAACCCCATAAAAC 3316
                         ---------      ---------i    i  -   i     v  v?  v
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAA 817

  chr2_124031861_   3317 AGTGGGCAAAGGACATGAACAGACACTTTTCGAAAGAAGACATACATGCG 3366
                          i           iv    i     i  i  v        i     vii 
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_124031861_   3367 GCCAACAATCACGATCACAATGAGATAC-CATC-TCACATAGAAT 3409
                              i  v   -  v -  --    i -  v -   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCAC-ATGA-AA--AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (136 / 84)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 2.51 (88 / 35)  


2956 27.78 1.44 0.56  chr2_124091163_124096602     4050  4949 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124091163_   4050 TGAAACAATATTCCATGTTCATGGATTGAAAGAATCGGTATCATTAAAAT 4099
                           i  vi    i                i    v iii   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124091163_   4100 GTCTATACTGTCCGAAGCAATCTACACATTCAGTGAAATTGCTATCAAAA 4149
                          v v     vi  i  vii       v     ii v   iv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124091163_   4150 TACCAATGACATTCTTTAAAAAAATAGAAAAAAGC-AATCCTGAAATATA 4198
                          v   iivi v  i   iv i    v  v  --  -i     i    vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr2_124091163_   4199 TATGGAATCACAGAAGACCAAGACTA-TTAGAAGATATCCTGAAAAAAGA 4247
                                vii  iii    v   v  -ii i  v -   i       ii 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACA-ATCTTGAAAAAGAA 197

  chr2_124091163_   4248 GAACAAAACTGGCGGATCAACATTACCTGACTTCAAATAATGCTATACAG 4297
                                ii   v   iiv   i v  ii i      vvv i   i v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_124091163_   4298 ATATAGTAACCAAAACATCATGGTACTGGCAGAAAAACAGACACATTGGG 4347
                         v  i     i   i   vii           v  ii i     i  -i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT-AGA 296

  chr2_124091163_   4348 CCAATGAAATAGAATAGAAAACTCAGAAATAAATCCATACATCTAAGGTG 4397
                         i     i        v  i iii          i        i  v   v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_124091163_   4398 AACTCATTCTCAACAA-AATGCCAAGAATATGCATTGGGGAAAACACAGT 4446
                           i v   i  i    -ii        vi  v  v        iv i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_124091163_   4447 CTCTTCAATAAATGGCCCTGGGAAAACTGGATATCCATGTACAGAAGTAT 4496
                           i     i      iv      v         ?   ii i  i   v  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_124091163_   4497 GAAACTTGATCCCTATCTTGC--CTTATACAAAAATCGAATCAAAATACA 4544
                            ii v  i     i  ii -- v           ii v       iv 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_124091163_   4545 TTAAAAATTTAAATCTAGGGCCTCAAACTATGAAACTACTACAAAAAATA 4594
                          i ? i ii     v  i iv  v       i     vi  v  i   vv
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_124091163_   4595 ATTGGAGAAACTCTCCAGGACATTGGTCTGGATAAAAATTTATTGAGTAA 4644
                           v  ? v  v   i iv   v    vi i ii  vii   v  iii  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA- 595

  chr2_124091163_   4645 TGCC-CTGCAAGCACAGGCAACTAAAGCAAAA--GGACAAATAGAATCCC 4691
                           v - iiv       i     v    v    --i  i    v i iii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_124091163_   4692 ATCAACTTTAAA-GCTTCTGTACAGGAAAAGAAACAATTAACAAATTGAA 4740
                              vv     -i   i   i vvv   i  v  v  i  v   v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_124091163_   4741 GAGACAACCCATAGAATGAGAGAAATTATTTGCAAAATACCCATCTGATA 4790
                         i          i      i      v          vi ivi        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_124091163_   4791 AGGGATTAATTATCAGAATATATAAGGAGCTCAAACAACTGTGTGGGTAA 4840
                              i vi vvi            i  i   vv      vvi iivv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_124091163_   4841 AAACCTAGTAATCCTATT-AAAAATGGACAAGGGATTTGAATAGACATTC 4889
                           iv v i   i  v   -        i   i                 i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_124091163_   4890 CTCGAAAGA---CATACAAATGGAAAACAGGCATATTAAAAAGTACTCAC 4936
                            v     ---i          vv  i i   i  v    ii i    v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_124091163_   4937 TATCGTTGATCAG 4949
                         i   i????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (153 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.38 (18 / 13)  


3259 26.54 0.55 0.55  chr2_124102031_124108298     4869  5776 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124102031_   4869 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATAAATATCATGAAAAT 4918
                              ii i  i     i      i v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124102031_   4919 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCTCCATCAAGC 4968
                            v     v     iv i  i           i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124102031_   4969 TACCAA-TGCCTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5015
                          v   i-       ii -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_124102031_   5016 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5065
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_124102031_   5066 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5115
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_124102031_   5116 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5165
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_124102031_   5166 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5213
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_124102031_   5214 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGAGGAAAGGATTC 5263
                         i vi    i  i     ivv  vv  i v  vv     i      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_124102031_   5264 CCTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGC 5313
                         i  v  i  i              v  i   v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_124102031_   5314 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5363
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_124102031_   5364 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5413
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_124102031_   5414 CCTAGGCCTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5463
                          v    ?v v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_124102031_   5464 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5513
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_124102031_   5514 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5563
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_124102031_   5564 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5613
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_124102031_   5614 AAGGGCTAATATCCAGAATCTACAATGAACTCCAAAAAATTTACAAGAAA 5663
                          i  i  vi          v  i  v      iv v  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_124102031_   5664 AAAACAAAGAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5713
                           i     v     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_124102031_   5714 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5763
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_124102031_   5764 CATCACTGGCCAT 5776
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1782 28.72 7.04 2.54  chr2_124118436_124121417.rev     1252  2118 (864)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_124118436_   1252 GGAGGACATACTATGTTCATGTGTTGATAGACTCAAACTTTTAAAGCTGT 1301
                          i i  i  v i         vi   iv     i  vv  v v   v  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_124118436_   1302 CAACTTTGCCTAAATGCACCTATAGATTTAATACAACCCCTATCAGAATT 1351
                            ivi v  i    vv i   i     i  ii   i        i   i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_124118436_   1352 GTGGAAGAATTTGTTGTAAATATAGACAAGCTGTTTCTAAAATTTACATG 1401
                         vii vv vv   v   i i v  v         v i        i i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_124118436_   1402 TAAAGGTAAAGCAAATAGAATAGCTAAGACAATTTTGAAAAAGAAGTATA 1451
                         v   v i  i v vvi        i  i     i            v i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_124118436_   1452 ATGTTGGAGCAATTACAACACATAATTTTAAGGCTTACTATAGAAGTACA 1501
                          v       v v i   viv vi     i  ii       i i iv    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_124118436_   1502 GCAGTCAAAACATTACGGTATTTGCAAAAAGATAGGCATACAAATTGA-G 1550
                          i i    i   v ii    i v   v  i     i    i i  ii - 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_124118436_   1551 AAACTGAACAAAGAACTTTAGAAA-AAGTCTGTGCAAATATGGCCAATTG 1599
                         i  iv   ivi   i- ii     -  ii ii i  vv     i      
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAG-TCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_124118436_   1600 ACTTT-GACAGAGGCGCAAAAACAAGTCA--GGAGACCTATGGA--GTAT 1644
                          i   -    ii  i  v  i  v v   --  i  --- v i --  v 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA---AAGAATAGTCT 398

  chr2_124118436_   1645 TTT-AACAAATGGAGTTGTAATAATTAAACATCCATATGAAAAAATGTTA 1693
                            -         v i  vi i  i ii i ?   i   ---------i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG---------CA 439

  chr2_124118436_   1694 AAAAAAAAAAACCTGATGCAGTTGTCAAACTTCATGTAAATACTAACTCT 1743
                            i  vi  iiiv  iv vvviv   v  ivi  ii   v i      v
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_124118436_   1744 AAATTTACCACTGATATAAA-----AAGTAAAAAGCATAAAAT------- 1781
                             vv i  ?v  iv    -----i  iv    vi      i-------
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_124118436_   1782 ---AAAC-T-GGAGAAATTCTTTGAGATATGGGTTTAGGTAAAG------ 1820
                         ---    - -  ? v  v    i v  iv v  v     i  v ------
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_124118436_   1821 -AGGCATAACACCAAAG---CAAG--ACA---TACAAAATA--TAATTAG 1859
                         -  ii  i        i---    --   ---v v      --   v v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_124118436_   1860 TACTTCATTATA-TTAACATGTTTTCT-CTATAAAACACACTCTTCAGAA 1907
                         v       i v -    v vv    v -  vi   iv     v iv    
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_124118436_   1908 AAGGAAAGCATAATCTATGAACT---AAAAAAAACTTGCAATTCACACAC 1954
                          iv    iv i  i i iii v --- i    v i      v   i i i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_124118436_   1955 CTGATAAAAAACTTGTATCCATAATATATAAAGAACTCTCAAAATTCAAT 2004
                                iii           v                 i v  i     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_124118436_   2005 --TAAGAAAACAAA--ACACAACTTTAAAAAAAATGAACAAAATATTTGA 2050
                         --   i  i     --  v   i ?----       ii    iv      
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTW----AAAAATGGGCAAAGGATTTGA 835

  chr2_124118436_   2051 ATAGCAATTTCACCAAG-----TATAT---TGGTTAATTCTCACACTGCT 2092
                             vv     v    i-----    i---   ii   vvv    ---- 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA----T 881

  chr2_124118436_   2093 GTAAAGGATACT--ACCTGAGAGTGGGC 2118
                          -   i   i  --  v v ????????
  L1M4_orf2#LINE/    882 G-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 2.86 (83 / 29)  


2457 27.46 2.30 2.95  chr2_124173667_124175930      859  1772 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124173667_    859 TGAAGAAATACTTTGTTCTCATAGATGGGAAGACACAATATTGTTAAAAT 908
                           i i i   iiiii vi    i   v       vi           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124173667_    909 ATTAATTCTTCTTAACTTGATCTATAGATTCAATGCAATCTCACTCATAA 958
                         ivi   v  i ii  v        i        i      i vv   v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124173667_    959 TTGCAGCAAGGCTTTTTTTGTATG--TTAACAAACTGGATTTTATAAGTT 1006
                          iv    --v  i       i vi--  i    i   -  ii  v  v i
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTC 147

  chr2_124173667_   1007 ATATAGAAATATAAAACATCTACAATAGTCAACACAATACCAAAGGAGAA 1056
                             i     ii  iiv i i v     i   v     viii  ii    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_124173667_   1057 CAACAGCATTGGAAGAATCTCACCACCTTATTTCAAGACTTATTATAAAG 1106
                         v    ivi     i  v  v   iv  iv       i     i  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_124173667_   1107 C-ACAGTAATTCAGAAAATGTGGCATTAGTAAAATGTTAGACACATAGGT 1155
                          -        iv   v i     i i i i v  v v      i    i 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_124173667_   1156 TAATGGAAGAGAATGAAAAGCCTAGAAATTAAACTCACACAAATGTAGTG 1205
                         i       v     vi i  i i      -    i  i   vv i i  v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAAT-AAACCCATACATTTATGGTC 346

  chr2_124173667_   1206 AAATAAATTTTTACAAAG-TCACAAGACAATTGAACAGA-AAAGGTTAGA 1253
                           v i v   iv    i - vv      v   v  ii i-    iv   v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_124173667_   1254 CTTTTTAACAAATGGTTATGGAACAATTGGAAGCTTACATGCAAAAACAA 1303
                              i          vv   i    i    vi?ii          i-  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AA 445

  chr2_124173667_   1304 TGAACTCAGACCCAGAACTTATACCTGAATA---AAAAATCAACTCAAAG 1350
                             v ii     vv v  i i   ---   ---      i        -
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACC---ATATACAAAAATTAACTCAAA- 491

  chr2_124173667_   1351 ATTGATTGTGGACTTGTATGTAAAATCCAAAGCTATAAAATCTCTAGAAA 1400
                           v   ii?i   i iv      i v i   i        iiii     i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_124173667_   1401 AAAATAGAAAAG-AAATCAAAT--GTGTCCTCAGGTTTGTTGATACATTT 1447
                             i v ii? -     --- --   v   ii    v vii  ivv  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_124173667_   1448 ATAGATACAAGAACAAAAGCACAAAATCCATAAAAGAAAGAGAGAGAAAA 1497
                         v      ii v v           i-- v i        ---------  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAG--CAACAAAAGAAA---------AA 627

  chr2_124173667_   1498 AAAGACAAGTTGAAATTTATTGAAATGACAAATTTCTGTTCTGTGAAAGA 1547
                          v   i  i   i v  i  ii    v v   i  i   v  vii  i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_124173667_   1548 CGCTATTAACAGAATTAAAA--CAAAGCACAGACTGGGAGAAAATATTTG 1595
                          i    i  v i i v    --   vv      v                
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_124173667_   1596 CAGAAGACATATATGATAAATAAAACTTGTATCTAAAACATA----GAAA 1641
                           i vv i    v      i--ii         i i  i   ----   v
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAG--GGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_124173667_   1642 TCTTGGAACTCAATAATAGATATTTTAAAAAGTCACTT--AAAGTAGACA 1689
                             iv            i v vviv  v  vi  v  --   i i i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_124173667_   1690 AAATATCTGAACAAAAAGCTCACCAAAGAAGATATTTAGAT--TTAAACT 1737
                           iv  i    i i v vi  v             vi i  --ii  -- 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA--T 873

  chr2_124173667_   1738 AAGAATATGAAAATATGAACAGCATCATTTTTCAT 1772
                            v i       v   vv  i     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (153 / 95)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.18 (48 / 22)  


3262 26.25 0.56 0.56  chr2_124178441_124180331.rev      501  1399 (492)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_124178441_    501 ATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATACT 550
                           i     i      i v      v i     i  v  i     v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_124178441_    551 GCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACCAA-TG 599
                         v     iv i  i           i  v     i     iv v   i-  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_124178441_    600 CCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAAC 647
                              i  -i     -   -- v  i  - iii    i           v
  L1M4_orf2#LINE/    110 CCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_124178441_    648 CAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGC 697
                         iiv  ii  v  v v  v     iv     i i ivv i          i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_124178441_    698 TGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAA 747
                               vv       v  ii i      viv        i          
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_124178441_    748 GCAAAACAGCATGGTATTGGTACCAAAACAGAGACATAGATCGATGGAAC 797
                         v   i    ii     i   i iv ii i   v i       i      i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_124178441_    798 AGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACTATCTGATC 845
                             i--    i  --        vv   i i  i  iiiii vi    i
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_124178441_    846 TTTGACGAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAA 895
                           i   i ivv  vv  i v  vv            i  vvi  v  i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_124178441_    896 TAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCTGAAACTGG 945
                         i              v  i   v  ?   i   i i  iiv    ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_124178441_    946 ATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGAC 995
                          i    v   i     v           i  i    i      i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_124178441_    996 TTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCCT 1045
                         i    i  v   v       i      vi i           v    ?v 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_124178441_   1046 TACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAA 1095
                         v viv   iv   v v  vv i     v ii   v ivv  vi       
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_124178441_   1096 AAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTA 1145
                              vvi           v     v  i    v   ii v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_124178441_   1146 AAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACC 1195
                           i i   i  ii vv    i  v    i  vv i      v  i     
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_124178441_   1196 TACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAA 1245
                         i   i             v  i    vii ivi      i  i  i  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_124178441_   1246 TATCCAGAATCTACAATGAAATCAAACAAATTTACAAGAAAAAAACAAAC 1295
                                   v  i  v   v  vv    v iv i  v     i     i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_124178441_   1296 AACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGA 1345
                              v  i?    i     i     iv    i     i     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_124178441_   1346 AGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGG 1395
                            i  vi viii     v  i          i       v     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_124178441_   1396 CCAT 1399
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.42 (136 / 96)
Gap_init rate = 0.01 (7 / 899), avg. gap size = 1.43 (10 / 7)  


2914 24.12 3.96 1.13  chr2_124206785_124210975.rev     2820  3702 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124206785_   2820 TGGAGACAAATTTCATATTTATGGATTGGAAGACTTTATATTGATAATAT 2869
                             i v v  ii   i  i                v      v   v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124206785_   2870 AACAATATCATCCAAAGCTT--TCTACAG-TTCAATACAATCTCTATCAA 2916
                         ii     iivi     --  --       -     ii     i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_124206785_   2917 AACCACAATGGTGC---TTTAGCAGAAATAGAAAAAG-AATCCTAGAATG 2962
                           i v  -- v   ---   v        v  v  iv-i      i   v
  L1M4_orf2#LINE/     99 AATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_124206785_   2963 TATTTGGAATCTCAAGCAAACCCTTACAGAA-----AAAACAATTTTCAA 3007
                         i  v     viv    -ii    ----    -----        i  v  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAG-GGACCC----AGAATAGCCAAAACAATCTTGAA 191

  chr2_124206785_   3008 AAGGAAGGATCAAGATGGAGGACCCATGCTTCTCAACTTTAAAACCTATT 3057
                           i    i iv   v        i  ii    i   i  i     i  i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_124206785_   3058 TAAAAGCTATAGCAATCAAAACAATATGGTACTGTCATAACAGTAGACAT 3107
                         vv       i  i      i   i i        v     vii       
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_124206785_   3108 TTTGGCCAATTAAATAGAAAAGAAAA-CCACAAAATAAACGTTTGTGTAA 3156
                         v v ii    vi       vv  i i-   -i        viv iii vv
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTT 340

  chr2_124206785_   3157 ATGGTCAAAAGATTTTGAACAATGGTTCGAAGACTATTGAATGAAGAAAG 3206
                                 vv      vi    v   v v     i   v    ii     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_124206785_   3207 GATAGTCATTCTAAGAGATAGAGCTAGGAAAACTAGATATCCGTATAAAA 3256
                         i      v  ii  v i  i v   i   v    i    ?  ii  iv  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_124206785_   3257 AAGAATGAAGGTTAACTC--ATTTTATACCATATA-AAAAATTAACACAT 3303
                                   v vi  i -- ii i i        -          v  v
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_124206785_   3304 AA--AATCAAAGACATGAAAGTAACAACTAAAATGACAAAATTCTTAGAA 3351
                           --i    ?    v i  v    v i      iv i    i        
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_124206785_   3352 GAAAACTT-GGTA-AAAGCTAGATGTCATTGGAATAACTGATGATTTCTT 3399
                               v -  ?i-   v  vvi  v v    iv  ivii   i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_124206785_   3400 GGGTA-AACACCAAACTCACAGGCAACAAAAAGAAAAGTAGATAAACTAG 3448
                         i i  -i        vv    i         ii    i        i i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_124206785_   3449 ACTTCATTAAAATTATTA-TTTTTTTGC--CAAAAGACACTATCAGAAGA 3495
                                i       vv -i    v   --    i          ii i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_124206785_   3496 GTTAAAAAA--ATTCACAAAATG--AGAAAATATTTTCACATTATAGATT 3541
                           v    i -- ii    i    --           v  v  i   v  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_124206785_   3542 TAGTAAGGGA-TAATATACAAAATATATAAAGGGTCTCTACAACACAACA 3590
                          ii       - vi   v  i           iiiiii      v   i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_124206785_   3591 ACAAACAGA---ACAAGCAAATC-AAAAATGAGCAATGGGCTTGAATAGA 3636
                          i   v   --- i  v v   i-       i    v  ii         
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_124206785_   3637 TATTTCTCCAAGTAAAACATATA--TGGCTAATAAGCACATGAAAAGATG 3684
                         i          iv  i i   i --    i                    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_124206785_   3685 TCCGATAACTTGAATCAT 3702
                         ii i i v v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (131 / 79)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 1.80 (45 / 25)  


2223 27.71 1.49 5.10  chr2_124258268_124261697.rev     1997  2938 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124258268_   1997 TAGAAAGACATCCTGTGATCACGGATTAGAGGAATTAATGTTGTTGAAAT 2046
                          i      i    ii  v   i     i  i  v     i     i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124258268_   2047 AACCATACTGCCCAAGC-AATCTGCCGATTCATTGCAATTCCTTTCAAAC 2095
                         ii v     v     ii-i    i v      vi     i   v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124258268_   2096 TACAAACATCATTCTTCATAGAAGTAGAAAAAACAATTCTAAAATTCATA 2145
                          v v i vv v  i  iii    i v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_124258268_   2146 AAACAA-ACAAAGAGCCCA-AATAGGCCAAAGTGATACTAAGCAA-AAGA 2192
                         viiv  -i   i ii    -     -     iii  vi i iv  -    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAG-CCAAAACAATCTTGAAAAAGAAGA 199

  chr2_124258268_   2193 ACAAAGCTAGAGGCATCGCATTACCTGAGTTCAAAATAGATTACAAGCCA 2242
                               i i    vv  i  i v  ii v       ivv i     iv v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_124258268_   2243 ATAGTAGCCAAAATAGCAAGACACTGGTAGAAAAATAGATACACAGACCA 2292
                          i    ii   i i  iiv ii     i v  ii     i i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_124258268_   2293 ATGAAACAGAATAAAGAACCCAGAAGTAATGCCACATACCTACAACCAAC 2342
                            i  i     vi   ii      i   vv   i i ii  iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_124258268_   2343 TGATGTTTGACAAAGTCAGCAAAAATATACACTGGGAAAAGAACACCCTA 2392
                             v  i     i viiv   i vi  v  v    i      i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_124258268_   2393 TTGAATAAATGATGCTGGGATAATTGGAGAGCCATATGCAAAAGAATGCA 2442
                           v  i     i        i  i    v ?   i             v 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_124258268_   2443 AATGGAGCCATATGTCTCACCATATATAAAAATTAA-----GGTAAATTA 2487
                         iv    v  v  iv  v         i         -----ii ii  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_124258268_   2488 AAGACTTAAATGCAAGACCTGAAAGGTCTTCTATAGGTCTACAAAAATCC 2537
                         ?    i      i    v  i   --------------   i    v  i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAA--------------CTATAAAACTCT 535

  chr2_124258268_   2538 TAGAGGAAATCCTAGGAA-AATTCTTCTGGACATTGTTCTAGGCAAATAA 2586
                             i    v v    ?i-  v     vv   v   vvi       - ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGG 584

  chr2_124258268_   2587 TTTATAACTAAGTCCACAAAAAGAAACGCAAAAAAAAAAAAAAAAAAAAA 2636
                            ----  v  ------ v v  v  -     iv v  iv  v    i 
  L1M4_orf2#LINE/    585 TTT----CTTAG------ATATGACAC-CAAAAGCACAAGCAACAAAAGA 623

  chr2_124258268_   2637 AAAAAAAAAAAAAAAAACCCAGAAAGAGGCAAATGGGACTTAGGTAAACT 2686
                              --------------i   ------i    v      vivi   v 
  L1M4_orf2#LINE/    624 AAAAA--------------TAGA------TAAATTGGACTTCATCAAAAT 653

  chr2_124258268_   2687 AATAGATGCCTGAACTGCAAAGGGAATAATGAACAGAGTAAACAGACAAC 2736
                         v v i ivii  vi  v      iv iv  v  v i   i  v       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_124258268_   2737 CAACAGAATGAAAGAAAATTTTTGAAAACAATTCATCTGAAAAAG---TT 2783
                          v        ii       v    v   iv  vi      v  i ---  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_124258268_   2784 ATGATTCAAAATCTA-AAGGAACTTAAACAACTCAACAGAAGAAAAGCAA 2832
                         i -  i  i   v  -  i     ivv         i iv i   ii   
  L1M4_orf2#LINE/    754 GT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_124258268_   2833 ATAACTCTATTGAAAAGTGAGCAAAGAATATAAAGAAACATTTTTCAAAA 2882
                              i v   ?    i  i      i  v i  v i      i  v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_124258268_   2883 GAAGACATACAAGAAGACAGCAAAGATATGAAAAAATGCTAAACATCACC 2932
                              i      ivi v  ii  iv i       i     v       ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_124258268_   2933 AATCAT 2938
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.60 (158 / 99)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.65 (62 / 17)  


3188 27.56 0.44 0.33  chr2_124272644_124279010.rev     4969  5875 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124272644_   4969 TGCAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5018
                           v  ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124272644_   5019 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5068
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124272644_   5069 TACCAATGACTTTCTTCACAGAA-TCGGAAAAAACT-ACTTTAAAGTTCA 5116
                          v   iivi i  i  ii     - i -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_124272644_   5117 TCTGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCC-AAGCCAAAAG 5165
                          v     viiv  ii  v  v v  v     i      i-i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_124272644_   5166 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATGCTACAAGCC 5215
                                i      vv    i  v  ii i      viv i      iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_124272644_   5216 CACAGTAACCAAAACAGCATGGTGCTGGTATCAAAACAGAGATATAGGCC 5265
                         i       i   i    ii    i    i  v ii i   v      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_124272644_   5266 AATGGAACAGAGCAGAGGCCTCAGAAATAACACCACACATCTACAACTAT 5315
                                i   iiv   ivii         vv   i    i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_124272644_   5316 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5365
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_124272644_   5366 ATTCAATAAATGGTGCTGGAAAAACTGGCTAGCCATATGTAGAAAGCTGA 5415
                         v     i            i v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_124272644_   5416 AATTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 5465
                          i     i    v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_124272644_   5466 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5515
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_124272644_   5516 AGGCA-ATACCATTCAGGACACAGGCATTGGCAAGGACTTCGTGACTAAA 5564
                            ?i- v i -   iv   viv  vv v     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_124272644_   5565 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5614
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_124272644_   5615 TAAACTAAAGAACTTCTGCACAGCAAAAGAAACTGCCATCCGAGTGAACA 5664
                         i   v v  i     i  ii vv    i  v   ii  vvvi      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_124272644_   5665 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5714
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_124272644_   5715 GGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAGAAAAA 5764
                           i  vi          v  i   v    ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_124272644_   5765 ATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAGTTTT 5814
                         iv    i     v  i?    i            v    i     v  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_124272644_   5815 TAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATTCTCATCA 5864
                         iv        i  vi viii     i ii          i  v    v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_124272644_   5865 TCACTGGTCCT 5875
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


2709 23.81 6.16 1.97  chr2_124282113_124287497     4040  4900 (485)    L1M4_orf2#LINE/L1       12   908 (0)  

  chr2_124282113_   4040 CTCATGGATTTCATGATCATTGGAAGAATCAATATTGTTAAAATGGGCAT 4089
                          i    ---      i--         v i           i    vv  
  L1M4_orf2#LINE/     12 CCCATG---TTCATGG--ATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_124282113_   4090 ATTGCCCAAAGCAATTTACAGATTCAATGCTATTTCTATTAAA---CCA- 4135
                          i v      vii  i           i  v  ii    i   ---   -
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_124282113_   4136 ---CC------------ATTGAGA--TTCATTTTAAAATCCATATGGA-- 4166
                         ---  ------------     v --i v  ii      i        --
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_124282113_   4167 TCCAAAAAAGAGCCCAGA-TAGCAAAGGCAATCCTAAGCAGAAAGAACAA 4215
                          v   iii ---      -    v  ii     i i iv ii        
  L1M4_orf2#LINE/    157 TGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_124282113_   4216 AGCTGGAGGTATCATGATACCCAACTT-GAAACTATATTACAAGTCTACA 4264
                           i      vv   iiv v     i  -i     -  i     iv     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACA 252

  chr2_124282113_   4265 GTAACCAAAACACCATGGTTACTGGTACAGAACCAGACACATAGACCAAT 4314
                             i   i   vii    -     i i iiivi     i     i    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGT-ACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_124282113_   4315 GTAACAAAAT----AGCCCAGAAATAAGACTGCACATCTACATGATC--- 4357
                          v  i i   ----  i          iv iii    i  --  i  ---
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA--TGGTCAAT 349

  chr2_124282113_   4358 TGATCTTCAACAAATCTGACAAAAGCAAGCAATCAGGAAAGGATTTTCTA 4407
                             i   i    ivv  v   i v  vv    vi      i  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_124282113_   4408 TTCAATAAATGGTGCTGGGATAACTGGATAGCCATGTGCAGAAGATTAAA 4457
                              i              i         ?   ii    i    v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_124282113_   4458 ACTGGATCCCTTCCTTAGATCATATATAAAAATTAACTCAAGATGGATTA 4507
                         ii    i    v   i v i      i              i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_124282113_   4508 AAGACTTAAATGTAA-ACCCAGTGCTATAAAAACTCT-GGACGATAACCT 4555
                         ?    i         - v i ivi        -    -i  v  v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr2_124282113_   4556 AGGCA-ATACCATTCAGGACATAGGCATGAGCAAAGATTTCATGACAAAG 4604
                            ?i- v i -   iv   v v  vv ii    v i    v iivv v 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_124282113_   4605 ATACCAAAAGCAATTAA--AACAAAAGCAAAAATTGACAAATGGGATCTA 4652
                          i          --i  --        v      v  i    v   ii v
  L1M4_orf2#LINE/    598 ACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_124282113_   4653 ATTAAA-CTAAAGA-------GC---AAAAGAAGTTATCAACAAGAGTAA 4691
                           i   -i    i -------  ---   i  vii      v  -   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA-AGTGA 694

  chr2_124282113_   4692 ACAAACAACCTACAGAATGGGAGAAAGTTTTTGCAAAATATGCATCTGAC 4741
                          v i      i               i v        vi  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_124282113_   4742 AAAGGTCTAATATCCAGCATCTATAGGGAACT--TA-AATTTACAAGAAA 4788
                           i  v  vi       v  v    ii     --  -  i i vv iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_124282113_   4789 AAAAACAAACAACTTTATTACAAAGTGGGCAAATGAAATGAACAAACACT 4838
                            i     i   iiv   ?v   i        v  vv    i i   i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_124282113_   4839 TC--AAAAGAAGACATACATGTGGCCAACAATCACATGAAAAAAGGCTCT 4886
                           --v        i     vi       i  v          i v    v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_124282113_   4887 ACGTCACTAATCAT 4900
                           i   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (126 / 75)
Gap_init rate = 0.03 (29 / 897), avg. gap size = 2.41 (70 / 29)  


2449 29.84 2.45 1.34  chr2_124296666_124299881     1827  2724 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124296666_   1827 TGGAAAAGCATCTGATGCTCAAGGATAGAAAGAATCAATATCACTGTAAT 1876
                               iii   iv   i   v    v i    v i     iii ivi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124296666_   1877 GGCTATACTGCCCAAAGCAATTTACAGATCCAATGCTCCTCCTCTCAAAC 1926
                            v     v      vii  i       i   i  vvii   v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124296666_   1927 TGCCTATCATTGAAATTATTCATAGAACTAGAAAAAAAACT-ATCTTAAA 1975
                          v  viiiiii----  v  iii    v v  v  i---  -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC----TTTTTTGCAGAAATTGACAAG---CTGATCCTAAA 143

  chr2_124296666_   1976 ATTCACATGGAACCAAAAAAGAACCCAAATAGCTAAGGCAATTCT--AAG 2023
                              i      viiv  ii  v  vi      i  ii    ii --  i
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_124296666_   2024 CGAACAAACAAAGCTGGATGCATCATGCTACCTGACTTCAAACTATAGCA 2073
                         v   -i       i    v vv   ii  v  ii i      viv  vi 
  L1M4_orf2#LINE/    194 AGAA-GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_124296666_   2074 CAAGGCCACAGTAACCAAATCAGAATGGTACTGGTACAAAAATAGGCACA 2123
                            i  i       i   iv   vi         i i  ii    i  i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_124296666_   2124 TAGACCAACAAAACAGAATAGAGAGCCCAGAAATAAGGCTGCACACCTAC 2173
                             i   iii  i     v     i          iv iii   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_124296666_   2174 AACCATCTGATCTTCAACAAAGCTGAGAAGAG---TCAATGGGAAAAAGA 2220
                         iii  vi    i   i    i v  vv    v---        i   ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_124296666_   2221 CTCCCTATTCAATAAACGGTGCTGGGATAACTGGCTAGACATGGGCAGAA 2270
                         ivvi  v     i   i          i      v  ?v  iiv   i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_124296666_   2271 GATTGAAGCTGAACCCCTTTCTTACACCGTATACAAAAATCAACACAAGA 2320
                           v     i  i      vi  i     i           i   v   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_124296666_   2321 C---TTAAAGACTTAAAGGTAAAACCCAAA-CTATAAACAATCT-GGAAG 2365
                         i--- i ?    i    v    i v i   -       - v   -i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAG 541

  chr2_124296666_   2366 ACAATCTAGGC---AATCCATCATGGACACAGGCACAGGCAAATATTTCA 2412
                          v  iv    ?---    i-  i  iv vii  i-i      vvi    v
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCT-TCGTGACCTTGGGT-TAGGCAATGGTTTCT 589

  chr2_124296666_   2413 T-GCTGAAGATGCTGGAAGCAATTGAAACAAAAGCAAAAATTGACAAATG 2461
                          - v - v  ii iii     vvv v        v      v  i    v
  L1M4_orf2#LINE/    590 TAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_124296666_   2462 AGATCT------AATTAAGAGCTTCTGCACAGCAAAATAAACTATTAACG 2505
                         i  ii ------      i i   i  ii vv    iv v     i  vi
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_124296666_   2506 GAGTAAATAGACAACCTACAAAATAGGAGAAAACATTTGCAAACTATGCA 2555
                         i   i  v        i   i   i        i         ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_124296666_   2556 TCTGACAAAGGTCTAATATCCAGCATCTATAAGTAACTTATACAAATTTA 2605
                              i  i  v  vi       v  v     iv    iv     v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_124296666_   2606 CAAGAAAAAACCAAACAATACCATTAAAAAGTGT-CAGATGATATGAACA 2654
                         i  v     iv    i  iv v   ?    i  v-  i v   v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_124296666_   2655 CACACTTTTTAAAAGAAAACATATATGAGGCCAACGAGCATATAGAAAAA 2704
                         v   i  i iv      i i   i viv      ii    i  ii   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_124296666_   2705 AACTCACTATCACTGAGTAT 2724
                         vi    vi    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (170 / 94)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


2676 27.54 1.99 1.55  chr2_124315385_124322126     3353  4256 (2486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124315385_   3353 TGGAAACATATACCATGCTCATGGGTTGAAAGAATCAGTATCATTAAAAT 3402
                               v    v     i      i   i    v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124315385_   3403 GGCCATACTTCCCAGAGCAATCTACAGATTCAATGCTATTTATGTCCAAC 3452
                            v     i    i vii              i  v  iiv i  v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124315385_   3453 TGCCAACATCATTTTTCACAGAA-TTGAAAAAAAACTTAGT-TAAAATTC 3500
                          v   i vv v     ii     -    v  i---  v vi-        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_124315385_   3501 ATGTGACACCAAT--AAAGAGCCCAGA-TAGCCAAAGTAAT-TTGAAGTA 3546
                           i  i- --   --  i ii      -        ii   -     i- 
  L1M4_orf2#LINE/    148 ATATGG-A--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-A 193

  chr2_124315385_   3547 AAAAGAACAAAGCTGGAGGCATCACACTACTTAACTTCAAATGATACTAT 3596
                          i          i      vv       v ii  i      vvv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_124315385_   3597 AAGGCTATAGTAACCAAAACAGCACAGTACTGGTACAAAAGCAGACACAT 3646
                           i    i     i   i    iiii       i i  iiii     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_124315385_   3647 AGACCAACGGTACAGAATAGAGAGCCCAGAAATAAAGTCACAGGCCTACA 3696
                            i   i  v i     v     i           vi  i viii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_124315385_   3697 GCCATTTGATCTTTGAAAAAGTTGACAAATATAAGCGAAGGGGAAATAAC 3746
                          i  v     i  i  v  i v  v   ivvi vv i v       v  i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_124315385_   3747 --TCTATTCAATAAATGGTGCTGGGATAGCTGGCAAGCCATGTGCAGAAC 3794
                         --   v     i              i i    vv ?   ii    i  v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_124315385_   3795 TATGACACTGAATGCTTACCTTTCACAATGTACAAAAATTAACTCAAGGT 3844
                         v    vii  i iv i     iv   v  i                 ii 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_124315385_   3845 GAATTAAAAATTTAAACATAAAATCTCAATATATAAGAATCCTAGAAGGA 3894
                          i  i ? i ii    ii   i v  v  vv     i v  i      i 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_124315385_   3895 AACCTAGAAA-ACACCATTTCTAGACATTGG-TCATGGCAAAGAATTTAT 3942
                            v   i?i- v i --   vv   v    - i -     v iv  iv 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC--TTCGTGACCTTGGGTTA-GGCAATGGTTTCTT 590

  chr2_124315385_   3943 GACTAAGTTCTCAACAGCAATTGGAACAAAACCAAAAATTGACAAGTGGG 3992
                         iiv  v vivi   v    vvv v       vv      v  i  i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_124315385_   3993 ACCTAATTAAACTAAAGAGCCTCTGCACAGCAAAAGAAACTATCAACAGA 4042
                           i v  i   v v  i i i i  ii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_124315385_   4043 GTAAACAGAAAACCCACAGAATGGGAGAAAATATTCGCAAACTACGCATC 4092
                           i  v   v                         i     ii iii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_124315385_   4093 TGACAAAGGTCTAATATCTAGCATCCATAAGAAACT--TA-AAC--AATT 4137
                            i  i  v  vi    i  v  vi    ii    --  -   --   v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_124315385_   4138 ATACAAATAATATTGAACAACCCCATT-AAAAATAGACAAATGGCATGAA 4186
                            v   -i i ---  i     v   -      i i    v iiv    
  L1M4_orf2#LINE/    791 ATAAAAA-GACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_124315385_   4187 CAGATGCCTGTCAAAAGAAGATATGCTAGCAGTCAACAA--ACATAAAAC 4234
                         i   iiii v  v           i v iii i   i  --    i   v
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_124315385_   4235 AATGTTCAATATCACCAGTCAT 4256
                         i   i    i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (153 / 93)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.52 (32 / 21)  

1951 28.43 4.99 1.87  chr2_124315385_124322126     5051  5852 (890)    L1M4_orf2#LINE/L1        1   827 (81)  

  chr2_124315385_   5051 TGGAAAGACATCTCATACTCATGAGTTAGAAAAATTAATGTTGTTAAAAT 5100
                                 i   i   ii     ii  i   i v     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124315385_   5101 GATTATACCACCCAAAGCAATCTACTGATTCAATGCAATCCCTATCAAAA 5150
                          iiv    iv      vii      v       i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124315385_   5151 TACCAATGAACATTTTCACA-AAATAGGGGTGA-AAGCT----CTAAAGT 5194
                          v   iiviv v    ii  -    -----   -     ----     i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-----TGACAAGCTGATCCTAAAAT 145

  chr2_124315385_   5195 TTGTATAAAACCAGAAAAGATCCCCAAAAGCCAAAATAATCTTGAGCAAA 5244
                          ii   ii  viiv  ii  i  vv  v        i        iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_124315385_   5245 ATGAAGAAAGCTCTAGCTATCAAACTACCTAATTTTAAAACATACTACAA 5294
                          v   v    i vv  vvv   v   v  i     i     v        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_124315385_   5295 GGTTATAGTAACCAAAACAATATAGTATAAGTATAAAAATAGATTCATAA 5344
                         i i  i     i   i   i i i   ivi i    ii     ivi   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_124315385_   5345 ACCAATGAAACAGAGGAAAGAA-CCAGAAAATAATCCCTCATAGTTACAG 5393
                          i     i  i   ivvi   i-       -   v   vi i v   ii 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGG 344

  chr2_124315385_   5394 CCAACTTACTTTTAACAAACACACCAAAAATGTACACTGGAGAGATGACA 5443
                         i   i v i   ii    iviii    i vii v  v   i  i vi i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_124315385_   5444 CCCTGTTCAATATATGGAGCTAGGAAAACTGTATATCTATATGCAGAAGA 5493
                         vi  v     i v    v   i   v     v   ? i i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_124315385_   5494 ATAAAACTAGAGACATATTTCTCCCTATATACAAAAATCAACTCAAAGTG 5543
                           i  ii i  vv v  ii  v v i            i        i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_124315385_   5544 GAATCA-AGAATTAAATGTAAGACCCCAAATGATAAAACTACTAAAAGGA 5592
                           -   -   vi           v iv   iv        vi  i   i 
  L1M4_orf2#LINE/    495 GA-TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_124315385_   5593 AACATTGGGG-AAATACTCTAGAACATTAGTATAGGTAAAATTTTTACGG 5641
                              v  ? -    -  iiivi  v  i vv    i  viv   ivii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_124315385_   5642 CTGAGGCCTCAAAAGCATAAGCAACATAAACAAAAATAGACAAATGCGAC 5691
                         v iv i vi        i        v  iv         i    vv   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_124315385_   5692 TAAATAAACCTTAAAAAAAATCTCTTA-GCA-AAAAGGAAAAAAAAAAAC 5739
                          vv  v  vv       ----  i  i-  v-v      v vv vv  --
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA----CTTTTGTGCTTCAAAGGACACTATCAA-- 686

  chr2_124315385_   5740 AGAAAG--AAGAGACA-CCAGCTGAATGGATGAACACATCTGCACAATAT 5786
                         -     --  i     -  vi v      iv   v i  i    v vi  
  L1M4_orf2#LINE/    687 -GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_124315385_   5787 TCATCTGACAATGGATTAATATCCA--ATA-ACAAAAAA----------- 5822
                         vi      i  v   i vi      --   - i   i  -----------
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_124315385_   5823 ---TAATAA---------TAATCTCATGAAAAAGTGGGCAAA 5852
                         ---      ---------   i iv  v?    i        
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

Transitions / transversions = 1.45 (133 / 92)
Gap_init rate = 0.02 (20 / 827), avg. gap size = 2.75 (55 / 20)  

 351 20.49 9.84 0.00  chr2_124315385_124322126     6129  6250 (492)    L1M4_orf2#LINE/L1      775   908 (0)  

  chr2_124315385_   6129 CTCTCACAA---AAAAAAAAAAAAAGAAAGAA---------AAAGCCGGC 6166
                             i    ---  v  v     i v   v  ---------   iiv   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_124315385_   6167 AAATAACATGAATAGAACTTCCTCAAAAGAAGACATACAAATGGCCAATA 6216
                            vi iv        vv  i   v        i                
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_124315385_   6217 GATGTATGAAAAAATGTTCAACATCACCAATCAT 6250
                         iiiii       i   i         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.01 (2 / 134), avg. gap size = 6.00 (12 / 2)  


2692 27.17 1.87 1.98  chr2_124329606_124336954     4132  5040 (2309)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124329606_   4132 TGGAAAAGCATTTCATCCTTGTGGATAGGAAGACTCAATATTGTGAAAAT 4181
                               iii  ii   vi ii     v        i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124329606_   4182 GGCCACACTGCCCAGCCCAAAGTAATTTATAGATTAAATGCTATTCCCAT 4231
                            v i   -   ----    v i  i  i     v  i  v  i  i  
  L1M4_orf2#LINE/     51 GGCAATACT-CCC----CAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_124329606_   4232 GAAACTACCA-CTGACATTGTTCACATAATTAGATAAATCTACTTTAAAA 4280
                         v   v v   -   v -  v  ii  v  v v  i  iiiv iii     
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_124329606_   4281 TTCATATGGAACCAAAAAAGATCCCATATAGCCAAGACAATCCAAAGCAA 4330
                                    viiv  ii  i  viv        i      ivi iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_124329606_   4331 AAAGAACAAAGTTTGAGGCATCACGTTACCTGACAT-GAAACTATACTTA 4379
                         i            v    vv    ii v  ii iv -i     -    - 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACT-A 242

  chr2_124329606_   4380 CAAGGCTGCAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGACACA 4429
                            i   i      i   i    ii       i i iv ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_124329606_   4430 TAGACCAATGGAACAGAATAGAGAGCTCAGAAAAAAGATCACACATCTAC 4479
                             i        i     v     ii      v  ivi  i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_124329606_   4480 AACCATCTGATCTTCAACAAACCTGACAAAAACAAACAATAAGGAAAGGA 4529
                         iii  vi    i   i    ivv  v   i v  vv    ii      i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_124329606_   4530 TTCTCTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAA 4579
                          vv   v  v  i              v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_124329606_   4580 AACTGAAACTGGATCCTTTCCTTACACCTTAAACAAAAGTTATCTCAAGA 4629
                         i v    ii    i  i v   i     v  v      i   v     i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_124329606_   4630 TAGATTA-AGACTCAAATGTAAAAACCCAAAACCTTAAAAACCGTGGAAG 4678
                          i   i -    ii        i i i-     iv     vi v i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAG 541

  chr2_124329606_   4679 AAAA--TCAGGGCAATACCATTCAGGATATAGGCATAGGCA--GACTTC- 4723
                             -- vi ? i  - i -   iv  iv v  vv      -- ii   -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_124329606_   4724 -----ATGACAAAAATGCCAAAAGCAATTTCAACAAAAGCCAAAACTGAC 4768
                         -----      ------         vvvv         vv    iv  i
  L1M4_orf2#LINE/    590 TAGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_124329606_   4769 AAAATGGGATCTAATTAAACCAAAGAGTTTCTGTACAGAAACAGAAACTA 4818
                            - v   ii v  i   viv  i ii  i   i vvv  vi  v    
  L1M4_orf2#LINE/    634 AAA-TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_124329606_   4819 TCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATC 4868
                            vv i      v  i     i                 v       vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_124329606_   4869 TACCCATCTGATAAAGGTCCACTATGCAGAATCTACATGAAACTTAAGCA 4918
                         i ivi         i  v ivv   v      v  i vii    ivvi  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_124329606_   4919 AATTTACAAGAAAAA---AAA-AACTCCATCAAAAAGTGGGCAAAGAACA 4964
                          v iv i  v     ---   -   i v  i?    i         i iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_124329606_   4965 TGAACAGACACTTCTTAAAAGAAGACATTTATGTGGCCAAGAATCATATG 5014
                             i     i    iv        i  vi vi       v  v  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_124329606_   5015 AAAAAAAGCTCAACATCACTGATCAA 5040
                             i v           ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.94 (35 / 18)  

3187 24.67 1.56 1.23  chr2_124329606_124336954     5962  6857 (492)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_124329606_   5962 ACCCTGTGCTTATGGACTGAAATATATAATATTGTGAAAACATCAACACT 6011
                          i  ii  i i     i  i  v iv         v  i iiv   i   
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_124329606_   6012 ACCCAAAGCGATCTACAGATTCAATGTTAAACCTATAAAAATCTCAAC-A 6060
                         v      vi               i iv vv     v      i  i -i
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_124329606_   6061 AGGTTCTTACAGAAAAAAACATATTCACTCTAAAATTAATATGAAATTTC 6110
                         vvv  i  i      vvi   vii v ii        v     i  v v 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_124329606_   6111 AAGGGATTCTGTATAGCTAAAAGAATGTTGAGTAAAAAGAAAAGAGTTGA 6160
                               ii v v     i    v   v    iv  i     v i     i
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_124329606_   6161 AGACCTCATTTCTCCTA-TTTCCAAACTTACTACAAGGCTATAGTAATCA 6209
                           iv    ivii   i -    v             i    i        
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_124329606_   6210 AAGTTGATTGGTACTAG---AAAGAGACAGATACAGATCAATGTACTAGA 6256
                          iiiv vv       i ---  i  v v v   i         v v    
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_124329606_   6257 ACAAATAATAAAAAAATAAAGATATACATATATGGACAAATGATTCTCTT 6306
                          ivi v i vv i       vvi      v     v   v     i  vv
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_124329606_   6307 CAAGAGTTCTAAGACCATTCAAGAGTGAAATGAGAATTGTTTTAATAATT 6356
                             i  v i            vi v    vi v i iv   i  i  v 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_124329606_   6357 GGTGCTGAGAAAAATCAATATGTCCATGCAGAAGA-TTAGGGTAGATCCT 6405
                                i  v  v vi   ?viv      i    - v i v i  i  i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_124329606_   6406 AATTTTTTACTTTACTTCACACAAAAAAAAATTAACTCAAGAGGGATTAA 6455
                         -------   i i  vi  i i v     --         i v    i ?
  L1M4_orf2#LINE/    460 -------TACCTCACACCATATACAAAAA--TTAACTCAAAATGGATCAW 500

  chr2_124329606_   6456 ACACCTAAATGTAAGATCTAAAACTA-AAAATTCCTTTGAA-AAACCATA 6503
                          v              v         -    i  -  v   -   v    
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTC-TTAGAAGAAAACATA 549

  chr2_124329606_   6504 GGAGAAAAGTCTCATGGCATTGGATTTGGCAGTGATTCCTTGGATCTGAC 6553
                           ? v   vii  i  i v    i  v    i  i  i   i   v    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_124329606_   6554 ACCAAAGTAACAGGCAACCAAAGTGCAAATAGAAAAATTGGACTTTATCA 6603
                               ivv   i     v    viv       v           i    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_124329606_   6604 AAAGTTAAAATGTTTGTGCTTCAAAAGGCACTACCAACAGAATAAAATGG 6653
                            v v    iv             i i     i   v i i i   v i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_124329606_   6654 CAACCAACAGAACTTGAAAAAATATTTTCTA-TCCCACATTTAATAAGAG 6702
                              v      ivv  i         v v -  vi i  i i     i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_124329606_   6703 ATTGATGTCCAGATTATGTAGAGAACTCCTAAAACTCAACAACGAAAAAC 6752
                          i vi i      v   i  i       i  v       i  i-     v
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAAAAG 798

  chr2_124329606_   6753 CCAAATAGCCCAATTCAAAAAT----AAAGAACTTGAATAGGCATTTCTC 6798
                         v      i       ?      ----    i i        i        
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_124329606_   6799 CAAAAAAG-TATTTAAATGGGCAATAAGCACATGAAAAGATGTTCAACAT 6847
                             i   -   vi      v                     i       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_124329606_   6848 CACCATTCAT 6857
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.21 (119 / 98)
Gap_init rate = 0.01 (13 / 899), avg. gap size = 1.92 (25 / 13)  


 431 28.04 0.00 0.00  chr2_124403728_124408693.rev     3406  3512 (1454)    L1M4_orf2#LINE/L1        1   107 (801)  

  chr2_124403728_   3406 TGGAAAAACTTCCCATGCTCTTGAATCAACAGAATCAATATTGTTGAAAT 3455
                               i iv       i  v  i  iiiv   v i         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124403728_   3456 TATCATATTGCCTAAAGCAACCTACAGATTCAATGCAATTCCTATCAAAA 3505
                         viiv   i v  i   vii i            i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124403728_   3506 TATCAAC 3512
                          vi  i 
  L1M4_orf2#LINE/    101 TCCCAGC 107

Transitions / transversions = 2.33 (21 / 9)
Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.00 (0 / 0)  

2439 26.06 1.70 3.27  chr2_124403728_124408693.rev     3650  4474 (492)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr2_124403728_   3650 AAAATC--AACATCATTTTTTACAGTATTAGGGAAAACAAATCTAAAATT 3697
                               -- i vv v      i   v v v iv  ivii vi        
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_124403728_   3698 CATATGGAA---CAAAAAAAACAGCCCA-AGTAGT-GAAACAATCCTAAG 3742
                                  ---   iii -----    - i   i-i        i i i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA-----CCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_124403728_   3743 CAAAATGAGCCAAACTACAGGCATCACATTACTTGACTTCAAACTATACT 3792
                         v  i v  i v  ii iv   vv     i v iii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_124403728_   3793 GCAGGGCTATAGTAACCAAAACAGCATGGTTCTTGTGTAAAAACAGACAC 3842
                         i  ii    i     i   i    ii    v  v ii   ii i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_124403728_   3843 ATAAATCAAAGAAACAGAATGGAGAACTCAGAAATAAAGCCTCATACCTA 3892
                            i     v i  i     v    iii          v  vi i ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_124403728_   3893 CAGTCAACTCATTTTTGACAAAGTTGACAAAAAATATAAAGTGGGAAAAG 3942
                         ii     i v     i     i v  v   i v-i  vv i    i    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAG 390

  chr2_124403728_   3943 GGCATCCTATTCAATAGATGGTTGC-AGGAAAATTGGATTCCTGTTATAC 3991
                         iii vi  v     i i     -  -i   v  i     v? iii-  i 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGT-GCTGGGACAACTGGATAKCCAC-ATGC 438

  chr2_124403728_   3992 AGCAGAATGAAACTGAACCACCATCTCTCACTGTATACAAATATTAACTT 4041
                          iv        ii  i   v i i   v   ii        v       i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_124403728_   4042 AAGATAGATTAAAAACTTAAATGTAAGACCTGAAATTATAAAACTACTAC 4091
                           i  i   i ? i  i           v  i   i         vi  v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_124403728_   4092 AAGAAAACCTAGG--TAAACCTCTCCTTGACATTGGCCTAGGCAAAGAGT 4139
                                 v    --    --   i v    v    vi       v iv 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_124403728_   4140 TCATGACTAAGAACTCAAAAGCAAATGCAACAAAAAACGAAAATAAACAA 4189
                           v iiv  v  vvi        v v         i -i      i i  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAA 635

  chr2_124403728_   4190 ATGGGACTTCATTAAGCTAAAAAGCTTTCATGCCACAAAAGAAATAATCA 4239
                           v         i  iv v    i    ii   iv    i  v iv    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_124403728_   4240 CCAGAGTGAACAGACACCCTGCAGAATGGAAGAAAATATTTGCAAATTAT 4289
                         vv i      v     v  ii        i                 i  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_124403728_   4290 GCATCCAACAAAAG---TATATCCAGAATCTACAAGGAATTCAAATATGT 4336
                         ii   ii i  ii --- i          v  i  i   i  --------
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC-------- 777

  chr2_124403728_   4337 GAGTAACAAGAACAACAACAACAACAACAACAAATAACCCCCTT-AAAAA 4385
                         --- v    --- v-   i  i  v  -i           vv  -     
  L1M4_orf2#LINE/    778 ---TTACAA---CT-CAATAATAAAAA-GACAAATAACCCAATTWAAAAA 819

  chr2_124403728_   4386 TGGAGAAAAGACATGAACAGACACTTTTCAAGAGAAGACATGTAAATGGC 4435
                            iv   i  iv    i     i  i  v i      i  ii       
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_124403728_   4436 CAACAATCACATGAAAAAATGTTCAACATCACTAATCAT 4474
                            i  v          i   i         ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (139 / 74)
Gap_init rate = 0.02 (18 / 812), avg. gap size = 2.28 (41 / 18)  


2590 26.94 1.07 0.67  chr2_124420266_124425147     3177  3922 (960)    L1M4_orf2#LINE/L1        1   749 (159)  

  chr2_124420266_   3177 TGTAAAAATATTCCATGTTGATGGATCAGAAGACTCAATATTATTAAAAT 3226
                           v   i    i       v      ii       i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124420266_   3227 AGCCAAACTACCCAAAGCAATCTACAACTTTAATGCAATCCCTATCAAAA 3276
                         i  v v   v      vii       iv  i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124420266_   3277 TACCAATGATATTCTTAACAGAAATAGAAAAAAAAGTATCCTAAAATTTA 3326
                          v   iiviiv  i  vi       v  v  ivvi--           i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCA 148

  chr2_124420266_   3327 TATGGAACCACAAAAGACCAAGAATAGCCAAAGCTACTTTAAGCAAAAAG 3376
                                vii   ii    v            i v ii  i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_124420266_   3377 AACAAAACTGGAGAAATCATATTACCTAATTTTAAATTGTACCACGGAGC 3426
                               ii     i v   i i v  i     i   viv   i  ii   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_124420266_   3427 TATAGCAACCACAACAGAATGGTACTGGTTTAAAAACAGACAGATAGACC 3476
                           i  i  i  vi    vi         iv   ii i     v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_124420266_   3477 AATGGAACAGATTAGAGAA-CCAGGAACAAATCCACACATCTACAGTGCA 3525
                                i   v v    i-    i  i   i   i    i  ii  vv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_124420266_   3526 CTCATGTTCTACAGAGGTTCTAAGAACATACACTGGGGAAAAGACACTCT 3575
                         i v  v   v   ii   v i    v   v  v        ii i v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_124420266_   3576 CTTCAGTAAACAATGCTGGCAAAACTGGATAATCCACATGAAGAAGAATG 3625
                         i    ii   iii      v v         -?       v i       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATA-KCCACATGCAAAAGAATG 447

  chr2_124420266_   3626 AAACTAGATGCTTATCTCTCATCATATACAAAAATAAAATAAAAATGGAT 3675
                           ii i  iv i  i   v  i             v  v v         
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_124420266_   3676 TAAAGTCTTCAATCTAAGACTTCAAACTGTGAAACTACTACAAGAAAACA 3725
                         i ?  v i v   v     vi v     i i     vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_124420266_   3726 TTGGGGAAAATCTCAAAGATATTGGTCTGGGCAAAAATTACTTGAGTAAT 3775
                          v  ? v      iviv  iv    vi i     vii  v   iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_124420266_   3776 AC-CCAACAAGCTCAGGCTACCAAAGCAAAAATGGACAAATGGGATTACA 3824
                           -    -    v  i  v  v    v      i  i    v   i v  
  L1M4_orf2#LINE/    598 ACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_124420266_   3825 TCAAG-TTAAGAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAG---- 3869
                             i-    i  -   i  ii vv       v  v     v    ----
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_124420266_   3870 -AGATAACATACAAAATAGTAGAAAATACTTGCAAGCTACCTATTTTACA 3918
                         -   i   vi   i   i v        i      iii iv   i v i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_124420266_   3919 AGGG 3922
                             
  L1M4_orf2#LINE/    746 AGGG 749

Transitions / transversions = 1.51 (119 / 79)
Gap_init rate = 0.01 (8 / 749), avg. gap size = 1.62 (13 / 8)  

 565 19.33 2.00 1.33  chr2_124420266_124425147     4241  4390 (492)    L1M4_orf2#LINE/L1      758   908 (0)  

  chr2_124420266_   4241 CTAAAATCTGTAAGGAGTTCGAACAAC--AATACATATAAAAATCTAATA 4288
                          i i   v i   i  ii  vv     --    -   v   i - v    
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAAAAGA-CAAATA 805

  chr2_124420266_   4289 GTGTGATC-AAAAATGGGCAAAATATTTGAATAGACATTTCTCAAAAGAA 4337
                         iivii  i-             iv                   v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_124420266_   4338 GACATACAAATGGCAAATAGGCATAAGAAAAGGTATTCAACATCACTGAT 4387
                           i           v    i   i v      i ii         ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_124420266_   4388 CAT 4390
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.03 (4 / 151), avg. gap size = 1.25 (5 / 4)  


 474 28.93 0.83 0.00  chr2_124435140_124438265      321   441 (2685)    L1M4_orf2#LINE/L1        1   122 (786)  

  chr2_124435140_    321 TGAAAACATATCCCATGTTTATGGGTTGGAAGAATCAGTATCATGAAAAT 370
                           i   v            i    i        v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124435140_    371 GACCATATTGCCCAAAGCAATCTGTAGATTCAATGAAATTCTTATTGAAA 420
                          i v   i v      vii    ii        i v   i i   ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124435140_    421 TATCAA-TGGCTCTACTGTAAA 441
                          vi  i-  v  i vi  i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA 122

Transitions / transversions = 2.50 (25 / 10)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 1.00 (1 / 1)  

2650 25.65 2.17 3.48  chr2_124435140_124438265      734  1653 (1473)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124435140_    734 TGAAAATATATCCCATGTTTATGGGTTGGAAGAATCGGTATCATGAAAAT 783
                           i   v            i    i        v iii   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124435140_    784 GACCATATTGCCCAAAACAATCTGTAGATTCAATGCAATTCTTATTGAAA 833
                          i v   i v      vii    ii        i     i i   ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124435140_    834 TATCAA-TGCCATTTTT-CAAAGAATTAGAAAAC-AATTCTACAATTCAT 880
                          vi  i-    v     -  i -    iiv  i -i  i   v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_124435140_    881 ATGAAAACAAAAAAGAGCCCAAATA----AAGCAACACTTAATAAA---- 922
                            i   iiv  ii  v  vi    ----  i   i-   i v   ----
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAG 198

  chr2_124435140_    923 -ACAAATCTAGAGGCATCACATTACCCAACTTCAAAGTATAATACAAGAC 971
                         -     vi i    vv     i v     i      iiv  v     ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_124435140_    972 TATTGTAACCAAAACAGCATGGTACTTGTATAAAAGTAGATACGTGGACC 1021
                           iv    i   i    ii       v i    iii    i ii i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_124435140_   1022 AATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTAAAACCAA 1071
                                i     v    ii           v   v i i   viii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_124435140_   1072 CTGATTTTTGACAAAACATACAAAAAC--TTAAATTGAGGAAAGGACA-T 1118
                         i       i     ii-i i v  i  --  v   - i      i i - 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAAT-GGGGAAAGAATAGT 396

  chr2_124435140_   1119 CATATTCAATAAATGATCCTGGGAAAACTGGATGGCCATATGTAAAAGAA 1168
                          v -     i     i v      v        i?   i   i       
  L1M4_orf2#LINE/    397 CTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_124435140_   1169 TGAAATTGGATCCCTATCTCTTCCTATAAACAAAAAAACAACTCAAGATT 1218
                             i     i     i   viv i   v       v-i       i  v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAACTCAAAATG 494

  chr2_124435140_   1219 GATCAAAGACTTAAATCTAAGA-CTGGAATCCTTAAGCATTCTGGAAGAA 1267
                              ?    i     v     -  ii  iiv v  i - ii i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAA 543

  chr2_124435140_   1268 AACTTAGAAAAAACTATCTG-GACATTGGCCTATGCAAAGAATTTATGAC 1316
                            v   i?iv  v v ii -   v    vi  v    v iv  iv iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_124435140_   1317 TAAGACCCCAAAAGCAAACGCAACCAAAACAAAAATAAATAAATGGGACA 1366
                           v   v         v v     v   iv       i      v    v
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_124435140_   1367 T-ATTTAAACTAAAAAGCTTCTGCACTGCAAAATAAATAATCATCAGAGT 1415
                          -  iv   i      -   i  ii  v    iv v iv    vv i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_124435140_   1416 AAACAGACAGCTTACAGAATGGGAAAAAAAGATGTTTGGAAACTATGTAT 1465
                         i  v     i ii           i    --- i    v   ii  i   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAA---TATTTGCAAATCATATAT 739

  chr2_124435140_   1466 CTGACAAAAGACTTATACCTGCAAGGAACTGCAAGAATCTCCAAGGATCT 1515
                             i  ii     i  i i-------------     v vi  i  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCC-------------AGAATATATAAAGAACT 776

  chr2_124435140_   1516 CAAACAAATCAGCAAAAAAATAAAAAATTAAAAAATAATCCCATTAGAAA 1565
                          vv    v   ----- v        i--- v      i  v   ?i   
  L1M4_orf2#LINE/    777 CTTACAACTCA-----ATAATAAAAAG---ACAAATAACCCAATTWAAAA 818

  chr2_124435140_   1566 CTGGACAAATTACATGACAAGAAAGCACTCCAAAGAAGATATCCAAATGG 1615
                         v   i    vv iv   vv   v viv               v       
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_124435140_   1616 CCAGCGA--ACAAGAAAAGATGTTCAACATTACTAATCAT 1653
                            iii --   v         i       i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (145 / 87)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.26 (52 / 23)  

2089 22.92 6.73 0.64  chr2_124435140_124438265     2011  2634 (492)    L1M4_orf2#LINE/L1      247   908 (0)  

  chr2_124435140_   2011 GCTATGTTAATCAAAACAGTGTGATGCTGGCAAAAACATAGACATATAGA 2060
                             iiv       i        i i      v  iv             
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_124435140_   2061 GCAATGGA-TAAAACTGAGAACCTAGAAATAAACT------TTTA----C 2099
                         v       -  i  i     ii i          i------    ---- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_124435140_   2100 AACATATTTT-GACAAAATTGCCAGGAATATTCATTGAGGAAAATAATAT 2148
                           ivv     -     iiv     i  vi     v  i     i-    v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAG 395

  chr2_124435140_   2149 TATTCTCAACAAATGGTCCTGAAACAACTGAGTAGCTACATACAAATGAG 2198
                          v  i            v   ii       ii  ? i    i    v  i
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_124435140_   2199 TGAAATTGGACTTTTACTTTACATTATATA--AAAATTAGCTCAAA-TGG 2245
                             i      iii   i i   ii     --       i      -   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_124435140_   2246 ACTAAAGAACAAAATATTAGAGCTAAAGCTATACAACTATTTGAAAAAAT 2295
                          ii ?   v v    i v         i     v    v  v   i   v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_124435140_   2296 TATGAGGGTTAATCAACATAACCTTCA-TTGGGCAATGAATCCTTAGATA 2344
                         i  ii ?  v    vv i i     vi-  i       iv i        
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_124435140_   2345 TGAATACAAAAGCAGAAGAAACAAAAAAAAA------TAAATTGAACATC 2388
                            vvv        v   v       i    ------       i  v  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_124435140_   2389 ATCAAA-TTATAAACTTT-GTGTTGTAAAGGATATTATCAAGGAAGATAA 2436
                               -   v       -   i vi      i i       i   vv  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_124435140_   2437 ATCACAAC--ACAGAATTTTTAAAAAT---TGCAAAATTACATATTTGAT 2481
                          vv     --       vvvvi     ---      - i i    i    
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGAT 744

  chr2_124435140_   2482 TTAAAA-------ATCTAGAATATGTGGAAAACTCATACAACTTGTTGAT 2524
                         --  ii-------   i       i ii i     v       iiv i  
  L1M4_orf2#LINE/    745 --AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_124435140_   2525 CAAAAGA----TAATTCAACTTAAAAACATGAAAAAGATCTAAATAAGTA 2570
                         v      ----   ii   i ?     iiv v   i   i i    iii 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_124435140_   2571 TTTCTCCCAAGAAGA-A-ACAAATGGCAGATAAATACAGGAAAATATGTT 2618
                                v       - -         vi    ii   v     v   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_124435140_   2619 TGACATTATTAGTCAT 2634
                         ii    i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (89 / 50)
Gap_init rate = 0.03 (19 / 662), avg. gap size = 2.42 (46 / 19)  


2172 28.06 3.67 2.90  chr2_124459812_124463758     2558  3455 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_124459812_   2558 AGAGTTATATTGTATTCATAGATTAGAAGAAAAAATACA--CAAGATGTC 2605
                          i  v   viii i     i    i     vvv    iv--i      v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_124459812_   2606 AATTACTTCC-AAATGGATCTGTAATTTTAGTACAAATACAATGAGGGTT 2654
                            -   i  -    v     ii iv  i iii   viv v  v iii i
  L1M4_orf2#LINE/     54 AAT-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_124459812_   2655 TCAGCAGGATGTTTTTGTAGTTACAGATGAGTTGATTATAAAATGTGTTT 2704
                         i    v vv -      i  vv iv  ii  i    iv      vii v 
  L1M4_orf2#LINE/    103 CCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_124459812_   2705 GAAAACCGAAAGGACT-AGAATAGCCAAAACAATTTTGGAAAAAATAAAT 2753
                          i   ivv  i    i-                 i   --     v  --
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG--AAAAAGAA-- 197

  chr2_124459812_   2754 GAATAAATCTTGAGGAGTTGCATTTTCTGCTTTTTAAGACTTACTATATA 2803
                            i   vi v     v ii  i  i iiv   i-  i        i v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTC-AAAACTTACTACAAA 246

  chr2_124459812_   2804 ACCAGGGTAATGCATACAGCATGGCATTGGTGTAGAGATAAGCACATATA 2853
                         i i vi     vv v    ii   i i   ii  ii    ii  i   v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_124459812_   2854 TCAATGGGAGAGAAGGGAGAAGACAGAAGTAGATCCACATGAATAAGCCT 2903
                                i v    vv    ivv     i  i i   i iivv  v vii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_124459812_   2904 AACTGATTTTTGACAAAGGTGCTAAAGAAATTAAATGCACAGAGCACAGT 2953
                           i       i     i     i  iivv   v    viv i  v i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_124459812_   2954 CTTTTCAACAAATG-TATTGAAACAATTGGATATTTGTATGCAAAAC--T 3000
                                       - ii  ii    i      ?iiii        v-- 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_124459812_   3001 GAA-CCATACCCTAAACCTATAACTTATTCAAAAAT-AATTCAA------ 3042
                            -iiiv    iv v ii i v v   v       -  i    ------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_124459812_   3043 -TAAACATCTCTATGTAAAAGGTAGAGATATACAACTTTTAGAATAAAGT 3091
                         -i ? v i  vv      i  v  i iv    v    i      v   ii
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_124459812_   3092 ATTTGAGGTAGACACAGGAAACGTCTGTGACCTTGGGT-AGGCAAATAAT 3140
                           ---   ?------- v   iv ii            -      vviv 
  L1M4_orf2#LINE/    547 AT---AGGN-------GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_124459812_   3141 TGTTAGCTATGATACCAAAAGCATAAGTAATAAAAGACAATATATGATAT 3190
                          v    v     i          i   i  i      v  v   -    v
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAA 635

  chr2_124459812_   3191 ATTGAACTTTATCAAAAATGTTTTAAAAGTGATCTGTG-----AAAGACA 3235
                             i    i       ----  v    v -- i    -----  i    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAA----TTAAAAACT--TTTGTGCTTCAAAGGACA 679

  chr2_124459812_   3236 CTATTCAGGGTATAAAAATACAAGGTACAGGTTTGAAAACATTCTTTCTA 3285
                             iv  iivi i    v    vvi    iv v i i v v v   vi 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_124459812_   3286 AATATTATATCTGAGAAAGGACTAGTATCTAGAATATATAAAAAAACTCT 3335
                            vv         v  i     v     i            i  -    
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTCT 778

  chr2_124459812_   3336 C-CATACTCAACAGTAGAAAAAGAAAAAA---AAT---AAATTGTTCAAA 3378
                         i-  -      i i  i   i v   v  ---   ---   v  vv    
  L1M4_orf2#LINE/    779 TACA-ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_124459812_   3379 AA----GATCAGACATTTTATCAAAGTATATATACTGATGGCAAATAAGC 3424
                         ii----  vi        ivi     v v      vi     v       
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_124459812_   3425 ACTTACAAAGAAATTCAACATCACCAGCCAT 3455
                           v iv     vii         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (144 / 105)
Gap_init rate = 0.03 (26 / 905), avg. gap size = 2.27 (59 / 26)  


3014 26.39 3.19 0.57  chr2_124543627_124547903     2909  3787 (490)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_124543627_   2909 GATAGTCCATATTCATGCATCAGGTGAATCAATATTATTAAAATGTCCAC 2958
                             vi    i      v  ii iv  v i      i    i   v v i
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_124543627_   2959 ATTACCCAAAACAATCTACAGATTCAATGCAATCCTTATCAAAATACCAA 3008
                          i v      vii              i       i         v   i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_124543627_   3009 TGACATCCTTCACAGAAATAGAAAAAAGAATTCTAAAACTTACATATAAT 3058
                         ivi v ii  ii       v  v  ivvi  i      i i i  iv  v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_124543627_   3059 TACAAAAGACCCAGAATAGCCAAAGCTATCTCAGCAAA-AAGAACAAAAC 3107
                          i   ii                 i v    iiiv   -         ii
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_124543627_   3108 TGGAGGAATCACATTACAGGACTTCAAATAATACTACAGAACTATAGTAA 3157
                                v     i v vvi i      vvv       i i   i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_124543627_   3158 CCAAAACCAGCATGGTACTGGAATAAAAGCAGACACATAGACCAATGGAA 3207
                         i   i  -  ii         v    iiii     i     i        
  L1M4_orf2#LINE/    257 TCAAGAC-AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_124543627_   3208 CAGAATAGAGAACCCAGAAATGAATTCATACATCTATAGTGAACTCATTT 3257
                         i     v    ii        i  ii       i   i  v  i v    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_124543627_   3258 TTTACAAAGTTGCCAAGGACATACATTGGAGAAAAGCCAGTCTCTTCAAT 3307
                          iv    i v       iv   v  v   i    iivi     i     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_124543627_   3308 AAATGGTGCTGGGAAAACTGGACATCCACATGCAGAAAAGTGAAACTAGA 3357
                                       v       i ?         i  i i    ii i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_124543627_   3358 TCTCTATCCCTCACCATACGCAAAAAATCCAATCAAAATGAATTAAAGCC 3407
                         i i   i i v       ii      - iv v        i  i ?  v 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGAC 504

  chr2_124543627_   3408 TTAACTTAAAGACCTCATACTATGAAACTCCTACAAGAAAACATTGGAGA 3457
                         i   v vv    v  v v     i      i  v          v  ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_124543627_   3458 AACTCCCCAGGATATTGGTCTGGGCAAAGATTTCTATAG---TAATACTT 3504
                           v  ii iv  iv    vi i     v i     -   --- i i  --
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT-TAGATATGACAC-- 601

  chr2_124543627_   3505 CACAAACACAGGGAACCAAAGCAAAAATGAACAAATGGTATCATATCATG 3554
                           v  i    i v   v    v      ii i    v v iivi    vi
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_124543627_   3555 TTTAAAAGCTTCTACACAGCAAATGAAACAATTAACAAAGTGAAGAGACA 3604
                         v      i   i iii vv    v  v  v  i  v        i     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_124543627_   3605 ACCCTCAAAGTGTGACAACATATTTGCAAACTACCCATCTGACAAGGGAT 3654
                             v  i i  v  v  v           ii ivi      i      i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_124543627_   3655 TAATAACCAGTACATATAAGGAGCTCAAACAATCCCATAG--GAAAGAT- 3701
                          vi  v    v i      i  i   vv    ii v   i--i     i-
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_124543627_   3702 --TGAC------------TGAG------ATCTGAATAGACTTTTCTC-AG 3730
                         -- i  ------------  i ------  i         v      - i
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_124543627_   3731 ATAAGACATAAAAATAGCAAACAGGCATATGAAAAGGTGCTCAGCATAAC 3780
                          v    i   v    i  v  i i   i        i      i   v ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_124543627_   3781 TGATCAT 3787
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.66 (143 / 86)
Gap_init rate = 0.01 (11 / 902), avg. gap size = 3.00 (33 / 11)  


 803 19.87 3.56 19.04  chr2_124556201_124558576.rev      736  1213 (1163)    L1M4_orf2#LINE/L1        1   404 (504)  

  chr2_124556201_    736 TGGACAGATACACAGTGTCCATGAATTAGAAAATTCAATATAGTACAGAT 785
                             v     iv vi   i    i   i   i i i     v  vv    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124556201_    786 GTCAGTTGTCCCCAAACCTGATTTACAGGTTTAACACAAGTCCGATCAAA 835
                          v  i vv        i-    i     i  i   i   vi  v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_124556201_    836 TTCCCAGCAAGATATTTTTGTATTCAATTATTTCACTTACAAAAACTGTA 885
                         v       ---- iii   ----------------i  i  i   i  --
  L1M4_orf2#LINE/    100 ATCCCAGC----TGCCTTT----------------TTTGCAGAAATTG-- 127

  chr2_124556201_    886 ATTAATTGTTATATTACTATTATTTTAAAATTTCTATAGAAAGGCAAAAA 935
                          iv ii  -------------  ii       iv   i    v    iii
  L1M4_orf2#LINE/    128 ACAAGCTG-------------ATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr2_124556201_    936 A---AGAATAGCTGAAACAATTTTTGAAAAAAAATGAGAAAGAAAGAAGG 982
                          ---        ii       i  -      -------------------
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTT-GAAAAA------------------- 194

  chr2_124556201_    983 AAAGCTGGAAAGAAGGAAAACAACAAAGAAGGAAGAAAAAATAAAAGGAT 1032
                         -----------    ------       vv   -------------   i
  L1M4_orf2#LINE/    195 -----------GAAG------AACAAAGTTGGA-------------GGAC 214

  chr2_124556201_   1033 AAATTAGTCTACTCAATTTTAAAACTTA-TGT----CTACAGCAATCAAG 1077
                         --- i vv  v i      i        - ii----      i       
  L1M4_orf2#LINE/    215 ---TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_124556201_   1078 AC--TGTGA-ACGTGGTAGAAAGAGGGACACATAAATCAATGAAAAAGAA 1124
                           --    i-  -   i v  i  vi    i   i       i  v    
  L1M4_orf2#LINE/    262 ACAGTGTGGTAC-TGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_124556201_   1125 A-GAGAACTTGGAAATAAACCCACAAAAATATGGACAATTGATTTTTGAC 1173
                         v-    iiiii            i v vv     v           i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_124556201_   1174 AAC----TCAAAAGCAATTCAGTAGAGAAAAGATAA-CTTTTTAA 1213
                           v----i   i v  -    i i i    ii   i-     i  
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCTTTTCAA 404

Transitions / transversions = 2.17 (65 / 30)
Gap_init rate = 0.05 (20 / 404), avg. gap size = 5.40 (108 / 20)  

 281 23.56 19.54 1.72  chr2_124556201_124558576.rev     1214  1387 (989)    L1M4_orf2#LINE/L1      522   726 (182)  

  chr2_124556201_   1214 AACTCTAAAACTTTTAGAAAAAAACA-----GTAAA-------AACT--- 1248
                             v       i      i      -----     -------i  i---
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_124556201_   1249 -ATT------TGGTATCTATAATACTAGACAAAGAGTGCATAATCCATAA 1291
                         -i  ------    v   vvi   iv v  v  i  --  i  v v i  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG--CACAAGCAACAA 619

  chr2_124556201_   1292 A----------GTCAGATTTGACTTTACCAAA-TAAAAAACTTTAATTCT 1330
                          ---------- vi i   v     i i    - v         vi v  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_124556201_   1331 ACAAAAGACCCTAAACATGGGAATGAAAA-ACAAGTTACAGAATGAGAGA 1379
                         v    i   v   v-  v ii i      -    vii        i    
  L1M4_orf2#LINE/    670 TCAAAGGACACTAT-CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_124556201_   1380 AAATATTT 1387
                                 
  L1M4_orf2#LINE/    719 AAATATTT 726

Transitions / transversions = 1.16 (22 / 19)
Gap_init rate = 0.04 (9 / 205), avg. gap size = 4.11 (37 / 9)  

 606 21.98 6.59 0.00  chr2_124556201_124558576.rev     1703  1884 (492)    L1M4_orf2#LINE/L1      715   908 (0)  

  chr2_124556201_   1703 GAGAAAGTATTTTCAAGCCACATATCTAACCAAGGGGTAGTATCCAGTAT 1752
                               i     v   ii  i      i iv i  iv v        v  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_124556201_   1753 ATATAA----CTCTTAAAAC--AACAGTAAG----TAAATGATCCAGTT- 1791
                               ----      v   --  i i   i----i    i i   i  -
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_124556201_   1792 ACAACTGGGCAAATGACATAAAGAGAAATTTCACCAAACAGGATATTCAG 1841
                          v  v        v  iv i  v   v     v     v i     v  i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_124556201_   1842 ATGGCAAATAAACACATTAAA-GATGTCCAACACCATCAGCCAG 1884
                              v     i     v   -    ii     i  ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (23 / 17)
Gap_init rate = 0.03 (5 / 194), avg. gap size = 2.40 (12 / 5)  


3198 26.84 0.66 0.77  chr2_124598899_124602630     2332  3240 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124598899_   2332 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 2381
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124598899_   2382 GGCCATACTGCCCAAGGTAATTTATAGATTTAATGCCATCCCCATCAAGC 2431
                            v     v     iv i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124598899_   2432 TACTAATGAATTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2479
                          v i iivivi  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_124598899_   2480 TATGGAACCAAAAAAGAGCCTACATTGCCAAGAAAATCCTAAGCCAAAAG 2529
                                viiv  ii  v  viv  v     i v    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_124598899_   2530 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCTATAGTACAAGGC 2579
                                i      vv    i  v  ii i     iviv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_124598899_   2580 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 2629
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_124598899_   2630 AATGGAACACAAC--AGAGCCCTCAGAAATAATACCACACACCTACAACC 2677
                                i v  i--    i  --        vv   i   ii  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_124598899_   2678 ATTTGACCTTTGACAAATCTGTCAAAACTAAGAAATGGGGAAAAGATTCC 2727
                          v    ii  i     ivv  i   i  i vvv          ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_124598899_   2728 CTATTTAATAAATGTTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2777
                           v  i  i     v        v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_124598899_   2778 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2827
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_124598899_   2828 GTAAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2877
                         vi ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_124598899_   2878 CTAGGCA-ATACCATTCAGGACATAGGCTTGGGCAA-GGTCTTCATGACT 2925
                         v    ?i- v i -   iv   v v  v  i     -   -   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGAT 594

  chr2_124598899_   2926 AAAACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCT 2975
                          vi            vvi   i      vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_124598899_   2976 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3025
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_124598899_   3026 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGAC 3075
                          v  i     i                 v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_124598899_   3076 AAAGGACTAGTATCAAGAATCTACAAAGAACTTCAACAAATTTACAAGAA 3125
                           i     v     v     v  i        iiv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_124598899_   3126 AAAAATCAAACAATCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 3175
                            i -    i  i  v  i?    i            v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_124598899_   3176 TACCCCAAAGAAGACATTTATGCAGCCAACAGACACACGAAAAAATGCTC 3225
                          v i          i  vi viii     i ii    i     i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_124598899_   3226 ATCATCACTGGCCGT 3240
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (149 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3307 26.87 0.44 0.44  chr2_124613083_124619362     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124613083_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124613083_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124613083_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_124613083_   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_124613083_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_124613083_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_124613083_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_124613083_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_124613083_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_124613083_   5327 GAAACTGGATCCCTTCCTTACACGTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i    vv           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_124613083_   5377 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_124613083_   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_124613083_   5477 AACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi   i      vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_124613083_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_124613083_   5577 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_124613083_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_124613083_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_124613083_   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5776
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_124613083_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 537 29.53 3.65 10.38  chr2_124671481_124674574.rev     1455  2138 (956)    L1M4_orf2#LINE/L1       28   665 (243)  

  chr2_124671481_   1455 GAAAGACTCAATACCATAAAGTTTGCAATTGTGATGTTCCCTAAATAGAT 1504
                          i      i    iii v   v v     ------ii    i    v   
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAAT------ACTCCCCAAATTGAT 71

  chr2_124671481_   1505 CTATGAATTCATTGAAATTCAATCCACACCCCATCTCAGAATTCCTTTTC 1554
                            iii     vi -----      ----- i   -- i   i  -----
  L1M4_orf2#LINE/     72 CTACAGATTCAACG-----CAATCC-----CTATC--AAAATCCC----- 104

  chr2_124671481_   1555 CTCTGTCCTTTCATTTTCTCCTTCCAGCTTTGCTTCCCTTTAACAAT-GA 1603
                         vv   -     -----------------     -------- iv   -  
  L1M4_orf2#LINE/    105 AGCTG-CCTTT-----------------TTTGC--------AGAAATTGA 128

  chr2_124671481_   1604 CAAGCTAATAGTAAAGTTTATTTAGAAGAGGAAAGACCCAAGAATATGCA 1653
                               i  vv    i  i  v i   iv v  i iv  v      vv  
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr2_124671481_   1654 AGATATTCCTGAAAAAGAAGAAAATAATGAGAAGAAATAC-CTTGGTACA 1702
                          i i v  i             v v i vi  i  vvi  -   vvi - 
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-A 227

  chr2_124671481_   1703 TATAAGGAATTA-TAGAAATCTGTAGTAATTG---CCGTGTGAATATTGG 1748
                          v v ii v   -  v   v  ii      ii--- v     i-  i   
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG-TACTGG 276

  chr2_124671481_   1749 CATG-GGATAGA-ATAT-TACCACTATAAAACAAAAT-AAGACTACCAGA 1794
                            i-       -    -v i  --  ii  i i   -i   v -     
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCA--ATGGAATAGAATTGAGAGT-CCAGA 323

  chr2_124671481_   1795 CACAGCCCCAGG-ATATATGG-CAATTTGGTTTATGATAGACTTGGTCCT 1842
                         v i iv    vi-  v     -     - i   vi  i ii---   v -
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATT-GATTTTCGACAAG---GGTGC- 368

  chr2_124671481_   1843 GCAAGGTTTTTTCCAGTAAGAAAGGAATAGAATTTACAGTTAATGGAAAA 1892
                         -    iiiv  --  i ii i  i      vv   v  iiv     vivv
  L1M4_orf2#LINE/    369 -CAAGACCATT--CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_124671481_   1893 AAAAAAAAAAGA-AATCATGTGGCAAGAAAT----CTGG---CATACTTC 1934
                         iii v  vvi  - ?i  ii  vv  ii   ----i   --- v   i  
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_124671481_   1935 TCATCCAGACACAAAA--TAATACATGCCAGATAGACTAAAGGTTTAATT 1982
                         v  -   v i      --   iv  ---- i  i  ii ?  iii   v 
  L1M4_orf2#LINE/    466 ACA-CCATATACAAAAATTAACTCA----AAATGGATCAWAGACCTAAAT 510

  chr2_124671481_   1983 GTAAAAGGGAAAACTGAAAAAAAAAACCTAAAA-AATATGTAAGACAATG 2031
                             i  vv      --- v    vv i  i  -  v ii  i ?vv vi
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACT---ATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_124671481_   2032 TCTTTATGACTTTAAGCTAAAAAACTATTTCTTAAGCAAAATACAGAGAA 2081
                             ii    i  ii i  iiv  ivi       iii vi i  vi i i
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_124671481_   2082 TTTAA--AATGTCAGAAAATAATGGACTAATTCCCCTATGTAAAAATTAA 2129
                         ivi  --  iivv      -   i  iv    vvv  vii v        
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_124671481_   2130 CAACTTCTG 2138
                         v     i  
  L1M4_orf2#LINE/    657 AAACTTTTG 665

Transitions / transversions = 1.49 (119 / 80)
Gap_init rate = 0.06 (36 / 638), avg. gap size = 2.67 (96 / 36)  

 395 31.00 2.50 1.00  chr2_124671481_124674574.rev     2412  2611 (483)    L1M4_orf2#LINE/L1      685   887 (21)  

  chr2_124671481_   2412 AAGGGAGTAAAAATCTAGGCCACAGATTGAAAGATAATTTTGGCAA-CCA 2460
                            ii   i    vvi iv       v  ii   v   v  v    -i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_124671481_   2461 TATAACTGACAAAATATTAGCATCTAGAATATATAAATAATTTCTACAAA 2510
                             v    i  iiv i v i   i            v  i ii     v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_124671481_   2511 TCGATTTGA-AAGAAGGCAGATGGCCCAGTAGAAAAATATTCAAAATATC 2559
                           i  --i -  i   i  i  ii    i v?      ivv    iv  i
  L1M4_orf2#LINE/    785 TCAAT--AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_124671481_   2560 TGAA--GACAAACTTAAAAAAAAGAAACTCAAATGGCTCACAATCTT-TA 2606
                             --    vvii vv   i    v iv        iv i  v vi- i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_124671481_   2607 AAAAG 2611
                              
  L1M4_orf2#LINE/    883 AAAAG 887

Transitions / transversions = 1.44 (36 / 25)
Gap_init rate = 0.02 (5 / 203), avg. gap size = 1.40 (7 / 5)  


3232 27.34 0.55 0.44  chr2_124830365_124836641.rev     4879  5785 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124830365_   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4928
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124830365_   4929 TGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                         v  v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124830365_   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_124830365_   5027 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_124830365_   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_124830365_   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_124830365_   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_124830365_   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_124830365_   5275 CTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i   i          v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_124830365_   5325 GAAACTGGATCCCTTCCGTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v  vi     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_124830365_   5375 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_124830365_   5425 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAC 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_124830365_   5475 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5524
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_124830365_   5525 TTAAAGTAAAGAGCTTCTGCACAGCAAAATAAACTACCATCAGAGTGAAC 5574
                          i   i v  i i   i  ii vv    iv v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_124830365_   5575 AGGCAACCTAAAAAGTGGGAGAAAATTTTCGTAACCTACTCGTCTGGCAA 5624
                           i     i v i i           v  i i  vii ivii    ii  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_124830365_   5625 AGGGTTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  ii vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_124830365_   5675 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_124830365_   5725 TCAAAAGAAGACATTTATGCAGCCAA-AAGCACATGAAAAAATGCTCATC 5773
                           v        i  vi viii     -             i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_124830365_   5774 ATCACTGGCCAT 5785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (150 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3209 27.53 0.44 0.44  chr2_124881178_124887449     4873  5780 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_124881178_   4873 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATGTCATGAAAAT 4922
                              ii i  i     i      i v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124881178_   4923 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 4972
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124881178_   4973 TACCTATGACTTTCTTCGCAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5020
                          v  viivi i  i  i      -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_124881178_   5021 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGGCAATCCTAAGCCAAAAG 5070
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_124881178_   5071 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5120
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_124881178_   5121 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5170
                                 i   i i  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_124881178_   5171 AATGGAACAGAGC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 5218
                                i   ii--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_124881178_   5219 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5268
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_124881178_   5269 CTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5318
                           v  i  i   i          v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_124881178_   5319 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5368
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_124881178_   5369 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5418
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_124881178_   5419 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5468
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_124881178_   5469 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5518
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_124881178_   5519 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTGAAC 5568
                          i   v v  i i   i  ii vv    i  v    ii vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_124881178_   5569 AGACAACCTAAAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5618
                                 i v i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_124881178_   5619 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 5668
                         i  i  vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_124881178_   5669 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5718
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_124881178_   5719 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5768
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_124881178_   5769 ATCACTGGCCAT 5780
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2747 25.23 5.99 2.93  chr2_124965178_124967601.rev     1071  1922 (501)    L1M4_orf2#LINE/L1        1   878 (30)  

  chr2_124965178_   1071 TGGAAAGATATCCCATGTTC--GAGTAATAAGAATAAATATTGTTACAAT 1118
                                             -- ii viv    v v          vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_124965178_   1119 GTTCATACTACCCAAAGTCATCTGTATATTTAATATAATCCCTATCAAAT 1168
                          viv     v      v v    ii v   i  iii             v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_124965178_   1169 TTCCAATGGCAGTCTTCATAGAAGTAGAATAAAAAAATCCTTACATTTGT 1218
                          i   iiv  vv i  iii    i v  -i  ivvi     v v   ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr2_124965178_   1219 ATGAAACCGAAAAAGACTTCAAATAGCCAAAGTAATCCTGAGGAAAAA-- 1266
                            i  vi v  ii   iivi          ii    i   ii  i  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_124965178_   1267 ATAAAGCTGAAAGCAC-CACATTTCCTAATTTCAAGGTATACCACAAAGC 1315
                          i    i  i i -  -    i    i        iiiv   i       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_124965178_   1316 CATAGGACTCAGAACAGTATGATGCTGGCATACAAACAGACACAGAGATC 1365
                         i i  v v   ii     i  i i        vii i     i v     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_124965178_   1366 AACAGAACAAAGAACTCAGAACTCAGAAATAAACTTAT------------ 1403
                           ii   i --   i v   iii           ii  ------------
  L1M4_orf2#LINE/    299 AATGGAATA--GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_124965178_   1404 -------------------TGC----AC-----AGTGGTGAAAGAATAGT 1425
                         -------------------   ----  ----- i   v           
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_124965178_   1426 CTCTTCAACCAGTGGTGTTGAGAAAAGTGGATATCCTCCTGCAAAAGAAT 1475
                           i      v i     i  i  v  v      ?  v v           
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_124965178_   1476 GAAATTAAGTCCTTGTCTTACAACACTCACAAAAATTAACTTGAAATGTA 1525
                            i  iiii  i ii  i   v  ivi             ii     v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_124965178_   1526 TTACAGACTTAAATATAATACCTGAAACCATAACACTCTGAGAAGAAAAT 1575
                          i ?    i     i   v v  i    i    v     v         i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_124965178_   1576 ATAGATGAATATATCCTTGACATTGGTCTAGGCAATGATTT--TGGATAT 1623
                             i? v v  v i v    v    vi         i   -- i     
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_124965178_   1624 TACACTAAAAATACAAGCAACAAAAGCAAAAATAGACATGTGGGATTACA 1673
                         v    i    ii              v         i vi v   i v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_124965178_   1674 TCAAACTAACAAATTTCTGCACAGCAAAGGA----AGCAACAGAATGAAA 1719
                              v v v   i  i  ii vv       ---- v   v i i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_124965178_   1720 AGGCAACCTACAGAATGGGAGAAAACATTTACAAGCTAGCTATCTGATAA 1769
                           i     i                i    i   iii vv          
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_124965178_   1770 GAGGGTACTATACAAAATATGCAAGAAACTCATAATATAACTCAATAGCA 1819
                          i iv vv   v  i     ii  ii     - --  i         ii 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTC-T--TACAACTCAATAATA 793

  chr2_124965178_   1820 AAAAACAAAACAAACAAACAAAAAACCCAAATAATATAATAAAAAGAGCA 1869
                             i------------     v       v ? ------    v i   
  L1M4_orf2#LINE/    794 AAAAG------------ACAAATAACCCAATTWA------AAAATGGGCA 825

  chr2_124965178_   1870 AAGACCTTCACTAGAGATTTTTCCAAAGAGGACATTGAAGTGGCCAACAG 1919
                            ivi  v v    v    i        i  i  vv  i       i i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_124965178_   1920 GTA 1922
                          i 
  L1M4_orf2#LINE/    876 GCA 878

Transitions / transversions = 1.81 (136 / 75)
Gap_init rate = 0.02 (15 / 878), avg. gap size = 5.07 (76 / 15)  


3192 26.98 0.55 0.55  chr2_125067194_125073475.rev     4883  5790 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125067194_   4883 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4932
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125067194_   4933 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATTGCCATCAAGC 4982
                            v     v     iv i  i           i  v  iv i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125067194_   4983 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5029
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_125067194_   5030 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5079
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_125067194_   5080 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5129
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_125067194_   5130 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5179
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_125067194_   5180 CAATGGAACAGAAC--AGAGTCCTCAGAAATAACACCACTTACCTACAAC 5227
                                 i    i--       --        vv   ivi ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_125067194_   5228 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5277
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_125067194_   5278 CCTATTTAATAAACGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5327
                         i  v  i  i   i i        v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_125067194_   5328 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5377
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_125067194_   5378 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5427
                           i ?   ii    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_125067194_   5428 CCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCA 5477
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_125067194_   5478 AAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTA 5527
                         vi            vvi     v    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_125067194_   5528 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5577
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_125067194_   5578 CAGGCAACCTGCAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5627
                         v  i     ii  iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_125067194_   5628 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5677
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_125067194_   5678 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGAAACTT 5727
                           i     i     v  i?    i     i     iv    i   v i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_125067194_   5728 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5777
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_125067194_   5778 CATCACTGGCCAT 5790
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2647 27.49 2.68 1.23  chr2_125100439_125106281     4457  5351 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125100439_   4457 TGGAAAAACACTACATGCTCATGGATAACAAGAATCAATATCATGAAAAT 4506
                               i i iiv    i        viv    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125100439_   4507 GGCCATACTTCCCAAAGCAATGTATAGATTCAGTGCTATTTCCATTAAAC 4556
                            v     i      vii  v  i       ii  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125100439_   4557 TACCATTGACGTTCTTCACA-AAATT-ACAAATAACT-ATTTTAAA-TTC 4602
                          v   vivi v  i  ii  -     -    i---  -  ii    -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_125100439_   4603 ATATGGAACCAAAAAAAAAGCTC-GCATAGCCAAGACAATCCTAAGCAAA 4651
                                 viiv  iii -- i - v        i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_125100439_   4652 AAGAACAAAGCTGGAGGTATCATGCTATATAACTTCAAACTATACTACAA 4701
                                   i      vv   ii  vivi  i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_125100439_   4702 GGCTGTAGTAAACAAAGCAATATGGTATTGCTACAAAAACAGGCATATAG 4751
                         i   ii     v   ii  i i     i  vi i  ii i  i       
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_125100439_   4752 ACCAATGGAACAGAATAGAGAATTCAGAAATGAAACCATACGTCTACAAC 4801
                          i        i     v    i i       i  v      i i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_125100439_   4802 CATCTCATCTTTGACAAACCTCACAAAAACAAGCAATGGGGAAAAGATTC 4851
                           vi v  i  i     ivv vv   i v  vv           ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_125100439_   4852 CCTATTTAATAA--GGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAAT 4899
                         i  v  i  i  --          v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_125100439_   4900 CGAAACTAGATCCCTTCCTTACACCTTATACAAAAATCAACTCAAGATGG 4949
                         i   ii i  i    v   i     v           i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_125100439_   4950 ATTAAAGACTTAAGGGCATAACCCAAAGCTAACAAACCCT-AGAAGAGAA 4998
                           i ?    i   iv i vi v i   i   vv    i  -      i  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_125100439_   4999 TCTAGGCA-ATACCATTCAGGACATAGGCAAGGGGAAAGACTTTATG--- 5044
                         iv    ?i- v i -   iv   v v  vvvi  v  v ii  iv i---
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_125100439_   5045 ATGAAATTGCCAAAAGCAATTACAACAAAACCAAAAATTGACAAATGGGA 5094
                             v ---         vvvi        vv      v  i    v   
  L1M4_orf2#LINE/    595 ATGACA---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_125100439_   5095 TCTAATTAAACTAAAGAGTTTCTGCACAGCAAATGAAACTATCATCAGAG 5144
                         ii v  i   v v  i ii  i  ii vv    v  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_125100439_   5145 CAAACAGACAACCTACAGAATGGGAGAACATTTCTGCAATTTATCCATC- 5193
                         ii  v        i              v  v i     v i  vi   -
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_125100439_   5194 GACAAAGGTCTAATATCCAGAATCTACAAGGAACTTAAGCAAACTCA--- 5240
                           i  i  v  vi          v  i  i     ivvi   -    ---
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATA 790

  chr2_125100439_   5241 -CAAGAAAATAAA--ACC--ATTAAAAAGTGGGCAAAGGATATTAACAGA 5285
                         -i  i  i i   --   --   ?    i            v v  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_125100439_   5286 CACTTCTC-AGAAAAGGCACACATGCGGCCAATAA--ACATGAAAATAAA 5332
                           i     - i i   ii i   vii         --         -i v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GAT 889

  chr2_125100439_   5333 GCTCAACATCACTGATCAT 5351
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (150 / 92)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.67 (35 / 21)  


2643 26.61 4.76 1.93  chr2_125199898_125202787.rev     1516  2398 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125199898_   1516 TAGAGAAATAGGCCAT-TTCATGGATTCAATGAGTTAATATTGCTAAAAT 1564
                          i  i i   vv    -          vi v  v         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125199898_   1565 GACCATACTACCCAAA-----------GTTCAATGCAATCATTATCATAA 1603
                          i v     v      -----------i     i      vi     v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125199898_   1604 TTTTAATGGTATTTTTCACACAAAAAAGGAAAAAATGATTCTACAATTTA 1653
                          iii iiv iv     ii  --i   vv  v  iv    i   v    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA--GAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_125199898_   1654 TAAGGAACCACAAAAGACCCTGAATAGTCAAATCAATCCTCAACAAGAA- 1702
                           v    vii   ii     v      i    v     i v  v     -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_125199898_   1703 --TAAAACTGGAGACATCACACTTCCTTATTTCAAA------TATAAAGC 1744
                         --i   ii     ivv          iv        ------  i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_125199898_   1745 TACAGTAGTCATAATAATATGGTACTATCATAAAAGCAGACATATAGGCC 1794
                                i   vi i i i       iv     iiii          ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_125199898_   1795 AACAGGACAGAATAAATAACCTCAAAATGAATCCAGGCACTTAGAGTCAA 1844
                           ii i i     vi v ii ivi    i  i   vi  i   vi     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_125199898_   1845 CT-ACCTTTGGCAAGAGTACAAAGGACAAAACA-TGGTGAAAGGTCAGTC 1892
                         i - ii  i i    i  i v   -  v vv  -   v     ivi    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAGTC 397

  chr2_125199898_   1893 TTTTCAATAAA-GATGTTTGAGAAAACTGTGTATCCACATGCAGAAAAAT 1941
                                i   - i  i - i  v     vi  ?         i  i   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_125199898_   1942 AAAACTGGACCCTTATCTCATGCAATATGTAAAAATCAACTAAAAATTGA 1991
                         i  ii       i  i    ii v    ii      i    v     v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_125199898_   1992 TTAAAAATTTAAACAAAAGACCTGTACCTGTAAAAATAACAGAAGAAAAC 2041
                          i ? i ii    iiv    v  iv v  i     v vvi          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_125199898_   2042 ACTGGATAAAATCTTCATGATGTTAGTCTGAACAACATTTTTTTAG-CAT 2090
                          iv  ?vv        i   iv  i vi iii   iiv   i    -i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_125199898_   2091 GACCCCAAAAGCACAGACAACAAAAGTAAAAATAAACCAGAGGGACTGTA 2140
                            v           ii         v       i iv ivv     vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_125199898_   2141 TCAAAAT-AAAAA----TATGCTTAAATTAAAAAAAATCAACAATCGAGA 2185
                                -     ---- i     ----i   ii v ii v   --  i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTT----CAAAGGACACTATCAA--GAAA 690

  chr2_125199898_   2186 GTGAAAAAATATCCTATGGAATACAGGGGAGGAAATGTTTGCAAACTATA 2235
                                i i v  i ii    ----     i    i        ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAAT----GGGAGAAAATATTTGCAAATCATA 736

  chr2_125199898_   2236 CATCTGATAAGGGGTTAATCATCAAAATCCATAAGAAACTGAAACAACTC 2285
                         i            ii vi vvi  i   vi    ii    vvv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_125199898_   2286 AATAGCAATAAATAAATAAATAAT--ATTTTAAAAG-----AAA-----T 2323
                             ---     v i i      i-- v  ?    i-----   ----- 
  L1M4_orf2#LINE/    787 AATA---ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_125199898_   2324 GAATAGACTTTTTTTTGAAGAAGACGTACAAATGGCTAACAAGTATATGA 2373
                                 v   i iii       ii          i  i   i i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_125199898_   2374 AAAGCTATTCAAAATCACTAATTGT 2398
                             v ii    v    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (154 / 77)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.95 (59 / 20)  


2791 27.22 1.67 0.78  chr2_125317067_125320562.rev     2107  3006 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125317067_   2107 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2156
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125317067_   2157 GACCATAGTGCCAAAAACAATGTACAAATTCAATACAATTCCCATCAAAA 2206
                          i v   v v  v   vii  v    i      ii    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125317067_   2207 CACCA----CCATCATTATAAAAA---ACAA-----TCCTAAAATTCAGA 2244
                         iv   ----  v iv  ii i   ---    -----            v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_125317067_   2245 TGGAACCAAAAAATAGCCCACATAGGCAAAGCAAGACTAAGCAAAAAGAA 2294
                              viiv  iiv v  viv    v    i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_125317067_   2295 CAAATATGGAGGCATCGCATTACCTGACTT-AAAATTATACTATTAGGCC 2343
                             vv      vv  i  i v  ii i  -    i -     iv i  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr2_125317067_   2344 ATAGTCACCAAAACAGCTTTGTACTAGTACAGAAATAGGCACATAGACTA 2393
                          i   v i   i    iv v     i i i iii    i  i     ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_125317067_   2394 ATGGAACAGAATAGAGAACCTGGAAATAAAGCCAAATATTTACGGCCAAC 2443
                               i     v    ii ii        v   v i     i  i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_125317067_   2444 TGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTA 2493
                             i   i    i vviv   i v   vv i         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_125317067_   2494 TTCAACAAATTGTATTGGGATAATTGTCAAGCCCCATGTAAAAGAATGAA 2543
                                   v  ii     i  i  vvv ?  v    i           
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_125317067_   2544 ACTGGATCCTCCATCTCTCATCTTATACAAAAATTAACTCAAGATGGATC 2593
                         ii    i  - i i   v  i v                   i       
  L1M4_orf2#LINE/    450 GTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_125317067_   2594 AAAGACTTAAATCTAAGACCTAAAGCCATAAAGATTCTAGAAGATAACAT 2643
                          ?    i     v     v     i i     iv ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_125317067_   2644 TGAAAAAAACTCTTCTAGACATTAGCTTAGACAAAGACTTCATGACCAAG 2693
                         v i?iv   -     vv   v  i v    i   v ii   v iivi v 
  L1M4_orf2#LINE/    549 AGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_125317067_   2694 AACCCCAAAGCAAATGCAAGAAAAGCAAATATAAATATGCAAACAGGACT 2743
                          vv  v      v v    v     v   v   i   ----  iv     
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA----AATTGGACT 643

  chr2_125317067_   2744 TAATTAAACTAAAAAGCTTCTGCAGAGCAAAAGAAATAATCAGCAGAGTT 2793
                          v  i   v v    i   i  iivvv    i  v iv    iv i   v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_125317067_   2794 AACAGAAAACCCA--GAGTGGGAGAAAATATTCACAATCTATACATCTGA 2841
                           v   v      --  i              ii   vii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_125317067_   2842 AAAAGGACTAATATCCAGAATCTACAAGGAACTCAAACAAATTAGCAATG 2891
                         v  i     vi          v  i  i      vv    v i ii   i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_125317067_   2892 AAAGAACAGACAATCTCATCAAAAAGTGGGCTAAGGACATGATTAGGCAA 2941
                            ii   i i  i iv  i?    i     v     iv   v   i  v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_125317067_   2942 TTCTCAAAAGAAAATATACAAATAGACAAAAAGCATATAGAAAACTACTC 2991
                              v      i          i v   v     i  ii   iv i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_125317067_   2992 AACATAACTAATTAT 3006
                              v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (137 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.44 (22 / 9)  


2580 24.71 3.74 7.17  chr2_125322060_125324026.rev      542  1476 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_125322060_    542 AGATAGCCCACATTCATAGATTAGAAGAATCATTATTGTTAAAATGTCCA 591
                              v    ii     i    i     v i v         i   v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_125322060_    592 TACCACCCCCAAAT-GAGCTACAAATTCAATGCAGTTCTTATTAAAATTC 640
                            i--        -  v     i      i   i i i   i     i 
  L1M4_orf2#LINE/     56 TACT--CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_125322060_    641 CAATTGTATATTTCAAAGCAATAGAAAAAC-AATTCTAGAGTTCATATGG 689
                           ii  iv v   iiv  v   v  v  i -i  i   i i         
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_125322060_    690 AATCAAAAAAGATCCCAAATAGCAAAAGGAATTTTGAGAAAGAAGAACAA 739
                           viiv  ii  i  vi      v   iv   i    i            
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_125322060_    740 GGCTGGAGGCATCACACTTCATAATTTCTAGCTATATTACAAAACTATAG 789
                         i i      vv         vi      v iviv  i      i   i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_125322060_    790 TGATCAAAAGCTTATGTTATCCATGCTGAATTCCTAATTAGAAACAAAAA 839
                          i     i -----------------------------------------
  L1M4_orf2#LINE/    254 TAATCAAGA----------------------------------------- 262

  chr2_125322060_    840 CAAAACAAAACAAAAAAATAGTATGGTACTGGCATCAAAACAGACACATA 889
                         ------------------i   i            v ii i     i   
  L1M4_orf2#LINE/    263 ------------------CAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_125322060_    890 GACTAAAGTAATAGAGGAGAGATCCCAGAAATAAACCTATACATTTGTGA 939
                           ii  v v      ivv    vi             i        i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_125322060_    940 TCAACTAAACTTTGATAAGAACAGCAAGAATACACAATGTAAAAAAGGAC 989
                             i i vi  i  i   iiiiv     vi iv     -iii    i i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAAT 393

  chr2_125322060_    990 AACCTCTTTAATAAATGGTGTTGGAAAAGATAGATACACACATACACATG 1039
                          ii  i  i  i        i   i v iv i    ?v     i  v v 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_125322060_   1040 TATTAAGTTGGATCC------------ACATACAAAAATTTACTTGAAA- 1076
                         v  v        i  ------------ i           v   ii   -
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_125322060_   1077 --AT-AAAGAGTTAAATATAAGATCTGAAACCATAAAACTCCTAGAAGAA 1123
                         --  - ?   vi     i     v  i    i         i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_125322060_   1124 AACATGGAGGAAAAACTCCTTAATATTAGTCTTGGCAATATTTGTTCTTT 1173
                              i i? v   v  i v i iv  i vi v      i---   ii  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG---GTTTCTT 590

  chr2_125322060_   1174 A--TATGACACCAAAAGAATACACAGCAAAATCCAAAATAAATAAATGAG 1221
                          --              v i vi  i     vvv      i      vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_125322060_   1222 ACCACATCACACTAAGAAGTTTCTGCACAATATAAGAAACAGTTGAAAAA 1271
                           iv     v v v i  ii  i  ii vvi v i  v  vi ii i   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_125322060_   1272 ATGAAAACGTGACCTAGAGAATGGGAAAAAATATTTGCA--CTACAGATC 1319
                         i      viii   i v         i            --ii i v   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_125322060_   1320 TGGCA-GGGATTTAATATCCAAAATATATAAAGAACTC----AACTCAAT 1364
                           ii -    i  i-      i                ----        
  L1M4_orf2#LINE/    741 TGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_125322060_   1365 AGCAAAGA-ATAAA-----CAATGACAAAAGTGAGCAAAAGTTCTGGATA 1408
                          ii   i - i   -----    v?-    i  i     i v i  i   
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATA 838

  chr2_125322060_   1409 GATATTT-TCCAAAGAAAACATACAA-TGACCAACAGATCTACAAAATGG 1456
                           i    -         i i      -  i    i iiivi ii   v i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_125322060_   1457 TGCTCAATATCGCTACTCAT 1476
                                i   i????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.20 (156 / 71)
Gap_init rate = 0.02 (19 / 903), avg. gap size = 5.37 (102 / 19)  


2073 24.18 1.58 8.67  chr2_125377747_125379499      501  1261 (492)    L1M4_orf2#LINE/L1      202   908 (0)  

  chr2_125377747_    501 AAAGCTGCAGGCATCTCACTCCCTGATTTCAAACTATATTGCAAAGCTGT 550
                             i  v   vv  v    i  ii        viv  i i       ii
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_125377747_    551 AGTAATAAAAAAAAAAGCATAATACTGGCATAAA-ACAGACACATAGACT 599
                               v  i v --- ii ii           i- i     i     ii
  L1M4_orf2#LINE/    252 AGTAATCAAGACA---GTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_125377747_    600 AATAGAATGGAATAGAGAAGCCAGAAATAAACCCAGGCTTATTTA--ATC 647
                            i    i    v    iv               vi --     --i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC--ATTTATGGTC 346

  chr2_125377747_    648 AACTAATCTTTGGCAAAATTTCCAAAAATGCATAATGAAGAAAATGTTGC 697
                           i i  i  i i   iiv v    i viiivi    ii    ivi v i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_125377747_    698 TTATTCAATAAATTGTGATGGGGAAATTGAATATCCACATGCAAAAGAAT 747
                         i v     i    v   v    iv  i  i   ?                
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_125377747_    748 AGAATTGGACCTTTATCTTATACCATATA--AAAATTAACTTGAAATGGA 795
                         ii i       ii  i  i i        --          ii       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_125377747_    796 TTAAAACCTTAAATATAAGACCTGAGACTGTAAA-CTCCAGGAAGGGAAC 844
                          i ? iv i     i     v  i i   i    -   ivi    ii   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_125377747_    845 ATAAGGACAGATCTCCTTAATATTGGTCTTGAAAATATATATATATGTTT 894
                            i ?ii i    i v i iv    vi v iv   i---------    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG---------GTTT 587

  chr2_125377747_    895 -----ACATGACACCAAAAGTATGATCAACAAGAGCGAAAATTTAAA-AA 938
                         ----- i             i ii v      i  vi     -- i -  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT--AGATAA 635

  chr2_125377747_    939 ATGGGACTGCATGAAACTAAAAAACCCTCTGTACAGCAAAGGACACAATC 988
                           v     v   v   v v      ii -   i vv          v   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATC 684

  chr2_125377747_    989 CACAAAAGGAAAAGGCAATCTACAGAATTGGAAAAAGAAATGTTTTTAAA 1038
                         v v   iv      i   i i       v   i   ---  i   vi   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA---ATATTTGCAAA 731

  chr2_125377747_   1039 CCATATGACTGATGAAGGGTTAGTATCCAAAGCATAAAAAGAATTAATAT 1088
                         i     iv     i i  ii v       i ii   v      i vv  i
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_125377747_   1089 AACTCAATAGCAAAAAAAAAAAAAAAAAGAAAGAAAGAAAAGAAAAACAC 1138
                                  ii     i v   v  vv--------------------  v
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACC--------------------CAA 811

  chr2_125377747_   1139 TTCAAAAAATAGGCAAAGGATGTGAATAGTTTTTTTTTGTTTTTTTTTGT 1188
                           -?      i          v       viv   i -------------
  L1M4_orf2#LINE/    812 TT-WAAAAATGGGCAAAGGATTTGAATAGACATTTCT------------- 847

  chr2_125377747_   1189 TTTTTTTTTTTTCCACAAAAGGCATACAAACATCCAACAGGTACATGAAA 1238
                         ------------   v i   ii       iiv    i i i        
  L1M4_orf2#LINE/    848 ------------CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_125377747_   1239 AGGTGCTTAACATCACTGATCGT 1261
                           i    i       ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (121 / 59)
Gap_init rate = 0.02 (15 / 707), avg. gap size = 5.20 (78 / 15)  


1142 21.29 1.94 1.61  chr2_125433119_125436275        1   310 (2847)    L1M4_orf2#LINE/L1      598   908 (0)  

  chr2_125433119_      1 ACACTAAAAGCAATCAGTAACACAA----ATTTAGATAAATTGGATGATA 46
                             i       -iv  i    v  ---- vv             ivvi 
  L1M4_orf2#LINE/    598 ACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_125433119_     47 TTCAAATTAAAATATTTTGTGTACCAAAGTATGTTCTCAAGAAAGCTAAA 96
                          iv         vv       ivi     v iii v         iv   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_125433119_     97 AGACAACCTATACAATGGAATACAATATTTGCAAATTATATATCACCTAA 146
                                 i i v     i v v             i       vvv   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_125433119_    147 GGGTTTAATATCTAGAATA-ATAATAATAAAACTTCTGCAACTCTACAAC 195
                            vi vi    i      -    ---- i    ii i      v i  i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAA----AGAACTCTTACAACTCAATAAT 792

  chr2_125433119_    196 AATAACGCCAGTAAACCATTTTAAAAGTGGTCATAAGCCTTGAATAGAAA 245
                           v  vi v i   v   v  ?    i   v  v i vi         v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_125433119_    246 CTTCTCCAGAGAAGATATACAAATGAC-AATAAACACATGAAAAGATGCT 294
                         i       i                i -     i                
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_125433119_    295 CAACATCATTAGTCAT 310
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (34 / 31)
Gap_init rate = 0.02 (5 / 311), avg. gap size = 2.20 (11 / 5)  

 582 28.32 4.90 3.85  chr2_125433119_125436275     1066  1351 (1806)    L1M4_orf2#LINE/L1       21   309 (599)  

  chr2_125433119_   1066 ATGGATTGGAAGACTTCACATAGTAAAGTTATTAATTCTCCCATTATAAT 1115
                                         v i  v  v   v ivi   v     ----i  v
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC----CAAA 66

  chr2_125433119_   1116 TTCATATATGAGTTTAACACAAAGCTTATAAAAATCCTAGCAATATCTTT 1165
                           v  v  iiii  i   i   vv i   v       i   -- ii    
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC--TGCCTTT 114

  chr2_125433119_   1166 TT-GTAGATATCAACCAGATTACTATAAAATATATATCCAAAGTGAAAA- 1213
                           - i   v  ii  v  v v iiv      vi    vv   -  v  i-
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA-TGCAAGG 163

  chr2_125433119_   1214 ---CTAGAACAGCTTAAACAATTTTGAAAAT--ATTATATA-TTGGAGGA 1257
                         --- i    i   iv       i       v-- vv i v -        
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_125433119_   1258 ---AAATGGTCTACCTGGTTTCAAGATTTG-TATA--GGTACAGTGGTCA 1301
                         --- v ----  v  iii      i i  i-  i -- v      ii   
  L1M4_orf2#LINE/    214 CTCACA----CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_125433119_   1302 AGATTATTTGCTATTTGCAAAGGGACAGATACATCAATCCATGGACCAGA 1351
                            ivi v  v  i v   v i   i   i i  vi   v     vi   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

Transitions / transversions = 1.19 (44 / 37)
Gap_init rate = 0.04 (11 / 289), avg. gap size = 2.27 (25 / 11)  

1526 24.90 8.62 0.96  chr2_125433119_125436275     2144  2665 (492)    L1M4_orf2#LINE/L1      347   908 (0)  

  chr2_125433119_   2144 AAATGATTTTTAACAAAGGTATAAATTCAATAAAATGGAGGAAA------ 2187
                           v       ii    i   iiv  vv v  vv     i i  i------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_125433119_   2188 -TTTTTAACCAATGCTGCTGGAGCAACTGGACATCCACAAGCAAAAGAAA 2236
                         -    i   v    v      ii        i ?     v         -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA- 445

  chr2_125433119_   2237 TTAATGTTGA---CCTAAGTCTCACATTTCATAAAAAAACTGACTCAAAA 2283
                         - i v    i---    --i      iivi   v     i i        
  L1M4_orf2#LINE/    446 -TGAAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_125433119_   2284 TGAATGACACACATAAATGTAAAAGGTAAAAGTAGAAAACT--TAAAA-A 2330
                           i  v ? v  v         i  v     v  v      --  i  - 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_125433119_   2331 AAATATAGGAGGAAATCTTTAGAATTCAGGGCTAGTCAAACAGTTCTTAG 2380
                            i     ? v       iivi iiiv   i   v   vviv       
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_125433119_   2381 ATA--ACAGTGTAAGCACAAACTATAAAATGAAGAATTGATAAACCAG-C 2427
                            --   viiv        i v i    vi  i   v      iii - 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_125433119_   2428 TTCATAAAAATGAAAAGCTTTTGTGCTTTGGAAGAAC-TTGTTAAAAGAT 2476
                              v     v    i           ii-   i  -i i i  i i v
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGAAAG 691

  chr2_125433119_   2477 TGAAATGGTCTGCTTCTGAGTGGGAGAAAATACTT-CAAACCATATATCT 2525
                              v iivvv iv v  i            i  -    i         
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_125433119_   2526 GACAAGGGACT-------AGAATGCACAAG----TCTCAAAATTCAAGAG 2564
                           i        -------     ii i  i----   i v  i    v i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_125433119_   2565 TAAAATACCAAACAATTCCATTAGAAAATGGGCAAAA----TAAGTTGA- 2609
                              viv    i  ii v   ?i            i---- i i v  -
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_125433119_   2610 -----------GGATATATACAAATGGTCAATAAGCACATGATATGATAT 2648
                         ----------- i v            i              v v   ii
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_125433119_   2649 TCCACATCATTAGGCAT 2665
                           v      ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (76 / 50)
Gap_init rate = 0.03 (15 / 562), avg. gap size = 3.33 (50 / 15)  


3246 26.48 0.55 0.77  chr2_125500697_125505482.rev     3385  4294 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125500697_   3385 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3434
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125500697_   3435 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCTATCAAGT 3484
                            v     v      v i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125500697_   3485 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAACT-ATTTTAAAGTT 3532
                          v   iivi i  i  ii     -   ---- v  i  -  ii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr2_125500697_   3533 CATATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAA 3582
                                  viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_125500697_   3583 AGAACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAG 3632
                                  i      vv    v  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_125500697_   3633 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 3682
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_125500697_   3683 CCAATGGAACTGAAC--AGAGCCCTCAGAAATAAGACCACACATCTGCAA 3730
                         i        iv   i--    i  --        iv   i    i iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_125500697_   3731 CCATCTGATCTTTGACAAACCCAACAAAAACAAGAAATGGGGAAAGGATT 3780
                         i  vi    i  i     ivviiv   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_125500697_   3781 CCCTATTTAATAAATGGTGATGGGAAAACTGGCTAGCCATATGTAGAAAG 3830
                         vi  v  i  i        v     v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_125500697_   3831 TTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 3880
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_125500697_   3881 AATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAA 3930
                         i  i ?    i       v   v       i      v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_125500697_   3931 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 3979
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_125500697_   3980 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 4029
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_125500697_   4030 TAATTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTG 4079
                          v  i   v v  i i   i iii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_125500697_   4080 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATATGA 4129
                           v  i     i                 v       vii ivi  v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_125500697_   4130 CAAATGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGG 4179
                         i  iv i  vi          v  i  v      vv    v iv i  vi
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_125500697_   4180 AAAAAACAAACAACCCCATCAACAAGTGGGCAAAAGATATGAACAGACAC 4229
                             i     i     v  i? v  i        i   v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_125500697_   4230 TTCTGAAAAAGAGACATTTATGTAGCCAACAGACACATGAAAAAATGCTC 4279
                             vv   ii   i  vi vi i     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_125500697_   4280 ATCATCACTGGCCAT 4294
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


3000 25.66 1.22 0.77  chr2_125505893_125508983.rev     1696  2599 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125505893_   1696 TGGAAACACATCCCATGCTCATGGGTATGTAGAATCAAGATTGTGAAAAT 1745
                               v i        i      i vv v   v i  v     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125505893_   1746 TACAATACTGCCCAAAGGAATCTACAGATTCAATGCAATTCCCATCAAAA 1795
                         vi       v      vvi              i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125505893_   1796 TACCC--CTATCATTCTTCACAGAACTAGAAAAAAAAATCTTAAAATTCA 1843
                          -   --  ii -  i  ii     v v  v  ivvi   i         
  L1M4_orf2#LINE/    101 T-CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_125505893_   1844 TATGGAACCAGAAAGGAACCCACA-TAGCCAAAGCAATACAAAGAGAAAA 1892
                                vi- v    i     v -        i    vivi i -  i 
  L1M4_orf2#LINE/    149 TATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGA 196

  chr2_125505893_   1893 AGAAGAAATCTGGAGGCATCACATTACATAACTTCAAATTATACTACAAG 1942
                             v   vi      vv     i v vi  i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_125505893_   1943 TCTACAGTTATCAAAACAGCATGATACTGGTATAAAAATAGACTCATAGA 1992
                         v       v     i    ii  i      i    ii      vi     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_125505893_   1993 CCAATGATATAGAATAGAGAACCAAGAAATAAAAACCAAACACTTTCAGC 2042
                         i     iv       v    ii v         v-   v   i  vii i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTTATGGT 345

  chr2_125505893_   2043 CAATTGATCTTCAACAAAGCATGTAAAAACAA---AGTGAGGAAGGAACA 2089
                                 i   i    i -i  iv  i  v --- i  i    i   i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_125505893_   2090 CCCTATTCAACAAATGGTGCTGGGAAAACTGGCAAGCCACATGTACGAGA 2139
                         vi  v                    v      vv ?       i vi   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_125505893_   2140 ATAAAACTGGATCTTCACTTCTCACCTTATACAAAAATCAACTAAAGATG 2189
                           i  ii    i iii  i  v    v           i    v  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_125505893_   2190 GATCAAAGACTTAAATCTAAGACCTGAAACCATACAAATTCT-AGAAGAC 2238
                              ?    i     v     v  i    i   -   i   -      v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAA 543

  chr2_125505893_   2239 AAGATTGGAAAAACTTCTCTAGACATTGGCTTAGGCAAATAATTCATGAC 2288
                           v  v  ?iv  v ii  vv   v    v        vviv   v iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_125505893_   2289 TAAAGCCCAAAAAGCAAATGTAACAAAAAAAAAAATGAATATGTGGGACC 2338
                           vii v v       v v i       i       ii   vi v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_125505893_   2339 TAATTAAACCCAACATTTTCTGCACAGCAAAAGAAATAATCAGCAAAGTA 2388
                          v  i   vii  v vi  i  ii vv    i  v iv    iv     i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_125505893_   2389 AACAGACAACCCCCAGAGTGGGAGAAAAAATTCACAAACTATGTATCCAA 2438
                           v         v    i          v   ii    ii  i    ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_125505893_   2439 CAAACGACTAATGTCCAGAATCTACAATAAACTCAAACAAATCAGCAAGA 2488
                         i  iv    vi i        v  i  vi     vv    v   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_125505893_   2489 AAAAAACAA----TCCCATTAAAAGGTGGGAAAATAACATGAATAGACAA 2534
                             i    ----i  v   ?   ii    v   vi iv          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_125505893_   2535 TTCTCAAACGAAGATATACAAGCTGCCAACAAACACATGAAAAAATGTTT 2584
                              v  v            iiv     i  i          i   i i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_125505893_   2585 AACATCACTAATGAT 2599
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (128 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


1042 30.56 0.83 1.11  chr2_125576410_125580378.rev     2291  2650 (1319)    L1M4_orf2#LINE/L1        9   367 (541)  

  chr2_125576410_   2291 TATTCC--GTTTGTGAATTGAAAAACTAAATGTTATTAAAATATTGATAC 2338
                            i  --   ii  i    i  i   v   i  i    i  ivii    
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr2_125576410_   2339 TACCCATTCTAATCTATAGATTCAATGCTATCTCAATCAAAATCCCAACG 2388
                          v    vvi i     i        i  v   i v            i v
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_125576410_   2389 ATCTTTATTGTAGATATTAACAAAAGTGTTCAAAAAATTTTATATGAGAA 2438
                         ii    v   i   v   i    iv-  v  vv      i-     ii  
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTC-ATATGGAAA 156

  chr2_125576410_   2439 -GCAAAAGACCTGGAATATTCACCACAATTCTAAAAAATAAAAACAAAAA 2487
                         -    ii    ii     vi  vv     ii i     v  i      --
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA-- 204

  chr2_125576410_   2488 GTTGGAAAACTGAAACAAATCTATATCAAGGGTGACTACAATGCTGTAAT 2537
                               ii   v v  vvvi v  v    iiv v       v   ii i 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_125576410_   2538 AATCAAGACAGGGTGGTATTGACAAAAGAAGGGATTCATAGATTTAGGAC 2587
                                    v      i  i  v   i vi  ivi      iv v iv
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_125576410_   2588 ACAGAATCAAGAGCTCAAAAATAGATGTACAGAAGTATGAATAATTGAAC 2637
                          i     ii    ii  i     i ivi i v vv    ivi      vi
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_125576410_   2638 TTTGGGCCGGGTG 2650
                           i ivvv     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTG 367

Transitions / transversions = 1.50 (66 / 44)
Gap_init rate = 0.01 (5 / 359), avg. gap size = 1.40 (7 / 5)  

1041 28.65 8.21 1.28  chr2_125576410_125580378.rev     2932  3479 (490)    L1M4_orf2#LINE/L1      323   908 (0)  

  chr2_125576410_   2932 AAATAAATAAATAAA---ATAAATAATTGATCTTTGATAAAGGAACTAAG 2978
                                ivv   v ---  iivi       i  i  i  i  vi i   
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_125576410_   2979 GAAATTCCATTAAGAAAGAATAGCATTTTTAAAAAA--ATGTTGTAATAA 3026
                         ivv    v  vii          iv    i  v   --i  i  vi i  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_125576410_   3027 TTGGACATTCACACGCAAAAACACAAACCCAGGCACAGACCTTACGCCTT 3076
                         i    i ?i    i      iv ii  viii i v vv    i  i  v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_125576410_   3077 TGACAAAAATTGCCTCAAAACATAT---AAATCTACATGTAAAATGTAAA 3123
                         vv         iv       iiv  --- i i   v      i vv    
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_125576410_   3124 ATAACAAAGCATCTGGAAGAAAGCATAGTAGGAAATCT--GTTACCATTG 3171
                          iv i   i vii i       i     v? v      --  v   -   
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC-TTG 571

  chr2_125576410_   3172 GGTT-GGTGACAATT-CTTAGATGCAGAACTGAAAGCCTAATCCATGAAA 3219
                             -  ii iii  -       iiiiv  ii     vi  v v ii   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_125576410_   3220 TCAAAATT-GAT---TTGAGCTTTATTAAAAT-AAAAACTTTTGCTCTGT 3264
                         vv    v -   ---   ii   i  i     -           iv  vi
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_125576410_   3265 GA--GATA--ATCTAAGAAAAATAAAAGATAAGCCA-----------AAA 3299
                         i --  i --   -      ivv      i  v   -----------   
  L1M4_orf2#LINE/    672 AAAGGACACTATC-AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_125576410_   3300 ACA----CAAATCTGAT----GAAAAAAAAATTACAAAGACAACAATA-A 3340
                          i ----      vv  ----  v  iii v  ii v--- v v    - 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTAT---CCAGAATATA 767

  chr2_125576410_   3341 TACAAATAC----ACAACTAAACAATAAGAAAGGAAACAACCCAGTTTTT 3386
                           v i -  ----      v  i     i  iiv   i      i  ?v-
  L1M4_orf2#LINE/    768 TAAAGA-ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA- 815

  chr2_125576410_   3387 AAAATGAGCAAACGATCTGAACACACACCTTACCAAAGAATATATACAGA 3436
                               i     v   i    i v   ii iv        v       i 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_125576410_   3437 TGGCAAATAAACATACGAAAAGAGATTCAACATGATTTTTCAT 3479
                             v     i  i i       vii       v ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (94 / 60)
Gap_init rate = 0.04 (21 / 586), avg. gap size = 2.48 (52 / 21)  


2810 29.14 0.77 0.55  chr2_125594284_125598880.rev     3200  4105 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125594284_   3200 TGGAAACACATCCCATACTTACATATGGGTAGAATCAATATTGTGAAAAT 3249
                               v i       ii i iiv  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125594284_   3250 TACCATACTGCCAAAAGCAATCTACAAATTTA-TGCAATTCTCATCAAAA 3298
                         vi v     v  v   vii       i   i -i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125594284_   3299 TACCAATATAATTTTTTATAGAACCAGAAGAAACAATACTAAAATTCATA 3348
                          v   iivvvv      ii    viv  vi ivii  v            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_125594284_   3349 AGGAACAAAAAAAGAGACC--ACATAGCCAAAGTAAGACTAAGCAAAAAG 3396
                         v    -- viv   i    --iv         ii  vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_125594284_   3397 AACAAATCTGGAAGCATCATATTACCTGATTTCAAACTATGCTATAAGGC 3446
                               vi    i vv   i i v  ii        viv i   i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_125594284_   3447 CATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCATATAGACC 3496
                         i i   v i   i    ii         i    ii    i        i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_125594284_   3497 AGTGGAACAGAATACTGAACCCAGAA-TAAACCCAAATACTTACAGCCAA 3545
                          i     i     vvv  ii      -        v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_125594284_   3546 CTGATCTTTGACAAAACAAACAGCAACATACAGTGGGGAAAAGACACCCT 3595
                         i    i  i     iivviv  iv v   v  i        ii i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_125594284_   3596 ATTCAACGAATGGTGGTGGGATATTTGGCAAGCCACATATGGAAGAATGA 3645
                         v      i       v     i vi   vv ?      iiii        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_125594284_   3646 AACTGGATTCTCATCTCTCCCCTTGTGTAAAA-TCAACCCAAGATGGATC 3694
                          ii    ii ii i   v v  v i ii    - i   i   i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_125594284_   3695 AAGGTCTTAAACCTAAGACCTGAAACTTTAAAAATTCTAGAAGATAACAT 3744
                          ?i v i    iv     v  i     v     v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_125594284_   3745 CGGAAAAAAACCTTCTAGACATTGGCTTAGGCAAGGATTTCATGAGCAAG 3794
                         v  ?iv   -i    vv   v    v        v i    v iiii v 
  L1M4_orf2#LINE/    549 AGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_125594284_   3795 AACCCTAAAGCAAATGCAATAAAAACAAGGATAAATAGCTGGAACTTAAT 3844
                          vv  v      v v    i    iv  ii   i   iv v i    v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_125594284_   3845 TAAACTAAAGAGCTTCTGCCCAACAAAAGGAACACT--CAGCAGAATAAA 3892
                         i   v v  i i   i  iv vv    i --     --  iv i i i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGG--ACACTATCAAGAAAGTGAA 695

  chr2_125594284_   3893 CAAACAAGCCATAGAGTGAGAGAAAATCTTCACAATCTATACATCTGACA 3942
                         v i    v   i   i  i        v  ii   vii   i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_125594284_   3943 AAGGACTAATATCCAGAATCTACAATGAACTCAAGCAAAGTAGTGAGAAT 3992
                          i     vi          v  i  v      vvi   vvi i i v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_125594284_   3993 AAAACAAACAATCCCATCAAAAAGTAGGCTAAGGACATGAACAGGCAATT 4042
                           i     i  i  v  i?    i i   v     iv    i  i  v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_125594284_   4043 CTCAAAAGAAGATATACAAATGGCCAACAAACATATGGAAAAATGCTCAA 4092
                            v                       i  i  i   i   i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_125594284_   4093 CATCACTAATGAT 4105
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (158 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


 393 32.28 1.27 1.27  chr2_125602294_125604560        1   158 (2109)    L1M4_orf2#LINE/L1       88   245 (663)  

  chr2_125602294_      1 ATCGCCATCAAGCTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT- 48
                            v i     iv v   iivi i  i  ii     -   -- v  i  -
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTG 135

  chr2_125602294_     49 ACTTTAGAGTTCATATGGAACCAAAAAAGAGCCCTCATTGCCAAGTCAAT 98
                          iii  i i           viiv  ii  v  vvv  v     iv    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_125602294_     99 CCTAAGCCAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAAC 148
                          i i ivv i          i      vv   ii  v  ii i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_125602294_    149 TATACTACAA 158
                         iv        
  L1M4_orf2#LINE/    236 CTTACTACAA 245

Transitions / transversions = 1.55 (31 / 20)
Gap_init rate = 0.02 (3 / 158), avg. gap size = 1.33 (4 / 3)  

2609 27.28 1.29 3.76  chr2_125602294_125604560      851  1781 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125602294_    851 TAGAAAAACACTCTATGCTCATGGATAGGATGAATCAATATTGTTAA-AT 899
                          i    i i ii i   i        v   v  v i           -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125602294_    900 GAACATAATGTCCCCCAAA---ATTTACAGATTCAATGCTATTCCTATCA 946
                          i---i   iii       ---  i           i  v  i       
  L1M4_orf2#LINE/     51 GG---CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_125602294_    947 AACTACCAATGACATTCTTCACAGAACTAGAAAAAGCT-ATTTTAAAATT 995
                           v v   iivi v  i  ii     v v  v  -   -  ii       
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATT 146

  chr2_125602294_    996 TATATGGAACCAAAAAAGAGCCCAAGTAGCCAAAACAGTACTAAGCAGAA 1045
                         i        viiv  ii  v  vi i           i vi i iv ii 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_125602294_   1046 AGAACAAAGCTGGAAACATTACATTTTCTGACTTCAAACTATGCTATAAG 1095
                                  i    iivv i   i  i ii i      viv i   i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_125602294_   1096 GCTACAAAAACAAAAACAGCATGGTTCTGGTAGAAAAACA--CACATAGA 1143
                               iv  iv  i    ii    v    i v  ii i --  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_125602294_   1144 CCAGTGGAATAGAATAGAGAGCCCAGAAGTAATGTCACACACCCACAACC 1193
                         i  i           v     i      i   vvi  i   iii iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_125602294_   1194 ATCTGATATTTGACAAAATTAACAAAAGTAAGCAATGAAGAAATGACT-- 1241
                          vi    v  i     iiv iv   i vi vv     ii    -  v --
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAG 395

  chr2_125602294_   1242 CCCCATCAGTAAATGGTGCTGGGATAACTGACTATCCACATGCAGAAAAC 1291
                         i iiv   ii              i     iv  ?         i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_125602294_   1292 TGAAATTGCACCCCTTGCTTACATCATATGAAAATCAATTTTTGTTGATA 1341
                             i   v      vv  i   i     ---------------------
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATAT--------------------- 474

  chr2_125602294_   1342 TACAAAAATAAACTCAACACGGATTAAAGAC--AAATATAAAACTCAAAA 1389
                         -        v       v i    i ?    --    i   i vii    
  L1M4_orf2#LINE/    475 -ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_125602294_   1390 CTATAAAAAACCTGGAAGATAACATAGAAAACACCCTTCTGGACATAAGA 1439
                                 vv i i     v       i?ivv vi    vv   v vi i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_125602294_   1440 CCAGGAAAATATTTCATGACAAAGACACCAAAAGCAATTGCAACAGAAAT 1489
                         ii   v  vvi    v iivv v             vvv      i  iv
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_125602294_   1490 AAAAATTGACAAATGGGACTTAATTAAA-CAAAGAGCTTCTATGCAGCAA 1538
                               v  i    v      v  i   -iv  i i   i i   vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_125602294_   1539 AAGAAACTATCAACTATCAACAGAGTAAACAGACAACCCACAGAATTGGA 1588
                          i  ------  -       v i   i  v                v   
  L1M4_orf2#LINE/    674 AGGA------CA-CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_125602294_   1589 GAAAATATTTGCAAAGTACGAATCTGACAAAGGTATAATATGCAGAATCT 1638
                                        vi iiv      i  i  vv vi   v      v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_125602294_   1639 ATGGGGAACTTAAACACATTAACAAGCAAAAACCAAACAACTCTATTAAA 1688
                           iii     ivv   vv i  i  vv    iv    i   i v   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_125602294_   1689 AAGTTGGCAAAGGACATGAACATACACTTTTCAAAAGAAGGCATAAACAT 1738
                           i v         iv    i v   i  i  v       ii   v v  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_125602294_   1739 GGGCCAACAAGCATGTAAAAAAATACTCAATGTCACTAATCAT 1781
                           -    i     ii i    i  i     ii   ????????
  L1M4_orf2#LINE/    867 GG-CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (154 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.36 (47 / 14)  


2373 27.56 3.78 0.85  chr2_125626202_125628011.rev      491  1310 (500)    L1M4_orf2#LINE/L1       37   880 (28)  

  chr2_125626202_    491 AGTATTTTCTAAAATGG--ACACAATCTAAAGCAATTTACAGATTCAACA 538
                          i    v -   i    -- i  vvi i   vii  i            i
  L1M4_orf2#LINE/     37 AATATTGT-TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACG 85

  chr2_125626202_    539 CTCTTCCTATCAAACTACCA-CTATCATTCTT-CATAAAATTAGAAGAAA 586
                          vv i         v v   -  ii v  i  -  v   v v v   vvi
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chr2_125626202_    587 ACTCTAAAATGTATATGGAACCAAAAATGAACCTGAATAGCAAAAGTAAA 636
                          ii       vi        viiv  iv  v  v       v   ii  v
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_125626202_    637 CTGAAGCAAAAAGAACAAAGCTTGAGACATCATACTACCTGACTTCAAAC 686
                           vi iv  i          i v   ivv   i   v  ii i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_125626202_    687 TATACTATAAGGCTATAGTAACCAAAACCTTATGGTATTCGTACAAAAAC 736
                         iv     i  i    i     i   i  vv i     i v i i  ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_125626202_    737 AGACACATA-ACCAATGGAACAGAATAGAGAACCCTGAAATAAAACCTCA 785
                              i   - i        i     v    ii  v        v  vi 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_125626202_    786 CACTTATAACCATTTGATCTTTAACAAGGGTGACAAAAGCAAGCAATGGG 835
                           i    iii  v     i  ii         v   i v  vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_125626202_    836 GAAAAGACTCCCTATTCAATGAATGGTTCTGGGATAACTGGCTAGCTAAA 885
                             ii ivvi  v     ii      v      i      v  ? i v 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_125626202_    886 TGCAGAAGAATGAAACAGGGTCCTTACCTTTTATCATATACAAAAACTAA 935
                             i         iiv  ii  i     ivi i            i   
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_125626202_    936 CTCGAGATGGATTAAAGA-----ATAT-----CCCAAACTATAGAAGTCC 975
                            i i      i ?   -----  i ----- iv        i  v  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_125626202_    976 TAGAAGAAAATTTAAG---AAATACACTTCATGATATAGGCTTGAGCAA- 1021
                                   iv  i ---    ---    i   iv v  v  ii    -
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_125626202_   1022 -ATTT-TTGTCTAAGTCCCCCAAAGCAATTACAACAAAAACAAAAGTTGA 1069
                         -i   -  ivv  v v v  v      vvvi        iv    i v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_125626202_   1070 CAAGTGGAACCTAATCGAA-CTACTGAGTTTT-TGCTTAGCAAAAGAAAC 1117
                         i  i v i  i v   i  -i  vvi v    -     --    i  v  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACAC 680

  chr2_125626202_   1118 TCTCAACAAAGTAAACAGAAAAACCTACAAAATGGGAGAAAATATTCACA 1167
                          v    v     i  v   v  -  i   i                ii  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAA-CCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_125626202_   1168 AACTATGCATCTGACAAATATCTAATATCCATAATCTATAAGGAACTT-- 1215
                           ii  ii      i  iviv  vi      v   v     i     i--
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_125626202_   1216 --AAATCAACAAGCAAAAAACAA----CCCCATTAAAAAGTGAGCAAAGA 1259
                         --  v    i  vv    i    ----   v   ?    i  i      i
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_125626202_   1260 ACATGAAAAGACACTTCTCAAAAGAAGACATAAAAGCCACCAACAAACAT 1309
                          iv    v     i     v        i   v  iivi    i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_125626202_   1310 A 1310
                          
  L1M4_orf2#LINE/    880 A 880

Transitions / transversions = 1.42 (131 / 92)
Gap_init rate = 0.02 (17 / 844), avg. gap size = 2.24 (38 / 17)  


2092 28.96 7.15 0.70  chr2_125690234_125691808.rev      231  1083 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125690234_    231 TAGAAAGACAGTCCATGCTAAATTATTGGAATAATTAATATTGCTAAAAT 280
                          i      i vi     i v vvv       v v         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125690234_    281 GACAATACTGACCCAAA--AATATACAGACTTTTTGCAATTTTTATAAAA 328
                          i       v-      --i  v      i ivvi     iii   v   
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_125690234_    329 ATAACAAGGATATTCTTCACATAAGTAGAAAGAAAC--ATCCTAAAATTT 376
                           vv  ivviiv  i  ii  v  i v  v -- i --           i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACA--AGCTGATCCTAAAATTC 147

  chr2_125690234_    377 GTATGGAACCAAAAAGAACCCCAAATCACCCAAGCAATCCTGAGAAAAAT 426
                         i       viiv  i i    vi   vi  v  i     i   i   i -
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA- 196

  chr2_125690234_    427 ATAACAAGGCTGGAGACATCACACAATAAGATCTGAAAATATGTTACAAA 476
                          v     i i     ivv      vvivvi  i v    iv ii      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_125690234_    477 TCTTTAGTAAACAACAC-----GCTACTAGCACAAAAACAAGTATGTAGA 521
                         v  vi     v   v  ----- v    i   i  ii i iii  i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_125690234_    522 CAAATGGAACAGAATAGGGAACACAGAAATTACTCTACATAGCTACAGCC 571
                         iv       i     v i  iiv       v vi i i i vi  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_125690234_    572 AACTGATTTTTGACAGAAGTGCCAAAAC-ACT-AATTGGGAAAGGACCGT 619
                           i       i    iii       i  - i -   v       i iv  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_125690234_    620 CTTTTCAATAACTAGTGCTAGGACAATTGGATATTCATGAACAGAATAAT 669
                                 i  v i     i      i      ?i  iivi  i  v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_125690234_    670 GAAATTAGATGTACACATTTTGTCTTTTACAAAAATCAACTCAAAATGGA 719
                            i  i  ivivi  v iviii v v         i             
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_125690234_    720 ACAGAGACTGGA--GGAAGACCTTAGA----GAAATGCTTCAGAAGA--- 760
                         v  ?    ivi -- v    v  v i ----i   iv   -      ---
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT-AGAAGAAAA 545

  chr2_125690234_    761 --TGGGT---------------CTTGA-------AAAGATTTTATAAGTA 786
                         -- i  ?---------------    i-------  v i   iv  ii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_125690234_    787 AGACCTCAAAAGCATAGGAAACAAAAGCAAACAT-GAAAAATGAGATTAT 835
                         v   vi        i i v        v   v  -  v    vi  i vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_125690234_    836 ATCAAACTAAATAACTTCTGTACAGTAAATAA----ATCAACAGAGTGAA 881
                               v v  v     i   i vvi   vi ----     v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_125690234_    882 AAGACAATCTACAGAATGGGATAAAATATTTGCGAAATACTCACCGAGTA 931
                                i i           v           i  vi ivi i vii  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_125690234_    932 GTGTATTAATATCCAGAATACGCTAGGCACTCAAACATCTCAACAACAAC 981
                         iv v i vi           iiiv i v    vv   v     i  i  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_125690234_    982 ----CAAA-ACTTCAGTTAAAAAATGAACAA----TCTGAACAGATATTT 1022
                         ----    - vii  i  ?       ii   ---- i    i   i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_125690234_   1023 CTCAAAAGAAGACATACAAAT---CGACAAAAACATGAAAAAATAGCTCA 1069
                            v        i        --- i i  iv         i  -     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCA 894

  chr2_125690234_   1070 ACATTATTAATCAT 1083
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.19 (67 / 21)  


2903 23.27 5.68 2.61  chr2_125777965_125780657     1322  2202 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125777965_   1322 TGGAAATATGCCCCATGTGCATGGATTCAAAGACTTAATGTTGTTAAGAT 1371
                               v  ii       v        vi          i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125777965_   1372 GTCAATACGACCCAAAT-GATATACAGATTCAATACAATTCTTAATGAAA 1420
                          v      vv       -   v           ii    i i  vii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125777965_   1421 TCTCAACAATGTTTACTTTTCAGAAATAGAAAAATCCACTCTAACCCCCA 1470
                           i  i --  ii vi   v       v  v  iiiv ii    vvii  
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_125777965_   1471 CCCCAATGGAATAATCTTTACAT-CAAGGGACCCCAAATAACGAAGATAA 1519
                         i----      ----------  -          vi    i v  i i  
  L1M4_orf2#LINE/    149 T----ATGGAA----------ATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_125777965_   1520 TCTTCAAAAAGAAGAGTGAAGTTTGAGGTCCTACACTTTCTGATTTCAAA 1569
                             v          iii     v    v ii      i ii        
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_125777965_   1570 CCTTATTACAAAATTACTTACAGTAATC--GAAAGTCTGGTACTGGCATA 1617
                         v    i      ii   ----       --  v   v             
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTAC----AGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_125777965_   1618 AACAGAAACATATAAACCAAGGAAATAAAAT--AGAGGCCAAAAACTACC 1665
                          iv v i       i i   v i    i   --    v   i   iv v 
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr2_125777965_   1666 TTCTACATATATGTTTATATACCTTATAACAAAGGCTCCAAAGCCATTCA 1715
                         iiv     v    v i vv ivi  vii    i  iv    ii       
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_125777965_   1716 ATGGGGGAAAAGACAATCTTTGTAATAAATGCTACTGGGAAAATTGGATT 1765
                               i  i - i i     vi  i     v i      v  i     v
  L1M4_orf2#LINE/    381 ATGGGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_125777965_   1766 TCTACATGCAGAAGAATGAAGTTGGATTCTTAATTTATACCATATGCCAA 1815
                         ? i       i               ii i  vi i i       i v  
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_125777965_   1816 AATTAACTCAAAGTTGATCAAATATATAAAT-TAAGGTCTAAAACTATAA 1864
                                     i v     ? v iv     -    iv            
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_125777965_   1865 CATTCTTAGAAGAAAACATAGATGAAAACTTTC-TGAAATTAAATTTGGC 1913
                         v i                  i? v   ii   -   vv  iii  v   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_125777965_   1914 AATGATTTATTGCATATATCACCAAAA-----------AAATGAAAA--T 1950
                             i   v  iv    iv        -----------   v     -- 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_125777965_   1951 AGATAAGTTGCAGTAACTCAAAATTAAAACTTTCTAAAAATCAGAAGACA 2000
                               i   v v vvv            vi  i ivivv   i i    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_125777965_   2001 C----AACAGATTGAAAAG-CAACCTGTCAAATGGGAGAAAATATTTGCA 2045
                          ----  v i v       -     iiivi                    
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_125777965_   2046 ACT-ATATACCTGATAAGGGGTTAATATT----GCATATAAAGTACTTCT 2090
                          v -     i          ii vi   i----ii        v   ii 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_125777965_   2091 ATGTAGTTCATTAACAACAACAACAAT--CCTGAT--AAATATAAGCAAA 2136
                          i-- ii   v   i  v  v vv   --  ii  --   v  ii     
  L1M4_orf2#LINE/    780 AC--AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_125777965_   2137 AGACTTGAA--------------AGCAAGATATACAAATTTCCTATAAGC 2172
                         i  i     -------------- iv             vv  v      
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_125777965_   2173 ATATGAAAAGATGCTCAAGAT-AGTAATCAT 2202
                          i                v  - ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (120 / 82)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.32 (73 / 22)  


2448 21.88 4.91 4.07  chr2_125789084_125791301.rev      525  1237 (980)    L1M4_orf2#LINE/L1        1   719 (189)  

  chr2_125789084_    525 TGGAAAGTCATCTCATGTTCATAGATTGGAAGGCATCATATTATAAATGT 574
                                vi   i         i         i v v     i v  vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125789084_    575 GATGATATTGCCCCAATTGATCTGCAG-TTCCCTGTCATCCATATCAAAA 623
                          iii   i v   v         i   -   vvi iv    v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125789084_    624 AACAAGATGA-TTTCTTGAGGAGATATATATATATATGTATATGTATATA 672
                         vv v  v  v-   i   vi  i  -----------------  - i vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-----------------TG-ACAAG 132

  chr2_125789084_    673 CTGGTTCTAAAATTTATAAGAAAAT---------TTGGAATTAACAAAAT 713
                            i i        i   v i    ---------iii    viv     i
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_125789084_    714 AAACTTGAAAGAGAAGAACAA-GTTGAAGAATTTACACTTCCTAAATT-- 760
                           v       i          -    i  i i i        i  v  --
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_125789084_    761 GAGCTAACTGTAAAGACAGAGTAGTGAAGACAGTGTGGCAATGACATTAG 810
                         i i  v   ii    vi v    i v            i v  i   v  
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_125789084_    811 GGTAGACATATAGATCAATGTAATAGAACTGACAGCCCAGACGTAAACCC 860
                          i                  v       i   v  i     vi       
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_125789084_    861 TCACATTTATGGTCAATTGATTTTTAACAAGACTACCCAGACAGATAAAT 910
                         vi                      ii     iv i  v    viv v   
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_125789084_    911 GGGAATAAAATGATCTTTTCAATAATTTCTGTTAGGACAACTAGATACC- 959
                            i v i   ii         i  v vv  i i        i    ? -
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_125789084_    960 ---TTTAAAA-AATAGTGTTGGATTCCGACCTCACAACATATACAAAAAT 1005
                         --- vi    -   iiv      ii  v        v             
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_125789084_   1006 TAACTGAAAATAGATCAAAGAC--AAATGTATAAGCTAAAACTATAACAC 1053
                              v     i     ?    --       vi              v  
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_125789084_   1054 TCTTACAAGAAAACCTAGACCTAAATATTTGTGACCTTAAATTAGGCATT 1103
                              v        v   i?v     v  i        iii       v 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_125789084_   1104 GA---CTTAAGCA-GAGTTTCTCAAAATACAAGCAAAAAATGATAAAATA 1149
                          i---    iii -  --iv iv   ii        v   v  v      
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_125789084_   1150 ----AACTGCATATCATCAAAATT-----TTTTTTATGTGTGTGTTTCAA 1190
                         ----  i  v iv           -----i    -------   i     
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTT-------GTGCTTCAA 673

  chr2_125789084_   1191 AGGACACCATCAATGCAACTAAAAA-ATAACACTAAAGAATGGAAAAA 1237
                                i     - v  v i    - i   - i v       i i  
  L1M4_orf2#LINE/    674 AGGACACTATCAA-GAAAGTGAAAAGACAAC-CCACAGAATGGGAGAA 719

Transitions / transversions = 1.39 (89 / 64)
Gap_init rate = 0.03 (19 / 719), avg. gap size = 3.37 (64 / 19)  

 468 21.90 10.48 2.86  chr2_125789084_125791301.rev     1516  1725 (492)    L1M4_orf2#LINE/L1      683   908 (0)  

  chr2_125789084_   1516 TCAAAAAAATAAAATAAAATAA---A-ATAATGAAAAAAAATACATTGAA 1561
                             i   i i   -- i i  --- - v    ii i      i-   v 
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAA--AGACAACCCACAGAATGGGAGAAAATAT-TTGCA 729

  chr2_125789084_   1562 AACCA------------GGGACTCACCTCTTGGATATGTAAAGAATTTTT 1599
                           i  ------------      iiiv  iv i    i       i i  
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_125789084_   1600 ACAACTCAATAATAAAA-TCCAAATAATCCACTCATTTAA---TGGCCAA 1645
                                          -vv       i   ---   ?  ---   v   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCA---ATTWAAAAATGGGCAA 826

  chr2_125789084_   1646 -GTAATTAAGTAGATGTTTTTTCAAAAAAAAAATGCAAATGAA-AATAAG 1693
                         - v v  i i    ii   i i    i  i v  i      iv-      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_125789084_   1694 CAAATGAATTGATAGTCAACATCATTAGCCAC 1725
                           v     vv   iv         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (30 / 15)
Gap_init rate = 0.04 (10 / 226), avg. gap size = 2.80 (28 / 10)  


2723 26.45 2.60 0.37  chr2_125809472_125813564     2793  3601 (492)    L1M4_orf2#LINE/L1       82   908 (0)  

  chr2_125809472_   2793 AATGCAATTCCTATGAAAATACCAATGACATTATTCACAGAAATAGA--A 2840
                           i     i     v     v   iivi v  v  ii       v  -- 
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

  chr2_125809472_   2841 AC--ATTTTTAAATTTATATGGAACCACAAAAGACCCAAAATAGCCAAAA 2888
                         i --  ii v     i        vii   ii      i           
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr2_125809472_   2889 CTATCCTGAGCAGAAAGAACAAAACTGAAGGAATAACATTACCTTACTTC 2938
                          v   i   iv ii         ii  i    v v   i v  iv i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_125809472_   2939 AAATTGTACTACAGAATTATAGTAACCAAAACGGCATGTTAATTGAATAA 2988
                            viv       i ii  i     i   i  i ii  v  v v v    
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_125809472_   2989 AAACAGTTATCTAGACCAATAGAACAGAATAGAGAACCCAGAAAAATATT 3038
                         ii i  vi  v    i    i   i     v    ii       v v ii
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_125809472_   3039 CAGACACCTACAGCGAACTCATCCTTGACAACGATGTAACAAACATACAC 3088
                           v   ii  ii iv  i v  ii i     v i  iv vi v   v  v
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_125809472_   3089 TGGGTAAA----AGTCTATCCAATAAATGGTGCTGAGAAAACTGGATATT 3134
                             v   ----     v i   i           i  v         ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_125809472_   3135 TATATGCAGAAGTCTGAAACTAGACCCATATCTCTCACCATATACAAACA 3184
                         i i     i   vv    ii i     v  i   v             v 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_125809472_   3185 TCAAATCAAAATGGATGAAATACTTAAATTTAAGACTTCAAGCTAGAAAA 3234
                          i  v           v ? v  i     v     vi v  i   v    
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_125809472_   3235 CTACTACAAGAAAACATTGGGGAAACTCTCCAGGACTTTAGTCTGGGCAA 3284
                           vi  v          v  ? v  v   i iv   i  i vi i     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_125809472_   3285 AGATTTCCT------GAGCCCCAAATCACAGGCAACCAAAGCAAAAACAG 3328
                         v i    i ------  vv  v   v    i     v    v     i  
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_125809472_   3329 AAAAAATGTGATCACATCAAG-TTAAAACACTTTTG-----CAAGATAAA 3372
                          v   v  -  iiv      i-      -       -----   iiv v 
  L1M4_orf2#LINE/    632 ATAAATTG-GACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACA 679

  chr2_125809472_   3373 TAATCAACAAAGTGAAGAGACAACCCACAGAATGGGAGGAAATACTTGCC 3422
                         iv     v        i                     i     i    v
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_125809472_   3423 AAGTATCCAACCAACAAGGGATTAATAACCAGAATATATAAAGCACTCAA 3472
                           vi  vi v ii i      i vi  v               v    vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_125809472_   3473 ACAACTTGATAGGAAAAAAAATTAATAATCTGACTTAAAA-TGGGTAGAA 3521
                               ii   iv     i -iv     i ii i ?    -    i i i
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_125809472_   3522 GATCTGAATAGACATTGCTCAAAAGAAGACATAGAAATGGCAAACACGTA 3571
                            i            v   v        i   v       v  i v i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_125809472_   3572 TATGTAAAGGTGCTCGGTGTCACCAATCAT 3601
                         i   v    i     iiii   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (123 / 87)
Gap_init rate = 0.01 (10 / 827), avg. gap size = 2.40 (24 / 10)  

 471 23.91 8.15 3.26  chr2_125809472_125813564     3830  4013 (80)    L1M4_orf2#LINE/L1       15   207 (701)  

  chr2_125809472_   3830 ATATGTATAAATCAGAAGATTTAATATTTTTAATCAGTT--CAGT-CTTC 3876
                           i vi  ii  ii     i        v    --- v --  i -  i 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAA---GATGGCAATACTCC 61

  chr2_125809472_   3877 TCAAATTGATCTACAGAGTTAATGCAATTCCAATTAAAAATTTAAGTCAA 3926
                         i                v i  i     i  v  i    - iiv  iii-
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCCAGCTG- 109

  chr2_125809472_   3927 ATCTTCATT--AGAAATTGAC---CC-ATC-TAAAATATATATGGAAGTA 3969
                         -i   iv  --          --- i-   -      vi        i i
  L1M4_orf2#LINE/    110 -CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_125809472_   3970 AAAGAGATTTAGTATAGCAAAAATGATTT-----AAAAAGAACAAAGTT 4013
                         v   i  iii  v     v    ii  i -----  i            
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

Transitions / transversions = 3.00 (33 / 11)
Gap_init rate = 0.05 (10 / 193), avg. gap size = 2.10 (21 / 10)  


1052 27.11 5.21 6.13  chr2_125817639_125819269      487  1139 (492)    L1M4_orf2#LINE/L1      262   908 (0)  

  chr2_125817639_    487 ACAATCATGTTACTG-TAAAGGGACAGACAAATAGGTTATTGGAA-AAAA 534
                            i -i  v     -i v i   i     v    i i v     - i  
  L1M4_orf2#LINE/    262 ACAGT-GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_125817639_    535 CTGAAGAACCAGAAAGAG---CATATCGTAGATA-TCA-CTGATATTTTA 579
                         i   iiiv       v i---    - i vv  i-   -i    v  iv 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATA-CATTTATGGTCAATTGATTTTCGA 359

  chr2_125817639_    580 CA--GATGT---GACCA----ATGAAAAGA-AATAAT---TTCATCAAAT 616
                           -- i  i---     ----   iii i -    i ---    v     
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_125817639_    617 GATGCTGGAACAACTGCATATTTATAAGAAAAATATTAATGTTT-ACCAA 665
                          i      i       v   ?ii i v v    v v i v   v-   vv
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_125817639_    666 TGTTTCCTACTATACACAAAAA--AACTAGTCGAGGAAGGATGATACACG 713
                          iii  vi  i   i       --    --- i i- v    v ? v  v
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACT---CAAA-ATGGATCAWAGACC 505

  chr2_125817639_    714 TAAATATCAAAGCTTTAAATGTAAAGCCTTTAGG-TAAAGCGTAGGAGTA 762
                              i v i    vv  v i    i ii    i-v   i i    ?   
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_125817639_    763 TACCATCATGACCCTAGAGTGTGCAGTGATAGCTTAAATAAGACACAAAT 812
                         v i v  i     i i iv iv   i  i vv    i   v     v  v
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_125817639_    813 AATGTTAATGAAATAAGAGAAAAAA-AGATAAATTTTACTTTATCAACAG 861
                          iiii-  - v  i  i        -         vv    i     v v
  L1M4_orf2#LINE/    606 AGCAC-AA-GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_125817639_    862 TAAGTGCATCCTCTTAT----CAAAAAACA-TGTTAAGAAACCAGAAAAA 906
                            ---- vv  i  i ----    ii   - i i      viii   i 
  L1M4_orf2#LINE/    654 TAA----AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_125817639_    907 CAAACCACAGGCTGGG-GAAAATACATTCAATGCATTTATATAATAAAAT 955
                            v      iv    -       iv v   vv   v   v i    iiv
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_125817639_    956 ATTTATATCTAAGTTATCTGAAGAATCTCTGCTAATTTATATATAATAGA 1005
                          i  i    i iiv   v i     -    vvi  i i ---      --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCA---ATAATA-- 793

  chr2_125817639_   1006 TATAAAACTAGTAAATGCATGACTTGGAAAACAGTTCAATATTTAAAATG 1055
                         ---    -------------   -----   i iii    - ?v      
  L1M4_orf2#LINE/    794 ---AAAA-------------GAC-----AAATAACCCAAT-TWAAAAATG 821

  chr2_125817639_   1056 AGCAAAG--TTTGAACACACATTTTATAATAGAAGAAATGTGAATGACTA 1103
                         i      --      i v      iviv v      v  iii    i i 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_125817639_   1104 TTATTCCCATGAAAAG-TGCTTGATATCATTAAGCAT 1139
                         v  vv v         -    ii i    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (103 / 70)
Gap_init rate = 0.05 (32 / 647), avg. gap size = 2.31 (74 / 32)  


3107 26.87 1.67 0.45  chr2_125831278_125837058     4393  5289 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125831278_   4393 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4442
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125831278_   4443 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4492
                            v     v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125831278_   4493 TCCCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 4541
                              iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_125831278_   4542 ATGGAACCAAAAAAAAGCCCACATTGCCAAGTGCATCCTAAGCCAAAAGA 4591
                               viiv  iii v  viv  v     ivvv   i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_125831278_   4592 ACAAAGCTGGAGGCATCATGCTACTTGACTTCAAATTATACTACAAGGCT 4641
                               i      vv   ii  v iii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_125831278_   4642 ACAGTAACTAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 4691
                                ii  i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_125831278_   4692 TTGGAACAGAAC--AGAGCCCTCAGAAATAAGACCACACATCTACAACTA 4739
                         v     i    i--    i  --        iv   i    i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_125831278_   4740 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 4789
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_125831278_   4790 TATTTAACAAATGGTGCTGGGA-AA----------ACATGTAGAAAGCTG 4828
                          v  i                 -  ----------     i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_125831278_   4829 AAACTAGAACCCTTCCTTACACCTTATACAAAAATTATTTCAAGATGGAT 4878
                           ii i  v    v   i     v             vi    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_125831278_   4879 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4928
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_125831278_   4929 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGATTTCATGTCTAA 4977
                             ?i- v i -   iv   v v  vv i     v i    v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_125831278_   4978 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5027
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_125831278_   5028 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5077
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_125831278_   5078 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5127
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_125831278_   5128 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5177
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_125831278_   5178 ACACAAACAACCCCATCGACAAGTGGGCAAAGGATATGAATAGACACTTC 5227
                          v     i     v  i? v  i            v          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_125831278_   5228 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5277
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_125831278_   5278 GTCACTGGCCAT 5289
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  


1401 26.53 11.16 2.99  chr2_125936440_125938368      703  1437 (492)    L1M4_orf2#LINE/L1      114   908 (0)  

  chr2_125936440_    703 TTTTGATGGTAATTAACAAGGCAATTCTAAAATTCATAGGAAAATACAAA 752
                              -ii v    i     vii  i            v i    i   i
  L1M4_orf2#LINE/    114 TTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_125936440_    753 GAACATAGAATAGGGAAAGCAATGT-AAACAAAAAGAATACATTTAGGAA 801
                          i  vi       vv   i    v -i  v  i     i v v  -   i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT-GGAG 211

  chr2_125936440_    802 GCCTCGTACCAGCTGATTACAAGACTTATTACAAAGTTATAGCAATGAAG 851
                          v   ii  ivv ii   v   i     i       i  i  i   v   
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_125936440_    852 ACAAGGTGGTA-TAATATAAGGATAGAAATAAAGCTTAGTGGAACACAGT 900
                            iv      - iii           v   v  v i i     i v i 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_125936440_    901 AGGGAGTTCCCAAACAGACT--TACACTGA-GGCCAATTTACTTTCAACA 947
                         v i    i vv   i i  i--    i v -  i     v i    i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_125936440_    948 AATGTGCCAAGATAAATAAATGGGGATAGAA-AGTCTTTTCAACATCTGA 996
                          iv         iv v v        v    -             vv  i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_125936440_    997 TACTGA-ACAACTAAATAAATGTATGGAAAATAATGAACCTTAACATTTT 1045
                          i   i-      ii   ?viii   v    v      vi vi  vii v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_125936440_   1046 CTTCACATCATTCTCAAATGTAATCTGAGAA-GGATTGTAAGTCTACATG 1094
                          i     i   viv    vi v v  v i  -    ii? iii   v   
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_125936440_   1095 TAAAAATTGAAGTTGTAAACATTCT-ACTGTAAAATAT-TGTGAAATATA 1142
                            i ii i  ii i    - i   - vviv    i  -v ? v  -  v
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAA-ATC 559

  chr2_125936440_   1143 TTTATGACTTTGGATT-GACAAATATTT-TGAGA------ACCAATTGAA 1184
                           ii    i    i  - i   vvi   - v   ------     ---- 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA----A 605

  chr2_125936440_   1185 AATAACCTTGTCATATAAGAAAAGAAATAATAAATAAA----ATCTTATC 1230
                          ii -------  vii  v        v    i     ---- ii i   
  L1M4_orf2#LINE/    606 AGCA-------CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_125936440_   1231 AAAA-------------------AAAG-----TATTAA------------ 1244
                             -------------------    -----   i  ------------
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_125936440_   1245 --AACCCA----AT-----AAATTATTGGTAATGCATACATCTGATAA-- 1281
                         --      ----  -----   v    v i  vv    i         --
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_125936440_   1282 --CTTATACTCAAAATATATGAAACAAAAACTCTTACAAGTCAACAATGT 1329
                         --   i  ii  i       i  i----           v    i   iv
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAG----AACTCTTACAACTCAATAATAA 794

  chr2_125936440_   1330 AA---CAACTAACCCCCAAAT--AAAAATGGTGAAAAGACTAAAACAGAC 1374
                           ---   v      ---   --        vv   i  i vi  i    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCC---AATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_125936440_   1375 ATTTTAGAATAAAAAGTGTAAGAATTG--AA--AGACCTTAAAAAGATGT 1420
                             ivvv v i  ii i  vi   v --  --  vv v i        i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_125936440_   1421 TTAACATCATTAGTATT 1437
                          i       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (115 / 77)
Gap_init rate = 0.04 (31 / 795), avg. gap size = 3.35 (104 / 31)  


2394 27.33 1.30 2.82  chr2_125954924_125959514.rev     1331  2252 (2339)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125954924_   1331 TGGATACACATCCCATGCTCAAGAATGGGTAGAATCAATATTGTGAAAAT 1380
                             v v i        i   v i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125954924_   1381 GACGATACTGCCAAAAGCAACCTACAAACTCAATGCAATTCTCATCAAAA 1430
                          i i     v  v   vii i     i i    i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125954924_   1431 TACCACCATCATTCTTCACAAGACTAGAAAAAAACAATCCTAAAGTTCAT 1480
                          v   v vv v  i  ii  ii v v  v  iv-ii        i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_125954924_   1481 ATGGTACCAAA-AAAAAAGAGCCTGATTGAAGCAAAAACAAACAAACAAA 1529
                             ----   -iv  ii  v  v  v --   v       v vvi-   
  L1M4_orf2#LINE/    150 ATGG----AAATGCAAGGGACCCAGAAT--AGCCAAAACAATCTTG-AAA 192

  chr2_125954924_   1530 AACTAACCAAAAAACAAATATGAGAGCA-TCACATTACCTGACTTAAAAG 1578
                           ------i  i      -i vi   v -     i v  ii i  v   i
  L1M4_orf2#LINE/    193 AA------GAAGAACAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_125954924_   1579 TATAATATAAGACCACAGTCACCAAAACAGCATGGTACTGGTATAAAAAT 1628
                         iv  v  i  ii i     v i   i    ii         i    ii  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_125954924_   1629 AGGCACATAGACCAATGGAACAGAATACAAAACCCAGAAATAAACCTAAA 1678
                           i  i     i        i     vv i ii             i v 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_125954924_   1679 TACTTACAGTCGATTGAGCTTTGACAAAGCAAACAAAAACATAAAGTGGG 1728
                         i i   ii   i     vi  i     i vviv   i v   vv i    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_125954924_   1729 GAAAGGACTCCCTATTCAACAAAAGGTGCTGGGATAATTGGCAAGCCAAA 1778
                              i ivvi  v         v          i  i   vv ?   --
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA-- 433

  chr2_125954924_   1779 CGTAATGTAGGGGAAAGAAACTGGATTCTCATCTCTCACCTTATACAAAA 1828
                          ---   i iii   v   ii    ii ii i   v    v         
  L1M4_orf2#LINE/    434 C---ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_125954924_   1829 ATCAACTCAAGATGGATCAAGGACTTAAATTTAAGTCCTGAAACTATAAC 1878
                           i       i        ?i   i     v    vv  i         -
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA- 529

  chr2_125954924_   1879 AATTCT-AGAAGATAACACTGAAAGAACGCTTCTAGACATTGGCTTAGGC 1927
                           i   -      v    iv i?iv  vv    vv   v    v      
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_125954924_   1928 AAAAACTTCATGACCAAGAATCCAAAAGCAAATGCAACAAAAACAAAGAT 1977
                           viii   v iivi v  vv         v v         iv   i  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_125954924_   1978 AAATAGATAAGACTTAATTAAACTACTGCACTTCTGCACAGCAAAAGGAA 2027
                          i   i  vi     v  i   v vvviv    i  ii vv    i iv 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_125954924_   2028 CAGTCA-----GCAAATAGACAAGGCACAGAGAGGGAGAAAACCTTAACA 2072
                          vi   ----- ii  v      vv      iv         iv  vi  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_125954924_   2073 ATCTACACATCTGACAAAGGATTAATATCCAGAATCTACAAGGAACTCAC 2122
                          vii i i      i  i   i vi          v  i  i      vi
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_125954924_   2123 ACAAATTAGCAAGTAAACAAATAAACAAACAATCTCATCAAAAAGTGGGC 2172
                             v ---   -   -i   v i     i  i iv  i?    i     
  L1M4_orf2#LINE/    780 ACAACT---CAA-TAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_125954924_   2173 TAATACCATGAATAGACAATTCTC-AAAAAAAA-ATACAAATGGCCAACA 2220
                         v  viviv          v     -   i  i -              i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_125954924_   2221 A--ACATCAACAAATGCTTAACATCACTAATGAT 2252
                          --    v  v i     i       ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (143 / 105)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.00 (38 / 19)  

1511 26.37 3.45 11.36  chr2_125954924_125959514.rev     3116  4101 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125954924_   3116 TGGAGAGATACATTGTGTTGACACACAGGAAAACTTAGCATAGTAAATAT 3165
                             i     iviii    v iiv iv    i     ii  v  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125954924_   3166 GGTAATTCTCCCCCAGTTGATCTACAGGTTTAGTGCAATTGCTATCAAAA 3215
                           i   v      v i           i  i ii     iv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125954924_   3216 TACCAGCAAGCTTCTTTGGAGACATGAACAAGCTTATTCTACAGTTTGTA 3265
                          v     viv   i    v   v  vi       v  i   v i  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_125954924_   3266 TG-AAAGACACAGGCCCTGTAATGGTTAGG-CAATCTTGAAAAGGAA-AA 3312
                           -   vi  vi  v  iiv   i ii ii-            i   -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_125954924_   3313 TAAAATGAGAGAAATCACTCTAGCTGAAATTAAGCCTTACTATATAGCCA 3362
                         i   i vi   i v    v  vv ii vv i  iv       i v   i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_125954924_   3363 CAGTCATCAAGGGAGAGTAGTACTAGCAAAAGCAAAGACACATTGATCAA 3412
                             v      iv  v  i     i   v   v v     i  v      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_125954924_   3413 TATAATGGAATAGAAAACTCAGAAATAGACTCACAGCAATTTGCACACGT 3462
                          iv   i    v  i iii        i  i  -----------------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCA----------------- 333

  chr2_125954924_   3463 GATTTTATATGAACTTTTTATAACAGCTTTATTGATAAATAACTTACATA 3512
                         -----  i  -------    ---- v iv      --------------
  L1M4_orf2#LINE/    334 -----TACAT-------TTAT----GGTCAATTGAT-------------- 353

  chr2_125954924_   3513 CCATAAAATTTAGCCTTTTAGGTATATAATTAGGTGTTTTCAGTAT-ATT 3561
                         ----------------   v ---- i  --i    i---  iv i-   
  L1M4_orf2#LINE/    354 ----------------TTTCG----ACAA--GGGTGC---CAAGACCATT 378

  chr2_125954924_   3562 CAGAGTATGCAGTCATCACCACTAATTATTTAGAACAACTTCTTTTTGAC 3611
                           ----   vi -----------  ------    i i--      ii  
  L1M4_orf2#LINE/    379 CA----ATGGGG-----------AA------AGAATAG--TCTTTTCAAC 405

  chr2_125954924_   3612 AAA-GGTGCATAAATAATTCAGTGGACAAACTATCACCTTTTCAAGAAAT 3660
                            -     vvii i  i ----   -----  ? vv v viv  ii   
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACT----GGA-----TAKCCACATGCAAAAGAAT 446

  chr2_125954924_   3661 CAGCCTTGATCTAAACTTCACATCTTAAACAAAAAT-AACTCAAGTTAGA 3709
                         v ivi v  i ivv  i     i v  v        -       iv i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_125954924_   3710 TCATGGACTTATATGTAAAACGGGAAACTATAACACTTTTACAG----AT 3755
                            ?i   i  v      i vvvi         v   i   v i---- i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_125954924_   3756 ATTGAGAGAAAGTATTCAGAATCTACTACTAGAAAAATATTTCTTAGAAT 3805
                           v - ? v  i v   ivi i  vvvii   iv  vvi         vv
  L1M4_orf2#LINE/    547 ATAG-GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_125954924_   3806 TAACGGCAAAAGCAGAGACAATAAAA-------TTGATAAATC-----TC 3843
                          i  iv        v ii   i    ------- v       i-----  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_125954924_   3844 ATCAAATTTTAAAACCTTTGGTCTGTGAAAGAAT-TTGACAAGAGAATGA 3892
                               v  v     i    vv  - v    i i-i iv     i i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAAGTGA 694

  chr2_125954924_   3893 AAAGACAAGT-ACAGACAAGAAAAAAAT----GCAATACCCATATTTGAC 3937
                                 vi-     vvi i i     ----    vv vi    i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_125954924_   3938 AAAGTATTAAACTTTAGAAGATATAAAAAACTC--ACAACTCAGTATTTT 3985
                           i v i vivv ii    v       i     --        i  ----
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA---- 790

  chr2_125954924_   3986 ACTAGAAAACCAAGT---TCTATTAGAAAATGATGAAAAGATATGAGCAA 4032
                          -  i   iv   i ---i v   ?i      ivv   i   v   ii i
  L1M4_orf2#LINE/    791 A-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_125954924_   4033 ATATTTTTTTGAA-AAGATTATACCATTGGCATGTAGCTACATGAAAAGT 4081
                          i    i iii  -     -    v v    vvi  ivi          v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGAT-ATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_125954924_   4082 TGTACAACATGATTGGTCAT 4101
                           iv      v ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (145 / 111)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 4.42 (146 / 33)  


2537 27.65 3.01 1.78  chr2_125973785_125976393.rev     1221  2117 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125973785_   1221 TGGGGAAACATTCCATGCTCATGAATAGGAAAAATCATCATTGTTAAAAT 1270
                            ii i i  i     i     i  v    i v i vi        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125973785_   1271 GGCCATACTACC-AAAGTCATTTATAGATTCAATGCTATTCCTATCAAAG 1319
                            v     v  -   v v  i  i        i  v  i         i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125973785_   1320 TACCAATTACATTCTTCACAGAATTAGAAAAA--AATCTCTTAAAATTCA 1367
                          v   ii i v  i  ii     v v  v  i--i   i--         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC--TAAAATTCA 148

  chr2_125973785_   1368 AATGGAACCAAAAAAAGAGCCCA-AGTAGCCAAGGCAATCCTAAGAAAAA 1416
                         v      -- viv  i ii    - i       ii     i i i   i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_125973785_   1417 AGAGCAAATCTGGAGGCATCATGTTACCTGATTTCAAACTATACTGCAAG 1466
                            i    vi      vv   iii v  ii        viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_125973785_   1467 GCTGCAGTAATCAAAAAAGCATGGTACTCGTACACAAATAGACACATACA 1516
                            i          i v  ii       v i i vii       i   v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_125973785_   1517 CCAGTGGAACAGAACAGAAAGCTCAGAAATAAAGCCACACACTTAGAACC 1566
                         i  i     i    iv  i  ii          v   i   i   viii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_125973785_   1567 ATCTGACCATCAATAAAGGTGACCAAAAC-AGGAAATGGGGAAAG----G 1611
                          vi   iiv  i i  i    -    i  - vvv           ---- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_125973785_   1612 CCTTCCTATTCAATACATGATCCTGGGATAACTGGCTAGCCATATGCAGA 1661
                         i   ----     i v   i v      i      v  ?   i     i 
  L1M4_orf2#LINE/    396 TCTT----TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_125973785_   1662 AGATTGAAACTGGACACCTTCCTTATGCCTTTTACAAAAATCAATTGAGG 1711
                            v    ii     v   v   i ii  v v         i  i v ii
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_125973785_   1712 ATGTAT--------TAAATGTAAAACCTAACACTATAAAAAAGTCTCTCA 1753
                            v  --------         i v    v         ----    i 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA----CTCTTA 537

  chr2_125973785_   1754 GAC---AACCT--GTGAAATACCATTCTGGACATAGGCCCTGGAAAAGAC 1798
                           v---   v -- ? v  - i -   vv   v v  viiv  v  v ii
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_125973785_   1799 TTCATGACAAAGATGCCAAAAGAATT-GCGATGAACGTTAAAATTTACAA 1847
                            v iivv v  ii       v iv-  i ii  v vv     vv i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_125973785_   1848 ATGAGACCTAATTAAACCAAAGAGCTTCTGTACAGCAATAGAAACTATAA 1897
                           vi   i v  i   viv  i i   i   i vv   vi  v     v 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_125973785_   1898 TCAGAGTAAGCAGACAACCTACAGAATGGGAGTAAATATTTGCAAACTAT 1947
                         vv i   i iv        i            v             ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_125973785_   1948 ACATCTGACAAAAATCTAATATAAAGAATCTATAACAAACTAA-ACAAAT 1996
                          i      i  iiiv  vi   vv     v     vi    vv-    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_125973785_   1997 TAACCAGTACAAAT-TAAACAACCCAATTAAAAAGTGGGCAAAGGACATG 2045
                         i  i- i  v   v-i   i         ?    i           iv  
  L1M4_orf2#LINE/    786 CAAT-AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_125973785_   2046 AATAGGCCCTTC--AAAAGAAGACATACATGCAGCTAAGAAGCTTATCAA 2093
                              i vi   --v        i     viii  i  v    vi  v  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_125973785_   2094 AAAATGCTCAGTATTACTAATCAT 2117
                           i       ii  i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.15 (43 / 20)  


1716 25.67 0.41 0.21  chr2_125976394_125981306.rev      599  1085 (3828)    L1M4_orf2#LINE/L1      421   908 (0)  

  chr2_125976394_    599 AACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACC 648
                               v  ?   i   i i  iiv    ii    i    v   i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_125976394_    649 TTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACATTAGACCTA 698
                         v              i    i      i ?    i    ii v   v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_125976394_    699 AAACCATAAAAACCCTAGAAGAAAACCTAGGCA-AAACCATTCAGGACAT 747
                             i      vi i           v    ?i-   i -   iv   v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT 569

  chr2_125976394_    748 AGACATGGGCAAGGACTTCATATCTAAAACACCAAAAGCAACAGCAACAA 797
                         v ivv i     v ii   v  vv  vi            vv        
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_125976394_    798 AAGCCAAAATTGACAAATGGGATCTAATTAAACTAAATAGCTTCTTTACA 847
                            vv     v  i    v   ii v  i   v v  v i   i v i v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_125976394_    848 GCAAAATATACTATCATCAGAGTGAATAGGCAACCTACAGAAAGGGAGAA 897
                         v    iv i       vv i      v  i     i      v       
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_125976394_    898 CATTTTTGCATTCTATCCTTCTGACCAAGGGCTAATATCCAGAATCTACA 947
                         v  v      vvii  viv     iv i  i  vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_125976394_    948 AAGAACTCAAACAAATTTACAAGAAAAAAA-AAACAACCCCATCAACAAG 996
                                 vv    v iv i  v     i -   i     v  i? v  i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_125976394_    997 TGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATGTATGCAGC 1046
                                     v    i     i     v        i  ii viii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_125976394_   1047 CAACAGACAAATGAAAAAATGCTCATCATCACTGGTCAT 1085
                            i ii  v       i       v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (64 / 57)
Gap_init rate = 0.01 (3 / 488), avg. gap size = 1.00 (3 / 3)  

2779 29.54 1.45 0.22  chr2_125976394_125981306.rev     3532  4428 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125976394_   3532 TAGATAGATATTCCATGTTTACAGATCAAAAGAATTAATATTATAAAAAT 3581
                          i  v      i       i ii   iii    v        i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125976394_   3582 GTCCATACTACCTAAAGTAATCTACAGATTCAATGCAATCCCTGTCAAAA 3631
                          v v     v  i   v i              i         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125976394_   3632 TACCAAGGACATCATTCACACAAGTAGGTAAA--------ACAATCCATG 3673
                          v   ivvi v iv  ii  v  i v ii  i-------- v   i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_125976394_   3674 TGAAATCACAGAAGACCCAGAATGGCCAAAGCTACCCTAAGCAA-ATGAT 3722
                           i  vii  iii          i      i v i i i iv  - v  v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_125976394_   3723 CAAAACTGAAGGAATCACATTACTTAAATTCAAATCATACCTCAGAACTG 3772
                             ii  i    v     i v ii  v      v v   iv  i i  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_125976394_   3773 CAGTAAACCAAATAGCATGATACTGGGATTAAAGCAGACACATAGACCAG 3822
                               v v i i  ii  i      v  v iiii     i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_125976394_   3823 TGGAACAGCATCAAGGACTGAGAAAAAAGCCCACACGCCTACAGTGAACT 3872
                              i  v  ii  iiiiv     v  i    i  iii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_125976394_   3873 CGTTTTCACCACAGTTTTCAAGAACATACACTGGAGGAAAAGACAGTCTC 3922
                         vi     iv  vi v vi     v   v  v   -     ii i     i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTT 399

  chr2_125976394_   3923 TTTAATAAATGGTGCTGAGATAACTGGATATCCATATGTAAAATAATAAG 3972
                           i  i           i  i         ?   i   i    v   i i
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_125976394_   3973 TTTAGACCCCTATATCTCACCATATATAAAAATCAAACCAAAATGTATTG 4022
                         v  i        iv  v         i      i  vi       v  ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_125976394_   4023 AAGACTTAAATCTAAAACCTTAAATTATGAAATTACTACAAGAAAACATT 4072
                         ?    i     v   i v  v   i   i   i vi  v          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_125976394_   4073 GGAGAACATCTTCAGGATATCGCCTT-GGCAAAAATTTCTTGAGCAGTGT 4121
                           ? v v      iv  iv i vv  -     vii      iiii -  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGA 598

  chr2_125976394_   4122 CCCCCACA-CACAGTCAACCAAGGAAAAAGTGCATAAATGGGATCACATC 4170
                          v  v v -    iv    v  i      i iv      v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_125976394_   4171 AAGTTAAAAAACTTCTGCACAGCAATGGAAACAATGAACAAAGCTAAGAG 4220
                           iv v        i  ii vv   v   v  v  v  v    iv  i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_125976394_   4221 ACAGCCCACAGGATAAGAGAAAATATTTTCAAACTGCCCAGCTGAAAAAG 4270
                            i       i  ii            v    iiiivi v    v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_125976394_   4271 GATTAATATCCAGAGTACATAAGGAGCTCAAACAACTCTACAGGAAAAAT 4320
                           i vi        i  i    i  i   vv       v i iv     v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_125976394_   4321 TCTGATAATACAATC-AAAAATGGACAAAACATGTAAACAGATATTTTTC 4369
                         v vi    iv    i-        i    iv  v i  i   i    i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_125976394_   4370 CAAATAAAGCATATAAGTGACAAGGATACCAATGAAAAGGTGCTTAA-AT 4418
                             v  iii   i  i  i v iv vi vv        i    i  -  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_125976394_   4419 CAGTACTACC 4428
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.59 (161 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


2244 25.18 2.83 7.56  chr2_125990208_125997714     4333  5285 (2222)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_125990208_   4333 TGGAAACAGATTCCATGCTTAAGGATTAGAAAAATCAATATTGTTAAAAT 4382
                               v v  i     i i v     i   i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_125990208_   4383 ATCCACACTGCC-AAAGTAATCTACAGATTCAACACTATTCCTATTCAAT 4431
                         iv v i   v  -   v i               i v  i     iv  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_125990208_   4432 TTCCAA-TGTAATTCTTCACTTAATTAAACAAAAT-ATTCTAAAATTTGT 4479
                          i   i-  iv-  i  ii vv  v vi    iv -  i        ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_125990208_   4480 ATGAAACCAAAACAAGAGTCT--GGATAACCAAAA-AACCT-AAGCAAAA 4525
                            i  --- vi    i v i-- i   i      -  i  -i iv  i 
  L1M4_orf2#LINE/    150 ATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_125990208_   4526 AGAACAAAGCTGGATACATCACACTACCCTACTTTAAACTATACTACAAG 4575
                                  i    vivv       v   v i  i   viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_125990208_   4576 GCTACAGTAACCAATAAAGCATTGTACTGATTAAAAAAAAAAGAAAGAGA 4625
                                   i   v v  ii v      ---------------------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTG--------------------- 275

  chr2_125990208_   4626 AAGAAAGAAAGAAAGAAAAAAGAAAAAGAAAAAGGAAAGATAAAAGAAAA 4675
                         --------------------------- v v     v   ----------
  L1M4_orf2#LINE/    276 ---------------------------GCATAAGGATAGA---------- 288

  chr2_125990208_   4676 TGTCACATGGATCAATGAAACAGAAT--AGAG---------AAAGCTGCA 4714
                         ---  i  i        i  i     --    ---------   v iii 
  L1M4_orf2#LINE/    289 ---CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_125990208_   4715 AAGCTACAACCAACTGATCTTCAACAAAGTTGACAAAAATGAACATTGGA 4764
                         v vi  iiii   i    i   i    i v  v   i viivv  v   i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_125990208_   4765 GGAAGAAAACCCTAACCGATAAATGGTGCTGAGAAAA-TGGCTATACATA 4813
                          i     v vi  vvi i i           i  v  -   v  ?v  i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_125990208_   4814 TGCAAAAGAATAAAACTGGGTGGGCACCTCTCATCATATA-AAAAATTTA 4862
                                    i  ii   iivvvi     v  i      -       v 
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_125990208_   4863 CTCAAGGTGGATTAAATACTTAA-TTTAAGATCTCAATCTGTAAAATGCC 4911
                              ii     i ? v  i   - v     v  v  v  i     iv i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_125990208_   4912 TAGAATAAAACCTAGG---AAATACCCTTCTATACATTGGCCTAGGCAAA 4958
                              v     v    ---    ---    vvv  v    vi       -
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA- 581

  chr2_125990208_   4959 TAATTTAT--GAC-TAAGTCCACAAATGCAAATCCAACAAAAAACAAAAA 5005
                          ii   v --  i- i vv   v  iii   i--        i -     
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAG--CAACAAAAGA-AAAAA 628

  chr2_125990208_   5006 TTGACAAGTGGGACCTAATTAAACTAAAGAGCTTCTGCATGGCGAGAGAA 5055
                          v  i  i v    i v  i   v v  i i   i  iiivv i ii  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_125990208_   5056 ACTACCAACAGAGTAAACACACAAGCTACATAATGAGAGAAAATATTTGC 5105
                             i   v i   i  v v    v i   v    i              
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_125990208_   5106 AAATCATGCATCTAACAAAGGTCTAATATTCAAAATCTGTAAAGAACTTA 5155
                                ii    i i  i  v  vi   i  i   v i         iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_125990208_   5156 AACAGATCAACAAGGAAACAACAAATAACCCCACTAAAATGTGGGCAAAA 5205
                         v   iv    i  vi   vi           v i ?   vi        i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_125990208_   5206 GGTATGAATACACATTTCTCAAAAGAAGACATACAAGCAGCCAATAAACA 5255
                          i v      v         v        i      iii        i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_125990208_   5256 TATGAAAAAACATTCAACATCATTAATGAT 5285
                         i       i iii         ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.50 (99 / 22)  

2785 19.92 7.73 3.15  chr2_125990208_125997714     6254  7016 (491)    L1M4_orf2#LINE/L1      111   908 (0)  

  chr2_125990208_   6254 CTTCTTTGCAAAAATTGAGAAGATAGTCCTAAAATTCATATGGAAATTCA 6303
                            i      i       v   v ii                     v  
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_125990208_   6304 AAGGACTATGAATATTCAAAATAATCTTGAA------GAACAAATTTGAA 6347
                          i    ivv     vi     i         ------       v   i 
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_125990208_   6348 AGATTCATACTTCCTAATTTGAAAAATTACTGCAAAACTACATTAATCAA 6397
                         i  i   i      i     v    v     i    i     v       
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_125990208_   6398 TACAGTGTGGTACGGTCCTAACAATA--CATGTAAACCAATGGAATCAAG 6445
                         v            v v v   vi   --   i  i i         vi i
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_125990208_   6446 TTGAAAGTTCAGAAATAAATCTTCACATT-ATATCTAATTAATTTTC--- 6491
                             i   i          i ivi     -  ivii    i      ---
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_125990208_   6492 -----TACT---------------GGATAGAATAGTAGCTTCAATAAATA 6521
                         ----- i i---------------   v        vvi     i    i
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_125990208_   6522 GTAATAAAGTGACTAAACAGCCACATG-AAAATAAT--AGTGTGTACCTC 6568
                           iv iiiiii   ii i ?       -    v   --   -  v   i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT-TGGACCCC 459

  chr2_125990208_   6569 TACCTTATACCATATGTCAGAATTAACCCAAAGTAAATGAAAAGCCTAAA 6618
                              i i       iiv i       i    i ii  v ? ii      
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_125990208_   6619 TGTAAAAGCTCAATCTATAAAA---TTAAAAGAAAAAAAACCTAGGCACA 6665
                              i    v  v        ---   i       ---- v    ?ii 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA----CATAGGNGTA 555

  chr2_125990208_   6666 A-TCTTTATGACCCTG------------------TAAATGCAACACAAAA 6696
                          -    ii     i  ------------------  i  iii    v   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_125990208_   6697 AGCAAAAGCAACAAAAGAGAAAAAATAGACAAATTGAACATCACCAAAAT 6746
                             v             --         i      i  v   i      
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGA--AAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_125990208_   6747 TAAAAACTATTGTGCTTTGATGGACCTCATCCATAAAGGACCTCATCAAT 6796
                                 v        i----------------       vii     v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTC----------------AAAGGACACTATCAAG 687

  chr2_125990208_   6797 AAAGTGACAACATAAGCCACACCGTGACAGAAAATACTTACACATCATAT 6846
                                v  v i  v     vvi  iv        i  i  v       
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_125990208_   6847 ACCTGATAAGGGACTTATATCTAGAAAATATGCACAACTATTAAAACTCA 6896
                          i              i    i    v    iv v    v   v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_125990208_   6897 ATAGTAAAAAGACAA-TAACCCAATTTAAAAATTTACAAAAGATTAGAAG 6945
                            i           -          ?      vvi    i    v   v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_125990208_   6946 AAATATTTTTTCAGAAGAAAAT-CACAAATGTGCAATGAGCACATGAAAA 6994
                          i i    i i  -     i  -i       vv    i            
  L1M4_orf2#LINE/    838 AGACATTTCTCCA-AAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_125990208_   6995 GATGCTCCACATCGCTAGCCAT 7016
                                v     i????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (94 / 54)
Gap_init rate = 0.02 (17 / 798), avg. gap size = 4.88 (83 / 17)  


2061 30.81 3.73 0.60  chr2_126019356_126025581     4904  5734 (492)    L1M4_orf2#LINE/L1       52   908 (0)  

  chr2_126019356_   4904 GCCATACTGTCCAAAGCAATTTATAAATTCAATGCCGTTC------AAAT 4947
                           v     vi     vii  i  i i      i  vi i ------    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_126019356_   4948 GTCA------TTTTTCACAGAAATAAAAAAAGT-ATTTCAAAATTCATGT 4990
                         vi  ------     ii       vi v  iv -  iii         i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_126019356_   4991 AGAACCAAAAAAGAGCTGCAATCACCAATACAACCCTAAGCAAAAACAGC 5040
                         i   viiv  ii  v iiv   vi    v    i i i iv  i  v i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_126019356_   5041 AAAGCCAGAGGCATTGCACTATCTGGCTTCAAACTACACTACAAGGTTAC 5090
                             iii    vv ii    vi iiii      vivi       i i   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_126019356_   5091 AGTAACCAAAAAAACATGGTACTC-TACCAAAACAGACATACAGATCAAT 5139
                              i   i v iii       v-i iv ii i       i        
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_126019356_   5140 TAAA-AGAATAGAGAACCCAAAAGTAAAGCTACACCCTTACAATCATCTA 5188
                         vi  -     v    ii   i  i    v i i  vi   iii   vi i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_126019356_   5189 ATTTTCAACAAACCTGA-AAGTAACAAACAACACAAAAAGGACCCCCTAT 5237
                               i    ivv  v-   - v  vv   iivii    i ivvi  v 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_126019356_   5238 TCAATAAATGATGCTGAGATAACTGGCTGACCATATGCCAAAGATTAAAA 5287
                             i     i     i  i      v i?   i    v     v i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_126019356_   5288 CTAAACCCTATCCTTTCACCATATATAAAAATTGACTCAAGATGGATGAA 5337
                         i ii    ivv   iv         i       i      i      v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_126019356_   5338 AGATTTAAATATAAGACTGAAGACAATAAAAATTCAAGAAGAAATCCTAG 5387
                            ii     i     viv  i  v      v iiv        v v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_126019356_   5388 G---AAATCATTTTG-GACTTCAGCCTTGGCAA--ATCTTTTATGACTAA 5431
                          ---     --  i -   i ii vi v     --i i i   -  -  v
  L1M4_orf2#LINE/    551 GNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GA-TAT 596

  chr2_126019356_   5432 GTCCTCAAAAGTAATTGCAGCCAAAACAAAAGTTGACAAGTGGGACCTAA 5481
                          v vi      i vvv   i v   iv    i v  i  i v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_126019356_   5482 TTAAACTAAAGAACTTCTGTACTGTAAAACAAGCTAACAGCAGAGAAAAC 5531
                          i   v v  i     i   i  vi   iv vi   v  iv i  vi  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_126019356_   5532 AGATAACCTACAGAATGGAACAAGTGATTTGCAAACTATGCCTCCAACAA 5581
                            i    i         i v  ivv         ii  iiv  ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_126019356_   5582 AGGTCTAGCATCCAGAATCTGTAAAGAACTT----AAATCAGCAAGCCAA 5627
                         i  v  v i         v i         i----  v   ii  vvv  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_126019356_   5628 AAACAA----CCCCATTAAAAAATGGGCAAAGTATATGAAGAGACGCTTC 5673
                          i    ----   v   ?              v  v    v    ii   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_126019356_   5674 TCAAAAGGAGACATACATGAGTCCAACAAATATATGAAGAAATG-TCATC 5722
                           v    i   i     viv v    i  ii i     i i   -   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_126019356_   5723 ACCATTAATCAT 5734
                          i  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (158 / 95)
Gap_init rate = 0.02 (16 / 857), avg. gap size = 2.25 (36 / 16)  


2419 26.57 1.92 5.02  chr2_126072029_126074744.rev     1288  2224 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_126072029_   1288 TAGAAAAACATCCTATACTCATGGATTAGAATAATTAATATTGTGAAAAT 1337
                          i    i i    i  ii         i   v v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126072029_   1338 TGCTATACTTCTCAAAACAATCTACAGATTCAATGCAATCCCAATCAAAA 1387
                         v  v     i i    vii              i        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126072029_   1388 CATCAACATCATTTTTCACAGAA-TTGGAAAAAAACAATCCTAAAATGTA 1436
                         ivi  i vv v     ii     -   -- v  ivii          vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_126072029_   1437 TATGGGATCAAAAAAGAGTCCCA--ATAGCAAGAGCAATC-------ATA 1477
                              i -- viv   i v    --     v i i     ------- v 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_126072029_   1478 AG--CAAAACTGGAGGCATCACATTATCTGACTTCAAATTATACTACAAG 1525
                           --    ii      vv     i vi ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_126072029_   1526 GCTGTAGTAGCCAAAACAGCATGATATTGGTGAAGAAAAAAAATTCAGAC 1575
                            ii    ii   i    ii  i  i   i----- v  ii  --    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGC-----ATAAGGAT--AGAC 289

  chr2_126072029_   1576 ACATAAATCAATATAACAGGTTAGAGAACCCAGAAGTAAAGCTACAAATT 1625
                          i   i      iv  i  iv v    ii      i    v i i v   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_126072029_   1626 TACTGCAAACTTATCTCTGACAATATCATCAAGAATATTCACTAGGGAAA 1675
                           iv iv  i v  i ii     viviii     vi     v i      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_126072029_   1676 GGACACTCTATTCAATAAATGATGCTAGGAAAATTGGATTGACATATGCA 1725
                          i i v   v     i     i    i   v  i     v?v  i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_126072029_   1726 GAAGGATACAATTGTACCGTAATCTTTCACTATATA-AAAAATCTACTCA 1774
                         i   i  iv i   v   viv i  iv   i     -      iv     
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_126072029_   1775 AGATGGAT---AAATTATTAAATATAAGACCTTAAAATATAATAATATTA 1821
                          i      --- i ii--     i     v  v   v     v v v   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACC--TAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_126072029_   1822 TAGGAAGCCTACAAAAAAACATTTCTG-GACTTTGTTTTAGGCAAATAAT 1870
                         v i   iv - i ii?iv v  i ii -   i   vv        vviv 
  L1M4_orf2#LINE/    538 GAAGAAAAC-ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_126072029_   1871 TCATGACCAAGATCTCAAAAGCACAGGAAACCAAAACAAAACTAGACAAA 1920
                           v iivi v  ivi          i v   v   iv    v    i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_126072029_   1921 TGAAACTTAATTAAACTTAAAAGCTTTTGCTAATTAAACTTAAAAGCTTT 1970
                          vii    v  i   v      i      i---------------    -
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGT---------------GCTT- 670

  chr2_126072029_   1971 TGCACAGCAAAAGAAATAATCAACAGAGTGAACAGACAACCAGCCAAATG 2020
                         -------    i  v iv     v i      v        vi vi    
  L1M4_orf2#LINE/    671 -------CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_126072029_   2021 GAAGAAAATATTTGCAAACTATGCATCAAACAGGAGATTAATATCCAGAA 2070
                          i                ii  ii   vi i i i  i vi         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_126072029_   2071 TTTATAAGGAACTCAAACAGCTCAACAACAACAATAAATAATAATAATAA 2120
                          v     i      vv   i     i  i  ----   -i i  --    
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAA----AAA-GACAA--ATAA 806

  chr2_126072029_   2121 TTCCAATAAATAGTGGGCAAAAGGCATAAAGAGACCTTTTTTTAAAAAAA 2170
                         ii v v ?  v i        i iiv i  v    v   i ii   i  -
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA- 855

  chr2_126072029_   2171 AAGACATGCAAATGACCAAAAAGCATATAAAAA-ATGCTCAACAACACTA 2219
                         --  i  i      i    v     i  i    -          v  ???
  L1M4_orf2#LINE/    856 --GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_126072029_   2220 ATAAT 2224
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.65 (153 / 93)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.25 (65 / 20)  


2774 28.48 1.10 0.88  chr2_126098900_126101086      790  1695 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_126098900_    790 TGGAAAAACCTTTGATGCTCATGGATAGGAAGAATCAATATTGGGAAAAT 839
                               i iv iiv   i        v      v i       vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126098900_    840 GGCCATACTGCTCACAGCAATTTATAGATTCAATGCTATCCCCATCAAGC 889
                            v     v i  v vii  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126098900_    890 CACCA-CTGACTTTCTTCACAGAATTTAAAAAAACT-ACTTTAAATTTCA 937
                         iv   -   v    i  -i     v  i v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_126098900_    938 TACAGAACCAAAAAAGAGCCTGTATAGCCTAGAAAATCTGAAGCAAAAAG 987
                           ii   viiv  ii  v  v v      v i v     vi iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_126098900_    988 AACAAAGGTGGAGGCATCATGCTACCTGACTTCAGACTATACTACAAGGC 1037
                                v      vv   ii  v  ii i    i viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_126098900_   1038 TACAGTAACTAAAACAGAATGGTACTGGTACCAAAACAGATATATAGACC 1087
                                 ii  i    vi         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_126098900_   1088 AATGGAACAGAACAGATGCCTCAGAAATCATGCCACACTTCTACAACTAT 1137
                                i    iv  vivii       v vv   i  v i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_126098900_   1138 CTGGTCTTTGACAAACATGACAAAAACAAGCAATGAGGAAAGGATTCCCT 1187
                         i  i i  i     ivi  v   i v  vv     i      i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_126098900_   1188 ATTGAATAAATGGTGTTGGGAAAACTGGCCAGCCATATGCAGCAAACTGA 1237
                         v  v  i        i     v      vi ?   i     iv i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_126098900_   1238 AACTGAACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 1287
                          ii  i      v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_126098900_   1288 AAGGACTTAAACTCATGATGTAAAATCATAACAACCCT-AGAAGAAAAGC 1336
                          ?i   i    ivi v  vv     ii    -   i  -         vv
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACA 547

  chr2_126098900_   1337 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAAACTTCATGACTAA 1385
                             ?i- v i -   iv   v v  vv i     viii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_126098900_   1386 AACACCAAAAGCAATTGCAAAAAAAGTCAAAATTGACAAATGGGATTGAA 1435
                         i            vvv    v     vv     v  i    v   i vv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_126098900_   1436 CTAAACTAAAGAGCTTCTTCACAGCAAAATATACTATCATCAGAGTGAAT 1485
                         ii   v v  i i   i vii vv    iv i       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_126098900_   1486 AGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTATCCTTCTGACAA 1535
                           i     i              v  v       vii  viv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_126098900_   1536 AGGGCTAATATCAAGAATCTACAAGGAACTTAAACAAATTTACAAGAAGA 1585
                         i  i  vi    v     v  i  i     ivv    v iv i  v  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_126098900_   1586 AAACAAACAACCCCATCAAAAGGTGGGCAAAGAATATGAACAGACACTTA 1635
                          i     i     v  i?   ii         i  v    i     i  v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_126098900_   1636 TCAAAAGAAGACATTTTTACA---GGCCAACAAACATTTGAAAAAAAGCT 1682
                           v        i  ----   ---      i  i  iv      i v   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATAT----ACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_126098900_   1683 CA---TCACTGGTCAT 1695
                           ---   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (143 / 111)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


2392 23.86 10.64 0.46  chr2_126109849_126112752.rev     1156  1813 (1091)    L1M4_orf2#LINE/L1        1   725 (183)  

  chr2_126109849_   1156 TGAAAAACTATCCTAAGTTCATGGCTTGAAAGATTTAACACTATTGAGAT 1205
                           i   iv     i v        v   i    i    i i i  i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126109849_   1206 AGTAATGCCCCTTGAACTGATCTACAGACTTAACTTGATCCCCATCAGAA 1255
                         i i   i i  iii  i           i i   vii     i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126109849_   1256 ACCCAGTGAGCTACTTTGTAGAAATTGACAAACTGATTTTAAAATTCATA 1305
                         v     iviv  vi    i            i     ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_126109849_   1306 TGGAATTGCAAGG-ACACAAAATCGTCAGAATAATT----AGAAAAAGAA 1350
                              v       -  v  i   v i  i  i   i---- i  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_126109849_   1351 CAATGTAGATAGACTCACATTTCTTGGATTCAAAACCT------------ 1388
                            v  v ivi        i   iiiiv        i ------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_126109849_   1389 ----------------GTGATACTGGTACAAGAGTAAA-ATGTAGATAAA 1421
                         ----------------   i      i i   ii  i -  i     v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_126109849_   1422 TGGAATATAATTGAGAATCCATAAATAAAATTATGCATCTATGATTAAAT 1471
                                v        i    v       vii  i   i    i i  v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_126109849_   1472 GATTTTTGACCAGGGTGCCAAGACTATACAATGGGGAAAGAATCAACTTT 1521
                               i   v             i  v               viv    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_126109849_   1522 -------------CTTGAA-AA---GATAGCCACATCCAGAGGAATAAAG 1554
                         -------------  v i -  ---    ?      v  i i    i   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_126109849_   1555 GTGTACTCTTATCTCACACTGTAT-TAAAAA-------AAAAAGTATCCA 1596
                         v  v  i i  i       ii   -i     -------    v v   v?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_126109849_   1597 AAACCTAAATGTAAAAACTAAAACT--------TTTAGTTAAAAACATAG 1638
                          i            i i        --------i    vvi         
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_126109849_   1639 AAGTATATATTTACGGCCCTAGATTTTTCAAAAGATTATTCAATGTAATA 1688
                         i?   v  v  iii i  i i i  vvv   vi v  v  vi  i i i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_126109849_   1689 CTAAAACCACAAGTAACATAGGAAAAAATAAATAAATTGCACTTCA--AA 1736
                          i    v      i    v i         i        v      --  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_126109849_   1737 ATTTAAAAACTTT-ATACTTAAGAGGACACTGCCAAAAAATAAATGGAAA 1785
                          v           -i i   v i        ii   i   ---i  i   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA---GTGAAAA 697

  chr2_126109849_   1786 GATAGCTCACCTAATGGGAGAAAATATT 1813
                           i i i   vv                
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATT 725

Transitions / transversions = 2.14 (105 / 49)
Gap_init rate = 0.02 (13 / 725), avg. gap size = 5.62 (73 / 13)  

 789 17.56 8.78 1.95  chr2_126109849_126112752.rev     2216  2420 (484)    L1M4_orf2#LINE/L1      690   908 (0)  

  chr2_126109849_   2216 AGTGACAAGACCAAACTCCTGGCACTTTGGCAACAATATTTGCAAATCAT 2265
                              v     --   i vii v -- v  vi v                
  L1M4_orf2#LINE/    690 AGTGAAAAGAC--AACCCACAGAA--TGGGAGAAAATATTTGCAAATCAT 735

  chr2_126109849_   2266 ATATCTGATGAGAGATTAATATCCAGAATATACAAATAACTATTAGAACC 2315
                                  i  i  i vi             i   v    v   v   i
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_126109849_   2316 CAATAATAAAAA--CA----------TTTAAAA--GAGCAAAGGATCTGA 2351
                                     --  ----------  ?    -- i         i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_126109849_   2352 ATAGATATTTTTCCAA----GACATATGAATGTTCAATAAGCGCAAGAAA 2397
                              i    i     ----  i   ii    vi        i  v    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_126109849_   2398 AGATGCTTTCCATGATTAGTTAT 2420
                                ivv   v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (20 / 15)
Gap_init rate = 0.03 (6 / 219), avg. gap size = 3.67 (22 / 6)  


3044 26.73 1.56 0.45  chr2_126148510_126152800.rev     2902  3799 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_126148510_   2902 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2951
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126148510_   2952 GACCATAATGCC-AAAGCAATCTACAAATTCAATGCAATCTCCATCAAGA 3000
                          i v   v v  -   vii       i      i      i i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126148510_   3001 TACCACCATCATTCTTCACAGAATTAGAAAAAAACTG-TTCTAAGATTCA 3049
                          v   v vv v  i  ii     v v  v  i--   - i    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_126148510_   3050 TAGAGAACCAAAAAAGAGCCTGCACAGCCAAAGCAAGACTAAGCAAAAAG 3099
                           vi   viiv  ii  v  v v i       i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_126148510_   3100 ACCAAATCTGTAGGCATCACACTACCTGATTTCAAACTACACTATAAGGC 3149
                          v    vi  v   vv       v  ii        vivi    i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_126148510_   3150 CATAGTAACAAAGATAGTGTGGTACTGGTATAAATATAAGCACATAGACC 3199
                         i i     iv    i             i    iv   ii  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_126148510_   3200 AATGGAACAGAATGGAGAATCCAGAAATAAACCCGAATACTTACAGCCAA 3249
                                i     v    i               iv i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_126148510_   3250 CTGATCTTCAACAAAGCAAAAAAAAAACATAAAGTGGGAAAAAGACACCC 3299
                         i    i   i    i -ivivv  i v   vv i    i   ii i vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_126148510_   3300 TTTTCAACCAATGGTGCTGTGATAAATGGCTAGCCACATGTAGGAGATTG 3349
                                 v          v  i  v   v  ?       i ii   v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_126148510_   3350 AAACTGGATCCTCATCCC-TGCCTTATACAAAAATCATCTCAAGATGGAT 3398
                           ii    i  ii i i -ii  v           i v     i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_126148510_   3399 TAAGGACTTAAAGCTAAGTCCTGAAACTATACAAATTCT-AGAAGATAAC 3447
                         i ?i   i    vv    vv  i        -   i   -      v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAAC 546

  chr2_126148510_   3448 ATTGGAAAAACCCTTCTAGACATTGGCTTAGTCAAGGATTTCATGATTAA 3497
                           v  ?iv  vi    vv   v    v    v   v i    v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_126148510_   3498 AAACCCAAAAGAAAATGCGATAAAAGAAAATATAAACAGCTGAGACTT-- 3545
                         i vv       v v v  i i         v   i i iv vi     --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_126148510_   3546 ----AACTAAAGAGCTTTGAATGGCAAAAGGAACAGTCAGT----TGAGA 3587
                         ----  i    i vi    viivv    i iv  vi   iv----   i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_126148510_   3588 AAACAGCCCACAGAATGGGAGAAAATCTTCACAATCTATATATCTGATAA 3637
                          i   i                    v  ii   vii             
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_126148510_   3638 AAGACTAACATCCAGAATCTACACCAAACTCAAACAAATCAGTAAGAAAA 3687
                         ii    vii         v  i vvi     vv    v   i   v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_126148510_   3688 AAATAAACAATCCTATCAAAAAGTGGGCTAAGGACATGAATAGACAATCC 3737
                          i i   i  i  v  i?    i     v     iv          v i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_126148510_   3738 TGAAAAGAAGATATGCAAATGGCCAACGAACATATGAAAAAATGCTCAAC 3787
                          vv           i           ii i  i       i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_126148510_   3788 ATCACTAATAAT 3799
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (136 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


1542 30.91 8.55 2.22  chr2_126163588_126167438     2506  3359 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_126163588_   2506 TGGAGAAATCATTTTTTGCTTA-GAATTGGACAACACAACAAAGCAAAGG 2554
                             i i  -  iiiv  i i - i      vi  vi  i vv iv   i
  L1M4_orf2#LINE/      1 TGGAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_126163588_   2555 TGGATGCCAATTCTCCTAAAACTGGT--ACAGGTTTAATGCAATTC-TAT 2601
                            ----    v    iv   i  i --    i  i  i     i -   
  L1M4_orf2#LINE/     50 TGG----CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_126163588_   2602 TAAAATTGCAACAAGATATTTTGCAGATATAGACCAACTTATTTTAAAAT 2651
                         i     iv  i vivv v         v  v   v i  v  ii      
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_126163588_   2652 TTATGTATAAAGACAAAGGAACTAAAATAGCTAGAATGATTTCGAAAATG 2701
                          i  i iv   vi   i   v i i      i i  ii  i i     v 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_126163588_   2702 AAAAATGCAATGGGAAGA-------------AT------ATTTATTGCAT 2732
                           i  iiv i v   i  -------------  ------ i   i i  v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_126163588_   2733 GGCTAGAGTAATTAAAAATATGTGCTATTGGCAAAAAGGTGTACAAATTG 2782
                         i    v      i  i vvi    v  i     v  i i iv   v  v 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_126163588_   2783 AACAGTTGAACATTAT-GAGGACCTAGAAATACACCCTTTCAAATTTGCC 2831
                          v  i v   i vv  -   iii i       v    v v  vv v  vi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_126163588_   2832 CAAGTGATTTTAGACAAAAGTACAAAAGCAATTTAATAACGGAAGTGGAG 2881
                            v       v     ii  i v  ii v   i   iiv i   viv  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_126163588_   2882 CCTTTTCAACAGGTGGTGCTGAAGTGATTCTGTAG--AC---CAAGAAAA 2926
                         i          ii        iiiii i vvi  ?--  ---   i i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_126163588_   2927 TGAACTTCTGCCTAAACATCATACTTTGTACAAAAAGTAACAAGAAATGG 2976
                             v  vvi  ivv  v   i  iv i        v    vvi      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_126163588_   2977 ATCATGGACTTAATTGTAGAATATAAAAGTGTATAACCTTTAGA-GAAAA 3025
                             ?i   i   v    ii vv     v i  v   ii     -     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_126163588_   3026 -ATAAAATAAAATGTTCAGGAATCTGAGCAAGGCAAATACTTTTTAGGCT 3074
                         -   ii?vv    v   iv  vii  i iv      vvii  i    iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_126163588_   3075 TGACAACAAAAGTGGGA----------AAAAAGTTGATGCTTTGTGTTTT 3114
                              v      iivi ----------     i v   ivv   vii  i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_126163588_   3115 ATCAAAATTAAAATTTTATCAATATTTTGCTGTGTGAAATGCTCT-AAGA 3163
                                      vi  -------  v    viiviii ii  v -    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTT-------TTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_126163588_   3164 GAATGAAAAG-----CTACACATTTGGAAAAAATATTTGCCAATCACATA 3208
                         i i       ----- i   v v v   i           v     i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_126163588_   3209 TTTG-CAAATCAC--ATATCTAACTGAAAACCAGTATCTACAATTTATAA 3255
                          i  -i  ivv  --i    i ---   v ----   vv v  i iv  v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCA---GAATA----TATAAAGAACTCTTAC 781

  chr2_126163588_   3256 AACTCAACAGTAAAAACAT------CCTGAT-AGAAAATAGGCAAACTAT 3298
                                i i      v i------  ii  -?i     i      vv  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_126163588_   3299 TC----AG---------CAAAGGGAATATG--GATCGCAGAAAAACACAT 3333
                          i----  ---------     iii    i--i  v  vi v  i     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_126163588_   3334 GAAA-TATGTTCAACATCATTAGCCAT 3359
                             -v   i         ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (154 / 106)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.54 (92 / 26)  


3538 20.00 3.53 1.29  chr2_126263166_126265007      501  1350 (492)    L1M4_orf2#LINE/L1       40   908 (0)  

  chr2_126263166_    501 ATTGT-AGAATGGCAATGATAACTAAATTAAT--ATAGACTGAAAATATT 547
                              - ii        iv vv i     i  -- i   i v  vii v 
  L1M4_orf2#LINE/     40 ATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

  chr2_126263166_    548 CCTTATCAAAATTCCAGCTTCCATTTTATACAGAAATTGACAAGCTGATC 597
                           i         i      v  v    - i                    
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATC 138

  chr2_126263166_    598 CTAAAATTCATTTGGAAATACAAGGGATGAAAAATAGACAAAACAATCCA 647
                                    v       i       ivv i     v          iv
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr2_126263166_    648 GAAAAGGAAAAACAAAGTTGGGGGACTCACACTTCTTGATTTCAAAACTT 697
                              i   i           i             iii            
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_126263166_    698 TCTACAAAGCTACAATAATCAAAACAGTACAGTGCTGGTACAAGGATAGG 747
                         v             i       i     iii  i    i i        i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_126263166_    748 TCTATAGATCAATGGAATAGAAATCAAAGTCCAGGAATAAATTCATACAA 797
                         iv                    v v i       i      ii      -
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA- 337

  chr2_126263166_    798 TCTGTGGTTGATTGATTTTCTACCAAG-TGCCAAGACTATTCAATGTGGG 846
                          i i    ii          v  v i -         i        -   
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGG 386

  chr2_126263166_    847 TATAAATAATAGTTTCATCAAATGATACTGGGACAACTCAATATCCATAT 896
                         v vi    i vv     v      i i           vi   ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_126263166_    897 AAAAAGGAAATAAGTTAGACCCCTTCCTCACATCATGCCCAAAAATTAAC 946
                         iv   i   vv     i       v       i   iiv           
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_126263166_    947 TCAAAATACATGATAAGCCAAAATGTAAAATCCCAAAATATAAAACAGTC 996
                                iv  v ? ii  v        i v iv   v        vv i
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_126263166_    997 AGAAGAAAATGTAGAAGTACATCCTCAGTATATTGGGTTAA-CATTA--T 1043
                                  ii   i?   v   i  ivv iv        i-  v i-- 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_126263166_   1044 TTTTAGATATGAC--CGAAAATAATCCAAAACAACAGAAGAAAAAAATAG 1091
                          i           -- i   ii ---   i-     i         -   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCA---CAAG-CAACAAAAGAAAAAA-TAG 631

  chr2_126263166_   1092 ATAAATTGGATTACATCAACATCAACATGTTTGCTGCATCAACCAATACC 1141
                                   i v      v  i  v vv   vv   v    vvi i  i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_126263166_   1142 ATCAAGGATGTGTGTAAAGGATA-CTAACAGAATGTCAGAAAATATTTGC 1190
                               i v   ---   i  i - iv        vv             
  L1M4_orf2#LINE/    682 ATCAAGAAAGTG---AAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_126263166_   1191 AAATCATGTATCTGAAAAGAGAATTATATCCAGGCTATATGAAAATATCT 1240
                                i       v   i  v  i       iv     i  i vv   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_126263166_   1241 TAGGACTCAATAACAAAT-GATAAATAAGCCAA-----------GTAAA- 1277
                           vi         i   v-  i      v    ----------- i   -
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_126263166_   1278 ------AATAAAAATTTTTCTAAAGAAGATACACAAATGTCCCATAAGCA 1321
                         ------    i v    i  i          i       v  v       
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_126263166_   1322 CATAAAGA-ATGCTCAACATCATTTGTCAT 1350
                            i  i -             ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (99 / 68)
Gap_init rate = 0.02 (18 / 869), avg. gap size = 2.28 (41 / 18)  


 601 29.22 2.88 1.23  chr2_126271750_126274137      663   905 (1483)    L1M4_orf2#LINE/L1        1   247 (661)  

  chr2_126271750_    663 TGGAAGGCCATCTGTTGTTCATTTATT---AGACT-AATATTGTTAGGGT 708
                              i vi   ivv       vv   ---     -          i i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126271750_    709 GTACATAATTCCCAAAGCAATCTTTAGATTCAATACAATTACTATCGAAA 758
                          vvv   v i      vii    vi        ii    iv     i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126271750_    759 TCCAAATGACATTTTTCAGAGAAATAGAAAAAATG-TCCTAATATTATTA 807
                            v iivi v     iiv      v  v  iv  -      v   vv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_126271750_    808 TGGAACCACAGATGACCCTAAATACCCTAAA-AATTTTTTTAG-GAAGAA 855
                              vii  iiv     vi    v  v   -   i  vvv i-      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_126271750_    856 CAAATACCCTGCAAATATCACATTCCCTGATTTTAAAATATATTACAAAG 905
                             v---i  v iivv     i i  ii    i    iv  i       
  L1M4_orf2#LINE/    201 CAAAG---TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

Transitions / transversions = 1.03 (36 / 35)
Gap_init rate = 0.02 (6 / 247), avg. gap size = 1.67 (10 / 6)  

1734 24.31 3.49 6.26  chr2_126271750_126274137     1210  1896 (492)    L1M4_orf2#LINE/L1      241   908 (0)  

  chr2_126271750_   1210 TACAAAGCTACAATAATTAAAACAGTATGGTACTGGCATTAAAA-AAA-- 1256
                                     i    i  i     i            v ii - i --
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_126271750_   1257 -ATAAACAAATTGAACAGTGTAGAGAGCACAGAAATAAACCCATGCATAT 1305
                         -   i iv   v   i  vi v     iv               i   v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_126271750_   1306 GCAGTCAACTGTTGTTCAAAAAGGGTGCCAATA--ATACA-TG---AAAA 1349
                         iii     i  v v   i v           v --  v  -  ---   i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_126271750_   1350 GATAGTCTCTCCAATGAACAATGTTTGGACATTTTTAAATCCACATTTAA 1399
                         i       i i   ii  iii  i v     vi vv v ?      vi  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_126271750_   1400 AATAATAAA-----ACCCTAATCTTAAACTATATAGAAAACTAAACCCCA 1444
                           v   i  -----    iv i  i v  i     v    v v   i v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_126271750_   1445 GATAGATTAAAGACCTAAACATAAACCCAGAAACAATAAAACCCTTAGAA 1494
                         i  i   i ?         ii   ivv vi    v       i       
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_126271750_   1495 GAATA-ATAGAGA-AAATGTTGGAGACATTGGTCTTGGCCATGGTTTCTT 1542
                            v -    i?i-    v  v v   v    vi v   v          
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_126271750_   1543 GGACATTAC-TCAAAAGCACATAAAACAAATTAAAAA-TAGATAAATTGG 1590
                         i  i  v  -i          viv      vv     -            
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_126271750_   1591 AC---ATCACAATGAAAAA-TTATGTGCAATCAACAAAGCAAAAATTATA 1636
                           ---    v   v     -  v     -- i--     --i v i   -
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGC--TT--CAAAG--GACACTAT- 683

  chr2_126271750_   1637 TAATCAGCACAGCAAAAAGCCAAATTATGGCACTGGAGAAAATATCGGCA 1686
                         ----  iv v  ii     v   vii ii v iv           iv   
  L1M4_orf2#LINE/    684 ----CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_126271750_   1687 GACCATATATCTTATAAGAGGTTAATATCCCAAATATGTGACAGTCTTCT 1736
                         i i         v     i ii vi     vi     i i viiv  ii 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_126271750_   1737 ACAACTCAATAGCAAAAAATAATATGCATCAATATCAGCAGCAGCAGCAG 1786
                                    ii     i-- i ------    v --------------
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAG--ACA------AATAAC-------------- 807

  chr2_126271750_   1787 CAGCAGCATTTCATTTTTAAAA-GGGCAAAAAACATGCATAGATATTTCT 1835
                         ----------i  v  ?v    -       ii iv  v     i      
  L1M4_orf2#LINE/    808 ----------CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_126271750_   1836 CTAAAGATGACTTACAGTTGGCCAATGCATATACAAAAAGGTGCTCAACC 1885
                          i     v  iv    iv        ivii i ii     i        v
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_126271750_   1886 TCACTAATCAT 1896
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (95 / 68)
Gap_init rate = 0.03 (20 / 668), avg. gap size = 3.35 (67 / 20)  


2443 24.01 2.13 2.56  chr2_126276063_126278399      581  1284 (1053)    L1M4_orf2#LINE/L1        6   706 (202)  

  chr2_126276063_    581 AGATATT--GTGTTCATGGATTGGAAGAC--AGTAT-GTGAAGGTTTCAA 625
                               i--i                   -- i   -  v   i vv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_126276063_    626 TACTACCCAAGT-GACCTACACATTCAAAGCAATTTTTATAAAAATAC-A 673
                             v     i -  i     v      v     iii   v     v - 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_126276063_    674 ATAATGTTTTTTGAAGAAATAGAAAAATCAATTCTTAAATTTATGTGGAA 723
                         iiviiv       v      v  v  iiii  i  v     i  i     
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_126276063_    724 TCTCAAGGAACTTTGAATGGCTAAAACAATCTTGTGAAATACAACAACAA 773
                         viv     i  iiv    i  i            --   -----------
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG--AAA----------- 192

  chr2_126276063_    774 CAACAACAACAACAAAATAGGAAGTGTCACTTTTCCTGGTTTCTATACTT 823
                         ----  v  v      i v   i vv    vi    iii    v v    
  L1M4_orf2#LINE/    193 ----AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_126276063_    824 ATTATAAAGCCATAGTAACCAAAACAGTTTGGTAACAGCATCAAGACAGA 873
                          i  i     i i     i   i     v     vii    v i  i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_126276063_    874 TGTATAGAGCAATGGAATACAATGAACAGCCCCTAAATAAACCTTCACAT 923
                         ii      v          v   vi v  i  vv         ivi    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_126276063_    924 ACACAGTCAAATAATTTTTGACAAGCAGACCAATATCATTCAATGGGAAA 973
                         vi ii     v i     i      vivi    v i           i  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_126276063_    974 AGGATACTCTTTTCAACTTACAATGTTAAGAAAATT--ATACATATATTC 1021
                           i   v          vv iii  i ii  v  i --   ?vi i  v 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_126276063_   1022 AGAAGAATGAAGTTGGACCCCTGTTT-ACATCACAAGCCAAAATTAACTC 1070
                          i                    iii -   i  i vi v           
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_126276063_   1071 ACAATGAATCAAAGATCTAAATATAAAAGGTAAAACTAGTAAAGTCTCAC 1120
                          v    i    ?   i      i   i  v        vv   v   i v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_126276063_   1121 AAGAAAA--TAGGGGAAAA-CTTCATGATTTGGGATT-TTTAATATTTTC 1166
                                --    ? v   -    i   ii v  i  -vvi   iv    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_126276063_   1167 TTGGATAAGAC-CCAAGAACACAAGCAAACAAGGAAACACACAGATAAAT 1215
                           i    v   -    i i         vv  i    v - i        
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAAT 637

  chr2_126276063_   1216 TAAACTACATGAAAATTTAAAACTTGTGTGAATCAAAGGACACTATCAAC 1265
                          ii   v   v      v       v    vv                 v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_126276063_   1266 AGAGTGATAAATCAACCCA 1284
                          i     v  iv       
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCA 706

Transitions / transversions = 1.31 (94 / 72)
Gap_init rate = 0.02 (14 / 701), avg. gap size = 2.36 (33 / 14)  

 849 18.14 1.96 1.47  chr2_126276063_126278399     1642  1845 (492)    L1M4_orf2#LINE/L1      704   908 (0)  

  chr2_126276063_   1642 CCATGAAATGAGAGAAAACATTTGTGAAT-ATATATCTGATACAGAATTA 1690
                            iii    i       i     ii   -            vi i i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_126276063_   1691 TTATCCAGAATACATAAAAAACG---ATAACTCAATAATACAAAACCCCC 1737
                         v           i     i   v--- i            v   iv ---
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC--- 800

  chr2_126276063_   1738 AAGAAACCCAATTAAAAAATTGACAAAGAACATGACTAGATATTTCTCTA 1787
                           iv         ?      v i     i iv   v    i       i 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_126276063_   1788 AATAGGATACACAAATGGCCAATAAACACATGAAAACTTGCTCAACATCA 1837
                           v i    i               i          vv            
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_126276063_   1838 CCAATCAT 1845
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.77 (23 / 13)
Gap_init rate = 0.01 (3 / 205), avg. gap size = 2.33 (7 / 3)  


3107 27.35 1.11 0.55  chr2_126298841_126305233     4999  5901 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_126298841_   4999 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATCATGAAAAT 5048
                              ii i  i     i i    i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126298841_   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126298841_   5099 TACCAATGACTTTCTTCACAGAATTGGAAAAAACAACTGTAAAGTTCATA 5148
                          v   iivi i  i  ii     v v  v  ivii iiv    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_126298841_   5149 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5198
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_126298841_   5199 CAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAGTCTA 5248
                              i      vv   vi  v  ii i      viv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_126298841_   5249 CAGTAACCAAAACAGCATGGTACTGGTACCGAAACAGAGATATAGATCAA 5298
                               i   i    ii         i iviii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_126298841_   5299 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5346
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_126298841_   5347 CTGATCTTTGACAAAC---CCAAGAAAAATAAGCAATGGGGAAAGGATTC 5393
                         i    i  i     iv---      vv v ---            i  vv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAAGAATAG 395

  chr2_126298841_   5394 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5443
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_126298841_   5444 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATAAATTCAAGATGG 5493
                             ii    i    v   i     v           v  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_126298841_   5494 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAGTCCTAGAAGAAAA 5543
                           i ?    i    i  v   v       i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_126298841_   5544 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTACATGTCTA 5593
                          v    ?i v viv   iv   v v  vv i     v ii v v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_126298841_   5594 AAACACCAAA-GCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5642
                         vi        -   vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_126298841_   5643 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5692
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_126298841_   5693 ----CAACCTACACAATGGGAGAAAATTTTTGCAACCTATTCATCTGACA 5738
                         ----     i   v             v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_126298841_   5739 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5788
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_126298841_   5789 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACGGACACTT 5838
                           i     i     v  i?    i           iv    ii    i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_126298841_   5839 CTCAAAAGAAGACATTTATGCAGACAAAAAATACATGAAAAAATGCTCGC 5888
                            v        i  vi viii v   v  ii         i      iv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_126298841_   5889 CATCACTGGCCAT 5901
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.50 (15 / 6)  


2067 28.71 5.28 1.23  chr2_126322758_126324566.rev      503  1317 (492)    L1M4_orf2#LINE/L1       61   908 (0)  

  chr2_126322758_    503 CCAAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACTACCAAGATC 552
                           v   vii  i           i  v  i         v v   ivvv 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr2_126322758_    553 ATTCTTCACA-AAATTGGGGAAAAAATTCTAAAATTCATGTGGTACCAAA 601
                         v  i  ii  -      ivi ivvi  i           i   ----   
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG----AAA 156

  chr2_126322758_    602 ---AAAAAAGCCGAAATCACCAAGGCGACCT--------AAGCATAAA-- 638
                         ---  iii v  ii   vi    ii i i  --------   v i   --
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_126322758_    639 -------------CTATCCAACTTAAAAGTATACTACAAGGCTATAGCAA 675
                         -------------  vi    i  v   iiv        i    i  i  
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_126322758_    676 CCAAAATAGCTTGGTACTGGTACAAAACCAGGCACATAGACTAAGGGAAC 725
                         i   i i  iv         i i  iivi  i  i     ii  v    i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_126322758_    726 AGAATAGAAACCTCAGGAATAAAGCCACACACCTACAGCCATCTGATCTT 775
                              v  i vii   i      v   i   ii  ii i  vi    i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_126322758_    776 CAGCAAGGCCAACAAAAACAGGCAATGGGTAAAGGACTCCCTGTTCAATA 825
                          ii     viiv   i v  vv       v    i ivvi  v     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_126322758_    826 AATGGTGCTGAGATAACAGGCTACTCATATGCAGAAAAATGAAACTAGAC 875
                                   i  i   v  v  ?i  i     i  i      ii i   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_126322758_    876 ATTTACCCTTCACCATGTATAAAAAGTAACACAAGATGAATTAAAGATTT 925
                         vii    iiv      i  i     v    v   i   i  i ?   ii 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_126322758_    926 AAATGTAAGACCTTAAAATATAAAAGCCCTAGAAGAAAAGCTAGG---AA 972
                                   v  v   v       vi i          vv    ---  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_126322758_    973 ATACCTTTCTCTACATCAGCCTTGGCAAAGAATTTAAGGCTAAGTCTCCA 1022
                           ---i   viv  v ii vi v     v iv  ivvi v  v v v   
  L1M4_orf2#LINE/    557 AT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_126322758_   1023 AAAGCAATTGCAATAAAAACAAAAATTGACAAGT-GGACCCTA-----AC 1066
                               vvv    i    iv      v  i  i -    iii ----- i
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_126322758_   1067 TAAAGAGATTCTGAACAGTAAAAGAAACCAGAAACAGAGTAAACAGACAA 1116
                             i v-  i  vi vvi   i  v  i vv  v i   i  v      
  L1M4_orf2#LINE/    654 TAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_126322758_   1117 CCTACAGAATGGGAGAAAATATTCACAAACTATGCATCTGAAAAAGGTCT 1166
                           i                    ii    ii  ii      v  i  v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_126322758_   1167 AAGATCCAGAATCTACAAGGAACTTAAACAAATCAGCAAGCGCAA---AA 1213
                         viv         v  i  i     ivv    v   ii  vviv  ---  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_126322758_   1214 ACAACACCAAT-AAAAAGTGGGTAAATC-TATGAACAGACCCTTCTC-AA 1260
                          i   -     -?    i    i   vv- v    i    vi     -  
  L1M4_orf2#LINE/    803 ATAAC-CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_126322758_   1261 AGAAGACATACAAGCAGCCAACAAACAT-TGACAAAAATGCTCATCATCA 1309
                               i      iii     i  i  i-   -   i       v     
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTCAACATCA 900

  chr2_126322758_   1310 CTAATGAA 1317
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.60 (142 / 89)
Gap_init rate = 0.02 (17 / 848), avg. gap size = 3.12 (53 / 17)  


2180 20.52 4.03 10.32  chr2_126498351_126500148.rev      464  1306 (492)    L1M4_orf2#LINE/L1      119   908 (0)  

  chr2_126498351_    464 CAGGAAT--GCAAGGCTGGTCTAGTATCTGAAAATCAATTATTGTAATAC 511
                            i   --i    -   i  ------  i   v   --   v v   i 
  L1M4_orf2#LINE/    119 CAGAAATTGACAAG-CTGATC------CTAAAATTCA--TATGGAAATGC 159

  chr2_126498351_    512 AACATATCAATAGAATAGCCAAAATAATCTTGAGTTCAATAAAAGAGCAA 561
                           viv i --i             i        ----  v i    i   
  L1M4_orf2#LINE/    160 AAGGGACC--CAGAATAGCCAAAACAATCTTGA----AAAAGAAGAACAA 203

  chr2_126498351_    562 --TT-------TTATAAATCCCCATTTCAAAGCATATTACAAAGCTACAG 602
                         --  ------- i i vv    v        i v  i             
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_126498351_    603 TTATCGAGACAATATGGTACTGGAATAAGAATAGATATATAGAACAATAG 652
                          v   i     i i         v     i     i       v    i 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_126498351_    653 AATAGAATTTAGA--TCACAAAT---TTCTCACATTTAAGATCAATTAAT 697
                                  v   --i  v    ---ii vi       v i      i  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_126498351_    698 TTTTTTGACATGAGTTCCAAAACAATTCAATAGTGAAAGAGTAGTCTTTT 747
                            i--    v i  v    i  v       i v      i         
  L1M4_orf2#LINE/    354 TTTC--GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_126498351_    748 CAATGAATGGTGCTGGCACAATTGGATATTCATATGTAAAATAACTATTT 797
                            ii           v    i      ?i  i   i    v  iv vv 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_126498351_    798 GAGATGCCTATCTCAAATACTATGCAATAATGAATTCAAAGTTAAACAGA 847
                         vi  iv    i    v ivv   i   v   v  i     ----------
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA---------- 491

  chr2_126498351_    848 CACAATGTAAGAAACCATATCTTCTTTCACATTCAGAATTGTGTCTGTAG 897
                         ----   ---  --------------------   ---------------
  L1M4_orf2#LINE/    492 ----ATG---GA--------------------TCA--------------- 499

  chr2_126498351_    898 AATTAAGACACAATTCTAAATGTAAGAG--AAGATTATAAAACTCTTAGA 945
                         ----?    ------             --  i i               
  L1M4_orf2#LINE/    500 ----WAGAC------CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_126498351_    946 AGAGG-TATAAAGATAAATTTTCTATACTTTCATTT-TGCAAAGGTTTTT 993
                            ii-i   ii?i     i   vvv  i  viv  -v    v     i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_126498351_    994 AAAATGCAAAATCAAAAGTACCTGGTAACCAATGAAGAAGCA--TAAATT 1041
                         v i  iii v i      i  v-i i   v  v   i  ii --      
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_126498351_   1042 GGACTTCACAAAAACTAAAAAGCTTTTGTACTTTAAAAGATCCCATAAAG 1091
                                 iv    i      -       i   i   i  iv i  v   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_126498351_   1092 AAAGTGATAAGATCACCTGCTGA-TTAGAGATAATATT-ATAATATCATA 1139
                                v    iv   ii v  - vi    v      -ii  -      
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATA 736

  chr2_126498351_   1140 CATCTAATATGATACTTGTGTCTCATACAGAATATGT--------CTTAT 1181
                         i    i   v iv      i  -----        i --------    i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATC-----CAGAATATATAAAGAACTCTTAC 781

  chr2_126498351_   1182 TACTCAATAATAAAATG-CAAGTAGATCAGTTTAAACATTGCCAGACCAT 1230
                         v              v -   i  ivi  i  ?   v  v v  i vv  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_126498351_   1231 CTGAATATACATTCCTCCAAAAAAAATATTCAAATGACCATTAAGCATAC 1280
                         i      v     i       i  i    v      i   v      i i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_126498351_   1281 AAAAA-ATGTGCAATATCATTAGTCAT 1306
                         i    -   iv   i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (102 / 67)
Gap_init rate = 0.04 (29 / 790), avg. gap size = 4.17 (121 / 29)  


2846 26.82 1.21 0.99  chr2_126527039_126531883.rev     3448  4353 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_126527039_   3448 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3497
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126527039_   3498 AATTATAATACCAAAAGCAATCCACAAATTAAATGCAATTCTCATCAAAA 3547
                         iiiv   v v  v   vii   i   i   v  i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126527039_   3548 TACCATCATCACTCTTCATAGAATTAGAAAAAGAAATCCTAAAATTCATA 3597
                          v   v vv vi i  iii    v v  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_126527039_   3598 AAGAAC--CAAAAAATAGTCCATA-CAGCCAAAGGAAGACTAAGCAAAAA 3644
                         vi   v--   iii i---   v -i       iv  vvi i iv  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_126527039_   3645 GAACAAATCTAGAGGCATCACATTACTCAATTTCAAACTATACTACAAGG 3694
                                vi i    vv     i v i          viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_126527039_   3695 CTATAGTCACCAAAACAGCATGGTACTGCCATAAAAATAGACACATAGAC 3744
                            i   v i   i    ii        v     ii       i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_126527039_   3745 CAATGGAACCAAATAGAGAACTCAGAAATAAAACCAAATACTTTCAGCCA 3794
                                 ivi   v    iii          v   v i i  vii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_126527039_   3795 ACTGATCTTTGACAAAGCATAAAAAAAC-GTAAAATGGGGAAAGGACACC 3843
                          i    i  i     i -i ivv  i  -i vv           i i vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_126527039_   3844 CTATTCAACAAATGATG-TGGGATAATTGGCCAGCCACATGTGGAAGAAT 3892
                           v           i  -     i  i   vi ?       iii      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_126527039_   3893 GACGCTGGATCCTCATCTCTCACCTTATGCAAAAATCAACTCAAGATGTA 3942
                           v i    i  ii i   v    v   i       i       i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_126527039_   3943 TCAAAGATTTCAATCTAAGACCTGGAACCATAAAAATTCTAGAAGATAAC 3992
                            ?   ii v   v     v  ii   i      v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_126527039_   3993 TTTGGAAAAGCTCTTCTAGACATTGGCTTAGGTAAAGATTTCAT-GAC-C 4040
                         v v  ?iv iv     vv   v    v     i  v i    v -  i-i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_126527039_   4041 AACAACCCAAAAGCAAATGGAATGAAA-ACAAAATAAATAGATGGGACTT 4089
                         i   --         v v v  ii   - v      i   i  v      
  L1M4_orf2#LINE/    597 GACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_126527039_   4090 AATTAAACTAAAGTGCTTCTGTACAGCAAAAGAAA-TATTCAGCATAGTG 4138
                         v  i   v v  ivi   i   i vv    i  v -   iv  v -    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA-AGTG 693

  chr2_126527039_   4139 AACAGACAACCCACAGAGTGGGAGAAAATAGTTTTGCAAACTACACATTC 4188
                           v              i            --        ii i i  ii
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATA--TTTGCAAATCATATATCT 741

  chr2_126527039_   4189 AACAAATGACTAATATCCAGAATCTACAAGGAAATCAAACAAACTAATAA 4238
                         i i  iv    vi          v  i  i   v  vv    vii     
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_126527039_   4239 GAATAA-ATTAATCATCTCATCAAGAAGTGGGCTAAGGTCAGGAATAGAC 4287
                         v  v  - iv   v i iv  i? i  i     v    vivv        
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_126527039_   4288 AATTCCCAAAAAAAGATATACAAATGGCCAACAAACATATAAGAA-ATGC 4336
                          v   i v   i                   i  i  i  i i  -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_126527039_   4337 TCAACATTACTAATTAT 4353
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.33 (20 / 15)  


 292 31.31 2.02 0.00  chr2_126607563_126609378        1    99 (1717)  C L1M4_orf2#LINE/L1   (807)   101     1  

C chr2_126607563_     99 TGGAGAGGTAT-CCATGTTCATGTATAGAAAAATTTAATATCAACAAAAT 51
                             i  i   -           v  v i  i i       iivi  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_126607563_     50 G-CAGCTCTTTCCCACTTTCTTTATTAATTCAAGGCAGCTCCAATCAAAG 2
                          -  iiv  ii  v v  vv i  ivi      v   iii  v      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_126607563_      1 T 1
                          
  L1M4_orf2#LINE/    101 T 101

Transitions / transversions = 1.82 (20 / 11)
Gap_init rate = 0.02 (2 / 101), avg. gap size = 1.00 (2 / 2)  

 612 30.41 13.52 3.13  chr2_126607563_126609378      554  1352 (464)    L1M4_orf2#LINE/L1       13   894 (14)  

  chr2_126607563_    554 CCATGGTCATGTTTTTCAAGGC--AAGTTGTTGTAAGAATAAAAATTTAT 601
                              v     vv  vv   i --  -- i    v ii  iiv   vivi
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAA--TATTGTTAAGATGGCAATACTC 60

  chr2_126607563_    602 CTTAAATTAACTTACAGATTCAGTGAAATCCTAATCAATAACCCAGGCAT 651
                          ii     i ii          ii v     iv     v v     ---i
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG---C 107

  chr2_126607563_    652 TACTTTTATGTGTACAAA---A-AAGTGTGAT-----AATT------AAA 686
                          i i   - v  i v   --- -   i-    -----    ------i  
  L1M4_orf2#LINE/    108 TGCCTTT-TTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATGGAA 155

  chr2_126607563_    687 AAGC---TGACCACGTAT-GT----ATA-TTTTAATACAAAAAAA----- 722
                          v  ---v    vv v  - i---- i - i  i v v i  i  -----
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_126607563_    723 --GGAACAC-CACATT----------AAGACTTATTATACAGTTATAGTA 759
                         --   iv  -    i ----------  i     i  i v  i  i    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_126607563_    760 ATTAAGACAGTATAATATTGGGAGTACAATAGAGATATATG-CAATAGAA 808
                           i        i ii  i   v vv vi     v     vi-    i   
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_126607563_    809 CAAAA---AGAATGAGCTAGAAACAA--TTATATATATATGGACATTTGA 853
                         i i  ---   i --- i     i  --ii   i  v     v  v    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGT---CCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_126607563_    854 TTTATGACATTGTTGATTCTATAAAAAT--AGTAAAGAAAAGATAATATT 901
                            vi    vv v  --- i vi vv  -- i iii    ii   i v  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTG---CCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_126607563_    902 TTCAATGTATGGT------ATAATT-----TTTATATAAATATGAAAAAA 940
                              iiv     ------ i  i -----?ii i  iv v v   vi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_126607563_    941 ATTTGACATGCACACCACA--ATATACGTGAAGCAGTTCCAG-TGGTATT 987
                         i  v   vivi  vi    --      ivi  vi ii  v i-   -  i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG-ATC 498

  chr2_126607563_    988 GTAGATTAAACTATAAAAGCCTAAACAATAAAATGTTTATAAAATAAAGT 1037
                         i?   iiv  v i   i   iv    v      ivi   v  i v  vi 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_126607563_   1038 AAAAA-AAATACATTCAAAAATTTGGTATGTGGAAGGATTTTTTAAA-AT 1085
                          ii?i-    - -   ivi vi    vv iv v  v i   i   i -  
  L1M4_orf2#LINE/    549 AGGNGTAAAT-C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_126607563_   1086 AAGAC-AAAAACA---GTAA-ATAAGTAAACGTATTGTTACATTTGGC-- 1128
                         i v  -    i  --- i  - v   v   vi  -- v  v   v i --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTT 644

  chr2_126607563_   1129 ----AAAA--AAGAA--TTAG------AAAGGTCCTATTATCAAAAAAGA 1164
                         ----    --  i  --  v ------     v -- i      i    v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC--ACTATCAAGAAAGT 692

  chr2_126607563_   1165 GGGAGAAAAAATA--CCATAGAATAGAA-AACATATTTGAAACACATAAA 1211
                          ----    i i --   i     i i -  v       v  vv    v 
  L1M4_orf2#LINE/    693 G----AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_126607563_   1212 T-TGA-AAGTGATGTACATTAAAAATATAGAAATA-TTCTTACAA----- 1253
                          -   -   v  iv ii  iv i      v   v -i        -----
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_126607563_   1254 --------AAACAGGTAACCTAACTTAAAAATGGGCAAGAAACTTGAATG 1295
                         -------- i   ii     i  i ?            iii i      i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_126607563_   1296 GTCATCTTTCAAAAAGAAGATGGGCACTTGGCAGTTCAACCTATAAAAAA 1345
                          v   i i  v   -      ivi  vv    viv v i vi  i    i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_126607563_   1346 GTCCTTA 1352
                         i v  i 
  L1M4_orf2#LINE/    888 ATGCTCA 894

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.05 (48 / 882), avg. gap size = 2.77 (133 / 48)  


1770 28.43 0.61 0.41  chr2_126633803_126640758     5291  5779 (1177)    L1M4_orf2#LINE/L1        1   490 (418)  

  chr2_126633803_   5291 TGGAAAAACATTCCATGCTCATGGATGGGAAGAATCAATATCATGAAAAT 5340
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126633803_   5341 GGCCAAAATGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5390
                            v v v v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126633803_   5391 TACCATTGACTTTCTTCACAGAATTACAAAAACT-ACTTTACATTTCATG 5439
                          v   vivi i  i  ii     v vv v  i  - iii  v v     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_126633803_   5440 TGGAACCATAAAAGAGCCCATATACCCAAGACAGTCTGAAGCAAAAAGAA 5489
                              viii  ii  v  viv   v    i   i   vi iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_126633803_   5490 CAAAACTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5539
                             ii      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_126633803_   5540 CAGTAACCAAAACTAGCATGGTACTGATACCAAAACAGATGTATAGACCA 5589
                               i   i  -  ii        ii iv ii i   ii      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGAC-AGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_126633803_   5590 ATGGAACAGAACAGAGGCCTTAGAAATAACTCCACACATCTACAACCATC 5639
                               i    iv   iviii        vi   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_126633803_   5640 TGGTCTTTAACAAACCTGACAAAAACAAACAATGGGGAAAGGAT--TCCC 5687
                           i i  ii    ivv  v   i v  vv            i  --  ii
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_126633803_   5688 ATTTAATAAATGGTGTTGGAAAAACTGGCTAGCCACATGCAGAAAACTGA 5737
                         -  i  i        i   i v      v  ?         i  i v   
  L1M4_orf2#LINE/    400 -TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_126633803_   5738 AACTGGACCCCTTCCTTATACCTTATAAAAAAATTAACTCAA 5779
                          ii         v   i i   v    v              
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

Transitions / transversions = 1.88 (90 / 48)
Gap_init rate = 0.01 (4 / 490), avg. gap size = 1.25 (5 / 4)  

 978 28.61 1.24 1.49  chr2_126633803_126640758     6051  6452 (504)    L1M4_orf2#LINE/L1      457   857 (51)  

  chr2_126633803_   6051 CTCTGTCTCAAAATAAATAAATAAATAAATAACTCAAGATGGTTTAAAGA 6100
                          i  ii    v vi v   v v    ---        i    v i ?   
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAAT---TAACTCAAAATGGATCAWAGA 503

  chr2_126633803_   6101 CTTAAATGTAAGACCTAAAGCCATAAACACCCT-ACAAGAAAACCTTGGC 6149
                          i           v     i i     -  i  - v        v v  ?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGN 552

  chr2_126633803_   6150 A-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAACAC 6198
                         i- v i -   iv   v v  vv i     v ii   v iiv  vi    
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_126633803_   6199 AAAAAGCAACGGCAAAAAAAAGCCAAAATCAACAAATGGCATCTAATTAA 6248
                         v       vvi    v    - vv     vi i    v v ii v  i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_126633803_   6249 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAGGC 6298
                          v v  i i   i  ii vv    i  v       vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_126633803_   6299 AACCTACAAAATGGGGGAAAATTTTTGCAATCTATCCATCTAACAAAGGG 6348
                             i   i      i      v       vii  vi    i i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_126633803_   6349 CTAATATCCAGAATCAACAAGGAATTTAAACAAATT--TAA-AAGAAAAA 6395
                           vi          vv i  i   i ivv    v i--   -  i  i v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_126633803_   6396 AAACAACCCCATCAAAATGTGGGTGAAGGATATAAACAGACACTTCTAAA 6445
                            i     v  i?   vi    ii      v i  i     i    vv 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_126633803_   6446 AAGAAGA 6452
                                
  L1M4_orf2#LINE/    851 AAGAAGA 857

Transitions / transversions = 1.11 (59 / 53)
Gap_init rate = 0.02 (8 / 401), avg. gap size = 1.38 (11 / 8)  

 613 28.89 1.11 1.11  chr2_126633803_126640758     6455  6634 (322)  C L1M4_orf2#LINE/L1   (728)   180     1  

C chr2_126633803_   6634 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 6585
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_126633803_   6584 GGCCATAGTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 6535
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_126633803_   6534 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6487
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chr2_126633803_   6486 TATGGAACCAAAAAAGAGCCTGCATCGCCTAA 6455
                                viiv  ii  v  v v  v   v  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

Transitions / transversions = 1.74 (33 / 19)
Gap_init rate = 0.02 (3 / 180), avg. gap size = 1.33 (4 / 3)  


3272 26.28 1.56 0.45  chr2_126652107_126658371.rev     4876  5773 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_126652107_   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4925
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126652107_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126652107_   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_126652107_   5024 TACGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5073
                           i    viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_126652107_   5074 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5123
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_126652107_   5124 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGATC 5173
                                 i   i    ii         i  v ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_126652107_   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCT------ 5215
                                i    i--    i  --        vv  ii i  i ------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_126652107_   5216 ----GATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5261
                         ----   i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_126652107_   5262 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5311
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_126652107_   5312 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5361
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_126652107_   5362 TTAAAGGTTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5411
                          i ?  iii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_126652107_   5412 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTGCAA 5461
                         v    ?i v viv   iv   v v  vv i     v ii   v ivii v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_126652107_   5462 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5511
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_126652107_   5512 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5561
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_126652107_   5562 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5611
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_126652107_   5612 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5661
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_126652107_   5662 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5711
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_126652107_   5712 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5761
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_126652107_   5762 ATCACTGGCCAT 5773
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 3.00 (18 / 6)  


 791 29.35 6.16 0.00  chr2_126728451_126731755.rev      974  1249 (2056)    L1M4_orf2#LINE/L1        3   295 (613)  

  chr2_126728451_    974 GAGAGATA--ACATATTCATGGATTGGGAGACACAGCATAGTAAAGATGT 1021
                           i     --v   i            i    vi ii  v  v      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_126728451_   1022 CACTTCTCTCTAAAT----CCATATGTTTTATTCAATTCGTATTAGAATT 1067
                           v v   i i    ---- i i vi  iv iv    i v   i i   i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_126728451_   1068 CCAAGAAGGTTTTGTATGGACATAGATAAGCTTATCCTAAAATTTATATG 1117
                            ivvivv    v iii  v  v  i     v           i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_126728451_   1118 AAAAGGCAAAGTTCT-----TAGTTAAAAAATTCTTATAAAAGAATAATT 1162
                         i   v    i vv i-----   ii    v v    iv       v  iv
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_126728451_   1163 AAGT-GGAAGAATCACTCTCCCCAATATTAAGGCCTGCCACAAAGCCACA 1211
                             -   i  v    v  i      v i  ii i i i       i   
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_126728451_   1212 GTGATCAG--TGGTGTGTTATTGGTGGAA--ACAGAT-TATAG 1249
                           i    i--ii     v  i   iiv  -- i   i-     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 1.53 (49 / 32)
Gap_init rate = 0.02 (7 / 293), avg. gap size = 2.43 (17 / 7)  

1821 26.07 3.44 0.98  chr2_126728451_126731755.rev     2204  2813 (492)    L1M4_orf2#LINE/L1      284   908 (0)  

  chr2_126728451_   2204 ATAGACATA--GATCAATGGAACAGAATAAAGA-TCCAGATATAAGCCCA 2250
                                  --           i     vi   -      v    i    
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_126728451_   2251 CAAAAATACACTCAACTGATGTTTGACAAAAGTGCAAAAGCTATTCAATG 2300
                         i v vv  iiv    i    v  i     ii    v  ii i        
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_126728451_   2301 GAAGAAGGATAGCTTTTTCAATAAATGATACCAAAACAATTACACATCCA 2350
                          iii   i    ii       i     i i iiii    i iv i ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_126728451_   2351 TAGATTAAA-AACGAACCTTGACCTAAATATCATAGCTTATATAAACGTT 2399
                         i viiv   -  i   vi v    ivv iv   i v v    i   vi  
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_126728451_   2400 AACTCCAAATGAATCATGGACTTAGAT-TAAAAAAATTTAGTGCTATATA 2448
                              v     i    ?i   i  i  -   i i---i  ivi     v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAG---CTAAAACTATAAA 530

  chr2_126728451_   2449 ACTTATAGA-TAATACATAGGAGAAAATTTTCAGAATGTGGAGTTAAGCA 2497
                            iv    -v  v       ? v    i   ivi iv v i    i   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_126728451_   2498 AAGAGTTCTTAGGTTTGACACTA----CACAATCCATTCAAGGAAA--TG 2541
                          v iv       i v      i ----     v v ivv   i   -- i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_126728451_   2542 TATAA-TTAGAAACCATCAAA-TTAAAAACTTGAGCTCACTGCAAAC--C 2587
                         v    -  i  vvi       -          vv i--i  v    v-- 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGT--GCTTCAAAGGAC 678

  chr2_126728451_   2588 CCTAATAAGAGGATGCAAAGACAAGGTACAGACTGGAGAAAAATATTTGC 2637
                         v   vi    iii  v        vvi     v   iii           
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_126728451_   2638 AAATGACATATCTAACAAAGGACCTGTAT--AGAATATAGAATATAAGTC 2685
                             v i      i i  i    i     --        v  - v  v  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA-AGAACTC 777

  chr2_126728451_   2686 TTA-AACTCAACAATAAAAATACAAATATTTCAATTAGAAAATTGGTAAA 2734
                            -       i        v       vii     ?i     v  i   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_126728451_   2735 GGACATGAATAGAAATTTCACTTGAG--GATATACAGATGGTAAATAAGC 2782
                            iv        v     v ivi  --        i    iv       
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_126728451_   2783 AAATAGAAAGGTGCACAGCATCATTAGACAT 2813
                          v  ii    i   v  i     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (92 / 63)
Gap_init rate = 0.03 (16 / 625), avg. gap size = 1.69 (27 / 16)  


3089 18.67 4.18 7.30  chr2_126740934_126743260      904  1835 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_126740934_    904 AGATATCCCATATTTATGGATCATAAGA----ATATTGTTAAGATGTCAA 949
                                    i  i      iiv    ----              v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_126740934_    950 T-TATCCAAAACAAATCTACAGATTCAACACAATCCCTATCAAAATCTCA 998
                          -ivi  v   ivi               i                 i  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_126740934_    999 GCTGATCTTCTCATACAGAGTAAC---CT-ATCTATATAGAAAAAAATAT 1044
                             vii  i iii v i v i  ---  -   i---  -   vvv    
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC---TA-AAATTCATAT 151

  chr2_126740934_   1045 GAAAATGCAATGGACCCAAAATAGCCAGAACAATCTTGAAAAACAA---T 1091
                          i        v       i        i               v  ---i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_126740934_   1092 ATATTTAGACAACCCACACAACCTGATTTTAAAACTTAAAAAGCTGAAAA 1141
                          v v  i  vi  i     vv  ii    i        -----  iv   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-----CTACAAA 246

  chr2_126740934_   1142 GCTACAATAACCAAGAAAGTGTGGTACTTGTATAAGGCTATATAAATATA 1191
                               i   i     v           v i      --   v v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG--ATAGACATATA 294

  chr2_126740934_   1192 G-TCAA----ATATAATTTGGAAGCCAGAAATAAACTACTATATA---AT 1233
                          -    ----   v    vi  iv            -- i   i ---  
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC--CCATACATTTAT 342

  chr2_126740934_   1234 GGTCAATTGATTTTAAACAAGGATATCAAGGCAATTAAATGGGGAAA-AA 1282
                                       vi      i ii    i v   v          -  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_126740934_   1283 TAGTCTTTTTAAGAAATAGTGTTGAGACAAGTAGATATTTACTTAGAAAT 1332
                                  i  v    i   i  i     v i    ?ii  v iv   v
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_126740934_   1333 CAATGAAGCTGAACCCCCACCTTAAGTCATATGCAGAAAT-AACTCAAAA 1381
                         v       i  i     i    i vii     i  i    -         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_126740934_   1382 TGGCTCATAGACATAAATGTCAATGC-AAAATT-TAAAGTACAATTTTAG 1429
                            v   ?    v       v iv  -    i -    --  -- i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA--AC--TCTTAG 538

  chr2_126740934_   1430 AAAAAACAAAAACATAGCTGTAAATTGTTGTGACCTCAGATTAGGCAATA 1479
                           i   -----      v?      iv i       ii i         i
  L1M4_orf2#LINE/    539 AAGAAA-----ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_126740934_   1480 ATTTCTTAATGAATGATA-GATATCAAATGCCCAAGTGACCCAAAAGAAG 1528
                         i       ------    -  i i    v  v    ii  --       i
  L1M4_orf2#LINE/    584 GTTTCTTA------GATATGACACCAAAAGCACAAGCAAC--AAAAGAAA 625

  chr2_126740934_   1529 ---TAGATCAATTAGGTTTGATTAAAATGTTTTGAAAAACT---GTGCT- 1571
                         ---     v    i ii  v  i     ---- -       ---     -
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAAT----T-AAAAACTTTTGTGCTT 670

  chr2_126740934_   1572 ------GCACAATCAGGAAAGTAAAAA-ACAACCTACAGAATGAGAGAAA 1614
                         ------i   v    i      i    -      i        i      
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_126740934_   1615 GTATATGCAAATCATACACTTGGTAAGGATAAGGTATCAAGAAAAAAACA 1664
                         i   v           i ii  i     ivvvv     v    -------
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA------- 763

  chr2_126740934_   1665 GGTTACATTTCTATCTAGATGGACACTCCCAGCTGATGAACTCATTAGCC 1714
                         -----------   v  i --  -    ii - -----      v  iiv
  L1M4_orf2#LINE/    764 -----------TATATAAA--GA-ACTCTTA-C-----AACTCAATAATA 793

  chr2_126740934_   1715 AAAAGATAATTGCAAGTAACCCAGTTAAGCAACGAGTAAAGTATTTGAAT 1764
                               ------   i       i  ? iv  i i i    v        
  L1M4_orf2#LINE/    794 AAAAGA------CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_126740934_   1765 AGACAGCTCTTCAAAGAAGATATACAAATGACCAACGATCGCAAGAAAAG 1814
                              vi   i                   i    ii v i  v      
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_126740934_   1815 ATTCTCAATACCATTTTATTA 1835
                           v     i i  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (108 / 62)
Gap_init rate = 0.04 (35 / 903), avg. gap size = 3.06 (107 / 35)  


2361 25.87 3.15 4.78  chr2_126766003_126769892     2482  3401 (489)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_126766003_   2482 AAAGATATTTTTTATGTTCATGGATCAGAATATTCAATATTGTTTCAATT 2531
                                 iii--            ii   v i i         vvi  v
  L1M4_orf2#LINE/      4 AAAGATATCCC--ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_126766003_   2532 TTAAC-CTTCTCAAATTGATGTATAGAGTCAATGAAATCTCAATAAAAAT 2580
                         vi  i-  i i         v  i   v    i v    i v  v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_126766003_   2581 TCCAGCTAGCCATGTTGTAGATATTGATGAAATCACTCTTGAATT-GTAA 2629
                         i      iv iv v   i   v     ii iv v ii  vi    -i  v
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_126766003_   2630 TAAAACTCAAAGAACCTACAGTAGCCAATACA-TCGCTGAAGAAGGAGAA 2678
                         vi   iv   i i   i v i       v   -  -i    i   i    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAAGAAGAA 200

  chr2_126766003_   2679 CCAGGTTATAGGACTCATACTATGCAAATTTAAGACTTCCTATAAAGCCA 2728
                          v i   iv        i   viv   v  i  i    v   i     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_126766003_   2729 CAGTATTCA-GCCAGCATGGAATTGGTGAAAGTATTAGACACATAGATCA 2777
                              v   - v   ii   v i   iiv   v  -     i        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGATCA 299

  chr2_126766003_   2778 ATGTAA-AGAGACTGAGAACCCAGAAGTAGATCCACACAAATATAGTCAA 2826
                            v  -   - i     ii      i  i i   i   vv   i     
  L1M4_orf2#LINE/    300 ATGGAATAGA-ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_126766003_   2827 TTGATCTTTGACAAATG-ACCAAAAGCAATTCAATAG-------ATAGCC 2868
                              i  i     iv -i    i v  -      i -------    i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTC 397

  chr2_126766003_   2869 TTTTCA-CAAATAATACTAGAACAGTTGGACATCCA-ATTAAAAAAAAAG 2916
                               -     ii i  i i   ii    i ?   -  -----------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT----------- 436

  chr2_126766003_   2917 AAAAGAAAAGAAAAAGAAAACAAATGAACCTAGACACAGACCTTAAAAGT 2966
                         --------- v       ------    vi i   v vv    i -----
  L1M4_orf2#LINE/    437 ---------GCAAAAGAA------TGAAGTTGGACCCCTACCTCA----- 466

  chr2_126766003_   2967 TACAACTTTCGCAAAAATTAACTAAGAATGAATAATAGGATTAAATTTAA 3016
                         --  v v vii            v i    i  v ?  ivi     v   
  L1M4_orf2#LINE/    467 --CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_126766003_   3017 AATGTAAAACTA-AAAATATGTAGAAAAAAACATAGGAGAAAATATATGT 3065
                         i vv        -    iviv     i          ? v    v vi  
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_126766003_   3066 AGCCCTGGATTTGGTAATGAGATTTTC----ATGCAACAACAAAATTACA 3111
                         ii  i   i  v  i    i---    ----  iii   v     vi   
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGG---TTTCTTAGATATGACACCAAAAGCACA 611

  chr2_126766003_   3112 ATTTATGAAAGAAAAAAACAATTAATTACACAC--TTAAAACTAAAAACT 3159
                          viv ii          vvi  v    iv  vi-- i    i        
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_126766003_   3160 TCT---TCTCAAAAGAGTCACTGTTAAGAGAAGAAAAGGACAAGCCACAG 3206
                          i ---ii     i  --    i i    i ivi   i     v      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGA--CACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_126766003_   3207 ACTAGGAGAAAATATTTGCAAAATACATGCCTAATTAAAAACTCAT-TCC 3255
                          v i                  vi i  ii  i  v iii   ii -   
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_126766003_   3256 AAAATATACAAATAACTCTTAGAAGTCAAGTAGAAGAAAGCAAACAACTC 3305
                          i      i   v        v  v    vv v  i  ii    i   i 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_126766003_   3306 ACTTTTAAAATGGCCAAAT-ATTTCAAAACACATCTCAACAAAGAAGATA 3354
                          v  ?v       v    v-    v  v v    i  vv           
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_126766003_   3355 GGCAGATG-CAAATA-GTGTCAGAAAACATGTTCAATACTACTTGTTGT 3401
                         vi  i   - v    - iiivv     v   i    i ii ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.03 (27 / 905), avg. gap size = 2.70 (73 / 27)  


2244 29.53 3.99 0.46  chr2_126809468_126814363     3528  4404 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_126809468_   3528 TGGAAAAACATTCCATGCTCATGAATTGGAAGAGTCAATATTGTGAAAAT 3577
                               i i  i     i     i         v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126809468_   3578 GGACACACTGCCCAAAGCAATCTATAAATTCAATGCTATTCTTATCAAAC 3627
                           vv i   v      vii     i i      i  v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126809468_   3628 TACAAACATCATGTTTCCCAGAATAGAAAAAACTAGTC-TAAAATTCAGA 3676
                          v v i vv v v   iv     vvvi v  i  ii  -         v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_126809468_   3677 TGGAACCAAAAAATAGCCCAAATAGCCAAAGCAATGCTAAGCAAAAAGAA 3726
                              viiv  iiv v  vi          i    vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_126809468_   3727 TAAAGCTGAAGCCATCTTATTACCTGACTTCAAACTATACTATGAGGATA 3776
                         i    i  i  vvv  vi i v  ii i      viv     ii i v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_126809468_   3777 TAGTAACCAAACCAGCATGGTACTGATACAAAAGCATACACATAGACCAA 3826
                         i     i   iv   ii        ii i  iiii v   i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_126809468_   3827 TGGAACAGGTTAGAGAACCGAGAAAGAAAGCCACACACCTACAACCATCT 3876
                              i  iv v    ii v     v   v   i   ii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_126809468_   3877 GGTCTTTGATAAACTTGACAA--CAATTAGCAATGGAGAAATTACTTCCT 3924
                          i i  i  i  ivv  v   -- v   --      i    vv ivvi  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATT--CAATGGGGAAAGAATAGTCT 398

  chr2_126809468_   3925 ATTAAGTAAATGGTGCTGGGATGACTGACTAGCCATAAACAGAAGACTGA 3974
                         v  v ii              ii    iv  ?   i vi  i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_126809468_   3975 AACTGGACCCTTTCTTT-CACCATATA-AAAAAGTAAAT-AAAATGAATT 4021
                          ii       i v i i-         -     v   v -      i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_126809468_   4022 AAATATTTAAATATAAGACCTCAAACTATAAAAATCCTAGACATAAACCT 4071
                          ? v ii     i     v  v           v  i    viv    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_126809468_   4072 AGGACGTA--CCATTCTGGACACAGGCCTTATCAAAATATTTATGGGTAA 4119
                            ?-   --i -   vv   viv  vi viv   vivv  iv i i  v
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_126809468_   4120 GTGCTCAAAAGCAATTGCAACAAAAACACAAATTGACAAGTGGGATCT-- 4167
                          vvvi        vvv         iv v    v  i  i v   ii --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_126809468_   4168 ---------AGAACTTCTGCAAAACAAAGAA-ACCGTCAACAGAGTAAAC 4207
                         --------- i     i  iivvv     i -  ii    v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_126809468_   4208 ATACAAC----AGAATTGGAGAAAATATTTGCAAACAATGCACCTGACAA 4253
                          v     ----     v                  iv  ii i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_126809468_   4254 AGGCCTAATATACAGAATCCATAAAGAAC-CT---AATGCAACAAGCAAA 4299
                         i  v  vi   v      vi         -  ---  iv   i  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_126809468_   4300 A-ACAAATAACTTCATTAAAAAGTAGGCAAAGAACATGAACCGACACTTA 4348
                          -         iiv   ?    i i       i iv    iv    i  v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_126809468_   4349 TC---AGAAGGCCTACAAGCAGCCAACAA--ACATGAAAAAA-GTTCATC 4392
                           ---     iiv     iii     i  --         i - i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_126809468_   4393 ATCACTAATGAA 4404
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (146 / 109)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.17 (39 / 18)  


2783 19.80 2.95 4.78  chr2_126814448_126816736      564  1275 (1014)    L1M4_orf2#LINE/L1        6   704 (204)  

  chr2_126814448_    564 AGACTTTCCATGTACATGAGTTGGATGAGTTCATATTAATAAGATGGCAA 613
                            iv i      v    ii     v  v  v     iv           
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_126814448_    614 TATTCTTCAAATTGATCAACAGATTTGATTCAGTTCTTACAAAAAACACA 663
                           i  ii          v       ii iv  i i i  iv    v v  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_126814448_    664 AGGTAGATTATTTGAAGAAATTGACAACATAACCCTAATATTTATATGGA 713
                         - v ivv  v    v            vv i i     v   i       
  L1M4_orf2#LINE/    106 -GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_126814448_    714 AATGTAAAGGATCTAGAATAGGCAAAATA-----------GAATAATAAT 752
                             i  i   i i       v     i -----------   v  i  v
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_126814448_    753 GTTGGAAGAATCACACT---CAGATTTAAAAATTATTGCACAGCTACAGT 799
                               i  v       ---  iv  i    v   i i  v         
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_126814448_    800 AATCAAGGCAGTGTTGTATTGGCATAAGGACAGGCATATAGATCAATGGA 849
                                i      v   i           i  i                
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_126814448_    850 TCAGAATTGAGAGTTCATAAAAAAAGAACAAACTCATAT-TTTG-GGACA 897
                         vi            i  v   -------i    i    i-   i-  v  
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAA-------TAAACCCATACATTTATGGTCA 347

  chr2_126814448_    898 CTTAAATTTTTACAAAGTTACCAAGATGATTCAATTACAAAATAATAATA 947
                         v  i v   iv    i v i      iv       vivi   v    i v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_126814448_    948 TTTTCA-CAAATGGTGCTGGGACAATTGGATATTCACATGCAAAAAAAAT 996
                               -                  i      ?i           i  --
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-- 445

  chr2_126814448_    997 TAGTAAAGTTGGACTCCTAAGTACTCCTACTCTACCATACACAAAAATTC 1046
                         --- i         i    -----i ii  ---      i         v
  L1M4_orf2#LINE/    446 ---TGAAGTTGGACCCCTA-----CCTCAC---ACCATATACAAAAATTA 484

  chr2_126814448_   1047 ACCAAAAATGAATTTAAGATCCAAATGTAAGAACTAAATGTAAAAACTGA 1096
                           iv      i  iv?   i i          i     -------   --
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA-------ACT-- 525

  chr2_126814448_   1097 ATCTATAAAACTCTTAGAATAAAACATAGCCATAAATCTGTATGACTTTG 1146
                         ----               v         v?i       vii    i   
  L1M4_orf2#LINE/    526 ----ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_126814448_   1147 GAAT-GGTAATGATTTCTTATGTATGGCACCAAAAGCACAAGCAACAAAA 1195
                          iv -  i    i       vi    i                       
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_126814448_   1196 GAAAAGA--AATAAATTGTCCCTTATCAAAATTTAAAATATTTGCTCTTT 1243
                              i --i        vv i i         v    iv    iv   i
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_126814448_   1244 AATGGATACCATTAAGAAATTGAATA-ACAGCC 1275
                           v   i  i  i      v    v -   i  
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

Transitions / transversions = 1.51 (83 / 55)
Gap_init rate = 0.02 (15 / 699), avg. gap size = 3.67 (55 / 15)  

 937 16.73 2.33 3.89  chr2_126814448_126816736     1542  1798 (491)    L1M4_orf2#LINE/L1      656   908 (0)  

  chr2_126814448_   1542 AAAACT---GTGTCTCAAAAAAAAAAAAAAAGAAAAAGAAAAGAAATTAA 1588
                               ---   ii     ii v vv vv      iv       ------
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA------ 699

  chr2_126814448_   1589 ATGACAACCCACAAAATGGGAGAAAACATTTACAAATCCTACATCTGATT 1638
                         ----         i            i    i      v  i       v
  L1M4_orf2#LINE/    700 ----CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_126814448_   1639 AAAGACTTCTATCAAGAACATATAAGTAACTCTCACAACTCGATGAAAAT 1688
                          ii     v    v    i      iv      i       i  i v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_126814448_   1689 ATGACAAATAACC-AATT-AAAAATAGGCAAAGAATATAAATAGACATTT 1736
                          v           -    -      i       i  v i           
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_126814448_   1737 CTCCTAAGAAGATGTACAAATGTTCAATATGCACATATAAA-ATGGTCAA 1785
                             v        i        vi     v      iv   -   v    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_126814448_   1786 CATCTAGACCCAA 1798
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.05 (22 / 21)
Gap_init rate = 0.02 (5 / 253), avg. gap size = 3.20 (16 / 5)  


 454 21.09 10.16 0.78  chr2_126826359_126828929      957  1084 (1487)    L1M4_orf2#LINE/L1      110   249 (659)  

  chr2_126826359_    957 CTTTTTTTGTAGAAATTGA---GTAGATTCTAAAAAATATTTGGAAACAG 1003
                          i       i         --- iv   i      vvi  v      iiv
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_126826359_   1004 AAAAGCCCCAGAATGCCCAAAACAATTTTTAAAAAGAAGATCAAAG---- 1049
                           ii v        iv          i  v          v     ----
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_126826359_   1050 --GCTTCACTACTGTC---TTTCCAAACTTACTG-AAGGCT 1084
                         -- vi    -   vi ---    v         i-  i   
  L1M4_orf2#LINE/    210 AGGACTCAC-ACTTCCCAATTTCAAAACTTACTACAAAGCT 249

Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.04 (5 / 140), avg. gap size = 2.80 (14 / 5)  

1267 25.14 3.57 9.34  chr2_126826359_126828929     1354  2081 (490)    L1M4_orf2#LINE/L1      223   908 (0)  

  chr2_126826359_   1354 CTCCATCTCAAAAAAACCTTATTGAAAAGTTATAGTAATGAAGACAATGT 1403
                          i v  i      ----    i iv    i  i      v      i   
  L1M4_orf2#LINE/    223 CCCAATTTCAAAA----CTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_126826359_   1404 ---ACTA-CATAAGGACAAAGAAATGGGCCA-TGGAATAGAACAGTGTAT 1448
                         ---   i-        i i v v  i ii  -          iv v - v
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG-AG 317

  chr2_126826359_   1449 TTCTGAA-TACACGTGTTTCAGGTGTTTTTTTTTTAAGTGCTAAAATATC 1497
                          i v   -  v  -----i  viii   ---------i  -------i  
  L1M4_orf2#LINE/    318 TCCAGAAATAAAC-----CCATACATTT---------ATG-------GTC 346

  chr2_126826359_   1498 AATTGACATTATTTATTTCCTTGCTCTTACAATAG---CAAAGTAATTCA 1544
                               ---------   -- i -----    vi ---   iiiv     
  L1M4_orf2#LINE/    347 AATTGA---------TTT--TCG-----ACAAGGGTGCCAAGACCATTCA 380

  chr2_126826359_   1545 ATGGTAATGAGATAATCTCTTTTTAAAAAATGATGCTAGAACAACTAGAT 1594
                             vi viii   i   --   i  v     i    i i      i   
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCT--TTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_126826359_   1595 AAAAATATGTAAAAATAAGAACCTTTATTCTTGCATCACACCATACATAA 1644
                          ?vv i   i    iv v   vi vv ii i i v          i i  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_126826359_   1645 AAATTAATTCAAAATGGATCATATAC-TAAA-GTA-GAATTAAAACTATA 1691
                                i             ? v  -    -   -  ii          
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_126826359_   1692 AAGCTCATTTAAGAAAGCA---GAATAATGTCTTCATGACCTTGATGTAA 1738
                           i   v vv      i  --- ?i   -i     i        ivv  i
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAG 577

  chr2_126826359_   1739 ATAAAGATTGCCTAAA-ATGACTCAAAGTGTATTAACTGTAAA-TAAAAA 1786
                         ii  v i  v i  i -     v v  iv i iv i vii   -v     
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_126826359_   1787 ATA-ATAAATTGGAATTCAACAAAATTTAAAACTTCAACAAAATTAAAAA 1835
                            -          v    v       v       ---------------
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTT--------------- 662

  chr2_126826359_   1836 CTTCTGCTTATTAAATACATGGTTCTGCAAGTGAAAAAGCAAGGCAAAGA 1885
                         -  v     -iv  iv   ivi ivv v         ii   vv  v   
  L1M4_orf2#LINE/    663 -TTGTGCTT-CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_126826359_   1886 CTTAGAAAATATATTCATAA--TATATATCTGAAAAAAGAGACTTATGTT 1933
                         v vi  i  v     iii  --i          v  -- i     i i i
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAA--GGGACTTGTATC 758

  chr2_126826359_   1934 TGAAATAGAGAAATAATGTATAAAAATCAATAGTAAAAGGACAACCAATC 1983
                         iii    v v   v  iviv  v  v      i     i     vi  i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_126826359_   1984 TAATTTCAATATGAGCAAGAGATGTGAA----CACTTTACAAAGGAATAC 2029
                         i    ?v  v   i    ii   v    ----  i  iv v  i   v i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_126826359_   2030 ATAGGAATGGCCTTCAA--AGTATGTGAAAAAGAACCTCAACATTGTTAG 2077
                            vi       ---  --  i ii      -  vv        ii????
  L1M4_orf2#LINE/    859 ATACAAATGGCC---AATAAGCACATGAAAA-GATGCTCAACATCAZZZZ 904

  chr2_126826359_   2078 CCAC 2081
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.49 (107 / 72)
Gap_init rate = 0.04 (30 / 686), avg. gap size = 3.13 (94 / 30)  


2898 26.03 2.68 1.34  chr2_126848770_126852347.rev     2198  3092 (486)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_126848770_   2198 GAAAAAATATTCCACGCTCATGGATAGGAAGAATCAATATCATTAAAATG 2247
                          i   i    i   i i        v      v i     ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_126848770_   2248 GCCATATTGCCCACAGCAATTTACAGATTCAATGCTATTCCTATCAAACT 2297
                           v   i v    v vii  i           i  v  i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_126848770_   2298 ACCAGTAACATTTTTAACAGAACTAGA-AAACAATATTTTAAAATTTATA 2346
                         v    ivi v     vi     v v  -  i vi-  ii       i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCATA 150

  chr2_126848770_   2347 TGGAACCAAAAAAGAGCCTGAATAGCCAAGGCAATCCTAAGCAAAAAGAA 2396
                              viiv  ii  v  v          ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_126848770_   2397 CAAAGCTGGAGGGATCACACTACCTGACTTCAAACTATACTACAGGGCTA 2446
                              i      iv       v  ii i      viv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_126848770_   2447 CAGTAACCAAACCAGCATGGTCCTGGTACAAGAACGGA---AGAGACCAG 2493
                               i   iv   ii    v    i i   i ii  --- v   i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_126848770_   2494 TAGAACAGAATCAAGAGCCCAGAAATAATAATGCACACTTGAAATCATTT 2543
                          i   i     ii    i          vvviii   i  ivii   v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_126848770_   2544 TATCTTTGACAAACCTGAAAAAAACAAGCATTTGGAAGGGACT--TCCTA 2591
                         v  i  i     ivv  vv  i v  vv  v v  i ii  v --  i -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT- 399

  chr2_126848770_   2592 TTCAATAAATAGTTCTGGGATAACTAGCTAGCCACATGCAGAAGACTGAA 2641
                              i    i  v      i    i v  ?         i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_126848770_   2642 GCTGGACCCTTACCTTACACCACATACAAAAATCAACTCAAGATGGATTA 2691
                          i       i     i      i          i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_126848770_   2692 ACGACTTAAATGCAAAACCTAAAACTGTAAAAACTCT-GGAAGATAACCT 2740
                         ?v   i      i  i v        i     -    -i     v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr2_126848770_   2741 AGG---AAATACCATTCTGAACATAGATACTGGCAAAGATTTC------A 2781
                            ---    -- v iv   v v i i -iv     v i    ------ 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--CTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr2_126848770_   2782 CGACATGCTGAAAGCAATCGCAACAAAAGCAAAGACTGACAAATGGGACC 2831
                         i    -- ii      vvv          v   i iv  i    v    i
  L1M4_orf2#LINE/    596 TGACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_126848770_   2832 TAATTAGACTAAAGAGCTTCTGCACAGGAAAACAAACTATCAACAGAGTA 2881
                          v  i i v v  i i   i  ii vvv   iv v        v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_126848770_   2882 AACAGACAAAATACAGAATGGAAGAAAATATTTCCAAACTATG-ATCCTG 2930
                           v      vvi         i           v    ii  i-   -  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC-TG 742

  chr2_126848770_   2931 AAAAAGGTCTAATACCCAAAAACTATAA-GAAATGTAAATA-AATTTACC 2978
                          v  i  v  vi  i   i  vv     -   v v ---  -  i i vi
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCT---TACAACTCAAT 789

  chr2_126848770_   2979 AGCAAAAA-----ACAACCCTGTTAAAAAGTGGGCAAAGGACATGAACAG 3023
                          ii     ----- i     vi  ?    i           iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_126848770_   3024 ATACTTTTCAGAAAAAGACATACACATGGCCAACAAGTGTATGAAAAGAT 3073
                          i i  i  vi  i    i     v        i   iii          
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_126848770_   3074 GCTCAGCTTCCCTAACCAC 3092
                              i v  v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (141 / 89)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 2.00 (36 / 18)  


2892 25.03 4.21 0.91  chr2_126867736_126872021.rev     2916  3794 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_126867736_   2916 TGGAAACACTTCCCATGCTTATGAATAGGTAGAATCAATATTGTGAAAAT 2965
                               v iv       i i   i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126867736_   2966 GACCATACTGCCATAAACAATCTACAAATTCAATGCAATTCCCATCAAAA 3015
                          i v     v  vv  vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126867736_   3016 TACCA-CCACCATTCTTCACAGAACTAGAAAACAAGATCTTAGAATTTAT 3064
                          v   - ii  -  i  ii     v v  v  vvv    i  i    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_126867736_   3065 ATAGAAC--CAA-------AGCATAGCCAAAGCAAGACTAAGCAAAAAGA 3105
                           i   v--   -------  v         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_126867736_   3106 ACAAAACTGGAGGCATCACATTACCTGATTTCAAGTTATATTATAAGGCC 3155
                              ii      vv     i v  ii       iviv  i  i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_126867736_   3156 ACAGTTACCAAAACAGCATGGTTCTGATATAAAAATAGGCACATAGATCA 3205
                              v i   i    ii    v   ii    ii    i  i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_126867736_   3206 ATGGGACAGAATAGAGAACCCAGAAATAAACCCAAATACTTATAG----- 3250
                             i i     v    ii               v i i    i -----
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_126867736_   3251 ----------CAAA-----CAAAAACATAAAGTGGGGAAAGGACACCCTA 3285
                         ----------   i-----   i v   vv i         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_126867736_   3286 TTCAACAAATGGTGCTGGGATAATTGGCAAAACACATGTAGAAGAACGAA 3335
                                             i  i   vv ?v      i i     i   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_126867736_   3336 ACTGGATCCTCTTCTCTCACCTTACACAAAAATCAACACAAGATGGATCA 3385
                         ii    i  iivi   v    v  i        i   v   i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_126867736_   3386 AGGACTTAAATCCATGACCTGAAACTATAAAAATTCTAGAAGATAACATT 3435
                         ?i   i     vi v  v  i           v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_126867736_   3436 GGAAAAACCCTTCTAAACATTGACTTAGGCA--GGGCTTTTATGATCAAG 3483
                           ?iv  vi    vvi  v   iv       --  vi i   -   - v 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GAT-ATG 597

  chr2_126867736_   3484 AGTCCAAAAGCAAATGCA-TAAAAACAAAGATAAATAGCTGGGACTTAAT 3532
                          vv         v v   -i    iv   i   i   iv v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_126867736_   3533 TAAACTAAAAAGCTCTTGCGCGGCTGAAGGA-ACAGTCAGCAGAGTAAAT 3581
                         i   v v    i  i   i  vv -i     -  vi   iv i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTC-AAAGGACACTATCAAGAAAGTGAAA 696

  chr2_126867736_   3582 AGACAACCCACACAGAGTGGGAGAAAATCTTCACAATCTATACACCTGAG 3631
                                     --  i           v  ii   vii   i i    v
  L1M4_orf2#LINE/    697 AGACAACCCACA--GAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_126867736_   3632 AAAGGACTGGTATCCAGAATCTACAATGAAC-CTAAAGTAATT-ATCAAG 3679
                           i     v           v  i  v    -  v --i  i - vi  v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAAT 792

  chr2_126867736_   3680 AAAAAAACAAACAATCCCGGTAAAAAGTGGGCTAAGGACATGAATAGAAA 3729
                              i     i  i  viv ?    i     v     iv        v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_126867736_   3730 ATTCTTAAAAGAAGACATATAAATGGCCAACAAACATATAAAAA-ATGCT 3778
                         v    iv        i   i          i  i  i  i    -     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_126867736_   3779 CAACATTACTAATGAT 3794
                               i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (127 / 89)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.65 (45 / 17)  


 386 17.65 12.75 4.90  chr2_126923927_126930986.rev      414   515 (6545)    L1M4_orf2#LINE/L1        1   110 (798)  

  chr2_126923927_    414 TGGAAAGATATCCTGTGTTTATAGACCAAAATAATTAATATTGTTAAAAT 463
                                      ii    i  i  iiii  v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126923927_    464 ----ATACTAGGCAAAGTGATC---------AATGCAATCCCTATCAAAA 500
                         ----     vvv    v     ---------  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126923927_    501 TTCTGCGGCAACTGC 515
                          i -----  i    
  L1M4_orf2#LINE/    101 TCC-----CAGCTGC 110

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.03 (3 / 110), avg. gap size = 6.00 (18 / 3)  

3198 27.61 0.22 0.33  chr2_126923927_126930986.rev     4160  5068 (1992)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_126923927_   4160 TGGAAGAACATTCCCTGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4209
                              ii i  i  v  i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_126923927_   4210 GGCCATACTGCCCAAGGTAATTTATAGATTCAATACCATCCCCATCAAGC 4259
                            v     v     iv i  i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_126923927_   4260 TACCAATAACTTCCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4307
                          v   iivi i ii  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_126923927_   4308 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 4357
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_126923927_   4358 AACAAAGCTTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 4407
                                -       vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    199 AACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_126923927_   4408 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 4457
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_126923927_   4458 CAATGGAACAGAACGGAGCCCTCAGAAATAATGCCGCATATCTACAACTA 4507
                                 i    iv   vvii         vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_126923927_   4508 TCTGATCTTTGACAAATCTGAGAAAAACAAGCAATGGGGAAAGTATTCCC 4557
                         vi    i  i     ivv  vv  i v  vv            v  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_126923927_   4558 TATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4607
                          v  i  i       i      v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_126923927_   4608 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAAGGAT 4657
                           ii    i    v   i     v              i    i v    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_126923927_   4658 AAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4707
                         v ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_126923927_   4708 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 4757
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_126923927_   4758 ACACCAAAAGCAATGGCCCCAAAAGCCAAAATTGACAAATGGGATCTAAT 4807
                                     vvi  vv      vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_126923927_   4808 TAAACTAAAGAGCTTCTGCACAGCAAAAGAGACTACCATCAGAGTGAACA 4857
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_126923927_   4858 GGCAACCTACAAAATGGGAGAAAATTTTCGCAGCCTACTCATCTGACAAA 4907
                          i     i   i             v  i   ivii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_126923927_   4908 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 4957
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_126923927_   4958 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 5007
                         i     i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_126923927_   5008 CAAAAGAAGACATTTATGCAGCCAAAAAACATATGAAAAAATGCTCACCA 5057
                          v        i  vi viii     v  i  i       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_126923927_   5058 TCACTGGCCAT 5068
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.25 (5 / 4)  

2355 24.34 9.13 1.72  chr2_126923927_126930986.rev     5814  6569 (491)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr2_126923927_   5814 AAAATTTCAATGGCATTTTCCACAAGAAATAGGAAAAC-AATCTGAAAAT 5862
                              ii  iiv  v    iii  -     v iv  i -i   iv     
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCA-GAAATTGACAAGCTGATCCTAAAAT 145

  chr2_126923927_   5863 TCATATGGAACCACAAAAGACTTCGAATAGTCAAAGCAAACTTGAACAAG 5912
                                   vii   ii   iiv      i    i   v      v   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_126923927_   5913 AA---CAAAGCTGGAGGCATCACACTTCCTGAATTCAAAATACATTACAG 5959
                           ---     i      vv          ii v       ivi i    i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_126923927_   5960 CGGTATAGAATTCCTAGCAGAATGACACTGGC------------------ 5991
                         v v  i  v v  vvii   vi  ii      ------------------
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_126923927_   5992 --CAATAAAAGAGAA--AAGCCAGCCCAGATATTTAATATAAATCCACAC 6037
                         --    ii  v    --i  --  i     -----    --  i   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAG--AGTCCAGA-----AATA--AACCCATAC 336

  chr2_126923927_   6038 ATTTATGATCAACTGATCTTTGACAAAGTTGCCAAGA--ATACAATGGGG 6085
                                i    i    i  i     i v        --  v        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_126923927_   6086 AAGGGATAGTCTCCTTAATAAACAGTGTAGGGAAAATTGGATATCCACAT 6135
                           i i       ii i  i   ii   iv    v  i      ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_126923927_   6136 GGAGGAGAAT------------------------ATACACAAATCTT--C 6159
                          v ii     ------------------------   i     vv  -- 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_126923927_   6160 TTAAGATAAATTAAATACTTAAATGTAAGACCTGAAACTGTAAAATGGCT 6209
                          i  i  ii  i ? v  i           v  i     i     ivvi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_126923927_   6210 AGAAGAAAACATAGAGGAAAAGCTTCTTGACATTGCTCTGGGTAACAATT 6259
                                       i? v   v    v    v   vvi i  i  iii  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_126923927_   6260 TTTTTTAATATGATCCTAAAAACACAGGTAACAAAAGCAAAAATAGACAA 6309
                          i  v-i      iv i    i    i i        v         i  
  L1M4_orf2#LINE/    587 TCTTA-GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_126923927_   6310 ATGGGGTTGCATCAAACTAAAAAGCTTCTATACAGCAAAGGAAACAATTA 6359
                           v  ii v       v v    i   i i i vv       v  v  i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_126923927_   6360 ACAAAGTCAAGAGACAACCTATAAAATAGGAGAAAATATTTGCAAACCAT 6409
                          v     v  i        i i i   i                  i   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_126923927_   6410 ACAT-TGGTAAG---TTAATATTCA--ATATACTTAATAATTT---CAAT 6450
                          i  -  i    ---i vi   i  --     - v  v  i i---   i
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATA-TAAAGAACTCTTACAAC 784

  chr2_126923927_   6451 TTAACAGCAAAAAAA-----AACGCACATTAAAAATAGGCAAGGGATT-G 6494
                          i  i ii     i -----   v  vv ?      i     i     - 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_126923927_   6495 AGCAGAAATTTCTCAAAAGAAGACACACAGATTGCCAACAGGTATATGAA 6544
                          ii   v       v        i i   i  v     i i i i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_126923927_   6545 CAAAATGCTCAACATCCCTAATTAC 6569
                         -  i            v????????
  L1M4_orf2#LINE/    885 -AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (119 / 61)
Gap_init rate = 0.02 (20 / 812), avg. gap size = 4.10 (82 / 20)  


3686 18.50 3.19 4.07  chr2_126973071_126977286     2817  3724 (492)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr2_126973071_   2817 TATTTTATGTTTGTAAATCAAAAAATTAATAATATTGTTAAAATGCTAGT 2866
                            iii     ii ii  iii  i i --            i   vi i 
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACT--TAATATTGTTAAGATGGCAAT 56

  chr2_126973071_   2867 ATATCCCAATTTCATCTACAGATTCAATGCAATCCCTATTAAAATTCTAA 2916
                          ivi     v  v              i           i     i i i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_126973071_   2917 CTAGTCATTTAT-CAGAAATTGGCAAGCTGATCCTAAAATATATATGCAA 2965
                           - i v   v -         i                 vi     v  
  L1M4_orf2#LINE/    107 CT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_126973071_   2966 ATGCAAGGAACCAAAAATAACCAAAACAATCCTGAAAAAGAATAACAAA- 3014
                                 i   v i    i           i          v      -
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_126973071_   3015 -TGGA---CTCCCACGTTGCCCATTTTTAAAA-TTACTACAAAGCTATGG 3059
                         -    ---   v   -  -    v   i    -              ii 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACAC-TT-CCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_126973071_   3060 GAATCAAGACAGTGTGGTACTGGCATAAAGACATACAGAGAGATCAATGA 3109
                         v                           i  i v   v v         i
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_126973071_   3110 ACTAGAATTGAGAGTACAGAAATAAACCCTCCCCATTTATGGCCAATTGA 3159
                          v             v             -viv         i       
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCC-ATACATTTATGGTCAATTGA 352

  chr2_126973071_   3160 CATTTTACACAGATACCAAGACAATTCGGTTTGAAAATGTT-GTCTTTTT 3208
                         iv  iv   vi i i       v    ii vv i   viv -       i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_126973071_   3209 AATGTATGGTGGTAGGACAACTGGATACCCACATGCAAAAGAATAAAGGT 3258
                           iiv      v i             ?                i   v 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_126973071_   3259 GGATTCCTTACTTATATCATAATTAATTTACAAACAATTCCTCACAAATA 3308
                            ii   vv  i i i    -------      --------------- 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATA-------TACAAA---------------A 480

  chr2_126973071_   3309 ATTAACTTTAAATTAATCATAAATGTGAATGTAAGAGTTAAAATTTTAAA 3358
                                iv    vi    ? i iv i          i     i v    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_126973071_   3359 AACC-----------CACAGGATTA-----TCATGATGTTAGATTAGTCA 3392
                          vi -----------  i   ?v  -----  i   iv  i i    v  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_126973071_   3393 ATGGTTTCTTTGATGTGACACCAAAAGCATAAGCAATAAAAGAAATAATA 3442
                                   v   i              i      i        v    
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_126973071_   3443 GATAAATTGGATTTCATCAAAACTACGAACTTTTATTATTCATAGGACAC 3492
                                    i          i  vi       i vv    v       
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_126973071_   3493 AATCAAGAAAGTGAAAATACAATCCACAGAATGGGAGGAAATACATATAA 3542
                         v                v    i              i     iv ii  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_126973071_   3543 ATCACATACATATATGTATACAAAGCAACTTCTATC-AAAATCTTTAAAG 3591
                             i   ---- v  -   ---  vi    v    - i   v v     
  L1M4_orf2#LINE/    731 ATCATATA----TCTG-ATA---AGGGACTTGTATCCAGAATATATAAAG 772

  chr2_126973071_   3592 AACTCTTATAATTCAATAATAA---GACAAA-AACTGAATTAAAATATAG 3637
                                 i  i          ---      -   iv    ?   v  i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_126973071_   3638 ACAAATTATTTCAATTGCTGTTTTTCCAAAGAAGATAATTTAAACAGCCA 3687
                         i    vv    v   v vii   i             - vi   ii    
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA-TACAAATGGCCA 871

  chr2_126973071_   3688 AGAAGCATAGGAAAATATGTTCTACATCATTAATCAT 3724
                          v     i v     v   i  v      ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (97 / 67)
Gap_init rate = 0.02 (21 / 900), avg. gap size = 3.14 (66 / 21)  


4144 19.02 1.90 0.34  chr2_127033588_127038070     3098  3991 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_127033588_   3098 TGGTAGTACATCCCATGTTCATGGTTTGGAACACTTAATATTGTTTAGAT 3147
                            v iv i               v      v             v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127033588_   3148 GGAAATACTATCCAAAGCAATAATCACATTCAAGGCAATTGCTGTCAAAG 3197
                           v      vi     vii  vvv  v      v     iv  i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_127033588_   3198 TCCCAACAGCCTTTTGTGTGGAAATGAAAAAGTGTATCCTCCAATTCATA 3247
                              i v       v  ii     vi v   ivv     vv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_127033588_   3248 TG-AAATGCAAGAGTGCCTGAATAGCCAGAACAGTCTTGACAAGGAA--- 3293
                           -         i vv  v         i    i      v  i   ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_127033588_   3294 CAAAGTTGTAAGGCTCACAATTACCAATTTCAAAACTTACTACAA-GCTA 3342
                                 v i i      v  v                      -    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_127033588_   3343 CAGCAATCAAAACAGTGTGGCACTGGCA-AAGGATAGACATTTAGCCTAA 3391
                            i      i         i       -            v   vii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_127033588_   3392 TTAAATAGAATTGAGAATCCATAAATAAACCTATACATCTATAGTCAATT 3441
                          vi             i    v         i      i   i       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_127033588_   3442 AATTGTTGACAAGTGTGCTAAGATCATTTAATGAGGAAAGAATAGTCTCT 3491
                         i   v i      v    i    i    i    i              i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_127033588_   3492 TCA-CAAGTGGTACTGGAATAACTAGATATCCAGAGGCAAAACAATAAAT 3540
                            -   i    i    i i    i    ?   v v      v   i  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_127033588_   3541 CTGAACTCATACCTTATACCATACACAAAAATTAACTCAAAATGGGTGAA 3590
                         i  i  i v     i i      i                     i v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_127033588_   3591 ATTCCTAAATATAAGAGCTAAAACTATAAAACTATTAGAAGAAAACATAG 3640
                          vv       i                      v                
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_127033588_   3641 GAGTAAATCTTCATTATCTTTAATTTTTTAGTGAATTATTAGATATAATA 3690
                          ?          i v i   vii  vvvi i  iv  v        i i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_127033588_   3691 CCAAAAGAATAAGCAACAAAATAAAAAAATACATAAAATGGATTTCATCA 3740
                                v i           -i        v     v    i       
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_127033588_   3741 AAATTAAAAACATTTG--CATCAAC--ACATTAATAAATAATTGAAAACA 3786
                                    v    -- v    v--   i  vi  iv  v      v 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_127033588_   3787 TCACCTAGGGAATGGGAAAAAATATTTGACAATGATATAGCTAATAAATG 3836
                         iv   i vi        i          vv   v     v  i    iv 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_127033588_   3837 TCTGGTATCCAAAACATGTAAAGAGCTCTTACAAGTCAACAACAAAAAGA 3886
                         v  v       i  i  i      i         v    i  i       
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_127033588_   3887 CAATTCAACTT--TTTAAA--TGGGCAAGGTACTTGAACAGACTTTACCC 3932
                            v -   ii--  ?   --       i v i     i    v  -i i
  L1M4_orf2#LINE/    800 CAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT-TCT 847

  chr2_127033588_   3933 CCAAAAAAGATA--CAAATGGCTAACAAGCAAATGAAAAGGTATCCAACA 3980
                              i      --        i  i     v        i iii     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_127033588_   3981 TCACTAATCAC 3991
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.21 (91 / 75)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


2814 25.82 4.44 1.14  chr2_127053560_127055442      534  1412 (471)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_127053560_    534 TGGAAAAATATTCTATGCTCATGGATAGGAAGAATCAATATCATGGAAAT 583
                               i    i i   i        v      v i     ii vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127053560_    584 GGCCACACTGCCCAAAGTAATTTATAGAATCAAATGCTATTCCCATGTAA 633
                            v i   v      v i  i  i   v    -i  v  i  i  vv  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAA 99

  chr2_127053560_    634 CTACCATTGATAGTCTTCACAGAATTAGAAAAAACTACTTC-AAAATTCA 682
                         v v   viviivv i  ii     v v  v  i-  iv i -        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_127053560_    683 TACGGAACCAATAAAGAGCCAGTATAGCCAAGACAATGCTAAACAAAAGG 732
                           i    viivv ii  v    v        i     vi i  v  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_127053560_    733 AACAAAGCTAGAGGTATCATGCTACCTGACTTCAAACTATACTACAAGGC 782
                                i i    vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_127053560_    783 TACAGCAACCAAAACAATATGGTACTGGTACAAAAACAGACACATAGACC 832
                              i  i   i   i i         i i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_127053560_    833 AATGGAACAGAATAGAAATCTCAGAA-TAAGACCACACATTTATAACCAT 881
                                i     v  i vii     -   iv   i        iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_127053560_    882 CTGATCTTCAACAAACCTGACAAAAACAAACAATGGGGAAAGGATTCCCT 931
                         i    i   i    ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_127053560_    932 ATTTAATGAATGGTGCTGGGAGAACTGGCTAGCCATATACAGAAAACAGA 981
                         v  i  ii             v      v  ?   i  i  i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_127053560_    982 AACTGGACTCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGATT 1031
                          ii     i   v   i    iv                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_127053560_   1032 AAAGACTTAAATGTAAAACCCAAAACTATAAAGACTCT-AGAAGAAAACC 1080
                          ?    i         i v i           -     -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chr2_127053560_   1081 TAGGCA-ATACCATTCAGGATAT--AGTCATGAGCAAAGATTTCAT-GAT 1126
                             ?i- v i -   iv  iv --i  i --i    v i    v -   
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGAT 594

  chr2_127053560_   1127 GAGAATGCCAAAAGCAATTACAACAAAAGCAAAAATTGAGAAATCGGATC 1176
                         - vi ii         vvvi         v      v  v    i   ii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_127053560_   1177 TAATTAAACTTAAGAGCTTCTGCACAGTTTG--TGAAACTATCCTCAAAG 1224
                          v  i   v    i i   i  ii --  ii--v  v      vvv    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGC--TTCAAAGGACACTATCAAGAAAG 691

  chr2_127053560_   1225 TGAACAGACAACCTACAGGATGGGAAAAAAGTTTTTGCAGCCTATCCATC 1274
                             v        i    i      i    - v      ivii  vi   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATC 740

  chr2_127053560_   1275 TGACAAAGGTCTAATATACAGAATCTACAAGGAACTTAAACAAATTTACA 1324
                            i  i  v  vi   v      v  i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_127053560_   1325 AGAAAAA-----ACAACCCCATTAAAAAGTGGG-AAA----------AGA 1358
                          v     ----- i     v   ?    i    -   ----------   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_127053560_   1359 CATTTCTCAAAAGAAGACATGTATGTGGC--------------AAAAATG 1394
                                 v        i  ii vi    --------------   i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_127053560_   1395 CTCAACACCACTGATCAT 1412
                                i  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.58 (49 / 19)  


2831 27.96 1.10 1.54  chr2_127077326_127081685     2957  3868 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_127077326_   2957 TGGAAAAACATTTCATGCTCATGGTTAGGAAAAATAAATATCATTAAAAT 3006
                               i i  ii    i      v v    i v v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127077326_   3007 GGCCATACTGCCAAAAGCAATTTACAGATTCAATACTATTCCTATCAAAT 3056
                            v     v  v   vii  i           ii v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_127077326_   3057 TACCAATGACATTCTTCACAGAACTAAAAAAAAAAAAAACT-ATTTTGAA 3105
                          v   iivi v  i  ii     v vi v  i-------  -  ii i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-------CTGATCCTAAA 143

  chr2_127077326_   3106 ATTTATATGGAACCAAAAAGGAGCTCTAACAGCTAAGGCAATGCTAAGCA 3155
                            i        viiv  i   v ivv  i   i  ii    vi i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_127077326_   3156 GAAAGAACAAAGCTGGAGGCAATATGCCACCCAACTGCAAACTATACTAC 3205
                         ii          i      vvvi ii iv     i v    viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_127077326_   3206 ATGGCTACAGTAATCAAAACAGTATGGTACTGGTACAAAAACAGACACAT 3255
                          vi              i     i         i i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_127077326_   3256 TGACCAATGGAACAGAAGAGAGAGCCCAGAAATAAGGCCAC----CTACA 3301
                         v  i        i    vv     i          iv   i----i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_127077326_   3302 ACCATCTGTTCTTTGACAAAGCTGAAAAAGAATAGGCAATGGGGAAAAGA 3351
                         ii  vi  v i  i     i v  vv  -  vi vv           ii 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAA 392

  chr2_127077326_   3352 C--TCCATATTCAATAAATGGTGGTGGGATAACTGGCTAGCCATATCCAG 3399
                         i--  -- v     i        v     i      v  ?   i  v  i
  L1M4_orf2#LINE/    393 TAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_127077326_   3400 AAGACAGAAACTGGACCCCTTCCTTACACCATTTACAAAAATCAACTCAA 3449
                             vv   ii         v   i       v         i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_127077326_   3450 AATAGATTAAAGACTTAATTTAAAAACCCAAAACTATAAAAACCCTGGAA 3499
                            i   i ?    i   v vv  i v i            vi i i   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_127077326_   3500 AACAATCTAGGTG-ATACCATTCTGGACATAGAAATGGGCAAAGATTTCA 3548
                         i v  iv    ? - v i -   vv   v v iiv i     v i    v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_127077326_   3549 TGACGAAAATGCCAAAAGCAATTGCAACAAAAGCAAAGGTTGACAAATGA 3598
                          iivv vi ii         vvv          v   ii v  i    vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_127077326_   3599 GATCCAATTAAACTTAAGAGATTCTGCATAACAAAAGAAACTATCAACAG 3648
                           iiiv  i   v    i iv  i  iiivv    i  v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_127077326_   3649 AGTAAACAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTACGCAT 3698
                            i  v        i                          ii iii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_127077326_   3699 CTGACAAAAGTCTAATATTCAGCATCTATAAGGAACTTAAACAAATTTAC 3748
                             i  ii v  vi   i   v  v     i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_127077326_   3749 AAAAAAAAAAAAAACCAACCCCATTAAAAAGCAGGCAAAGGATATTAACA 3798
                           v     i v   i-     v   ?    iii          v v  i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_127077326_   3799 GACACTCTTCTAAAGAAGACA--CAGATGCAGTTAACAAGCATATGAACA 3846
                             i ii  i        i --  i   -- ii  i     i     v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAA 886

  chr2_127077326_   3847 AAAGCTCAGTATCACTGATCAT 3868
                         i v     ii    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (153 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.18 (24 / 11)  


 323 16.36 0.00 0.00  chr2_127103399_127106430      460   514 (2518)    L1M4_orf2#LINE/L1        1    55 (853)  

  chr2_127103399_    460 TAGAGACATATTCCATGTTCATGGGTAGGAAGACTCAATATTGCTAAGAT 509
                          i  i v    i            i v        i       i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127103399_    510 GTCAA 514
                          v   
  L1M4_orf2#LINE/     51 GGCAA 55

Transitions / transversions = 2.00 (6 / 3)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.00 (0 / 0)  

2551 24.15 4.15 4.92  chr2_127103399_127106430     1626  2540 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_127103399_   1626 TGAAGAGCTATTCCATGTTTATGGAAAGGAAGACTCAATATTGCTAAGAT 1675
                           i i  v   i       i     vv        i       i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127103399_   1676 GTCCATTCTTCCCAACTTGAACTATAGATGCAATGTAATCCCCCCAAAAA 1725
                          v v  v  i     v    v   i    v   i i      iviv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_127103399_   1726 TCCCAAGATGC-TATTTTGTGGATGTCAACAAACTCTTTTTAAAGTTTAT 1774
                              - v   - v     ii  vi ii    i  vv ii    i  i  
  L1M4_orf2#LINE/    101 TCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_127103399_   1775 ATCAAAACTCACAAAAGAAACAGAATAGCAAACACAATACTAAATA---- 1820
                           vi   i--i   ii  vv         v  v     vi i  v ----
  L1M4_orf2#LINE/    150 ATGGAAAT--GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_127103399_   1821 TAACAAAGTTGGACAACTGACACTACCTTAACTTCAATAATTACCTTCAA 1870
                         v            vi   v     v  i-  i     -----------  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCC-AATTTCAA-----------AA 235

  chr2_127103399_   1871 CATTACTTCAATAGCTACAGTAACCAGGACAGTGTCATACTGGCAAAAAA 1920
                          -     v   -           i  i        vi        v  ii
  L1M4_orf2#LINE/    236 C-TTACTACAA-AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_127103399_   1921 AAAAATGGACAAATAGAACAGAATAGAAAACAGATCAATAGAACAGAATA 1970
                          ---- i    v     -----------------     i   i     v
  L1M4_orf2#LINE/    284 A----TAGACATATAGA-----------------TCAATGGAATAGAATT 312

  chr2_127103399_   1971 AAGAGCCCAGAAATAGACACAAA----TATAGTCAACTGATCT-AGACAA 2015
                         i    i         i  v  v ----   i     i    i -v     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_127103399_   2016 AGGAAGAAAGGCAATACAATGGAGAAAAATATCACCTTTTCAAAAAATTT 2065
                         i  vivv   i v  v      i    i -  vii        v    vv
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACAAATGG 411

  chr2_127103399_   2066 CACTAAAACAGCTGGACTGTCATATTAAAAAAAGAATGAACCTAGATACA 2115
                         ii  iii   i     iv?i  i  --iv           vi i  iv v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACAT--GCAAAAGAATGAAGTTGGACCCC 459

  chr2_127103399_   2116 AACCGTATGTCTTTCACAAAAATTTACTCAAAGTAGATCATACACTTAA- 2164
                         v   vi iii v vi         v       i i     ? v  i   -
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_127103399_   2165 TGTAAAATGC-AAAGCTATAAAATATCTAGAAGATAACATAGAA-TAAAT 2212
                              i -  -   i        ivii       v       i?-     
  L1M4_orf2#LINE/    510 TGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_127103399_   2213 TCTCAATGACCTTGGGTTTAGGAATGAGTTTTTAGACACAACATCAACAT 2262
                         ii  i-            vi v    iv  i     i ii   i   v v
  L1M4_orf2#LINE/    559 CTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_127103399_   2263 CACCATCCGTGAATAAAAATTACTCG-TAAGTTGCACTTCACTAAAATTA 2311
                            v v viii  vi    -- v v -   i   v      ii       
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAA--AATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_127103399_   2312 AAAAATTCTGCTCTGGAAAAGACATCGTTAAGAGACTGAAAAGACAAC-- 2359
                             v  i  iv  vv   i    iii i    i v            --
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_127103399_   2360 --AGTA-GGGAAAAAATCTTAGCGAAACACATATCAAATGAAGGACTTGT 2406
                         --  v -    i     v  v  i  v  i     vi  i i        
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_127103399_   2407 ATCCAAAATATACAAAGAGCTCTTA-AACTCAATGATAAGAATACAAACA 2455
                              i      i     i      -        i    i  v     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_127103399_   2456 ACCCAATT-AAAAATAAGTAGATAATCTGTACAGGTACCT---------A 2495
                                 -      ii i i vi  i  v i  ii ii --------- 
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_127103399_   2496 GATGT-CAAAT-------AAGTATATCAAGAGTTGTTCAACATTATATGT 2537
                            i -     -------   i i  v  i  v  i       i ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_127103399_   2538 GTT 2540
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.60 (134 / 84)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.96 (83 / 28)  


2092 26.60 4.31 1.63  chr2_127315867_127322174     2504  3176 (3132)    L1M4_orf2#LINE/L1        1   691 (217)  

  chr2_127315867_   2504 TGGCAAAATATATTATGTTCATGATTTGGAAGAGTTAATATTATTATAAT 2553
                            v  i    vii         iv        v        i   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127315867_   2554 GTTAATTC-CCCCAAATTAATCAATAAGTTCAGTATCATTCAAATCAAAA 2602
                          vi   v -         i   v i ii    iiiiv  i vv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_127315867_   2603 TTTCAATAGACTCTTTGACAGAAATCAACATCTTTATTTTAAACTTTATT 2652
                          ii  iiv v  i   vi       ii   vvi v  ii    v  i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_127315867_   2653 TTGAAATGCAAAGGACCTAAAGTAACCAAATCAGCCTTGAAACAAAAGAA 2702
                          v         i     i i i  i     v  ii       v i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_127315867_   2703 CAAAGTTGGAGGACCCACAACTCCTGATTTCAAGACTTGCAATAAAGTTA 2752
                                       i    vi   ii       i    i v i    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_127315867_   2753 CAATAATCAAGGCAGTATGGTATTTACTTAA--------ACATAGATTAA 2794
                           i        i    i     i vi v   -------- i      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_127315867_   2795 TGGAACTGAATAAAAAGTCCAGGCATAGACTCACACACATATAGTC---- 2840
                              iv    vi i       iv   i  i  i   iv   i   ----
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_127315867_   2841 GATTTTTGACAAAGTCGTCAAAAAAATCTTATGGAAAA------GTCTTT 2884
                               i     i vi i   i vv  iiv    ii  ------      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_127315867_   2885 TTAAAAATTGGTGCTGG---AACTGGAAAAACACATGGTAAAAAAATTAA 2931
                          i  v  v         ---       v ?v      -i    i   v  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAATGAA 449

  chr2_127315867_   2932 TCTCAAACTCTACTTCATACCACACACACTCACACAAATTAGTTCAAGAT 2981
                         vi vi v i    i   i    i i   ----- -      ii    i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACA-----A-AAATTAACTCAAAAT 493

  chr2_127315867_   2982 GGATCACAGATCTAAACA-AATAGTTTAAACTGTAACACTTTTAGAAAAA 3030
                               ?   i     ii-  v  i v     i   v   i      i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_127315867_   3031 AATATGGGAAAATACCTTCCCAGCTTTGGGATAGGCAAAGACTTTTTATA 3080
                           i  i  ?iv v i    viii i     v       v ii  i   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_127315867_   3081 AAAGACACTA---TTTCTAACCATGAAAGAAGAAAAATGATAAATCAAAA 3127
                         v v     i ---viv v i v ii      i   v -       i-ii 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATT-GGA 641

  chr2_127315867_   3128 CTTCATCAAAATGTTTAAATGTTTTA-GCTACAAAAAATA-TAT-AAGAT 3174
                                     -- v   vv    i-   v    ii i -   -    v
  L1M4_orf2#LINE/    642 CTTCATCAAAAT--TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_127315867_   3175 AG 3176
                           
  L1M4_orf2#LINE/    690 AG 691

Transitions / transversions = 1.79 (113 / 63)
Gap_init rate = 0.02 (16 / 691), avg. gap size = 2.50 (40 / 16)  

3146 23.05 3.03 4.76  chr2_127315867_127322174     3266  4189 (2119)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_127315867_   3266 TGGAAAGATATCCTGTGTTCACAGATTGGAAGA---AATAATGTTAAAAA 3312
                                      ii      ii          ---    v      i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127315867_   3313 GTCCATATTACCCAAAGCAATCTACAGATTCAGTGCAATTCCTATCAAAA 3362
                          v v   i v      vii             ii     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_127315867_   3363 TACCAA---------TAACAGAAATAGAAAAAACAATTCTAAAATTTATA 3403
                          v   i--------- vi       v  v  ivii  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_127315867_   3404 TGAAACCACAAAAGACTTTGAATAGCGAAAGCAATCTTGAGCAAAAAAAA 3453
                           i  vii   ii   iiv       v   i         iv  i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_127315867_   3454 GAAAGCTGGAGGCATCACACTGCCCAACTTCAAAATATGCTACAGAGCAG 3503
                         v    i      vv       v     i       iv i     i   vi
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_127315867_   3504 TAGTAACAAAAACAGAATGGTACTGGCATCAAAACAGACACACAGACCAA 3553
                         i     iv  i    vi            v ii i     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_127315867_   3554 TGGAACAGCACAGA-AGCCCAGAAATAAATCTGTACATATATACAAAAAA 3602
                              i  v iv  -  i           i ii     v   i-------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG------- 343

  chr2_127315867_   3603 CATATGTACCTACACACATACAAAAAGCAGCCAACTGATTTTTGACAAAG 3652
                         ----------------------------- i   i       i     i 
  L1M4_orf2#LINE/    344 -----------------------------GTCAATTGATTTTCGACAAGG 364

  chr2_127315867_   3653 AGGCCAAGAACACACACAGAGAAAAGGACAGTCTCTTCAATAAATGGTAT 3702
                         iv       v  iv  vv i i    i i     i     i       ii
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_127315867_   3703 TGGAAAAATTCGATATCTGAGTACAGAAGAATGAAACTGGATCACTTTCT 3752
                            i v  i v    ? iivi i  i         ii    i v  vi  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_127315867_   3753 TTTGCCATATAAAAAAATCAACTCAAAATGAATTAAAGGCCTAAATGTAA 3802
                         ivii       v      i           i  i ?  i           
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_127315867_   3803 GACTCAAAGCTGTGAAACTACTAGAAGAAAACTTAGGGG-AAATGCTCCA 3851
                           vii   i  i i     vi           v    ? -    -  i i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCG 563

  chr2_127315867_   3852 TGACATTGGGCTGGGCAAAGATTCTTTTGGATAAGACCTCAAAAACAAAA 3901
                             v     i i     v i  - i  i    v   vi     i  v  
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTT-TCTTAGATATGACACCAAAAGCACAA 612

  chr2_127315867_   3902 GGCAACAAAAGCAGAAATAGACAAATGGGATTACAT-AAAACTAAAAAGC 3950
                          -         v i       i    v   i v   -    i      vi
  L1M4_orf2#LINE/    613 G-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_127315867_   3951 TT----CTTCCCAGGAAAGGAAACAATCACCAAGGTGAAGAGGATGTCTA 3996
                           ----    -----      v  v    vv  i     i  ivvii i 
  L1M4_orf2#LINE/    662 TTTGTGCTTC-----AAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_127315867_   3997 TAGAATGAGAGGAAATATTTGGAAAGTATACATCTGATACGAGGTTAATA 4046
                         i      i   i         v   vi   i        v i ii vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_127315867_   4047 TTCAGAATATAT------TTTTTA-AATT-AACAACAAAAA-ACTCATAA 4087
                          i          ------i i   -  i -  i  i     -  vv    
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_127315867_   4088 CCCTATTTTAAAATGAGGAAAAGACCATAATAGACATTTATCAAAAGAAG 4137
                            v   ?v      i v   i  iivv           v  v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_127315867_   4138 ACACACAAATGGTCCACAGGTATATGAAAAAATGCTCAGCATCAGTAATC 4187
                          i i        i v i i i i       i       i     ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_127315867_   4188 AT 4189
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.94 (138 / 71)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.80 (72 / 15)  

 816 18.95 9.27 4.44  chr2_127315867_127322174     5570  5817 (491)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr2_127315867_   5570 AAAATTTAA---TTTTGTTTATTCAAAGG-CACTATTCAGAAAATGAAAA 5615
                               v  ---      vi-        -      iv     i      
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_127315867_   5616 AGCAAGTCATAGACTGGG-GAAAATATTCACAAGACATATATCTGATAGA 5664
                         ii   vi  i   v    -         ii   iv             ii
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_127315867_   5665 GGGCTTGTATTCCGATTATGCATTTTTAAAG---CCCTACAAATCAATAA 5711
                           i       i v  v   i------     ---i i     v       
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATA------TAAAGAACTCTTACAACTCAATAA 791

  chr2_127315867_   5712 TAAAGAGATAAACAACTTAATTTTTTTAAAGAC---CAAAAGACTTGAGC 5758
                             i   i   i   ii    ?----   i i---    i  i    ii
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTW----AAAAATGGGCAAAGGATTTGAAT 837

  chr2_127315867_   5759 AGGT-----------GAAGATATACAAGTGGCCAATAAACACATAAAAAT 5797
                           ii-----------            i          i     i    v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_127315867_   5798 -TTCTCAAGATCGTTTGTATT 5817
                         - v     v   i????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.83 (34 / 12)
Gap_init rate = 0.04 (10 / 260), avg. gap size = 3.40 (34 / 10)  


2878 23.45 6.09 1.72  chr2_127342793_127348472     4319  5188 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_127342793_   4319 TGGAAAGATATCCTATACTCAAGGATTGGAAGACT----ATTGTAACAGA 4364
                                      i  ii   v             ----     v -   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGA 49

  chr2_127342793_   4365 TGCCAATTCTATCCAAATTGATCTATAGATTCAATGAAATCACCAGTCAA 4414
                           v    v  vi             i        i v    v i -    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAA 98

  chr2_127342793_   4415 AACCCCAGCAGGATTTATTATAGAAACTGACAAGCTGATTCTAAAATTTA 4464
                           i      v vv   v  ii     i            i        i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_127342793_   4465 TACAGAAATGCAAAGGACCTAGAATAGCCAAAGCAATCT--AGAAAGA-G 4511
                           ii         i     i            i      -- i     - 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_127342793_   4512 AACAAAATTGGAGGACTTATGGTAGCTGATTTCAAAACTTGATATGAAGC 4561
                               i          i iiv vv ii            iv  ii    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_127342793_   4562 AAAAATTATAAAGACTGTGGGCTGTTAGCTCAAGGATAGAAAAAGACATC 4611
                         v v i v  v     v   v v ii i  vi         v v v v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_127342793_   4612 AAAGTAGCAGAAAATAAAGTCCAGAAATTGACCCACACCCGTATGGCCAA 4661
                           v v ii    vvv i           vi     i  viv     i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_127342793_   4662 GTGATTTTTGGCAAAGACACAAAAAC-----AGTGAGGAGAGAACAGTCT 4706
                         v       i i   i iii v  i  ----- i  i   i    i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_127342793_   4707 TTTTAACATACAGTGCTGAAATAACCGCAGAGC-ACATGGAAGA-AATTA 4754
                            i    v ii      ii i   i v v ? -     v  i -   v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_127342793_   4755 A-CTGG-CTATCACCTTGCCCCATTCACACAACTTCATTCAAGATGGACC 4802
                          -i   - ivii    ii v    vi   v  v  v i    i     i 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_127342793_   4803 ATAGCCTTAAATATCAAAGCTAAAACTAAAAATATTCT-GGAAGGAAAAA 4851
                          ?  v i     i v i           v   - i   -i    i   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chr2_127342793_   4852 TAGGAGGATATTTTTACAATCGTAGG----------ATTTATTAGACACG 4891
                             ? v v  i  iiii i v i  ----------i   v     i i 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_127342793_   4892 TC-CTAAAAGCATAAGCCATAAAATTTAAAAAATGAATAAATTACACTTT 4940
                         v - i       i    v i    v--       ii       iv    i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAG--AAAAAATAGATAAATTGGACTTC 645

  chr2_127342793_   4941 ATCAAAATTAAAATCTTTTGCTCATAAAAACACACTATTATTTTAAAAG- 4989
                                      v      iv v v   iv       i v---i    -
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA---GAAAGT 692

  chr2_127342793_   4990 GAGAAGGAAAGCTATAGATTTGTCTGTGAAATAATTATTG--AATCACAT 5037
                           i   iv  v i i   -----v  v  i v   vv   --     -- 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGA-----ATGGGAGAAAATATTTGCAAATCA--T 735

  chr2_127342793_   5038 ATATCAGACCAAAAAATTATATCCAAAATGTGTAAAGAACTCTTACAAGT 5087
                              v  iv iii v  i      i   i i                v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_127342793_   5088 CAATGAGAAACAGCCAGACAACCCAATT-----ATTG-TAAAGGA---GA 5128
                             i v   v  v  i i         -----  v -i      ---  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_127342793_   5129 A-------------AAAGAAAACACACAAATGGCCAGGAAGTACATGAAA 5165
                          -------------      i i i           iv   i        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_127342793_   5166 AGGTGCTCAACATCATCACCCGG 5188
                           i            ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (119 / 82)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.83 (68 / 24)  


3020 25.25 1.42 2.19  chr2_127431670_127437441.rev     4366  5280 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_127431670_   4366 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4415
                               i i  i    vi        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127431670_   4416 GGCCATACTGCTCAAAGTAATTTATACATTCAATGCTGTTCCCATCAAAC 4465
                            v     v i    v i  i  i v      i  vi i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_127431670_   4466 TACTATTGACATTCTTTACAGCATTAGAAAAACT-ACTTTAAATTTTATA 4514
                          v i vivi v  i   i   v v v  v  i  - iii    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_127431670_   4515 TGGAA-T-CAAAGAAGACCCCTTAAAGCCCAGACAATCCTAAGCAAAAAG 4562
                              - -   i --     vvv v    v i      i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_127431670_   4563 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAAGTATACTACAATGC 4612
                                i      vv   ii  v  ii i      iiv        v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_127431670_   4613 TACAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACC 4662
                                 v   i    ii         i iv ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_127431670_   4663 AATGGAACAGAA--GAGACCTCAGAAATAACACCACACATTTACAACCAT 4710
                                i    --    vii         vv   i       iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_127431670_   4711 CTGATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATCTCCT 4760
                         i    i        ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_127431670_   4761 ATTCAATAAATGGTGCTGGGAAAAGTACATTAAATTTTCTGCTATCCATA 4810
                         v     i              v  -----i ii  -------- ?   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAA-----CTGGAT--------AKCCACA 435

  chr2_127431670_   4811 TGCAGAAAATGGAAACTGGACCCCTTCCTTACACATTATACAAAAATTAA 4860
                             i  i vv   ii         v   i    vv              
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_127431670_   4861 CTCAAGATGGATTAAAGACTTAAATGTAAAACCCCAA-CCATAAAAGCCC 4909
                              i      i ?    i         i v iv  - i      vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_127431670_   4910 TAGAAGAAAACCTGGGCA-ATACCATTCAGGATATAGGCACGGGCAAAGA 4958
                                    v i  ?i- v i -   iv  iv v  vvii     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_127431670_   4959 CTTCAT-GATGAAATCACCAAAA--ACAATTGCAACAAAAGCCAAAATTG 5005
                         i   v -   ivi -        --    --          vv     v 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGA-CACCAAAAGCACAA--GCAACAAAAGAAAAAATAG 631

  chr2_127431670_   5006 ACAAATGGGATCTAATTAAA-TGAAAGAGCCTCTGCACAGCAAAAGAAAC 5054
                          i    v   ii v  i   - v   i - i i  ii vv    i  v  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACAC 680

  chr2_127431670_   5055 CATCATCAGAGTGAAAAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAA 5104
                         i    vv i         i  i  i                 v       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_127431670_   5105 TCTACCTGTCTGACAAAGGTCTAATATCCAGAATTTACAAGGAACTTATG 5154
                         vii iv i     i  i  v  vi          v  i  i     iv i
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_127431670_   5155 CAAATTTACAAGAAAAA-ACAAACAATCCCATTAAAAAGTGAGAAAAGGA 5203
                            v iv i  v     -     i  i  v   ?    i  i v      
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_127431670_   5204 TATGAACAGATACTTCTAAATAGAAGACATTTACGTGGCCAACAAACGT- 5252
                          v    i   i i    vv v      i  vi vi       i  i ii-
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_127431670_   5253 TGAAAAAATGCTCAACATCACTAATCAT 5280
                               i             ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (134 / 93)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.83 (33 / 18)  


2363 26.24 2.01 3.21  chr2_127599295_127601033.rev      501  1247 (492)    L1M4_orf2#LINE/L1      171   908 (0)  

  chr2_127599295_    501 AATAGCTAGAGCAACTTCAAAAAGGAAGAATAAA-TTGG-GGA---AAAC 545
                               i i i   ii ii    i      i   -    -   --- v  
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_127599295_    546 CTCTCTACCT----GCTTTC-ATATAGGTACAGTAATTAACTCTACATGG 590
                         i  i v ii ----i   v - i v  v         i  vv viii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_127599295_    591 GATCAGCAAAGGAACAGACACACAGATAAAGCAACAAAATAGAGAACCAC 640
                         v iii   v i i i     i i    ----   iii      ----- i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGAT----CAATGGAATAGA-----AT 311

  chr2_127599295_    641 TCCCAAAAAAGAGAATCCAGAAATAGCCCCTCAGAAGTGTTGCCAATTGA 690
                          ---------    i          iv   vi v vv i v i       
  L1M4_orf2#LINE/    312 T---------GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_127599295_    691 TTTTTGACAAAGGTGCAAAGGTTAT-CAATGGAAGGATGATAGTCATTTC 739
                             i     i     v   iii  -      iiii vi      v    
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_127599295_    740 AATGACTGGTGCTGGAGCAATTAGGTACTGAGAGGCAAAAAAATAGACCT 789
                           ii v         ii   i i i  ?iv v v      i   -  vv 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT-GAAGT 451

  chr2_127599295_    790 TG---CCCTAAACTTCACATCTGTTGCAAAAGCTGACTCAAAATGGATCA 836
                           ---     -- i     i vvv i     ii i               
  L1M4_orf2#LINE/    452 TGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_127599295_    837 TAGAT-TAAACGTAAGTTATAAAACTAGAAATCTTTTAGAAGGCAATATA 885
                         ?   i-    i     vvv        v   v  i       iv  i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_127599295_    886 TGGAAAAATCTTTTGGACCCAAGGCTTGGTGAAGAGTTCTTAAATATGAC 935
                         v ?iv       ivv    ivi  i v  ii v iv      i       
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_127599295_    936 ATCAAAAGTACAATCCTTGAAAGAAAAAAAATGGATCAATTGAATTTCAT 985
                          i      i    v vvii          -- i   v     i i     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAAATTGGACTTCAT 647

  chr2_127599295_    986 CAAAATTAAAAAATTTTGCTCTGCAAAAGACCCTCTTAGATGGATAAAAA 1035
                                     v     iv  v    i   v  v i iiviii i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_127599295_   1036 GACAAGCTACGGACTGTGAGAAAATATTTGCAAACCACATTTCCTACAAA 1085
                              v i  i  v  v                 i  i  v  iv i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_127599295_   1086 GGACTATTATCTGGAATACATAAAGAGCTCTCAAAACTCAACAGTGAAAA 1135
                              vv    ii     i       i    i v       i i -    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAAA 796

  chr2_127599295_   1136 AAAGAAGCAATCCAATTAGAAGTTAGGCAGAAGCCATAAAGAGACATTTC 1185
                          i v  ii  i      ?i  iv i    i i viv i  v         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_127599295_   1186 ACTGAAGAGGAGATACAGATGGCAAACAAGCACATAAAAAGATGTTCAGC 1235
                         v ii    i  v     i     v  i        i        i   i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_127599295_   1236 ATCACTAGCCAT 1247
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (124 / 68)
Gap_init rate = 0.02 (15 / 738), avg. gap size = 2.60 (39 / 15)  


2902 26.73 1.67 0.56  chr2_127682300_127688371     4688  5585 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_127682300_   4688 TGGAAAAACATTCCATCCTTATGGATAGGAAGAATCAATATCGTGAAAAT 4737
                               i i  i    vi i      v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127682300_   4738 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 4787
                            v     v      v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_127682300_   4788 CACCATTGACATTCTTCACAGAATTAGAAAAAAAAAAACTTAAATTTCAT 4837
                         iv   vivi v  i  ii     v v  v  ivvi v- i    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chr2_127682300_   4838 ATGGAATTG-AAG--ACCCCATATAGCCAAAACAATCCTAAGCAAAAAGA 4884
                               v  -   --    viv               i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_127682300_   4885 ACAAAGCTGGAAGCATCACGATACCTGACTTCAAACTATACTACAAGGCT 4934
                               i    i vv    iv v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_127682300_   4935 ACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACCA 4984
                           i    i   i    ii         i iv ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_127682300_   4985 ATGGAGCAAAACAAAGACCTCAGAAATAGCACCACACATCTACAACCATC 5034
                              ii i  ivi   vii        ivv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_127682300_   5035 TGCTCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGA-ACTCCT 5083
                           v i  i     ivv  v   i v  vv            i - v  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_127682300_   5084 ATTCAGTATATGGTGCTGGGAAAACTGGCTAGCCATATGCATAAAACTGA 5133
                         -    ii v            v      v  ?   i     v  i v   
  L1M4_orf2#LINE/    400 -TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_127682300_   5134 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAACGCAAGATGAATT 5183
                          ii         v   i     v               v   i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_127682300_   5184 AAAGACTTAAATGTAAAACCCAGAGCCATAAAAACCCTAGAAGAAAACCT 5233
                          ?    i         i v i i i i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_127682300_   5234 AGGCA-ATACCATTCAGAACACAGGCATCTGCAAAGATTTCCT-GATGAA 5281
                            ?i- v i -   ivi  viv  vv vv    v i    i -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr2_127682300_   5282 GACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAA-CTAGA----A 5326
                                      vvv          vv     v  i  -i i  ---- 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_127682300_   5327 TCAAA-TTAAAGAGTTCCTGCACAGCAAAAGAAACTATCATTGGAGTGAA 5375
                              -     i v  i-  ii vv    i  v       vvii      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_127682300_   5376 CAGGCAACCTACAGAATGGGAGAAAGTTTTTGCAATCTACCCATCTGACA 5425
                         v  i     i               i v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_127682300_   5426 AAGGTCTAATAGCTGGAATTTACAAGGAAATTGAACAAATTTACAAGAAA 5475
                          i  v  vi  v ii    v  i  i   v ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_127682300_   5476 AAAACAAATGGCCCCATCAAAAATTGGGCAAAGAATATAAACAGACACCT 5525
                           i      ii   v  i?    v         i  v i  i     ii 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_127682300_   5526 CTCAAAAGAAGACATTTATGTAGACAACAA--ACATGAAAAAAAGCTCAA 5573
                            v        i  vi vi i v   i  --         i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_127682300_   5574 TGT-ATAATGTAT 5585
                         ii - ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.33 (20 / 15)  


2326 10.89 4.19 23.21  chr2_127688453_127690277      498  1333 (492)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_127688453_    498 AAGACTTAGTACAAAGCTACAGTAACCAAGACAGTGCAGTAATGGCATAA 547
                           i     v                i          ii   v        
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_127688453_    548 ---------------TCATTGGCTTAGATTTAAGA-------------CT 569
                         ---------------   v   vv    v  i   ------------- i
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_127688453_    570 CAAACATCTATGGTCAACTGATTTTCATCAAGAGTTCCAAGATCTTTCAA 619
                           v    i         i        iv    i  v      i v     
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_127688453_    620 TAGGAAAAGGATTTAATAGTCTCTTAAACAAATGGCACAGGGACAACTGG 669
                          i  i    -----        i  v         ii v           
  L1M4_orf2#LINE/    382 TGGGGAAAG-----AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_127688453_    670 ATAGCCACAAGCAAA-GAATCAATTTTTACCTTTTTCTCACACTATATAA 718
                            ?     v     -    v  v  vv   ii vi       i     v
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_127688453_    719 AAAAATTATCTCAAAATGGATCAAAGCTCTAAATGTAAATGCTAAAACTA 768
                                 v              ?  vi          iv          
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_127688453_    769 TAAA-CTCTTAGAAGAAAACATAAGGGTAAATCTTCATGACCCTGGGTTT 817
                             -                  i ?          i     i      v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_127688453_    818 GGCA-TAATGTCTTAAGATATGATCCCTAAAGTGCAAGTAACAAAAGAAA 866
                             - ii v     -       iv  v    ii    i           
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTA-GATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_127688453_    867 AAAATCGATAA-TAGGACTTCATCAAAATTTAAAACTTTTATGCTTTAAA 915
                            - v     - v                v         i     i   
  L1M4_orf2#LINE/    626 AAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_127688453_    916 GAACACTATTAAGAAAGTGAAAACAAGGCCGGCCATAATGGCTCAGGCAT 965
                          i       i             ---------------------------
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAA--------------------------- 697

  chr2_127688453_    966 GTAATCCTAGCACTCTGGGAGGCCAAGGCAGGTGGATTGCTTGAGCCCAG 1015
                         --------------------------------------------------
  L1M4_orf2#LINE/    698 -------------------------------------------------- 697

  chr2_127688453_   1016 CCTAGGCAACATAGCAAGACCCTGTCTCATTAAAAAATAAAAATAAAATG 1065
                         -------i   -------    -------------------- i i    
  L1M4_orf2#LINE/    698 -------GACA-------ACCC--------------------ACAGAATG 713

  chr2_127688453_   1066 TAAAAATAAAAAGCAAAAACAACCTTCGGATGGAGAAAATATTTGCAAAG 1115
                         -------------------------------                  v
  L1M4_orf2#LINE/    714 -------------------------------GGAGAAAATATTTGCAAAT 732

  chr2_127688453_   1116 CACATATCTGATAAGGGACTTGTACCCAGAATATATAGAAA---CTTACA 1162
                           i                     i            i i ---      
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_127688453_   1163 AATCAGTAGAGGAAGGGAGGGAGGGAGAGAGAGAGGGAGGGAGGGAGGAA 1212
                          v   i  i-----------------------------------------
  L1M4_orf2#LINE/    783 ACTCAATAA----------------------------------------- 791

  chr2_127688453_   1213 GGAAGAAGAGAGAAAAGAACCCAATTAAAAACTGGACAAAGGATTTCAAT 1262
                         -v  i    v ---  v         ?    v   i          v   
  L1M4_orf2#LINE/    792 -TAAAAAGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_127688453_   1263 GGATATTTCTCCAAAGAAGATATACAAATGGTAAATAAGCACATGAAAAT 1312
                         i  i                           iv                v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_127688453_   1313 ATGCTCAACATCATCAGTCAT 1333
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (49 / 38)
Gap_init rate = 0.02 (16 / 677), avg. gap size = 14.31 (229 / 16)  


 265 19.10 5.62 1.12  chr2_127830822_127832529        3    91 (1617)    L1M4_orf2#LINE/L1      773   865 (43)  

  chr2_127830822_      3 AACT-TCACACACACAAAAATAAAAT----AATCATCCCATTAAAACATG 47
                             - i   -  v   v       v----   v i  v   ?   v   
  L1M4_orf2#LINE/    773 AACTCTTACA-ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_127830822_     48 GGCAAAGGACATGAACAGACATTTTTCAAAAGAAGTTTGACAAA 91
                                  iv    i        i  v       v vv     
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

Transitions / transversions = 0.45 (5 / 11)
Gap_init rate = 0.03 (3 / 93), avg. gap size = 2.00 (6 / 3)  

 259 25.69 25.69 0.69  chr2_127830822_127832529      155   298 (1410)    L1M4_orf2#LINE/L1        3   182 (726)  

  chr2_127830822_    155 GAACAAAATGCCATGTTC--GGACCAGAAGACTCAATGTTGTTA------ 196
                            vi v  v        --   iii       i   i      ------
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_127830822_    197 ----------CAAA-----------ATTCAATGAAATC----TTAAATAT 221
                         ----------    -----------      i v    ---- i   -  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA-AT 101

  chr2_127830822_    222 CCTGGCAGCCAATACTGTGAAAACTGAAAAGCTGATTGTAAAATTTACAT 271
                           ii  v   vv vi  iii   i   v        iv       i i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_127830822_    272 TGACA-GTCTGGG---CAACATAGCAAGAAC 298
                         v  v - ivv   ---  iv     v i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

Transitions / transversions = 1.31 (21 / 16)
Gap_init rate = 0.04 (7 / 180), avg. gap size = 5.43 (38 / 7)  

2115 21.23 10.47 4.75  chr2_127830822_127832529      501  1216 (492)    L1M4_orf2#LINE/L1      152   908 (0)  

  chr2_127830822_    501 GGAAATGTGAAGGACCTAGAAATTCTAAAACAAGTTTGAAAAAGAAGAA- 549
                                ii i     i    vvv i       vi              -
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_127830822_    550 ------AGAGAACTTAAATTATGTAACTTCAAGACTTATTATAAAGCTAT 593
                         ------i   i   i v i vivi  i     i     i  i       i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_127830822_    594 AATAATCAAGACAGTGTGTTATTGGCATACAGGTAGATAAATGG-TTAAT 642
                          i                v  i       vi i    i v  i - i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_127830822_    643 GAAACAGA-TTA----TCTAGAAACAGACCCATATATACATGACCAGTTA 687
                          i  i   -  i----  i     i i       i  vi   ii  i  i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_127830822_    688 ATTTTTTTTAAAGG-GCTAAGGCTATTCAATGGGGAAAGGATAATCTTTT 736
                              ivvi  i  -  i   i i               i   i      
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_127830822_    737 CTATACACTGTGGTACAACAGCTGGATA-CCTCA--------------GC 771
                          v i v iv   v ivi   i       -  v  -------------- i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_127830822_    772 TG-----TCACCTCATA--ACAGACAAAAACTAACTCAGAATAGATCATA 814
                           -----ii      i -- i v       i       i   i     ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_127830822_    815 AACCTACATATAAGGACTAAAACTATAAAACTTGTAGAAAAAAAT-TATG 863
                         i     v  i    ii                iv     i    i-  v 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_127830822_    864 -----------GTGACCTTGACTTTGGCAAAGATTTCTTTGCATTTTTTA 902
                         -----------         iv  v     v i      v -  ------
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-AT------ 594

  chr2_127830822_    903 ATGGTGTCTTTTGAAGAGCAAAAGTACAGTACATATCTTAAAAGAAAAAA 952
                            iiii -----  i    v   i ----   -------          
  L1M4_orf2#LINE/    595 ATGACACC-----AAAAGCACAAGCA----ACA-------AAAGAAAAAA 628

  chr2_127830822_    953 ---ATGCATTGAACTTCA--AAAATTAAAAATGTTTACCCTTCAAAAAAC 997
                         ---  iv    i      --           iv   iiv       ii  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_127830822_    998 ACCATTAAAAAAATAAAAACACAAGCCACAGACTACGAGAAAAAATGTAC 1047
                           i  i  i   i i    v    v       v iv       v  v i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_127830822_   1048 TAAACACATACCTGACAAAATATTTGTATCCAGAATATCTAAAGTACTCT 1097
                         v  v  i   i    i  iiv i               v     v     
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_127830822_   1098 TACAACCCAACAA-AAAAAGACAAACA------TT-------------AA 1127
                               i   i  -           i ------  ------------- i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_127830822_   1128 GATTAGGACATACACTTCACCAAA-AAGACAT-TAAGGATGGCAAATAAA 1175
                             v i i v   i   v     -    i  -i  --     v     i
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAA--ATGGCCAATAAG 876

  chr2_127830822_   1176 GCCATGGTCAATAAGATAAGATGCTCAATATCATTAGTCAT 1216
                         vv    ------  ---           i    ????????
  L1M4_orf2#LINE/    877 CACATG------AA---AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (103 / 48)
Gap_init rate = 0.03 (26 / 757), avg. gap size = 4.19 (109 / 26)  


3408 21.84 2.20 2.52  chr2_127885972_127888081      708  1618 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_127885972_    708 TGTAGAGAAATACCATGCTAATAGATGAGAAGACTCAACATT---AAGAT 754
                           v i   v  v     i v  i   vi       i  i   ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127885972_    755 GTCTTTTATTCCTAAATTGTTCTATAGATTCAATTCAATCCAAATCAAGA 804
                          v vv vv i  i      v    i        iv      vv     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_127885972_    805 TTTCACCAGGAATTTTTTTTTTAGAAATTGAGAAATTGGTTCTAAAATTT 854
                          ii  v v ---ii      vi         v  ii  i i        i
  L1M4_orf2#LINE/    101 TCCCAGCTG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_127885972_    855 ATATAGAAGTAGAAAGGACCTAGAATAGCCAAAACAATTTTGAAAAATAA 904
                             i   i iv  i     i                 i        v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_127885972_    905 GAACAAAGTTGGAGGACTTACACTACTTGATTTCATGAGTTACT-TGAAT 953
                                           i     v iii      vi v     -ii  v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_127885972_    954 CTTGTAATAGCAATTAAGACATTATAATGTTGGCATAAAAAT-GAAAGAT 1002
                           ---- i  i   i      v i ii ii        ii  -  v v  
  L1M4_orf2#LINE/    248 CT----ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_127885972_   1003 AGATTAACAGAACAAAAT--AGAGTCCAGAAGTAGATGTATGCATATACG 1050
                             i  ii   i i   --           i  i ivi  i   v  i 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_127885972_   1051 GTCAATTGATTT-CAACAAAG-CACCAAAGCAATTCAATGGGAGAAAGGA 1098
                                     - i    i -ii    ii v          -     i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAA 392

  chr2_127885972_   1099 TAGTGTTTGCAAGAAATGGGACTGTGACAACTAGATCTCCATATATTTTA 1148
                             v   v   v      vi   v       i   v?   i  iiv-- 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA--A 440

  chr2_127885972_   1149 AAGAATGATTCTTGGCCCCTACCTCACACCATATACCAAAATTAACGAAT 1198
                                 vvi v i                     v         ----
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC---- 486

  chr2_127885972_   1199 TCAAAATGGGTCAGAGATGTAAATGTAAGAGTGAAAAACCATAAAGCTTC 1248
                                  i   ?   iv            iv    - i     i  ii
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCT 535

  chr2_127885972_   1249 TAGAAGAAAACATAAGAGAAAGCCTTTGTGACCTTGAATAAGGCAGTG-- 1296
                                       i ? v  ii   i         ii v     i  --
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_127885972_   1297 TTCTTTGGTAGGACAC-AAAAGCACGAATCATAAAAGAAAATGTTGATAA 1345
                              v i  v     -        i iiv i         vi v     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_127885972_   1346 -TTGGACTTCATCAAAATTACAAACATCTGTTCATTAAAAGACACTGTTA 1394
                         -                   v    v i   v v i   i      i i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_127885972_   1395 AGTA--T-AAAAGACAAGTCACAGACTGAGAGGAAATTTTTGCAAAATAC 1441
                           v -- -         vi      v  i   i    v        vi i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_127885972_   1442 TTAGCTGACAAAGGGCTTGTTACTAGGATACATACA-AATTCTAAAAACT 1490
                         v  v    i  i  i     vv i  i   i   v -  i   v v    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_127885972_   1491 CAATTTAAAAAACCCTCAAAAACAAAGAAACAAAC-AAAAAACAGCCCAA 1539
                             --  v   ------  i     v  v v  i-?     ii v v  
  L1M4_orf2#LINE/    786 CAAT--AATAAA------AAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_127885972_   1540 AGACTTAAACTGGCACTTCACCAAAGAAGATATA--AATAGCAAATTAGC 1587
                         i  i  i  iv i  i   v              --   i  v   v   
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_127885972_   1588 ACAGGAAAAGATGCTCAAAATCACCAGAGAA 1618
                            v              v    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (117 / 78)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.95 (43 / 22)  


 445 22.22 9.03 5.56  chr2_127916189_127918812.rev      626   769 (1855)    L1M4_orf2#LINE/L1        1   149 (759)  

  chr2_127916189_    626 TGGAGAGATATCCATCCCAT---CACAGAGATCTTG----ACTCAGTGTT 668
                             i        ----   ---  ii  ----   ----   i i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCC----CATGTTCATGGA----TTGGAAGACTTAATATT 42

  chr2_127916189_    669 GTCAAGATGTC--TCTTCTGCAATTTGATC----GATTCAATGTAATCCC 712
                           i      v -- vi  iv   v      ----       i i      
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chr2_127916189_    713 AGTCAAAATCCCAGCAAGTTATTTTATAGATATTGGAAAACCGATTCTAA 762
                         vi             vivi v    ii   v    iv  i i   i    
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr2_127916189_    763 AGTTTAT 769
                          i  i  
  L1M4_orf2#LINE/    143 AATTCAT 149

Transitions / transversions = 2.20 (22 / 10)
Gap_init rate = 0.04 (6 / 149), avg. gap size = 3.50 (21 / 6)  

1714 14.57 1.97 29.42  chr2_127916189_127918812.rev     1069  2132 (492)    L1M4_orf2#LINE/L1      137   908 (0)  

  chr2_127916189_   1069 TTCTAAAGTTTATATGAAAAGGCAAAGGTGCCAGGATAGCCAACACAATA 1118
                          i     i  i     i   v    i  vv    i        v     v
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_127916189_   1119 TTGAAGGAAAAGAACAAA-TTGAAGAACTGATACT----GACGTCAAGCC 1163
                              ii i         -   i  i   v i   ----i iv    iv 
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_127916189_   1164 TTTCTATAAAGCTACAGTAATTAAAACAGTGTGGTATTGGTGAAAGAATT 1213
                           v   i              i  i           i   iiv   i  v
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_127916189_   1214 GACAAATAGATCAATGGAACAGAAAAGAGAGCCCAGAAATAGACCTACAC 1263
                             v              i    vv     i         i   i i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_127916189_   1264 AAATAAAGTTTGCTGATCTTTGCCAAAGGAGCGAAAGCAATTCAATGGAG 1313
                          vv  vi  ivii    i  i v   i  v  v  ii v         i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_127916189_   1314 AAAGGATAGTCTTTTCAACAAATGGTGCTAGAACCGCTGGATATCCACAT 1363
                             i                        i i  vi       ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_127916189_   1364 GCAAAAATGAATCCATGCTGGGTGTGGTGGCTCACACCTGTAATCCCAGC 1413
                               --    --------------------------------------
  L1M4_orf2#LINE/    437 GCAAAA--GAAT-------------------------------------- 446

  chr2_127916189_   1414 ACTTCAGGAGGCCAAGGAGGGCGGATTGCTTGAGTTCACGAGTTCGAGAG 1463
                         --------------------------------------------------
  L1M4_orf2#LINE/    447 -------------------------------------------------- 446

  chr2_127916189_   1464 CAGCCTGGGCAACATGTCAAAACCCCGTCTCTACAAAAAATACAAAACTT 1513
                         --------------------------------------------------
  L1M4_orf2#LINE/    447 -------------------------------------------------- 446

  chr2_127916189_   1514 AGCTGGGCATGGTGCTATGCGCCTGTAGTCCCAGCTATTTGGGAGGCTGA 1563
                         --------------------------------------------------
  L1M4_orf2#LINE/    447 -------------------------------------------------- 446

  chr2_127916189_   1564 GGTAGGAGGATGGCTTGAGCGCAGAGGTTGCAGTAAGCTGAGAGCACACC 1613
                         -----------------------  i    -----------  -----  
  L1M4_orf2#LINE/    447 -----------------------GAAGTTG-----------GA-----CC 457

  chr2_127916189_   1614 CCTCCACTCTAGCCTGGGGGACACAGCCAGACCTTGTCTCAAAAAAAAAA 1663
                            -----------------------------------------------
  L1M4_orf2#LINE/    458 CCT----------------------------------------------- 460

  chr2_127916189_   1664 AAAAAAAAAATCCGTACACAGACCTTACACC-TGTACAAAAATTAACTCA 1712
                         ---------------------    i     - i                
  L1M4_orf2#LINE/    461 ---------------------ACCTCACACCATATACAAAAATTAACTCA 489

  chr2_127916189_   1713 AAATGGATCATAGACCTAAATGAAAAATGC-AAAACTATAA--CTTCTAG 1759
                                   ?           v  i -  -          --  ii   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAG 538

  chr2_127916189_   1760 AA---AATGTAGGAGAAAATCTAGATGACCTTGGGTTTGGCAATGACTTT 1806
                           ---  ii    ? v      vvi            v       ii  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_127916189_   1807 TTAGATACAACACCAAAGGCACAATCTATGGAAGAAAATATTGATAAGCC 1856
                                ii        i      v v iii       v  v     iii
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_127916189_   1857 GGACTTCATTAAAATTAAAAACACATGCTCCGCGAAAGATAGTTT--GGA 1904
                                  i            viv  iv iv i  i  i v v --i  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_127916189_   1905 AAATGAAAAGACATGCCATAGACTGGGAGAAAATCTTTGCAAAATACCTA 1954
                           i          vv   i   v           v        ----ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA----TCA 734

  chr2_127916189_   1955 TATATTTG------GATGGGTGTCCAAAACATATAGATACACACACAAAA 1998
                              i  ------  ivv  i    i  i     i ---------i  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAA---------GAAC 775

  chr2_127916189_   1999 TCTTACAACTCAACAGTAAGAAAACATACAATCCAAAATGTAAAAG-AGG 2047
                                      i i   i  i   v i  i    -- v?    i-i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAA--TTWAAAAATGGG 823

  chr2_127916189_   2048 CAAAAGATCTGAACAGACATCTCATCAAAGAAGATATACAGATGGCAAAT 2097
                             i   i    i      i  vi               i     v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_127916189_   2098 ATACTTATGAAAAGATATCCAACATCAGATGTCAC 2132
                          vi vi          iii        ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (100 / 51)
Gap_init rate = 0.02 (18 / 772), avg. gap size = 18.56 (334 / 18)  


 223 24.00 4.00 0.00  chr2_127930856_127936771     3867  3916 (2000)    L1M4_orf2#LINE/L1        1    52 (856)  

  chr2_127930856_   3867 TGGAAAAACATTCCATATTCGTAAGTCTGTAGACTTAACA--GTTAAGAT 3914
                               i i  i    i   i iii iv v        i --        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_127930856_   3915 GG 3916
                           
  L1M4_orf2#LINE/     51 GG 52

Transitions / transversions = 5.00 (10 / 2)
Gap_init rate = 0.02 (1 / 52), avg. gap size = 2.00 (2 / 1)  

1614 18.24 1.52 2.43  chr2_127930856_127936771     4073  4401 (1515)    L1M4_orf2#LINE/L1       38   363 (545)  

  chr2_127930856_   4073 ATATTGTCAAGATGGCAACATGCCCCAAACCCAAATTGATCTATAGATGC 4122
                                i          i iv       ------        i    v 
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAA------TTGATCTACAGATTC 81

  chr2_127930856_   4123 AATGTAATCCCTATCAAAATCCCAGTTGGCTTCTTTGCAGCTATCAACAA 4172
                           i i                    i  v   i       vv  ii    
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

  chr2_127930856_   4173 GATGATCCTACAATTCATATAGAACTTTGGGGGACTCAGAACAGCCAAAA 4222
                          v        v         i   v viii     i     i        
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr2_127930856_   4223 CAATCT-GCAAAAGAA---TGAAGTTGAACGATTTACACTTCCTGATTTC 4268
                               - v       ---ii      i v  i i        ii     
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_127930856_   4269 AAATCTTCTTACAGTGTTATAATAATCAAGAGAGCGTGTCGCTGGCAAAA 4318
                            v   vi    iv i  i i         v  i   vii      v  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_127930856_   4319 GGACAGACATACAGATAAATGGAATAAAATGGAAAGTCCAGAAATAAACC 4368
                            i       i    v         i   v  i                
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_127930856_   4369 CTTACACATATATGTTCAATTTATTTTTAA-AAG 4401
                          -- i    v    v      v     ii -   
  L1M4_orf2#LINE/    332 C--ATACATTTATGGTCAATTGATTTTCGACAAG 363

Transitions / transversions = 1.73 (38 / 22)
Gap_init rate = 0.02 (5 / 326), avg. gap size = 2.60 (13 / 5)  

2529 15.13 8.62 0.57  chr2_127930856_127936771     4903  5424 (492)    L1M4_orf2#LINE/L1      345   908 (0)  

  chr2_127930856_   4903 TCAATTAAATTTTGACAAGGGTGCCAAGACCATTCAATGAAGGAAAGA-- 4950
                               i v   i                          i-       --
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAAT 393

  chr2_127930856_   4951 -GTTTTTTCAATAAATGAAGCTGGAACAACTGTATAGTCACATACAAAAG 4999
                         -  i       i     iv     i       v   ?i     i      
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_127930856_   5000 AATGATTTTGGACCCCTACGTCATGCCATATACAAAAATTAA-------- 5041
                              vv            v   ii                 --------
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_127930856_   5042 ----------------TGCAACAGT----GCTGTAAAATCTCTTAGAAGA 5071
                         ----------------  i  v  i----i  i     -           
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGA 542

  chr2_127930856_   5072 AA-CACAGGAGTAAATCTT---------GCATTAGGCAATGGATTCCTAG 5111
                           -  i   ?         --------- vi           v   i   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_127930856_   5112 TTATTACACCAAAAACACAGGCAAATAAGAAAAAAATAGATACACTGAAT 5161
                         v   v         i    i    vv  ii            v i  i i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_127930856_   5162 TCCATAAAAATTAAAAACTTCTGTGCTTCAAAGGATACTATGAAGAAAGT 5211
                          i   v              i              i     v        
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_127930856_   5212 AAAAAGACAATCCATAGAATGGGAGATCATTTTTGCAAATCCTTTACCT- 5260
                         i         i   i           vv  v          v v  i  -
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_127930856_   5261 --AAGGAGCTTATATACAGAATTTATAAAGAACTCCTATG-CTCCACCAG 5307
                         --    ii   i   v      v            i  ii-   v iv v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_127930856_   5308 AAAAAGACAAATAACCCAATGTTTTAAATGGGCAAATAATCTGAATAGAC 5357
                                             - ?vv           vi  i         
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_127930856_   5358 ATTGGTCCAAAGAAGAGATACAAACGGCCAAAGAGCACATGAAAAGATGC 5407
                            vv           v       i      vi                 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_127930856_   5408 TCAACATCATTAGCCAT 5424
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (43 / 33)
Gap_init rate = 0.02 (10 / 564), avg. gap size = 4.80 (48 / 10)  


3191 19.49 9.63 0.84  chr2_127947367_127952092     3404  4234 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_127947367_   3404 AAGATATTCCATGGTCATG-ATTCAAAGACTTAATATTGTTAAGAAGTCA 3452
                                i     v     -   vi                    v v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_127947367_   3453 ATACTACCCAGAGCACCTCTACAGATTCAATGCAATTCCTAACAAAATAC 3502
                              v    i viiv-             i     i    v      v 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGA-TCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_127947367_   3503 CAATAATGTTTACTGCATATATAGAAAAATCCATTTTAAAATTCACATG- 3551
                           iiviiv   vi    v v  v  v  iiiv  ii         i   -
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_127947367_   3552 AAAT--------CTCA-AATAGCCAAAACAATCTTGAAAAACAA---CAA 3589
                             -------- i  -                        v  ---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_127947367_   3590 AGTTGGAAGACTCACACGTCCTGACTTCAG---TGGGGACAGA--CACA- 3633
                                i         v   ii i    i--- vivv   i --i   -
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_127947367_   3634 ----CA-GACAGTTCTATATTG-CA---------ACATGCAGACCAATGG 3668
                         ----  -      vivi  i  -  ---------    ii   i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_127947367_   3669 AAAAGAA--GAAAGTCCAGAAATCAACTCTTACACATATGGTCAAATGAT 3716
                           v    --  i           v   i v    iv         v    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_127947367_   3717 TTTTGAAAAGACTTGCAAGACCATTCCATGGGGAAA--ATAAGTTTTTTT 3764
                            i  v   iv vv           v         --   i-- i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG--TCTTTT 401

  chr2_127947367_   3765 CAGTAAATGTTGCTGGGGAAACTTGATATCCATATGCAAATGGATAAAGT 3814
                           ii     v       iv    v    ?   i       v i  i    
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_127947367_   3815 TGGAACCTTATTTTACACAACATACAAAAAATCAACTAGAAATGGATCAA 3864
                             v  i  ii i    v i         - i    vi          ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAW 500

  chr2_127947367_   3865 AGACCTAAACATAAGAACTAAACTTACAAAATT-------------ATAG 3901
                                  ii     i     vi  i    i -------------    
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_127947367_   3902 GGTAAAAGCTTCATAATATTGAATTTGGCAATAATTTTTTTGATATGACA 3951
                          ?vv   v    i i iv   ii  v      ii   i  v         
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_127947367_   3952 CCAAAAGCACAGGCAATAAAAGAAAAAAGTGAGATA----------CAGC 3991
                                    i    i           - -     ----------  v 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAA-T-AGATAAATTGGACTTCATC 648

  chr2_127947367_   3992 AAAATTTAAA---TGTGTGCAACGAAGAACACAATCAAGA--GTGAAAAG 4036
                               v   --- v     vv i   i    v       --        
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_127947367_   4037 GCAATCTAAAGAATGAAAGAGAGTATTTGCAAATCATATAGCTGATAAAG 4086
                         i   i i v      ii   i i                 v       i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_127947367_   4087 CATTAACAT---GAGTACACAAAGCACTCCTACAACTCACAC-------- 4125
                         v i vii  ---  i  i i    v    i         - i--------
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-ATAATAAAAA 797

  chr2_127947367_   4126 --CAAACAACCCAATATAAAACTGGGCAAATGACTTGAATAGACATTTCT 4173
                         --    i        v?    v        v  i                
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_127947367_   4174 CCAAGGAAGATATATAAATGGTCAAAAAGTACATTAAAAGATGCTCTACA 4223
                             i         i      i   v   i    v           v   
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_127947367_   4224 TCACTATCATT 4234
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (93 / 65)
Gap_init rate = 0.03 (25 / 904), avg. gap size = 3.48 (87 / 25)  


2373 24.22 1.09 1.24  chr2_128030929_128032562      499  1142 (492)    L1M4_orf2#LINE/L1      266   908 (0)  

  chr2_128030929_    499 TGTGGTATTGGTATAAAAATAGGCATATAGACCAATGGAACAAAATAGAG 548
                                i   i    ii    i        i        i i   v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_128030929_    549 AACCCAGTAATAAACCCAATTGCTTACAGCCAACTGACCTTCAACAAAGC 598
                          ii    v          vviii   ii i   i   ii   i    i v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_128030929_    599 AAACAAAAACGTAAAGTGGGGAAATAACACCCTATTCAACAAATGGTACT 648
                         viv   i v i vv i        v  i vi  v             i  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_128030929_    649 GGGATAATTGAAAAGCCACATGTAGGAGAGTGAAACTGAATCCTCATCTC 698
                             i  i  i v ?       i ii   i    ii  i i  ii i   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_128030929_    699 TCACCTTATATAAAAATCAACTCAAGATGGATCAAGGACTTAAATCTAAG 748
                         v    v    i      i       i        ?i   i     v    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_128030929_    749 ACCTAAAACTATAAAAATTCTAGACTATAACATCAGA--AAATCCCTTCT 796
                          v              v ii    vv v     vi ?--     --   v
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC--TTCG 563

  chr2_128030929_    797 AGACATTGGCTTAGGCAAAGATTTCATGACCAAGAGCCCAAAAA-ACAAA 845
                         v   v    v        v i    v iivi v  vv      i-    -
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA- 612

  chr2_128030929_    846 TGCAACAAATACAAAGATAAATAGGTGGGACTTAATTAAACTAAAGAGCT 895
                         -        viv   i   i   ii v      v  i   v v  i i  
  L1M4_orf2#LINE/    613 -GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_128030929_    896 TTTGCACAGCAAAATGAACA--GTCAGCAGAGCAAACAGATAACCCATAA 943
                             ii vv    -- i   --i   iv i  ii  v   i      i i
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAA--GGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_128030929_    944 AGTGGGAGAAAATCTTCACAAACTATGCATCTGACAAAGGACTAATATCC 993
                          i           v  ii    ii  ii      i  i     vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_128030929_    994 AGAATCTACAAGGAACTCAAACAAATTAGTAAGAAAAAAAACCAAACAAT 1043
                              v  i  i      vv    v i i   v     i --    i  i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CAAATAAC 807

  chr2_128030929_   1044 CCCATCAAAAAGTGGGCTAAGGTTATGAATAGACAATTCTCAAAAGAAGA 1093
                           v  i?    i     v    v v          v     v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_128030929_   1094 TATATAAATGGCCAACAA--ACATGAAAAAATGCTCAACATCACTAATGA 1141
                             i          i  --         i             ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_128030929_   1142 T 1142
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.71 (96 / 56)
Gap_init rate = 0.01 (8 / 643), avg. gap size = 1.88 (15 / 8)  


2356 25.50 8.11 2.94  chr2_128071655_128076329.rev     3334  4184 (491)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_128071655_   3334 CATGTTTATGGATTGGAAGA-TGGATTTAGTAGAGATGTTAAT---TCTC 3379
                               i             - vi  v v  vi     vi   ---i i 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_128071655_   3380 AAATTG--CTATA----CAAGCCTATTACTATCAAAAATCCCAACAAGGT 3423
                               --   i ----   vv v  iv         -     i --v i
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCCAGC--TGC 110

  chr2_128071655_   3424 TTTTTTTGTAGATATAGACAAAATTATTTTTATATGTACATGGAAATGCA 3473
                         i       i   v  v     iv v  ii v v  vi i           
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_128071655_   3474 AAGGAACTACAATAACTAAAACACTTTTGAAGAAGAA-----AAGTGGGA 3518
                          i   v i v    i i      v i     i     -----    v   
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_128071655_   3519 AGAATTAGTCTACACAGCTTTAAGACTTATTATATAACTATGATAAACAA 3568
                         i  v i vv  v v  ii  i  i     i  i v i   iii   v   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_128071655_   3569 GATGTTGTGACATTG-TGGAGGGATAGAGTCATCGACCAATGGAATGGGA 3617
                           iiv    ii i  -iiv i       vvi  v  i         i i 
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_128071655_   3618 TAGAGAACATAGAAACAGACCCACACCGCTA-GGT---------TTTGAT 3657
                          v    iivi     i i     i  vvi  -   ---------  i  i
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_128071655_   3658 AAAGATGT-AAAAGCATTTCATTGAAGGAAGGATAGACTTTTTTTTATGA 3706
                           i i  i-  i v    -  v  ii i   i    -- i    iv ii 
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAG--TCTTTTCAACAA 407

  chr2_128071655_   3707 ATAATACTGGGG-----AGACAACCATA-G-AAAAAAATTTAAAA--GAA 3747
                           ii i     i-----i  i ?   i - -    i   --i  i-- i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT--GAAGTTGGA 455

  chr2_128071655_   3748 CCTTGACCTAAGTGTCACGCTCTACACAAAAATTAATTCAAAATGGGAAT 3797
                           iiv    ------   i iv  i           i         ----
  L1M4_orf2#LINE/    456 CCCCTACCT------CACACCATATACAAAAATTAACTCAAAATGG---- 495

  chr2_128071655_   3798 GTATCATGGACCTACATGTAACATATTTAAAACTATAAAAACTTTTAGAA 3847
                         --    ?i      v      v v--i             -  i      
  L1M4_orf2#LINE/    496 --ATCAWAGACCTAAATGTAAGAG--CTAAAACTATAAAA-CTCTTAGAA 540

  chr2_128071655_   3848 --AAACACAAAAGAAAATCTT---GAC----------GAAAAGAGTTCTT 3882
                         --     i ii? v       ---   ---------- v  v iv     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_128071655_   3883 AGACTTAACACTAAAAGCACGATCTATGAAAGAGAAATTTGACAA-TTAG 3931
                            iv i    i        i v v ii     i   v v  i  -  i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_128071655_   3932 ACTTTACGAAGATTAAAAACTTTTGCTCTGCAAAG--CCCTCTTAAGAGG 3979
                             i iv  i              iv  v     -- v  v i    ii
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_128071655_   3980 ATGAAGAGACAATCTACAGACTAGGAGAAAATATTCACAAACCACATAGC 4029
                         i    i      i i     v i            ii    i  i   v 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_128071655_   4030 TGACAGAGGACTAGTATCTAGAATATATAAAGAACTCTCAAAACTCAACA 4079
                            i ii     v     i                   i v       i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_128071655_   4080 A-----AGAC------TCCAATTAGAAAACAGGCAAGCAACATGCACAGA 4118
                          -----    ------i      ?i    ii     ivi iv  v i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_128071655_   4119 CAGGTCACCAAAGAGGGGACACATACATGAC----AAGCACACACAAAGG 4164
                           vv  v       i -- i i i v   i ----       iiv    i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAG--ATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_128071655_   4165 TGTTCCACATCGGGAAATGG 4184
                           i  v     i????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (141 / 72)
Gap_init rate = 0.03 (31 / 895), avg. gap size = 3.03 (94 / 31)  


1089 15.42 1.32 4.85  chr2_128140627_128144206     1362  1588 (1992)    L1M4_orf2#LINE/L1        4   222 (686)  

  chr2_128140627_   1362 AAAGATATCCCATGTTCATGGATTGGAAAACTTAATATTGTTAAGATGGC 1411
                                                     i                     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_128140627_   1412 AATACAACACTACATCAAATTGACCTATAGATTCAATACAATCTCCATTA 1461
                              ----- v -i        i   i        ii     i i  i 
  L1M4_orf2#LINE/     54 AATAC-----TCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_128140627_   1462 AAATTCC---TGCCTTTTTTAAAGAAATAGACAAGGCATTCCTAAAATTT 1508
                             i  ---          iv      v      viiv          i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_128140627_   1509 ATATGAAAATGCAAGTGACACAGAATAATCAAAACAACTTTAAAAAAAAA 1558
                              i         v   v       ii        ii  i     i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_128140627_   1559 CAAAGAGGCCAGGTGCAGTGGCTCACACCT 1588
                         v  vi ----  v  v  - i       i 
  L1M4_orf2#LINE/    198 GAACAA----AGTTGGAG-GACTCACACTT 222

Transitions / transversions = 2.18 (24 / 11)
Gap_init rate = 0.02 (5 / 219), avg. gap size = 2.80 (14 / 5)  

 286 24.22 10.16 2.34  chr2_128140627_128144206     1868  1995 (1585)    L1M4_orf2#LINE/L1      190   327 (581)  

  chr2_128140627_   1868 AAAAAAAAAAAAAAAA--AAAAAACACCTTACTTAAAAATTACAATTTAC 1915
                              i  i  v   i--ii ii  -i vi    vvv    v   v--  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAA--AC 236

  chr2_128140627_   1916 TTACTAAAAAATT---GTAA--------GTGTGGCAGTGGTGTAAGGATA 1954
                               v   ii ---    --------      i v   ii        
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_128140627_   1955 GACATATACACCCATAGAACAGAACCAAGAGTCCAGAAATA 1995
                                 v i v  i   i    iii              
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

Transitions / transversions = 1.82 (20 / 11)
Gap_init rate = 0.04 (5 / 138), avg. gap size = 3.20 (16 / 5)  

1392 16.42 24.34 0.29  chr2_128140627_128144206     2269  2609 (971)    L1M4_orf2#LINE/L1      311   733 (175)  

  chr2_128140627_   2269 TCGAGAGTCCAAAAATAATCCCATATATTTGTGGTCAACTGATTTTTGAC 2318
                          i         i      v      i    i       i       i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_128140627_   2319 AAGAGTGCCAAGACCATTCAATGGGGCGAAGAGTAGTCTTATCAACAAAT 2368
                            i                      -i    i       v         
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAAT 409

  chr2_128140627_   2369 GATGCTAGGACAACTGGATAGCTACATGC--------------------- 2397
                          i    i             ? i      ---------------------
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_128140627_   2398 -----------------------TAAC--------------AG------- 2403
                         -----------------------    --------------  -------
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_128140627_   2404 ---------------TATAAAACTCCTAGAAGAAAACAGATGTTTTCAT- 2437
                         ---------------          i            v v ?v vv  -
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_128140627_   2438 TTCATGAGCCAGGATTAGGCAATAGTTTCCTAAACATGACAAAAAAAACT 2487
                            i   v iv  i         i     i  i i      vv    i v
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_128140627_   2488 CAAGCAACTAAAGAATAAGGAAATAAATTGGATTTCATTAAAAGTTAAAA 2537
                                 v      v  iv i          i     i    v v    
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_128140627_   2538 CGTGTGTA--TCAAACGACACAATCAAGAAAGTGAAAAGATGATCCACAG 2585
                          v v   i--     v     v                  ii i      
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_128140627_   2586 AAAAGGAAAAAATATTTGTAAATC 2609
                           vi   i          i     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATC 733

Transitions / transversions = 1.45 (32 / 22)
Gap_init rate = 0.01 (6 / 423), avg. gap size = 14.00 (84 / 6)  

1004 13.76 2.65 0.53  chr2_128140627_128144206     2900  3088 (492)    L1M4_orf2#LINE/L1      716   908 (0)  

  chr2_128140627_   2900 AAAAAAAATTTGCAAATCATATGTCTGAGAAGTGTCTAGTATTCA-AATA 2948
                          i    v               i     v   v v  v    i  -    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_128140627_   2949 AATAAGGAACTCTTACAATTCAACAATAAAAAGACAA----CCCGATTTA 2994
                         v    i            i    i             ----   i   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_128140627_   2995 AAAAATGGGCAAAGAGTTTGAATGGACATTTTTCCAAAGAGGATTTACAA 3044
                             -         ii       i       i        i   v     
  L1M4_orf2#LINE/    816 AAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_128140627_   3045 GTGGCCAACAGATACATGAAAAGATGCTCAACATTATCAGTCAT 3088
                         i       i iii                     i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.02 (3 / 193), avg. gap size = 2.00 (6 / 3)  


2146 16.83 1.97 20.95  chr2_128677364_128681136     2165  3281 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_128677364_   2165 AAAGACATACTGTGTTCATGAATTGGAAGATGTAATGTTGTTAAAATGAC 2214
                              i  v ii        i         iv    i       i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_128677364_   2215 AATACTCTGCAAATTGATCTAAAGATTCAATGTA-TTTTTGTCAAAATCC 2263
                                iv            v        i i - iii i         
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_128677364_   2264 CA-CTGTTGTTTTCTGCAAAAATATAAAAATTCATCCTAAAATACATATA 2312
                           -   ii-    i    i    vv v  ii v          v     i
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_128677364_   2313 GAATTTCAGCAGACCCTGACTAGGCATTCTTGATAAAACAGAACAATGTT 2362
                            v v  ivi     v  v   ----- ---------  i      v  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAG-----C---------CAAAACAATCTT 188

  chr2_128677364_   2363 GATAAAAACAGAACAATATTGGAGAACACATACTTCCCAATTTGAAAACT 2412
                           -    iv       vi      i  v  i            v      
  L1M4_orf2#LINE/    189 GA-AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_128677364_   2413 TACTACAAAGCTACAGTATTCAAAACAGTATGGTACGAGCATAAGAATAA 2462
                                           v    i     i      vi       i   i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_128677364_   2463 ACATGTAGACAGATGGAACTGAA----------AGAAA--AACCCTTATA 2500
                             i    ivi      iv   ----------     --     v  i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_128677364_   2501 TATGTGGTCAATTCACTTTTGATGTGGGTGCCAAAACAATTAAATAAAGT 2550
                          v i         v i   i  iiv         i  v   v   iii v
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_128677364_   2551 AAGAACAGGCTGGGCACGGTGGCTCATGCCTATAATTCCAGCACTTTGGG 2600
                              i  v  -------- --i   ----- i  v --i ii  --   
  L1M4_orf2#LINE/    388 AAGAATAGTCT--------T--TTCA-----ACAAAT--GGTGCT--GGG 418

  chr2_128677364_   2601 AGGCCAAGATGGGTGGATCACGAGGTCAGGAGTTCAAGACCAGCCTGGCC 2650
                          ---   v-   i i?-i   iv --  i------    -----------
  L1M4_orf2#LINE/    419 A---CAAC-TGGATAK-CCACATG--CAA------AAGA----------- 444

  chr2_128677364_   2651 AAGATGATGAAACCCTGTCTC-TACTAAAAATACAAAAAAATTAGCCGGG 2699
                          v  v v  i v    ii   -i  i ----  i v        ------
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCA----TATACAAAAATTA------ 484

  chr2_128677364_   2700 CATGGTGGCAGGCACCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGAG 2749
                         -----------------------------    iii ---  iiv  ?  
  L1M4_orf2#LINE/    485 -----------------------------ACTCAAAA---TGGATCAWAG 502

  chr2_128677364_   2750 AATTGCTTGAACCTGGGAGGCAGAATCTGCAGTGAGCTGAGATCATGCCA 2799
                          ---- i i  ----------------  i i-     i i --------
  L1M4_orf2#LINE/    503 A----CCTAAA----------------TGTAA-GAGCTAAAA-------- 523

  chr2_128677364_   2800 CTGTACTCCAGCCTGGGCAACAGCGAGACTCCATCTTGGATAAAAAAACA 2849
                           i  -------------------- i    ----  i  -- i      
  L1M4_orf2#LINE/    524 CTATA--------------------AAACTC----TTAGA--AGAAAACA 547

  chr2_128677364_   2850 -AAAAGTAAGAACAGTCTTTTCAAAAATAGTGCTGAGACAGCTGAATAGC 2898
                         - ii?    i------- i   -------   -----  --  -------
  L1M4_orf2#LINE/    548 TAGGNGTAAA-------TCTTC-------GTG-----AC--CT------- 569

  chr2_128677364_   2899 CACATGCAAGAGGATGAAGTTTAACTCTACTAAGTTGGCAATGGTTTCTT 2948
                         ----  -----  -------   -------------              
  L1M4_orf2#LINE/    570 ----TG-----GG-------TTA-------------GGCAATGGTTTCTT 590

  chr2_128677364_   2949 CAGTATACCACCAAAAGCACAGGTAACAGAAGAAAAAAACAGATAAATTG 2998
                         vii   iv             i i    i         -i          
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTG 639

  chr2_128677364_   2999 GGATTCATTAAAATAAAAAACTTGTGTGCACCAAGGGACA---TCATGAG 3045
                          iv     i     v        v     vi   i     ---   v  i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_128677364_   3046 AGTGAAAAGACAACTTAGGGAATAAGA-ATAATATTTGTGCCTCATACAT 3094
                                       ii vi    ii  - v        iivv     i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_128677364_   3095 CTGATGACAGATTAATA-CCAGATCATATAGGAAACTCCTACAACTGAGC 3143
                              i vi  i vi  -     vi     iii     i       --- 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---C 786

  chr2_128677364_   3144 AGAAAAGAAAAAACAAAAAAAGCAAACAAAAGACCTGCCCAGTGAAAAAC 3193
                          -------- v  i     i -    i  --------    i v?    v
  L1M4_orf2#LINE/    787 A--------ATAATAAAAAGA-CAAATAA--------CCCAATTWAAAAA 819

  chr2_128677364_   3194 TGGGTGAAGGATTTGAATAGATATTTC-CCAAAGAAGAGATACAAATGAA 3242
                             ii               i     -          v         iv
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_128677364_   3243 CAATAAGCCCATGAAAAGATCTTCAATATCATTAGTCAT 3281
                                 v           vi    i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (123 / 61)
Gap_init rate = 0.05 (48 / 905), avg. gap size = 5.33 (256 / 48)  


 790 24.37 1.52 0.00  chr2_128768758_128772385     1777  1973 (1655)    L1M4_orf2#LINE/L1        1   200 (708)  

  chr2_128768758_   1777 TGGAAAATCATCCCATGTCCATGAACTGAAAGACCTACTATCATTAAGAT 1826
                               ivi         i    i i  i     i  v   ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_128768758_   1827 GTAAATACTACTCATGT-AATCTACAGATTTAATGAAATCCCTATCACAA 1875
                          vv      v i  vi -i           i  i v           v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_128768758_   1876 CCCCAACAGTATTTGCTGCATAAATAGAGTAACTTAACCTAAAATTCATA 1925
                         i    i v iv   vi    v    v  vv i  v v             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_128768758_   1926 TGAAATTTCAAGGGATTTTGAATAGCTAAAGTA--CTTGACAAAAAAGAA 1973
                           i  v v       iiiv       i   ii --     v   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

Transitions / transversions = 1.29 (27 / 21)
Gap_init rate = 0.01 (2 / 200), avg. gap size = 1.50 (3 / 2)  

2252 17.63 7.47 0.41  chr2_128768758_128772385     2115  2596 (1032)    L1M4_orf2#LINE/L1      154   669 (239)  

  chr2_128768758_   2115 AAACAAAAAAAACCCCAAA---CCAAAACAA-------ATACAA-AACAA 2153
                            iiv  iii    vi  ---         ------- v v  -     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_128768758_   2154 AGTTGGA---CTCCCATTTCCTGATTTCAAAACTTAACTACAAAGCTATG 2200
                                ---   v  i    ii             -           ii
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAAAGCTACA 252

  chr2_128768758_   2201 GTAGTCAAATCAGTGTGGTACTGTCATAAAGATAGGCATATAGACCAATG 2250
                            i    iv             v     i     i        i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_128768758_   2251 GAATACGATAAAGAGCCCAGAAATCAACCCTTGCATATATGGTCAA---A 2297
                              vi  vi    i        v     v i   v         --- 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_128768758_   2298 T----------GGTGCCAAGACCATTCAATGGGGAAAACACACTCTTTTC 2337
                          ----------                          iv i v       
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_128768758_   2338 AACAAATGGTGCTGGGGAAACTGGATTTCCACATGTAAAAGAAGGAAATT 2387
                                         iv        v?       i       v   i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_128768758_   2388 GGACCCTTATCTAACATTATACATAGAAATTAACTCAAAATGGATTAATG 2437
                               i  i  v   ii   i i i                   i ?v 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_128768758_   2438 ACC--AATGGTAAGACCTAAAACTGTCAA-CTCTTAGAA-----CACAGG 2479
                            --    -     v        i v  -         -----  i   
  L1M4_orf2#LINE/    503 ACCTAAATG-TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_128768758_   2480 AAAAAAGCTTTATGATACTAGATTTGGCAATGATCTCTTGAATATGACAT 2529
                         ?iv   v   ii   ivi i i  v       i i    ii        i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_128768758_   2530 CCAAA-CACAGGTAACAAAAGAAAAGCTAGATTAATTGGGCTTCATCAAA 2578
                          v   -    i i            iv     v      i          
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_128768758_   2579 ATTAAAAACATTTAGGCT 2596
                                  v   iv   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCT 669

Transitions / transversions = 1.73 (52 / 30)
Gap_init rate = 0.02 (12 / 516), avg. gap size = 3.17 (38 / 12)  

1170 13.45 9.24 0.00  chr2_128768758_128772385     2900  3137 (491)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr2_128768758_   2900 AAAATTGAAAATATTTGTGCATCAAAGGATAGTATCAACAGAGTGAAACG 2949
                               i    iv       v        i v      v i       v 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_128768758_   2950 -CAACCCACAGAATGGAAGAAAATATTTGTAAATCATATATCTGATAAGA 2998
                         -               i            i                   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_128768758_   2999 GATTAATATCCAGAATATATAAAGAACTCCTATAACTTAACAA------- 3041
                           i vi                       i  i    i  i  -------
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_128768758_   3042 --------CCCAATTAAAAAATGTGCGA--CATTTGAGTAGACATTTCCC 3081
                         --------       ?       v  i --v      i          i 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_128768758_   3082 CAAAGAAGACAGACCAATGGCCAACAAGCAGAT-ATAAGATG---AACAT 3127
                                  i v  v         i     v  - v      ---     
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_128768758_   3128 CGTTAGCCAT 3137
                          i????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.58 (19 / 12)
Gap_init rate = 0.02 (5 / 260), avg. gap size = 4.40 (22 / 5)  


2069 24.32 14.39 1.74  chr2_128810410_128812347      643  1448 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_128810410_    643 TGGAGAAATATACCATGTTCATAGATTAGAGTTCTTGGATATTGAGAAGA 692
                             i i    v          i    i  ivv   i-      vv    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTA-ATATTGTTAAGA 49

  chr2_128810410_    693 AGTTGATTTTCTCCAAATTGCTTTGTAGATTCAACACAATCTCAAGAAAA 742
                         v vii  vi  i        v i ii         i     i v vv   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_128810410_    743 AATGTCAG-TGTCTTTTT----GAA---GA-AAGCTGATTCTAAATTT-- 781
                          - vi   -  i      ----   ---  -        i     v  --
  L1M4_orf2#LINE/    100 A-TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_128810410_    782 --------------------------------------TT--AAAAG--- 788
                         --------------------------------------  --     ---
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_128810410_    789 --------TGGACAACTTACACTAACTGCTTTTCAGACTTCCTATAAGGC 830
                         --------    vi   i     vv iiv   iv i    v   i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_128810410_    831 TACAGTAATCAAGATGGTATCGTACTGACATAAGGATAGACAAATGGATC 880
                                       ii  i v      i              v  i    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_128810410_    881 CATGGAACAGAGTAGAGAGTTAGGCAATAAATCTCCACAAT-ATGGTTAA 929
                         v      i   i v      ivi v      i ivi   v -     i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_128810410_    930 TTGATTTTTGAACAAGGA-ATCAAATTAATTCAAAGCAGAAAAGAA-AAC 977
                                 i  -     i-ii   iviv      v -i i      - ii
  L1M4_orf2#LINE/    349 TTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGT 396

  chr2_128810410_    978 CTTTTAAACAAATGGTGCTAAAACAAACCGGATATTTATAT---AAAAAA 1024
                              v             iii    - i     ?ii i  ---   i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAA 445

  chr2_128810410_   1025 TAAACTTAACCCCC---------------ACGGAAAATAATTTAAGATGA 1059
                          i  v  iiv    ---------------  ii   v   i i  i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_128810410_   1060 ATCATTGACCTAAAATGTAA-ACTTAGAACCCTGAATCTTTTAGAAAAAA 1108
                             ?v        -     - vi  i   iv i  v  i      i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_128810410_   1109 ATATAGCAGGGTA----TTTGCAAATTTGGGGAATGCAAAGACACCAACC 1154
                          i    -- ?   ----  i ii vi     vv v    v iivi --ii
  L1M4_orf2#LINE/    545 ACATAG--GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC--TT 590

  chr2_128810410_   1155 AAAT-TAGCACAAAAAACTTTAACTATAAATAAAAAAAATAAG--AATTG 1201
                          i  - ii   v    i viv i v i   - i        ii--     
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAA-AGAAAAAATAGATAAATTG 639

  chr2_128810410_   1202 GACATCATCAGGAT---GAACATTTCTACTCATCAAAAGATACAATTAAG 1248
                            v      ii  ---i   v   v i  --     i  i  v  i   
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTATCAAG 687

  chr2_128810410_   1249 AAAATGAACAAGCAAGCCACAGA-TG--AGGAAATATTCACAG------- 1288
                            i    v ii   v       -  --  i       ii  i-------
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_128810410_   1289 ---TGATAAAGAATCCATATTCATAATATGTAAAGAATTACTA-AA---A 1331
                         ---      i i iiii   i  v     i       i vi  -  --- 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_128810410_   1332 ATAATAAAAAGGCAGACAGCCCAGTT--AAAATGGTAATAAGACTC--AT 1377
                                    i  i i i    i  --       vv v i  i i--  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_128810410_   1378 AGACACTT-TACAATGCAAGATATGTAAATGGCCAATAAGCACATGAAAA 1426
                              i  - v   v -       ii                        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_128810410_   1427 GATATTCAACATTGTTGAAAAG 1448
                            ii       ii????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (131 / 62)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 3.61 (130 / 36)  


4392 16.49 6.55 0.35  chr2_128829683_128831633.rev      605  1459 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_128829683_    605 TGAAAAGACAGCTGGTGTTCATGGATCAGAAGACTTACTATTGCTGAAAT 654
                           i     i v ivi           ii         v     i i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_128829683_    655 GTCAGCACTTCCCAAATTGATCAACAGACTCAATGCAATTCCTATCAAAA 704
                          v  ii   i            v     i    i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_128829683_    705 TTCTAAAGGTCTTTTTCACAGAAATGGGCAAGCTGATTCTAAAATTCATA 754
                          i i ivv i      ii       v i         i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_128829683_    755 TGAGAATCCAAGGAACTCAGAGTAGTCAAAACAATCTTGAAAAGGAAGGA 804
                           ii   v     i  i    i   i                 i    i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_128829683_    805 AATATTTGGAGGATTTGCATTTCCCAATCTCAAAACTTACTACAAAGCTA 854
                         v v v        i ii  i        i                     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_128829683_    855 CAGTAATCAAAACTGTGTTGTACAGGCACAAGGACAGACAAATAGATTAA 904
                                   i  v    v    v    i     i     v      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_128829683_    905 TGGAATAGAATTGAGAGTC-AGAAATAAACTCATACATTTGTGGTCATCT 953
                                            -          i         i      vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_128829683_    954 GAGTTTCAACCAGG-TGCCAAGAC-------------------AGT---- 979
                           v    i  v   -         -------------------   ----
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_128829683_    980 TAAACAAA-GGCAGTAGGACAACGAGATAGTGACATGCAAAAGAATTGAT 1028
                          v      -  iiv i       vi    ?iv              vi v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_128829683_   1029 TTGAACCCCTACCTCATGCCACATACAAAAATTAATTCAAAATGAATCAA 1078
                            i            ii   i             i        i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_128829683_   1079 AG-TCTAAAAGTAAGAGCTGAAACTATAAAACTCTTAGAAGAAAACACAG 1127
                           -i     v         i                           i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_128829683_   1128 GTGAAAATCTTCATGACCTTGAGTTTGGCCATGGTTTCCTAGATATGATG 1177
                          ? v        i        i   v   v        i         ii
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_128829683_   1178 TCTACAATACAAGTAACCAAAGAAAAAAATAGATAAATTGGACTTCATCA 1227
                         i v v ii     i   v          -                     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCA 649

  chr2_128829683_   1228 AAATTTAAAACTTT-GTTTATCAAGGGACACTATCAAGAAAGTGAAAAAA 1276
                              v        -  viv    i                       i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_128829683_   1277 ACAACCCACAGAATGGGAAAAAATATTCTTAACTCATATAATTGATAAGG 1326
                         -                 i        ivi  v       vi        
  L1M4_orf2#LINE/    700 -CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_128829683_   1327 G-CCTATAACCAGAATATA--------------------------AAAAG 1349
                          - i i  v          --------------------------     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_128829683_   1350 GCAAGTAATCTAATTTTAAAACAGGCAAAGTATTTGAATAAACATTTCTC 1399
                         i   i   i i    ?v    ii       v         i         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_128829683_   1400 CAAAGAAGGTATGCAAATGACCTATGAACACAGTGGATGG-TACTCAATG 1448
                                 i   i      i  v  i i    -  i vi - i     ii
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACA-TGAAAAGATGCTCAACA 897

  chr2_128829683_   1449 TCACCATTTAT 1459
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.19 (94 / 43)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.54 (59 / 13)  


1750 24.81 4.36 2.46  chr2_128870150_128873628.rev     1669  2196 (1283)    L1M4_orf2#LINE/L1        1   538 (370)  

  chr2_128870150_   1669 TGAAGAGACATACAGTGTTCATGGATTGAAAGATTCGATTTAGTAAAGAT 1718
                           i i   i  v vi             i    i ii  v v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_128870150_   1719 ACAAATTCTCCCTAAAAGGACCTATAAGTTTAACGCAA---CTATCAAAA 1765
                         ivv   v     i   vv  i   i ii  i       ---         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_128870150_   1766 TTCCGGCAAGAAATGTTGAAGACATAGACAAAATTATTCCAAAATGTATA 1815
                          i  i  vivvvv v   v   v  v     iv v  i i     vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_128870150_   1816 TGGAAAGGCAAAGAAACTAGGATAACTAAAACAATTTTGAAAA----GAA 1861
                               v    i i v i  i   i i        i       ----   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_128870150_   1862 TAAAATGGGAAGAATCACTCTACCCAATTTTAAGACTTA-TATA--GCTA 1908
                         i   i v   i  v    v  v        i  i     -  i --    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_128870150_   1909 CAGGAATCAAGACCATGTGGTATGGGCAGAGGGACAGACCCATAAAT-AG 1957
                            v         vi       iv    v i   i    vi   i  - i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_128870150_   1958 TGGAACAGAATCAAGAGATCAGAAATAGACCCACACACGTATGGCCAACA 2007
                              i     ii    vi        i     i   iv     i   iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_128870150_   2008 GATTCTGGACAAAGGTGCAAAAGCAA--CA--GAGGAAAGA-TGGTCTTT 2052
                             i v     i     v  ii v --  -- i       - i      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_128870150_   2053 TCAAGGAATGGTGCTGGAGTAATTACATACCCACAGGCAAAAAAAAAAAA 2102
                             vi           iii  i iv   ?     v      i  vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_128870150_   2103 AAAAAAAAGAGACCTTGACCTAAACCTCGCAGCTTGTACAAAAATGAACT 2152
                         -------------i v    ivv     i  v v i         v    
  L1M4_orf2#LINE/    451 -------------TTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_128870150_   2153 CAAAATGAATT-------TAAGTGCAAAACATAAAACTTCAAAACTTTCA 2195
                                i  i-------   i  i  i vv       vi      i i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_128870150_   2196 G 2196
                          
  L1M4_orf2#LINE/    538 G 538

Transitions / transversions = 1.50 (78 / 52)
Gap_init rate = 0.02 (10 / 538), avg. gap size = 3.60 (36 / 10)  

 852 28.68 1.47 1.10  chr2_128870150_128873628.rev     2488  2759 (720)    L1M4_orf2#LINE/L1      507   779 (129)  

  chr2_128870150_   2488 AAAGGCAAAAAACAAAACTATAAAACTTCTAGAAGAAAACATAGAAGATC 2537
                            v i  i ivi              ii               i? vvv
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_128870150_   2538 ATCTTCAGCACCTCAGGCTTGGTGAACATTCCTTGGACGTGACACTAAAG 2587
                               ivv    ii  i v  ii vvi  i   i  ii      i   i
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_128870150_   2588 GTAAGATCTATAAAAGATAAATATCAATTAATTGTACTACATTGAAATTT 2637
                          i vi v v i      v   -  vi  v     v   v   ii     v
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_128870150_   2638 AAAACTTTCACTCTGTGAGCAACCCTGCTAAGAGGATGAAA-GACAA--- 2683
                                 iiiv  vii ivi  v  iii    iii     -     ---
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_128870150_   2684 GTAGGCTGGGAGAAAATATTTGCAAACCACATAGCTGATAAATGACTTGT 2733
                         ii  iv                    i  i   v       iv       
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_128870150_   2734 TTCTCTAATATGTAAAGAATGTTCTT 2759
                         v  ivv     i       --i    
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAA--CTCTT 779

Transitions / transversions = 1.66 (48 / 29)
Gap_init rate = 0.01 (4 / 273), avg. gap size = 1.75 (7 / 4)  

 461 26.34 1.79 8.04  chr2_128870150_128873628.rev     2765  2988 (491)    L1M4_orf2#LINE/L1      699   908 (0)  

  chr2_128870150_   2765 ATAATTTACAAAACGTATGAAAGTTTTTAAAATTTATACATTT-ATAAAT 2813
                          i  iii   i  i viv    i v   iv  v i   i  i -    iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_128870150_   2814 AATTTATCAAACTTCATATATATATATACATATATATATATATACTTCTA 2863
                         i i  i --- - i  v ---       v v -----------   ii  
  L1M4_orf2#LINE/    749 GACTTGT---A-TCCAGA---ATATATAAAGA-----------ACTCTTA 780

  chr2_128870150_   2864 AAACTCAACAGAAAAATAACAAATAATCCGATTGGAACGTGGGCAAAAAG 2913
                         v       i iv    vi        i  i   ?i  vi        iii
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_128870150_   2914 CACCAAGAGACGTTTCAC---AGAGGATACCCAGATGCCTAATAAGCACA 2960
                         iviv  v    i    v ---   i    iv  i   v i          
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_128870150_   2961 TGAAAAGATGTTCAGCATCGCTAAGCAC 2988
                                   i   i    i????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (39 / 19)
Gap_init rate = 0.03 (6 / 210), avg. gap size = 3.67 (22 / 6)  


2458 22.33 12.39 0.98  chr2_128901961_128906091.rev     2837  3651 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_128901961_   2837 TGAAGAGACATTCCATGTTCATGGATTGGAAGACTTAAAATAGTAAAGAT 2886
                           i i   i  i                          v  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_128901961_   2887 GCCAATTATTTCTCAAATTGTTTGATAGATTTAATGTAATTGATATCAAA 2936
                          v    - i i i       v iv i     i  i i   ivv       
  L1M4_orf2#LINE/     51 GGCAAT-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_128901961_   2937 ATCCCAGCAAGGTTTAATGCAGA------CAAATTTATTCTAAAATGTAT 2980
                                 vivv   vv      ------   ii v  i       vi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_128901961_   2981 GTGGAAAGACACAGGAACTAGAATAGT--AAACAATCTTGAAATAAGAAA 3028
                         i      vi  vi   v i       i--              -     i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGAAG 198

  chr2_128901961_   3029 AACTAAAGTGAGAG-------------TAACTTGA-----TATTA--AAG 3058
                            -     vi   -------------i  i  v -----  i  --   
  L1M4_orf2#LINE/    199 AAC-AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_128901961_   3059 CTACGGTAAACAAGACACTGTGGCATTGTGCA--GGGATAGACGCATAGA 3106
                             i    v       v     i i  -   --i        ii     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTG-GCATAAGGATAGACATATAGA 296

  chr2_128901961_   3107 TCAACAGAACAGAATAGAGAACCCAGAAATAGACCCACACAAATATGCAC 3156
                             ii   i     v    ii         i     i   vv    vv 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_128901961_   3157 AAGTGATGTTTGACAAAAGTGTGAAATCTATTCAATGG---AAGGATAGT 3203
                           v    v  i     ii   iv  iv i         ---   i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_128901961_   3204 CTTTTC--CAAAAG---------CAA----A-AACCA---ACAAACAAAC 3234
                               --    v ---------   ---- - ?   ---i    vi  i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_128901961_   3235 AAA-------------------------ACAA----CAAC---AAATGGA 3252
                         i  -------------------------    ----i   ---       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_128901961_   3253 TCATGGACTTAAACGTAAAA-C---AACTCAATAAAACTTTCAGGAGAAA 3298
                            ?i   i    i    i - ---    --        i i  i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACT--ATAAAACTCTTAGAAGAAA 544

  chr2_128901961_   3299 -CATGATAGAAAATCTTCAGAATCTAGGGCTAGGCAATGAATTCTTAGAC 3347
                         -   iiv? v        ivi i  v   i         iv        i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_128901961_   3348 TTGACACCCAAAGCATCATCCATAAAAGAAAAACT-GATAAATTAGACCT 3396
                         v       v      iv v v i          v -        i   i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_128901961_   3397 CACCACAATTTAAAACTTT-GTTCTGTGAAAGCACAC-ATAAAGAAGATG 3444
                           i  v    v        -  v  - v    v    -  v     ii  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAAGTG 693

  chr2_128901961_   3445 AAAAGACAGGCTGCAGACGGCAAGAAAATATCCGCAAACCACATATCTGA 3494
                                 iv ii    vv vi         ii     i  i        
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_128901961_   3495 GAAAGGGCAAGTATCTAGAACATAGAGAGA-CTATCAAAACTCAATACTT 3543
                         v  i  i vv     i    i   v i   -  v i v         v v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_128901961_   3544 AAAAAA-AAAT---TCAGTCAGAGAATGAGCAAATAACATAA---GACAT 3586
                             i -    ---i  i i?i i    i     vi iv i ---     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_128901961_   3587 TTCATTAAACAGAGTATACAAATGACTGATAAGTACATGAAAAGACAGCT 3636
                            vii   v iii          i ii     i           i-   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCT 892

  chr2_128901961_   3637 -GATGTCATTAGCCAC 3651
                         -i ii   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (112 / 66)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.30 (109 / 33)  


2915 19.71 19.84 0.53  chr2_128953466_128958241     3534  4284 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_128953466_   3534 CTGTGTTTATAAATCACA-GATTTAATCATGTTAAGAGGGCAATACTTCC 3582
                          ii    i  ii  iiv -  i     vv        v         i  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_128953466_   3583 CCAATTGATCTACGTATTTAATATAATCCCTATCTGAATACCAGTTATTT 3632
                          v           iv   i  iii          vi   v    i iii 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_128953466_   3633 TCTTTGTTGAAATTGACAACTTAATTCTAAAATCCATATGGAATTACAAG 3682
                          i    iv           vi i  i       i         v i    
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_128953466_   3683 GAGTTACAAATACCTAACACAATTTTGAAAGAGAAGAACAAAATACAAGG 3732
                          iiiivvi    v i  v     i      i           i vvi   
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_128953466_   3733 ATTCACATTTCCCAATTTCAAAACTTACTACAAA-CAATGATAATGAAGA 3781
                          i     i                          - v iii    v    
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_128953466_   3782 CAGAGGAGGCAATGGCACAAGGATAGACATGTAGATCAATAAAATATAAT 3831
                            v v-  i v     i            i         ii    v   
  L1M4_orf2#LINE/    263 CAGTGT-GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_128953466_   3832 TGAGAGGCCAGAAACAAATCCATACATCTATGGTCAACTGATCTTCAACA 3881
                               v       i   i        i         i    i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_128953466_   3882 AGGATTTCAATACCATTCAATGGGGGAAAAATATTCTTTTCAGCAAATGG 3931
                            i vi   v              i  i    v        i       
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_128953466_   3932 TGCTG--------------CCACATGTAAAAGAATAATGTTGGATCCTTA 3967
                              --------------       i        i v      i  i  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_128953466_   3968 CCTCATACCATATACAAACATTAATGTAACATAAATTAAAG--CT----- 4010
                              i            v     ivi  v  ii  i ?  --  -----
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_128953466_   4011 -----GTTATAACCATAAAACTGTCAGGAAAAAACAT--GGGTAAATCTT 4053
                         ----- i  v   i        v i  i i       -- ?         
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_128953466_   4054 CATTATCTTGGACTTGGCAAAGGATTCTCAGATATGATATTAAAAGCATA 4103
                          i v i     ii v     v  v    i        i ii       i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_128953466_   4104 AACAACCAAAGAAAAAATAGATAAGTTGGAC---------ATT------- 4137
                          i    v                 i      ---------   -------
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_128953466_   4138 -------------------------------------------------- 4137
                         --------------------------------------------------
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_128953466_   4138 ---------------------CATATAT---------------------- 4144
                         ---------------------       ----------------------
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_128953466_   4145 ---GTAGAAAGAGCTCTTACAATTCAATAA------GACAA-TGACGTTC 4184
                         ---i  v     i         i       ------     - i  --- 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC---C 808

  chr2_128953466_   4185 TAATTTTAAAATAGGCAAAGGGTATAAACAGTCATGTCTCCAAGTAAGAT 4234
                         i    ?v     i        i v i  i  v   v       iv     
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_128953466_   4235 GTATAAATGGCTAATAAGTACATGAAAAAATACTCAATTTCATCATTATC 4284
                         i  i       i      i         i  i     iv   ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.22 (100 / 45)
Gap_init rate = 0.01 (13 / 896), avg. gap size = 11.77 (153 / 13)  


2478 24.97 2.21 2.90  chr2_129004213_129006311      503  1227 (872)    L1M4_orf2#LINE/L1      109   828 (80)  

  chr2_129004213_    503 GCATTTTTCACAAAAATAGAAAAACCAAATCTAAAATTCATA-GGAAAC- 550
                           v     ii  i    v  v  i ii vi            -     i-
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_129004213_    551 CATCAAAGACCCAAAATCGCCAAGACAATCTTGAGCAAGAAGAATGAAGC 600
                           -- ii      i   v     i          iv        ii   i
  L1M4_orf2#LINE/    159 CA--AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_129004213_    601 TGGAGGCATGATGCTTCCTGGTTTAGAAGTATACTACAGAGCAATAGTAA 650
                               vv v ii     iii   vi  iiv       i   v i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_129004213_    651 TCAAAGGAGTGTGGTAGTGCTGTAAAAACAGATATAGAGACCAGTAGAAC 700
                             iiv         v  vii   ii i   i   v   i  i i   i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_129004213_    701 AGAATAGAGAGCGCAGGAGTAAATCCATACATTTATAACAGACTGATCTT 750
                              v     iv   i i    i            iiivi i    i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_129004213_    751 CAACAACGATGCCAAGA--ATGCACTGTGGTGTAAGGATTGTGTCTTCAG 798
                          i    v i        --  v  --i   v v   i  v  v i    i
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_129004213_    799 TAAACGGTGTTGGGGAAACTGGATATTCACATACACAGCAATGAAAGTGA 848
                         i   i    i    iv         ?i     i  v iv      iv  i
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_129004213_    849 AACTTTGTCTCAGCCTATGTACAAAAATCAACTCAAAATGGATTGAAAAC 898
                          v ii ii    vv i  i         i              ii? i  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_129004213_    899 TTAAACTTAAGACCTGAATCCATAAAACTGCTAGAAGCAAACAAA----- 943
                         i    iv     v  i  v i        vi      v     v -----
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_129004213_    944 AAATCTTCTTGACATTGGTTTGGGTAGTGTTATTTTGAATACAACCTCCC 993
                                 v    v    v  i  i i  v v i  ii   ii  v-  v
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA-CCA 603

  chr2_129004213_    994 AAAGCACAGGCAACTGAAGCAAAAATAGACAAATGGGATTGTCTATTTTT 1043
                                 i     vi   v         i    v   i ----------
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT---------- 643

  chr2_129004213_   1044 TTTTTATAGAAACTAAAAAGCTTCTGTACAGCAAAGGAAAAAAAATCAAC 1093
                         --- i  vi   i      -   i   i vv       v vv --    v
  L1M4_orf2#LINE/    644 ---TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA--TCAAG 687

  chr2_129004213_   1094 AGGGTAAAGAGACAACCTACAGTATGGGAGGATATATTTACAAACCATAC 1143
                          ii  i  i        i    v       i v      i    i    i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_129004213_   1144 ATCCGATAAGGGGTTAATATGAAAAATATGTACA-AACTCAAACA-CTCA 1191
                            i        ii vi   vv i     i  v -     vv   -    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_129004213_   1192 ATAATGAGAAGACAG----TCTGATT-AAAAATGGGCAAAG 1227
                              i i      i----i ii   -              
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.84 (116 / 63)
Gap_init rate = 0.02 (14 / 720), avg. gap size = 2.64 (37 / 14)  

 435 19.47 2.65 1.77  chr2_129004213_129006311     1495  1607 (492)    L1M4_orf2#LINE/L1      795   908 (0)  

  chr2_129004213_   1495 AAAACCAAACAAACAAA---GAAAATGGGCAAATGACTTAAATTGACATT 1541
                            iv    i  v v  ---i            v  i  i   v      
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_129004213_   1542 TTTTTCCAAAGGATACATACAAATGGCCAACAGGTACTTGAAAAGGGGCT 1591
                          i --      i v i              i i i  v       iv   
  L1M4_orf2#LINE/    845 TCT--CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_129004213_   1592 CAATGTCACTAATCAT 1607
                            ii   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.02 (2 / 114), avg. gap size = 2.50 (5 / 2)  


2067 24.25 3.12 4.74  chr2_129107333_129109709.rev      679  1416 (961)    L1M4_orf2#LINE/L1        1   726 (182)  

  chr2_129107333_    679 TGGAGAAGTATTGAACG--CATGGGTTAGAAGGCTCGACATTGTTAAGAT 726
                             i ii   ivv i --     i  i    i  ii i           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129107333_    727 GGCAGTTCTTCCCACACTGATCTATAAATTCAAGGCAAACCC-ATTAAGA 775
                             i v  i    v i       i i      v    v   -  i  - 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-A 99

  chr2_129107333_    776 ATTTCTATAGACTTTTGAGAAGTAAATTAACAGGTGGGTTCTAAAACTTA 825
                           ii viiv v     vv v  -     i   i iv i i      i i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAG-AAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_129107333_    826 AATTGAAAAGCAAAAAATGTCAGAATAGCCAAAACAATTTGGAAGAAAAA 875
                         v  v    v    iii i-i                  i v   --   i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAA--AAAG 195

  chr2_129107333_    876 AAGAAGAAATTTGGAGGAATCTCACAC---CAGACGTAAATACTAAATAA 922
                              v   v        --       --- vi iv v  v   v v  v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGA--CTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_129107333_    923 AAAGCTACAGTATTCATAATAGTGTGGTATTAGAATAAGGACAGGCATAG 972
                                     v   vi i         i i v       i  i    v
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_129107333_    973 AGATTGATAGAATATAATTGAATTGAGAGTTCAGGGATAAAGTCACACAT 1022
                             ii  i     -----           i   ii     vi  i    
  L1M4_orf2#LINE/    294 AGATCAATGGAATA-----GAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_129107333_   1023 ATATGATCAATTAATTTTCAACA-GCATGCCAAG-CAATTCAACAGGGAA 1070
                         v    i      i      i   - vi       - v      ii     
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_129107333_   1071 AGTTCACTCTTTCCAACAAAGAGT-CAGAAACATCAGGACATCCTTATTT 1119
                           vvi v     i       vi  - v ii   v v   i ?  vi  vi
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_129107333_   1120 TAAA--ATGCACCACAACCCTTCCCTTGTACCTTATCCCGAAAACAAAAA 1167
                         v   --   v vivvi    i v   iii   v   -------       
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATAT-------ACAAAAA 481

  chr2_129107333_   1168 ACCAAAAAAACTAACT-GAAATACAGTATAAGCCTAAATGTAAAA-CCAA 1215
                         ----------i     -i    iv vi ? ii           i - i  
  L1M4_orf2#LINE/    482 ----------TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_129107333_   1216 AGCC-TAAACCTCTTAAGAGA-----TAGGAGAAAAACAT-GTGTGCTTG 1258
                          i i-    v      ii   -----    ? v   v v -   vv    
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_129107333_   1259 GATTCGGCAAACATGTTTCA-ATAGGACAAAAAAAGGCACAAAACTACAA 1307
                          i  v     vvi v i i -   v    vv     -     i- v    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG-CACAAG-CAACAA 619

  chr2_129107333_   1308 ATGAAAAAAATTGATAAACTGGACTTCGTCAAAATCAAAA-CTTCTGTTT 1356
                          v       - v      i        i       i    -   i   vi
  L1M4_orf2#LINE/    620 AAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_129107333_   1357 TTTGTAAAACACTGTTTTAAGAAA-TGGAAAGTCAAGCCACAGACTTGGA 1405
                           iiv ii     i i--      -  i    v   v       v v   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATC--AAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_129107333_   1406 AAAACACATTT 1416
                         i   - i    
  L1M4_orf2#LINE/    717 GAAA-ATATTT 726

Transitions / transversions = 1.38 (102 / 74)
Gap_init rate = 0.04 (28 / 726), avg. gap size = 2.07 (58 / 28)  

 515 23.50 7.10 1.64  chr2_129107333_129109709.rev     1715  1897 (480)    L1M4_orf2#LINE/L1      716   908 (0)  

  chr2_129107333_   1715 AAAAAACATTTTAAAAACATGTATCTGATAAAGGACCT---TCCTGAA-A 1760
                          i    i    vv   v   i          i    i ---   v   - 
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_129107333_   1761 TATTGAAAGAACATTTATAACTTTATAATAAGAAGACAAACAATTCAATA 1810
                            --       vi   i    iv       i        i  ii    -
  L1M4_orf2#LINE/    766 TAT--AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT- 812

  chr2_129107333_   1811 TGGAATATAGACAAAAGATTT---TGGACACTTCACCAAAAACTATATGT 1857
                          ?i  v  i i    i     --- i    i   v     i vv    ii
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_129107333_   1858 GAGTGGC----AAGTGCATACAAA--TGCACAGTACTATTAGTCAT 1897
                         i i    ----   ii   iv   --   v  ii ii ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (30 / 12)
Gap_init rate = 0.04 (7 / 193), avg. gap size = 2.29 (16 / 7)  


1127 26.60 10.60 4.00  chr2_129122065_129125944.rev     2244  2743 (1137)    L1M4_orf2#LINE/L1        1   533 (375)  

  chr2_129122065_   2244 TGGAGAAACATACCATTTTCATATGCTGGACGTGTCAGTATAGTAAAGCT 2293
                             i i i  v    v     ivii    v vv i i   v  v   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129122065_   2294 GTCAATTCTCCTAAAACTGATATAAAGTTAAAATACAATTTCTATCAAAA 2343
                          v    v    iv   i    v  v  v vv  ii    ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129122065_   2344 CCCCAGCAATATACCT-----GCATATTTTTATAGAC--------AAATG 2380
                         i      ---- i   -----   v vv  v i ii --------    v
  L1M4_orf2#LINE/    101 TCCCAGC----TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_129122065_   2381 TTTGTGAAAATGCAAAGGAGCATGAA--GCATTAAACATTTTTGAAAAAG 2428
                         iv i  i        i   v vv   --  -iv     v i         
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGC-CAAAACAATCTTGAAAAAG 195

  chr2_129122065_   2429 AAGAATGAAGTGAAAGGAATCAATCTATCTGATTTCAAAACTTATTATAT 2478
                              ii    vii    v   vv  vi ii             i  i v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_129122065_   2479 AACCCCAGTAATCAAGACTATGTGGTATTGGTGGAGGAACAGACA----- 2523
                          i iv             vi       i   iiv i i i     -----
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_129122065_   2524 ---AA--GAACAGTA--GAGAACCCAAAAATAGACCCATGCAAATACATC 2566
                         ---  --   i  v --    ii   i     i      i  vv  iivi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_129122065_   2567 CAACTGATTTTTCACAAAGGTGCAAAAGCAATTCAATCAAGGAAAG---- 2612
                            i       iv    i     v  ii v       -ii      ----
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATA 394

  chr2_129122065_   2613 --CTTTTCAAT-----------GAACAATTAGATGTGCATAAGCAGAAAA 2649
                         --        i----------- i    i i   i?v  i v   ---  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA---AA 441

  chr2_129122065_   2650 AAAACAAAAACTCCAAAACCTTGG-CCTAAACCTCAAACCCTAAACAAAA 2698
                          i  ii  i-----------    -  ivv      v   v  v      
  L1M4_orf2#LINE/    442 AGAATGAAG-----------TTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_129122065_   2699 CTTAACTCA----GGGTCT----TTTGCATGTAAAATATAAAACTATCAA 2740
                         v        ----  i  v----ii iv      i vv         v  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_129122065_   2741 ACT 2743
                            
  L1M4_orf2#LINE/    531 ACT 533

Transitions / transversions = 1.32 (75 / 57)
Gap_init rate = 0.03 (16 / 533), avg. gap size = 4.56 (73 / 16)  

 894 23.42 10.74 1.65  chr2_129122065_129125944.rev     3026  3388 (492)    L1M4_orf2#LINE/L1      513   908 (0)  

  chr2_129122065_   3026 AAAAATTAAA-CTATAAAA-----AAAAGGAAA-------GTA----TTT 3058
                           i ii    -        ----- i   i   -------   ----  i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_129122065_   3059 GGGATCTAGGACTAGACAAAGAGAACTT-TATAT---------AGTATAA 3098
                          v  i  v  ii   i   v ivvv   -v    ---------  i i  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_129122065_   3099 CCTACAAAA----AAAT-GAAAAATTGGACTTTATTAAAGTTAAAAATGT 3143
                         v v      ----    -  v           i  i   i       iv 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_129122065_   3144 TTG--CTTTGAGAAAAAGCCTATTAAGAGGATGAAAATACAAGTTATGTA 3191
                            --   ii iii v --    i    iii      v    vii iiv 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACA--CTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_129122065_   3192 CTTGTAGAAAATATTTGCAACCCACACGTCTAACAAGG-ACTAGTA-CCA 3239
                         v v v               vi  i ii   i i    -   v   -   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_129122065_   3240 GACATATATAAAGAATTCTCAAAACTCAGCAGTAAAAAAATCAAACTTAC 3289
                           -            i   i v      ii i      i -    - v  
  L1M4_orf2#LINE/    761 GA-ATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAA-TAAC 807

  chr2_129122065_   3290 C--ATTTAGAATATGGGCAA-GGATCTGAACAAACATTTCACTGAAAAGG 3336
                          --   ? i  -        -    i    i i       v ii  i i 
  L1M4_orf2#LINE/    808 CCAATTWAAAA-ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_129122065_   3337 ATATAGAGATGGCAAAAAAGTACATGACAGTGTGTTCAGCATCACTAACC 3386
                              v i     v  v   i      v ivi  i   i     ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_129122065_   3387 AC 3388
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.00 (56 / 28)
Gap_init rate = 0.05 (18 / 396), avg. gap size = 2.50 (45 / 18)  


4079 18.05 3.52 0.68  chr2_129172195_129178853.rev     2550  3430 (3229)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_129172195_   2550 GAAAGATTTCCCACATTCATGAATCAGAAGACCTAATACTGTTAAGATGT 2599
                                v     ii      i  ii      i     i          v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_129172195_   2600 CAATACTTCCCAAATTGATCTA--AATTCAACGCAA-------CAA---- 2636
                                i              --i           -------   ----
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_129172195_   2637 ---GTTAGGTTTTTTGCAGAA-TTGACAATCTGATCCCAAAATTCATAAA 2682
                         --- i ivv            -       v       i          vi
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_129172195_   2683 GAAATTCCAGAAAGCCAGAATTTTCAGAACAATCTTTGGAGAAAAAAGAA 2732
                              v v  ii v       vvi  i         --  i   i     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--GAAAAAGAAGAA 200

  chr2_129172195_   2733 ---AGTTGTAG-ACTCCCATTTTATTATTTCAAAACTTACTATAAAGCTA 2778
                         ---     v  -    v  i  iviv                i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_129172195_   2779 -----ATGAAGACAGTATGATATTGGCATAAGGATAGAAATACAGATAAA 2823
                         -----  v        i  i  i               v   i    v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_129172195_   2824 TGGAATAGAATTCAAAGTCCAGAAATAAGCCTTTACATTTACAATCAAGT 2873
                                     v i             i  iv        iii    v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_129172195_   2874 AATTTTTTACAATGTTGCCAAGAAAACTTAATAAGAAAAAGAATAAACTT 2923
                         i     iv    v v        vv i i   ii i   -     iv   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTT 399

  chr2_129172195_   2924 TTCAAATAATGGTGCTGGGTCAGCTGGATATCGACATGCAAAAGAATGAA 2973
                              vv            v  i       ? v                 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_129172195_   2974 TTTAGTGTTATTTTTCACAGCATACAGTAAAACTAAGTCAAC-TGGATCA 3022
                         v  i vviiv vii     v    i vv    i   v    v-       
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_129172195_   3023 CAGACTTAAAACTAAGAGCTAAAATTATAAAAACATCTGGGAA--AAATA 3070
                         ?    i    vv            i       - -   vi   --   i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-C-TCTTAGAAGAAAACA 547

  chr2_129172195_   3071 TAGTAGTAAACCTTCACAAGCTTTGGTTAGGAAAAGCCTTCTTAGATATG 3120
                            v?     i    iii v   v       v  v vi            
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_129172195_   3121 ACACCAGAAGCACAAGTAAAGAAAGAAAAAATAGATAAATTGAACTTCAT 3170
                               i         i  vi                     i       
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_129172195_   3171 CAAAATTTAAAACTTTGATGCTTCAAAGGACACCATGAATGAAGTGAAAG 3220
                                v        vi               i  v  vi        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_129172195_   3221 GACAACT-ACATAATAGGAAAACATTTTTGCAAATCATGTATCTGATGAG 3269
                               i-   v   i   i  v  v            i        i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_129172195_   3270 GAGCTTGTATCTAGAATAGATAAAGGACCCTTATTACTCAATAGTATAAC 3319
                          ii        i      v      i  i    iv        i  v  v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_129172195_   3320 -ACAAATAACCCAATCAAAAATCTAGGAAAAAGATCTGAATAGACATTTC 3368
                         -              i?    -v i  v   i   i              
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_129172195_   3369 TTCAAAGAAGATATGCAAATGGTGAGTAAGCACATAAAAACATGCTCAGC 3418
                          i            i       iv i         i    v       i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_129172195_   3419 ATTATTAGCCAT 3430
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (89 / 66)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 2.31 (37 / 16)  

3511 23.24 2.79 1.34  chr2_129172195_129178853.rev     3910  4804 (1855)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_129172195_   4804 TGGAAAGATATCCTGCGTTCATGCATTGGAAGAAACAGTGTTCTTAAAGT 4755
                                      iii       v         vvi i i  v    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_129172195_   4754 GTTCATACTTTCCAAAGTTATCTACAGATTCAGTGCAATCCCTATCAAAA 4705
                          viv     ii     v v             ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_129172195_   4704 TTTCAA-TGTCATTTCTTACAGAAATAGAAAAAA-AATCCTAAAATTTGT 4657
                          ii  i-  i -   i  i       v  v  iv-i           ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

C chr2_129172195_   4656 ATGGAGCCTATAGAAGACCCCAAATAAGCCAAAGCAATCTTGAGTAAGAA 4607
                              iv- ii iii     vi    -      i         iv     
  L1M4_orf2#LINE/    150 ATGGAAA-TGCAAGGGACCCAGAATA-GCCAAAACAATCTTGAAAAAGAA 197

C chr2_129172195_   4606 GAACAAAGTTGAAAGCATCACTTTTTCCAATTTCGAACAAC--ATTACAA 4559
                                    i i vv    vi  i        i  --  -- i     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAA 245

C chr2_129172195_   4558 AGCTGTAGTAATGAAAACAGTACAGTATGATATTGGCATAAAAACAGATA 4509
                             ii      v  i     i-----  i  i        ii i   i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTG-----TGGTACTGGCATAAGGATAGACA 290

C chr2_129172195_   4508 TGTAGA-CATATGAAATATAATAGAGAGCCCAGAAATAAAGCCACACATA 4460
                          i    -  -   i    v   v     i           v   i    v
  L1M4_orf2#LINE/    291 TATAGATCA-ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

C chr2_129172195_   4459 TACAGTCATCTAATCTTTGACAAGAGCATCAAAAGTACACAATGGGGAAA 4410
                           ii    vi i  i  i      i iii   i vi iv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

C chr2_129172195_   4409 GTACACTGTCTTCAG----TGGTGCTGAGAAAACTGGATATCCACATGCA 4364
                          v i v v i    i----        i  v         ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

C chr2_129172195_   4363 AAAGAATAAAATCAAACCCTTATCCTACACAATACAGATAAGTTAACTCA 4314
                                i  i iii    i  i ii    v   i v v  i        
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

C chr2_129172195_   4313 GAATGGATTAAAGACTCAAAAGTAAAACCTGAAACAATAAAATTGCTAGA 4264
                         i       i ?    ii   v    i v  i    v      i vi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

C chr2_129172195_   4263 AGAAAACATAAGGAAAGGGCTGTTTGACGTTGATCTTGGCTATGATTT-T 4215
                                   i ?iv iiv  viv    v   ivi v   v   i   - 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

C chr2_129172195_   4214 TAAAAATGACTCCAAA-GCACAGGCAACAAAAACAAAAATAAATAAGTGG 4166
                           i v     v     -     i         iv       i    i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

C chr2_129172195_   4165 TGCTACATCAA--CTAAACAGCTTCTGCACAGCAAAGGAAAC-ATTAAAA 4119
                         vi  v      --i    - i   i  ii vv       v  -  i  i 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGA 688

C chr2_129172195_   4118 AAATGTAAAGGCAACCTACGGAATGGGGGAAAATATTTGTAAATCATATA 4069
                           i  v    i     i  i       i           i          
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

C chr2_129172195_   4068 TCTGATGAGGGGTTAATATCCAAAATATTTAAGGAACTCATACAAATCAG 4019
                               i    ii vi      i     v   i      v     v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

C chr2_129172195_   4018 TAGCAAA----CAAAAAACC---TCTCCAAACAGGCAAAGGACTTGAAGA 3976
                           ii   ----    v    --- i?vv   ii         i     v 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

C chr2_129172195_   3975 GACATTTTTC----AAAGACGTACAAATGGCCAAAAGGTATATGTAAAAG 3930
                                i  ----i    ii             v i i i   v   ii
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

C chr2_129172195_   3929 TGTTCAATATTACTATCATC 3910
                           i    i  i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.19 (140 / 64)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.95 (37 / 19)  


2925 25.80 1.88 1.33  chr2_129232184_129237263.rev     1623  2525 (2555)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129232184_   1623 TGGAAAAATATTCCATCCTCACAGATAGGAAGAATCAATATCATGAAAAT 1672
                               i    i    vi   ii   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129232184_   1673 GGCCATATTGCCCAAAATAATTTATAGATTCAATGCTACTCCCATCAAAC 1722
                            v   i v      v i  i  i        i  v ii  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129232184_   1723 TACCA-CTGACATTCTTCACAGAATTAGAAAAACT-ATTTTAAATTTCAT 1770
                          v   -   v -  i  ii     v v  v  i  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_129232184_   1771 ATGGAA-T-CAAAGAAGACCCCATACAGCCAAGACAATCCTAAGCAAAAA 1818
                               - -   i --     viv i      i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_129232184_   1819 TAACAAAGCTGGAAGCATCATGCTACCTGACTTCAAACTATACTACAAGG 1868
                         v       i    i vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_129232184_   1869 CAACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAAATATAGAA 1918
                          v       i   ii   ii         i iv ii i   v       v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_129232184_   1919 CAATGGAGCAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCA 1968
                                ii    iv    vii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_129232184_   1969 TCTGATCTTCAGCAAACCTGACAGAAAACAAACAATGGTGAAAGGATCTC 2018
                         vi    i   ii   ivv  v  - i v  vv      v     i  vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGT 396

  chr2_129232184_   2019 CTATTCGGTAAATGGTGCTAGAAAAACTGGCTAGCTATATGCATAAAACA 2068
                           v   iii          i i v      v  ? i i     v  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_129232184_   2069 GAAACTGGACCCCTTTCTTACACCTTATACAAAAATTAACTCAAGATGGA 2118
                            ii         vi  i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_129232184_   2119 TTAAGGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAAT 2168
                          i ?i   i         i v i     i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_129232184_   2169 CTAGGCA-ATACCATTCAGGACAT-AGGCACAGCAAAAATTTCAT-GATG 2215
                         v    ?i- v i -   iv   v -i  ivvi    vii    v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr2_129232184_   2216 AAAACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCT 2265
                          vi            vvv          v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_129232184_   2266 -ATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCATCAGGGTGA 2314
                         -  i   v v  i i   i  ii vv    i  v       vv ii    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_129232184_   2315 A----CAACCTAGAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 2360
                          ----     i v               v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_129232184_   2361 AATGTTCTAATATGCAGAGTCTACAAGGAACTTGTATTCTTA-AATACAA 2409
                           v vv  vi   v    i v  i  i     ------    -  iv   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACT------CTTACAACTCAA 788

  chr2_129232184_   2410 GAATAAAAA---AAAAGACTTCATTAAAAAGTGAGCAAAGGACATGAGCA 2456
                         v        ---   vi  iiv   ?    i  i        iv   ii 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_129232184_   2457 AACACTTCTCAAAAGAAGACATACATGTGGCCAACAAACATATGAAAAAA 2506
                         i   i     v        i     vi       i  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_129232184_   2507 -GCTCAACATCACTGATCCT 2525
                         -           ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.61 (29 / 18)  

3834 17.24 7.51 0.74  chr2_129232184_129237263.rev     3769  4580 (500)    L1M4_orf2#LINE/L1        1   867 (41)  

  chr2_129232184_   3769 TGGAAAGAC-TCCCATGTTCATGAATTGGAAGA--TAATATTATTAAGAT 3815
                                 i-             i         --       i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129232184_   3816 AGCAATTTTCTCCAAATTGATTTTCAGATTCAATACAATCTCTGTCAAAT 3865
                         i     vi  i          i v         ii     i  i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129232184_   3866 TCCCAATT-CACTATTTGCAAAAATAAACAAGCTGGTCCTAAAATTTATA 3914
                              ii - vi v      i    vi        i          i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_129232184_   3915 TGAAAATGCAAGGGACCCATAATAACCAAAACCATTTTGA----GCTAGA 3960
                           i                v    i       v  i    ---- v-   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA-AGA 199

  chr2_129232184_   3961 ACAAAGTTGGATGACTCATATTTTTCAA---------------CAGAACT 3995
                                    v      i i  ii   ---------------  i i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_129232184_   3996 ACACTACTCAGGACAATGT---ACTGGCATAAAGATGAACAGGCAGAGTA 4042
                            v  v   i    i   ---          i   ii   vii   vi 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_129232184_   4043 ATGGAATATAATTACAAGTCCAGAAATAAACCCACAACTTTAAAGTCAAT 4092
                                 v    ivi                  i vv    vi      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_129232184_   4093 TGATTTTTGCCAAGAGTACCAAGATCATTCAGTGGG-AAAGAATAGTCTC 4141
                                i v    i  i      i      i    -            i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_129232184_   4142 CTCAGCAAATAGTGTTCGGACAACTGGATATC------------------ 4173
                         i   i     i   i v             ? ------------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_129232184_   4174 GT-------------CACACCATATATAAAAATTACCTTAAAATGGATCA 4210
                           -------------           i        v  i           
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_129232184_   4211 TAGGCCTAAATGTAAGAGCAGAAACTAACAAACTCTCTAGGAGAAAGCAC 4260
                         ?  i               vi      vv       -   i     i  i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAACAT 548

  chr2_129232184_   4261 AGGAGTAAATATTGCTTACCTTGTGTTAAGCATTGGTTCCT-AGATAAAA 4309
                            ?      v  vv v      v    i   v     i  -     vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_129232184_   4310 CACCAATAGCACAAGCAATAAATAAATAAATAAATAAATAAATTGCATTT 4359
                               v           i   --- v   -     i        v i  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAA---AGAAA-AAATAGATAAATTGGACTT 644

  chr2_129232184_   4360 TATCAAAATTAAATGTTTTTGAGCTTCAAAGGCCATCATTAA-AAAGACA 4408
                         i            vii     v          v  ii  i  -    vv 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_129232184_   4409 AAAGACAGCCTATAGAATGGGAGAAAATATCTGCAAACCATATATCTGAT 4458
                                i  i i                 i      i            
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_129232184_   4459 AAGTAACTTGTATGCAGGCTATATAAAGAATTATTACAACTCTACATTAA 4508
                            vi        v   iv           i v         v i v   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_129232184_   4509 AAAGACAAATAATCCCATT-AAAAATGGGAACTATATTCCAGTAGATAGT 4557
                                     i  v   -         v vviv   iv i    i v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_129232184_   4558 TCTCTAAAGAAGATATGCAAATG 4580
                             i           i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATG 867

Transitions / transversions = 1.58 (84 / 53)
Gap_init rate = 0.02 (16 / 867), avg. gap size = 4.19 (67 / 16)  


 966 22.27 0.00 0.00  chr2_129296701_129304400     3278  3515 (4185)  C L1M4_orf2#LINE/L1   (0)   908   671  

C chr2_129296701_   3515 CAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAA 3466
                             i  v    i  vv i      v  i     i               
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

C chr2_129296701_   3465 ATTTTTGCAACCTACTCATCTGACAAAGGGCTAATCCCCAGAATCTACAA 3416
                           v       vii ivi      i  i  i  vi vi       v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

C chr2_129296701_   3415 TGAACTCAAACAAATTTATAAGAAAAAAACAAACAACCCCATCAAAAAGT 3366
                         v      vv    v iv    v     i     i     v  i?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

C chr2_129296701_   3365 GGGCAAAGGATTTGAACAGACAATTCTCAAAAGAAGACATTTATGCAGCC 3316
                                         i     v     v        i  vi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

C chr2_129296701_   3315 AAAAAACACATGAAAAAATGCTCGTCATCACTGGCCAT 3278
                           v  i          i      iv     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (29 / 23)
Gap_init rate = 0.00 (0 / 238), avg. gap size = 0.00 (0 / 0)  

3093 26.48 1.79 0.45  chr2_129296701_129304400     6315  7209 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_129296701_   6315 GGAAAAATATTCCATGCTCATAGATAGAAAGAATCAATATTGTGAAAATG 6364
                              i    i     i    i   v i    v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_129296701_   6365 GCCATAGTGCCCAAAGTAATTTATAGATTCAATGCTATCGCCATCAAGCT 6414
                           v   v v      v i  i  i        i  v   v i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_129296701_   6415 ACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCAT 6462
                         v   vivi i  i  ii     -   -- v  i  - iii    v     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_129296701_   6463 ATGAAACCAAAAAAGAGCCTGTGTAGCCAAGACAATCCTAAGCAAAAAGA 6512
                            i  viiv  ii  v  v vi       i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_129296701_   6513 ACAAAACTTGAGGCATCACACT----GACTTCAAACTACACTACAAGGCT 6558
                              ii v    vv       ----i i      vivi       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_129296701_   6559 ACAGTAACCAAAACAGCATTGTACTGGTACCAAAACAGATATATAGACCA 6608
                                i   i    ii v       i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_129296701_   6609 ATGGAACAGAACAGAGGCCTCAGAAATAATGCTGCTTATCTACAACCATG 6658
                               i    iv   ivii         vv iiivi  i  iiii  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_129296701_   6659 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATTTCCTA 6708
                             i  i     ivv  v   i v  vv      i     i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_129296701_   6709 TTTAATACATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 6758
                           i  i v      i     v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_129296701_   6759 ACTGGGCCCCCTTCCTTACACCTTATACAAAAGTTAACTCAAGATAGATT 6808
                         ii   i    - v   i     v         i         i  i   i
  L1M4_orf2#LINE/    450 GTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_129296701_   6809 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 6858
                          ?    i           v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_129296701_   6859 AGGCG-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 6907
                            ? - v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_129296701_   6908 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 6957
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_129296701_   6958 TAAACTAAAGAGCTTCTGCACAGGAAAGAA-ACTATCAGCAGAGTGAACA 7006
                         i   v v  i i   i  ii vvv    i -       iv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_129296701_   7007 GGCAACCTAAAGAATGGGAGAAAATTTTTTCAATCTATCCATCTGACAAA 7056
                          i     i v               v   v   vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_129296701_   7057 GGGCT--AATCCAGAATCTACTAAGAACTTAAACAAATTTACAATAAA-- 7102
                           i  --v         v  iv       ivv    v iv i      --
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_129296701_   7103 --TAAACAACCCCATCAAAAAGTGGACAAAGGATATGAACAGACACTTCT 7150
                         --i   i     v  i?    i   i        v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_129296701_   7151 CCAAAGAAGACATTTATGGGGCCAAGAA--ACATGAAAAAAAGCTCATCA 7198
                                   i  vi viv      v  --         i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_129296701_   7199 TCTCTGGTCAT 7209
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.38 (135 / 98)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 1.82 (20 / 11)  


1603 24.92 7.36 2.84  chr2_129318314_129321737.rev      501  1098 (2326)    L1M4_orf2#LINE/L1      284   908 (0)  

  chr2_129318314_    501 ATAGATACACCAGTAGATCAATGGAAAACAAT--AAAATCCAGAAATAGA 548
                              i i ----             v v   -- i i          i 
  L1M4_orf2#LINE/    284 ATAGACATA----TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_129318314_    549 TCCACATATATGTGAGCAACTTATTTTTGACAAGG-----AA----ATTT 589
                         i   i i  v i  iv   i v     i       -----  ----   i
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_129318314_    590 AGTAGAGAAAAGGACAGTCTTTTCAACAAATGATGTTGGAACAACTAGGC 639
                          i i i    - i i                 i  i   i      i ii
  L1M4_orf2#LINE/    380 AATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_129318314_    640 ATTCATATGCAAAAAGAAACATTT--ATCCATAACATTCACTATACACAC 687
                          ?i  i        ii viv v  -- i  v  v viv   i   i   v
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_129318314_    688 AAAAAAATTTTAA-TGAGTTATAAACCTAAATTTAAAACCTAAAATTATA 736
                            vv  i iv  -  ii i ? i        v   i v      i    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_129318314_    737 AAACATTCAAGAGAAAACATA-----AAATATTTTTTTCAAAATTTTAAG 781
                             vi i ii          -----    -----i   ivi ii  ii 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAAT-----CTTCGTGACCTTGGG 573

  chr2_129318314_    782 CTAGGCAAATGTTGCTCAGATAT---ATCAAAAGTATATCCCATAAAATA 828
                         i       vv   v  i      --- i      i i vv v i    v 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_129318314_    829 ACAAACTGATTAAT-ATATGTCATCAAAATTGGAAATTTTTGCTCTTTAA 877
                          v   iv   v   -iv iv           ii   i     iv   i  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_129318314_    878 AATGCA--GTTATGAAAACAAAAAGGCAAGCCAAAGACTGGG-GCAAATA 924
                          ivi  --i i v    iii     i   v   v   v    - v     
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_129318314_    925 TTTTCAAAGCGTAT---------GG--------TCCAGAATCTAGAAAGA 957
                            v    v i   ---------  --------        v  v     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_129318314_    958 ACTCTCAATACTCACCAATAAAGAAACAAACAACTCAATGTTTTTAATGG 1007
                              i vv     vi      i i     i   i    - ?vvv     
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT-TWAAAAATGG 822

  chr2_129318314_   1008 A-AAAAAATTTTAACAGACAATTCCCCAAAGAAGATATATGGCTGGTTAA 1056
                         i-   ii    v  i     v   i              iiiv   ii  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_129318314_   1057 TAAGCACATGAAAACATGTTCACCTGAGATATCATTAGGAAA 1098
                                       v   i   ------ i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCA------ACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (93 / 53)
Gap_init rate = 0.03 (18 / 625), avg. gap size = 3.39 (61 / 18)  

3616 17.49 5.51 2.63  chr2_129318314_129321737.rev     2098  2932 (492)    L1M4_orf2#LINE/L1       50   908 (0)  

  chr2_129318314_   2098 TGTCAATACTAGCCAAAGTGATCTACAGATTCAACATAATCTCTGTCAAA 2147
                           v       vv     v                 ii    i  i     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_129318314_   2148 ATTCCAGTGACATTTCCTTACAGAAACAGAAAAACCCACCCTAAAATGTA 2197
                           i    ivi v   i-  i      iv  v  i iv i        vi 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_129318314_   2198 TATGAAATCTCAAGGGACCCCAAATAACTAAAATAACCTTGAAAAAGAAG 2247
                             i  viv          vi    i i    i  i             
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_129318314_   2248 AACAAAGTTGGGAGTCTCACACTTCTTGATTTCAAAACTGACTGCAAAAC 2297
                                    ii v          iii           v   i    i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_129318314_   2298 AACAGTAATCAAAATAATGTGG------CATAAAGACAGACA-------- 2333
                         v           i i i     ------     i  i     --------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_129318314_   2334 AATAGAATAGAATAAAGATCCCAGAAATAAACCCTTGCATGTAT--TCAA 2381
                            i         vi   vi              v i   v   --    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_129318314_   2382 TATTTTGAATTATTTGCATATATTCAAATAATTTTCTAACAAGACCATTC 2431
                          ----   -  -  i ----- --   ivi------ iv           
  L1M4_orf2#LINE/    349 T----TGA-TT-TTCG-----A--CAAGGG------TGCCAAGACCATTC 379

  chr2_129318314_   2432 AATGGGGGAAAGGACAGTCTTTTCAACAAATGGTGTTGAGAAAACTGAAT 2481
                                -    i i                    i  i  v     i  
  L1M4_orf2#LINE/    380 AATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_129318314_   2482 ATCCACATGGAAAAAAATGAAGGTGGACACTTACCTTGTACCACATATGA 2531
                          ?       v    i       v     v i     iii    i   ii 
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_129318314_   2532 AATTTAACTAAAATTAGATCAAAGACCTAAATGTAAGAGCTAAAAC---- 2577
                           v      v   v i     ?                        ----
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_129318314_   2578 --------------------AGGGG-AAGTCTACATGACATTGGATTTGG 2606
                         --------------------   ? -  i   v i    v    i  v  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_129318314_   2607 CAATGATTTCATAGATACATCACCAAAAGCACAGGCAACAAAACCAATAA 2656
                              i    v      iiv             i         vv  -  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA-AA 627

  chr2_129318314_   2657 ATAGATAAATTGGATCTTATCAAAATTTAAAACTTTTATGCATAAAAGGA 2706
                                       ii i         v         i   v v      
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_129318314_   2707 CACTATCTACAAAATGAAAAAGCAACCCACACA-TGGAAGAAAGTATTTG 2755
                                v v   i      ii         v -   i     i      
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_129318314_   2756 CAGATCATATATCTGATAAGGGATTAATAGTCACAATATACAAAGAACTC 2805
                           i                    i vi  vi  v      i         
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_129318314_   2806 CT-TAACTT--TAATGAAAACACAAAACAAACAATTCATAAATGAGTAAT 2852
                         i -i    i--    i    v     vv vv     ? v     i i  v
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_129318314_   2853 GACTTT-AATAAACATTTCTCCAAAGTAGATGTACAAATGGCCAATAAGC 2901
                          iv   -    i              v    i                  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_129318314_   2902 ACATGAACAGATGCTCATCCTCACTGGCCAT 2932
                                v         v v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (85 / 57)
Gap_init rate = 0.02 (18 / 859), avg. gap size = 3.78 (68 / 18)  


3219 27.20 0.44 0.44  chr2_129333041_129339320.rev     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129333041_   4881 TGGAAGAACATTACATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  iv    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129333041_   4931 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129333041_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_129333041_   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_129333041_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_129333041_   5129 TACAGGAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                              v  i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_129333041_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5226
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_129333041_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_129333041_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_129333041_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_129333041_   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_129333041_   5427 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_129333041_   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_129333041_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_129333041_   5577 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_129333041_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_129333041_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_129333041_   5727 TCAAAAGAAGACATTTATGCAGCAAAAAAACACATGAAAAAATGCTCATC 5776
                           v        i  vi viii  v  v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_129333041_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3828 19.34 3.96 1.24  chr2_129358944_129362549.rev     2235  3118 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129358944_   2235 TAGAAA-ATATCC-ATGTTCATGGATTAGAACAATTAATATTATTAA-AT 2281
                          i    -      -             i   v v        i    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129358944_   2282 GGGATTACTTCCCAAACTGATATCCAGACTAAATGTAATCCCTATCAAAA 2331
                           v v    i      i    v v    i v  i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129358944_   2332 TCCTATCTGGCTCTCTTGCTAATATTGTCAGGCTGATACTAATAATCCAT 2381
                            i v   v  i i    vi v    v  i      v    -   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA-AATTCAT 149

  chr2_129358944_   2382 ATGGAAATACATGGGACCTAGAATAGCCAACATA---TTGAATAAGA--- 2425
                                 i  v      i           v i ---     v    ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_129358944_   2426 -CAAAGTTGGAAAATTCACACTTCTAAATTTCAAAACTTACTACAAAGCT 2474
                         -          ii i         iv                        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_129358944_   2475 ATGGTAATCCAAACAGTGTGGTACTGGCATAAGGGTAGACACATTGGTCA 2524
                          ii      v i                      i      i  v i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_129358944_   2525 ATAGAATAGAATTGTGAATGCAGAAATCAATCCATATGTCTATGAACAAG 2574
                           i           v  i v       v  i     ii i    iv   -
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA- 348

  chr2_129358944_   2575 TTG-TTTTTGACAAGGG------GAT-ATTCAATGGGCAAAAAAATAGTC 2616
                            -    i        ------  i-          -i   i       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTC 397

  chr2_129358944_   2617 CTTTCAACAAATGATTCTGTGACAGCTGGAT-TTTACTTGTGAGGAAAAA 2665
                         i            i v   v    i      -?ii  v  ii iii  vi
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_129358944_   2666 AAGTTGGACCCATATCTTACACCATACACAAAAATTTACTCAGAATAGAT 2715
                                    v  i  i        i         v     i   i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_129358944_   2716 GATGGTGCTTAAATGTATGAGCTGAAATTATAAAACTCTCTAAGAAGAAA 2765
                         v ?i -i i        v     i   i           i--        
  L1M4_orf2#LINE/    498 CAWAG-ACCTAAATGTAAGAGCTAAAACTATAAAACTCTT--AGAAGAAA 544

  chr2_129358944_   2766 ACTTAGGAGTAAGTGTTCATCATATTGGTTTA---ACTTATTCTTTTGAT 2812
                           v    ?    i v   i v iv    v   --- v vi  ii  v   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_129358944_   2813 ATGACAGCAAAAACACAAGCAGCAAAAGAAAAA-TCTATAAATTGGAGTA 2861
                               v     i        i           - vv          v v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_129358944_   2862 TATCAAAATTAAAACCTTTTATACTGCAAATAATACTACCAAGAAAGTGA 2911
                         i             v     i i  v    vi i    i           
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_129358944_   2912 AGGAAAAACACCACACAGAATGGGAAAATATATTTGTAATTCCTATACCT 2961
                          ---  i   v v            i  v       i  v  v    i  
  L1M4_orf2#LINE/    695 A---AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_129358944_   2962 GATAAGAGAGTTATATC----------AAATTCCCCTT-TAAATCATTTT 3000
                               i  v  i    ----------   vvv i   -i  v   v vv
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_129358944_   3001 TAAAAATATGAATAATCCAACTTTAAAAGTGGACAATGAAACTCAGTAGA 3050
                               v ii     i    -  ?    i   i   v i vi v i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_129358944_   3051 TATTTCTCTGAAGAATATGTGCAAATAGCCAGTAAGTACATGTAGAGGTG 3100
                         i       ii     v  i i     i    i    i     v i  i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_129358944_   3101 -TCAACAGTTACCATATTA 3118
                         -      - i ????????
  L1M4_orf2#LINE/    891 CTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (101 / 66)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.09 (46 / 22)  


 710 26.52 30.77 1.21  chr2_129385757_129387471       19   512 (1203)  C L1M4_orf2#LINE/L1   (184)   724    85 *

C chr2_129385757_    512 GCAATTC-TAT----ATGCAAGCAACCTTTTTTGTAGATATTAACAATCA 468
                              i -   ----  v v   vi         i   v   i    v v
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

C chr2_129385757_    467 AATTTTAAAGTGTACATGGAAAGGCAAAAGACCCAGAGCAATTAACACAA 418
                         i  ii    i vi i       v    ii        ii iii  v    
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

C chr2_129385757_    417 TACTGAA---GAAGAATAATGCTGGAGGACTCA-ACT-----ATTTGA-- 379
                          vi    ---      i  v i           -   -----    v --
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

C chr2_129385757_    378 ---TGTTG--AGACTACAGGAATCTAGATAGTGTGGTATTGGTGAAAGAA 334
                         --- ii i-- ii      v    v   i         i   iiv   i 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

C chr2_129385757_    333 GGCACATATAGATTAA-------------------CAGAA---------- 313
                         viv          i  -------------------     ----------
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

C chr2_129385757_    312 -------------------------CAAA--TGC---------------- 306
                         -------------------------   i--   ----------------
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

C chr2_129385757_    305 -AAAAGAA----------AA-AAATGA-----------------AACCAT 285
                         -i      ----------  -     i----------------- ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

C chr2_129385757_    284 ACACAGA--------------------CCTTACAATGTCCACAAACATTA 255
                          ii  i --------------------   i   vii vi     v    
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

C chr2_129385757_    254 ATTCAAACTGTATCATAGACCTAAATGTAAAATTAAAAACTATAAAAC-C 206
                          i     v  v    ?              i viv             - 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

C chr2_129385757_    205 TCCAAAGAAAACA--GGAG-AAATCAAAGTTCCCTTGGGTTGGGTGAAGG 159
                          ivi         --  ? -     vvv  vv         i  ii v  
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

C chr2_129385757_    158 CTCTTTACATGCAACAATAAGATGATGATCCTTGAAGGAAAAAAGAGTGA 109
                         i ii   v  iii   vi  i vv ii v vvii  i       v  -- 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG--A 632

C chr2_129385757_    108 TAAGTATAATTTTATTAAAATTAAAAGCTTCACTCTGTG----AAA--AC 65
                            i vvi i  i  i          i   i----    ----   --  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTT----TGTGCTTCAAAGGAC 678

C chr2_129385757_     64 AATACTAAGAGCATAAAACAGCAAGTCACAGACTGGGGAAAAATGT 19
                          v  ii    ivi i   vii   vi      v    ii     i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

Transitions / transversions = 1.78 (82 / 46)
Gap_init rate = 0.03 (22 / 640), avg. gap size = 7.18 (158 / 22)  

3043 19.34 6.35 1.10  chr2_129385757_129387471      500  1223 (492)    L1M4_orf2#LINE/L1      147   908 (0)  

  chr2_129385757_    500 CATATAGAATTGCAAGAAACCCC-ACTAGCCAAAACAATCTTGAAAAAAA 548
                              i   v      ii    v- v                      i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_129385757_    549 AAAAAAAGAACAAAGTTGGAGGACTCATACTTCCTGATTTCAAAACATAC 598
                          ------                    i      ii          v   
  L1M4_orf2#LINE/    197 A------GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_129385757_    599 TACAAAGCTGCAGCAATCTAAAAGGTTTGGTACTGTAATAAAACTAGACA 648
                                  i   i    v i vi  v        vv    iiv      
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_129385757_    649 AATACACCAGTGAAATAGAACTGAGAGCCCAAAAAGAAGCCCTTACAGTA 698
                         v   v i  i  i       i      i   i   v  i   v    v v
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_129385757_    699 ATGGGCAATTGATTTTCAACAAGTGTGCCAAGATCATTTAATAGTGAAGG 748
                             v            i     v         i    i   i v   i 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_129385757_    749 GAGAGTGTCTTGAACAAATTATGCTGGGGCAACTGTATATCCACATTCAG 798
                         i v   v i  v       vi       i      v   ?      v  i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_129385757_    799 TAAAATGAA-TTGGACTCCTATCTCATACTATATATAAA--TTAACTCAA 845
                         v i      -      i    i    i  i     i   --         
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_129385757_    846 AGTAGTACAAACACGCAAATATAAGGGCTAAG-TTATAAAACTCTTGGAA 894
                          i i vv  ? v  vi    i    i     i-i            i   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_129385757_    895 GAAAACA--GGAGTAATTATTGTTGACCTTGGATTTGTTAAAGGAGTCCT 942
                                --  ?    v v  vv         i  v vi  v  vv  i 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_129385757_    943 AAATATGATGCCAAAAGCAAGAGCAACACAAGCAAAAATAGATAAACTGG 992
                          i      ii         vi       v   v             i   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_129385757_    993 ATTCCATTAAAATTAAAAACTTTTGC-CATAAAATGACACTATCAAGAAA 1041
                          i i   i                 i- v v   v               
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_129385757_   1042 CTGAAAAGAAAACCTACAACATG-----------------ATCATTCA-- 1072
                         v        v    i   iv   -----------------     vi --
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_129385757_   1073 -------------GTATCCAGTATATATAAAGAACTCCTATAACTCAAAT 1109
                         -------------        v               i  i       vv
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_129385757_   1110 ACAATAAGACAGATACCCC--TCAAAAAATCTGGACAAAGAACTTGAATA 1157
                          i  v      i   v   -- i?      --  i     i i       
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAAT--GGGCAAAGGATTTGAATA 838

  chr2_129385757_   1158 GACATTTCTCCAGAGA---TACACATATTCACAA-AAATATTTGAAAAGG 1203
                                     i   ---  i   v  vvv   -  ii iv       i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_129385757_   1204 TGTTGAATGTCATTAGTCTT 1223
                           i v  ii   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (76 / 60)
Gap_init rate = 0.02 (13 / 762), avg. gap size = 4.15 (54 / 13)  


3300 26.54 0.44 0.44  chr2_129417365_129419083.rev      320  1227 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129417365_    320 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTTAAAAT 369
                              ii i  i     i        v      v i     i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129417365_    370 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 419
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129417365_    420 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 467
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_129417365_    468 TATGGAACCAAAAAAGAGCCTGTATTGCTAAGACAATCCTAAGCCAAAAG 517
                                viiv  ii  v  v v  v  i  i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_129417365_    518 AACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTGCAAGGC 567
                                i      vv    v  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_129417365_    568 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 617
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_129417365_    618 AATGGAACAGAACAGAGACCTCAGAAATAATACCACACATCTACAACCAT 667
                                i    iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_129417365_    668 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGTAAGGATTCCCT 717
                         i    i  i     ivv  v   i v  vvv       v   i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_129417365_    718 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAGAGCTGA 767
                         v  i  i              v      v  ?   i i i i iiiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_129417365_    768 AACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGATT 817
                          ii    i    v   i   i v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_129417365_    818 AAAGACTTAAATGTTCGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 867
                          ?    i       vv  v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_129417365_    868 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCGTGTCTAAA 916
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_129417365_    917 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCAT 966
                                     vvi          vv     v  i    v   ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_129417365_    967 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGCACC 1016
                         i   v v  i i   i  ii vv    i  v    i  vv i    v vv
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_129417365_   1017 AGCAACGTACAGAATGGGAGAAAATTTTTGCAATCTATTCATCTGACAAA 1066
                         ii    vi                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_129417365_   1067 AGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAA 1116
                         i i  vi          v  i         vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_129417365_   1117 -ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 1165
                         -     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_129417365_   1166 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAAATGCTCACC 1215
                          v        i  vi viii     i ii          i -      v 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAAC 896

  chr2_129417365_   1216 ATCACTGGCCAT 1227
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


2009 29.18 3.34 3.46  chr2_129463908_129467363     2129  2995 (461)    L1M4_orf2#LINE/L1       26   891 (17)  

  chr2_129463908_   2129 TTAGAAGATTCATCACAATAAAGATAGCAATTCTTCTCAAATTGATATAG 2178
                           i     i i vi ivi v     i     v  i i         v  v
  L1M4_orf2#LINE/     26 TTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chr2_129463908_   2179 AGGTTCAATGCCATTCTTATCAAAATCTCAGCAAGACTTTTTTTGTCAAT 2228
                           i     i  v  i i          i    --vi i       ivi v
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGC--TGCCTTTTTTGCAGAA 123

  chr2_129463908_   2229 ATAGGCAAGGTTATTCTAAAATGTATATGGAAAGGCAATGGAACTAAAAA 2278
                           v i    v v  i       vi         v    -  i  iv i  
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA-GGGACCCAGAA 172

  chr2_129463908_   2279 TAGCTAAAACAATTATGAAAA----GAGTTAAAGTGGAGGTATCAGCGTA 2324
                             i        iv      ----  iiv  iv      vv   vvv v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr2_129463908_   2325 GCTGATTTCAAGACTTCTTATATAGACTGTTTGGTCTTGGAGGAGGGATA 2374
                         v ii       i    vi  i v  -  ii--i  vv vi  ivi vi i
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAG-CTAC--AGTAATCAAGACAGTGTG 269

  chr2_129463908_   2375 GACACTTGGAGGGAGAACAGACAAATAGATCAATGGGACACAATGGAGAA 2424
                          -i   -  vivi  i i     v            i i v   v    i
  L1M4_orf2#LINE/    270 G-TACT-GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_129463908_   2425 CCCA-ATGTAGGCTTACACAGATATGCCAAAGAGATTTCTCACAAAGGTG 2473
                         i   - vi  ii ii i   vv    viv  vv     iiv    i    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_129463908_   2474 CGAGAGCAATTCAAAGGGGGAAATTATAGCCTTTTTAACAAATAATGTTG 2523
                          v iii v      -v       vv    i     i       ii  i  
  L1M4_orf2#LINE/    368 CCAAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_129463908_   2524 GAGCAATTAGGCATTCATAAGTCAAAAAATGAGCCTAAACCAAAATCTCA 2573
                          ii   i i ii ?i  i v iv   i     ivi ii   vvv i    
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_129463908_   2574 CATCTTTTGCAAAAATTAATGCAAAATGAATCATAGGTGTACATGTAAAA 2623
                           i v v i          iv       i    ?  iiv  v      i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_129463908_   2624 TGTAAAATTATAAAACT-TGAGAAAAAAAACACAAGA--AAATCTTTGGG 2670
                         vv     i         - v    i    -  i i ?--       i v 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGTAAATCTTCGTG 565

  chr2_129463908_   2671 ATTTAGGGCTCG--AAC----TCTTTAATTTTACA----AAATGTAAATT 2710
                          ii v   i v --  i----    vi  v v   ----  iiii  iiv
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_129463908_   2711 TCTG--GGAAAAATTGATAAATTTGGA-TTCATCAAGGTTAGAAACTTTG 2757
                         v vi-- i      v        -   -        ii   i       v
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATT-GGACTTCATCAAAATTAAAAACTTTT 664

  chr2_129463908_   2758 GCTCTGTTAAAAAAATTAACCTGTCAAGAAGATGAAAAGACAACCTTCAA 2807
                          iv  - i   ii --i --  i       ii             iv  i
  L1M4_orf2#LINE/    665 GTGCT-TCAAAGGA--CA--CTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_129463908_   2808 AGTGAGAGAAAATATTTGTAAACCATA--------AAACAACTAGTAATT 2849
                          i  i             i   i    --------  ivi   v   vii
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_129463908_   2850 AGAATATTTAGATAACAGTCAAAATTCAACAGTAAAAAATACAACAAGAC 2899
                                v  i v   vv i v  i    i i      i----    - i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG----ACAA-AT 804

  chr2_129463908_   2900 AATCTAATTATAAAATGGGCAAAAACCATGAAGACAGATTTCACCATAAA 2949
                           i i    ?v            iiviv    v v v     v   v i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_129463908_   2950 AAATATAGATGAGGATGGTTAACATCATTAGCAATTAGGGAGATGC 2995
                          i     v ----i    ii  i -----    vv iiii      
  L1M4_orf2#LINE/    855 AGATATACA----AATGGCCAATA-----AGCACATGAAAAGATGC 891

Transitions / transversions = 1.57 (152 / 97)
Gap_init rate = 0.03 (26 / 866), avg. gap size = 2.27 (59 / 26)  


3040 25.31 3.06 0.57  chr2_129486565_129488437.rev      501  1381 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_129486565_    501 AGACATCCCATGTTCATAGATTGAAAAA-TTAATATTGTT-----GTCTA 544
                            i             i     i  i -           ----- v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_129486565_    545 TACTAATCCAAAGCAATACACAGATTCACCGCAATCCCTATAAAAATGCT 594
                             v-i     vii  vi         v            v     v i
  L1M4_orf2#LINE/     56 TACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_129486565_    595 GATTGCATTCTTTACAGAA---GAAAAAAT-ATCCTAAAATACTTCTGAA 640
                         iii   v  i   i     ---  v  iv -          v v v  i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_129486565_    641 ACCACAAA--ACCCTGAGGAGCCAAAGCAATACTGAGAAGATAAAACAAA 688
                          vii   i--    v  iv       i    vi   i  iiv i      
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_129486565_    689 GTTGAAAGCATTACACTTACTCATTT-AAGACTATATTACAAAGCCATAG 737
                             i i vv i      v iv    -  i   -  i        i i  
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAG 253

  chr2_129486565_    738 TAATCAA-ATAGTATGGAATTGGCATAAAAACAGAAACATAGACCAATGG 786
                                - i   i   v i        ii i   v i     i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_129486565_    787 AACAGACTAGAGAGCCCAGAAATAAGTCCAGACTTAAATGGTCAAGTAAG 836
                           i   v v     i          ii   v  v vv        v i v
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_129486565_    837 TTTTGACAAGGGCACTAAGAGGACACAACAGGGAAAGGACAGTCTTTTCA 886
                            i        ii i    vv iv   ii       i i          
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_129486565_    887 ATAAATGATGCTGGGAAAACTT-ATTTTCATATGCAAAATAATAAAATTG 935
                          i     i        v    v-  v?i  i        v   i  i   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_129486565_    936 GACTCTTGTTACACACTATACACAAAAATAAACTTGAAATAAATAAAAGA 985
                            i i iiiv     i   i        v    ii    ii  v ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_129486565_    986 CCTAAATGTAAGATCTGAAACCATAAAACTCTGGCAAGAAAAAAATTGGG 1035
                                      v  i    i          viv       v vvv ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_129486565_   1036 CAAATGTTCCTTGACACTGGTCTTTGCAATGAATTTTTTGGATATCACAC 1085
                         i    v   v -   vi   vi vv      i-   i  i     v    
  L1M4_orf2#LINE/    554 TAAATCTTCGT-GACCTTGGGTTAGGCAATGG-TTTCTTAGATATGACAC 601

  chr2_129486565_   1086 CAAAAGCTCAGGCTACAAAAGCAAAAACAAATGA---GGCAATC-TCAAA 1131
                                v  i  v       v     i i  i ---  vvv  -     
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_129486565_   1132 CTGAAAAACTCCTACACAGTAAAGAA-ATCAATAAGTGAAATGATAAGGT 1180
                         v v       ii iii vvi    i - ii vi   -i  i   v   ii
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAAAGAC 700

  chr2_129486565_   1181 AACCTACTGACTAGGTATAAACATTTGCAAACCACATATCTGATAAGGAG 1230
                             i  v  v i  viv   i         i  i             ii
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_129486565_   1231 TTAATATTCAAAATCTACAAAGAACTCTTATGAC-CAGTAGCAGAATAAC 1279
                         i vi   i  i   v  i            ii  -  i  ii i  vi  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_129486565_   1280 A--TGAT----TTTAAAAATGAGTAGAGGACCTGAAAATATATATTTCCA 1323
                          -- i i----  ?       i i i    ii    v v i  v i    
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_129486565_   1324 AAGAAGACATAATAATGACCAATACATAGATGAAAAGGTGTTCAATATCA 1373
                                i   vv    i      vii v        i  i    i    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_129486565_   1374 CTAATCAA 1381
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.64 (136 / 83)
Gap_init rate = 0.02 (19 / 903), avg. gap size = 1.68 (32 / 19)  


2757 27.91 2.44 1.88  chr2_129496382_129500370.rev     2585  3487 (502)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129496382_   2585 TGGAAAAACATTCGATACTCATGGACTGGAAGAATCAATATCATTAAAAT 2634
                               i i  i v  ii       i       v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129496382_   2635 GATCATACTTCCCAAAGCAATCTACAGATTCCACAATATTCCTATCAAAC 2684
                          iiv     i      vii            v  ivv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129496382_   2685 TACCAA-TGTCATTTTTCACAGAATTCCATAAAACT-ATTCTAAAATTCA 2732
                          v   i-  i -     ii     v iv i  i-  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_129496382_   2733 TTTGGAACCAAAGAAGAGCCTGAATGTCCAAAACAATCCTAAACAAAAAG 2782
                          v     viiv iii  v  v    iv           i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_129496382_   2783 AATAAAGCCAGAAGCAC-CACACTATTTGACTTCAAACTATACTATAAGG 2831
                           i    iii  i -  -      viiii i      viv     i  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_129496382_   2832 CTACAGTAACCAAAACAGCATGGTAATGGTAAACAAACACACAAAAAAAC 2881
                                  i   i    ii     v   ------------  v  ii i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGG------------CATAAGGAT 285

  chr2_129496382_   2882 AGACACATAGACCAATGGAACAGAATAGGGAACCCAGAAATAAAGCCTGA 2931
                              i     i        i     v i  ii           v  vv 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_129496382_   2932 CACCTACAGCTATCTGATCTTTGACAAAACGGACAAAAATAAGAACTGGG 2981
                           ii  ii ii vi    i  i     iivv v   i vi vvv v    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_129496382_   2982 GAATGGACTGTATT--CAATAAATGATGCTGGGATGACTGGCTAGCTATA 3029
                            v i iv  v  --   i     i        ii     v  ? i i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_129496382_   3030 TACAAAAGAATAAAACTGGACTCCTACATTTTACCACACACAAAAATTAA 3079
                          i         i  ii     i     v ivi    i i           
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_129496382_   3080 CTCAAAATGAATTAAAGATTTAAATGTAAGACCTTAAACTAGAAGGATTT 3129
                                  i  i ?   ii           v  v      v  iiv i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_129496382_   3130 CAGAAGAAAACCTAGGAA-ACACCACTATGTACATTGGCTTTAGGGAAAG 3178
                         i          v    ?i- v i viii  -  v    v  -   v  v 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTT-AGGCAATG 583

  chr2_129496382_   3179 AATTTATGTTTAAGTTATCAAAGGCAATTGCAACAAAG---AAAACTGAT 3225
                         iv  iv ivv  v vi i    i   vvv        i---    iv   
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_129496382_   3226 GAGTGGAATCTAATTAAACTAGAGAGCATTTGCACAGCAAAAGAAAATAT 3275
                         i i v i ii v  i   v vi i i v    ii vv    i  v v   
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_129496382_   3276 CGACAGAGTAAA----TAACCTACAGAATGGGGGAAAATATTCACAAACT 3321
                          i v i   i  ----i    i          i         ii    ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_129496382_   3322 ATGCATCTGACAAAGGCCTACTATTCAGAATCTACAAGGAACTT----AA 3367
                           ii      i  i  v  vv   i      v  i  i     i----  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_129496382_   3368 TTCAACAAGCAAAAAACAA----TCCCATTTAAAAGTGGGCAAAGGACAT 3413
                         i    i  vv    i    ----i  v   ?    i           iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_129496382_   3414 TAATAGACACTTCTCAAACAAAGACATACAAGCAGCCAGCGTGTAT-TAA 3462
                         v        i     v  vi    i      iii    iiiv i i- i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_129496382_   3463 AAAAATGTGCAACATCGCTAATCAT 3487
                            i   iv       i????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (162 / 86)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.44 (39 / 16)  


2939 24.72 3.97 1.02  chr2_129506075_129508254      807  1688 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129506075_    807 TGAAAAAACATTCTATGCTCATGAATTGGAAGATTCAATATTATGAAAAT 856
                           i   i i  i i   i     i         i i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129506075_    857 GACAACACTGCCCAAAGCAATCTACAGATTCAATGCAATTCCTATTAAA- 905
                          i   i   v      vii              i     i     i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129506075_    906 TGCCAA-TGTCATTTTTCACAGAATTAGAAAAAATAATCCTAAAATTCAT 954
                          v   i-  i -     ii     v v  v  iv i              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_129506075_    955 CTGGAACCAAAAAAGAGCCTAGG-TAGCCAAAGCAATCCTAAACAAAAAG 1003
                         v     viiv  ii  -  i  i-        i     i i  v  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_129506075_   1004 AACAAACCTTGAGGCATCACATTACCTGACTTCAAAATTATACTGCAAAG 1053
                               vi v    vv     i v  ii i       i -    i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_129506075_   1054 TGATAGTCAATAAAACAGCATGGTATTGGTGCAAAAATAGACACACAGAC 1103
                         iv i   v vi  i    ii     i   iii  ii       i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_129506075_   1104 CAATGGAACAGAATAGAGAACTCAGAAATAAATCCAAATACTTATAACCA 1153
                                 i     v    iii          i   v i i    iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_129506075_   1154 ACTGATTTTTGACAAAGCAGACAAAAACATACATTGGAGAAAGGACATGC 1203
                          i       i     i vv v   i v   v  v   i     i i vv 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_129506075_   1204 TGTTAAATACATGGTTCTGGAAAAACTGAATTGCCACATGCAGAAGCGAA 1253
                          v  v  i v     v    i v     i  v?         i   --  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG--AA 445

  chr2_129506075_   1254 AAAACTTG-ATCCCTATTTCCCACCATATGCAGAAATTAACTCAAGATGA 1302
                         vi  v   - i     ii  v        i  i            i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_129506075_   1303 ATTAAAGAC--AAATCTAGAATCCTAAATCATAAAAATTCTGGGAGAAAA 1350
                           i ?    --    v  ii v iv   ii      v ii i i      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_129506075_   1351 CCTAGGA--AAATTTCTTCTGGATATTGGCCTAGGCAAATAATTTAT--G 1396
                          v    ?--    --    vv  iv    vi       - ii   v -- 
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAG 592

  chr2_129506075_   1397 ACTAAGAACCCAAAAGCAAATGCAACAAAAACAAAAATAAATAAATGGCA 1446
                          -  v  vv         v v         iv       i      v v 
  L1M4_orf2#LINE/    593 A-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_129506075_   1447 CTTAAATAAACTGAAAAGCTTCTGCACCACCAAAGAAAGAATCAACAGAG 1496
                            v vi   v v    i   i  ii iv v  i  v vv     v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_129506075_   1497 TAAACAGACAACCTACAGAATTGGAGAAAATATATTCAAACTATACATCT 1546
                          i  v        i       v           v v    ii   i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_129506075_   1547 GACAAAGAGCTAATATCCAGAATCTGTAAAGACCTCAAACAAATCAGCAA 1596
                           i  i ii  vi          v i      v   vv    v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_129506075_   1597 GACAAAAACAAATCATCCTATTAAAAAGTGGGCAAATGACATGAATA--- 1643
                         v v   i      v i  v   ?    i        v  iv      ---
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_129506075_   1644 -------CAAGGG-----TAC---CG--CAA-----ACATGAAAAAATGC 1671
                         -------   i i-----   ---i --   -----         i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_129506075_   1672 TCAGCATCACTAATCAT 1688
                            i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (131 / 83)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.32 (44 / 19)  


 478 16.34 9.15 3.92  chr2_129512194_129518555.rev      337   489 (5873)    L1M4_orf2#LINE/L1      748   908 (0)  

  chr2_129512194_    337 GAACTTAAAGTAT----AATAAAAAAAAAAATTTTTTTAAAACTCAACAA 382
                          i    ---    ----    v v   i  ---i i   v       i  
  L1M4_orf2#LINE/    748 GGACTT---GTATCCAGAATATATAAAGAA---CTCTTACAACTCAATAA 791

  chr2_129512194_    383 TAAA--------CAACTGAATTCAAAAACAGGCAAAGTACTTGAATAGAC 424
                             --------i   iv    ?     ii       v i          
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_129512194_    425 ATTTCTCCAAAGAAGATATACCAATCTTCAA--AGCATGTGAAAAGATGT 472
                                              v   vvi   --    ii          i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_129512194_    473 TCAACAAAACTAATCAT 489
                               vv ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (14 / 10)
Gap_init rate = 0.03 (5 / 161), avg. gap size = 4.00 (20 / 5)  

3189 27.56 0.33 0.44  chr2_129512194_129518555.rev     4964  5870 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_129512194_   4964 GGAAGATCATTCCATGCTCATGGGTAGGAAGAATCAGTATGGTGAAAATG 5013
                          i     -  i     i      i v      v i i   v  v  i   
  L1M4_orf2#LINE/      3 GAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_129512194_   5014 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 5063
                           v     v     iv i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_129512194_   5064 ACCAACGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 5111
                         v   i vi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_129512194_   5112 ATGGAACCAAAAAAGAGCCTGCATTACCAAGTCAATCGTAAGCCAAAAGA 5161
                               viiv  ii  v  v v  vi    iv     v i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_129512194_   5162 ACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGGCT 5211
                               i      vv    v  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_129512194_   5212 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGACCA 5261
                                i   i    ii         i iv ii ii  v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_129512194_   5262 ATGGAACAGAACAGAGACCTCAGAAATAATGCTGCATATCTACAACCATC 5311
                               i    iv    vii         vv iii i  i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_129512194_   5312 TGATCTTTGACAAACCTGACAAAAACAAGATATGGGATAAGGATTCCCTA 5361
                             i  i     ivv  v   i v  vvvv     iv   i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_129512194_   5362 TTTAATAAATGGTGCTGAGAAAACTGGCTAGCTGTATGTGGAAAGCTGAA 5411
                           i  i           i  v      v  ? iii   iii  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_129512194_   5412 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA 5461
                         ii    i    v   i     v              i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_129512194_   5462 AAGACTTAAATGTTAGATCTAAAACAATAAAAACCCTAGAAGAAAACCTA 5511
                         ?    i       v   v       v      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_129512194_   5512 AGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTTGTGTCTAAAA 5560
                         i ?i- v i -   iv   viv  vv i     v ii  iv ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_129512194_   5561 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5610
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_129512194_   5611 AAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGAACAG 5660
                            v v  i i   i  ii vv v  i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_129512194_   5661 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAG 5710
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_129512194_   5711 GGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAT 5760
                          i  vi          v  i         vv    v iv i  v     v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_129512194_   5761 ACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTC 5810
                              i     v  i?    i     i      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_129512194_   5811 AAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCAT 5860
                         v        i  vi viii     v ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_129512194_   5861 CACTGGCTAT 5870
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.01 (6 / 906), avg. gap size = 1.17 (7 / 6)  


1199 16.31 8.51 0.71  chr2_129518757_129525121.rev      206   487 (5878)    L1M4_orf2#LINE/L1      490   793 (115)  

  chr2_129518757_    206 AAGTGGGTCAAAGAGCTAAATGTAAGATCTAAAACTATAAAACTCTTAGA 255
                           i   i   ?   v            v                      
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_129518757_    256 AGAAAATGTAGGACAAAAGCTTCACACTATTG---TA--------TTTGT 294
                               ii    ?vv   v    iiiviv   ---  --------   v 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_129518757_    295 TGGTTATGACACCAAAGGCACACTCAACAAAAGAAAAAAAATACAAAAAT 344
                          i v            i     vv               --  v v    
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAAAT 637

  chr2_129518757_    345 TGGACTTCAT-AAAATT--------TTGTGCATGAAAAAACAACATCAAC 385
                                   -      --------      v v   ii   vi     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_129518757_    386 AGAGTAAAAAGGCAGCCAACAGAGTGAGAGAAAATATTTTCAAATCATAT 435
                          i   i     i  i  v     i  i            v          
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_129518757_    436 ATCTGACAA----TTAATATTCAGAATATATAAAGAACTCTTAAAACTCA 481
                               i  ----i vi   i                      v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_129518757_    482 ATAATA 487
                               
  L1M4_orf2#LINE/    788 ATAATA 793

Transitions / transversions = 1.10 (23 / 21)
Gap_init rate = 0.02 (6 / 304), avg. gap size = 4.33 (26 / 6)  

3011 28.00 0.88 0.77  chr2_129518757_129525121.rev     4967  5873 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129518757_   4967 TGGAAAAACATTCCATGCTCATGAACAGGAAGAATCAATATCATGAAAAT 5016
                               i i  i     i     i iv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129518757_   5017 GGCCATACTGTCCAAAGTAATTTAAAGATTCAATGCTATTCCCATCAAAT 5066
                            v     vi     v i  i  v        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129518757_   5067 TACCATTGACTTTCTTCACAGAAATGAAAAAAACT-ACTTTAAATTTCAT 5115
                          v   vivi i  i  ii       vi v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_129518757_   5116 ATGGAACCAAAACAAAAA--CCAAACCATA-TGGAACCAACCCTAAGCAA 5162
                               --- vi   iii--   i --   -ivi  v   i i i iv  
  L1M4_orf2#LINE/    150 ATGGAA---ATGCAAGGGACCCAGA--ATAGCCAAAACAATCTTGAAAAA 194

  chr2_129518757_   5163 AAAGAACAAAGTTGGAGGCCTCACACTACTTGACTTTAAACTATACTACA 5212
                         i                 v        v iii i  i   viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_129518757_   5213 AGGCTACATTAACCAAAACAGCATGATAGTGGTACCAAAACAGGTATATA 5262
                          i      v   i   i    ii  i  v   i iv ii i  ii     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_129518757_   5263 GATGAATGGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACAA 5312
                            v       i     v   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_129518757_   5313 CCATCTGATCTTTGACAAACCTGACAAAAACAAGCATTAGGGAAAGGATT 5362
                         i  vi    i  i     ivv  v   i v  vv  v i       i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_129518757_   5363 CTCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTGGAAAG 5412
                         v   v  i  i        i     v      v  ?   i   iii  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_129518757_   5413 ATGAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAACTCAAGATG 5462
                              ii    i    v   i   i v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_129518757_   5463 GATTAAAGACTTAAACATAAGACCTAAAATCATAAAAATCGTAGAAGAAT 5512
                            i ?    i    ii     v      ii      v  v        v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_129518757_   5513 ATCTAGGCA-ATACCATTCATGACATAGGCATGTGCAAAGACTTCATGAC 5561
                          iv    ?i- v i -   i    v v  vv iv    v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_129518757_   5562 TAAAACACTAAAAGCAGCGGCAACAAAAGCCAAAATAGACAAATGGGATC 5611
                           vi    i       vvi          vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_129518757_   5612 TAATTAAACTAAAGAGCTTCTACACAGTGAAAGAAACTATCATCAGAGTG 5661
                          v  i   v v  i i   i iii vvii  i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_129518757_   5662 AACAGGCAACCTATAGAATGGGAGAAAAATTTTGTGAGATATCCATCTGA 5711
                           v  i     i i              vv    ii ivi  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_129518757_   5712 CAAAGGGCTAATATCCAGAATCTACAAAGCACTTAAACAAATTTACAAGA 5761
                         i  i  i  vi          v  i    v   ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_129518757_   5762 AACAAACAAACAATCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5811
                           v i     i  i  v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_129518757_   5812 TTCTC-AAAAAGGACATTTATGCAGTGAACAA--ACATGAAAAAATACTC 5858
                              -   i i  i  vi viii iv  i  --         i  i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_129518757_   5859 ATCATCACTGGTCAT 5873
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (156 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2453 14.55 1.77 25.40  chr2_129525447_129527810      684  1872 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129525447_    684 TGAAAAGACATGTCGTGCTCTTAGATCAGAACACTTACTATTGTTTAGAT 733
                           i     i  vi i  i  v i   ii   v     v       v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129525447_    734 GGCAATGCTCCTTAAATTGATCTATGAAAACAACTCAGCTCTTAATAAAA 783
                               i    ii           iii vv    v  iii i  vi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129525447_    784 TCCCAGGTGGGTTTTTTATATCAACTGATAAGCTGATTCTAAAATTAATA 833
                               v  vv      ii vv  i   i        i        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_129525447_    834 TGAAACTATAAAA-ACTCTGAAGAGCAAAAACAATCTTGAAAAAGAA--- 879
                           i  v ii  ii-  i v   v   v                    ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_129525447_    880 CACAATTAGAGGACTCAGAGTTCCCAATTTAAAAATTTGCTGTAAA-CTT 928
                           v i  i         v v          v    i  i  ii   -  v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_129525447_    929 CAATAATCAAGACAGTGTGGTA-TGGCATAAAGATAAACACATAGATTAA 977
                           i                   -        i    i   i      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_129525447_    978 C--AACACATACGGAAAGTCCAGAAATAAATCT-TACATTTATGGTCAAT 1024
                         i--  i v - iv  i              i i-                
  L1M4_orf2#LINE/    301 TGGAATAGA-ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_129525447_   1025 TGATTTTTGAGAAGAGTGCCAATA--AATCAATAAGAAAA-ATCAGTTTT 1071
                                i  v   i       v -- v     ii i   - vi   i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_129525447_   1072 CATAACAAATGGTGCTGGGACAATTGGATATCTGCATTCAAAAGAATGAA 1121
                         ivi                    i      ? ii   v            
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_129525447_   1122 GTTGTACCCTTTCCTCATACCTTACTCAAAAATTAACTCAGGCCTGTAAT 1171
                             v    i v     i   v  iv              ----------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA---------- 489

  chr2_129525447_   1172 CCCAGCACTTTGGGAGGCCGAGGCAGGTGGATCACGAGGTCAGGAGTTCA 1221
                         ------------------------ ii       ---------------?
  L1M4_orf2#LINE/    490 ------------------------AAATGGATCA---------------W 500

  chr2_129525447_   1222 AGACCATCCTGGCCAACACGGTGAAACCCTGTCTCTACTAAAAATACAAA 1271
                              ---------------------------------    --------
  L1M4_orf2#LINE/    501 AGACC---------------------------------TAAA-------- 509

  chr2_129525447_   1272 AAAATTAGCTGGGTGTGGTGATGGGTGCCTGTACTTCCAGCTACTCGGGA 1321
                         -----------------------------    -----------------
  L1M4_orf2#LINE/    510 -----------------------------TGTA----------------- 513

  chr2_129525447_   1322 GGCTGAGGCAGGAGAATGGCGTGAACCTGGGAGGCAGAGCTTGCAGTGAG 1371
                         -----------------------------------      ---------
  L1M4_orf2#LINE/    514 -----------------------------------AGAGCT--------- 519

  chr2_129525447_   1372 CCAAGATCGCACCACTGCACTCCAGCCTGGGCGACAGAGTGAGACTCCGT 1421
                         --------------------------------------------------
  L1M4_orf2#LINE/    520 -------------------------------------------------- 519

  chr2_129525447_   1422 CTCAAAAAATAAATAAATAAAAATAAAAAAAATAAAAAAACCTCAGAGTG 1471
                         ---------------------------    v  v    vi  i   ivi
  L1M4_orf2#LINE/    520 ---------------------------AAAACTATAAAACTCTTAGAAGA 542

  chr2_129525447_   1472 AAGCATAGAACTAAATACAAGAGCTGAAACCATACAGCTTAAAGAAATAC 1521
                           i     i?v     ----------------------------------
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT---------------------------------- 558

  chr2_129525447_   1522 CAGAACAAACCTTGTGACCCCAGGCTAGGCAATGGATTCTTAGATTTGAC 1571
                         --------- i i      iii  i          v         v    
  L1M4_orf2#LINE/    559 ---------CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_129525447_   1572 AGCAAATGTG--AGCAAGAAATGAAAAAATAGAGAAAATAAACTTCATCA 1619
                          v    v ii--     v   v           v   v ii         
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_129525447_   1620 AAGTTAA---CTTTTGTGCATGAAAGAACATTATCAAGAAAGGGAAAAAA 1666
                           i    ---         v v    i   i           v     i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_129525447_   1667 --ACATACAGAAAGGGAGAAAATATTTTCATTTCATACATCTGATAAAGG 1714
                         --  vi      v              v  vv     i         i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_129525447_   1715 TTTAATATTGAGAATGTATAAAGAATTCTTACAACTCAACAACAAAAAGA 1764
                         vi vi   iv     i         i             i  i       
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_129525447_   1765 CAAACAACTCAATTAAAAAATTGG-AAAGTGAATTGAATAGACATTTCTT 1813
                             i   i     ?      v  -    -  v                i
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAG-GATTTGAATAGACATTTCTC 848

  chr2_129525447_   1814 CAAAGAACATACACAAGTGGCAAGCAAGCATATAAAAA-ATGTTCAACAG 1862
                                v   i    i    v ii     i  i    -   i      v
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_129525447_   1863 CATTGGCCAT 1872
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.60 (104 / 65)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 14.68 (323 / 22)  


1352 28.52 12.38 3.64  chr2_129556267_129558283.rev      708  1531 (486)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_129556267_    708 CCATTTTCATGTATTAAAAGCCTCAATATT---AAAATGTTTCAATTCTC 754
                             v      v   ii   v  i      ---  i   v--    v   
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG--CAATACTC 60

  chr2_129556267_    755 ACCCATATTGATTTACAAATTCAATGCAATTCCAATCAA----------- 793
                         -    v      i    i      i     i  v     -----------
  L1M4_orf2#LINE/     61 -CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_129556267_    794 --TTTTTCAT-------------CTGATTC-AAAATTTATATGAAAACAC 827
                         --     iii-------------     i -      i     i   ii 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_129556267_    828 AAAAAATTGCAAGAATAGCAAAGATAGTCTTCAA---GAAAAGCAAAGTT 874
                           iii i-- v        v  i i i    v  ---   i i       
  L1M4_orf2#LINE/    160 AAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_129556267_    875 GGAAGACTTACACTGC--AATATACTAAGACTT-TTAATAACTTACAGTA 921
                            i    i     v --   v --i  i    -i  vv  vi       
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTT--CAAAACTTACTACAAAGCTACAGTA 255

  chr2_129556267_    922 ATTAAAACAGTATAATATTGGTGAAAGAAGGAAAAAATAGATCA---GAA 968
                           i  i     i ii  i   iiv   i vii v v        ---   
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_129556267_    969 CAGACCAACACACACTAAGAGCCCAATAATAGATGCTTTCATGCACAATC 1018
                         i   --------- i i    i   iv    i iv v v   vi iii  
  L1M4_orf2#LINE/    306 TAGA---------ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_129556267_   1019 ACCTCAGCAAAGGCAGAGGTGACAATGCGATGCAGTGTAAAAATTGTGAT 1068
                          vi v vivvv i  ii    v   vi v  v  i  vii   vvi ii 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_129556267_   1069 CTTTTCAA------GTA---GGCCAATTTGATATCCATGTAGGATGCAAC 1109
                                 ------  i---  v   i v    ?   i-----      v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC-----ATGCAAA 441

  chr2_129556267_   1110 AGA-TG---TTGA---CCTATCTTATACCCAGA-ACAAAAACCGATTCTT 1151
                            -  ---   i---    i  i i   - v -       iii i  vv
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACC-ATATACAAAAATTAACTCAA 490

  chr2_129556267_   1152 GATGGGTCATATAGCTTAATGTGAAAGACACATGCATAAAGCTTCTAGAA 1201
                         i    i   ? v v  v     i i  vi v vvi     i  ii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_129556267_   1202 AGAACTGTGGGAG--AATAT--GTAAGC---AGTCAA--AATGCTTT--- 1239
                         ii  vii i  ? --   v --  i v ---i  i i--    v   ---
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_129556267_   1240 AG-CAGGATGTTCATGTCCCTAGCCACAAAGGAAAAGGTTGATACATTAG 1288
                           -i v  iiiiv viv v v   v     i     ii v    v   i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_129556267_   1289 AC---ATTAAGATTCAGCACTTCTG-GCTATTAAA--ACACTATTGAGAG 1332
                           ---  i  i   v iv    i  -   - i   --       ii   i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAA 689

  chr2_129556267_   1333 AGCAAAAAAGCAAACCACA--ATGGGC-----TATCTTTC---TCAGTAT 1372
                           ii    ii   v     --     v-----   -  v ---   -   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATAT-TTGCAAATCA-TAT 737

  chr2_129556267_   1373 A-CTTATAAAATTGAGAATTATTACACAGAA-A-ATAAAAAAATCCTACA 1419
                          -  v    ---- i  v  i - iv     - -     i  v  i    
  L1M4_orf2#LINE/    738 ATCTGATAA----GGGACTTGT-ATCCAGAATATATAAAGAACTCTTACA 782

  chr2_129556267_   1420 AGGCAATAAGTAGGAACCGGACAATCTCATATACAAATTGGAAAAATCTT 1469
                          vv      vv ii iv ii i  i iv  v? v    v  v   ivv  
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_129556267_   1470 TGAACAGATACTTCCT--------------AAGTGGTTAATAGGCATATG 1505
                             i   i i   ii--------------  i   ii    i   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_129556267_   1506 AGACAGTGCTCACTGTCATTAGTCAT 1531
                          i vii      vii   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (145 / 86)
Gap_init rate = 0.05 (42 / 896), avg. gap size = 3.14 (132 / 42)  


3278 24.78 1.21 1.64  chr2_129620567_129624884.rev     2916  3827 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129620567_   2916 TGGAAAGTTATTCCATGTTCACAGATTGGAAAAATCAATATTGTTAAAAT 2965
                                v   i         ii        i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129620567_   2966 GTCCATATTACCCCCAAA---ATCTGCAGATTCATTGCAAATCCTTTAAA 3012
                          v v   i --       ---    i        vi    vi   v v  
  L1M4_orf2#LINE/     51 GGCAATACT--CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_129620567_   3013 AATCCCAA-TGCCATTCTTCACAGAAATATAAAAAA--AATCTAAAAATT 3059
                                i-    -  i  ii       - i v  i--i   iv      
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATT 146

  chr2_129620567_   3060 TATATGAAATCACAAAAGACCCAGAATATCCAAAGCTATCCTAAGCAAAA 3109
                         i     i  vii   ii           v     i v   i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_129620567_   3110 AGAACAAAACTGGAGACATTGCATTGCCTGACTTCAAATTATACTACAGA 3159
                                 ii     ivv ii  i v  ii i      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_129620567_   3160 GCTATAGTAACCAAAACAGCCTAATAGGGACACTCATTAAAAACAGACAC 3209
                             i     i   i    iv ii  vv i  -----   ii i     i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCA-----TAAGGATAGACAT 291

  chr2_129620567_   3210 ATAGACGAATGGAACAGAATACAGAACCCAGAAACAAATCCATTCACCTA 3259
                              iv       i     vv   ii       i   i    v  ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_129620567_   3260 CAGTGAACTCATTTTTGACAAAGGTGCCAAGAACACTGATTGGTGAAAAG 3309
                         ii  v  i v     i     i          v  i v v   v    ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_129620567_   3310 ACATTCTCTTTAATAAATGGTGTTGGGAAATTTGGTTATCCATATGCAGA 3359
                          i v   i  i  i        i     v vi   v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_129620567_   3360 AGAATGAAACTTAATTCCTATCTCTCACTTTTTACAAAAGTAAAATCAAA 3409
                                 ii vi ii    i   v   iv v       i v  v     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_129620567_   3410 ATGGATTAAAGACTTAAATTTAATAGCTCAAACTGTAAGACTCTTACAAG 3459
                               i ?    i     v   v    v     i   i       v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_129620567_   3460 ACAATATTGGA--AACTCTTTAGGACATTGGTCTGGGCAAAAATCTCTTG 3507
                          v  i  v  ?--  v    iiv   v    vi i     vii i    -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT- 590

  chr2_129620567_   3508 AGTCAT-ACCCCACAAGCACAGACAACCAAAGCAAAAATGGACTAATAAG 3556
                           vi  -  v   v       ii    v    v      i  iv   vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_129620567_   3557 ATCACATCAAG-TTAAAAAGCCTCTGCACAGCAAAGGAAACAATCAACAA 3605
                          iiv      i-       - i i  ii vv       v  v     v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_129620567_   3606 AGTGAAGAGATAACC-ACAGAATGAGGAAAAATATTTGCAAACCACCCAT 3654
                               i   i    -        i ii              i  ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_129620567_   3655 ATGACAAGGGATTAATGACCAGAATATATAAGGAGCTCAAACAGCCCTAT 3704
                         v   i      i vi iv             i  i   vv   i i v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_129620567_   3705 AGGAAAAAAAAATCTAAGAAGCTGATTTTTTAAATGAGCAAAATATTTGA 3754
                          iv     i v ---  v  v ii   ?vv-     i     iv      
  L1M4_orf2#LINE/    790 AATAAAAAGACA---AATAACCCAATTWAA-AAATGGGCAAAGGATTTGA 835

  chr2_129620567_   3755 ATATACATTTCTCAAAAGAAGACATACAAATGGCAAACAGGTATACGAAA 3804
                            v         v        i           v  i i i i i    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_129620567_   3805 AGGTTCTCAACATCGTTGATTAT 3827
                           i v         i????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (138 / 84)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  


2361 26.70 3.91 4.80  chr2_129645166_129647124      565  1459 (500)    L1M4_orf2#LINE/L1        1   887 (21)  

  chr2_129645166_    565 TGGTGAGATATATTGTGTTCATGAATTGGAGGACTCAATGTAG---AAAC 611
                            vi      viii        i      i    i   i v --- i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129645166_    612 ATCAATTTTCTAAAAATTGATCTACAGGTTTAATGCAATTTTTATCAATG 661
                         iv    vi  ivv              i  i  i     iii      vi
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129645166_    662 TCTCAGCAAGTTATTTTATAGTTTTAGACAATATTATACTAAAATGTACT 711
                           i    vivi v    ii  vvv v     vv v  v       vi iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_129645166_    712 TGTAAATTCAAAGGAACAAGAACAGATAAAACACTCTCATAAAAGAAGAA 761
                           v    v   i   v v    i  vi      v   iiv          
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_129645166_    762 TAAAATAGGAGAAATCAGTGTACCTC---ATTTCAAGA-TTATTGTATAC 807
                         i   i v    i v   ---i  i  ---       i -   i ii v v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCA---CACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_129645166_    808 CTACGGTAATCAAGACTGTATGGTATTGGTGAAGGGATAGTCACAGGCAT 857
                             i           v  i     i   iiv i      v  i viv  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_129645166_    858 CAATGGAAGA-AATAGAGAACTGGGAAACAGACCTGTACAACTATAACGA 906
                                 v -   v    iiivi    i i   ii    vi   iiiv 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_129645166_    907 ACTGATTTTTGACAAAAGTGTAAAATCAATTCAATAGAGAAAGAGTGGCC 956
                          i       i     ii   iv  iv v       i i      i i i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_129645166_    957 TTTTCAACTAATGGTACTACATAAAATCTATAGCAATATAAACTCTATGA 1006
                                 v      i  -------------- vi i ---   vv  --
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCT--------------GGGACA---ACTGGAT-- 428

  chr2_129645166_   1007 AATTAAATGCAAA-GAAAAAGATTGCATGACTGAAGAGAAAACAGGAAAC 1055
                          ?ii v       -   vi ii   v ivv  ---------  ------ 
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCT---------AC------C 463

  chr2_129645166_   1056 TTGCACATTATACAAAAATTAATTCAAAATAGGCCATACCTCCTACTGTA 1105
                          ii   vv              i       i ii  ? vvi iv v    
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_129645166_   1106 AAATATGAAAATATACAACTTTTAGGAGAAAACATAAGAGAAAAACCTTT 1155
                          i vv i   v    v    i    i          i ? v   -i   i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTC 562

  chr2_129645166_   1156 GAATCCTAGGGTTTGCTGAAAAGTTTTTAGACATGATGCCAAAAGCATTA 1205
                          viv   v     v vii viiv  i     i    ii         iv 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_129645166_   1206 TTCATAAAATAAAATCACA-ACACATTGGACTTAATCAAAGTTAAAAACT 1254
                         viv i    v    -v i - i v         v      i         
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_129645166_   1255 TTTGTTCTGTGAAAGACTCTGATAAGAGGATGAAAAGGCAAACTACATTC 1304
                              v  vii  i   v  ivi    iii       i   v i   ---
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA--- 708

  chr2_129645166_   1305 TGAA---AAGGGAACATTTGCAAACCATGTATTTGACAAGGAACT----- 1346
                         -   ---i  ii  i         i   i   i   i    i   -----
  L1M4_orf2#LINE/    709 -GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_129645166_   1347 --GGAATATATAAAGAACTG---------AGCAGTAAAAA---AAAT--- 1379
                         --i                v--------- ii i      ---    ---
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_129645166_   1380 TCAATTATAAAATGGGCAAAAGATATGAAGAGGCATTTCATCAGAAAGGA 1429
                         i     ?v            i   v    v  i      vi  i i i  
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_129645166_   1430 TGTGCAGATGGCAAATAAGCACATGAAGAG 1459
                          i i  i     v              i  
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAG 887

Transitions / transversions = 1.61 (145 / 90)
Gap_init rate = 0.02 (20 / 887), avg. gap size = 3.90 (78 / 20)  


2958 24.83 3.67 2.56  chr2_129741712_129746623     3523  4420 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129741712_   3523 TGGCAAGATATAATGTGTTCATGGATTCAATAAATCAATATTTTAAAAAT 3572
                            v       vvii            vi vi v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129741712_   3573 GGTCATACTACCCAAAGTCATATACAGATTCAACATAATCCTTATCAAAA 3622
                           iv     v      v v  v            ii     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129741712_   3623 TTCCAATGATATTCTTTACAAAAATAGAACAA-----TTATAAAATTCCT 3667
                          i   iiviiv  i   i  i    v  -   ----- iv        v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr2_129741712_   3668 GTAGAATCACAACAAAAGATCCCAAATAACCAAAGCAATCCTGAGAAAGG 3717
                         i i   -- ii-   ii  i  vi    i     i     i   i    i
  L1M4_orf2#LINE/    150 ATGGAA--ATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_129741712_   3718 AAGACAAATTTGGAACCGTCACACTCCCTGATTTCAAATTGTACCACAAA 3767
                          ii     v     ivvv       i  ii        viv   i     
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_129741712_   3768 GCTGTAGTAATCAAAACAGCAAGGTACTGGCATAAAAATCAGATGCGCAG 3817
                            ii         i    iiv             ii  -   iiiii  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAG 295

  chr2_129741712_   3818 ACCAATGGAACAGAATAGAAAGCTCA--AATAATCTCAACCATATTTGGT 3865
                          i        i     v  i  ii  --     v i  vv   v v    
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_129741712_   3866 CTACTAATTTTCAATGAAG------AAAT-----AATGGGGAAAGAATTA 3904
                          v i i      i ii i ------ i i-----              vi
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_129741712_   3905 TCTCTTGAATAAATGGTGTTGAGAAAACTAGGTATCTACTTGCAAAAGAA 3954
                            i  v  i        i  i  v    i i  ? i  v          
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_129741712_   3955 TAAAATTAGACCCTTAT-----GCCATTTACAAAAAGCAACACAAAATAG 3999
                          i  i  i     i  i-----i    v        vi   v      i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_129741712_   4000 ATTAGAGACCTAAATGTAAAACTTGAAATAATAAGAATCTTAGAAGAAAA 4049
                           i ?              i vi i   iv    i v             
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_129741712_   4050 CTTAGGAA-AAACACTCATTGACATTGGTCTTGGCAATGATATTTTGACT 4098
                          v    ?i-   ivi  i -   v    vi v       i v i  iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_129741712_   4099 AGGATTCTACAAGAACACAAGTAACAAAAGCAAAAATAAACAGATGGGAC 4148
                          v  iv --   i i      i        v       i i i  v    
  L1M4_orf2#LINE/    595 ATGACAC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_129741712_   4149 TACAATAAGCTAAAAAGCTTCTGTACAGCAAGAGAAAC---CAACAAAAT 4195
                          v  vi  iv v    i   i   i vv   ii  v  ---   v   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_129741712_   4196 GAAAAGG--ACCTAAAGATTTGGAGAAAGTATTTGCAAACTGTATATCCG 4243
                               i--   i v   v v       i          iii      i 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_129741712_   4244 ATAAGGGGTTAATATGCCAAATATATAAGAAATGCACACAACTAAATAGC 4293
                                ii vi   v vi         ii  iv vi      v    ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_129741712_   4294 AAAAAAAAAAAAAAAAAAAAAATTAATACCCTGATTTAAAAACGGGCAAC 4343
                              i v   ------------   ---  ii   ?     i      v
  L1M4_orf2#LINE/    793 AAAAAGACAAA------------TAA---CCCAATTWAAAAATGGGCAAA 827

  chr2_129741712_   4344 GGACCTGAATAGACACTTTTCTAAAAA---TATACAAATGTCCAATAGAT 4390
                            ii          i  i  i   i ---          v      iii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_129741712_   4391 ATATAAAAA-ATGTTCAACATCACCAATCAT 4420
                          i  i    -   i         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (145 / 74)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.11 (56 / 18)  


1813 17.31 6.15 1.59  chr2_129816600_129820906     3379  3817 (490)    L1M4_orf2#LINE/L1      450   908 (0)  

  chr2_129816600_   3379 GTTGTAATCCTACCTCACACCATACTCAAAAATAAACTTAAAAT----CA 3424
                             v vi                iv       v    i     ----  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_129816600_   3425 TGGACCTGAAGGTAAGATCAAACACTATAAAACTCTTAAAAGAAAATACA 3474
                         ?i     i  v      v v  v               i       i i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_129816600_   3475 GGAGCAACTCTTTCTGAC-TTGGATTAGACAATAGCTTCTTAGCTATAAC 3523
                           ? i  v    iv    -    i    i    i i       v   i  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_129816600_   3524 CACAAAA--ACAAATGGCAAAATAAAAAAATAGATACATTGCAGTTAATC 3571
                         vv     --    iiii     -i            v    v v  v   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATC 648

  chr2_129816600_   3572 AAAATTAAAG--CTTTATATTTCAAATGATACCGTAAAGAAAATGAAACA 3619
                                  i--i   i ii      v  i  ii v      i     vi
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_129816600_   3620 GCAATCCAGAAAATAGGAGAAAATATTTGCAAATCATATATCTGATAAGG 3669
                         i   i   v i   i                                   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_129816600_   3670 GCCTTATATCCAGAATATGTATTTAAAACAAC----ACAACTCAAGAATA 3715
                          v   i            i  -----  v   ----         v    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATA-----AAGAACTCTTACAACTCAATAATA 793

  chr2_129816600_   3716 AAAGGACAA----TTCAATTAAAAA-----CAGACTATCTGAATAGTCAT 3756
                            i     ----ii     ?    -----  i vv  i       v   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_129816600_   3757 TTCT----AAAAAATATGGTAAATAGCCAATAAGCACATGAAAAGATGCT 3802
                             ---- i  i    i-i    i                         
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATA-CAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_129816600_   3803 CAACA-CATTTAGTCC 3817
                              -  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (46 / 27)
Gap_init rate = 0.03 (12 / 459), avg. gap size = 2.83 (34 / 12)  


2591 24.97 6.50 2.96  chr2_129822606_129824897.rev      924  1800 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129822606_    924 TGGAGAGATATTCCATGTATATAGATAGGAAGAC--AACATTGTCAAGGC 971
                             i      i      vi  i   v       --  i     i   ii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129822606_    972 GTCAGTTCTTCCCAACTTGATCTATACATTCAATGAAAGCCTGATTAAAA 1021
                          v  i v  i     v        i v      i v  v  iv  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129822606_   1022 TCCCTGCAAGCTATTCTGTGGATGGGGATAAACTGATTTTAAAGTTCATA 1071
                             v  viv  v  i  ii  vivv  i  i     ii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_129822606_   1072 AGGAAG-GCAAAG-ACCCAAGATAGCAAGTGCAATATTGAAGGACACAAA 1119
                         v    i-    i -     ii     v ivi    v     ii v vi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_129822606_   1120 CAAAAGTCAGAGAACTGACACT-----------------ACCA------- 1145
                             -  ii   i   v     -----------------  i -------
  L1M4_orf2#LINE/    201 CAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_129822606_   1146 ACGATAATCAAGACAGTGTGATATTGGCAAAAAAAGAAAAAAAAAAAGAG 1195
                           ii                i  i     v  i---------------- 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAG----------------G 283

  chr2_129822606_   1196 AGAGACAGACAAATCAAGGGAACAGAATAGAAAGCCTAGAAATGAATCCA 1245
                          v     v i i     v    i     v  i  i i      i  i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_129822606_   1246 CAGAAATATAGTCAACTGATATTTGACAACGA-GCAAAGGC-ATTCCAAT 1293
                         i v vv   i     i    v  i     v i-  v   i -    -   
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC-AAT 382

  chr2_129822606_   1294 GGAGAAAAGAGAGGCTTTTCAACAAATAGTACTGAAAAAAGTAGACATCA 1343
                           i    ii v  v             i  i   ii v  v i  i ? v
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_129822606_   1344 ACATGCCAAAAAAATA------GACACAGATTTTTCACTGTTCACAAAAA 1387
                               -    i   i------   v vv ii iv   ii vi       
  L1M4_orf2#LINE/    433 ACATGC-AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_129822606_   1388 TTACCTCAAAATAGATCATAGTC-------TAAG-GCACACAATTGTAGA 1429
                            v        i     ?  v -------    -  -i v  i i  i 
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAA 530

  chr2_129822606_   1430 ACTCCTAGAAGGTATCACAGGAG-AAATTCTCGGAGACTTGGGTTTGGTG 1478
                             i      iv v  i   ? -    ii   viiv        v  ii
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_129822606_   1479 GAGACTTTTTAGATACAACACCAAAAGCACTTTCCATGAAAGAAGAAGT- 1527
                         iv ii  i       ii             vvv v ii      i  i -
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_129822606_   1528 --TAAATTGAACACCACTAAAATTAAAAGTTTCTGATTTGCAAAAGACAT 1575
                         --       i  vi  ii          ii  i  vvi v    i    i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_129822606_   1576 GGATAAGATAATGAAAACAGAAACTATTGACTGAAGAAAAAACAACGTTT 1625
                         vivi    v i      v v  v i iv  v  i-  i    i ---   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGG-GAGAAAATA---TTT 726

  chr2_129822606_   1626 GCCAAACAAATATCTGATCAAGGACTGG-ATCCA-AATACACAAAGAACT 1673
                           v  v  v         v i     v -     -    i i        
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_129822606_   1674 CTTAAAACTTAACAACAAAACAACA-------CAATTTAAAAAGCAGAAA 1716
                             v    i  i  i    vi   -------     ?     v-- iiv
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT--GGGC 824

  chr2_129822606_   1717 AAAAGATTTGAACAGGCACCTCACCAAAGAAGACATACAGATGGCAAATA 1766
                            i        i  i  ii  v          i     i     v    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_129822606_   1767 AGCATATAAAACGATGCTCAGCATCATATGTCAG 1800
                             i  i   v        i     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (134 / 81)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.61 (83 / 23)  


2243 26.58 8.98 1.46  chr2_129855377_129859905.rev     3214  4037 (492)    L1M4_orf2#LINE/L1       23   908 (0)  

  chr2_129855377_   3214 GAGTTGGAAGACTTA---TCATACAGAAAGCAATTCTCCTTACATTGATA 3260
                          ii            --- ii vv   vi     v    ii v      v
  L1M4_orf2#LINE/     23 GGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATC 72

  chr2_129855377_   3261 TATGTAGGTTTAACACAATTTCTATCAAAATTCTAGCAAGGCACTTTGAG 3310
                           i--  i  i   i    ii          i i   vivvivi    vi
  L1M4_orf2#LINE/     73 TAC--AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr2_129855377_   3311 GATATAGACAAGCATGCTT-TAAAATTTATATGGAAAGGGAAAC-ACTCT 3358
                           v  v       -  v i-       i         v v  iv-  i v
  L1M4_orf2#LINE/    121 GAAATTGACAAGC-TGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_129855377_   3359 AAATATCCAGAACACAGCT---AAAAGAGG--TAAAGT--GAAAATT--- 3398
                         i    v   i    - v  ---      i --i     --  ii i ---
  L1M4_orf2#LINE/    170 GAATAGCCAAAACA-ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_129855377_   3399 GCTCTCCTGATGTTAAGACTTGCTGTATAGCTACAATAATCAAGACACTG 3448
                         i  -   ii  v i  i    i  ii v       i           v  
  L1M4_orf2#LINE/    219 ACT-TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_129855377_   3449 TGGTGCTGGCAGAGGAACAGA--TACAGATCAGTGAGACAGAACAGAAAG 3496
                             i      v i i i   --  i      i  ii i    iv  i  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_129855377_   3497 TCCAGAAGAAGATCCATACAAACATGTCCCATTAATTTTTGGCAAAGGAA 3546
                                iv i i       vvi   vi v   i     i i   i  vi
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_129855377_   3547 CAAAAACAACTCGGTTGAGGAGGGATGACCTTTTTAATAACTGTTGCTAG 3596
                          v  i  v i  ii v i i i i  iii     i  i  v  v    i 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_129855377_   3597 GGTGACTGGATATCCACAGGCAAAAAAAGGAATTATGAGCTAAACTTCAT 3646
                          iii        ?     v      i  v   v vv  v ivv  i   i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_129855377_   3647 ATCTTATACGAAAATTAAAACAAAATGTATCACCATGCTTAAATGTAAAA 3696
                          i v     i        vv       v    ?- vi i         i 
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAW-AGACCTAAATGTAAGA 516

  chr2_129855377_   3697 CAGAAACCTGTAAAACTTTTAGAATAAAATATAGG--------------- 3731
                         vvv   v  i       i      v    i     ---------------
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_129855377_   3732 ---------AGACGATA-----TTAAGCCTGAAGCCAAATGCACAAT--A 3765
                         ---------  i i  i-----   iiiv   vi     v      v-- 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_129855377_   3766 CATAAGAGGAAA--ACTAAATTGAACCTCATCAAAATTAAAAACT---G- 3809
                           v    ii   --iv       i  i                  --- -
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_129855377_   3810 ACTCTGGAAGACCCTGTTA--------------CAAATTACAGACTGGAA 3845
                         i  iiii i   v  i i --------------   vii     v   i 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_129855377_   3846 GAAAATATTTGCCAATTACATATACAAGAAATGACTCATGTCTAGAATAT 3895
                                     v   i i    vii v  iv    ii i  i       
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_129855377_   3896 ATTTAAAAATCCCTCTCAAACTCAGTAGTAAAAC-ACAAGTAATTCAA-- 3942
                           --   i v i  iv   -    i  i     v-    i   ii   --
  L1M4_orf2#LINE/    767 AT--AAAGAACTCTTACAA-CTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_129855377_   3943 -AAGCAAATGGGCAAAGAAAT-GTACAGGCATTTCACTGAAGAGATTATA 3990
                         -  --            i v - v i  i      v ii    iiv    
  L1M4_orf2#LINE/    814 WAA--AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_129855377_   3991 TAGATG-CCACATAGGCAGATGAAAATATGTTTAACATCATTAGCCAT 4037
                         i i   -   -   i   v       v   i i       ????????
  L1M4_orf2#LINE/    862 CAAATGGCCA-ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (141 / 76)
Gap_init rate = 0.03 (28 / 886), avg. gap size = 3.07 (86 / 28)  


3292 26.87 0.44 0.44  chr2_129885109_129891703.rev     5196  6103 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129885109_   5196 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5245
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129885109_   5246 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5295
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129885109_   5296 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5343
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_129885109_   5344 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5393
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_129885109_   5394 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5443
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_129885109_   5444 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5493
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_129885109_   5494 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5541
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_129885109_   5542 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5591
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_129885109_   5592 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5641
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_129885109_   5642 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5691
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_129885109_   5692 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTACAAGAAAAC 5741
                          i ?   ii    i  v   v       i      vi i  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_129885109_   5742 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5791
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_129885109_   5792 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5841
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_129885109_   5842 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5891
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_129885109_   5892 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5941
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_129885109_   5942 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5991
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_129885109_   5992 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 6041
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_129885109_   6042 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 6091
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_129885109_   6092 ATCACTGGCCAT 6103
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1730 22.57 1.81 1.58  chr2_129926017_129928313        1   443 (1854)    L1M4_orf2#LINE/L1      249   692 (216)  

  chr2_129926017_      1 TATAGTGATCAAGAAAGTGTGGTGCTGGCATTATGTTAGAAATGTAGATG 50
                           i   i       v        i       v v v    v  i     v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_129926017_     51 AATAAATACAATGGAATTGAGGGTCCAAATATAAACTTGTA-ATTATATG 99
                            ii ----  i        i     i v      iii  -   -    
  L1M4_orf2#LINE/    299 AATGGA----ATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATG 343

  chr2_129926017_    100 GTTAACTGATGATTGGCACTTATGCCTAAATCATGTAAGGGGATACAGAA 149
                           i  i    vv i i  vvvi    v i i   vi  v   i- v    
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAA 392

  chr2_129926017_    150 TAACCTTTTTGTCAAATGATGGTTGTACAACTGAATGTATACATGCTAAA 199
                           ii     iiv      i  v v v       i  i?vi      v   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_129926017_    200 AAATGAACTTGGAACTCTACCTCAAATGGTATACAAAAAACAACTCAAAA 249
                         i      v     v i        v ivi          vi         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_129926017_    250 GGGAATCA-AGACCTAGATGCAAGAGCTAAAATTACAAAACCATTAGAAG 298
                         v   -   -       i   i           i  i     iv       
  L1M4_orf2#LINE/    493 TGGA-TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_129926017_    299 AAAGAATAGGTATAAATCTACATGATTTTGGATTAGGGAACAATTTCTTA 348
                            iv     ?i       v i   ii    i     v  iii       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_129926017_    349 GATATGACA---AATGCATGAGCAACCAAAGAAAGAGTAGATAAATCT-A 394
                                  ---  v   ii      v       i i         iv- 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_129926017_    395 CTTCATCAAAATTAAA--TTTTTATTCATCAAAACATACTATCTAAATAG 442
                                         --i    i v v     iv i      v i v  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_129926017_    443 T 443
                          
  L1M4_orf2#LINE/    692 T 692

Transitions / transversions = 1.45 (58 / 40)
Gap_init rate = 0.02 (9 / 444), avg. gap size = 1.67 (15 / 9)  

1800 26.74 11.63 0.91  chr2_129926017_129928313      583  1244 (1053)    L1M4_orf2#LINE/L1        8   740 (168)  

  chr2_129926017_    583 ACATGTCATGTTTACGGATTGGAACATTCAACATTGTGCAAACATCAACT 632
                          i  vi      i i         v i i  i     vv i iiv   iv
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_129926017_    633 CTTCGCAAATAGATCAGTAGGTTTAACAGAATCCTGATCCAATTCCCAGA 682
                           i v     v    vii  i  i   iv     iv   v  v      v
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_129926017_    683 -AAAGTTTTTGTAGACATAGAT--GCTTACTCATAAATGTACATGAAAAA 729
                         -ivvv      i   v  v  i--   v ii vv    vi i   i   v
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_129926017_    730 GCAAAGGACTTATGATAACTAAACATGATTTT-AAAAGGAAGAGTAAAGT 778
                             i    ii vi   i i   - ii  i  -    i     ii     
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_129926017_    779 TAGAGGGATAACTCTACCCAATGTTAATGATAACTATATAGCTAAAGTAA 828
                          i    iv v  v  v      v i  viv v    i v     v     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_129926017_    829 TCAAGGCAATGTAGTATTGGCACACGAATAAACACATAGACCAATGAAAC 878
                              i  i   i   i     i v i   i   i     i     i  i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_129926017_    879 ACAATAGAAAGCCCAGAAATAGACTGATACAAATATACCCAACTGATTTT 928
                          v   v  i  i         i  iv     vv   ivi   i       
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_129926017_    929 TGA-AAAGGTGCAAACGCAGTTCAGTAAAGGAAAGGAAGAAGAG-CTTTT 976
                         i  -  i     v  vi vi    i ii-      ----  v  -     
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGG-GGAAAG----AATAGTCTTTT 401

  chr2_129926017_    977 CAACAAATGGTCCTGGAGCAATTGATCATCCACAGGCAAAAAAA-GAG-- 1023
                                    v    ii   i  ivi ?     v      i  -  i--
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_129926017_   1024 --------------------------AAGAT---------ATG------- 1031
                         --------------------------  i  ---------   -------
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_129926017_   1032 --CTTAAATGTAACACCTAAAACCACAAATCCTTTAGAA---AGCATAGG 1076
                         -- i         v v       i i   v ii      --- i      
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_129926017_   1077 AGGAAATCTTTGGGACTTAGAGCTAGCTGAAG--TTATTAAAGTTGACAC 1124
                         ? v       i v   i v i i   vii v --  v   i vv      
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_129926017_   1125 --------------ACAAAA----AAATATGTAA-TTGAATCTCATCAAA 1155
                         --------------      ----     vi   -   i ii        
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_129926017_   1156 ATTTAAAACATTTGGTCCGTAAAAGACCCTTTAAAGACAATGAAAAGACA 1205
                            v     v    vv ivi   i   v  v v    v i          
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_129926017_   1206 AGCTACAGAGTGGAAGACAATGTTTTCAAATCACATATC 1244
                          v i     i   i   v   i   v       i     
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

Transitions / transversions = 1.40 (102 / 73)
Gap_init rate = 0.02 (17 / 733), avg. gap size = 4.88 (83 / 17)  

 574 21.79 1.68 1.12  chr2_129926017_129928313     1630  1808 (489)    L1M4_orf2#LINE/L1      729   908 (0)  

  chr2_129926017_   1630 AAAACGCATATCCTTA-AAGGGACTTATATAGAGAGGATATAATACACTC 1678
                            v ii     - v -         i   vv   iv      viv    
  L1M4_orf2#LINE/    729 AAATCATATATC-TGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_129926017_   1679 TCAAAACTTAACAGTAAAAAATGCAAATAATACAATGAGAAAATGG-CAA 1727
                          i v    i  i i      i-i       iv    v?i       -   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_129926017_   1728 AAGACATACAGAAACATTTTACCAGAAAGGATATACAAATTGCAAATAAG 1777
                          i  iv iv v i      iv   i i i           v  v      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_129926017_   1778 CACATGAAAAGATGTTCAAC-TCACTAGCTAT 1808
                                       i     -   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (22 / 16)
Gap_init rate = 0.03 (5 / 180), avg. gap size = 1.00 (5 / 5)  


4199 17.83 3.03 1.23  chr2_129945564_129948054.rev     1108  1999 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129945564_   1108 TGGAAACACATTCTGTGTTTCAATCCATGGATTGAAAGACTTA---CTGT 1154
                               v i  i ii    ------         i        ---i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTT------CATGGATTGGAAGACTTAATATTGT 44

  chr2_129945564_   1155 TAAGGTGACAATACTATC-AAGTAAAAGTATAGATTTATTGCAATCC-TA 1202
                             i  i       vi -  i vi vv  i     i vi       -  
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_129945564_   1203 TCAAAATCCAAACAACACTTTTTTATAGAAATAGAAAAACCCATCTTAAA 1252
                                  v i vi -       ii      v  v  i iv   i    
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_129945564_   1253 GTTTATATGGAATCTCAGTGGAACCCA-AACAGCCAAAACAATATTGGAA 1301
                         i  i        viv  i-  i     -  i            v   i  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_129945564_   1302 AGAAAGAACAAAGTTGGAAGACTCACACTTCCTTATTTCAAAACTTATTA 1351
                          ii               i             iv             i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_129945564_   1352 AAAACCTACTGTAATCAAAAGAGTGTATTACTGGCATAAGTACAGGCATA 1401
                         v   v    v        i v     iv            v i  i    
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_129945564_   1402 TAGATCAATGTAATAGAATAGACAGCCCAGGAAGAAATCC-----TT--- 1443
                                   v        v  v  i    i  v   i  -----  ---
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_129945564_   1444 -GTCAACGGATTTTTGACAAGGGCATCAAAACTCTTCAATGGAGGAAAAG 1492
                         -     iv      i        iii   i  iv        i --    
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAAG 390

  chr2_129945564_   1493 AACAGTTTTATCAA-AACTGGCGCTGGGAAAACTGGATATACACATGCAA 1541
                           i   i  v    -  v   i       v         ?v         
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_129945564_   1542 AATATTGATGCTGGACTCTTACATTCTAACATATGCAAAAATTAACTCAA 1591
                           v v   v i     i i   v ivi v     i               
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_129945564_   1592 AATGGATTAGAGACCTAAACATAAGAGCTAAACTTATAAAACCCTTAGAA 1641
                                i ?         ii           vi        i       
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_129945564_   1642 GAAAACATAGGGGAAAAACTTCATGACATTGGACTCGGCAATAATTTCTT 1691
                                    ? v   v    i    v    ii v      ii      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_129945564_   1692 GGATATGACACCAAACGCTCAGGCAACAGAAGAAAACAATATATAAGTCG 1741
                         i              v  v  i      i       -    v    i i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTG 639

  chr2_129945564_   1742 TATTTCATCAAAATTAAAATTTGTTGTGCATCAGAGAACACTATCAAGAG 1791
                         v i                vi v      v   i  i            i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_129945564_   1792 GGTGAAAAGGCAATTCACAGAATGGGA--AAATATTTGTAAATTATATAT 1839
                         i        i   ii            --         i    i      
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_129945564_   1840 CTAATAAGATATTAATATCTAGCATATATAAAGAATTC----AAC--AAT 1883
                           i     iv i vi    i  v            i  ----   --   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_129945564_   1884 AA--AAAACCCAAACAACCCAATTCAAAA-TAGGCAAATAACTTGAATAA 1930
                           --    vv    i         ?    - i      vi i       i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_129945564_   1931 ATATTTCTCCAAAGAAGAAATACAAATGGCTAATAAGCACATGAAAACAT 1980
                          i                v           i                v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_129945564_   1981 GCTCAGTATCACTAGTCAT 1999
                              ii    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (98 / 57)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  


2671 25.24 1.26 6.18  chr2_129990582_129995210.rev     3183  4137 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_129990582_   3183 TGGAAACATATCCGATGTTCATGGAGGGATAGAATCAATATTGTAAAAAT 3232
                               v      v           vv iv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_129990582_   3233 GATCATATTGCCAAAAGCAACCTACAAACTCAATGAAATTCCCATCAAAA 3282
                          iiv   i v  v   vii i     i i    i v   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_129990582_   3283 TAC-AACCATCATTCTTGACAGTACTAGAAAAAACAATTCTAAAGTTCAT 3331
                          v - i iii v  i   -   v v v  v  ivii  i     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_129990582_   3332 ATGGAACTAAAAAGGAGCCCCACATAGCCAAAACAA----GACAAAGCAA 3377
                               v iv  i   -   viv             ----  v    ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAG--- 195

  chr2_129990582_   3378 AAAGAACAAATCTGGAGGCATTACATTACCTGATTTCAAACAATACTATG 3427
                         -         vi      vv i   i v  ii        vvv     ii
  L1M4_orf2#LINE/    196 -AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_129990582_   3428 AGGCCATAGTTACCAAAACAGCATGGTTCTGTTACAAAAACAGGCATACA 3477
                          i  i i   v i   i    ii    v   vi i  ii i  i    i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_129990582_   3478 AGAAAAAAAAACAAAAAAACAAAAAAACAAAAAAAAAACAACAGGTATAC 3527
                         --------------------------------------------------
  L1M4_orf2#LINE/    295 -------------------------------------------------- 294

  chr2_129990582_   3528 GGACCAGTGCACTAGAATAGAGAACCCAGAAATAAAGCCAAA----TATA 3573
                         -  i  i  v v      v    ii           v   v ----   i
  L1M4_orf2#LINE/    295 -GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_129990582_   3574 ATCAACTGATCATAGACAAAACAAACAAAAACATAAAGTGGGGAAAAGAC 3623
                         i    i    iv v     iivviv   i v   vv i        ii i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_129990582_   3624 ACCCTATTCGACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAG 3673
                          vi  v   i                i  i   v  ?       i ii  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_129990582_   3674 AATGAAACTGGATCCTCATTTCTCACCTTATAAAAAAATCAACTCAAGAT 3723
                               ii    i  ii ii  v    v    v      i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_129990582_   3724 TGATCAAATACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGAT 3773
                         v     ? v  i     v     v  i           v ii       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_129990582_   3774 AACATTGGAA-AAACCGTTCCGGACATTTGCTTAGACAA-AGCTTCATGA 3821
                              v  ?i-   i -   vv   v  v v    i   -i i   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_129990582_   3822 CCAAGAACCCAAAAGCAAACAAAACAAAAACAAAGATAAATAGATGAGAC 3871
                         vi v  vv         v viv       iv   i   i   i  vi   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_129990582_   3872 TTAATTAAACTAAAAAGCTTCTGCGTGGCAAAAAA-ATTATTCAGCAGAG 3920
                           v  i   v v    i   i  i ivv    ii - i   iv  - i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAG 691

  chr2_129990582_   3921 TAAACAGACAACTCACAGAGTGTAAGAAAATCTTCACAATCTATACTTCT 3970
                          i  v       i      i  vi       v  ii   vii   iv   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_129990582_   3971 GACAAAGGACGAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAG 4020
                           i  i    vvi          v  i  i      vv    v   ii i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_129990582_   4021 GATAAAAACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGAC 4070
                         v v   i     i  i  v  i?    i     v     iv         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_129990582_   4071 AATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAAGGC 4120
                          v     v                       i  i  i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_129990582_   4121 TCAGTATCACTAGTTAT 4137
                            ii    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (137 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 5.92 (71 / 12)  


3118 27.47 0.66 0.88  chr2_130007989_130011518     2129  3038 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_130007989_   2129 TGGAAGAACATTTCATGCTCATGGATAGGAAGAATCAATATTATGAAAAT 2178
                              ii i  ii    i        v      v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_130007989_   2179 GGCCATATTTCCCAAGGTAATTTATAGATTCAATACCATCCCCATCAGGC 2228
                            v   i i     iv i  i  i        ii v     i    iiv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_130007989_   2229 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2276
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_130007989_   2277 TATGGAAGCAAAAAAGAGCTCACATTGCCAAGACAATCCAAAGCCAAAAG 2326
                                iiiv  ii  v iviv  v     i      ivi ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_130007989_   2327 AACAAAGCTGGAGGCATCACACTACGTGACTTCAAACTATACCACAAGGC 2376
                                i      vv       v vii i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_130007989_   2377 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGACC 2426
                                 i   i    ii         i i  ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_130007989_   2427 AATGGAACAGAAT--AGAGCCCTCGGAAATAATACTACACATCTATAACC 2474
                                i     --    i  --i       vv i i    i   iii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_130007989_   2475 ATCTGATCTTTGACAATGCTGACAAAAACAAGAAATGGGGAAAGGATTCC 2524
                          vi    i  i     v v  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_130007989_   2525 CTATTTAATAAATGGTGCTGGGAATACTGGTTAGCCATATGTAGAAAGCT 2574
                           v  i  i              vv     v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_130007989_   2575 GAAACTGGATCCCTTCCTTACACCTAATACAAAAATTAATTCAAGATGGA 2624
                            ii    i    v   i     vv             i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_130007989_   2625 TTAAAGACTTAAATGTTAGATGTAAAACCATAAAAACCCTAGAAGAAAGC 2674
                          i ?    i       v   vv      i      vi i         i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_130007989_   2675 CTAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGATT 2722
                         v    ?i- v i -   i- i  v i  i- i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_130007989_   2723 AAAGCATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCT 2772
                          vii  i        vvi          vv     v  i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_130007989_   2773 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTACCATCAGAGTGA 2822
                         v  i   v v  i i   i  ii vv    i  v i  i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_130007989_   2823 ACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 2872
                          v  iv    i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_130007989_   2873 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 2922
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_130007989_   2923 AAAAATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAAATAC 2972
                            i -    i     v  i?    i     i      v    i i i i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_130007989_   2973 TTCTCAAAAGAAGACATTTATGTAGCCAACAGAAAAATGAAAAAAATGCT 3022
                              v        i  vi vi i     i iiv v       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr2_130007989_   3023 GATCATCACTGGCCGT 3038
                         v v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (155 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


1710 24.20 9.80 1.68  chr2_130021014_130022658.rev      501  1153 (492)    L1M4_orf2#LINE/L1      203   908 (0)  

  chr2_130021014_    501 AAGTTGGTAGAAGTGATGTTACCTGATCTCAAGACTTCTTAGAAAGCTAA 550
                                -  i v v iii v  ii  i    i    vi  v       v
  L1M4_orf2#LINE/    203 AAGTTGG-AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_130021014_    551 AGTATTAGATACAGTGTGGTATTGACATAAGAACAGATGAAAAGATCAGT 600
                             v vi v           i  i      i i   iiv v      i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_130021014_    601 GGG---GCATACAAAGGCCA--AAGAGATCCATG--TTAATAGAGTCAAT 643
                           i--- v  vv i  v   --  v i i    i--  --  vi      
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAAT 349

  chr2_130021014_    644 TGATTTTGAACAGACACATGAAAGCAAGTCAATGAGTAAAG-----TCTT 688
                                vi   iiviiiiv  ii v v      i v    -----    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_130021014_    689 TTAAACAATTGGTGCTATAACAACTGAATAA----AGGAGAGAGAAAAAA 734
                           v     v       ivi       i   ?---- v vi i    vi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_130021014_    735 ATTTCCATCTTCTTCTACACACCATATACAGAAATTAACTTAAGAGGGAT 784
                         i  v--iv ii  v iv             i         i  i v    
  L1M4_orf2#LINE/    450 GTTG--GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_130021014_    785 CATAGACCTAAACATAAAAGCTAAAACTATAAAGATTTTAGAAGAAAGCA 834
                           ?         ii   i               iv i          i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_130021014_    835 -AGAAAAAATATCTTGGTGGC-TTGGGATAAGCAGATA-TTTTTTAAGTA 881
                         -  i?iv  -     v   i -     v  i   -  i-   i   ii  
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAGATA 595

  chr2_130021014_    882 -GGC-TTAGAAATTGATAACCA-CAAAAGAAAAAAGATGATTAATTAGAC 928
                         - i -ii i  ii-- i  v  -            v -   v    i   
  L1M4_orf2#LINE/    596 TGACACCAAAAGC--ACAAGCAACAAAAGAAAAAATA-GATAAATTGGAC 642

  chr2_130021014_    929 TTCACAGAAAT----------------------GATACCATTAGGAAAAT 956
                             ivi    ----------------------  i  i  i i    i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_130021014_    957 GAAATGACAAGCC-TAAAA---GATAAAATATTCACAAAAAATATCTCTA 1002
                             v     v  -i i  ---  v        ii    vv    v   i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_130021014_   1003 ACAAGGAATTT----CAAGAATATATAAGGAACTCAAACAACTCAGTAAT 1048
                          i    i i  ---- v           i      vv        i    
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_130021014_   1049 ATAAA-AC---TGTCACA--TTAAAAATGG-CAAAACATTTG----GACA 1087
                          v   -  --- iv v  -- ?        -    iv     ----    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_130021014_   1088 CT-CTACAAATGAAGATATATGAATGGTCAATAAACACATGGAAAGGTTC 1136
                         i -  v    -         ii     i      i      i    i v 
  L1M4_orf2#LINE/    843 TTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_130021014_   1137 TTAACATTATTAGTCAT 1153
                          i     i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (97 / 57)
Gap_init rate = 0.04 (29 / 706), avg. gap size = 2.59 (75 / 29)  


4151 19.11 2.17 3.58  chr2_130028767_130030700.rev      522  1442 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_130028767_    522 TGGAGAAGCAGTCTGTATTCATGGATCAGAAGACT-AGCGCTGTTTAGAT 570
                             i iii vi ii i         ii       - iiii    v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_130028767_    571 GGCAATGCTTCCCAA-TTGACCTATAGATTCAAGGCAGTCCCCATGAGAA 619
                               i  i     -    i   i        v   i    i  v i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_130028767_    620 TCTCAGGTAACTTCCTTATAGGAATTAAGAAGCTGATTCTAAAATGTATA 669
                           i   v iv   ii  ii  i    i v        i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_130028767_    670 TGGACTTGCAAGGGACCCAGAAGAGCCAAAATAATCTTGAAACAGAAGAA 719
                             vv                v        i          v       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_130028767_    720 TAAGGTAGGTGTACTCATACTTCCTGATTTCACAACTCACTACAAAGCAA 769
                         i  i  v  v v     i      ii      v    i          v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_130028767_    770 AAGAAATCAAGACGATATGATCCTGGCATTAAGA-AAACAGAGAGATCAA 818
                         v  v         ii i  i v       v i  - i   v v       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_130028767_    819 TGAAATGTCATGGAGAGAGTCCAAAAATAAATCCACACATTTAATAGTCA 868
                           i   ivv  v     --    i       i   i       - i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAG--TCCAGAAATAAACCCATACATTTA-TGGTCA 347

  chr2_130028767_    869 ACTGATTTTTGACAATGGTGTCAAAACCATTCAGTGAGTAAAGAATAATC 918
                          i       i     v    i   i        i  i v        i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_130028767_    919 TTTTCAACAAATGGTACTGGGACAAATGTATGCAGCCATATGCAAAAGAA 968
                                        i         v  v  -- ?   i           
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGAT--AKCCACATGCAAAAGAA 445

  chr2_130028767_    969 TGAAGTTGAACTCTTACTTCAC-TCA-ATTTAAAAGTTAACTTTAAATGG 1016
                                 i  i i   i    -i  -  vi    i      iv      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_130028767_   1017 AGCAAAGACCTAAATATAAAAAGCAAAACCAAAGAAATCATGGAAGAAAA 1066
                          v  ?          i   i ivi     i v i  v  v i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_130028767_   1067 AGTAGGATTAAGTCTTCATGATCTTGAATTTAGCAAAGGATTCTTAGATG 1116
                         vi    ?v   i     i   i    ii  vi    v  v         i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_130028767_   1117 TGATATCAAGAGTACAAGCAATAAAA-------------AATTATACTTT 1153
                            i i   i  i        i    -------------    iv    i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_130028767_   1154 GTCAAAATTAAAAACTTTTGTGCTCCAAAGGAAACCATAAACAAAATGAA 1203
                         i                       i       v  i  v  v   i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_130028767_   1204 AAGACAACACACAGAACGGAAAAAAAT--CTGCAAATCACATATCTAAAA 1251
                                 v       i  i i     --i         i      i v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_130028767_   1252 AGGGACTTATATCCAGAACAGATAAAGAGCTCTTCAGTTCTTTATTACTG 1301
                                 i         i v       i     ------------  --
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTT------------AC-- 781

  chr2_130028767_   1302 AACTTTCAGTTCAGTCCTCAGTAATAAAACAACAAATAATCTAATTAAGG 1351
                             --------------  i        vi        i i    ? ii
  L1M4_orf2#LINE/    782 AACT--------------CAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_130028767_   1352 AATGGACAAAGGATCTGAGTAGACATTTCTCCAGGGAATATGTACAAATG 1401
                              i        i   i              ii   v  i        
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_130028767_   1402 ACCAATGAGCACATGAGAAGATAATCAGCCTCACTAGTCAT 1442
                         i     i         i     iv   i v   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (119 / 53)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.08 (53 / 13)  


3083 26.08 1.66 0.89  chr2_130042705_130048505     4410  5310 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_130042705_   4410 TGGAAA--CATCCCATGCTCATGGATAGGAAGAATCAATATCAGGAAAAT 4457
                               --i        i        v      v i     iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_130042705_   4458 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCTCCATCAAGC 4507
                            v     v      v i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_130042705_   4508 TACCATTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTCA 4556
                          v   vivi i  i  ii     v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_130042705_   4557 TATGGAACCAAAAAAAGAGCCCCT--ATAGCCAAGACAATCCTAAGCAAA 4604
                                --- viv   i v   v--        i      i i iv  i
  L1M4_orf2#LINE/    149 TATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_130042705_   4605 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAA 4654
                                   i      vv   ii  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_130042705_   4655 GGCTACAGTAACTGAAACAGCATGGTATTGGTACCAAAACAGATATATGG 4704
                         i          iii i    ii     i   i iv ii i   i    i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_130042705_   4705 ACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAAC 4754
                          i        i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_130042705_   4755 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 4804
                           vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_130042705_   4805 CCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAAC 4854
                         i  v  i  i        i     v      v  ?   i   i i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_130042705_   4855 TGAAACTGGACCCTTTCCCTATACCTTATACAAAAATTAACTCAAGATGG 4904
                             ii       i v  ii i   v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_130042705_   4905 ATTAAAGACTTAAACATAAGACCTAAAACCATAAAAATCTTAGAAGAAAA 4954
                           i ?    i    ii     v       i      v             
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_130042705_   4955 CCTAGGCG-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACT 5003
                          v    ? - v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_130042705_   5004 AAAACACCAAAAGCAATGGCAAGAAAAGCCAAATTTGACAA-TGGGATCT 5052
                          vi            vvi    v     vv   v v  i  - v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_130042705_   5053 AATTTAACTAAAGAGCTTCTGAGCAGCAAAAGAAACTATCATTAGAGTGA 5102
                         v  iv  v v  i i   i  v  vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_130042705_   5103 AAAGGAAAGCTACAAAATGGGAGAAAATTTTTGCAATCTATTCATCTGAC 5152
                             iv  v i   i             v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_130042705_   5153 AAAGGGCTAATATCCAGAATATACAAGGGAATTAAACAAATTTACAAGAA 5202
                           i  i  vi             i  i i v ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_130042705_   5203 AAA-ACAAACAAGCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5251
                            -     i  v  v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_130042705_   5252 TCTCAAAAAAAAATTTGTGCAA----CCAACAA--ACATGAAAAAA-ACT 5294
                             v   i  i  --i i   ----    i  --         i -i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGAT--ATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_130042705_   5295 CATCATCTCTGGTCAT 5310
                           v    v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


 431 25.57 15.57 6.39  chr2_130052123_130053721.rev      490  1099 (500)    L1M4_orf2#LINE/L1      229   894 (14)  

  chr2_130052123_    490 TTCAATA--TGCAATAAAGC--CTATAAGTAAAGCAGTGTGACATAGGTC 535
                              v -- i v i     -- vi   vi  ii       ii iv  --
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG-- 276

  chr2_130052123_    536 CATGAAGA---GCAGACAGATTAATAGAATAAAAT-----ATCCAGAAAC 577
                            i i  ---i  v i    i   i     i   -----i        i
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_130052123_    578 AGA----TACACTTACATTTAAAAGTTTACCGTAACAGGAAAGTGGGATT 623
                          i ----    i   iiv i  vv v  vi  --   -- ii   -----
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCG--ACA--AGGGTG----- 367

  chr2_130052123_    624 TCAA-ATCAT-CA--GGGGATAAGAAAAA-CTTT--AAAAAAT-----TG 661
                         i   - i   -  --     -     v i-    --  v    -----  
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGA-AAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_130052123_    662 A-ATAACTGAGTGACCCTATGGGAAAAAAAAAAAGAAGTTGGATTCGTTT 710
                         i- i     ii i?  vi   v----    i  v         ii v vi
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGC----AAAAGAATGAAGTTGGACCCCTAC 462

  chr2_130052123_    711 TTCATGTATCATGT-CAA---TTA---CAAAA-GGATAAGAGATTTCAAT 752
                         i   i-- i   i -   ---   ---     -    v ?   ii v   
  L1M4_orf2#LINE/    463 CTCAC--ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_130052123_    753 GTAAAAAAATGGAATCACA----TGTACAGTAAAAGAAAACACAGATGAA 798
                             i iv- ii  ii i ---- v ----  i         i  i? v 
  L1M4_orf2#LINE/    511 GTAAGAGC-TAAAACTATAAAACTCT----TAGAAGAAAACATAGGNGTA 555

  chr2_130052123_    799 ATTCCTATATAATTTGGCAT----CAAT------TTAAA-AT----TCAG 833
                          v  i -ii i ii v vi ----    ------   i -  ----i  i
  L1M4_orf2#LINE/    556 AATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_130052123_    834 AA-----AG-AGTAAGAATAAAATTGGATATGTTTGAAT-AATAAAAATT 876
                           -----  - ii  i iv    v i    vi  v  v -v  v      
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_130052123_    877 TTAAAAA-----GTAATTTTCAAGGCAACACCATAAACAAAGT--AATGA 919
                         --     -----  i--i     i -i    i  v  v     --  v  
  L1M4_orf2#LINE/    655 --AAAAACTTTTGTG--CTTCAAAG-GACACTATCAAGAAAGTGAAAAGA 699

  chr2_130052123_    920 CAA---AC----TAGGAAAAGATATTTGCAACTTATATTGCAGAGAAAGG 962
                            ---  ---- i   i  i          v i    vv v  v  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_130052123_    963 GTTTATATTCTTAATATCCAAAGAGCTTCTA-------ATACTACAGAAG 1005
                         ii  i   i vv     vi     i  ii  -------   v  - i   
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA-AAAAG 798

  chr2_130052123_   1006 A-AAATAACCTAG-----AGCCCTATGG---AAAGATCAGAGTA-ATGTT 1045
                          -        i i----- i----    ---  i   iv  i  - ii  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAA----ATGGGCAAAGGATTTGAATAGACATT 844

  chr2_130052123_   1046 TCATTCACAGAAAAATAAGTGCAAATGATTC-TACACCACATGAAAAGAT 1094
                           - i  v    i -  -- i      iiiv-  - v             
  L1M4_orf2#LINE/    845 TC-TCCAAAGAAGA-TA--TACAAATGGCCAATA-AGCACATGAAAAGAT 889

  chr2_130052123_   1095 GCTCA 1099
                              
  L1M4_orf2#LINE/    890 GCTCA 894

Transitions / transversions = 2.12 (104 / 49)
Gap_init rate = 0.08 (53 / 666), avg. gap size = 2.53 (134 / 53)  


2252 25.50 4.75 4.64  chr2_130062384_130067108     3328  4233 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_130062384_   3328 GGAAACATA--CTGTATTTATGAGTTGGATGACTCAACATAGAAAAGTTG 3375
                              v   -- ii i  i   ii     v    i  i  v vv   v  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_130062384_   3376 TCCATTCTTCCCAAATTGATCTACAGATATAATCCAATTCCTACAAAAAT 3425
                         v v  v  i                   vi  iv    i    iv     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_130062384_   3426 CCCAGCAAGGGATTTTGTAGACATAGAACACCTTATCCCAAAATGTATCT 3475
                               vivvvv     i   v  v  vv v  v    i     vi  v 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_130062384_   3476 GGAAA-GCACCAGGCCCTAGAATAGCTAAAAAAAAAAAAAAAAAAAAAAA 3524
                              -   v-i  v  i        i    v  vvvvi     i  ---
  L1M4_orf2#LINE/    152 GGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA--- 197

  chr2_130062384_   3525 AAAAAAAAAAAAATCTGTACTAAGAACAGAATGGGAGGAATTATTCTACG 3574
                         -----------------------     i i v      v i iv  v v
  L1M4_orf2#LINE/    198 -----------------------GAACAAAGTTGGAGGACTCACACTTCC 224

  chr2_130062384_   3575 TGGTATTAGA-TTTGCTATGTAATCATAGCAATCAAGACACTGTGGCATT 3623
                         iii v i i -i  i   iiv iii i  i          v     i i 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr2_130062384_   3624 G--AAAATGCAATAGACATATTGATAAATGGAACAAAACAGAGAACCCAG 3671
                          -- v  v --          v   v       i i  iv    ii    
  L1M4_orf2#LINE/    275 GGCATAAGG--ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_130062384_   3672 AAATAGACCTACACAAATATGCCCAACTGAGTTTTTTATAAAGATACAAA 3721
                              i   i i   vv    vi   i   -    iv i  i i i v  
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGA-TTTTCGACAAGGGTGCCAA 371

  chr2_130062384_   3722 AGCAATTCAATGGAAGAAGGAAAATCTTTTCAACAAACAGTGCTGGAGGA 3771
                         ii v         iii   i v i             ii       iiv 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_130062384_   3772 ATTTAACATCGATAGGCACAATAATGAAC----ACAACCTAAGTCTCACA 3817
                          i vi i ? v i v   v  v      v----  v-    --i      
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC-CCTA--CCTCACA 468

  chr2_130062384_   3818 GCTCATA-AAAAATTAA-TCAAAATAGAT-ACAAACATAAATGTGAGACA 3864
                         v vi   -         -       i   - ? i  v       i   vv
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_130062384_   3865 TAAA-CTTTAAAACTTTTAGAAAAAAATAGAAAG---AATCTTCAGGATC 3910
                             -  v       i      i    i v ii?---       iv  i 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_130062384_   3911 T----------AA-GATTTCTTAAACTTTACACCAAAAGCATGATCCATA 3949
                          ----------  - i       i iv v            ii v v i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_130062384_   3950 AAAGGAAAAACTAATAAATTTAACGTTATCAAAATTAAAAAATTTTA--C 3997
                             i     ivi       vi  v i              v    i-- 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_130062384_   3998 TTAGTGAAAGATCCCATTAAAAGAATGAAAAGACAAGCTATAGACTGGG- 4046
                           --ii  i  iv i  i  i i i           v i i   v    -
  L1M4_orf2#LINE/    669 TT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_130062384_   4047 GAAAATGTTTGCAAATGCCAC-TACC-AATGAAGAATTAGTATCTAGAAT 4094
                               i         --  i-  i -i  i i i i v     i     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAAT--CATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_130062384_   4095 TAAGAAAAAAAAACTCTTAAAATTTAATAGTAAAAA-------AATCCGG 4137
                         ---iv v   i        v  i i    i      -------  i  ii
  L1M4_orf2#LINE/    765 ---ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_130062384_   4138 T---AACATGAGCAAAAGACATGCACAGAAATTTCGCTGAAGAGGAGATA 4184
                          ---  v   i     i  iv  v i   v     v ii    i  v   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_130062384_   4185 CAGCTGTGGAAAATAAACACATGAAAAGATGTTCAGCACCACTAGCTAT 4233
                           i--i   vv     i              i   i  i  ????????
  L1M4_orf2#LINE/    862 CAA--ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (137 / 91)
Gap_init rate = 0.03 (28 / 907), avg. gap size = 3.04 (85 / 28)  


3925 18.36 4.53 0.37  chr2_130165696_130169840     2829  3645 (500)    L1M4_orf2#LINE/L1       18   868 (40)  

  chr2_130165696_   2829 TTTATTGATCTGAATATTTAATATTGTTAAGATAGTAATACTTCCAAAAT 2878
                           i  v   iv   v i                i i      i  v    
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chr2_130165696_   2879 GTAGCTACATATTTGACAAAATCCCTAACAAAATCAAAAATTAATTTTTT 2928
                         vv v     v   ii  iv        v       vv iv vvv      
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr2_130165696_   2929 TCAGAAATTGGCAAATTGATCCTAAAATTTATGTAGAAACACAAGAGACC 2978
                         v         i   ii             i  i i    ii    i    
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_130165696_   2979 CAGAATAGCCAAAAT--TCTTACAAAGGAAAAGCAAAGCTGAAGGATTCA 3026
                                       i--    iv   i   i i     i  i    i   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_130165696_   3027 CCCTTTTCAATTTCAAAACTTA-TACA--TCTATAATAATCAAGGTGATA 3073
                          v   ii               -    --v   i i        iiii i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_130165696_   3074 TGATTC------------AGTTATATA---------AATAGACATTGAGA 3102
                           i v ------------  vi     ---------      -       
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA-ATTGAGA 316

  chr2_130165696_   3103 GTCCAAAAGTAAATTCATATATTTATCATCAATTGGTTTTCCACATGGGT 3152
                              i  i    ii    i      vi       i     v   v    
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_130165696_   3153 GCCAAGAGCATCCAATGGGGAAAGAATCGTCTTTTCAAAAAATAATGCTG 3202
                                v   i               v          v    ii     
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_130165696_   3203 AAACAACTGGCTATCCACATGCAAAAGAATGAAGTTGGACCCTTATCTCA 3252
                         ii        v  ?                            i  i    
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_130165696_   3253 AGCCATACACAAAATTTAA-TCAAAAGGAGTCATAGACCTAAATGTAGGA 3301
                         vi     i      v    -      v ii   ?             i  
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_130165696_   3302 GCTAAAACTATAGACAC-CTGAGAAGAAAACATAGAAGTAAATC---ATG 3347
                                     i -  -  v              i?       ---i  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_130165696_   3348 GCCTTAAGTTAGGGAATAGTTCCTTAGGTGCAACACTCTAAGCACAAATG 3397
                         i    ii      v   i   i     i iii    ivv        iii
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_130165696_   3398 ATGAAAGAAGAAAT-GATAAATTG-ACTTCATCAAAATTTAAAACTTTTG 3445
                          ii      i    -         -              v          
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_130165696_   3446 TGCTTCTAATAATACTATCAAGAAAGTGAAAAGAAAATCCACAGAATGAG 3495
                               v  vi i                     v  i          i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_130165696_   3496 GGAATATGTTTGCAAATCTTATATCTAGTATGAGGCTTATATTCAGACTA 3545
                         i   v  i          v       ii  v i i   i   i    v  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_130165696_   3546 TATAAAGAACATTTACAACTCAATGATAAA--GATAAATAATCCAATATT 3593
                                   vi            i     --  i      i     - ?
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT-TW 814

  chr2_130165696_   3594 AAAATTGGGCAAAGAATTTAAA--GAAAATTCTGCAAAGAAGGTATGCAA 3641
                             v         i    i  --  v v    v        i   i   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_130165696_   3642 GTGG 3645
                         i   
  L1M4_orf2#LINE/    865 ATGG 868

Transitions / transversions = 1.98 (97 / 49)
Gap_init rate = 0.02 (15 / 851), avg. gap size = 2.67 (40 / 15)  


2245 22.77 4.95 1.16  chr2_130191604_130193194      494  1099 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_130191604_    494 AAGGTGTAGGTACACTGACCAATGGAACAGGAATAAACAGCCCAGAAATA 543
                             -i   ii i iv  i        i  -   vi v  i         
  L1M4_orf2#LINE/    280 AAGG-ATAGACATATAGATCAATGGAATAG-AATTGAGAGTCCAGAAATA 327

  chr2_130191604_    544 AACCCATGCATCTCCATTCTATTGATTTT-GACAAAAATGCCAAGAATAT 592
                                i   i viiv  v         -     iii        vi  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_130191604_    593 ACATTGGGGAACTAACAGGCATTTCCATAAA-GGTGCTGGGAAAACTAGA 641
                         v  v       vv  i  v v    v i   -          v    i  
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_130191604_    642 TATCCACATATAAAAGAATACAATTGGATGCTTATCTCACACCATGTGCA 691
                           ?      ii        iv i     iv i  i          i i  
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_130191604_    692 AAAAATCAACTCAAAGTTGACTAAAGACTTAAATGAGAGACCCAAAACTG 741
                             - i        i v  ii ?    i      vi   v i      i
  L1M4_orf2#LINE/    478 AAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_130191604_    742 TAAAGCTACTAGAAGAAAACATGGGGGAAAA-CTACACAACATTGGTCTG 790
                             i  vi             i  ? v   -  v iii  v    vi i
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_130191604_    791 GGCAATAACTTTTTTTTGATTTGACCCCAAAAGTA--GGCAACAAAAGAA 838
                               ii--   i  v   v    v       i --i            
  L1M4_orf2#LINE/    577 GGCAATGG--TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_130191604_    839 AAAATAGACAAACTA---------------AAAAGCTTCTACACAGCAAA 873
                                 i   i i---------------    i   i iii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_130191604_    874 GAAAATAATTAATAGTGTGAAGAGGCAACCTACAGACTGGGAGAAAATAT 923
                          i v iv  i  v iv     i  i     i     v             
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_130191604_    924 CTACAAATCCTAGAGCAGATAAGGG-CCCATATCTAAAATGCATCA-GAA 971
                         i i      v  v v v        - iii    i i   ii  v -   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_130191604_    972 --------ACTCAATAACGAGAAAACAAATAACCCTATTTAAAAATAGGC 1013
                         --------         ii i  i           v   ?      i   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_130191604_   1014 AAAAGACCTAAATAGGCATTTCTCAAAAGAAGACTTACAAAGGGCCAACA 1063
                            i  ii i     i        v        iv      v      i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_130191604_   1064 GATACATGAAAAAAAATGCTCAACATCACTAATCAT 1099
                         iii         i --            ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (90 / 44)
Gap_init rate = 0.02 (13 / 629), avg. gap size = 2.85 (37 / 13)  


1759 24.69 8.50 4.66  chr2_130223712_130225432      501  1229 (492)    L1M4_orf2#LINE/L1      152   908 (0)  

  chr2_130223712_    501 GGAAAAAGAAGGG-CCCA-AATAGCCAAAGAAATTTTACGCAGAAAAAAT 548
                              viv     -    -          iv   i  iviv ii  i  i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_130223712_    549 AAAGCCAGAGGCATCACATTATCCAACTTCAAA-CATACTACAAGGCTAC 597
                             iii    vv     i vi    i      - v        i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_130223712_    598 AGTAACCCAAACAGCATGGTACTGATACAAAAACAAACACATAAACGAAT 647
                              i v i    ii        ii i  ii i i   i   i iv   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_130223712_    648 GGAACAGAACAGAGACTCCTGAAATAGAGCCACATACCTATAACCAACTC 697
                             i    iv    v   v      i v   i i ii   iii   i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_130223712_    698 ATCTTTGACAGTCAACAAAAAAAAAAAAAAAAAAAATGGGGAAAGGACAC 747
                           i  i    ------ iiivivv  i vv vvv           i i v
  L1M4_orf2#LINE/    352 ATTTTCGACA------AGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_130223712_    748 ACTATTTAATAAATGGTCCTGGGAAAACTGGCTAGCC-TAT-CAA----- 790
                         v  v  i  i       v      v      v  ?  -i  -   -----
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_130223712_    791 ------------------------CATATATAAAAATTAATGCAAG-TAG 815
                         ------------------------      i         iv   i- i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_130223712_    816 ATTAAATACTTAAATGTAACACCTCAAACTACAAAAATCC-AGAAGAAAA 864
                           i ? v  i         v v  v      i    v  i-         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_130223712_    865 TCCAGAAAATACTCTTCTAGACATTGGCCTAGGCAAATAATTTAT--GAT 912
                         ivi  i?ivv v     vv   v    vi       - ii   v --   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT 594

  chr2_130223712_    913 GAAGACCCCAAAATCA---------------AAAATAGACAAATGAGACT 947
                         - v   v      v  ---------------        i    vi    
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_130223712_    948 T-----AACTGAAGAGCTTTTGCACAGAAAAAGAAAAAAAAAAGAAACAA 992
                          -----  v v  i i      ii vvv   i  ----------------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA---------------- 677

  chr2_130223712_    993 ACAAAAAAACACCTCTCAACAGAATAAACAGACAACCTACAGAATGGGAT 1042
                         ---------   - v    v i i i  v        i           v
  L1M4_orf2#LINE/    678 ---------CAC-TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_130223712_   1043 AAAATATTTGCAAATCATGTACTCGACAAAGGACTAATCTCCAGAATCTA 1092
                                           i  iii  i  i     vi v        v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_130223712_   1093 TAAGGAACTTAAATGAATCAACAAGAAAGAAACAA----CCCCATTAAAA 1138
                            i     ivv ii v    i  v   i i    ----   v   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_130223712_   1139 AGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATACAAGCA 1188
                          i           iv    i     i     v        i      iii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_130223712_   1189 GCCAACAAACATATGAGAAAATGTTCAACATTACTAATCAC 1229
                              i  i  i    i  i   i       i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (108 / 68)
Gap_init rate = 0.02 (17 / 757), avg. gap size = 5.65 (96 / 17)  


1912 28.11 7.95 1.78  chr2_130256812_130258765      620  1462 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_130256812_    620 CGTGCTCATGGATTAGAAGGCTCAGCATAGGAAAGATGCCAGTACTACCA 669
                          i  i         i    i  i ii  v vv      v  i    v  v
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_130256812_    670 AAACTATTCTACATGCTGAACACAATTCCTAACAAAAGCTTAGCAAGAGT 719
                            i iv      vii v   i    i    v     v ii   vivvv 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_130256812_    720 TTTTGTTCAAATAGACAATCTCGTTCTAAAATGCATATACGGAAAGG--- 766
                              ivv    v     v  vi i       v     --     v ---
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT--GGAAATGCAA 161

  chr2_130256812_    767 GGGA------------AAAATAA-------AGATAAGAA---AGTGGGAG 794
                             ------------    i  ------- i v     ---   v    
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_130256812_    795 GAATCACTCTTCTTGGTGTTAAGGCTTCCTGTGTAACCACAGAAATCAAG 844
                           v    v    iiii v i  ii   v  iiiv i i    v       
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_130256812_    845 ACAGTATAGTTAGTATTGGCAGAGACATAGACACATTGATCAACAGGAAA 894
                              i i  ---- i     v iiv       i  v      i-    v
  L1M4_orf2#LINE/    262 ACAGTGTGGT----ACTGGCATAAGGATAGACATATAGATCAAT-GGAAT 306

  chr2_130256812_    895 AAAACAGAGAACCCAGAAATAGACCCAAACAAATAGACCCACATGGATGT 944
                          i  iv    ii         i     v   vv  vivi  -  v   v 
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA-ATTGATTT 355

  chr2_130256812_    945 ATTATAAAAGTGGAAAAGCAAATTAAGGGAGGAAGGACCACCTTTTCAAT 994
                         viv i  ii   vv  ii v v i  v  i i   i ivii        i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_130256812_    995 AAATGGTGCTGGAAGAAGTTGAATCTCCATAACCCAAAACATGAACCTCA 1044
                                     i v  -i  i  v?   i vv v   iv     vi vi
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_130256812_   1045 ACCTAAGTCCCACACCTTCTATAAAAATTAACTCAAAAC-------AGAC 1087
                            ivvii i      v v  i                i-------    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_130256812_   1088 --AAGTGTACAATGAAAAATTCTAAAACTTTAAGTGAAAAAATACAGGGG 1135
                         --  i    vi vvv    i v       i v  -i i    i i   ? 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAG-AAGAAAACATAGGNG 553

  chr2_130256812_   1136 AAAATCTCTAGGACCCAGGGCTAGGGGA-GGTGTTCTTAGAATTGACACC 1184
                         v      iiiv    iv   i    vi -   -        vv       
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATATGACACC 602

  chr2_130256812_   1185 AAAAGCCCAATCCACAAAAGAAGACA---ATAAATCAAACT-CATCGAAA 1230
                               v   v v         i v ---      iii   -    i   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_130256812_   1231 TTAAAAATGTCTACTCCTCAAAAGGTCAC----------ATGAAA-GATT 1269
                                iv i iiv i     -  v   ----------i     -  iv
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_130256812_   1270 TTTT------TTGTA-AAATCATTTGCAGACCACATATCCAACAAAGGAC 1312
                         viii------ v v -   vi       i i  i     ii i  i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_130256812_   1313 TTGCCTTTAGAATACATAGAAAGC----A-AACTCAACAATAAAGAAAAC 1357
                            iv ii      i   i i i ---- -       i      -  i  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGAC 800

  chr2_130256812_   1358 AAAT----CAATTAGAAAATAA-CAAAAGGCAAGAACAGAGAGTTCACTG 1402
                             ----     ?i     ii-    i iivv   i   v v   v ii
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_130256812_   1403 CTGAGCATATACAGATGTCAAAAAAAAACACATGAAAAGATGTTGAATAT 1452
                         vv  iv       i   v v  v  i--              i v  i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAG--CACATGAAAAGATGCTCAACAT 898

  chr2_130256812_   1453 CATTAGTAAT 1462
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.36 (135 / 99)
Gap_init rate = 0.03 (27 / 895), avg. gap size = 3.04 (82 / 27)  


1920 24.95 2.59 0.00  chr2_130308873_130310894        1   501 (1521)    L1M4_orf2#LINE/L1      316   829 (79)  

  chr2_130308873_      1 AGCCCAGAAATAAACTCATACATCAATAGCTAATTGATTTTCAACCAAAT 50
                           i            i       iv  i ii           i  v iiv
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_130308873_     51 TGCCAAAAGCACACAATGGGGAAAGAACAGTCTCTTCAATAAATGGTGT- 99
                               i v  iv              i     i     i        i-
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_130308873_    100 -----AATTGTATATTCAAA-ACAGAAGAATGAAAATGGACTCTCGTCTC 143
                         -----  i  v   ?i  v -i  i         iv     i iiii   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_130308873_    144 ACTCCTTATACAAGAATCATCTCAAAATAAATTAAGGACTTAAATGTGAG 193
                           v  v       i   i v        ii  i ?i   i       i  
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_130308873_    194 ACCTAAAGCTACAAAACTACTAGAAGAAAGCATAGGGGGAAAGCTCCATG 243
                          v     i   i      vi         i      ? v   v  i i  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_130308873_    244 ACATTGGTTTGGACAGAAATTTCT---GCATAATTCCAAAAGCATAGTAA 290
                           v    v  i i  ivii     ---ii  i iv         i ivv 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_130308873_    291 ACAAAAGCAAAAATAGACAAATAGGATTACAGTAAACTAAAAAACTTTTG 340
                                v         i    v   i v  vi   v v           
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_130308873_    341 CACAGCAAGGAAAACAATTCATAGAGTGAAGACACAGCCGACAGACTGGG 390
                         ii vv   i i v  v  iv v i      i v   i  v     v    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_130308873_    391 AGAAGATATTTGCAAATCATACAGCAGATAAAGGGTTAATATCCAAAATA 440
                             i                i v v     i  ii vi      i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_130308873_    441 TACAAGGAACTCAAAGTAGTCAACAAGCAAATGA---ATAATTCTATTAA 487
                           i  i      vv vv v    i  vv   v  ---    ii v   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_130308873_    488 AAAATGGGCAAAGG 501
                                       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGG 829

Transitions / transversions = 1.52 (73 / 48)
Gap_init rate = 0.01 (4 / 514), avg. gap size = 3.25 (13 / 4)  

1249 15.66 0.58 30.93  chr2_130308873_130310894      503  1530 (492)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr2_130308873_    503 AAAAAGAACAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTA 552
                           i         ii       v     i v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_130308873_    553 TAA-GCTATAGTAACCAAAACAGCATGGTACTGGTAAAAAAAACAGACAC 601
                         i  -    i     i   i    ii         i v  ii -i     i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACAT 291

  chr2_130308873_    602 ATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAATTCATAAACAAG 651
                              i        i     v    ii           ii    v ivvi
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_130308873_    652 CAGTAAACTCATTTTTGACAAAGGTGCCAAGAATATACACTGCAGAAAAG 701
                         ii  v  i v     i     i          vi  v  v  vi    ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_130308873_    702 ACAGTCTCTTCAGTAAATGGTGCTGGGAAACCTGGATATCCATATGCAGA 751
                          i     i    ii              v v       ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_130308873_    752 AGAATGAAACTAGACCCCTGTCTCTCGCCATATACAAAAATCAAATCAAA 801
                                 ii i       ii   v i              i  v     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_130308873_    802 ATGGATTAAAAGAATTTAAATTGGCTGGGTGGGGTCTCATGCCGGTAATC 851
                               i ? ----------------------------------------
  L1M4_orf2#LINE/    492 ATGGATCAWA---------------------------------------- 501

  chr2_130308873_    852 CCAGCCAGCACTTTGGGAGGCCCAGGTGGGCAGATCACTTGACGTCAAGA 901
                         --------------------------------------------------
  L1M4_orf2#LINE/    502 -------------------------------------------------- 501

  chr2_130308873_    902 GTTGGAGACCAGCCTGGCCAACAGGTTGAAAGCCTGTCTCTACTAAAAAT 951
                         ------    ---------------------------------    ---
  L1M4_orf2#LINE/    502 ------GACC---------------------------------TAAA--- 509

  chr2_130308873_    952 ACAAAAATTAGCTGGGCATGGTGGTGTGCACCTGTAAGTCCAGCTACTCG 1001
                         --------------------------------      ---     ----
  L1M4_orf2#LINE/    510 --------------------------------TGTAAG---AGCTA---- 520

  chr2_130308873_   1002 GGAGTTTGAGGCACAAGAATGGCTTGAATCTGGGAGGCAGATATTGCAAT 1051
                         --------------------------------------------------
  L1M4_orf2#LINE/    521 -------------------------------------------------- 520

  chr2_130308873_   1052 GAGCCAAGATGGTGCCACTACTCTCCAGCCTGGGTAACACAGTGAGACCC 1101
                         --------------------------------------------------
  L1M4_orf2#LINE/    521 -------------------------------------------------- 520

  chr2_130308873_   1102 TGTCTCAAAAAAAAAAAAAGAACTAAATCGAAGACATTAAACTATAAAAC 1151
                         --------------------------------------            
  L1M4_orf2#LINE/    521 --------------------------------------AAACTATAAAAC 532

  chr2_130308873_   1152 TGCCACAAGAAAATATTGAGGAAACTCTCCAGGACATTGGTCTGGGCAAA 1201
                          vii v       i  v i? v  v   i iv   v    vi i     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_130308873_   1202 ATTTTCTTGAGCA--ACACTTCATAAGTACAAGCAGGCAACCAAAGCAAA 1249
                         iv      iiii --    --  v   i       ----  v    v   
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACAC--CAAAAGCACAAGCA----ACAAAAGAAAA 626

  chr2_130308873_   1250 AATGGACAAATGGGGTTACCTCAAG-TTAAAAAGCCTCTGCACAGCAAAG 1298
                            i  i    v  ii v v    i-       - i i  ii vv     
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAG 675

  chr2_130308873_   1299 GAAACAATCAACAAAGTGAAGAGACAAACTGCAGAATGGAAGAAAATACT 1348
                           v  v     v        i      v ii        i        i 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_130308873_   1349 TGCAAACTACCCATCTAACAAGGTATTAATAACCAGAATACATAAGGAGC 1398
                               ii ivi    i i    v i vi  v        i    i  i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_130308873_   1399 TCAAACAAGTCTACAGAAAAAAAATCTAGTAATCCAATCAAAAAATGGGC 1448
                           vv    v  v i iv     i - v i   i     i?          
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGC 824

  chr2_130308873_   1449 AAAAGATTTGAATAGACATTTCTAAAAAGAAGACATACAA-TGGCAGACA 1497
                            i                   vv        i      -    vi i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_130308873_   1498 GGCATATGAAAGGG-GCTCAACATCATTGATTAT 1530
                         i   i      i i-           ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (103 / 54)
Gap_init rate = 0.02 (15 / 716), avg. gap size = 21.60 (324 / 15)  


 228 18.03 6.56 0.00  chr2_130315759_130321508.rev     2309  2369 (3381)    L1M4_orf2#LINE/L1      140   204 (704)  

  chr2_130315759_   2309 TAAAATTTGTATGGAAATG-AAGGG-TCCAGAG-ACCTAAGACAGTCTTG 2355
                                ii          -     -i     i- v i  i   i     
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_130315759_   2356 AAAAAACA-AACAGA 2369
                              iv -    i 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAA 204

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4)  

1210 23.15 6.23 9.94  chr2_130315759_130321508.rev     2482  3155 (2595)    L1M4_orf2#LINE/L1      260   908 (0)  

  chr2_130315759_   2482 AAACAATGTGGTA---GCATTCAAGAATGGACA-ATGAGACCAGTGGAAC 2527
                          i   i       ---    --   i  i    -  -   i  i     i
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCAT--AAGGATAGACATAT-AGATCAATGGAAT 306

  chr2_130315759_   2528 AGAAT--AGAGTCCAGAAACAGCCCCGTATGTA-ACAGTCACTTGATTTC 2574
                              --            i iv   i  ii v- ii    v       i
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_130315759_   2575 CCCACAGATAACACTGC--AGTGCATT-----GGGAAAGGATGGAGGCTT 2617
                          -----  i  viv   --  vv    -----       i  --  v   
  L1M4_orf2#LINE/    357 C-----GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT--AGTCTT 399

  chr2_130315759_   2618 CT-ATCAAA-GATGCTAG----------TGTCCATATGGGAAA--ACCAT 2653
                         i - v    - i    i ---------- i?   i   vi   -- iv v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_130315759_   2654 CTTG---CCCT-CTGCACAACATACAAAAATAATCCCACAAGCAAAAAAA 2699
                         v   ---    - iv    v    i ----------------      --
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATA----------------CAAAAA-- 481

  chr2_130315759_   2700 AACCTGAATTTCAAATAGATTGCAGATCTAAATACATCTCAGTAGGATCA 2749
                         ---- v  i iv    i   ii?   i      --------   i  v -
  L1M4_orf2#LINE/    482 ----TTAACTCAAAATGGATCAWAGACCTAAAT--------GTAAGAGC- 518

  chr2_130315759_   2750 CAGATCTAAACAAAAGTTGTAGAAGAATAGCACAATTGT----CTACATG 2795
                         i i v   --i    v iv        - i  i iv?  ----  v i  
  L1M4_orf2#LINE/    519 TAAAACTA--TAAAACTCTTAGAAGAA-AACATAGGNGTAAATCTTCGTG 565

  chr2_130315759_   2796 AACTTGAAT-AAGCAGAGGCTTCTCTAAATGAGAAACAAAGATGGTAGAC 2844
                          v    ii - i   iv  i    -  i  iv  v  v  i vvii ii 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCT-TAGATATGACACCAAAAGCACAAGC 614

  chr2_130315759_   2845 A-CAAAGGAAAAGATTGATCAAATGGACTATGTTAAAATTAAGACCTTTT 2893
                          -    i     i  v   v  v      vii i        i v     
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_130315759_   2894 AAAGAAATCAAAAGATACCTTTAAGAGAGTGAAAAGTCAGCCCCGAAAAT 2943
                         i--vivv     i  i  iv i    i         v  i   vv i   
  L1M4_orf2#LINE/    665 G--TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_130315759_   2944 GGGAGAATGTATTTTAATAGA-CATA-ATATAACAAAGAACTAGGATCTA 2991
                                vi     --ii i -    -  v i i  i i   v v   i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTT--GCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_130315759_   2992 GACTATATAAAGAACTCCTACAAATCAGTAAGAAAAGAACAA-CAACCCA 3040
                           v              i     v   i   v    ii    -i      
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_130315759_   3041 ATAACAAAATGAGGGGAAAAACAAACCAAAAATCAAAAATTGACTAGGTA 3090
                           v?v      i --------    ----ii  ------    v   ii 
  L1M4_orf2#LINE/    811 ATTWAAAAATGGG--------CAAA----GGAT------TTGAATAGACA 842

  chr2_130315759_   3091 CTTCACAAAAGA-GACGTCCAAATGGCCAATAAACATTTGAAATGATGCT 3139
                         i   v v     -  ii v              i  iv     v      
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_130315759_   3140 CAACCTCTTAAGTTAT 3155
                             v  v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (93 / 59)
Gap_init rate = 0.05 (35 / 649), avg. gap size = 3.11 (109 / 35)  

3261 26.89 0.44 0.77  chr2_130315759_130321508.rev     4348  5258 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_130315759_   4348 TGGAAGAACATTCTATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4397
                              ii i  i i   i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_130315759_   4398 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATTCCCATCAAGC 4447
                            v     v     iv i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_130315759_   4448 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAACT-ACTTTAAAGTT 4495
                          v   iivi i  i  ii     -   ---- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr2_130315759_   4496 TCATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGTAAA 4545
                         -         viiv  ii  v  viv  v     i      i i iv  i
  L1M4_orf2#LINE/    147 -CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_130315759_   4546 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAG 4595
                                   i      vv   ii  v  ii i      viv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_130315759_   4596 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 4645
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_130315759_   4646 ACCAATGGAACAGAATAGAGGCCTCAGAAATAATACCACACATCTACAAC 4695
                          i        i     v   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_130315759_   4696 CATCTGACTTT-GACAAACCTGACAAAAACAAGAAACGGGGGAAAGGATG 4744
                           vi   i   -     ivv  v   i v  vvv  i    -    i  i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chr2_130315759_   4745 ACCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 4794
                         ii  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_130315759_   4795 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAAATG 4844
                         v    ii    i    v   i     v              i        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_130315759_   4845 GATTAAAGACTTAAATGTTAGACCTAAAACGATAAAAGCCCTAGAAGAAA 4894
                            i ?    i       v   v       v      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_130315759_   4895 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGAC 4943
                           v    ?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_130315759_   4944 TAAAACACCAAAAGTAATGGCAACAAAAGCCAGAATAGACAAATGGGATC 4993
                           vi          i vvi          vv i      i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_130315759_   4994 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAGCTACCATCAGAGTG 5043
                          v  i   v v  i i   i  ii vv    i  vi   i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_130315759_   5044 AACAGGCAACCTACAGAATGGGAGAAAATCTTTGCAATCTACCCATCTGA 5093
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_130315759_   5094 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACACATTTACAAGA 5143
                         i  i  i  vi          v  i        ivv   vv iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_130315759_   5144 AAAAAACAAACAGCCCCAACAAAAAGTGGGCAAAGGATATGAACAGACAC 5193
                             i     i i   v vi?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_130315759_   5194 TTCTCAAAAGAAGATATTCATGCAGCCAACAGATAGATGAAAAAATGCTC 5243
                              v           v  viii     i iii v       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_130315759_   5244 ATTGTCACTAGTCAT 5258
                          vii   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (150 / 91)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2338 25.93 7.48 1.40  chr2_130551374_130553614      895  1750 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_130551374_    895 TGAAAATACATCCTATGTTCATGGACTGAAAGAACTGATATAGTGAAAAT 944
                           i   v i    i           i  i    vi i    v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_130551374_    945 GACCATAGTGCCCAAAGCAGTCTACACATTCTATACAATACCTACCAAAG 994
                          i v   v v      viii      v    v ii    v    i    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_130551374_    995 TACCAA-TGTCATTCTTCACAGAATTATTT-TAAAATG---CTGACATTC 1039
                          v   i-  i -  i  ii     --   v-i  iv  ---  i v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chr2_130551374_   1040 ATGTAGAACCACAAAAGAGCCTGAACAGCAACAGACATACCAAGCAAAAG 1089
                           i i   vii   ii  v  v   i   v - i   - i vv v     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCA-AAACA-ATCTTGAAAAAG 195

  chr2_130551374_   1090 --GAACAAATATGTTGGCA---TCACATTACCTGACTTCAAATGATACTC 1134
                         --       ---     vi---     i v  ii i      vvv    v
  L1M4_orf2#LINE/    196 AAGAACAAA---GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_130551374_   1135 TAAGACCACAGTAACAGAAGCAGCGTGGTACTCGTATAAAAACAGATACA 1184
                         i  ii i       ivi ii   i        v i    ii i   i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_130551374_   1185 TAGATCAATGGAACAGAACAGACAACTCAGAAATAAAGCCACTACA---- 1230
                                      i    iv  v iii          v   -    ----
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTA 341

  chr2_130551374_   1231 --ACCAAGTGATCTCTGAGCAAGGATACAAAAAC-ATACACTGGAGAAAG 1277
                         --ii   v    i ii  -     i i v  i  -  v  v   i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_130551374_   1278 TACAGGTTATTCAATAAATGGTGCTGGGAAAAAAAGATAGCCACATGTGG 1327
                         v i  vi v     i              v  vvi    ?       iii
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_130551374_   1328 AAGAATGAAACTGGATCTCTATCTCTCACCATATACAAAAATTAATTCAA 1377
                                  ii    i i   i   v                   i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_130551374_   1378 GATGGATGAAAGGCCTAAACCTAAGACCT--------------------- 1406
                         i      v ?  i      iv     v  ---------------------
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_130551374_   1407 GAAAACAT---------------TGGCCT------AGGCAAAGGATTTAT 1435
                                 ---------------  i   ------      v  -   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCT 589

  chr2_130551374_   1436 GAGGAA-GACCCTAAAAGCAAATCCAACAAAAATGAAAATAAATAAATAA 1484
                         v  iv -   v i       v vv        ivi      i      vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_130551374_   1485 GACCTAATTAAACTAAAAAGCTTCAGCACAGCAAAAGAAATAATCATCAG 1534
                            i v  i   v v    i   iv ii vv    i  v iv    vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_130551374_   1535 AGTAAAACAACAACTTATACAATGGGA--AAAT-TTTGAAAATTATG-AT 1580
                            i   vi     ii i v       --    -    v    i  i-  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_130551374_   1581 GCTAACAAAGGACTAATATCTATAACCTACAAGAAACTCAAACAAATCAA 1630
                         -  i i  i     vi    i v  iv  i  ii     vv    v    
  L1M4_orf2#LINE/    740 -CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_130551374_   1631 CAGGAAAAACGCAAATAATTCCATTGGAAAGTGGCCAAATTACATGAATA 1680
                         i iv     vi       ii v   ?i   i   v    vv iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_130551374_   1681 GACATTTCTCAAAAGAAGATGTACAAACGGTAAACAAGCATATAAAAACA 1730
                                   v         i      i  iv  i     i  i    v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_130551374_   1731 CGCTAAATATCTCTAATCAT 1750
                         i   v  i   v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (131 / 88)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.30 (76 / 23)  


3562 15.38 5.08 1.92  chr2_130838655_130840354.rev      490  1217 (483)    L1M4_orf2#LINE/L1      158   908 (0)  

  chr2_130838655_    490 GCAGGGGACCTACCCAAAATAGCCAAAACAATCTTGGAAAA-AAGAACAA 538
                            i      ----  i                   i    -        
  L1M4_orf2#LINE/    158 GCAAGGGACC----CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_130838655_    539 ATTTGGAAGACTCATACTTCCTGATTTCAGAACTT-CTACAAAGGTATAA 587
                          v     i      i      ii      i     -        v  i i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_130838655_    588 TAATCAAAACTATGTTACACTGGCACAAGGATAAACACATCAATCAGCTT 637
                                i  vi   vii       i       i   i  vi    iivv
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_130838655_    638 AATAAAATTGAGAGTTCAGAAATAAACCCTTATATTTATGGCCAATTAAT 687
                             i          i             v  i        i     i  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_130838655_    688 TTTCAACAAAGGGGCCAAGACGGTTCAATGGGCAAAGCATAGTCTTTTCA 737
                             i    i  v        vi         v    v            
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_130838655_    738 ACAAATGGTGCTGGAACAACTGGATAGTCACATGCAAAAGAGTGAATGTG 787
                                       i           ?i             i    vv  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_130838655_    788 GACCCCTATCTCACATCACATACAAAAGTTCATTCAAAGTAAATCTGAGA 837
                                 i      i  i        i  v i     i ii   v?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_130838655_    838 CCTAACTGTAAGCAAGAAAACTATAAAACACTTAGAAGGAAGAACAGGAG 887
                              v      vivv             v        i  iv i   ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_130838655_    888 TAAGTCTTTATGACCTCTGATTAGACAATGACTTCTCAGATA---CACCA 934
                            i    ii      iv i    i     ii    i     ---     
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_130838655_    935 AAAGCACA-GCAACACAA-----------TAGATTGGA----ATTAAAGT 968
                                 -      v  -----------  i      ----  i   i 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_130838655_    969 TTCACAAAATGTTTGTGCTTCAAAACACACCATCAAGAAAGTGGAATGAC 1018
                          -- -    iv             iv    i            i  v   
  L1M4_orf2#LINE/    654 T--A-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_130838655_   1019 AACCCACAGAATGGGA-AAGACATTT-TAAATCATGTA-CTGATAAGGGA 1065
                                         -  i i    -i       i  -           
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_130838655_   1066 CTTATATACAGAATA--------ACGCTTACAACTCAATAATAAAAAGAC 1107
                            i   v       --------  v                        
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_130838655_   1108 AACCCCAAATAGCCCAATTTTAAAATGAATAAATGACATGAATAGACATT 1157
                           ------   i       ?v      iii   v  iv            
  L1M4_orf2#LINE/    801 AA------ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_130838655_   1158 TGGCCAGAGAAGATATACAAATGGACGAATAAGCACATGAAAA-----CC 1202
                          vv   i                 v -                -----i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCC-AATAAGCACATGAAAAGATGCTC 893

  chr2_130838655_   1203 AAAACCACAATGAGG 1217
                           v i  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (72 / 36)
Gap_init rate = 0.02 (16 / 751), avg. gap size = 3.19 (51 / 16)  


 601 22.13 0.00 0.82  chr2_130871629_130873770      455   576 (1566)    L1M4_orf2#LINE/L1        1   121 (787)  

  chr2_130871629_    455 TGGAAAGATATTCTGTGTTCACGGATGGGAAAACTCGATATAGTTAAGAT 504
                                    i ii      i    v    i   ii    v        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_130871629_    505 GACAATACTACCCAATGTGATCTAAAAATTCTGTGTAATCTCTATCCAAA 554
                          i       v     vv       v i    vii i    i     v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_130871629_    555 TCTTAATGGCATTTTTTTGCAG 576
                           ii iiv  -i          
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAG 121

Transitions / transversions = 2.00 (18 / 9)
Gap_init rate = 0.01 (1 / 121), avg. gap size = 1.00 (1 / 1)  

3479 17.83 4.29 0.67  chr2_130871629_130873770      905  1650 (492)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr2_130871629_    905 ATTCTGAAATTCATTTGGAATTTCAAAGGACCCTGATTAGCTAAAACAAT 954
                           i  i        v     v v   i      v  v    i        
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_130871629_    955 CTTGGAAAA------C----TTGGAGGATCCACATTTCTTGATTTCAAAA 994
                             i    ------ ----        ii    i   iii         
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_130871629_    995 CTTACTACAAAACTACAGTAATCAAAA--GTGTGGTACTGGCATAAGGAC 1042
                                    i             i --                    i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_130871629_   1043 AGAAATATAGACCAATGAAATAGAATACAAAGCCCAGCAATAAACCCTCA 1092
                            v       i     i        vv i  i    v         vi 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_130871629_   1093 CATTGATTTTCAACTGATTTTCTACTATACTGTCAAGACCATTGAATGGG 1142
                             v  vv    i        v  v viv  i          v      
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_130871629_   1143 -----AACAGTCTTACTAACAAATGGTACTGAGAAAACTAGATATCCATA 1187
                         -----  i      vii          i   i  v    i    ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_130871629_   1188 TGCAAAAAAATGAAATTGGACCCTTACCTCACCTCACATACAAATATCAA 1237
                                i      i        i        vi  i       v  i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_130871629_   1238 CTCAAAACATATCAAAGACCTAAACGTAAAAGCTAAAACTACAAAATTCT 1287
                                iiv    ?         i    i           i    i   
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_130871629_   1288 TAG--GAAAAAATAGGAAAGAATCCTCATGAC-TTGAATTTGGCAATAAT 1334
                            --     v     ?ivi    i  i    -   ii  v      ii 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_130871629_   1335 TGCTTAAACATGACCACAAAAGCATG-GCAGCAAAAGAAAAAATAGATAA 1383
                          v    i i     vv        ii-   i                   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_130871629_   1384 ATCAGATTCCATCAAAATTTAAA-CATTAGTGCATAAAAGGAAACTACAG 1432
                           ii  i i          v   - v  v    v v      v    ---
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA--- 682

  chr2_130871629_   1433 TATCAACAGAGTAAAAAGATAATTCATGGAATGGCAGAAAGT-TT--CAA 1479
                         --    v i   i      i  ii  ii      v     i -  --   
  L1M4_orf2#LINE/    683 --TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_130871629_   1480 ATCATGTATCTGTTAAGTGATTAATATCTGGAATATACAAA-AATTCCTA 1528
                              i      v    v  i vi    ii       i   -  i  i  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_130871629_   1529 CAGCTGAACAA-AAAAATTCAA-----CCAAATTAACACTGGGCAAGGGA 1572
                           i  v  i  -     vv   -----    v ?  v v       i   
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_130871629_   1573 TTTGCATAGACGTTTCTCCAAAGAAGATATACAAATAGACAACAAGCACA 1622
                             v      i                        i v   i       
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_130871629_   1623 TGAAAAGATGCCCAACATCATCAGTCAC 1650
                                    i        ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (81 / 48)
Gap_init rate = 0.02 (14 / 773), avg. gap size = 2.64 (37 / 14)  


2234 26.35 8.12 1.29  chr2_130939942_130942176      895  1744 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_130939942_    895 TGAAAATACATCCTATGTTCATGGACTGAAAGAACTGATATAGTGAAAAT 944
                           i   v i    i           i  i    vi i    v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_130939942_    945 GACCATAGTGCCCAAAGCAGTCTACACATTCTATACAATACCTACCAAAG 994
                          i v   v v      viii      v    v ii    v    i    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_130939942_    995 TACCAA-TGTCATTCTTCACAGAATTATTT-TAAAATG---CTGACATTC 1039
                          v   i-  i -  i  ii     --   v-i  iv  ---  i v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chr2_130939942_   1040 ATGTAGAACCACAAAAGAGCCTGAACAGCAACAGACATACCAAGCAAAAG 1089
                           i i   vii   ii  v  v   i   v - i   - i vv v     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCA-AAACA-ATCTTGAAAAAG 195

  chr2_130939942_   1090 --GAACAAATATGTTGGCA---TCACATTACCTGACTTCAAATGATACTC 1134
                         --       ---     vi---     i v  ii i      vvv    v
  L1M4_orf2#LINE/    196 AAGAACAAA---GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_130939942_   1135 TAAGACCACAGTAACAGAAGCAGCGTGGTACTCGTATAAAAACAGATACA 1184
                         i  ii i       ivi ii   i        v i    ii i   i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_130939942_   1185 TAGATCAATGGAACAGAACAGACAACTCAGAAATAAAGCCACTACA---- 1230
                                      i    iv  v iii          v   -    ----
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTA 341

  chr2_130939942_   1231 --ACCAAGTGATCTCTGAGCAAGGATACAAAAAC-ATACACTGGAGAAAG 1277
                         --ii   v    i ii  -     i i v  i  -  v  v   i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_130939942_   1278 TACAGGTTATTCAATAAATGGTGCTGGGAAAAAAAGATAGCCACATGTGG 1327
                         v i  vi v     i              v  vvi    ?       iii
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_130939942_   1328 AAGAATGAAACTGGATCTCTATCTCTCACCATATACAAAAATTAATTCAA 1377
                                  ii    i i   i   v                   i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_130939942_   1378 GATGGATGAAAGGCCTAAACCTAAGACCT--------------------- 1406
                         i      v ?  i      iv     v  ---------------------
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_130939942_   1407 GAAAACAT---------------TGGCCT------AGGCAAAGGATTTAT 1435
                                 ---------------  i   ------      v  -   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCT 589

  chr2_130939942_   1436 GAGGAA-GACCCTAAAAGCAAATCCAACAAAAATGTAAATAAATAAATAA 1484
                         v  iv -   v i       v vv        iviv     i      vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_130939942_   1485 GACCTAATTAAACTAAAAAGCTTCAGCACAGCAAAAGAAATAATCA---- 1530
                            i v  i   v v    i   iv ii vv    i  v iv    ----
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_130939942_   1531 --TCAAACAACAACTTATACAATGGGA--AAAT-TTTGAAAATTATGACG 1575
                         -- v   vi     ii i v       --    -    v    i  ivvv
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_130939942_   1576 CTAACAAACGACTAATATCTATAACCTACAAGAAACTCAAACAAATCAAC 1625
                           i i  iv    vi    i v  iv  i  ii     vv    v    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_130939942_   1626 AGGAAAAACGCAAATAATTCCATTGGAAAGTGGCCAAATTACATGAATAG 1675
                          iv     vi       ii v   ?i   i   v    vv iv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_130939942_   1676 ACATTTCTCAAAAGAAGAGGTACAAACGGTAAACAAGCATATAAAAACAT 1725
                                  v        vi      i  iv  i     i  i    v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_130939942_   1726 GCTAAATATCTCTAATCAT 1744
                            v  i   v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (128 / 93)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.64 (80 / 22)  


2234 26.35 8.12 1.29  chr2_131245180_131247414.rev      895  1744 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_131245180_    895 TGAAAATACATCCTATGTTCATGGACTGAAAGAACTGATATAGTGAAAAT 944
                           i   v i    i           i  i    vi i    v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_131245180_    945 GACCATAGTGCCCAAAGCAGTCTACACATTCTATACAATACCTACCAAAG 994
                          i v   v v      viii      v    v ii    v    i    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_131245180_    995 TACCAA-TGTCATTCTTCACAGAATTATTT-TAAAATG---CTGACATTC 1039
                          v   i-  i -  i  ii     --   v-i  iv  ---  i v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chr2_131245180_   1040 ATGTAGAACCACAAAAGAGCCTGAACAGCAACAGACATACCAAGCAAAAG 1089
                           i i   vii   ii  v  v   i   v - i   - i vv v     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCA-AAACA-ATCTTGAAAAAG 195

  chr2_131245180_   1090 --GAACAAATATGTTGGCA---TCACATTACCTGACTTCAAATGATACTC 1134
                         --       ---     vi---     i v  ii i      vvv    v
  L1M4_orf2#LINE/    196 AAGAACAAA---GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_131245180_   1135 TAAGACCACAGTAACAGAAGCAGCGTGGTACTCGTATAAAAACAGATACA 1184
                         i  ii i       ivi ii   i        v i    ii i   i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_131245180_   1185 TAGATCAATGGAACAGAACAGACAACTCAGAAATAAAGCCACTACA---- 1230
                                      i    iv  v iii          v   -    ----
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTA 341

  chr2_131245180_   1231 --ACCAAGTGATCTCTGAGCAAGGATACAAAAAC-ATACACTGGAGAAAG 1277
                         --ii   v    i ii  -     i i v  i  -  v  v   i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_131245180_   1278 TACAGGTTATTCAATAAATGGTGCTGGGAAAAAAAGATAGCCACATGTGG 1327
                         v i  vi v     i              v  vvi    ?       iii
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_131245180_   1328 AAGAATGAAACTGGATCTCTATCTCTCACCATATACAAAAATTAATTCAA 1377
                                  ii    i i   i   v                   i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_131245180_   1378 GATGGATGAAAGGCCTAAACCTAAGACCT--------------------- 1406
                         i      v ?  i      iv     v  ---------------------
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_131245180_   1407 GAAAACAT---------------TGGCCT------AGGCAAAGGATTTAT 1435
                                 ---------------  i   ------      v  -   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCT 589

  chr2_131245180_   1436 GAGGAA-GACCCTAAAAGCAAATCCAACAAAAATGTAAATAAATAAATAA 1484
                         v  iv -   v i       v vv        iviv     i      vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_131245180_   1485 GACCTAATTAAACTAAAAAGCTTCAGCACAGCAAAAGAAATAATCA---- 1530
                            i v  i   v v    i   iv ii vv    i  v iv    ----
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_131245180_   1531 --TCAAACAACAACTTATACAATGGGA--AAAT-TTTGAAAATTATGACG 1575
                         -- v   vi     ii i v       --    -    v    i  ivvv
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_131245180_   1576 CTAACAAACGACTAATATCTATAACCTACAAGAAACTCAAACAAATCAAC 1625
                           i i  iv    vi    i v  iv  i  ii     vv    v    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_131245180_   1626 AGGAAAAACGCAAATAATTCCATTGGAAAGTGGCCAAATTACATGAATAG 1675
                          iv     vi       ii v   ?i   i   v    vv iv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_131245180_   1676 ACATTTCTCAAAAGAAGAGGTACAAACGGTAAACAAGCATATAAAAACAT 1725
                                  v        vi      i  iv  i     i  i    v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_131245180_   1726 GCTAAATATCTCTAATCAT 1744
                            v  i   v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (128 / 93)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.64 (80 / 22)  


3054 15.52 7.20 0.48  chr2_131342956_131344572      501  1125 (492)    L1M4_orf2#LINE/L1      242   908 (0)  

  chr2_131342956_    501 ACAAAGCTACAGTAATCGAAACAGTGTGGTAC------AAAGACAGACAT 544
                                          i i            ------  i  i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_131342956_    545 ACAGACCGATAAAATAGGATAGAGAGCCCAGAAACAAATCCTCAGGTATT 594
                          i   i i  ii     i  v     i       i   i  -- vii   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC--ATACATT 339

  chr2_131342956_    595 TA--GTCAAATGATTTTCAACAAGGATGCCAAGACCATTCAATGGAGAAA 642
                           --     v        i      i                   i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_131342956_    643 GGACAGTCTTTTCAACAAATTATGCTGGGAAAACTGAATAGTCACAT-CA 691
                          i i                vi        v     i   ?i     -  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_131342956_    692 AAA-AATGAAACTGGACTCTTACCTTCTGCCATATACAAAAATTAACTAA 740
                            -      ii     i i     ivii                   v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_131342956_    741 AAATTGATCG-------------AAGAGCTAAAAGTATAAAACTTTTACA 777
                             v    i-------------           v         i   v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_131342956_    778 AGAAAACCTAGA---AAATCTTTGTGACATTGGATTTTGCAATGATTTAT 824
                                v   i---       i     v    i  vv      i   v 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_131342956_    825 TTGATATGACACCAAAAGTTCAAGAAATAATACACAAAATAAATAACCTG 874
                          v                iv    v  i  v v v      i    vi  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_131342956_    875 GACTTTATCAAAATTAA-------TG-------AAAACCACTCATCAAGA 910
                              i           -------  -------  iiv    -       
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGA 688

  chr2_131342956_    911 --GTGACAAGGCAATCCACAGAATGAGAAAAAATATTTGCAAATCATCTA 958
                         --    v   i   i          i  i                  v  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_131342956_    959 CTGGGTAGGGGATTAACATCCAGAATATATAAACAACTCCTAGAACTCAA 1008
                         iiv i  i    i vii                v     i  v       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_131342956_   1009 CAATAAA--GACAAACAATCTAATT-AAAAATGGAGAAAGGACTTGAATA 1055
                         i      --      i  i i    -        iv      i       
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_131342956_   1056 GATACTTCTCCAAAGAATATATACAAATGGCCAATAAGCATATGAAAAGA 1105
                           i i            v                      i         
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_131342956_   1106 TGCTCAATATCACTAATCAT 1125
                                i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (65 / 31)
Gap_init rate = 0.02 (13 / 667), avg. gap size = 3.69 (48 / 13)  


 312 27.57 19.46 0.00  chr2_131383556_131385511.rev      113   297 (1659)    L1M4_orf2#LINE/L1      688   908 (0)  

  chr2_131383556_    113 AAAACAAAAAGAAAACCCATAGATAGGAAGAAAATA---GTAAATTA--- 156
                            iii      v      i   vv  i        --- i    i ---
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_131383556_    157 ----------------GTATCCAGAATGCATAAAGAATTTACAAAAATCA 190
                         ----------------           ii        i ivi v  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_131383556_    191 ATAA---------GAATA--TTAA---AAAAATGGATCAAAGACATGAAA 226
                             ---------i    --ii  ---        iiv  i  iv    v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_131383556_    227 AAGCATTTCACAGATGAGGAAGTGTGGATGGGCAGGAAGTACCTAAAAAG 276
                          ii      v vi v  i  vi iiii    v  iv   i  v i     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_131383556_    277 ATGCTTTGCCTCATTAGTCAC 297
                              ivi v   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (33 / 18)
Gap_init rate = 0.02 (5 / 221), avg. gap size = 7.20 (36 / 5)  

4032 18.00 4.71 1.18  chr2_131383556_131385511.rev      607  1456 (500)    L1M4_orf2#LINE/L1        1   880 (28)  

  chr2_131383556_    607 TGGAAGGACATCTTATGTTCGTGAATTGGAACACTTAATGTTGTTAAGAT 656
                              i  i   ii      i  i       v       i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_131383556_    657 GGAAATACTCTCCAAACTGATCTATAGATTCATCACAATCCCTATCAAAA 706
                           v       i     i       i       v i               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_131383556_    707 TCTCTGCTAGCTTTTTCGAAGAAATTGACAAGTTGAACATGAAGTTCATG 756
                           i v   iv      i v             i   v v i  i     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_131383556_    757 TGGAAA-GTTAGGGACCCAGAATAGCCAAAACAATTTTGAAA-------- 797
                               - iv                         i      --------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_131383556_    798 --------GAAAATTCATACCTCCCTATTACAAA-CCTACTACAAAGCTG 838
                         --------  ii i   i  i    v   v    - i            i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_131383556_    839 TAGTAATCAAGATAGTGTGTTAATGGTATAGGGAGAGACACA-AGATAAA 887
                         i           i      v  v   i   i   v     i -    v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_131383556_    888 TGGAATCAAATGGAACCAAAGGTTCAAATAGAAACCTTCACAATTATGGT 937
                               vi   v  -----ii  i  i v v     ivi   v       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGA-----GAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_131383556_    938 AAAGTAATTTTTGACAAGTGGGCAAAGACAATTCAATGAAGGAAAGAATA 987
                         v  v i     i      v v  v     v        -i          
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATA 394

  chr2_131383556_    988 TTCTTTTCAATAAATGGTGCTGGGACAA-TGGATGTCCACAAGCAAAAGA 1036
                         v         i                 -     i?     v        
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_131383556_   1037 ATAATGTCATACCC-TACCTCAGACCATATACAAAAATTCCCTCTAAATG 1085
                           i v  iiv    -       v                vv   v     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_131383556_   1086 GATCATAGACATCAATGCGAGACCTAAAACTATCAAACTCTTAGAA---A 1132
                              ?    v v    ii   v          v            --- 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_131383556_   1133 ATATAGGAGTAAATCTTCATGAACTTGGGTTAAGCAATGGTTTCTTATAT 1182
                          i     ?          i   v         i              v  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_131383556_   1183 ATGGCACCCAAAGCATAGGCAACAAAAGAAAAAAACAGATACACTGAATG 1232
                            i    v      i i                -i     v i  i iv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACT 643

  chr2_131383556_   1233 TCATCAAA-TCGAAAGTTTTTGTTCATCAAAGAACACCATCAATAAAGTG 1281
                                 - ii   ii      v v      i    i     v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_131383556_   1282 AAAAGATAACCCACAAAATGAGA-AAAATATTTGCAAAATATGTATCTGA 1330
                               i        i    i  -              vi  i       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_131383556_   1331 TGAGAGTCTAGTAACCAACACATATTTTTAAAAACTCTTAAAATTCAGCA 1380
                          i  i v  v   v   iv i    ---v  i        v  i   ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATAT---AAAGAACTCTTACAACTCAATA 790

  chr2_131383556_   1381 GTAAGAAGACAAAATTCTCAGTGAAAAACCAGGCAAAGG-TTTGAATAAG 1429
                         i   i        vvv i  i v?    vii        -        ii
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_131383556_   1430 CATTTCTTCAA-------------GTGGTCAATACGCACA 1456
                                i   -------------i   i     v     
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

Transitions / transversions = 1.48 (89 / 60)
Gap_init rate = 0.02 (15 / 880), avg. gap size = 3.33 (50 / 15)  


2345 25.72 1.82 0.45  chr2_131401645_131403297.rev      501  1161 (492)    L1M4_orf2#LINE/L1      239   908 (0)  

  chr2_131401645_    501 ACTACAAGGCTACAGTAACCAAAACAGCATGGTACCGGTACAAAAACAGA 550
                                i          i   i    ii      i  i i  ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_131401645_    551 CACATACACCAATGGAACAGAATAGAGAACTCAGAAATAAGATCACATAT 600
                           i   v i        i     v    iii         ivi  i i  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_131401645_    601 CTACAACCATCTGATCTTTGACATACCTGACAAAAACAAGCAACAGGGAA 650
                         i  iiii  vi    i  i    vivv  v   i v  vv   ii     
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_131401645_    651 TGGATTCCCTATTTAATAAATGGTGCTGGGAGAACTGGCTAGCTATATGT 700
                         v i  vvi  v  i  i              v      v  ? i i   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_131401645_    701 AGGAGATTGAAACTGGACCCCTTCTTTACACCTTATACAAAAATTAACTC 750
                          ii   v    ii         v i i     v                 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_131401645_    751 AAGATGGATTAAAGACTTAAATGTAAAAGCCAAAACTATAAAAACCCTAG 800
                           i      i ?    i         i   i            vi i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_131401645_    801 AAGAAAATCTAGGCAGTA--CCATTCAGGACATAGGCACAGGCAAAAATT 848
                                iv    ?-   --i -   iv   v v  vvi      vii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_131401645_    849 TCAC-GATGAAAACGTCAAAAGCAATTACAACAAAAGCAAAAATTGACAA 897
                           vi-   - vi  ii        vvvi         v      v  i  
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_131401645_    898 ATGGGGTCTAATTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTATCA 947
                           v  iii v  i   v v  v i   i  ii vv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_131401645_    948 TCAGAGTGAACAGACATCCTACAGAATGGGAGAAATTTTTTGCAATCTAT 997
                         vv i      v     v  i               v v       vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_131401645_    998 CCATCTGGCAAAGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAAT 1047
                         vi     ii  i  v  vi          v  i  i     ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_131401645_   1048 TTACAAGAAAAA---AAACAACCCCATTAGAAAGTGGGCAAACAACATAA 1094
                         iv i  v     ---   i     v   ?i   i        vi iv i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_131401645_   1095 ACAGACACTTCTCAAAAGAAGACATTCATTTGGCCAG------CATGAAA 1138
                          i     i     v        i  v  vv      i------       
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_131401645_   1139 AAAGGCTCAACATCACTGATCAT 1161
                          i v           ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (99 / 67)
Gap_init rate = 0.01 (7 / 670), avg. gap size = 2.14 (15 / 7)  


 496 24.62 3.85 0.00  chr2_131561479_131563610.rev      501   630 (1502)    L1M4_orf2#LINE/L1        6   140 (768)  

  chr2_131561479_    501 AGATGTATGATGTTTCTAAACTG----ACTCCATACTGTTAAGATTTCAA 546
                             i viv     iv ii i  ----   iv   i         vv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_131561479_    547 TCCTCCCAAAACTGATCTACAGATTCAACACAATCCATATCAAAA-CTCA 595
                          v     v   i                 i      v        - i  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_131561479_    596 AGAGGATATTCTGTAGATACTGACAAGTTGATTCT 630
                         ivv vv v  i  i   v i       i    i  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 1.13 (17 / 15)
Gap_init rate = 0.01 (2 / 135), avg. gap size = 2.50 (5 / 2)  

2255 23.14 11.36 0.84  chr2_131561479_131563610.rev      928  1640 (492)    L1M4_orf2#LINE/L1      121   908 (0)  

  chr2_131561479_    928 GATATTGACAAGTTGGTTCTAAAATGTATATGAAAAGGCAAAAAAGA-AG 976
                           v         i  i i       vi     i   v    iii vv-  
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr2_131561479_    977 AAGAATTAAAACAATGTTGAAAAAGAAGAACAAAATTGGAGGACTCACAT 1026
                           v iii        v                  i              i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_131561479_   1027 -------------AACTGACT-TAAAACTACAGCA--------------- 1047
                         -------------    v   -i   i      i ---------------
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_131561479_   1048 ------------------------------TGGAACAGAAC--AGAG-CT 1064
                         ------------------------------     i    i--    - i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_131561479_   1065 AGAAATAGACCAACACAAATATAGACTGTTGTTTTTTGACAAAGGTACAA 1114
                                i   v i   vv   i v vi   v    i     i   i v 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_131561479_   1115 AGGAAATT-AATGGAGAAAAAA-AGTCTTTTTAACAAATGGTGCTATAAA 1162
                           ivv   -     i    i  -        i             ivi v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_131561479_   1163 AATTGGACATGCATATGCAAAAAAATGAACCTTCACTCTTATCTTGAACC 1212
                           i    i ?v  i        i      vi vv  i i  i  iiv   
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_131561479_   1213 TTA---AAAAATTAACTCAAAATAGATCATAGATCTAAGTACAAAATATA 1259
                         v  ---                 i     ?   i    i ii  i vv  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_131561479_   1260 AAACTGTAAAACCTTCTAGAAGGAAACAAACATAAAAGAAACTCTCTGTG 1309
                              i      ii -      i     ----  ii? v  v   ii   
  L1M4_orf2#LINE/    521 AAACTATAAAACTCT-TAGAAGAAAACA----TAGGNGTAAATCTTCGTG 565

  chr2_131561479_   1310 ACCTCAGGTTACATAAAGATTTCTGAGATGT-ACACCAAAAGTATGTTTT 1358
                             ii     vii  v i     v    i -          i iivviv
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_131561479_   1359 ATAAGACAGAGAGAT-GAAAAATTGGATTCCGTCAAAATTACAAACTTTT 1407
                          i  i v i i -  -  v        i i i         v        
  L1M4_orf2#LINE/    616 ACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_131561479_   1408 GTTCAGCAAAAGACACTATTA-GCAAGT-AAAACACAAGCCACAGACTAG 1455
                           v vv    i        i - v    -    v    v       v i 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_131561479_   1456 AATAAA-TATTTGCAAATCACATATCTAACAAAGTACTTGCACTCAGAAT 1504
                         i v   -             i      i i  i v     i ii      
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_131561479_   1505 ATATAAAGAACTCTCCAAATACAACAATAAGAAAACAAACAATCCAAT-A 1553
                                       ivv  iv   i     i  i     i  i     -?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_131561479_   1554 AAAATTATGT---GGGTCTG----GATGCTTCAACAAAGAAGATATGCAT 1596
                             v iv i---  i i  ----  iii   vv            i  v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_131561479_   1597 ATGCCAAACACCCACATGAAAAGATGCTCAGCATTAGGAGTTGC 1640
                            v v  i vv                  i   i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (102 / 59)
Gap_init rate = 0.03 (20 / 788), avg. gap size = 4.35 (87 / 20)  


 493 21.43 2.68 0.00  chr2_131609137_131611991.rev     1158  1269 (1586)    L1M4_orf2#LINE/L1        3   117 (791)  

  chr2_131609137_   1158 GAAAGACGTCCCATGTTCATAAATTGAAAGTCTTAATATATTTAAGATGA 1207
                               ii            ii    i   v        vv        i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_131609137_   1208 CAATACCACCTAAAGCAATCTGTGTATTCAATGCA-TTCCTATAAAAATC 1256
                               iv  i   vii    iiiv      i   - i     v      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_131609137_   1257 CAA--TGACTTTTTT 1269
                          v --  v       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT 117

Transitions / transversions = 1.67 (15 / 9)
Gap_init rate = 0.02 (2 / 115), avg. gap size = 1.50 (3 / 2)  

3653 17.95 2.60 2.72  chr2_131609137_131611991.rev     1556  2363 (492)    L1M4_orf2#LINE/L1      102   908 (0)  

  chr2_131609137_   1556 CCCAGTGGCATTTTTTTACACACATAGAAAAATTCATCATTAAAATTCAC 1605
                              iv  -i      i  v v  v  v  ii v   -i         i
  L1M4_orf2#LINE/    102 CCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATC-CTAAAATTCAT 149

  chr2_131609137_   1606 ATGGAATCTCAAGGGGTCCTGACTAGCCAAAATTATTTTGAAAAA----A 1651
                               viv      ii  v  v         iv  i        ---- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_131609137_   1652 ACAAAGTTGGAGGACCCGCATTTCCTGATTTCAAAACTTACTACAAAGTC 1701
                                        i i  i    ii                     ii
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_131609137_   1702 ACAATAATCAA-ATAATGTGGAAATGGCATAAGGATAGATATATAGACCA 1750
                            i       - i i     v v               i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_131609137_   1751 ATAGAACTGAATAGAGGATCCAGAAATAAACCCTCCCATATGTGGTCAAT 1800
                           i   iv    v   ii               viv   v i        
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_131609137_   1801 TGATTTTCGACAAAGGTGCTAACACTGTG----AGGGAAAAGACAGTCTT 1846
                                      i     i  v  ii v----i      ii i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_131609137_   1847 TACAGCGAACAGTGTTGGGA-AGCTGGATATCCAAATGCAAAATAATGAA 1895
                          v  i i  ii   i     - i       ?   v        v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_131609137_   1896 GTTAAACCCTTACCTAACAC---ACATAAAAATTAACTCAAAATGGA-CA 1941
                            ii    i     v    --- i i                    -  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_131609137_   1942 AAGTCCTAAATATAAAAGTTAAAACTATAATACTCTTAGAAGAAAACA-- 1989
                         ?  v       i   i  i           v                 --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_131609137_   1990 GGGG-AAAGCTTTACAGCAGTGAATCTGTAAATAATTTCTTGGATATAAG 2038
                           ? -   v   iiiii vv  ii iv vv   ii      i     i v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_131609137_   2039 ACCAAAAGCACAGGCAACAGGA-AAAAAATAGGTAAATTGAACTGTATCA 2087
                                     i      ii -         i       i   vi    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_131609137_   2088 AAATTTAAATCTTTTGTGCATTAAAGGACAGTATCAAGAGAG--AAAAGG 2135
                              v   v         v i        v        i  --     i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_131609137_   2136 CAACCCATAGAATGGAAGAAAATATCTGCAAATCATATATCTGATAAGGG 2185
                                i       i         i                        
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_131609137_   2186 AATAACATCCAGAATACATTTTTGAAAAACTCCCACAACTCAAAAAACAA 2235
                          v vii          i  ----i  i     ii         v  -i  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATAT----AAAGAACTCTTACAACTCAATAA-TAA 794

  chr2_131609137_   2236 AACAAACAAAAAACTCAAAAACTAGCCCAACTCAAAAATAGGCAAAGGAT 2285
                           - i     ------------  i     i ?      i          
  L1M4_orf2#LINE/    795 AA-AGACAAA------------TAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_131609137_   2286 TTGAATAGACATTTCTTCAAAGAAGACATACGAATGGTCAATA-GCATAT 2334
                                         i         i    i     i     -   i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_131609137_   2335 AAATAAGGACATACGACATCACTAATCAT 2363
                         i  -- i  iiiv i      ????????
  L1M4_orf2#LINE/    882 GAA--AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.36 (99 / 42)
Gap_init rate = 0.02 (18 / 807), avg. gap size = 2.39 (43 / 18)  

 809 26.65 0.26 10.82  chr2_131609137_131611991.rev     2477  2855 (0)  C L1M4_orf2#LINE/L1   (541)   367    29  

C chr2_131609137_   2855 GAGGGCTCAACAGAGTAAAGATTTCAGTTGTCTCCGAGTTGATACATAGG 2806
                           i i  i  i vv  v     vv  i vv  i  i i     vi i  i
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

C chr2_131609137_   2805 TTTAATGTAATTCCTATCAAAATCTCAGCAGGATTTTTTTCTAGCTATAG 2756
                           i  i i   i            i    -v vi      vi  vv  v 
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGC-TGCCTTTTTTGCAGAAATTG 127

C chr2_131609137_   2755 ACAAGATTATTCTAAAATTTATATGGAAAGGCAAAGGAACAGGAATAGCT 2706
                              v v  i        i         v    i   v vi       i
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

C chr2_131609137_   2705 AAAACAGGAGGCCAGGGGAGGAAACAAAAAAGAATAGCTAAAACATTTCT 2656
                               --------------------------------------  i iv
  L1M4_orf2#LINE/    178 AAAACA--------------------------------------ATCTTG 189

C chr2_131609137_   2655 GAAAAGAGGAATTAAGTAAGATGAACCACTCTACCAAATTTCAAGAATTA 2606
                         i      i   iv    vi  v  vi   v  v  v        i v   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

C chr2_131609137_   2605 TTTTATACCCACAGAAAACAAGACTATTTGGTA-TGAGAGGTGGATGAAC 2557
                         i vi v v i    v  v      vi v     -  iv viv    ii  
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

C chr2_131609137_   2556 ACATTGATCAATGGGACAGAATAGAAAATCCAGAAATAGTGCCAAACAAG 2507
                          i  v         i i     v  i i          ivv   v   vv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

C chr2_131609137_   2506 TACAGCCAACCAGTTGTTTAAACAATTGTG 2477
                           ii i   iiii  --  vi    vv   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATT--TTCGACAAGGGTG 367

Transitions / transversions = 1.10 (53 / 48)
Gap_init rate = 0.01 (4 / 339), avg. gap size = 10.50 (42 / 4)  


 613 21.31 0.00 0.82  chr2_131751555_131756139.rev     2896  3017 (1568)    L1M4_orf2#LINE/L1        1   121 (787)  

  chr2_131751555_   2896 TGGAAAGATATTCTGTGTTCACGGATGGGAAAACTCGATATAGTTAAGAT 2945
                                    i ii      i    v    i   ii    v        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_131751555_   2946 GACAATACTACCCAAAGTGATCTAAAAATTCTGTGTAATCTCTATCCAAA 2995
                          i       v      v       v i    vii i    i     v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_131751555_   2996 TCTTAATGGCATTTCTTTGCAG 3017
                           ii iiv  v   -       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAG 121

Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.01 (1 / 121), avg. gap size = 1.00 (1 / 1)  

3502 17.43 4.42 0.80  chr2_131751555_131756139.rev     3348  4093 (492)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr2_131751555_   3348 ATTCTGAAATTTATTTGGAATTTCAAAGGACCCTGATTTAGCTAAAACAA 3397
                           i  i     i  v     v v   i      v  v -   i       
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT-AGCCAAAACAA 184

  chr2_131751555_   3398 TCTTGGAAAA------C----TTGGAGGATCCACATTTCTTGATTTCAAA 3437
                              i    ------ ----        ii    i   iii        
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_131751555_   3438 ACTTACTACAAAACTACAGTAATCAAAA--GTGTGGTACTGGCATAAGGA 3485
                                     i             i --                    
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_131751555_   3486 CAGAAATATAGACCAATGAAATAGAATACAAAGCCCAGCAATAAACCCTC 3535
                         i   v       i     i        vv i  i    v         vi
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_131751555_   3536 ACATTGATTTTCAATTGATTTTCTACTATACTGTCAAGACCATTCAATGG 3585
                              v  vv             v  v viv  i                
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_131751555_   3586 G-----AACAGTCTTACTAACAAATGGTACTGAGAAAACTAGATATCCAT 3630
                          -----  i      vii          i   i  v    i    ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_131751555_   3631 ATGCAAAAAAATGAAATTGGACCCTTACCTTACCTCACATACAAATATCA 3680
                                 i      i        i     i  vi  i       v  i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_131751555_   3681 ACTCAAAATGTATCAAAGACCTAAACGTAAAAGCTAAAACTACAAAATTC 3730
                                   v    ?         i    i           i    i  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_131751555_   3731 TTAG--GAAAAAATAGGAAAGAATCCCCATGAC-TTGAATTTGGCAATAA 3777
                             --     v     ?ivi    ii i    -   ii  v      ii
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_131751555_   3778 TTGCTTAAACATGACCACAAAAGCATG-GCAGCAAAAGAAAAAATAGATA 3826
                           v    i i     vv        ii-   i                  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_131751555_   3827 AATCAGATTCCATCAAAATTAAAA--CATTATGCATAAAAGGAAACTACA 3874
                            ii  i i              --iv  i   v v      v    --
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-- 682

  chr2_131751555_   3875 GTATCAACAGAGTAAAAAGATAATTCACAGAATGGCAGAAAGT-TT--CA 3921
                         ---    v i   i      i  ii          v     i -  --  
  L1M4_orf2#LINE/    683 ---TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_131751555_   3922 AATCATGTATCTGATAAGTGATTAATATCTGGAATATACAAA-AATTCCT 3970
                               i           v  i vi    ii       i   -  i  i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_131751555_   3971 ACAGCTGAACAA-AAAAATTCAA-----CCAAATTAACACTGGGCAAGGG 4014
                            i  v  i  -     vv   -----    v ?  v v       i  
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_131751555_   4015 ATTTGCATAGACGTTTCTCCAAAGAAGATATACAAATAGACAACAAGCAC 4064
                              v      i                        i v   i      
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_131751555_   4065 ATGAAAAGATGCCCAACCTCATCAGTCAC 4093
                                     i    v   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (81 / 45)
Gap_init rate = 0.02 (15 / 773), avg. gap size = 2.60 (39 / 15)  


2336 25.93 7.48 1.40  chr2_131850422_131852661.rev      894  1749 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_131850422_    894 TGAAAATACATCTTATGTTCATGGACTGAAAGAACTGATATAGTGAAAAT 943
                           i   v i   ii           i  i    vi i    v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_131850422_    944 GACCATAGTGCCCAAAGCAGTCTACACATTCTATACAATACCTACCAAAG 993
                          i v   v v      viii      v    v ii    v    i    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_131850422_    994 TACCAA-TGTCATTCTTCACAGAATTATTT-TAAAATG---CTGACATTC 1038
                          v   i-  i -  i  ii     --   v-i  iv  ---  i v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chr2_131850422_   1039 ATGTAGAACCACAAAAGAGCCTGAACAGCAACAGACATATCAAGCAAAAG 1088
                           i i   vii   ii  v  v   i   v - i   -   vv v     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCA-AAACA-ATCTTGAAAAAG 195

  chr2_131850422_   1089 --GAACAAATATGTTGGCA---TCACATTACCTGACTTCAAATGATACTC 1133
                         --       ---     vi---     i v  ii i      vvv    v
  L1M4_orf2#LINE/    196 AAGAACAAA---GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_131850422_   1134 TAAGACCACAGTAACAGAAACAGCGTGGTACTCGTATAAAAACAGATACA 1183
                         i  ii i       ivi i    i        v i    ii i   i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_131850422_   1184 TAGATCAATGGAACAGAACAGACAACTCAGAAATAAAGCCACTACA---- 1229
                                      i    iv  v iii          v   -    ----
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTA 341

  chr2_131850422_   1230 --ACCAAGTGATCTCTGAGCAAGGATACAAAAAC-ATACACTGGAGAAAG 1276
                         --ii   v    i ii  -     i i v  i  -  v  v   i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_131850422_   1277 TACAGGTTATTCAATAAATGGTGCTGGGAAAAAAAGATAGCCACATGTGG 1326
                         v i  vi v     i              v  vvi    ?       iii
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_131850422_   1327 AAGAATGAAACTGGATCTCTATCTCTCACCATATACAAAAATTAATTCAA 1376
                                  ii    i i   i   v                   i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_131850422_   1377 GATGGATGAAAGGCCTAAACCTAAGACCT--------------------- 1405
                         i      v ?  i      iv     v  ---------------------
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_131850422_   1406 GAAAACAT---------------TGGCCT------AGGCAAAGGATTTAT 1434
                                 ---------------  i   ------      v  -   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCT 589

  chr2_131850422_   1435 GAGGAA-GACCCTAAAAGCAAATCCAACAAAAATGAAAATAAATAAATAA 1483
                         v  iv -   v i       v vv        ivi      i      vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_131850422_   1484 GACCTAATTAAACTAAAAAGCTTCAGCACAGCAAAAGAAATAATCATCAG 1533
                            i v  i   v v    i   iv ii vv    i  v iv    vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_131850422_   1534 AGTAAAACAACAACTTATACAATGGGA--AAAT-TTTGAAAATTATG-AT 1579
                            i   vi     ii i v       --    -    v    i  i-  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_131850422_   1580 GCTAACAAAGGACTAATATCTATAACCTACAAGAAACTCAAACAAATCAA 1629
                         -  i i  i     vi    i v  iv  i  ii     vv    v    
  L1M4_orf2#LINE/    740 -CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_131850422_   1630 CAGGAAAAACGCAAATAATTCCATTGGAAAGTGGCCAAATTACATGAATA 1679
                         i iv     vi       ii v   ?i   i   v    vv iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_131850422_   1680 GACATTTCCCAAAAGAAGATGTACAAACGGTAAACAAGCATATAAAAACA 1729
                                 i v         i      i  iv  i     i  i    v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_131850422_   1730 CGCTAAATATCTCTAATCAT 1749
                         i   v  i   v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (131 / 88)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.30 (76 / 23)  


3135 28.08 0.33 0.33  chr2_131933037_131939470.rev     5035  5942 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_131933037_   5035 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5084
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_131933037_   5085 GGCCATACTGCCCAAGGTCATTTATAGATTCACTACAATCCCCATCAAGC 5134
                            v     v     iv v  i  i       vii       i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_131933037_   5135 TGCCAATGACTTTCTTCACAGAATTGGAAAAACCTACTGTAAAGTTCATA 5184
                          v   iivi i  i  ii     v v  v  i iv iiv    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_131933037_   5185 TGAAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTGAGCCAAAAGAA 5234
                           i  viiv  ii  v  v v  v     iv     i   ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_131933037_   5235 CAAAGCAGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5284
                              iv     vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_131933037_   5285 CAGTAACAAAAACAGCATGGTACTGGTGCCAAAACAGAGATATAGATCAA 5334
                               iv  i    ii         iiiv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_131933037_   5335 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCTTAGCTACAACCAT 5382
                              i    i--    i  --        vv iiivi vi  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_131933037_   5383 CTAATATTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5432
                         i i  v  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_131933037_   5433 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5482
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_131933037_   5483 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5532
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_131933037_   5533 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5582
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_131933037_   5583 AGGCA-ATACCATTCAGGACATAGGCAGGGGCAAGGACTTCATGTCTAAA 5631
                            ?i- v i -   iv   v v  vvvi     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_131933037_   5632 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACCAATGGGATCTAAT 5681
                                     vvi          vv     v  iv   v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_131933037_   5682 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5731
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_131933037_   5732 GGCAACCTACAGAATGGGAGAAAATTTTCACAACCTACTCATCTGACAGA 5781
                          i     i                 v  ii   vii ivi      i ii
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_131933037_   5782 GGGCTAATATCCAGAATCTACAATGAACTCCAATAAATTTACAAGAAAAA 5831
                           i  vi          v  i  v      iv i  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_131933037_   5832 AACAAACAACCCCATCAAAAACTGGGCGAAGGATATGAACAGACACTTCT 5881
                         i     i     v  i?    v     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_131933037_   5882 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGTTCATCA 5931
                          v        i  vi viii     v ii          i   i   v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_131933037_   5932 TCACTGCCCAT 5942
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.39 (146 / 105)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3181 26.62 0.44 0.99  chr2_131964707_131970498     4388  5300 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_131964707_   4388 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4437
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_131964707_   4438 GGCCATACTGCCCAAGGTCATTTATAGATTCAATGCCATCCCCATCAAGC 4487
                            v     v     iv v  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_131964707_   4488 TACCAATGACTTTATTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4535
                          v   iivi i  v  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_131964707_   4536 TATGAAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTGAACCAAAAG 4585
                             i  viiv  ii  v  v v  v     iv     i    vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_131964707_   4586 AACAAAGCCAGAGGCATCATGCTACGTGACTTCAAACTATACTACAAGGC 4635
                                iii    vv   ii  v vii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_131964707_   4636 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATA 4685
                                 i   i    ii         i iv ii i   v        v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_131964707_   4686 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 4733
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_131964707_   4734 ATCTGATCTTTGACAAACCTGGGAAAAACAAGCAATGGGGAAAGGATTCC 4783
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_131964707_   4784 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4833
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_131964707_   4834 GAAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4883
                            ii    i i  v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_131964707_   4884 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTGAAACCCAAG 4933
                          i ?    i    i  v   v       i      - i  v i ----  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGA----AG 541

  chr2_131964707_   4934 AAAACATAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 4983
                                   ?i v viv   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_131964707_   4984 TCTAAAACACCAAAAGCAATGGCAAGAAAAGCCAAAATTGACAAATGGGA 5033
                         vv  vi            vvi    v     vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_131964707_   5034 TGTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5083
                         iv v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_131964707_   5084 TGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCCACTCATCT 5133
                             v  i     i   i             v  i    vi  ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_131964707_   5134 GACAAAGGGCTGATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 5183
                           i  i  i  vi          v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_131964707_   5184 GAAAAAAACAAACAAGCCCATGAAAAAGTGGGCGAAGGACATGAACAGAC 5233
                         v     i     i  v  v  v?    i     i     iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_131964707_   5234 ACTTCTCAAAAGAAGACATCTATGCAGCCAAAAAACACATGAAAAAATGC 5283
                          i     v        i  vi viii     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_131964707_   5284 TCACCATCACTGGCCAT 5300
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (137 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2130 27.89 3.85 0.93  chr2_132143078_132144820.rev      499  1251 (492)    L1M4_orf2#LINE/L1      134   908 (0)  

  chr2_132143078_    499 TAATTCTAAAATTCATATGGAATCAAAACAGAGCCCACATAGCCAAAGCA 548
                          i  i                 viiv  vi  v  viv         i  
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr2_132143078_    549 AGACTAAGCAGAAAGAACAAATCTGGAGGCATTACATTACCTGACTTCAA 598
                          vvi i iv ii         vi      vv i   i v  ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_132143078_    599 TCTATACTACAAGGCCATAGTCAGCAAAACAGCATAATACTGGTATAAAA 648
                         vviv        i  i i   v v   i    ii ii      i    ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_132143078_    649 ATAAGCACATAGACCAATGGAATAGAATAGAGAACCCAGAAACAAACCCA 698
                            ii  i     i              v    ii       i       
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_132143078_    699 AATACTTACAGCCAACTGGTCTTTGACAAAGCAAACAACAATATAAAGTG 748
                         v i i   ii i   i  i i  i     i vviv   v vi  vv i  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_132143078_    749 GGGAAAGGACACCCTACTCAACATATGGTGCTTGGATAATTCGCAAGCTA 798
                                i i vi  vi      v        v   i  i v vv ? i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_132143078_    799 CATCCCAAGAAATGAAACTGGATCCCCATCTCTTACCTTATACAAAAGTC 848
                            v v  ii      ii    i   i i   vi   v         i i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_132143078_    849 AACT------------------TAAATCTGAGACCTGAAACCATAAAAAT 880
                             ------------------     v i   v  i    i      v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_132143078_    881 TCTACAAGGTAACATTGGAAAACCCCTTCTACACATTGGCTTAGGCAGAG 930
                         ii  v   iv     v  ?iv vvi    vvv  v    v       iv 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_132143078_    931 ACTTCATGACCAAGAACCCAAAAGCAAGTGTGACAACAAAATGAAGATAA 980
                         ii   v iivi v  vv         viv ii    v i  --  i   i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA--AAAATAG 631

  chr2_132143078_    981 ACAGGTGAGACTTAATTAAGCCAAAAAGTTTCTGCACAGCAAAAGAAACA 1030
                          i ii vi     v  i  iviv    ii  i  ii vv    i  v  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_132143078_   1031 ATTAGCAGAGTAAACAGACAACCCACAGAAAGGGAGAAAA-ATCTTCACA 1079
                           i iv i   i  v               v         -  i v  - 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-A 730

  chr2_132143078_   1080 ATCTATACATCTGACAAAGGACTAATATCCAGAATCTACAAGGTACTC-- 1127
                            -   i      i  i     vi          v  i  i v    --
  L1M4_orf2#LINE/    731 ATC-ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_132143078_   1128 --AAATTAGCAGGAAAAAAAACCAAT--CCC--TTCAAATAATGGGCTAA 1171
                         --  v i ii iv     i - v   --   --  ?   -       v  
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAA-AATGGGCAAA 827

  chr2_132143078_   1172 ATACTTGAATAGACAATTCTCAAAAGGAGATATAAAAAATGGCCAACAAG 1221
                         iv i           v     v    i       v   -       i   
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAG 876

  chr2_132143078_   1222 TA--TGAAAAAATGCTCATCATCACTAATGAT 1251
                         i --      i       v     ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (122 / 85)
Gap_init rate = 0.02 (12 / 775), avg. gap size = 3.00 (36 / 12)  


2796 27.26 1.97 0.93  chr2_132160648_132163109     1101  1962 (500)    L1M4_orf2#LINE/L1        1   871 (37)  

  chr2_132160648_   1101 TAGAAAAACATCCCATATTTATGGATTTGAAAAATTAATATTGTCAAAAT 1150
                          i    i i       i  i       v   i v          i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132160648_   1151 TTCAATGCTAACAAAAGCAATCTGCAGATTAAATGCAATCACTATCAAAA 1200
                         vv    i  vv v   vii    i      v  i      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_132160648_   1201 TCCAA--TGCCATTCTTCACAGAAATAGAAAAATTAGTCCTAAAATCTGA 1248
                            v --    -  i  ii       v  v  ii ii         iiiv
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_132160648_   1249 GTGGAACCACAAAAGACGCTGAAAAACCAAAGCAATCTTGAGCAAAAAGA 1298
                         i     vii   ii   v v   v i     i         iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_132160648_   1299 ACAAAGCCAGAGGCATCAGACTACTTGATTTCAAACAATATTAAAAAGTT 1348
                               iii    vv   v   v iii        vvv  i  v    i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_132160648_   1349 ATAGTACTTAAAACAGCATAGCACTGGCATAAAAACAGACACCTAGACCA 1398
                          i    v i  i    ii i i          ii i     iv    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_132160648_   1399 GTGTGAA-GGAATATAGAACCTATAAATAAATCCATGTGTCTGTGGTCAA 1447
                         i  -   -i    vv   ii i v       i    iii i i       
  L1M4_orf2#LINE/    300 ATG-GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_132160648_   1448 TTGATTTTTGGTAAAAGGACAAAGAATACACAATGGGGAAAGAAAATTCT 1497
                                 i ii  ii vi v    vi iv              v v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_132160648_   1498 CTTTAATAAATAATGTAGAGAAAAACTGACTATTCACATACAGAAGAATA 1547
                         i  i  i    ii  iv i  v  -   iv  ?i     i  i      i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATG 447

  chr2_132160648_   1548 AAATTGGATCATTATTTCACTCTTTATACCAACATCAATTAGCAATGGAT 1597
                           i     i vi  ii    v iv     v  v  i  i viv       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_132160648_   1598 GAAAGACTTAAATATAA-ACCTGAAACTGTAAAACCACTACAAGCAGAGA 1646
                         v ?    i     i   - v  i     i      ivi  v   v i v 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_132160648_   1647 TAGGAGAAAACCAT-ATGACAATGGCCTCAGCTATGATTTTCTACAGATG 1695
                             ? v   i v -i    vv   vi vi  v   i   ii  v v   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_132160648_   1696 ACCCCAAAAGTACAGGCAACAAAAGCAAAAATACACAAACGAGATTCCAT 1745
                           v       i   i          v       v i   ivi  i i   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_132160648_   1746 -AAAACTAAGAAGCTTCTCTGCACAGCAAAAGGAAC-AGTAATAGAGTGA 1793
                         -    i   i  -   i v   vi--    i iv  - vi  v i     
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGA 694

  chr2_132160648_   1794 AGAGACAACCCACA-AATGGGAAGAGAATGTTTTTAAACCATACCTCAGG 1842
                          i            -       -  i   i   vi   i    iv  v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGA-GAAAATATTTGCAAATCATATATCTGA 743

  chr2_132160648_   1843 TAAGGGGTTCATACCAATAATATGTAAGGAACTC----AACCCAGAAATG 1888
                               ii ii  i v v     i   i      ----   i  iv   i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_132160648_   1889 AGAAAACAAG----CTTACTAAAAAATAAGTAAAGGACTTGAATAGACAT 1934
                          i  i    i---- iv i ?      ii i      i            
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_132160648_   1935 TT-TCTAAAAACAGACATACAGAAGGCCA 1962
                           -  i   i -   i     i v     
  L1M4_orf2#LINE/    844 TTCTCCAAAGA-AGATATACAAATGGCCA 871

Transitions / transversions = 1.89 (151 / 80)
Gap_init rate = 0.02 (17 / 871), avg. gap size = 1.47 (25 / 17)  


2629 28.47 3.76 0.34  chr2_132164294_132166842.rev     1180  2057 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_132164294_   1180 TGGAAACACCTCTCATGCTCATGGATGGGTAAAATCAATATTGCAAAAAT 1229
                               v iv  i    i        v  v i v i       iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132164294_   1230 GACCATAACATCAAAAGCAATTTATAAATTCAAAGCAATTTCCATCAAAG 1279
                          i v   vivi v   vii  i  i i      v     ii i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_132164294_   1280 TATCACCATCATCCTTCACAGAACTAAAAAAGATAATTTGAAAATTCATA 1329
                          vi  v vv v ii  ii     v vi v   v i  iiv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_132164294_   1330 TGGAACCAAAAAAGAGCCCGCATAGCCAAAGCAAGACTAAGCGGAAAGAA 1379
                              viiv  ii  v  v v         i   vvi i iviii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_132164294_   1380 CAAATCTGGAGGCATTACATTACCTGGCTTCAATCTATACTACAAGGCCA 1429
                             vi      vv i   i v  iiii     vviv        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_132164294_   1430 TAGTCAGCAAAACAGCATGATACTGGTATAAAAATAGGCACATAGACCAA 1479
                         i   v v   i    ii  i      i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_132164294_   1480 TGAAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGTCAACT 1529
                           i  i     v    ii               v i i   ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_132164294_   1530 GATCTTTGACAAAGCAAACAAAAACATAAAGTCGGGAAAGGACAATCTAC 1579
                            i  i     i vviv   i v   vv i v       i i i   vi
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_132164294_   1580 TCAACATATGGTGCTTGGATAATTGGCAAGCTACATCCCAAGAAATGAAA 1629
                               v        v   i  i   vv ? i    v v  ii      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_132164294_   1630 CTGGATCCCCATCTCTTACCTTATACAAAAGTCAACT------------- 1666
                         i    i   i i   vi   v         i i    -------------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_132164294_   1667 -----TAAATCTGAGACCTGAAACCATAAAAATTCTACAAGGTAACATTG 1711
                         -----     v i   v  i    i      v ii  v   iv     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_132164294_   1712 GAAAACCCCTTCTACACATTGGCTTAGGCAGAGACTTCATGACCAAGAAG 1761
                          ?iv vvi    vvv  v    v       iv ii   v iivi v  vi
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_132164294_   1762 CCAAAAGCAAGTGTGACAACAAAATGAAGATAAACAGGTGAGACTTAATT 1811
                                  viv ii    v i  --  i   i i ii vi     v  i
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAA--AAAATAGATAAATTGGACTTCATC 648

  chr2_132164294_   1812 AAACCAAAAAGTTTCTGCACAGCAAAAGAAACAATTAGCAGAGTAAACAG 1861
                            viv    ii  i  ii vv    i  v  v  i iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_132164294_   1862 ACAACCCACAGAATGGGAGAAAATCTTCACAATCTATACATCTGACAAAG 1911
                                                 v  ii   vii   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_132164294_   1912 GACTAATATCCAGAATCTACAAAGAACTC---------AGCAGAAAAAAA 1952
                             vi          v  i         --------- ii iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_132164294_   1953 ACCAAT--CCC--TTCAAATAATGGGATAAGGACTTAAATAGACAATTCT 1998
                           v   --   --  ?   -      vv     i  i        v    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_132164294_   1999 CAAAAGAAGATATAAAAATGGCCAACAA--ACATGAAAAAATGCTCATCA 2046
                          v            v          i  --         i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_132164294_   2047 TCACTAATGAT 2057
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 5.14 (36 / 7)  


 841 33.47 8.09 2.06  chr2_132169750_132171481.rev      512  1240 (492)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr2_132169750_    512 ATGCTAAAATTCCCATGGGACCACGAAATGCTCTGAAACTCCAAAGCCAT 561
                           v         vi    i vii i iivi i v   vvv     i v  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_132169750_    562 GCTGGGAGATCCAGACGATGTCAGATGGAC-CACGATCTCCAATTTCAAA 610
                         vi  ii i vvvii  i v  ii  -    -   iv ii           
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGA-GGACTCACACTTCCCAATTTCAAA 234

  chr2_132169750_    611 TTTCACAGAAAAGCTACAG--ACC------------CACCTCCACC---- 642
                         vi i  viv          -- i ------------i  ivv  iv----
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_132169750_    643 TAGACA------------GAATAGGA-----AACCCAGAAGCAA-CCCAC 674
                               ------------      i ----- ii      ii  -    i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_132169750_    675 ATACCTGCAACCATCTGACCTTTGA-AA---CACCAAAA---TTCAGACG 717
                          i ii iiiii  vi   ii  i  -  ---ii    i ---    - i 
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA-ATG 383

  chr2_132169750_    718 TGGAAAGGGCTCACTGTGCGATGAAAGGCACTGGGATAG-TGTCTAGCCA 766
                         v      iiivvv  v v i ii  v  ii      i i-  vv  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_132169750_    767 CTTGCAGATGAACAACACTGGAGCCTCACCTCTCACAAGATGCAAAAACT 816
                          v    i v   ii vii    v  ii     v   v v  i      i 
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_132169750_    817 AACTCAAGGTGAATGAAAGATTTCAGCAGAAGACCGCAAACTATACAAGT 866
                                ii  i  v ?   ii v iiiv    v vv        v  v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_132169750_    867 CCTACAAGAAAAACTAGG---AAATACCTTTCTCAACACAGGCTTTGGTA 913
                          i  v       vv    ---    ---i   vii  viv  v  v  i 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCA 580

  chr2_132169750_    914 AAGAATT--TAGATGACTTGGTCCCTAAAAACAACAGCAAGAAAAACCAA 961
                          v iv  --     i---  iiv  -    i  vv     v    ivv  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATA---TGACACC-AAAAGCACAAGCAACAAAAGAAAA 626

  chr2_132169750_    962 AATGGACAAGTTGGGCCTAA--GAAACTAAAACACTGCCAGATAGCAAAA 1009
                            i  i  i    i i v --i   i     -   viiiviivv    i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAG 675

  chr2_132169750_   1010 TAAATCACCAGCACAGTAAAAACATAGCCTACAGGATGGGAGAAAATGTT 1059
                         v v ii i  iv v   i    v i i  i    i            i  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_132169750_   1060 CCCAAACTACGCTTCTGACCAAGGTCTAATAGCCAGACTCTAACATGACC 1109
                         iv    ii iiiv     iv i  v  vi  v     v v  vv v  v 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_132169750_   1110 TTAAAAAAATCAAGAGGCAGAAAAACAAATAATC-----AAACAATGGGC 1154
                          ivv v  v    v i-i i   i        i -----?  v       
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_132169750_   1155 AAAAAGACATGGAGACATACTTGTAAAAAAAAAAAGACGTACAAGTGACC 1204
                            i-  iv  i v v i i  v vv   i  ---  ii     i  i  
  L1M4_orf2#LINE/    825 AAAG-GATTTGAATAGACATTTCTCCAAAGAA---GATATACAAATGGCC 870

  chr2_132169750_   1205 AATAGACA-AGAAAAAAACA-TCAACATCACTCATCAT 1240
                             ii  - vi    i ii-         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.03 (26 / 773), avg. gap size = 2.85 (74 / 26)  


2258 26.43 7.45 1.75  chr2_132212672_132214915.rev      895  1753 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_132212672_    895 TGAAAATACATCCTATGTTCATGTACTGAAAGAAGTGATATAGTGAAAAT 944
                           i   v i    i         v i  i    vv i    v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132212672_    945 GACAATAGTGCCCAAAGCAGTCTACACATTCGATACACTTCCTACCAAAG 994
                          i     v v      viii      v    i ii  v i    i    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_132212672_    995 TACCAA-TGTCATTCTTCACAGAATTATTT-TAAAATG---CTGACATTC 1039
                          v   i-  i -  i  ii     --   v-i  iv  ---  i v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chr2_132212672_   1040 ATGTAGGACCACAAAAGAGCCTGAACAGCAACAGACATACCAAGCAAAAG 1089
                           i i i vii   ii  v  v   i   v - i   - i vv v     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCA-AAACA-ATCTTGAAAAAG 195

  chr2_132212672_   1090 --GAACAAATATGTTGGCA---TCACATTACCTGACTTCAAATGATACTC 1134
                         --       ---     vi---     i v  ii i      vvv    v
  L1M4_orf2#LINE/    196 AAGAACAAA---GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_132212672_   1135 TAAGACCACAGTAACAGAAGCAGCGTGGTACTCGTATAAAAACAGATACA 1184
                         i  ii i       ivi ii   i        v i    ii i   i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_132212672_   1185 TAGATCAACGGAACAGAACAGACAACTCAGAAATAAAGCCACTACA---- 1230
                                 i    i    iv  v iii          v   -    ----
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTA 341

  chr2_132212672_   1231 --ACCAAGTGATCTCTGAGCAAGGATACAAAAAC-ATACACTGGAGAAAG 1277
                         --ii   v    i ii  -     i i v  i  -  v  v   i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_132212672_   1278 TACAGGTTATTCAATAAATGGTGCTGGGAAAAAAAGATAGCCACATGTGG 1327
                         v i  vi v     i              v  vvi    ?       iii
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_132212672_   1328 AAGAATGAAACTGGATCTCTATCTCTCACCATATACAAAACTTAATTCAA 1377
                                  ii    i i   i   v              v    i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_132212672_   1378 GATGGATGAAAGGCCTAAACCTAAGGCCT--------------------- 1406
                         i      v ?  i      iv    iv  ---------------------
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_132212672_   1407 GAAAACAT---------------TGGCCT------AGGCAAAGGATTTAT 1435
                                 ---------------  i   ------      v  -   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCT 589

  chr2_132212672_   1436 GAGGAA-GACCCTAAAAGCAAATCCAACAAAAATGAAAATAAATAAATAA 1484
                         v  iv -   v i       v vv        ivi      i      vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_132212672_   1485 GACCTAATTAAACTAAAAAGCTTCAGCACAGCAAAAGAAATAATCATCAG 1534
                            i v  i   v v    i   iv ii vv    i  v iv    vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_132212672_   1535 AGTAAAACAACAACCTATACAATGGGAAAAA---TTTGAAAATTATGACA 1581
                            i   vi      i i v       i   ---    v    i  - i 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-ATA 738

  chr2_132212672_   1582 -CTAACAAAGGACTAATAATATCTATAACCTACAAGAAATTCAAACAAAT 1630
                         -  i i  i     -- i-    i v  iv  i  ii  i  vv    v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACT--TG-TATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_132212672_   1631 CAACAGGAAAAACACAAATAATTCCATTAGAAAGTGGCCAAATTACATGA 1680
                            i iv     v        ii v   ?i   i   v    vv iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_132212672_   1681 ATAGACATTTCTCAAAGGAAGATGTACAAACGGTAAACAAGCATATAAAA 1730
                                      v  i      i      i  iv  i     i  i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_132212672_   1731 ACACGCTAAATATCTCTAATCAT 1753
                          v i   v  i   v????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (136 / 88)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.29 (79 / 24)  


2283 26.61 3.43 0.57  chr2_132241115_132242820.rev      516  1214 (492)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr2_132241115_    516 AAATAAATAAATAAAACTGGAGGAATTAT-----CTGACTTCATATTATA 560
                            v i vi  i   ii       v i i----- ii i    v viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_132241115_    561 CTACAGAATTATAGTAACAAAAAGAGTATGGTACTGGCATAAAAACAGAT 610
                              i ii  i     iv  i v   i              ii i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_132241115_    611 CCATAGATCAATGGAACAGAATACAGAACCCAGTAACAAATCTACATACC 660
                         vi              i     vv   ii    v  i   i i i i ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_132241115_    661 TACAGTGAACTCATTTTTGACAAAGGTGCCAAGAACATACACTGGTGGGA 710
                           ii  v  i v     i     i          v   v  v   v ii 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_132241115_    711 -----------------AATGGTGTTGAAAAAACTGGATATCCATATGCA 743
                         -----------------       i  ii v         ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_132241115_    744 TAAGAATGAAAACAGACTAGTATCTATCACCAAATACAAAAGTAAAATCA 793
                         v         ivii   ivv  i  vv     v        i v  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_132241115_    794 AAGTTGTTTAAAGATGTAAAGCTAAGACCTCAAACTATAAAACTAGTACA 843
                           i v v i ?   iv    vv     v  v             vv  v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_132241115_    844 AAAAAACTTTGGGGAAAATCTCCAGGACATTGGTCTGGGCAAAAATATCT 893
                          i     v v  ? v      i iv   v    vi i     vii v   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_132241115_    894 TGAGCAATACCCCACAAGAACAGGCAATCAAAGCAAAAATGGACAAAT-G 942
                          iiii vv  v   v   v   i    iv    v      i  i    - 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_132241115_    943 GATCGCATTAAG-TTAAAAAGCTTCTGTACAGAAAATGATACAATCAACA 991
                           iiv   i  i-       -   i   i vvv   v  i  v     v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_132241115_    992 AAGTTAAGAGACAATCCACAGAATGGGAGAAAATATTTGCAAACTACTCA 1041
                             v  i      i                            ii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_132241115_   1042 TCTGACAAAGGATTAATAATCAGAATAAATAAAAAGCTCAGACAACTCTT 1091
                              i  i   i vi  vi       v     i i   vv       vv
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_132241115_   1092 TAAGAAACAATCTAATGACCTGGTTAAGAAAAAGGGGGCAAAAGATTTGA 1141
                            v   v iv v   i   iii  ? i   ---v       i       
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAA---TGGGCAAAGGATTTGA 835

  chr2_132241115_   1142 ATAGATATTTCTCAAAAGGAGACCTACAAATGGCAAACAGGTATAAGAAA 1191
                              i       v    i   iv          v  i i i i v    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_132241115_   1192 AGGTGCTCAATATCACCGATCAT 1214
                           i       i    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (104 / 78)
Gap_init rate = 0.01 (6 / 719), avg. gap size = 4.67 (28 / 6)  


2480 28.62 3.99 0.46  chr2_132246356_132248611.rev      890  1766 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_132246356_    890 TGGAGAAACATCCTTTATTGATGAATTCAAAAA-TTAGAATTGTAAAAGT 938
                             i i i    iv i  v   i   vi  i -   iv     v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132246356_    939 GTCAATGCTACCCAAAGCAATCTACAGAGTAAATGCAACCACTATCAAA- 987
                          v    i  v      vii         v v  i    i v        -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_132246356_    988 TTCCAA-TGTCATTCTTCACAGAAATAGAAAAATTACTGCTAAAATTTGT 1036
                          i   i-  i -  i  ii       v  v  ii iv v        ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_132246356_   1037 ATGGAACCACAAAAGACCTGGACCAACCAAAGCAATCTTGAACAAAAAGA 1086
                               vii   ii    ii  vi i     i          v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_132246356_   1087 ACAAAGCTGGAGGCATCAGACTACCCGACTCCAAACTCTATTACAAAGCT 1136
                               i      vv   v   v   i i i    vii  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_132246356_   1137 ATAGTAATTAAAACAGCATAGTAATGGCATAAAAACAGACATGTAAAACA 1186
                          i      i  i    ii i   v        ii i      i  i v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_132246356_   1187 GTACAAAGGGATATAGAACCCGTAAATAAATCCGTGTGTCTGTGGTCAAT 1236
                         i iv  vi i  vv   ii  iv       i  i iii i i        
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_132246356_   1237 TGATTTTTTTGATAAAATAACTAAAAATACACAATGAAGAAAGAAAATTA 1286
                                i--  i  iivvi i  i vi iv     ii       v v v
  L1M4_orf2#LINE/    350 TGATTTTC--GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_132246356_   1287 CTTTCAATAAATGGTGTAGAAAAAACTGACTATCCACATACAGAAGAATA 1336
                         i      i        iv ii v     iv  ?      i  i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_132246356_   1337 AAATTTGACTTTTATTTTGCTCTTTATACAAGCATCAAATCAAAAT---- 1382
                           i  v   iii  ii ii v iv       iv  i  v       ----
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_132246356_   1383 TAAAGTCTTAAAT-------TTAAAACTAC--------TACAAGGAAATA 1417
                         i ?  v i     -------i        i--------  v   i   i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_132246356_   1418 TAGAAGAAGA-CTGTATGACATTGGCCTGAGCTATGATTTTCTGTAGATT 1466
                            i? v i -  vii    v    vi ii  v   i   ii iv v  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_132246356_   1467 ATTCCAAAAGCACAGGCAACAAAAGCAAAAACACACAAATGAGACTGCAT 1516
                          iv           i          v     i v i    vi    v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_132246356_   1517 AAAACTTAAAAGCTTTTCCACAGGAAATGAAGCAAT-AACAGAATGAAGA 1565
                         v   v      i     vii vvv   v  vi v  -  v i i    i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_132246356_   1566 GA--ACCCACA-AATGGGATAACATTTTT--AAACCATACATCATATAAG 1610
                           --       -       v  v  v   --   i    i   vv     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_132246356_   1611 GGGCTCATATA-ATAATATATAAGTAACTCAACCTACTCAAAAATAAGAA 1659
                           i  ii   v- v         iv     vvv v      v     i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_132246356_   1660 AAAAACTATGCTTATTAAAAAAATAAGCAAAGAATCGGAATAGACATTT- 1708
                         i v  v  vv iv   ?     - ii      i  iv            -
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_132246356_   1709 TCTATGG----CATACAAAAGACCAACAGGTGCATGAAAAAATCATAAAC 1754
                           i vi ----i       v i    i i ii        i  vv v   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_132246356_   1755 ATTCCTAATTAT 1766
                           iv????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (152 / 95)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.29 (39 / 17)  


1173 30.72 6.87 2.66  chr2_132277826_132279534.rev      497  1209 (500)    L1M4_orf2#LINE/L1      136   878 (30)  

  chr2_132277826_    497 ATGCTAAAATTCATGCAGAC-CACAAAACACCCTGAATTTCTAAAGCAAT 545
                           v           iii  v-ii   iiv    v    vv i   i    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_132277826_    546 CCTGAGAAGTCCAAACTACATTGGTTGTGTCACACTTCCTGATTTTTAAT 595
                          i   i  ivvvi   v vi    vv vv          ii    iv  v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_132277826_    596 TTCATTGAAAAGCTA------------------GGGACCC-CATT----T 622
                         i i i iv       ------------------  v  iv-   v---- 
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_132277826_    623 ---CACACAGAGCAGTGGAACAAATTAGAGGACCCAGATGTAAACCCACA 669
                         ---  i i   v  i     i i v v   iii     vi        i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_132277826_    670 CCCCTAACACCATCTGATCTTCAA-AAAAAT-CCACGAAAAT--AAGCTT 715
                          vii  vvii  vi    i   i -  iii -   v  vv  --  ----
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA---- 381

  chr2_132277826_    716 TGGAGAAAGGACTCCCTCCTCTCAATAGATGGTGCCAGGATAAACTGC-T 764
                            i     i i--vv  i i    i i       ii   i  -   v- 
  L1M4_orf2#LINE/    382 TGGGGAAAGAAT--AGTCTTTTCAACAAATGGTGCTGGGACAA-CTGGAT 428

  chr2_132277826_    765 AGCCAGTTGCAGAAGAAAAACAGTGGGCCCCTGTGTCTCACCCTGTACAG 814
                          ?   vv    i     vi viv   i     iiv  v    v i    i
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_132277826_    815 AAATTAACTCAAGATGAATGA-AGATGTAAACGCAAGACCTCAAACTATG 863
                                     i   i  v -   iv    i i    v  v       i
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_132277826_    864 AAAAGCCTGCAAGAGAACTTGGAAATAC-CCTTCTTGACAGAGGATTTGG 912
                            vv i iv    i   v i i?i  v-i    v    vvv  i  v  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_132277826_    913 CAGAGCATGGCTGTGCCTAAGT----CCCCAAAAGCAATTGCAACTAAAA 958
                           ----    i - - i  ii ---- v         vvv     v   i
  L1M4_orf2#LINE/    579 CA----ATGGTT-T-CTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_132277826_    959 CAATTATTGACAAGTGGGGCCTAATATACAA--AAGAGCTGCTGCACAGC 1006
                         v  vv  v  i  i v  i i v  -i v  --  i i  vi  ii vv 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCAT-CAAAATTAAAAACTTTTGTGCTTC 671

  chr2_132277826_   1007 AGAAGAAATTACCAACACAGTAAACAGACAGCCTACACAATGGGAGAAAA 1056
                          i i  v i  i   v v   i  v     i  i   v            
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_132277826_   1057 TGTTCCCACATC-TGCATCTGATGAAGT-CTAATATCCAGAATCTACTTC 1104
                          i  iv  v   - ii       i i v-  vi          v  -- v
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA--TA 769

  chr2_132277826_   1105 AAATACATTAAGCAAATAAAT--CAGAAAAACAAA-AACTCAATGAAGAA 1151
                           iv  vi v -   v v   --i i   i     -   i    v? i  
  L1M4_orf2#LINE/    770 AAGAACTCTTA-CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_132277826_   1152 A-GGGTAAGGGGCATGAA--AACATGCATCTCAAAAGAAGGTTTACAG-C 1197
                          -   i  i  iiv    --i    v--    v       i v    i-i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATT--TCTCCAAAGAAGATATACAAAT 866

  chr2_132277826_   1198 AACCAACAGACA 1209
                         ii    i ii  
  L1M4_orf2#LINE/    867 GGCCAATAAGCA 878

Transitions / transversions = 1.32 (123 / 93)
Gap_init rate = 0.04 (30 / 743), avg. gap size = 2.27 (68 / 30)  


2225 23.17 9.36 4.20  chr2_132455343_132458187.rev     1521  2353 (492)    L1M4_orf2#LINE/L1       33   908 (0)  

  chr2_132455343_   1521 ACTAAATATTGTTAAGATGTTAATTCTCTCCTATTTGATGAATATATTCA 1570
                            v               vi   v   i  v v     vv i v     
  L1M4_orf2#LINE/     33 ACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCA 82

  chr2_132455343_   1571 ATGCAATCCCAATTTTTTAGAA----AAATACTTTTTT---AGATATCAA 1613
                          i        v  i---- i  ---- iv i i     ---   v  ii 
  L1M4_orf2#LINE/     83 ACGCAATCCCTATC----AAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chr2_132455343_   1614 CAAACAGATATATAAAGTTTATATG-AAACGTCAAAAAACCTGAAATACT 1662
                            i v   vi-    i  i     -   i -   iii   iii    vi
  L1M4_orf2#LINE/    129 CAAGCTGATCC-TAAAATTCATATGGAAATG-CAAGGGACCCAGAATAGC 176

  chr2_132455343_   1663 CAATACAAACT-GAAAAACCA---TAAAGTTGGAGGATGCATACTACCCA 1708
                            v    v  -      vv ---i            iv  i   v    
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_132455343_   1709 ATTTTAAGACTTACTATAAAGGCACAGTG-TCAAGACAGTGTGGTATTGA 1757
                             i  i        i    vi     i-                i  i
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_132455343_   1758 CTAAAGAATTCACACATAGTTCAATGGAACTAG---TGGG--TCCAGAAA 1802
                          vv   i  vv   i    v         -   ---  i --        
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAA-TAGAATTGAGAGTCCAGAAA 325

  chr2_132455343_   1803 TAGGCCTCATACAAATGTAATCAACTGATCTTTGACAAAGGAGCAAAATG 1852
                           ii  -      vv i ii    i    i  i     i  v  v  i-i
  L1M4_orf2#LINE/    326 TAAACC-CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG-A 373

  chr2_132455343_   1853 CAATTCAATAGCAAAGGAATAGTCTTTGCAATAAATGCAGTAAGTGGTGC 1902
                          v       i vi  i           v   i     ---------    
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG---------GTGC 414

  chr2_132455343_   1903 TGCAACAATGGGATATCCTTCTGCACACACATAAAAAAAATGAACCTGGA 1952
                           vi    iv     ?  ------   ii  ---   i      vi    
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCC------ACATGCA---AAAGAATGAAGTTGGA 455

  chr2_132455343_   1953 CACACGAACCTCAGAGCTT-CACAAAAAATCAACTTAAAATAGAACATAG 2001
                          v vi--      v v v -i       - i    i     i  v  ?  
  L1M4_orf2#LINE/    456 CCCCT--ACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAG 502

  chr2_132455343_   2002 ATTTAAATGCAA-------AACTACAAA---------------TATAGGA 2029
                          ii      i  -------     i   ---------------i     ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_132455343_   2030 GCAAATTTAGGTGACCTTGAATTTGGCCATAAGATTTC--AGATACAAC- 2076
                          i    i vv         ii  v   v  -- i    --     ii  -
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAAT--GGTTTCTTAGATATGACA 600

  chr2_132455343_   2077 -------CACAA------AAAGATTCTGT-GAAAGCTTAGATGTTACTAA 2112
                         -------     ------     vvvvi -  v iv  i  iv i ii  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_132455343_   2113 AATTAAAAACTTCAGCCCTGTGAAAGTCACTGTTAGGATAATTTTTAAAA 2162
                                     iv iv  vii  i v    i i i  v i v---    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG---AAAA 697

  chr2_132455343_   2163 AGTAAT----AGACTGGGAAAAAAT--TTGCAAGACATGCATCTGATAAA 2206
                         iii  i----   v     i     --      iv   ii         i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_132455343_   2207 AGGCTTGTATCCAAAATATACAATAAACATTTAAGACTCAACAATAAGAA 2256
                         i i          i      i  vi   vi   vi      i     i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_132455343_   2257 AACAA-TCAC---ATTTGAAAGTTGGCAAAAGATTTAAATAGACACCTCA 2302
                         i    - v  ---   ?i   i v      i     i        ii  v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_132455343_   2303 TCAAAGAAGATACACAGATAGAAAATAA----------AGATGGTCAACA 2342
                         i           i   i  i vv     ----------     v      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_132455343_   2343 TCATTTGTTAC 2353
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.70 (119 / 70)
Gap_init rate = 0.04 (33 / 876), avg. gap size = 3.42 (113 / 33)  


2261 24.71 3.48 4.64  chr2_132461793_132463637.rev      506  1367 (478)    L1M4_orf2#LINE/L1       57   908 (0)  

  chr2_132461793_    506 ACTCTACCCAAAAGAATCTACACATTCAATGCAATGCCTTTCAAAATACA 555
                             --      vvi       v      i     v   v       v v
  L1M4_orf2#LINE/     57 ACTC--CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_132461793_    556 AATGACATTCCTCAAAGAAATATTTTTAAA--AATCGTAAAATCTGTGTG 603
                          iivi v  ii iiv      -- vvi  i--i   v      iii i  
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCATATG 152

  chr2_132461793_    604 GAACTACAAAAGGGCCCA-AGTAGTCAAAGAAAGAAATTTTGAGCAAAAC 652
                            v i   i-  i    - i   i    iv  ---- i    --    -
  L1M4_orf2#LINE/    153 GAAATGCAAG-GGACCCAGAATAGCCAAAACAA----TCTTGA--AAAA- 194

  chr2_132461793_    653 AGACAAACAAACAAAAAGCTGCAGACATCATGCCACCTGATTTCAAAATA 702
                         -  vi      ------ i  v  ivv   ii iv  ii         iv
  L1M4_orf2#LINE/    195 -GAAGAACAAA------GTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_132461793_    703 TACTGCAAAGCTATAGTAACCAAAATAAAATGGCATTGGTATAAAAACCA 752
                             i        i     i   i i ivi   i i   i    ii i- 
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-A 286

  chr2_132461793_    753 GACACGTAGATCAATGGAACAGAAGAGATAATCCAGAAATAAATCCACGG 802
                             ii             i    vv  v i            i   iiv
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_132461793_    803 ATTTAGAGCCAATTGATTTTTGACAAAGACATCAAGAACATACATTGAGG 852
                              vi i           i     i iiii     v   v  v  i  
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_132461793_    853 AAAAGACAGTATCTTCAATAAATGGTGCCAGGATATTTGGATATCAATAC 902
                            ii i   v i     i         ii   i vi      ? v i i
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_132461793_    903 ACAGAACAGCTAAATGAGGCCCTT-----------TAAACAAAATTTAAC 941
                         i  i  v iiv  i vi i   i -----------  v      v     
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_132461793_    942 TTAAAATT-ATTAAAGACTTAAATGTAAGATGC-AAAACTATAAAAGTAA 989
                          i     v-  i ?    i           -  -            v vv
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCT 535

  chr2_132461793_    990 TAGAAAACAAGTTAGGGAAAATTCATCAGGACATTGGTCTAGGAAAAGAT 1039
                              i v  vv    ?iv  v  v  iv   v    vi    v  v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_132461793_   1040 TTCATTGATGAGACCTCAAATGCACAGGCAACAAAAGTTAAAACAGACAA 1089
                            v v   iv   vi    v     i          vv    i   i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_132461793_   1090 ACAAGAATATATCAAACT--AAAACTCCC-TGCATAAATAACAAAGGAAA 1136
                          ivi  v vi      v --      iii-   v ------       v 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT------CAAAGGACA 679

  chr2_132461793_   1137 C----AACAACGTGAGGAAACTATCTGTAGATTAGGAGAAAATATTTGCA 1182
                          ----  v  v    ii i  v i iii   v i                
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_132461793_   1183 AACTAACTATGCATCTGACAAGGGATTAATACCCAGAATATATGAGGAAC 1232
                           ii --   --      i      i vi  i           i i    
  L1M4_orf2#LINE/    730 AATCA--TAT--ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_132461793_   1233 TCAGACAACTCAACAACAACAGCAACAAAAAAAAATCCA-TTAAAACACA 1281
                           vv         i  i  ----  vi v   v  i   -  ?   v ii
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAA----AAAGACAAATAACCCAATTWAAAAATG 821

  chr2_132461793_   1282 GGCA-----TTTCTGAGTAGACATTTCTCAAAAGAAAGACATACAAATGA 1326
                             -----   --  i            v      -  i         i
  L1M4_orf2#LINE/    822 GGCAAAGGATTT--GAATAGACATTTCTCCAAAGAA-GATATACAAATGG 868

  chr2_132461793_   1327 TCAACAAGTATATAAAAA-ATCCATCACAAATCATCAGAGAA 1367
                         i   i   i i  i    -  v -   - v    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGC-TCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (129 / 80)
Gap_init rate = 0.03 (28 / 852), avg. gap size = 2.50 (70 / 28)  


2698 23.58 2.91 4.13  chr2_132533394_132535261      485  1379 (489)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr2_132533394_    485 ATTGAATAAAACTTCAT---GTTAAAATGTCCATACTATCCAAAACAGGG 531
                             i -- i    v  ---     i   v v     vi     viiivv
  L1M4_orf2#LINE/     25 ATTGGA--AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATC 72

  chr2_132533394_    532 TATAGATTCAATAACATCCCTATGAAAATCCCAATGGCAAGTTTTTACAA 581
                           i        iivv        v         iiv  v-v     i  i
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAG 121

  chr2_132533394_    582 AAATTGA-AAAC-AATTATAAAATTCATATGGAACCACAAAAGACCCTGA 629
                                -  i -i  iv                vii   ii     v  
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_132533394_    630 GTAACCAAAGCAATCTTGTGAAAGAAGAACAAAGATGAAGGCATAACACT 679
                         i  i     i        vi              v  i   vv v     
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_132533394_    680 ACCAGGTTTCAAAATACATTACAAAGCTACAATAATTAAAACAGCATAAT 729
                         v  vii        ivi i            i    i  i    ii ii 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_132533394_    730 AGTAGCATAAAG-CAGACAGATACACCAATGAAATAGAATAGAGAGTACA 778
                          v i      i -i     v   v i     i        v      v  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_132533394_    779 GAAATAAATCCATACATATATTGTTATGTACTGTCACATATACTTGAATT 828
                                 i        ------     ----    ---  ---   v  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACAT------TTATG----GTCA---AT---TGATTT 355

  chr2_132533394_    829 TTGACAAGTGCGACAAAAATACAAAATGGGAAAGGGATAATGTCTTCGAC 878
                          i      v i v   i vi ivv      i  i i   i v i   i  
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_132533394_    879 ACATGGTATTGGAAAAACTGAATAACCTCATGCAAAC-AATGAAATTGGA 927
                          v     ii   i v     i   ?  v        v-      i     
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_132533394_    928 TCCTTATCTTACACTATACAAAAAACATCAACTCCACATGGATTAAATTT 977
                         i  i  i  i    i   i v    -  i     v v      i ? vvi
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATGGATCAWAGAC 504

  chr2_132533394_    978 TGTAATGTAAGACCTGAAACTGTAAAACTCCTAGAA-AAAATATAGAAA- 1025
                         ivv         v  i     i        i     -    i    i?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_132533394_   1026 AAATGCTTTATGATATTGGTGTT-GGCAATGATTTCTTGAATGTAATAGC 1074
                             -   ii   iv    -   -       i      ii  i i i v 
  L1M4_orf2#LINE/    555 AAAT-CTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_132533394_   1075 AAAAGCACAGGCAACCAAAACAAACATAGACAAGCAGAACTACATTAAAC 1124
                                  i     v   iv   v     i  iiv i   v   i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_132533394_   1125 TAAAAAGCTTGTGCACAGCAAAGGAACCAATCAACAGAGTGACAAGGAAA 1174
                          v    i   v  ii vv       vv v     v i     v   iv  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_132533394_   1175 CATATGAACTCAGGGAAAATGTATGTTTTTCCAAACCATGTATCTGTTAG 1224
                          vi iii v vi i      i v  ------    i   i      v  i
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTG------CAAATCATATATCTGATAA 746

  chr2_132533394_   1225 ATG-TTAATATGTAAAATATAT---GAACT---ACAATGCAATAATTAAA 1267
                         iv -i vi   vi i       ---     ---    iv       --  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT--AA 794

  chr2_132533394_   1268 AAAAGCAGATCAAGCCA---------TAGGCAAAGGACTTGAATAGACAT 1308
                            ii  i  -  v   --------- i         i            
  L1M4_orf2#LINE/    795 AAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_132533394_   1309 TTAGCCAAAAAAAAAAAATACAAATAGCCAACAGCTATATGAAAAATATG 1358
                           vv     i  i v --       i     i ivi i       ---- 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATA--TACAAATGGCCAATAAGCACATGAAAA----G 887

  chr2_132533394_   1359 ATAATCATCATCACTAATCAG 1379
                           iv   v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (126 / 82)
Gap_init rate = 0.03 (26 / 884), avg. gap size = 2.42 (63 / 26)  


 897 26.13 2.79 1.05  chr2_132542236_132544408.rev      468   754 (1419)    L1M4_orf2#LINE/L1        2   293 (615)  

  chr2_132542236_    468 GGAAAACTATTCCATACTCATTAATTAGAAAAATTAATTTGATTCATATG 517
                              iv   i    ii    vi   i   i v     v vi  v v   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_132542236_    518 ACAATATTACCCAAAACAATTTATAAAT-CAATTTCACTCCCTATCAAAA 566
                         i     i v      vii  i  i i  -   iv-  v            
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACG-CAATCCCTATCAAAA 100

  chr2_132542236_    567 TACTCA--TG--TTTCTCACATAAATAGA-AAGCAAATCCTGAAATTGAT 611
                          - i  --  --   i ii  v    v  -    vi     i     v  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_132542236_    612 ATAGAACCACAAAAAACCCAG--TAGCCAAAGCAATCCTGAGCAAAATGA 659
                           i   vii   iii      --        i     i   iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_132542236_    660 ACAAAGCTTGGAGACATCACACTATATGACTTCAAAATTTACTACAATGC 709
                               -      ivv       vivii i       i         v  
  L1M4_orf2#LINE/    200 ACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_132542236_    710 TATAGTAACCAAATCAACATGTTCCTGGCATAAAAACAGAAACAT 754
                           i     i   iv  iii  v v         ii i   v i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

Transitions / transversions = 1.78 (48 / 27)
Gap_init rate = 0.03 (8 / 292), avg. gap size = 1.38 (11 / 8)  

1743 27.74 3.06 2.58  chr2_132542236_132544408.rev     1064  1683 (490)    L1M4_orf2#LINE/L1      286   908 (0)  

  chr2_132542236_   1064 AGAAACACAGACTAATGAAACATCATAGAGAACCCAGATGTAAATCACGC 1113
                            v i i   ii    i  i vv  v    ii     vi    i --- 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC---C 332

  chr2_132542236_   1114 ATTTACAACATTTACGCAAATGAGCCAATTCATTTTTGACAAGGATGCTG 1163
                           -----       i ------- i     v     i       i   ii
  L1M4_orf2#LINE/    333 AT-----ACATTTATG-------GTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_132542236_   1164 GAAATACACAATGGGAAAAGGACAGTCTCTATAATGAATGGTGCTAGGA- 1212
                         ii vi iv       i    i i     i vi  ii         i   -
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_132542236_   1213 AACCAGATAACCATATGCAGAAGAATGAAACTAACCCCTTATTTCTTACC 1262
                            ii    ?   i     i         ii iiv   i  ii  vi   
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_132542236_   1263 ATATACAAAAATCAAATCAAAATGACTTAAAGACTTAAATCTAAGATATA 1312
                                     i  v        iv i ?    i     v     vv  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_132542236_   1313 AAACTATGACACT---AGAAGTATACTTTTGGGAAGCACTCCAGGACATT 1359
                                i v   ---     v v  v vv ? v ivv  i iv   v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_132542236_   1360 GGTCTGGGCAAAGATTATTTT---TAAGACCTCAAAATCACAGGCAA--- 1403
                           vi i     v i  - i  ---  v   vi     v    i    ---
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTT-TCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_132542236_   1404 AAGCAAAAGCAGATAAATGGGATTACATTAAGCTAAAAAGCTTCTGTCTA 1453
                            v    ii        v   i v   i  iv v    i   i   viv
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_132542236_   1454 GCAAACAAGACCATCAACAAACTGAAGATAAAGGCCATGGAGTTGAATAA 1503
                         v    vi v  i     v   v    i v v iv   ii  i v i v  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_132542236_   1504 TGTATTTGCAAACTGTCAATCTGACAAGTAATTAGTAACCAGAGTATATG 1553
                         vi          iii vv      i   vi i v   v     i     i
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_132542236_   1554 AGATGCTTAAACAGTCCAATAG--AAAAGA-----AATCTGATTAAGAAC 1596
                          iivi  ivv   iii     i--      -----  i ii   ? i  v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_132542236_   1597 TGGGCAAAAGATT-AAATAGACATTTCTCACTAGGAAACATGCAAATGGC 1645
                                 i    -i              vvv  i i i  i        
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_132542236_   1646 AAATAGGTGTATGAAAA-AGGTTTAACATGACTGATCAT 1683
                         v    i iii       - v i i     v ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (103 / 65)
Gap_init rate = 0.02 (12 / 623), avg. gap size = 2.92 (35 / 12)  


2770 24.25 3.52 1.30  chr2_132546259_132548524.rev      653  1419 (847)    L1M4_orf2#LINE/L1       25   808 (100)  

  chr2_132546259_    653 ATTGAGAGACTTAGTATTGTTATGTTTCCAATTCTACCCAAAGTGATCTA 702
                             ii       i        v v vv    v  v      v       
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr2_132546259_    703 CAAGTTCAAAGCAATTCTTATCAAAATTCCAACAGCCCCTTT-GCAGAAA 751
                           ii     v     i i         i   i v   ii   -       
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr2_132546259_    752 TGAAAAAGCCAGTCCTCAAACTCATATGGAGTTGCAAAGGGATCT-GAAT 800
                          vi v    iii    v   i         iv     -    i i-    
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA-GGGACCCAGAAT 173

  chr2_132546259_    801 ACTCCAAACAATGCTGAAAAAGAAAATAACAAAATGAAAGGACTCACACT 850
                          vi v       vi          i --     i vii            
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGA--ACAAAGTTGGAGGACTCACACT 221

  chr2_132546259_    851 TCCCAATT---------ACTGCAAAACTAGA-TGGTCAAATCAGTATGGC 890
                                 ---------   i    i   v - ii    iv    i   i
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_132546259_    891 CCTGGCAAACAGTTAAACATACAAGCCAATAGAATTAAACAGAGAGTCCA 940
                         v      v vi v  i     i iii    i    vi  iv         
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_132546259_    941 GAAATAAACCCATACATCTATGGAACACTGATTTTTAATAAAAGCACCAA 990
                                          i     vvv i       ii i  ii ii    
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_132546259_    991 GTGTATTTTATGGGGAAAAGAATAGTCTTAGCAACAA-TGGTG-TGGGAC 1038
                          vvi   iv         -          vv      -     -      
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_132546259_   1039 AACTGTATTTCTACATTTAAAAGAATAAAATTGGGTCTGCGTTTTATGCC 1088
                              v  v? i    vi        i  i    ii iviiii i ii  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_132546259_   1089 ATATA-GCAAATTACTTCAACGTGATTCATTGACCCAA-TATAAGAGCTA 1136
                              -iv      vi    vi  iv   ?v    i  - i         
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_132546259_   1137 AACTTATAGCATGCTTAGAAGAAAACAT--GAGTAAATCTACATGATTTT 1184
                           vi    iv iv               -- ?        v i   ii  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_132546259_   1185 TAAATTTGGCATTTAATCTATTTTTG--TGTAAAACTAAAATAATGAGCA 1232
                         -iii  v    v -ii ---  i  i-- i i v  i    vv ii    
  L1M4_orf2#LINE/    571 -GGGTTAGGCAAT-GGT---TTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_132546259_   1233 ACAAAAGAAAAGTTAGACAAATTGAAATTCATCAAAATTTAAATATATTG 1282
                                    iv    i      i v            v   vv v   
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_132546259_   1283 TTTATCAAAGGACATTAT----AAAGTGAAA---TAACGTATAGAAGTGG 1325
                          viv          i   ----         ---i   vi i    -   
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA-TGG 714

  chr2_132546259_   1326 ATAAAAATATTTGCAAATTATATATCTAATAGGGGTTTAATAATCAGAAT 1375
                         ivi               i        i   i   vi vi  vi      
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_132546259_   1376 CTACAAGGAAGACCTACAACTCAACAACAGAAATGCACACAACC 1419
                         v  i  i   vv i          i  i i   vi  v i    
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

Transitions / transversions = 1.65 (114 / 69)
Gap_init rate = 0.02 (19 / 784), avg. gap size = 1.95 (37 / 19)  

 316 17.33 1.33 1.33  chr2_132546259_132548524.rev     1702  1776 (490)    L1M4_orf2#LINE/L1      834   908 (0)  

  chr2_132546259_   1702 GAATAGATGTTTCT-CAAATAAGTTATACAAACGACCAATAAGCACACAA 1750
                                ii     -    v   v        i i            ii 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_132546259_   1751 AAAAGACGTCCAACATTTTTAGCCAT 1776
                            -  i ii      iv????????
  L1M4_orf2#LINE/    884 AAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.00 (2 / 2)  


1758 29.33 2.83 4.95  chr2_132572334_132574150      477  1325 (492)    L1M4_orf2#LINE/L1       78   908 (0)  

  chr2_132572334_    477 ATTCAATA-AGTCTCTAGGAAGTTCCAAACTACCATGTCATTTTTTTTCT 525
                               ii- i  i   vv  iv   v i  i  ----------    i 
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCC----------TTTTTT 117

  chr2_132572334_    526 ATAAAACCAGAAAAAAACT-AT--TAAATAATTCATATGAAACTCCAAAC 572
                         ii i  -- vvi v  i  -  --    --         i  v v   iv
  L1M4_orf2#LINE/    118 GCAGAA--ATTGACAAGCTGATCCTAAA--ATTCATATGGAAATGCAAGG 163

  chr2_132572334_    573 -AGCCAAAATAGCCAAAGTAATCTTAATCACAAAGAACAAAGCCAGAGGC 621
                         - v   i          ii      i vv vi          iii    v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_132572334_    622 ATCATGTTTGCTGACTTCCAAATATACTATCAGGTGATGGTAACCAAAAT 671
                         v   iii  v ii i   v   iv     iv i iv ii    i   i -
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA- 262

  chr2_132572334_    672 AGCATGGTACTGGTGCCAGAACAGCATGGTACTGGTACAAAAACAGACAC 721
                         ---------------------   ii         i i  ii i     i
  L1M4_orf2#LINE/    263 ---------------------CAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_132572334_    722 ATAGACCAATGGAATGGAACAGAAAACCCAGAAATAAAGCTGCACACCTA 771
                              i         i   iv  i ii           v iii   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_132572334_    772 CAGATATCTGATCTTTAACAAAGTTAAGAAAAATAACCAACAGGGAAAAG 821
                         ii vi vi    i  ii    i v ivv  i vi vi   ii      - 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-G 390

  chr2_132572334_    822 ACTACTCTGTATTCAATAAATGGTG-TGGGCTAGTTGGGTAGCTGTATGT 870
                          v  v   - -     i        -    vi ii   i  ? iii   i
  L1M4_orf2#LINE/    391 AATAGTCT-T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_132572334_    871 AGAAGAATGAAACTCAACCCC-ACCTTTCACCATATAAAAAAATTAACTG 919
                          i         ii vi     -    iv         v           v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_132572334_    920 AGGTTGGATTAAAGATTGAAACACAAGACCTCAAACTACAAGAATCCTAG 969
                          iiv     i ?   iiv   iii    v  v      i  i v  i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_132572334_    970 GAAACTCCAT---------TCT--G-GACATTGGCCTTGGGAAATAATTT 1007
                         i i vvv   ---------   -- -   v    v-  i  v   ii   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTT 587

  chr2_132572334_   1008 AT--GACTAAGTCCTCAAAAGCAATTGCAACCAAAACAAAAATTGACAAG 1055
                         v --  -  v v vi        vvv     v   iv      v  i  i
  L1M4_orf2#LINE/    588 CTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_132572334_   1056 TGGGGTCTAATTAAA-TTAAAGAGCTCTACACAGCAAAAGAAATTATCAA 1104
                          v  iii v  i   -     i vi i iii vv    i  v i      
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_132572334_   1105 CAGAGAAAACAGGCAACCTACAGAATGAGATAAAATACTCACAAACTACA 1154
                         v i  vi  v  i     i        i  v      i ii    ii i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_132572334_   1155 CTTCCAACAAAGGTCCCAATACCCCAAATCTATAAGAAAATTAAACAAAT 1204
                         iv  ii i  i  v iii-  i  vi   v     ii  v ivv    v 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_132572334_   1205 TAATAAGCATAAAACAAATAACATGAAT-ACAAATGAACAAAAGACATGA 1253
                         i     vv v  i         vii v - v     ii    i  iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_132572334_   1254 ATAGACACCTCTCAGAAGAAGACATAAAAGTGGTTTACAAACATATAAAA 1303
                                ii    vi       i   v  i   iiv i  i  i  i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_132572334_   1304 A-ATTCTCCACATCACTAATCAT 1325
                          -  v   v      ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (159 / 88)
Gap_init rate = 0.03 (23 / 831), avg. gap size = 2.87 (66 / 23)  


2788 23.25 6.56 2.65  chr2_132610098_132612849.rev     1392  2260 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_132610098_   1392 AAATGTCTTATAGCCATGAATTGGAAGATTTAATATTGT---------AG 1432
                          i  i  ii  ivi    i         i          --------- i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_132610098_   1433 TACTTTACAATTTGAACTACAGATTTGATGAAATCCCTA--AAAGTATCC 1480
                             iiv   v    v         ii i v        --   --    
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA--ATCC 103

  chr2_132610098_   1481 CAACAGACTTCTGTCTAGAAACTGACAAGCTGATTCTAAAATACACATGG 1530
                           i v v   i v vi     i            i       v  i    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_132610098_   1531 AATCGCAAGGGACTCAAAATAGCCAAAATAACCTTGAAAAAAGAAAACAT 1580
                           vi         i  i           i  i         ii i    v
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_132610098_   1581 AATAGGATAATTCACACCCCCGTGCTGCACACCTTACTGCAAAGCATCAG 1630
                          i v   vi i      ii  vvii v  v v      i      vv   
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_132610098_   1631 TAATCAAGACAACACAATACTGATG-AAGGA-AAA---ATAGATTGATGG 1675
                                    iiiiii     iii-     - i ---      ii    
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_132610098_   1676 AAGAGAATGGAGAGTCCATATATAAAACTATGTATCTATAGTCAATGGAT 1725
                           v     v         v v     v i  ii  i   i      v   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_132610098_   1726 TCTT-ACAGTGGTGCCATGTGCAATTCAATGAGGAAGAGACAGTCTTG-- 1772
                          i i-   iv       v -i v        i    iii i      v--
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_132610098_   1773 AACAA-----GCTGGGTCAACAACGTACACATGGATCACCACTTGCAAAA 1817
                              -----      ---     -------     v?    v       
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGG---ACAAC-------TGGATAKCCACATGCAAAA 442

  chr2_132610098_   1818 TAATAAATTCGAACCCTTACCCCAAAGCATACAAAAATATTAACTCAAA- 1866
                         v   i  v i i    i    i  v v    i v   v           -
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_132610098_   1867 TGAATTAAAGACATACATGCAAGAGCTA-----------------GAATA 1899
                           i  i ?    v  v   i        -----------------   v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_132610098_   1900 AAGCATATGGGAAAATCTTCAGGATTTTGGATCTAGCAAAGA---AATAG 1946
                           i    v ? v        iv  ii    i ivi    v i---vv   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_132610098_   1947 CTGTAACACCAAAAACATGAGCAACAAAATAAAAATTAGATATTTAAAAT 1996
                         v i i         i  ii          v     v      vv vii i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_132610098_   1997 TTCTTAAAAATTAAAGACATTGGTGTTTCAAAGGACA--ACCAAGCAAGT 2044
                            v v         i  v  v   i           -- i    v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_132610098_   2045 CAAAAGGCAGCTCAAAAATTGTGAGAAGATATTTGAAAAACACGTGTCTA 2094
                         v     i  i i  v i v  v     i       v   -------  - 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-------TC-A 734

  chr2_132610098_   2095 TATGTCTGTATATATATATATGTATCTTGAATATAGAAA-AATTGTTTTA 2143
                            i    -   - viv iv      iv       v   -  i v  vi 
  L1M4_orf2#LINE/    735 TATATCTG-ATA-AGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_132610098_   2144 ACTCAGTAA--------CAAATATCCCAACTCAAAACTGA-TAAATGATA 2184
                              i   --------      v     i ?    v  i-i   v   v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_132610098_   2185 GGAATAGATGTGTTTCCCAAGAAGTTACACGAACGGCCAATAATCCCATA 2234
                         v       ii v i   v      v  i  i  i         v v   i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_132610098_   2235 AAAATATACTCAATAGCATCACTCAT 2260
                             v  i     i v  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (114 / 84)
Gap_init rate = 0.03 (23 / 903), avg. gap size = 3.48 (80 / 23)  


2922 27.44 1.78 0.89  chr2_132654430_132660821.rev     5001  5900 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_132654430_   5001 TAGAAGAACATTCCATGCTCATGGGTTGGAAGAATCAATATCATGAAAAT 5050
                          i   ii i  i     i      i        v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132654430_   5051 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5100
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_132654430_   5101 TACCAATGACTTTGTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 5148
                          v   iivi i  v  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_132654430_   5149 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5198
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_132654430_   5199 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATAGTACAAGAC 5248
                                i      vv    i  v  ii i      viv  v     ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_132654430_   5249 TACAGTAACCAAAACAACATGGTACTGGTACCAA-ACAGAGACATAGATC 5297
                                 i   i   iii         i iv i- i   v i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_132654430_   5298 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATAACTACAACT 5345
                                i    i--    i  --        vv   i i vi  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_132654430_   5346 ATCTGATCTTTTACAAACCTGACAAAAACAAGCAATGGGGAAAGATTC-C 5394
                          vi    i  iv    ivv  v   i v  vv             v v-i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_132654430_   5395 CTATTTAATAAATGGTGTCAGGAAAACTGGCTAGCCTTATGTAGAAAGCT 5444
                           v  i  i        iii   v      v  ?  vi   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_132654430_   5445 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5494
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_132654430_   5495 TTAAAGACTTACATGTTAGACCTAAAACTATAAAAACCCTAGAAGAAAAC 5544
                          i ?    i  v    v   v              vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_132654430_   5545 CTAGGCA-ATACCATTCAGGACATAGGCATGGGAAAGGACTTC--AGGTC 5591
                         v    ?i- v i -   iv   v v  vv i  v  v ii   --  i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_132654430_   5592 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5641
                          i --           vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    596 TGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_132654430_   5642 TAATTAAACAAAAGAGCTTCTGCACAGCAAAAGAAACTACCACCAGAGTG 5691
                          v  i   vvv  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_132654430_   5692 AACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTTCTCT-TCTG 5740
                           v  i     i   i             v  i    v- iv v -    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTG 742

  chr2_132654430_   5741 ACAAAGGGCCGATATTCAGAAACTACAATGAACTC----AAATTTACAAG 5786
                          i  i  i ivi   i     vv  i  v      ----  v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_132654430_   5787 AAAAAAACAAACAATCCCATCAAAAAGTGGGTGAAGGACACGAACAGACA 5836
                              i     i  i  v  i?    i    ii     ivi   i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_132654430_   5837 CTTCTCGAAAGAAGACATTTATGCAGCCAAAAA--ATATGAAAAAATGTT 5884
                         i     v        i  vi viii     v  -- i       i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_132654430_   5885 CATCATCACTGGCCAT 5900
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.60 (24 / 15)  


2191 28.34 5.10 2.15  chr2_132680496_132682765.rev      897  1778 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_132680496_    897 TGCAAAAAGATTTCAAGCTTATGAACTGGAAGAATAAATATTATAAAG-T 945
                           v   i v  ii  v i i   i i       v v      i v   - 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132680496_    946 ACCA-TATGATTCAAAGTGATCTACAGCTTCAATGAACTCTCTATTAAAA 994
                         iv  -  ivvii    v          v     i v v  i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_132680496_    995 ATCCAGTGACATTTTTCACAGTAATGGA--AATTACAATTCTAAAATTTA 1042
                         vi    ivi v     ii   v   v  -- ii i--  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCA 148

  chr2_132680496_   1043 CATGAAACTATGATAGGCTTTGAAAAACCAAAGCAATCTAGAGGAAAAGG 1092
                         i   i  v iii vi i iiv   v i     i      v  ii  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_132680496_   1093 GACAAAGCAACCAAACTTCATACTTTATGATTTCAAACTATATTTTAAGA 1142
                         i      ivivvii   -  i    ivii        viv  i vi  ii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACT-CACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_132680496_   1143 TTGTAGTAA-AAAAACAGGATGATACATGCA-AAATATGGACACAATAAA 1190
                         i ii     -v  i    vi  i   vv   -  iv  i    i -  i 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGA 296

  chr2_132680496_   1191 CCAATGGAACAGAAT--AGAGCCCAGAAATAAACCCAGGCATATAAAGTT 1238
                         i        i     --    i               vi   v  vi  i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_132680496_   1239 TACTAATCTTTGACAAGTGCACCAAAAATACACAATGAACGAAGTATAGT 1288
                         v i i  i  i      v ii    i vi iv     iivi   v     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_132680496_   1289 CTTTTTAATATTTGGTTCTGAAAAAACTGGATACCTTCAGGCAAAAGAAT 1338
                              i  i vv    v   ii v         ? iv  v          
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_132680496_   1339 AAAATTAG---CTTATTTTTCTTACACCATGC-TAAAAGTTAA------- 1377
                         i  i  i --- i  i----  i       ii-i    i    -------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTAC----CTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_132680496_   1378 ---ATTACAGACTTAAATATGAATCCTTAAA-----AAACCTGAAAAAGA 1419
                         ---  i ?    i     i i ivv  v   -----    iivv i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_132680496_   1420 ATACATGGA---AAACCCTCATGATATGGTCTTAA-CAATAATTTGTTAG 1465
                          v    i i---   i i  i   iv v vv   i-    ii   v    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_132680496_   1466 ACATAATACCAAAAGTACA-GCAACAAAAGCAAATATAAACAAGCTGGAC 1514
                          i  i i        i   -          v   v   i i  ii     
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_132680496_   1515 TGCATCAAACTAAAAACCTTCTGCACAGAAAAGGGAAC----AATAAAAT 1560
                          v       v v    v   i  ii vvv     iv  ----  v   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_132680496_   1561 AAAAA---AATTTGTAGAATGGGAAAAAATATTTGCAAACCATACATCTG 1607
                         i    ---  iiiii         i              i    i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_132680496_   1608 ATAAAAGATTGATATACAAAATATATAAGAAATGCAAGCAGATTGAAAGC 1657
                             ii  i vi   v  i         ii  iv vvi  iv ii v ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_132680496_   1658 AAGAACAACAGTAACCCAGTTCAAAA-TAGGCAAAA-ATCTAAACTGATA 1705
                           i  v vv i       i  ?    - i      i-  i i  iv  i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_132680496_   1706 TTTGTCCAATGAAGACATACAAATGGCCATACATATGGCCATAAGC-CAT 1754
                            v     v     i             -----------      -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCA-----------ATAAGCACAT 881

  chr2_132680496_   1755 --AAAG-TACTCAATATCACCAAATAT 1778
                         --    - i     i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (162 / 85)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.56 (64 / 25)  


1874 30.49 4.44 1.48  chr2_132700553_132705313      478  1356 (3405)  C L1M4_orf2#LINE/L1   (0)   908     4  

C chr2_132700553_   1356 AAAGATATTTCTAATTCATAAATGGGCATGA-TTAATATTGTTAA-ATAT 1309
                                 ii vvi     ii  v  v -  -             -  iv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAA-GACTTAATATTGTTAAGATGG 52

C chr2_132700553_   1308 CTGCATTACACAAACTGATATACAGATATAATAAAACTTCTATTAAAATA 1259
                          vii i v v    i    v       vi  iiv  iii    i     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

C chr2_132700553_   1258 CCAGTTAAATTCTCCACAGAAATATTTTTAAA--AATC-TAAAATGTATA 1212
                             i ivv  i iii       -- vvi  i--i   -      vi   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCATA 150

C chr2_132700553_   1211 TTGCCCCACAAAAGGCCT-TAATAGCTAAGAAAATCAAGCAAAAAATGGA 1163
                          v vvvii   ii i  i-v      i  i v    vv v    i --- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA---A 197

C chr2_132700553_   1162 AAATAAAAGGCTGAAGGAATCACTCTACCTGACTTTTAAATGTCCAACAA 1113
                         i  i   -- i  i    v    v  v  ii i  iv   iv v v    
  L1M4_orf2#LINE/    198 GAACAAA--GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

C chr2_132700553_   1112 AGCTACAGTAATCAAAACAGAGTGTTACTTACATAAAAATGGACACAAAG 1063
                                        i    v   v    vi     ii  i    i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

C chr2_132700553_   1062 GCCAACAGAGCAAAAGAGAAAGACCAGAAATAAATTC-TGTAATTACAGA 1014
                         ii   ii  ii i  vv  i  v           ii - ii v   ii v
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

C chr2_132700553_   1013 CAACTGATTGTAAATAAAGATGACAATTTTTTTTAA----AAAAGAACAG 968
                            i     v vi i  i i  v   vviiv  i  ----i      i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

C chr2_132700553_    967 TCTCTTTTATAAATGACATTGAGAAAA-TATATATCCACGTGCAAAATAA 919
                            i  iv i     iiii  i  v  - iv   ?    i       v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

C chr2_132700553_    918 TAAAATCAGACCTTCATCTCACACCATATACAAAAATTAACTCAAA---- 873
                          i  i ii    iii i                             ----
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

C chr2_132700553_    872 -TTAAATACTTAAATATGAGACCTGAAAATCTAAAACTA--AGATGAGGA 826
                         - i ? v  i     i i   v  i   v v       v--   --  i 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA--AGAA 543

C chr2_132700553_    825 AATATAGAA-TGAATGCCCCATAACATTGGTCTGGGCAGTGACT-CTTGG 778
                           i    i?- i   - ii i i  v    vi i    i  ii -   i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

C chr2_132700553_    777 GTTTAACCTCAAAATTTTAGG---------GGGAAATAGACAAATCAGA- 738
                         i v i  vi     vivi i ---------iii       i    ii  -
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

C chr2_132700553_    737 TTCCTTAAAATTAAGAAACTGCTGCACACCAACAGATACAATCAGCAGAA 688
                            v i        -     vi  ii vi   vi  i  v    iv i i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

C chr2_132700553_    687 TGACA---TAACTGA-AAAATGGAAGAAAATGTTTGCAAATTACACATGT 642
                            v ---i   iv - i     i       i         i i i  v 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

C chr2_132700553_    641 GAAAAGCAGTTAATATAAAAAATATACAAGAAACTCAAAGGACTATACAA 592
                           v   viii vi   vv i      i  ii     vv vi   vv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

C chr2_132700553_    591 CAAAAAAACAAATAACC--AT-GAAAAATAAGCAAAAGATCTATATAAAT 545
                         i     i          --  -?      ii     i   i iv   i i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chr2_132700553_    544 AATTTTCAAAGAAAGACATACATATAGCTTGGCAGACAGATGAATATG-G 496
                          v  i  v  ii    i     v  i  i-iii ii  v     v vi- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCC-AATAAGCACATGAAAAGATG 890

C chr2_132700553_    495 CTCAAAGTCAATTATCAT 478
                              vi   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (174 / 90)
Gap_init rate = 0.03 (27 / 905), avg. gap size = 1.93 (52 / 27)  

1508 28.55 11.35 2.87  chr2_132700553_132705313     3435  4271 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_132700553_   3435 TGGAATAGTATTTCATGCTAATGGATTAGAAG---------TATTAAAAA 3475
                              vii   ii    i v       i    --------- i    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132700553_   3476 GTTCATACTGCCCAAAGCAATTGACAG-TTTATTTCTATTTCTATTACTC 3524
                          viv     v      vii  iv    -  i viv v  ii    i vvv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_132700553_   3525 TACCAA-TGCCATTTTTTATAAAATTAGACAAAAAAACT-ATTCTAAAAT 3572
                          v   i-    -      ii i  v v     i----  -  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG----CTGATCCTAAAAT 145

  chr2_132700553_   3573 TTATATGAAAA--CAAAAAAGCTCAAATAGCCAAGGCTATACTAAATAAA 3620
                          i     i   --   iii v ivi         ii v  vi i  v  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_132700553_   3621 AAGAATAAACCTGGAGACATTATGTTACCAAACTTCAAACTTTACCACAA 3670
                              i   vi     ivv i iii v  v  i      vi    i    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_132700553_   3671 -GCTACGGTAACCAATATAATATGAATGCAGATACACACACACACACATA 3719
                         -     i    i   v i i i  i- i v ii i viv i v   i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGG-TACTGGCATAAGGATAGACATATA 294

  chr2_132700553_   3720 CACCCCTATTGAACAGAAGAGAGAGCCCTGAAATGAAGCTGAACTCTTAC 3769
                         v i v--  v   i    vv     i  v     i  v iiv  vi   i
  L1M4_orf2#LINE/    295 GATCA--ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_132700553_   3770 AATTAATTGATTTTTGACA---GCATCAACAGAAACAAATGG--AAAGAA 3814
                         ii i          i    --- iii   v vv viv     --      
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_132700553_   3815 CTCCCTACCCAATAAAAGGTGCTGGAAAAACTGGTTAGTCATATGCAGAA 3864
                         ivvi  vii   i   v        i v      v  ?i  i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_132700553_   3865 GAGGAAAACTCGACCGCTACTTCTCATGATATA-GAAAATTAACTCAAGA 3913
                           ivi  ii v    v    i  v  iv     -i             i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_132700553_   3914 TACATTAAAGACTTATCTGTAAGAGTTCAACCTATAAAAATCCTAGAAGA 3963
                          iv  i ?    i  vv        i v  v        v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_132700553_   3964 ACACCTAGA---AAATTCTC-T--CCTTGG------CATTGGTCTCTGTA 4001
                          v  v   i---    ii  - --      ------  v    i   -  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT-TA 591

  chr2_132700553_   4002 AAGAATTAATGACTACATCCTCAAAAGTGAAAGCAACAAAAATAAAAATT 4051
                         i ----  -    -  -----      iiv           iv      v
  L1M4_orf2#LINE/    592 GA----TA-TGAC-AC-----CAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_132700553_   4052 AA-AAATTGTGACCT--------------------GCACAGCAAGAGAAA 4080
                         i -      -   i -------------------- ii vv   ii  v 
  L1M4_orf2#LINE/    631 GATAAATTG-GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_132700553_   4081 CTATTAACAAAAT----AGACAACCTATAGTATGGGCTAAAATATGTGTA 4126
                             i  v   i ----        i i  v     vv       v  i 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_132700553_   4127 AACTGCATAC--AATAAATAACTAATATATATGTTTTATAAGGAATTT-- 4172
                           iiii   i--i    ivi   vi   vi viv v     i   i i--
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_132700553_   4173 ----------------AAGA---------------AAAAATGTTGACAAA 4191
                         ----------------    ---------------       -- i    
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG--GGCAAA 827

  chr2_132700553_   4192 AAATGTGAACATATACTTTTAAAAGAAAGACAAAAAAAGCAGCCAACAA- 4240
                         ii  v    i v i i  i vv  ii    i v v   -ii     i  -
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAG 876

  chr2_132700553_   4241 -ACATGAAAAATTGATCAACATTTCTAATTAG 4271
                         -         iv  v       iv????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 3.72 (119 / 32)  


2722 26.81 8.07 0.36  chr2_132822131_132828341     4877  5719 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_132822131_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4926
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132822131_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCTTCCCCATCAAGC 4976
                            v     v     iv i  i           i  vv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_132822131_   4977 TACCAA-TGCCTTTCTTCACACAATTGGAAAAATCTACTTTAAAGTTCAT 5025
                          v   i-       i  -i  v  v v  v  iiiv iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_132822131_   5026 ATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGA 5075
                               viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_132822131_   5076 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTGCAAAGCT 5125
                               i      vv       v  ii i      viv    i       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_132822131_   5126 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5175
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_132822131_   5176 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCCACAACTA 5223
                               i    i--    i  --        vv   i i  ii iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_132822131_   5224 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5273
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_132822131_   5274 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5323
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_132822131_   5324 AAACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAGATGGAT 5373
                           ii    i    v   i     v  i        i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_132822131_   5374 TAAAGACTTAAACGTTCAACCTAAAACCATAAAAACCCTAGAAGAAAACA 5423
                         i ?    i    i  vvi v       i      vi i            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_132822131_   5424 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5473
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_132822131_   5474 ACACCAAAAACAATGGCAACAAAAGACAAAATTGACAAATGGGATCT--- 5520
                                  i  vvi           v     v  i    v   ii ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_132822131_   5521 -------------------------------------------------- 5520
                         --------------------------------------------------
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_132822131_   5521 ------------AATGGGAGAACATTTTTGCAACCTACTCATCTGACAAA 5558
                         ------------          v  v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_132822131_   5559 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5608
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_132822131_   5609 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACACATACTTCT 5658
                         i     i     v  i?    i           iv    i v i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_132822131_   5659 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5708
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_132822131_   5709 TCACTGGCCAT 5719
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (131 / 91)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 14.20 (71 / 5)  


1192 30.27 0.50 0.25  chr2_132890084_132892631.rev      842  1244 (1304)    L1M4_orf2#LINE/L1        1   404 (504)  

  chr2_132890084_    842 TGGAAACACATCCCATGTTCATGAATGGGTAAA-TCAATATTGTAAAAAT 890
                               v i              i  v  v i - i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132890084_    891 GACCATACTGCCAAAAGTTG-TTTACAAATTCAATGCAAGTTCCATCAAA 939
                          i v     v  v   -   - i    i      i    vii i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_132890084_    940 ATACCACCATCATTTTTCCCAGAACTAGAAAAGACAATTCTAAAATTCAT 989
                           v   v vv v     iv     v v  v   vii  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_132890084_    990 ATGGAACCAAAGAAGAGCCCGCAGAACCAAAGCAAGGCTAAGCAAAAAGA 1039
                               viiv iii  v  v v v i     i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_132890084_   1040 ACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATACCATAAGGCT 1089
                              vi      vv     i v  ii i      viv   i i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_132890084_   1090 GTAGTCACCTGAACAGCATGGTACTGGTATAAAAATAGGCACAAAGACCA 1139
                         ii   v i vii    ii         i    ii    i  i v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_132890084_   1140 ATGGAACAGAATACAGAACCAAGAAATAAATCCAAATACCTACAGCCAAC 1189
                               i     vv   ii v         i   v i ii  ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_132890084_   1190 TGATATTTGACAAAACAAACAAAAACATAAAGTAAGGAAAAGACCCCCTA 1239
                             v  i     iivviv   i v   vv i ii     ii ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_132890084_   1240 TTCAA 1244
                              
  L1M4_orf2#LINE/    400 TTCAA 404

Transitions / transversions = 1.44 (72 / 50)
Gap_init rate = 0.01 (3 / 404), avg. gap size = 1.00 (3 / 3)  

1618 27.52 1.55 0.39  chr2_132890084_132892631.rev     1541  2056 (492)    L1M4_orf2#LINE/L1      387   908 (0)  

  chr2_132890084_   1541 AAAAGACACCCTATTCAAACAAATGGTGCTGGTGTAATTGGCAAGCCACA 1590
                            ii i vi  v     -             vii  i   vv ?     
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAA-CAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_132890084_   1591 TGTAGAAGAATGTGAATGGATCCTCATCTCTCACCTTATACAAAAATCAA 1640
                           i i       viiv    i  ii i   v    v           i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_132890084_   1641 CTCAAGATGGATCAAAAACTTAAA------ACTTGAAACCATAAAAATTC 1684
                              i        ? i  i    ------ vi i    i      v ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_132890084_   1685 TAGATGATAATTCAGAAA-AACCCTTCAAAACATTAGCTTAGGCAAAGAC 1733
                             v  v  ivi  i?i-  vi    ivi  v  i v        v ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_132890084_   1734 TTGATGACCAAGATCCTAAAAGCAAATTCAATAGAAAAAATGATAAATAG 1783
                           vv iivi v  iv i       v vv   i i  i   vi   i   i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_132890084_   1784 GTGAGACTTAATTTAAGTAAAAAGTTTCTGCACAGCAAAAGAAAC-ACTG 1832
                         i vi     v  iv  i v    ii  i  ii vv    i  v  - iii
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_132890084_   1833 AGCAGATTAAACAGACAACCCACAAAGGGGGAGAAAATCTTCACAATCCA 1882
                           v ii v   -            i iv          v  ii   vi  
  L1M4_orf2#LINE/    686 AGAAAGTGAAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_132890084_   1883 TACATCTGAAAAAGGATGAATATCCAGAATCTAGAAGGAACTCAAACAAA 1932
                           i      v  i   ivvi          v  v  i      vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_132890084_   1933 TTAGCAAGAAAAATACGAAGAATCCCATCAAAAAATGGGCTAAGGACATG 1982
                          i ii  v     v  i  v  i  v  i?          v     iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_132890084_   1983 AATAGACAATTCTACAAAGAAGATATACAAATAGCCAACAAACATATGAA 2032
                                 v    v                  i     i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_132890084_   2033 AAAATGCTCAACATCACGAATGAT 2056
                           i             ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (82 / 56)
Gap_init rate = 0.01 (5 / 522), avg. gap size = 2.00 (10 / 5)  


2103 24.35 8.03 3.34  chr2_132917510_132919294.rev      501  1309 (476)    L1M4_orf2#LINE/L1       62   908 (0)  

  chr2_132917510_    501 CCAAATTGATCTATAAAGTCAACACAGTATCAATCAAATTTAGAGCAGGC 550
                                      i i v     i  i vi v      v ivv   v v 
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_132917510_    551 TTTTT-GCAGAAA--------CTAATATTAAGATTTACATTGATATGCAA 591
                              -       --------  i  vi   i   i i  v  v      
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_132917510_    592 AAAACAGCCAACTAAAAAAACTAGAATAGTCAAAATTGTTTTGAAAAGGA 641
                         iii  --------------- i       i     ivi i       i  
  L1M4_orf2#LINE/    162 GGGAC---------------CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_132917510_    642 AGAACATCATTAGAGGAATAACAGTATCAGATTTCAAAACTTATTCTAAA 691
                               vvi  i     v v   v vi vi             i vi   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_132917510_    692 GCTCCTGTAGTCAAGACATAGTGAAA---GCTTAACAATATTTATATAAA 738
                            v v   i        vv   iv ---  v   vi   vvi     i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_132917510_    739 TCAGTGGAACAGAAGTGAT--TCCAGAAAATACAGCCAAGTATATATGAT 786
                            i     i    v   v--        -  v v   vii  v    i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGT 345

  chr2_132917510_    787 CAGTTTATTTTCGGTGCAGCCACAAAGGTAATTCAATGGG---AGAA-AG 832
                           i  v       iiivi vii v   iiv          ---    -  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_132917510_    833 TTGTTTCAAAAAATAGCACTAGAACAACTGGACACCTATTCG-AAAATTA 881
                          iv      v    i ii  i i         i ? i ivi -    vv 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_132917510_    882 TGAACCTCAACACTTACCTCACGTCATACACAAAAAG-AACTCAAAATAG 930
                             vi vi  v i        ii    i       v-          i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_132917510_    931 GTAACAGACCTAAATG-AAAAGCTAAAACTACAAATGTTATACAAGAAAA 979
                         i v ?           -  i           i   vv iv  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_132917510_    980 TATAGGAGAACATTTTCAAAACCTTGGGATAGGCAAAAAAAGATTTCATA 1029
                         i     ? v v  i   ivi        v       v---- i    v  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT----GGTTTCTTA 591

  chr2_132917510_   1030 GGCAAAA----AAGAGCACAAA-ATCTAATTTAAAAA--GATAAACCAGA 1072
                          ii vi ----  i       i- v v  vvv     --      iii  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_132917510_   1073 ACTTCATCAAA-TTAA-----CTTACTCTCTTAAAAACATTAACAAAA-- 1114
                         -          -    -----i  iiv  iiv  ii   i  v   i --
  L1M4_orf2#LINE/    642 -CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_132917510_   1115 -TGAAGAGGCAAGCTA-AGACTAGGAAAAAATATTAATAATGTATTTATC 1162
                         -    i  i   v i -   v i   i        vii  vvi  v    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_132917510_   1163 TGAGAAAGGATTTGTATCTAGGCTATATTAAGAAATCTTACAACTCAACA 1212
                            v  i   i       i  iv     v     v             i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_132917510_   1213 GTAAGGAAGCAAA--ACT---TT----------CAAAAG-TTC------- 1239
                         i   ii ii    --  i---  ----------    i -  i-------
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_132917510_   1240 ---TTTTCCAAAGAAGATATA-AAATGACCAATCAGCACATGATAAAATG 1285
                         ---  i               -     i     v         v  i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_132917510_   1286 ACTGATAACCACATCATTACTTAT 1309
                         -  ----- v      ????????
  L1M4_orf2#LINE/    891 -CT-----CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (112 / 82)
Gap_init rate = 0.03 (28 / 847), avg. gap size = 3.29 (92 / 28)  


3407 18.99 6.64 2.75  chr2_132944765_132947848.rev     1720  2593 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_132944765_   1720 TGGAAAGACATTCTGTGTTCACGGGTTGTAAGAC--AATATTGTTAAGAT 1767
                                 i  i ii      i  i   v     --              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132944765_   1768 GACAATACCATCTAAAGTAATCTACAGATTCAATGCAATACC-ATCAAAA 1816
                          i      ivi i   v i              i     v  -       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_132944765_   1817 TCCCAAAGGCATTTTT-GCAGAAACAAAGAAACTCATTCTAAAAT-CATA 1864
                              ivv  v     -       ivi v  i  v  i       -    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_132944765_   1865 CAAAAATTCAAAGGATCTG--ACAGACAAAACAGTCTTGAAAAAGAA--- 1909
                         iii    v   i   i ii-- i  v       i             ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_132944765_   1910 CA---TTGGAAAACTCACATTTTTCAGTTTCACAGCCTACTACAAATCTA 1956
                           ---     ii       i  ii  i     v i i         v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_132944765_   1957 CAGTCATCAAGAGAGTGTGGTACTGGCATAAGACCAACAGACTTTTAGAC 2006
                             v       v                   i--- i    v v    i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGG---ATAGACATATAGAT 297

  chr2_132944765_   2007 CAATACAATAGAACAGATTTGAGATCCTACAAATTAGTCCTCACATATAT 2056
                             iv       -----      vi i v    v ii  vi    v   
  L1M4_orf2#LINE/    298 CAATGGAATAGAA-----TTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_132944765_   2057 GGTCAAT-GACTGTTCAACAAGGTGGCCAAGTCTAGTCAAGGGAGGAAAG 2105
                                -  i -   i      vv      v i v    v  -      
  L1M4_orf2#LINE/    343 GGTCAATTGATT-TTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAG 390

  chr2_132944765_   2106 AACAGTCTCTTCAACAG---------------CTGGAT-GTCA-GTGCAC 2138
                           i     i       i---------------      -?i  -i    v
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_132944765_   2139 AGGAGAGAAATTAGACCCCTACCTTGCAGTATATACAAAAATTAATTCTA 2188
                          i  iv   i  i           ii  vi               i  v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_132944765_   2189 AATTAATAAAAGACTTAAATGTAAGGACTAAAAGTATGTAACTCTTAGAA 2238
                            vi  v ?    i          ii      v   iv           
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_132944765_   2239 GAAAACACACG-GTAAACCTTTATGACCTTTGAGTTTTAAG---TGTATT 2284
                                i v -     i   ii       - i   -- i ---  vv  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTT-GGGTT--AGGCAATGGTTT 587

  chr2_132944765_   2285 TTGAAATATGACAG-AAAAGCACAGATAACAAAAGAAAATACATGTAAAT 2333
                         i v i        v-         iii            v i vi     
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_132944765_   2334 TAGATTCAATCAAAATAAAAACCCTTTATGCATCAAAGGATACTATCAAG 2383
                          i  i iv        v    v i   i   v        i         
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_132944765_   2384 GGAGTGAAAAGACAACCCATAGTATGTGAGAAAATATGTATCTGCTAAAA 2433
                         ii                 i  v   v          ----i   --   
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT----TTGC--AAA 731

  chr2_132944765_   2434 TCAAAGTGTGTATCTGATAAAAG-CTT--------AATAT---------- 2464
                            ----- i          ii -   --------     ----------
  L1M4_orf2#LINE/    732 TCA-----TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_132944765_   2465 CCCACAACTCAACAG---AATTTCTAAGATCCCAATTAAAAAAGAGGCAA 2511
                          ii         i i---  vvv v  v v       ?     vi     
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_132944765_   2512 AGGACTTGAATAGACATTTCTCCAAAAAAGATACACAAATGTCTAAGAAG 2561
                             i                     i      i       v i  v   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_132944765_   2562 GACAAGAAAAGATGCTAAACACCGTTATTCAT 2593
                         v   v           v    i i????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (101 / 62)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.04 (82 / 27)  


1452 28.43 2.39 1.99  chr2_132949129_132951636      506  1008 (1500)    L1M4_orf2#LINE/L1       47   551 (357)  

  chr2_132949129_    506 AGATGAGTATACTGCTCAAAGCGATTTACAGATTCAATGCTTTTCCTATC 555
                              ivv     v i    vi   i           i  vv i      
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_132949129_    556 AAACTACTAA-TGTCATTTT-GCACAAAATAGA-AAAC--ATC-TAAAAT 599
                            v v i i-  i v    -   -i    v  -  i --   -      
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCA-GAAATTGACAAGCTGATCCTAAAAT 145

  chr2_132949129_    600 TTATATGGAACCTAAAAGGAGTCTGAATAGCCAAGCCAAAGCAATACTAA 649
                          i        vivv  i   vi v          ----- i    vi i 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAA-----AACAATCTTGA 190

  chr2_132949129_    650 GGCTAGAGA-CATAGGCTAGAGACATCATATTACATGACTTCAAACTATC 698
                         iivvii   -  - i i i   ivv   i i v vii i      viv v
  L1M4_orf2#LINE/    191 AAAAGAAGAACA-AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_132949129_    699 CTAGAAGACTATAGTAATCAAAACAACATGGTACTGGTAGAAAAACAGAC 748
                            v  ii   i         i   iii         i v  ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_132949129_    749 ACATAGACCAATGGAACAGACT--AGAGTACTAGAAACTAAGGCCACATG 796
                          i     i        i   v --     - i     -   iv   i ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGT-CCAGAAA-TAAACCCATACA 337

  chr2_132949129_    797 CCTGCAACCATCACATCTTTAACAAAGTTGACAAAAGTAAGCAATGGGAA 846
                         ii iiiii  vivv  i  ii    i v  v   i vi vv       i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_132949129_    847 AAAGAC--TTTTATTTAATAAATAATGCAGGGATAACTGGCTAGTCATAT 894
                           ii i-- i  -  i  i    ii   v    i      v  ?i  i  
  L1M4_orf2#LINE/    388 AAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_132949129_    895 GCAGAAGAATAAAACTAGACCCCCATATTTCACCAAATACAAAAATTAAC 944
                            i      i  ii i      i iv iv     v              
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_132949129_    945 TTAAGATGGATTAAAGAGTTAAATGTAAAATCTCAAGCTATAAGACGCCT 994
                          i  i      i ?   vi         i v  v  i      i  v i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_132949129_    995 AGAA-AAATCCTAGG 1008
                             -   v v    
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGG 551

Transitions / transversions = 1.94 (93 / 48)
Gap_init rate = 0.03 (15 / 505), avg. gap size = 1.47 (22 / 15)  

 990 26.49 0.60 1.79  chr2_132949129_132951636     1681  2016 (492)    L1M4_orf2#LINE/L1      577   908 (0)  

  chr2_132949129_   1681 GGCAAATAATTTAT-GGCTAAGTCCTCAAAAGCAATTGCAACTAAAACAA 1729
                              - ii   v -i v  v v vi        vvv     v   iv  
  L1M4_orf2#LINE/    577 GGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_132949129_   1730 AAATTGACAAGTGGTAGTTAATTAAACTGAGAAACTTTTGCACAACAAGA 1779
                             v  i  i v v v  v  i   v v i         ii vv   ii
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_132949129_   1780 GAAACTATCAAGGTAGTAAAGAGATAACCCACAGTATGAAAGAAAATATT 1829
                           v         iv   i  i   i         v   ii          
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_132949129_   1830 CACAAACTACGCATCTAACAGAGGTCTATTATTCAGAACCTATAAGGAAC 1879
                         ii    ii iii    i i ii  v  vv   i     iv     i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_132949129_   1880 TCAAACAAATCAACAAGCAGCAG-CAAGTAACTCCATTAAAAAGTGGGCA 1928
                           vv    v    i  vv iv  -   i    i v   ?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_132949129_   1929 ACAGGACATGAACAGACACTTCTCAAAAGAAGACATACACACAAGCACCC 1978
                          -    iv    i     i     v        i     v iii----  
  L1M4_orf2#LINE/    826 A-AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG----CC 870

  chr2_132949129_   1979 AACAAACATATGTAAAAGTGCTCATCATCATTATTTAT 2016
                           i  i  i   v   ii      v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (50 / 38)
Gap_init rate = 0.02 (5 / 332), avg. gap size = 1.60 (8 / 5)  


4019 22.00 0.88 0.99  chr2_132996527_132998537.rev      611  1519 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_132996527_    611 TGGAAAGATATCTCATATTCATGAGTTGAAAGAATTAATATTGTTAAAAT 660
                                     i   i      ii   i    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_132996527_    661 GGCCATGCTACCCAAAGCAATATACAGATTTAACATAATCTCTATCAAAA 710
                            v  i  v      vii  v        i   ii    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_132996527_    711 TTCCAGTGGCATTTTTCACAGAAATATGAAAAAC-AATTCTAAAACTCAT 759
                          i    iv  v     ii       -   v  i -i  i      i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_132996527_    760 GTGGAACTACAGAACACCCTAAATAGCCAAAACAATCTTGAAAAAGAAAA 809
                         i     v i  iiiv    vi                           i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_132996527_    810 ACAAAGCTGGAGGCATCACACTTCCTGATTTCAAATTATATTACAAAGTT 859
                               i      vv          ii        viv  i       i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_132996527_    860 AGAGTAATCAAAGCACTATGGTACTGGCATAAAAACCGACATGTAGACCA 909
                          v         ii  v i              ii iv     i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_132996527_    910 ACGGACCAGAACAGAGCACCCAGAAATAAACCCATGCATATATGGTCAAC 959
                          i   vi    iv   vii                i   v         i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_132996527_    960 TAATTTTAGACAAGGCCACCAAAAATATACAATGGGGAAAGAACAATCTT 1009
                          i     v       vii    i vi  v              i i    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_132996527_   1010 TTCAATCAATGGCATTGGGAAAAGTGGATAGCTACGTGCAAAAGAATAAA 1059
                              iv     iii     v  v      ? i  i           i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_132996527_   1060 ACTGGACCCTTATTTTACACTACACACAAAATTCAACCTAAAATGAATAA 1109
                         ii       i  ii i    i i i      v i   ii      i  v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_132996527_   1110 AAGACGTGAACGTAAGACCTGAAACCATAAAATT-GTAGAAGAAAATATA 1158
                         ?    v i  i      v  i    i      i -v          i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_132996527_   1159 G-TGAAAAGCTCCTTGATATTGGCCTCGGCAGTGAATGTTT-TTAGATAT 1206
                          -? v   v  i v   iv    vi v    i  ---    -        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG---GTTTCTTAGATAT 596

  chr2_132996527_   1207 CACACTGAAAGCTCAGGCAATAAAAGCAAAAGAAAACAAGT-GGATCTCA 1255
                         v    ii     v  i    i     v    iv i i  i -   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_132996527_   1256 TCAAA--CAAAAGTTTCTGCATACCAAACAAAACAATTAATAAAATGAAA 1303
                              --i    ii  i  iiivi    vi v  v  i  v   i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_132996527_   1304 AGGCATCCTACAGACTGAGAGAAAATATTTGTAAACCATATATCTGATAA 1353
                           i  v  i     v  i             i   i              
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_132996527_   1354 GGGGTTAATATCCAAAATATATAAGGAATTTAAACAACTCAACAGCAAAC 1403
                            ii vi      i         i   i ivv         i ii   v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_132996527_   1404 AAACAAACAGATAACCTGAATTTAAAA-TAGACAAAGGACTTGTATAAAC 1452
                          i     ----     i-    ?    - i i       i   v   i  
  L1M4_orf2#LINE/    797 AGACAAA----TAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_132996527_   1453 ATTTTTCCAAAGAAGATGTAAAAATGGCCAACAGGTATAGGAAAAGGTGT 1502
                             i            i  v          i i i i v      i  i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_132996527_   1503 TCAATACCATTAATCTT 1519
                             i i  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (138 / 58)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


3023 27.12 0.99 0.88  chr2_133044037_133050066.rev     4632  5538 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_133044037_   4632 TGGAAGAACATTCCATGATCATGGATAGGAAGAATCAATATCATGAAAAT 4681
                              ii i  i     v        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_133044037_   4682 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCTGCATCAAGC 4731
                            v     v      v i  i  i        i  v   ivi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_133044037_   4732 TACCTATTACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4779
                          v  vii i i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_133044037_   4780 TATGGAACCAAAAAAGAGCCCACATTGCCAGGACAATCCTAAGCCAAAGG 4829
                                viiv  ii  v  viv  v    ii      i i ivv i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_133044037_   4830 AACAAAGCTGGAGGCATCACACTACCTGACTTTAAACTATACTACGAGGC 4879
                                i      vv       v  ii i  i   viv      i i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_133044037_   4880 TACAGTAACCAAAACAGCATGGTGCTGATACCAAAACAGACATATAGACC 4929
                                 i   i    ii    i   ii iv ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_133044037_   4930 AATGAAACAGAA--GAGAGGCCTCAGAAATAACACCAAATATCTACAACC 4977
                             i  i    --     v  --        vv   v i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_133044037_   4978 ATCTGATCTTTGACCAACCTGACAAAAACAAGAAATGGGGAAAGGGCATC 5027
                          vi    i  i   v ivv  v   i v  vvv           iii vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_133044037_   5028 CCTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGCAGAAAGC 5077
                          i -  i  i              v     iv  ?   i     i  iiv
  L1M4_orf2#LINE/    397 CTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_133044037_   5078 TGAAACTGGATCCCTTCATTACACCTTATACAAAAATTAATTCAAGATGG 5127
                             ii    i    v v i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_133044037_   5128 ATTAAAGACTTAAATGTTAGACCTAAAACC-TAAAAGCACTAGAAGAAAA 5176
                           i ?    i       v   v       i-     vivi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_133044037_   5177 CCTAGGGA-ATATCATTCAGGACATAGGCATGGGCAAGGACCTCATGACT 5225
                          v    ?i- v   -   iv   v v  vv i     v iii  v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_133044037_   5226 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGATAAATGGGATCT 5275
                          vi            vvi          vv             v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_133044037_   5276 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTGTCAGAGTGA 5325
                         v  i   v v  i i   i  ii vv    i  v    iiivv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_133044037_   5326 ACAGGCAACCTACAGAATGGGAAAAAATTTTTGCAATCTACTCATCTGAC 5375
                          v  i     i           i     v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_133044037_   5376 AAAAGGCTAATATCCA-AACACTACAAAAAACTCAAACAAATTTACAAGT 5424
                           ii i  vi      -  i -  i   i     vv    v iv i  vv
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATA-TATAAAGAACTCTTACAACTCAATAATA 793

  chr2_133044037_   5425 AAAAAACAAACAACCCCAAC--AAAATTAGGCAAAGGATATGAACAGACA 5472
                             i     i     -  i--    v i          v    i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_133044037_   5473 CTTCTCAAAAGAAGACATCTATGCCACCAACAGACACATGAAAAAATGCT 5522
                         i     v        i  vi viivi    i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_133044037_   5523 CATCATCACTGGTCAT 5538
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (150 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.31 (17 / 13)  


2795 26.05 2.98 2.87  chr2_133089621_133093919.rev     2902  3807 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_133089621_   2902 GGAAACATATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAATG 2951
                              v          i        v  v   v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_133089621_   2952 ACCATTCTGCCAAAAGCAGTCTACAAATTCAATGCAATTCTTATCAAAAT 3001
                         i v  v  v  v   viii      i      i     i i         
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_133089621_   3002 ACCA-CCATCATTCTTAACTAGGAA-----AAAC-AATCCTAAAATTCAT 3044
                         v   - iii v  i  i--i  i  -----  i -i              
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTG--CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_133089621_   3045 ATGGAATCAAAAAAGAGCCCGCATAGTCAAAGCAAGACTAAGCAAAAAAC 3094
                               viiv  ii  v  v v    i    i   vvi i ---------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--------- 190

  chr2_133089621_   3095 AAACAACAACAACAAAAAAAACCACAAATCTAGAGGTATCACACCCCCCA 3144
                         --------------    i  vv     vi i    vv      ii    
  L1M4_orf2#LINE/    191 --------------AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_133089621_   3145 ACTTCA-----CACTATAAGGCCATAGTCACCAAAACAGCATGGAACTGG 3189
                          i    -----i    i  i  i i   v i   i    ii   v     
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_133089621_   3190 TATAAAAATAGGCACCTAGACCAAGGGAACAGAAC-------CCAGAAAT 3232
                         i    ii    i  iv    i   v    i    i-------        
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_133089621_   3233 CAAGCCAAATGCTTACAGCCGACTGATTTTTGGCAAAGCAAACAGAAACA 3282
                         v  v   v iii   ii i i i       i i   i vviv  ii v  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_133089621_   3283 TAAAGTGGGGAAAAGACACCCTATTCAACAAATGGTGCTGGGATAATTGG 3332
                          vv i        ii i vi  v                    i  i   
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_133089621_   3333 CAAGCCACACGTAGAAGAATGAAACTGGATCCTCATCTCTCACTTCATAT 3382
                         vv ?     i i i         ii    i  ii i   v   ivi   i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_133089621_   3383 AAAAATCCACTCAAGATGGATCAAAGACTTAAATCTAAGACCCTGAAACC 3432
                               iv      i        ?    i     v     v - i    i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACT 525

  chr2_133089621_   3433 ATAAAGATTCTAAAAGATAACTTAGGAAAAACACTTCTAGACATTGGCTT 3482
                              iv ii  i    v   v    ?iv  vv    vv   v    v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_133089621_   3483 AGGCAAAGCCTTCATGACCAAGAACCCAAAAGCAAATACAACAAAAACAA 3532
                               v vi   v iivi v  vv         v vi        iv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_133089621_   3533 AGATAAATAGATGGAATTTAATTAAA-CTAAAAAGTTCTGCTCAGCAAAA 3581
                          i   i   i  v i i  v  i   -i      v  i  iv vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_133089621_   3582 GAAATAAGCAGCAGAGTTAACAGACAACCCACAGAGTGGGA---AATCTT 3628
                           v iv v  iv i   v  v              i     ---   v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_133089621_   3629 CACAATCCATACATCCGACAAAGGACTAATATCCAGAATCTATAGAGAAC 3678
                         ii   vi    i   i  i  i     vi          v    i     
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_133089621_   3679 TC----AAATCAGTAAGAAAAAAAAGAACAATCCCATCAAAAAGTGGGCT 3724
                           ----  v   i   v     i vi  i  i  v  i?    i     v
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_133089621_   3725 AAAGACATGAACACACAATTCTCAAAAGAAGATACACAAATGGCCATTAA 3774
                           i  iv    i v   v     v          i           v   
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_133089621_   3775 GTATGTGGAAAAATGCTCAGCATCACTAATTAT 3807
                          i ii  i   i       i     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (140 / 92)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 4.82 (53 / 11)  


 651 29.44 0.51 0.00  chr2_133119687_133126055        1   197 (6172)  C L1M4_orf2#LINE/L1   (710)   198     1  

C chr2_133119687_    197 TGGAAA-ACATTCCATCCTCATAGATAGGAAGAATCAATAGTGTGAAAAT 149
                               - i  i    vi    i   v      v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_133119687_    148 GGCCATATTGCCCAAAGTAATTTAGAGATTCCATGCTCTTCCCATCAAAC 99
                            v   i v      v i  i  v      v i  vv i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_133119687_     98 TACCATTGACATTCTTCACAGAATTAGAAAAAACTATTTTAAATTTCATA 49
                          v   vivi v  i  ii     v v  v  iviv  ii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr2_133119687_     48 TGGAACCATAAAAGACCCTGTATAGCCAAGACAATCCTAAGCAAAAAG 1
                              viii  ii     v v        i      i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

Transitions / transversions = 1.15 (31 / 27)
Gap_init rate = 0.01 (1 / 198), avg. gap size = 1.00 (1 / 1)  

3175 26.89 1.44 0.56  chr2_133119687_133126055     4978  5877 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_133119687_   4978 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5027
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_133119687_   5028 GGCCATACTGCCCCAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 5077
                            v     v   v iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_133119687_   5078 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5125
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_133119687_   5126 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCGAAAAG 5175
                                viiv  ii  v  v v  v     iv     i i ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_133119687_   5176 AACAAAGCTGGAGGCATCCCACTACCTGACTTCAAACTATATTACAAGGC 5225
                                i      vv  v    v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_133119687_   5226 TACAGTAACCAAAACAGCATGGTACTGGTACCACAACAGAGATATAGACC 5275
                                 i   i    ii         i iv vi i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_133119687_   5276 AATGGAACAGAACAGAGCTGTTAGAAATAATGCTGCATATCTACAACTAT 5325
                                i    iv   vvvii        vv iii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_133119687_   5326 CTGATCTTTGACAAACCTGAGAAAAGCA----ATGGGAAAAGGATTCCCT 5371
                         i    i  i     ivv  vv  i v  ----     i    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_133119687_   5372 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5421
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_133119687_   5422 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5471
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_133119687_   5472 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5521
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_133119687_   5522 ACG---AAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5568
                          v ---    -- -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_133119687_   5569 AAACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAGATGGGATCTA 5618
                         vi            vvi          vv     v  i i  v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_133119687_   5619 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGTGTGAA 5668
                           i   v v  i i   i  ii vv    i  v       vv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_133119687_   5669 CAGACAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5718
                         v        i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_133119687_   5719 AAGGGCTAATATGCAGAATCTATAATGAACTCAAACAAATTTACAAGAAA 5768
                          i  i  vi   v      v     v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_133119687_   5769 AAAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5814
                           i    ----   v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_133119687_   5815 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGTTCAT 5864
                            v        i  vi viii     v  i          i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_133119687_   5865 CATCACTGGCCAT 5877
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.25 (18 / 8)  


 606 22.29 3.43 3.43  chr2_133166507_133170414.rev     1583  1757 (2151)    L1M4_orf2#LINE/L1       14   188 (720)  

  chr2_133166507_   1583 CATGTTCATAAATTATAAGACTCAATATAGTACAGCTGTCAATTCTCCTC 1632
                                  ii   iv      i     v  vv  v  v    v    i 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_133166507_   1633 AAATTGATATACAGATTTAATACAATTCCTTTCAAAATCCACATAAGAGT 1682
                                 v        i  ii    i   v         -  ----- i
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC-CA-----GC 107

  chr2_133166507_   1683 TG------TTGTTGATATAGATAAGGTTATTCTAATATTTATATTGAAAG 1726
                           ------   iv  v  v  i   v v  i    v   i    v    v
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_133166507_   1727 GCAAAGGAACTAGAATATCAAGAATAATTTT 1757
                             i   v i      v v i  i   i  
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTT 188

Transitions / transversions = 0.95 (19 / 20)
Gap_init rate = 0.02 (3 / 175), avg. gap size = 4.00 (12 / 3)  

1038 24.43 6.30 4.03  chr2_133166507_133170414.rev     2033  2429 (1479)    L1M4_orf2#LINE/L1      174   579 (329)  

  chr2_133166507_   2033 AGCCCCAAAAACAGTTTTGAAAAAAAAAAA-----TGGGAGGAATTTGTC 2077
                             ---      i i        i  i  ----- v      v ivvv 
  L1M4_orf2#LINE/    174 AGCC---AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_133166507_   2078 TACCTCATTTTGAGACTTA-TATA--GCTAAAATAATCAAGA--ATGTGG 2122
                          v  iv    ii i     -  i --    v i         --i     
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_133166507_   2123 TATTGGTAGAGGTATAGTCATATAGATCAATAAAACAAAATAAGGA---- 2168
                           i   i v i v    v             ii  i i   vii  ----
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_133166507_   2169 --AAACAAATTCAAACAAATATGCACAACCGATTTTTGATAAGCATGCCA 2216
                         --   i   ii  v   vv    vv   ii      i  i   vi     
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_133166507_   2217 A-ACAATTAAGTGGAGAAAAGATAGCCTTTTCAACAAATGGTATTGAAGC 2265
                          -  v   v i   i    ii    i                ii  iii 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_133166507_   2266 AACTGGACATCGG-AGGCCAAAAAACAACAACAAAAACCTTGG-CCTAAA 2313
                                i ? vi- v  -    i ----- ii  i---    -  ivv 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGC-AAAAGA-----ATGAAG---TTGGACCCCTA 461

  chr2_133166507_   2314 TCTCACACCCTTATGTGAAA-TTAACTCAAAATGGATCACAGACTTGCAT 2362
                         i        v -  iii   -                  ?    i iv  
  L1M4_orf2#LINE/    462 CCTCACACCAT-ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_133166507_   2363 ATAAAA-CTAAATTTCTGTAAAATT-TTAGAAAAAAAATTTAAA---AAA 2407
                         i   i -     v--  i     i -      i    -iv  ii---   
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAA--CTATAAAACTCTTAGAAGAAAA-CATAGGNGTAAA 557

  chr2_133166507_   2408 TGTTCAGGACTGAGGGCTAGGC 2429
                          v   iv   ivv   i     
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGC 579

Transitions / transversions = 1.97 (63 / 32)
Gap_init rate = 0.05 (19 / 406), avg. gap size = 2.16 (41 / 19)  

 882 26.87 5.97 0.00  chr2_133166507_133170414.rev     2714  2981 (927)    L1M4_orf2#LINE/L1      547   830 (78)  

  chr2_133166507_   2714 ACAGGTGTGAGCCATCAC-ACCT--GGCTAGGC---------TTAGCCTT 2751
                          i   ?  i ii v  ii-    --  i     ---------    viv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_133166507_   2752 GATATCAAAAGCACAATC--CAAAA--AAGAACTGATAAACCGCACTTTG 2797
                           i i           v --     --  i  iv      ii v    ii
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_133166507_   2798 TCAAAATTTAAAACTTTTGCTCTGTGATAGACCCTGTTAAGAGGAGAAAA 2847
                                 v          iv  vii vi   v  i i    iiivi   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_133166507_   2848 AGATAAGCAACCAACTGAGAGAAAATATTTTCAGACCACATATCCAACAA 2897
                            i  v v  vi v  i            v  i i  i     ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_133166507_   2898 AGGACTAACACCTAGAATATATAAACAACTCTCAAAATTCAACAGTAAAA 2947
                         i     vii i i            v      i v  i    i i     
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_133166507_   2948 AAAGAAATAATTCAATTAGAAAATGGGCAAAAGA 2981
                          i v      ii     ?i            i  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 2.33 (49 / 21)
Gap_init rate = 0.02 (5 / 284), avg. gap size = 3.20 (16 / 5)  

 272 25.81 8.06 2.42  chr2_133166507_133170414.rev     3293  3416 (492)    L1M4_orf2#LINE/L1      778   908 (0)  

  chr2_133166507_   3293 TTACATCATATCAATTTTAGGAGGACAAA-----CATTTAGACAACAG-C 3336
                              v ---     vv  ii i      -----  v  ?i v  ii - 
  L1M4_orf2#LINE/    778 TTACAAC---TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_133166507_   3337 A---GATGTGAAGAGACAGTTCACTAAAGAGGAATTGTAGATGGTAAGTA 3383
                          ---   v    v     v   v i     i  vv ii i    iv i  
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_133166507_   3384 AGCACATGCAG-GACATTCAATATCATTAGCCCT 3416
                                 v i-  iii    i    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (18 / 13)
Gap_init rate = 0.04 (5 / 131), avg. gap size = 2.60 (13 / 5)  


3488 23.02 3.39 0.90  chr2_133190919_133194602     2307  3192 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_133190919_   2307 TGGAAAGATAACCCATGCTCATGGATTAAAAGA----ATATTGTTAAAAT 2352
                                   v      i         ii    ----          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_133190919_   2353 GACAATACTACCCAAAGCAAGCTACAGAT----------CTCTATCAAAA 2392
                          i       v      vii v        ---------- i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_133190919_   2393 TACCAATGACATTCTTCACAGAAATAGAAAAAAAAAAACCTTAAATTAGT 2442
                          v   iivi v  i  ii       v  v  ivvi v-   v     vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chr2_133190919_   2443 ATGGAACCACAAAAGACCCCAAATAGCCAAAGCAATACTGAGCAAAAATA 2492
                               vii   ii     vi          i    vi   iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_133190919_   2493 ACAGAGCAGGGAGCATCATACTACCTGACTTCAAAATATACCACAAAGCT 2542
                            i  iv  ii vv   i   v  ii i       iv   i        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_133190919_   2543 ATAGTAACCAACACAGCATAAT---GGTATAAAAACAGACATATAGACCA 2589
                          i     i   v    ii ii ---  i    ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_133190919_   2590 ACATAACAA----GAGAATCCAGAAATAAATCCATATATTTACAGCCAAC 2635
                          iiv  i i----    i            i     i     ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_133190919_   2636 TGATTTTCAGCAAAGGTGCCAAGAATACACACTGGGGAAAGGACACTCTC 2685
                                 ii   i          vi iv  v         i i v   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_133190919_   2686 TTCAATAAATGGTGCTGGGAAAACTAGATATCCAAATGCAGAAAAATGAA 2735
                              i              v    i    ?   v     i  i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_133190919_   2736 ACTAGGCTCTTATCTCCTACCATATACAAAAATTAATTCAAAATTGGAT- 2784
                         ii i i i i  i   vi                  i       -    -
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT-GGATC 498

  chr2_133190919_   2785 AAAGATTTAAATAAATGCAAGACCTGAAACTATAAAACTACTAGAAGAAC 2834
                          ?   ii     ---- i    v  i             vi        v
  L1M4_orf2#LINE/    499 AWAGACCTAAAT----GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_133190919_   2835 ACATAGGGG-AAATGCTTCAGGATGTTGGTCTAGGCAAAGATTTTTTGGG 2883
                                ? -    -    iv  iv    vi       v i   i  i i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_133190919_   2884 TAAGACTTCAAAAGCACAGACAACAAAA-----AATAGGCAAATGGAACT 2928
                           v   vi          ii        -----     ii    v i   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_133190919_   2929 ATATCAAACTAAAAAGCTTCTGCACAGCAAAGGAAACAATGAAGTGGGTG 2978
                         vi      v v    i   i  ii vv       v  v  v   vii   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_133190919_   2979 AAGAGAAAACCTGTAGAATGGGAGAAAATATTTGCAAACTATACATCCAG 3028
                           i   v    iii                        ii   i   iii
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_133190919_   3029 CAAGAGACTAATATCCAGAATCTACAAAGAATTCAAATAACTCAAAAGCA 3078
                         i   i    vi          v  i      i  vv i       v ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_133190919_   3079 AAAAACTGAATAATCTGATGTAAAA-TGGGCAAATGATTTGAATAGACAT 3127
                             ivii     i ii  v?    -        v               
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_133190919_   3128 TTCTCTAAAAAAAAAGACACAAGTGGCCAATAAGTATATGAAAAAA-ATT 3176
                              i   i  i -v i    i           i i       i -ii 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGA-TATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_133190919_   3177 CAACATCACTAATCAT 3192
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.23 (138 / 62)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.71 (38 / 14)  


3149 26.37 1.68 0.22  chr2_133397327_133401604.rev     2893  3787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_133397327_   2893 TGGAAACACATCCCATGCTCATGGATGAGTAGAATCAATATTGTGAAAAT 2942
                               v i        i        vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_133397327_   2943 GACCATACTACCAAAAACAATCTACAAATTCAATGCAATCCCCATAAAAA 2992
                          i v     v  v   vii       i      i        i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_133397327_   2993 TACCACCATCATTCTTCACAGAATTAGAAAAAAACAATTCTAAAATTCAT 3042
                          v   v vv v  i  ii     v v  v  iv-ii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_133397327_   3043 ATGGAACCATAAAAGAGCCACA-TAGCCAAAGCAAGACTAAACAAAAATA 3091
                               viii  ii  v   v -        i   vvi i  v  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_133397327_   3092 ACAAATCTGGAGGCATCACACTAACCAATTTCAAACTATACTATAAGGCC 3141
                              vi      vv       vv           viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_133397327_   3142 ATAGTCACCAAAACAGCATGGCACTGGTATAAAAATAGGCACATAGACCA 3191
                          i   v i   i    ii   i     i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_133397327_   3192 AAGGAACAGAACAGAGAACCCAGAAATAAACCCAAATACTTAACAGCCAA 3241
                          v    i    iv    ii               v i i   -ii i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAA 348

  chr2_133397327_   3242 CTGATCTTAGACAAAGCAAACAAAAACATAAAGTGGGGAGAAGACACCCT 3291
                         i    i  v     i vviv   i v   vv i      i ii i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_133397327_   3292 TTTCAACAAATGGTGCTAGGATAATTGGCTAGCCGCATGTAGGAGAATGA 3341
                                          i   i  i   v  ?  i    i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_133397327_   3342 AACTAGATCCTTACCTCTCGCCTCATACAAAAATCAACTCAAGATGGATT 3391
                          ii i  i  i      v i  vi          i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_133397327_   3392 AAGGACCTGAA-------------ACTATAAAATTTCTAGAAGATAACAT 3428
                          ?i     i  -------------         i ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_133397327_   3429 TGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGA 3478
                         v  ?iv  vi    vv   v    v        v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_133397327_   3479 ACCCAAAAGCAAATGCAATAACAACAAAGATAAATAGCTGGGACCTAATT 3528
                         vv         v v    i  v iv   i   i   iv v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_133397327_   3529 AAA-CTAAAGAAATTTGCACAGCAAAAGGAACAGTCAGCACAGTAAACAG 3577
                            -i    i vv    ii vv    i iv  vi   iv v   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_133397327_   3578 ACAGCCCACAGAGTGGGAGGAAATCTTCACAATCTGTACATCTGACAGAG 3627
                            i        i      i    v  ii   viii  i      i ii 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_133397327_   3628 GACTAATATCCTGAATCTACAATGAACTCAAATAAATCAGTAAGAAAAAA 3677
                             vi     v    v  i  v      vv i  v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_133397327_   3678 ACAAACAATCCCATCAAAAAGTGGGCTAAGGACGTGAATAGACAATTCTC 3727
                              i  i  v  i?    i     v     iv          v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_133397327_   3728 AAAAGAAAATATACAAATGGCTACCAAACATATGAAAAAATGCTCAATAT 3777
                         v      i             i vi  i  i       i        i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_133397327_   3778 CTCTAATGAT 3787
                          v????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 3.40 (17 / 5)  


3106 25.17 2.81 0.79  chr2_133423928_133427151.rev     1842  2731 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_133423928_   1842 TAGAAAATCATCTAATTCTCAGGGATAAGCAGAATTAATATCATTAAAAT 1891
                          i    ivi   iv  vi   v    vi v   v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_133423928_   1892 AACCATACTACCC----TAATCTAGAGATTCAATGCAATCCCTATCAAAA 1937
                         ii v     v   ---- i     v        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_133423928_   1938 TGCCAA-TGTCACTGTTTCGCAGAATTAGAGAAAC-ATTCCTAACATTCA 1985
                          v   i-  i -- v   i      v v  v  i -iv      v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_133423928_   1986 TATGGAATGAAAAAAGACCCCAAATAGTCAAAGTAATCCTAAGCAAAAAG 2035
                                vviv  ii     vi     i    ii    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_133423928_   2036 AACAAAGCTGGAAGCATCACATTACCTGACTTCAAATTATATTACAAGCC 2085
                                i    i vv     i v  ii i      viv  i     iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_133423928_   2086 TATAGTAATCAAAATGGCATGGTATTGGTATTAAAATATTC-TGT---TC 2131
                           i         i ii ii     i   i  v ii   vv - i ---  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_133423928_   2132 AATGGAACAGAATAGAGAACTCAGAAATAAACACACATTATTTACAGCCA 2181
                                i     v    iii           v  i i-     ii i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC-ATTTATGGTCA 347

  chr2_133423928_   2182 ACAGATCTTTGACAAAGCTGACAAGAGCATGCATTGGATAAAGAACACTC 2231
                          iv   i  i     i v  v     v   v  v   iv      i v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_133423928_   2232 TTTTGAATAAATGATTCTGGGAAAATTGGATTGCCATTTGCAGAAGAATT 2281
                             v  i     i v      v  i     v?   iv    i      v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_133423928_   2282 AAGCTGAAGCCACATCGCTCACCATGTACAAAAATCAACTCAGGATGGAT 2331
                            i  i v  vi i v v      i         i      ii      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_133423928_   2332 TAAAGTCTTAAACATAAGACCCAAAACTAC--------TAGAAGAAAACA 2373
                         i ?  v i    ii     v i       i--------            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_133423928_   2374 TAGGGGAAACATTTCAGGACACTGATCTAGGCAAAGATTTTTATGGATAA 2423
                             ? v  vvi   iv   vi  ivi       v i   i - i    v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT-TAGATAT 596

  chr2_133423928_   2424 GACTTCAAAAGCACAGGCAACAACAACAAAAAATAGACAAA---GAAACC 2470
                            vi          i       -  v          i   ---  vvi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAA-AAGAAAAAATAGATAAATTGGACTTC 645

  chr2_133423928_   2471 ATATAAAGCTAAAAAGCTTCTGCACAGCAAATGAAATAATCGACAGAGTG 2520
                           -i   ii      -   i  ii vv    v  v iv   i v i    
  L1M4_orf2#LINE/    646 AT-CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_133423928_   2521 AACAGA--ACCTGCAGAATGGGAGAATACATTTGCAAACTATTGATCTGA 2568
                           v   --   ii             v i         ii  vv      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_133423928_   2569 CAAGGGACTAACATCCCGAATATACAAGAAACTCAAACAATTCAGCAACA 2618
                         i        vii    v       i  ii     vv    i   ii  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_133423928_   2619 ACAATG-AAATAATCCCATTAAAAATGGGGTAAAGGACATGAATAGACAT 2667
                          v  vi-      i  v   ?    vv   i      iv           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_133423928_   2668 TTTTCAAAAGAGGGCATACAAATGACCAACAGGTATATGAAAAAA-GCTA 2716
                           i  v     i ii         i    i i i i       i -   v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_133423928_   2717 AACATCACACATCAT 2731
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (133 / 87)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.00 (32 / 16)  


 354 19.80 8.91 4.95  chr2_133775522_133779995.rev      949  1049 (3425)  C L1M4_orf2#LINE/L1   (790)   118    14  

C chr2_133775522_   1049 CATACTTATGGATTGGAAGACTTAA--------AGATGTCAAT-TTTCCC 1009
                            ii i                  --------     v    -i i   
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

C chr2_133775522_   1008 AAATTGATATTTAAATTTAATGCCATTTCTATAAAATTTCCAGTGAGATG 959
                                 v vi i   i  i  v  ii    v   v i    i----  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC----TG 109

C chr2_133775522_    958 GCCTTCTTTG 949
                         -    i    
  L1M4_orf2#LINE/    110 -CCTTTTTTG 118

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.04 (4 / 105), avg. gap size = 3.50 (14 / 4)  

2970 26.08 1.99 1.66  chr2_133775522_133779995.rev     3078  3982 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_133775522_   3078 TGGAAAAATATTTTATGCTTATGGATCAGAAAAATCAATATTATTACAGT 3127
                               i    iii   i i      ii   i v i      i   -  v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGA 49

  chr2_133775522_   3128 TGGCCATACTGCCCAAAGCAATTTATAGGTTCAGTGCTGTTTCTGTCAAA 3177
                             v     v      vii  i  i  i    ii  vi ii  i     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_133775522_   3178 ATACTAA-TGTCATTTTTCACAGAAATAGAAAAAAAAACTG-TTCTAAAA 3225
                           v i i-  i -     ii       v  v  i----   - i      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG----CTGATCCTAAAA 144

  chr2_133775522_   3226 TGTATATGGAACCAAAAAAGAGCGTAAATAGTCAAAGAATTCTGGAGCAA 3275
                          vi        viiv  ii  v vvi     i    iv v   v  --  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AA 192

  chr2_133775522_   3276 AAGAAG--CATAGCTGGAGGTATTACATTACCCAACTTCAAACTATACTA 3323
                               --  v  i      vv i   i v     i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_133775522_   3324 TAGTGCCACAGTAACCAAAACACCGTGGTACTGGTGCAAAAGCAGACACA 3373
                         i iv  i       i   i   vi          iii  iiii     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_133775522_   3374 TAGACCAGTGAGAAAGAATAGAAAACACTGAAATAAAGCTGCACACCTAT 3423
                             i  i  ii v     v  i iiv v        v iii   ii   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_133775522_   3424 AACCATCTGATCTTTGACAAAGTTGACAAAAAATAAGCAATAGGGAAAGG 3473
                         iii  vi    i  i     i v  v   i v-i vv    i       i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGA 391

  chr2_133775522_   3474 A-ATCCTATTCAATACATGATGCTGGAATAGCTGGCTAGCCATACGCAGA 3522
                          - vi  v     i v   i      i i i    v  ?   i i   i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_133775522_   3523 AGAATGAAATTGGACCCCTAGCTCTCATCCTATACAGAAATTAACACAAG 3572
                                 i           v   v  i v      i        v   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_133775522_   3573 ATGGACAAAAGACTTAAATGTGTGAATTCAAACTATAAAAATTCTGGAAG 3622
                              iv ?    i       iv  ii v           v ii i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_133775522_   3623 AAATCCTAG---CAAATACTCTTGTAGATAGTGGTCTAGGCAATGAATT- 3668
                            v v   ---i    -  - i  -  ivv   vi         iv  -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CT-TCGT-GACCTTGGGTTAGGCAATGGTTTC 588

  chr2_133775522_   3669 TAAGATGAAGACCCCAAAAGCAAAAGCAACAAAATAAAAAATAGGCAAAT 3718
                          v    - v   v         v           v         ii    
  L1M4_orf2#LINE/    589 TTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_133775522_   3719 GAGACTT------AACTAAAGAGCTTCTGCATAGCAAAATAAACTTTCAA 3762
                         vi     ------  i    i -   i  iiivv    iv v   v    
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_133775522_   3763 CAGAGTAAACAGAAAACCTGTATGTTGGGAGAAGATATTTGCAAACTATG 3812
                         v i   i  v   v    iii viv        i           ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_133775522_   3813 CATCTGACGAAGGTCTAATATCCAGAATCTATAAGAAACTTAAACAAATT 3862
                         i      ii i  v  vi          v     ii    ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_133775522_   3863 AACAAGCAAAATACAAACCAACCCC-TTAAAAAGTGGGCAAAGAACATGA 3911
                           i  vv    v     i-     v-  ?    i         i iv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_133775522_   3912 ATAGACACTTCTCAAAAGAATACATGGAAGCAGCCAACAA--ACATGAAA 3959
                                i     v      v i  iv  iii     i  --        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_133775522_   3960 AGATGTTCAATATCACTAGTCAT 3982
                              i    i    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (148 / 85)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.65 (33 / 20)  


1619 27.98 10.04 1.34  chr2_133782765_133784459      462  1208 (487)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr2_133782765_    462 AAAATTCCAGTGAGATATTTTTTAAATATATG-CAGGATTATTCTAAAAT 510
                              i    ivivv v    vi i v  -  -  i v v  i       
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAAT 145

  chr2_133782765_    511 ATATATGGAAAGGCAA------------AGCTAAAACTAATGTGAAAAAT 548
                         vi         v    ------------   i     v viv       -
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA- 194

  chr2_133782765_    549 GAAGAATAAAGTGAGATGAATC-TACT---AAATTCCATGACTTATTATA 594
                               i     vi  v  v  -i   ---v    i  vi     i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_133782765_    595 TTGCTGCAGTAATCATGACTGTGTGTTATCAGTGGAGGGACGGACATA-- 642
                         vv   i         v   v     v  iii iiv i   ii      --
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_133782765_    643 GATAAATGGGACCCAATAAAGAAACCAGAAATACACC--TGCATGAATAA 690
                            v     i ivv   vi   iv         v   -- i   vv  i-
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG- 343

  chr2_133782765_    691 GTCCAACTAATTTTTGACAAATATGCAAAAGTAATTCCATGTGGGAAAAA 740
                            -  i i     i     ivi   v  iiiv    v   v  i  i  
  L1M4_orf2#LINE/    344 GTC-AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_133782765_    741 CAGTCTT--CAAAAAATAGTG---GAAAAATTGGCCATCTATAGGCAACA 785
                         i      --   v    i   --- i v  i   vi ? i i v    v 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_133782765_    786 AAAAGAACTTCAACCTAAGTCTTATACCA-------------------AA 816
                         i  v   v  vi   ivvii  i i    -------------------  
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_133782765_    817 TGTATCACAAGCTTTAAAT--------TGAAACTGTAGATCTTTTAGAAA 858
                           v    ? ii i -    -------- i     i  i v  i      i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCT-AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_133782765_    859 A-----TAGGAGAAAATTGTTGAGAACTAAACCTACGCAAATAGTT-CTT 902
                          -----    ? v    iv i v  v  viivi  v    - i   -   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTT 590

  chr2_133782765_    903 AGACTTGCTACCAGTAGCACAAATCCATAAAAGGGAAAAC-------CTG 945
                            iv  vi    iv       i- v i     ii    i-------i  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTG 639

  chr2_133782765_    946 GGCATCATCGAAAT-GAAAACTTTTGTTCTGTGAAATATCCATGTTAAGA 994
                          i v     i    -i           v  vii  iv iv - i i    
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC-TATCAAGA 688

  chr2_133782765_    995 GGATGTAAA--TCAGTTATACACTGGGAGAAAACATTTACATACCACATA 1042
                         iii  v   --iv vii i v v          i    i  v i  i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_133782765_   1043 TACTACCAAGG-ACTAGTTTCCAGAATATATAATGGACTCTCAAAGCTCG 1091
                          -  ivi    -   v  v              v i     i v i   i
  L1M4_orf2#LINE/    739 T-CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_133782765_   1092 A-AAGAAAAAAAAATACAATTCAATTAGAAAACGGGCAAAAAGACATGTA 1140
                          -  v     i v v i  ii     ?i    i       i-  iv  v 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG-GATTTGAA 836

  chr2_133782765_   1141 GAGACATTTC---AAAGATTATACACAAATGACAAATAAGCACAT-AAAA 1186
                         v         ---     vv   i       i v           -    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_133782765_   1187 GATATTCAATGCCACTAACCAT 1208
                            ii    iii  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (120 / 85)
Gap_init rate = 0.04 (29 / 812), avg. gap size = 2.93 (85 / 29)  


1975 24.22 10.12 2.29  chr2_133789393_133791289      577  1406 (491)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_133789393_    577 CATATTTGTGGATTAAAAGATTCAATATT-TTAAGATGTCACTTCTGCCC 625
                            i  ii      ii    i i      -        v  v v  v   
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_133789393_    626 ACATTGATACAGAGATTCAATGCTAT---TATTAAAAAGTCA-CTGGAGG 671
                          v      vi v        i  v  ---   i    vvi  -   vvvv
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_133789393_    672 TAGTGTGAGGAAATTGACAAGCTGTTTCCAATACTGACATGGAAATTACA 721
                          -- v  vi               v i i  v i v i        vvv 
  L1M4_orf2#LINE/    114 T--TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_133789393_    722 GGGACCTAGAACAGCAAAAATA-TCTTGGAAACGAA---CAAAGTT---- 763
                               i    i   v    i -     i   v   ---       ----
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_133789393_    764 --------CTTT----TTTTAAAATCTTATTACACAATCAAAATAATCAA 801
                         --------   i----   i    -    i    v iii v i       
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAA-CTTACTACAAAGCTACAGTAATCAA 260

  chr2_133789393_    802 -ACAGTGTGGTATTTGCA-AAGCACAAACAAACAGA--AATAAAA--GAA 845
                         -           i v   -   v i i   v i   --   ii  --   
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_133789393_    846 GTTAGAGTCCAGATATTGAGTTGTGCATGTAGAGACAAAGGGTTTTCAGC 895
                         v v          v  vi viii i   v  vi v   vv i     ii 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_133789393_    896 AAAGGAACCAAGAA-ATTCAATAAAGGAAATAA-ATTCATTTCAAAAAAT 943
                           i  vi      v-       ii-     v  - v  v      v    
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_133789393_    944 GATAC--AAATG--TGGATATCTACATTTAAAAAAATACAACTTAACCCC 989
                          i i --ii ii--      ? i    vi    i   iv ii vi     
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_133789393_    990 TAAACACACATCATAGATAAAAATTAAGTCCCAACAGATCATGGACCTAA 1039
                           v- v    i    v i         v  vv  ii     ?i       
  L1M4_orf2#LINE/    460 TAC-CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_133789393_   1040 AACATAAAATCTAAAACTATAAAACTTGTAGAAGAAAACACAAAACAATA 1089
                          -ii   i v                iv            i ii?vv v 
  L1M4_orf2#LINE/    509 A-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_133789393_   1090 TTTTTTGTAAACATAGGGTAGGCAAACGTTCCT-AGA----ATACAGAAA 1134
                          i  i-  i v v i  v       vv   i  -   ---- i  vi   
  L1M4_orf2#LINE/    558 TCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_133789393_   1135 GCATAAAC--TAGAAAAATAAATAGAGTTTTAATACTAGACT-------- 1174
                            i  i --i i  i  v       ----   - i i    --------
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGA----TAA-ATTGGACTTCATCAAA 651

  chr2_133789393_   1175 -------GCTTCTGTTCACCTAAAGACGCCATTATTTAAAATAAATATGC 1217
                         -------i   i   v vi v  i   i i  i vv-   i i  v vi 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAAAGAC 700

  chr2_133789393_   1218 AAACCAAAGAATGGGGGAAAA-ATT-GCAACACATAT-TTTGACAAGAGA 1264
                           v   v        i     -   -    vv     - i   i   i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_133789393_   1265 CTTATATTCAAAATATGTAAAGAACTCATACCACTCAATGATTTCTTTAA 1314
                            i   i  i     i          v   v       i  ------  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT------AA 794

  chr2_133789393_   1315 AAAG-CAGTCACCTCCCTC---AAATAGGCAAA--------ATA---ATT 1349
                             -  ivi v i vv i---    i      --------   ---   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_133789393_   1350 T-----AACAA-ATACATAAATGGACAATAAGCACATGAAAAG-TACTCA 1392
                          -----  v  -   i i      v                  - i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_133789393_   1393 ACATCTTTTATCAT 1406
                              v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (112 / 86)
Gap_init rate = 0.04 (39 / 895), avg. gap size = 2.64 (103 / 39)  


3278 25.95 1.56 0.45  chr2_133974620_133980988.rev     4980  5877 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_133974620_   4980 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5029
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_133974620_   5030 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5079
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_133974620_   5080 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTC 5126
                          v   i-       i  -i     -   -- v  i  - iii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_133974620_   5127 ACATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAGTCCTAAGCCAGAA 5176
                          i      viiv  ii  v  v v  v     iv  i  i i ivv    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_133974620_   5177 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5226
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_133974620_   5227 CTACAGTAACCAA-ACAGCATGGCACTGGTACCAAAACAGAGATATAGAC 5275
                                  i   -    ii   i     i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_133974620_   5276 CAATGGAACAGAACAGAGACCTCAGAAATAATACCACACATCTATAGCTA 5325
                                 i    iv    vii         vv   i    i   i ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_133974620_   5326 TCTGATCTTTGACGAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5375
                         vi    i  i   i ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_133974620_   5376 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5425
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_133974620_   5426 AAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTAAAGATGGAT 5475
                           ii    i    v   i    iv              i v  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_133974620_   5476 TAAAGACTTACATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAACT 5525
                         i ?    i  v    v   v  i    i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_133974620_   5526 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5574
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_133974620_   5575 AACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGGATCTAA 5624
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_133974620_   5625 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5674
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_133974620_   5675 AGGCAACCTACAGAATGGG-GAAAATTTTTGCAATCTATTCATCTGACAA 5723
                           i     i          -      v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_133974620_   5724 AGGGCTAATATCCAGAATCTACAAAGAACTC----AAATTTACAAGAAAA 5769
                         i  i  vi          v  i         ----  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_133974620_   5770 AAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 5815
                          i    ----   v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_133974620_   5816 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTTGTC 5865
                           v        i  vi viii     i ii          i     iiv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_133974620_   5866 ATCACTGGCCAT 5877
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (137 / 92)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


1999 22.59 1.15 8.06  chr2_134020875_134022561.rev      501  1195 (492)    L1M4_orf2#LINE/L1      262   908 (0)  

  chr2_134020875_    501 ACAGT-TGGTGCTGGTACAAAAATAGACATATAGACCAATGGAACAGAAT 549
                              -    i    i i  ii             i        i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_134020875_    550 AGAGAACACTGAAATAAAGCTCTACACTCATGACTAACTCATCTTCAACA 599
                         v    iiv v        v iv    i i   iii  i v  i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_134020875_    600 -----GTCAACAATAATAAGCAATGGGGAAAGGACTCCCTATTCAATAAA 644
                         ----- i   v vi v ---            i ivvi  v     i   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATT---CAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_134020875_    645 TGGTGCTGGAAAAACTGGCTAAGTATATGCAGAAGAATGAAACTGGACCC 694
                                  i v      v  ?vi i     i         ii       
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_134020875_    695 CTACCTCTCATCATATGTAAAAATTAACTCAAGATGGATTAAAGACTGAA 744
                                v  i     ii              i      i ?    iv  
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_134020875_    745 ACGTATGACCGCAAATTATAAAAATGCCAGAAGAAAACCTAGGAAATACT 794
                          i   v  v vv   i       v vii          v    ?ivv v 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_134020875_    795 CTTCACGTCATTGGCTTAGGCAAAGAATTTAT-GATGAAGACTCCAAAAA 843
                             ii v v    v        v iv  iv -   - v   v      i
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAG 607

  chr2_134020875_    844 CAAAAGCAACAAAACCAAAGG-AGACAAATGAGACTTAATTAAACTAAAG 892
                           v           vv   ii-   i    vi     v  i   v v  i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_134020875_    893 AGCTTCTGTACAGCAAAAGAAACTCTCAACAGAGTAAACAGACAAACTAC 942
                          i   i   i vv    i  v   v    v i   i  v      v i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_134020875_    943 ACATTGGGAGAAAATATTTGCAAACTATGCATCCAAGAAAGGACTAATAT 992
                          v v                    ii  ii   ii v  i     vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_134020875_    993 TCAGAATCTACAAGAAACTTAAATGAGTCAACAAGAAAAAACAAATTTAT 1042
                         i      v  i  ii    ivv ii v    i  ----------------
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAA---------------- 791

  chr2_134020875_   1043 TAAAAAGTGGGCAAAGATAATTGTATATACCTACTATGTACCCACAAAAA 1092
                                --------- i  ------   ----------     ----- 
  L1M4_orf2#LINE/    792 TAAAAAG---------ACAA------ATA----------ACCCA-----A 811

  chr2_134020875_   1093 TTAAAAAATCAAGAAGAGCAAAGGACATGAACAGTTATTTCTCAAAACAA 1142
                           ?      ------ i        iv    i  vi       v   v  
  L1M4_orf2#LINE/    812 TTWAAAAAT------GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_134020875_   1143 GACATAGAAGCAGCCGACAAACATATGAAACAATACTCAACATCACTAGT 1192
                           i   v  iii   i i  i  i      vi  i          ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_134020875_   1193 CAG 1195
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.43 (90 / 63)
Gap_init rate = 0.02 (12 / 647), avg. gap size = 5.33 (64 / 12)  


3332 26.13 0.55 0.55  chr2_134056563_134062841.rev     4881  5787 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_134056563_   4881 GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATG 4930
                             ii i  i     i      i v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_134056563_   4931 GCCATACTGCCCAAGGTAATTTTTAGATTCAATGCCATCCCCATCAAGCT 4980
                           v     v     iv i  i vi        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_134056563_   4981 ACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                         v   i-       i  -i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_134056563_   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_134056563_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_134056563_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGGGATATAGATC 5177
                                 i   i    ii         i iv ii i  iv         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_134056563_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_134056563_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_134056563_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAATCT 5325
                           v  i  i              v      v  ?   i   i i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_134056563_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_134056563_   5376 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_134056563_   5426 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_134056563_   5476 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTCA 5525
                         i            vvi           v     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_134056563_   5526 TTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i     i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_134056563_   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_134056563_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_134056563_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_134056563_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5775
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_134056563_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 1.43 (10 / 7)  


3552 18.82 3.81 3.93  chr2_134125888_134129406.rev      656  1521 (1998)    L1M4_orf2#LINE/L1        1   865 (43)  

  chr2_134125888_    656 TGGAAAGACATCAAATTTTCATGGACCAGAAGACTGAGCATTGTTAAGAT 705
                                 i   vv  v        iii       v ii           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_134125888_    706 GGCACTACTCCCCAGATTGATCTACAAACTCAATGCAATC---------- 745
                             v         i           i i    i      ----------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_134125888_    746 TCCCAGTTGGATTTTTTTGCAGACATTTATAAGTTGATCTCAAAATTCAT 795
                               i  v-i           v   v i   i     ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_134125888_    796 ATGAATTTCCATATGGAAATGCAAGATATCAAAAACAGCCAAATCA-TCT 844
                            ------------          iv i v i  i       v  -   
  L1M4_orf2#LINE/    150 ATG------------GAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_134125888_    845 TGAAAATAAAGAATGAAGTTGGAAGATTCACACCTCC-AATTTCAAA-CC 892
                               vi     ii        i  i      i   -         - i
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_134125888_    893 TACTATAAATCTATAGTAATCAAGATAGTACTGTGCTGACATAAGGCTAG 942
                              i   v   i           i   iiv  i   i       v   
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_134125888_    943 ACATATACATCACAGGTAGAGAATTAAGAGTGCAGAAATGAATTCTCTCA 992
                                v    vv  v v      i     v       i  ii viv  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_134125888_    993 CTTATAGTCAATAGACTTTTGACAAGGGAGCCAAAACAGTTCTGTGAGAA 1042
                         i    i      v  i   i        v     i  vi   vi  i i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_134125888_   1043 AAAGAATAATCTTCTCAACAAATAATGTTAGGATAATTGGAGATTCATGT 1092
                           -     i    i         ii  i i   i  i    v ?i  ii 
  L1M4_orf2#LINE/    388 AA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_134125888_   1093 ATAAAAGAG-GAAATTCGGATTCCTATCTCAAACC-TAC-CAAAAA--AA 1137
                         ii      i-   i  -   ii    i    v   -  i-      --  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTT-GGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_134125888_   1138 CCCTTAAAATGAATTATAGACCTAAATGTAAGAGCTAAAATTATAAAACT 1187
                          -- i      i  i ?                       i         
  L1M4_orf2#LINE/    486 C--TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_134125888_   1188 TCCATAA-------TAGAAGTAAATCTTCACTGCCTTGGATTAAGCAATA 1230
                         iii v  -------   i?          iivi      i   i     i
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_134125888_   1231 GTTTC--AGATCTGACATCAAAACCATAAGCAACAATA-AAAAAACAGAT 1277
                              --    v     i     v  i         v -      i    
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_134125888_   1278 AGCTTGGACATCAGTAAAATTTAAAAAAAAATGTGCCTCAAAGGATATTA 1327
                          iv      v   vi      -     vvvv     i        i i  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_134125888_   1328 GCAGGAAAGAAAAAAAGC--CCCATGAAATAGGAGAAAATATTTGCAAAT 1375
                         v  i     vi    ii --    iii   i                   
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_134125888_   1376 ATTATATGTGACAAGGAACTTCTAACCAGAATATATAAAAAAAACTCTTA 1425
                         vv     v   i    i    v  v              i  --      
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA--CTCTTA 780

  chr2_134125888_   1426 GAACTCAATAATAAAAAC-CAAATCACCCAATT--AAAATGGACAAAAAT 1472
                         v                v-     v        --       i    ii-
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG- 829

  chr2_134125888_   1473 CTGAATTGATATTTGGAATACAGATATTTCTCTTAAAAAGACATGCAAA 1521
                         ----------     -    --  i       iv  i    i  i    
  L1M4_orf2#LINE/    830 ----------ATTTG-AATA--GACATTTCTCCAAAGAAGATATACAAA 865

Transitions / transversions = 2.08 (108 / 52)
Gap_init rate = 0.03 (24 / 865), avg. gap size = 2.79 (67 / 24)  

2645 25.32 0.86 0.14  chr2_134125888_134129406.rev     1522  2220 (1299)    L1M4_orf2#LINE/L1      205   908 (0)  

  chr2_134125888_   1522 GCTGGAGGTATCACATTACATGACTTCAAATTATACTACAAGGCTATACT 1571
                          i      vv     i v vii i      viv        i    i v 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_134125888_   1572 GGCCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGATTAATGGA 1621
                         iii   i    ii         i i  ii i     i      i      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_134125888_   1622 AGAAAATACAGAACCCAGAAATAAAGGCACATACCTACAATCAACTGAAT 1671
                          v i   vv   ii           vv  i i ii  iii    i   v 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_134125888_   1672 TTTGACACAGTTGTCAAAAATATACAATGGGGAAATGACACCCTAATATA 1721
                           i    vi v  i   i vi  v           vi i vi  vv vv 
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_134125888_   1722 TAAGTGGTGCTGGGAAAACTAGAAAGCCATATGTAGAAGAATGAAACTGG 1771
                         i  i           v    i  v ?   i   i i         ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_134125888_   1772 ACCCCTACCTCTCACCATATATAAAAATTAACTCAAGATGGATTAAAGAT 1821
                                    v         i              i      i ?   i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_134125888_   1822 TTAAGTGTAAGACCTGAAACTATAAAAATCCTAGAAGAAAACCTTGGAAA 1871
                         i   i       v  i           v  i           v v  ?iv
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_134125888_   1872 TACTCTTCTGGACATAGGCCTAGGCAAAGAATTTATGACTAAGACCTCAA 1921
                         v v     vv   v v  vi       v iv  iv iiv  v   vi   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_134125888_   1922 AAGC-CAATGCAACAAAACAAAAA-TAGACAAATAGGACTTAATTAAACT 1969
                             -   -         v     -    i    v      v  i   v 
  L1M4_orf2#LINE/    605 AAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_134125888_   1970 AAAAAGCTTCTGCACAGCAAAAGAAATAAACAATAGAATAAACAGACAAC 2019
                         v    i   i  ii vv    i  v iv v   v i i i  v       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_134125888_   2020 CTACAGAATGAGAGAAAATATTTGCAAGCTATGCATCTGACAAAGGACTA 2069
                          i        i                iii  ii      i  i     v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_134125888_   2070 ATATCCAGAGTCTACAAGGAACTCAAACAACTCAGCAAGAAGAAAACAA- 2118
                         i        i v  i  i      vv        ii  v  i  i    -
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_134125888_   2119 ---CTGCATTAGAAAGTGGCCAAAGGAGGTGAACAGACATTTTTCAAAAG 2165
                         --- ivv   ?i   i   v       vv    i        i  v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_134125888_   2166 AAGACGTACAAGTGACCAACAAACATTTGAAAAAATGCTCAACATCTCTA 2215
                             ii     i  i    i  i  iv      i            v???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_134125888_   2216 ATTAT 2220
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.51 (104 / 69)
Gap_init rate = 0.01 (4 / 704), avg. gap size = 1.75 (7 / 4)  

 296 13.79 0.00 0.00  chr2_134125888_134129406.rev     2970  3027 (492)    L1M4_orf2#LINE/L1      851   908 (0)  

  chr2_134125888_   2970 AAAACAATATACAAGTAGCCAATAAACACATGAAAAGATGCTGAACATTA 3019
                           i vi        i i        i                v     i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_134125888_   3020 TTAGTCAT 3027
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.00 (0 / 0)  


3313 26.98 0.22 0.22  chr2_134205091_134215364     3880  4787 (5487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_134205091_   3880 TGGAAGAACATCCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3929
                              ii i        i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_134205091_   3930 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3979
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_134205091_   3980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTCA 4027
                          v   iivi i  i  ii     -   -- v  i  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_134205091_   4028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_134205091_   4078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_134205091_   4128 TACAGTAACCAACACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4177
                                 i   v    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_134205091_   4178 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCCCATATCTACAACTAT 4227
                                i    iv   ivii         vv  vi i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_134205091_   4228 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 4277
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_134205091_   4278 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 4327
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_134205091_   4328 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 4377
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_134205091_   4378 AAAGCCTTAAACGTTAGACCTAAAACCATGAAAACCCTAGAAGAAAACCT 4427
                          ?  v i    i  v   v       i  i   vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_134205091_   4428 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 4477
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_134205091_   4478 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 4527
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_134205091_   4528 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 4577
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_134205091_   4578 GCAACCTACAAAATGGGAGAAAATTTTCACAACCCACTCATCTGACAAAG 4627
                         i     i   i             v  ii   vi  ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_134205091_   4628 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 4677
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_134205091_   4678 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 4727
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_134205091_   4728 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 4777
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_134205091_   4778 CACTGGCCAT 4787
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  

2886 27.09 1.56 0.45  chr2_134205091_134215364     8886  9782 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_134205091_   8886 GAAAACACACTCCATGCTCATGGATGGGTAGAATCAGTATTGTAAAAATG 8935
                          i   v i ii     i        v  v   v i i      v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_134205091_   8936 ATCATACTGCCAAAAGCCACCTATAAATTCAATGCAGTTCTCATGACAAT 8985
                         iiv     v  v   viv i   i i      i   i i ii  v v   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_134205091_   8986 ACCATCAGTCTTC---ACAGAACTAGAAAAA---ATCCTAATATTCATAT 9029
                         v   v v i   i---i     v v  v  i---       v        
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_134205091_   9030 GGAATCAAAAAAGAGCCCACATAGCCAAAGCAAGCCTAAGCAAAAAGGAC 9079
                             viiv  ii  v  viv         i   v i i iv  i   i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_134205091_   9080 AAATACGGAGTCATCACATTACTCAACTTCAA--CTATACTATAAGGCCC 9127
                            vvi    vvv     i v i   i     --  -     i  i  iv
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTA 250

  chr2_134205091_   9128 TAGTCACCAAAACAGCATGATACTG-TATAAAAATAGGCACATAGACCAA 9176
                         i   v i   i    ii  i     -i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_134205091_   9177 TGCAACAGACTAGAGAACCCAGAAATAAAGCCAATTGCTTACAGCCAACT 9226
                           v  i   v v    ii           v   vviii   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_134205091_   9227 GATCTTTGACAAAGTAAACAAAAACATGAGGTGAGAAAAGGACAGCCTAT 9276
                            i  i     i vviv   i v   vvii  i i    i i  i  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_134205091_   9277 TCAACAAATGGTGCTGAGATAATTGGCAAGCCAAATGTAGAAGAATGAAA 9326
                                         i  i  i   vv ?   v   i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_134205091_   9327 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGAATCAA 9376
                         i    i  ii i   v    v           i       i   i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_134205091_   9377 AGACTTAACTCTAAGACCTGAAACCATAAAGACTCC-AGAAGATAACATC 9425
                             i   v v     v  i    i     -    i-      v     v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATA 549

  chr2_134205091_   9426 GGAAAAACTCTTCTAGACATTGGCTTAGGCAAAGACTTCAT-GACCAATA 9474
                           ?iv  v     vv   v    v        v ii   v -  i--  i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATG 597

  chr2_134205091_   9475 AC-CCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATAGGATTTAAT 9523
                           -         v v         iv   i   i   i  v   i  v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_134205091_   9524 TAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATGAGCATGGTTAACA 9573
                         i   v v    i   i  ii vv    i  v iv  v iv vi  v  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_134205091_   9574 GACAACCCAGAGG--GGGAGAAAATCTTCACAATCTATACACCTGACAAA 9621
                                  v  i--          v  ii   vii   i i    i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_134205091_   9622 GGACTAATATCCAGAATCCACAAAGAACTCAAACAAATAAGCAAGAAAAA 9671
                              vi          vi i         vv    v v ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_134205091_   9672 ATCAAACAATCCCATCAAAAACTGGGATAAGGACATGAATAGGCAGTTCT 9721
                         iv    i  i  v  i?    v    vv     iv       i  v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_134205091_   9722 CAAAAGAAGACATAAAAATGGCCAACAAGCATATGGAAAAATGTTCAACA 9771
                          v        i   v          i     i   i   i   i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_134205091_   9772 CCACTAATTAT 9782
                         i  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 1.64 (18 / 11)  


1258 24.86 3.01 1.09  chr2_134238701_134243219     2830  3195 (1324)    L1M4_orf2#LINE/L1        1   373 (535)  

  chr2_134238701_   2830 TGAAAAGATATCCTATGTTTATGGATTGGAAGACTTAATATTGTTTAAAT 2879
                           i          i     i                         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_134238701_   2880 GTTTATGGTACTCAAAGTGATCTACAGATTCAATCTAATAACTAAAAAAA 2929
                          viv  iv v i    v                ivi   vv   vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_134238701_   2930 AGTCAAATGGTACTTTTTACAAAAATAGAAAATACAATC--AAAATACTC 2977
                         vvi  iv  vi-i     i  i    v  v  vvii   --     --  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT--TC 147

  chr2_134238701_   2978 ATAGAGAATAT-CAAAAGACCATGAATAGCCAAGTCAATATTGAGAAAGA 3026
                            vi   -  -   ii    vv          iv    v    i     
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_134238701_   3027 A---CTAAGCTATAAGTATTACACTTCCAGATTTTAAAATATATTACAAA 3073
                          --- v   i iv i vv i        vi    i    iv  i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_134238701_   3074 GCTATGATAACCAAAACAACATGATGCTGACATAAAGACAAACATATAGA 3123
                             iii   i   i   iii  i i   i     i  i i         
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_134238701_   3124 TCAATAGAACAGAAC--AG---CCAGAAATAAATCCACACATATGGGGTC 3168
                              i   i    i--  ---           i   i    v iv    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_134238701_   3169 AACTGTTGTTTAATAAAGGTTCCAGGA 3195
                           i  v v  ii i  i   v   i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGA 373

Transitions / transversions = 1.60 (56 / 35)
Gap_init rate = 0.02 (8 / 373), avg. gap size = 1.88 (15 / 8)  

2012 22.61 6.32 1.34  chr2_134238701_134243219     3506  4027 (492)    L1M4_orf2#LINE/L1      361   908 (0)  

  chr2_134238701_   3506 AAAGGTACCAGGAATACACAATCTAGAAAGACCA-TCTCCTCAACAAAAG 3554
                           i   i   i  vi iv    vvi      vi -   ii        v 
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_134238701_   3555 GTGTTGGGAAAACTGGATATTCACAGGCAAAAGAATGAAATTGAATCCTT 3604
                            i     v         ?i    v             i   i i  i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_134238701_   3605 ATTTTACCCTACACACAAACATCAACTTAAAATGGATTGAAGACTGAAAC 3654
                          ii i  v i i i     v  i    i         ii?    iv   i
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_134238701_   3655 GTAAGACCTGAAACTGTAAAACTCCTAGATGAAAACATAGAGG-AAAT-- 3701
                               v  i     i        i    v          i? -    --
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_134238701_   3702 --ATGGCATTGGTCCTGACAATGATTTC----ATATGATACCAAAAATAC 3745
                         --i  i v    viiv i     i    ----      i       ii  
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_134238701_   3746 AGGCAACAATAATAAAAATAGACAAGTTGGACTTCTGCA----TAA---- 3787
                          i       v iv         i  i         vv  ----   ----
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_134238701_   3788 ----------CAAA--ACA--ATCAACAGAGTGAAAGG-TAACCTGTATA 3822
                         ----------    --   --     v i       i -i    iii v 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_134238701_   3823 ATGTAAGAAAATATTTGCAAATCACATATTGGAAAAGGGGTTAATCTCCA 3872
                            vi                   i    iv  v     ii vi v    
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_134238701_   3873 AGATATGTGAGGGACTCCTGCTATTCAAGAGTAAAACAAACTAAAACTAA 3922
                         ii    i i i i    i i v i    v i     ------- i  v  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAA-------AGACAAA 803

  chr2_134238701_   3923 TAACCTGACTAAAATATGGGCTAAGGACTTGGATAGACATTTCTCCAAAG 3972
                              ii i ?   v      v     i   i                  
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_134238701_   3973 AAGACATACACATGGCCATGAGGTATATGAAAAAGTGTTCAACATCACTA 4022
                             i     v       vv i i i       ii  i         ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_134238701_   4023 ATCAT 4027
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.26 (79 / 35)
Gap_init rate = 0.02 (10 / 548), avg. gap size = 4.00 (40 / 10)  


 655 30.46 1.02 0.00  chr2_134387528_134389880.rev      306   502 (1851)    L1M4_orf2#LINE/L1        8   206 (702)  

  chr2_134387528_    306 ATATTCTGTGGTTGTAGATTAGAAGACTCTATGTTATTAAGATGTGAATT 355
                             i ii  v ii i    i       iv  i  i        vv   v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_134387528_    356 CTTTCCAATTTGATCTATGGATTTAAGGCAATTTCAGTCAAAGTCCAATA 405
                           ii    v        ii    i  v     ii vi     i   v vv
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_134387528_    406 AAGCTATTTTGTGGATATTGATAAACGGTTTCTAAAGTTTATATAGAAAG 455
                         viv  v     ii  v     i  i v v i     i  i    i    v
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_134387528_    456 GCAAAAG-CCTAGAATAGCCA-CACAATACTAAAGAGAAAAAATAGAAT 502
                             ii -  i          -v     vi i  i ii  i  i i i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

Transitions / transversions = 2.00 (40 / 20)
Gap_init rate = 0.01 (2 / 199), avg. gap size = 1.00 (2 / 2)  

3007 22.53 3.33 5.22  chr2_134387528_134389880.rev      961  1861 (492)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr2_134387528_    961 ATCAGAAAAATCAGTATTGTGTCAAAATATCCACACTACCCTAAGTCATC 1010
                           ii   i v i i      --i  i  iv v i   v   v  v v   
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGT--TAAGATGGCAATACTCCCCAAATTGATC 72

  chr2_134387528_   1011 TACAGATTCAATGCAATCCCTGTCAAAATTTCAATGGCATTTTTTACAGA 1060
                                    i         i       ii  iiv  v      i    
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chr2_134387528_   1061 AATAGATTTTAAA--AATCCTAAAATTCATATGGAACCACAAAAGATCCT 1108
                            v  i---  i--i                    vii   ii  i  v
  L1M4_orf2#LINE/    123 AATTGAC---AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_134387528_   1109 GAATAGCTAAAGCAATCTTGAGCAAGAAGAACAAAGCTAGAGGCATCACA 1158
                                i   i         iv             i i    vv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_134387528_   1159 CTTCTTGACTTTAAATTATATTGCAGAGCTGTAGTAGTCAAAACAGTATG 1208
                             iii i  i   viv  i i  i    ii    i    i     i  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_134387528_   1209 GTACTGGCATAAACTCATATACTTAGAAAAATGGAATAGA-----GAGCC 1253
                                     ivvi v i iv    vv           -----   i 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_134387528_   1254 CAGAAATAAACCCATACATATATGGTCAATTAATAGTCTACAAAGTCTCC 1303
                                            v           i  vv  v    i viv  
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_134387528_   1304 AAAAATAGACAGTGGGGGAAAGGATAGTATCTCCAATAAA--GTGTTAGG 1351
                           i vi vv  i     -    i     v i i   i   --   i i  
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_134387528_   1352 AAAACTGGATGTCCATTTGCAAAAAAGTGAAATTGGATCTTTATCTTATA 1401
                          v        i?   iv       i i    i     i ii  i  i i 
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_134387528_   1402 CTATATATAACAATCAACTCAAAATGAATTAAAGATTTGAACATAAGATC 1451
                          i     i  v   i           i  i ?   ii i  ii     v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_134387528_   1452 TGAAACTATAAAATTCCTATGAGAAAAC-T-GGGGAAAAGCTCCATGATA 1499
                          i           i  i  vi       - -  ? v   v  i i   iv
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_134387528_   1500 TTGGTCTTGGCAATGATTTTTTTAATATGGTG--AAAAACACA--CACCA 1545
                             vi v       i   i  vi     iii--    i    --  v  
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_134387528_   1546 AAAGCAAAACTAAACAAGTGGGACTACATCAAA--TAAACAAACTTCTGC 1593
                             v    v  i i  i v     v       --    --     i  i
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA--AACTTTTGT 666

  chr2_134387528_   1594 ATGGCAAAG-ACAATAATCAA---AGCAAAAAGGCAACAAACCAAATGAA 1639
                         iivv     -   v  -    ---  ii     i    vv  vi    ii
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_134387528_   1640 AGAAAATATTTGCAAA-CATATACCCAATAAAGGGTAAATATCCAAAATA 1688
                                         -      i ii    i  iivvi      i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_134387528_   1689 TATAAGGAACTCATGCAACTCAATAGGAAAAAAAAAAAAAAAAAAACCCA 1738
                              i      v i          ----- v     i v   v      
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATA-----ATAAAAAGACAAATAACCCA 810

  chr2_134387528_   1739 AACCAAAACCCCCACCTGAAAAAAGGCTTCGATTTTAAAATGGTCAAAGG 1788
                          -------------------------------  ?v       v      
  L1M4_orf2#LINE/    811 A-------------------------------TTWAAAAATGGGCAAAGG 829

  chr2_134387528_   1789 ACCTTAGTAGACATTTT--CAT------TTTACAGCAATGGCTAACAGGT 1830
                          ii v i         i--  v------ v    --      i  i i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACA--AATGGCCAATAAGC 877

  chr2_134387528_   1831 ATACAAAAAGGTGCTCAGCATCACTAATCAT 1861
                          i ii     i      i     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (133 / 66)
Gap_init rate = 0.02 (21 / 884), avg. gap size = 3.67 (77 / 21)  


 618 26.55 3.10 8.97  chr2_134459167_134462591     1487  1776 (1649)    L1M4_orf2#LINE/L1        7   279 (629)  

  chr2_134459167_   1487 GAAATACTATGTTCCTGAATTAGAAGTTTCAATATTATAAATGTGTCAAA 1536
                           v  v i      v  i   i    vi i      i v  vi  v   -
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA- 55

  chr2_134459167_   1537 TTCTCCCCAAAGTGATCTATAGATTCAA-----TTCCAATCAAAATCTCA 1581
                          v         v       i        ----- i  v         i  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_134459167_   1582 ACAAGACTTATGCGTGTGTGTGTGTGTGTGTGTGTGTGTAATCTGACAAA 1631
                         i --------   v v v ---------------  iiv  vi      i
  L1M4_orf2#LINE/    106 GC--------TGCCTTTTT---------------TGCAGAAATTGACAAG 132

  chr2_134459167_   1632 CTGTTTCTAAAACTGATACAGCAGTGTAAAGTACCAAGAATACCCACAAC 1681
                            v i      i v   ii v i  i  i v   v      v   v   
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_134459167_   1682 AAATTCAGACAAGAGCAAAAAAG---AAATATTTACTTTTGAAGACGTCA 1728
                           vi iii v    iv  v    ---i iv i i  vi  vvvi iv   
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_134459167_   1729 AGACTTATAATAAAGCGACAG-AATTACATCAGCATGGTACTCAGGCAT 1776
                          i     iv i     v    -   i viv   ii       --     
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT--GGCAT 279

Transitions / transversions = 1.14 (41 / 36)
Gap_init rate = 0.03 (7 / 273), avg. gap size = 5.00 (35 / 7)  

1372 27.35 5.79 2.03  chr2_134459167_134462591     2257  2947 (478)    L1M4_orf2#LINE/L1      192   908 (0)  

  chr2_134459167_   2257 AAAGAAAAAAAACTATTTGGAGGAAGCACAACTGGCATGATAAAAAGTTA 2306
                               i  v  -- v        vv    vi vv  vvv v    v   
  L1M4_orf2#LINE/    192 AAAGAAGAACAA--AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_134459167_   2307 ----AAAA-TAAACTAAAAAACATCAGTGTGGTACTGGTGCAAGAA-A-- 2348
                         ----   i-  v v   vv  v -              iii   i - --
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_134459167_   2349 -ATACAGTTAAAAAGAATGGAATAGAAATTTCAGAAACAGACCCATGCAG 2397
                         -   i  v v  vi    i    v  i v i      i i      i  v
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_134459167_   2398 T-ATGGACACTTGATTCATGACACATGTGGCACTGAAAGCAT------GG 2440
                          -    v  v      ivi    viv   v  --- i v   ------  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCA---AGACCATTCAATGGG 385

  chr2_134459167_   2441 GAAAAGATAGTCTTGTCAATAGGTATTGCTGAT-CAATTAGACAGCCATA 2489
                             ii        v    i ii iv     iv-   i i  i ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_134459167_   2490 TTTAAAGACATAAAAATCTGATTCCTACCTCACACCATATGAAATACTTA 2539
                          vi   iiv  i  i- iv  ii                 iv  v v   
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_134459167_   2540 ATTCCACACAGATTGCATATCTACATATGAAA--TATAAATGATTAATCT 2587
                          i  v v ii   ii? v i   v  i i i --  -   iv  v  v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACT 533

  chr2_134459167_   2588 TCTAAAAGATAATA-AGGAGTAGAATATTTTTATGCCCTTGGCATAGA-- 2634
                         ii  i    v  i -   ?   i --- i  ii  v      vv   i--
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCA 580

  chr2_134459167_   2635 ----TTTCTGAAA-AGGACACAAAATCTACTAACA-TAAAGGAAAAGGT- 2677
                         ----     v i - v     v   vvi  v i  -i   i     ii -
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_134459167_   2678 GATAAATTAGGCTAATTTAAAAATAAAAACTTGCATTCATCAAAAGATAC 2727
                                 i i  vvv i    v         vii v v     i  i  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_134459167_   2728 TATTAGGAGTATGAAAAGACAGCCAA-AGAATGGGAGA---TTTTTATAA 2773
                            i i  ivi          i  v -           --- v   ii  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_134459167_   2774 TATAA-ATAACT-AGAAGGGACACATATCTAGACAATATGAA-AACTCCT 2820
                         -  v -   v  - v       vii    i   vv    i  -     i 
  L1M4_orf2#LINE/    731 -ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_134459167_   2821 ACCAATAAATAAGAAAAAGACAGACAAGCTTATACAGAAATAGG-AAAGA 2869
                           v v v     v         i i  v iv  v? i    i  -    i
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_134459167_   2870 CATTTGAATAGGCACTTCACATAAATGAG-TATCCAAATGACCAATCA-- 2916
                         -          i  i   v -i   vi  -   v      i     v --
  L1M4_orf2#LINE/    830 -ATTTGAATAGACATTTCTC-CAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_134459167_   2917 ACATGAAAATGTGGCCAGATTCATTAAAGAA 2947
                                  vi  vi  ivv   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.13 (98 / 87)
Gap_init rate = 0.04 (30 / 717), avg. gap size = 1.80 (54 / 30)  


3262 26.77 0.88 0.44  chr2_134501284_134507555     4877  5780 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_134501284_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_134501284_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_134501284_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_134501284_   5025 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_134501284_   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_134501284_   5125 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_134501284_   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5222
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_134501284_   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_134501284_   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_134501284_   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_134501284_   5373 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_134501284_   5423 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5472
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_134501284_   5473 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5522
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_134501284_   5523 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_134501284_   5573 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5622
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_134501284_   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5672
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_134501284_   5673 AAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5718
                          i    ----   v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_134501284_   5719 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5768
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_134501284_   5769 ATCACTGGCCAT 5780
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2027 27.51 7.91 2.01  chr2_134523107_134525424.rev      980  1826 (492)    L1M4_orf2#LINE/L1       12   908 (0)  

  chr2_134523107_    980 CCCATTTTTGTGGTTTAGAA---TTAAAATGGTCAGGATGTAAATTGTCT 1026
                              v  ii   v  i   ---    v  v  i i    vv   vv  i
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chr2_134523107_   1027 CCAAACTAATCTTTAGATTAAACACAATCCTGATTAAAATCTCAGCAGG- 1075
                              i i    vi     v   i      iv  i      i    v v-
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_134523107_   1076 TTTTGTGTAGAAATTGACAAGCTGATTCTAAAATTCATATAAGAATGCAA 1125
                             v  i                  i             iii       
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_134523107_   1126 ACGGCAAAACATAGTCAAGGAGATTATTTATAAAAAGAAAGATTA-TTTT 1174
                         iv i vv iv    i   i--- iv  i vv        ii iv -v  v
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAA---ACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_134523107_   1175 GAGGACTTACACTCTCAGATATTGAGACATATCACAAAGCTATTGAAATT 1224
                                i     ii vi  v ii i  v  ii         iv v   i
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_134523107_   1225 AAGAGAGATTGAAGTTTGCATAACAATAGATAAAAAGACCAGTGGAACAG 1274
                             v  vv  ivii v      vi     i v v   i  i     i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_134523107_   1275 AACAGAGAGTCCA----------CAT-C-TCTATAGTTATCTGATATTTT 1312
                           iv         ----------   - - i   i  i vi    v  iv
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_134523107_   1313 ACAAAAGTG---ATACTGCTGTATAGGGTAGAAAGGATGACCTTTTTAAC 1359
                             ii   --- v  iii vv  i   ---    i  iii     i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGG---AAAGAATAGTCTTTTCAAC 405

  chr2_134523107_   1360 AAATGGTGCTGTTAT--TTGGATATCCACATGGGAAA-AATGAA------ 1400
                                    vv i--i      ?       vi   -      ------
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_134523107_   1401 TCTTTATCTTACAC---------AAGTCAATTCCAGTCAGATTGTAGATC 1441
                         i ii  i  i    ---------  i i  i  v ivii   ii?   i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_134523107_   1442 TATAGGCAAAAGTTAAACAAATAAATGCTTTTAGGAAAAAAAAAACCCAC 1491
                           v v i  i  i    vvv     -i  i    i i    ------  i
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA------CAT 548

  chr2_134523107_   1492 AGAAG-ATATATTTATTATCTCAGGT-AGACAAAATTTTCTTAATTCGGA 1539
                           i? - v  v  ii v i  ii   -  i   viv       iv vv  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_134523107_   1540 TATAAAATGTACTAGTTATAAAA-------T-GTTCACTTGGACTACATT 1581
                         i iv   v i  v  iv i    ------- - v v v       v   i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_134523107_   1582 AAAGTTAGAAATTTCCTATTCATTAAAAGACACCATTAG---AGTGAAAA 1628
                            i   i   i  i- i v v i   i     i  i i---        
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_134523107_   1629 CATAAGCCACACAATATTGAG----TATATTGTTAATAAATATA------ 1668
                         v i  v     v   iv-   ----   -   iv   v -    ------
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGG-GAGAAAATAT-TTGCAAATCA-TATATCTGAT 744

  chr2_134523107_   1669 AAAAGACTCATATCCAGAATATATAAAGAACT---GAAAATCATTGAGAA 1715
                           ii    ii                      ---iv  v   v i v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_134523107_   1716 AAAT-TAAATAATGCAATATAAAAATAGGCAAATGACTTAAATAGTCATT 1764
                            v-i      iv    v?      i      v  i  i     v    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_134523107_   1765 TCATGAAAGAGGATATCCAAATGGTCAATAA--ATGTGAGAGCATGTTTA 1812
                           viv     i     v       i      -- ii   i iv   i i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_134523107_   1813 ACCTCATCATCAAG 1826
                           v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (137 / 92)
Gap_init rate = 0.03 (29 / 897), avg. gap size = 2.90 (84 / 29)  


4746 14.65 1.63 1.74  chr2_134537917_134539765      498  1357 (492)    L1M4_orf2#LINE/L1       50   908 (0)  

  chr2_134537917_    498 TGG-AATATTCCCCAAGCTGATCTACAAAT-CAATGCATTCCTTGTCAAA 545
                            -    i       ii         i  -   i   v   i i     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_134537917_    546 ATCCCAGCTGGCTTTTTTTTTTTTTTGCATAAACTGACAAAGTTATCCTA 595
                                   v       --------   v   i      iv v      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT--------GCAGAAATTGACAAGCTGATCCTA 141

  chr2_134537917_    596 AAATTCATACAGAAATGCAAGGAATCCAAAATAGCCAAAACAATCTTGAA 645
                                  ii           i i   i                     
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_134537917_    646 AAGGAAGAGCAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACCTACT 695
                           i     i                                    i    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_134537917_    696 ACAAAGTTTCAGTGATTAAGATTGTGTGGTACTGGCATAAGGATAGACAT 745
                               i v    i  i    iv                           
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_134537917_    746 ATAGATCAGTGGAATAGAACTGAGAATCCAGAAATAAATCTTCACATTTA 795
                                 i          i     i            i ivi       
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_134537917_    796 CAGTCAATTGATTTTTACGAAGGGTGTGAAGA-------ATGGGGAAAGA 838
                         ii             iivv       iv    -------           
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_134537917_    839 ATAGTCTTTTCAACAAATGGTACTGGGACAACTGTCTATTCACATGCAAG 888
                                              i            vv  ?i         i
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_134537917_    889 AGGATT--TTTGGACCCCTACCTCACACTATATATAAAAATGAAGTCAAA 936
                           i  v--v                   i     i      v  v     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_134537917_    937 ATGGATAATATACCTAAACATAAAAGCTAAAACTGTAAAACTCTTAGAAA 986
                               v ? v       ii   i          i              i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_134537917_    987 AAAACATAGAAGTACATCTTTGTAGCCTTGGATTAGGCAATGGTTTCTTA 1036
                                  i?   v     i  ii      i                  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_134537917_   1037 GATTGGTCATCAAAAGCACAAGCAACAAAAGAAAAAATAGGCAAATGGGA 1086
                            vv v  i                              ii    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_134537917_   1087 TATCATCAAGGTTACAAACTGTTTTCACTTCCAAAAACACCATCAAAAAG 1136
                         iv       ii   v     -   vii    v  ii    i     i  i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_134537917_   1137 GTGAAAAAACAACCCACAGAATGAGAGGACATATTTGCATAATATATACT 1186
                                i               i   i v         v vi     --
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA-- 738

  chr2_134537917_   1187 GTCTGATAGGAAACTAGAATTCAGAATATATAAAGAACACTTACAACTTA 1236
                         -       i ii   v v  i                 v         i 
  L1M4_orf2#LINE/    739 -TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_134537917_   1237 ACC-CAAAAAG-CAAATAACCTAATTTTTAAATGGGCAAAGGATTTGA-T 1283
                          iv-i      -         i    ?vv                   - 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_134537917_   1284 AGACATTTCTTCAGAGAAGACATTGTACAGATAGCTAATGAGTACAAGAA 1333
                                   i  i      i  ---   i  i  i   i  i   v   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATAT---ACAAATGGCCAATAAGCACATGAA 884

  chr2_134537917_   1334 AAAATAGTCAACATCATTAGCGTT 1357
                           i  iv         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (83 / 39)
Gap_init rate = 0.01 (11 / 859), avg. gap size = 2.64 (29 / 11)  


3238 27.97 0.11 0.11  chr2_134633583_134642532     4975  5882 (3068)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_134633583_   4975 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5024
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_134633583_   5025 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5074
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_134633583_   5075 TACCAATGACTTTCTTCACAGAATTGGAAAAAAGTACTTTAAAGTTCATA 5124
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_134633583_   5125 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5174
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_134633583_   5175 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAAGGCTA 5224
                              i      vv    i  v  ii i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_134633583_   5225 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGATCAA 5274
                               i   i    ii         i iv ii i   v  i        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_134633583_   5275 TGGAACAGAACAGAGGCCTCAGAAATAATGCCACATATCTACAACTATCT 5324
                              i    iv   ivii         vv   i i  i  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_134633583_   5325 GATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCTAT 5374
                            i  i     ivv  vv  i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_134633583_   5375 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5424
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_134633583_   5425 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 5474
                         i    i    v   i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_134633583_   5475 AGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCCAG 5524
                             i       v   v       i      vi i           vi  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_134633583_   5525 GCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAAC 5573
                          ?i- v i -   iv   v v  vv i     v ii   v ivv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_134633583_   5574 ACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAATGA 5623
                                   vvi      i   vv     v  i    v   ii v  v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_134633583_   5624 AACTAAAGAGCTTCTGCACAGCAAAGGAAACTGCCATCAGAGTGAACAGG 5673
                           v v  i i   i  ii vv       v   ii  vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_134633583_   5674 CAATCTACAGAATGGGAAAAAATTTTTGCAACCTACTCATCTGACAAAGG 5723
                            i i           i     v       vii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_134633583_   5724 GCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAA 5773
                         i  vi          v  i  v      vv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_134633583_   5774 CAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCA 5823
                             i     v  i?    i     i      v    i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_134633583_   5824 CAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCATC 5873
                         v       i  vi viii     v ii          i       v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_134633583_   5874 TTTGGCCAC 5882
                         v????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.40 (146 / 104)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 1.00 (2 / 2)  

1354 28.31 1.56 0.00  chr2_134633583_134642532     7239  7623 (1327)    L1M4_orf2#LINE/L1        1   391 (517)  

  chr2_134633583_   7239 TGGAAAGATGTTCCATACTCATAGATAGGAAGACACAATATTGTCAACAT 7288
                                  i i    ii    i   v       vi        i  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_134633583_   7289 GTCAATTTTTCTCAGTTTGATCTATATATTCAATGCAATGCCTATCAAAA 7338
                          v    vi i i  iv        i v      i     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_134633583_   7339 TCCCAATAAATTATTTTGTGAATATCAACA----GAT-CTAAAGTTTGTA 7383
                              iivivi v     iii v  ii   ----   -     i  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_134633583_   7384 TATAGAAGCAAAAGATCCAGAATTTCCAACACAATATTAAAGGAGAAGAA 7433
                          iv i v    ii  i       vv    v     v  i  ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_134633583_   7434 CAAAGTTAGAGGAGTGATGCTGTAT-ACTTCAAAAGGTATGATAAAGCTA 7482
                                i     v v ii  vivi- i       vv  iv i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_134633583_   7483 TACTAATGAAGACAGTTTGGCATTGGAGAAAGGATAGACAAATAGATCAA 7532
                         i v    v        v   i i   viv           v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_134633583_   7533 TGGAGCAGAATAGGGAGCCCGGAAATAGGCTCACATAAAAATAGTCAACT 7582
                             ii     v i   i  i      ii i  i i vvv  i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_134633583_   7583 GATCTTTGACCAAGGAACAAGGGAAATATGATAAGAAAAGA 7623
                            i  i   v i  vi v i ivv  vii  ii i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

Transitions / transversions = 1.66 (68 / 41)
Gap_init rate = 0.01 (3 / 391), avg. gap size = 2.00 (6 / 3)  

1872 24.57 0.76 2.08  chr2_134633583_134642532     7930  8458 (492)    L1M4_orf2#LINE/L1      387   908 (0)  

  chr2_134633583_   7930 AAAAGATAATATTTTTAACAAATAGTGTTGGAGCAACTGGACATCTACAT 7979
                            ii   i v    i       i   i   ii        i ? i    
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_134633583_   7980 GCAAACAGTAATGAACCTAGGCACAGATTTTAGACTCTTCACAAAAATTT 8029
                              -  -      vi i i v vv ii i v  iv vi         v
  L1M4_orf2#LINE/    437 GCAAA-AG-AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_134633583_   8030 ACCCAAAATGGATCACAGACCTAACTGTAAAACTATATGTAAAAACTATA 8079
                           i            ?        v     i ------ iv         
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGA------GCTAAAACTATA 528

  chr2_134633583_   8080 AAACTCCTGAAAGATAGCATAGGAAAAAATCAAGATGACCTTAGGTTTGG 8129
                               i ii    v i      ?iv     vvvi       i    v  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_134633583_   8130 CAGTGACATTTTAGATATGATATCAAAGTCATGATTCACGTTAGAAATAA 8179
                           i  iiv i          i i    iv  ii viv  ivv     v  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_134633583_   8180 TTGATG--TTAGACTTCCCTAAAATTAAAAACTTCTGTTCTTTGAAAGAT 8227
                          v   i--  i      vii              i   v   ii  i  i
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_134633583_   8228 ACTGTCAAGAGAATGAAAACACAAGTCAGAAACGGGGAGAAA-TATTTGC 8276
                            i      i i      v    vi  v i vv        -       
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_134633583_   8277 AAAAGACATATCTAATAAATAACTGTTATCCACAATGTACAAAAAACTCT 8326
                            vv i      i    ivi   vv      v   i  i   i      
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_134633583_   8327 GAAACCTCAGCAATAAGAAAACAAACAACCAGACTAAAAAATGGGTCAAA 8376
                         v v v    ii     i  i     i    vi i ?         iv  i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_134633583_   8377 GATCTTAATAGCCACCTCACCAAAGAAGATAAATATAGATGGCAAATAGA 8426
                            i v     v  ii  v            --  i i     v    ii
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATA--TACAAATGGCCAATAAG 876

  chr2_134633583_   8427 CATATGCAAAGATA-TCACACATCATGTGTCAT 8458
                           i   v      i-   -      ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (78 / 48)
Gap_init rate = 0.02 (8 / 522), avg. gap size = 1.88 (15 / 8)  


2084 25.52 4.49 0.64  chr2_135006174_135007782.rev      496  1118 (491)    L1M4_orf2#LINE/L1      262   908 (0)  

  chr2_135006174_    496 ACAG-GTGATTTTGGCATAAAAACAGACATACAGACCAATGGAACAGAAC 544
                             -   i vi        ii i       i   i        i    i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_135006174_    545 AGAGAAACCAGAAAAGAAC-------------------TGATTCCCAACG 575
                         v    iv       vi   -------------------     ii i  i
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_135006174_    576 ACGCTGACAAGAATACACAATGGAGAA-GCACAGTGTCATCAATAAATAA 624
                          v v  v     vi iv      i   - v i   v iv    i    ii
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_135006174_    625 TATTTGGAAAACTTGATTTCCACAAGCATAAGAATGAAATCAAATCTTTA 674
                          ii v   v    v   v?     v   v         i iii i ii  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_135006174_    675 TCTCACACTATCTATAAAAATGAATTCAAAATTGATTA--GACTTCAATA 722
                         i       i  v  i      v  i       v   i --   i v   i
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_135006174_    723 TAAGACCTGAAACAGCACAACTAC--GAGGAAAAAAAAAGTGCAAAAGCT 770
                              v  i    vii v    vi--  i     v v i ? i   -v  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCT 560

  chr2_135006174_    771 TCTTGACACTAGTCTGGGCAATGATGT-TTGGGTATGATACTAAAAGCAC 819
                           v    vi i vi i       i v -  i i     i  i        
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_135006174_    820 AGGCAACAAAAGCAAAAACAGGCAACTGAGATTGCATCAAACTAAAGAGC 869
                          i          v     i  ii  v vi  i v       v v  i i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_135006174_    870 TTCTGCACAGCAAAGGAAACAATCAATAGAGTGAAAAGGCAACCTATGGA 919
                           i  ii vv       v  v     v i         i     i ii  
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_135006174_    920 ATGGGAGAAAATATTTGCAAACCACATATTTAATAAGCGGTTAATTCCCA 969
                                              i  i    i i     v ii vi vi   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_135006174_    970 AAGTATATAAGGAACTCCTACAACTCAACTGCGGAAAAAACCCAACCAAT 1019
                         i i       i      i          - ivvi    i  --  vi  i
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAA-TAATAAAAAGAC--AAATAAC 807

  chr2_135006174_   1020 CAAATTAAAATATACGCAAATAACCTGAA--GACATTTCTCGAAAGAAGA 1067
                          v    ?   v  iv     vi ii    --          v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_135006174_   1068 CATACACAAGGCAAACAAACATATGAAAAGGTGCTCAACATCTTTCATCA 1117
                         i     v v   v  i  i  i        i           v???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_135006174_   1118 T 1118
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.64 (97 / 59)
Gap_init rate = 0.02 (10 / 647), avg. gap size = 3.20 (32 / 10)  


2118 23.81 8.47 5.98  chr2_135063472_135067544     2696  3581 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_135063472_   2696 TGGAAAGATATACTGTGTTCA---ATT------------ATTATTAAAAC 2730
                                    v ii      ---   ------------   i    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_135063472_   2731 GTTAGTTCTCCCCAAACCGATCTG--GATGCAAAAGCCACCCTAAGCCAA 2778
                          vi i v         ii     i--   v   v-  v i  iv v v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAAC-GCAATCCCTATCAAA 99

  chr2_135063472_   2779 ATCCCAGCAGGCTTTTTTAAAGAAATAAAAATGGACAAGTTGATTTTAAA 2828
                                 v v       iv      -----  -     i    ii    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAAT-----TG-ACAAGCTGATCCTAAA 143

  chr2_135063472_   2829 AGTTATGTGTAAATGAAAGGG-CTTACAATAAGTAAAGTGATTTTGAAAA 2877
                          v i  i  v     v     - ii v    ivi   iii  i       
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_135063472_   2878 AGAA---CAAGTTTCAAAGGTTTACACAAGGCCTTTCCTTATTTGATTTA 2924
                             ---   iv  vi i ii i    -------    iv    ------
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACAC-------TTCCCAATTT------ 230

  chr2_135063472_   2925 TGAAATAAGTCATTTCCAAACTGATTTATTATGAAGCTATTGTAATCAAG 2974
                         ----------------    --- i   i  ii      iv         
  L1M4_orf2#LINE/    231 ----------------CAAA---ACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_135063472_   2975 A-AGTA--ATACTGTCATAAAGCCAGACAGACATACAGATCAACAGAACA 3021
                          -   i--i     v     i ---- i       i       ii   i 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGG----ATAGACATATAGATCAATGGAATA 307

  chr2_135063472_   3022 AAAT----AGCCTAGAAATCATCCCACTCTCAGATATAGTCATTTAGTTT 3067
                         i   ----  i i      v v    iv -- vv   i    v  ii   
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATAC--ATTTATGGTCAATTGATTT 355

  chr2_135063472_   3068 TAGACAAAAGCACAAAAGCAATCCAGTGGAAAATGTAAAGTCTTTACAAC 3117
                          v     ii ii v  ii v  i  i   ii  v v v       v    
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_135063472_   3118 TAACAGCACTAGAACAATTGGATATGTGTACAGAAAGAAATAAATCCTGA 3167
                         v  ii ii  i i    i      ?viii iiv   ii   i  viiv  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_135063472_   3168 TCCTTATTTCACACTATATATAAATTTTAATTTTAGATGGACTGCAGATC 3217
                         i  i  ii      i     i   vv    i iv i     iii?   i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_135063472_   3218 TCAAAGTGA-AGCTAAAACTGTAAAACT--------AAATTAT----GTA 3254
                          v  v  i -          i       --------   vi  ----   
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_135063472_   3255 --------TGACCTTGGGTTAGGCAAAATATTTCCTA----TGACA--AA 3290
                         --------                  vi-i    i  ----     --  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTAGATATGACACCAA 604

  chr2_135063472_   3291 AA--ACAAGCACTAATCATTAAGAAAACTGTGATTAATTAGACTTTATCA 3338
                           --       vi  -----       vvvv   v    i     i    
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAA-----AAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_135063472_   3339 AAATTAAAA-CTTTTGCTCCTTGAAAG---ACTATTAAGAAAATGAA--G 3382
                                  -      - v   v    ---     i      i    -- 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_135063472_   3383 GCAAGCCATGATACAGAAAAAAAAATT-GTAAA--ACATATCTGATACAG 3429
                         i   v   iiiv ii i i    v   - i   -- i          vi 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_135063472_   3430 AACTGGTATCCAGAATATTTAA-TAATTTCTACATCTCAGTAAGAAAA-- 3476
                         i   v             v   -v  i ii    v    i   v    --
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_135063472_   3477 -CAGATGACTCAATTAAAACAGAAGGCAAAA-ATTTAAA----CACTTTA 3520
                         -  i  i  i     ?   - ivi      i-    i  ----  i  iv
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_135063472_   3521 CCAAATAAGATGTAAGAACAGCAAATAAGCACAAATAAAGATAATCAACA 3570
                              v     i  vi  ii  v          viv      iv      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_135063472_   3571 TTATTGGTCAA 3581
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.89 (136 / 72)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 3.56 (128 / 36)  


 726 27.74 11.38 8.39  chr2_135077846_135080688      896  1598 (1245)    L1M4_orf2#LINE/L1       21   744 (164)  

  chr2_135077846_    896 ATGGAAGGGAGGATGCAAT--TGTTAAAGCAAGCCAATTCTCTCAGAATT 943
                              vv   i  ivi   --      i-- v v    v   i vi    
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAG--ATGGCAATACTCCCCAAATT 68

  chr2_135077846_    944 AAT----AAATTCGATGCAACTTCACACAACACCCCAACAGGATTTTTCA 989
                         i  ---- i    i i    iii vvv   v i    i v vv     ii
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG 118

  chr2_135077846_    990 TTAAACTTGGCAAACCAGTTTTGAAATTCGTATGGAATATTACTAATGCA 1039
                         ivi  v   i   i iii ii i      i       --------     
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA--------ATGCA 160

  chr2_135077846_   1040 ATGT--------TAGTCAAAACCACTTTGAAAATCCAAGAA--AAGATGG 1079
                          v v--------   i      v ii       -vv     --   v   
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAA-AGAAGAACAAAGTTGG 209

  chr2_135077846_   1080 -TGAC-CAAAC------ATT--AAGACTCATTGTAA--TTACAGGAATTT 1117
                         -v   -  v  ------   --  i   i i ii  --i     v   iv
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_135077846_   1118 TAGAGAATG--ACTCTAGAACAAA-ATGGACCCACGCATCCACAGAATGG 1164
                         -   v i  --iiv  i v i  i-  i   vi iiv   v ii    i 
  L1M4_orf2#LINE/    260 -AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_135077846_   1165 AACGGCAAGTCCAGGGACAG--CTGTGCACCTATGA------GA------ 1200
                           iv vi       ii i i-- ii i  ii    i------  ------
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_135077846_   1201 ACATGG----CA----CAT--GATGGAGG-----TGGCCTTTG----AAA 1231
                            v  ----  ----   --i    i i----- i i    v----   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_135077846_   1232 TCATCTTGGG-CAAGTTGTATATTCATCTGAGTAAAAGAAAAACCAAATT 1280
                          vi vi    -   -i  v   ?i  iv  --i       vi --- i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAA-CTGGATAKCCACATG--CAAAAGAATGA---AGTT 452

  chr2_135077846_   1281 GGATCCCTACCTCATACCAAATACAAA------TTCTAGATGAATTAAAG 1324
                            i          i    v       ------i  v i   i  i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_135077846_   1325 ATCTAATTTTAAAGTCTAAC-CTTTAATATCTTTTAAAAGATAATACAGG 1373
                          i    v v   iiv    v-  v   v -  i   i    v  i i   
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGG 551

  chr2_135077846_   1374 TATATATCTTCATGGCATCAGG----GCAATAGACCTTCTTAAACCTCTA 1419
                         ?i  v      i  i v ii  ----     i --i      i ----  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGG--TTTCTTAGA----TA 595

  chr2_135077846_   1420 TGTCCTCCCTTGCCAAACAAAAACAAACCACCACAATCTCCATTTAAAAA 1469
                           v -------i     -- iv    i v  ---------------    
  L1M4_orf2#LINE/    596 TGAC-------ACCAAA--AGCACAAGCAAC---------------AAAA 621

  chr2_135077846_   1470 AAAAAAAGACTGATAAATTTGATCACACCAAAATGGAAAGG----GTGGG 1515
                         i      v --        v  iiv  i      vi   iv----   --
  L1M4_orf2#LINE/    622 GAAAAAATA--GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG-- 667

  chr2_135077846_   1516 AAGATTTCTAATAGCAACAGATAGACAATATTAAAAGAAAAACTAAATAT 1565
                         ----i   v  vii  vi vvv   v i i--      v  v i v v v
  L1M4_orf2#LINE/    668 ----CTTCAAAGGACACTATCAAGAAAGTG--AAAAGACAACCCACAGAA 711

  chr2_135077846_   1566 TAGGCGAAATTATTTGCAATGCACATATGTGAT 1598
                          i  v    v         vv  i    v    
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGAT 744

Transitions / transversions = 1.49 (115 / 77)
Gap_init rate = 0.06 (40 / 724), avg. gap size = 3.48 (139 / 40)  

 221 32.69 3.85 1.28  chr2_135077846_135080688     2196  2351 (492)    L1M4_orf2#LINE/L1      749   908 (0)  

  chr2_135077846_   2196 GACTGGTACCTGGAACACAGATAAATAACTCCTAAAAACCTGTGGGAAAA 2245
                             v   i ii   i i --    v     i  v  vi vi iiv    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATA--TAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_135077846_   2246 AGATAA------CAATAGATAAATGGGCAAAACATATAAAGCAGCAATTT 2289
                            i  ------    v? v           iv  v i  vvii  v  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_135077846_   2290 ATAAAAGAGGAAACATAAAAAGTCAGCAGATGCATAAAAATATAATCAAC 2339
                         viv     i  v i i   vi i  ii iiii   i    v  iv     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_135077846_   2340 TTCACCAATAAC 2351
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (30 / 20)
Gap_init rate = 0.01 (2 / 160), avg. gap size = 4.00 (8 / 2)  


 254 26.37 3.30 1.10  chr2_135154207_135156560      779   869 (1485)    L1M4_orf2#LINE/L1       91   183 (725)  

  chr2_135154207_    779 CCAATTAAAATCCTAGCAGG--TGGTGACAGAA-TTGATAAGATGAAGCC 825
                           v  i       i   v v-- vv vi     -    i   v   vv i
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_135154207_    826 AGAGTTCATGTGGAAAGTGAAAAGAATCAGGAATAGCCAAGACA 869
                          i i     i      -  v  i i i vi          i   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACA 183

Transitions / transversions = 1.18 (13 / 11)
Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.33 (4 / 3)  

1324 26.93 10.63 2.91  chr2_135154207_135156560     1179  1865 (489)    L1M4_orf2#LINE/L1      169   908 (0)  

  chr2_135154207_   1179 AGAATAGCCAAGACAACCGTTAACAACCACAACCAAAAAAACCTGGAAGA 1228
                                    i    i -  i v  -- v  --i  v   vi    i  
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATC-TTGAAAA--AGAA--GAACAAAGTTGGAGGA 213

  chr2_135154207_   1229 CAGTCACTACCAGATACGAAGATTT----CAAAGCTACAGTAAATAAAA- 1273
                          vvv    v  vi  viv  i i  ----              vi  i -
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_135154207_   1274 ----TGATATTAGCACAAGGATAAACAAAGAGACCA------CAGAA--- 1310
                         ----  i  i i   i       i   v v   i  ------i    ---
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_135154207_   1311 ------CAAAAGAAGACCCACACAGATATGGTTACTTGATTTATATATTT 1354
                         ------  i  iv i     i   vv      i v       - vv ---
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT-TCGA--- 359

  chr2_135154207_   1355 CAAAAGTACCCCTAAAA---TACACGGGGGAAAGAA-AGTTCTTTTCAAT 1400
                            ii  i  ---  i --- v  vv          -   -        i
  L1M4_orf2#LINE/    360 CAAGGGTGCC---AAGACCATTCAATGGGGAAAGAATAGT-CTTTTCAAC 405

  chr2_135154207_   1401 AAATGGTACTGGGCCAGTTGGACATCCATATG-AAATGACTGAATTATGA 1449
                                i     v  ii    i ?   i   -   v  v    v vv  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_135154207_   1450 CCC-TACCTTACTCCATATAGAGAAA---ACTGTCGATGAGCTGTAGATA 1495
                            -     i  v       v i   ---   vvvi   iiiii?   iv
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_135154207_   1496 TAAAAGTGTAAG-GTTAACATAGGAGAGGTCTGA-AATAGAATATTGGCA 1543
                             --      - i   v iviv i iv   v -  v i  i  v  ?i
  L1M4_orf2#LINE/    506 TAAA--TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_135154207_   1544 TGGAGTTTCATAATCTTGGGGAAAGGTAAAGATTTTTTAAACTA-GACAT 1592
                          ii vi   i i i      vv -  i  v i   i   i -  -    i
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGA-TATGACAC 601

  chr2_135154207_   1593 -AAATGCATTCATCATAAGGGAAAGGACTCGTAAACTGAACTACAT---- 1637
                         -   v   ivviiv i  ii    ii ivvi    i  i   v   ----
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_135154207_   1638 --TAAAGACCTC----CTTCAAAGAGCA--------------AAACAGCA 1667
                         --    i  i i----        ii  --------------   vii  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_135154207_   1668 AGCCATCGAGTTTATTGAGAAGATATTTATAAA--ACATAACTACCAGGG 1715
                          v   iv  i vv---     i      ii   -- i   v  ivi i  
  L1M4_orf2#LINE/    702 ACCCACAGAATGG---GAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_135154207_   1716 GACTTATATCCAGAACATATAGA-----CTTATAAATCACTAAGAAAGAG 1760
                              i         i     i -----    i  v   v   v   i  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_135154207_   1761 A-AATCAACCCAATAGGAAAATGGGTGAAAGACTT-AACAAGC--TTCAT 1806
                          -  vi        v?i        ii  i  i  -  i ii --   vi
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_135154207_   1807 GAAAGATGATACACAAATGACCAATAAACATATGAAAATATACTCTAC-T 1855
                         v     v    i       i       i  i       v  i   v  - 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_135154207_   1856 TATTGGTAAC 1865
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.59 (111 / 70)
Gap_init rate = 0.04 (33 / 740), avg. gap size = 2.82 (93 / 33)  


 850 17.91 0.50 7.46  chr2_135208545_135213038     2815  3015 (1479)    L1M4_orf2#LINE/L1       45   231 (677)  

  chr2_135208545_   2815 TAACATGGCAATAATCCCCAAACTGATCTATAGATGTAATACATACACTA 2864
                            v         v        i       i    vi  ii  vv v   
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_135208545_   2865 TTAAA-TCCCAGCAGGTTTACTTATTTATTTATTTTTATAGAAACTGACA 2913
                          i   -       ----- i i ---------     ii     i     
  L1M4_orf2#LINE/     95 TCAAAATCCCAGC-----TGCCT---------TTTTTGCAGAAATTGACA 130

  chr2_135208545_   2914 GGCTGATCCTAAAACTTATATGGAAATGCAAAGTATCCAAAATAGCCAAA 2963
                         i             i i              i v i   i          
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr2_135208545_   2964 AACAATTGTTAGAAAGAAAAACAAAGTTGGAGGATCTAAACTATCTAATT 3013
                          -    iv v i      i               iii v   vi i    
  L1M4_orf2#LINE/    181 A-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_135208545_   3014 TC 3015
                           
  L1M4_orf2#LINE/    230 TC 231

Transitions / transversions = 2.27 (25 / 11)
Gap_init rate = 0.02 (4 / 187), avg. gap size = 4.00 (16 / 4)  

2446 23.01 2.17 2.03  chr2_135208545_135213038     3315  4005 (489)    L1M4_orf2#LINE/L1      217   908 (0)  

  chr2_135208545_   3315 ACACTACCTAATTTCAA----CACTATAAAACTACAGGAATCAAAA-AGT 3359
                              v  i        ----i    i   i      v      i -   
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_135208545_   3360 G--GCACGGTTGTAAAGACAGAAATATGTATAAATGAAATATAGTTGAGA 3407
                          -- i  v vii   i  i   v    iv  v    i    v i      
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_135208545_   3408 GTGCAGGGAGGAAAAATCTTTCATTTATGGTGAATTAATTTTTAATAAAG 3457
                           v   ii v--   vi v v          v    i     ii i  i 
  L1M4_orf2#LINE/    317 GTCCAGAAAT--AAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_135208545_   3458 TTG--AATGCAATTCAATACAGAGGAAGCTTGGTCTTTTCAATATATGGT 3505
                         v  --  vi v       i-- i i   vv i          i v     
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATG--GGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_135208545_   3506 GCTGGGACAACTGAATACCCATATACAAAGAAAGAAAATTGAACTTAAAC 3555
                                      i   ?   i  i    ---    ---    v  ii  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAA---AGAA---TGAAGTTGGAC 456

  chr2_135208545_   3556 CGTTACCTCATATAATATACAAGAACTGAG-AAAAATGAGTAACAGCACT 3604
                          vi       i iv        i  i i v-v      ii v ?  vv  
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_135208545_   3605 AAATGTAAGAGCTAAAACTACAAAACTCATAAAGGAAAACATAGGAGAAA 3654
                                             i       v  i i           ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_135208545_   3655 ATCATCATGACCTTGGATTAAGGGCCAAGATTTCCTAGACGCAACACCAA 3704
                            v  i         i   --   v v i    i    iiii       
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_135208545_   3705 AAACACAATTCCCAAAGGAAAAAGTTGATAA-CCGAATATAGTCAAAAT- 3752
                           i     vivv    i      i v     -ii i iv vi       -
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_135208545_   3753 AAAATTTTCTGTGCTTCAAAAAATATCTTTAAGAAAATGAAAAGACAAGC 3802
                             vi  i           ii i iiv i      i           v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_135208545_   3803 TACTTACTGTGAAAAAATAATTGCAAATCATATTTCTGATAAACTACTTG 3852
                         i  vv v  v  i      v             v        ivv     
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_135208545_   3853 CATCCAGAATATATA--TCCCTCGTATCATTCAATAA-AAGGAGTAAAAC 3899
                         i              --vvv   v  iv i       -  ii  vv   i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_135208545_   3900 AGCTCAATTTTAAAAACAGGCTAATGATTTGAGCATATATTTCACCAAAG 3949
                          i i     ?-     ii   v  v       ii v i     v      
  L1M4_orf2#LINE/    805 AACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_135208545_   3950 AAGAAAACACACATGGCTAATAAGCACATGAAGAGATGCTTAATAATATT 3999
                             v -i   v     i              i       i  i vi ??
  L1M4_orf2#LINE/    854 AAGATA-TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_135208545_   4000 AGTCAT 4005
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.42 (91 / 64)
Gap_init rate = 0.02 (16 / 692), avg. gap size = 1.81 (29 / 16)  


2535 24.01 4.41 4.41  chr2_135234517_135236828      913  1820 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_135234517_    913 TGGAGAGACATACTGCATTCAAGAATTGAAAGACTAAACACAGTAAAGAT 962
                             i   i  v iiii    v i    i      v  i iv  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_135234517_    963 G----TACATGTCTGTAAACTTATCTATAGATTTAAGAAAAGGCC-ATTG 1007
                          ----   ---  ivi   i v     i     i  viv  vv  -  ii
  L1M4_orf2#LINE/     51 GGCAATAC---TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_135234517_   1008 AATTCCAGAGAGATTTTTTTTCTAGATATAGAGGAGTTGATTCTAAAATT 1057
                           v   v-  vviii      vi   v  v  vi  i    i        
  L1M4_orf2#LINE/     98 AAATCCC-AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_135234517_   1058 CTTAGGGAAAGCCAACGGAACTAGAACAACTAAAACGATGTTTTTGAAAA 1107
                          v  v     vv   v   v i    i i i     i  ---i       
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT---CTTGAAAA 193

  chr2_135234517_   1108 AGAAAAATA---TTAAAGGAAT-ACACTACCCAATTTGAAGACTTACTAG 1153
                             i  i ---  ii    v -     v        v  i        v
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_135234517_   1154 AAAGCTACGGTAATTAAGACCATGGGGTATTAGCAAAAGAA-AAACAAGT 1202
                                 i     i     vi  v    i i   v   i - i   vi 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_135234517_   1203 AGCTCA---GAACAGA-------GTCCAAAAACA--CCCGCAGAAATATG 1240
                           v   ---   i   -------     i   i --   ii v vv    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_135234517_   1241 GCCATATGATTCCTTTCACA--GATACTAATGCGATTCAATTTAAAAAGG 1288
                          i  vv     --  iv   -- i i i  vi v       vvii    i
  L1M4_orf2#LINE/    344 GTCAATTGATT--TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_135234517_   1289 -TGGCCCCTTCAACAAATGATGTTAGAACAACCAAACATTCATATGCAAA 1337
                         - i i ii           i  i i i     iii i ?i  i       
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_135234517_   1338 AAATAAGTTGCAATCTATACACATCATAATTAGTTGCAACCTATACCTCA 1387
                          i ----------------------  i --     -i   iv       
  L1M4_orf2#LINE/    442 AGA----------------------ATGA--AGTTG-GACCCCTACCTCA 466

  chr2_135234517_   1388 TAC-AT---CAAAAATTAATTCAAAATAGATAATAAATCTAAGTGTAAAA 1433
                         i  -  ---          i       i   v ? i i    i     i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_135234517_   1434 CATAAAACTATCAAAATTTTAGAA-AAAACATAGGAG-AAATCCGTTGGG 1481
                         vv         v   v i      -          ? -     i- i v 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT-TCGTG 565

  chr2_135234517_   1482 ATCTGAAGTTAGGCAAAGAGTTTTTAGACACGACACCAAAAGCATGCTCC 1531
                          i  vii         v iv  i     i i             iivv v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_135234517_   1532 ATAAAAGAAAAAATTGATCAACTG-ACTTCACCAAAATGAAAAATATTTT 1580
                          i            v   v  i  -      i      v     iv   v
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_135234517_   1581 T-CTGCAAAAGATGCTATAAAGAGAATGAAAAAAACAAGCTACC-ACTGG 1628
                          -  v    i  ii    v    i i      i -   v i  v- v   
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA-CAACCCACAGAATGG 714

  chr2_135234517_   1629 GAGATAATATTTTCAAATCACATATCCACCAAAGGTCATGGATTCAGACT 1678
                             v       v       i     iivi  i  v v  v  i    v 
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_135234517_   1679 ATATTAAAAACTGTCAAAACTCAACTGTAAG----TAAACAACACAATTT 1724
                             v  i    v i v       ivi   i----i   i   v     ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_135234517_   1725 TGAAAAACGGTTAAAAGCCTTGAAAAGCCACATTACT--AAAAAAGATAT 1772
                         --     i  vi   i vi     v  --     v  --   i       
  L1M4_orf2#LINE/    815 --AAAAATGGGCAAAGGATTTGAATAG--ACATTTCTCCAAAGAAGATAT 860

  chr2_135234517_   1773 ACAAATGGCAAACAAGCACATGAAAAGGTATTTGACATCATTACCCAT 1820
                                  v  i              i ii ii      ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (130 / 84)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.67 (80 / 30)  


3202 27.53 0.44 0.44  chr2_135242097_135248376.rev     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_135242097_   4881 TGGAAGAACATTGCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  iv    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_135242097_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATTCCCATAAAGC 4980
                            v     v     iv i  i           i  v  i  i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_135242097_   4981 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 5028
                          v   iivi i  ii ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_135242097_   5029 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_135242097_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_135242097_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_135242097_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_135242097_   5227 ATCTGATCTTTGACAAACCTGAGGAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vvi i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_135242097_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_135242097_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_135242097_   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_135242097_   5427 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_135242097_   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTAA 5526
                         i            vvi          vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_135242097_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_135242097_   5577 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_135242097_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_135242097_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_135242097_   5727 TTAAAGGAAGACATTTATGCAGCCAAGAAACACATGAAAAAATGCTCATC 5776
                          iv  i     i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_135242097_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3218 27.20 0.66 0.66  chr2_135338064_135344440.rev     4978  5885 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_135338064_   4978 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5027
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_135338064_   5028 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5077
                            v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_135338064_   5078 TACCAATGACTTTCTTCACAGAA-TTGGAAACAA-CT-ACTTTAAAGTTC 5124
                          v   iivi i  i  ii     -   ---    -  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_135338064_   5125 ATATGGAACTAAAAAAGAGCTCGCATTGCCAAGTCAATTCTAAGCCAAAA 5174
                                 v iv  ii  v iv v  v     iv    ii i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_135338064_   5175 GAACAAAGCTGCAGGCATCATGCTACCTGACTTCAAACTATGCTACAAAT 5224
                                 i  v   vv   ii  v  ii i      viv i       v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_135338064_   5225 CTACAGTAACCAAAACAGCGTGGTACTGGTACCAAAACGGAGATATAGAC 5274
                                  i   i    i          i iv ii ii  v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_135338064_   5275 CAATGGAACAGAATAGAGCCTTTGGAAATAATACCACACATCTACAACCA 5324
                                 i     v   vv iii       vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_135338064_   5325 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5374
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_135338064_   5375 TGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGGTG 5424
                          v  i  i              v      v  ?   i   i i  iii  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_135338064_   5425 AAACTGGATCCCTTCCTTACGCCTTATACAAAAATTAATTCAAGATGGAT 5474
                           ii    i    v   i  i  v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_135338064_   5475 TAAAGACTTAAATGTTAAACCTAAAACCATGAAAACCCTAGAAGGAAACC 5524
                         i ?    i       v i v       i  i   vi i      i    v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_135338064_   5525 TAGG--TAATACCATTCA-GGTCATAGGCATGGGCAAGGAATTCGTGACT 5571
                             --   - i -   i- ii v i  i- i     v iv   v iiv 
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_135338064_   5572 AAAACATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATTG 5621
                          vi   i        vvi          vv     v  i    v   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_135338064_   5622 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGTGA 5671
                         v  i   v v  i i   i  ii vv    i  v    i  vv v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_135338064_   5672 ACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACACATCTGAC 5721
                          v  iv    i                 v      ivii i i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_135338064_   5722 AAAGGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAACAA 5771
                           i  i  vi          v  i   v    ivv    v iv i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_135338064_   5772 AAAATCAAACAACCCCACCAAAAAGCGGGCAAAGGAGATGAACAGACACT 5821
                            iv    i     v ii?    ii          vv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_135338064_   5822 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5871
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_135338064_   5872 TCATCATTGGCCAT 5885
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (151 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2588 20.11 1.20 17.15  chr2_135344763_135350559     4234  5312 (485)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_135344763_   4234 GGAAAGATATTCCATGCTCATGAATAGGAATAATTAATGTCATTAAAATG 4283
                                   i     i     i  v    v v     i ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_135344763_   4284 ACAATACTACTTAAACCAATTTGCAGATTTAATGCAATCCCTATCAAAAT 4333
                         i       v ii   iii  i i      i  i                 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_135344763_   4334 ACCAATGACATTCTTCACAGAAATAGAAAAAACAATCCTAAAATGTATAT 4383
                         v   iivi v  i  ii       v  v  ivii          vi    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_135344763_   4384 GGCACCACAAAAGACCCCCCATAGCCAAAGCAATCCTGAGTAAAAAGAGC 4433
                           v vii   ii     vvv         i     i   iv  i    i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_135344763_   4434 AAAGTTG-AGGCATCATGCTACCTGACTTTAAAATATATTACAAAGCTAT 4482
                                -   vv   ii  v  ii i  i    iv  i          i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_135344763_   4483 AGTAACCAAATGAGCATAGTACTAGCATAAAAGCAGATATATAGGCTAGG 4532
                              i   ivv  ii i     i      iiii   i      ------
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG------ 295

  chr2_135344763_   4533 CATGGTGGCAGGTGCCTGTAATCCCAGCTACTCAGGAGGCAGAGGCAGGA 4582
                         --------------------   ---------------------------
  L1M4_orf2#LINE/    296 --------------------ATC--------------------------- 298

  chr2_135344763_   4583 GAAACGTTTGAACCTGGGAGGTGGAGTTTGCAGTGAGCTGAGATTGCACC 4632
                         --------------------------------------------------
  L1M4_orf2#LINE/    299 -------------------------------------------------- 298

  chr2_135344763_   4633 ACTGCATTCTAGCCTGGGCGACAGTGCAAGACTCTGTTTCAAAAAAACAA 4682
                         --------------------------------------------------
  L1M4_orf2#LINE/    299 -------------------------------------------------- 298

  chr2_135344763_   4683 AAACAAAAACAAAACAGATGCATAGACAAATGGAACATAATAGAAAACCT 4732
                         ----------------------------       i v   v  i ii i
  L1M4_orf2#LINE/    299 ----------------------------AATGGAATAGAATTGAGAGTCC 320

  chr2_135344763_   4733 AGATATAAAGCTACTCTTTTACAGCCAACTCATTTTCAACAAAGGAGCCA 4782
                            v     v i iv v    ii i   i v      i    i  v    
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_135344763_   4783 AGAACATACAATGGGGAAAG-----TCTCTTCAATAAATGGTGCTGGGAA 4827
                            v   v            -----   i     i              v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_135344763_   4828 AAATGGATAACTATTTGCAGCAGAATGAAACTAGACTCCTATCTCTCAAC 4877
                           v      ? i iv    iv        ii i   i    i   v  v 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_135344763_   4878 ATACACAAAAATCAAATCAAAATGGATTAAAGAATTAAAT-CAAGACTCA 4926
                            i        i  v           i ?   vi     -i    vii 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_135344763_   4927 AAACTATGAAACTACTAGAAGAAAACTTGGGG--AAATGCTCGACTCCAT 4974
                                i     vi           v i  ?--    vi   vvv  - 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC-T 569

  chr2_135344763_   4975 TGGTCTGGGCA--GATTTTTGTGTGTGTAAGACCTAAAAAGCACAGGCAA 5022
                            vi i    -- i   i - ivi i i v   --         i    
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCT-TAGATATGACACC--AAAAGCACAAGCAA 616

  chr2_135344763_   5023 CTAAAGCAAAAATAGACAAATAGGTTTACATCAAGCTAAACAGCTTCTGC 5072
                          v    v         i    v  vi v      iv v  v i   i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_135344763_   5073 ACAGCAAAGGAAACAATCAACAAAGTGAAGAAATGACTCATAAAATGGGA 5122
                         i vv       v  v     v        i i ii  i  i i       
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_135344763_   5123 GAAAATATTTGCCAACTATGCATCTGA-AAGGGATTAACAACCACAATAT 5171
                                     v  ii  ii      -      i vii v   v     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_135344763_   5172 AGAAAGAGCTCAAACTATTCAACAGCAAAAAAACAAATAACCTGATT-AA 5220
                          v     i   vv  v i    i ii     i          ii   -  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_135344763_   5221 AAATGAGTAAAAGATCTCAATAGACATTTCTCAAAAGAAGACATACAAAT 5270
                              i i   i   i v              v        i        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_135344763_   5271 GGCCAAAAGGTACATGAAAAGGTGTTCTACATGACTAATAAT 5312
                               v i i          i  i  v    v ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (137 / 77)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 16.50 (198 / 12)  


3298 26.13 0.66 0.55  chr2_135416254_135422515     4864  5770 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_135416254_   4864 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4913
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_135416254_   4914 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCC-ATCAAGC 4962
                            v     v     iv i  i           i  v     -     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_135416254_   4963 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5009
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_135416254_   5010 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5059
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_135416254_   5060 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5109
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_135416254_   5110 CTGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5159
                           i      i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_135416254_   5160 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5207
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_135416254_   5208 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5257
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_135416254_   5258 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5307
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_135416254_   5308 TGAAACTGGATCCCTTCCTTACACCTTATACCAAAATCAATTCAAGATGG 5357
                             ii    i    v   i     v     v     i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_135416254_   5358 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5407
                           i ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_135416254_   5408 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5457
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_135416254_   5458 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5507
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_135416254_   5508 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5557
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_135416254_   5558 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5607
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_135416254_   5608 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5657
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_135416254_   5658 AAAACAAACAACCCCATCAAAACGTGGGCGAAGGATATGAACAGACACTT 5707
                           i     i     v  i?   vi     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_135416254_   5708 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5757
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_135416254_   5758 CATCACTGGCCAT 5770
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1068 24.43 10.75 0.00  chr2_135476914_135480084     1489  1795 (1376)    L1M4_orf2#LINE/L1        1   340 (568)  

  chr2_135476914_   1489 TGGAAAGTTCTATCATGTTTATGGATCAGAGAACTCTACGATGTTAAGAT 1538
                                v v vi      i      ii  ii   iv iiv         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_135476914_   1539 ATCAATTCTCCTCACATTGATCTATAGAGTCAATGTAATCCA-AGCTAAA 1587
                         iv    v    i  v         i   v    i i     v- v v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_135476914_   1588 TCT----------------AAAAAT-------------CTAAAATGTATA 1608
                           i---------------- i    -------------       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_135476914_   1609 CAGATATACAAAGGACT-AGAAGAGCCAAAATAATCTTGAAAAAGAAAAA 1657
                         ii  v  i   i    i-    v        i               i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_135476914_   1658 TAA-GTTAAAA-ACTTGCATTAACTGACCTCAAGGGTTACTACAGAACAA 1705
                         i  -   ii i-   ii  i vv ii ii    iiv        i i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_135476914_   1706 CAGCAATCAAGATAGTGTGATATTGGCATAAGGAAAGACAAATAGATTAA 1755
                            i        i      i  i           v     v      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_135476914_   1756 TGGAATAAACTAAAGAATCCAGATATATATCCATTCTTTT 1795
                                i v vi   i      v   v i    v v   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

Transitions / transversions = 1.78 (48 / 27)
Gap_init rate = 0.02 (6 / 340), avg. gap size = 5.50 (33 / 6)  

1781 27.82 1.52 1.52  chr2_135476914_135480084     2087  2679 (492)    L1M4_orf2#LINE/L1      316   908 (0)  

  chr2_135476914_   2087 AGCCCAGAAATATATTCATCCTTATACGGTCAATTAATTCTTGACAGAGA 2136
                           i         v ii   v v v  i        i   i i    ii i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_135476914_   2137 CACGAAAGCAATTACATGGGGAAAGGAAAGCCTTTTCA-CAAATGGTGCT 2185
                         ii v  ii v   vv          i v  i       -           
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_135476914_   2186 GAAGCAA--GAAT--CCATCATATGGGGGGGAAATGAACCCTGACCC-TA 2230
                          iii   -- i  --   -   iiiiii ---      viiv     -  
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCA-CATGCAAAAG---AATGAAGTTGGACCCCTA 461

  chr2_135476914_   2231 TCTCATACCAGCCATACACAAAACTTAATTTGAGCAAGATTATACAACTA 2280
                         i    i    ----  i      v    i ii ivvi   i ? v v   
  L1M4_orf2#LINE/    462 CCTCACACCA----TATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_135476914_   2281 AACAAAAAAGCTAAAACAGTAAAGCTTCAAGAAGAAAATATAGAAGAATA 2330
                           iiv  i         vi    i  iiv         i    i? v v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_135476914_   2331 TCTCTTCAACCTGGAAGCAGGCAAAAATTTCTTGGACAAGATGCAGAAAG 2380
                            iivii    v iivi      vii      i  i v  ii vi    
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_135476914_   2381 CAATAAAACCATAAAGAAGAATTTGACAAATTAGACTTCATCACA-TTAA 2429
                           vv iv v  -      i  v v  i     i          v -    
  L1M4_orf2#LINE/    608 CACAAGCAACA-AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_135476914_   2430 ACACTTTAGCTCATCCTAAGACAACATTAGCAACATGAATAAGTAAGCCA 2479
                          v     v iv v  vv i    vi  i iv  vi    v iii  v   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_135476914_   2480 CAGAATGATAGGAAATGTTCATAAAGCATATATATGACAAAGGACTTATA 2529
                                iv  i    i  iii   v       v   i  i      i  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_135476914_   2530 TCCAAAATTTATAAAGAACTACTAAAACTCA-TGATGAAAAGTCCAACAA 2578
                             i   v           vi  v      - i  i     v v  i  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_135476914_   2579 TCCTATTTAAAAGTGGGCAAAAGGCTTAAATGGCCACTCCCAAAAAGAAG 2628
                         i  v   ?    i        i ii  i   i v  i i ivv       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_135476914_   2629 GTA-ACAATTAGCCAATAAACATATTTAAAGGTGCTCAACATCATTAGTT 2677
                         i  -    v i        i  i  vv    i            ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_135476914_   2678 CA 2679
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.70 (102 / 60)
Gap_init rate = 0.02 (11 / 593), avg. gap size = 1.64 (18 / 11)  


1508 22.16 24.11 1.60  chr2_135677306_135679657.rev      824  1387 (965)    L1M4_orf2#LINE/L1        4   694 (214)  

  chr2_135677306_    824 AGAGATACATCACATACATGGATTGAAAGATAAAACACTGTGAACACACC 873
                          i     ivi  ii v         i    ivv  i i   v  v iiv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_135677306_    874 AGTTCTCCCCAAGTTAATCTATATATTCAACATGATCCCAATCAAAACAT 923
                          i v        i  i     i v       iii     v       ivi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_135677306_    924 CAGCAACAGGCATTTTGTAGAAATTGACAAGTTGATTTTAAAACTAATAT 973
                             vi v--iv     i             i    ii     i v    
  L1M4_orf2#LINE/    104 CAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_135677306_    974 GAAAATCCAAAGAACCTAGAACAGCTAAAATAATTTTGATGAATAAG--- 1020
                          i    v   i i   i    i   i    i   i    vi  v   ---
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_135677306_   1021 --------------TATACTACCTGATTTTAACACTT--T-----GCTAC 1049
                         --------------i i   v  ii    i  v    -- -----     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_135677306_   1050 AATAATTAAGACAGTATAGTATAGGCATAAAGACAGACAAACAGATCAAT 1099
                          i    i        i i   iv       i  i     v i        
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_135677306_   1100 GAAATAGA-------GTCCAGAAATAA---CATTCGCACTTA----CATT 1135
                          i      -------            ---   --i  i   ----  v 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCAT--ACATTTATGGTCAAT 349

  chr2_135677306_   1136 TGACTTCACAACAGAGGTGCTACTGGA--ATTCAGGGGGGAAATAATAGT 1183
                            i  i- i   ii     i --i  --     iv       v      
  L1M4_orf2#LINE/    350 TGATTTT-CGACAAGGGTGCCA--AGACCATTCAATGGGGAAAGAATAGT 396

  chr2_135677306_   1184 CTTTTCAACAAATGGTGCTGGAATAATTAAATATTCACATGGAAGAAAA- 1232
                                              i i  i ii   ?i      v  i i  -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_135677306_   1233 -----------------------CATG----AGAAT-------------- 1241
                         -----------------------   i---- i   --------------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_135677306_   1242 ------ATCT-----TGGGA----------------TCTT---------- 1254
                         ------ i  ----- ii  ----------------    ----------
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_135677306_   1255 ------GCAAAT-------ACCTTGGGATAGGCAAAGATTCCTTTGACCA 1291
                         ------ i    -------        v       v i  i   v  ivv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_135677306_   1292 GACACAAAAAGCACTAACAATAAAATTAAAAATAGAGAAAATGAACTTCA 1341
                              v        v i   i    vv         v   v  i      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_135677306_   1342 TCTAAAT-AAAA---TTTGTGCTTATCAAAAGACACAGTTAAGAAAACGA 1387
                           v    -    ---         --    i     vi i      ii  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGA 694

Transitions / transversions = 2.18 (85 / 39)
Gap_init rate = 0.03 (21 / 691), avg. gap size = 6.90 (145 / 21)  


3104 24.55 2.79 1.45  chr2_135699237_135701126.rev      503  1398 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_135699237_    503 TAAAGAAATATTCTATATTCATGGATAGGAAGA--TAATATTATCAAGAT 550
                          ii i i    i i  i         v      --       i i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_135699237_    551 ATTAGTTCTTTCCAACTTCATCTACAGATTCAATGCAATCTCAATCAAAA 600
                         ivi i v  ii    v  v              i      i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_135699237_    601 TCTCAGCAAGTTATCGTGAGGATATCCACAAACTGAGTTTAAAGTTCACA 650
                           i    vivi v iv  vi  v  iv    i    vii    i    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_135699237_    651 AGCAGAAGCAAAAAAAGACTCAAAGTAGCCAATAAAATATTGAAGAAGAA 700
                         v v i v    ii---   i  i i       v v   v     i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG---GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_135699237_    701 GAA---AGTTGGAGAACTAACACTATCAAACTTCAAGCACT-ACTATAAA 746
                            ---        i   v     vi v  i     i-   -    i   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-ACTTACTACAAA 246

  chr2_135699237_    747 GCTACAGAAATCAATACAGTGTGGTAATGGCAAAAGAACAAA--TAGGGA 794
                                v      v           v     v   i i i --  vi  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_135699237_    795 TCAATGGAACAGAATAGACAGCCTAAAAATAGACCCAGATAAATATAGTC 844
                                  i     v  v  i i i     i     v i vv   i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_135699237_    845 AACTAATCTCTGAAAAGGA-ACAGAGGCAATACAATGGAGA-----TAGT 888
                           i i  i ii  v    i-i vi  i v  v      i  -----    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_135699237_    889 CTTTTCAACAAATGGTGTTAGAACAACTGGACATCCACATACAAAAAAAT 938
                                          i i i         i ?      i     i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_135699237_    939 TAATCTAGA----TAGGCTTTACATTCTCCACAAAAACTAACTTAAAATG 984
                         v  vi i  ----  -- i i   iiv vi       i     i      
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_135699237_    985 GATTACAGACCTGAATATAAAATGC-AAAGTTATAAAACTCCTAGAA--- 1030
                            i ?      i   i   i -  -   ii          i     ---
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_135699237_   1031 --CACAGAATAAAATCTAGATAACTTTGAGTTTGTTGATGACCTTTTAGA 1078
                         --  i  i?vv      vvi i  i   i   v vii   iii i     
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_135699237_   1079 TGCAACACCAAAGGCACAATCCAGAAAAGAACAAACTGATACGCTAGACT 1128
                          iii        i      v v v       v   iv    vii i    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_135699237_   1129 TCATTAAAATTAAAAATTTTTGCTCTGCAAAAGACACTGTCAAGAGAATG 1178
                             i           i     iv  v    i      i      i i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_135699237_   1179 AAAGAGAAAACC-ATAGTCTGGGAGAAAATATTTGCAAAAGACATTTCAG 1227
                            -   v    - i  vv                    vv i  v  v 
  L1M4_orf2#LINE/    694 AAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_135699237_   1228 ATAGAGGACTGTTATCTAGAATCTACAGAGAACTCTTAAAACTCAAAAAT 1277
                            ii     vv    i     v  i i          v       v   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_135699237_   1278 AAGAACATAATCGAAGCTAAAAAAAAAAAAAAGCCCCAAAGACTTCAACC 1327
                           i  v i  vi-  v i  vv?     viii----     iv  ii vi
  L1M4_orf2#LINE/    793 AAAAAGACAAAT-AACCCAATTWAAAAATGGG----CAAAGGATTTGAAT 837

  chr2_135699237_   1328 AGACACCTCACCCAAGAAGATATAAAGATAGCAAACAAGCGTATGAAAAG 1377
                              ii  v  v           v i  i  v  i    ii        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_135699237_   1378 ATGTTCCATATCACATGTAAT 1398
                            i  v i    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (136 / 80)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  


1939 26.12 6.18 2.78  chr2_135731844_135735306.rev     1838  2484 (979)    L1M4_orf2#LINE/L1       32   700 (208)  

  chr2_135731844_   1838 GACTCAATATT---AAGATGTCAATTCTCCATAAATTGATCTACAAATTC 1884
                             i      ---      v    v    vi             i    
  L1M4_orf2#LINE/     32 GACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTC 81

  chr2_135731844_   1885 AATGCAATCTGAATTAAAATCCCAGCAAGATTTTGAATATGTGTTTGTTT 1934
                           i      ivv  i           -------------  iv   -   
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGC-------------TGCCTTT-TTT 117

  chr2_135731844_   1935 ATAAAAATTAACAAGCTGATTCTCAAATTGATATAACAATGCAAAGGACC 1984
                         ii i     i          i  v     v    iiv       i     
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_135731844_   1985 TAGAATAGCTAAGATAATGTTGAA---GAGTAACAAAGTTAGAAGATTTA 2031
                         i        i  i i   v     ---  iv         i  i  i i 
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_135731844_   2032 CACTACCAGAT----AGACTTATTATAAAGCTACAATAATGATGACAGTA 2077
                             v  vi  ---- i     i  i         i    v v      i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_135731844_   2078 CATTACTGGCACACG-ACAGA------GACCAACGGAACAGAATAAATAG 2120
                         iiv        i v - i   ------  i   i    i     vi v  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_135731844_   2121 TCCAGAAATAGACCAAAACACATACAGTTGCTTGATTTACATCAAAGATA 2170
                                   i   v v   iv  ii  iiv       v iv   i i i
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_135731844_   2171 TCACTGCCACTCAATGGGAAAAGGCAGATCTTTTCAACAG-TGGTGGTGG 2219
                         i  vvi   i        i    ivvii           i-     v   
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_135731844_   2220 AACAATTCAATCTCCCTATAGAGAAAAGAGAATCTTAACCTGTTCCTCTT 2269
                         i    i vi  v?  vi  iv i  i iv   vi vi   iv v    vi
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_135731844_   2270 ACCA-----AACAATTAATTTGAGGTGGGTCACAAAC--AAATGATATAG 2312
                             -----  v      i ii ii   i   ? i  --     vv v  
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_135731844_   2313 GTAAAACAATAAAGCTTCCAAAAGAAAA-----GAAAATATCTTCAGTAC 2357
                         v      v     i  iii i       ----- ?iv v      ivv  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_135731844_   2358 TT-------GGTAAAGAGTTCTTAAGCAGAACACAAAAAGCACTAACCAC 2400
                         i -------  i  v iv      iii vi    v        v i v  
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_135731844_   2401 ATAAGAAAAACAAGGATAGATGAGACTGTATTAAAATTAAGAACACCT-- 2448
                          v        - vi    i  vi    vi  i        i   vii --
  L1M4_orf2#LINE/    618 AAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_135731844_   2449 -CTTCAACCCAAGGCATCATTAAGAAAGTGAACAGGC 2484
                         -      --- i i  ii  i           v  i 
  L1M4_orf2#LINE/    667 GCTTCAA---AGGACACTATCAAGAAAGTGAAAAGAC 700

Transitions / transversions = 1.68 (104 / 62)
Gap_init rate = 0.02 (15 / 669), avg. gap size = 3.87 (58 / 15)  

 556 20.59 11.76 1.96  chr2_135731844_135735306.rev     2778  2981 (482)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_135731844_   2778 AAGTAAGTGAATAGATAAGCAACA----------AAATATTTGCAATACA 2817
                            v       v   i  v v   ----------            vv  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_135731844_   2818 AGTATCTAA----GGACTCATATCCAGAATATATGAAGAATTCCTATAAA 2863
                         vi     i ----     ii              i     i  i  i  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_135731844_   2864 GTAATAAGAAAAAAAAAGACAACTGCTTTAAGAAAAAAATAGGCAAAGGC 2913
                         vi     v     i v i i   i----i  vv?      i        v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACC----CAATTWAAAAATGGGCAAAGGA 830

  chr2_135731844_   2914 CTTGAACAGGCTTTTCACCAA-GAAGATAGACAAATGGGCAATAAATATA 2962
                         i     i  i v    v    -       v        v      ii i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_135731844_   2963 T----ATATGCT-----TCAGGAAAATG 2981
                          ---- v     -----   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (22 / 19)
Gap_init rate = 0.03 (6 / 224), avg. gap size = 4.67 (28 / 6)  


 449 21.78 0.00 0.00  chr2_135781354_135785089     1655  1755 (1981)    L1M4_orf2#LINE/L1        1   101 (807)  

  chr2_135781354_   1655 TGAAAACACATTCCATGTTCATGGATTGGAATAGTTAATATAGTAAATGT 1704
                           i   v i  i                   v v       v  v  vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_135781354_   1705 GTCAATACTACTCATAGTGATCTACAGATTCAATGCAATATTTATTGATA 1754
                          v       v i  v v                i     vii   ii v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_135781354_   1755 T 1755
                          
  L1M4_orf2#LINE/    101 T 101

Transitions / transversions = 0.83 (10 / 12)
Gap_init rate = 0.00 (0 / 101), avg. gap size = 0.00 (0 / 0)  

4151 17.95 2.48 0.12  chr2_135781354_135785089     2437  3244 (492)    L1M4_orf2#LINE/L1       82   908 (0)  

  chr2_135781354_   2437 AACACA---CCTATCAAAATCTTA-CTGATATGTCTGTAGAAATAGAAAA 2482
                            i  ---            ii -   viv v i  i      v  v  
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

  chr2_135781354_   2483 GTCCATCCTAAAATTTATATGGAATCTCAAGGGACCCCAAATAGCCAAAA 2532
                          iiv           i        viv          vi           
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr2_135781354_   2533 CAATCTTGTAAAGAAA--------TCAGAGGTCTCACATTTCCTGATCTC 2574
                                 v   ii  -------- ii    v      i    ii  i  
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_135781354_   2575 AAAATTTACTACAGAGTTACAGTAATCAAAACAGTGTGGTACTGGCATAA 2624
                             i        i  i            i                    
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_135781354_   2625 AGGCAGACATATAGACCAATGGAATAAAGTACAGAGCCCAGAAATAGATC 2674
                         i ii           i          i i vv    i         i i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_135781354_   2675 CACACTTACATGGTCAAATGATTTCCAACAAGGGTGCCAAGATCATTCAA 2724
                           i  v vi        v      i i               i       
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_135781354_   2725 TGGGGAAAGGACAGTCTTTTCAACAAATGGTGCTGGGGAAACTGCACATC 2774
                                  i i                         iv     v i ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_135781354_   2775 TACATGTAAAAGAATGAAGTTGGACCT-TAGCTAATACTAAATACAAAAA 2823
                         i     i                   i-  v  v i  i v         
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_135781354_   2824 TTAACATGAAATAGATCAAAGACTTAAATGTAGGAACTAAAACTATAAAA 2873
                              vii    i     ?    i        i  i              
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_135781354_   2874 CTCTTAGAAGAAAACACAGGGGAAAGGCTTCAAGGCATTGGACTTGGCAA 2923
                                         i   ? v  iv    iv i v    ii v     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_135781354_   2924 TGACTTCCTAGATCTGACATCAAAGGCACAGGCAACAAAAGAAATAACAG 2973
                           ii   i     v     i    i     i             v  i  
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_135781354_   2974 ACAAATTGGGCTTCATAAAAAATTTAAAACTTTTGTGT---AAAGTTCAT 3020
                          i       i      v    -  v            i---    vv  i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_135781354_   3021 T--CAACTGAGTAAAACGACGATTCACAGAATAAGAGAGAAGATTTGCAA 3068
                          --   vvi   i   v   i ii        ii    i  v        
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_135781354_   3069 ATCACATATCTGGTAAGTAATTAATGTCCAGAAGATACAAATAACTCCTA 3118
                             i       i    vi i vi i       v   i   v     i  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_135781354_   3119 AAGCTCAACAATAAAAG--CAAATAATTCAATTCAAAAATGGGCATAGGA 3166
                         v i     i       i--       ii     ?           v    
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_135781354_   3167 CTTGAATAGATATTTCTCCAACAGTAATATACAAATGGCCAATAAGCATA 3216
                         i         i          viivi                      i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_135781354_   3217 TGAAAAGATGCTCAACATCACTAATCAT 3244
                                             ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (96 / 45)
Gap_init rate = 0.01 (8 / 827), avg. gap size = 2.62 (21 / 8)  


3231 26.95 0.55 0.66  chr2_135822613_135829004     4992  5900 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_135822613_   4992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATGTCATGAAAAT 5041
                              ii i  i     i      i v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_135822613_   5042 GGCGATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5091
                            i     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_135822613_   5092 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5139
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_135822613_   5140 TATGGAACCAAAAAAGAACCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5189
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_135822613_   5190 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAGCTATACTACAAAGC 5239
                                i      vv       v  ii i     iviv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_135822613_   5240 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5289
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_135822613_   5290 AATGGGACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5337
                              i i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_135822613_   5338 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5387
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_135822613_   5388 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5437
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_135822613_   5438 GGAAGTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5487
                          i iv    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_135822613_   5488 TTAAAGACTTACCATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAA 5537
                          i ?    i  v-    v   v       i      vi i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAA-ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_135822613_   5538 CCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCT 5586
                          v    ?i- v i -   iv   viv  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_135822613_   5587 AAAACACCAAAAGTAATGGCAACAAAAGCCAAAATTGATAAATGGGATCT 5636
                          vi          i vvi          vv     v       v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_135822613_   5637 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5686
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_135822613_   5687 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5736
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_135822613_   5737 AAAGGGCTAATATCCAGAATCTACAATTAACTCAAACAAATTTACAAGAA 5786
                           i  i  vi          v  i  vv     vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_135822613_   5787 AAAAACAAACAACCCCATCGACAAGTGGGCGAAGGATATGAACAGACACT 5836
                            i     i     v  i? v  i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_135822613_   5837 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5886
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_135822613_   5887 TCATCACTGGCCAT 5900
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3025 27.34 0.44 0.77  chr2_135877470_135882435.rev     3568  4474 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_135877470_   3568 AACACATCCCATGCTCATGGATTGGTAGAATCAATATTGTGAAAATAACC 3617
                           v i        i           v   v i        v  i  ii v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_135877470_   3618 ATATGGCCAAAAGCAATCAACAAATTCAATGCAATTCCCATCAAAATAAC 3667
                            ivv  v   vii   v   i      i     i  i        v- 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC-C 103

  chr2_135877470_   3668 CATCATCATTCTTCACAGAAGTAGAAAAAACAATCCTAAAATTCATATGG 3717
                           v vv v  i  ii     i v  v  ivii                  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_135877470_   3718 AACCAAAAAAGACTCATCATAGCCAAAGCAAGACTAAGCAAAAAAGAACA 3767
                           viiv  ii   i  vv         i   vvi i i-   i       
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAACA 202

  chr2_135877470_   3768 AATCCAGGGGTATCACATTACATGACTTTGAACTGTACTGTAAGGTTATA 3817
                           viii i  vv     i v vii i  ii  viv    ii  i i  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_135877470_   3818 GTCACCAAAACAGCATGGTACTTGTATAAAAATGGGCACATAGACTAATG 3867
                           v i   i    ii       v i    ii  i i  i     ii    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_135877470_   3868 GTACAGAATAGAGAACCCAGAAATAAAGCCAAATATTTACAGCCAACTGA 3917
                          v i     v    ii           v   v i     ii i   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_135877470_   3918 TCTTCAACAAAGCAAACAGAAAGATAAAGTGGGGAAAGAACACTCTATTC 3967
                          i   i    i vviv  ii vv  vv i           i v   v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_135877470_   3968 AATAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGAAGAATGAAACT 4017
                           i              i  i   vv ?       i i         ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_135877470_   4018 GGATCCTCATCTCTCACCTTATGCATAAATCAACTCAAGATGGATCAAAC 4067
                            i  ii i   v    v   i  v    i       i        ? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_135877470_   4068 ACTTAAATCT--GACCTAAAACCATAAAAATTCTAGAGGATAACATTGGA 4115
                           i     v --  v       i      v ii    i  v     v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_135877470_   4116 CAACCCCTTCTAGATATTGGCCTAGGCAAAGAGTTCATGACCAAGAACCC 4165
                         vv vvi    vv  iv    vi       v iv   v iivi v  vv  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_135877470_   4166 AAAAGCAAATGCAACAAAAACAAAGATAAATAGATGAGACTTAAATAAAT 4215
                                v v         iv   i   i   i  vi     v vi   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_135877470_   4216 GTAAAAGCTTCTGCACAGCAAAAGGAGCAGTCAGCAGAGTAAACAGACAA 4265
                         v     i   i  ii vv    i ivi vi   iv i   i  v      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_135877470_   4266 CCCACAGAGTGGGAGAAAATCTTCACAAACTATGCCTCCAACAAAGGACT 4315
                                 i           v  ii    ii  iiv  ii i  i     
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_135877470_   4316 AATAGCCAGAATCTACAAGGAACTCAAACAAGTCAGCAAGAAAAAAATAA 4365
                         vi  v       v  i  i      vv    v   ii  v     i i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_135877470_   4366 TAATAATAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCT 4415
                         -----    i  v  i?    i     v     iv          v    
  L1M4_orf2#LINE/    803 -----ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_135877470_   4416 CAAAAGAAGATATGCAAATGGCCAAAAA--AAATGAAAAAATGCTCATCA 4463
                          v           i           v  -- v       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_135877470_   4464 TCACGTATTAT 4474
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.01 (5 / 904), avg. gap size = 2.20 (11 / 5)  


3211 27.37 0.66 0.44  chr2_135883149_135889513.rev     4968  5873 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_135883149_   4968 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATGTCATGAAAAT 5017
                              ii i  i     i      i v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_135883149_   5018 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5067
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_135883149_   5068 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5115
                          v i iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_135883149_   5116 TATGGAACCAAAAAAGAACCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5165
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_135883149_   5166 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAGCTATACTACAAGGC 5215
                                i      vv       v  ii i     iviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_135883149_   5216 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5265
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_135883149_   5266 AATGGGACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAGCT 5313
                              i i    i--    i  --        vv  ii i  i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_135883149_   5314 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5363
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_135883149_   5364 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5413
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_135883149_   5414 GGAAGTGGGTCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5463
                          i iv   ii    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_135883149_   5464 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAACCCCTAGAAGAAAAC 5513
                          i ?    i       v   v       i       i i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_135883149_   5514 CTAGGCA-ATACCATTAAGACATAGGCATGGGCAAGGACTTCATGTCTAA 5562
                         v    ?i- v i v iiv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_135883149_   5563 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGTCAAATGGGATCTAA 5612
                         i            vvi          vv     v vi    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_135883149_   5613 TTAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTACCATCAGAGTGAAC 5662
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_135883149_   5663 AGGCAACCTACAGAATGGGAGAAATTTTTTGCAGTCTACTCATCTGACAA 5712
                           i     i               v v      ivii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_135883149_   5713 AGGGCTAATATCCAGCATCTACAATGCACTCAAACAAATTTACAAGAAAA 5762
                         i  i  vi       v  v  i  v v    vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_135883149_   5763 A-ACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 5811
                          -     i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_135883149_   5812 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5861
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_135883149_   5862 ATCACTGGCCAT 5873
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 570 26.05 11.16 0.00  chr2_135899707_135903025     1319  1533 (1786)    L1M4_orf2#LINE/L1        3   241 (667)  

  chr2_135899707_   1319 GAACGATACTC--TTTTCAGGGACCAGAAGACTAAATATTATTCAGAAGT 1366
                            v    ii -- v    v   iii       v      i  v   v v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_135899707_   1367 AAATTCTTCC-AAATTAGTCAACAGATCCAACACAATTCCAA-CAAAATT 1414
                         v   v  i  -     ii  v      i    i    i  v -      i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_135899707_   1415 GTA--TACACTT------AAAAT------GCTGATTCTAAAATTCATACA 1450
                         vi -- i vi  ------i    ------      i            ii
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_135899707_   1451 GAAAAGCGAAGGACCTACAAAAGACAAAGCAATATTGAAAAGGAA---TA 1497
                             v  i i     i v  v  v    i    v       i   ---i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_135899707_   1498 CAGTAGGGTAA---ACACTATATAATTTCAAGGCTTATT 1533
                         v   v  ivi ---     vivi        ii    i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

Transitions / transversions = 1.43 (33 / 23)
Gap_init rate = 0.03 (8 / 239), avg. gap size = 3.00 (24 / 8)  

 755 22.86 3.81 12.70  chr2_135899707_135903025     1833  2147 (1172)    L1M4_orf2#LINE/L1      229   515 (393)  

  chr2_135899707_   1833 TTCAAGACTTATTATAAAGCTACAGTAATCAAGCCATTGTAGTA------ 1876
                              i     i  i                  v  v   i   ------
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_135899707_   1877 TAAGGCT-GATGAATAGACCAATGAATGAGAAT--AGAGTTCAGAAACAG 1923
                              v -  iiv     i     i vv     --     i      i i
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_135899707_   1924 ACCTACACATACATTGCCAATTGGTTTTTGGTGAAGGTGCCAAGGAAATT 1973
                            i i    vi  v i      i    i iii i         ivv   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_135899707_   1974 TAAGGAGGGCAAAATAGTCTTCTGTGTTTTGATGA---GTGTTGTAACAA 2020
                         i  v i  iv i         ------  ii ii ---   i  vi    
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTT------TTCAACAAATGGTGCTGGGACAA 422

  chr2_135899707_   2021 CTGAAAATCCATATGTAAAATGACAAACCAAAACAAAAATAAAAAAATCA 2070
                            i v ?   i   i    ----------------i   i  i--- ii
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAA----------------GAATGAAG---TTG 453

  chr2_135899707_   2071 GAACTGCTACCTTTATTTTGTAGCATATAAAAGAATTATATGCTACAAAA 2120
                           -------  ii  ii iii v      v  i     ---i  -     
  L1M4_orf2#LINE/    454 GA-------CCCCTACCTCACACCATATACAAAAATTA---ACT-CAAAA 492

  chr2_135899707_   2121 ATAATAGTTTATAGACCTACATCTAAG 2147
                         ---- i v i ?       v  v    
  L1M4_orf2#LINE/    493 ----TGGATCAWAGACCTAAATGTAAG 515

Transitions / transversions = 2.68 (51 / 19)
Gap_init rate = 0.04 (11 / 287), avg. gap size = 4.73 (52 / 11)  

 849 26.33 10.92 1.40  chr2_135899707_135903025     2471  2827 (492)    L1M4_orf2#LINE/L1      518   908 (0)  

  chr2_135899707_   2471 CTAAAGCTATGGCATTTTTAGAAGAAAATATAAGAGGGTATCTTTGTGAA 2520
                              i    iiv i i           i   i ? viv     i    v
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_135899707_   2521 CTTAGATTAGGCAAAAATTTCTTAG----GAC-TCAAAA-TACAAAAAAA 2564
                            i i        vii        ----   -i     -i    iv  v
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_135899707_   2565 AAAAGGAAGAAAAAAATTGATATACTAGATTGTTTCCAAATTTAAAACTT 2614
                              -----       v    v i i  i viv  v     v       
  L1M4_orf2#LINE/    618 AAAAG-----AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_135899707_   2615 CTGTTCTCTGAAAGACAATGTTAATAAAATAGAAATCAAATCCATAGACT 2664
                         i   v  iii  i    v i i  v   i ii   vvv  i   i   v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_135899707_   2665 TGGAGGACATATTTGTAAAAGATATATATATTACAGAACTTGTTTCCAAA 2714
                         v    i v       i   vv      v iv  vi i      v    i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_135899707_   2715 ATA----AAGAGTTCTTATTACCCCATA---------TAAATA------- 2744
                            ----    ii     iv  i v   ---------i     -------
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_135899707_   2745 -------TGGACTCA--ATATGAACAGATACTTCACAAAAGAAAATG--- 2782
                         -------   i vv --  v    i   i i   v v      i  i---
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_135899707_   2783 -AATAGACAAAAGGCACCAAAAAACATGCTCAACACCATCAGTCAT 2827
                         -   i v   v i    vvi    v          i  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (53 / 40)
Gap_init rate = 0.02 (9 / 391), avg. gap size = 4.89 (44 / 9)  


2968 27.85 0.88 0.77  chr2_135971670_135978055     4990  5894 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_135971670_   4990 GAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGC 5039
                            ii i  i     i      i v      v i        v  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_135971670_   5040 CCATACTGCCCAAGGTAATTTATAGATTCAATGCCACCCCCATCAAGCTA 5089
                          v     v     iv i  i  i        i  v i   i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_135971670_   5090 CCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATATG 5134
                            iivi i  i  ii     v v  v  i--- --     i        
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_135971670_   5135 GAACCAAAAAAGAGCCTGTATTGCCAAGACAATCCTACACAAAGAAAAAC 5184
                            viiv  ii  v  v v  v     i      i iv -      i   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAAC 201

  chr2_135971670_   5185 AAAGTTGGAAGCATCATGCTACCTGGCTTCAAACTATACTATAAGGCTAC 5234
                                  i vv   ii  v  iiii      viv     i  i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_135971670_   5235 AGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGATATATTGAGCAAT 5284
                              i   i    ii     v   i iv ii i   i    v  v    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_135971670_   5285 AGATCGGGAACAGAG-GTCTCAGAAATAACACCACACATCTGCAACCATC 5333
                         i  vii -  iv   -   -         vv   i    i iiiii  vi
  L1M4_orf2#LINE/    302 GGAATAG-AATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_135971670_   5334 TGGTCTTTGACAAACCTGACAAAAACAAAAAATGGGGAAAGGATTACCTG 5383
                           i i  i     ivv  v   i v  vvv           i  vii  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_135971670_   5384 TTTAATAAATGGTGATCAGAAAACTGGCTAGCCATGTGTAGAAAGCCGAA 5433
                           i  i        v vi  v      v  ?   ii  i i  iivi   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_135971670_   5434 ACTGGATCCCTGCTTTACACCTTATACAAAAATTAACTCAAGATGGATTA 5483
                         ii    i    i i i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_135971670_   5484 AAGACTTGAATGGTTTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5533
                         ?    i i    --- v   v       i      vi i           
  L1M4_orf2#LINE/    500 WAGACCTAAATG---TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_135971670_   5534 CTAGGCA-ATACCATTCAGGACAGAGGCATGGGCAAGGACTTCATGACTA 5582
                         v    ?i- v i -   iv   vvv  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_135971670_   5583 AAACACCAAAAGCAATGGCAACAAAAGCCAAAAGAGACAAATGGGGTCTA 5632
                         vi            vvi          vv    v   i    v  iii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_135971670_   5633 ATTAAAGTAAAGATCCTCTGCAAGGCAAAAGAAACTACCATCAGAGTGAA 5682
                           i   i v  i v i i  iivvv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_135971670_   5683 CAGGCAACATACAGAATGGGAGAAAATTCTTGCAATCTACCCATCTGAGA 5732
                         v  i    vi                 vi      vii ivi      v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_135971670_   5733 AAGGGCTAATATCCAGAATCTACAGAGAACTCAAACAAATTA-CAAGAAA 5781
                          i  i  vi          v  i i       vv    v i -i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_135971670_   5782 AAAACAAACAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5831
                           i     i   i v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_135971670_   5832 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5881
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_135971670_   5882 CATCACTGCTCAT 5894
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.50 (15 / 10)  


3335 26.35 0.33 0.44  chr2_135996954_136000038     1687  2593 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_135996954_   1687 GAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGG 1736
                            ii i  i     i      i v      v i     i  v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_135996954_   1737 CCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 1786
                          v     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_135996954_   1787 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 1834
                            iivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr2_135996954_   1835 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 1884
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_135996954_   1885 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 1934
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_135996954_   1935 CAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGAGATATAGACCAA 1984
                               i   i    ii       i i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_135996954_   1985 TGGAACAGAACAGAGACCTCAGAAATAATGCCGAATATCTACAGTCATCT 2034
                              i    iv    vii         vv  iv i  i  ii    vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_135996954_   2035 GATCTTTGACAAACCTGACAAAAACAATAAATGGGGAAAGGATTCCCTAT 2084
                            i  i     ivv  v   i v  v v           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_135996954_   2085 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 2134
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_135996954_   2135 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 2184
                         i    i    v   i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_135996954_   2185 AGACTTACCACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 2234
                             i  v- i  v   v       i      vi i           v  
  L1M4_orf2#LINE/    501 AGACCTAA-ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_135996954_   2235 GGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 2283
                           ?i- v i -   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_135996954_   2284 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGTCAAATGGGATCTAATT 2333
                                    vvi          vv     v vi    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_135996954_   2334 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 2383
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_135996954_   2384 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAG 2433
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_135996954_   2434 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 2483
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_135996954_   2484 ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 2533
                              i     v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_135996954_   2534 AAAAGAAGACGTTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCAT 2583
                         v        ii vi viii     v ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_135996954_   2584 CACTGCTCAT 2593
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (6 / 906), avg. gap size = 1.17 (7 / 6)  


3105 25.63 3.64 0.23  chr2_136000166_136002671     1137  2014 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_136000166_   1137 TGGAAAAACATCTCATGCTCATGGACACAAAGAATCAATATCATTAAAAT 1186
                               i i   i    i       ivvi    v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_136000166_   1187 GGCCACAGTGCCTAAAGCAAAGTACAGATTCAATGCTATTCCTATCAAAC 1236
                            v i v v  i   vii vv           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_136000166_   1237 TACCAATGGCATTCTTCACAGGACTAGAGAAAAGTATTTTAAAATTCATA 1286
                          v   iiv  v  i  ii   i v v  v  ivvv  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_136000166_   1287 TG-AAACAAAAAAGAGCCCCAATAGCCAAGGTAATTCTAAGCAAAAAGAA 1335
                           -   iiv  ii  v  vv         iii   ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_136000166_   1336 CAAAGCTGGAGGCATCACACTACCCAACTTCAAACTATACAACAGGGCTA 1385
                              i      vv       v     i      viv   v   ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_136000166_   1386 CAGTAACCAAAACAGCATGATATTGGTACAAAAAGAGACACATAGACCAA 1435
                               i   i    ii  i  i   i i  ii v     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_136000166_   1436 TGGAACAGGATAGAGAGCCCTGAAATAAGGCCACACAACTACAAGCACCT 1485
                              i  i  v     i  v       iv   i   vi  iiiv  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_136000166_   1486 AATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGACTCTATAT 1535
                         i  i  i     i v  v   i v  vv            i ivv v v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_136000166_   1536 TCAATAAATGGTACTGGGATAACTGTCTAGCCATATGCAGAAGAATGAAA 1585
                             i       i      i     vv  ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_136000166_   1586 CTGGAACTCTACATATCACCATATATAAAAATTAACTCAAGATGGTTTAA 1635
                         i    v i    v vv         i              i    v i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_136000166_   1636 ATACTTAAATGTAAGACCTCAAACTACAAAATTCCTAGAAGAAAATCTAG 1685
                          v  i           v  v      i    i  i          iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_136000166_   1686 GA--AAATCTCTTCTGGACACTGGACTAGGCAAAGAATTTATGATTAAGA 1733
                          ?--      --  vv   vi   ii       v iv  iv iiv  v  
  L1M4_orf2#LINE/    551 GNGTAAATCT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_136000166_   1734 CCTCAAGAGTAAATGCAACAGAACAAAAAATAGGTATATGGGACTT---- 1779
                          vi   i  i v v      i  v         i  v  v      ----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_136000166_   1780 ----------------GCACAGCAAAAGAAACAATCAACAGAGTAAACAG 1813
                         ---------------- ii vv    i  v  v     v i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_136000166_   1814 ATGACCTACAGAATGGGAGAAAATATTTGCAAACTATGCAACTGAAAAAG 1863
                          ii   i                          ii  ii v    v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_136000166_   1864 GACTAATATCTAGACTCTATAAGGAACTGGAACGAATCAACAAGGAGAAA 1913
                             vi    i   v v     i     vvv  i v    i  vi i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_136000166_   1914 ACAA----CCCCATTGAAAAGTGGGCAAAGGGCATGAACAGACACTTCTC 1959
                             ----   v   ?    i          iiv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_136000166_   1960 ---AAAAGACATACAAGTTGCCAAAAA--ACATGAAAAAATGCTCAACAT 2004
                         --- i    i      i v     v  --         i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_136000166_   2005 CACTATCATT 2014
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (129 / 92)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 4.86 (34 / 7)  


3308 26.02 0.55 0.66  chr2_136004568_136009174     3209  4115 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_136004568_   3209 GAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGG 3258
                            ii i  i     i      i v      v i     i  v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_136004568_   3259 CCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 3308
                          v     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_136004568_   3309 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 3356
                            iivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr2_136004568_   3357 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 3406
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_136004568_   3407 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 3456
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_136004568_   3457 CAGTAACCAAAACAGCATGGTCCTGGTACCAAAACAGAGATATAGATCAA 3506
                               i   i    ii    v    i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_136004568_   3507 TGGAAGAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACTAT 3554
                              v    i--    i  --        vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_136004568_   3555 CTGATCTTTGACAAACCTCAGAAAAACAAGCAATGGGGAAAGGATTCCCT 3604
                         i    i  i     ivv vvv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_136004568_   3605 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAAAAAGCTGA 3654
                         v  i  i              v      v  ?   i   i    iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_136004568_   3655 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3704
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_136004568_   3705 AAAGACTTACCACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 3754
                          ?    i  v- i  v   v       i      vi i           v
  L1M4_orf2#LINE/    499 AWAGACCTAA-ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_136004568_   3755 TAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGACTAA 3803
                             ?i- v i -   iv   viv  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_136004568_   3804 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3853
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_136004568_   3854 TTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3903
                          i   v v  i i      ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_136004568_   3904 AGGCAACCTACAGAATGGGAGGAAATTTTTGCAATCTATTCATCTGACAA 3953
                           i     i            i    v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_136004568_   3954 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4003
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_136004568_   4004 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 4053
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_136004568_   4054 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 4103
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_136004568_   4104 ATCACTGGCCAT 4115
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (136 / 96)
Gap_init rate = 0.01 (8 / 906), avg. gap size = 1.38 (11 / 8)  


 793 28.25 5.71 2.86  chr2_136087894_136091409      518   832 (2684)    L1M4_orf2#LINE/L1        1   324 (584)  

  chr2_136087894_    518 TGTAAAAATAATTCATATTCATGGAATGAAATACTCTGTATTATAAATAT 567
                           v   i   vii   i        v  i  v   ivi    i v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_136087894_    568 ATAAATTCTCCCCAAACTGATCTATAGATGCAGTAAAACTCCATTCACAA 617
                         ivv   v         i       i    v  iiiv  ii  vv   v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_136087894_    618 ATCCAGC-AC---TTTTGTGAAAATTGATAAA-TGACTTCTACAATTTAT 662
                         vi     -i ---     iii       i  i-   - i   v    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_136087894_    663 ATGTAA-TGCAGAG--TCAATAATAGCTGAGACAATTTTGAAAAAGAG-- 707
                            v  -    ii --i v v      ii i     i          i--
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_136087894_    708 -TAAGGCTGAAAGATTTATACTGCCTGATACCAGAATATTTATTATAAAG 756
                         -i  i i  i i  i i i   v  ii  vi  i  i--   i  i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC--TTACTACAAAG 247

  chr2_136087894_    757 CTACGCTAAGAAGTATGAAGA-AGTATGGTACTGACACAAAGATGG-CAA 804
                             iv   ------ v    -   i        i  i  i   i -  v
  L1M4_orf2#LINE/    248 CTACAGTAA------TCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_136087894_    805 ACAGA-----GAAACAAAACAAAGAATCTACAA 832
                          i   ----- i  i i  ivi   i  i v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

Transitions / transversions = 2.30 (62 / 27)
Gap_init rate = 0.04 (12 / 324), avg. gap size = 2.25 (27 / 12)  

 320 29.91 5.13 0.00  chr2_136087894_136091409     1050  1166 (2350)    L1M4_orf2#LINE/L1      333   455 (453)  

  chr2_136087894_   1050 ATACACATAAAATTACTTGATTTATGACAAAAGTAACATTACAATGCAGT 1099
                              iv  vii i v       vi     ii  iv  vv  v  v  i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_136087894_   1100 AGGAAAA----AGTCTTTTCAATAAATTGTGCTGGATCAAGTAGACATTC 1145
                         i  i   ----           i    v       iv   v i  i ?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_136087894_   1146 ATATGTAAAA--ATAAATTTAAA 1166
                          i   i    --  i  v  ii 
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGA 455

Transitions / transversions = 1.62 (21 / 13)
Gap_init rate = 0.02 (2 / 123), avg. gap size = 3.00 (6 / 2)  

 433 24.17 2.50 4.17  chr2_136087894_136091409     1516  1635 (1881)    L1M4_orf2#LINE/L1      454   571 (337)  

  chr2_136087894_   1516 GATGTCTACTTCATACCATATACACAAAACAATTCCAAGTAGATTGTAAA 1565
                           ivi    i   i          v   vi  i  v  i i   ii? i 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_136087894_   1566 TCGAATTAGTGTAAAAATTAAAACAATAAAGCTTTTAGAGGAAAACACAG 1615
                         i v  ---i     i ii      v     i  i     i       i  
  L1M4_orf2#LINE/    504 CCTAA---ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_136087894_   1616 G---AAATCTCTTCATGACTTTG 1635
                          ---      --  i    i   
  L1M4_orf2#LINE/    551 GNGTAAATCT--TCGTGACCTTG 571

Transitions / transversions = 3.67 (22 / 6)
Gap_init rate = 0.03 (3 / 118), avg. gap size = 2.67 (8 / 3)  

 678 28.53 2.31 6.05  chr2_136087894_136091409     2683  3029 (487)    L1M4_orf2#LINE/L1      575   908 (0)  

  chr2_136087894_   2683 TAGACAAAGATTTTTAAAATTTGATGAAAGAAGTGCCAGCCATA---GAA 2729
                            i   v i   i v i  v   iivv i   ii v   v i ---   
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_136087894_   2730 TGAATGCGGATAAAGATTATGTAAGATGACATTAAAATTGAGAATCTCTG 2779
                         vi   i--      --  i-----  ivv   i      i i  ii i  
  L1M4_orf2#LINE/    625 AAAATA--GATAAA--TTG-----GACTTCATCAAAATTAAAAACTTTTG 665

  chr2_136087894_   2780 CTTATCAGAAGACATCATTAAGACAAGGAAAAGGCAAAACACAACCTGAG 2829
                         iviv   i i    ii  i    v iv      i   vv    ivv  i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_136087894_   2830 AAAATTTACTTGCCATAAATATACCTGATAAAAGACTCATATCCAGAGTA 2879
                          i  vv  i    v vvv     i       ii    ii        i  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_136087894_   2880 TACATATGACAAAAGGACTCCTACAAAACAATAAGAAAAAGGCAAATAGA 2929
                           i --------   i    i     vv      v      i      --
  L1M4_orf2#LINE/    766 TATA--------AAGAACTCTTACAACTCAATAATAAAAAGACAAATA-- 805

  chr2_136087894_   2930 CAATCCAGAAGAAAAACAGATAAGAAAT--GAACAGGCATTTA---AAAA 2974
                         -- i   ivv?     ii ii  iii  --   i  i     v---   i
  L1M4_orf2#LINE/    806 --ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_136087894_   2975 AAGATGTCCAAATGGCTAATAAGCGTATGACAAGGTATTAAATTTTACTT 3024
                              i v        i       ii    v   i ii v  iv i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_136087894_   3025 ATCAT 3029
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.88 (64 / 34)
Gap_init rate = 0.02 (8 / 334), avg. gap size = 3.62 (29 / 8)  


3049 17.14 5.81 1.64  chr2_136364587_136366862      608  1278 (998)    L1M4_orf2#LINE/L1        1   699 (209)  

  chr2_136364587_    608 TGGAAAG-TATCCTATGTTCATGGATAAGAATACTTAACATTGTTAAGAT 656
                                -     i            vi   v      i           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_136364587_    657 GATAATCCTCCCTAAACTGATCTAACTGATCTATAGATTCAACAC---TC 703
                          ii   v     i   i       ---------i         i ---i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTA---------CAGATTCAACGCAATCC 91

  chr2_136364587_    704 CTATCAAAATTCCAGCTGGCTTTTTTCCATAAATT-ATAAAC-----CTA 747
                                   i       v       v  v     - i  i -----   
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr2_136364587_    748 AAATTCATATGGAAATGCAAGAAACACA--ATAGTTAAAACAAACTGGAA 795
                                              ii  v  --    ii       v  v   
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_136364587_    796 AATGAAGA-------TAGATGACTCATACTTCCTGATTTTCAAACTTACT 838
                           v     ------- i  v      i      ii    iv         
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_136364587_    839 GCAAAGCTATA----------CAGTGATGTAATGGTATAAG-ATGAACAT 877
                         i        i ----------     vv   v   i     -  ii    
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_136364587_    878 ACAGGTCATTGTAATAGAATGGAGTCTCTAGAAATAAACCCTTACATTTA 927
                          i  i   v  v        v   vv  i            v        
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_136364587_    928 TGAACTGTTTATTTTTGAAAAGGGTACCAAGACTATTCAGTGGG-AAAGA 976
                           iv vi  v     i  v      i       i     i    -     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_136364587_    977 AGAATCTTTTCAACAAAAGGTGCTTGGACAACTGAATATCTACATGCAAA 1026
                          v i             v      v         i   ? i         
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_136364587_   1027 ATAATGAATTTGGACCTTTACCTCACACCATGTACAAAA-TTAACTTAA- 1074
                          v      v       ii             i       -      i  -
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_136364587_   1075 -TGGATCATCTACCAAAAAGTAAAA-CTATAAAATATATA-TTCTTAGAG 1121
                         -       ?vv   v   v    i -   -   v    v -i       i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAA 540

  chr2_136364587_   1122 GAAAAAAGAGGAATATATTTTTGTGATCTAGGAGTAGCCAATGGATTGTT 1171
                              v v   ?i  v  i  i    i  v  iv   v      v  v  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_136364587_   1172 AGACATGGCACTAAAAGCACAGG-AACAAAATTTAAAAATAGGTAAATCG 1220
                            i   i   i         i -       vv-        i     i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTG 639

  chr2_136364587_   1221 CACTTC--CAAAATTTAAAACTTTCGTGCTTTGAAGGATATCATCAAGAA 1268
                         v     --       v        i      ii     i ii        
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_136364587_   1269 AGTGCAAAGA 1278
                             v     
  L1M4_orf2#LINE/    690 AGTGAAAAGA 699

Transitions / transversions = 1.29 (63 / 49)
Gap_init rate = 0.03 (18 / 699), avg. gap size = 2.78 (50 / 18)  

1193 12.61 6.09 0.43  chr2_136364587_136366862     1555  1784 (492)    L1M4_orf2#LINE/L1      666   908 (0)  

  chr2_136364587_   1555 TGTCTCAAAAAAAA-----AAAAAAATGCAAAGAACAACCCATAGAATTG 1599
                           ii     ii v -----  i   i  v     -       i     v 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA-CAACCCACAGAATGG 714

  chr2_136364587_   1600 GAGAAAATATTTGCAAATCATATATTTGATGAGAGACTTGTGTCTAGAAT 1649
                                                  i    i  i       i  i     
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_136364587_   1650 ATAAAAAGAACC--TGTGACTCAATTATAAA--GACA-----CCCAGTTC 1690
                            v       i-- iii       v     --    -----    i  ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_136364587_   1691 AAATATGTGGAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAAACAA 1740
                            v   v v                                   v    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_136364587_   1741 ATGGCCAGTAAGCACATGAAAAGATGTTCAACATCATTAGTCAT 1784
                                i                  i         ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (19 / 9)
Gap_init rate = 0.02 (5 / 243), avg. gap size = 3.00 (15 / 5)  


3156 26.72 1.22 0.55  chr2_136529398_136533719     2929  3830 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_136529398_   2929 TGGAAGAACATTGCATGCACATGGATAGGAAGAATCAATATTGTGAAAAT 2978
                              ii i  iv    iv       v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_136529398_   2979 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3028
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_136529398_   3029 TACCAAGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3076
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_136529398_   3077 TATGGAACCAAAAAAGAGCCTGCATTGCGAAGACAATCCTAAGCCAAAAG 3126
                                viiv  ii  v  v v  v  v  i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_136529398_   3127 AACAAAACTGGAGGCAC-CACGCTACCTGACTTCAAACTATACTACAAGG 3175
                               ii      -  -   i  v  ii i      viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_136529398_   3176 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGA--TATAGAT 3223
                                  i   i    ii         i iv ii i   --       
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_136529398_   3224 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAAC 3271
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_136529398_   3272 TATCTCATATTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 3321
                         i vi v  v  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_136529398_   3322 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3371
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_136529398_   3372 TGAAACTGGATCCCTTCCTTACACCTTATACAAGAATTAATTCAAGATGG 3421
                             ii    i    v   i     v       i      i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_136529398_   3422 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3471
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_136529398_   3472 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3521
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_136529398_   3522 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3571
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_136529398_   3572 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3621
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_136529398_   3622 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 3671
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_136529398_   3672 AAGGGCTAATATTCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 3721
                          i  i  vi   i      v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_136529398_   3722 AAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 3767
                           i    ----   v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_136529398_   3768 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 3817
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_136529398_   3818 CATCACTGGCCAT 3830
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


3062 26.55 1.00 0.55  chr2_136851983_136858999.rev     5622  6525 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_136851983_   5622 TGGAAAAACATTCCATGCTCATGAATAGGAAGAATTAATATCATGAAAAT 5671
                               i i  i     i     i  v      v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_136851983_   5672 GGCCATACCACCCAAAGTAATTTATAGATTCCATGCTATTCCCATCAAGC 5721
                            v    iv      v i  i  i      v i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_136851983_   5722 TACCATTGACTTTCTTCGCAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5770
                          v   vivi i  i  i      v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_136851983_   5771 GTGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAGCAAA-AAGA 5819
                         i     viiv  ii  v  v v        i      i iiv   -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_136851983_   5820 ACAAAGCTGGAGGCATCACGCTACCTGACTT-GAAACTACACTACAAGGC 5868
                               i      vv    i  v  ii i  -i     -i       i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_136851983_   5869 CACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATACAGACT 5918
                         i       i   i    ii  i      i iv ii i   i   i   ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_136851983_   5919 GATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5968
                         i      i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_136851983_   5969 TTGATCTCCGGCAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 6018
                              i i  i   ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_136851983_   6019 ATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCACGTGCAGAAAACTGA 6068
                         v  i  i              v      v  ?    i    i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_136851983_   6069 AACTGGACTCCTTCCTTACACCTTATACAAAAACTAACTTAAGATGGACT 6118
                          ii     i   v   i     v          i     i  i     ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_136851983_   6119 AAATACTTAAATGTAAGACCTTAAACCATAGAAACCCTAGAAGAAAACCT 6168
                          ? v  i           v  v    i   i  vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_136851983_   6169 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCA-AGACTAA 6216
                            ?i- v i -   iv   v v  vv i     v ii   v-   -  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TAT 596

  chr2_136851983_   6217 AACACTAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 6266
                         i    i    i  vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_136851983_   6267 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 6316
                          i   v v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_136851983_   6317 ACGCAACCTACAGAATGGGAAAAAAAAATTCGCAATCTATCCATCTGACA 6366
                          vi     i           i    v -  i    vii  vi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATA-TTTGCAAATCATATATCTGATA 745

  chr2_136851983_   6367 AAGGGCTAATATCCAGAATCTACCAGGAACTTAAACAAATTTACAAGAAA 6416
                          i  i  vi          v  iv i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_136851983_   6417 AA-ACAAACAACCCCATCAAAAATTGGGCAAAGGATATGAACAGACACTT 6465
                           -     i     v  i?    v            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_136851983_   6466 CTCAAAAGAAGACATTTATGTGGCAAACAA--ACATGAAAAAAAGC-CAT 6512
                            v        i  vi vi    v  i  --         i v  -  v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_136851983_   6513 CATCACTGGTCAT 6525
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.08 (14 / 13)  


3585 22.34 4.08 1.13  chr2_136861518_136866497     3607  4488 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_136861518_   3607 TGAAAACATATTCTATGTTCATGGATTGGAAGAATTAATATTGCTAAAAT 3656
                           i   v    i i                   v         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_136861518_   3657 GTTCATACTACCCGAAGCAATCTATAGATTCATTGCAATCTCTATAAAAC 3706
                          viv     v   i  vii     i       vi      i    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_136861518_   3707 TTCCAG-TGACATTTTCATGGAAATAGAAAAAGCAATCTTAAAATTCATA 3755
                          i    -  v v    iiii     v  v  ivii   i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_136861518_   3756 TGGAACTAT----GACCCTGAA-------AGCAATCTTGAAAGAAAA--- 3791
                              v ii----     v   ------- i           i i  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_136861518_   3792 -AAAGCTAAAAGAAGTATCTTTCCTGATTTCAAATTATATTACAAAATTA 3840
                         -    i ii i  vvi ivi    ii        viv  i      ii  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_136861518_   3841 TAGGAATCAAAGCAGTATGATATTGGCATAAAAACAGACACATAAACTAA 3890
                         i  v      ii    i  i  i        ii i     i   i ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_136861518_   3891 TGAAATAGAATGAAGAGCCCAGAAATAAACCCACACATATATGGTCACCT 3940
                           i        vi    i               i    v        vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_136861518_   3941 AATTTTCTATAAGGGTGCCAAGAATACACAGTGGAGAAAGGATAGTCTCT 3990
                         i      v i             vi iv  i   i     i       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_136861518_   3991 TCAACAAATGGTGTTGGGAAAACTGGATATCCACATGCAAATAAAGGAAG 4040
                                      i     v         ?           vi  v    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_136861518_   4041 TTGGGTCGTTATCTTGCACCCTACACAAAAATCAACCCAGAATTTATTAA 4090
                             ii vi  i  ii    v  i        i   i  i   vv  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_136861518_   4091 AGACTTAAATATAAGACCTGAAACTGTAAAACTCCCAGAAGAACTCATAG 4140
                             i     i     v  i     i        ii       vv     
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_136861518_   4141 GAA-AAAGCTCTTTGACATTATCCTTGGCAATGATTTTTTGGCTTTGATA 4189
                          ?i-   v  iiv    v  ivvi v       i   i  i v v   i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_136861518_   4190 CCAAAAACACAGACAACAAAAGCAAAAATGAACAAGTGGTACTACATCAA 4239
                               i    ii         v      ii i  i v v   v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_136861518_   4240 ACTAAAAAACTTCTGTGCAGCCAAAGAAACAATTAACAAAATTAAGA--- 4286
                          v v        i     vv v  i  v  v  i  v   i v  i ---
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_136861518_   4287 ---------AATGAGAGAAAATATTTGCAAACCATATATCTGATAAGGGA 4327
                         ---------    i                 i                  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_136861518_   4328 TTT-TATCCAAAATATAGAAGGCATTTATGCAACTGAATAGCAAAAACAT 4376
                         i  -      i      v  i v i iv i     v    ii     ---
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA--- 797

  chr2_136861518_   4377 AACAAA-AACCAAATAATTAAATTAAAAATGGGCAAATGTTCTGAA-AGA 4424
                         i     -    v   ------- ?             v v i    -   
  L1M4_orf2#LINE/    798 GACAAATAACCCAAT-------TWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_136861518_   4425 CATTTCTCCAAGGAAGA----CAAAAGGCCAACAGGTATATGACAATGTG 4470
                                    i     ----    v      i i i i    v  vi  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_136861518_   4471 CTCACCATCATTAATTAT 4488
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (123 / 70)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.83 (46 / 12)  


2936 25.03 2.38 4.23  chr2_136958236_136962012     2363  3285 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_136958236_   2363 GAAAGATATCCTATGTTCATCAATTAGAAGAATTAATATTGTTAAAATGT 2412
                                    i        vi   i     v             i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_136958236_   2413 CCATACTAGACTATCTAAAGTGATTTATAGATTCAATACAATCTCTATAA 2462
                          v     --- i-- i   v    i  i        ii     i    v 
  L1M4_orf2#LINE/     53 CAATACT---CC--CCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_136958236_   2463 AAACTCCAGTAACATCTTCCACAGAAA----CAAAAAAATCCTAAAATTT 2508
                            ii    ivi v i  iii      ----   ivvi           i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_136958236_   2509 GTAAAGAACTACAAAAGACCTTAAATAGCCAAAGCTATTTAAGAACAACA 2558
                         i  vi   v i   ii    ivi          i v  i vi------- 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-------A 190

  chr2_136958236_   2559 AAGAGAAGAACAAAGCTAGAGGCATTACACTTCCTGATCTCAAGCTAAAT 2608
                           i            i i    vv i        ii  i    ivivv i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_136958236_   2609 TATAAAACAATAGTAATCAAAGCAGTATGGCAGTGGCATAAAAACAGACA 2658
                           i   i v i         ii    i   i v        ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_136958236_   2659 CAGAGGCTAATGGAACAGAACAGAGAGGCCAGAAATAAACTCAAACATAT 2708
                         i v  iii       i    iv     v            i  v    v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_136958236_   2709 ATAGTC---TAACATTTGACGAGGGTGCTAATAATAT--GATAGGGAAAG 2753
                           i   --- i iv  i   i       i  v vi  --i  i       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_136958236_   2754 GGCAGTCTCTTCAATAAGTGGTATTGGGAAAGCTGGATATCCACATGCAA 2803
                         iii     i     i  i    ii     v i       ?          
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_136958236_   2804 AAGAATGAAGCTGGACCTCTATCTTATACCACTTACATAAATTAACTCAG 2853
                                   i      i   i  i i    iv    v           i
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_136958236_   2854 AATGAATTACACAT-TAAATGTAATACTTAG-----TAAAACTCCTAGAA 2897
                             i  i ? v i-         v vi  i-----        i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_136958236_   2898 GAAAACA--GGAAAAAAGCTCATTGACATTGGGCTTGGGCTTGGCAAAGA 2945
                                --  ?iv   v  ivv    ------      i v     v i
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGAC------CTTGGGTTAGGCAATGG 584

  chr2_136958236_   2946 TTTTTTGAATATAGCACTAAAAGCACAGGCAACAAAAATGAAAATAAACA 2995
                            i  ii    ii   i         i         ivi      i i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_136958236_   2996 AGTGCAACTACAG-AAAACTAAAGTGTCTGGATAGCAACAAACCAATGAA 3044
                          i vvi   v  v-    i    -----------------   ivv  vi
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAA-----------------AACTTTTGTG 667

  chr2_136958236_   3045 CAACACAAAAAACAAAAACCAACAAAATGAAAGG-TAACTTATATAAT-- 3091
                          --iv    ii   vv -i   v   i     i -i   ii i v   --
  L1M4_orf2#LINE/    668 C--TTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_136958236_   3092 -AGAAAATAAATGCAAACCGTATATCTGGAAAGAGATTAACATACTAAAT 3140
                         -        vv      i i        iv   i  i vii  v vi   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_136958236_   3141 ATGTAAGAAGCCCACACAACTCAATAGCAAGGAAACAAAAAAATCCAATT 3190
                           i   ii i i vi           ii  ii i     v  -i      
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA-CCCAATT 813

  chr2_136958236_   3191 AAAAACTCAACAAAAGACCTAAATAAACATATTTCCAAAGAAGACATACA 3240
                         ?    v vii    i  ii i    i    v i           i     
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_136958236_   3241 AATGACTGGCAGGTATCTGGAAAGGTGCTCACCATCACTAACCAT 3285
                             i iiii i i iv  i    i      v     ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.34 (159 / 68)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 3.59 (61 / 17)  


 551 21.32 5.15 0.74  chr2_137020344_137022135.rev      187   322 (1470)    L1M4_orf2#LINE/L1        6   147 (761)  

  chr2_137020344_    187 AGTTATTCCATGTTCATGGATAGAAAGCCTCAATATCGTCAAAATATCAA 236
                           v   i              v i   v  i     i  i  i  iv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_137020344_    237 TTATTTTC--AACTGATCTATAGATTCAAGGCAATCTCAATCAAAATCTC 284
                          - i ii --  i       i        v      i v         i 
  L1M4_orf2#LINE/     56 T-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_137020344_    285 AGCAGACTATTTTGAAGATATTAACAA-----TTCCACAATTC 322
                            v v  v     v   v   i    ----- i i v     
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

Transitions / transversions = 1.42 (17 / 12)
Gap_init rate = 0.02 (3 / 142), avg. gap size = 2.67 (8 / 3)  

2360 22.65 2.35 6.31  chr2_137020344_137022135.rev      502  1309 (483)    L1M4_orf2#LINE/L1      133   908 (0)  

  chr2_137020344_    502 CTAATTCTAAAGTTTATACAAAAAGACAAAAGATCCAAAATAGTCAAAAT 551
                           i  i     i  i   iii   vi   ii  i   i     i     i
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_137020344_    552 AATACTGAA---GAAGATCAAAGTTGGAGGAATGACATTACTCAGCTTCA 598
                            vi    ---     v             v v   i v i  ii    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_137020344_    599 AGAATTACAGTACTAAAAGTAAACTAAAACAAGTCAACTTGATGACCAAA 648
                          -  i ----     -------------------------------    
  L1M4_orf2#LINE/    233 A-AACT----TACTA-------------------------------CAAA 246

  chr2_137020344_    649 GCTACAGTAATCAAAACAGTGTGGTATGGGCCTAAAAAAAAAAAAAATAC 698
                                       i           iv   v   ii v i ------- 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA-------C 289

  chr2_137020344_    699 AAATAGATAAATGGAACAGGATAGAGAGCTCAGAAATAGACCTACATAAA 748
                          v      v       i  i  v     ii        i   i i i vv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_137020344_    749 TATAGTCA-CTGGTTTATGGCAAAA-TGA-AAGGCAACACA-TGGAGAAA 794
                            i    -i  i   vi i   ii-  v-   i v iv  -   i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_137020344_    795 AGATAATATTTTCAACAAATGGTTATAGAAAAACTG-ACACCCGCATAAA 843
                         ii   i v               vv i i v     - i ?  i   iv 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_137020344_    844 AAAAAAAAAGAATTTAGACACAGACGTTACAACCTTCACAAAAACTAACT 893
                            i  v--   v  i   v vv  v i   v v vi       i     
  L1M4_orf2#LINE/    440 AAAGAAT--GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_137020344_    894 CGAA-TAGATCAAAGACCTAA-TATAAAATGC-AAAACTGTAAAACTCTC 940
                          i  - i     ?        - i   i -  -      i         i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTT 536

  chr2_137020344_    941 AGAAGATGACATAGATGAAAATCGAGATGACCT-GGGTTTGGCAAAGACT 989
                               vi      i? v     vvvi      -     v     v ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_137020344_    990 TTTTAGATACAACATCAAAGGAACAATCCATGAAAGAAAGGGCTGATAAG 1039
                          i       ii   i    i v    v v ii       iiiiv     i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_137020344_   1040 CTGGATTTCAGTAAAATTCAAA--TTTTCTGCTCTATGAAAGTCACCATC 1087
                         i    i    vi      v   --    v    ii --  i v   i   
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATC 684

  chr2_137020344_   1088 AAGACAGTAAGAAGAG---CCACAGACTGCAAGAAAATATTTGTCAAAT- 1133
                             v   i i    v---       v  vi            -     -
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG-CAAATC 733

  chr2_137020344_   1134 ATGTGTCTCTTAAAGGACTAATATCCAAAATATACAAAGAACTCTTAAAA 1183
                           i i   vv   i     vi      i      i            v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_137020344_   1184 CTCAACAATAAGAAAACAAAACAACCTAATTTTTTAAATGGCCCGAAGAC 1233
                              i     i  i     -i    i    ?vv-      v vi i  i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAA-TAACCCAATTWAA-AAATGGGCAAAGGAT 831

  chr2_137020344_   1234 CTAACCAGATACCTCACCAAAGAAGATATACAGATTGCAGATAAGCATAC 1283
                         i i vi   i ii  v                i  v  vi       i i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_137020344_   1284 GAAAAGATGTACC-CATCATTTGTTAT 1309
                                  iv v-     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (114 / 65)
Gap_init rate = 0.03 (24 / 776), avg. gap size = 2.92 (70 / 24)  


3069 26.40 2.46 0.89  chr2_137059789_137065876     4703  5596 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137059789_   4703 TAGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4752
                          i   ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137059789_   4753 GGCCATACTGCCCATGGTAATTTATAGATTCAATGCCATCCCCATCAAAC 4802
                            v     v    viv i  i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137059789_   4803 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTCA 4850
                          v   iivi i  i  ii     -   -- v  i  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_137059789_   4851 CATGGA---GCCAAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCA 4897
                         i     ---  ----  ii  v  v v  v     i      i i ivv 
  L1M4_orf2#LINE/    149 TATGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_137059789_   4898 AAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACA 4947
                         i          i      vv       v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_137059789_   4948 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAATATGTA 4997
                          i          i   i    ii         i iv ii i i i  i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_137059789_   4998 GACCAATGGAACAGAACAGAAGACTCAGAAATAACACCACACATCTACAA 5047
                           i        i    iv  iiiii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_137059789_   5048 CCATCTGATCTTTGACAAACCTGACAAAAAGAAGAAATGAGGAAAGGATT 5097
                         i  vi    i  i     ivv  v   i vv vvv    i      i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_137059789_   5098 CCCTGTTTAATAAATGGTGCTGGGAAAACTAGCTAGCCATATGTAGAAAG 5147
                         vi  v  i  i              v    i v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_137059789_   5148 CTGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATG 5197
                         v    ii    i    v   i     v  i           i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_137059789_   5198 GATTAAGGACTTAAAC-------CTAAAACCATCAAAACCCT-AGAAGAA 5239
                            i ?i   i    i-------       i  -     i  -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAA 543

  chr2_137059789_   5240 AACCTAGGCA-ATACCATTCAGGACACAGGCATGGGCACGGATTTCATGA 5288
                            v    ?i- v i -   iv   viv  vv i    vv i    v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_137059789_   5289 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGAT 5338
                         v  vi            vvi          vv        i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_137059789_   5339 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5388
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_137059789_   5389 GAACAGGCAACCTACAGAACGGGAGAAAAATTTTGCAATCCATCTATCTG 5438
                            v  i     i      i         vv       vi   v      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_137059789_   5439 ACAAATGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAG 5488
                          i  iv i  vi          v  i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_137059789_   5489 ACAAAAA-----AACCCAATCAAAAAGTGGGCAAAGGATGTGAACAGATA 5533
                          v   i -----        i?    i            v    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_137059789_   5534 TTTCTGAAAAGAAGACATTTATGCAGGCAACAGACATATGAAAAAATGCT 5583
                              vv        i  vi viii v   i ii  i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_137059789_   5584 CA---TCACTGGCCAT 5596
                           ---   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (143 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.50 (30 / 12)  


3171 27.15 0.88 0.66  chr2_137186868_137193226     4963  5868 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137186868_   4963 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5012
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137186868_   5013 GGGCATACTGCCCAAGGTAGTTTATAGATTCAATGCCATCCCCATCAAGC 5062
                           vv     v     iv ii i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137186868_   5063 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5110
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_137186868_   5111 ATATGGAACCAAAAAAGAGCCCGCATTGCCATGACAATCCTAAGCTAAAA 5160
                                 viiv  ii  v  v v  v    vi      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_137186868_   5161 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5210
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_137186868_   5211 CTGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGAC 5260
                           i      i   i    ii         i iv ii i   v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_137186868_   5261 CAATGGCACAGAAC--AAAGCCCTCAGAAATAATACCACACATCTACAAC 5308
                               v i    i-- i  i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_137186868_   5309 CATCTGATTTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5358
                           vi       i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_137186868_   5359 TCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGC 5408
                            v  i  i              v      v  ?       i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_137186868_   5409 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGT 5458
                             ii    i    v   i     v           i  i    i   v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_137186868_   5459 GTTAAAGACTTAAATGTTAGATGTAAAAACCATAAAAACCCTAGAAGAAA 5508
                         i i ?    i       v   - iv     i      vi i         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_137186868_   5509 ACCTAGGCAATACCTTTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5558
                           v    ?ivv vii   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_137186868_   5559 AAAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5608
                          vi    v       vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_137186868_   5609 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5658
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_137186868_   5659 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5708
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_137186868_   5709 AAATGGCTAATATCTAGAGTGTACAGAGAACTC--A-AATTCA-CAAGAA 5754
                           iv i  vi    i   i i  i i       -- -  i   -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_137186868_   5755 AAAGACAAAGAACCCCATCAAAAAGTAGACGAAGGATATGAACAGACACT 5804
                                  v     v  i?    i i i i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_137186868_   5805 TCTCAAAAGAGGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5854
                             v     i  i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_137186868_   5855 TCATCCCTGGCCAT 5868
                         v    v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3044 26.29 2.13 0.11  chr2_137275063_137280384     3941  4830 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137275063_   3941 TAGAAACACATCCCATGCTCATGGATGGATGGAATCAATATTGTGAAAAT 3990
                          i    v i        i        v ivi  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137275063_   3991 GACCATACTGCCAGAAGCAATCTACAAATTCAATGTAATTCCCATCAAAA 4040
                          i v     v  vi  vii       i      i i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137275063_   4041 TACTACCATCATTCTTCACAGAACTAAAAAAA---ATCCTAAAATTCATA 4087
                          v i v vv v  i  ii     v vi v  i---               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_137275063_   4088 TAGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 4137
                          i   viiv  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_137275063_   4138 CAAATCTGGAGGCATCACATTACCCAACTTCAAACTATACTATAAAGCCA 4187
                             vi      vv     i v     i      viv     i     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_137275063_   4188 TAGTCCCCAAAACAGCATGGTACTGGTATAAGAATAGGCACATAAATCAA 4237
                         i   vvi   i    ii         i     i    i  i   i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_137275063_   4238 TGGA-CAGAATAGAGAACCCAGAAATAAAGCCAAA----TGCGGCAAACT 4282
                             -i     v    ii           v   v ---- ii  iv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_137275063_   4283 TGTCTTCAACAAAGCAAACAAAAACATAAAGTGGAGAAAC-----CCTAT 4327
                         vi i   i    i vviv   i v   vv i   i    v-----i  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_137275063_   4328 TCAACAAATGTTGCTGGGATAATTGGCAAGCCACATATAGAAGAATGGAA 4377
                                   v        i  i   vv ?      ii i       i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_137275063_   4378 CTGGCTCCTCATCTCTCACCTTATACAAAAATCAACTCAAGCTGGAACAA 4427
                         i   vi  ii i   v    v           i       iv    v  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_137275063_   4428 AGACTTAAATCTAAGAACTGAAACTATAAAGATTCTAGAAGATAACATCA 4477
                             i     v     i  i          iv ii       v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_137275063_   4478 GAAAAAATCTTCTAGACATTGGCTTAGACAAAGACTTCATGACCAAGAAC 4527
                          ?iv        vv   v    v    i   v ii   v iivi v  - 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-C 599

  chr2_137275063_   4528 AC-AAAAGCAAATGCAACAAAA-ACAAAGTAGATG----GGACTTAACCA 4571
                           -       v v         - v   i     i----      v i  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_137275063_   4572 AACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTTAACAGA 4621
                           v v    i   i  ii vv    i  v iv    iv i   v  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_137275063_   4622 CAACCCATAGAGTCAGAGAAGATCTTCACAATCTATATATCTGACAAAGG 4671
                                i   i vi     i  v  ii   vii          i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_137275063_   4672 ACTAATATCTGGAATCTACAAGGAACATAAACAAATCAGCAAGGAAAAAA 4721
                            vi    ii    v  i  i    vivv    v   ii  vi    i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_137275063_   4722 TAAACAATCTAATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCA 4771
                         i   i  i i   i?    i     v     iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_137275063_   4772 AAAGAAGATATACAAATGGCAGACAAGCATATGGAAAAATGCTCAACATC 4821
                                             vi i     i   i   i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_137275063_   4822 ACTAATTAT 4830
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.42 (135 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.50 (20 / 8)  


2441 26.87 6.00 1.27  chr2_137313586_137317123.rev     2207  3073 (465)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137313586_   2207 TGGGAACATATTCCATGCTCATAGATTGGAAGAATCAATATTGTTGAAAT 2256
                            i  v    i     i    i          v i         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137313586_   2257 GACAATACTGCACAAAC-AATTTACAGAATCAATGCTATCCCTATTAAAA 2305
                          i       v v    i-i  i      v    i  v        i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137313586_   2306 TACCAACATCATTTTTAACAGAA-TAGAAAAATATATTCTAAAATTCATT 2354
                          v   i vv v     vi     - v  v  iivv  i           v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_137313586_   2355 CGGAACCAAAAAAGAGCCCAAATAGCCAAAGCAATCCTAACCAAAAAGAA 2404
                         i    viiv  ii  v  vi          i     i i vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_137313586_   2405 CAAAGCCAGAGGTATCACATTGCCTG-TCTCCAAACTATACTGTAAGGAA 2453
                              iii    vv     i v  ii- i  v     -    ii  i vv
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr2_137313586_   2454 ATAGTAACCAAAATAGCATGGTCCTTGT-TCAAAACAGACACACATACCA 2502
                          i     i   i i  ii    v  v i- v ii i     i i v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_137313586_   2503 AAGGAACAGAATGGTGAACCTAGAAATAAAACTGCACACCTACAACCATG 2552
                          v    i     v v  ii i         v iii   ii  iiii  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_137313586_   2553 TGATCTTTGACAAAATTGACAAAAAAATAAGCAGTGGGGAAA-------- 2594
                             i  i     iiv  v   i vv  --v  i        --------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAATAGTC 397

  chr2_137313586_   2595 --TTCAATAAATGATGTTGAGATCACTGGTTAGCCATATGCAGAAAAATG 2642
                         --     i     i  i  i  iv     v  ?   i     i  i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_137313586_   2643 AAACTGGACCCTTATCTATCATGATATACAAAAATTATCTCAAGGTAGAT 2692
                           ii       i  i  vv  iv              v     ii i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_137313586_   2693 TAAAAATTTAAGCCTAAGACCTCAAAGTTTACAAATTCT-AGAAGAAATC 2741
                         i ? i ii   iiv     v  v   v v  -   i   -        v 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAAC 546

  chr2_137313586_   2742 CTAGG---AAATACCCTTC-TCATCATTGGCTTTGTTAAAGGATTTATGG 2787
                         v    ---    ---    - v i -    v  v vi  v  v  iv i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT---CTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_137313586_   2788 CTAAGTC-CCAAAAGCAATTGCAGCAAAAACAAAAATTGACAAGTGAAAT 2836
                         v  v v -         vvv   i     iv      v  i  i vii i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_137313586_   2837 TTAATTAAACTAAAGAGCTTCTTCATAGTAAAAGAAACTACCAACA---- 2882
                           v  i   v v  i i   i viiivvi   i  v    i   v ----
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_137313586_   2883 GAATAAACAGCCTAGAGAATGGGAGAAA-CATTTGCAAATTATGCATCTG 2931
                            v i   i  i v             -i          i  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_137313586_   2932 ACAGAAATCTAATATCCAGAATCTACAAAGAACTT----AAATCAACAAG 2977
                          i iiiiv  vi          v  i        i----  v    i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_137313586_   2978 CAAAAAAGAAATAATGCAATTTAAAAAATGGGTAAAGGACATGAACAGAC 3027
                         v    i v      iv     ?     -    i      iv    i    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGAC 841

  chr2_137313586_   3028 ACTTC-CCAAA----ATAT------------------CATGAGAAAAATT 3054
                          i   -     ----    ------------------     i  i -- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--T 889

  chr2_137313586_   3055 GCTGAACATCACTAATTAT 3073
                            v       ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.86 (63 / 22)  


2256 22.59 3.16 1.99  chr2_137487133_137488730.rev      497  1098 (500)    L1M4_orf2#LINE/L1      266   874 (34)  

  chr2_137487133_    497 TATAGTACTGGCATAAGGATTATGTATAGAC-TATAGATCAATGGAACAG 545
                          i i                -------    -               i  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGAT-------AGACATATAGATCAATGGAATAG 308

  chr2_137487133_    546 AACAGACATTCCAGAAATAAACTCTAATATTTACATTTAATTGATTTTCA 595
                           iv  v v             i vv i     iiv i           i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_137487133_    596 ACAAAGATGCCAAGGCAATTCAATGAAGAATTTCCATAGTTTTTACAACA 645
                             i i       i v        ii   vv--v     i   v     
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAG--AATAGTCTTTTCAACA 406

  chr2_137487133_    646 AATTATGCTAGCACAATTGAATAGCCACATGTAAAAAATTGAACTTAGAC 695
                            vi    i v    i  i   ?       i    i v    v  i   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_137487133_    696 TTTTAT-TCATACCA-A---AGAAATTAATTTGAAATGAGTCACAGACTT 740
                         iii  i-   i    - --- i       i ii     ii   ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_137487133_    741 AAATGTAAGAGTTAAAACTATAAAAATTTTAGAAGACGACATAGGAGAAA 790
                                    i             v i        vi       ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_137487133_    791 ATCTT-GAGACTCTGAACAGGGCAAAGATTTCTTAGATAAAAGACCAAA- 838
                              - v   ii  iiivi     v i           vi v      -
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_137487133_    839 GTATAATCCATTAATTTTTTTAAATTGGA-AAACTAGGCTTCATAAGAAT 887
                          i i  v v iv  vvvv---   v i  -   i i i      v i   
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAA---AAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_137487133_    888 ACAAAACTTTTGCACTTCAAAAGACACCATTGA---ACTGAAAAGAAAAG 934
                         vv          ii       i     i  ii --- v        v  v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_137487133_    935 CCACAAGCTGGGAGAAAATATTTGCAAAACTCACATCCAATAAAGGATTT 984
                              iiv                    v vi i   ii    i   i  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_137487133_    985 GCATCCAGAATGTACAAAGGACTCTTGAAACTCACTAATAGGAAAACAGT 1034
                          i         i  i    i      iv      v     ii  i   iv
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_137487133_   1035 T-------TTAAAAAATGCAAAAAAGATGTACATAAACATTTCACCAAAG 1077
                          -------  ?       viv   i   v iv   i       v      
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_137487133_   1078 AAAATATACAAGTGGCTAATA 1098
                           i        i    i    
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.75 (84 / 48)
Gap_init rate = 0.02 (12 / 609), avg. gap size = 2.58 (31 / 12)  


3086 27.97 1.33 0.55  chr2_137532409_137537043.rev     3243  4143 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137532409_   3243 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 3292
                              ii i  i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137532409_   3293 GGCCTTACTGCCCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 3342
                            vv    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137532409_   3343 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAAACTGCTT-TAAAGT 3390
                          v   iivi i  i  ii     -   ----- v  i   v i-    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-----ACAAGCTGATCCTAAAAT 145

  chr2_137532409_   3391 TCATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCCAACCAAA 3440
                                   viiv  ii  v  viv  v     i      iii vv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_137532409_   3441 AATAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATATTACAA 3490
                           v       i      vv   ii  v  ii i      viv  i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_137532409_   3491 GGCTACAGTGACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAG 3540
                         i        i i   i    ii         i iv ii i   v   i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_137532409_   3541 TCCAATGGAACAGAACAGAGGACTCAGAAATAACACCACACATCTACAGC 3590
                         vi        i    iv   iiii         vv   i    i  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_137532409_   3591 CATCTGATATTTGACAAATCTGACAAAAACAAGAAATGGGGAAAGGATTC 3640
                           vi    v  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_137532409_   3641 TCTATTTAATAAATGGTGCTAGGAAAACTGGCTAGCTATATGTAGAAAGC 3690
                            v  i  i          i   v      v  ? i i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_137532409_   3691 TGAAACTGGATCCCTTCCGTACACCTTATACAAAAATTAATTCAAGATGG 3740
                             ii    i    v  vi     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_137532409_   3741 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3790
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_137532409_   3791 CCTAGGCAATACCTTTCAGGACACAGGCATGGGCAAGGACTTCATGACTA 3840
                          v    ?ivv vii   iv   viv  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_137532409_   3841 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAAACAAATGGGATCTA 3890
                         vi            vvi          vv      i i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_137532409_   3891 ATTAACCTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3940
                           i  vv v  i ii  i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_137532409_   3941 CAGGCAATCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACA 3990
                         v  i   i i                 v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_137532409_   3991 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTTCAAGAAA 4040
                          i  i  vi          v  i        ivv    v ivvi  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_137532409_   4041 AAAA----------AATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 4080
                           i ----------   i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_137532409_   4081 CTCAAAAGAAAACATTTATGCAGCCAACAGTCACATGACAAAATGCTCAT 4130
                            v      i i  vi viii     i iv       v  i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_137532409_   4131 CATCACCGGTCAC 4143
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 4.25 (17 / 4)  


2689 28.64 1.90 0.34  chr2_137565752_137572159.rev     5023  5916 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137565752_   5023 TGAAAAAGCATTTTATGCTCATGGATAGGAAGAATCAATATCATAAAAAT 5072
                           i   iii  iii   i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137565752_   5073 GGCCATACTGCCCAAAGCAATTTATAGATTGAATGCTATTTCCATCAAAC 5122
                            v     v      vii  i  i     v  i  v  ii i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137565752_   5123 TACCATTGACATTCTTCACTGAACTAGAAAAAACT-ATTTTAAAATTCAT 5171
                          v   vivi v  i  ii v   v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_137565752_   5172 GTAGTACCAAAAAAGAGCCTATACATCCAAGACAACCTTAAGAAAAAAGA 5221
                         i i v viiv  ii  v  viv i v    i    i   i i   i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_137565752_   5222 ACAAAGCCAGAGGCATCAAACTACCTGACTTCAAACTATATTACAAGGCC 5271
                               iii    vv   v   v  ii i      viv  i     i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_137565752_   5272 ACAGTATCCAAAACAGCATGGTACTGATGCAAAAACAGACACATAGACCA 5321
                               vi   i    ii        iiii  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_137565752_   5322 ATGGAACAGAATAGAGACCTCAAAAATGAGACCACACATCCACAACCATC 5371
                               i     v    vii  i    i iv   i    ii iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_137565752_   5372 TTATCTTTGATAAACCAGACAAAAATGAACAATGGGAAAAGCATCCCCTA 5421
                          v  i  i  i  ivvv v   i viivv       i    v  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_137565752_   5422 TTCAATAAATAGTGCTGGGAGAACTGGCTAGCCCTATGCAGAAGATTGAA 5471
                              i    i         v      v  ?  vi     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_137565752_   5472 ACCAGACCCCTTCCTTACACCTTATACAAAAATTAAGT-----------A 5510
                         iiii       v   i     v              v ----------- 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_137565752_   5511 AAGACTTAAATGTAAAGCCCAAAACTATAAAACCCT-AGGAGAAAATCTA 5559
                         ?    i         iiv i             i  -  i      iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_137565752_   5560 GACA-ATACCATTCAGGACATAGGCACAGGCAAAGATTTTAT-GATGAAA 5607
                          i?i- v i -   iv   v v  vvi      v i   iv -   - vi
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr2_137565752_   5608 ACATCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTAAT 5657
                            i        vvv          v      v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_137565752_   5658 GAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 5707
                         v   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_137565752_   5708 GGCAACCTACAGAATGGGAGAAAAATTTTGCAATTTATCCATCTGACAAA 5757
                          i     i                vv       v i  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_137565752_   5758 GGTCTAATATCCAGAGTCTACCAGGAACTTAAAAGAATTTACAAAAAAAA 5807
                           v  vi        i v  iv i     ivv vi v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_137565752_   5808 AAAAAACAAACCA-TTAAAAAGTGGGCAAAGGACATGAAAAGACACTTCT 5856
                         i v   i  v   -  ?    i           iv    v     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_137565752_   5857 CAAAATAAGACATTTATGTGGCCAAAAAACATATGAAAAAAC-CTCAACA 5905
                          v   v    i  vi vi       v  i  i       i i-       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_137565752_   5906 TCACTGACCTT 5916
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.42 (148 / 104)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2645 25.34 4.17 1.91  chr2_137650919_137655114.rev     2817  3704 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137650919_   2817 TGGAGAGATATCCTATGTACCAGAATAGGATGACTCAGTATTATCAATAT 2866
                             i        i    v vv i  v   v    i i    i i  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137650919_   2867 ATTAGTTCTTCCCAAATTGATCTTCC-ATTACATGCAATCCCAATCAAAA 2915
                         ivi i v  i             v v-   vv i        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137650919_   2916 TCTTGGAAGT-TATTTTGTGGATATCAAAAAG-TAGTTCCAAAGTTTATA 2963
                           iii vv i- v     ii  v  ii v   - ii i i   i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_137650919_   2964 TGAAAAAGCAAAAGATTCACTGCAGACAACACA-T----AGGAAGAAAAA 3008
                           i   v    ii  ii  vvii  v   v   - ---- ii     i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_137650919_   3009 --AAATAGGAAGACTGACACTTCTCTGCTTTACAATTTACTATAAAACTA 3056
                         --  i v   i    v       i vii  i v  i      i   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_137650919_   3057 CATTACTCAAAACATTGTGTTACTAACA-AATAATAGATA-GTAAA---A 3101
                           v  v    i   v    v    ii  -  vi     i -i  i --- 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_137650919_   3102 TAGAATAAAAATTGAAGGCATAGAA-CAGACTCATATCAACATAGTCAAT 3150
                          i     i  -    ii ivi    -i i  i    ivvvi  i      
  L1M4_orf2#LINE/    301 TGGAATAGAA-TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_137650919_   3151 TGATCTTTGTCAAAAAAGCATAGGTAACTCAATAGAGAAAAGATATTCTT 3200
                             i  i v   iiiv  vv  iiv i     i i    ii   v    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_137650919_   3201 TACAATAAATGGTGCTGGAACAACTGAACATATA-ATAATCTTTTTTAAA 3249
                          v   i            i       i i ?vi -  i-- -------  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG--C-------AA 440

  chr2_137650919_   3250 AAGAATGCAGACATAGACCCTATACCTTTCACCA-----AAAAAC---CT 3291
                                v  v-- i     i-     iv     -----     i---  
  L1M4_orf2#LINE/    441 AAGAATGAAGT--TGGACCCC-TACCTCACACCATATACAAAAATTAACT 487

  chr2_137650919_   3292 CAAAATGAATGATAGACCTAAATATAATAAACAAAATTATGCAACTCGTA 3341
                                i  v ?          i   v ivi    i   iv     v  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_137650919_   3342 GAAGAAAATATAAGAGAAAAATTGAGTTGACTTTGGGTTTAGTGATA--T 3389
                                 i   i ? v   vi vv  -   i       vi ii  i-- 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTT 586

  chr2_137650919_   3390 TTTTAAACA--ACACCAAAAAAAAAAG--ATCCTTGAAAAAATATTGAGA 3435
                          i   i i --         iv v   -- ivvvv         --  v 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATA 634

  chr2_137650919_   3436 AGTTGGACTTCATTAAAATTAAAAATATTTTCT-CTGTGAACAACACCAT 3484
                          i           i           i-    v -  vii  vi    i  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTAT 683

  chr2_137650919_   3485 CAAGAAAATGAAAACACAAATCATAGACTGTCA-AAAATATTTGCAAAAC 3533
                                i      v    vi  i   v  vv -              v 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_137650919_   3534 ACATATCTGATAAAGGACTGGTATCCAAAATATACAAATAACTCTTAAAA 3583
                          i           i     v       i      i   v        v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_137650919_   3584 TTCAACAATAAGAAAACAA----CTCAATTAAAAAATAGACAAAACATCT 3629
                         i    i     i  i    ---- i     ?      i i    iv  i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_137650919_   3630 GAATAGACACCTTATCAAATAATATATACAGATGGCAAGCAAGTGTATGA 3679
                                  ii ivi    v  v       i     v ii   iii    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_137650919_   3680 AAAGATGTTCAGCATCACATGTCAT 3704
                                i   i     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (140 / 81)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.00 (54 / 27)  


2976 25.13 0.63 5.65  chr2_137662111_137668539.rev     4983  5937 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_137662111_   4983 GGAAGAACAATGCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATG 5032
                             ii i viv    i      i v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_137662111_   5033 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCATCAAGCT 5082
                           v     v     iv i  i  i        i  v    ii     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_137662111_   5083 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 5130
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_137662111_   5131 ATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCA-AAGA 5179
                               viiv  ii  v  v v  v     iv     i i ivv -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_137662111_   5180 ACGAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5229
                           i   i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_137662111_   5230 ACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGACCA 5279
                                i   i    ii  i      i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_137662111_   5280 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTGCAACTA 5327
                               i    i--    i  --        vv  ii i  i iiiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_137662111_   5328 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5377
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_137662111_   5378 TGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5427
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_137662111_   5428 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5477
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_137662111_   5478 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5527
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_137662111_   5528 TAGGCAATACCTAGGCAATATCATTCAGGACATAGGCAACACCTAAAACC 5577
                             ?--------- i  -   -   iv   ----------------- i
  L1M4_orf2#LINE/    548 TAGGN---------GTAA-ATC-TTCGTGAC-----------------CT 569

  chr2_137662111_   5578 TAGGCAATACCATTCAGGACATAGGCACAGGCAAGGACTTCATGTCTAAA 5627
                          i  --------  --------------      v ii   v ivv  vi
  L1M4_orf2#LINE/    570 TGGG--------TT--------------AGGCAATGGTTTCTTAGATATG 597

  chr2_137662111_   5628 ACACCAAAAGCAATGGCAACAAAAGCCAATATTGACAAATGGGATCTAAT 5677
                                     vvi          vv  v  v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_137662111_   5678 TAAACTAAAGAGCTTCTGCACAGCAAAAGTAACTACCATCAGAGTGAACA 5727
                         i   v v  i i   i  ii vv    i vv    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_137662111_   5728 GGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5777
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_137662111_   5778 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5827
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_137662111_   5828 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5877
                         i     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_137662111_   5878 CAAAAGAAGACATTTATGCAGCAAA-AGACACATGAAGAAATGCTCATCA 5926
                          v        i  vi viii  v  - ii        i i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_137662111_   5927 TCACTGGCCAT 5937
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 4.62 (60 / 13)  


 962 27.45 1.31 2.29  chr2_137678075_137680684      892  1197 (1413)    L1M4_orf2#LINE/L1        1   303 (605)  

  chr2_137678075_    892 TGGAAACACATCCCATGCTTATGGATGGGTAGAATCTATATCGGGAAAAT 941
                               v i        i i      v  v   v iv    i vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137678075_    942 GACCATACTGCCAAAAGCAATCTACAAATTCAGTGCAATTCCTAT-AAAA 990
                          i v     v  v   vii       i     ii     i     -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137678075_    991 TAT--ACTACCATTTTTCTTCACCAAATTAGAAAAAACAATTCTAAAATT 1038
                          vi--i  i  --    i v  v-     -  v  ivii  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAG-AAATT-GACAAGCTGATCCTAAAATT 146

  chr2_137678075_   1039 CATATGGAACCAAAAGAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAA 1088
                                  viiv   i  v  v v         i   vvi i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_137678075_   1089 AGGACAAATCTGGAGTCATCACATTACCTGATTTCAAACTATATTATAAG 1138
                           i     vi     vvv     i v  ii        viv  i  i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_137678075_   1139 GCCATAGTCACCAAAACAGCATGGTACTGGTATAAA-ATAGGTACACAGG 1187
                           i i   v i   i    ii         i    i-    ii i i  i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_137678075_   1188 CCAGGCATGG 1197
                         i  ---    
  L1M4_orf2#LINE/    297 TCA---ATGG 303

Transitions / transversions = 1.62 (52 / 32)
Gap_init rate = 0.02 (7 / 303), avg. gap size = 1.57 (11 / 7)  

2114 26.09 1.77 0.32  chr2_137678075_137680684     1498  2118 (492)    L1M4_orf2#LINE/L1      279   908 (0)  

  chr2_137678075_   1498 TAAAAAAAGGTGCATAGACCAATGGAACAGAATAGAGAACCCAGAAATAA 1547
                            ii v  iiii     i        i     v    ii          
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_137678075_   1548 ACCCAAATACTTACAGCCAACTTACCTTCAACAAAGCAAACAAAAACATA 1597
                              v i i   ii i   i v ii   i    i vviv   i v   v
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_137678075_   1598 AAATGAGGAAAGAACTCCCTTTTAAACAAATGGTACTGGGATAATTGGCT 1647
                         v    i        ivvi     v          i      i  i   v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_137678075_   1648 AGCCACACATAGGAGAAAGAAACTGGATCCTCATCTCTCACCTTATACAA 1697
                          ?     iii ii    v   ii    i  ii i   v    v       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_137678075_   1698 AAATCAACTTAAGATGGATTAAGGACTTAAATCTAAG-GCATGAAACTTT 1746
                             i    i  i      i ?i   i     v    -  - i     v 
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTAT 527

  chr2_137678075_   1747 AAAAATTCTGGAAGATAACATTGGAAAAACCCTTCTAGACATTGGCTTAG 1796
                             v ii i     v     v  ?iv  vi    vv   v    v    
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_137678075_   1797 GCAAGGGTTTCATGACCAAGAGCCCAAAAGCAAATGCAATAAAAAAAAAA 1846
                             v      v iivi v  vv         v v    i    i     
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_137678075_   1847 AAAAATAGCTGGGACTTAATTAAACCAAAGAGCTTTTGCATGGCAATAGG 1896
                          v i   iv v      v  i   viv  i i      iiivv   -   
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA-AGG 676

  chr2_137678075_   1897 A-ACCATCAGCAAAATAAACAGACAACCCACAGAGTAGGAAAAAATCTTC 1945
                          -  i    iv   i i  v              i i   i     v  i
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_137678075_   1946 ACAATCTATACATGTGACAAAGTACTAATATCCAGATTCTACAATGAACT 1995
                         i   vii   i  v   i  i v   vi        v v  i  v     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_137678075_   1996 C----AAACCAACAAGAAAAA-----ACAATTCCATCAAAAAGTGGGCTA 2036
                          ----  vi   i  v     ----- i  ii v  i?    i     v 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_137678075_   2037 AGGACATAAATAGACAATTCTCAAAAGAAGATATACAAATGGCCAACAAA 2086
                             iv i        v     v                       i  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_137678075_   2087 CATTTGAAAAAATGTTGAACATCACTAATGAT 2118
                           iv      i   i v       ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (95 / 63)
Gap_init rate = 0.01 (6 / 630), avg. gap size = 2.17 (13 / 6)  


3153 27.49 0.89 0.22  chr2_137692450_137698604     4762  5663 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137692450_   4762 TGGAAAAACATTCCATGCTCCTGGATAGGAAGAATCAATATCATGAAAAT 4811
                               i i  i     i  v     v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137692450_   4812 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAGG 4861
                            v     v      v i  i  i       ii  v     i     ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137692450_   4862 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 4910
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_137692450_   4911 GTGGAACCA-AAAATACCCCATATAGCCAAGAGATATCCCAAGCAAAAGG 4959
                         i     vii-  iiv    viv        i v -   iii iv  i i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACA-ATCTTGAAAAAGAAG 198

  chr2_137692450_   4960 AACAAAGCTGGAGGAATCACGCTACCTGACTTCAAACTATACTACAAGGC 5009
                                i       v    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_137692450_   5010 TACAGTAACCAAAATAGCATGTTACTGGTACCAAAACAGATATATAGACC 5059
                                 i   i i  ii  v      i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_137692450_   5060 AATGGAGCAGAACACAGACCTCAGAAGTAATGCCACACATCTACAATCAT 5109
                               ii    ivv   vii     i   vv   i    i  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_137692450_   5110 CTGATCTTTGACAAACCTGACACAAACAAGCAATGGGGAAAGGATTCCCT 5159
                         i    i  i     ivv  v  vi v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_137692450_   5160 GTTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5209
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_137692450_   5210 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 5259
                          ii         v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_137692450_   5260 AAAGACTTAAACATAAGACCTAAAACTATAACACCCT-GGAAGAAAACCT 5308
                          ?    i    ii     v            v  i  -i         v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_137692450_   5309 AGGCGATAGCATTCGGGACATAGGCATGAGCAAAGACTTCATGACTAAAA 5358
                            ? vv iiv    v   v v  vv ii    v ii   v iiv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_137692450_   5359 CACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATGTAGTT 5408
                                    vvi   i      vv     v  i    v   iv vi i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_137692450_   5409 AAGCTGAAGAGCTTCTGCACAACAAAAGAAACTATCATTAGAGTGAACAG 5458
                           iv v  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_137692450_   5459 GAAACCTACAGAATGGGAGAAAAT-TTTTCTATCTATCCATTTGACAAAG 5507
                         iv    i                 -   v v vii  vi  i   i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_137692450_   5508 GACTAATATATAGAATCTACAAGGAACTTAAACAAAT---TTACAGGAAG 5554
                             vi   vi     v  i  i     ivv    v --- v i ii   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_137692450_   5555 A-AAACAACCCCATTAAAAAGTGGTCAAAGGATATGAACAGACATTTCTC 5603
                          -   i     v   ?    i   v        v    i           
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_137692450_   5604 AAAAGAAGACATTTATGCGGCCAACAAACATATGAGCAAAAGCTCATCGT 5653
                         v        i  vi vii      i  i  i    iv i v     v i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_137692450_   5654 CACTGGTCAT 5663
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


2717 26.31 4.56 1.14  chr2_137776789_137778785.rev      628  1505 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137776789_    628 TGGAAAAACATCC-ATGTTCATGGATTGGAAGAATCAATATT---AAAGT 673
                               i i    -                   v i      ---  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137776789_    674 GGTCATACTGTTCAAAACAATGTATAGATTCAACACTATTTCTATCAAAC 723
                           iv     vii    vii  v  i         i v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137776789_    724 TACAAA-TGTTATTTTTTATACAAGTAGAAAAAATAATTCTAAAATTCAT 772
                          v v i-  ii-      ii v  i v  v  iv i  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_137776789_    773 CTGGAACCAAAAAAGAGTCCTAATAGTCAAAGTAATCCTAAGCAAAGAGA 822
                         v     viiv  ii  vi vv     i    ii    i i iv  ii   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_137776789_    823 ACAAATTCAGAGGAATCATGTTACCTGACTTCAAACTACACTACAAGACA 872
                              v ii     v   iii v  ii i      vivi       ii v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_137776789_    873 ACAGTAATCAAACCAACATAGTATGGGTACAAACACAGACAAAAAGATCA 922
                                    iv  iii i   iv  i i  iv i     v v      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_137776789_    923 ATGGAACAAAACAGAGAACTCAAAAATAAAGCCACACATCTACAGTCA-- 970
                               i i  iv    iii  i       v   i    i  ii    --
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_137776789_    971 ------TC--CAA--------AGTCCATAAAGCAATAAGGAAAGGACTCC 1004
                         ------  --   --------  v    ---v    ii      i ivvi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCAT---TCAATGGGGAAAGAATAGT 396

  chr2_137776789_   1005 CTATTCCATAAATGGTGCTGGGATAACTGTCTAGCCATTTGCGGAAGAAT 1054
                           v   v i              i     vv  ?   iv   ii      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_137776789_   1055 AAAACTGAACCCTTACCTTTCACCATATACAGAAATTAACTCAAGAT--- 1101
                         i  ii  i    i     iv           i            i  ---
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_137776789_   1102 --AAAGACTGAAATAGAAGACCTCAAACTACAAAATTCTTAGAAGAAAAC 1149
                         -- ?    iv    iv    v  v      i    i              
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_137776789_   1150 CTAGG---AAATACCCTTCACAACACGGGCTTTGGCAAATAATTTAT-GG 1195
                         v    ---    ---    iii  viv  v  v     - ii   v -i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAG 592

  chr2_137776789_   1196 CTAGGTCCTTAAAAGCAATTGCAACAAAAACAAAAATTGACAAGTGAAAC 1245
                         v  v v vii       vvv         iv      v  i  i vii  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_137776789_   1246 CTAATTAAA-TTAAAGAGCTTCTGCACAGCAAGAAAAACTATCGATGGAG 1294
                         i v  i   -     i -   i  ii vv   iii v      i vii  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_137776789_   1295 TAAACAGACATCCTATAGAATGGGAAGAAATATTTTCAAACTCTGCATCC 1344
                          i  v     v  i i         ii        v    iiv ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_137776789_   1345 AACAAAGGCCTAATATCCAAAATCAACAAGGAACTT----AAATCAACAA 1390
                         i i  i  v  vi      i   vv i  i     i----  v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_137776789_   1391 GCAAAAACA-AAATAACCACACTAAAAAGTAGGCAAAGGATATGAACAGA 1439
                         -i     v -        vv i ?    i i          v    i   
  L1M4_orf2#LINE/    792 -TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_137776789_   1440 TACTTCTCCAAAGAAGATATACAAGTGGACAACAA--ACATGAAAAAATG 1487
                         i i                     i   v   i  --         i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_137776789_   1488 CTCAACATCACTAATCAT 1505
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (146 / 82)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.63 (50 / 19)  


3190 26.40 0.77 0.88  chr2_137872957_137877387.rev     3031  3939 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137872957_   3031 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATTATCGTGAAAA 3080
                              ii    i     i      i v      v i   -  i  v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT-ATTGTTAAGA 49

  chr2_137872957_   3081 TGGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAG 3130
                             v     v     iv i  i  i        i  v     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_137872957_   3131 CTACCAATGACTTTCTTCACAGAA-TTGAAAAAAACT-ACTTTAAAGTTC 3178
                         v v   iivi i  i  ii     -    v  i--  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_137872957_   3179 ATTTGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGTCAAAA 3228
                           v     viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_137872957_   3229 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 3278
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_137872957_   3279 CTACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGATATAGAC 3328
                                  i   i    ii   i     i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_137872957_   3329 CAATGGAATAAAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 3376
                                   i  i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_137872957_   3377 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 3426
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_137872957_   3427 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3476
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_137872957_   3477 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATTG 3526
                             ii    i    v   i     v              i    i  v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_137872957_   3527 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAAAAA 3575
                           i ?    i       v   v       i      -    -    i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr2_137872957_   3576 ACCTAGGCA-ATACCATTCAGGACATAGGCACAGGCAAGGACTTCATGTC 3624
                           v    ?i- v i -   iv   v v  vvi      v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_137872957_   3625 TAAAACACCAAAAGCAATGGCAACAAAAGCCAACATTGACAGATGGGATC 3674
                           vi            vvi          vv  v  v  i i  v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_137872957_   3675 TAATTAAA-TTAATGAGTTTCTGCACAGCGAAAGAAACTACCATCAGAGT 3723
                          v  i   -    -i ii  i  ii vv i  i  v    i  vv i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_137872957_   3724 GAACAGGCAACCTACAGAACGGGAGAAAACTTTTGCAACCTACTCATCTG 3773
                            v  i     i      i         iv       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_137872957_   3774 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 3823
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_137872957_   3824 AAAAAAACAAACAACCCCATCAACAAGTGGGCAAAGGACATGAACAGACA 3873
                              i     i     v  i? v  i           iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_137872957_   3874 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 3923
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_137872957_   3924 CATCATCACTGGCCAT 3939
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


3230 27.64 0.22 0.22  chr2_137901057_137907336.rev     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137901057_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137901057_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137901057_   4981 TACCAATGACTTTCTTCACAGAATTGGAAAAAAATACTTTAAAGTTCATA 5030
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_137901057_   5031 TGGAAGCAAAAAAGAGCCCGCATCACCAAGTCAATCCTGAGCCAAAAGAA 5080
                              iiiv  ii  v  v v  vi    iv     i   ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_137901057_   5081 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5130
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_137901057_   5131 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5180
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_137901057_   5181 TGGAAGGGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5228
                              vi   i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_137901057_   5229 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5278
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_137901057_   5279 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5328
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_137901057_   5329 AACTGGATCCCTTCCTTATGCCTTATACAAAAATCAATTCAAGATGGATT 5378
                          ii    i    v   i ii  v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_137901057_   5379 AAAGCCTTAAACCTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5428
                          ?  v i    iv v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_137901057_   5429 AGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAAAA 5478
                            ?i v viv   iv   v v  vvii     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_137901057_   5479 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCATT 5528
                                    vvi          vv     v  i    v   ii    i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_137901057_   5529 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5578
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_137901057_   5579 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 5628
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_137901057_   5629 GGCTAATATCCAGAAACTACAATGAACTCAAACAAATTTACAAGAAAAAA 5678
                          i  vi         vv  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_137901057_   5679 ACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 5728
                              i     v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_137901057_   5729 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5778
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_137901057_   5779 CACTGGCCAT 5788
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (145 / 102)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


2846 21.02 2.60 8.43  chr2_137932000_137934884.rev     1433  2393 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_137932000_   1433 AAATATATTCCATGCTCATGGATTGAAAGA----ATATTGTTAAAATGTC 1478
                            v    i     i          i    ----          i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_137932000_   1479 CACACTACCCAAAGTAATCTACCAATTCAATGCCAATTCAATACTAATTT 1528
                         v i   v      v i      vi      i  -   i -----------
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGC-AATCC----------- 91

  chr2_137932000_   1529 TATCTCTATTAAAATGTCAA-TGTCATTTCATATAGGCATAGAAAAA--A 1575
                         -----    i     vi  i-  i v   i- ii  iv  v  v  i--i
  L1M4_orf2#LINE/     92 -----CTATCAAAATCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTG 135

  chr2_137932000_   1576 ACCCTAAAATTCATATGGAGCAACAACAACAACAAAAGTCTT-GAATAGC 1624
                          i                 --------  ii-   ii v ii-       
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGA--------AATG-CAAGGGACCCAGAATAGC 176

  chr2_137932000_   1625 CAATACAATCATGATAAAAAAACAAAAAAACAAACAAAAAACAGCTGGAG 1674
                            v      v   ---------    i  -i      ----- i     
  L1M4_orf2#LINE/    177 CAAAACAATCTTGA---------AAAAGAA-GAACAAA-----GTTGGAG 211

  chr2_137932000_   1675 GTATAACATTACCTGATATCAAGTTTTACTATGGAGCTATAGTAATTAAA 1724
                          vv v   i v  ii  v    ivi      iii     i      i  i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_137932000_   1725 ACAGAATGCTTCTGGCAGAAAAAAGAAAGACACATTAACCAACGGAACAA 1774
                             vi  v v      v  i---  v     i  vi i   i    i i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAG---GATAGACATATAGATCAATGGAATAG 308

  chr2_137932000_   1775 AATAGAGAGTCCATAAATGAACCCATATACGTATGGTCAATTGATTTTTT 1824
                            v         v    i        i iv                 iv
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_137932000_   1825 ATAAAAGTGCCTAAGAATATGCAATAGTAAAAAGGACAATCCCTT----A 1870
                          i  ii     -    vi  v    i -ii    i i i  ii  ---- 
  L1M4_orf2#LINE/    359 ACAAGGGTGCC-AAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACA 406

  chr2_137932000_   1871 AATGGTATTGGGAATACTGGGTATCTATATGCAGAAGAATGAAAGTGGAC 1920
                               ii     vv     i  ? i i     i         iv     
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_137932000_   1921 CTTAATCCCACAACACATACAAAAATCAACTCTAAATGGATTAAACACTT 1970
                          iiv i i    v  i          i     v        i ? v  i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_137932000_   1971 AAACATAAGACCATAAAA-TGTGAAACTACTT-GAAGAAAATGTAGGGGA 2018
                            ii     v -     - i i     -   -        ii    ? -
  L1M4_orf2#LINE/    507 AAATGTAAGAGC-TAAAACTATAAAACT-CTTAGAAGAAAACATAGGNG- 553

  chr2_137932000_   2019 AAAATAAAAATAACAACAAAAAAACTACATGACATTGATCTAGGCAATGA 2068
                         ----    -- -------------  v i    v   ivi         i
  L1M4_orf2#LINE/    554 ----TAAA--T-------------CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_137932000_   2069 TTTTTTGTTTGTTTTTTTATTTGACCCCAAAAATGCAGTCATCAAGAACA 2118
                            i  i--- -------  v    v      iii  iv  v   i iv 
  L1M4_orf2#LINE/    585 TTTCTTA---G-------ATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_137932000_   2119 AAAGGAGACAAATAGGATTACAT-AAAACTAAAAAGCTTCTACATAGCAA 2167
                            iv   i    v   i v   -    i      -   i iiiivv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chr2_137932000_   2168 GGAAAACAATTAAGAGTGTGCAGAGACAACCTAT-GAA---GAAAAAATA 2213
                         i i v  v  i    iv   v i        i i-   ---  i      
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_137932000_   2214 TTTGCAAACCATATATCTGAGAAGGGGTTAATATTCAATATATATAAGGA 2263
                                 i           v     ii vi   i  iv        i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_137932000_   2264 GCTCAAACAACTCAACAGCAAGAAAAACAAA------AATTAAAAAATGG 2307
                         i   vv         i ii  -   i     ------    ?        
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_137932000_   2308 GCAAGGGATATGAATAGACATTTTTCAAAAGAAGATATACAAATGGCCAA 2357
                             i    v             i  v                       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_137932000_   2358 CATATAAATGAAAAAATGCTCAACATCACTAATCAT 2393
                         i vii v       i             ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (132 / 66)
Gap_init rate = 0.03 (31 / 905), avg. gap size = 3.42 (106 / 31)  


3066 27.12 0.99 0.88  chr2_137951500_137957454     4557  5463 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137951500_   4557 TGAAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4606
                           i   i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137951500_   4607 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4656
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137951500_   4657 TGCCAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTTCA 4704
                          v   iivi i  i  ii  -      -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_137951500_   4705 CATGGAAC--CAAAAAACAGCCCACATTGCCAAGACAATCCTAAGCCAAA 4752
                         i      v--   iii  --  viv  v     i      i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_137951500_   4753 AGAATAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAT 4802
                             i    i      vv       v  ii i      viv        v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_137951500_   4803 GCTACAGCACCCCAAACAGCATGGTGCTGGTACCAGAACAGAGATATAGA 4852
                                i vi v i    ii    i    i iv  i i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_137951500_   4853 CCAGTGGAACAGAACAGAGGCCTCAGAAATAACACCACACACCTACAGCC 4902
                         i  i     i    iv   ivii         vv   i   ii  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_137951500_   4903 ATATGATCTTTGACAAACATGACAAAAACAAGAAATGAGGAAAGGATTCC 4952
                          vv    i  i     ivi  v   i v  vvv    i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_137951500_   4953 CTATTCAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGAAGAAAGCT 5002
                           v     i   i          v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_137951500_   5003 GAAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5052
                            ii    i i  v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_137951500_   5053 TTAAAGACTTACCTGTTAGATCTAAAACCATTAAAACCCT-AGAAGAAAA 5101
                          i ?    i  vv   v   v       i  -     i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chr2_137951500_   5102 CCTAGGC---AATGCCATTTAGGACATAGGCATGGGCAAGGACTTCATGA 5148
                          v    ?---   -- -  iiv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_137951500_   5149 CCAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5198
                         vi vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_137951500_   5199 CTAAGTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5248
                         i v vi   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_137951500_   5249 GAACAGGCAACCTACAGAATGGGAGAAAATTTTCACAATCTACCCATCTG 5298
                            v  i     i                 v  ii   vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_137951500_   5299 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAG 5348
                          i  i  i  vi          v  i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_137951500_   5349 AAAAAATCAAACAACCCA-TCAAAAAGTGGGCAAGGTATATGAACAGACA 5397
                              iv    i      - i?    i       i v  v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_137951500_   5398 CTTTTCAAAAGAAGACATTTATGCAGCCAACAGACACATGGAAAAATGCT 5447
                         i  i  v        i  vi viii     i ii      i   i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_137951500_   5448 CATCATCACTGGTCAT 5463
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


2717 26.73 3.12 2.00  chr2_137980111_137984546.rev     3047  3944 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137980111_   3047 TGGAAGGACATCCCACGCTCATG-ACCAAAAGAATTAATATTGTAAGAAC 3095
                              i  i      i i     - iiii    v          v ii i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137980111_   3096 GACCACACTACCCAAAGCAATCTGCTGATTCAGTGCAATCCCTATCAAAA 3145
                          i v i   v      vii    i v      ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137980111_   3146 TACCAATGTCGTTTTTTTCACAGAAATAGAAAGGGTAATCCTAAAATTTG 3195
                          v   -- ii ii     ii       v  v i v i           ii
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_137980111_   3196 TGTGGAGCT-CAAAAGAGCCAGTTTAGCTGAACCAATCCTGAGCAAAAAG 3244
                          i    iv -   ii  v    vv    ii  v     i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_137980111_   3245 AACAAAGCTGGAGGCATCGCACTACCTGACTTCAAAACC-----CCAAAC 3289
                                i      vv  i    v  ii i        i----- v  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_137980111_   3290 -------ATCA------TCT--CATTGGTATAAAAACAGAAACACACACT 3324
                         -------    ------ v --i i   i    ii i   v i i v ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_137980111_   3325 AATGAAACAGAATAGAGAATCTAGAAATAAGTTCATGTACTTACAGCCAA 3374
                             i  i     v    i  i        iii   ii i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_137980111_   3375 TAGATTTTTTACAAAGGTACTAATAACATACATTGCTGAAAAGAA-ACCC 3423
                          v      iv    i   i i  v v   v  v  v- i      - vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTC 397

  chr2_137980111_   3424 TTTTTAATAAATTGTGCTGG-ACAACTGAATATCCACATACAGATGAATA 3472
                             i  i    v       -       i   ?      i  i v    i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_137980111_   3473 AAAATAGACATTGTGTTTCTCACCACGTACAAAAAGCAACTCAAAATTGT 3522
                           iv i   vii- iii  v     ii        vi          v v
  L1M4_orf2#LINE/    448 AAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_137980111_   3523 TTA-AAACCTAAGCATAAGATGC-AAAAGTATAAAAATACTAGATGAAAA 3570
                          i - i      iii     -  -    v       v vi    v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_137980111_   3571 CCTAGGGAAAACTTTTCTGGACATTGGTCTAGGCAAAGATTTTATAGGTA 3620
                          v    ?iv  v i   vv   v    vi       v i   iv   i  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_137980111_   3621 AGACCTCAAAAACATGAACAAGAAAAATGAAAATAAACAAATGGGACTAT 3670
                         v   vi     i  ii i   v    ivi      i i    v     vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_137980111_   3671 AGTAAAATAAAAAGTTTCTGCACAGCAAAGAAAACAATCAAGA--GTGAA 3718
                          vi     v    ii  i  ii vv     i v  v       --     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_137980111_   3719 GAGACAGCCTGTTAAATGGAAGCAAATATTTGCAAACTATCCATCTGACA 3768
                         i     i  iiivi     i  v             ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_137980111_   3769 AGAGACTAATATCCAGAATATAGAAGGAACTCAAACAACTGCACAGCAAA 3818
                           i    vi             v  i      vv      ------   v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT------CAAT 789

  chr2_137980111_   3819 AAAAAAAAAAAAAAAAAAAAAAAATCACATTAAGAAGTGGTCAAACTATC 3868
                           v     i v   v  v------i  -   ? i  i   v    vv  i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAAC------CCA-ATTWAAAAATGGGCAAAGGATT 832

  chr2_137980111_   3869 TGAATGGACACTTCTCAAATAAAGACAAACAATTAGCCAAGAGGTATATT 3918
                              i    i     v  vi    i v    v i     v i i i  v
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_137980111_   3919 GAAAAATAGTTAATATCACTTATCAT 3944
                         i   i  iv i  i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (150 / 87)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.56 (46 / 18)  


3192 27.20 0.55 0.55  chr2_137984714_137990992.rev     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_137984714_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_137984714_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_137984714_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_137984714_   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_137984714_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_137984714_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_137984714_   5178 AATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATCTACAACT 5225
                                i    i-- v  i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_137984714_   5226 ATCAGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          viv   i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_137984714_   5276 CTATTTAATAAACAGTGCTGGGATAACTGGCTAGCCATATGTAGAAAGAT 5325
                           v  i  i   ii         i      v  ?   i   i i  ii  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_137984714_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_137984714_   5376 TTAAAGCCTTAAACCTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?  v i    iv v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_137984714_   5426 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCACGGACTTCATGACCA 5474
                         v    ?i- v i -   iv   v v  vv i    vv ii   v iivi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_137984714_   5475 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5524
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_137984714_   5525 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5574
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_137984714_   5575 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5624
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_137984714_   5625 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5674
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_137984714_   5675 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5724
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_137984714_   5725 CTCAAAAGAAGACATTTATGCAGCCAAAAAACATATGAAAAAATGCTCAT 5774
                            v        i  vi viii     v  i  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_137984714_   5775 CATCACTGGCCAT 5787
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (149 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3176 24.32 4.68 1.03  chr2_138016489_138018859     1004  1879 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_138016489_   1004 TGGAAAGATATCCTGTTTGTTCATAGATCAAAGTAATAAATATTGTCAAA 1053
                                      ii --      i   iii iv v v        i  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT--GTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_138016489_   1054 ATGTTTATACTATTCAAAATCATCTACAGACTCAATGCAACCCTTATCAA 1103
                            viv     vii    v v         i    i    i  i      
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_138016489_   1104 AACCTCAATGGCACTTTTCACAAAAATAGAAAAAAAAAATCCTACAATTC 1153
                           i i  iiv  vi    ii  i    v  v  ivvi -     v     
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTC 147

  chr2_138016489_   1154 ATATGGAACCACAAAAGACCTTGAATAGGTAAAGTAATATTGAACAAGAA 1203
                                 vii   ii    iv      vi   ii   v     v     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_138016489_   1204 GAACAAAGCTGGAGGCAC-CACACTTCCTGAGTT-AAAATTATCTTACAA 1251
                                 i      -  -         ii v  -    i - vi     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chr2_138016489_   1252 AGCTATAGTCATCATTAG-CAGTATGGTACAGGCATAAAAACAGACACAT 1300
                              i   v    --  -    i      v       ii i     i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCA--AGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_138016489_   1301 AAATCAATGGAACAGAATATAAAGCTCAGAAATAAATG-------TTGCG 1343
                          i          i     vv i  ii          iv-------  ii 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_138016489_   1344 CT--AGTAATCTTTGACAAAGTTACCAAGAATACACAATGGGGAAAAGAG 1391
                         v -- v i  i  i     i v i      vi iv           ii v
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_138016489_   1392 AGTCTCTTTGATAAATGGTATTGGATAAACTAGATATC------------ 1429
                              i  ii i       ii   ivv    i    ? ------------
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_138016489_   1430 -ATGAAATTGAATCCTTATCTTACATCATGCACAAA------CTCAAAAT 1472
                         -     i   i i  i  i  i   i   ii     ------        
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_138016489_   1473 AGTTTAAAGATTTGAATGTAAGACTTGAAGCAATAAAACTACTCAAAGAA 1522
                         i v i ?   ii i         vi i  i v        vi vi     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_138016489_   1523 GACATAAGGG-AAACATTCATGACATTGGTCTTGACAATGATATTTTGGA 1571
                         i     i ? -   iv   i    v    vi v i     i v i  i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_138016489_   1572 TATGACGCCAAAAATACCAGCAACAAAAACAAAAATAAGT------GACC 1615
                               i      ii  v          iv       ii ------   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_138016489_   1616 ACAT--AAACTAAAATTTTCTGCACAAGAAATGAAACCATCAATAAAATG 1663
                         v   --   i     vi  i  ii vvv   v  v  i     v   i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_138016489_   1664 AAGAGGCATCCCATGGAATAGGAAAAAATATTTGGATACCATATATTCAA 1713
                           i  i  v    ii    i   i          v v i       iii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_138016489_   1714 TAAGGGGTTAATACCCAAAATATATTTAAAAACTACTACAACTCAATAGT 1763
                               ii vi  i   i       v-  i    vi            i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATA-AAGAACTCTTACAACTCAATAAT 792

  chr2_138016489_   1764 GAAAA-ACAAATAGCCCAATTTTAAAAGGGGCAAAGGATCTTAGTAGACA 1812
                         i    -       i       ?v    v           i v i      
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_138016489_   1813 TTTTTTTCAAGGAAGACATACAAACAGCCAACAAGGATATGAAAAGTTGC 1862
                            i i-   i     i       ii     i   v i        v   
  L1M4_orf2#LINE/    843 TTTCTC-CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_138016489_   1863 TGAACATCACTCGTTAT 1879
                          v       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (142 / 67)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.78 (50 / 18)  


 822 20.38 8.06 2.37  chr2_138133483_138135679      499   709 (1488)    L1M4_orf2#LINE/L1      146   368 (540)  

  chr2_138133483_    499 TCATACAAAGTATTCAAGGGAAACA--ATAGCCAAAACAGTCTTGGAAAA 546
                              iii i-  v       vv  --            i     i    
  L1M4_orf2#LINE/    146 TCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_138133483_    547 AAA---CAAATTTGGAGGACTGACTTACACTTTTTCATTTCAAAGCTTAC 593
                         i  ---    v          ----i      iiiv        i     
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACT----CACACTTCCCAATTTCAAAACTTAC 240

  chr2_138133483_    594 TACAAAGCT-CAATAATCACAATCGTGTTGTACTAACATAAGGATAAACC 642
                                  -  i      vi iv    v     ii          i  v
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_138133483_    643 TGTAACTCAAT-----AGAAGTGAGAGCCTGAAAATACACCAAAACATTT 687
                          i  iv     -----    v      i iii     v   v v      
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_138133483_    688 ATGATCG------TTTTGGCAATGGTGC 709
                            i  i------   i i   v     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGC 368

Transitions / transversions = 1.87 (28 / 15)
Gap_init rate = 0.03 (7 / 223), avg. gap size = 3.14 (22 / 7)  

2157 20.83 4.36 2.27  chr2_138133483_138135679     1170  1697 (500)    L1M4_orf2#LINE/L1      356   894 (14)  

  chr2_138133483_   1170 TTAACACAGGTGCCAAGGCAATGCAATGAAGAAAAACT-GTCTTTTTGAC 1218
                          ii   vi         i v  v     ii    i v -       ii  
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_138133483_   1219 AAATAGTGCTTGGACAACTGGATATCCACATGCAAA-GAATGAATTTAGA 1267
                             i     v             ?           -       v  i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_138133483_   1268 CCACTCCCTCATATCATATGAAGACAGTTATTTAGC-TGGATTAAAGACC 1316
                           v  v     i i     iv i v v v i i iv-     i ?     
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_138133483_   1317 AAAATATAAGCACCAAAGCTGTAAAGCTGTTAGAAGAAAACATTGATATA 1366
                         v    i    vi i   i  i    i  v              v i?i  
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_138133483_   1367 CATCTTTATGATCATGGATTAAGCAAT-------------TGACAATGAA 1403
                         v     ii   i v   i   i     -------------     vii  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_138133483_   1404 AGCTCATGTAACCAAAGAGAAAAGAGATAAATTGGACCTTATCAAAAT-G 1452
                            v  v i   v     i    v             i i        -i
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_138133483_   1453 AAAACATTTTCAATTTAAAG-ACACCATCAAGAAAGTGTGAAGGCAATCC 1501
                              v   viiv  i    -    i            vi   i   i  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_138133483_   1502 ACAGAATGGGATAAAATATTTGCAAACCATACATCTGATAAGGGTGTAGT 1551
                                    v              i    i            vv v  
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_138133483_   1552 ATTGAGGATAAATAAAGAACTCTTACAACTGAACAACAGGAACACAAATA 1601
                           iv  i   v                   v  i  i ii  v       
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_138133483_   1602 ATCTGATTAATAAATGGGCTCAGGACTT----AGACATTTCTCCAAAATA 1647
                          i ii   ? v        vv    i  ----               ---
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA--- 852

  chr2_138133483_   1648 TGTCTTGGAGAAGATAAACAAGCAGTCAA-AAGGACCCGAAAAAATGCTC 1696
                         ---------       v    iii i   -   v  vi     i      
  L1M4_orf2#LINE/    853 ---------GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_138133483_   1697 A 1697
                          
  L1M4_orf2#LINE/    894 A 894

Transitions / transversions = 1.52 (64 / 42)
Gap_init rate = 0.02 (9 / 539), avg. gap size = 3.89 (35 / 9)  


2940 28.24 1.11 0.55  chr2_138145363_138151774     5018  5920 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_138145363_   5018 TGGAAGAACATTCCAAGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5067
                              ii i  i   v i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_138145363_   5068 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5117
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_138145363_   5118 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5165
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_138145363_   5166 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA- 5214
                                viiv  ii  v  v v  v     iv     i i ivv i  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_138145363_   5215 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTGCAAGGC 5264
                                i      vv    i  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_138145363_   5265 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACA 5314
                                 i   i    ii         i iv ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_138145363_   5315 AATGGATCATAAC--AGAGCCCTCAGAGATAATACCACACATCTACAACT 5362
                               vi v  i--    i  --   i    vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_138145363_   5363 ATCTGATTTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5412
                          vi       i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_138145363_   5413 CTATTTAACAAGCGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5462
                           v  i     ii          v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_138145363_   5463 GAAACTGGATCCCTTCCTTACACAGTATACAAAAATTAATTCAGGATGGA 5512
                            ii    i    v   i    vi              i   ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_138145363_   5513 CTAATGACTTAAATGTTAGACCTAAAACCATGAAAACCCTAGAAGAAAAC 5562
                         ii ?v   i       v   v       i  i   vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_138145363_   5563 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTA 5611
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_138145363_   5612 AAATACCAAAAGCAATGGCAACAAAAGCCAAAATTCACAAATGGGATCTA 5661
                         vi i          vvi          vv     vv i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_138145363_   5662 ATTACACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCCAATTGAA 5711
                           i v v v  i i   i  ii vv    i  v    i  vvv  v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_138145363_   5712 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5761
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_138145363_   5762 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAGGAAA 5811
                          i  i  vi          v  i         vv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_138145363_   5812 GAAACAG----CCCCATCAACAAGTGGGTGAAGGATATGAACAGACACCT 5857
                         i i   i----   v  i? v  i    ii      v    i     ii 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_138145363_   5858 CTTAAAAGAAGACATTTATCCAGCCAAGAGACACATCAAAAAATGCTCAT 5907
                           iv        i  vi vvii     v ii     v    i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_138145363_   5908 CATCACTGGCCAT 5920
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (147 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3072 26.41 1.44 1.10  chr2_138173894_138180236.rev     4948  5852 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_138173894_   4948 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4997
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_138173894_   4998 GCCCATACTGCCAAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 5047
                          v v     v  v  iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_138173894_   5048 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5095
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_138173894_   5096 TATGGAACCAAAAAAGAGCCCACATTGCCAAGAGAATCT-AAGCCAAAAG 5144
                                viiv  ii  v  viv  v     i v     -i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_138173894_   5145 AACAAAGCTGGAGGCATCACGTTACCTGACTTCAAACTATACTACAAGGC 5194
                                i      vv    ii v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_138173894_   5195 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5244
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_138173894_   5245 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACT 5292
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_138173894_   5293 ATCTGATCTTTGACAAACCTGAGAAAAACAAATAATGGGGAAAGGATTCC 5342
                          vi    i  i     ivv  vv  i v  vvi           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_138173894_   5343 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5392
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_138173894_   5393 GAAACTGGATCCCTTCCTCACACCTTATACAAAAATTAATTCAAGATGGA 5442
                            ii    i    v         v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_138173894_   5443 TTTAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5492
                          iv?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_138173894_   5493 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCGTGTCTA 5541
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_138173894_   5542 AAACACCAAAAACAACGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5591
                         vi         i  vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_138173894_   5592 ATTACACTAAAGAGCTTATGCACAGCAAAAGAAACTACCATCAGAGTGAA 5641
                           i v v v  i i   v  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_138173894_   5642 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTCACA 5691
                         v  i     i                 v       vii ivi    v i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_138173894_   5692 AAGGGCTAATATTCAAAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5741
                          i  i  vi   i  i   v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_138173894_   5742 AA---AAACAAGCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5788
                           ---   i  v  v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_138173894_   5789 CTCAAATGAAGACATTTTATGCA----GCCAACAGACACATGAAAAAATG 5834
                            v  v     -----   i  ----     i ii          i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGA-----TATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_138173894_   5835 CTCATCATCCCTGGCCAT 5852
                             v    v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


 553 25.50 4.03 0.00  chr2_138239822_138241615.rev       85   233 (1561)    L1M4_orf2#LINE/L1        1   155 (753)  

  chr2_138239822_     85 TGGAAAGATATTCTATGCACATGGATTGGAAGAACTAGTATT---AAAAT 131
                                    i i   iv              vi  i    ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_138239822_    132 GATGATACTTCC-AAAGCAATTTACAGATCTAGTGCAATCCCCATCAAAA 180
                          iii     i  -   vii  i       ii ii        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_138239822_    181 TACCAAAGACATTCTTCACATACATAGAAAAAC--ATCGTAAAATGTATA 228
                          v   ivvi v  i  ii  v v  v  v  i --   v      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_138239822_    229 TGGAA 233
                              
  L1M4_orf2#LINE/    151 TGGAA 155

Transitions / transversions = 1.92 (25 / 13)
Gap_init rate = 0.02 (3 / 155), avg. gap size = 2.00 (6 / 3)  

2359 24.19 1.00 6.73  chr2_138239822_138241615.rev      501  1302 (492)    L1M4_orf2#LINE/L1      153   908 (0)  

  chr2_138239822_    501 GAAACTCAAAATATCTTGAATAGCCAAAGCAATCCTGAGCAAAAAGAACA 550
                             iv   iiv i iv           i     i   iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_138239822_    551 ATGCTGAAAGCATCACACTACTTGACTTCAAAATACACTACAAACCTGTA 600
                          v i  i i vv       v iii i       ivi        v  ii 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_138239822_    601 GTAGGCAAATCAGCATGGCACTGGCATAAAAACAGATACTTAGACAAATG 650
                            iv   iv   ii   i          ii i   i iv    iv    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_138239822_    651 AAACAAAATAAAAAACTCAGACTTATATGCATGATAAAAACCCCAGATTT 700
                         i  i i   vi i iii    -----------i     ---    -----
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGA-----------AATAAA---CCCA----- 333

  chr2_138239822_    701 ATATCCAGATTTATATTCATGCATTTATAGACAACTCATTTTTGACAAAG 750
                         ------------------- i       i v   i v     i     i 
  L1M4_orf2#LINE/    334 -------------------TACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_138239822_    751 GTGCCAAGAACATGCAGTGGGGAAAGGATAGTCTCTTCAATAAATATTAC 800
                                  v   v  i         i       i     i    iv i 
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_138239822_    801 CGGGAAAACTGGATAAGCATATGCAGAAAAATAAAACTAGTCCTCTACCT 850
                         i    v         ?v  i     i  i   i  ii i v  i      
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_138239822_    851 TTCAACATACAAGAAAATCAAATCAAAATGTATTAAAGTCTTAAACCTAA 900
                         iv  v    i vi     i  v        v  i ?  v i    iv   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_138239822_    901 GAACCGAAATTTTGAAACTACTAGAAGAAAAGAACTTTGGGAATATG-CT 949
                           i ii   i v i     vi          v ---- i  ?i  vi-  
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACA----TAGGNGTAAATCT 560

  chr2_138239822_    950 CCAGGATATTGGTCTGGGAAAAGATTTTTTTTCTTTTGTGTCAGATATCA 999
                         i iv  iv    vi i  v  v i   -----   vvi i --  i i  
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTT-----CTTAGATAT--GACACCA 603

  chr2_138239822_   1000 AA-GCACAGGCAATCAAAGCAAAAATAGACAAATGGGAGTACAACAGGCT 1048
                           -     i    iv    v         i    v   v v  v  iiv 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_138239822_   1049 AAAAAGCTTCTG-----CATAGCAAACAATCAACAAAGTGAAGAGACAAC 1093
                         v    i   i  -----  v  v v  v     v        i       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_138239822_   1094 CAACAGAATGGGAGAAAATGTTTGCAAACTACCCATGTGACAAGG-ACTT 1142
                          v                 i        ii ivi  v   i    -    
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_138239822_   1143 AATAACCAGAATAAATAAATAGTTCAAAGAACTCAACAGCAAAAAACCCC 1192
                         i-  v        v     v ii  vv v       i ii     iv --
  L1M4_orf2#LINE/    754 G-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC-- 800

  chr2_138239822_   1193 CAAATAATCCAATTTAAAAATGGGCAAAATACCTGAGTAGACATTTCTCA 1242
                         -      i      ?             iv ii   i            v
  L1M4_orf2#LINE/    801 -AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_138239822_   1243 AAAGAAGACATGCAAATAGCCAACTGCCATATGAAAAAAAAGTTCAACAT 1292
                                 i  i     i     iviv  i       i v- i       
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACAT 898

  chr2_138239822_   1293 TAGTACTTAT 1302
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.75 (121 / 69)
Gap_init rate = 0.02 (13 / 756), avg. gap size = 4.77 (62 / 13)  


3215 23.91 3.48 1.57  chr2_138322168_138326384.rev     2835  3725 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_138322168_   2835 TGGAAAGATATTCTGTGTTCATAGATTTAAAGACTTAATATTATTAAAAT 2884
                                    i ii       i    vi             i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_138322168_   2885 GTTCATGCAACACATAGTAATCTACAGATTCAAAATACTATCCCTATCAA 2934
                          viv  i vv v  v v i              vii --           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA--ATCCCTATCAA 98

  chr2_138322168_   2935 AATCCCAATAGCATTTTTTATAGAAATAGAAAAAC-AATTCTAAAATTAA 2983
                                iiv  v      ii      v  v  i -i  i        v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_138322168_   2984 TGTGAAACCACAAATGACCCCAAATAGTCAAATCAGTCTTGAGAAAGAAG 3033
                          i  i  vii   iv     vi     i    v  i      i       
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_138322168_   3034 AACAAAACTGGCAGTAC-CACACCTCCTGATATTAAAATATATCACAAAG 3082
                               ii   -  v  -     i   ii  v i    iv  ii      
  L1M4_orf2#LINE/    199 AACAAAGTTGG-AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_138322168_   3083 CTACAATAATTAAAAATGTATGGTACTGGCATAAAGCTAGGCATATGGAA 3132
                              i    i  i vv  i              i v   i     i  v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_138322168_   3133 CAATGGAACAGAA--AAGAGCCCAGAAATAAATTCATGCACATATTGTGA 3180
                                 i    --i    i           ii   i  iv   v  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_138322168_   3181 ACTGGT------CAAGAGTGCCAAGTATACACAATGGGGAAAAGATAGTT 3224
                          i  i ------    i        vvi iv           ii     i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_138322168_   3225 TCTTCAACAAATGGTGCAGGGAAAACTGATCATCCACATGCAAAAGAACA 3274
                          i               v    v     ivi ?               ii
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_138322168_   3275 AAATTAGAGCTTTGCCTTATACCATACACAAAAATCAATTTGAAATGGAT 3324
                           i  i  v ii i   i i      i        i  i ii        
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_138322168_   3325 TAAAGGCTCAGATAAACAAACTAAAACCTCAAAACTTCCAGAAGAAACGA 3374
                         i ?  i ii i  iv vi i       ivi      iii        vv 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_138322168_   3375 T-GGGGCAAAGTTACACGACAGTAGTCTTGGCAATCATTTCATGGATATG 3423
                          -  ? i   vi v ii   vv i vi v      vi    v i      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_138322168_   3424 ACACCAAAAGCACAGGCAACAAAAGCAAAATCAGACAAGTGGAACTACAT 3473
                                       i          v    vi   i  i v i   v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_138322168_   3474 CACACTAAAAAGCT---GTAC-----AGAAAA-----AAGAAATTTGTAA 3510
                           v v v    i  ---  i -----  i v -----      ---  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA---GTGA 694

  chr2_138322168_   3511 AAAAAAAAAAACCTATGGAATTGGATAA----TTTGCAAAGCACATATCA 3556
                            i v  ---  i ii    v   v  ----        v  i     v
  L1M4_orf2#LINE/    695 AAAGACAA---CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_138322168_   3557 ATTAAGGGACTAATTTGTAAAATATATTTAAAAACTCCTAAAATTCATTA 3606
                         iv         vi v vi i       v-  i     i  v  i   v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATA-AAGAACTCTTACAACTCAATA 790

  chr2_138322168_   3607 GCAAAAATACCCTTAAA--ATCCATTTTTAAAATGGCTAAAG-ACTTGAA 3653
                         ii     v  ----   -- i   v  ?v       vi    - i     
  L1M4_orf2#LINE/    791 ATAAAAAGAC----AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_138322168_   3654 CAGATCTTTCCTCAAAGAAGACATACAAATGGCCAACAAGTATATAAATA 3703
                         i   iv    ii         i              i   i i  i  v 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_138322168_   3704 GATGCTTAATGTCACTAATCAT 3725
                               i  ii   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (135 / 74)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.65 (45 / 17)  


3352 24.35 2.39 1.37  chr2_138436655_138438794.rev      762  1640 (500)    L1M4_orf2#LINE/L1        1   888 (20)  

  chr2_138436655_    762 TGAAAGGAAATTCTGTGTTCCTAGCTGGGAGTAATTAATATTGTTAAAAT 811
                           i  i  v  i ii     v i v v   iv v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_138436655_    812 CTCCATACCACCCCCATAA--AATCTATAGATTCAATTCAATCCCTATCA 859
                         vv v    i--     -  --i     i        iv            
  L1M4_orf2#LINE/     51 GGCAATACT--CCCCA-AATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_138436655_    860 AAATTCCAA--ATCCTTTTCACAGAAATAGAAAAAA-AATTCTAAAATTC 906
                             i   i--ii i    ii       v  v  iv-i  i         
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_138436655_    907 ATATGGAACTGCAAATTATCCTGAATAGCCAAGGTAATTTTGA------- 949
                                 v     ivv i  v          iii   i    -------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_138436655_    950 GAACAAAGTTGGAGGCATCAAACCACCTGATTTTAAAATATGTTACAAAG 999
                                        vv   v  iv  ii    i    iv ii       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_138436655_   1000 TTATAGTAATTAAAACAGTGTGGTATTGGCATAAAAACAGACAC-CA--- 1045
                         i  i      i  i           i        ii i     i-i ---
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_138436655_   1046 CAATAAAACAGGATAGAAAAACCCGAAATAAACCTACAGATTTACAAGCA 1095
                             ii  i  i  v  i iv  v          i i v     iiiv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_138436655_   1096 ATTGATTTTTGTCAAAGATGGCGAGAACACTCAATGGA-AAAGTTCTGTC 1144
                                  i v   i i  v i   v  i       i-    vviv   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_138436655_   1145 TCTTCAATTCAATAAGTCATGCTGGGAAAACTGGATATCCTCATGCAGAA 1194
                          i     i-----  i vi        v         ?  v      i  
  L1M4_orf2#LINE/    398 TTTTCAAC-----AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_138436655_   1195 GAATAAATTTGGGACTTTATCTTACACCACATACAGAAATAAACTCAAAA 1244
                             i  v    iv ii  i  i      i     i    v         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_138436655_   1245 TAGATAAAAGACCTAGACATAATAATGGAAACTGTAATACCACTAGAATA 1294
                          i   v ?       i ii   v iivi     i   v  ivi     v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_138436655_   1295 AAACATAAGGGAAAATCTCTACATCATTTGTCTGGGCAATGATATTTTAG 1344
                                i ? v      iiiiiv v  v vi i       i v i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_138436655_   1345 ATTTGATCCCAAAAGCTTAGCCAATAAAAGAAAAAATAAACAAATGGGAT 1394
                           v   iv        vi iv   i             i i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_138436655_   1395 TGCTTCACTCTAAAAAGCTTCTGTACAGCAAAGGAAACAGTGTTAATAGA 1444
                          v v   vvv v    i   i   i vv       v  -- i i  v i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC--TATCAAGAAA 690

  chr2_138436655_   1445 GTGAAAAGACAACCTACAGATTGAGAGAAAAAAATTTGCAAACCATACAT 1494
                                       i     v  i       v -        i    i  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATA-TTTGCAAATCATATAT 739

  chr2_138436655_   1495 CATATAAGGGATTCATATCCAAAATATGTAAGGAATTC----AACTCAAT 1540
                          vv        i ii      i     i   i   i  ----        
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_138436655_   1541 AGCAAGAAAACAAGTAATTCGATTTTAAAAATGGGCAAAGGACCTGAATA 1590
                          ii  i  i    i   ii i   ?-                ii      
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATA 838

  chr2_138436655_   1591 AACTTTTCTTGAAAGAAGACATACAAATAGCCAACAAGTATATGAAAAAA 1640
                         i  v     iv        i        i     i   i i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.92 (138 / 72)
Gap_init rate = 0.02 (14 / 888), avg. gap size = 2.36 (33 / 14)  


2907 24.01 1.50 0.00  chr2_138580648_138582360.rev      489  1221 (492)    L1M4_orf2#LINE/L1      165   908 (0)  

  chr2_138580648_    489 ACCCATAATCTGCAATATAATATGGAAAGAGAAGAATAAAGTTGGAGAAC 538
                              v   vvv   v i   v v    i       i          i  
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_138580648_    539 CGACACTATCTGACTTCAAGACTTACTATAAAGCTATATGAATCAAAACA 588
                         iv     vi ii i     i        i       i vv      i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_138580648_    589 GCCTGGTAATGGCAAAAGAATAGACAGATAGATCAGTGGAACAGAATAGA 638
                          iv     v     v   i       v        i     i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_138580648_    639 GAGACCAGAAATAGACCCACATAAATATAGTGAATTGATCTTTGACAAGG 688
                            v         i     i i vv   i  v       i  i       
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_138580648_    689 GAGCAAAGGCAATACAATGGAGCAAAGATAGTCTTTTCAACAAATGGTGC 738
                          v  v   i v  v      i v  ii                       
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_138580648_    739 TGCAACAACTGGATACCCACCTGCAAAAAAATGAATCTAGACAAGGACCT 788
                           vi           ?    v       i      vi i   vvvv    
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_138580648_    789 TACATCCTTCACAAAAATTAACTCAAAATGAATCATAGAACTATGTGTAA 838
                         i   i v vi                    i    ?   v   vi     
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_138580648_    839 AACATAAAACTGTAAAATTCCTAAAATATAACACAGAGGAAAACCTAGAT 888
                         i vv       i     i  i  i  v v    i  i? v   i  vvi 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_138580648_    889 GACCTTGGGTACGGCGATGACTTTTTAAATA-GAAACCAAAGGCATAATC 937
                                   vv   i   ii  i   i   -  v      i   i  v 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_138580648_    938 TATGAAATAAGTAATTAATAAGCTGAACTTTATTAAAATTAAAAACTTCT 987
                         v ii   v  iv   vi    ii  i    i  i              i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_138580648_    988 GCTCTACAAAAGAAAATGTCAAGAGAATGAGATGACAA------GCATGA 1031
                          iv  v    i  v v i      i i   i v     ------ v   i
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_138580648_   1032 AAGAAAATAATTGAAAAGAGCATATCTGATAAAGGATTACTATCCAAAAT 1081
                         i        v   v   vvii           i   i vv      i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_138580648_   1082 ATACAAAGAACTCTTAAAGCTCAACGATAAGAAAACAACCAGCCCAATTA 1131
                            i            v i     ii    i  i    vi i       ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_138580648_   1132 ACAATTGGGCCAAAGACCTAAA----CACCTCACCAAAGAAGATATACAG 1177
                          v  v     v  i  ii i  ----  ii  v                i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_138580648_   1178 ATGACAGATAAATATATAAAGAGATATTTCATATCATATGCCAT 1221
                            i vi    ii i  i  i    ii iv i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (101 / 71)
Gap_init rate = 0.00 (3 / 744), avg. gap size = 3.67 (11 / 3)  


3015 26.32 1.21 1.21  chr2_138583497_138589235     4341  5248 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_138583497_   4341 TGGAAAAACATTCCATCCTCATGGATAAGAAGAATCAATATTATGAAAAT 4390
                               i i  i    vi        vi     v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_138583497_   4391 GACCATACTGCCCAAATTGATTTATAGATTCAATGCTATTCCCATCAAAC 4440
                          i v     v           i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_138583497_   4441 TACCATCGACATTCTTCACAGAATTAGAAAAAGTTATTTTAAATTTCATA 4490
                          v   v vi v  i  ii     v v  v  iv v  ii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_138583497_   4491 TGTAA-T-CAAAGAAGACCACATATAGCCAAGACAATCCTAAGCAAAAGG 4538
                           v  - -   i i v-   v -        i      i i iv  i i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC-CCAGA-ATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_138583497_   4539 AGCAAAGCTGGAGGCATCATGCCACCTGACTTCAAACTATACTA-AAAGT 4587
                          i     i      vv   ii iv  ii i      viv     -    -
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG- 247

  chr2_138583497_   4588 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 4637
                                  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_138583497_   4638 CAATGGAACAGAACAGAGACCTCAGAAATAACACCACACACCTACAACCA 4687
                                 i    iv    vii         vv   i   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_138583497_   4688 TCTGATCTTCAACAAACCTGACAAAAACAAGCAACGGGGAAAGGATCTCC 4737
                         vi    i   i    ivv  v   i v  vv   i        i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_138583497_   4738 TATTCAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 4787
                          v    ii              v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_138583497_   4788 AAACTCGACCCCTTCCTTACACCTTATAACAAAAATTAACCCAAGATGGA 4837
                           ii v       v   i     v    -           i   i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATA-CAAAAATTAACTCAAAATGGA 496

  chr2_138583497_   4838 TTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGACAAC 4887
                          i ?    i         i v i     i      vi i       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_138583497_   4888 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTC------A 4930
                         v    ?i- v i -   iv   v v  vv i     v ii   ------ 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_138583497_   4931 TGACAAAAATGCCAAAAGCAATTGCAACAAAAGCCAACATTTACAAATGG 4980
                              ------         vvv          vv  v  vv i    v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_138583497_   4981 GATCTAATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCAG 5030
                           ii v  i   v v  i     i  ii vv    i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_138583497_   5031 AGTGAACAGGCAACCTACAGAATGGGATAAAATTTCTGTGCTCTACCCAT 5080
                               v  i     i           v     v i  iivvii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_138583497_   5081 CTGACAAAGATCTAATATCCAGAATTTACAAGGAACTTAAATGAATTTAT 5130
                             i  i iv  vi          v  i  i     ivv ii v iv  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_138583497_   5131 AAGAAAAAAA-AAGCCACCCCATCAAAAACTGGACAAAAGATATGAACAG 5179
                           v     i -  iiv    v  i?    v   i    i   v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_138583497_   5180 ACACTTCTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAA 5229
                            i     v        i  vi vi       i  i  i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_138583497_   5230 GCTCAATATCGCTGATCAT 5248
                               i   i????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


2118 26.03 4.75 0.46  chr2_138599320_138600961      498  1150 (492)    L1M4_orf2#LINE/L1      228   908 (0)  

  chr2_138599320_    498 TTCCAAACCATACTATAGGGGGGTACAATAACCAA-ACAGCATGGTACTG 546
                           i    v v     i ii v--    i   i   -    ii        
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGC--TACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_138599320_    547 GTACAAAAACAAGCACATAGACCAATGAAACAGAATAGAGAGACCAGAAA 596
                          i i  ii i ii  i     i     i  i     v     v       
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_138599320_    597 TAAGGCCGCACACCTACGACCATCTGATCTTTGACAAAGCTGACAAAAAC 646
                            iv  ii   ii  i ii  vi    i  i     i v  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_138599320_    647 AAGCAATGGGGAAAAGACTTCCTATTCAATAAATGGTGGTGGGATAACTG 696
                          vv           ii ivvi  v     i        v     i     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_138599320_    697 GCTAGCCATATGCAGAAGACTGAAGCCAGTCTCCTTCCTTATACTATATA 746
                          v  ?   i     i    v     iii v i   v   i i  i     
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_138599320_    747 CAAAAATCAACTCAATGTGGCTTAAAGACT----------ACCTAAAACT 786
                                i       vi   v i ?    i---------- v        
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_138599320_    787 ATAAAAACCT-GGAAGACAACCTAGGCA-ATACCATCCTGCACATAGGAA 834
                               vi  -i     v   v    ?i- v i v  v  -  v v  iv
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGT 574

  chr2_138599320_    835 CAGGCAAAGATTC------TGTGACA---AAGACACTAA-AATCAATAAA 874
                         i      v i  i------ i     ---  ii   v i-  iv  vi  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_138599320_    875 AACATTGGCAAATGGCATCTCATTAAACTTAAGAGCTTCTGTACAGCAAA 924
                           v  v ii    v v ii    i   v    i i   i   i vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_138599320_    925 AGAAACTATCAATAGAATAAACAGACAACCTACGGAATGGTAGAAAATAT 974
                         i  v        v i i i  v        i  i      v         
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_138599320_    975 TTGCATAGTATGCATTTGACAAAGGTCTAATATCCATCATCTATAAGGAA 1024
                              v vi  ii  i   i  i  v  vi      vv  v     i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_138599320_   1025 CT--TA-AATTTAC-----AAGAGAGAAACAACCCCATTAAAACGTGGGC 1066
                           --  -  i i v-----  i   v   i     v   ?   vi     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_138599320_   1067 AAAGGACATGAATAAACAATTCTCAAAAGAAGACAGAGATGTGGCCAAGA 1116
                               iv      i   v     v        i v v vi       v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_138599320_   1117 AGCATTTGAAAAAAAGCTCAACATCACTGATCAT 1150
                             iv      i v           ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (99 / 67)
Gap_init rate = 0.02 (12 / 681), avg. gap size = 2.83 (34 / 12)  


2738 26.87 0.87 0.62  chr2_138732427_138734225.rev      504  1307 (492)    L1M4_orf2#LINE/L1      103   908 (0)  

  chr2_138732427_    504 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 551
                            iivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr2_138732427_    552 TAGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAGAA 601
                          i   viiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_138732427_    602 CAACGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 651
                            v i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_138732427_    652 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGA--TATAGATCAA 699
                               i   i    ii         i iv ii i   --          
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_138732427_    700 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTGCAACCAT 747
                              i    i--    i  --        vv   i    i iiiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_138732427_    748 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGTAAAGGATTCTCT 797
                         i    i  i     ivv  v   i v  vvv      v    i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_138732427_    798 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 847
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_138732427_    848 AACTAGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 897
                          ii i  i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_138732427_    898 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAGGAAAACCT 947
                          ?    i       v   v       i      vi i    i      v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_138732427_    948 AGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAAA 996
                            ?i- v i -   iv   v v  vv i i   v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_138732427_    997 ACACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATCTAAT 1046
                                     vvi          vv   i v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_138732427_   1047 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1096
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_138732427_   1097 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 1146
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_138732427_   1147 GGGCTAATATCCAGAATCTACAATGAACTAAAACAAATTTACAAGAAAAA 1196
                           i  vi          v  i  v     vvv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_138732427_   1197 AACAAACAACCCCATCAAAAACTGGGCAAAGGATATGAACCAACACTTCT 1246
                         i     i     v  i?    v            v    ivi   i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_138732427_   1247 CAAAAGAAGACATTTATGCAGCCAAATGACACATGAAAAAATGCTCATCA 1296
                          v        i  vi viii     vvii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_138732427_   1297 TCACTGGCCAT 1307
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (124 / 88)
Gap_init rate = 0.01 (8 / 806), avg. gap size = 1.50 (12 / 8)  


2258 28.01 4.84 2.70  chr2_138757416_138762356     3561  4449 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_138757416_   3561 TGGAAAAACATTCCATGCTCATGAACTGAAAGAATCAATCTCATTTAAAT 3610
                               i i  i     i     i i  i    v i   v ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_138757416_   3611 GATCATACTGTCAAAAGTAATTTACAGATTTAATGCTATTCCTATCAAAC 3660
                          iiv     vi v   v i  i        i  i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_138757416_   3661 TACCAACATCATTTTTCACAGAACTAGAAAAAAAACT-ATTTTAAAATTC 3709
                          v   i vv v     ii     v v  v  i---  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_138757416_   3710 ATATGGAACCAAAAAGAGCCCA-AATAGTCAAAGTAATTCTAAGCAAAAA 3758
                                 viiv  i ii    -     i    ii   ii i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_138757416_   3759 GGCCAATGCTGGAGGCATCACGTATCCAAAGTC--AAACTATATAATATA 3806
                          iv   v i      vv    iiv   v  v i--     ---  v  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT---TACTACA 244

  chr2_138757416_   3807 AGGCTACAGTAGCCAAAACAGCACAGTTCTGGTACAAAAACTGGCACATA 3856
                          i         ii   i    iiii  v    i i  ii iv i  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_138757416_   3857 AATCAGTGAAACAGAATAGAGAAACCAGAAATAAAGCTATATACCTCCAG 3906
                         i    i  i  i     v    iv           v i   i ii vii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_138757416_   3907 CCATCTGATCTTTGAAAAAGTCAACAAAAATAAGTGGTGAGGAAAAGACT 3956
                         i  vi    i  i  v  i viiv   i vi vviii  i     ii iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_138757416_   3957 CCCTATTCAATAATTGGTGCTAAGACACCTGGCTAGCAATATGCAGAAGA 4006
                         vi  v     i  v       ii    v    v  ? v i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_138757416_   4007 ATGAAACTGGACAT-TGCCTTTCAACGTATATACAAATTAACTCAAGATG 4055
                              ii     vi- i   iv  v i    i v            i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_138757416_   4056 GATTAAAGATTTAAATATAAGACCTCAAACTATAAGAATCCTACAAGAGA 4105
                            i ?   ii     i     v  v         i v  i  v    i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_138757416_   4106 ACCTAGGA-TATACCATTCTGGATATCAGCCTTGGAAAATAATTTAT--G 4152
                           v    ?-  v i -   vv  iv ii v-  i iv   ii   v -- 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAG 592

  chr2_138757416_   4153 ACCAAGTCCTCAAAAGCAATTGCAAAAAAAAAAAAAAAAAAAAAAAAATG 4202
                          i- v v vi        ----   iv  v    i      v ------ 
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCA----CAAGCAACAAAAGAAAAAATA------G 631

  chr2_138757416_   4203 ACAAGTGGGACCT------AATTAAAGACCTTCTGCACAGAAAAAGAAAC 4246
                          i  i v    i ------       i  i  -  ii vvv   i  v  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACAC 680

  chr2_138757416_   4247 AATCAATAGAATAAATA------------AATGAGAGAAAATATTTGCAA 4284
                         v     v i i i  v ------------    i                
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_138757416_   4285 ACTATGCCTCTCACTAGGATTTAATATCCAGAATGTATAAGGAACTTAAA 4334
                          ii  iiv   v iv   ivi vi          i     i     i---
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--- 777

  chr2_138757416_   4335 TTAGCAAGCCAA-AATAAAA-----------CCA--TTAAAAATAGGCAA 4370
                            -   vi   -       -----------   -- ?      i     
  L1M4_orf2#LINE/    778 TTA-CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_138757416_   4371 AAGACGCAAACAGACACTTCTCTAAAGAAGACATACAAGCAACCAACAA- 4419
                          i  ivii  i     i     i        i      iiii    i  -
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_138757416_   4420 -ATATAAAAAC-TGCTCAATATCACAAATCAT 4449
                         - i  i    v-       i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (160 / 85)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.91 (67 / 23)  


3009 27.04 2.35 1.01  chr2_138851564_138853511.rev      562  1456 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_138851564_    562 GGAAAAACATCCCATGCTCATGGATAGGAAGAATCAATATCATTAAAGTG 611
                              i i        i        v      v i     ii    ii  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_138851564_    612 GCCATACTGCCCAAAGCAATTTACAGATTCGATGTTATTCCTATCCAAAA 661
                           v     v      vii  i         i i iv  i      v   v
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_138851564_    662 ACCAATGACATTCCTCACAGAACTAGAAAAAACT-ATTTTGAAATTCATA 710
                         v   iivi v  ii ii     v v  v  i-  -  ii i         
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr2_138851564_    711 TGAAACCAAAAAAAGAGCCTGAATAGCCAAGGCAATCCTAAGCAAAAAGA 760
                           i  viiv  ii-  v  v          ii     i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_138851564_    761 ACAAAGCTGGAGGCATCATGTTCTCTGACTT-AAAACTATACTACAGGGC 809
                               i      vv   iii ii ii i  -      -       ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_138851564_    810 TACAGTAGCCAAAACAGCATGGTACTGGTACAAGAACAGACACATAGAAC 859
                                ii   i    ii         i i   i i     i     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_138851564_    860 AATGTAACAGAATAGAGAACCCACAAATAAGGCCACACACCTACAACCAT 909
                             v  i     v    ii   v      iv   i   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_138851564_    910 CTGATCTTCAACAAAGCCGACAAAAACAAGCAATGGGGAAAGGACTCCCT 959
                         i    i   i    i vi v   i v  vv            i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_138851564_    960 ATTCAAAAAATGGTACTGGAATAACTGGCTAGCCATATGCAGAAAACTGA 1009
                         v     v       i    i i      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_138851564_   1010 AACTGGACCCCTTCCTTACACTATATACAAAAATCAACTCATGATGGATT 1059
                          ii         v   i    i            i      vi      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_138851564_   1060 AAAGACTTAAATAAAATGTAAAACTCAAAGCTATAAAAACCCTGGAAGAT 1109
                          ?    i     -----    i vii   i        vi i i     v
  L1M4_orf2#LINE/    499 AWAGACCTAAAT-----GTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_138851564_   1110 AACCTGGACA-ATATC------ATCT-------GGTAAAGATGTTGTGAT 1145
                            v i i?i- v   ------ i  -------  i  v i v iv iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_138851564_   1146 TAAGATGCCAAAAGCAATTGTAACAAAAACAGAAATTGACAAAT-GGAAT 1194
                           v  ii         vvv i       iv i    v  i    -   v 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_138851564_   1195 GCAATTAAACTTAAGAGTTTCTGCACAGCAAAAGAAACTATCAACAGAGT 1244
                         v  - i   v    i ii  i  ii vv    i  v        v i   
  L1M4_orf2#LINE/    644 TCA-TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_138851564_   1245 AAACAGACAACCTGCAGAATGGGAGAAAATATTTGCAAACTATGCATCTG 1294
                         i  v        ii                         ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_138851564_   1295 ACAAAGGTCTAATATTTAACATCTATAAGGAACTTAAACAAATTTACAAG 1344
                          i  i  v  vi   ii iv  v     i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_138851564_   1345 AAAAA----AATAACCCCTTTAGAAAGTGGACAAAAGACATGAACACACA 1390
                              ----        vv  ?i   i   i    i  iv    i v   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_138851564_   1391 CTTTTCAAAAACAGACATAGATGTGGCCAACAAAGATATGAAAAAAAGCT 1440
                         i  i  v   iv   i   v vi       i  iv i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_138851564_   1441 CAATATCACTGATCAT 1456
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (156 / 82)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 2.50 (30 / 12)  


3159 27.20 0.55 0.55  chr2_138880068_138882080.rev      614  1521 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_138880068_    614 TGAAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCGTGAAAAT 663
                           i  ii i  i     i        v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_138880068_    664 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCGCATCAAGC 713
                            v     v     iv i  i  i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_138880068_    714 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCG 761
                          v   iivi i  i  ii     -   -- v  i  - iii    i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_138880068_    762 TATGGAAAGAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 811
                                 viv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_138880068_    812 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTATAAGGC 861
                                i      vv    i  v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_138880068_    862 TACAGTAACCAAAGCAGCATGGTACTGCTTCCAAAACAGAGATATAGACC 911
                                 i   ii   ii        viviv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_138880068_    912 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 959
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_138880068_    960 ATCTGATCTTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCC 1009
                          vi    i  i     ivv  v   i vv vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_138880068_   1010 CTATTCAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGGT 1059
                           v                    v      v  ?   i   i i  iii 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_138880068_   1060 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1109
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_138880068_   1110 TTAAAGACTTAAATGTTATACCTAAAACAATAAAAACCCTAGATGAAAAC 1159
                          i ?    i       v v v       v      vi i    v      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_138880068_   1160 CTAGGCA-ATACCATTCAGGGCATAGGCATGGGCAAGGACTTCATGTCTA 1208
                         v    ?i- v i -   iv i v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_138880068_   1209 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1258
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_138880068_   1259 ATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1308
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_138880068_   1309 CAGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTACTCATCTGACA 1358
                         v  i     i                 i       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_138880068_   1359 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 1408
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_138880068_   1409 AAAACAAACAACCCCATCAACAAGTGGCGGAAGGATATGAACAGACCCTT 1458
                           i     i     v  i? v  i   vvi      v    i    vi  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_138880068_   1459 CTCAAAAGAAGACATTTATGCAACCAACAGACACATGAAAAAATGCTCAT 1508
                            v        i  vi viiii    i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_138880068_   1509 CAACACTGGCCAT 1521
                           v  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2980 25.09 4.99 0.73  chr2_138972763_138974571      497  1317 (492)    L1M4_orf2#LINE/L1       53   908 (0)  

  chr2_138972763_    497 CAAAACTATCCATAGTAATTTACAAATTCATTGCAATCCCTATCAAAATT 546
                            v   vi   v v i  i    i     vi                 i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_138972763_    547 CCAATGATATTTTCCACAGAAAT--A-AAACAAATCCTAAAATTCACATG 593
                            iiviiv    iii       -- -  i vi             i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_138972763_    594 GAAA--CCAACGACCCTAAAGAGCCAAAGCAACCTTAAGCAAAGAGAAAA 641
                             -- v iv     vi  v       i   i   i iv  ii    v 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_138972763_    642 AGGCTGAAAGCCTCACACTACCTGACTTCAAAATATACTGTCAAGTTTTA 691
                          i i  i i v        v  ii i       iv    iiv   i vi 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_138972763_    692 GTAATCAAAATAGTAT--------------------CATACAAAT-ACT- 719
                                 i i   i --------------------    i i  - v -
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_138972763_    720 -AACAGAATAGAGATCCCAAAAATAAATCCACACACTTAAAGTTAATT-A 767
                         -  i     v    vi   i       i   i   i   vi  i    - 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_138972763_    768 TATTTGACAAAGGTGCCAATAACACACA-TAGGGAGAGGACAGTCTCTT- 815
                          v  i     i        v v  iv  - i    i  i i     i  -
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_138972763_    816 ----AATAGTGTTAGAAAAACTGGATATTTTCATGCAGAAGAATAAAATT 861
                         ----   i   i i i v         ?iiv      i      i  i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_138972763_    862 AGACCCTTATCTTGGAACATATACAAAAATGAACTTAAAATGAATTGAAG 911
                         i     i  i  iiv v             v    i      i  ii?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_138972763_    912 ACTTAAATGTAATACCTGAAACTGTAAAAGTATTCAAAGAAAACATAGGG 961
                           i         v v  i     i     v v  vi             ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_138972763_    962 GCAAGT-TCCATAACATCAGTCTGGGCAATTACTTTTTGG-TATGAACCT 1009
                          i  i - i i i  v ii vi i      vii  i  i -     vv i
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_138972763_   1010 GAAAGCACATGCCACAAAAGCAAAAATAGACACATGAGATTACATCAAAC 1059
                         i        v  v       v         i v  vi  i v       v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_138972763_   1060 TAAAAAGCTTCTGCACAGCCAAGGAGACAGTCAGTAGAGTGAAGAGTCAA 1109
                          v    i   i  ii vv v     v  vi   iv i      i  v   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_138972763_   1110 TCTGTGGAGTGGGAGAAAACATTTGCAAACCATACATCTGATGAAGGGTT 1159
                         i iiii  i          i         i    i       i i  ii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_138972763_   1160 AATATCCAAAATACATAAGGAACTCACACAACTTAGTAGTAAGAA----A 1205
                         vi      i    i    i      vi      i i  i   i  ---- 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_138972763_   1206 ATAACCTGATTTAAAAATGGGCAAAGGCTATGAATAGACATTTCTATTCA 1255
                               ii   ?               v v               --i  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT--CCA 850

  chr2_138972763_   1256 CAGAAAGAAAATGTACAAACGGCCAACAGCTATATGAAATAATGCTCAAT 1305
                         ----     i  i      i      i ivi i      vi        i
  L1M4_orf2#LINE/    851 ----AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_138972763_   1306 ATCACTAGTCAT 1317
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (139 / 63)
Gap_init rate = 0.02 (14 / 856), avg. gap size = 3.36 (47 / 14)  


3221 25.03 1.78 0.78  chr2_138989721_138993910     2800  3698 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_138989721_   2800 TGGAAAGACATTACATATTCATGGATTATAAGAATCAGTATTGTTAAAAT 2849
                                 i  iv   i          iv    v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_138989721_   2850 GTCCATACTACCCAAAGCAATCTATAGATTAAATGCAATCCCCTATCAAA 2899
                          v v     v      vii     i     v  i        -       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC-TATCAAA 99

  chr2_138989721_   2900 ATACTCA--TGACAGTCTTCACAGAAATAGAAAAAAAAAACCCCAAAACT 2947
                           - i  --  v -v i  ii       v  v  ivvi -i  i    i 
  L1M4_orf2#LINE/    100 AT-CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATT 146

  chr2_138989721_   2948 TATATGGAACCACAAAAGATCCAGAATCGCCAAAGCTATCCTGAACAAAA 2997
                         i        vii   ii  i       v      i v   i    v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_138989721_   2998 AGAACAAAACTGGAGAAATTATATTACCTGACTTCAAATTATACTACAGA 3047
                                 ii     i v i i i v  ii i      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_138989721_   3048 GCTATAGTAAACAAAATAGTATGGCACTGGCATAAAAACAGACTTACAGA 3097
                             i     v   i i   i   i          ii i    v  i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_138989721_   3098 CCAATGGAACAGAATAGGGAACCCAGAAAAAAGTCCATACATTTACAGG- 3146
                         i        i     v i  ii       v  ii           ii v-
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_138989721_   3147 AACTCATTTTCAGCAAA--TG--AGGAC-ATACA-TTGGAAAAGTACAGT 3190
                           i v      ii   i--  -- i   -  v  - v  i    v i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_138989721_   3191 CTTTTCCATAAACGGTCCTGAAAAAAATGGATATCTATAGGCAGAAGAAG 3240
                               v i   i   v   ii v  v      ? i i v   i     v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_138989721_   3241 AAAACCAGACCCCTATCTCTCACTATGTACAAAAATCAAGCCAAAATAGA 3290
                         i  iiii        i   v   i  i         i  vi      i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_138989721_   3291 TTAAAGACTTAAATCTAAAACCTCAAACTATAAAACTACTACAAGAAAAC 3340
                          i ?    i     v   i v  v             vi  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_138989721_   3341 ATTGAGGAAACTCTCCAGGACATTGGACTGGGCAAAGATTTCTTGAGTAA 3390
                           v i? v  v   i iv   v    ii i     v i      iii  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_138989721_   3391 TACCCCACAAGCACAGGCAACCAAAGCAAAAA-GGACAAATGGGATCACA 3439
                         v  v   v       i     v    v     -i  i    v   iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_138989721_   3440 GCAAGCCAAAAGGCTTCTACATAGCAAAGGAAACAATCAACAAGGTGAAG 3489
                         v   iviv   ii   i iiiivv       v  v     v  i     i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_138989721_   3490 GGGCAACCCACAGAATGTGAGAAAATATTTTCAAACTACCCATCTGATAA 3539
                         i i              v            v    ii ivi         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_138989721_   3540 GAGATTAATAACCAGGTGATATAAGGAGTTGAAACAACTCTATAGAAAAA 3589
                          i  i vi  v    ivv      i  ii vvv       v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_138989721_   3590 AAAATCTTGTAATCTGATTTTAAAAATAGGCAGAATATCTGAATAGACAT 3639
                          i -- vvi   i ii   ?-      i    i iv  i           
  L1M4_orf2#LINE/    797 AGA--CAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_138989721_   3640 TTCTCAAAAGAAGATATACAAATGGC-----AG-ATATAAAAACATGCTC 3683
                              v                    -----  - i  i    v      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_138989721_   3684 AACATCATTGGTCAT 3698
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (138 / 83)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.53 (23 / 15)  


2990 24.58 8.95 0.60  chr2_138996991_138998953.rev      634  1471 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_138996991_    634 TGGAAGGATGTTTTGTGTTCATAGATTGGAAGAGTTAATATTGTTAAAAT 683
                              i   i iiii       i          v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_138996991_    684 CTTTATACTATTGAAAATAATCTACACATTCAATGAAATATTTATGAAAA 733
                         vviv     viiv   v i       v      i v   vii   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_138996991_    734 TCCTGATGGCAATTTTTGCAGGCATAGAAAAAAACCAATTCTAAAGTTTA 783
                            iiiiv  vv         iv  v  v  i-- ii  i     i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_138996991_    784 TTTGGAACCACAAAAGACCCTGAATAGCCAATGTAATTTTGAGAATAAAG 833
                          v     vii   ii     v          vii   i    i  vi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_138996991_    834 AACAAAGCTG-----TTCATGCTCTCTGATTTCATAATATATAACAA-GC 877
                                i  -----i   ii  ii ii      v  iv  iv    -  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_138996991_    878 TACAGAAATAAATACACTATGGTACTTACTTAAATGCAGCCATATAGATA 927
                              v   v  v   v i       vi v   ivii  v         v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_138996991_    928 AATGAAACAGAATAGAGAGCCCAGAAACAAAACTATACACATAAAGTCAA 977
                             i  i     v     i       i   v i     iv  vi     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_138996991_    978 CTAATCTT-GATGATGGTATCAAGAATACATAATGGGGAAAAGATAGTCT 1026
                         i i  i  -  ii v   ii     vi ivi          ii       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_138996991_   1027 CTTCAATAAATGGTATTGGGAAAACTGGATACCCACAGGCAAA-GAATGA 1075
                         i     i       ii     v         ?     v     -      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_138996991_   1076 CTTTGGATTCTTATCTCATACCATATACAAAAATCAACTCAAAATGATTT 1125
                         vv     ii i  i    i               i           iv i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_138996991_   1126 AAGGGCTTCAGTGCAAAACCTGAAGC---AAAACTCTTAGAAGAAAACA- 1171
                          ?i i i v i  i  i v  i  i ---                    -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_138996991_   1172 --GAGTAAAAGCTTCCAGACATTGGATTTGACAATGATTTCTTGGATATG 1219
                         -- ?     -v    vv   v    i  v i     i      i      
  L1M4_orf2#LINE/    549 AGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_138996991_   1220 ACACCAAAAGCGTAGGTAACAAAAGCAAGCATAGACAAGTGGGATTATAT 1269
                                    ii i i        v  iv     i  i v   i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_138996991_   1270 CAAACCAAGAAGCTTCTTCACAACGAAGAGAACACT--CAACAAAAAGTA 1317
                             viv i  i   i vii vv i   i--     --   v   iv v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGG--ACACTATCAAGAAAGTGAA 695

  chr2_138996991_   1318 AAGACAACCTACTGAATGGGTGAAAGTATTTGCAAACCATCCATTTGATA 1367
                                  i  v       v    i          i   vi  i     
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_138996991_   1368 AGGGGTTAATATCAAAAACATATAA------------------------- 1392
                             ii vi    v i  i      -------------------------
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_138996991_   1393 ---------------------------------GATTT-AGTAGACATTT 1408
                         ---------------------------------     - i         
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_138996991_   1409 CACCAGAGAAGACATATAAATAGCCAACAAGTATATGCAAAGGTACTCAA 1458
                          v   i      i   i    i     i   i i   v    i i     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_138996991_   1459 CATCACTAATTGT 1471
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (131 / 72)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 6.67 (80 / 12)  


 565 26.63 0.54 0.54  chr2_139053992_139055994        1   184 (1819)  C L1M4_orf2#LINE/L1   (68)   840   657  

C chr2_139053992_    184 AAGCTTCTGAACAGCAAAAGAAACCGTCATCAGAGTGAATAGGCAAACTA 135
                           i   i  vi vv    i  v  ii   vv i      v  i   v i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

C chr2_139053992_    134 CAGAATGGGGGGAAAAT-TTTGCAATCTATCCATCTGACAAAGGGCTAAT 86
                                  i -     -       vii  vi      i  i  i  vi 
  L1M4_orf2#LINE/    707 CAGAATGGGAG-AAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

C chr2_139053992_     85 ATCCAGAATCTACAAGAAACTTAAACAAATATACAAGAAAAAAACAAACA 36
                                  v  i  ii    ivv    v vv i  v     i     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

C chr2_139053992_     35 ACCCCATGAAAAAGTGGGCAAAGGATATAAACAGA 1
                             v  v?    i            v i  i   
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

Transitions / transversions = 1.29 (27 / 21)
Gap_init rate = 0.01 (2 / 184), avg. gap size = 1.00 (2 / 2)  

2444 28.27 0.64 3.43  chr2_139053992_139055994      578  1511 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_139053992_    578 TAAAAACACATCCCATACTCATGGATGGGCAGAACCAATAATGTCAAAAT 627
                          ii   v i       ii        v  v   vii    v   i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139053992_    628 GACCATGCTGCCAAAAGCAATCTAAAAATTTAATGCAATTCCCATCAAAA 677
                          i v  i  v  v   vii     v i   i  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139053992_    678 TATCA-TTATAATTCTTCACACAACTAGAAAAAACAACCCTAAAATTCAT 726
                          vi  -i iiv-  i  ii  v  v v  v  ivii i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_139053992_    727 ATGGAACTAAAACAAAAAAAAAGCCTGCATAGCCAAAGCCAGACTAAGCA 776
                               v i---   iii v---  v v         i v vvi i iv 
  L1M4_orf2#LINE/    150 ATGGAAATG---CAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_139053992_    777 GCAAAAAAACAAATCTGGAGGCATCACATTACCTGGCTTCAAACTATACT 826
                         -- i  i      vi      vv     i v  iiii      viv    
  L1M4_orf2#LINE/    194 --AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_139053992_    827 ACAAGGCTATAATCACCAAAACTGCATGGTTCTGGTATAAAAATAAGCAT 876
                             i    i i v i   i  v ii    v    i    ii   ii   
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_139053992_    877 GTAGACTAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTA 926
                         i    ii       i     v    ii           v   v i i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_139053992_    927 CAGCCAGCTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGAGAAAGT 976
                         ii i  ii    i   i    i vviv   i v   vv i   i     v
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_139053992_    977 ACACCCTATTTAACAATTGGTGCTGGGATAATTGGCAAGACACATGTAGG 1026
                          i vi  v  i     v           i  i   vv ?v      i ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_139053992_   1027 AGAATGAAACTAGATCCTAATCTCTCACCTTATACAAACATCAATTCAAT 1076
                                 ii i  i  iv i   v    v        v  i  i    v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_139053992_   1077 ATGGATCAAAGATTTAAATCTGAGACCTGAAACTGTAAACATTCT-AGAA 1125
                                 ?   ii     v i   v  i     i    - i   -    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAA 540

  chr2_139053992_   1126 GGTAACATCAGAAAAACCCTTCTAAACATTGGCTTAGGCAAAGACTTCAT 1175
                          iv     vi ?iv  vi    vvi  v    v        v ii   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_139053992_   1176 GACCAAGAACCCTAAAGCAAATGCAACAAAAACAAAAATAAAAAGGTGGA 1225
                         iivi v  vv  v      v v         iv       i v ii v i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_139053992_   1226 ACTTAATTAAACTAAAAAGCTTCTATACCGCAAAAGAAATAATCAGCAGA 1275
                             v  i   v v    i   i i i iv    i  v iv    iv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_139053992_   1276 GTAAACAGA--ACCCTCAGAGTGGGAGAAAATCTTCACAAACGAAGCATT 1323
                           i  v   --    v    i           v  ii    iv vii  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_139053992_   1324 CAACAAAGGAATAATATCCAGAATCTACAAGGCAATCAAACAAATCACAA 1373
                         ii i  i   v vi          v  i  i v v  ------- i    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTC-------TTACAA 783

  chr2_139053992_   1374 GACAAAAAAAAAAAAATCCAACCAAATACAAATAATCACATCAAAAAGTT 1423
                         vv   v  v     i ------------       i vv  i?    i v
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGA------------CAAATAACCCAATTWAAAAATG 821

  chr2_139053992_   1424 GGCTAAGGACATAAATAGACAATTATCAAAAGAAGATATACACATGGCCA 1473
                            v     iv i        v  v  v              v       
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_139053992_   1474 ACAAACATATTTTTAAAA--TGCTCAGTATCACTAATTAT 1511
                          i  i  i  v---    --      ii    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATG---AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (152 / 108)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.17 (38 / 12)  


3015 27.91 1.11 0.55  chr2_139130303_139135318.rev     3622  4524 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_139130303_   3622 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 3671
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139130303_   3672 GGCCATACTGCCAAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3721
                            v     v  v  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139130303_   3722 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 3769
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_139130303_   3770 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 3819
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_139130303_   3820 AACAAACCTGGAGGCATCACTCTACCTGACTTCAAACTATATTACAAGGC 3869
                               vi      vv    v  v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_139130303_   3870 TACAGTAACCAAAACAGCATGGTACTGGTAACAAAACAGAGATATAGACC 3919
                                 i   i    ii         i vv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_139130303_   3920 AACGGAACAGAAC--AGAGCCCTCAGAAAGAATGCCGCGTATCTACAACC 3967
                           i    i    i--    i  --     v  vv  iiii  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_139130303_   3968 ATCTGATCTTTGACAAATCTGACAAAAACAAGAAATGGGGACAGGATTCC 4017
                          vi    i  i     ivv  v   i v  vvv        v  i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_139130303_   4018 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4067
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_139130303_   4068 GAAACTAGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4117
                            ii i  i  i v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_139130303_   4118 TTAAAGACTTA----TTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4163
                          i ?    i  ---- v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_139130303_   4164 CTAGGCA-ATACCGTTCAGGACATACGCATGGGCAAGGACTTTATGTCTA 4212
                         v    ?i- v i -   iv   v vv vv i     v ii  iv ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_139130303_   4213 AAACACCAAAAGCAATGGCAACAAA-GACAAAATTGACAAATGGGATCTA 4261
                         vi            vvi        -  v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_139130303_   4262 ATTAAACTAAAGAGCTTCTGGACAGCAAAAGAAACTACCATCAGAGTGAA 4311
                           i   v v  i i   i  vi vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_139130303_   4312 CAGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTACTCATCTGACA 4361
                         v  i     i                 i       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_139130303_   4362 AAGGGCTAATATTCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 4411
                          i  i  vi   i      v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_139130303_   4412 AAAACAAACAACCCCATCAAAAAGTGGCTGAAGGATATGAACCAACAGTT 4461
                           i     i     v  i?    i   vii      v    ivi   v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_139130303_   4462 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 4511
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_139130303_   4512 CATCACTGGCCAT 4524
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


1124 24.88 8.87 4.93  chr2_139152809_139155307      559   964 (1535)    L1M4_orf2#LINE/L1       16   437 (471)  

  chr2_139152809_    559 TGTCCATGGACTGAAAGTCTCAATATTGTTAAAATGTCAGTTGTCTTTAA 608
                            i      i  i   v  i           i   v  i vv  iii  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_139152809_    609 AATTGATA-GTAGACGCAGCATG-TTCCTCTCAAGATCCTAGCAGTCTTT 656
                          -     v-ii   iv  i iii- i   v    i    i   v i    
  L1M4_orf2#LINE/     66 A-TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr2_139152809_    657 TTTCTTTTTTTTTTTTCAGAAGTTGACAAGCTGATT-TAAAATTT-TAT- 703
                            v------------     i             i-       i-   -
  L1M4_orf2#LINE/    115 TTTG------------CAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_139152809_    704 ---------------TATAATAACT-------TTGGGGAAAAAAAGAATA 731
                         ---------------i v    i i------- ivv i    i     i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_139152809_    732 AAGT-AGAGGACTAACACTACTTGATATCATGACTTACTATAAAGCTTTA 780
                             -i       v     v iii  v   vi        i      vi 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_139152809_    781 GAAATTAAGACAGTGTTGTATTGGTGTTAAGATGGGCAAATA-----ATG 825
                          v   i          v   i   ii v i   i i  v   -----   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_139152809_    826 GAACAGAATAAAGAATATGAATATGAAAATAGACC-ATCACATT-ATGAA 873
                            i     vi   i viii ------    i   -  -     -   iv
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGA------AATAAACCCAT-ACATTTATGGT 345

  chr2_139152809_    874 TATTTAATTTTTGACAAAAGTGCAAAGACAGTTCAGTAGAAAAAGGATAA 923
                         i v  i     i     ii    v     vi    i i ii    i   i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_139152809_    924 TCTTT-AAACAAGTGGTGCAGGAGCAGTTGAATACCTACATG 964
                              -v     i      v  ii  ii  i   ? i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

Transitions / transversions = 2.45 (71 / 29)
Gap_init rate = 0.04 (15 / 422), avg. gap size = 3.73 (56 / 15)  

 949 21.71 11.22 5.85  chr2_139152809_139155307     1293  1702 (797)    L1M4_orf2#LINE/L1      477   908 (0)  

  chr2_139152809_   1293 AAAAAGTAATGCAAAATGGATCATAAACCTAAA------ATCTAAACCTC 1336
                              v   iv            ? i       ------ v     v  v
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_139152809_   1337 TAAAA---------GAAAACATAAAAGAAAGTGTTTGTGATGTTAGGTTA 1377
                              ---------         ii? v  i v  i    iv  i     
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_139152809_   1378 GGCAGAGATTTCTTAGCTGTGACACCAAAAATTCT-GTAA-AAGAAAAAA 1425
                             iv i        v i           iiv v- i  -  i i    
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_139152809_   1426 AAT-GATAAAATAGACTTCAATAAAATTTCAA-CTTCTTTTCTTCGAAAG 1473
                            -      v i       vi      vv  -   i v v    i  i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_139152809_   1474 ACA-------GAA--TAAAAAGATTAGCCACAAACTGGGAGAAAATATTT 1514
                            -------   -- i      iv v     i v               
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_139152809_   1515 GCACAGCAGATATCTAATGAACAACTTTTATTCAGAATATATCTGACTTT 1564
                            v v  v      i  i ivi    -----------------------
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTT----------------------- 753

  chr2_139152809_   1565 TGTATTCAGACTATATAAAGAATTCTCAAAACTCAGTTATAAGAAAACAA 1614
                         -    i    v           i   i v      i v    i  i    
  L1M4_orf2#LINE/    754 -GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_139152809_   1615 -TG--TTATTTCTAAAA--GACAAAACGTTTGAGCAAACATTT-TCTGAA 1658
                         - i--ii v  ?v    -- i    ivi     ii i      -  ii  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_139152809_   1659 ----ATA-----ATGTCTGA--AATACATAAAAAGATATTCTA-GTCAAG 1696
                         ----   -----   v ii -- ii    i       ii  v -i   ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_139152809_   1697 CATGGT 1702
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.61 (53 / 33)
Gap_init rate = 0.04 (17 / 432), avg. gap size = 4.12 (70 / 17)  


1303 20.70 2.78 21.86  chr2_139183763_139185924.rev      556  1671 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_139183763_    556 AAATATAACATATTCATAGATTCAGAGGCTCGATATCGTTAAGATGTCAA 605
                          i    vv   i     i    vii  i  ii    i         v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_139183763_    606 TACTTCTCAAAGTTTGAATTTATTTATAAATTCAATACCTTCTGAACCAA 655
                             i i    --    ----- i  i i      ii vv  ivv i   
  L1M4_orf2#LINE/     56 TACTCCCCAAA--TTGA-----TCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_139183763_    656 AATATTACCAG--GCTTTATTTTAATAGAAAATGACAAGCTAATTTTAAG 703
                            v---    --  i  -    i-i     v         i  ii   i
  L1M4_orf2#LINE/     99 AATC---CCAGCTGCCTT-TTTTG-CAGAAATTGACAAGCTGATCCTAAA 143

  chr2_139183763_    704 ATTTATAGAGAAATACAAAGGACTTTGAGTAGTCAAGATAATATTGAAAA 753
                            i   vi     i   i    iiv  i   i   i i   v       
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_139183763_    754 ATAA---TAAAGTTGGAAAACTTACAA--CATGATTTTAAGACTTGCTAT 798
                          v  ---i         ii   i   v-- vii    i  i    i   i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_139183763_    799 AAAGCTACAGTGACCAAAGAC-TTGCTTTGCTGGCATATGACTAGATATA 847
                                    i i   -   -v  ivv i        v iv    i   
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAA-GACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_139183763_    848 TAGGTTAGTAGAACAAAATTGAGACCGGAACATATTGGTCAGCTCATTGA 897
                            i i i i   i i        -------------   ----------
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGA-------------GTC---------- 319

  chr2_139183763_    898 TTTTCAAAAAAAAGTATCAGGGAAGGCAGAATGGGGGAGTGACTGCTTAA 947
                         --------------------------     -------------------
  L1M4_orf2#LINE/    320 --------------------------CAGAA------------------- 324

  chr2_139183763_    948 TGGACATGGGGTCTCCTTTGGGAGCAATGGAAAATTTATGGACTAGATAT 997
                         ------------------------------------------------  
  L1M4_orf2#LINE/    325 ------------------------------------------------AT 326

  chr2_139183763_    998 AGGCAATGGTTGCACAACCTCAGGAAGGCACTGACTGCCACTGGACTGTA 1047
                          --------------    -------------------  --------  
  L1M4_orf2#LINE/    327 A--------------AACC-------------------CA--------TA 335

  chr2_139183763_   1048 CACTTTTAAATGGTTAATTTTATGTTATATGAATTTTACCCTAACAAAGA 1097
                           i  ----     i    ------------i     ------- ---  
  L1M4_orf2#LINE/    336 CATTT----ATGGTCAATT------------GATTTT-------C---GA 359

  chr2_139183763_   1098 CAGCAGAAGGGTATCAAG-CAATTCA-TGGGGGTAAAGAAGAGTATTGTC 1145
                           -----     ii    - v     -     --      v   v  v  
  L1M4_orf2#LINE/    360 CA-----AGGGTGCCAAGACCATTCAATGGGG--AAAGAATAGTCTTTTC 402

  chr2_139183763_   1146 AACAAAATGGCACTAGGATCAACAGAACAGGATATCCATTCTAAATTTAA 1195
                               -   ii  i   i------   v     ?   i-----  vi  
  L1M4_orf2#LINE/    403 AACAAA-TGGTGCTGGGAC------AACTGGATAKCCAC-----ATGCAA 440

  chr2_139183763_   1196 AAAGAATAAAAGAACCTTGAAACTTTACCCAATGGCATTCACAAAAATCA 1245
                           -    i  i-----   i v ii    iv iiv   vi        i 
  L1M4_orf2#LINE/    441 AA-GAATGAAG-----TTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_139183763_   1246 ATTCGAAATGAGTCATAAAGCCGTATGTATAATCTAGAATT-TGGATGTG 1294
                          i  i     ii   ? i v iiv     vi v   i  i - ii vv v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_139183763_   1295 TTAAAGGAAAACAGAAAA--AAATGTCAACATGAATGTAGGGTAGACAAA 1342
                            i i       v ii?--    v i-- i   viv i  v   i   v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTT--CGTGACCTTGGGTTAGGCAAT 582

  chr2_139183763_   1343 AATTGTTTTAGACAGGACACAAAAATTAC---TAACCATAGAAAA--TAG 1387
                         ii  - i     i v     v    vi  ---i   v v      --   
  L1M4_orf2#LINE/    583 GGTT-TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_139183763_   1388 AAAAATTATATTTTATCAAAATGTAAAACTTCTTGTTCCTCAAAAGTTAC 1437
                          v     iv i  i        vv       -    v i     i vi  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTT-TTGTGCTTCAAAGGACAC 680

  chr2_139183763_   1438 CATTAAGAAAATGAAGAGACAAATCACAGACT-----AAGATTTTCTTAA 1482
                         i  i      i    i      vi      v -----  i  v  ivi  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_139183763_   1483 ATGGTATATTTGGCCAAGGATTTATATCTGGAATATA---AAAATTACTA 1529
                           vi     i  iiv i   i  i    ii       --- i  i vi  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_139183763_   1530 TAAATTAATAA--AAACAATTAATAATCATAAATACAATAAAATAAAAAC 1577
                         i  v i     --   vi iv     i -------    ---- ?    -
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACC-------CAAT----TWAAAA- 818

  chr2_139183763_   1578 ATTTAAAGTAGATAAAACTCTTGAACAAGCACTTTACAAAAGAAGATATA 1627
                         -------i i ii   ivvi     i ii  i  iv v            
  L1M4_orf2#LINE/    819 -------ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_139183763_   1628 TAGATAACCAACA-GCACTTAAAAA--TGTTCAATGTCCCTGTTTTC 1671
                         i i  ii    i -    v i    --  i    ii  v????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.20 (156 / 71)
Gap_init rate = 0.05 (44 / 903), avg. gap size = 6.25 (275 / 44)  


2740 25.52 6.84 1.51  chr2_139345768_139348043.rev      923  1784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_139345768_    923 TGGAGAGCCAGTGCATGTTTGTGAATTGGAAAACTCAATATTGTTAAAAT 972
                             i  vi viv      ii  i       i   i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139345768_    973 GTCATTTATTCCTAACTTGATCAACAGAGTCAATGCAATACCAATTTAAA 1022
                          v  v vv i  i  v      v     v    i     v  v  iv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139345768_   1023 TTCAAGCAGGCTACTTCGCAGATATTG-CAAACTGGCTCTAAAATTTTTA 1071
                          i v   v v  vi  i     v    -   i   iii        iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_139345768_   1072 TAGAAAGTCCAAT--ACCTAGAATATCCAACATAATACTGAGAAA----- 1114
                          i    - v   v--   i      v    v i   vi   i   -----
  L1M4_orf2#LINE/    151 TGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_139345768_   1115 -CAAAACTGAAGGGCTCACATTACCTGATTTTAAGACTTACTATTAGGCT 1163
                         -    ii  i   i      i v  ii    i  i        iv i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_139345768_   1164 GTAGTATTCAATACACCATGGTATTGGTTAAAAAAAGCAAATATAGACAC 1213
                         ii    v    v   vii     i   i--- v  i -----       i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGC---ATAAGG-----ATAGACAT 291

  chr2_139345768_   1214 ATAGATCAATGGTGCAAAAAAGAGAACTAAGAAACAGCCCTGCACAAATA 1263
                                     vii i  vv    iiiv     i iv  iii   vv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_139345768_   1264 TAGTCAGCTGATTTTTGACAAAGGAACAAAGGCAATTCAATGGAGAAAGT 1313
                          i    ii       i     i  vi v   i v         i     v
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_139345768_   1314 ATAGCCTTTTCAACAAATGATGCTGGAACAGTTGGTCATTCATATGCAAC 1363
                             i              i      i   ii   vi ?i  i      v
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_139345768_   1364 ATA-TGTATGTAGACATAAAACTTACACCTTTCACAGCAGT-AATTCAAA 1411
                          v -  v vv i   vivv v  i     v vi   iv i -  i     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_139345768_   1412 ACAGACCATAGACATAAATTTAAAATGC-AAAACTACAAAACTTCTAGAA 1460
                          ii  i  ?    v     v   i -  -       i      ii     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAA 540

  chr2_139345768_   1461 AAAAACCACAGGAGAAAATCTATGTGACCTTGGGTCA------------- 1497
                         i     - i   ? v      vi            i -------------
  L1M4_orf2#LINE/    541 GAAAAC-ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_139345768_   1498 ----TAT------AGAGGCACACTTTGCGAAAGAAAAAATTGACAGCTTG 1537
                         ----   ------ i i     vvivi i           v  i iv   
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_139345768_   1538 AACCTTATTGTAATTAAAAACTTCTCAGTG----AAAG--CACTATTAAA 1581
                         i  i i  iiv            i --   ----    --      i  i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTT--GTGCTTCAAAGGACACTATCAAG 687

  chr2_139345768_   1582 AGAATGAAAAGATAAGCCGTATACTGAGATA---TATATGCTGAATATAT 1628
                          i i        i  v  ii v v  i  v ---   v   vi vi    
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_139345768_   1629 ATCTGATAAAGAACTTGTATGCAACATATACAAAGAATTCTTAGAACTCA 1678
                                  i i        v  iv     i      i     v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_139345768_   1679 ACAGTAAAAAG----------CAATTTAAAGATGGCCAAAAGATCTGA-- 1716
                          i i       ----------     ?   i    v    i   i   --
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_139345768_   1717 ---TACCTAATCATAGAAGATGTACTGATAACACATAAACATATGTAAAG 1763
                         ---i ii vvi  v       i   vi  ii vv    i  i   v    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_139345768_   1764 ATGCTTAACATCATTTGTCAT 1784
                              i       ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (134 / 82)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.79 (72 / 19)  


1805 28.27 1.36 0.97  chr2_139380141_139386186.rev     4338  4850 (1196)    L1M4_orf2#LINE/L1        1   515 (393)  

  chr2_139380141_   4338 TGGGAAAACATTCCATACTCACGGATAGACAGAATCAATATCATAAAAAA 4387
                            i  i i  i    ii   i    v iv   v i     ii v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139380141_   4388 GAGCACACTGCCCAAAGTAATTTATAGATTTAATGCTATTCCCATTAAAC 4437
                          ivv i   v      v i  i  i     i  i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139380141_   4438 TTCCATTGACGTTTGTCACAGAATTAGAAAAAAAACT-ATTTTAAAATTC 4486
                          i   vivi v   v ii     v v  v  i---  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_139380141_   4487 ATATGGAACCAAAAAAGAACTTGAATAGCCAAGACAACCCTAAGCAAAAA 4536
                                 viiv  ii  v iv          i    i i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_139380141_   4537 GAACAAAGCTGGAAGCATCATGCTACCTGACTTCAAACTATACTACAACG 4586
                                 i    i vv   ii  v  ii i      viv        v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_139380141_   4587 CTATGGTAACCAAAACAGCATGGTACTGTTACAAGAAAAGACACATAGAC 4636
                            ii    i   i    ii        vi i   i v     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_139380141_   4637 CAATGGAACAGAATAGAGAACTCAGAAATAAGACCACACACCTACAACCT 4686
                                 i     v    iii         iv   i   ii  iiii v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_139380141_   4687 -CTGATCTTCAGCAAATCTGACAAAAACAAACCATGGGGAGAGGAT--TC 4733
                         -i    i   ii   ivv  v   i v  vv v       i  i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_139380141_   4734 CTTATTTAACAAATGGTGCTGGGAGAACTGGCTAGCCATGTGTAGAAAAT 4783
                         i  -- i                 v      v  ?   ii  i i  i v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_139380141_   4784 TGAAACTGGGCTCT--CCTTACACCACATACAAAAATTAAC-CAAGACGG 4830
                             ii   i i i--   i      i              -   i i  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_139380141_   4831 ATTAAAGACTTAAATGTAGG 4850
                           i ?    i        i 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAG 515

Transitions / transversions = 2.25 (99 / 44)
Gap_init rate = 0.01 (7 / 515), avg. gap size = 1.71 (12 / 7)  

 941 25.89 7.81 2.46  chr2_139380141_139386186.rev     5107  5554 (492)    L1M4_orf2#LINE/L1      437   908 (0)  

  chr2_139380141_   5107 GCAACAGAGTGA-----GACTC-TACCTCA----------AAAAAAGAA- 5139
                             v   i   -----   i -       ----------     vv  -
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_139380141_   5140 --AAAAAGGA----ATACTTAAATTTAAAACCCAAATCTATAAAAACCCT 5183
                         --    v   ---- v  i     v   i v i   v        vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_139380141_   5184 GTAAGAAAATCTAGG--TAATACCATTCAGGAACTAGGTATGGGCAAAAA 5231
                         iv       iv    --   - i -   iv  v  v  vv i     vii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_139380141_   5232 TTTCAT-GATGAAAATGCCAAAAGCAATTGCAACAAAAGCAAAAATTGAT 5280
                             v -   - vi ii         vvv          v      v   
  L1M4_orf2#LINE/    585 TTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_139380141_   5281 ---------CTAATTAAACTAAAGAGCATCTGCACAGCAAAAGAAACTAT 5321
                         ---------i v  i   v v  i i v i  ii vv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_139380141_   5322 TATCAGAGTGAACAGACAACCTAGAGAATGAGAGAAAATTTTTACAATCT 5371
                         i vv i      v        i v      i        v   i   vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_139380141_   5372 ATTCATCTGTCAAAGGTCTAATATTCAGAGTCTGCAAGGAACTTAAACAA 5421
                           vi     vi  i  v  vi   i    i v ii  i     ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_139380141_   5422 ATTTACAAGAAGAAAACAAACATTAAACATTGCCTAGTAAAAAGTGGGCA 5471
                         v iv i  v  i  i     i ----  ----  v v ?    i      
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATA----AC----CCAATTWAAAAATGGGCA 825

  chr2_139380141_   5472 AAGGACATGAACAGACACTTCTCAAAAGAAGACATACATGCAGCCAACAA 5521
                              iv    i     i     v        i     viii     i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_139380141_   5522 ACATATACAAAAAACCTCAACATCACTGCTCAT 5554
                         i  i  iv   i vv          ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (60 / 55)
Gap_init rate = 0.03 (13 / 472), avg. gap size = 3.54 (46 / 13)  


3134 26.72 0.44 1.42  chr2_139386459_139393145     5279  6195 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_139386459_   5279 TGGAAAAACTTTCCATACTTATGGATAGGTAGAATCACTATCATGAAAAT 5328
                               i iv i    ii i      v  v   v i v   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139386459_   5329 GGCAATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCTATCAAGA 5378
                                  v      v i  i  i        i  v  i        i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139386459_   5379 TACCAGTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5427
                          v    ivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_139386459_   5428 ATGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGA 5477
                               viiv  ii  v  v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_139386459_   5478 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGACT 5527
                               i      vv       v  ii i      viv        ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_139386459_   5528 ACAGTAACCAAAACAGCATGATACTGGTATCAAAACAGTTAATATAGATC 5577
                                i   i    ii  i      i  v ii i  vi -        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA-TATAGATC 298

  chr2_139386459_   5578 AATGGAACAGAACAGAGATATCAGAAATAACACCACACATCAACAACCAT 5627
                                i    iv    vvi         vv   i    iv iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_139386459_   5628 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5677
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_139386459_   5678 ATTTAATGAATGGTGTTGGGAAAACTGGCTTTCCATATGCAGAAAACTGA 5727
                         v  i  ii       i     v      v v?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_139386459_   5728 AACTGGACCACTTCCTTACACCTTTTACAAAAATTAGCTCAT--TGTATT 5775
                          ii      v  v   i     v v           i    v--  v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_139386459_   5776 AAAGATTTAAACATAACACCGAAAACCATAAAAACCCTGGAAGAAAACCT 5825
                          ?   ii    ii   v v v     i      vi i i         v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_139386459_   5826 AGGCA-ACACCATTCAGGACATAGGCATGGGCAAAGACTTTATGACTAAA 5874
                            ?i- v i -   iv   v v  vv i     v ii  iv iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_139386459_   5875 ACACCAAAAGCAATTGCAATGAAAGCCAAAATTGACAAATGGGATCTAAT 5924
                                     vvv    ii    vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_139386459_   5925 TACACTAAAAAGCTTCTGCACAGAAAAAAGAAAAATAAAAAACTATCATC 5974
                         i v v v    i   i  ii vvv   ii---------- v       vv
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGG----------ACACTATCAAG 687

  chr2_139386459_   5975 AGAGTGAATAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCC 6024
                          i      v  i     i                 v       vii  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_139386459_   6025 ATCTGACAAAGGGCTAATATCCAGAATATACAAGGAACTTAAACAAATTT 6074
                               i  i  i  vi             i  i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_139386459_   6075 ACAAGAAAAAAACAAACAATCCCATCAAAAAGTGGGCAAAGGATATGAAC 6124
                          i  v     i     i  i  v  i?    i            v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_139386459_   6125 AGACATTTCTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAA 6174
                                    v        i  vi vi       i  i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_139386459_   6175 AAGCTCATCATCACTGGTCGT 6195
                          v     v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (138 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.43 (17 / 7)  


2301 23.81 6.05 2.70  chr2_139397741_139399517.rev      501  1277 (500)    L1M4_orf2#LINE/L1       67   869 (39)  

  chr2_139397741_    501 TTGATCTATAGATTCAAAATGAAATCCAAATATAAATAACAGAAAGATTT 550
                                 i        --i v     vv  vv    vv   vv- vi  
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAA--CGCAATCCCTATCAAAATCCCAGCT-GCCTT 113

  chr2_139397741_    551 TGTTTGTACATATTGATATGCTTATTCCAAACTTTACATGGAAAGGCAAA 600
                          -    i v v     i v   v  i i   v  i i       v    i
  L1M4_orf2#LINE/    114 T-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_139397741_    601 GGAACTAAAATAGGTAATTCCAA-AATTCTGAAAAAGAAAAGAACAAAGT 649
                            v i i     vi  ----  -   ii          --         
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAA----AACAATCTTGAAAAAGAA--GAACAAAGT 206

  chr2_139397741_    650 CAGAATCCTCACATTACCCAGTTGTAAGTCTTATTCTTATAAAGCTACAG 699
                         ii  ivv      i v    i  vi  iv    i --- i          
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACT---ACAAAGCTACAG 253

  chr2_139397741_    700 TAATCAAGTCGATCCTGTATTGTCAAAAGGATAGACACACAGATCAATTA 749
                                 v ii viv   i  v  v           i i        vi
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_139397741_    750 AACAGAATAGAAAGCCCAGAAATAGATCTACACAA--ATAGTTAACTGAT 797
                           i     v  i  i         i i i i   v--  i  i  i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_139397741_    798 TTTTGATAAAGATTCAAAGGCAATTCAATGGAGAAA----AG-CTTCTCA 842
                            i  i  i i v v   i v         i    ----  -   i   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_139397741_    843 ACAAATGATGCTTGAATAATTTGGACATCCATATGGGAAAAAGAA-GAAG 891
                                i    v i i  i -   i ?   i   v--       -    
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACT-GGATAKCCACATGC--AAAAGAATGAAG 450

  chr2_139397741_    892 --AAA-----------------AAACAAAAA--ACCTCCAAATGGCT-AC 919
                         --ii ----------------- v       -- v   v      v - ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_139397741_    920 AGACCTAAAGGTATCATGTAAAAGTA-AAGACAGTATCTT---------C 959
                                  v   vv vv     v  -  i  ----    --------- 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAAC----TCTTAGAAGAAAAC 546

  chr2_139397741_    960 -TAGGCG-ATACCTGTGTTGCACTGGTTTTGTCAATGTGTTTTTAGATAC 1007
                         -    ? - v i  vi  vi vi   v  v v     vv  i       i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_139397741_   1008 AATACCAAAAGCATACACCATTAAAGAAAATATTGATTAACTGGACTCTA 1057
                         i i          i vi v iv        v  v   v  i      ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_139397741_   1058 TCAAAGTTTTAAGCTGTAGCTCCACAAAAGACACTGTTGAGAGAATTAAC 1107
                              i  vv  i  v v iv iv    i      i ii   i i v  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_139397741_   1108 AGACAACCCATAGAATAGGAGAAAATAT--GCAAATCACATATCTGATAA 1155
                                   i     i           --        i           
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_139397741_   1156 AAGACATGTACCAAGAGTATATAAATA-CTCCCA-AATTCAATAATAAAA 1203
                         ii   v    i v   i        v -   ii -  i            
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_139397741_   1204 AAACCAAGCACCACAATTAAAAAATAGGTGAAACATTTGAACAGACACTT 1253
                          i  v  vv   -     ?      i  ii  iv       i     i  
  L1M4_orf2#LINE/    797 AGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_139397741_   1254 TAGGAAAGAAGATATATGGATGGC 1277
                         ivvv            iii     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGC 869

Transitions / transversions = 1.29 (102 / 79)
Gap_init rate = 0.03 (26 / 803), avg. gap size = 2.62 (68 / 26)  


1792 26.54 10.07 1.70  chr2_139426905_139429232.rev     1078  1842 (486)    L1M4_orf2#LINE/L1       80   908 (0)  

  chr2_139426905_   1078 TCACTGCAGTCCCAATCAAAATCCCATCACACATTTTTGCACAAACCAAC 1127
                            vi   i    v            v vvv v        v   iii  
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chr2_139426905_   1128 AAGCCAAGTCCAAAATATA-ATTGAAACACAAAGGAGCTAGAATAGCCAA 1176
                             ii vi i     vi -  v    ii   i   v i           
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_139426905_   1177 ACTCTTTTTTTTAAAGTT---CAAAGTCGAAGGACTC-------CTAATT 1216
                          vivv i  vvv    vv---      i i       ------- i    
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_139426905_   1217 TCAAG--------TAAAGTTACGGTAATCAAGACAGTGTCATACTGATGT 1258
                             i--------i    i   i                vi     iii 
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_139426905_   1259 AAAAACAGACATACACATCCATGGAACAGAATCAGTAATTCAGAAATAGA 1308
                           ii i       i v   v      i     iiiv i i        i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_139426905_   1309 TC--TACA---------AATTAATTTTTTATAAAT-TGCTAA-------- 1338
                         i --    ---------    i     iv i  iv-   i  --------
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_139426905_   1339 --TGGAAAAAG--TAGCATCTTTTTCCATAAATTATGTGGGAACCACTGG 1384
                         --   ii    --   --      - v i    vi  iv  i  v     
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAG--TCTTTT-CAACAAATGGTGCTGGGACAACTGG 426

  chr2_139426905_   1385 ATATTGATAC---AGATATTGATATTG-ATATTGACCTTATACTATACAT 1430
                            ?iv i i--- i v v   vi   - iviiv    i i  i   i i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_139426905_   1431 AAAA-TTAATTCAAA-TAGATCATCGACCTGTTTGTAACAGTGAAGATTA 1478
                             -    i     - i     ?v     ivv     v  iv  i i  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_139426905_   1479 TGAGACTTCTAAAAGAAAACATAAGAGAAAAT----ATGATTATGAGATA 1524
                          i i   ii  i           i ? v    ----i   iiv  i v  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_139426905_   1525 GGCAAGGATTTCCTAGG-----CACAAAAAACACAAAGCATATAAGACAA 1569
                              v i    i   i-----   v    i     ivv i v    v  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_139426905_   1570 AAT-GATTTATTGAATTTGATCAAAATTTGAA-TGTTTACTCTTCAAAAA 1617
                            -   vv    i i  v         vi  -iv   iiv       i-
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG- 675

  chr2_139426905_   1618 GACACCATTTTTTTAA-------AAAAGGCAAGTCAGAGACTG--AGCAA 1658
                              i  i-----  -------     i   vi  v   v  --  v  
  L1M4_orf2#LINE/    676 GACACTATC-----AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_139426905_   1659 GTGTTCACAGCATGTATATATCTGACAAAATACTTTTATCTAAAATATGT 1708
                         i i  ii  i-  -i          i  iiv    v    i i     i 
  L1M4_orf2#LINE/    721 ATATTTGCAA-AT-CATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_139426905_   1709 GAAAAA-TCATACATCT---TTATAAGAAAATAAACAACATA-TTTAAAA 1753
                         i  i  -  v    v  --- v    i  i i   i   vi -  ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_139426905_   1754 ATA--CAAAAATATTTCAATAGACACTTCACAAAATAAGAAATTACAG-T 1800
                           i--    ii-    v        i   v v   v    v  -   i- 
  L1M4_orf2#LINE/    819 ATGGGCAAAGG-ATTTGAATAGACATTTCTCCAAAGAAGATAT-ACAAAT 866

  chr2_139426905_   1801 AGTCTTTAAGGACATGAAAAGATGCTCATCCCCATTATTCAA 1842
                         i i vv    v                 v vi  ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (123 / 76)
Gap_init rate = 0.04 (32 / 829), avg. gap size = 2.81 (90 / 32)  


1368 26.39 11.38 4.00  chr2_139490260_139492491.rev      920  1745 (487)    L1M4_orf2#LINE/L1       22   908 (0)  

  chr2_139490260_    920 TGAATTGAAACTCTCAGTATT---AATATTTTATTTGTCTCCAGATAGCT 966
                           i    i  vv  i i    ---  v  vvi v vv  i   i  v v 
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGAT 71

  chr2_139490260_    967 ATATAAACTCAGAAACAATGCCAGACAAAATCCTACAGAAATG---TTTC 1013
                         v  i i i   - vi    v  viv        --   v--  ---   i
  L1M4_orf2#LINE/     72 CTACAGATTCA-ACGCAATCCCTATCAAAATCC--CAGC--TGCCTTTTT 116

  chr2_139490260_   1014 TACAAAA--TGACCAGCTGATTC--AAATTCATTTTTAGAAATTCAAAAA 1059
                          i  i  --    v       i --        v --i     v   iii
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATAT--GGAAATGCAAGGG 164

  chr2_139490260_   1060 AACTCAGA---GTTAAAACAATCTGGAAAATGTTGA-------TAGAGA- 1098
                          - i    --- ii          v     v vv  ------- i   i-
  L1M4_orf2#LINE/    165 A-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_139490260_   1099 --TACAGTAGCTTATTCTAAGACTTGTTCTATAGCTACAATAGTTTAAAA 1146
                         --i   v vv iv   ii  i    ii vi v       i  i i-  i 
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC-AAGA 262

  chr2_139490260_   1147 AAAAGTGGTATAGGCATACGAATAAAAAAATAAATCAACTGAATAGAAT- 1195
                         v iv      iv      v i   i v v   i     iv         -
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_139490260_   1196 -ATGCTCTAGAACTAGAACCACATACAT--AGGATCAATTGATTTTCAAC 1242
                         - viv  i    v  -    -       -- v i             i  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATA-AACC-CATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_139490260_   1243 AAAA-CGCCAAGATAAT--ATTTGGGAAAAAA-AATATTTTTAACAAATA 1288
                           ii-i       iv  -- v v      i  - i v    i       i
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_139490260_   1289 GTGCTAGAACAACTGTATATTCATATGGGGAAAAAAATGAGCTTCACCCC 1338
                              i i       v   ?i  i   v--    i     iv  viv   
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGC--AAAAGAATGAAGTTGGACCC 458

  chr2_139490260_   1339 CCCATTTCATATTATACATGAAAATTATATCCCTGCCAAATGGATCAAAG 1388
                          i- ii   i ii   i ii       - ---  - v          ?  
  L1M4_orf2#LINE/    459 CT-ACCTCACACCATATACAAAAATTA-A---CT-CAAAATGGATCAWAG 502

  chr2_139490260_   1389 ACCTAAATATAGAAACTATAAATTTAAATTATCTAGAATAAAATACAGGA 1438
                                 i  ii i   v  v v    vivii     v    i i   ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_139490260_   1439 --AATTATCTTC----TCTAAAAATTTA--CAAATATTTATT-------- 1472
                         --  --      ----i  viii--   --   vvi   v  --------
  L1M4_orf2#LINE/    553 GTAA--ATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGATATGA 598

  chr2_139490260_   1473 CAACAGAAAACACTAACCATA----------TTGATAAATT-----TCAT 1507
                           v  -   i   v i v i ---------- v        -----    
  L1M4_orf2#LINE/    599 CACCA-AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_139490260_   1508 CAAATTTTAAAA-TCTTGTGCCTCAAA----------------------A 1534
                             v  v    - i      i     ---------------------- 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_139490260_   1535 GGCAAACCATTGTTTGGAATAAAACATTCTTAGTACATACGTACAACAAA 1584
                          i   v   iv vv   i v    i   ivi ivv    ii vii i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_139490260_   1585 GAACTTGTATCGAAAATATATTTTTTTTAA-----TCTGCTACACTTCAA 1629
                          i         v i       -------  -----   --    vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATAT-------AAAGAACTCT--TACAACTCAA 788

  chr2_139490260_   1630 TAGTAAAAA--TAACCAACC-AGTTTAAAAATGAGCAAAAGACTTGGACA 1676
                           i      --i  vi    - i  ?       i     i  i   i i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_139490260_   1677 AATACTTCACCATAAAA-ATATTAAGATAGCCAGTGAATATGTTAAAGAA 1725
                         i i i   v   v i  -    vv i  i    i i ii ii v   ii 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_139490260_   1726 TGCTCAAACTCATTAGTCAC 1745
                                vv   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (129 / 85)
Gap_init rate = 0.05 (42 / 887), avg. gap size = 3.02 (127 / 42)  


2777 27.15 1.43 1.21  chr2_139523166_139526511     1962  2867 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_139523166_   1962 TGGAAAAACATTCCATCTTCATGTATAGTAAGAATCAATATCATGAAAAT 2011
                               i i  i    v      v  v v    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139523166_   2012 GGCCATACTGCCCAAAGTAGTTTATGGATTCAATGCAATTCCCATCAAAT 2061
                            v     v      v ii i  ii       i     i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139523166_   2062 TAGCATTGACATTTTCCACAGAATTAGAAAAAACTAATTC-AAATTTTAT 2110
                          vv  vivi v    iii     v v  v  i-  i  i -   v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_139523166_   2111 GTAGAA-T-CAAAGAAGACCCCGCATAGCCAAGACAATCCTAAGCAAAAA 2158
                         i i   - -   i --     v v        i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_139523166_   2159 GAACAAAGCTGCAGGCGTTATGCTACCTGACTTCAAACTACACTACAAGG 2208
                                 i  v   vv i ii  v  ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_139523166_   2209 CTCCAATAAAAAAAACAGCATGATACTGGTACCAAAACAGACATAAAGAC 2258
                           v  i   vv  i    ii  i      i iv ii i       v   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_139523166_   2259 CAATGGAACAGAACAGAGGCCTTAGAAATAACACCAAAAATCTACAGTCA 2308
                                 i    iv   iviii        vv   v v  i  ii    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_139523166_   2309 TCTGATCTTCAACAAACCTGAACAAAACAAG-CAATGGTGAAAGGTGAAA 2357
                         vi    i   i    ivv  v-   i  v v-      v     ----  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAG----AA 392

  chr2_139523166_   2358 TGGTG----AAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGCAGAA 2403
                          i  v----v  i   i          v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_139523166_   2404 AACTGAAACTGGACCCCTTTCTTACACCTTATACAAAAACCAACTCAAGA 2453
                         i v    ii         vi  i     v          ii       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_139523166_   2454 TGAATTAAAGACTTACATGTAAAACTCAAAACCATAAAACCCT-AGAAAA 2502
                           i  i ?    i  v      i vii     i       i  -    i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_139523166_   2503 AATCCTAGGCA-ATACCATTCAGGATATAGGGATGGGCAAAGACTTCAT- 2550
                           v v    ?i- v i -   iv  iv v   v i     v ii   v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_139523166_   2551 GATGAAAATACCAAAAGCAATTGCAA-AAAAGCCAAAATTGACAAATGGG 2599
                            - vi i          vvv    -     vv     v  i    v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_139523166_   2600 ATCTAATTAAACTAAAGAGCTTCTACGCAGCAAAAGAAACTATCATCGGA 2649
                          ii v  i   v v  i i   i ii  vv    i  v       vvii 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_139523166_   2650 GTGAACAGGCAACCTACAGAATGGGAGATAATTTTTGCAATCTACCCATC 2699
                              v  i     i             v   v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_139523166_   2700 TGACGAAGGTCTAATATCCAGAATTTACAAGGAACTTAAACAAATTTATA 2749
                            ii i  v  vi          v  i  i     ivv    v iv   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_139523166_   2750 AGAAAAAAA-AAACAGCCCCTTCAAAAAGTAGGCAAAATATATGAATAGA 2798
                          v     i -   i i   vv i?    i i      iv  v        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_139523166_   2799 CACTTCTCAAAAGAAGACATTTACATGGCCAGCAAACACATGAAAAAAAA 2848
                           i     v        i  vi v       ii  i          i vi
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_139523166_   2849 CCTGAACATTACTGATCAT 2867
                          - v     i ????????
  L1M4_orf2#LINE/    891 C-TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (140 / 102)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.41 (24 / 17)  


3164 27.28 0.66 0.77  chr2_139528456_139534913.rev     5058  5966 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_139528456_   5058 TGGAAGAACTTTCCATGATCATGGATAGGAAGAATCAGTATCATGAAAAT 5107
                              ii iv i     v        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139528456_   5108 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5157
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139528456_   5158 TCCAAATGACTTTCTTTCCAGAA-TTGGAATAAACT-ACTTTAAAGTTCA 5205
                            v iivi i  i   v     -   -- i  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_139528456_   5206 TATGGAACCAAAAAAAGAACT--GCATACCCAAGACAATCCTAAGCAAAA 5253
                                -- viv  i i  i-- v   v    i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_139528456_   5254 AGGACAAAGCTATAGGCATCATGCTACCTGACTTCAAACTATGCTACAAG 5303
                           i      i iv   vv   ii  v  ii i      viv i      i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_139528456_   5304 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATGGA 5353
                                   i   i    ii         i iv ii i   i    i  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_139528456_   5354 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACTTCTACAACC 5403
                         i        i    iv   ivii         vv   i  v i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_139528456_   5404 ATCTGATCTTTGACAAAACTGACAAAAACAAGAAATTGGGAAAGGATTCC 5453
                          vi    i  i     iiv  v   i v  vvv   v       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_139528456_   5454 CTATTTAATAAATAGTGCTGGGAAAACTGGCCAGCCATATGTAGAAAGCT 5503
                           v  i  i    i         v      vi ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_139528456_   5504 GAAACTGGATCCCTTCCTTACACCATATACAAAAATTAACTCAAGATGGA 5553
                            ii    i    v   i                         i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_139528456_   5554 TTAAAGACTTAAATGTAAGACCTAATACCATAAACACCCC-AGAAGAAAA 5602
                          i ?    i           v    v  i     -  i i-         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chr2_139528456_   5603 CCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAAGACTTCATGACT 5651
                          v    ?i- v   -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_139528456_   5652 AAAACACCAAAAGAAATGACAACAAAAGCCAAAATAGACAAATGGGATCT 5701
                          vi          v vvii         vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_139528456_   5702 AATTAAAATAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5751
                         v  i     v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_139528456_   5752 ACAGGCAGCCTGGAGAATGGGAGAAAATCTTTGCAATCTACCCATCTGAC 5801
                          v  i  i  iiv               v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_139528456_   5802 AAAGGGCTAATATTCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5851
                           i  i  vi   i      v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_139528456_   5852 AAAAAATAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 5901
                            i -i   i     v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_139528456_   5902 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTC 5951
                              v        i  vi viii     i ii  i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_139528456_   5952 ATCATCACTGGCCAT 5966
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (155 / 89)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3468 17.60 12.64 0.37  chr2_139561039_139563165.rev      829  1635 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_139561039_    829 GAAAGACATCTCATGTTTATGAATTGGGTGACTTAGTATTGTTAAGATGA 878
                               i   i      i   i     iv      i             i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_139561039_    879 CAATACTATGCAGAGTGAGCTACAAATT-AATTCAACCCCTATAAAAATT 927
                                viv  i v   v     i   -  iv   i      v     i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_139561039_    928 TTAA--GCCATTTT-GCAGAACTGGAAAAGCCAAACCTCAAATTCATATG 974
                         ii i--   v    -      v v  v    ii v   v           
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_139561039_    975 GAATTTCAAGGGGTCTCGAATAGTCAACACAATCTTGAAAAATAAGAACA 1024
                            v v      ii iv      i   v              v       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_139561039_   1025 AAATTGGAGGAATCCCACTT---GATTTCAAAACTTTCTACAAAGCTACA 1071
                           i        v  v     ---i            v             
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_139561039_   1072 GTA-------------------------------GACAT----------- 1079
                            -------------------------------     -----------
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_139561039_   1080 ---------------------------CTC---------TAACCAATTGA 1093
                         --------------------------- i --------- iii       
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_139561039_   1094 TTTTTCAACAAGGGTGCCAAGTCCATTCAGTGGGGAAA---TAGTCTATT 1140
                             - i              v       i        ---      v  
  L1M4_orf2#LINE/    353 TTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_139561039_   1141 CAACAAATGCTGCTTGGACAACTAAATTTTCACAGGCAGAAGAATGAGGT 1190
                                  v    v        ii  v?i    v   i        i  
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_139561039_   1191 TGGACCCCTATCTCACACCATATTAAGAAAAAGAACTCAAAATAGATTAA 1240
                                   i            - vi    vv          i   i ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGATCAW 500

  chr2_139561039_   1241 TGAC-TAAATGTAAGAGTTAAAACCATAAAATTCTTAGAAGAAAATATAC 1289
                         v   -            i      i      i             i   v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_139561039_   1290 TGGTAAATCTTCATAATTTGGGATTTAGCAATGAGTTCTTAGACATGACA 1339
                         v?          i i ii v  i  vi      iv        i      
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_139561039_   1340 CCAAAAGCACAGGCAACAAAATAAAAAA---ATAAATTAAACTTCATCAA 1386
                                    i         v      ---       ii          
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_139561039_   1387 TATTAACA--TTTGACACATCAAAGGACACTATCAAGATATTAAAAAGAC 1434
                         v     v --   viii v                   v v i       
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_139561039_   1435 AACCTACAAAATTGGAGAAAGTATTTGACAAA-CATATATCTGATAAGAG 1483
                             i   i   v       i      -    -               i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTG-CAAATCATATATCTGATAAGGG 749

  chr2_139561039_   1484 TTTACTAGCCAGAGTGTATAAAGAACTCA-AAAATTTAACAACAAAGATA 1532
                         vi vv  v     i i            v- v  i i  i  i   i v 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_139561039_   1533 CAA----TTTGAT--AAAAATGAGCAAAATACTTGAATAGATAGCTTTCC 1576
                            ----iiii  --       i     iv i         i vi i   
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_139561039_   1577 AGAAAAGATATACTAATGGCCAATAAACACATGAAAAGATTCCCAACATC 1626
                          i i         v            i             v i       
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_139561039_   1627 ATTAATCAT 1635
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.53 (84 / 55)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 5.83 (105 / 18)  


2337 27.60 3.51 2.57  chr2_139603501_139609364.rev     4506  5360 (504)    L1M4_orf2#LINE/L1        1   863 (45)  

  chr2_139603501_   4506 TGGAAAATCATGCCATACTCATGGATAGGAAGAATCAATATCATTAAAAT 4555
                               ivi  v    ii        v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139603501_   4556 GGCCATAATGTCCAAAGCAATTTACAGATTCAATGGTAATCC-TATCAAA 4604
                            v   v vi     vii  i           i -i     -       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACG-CAATCCCTATCAAA 99

  chr2_139603501_   4605 CAACCAATTACATTCTTCATAGAACTAGAAAAAAACCTAGTTA-AAAATT 4653
                         vvv   ii i v  i  iii    v v  v  i---  ii iv-      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chr2_139603501_   4654 CACAGGGAACCAAAAAAGAGC-AGAATAGCCAAAGCCATCCTAAGCAATA 4702
                           i v    viiv  ii  v -            i v   i i iv  v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_139603501_   4703 AGAACATACATGAAGGTATCACACTACCCAACTTCAAACTATACTACAGA 4752
                               v vv  i   vv       v     i      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_139603501_   4753 GCTACAGTAAGCAAAATAGCATAGCACTTGT-TAAGAAAAAAAAAATGAC 4801
                                   v   i i  ii i i   v i-    i v -------   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-------GAC 289

  chr2_139603501_   4802 ACATAGACCAATGGAACAGAATAGAGAGCTTGAGCTCAGAAATAAGGCCC 4851
                          i     i        i     v     ii------         iv  v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTC------CAGAAATAAACCCA 333

  chr2_139603501_   4852 CACACCTACAACCATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATG 4901
                         i   ii  iiii  vi    i  i     i v  v   i v  vv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_139603501_   4902 TGGAAAGGAT--TCCTTATTCAATAAATGATGCTAGCATAACTGGCTAGT 4949
                         v      i  --  i  --    i     i    i v i      v  ?i
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_139603501_   4950 CATATGCAGAAGATTGAAACTAGACCCCT---TAACACCATATGCAAAAG 4996
                           i     i    v    ii i       --- v         i     i
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_139603501_   4997 CCAAATCAAAATGAATTAAAGACTT-----------C----ACTATAAAA 5031
                         ii  v        i  i ?    i ----------- ----         
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_139603501_   5032 ACACTGGAGGACAACCTAGGCAATACTGTTC-TGCACATAGGAACGAGCA 5080
                         vivi i  i  v   v    ?ivv v v   -  -  v v  iviii   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCA 580

  chr2_139603501_   5081 AAGATTTCAT-GATGAAGCTGCTAAAAGCAACTGCAACAAAAGCAAAAAT 5129
                          v i    v -   - v vii i       vvv          v      
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_139603501_   5130 TGACAAATGGAATCTAATTACACTTAAGAGCTTCTGCACAGTGAAAGAAA 5179
                         v  i    v i ii v  i v v    i i   i  ii vvii  i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_139603501_   5180 CTATCAAAAGAGTAAACAGGCAACCTACAGAGTGGGGGAAAAAAATTGCA 5229
                                i i   i  v  i     i     i    i     v v     
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_139603501_   5230 AACTGTGCATCTGAAAAAAGTCTAATATCCAGCATCTATAAAGGACTTAA 5279
                           iii ii      v  ii v  vi       v  v       i   ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_139603501_   5280 ACAAATTTACTAGTAAAAACCCAA----CTTTATTAAAAAGTGGGCAAAA 5325
                             -i i v  i      vv   ---- iiv   ?    i        i
  L1M4_orf2#LINE/    780 ACAA-CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_139603501_   5326 GATATGAACATATACTTTTCAAAAGAAGACATGCA 5360
                            v    i v i i  i  v        i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.02 (19 / 863), avg. gap size = 2.74 (52 / 19)  

1546 25.74 0.91 0.00  chr2_139603501_139609364.rev     5362  5800 (64)    L1M4_orf2#LINE/L1      466   908 (0)  

  chr2_139603501_   5362 ACACTCTGTGCAAAAATCAACTCAAAATGAATAAAAGAGCTAAATATAAA 5411
                             iv i i       i           i  v ?   v      i   i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_139603501_   5412 ACTTGAAACCACCATACTCCTACAAGAAAACACAGGGGAAAAGTTCCTTG 5461
                          vi i    i iv v    i  v         i   ? v   vi i v  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_139603501_   5462 GCATTGGCCTTGGCAATGATTT-TTAGATGTGACACCAAA-GCTCAGGCT 5509
                         i v    vi v       i   -      i          -  v  i  v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_139603501_   5510 ACAGAAACAAAAATATATAAATGGCACTACATCAAACTAAAAAGTTTCTG 5559
                            i  iv       v      v v   v       v v    ii  i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_139603501_   5560 CACAGCAAAGGAAACAATTAATAAAATTAAAAGGCAGCCTATGAACTGGG 5609
                         ii vv       v  v  i  v   i v     i  i  i iii v    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_139603501_   5610 AATAAATCACTGCAACT-GCACATTTGATAAAGGATTAATACCTAAAATT 5658
                          iv    vvi     v -ii i  i      i   i vi  i i i   v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_139603501_   5659 TATAAAGAACTC-AACAACTCAATAGAATAAAAACGAATAGCACAATTGA 5707
                                     -v           iv v   i  i    i v     ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_139603501_   5708 AATATGTGCAAAGGACCTGAGAAGATGTTTCTCTAAAGAAGACATAAAAA 5757
                           v   v        ii   iv   ii      i        i   v   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_139603501_   5758 TGGGCAACAGGTATTTGAAGAGATACTCAACATCGCTAATCAT 5800
                            v   i i i iv    i    i         i????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (65 / 45)
Gap_init rate = 0.01 (4 / 443), avg. gap size = 1.00 (4 / 4)  


 839 25.67 6.13 2.30  chr2_139677561_139680772.rev     1574  1834 (1378)    L1M4_orf2#LINE/L1        1   271 (637)  

  chr2_139677561_   1574 TGGAAAGATATTTTATGTTCATAGACTGGAAAAAATAATGTTGTGAAAAA 1623
                                    iii        i  i     i vv    i    v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr2_139677561_   1624 TGTCCACACTACCCAAAGTGATCTACAGAT----------CCCTATCAAA 1663
                           v v i   v      v            ----------          
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_139677561_   1664 ACTCCAATGGCATTTTTTCACAGAAATAGAAAAGTCAAATCTTTTAAATT 1713
                          ii   iiv  v      -i       v  v   - vi   -i v     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATC-CTAAAATT 146

  chr2_139677561_   1714 TGTCTGAAACCATGAAAAACCCCAAAGAGCGAAAACAATTTTGAGCAAAA 1763
                         ii v  i  viiii iii    vi  v   v        i    iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_139677561_   1764 AGAGGAAAGTTGGAGGCATCACACTCCCTGATTTCAAAATATATT----- 1808
                            iv           vv       i  ii         iv  i -----
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_139677561_   1809 -TTCCAGTGATTACAGATGGACATGGT 1834
                         -i v    i  i -   ii -ii    
  L1M4_orf2#LINE/    247 GCTACAGTAATCA-AGACAG-TGTGGT 271

Transitions / transversions = 1.79 (43 / 24)
Gap_init rate = 0.03 (8 / 271), avg. gap size = 2.75 (22 / 8)  

2383 25.44 1.60 1.89  chr2_139677561_139680772.rev     2039  2726 (486)    L1M4_orf2#LINE/L1      223   908 (0)  

  chr2_139677561_   2039 CCCTGTCTCAAAA---A--ACAAATGTGATTATAAT-AACACAGCATTGT 2082
                            vi i      --- --     - iv ivi    -  v    ii v  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAA-GCTACAGTAATCAAGACAGTGTGGT 271

  chr2_139677561_   2083 ACTGGTATAAAAACAGACACATTGGCCAATGGAATAGGATAGAAAACCCA 2132
                              i    ii i     i  v ii           i  v  i ii   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_139677561_   2133 GAAATAAACCCATGTACTTATGATTAATAGACTTTTGACATGAGTGTCAA 2182
                                      ii i     i i   v  i   i    v i   i   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_139677561_   2183 GAACACATAATGGGAAAAGGGACAATCTCTTCAA-AA--GGTGTTGGGAA 2229
                           v  ivi      i    i- i i   i     -  --    i     v
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_139677561_   2230 AACTGAATATTCACATGCAGAAGGACGATATTGGACTCTTTTCTCACACC 2279
                              i   ?i        i   i i  vi      i i vi        
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_139677561_   2280 TTATACAAAAATTAATTCAAAATGGATTAGACACTTAAATATAAGACCTG 2329
                         v              i           i ? v  i     i     v  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_139677561_   2330 AACCTGTAAAACTGCTAGGGAATTAAAAAAAAAAAACAGCGGAAAGTTCT 2379
                           v  i       -  -------  i  i    v vvi ? v   vi ii
  L1M4_orf2#LINE/    521 AAACTATAAAACT-CT-------TAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_139677561_   2380 ACAATATTTGTCTGGGCAATGATTTTTTGGCTATGACCACAATAGCTCAG 2429
                         iii iv  v vi i       i   i  i v      vv   v   v  i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_139677561_   2430 ACAACAAAAGCAAAAATAAACAAATGGAATGCTATCTAA-CCAAAAATAT 2478
                         i         v       i i    v i ivii   v  -ii     i- 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC-T 661

  chr2_139677561_   2479 TCGGCACAGCAAAAGAAACAATTAAGAA-GTGAAGAGACAATTTACAGAA 2527
                          iv ii vv    i  v  v  i     -     i      iii      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_139677561_   2528 TAAGAGAAAACATTTGCAAACCACACAACTTATAAGGGGTTAATATCCAA 2577
                          ii       i         i  i i v  v       ii vi      i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_139677561_   2578 TCTATACAATAAATTCAGACAATTCAATAACAAGAAAACAAATAACCCTA 2627
                         vv    i  vi  i  vv    i       i  i  i           v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_139677561_   2628 TTAAACGAGTTCAGCAAAGGACCTGAACAGACATATCTCAACAGAAGATG 2677
                           ?  vi -- vi        ii    i      v    v v       i
  L1M4_orf2#LINE/    812 TTWAAAAA--TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_139677561_   2678 TACAAATAGCCAATGGGTACATGGAAAAATGCTCAGAGTCACTAACCAT 2726
                                i      ii i     i   i       ivi   ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (116 / 55)
Gap_init rate = 0.02 (13 / 686), avg. gap size = 1.85 (24 / 13)  


2844 27.73 1.33 0.99  chr2_139696675_139699364.rev     1294  2198 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_139696675_   1294 TGGGAAAACATTCCATCTTCGTGGATAGGAAGAACCAATGTCATGAAAAT 1343
                            i  i i  i    v   i     v      vii   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139696675_   1344 GGCCATACTGCCCATAGTAATTTATACATTCAATGCTATTCCCA-CAAAA 1392
                            v     v    v v i  i  i v      i  v  i  i -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139696675_   1393 CTGCCATTGACATCCTTCACAGGATTAGAAAAAAACATTTTAAATTTCGT 1442
                         - v   vivi v ii  ii   i v v  v  ivvv  ii    v   i 
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_139696675_   1443 ACGGAATCAAAAAAGACCCTGTATAGTCAAGACAATCCTAAGCGAAAAGA 1492
                          i    viiv  ii     v v    i   i      i i ivi i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_139696675_   1493 ACAAAGCCGTAGACATCACCCTACCTGACTTCAAACTATACCAGAAGGCT 1542
                               ii v  ivv    v  v  ii i      viv   i v  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_139696675_   1543 ACAATAACCAAAACAGCATGGCACTGGTACCAAAACAGACATATAGACCA 1592
                            i   i   i    ii   i     i iv ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_139696675_   1593 ATGGAGCAGAACAGAGACCTCAGAAATAACACCACACATCTACGACCATC 1642
                              ii    iv    vii         vv   i    i  i ii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_139696675_   1643 TGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAATGATCTCCTA 1692
                             i  i     i v  v   i v  vv           vi  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_139696675_   1693 TTCAGCAAATGGTGCTGGGAAAACTGGCTAGCCATAAGCAGAAAACTGAA 1742
                             i               v      v  ?   i v   i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_139696675_   1743 ACTGGATCCCTTCCTTACACCGTATACAAAAATTAACTCAAGATGTATTA 1792
                         ii    i    v   i     i                   i   v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_139696675_   1793 AAGACTTAACTGTAAAACCCAAAACCATAAAAATCCTAGAAGAAAAC-TA 1841
                         ?    i   v     i v i     i      v  i           -  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_139696675_   1842 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTTATGACTAAAA 1890
                           ?i- v i -   iv   v v  vv i     v ii  iv iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_139696675_   1891 TACAAAAAGCAATTGCAACAAAAGCCAAAACTGACAAATGAGATCTAATT 1940
                         i  v       vvv          vv    iv  i    vi  ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_139696675_   1941 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 1990
                            v v  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_139696675_   1991 GCAACCTACAGAATGGGAGAAAATTTTTGCAACCTATCTGTCTGACAAAC 2040
                         i     i                 v       vii  v i     i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_139696675_   2041 ATCTAATATCCAGAATTTACAAGGAACT--TA-AATATATTTACAAGAAA 2087
                         iv  vi          v  i  i     --  -  ivi v v i  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_139696675_   2088 A-AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAA-AGATAATTCTT 2135
                          -   i     v  i?    i            v    -   i v    i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_139696675_   2136 AAAAAAAAAAGACATTTATACAA----CCAGCAAACGCATGAAAAATAGC 2181
                         v   i  i -------       ----   ii  i i        ivv  
  L1M4_orf2#LINE/    849 CAAAGAAGA-------TATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_139696675_   2182 TCAACATCACTGATGAT 2198
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.91 (21 / 11)  


2777 26.57 2.91 1.12  chr2_139839273_139841495.rev      840  1731 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_139839273_    840 TGGAAAAACATTCCATGCTCACGGATAGGAAGAATGAATATCATGAAAAT 889
                               i i  i     i   i    v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139839273_    890 GGCCATATGGCCCAACGTAATCTATAGATTCAATGCTTTTCCCATTAAAC 939
                            v   ivv     vv i     i        i  vv i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139839273_    940 TACCATTGACATTCTTCACAGAATTAGAAGAAACT-ATTCAAAAACTCAT 988
                          v   vivi v  i  ii     v v  v-  i  -  i v    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr2_139839273_    989 ATGGAACAAAAAAAGTGTTCATAGTCAAGCCAAACATAATC------AAA 1032
                               - viv  i viii  v i --       - i    ------  i
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAAT--AGCCAAA-ACAATCTTGAAAAAG 195

  chr2_139839273_   1033 AAGAACAAAGCTGGGGGCATCACACTACTGGACTTCAAACTGTACTACAA 1082
                                   i   i  vv       v ivi i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_139839273_   1083 GGCTGGAGAAACCAAAATAGCATAGTACTGGTACAAAAACAGAC------ 1126
                         i   iv  v  i   i i  ii i       i i  ii i    ------
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_139839273_   1127 --TAATGGAACAGAATAAAGAATTCAGAAG---ACC-ACACATCTACAAC 1170
                         --i       i     vi   i i     i---   - i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_139839273_   1171 CATCTGATCTTTGACAAACTTGACAAAAACAAGCAATAGGGAAAGGATTC 1220
                           vi    i  i     ivv  v   i v  vv    i       i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_139839273_   1221 CCTATTTAATAAAAGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAAC 1270
                         i  v  i  i   v          v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_139839273_   1271 TGAAACTGGACCCCTTTCTTACACCTTATACAATAATTAACTGAAAATGG 1320
                             ii         vi  i     v       v        v       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_139839273_   1321 ATTAAAGACTTAACTGTAAAACCCAAAACTATAAAAACCCTAGAAGAAAA 1370
                           i ?    i   v     i v i            vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_139839273_   1371 CCTAGGCA-ATACCATTCAGAACATAGGCATGGGCAAAGATTTCATGACG 1419
                          v    ?i- v i -   ivi  v v  vv i     v i    v i-- 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA--G 592

  chr2_139839273_   1420 AAAT--CACCAAAAGCAATTGAAACAAAACCCAAAATTGATAAATGGGAT 1467
                          v  --           vvv v       vvv     v       v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_139839273_   1468 CTAACTAAA--TAAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGA 1515
                         i v ii   --     i--   i  ii vv    i  v       vv i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_139839273_   1516 GAGAACGGGCAACTTACAGAGTGGGAGAAAACTTTTGCAATCTATGCATC 1565
                          v   vi i    ii     i          iv       vii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_139839273_   1566 TAACAAAAGTCTAATATCCAGAATCTGCAAGAAACTTAAAAAAATTTACA 1615
                          i i  ii v  vi          v ii  ii    ivv v  v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_139839273_   1616 AGAAAAAAATGAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGA 1665
                          v     i ii  i     v   ?    i           iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_139839273_   1666 CATTTCTCTAAAGAAGATATTCATGTGGCCAACAA--ACATGAAAAAAAT 1713
                                 i           v  vi       i  --         i vv
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_139839273_   1714 CTCAACATCACTGATAAT 1731
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (135 / 98)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.25 (36 / 16)  


1715 25.10 2.69 11.88  chr2_139847554_139849507      499  1466 (488)    L1M4_orf2#LINE/L1       30   908 (0)  

  chr2_139847554_    499 AAGATTCAACATAGTAAAGATGACAAT-TTCCCCAAATATATATATATAT 547
                             i i  i  v  v      i    -i         --- i-  v  i
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT---TG-ATCTAC 75

  chr2_139847554_    548 AGGTTTTAAATAATTCTTATCGAAATCTCA-CCAAGATTTTTGATGATAT 596
                           i  iv vii   i i    i     i  - iivvv      vv  v  
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr2_139847554_    597 AGAAAATATAATTCTAAAATTTATATTAAAAGACAAAGAAGCTTTAATAG 646
                         v  v  vv i  i        i    vi   vi   i i v ivv     
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr2_139847554_    647 CTAAAACAATTTTGAAAAAAAAGAAAAAAAATCAAGTGGGAGGAATC--- 693
                          i        i        i     v   ------  v      v  ---
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAA------GTTGGAGGACTCACA 219

  chr2_139847554_    694 CTTC--GACCT-AAGATGCATTTTATAGCTACACTAATCAAGACTATGTA 740
                             --i ii -  i ivi i vi v       v          vi   i
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_139847554_    741 GTATTAGTGGAATGAAATACACAGAGACAAATGGAGTGAAACAGAGAATG 790
                            i i iiv  v  v v   i v   iv      i ii  iv    i v
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_139847554_    791 CAGAAATACAGTATATTTCCATATATATATACCCAATTAATTTATATATA 840
                                 -------------------- -     ---------------
  L1M4_orf2#LINE/    320 CAGAAATA--------------------A-ACCCA--------------- 333

  chr2_139847554_    841 TATACACCCAATTAATTTATATATATATATATACACCCAATTAATTTTTG 890
                         --    ---------     i---------i -----     i     i 
  L1M4_orf2#LINE/    334 --TACA---------TTTATG---------GT-----CAATTGATTTTCG 358

  chr2_139847554_    891 ACAGAGATGCAGAAGTACTTCAATGGAGAAAAGACAACCTTTTCAGCAAA 940
                            ii i   vi iiivv        i    ii i ii       i    
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_139847554_    941 TGATGCTGGAATAATTGGACATCCATAGGCAAAACAAACAAAAAGACCTT 990
                           i      i i  i    i ?   i v      -i  ii  i-----  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAAG-----TT 452

  chr2_139847554_    991 GGGAGAAGTCTCATGCTTTATATGTAAAAACAAAACAAAACAAAACAAAC 1040
                           i------ i v i i i i i-----------------  ---i v  
  L1M4_orf2#LINE/    453 GGA------CCCCTACCTCACAC-----------------CA---TATAC 476

  chr2_139847554_   1041 AAAAAACAAAAACCTCCAAATAAATTCATGGACTTCAATGTAAAATATAA 1090
                              vi  ----   v    ii  -  ?i   i v       i vv   
  L1M4_orf2#LINE/    477 AAAAATTAA----CTCAAAATGGAT-CAWAGACCTAAATGTAAGAGCTAA 521

  chr2_139847554_   1091 AACTAAAATAGTTTTGATTTAAAAAAAAACCCTAGAAGAAAATATTCAGG 1140
                              v  v v i  ----- i  i     v-   i? v    v   iv 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTT-----AGAAGAAAACA-TAGGNGTAAATCTTCGTG 565

  chr2_139847554_   1141 ATCTAGAGGTTGGCA--GAGTTCTTAGCCTTGGTACTAAAAGCACAATT- 1187
                          i  v i v v    -- iv       viv  ii  i          vi-
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_139847554_   1188 -CATGAGAAAAAGTTGAACAATTGAACTTGATGAAAATTAAAAACTTTTA 1236
                         -  vi       i v  vv     i    v  v                i
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_139847554_   1237 CTCTGTTAAAGCCCCCATTAATGG-GTGAAAA-------CACAGAGTGGG 1278
                         iv  viv  i v v i  i  vii-       -------      i    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_139847554_   1279 TAAAAATTCTTGCAAAGTACATATCTGACAAAAAGCTAGTGTGCAGAATA 1328
                         vi     vi       vi i        i  iiii  v  i v       
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_139847554_   1329 TATTAACTGCTCTTAAAAGTCAATGGGAAAATAACAA----TCTGATTAG 1374
                            v  vvi      v  v     iiv    vi    ----i ii   ?i
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_139847554_   1375 AAAATGGGCCAAAGATATGAAGAGAAATTTCATTGGTGAAAATACACAGA 1424
                                  v  i   v    v   v     viiiiv   i   i   i 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_139847554_   1425 TA--TAATTAAGCACATGAAAAAATGTTCAACCTTATAAGCCAT 1466
                          i--i   -             i   i     v i ????????
  L1M4_orf2#LINE/    866 TGGCCAAT-AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (147 / 92)
Gap_init rate = 0.03 (30 / 879), avg. gap size = 4.70 (141 / 30)  


2285 28.52 4.89 0.72  chr2_139873392_139878751     3682  4519 (840)    L1M4_orf2#LINE/L1        1   873 (35)  

  chr2_139873392_   3682 TGGAAACACATCCCATGTTCATGGATGTGTAGCATCAATATTGTGAAAAT 3731
                               v i                 vv v  vv i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139873392_   3732 GATCTTACTGCCAAAAGCAATCTGCAAATTCAATGTAATTCCCATCAAAA 3781
                          iivv    v  v   vii    i  i      i i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139873392_   3782 TACCACCATCATTCTTAACAGAACTAAAAGAAAACAATCCTAAAATTCAT 3831
                          v   v vv v  i  vi     v vi v-  ivii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr2_139873392_   3832 ATGGAACCAAAAAAGAGCCCATACAGCCAAAGCAAGACTAAGCAAAAAGA 3881
                               viiv  ii  v  viv i       i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_139873392_   3882 ACAAATCTGGAGGCATCACGTTGCCTAATTT--AAACTCTACTATAAGAC 3929
                              vi      vv    ii v  i     --     -     i  ii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_139873392_   3930 CATAGTCACCAAAATAGCATGGTACTGGTATGAAAATAGCCACATAGACC 3979
                         i i   v i   i i  ii         i  i ii    v  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_139873392_   3980 AATGGAACAGAATAGAGAACCCAGAAATAAAGCAAAATACTTACAGCCAA 4029
                                i     v    ii           v v v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_139873392_   4030 CTGATCTTTGACATAGCAAACAAAAACAA---AGTCAGGAAAGGACACCA 4076
                         i    i  i    -  vivi v  i  v --- i vi      i i viv
  L1M4_orf2#LINE/    349 TTGATTTTCGACA-AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_139873392_   4077 TATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGAAAAATG 4126
                          v                    i  i   vv ?       i i  i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_139873392_   4127 GAACTGAATCCTCATCTCTCACCTTATA-AAAAATCAACTCAAGATGGAT 4175
                         i ii  i i  ii i   v    v    -      i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_139873392_   4176 CAAGGACTTACACCTAAGACATGAAACCATTAAAATTCT-AGAAAATAAC 4224
                           ?i   i  v iv     vv i    i  -    i   -    i v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAAC 546

  chr2_139873392_   4225 ATCAGGA--AAACCTTTCTAAACATTGGCTTGGGTGAAGACTTCATGACC 4272
                           -   ?--   i   iv i v -    v  i  ii v ii   v iivi
  L1M4_orf2#LINE/    547 AT-AGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_139873392_   4273 AAGAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGAACTT 4322
                          v  vv         v v         iv   i   i   i  v i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_139873392_   4323 AATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACAATCAGTACAGTAA 4372
                         v  i   v v    i   i  ii vv    i  v  v    iv v   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_139873392_   4373 A----CAATCCACTGAGTTGGAGAAAATCTTCACAATCTATACATCCAAC 4418
                          ----   i    v  i v         v  ii   vii   i   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_139873392_   4419 GACAAACTAATATCCAAAATCTACAAGGAATTTAAACAAATCAGCAA--- 4465
                         i vii   vi      i   v  i  i   i ivv    v   ii  ---
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_139873392_   4466 ---GACA--TGAC-------------GGACA-------TGAATAGACAAT 4490
                         ---    -- i  -------------  i  -------          v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_139873392_   4491 ACTAAAAAGAAAATATAAAAACAGCCAGT 4519
                         v  vv      i     v   ii    i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAAT 873

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.02 (16 / 873), avg. gap size = 2.94 (47 / 16)  

 211 16.95 0.00 0.00  chr2_139873392_139878751     4810  4868 (491)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr2_139873392_   4810 AAACAAAACAAAAAAATGGCCAAAGAACATATGAAAAAATGCTCAACATC 4859
                            v  i i v v          vi i  i       i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_139873392_   4860 ACTAATGAT 4868
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.50 (6 / 4)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


1914 25.57 7.39 4.20  chr2_139982667_139984715.rev      678  1557 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_139982667_    678 TGGAGAGACATG--GTATTCATGAATTGGAAGACCAAAAATTAATAAA-- 723
                             i   i  v--i i      i          iv  v   iv   i--
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139982667_    724 GACATGCATTCTACCCAAAATGATATACAGTTTTAATGTAACTCCTATCA 773
                          i  ---  v  v      v    v     v  i  i i  ii       
  L1M4_orf2#LINE/     51 GGCA---ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_139982667_    774 AATTCC-----------TTTG--GATATGAACAAGACTG-TTTTAAAATT 809
                           v   -----------    --  v  vi     -   - ii       
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chr2_139982667_    810 TATATGGAAATATACAAAAT--AGAAAAGCCAACAAAAG--TGAAAAAGA 855
                         i          ii viii i--    v      v v  v--         
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_139982667_    856 GGAATAAAATAGGAAGACTCTGTCTACCTAATTTCAAGAGGTATAATATA 905
                         i   i   i v   i     vvv  v  i        i vv  iv i v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_139982667_    906 GCAACAGCAGTCAAGACTGCAGGATATTTGTGCAGAGACAAACACACAGA 955
                           v    i i       v iiv i  i v iii ii  i i   i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_139982667_    956 TAAATTGAACAGCACACAGGAACCAGAAATAGACCAATACAAACATGCCC 1005
                          v   v   i  v ivv  iiv         i   v     vvi   vi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_139982667_   1006 AAAACAAATTT--GACAAAAGT------ACAATTCAATTGAGGAAAGA-T 1046
                           --ivi    --     ii  ------  v       - i       - 
  L1M4_orf2#LINE/    347 AA--TTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAAT 393

  chr2_139982667_   1047 AGA--TTTCAACAAATAGTGCTAGAGCAAGTGGATATCCATAGACAAAGA 1094
                           v--           i     i ii   v      ?   i vi    --
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-- 441

  chr2_139982667_   1095 AGAAGAAAAAAAGAAGCTTGG---TCTAAGTCTCACATTTCAAGCAAAAA 1141
                         ------- i  v    -    ---i   --i      iivi vi      
  L1M4_orf2#LINE/    442 -------AGAATGAAG-TTGGACCCCTA--CCTCACACCATATACAAAAA 481

  chr2_139982667_   1142 TTAACTGAAAATGGAGAACAGACTTATATTCAAGATGTAAAACTGTAAGC 1191
                               v        vv ?    i  v  vi    vv       i   iv
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_139982667_   1192 C-----AAAGCAAA-ATAGGAAAAAATTTTCAGAATCTAAGGCTAGAAAA 1235
                          -----i   v   -     ?iv    i   ivi i  vi  i   iv  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_139982667_   1236 AAGGC-----------ACACCAAAAGCACAATCTATATAAGTGAAACTAA 1274
                         vi vi-----------               v v i v   vi   v  i
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_139982667_   1275 ATCAATTGTACTTTATCAAAATTAAAAATATTTTGCTCTGTCTGTAAAAA 1324
                           v     v    i              i-     ---  -  vi   ii
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAAC-TTTTG---TG-CTTCAAAGG 676

  chr2_139982667_   1325 AATAAATACACAAATCCCTTAAGAGGATGAAAAGATAAGCTATAGAGTAG 1374
                          -------   v ----- i    iii        i  v i i   i i 
  L1M4_orf2#LINE/    677 A-------CACTA-----TCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_139982667_   1375 GAAAAAATATTTGTTAACCACATGTATGACAAAGGTCTAGTATCTAGAAT 1424
                           i          iv  i  i  i v   i  i  v  v     i     
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_139982667_   1425 ATATACACA-CTCTCAAAACTAAA-GTTAAAAAAATTGGATAAT------ 1466
                              v v -    i v    v  -iv      i i-ii    i------
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATT 813

  chr2_139982667_   1467 --AAAATGGG-AAAAGACATAAAGAGATATTTTACTGAA-AGCATACACG 1512
                         --        -   i  iv i  v   i    iv ii  - iv   i  i
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_139982667_   1513 AATGGCAAAAATGTACATAAAAAGATATTCAACATCATTATCACT 1557
                               v  v v i    i       ii         ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (133 / 89)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.09 (102 / 33)  


2326 28.45 3.87 0.73  chr2_139988485_139992029     2220  3045 (500)    L1M4_orf2#LINE/L1        1   852 (56)  

  chr2_139988485_   2220 TGAAAAAACATTCCATGCTCATGGATAGAAAGAATCAATATCGTGAAAAT 2269
                           i   i i  i     i        v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_139988485_   2270 GGCCATACTGCCCAAAGTGATTTATAGATTTAATGCTATTCCCATGAAAC 2319
                            v     v      v    i  i     i  i  v  i  i  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_139988485_   2320 TACTATTGACATTCTTTACAGAATTAGAAAAAACT-ACTTTAAAATTCAT 2368
                          v i vivi v  i   i     v v  v  i-  - iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_139988485_   2369 ATGGAAGCAAAAAAGACCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 2418
                               iiiv  ii     viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_139988485_   2419 ACAAAGCTGGAGGCATCATGGTACCTAACTTCAAACTACACTACAAGGTA 2468
                               i      vv   iiv v  i  i      vivi       i iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_139988485_   2469 ACAGTAACCAAAACAGTGTAGTACTGGTACAAAAACA--CACATAGACCA 2516
                                i   i       i       i i  ii i --  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_139988485_   2517 ATGGAACAGAATAGAGATCTCGGAAATAAGACCACACATCTACAACCATC 2566
                               i     v    vii i       iv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_139988485_   2567 TGATCTTTGACAAACTTGACCAAACAAGT-AATAGGGAAAGGATTTCCTA 2615
                             i  i     ivv  v v i  v v -   i       i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_139988485_   2616 TTTAATAAATGGTGCTAGGAAAACTGACTAGTCATATGCAGAAAATTGAA 2665
                           i  i          i   v     iv  ?i  i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_139988485_   2666 ACTGGATCCTTTCTTTACACCTTATACAAAAGTTAACTCAAGGTGGATTA 2715
                         ii    i  i v i i     v         i         ii     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_139988485_   2716 AAGACTTAAA------ATCCAAAACTATAAAACCCT-AGAAGAAAATCTA 2758
                         ?    i    ------ v i             i  -         iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_139988485_   2759 GGCAACACTATTCAGGACATAAGCGCAGGGAAATATTTCAT-GATAAAAA 2807
                           ?ivv v v   iv   v vi vvi   v  vvi    v -    vi -
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA- 598

  chr2_139988485_   2808 TATCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTAATT 2857
                         i i        vvv          v      v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_139988485_   2858 GAACTAAAGAGCTTCTGCAC--------ACACACACACACACACACACAC 2899
                         i  v v  i i   i  ii --------    vvv  viv viiiv v v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_139988485_   2900 ACACACACACACAA--ACACAAACTATT-----ATCAGAG---TGAACAG 2939
                            -  v    v  --iv v   v    -----    v v---   vv  
  L1M4_orf2#LINE/    699 ACA-ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_139988485_   2940 AAATCCTGCAGATCCAGAATCTATAAGGAGCTTAAACAAATTTACGAGAA 2989
                         ii - i  i --        v     i  i  ivv    v iv ii v  
  L1M4_orf2#LINE/    748 GGA-CTTGTA--TCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_139988485_   2990 AAAAA--AACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACT 3037
                            i --  i     v   ?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_139988485_   3038 TCTCAAAA 3045
                             v   
  L1M4_orf2#LINE/    845 TCTCCAAA 852

Transitions / transversions = 1.38 (134 / 97)
Gap_init rate = 0.02 (16 / 852), avg. gap size = 2.38 (38 / 16)  


 582 27.56 1.28 0.00  chr2_140005457_140007168.rev       11   166 (1546)    L1M4_orf2#LINE/L1      292   449 (459)  

  chr2_140005457_     11 ATAGATCAATTGAACCAAACTGAGAGTCCAGAAATAGAACCATATACAGC 60
                                   v   ivi  i                i v     i ivvv
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_140005457_     61 CAGTCAATTTATTTTTAATGAAAGCAGCAAGGTAATTTAATGAGGAAAGA 110
                         ii       v     ii ii ii iiv    iiv   i    i       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_140005457_    111 AAAGTCTTTTCAACAGA--GTCCTGGAACAACTAGAAAGCTCTGTGAAAA 158
                          v             i --  v    i      i  v ? ivii  v   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_140005457_    159 ATAATAAA 166
                          v   i  
  L1M4_orf2#LINE/    442 AGAATGAA 449

Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.01 (1 / 158), avg. gap size = 2.00 (2 / 1)  

 587 27.93 1.12 0.56  chr2_140005457_140007168.rev      171   349 (1363)  C L1M4_orf2#LINE/L1   (728)   180     1  

C chr2_140005457_    349 TGGAAACACATCCCATGGTCATGGATGGGTAGAATCGATATTGTAAAAAT 300
                               v i        v        v  v   v ii       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_140005457_    299 GACCATACTGCCAAAAGCAGTCTACAAATTCAATGCAATTCCCACCAAAA 250
                          i v     v  v   viii      i      i     i  i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_140005457_    249 TACCA-CCATCATTTTCACAGAACTAGGAAAAATAATCTTATAGTTCATA 201
                          v   - iii v    ii     v v iv  iv i   i  v i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr2_140005457_    200 TCAAACCAATAAAGAGCCCA-CATAGCCAAA 171
                          vi  vi-ii  i ii    -v         
  L1M4_orf2#LINE/    151 TGGAAAT-GCAAGGGACCCAGAATAGCCAAA 180

Transitions / transversions = 1.50 (30 / 20)
Gap_init rate = 0.02 (3 / 180), avg. gap size = 1.00 (3 / 3)  

2446 26.86 0.55 0.41  chr2_140005457_140007168.rev      495  1220 (492)    L1M4_orf2#LINE/L1      182   908 (0)  

  chr2_140005457_    495 CAA-CTTGCAAAA--AGAACAAATCTGGAGGCATCACATTAACTGATTTC 541
                            -    v    --        vi      vv     i vv ii     
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_140005457_    542 AAACTATACTATAAGGCCATAGTCAACAAAACAGCATGGTACTGGCATAA 591
                            viv     i  i  i i   v v   i    ii              
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_140005457_    592 AAATAGGCTCATAGATCAATGGAACAGAATAGAGAACAGAGAAATAAAAG 641
                         ii    i vi              i     v    iivv         v-
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC- 330

  chr2_140005457_    642 CCAAATACTTACAGCCAACTAATCTTTGACAAAGCAAACAAAAACATAAA 691
                            v i i   ii i   i i  i  i     i vviv   i v   vv 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_140005457_    692 GTGGGGAAAGGACACCCTATTCAACAAATGGGGCTGGGATAATTGGCTAG 741
                         i         i i vi  v            v       i  i   v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_140005457_    742 CCACATGTAGGAGAATGAAGCTGGATTCTCATTTCTCGCCTTATACAAAA 791
                                i ii         i    ii ii ii  v i  v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_140005457_    792 ATCAACTCAAGATGGATCAAGGATTTAAATCTAAGACATGAAACTATAAC 841
                           i       i        ?i  ii     v     vv i         v
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_140005457_    842 AATTTTTGAAGATAACATCAGAA-AAATCCTTCTAGACATTGGTTTAGGC 890
                          v i  v     v     vi ?i-     -   vv   v    v      
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGC 579

  chr2_140005457_    891 AAATATTTTATAACAAAGAACTCAAAAGTGGATGTAACAAAAACAAAGAT 940
                           vvi   iv  ivv v  vvi      iiv v i       iv   i  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_140005457_    941 ACATAGGTGGGACTTAATTAAACTAAAGAGCTTGTGCACAGCAAAAGGAA 990
                          v   ii v      v  i   v v  i i   v  ii vv    i iv 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_140005457_    991 CAGTCAGCAGAGTAAACAGACAAACCTCAGAGTGGGAGAAAATCTTCACA 1040
                          vi   iv i   i  v      v  v    i           v  ii  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_140005457_   1041 ATCTACACATCTGATAAAGGACGAATATCAAAAATCTACCCAAAACTCAA 1090
                          vii i i         i    vvi    v i   v  ivv i     vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_140005457_   1091 ACAAATTAGCAAGAAAAAAAACAAACAATCCCATCTAAAAGTGGGCTAAG 1140
                             v i ii  v     i -    i  i  v  i?    i     v   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_140005457_   1141 GACATGAATAGACAATTCTCAAAAGATGATATGCAAATGGACAACAGGTA 1190
                           iv          v     v     v     i       v   i i i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_140005457_   1191 TCTGAAAAAATGCTCAACATCACTAATGAT 1220
                         iv      i             ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (106 / 85)
Gap_init rate = 0.01 (6 / 727), avg. gap size = 1.17 (7 / 6)  


2622 26.84 1.40 1.75  chr2_140042622_140044408.rev      439  1295 (492)    L1M4_orf2#LINE/L1       55   908 (0)  

  chr2_140042622_    439 ACACTGCCCAAAACAATCTGTAGTTTCGATGTAATCCATATCAAAATAAC 488
                          i   v      vii    ii  v   i i i     v         vv 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_140042622_    489 AA-TGTTATTTTTCACAGAAATAGAAAAACTTAGCCTACAATTTGTATAA 537
                          i-  ii-     ii       v  v  i  v v    v    ii   ii
  L1M4_orf2#LINE/    105 AGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_140042622_    538 AA--GCAAAAAAAAAAAAAAAAGCCAGAATATACAGAGCAATCTTGAGCA 585
                           --    iii v----------        vv  i i         iv 
  L1M4_orf2#LINE/    154 AAATGCAAGGGAC----------CCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_140042622_    586 AAAAGAACAAAGCTGAAAACATTACACTACTTGATTTTAAAATATATAAC 635
                          i          i  i iivv i     v iii    i    iv  iv  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_140042622_    636 AAACCTATCGTAACCAAAACTGCATGATA-TGATATAAAAATAGAGATAT 684
                            v   iv    i   i  v ii  i  -  ii    ii     v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_140042622_    685 AGACCAATGGAGCAGAATTGAGAACATACAAACAAATACATATATATTAT 734
                            i       ii          iivi v   i   iv    i  -    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-TTAT 342

  chr2_140042622_    735 AGCAAACTTCTCTTTGACAAAGACATCAAGAACATACAGTAGC-AAAGGA 783
                         i iv  i vv i  i     i iiii     v   v  i i v-    i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_140042622_    784 TACCATCTTCAATAAACGGTGCTGGGAAAATTAGATATCTATATGCAGAA 833
                           viv i     i   i          v  i i    ? i i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_140042622_    834 GAATGAAACTGGACCCATATCCCTCACTATATACAAAAATTAATTCACAA 883
                                ii       v  i i v   i               i   v  
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_140042622_    884 TGGATTAGTTACATAAATGGTAAGACCTCAAAATATAAAACTACTAGAAA 933
                              i ?vv  v      -     v  v   v         vi     i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATG-TAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_140042622_    934 AAAA--TAGGGAAAACACTTCAGGAGATTGGTCTAGGTAA--ATATTTTA 979
                             --    ?iv  vv    iv  vv    vi    i  --i v i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_140042622_    980 CGGCTAACACCTCAAAAGCACAGACAACTCAAACAAAAATAGACAAATGG 1029
                         vivv i     --         ii    vv  iv         i    v 
  L1M4_orf2#LINE/    592 GATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_140042622_   1030 GACTATATTAAACTAAAAAGCTTCTGCACAGCAAAGAAAAAAATCAACA- 1078
                             vi  i   v v    i   i  ii vv     i v vv     v -
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_140042622_   1079 -GTAAAGAAACAACCTGTAGAATGGGAGAAAATATTTTCAAACTATTCAT 1127
                         -  i  i i      iii                   v    ii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_140042622_   1128 CCAACAATGGACTAATATCTAGAATACATAAGAAACTCAAACAACTCAGC 1177
                          ii i  v     vi    i      i    ii     vv        ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_140042622_   1178 AATAGAAAATAAAACAATCTCATT-AAAAATGGGCAAAGGACATGAATAG 1226
                             i   ivv   i  i iv   -                iv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_140042622_   1227 ATAATTTTCAAAACTAAACATGCAAATGTCCAACAGGTTTATGAAAAAAT 1276
                          i v  i  v   vv i i  i      v    i i ivi       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_140042622_   1277 GCTCAATATCACTAATCAT 1295
                               i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (141 / 86)
Gap_init rate = 0.02 (13 / 854), avg. gap size = 2.08 (27 / 13)  


1708 28.54 3.33 5.90  chr2_140073433_140076021.rev     1179  2110 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_140073433_   1179 TGGAAGCAAATGCGATGTTCACAGGTTAGAAGATTCAAAACTATAAAGAT 1228
                              iv v  v v       ii i  i     i i  v i i v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_140073433_   1229 AGCAACTCTCCATCAGATTTATCTATAAAGTCAAGGCAGTCTTAATCAAA 1278
                         i    iv    -i  i   v     i i v    v   i  iiv      
  L1M4_orf2#LINE/     51 GGCAATACTCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_140073433_   1279 ATCTC-TCCATTATTTTCTTACAAATTTACAAGCTTATTTTGAAACTTAC 1327
                            i -v iiiiv    ivi v     v       v  ii i   i i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_140073433_   1328 ATTGCAATACAAAGAGCTAAGAATAGCCAAGACAATCTTGAA------GA 1371
                           v v   i   i ii iv           i           ------  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_140073433_   1372 ACAAAGCCAGGGCACTTATGCTTCCAGAAATCAAAACTTGTCATGAAACT 1421
                               iii i v   i ii     vi vv         iii ii  i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_140073433_   1422 ACAGTAATTTAGATAATATTATGTTGGTACATAGAAAGTCCAATAGACAG 1471
                                 iv   i i i vi ii   --    -- i ----       v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGG--CATA--AGG----ATAGACAT 291

  chr2_140073433_   1472 A-AGA--AATGGGG-AGAA--AAGAGACCTGATTCAATGCAGATTCACAC 1515
                          -   --     ii-    --i    v  v  ---   -- i ii  i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGA---AAT--AAACCCATAC 336

  chr2_140073433_   1516 AAATATAATAATTTGCTTTATAACAAAGTTGCTTGCTTTATAACACTGCA 1565
                          vv   ii v v   v   vii    i v   i--------  v  --  
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCC--------AAGAC--CA 376

  chr2_140073433_   1566 GTGCATAAGACAAAGAA--GGCCTTTCAATAAATGATGCTAATGTA-TTA 1612
                         v vv  ii i-      -- v i      i     i    iivii -i i
  L1M4_orf2#LINE/    377 TTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_140073433_   1613 GAGTTTCCATATGGGAAAAAAAAATTGAAACTTTACCTCTACCTCACACC 1662
                           - v?   i   vi   i  ----    ii vv   i            
  L1M4_orf2#LINE/    426 GA-TAKCCACATGCAAAAGAA----TGAAGTTGGACCCCTACCTCACACC 470

  chr2_140073433_   1663 ACAGATAAAAACCAGTTCCAGATGGATTACAGATCTAAATATAAATGTTA 1712
                          i v i     ii ii  v i      i ?   i      i   iv i  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_140073433_   1713 AAATAATTAGCTATTTGGACAAAAACA--GTAATAATATCACGGTAGTTC 1760
                            iv  v ivivi  i  vi      -- v?i   -   viv  iiiii
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCT 569

  chr2_140073433_   1761 TGAAGAAAGCAA-AGTTT-TAAAAAATGAAACACAAGAAGAACTACCTAT 1808
                           iivv i    -i    - v i v    --   v i   v  v v v i
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGA--CACCAAAAGCACAAGCAAC 617

  chr2_140073433_   1809 ACTGGAAAATATTGGTGAAATGAAATTTATTAAAAATGAAAACTTA---G 1855
                          vvi     v  v i i  v  i v  i  i    v i       v--- 
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_140073433_   1856 ATTAAAATAAAATGAAATCAAAAGTTTCAGAGAATGAAAATACAGGCCAC 1905
                         v  v   vi v iv --    --------  i i      v   iv    
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTA--TCAA--------GAAAGTGAAAAGACAACCCAC 707

  chr2_140073433_   1906 AGAGTTATGATGGA---TATTTTCAAAACATATATGCCACAGTGAACTCA 1952
                            ---   ivi  ---     v    v       viv i iv i   ii
  L1M4_orf2#LINE/    708 AGA---ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_140073433_   1953 CATCCAGGATATTCAAAGAACTTTTACAGATCTATAG-AAAAAG-TAAA- 1999
                         i      i    vi        i     iv  v   i-      -i   -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_140073433_   2000 GACTCAAAAGAAAAATTGGCCAAAACTTTTG--CAGACACTTTTCAAAAG 2047
                         i  i   vv?      v   -   ivv    --i     i  i  v    
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGC-AAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_140073433_   2048 AAGATATTCAAATAATTATTAAATATATGGAAAAGATCCTCATGCATAGA 2097
                                v     iiii v   ii i   -       v    ------- 
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTCA-------A 895

  chr2_140073433_   2098 CACCAGAGAAATG 2110
                           i  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (163 / 99)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 2.39 (86 / 36)  


2950 26.42 2.23 1.00  chr2_140089490_140093961     3084  3980 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_140089490_   3084 TGAAAAAACATTCCATGTTTATGGATAGGAAGAATCAATATCATTAAAGT 3133
                           i   i i  i       i      v      v i     ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_140089490_   3134 GGCTATACTTCCCAAAGCAAT-TACAAATTCAATGCTATTCCTATGAAAC 3182
                            v     i      vii  -    i      i  v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_140089490_   3183 TACCAACAACATTATTTACAGAACTAGAAAAAATTACTTTAAAATTTATA 3232
                          v   i vi v  v   i     v v  v  iv v iii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_140089490_   3233 TGGATTCAAAAGCAAG----CCTGAATAGCCAAGGCAATCCTAAGCAAAA 3278
                             ----  v     ----  v          ii     i i iv  i 
  L1M4_orf2#LINE/    151 TGGA----AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_140089490_   3279 AGAACAAAGCTGGAGGCATCACACTAACTGACTTTA-----TATTACAAG 3323
                                  i      vv       vv ii i  i -----  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_140089490_   3324 GCTACAGTGACTAAAACAGCGTGGTACTGGTACAAAAACAGAAATATAGA 3373
                                 i ii  i    i          i i  ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_140089490_   3374 CCAATGGAACAGAATAGAGAGCCCAGGAATAAGACTGCACATACACAACT 3423
                         i        i     v     i    i     iv iii    vi iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_140089490_   3424 ATCTGATATTTGACAAAGCTAACAAAGACAAACAATGGGAAAA--ATGCT 3471
                          vi    v  i     i v iv   iiv  vv       i   --  iv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_140089490_   3472 CCCTATTCAATAAATGGTGTTAGAAAAATTGGATAGCCATATGCAGAAGA 3521
                          -- v     i        i i i v  i      ?   i     i    
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_140089490_   3522 TTGAAGCTGGATCCCTTCCTTATGCCATATACAAAAATCAACACAAGATG 3571
                         v     i    i    v   i ii              i   v   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_140089490_   3572 GCTTAAAGACTTAAACTTAAAACCCAAAACTATAAAAACCCTGGAAGACA 3621
                          v i ?    i    iv   i v i            vi i i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_140089490_   3622 ACCCAGGCA-ATACCATCCTGGACATAGGAATAGGCAAAGATTTCATGAC 3670
                           vi   ?i- v i v  v  -  v v  iv       v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_140089490_   3671 AAAGACACCAAAA--ACAATTACAACAAAAACAAACATTGACAAATGGGA 3718
                         v v          --    --i        iv   v  v  i    v   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_140089490_   3719 TCTAATTAAACTAAATAGCCTTTGCATATCAAAAGAAACTATCAACAGAG 3768
                         ii v  i   v v  v i i    iiiv     i  v        v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_140089490_   3769 TACACAAACAACCTACAGAATTAGAGAAAATATTTGCAAACCATGCATCT 3818
                          iv v i      i       vi                 i   ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_140089490_   3819 GACAAAGATCTAATATCCAGCATCTATCAGGAACTTAAACAAATTTACAA 3868
                           i  i iv  vi       v  v   v i     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_140089490_   3869 GAGAAAAACAA----CTCA-TAAAAAAGTGGTCAAAGGACATGAACAGAC 3913
                         v i   i    ---- i  - v?    i   v       iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_140089490_   3914 GCTTCTCAAAAGAAGAAATACATGGGGCCAACAATCATAGGAAGAAAAGT 3963
                         ii     v        v     viv      i  v  i v   i i v i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_140089490_   3964 TCAGTATCACTGATCAT 3980
                            ii    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  


3231 27.06 0.55 0.66  chr2_140124369_140130776.rev     5008  5916 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_140124369_   5008 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5057
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_140124369_   5058 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5107
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_140124369_   5108 TACCAATGACTTTCTTCGCAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5155
                          v   iivi i  i  i      -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_140124369_   5156 TATGGAACCAAAAAAAGAGCCC-TCATCGCTAAGTCAATCCTAAGCCAAA 5204
                                -- viv  i ii   -vv  v  i  iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_140124369_   5205 AGAACCAAGCTGGAGGCATCGCACTACCTGACTTCAAACTATACTACAAG 5254
                              v   i      vv  i    v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_140124369_   5255 GCTACAGTGACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5304
                                 i i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_140124369_   5305 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAA 5352
                                  i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_140124369_   5353 CTATCTGATCTTTGACAAATCTGAGAAAAACAAGCAATGGGGAAAGGATT 5402
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_140124369_   5403 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5452
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_140124369_   5453 CTGAAACTGGATCCCTTCCTTATGCCTTACACAAACATCAATTCAAGATG 5502
                         v    ii    i    v   i ii  v  i     v  i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_140124369_   5503 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5552
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_140124369_   5553 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGGCTTCATGTAT 5602
                           v    ?i v viv   iv   v v  vv i     v  i   v iv  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_140124369_   5603 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCT 5652
                          vi            vvi          vv     v  i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_140124369_   5653 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5702
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_140124369_   5703 GCAGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5752
                         iv  i         i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_140124369_   5753 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5802
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_140124369_   5803 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACT 5852
                            i     i     v  i?    i    ii     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_140124369_   5853 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5902
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_140124369_   5903 CCATCACTGGCCAT 5916
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


2710 25.51 4.27 2.25  chr2_140144604_140148769.rev     2797  3686 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_140144604_   2797 TGGAAAAATATTTTTTATTTATGTATTGGAAGAATTAATATTGTAAAAAT 2846
                               i    iiiv i  i   v         v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_140144604_   2847 GTCCATGTTACACAAAGCTATCTACACATTTATTGAGATCTCTATCAAGA 2896
                          v v  ii v v    viv       v   i vi vi   i       i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_140144604_   2897 TTCCAA-TGTCATTTTTCGATATACAGAAA---ATAA-CT-ATCCTAAAA 2940
                          i   i-  i -     ----- i      --- i  -  -         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTT-----TGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_140144604_   2941 --CGTATGTGAACCATAACAAAAAGC---AAATTGCCAAGGCAATATAAG 2985
                         -- i    -   --  i-   iiii ---i   v     ii    v vii
  L1M4_orf2#LINE/    145 TTCATATG-GAA--ATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_140144604_   2986 AAAAGA-GAACAAAGCTAGATGTATCTCACTCCATGATTTCAAGCTATAC 3034
                               -        i i  v vv  v    i vii       iviv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_140144604_   3035 TTTAAAGCAATAATATTTAAAATAGCATGGCACTAACATAAAAATAGACA 3084
                          vi     v i i  v i  i i  ii   i   ii     ii       
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_140144604_   3085 CATCAACCAATGGAACAGAATAGCAAGCCCAGAAAAGAATCCATACCTCT 3134
                         i  vi i        i     v vi  i       vi  i      v i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_140144604_   3135 GCAGTCAATTGATTTTCAACAAAATTACCAATAATATACAATGGAAAATG 3184
                         iii              i    iiv i    v vi  v      ii  v 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_140144604_   3185 TATAATCTCCTCAATAAATGGTGCTAGGAAAACTGGATATCCATATGTAA 3234
                         v   i   ii    i          i   v         ?   i   i  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_140144604_   3235 AAGAATAAAATTGGACCTTCATCTTACACCATATACAAAAGTCTACTCAA 3284
                               i  i       iii i  i               i iv      
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_140144604_   3285 AATAGATGAAAAAATTAAACA----ATCTGAAACTATAAAACTACTAGAG 3330
                            i   v ? i vi    ii---- v  i             vi    i
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_140144604_   3331 GAAAATACAAAATGACATTGGAAAAACTACATGACACTGGTCTGGGCAAT 3380
                              i i ---- i?i ----   v  v i    vi   vi i      
  L1M4_orf2#LINE/    541 GAAAACATA----GGNGT----AAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_140144604_   3381 AATTTTTAAAATTTGACCCCAAAAGTACAAGGCAACAAAAGGAAAGGTA- 3429
                         ii   i v i  v    v       i     -         i   ii  -
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAG 631

  chr2_140144604_   3430 ACAAAT-GAA----ATCATATTTAAAACCTTCTGCCTATCAAAGAAAACA 3474
                          i    - i ----    v v      v   i  iviv      i v  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_140144604_   3475 ACTAACAAAGCGAAGAGACAACCTACAGATTGAGATAAAATATTTGCAAG 3524
                          ii  v    i   i        i     v  i  v             i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_140144604_   3525 CCATACATCTGATAAA--------------AATACGTTAGAAACTCCAAC 3560
                         i    i         i--------------    ii v ii     iv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_140144604_   3561 AACTCTATAGAAAGAAAATACATAATCCAATTAAGAAATGGTCAAGGGAA 3610
                              v   iv  i  i i v    i      ? i      v   i   v
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_140144604_   3611 TTGAATGGATATTTCT--AATAAAAAACAACCAAATGGCTAACAGATACA 3658
                               i  i      --  - i  i i vv        i  i iii   
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAA-AGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_140144604_   3659 TGAAAAAAATATCTACCTCACCAATCAC 3686
                               i vvv  v  v   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (149 / 74)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.64 (58 / 22)  


2881 26.67 1.56 0.67  chr2_140157775_140159872      707  1606 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_140157775_    707 TGGAAAGATATATCATGTTCCTCAATTGGAAGGATTAATATTGCTAAAAT 756
                                    vi       v vi        iv         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_140157775_    757 GTCCATACTACCCAAGC-AATCTACAAATGCAATGCAATCT-TATCAAAA 804
                          v v     v     ii-i       i  v   i      i-        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_140157775_    805 CACCAATGACATTCTTAAAAGAAA--GACAAAAAAATCCTAAAATTTATA 852
                         iv   iivi v  i  viv     --     ivvi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_140157775_    853 TGGAACCA-AAAATACCCAGAATAGCCAAAGTTATTCTATGCAAAAAAAA 901
                              vii-  iiv                iiv  -  -  v    i  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGAAG 198

  chr2_140157775_    902 AA-AAAGT-GGGGAAATCACATTATCAGATTTTAATAA--TACCACAGAG 947
                           -     -  i i v     i vi vi    i  -  --   i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAA-AACTTACTACAAAG 247

  chr2_140157775_    948 CTACAATTACCAAAACAGCATGATATTGGCATGAAAACAGAAACATTTAT 997
                              i v i   i    ii  i  i      i ii i   v i  vv  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_140157775_    998 CAATGGAACAGAATAGAGAATCAAAAGACAAATCCATACATCTACAGTGA 1047
                                 i     v    i  v i i i   i        i  ii  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_140157775_   1048 ACTCGTTGTTGACAAAGGTTCCAAGAACATACACTGGGGAAAGAACAGTC 1097
                          i vi  v i     i   v      v   v  v           i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_140157775_   1098 TCTTCAATAAATGGTGCTGGGAAATTTGGGTAACCATATGAAGAAGAATG 1147
                          i     i              v vi   i  ?   i   v i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_140157775_   1148 AAACTAGGCCCTTGTCTCTCAATACATTAAAAAATCAAATCAAAATGGAT 1197
                           ii i i   i ii   v  vi i  vv      i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_140157775_   1198 TAAAGACTTA--TATAAGACATCAAACTATGAAACCACTAAAAGAAAAGA 1245
                         i ?    i  -- i     vv v       i    ivi  i       v 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_140157775_   1246 TTGAGGAAAGTTTGTAGGACATTGGATTTGGCAAAAATTTCTTGAGTAAT 1295
                          v i? v  i i viiv   v    i  v     vii      iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_140157775_   1296 ACCCCACAAGCA-AGGCAAGCAAAGCAAAAAAGGACAAATGGGATCAAAT 1344
                           v   v     - i    vv    v     vi  i    v   iivv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_140157775_   1345 -GAAGTTAAAAACCTTCTACAGAGCAAATAAAACAATCAATAAAATGAAG 1393
                         -i  i        i  - iiivvv    vi v  v     v   i    i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_140157775_   1394 AGAGAATTCACATAATGGGAGAAAATATTTGCAAACTATTCATCTCACAA 1443
                            v  ii    v                      ii  vi    v i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_140157775_   1444 AAGATTAATAACTAGAATATGTAAGGAGATTAAACGACACTATAG-AAAA 1492
                         ii  i vi  v i       i   i  iv ivv  i  v v   i-    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_140157775_   1493 ATATCTAATAATCTGGTACAAAAAATGGGCAAGAAATCTGAATTGGCATT 1542
                          v - v     i iii -i?            iii  i     v i    
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_140157775_   1543 TCTTAAAAGAAGACATACAAATGGCAAATAGGTAAATGTAAACATATTCA 1592
                            iv        i           v    i i v   v   v  ii   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_140157775_   1593 GCATCACTGATCAT 1606
                         i     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.18 (20 / 17)  


2812 27.94 1.55 1.11  chr2_140194892_140198208.rev     1924  2825 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_140194892_   1924 GAAAGATATTCCATATTAATGGAATGGAAGAATCGATATTGTTAAAATGT 1973
                                  i    i  v     v       v ii          i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_140194892_   1974 TCATACTCCCCAAAGCAATCAACAGATTCAATGTAATTCCCTATTAAAAC 2023
                         iv            vii   v          i i   -      i    i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAAT-CCCTATCAAAAT 101

  chr2_140194892_   2024 ACTAATAAAATTCTTCACAGAAATAGTAAAACAG-TCCTAAAATTTAAAT 2072
                         v i iivivv  i  ii       v vv  i v -          i v  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_140194892_   2073 GAAACCACAAAAGACCCAGAATAGTGAAAGCTATCCTAAGCAAAAAAAAA 2122
                          i  vii   ii            iv   i v   i i ----    i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA----AAAAGAA 197

  chr2_140194892_   2123 TAAAAAAGTCTGAAGGAATCACGTTACCTGACTTCAAATTGTACTATAGA 2172
                         v  v     -  i    v    ii v  ii i      viv     i i 
  L1M4_orf2#LINE/    198 GAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_140194892_   2173 GCTGTAGTGACAAAAACAGCATGGCACTGGCATCAAAACAGACACACAGA 2222
                            ii   i iv  i    ii   i        v ii i     i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_140194892_   2223 CCAATAGACTACAATAAAGAACCTAGGAACAACTCCACACACCTACAGTG 2272
                         i    i  v  v   vi   ii i  i  i  vi   i   ii  ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_140194892_   2273 AACTCCTTTCTGACAAAGGTGTCAAGAACATACACTTGGGAAAAGACAAT 2322
                           i vv   ii     i    i     v   v  v v      ii i i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_140194892_   2323 CTCTTTAATAATTGGCACTGGGTAAACTCAGTATCC-TATGCAAA-GAAT 2370
                           i  i  i  v   ii     vv    vii  ?  -i       -    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_140194892_   2371 GAAGCTAGACCCTTTATTTCTCACCATATG-AAAAATCAAATCAAAATGA 2419
                             i i     i - ii  v        i-      i  v        i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_140194892_   2420 AT-AAACACTTAAATCTAAGACCTCA--CTAAGAAATTACTACAGAAAAC 2466
                           - ? v  i     v     v  v --   vi   i vi  v ii   v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_140194892_   2467 CATGGGGGCATAAATCTGCAGGACATTGGTGTGGGCAAAAATTTCTTAAG 2516
                            i  ? --       v iv   v    vv i     vii       ii
  L1M4_orf2#LINE/    546 CATAGGNG--TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_140194892_   2517 CAATACCTCACAAGCGCAGGCATCTGAAGGAAACATGGACAAATGGAATC 2566
                         i vv  vi  v    i  i   v vi   i   v  i  i    v i ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_140194892_   2567 ACATCAAG-TC-----CTTCCACACAGCCAAGGAAACAATCACCAAAGTG 2610
                         v      i- i-----   iiiii vv v     v  v    vv      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_140194892_   2611 TAGAGACAATCCACAGGCTGGAAGGAAATATTTGCAAACTACCCATCTGA 2660
                         v i      i      iv   i  i             ii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_140194892_   2661 TT-GGGATTAATAACCAAAATACATAAGTATTTCAAACAACTGTATAGGA 2709
                          v-    i vi  v   i    i    iv vi  vv      vv   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_140194892_   2710 AAAAATCTAATAATCTGATTTTTTAAATGGGCAAAAGATTTGAATAGACA 2759
                             iv v     i ii   ?vv-           i              
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACA 842

  chr2_140194892_   2760 TTTGTCAAAAGAAGACATAAAAATGGCAAACACGTATATGTAAAGGTACT 2809
                            v  v        i   v       v  i v i i   v    i i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_140194892_   2810 CAACTTCACTGATAAT 2825
                             v   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 1.60 (24 / 15)  


1603 25.66 5.59 6.03  chr2_140325376_140327372.rev      594  1505 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_140325376_    594 TGGCAAAATATATAATGTTTATGGATTGGAATACTTAATATTGTTAAAAT 643
                            v  i    viv     i           v               i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_140325376_    644 GTGAATTAATTT---AGATTGATCTATAGTTTCAATGCAAGTGCTAT--- 687
                          vv   -- i i--- i         i  v     i    viv    ---
  L1M4_orf2#LINE/     51 GGCAAT--ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_140325376_    688 AATTCCAGCAGACTTTTTTTTTTAGAAATAATCAAGATGATTC-AAAGTT 736
                            i     v v       vi--      viv    v    i -   i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGC--AGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_140325376_    737 TATGTGAAAATGCAAAA-ATCTGGAGTATTCAAAGCAATCTTGAATTAAA 785
                         i  i  i        ii- i ii  i  vi    i          vv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_140325376_    786 AAAATAAACTTACAGGA--------------TTTTAAACTTTACTATAAT 821
                          i  i   v  iv    --------------   i   vi      i  v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_140325376_    822 GCTACAGTAAATATCACAGAATGATGCTGGCATAAAGATAGACA----AA 867
                                   vi vv    vi  i i         i        ----i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_140325376_    868 TTAGTAGAAGAGAACAGAGAACTCAGAAATAATCCTTCA-ATTATATAGT 916
                          i i i   v    iv    iii         v  ivi -   -   i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGGT 345

  chr2_140325376_    917 CAACCAATTCTCAATAAAGTTGCAAAG-CAATCCAATGAGAAAAGGAAAA 965
                            iii   i  i i  i v   v   - v  i     i i    i v i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_140325376_    966 TCTATTTAACAAAATATGCTGAAACAACTAGAGTTTTTA-AT---AAAAA 1011
                            v  i      vvi     ii      i  - v?ii -  ---   i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGA-TAKCCACATGCAAAAGA 444

  chr2_140325376_   1012 ATAAACT--AACTGC-AGCT-GCACTACCCACAAAATTTAAATTTAAATG 1057
                           i  v --i  iv - v  -i   i ivi      v    v iv     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_140325376_   1058 AGTTGGAAACCTAAGCATTAAAGCTAAA--TATTTATGCTTGTAAAA-AA 1104
                         ii ii? i      iii v i       --   vv -i  iv  i  -  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAA 543

  chr2_140325376_   1105 GAGAAAGCAGTA--TCATTGCAACTTGGAAGTATGCAAAGGTATTTTAGA 1152
                         i v v  v?   --  v i ii  i v iiv  v    v   v i     
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_140325376_   1153 CAGGATGCAAAAAGGTATAACCA-TAAAAGAAAAAATAAAAGCTAAATTA 1201
                         i v  ii v     -i i  v  -i             i ---      i
  L1M4_orf2#LINE/    594 TATGACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGA---TAAATTG 639

  chr2_140325376_   1202 G--TTCA-CACATTTAGAAAATGAATAAGCATTCATAGATGGGAGAAAAT 1248
                          --    -  v v   -    ivvv iv  -    v  ------  v v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTA-AAAACTTTTGTGC-TTCAAAG------GACACT 681

  chr2_140325376_   1249 ATTTTACAAACATAATTTTGAAATATATATATATATGAAATCTACATGTA 1298
                           ----   iv - i ---    ------- v i ---- i i   - - 
  L1M4_orf2#LINE/    682 AT----CAAGAA-AGT---GAAA-------AGACA----ACCCACA-G-A 710

  chr2_140325376_   1299 GTTAGATACCTCTCCATATAAATATAAATTTTTTATCT-ATATGAAATAT 1347
                         i vi  v ------- v   vv ii    iv v     -   v ii iv 
  L1M4_orf2#LINE/    711 ATGGGAGA-------AAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_140325376_   1348 ATATTTTTCATATATATACATGAAAAAGTCT-ATAATTCAGCAATAAAAG 1396
                         i   i---  v ---   i  i  i  v   - i  i   ii       i
  L1M4_orf2#LINE/    754 GTATC---CAGA---ATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_140325376_   1397 GACAAAGA---CAAATTTTTTAAATGGGCAAAAGAATAGAATGATCACTT 1443
                               v ---   --  ?vv           i  v v    iiv  i  
  L1M4_orf2#LINE/    798 GACAAATAACCCAA--TTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_140325376_   1444 CACAAAAGGAGATATACAAATGGCCAATAAGGTCATGAAATGAT-TTCAA 1492
                          v v    i                      vv       v   -i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_140325376_   1493 CATCATTACTGAT 1505
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (136 / 94)
Gap_init rate = 0.05 (44 / 908), avg. gap size = 2.41 (106 / 44)  


 908 26.15 1.54 0.38  chr2_140433291_140434927       63   322 (1315)  C L1M4_orf2#LINE/L1   (645)   263     1  

C chr2_140433291_    322 TAGAAAGATATTCCATGCCCATGAATTAAAATA---AATATTGTTAAAAT 276
                          i         i     ii    i   ii  v ---           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_140433291_    275 GACAAACCTACCCAAAATAATTTACAGATTCAATGCAATCCGTAGCAAAA 226
                          i   vv  v      v i  i           i       v  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_140433291_    225 TACCAATTACACTTTTTCACAGAAATGTAAAAAAAAATCCTAAAATGTAT 176
                          v   ii i -      ii       vv v  ivvi          vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

C chr2_140433291_    175 ATGGGACCACAAAATAATTTGTATAGTCAAAGCAATCT-GAGCAAAAAGA 127
                             i vii   iiv viiv v    i    i      -  iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

C chr2_140433291_    126 ACAAAGCTGAAGGCATTACATAACACGAGTTTAAAATATACTACAAAGCT 77
                               i  i   vv i   ivv v i v  i    iv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

C chr2_140433291_     76 GTAGTAATCAATAC 63
                         ii         v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGAC 263

Transitions / transversions = 1.43 (40 / 28)
Gap_init rate = 0.01 (3 / 263), avg. gap size = 1.67 (5 / 3)  

1987 22.02 4.96 4.96  chr2_140433291_140434927      501  1145 (492)    L1M4_orf2#LINE/L1      264   908 (0)  

  chr2_140433291_    501 AGTGTGATACTGGCATAAAAATGAACATATAGATCAATGGAACAGACTAG 550
                               i           ii  ii                  i   v v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_140433291_    551 AGAATCCAGATACAAATCTATACATTTGTAGTGAACTTATTTTTCACAAA 600
                            i      v i   i i        i i  v  i v     iv    i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_140433291_    601 GTTGCCAATAACATACAATAGGATAAGAACAGCATCTTAAACAAATGATG 650
                          v      v v   v    i  iv     i  iv i  v        i  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_140433291_    651 CTGGGA-AAGTGGATT------TGTAGAAGAATAAAACTATACTC-TCTC 692
                               -  v     v------  i i      i  ii iv  i - vi 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_140433291_    693 TTTCATCATATATATAAAATCAAACCAAACTGCATTAAAGACTTAAATCT 742
                          iv  i      i -     i  vi    v  v  i ?    i     v 
  L1M4_orf2#LINE/    464 TCACACCATATACA-AAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_140433291_    743 AAGACCAGAAACTATGAAACAACTAGAAGAAAACATTGG-GTA------- 784
                             v vi       i    vvi             v  -   -------
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_140433291_    785 -TGCTCCAGGGT-----AAAGATATTTTGTGTAAGACCTTAAAAGCACAG 828
                         -  vi iv    -----  v i v i  ivi  v   vii         i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_140433291_    829 GCAACAAAAGCAAAAATAGACAA--TGGGTTTTACATCAAACTAAACATC 876
                                   v         i  --   ii  --       v v  v v 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTT--CATCAAAATTAAAAAC 660

  chr2_140433291_    877 TTCTGCACAGCAAAGGAAATAATCAACAAAAGGAAAATAAAACCCACAGA 926
                           i  ii vv       v iv     v   iv     v v          
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_140433291_    927 ATGGGAACAAATATT-GCAAACTACCCCTCTGACAAGGGATTAATAACCA 975
                               iv       -     ii iviv     i      i vi  v   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_140433291_    976 GAATATGTAAGGAGCTCAAGCAACTCGATAGCAAACAAAACAAAACACCA 1025
                               i   i  i   vvi      i   ii   -  i     ------
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAAA------ 803

  chr2_140433291_   1026 ATAATAATAATAATCATCATCATCATCTTATTTAAAAATGGGCAAAT-AT 1074
                         ----------   i --------  ----   ?             v-  
  L1M4_orf2#LINE/    804 ----------TAACC--------CA----ATTWAAAAATGGGCAAAGGAT 831

  chr2_140433291_   1075 CTGAATAGACATTTT------AAATACATACAAATGACCAACAGGTATTT 1118
                         i             i------i  v i         i    i i i iv 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_140433291_   1119 GAAAAGATGTTCAACATCACTAGCAGT 1145
                                  i         ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (83 / 57)
Gap_init rate = 0.02 (16 / 645), avg. gap size = 4.00 (64 / 16)  


2234 22.39 1.87 1.31  chr2_140452280_140454489      501  1036 (1174)    L1M4_orf2#LINE/L1        2   540 (368)  

  chr2_140452280_    501 GAAAAGACATCCCATGATAATGGATTGGTTGAACTACTATTGTTAGGAGG 550
                          i     i        v v         vv  vi  v        i  v 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_140452280_    551 GCAATACTACTCAAA---ATCTTCAGACTTAATTTGATCCTTATTGAAAT 597
                                 v i    ---    v    i i  ivii    i   ii    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_140452280_    598 CCCCAAAGTG---TTTTTGCATAAATTAAAAAAATCAATACTAAAATTTG 644
                            -- iv  ---        v     i v  iv -i  v        ii
  L1M4_orf2#LINE/    102 CCC--AGCTGCCTTTTTTGCAGAAATTGACAAGCT-GATCCTAAAATTCA 148

  chr2_140452280_    645 TATGAAATTTCAAAAGACTTTGAATAGTCACAACAATCTTGTAAAGGAAG 694
                             i  v v   ii   iiv      i  v          v   i    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_140452280_    695 AACAAAGTTGAAGAATTCACACTTCCTGATTTTAAGAATGACTCTTAATG 744
                                   i  i i          ii    i  i v v   viv  - 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-G 247

  chr2_140452280_    745 CTACAATAATCAAAACAGTGTGGTACTGGCATAAAGAGAGATATAGAGAC 794
                              i       i                    i  v   i   v   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_140452280_    795 CTGTGGAGTTGAATAGAGAATGCAGAAATAAAATCTATACAT----AGTC 840
                          vi    i v    v    i v          -i i      ----i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTC 346

  chr2_140452280_    841 AAATGATTTTTGAAAGGGATGCTAAGACTACTCAGTGCAGAATGAACCGT 890
                           v       i  v i  i   i     i i   i  vi   v   iv  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_140452280_    891 CTTTTTAACAAATTGTGGTGGGAAAACTAGTTATCCACATGTAAAAGAAT 940
                              i       v   v     v    i v  ?       i        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_140452280_    941 AAAATTGGATCACAGCCTTATGCAACATACCAACATTAAATCAAAATGGA 990
                         i  i     i v vi   i ii v i    v  v     v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_140452280_    991 TCAAAGACATAAACATGGGATCTAAAACTATAAAACACATTTAAAA 1036
                            ?    v    ii ii  v               v --   i  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC--TTAGAA 540

Transitions / transversions = 1.46 (70 / 48)
Gap_init rate = 0.01 (8 / 539), avg. gap size = 2.12 (17 / 8)  

1109 21.75 5.93 0.85  chr2_140452280_140454489     1365  1718 (492)    L1M4_orf2#LINE/L1      537   908 (0)  

  chr2_140452280_   1365 AAAAAAAAAAATAGAGG-AAATGATAGATGATATTGGATTTGG-AATAGC 1412
                          i  i    v    i? -    vv v -   iv    i  v  -   i i
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGT 585

  chr2_140452280_   1413 TTCTTTAATATGATGTAAAAAGCACAGGAAACAAAAGAAAAAATGAATAA 1462
                              vi      iiiv         i v               ii    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_140452280_   1463 ATTATACTTCA--AAATTTAAAAGAAATTGTGCAACAAAGGACACTATGA 1510
                            iv      --   v      ivvv      vv             v 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_140452280_   1511 AGAACATGAAAAT-CGATCCATAGAGTGAAAGAAACTATTTTCAAATAAT 1559
                             vi      v- i i   i   i  ii     v     v     v  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_140452280_   1560 ATACTTGATAAAATATTAATATTCAGAATATGTAAAGAACTCTTACAAGT 1609
                            ii      iiv i vi   i        i                v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_140452280_   1610 CATCAACAAAGA------TAAC---------AAATGGACAAAGAACAAGA 1644
                           vi  i   i ------    ---------      i     i ivv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_140452280_   1645 ATAGCTTTTTTCTTCTGAAGAAAAAATACAAA-AACCAATAAGCACATGA 1693
                             viv   i--  ii     i v       -ii               
  L1M4_orf2#LINE/    836 ATAGACATTTC--TCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_140452280_   1694 AAAGATGCTCAATATCATTAATCAT 1718
                                     i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (45 / 31)
Gap_init rate = 0.02 (9 / 372), avg. gap size = 2.67 (24 / 9)  


 450 23.66 0.00 0.00  chr2_140575096_140578384.rev     1690  1782 (1507)    L1M4_orf2#LINE/L1        1    93 (815)  

  chr2_140575096_   1690 TGGAAAAACATTCCATGCTCATAGACTGGAAGAATCAATATTGTTAAAAT 1739
                               i i  i     i    i  i       v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_140575096_   1740 GCCCATATTGCCCAAAGCAATCTCCAGATGCAATGTTATTCCT 1782
                          v v   i v      vii    v     v   i iv  i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.00 (0 / 0)  

1092 21.17 5.10 8.16  chr2_140575096_140578384.rev     1784  2175 (1114)    L1M4_orf2#LINE/L1      317   696 (212)  

  chr2_140575096_   1784 GTCCAGAAGTAAAGCCACACACTAACAATCATTTGATATTTCG-CAAAAA 1832
                                 i    v   i   i v iii   v     -     -   iii
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGAT-TTTCGACAAGGG 365

  chr2_140575096_   1833 ---CAAG------CAGTAAGGAAAGGACTCCCTATTCAAGAAATGGTGCT 1873
                         ---    ------  i ii      i ivvi  v     v          
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_140575096_   1874 GGGATAGCTGAGTAGCCATACTCAGAAGAATGAAACTGGACCCCTTCCTT 1923
                             i i   ii  ?   i iv  i         ii         v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_140575096_   1924 ATACCATATAGAAAAATCTACTCAAGATGGATTAAAGACTTAAATGTAAA 1973
                          i        v      iv      i      i ?    i         i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_140575096_   1974 ACCTAAAAATATAGAAACCTTGCAAGCTAATGTAGG---AAATATTGATA 2020
                          v      v    i  vi   iv   vv  ii    ---    v  ----
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT---- 561

  chr2_140575096_   2021 CCATTCTGGACATAGGCTCCAGCAAAGATTT------TATGACAAAGAGG 2064
                         - i ----   v v  v ivi    v i   ------       v-----
  L1M4_orf2#LINE/    562 -CGT----GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC----- 601

  chr2_140575096_   2065 ACAAAAGCAATTGCAACAAAAGCAATTGCAACAAAAACAAAAATTGACAA 2114
                         -        -------------   --         iv      v  i  
  L1M4_orf2#LINE/    602 -CAAAAGCA-------------CAA--GCAACAAAAGAAAAAATAGATAA 635

  chr2_140575096_   2115 ATGGGACCTCATTAAA-TTAAAGAGCTTCTGTAGAGCAAAGAAAACTATC 2163
                           v    i    i   -     i -   i   ivvv     i v      
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chr2_140575096_   2164 AACAGAGTGAAA 2175
                           v i       
  L1M4_orf2#LINE/    685 AAGAAAGTGAAA 696

Transitions / transversions = 1.53 (49 / 32)
Gap_init rate = 0.03 (13 / 380), avg. gap size = 4.00 (52 / 13)  

 608 28.88 2.59 0.43  chr2_140575096_140578384.rev     2568  2799 (490)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr2_140575096_   2568 AAAATAGACTAATACAGAGAGTTAATAACCAACCCACAGAATAGGAGAAA 2617
                            iv v    vi -   i   v  v iv             i       
  L1M4_orf2#LINE/    672 AAAGGACACTATCA-AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_140575096_   2618 ACACTTAAAGACTATGCATCTGACAAAGGTCTACTATTCAGCATGTATAA 2667
                          i i  iv i ii  ii      i  i  v  vv   i   v  i     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_140575096_   2668 GGAACTTAAACAAATTTATAAGCAAAAAACAA----TGCCATTAAAAAGC 2713
                         i     ivv    v iv    vv    i    ----iv v   ?    ii
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_140575096_   2714 TGGCAAAGGACATGGACAGACACTTTTCAATAGAAAATATATTTGCGGCC 2763
                         v         iv  i i     i  i  v v    i     ivvii    
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_140575096_   2764 AACAA--AAATAGAAAAATGTTCAACATTGCTAATCAT 2799
                           i  -- v  ii   i   i       ii????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (40 / 26)
Gap_init rate = 0.01 (3 / 237), avg. gap size = 2.33 (7 / 3)  


 392 22.35 1.18 12.35  chr2_140920043_140922776     1016  1185 (1549)    L1M4_orf2#LINE/L1        3   153 (755)  

  chr2_140920043_   1016 GAAAAAAACCTACCATGCTCATGGGTAGAAAGAATCAATATTGTGAAAAT 1065
                             i v i --     i      i v i    v i        v  i  
  L1M4_orf2#LINE/      3 GAAAGATATC--CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_140920043_   1066 GGCCATACTACCCAAAGTAATTTATACATTCACTGCTATTCCTGTTAAAC 1115
                            v     v      v i  i  i v     vi  v  i   i i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_140920043_   1116 TACCA-TTGACATCCTTCACCAAATTAGAAAAAAAAACAAAAACAAAAAA 1164
                          v   -i  ----    i------  v ---------  i   ivi v  
  L1M4_orf2#LINE/    101 TCCCAGCTG----CCTTT------TTTG---------CAGAAATTGACAA 131

  chr2_140920043_   1165 ACT-ACTTTAAAATTCATATGG 1185
                         i  - iii              
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGG 153

Transitions / transversions = 1.53 (23 / 15)
Gap_init rate = 0.04 (6 / 151), avg. gap size = 3.83 (23 / 6)  

2414 25.67 3.36 1.08  chr2_140920043_140922776     1499  2242 (492)    L1M4_orf2#LINE/L1      148   908 (0)  

  chr2_140920043_   1499 ATATGGAGCCAAAAAAGAGCCCGTATAGCTAAGATAATCCTAAGCAGAAA 1548
                                iviiv  ii  v  v v     i  i i    i i iv ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_140920043_   1549 GAACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAAGG 1598
                                 i      vv     i v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_140920043_   1599 CTATAGTAACCAAAA-GCTATGGTACTGGTACA------GACACATAGAC 1641
                            i     i   i -iv i         i i ------    i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_140920043_   1642 CAATGGAACAGAATAGAGAGCTCAGAAATAAGACTGCACATTTACAACCA 1691
                                 i     v     ii         iv iii       iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_140920043_   1692 TCTGATTTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGA--GTT 1739
                         vi        i    ivv  v   i v  vv            i --  i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_140920043_   1740 TGTATTTAATAAATGGTGCTAGGAGAACTGGCTAGCCATATGCAGAAAAT 1789
                          - -  i  i          i   v      v  ?   i     i  i v
  L1M4_orf2#LINE/    398 T-T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_140920043_   1790 TGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTTAATATAG 1839
                             ii         v   i     v                i  v  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_140920043_   1840 ATTTAAGACTTAAATGTAAAACCCAAATCTATAAAATTCCTAGAAGAAAA 1889
                           iv?    i         i v i   v        i  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_140920043_   1890 TCTTGG---AAATACCATTCA-GGTCATAGGCAAAGGCAACGATTTCAT- 1934
                         iv v  ---    -- -   i- ii v i  iv -     i i    v -
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTA-GGCAATGGTTTCTTA 591

  chr2_140920043_   1935 GATGAAGATGCCAAAAGCAATTGTTAACAA--GAAAAAATTGACAAATAG 1982
                            - v  ii         vvv i-     --        v  i    v 
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTG 639

  chr2_140920043_   1983 GATCTAGTTTAACTAAAGTGCTTCTGCACAGCAAAATAAACTATCAG--- 2029
                           ii vi iv  v v  ivi   i  ii vv    iv v       i---
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_140920043_   2030 AGTGAACAGACAACCTACAGAATGGTAGACAATTTTTGCAATCCACCCAT 2079
                               v        i         v   v   v       vi  ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_140920043_   2080 CTGACAAAAGTCTAA-ATTCAGAATCTACAAGGAACTTAAACAAATTTAC 2128
                             i  ii v  vi-  i      v  i  i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_140920043_   2129 A-CGAAAAAACAA----CCCCAGTAAAAAGTGTGCAAAGGACAAGAACAG 2173
                          -ii    i    ----   v v ?    i  v        ivv   i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_140920043_   2174 ACACTTTTCAAAAGAAGACATGCCTTTGGCCAACAAACATATGAAAAAAA 2223
                            i  i  v        i  i vvv       i  i  i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_140920043_   2224 GCTCAGCATCACTGATTAT 2242
                              i     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (115 / 73)
Gap_init rate = 0.02 (18 / 761), avg. gap size = 1.83 (33 / 18)  


 208 30.55 14.63 5.26  chr2_140933217_140934988      508  1286 (486)    L1M4_orf2#LINE/L1       57   908 (0)  

  chr2_140933217_    508 ACTTCTCACAAATTAATCTAGAAATGCAATGCAACATCAATCTAATTCTA 557
                            i i  --    i     v i  v   i    ivi v   v  v  iv
  L1M4_orf2#LINE/     57 ACTCCCCA--AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_140933217_    558 ATGTGTTTATTCTTATA-ATATTC-CAAAACAATTTTAGAA---ATA-AA 601
                          vv  ii -  i  ii - v   v-   ivii  ii  i  ---   -ii
  L1M4_orf2#LINE/    105 AGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_140933217_    602 AAATGCAAG---------ATTTTCAAA-TAATTTTTAAAT----GAATGA 637
                                  ---------  vvi    -i   i  v   v----   ii 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_140933217_    638 CTGTGGAG--TTCATA--------TATAGAGATATGCTATAATGCTACAG 677
                         vvv     --i   i -------- v vi i iv i   i  v       
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_140933217_    678 -AACATTTTTAAAATA-TGT--TAATGGTGCACAGATCCACAAAGAGATC 723
                         -  ----- i  i i -   --  v   iii vi   vv   v v     
  L1M4_orf2#LINE/    254 TAA-----TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_140933217_    724 CAAAGAATAGGATGGGGACTCCA----TACTCACGTATACGTTT-TGA-- 766
                         v vi      i  v i  v    ----  v--  vi    i   -  i--
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAA--ACCCATACATTTATGGTC 346

  chr2_140933217_    767 ----GAGTTT-------AGTGCCACAGA--A--CAATAGA-----AATC- 795
                         ----  v   -------i      -   -- --    i i-----   v-
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAG 395

  chr2_140933217_    796 CCTACTCAATCA------CCAG-AGAAATGAAAGACTA-ATATTTAGGGT 837
                         i  vi    iv ------ ii - v  v  i vi? i -  iivv i iv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_140933217_    838 GGAAGTTAAATCTCTACATCAAACCATATACACATAAATGCATTCAGA-T 886
                         v      ii i i    v   v          - -    vv i   i - 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACA-A-AAATTAACTCAAAAT 493

  chr2_140933217_    887 ACATCAGAAACATAAATAT-----TTAAAA--GTAAAAGTATTAAAAGAA 929
                         iv    ? i  v     i -----i     --i     v v   i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_140933217_    930 AGAATAGA---AAATGT--GTG--CATGTGCTGGATAAAAGACTTTCCTA 972
                          iv    i---    v --   -- v  v i i ii  vi --    i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG--TTTCTTA 591

  chr2_140933217_    973 AATATGATGTGATGTCCAGAAACACTGAAGGAAAAGACAGTCAGATCTGA 1022
                         i      iiiv vivv  v  i  vii  i     i i  vi i  iv  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_140933217_   1023 CTACATAAGAAGTAAAT-CTTCTATATAGCAAAA---ACCATCA-GAAAC 1067
                           v   v i  v    v-   i i iivv    i---  i    -    v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_140933217_   1068 ---AAAGCAAATTCAT----TTGAAGGAATTTTTTTTGTGTGTGGGGTGT 1110
                         ---    vv  ii  i---- v i  i  v v   ------ iiiivii 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTT------GCAAATCAT 735

  chr2_140933217_   1111 ATATCTTACAAAAGCTCAGTATTTACAGTATATAAATAGTGC-------- 1152
                               v i  ii viiv    ii v i        v iiv --------
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_140933217_   1153 --ATAATAAGATCTTATGGA-AAATGAAACATTTTAAGGAAAAAAATAAG 1199
                         --       i ------i  -    i vv  v  ?  ------    ii 
  L1M4_orf2#LINE/    786 CAATAATAAAA------AGACAAATAACCCAATTWAA------AAATGGG 823

  chr2_140933217_   1200 CATAG-ATCAAAATAAGAC---CCTTGGAAGAAGCAGAATTT-TGAATGT 1244
                           v  -  ivi    -   ---i  ivi      ----  v -ii    v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATA-GACATTTCTCCAAAGAAG----ATATACAAATGG 868

  chr2_140933217_   1245 TTAATAAA-ACATGAGAAAATATGTTCAAACTTCACAGTATAG 1286
                         ii     i-      --   v   i    - v   ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGA--AAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.06 (55 / 852), avg. gap size = 2.82 (155 / 55)  


2893 27.13 2.16 0.34  chr2_140996954_140999390     1065  1945 (492)    L1M4_orf2#LINE/L1       12   908 (0)  

  chr2_140996954_   1065 CCCATGTTCATGGATGGAAAGAATGAATGTTGTGAAAATGAACATACTCT 1114
                                        v i    v v   i    v  i   ivv      i
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chr2_140996954_   1115 CCAAAGCAATCTATAGATTTAATGCAATTCCTATCAAAATGCCA-TTATC 1163
                              vii     i     i  i     i           v   -i ii 
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_140996954_   1164 ATTTTTCACAAAACTAGAAAAAACAATCTTAAAAATCATATGGAACCAAA 1213
                         -     ii  i  v v  v  ivii   i     v          viiv 
  L1M4_orf2#LINE/    112 -TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_140996954_   1214 ACAGAGCCTGAATAGCCAAAGCAATACTACGTAAAAAGAACAAATCTGGA 1263
                          vi  v  v           i    vi iviv  i         vi    
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_140996954_   1264 GGCATTACAGTACCAGACTTCAAATCATATTGCAAGGCTATGATTACCAA 1313
                           vv i   v v  vi i      v v  i i   i    iii v i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_140996954_   1314 AACAGCATGGTGCTGGTATAAA-ATCGGCACGTAGGCCAGTAGAACAGAA 1362
                         i    ii    i    i    i-  v i  ii   ii  i i   i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_140996954_   1363 CAAAGAATCCAAAAATAAAGCTGAATATTTATAGCCAACTGATCTTTGA- 1411
                         ivi   i    i       v iiv i      i i   i    i  i  -
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_140996954_   1412 GAGAGTATACAGAAACATAAACTGGGAAAAGTACATCCCATTCAATAAAT 1461
                         i  i  ii-  ii v   vv v    i    v i vi iv     i    
  L1M4_orf2#LINE/    361 AAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_140996954_   1462 GGTGCTGGGAAAACTGGCAAGCCACACATAGAAGAATGAAACTGGAACCC 1511
                                   v      vv ?     iii i         ii    -   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA-CCC 458

  chr2_140996954_   1512 CTCTCTCACGT--TATACAAAAATCAGTTCAAGAGGGATCAAAGACCTAA 1559
                           vi     ii--           i ii    i v      ?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_140996954_   1560 ATCTAAAACATAAAACCATAAAAATTATAGAAGACAACATTGAAAAAACT 1609
                           v   i vv      i      v iv       v     v i?iv  v 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_140996954_   1610 ATTCTGGACATTGGCCTAGGCAAAGAATTTATGACTAAGACCCCAAAAGC 1659
                         v   vv   v    vi       v iv  iv iiv  v   v        
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_140996954_   1660 AAATGTGACAAAT------ATA-ATAAATGGGATCTAATTAAACTAAAAA 1702
                          v v ii     v------   -      v   ii v  i   v v    
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_140996954_   1703 GCTTCTGCACAGCAAAATAAATAATCG-----GTAAACAGAAAACC-ATA 1746
                         i   i  ii vv    iv v iv   i-----  i  v   v    - i 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_140996954_   1747 GAATAAGAGACAATATTTGCAAACTCTGCATCCGACAAAGGAATAGTATC 1796
                             ii    v            iiv ii   i  i  i   v v     
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_140996954_   1797 CAGAATGTACAAGGAACTCAAGCAAATCAGCAAGAAAAGGACAAATAATC 1846
                               i  i  i      vvi   v   ii  v    i         i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_140996954_   1847 CCATTAAAAAGTGGGCAAATGACATGGATAGACATTTCTCAAAATAAGAT 1896
                          v   ?    i        v  iv  i             v   v     
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_140996954_   1897 ACACAAACAGCCAACAAACATATAAAAA-ATGCTCAACATTACTGATCAT 1945
                          i     ii     i  i  i  i    -           i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.01 (12 / 897), avg. gap size = 1.83 (22 / 12)  


2638 26.09 3.70 2.02  chr2_141159240_141164207     3584  4476 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_141159240_   3584 TGGAAAGACATCCCATGTCTATGGTTTAGATGAATCAATACTGTGAAAAT 3633
                                 i         ii    v  i  v  v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_141159240_   3634 GACA---CTACCAAAAGTGATTTATAAATTCAATGCAATCCCTATCAAAA 3680
                          i  ---  v  v   v    i  i i      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_141159240_   3681 TACCAATGACATTTTTTTACAGAAATAGA-AAG--AACCCTAAAACTTAT 3727
                          v   iivi -i      i       v  -   --i i       i i  
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_141159240_   3728 ATGAAATCACAAAATTTCCCAAATAACCAAAGCAATCCTGAGAAAAGTAA 3777
                            i  vii   iivvi  vi    i     i     i   -     ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAG--- 195

  chr2_141159240_   3778 AAAAACAAAGATAAAGACATCACAAAACCTAACTTCAAAA-----TATA- 3821
                           i       v ii  ivv     vvv  i  i       -----  i -
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_141159240_   3822 -GTTGTAAAAATCCAAAACAGCATGCTGCTGGCATAACAATGGACAATTA 3870
                         - i ii iv    -  i    ii  v i         vi  i    vv  
  L1M4_orf2#LINE/    246 AGCTACAGTAATC-AAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_141159240_   3871 GACCAATGCAACAACA--GATAACTTAAAAATAAAGTTATGTTTTTACAG 3918
                           i     v  i iv --  v iiii i       vii  iiv    ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_141159240_   3919 CCAACTCATTTTTGACAAAGACTTGAAGAATATTGATTGGGGA-----TA 3963
                         i   i v     i     i iiviv    vi   v v      -----  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_141159240_   3964 GTCCCCTCAATAAGTGGTGTTGGGAAAACTAGATATCCATATGCAGATGA 4013
                            iii    i  i     i     v    i    ?   i     i v  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_141159240_   4014 ATGAAACTAGAACCTTGTATCTCATCATATAAAAAAATT----CAAAATG 4059
                              ii i  v  i iiv  v  i      v       ----       
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_141159240_   4060 GATTAAAGACTTAAATGTAAAACTTGAAGCTATAAAACTACTAAAAGAAA 4109
                            i ?    i         i vi i  i          vi  i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_141159240_   4110 ACATAAAGG-AAATGCTTTAAGATATTATAGGTCTTGAAAAATATTTTAT 4158
                              ii? -    -   iiv  iv  i--   -- iiiv   iv   v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTG--GGT--TAGGCAATGGTTTCT 589

  chr2_141159240_   4159 GAAAAA-GACCTCACAAACAGAGACAACATAAGCAAAAATAGACAATTGG 4207
                         v i v -   vi  v  i  v ii     v   v         i  v v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_141159240_   4208 GATTATATGAATCTAAAAAGCTTCTGCACAGCAAAGAAAACAATTAATAG 4257
                           i vi  v  vv v    i   i  ii vv     i v  v  i  v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_141159240_   4258 AGTGAAGAGACAATCTACAGA---GAAGAAAATATTTGTAAACTATTTAT 4304
                               i      i i     --- i            i   ii  v   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_141159240_   4305 TTGGTAAGTGATTAATATCCACAATACATAAGGAAC-CTAAAAAGCTCAA 4353
                         i  i    v  i vi      v    i    i    -  v v  -     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAA 788

  chr2_141159240_   4354 CAGAAAAAA---AAATCATTCAATTAAAAAAAGTGGGCAAATAAGCTGAA 4400
                         i iv     ---    v ii     ?     --        vi vi    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAA 836

  chr2_141159240_   4401 TAGACATCTCTCAAAAGACGACATGCAAATAAATGGCCAACAGGTATCTG 4450
                                i    v     v  i  ---- i          i i i iv  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATAT----ACAAATGGCCAATAAGCACATG 882

  chr2_141159240_   4451 AAAAAACGGTCAACATCACTAATCAT 4476
                             i i v         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (147 / 82)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.22 (51 / 23)  


2855 20.46 12.23 2.30  chr2_141196592_141198998     1093  1918 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_141196592_   1093 TGGAAAGATA-ACAATGTTCATGGAATGGAAGGCCTAATATTATGAAGAT 1141
                                   -v v           v      i i       i v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_141196592_   1142 GACAATTCTATCCAAATAGACCTACAGATTTAATG-------TATAGAAA 1184
                          i    v  vi      v  i         i  i -------   vi   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_141196592_   1185 TCCCAGCTGGCTTCTTCCCAGAAATTGACAAGCTGACCTTAAAATGCATA 1234
                                  v   i  iv                  i i      v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_141196592_   1235 TGGAAATACAAGGGACCCAGAAAAGCCAAAAGAATCTTAAATGAAAAAAA 1284
                                i              v        v      i  vi i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_141196592_   1285 CAAAGTTAGTGGGCTCACACTTCCTGATTTCAAC-CTCAGTATAAAGTTT 1333
                                i v  i           ii       v-  i v  i    i -
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT- 249

  chr2_141196592_   1334 ATAGTAATAAAGAGAGTTTGA-------ATAAGAATAGACA--------- 1367
                          i      v    v   v  i-------     i       ---------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_141196592_   1368 --------------------CAG-------C---TACAT----------- 1376
                         --------------------   ------- ---     -----------
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_141196592_   1377 ---------------GTACCAGAAAAGTCCAATGAGAAAAAAA-ATTATC 1410
                         ---------------  i   ii vvi i     i i   i  - v v i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_141196592_   1411 TCAAATATATAGTACTCCCAACAATTGTATAGCCACATGTAAAAGAATGA 1460
                          iv  i v  i  i  vv-i    i  v   ?       i          
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGG-GACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_141196592_   1461 TATTTGATTCCTTCTTCATATCACACACACACTCATACACCCACACATAT 1510
                         vi  v  ii   v i   i i  i i   v ------------- -  - 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAA-------------A-AT-T 483

  chr2_141196592_   1511 AACTAAAAATATACCTTAAACCTAAACATAGATGGTAGA-TGATGAAACT 1559
                             v     iv i v? i       ii  iiv v  i -iv  i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_141196592_   1560 CTTAGGATAAAAAATAGGAAGAAATCTTCATAACTTTGGGTTAAGCAAAG 1609
                              i v    v     ?iv        i i  i        i    v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_141196592_   1610 CCTTCTTAAACATGACACAAAAAATACAAATGAAAAAAGAAAAA-CAGAT 1658
                         vi      i i       v    ii    iii v          -i    
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_141196592_   1659 G--TTAGATCTCATCAAAATGAAAAACTTGTATGCTTCAAAAGACA---- 1702
                         i--  i  ii          v        v i         i    ----
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_141196592_   1703 ----------AAAAGTCAACTGACAGAATGGGAGACAATATTTGCAAATC 1742
                         ----------     v    iv             v              
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_141196592_   1743 ACTTATGTGATAATGGACTTGTATCTTGAATAAATAATGAATGCTTTATA 1792
                          iv   v      v           iv     v    v   iv   - i 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT-ACA 782

  chr2_141196592_   1793 CACTCAACAATAAAACAACAACTAATCCAATTAAATAATGGGCAAATAAT 1842
                         -      i       vi    v   i      ?  v          vi  
  L1M4_orf2#LINE/    783 -ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_141196592_   1843 TTGAATAAATATTTCTCCAAAGAAGATACACAAATGACTGATGAACACAT 1892
                                i i                  i       i ii  i i     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_141196592_   1893 AAAAA-ATGCTCAACACTATTAGACAT 1918
                         i    -          ii ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (103 / 62)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 5.71 (120 / 21)  


3457 20.45 3.84 1.24  chr2_141345248_141348873     2251  3135 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_141345248_   2251 TAGAAAGCTATCACAT--TGATATACTGGAAGATTTAATATTGTTAAGAT 2298
                          i     v    v   -- v  iv i       i                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_141345248_   2299 CACAATAATCCTCAG-TTGTTTTCTACAGCTTCCTCACAATCTCTCTCAA 2347
                         vi     v   i  i-   v --      v   vv i     i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT--CTACAGATTCAACGCAATCCCTATCAA 98

  chr2_141345248_   2348 AATCTCTGCTAGTTTATTTGCCAAAATTGGCAGGCTAATCCTTAAACTCA 2397
                             i v   ivi  v     vi      i  i   i     v   i   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_141345248_   2398 TAAGACAATACAAGGACTCAAAAATAACCAAAAAAGTCTTGAAAAATGAG 2447
                           v iv   i     ivi v i    i      v i          vi  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_141345248_   2448 AACAAAGTTGAAAGCCTCACACTTCC-AATGTTAAAGCTGAATACAAAGC 2496
                                   i i v           -   v i   i  v v        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_141345248_   2497 TATAGTAATCAAGACAAT-TGATACT--CATAAAAATAAAATAGATATAT 2543
                           i             i -  i    --     ii   -----  i    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-----GACATAT 293

  chr2_141345248_   2544 AGATCAATGAGATAGAATTTAGA-T----AAATAAAGCCTCACATTTACA 2588
                                  ii        v   - ----       v  vi       ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_141345248_   2589 ATCAAATGATTTCCAACAATT-TGCCAAGATAATTTAATAGTGGAAAGAC 2637
                         i    v      i i    vv-        iv   i   i -       v
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAA 392

  chr2_141345248_   2638 TCGTCTTTTATACAAATGATACTGGGATAAGTAAATATCCATATGCAAA- 2686
                          v       vv       i i      i  v ii   ?   i       -
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_141345248_   2687 ---TCCACATGGA----TATC-CATATGTGTATAGCAAAATTAACTAAAA 2728
                         --- vv vv    ----  i -  i i-ii    vv          v   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACAC-CATATACAAAAATTAACTCAAA 491

  chr2_141345248_   2729 GTGGATCATAAATCTAAATTTAAAAGTTAAAAC-ATTGCATT--TAAAAA 2775
                         i       ? i i      v   i  i      -  viv i --  i  i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_141345248_   2776 GAAACATGGAATTAAATGTTAGTATCTTTGGATTAGGCAATGGTTTCTTA 2825
                         i      i i?v     v  v  iv i    i                  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_141345248_   2826 GATATGATACAAAAAGCACAAGCAACAAAAGAAACAAATAGCTAAATTAT 2875
                                i  v                       -      v      iv
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGG 640

  chr2_141345248_   2876 ACTTCATCAAAATTTAAAACTTTTGTGATTCAAAAGGCACCTTTGA-AAA 2924
                                       v            v      i i   iv ii -   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_141345248_   2925 GAGAAAA---AAACTATAGCATGGCAGAAAACTTTTGCAAAT----TATC 2967
                          v     ---  v i i  v    v      iv         ----    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_141345248_   2968 TTACAAGGGAGTTTTATCTAGAATGTATTCAAAATTCTAGTAACTCAATA 3017
                          v i      v  v    i     i   vv i  i   vii         
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_141345248_   3018 TTAAAAAGACAAAGACCCCAGTAATAAAATGGGCAAAAGCTTTAAATAGA 3067
                         v            v v    i v?v            i v   i      
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_141345248_   3068 CATTTCTTCATATAC-ACATATAAATGGCTAATAAGCACATTAAAAAGAT 3116
                                i  v v v- i   i       i           -i       
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-GAAAAGAT 889

  chr2_141345248_   3117 ACTCAACATCTTTAGGCAT 3135
                         i         v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (98 / 79)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.96 (45 / 23)  


2771 26.01 5.43 0.81  chr2_141418377_141423730     3998  4862 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_141418377_   3998 AAAGATATTCCATGCTCATGGAGTAGAACAATTAGAATTGGTAAAATGTC 4047
                                 i     i       v i   v v   iv    v   i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_141418377_   4048 AACACTACCCAAAGCTACCCACAGATTATATGCAATCTCTATCAA----- 4092
                           i   v      viv i i       vv i      i       -----
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_141418377_   4093 -----------------GAAAC---CAA--TGATGTTA-----CA----G 4111
                         -----------------    i---   --    vi  -----  ---- 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_141418377_   4112 AGCCACAAAAGACCCCAAATAGCCAAAACAATCCTAAGCAAATAAATAAA 4161
                          ivii   ii     vi                i i --   vi  -i  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAA-GAA 200

  chr2_141418377_   4162 TAAAGACAGAGACATCACATTACTTGACTTCAAAATGTAGTACAAAGACA 4211
                         i    vii   ivv     i v iii i       iv  v       vi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_141418377_   4212 TAGTAAACAAAACGGCATGGTGC-GATATAAAAACAGACATAGAGAACAG 4260
                         i     v   i  i ii    i - ii    ii i       v   v  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_141418377_   4261 TGGAACACGCTAGAGAACTCAGAAATAAATCCATACACTTACAGCCAATA 4310
                              i viv v    iii          i       i   ii i    v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_141418377_   4311 CATTTTTGACAAAGGCACCATGAACATACA-TGGTAGAAAGGACAATATC 4359
                         v     i     i  ii   v  v   v  -   -i     i i i v i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTT 399

  chr2_141418377_   4360 TTCAATAAATAGTGCTGGGAAAACTAGATATCCCTATGCAGAAGAATGAG 4409
                              i    i         v    i    ?  vi     i        i
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_141418377_   4410 ACTAGATTCCTATCTCTTGCCAAATATAAAAGTCAAATCAAAATGAATCA 4459
                         ii i  ii    i   vii   v   i    i i  v        i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_141418377_   4460 AAG-CTTGAATCTAAGATGTAAAACTATTAAACTACTGAAAGAAAACATT 4508
                         ?  - i i   v     vv         v     vi ii          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_141418377_   4509 TGGGCAACACTTCAGGACAT-GGGTCTGGGCAATGATTCCTTGGCTAAAC 4557
                         v ? i  vv    iv   v -    - i       i  i   i v  viv
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGA 598

  chr2_141418377_   4558 TTTCAAAAGCACAGGCAACAAAAGCAAAAATAG-CAAATGGGATTATATG 4606
                         ivi          i          v        -i    v   i vi  v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_141418377_   4607 AAA--CAAAAAGGTTTCTGCACAGCAAAGGAAACAATCAACAAAGAGAAG 4654
                            --i     --i  i  ii vv       v  v     v    v   i
  L1M4_orf2#LINE/    649 AAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_141418377_   4655 AACAAATCTACAGAATGGAAGAAAATATTTACAAACTATCCATCTGACAA 4704
                          ivv  i i         i           i    ii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_141418377_   4705 GATATCAATAACCAAAATATATAAGGAACTC----AATTCAATAGCAAAA 4750
                          iv iivi  v   i         i      ----  i      ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_141418377_   4751 TAACTAATAATGTGATTTTAAAATGGGCAAAAGATCTGAGTAGGCATGTC 4800
                         vi  v     ivii   ?v            i   i   i   i   v  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_141418377_   4801 TCAAAAAAAGACACACAATTGGCCAACAGATATATGAAAAAATGTTTAAC 4850
                           v   i    i i    v       i iii i       i   i i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_141418377_   4851 ATCACTAACCAT 4862
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (144 / 77)
Gap_init rate = 0.02 (17 / 905), avg. gap size = 3.18 (54 / 17)  


2716 26.56 2.33 1.78  chr2_141533040_141537911     3493  4392 (480)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_141533040_   3493 AAAAATCATTTCATGCTCATGGATTGCAATAATCAATATTATTAAAATGT 3542
                            i  -  ii    i          v  v v i      i    i   v
  L1M4_orf2#LINE/      4 AAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_141533040_   3543 TCATACTGCACATAGCAATCCACAGATTCAACACCATTCCTATCAAAACA 3592
                         iv     v v  v vii   i           i v  i          iv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_141533040_   3593 CCAGCATCAATTTTCACAGAATTAGA-AAGCC-ATTCTAAAATTCATATA 3640
                              vv vv    ii     v v  -    i-  i             i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_141533040_   3641 GAAA-ATAAT---TCCA-AATAGCCAAAGCAACCCTAAGCAAAAAGAATA 3685
                             -ii  v---i   -          i   i i i iv  i     i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_141533040_   3686 TAGCTAGAGGCATCAGATTATCCAACTTCAAACTATACTACAAGGCTACA 3735
                         v  i i    vv   v i vi    i      viv        i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_141533040_   3736 GTAGCCCAAACAGCATGATAATGGTACAAAAATAGACACACAGATCAACG 3785
                            ii v i    ii  i  v   i i  ii       i i       i 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_141533040_   3786 GAACAGAATAAAGAGCTCAGAAATAAAGCTGCACACCTACAGCTGACTGA 3835
                            i     vi    ii          v iii   ii  ii iii i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_141533040_   3836 TCTTCAACAAAGTCAACAAAAATAAGCAATGAGGAAAGGAC--TCCGTAT 3883
                          i   i    i viiv   i vi vv     i      i i--  -- v 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC--TTT 400

  chr2_141533040_   3884 TCAATAAATGGCGTTGGGAGCATTGGCTAACCATATGCAGAAGAATGAAA 3933
                             i      i i     vv i   v  ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_141533040_   3934 TTGTAGCCCTATT----ACTATATACAAAAAAAAATAAAAACTCAAGACA 3979
                            v v     ii----  i           ---- v  --     i ii
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAA----TTAA--CTCAAAATG 494

  chr2_141533040_   3980 GCTTAGAGACTTAAATGTAAAACTTTAAACTATAAAAATCCTAGAAGAAA 4029
                          v i ?    i         i vi v           v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_141533040_   4030 ACCTAGGAAGTACTCTTCTAGATATTGGCATAGGCAAAGAATTTATGACT 4079
                           v    ?ivv v     vv  iv    vv       v iv  iv iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_141533040_   4080 AAGTCCTCTAAAGCAATTGCAACAAAAGATA---TTTATAAGTGAGACCT 4126
                          v v vi v      vvv           v --- vv    i vi   i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_141533040_   4127 AATTAAA-CTAAAGACCATTTGTCAAGCAAAATAAACTGCCAACAGAGTA 4175
                         v  i   -i    i  i-     vvvv    iv v   ii   v i   i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_141533040_   4176 AACAGACAACCTGCAGAATGGGGGCAAGTCTTTGCAAACTACACATCTGA 4225
                           v        ii         i v  i v        ii i i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_141533040_   4226 CAAGGAACTAATAGCCAGAATTTATAAAGAACTGAAAGAAATCAATAAGA 4275
                         i    i   vi  v       v           vvv v  v       v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_141533040_   4276 AAAAAACAAGT---TCA-TCAGAAAGTAGGCCAAAGACATGAACAGACAC 4321
                             i    i ---i  - i?i   i i   v  i  iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_141533040_   4322 TTCTCAGAAAGAAGACATGCAAGTGGCCAGGAAACATATGAAAAAATGCT 4371
                              v-        i  i   i      iv  i  i       i     
  L1M4_orf2#LINE/    844 TTCTCC-AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_141533040_   4372 CCACTAATAATCAGAGAAATG 4392
                          v  -----    ????????
  L1M4_orf2#LINE/    893 CAAC-----ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.02 (18 / 905), avg. gap size = 2.06 (37 / 18)  


2882 27.71 2.35 0.89  chr2_141557107_141562394.rev     3902  4796 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_141557107_   3902 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATGTCATGAAAAT 3951
                              ii i  i     i        v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_141557107_   3952 GGCCATACTGCCTGAGGTAATTTATAGATTTAATGCCATCCCCATCAAGC 4001
                            v     v  ii iv i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_141557107_   4002 TACCAATGAGTTTCTTCATAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 4050
                          v   iivivi  i  iii    v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_141557107_   4051 ATGGAACCAAAAAAGAGCCCTCATTGCCAAGACAATCCTAAGGCAAAAGA 4100
                               viiv  ii  v  vvv  v     i      i i iiv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_141557107_   4101 ACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGTCT 4150
                               i      vv    v  v  ii i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_141557107_   4151 ACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATACAGACCA 4200
                                i   i    ii i       i iv ii i   v   i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_141557107_   4201 ATGGAACAGAAC--AAAGCCCTCAGAAATAATACCACACATCTACAACCA 4248
                               i    i-- i  i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_141557107_   4249 TCTGATCTTTGACAGACCTGACAAAAACAAGAAACGGGGAAAGGAT--TC 4296
                         vi    i  i    iivv  v   i v  vvv  i        i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_141557107_   4297 CATATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTGGAAAGC 4346
                         -- v  i  i              v  i   v  ?   i   iii  iiv
  L1M4_orf2#LINE/    398 --TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_141557107_   4347 TGAAACGGGATCCCTTCCTTACACCTTATAAAAAAATTAATTCAAGAGGG 4396
                             iiv   i    v   i     v    v         i    i v  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_141557107_   4397 GTTAAAGACTTAAATCTTAGACTTAAAACCATAAAAACTCT-AGAAGAAA 4445
                         i i ?    i     v v   vi      i      -    -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr2_141557107_   4446 AGCTAGGCA-ATACCATTTAGGACATAGGCATGGGCAAGGACTTTATGTC 4494
                          vv    ?i- v i -  iiv   v v  vv i     v ii  iv ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_141557107_   4495 TA-AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATC 4543
                           -i            vvi           v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_141557107_   4544 T------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTTCCATCAGAGT 4587
                          ------       i -   i  ii vv    i  v   vi  vv i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_141557107_   4588 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTG 4637
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_141557107_   4638 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAG 4687
                          i  i  i  vi          v  i         vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_141557107_   4688 AAAAAAACAA----CCCTATCAAAAAGTGGGTGAAGGATATGAACAGACA 4733
                              i    ----   v  i?    i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_141557107_   4734 CTTCTCAAAAGAAGACATTTATGCAGCCCACAGACATGTGAAAAAATGCT 4783
                         i     v        i  vi viii   v i ii  ii      i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_141557107_   4784 CA---TCACTGGCCAT 4796
                           ---   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (151 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.93 (29 / 15)  


2174 26.23 6.61 3.31  chr2_141728716_141731404     1321  2197 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_141728716_   1321 GAAAGATAGGCCTTGTTTATGGGGTAGAAGGCATAATATTGTCAAGATGT 1370
                                 vv  v    i    iv i    i v         i      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_141728716_   1371 CTGTTCTCTCCAAACTTATC---AG-TTCAATGAAATATCCTCT-AAAGT 1415
                          vi v   i     i v   ---  -     i v   -i   v -   i 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAAT-CCCTATCAAAAT 101

  chr2_141728716_   1416 C--GGTCACACTTTCTGTAAATATTGGGAAAATGATTTAAAAATTCACAT 1463
                          --i iii vi   i  i i v    iv  iv    iiv        i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_141728716_   1464 AGAAATTTGAAAGACCTAGAATAGCCAATAACAGCTTTGGATAA--ACAA 1511
                         i     vii ii    i           -    iii   i v  -- v  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAA-AACAATCTTGAAAAAGAAGAA 200

  chr2_141728716_   1512 CAAAATTGGATAGA-TAAGAGTGCCTAATTTTAAGAATTGAGATAAAG-- 1558
                             i     -i  - v v v v  i     i  i v  ivv i    --
  L1M4_orf2#LINE/    201 CAAAGTTGGA-GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_141728716_   1559 -------TCAAAATAGTGTGATATT--TATGAA-ATAGA----TAAATCA 1594
                         -------    i i      i  i --i  i i-     ----  i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_141728716_   1595 ATAGGACAGAATAAATATTTTAGAAATAAATCTATAGCTAAATGAATAGC 1644
                           i i i     vi v v ii         i i   vv vv   ivi ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_141728716_   1645 TTATTTGTGGCAAAGATATGAAGGCACTAT--AGTAGAGAAACAATAGTT 1692
                          v    vi i   i i iiv   --  i  -- i i i    v      i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAG--ACCATTCAATGGGGAAAGAATAGTC 397

  chr2_141728716_   1693 TTTTCAACAAATGGTGCTGGAAAAATTAGACATCTATATGCAAAATATTC 1742
                                             i v  i i  i ? i i        v v v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_141728716_   1743 ---TTAGATTCATGCCTTATACCATACACAACAATTAACTCGATATGAAT 1789
                         ---  i  ii v i   i i      i    v         ---------
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC--------- 488

  chr2_141728716_   1790 CCTCTAAAAAAAGATGAATCATAAAATGAAATGTAAAGTCCTGAACTATA 1839
                         ----------  i   i    ? i viv        iiv ivi       
  L1M4_orf2#LINE/    489 ----------AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_141728716_   1840 AAACTCCTAGAAGAAAACATAAAACAAAATCTTTATAACATTTGGTTAAG 1889
                               i              ii?vv       ii i  v  v     i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_141728716_   1890 CAAAGATT----AAATTTAACACCAACATCACAGTCTATAAAA---AAAA 1932
                            v i  ---- i  v i       v v    iv v i    ---    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_141728716_   1933 T-GATAAA-----CTTCATCAAATATTAAA--CTTTCATTTTTCTAAAGA 1974
                          -      -----          -      --    ii vi   v  i  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_141728716_   1975 CACTGTTAGGAGAATAAAAAGATAAGTCACAGATTGGGAAAAAAATCTTT 2024
                             i i i  i i i      i  vi      v     i    - v   
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTT 726

  chr2_141728716_   2025 ATAAGGCTTTTATCTGATAAAATATTGGTGTATACTATATATAAAGAACA 2074
                         ii  iv v v          iiv i v  i vi vv             v
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_141728716_   2075 CTCAAAACCCTCCAATAAGAAAAAAA--AATTATCCTACACAAAAA-GGG 2121
                           i v   i ---     v     i --   v i  v iv?     -   
  L1M4_orf2#LINE/    777 CTTACAACTC---AATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_141728716_   2122 CAAAGG--CCAAAAAGGG-------CAAAGGGAATATATGAATGGCAAAT 2162
                               --iii  v  iv-------     iii     ii      v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_141728716_   2163 AAGGACATGAAAAAAAATTCAATATCATTAGTAAC 2197
                            v         i vii    i    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (144 / 82)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 3.00 (87 / 29)  


2440 26.99 5.88 1.38  chr2_141810312_141816058     4389  5255 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_141810312_   4389 GAAAAACATTTTGTGCTCATGGAT-AGAAGAATCAATATTATGAAAATGG 4437
                             i i  iiii  i        -i     v i      i v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_141810312_   4438 CCATACTGCCCAAAGCAGTTTATAGATTCCATGCTATTCCCATTAAACTA 4487
                          v     v      viii i  i      v i  v  i  i  i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_141810312_   4488 CCA-TTGACATTCTT-CAGTGAATTAGAAAAAACT-ATTTTAAAATTCAT 4534
                            -i  v v  i  -   -i    i-- v  i  -  ii          
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAG-AAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_141810312_   4535 ATGACATCAAAAAAGAGCCTGTATAACTAAGCCAATCCCAAGAAA-AAGA 4583
                            iv viiv  ii  v  v v   i i  iv     iii i   -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_141810312_   4584 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 4633
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_141810312_   4634 ACAGTAACCAAAACTGGTACATGGTACTGGTACAAAAACAGACACA--GA 4681
                                i   i  -i  i--         i i  ii i     i --  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGAC-AGTG--TGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_141810312_   4682 CCAGTGGAACAGAATAGAGAACTCAGATTTAAGACCACACATCTACAACC 4731
                         i  i     i     v    iii    vv   iv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_141810312_   4732 ATTAGATCTTTGACAAACCTGACAGAAACAAGCAATGGGGAAATGATTCC 4781
                          v v   i  i     ivv  v  ii v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_141810312_   4782 CTATTTAATAAATGGTGCTGGGCAAACTGGCTAGCCATATGCAGAAAATT 4831
                           v  i  i             vv      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_141810312_   4832 GAAACTGGACTCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 4881
                            ii     i   v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_141810312_   4882 TTAAAGATTTAAATGTAAAACTCAAAACTATAAAAACCCTGGAAGAAAAT 4931
                          i ?   ii         i vii            vi i i        i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_141810312_   4932 CCAGA--TAATACCACTCAGGACATAGGCACGGGCAAAGATTTCCT-GAC 4978
                         vi  i--   - i -i  iv   v v  vvii     v i    i -  i
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_141810312_   4979 AAAATTGCTGAAA--ACAATTGCAACAAAAGCAAAAATTGACGAATGAGA 5026
                          vi i-i ii   --    --          v      v  ii   vi  
  L1M4_orf2#LINE/    595 ATGAC-ACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_141810312_   5027 TCTAATTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTATCATTAGAG 5076
                         ii v  i   v v  i i   i  ii vvi   i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_141810312_   5077 CAAACAGACATCCTACAGAATGGAAGACAATTTTTGCAA--------TCT 5118
                         ii  v     v  i         i   v   v       --------   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_141810312_   5119 -ACAAGGAACTT---------------AAACAAAT-TGACACAC------ 5145
                         - i    i    ---------------   v  v - v   -  ------
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCAATA 790

  chr2_141810312_   5146 ACACACACACAAACA------TTAAAAAGTGAGCAAAGGACATGAACAAA 5189
                          i v v v     i ------  ?    i  i        iv    i i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_141810312_   5190 CAC--CTCAAAAGATGACATGTATATGGCCAGCAAACATGTGGAAAATAG 5237
                           i--   v     v  i  ii v       ii  i  ii  i   ivv 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_141810312_   5238 CTCAACATCACTGATTAG 5255
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (148 / 83)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 2.52 (63 / 25)  


1728 26.06 8.17 7.94  chr2_141852951_141855044.rev      717  1610 (484)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_141852951_    717 CCATATTTTTTAATTAGAAGGCTCAGTAGTGTTAAGATGTCAATATCCCC 766
                             i  iv vi   i    i  i i  v          v     ii   
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_141852951_    767 CAA-----TCTATAAATTTAACATAATTCCAATTAATATCCTAGTAGGAT 811
                            -----    i i   i   ii   i  v  i  v    i  iv vv 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_141852951_    812 TCTTT--AGGAACTGAAAAGCTATTTCTAAAATTTACATGGAAATATAAA 859
                          i   --  i  i   v     iv i        i i        ii  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_141852951_    860 GGACCTAGAAT--CTAAAGGAATCT-AAAAATATAAAAGAACAAGGCATA 906
                              i     -- i   iv     -i    --- i        i ivvi
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAA---AGAAGAACAAAGTTGG 209

  chr2_141852951_    907 AAAATTTATGCTACCAGATTTCAAGATTTGCT-----------GTCATCA 945
                          ii i i ii  v  vi       i i  i  -----------  v    
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_141852951_    946 AAATAGCATAATTTATAGA---AAGGACAGACATACAGATTAACGAAACA 992
                          i i  ii ii -- iv i---     i       i    i  i i  i 
  L1M4_orf2#LINE/    260 AGACAGTGTGGT--ACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_141852951_    993 ----TAAGGGTACAAAAATATACCCATGGATACTTGGTCAATTCATTTTT 1038
                         ---- i  i  v  i     v      iv  viv         v     i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_141852951_   1039 GACAAAGGTACAAAGATAATTCAACAGAGAAATGTTAGTAATCTCACTAA 1088
                              i   i v    iv      ii i    viv    vv i   vi  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_141852951_   1089 ATGGTACTGGAACAATTTAACATTTGTGTACAAAATGATGAACCTTCAGT 1138
                              i    i    i vi i ?iiiii i     vi     vi vv vi
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_141852951_   1139 CATAGATTTTACCATTTATGGAAATTAAACAAAAATAAACTA------CA 1182
                          v  vv ivi     v  iii       viv     ii ii ------i 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_141852951_   1183 AAT-------CTAAAACT-TAAAATTTCTAGAAGAAG-TATAGGC-TAAA 1222
                            -------        -     i ii        i-i     ?-    
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_141852951_   1223 T-----------TGAGTCAG-TAATGGATTTCTTAGA----ACTCCCGAA 1256
                          -----------  i  i  -i     -         ----  v  vi  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGACACCAAAA 606

  chr2_141852951_   1257 GCAGGATTTATGACAGAATATATTGA--GATTTGATTTTATGAAATGTAA 1304
                            vi viv ii v    v v  v  --i   v  i  i  v   vv   
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_141852951_   1305 GATTTTTTTCTTTGAAATTGTGTTATTTGAAAAGCAGTAATAAGAGAATG 1354
                         i vi    -----------   i -- ii  iii  v  vi    i i  
  L1M4_orf2#LINE/    657 AAACTTTT-----------GTGCT--TCAAAGGACACTATCAAGAAAGTG 693

  chr2_141852951_   1355 CAAAGAGAAACTATAGGCTAGGAGAAACGATATACAAATCATATATCTCG 1404
                         v     v  v i i  iv i       vv  v i              vi
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_141852951_   1405 TAACAAACTTGTATCCAGAATACATATACACGCTCACACATGCACGCACA 1454
                            vii                i   v v --------------------
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGA-------------------- 773

  chr2_141852951_   1455 CACACACACACACTCCGTCTCGCTCTCTCTCTTTCAGAGCTCAATAATAA 1504
                         -----------    ------------------ i v i           
  L1M4_orf2#LINE/    774 -----------ACTC------------------TTACAACTCAATAATAA 794

  chr2_141852951_   1505 GAAAACAA----CCTAAT--AACAGTCGGCAGAAGATT-GAACAGA-ATT 1546
                         i  i    ----  i   --  v i v    i i    -   i   -   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_141852951_   1547 TCTCTGCAGATAACATATATGACTAGCTAATAAGCACAATGAAAAAAT-- 1594
                             --  i v  v     ii v i  i          -      i  --
  L1M4_orf2#LINE/    845 TCTC--CAAAGAAGATATACAAATGGCCAATAAGCACA-TGAAAAGATGC 891

  chr2_141852951_   1595 -CAATAATAATTAGAAA 1610
                         -   i vi ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (153 / 78)
Gap_init rate = 0.03 (30 / 896), avg. gap size = 4.80 (144 / 30)  


2866 19.97 3.51 0.30  chr2_141863810_141865773      818  1473 (491)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_141863810_    818 AAAACGTACTACAAATCTATAATCATCAAGACAGGGTGGTACTGGCATAA 867
                              v         v   i i v          v               
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_141863810_    868 AGATGCACACATAGATAAATGTAACAGAATTGAGAATCCAGAAATAAACT 917
                         i   iv   i      v    v  i          i             i
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_141863810_    918 CTCACATCTATGGTCAATTACTTTTTG-C-AGGGTGCCAAGAAAGTTCAA 965
                          vi    i           iv    i - -            vvi     
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_141863810_    966 TGGGGAGGAATTAATTTTTCCAACAAATTGTACTAGGTCAACTGGAAATC 1015
                               iii v  i i   i        v  i  i  v        v ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_141863810_   1016 CACATGCAAAAAAAATAAAGTTGGAAACTT-CCT-ATGCCACATACAAAA 1063
                                    i  - i        vv i -   - ii   i        
  L1M4_orf2#LINE/    432 CACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_141863810_   1064 ATTAACTCAGAATGGACTGCTGGCCTCAGTAAAAGAGTTACAACGAGAAA 1113
                                  i      iii?v i   v i iv     i  v   v v   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_141863810_   1114 ACTCTTAGAAGAAAAAATGTGAGTAAATCCTTGTTTCCTTGGGTTAGAAA 1163
                                        v  iv ?       i i  vv           iv 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_141863810_   1164 AAAGGCTTGTTTGGTATGATATAAAATGCACAAGTGACAAAGGAAAAAAT 1213
                          -v  i  v  v i     i iv   v       ii     i        
  L1M4_orf2#LINE/    581 A-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_141863810_   1214 ACATGCATTGGACTTAA-CAAAAGTA------TTTATGCTTCAAATAACA 1256
                          v  iv         v -     v  ------   i         vi   
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_141863810_   1257 CCATCAAAAAAGTGAATAAACAATTCATACAATGCGAGAAAACATTTTCA 1306
                          i     i        v i    ii  i v    v       i    v  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_141863810_   1307 GATC-CA-ATCTGGTGAGAGACTTGTATTCAGAATATACAAATAACTCTT 1354
                         i   -i -     i i  i         i         i   v       
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_141863810_   1355 ATAATTCAGTAATAAAAAG---GA-AACCCAATATAAAAA----CAAAGG 1396
                          i  i   i          ---i -        v?     ----      
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_141863810_   1397 ATCTG--CAGATATTTCTGTAAAGAAGTTACACAAATGTCCAATAAACAC 1444
                           i  --i   i      vi       v  i       v       i   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_141863810_   1445 ATAAATGGATATTCAACGTCTGTAATCAT 1473
                           i  vi   ii     i  v????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (78 / 49)
Gap_init rate = 0.02 (14 / 677), avg. gap size = 1.79 (25 / 14)  


1546 26.38 4.82 0.23  chr2_141894815_141899424.rev     2891  3326 (1284)    L1M4_orf2#LINE/L1        1   456 (452)  

  chr2_141894815_   2891 TGCAAAAATATCCCACTTTCATGGATTGGAAGAATTAATATTTTTAAAAT 2940
                           v   i        iv                v        v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_141894815_   2941 GACCATTCTACCCAAAGCAGTCTACAGATTCATTGTAATCCCTATCAAAA 2990
                          i v  v  v      viii            vi i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_141894815_   2991 TGCCAA-TGTCATTTTTCACAAAAATAGAAAAAGCAATTATAAAATTTGT 3039
                          v   i-  i -     ii  i    v  v  ivii  iv       ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_141894815_   3040 ATAGAACAACAATAACAACAAAATA--CAAAGCAATCCTAAGCAAAAAGA 3087
                           i   vvi   viivvv  i    --    i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_141894815_   3088 ACAAAAATGTAGGCATCACATTACCTGTCTTCAAAA-------------T 3124
                              iv  v   vv     i v  iivi       ------------- 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_141894815_   3125 ATAGTAATTAACATAGCGTAATATTGGTACGA----AAACACATAGACCA 3170
                          i      i  v i  i  ii  i   i ii ---- i   i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_141894815_   3171 ATGGAACAGAATAGAGAACCCAGAAATAAATTAATGTATTTACAGCTAAC 3220
                               i     v    ii           iiv  ii     ii ii  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_141894815_   3221 TGATTTTTGACAAAGGTGCTAAGAAGAAACATCAAGGAAAGA-TACCCTT 3269
                                i     i     i    vv vv  viii       -  vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_141894815_   3270 TTGAATAAATAGTGCTGGGAAAACTGAGTATTCATATTCAAAAGAATGAA 3319
                           v  i    i         v     ii  ?i  i  v            
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_141894815_   3320 ACTGGAC 3326
                         ii     
  L1M4_orf2#LINE/    450 GTTGGAC 456

Transitions / transversions = 1.92 (75 / 39)
Gap_init rate = 0.01 (6 / 456), avg. gap size = 3.67 (22 / 6)  

1441 26.22 0.63 1.27  chr2_141894815_141899424.rev     3646  4118 (492)    L1M4_orf2#LINE/L1      439   908 (0)  

  chr2_141894815_   3646 AAATGAATGAAACTGGACTCCTACTTT-CTCAATATACAAAAAGCAATTC 3694
                            v       ii     i     i i- v v           vi  i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_141894815_   3695 AATATGTCTTAGAGACATGAAACTATAAAAGACCTAAAATTATAAAATCA 3744
                           v   vv i ?    v i  -- i   i  --      i       iiv
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAA--TGTAAGAG--CTAAAACTATAAAACTC 534

  chr2_141894815_   3745 CTAGAAGAAAATTTAACGGTAAGACTTCAATACGTTGATCTAGGCAAATA 3794
                         i          iv  iv?    iv    ivv  v   ivi       vvi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_141894815_   3795 TTTTATGACTAAGACCTCAAAATCACAGGTAACAAAAATAAAAATAGGTA 3844
                            iv iiv  v   vi     v    i i       iv        i  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_141894815_   3845 CACAGGACAT-ATTAAA-TGAAAAAGCTTCTGTGCAGTAAAGGAAACAAT 3892
                         v iv    v -  i   - v     -   i     vvi      v  v  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chr2_141894815_   3893 CATCAGAGTAAAATGACAGTCTGTTCAATGGGAGAAAATACTTGAGAAGT 3942
                           vv i   i   v    ii iiivv              i   vi  vi
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_141894815_   3943 ATTCATCCAACAAGGGACTAATATCCAGAATATACAAGGAACTCAAACAA 3992
                           vi   ii i        vi             i  i      vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_141894815_   3993 CTCAAGAGTGAAGAAACAAATAATCCCATTAAAAAGTAGGTAAAGGAAAT 4042
                              v i i  i i        i  v   ?    i i  i      vv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_141894815_   4043 GAGTAAATATTTCTCAAAAGAATACATAGAAATGACCAATAGACATATTT 4092
                           i  i i       v      v i   v     i      ii  i  -v
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-G 882

  chr2_141894815_   4093 TTAAAATGCTCAACATCACTAATCAT 4118
                         vv  i             ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (68 / 53)
Gap_init rate = 0.01 (7 / 470), avg. gap size = 1.29 (9 / 7)  


1912 20.34 1.33 21.04  chr2_141961202_141965527.rev     2704  3834 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_141961202_   2704 TGGAATAACATCCCGTGGTCATGGATTGGAAGAATTAATATTGTTAAAAT 2753
                              vi i     i  v               v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_141961202_   2754 AACCATATTGCTCAAAGCAATCTACAGGTTCAATGTAATCTTTATCAAAC 2803
                         ii v   i v i    vii        i     i i    ii       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_141961202_   2804 TACCAA-TGTCATTTTTCACAGATTTAGAAAAAACAATTCTAAAATACAT 2852
                          v   i-  i -     ii    vv v  v  ivii  i       v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_141961202_   2853 TTGGAACCAATAAAAAG--CCCA-AATAGCCAAA-CAACCCTAATCAAAA 2898
                         v     ---  iv  i --    -          -   i i i vv  i 
  L1M4_orf2#LINE/    150 ATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_141961202_   2899 TGAACAAAGCTAGAAGCATTACATTGTCTGACTTCAGATAATACTAAAAT 2948
                         v        i i  i vv i   i vi ii i    i vvv     v  v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_141961202_   2949 GCCATAGTAACTGAAAGAACATGTTACTGGTATAAAAATAGACACATATA 2998
                           i i     iii i v iii  v      i    ii       i   v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_141961202_   2999 TCAATGGAATAGAATAGAGAACTAAGTTCAGGACCAGCCTGGCGAACATG 3048
                                        v    -----  i   -------------------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGA-----GTCCAG------------------- 322

  chr2_141961202_   3049 AACATGGTCTCTACTAAAAATACAAAAATGTACCTGGCGTGGTGGTGCAT 3098
                         -----------------     ----------------------------
  L1M4_orf2#LINE/    323 -----------------AAATA---------------------------- 327

  chr2_141961202_   3099 GCCTGTAATCCCAGCTACTCAGGAGGCTGAGGTAGGAGAATCACTTGAAC 3148
                         -----------------------------------------------   
  L1M4_orf2#LINE/    328 -----------------------------------------------AAC 330

  chr2_141961202_   3149 CCAGAAGGCAGCGGTTGCAGTGAGCCGAGATCACGCCACTGCACTCCAGC 3198
                            ------------------------------------ i  i -----
  L1M4_orf2#LINE/    331 CCA------------------------------------TACATT----- 339

  chr2_141961202_   3199 CTGGGCCACGAGAGCGAAACTCCATCTCAAAAGAAAGAAAAGAAAAGAGA 3248
                         --------------------------------------------------
  L1M4_orf2#LINE/    340 -------------------------------------------------- 339

  chr2_141961202_   3249 ACTCAGAAATACAGCCATATAATCAAAGGCTACTGATTTTTGCCAAACTT 3298
                         -----------------   ii    ------i       i v   ivv 
  L1M4_orf2#LINE/    340 -----------------TATGGTCAA------TTGATTTTCGACAAGGGT 366

  chr2_141961202_   3299 GGAAATACTATATACTGAGGAAAGGATACAGTTTTCAATAAATGGTGCTG 3348
                          vv  v  i  vi v  i      i   vvv       i           
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_141961202_   3349 GGAAAAATGGACTGCCGTATGCAGGAGAATGAAACTGGATCCATATATCT 3398
                            v  v    iv?  ii     ii        ii    i  v  iv  v
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_141961202_   3399 CATCATATATAAAAATCAACTCAAGATGGATTACAGACTTGAATATGAGA 3448
                           i      i      i       i      i ?    i i   i i   
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_141961202_   3449 CCTGAAACCGTAAACATATTAGAA-AAAACCTGGGGAATACTCTTCTAGA 3497
                         v  i    ii    vv v      -     v i  ?ivv v     vv  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_141961202_   3498 CACTGGTCTAGGCAAAGAATTCACGAATAAGACTTCAAAAGCACAGGAAA 3547
                          vi   vi       v iv   viii   v   vi          i v  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_141961202_   3548 CAAAAACAAAAAATAGACAAATGGGATTTAAACAAAA----AAGCTTCTG 3593
                              i-          i    v   i  v v     ----  i   i  
  L1M4_orf2#LINE/    617 CAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_141961202_   3594 CACAGCAAAAGAAA-TAACAAAGGAGTGAAACAACAACTTGCAGAATGGG 3642
                         ii vv    i  v -  v   iii       vi     iii         
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_141961202_   3643 AGAAAATATTTGTAAAGTATACATTCAACAGGGGACTCATATCCAGGATT 3692
                                     i   vi   i  iii i i      ii       i  v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_141961202_   3693 TACGAAGAACCCAAACAACTCAACAA-AAAACAACCCCAAATAATCCCAT 3741
                           ii      i vv         i  -    vi  ---      i  v  
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGAC---AAATAACCCAAT 812

  chr2_141961202_   3742 TGAAAAGTAGGC---TGACATGAATAAACATTTCTCAAAAGAAGACAAAC 3788
                          ?    i i   ---v  iv      i         v        i v  
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_141961202_   3789 AAATGGCCAAGAAGTCTATGAAAAAACATTGAACATCATTAATCAC 3834
                                   v   ivi       i iii v       ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (139 / 87)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 13.32 (253 / 19)  


3551 19.37 3.64 2.35  chr2_141977143_141982005     3163  4014 (849)    L1M4_orf2#LINE/L1        1   863 (45)  

  chr2_141977143_   3163 TGGAATCATATCC-GTGTTCATAGATTTGAA-ACTTAATAT-ATTAAGAT 3209
                              vv      -i       i    v   -         -i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_141977143_   3210 GCCACTACTACTCACACT-------AGATTCAGTGTTAGCC-TATTAAAA 3251
                          v  v    v i  v i -------       ii iv v  -   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_141977143_   3252 TTCCAACAAGCTTTTTTACAGAAATAGAAAAGCCAATCCTCAAATTCTTA 3301
                          i   i viv       i       v  v    ii     v      v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_141977143_   3302 TGGAATTACAAGGGTCTCTGAGTAGCCGAAAGAACCT---AGAATAAGAA 3348
                              v i      v i v  i     i   v  i  --- i  v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_141977143_   3349 CAAA-TTGGAGGACTCATG--TCCTGATTTCAACACTTACAATAAAGCTA 3395
                             -            ii--   ii       v      v i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_141977143_   3396 CAATAATCAAAACAATGTGTTATAGGCATAATGGCATACATGTAGATCAA 3445
                           i       i   i    v  iv       v ii v    i        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_141977143_   3446 TGGAATAGAATTAAGAGTATA-AAATA----TATATATCTAGGGGCACTT 3490
                                     i     vi -     ----i   i  i  v  v  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_141977143_   3491 GATTTTGGACAAAAGGTGCTGAGACCAGTCAATGGGGGATAAATAGTCTC 3540
                               v     i-     ii      v         i vi        i
  L1M4_orf2#LINE/    351 GATTTTCGACAAG-GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_141977143_   3541 TTCAACAAATGGTGCTGGGATAACCAGATATCCACATGCAAAAGAATGAA 3590
                                             i   ii    ?                   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_141977143_   3591 GTTAGGCTCCTATTTCACACCATACGCAAAAATTAACTCAAAGTGAACCA 3640
                            i i i    ii          ii                i  i i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_141977143_   3641 AAGAGTTAAACATAGGGAGAGCTAAAATCA--AAACTCTTTTTA-AAATC 3687
                         ?   vi    ii  ---          ii --        vvv -   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTA---AGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_141977143_   3688 ATGAACG--AATATTCATTAATTTAGCATTGGCAATGAATTCTTAGATAC 3735
                           iii? --   v   i v vi  i vv v       iv          i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_141977143_   3736 GAGAACAAACGCACGAGGAGCAACAACAACAACAACAACAACAAAACAGA 3785
                           v v    v    i  ------------      -  v  -    i   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAG------------CAACAA-AAGAA-AAAATAGA 632

  chr2_141977143_   3786 TAAACTGGACTTCATCAAAATTAAAACCCTTTGGTGCATAAAAGGACATT 3835
                             i                     v i    -   v v        i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACT 681

  chr2_141977143_   3836 ACCAAGAAAGCGAAAAAGCAATCTACAGAAGGAGAGAAAATATTTTCAAA 3885
                          i        i     ii   i i      v i            v    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_141977143_   3886 TAATATATCCGATAAGGCTCTAGTATACAAAATATATATAATACTCTTAC 3935
                          v       i       vv  v    v  i        v iv        
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_141977143_   3936 AACTCAACAA---AAAGGCAAACATCCCAGTTAAAAAGTGGGCAAACAAC 3982
                                i  ---    i    i v    i  ?    i        vi i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_141977143_   3983 ATTGA-TGGACATTTCTTTAAAGTAGATGAACA 4014
                         -    - i         ii    v    iv   
  L1M4_orf2#LINE/    832 -TTGAATAGACATTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.48 (96 / 65)
Gap_init rate = 0.03 (22 / 863), avg. gap size = 2.32 (51 / 22)  

 280 13.56 0.00 0.00  chr2_141977143_141982005     4313  4371 (492)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr2_141977143_   4313 AAAGTAGATGAACAAAGCACCAATGAGCACAGGAAAAGATGCTCAACATC 4362
                             v    iv     vvi     i      v                  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_141977143_   4363 ATTCATCAT 4371
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 0.60 (3 / 5)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


3368 22.67 2.52 3.07  chr2_142008781_142010968.rev      784  1696 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_142008781_    784 TGGAAAGACCTCCTATGTTCATGGATCAGAAGACTTGATACTGTGAAAAT 833
                                 iv   i            ii        i   i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_142008781_    834 GTCCATACTATTCAAAGTGATCTACAGATTCAGTGGAATTCCTCTCAAAA 883
                          v v     vii    v               ii v   i   v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_142008781_    884 TCCTAATGGCATTTTTTACAGAAATAGAAAAAAAAAATTCTAAAATTCAT 933
                            i iiv  v      i       v  v  ivvi - i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_142008781_    934 ATGGAACCCCAGTGGATCCCAAAGAGCCTAAATCACCTTGGGGAAGATGG 983
                               viv  iv   i  vi  v    v   iv i    iii    v i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_142008781_    984 ACAAAGATGGAGTACTTTCATTTCCTCTTTTTAAAACACATTAATTACAG 1033
                               v     v   iv  i    ivv   i     ---   -i    i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC---TTA-CTACAA 245

  chr2_142008781_   1034 AGCTACAGAAATCAAAGCTGTGTAGTACTGCTATGAAGGCAGCCAT-TAC 1082
                                 v      ii v    i      vi  i i ii  v   -  v
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_142008781_   1083 TTCAATGGAACAGAACACAGAGCCCAGAAATAAACCCACACAT----ACT 1128
                         v         i    ivv    i               i    ----iv 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_142008781_   1129 CAAATGATCTTTGACAAGAGTGCCCAAACTGGACAATGAGGAAAGGGTAG 1178
                            v    i  i      i     v i  iivv     i      ii   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_142008781_   1179 CCTCTTCAACAAATGATGTTGAG-TAACTGGGTATCCACATGCAAAAAAA 1227
                         i  i           i  i  i -i      i  ?            i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_142008781_   1228 AAAAAAAATATTGTGCTC-TGTTTTACAC--TACACAAAAATCAACTCCA 1274
                         vi  i-----   vi i - iii i    --  i        i     v 
  L1M4_orf2#LINE/    446 TGAAG-----TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_142008781_   1275 AATGGATGAAAGACTTAAATGTAAGCTCTGAAA-TGTAAAATTTAAAGAA 1323
                                v ?    i          vv  i   - i     i ivv    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_142008781_   1324 AAGAATGTAGGGCAAAAGGGTTATAACATTGA--TATTCA-TGATTTTTT 1370
                         i i  ii    ?vv   vvv ii i  v   i--  vv  -  i   i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_142008781_   1371 GAATATAATACCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGAG 1420
                         ii    i i            i          v         i  i vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_142008781_   1421 ATTACATCAAA-CTAAAAA--TCTGCTTTTCAACCAAGGAAACAATCAAC 1467
                          i v       -i      -- i  ivi     ---    v  v     v
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAA---AGGACACTATCAAG 687

  chr2_142008781_   1468 AGAGTGAAA------CCTAAACAGTGGGAGAAAATATTTGAAAACCATAT 1511
                          i       ------  i v v i                v   i     
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_142008781_   1512 ATCTGATAAAGGGTTAATGTCCAAAATATATAAGAAACTCATACAACTCA 1561
                                  i  ii vi i    i         ii     v         
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_142008781_   1562 ATAGCAAACAACAACTAAAAACCTGATTTTAAAAAATGGGCAAAGGACTT 1611
                            ii   -  -i  v  v    ii   ?--                i  
  L1M4_orf2#LINE/    788 ATAATAAA-AA-GACAAATAACCCAATTW--AAAAATGGGCAAAGGATTT 833

  chr2_142008781_   1612 GCATAGGCATTTCTTCATCTTTGTCCAGTGAAGACATACAAATGACTAAT 1661
                          v    i       ----------   iv     i         i i   
  L1M4_orf2#LINE/    834 GAATAGACATTTCT----------CCAAAGAAGATATACAAATGGCCAAT 873

  chr2_142008781_   1662 AGAGT-TATGAAAAGATGTACAATATCATTCATCAT 1696
                          -  i-i           iv   i    ????????
  L1M4_orf2#LINE/    874 A-AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (130 / 73)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.32 (51 / 22)  


3009 27.83 0.66 0.77  chr2_142033982_142040662.rev     5281  6189 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_142033982_   5281 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5330
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_142033982_   5331 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATACCCATCAAGC 5380
                            v     v      v i  i  i       ii  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_142033982_   5381 TACCA-TTGCCTTTCTTCACAGAATTAGAAAAAAAAACT-ACTTTAAATT 5428
                          v   -i       i  -i     v v  v  i----  - iii    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG----CTGATCCTAAAAT 145

  chr2_142033982_   5429 TTATAGGGAACCAAAAAAGAGCCTGTATATCCAAGACAATCCTAAGCAAA 5478
                          i   v    viiv  ii  v  v v   v    i      i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_142033982_   5479 AAGAACAAAGCTGGAGGCATCACGTTACCTGACTTCAAACTATACTGCAA 5528
                                   i      vv    ii v  ii i      viv    i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_142033982_   5529 GGCTACATTAATCAAAACAGCATGGTAGTAGTACCAAAACATATATACAG 5578
                         i      v       i    ii     v i i iv ii i v i   i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_142033982_   5579 ACCAATGGAACACAGCAGTGGCCTCAGAAATAATGCCACACATCTACAAC 5628
                          i        i v iiv v ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_142033982_   5629 CATCTGATCTCTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5678
                           vi    i ii     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_142033982_   5679 CCTGTTTAATAAATGGTGTTGAGAAAACTGGCTAGACATATGCAGAGAAC 5728
                         i  v  i  i        i  i  v      v  ?v  i     i ii v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_142033982_   5729 TGAAATTGTACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGG 5778
                             i   v      v   i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_142033982_   5779 ATCAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGACAA 5828
                             ?    i    ii     v       i      vi i       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_142033982_   5829 CCTAGGCA-ATACCATTCAGGACA--GGAATGGGCAAAGACTTCATGACT 5875
                          v    ?i- v i -   iv   v--  iv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_142033982_   5876 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCAGATCT 5925
                          vi            vvi          vv     v  i    ii  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_142033982_   5926 AATTCAACTAAAGAGCTCCTGCACAGCAAAAGAAGCTATCATCACAGTGA 5975
                         v  iv  v v  i i  ii  ii vv    i  vi      vv v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_142033982_   5976 ACAGGCAACCTGCAGAATGGGAGACAAAT-TTTGCAACCTATCCATCTGA 6024
                          v  i     ii            -    -       vii  vi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGA-AAATATTTGCAAATCATATATCTGA 743

  chr2_142033982_   6025 CAAAGTGCTAATATACAGAATCTATAAGAAACTTAAACAAATTTACAAGA 6074
                         i  i vi  vi   v      v     ii    ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_142033982_   6075 AAAAAACAAACAGCCTCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 6124
                             i     i i  iv  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_142033982_   6125 TTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTC 6174
                              v        i  vi viii     i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_142033982_   6175 ATCATCACTGGTCAT 6189
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (149 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2784 25.53 3.46 2.23  chr2_142161850_142167658     4421  5317 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_142161850_   4421 TGGAAAAACATTCCATTCTCACGGACAGGAAGAATCAATATTGTGAAAAT 4470
                               i i  i    vi   i   iv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_142161850_   4471 GGCCATACTGCCCAAAGCAGTTTATAGATTCAATGCTATTCCCGTCAAAC 4520
                            v     v      viii i  i        i  v  i  ii     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_142161850_   4521 TACCATTGACATTCTTCACAGAATTTGGAAAAAAAAAACT-ATTTTAAAT 4569
                          v   vivi v  i  ii     v   ------ v  i  -  ii    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG------ACAAGCTGATCCTAAAA 144

  chr2_142161850_   4570 TTTATATGGAA-T-CAAAGAAGACCCTGTATAGCCAAGACAATCCTAAGC 4617
                           i        - -   i --     v v        i      i i iv
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_142161850_   4618 AAAAAGAACAAAGTTGGAAGCATCACGCTACCTGACTGCAAACTATACTA 4667
                           i               i vv    i  v  ii i v    viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_142161850_   4668 CAAGGCTACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGACATA 4717
                            i          i   i    ii     i   i iv ii i       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_142161850_   4718 TAGACCAATGGAGCAGGACAGACACCTTAGAAATAATGCCACACATCTGT 4767
                             i       ii  i iv  v viii        vv   i    i i 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_142161850_   4768 AACCATCTGATCTTCGACAAACCCGACAAAAACAAACAATGGGCAAAGGA 4817
                         iii  vi    i        ivvi v   i v  vv       v    i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_142161850_   4818 -ACTCCTATTTAGTGAATGATGCTGGGAAAACCGGCAAGCCATATGCAGA 4866
                         - v  i -  i iii    i        v   i  vv ?   i     i 
  L1M4_orf2#LINE/    393 TAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_142161850_   4867 AAACTGCAACTGGACCCCTTCCTTACACCTTATAC----------TTAAG 4906
                          i v  v ii         v   i     v     ---------- i  i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_142161850_   4907 ATGGATTAAAGACTTAAATGTAAAACCCCAAACCATAAAAACCCTAGAAG 4956
                               i ?    i         i v iv    i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_142161850_   4957 AAAAACTAGGCA-ATATCATTCAGGACACAGGCATGGGCAAAGACTTC-- 5003
                             vv    ?i- v   -   iv   viv  vv i     v ii   --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_142161850_   5004 ----ATGACAAAAATGCCAAAAGCAATTGCAACAAAAGCCAAAATTTACA 5049
                         ----      ------         vvv          vv     vv i 
  L1M4_orf2#LINE/    591 AGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_142161850_   5050 AATGGGATCTAATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATC 5099
                            v   ii v  i   v v  i     i  ii vv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_142161850_   5100 ATCAGAGTGAACAGACAATCTACAGAATGAGAGAAAACTTTTGCAA-TC- 5147
                          vv i      v      i i        i       iv       -  -
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_142161850_   5148 TA---CTGATCTAAGGTCTAATATCCTGAATTTATAATGAACTTAAACAA 5194
                           ---     v- i  v  vi     v    v     v     ivv    
  L1M4_orf2#LINE/    735 TATATCTGATA-AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_142161850_   5195 TATTTACAATTAAAAAAAAAAAACAACTCCGTCAAAAAGTGGCCAAAG-A 5243
                         i- iv i   --     i v   i   i vi i?    i   v     - 
  L1M4_orf2#LINE/    784 C-TCAATAAT--AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_142161850_   5244 TATGAACAGACACTTCTCAAAAGAAGATATTTATGTGGGCAA----CATG 5289
                          v    i     i     v           vi vi   v   ----  ii
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_142161850_   5290 TGAAAAAAAGCTCAACATCACTGATCAT 5317
                               i v           ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (130 / 95)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.55 (51 / 20)  


 764 24.41 1.41 1.88  chr2_142332348_142336435.rev     2371  2583 (1505)    L1M4_orf2#LINE/L1        1   212 (696)  

  chr2_142332348_   2371 TGGGAAGATATTCCATGT-CATGGATTTGAAGAAACAATATTGTTAAAAT 2419
                            i       i      -        v     vvi           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_142332348_   2420 GTCCATACTACCCAAAGCAATCTACAGATTCAAT-CAATTCCCAGCAAAA 2468
                          v v     v      vii              i-    i  i v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_142332348_   2469 TACCAATGACATTCTTCACAGAAATCAAAAAAA-AATCCTAAAATGTATA 2517
                          v   iivi v  i  ii       ii v  iv-i          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_142332348_   2518 TGGAATCACAAAAGACTCAAAATAGCTAAAGCTTTACTGAGCAAATGCTA 2567
                              vii   ii   i  i      i   i vv vi   --   v -- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAG--A 196

  chr2_142332348_   2568 AGGACAGAACTGGAGG 2583
                           i   i ii      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG 212

Transitions / transversions = 1.74 (33 / 19)
Gap_init rate = 0.02 (5 / 212), avg. gap size = 1.40 (7 / 5)  

2618 25.21 1.26 0.56  chr2_142332348_142336435.rev     2883  3596 (492)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr2_142332348_   2883 AGAAAGAAAAAAAAAACTGGAGGAATCACATTACCTGACTTCAAGTTATA 2932
                          i      i  v   ii       v     i v  ii i     iviv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_142332348_   2933 CTACAGAGCTATAGTAACTACGATGGCATGGTACTGGCATAAAAACAGAC 2982
                              i     i     ii v  ii ii              ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_142332348_   2983 ACATAGACCAGTGGAACAGAATATAGAAAACATAAATAAATCCAGACATC 3032
                          i     i  i     i     vv   ivv  v       i   v    i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_142332348_   3033 TACAGTGAACTCATTTTTGACAAAGGTGTCAAGAACATACATTAGGGAAA 3082
                           ii  v  i v     i     i    i     v   v  v i      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_142332348_   3083 GGACAGTCTCTTCAATCAATGTTGCAGGGAAAACTGGATATTCATATGCA 3132
                          i i     i     iv    v   v    v         ?i  i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_142332348_   3133 GAAGAATGAAGCTAGACGCCTATCATTTGCCATATACAAAA-TCAAATCA 3181
                         i          i i   v    i vivii            - i  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_142332348_   3182 AAATGTATTAAAGACTTAAATCTAAGATCTCAAACCATGAGACTACTGAA 3231
                              v  i ?    i     v     v  v    i  i i   vi ii 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_142332348_   3232 AGAAAGCAATGGAGAAACTCCCCAGGATATTGGAGTTGTCAAAGATTTCT 3281
                              i  vv  ? v  v  ii iv  iv    iv v v   v i     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_142332348_   3282 TGCGCAATAT--C-CCACAAGCACAGGAGACCAAAGCAAAAATGGACAAA 3328
                          i---i    -- -   v       i vi  v    v      i  i   
  L1M4_orf2#LINE/    590 TA---GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_142332348_   3329 GAAGATCATATCAAG-TTAAAAAGCTTCTGCAGAGCAAAGGAAATAATTA 3377
                         vvi  iivi     i-       -   i  iivvv       v iv  i 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_142332348_   3378 ACAAAGTGAAGAGGTAAACTACAGAATGGGAGAAATTATTGGCAAACTAC 3427
                          v        i  ii  v i               v    v     ii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_142332348_   3428 CCATCTGAC--GAGATTAATAACCAGAATATGTAAGGAACTCAAACAACT 3475
                         vi      i-- i  i vi  v         i   i      vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_142332348_   3476 AAATAA--AATAAACTAATAATCTGATTTAAAAATGGGCAAAAGATCTGT 3523
                         v     --  v i  v     i ii   ?             i   i  v
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_142332348_   3524 ATAGACACTTCTCAAAAGAAGACATACAAATGGCAAACAGGAATATGAAA 3573
                                i     v        i           v  i i v i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_142332348_   3574 AGGTGCTCAATACCACTGATCAT 3596
                           i       i i  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (108 / 68)
Gap_init rate = 0.01 (8 / 719), avg. gap size = 1.62 (13 / 8)  


2216 24.09 3.35 11.08  chr2_142505251_142507641      916  1899 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_142505251_    916 TGGAAAAACATTTTATTCTCATGAATTGGAAGAATCAATATCATAAAAAT 965
                               i i  iii  vi     i         v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_142505251_    966 GGCCATACTACCCAAAGT-ATCTATAGATTCAATATTATTTCTGTCAAAC 1014
                            v     v      v -     i        iiiv  ii  i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_142505251_   1015 TACCAATATCATTTTTCATAGAATTAGATAAACTAATC-TAAAATTCATA 1063
                          v   iivv v     iii    v v  i  i  i   -           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_142505251_   1064 TGGGACAAAAAAAGAGACC--AAATAGCCAAAGCAATCCCAAGCAAAAAG 1111
                            i -- viv   i    --i          i     iii iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_142505251_   1112 AACAAAATCACAGGCATCACATTGCCTGACTTCAAACTATACTATAGAGC 1161
                               i iiv   vv     i v  ii i      viv     i i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_142505251_   1162 TACAGTAATCAAAACAGCATGG-ACTGGTACAAAAACAGACACTTAGACC 1210
                                     i    ii   -     i i  ii i     iv    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_142505251_   1211 AATGGAACAGAATACAGAACCTGGAAATAAAGCAGCGCACCTATAGCCAT 1260
                                i     vv   ii ii        v viii  ii   i i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_142505251_   1261 CTGATTTTCAACA-----GTCAACACAAATATGCAAAGGGGAGAGGAC-- 1303
                         i        i   ----- i   v  ---i  v   v     i  i i--
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAAAGAATAG 395

  chr2_142505251_   1304 TCCATATTCAATCAATTGTTTTGGGATAGCTGGCTAGCCACATGAAGGAG 1353
                           -- v     iv   v  vi     i i    v  ?       v ii  
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_142505251_   1354 AATGAAACTGAACCTTTCACCATATACAACAATACAGCATACAAAACACA 1403
                               ii  i   ii ---------------------------------
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCT--------------------------------- 460

  chr2_142505251_   1404 CCATACAAATACACCATACAAATGTGTCATACAAAAATTCACCATACAAA 1453
                         --------------------------------------------------
  L1M4_orf2#LINE/    461 -------------------------------------------------- 460

  chr2_142505251_   1454 AATTGTATATGGTGAACCTTTCACCATATACAAAAATTAACTCAAGATGG 1503
                         ---------------    iv                        i    
  L1M4_orf2#LINE/    461 ---------------ACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_142505251_   1504 ATTAAAAAATTAAATGTAAGACCTCAAAGTA-----------GAAGAAAA 1542
                           i ? i vi           v  v   v  -----------        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_142505251_   1543 CCTGGG---AAATACCATTCTGGACTTTGGCCTTGGGAACAAATTTATGA 1589
                          v i  ---    -- -   vv   i    vi v  v  iiiv  iv ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_142505251_   1590 CTATTCCATCAAAAGAAATTGCAACAAAAACAAAAATTTACAAGTGAAAT 1639
                         v   vv  i      v vvv         iv      vv i  i vii i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_142505251_   1640 CTAATTAAGCTAAAGAGCTACTGCACAGCAAAAGAAACTATCAACAGAAG 1689
                         i v  i  iv v  i i  vi  ii vv    i  v        v i iv
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_142505251_   1690 AAACAGACCAACTAAAGAATGAAAGAAGACATTCACAAAGAATGCATTTG 1739
                         i  v    v v i v      ii    i i   ii    vv  ii  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_142505251_   1740 ACAAAGGTCTAATATCCAGAATGTGTAAAGAACTTAAACAATTCAACCAA 1789
                          i  i  v  vi          i i         ivv    i    i-  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-AA 791

  chr2_142505251_   1790 TAAAAA-ACAAATAACC--ATTCAAAAGTGGGCACAAGACATCAACAGGC 1836
                               -          --   ?    i      v i  iv v  i  i 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_142505251_   1837 ACTTCTC--AAGA-GACAGACAAGTGGCCAACAAACATATAAAAA-ATGC 1882
                          i     --    -  i v    i       i  i  i  i    -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_142505251_   1883 TCAACATCACTAATTAT 1899
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (149 / 85)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 7.10 (142 / 20)  


3446 21.32 4.08 1.47  chr2_142744678_142746904.rev      854  1735 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_142744678_    854 AAAGATATCTTACGTTTATAGATCAGAAAATGTAATATTGTTAAGATGGT 903
                                  ii i   i  i   ii   i iv                 i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_142744678_    904 AATGCTCCTCAAAATAGAACAATA-ATGCAGTTCAGTTTTTATAAAAAAC 952
                            i    i    v -  v v i -  v  iiv  i iii   v    v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATT-GATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_142744678_    953 CCAGC--CTTCCTTTGGCACAAAGGAATCACCTCATCCAAACATTTATAT 1000
                              -- i ii    -  v   vvi iv v  v    v  v   i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_142744678_   1001 GTATATGCAAGGGACACAGAATAGCAAGAACAATCTTGAAAAAGAA---T 1047
                          v v           v         v i                  ---i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_142744678_   1048 GCAGTTAGAGGACTCATACG----GATTTCAAATCTTACTACAAA-CTTT 1092
                         iv    i         i  v----i        v           -  vi
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_142744678_   1093 AATAAATAAAGACAATGTGGCACTGGCACAAAAATATGCATATAGATCAA 1142
                          i   - v      i     i       i  ii   vi            
  L1M4_orf2#LINE/    252 AGTAA-TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_142744678_   1143 TGGAATGAAATT-----TCCAGATATAAACTCTTACATTTATGGTCAATT 1187
                               ii    -----      v      i v                 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_142744678_   1188 AATTTTTCACAAGGGTGCCAACATGACTCACTGGGGGGGGGGGAAGCCTT 1237
                         i     iv             v iv i   v     iii iiv - i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-GTCTT 399

  chr2_142744678_   1238 TTCAAATAGTGGTACTGGAACAACTGGATTTCCACAGG-AAAGGAATGAA 1286
                              vv i    i    i          v?     v -   i       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_142744678_   1287 GTTTGACTTCTACCTCACTCCATACACAAAAATTAAATCAAAATTGGTCA 1336
                            v   ii         v     i           v       v i   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_142744678_   1337 TCAACCTGAATGTAAGAACTAAAATCTATAAAACTCTTACAAAAAAA--- 1383
                         ?vi    i         i      -              v  i    ---
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACAT 548

  chr2_142744678_   1384 -----------TCCATGATCTTGGATTAGGCAATAGCTTCTTAGATTTGA 1422
                         ----------- i i   i     i         i i         v   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_142744678_   1423 CACTAAAAGAAAAGGGGACTAAATTTAAAAAAGGGATAAATCGGATTTCA 1472
                            i     v v i vi  v   v--      vi       i   i    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAG--AAAAAATAGATAAATTGGACTTCA 646

  chr2_142744678_   1473 TCAATATTATGACCTTTTGTGCTTTACAGTATACCATCAAGAAAGTGAAG 1522
                             v    vi v           i v  v i  i              i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_142744678_   1523 AGACAAACCACAGATTGGGAGCATATTTTTATTCATACTATAAGTGATAA 1572
                               v       v      v v  v   iivv  vv    vv      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_142744678_   1573 AGGTCATGTATTTCAAATATTTTTTGCAGCCCTTACAATTCTACAAAATA 1622
                         i  v v     iivi     v vvv - i i       i  v i  v v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAG-AACTCTTACAACTCAATAATAAA 795

  chr2_142744678_   1623 ATGACA--TCACA-AAT--GAAAATGTGAAAATGATTCAAATAGGGCATT 1667
                          v    -- v  v-   --i      v v   v    ii     i-    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA-CATT 844

  chr2_142744678_   1668 TCTTTAAAGACAAAAAATAAATAAATGGCCAATAAGCATATGAAAATATG 1717
                            ii     ---- i   v i                i       v   
  L1M4_orf2#LINE/    845 TCTCCAAAGA----AGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_142744678_   1718 CTCAATGTCACTGGTCAT 1735
                              ii   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (102 / 84)
Gap_init rate = 0.02 (20 / 905), avg. gap size = 2.45 (49 / 20)  


1675 27.70 8.39 4.02  chr2_142804620_142808861.rev     2882  3751 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_142804620_   2882 TGAAGAGATACGCCATGTTCATGGACTGGAGGACTCAATATAGTCATCAC 2931
                           i i     iv             i    i    i     v  i vv i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_142804620_   2932 GTTTATTCTAGCCAAAT-GGCATAAATGTTTAACACAATTTTTATCAAAA 2980
                          viv  v  vv      - iiv  v vi  i   i    iii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_142804620_   2981 TCTCAGCAGAATTCTTTTGTATATATAGACAAGATTATGTGAACATTTAT 3030
                           i    v vv  -     i v v  v      v v  viv  v   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_142804620_   3031 ATGGAAAGTTACAGGAAGTAGAATGGCTAGGACAATTTTGAAAAATAATA 3080
                                vvi vi   vvi     i  i ii     i        v  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_142804620_   3081 AAAAAAA-AGAGG-------------------------TACGGGTGGAAA 3104
                          v   iv-i    -------------------------   --- iv   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC---TACAAA 246

  chr2_142804620_   3105 A-TATGATATT-------GTGTGATATTGGGGAAGAGGCAGGCACATAAA 3146
                         i-  iii  v -------     i  i   viv ii ii  i  i   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_142804620_   3147 CCAGTGGAAAAGAGGAGGAAACCCAGAAAGAGACCCATACAA--ATGTCC 3194
                         i  i     v   ivv ii ii       v i         v--   vi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_142804620_   3195 AACTGATTTTTGACAAAGGTACAAAAGCAATTCAATGGAAAAAGA-TAGC 3243
                           i       i     i   i v  ii v         ii     -   i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_142804620_   3244 CTTTCTAACAAATAGTACTGGATCAATTGGACATCCATAGATTAA-GAAT 3292
                             ii       i  i    iv   i    i ?   i viiv  -    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_142804620_   3293 GTAAATATCAAAATAAATCTC-ACCTC------TATCCAAAAAATAACTC 3335
                          -  i ------- ii i i -     ------   v      v      
  L1M4_orf2#LINE/    447 G-AAGT-------TGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_142804620_   3336 ATA-TTGATTATGTATTTAAAAGTAAAACATAAAATTATAAAAACTTTAG 3384
                          v - v   i ?iv ii    v    i vv     i       vii    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_142804620_   3385 AGAAAAAAACAAAAAACAAAAACAAAAAAACCTAGGAGAAAATCTTGG-G 3433
                          --------- i      --------------    ? v       v - 
  L1M4_orf2#LINE/    539 A---------AGAAAACA--------------TAGGNGTAAATCTTCGTG 565

  chr2_142804620_   3434 ACATAGGAGTAGACAA---------AAAAAAAAAA--AAAAAAAAAAGC- 3471
                           v v  iv   i   --------- i v vi v --    iv v    -
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_142804620_   3472 -CAGAA--AAAAAT-GAAACATTCAACCTTATCAAAAGTAAAA--CTTTG 3515
                         -  i  --      -  v v   vi  i i       v     --i    
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_142804620_   3516 TTCCGCAAAATACTTCATTAAAAGGAAGAAAAGACAAGTTACAGACTTAG 3565
                          v iv    iv  vii  i  i iiiv          vii     v vi 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_142804620_   3566 AGAAAATATTT-CAAACTACATGTCTGACAGATGA-TTGTATCTAACATA 3613
                                    -    ii i  i     i iiv  -       i iv   
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_142804620_   3614 TATAACCAACTCTCAAAACTCATCAGTAGTAA---AAACAATTCGATTTA 3660
                              vv      i v      vi i  iv  ---   i  ii i   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_142804620_   3661 AAAATGGAAAAATGAC--AAAGATATATTTCACTAAAGAGAAGATATGGA 3708
                                iv   v  i--i  v v i     v i     ii v   iii 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_142804620_   3709 TGGCAAATAAACACACAAAAATATAGTAAACATCTTAGCTGTT 3751
                             v     i    ii    v  iv v      v????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.86 (108 / 28)  


2598 23.30 3.20 2.43  chr2_142822949_142824662      442  1222 (492)    L1M4_orf2#LINE/L1      122   908 (0)  

  chr2_142822949_    442 AAGCTGA-AAGCTATTCCACTAAGATTCAGTCCAAGGAAA-G-AATGCAC 488
                           ii   -     iv   --   i     ---i v     - -  v v  
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCC--TAAAATTCA---TATGGAAATGCAAGGGAC 166

  chr2_142822949_    489 ACAGAGTGGC-AA---------GAGAAAGAAAAAGAAAGTTGGAAGCATC 528
                         v    i i  -  ---------  i      i  v         i vv  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr2_142822949_    529 AGACTTCCTGATTT-AAAATTATTCTACAAAGCTATAGTAATCAAATCAG 577
                          v      ii    -    i - v           i         iv   
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_142822949_    578 TATATTACTAGCATAAA-ACAGACA-ATAAACCAGTGCAACAGAATAGAA 625
                          i iv    i      i- i     -   i i  i  v  i     v  i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_142822949_    626 AACCCAGGAATAAATCTAAACATACACAGTCAACTAATTTTTGACAAGGG 675
                          ii    i      i i v    vi ii     i i     i        
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_142822949_    676 CATCAAGAAGACCCAATGGGGAAGGGATAGTCTCTTCAAAAAATGGTGCT 725
                         iii     vv ii          i i       i     v          
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_142822949_    726 GGCAAAACAGGATTTCCACAGGCAAAAGAATAAAACTGGACTCTTATCTT 775
                           v v   v    v?     v          i  ii     i i  i  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_142822949_    776 ACCTATTATTTTATCCTAAACAACAATCAACTCAAAATGGATTTAAAAAC 825
                           ---------- i v  v    v   i              i- ? i  
  L1M4_orf2#LINE/    466 AC----------ACCATATACAAAAATTAACTCAAAATGGATC-AWAGAC 504

  chr2_142822949_    826 CTAAATATAAGATCAGAAACTATAAAATTCTCAGAAGACAACATAGGGAA 875
                               i     v vi           i   i      v        ?iv
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_142822949_    876 AAAGCTACTGAAGATTGGTCTTGGTTATTATTTTTTGGATATCACATTAT 925
                            v  v vvi vv    vi v  iv  vi   i  i     v   ii v
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_142822949_    926 AAGCTCAGTCCACAAAAAGAAAAACTAAATAAATGAAAATACATTAAACT 975
                             v  iv v      -      v  i      vii v v   i   v 
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_142822949_    976 AAAAACCTTCTTCACAGCAAAGGA----ATTGACGAAAG-GAAATGGCAT 1020
                         v    v   i vii vv       ----  ii -     -    v i  v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAA-GAAAGTGAAAAGACAA 702

  chr2_142822949_   1021 TCTATGGATTGGGAAAAAATATTTGCAAACCATATATCTAATAGATGATT 1070
                         i i ii  v     i              i         i   iiv  i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_142822949_   1071 AATATCCAAAATATATAAAGAACATGTAAAACTCAATACTGGAGA-ATAA 1119
                         vi      i              viv  v         v ii i - i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_142822949_   1120 A-AACCCAATTAAAAAATAGGCCAAATATCTGAATAGATATTTTTCCAAA 1168
                          -         ?      i   v  iv  i        i    i      
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_142822949_   1169 AAAGACA-A-AAATGACCAACAGGTACACGAAATGGTGCTCAGCATCATT 1216
                         i    i - -     i    i i i   i    v i      i     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_142822949_   1217 AATCCT 1222
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.62 (110 / 68)
Gap_init rate = 0.03 (21 / 787), avg. gap size = 2.10 (44 / 21)  


3291 20.13 2.50 0.92  chr2_142941922_142943682      510  1269 (492)    L1M4_orf2#LINE/L1      137   908 (0)  

  chr2_142941922_    510 TTCTTGAATCCCTATGGAATCTCAAGAGACATCAAAGAGCCTAAACAAT- 558
                          i  vi   i v       viv    i   vivi  v    v       -
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_142941922_    559 --AATAAAAAGGAGCAACTCTGGAGGCCCCACACTTTCTTATTTCAAAAC 606
                         --i v   i i  i   vvi      v i       i iv          
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_142941922_    607 ATATTTCAAAGGTACATTGATCAAAACCATATAGCACTGGCATAAAGACA 656
                         v  i v     v    v i     i  vi i i i          i  i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_142941922_    657 GACATATAAACCAATGGAACTGAATAGACAGCCCAGAAATAAATCCTCAC 706
                                 i i        iv    v  v  i           i  vi  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_142941922_    707 ATATATAGTAAAATGATTTTCAATA-GGGTGCCAAAGACCACTCAATGGG 755
                           v   i  v  v        i i -         -     i        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGG 385

  chr2_142941922_    756 GAAATGACAGTCTCCTAAAAAAAAAAAAAAGGTGCTGGAAAAACTGTATA 805
                             vi i     ii v  v   v------        i v     v   
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAAT------GGTGCTGGGACAACTGGATA 429

  chr2_142941922_    806 ACCA--TGCAAAAGAATGAAGTTGGACCTTTATCTTATATCATATACAAA 853
                         ?   --                      ii  i  i i i          
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_142941922_    854 AATTAACTCAAAATGGATCAAAGACCTAAACATAAGATCTAAAACCACAA 903
                                             ?         ii     v       i i  
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_142941922_    904 AACTCATAGAAGAAAACATAGGTA-AAACCTTCATGCAATTGGATTTGGC 952
                              v                ?i-   i    i  vvv    i  v   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_142941922_    953 AATGATTTATTGGGTATGACATTAAAAGCACAGGCAACAAT-TAAAAAAT 1001
                             i   v  i i       ii         i       v-v       
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_142941922_   1002 AAATAAATAGAATCACATCAAAATTTAAAACTTTTGTGCACCGAGGGATA 1051
                          i      v i iiv          v             vi i i   i 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_142941922_   1052 CAATCGACAGAATGAAAAAGCAATCCACAGAATGGAAGAACATACTTTCA 1101
                          v   i v i i      ii   i           i    v   i  v  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_142941922_   1102 AATAATATACCTGATAAAGAATTGATATCCAGAATACATAAAGAACTCCT 1151
                            v     i       i i i vi           i           i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_142941922_   1152 ACAAC--------AACAAAACTAACAACC-AATTTTAAAATGGACAAAAA 1192
                              --------  v  i  v  i    -    ?v       i    ii
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_142941922_   1193 AGTT-AATAGATATTTCTCCAAATAAAATATATAAATAGCCAA-AAGCAT 1240
                          v  -      i           v  i     i    i     -     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_142941922_   1241 ATAAAAAGATGTTCAACATCAGTGATCAT 1269
                           i        i         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (94 / 55)
Gap_init rate = 0.01 (11 / 772), avg. gap size = 2.36 (26 / 11)  


2803 28.22 1.00 0.89  chr2_142943718_142949022     3914  4813 (492)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_142943718_   3914 ATACGCCATGCTCATGTATGGGTAAAATCATTATTGTGAAAATGACCATA 3963
                            iv     i     v  v  v i v i v      v  i   i v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_142943718_   3964 TTGTCAAAAGCAGCCTACAAATTCAATGCAATTCCCATCAAAATACCACC 4013
                         i vi v   viiii     i      i     i  i        v   v 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_142943718_   4014 ATCATTCTTCACAGAATTAGAAATGACATTCCTAAAATTCGTATGGAACT 4063
                         vv v  i  ii     v v  v v viiv           i       v 
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_142943718_   4064 AAAAAAGAGCGCTCA---TAGCCAAACCAAGCCTAAGGAA-AATAACAAA 4109
                         iv  ii  --- i  ---        v   v i i ii  -  v      
  L1M4_orf2#LINE/    158 GCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_142943718_   4110 TCTGGAGGCATTATATTACCTGATTTCAAACTACACTGTAAGGCTGTAGT 4159
                         vi      vv i i i v  ii        vivi   ii  i   ii   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_142943718_   4160 CACCAAGACAGCATG-TACTGGTATAAAAACAGGCATATAGACTGATGAA 4208
                         v i        ii  -      i    ii i  i        iii   i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_142943718_   4209 ACAAAATAGAGAA-CTGGAAATAGAGCTAAATACTTACATTCAACTGATC 4257
                          i i   v    i- ii      i v i v i i   iiv    i    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_142943718_   4258 TTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGAGTACCCTATTCAA 4307
                           i     i vviv   i v   vv i          i  vi  v     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_142943718_   4308 CAAAATGATGCTGGGATAATTGGCAAGCAACATGTAGAAGAATAAAACTG 4357
                             -  i        i  i   vv ? v     i i      i  ii  
  L1M4_orf2#LINE/    405 CAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_142943718_   4358 GGACCTCTTCC-CTCACCTTATA-AAAAATCAACTCAAGATGGATCAAGG 4405
                          -   i  v  - v    v    -      i       i        ?i 
  L1M4_orf2#LINE/    454 G-ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_142943718_   4406 ACTTAAACCTAAGACCTGAGGCCATAAAAATATCTAGAAGATATCATTGG 4455
                           i    iv     v  i ii i      v v -       v v   v  
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAACATAGG 551

  chr2_142943718_   4456 AA-AAACCTTTCTAACATTGGCTTAAGCAAAGACTTGATGACCAAGAACC 4504
                         ?i-   i   iv i  v    v   i    v ii  vv iivi v  vv 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_142943718_   4505 CAAAAGCAAATGTGACATAAACAAAGATAAATAGATGGGACTTAATTAAG 4554
                                 v v ii   v  iv   i   i   i  v      v  i  i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_142943718_   4555 CTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTAAACAGACA 4604
                         v v    i   i  ii vv    i  v iv    iv i   i  v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_142943718_   4605 ACCTAGAGAGTGGGAGAAAATCTTTGCAAGCTATGCATCGAACAAAGGAC 4654
                            i v   i           v       iii  ii   vi i  i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_142943718_   4655 TAATATCCAGAGTCTACAAGGAACTCAAACAAATCAGCAAGACAAAAAAC 4704
                          vi        i v  i  i      vv    v   ii  --i     iv
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA--TAAAAAGA 799

  chr2_142943718_   4705 CAAACAATCCCATCAAAGAGTGGGCTAAGGACATAAATAGACAATTCTTA 4754
                             i  i  v  i?  i i     v     iv i        v    iv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_142943718_   4755 AAAGAAGATATACAAACAGCCAACAAATATATGAAAACATGCTCAACATC 4804
                                         ii     i  ii i       v            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_142943718_   4805 ACTAATTAT 4813
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.55 (152 / 98)
Gap_init rate = 0.01 (12 / 901), avg. gap size = 1.42 (17 / 12)  


2141 27.39 5.19 0.53  chr2_143044578_143046249      429  1180 (492)    L1M4_orf2#LINE/L1      122   908 (0)  

  chr2_143044578_    429 AGATTAATAAGCT-ATC------TCCACTATAAAA---CA-GAAACCTA- 466
                          i   i i     -   ------ i  -   ii  ---  - ii   i -
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCA-TATGGAAATGCAAGGGACCCAG 170

  chr2_143044578_    467 AATACTCAAT-TAAT--TGGAAA-GAA-AATGAAGT----AGACTGAC-- 505
                             vi   v-i   --  i   -   -  ii    ----i    v  --
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_143044578_    506 --------TTCAAACTATAATATAAGTCTACAGTAACCAAAACAGCATGC 547
                         --------      viv  v  i  iv         i   i    ii  v
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_143044578_    548 TACTGGTACCAAAACAGATATATAGTCCAGTGGAACAGAATAGAAACCTC 597
                               i iv ii i   i      vi  i     i     v  i vii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_143044578_    598 AGGAATAACACTATACGTCTACAGCTATCTGCTCTTCAACAAATCTGACC 647
                           i     vv i    i i  ii ii vi  v i   i    ivv  -  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG-CC 369

  chr2_143044578_    648 AAG------CAATAGGGAAACGATTCCCTATTTAATAAATGGTGCTGGGA 691
                            ------    i      vi  vvi  v  i  i              
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_143044578_    692 AAACTGGCTAGCCATATGCAGAAAACAGAAACTGGACCCCTCTCTTAAAC 741
                         v      v  ?   i     i  i vv   ii         vi  i v  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_143044578_    742 CTTATACAAAAATTAACTCAAGATGGACTAAAGACTTAAATGTAAAACCC 791
                          v                   i     ii ?    i         i v i
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_143044578_    792 AAAACCATAAAAGCTCT-AGGAGAAAACCTAGGCA-ATACCATTCAGGAC 839
                              i      -    -  i       v    ?i- v i -   iv   
  L1M4_orf2#LINE/    520 AAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGAC 567

  chr2_143044578_    840 ATAGGCATGGGAAAAGACTTCATTACTAAAACACCAAAAGCGATTGCAAC 889
                         v v  vv i  v  v ii   v viv  vi           ivvv     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_143044578_    890 AAAAGCCAAAATTGACAAATGGGATCTAATCAAACTAAAGAGCTTCTGCA 939
                              vv     v  i    v   ii v      v v  i i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_143044578_    940 CAGCAAAAGAAACTATTATCAGAGTGAACAGGCAAACTACAGAATGGGAG 989
                          vv    i  v     i vv i      v  i   v i            
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_143044578_    990 ACAAGTTTTATAATCTACCCATCTGACAAAGGTCTAATATCCAGAATCTA 1039
                          v  vv   ii  vii ivi      i  i  v  vi          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_143044578_   1040 CAAGGAACTTAAACAAATTTACAAGAAAAAGACAAGCTACCCCATCAAAT 1089
                         i  i     ivv    v iv i  v          iiv    v  i?  v
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_143044578_   1090 AGTGGGCGAAGGATAGGAACAGACCCTTCTCAAAAGAAGGCATTTATGTG 1139
                          i     i      vv   i    vi     v       ii  vi vi  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_143044578_   1140 GCCAACAAATACATGAAAAAAAGTTCATCATCACTGGTCAT 1180
                              i  ii         i v i   v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (118 / 84)
Gap_init rate = 0.02 (18 / 787), avg. gap size = 2.39 (43 / 18)  


2913 26.14 2.93 0.82  chr2_143139646_143142552     1558  2410 (497)    L1M4_orf2#LINE/L1        1   871 (37)  

  chr2_143139646_   1558 TGAAAAAGCAGCTCATATTCATACATTAGAAGAATTAATATTGTTAAAAT 1607
                           i   iii v i   i     iv   i     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_143139646_   1608 GTCCATAGCACTGGAAGTAATCTGCCTACTCAATGTAATTCCTACTAAAA 1657
                          v v   viv ivi  v i    i vv i    i i   i    ii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_143139646_   1658 TTGCCATGGAATTTTTTTTTCACAGTAGTAGACAAAACACTTCTAAAATT 1707
                          i-   ---iv vii     ii   v i v     iviiv i        
  L1M4_orf2#LINE/    101 TC-CCA---GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_143139646_   1708 TGTATGAAACCACAAAAGACAATGAATAGCCAAAGCATTCT-GACAAAGA 1756
                         ii    i  vii   ii   vvv           i  v   -  v     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_143139646_   1757 GGAA---AGCCTGAAGTGTCACACTTTCTGATTTCAAAGTATATTACAAA 1803
                         i   ---  iiv  i vv        i ii        iiv  i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_143139646_   1804 GCTCTACTAATCAAAATAGCATGGTACTGACATA------GACATATGAA 1847
                            vi v       i i  ii        i    ------       ii 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_143139646_   1848 CCAATGGCACAGAACAGAGAAGTCAGAAGTAAATCCATGTATATAAGG-- 1895
                         i      v i    iv    ivi     i    i    ii  v  v  --
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_143139646_   1896 -----ATCTTTGACAGTGGTGCCACGTGTACACAATAGGGAAAGGATAGT 1940
                         -----  i  i    iv       v vvi iv    i       i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_143139646_   1941 CTCTTCAATAAATGGTGTTGGGAAAACTGGATATCAACAAGAAAAAGAAG 1990
                           i     i        i     v         ? v   v v       v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_143139646_   1991 AAACTTGGACCTTTATCTTACACCATACAGAAAAATCAACTCAAAATTGA 2040
                         i  v       ii  i  i        i v      i          v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_143139646_   2041 TTGAAGACTTAAATGTAAGATACAAAACAATAAAACTCCTAGAAGAAAAC 2090
                          ii?    i           vvi     v         i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_143139646_   2091 ATAGGAGAAAATTTTCATGACATTGGTTT-GGCAGTGGTTTCATGAATTT 2139
                              ? v    i   i    v    v  -    i       v ii  v 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_143139646_   2140 GACACCAGAAGCTCAGGCAACAAAAACAAAAATTAAAAAGCAGGACTAAA 2189
                                i    v  i         iv      vi v  iiv     vv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_143139646_   2190 TCAAA-CTATAATCTTCTTCACGGCAAAGGAAAAATTCAATGCAGTGAAA 2238
                              -i  v  v   i vii vv       v vvv    viv       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_143139646_   2239 AGCCAACCTAGGAAATGAGAGAAAATATTTTAAAGTAACATATTTGATGA 2288
                           v     i vii    i            vv  i v i    i    i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_143139646_   2289 GG--CTTTAATCTCTAAAATATACAAGGAACTCATCTAAA--AATCATAA 2334
                           --   --i v  i i      i  i      v vi  v--   v    
  L1M4_orf2#LINE/    747 GGGACTT--GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_143139646_   2335 AAACAACTAATAACT-AATATGATAATGGGTTAAGAACTTAAACAGACAT 2383
                            -i  v      i-   v?i v      iv   i i  i  i      
  L1M4_orf2#LINE/    795 AAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_143139646_   2384 TTATTTAAAGAAAACATGCAAATG-CCA 2410
                           v ii      i i  i      -   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.49 (131 / 88)
Gap_init rate = 0.02 (14 / 871), avg. gap size = 2.29 (32 / 14)  


3121 27.31 0.66 0.66  chr2_143199333_143205613.rev     4882  5789 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_143199333_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_143199333_   4932 GGCCATACTGCCCAAGGTAATTTACAGTTTCAATGACATCCCCATAAAGC 4981
                            v     v     iv i  i     v     i vv     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_143199333_   4982 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 5030
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_143199333_   5031 ATGGAACCAAAAAACAGCACTCA---TCGCCAAGGCAATCCTAAGCCAAA 5077
                               viiv  i--- v  i  --- v     ii     i i ivv i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG---GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_143199333_   5078 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAGACTATACTACAAG 5127
                                  i      vv       v  ii i    i viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_143199333_   5128 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGA 5177
                                   i   i    ii         i iv ii i   v   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_143199333_   5178 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAA 5225
                                  i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_143199333_   5226 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGAGGAAAGGATT 5275
                         ii vi    i  i     ivv  vv  i v  vv     i      i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_143199333_   5276 CCCTATTTAATAAATGGTGCTGGGAAAACTTGCTAGCCATATGTAGAAAG 5325
                         vi  v  i  i              v    v v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_143199333_   5326 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5375
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_143199333_   5376 TATTAAACACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5425
                         v  i ? v  i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_143199333_   5426 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCC 5475
                           v    ?i v viv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_143199333_   5476 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5525
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_143199333_   5526 AATTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGA 5575
                         v  i   v v  i i   i  ii vv v  i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_143199333_   5576 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5625
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_143199333_   5626 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5675
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_143199333_   5676 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5725
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_143199333_   5726 TCTCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5775
                             v           vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_143199333_   5776 TCATCACTGGCCAT 5789
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3156 27.42 0.55 0.55  chr2_143318669_143325067     5000  5907 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_143318669_   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAAGATCGTGAAAAT 5049
                              ii i  i     i      i v      v i  v  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_143318669_   5050 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5099
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_143318669_   5100 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5147
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_143318669_   5148 TAGGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5197
                           v    viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_143318669_   5198 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTAAACTACAAGGC 5247
                                i      vv   ii  v  ii i      vivv       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_143318669_   5248 TGCAGTAACCAAAACAAAATGGTACTGGTACCAAAACAGAGATATAGATC 5297
                          i      i   i   ivi         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_143318669_   5298 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATACCTACAACT 5345
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_143318669_   5346 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5395
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_143318669_   5396 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5445
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_143318669_   5446 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5495
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_143318669_   5496 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCGAGAAGAAAAC 5545
                          i ?    i  v    v   v       i      vi iv          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_143318669_   5546 CTAGGCA-ATACCATTCAGGACATAGGCATGCGCAAGGACTTCATGTCTA 5594
                         v    ?i- v i -   iv   v v  vv iv    v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_143318669_   5595 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5644
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_143318669_   5645 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAA 5694
                           i   v v  i i   i  ii vv    i  v    i ivv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_143318669_   5695 CAGGCAACCTACAGAATGGGGGAAAATTTTTGCAACCTACTCATCTGACA 5744
                         v  i     i          i      v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_143318669_   5745 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5794
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_143318669_   5795 AAAACAAACAACCTCATCAAAAAGTGGGCGAAGGATATGAACAGACACTG 5844
                           i     i    iv  i?    i     i      v    i     i v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_143318669_   5845 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5894
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_143318669_   5895 CATCACTGGCCAT 5907
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1387 28.38 6.32 2.22  chr2_143370604_143372806      516  1100 (1103)    L1M4_orf2#LINE/L1        1   609 (299)  

  chr2_143370604_    516 TGGAGAAATGTATTGTGTTCATGAGTCCGAAGATTACATAT-----GGAT 560
                             i i  i viii        ii iv     i vv    -----i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_143370604_    561 G-TAAT-TTC-------TG--CCACAAATTCAGTACAATCCCAATCAAAA 599
                          -i   -i  -------  -- i   i     iii       v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_143370604_    600 TTTTCGTAGGCTTTTTTTTGGGTAGATATTGATT-GCTGATTCTAAGATG 648
                          iiiv iv v       ---- i   v     iv-      i    i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT----GCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_143370604_    649 CATATGGAAATGAAAGTAGCCAAGAGAAACTCAAGCAACTTTTTTTTAAA 698
                                     v   vii  v   iv i iv  i   ---- i  v   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA----TCTTGAAA 192

  chr2_143370604_    699 AAGAGGAA---AGTTTAAGGTCTAATCCTGTCTTATTATTTCCAGACTTA 745
                             i   ---    vi   v  v iv  -  ii --     v i     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACT-TCCCA--ATTTCAAAACTTA 239

  chr2_143370604_    746 TTA-AAAGCTACTATAATCAGGATAGTGTGGCATTGGCATGAATATAAAC 794
                         i  -        vi      i  i       i i      i iv   i  
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_143370604_    795 AAATATTTCACTGGAACAGACTATATTATCCAGAAATAGACTCACACATA 844
                          v   vv   v     i   v vv vvi          i  i  i    v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_143370604_    845 TTTTTTCAACTGATAT-CAACAAGG----CAA-----TTCATTGGAGAAA 884
                          v vv    i    v - i      ----   -----    v   i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_143370604_    885 TGAT-GTCTTTT--ATAAAGGGCAGTAG--CAATTGCATATCCATATTTT 929
                         vi  -       -- i   v  iiv i --   i  v   ?   i  viv
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_143370604_    930 TAA-AATCAACTTTAATTCTTCTTTTACACCTTAAACAAAAACAAACTAC 978
                         v  -   v  v  vi ii i vii i     v  v       iv    vv
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_143370604_    979 AAATGGATCTTACACCTAAATGCAAAACTTTAAGCTTGGAAACTTCTAGA 1028
                                  v? v         i  i vi v  i  vvi     ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_143370604_   1029 AATAAAACAAAGTAGAAAAATTTATATGCTTTTGGTTTAGGTAAAGACTT 1078
                          i-      v  v? v   vi  -ii  vii    v     i  v ii  
  L1M4_orf2#LINE/    540 AG-AAAACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_143370604_   1079 ATTAGATGCAACAAGAACAGCA 1100
                         v      iii   vv  v    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCA 609

Transitions / transversions = 1.26 (91 / 72)
Gap_init rate = 0.03 (21 / 609), avg. gap size = 2.38 (50 / 21)  

 311 24.39 6.27 7.32  chr2_143370604_143372806     1426  1712 (491)    L1M4_orf2#LINE/L1      625   908 (0)  

  chr2_143370604_   1426 AAAAT-GTTAAATCAGACCCTATCAAAATTTAAAAACTTCTGTTTCTTCA 1474
                              - v     ii   iii         -        i   v-     
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATT-AAAAACTTTTGTG-CTTCA 672

  chr2_143370604_   1475 AAGATACTGTTAAATTCACTTTCAGTAGAAAAACATTGAGAAAACCAGCC 1524
                            i-  ----------   v   --     i----   i  i  v v  
  L1M4_orf2#LINE/    673 AAGG-AC----------ACTATCA--AGAAAG----TGAAAAGACAACCC 705

  chr2_143370604_   1525 ACTCTCTGAGACAAAATAGTAGAAAA--A-ATAT----TA-------TGT 1560
                           vvvv  i  v      v v v   -- -    ----  -------   
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_143370604_   1561 ATCTGGAATAAATAA-GAACTCTCAAAATTTATTGCTAAGAAAACAAGTG 1609
                            ii     v    -       i v  i i v iv   i  i    i i
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_143370604_   1610 ACTCAATAAAGAAATTATTTA-TAACTTACAAAGACACTTCAACAATAAA 1658
                           i    v? i    viviv -vi i  iv v     i   vv   vi  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_143370604_   1659 TATATGTAG-TGTAAAAATAAGCACATAAAAAACATTCTCACCATCTTTC 1707
                         v    ii i-  -ivv           i    i-  v    v    v???
  L1M4_orf2#LINE/    856 GATATACAAATG-GCCAATAAGCACATGAAAAG-ATGCTCAACATCAZZZ 903

  chr2_143370604_   1708 CATAA 1712
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.09 (36 / 33)
Gap_init rate = 0.06 (16 / 284), avg. gap size = 2.44 (39 / 16)  


2777 25.51 2.38 4.43  chr2_143379199_143384003     3389  4313 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_143379199_   3389 GAAAAACATCCCATGCTCATGGATAGGCAGAATCAATATCATTTAAATAG 3438
                             i i        i        v  v   v i     ii  v i  i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_143379199_   3439 CCATACTGCCCAAAACAATTTATAGATTAAATGCTATTCCTATCAAATTA 3488
                          v     v      vii  i  i     v  i  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_143379199_   3489 CCAATGATATTCCTCTTAGAACTAGAAAAA--AAATTTAAAATT-ATATG 3535
                            iiviiv  ii ivi    v v  v  i--i vii       -     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_143379199_   3536 GATACAAAAAAGAGCCCAAGTAGCCAAGTCAATACTAACAAA-AAGAACA 3584
                           v iiv  ii  v  vi i       iv    vi i v   -       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_143379199_   3585 AAACTGGAGGCATCACATGACCCAACTTCAAACTATACTGCAGGGCTACA 3634
                           ii      vv     ivv     i      viv    i  ii      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_143379199_   3635 GTAACCAAAATAGAATAGTACTGGTACAAAAACAGGAACTTAGACCAGTA 3684
                             i   i i  vi i       i i  ii i  iv iv    i  i i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_143379199_   3685 GAACAGAATAGAGAGGCCAGAAACAAGGCCACAAACCTATGACCATCTGA 3734
                            i     v     v       i  iv   i v ii    ii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_143379199_   3735 TCTTTGACAAAGCTGACAAAAACAAACAATGGGAAAAAACT--TCCTATT 3782
                          i  i     i v  v   i v  vv       i   i v --  i -  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-TT 401

  chr2_143379199_   3783 TAATAAATGGTGCTGGGATAACTGGCCAGCCACATGCAGAAGATTGAAGC 3832
                         i  i              i      vi ?         i    v     i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_143379199_   3833 TGGATGTCTTCCTTATACCATATACAAAAATCAACTCAAGATGTATTAAA 3882
                             ivi  v   i i               i       i   v  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_143379199_   3883 GACCTAAATGTAAAACCCAAAACTATAAAATCCCTGGAGGATGACCTAAG 3932
                                      i v i            ii i i  i  vi  v  i 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_143379199_   3933 CAATACAATCTT-G-GACATAGAAATGAGCAAAAATTTCATGACAATGAT 3980
                         ?i-  -      - -   v v iiv ii    vii    v iivv    i
  L1M4_orf2#LINE/    552 NG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_143379199_   3981 GCCAAAAGCAACTGAG--ACAAAAGCAAAAATTGACAAATGGGATATAAT 4028
                         i         --ii  --       v      v  i    v   iv v  
  L1M4_orf2#LINE/    600 ACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_143379199_   4029 TAAACTTAGAAACTTCTGCACAGCAAAAGCTTTTTGCATACCAAAAGCTT 4078
                         i   v   i      i  i---------    ---------    i ---
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGT---------GCTT---------CAAAGG--- 676

  chr2_143379199_   4079 GTTGATAGTTGCTAAGAACTATCAATAGAAT-AACAGGCAACCTACAGAA 4127
                         ---- i -----------       v i i -  v  i     i      
  L1M4_orf2#LINE/    677 ----ACA-----------CTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_143379199_   4128 TGGGAGAGAATTTTTGCAAACTATGCATCTGACAAAGGTCTAATATCTAG 4177
                                i   v        ii  ii      i  i  v  vi    i  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_143379199_   4178 CATCTATAAATAATT--TACAA---------GAAGAAACAAACAGCCCCA 4216
                         v  v      v  i --     ---------i  i i     i i   v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_143379199_   4217 TTAAAAAGTAGGAATAGGACATTAACAAACACTTTTCCAAAGAAGACATA 4266
                           ?    i i  v v    iv v  i i   i  i           i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_143379199_   4267 CATGTGAGCAACAAGCATATGAAAAAAAGCTCAATATCACTGATCAT 4313
                           vi  iv   i     i       i v      i    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (150 / 82)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 3.50 (63 / 18)  


 931 26.76 2.46 0.35  chr2_143397828_143404094.rev       10   293 (5974)    L1M4_orf2#LINE/L1      619   908 (0)  

  chr2_143397828_     10 AAAACAAAAATTGACAAGTTGGATCT------AATTAAAGAGCTCTGCAC 53
                            iv      v  i  i     ii ------       i vi i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_143397828_     54 AGCAAAAGAAATTATCAACAGAGTGAACAGACAACTTACAGAAAGGAAGA 103
                         vv    i  v i      v i      v       ii      v  i   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_143397828_    104 AAATATTCGCAAACTATGCATTTGACAAAGGTCTAATATCCAGAATCCAT 153
                                i     ii  ii  i   i  i  v  vi          vi  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_143397828_    154 AAGGAACTTAAACAGTTCAACAAACAAAAAACAAATAACCCCATT-AAAA 202
                           i     ivv   ii    i  vv    i           v   -    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_143397828_    203 ATGGGTAAAAAACATGAACAGATGCTTCTCAAAAGAAGACATGTAGGCAG 252
                              i   ii iv    i   iii     v        i  ii iiii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_143397828_    253 CCAACGAATATATGAAAAAAATGTCCATTATCACTAATCAT 293
                             ii ii i       i -  ii  vi    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.80 (56 / 20)
Gap_init rate = 0.01 (3 / 290), avg. gap size = 2.67 (8 / 3)  

3221 27.13 1.00 0.44  chr2_143397828_143404094.rev     4873  5775 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_143397828_   4873 TGGAAGAATATTCCATGCTCATGTGTAGGAAGAATCAATATCGTGAAAAT 4922
                              ii    i     i     vi v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_143397828_   4923 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCTATCAAGC 4972
                            v     v     iv i  i           i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_143397828_   4973 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5020
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_143397828_   5021 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5070
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_143397828_   5071 AACAAAGCCGGAGGCATCACACTACCTGACTTCAAACTTTACTACAAGGC 5120
                                ii     vv       v  ii i      vi         i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_143397828_   5121 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5170
                          i      i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_143397828_   5171 AATGGAACAGAA--AAGAGCCCTCAGAAATAACGCCACATATCTACAACT 5218
                                i    --i    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_143397828_   5219 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5268
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_143397828_   5269 CTATTTAATAAATATTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5318
                           v  i  i    iv        v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_143397828_   5319 GAAACTGGATCCCCTCCTTACACCTTATACAAAAAGCAATTCAAGATAGA 5368
                            ii    i   iv   i     v          vi  i    i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_143397828_   5369 TTAAAGACTTAAATGTTAGACCTAAAGCCATAAAAACCCTAGAAGAAAAC 5418
                          i ?    i       v   v     i i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_143397828_   5419 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5468
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_143397828_   5469 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5518
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_143397828_   5519 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCGGAGTGAAC 5568
                          i   v v  i i   i  ii vv    i  v    i  vvii      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_143397828_   5569 AGGCAACCTACAAAATGGGAGAAAACTTTTGCAACCTACTCATCTGACAA 5618
                           i     i   i            iv       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_143397828_   5619 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5668
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_143397828_   5669 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5718
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_143397828_   5719 TC-----AAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5763
                           -----    i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_143397828_   5764 ATCACTGGCCAT 5775
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.17 (13 / 6)  


2449 27.63 2.93 1.34  chr2_143500854_143505781.rev     3269  4086 (842)    L1M4_orf2#LINE/L1        1   831 (77)  

  chr2_143500854_   3269 TAGAAAAACATTCCATACTCATGGATTGGAAGAATCAATATCATGAAAAC 3318
                          i    i i  i    ii               v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_143500854_   3319 CACCATATTGCTCAAAGCAATTTATAGATTCAAAGCTATTCCTATCAAAC 3368
                         vi v   i v i    vii  i  i        v  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_143500854_   3369 TACCTA--TGTCATTTCTCACAGAAATAGAAAAATCTATTCTAAAATTCG 3416
                          -  i --  i -   i ii       v  v  iiiv  i         i
  L1M4_orf2#LINE/    101 T-CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_143500854_   3417 TATGTGACCAATA-AAGAG--CCTGAATAGCCAAAGCAATCCCAAGCAAA 3463
                             -  --   i-   i --  v           i     iii iv  i
  L1M4_orf2#LINE/    149 TATG-GA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_143500854_   3464 AAGAACAAGGCTGATGG---CATCATTACCTGACTTCAAA-----CTACA 3505
                                 i i  iv  ---  -  i v  ii i      -----     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACA 244

  chr2_143500854_   3506 AGGCTACAATAACCAAAACACCATGGTACTGGGACCAAAACATATACATA 3555
                          i      i   i   i   vii         v iv ii i v i i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_143500854_   3556 GACCAATAGAACAGGTTAGAGAACCCAGAA-TAAAGCCACATATCTACAA 3604
                           i    i   i  iv v    ii      -    v   i i  i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_143500854_   3605 -CAGTCTAATCTTTAACAAAGTTGACAAAAACAAGCAATGGGGTAAGAAC 3653
                         -  i - i  i  ii    i v  v   i v  vv        v     i
  L1M4_orf2#LINE/    345 TCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_143500854_   3654 --TCTTATTCAATAGGTGGTGCTGGGATAACCAGCCAGAAATATGCAGAA 3701
                         --    -     i ii           i   ii vi ?vv i     i  
  L1M4_orf2#LINE/    394 AGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_143500854_   3702 GAATGGAACTGGACCCCTACCTTTCACCAAATACAATTATTGACTCAAGA 3751
                              i ii             iv     v      vv   i      i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_143500854_   3752 TGGAT--AAGACTAAAATGTAAGACCTAAAATTATAAAATTCCTAGAAGA 3799
                              --?    iv          v      i       i  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_143500854_   3800 AAACCTAGGAA-ATATCATCCTGGACAGTGGCTTTGACAAAGGATTTGTG 3848
                             v    ?i- v   v  v  -  vv   v  v i   v  v  iv i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_143500854_   3849 ACTGAGTCCTCAATA--ACAATTGCAAAAACCCCCCAAACTGACAAGTGG 3896
                         iv iv v vi   v --    --    v  vvvvvv   iv  i  i v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_143500854_   3897 GACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAGCAG 3946
                            i v  i   v v  i i   i  ii vv    i  v       iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_143500854_   3947 AGTAAATAGACAACCTACAGAATGGGAGAAGATATTCACAAAC--TATTC 3994
                            i  v        i              i     ii    i--   vi
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_143500854_   3995 CTTGCAAATATTTAATATCCAGACTCTATAAGGAATTTAAGCAATTCGAC 4044
                           vii  ivivi vi        v v     i   i ivvi   i  i i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_143500854_   4045 AAGCGAGAAACAAATAACCCCATTAAAAAATGGGCAAAGAAT 4086
                           vvi i i           v   ?              i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.67 (139 / 83)
Gap_init rate = 0.03 (21 / 831), avg. gap size = 1.67 (35 / 21)  

 426 18.09 0.00 0.00  chr2_143500854_143505781.rev     4343  4436 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_143500854_   4343 AAAAAAAGGCAAAGAACATGAATAGACACTTCTTGAAAGAAGACATACAT 4392
                              vi       i iv          i    iv        i     v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_143500854_   4393 ACAGCCAACAAATATATGAAAAAATGCTCAACATCAATAATTGT 4436
                          ii     i  ii i       i             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3167 27.86 0.44 0.44  chr2_143596844_143603125     4883  5790 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_143596844_   4883 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4932
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_143596844_   4933 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4982
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_143596844_   4983 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5030
                          v i iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_143596844_   5031 TATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 5080
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_143596844_   5081 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGCC 5130
                                i      vv       v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_143596844_   5131 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5180
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_143596844_   5181 AATGGAACAGAAC--AGAGCCCTCATAAATAATGCCGCATACCTACAACT 5228
                                i    i--    i  -- v      vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_143596844_   5229 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5278
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_143596844_   5279 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 5328
                           v  i  i              v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_143596844_   5329 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5378
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_143596844_   5379 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5428
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_143596844_   5429 CTAGGCATGGCCATTCAGGACATAGGCATGGGCAAGGACTTCATGTGCAA 5478
                         v    ?i iiviv   iv   v v  vv i     v ii   v ivii v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_143596844_   5479 AACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAA 5528
                         i            vvi     v    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_143596844_   5529 TTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGAAC 5578
                          i   v v  i i   i  ii vv v  i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_143596844_   5579 AGGCAACCTACAAAATGGGAGACAATTTTTGCAACCTACTCATCTGACAA 5628
                           i     i   i         v   v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_143596844_   5629 AGGGCTAACATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5678
                         i  i  vii         v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_143596844_   5679 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5728
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_143596844_   5729 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5778
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_143596844_   5779 ATCACTGGCCAT 5790
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (151 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2531 24.64 1.86 8.25  chr2_143608744_143612505.rev     2424  3393 (369)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_143608744_   2424 TGGAAAAACATTCCTTGCTCATGGA----A----TCAATATTGTTAAAAT 2465
                               i i  i  v  i       ---- ---- i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_143608744_   2466 GACTATACCGTTCAAAGCAATCTACAGATTCAACACCATTCCTATATCAA 2515
                          i v    ivii    vii               i v  i     --   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT--CAA 98

  chr2_143608744_   2516 GCTACCAACATTATTTTTTCACAGAACTAGAAAAAACT-ATTCTAAAATA 2564
                         iv v   i - vvi     ii     v v  v  i-  -  i       v
  L1M4_orf2#LINE/     99 AATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chr2_143608744_   2565 TAGAGAGAACCAAAAAAGAGCCCAAATAGACAAAGCAATCCTAAGCAGAA 2614
                         i v vi   viiv  ii  v  vi     v    i     i i iv ii 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_143608744_   2615 ATAACAAAGCTGGTGGCATCACATGACTTGACTTCAAACTATACTCTAAG 2664
                          v       i   v  vv     ivv iii i      viv    vi  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_143608744_   2665 GCTACAGTAATCAAAATGGCATGATACTGGTACAAAAACAGACACATAGA 2714
                                       i ii ii  i      i i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_143608744_   2715 CCAATAGGACAGGACAGAGAATCCAGAAATAAAGCTGCATA---ACAGCC 2761
                         i    i i i  i iv    i            v iii i --- ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_143608744_   2762 ATCTGATCTTTGACAAAGTAGACAAAACAAG-CAATCGGAAAAGGACTCC 2810
                          vi    i  i     i vv v   i  v v-    v  i    i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_143608744_   2811 CTACTCAATAAATGGTGTTGGGATAACTGGCTGTCAATATGCAGAAGAAT 2860
                           vi    i        i     i      v i? v i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_143608744_   2861 AAAACTGGACCCCTACCTTTTACCATATAGAAAAATTAACTCGAGATGGA 2910
                         i  ii             ivi        v            i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_143608744_   2911 TTAAAAGCTTAAATATAATACCTAAAACTATAAAAGTCTTAGAAGAAAAC 2960
                          i ? ii i     i   v v              v              
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_143608744_   2961 CTAGG---AAATACCATTCTGGATATCAGCTTTGGCAAAGAATTTATGAC 3007
                         v    ---    -- -   vv  iv ii v  v     v iv  iv iiv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_143608744_   3008 TGAGTCCTCAAAAGCAATTGTGAGAAAAACAAAAATAGACAAGTGAGACC 3057
                          iv v vi        vvv ii v    iv         i  i vi   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_143608744_   3058 TAATTAAACTAAAGAGCTTCTTCACTGCAAAAGAAACTATCAACAGAGTA 3107
                          v  i   v v  i i   i vii  v    i  v        v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_143608744_   3108 AACATACAACCTATAGAATGGGAGGAAATATTTACAAACTATGCATCTGA 3157
                           v v      i i          i        i    ii  ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_143608744_   3158 CAAAGTTCTAATATCCAGAATCTATAGGGAACTTAAGCAATTG-AACTAA 3206
                         i  i vv  vi          v    ii     i------  i-    v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTC------TTACAACTCA 787

  chr2_143608744_   3207 ATATTTTGCCCACTAAAATATGGGCAAAATACATGAACAGATGCTTCTCA 3256
                            --------------   -----    v   -----------------
  L1M4_orf2#LINE/    788 ATA--------------ATA-----AAAAGACA----------------- 801

  chr2_143608744_   3257 AAAGAAATGAACTTAAGCAATTGAACTAAATATTTTGCCCACTAAAATAT 3306
                         -----   -   i----     --------------------?    -  
  L1M4_orf2#LINE/    802 -----AAT-AACC----CAATT--------------------WAAAA-AT 820

  chr2_143608744_   3307 GGGCAAAATACATGAACAGATGCTTCTCAAAAGAAGACATACAATTGGTC 3356
                                iv iv    i   iii     v        i      v   i 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_143608744_   3357 AACAAACATATGAAAA-ATGCTCAACATCACTCAGAAA 3393
                           i  i  i       -             ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (149 / 87)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.67 (98 / 21)  


1886 27.36 1.89 10.27  chr2_143655879_143659629     2311  3264 (487)    L1M4_orf2#LINE/L1        6   879 (29)  

  chr2_143655879_   2311 AGATATTCTGTATCCATGGATTGGAAGAGTCAACATAATAAAGATGACAG 2360
                               i ii i i              v i  i  vi v      i  i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_143655879_   2361 TTCTCCCTAAAT----CTGTAAGTTTAAGACAATTTCTATTAAAAATCTT 2406
                          v     i    ----  ii ii  i  vi    ii    i    -  i-
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCC- 103

  chr2_143655879_   2407 GTCAGCTTTGTATATTTTTATTTATTTATTATTAGCTGGTTACTTGAAGC 2456
                         --     ---------------------------  ------   -----
  L1M4_orf2#LINE/    104 --CAGCT---------------------------GC------CTT----- 113

  chr2_143655879_   2457 TTTTTATAGATGTAGACAAGTCTAGTCTAAAATTTATATGCAA-TGCCAA 2505
                         -    ii   vi v      iiv vi        i     v  -   v i
  L1M4_orf2#LINE/    114 -TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_143655879_   2506 AGATGTACACCAGCAAAAACTATTCTATATTGTATGAAAAGAAATAATGT 2555
                         i  ivi v vi   v     v  i-----   v vi i     vv  vv 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATC-----TTGAAAAAGAAGAACAAAGTT 207

  chr2_143655879_   2556 GAAAAAATCACTCTACTTGACATTGAGGCTTACTATATAGGTACAATATT 2605
                          i ii v    v  v iii iv ii ii       i v  v    i  v 
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_143655879_   2606 CAAGACAGTGTGGTACTGGAGGAGGAATAGATAAAAAGATCAACAGAACA 2655
                                            viv i i     i v v       ii   i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_143655879_   2656 GAAGAGAGAACCAAGATGGAGACCCATACAAAAGTGTCCCAGTGATTTTT 2705
                            vv    ii v   viv i         vvvi  vi v v       i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_143655879_   2706 TTCAAAGGTGAAAAAGCAATTCAACAGAGGAAGG-TACCCTTTTCAAGAA 2754
                         vv   i    vv  ii v      ii i i   i-  vi        v  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_143655879_   2755 ATGGTACAGGAGCAATACCATTAGATAATACAGGAAGATACCCTTTTTAA 2804
                              i v  ii   i----- i    ?i---------------------
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAAC-----TGGATAKC--------------------- 431

  chr2_143655879_   2805 GAAATGGTATGGGAGACACTCATCAGCAGAAGAAGAGACCTTGACCTAAA 2854
                         ----------------   --  --   i     vii vi v    ivv 
  L1M4_orf2#LINE/    432 ----------------CAC--AT--GCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_143655879_   2855 CTTCACACCTCATACAAAAATGTGCTAAAAATGAATCACAGACTTAAATG 2904
                          i       vi          vvi  v      i    ?    i      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_143655879_   2905 TGAGACATAAAACCATAAA-CTATTAGAAAAATACTTAGGAGAAAATTAT 2953
                          i   vv      i     -  v      i  v  v    ? v    iv 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_143655879_   2954 TGGAACCTAGGGATAGGCAAACAGTTCTTGGACTTGATACCAAAAATATA 3003
                         i vi    v   v       vviv     i  iv   i       ii i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_143655879_   3004 GTTCAT----TAAAAAAT---TAAGTTGAACCTTATCAGGACTGGAAAGA 3046
                         iviv i----v       ---   i   i  i i    ii i --   i 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT--AAAAA 659

  chr2_143655879_   3047 CCT----GCTCCAAGAAAGATCCTGTTAAAAACATGAAAATACAGCCTAC 3092
                          i ----   i   -- i  iv  i i  i  vi      v   i  i  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAA--AGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_143655879_   3093 ACAGTGAGATAAAATATTTTCAGACCACACATTTAAGAAATGTCTTCTAG 3142
                          v i  i  v         v  i i  i i  i i v  iv v   v  v
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_143655879_   3143 CTAGAATATATAAATAATCCTCAAATCTCAGCATTAGTAAGACAAATAAT 3192
                          i            v  ii  i v v    ii v  iv           i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_143655879_   3193 CCAAATAGCCAATGGGCAAAAACCCTAAAGAGATATTTCACTGAGGAGAA 3242
                             v ?ivv          iivii i  v   i     v ii i  ii 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_143655879_   3243 TATACAGATTTTAGATAAGCAC 3264
                               i  vvivi        
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCAC 879

Transitions / transversions = 1.50 (154 / 103)
Gap_init rate = 0.02 (19 / 874), avg. gap size = 6.11 (116 / 19)  


3608 23.91 1.90 0.45  chr2_143706312_143708756     1059  1953 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_143706312_   1059 TGATAAGATATTTCATGTTTATGGATAGGAAGAATTTATATCGTTAAAAT 1108
                           iv       ii      i      v      v  v    i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_143706312_   1109 GTCCATACTACTCAAAGTGATTTACAGATTTAATGCAATGCCTATCAAAA 1158
                          v v     v i    v    i        i  i     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_143706312_   1159 CTCCAA-TGTCATTTTTTTTCAGAAATAGAAAAAACAATCCTAAAATTTG 1207
                         ii   i-  i --      v       v  v  ivii           ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_143706312_   1208 TATGGAATCACAAAAGATTCCAAAGAGCCAAAGCAAT-TTGAGCAAAAAT 1256
                                vii   ii  ii vi  v       i    -    iv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_143706312_   1257 AAGAAAGGTGAAGACATTGCCCTACCTGATTTCAAAATTGACTACAAAGC 1306
                           v    v  i  ivv ii v  v  ii         i v          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_143706312_   1307 TCTAGTAATCAAAACAGCATGATACTAGCATTTAAACAGACACATAGATA 1356
                          vi         i    ii  i    i    vvii i     i      v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_143706312_   1357 AATGGAACAGAATACTGAGTCCACAA-----TCTACACACTTAATGTCAA 1401
                                i     vvv       v  -----i i i   i   vv     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_143706312_   1402 TTGATTTTTGACAAAGATGCCAAGAGCACATAATGGAGAAACAACAGTCT 1451
                                 i     i i        v  ivi     i    v  i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_143706312_   1452 GTTCTATAAATGGTACTAGGA-GACTGAATATTCATATGCAGAAGAATGA 1500
                         v   v i       i  i   -i    i   ?i  i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_143706312_   1501 TATTAGACCCTCATCTCACACCATTTACAAAATCCAACTCAAAATAAATT 1550
                         vi  i     ii i          v       vii          ii  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_143706312_   1551 AAAGAGTTACACGTAAGACCTGAAACTGTAAAACTACTAGAAGAAAACAT 1600
                          ?   vi  v i      v  i     i       vi             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_143706312_   1601 AGGAGGAAAGCTCTGTGAGAT-GGGTCTTGGAAAAGATTTCTTAGATATG 1649
                            ? v   v  ii    vv -    - v  v  v i             
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chr2_143706312_   1650 ATCTCAAAAGTATGGGCAACAACA---AAAATAGACAAATGGGATTACAT 1696
                          ivi      i iii       v ---        i    v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_143706312_   1697 TAAAGTAAAAAGCTTCTGCATAGCAAAGGAAGCAATCAATGGAATAAAAA 1746
                         i   i v    i   i  iiivv       vi v     vii i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_143706312_   1747 GACAATCTATGGAAT---AGAATATATTTGCAAGCCATGTATCTGATAAG 1793
                              i i ii    ---    v          ii   i           
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_143706312_   1794 GGATTAATGTGTAAACTCCATATGGAACTCAAACAACTCAACAGTAAGAA 1843
                            i vi i vi i v vi   vi      vv         i i   i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_143706312_   1844 AATAAA-AATCCGATT-AAAAATATACAAAGGATCTGAATAGACATTTTT 1891
                         i i   -  i  i   -      ivi        i             i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_143706312_   1892 TCAAAAGAAAACATACAAATAGTTAACAAGTATATGAAAAGATGCTCAAC 1941
                         i    -   i i        i ii  i   i i                 
  L1M4_orf2#LINE/    848 CCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_143706312_   1942 ATCACTAATCAT 1953
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (138 / 73)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


3277 26.43 0.66 0.66  chr2_144127930_144134325.rev     4997  5904 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_144127930_   4997 TGGAAGAATATTCTATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5046
                              ii    i i   i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_144127930_   5047 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_144127930_   5097 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 5144
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_144127930_   5145 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5194
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_144127930_   5195 AACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTACACTACAAGGC 5244
                                i     ivv   ii  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_144127930_   5245 TACAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGATATAGATC 5294
                                 i   i    ii           iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_144127930_   5295 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAGCC 5342
                                i    i--    i  --        vv iii i  i  ii i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_144127930_   5343 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5392
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_144127930_   5393 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 5442
                           v  i  i              v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_144127930_   5443 GAAACTGGATCCCCTCCTTACACTTTATACAAAAATTAATTCAAGATGTA 5492
                            ii    i   iv   i    iv              i    i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_144127930_   5493 TTAAAGACTTACATGTTAGATCTAAAACCATAAAAACTCT-AGAAGAAAA 5541
                          i ?    i  v    v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr2_144127930_   5542 CCTAGGCA-ATACCATTCAAGACATAAGCATGGGCAAGGACTTCATGTCT 5590
                          v    ?i- v i -   iv   v vi vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_144127930_   5591 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5640
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_144127930_   5641 AATTAAACTAAAGAGCTTCCGCACAGCAAAAGAAACCACCATCAGAGTGA 5690
                         v  i   v v  i i   ii ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_144127930_   5691 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACTTACTCATCTGAC 5740
                          v  i     i                 v       v i ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_144127930_   5741 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAAGAAATTTACAAGAA 5790
                           i  i  vi          v  i  v      vv v  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_144127930_   5791 AAAAACAAACAACCTCGTCAAAAAGTGGGCAAAGGATATGAACAGACACT 5840
                            i     i    ivi i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_144127930_   5841 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5890
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_144127930_   5891 TCATCACTGGCCAG 5904
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3141 27.64 0.44 0.44  chr2_144252364_144258632     4870  5777 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_144252364_   4870 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4919
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_144252364_   4920 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCAACCCCATCAAGC 4969
                            v     v     iv i  i           i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_144252364_   4970 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5017
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_144252364_   5018 TATGGAACCAAAAAAGAGCCCACATCCCCAAGGCAATCCTAAGCCAAAAG 5067
                                viiv  ii  v  viv  vv    ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_144252364_   5068 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGAC 5117
                                i      vv       v  ii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_144252364_   5118 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5167
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_144252364_   5168 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATGTCTACAACT 5215
                                i    i--    i  --        vv  ii ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_144252364_   5216 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5265
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_144252364_   5266 CTATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATGTACAAAGCT 5315
                           v  i  i              i      v  ?   i   i v  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_144252364_   5316 GAAACTGTATCGCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5365
                            ii  v i v  v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_144252364_   5366 TTAAAGCCTTAAACCTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5415
                          i ?  v i    iv v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_144252364_   5416 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5465
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_144252364_   5466 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5515
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_144252364_   5516 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5565
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_144252364_   5566 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5615
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_144252364_   5616 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5665
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_144252364_   5666 AAACAAACAACCCCATCAGAAAGTGGGCTAAGGACATGAACAGAGACTTC 5715
                          i     i     v  i?i   i     v     iv    i   v i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_144252364_   5716 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5765
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_144252364_   5766 ATCACTGGCCAT 5777
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (145 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3254 27.20 0.44 0.44  chr2_144451758_144458036     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_144451758_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_144451758_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_144451758_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_144451758_   5028 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_144451758_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_144451758_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_144451758_   5178 AATGGAACAGAAC--ACAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i-- v  i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_144451758_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_144451758_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTATCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_144451758_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_144451758_   5376 TTAAAGATTTAAACATTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    ii v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_144451758_   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_144451758_   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_144451758_   5526 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_144451758_   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_144451758_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_144451758_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_144451758_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_144451758_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3277 26.00 1.45 0.11  chr2_144678775_144681021      860  1755 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_144678775_    860 TGGAAAAACATCCCACACTTATGGATTGGAAGAATTAATATTGATAAAAT 909
                               i i      iii i             v         v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_144678775_    910 GACCACATAGCCCAAAGCAGTCTACATATTAAATGCAATCCCTATCCAAA 959
                          i v i ivv      viii      v   v  i            v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_144678775_    960 TACCAA-TGTCATTCTTCACAGAATTAGAAAAAACAATTCTAAA-TTTAT 1007
                          v   i-  i -  i  ii     v v  v  ivii  i     -  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_144678775_   1008 ATGGAACTAAAAAAGAGCCTAAATAGCCAAAACATTCCTAGGCAAAAACA 1057
                               v iv  ii  v  vi             v  i iiiv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_144678775_   1058 ATAAAGCTGGTGGCATCACACTATCTGATTTCAATACATATTACAAGTCT 1107
                          i    i   v  vv       vi ii       v  v  i     iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_144678775_   1108 ACAGTAAACAGAACAGCATGGTATTGGTATAAAAATTGGCATATAGATCA 1157
                                v  ii    ii     i   i    ii  v i           
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_144678775_   1158 ATGGAATAGAATTGAGAACCCAGAAATAAAGCCACATATTCATAGCCAAC 1207
                                          ii           v   i i   i  i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_144678775_   1208 TGGTCTTCAACAAAGCTGACAAGAACTTACATTGGGGAAAGGACATTCTC 1257
                           i i   i    i v  v     v v v  v         i i v   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_144678775_   1258 TTCAATAAATGATGCTGAGAAAACTGGATAGCTACAGGCAGAAAAATAAA 1307
                              i     i     i  v         ? i   v   i  i   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_144678775_   1308 ACTAGATGACTATCTCTCAACATACACAAAAATCAAGACAAAATGGATTA 1357
                         ii i  ivv   i   v  v    i        i  vv          i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_144678775_   1358 AAGATTTAAACATAAGACCTGAAACTATAAAAATATTAGGAGTAAGCCTA 1407
                         ?   ii    ii     v  i           v v    i  v  i v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_144678775_   1408 GGAAAAACTCTCCTGGACACTGGCCAAGGCAAAAATTTA-TGGCTAAGAC 1456
                           ?iv  v   i vv   vi   viv      vii   v- i v  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_144678775_   1457 CTAAAAAGCACAAGCAATTAAAACAAAAATAG--------GACTTACTTA 1498
                         viv              iv   iv        --------     vv i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_144678775_   1499 AACTAAAAAACTTCTACACAGCAAAAGAAATATTCAACAGTGTGAAGAGA 1548
                           v v        i iii vv    i  v ivv    v iv     i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_144678775_   1549 CAACCTGTTGAATGAGAGAAAATATCTGCAACCTATTCATCTGACAGGAG 1598
                              iiiv     i          i     vii  vi      i i i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_144678775_   1599 ACTAATATCCAGAATATACAAGGAACTCAAGCAACTCAACAGGAAAAAAG 1648
                            vi             i  i      vvi        i iv     ii
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_144678775_   1649 TAA-TAATCCTATTAAAAAGTAGGCAAAGGACATGAGTAGACATTTCTCA 1697
                         i  -   i  v   ?    i i         iv   i            v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_144678775_   1698 AAAGAAGACATGCAACAGGTCAACAGGTATGTGAAAA-ATGATGAACATC 1746
                                 i  i   vv  i   i i i ii      -   v v      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_144678775_   1747 ATCAAGCAT 1755
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  


2933 26.10 3.73 1.13  chr2_144694921_144701601     5305  6189 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_144694921_   5305 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAACATCATGAAAAT 5354
                              ii i  i     i        v      v i  i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_144694921_   5355 GGTCGTACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5404
                           ivi    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_144694921_   5405 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCG 5452
                          v   iivi i  i  ii     -   -- v  i  - iii    i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_144694921_   5453 TATGGAA-----------CCAAAA-------GACAATCCTATGCCAAAAG 5484
                                -----------   i  -------i      i ivivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_144694921_   5485 AACAAATCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5534
                               vi      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_144694921_   5535 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAAATAGACC 5584
                                 i   i    ii         i iv ii i   v v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_144694921_   5585 AATGTAATAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5632
                             v       i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_144694921_   5633 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5682
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_144694921_   5683 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5732
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_144694921_   5733 GAAACTGGATCCCTTCCTTATACCTTACACAAAAATTAATTCAAGATGGA 5782
                            ii    i    v   i i   v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_144694921_   5783 TTAAAGACTTAAATGTTAGACCTAAAAACCATAAAAACCCTAGAAGAAAA 5832
                          i ?    i       v   v      - i      vi i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAA 545

  chr2_144694921_   5833 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTTC 5881
                          v    ?i- v i -   iv   v v  vv i     v ii   ---- i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC----TT 590

  chr2_144694921_   5882 AGA----ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 5927
                            ----            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_144694921_   5928 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATCACCATCAGA 5977
                          ii v  i   v v  i i   i  ii vv    i  v ii i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_144694921_   5978 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATC 6027
                              v  i     i                 v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_144694921_   6028 TGACAAAGGGCTAATATCCAGAATCTACAA-TAACTC----AAATTTACA 6072
                            i  i  i  vi          v  i  -v     ----  v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_144694921_   6073 AGAAAAAAA-AAACAACCCCACCAAAAAGTAGGCAAAGGATATGAACAGA 6121
                          v     i -   i     v ii?    i i          v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_144694921_   6122 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATG 6171
                           i     v        i  vi viii     v ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_144694921_   6172 ATCATCATCACTGGCCAT 6189
                         v   v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (142 / 85)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.87 (43 / 15)  


3962 17.39 5.15 1.83  chr2_144895681_144898063.rev     1027  1900 (483)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_144895681_   1027 AGACATCCCATGTTCATGGATCTAGATGACTTAATATTGTTAAGATGTCA 1076
                            i                 - i  v                    v  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGAT-TGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_144895681_   1077 GTATTATCCCAAAT-GATCTACAGATTCAAGGCAATCTC----------- 1114
                         i  i -i       -               v      i -----------
  L1M4_orf2#LINE/     55 ATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_144895681_   1115 -AGCTGCCATTTTTCTTCTTCAGAAAAGGCAAAGCTGATCCTAAAAGTTA 1163
                         -       -     ---- v      vv vv               v i 
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTT----TGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_144895681_   1164 CATGGAAATTCAGGGTAGTCAGAATTTTTAAAACAGCTTTGAAAAAGAAC 1213
                         i        v  i  v vi      vvii      iii           v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_144895681_   1214 AACAAAAGTGAAGGAGTCACAGTTCTTGATTTCAAAACTTAATACAAAGC 1263
                               iv  i    v     v   iii             v        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_144895681_   1264 TACAGTACCCAAAACAGGGCGATACTGGTATAATGATAGACATATAGGTC 1313
                                vi   i    v i i      i    v             i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_144895681_   1314 ACTGGAATATAATTGAAAGCCCAGAATTAAACCCTGACTTTTATGTTCAA 1363
                          v       v      i  i      v       vv  v      v    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_144895681_   1364 TTGATTTTTAA--AGGGTGTCATGACAATTTAATAAAGAAAGAATAGTCT 1411
                                 ii --      i  v   v   i   iii             
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_144895681_   1412 TTTCAACAGATGGTGCTGGGATAACTGTGTATCCACTAGCAAAAGAATAA 1461
                                 i            i     vi  ?    vv          i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_144895681_   1462 AGTTGGACCCCTTTCATGTACTATATATTAAAATATTAATGCCAAATGGA 1511
                                     vi viii  i     i-    -     iv v       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATAC-AAAA-ATTAACTCAAAATGGA 496

  chr2_144895681_   1512 TTATGGACCCAAATGAAAGAACTAAAACTATAAA-CTCTTAAAAGAAAAC 1560
                          i ?i    i     v    i             -      i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_144895681_   1561 ATAAGAGTAAGTCTACTTGTTCTTGGGTTAGTCAAAGCCTTTTTA--CAA 1608
                            i ?    i   v v  vi          v   v vi  i   --i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_144895681_   1609 GACACCAAAAGCACAAGTGACAGTAGAAAAAATAAATATGTTGGACTTCA 1658
                                          ii   iv          i   vi          
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_144895681_   1659 TCAAAATTAAAAACTTT-ATACTTTAAAAGACACTATCAAAAATAAAGTG 1707
                                          -i i   i   i           i  ---    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA---AGTG 693

  chr2_144895681_   1708 AAAAAAACCAACACACAACATGCAAGAACATATTTGTCAGTTATATTTGT 1757
                             i --    v    iv   vi    v       iv i i    v v 
  L1M4_orf2#LINE/    694 AAAAGA--CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_144895681_   1758 GATAAGGGACTTGTATCCACAATATATAAAGAACTGTTACAATTCAATAA 1807
                                            v               v      i       
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_144895681_   1808 TCAAGA-----------CAATTCAAAAATATGAAAAGTATCTGAATAGAA 1846
                          v  i -----------     ?      iv v    v  i        v
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_144895681_   1847 ATTT-TCCAA----------CAGA----CAGTAGGCATATGCATAGATGC 1881
                             -     ----------  i ----  i  i   i   v v      
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_144895681_   1882 TCTCAGTGTCATTTACTGT 1900
                           -- iii   ????????
  L1M4_orf2#LINE/    892 TC--AACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (84 / 64)
Gap_init rate = 0.02 (19 / 903), avg. gap size = 3.21 (61 / 19)  


3056 28.09 1.23 0.22  chr2_145375784_145382451     5280  6176 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_145375784_   5280 GAAAAACATTCCATGCTCATGTATAGGAAGAATCAATATTGTGAAAATGG 5329
                             i i  i     i     v  v      v i        v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_145375784_   5330 CCATATTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGCTA 5379
                          v   i v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_145375784_   5380 CCATTGACTTTCTTCACAGAATTAGAAAAATCTACTTTAAATTTCATGTG 5429
                            vivi i  i  ii     v v  v  iiiv iii    v     i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_145375784_   5430 GAACCA-AAAAAAGCCTGTATAGCCAAGACAATCCTAAGCAA-AAGAACA 5477
                            vii-  iii v  v v        i      i i iv  -       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_145375784_   5478 AAGCTGGAGGCATCATGCTACTTTACTTCAAACTACACTACAAGGCTACA 5527
                            i      vv   ii  v iiv i      vivi       i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_145375784_   5528 GTAATCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAATG 5577
                                 i    ii         i iv ii i   i       i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_145375784_   5578 GAACAGGGCAGAGGCCTCAAAAATAATGCCACACATCTACAACCATCTGA 5627
                            i  iiiv   ivii  i      vv   i    i  iiii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_145375784_   5628 CCTTTCACAAACCTGACAAAAACTAGCAACGAGGAAAGGATTCCCTATTT 5677
                         ii  iv    ivv  v   i v vvv   i i      i  vvi  v  i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_145375784_   5678 AATAAATGGCATTGAG-TAATTGGCTAGCCTTATGCAGAAAACTGAAACT 5726
                           i      iii  i -i  i   v  ?  vi     i  i v    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_145375784_   5727 GGACCCCTTCCTTACACCTTATACAAAAATTGACTCAAGATGGATTAAAG 5776
                                 v   i     v            i      i      i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_145375784_   5777 ACTTAAACGTAAGACCTAAAACCATAAAATCCCTAGAAGAAAACCTAGGC 5826
                           i    i      v       i      ii i           v    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_145375784_   5827 A-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAACAC 5875
                         i- v i -   iv   v v  vv i     v ii   v iiv  vi    
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_145375784_   5876 CAAAAAGCAGTGGCAACAAAAGCCACAATTGACAAATGGGATCTAATTAA 5925
                              -   vvi          vv v   v  i    v   ii v  i  
  L1M4_orf2#LINE/    602 CAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_145375784_   5926 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCTGAGTGAACAGGC 5975
                          v v  i i   i  ii vv    i  v       vvvi      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_145375784_   5976 AACCTACAGAATGGGAGAAAGTTTTTGCAATCTATCCATCTGACAAAGGG 6025
                             i               i v       vii  vi      i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_145375784_   6026 CTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAAC 6075
                           vi          v  i  i     ivv    v iv i  v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_145375784_   6076 A------CCA-TCAAAAAGTGGGCAAAGGATATGAACAGACTCTTATCAA 6118
                          ------   - i?    i            v    i    vi  v  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_145375784_   6119 AAGAAGACATTTATGTGGCCAACAAACATATGAATAAAAGCTCATCATCA 6168
                                i  vi vi       i  i  i     v i v     v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_145375784_   6169 CTGGTCAT 6176
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.01 (8 / 906), avg. gap size = 1.62 (13 / 8)  


3969 19.37 5.34 0.23  chr2_145412911_145416257     2008  2869 (478)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_145412911_   2008 GAAGAATA-CTCATGTTT-TGCATCGGTAGACTTAATATTGTTAAGATAC 2055
                            ii   - i      i-  v  i  v                    iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_145412911_   2056 CTGTAATCTCCTAATCGCTCTACAGATTCAATGCAATCCTTGTCAGAATA 2105
                          vi  v  i  v   i v             i       i i   i   v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_145412911_   2106 GCAGCTGGCTTCTTTGTAGAAATTAA-AAGTCTGATCCTAAAATCTGTAT 2154
                         v      v   i    i       i -   -             iii   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr2_145412911_   2155 TGAATTTTGAAACACC---AATA--TAAAACAATCTTTAAAAAGGAGAAC 2199
                         v   v vii iiv   ---    --i           v      i     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_145412911_   2200 AAAGTTGGAGGACTCACACTTCCCAATTTTGAAACAGAATATAAAACAAA 2249
                                                      ii    vv v  i   i v v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_145412911_   2250 AGTAATCAAGAAAGTGTGATACTAGCATCAAGATAGACATATACATCTAT 2299
                                    v      i    i    v i            v   v  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_145412911_   2300 GGGGCAGGATAAAGAGTCCAGAAATAAACACATGGCTTCTATGGTTTACT 2349
                           iii  i  vi                 v   i- v i      iv i 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGTCAATT 350

  chr2_145412911_   2350 GACTTTTGGCAAGGGTATTGAGGCTATCCAATGGGAAAAGAATACTTTGT 2399
                           i   i i       iiii  i i  i       i        v i v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_145412911_   2400 TTAACAAATAGTGGTGGAACAACTGGATAGCCATAGGCAATACAATAAAA 2449
                          i       i   v   i           ?   i v    v v   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_145412911_   2450 TTACACTTTTACTTCATACTTTATTCAAAAATTAACTCAAAATTAGTCAA 2499
                           iv  iii   i   i  iv   v                  vii   ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_145412911_   2500 ACATCTAACTG------CTAAAACCATAAAACTCTTAGAAGAAAGCATAG 2543
                          v i    v  ------       i                   i     
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_145412911_   2544 AGGTAAATGGCCATGAC-TTAGATTTAGCAATGAATTTTTAGATATGACA 2592
                         i?      vvi i    -  i i  vi      iv  i            
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_145412911_   2593 CCAAAAGCATAAGCAAAGGCAAAAATAATTGATAAATTAGACTTCATAAA 2642
                                  i      viiv i   v   v        i        v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_145412911_   2643 AATT-----------------------CACATTCAAGAAAGTGAAAAGAC 2669
                             -----------------------   vv                  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_145412911_   2670 AAAGCCCAGAATAGGAAAAAATATTTGTAAATCATATATTTGTTAAGGGA 2719
                           vv v      i   i          i           i  v       
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_145412911_   2720 CTCATATCCAGAATATATAAAGAATCGTTACAACTCAATAATAAAAAGAC 2769
                           ii                    iiv                       
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_145412911_   2770 -------CCAATTGACAAATGGTTAAAGAGGCTTAACAGATATTTCTCCA 2812
                         -------      ? v      vi    iivi v  i   i         
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_145412911_   2813 AAGAAGATATACAAATGGCCAATAAGCACATGAAACT-TTCTTGACATCA 2861
                                                            vv- v  ii      
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_145412911_   2862 TTTGTCAT 2869
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.59 (100 / 63)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 4.00 (48 / 12)  


3176 26.63 1.10 0.77  chr2_145489149_145495402.rev     4858  5762 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_145489149_   4858 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4907
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_145489149_   4908 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4957
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_145489149_   4958 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5005
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_145489149_   5006 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCGAAGCCAAAAG 5055
                                viiv  ii  v  v v  v     iv     ivi ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_145489149_   5056 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5105
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_145489149_   5106 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAATAGAT 5155
                                 i   i    ii         i iv ii i   v   -     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGAT 297

  chr2_145489149_   5156 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5203
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_145489149_   5204 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT-- 5251
                         i vi    i  i     ivv  vv  i v  vv            i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_145489149_   5252 TCCCTAATTAATAAATAGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5301
                           ii -- i  i    i         v      v  ?   i   i i  i
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_145489149_   5302 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGAT 5351
                         iv    ii    i    v   i     v           i  i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_145489149_   5352 GGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5401
                             i ?    i    i  v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_145489149_   5402 AACCTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTC 5451
                            v    ?i v viv   iv   viv  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_145489149_   5452 TAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATC 5501
                           vi            vvi           v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_145489149_   5502 TCATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5551
                             i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_145489149_   5552 AACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGA 5601
                           v  i     i   i             v  ii   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_145489149_   5602 C----GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5647
                         i---- i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_145489149_   5648 CAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAC 5697
                         v   i     i     v  i?    i     i     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_145489149_   5698 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAATAAATGCTC 5747
                              v        i  vi viii     v  i        v i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_145489149_   5748 ATCATCACTGGCCAT 5762
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


1462 20.00 1.38 0.69  chr2_145691690_145694928     1452  1741 (1498)    L1M4_orf2#LINE/L1        1   292 (616)  

  chr2_145691690_   1452 TGGAAAGACATCTGATATTCATGGATCAGAAGATTTAATGTTGTTAAGGT 1501
                                 i   iv  i         ii     i     i        i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_145691690_   1502 GGCAATGCTCTCCAAAGT-ATCTACAGAGTCAATACAATCCTTATCAATA 1550
                               i   i     v -         v    ii      i      v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_145691690_   1551 TCTCACTTGGGTTTTGTGCAGAATTTCACAAGCTGGTCCTGAAACTCATA 1600
                           i  vi  vv    v       v  v        i    i   i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_145691690_   1601 AGAAAATCCAAGGAACCAAGAGCAGTCAAAATAATCTTGAAAAGGAA--- 1647
                         v i    v     i   v   ii  i     i           i   ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_145691690_   1648 CAAAGTTGAGGGGTTCATACTTCTCAATTTAAAAACCTACCACAGAGCTA 1697
                                 ii  ii   i     i      v     i   i   i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_145691690_   1698 TATGAATCAAGACATTTTGGTACTCACATAAAAACAGATTCATA 1741
                         i vv          v v       vi     ii i   --    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA--CATA 292

Transitions / transversions = 2.05 (39 / 19)
Gap_init rate = 0.01 (3 / 292), avg. gap size = 2.00 (6 / 3)  

2662 21.33 3.17 0.00  chr2_145691690_145694928     2148  2747 (492)    L1M4_orf2#LINE/L1      290   908 (0)  

  chr2_145691690_   2148 ATCTAGATAAATGGGATACAATGGAAATTCTAGAAATAAATCTTTATGTT 2197
                           v     v     i   v   v  i v  i         i iv  ii  
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_145691690_   2198 TATAATTAATTGATTTTCAATAAGGATGCTAAGACAATTCAATAAGGAAA 2247
                            ii i           i i    i   i     v       ii     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_145691690_   2248 CA-TAGTCTTT-CAAC------TGC---GACCACTGAAGATCCACATTCA 2286
                         v -        -    ------   ---   v    i v ?      v  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_145691690_   2287 AAAGAAAGAAGTTGCACTC-TGCCTCCCATCGCATACAAAAATTAACTCA 2335
                               v       v  i - i    v  i ii                 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_145691690_   2336 AAATGGATCACAGTTGTAAATGTAAGAACTAAAATTATAGAAATCTTTGG 2385
                                   ?  viv           i      i    i  v    v i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_145691690_   2386 AAAAAATATAGAAACACATCTTAATTGTCTTGAATTAGGCAAAGACTTCT 2435
                          i    i    i?ii v     vi vii    ii        v ii    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_145691690_   2436 TAGAGATGAGACTAACAACACAAGTGACAAAAGAAAAA-----TGGTTTG 2480
                             v    v  i  v i      ii            ----- iiv   
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_145691690_   2481 GGCTTCATCAAAACTGAAAGCTTTTGAACTTCAAAGGATGCAATCCAGAA 2530
                          i           i i   i      vi          ii v   v    
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_145691690_   2531 AGTGAAAGG-CAGCCTAGAATATGGAAGCAAATATTTACAAATCACATAT 2579
                                i -  i  i v iv    i  v        i       i    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_145691690_   2580 CTGAAAAGGAACTTGTATCTAGACTATGTAAATATTTCTTACAACTTAAT 2629
                             v    i         i   v   i    v vi          i   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_145691690_   2630 GATACAAATGCAAATATTCCAACT-GAAATTTGGCAAAGGGTGTGAATAG 2678
                         i   v   vi      vi    i -i   v v        i v       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_145691690_   2679 AAGCTCCTTCAAAGAAGACATGCAAAGGACCGATAAGCTCATGAAAAGGT 2728
                          vii i  i         i  i    v i  i      v         i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_145691690_   2729 GCTCCACATCATTAGCCAT 2747
                             v      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (79 / 46)
Gap_init rate = 0.01 (8 / 619), avg. gap size = 2.38 (19 / 8)  


2202 26.44 8.70 2.59  chr2_145715154_145717432      973  1823 (456)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_145715154_    973 AGACATACTGTGTTCATATGTTGGAAGACTCAACATAGTAAAGATATCTA 1022
                            i  v ii       ivi          i  i  v  v     iv v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_145715154_   1023 TTTTCACCAGATTGATACACAAGTTTAATGCAATTCCTACTAAAATGCCA 1072
                          vi  v   i      vi   ii  i  i     i    ii     v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_145715154_   1073 ACAAAATTCTTTGGTAGATATAGAGAACATTATTGTAAAATTTATATGGA 1122
                         i vivv  i    -i   v  v  v  vv v  iv       i       
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_145715154_   1123 ACAGCAGAGAAACTAAAATAGCTAGCACAATTTTGAGAAAGAGAAATGGA 1172
                          vv   ii i v i i      i iv     i    i     ii  iii 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_145715154_   1173 AGAGGAGAAATAGGTATAC---CTAATTTTAAAACTTATTATTATAACTA 1219
                         ivv    i v ---i i  --- i     i        i  iv - i   
  L1M4_orf2#LINE/    205 GTTGGAGGACT---CACACTTCCCAATTTCAAAACTTACTACAA-AGCTA 250

  chr2_145715154_   1220 CTGTATTCAAGATTGTGTGACGGTGG--TGAG-ACAGGTACATAGATCAA 1266
                          v   v      iv     iiiv   -- i  - i  ii i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_145715154_   1267 TAGAACACGATGGAGAGCCCATTATTAGATGAACACAAATATACTCAACT 1316
                          i   i vi  v     i   vv v  i ivv i   vv   iv    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_145715154_   1317 AATTTTTGACAAAGATGCAAAAGCAATTCAAT----AAAGA-TAGCCTTT 1361
                         i     i     i i   v  ii v       ----     -   i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_145715154_   1362 TTCCCCAAAAGATGGTGTAACAATTGGATATCCATAGGCAAAAAATAAAT 1411
                          - vv    v i  v  vi    i      ?   i v      i -----
  L1M4_orf2#LINE/    401 T-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA----- 444

  chr2_145715154_   1412 AAATAAATAAAACTTGACCTAAGTCTCACATCTTA------AATTAAAAA 1455
                         ------  i  ii v    ivvii      i v  ------      vvv
  L1M4_orf2#LINE/    445 ------ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_145715154_   1456 AAAATGCATCATGGACTTAAATGTAAAACACAGAATTATGAAACATTTAG 1505
                               v    ?i   i         i vvi i  i   i    vi    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_145715154_   1506 AAAAAATAATAGTAGAAAATCTTTG------------------------- 1530
                           i   vv    v? v       i -------------------------
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_145715154_   1531 --AGATCTGA------AAGCATAATTCATAGAAGAAAAAATAGATTAATT 1572
                         --    v   ------     i  viv i i              v    
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_145715154_   1573 GGACTTCATCACAATTAAAAACTTTTGCTTTGTAAAAGATGCTATTAAAA 1622
                                    v               ivi vi   i  ii    i  i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_145715154_   1623 ATATGAAAAGAGGAGCTACAGACTTGGAGAAAATATTTGCAAACCATATA 1672
                          vi        vi v i     v v                  i      
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_145715154_   1673 TCTTCCAAGAGAGTAGTATTTAGAACATATAAAGAACTCTCAGAATTCAA 1722
                            vvi   i  v v    ii    i              i v  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_145715154_   1723 CAATAAAAAG-CAAAGCAATGCAATTTTA---------------CTGAAC 1756
                         i         -    -i  iv     ?v ---------------i    i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_145715154_   1757 AGACATTTTACTGAAGG-GATATAT---TGGC----AACCACACAACTTC 1798
                                 iv ii   i-      i---    ----  v    ii ----
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA---- 883

  chr2_145715154_   1799 AGTGATATTCAACCTAATTATCCAT 1823
                          iv   ii     v v ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (132 / 89)
Gap_init rate = 0.02 (20 / 903), avg. gap size = 4.80 (96 / 20)  


1875 25.94 9.68 2.42  chr2_145738840_145742028.rev     1539  2282 (907)    L1M4_orf2#LINE/L1       13   810 (98)  

  chr2_145738840_   1539 CCATGCCCATTGGTTGGGAAAGTCAATAGAGTTAATTTACCAATTTTCTC 1588
                              ii   v i    i i v i    vv     vv iv    vi  i 
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_145738840_   1589 CAAATTTTTCTACAGATTTAATACAGTCTCAAACAAAATCCCAGAAGGGT 1638
                               vv          i  ii  i  i v v           vv vv 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_145738840_   1639 GTCTGG-AGAAA--GACAAGTTGATTCCAAAAATTATATGGAAAAGGAAA 1685
                         v i v -     --      i    i i    v i         v v  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_145738840_   1686 GGATCTAGAATAGCCAAAACAATATTATGAAAGAAGAACATATTTG-AGG 1734
                            i i                 v  ivi           v v   -   
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_145738840_   1735 GCTGAAACTACTTGATTTCAAGACTAGC-ATAATGTGACAACAATCAAGA 1783
                         i  v v   v iii       i   vi - i  v iv   ii        
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_145738840_   1784 AAGAATGGTATTGGCATAAAGACAGA-------------AGAATAGA--- 1817
                         v  vi     i        i  i   -------------i       ---
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_145738840_   1818 ---------------------------TATGGATAACTTACTTTTGACAA 1840
                         ---------------------------     vi  i v i   i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_145738840_   1841 GTGTG--AAGCTCATTCAGTGGAGAAAGCTTATGCTATTTAACAAATGGT 1888
                          v   --   vi      i   i     vv  vv  v  i          
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_145738840_   1889 TCTGAAACAATCGAATATTAATATTCAAAGAAAAACAAACTTTGATCCTT 1938
                         v   ii    ii i   ?iv i  v    -- i  ii  v  v  i  i 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAA--AGAATGAAGTTGGACCCCT 460

  chr2_145738840_   1939 ACTTTGAACCGTATTTGAAAATTAATTCAAC-TGGATAATACAGACTTAA 1987
                           i iiv   i   vii        i    v-     --i ?    i   
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGAT--CAWAGACCTAA 508

  chr2_145738840_   1988 ATGCAAAATATAATACCATAAAACTTCTAAAAGAAAA------------T 2025
                            i  i vv   v  i        ii  i       ------------ 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_145738840_   2026 CTTTGTGACATTTGACTAGGCATAAATACTTT-TAAAATATAACACTAAT 2074
                            i     v  v ii      ---  iv   - v i    i    i  v
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCA---ATGGTTTCTTAGATATGACACCAAA 605

  chr2_145738840_   2075 AGCATTTTTCTAAAAATAAAATTTTTTAAAAATAAATCTATTG-ACT--A 2121
                             ----- v iv  i    vv----       i  vv    -   -- 
  L1M4_orf2#LINE/    606 AGCA-----CAAGCAACAAAAGA----AAAAATAGATAAATTGGACTTCA 646

  chr2_145738840_   2122 TCAA--TTAAAAA--TCAGTTCTTTAAATAAACAGTGTTAAGATAATCGA 2167
                             --       -- iv  v   i   -ii   v i i    v i vi 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAA 695

  chr2_145738840_   2168 AGG-CAATGTGTAGACTGAGGGAAAATATGTATCAAACATATATCTGAGA 2216
                          i -   iviii   v  i i        v iiv  v           v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_145738840_   2217 AAGGACTTTTATTCAGAAAAAAATAAATATCTCTTAAAGCTCAGCAATAA 2266
                          i      v   i     v v -    v v      v i    ii     
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATA-TAAAGAACTCTTACAACTCAATAATAA 794

  chr2_145738840_   2267 AAAAACAAACAGGCCA 2282
                            i     i iv   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCA 810

Transitions / transversions = 1.33 (109 / 82)
Gap_init rate = 0.03 (22 / 798), avg. gap size = 4.09 (90 / 22)  

 511 16.52 0.87 0.00  chr2_145738840_145742028.rev     2585  2699 (490)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr2_145738840_   2585 AAGAAAACAAATAGCCCAATT-AAAAATGGACAAAAGATTTGAATAGACA 2633
                           i  i       i       -        i    i              
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_145738840_   2634 CTTCACCAAAGGAGATAAGCAGATGGCATATAAGCACATACAAAGATATT 2683
                         i   v      i     vi  i     vv          iv      ii 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_145738840_   2684 AAACATAATTACTAGA 2699
                         v     v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.01 (1 / 116), avg. gap size = 1.00 (1 / 1)  


2367 25.14 4.45 3.45  chr2_145909647_145912552     1538  2436 (470)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_145909647_   1538 TGAAAAGATATCCTGTGTTCGTGGATTAGAAAACTCAATGTTATTAAGAA 1587
                           i          ii     i      i   i   i   i  i      v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_145909647_   1588 GCTGCTTTTCCTCAAAT-GATTTATAGATTTGATGCAACGCCAATCAAAA 1636
                          viiv vi   i     -   i  i     ii i    iv  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_145909647_   1637 TTTCAGCAGGCTATTTTGTAGAAATTAACTAGATGATTCTAAATTTTGTG 1686
                          ii    v v  v     i       i  v  v    i     v  ii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_145909647_   1687 GGGAAATACAAAAGACCTA-ACTAGATTAAACAATTTCGAAAAAGCAGAA 1735
                         v      i   ii    i - v   viv       i i       v    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_145909647_   1736 CAACGTGGTACCTTTTATACTAACTGATCTTAAAAATTATTTGAAAGCTA 1785
                            v  v v vvvi i i   vv ii  i i    v   i vv       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_145909647_   1786 -AGCTAATGAAGATTATGTGGAATTGGCATGAAAAGAGATATATAAATCA 1834
                         -  -    v    ivi     v i      i ii v   i     i    
  L1M4_orf2#LINE/    251 CAG-TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_145909647_   1835 ATTGAACAATATATAGAGTGCAGGAATAAATCTGTTTATACATGGTCAAT 1884
                           v   i iv  vv     v   i      i ii vi  vi         
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_145909647_   1885 TGATTTTAGACAAAGGTGTAAAGGCAATTCAATGGAGAAAAAGTTACTCT 1934
                                v     i    iv   i v         i    i i - v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT-AGTCT 398

  chr2_145909647_   1935 TTTTCAACAAATGGCTCTATAGCTATTGCAT--TAACATGTGAAGTATTA 1982
                            -          iv  ivii v i  v  --iv     ii  iv ---
  L1M4_orf2#LINE/    399 TTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA--- 444

  chr2_145909647_   1983 ATGAAATTATCCCCAACCCCTACCTCACA--ATATGCACAAA--AACTTA 2028
                              i  i-----i              --    i  v   --    i 
  L1M4_orf2#LINE/    445 ATGAAGTTG-----GACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_145909647_   2029 GAGATGGATCATACACCTAAACGTAAAAGCTAAAACCATACATTTCAAAA 2078
                         i -        ? v       i    i         i   v vi  vv i
  L1M4_orf2#LINE/    490 AA-ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_145909647_   2079 AAGTAATTATTAGAGAATTTCTTTATGACCTTTTGATATGGAAAGATATT 2128
                            v  vi  vi ? v vv    ii       vv v  v v  v i v i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_145909647_   2129 TTAG------CA--AAAAACAAACAGCAACAACCATAAGAAAAATTAAGT 2170
                             ------  --    i  v -        ----        v  ii 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACA-AGCAACAA----AAGAAAAAATAGAT 633

  chr2_145909647_   2171 TTAGAAAGTGGACCTCACCAAAGTGATTTTTTAAAAAACT---GCCCATC 2217
                         ----   v     i   i    ---   -----       --- iv v  
  L1M4_orf2#LINE/    634 ----AAATTGGACTTCATCAAA---ATT-----AAAAACTTTTGTGCTTC 671

  chr2_145909647_   2218 AAAAGTTATTATTAAGAAAATAAAAAGGCAAGACACAGAATGA-AGAAAA 2266
                            i vi i   i      i i     i   vv         i-      
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_145909647_   2267 TAT----AATACCAAA-ATTTTAAAAAGGAGCTATATCCAGAATACGCAA 2311
                            ----  - i  v -  i v v  i   vi i           iii  
  L1M4_orf2#LINE/    722 TATTTGCAA-ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_145909647_   2312 AGAA-TCT-ACAAATCATTAATGAAGAG-TAAACTAGTCAAT--ACAAAT 2356
                             -   -    v   v    i  i  -i   iv vi    -- v    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_145909647_   2357 GG-CAAGATAATTGAACAGCCACTTATC-----AAAATATATGGCAGGCC 2400
                           -   iiv v     i  v  i  v  -----  i     iiivv    
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_145909647_   2401 AGTAAGTCCGCTGAACAG-TCCTT--CATTAGGACCAAG 2436
                          i    iv i-    v  - v  i--   i ????????
  L1M4_orf2#LINE/    871 AATAAGCACA-TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (130 / 94)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 2.15 (71 / 33)  


2978 22.96 5.60 3.92  chr2_146016132_146018111      596  1488 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_146016132_    596 TGGAAAGATAGCCTGTGTTAATG-ATTGAAATAATTAATGTTGTTCAAAT 644
                                   v  ii    v   -    i  v v     i     v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_146016132_    645 GTCCACCTTACCTGAAGTGATCTGCAAATTCAAAGCA-----TGGCA--- 686
                          v v ivi v  ii  v      i  i      v   ----- iv  ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_146016132_    687 ----------TTTTTTTACTTAAATAAGAAAAAATAATCCTAAAATTTGT 726
                         ----------i      i vv    v-  v  iv i           ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chr2_146016132_    727 AGAGAACCACAAAAGACCCCAAATAGCTAAAACAATCTGGAACAAAATAA 776
                          vi   vii   ii     vi      i          v   v  i vi 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_146016132_    777 TTAAAGCCAGAGGCATCATATTTCCTTATTTTAAA--TTATCCTAATATG 824
                         vi    iii    vv   i i    iv    i   --   --   vv v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAG 247

  chr2_146016132_    825 CTATAGTAATCAAAACAGTATAGTATTGGCATATAGATAAACATATAGAC 874
                            i         i     i i   i       vi    i         i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_146016132_    875 CAATGAAACAGAAT--AGAGTGTAGAAATAAACCCATACAT--ATAGTCA 920
                              i  i     --     vi                  --  i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_146016132_    921 ACTAAACTTTGACAAAAGCAGCAATGATACA--CCATGGGGAAAGGATGA 968
                          i i vi  i     ii iiv   -  i-  -- v          i  ii
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAA-GAC-CATTCAATGGGGAAAGAATAG 395

  chr2_146016132_    969 TCTCTTTATTAAATGGTGTTGGGA-AA----------ACATGCGAAATAA 1007
                            i  i vi        i     -  ----------      i   v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_146016132_   1008 TACATTTTGACCCTTATCTTGCACCATACGCAATAATCAACTCAAAACTA 1057
                          iv v  v     i  i  ii       ii   v   i         ivi
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_146016132_   1058 ATTAAAGGCTTAAATGTAAGACCTTAAACCATAAAACTCCTGTAAGAAAA 1107
                           i ?  i i           v  v    i         i iv       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_146016132_   1108 CATAGGGGAAAAGCTCCTTCACATTGCTTT-GGCAATAATTTTGTGGATA 1156
                               ? v   v  i v v  v   vv  -      ii   iv i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_146016132_   1157 AGACACCAAAAACCCAGACAACAAAAGCACAGACAAGCAAGTGGGAC--- 1203
                         v          i v  ii         v v i i iii  i v    ---
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_146016132_   1204 ATCAAATTTGAATGCTTCTGCACAGCAAAGGAAACAATCAACAAAATGAA 1253
                               v  i  vi   i  ii vv       v  v     v   i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_146016132_   1254 AAGGCAACCTATGGAATGGGAGAAAATATTTGTGAA-CATATGTCATATG 1302
                            i     i ii                   ii  -     i  vv  i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_146016132_   1303 AGTGATTAATATTCAAAATATATAAGGAACTCATACAACTCAATAGCAAA 1352
                           v  i vi   i  i         i      v            ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_146016132_   1353 AAACAAACAAGAACAAAAACAACACACGCAAAAACAAATAATCCAACTTA 1402
                           i------------------------------        i    i ? 
  L1M4_orf2#LINE/    796 AAG------------------------------ACAAATAACCCAATTWA 815

  chr2_146016132_   1403 AAAATGGGCAAAAGACCTGATTGGACATTTTCCCAAAGAA----TACATA 1448
                                     i  ii   v i       ii        ----    v 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_146016132_   1449 TG---AAGAGGTATATGAAAAGCTACTCAACATCACTAATCAT 1488
                           ---  v i i i        v i          ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (128 / 74)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 4.47 (85 / 19)  


3337 21.86 3.93 4.70  chr2_146105606_146109390     2379  3293 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_146105606_   2379 TGGAAAAACACCCCATGCTCATGGGTAATTAGACTTAGTATTGTTAAGAT 2428
                               i i i      i      i vivv       i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_146105606_   2429 GGCAATAATATCAGAATTTATTTATAAGTTTAATGTAATTCCTTTCAAAA 2478
                                v vi vi    v  i  i ii  i  i i   i   v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_146105606_   2479 TCCCAGCCGATTTTTTTACAGAAATTGACAAATGGATCCTAAAATTCATA 2528
                                i vi      i             iiv                
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_146105606_   2529 TAAAAATATAAGAAACTCAGAATAGCCAAAACAACTTTACAAAGGAAAAA 2578
                          ii    ii   ii  i                 ii  iv   i   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_146105606_   2579 AAATGTTGGAAGACTCACATTTTTAGATTTCAAGATTTACCAAGGCTTAC 2628
                         v  v      i        -------------------------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACA------------------------------- 219

  chr2_146105606_   2629 ACTTCCAGATTTCAAGACTTATTACAAAGCTATAGTAACCAATATAAGGT 2678
                         -     vi       i     i          i     i   v i iv  
  L1M4_orf2#LINE/    220 -CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_146105606_   2679 AATACTT-CATAAAAACATACATATACATCAACAACATAAAACCACAAGT 2727
                         ii    v-     ii i v       v     iiiv   i  iiivi   
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_146105606_   2728 CCCAGAAATAAATCTTCATATTTATCATCAATTTACTCTTGACAATGATG 2777
                           -         i ivi i      vi      v i i i     v i  
  L1M4_orf2#LINE/    319 CC-AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_146105606_   2778 CTGAGGCCATTCAATAGTGAAAGAATAGTCCTTTTAATAAATGGTGCTGG 2827
                          ii  i         i v            i   i  i            
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_146105606_   2828 ---AATTGGATATCCATATGAATCCATACGCAAAAGAAGATAGCTGAAGC 2874
                         ---  i      ?   i   ----------        viv  i  i v 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATG----------CAAAAGAATGAAGTTGGACC 457

  chr2_146105606_   2875 ACCACCTCACACCAGATACAAAATGTAACTCCAGCTGCATCATAGATCTC 2924
                         v i           v        vv      v iv  v    ?   i  v
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_146105606_   2925 A-TATTCTAGCTAAAACTATGAAGATGTTAGAAGA---CGTA--CTTAAA 2968
                          - i vvv            i  iv v        --- i  --?v    
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_146105606_   2969 TTTTTATAACCTTGGGTT-TTCAATGGTTTCTTAGAGATGATATCAAAAG 3017
                          i  ii i          -vv               v    i i      
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_146105606_   3018 CATAAGTGACAAAGAAAAAAACAAGTAAATTA-ATTTGATCAAAATT--- 3063
                           i   ii     ii      i ii      i- i  v         ---
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_146105606_   3064 ---TTT----CTTCAAAGGAAAGCATCAAGCAAAGAAAAAGGCAACT--- 3103
                         ---   ----          v vi      v  ivi     i    i---
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_146105606_   3104 --GATAAGATAAAAGATTCACAAATTATACATCTGATAAGAAAATTTTAC 3151
                         --i  ii  v    v   ii     i   i          ii v  v  i
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_146105606_   3152 ACAGACTATATAAGGAATTTGTACAACTCAACAATAAAACT-CAA----- 3195
                         v    v       i   i iv          i       vv-   -----
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_146105606_   3196 TCGATTTAACAATGGGCAATG--TTT-AATCGCTATTTCTCCAAAAAAGA 3242
                         i i   ?  v         v --   -   v vi           i    
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_146105606_   3243 TATATGAGTGGTCAGTAAACACACGAATATATGCTTAACATCATGAGCCA 3292
                             ii i   i  i   i    i   v v     i       ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_146105606_   3293 T 3293
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.97 (130 / 66)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.65 (79 / 17)  


2162 24.59 21.22 0.27  chr2_146291579_146293310.rev      501  1240 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_146291579_    501 CATGTTCATGGATTTGAAGAATCAATATTGCTAAAATGTCCATACTACCC 550
                                       v     v i       i   i   v v     v   
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_146291579_    551 AAAGCAATCTACAGATTCAGTGCAATCCCTATCAAAGTACCAATGATATT 600
                            vii             ii               i v   iiviiv  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_146291579_    601 CTTCATGGAAAT-AAAAA----ATTCCAAAATTTATATGGACTCACAAAA 645
                         i  iiii     -i v  ----  i i      i       vvii   ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_146291579_    646 GACCCCGAATAGCCAATGCTATCCTGAGCAAAAAGAGCAAA-CTGGAGGA 694
                              v          vi v   i   iv  i    i    -i       
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_146291579_    695 ATCACTTTACCTGACTTCACATTTTACTACAGAAGTATGATAACCAAAAT 744
                         v    vi v  ii i    v vi        i iv  iii   i   i i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_146291579_    745 AACATGATACTGGCATAAAAACAG---TACAGA--------ATAGA---- 779
                          iii  i           ii i  ---  i   --------     ----
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_146291579_    780 -GAACCCAGAAACAAATCCACATACCTATGGTGAACTCATTTTTGACCAA 828
                         -  ii       i   i   i i ii      v  i v     i   v i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_146291579_    829 AGTGTCAAGAGCATACACTGGGGAAAAGACAGTCTCTTCAATAAATGGTA 878
                         i   i     v   v  v        ii i     i     i       i
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_146291579_    879 CTGGGAAAACTGGATATCCATATGCAGAAGAATAAAACTTGATCCCTATC 928
                               v         ?   i     i      i  ii v  i     i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_146291579_    929 TC---------------------TCA------------------------ 933
                           ---------------------   ------------------------
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_146291579_    934 --------------------------------------------TCTTC- 938
                         --------------------------------------------     -
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_146291579_    939 --------------------------------------------TACAGG 944
                         --------------------------------------------i   i 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_146291579_    945 CAACCAAAGCATAAATGGATAAATGGGATCACATCAAGCTATAAAGTTTC 994
                             v    v v    i       v   iiv      iv vv   ii  i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_146291579_    995 TGCCCAGCAAAGGAAACAATCAGTGAAGTGAAGAGACAACCCACAGAATG 1044
                           iv vv       v  v    ivi       i                 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_146291579_   1045 GGAGAAAATATTTGCCAACTACTCATCTGACAAGGAAATAATAATCAGAA 1094
                                        v  ii ivi      i    i v vi  vi     
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_146291579_   1095 TTTATGTGGAGCTCAAACAACTCTATAAGAAAAAAATCTAATAATCCTAA 1144
                          v   ivi  i   vv       v    v     i - v     i  -  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCC-AA 811

  chr2_146291579_   1145 TTAAAAAAGGGG-AAAAGATTTAAAGAGACACTTCTCAAGAGAAGGCATA 1193
                           ?     v   -   i     i  v     i     v i     ii   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_146291579_   1194 CATATGGCAAACAATAGTATGAAAAAGTGGTCAGCATCATTGATCAT 1240
                           v     v  i  vvii       ii  v   i     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (116 / 64)
Gap_init rate = 0.01 (12 / 895), avg. gap size = 13.25 (159 / 12)  


2701 26.53 2.68 1.45  chr2_146297052_146301607.rev     3168  4064 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_146297052_   3168 TGTAAAGATATCCCACGTTGATAGATTAGAAGAATTAATATTGTTTAAAT 3217
                           v            i   v  i    i     v           v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_146297052_   3218 GCCCATACTGCTCAAACCAATCTACATATTCAATGCCAACTCTGTCAAAA 3267
                          v v     v i    iii       v      i  v v i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_146297052_   3268 TCCCAATGGCATTTTTCACAAGAATAGAAAAAAAAACT-ATTTTAAACTT 3316
                              iiv  v     ii  ii   v  v  i----  -  ii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chr2_146297052_   3317 CATATGTAACTCCTAAAGA----GAA-AGC-AAAGCAATCTTAAACAAAA 3360
                               v  v v v ii  ----   -   -   i       i  v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_146297052_   3361 GAAAAAAAGATAGAAGCATCATATTTCCTGGTTTCAAAATATATTAGAAA 3410
                         ii  v    v i  i vv   i i    iii        iv  i  v   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_146297052_   3411 GCTATAGTAATCAAAATTACGTGGTACTGCTATAAAAAAAAAAACACATA 3460
                             i         i ivii         vi    ii v i --  i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA--CATATA 294

  chr2_146297052_   3461 AAAAATTGGAACAGAATGGAGAGCACAGAAAT----CCAT-----TACAG 3501
                         i vv v     i     v     iv       ----    -----  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_146297052_   3502 CCTAATGATCTTTGCTAAGGGTGCCAGGAACACAAAATGGGGAAGGTTAA 3551
                         i v v    i  i vi          i  v  ivv         i --  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG--AA 392

  chr2_146297052_   3552 TGGTGTT--CAGTAAATGGTGTTGGTAAAACTGAATATCCACCTGCGGAA 3599
                          i  v  --  ii        i   v v     i   ?    v   ii  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_146297052_   3600 AAGTGAAATTGTACTATTTTTTCACACCATATA-AAATATCAACTCAAAA 3648
                         i i    i   v  ivi vii            -   v  i         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_146297052_   3649 TAGATTAAAGGCTTAAATATAAAATTTCAAACTGTAAAACAACTAGAAGA 3698
                          i   i ?  i i     i   i vi v     i      vvi       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_146297052_   3699 AAACATACAGAAAAAGCTTC-TGACATTTATCTGAGCAATGAAATTTTGG 3747
                                vi?iv   v    -    v  vivi ii      ivv i  i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_146297052_   3748 ATAAAAT-CCAAAAATACAGGCAACAAAAGCAAAAATAAACAAATAGAGT 3796
                            vi i-      ii   i          v       i i    v iii
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_146297052_   3797 TGCATCAAA-TTAAAAATCTCCTGAACATCAATGGAAACAATCAACAGAG 3845
                          v       -       -  ii  vi v    v   v  v     v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_146297052_   3846 TGAAGAGAAAATATATGCAGTAGGAGATAATATATGCAAA-CATACTA-C 3893
                             i   v  ivi iiv i i     v     v      -    -  - 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA-TATC 740

  chr2_146297052_   3894 TGGTAAAAGGTTGATATACAAAATATACAAGAAATTCAAACAATTTTATA 3943
                           i   ii ii vi   v  i      i  ii  i  vv    i iv   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_146297052_   3944 ACAAATATATCTTAAATAATTAAATTTAAAATTATACAAAACACCTGAAT 3993
                          i   v v i---      iiv    ?    v ivi    iv ii     
  L1M4_orf2#LINE/    791 ATAAAAAGAC---AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_146297052_   3994 AGACATTTCTTCAAAGAAGATGCTCAAATATCAAATACCTATATGAAAAC 4043
                                   i          iiv     iv v    vvi i       v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_146297052_   4044 GTCCTCAACATCACTGATCAT 4064
                         i v          ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.95 (37 / 19)  


3103 25.97 3.99 0.57  chr2_146373202_146379547     4977  5854 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_146373202_   4977 TGGAAGAACATTCCATGCTCATGGATACGAAGAATCAATATTGTGAAAAT 5026
                              ii i  i     i        vv     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_146373202_   5027 GGCCATACTGCTCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 5076
                            v     v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_146373202_   5077 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCC 5124
                          v   iivi i  i  ii     -   -- v     - iii    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_146373202_   5125 TATGGAACTAAAAAAGAGCCCGCATTGCCATGACAATCCTAAGCAAAAAG 5174
                                v iv  ii  v  v v  v    vi      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_146373202_   5175 AACAAGGCTACAGGCATCATGCCACCTGACTTCCAACTATACTACAAGCC 5224
                              i i iv   vv   ii iv  ii i   v  viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_146373202_   5225 TACAGTAACCAAAACAGCATGGTACTGGTACCAAGACAGAGATATAGACC 5274
                                 i   i    ii         i iv i  i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_146373202_   5275 AATGGAACAGAAC--AGAGCCCTCAGAAGTAACACCACACATCTACAACC 5322
                                i    i--    i  --    i   vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_146373202_   5323 ATCTGATCTTTGACAAACCTGACGAAAGTAAGAAATGGGGAAAGAATTCC 5372
                          vi    i  i     ivv  v i i vi vvv              vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_146373202_   5373 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5422
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_146373202_   5423 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5472
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_146373202_   5473 TTAAAGACTTAAATGTTAGACCTAAACCCATAAAAACCCTAGAACAGGAC 5522
                          i ?    i       v   v     v i      vi i     v ii  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_146373202_   5523 ATAGG----------CATG-----------GGCAAGGACTTC------AT 5545
                              ---------- i  -----------     v ii   ------  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_146373202_   5546 GACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 5595
                                      vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_146373202_   5596 TTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5645
                          i   v v  i     i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_146373202_   5646 AGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTACCCATCTGACAA 5695
                           i     i                 i       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_146373202_   5696 AGGGCTAATATCTAGAATCTACCAAGAACTTAAACAAGTTTACAAGAAAA 5745
                         i  i  vi    i     v  iv       ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_146373202_   5746 AATCAA----CCCCATCAACAAGTGGGCAAAGGATATGAACAGACCTTTT 5791
                          iv   ----   v  i? v  i            v    i    v   i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_146373202_   5792 TCAAAAGAAGACATTTATGCAGCCAATGGACACATGAAAAAAATGCTCAT 5841
                           v        i  vi viii      iii          i -      v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

  chr2_146373202_   5842 CATCACTGATGAA 5854
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (137 / 88)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 4.00 (40 / 10)  


1386 27.73 10.38 1.64  chr2_146495981_146497656.rev      453  1184 (492)    L1M4_orf2#LINE/L1      113   908 (0)  

  chr2_146495981_    453 TTTTTGTCACAATTTCAAAAGTTTTATTTCTGAACTGATTCATCTG---- 498
                               -  v  v  v v   i --iv i  i  ---      v  ----
  L1M4_orf2#LINE/    113 TTTTTG-CAGAAATTGACAAGCT--GATCCTAAA---ATTCATATGGAAA 156

  chr2_146495981_    499 TTCAATAGATGAAGAATAGCATAGACAACTATGAGGAA-ATGAATAAAAT 547
                          v   vi  ivv        vv i    iiv   ii  - v   i   i 
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_146495981_    548 TGGAGAATGTATATTAAGTATACATGAAGACTTA--ATAAATCTAGAGAA 595
                              i ivi i i vvvi - iv v  i     -- i   v   v  v 
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_146495981_    596 ACTGAAAC------------GAATA-GGTTAGA-----AAATTAACAAAA 627
                          iii i  ------------ v   -  v    ----- i  i  iii  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_146495981_    628 CAAAA--GAGAAGTCACAAATA------TACA------GTCAGCTATTAT 663
                         i i  --    ivi  v     ------    ------    ii iv v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_146495981_    664 ATGATAAAGGTGGTACTGCAATTTAATGAA-AAAGAAT---CTT------ 703
                         vi  i  i    vi vvi v   i    ii-       ---   ------
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_146495981_    704 AAATAATGTTGAATCAATTTTATATTCAAATATAAAGAAAAGGAACTTTG 753
                             ii  i  iiv   i vv   ?i  v  ii   - i  v   v  v 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-AGAATGAAGTTGG 454

  chr2_146495981_    754 ACCAGTACTTCACAGCATAGTCAAAGACCAATTCTAGATGACTCATA-AT 802
                            vv   i     v    vv    i ii  i  v i   iv   ? - i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_146495981_    803 CTAAATTTGAAAGTTAA---TACACCAC-------AGATAACA-----GT 837
                               v i i  i   ---  i vv  -------   v    -----  
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_146495981_    838 AAAAGGTTTTCATGAACTTGAGACAGGTAAAAATTTCTCAAGCAGAACA- 886
                            --- i   i   v    i vi   i  vii     i iii vi   -
  L1M4_orf2#LINE/    555 AAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_146495981_    887 -AAAA----AAGTATTAAGACAAAGATTTG-TAATTTCTACTAAATTAAA 930
                         -    ----   i vi  i v   i v v -   v  vv   vv  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_146495981_    931 ATTTAAAACTTCTGTTCATCATAAGACAATATTAAGA--GTGAAAAGGCA 978
                            v       i   v v   v i    v   i    --        i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_146495981_    979 ATCCACAGAGTGGGAGAAGAAATTTGCAATGCATATATTTAACAATGGAC 1028
                          i       i        i v        vv       i i i  v    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_146495981_   1029 TCTTATCTAGAATGTATAAAGGACTCTTACAAATTGAGATTAAAAAGACA 1078
                          iv    i     i       i          v ii v v          
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_146495981_   1079 GACGACCCAATTGAAAAATTGTCAAAAGACTTGAACA-ACACTT-TACAA 1126
                         i ii        ?      v v    i  i     i -   i  - v   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_146495981_   1127 AAGAGATTGTCAGAATGGTCAATAAGCATATGAAAAGTTCCCCAACTTCA 1176
                          ii    vvv  -     i         i        v v i    v   
  L1M4_orf2#LINE/    852 AGAAGATATACA-AATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_146495981_   1177 TTATTCAT 1184
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.30 (113 / 87)
Gap_init rate = 0.04 (29 / 796), avg. gap size = 3.03 (88 / 29)  


1638 24.63 3.46 9.05  chr2_146533464_146537685.rev     2462  3212 (1010)    L1M4_orf2#LINE/L1        1   709 (199)  

  chr2_146533464_   2462 TAAAAAGATATTCCATGTTCCTAAATAGGAAGAATTAATTTTATTAAAAT 2511
                          ii        i        v ii  v      v     v  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_146533464_   2512 TTCTATACT----AAAGTGATTTACATATTTGACGCCATACTTATCATAA 2557
                         vv v     ----   v    i    v   ii    v  v i     v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_146533464_   2558 TTCCAATGACATGTTTCTCAGAAGTAGAAAAAA-AACCCTAAAATT--TG 2604
                          i   iivi v v   iv     i v  v  iv-i i         -- i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_146533464_   2605 TGCAAATCTAAAATGACCCTGAATAGCTAAAACACTGTTGTG-------- 2646
                           v    vi  ii-     v       i      v v   vi--------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_146533464_   2647 -CAA--CTGGAAGCACT-AGACTTCCTGATTTCAAA--TTAAATTATAAC 2690
                         -   --i    i -   - v      ii        --   --i  i  v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTA--CTACAAA 246

  chr2_146533464_   2691 TCTGTAGCAATCAAAACATTATGGCAATACCATAAAAACAAACACATATA 2740
                         v  ii  i      i   v i   i v iv     ii i i   i   v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_146533464_   2741 GTAATAAAATAGAATAGAAAGCTCACAAATAAAGTGATATGTGTGTATAC 2790
                         vi   ii        v  i  ii  v       vi----------i    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACC----------CATAC 336

  chr2_146533464_   2791 ATTACATATATATATAATGTATACACACACACACATATACATATATATAG 2840
                            ------------------------------------------   i 
  L1M4_orf2#LINE/    337 ATT------------------------------------------TATGG 344

  chr2_146533464_   2841 TCAACTAGTCTTCCACAAAGCTTCCAAGAATACACAATGAGTAAAGGATA 2890
                             i ii i   v    i v v      vi iv     i v    i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_146533464_   2891 ATGTCTTCAATAAATAACACTGGGAATACGTTGAATATCAATATGCAAAA 2940
                         i v i     i    iiii      vv  --  i   ? v i        
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAAC--TGGATAKCCACATGCAAAA 442

  chr2_146533464_   2941 GAAAGAAACTGGACTCATACCTTATATTATACACTAAAATCAACTCAAAA 2990
                            v   ii     i v     i i ii   i  v     i         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_146533464_   2991 GGGATTAAAGAAATAGATTTAAGATGTGAGACTGTAAAACTACTAGATGA 3040
                         v    i ?   vv  i  v     vv i i   i       vi    v  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_146533464_   3041 AAA-ATAGGA--AAATGTTCCTTGACATTGT-TTGGGCAATGATTTTTTT 3086
                            -     ?--    v   v -   v   v-  i       i   i  -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTT- 590

  chr2_146533464_   3087 GGATATGACCTCAAAAGCACAGACAAAAAAGCAAAAAGCAAAAATATTAC 3136
                         i        vi          ii   -----     - v       v- i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAA-----CAAAA-GAAAAAATAG-AT 633

  chr2_146533464_   3137 AAATTATGCCACATCAAA-TTAAATAGTTTCTTTTCACCAAAAGAAACAA 3185
                              ivi iv       -     - ii  i v v vi    i  v  v 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTA 682

  chr2_146533464_   3186 TCAACACAATTAAAAGGCAACTTATGG 3212
                             v v i v     i    ii ii 
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAG 709

Transitions / transversions = 1.46 (108 / 74)
Gap_init rate = 0.03 (23 / 709), avg. gap size = 4.09 (94 / 23)  

 830 22.49 0.40 6.83  chr2_146533464_146537685.rev     3482  3730 (492)    L1M4_orf2#LINE/L1      676   908 (0)  

  chr2_146533464_   3482 GACTCTATCTCAAAAAAAAAAAAAAAAAAGGCAACTTATAGA-TAGGACA 3530
                            v     -------  i   ivi     i    ii i   - i   v 
  L1M4_orf2#LINE/    676 GACACTATC-------AAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_146533464_   3531 AAATATTTGCAAATCATGTATCCAAGAACAGGTTAATACCCAAAATATAT 3580
                                          i    ii v  vi ii vi  i   i       
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_146533464_   3581 AAGGAATTCATCCAAGTCAACAGCATAAAAGCATGTAGCCTGATTAAAGA 3630
                           i   i  v v   v    i ii v   ii  vi  i  ii   ?  i 
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_146533464_   3631 ATGGGCAAAGAATCTGAATAGACTTCTTTTTTTTTTTTCCCAAAGAAGAG 3680
                                   i  i         v i i ----------          v
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCT----------CCAAAGAAGAT 858

  chr2_146533464_   3681 ATACAAATGGCCAACAGGTATATGAAAAAGTGCATAATATCACCAATAAC 3730
                                       i i i i       ii   vi  i    ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.93 (41 / 14)
Gap_init rate = 0.01 (3 / 233), avg. gap size = 6.00 (18 / 3)  

 359 30.08 1.50 0.75  chr2_146533464_146537685.rev     4047  4179 (43)    L1M4_orf2#LINE/L1       68   201 (707)  

  chr2_146533464_   4047 TGATTTACATATTTGATGCCATACTTATCATAATTCTAATGACATTTTTC 4096
                             i    v   ii i  v  v i     v   i i iivi v     i
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr2_146533464_   4097 TCAGAAGTAGAAAAAAAAATCCTAAAATTTGTAC--AAATCTAAACTGAC 4144
                         v     i v  v  ivvi           ii  i--    vi  iv-   
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG-GAC 166

  chr2_146533464_   4145 CCTGAATAGTTAAAACAATGTTGTGCAAGAACAAC 4179
                           v      ii        v   viv     v   
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

Transitions / transversions = 1.22 (22 / 18)
Gap_init rate = 0.01 (2 / 134), avg. gap size = 1.50 (3 / 2)  


3026 27.75 0.44 0.55  chr2_146537736_146544133.rev     4999  5906 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_146537736_   4999 GGGAAGAGCATTCCATGCTCATGGATAAGAAGAATCAATATCATGAAAAT 5048
                           i    -i  i     i        vi     v i     ii v  i  
  L1M4_orf2#LINE/      2 GGAAAGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_146537736_   5049 GGCCATACTGTCCAAGGTGATTTAGAGATTCAATGCCATCCCCACCAAGC 5098
                            v     vi    iv    i  v        i  v     i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_146537736_   5099 TACCAATGACTTTCTTCACAGAACTGGACAAAACT-ACTTTAAATTTTAT 5147
                          v   iivi i  i  ii     v v     i-  - iii    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_146537736_   5148 ATGGAACCAAAAAAGAGCTCGCATTGACAAGACAATCCTAAGCAAAAAGA 5197
                               viiv  ii  v iv v  v v   i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_146537736_   5198 ACAAAGCTGGAGGCATCAGGCTACATGACTTCAAA--TTATTCTACAAGG 5245
                               i      vv   vi  v vii i      --   --      i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAG 247

  chr2_146537736_   5246 CTATAGTAACCAAAACAGCATGGTACTGGTACCAAAATAGAGATATCGAC 5295
                            i     i   i    ii         i iv ii     v    v  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_146537736_   5296 CAATGGAACAGAACAGAGGCCTCAGAAATAATACAACACATCTACAACCA 5345
                                 i    iv   ivii         vv v i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_146537736_   5346 TCTGATCTCGGACAAACCTGACAGAAACAAGAAATGGGGAAATAATTCCC 5395
                         vi    i iv     ivv  v  ii v  vvv          v   vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_146537736_   5396 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGAAGAAAGCTG 5445
                          v  i  i              v      v  ?   i   v i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_146537736_   5446 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATCGAT 5495
                           ii    i    v   i     v              i    i  v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_146537736_   5496 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAAAAGAAAACC 5545
                         i ?    i  v    v   v       i      vi i  i        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_146537736_   5546 TAGGCAATAGCATTCAGGACATAGGCATGGGAAAGGACTTCATGACTAAA 5595
                             ?ivv iiv   iv   v v  vv i  v  v ii   v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_146537736_   5596 ACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGAATGTAAT 5645
                                     vvi          vv        i    v i iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_146537736_   5646 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5695
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_146537736_   5696 GGCAACCTACAGAATGGGAGAAAATTTTTACAA-TCTTCCCATCTGACAA 5744
                          i     i                 v   i   -  v vi-      i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAA 746

  chr2_146537736_   5745 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5794
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_146537736_   5795 AGTCAAACATCTCCATCAAAAATTGGGCAAAGGATATGAACAGATGCTTC 5844
                           v    i v i v  i?    v            v    i   iii   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_146537736_   5845 TCAAAAGAAGACACTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5894
                           v        i ivi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_146537736_   5895 ATCACTGGCCAT 5906
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (141 / 107)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 1.29 (9 / 7)  


2857 25.58 1.98 1.87  chr2_146587864_146593491     2127  3033 (2595)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_146587864_   2127 TGAAAAAAAATTTCATGCTCATGGATTAGAAGAATCAATATCATTAAAAT 2176
                           i   i v  ii    i         i     v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_146587864_   2177 GACCATACTGCCCAAAGCAATCTACAGATTCAACACTATTTCTATCAAAC 2226
                          i v     v      vii               i v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_146587864_   2227 TGCCAAG-GCCATTTTTCACAGAACTAGAAAAACT-ATTCTAAAATTCAC 2274
                          v   iv-   -     ii     v v  v  i  -  i          i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_146587864_   2275 ATGGAAACAAACATAAAAAGCCTGAAGAGTCAAAGCAATCCTATGTGAAA 2324
                                ii--  - iii v  v   v  i    i     i ----    
  L1M4_orf2#LINE/    150 ATGGAAATG--CA-AGGGACCCAGAATAGCCAAAACAATCTT----GAAA 192

  chr2_146587864_   2325 AGGAAAAAC-----TGGAGGCATCA-ATTACCCCATTTCAAACTACACTA 2368
                          i   i   -----      vv   - i v   v        vivi    
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_146587864_   2369 GAAGGTGACAGTAAACCAAAACA-CATAGTACCTATATAAAAATAGACAC 2417
                         v  i iv       -i   i   -ii i    ivii    ii       i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAA-TCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_146587864_   2418 ACAGAACAATGGAGCAGAATAGAGAACCCAGAAATAAAGCAGCACACCTA 2467
                          i   v       ii     v    ii           v vii   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_146587864_   2468 CAACCAACTCATCTTCGACAAAGTTGACAACAATAAACAATAGGGAAAGA 2517
                         iiii   i v  i        i v  v   v vi vv    i        
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_146587864_   2518 CC-TTCTTATTCAATAAATTGTGCTGAGATAACTGGCTATCCATATGCAG 2566
                         vi-v    -     i    v      i  i      v  ?   i     i
  L1M4_orf2#LINE/    392 ATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_146587864_   2567 AAGATTGAAACTGGACCCCTACATATCACCATATACAAAAATTAACTCAA 2616
                             v    ii           v vv                        
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_146587864_   2617 AAAGGATTAAAGACTTAAATGTAAGACCCAAAACTATGAAAATCCTAGAA 2666
                           v    i ?    i           v i        i   v  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_146587864_   2667 GAAAACCTAGG---AAATACCCTCATGGTCATCAGCCTTGGCAAATAATT 2713
                               v    ---    -- i  i  ii - ii vi v     - ii  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT--CTTCGTGACC-TTGGGTTAGGCAA-TGGTT 586

  chr2_146587864_   2714 TAT--GACTAAGTC-TCAAAAGCAATTGCAACAAAAACTAAAATTGAGAA 2760
                          v --  -  v v -i        vvv         ivv     v  v  
  L1M4_orf2#LINE/    587 TCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_146587864_   2761 GTGGGACTTAAGTAAACTATCTTTAGCTTCTGCACAGAAAAAGAAACTGG 2810
                         i v      v vi   --  ivvv i   i  ii vvv   i  v   iv
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAA--ATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_146587864_   2811 CAATGGTGTAAACAG-CTATCTACAGAATGGGAAATAATATTCACAAACC 2859
                            viiv  i  v  - v i i           i v      ii    i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_146587864_   2860 ATGCATCTGACAAAGCTCTTATGTCCGGAATCTATAAAGAATTTAAACAA 2909
                           ii      i  i vv   i i   i    v         i ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_146587864_   2910 TTCAACAGGCAAAAAA-AAACAACTCCATTAAAAAGTGGACAAAGGACAT 2958
                         i    i ivv    i -   i   i v   ?    i   i       iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_146587864_   2959 GAACAGATACTTCTCAAAAGAAGACATGAAAACAGTCAGCAAACATATGA 3008
                            i   i i     v        i  iv   ii i  ii  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_146587864_   3009 AAAAATGCTTATCACTAATCATAAA 3033
                            i     i v  ii ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (142 / 87)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.59 (35 / 22)  

3584 20.31 3.42 3.20  chr2_146587864_146593491     4231  5136 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_146587864_   4231 TAAAAAGATATACCATGTTCATGCATAGGAAGACTTAATAGTGTCCCAAT 4280
                          ii        v           v  v             v   ivvi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_146587864_   4281 AGCAACAATCCCCAAATTGATCTACAGATTCAGTGTAATCCCTGACAAAA 4330
                         i    i v                        ii i       iv     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_146587864_   4331 TCTTGGCTGC-TTTTTTATATAAATGGATACGCTGATCCTAAAACTCATG 4379
                           iii     -      ii v    v  i v             i    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_146587864_   4380 TGGAAATGCAAGAGACCTCTCCTCCACCCAAATAATAATCTTAAAAAAGA 4429
                                     i    ivvvv -- v     -- i      i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAAT--AGCCAAA--ACAATCTTGAAAAAGA 196

  chr2_146587864_   4430 AGACCAAAGTCTGAGGACTCAAATTTATCAGTTTAAAAATTTGCT----- 4474
                            v      iv         v i  vi  i   v    i  i  -----
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_146587864_   4475 -TTCCAGTAACCAAGATAATGTGTTACTGTCTCAA---TAGATATATAGA 4520
                         -i v      i     i i    v     v vi  ---    i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_146587864_   4521 CCAATGAAATAGAATTAAAGGTCCAGAAGTAAACTTTCAAATTTATGGTC 4570
                         i     i         i ii        i     iivi v          
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_146587864_   4571 AATTGATTTTCTACAAAGCTGCCAAGAA-ATTCAGTAAGAAAAAGAATAG 4619
                                    v    i v        v-     i ii i   -      
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAG 395

  chr2_146587864_   4620 TCT---CAACAAACGGTGCTGA---------ATACGAACATGCAAAATAA 4657
                            ---       i       i---------   ?vv          v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_146587864_   4658 TAAAACTGGACTCCTGCATCAGACCACATACAAAAATGAAGTCAAAATGA 4707
                          i  ii     i   i v   v    i          v  v        i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_146587864_   4708 ACCACCGACCCAGAAACAAGCACTAGTACTATAAAACTCTCAGAAGAAAG 4757
                          i  ?v    i i vii   vi   iv             i        i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_146587864_   4758 CTTATGCATAAATCTTTATGAT-TTGTGGTAGGCAAAATCTTGTTAGATA 4806
                          v  v ?i        ii   i-   v v       vivi  v       
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_146587864_   4807 CAATGCTTGAAGCACAAGTGACAAAATCAACAAAAATACATAAATTTAAT 4856
                         ii ii ivi         ii      --i -       v       vi i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAA--GA-AAAAATAGATAAATTGGAC 642

  chr2_146587864_   4857 GTTGCCAATAAT--AAAATATTTATACTGCAAACAATGCTATCAAGAAAG 4904
                         v iii   -   --    iv   i i  v    vi ii            
  L1M4_orf2#LINE/    643 TTCATCAA-AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_146587864_   4905 TTAAAAGAGAATCCACAGAATGAGAGAAAACATTTGGAAATTATAGACCT 4954
                          v      v  i          i       i     v    i   v i  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_146587864_   4955 GATAAAGTATTTGCATCCAAAA---ATAAAGAACCCTTAAAACTCAAAGC 5001
                              i v i   i     i  ---         i    v       viv
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_146587864_   5002 TAAAAAGACAAGAAAGAGAAGAAAGAGAAACAATTCATAATTTAAAAATG 5051
                                    ------------------ i  ii  --   ?       
  L1M4_orf2#LINE/    792 TAAAAAGACAA------------------ATAACCCA--ATTWAAAAATG 821

  chr2_146587864_   5052 AGAAAAGGATATGAATAGATATTTCTCCAGAGACCATACACCA-TGGCCA 5100
                         i v       v        i         i   vv   i  v -      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_146587864_   5101 ATAAGCACATAGAAA-ATGCTCAACATCACTGGCAGT 5136
                                   ii   -             ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (112 / 68)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.16 (60 / 19)  


2754 25.48 4.40 2.03  chr2_146702619_146705508     1560  2446 (444)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_146702619_   1560 TAGAAAGATATCCTATATTCATAGGTTCGAAGA------ATTGTCAAAAT 1603
                          i           i  i     i i  v     ------     i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_146702619_   1604 GTCTATATTG---AAAGCAATCCGCTGATTCAACGCAATCGCTATCAAAA 1650
                          v v   i v---   vii   ii v              v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_146702619_   1651 TTCCAACGGAGTTTTTCACAGAAATAGAAAAAACAATACTAAAATTTGTG 1700
                          i   i v vv     ii       v  v  ivii  v        ii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_146702619_   1701 TGGAAGTATAACAGACTCCATGTACCTAATGCAATCTTGAGAAAGAAGAA 1750
                              i ii  vi   i vivi  v i  vi         i         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_146702619_   1751 TAAAGCTGGAGACATCACACTACCTGATTTCAAATTATATTACAAAGCTG 1800
                         i    i     ivv       v  ii        viv  i         i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_146702619_   1801 TACTTATCAAG-CAGTACAGCACTAGTATAAAAATAGACACATAGACCAA 1849
                         i v v      -    iii i   i i    ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_146702619_   1850 TGGATTAAAATAGAAAGCACAGAAATAAACACACAGGTAGATGATCATCT 1899
                             v  i   v  i  iv           v  i vi vv   i   vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_146702619_   1900 AATCTGCAACAAAGGTACCAAGAATATACAATGGAGAAGGGATAGTTTCT 1949
                         i  i v i    i   i      vi  v      i   i i     i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_146702619_   1950 TCAATAA----------GAAAACC--ACATTTTCATGTGAAAAAA--AAA 1985
                             i  ----------  v   i-- i ?iiv    ii   i  --  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_146702619_   1986 TTGGTTCCTAATTTTATACTAGAGATGAAAAATCAACTCAAAATTG-TTA 2034
                             vi  iv ii i i  i v v i-      i          v - i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAAATGGATCA 499

  chr2_146702619_   2035 AGGACTTAAATGTAAGACATGAA-TTGTAAAACTCCTAGAAGAAAACA-A 2082
                         ?i   i           vv i  -i i        i            - 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_146702619_   2083 GGAGAAGAGCTCCATGACATTGGTCTTGTGAATAATGTTTTTGGAGATGA 2132
                           ? v i v  i i    v    vi v vv   ii -  i  i  v    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATATGA 598

  chr2_146702619_   2133 AGTCAAAAGCACAGGCAACAAAAGAAAAAAATAAACAAGTGGGTCTACAT 2182
                         vii          i                -  i i  i v  v  v   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCAT 647

  chr2_146702619_   2183 CAAA-CTAAAAAGTTTGGACACAGCAAAGGAAATATTCAACAAAATGAAG 2231
                             -i      v   v -ii vv       v ivv    v   i    i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_146702619_   2232 AAGCAATCTATAAAATGGGAGAAAATATTTGTTAACCATGCATATAATAA 2281
                          ii   i i i i                  iv  i   ii  v i    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_146702619_   2282 GGGATTAGTTAATATCCAAAATATATAAGGAACTCATACAATTCAATC-T 2330
                             i v  ----     i         i      v     i     v- 
  L1M4_orf2#LINE/    747 GGGACTTGT----ATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_146702619_   2331 CAAAAAACAA-----CCTGTTTGAAAATGGTTAAAGTACCTGTATAGACA 2375
                         v    i    -----  vi  ?i       vi    v ii  v       
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_146702619_   2376 TTTTTACAAAGATGAAAATGTGTTCAACATCACCAAT-----CATGAGGG 2420
                            i v      --- i  i i--   -  vi     -----     ii-
  L1M4_orf2#LINE/    843 TTTCTCCAAAGA---AGATATA--CAA-ATGGCCAATAAGCACATGAAA- 885

  chr2_146702619_   2421 AAATGCAAATCAAAATCACAATATCA 2446
                          i    ---    v    ????????
  L1M4_orf2#LINE/    886 AGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (143 / 79)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.48 (57 / 23)  


2680 27.18 5.81 0.35  chr2_146890547_146895558     3660  4520 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_146890547_   3660 TGGAAACACATCCCATGCTCATGGCTAGGTAGAATCAACATTGTGAAAAT 3709
                               v i        i      v v  v   v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_146890547_   3710 GACCATACTACCAAAAGCAATCTACAAATTCAATGCAATCCCTATCAAAA 3759
                          i v     v  v   vii       i      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_146890547_   3760 TACCA-CAATCATTCTTCACAGAATTAGAAAAAAACAATTTAAAATTCAT 3808
                          v   - vii -  i  ii     v v  v  ivvv vii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_146890547_   3809 ATGGAACCAAAAAAGAGCCTGTATAGTCAAAGCAAGACTAAGCAAACAGA 3858
                               viiv  ii  v  v v    i    i   vvi i iv  iv   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_146890547_   3859 ACAAATCTGGAGGCATCACACAACCTGATTTCAAACTACACTATAAGGGC 3908
                              vi      vv      vv  ii        vivi    i  i vi
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_146890547_   3909 ATAGTAACCAAAACAGCATGGTACTTGTATAGAAATAGGCACATAGACCA 3958
                          i     i   i    ii       v i   iii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_146890547_   3959 ATGGAATGGAATAGAGAACTCAGAAATAAACCTAAATACTTACAGCCAAC 4008
                                i    v    iii            i v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_146890547_   4009 TGATCTTCAACAAAGCAAACAAAAACTATAAAGTGGGGAAAGGACACCCG 4058
                             i   i    i -ivi v  i  i  vv i         i i vi v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_146890547_   4059 TTTCAACAAATCACGCTGGGATAATTGGCTAGCCAAATGTAGGAGAATGA 4108
                                    vii       i  i   v  ?   v   i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_146890547_   4109 AACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATT 4158
                          ii    i  ii i   v    v           i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_146890547_   4159 AAGGACTTAAACTTAATACCTGAAACTATAAAAATTCTAGAAGATAACAT 4208
                          ?i   i    iv   v v  i           v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_146890547_   4209 TGGAAAAGCCCTTCTAGACATTGACTTAGGCAAAGATTTCAT-GATGAAG 4257
                         v  ?iv ivi    vv   v   iv        v i    v -   - v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr2_146890547_   4258 AGCCCCAAAGCAAATGCAATAAATACAAAGATAAATAGCTGAGACCTAAT 4307
                          vv  v      v v    i   viv   i   i   iv vi   i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_146890547_   4308 TAAACTAAAGGGCTTTTGCACGGCAAAAGGAACAGTCAGCAGAGTAAACA 4357
                         i   v v  iii      ii vv    i iv  vi   iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_146890547_   4358 GACAAC---------------AAATAT----------------------- 4369
                               ---------------      -----------------------
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_146890547_   4370 ----------CCAGAATCGACAACAGATTCAAACAAATCAGTAAGGAAAA 4409
                         ----------       vv i  vii i  vv    v   i   vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_146890547_   4410 AACAAACACTCCCATCAAAGAGTGGGCTAAGGACATGAATAGACAATTCT 4459
                         i     i vi  v  i?  i i     v     iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_146890547_   4460 CAAAAGAAGACATACAAATGGCCAACAAACATATGAAAAAATGCTCAACA 4509
                          v        i              i  i  i       i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_146890547_   4510 TCACTAATGAT 4520
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 7.57 (53 / 7)  


3232 20.07 5.46 4.46  chr2_146920729_146922994.rev      878  1774 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_146920729_    878 GAAACACGTCCCATGTTCATTGATTTGAATAGTTAATATTGATAAGATGG 927
                             v ii            v    v   v v         v        
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_146920729_    928 CAATATATCCCAAATCAATCAAAGGACTTA-TGCAACTCCTATCTAATTT 976
                              ivi       ii   v vi  i i -i    ii      v  v i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_146920729_    977 CCAGCTGTTTTATTTCTTTGCA-AAATTGGTGAGCTGATCTTAAAATTAA 1025
                                ii  ----i      -      iii        i       v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTT----TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_146920729_   1026 TGTGAACATTCAGTGCATCCAGCAAAGTCAAAATAATCTTGAAAAATAGA 1075
                          i  i v  v  iv v i    v v  i     i            v ii
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_146920729_   1076 AACAATGTTGAAGGATTCACA--------TTTCAAAACTCGCTACAA-TT 1116
                              v    i    i     --------          ii      -vi
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_146920729_   1117 TATAGTAAT------AATCTGGTAGTGGCATAAGGATAGACCCAAAAAAA 1160
                           i      ------ i v     v                ---- v v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC----ATATA 294

  chr2_146920729_   1161 AACCAACAGCAATGGAACTGATAATAATCCATAAGATAA-CCCTTCTATT 1209
                         i i   ii -   i   i   v i ---   v  -    -   v vi   
  L1M4_orf2#LINE/    295 GATCAATGG-AATAGAATTGAGAGT---CCAGAA-ATAAACCCATACATT 339

  chr2_146920729_   1210 TATAGTCAAACAATTTTCAAAAATGATTTCAAGACAATTCAATGTAAGAC 1259
                            i     vii      i v  v i vi      v        ------
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG------ 383

  chr2_146920729_   1260 TGGGGGTAAGGGTGGGGATAATATTATCAACACGTGATGCTGGGACAACC 1309
                         ---   v   i------   i v  v      vi  i            i
  L1M4_orf2#LINE/    384 ---GGGAAAGA------ATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_146920729_   1310 AGATATTAACATGCAAAAGAATGATGTTGAAATCTTTTGCTCGTATCATA 1359
                         i    ?iv                v    i vi i vi-   ii i    
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC-CTCACACCATA 473

  chr2_146920729_   1360 --CAAAAAT-AGCCCCCAATAGATCAAAGACCTAAAAGTAAGAGCTGAAA 1406
                         --       - i i vv   i     ?         v         i   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_146920729_   1407 CTATAAAACTCTTAGAAGTGAACA--GGTGTAGATCTTTTTCACCTTGGA 1454
                                           vi    --  ?   i     iv v       i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_146920729_   1455 TT-GGCAATGGTTTCTTCAAAATGAAGCACGTTGTGCTTCAGAAGCACAG 1503
                           -              vi v    --   ---------  i       i
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGA--CAC---------CAAAAGCACAA 612

  chr2_146920729_   1504 ----TGAAAGAGAAAAGAGATAAACTGTTCCCCTGCAAAATTAAAAACTC 1549
                         ----ii     i    v       i  vv ii vv              i
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_146920729_   1550 TTGTTCATCAAAGGACAATGTTA-GAAAGTGAAAAGGCAACCCATAGAAT 1598
                             v v          v i i -            i       i     
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_146920729_   1599 GGAAGAAAATATCTGTAAATCATATATCTAATAGATGTCCAGTATCCAGA 1648
                           i         i  i             i   iiv v iv         
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_146920729_   1649 ACGTATGAA------------TTCAAGAATATAAAGAAAAA-AATCTAA- 1684
                          ii   i  ------------i    v    v     v   -  i i  -
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_146920729_   1685 ------ATGAGCAAAATATTTCAATAGACATTATTTCAAAGAAAATATAT 1728
                         ------   i     iv    v          vi i       i     i
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_146920729_   1729 AAATGGCCATTAAGCACATGAAAAGTTGTTAAATGTCATTAGTAAT 1774
                                  v               v  i v  ii   ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (107 / 70)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 3.56 (89 / 25)  


1832 25.93 4.66 1.24  chr2_147038123_147039758.rev      501  1144 (492)    L1M4_orf2#LINE/L1      243   908 (0)  

  chr2_147038123_    501 CAAAGCT----TAATCAATACAGTGTGGCATTGGTGAAAAAGTAGACAAA 546
                                ----       v         i i   iiv  iii      v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_147038123_    547 TAAATCAATGGAACAAAATATAGAGCCCA-AAACAGACCCATACAC--AC 593
                           i          i i   vv    i   -   i i         i-- i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_147038123_    594 AAACACAAAACTGATTTT-GACAAAGGAGTAAAGATAGTACAATCG--AA 640
                         iiv  ---- i       -     i  v iv    ivi v    v --  
  L1M4_orf2#LINE/    343 GGTCA----ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_147038123_    641 CACATAGTTTTTAAAGCAAATACTGCTGGAACAACTAGACATTCACTTGT 690
                         viv     i   vv i     iv      i      i  i ?i   v  i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_147038123_    691 AAAACCATGAATCTAGACACAGACCTTACAATGATCATGCAAA--TGAAG 738
                             vv     vi i   v vv    i   vi-  -  i    -- v  v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACC-AT-ATACAAAAATTAAC 486

  chr2_147038123_    739 TCACAATGAATCATAGACCTAAATGTAAAATGC-AAAACAATAAAACT-- 785
                            v    i    ?              i -  -     v        --
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCT 535

  chr2_147038123_    786 -AGATGATAACATAAGAGAAAACCTAGATGACCTTGGATATGG---TGAT 831
                         -   v  v      i ? v   i  vvi         i vv  ---  i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_147038123_    832 TACTTTAGATGCAACACCAAAGTCAAGATCCATGAAAGAAATAATAGATA 881
                          v   -    iii        iv  vi v v ii       v        
  L1M4_orf2#LINE/    586 TTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_147038123_    882 AGCTTGACCTCACTAAAATTAAATACTTCTGCTCTTTTAAA-ATGCCAG- 929
                          ii v   i   ii         v    i  iv   iv  i- ii i v-
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_147038123_    930 GAGAATGTGAAAAGG--AGCCACATACTGGGAGAAAATACTTGCAAAAGA 977
                         i    v        i-- v     v v            i       vv 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_147038123_    978 CACATCTGACAAAAGACTGTTATTTGAATTATACACAAAATTC--AAAGT 1025
                         i i      i  ii    vv   iiii v    i v i  i  -- v ii
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_147038123_   1026 TTGACA-TAAGAA----AATAATCTGATTAAAAAATGGGCCAAAGACTGT 1070
                          ii i -   i  ----     i ii   ?          v  i  i vv
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_147038123_   1071 AACAGGCACCTCACCAAAGAAGATATACAGTTGTCCAGCAAGCATAGGAA 1120
                           i  i  ii  v                iv  v   ii     i v   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_147038123_   1121 AAGTTGCTTCACATCATATGTAAT 1144
                            v    iv      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (97 / 66)
Gap_init rate = 0.03 (20 / 666), avg. gap size = 1.90 (38 / 20)  


2789 27.40 1.99 1.66  chr2_147050878_147056627.rev     4354  5258 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_147050878_   4354 TGAGAAGCCATTCCATGCTTCTAGATAGGAGGAAGAATCAATATCATTAA 4403
                           ii   vi  i     i iv i   v   ---   v i     ii    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGA---AGACTTAATATTGTTAA 47

  chr2_147050878_   4404 AATGGTCGTACGGCTTAAAGAAATTTATAGATTCAATGCTATTCCTATCA 4453
                         i    ivi   vv ii   vvi  i  i        i  v  i       
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_147050878_   4454 CACTACCAATAACATTCTTCACAGAACTAGAAAAGACGATTTTAAAATTC 4503
                         v v v   iivi v  i  ii     v v  v   vi   ii        
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_147050878_   4504 ACATGAACCAAA---AAAGAGCCCA-AATAGCCAAGGCAATCCTAAGCCA 4549
                          i   i ---  ---  i ii    -         ii     i i i-- 
  L1M4_orf2#LINE/    148 ATATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--A 192

  chr2_147050878_   4550 AAGTAG--CAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTA 4597
                            v  --     i      vv     i v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_147050878_   4598 CAGGGCTACACTAACCAA-ACAGCATGGTACTGATACAAAAATAGACATA 4646
                           ii      v   i   -    ii        ii i  ii         
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_147050878_   4647 TAAGCCAGTGGAACAGAATAGAGATCCCAGAAATAAAGCTGCACACCTAC 4696
                           iii  i     i     v    vi           v iii   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_147050878_   4697 AACCTTCTGATCTTTGGCAAAGCTGACAAAAA-A--CAATGGGGGAAAGG 4743
                         iii vvi    i  i i   i v  v   i v- --        -    i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGA 391

  chr2_147050878_   4744 ACCATCCATTCAATAAATGATGCTGGGATAATTGGCCAATCATATGCAGA 4793
                          ivi  iv     i     i        i  i   vi ?i  i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_147050878_   4794 AGATTGAAATTGGATCCCTACCTGACACTACATGTAAAAAAGTCAACTCA 4843
                            v    i     i        v    --   i  v    i i      
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACAC--CATATACAAAAATTAACTCA 489

  chr2_147050878_   4844 AGGTGGATGAAAGACATAAATACAAAACCTAAATAAATAAAAACCCTGGA 4893
                          ii     v ?    v     ii  i v     vvv      vi i i  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_147050878_   4894 AGATAACCTAGG---AAATACCATTCTGGACATAGGACTTGGCAAAGATT 4940
                            v   v    ---    -- -   vv   v v  ii v     v i  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_147050878_   4941 TTAT-GATCAAGATACCAAAAGCAGTTGCAACAAAATCAAAAATTAACAA 4989
                          iv -   - v  i          vvv         vv      vi i  
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_147050878_   4990 ATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCA 5039
                           v   ii v  i   v v  i i   i  ii vv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_147050878_   5040 ACAGAGTACATAGGCAACCTAGAGAATGAGAGAAGATTTTTGCAAACTAT 5089
                          v i   iv v  i     i v      i     i  v        ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_147050878_   5090 GGATTCAACAAAAGTCTAATATTCCGAATCTATAGGAAACTTAAACAAAT 5139
                         iv  iii i  ii v  vi   i v    v    iii    ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_147050878_   5140 TTACAAGCAAAAAACAG----CCCCATTAAAAAGTGGGCAAAGGTTATGA 5185
                         iv i  vv    i   i----   v   ?    i          v v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_147050878_   5186 ACAGACACTTTTCAAAAGAAAACATTCATGTGGCCAACAAGCATGTGAAA 5235
                          i     i  i  v      i i  v  vi       i     ii     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_147050878_   5236 AAATGCTCAACATCACTGAAATG 5258
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (153 / 92)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.94 (33 / 17)  


2873 24.63 5.22 2.16  chr2_147201627_147205133.rev     2144  3024 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_147201627_   2144 TGGAAAGATATCCTGTGTTCACGGATTTAAAAAATCAATATTGTTAAAAT 2193
                                      ii      i     vi  i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147201627_   2194 GTCCATACTACCCAAGT-GATCTACAGATTCAATGTAATCCCTATCAAAA 2242
                          v v     v     i -               i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_147201627_   2243 TGCCAATGACATTTTTTACTGAAATAGAAAAATAAAATCCTGAAAGTTTT 2292
                          v   iivi v      i v     v  v  iivi -    i   v iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_147201627_   2293 ATGGTATTATG-AAAGAATTCA-AATAGCCAAAGCAATATTGGGGTATGG 2340
                             v --   -  i i ii  -          i    v   iiiv ---
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA--- 194

  chr2_147201627_   2341 GGGATGGTCATGGAAACAAAGCTAGAGGTATCACACTATCTAACTTCAAA 2390
                         --  v --------       i i    vv       vi i  i      
  L1M4_orf2#LINE/    195 --GAAG--------AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_147201627_   2391 TTCTTCTACAAAGTAATTGTAATCAA-ACACCATAATAGTGGACTAAAAA 2439
                         vii v        iv iv        -   vii ii  v   vv   ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_147201627_   2440 CAGGCACATAAACCAATGGAACAGAATGGAGAG-CCTGAAATATATCCA- 2487
                         i  i  i   i i        i     v     -  v      v i   -
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_147201627_   2488 -CATTTATGGTCAATTGATTTTTCACAAAGCTGCCAAGAGCACGCAATGG 2536
                         -                     iv    i v        v  iv      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_147201627_   2537 GGAAA--AGAGTTTCTTCAATAAATG-TATTGGAAATACTGGATGTCCAT 2583
                              -- v   i i     i     - ii   i vv       i?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_147201627_   2584 ATACAGAAAAAT-----TAGATTTTTATTTCATACCAAATAAAAATATCA 2628
                           i  i  i   ----- i  iiii  ii   i    v   v   v  i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_147201627_   2629 CCTCAATATTGATTAAAGATTTAAACATAAGACCTGAA-CTATAAAAGTA 2677
                         v     v  v   i ?   ii    ii     v  i  -        v v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_147201627_   2678 CTAGAAGAAAACATAAGGGAAAAGCCCCATGACAT-GGATCTGGGAAATT 2726
                         i              i ? v   v ii i    v -  i - i  v   v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATG 583

  chr2_147201627_   2727 ACTTTTTGAATATGACCTCAAAAGCACAA----CAAAAGCAAAAATAGGC 2772
                         ii  i  ii       vi           ----      v        ii
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_147201627_   2773 AAGTAGAATTATAACAAACTATAAAGCTTCTGCACAGCAAAGGAAATCAT 2822
                           i v i i vi v    v vv   i   i  ii vv       v ii  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_147201627_   2823 CAACAGAGCGAAGAGACAGTCTATTAAATGTGGAAAAATATTTGTAAACA 2872
                            v i  i   i     ii i ivi    v ii          i   iv
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_147201627_   2873 ATGCATCTGATAAGAGGTTAATATCCA--ATATATACA------TTAAAC 2914
                           ii          i ii vi      --       v ------   -- 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--C 781

  chr2_147201627_   2915 AACTCGATAGCAAGGAAACAAATAATCCTATTGAAAAACGAGCAAAGGAC 2964
                              i   ii  ii i        i  v   ?     i i        i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_147201627_   2965 TGGAATAGA---------------GATACA-AAATGGCCAACAGGTATAT 2998
                          v       ---------------    i -          i i i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_147201627_   2999 GAAAAAATGTGCA-TATTACTAATCGT 3024
                              i   iv  -i  i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (140 / 73)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.83 (65 / 23)  


3125 27.98 0.22 0.98  chr2_147232632_147240757     5019  5933 (2193)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_147232632_   5019 TGGAAGAACTTTCCATGCTCATGGACAGGAAGAATCAATATCGTGAAAAT 5068
                              ii iv i     i       iv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147232632_   5069 TGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5118
                         v iv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_147232632_   5119 TACCAATGATTTTCTTCACAGAATTGGAAAAAAATACTTTAAAGTTCATA 5168
                          v   iiviii  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_147232632_   5169 TGGAACCAAAAAAGAGCCCGCATAGCCAAAACAATCCTAAGCAAAAACAA 5218
                              viiv  ii  v  v v               i i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_147232632_   5219 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5268
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_147232632_   5269 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATACATAGACCAA 5318
                               i   i    ii         i iv ii i   i i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_147232632_   5319 TGGAACAGAACAGAGGCCTCAGAAATAACATCACACATCTACAATCATCT 5368
                              i    iv   ivii         vvi  i    i  iii   vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_147232632_   5369 GATCTTTGACAAACCTCACAAAAAAATAGAAATGGGGGAAGGATTCCCTA 5418
                            i  i     ivv vv   i vv  -vv       i   i  vvi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGTCTT 399

  chr2_147232632_   5419 TTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGTGGAAAGCTGAA 5468
                           i  i     i        v      v  ?   i   iii  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_147232632_   5469 ACTGAATCCTTTCCTTACTCCTTATACAAAAATTAATTCAAGATGGATTA 5518
                         ii  i i  i v   i  v  v              i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_147232632_   5519 AAGATTCAAATGTTTGACCTAAAACCATAAAACCATAAAAACCCTAGAAG 5568
                         ?   iii      vv  v       i       --------i i      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAAC--------TCTTAGAAG 541

  chr2_147232632_   5569 AAAACCTAGGCAACAACATTCAGGACATAGGCATGTACAAGGACTTCATG 5618
                              v    ?ivv  iv   iv   v v  vv ivi   v ii   v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_147232632_   5619 ACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGAA 5668
                         iv  vi            vvi          vv        i    v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_147232632_   5669 TCTAATTAAACTAAAGAACTTTTGCACAGCAAAATAAACTATCATCAGAG 5718
                         ii v  i   v v  i        ii vv    iv v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_147232632_   5719 TGAAAAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCT 5768
                                i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_147232632_   5769 GACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAA 5818
                           i  i  i  vi          v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_147232632_   5819 GAAAAATACAAACAATCCCATCAAAAAGTGGGCAAAGGATGTGAACA--C 5866
                         v     v     i  i  v  i?    i            v    i -- 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_147232632_   5867 CCTTCTCAAAAGAAGACATTTATGCAGCCAATAGACACATGACAAAATGC 5916
                         vi     v        i  vi viii       ii       v  i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_147232632_   5917 TCATCATCACTGGTCAT 5933
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (149 / 103)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 3.67 (11 / 3)  

2740 27.43 2.29 0.34  chr2_147232632_147240757     6760  7634 (492)    L1M4_orf2#LINE/L1       17   908 (0)  

  chr2_147232632_   6760 GTTCTATATATTAAAA-ACTCAAAATTTTTATGATTGTAATTCTCCCCGA 6808
                             -  iv   ii  -   i  v   v   v   v i   v      i 
  L1M4_orf2#LINE/     17 GTTC-ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_147232632_   6809 ATCCATCTGTGGCTTCAAAGTAGCCCCAGTAAACATTCAGAAAGACTTTC 6858
                           iv    iii v     v i ii   vi v  v  i v- ivvi i  i
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC-AGCTGCCTTT 114

  chr2_147232632_   6859 TTTGTAGTAATTGACAATCTGAATTTAAAATTTATATAAAAAATTAAAGT 6908
                             i  v         v    vii       i    ii   vvi  i v
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr2_147232632_   6909 ACCTACAATAGCAAAAACAACTGTGAGAAAAAGAGAACAAAATTGGAGGG 6958
                            i v      v       iiv   i   i -        i       i
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGA-AGAACAAAGTTGGAGGA 213

  chr2_147232632_   6959 CTAACATTAATTGATATTAAAACATATTAGAAAGCAAGAATAAGCAAAAT 7008
                           v   i vviii  v i     v  i  v     v v i   v   i i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_147232632_   7009 -GTGTGGTATTGGCATCATGATAGATGAATAAATCAATGCAACAGAA--G 7055
                         -        i      v v      iiv   i       v  i    -- 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_147232632_   7056 AGAGTTCTAAAATAGGCTTGTGTAC--ATAGACAACTGATTTTAGACAAA 7103
                              i vi     ii iii ii i--  i v   i       v     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_147232632_   7104 GATGCAAAAGCAATTCTGTAGAGAAAGAATAGT-TTTTCAGTAAATGGTA 7152
                          i   v  ii v    vi i i           -      ii       i
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_147232632_   7153 TGGGAACAACTGTATATCCACATTTAAAAAAACGAACTTTGATTCATACC 7202
                         iv  i       v   ?      vi    i  i   v  v  ii v    
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_147232632_   7203 ACATGCTACATGCAAAA-TTAACACAAAGTAGATCATACTATTAAATGTA 7251
                         v  ii i i  i     -     v    i i     ? vvvi        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_147232632_   7252 ATATTTAAGACTGTAAAATGTATAGATGAAAATATGAAAAAAAATCTTTT 7301
                          v vi   i   i     iviv    v     i  iii?iv       iv
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_147232632_   7302 TGACCTTGGGTTAGGCAAGGCTTTCTTAAATATGACACAAAAAGCATGAT 7351
                                           v v       i         v       ii v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_147232632_   7352 CTATAAAATAAAAC-TA-ACAAATTTGATTCTTTCTATATTAAAAACTTC 7399
                          v i    v    v-  - i     v  i iiv  v v           i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_147232632_   7400 TGTTCTTTGAAAGAT--TTTTAGGAGAAAGAAAAGACGAGCCCCAGACTG 7447
                            v   ii  i  i-- v i i  i iv        i v  v    v  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_147232632_   7448 TGAGAAAATAATTGCAAATTATATTTCTAATAAAGAACTTATATCCAGAA 7497
                         v         v        i    v   i    i i    i         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_147232632_   7498 GAGATAAAGA-CTCTTAAAAATCAACAACAAAGAAACAA-----TCTGCT 7541
                         v v       -      v  v    i  i   i i    -----i vii 
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_147232632_   7542 AAAAGAGGGGAAAAGAATATGAAAGGGCACTTAATCAAGGAAAATGCATA 7591
                         ?   i v   v    i  v    vi i  i  vvi   i   i  ii i 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_147232632_   7592 CAT--CAAATAAACGCATGAAATGATGCACACCATCAACTATTAA 7634
                         v  -- v     i i       v     v  v     ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.02 (15 / 892), avg. gap size = 1.53 (23 / 15)  


3295 23.90 3.49 1.13  chr2_147293749_147298286     3160  4046 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_147293749_   3160 TGGAAAAATATTCCATGTTCATGGATTGGAAGAATCAATATTATTAAAAT 3209
                               i    i                     v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147293749_   3210 GTCCATATTACCCAAAGTAATTTACAAATTCAATGCAGTCCCTATCAATA 3259
                          v v   i v      v i  i    i      i   i          v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_147293749_   3260 TACCAATGATACTCTTCACAGAAATAGAAAA--TAAAAGTCATAAAATTT 3307
                          v   iiviivi i  ii       v  v  -- i ---  v       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA---TCCTAAAATTC 147

  chr2_147293749_   3308 ATATGGAACCACAAACTACCCAGGACCACAAAAGTCCCAGACCCTAAGCA 3357
                                 vii   ivv      i ivi v   i---  - i i i iv 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAA---CA-ATCTTGAAAA 193

  chr2_147293749_   3358 AAAAGAACAAAACTGTATGATTCACGTTACTTGACTTCAAACAATA-TAT 3406
                          i         ii  v v  i    ii v iii i      vvv  -  i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_147293749_   3407 ATAGCTGTAGTAACCAAAATAGCATGGTACTGGCATAAAAACAGACACAT 3456
                          v    ii     i   i i  ii              ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_147293749_   3457 AGAGCAATGGAACAGAATAGAGAACCCAGAAACAAATCTACACACCTAGA 3506
                            v        i     v    ii       i   i i i   ii  vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_147293749_   3507 GTGAACTGGTTTTTGATAAAAGTTCCAATAACATGCACTG---------- 3546
                           v  i  i    i  i  ii  v    v v   v  v  ----------
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_147293749_   3547 --TCTCTTCAACAAATGGTACTGGGAAAACTGGATATCCACATGCAAAAG 3594
                         --   i             i      v         ?             
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_147293749_   3595 AATGAAACTAGACCCCTGTACTCTCACCATATACAAAAATCAAATCAAAA 3644
                               ii i       ii-   v                i  v      
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTAC-CTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_147293749_   3645 GGGATTAAAGACTTAACTCTAAGACCTCAAACTATAAAACTACTACAAGA 3694
                         v    i ?    i   v v     v  v             vi  v    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_147293749_   3695 AAACATTGGAGAAAATCTTTAGGACATCATTCTGGGCAAAGATTTCTTGA 3744
                               v  ? v       iiv   v iivvi i     v i      ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_147293749_   3745 GCAATAC-CCAACAAGCACAGGCAACTAAGG----------CAAATGGGA 3783
                         ii vv  -    -       i     v  i ----------i    v   
  L1M4_orf2#LINE/    593 ATATGACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_147293749_   3784 TCACATCAAG-TTAAAAAGCTTCTGCATAGCAAAGGATACAATCAACAAA 3832
                         iiv      i-       -   i  iiivv       i  v     v   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_147293749_   3833 GTGAAGAGACAACCCATAGAATGGGAGAAAGTATTTGCAAACTACCCCTC 3882
                              i          i             i          ii iviv  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_147293749_   3883 TGACAAGAGATTAAAAACCATAATGTATAAGGACCTCAAACAACTCTATA 3932
                            i   i  i viv v   v   i     i  v   vv       v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_147293749_   3933 GGAAAAAATCCAATAATCCAGTTGAAAAAAGGACAAGAGATTTGAATAGA 3982
                         iv     iv v     i   i  ?     v  i   ii            
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_147293749_   3983 TATTTCTCAAAAGAAGACATACAGATGAC----AAACATATAAAAAAGTT 4028
                         i       v        i     i   i ----  i  i  i    ii v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_147293749_   4029 CTCAACATCACAGATCAT 4046
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (132 / 76)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.15 (41 / 13)  


2315 26.70 4.80 3.58  chr2_147315143_147317548     1020  1914 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_147315143_   1020 GAGAGATATTCCATGCACTTAAATCAGAAGATTGATTGTTGTCAAGATAT 1069
                           i      i     iv v ii  ii     i v v i    i     iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_147315143_   1070 CAGTTCTTCCCAACTTGATCTATAAATTCAACGTAATCCCAATTAAAACC 1119
                           i v  i     v        i i        i      v  i    i 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_147315143_   1120 -------------------------ACAAATTGATTC-AAAATTCCATAT 1143
                         -------------------------    ii    i -       -    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC-ATAT 151

  chr2_147315143_   1144 AGAAAAGCAAAGG-CCCAGAATAATCAATATTCAAGTTCAATACACAACT 1192
                         i    v    i  -         ii   v --   vi ii v v v  v-
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAA--CAATCTTGAAAAAGAAG- 198

  chr2_147315143_   1193 TCAACTACTGAAATACTAGAACTGAAAATACTAAACTTCAAGGCTTA-TA 1241
                         --   ----i  i vvv  i   v v v v iv  i     ii    -  
  L1M4_orf2#LINE/    199 --AAC----AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_147315143_   1242 TAGAACTATAGTAATCAAGGAAGAATGGTATTTGTGAAAGAATAGACAAA 1291
                         i i i   i          iv  vi     i v iiv   i       --
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA-- 290

  chr2_147315143_   1292 TATAATACATCAATGTAACAGAAAAGAGAGCCCAGAAACAGACACACACG 1341
                             i---       v  i    vv     i       i i  v  i  i
  L1M4_orf2#LINE/    291 TATAG---ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_147315143_   1342 AACATAATCAACTGACCTTTTAGAAGCA-GCAAGGGTAATGTAATAGTGA 1390
                         vvi  ii    i   ii  iv v   vi-  v i iiv  vi   i v  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_147315143_   1391 AGGGATGATTTTTTTCAACAG-TGCTACTAGAACAATTTGGCATCTACAT 1439
                          i i  - v i         i-  v i  i i    i v ii ? i    
  L1M4_orf2#LINE/    388 AAGAAT-AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_147315143_   1440 GAAAAAAAAAAAAGATCTAAGTACATACCATACATCTTTCACAAAAGTTA 1489
                          v    i  vi   --i iiiiv v    vi   i v vi      i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAG--TTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_147315143_   1490 ACT------GGATAGCAGTTGTAAATGTAAAATGC-AAAACTATAAAACT 1532
                            ------    vi?  viv         i -  -              
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACT 533

  chr2_147315143_   1533 TCTGTAAGATAACA--GGAGAAAATCTAGGTGACCTTCAATTTTGTAATG 1580
                         ii iv    v    --  ? v      vv        vii  vv i    
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_147315143_   1581 GCATTTTAGATACAGCACCAAAAGCATTAACAATGAAAGAAAACATTGAT 1630
                          iv i       iii           iv i   ii        v  v   
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_147315143_   1631 AAGTTGGACTTTGTTAAAATTAAAAAGTTCTGCTCTATGAAAGACACTAT 1680
                           i        ii i           v  i  iv  vii  i        
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_147315143_   1681 GAAGACACTGCTCTAAAAAAGACATGCTACAGACTGGGAGAAAATCTATG 1730
                         v    v v  ------        vv i     v           v v  
  L1M4_orf2#LINE/    684 CAAGAAAGTG------AAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_147315143_   1731 CAAAACATATACCTGATAAAGTGCTTTTTTCTAAAATA---AAAGAACCC 1777
                             v      i       i vi   v v  i i    ---       i 
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_147315143_   1778 TTAAAATGAAACAATAGCAA-ATAAGCAACCTAATTAACCAATGGACAAT 1826
                            v  ivv  i    iv  - i  ii    i    ? vv     i   v
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_147315143_   1827 AAATCTAAACAGATATCTCAACAAAAAAGATATACAGGTGGTAAAAAAAA 1876
                         ii  i i  i   i  i  vv    i          ii   iv  v  --
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA-- 875

  chr2_147315143_   1877 AAAAAGCATATGAAAAGATGGTCAATGTCATGATCATT 1914
                         -----   i           v    ii   ????????
  L1M4_orf2#LINE/    876 -----GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.02 (22 / 906), avg. gap size = 3.41 (75 / 22)  


3049 26.67 1.67 0.78  chr2_147379204_147385592     4998  5897 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_147379204_   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5047
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147379204_   5048 GGCCATACTGCCCAAGGTAATTTATAGAGTCAATGCCATCCCCATCAAGC 5097
                            v     v     iv i  i  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_147379204_   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_147379204_   5146 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5195
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_147379204_   5196 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_147379204_   5246 TACAGTAACCAAAACAGCACGGTACTTGTACCAAAACAGAGATACAGACC 5295
                                 i   i    iii      v i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_147379204_   5296 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5343
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_147379204_   5344 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5393
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_147379204_   5394 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCCTATGTAGAAAGCT 5443
                           v  i  i              v      v  ?  vi   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_147379204_   5444 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5493
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_147379204_   5494 TTAAAGACTTAAATATTAGACCCAAAACCATCAAAACCCT-AGAAGAAAA 5542
                          i ?    i     i v   v i     i  -     i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chr2_147379204_   5543 CCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCT 5591
                          v    ?i- v i -   iv   viv  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_147379204_   5592 AAAACACCAAAAGCAATGGCAACATAAGCCAAAATTGACAAATGGGA--- 5638
                          vi            vvi      v   vv     v  i    v   ---
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_147379204_   5639 --TCTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5686
                         --  v   i    i -   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_147379204_   5687 AACAGGCAACCTACAGAATTGGAGAAAATTTTTGCAATCTACTCATCTGA 5736
                           v  i     i       v         v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_147379204_   5737 CAAAGGGCTAATATCCACAATCTACAATGAACTCAAACAAATTTACAAGA 5786
                         i  i  i  vi      v   v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_147379204_   5787 AAAAAACAA----CCCCATCAAAAAGTGGGTAAAGGATATGAACAGACAC 5832
                             i    ----   v  i?    i    i       v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_147379204_   5833 TTCTCAAAAGAAGACATTTATGCAACCAAAAGACACATGAAAAAATGCTC 5882
                              v        i  vi viiii    v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_147379204_   5883 ATCATCACTAGCTAT 5897
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


1952 29.73 0.64 0.64  chr2_147399306_147405845     4378  5006 (1534)    L1M4_orf2#LINE/L1        1   629 (279)  

  chr2_147399306_   4378 TGAAAAAACATTCTATCTTCATGGATAGGAAGAATCAGTATAATGAAAAT 4427
                           i   i i  i i  v         v      v i i   vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147399306_   4428 GGCCATATTGTCCAAAGTAATTCATAGATTCAAAGCTATTCCCATCAAAC 4477
                            v   i vi     v i  ii i        v  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_147399306_   4478 TACCATTGAGATTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTAAT 4526
                          v   vivivv  i  ii     v v  v  i-  -  ii    v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_147399306_   4527 ATGGAA-T-CAAAGAAGACCCCACATAGCCAAGAAAATACTAAGCCAAAA 4574
                               - -   i --     viv        i v   vi i ivv i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_147399306_   4575 GAACAAAGCTGGAGGCATTATGCTACCTAACTTCAAACTATACTACAGGG 4624
                                 i      vv i ii  v  i  i      viv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_147399306_   4625 CTATAGTAACCAAAACAGCATGGTATTGGTACCAAAATAGACATACAGAC 4674
                            i     i   i    ii     i   i iv ii         i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_147399306_   4675 CAATAGAGCTGAACAGTGACCTCAGAAATAAGACCACACATCTACAACCA 4724
                             i  iiv   iv v  vii         iv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_147399306_   4725 TCTGATCTTCGACAAACCTGACAGAAACAAGCAATGGAGAAAGGCTCTCC 4774
                         vi    i        ivv  v  ii v  vv      i     iv vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_147399306_   4775 TATTCAGTAAATGGTGCTGGGAAAACTGGCTAGTCATATGCAGAAAACTG 4824
                          v    ii              v      v  ?i  i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_147399306_   4825 AAACTGTACCCCTTCCTTACACCTTATACAAAAATTAACTTGAGATAGAT 4874
                           ii  v      v   i     v                ii i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_147399306_   4875 TAAAGACTTAAATGTGAAACCCCAAACCATAAAAACCCTATAAGAAATCC 4924
                         i ?    i       i i v iv    i      vi i  v      v v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_147399306_   4925 TAGGCA-ATACCATTCAGGGTATAAGCATGGGCAAAGATTTCATGACAAA 4973
                             ?i- v i -   iv iiv vi vv i     v i    v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_147399306_   4974 AACGCCAAAAGCAATTGCAACAGAAGACAAAAT 5006
                         i  i         vvv      i    v     
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

Transitions / transversions = 1.42 (108 / 76)
Gap_init rate = 0.01 (7 / 629), avg. gap size = 1.14 (8 / 7)  

 659 26.53 3.27 1.63  chr2_147399306_147405845     5284  5528 (1012)    L1M4_orf2#LINE/L1      609   857 (51)  

  chr2_147399306_   5284 ATAAAAAATAAAAAAAGCCAAAATCGACAAATGGGATCTAATTAAACTAA 5333
                          i  iv  i    i  ---     v  i    v   ii v  i   v v 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAA---AAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_147399306_   5334 AGAGCGTCTGCACAGCAAAAGAAACTATCAG---ACTGAACAAGCAACCG 5380
                          i i v i  ii vv    i  v       i--- v    v ii     v
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_147399306_   5381 ATGGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAGGTCTAAT 5430
                          ii              v       vii ivi      i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_147399306_   5431 ATCCAGAATTTACAAGGTACCTGAACATATTTACAAGAAAAAAACAA--- 5477
                                  v  i  i v  iivv   vv iv i  v     i    ---
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_147399306_   5478 -CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACATTTCTC-AAAGTA 5525
                         -   v  i?    i            v    i           -    - 
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG-A 854

  chr2_147399306_   5526 AGA 5528
                            
  L1M4_orf2#LINE/    855 AGA 857

Transitions / transversions = 1.29 (36 / 28)
Gap_init rate = 0.02 (5 / 249), avg. gap size = 2.40 (12 / 5)  

 233 17.24 1.72 0.00  chr2_147399306_147405845     5991  6048 (492)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr2_147399306_   5991 AAGGAAGACATTTACATGGCCAACAAACATA-GAAAAAAAGCTCAACATC 6039
                           i     i  vi v        i  i  i -     i v          
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_147399306_   6040 ACTGATCAT 6048
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1)  


2483 23.18 12.90 4.42  chr2_147406662_147408953.rev      970  1806 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_147406662_    970 TGGAACAATATCCAGTGTTCATTGATTGGAAAATTTCATATTGTCAGAAT 1019
                              vi      vi       v        i i  v       i ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147406662_   1020 ATCCATGCTACCCAAAGCACTCTACAGATTCAATGCAATCCTTGTCAGAA 1069
                         iv v  i  v      viiv             i       i i   i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_147406662_   1070 TTTTAAAGCTG--TTTATTACAGAAATAGAAAAAACAATCCCAACATTAA 1117
                          iii --    --   v  i       v  v  ivii    i  v   v 
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_147406662_   1118 TATGGAACCAAAAAAGACCCCAAATAACCAAACCAATCTTGAGCAAAAAG 1167
                                viiv  ii     vi    i     v         iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_147406662_   1168 AACAAAGCTGGAGTTGTCGTACTATCTGACTTTAAAATATACTACAAAAC 1217
                                i     vvv  ii   vi ii i  i    iv         i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_147406662_   1218 TAT----------------------------------------------- 1220
                           i-----------------------------------------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_147406662_   1221 ----------------------------------------------TCAA 1224
                         ----------------------------------------------    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_147406662_   1225 TTAATTTTTTACAAAGGTCCCCCAAACA--CAATGCAGGAAGAACAGTCT 1272
                           i     iv    i   v  vvi v  --     vi i     i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_147406662_   1273 CTTCAATAAATGATGTTGGAAAAACTGGCTATTCCTATGAAAAAAAATAA 1322
                         i     i     i  i   i v      v  ?i vi   v    i   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_147406662_   1323 AATTAGAACCTTATCTCACATTGTACACAAAAATCAACTTAAAATGGATT 1372
                          i  i  v  i  i      iii  i        i    i         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_147406662_   1373 CAAAACTTAAATGTAAGTCCTAAACCTATAAAATTACTAGAAGAAAACAT 1422
                         v? i  i          vv     v        i vi             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_147406662_   1423 AGTAGAAAGGCTCCATGACATTGGCCTAGGCAATAACTTTTTTTAATATG 1472
                           v? v  iv  i i    v    vi        ii-   i  vi     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATG 597

  chr2_147406662_   1473 TCCCCAAAAGCCCAAAATAGACACGATTGTTGCCCAAGAGGCAACAAAAG 1522
                         v v        v   -------------------------          
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA-------------------------GCAACAAAAG 622

  chr2_147406662_   1523 CAAAAATAGACAAATGGGATTACATCAAACTAAAAACACTTCTATACAGC 1572
                         v         i    v   i v       v v    -    i i i vv 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTC 671

  chr2_147406662_   1573 AAAGAA-------AAGAACACAGTGAAGAGAAAACCTATAGAATGGGAGA 1615
                             i -------     ---      i   v    i i           
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAA---AGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_147406662_   1616 ACATATTTGCAAACCATACATCTTATCAGGGGTAAGTTAATATCCAAAAT 1665
                          v           i    i    v  v    --- v  i-      i   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGG---ACTTG-TATCCAGAAT 764

  chr2_147406662_   1666 ATGTAAGGAATTCAAGCAACTTAATAGCAAGAAAACAA----CCCAATTT 1711
                           i   i   i  vvi     i    ii  i  i    ----       ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_147406662_   1712 AAAAATGAACAAAGGACCTGAATAGACATTTCCCAAGAGAAGACTTACAA 1761
                                ii       ii              i v i      iv     
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_147406662_   1762 ATGGTCAGCAGATATATTTTAAAAATGCTCATTACTAGTGAAGAA 1806
                             i  ii iii i  vv-   i       vi ii ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGA-AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (121 / 69)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 11.15 (145 / 13)  


2857 24.79 2.17 1.93  chr2_147455157_147456973      498  1328 (489)    L1M4_orf2#LINE/L1       76   908 (0)  

  chr2_147455157_    498 AAATTCAACACAATCCCCATCAAAAT----ACTGCCATCATTCTTCACAG 543
                          i       i       i        ----i     ----  i  ii   
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC----TTTTTTGCAG 121

  chr2_147455157_    544 AATTAGAAACAAC-AATTCTAAAATTCATATGGAACCAAAAAAGAGCCCG 592
                           v v  v - i -i  i                 viiv  ii  v  v 
  L1M4_orf2#LINE/    122 AAATTGACA-AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr2_147455157_    593 CATAGCCAAAGCAAGACTAAGCAAAAAGGACAAATTTGGAGGCTTCAGAC 642
                         v         i   vvi i iv  i   i     v       vi   v  
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_147455157_    643 TACCTGATTTCAAACTATACTACAAAGCCATAGTCACCAAAACAGCATGG 692
                          v  ii        viv           i i   v i   i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_147455157_    693 TACTGACTGGAATAGAAATAGGCATATAGACCAATGGAACAGAATAGAGA 742
                              i ----   iii    i        i        i     v    
  L1M4_orf2#LINE/    271 TACTGGC----ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_147455157_    743 ATCCAGAAATAAACCCAAATACTTACAGCCAACTGATCTTTAACAAAGCA 792
                         i                v i i   ii i   i    i  ii    i vv
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_147455157_    793 AACAAAAACAGAAAGTGGGAAAAGGACATCCTTTTCAACAAACAGTCTTG 842
                         iv   i v  vvv i    i    i i vi            ii  vi  
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_147455157_    843 GGATAATTGGCTAGCCACATCTAAGAGAATGAAACTGGATCCTCATCTCT 892
                            i  i   v  ?      vi  i        ii    i  ii i   v
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_147455157_    893 CACGTTATATAAAAATCAACTCAAGAAGGATTAAGGACTTAAACCTAAGA 942
                            vv    i      i       i v    i ?i   i    iv     
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_147455157_    943 CCTGAAACTATAAAAATTCTAGAAGATAACATTGGAAAAACTCTTCTAGA 992
                         v  i           v ii       v     v  ?iv  v     vv  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_147455157_    993 AATTGGCTTTGGCAAAGATTTCATGACCAAGAACCCAAAAACAAATGCAA 1042
                         vv    v  v     v i    v iivi v  vv      i  v v    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_147455157_   1043 TAAAAACAAAGATAAATGGCTGGGACCTAATTAAACTAAAGAGCTTTTG- 1091
                         i    iv   i   i  iiv v    i v  i   v v  i i      -
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_147455157_   1092 ----CAAAATGAACA--GTCAGCAGAGTAAACAGACAATCCACAGCACAG 1135
                         ----    -- i   --i   iv i   i  v      i      -----
  L1M4_orf2#LINE/    667 GCTTCAAA--GGACACTATCAAGAAAGTGAAAAGACAACCCACAG----- 709

  chr2_147455157_   1136 AGTAGGAGAAAATCTTCACAATCTATGCATCTGACAAAGGACTAATATCC 1185
                          i i         v  ii   vii  ii      i  i     vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_147455157_   1186 AGAATCTACAATGAACTCAAACAAATCAGTAAGAAAAAAA-----AATCC 1230
                              v  i  v      vv    v   i   v     i -----  i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_147455157_   1231 CATCAAAAAGTGGGCTAAGGACATGAATAGATAATTCTCAAAAGAAGATA 1280
                         v  i?    i     v     iv        i v     v          
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_147455157_   1281 TACAAATGGCCAACAAACATATGAAGAAATGCTCAAC-TCACTAATTAT 1328
                                      i  i  i     i i         -   ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (124 / 78)
Gap_init rate = 0.01 (11 / 833), avg. gap size = 3.09 (34 / 11)  


2435 23.39 6.74 0.86  chr2_147523436_147525117      494  1190 (492)    L1M4_orf2#LINE/L1      171   908 (0)  

  chr2_147523436_    494 AACAATAAAAGCAACTTTGAGAAAGAAGAACAAAGCTAGAGGCAGCACAC 543
                           i iiv   i   ii    i              i i    vvv     
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_147523436_    544 T-CTTAATTTCAAACTATATTACAAAACTGTAGTAATCAAAGCAGTATG- 591
                          - ii         viv  i      i  ii         ii    i  -
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_147523436_    592 TAATGACATAGAAACACTCACATAGATCAAAGGAACAAATTAGAGAGACC 641
                           v  i    iii i vv  i         v    i i v v     v  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_147523436_    642 AGAAATAA-----TACA------ACCATCTAATCTTTGATAAGGATACCA 680
                                 -----    ------ii  vi i  i  i  i    i i   
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_147523436_    681 AGA------------------ATA-------CA-CAA-TGGTGTTAGAAA 703
                            ------------------   -------  -   -     i i i v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_147523436_    704 AACTGAATATCTACACACCAAAGTATAATATTGGACCCTTGTCTTACACC 753
                              i   ? i   ii v    v  i vi        i ii  i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_147523436_    754 ACACACAAAAATTAACTCAAAATGAATTAAAAATTTACATGTAAATTCTG 803
                          i i                    i  i ? i ii  v      ivv  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_147523436_    804 AAATCATAAAACTTCCAGAAGAAAACATAGGGAAGAAGCTTTTAGACACT 853
                            ii        iii               ?ivi  v   ivv   vi 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_147523436_    854 GGCCTTAGCAATTATTTTTT-GATATAACACCAAAAGAACAGGTGACTAA 902
                           vi vi     vi   i  -     i          v   i ii  v  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_147523436_    903 AGAAAAAA---ATAAGTAAGACTACATCAAACTAAAAAGCTTCT-TCCTA 948
                                 ---    i vi    v       v v    i   i - v  -
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT- 669

  chr2_147523436_    949 GCAAAGGA-ACAATCAACAAAATGAAAAGGCAACACATGGAATGGGAGGA 997
                         v       -  v     v   i       i    v  ii         i 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_147523436_    998 AATATTTGCAAACCATATATTTGATAAGGGGTTAACATCTACAATATATA 1047
                                     i       i         ii vii   i v        
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_147523436_   1048 AGAAACTAATGTAAGTCAATAGCAAAAATAAAAACAAA-AACCTGATTTT 1096
                          ii    vv ii  v      ii     ----i     -    ii   ?v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAA----GACAAATAACCCAATTWA 815

  chr2_147523436_   1097 AAAATGAGCAAAGGACCTGAATAGACATTTTTTCCAAAGGATACATGTAA 1146
                               i        ii             i -      i v i  ii  
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCT-CCAAAGAAGATATACAA 864

  chr2_147523436_   1147 ATGGCCAAGAGGCAAATGAAAAGATTCTCAACATCACTAGTCAT 1190
                                 v i   v          v          ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.18 (109 / 50)
Gap_init rate = 0.02 (16 / 738), avg. gap size = 3.31 (53 / 16)  


2115 26.11 1.53 0.92  chr2_147562099_147563745.rev      501  1155 (492)    L1M4_orf2#LINE/L1      250   908 (0)  

  chr2_147562099_    501 ACAGTAACCGAAACAGCATGGTACTGGTACCAAAACAGACATA--GACCA 548
                                i i i    ii         i iv ii i       --  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_147562099_    549 GTGGAACAGAACAGAGGCCTCAGAAATAACACCACACATTTACAACCATC 598
                         i     i    iv   ivii         vv   i       iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_147562099_    599 TGATCTTTGA-AAGACCTGACAAAAACAAGTGATGGGGAAAGGATCTCCT 647
                             i  i  -   iv-  v   i v  vvii          i  vvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_147562099_    648 GTTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 697
                         v     i              v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_147562099_    698 AACTGGACTCCTTCCTTGCACCTTATACAAAAATTAACTAAAGATGGACT 747
                          ii     i   v   ii    v                v  i     ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_147562099_    748 AAAGACTTAAAAGTAAAACC--AAACCGTAAAAACTCT-AGAAGAAAACC 794
                          ?    i    v    i v --    ii     -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr2_147562099_    795 TAAGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCAT-GATG 841
                           i ?i- v i -   i- i  v i  i- i     v ii   v -   -
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT- 594

  chr2_147562099_    842 AAAATGCCAAAAGCAATAGCAACAAAAGCCAAAATTGACAAATGGGATCT 891
                          vi ii         vv           vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_147562099_    892 AATGAGACTAAAGAGCTTCTGCACAACAGAAAAAAATTATCATCAGAGTG 941
                         v  v i v v  i i   i  ii vv  -  ii v i     vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGAAAGTG 693

  chr2_147562099_    942 AACAGGCAACCTACAGAATGGGAGGATATTTTTGCAATCTACCCATCTGA 991
                           v  i     i            i v  v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_147562099_    992 CAAATGTCTAATATCCAGAATCTGCAAAGAACTTAAACAAATTTACAAGA 1041
                         i  iv v  vi          v ii        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_147562099_   1042 CAAA-ACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGGACAGACAA 1090
                         v   -     i     v  i?    i           iv  i i     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_147562099_   1091 TTCTCAAAAGAAGACATTTACACGGCCAACAGACATATGAAAATAAGCTC 1140
                              v        i  vi v i      i ii  i       v v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_147562099_   1141 AACATCACTGATCAT 1155
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (101 / 66)
Gap_init rate = 0.02 (14 / 659), avg. gap size = 1.14 (16 / 14)  


2863 25.25 2.55 1.99  chr2_147663753_147666575.rev     1429  2331 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_147663753_   1429 TGAAAAAACATCCCATGCTAATGAATTG-AAGAATGAATATTGTTAAAAT 1477
                           i   i i        i v   i    -    v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147663753_   1478 GACCATACTGCC-AAAGCAATCTAGAGATTCAATGAAAGTCCTATCAAAT 1526
                          i v     v  -   vii     v        i v  vi         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_147663753_   1527 TACCAA-TGTCAGTCTCCACAGAATTAGAAAAAAAAACAATTCTAATGTT 1575
                          v   i-  i -v i iii     v v  v  iv---ii  i    vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC---TGATCCTAAAATT 146

  chr2_147663753_   1576 CATATGGAACCAAAAAAGAGCTCAAATAGCCAAAGTAATTCTAAGCAAAA 1625
                                  viiv  ii  v ivi          ii   ii i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_147663753_   1626 AGAA-AAAGCTAGAGGCATCACATTACCTGACTTCATATTATACTACAAG 1674
                             -    i i    vv     i v  ii i    v viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_147663753_   1675 GCTACAGTAACCAAAACAGCATGGTACTGGTGTGAAAACTGACACACAGA 1724
                                   i   i    ii         ii i ii iv    i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_147663753_   1725 TCAATG-AACACAATAGAGAACCCACAAATAAAGCCACATATCTACAGCC 1773
                               -  i v   v    ii   v       v   i i  i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_147663753_   1774 AAGTGATCTTTAATAAAGTTAACAAAAACATACACTGGAGAAAGGACACC 1823
                           v    i  ii i  i v iv   i v   v  v   i     i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_147663753_   1824 CTCTTTAGTAAATGGTG-TGGGAAAATTGGATAGCCATAGGCAGAAGAAT 1872
                           i  i ii        -     v  i      ?   i v   i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_147663753_   1873 TAAACTGGACCCCTATCTCTCACTATATACAAAAGTTAACTAAAGGTTAA 1922
                         v  ii          i   v   i          i      v  ii vi 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_147663753_   1923 TTAAAAACTTAAAGGGAAGACCTGAAATTTAAAAAAAGCCTAGAAGAAAA 1972
                          i ? i  i    v v    v  i   i - v    vv i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTTAGAAGAAAA 545

  chr2_147663753_   1973 CCTAGAAAAAACTCTTCTGGGTGTTGGTCTAGGCAAAGAATT------TA 2016
                          v   i?iv  v     vv iiv    vi       v iv  ------  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_147663753_   2017 TGACTAATTCTCAAAA--ACAATTACAACAAAAACAAAAATAGATAAATA 2064
                             -- i---     --    --i        iv              v
  L1M4_orf2#LINE/    596 TGAC--AC---CAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATT 638

  chr2_147663753_   2065 GGATTT------AATTAAAAAGATTCTGCACAGCAAAATAAACAATCAAC 2108
                            i  ------         v-  i  ii vv    iv v  v     v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_147663753_   2109 AGAGTAAATAGAAAACCTACAGAATGGGAGAAAATATTTGTGAACTATGC 2158
                          i   i  v   v    i                      ii  ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_147663753_   2159 ATCTGACAAGAG-CTAATATCCAGAACTTATAAGAAACTCAATTA--GCT 2205
                               i   i -  vi         iv     ii     --   --i  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--TTACAACT 785

  chr2_147663753_   2206 TAACAATAACAACAACCAAATAATCCAATTAAAAAGTGGACAAAAAAACA 2255
                         i  i     v  v --       i      ?    i   i    ii vi-
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATT- 832

  chr2_147663753_   2256 TGAATAGACATTTTTCAAAAGAAGGCATATAAGCGGCCAACAAAAATATG 2305
                                      i  v       ii   i  ii      i  iv i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_147663753_   2306 AAAACATGCTCAAAATCAGAGAAATG 2331
                             v        v    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (143 / 81)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.95 (41 / 21)  


2402 23.50 6.12 5.35  chr2_147705505_147709597.rev     2704  3601 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_147705505_   2704 AAAGATATGTACCTTGTTAATCAATGAGTAGACTCAATAATGTTAACATG 2753
                                 v--  v    v  vi  vi v     i    v      v   
  L1M4_orf2#LINE/      4 AAAGATATC--CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_147705505_   2754 GCAACTTTATCCGTATTCATCTGTAGCTTTAATATGATCCCAGTCAAAAC 2803
                             ivi vi  iv   v    ii  v  i  iiii     vi      -
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA- 100

  chr2_147705505_   2804 TATTCAAGCTAT-TTTTTTGTAGAAATC-ACAAAATGATTTTAAAATTTA 2851
                         -- i v    ii-       i      i-    iv    ii       i 
  L1M4_orf2#LINE/    101 --TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_147705505_   2852 TGTAAAATTACAAAAGACCTAGAATAGCCAAAACAACTTTGAAAAAGAAG 2901
                          i ii  v i   ii    i                ii            
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_147705505_   2902 AATAAAGTTGAATAACTTAAACACTATTTGATTTCAAGACTTGTTAGAAA 2951
                           i       i vi   i --    viiii       i    ii  v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCA--CACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_147705505_   2952 GCTAAAGTATGCAAG-----------------TATGGAT---CAT-TAGA 2980
                             v    vv    -----------------  v    ---   -    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_147705505_   2981 AC--TGGA-TAAAAT----ACTC--AAAATAGGATCACACAT--ACAGTC 3019
                         v --    -  i   ---- v  --i     iivi  i    -- ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_147705505_   3020 AATTGACTTTTTACAAAGGAACAAAAGCAATTTAATTGGGGGGAAATTAG 3069
                               i   iv    i  vi v  ii v   i   -    ii i v   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAG 395

  chr2_147705505_   3070 CATTCTCTTCAACAA------TTAGAACAACCTGA----CAGATGTAGAA 3109
                         ---   i        ------i i i     iv  ----  v   i ---
  L1M4_orf2#LINE/    396 ---TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA--- 439

  chr2_147705505_   3110 AACAAAAAACAAAAATAACCCTCCCCTACAAAACCACCTTGGACCT-TAC 3158
                         ---   i  ii  i------------------------       i-   
  L1M4_orf2#LINE/    440 ---AAAGAATGAAG------------------------TTGGACCCCTAC 462

  chr2_147705505_   3159 TTCACACCACATACCATACCATAATTAACTTGAATTGGATCATATACCAA 3208
                         i        i    v ---- -        ii  v       ? v   v 
  L1M4_orf2#LINE/    463 CTCACACCATATACAA----A-AATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_147705505_   3209 AATGTAAGAGCTTACA-TATACAATTACTGGAATGAAACATTGGAAAATA 3257
                                     v v -    v  i vi i   vi      v  ?iv v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_147705505_   3258 TCTTAAAGATCTTGGGTTTGGCAAAAATTTCTTAAATATAATGCAAAGAG 3307
                             viv  i        v     vii       i    i ii v  i  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_147705505_   3308 CATGAACTATTAAATAATAAAATCAATAAATTTATCTTAAGCAAGTTTAA 3357
                           ii i v iv   v  -     vi       viv   v v   iv    
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAA-AAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_147705505_   3358 AA-CTTTTGTTATTTTAAAACCCCTGTTATGAAAAATGAAACAGCAGGCA 3406
                           -       vv  iv  iiv v  i i v    i-     vii  iv v
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG-TGAAAAGACAACCC 705

  chr2_147705505_   3407 ACAGACTGGGACAAAATACTAGCAAATCATATATCTGACAAAGGACTTGT 3456
                              v     v      i v                 i  i        
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_147705505_   3457 TTCTAGAATATGCAAAGAACTC--AGAAGTTGATAATAAAAACACAGATA 3504
                         v  i       ii         -- v  v ii          v   i   
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_147705505_   3505 ACTCA-TTTAAAAATGGACAACATATTTAAACAGACCCTTCACCAAA--- 3550
                           i  -  ?        i   viv    i  i    vi   v     ---
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_147705505_   3551 --TATACAGATGGCAAATAAGAACATGAATATGTGCTCAACATCAATTGT 3598
                         --      i     v      v       v vi            ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_147705505_   3599 CAT 3601
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.48 (124 / 84)
Gap_init rate = 0.03 (29 / 905), avg. gap size = 3.55 (103 / 29)  


3169 25.76 1.52 2.83  chr2_147733059_147734978.rev      522  1441 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_147733059_    522 TGGAAAGGTATTTAATGTTTACAGACCAGAAGACTTAATATTCTTAAAAT 571
                                i   iiv     i ii  iii              v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147733059_    572 GTCTATGCTGCTCAAAGCAATATACAGATTTAACATAATCCCTATCAAAA 621
                          v v  i  v i    vii  v        i   ii              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_147733059_    622 TTTCAATGGCATTCTTCACAGAAGTAGAAAAAAGAATTCTAAAGTTTGTA 671
                          ii  iiv  v  i  ii     i v  v  ivvi  i     i  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_147733059_    672 GGGAACCACATACAACTCTGAATCACAAAAGCAATACTGAGAAAGAAAAA 721
                         v    vii  vivi  i v    vi v   i    vi   i      i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_147733059_    722 CAAAGTTGGAAGCATTATACTTCCTAATGTAAAATTTTATTACAAAAGTA 771
                                   i vv i i      i   v v   vi   i      iv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_147733059_    772 TATTAATCAAAGCAGTATAGTACTGTTATAAAAACAGAAACATAGACCAG 821
                         i v       ii    i i      vi    ii i   v i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_147733059_    822 TGGAACAGAATAGAGAGCCAAGAAATAAATTTATACACATGTAGTCAACA 871
                              i     v     i v         iii     iv i i     iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_147733059_    872 AATTTTTGACAAGGGCACTAAGAAGACACAATGGGGAAAGGATAGTCTCT 921
                         i     i        ii i    vv iv            i       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_147733059_    922 TCAATAAATGGTACTGGGAAAACTAGGTTTCCACATGCAAAAGAATGAAA 971
                             i       i      v    i i v?                   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_147733059_    972 CCAAATCCTTATCTTGTACCAGACCAAAAAAAAAAAAAAAAAAAAAAAAA 1021
                         iiii i  i  i  iii    v i--------------------- v   
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATAT---------------------ACAAA 479

  chr2_147733059_   1022 AGTCAACTGAAAATAGATAAAAAATCTAAATATAAGACCTGAAATCA--- 1068
                          i i    v     i   v ? i i      i     v  i   ii ---
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_147733059_   1069 -ACTCCTAGAAGAGAACACAGAGG-AAATGCTTCTTGAAACTGGATGTTG 1116
                         -    i       i    i  i? -    -    v   vvi   i - v 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGT-TAG 577

  chr2_147733059_   1117 GTATTAATTTTGTGAATATCACACCAAATAGC-CAGGCTACAAAAGCAGA 1165
                          i v ii   iv ii    v        -   -  i  v       v i 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAA-AGCACAAGCAACAAAAGAAAA 626

  chr2_147733059_   1166 AATTAATAAATGGGA--TCACTCCAAACCAAAAAGCTCCTGTACAACAAA 1213
                            vi      v   --   -  v   ii     -  ii   i vv    
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCA-TCAAAATTAAAAA-CTTTTGTGCTTCAAA 674

  chr2_147733059_   1214 AGAAACAATCAACAAAATGAAAAGGCAACCTATGAACTGGGAAAACATAT 1263
                         i  v  v     v   i       i     i iii v     i  v    
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_147733059_   1264 TTGCAAACCACATATCTGATAAGGGTTTTATGCTCAAAAGTTATAAAGAA 1313
                                i  i              vi  i iii  i  vv         
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_147733059_   1314 CTCTTACAATTTAATAGCAGAAA-----ACAACCCAATTGAAAAATGGGC 1358
                                  i i    ii i   ----- i         ?          
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_147733059_   1359 AAGAAACCCAAACAAACATTTCTTCAAAGAAAACATTAAAAGGGCCAATA 1408
                           iii iiii  i i        i       i i  vv   v        
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_147733059_   1409 CGTATATGAAAAG-TGTAAAATATTACTAATTAT 1441
                         v i i        -  ivv  i  i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (161 / 72)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.33 (40 / 12)  


3295 26.02 0.66 0.55  chr2_147741593_147748019     5029  5935 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_147741593_   5029 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5078
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147741593_   5079 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5128
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_147741593_   5129 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5176
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_147741593_   5177 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5226
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_147741593_   5227 AACAAAGCTGGAGGCATCACACTACCTGACTCCAAACTATACTATAAGGC 5276
                                i      vv       v  ii i i    viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_147741593_   5277 TACAGTAACCAAAACAGCCTGGTACTGGTACTAAAACAGAGATATAGATC 5326
                                 i   i    iv         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_147741593_   5327 AATGGAACAGAAC--AAAGCCCTCAGAAATAATGCCGCATATCTACAACC 5374
                                i    i-- i  i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_147741593_   5375 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACAATTCC 5424
                          vi    i  i     ivv  v   i v  vvv          v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_147741593_   5425 CTATTTCATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5474
                           v  iv i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_147741593_   5475 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5524
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_147741593_   5525 TTAAAGACTTAAATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAAC 5574
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_147741593_   5575 CTAGGCA-ATACCATTCAGGACATAGGCATAGGCAAGGACTTCATATGTA 5623
                         v    ?i- v i -   iv   v v  vv       v ii   v  vi  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_147741593_   5624 AAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTA 5673
                         vi            vvii         vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_147741593_   5674 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5723
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_147741593_   5724 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5773
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_147741593_   5774 AAGGACTACTATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5823
                          i     vv          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_147741593_   5824 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5873
                           i     i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_147741593_   5874 CTC-AAAGAAGACATTCATGCAGCCAAAAAACACATGAAAAAATACTCAT 5922
                            -        i  v  viii     v  i          i  i    v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_147741593_   5923 CATCACTGGCCAT 5935
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3068 26.30 1.33 0.78  chr2_147773020_147779582     5171  6071 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_147773020_   5171 GAAAAACTTTCCATGCTCATGGATAGGAAGAATCAGTATTGTGAAAATGG 5220
                             i iv i     i        v      v i i      v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_147773020_   5221 CCATACTGCCCAAAGTAATTTATAGATTCGGTGCTATTGCCATCAAGCTA 5270
                          v     v      v i  i  i      iii  v  iv i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_147773020_   5271 CCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCATGT 5319
                            vivi i  i  ii     v v  v  i-  - iii    v     i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr2_147773020_   5320 GTAAC--CAAAAAACAGCCTGTATAGCCAAGGCAATCCTAAGCAAAAAGA 5367
                          v  v--   iii  --  v v        ii     i i iv  i    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_147773020_   5368 ACAAAGCTGGAGGCATCACGCTTTCTGACTTCATACTATACTACAAGGCT 5417
                               i      vv    i   i ii i    v viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_147773020_   5418 GCAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATCTAGACCA 5467
                         i      i   i    ii  i      i iv ii i   i  v    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_147773020_   5468 ATGGAACAGAAC--AGAGTCCTCAGAAATAATACCACACATCTAAAACCA 5515
                               i    i--       --        vv   i    i  viii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_147773020_   5516 TTTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5565
                         v     i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_147773020_   5566 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5615
                          v  i  i        i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_147773020_   5616 AAACTGGACCCCTTCCATACAACCTACACAAAAATTAACTCAAGATGGAT 5665
                           ii         v  vi   v v  i                i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_147773020_   5666 TAAAGATTTAAATGTAAGACCTAAAACCATAAAAACTCT-AGAAGAAAAC 5714
                         i ?   ii           v       i      -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr2_147773020_   5715 CTAGGCA-ATACCATTCAGGACATAGGCATGAGCAAAGACTTCATGACTA 5763
                         v    ?i- v i -   iv   v v  vv ii    v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_147773020_   5764 AAACACCAAAAGCAATGGCAACAAAAGCCACAGTTGACAAATGGGATCTA 5813
                         vi            vvi          vv v i v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_147773020_   5814 ATTATACTAAAGAGCCTCTGCACAGCAAAAGAAATTATCATCAGAGTGAA 5863
                           i v v v  i i i i  ii vv    i  v i     vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_147773020_   5864 CAGGCAATCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACC 5913
                         v  i   i i                 v       vii  vi      iv
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_147773020_   5914 AAGGTCTACTACCCAGAATCTACAAGGAACT-TAACAAATTTATAAGAAA 5962
                          i  v  vv  i       v  i  i     - v    v iv    v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_147773020_   5963 AAAA-AAA-AACC--ATCAAAAAGTGGGCAAAGTATATGAACAGACACTT 6008
                           i -   -    --  i?    i         v  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_147773020_   6009 CTCAAAAGAAGACATTTATGTGCCCAAGAAACATATTAAAAAAAGCTCAT 6058
                            v        i  vi vi  v    v  i  i  v    i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_147773020_   6059 CATCACTGGTCAT 6071
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (133 / 100)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 1.36 (19 / 14)  


3685 22.85 2.01 0.78  chr2_147781299_147785622     2936  3832 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_147781299_   2936 TAGAAAGACATCT-GTGCTTATGAAGTGGAATAATTAATATTGTTAAACT 2984
                          i      i   i-i  i i   i v     v v             iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147781299_   2985 ACT--TATTCAACTCAAAGTGATTTACAGATCCAATGCAATGCCTATCAA 3032
                         ivi--  i  -- i    v    i       i   i     v        
  L1M4_orf2#LINE/     51 GGCAATACTC--CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_147781299_   3033 AATTGCAA-TGTGTTTTTTGCAGAAAAAAATAAGA-AATACTAAAATTCG 3080
                            iv  i-  iv             vvi i   v-i  v         i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_147781299_   3081 TATGGAATCTAAAGGAACCCTAAATAGACAAAACAATCTTCCAAA----G 3126
                                vivv    i    vi     v            vv   ---- 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_147781299_   3127 AATAAAATTGGAGGCTTCACACTCTCTAATTTCAAAACTTATTATGAAGC 3176
                           i   i       vi       ii i              i  ii    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_147781299_   3177 TGCAGTAATTGAAGTAGCATGGTCCTGGCATAAAGGCAGACATACAGACC 3226
                          i       ii iii  ii    v         i ii       i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_147781299_   3227 AATGAAACAAAATAGAGAGTCCAGAAATAAACTCCCATGCAT--ACGGTT 3274
                             i  i i   v                  --    i   -- i   i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAAC--CCATACATTTATGGTC 346

  chr2_147781299_   3275 AAATGAACTTTGA-AAGACTACAAAGATGATACAATGGGCGAAGGACAGT 3323
                           v   vi  i  -   iv i v    iv  v       vi   i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_147781299_   3324 CTCTTTAACAAATGATGCTGAAAAAACTGAGTATCTGCATGCAAAAGAAT 3373
                           i  i        i     ii v     ii  ? ii             
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_147781299_   3374 AAAGTTGGACCCTTATCTTGCACTATACATAAAAATTAACTCAAGATGAA 3423
                         i           i  i  ii   i   i i              i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_147781299_   3424 TTAAAAGCCTAAACA-AAGACCTAAAACTATAAAAGTCTTATAAAAACTC 3472
                          i ? ii      ii-    v              v     v  i  vv 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_147781299_   3473 -CAAGGGAAAAACTTCATGACATTGGATTTGG-AATGATTTTGTTTGAAT 3520
                         -i i ? v   v    i    v    i  v  -    i   i--  ii  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC--TTAGAT 594

  chr2_147781299_   3521 ATGACACCAAAATCACAGGGAATAAAAGCAAATTCAGACAAATGGGACTA 3570
                                     v    i v  i     v   vvi   i    v     v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_147781299_   3571 CATTAAATTTAAAAACATTTGTGCATCAGAGGCAACAATCAATGGAATAA 3620
                            i   v        v       v   i   vv  v     vii i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_147781299_   3621 AAAGGCAGCCTATGGAGTGGGAGAAAATGTTTCTGAA-CATGCATCTCAT 3669
                             i  i  i ii  i           i   vii  -   ii    v  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_147781299_   3670 AAGAAGTTAATATCTAGAATACATAAA-AACTTCCACAACTCAACAACAA 3718
                            iiii vi    i      i     -    iii         i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_147781299_   3719 CAACAACAAA-AACGTGATTTTAAAATGGGCAAAGAACCTGAATGCACAT 3767
                         v  -i     -   vii   ?v             i ii     iv    
  L1M4_orf2#LINE/    795 AAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_147781299_   3768 GTCTTCAAAGAAGATATACAAATGCCCAATGAACATATGAAAAGATGCTC 3817
                         v   i                   v     i i  i              
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_147781299_   3818 AACATCACTAATCAT 3832
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.19 (138 / 63)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.47 (25 / 17)  


3117 26.54 0.70 0.93  chr2_147853235_147856980.rev     2388  3246 (500)    L1M4_orf2#LINE/L1        1   857 (51)  

  chr2_147853235_   2388 TAGAAAGATATTCCATGCTCATGGATTAGT-GAATCAATATTATTAAAAT 2436
                          i         i     i         i v-  v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_147853235_   2437 GGCAATATTGCCCAAAGTAATTTACAGATTCAATGCAATTCCTATCAAAA 2486
                                i v      v i  i           i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_147853235_   2487 TACCAATGACAGTCTTCACAGTAATAGAAAATACAATTCTCAAACTTATA 2536
                          v   iivi vv i  ii   v   v  v  vvii  i  v   i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_147853235_   2537 TGAAACCATAAAAGACTCCAAATAGCTCATGCAGTCCTGAGTGAAAAAAG 2586
                           i  viii  ii   i vi      iv vi  i  i   i--   i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--AAAGAAG 198

  chr2_147853235_   2587 AATAAAGCTAGAGGCATGACACTACCTGTCTTTAAAATTTACTACAAAGC 2636
                           i    i i    vv v     v  iivi  i    i            
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_147853235_   2637 TACAGTAACCCAAACAGCATGGTACTGGTGTAAAAACAGACACATAAAAC 2686
                                 i v i    ii         ii   ii i     i   i v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_147853235_   2687 AATGGAACAGAATAGAGAATCCGGATATAAACCCCCATGTTTACAGCAAA 2736
                                i     v    i   i  v        vi ii    ii iv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_147853235_   2737 CTCATCTTTGACAAAGGTGCCAAGAACATACATGGGGGAAAGGACAATCC 2786
                         i v  i  i     i          v   v  vv        i i i  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_147853235_   2787 TTTCCATAATTGGTGCTGGGAAAACTGGATAACTTTATGAAGAAGAATGA 2836
                             v i  v           v         ? ivi   v i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_147853235_   2837 AACTATATTCTT----CACACTATATACAAGAATCAAGTGAGAATGGATG 2882
                          ii iv ii i ----     i        i   i  v v i       v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_147853235_   2883 AAAGACTTAGATCTAAGACCTGAAGCAATGAAAACACC-AGAAGAAACCA 2931
                          ?    i  i  v     v  i  i v  -     v i-        v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chr2_147853235_   2932 TTGCAGTAACACTCCAGGACAGTGGTCTGAACAAAGATTTTTGTGTGTAT 2981
                          v v?    vv  i iv   vv   vi iii   v i   i - ivi   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT-TAGATAT 596

  chr2_147853235_   2982 GACCCCAAGAGTACAGGCAACAAAAGCAAAAATAGACAAGTGGGATTATA 3031
                            v    i  i   i          v         i  i v   i vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_147853235_   3032 TGAAGCTAAAAAGCTACTGCACAGCAAAGGAAACAATCAGCAAAGCAAAG 3081
                          v  iv v    i  vi  ii vv       v  v    iv    ii  i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_147853235_   3082 CGACAACACCCAGAATGGAAGAAAATATTTGTAAACCACTCATCTGACAA 3131
                         v      v v        i            i   i  ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_147853235_   3132 AGGATTAATAACAAGAATATGTAGGGAACTCAAATAACTCAACAGTAAAA 3181
                         i   i vi  v v       i  ii      vv i       i i     
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_147853235_   3182 AAAAATAATAATAATCCCATTAAAAAGTGGGCAAATGATCTAAATAGACA 3231
                          i v ----     i  v   ?    i        v   i i        
  L1M4_orf2#LINE/    797 AGACA----AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_147853235_   3232 TTTCTCAAAAAAAAA 3246
                               v   i  i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGA 857

Transitions / transversions = 1.67 (140 / 84)
Gap_init rate = 0.01 (7 / 857), avg. gap size = 2.00 (14 / 7)  


2157 26.04 2.66 6.27  chr2_147995564_147997534      541  1481 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_147995564_    541 GGAGAGATATACTGTGTTTAAGGATAAAAAGACTTTACATAGTAAAAATA 590
                            i      v ii    i v    vii       v i  v  v  i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_147995564_    591 TTAGTTTTCCACAAATTTATATGCAAGTGTAATGCAATTCCTATTAAAAT 640
                         vi i vi   v      v  v i  ii vi  i     i     i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_147995564_    641 CCTTGCT-CATTTTTCATAGATATAGACAAGATTATTCAAAAAATAATAT 689
                           iv   - v     iii   v  v      v v  i v    v v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_147995564_    690 GAAAAGGCTAAAGAAGTGGAATAGTTAAAAACAA-ATTGCAAAAGAAAAA 738
                          i   v  v ii  vvii      ii    -   -v   v       i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAA 200

  chr2_147995564_    739 TAA---TGGAAGAGTAAAGAGTCTACCTGATTTTAAGACTTTTTGTCTGG 785
                         i  ---    i  v v vi---  v  ii    i  i    vi iivvi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACA---CTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_147995564_    786 CTGCAGTAGTCAAGACTGTGTGATACTAATGGAGCAATCTACACACAGAT 835
                           i     i       v     i    iiiiv ivi  vv   i i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_147995564_    836 CAATAGAACAGAAGAGAGAAACCATAAAGAGATCAACACAAATATGTCCA 885
                             i   i    vv    iv   v   v i i v i   vv    vi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_147995564_    886 ATTGAATTTTGACAAAGAAGCAACAACCA----ATGG---------AGTC 922
                              v   i     i iv  v vi    ----    ---------    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_147995564_    923 TTTTCAACAAAAGGTGCCAGAACAACTGGACATTCATAGGCAAAAATAAT 972
                                    v     ii i         i ?i  i v      i-   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AAT 446

  chr2_147995564_    973 AGTAATCTTGTCATAAACCTTACACCTCACACT-TATACAAATTTGCGTA 1021
                         i--  ----  -- ii   ii-i         i-        --------
  L1M4_orf2#LINE/    447 G--AA----GT--TGGACCCC-TACCTCACACCATATACAAA-------- 479

  chr2_147995564_   1022 ACCTTGCACCTTACACAGATTAACTCAAAATGCATCACAGACTTAAAGGT 1071
                         -----------------i              v    ?    i    v  
  L1M4_orf2#LINE/    480 -----------------AATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_147995564_   1072 AAATTGTACAAGTATAAAATTTGGGGGAAAAAATTACAGGAGAAAATATT 1121
                           ivvv  v  v       i ivvi i i    i- i   ? v    v  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC-ATAGGNGTAAATCTT 561

  chr2_147995564_   1122 TG-GGCTCCAGGTCTTGGCAAAGTGTTTTTAGACTTGACAACAAA-GCAT 1169
                         i - i iiii   - v     v vv  i     iv     v    -   i
  L1M4_orf2#LINE/    562 CGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_147995564_   1170 ATATATAAAGAGAAATATTA-ATAAATTAGAC--CATGAAAGTTAAAAAC 1216
                          vii vv  i     v v  -       i   --   v   i        
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_147995564_   1217 TTTTGCTCTGAGAAAAAACTATATTAAGAGAGTGAAAAGACAAACTACAC 1266
                              iv  vv-   ii  vv   i    i             v i   v
  L1M4_orf2#LINE/    661 TTTTGTGCTTC-AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_147995564_   1267 ACAGGAAGTAGGTATTTGTAAACCACATATCAGACAAAGAACTAGTATCT 1316
                          vv  i  v ii      i   i  i     v  i  i i   v     i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_147995564_   1317 ATAATAGTATATATATAAAGAACTATCAAAACTCAATAGTAAAAAAAGCT 1366
                          v    -------           v i v         i      i ---
  L1M4_orf2#LINE/    760 AGAATA-------TATAAAGAACTCTTACAACTCAATAATAAAAAGA--- 799

  chr2_147995564_   1367 GAAATCAAACAATACAACTAGAAAATAGGCACAAATGAGT-GAACAAATA 1415
                         -----    i  iv   i ?i     i    --  v  v -   i i i 
  L1M4_orf2#LINE/    800 -----CAAATAACCCAATTWAAAAATGGGCA--AAGGATTTGAATAGACA 842

  chr2_147995564_   1416 GTTCACCAAAGAAAGTAAATAGATAGCAAATAAGCATATGAAATTATGTC 1465
                         v   v        ii  v i i  i  v        i      vv   ii
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_147995564_   1466 CAATATAATTAGCTAT 1481
                            i  v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.03 (25 / 907), avg. gap size = 3.36 (84 / 25)  


2809 27.82 2.35 0.89  chr2_148001507_148007246.rev     4354  5248 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148001507_   4354 TGGAAAAACATTCCATCCTCATGGATAGAAAGAATCAATATTGTGAAAAT 4403
                               i i  i    vi        v i    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148001507_   4404 GGCCATACTGCCTAAAATAATTGATAGATTTAATGCTATTCTCATCAAAC 4453
                            v     v  i   v i  iv i     i  i  v  i ii      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148001507_   4454 TACCA-CTGACATTCTTCACAGAGTTAGAAAAAATTACTTTAAATTTCAC 4502
                          v   -   v -  i  ii    iv v  v  iv v iii    v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_148001507_   4503 ATGGAACCA-AAAAGAGCCTGTATAGCCAAGATAATCCTAAGCAAAAAGA 4551
                               vii-  ii  v  v v        i i    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_148001507_   4552 ACAAAGCTAGAGTCATCACACTACCTCACTTCAAACTATATTACAAGGCT 4601
                               i i   vvv       v  iv i      viv  i     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_148001507_   4602 ACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGACATATAGACCA 4651
                                i   i    ii         i iv ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_148001507_   4652 ATGAAACAA-----------CAGAAATAACACCACATATCTACTGCCATC 4690
                            i  i i-----------         vv   i i  i  iv i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_148001507_   4691 TAGTCTTAGACAAACCTCACAAAAATAAGCAGTGAAGAAAGGATTTCCTA 4740
                          ii i  v     ivv vv   i vi vv  i  ii     i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_148001507_   4741 TTTAATAAATGGTGCTGGGAAAACTGGCTAGACATATGCCGAAAACTGAA 4790
                           i  i              v      v  ?v  i    vi  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_148001507_   4791 ACTGGACCTCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 4840
                         ii      i  v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_148001507_   4841 AAGACTTAAATGTAAAACCAAAAAGCATAAAAACCCTAGAAGAAAACCTA 4890
                         ?    i         i v v    vi      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_148001507_   4891 GACA-ATACCATTCAGGACGTAGGCCTCGGCAAAGACTTC------ATGA 4933
                          i?i- v i -   iv   v v  vi v     v ii   ------    
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_148001507_   4934 CAAAAATGCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGGAT 4983
                           ------         vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    599 CA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_148001507_   4984 CTAATTAAACTAAAAAACTTTTACACAGCAAAAGAAGGTATCATCAGAGT 5033
                         i v  i   v v          iii vv    i  viv     vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_148001507_   5034 GAACAGGGATCCTATAGAATGGGAGAAAATTTTTGCAATCTACCCATCTG 5083
                            v  iv v  i i               v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_148001507_   5084 ACAAAGATCTAATATCTAGA-TCCACAAGAAACTTAAACAAATTTATAAG 5132
                          i  i iv  vi    i   - vi i  ii    ivv    v iv    v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_148001507_   5133 AAGGAAACAAACAATCCCATCAAAAAGTAGGCAAAGAATATGAACAGACA 5182
                           ii i     i  i  v  i?    i i       i  v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_148001507_   5183 CTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAGAAAAGCT 5232
                         i     v        i  vi viii     i  i  i     i i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_148001507_   5233 CAACATCACTGATCAT 5248
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.22 (29 / 9)  


3225 27.37 0.55 0.33  chr2_148172012_148178702.rev     5294  6199 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148172012_   5294 TGGAAAAACATTCCACGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5343
                               i i  i   i i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148172012_   5344 GGCCATACTGCCCAAAGTAACTTATAGATTCAATGCTGTCCCCATCAAGC 5393
                            v     v      v i ii  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148172012_   5394 TACCATTGACTTTCTTCACAGAATAAGAAAAAACT-ACTTTAAATTTCAT 5442
                          v   vivi i  i  ii     - vvi v  i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_148172012_   5443 ATGGAACCAAAAAAGAGCCTGTATAGCCAAGGCAATCCTAAGCAAAAAGA 5492
                               viiv  ii  v  v v        ii     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_148172012_   5493 ACAAAGCTGGAGGCATCATGCTAGCTGACTTCAAGCTATACTACAAGGCT 5542
                               i      vv   ii  vv ii i     iviv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_148172012_   5543 GCAGTAACCAAAACAGTATGGTACTGGTACCAAAAAAGATATACAGACCA 5592
                         i      i   i     i         i iv ii v   i   i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_148172012_   5593 ATGGAACAGAACAGAGGCCTCAGACATAATGCCATATGTCTACAACCATC 5642
                               i    iv   ivii    v    vv     ii i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_148172012_   5643 TGATCTTTGACAAATCTGACAAAAACAAGAAAGGGCGAAAGGATTCCCTA 5692
                             i  i     ivv  v   i v  vvv  v  v     i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_148172012_   5693 TTTAACAAATGGTGTTGGGAAAACTGGCTGGCCATATGCGGAAAACTGAA 5742
                           i           i     v      v i?   i    ii  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_148172012_   5743 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAAGCGTATTA 5792
                         ii    i    v   i     v                    ii v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_148172012_   5793 AAGACTTAAATGTAAGACCTAAAACCATAAGAACCCTT-GAAGAAAACCT 5841
                         ?    i           v       i    -   i   -         v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACAT 548

  chr2_148172012_   5842 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 5890
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_148172012_   5891 ACACCAAAAGCAATGGTAACAAAAGCCAAAATTGACAAAT-GGATCTAAT 5939
                                     vvi i        vv     v  i    -   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_148172012_   5940 TAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAGTGAACA 5989
                         i   v v  i i   i  iiivv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_148172012_   5990 GGCAACCTACAGAATGGGAGAAAGT-TTTGCAATCTATCCATCTGACAAA 6038
                          i     i               i -       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_148172012_   6039 AGGCTAATATCCAGAATCTATAAGGAACTTAAACAACTTTACAAGGAAAA 6088
                         i i  vi          v     i     ivv      iv i  vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_148172012_   6089 AATGAACAACCCCATCAAAAAGTGGGTGAAGGATATGAAAAGATACTTCT 6138
                         i ii  i     v  i?    i    ii      v    v   i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_148172012_   6139 CGAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTCATCA 6188
                          v        i  vi vi       i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_148172012_   6189 TCACTGGTCAT 6199
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (149 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.00 (8 / 8)  


3278 26.98 0.44 0.44  chr2_148317806_148324080     4876  5783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148317806_   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148317806_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCTATCAAGC 4975
                            v     v     iv i  i           i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148317806_   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_148317806_   5024 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAACCCAAAAG 5073
                                viiv  ii  v  v v  v     iv     i i vvv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_148317806_   5074 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5123
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_148317806_   5124 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5173
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_148317806_   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5221
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_148317806_   5222 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5271
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_148317806_   5272 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5321
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_148317806_   5322 GAAACTGAATCCTTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5371
                            ii  i i  i v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_148317806_   5372 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5421
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_148317806_   5422 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5471
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_148317806_   5472 AACACCAAAAGCAATGGCAACAAAAGACAAAACTGACAAATGGGATCTAA 5521
                         i            vvi           v    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_148317806_   5522 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5571
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_148317806_   5572 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5621
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_148317806_   5622 AGGGCTAATATCCAGAATCTACAATGAATTCAAACAAATTTACAAGAAAA 5671
                         i  i  vi          v  i  v   i  vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_148317806_   5672 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5721
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_148317806_   5722 TCAAAAGAAGACATTTATGCATCCAAAAAACACATGAAAAAATGCTCATC 5771
                           v        i  vi viiiv    v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_148317806_   5772 ATCACTGGCCAT 5783
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1228 28.21 0.56 0.00  chr2_148324641_148328181     1469  1826 (1715)    L1M4_orf2#LINE/L1        1   360 (548)  

  chr2_148324641_   1469 TGGAAAAACAT-CTATATTCATAAATTGGAAGAATTAATATTGAGAAAAT 1517
                               i i  - i  i     ii         v         vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148324641_   1518 GATCATACTACCAAAAGCAATCAACAGAGGCAATGCAATGCCTATCAAAA 1567
                          iiv     v  v   vii   v     vv   i     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148324641_   1568 TACCAA-TGACATCCTTGAAGAAATAGAAAAAACAATGTTAAAATTCACA 1616
                          v   i-  v v ii   v      v  v  ivii  vi         i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_148324641_   1617 GGGAGCCACAGACGACCCCAAATAGCCAAGGTAATACAGAGCAAAAATAA 1666
                         v   ivii  iiv     vi         iii   viv  iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_148324641_   1667 CAAAACTGGAGGCATCACACTACTGAACTTTCAAATATACTACAAAGCTA 1716
                             ii      vv       v iv  i  iv   iv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_148324641_   1717 TAGTAACCAAAGCAGCATTGTGCTGGCATAAAAACAAACACATAGACCAA 1766
                         i     i   ii   ii v  i         ii i i   i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_148324641_   1767 TGAAACAGAATAGAGAACGCAGAGATAAATCCATGTAGTTAAGACCAACT 1816
                           i  i     v    iiv    i     i    ii v   v ii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_148324641_   1817 GATTTTTGAC 1826
                               i   
  L1M4_orf2#LINE/    351 GATTTTCGAC 360

Transitions / transversions = 1.66 (63 / 38)
Gap_init rate = 0.01 (2 / 360), avg. gap size = 1.00 (2 / 2)  

1383 21.43 0.34 0.00  chr2_148324641_148328181     2136  2429 (1112)    L1M4_orf2#LINE/L1      346   640 (268)  

  chr2_148324641_   2136 CAACTGATTTTCAACAAAGGTGTCAAGAACATTCAGTGGGAAAAGGACTG 2185
                            i        i    i    i     v      i    i    i iv 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_148324641_   2186 TCTGTTCAACAAATGGTGCCGAGAAAACTGTATATCCATTGGCAGAAAAA 2235
                            v               i i  v     v   ?   ivv   i  i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_148324641_   2236 TGAAAATAGATCCCTATCTCTCACCATACACAAAAATTAAATCAAAATGG 2285
                             iv i  i     i   v       i           v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_148324641_   2286 ATTAAAGACTTAAATGCAAGACCTGAAACTATAAAATTGCCACAAGAAAA 2335
                           i ?    i      i    v  i           i vii v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_148324641_   2336 TATTGGGGAAACACTTCAGGACATTGGTCTGGGAAAC-ATTTGTTGGATA 2384
                         i  v  ? v  vv    iv   v    vi i  v  i-i   v  i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_148324641_   2385 AGACCTCAAAAGCACAAGCAACAAAAGTAAAAATAGACAAATGGG 2429
                         v   vi                     v         i    v  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

Transitions / transversions = 1.31 (34 / 26)
Gap_init rate = 0.00 (1 / 295), avg. gap size = 1.00 (1 / 1)  

 806 21.94 3.55 5.16  chr2_148324641_148328181     2740  3049 (492)    L1M4_orf2#LINE/L1      604   908 (0)  

  chr2_148324641_   2740 AAAGAA-AAGAAAGAAAGAAAAAAATAGACAAATGGGA--TCACTCAAAC 2786
                             v -   v  v   ii          i    v   --   iiv   i
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_148324641_   2787 TAAAATGCTTCTGCACAGCAAAGGAAACAATCTACAGAGTGAG----TAA 2832
                              -i   i  ii vv       v  v   v v i     i----i  
  L1M4_orf2#LINE/    654 TAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_148324641_   2833 ---ACAGAATGGGAGGAAATATTTGCAAACTACCCATCCAACATGGGATA 2879
                         ---            i             ii ivi   ii i v    iv
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_148324641_   2880 AACAACCAGAAAGTGTAAGAAACTCAAACAACTCAACTGCAAAAAAAAAA 2929
                         vii v      vi i   ii     vv         i--------  v  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAAT--------AATAA 794

  chr2_148324641_   2930 AAAAAAAAAAAACAAGAGTCTGATTAAAAAGTGGGCAAATGATCTGAATA 2979
                            i v   v   ------ ii   ?    i        v   i      
  L1M4_orf2#LINE/    795 AAAGACAAATAAC------CCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_148324641_   2980 GACATTTCTC-AAAGAAGACATATACATGGTCAACAGGCATATGAAAAAA 3028
                                   -        i   i v    i   i i   i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_148324641_   3029 GTGCTCAGTATCACTCATCAT 3049
                         -      ii    ????????
  L1M4_orf2#LINE/    889 -TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (43 / 24)
Gap_init rate = 0.03 (9 / 305), avg. gap size = 3.00 (27 / 9)  


3259 26.76 0.55 0.55  chr2_148360590_148363693     1705  2612 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148360590_   1705 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1754
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148360590_   1755 GGCCATACTGCCCAAGGTAATTTATAGAGTCAATGCCATCCCCATCAAGC 1804
                            v     v     iv i  i  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148360590_   1805 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1852
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_148360590_   1853 TATGGAGCCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAACCCAAAAG 1902
                               iviiv  ii  v  v v  v     iv     i i vvv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_148360590_   1903 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGT 1952
                                i      vv       v  ii i      viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_148360590_   1953 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGACC 2002
                                 i   i    ii         i  v ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_148360590_   2003 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATTTCTACAACC 2050
                                i    i--    i  --        vv   i iv i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_148360590_   2051 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2100
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_148360590_   2101 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2150
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_148360590_   2151 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2200
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_148360590_   2201 TTAAAGACTTAAATATTAGACCTAAAACCACAAAAACCCTAGAAGAAAAC 2250
                          i ?    i     i v   v       i i    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_148360590_   2251 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 2299
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_148360590_   2300 AAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTA 2349
                         vi            vvi      i   vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_148360590_   2350 ATTAAACTAAAGAGCTTCTGAACAGCAAAAGAAACTACCACCAGAGTGAA 2399
                           i   v v  i i   i  vi vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_148360590_   2400 CAGGCAACCTACAGAATGGGGGAAAATTTTTGCAATCTACTCATCTGACA 2449
                         v  i     i          i      v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_148360590_   2450 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 2499
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_148360590_   2500 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 2549
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_148360590_   2550 CTCAGAAGAAGACATTTATGCAACCAAAAGACACATGAAAAAATGCTCAT 2599
                            vi       i  vi viiii    v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_148360590_   2600 CATCACTGGCCAT 2612
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 537 23.42 0.90 0.00  chr2_148414246_148420906     3060  3170 (3491)    L1M4_orf2#LINE/L1       43   154 (754)  

  chr2_148414246_   3060 GTTAAAATGGCAGTATTA-CCAAATTGATTCACAGATTGAGCATAATTTT 3108
                              i      i  i v-          ii       v i ii   iii
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chr2_148414246_   3109 TATCCAAACCCCAGCTAGCTTTTCTGCAGAAATTAATAACTTGATCTTAA 3158
                             v   i       iv     i          i i  vi     i   
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr2_148414246_   3159 AACTCACAAGGA 3170
                           i   i v   
  L1M4_orf2#LINE/    143 AATTCATATGGA 154

Transitions / transversions = 3.33 (20 / 6)
Gap_init rate = 0.01 (1 / 112), avg. gap size = 1.00 (1 / 1)  

1243 17.96 14.79 0.00  chr2_148414246_148420906     3470  3753 (2908)    L1M4_orf2#LINE/L1      141   466 (442)  

  chr2_148414246_   3470 AAAACTCACAAGAAAATGCAAAGGACTCCAAATTGCCAAAATGATCTTAA 3519
                             i   i v i        i    i vi   v       ii     i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_148414246_   3520 AAAACAGGAACCTACTTGGAGG-CTCACACTTCCCGATTTGAAAACTTAC 3568
                             v i    vv v       -            i    v         
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_148414246_   3569 TACAAAGCTACAGTGACAAAAATAGTGTAGTATAGGCATAGAGTTA---- 3614
                                       i iv  i i     i   iv      ii v  ----
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_148414246_   3615 --------------------TTGGGAATCCAGAAATAAACCCTTACACT- 3643
                         --------------------   i  i               v    i -
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_148414246_   3644 ATCTTCAATTGATTTT-AACAAGCTTGCCAAGACAACTCAATAAGGAAAG 3692
                           vv            -i     vv         v i     ii      
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_148414246_   3693 CTCAGTCTTTTCAACA----GTTTTGAGAC-----------CACATGCAA 3727
                         vvi             ----  vi  i   -----------         
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_148414246_   3728 AAGTATGAAGTTGGACCCCCACCTCA 3753
                            v               i      
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCA 466

Transitions / transversions = 1.43 (30 / 21)
Gap_init rate = 0.02 (6 / 326), avg. gap size = 7.00 (42 / 6)  

 369 21.74 0.00 0.00  chr2_148414246_148420906     5208  5299 (1362)    L1M4_orf2#LINE/L1      466   557 (351)  

  chr2_148414246_   5208 ATACCATACAGAACAATTAATTCAAAATGCAGGAGAGACCTAAATGTAAC 5257
                          i      i v  v      i        v vv ?              v
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_148414246_   5258 ATGTAAAATTATAAAACTCTTAGTAGAAAACACTGAGATAGA 5299
                          vv     i              v        iv i?i  i 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

Transitions / transversions = 0.80 (8 / 10)
Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.00 (0 / 0)  

 422 17.31 2.88 2.88  chr2_148414246_148420906     5632  5735 (926)    L1M4_orf2#LINE/L1      649   752 (156)  

  chr2_148414246_   5632 AAAATTTAAAACCCTAAGCACTTCAAAGGAATTCCACCAAGAAACTGAAA 5681
                               v     ii v- ii          -iv i i       v     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTT-GTGCTTCAAAGGA-CACTATCAAGAAAGTGAAA 696

  chr2_148414246_   5682 GTGACAGCCTACAGAATGTGAGAAAATATTTTTAAATCATATAT---ATA 5728
                         i-    i  i        v            vi           ---   
  L1M4_orf2#LINE/    697 A-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_148414246_   5729 AGGGATT 5735
                              i 
  L1M4_orf2#LINE/    746 AGGGACT 752

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.04 (4 / 104), avg. gap size = 1.50 (6 / 4)  

 746 11.11 0.74 0.00  chr2_148414246_148420906     6035  6169 (492)    L1M4_orf2#LINE/L1      773   908 (0)  

  chr2_148414246_   6035 AACTCTTATAACTCAATAATAGAAGGACAAATAACCCGATTTAAAAATAG 6084
                                 i            i  i            i   ?      i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_148414246_   6085 GGAAATTATTTGAAAAGACATTT-TCCAAAGAAGATATTCAAATGGCCAA 6133
                          v   vv       v        -              v           
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_148414246_   6134 TAAGTACAAGAAAAGATGCTAGACATCATTAATCAT 6169
                             i   v           vi      ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (7 / 7)
Gap_init rate = 0.01 (1 / 136), avg. gap size = 1.00 (1 / 1)  


2074 26.89 4.19 2.03  chr2_148484475_148486120.rev      458  1197 (449)    L1M4_orf2#LINE/L1      153   908 (0)  

  chr2_148484475_    458 GAAAAACAAGGAAACTGGAATACCCAAAATAATTCTGAAAAAGAAGTACA 507
                             vi     i v ii     v      i   ii           v   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_148484475_    508 AAG---GAGAATTCATACTAACTGATTTTAAGACTTACTATAAAACTTCA 554
                            ---   i i   i   vv ii    i  i        i   i  v  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_148484475_    555 GCAATAAAAACAGTATGGTTATAGTGAAAAGACAGAAACATGTATCAATG 604
                          i   v  i     i    vv i iiv  i  i   v i  iv       
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_148484475_    605 GGACAGAACAGAGAACCCAGAAATAGACCCACATATAAATGGTCAACTGA 654
                          i i    iv    ii         i     i i  vv        i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_148484475_    655 TGTAGAGAAAAGATGTCAAGGCAATTCAATAGAAAAACGATAGTCGTAGC 704
                          v vviiv  i i  i    i v       i ii   vi      v vv 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_148484475_    705 AACCACAGATGCTGGAGCAATTGAATATCCATACACAAAAAGAAAAAACA 754
                            v vv i      ii   i  i   ?   i ii     ii vi  i--
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG-- 450

  chr2_148484475_    755 AACAACTTCAACCCATATATCACGCCATATACAAAAATTAATTCTAAACA 804
                         ------  vi    v  iv    i                 i  v   ii
  L1M4_orf2#LINE/    451 ------TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_148484475_    805 TATCATAGACCTAAA-ATAATACCTGAAACTATTAAACTTCCAAAAGAAA 853
                         v    ?         -i   v v  i       v     iii i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_148484475_    854 ACATGAA---AAATCTTTGTGACCCTGAATTACGAAA-GATTTCTTAGA- 898
                             iii---       i      i  ii   v v  - i         -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_148484475_    899 ACAACAC-ATATG-ACCTACAA-AAAAGACAGAACCGATAAACTGAACCT 945
                          ii    - v v -  vvi   -      v i  iv      i  i  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_148484475_    946 CACTAAAAT-GAAAACTTCTACTCTTTGAAGG---CTA---AGGGGATGA 988
                           ii     -i       i iiv   ii    ---   ---  iiii   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_148484475_    989 AAA---AAGTCACAGACTGGAAGAAAATACTTGCAAAACACATTTCTAAA 1035
                            ---  vi      v   i        i       v  i  v   i v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_148484475_   1036 AAAGGACTGATGCTCAGAAAATATAACGGCCTCTTACAAGTCAATCATAG 1085
                           i     vi iii     v      v iv         v     v   i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_148484475_   1086 GAAAAAACACTGTCCAATT--ATTTAAATGGGCAAAAGATTCAAATAGGT 1133
                         i  i v v ivii      -- ---           i    ii     ii
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAA---AAATGGGCAAAGGATTTGAATAGAC 841

  chr2_148484475_   1134 CCTTTGCCAAAGAGCAAAGA-ATAAAAATTTTTTTTGAA------AAAAG 1176
                         vi  iv       ----   -   v    vviivv i i------     
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGA----AGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_148484475_   1177 CTACCCAATATTATCAATCAT 1197
                         v i i   i  i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (129 / 68)
Gap_init rate = 0.02 (18 / 756), avg. gap size = 2.56 (46 / 18)  


2826 26.68 3.03 1.23  chr2_148555662_148560347     3303  4194 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148555662_   3303 TGAAAAGACA-CCCATACTCACATGATAGAAAGAATGAATATTGTTAAAA 3351
                           i     i -     ii   ii-   v i    v v           i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATG-GATTGGAAGACTTAATATTGTTAAGA 49

  chr2_148555662_   3352 TTACTATATTACCAGAAGCAATCTACAGTTTCAATGATATTCCTATCATA 3401
                          vi v   i v  vi  vii        v     i vv  i       v 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_148555662_   3402 ACACTAATGATATTCTTCACAGAGATAGAAAAAA-AATCCTAAAATTCAT 3450
                          iv i iiviiv  i  ii    i  v  v  iv-i              
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_148555662_   3451 ATGAAACAACAAAAGATGCCAAATCGCTAAAGCAATCTTGAGCACAAGGA 3500
                            i  vvi   ii  iv vi   v  i   i         iv vi i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_148555662_   3501 ATAAGGCTGGAGTCAAC--ATACTGCCTTACTTCAAA-TATACTACAAAG 3547
                          i  i i     --i  -- i   v  iv i      -iv          
  L1M4_orf2#LINE/    200 ACAAAGTTGGAG--GACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_148555662_   3548 CTGTAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACATGTAGAC 3597
                           ii     i   i    ii              ii i      i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_148555662_   3598 CAATAGAACAGAATAGAGAACCCAGAAATTAATCTGCTTATCAACAGCCA 3647
                             i   i     v    ii        v  i iiivi  iv ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_148555662_   3648 ACTGATTTTT-ACAAAGG--CCAAGAACACTCACTCATCAGGGAAAGGGC 3694
                          i       i-    i  --      v  i   ---  -i       iii
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCA---AT-GGGGAAAGAAT 393

  chr2_148555662_   3695 AATTTCTTCAATAAATGGTGCTGAGAAAACTGGATA------TGCAGAAG 3738
                          i i i     i           i  v         ------    i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_148555662_   3739 AATTAAACTAGATTCCCATCTCTCATCCTGTACAAAAATCATTTCATAAT 3788
                            v  ii i  ii  i i   v  i v i         i vi   v   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_148555662_   3789 AGATCAAAGACCTCAATGTTAAGACCTGAAACTATAAAACTACTAGAAGA 3838
                         i     ?      v     -    v  i             vi       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_148555662_   3839 AAACATAGGGGTAATACTTCAGGACACTAGTCTAGGAAA--ATATCTTAT 3886
                                  ?    vv    iv   vi i vi    v  --i v     -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA- 591

  chr2_148555662_   3887 GAATA-AAAACTGCAAATCACAGACAACATAA--AAAAATAGACAAATCT 3933
                         -i   -i v  ii-   v    ii     v  --         i    iv
  L1M4_orf2#LINE/    592 -GATATGACACCA-AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_148555662_   3934 GCTAACATCAAACTCAAAAGCTTCTGCATAGCAAGGGAAACAATCAACAG 3983
                          vivv       v i    i   i  iiivv   i   v  v     v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_148555662_   3984 CATGAAAAGACAATCTACAGAATAAATGAAAATATCTGCAAAGTATTCAT 4033
                         vi           i i       iiiv        i      vi  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_148555662_   4034 CTCATA-GGGATTCATATCCAGATTACACAAGGAACTCCAGTATCTCAAA 4082
                           v   -    i ii        v  i i  i      ivii v     v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_148555662_   4083 AGCAAAAAACCAATTTGC----TTAAAAAACAGGCAAATTATCTGAACAG 4128
                          ii     iv   v vi ----  ?     ii      vv  i    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_148555662_   4129 ACATTTCT---GAAAGGACATACATATAGCCAACGAATACATGAAGAAAT 4175
                                 ---i i i  i     v  i     ii ii       i i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_148555662_   4176 GCTTAACATCATCAATCAT 4194
                            i       ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (158 / 77)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.90 (38 / 20)  


2934 23.50 4.23 3.12  chr2_148600142_148604651     3121  4018 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148600142_   3121 TGAAAAGACATCCCATGCTCATGGGTTGAAAAAAATTGTATTGTTAAAAT 3170
                           i     i        i      i   i  i vv vi         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148600142_   3171 GACAATACTTCCCACAGCAATCTACAGATTCAAAGCCATCCCTATCAAGA 3220
                          i       i    v vii              v  v           i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148600142_   3221 GC--AATGACATTCTTCACAGAAATAGAAAAAAAAAATCCTAAAATT-GT 3267
                         v -- iivi v  i  ii       v  v  ivvi -          -i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_148600142_   3268 ATGGAAGCACAAAAGACCCCAAATAGCCAAAACAATCCTGACCAAAAAGA 3317
                               iii   ii     vi                i   vv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_148600142_   3318 ACAGAGCTGGTAACTGGTAGACTTACCACACTACCAAACCTCAAAATATA 3367
                            i  i   - i------    ---      v  v  ii      iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGG-AG------GACT---CACACTTCCCAATTTCAAAACTTA 239

  chr2_148600142_   3368 CTACAACGCTATAGTAACCAAAATAGCACGATAGTGGCATAAAAACAGAC 3417
                               v    i     i   i i  iii i  v        ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_148600142_   3418 ATGTAGAACAACAGAACAGA-----GAGTCCAGAAATTAATCTGTGTATT 3462
                           i    v   ii   i   -----            v  i ii ii   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_148600142_   3463 TAAAGCCAATTAGTTTTTTACTAAGGTGCCAAAAACACTCA-TTGGGAAA 3511
                           vi i     ii    iv  v i        i v  i   - v      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_148600142_   3512 GGACAGTCTCTTCAATAAATGGTGTTGGGAAAACTGGATGCCCACATTCA 3561
                          i i     i     i        i     v        i?      v  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_148600142_   3562 GAACAACAAAAGTAGACCCC-AACTCTTGCCATATACAAAAATCAAAGAA 3610
                         i  v  ii  iv i      - v   vii              i  vvv 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_148600142_   3611 AAATGCATTAAAGACTTACAT-------------CTATGAAACTAATCAA 3647
                              v  i ?    i  v  -------------    i     vv vi 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_148600142_   3648 GGAAACCATTAGGCAAAAA-CTCCAGGACATTGGTCTAGGCAAAGACTTC 3696
                         i    v   -   ?iv   -  i iv   v    vi       v ii   
  L1M4_orf2#LINE/    540 AGAAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_148600142_   3697 TTAAATAAGACCTCAAAAACACAAGCAACTAAAGCAAGAAAATAAAATAA 3746
                            i   v   vi     i          v    -- i      i ----
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAG--AAAAAATAGA---- 632

  chr2_148600142_   3747 AATAACAACAAATGAGATCTC-TCCAAGCCAAAAAGCTTCTGCACAGCAA 3795
                         --------i    vi  ii  -  v  iii     -   i  ii vv   
  L1M4_orf2#LINE/    633 --------TAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chr2_148600142_   3796 TGAAAAC----AATAAAATGAAGATATAACATGTAGAATGGGAGAAAATA 3841
                         v i v  ----  v   i    i v i   viii                
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_148600142_   3842 TTT-CAAACTA-ATATCTGACAAAGGATTAATAACCAGAATATATAAGAA 3889
                            -    ii -        i  i   i vi  v             ii 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_148600142_   3890 TCTCAAACGACTCAATAGGAAAAAAA-----AATCTGATTTTAAAATGGG 3934
                         v   vv  i        iv     i -----  i ii   ?v        
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_148600142_   3935 CAAAAGATCTGAGGAGACATTTCTC--AAAAAGACATACAAATGGCAAAC 3982
                             i   i   iv           --  i    i           v  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_148600142_   3983 AGGCATATGAAAAAAATGTTCCACATTATTAATAAT 4018
                          i   i       i -  i  v    i ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (136 / 71)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.00 (66 / 22)  


2447 16.19 21.33 7.40  chr2_148641084_148643516.rev     1146  1942 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148641084_   1146 TGAAAAGACATAC--TGTTCATGGACTGGAAGAGTTACTACTGTTAAGAT 1193
                           i     i  v --          i       v   v  i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148641084_   1194 GGCAATAATTCCCAAACTGATCCACAGACTCAATACAATCTCCTACTAAA 1243
                                v i      i     i     i    ii     -    ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC-CCTATCAAA 99

  chr2_148641084_   1244 ATTTCAACAGTCTATTTTTCATTTTCAGAAAGGGACAAGCTGATTTTAAA 1293
                           ii  i v i  -     v-----      vv           ii    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCT-TTTTTG-----CAGAAATTGACAAGCTGATCCTAAA 143

  chr2_148641084_   1294 ATTCATATGAAAATATAAGGAACCCTGAATAGCTAAAACAATCTTAGAAA 1343
                                  i    ii    i    v       i           ii   
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_148641084_   1344 AATCAAGAAACAAAAAAACTATAGTAAGGAAACACACTTCTTGATTTCAA 1393
                          i--     -    i---- - i --    vv        iii       
  L1M4_orf2#LINE/    194 AG--AAGAA-CAAAG----T-TGG--AGGACTCACACTTCCCAATTTCAA 233

  chr2_148641084_   1394 AACTTACTACACAAAGCTACAGTAATCAAAACAGTGTAGTATTGATATAA 1443
                                    --                i       i   i  ii    
  L1M4_orf2#LINE/    234 AACTTACTACA--AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_148641084_   1444 GGAGAGACGTACAGACCAACAGGATATTACTGAAAG-CCTGAAATACACC 1492
                            v    i  i   i   ii i   vv i   i  -  v      v   
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_148641084_   1493 CACATGTCTTTGATTAACAGATTTTTGACAGGAGTGCTAGGGCAATTCAA 1542
                           i ii i v  i i  iv      i    i i    i i i v      
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_148641084_   1543 TGGGGGGATA-TAGTCTCTTCAA---------------------GATA-- 1568
                              ii v -      i     ---------------------    --
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_148641084_   1569 -------------------------------------------------- 1568
                         --------------------------------------------------
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_148641084_   1569 -TAA---------------------------------------------- 1571
                         -   ----------------------------------------------
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_148641084_   1572 --------------------TGTAAATTTTCATAACCTTGGAATAGGCAA 1601
                         --------------------?      i   i i       iv       
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_148641084_   1602 TAATCTATTAAAT-TAACACCAAAAGTTAAAGTAACAAAAGAAAAAA--- 1647
                          ii i v   i  - i          ivv   i              ---
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_148641084_   1648 ----ATT-------ATTGAGAC--AAAATTTTTGTGGATCAAATGACATT 1684
                         ----   -------  ii i i--    i       vv     v    i 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_148641084_   1685 AT--AGAGAGTGAAAAGACAGCACACAGAATGGGAGAAAATATT-GCAA- 1730
                           --   i            i v                     -    -
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_148641084_   1731 TCATATAT--GATAAGGGTCTAGTATCCAAAATGTATAAAGAACTCTTAC 1778
                                 --        v  v       i   i                
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_148641084_   1779 AATTCAATAATAAAAAGATAATGAAAAGGCAAACACGAAAAAGTGGAAAA 1828
                           i               i  -----------------------------
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAA----------------------------- 802

  chr2_148641084_   1829 GGATTTGAATAATC--ATTTCTCTAAAATGGA-AAAGGATTTGAATAAAC 1875
                         --------    i --   ?v---       i-              i  
  L1M4_orf2#LINE/    803 --------ATAACCCAATTWA---AAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_148641084_   1876 ATTTCTCTAAAGAAGGTATGCAAATGGCTAATAAGCACATGAAAACATTT 1925
                                i       i   i        i                v  vi
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_148641084_   1926 GGAACATCGTTAGCCAT 1942
                         vv      i????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.63 (92 / 35)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 8.48 (229 / 27)  


2925 27.67 0.88 0.77  chr2_148678963_148683870     3510  4416 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148678963_   3510 TGGAAACACATCCCATACTCACAGATGGGTAGAATCAATGTTCTGAAAAT 3559
                               v i       ii   ii   v  v   v i   i  v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148678963_   3560 GACCTTACTGCCAAAAGTAAGCTACAAATTCAGTGCAGTTCCCATCAAAA 3609
                          i vv    v  v   v i v     i     ii   i i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148678963_   3610 TACCATCATCATTCTTCACAGAACTAGAAAAAACAATCCTCAAATTCATA 3659
                          v   v vv v  i  ii     v v  v  ivii     v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_148678963_   3660 TAGAACCAAAAAAGAACCCGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 3709
                          i   viiv  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_148678963_   3710 CAAATCTAGAGGCATCACATTACCTGACTTCAAACTGTACTACAAGGCTA 3759
                             vi i    vv     i v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_148678963_   3760 TAGTTACCAAAACAGCATGGTACTGATATCCAAATAGGCACGTAGACCAA 3809
                         i   v i   i    ii        ii  vvii    i  ii    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_148678963_   3810 TAGAATAGAATAGAACACCCAGAAATAAAGCCATATGCTTACAGCCAACT 3859
                          i         v  ivii           v     iii   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_148678963_   3860 GATCTTCAACAAAATAAACAGAAACATAAAGTGGAGAAAGGATACCCTAT 3909
                            i   i    iivviv  ii v   vv i   i     i   vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_148678963_   3910 TCAAAAAATCATGCTAGGATAATTGGCAAGCCACATTTAGAAGAATGAAG 3959
                             v    vi    i   i  i   vv ?      vi i          
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_148678963_   3960 CTGGATCCTTATCTCTCACCTTATACAAAAATCCATTCAAGACAGATCAA 4009
                         i    i  i  i   v    v           iv i    i ii     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_148678963_   4010 AGACTTAAATATAAGACCTGAAACCATAAAAATTCTAGAAGATAACATTG 4059
                             i     i     v  i    i      v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_148678963_   4060 GAGAAACTCTACTAGACATTGGCTTAGGCAAAGAGTTGATGACCAAGAAC 4109
                          ? v  v   v vv   v    v        v iv  vv iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_148678963_   4110 CCAAAAGCAAATGCAACAAAAACAAAAACAAAGATAAACGGATGGGACCT 4159
                                  v v         iv     i --      ---- v    i 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAA----TTGGACTT 644

  chr2_148678963_   4160 AATTAAACTAAAAAGTTTCTGCACAGCAGAAGAAGTAATTAGCAGAGTAA 4209
                         v  i   v v    ii  i  ii vv  i i  viiv  i iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_148678963_   4210 ACAGACAACCCA-AGAGTATGAGAAAATATTCTGCAACT-ATGCATCTGA 4257
                          v          -   i iv           -     v -  ii      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATT-TGCAAATCATATATCTGA 743

  chr2_148678963_   4258 CAAAGGACTAATATCTGGAATCTACAAGGAACTCAAACAAATCATCAAGA 4307
                         i  i     vi    ii    v  i  i      vv    v   vi  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_148678963_   4308 AAGAAACA----GTCCCATCAAAAAGTCAGCAAAGGATATAAATAGACAT 4353
                           i i   ----ii  v  i?    i vi         v i         
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_148678963_   4354 TTCCCAAAGGAAGACATATAAATGGCCAATAA--ACATGGAAAAATGCTC 4401
                            i v  i     i   i             --     i   i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_148678963_   4402 AGCATCACTTATTAT 4416
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (144 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.14 (15 / 7)  


 935 14.80 6.12 1.02  chr2_148710065_148711704.rev        1   196 (1444)    L1M4_orf2#LINE/L1       39   244 (664)  

  chr2_148710065_      1 TATTGTTAAAATGTCAATAATCCCAAAATTGATTTACATATTCAACGCAA 50
                                  i   v     v    v        i    v           
  L1M4_orf2#LINE/     39 TATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAA 88

  chr2_148710065_     51 TCCCTATCAAAACTCAAGCTGGCGATTTTGCAGCAACTGACAAGCTGAT- 99
                                     ii v     v vv        v  i            -
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chr2_148710065_    100 -TAGAATTTCACATGGAAATGCAGG--------AATAACCAAAACCATCT 140
                         -  i    -  i           i --------    i       v    
  L1M4_orf2#LINE/    139 CTAAAATT-CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_148710065_    141 TAAAAAGAGAGAAACAAAGTTAGAAAACTCACACTTTACAATT-CAAAAT 189
                          i    -   ii         i  ii          iv     -     i
  L1M4_orf2#LINE/    188 TGAAAA-AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_148710065_    190 GTA-TACA 196
                         v  -    
  L1M4_orf2#LINE/    237 TTACTACA 244

Transitions / transversions = 1.42 (17 / 12)
Gap_init rate = 0.03 (6 / 206), avg. gap size = 2.33 (14 / 6)  

2980 18.21 3.70 0.31  chr2_148710065_148711704.rev      501  1148 (492)    L1M4_orf2#LINE/L1      239   908 (0)  

  chr2_148710065_    501 ATTACAAAGCTATAGTAATCAAGACAAGATGGTACTGGCATAGGG-TAGA 549
                          i          i             ivi             i  -    
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_148710065_    550 CATATAGATTAATGGAACAGA-----GAGTC-AGAAGTAAATCCTTGCCT 593
                                  i       i   -----     -    i    i  v i v 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_148710065_    594 TTGCAGTCAACTGTTTTTGGACAAGGGTACTAAGAACATTCAATCAG--A 641
                           iii     i  v    v         i i    v        vi -- 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_148710065_    642 AGAATCACCTT--CAATAAATGTTGCTGGGTAAACTGGAGAGCTACATGA 689
                              vii   --   i     v       vv       v ? i     v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_148710065_    690 AAAAGAATGATATTGGATCACTTCCTCACACCATACATAAAAATTAACTC 739
                                   vi     i v  v            i i            
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_148710065_    740 AAAATG-ATCATATACCTTTATGTAAGAGCTACAACTATAACA-TCTTAA 787
                               -    ? v    vv            v        v -     i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_148710065_    788 AAGAAAACACAGGAAACAATCTCTGTGACCTTAGGTTAGGCAAAGAACTC 837
                                  i   ?ivv     ii        i          v ivi  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_148710065_    838 TTTAGGTATGTCACCAAAAGCACAAGTAAAAGAAGAAAAAAATAATAAAT 887
                           -  i    v               i  v i         vvi      
  L1M4_orf2#LINE/    589 TT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_148710065_    888 TTGACTTCATCAAAACTAGGACATTTCGTACTGCATAGAACACCATCAAG 937
                          v             i  ii vv   i  i  v  v  i    i      
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_148710065_    938 AAGGTGAAAA-----CCCATAGGATAAGAGAAAATATTTGTAAATCACAT 982
                           i       -----    i  i  ii             i      i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_148710065_    983 AG--GATTAAAAAACTTGTAATCAAAATACATAAATAACACTTAAAACTC 1030
                          v--   -  iii       vi  i    i     v   v    v     
  L1M4_orf2#LINE/    738 ATCTGAT-AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_148710065_   1031 AGTAATAAAAAGACAA----TTCAATTAAAAATTGCACAAAGGATTTAAA 1076
                          i              ----ii     ?    v  vi          i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_148710065_   1077 TAGACATTTCTCCAAAGAAGTTATAAATGTGGCCTATAAGGACAGAAAAA 1126
                                             v    v vi     v     v   vi    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_148710065_   1127 GATGTTAAATATCATTAGTCAT 1148
                             i v  i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (66 / 48)
Gap_init rate = 0.02 (12 / 670), avg. gap size = 2.17 (26 / 12)  


3262 27.31 0.33 0.33  chr2_148740492_148746757.rev     4867  5774 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148740492_   4867 TGGAAGAACATTCCATGCTCATGGGTCAGAAGAATCAATATCGTGAAAAT 4916
                              ii i  i     i      i ii     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148740492_   4917 GGCCATACTGCCCAAGGTAATTTACAGATTCAAGGCCATCCCCATCAAGC 4966
                            v     v     iv i  i           v  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148740492_   4967 TACCAATGACTTTCTTCACAGAATTGGAAAAAAATACTTTAAAGTTCATA 5016
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_148740492_   5017 TGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5066
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_148740492_   5067 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5116
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_148740492_   5117 TAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5166
                         i     i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_148740492_   5167 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5214
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_148740492_   5215 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTTCCT 5264
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_148740492_   5265 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5314
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_148740492_   5315 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5364
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_148740492_   5365 AAAGACTTAAATGTTAGACCTAAAACCATCAAAACCCT-AGAAGAAAACC 5413
                          ?    i       v   v       i  -     i  -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chr2_148740492_   5414 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5463
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_148740492_   5464 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5513
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_148740492_   5514 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5563
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_148740492_   5564 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5613
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_148740492_   5614 GGGCTAATATCCAGGATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5663
                           i  vi       i  v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_148740492_   5664 AACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCT 5713
                         i     i     v  i?    i    ii     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_148740492_   5714 CAAAAGAAGACATTTATGCAGCCAAATAACATATGAAAAAATGCTCATCA 5763
                          v        i  vi viii     vv i  i       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_148740492_   5764 TCACTGGCCAT 5774
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3184 24.13 1.64 2.51  chr2_148764551_148766509      554  1469 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148764551_    554 TGGAAAGATATCCCATGTTTATGCATTGAAGAAACTAATATTCTTAAAAT 603
                                            i   v    i ii vi       v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148764551_    604 GCTCATATTACCCAAAATTATCTACAGATTCAATACAATCCATATCAAAA 653
                          viv   i v      v v              ii      v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148764551_    654 TTCCAACATCATTTTTCATAGAAATAGATTAAGA-AATCCTAAAATTTAT 702
                          i   i vv v     iii      v  i-   v-i           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr2_148764551_    703 ATGGAACCACAACAAAAACTTGCATAGCCAAAGCAATCATGAGCAAAAAA 752
                               vii   -iii v iv v         i     v   iv  i  i
  L1M4_orf2#LINE/    150 ATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_148764551_    753 ATCAAAGCTGGAGGCATCACACTACCTGAATTCAAATTGTACTACAAACC 802
                          v     i      vv       v  ii v      viv         v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_148764551_    803 TATAGTAATTAAAAATACTGTAGTGCTAGCAAAAAAAATTAAA-ATAAAA 851
                           i      i  i -i v   i  i  i   v  ii --  i -   v i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGA--TAGACATATAG 295

  chr2_148764551_    852 ATGAACACATCCCCAGTGGACTGGAATAGAGAGCTTAGAAATGAGCCCAT 901
                           -----------  i    v i    v     iii      i i     
  L1M4_orf2#LINE/    296 AT-----------CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_148764551_    902 GCATGTATGGTCAATTGATTTATGACAAAGATGTCAACAATAAACAATGG 951
                         i   v                vi     i i  i   v vi vv      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_148764551_    952 C-AAAGGATAGTCTCTTTAATAAATGATGTTGGGGAAAGCTGGATATCCA 1000
                         v-    i       i  i  i     i  i    iv  -       ?   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCA 433

  chr2_148764551_   1001 CATATAGAAGAACAAAATTGGACCCTTATTTCACTCCATATACAAAAATC 1050
                            ii i     ii  i        i  ii    v              i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_148764551_   1051 AACTCAAAATGGATTAAAGACTTAAATGTTAAGACCAGAAACTGTAAAAC 1100
                                       i ?    i       -    v vi     i      
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAAC 532

  chr2_148764551_   1101 TCCTAGAAGAAAACTTAGGGGGAAAACTGCAAAA--TTGGTCTGGGTATT 1148
                           i           v    ? v   v  v ivi --    vi i  i v 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_148764551_   1149 GATTTTTTGGATTTGACCGCAAAAGTGCAGGCAACGAAAACAAAAATAGA 1198
                          i   i  i   v    vv      ii  i     i   iv         
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_148764551_   1199 TAAAGGGGATTATATCAAA-TGAAAAAGCTTCTGTACAGCAAAAGAAACA 1247
                             vv   i vi      - v     -   i   i vv    i  v  v
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT 681

  chr2_148764551_   1248 AT-------GTACAGAGACAGCCTACAGATTGGGAGAAAATATTTTCAAG 1290
                           -------  iv i     i  i     v               v   i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_148764551_   1291 TCATACATTGAATAAGGGGTTAATATCCAAAATATATAAGAAGCCGAAAC 1340
                              i  ivi       ii vi      i         ii i ivvv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_148764551_   1341 ACCTGAATAGCAAGAAAATTTTAAAAAAAAACA--TTAAAAATTGGAAAC 1388
                          v  v    ii  i  i i----   v  vv  -- ?      v  v  v
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGAC----AAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_148764551_   1389 GGACCTGAATATACATTTCTCAAAAAAAGGCATCCAAAAGTCCAACTGAT 1438
                            ii      v         v   i   ii  v    v v    iviii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_148764551_   1439 ACAAGAAAAACTTCTCAACATTGCTAATCAT 1469
                            v     iv v        ii????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (129 / 88)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.38 (38 / 16)  


3333 26.46 0.55 0.44  chr2_148779547_148785822     4878  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148779547_   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4927
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148779547_   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148779547_   4978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_148779547_   5026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCAA-AAG 5074
                                viiv  ii  v  v v  v     iv     i i iv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_148779547_   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_148779547_   5125 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_148779547_   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5222
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_148779547_   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_148779547_   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_148779547_   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5372
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_148779547_   5373 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_148779547_   5423 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5472
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_148779547_   5473 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5522
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_148779547_   5523 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_148779547_   5573 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5622
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_148779547_   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5672
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_148779547_   5673 AAGCAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5722
                          ii    i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_148779547_   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5772
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_148779547_   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3076 27.67 1.22 0.56  chr2_148812316_148816890.rev     3184  4083 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_148812316_   3184 GAAAGATACTCCATGTCCATGGATTGGAAGAATCAATATTATTAAAATGT 3233
                                 ii      i              v i      i    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_148812316_   3234 CCATACTGCCCAGTGCAATTTACAGAATCAGGTCTATCCCTATCAAAATA 3283
                          v     v    ivvii  i      v   ivv v              v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_148812316_   3284 CCAATGACATTCTT--CAAACACACACACATAAATTTTGTAAAATTTATA 3331
                            iivi v  i  --  i v ivv   viivi  ii --      i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCATA 150

  chr2_148812316_   3332 TGGAACCACAGAAAATTCAAAATAGTCAAAGCTATCCTAAGCAAAAAGAA 3381
                              vii  iiii ii  i     i    i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_148812316_   3382 CAAAACTGAGAAAATCACATTACCTGACTTCAAATTATACTACAGAGCTA 3431
                             ii  iiii v     i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_148812316_   3432 TAGTAATCAAAACAGCATGGCACTGACATAAAAACACACATGTAGACCAA 3481
                         i         i    ii   i    i     ii i v    i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_148812316_   3482 CGGAACAGAATAGAGAACCCAGAAACAAATTCACACACCTACAGTAAACT 3531
                         i    i     v    ii       i   ii  i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_148812316_   3532 CATTTTCAACAAATGTGCCAAGAACATACACCGTGGAAAAGACAGTCTCT 3581
                         v      i    iv         v   v  vi v     ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_148812316_   3582 TCAATAAATGGTGCTGGGGAAAATGAATATCCATATGCACAAGAATGCAG 3631
                             i             iv  v  i   ?   i     v       v  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_148812316_   3632 TTAGACTGCTATTTCAAGCCATATAGAAACATCACATAGAAATACATTAA 3681
                           i   iv   ii   vi       v   v  i vv vi    iv  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_148812316_   3682 AGATTTAAACCTAAGACCCTCAGATTATGAAACTACTACAAGAAAACATT 3731
                            ii    iv     v - v i i   i     vi  v          v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_148812316_   3732 GGGGAAAAATCTCCAAGACATTGGTCTGAATAAAAATTTATTGAGTAATA 3781
                           ? v   -   i iv   v    vi iiii  vii   v  iii  vv 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_148812316_   3782 CCCTACGAGCACAGGCAATCAAAACAAAAATAGACAAATGGGATCATATC 3831
                          v i vi      i    iv   iv         i    v   iivi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_148812316_   3832 AAC-TTAAGAAGTTTCTGCACAGCAAAGGAAAC----AACAAAGTGAAGA 3876
                           v-    i  v   -  ii vv       v  ----  v        i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_148812316_   3877 GACACCACAAAGAATTGGAGAAAATATTTGCAAACTACCCATCAGACTAG 3926
                             v v  v     v                  ii ivi   v  iv  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_148812316_   3927 GGGTTAATAACTAGAATATACAAGGAGCTC----AACTCTATGGGAAAAA 3972
                           ii vi  v i        i  i  i   ----     v  iiv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_148812316_   3973 ATCTGATAATCTGATTAAAAAATGGGCAAAAGATTTGAGTAAACATTTCT 4022
                         iv vi    i ii   ?             i       i  i        
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_148812316_   4023 CAAAAGAAGCCATGGAAATGGCAAACATGCATATGAGAAAGTGCTCAACA 4072
                          v       vi  iv       v  i v   i    i  ii         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_148812316_   4073 TCACTGATAAT 4083
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.72 (155 / 90)
Gap_init rate = 0.01 (8 / 906), avg. gap size = 2.00 (16 / 8)  


 931 20.10 0.52 2.06  chr2_148882451_148884284        4   197 (1637)  C L1M4_orf2#LINE/L1   (714)   194     4  

C chr2_148882451_    197 AAAGACATCTCATGTTCATGGATCTG-AGCTCTACTATTGTTAAGATGAT 149
                              i   i             iv -  vii  v             ii
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

C chr2_148882451_    148 AAAATTCTCCAAATTGATCTACTGATTCAATGTAATCTCTATCAAACTCC 99
                           v i  i              v       i i    i        v   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

C chr2_148882451_     98 CAGCTAGCTTTGTTGCTAAAATTGGTACGTTGATCTTAAAATTCACATGG 49
                              iv    v    vi      ii v i     i         i    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

C chr2_148882451_     48 AAATTGATAGAACGTAGAATAGCCCAAACACACCATTTTAAAAAA 4
                             vv vi i  vi         v     ----  i  i     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACA----ATCTTGAAAAA 194

Transitions / transversions = 1.60 (24 / 15)
Gap_init rate = 0.01 (2 / 191), avg. gap size = 2.50 (5 / 2)  

3045 25.53 0.71 1.07  chr2_148882451_148884284      501  1342 (492)    L1M4_orf2#LINE/L1       70   908 (0)  

  chr2_148882451_    501 ATATATAAAATCAGTGTAATGCCTATCAAAATACCAATGACATCCTTCAC 550
                           v  i i v   ii i   v           v   iivi v ii  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chr2_148882451_    551 AGAAATAGAAAAAACAATCCTAAAATGTATATGGAATCACAAAAAATCCA 600
                               v  v  ivii          vi        vii   iii i   
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_148882451_    601 AAATAACCAAAGCTG-CTCTAAGCAAAAGAACAAAACTGGAGGAATCACA 649
                         i    i     i vi-  iv  iv i         ii       v     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_148882451_    650 TTACCTGACTTCAAA-TATACTACAGAGTTGTACTAACTGAAAACAGCAT 698
                         i v  ii i      -iv       i  i ii v   - v  i    ii 
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA-TCAAGACAGTGT 268

  chr2_148882451_    699 GGTCCTGGCATAAAAACAGACACATAGACCAATGGAACAGAAT-GAGAAC 747
                            v         ii i     i     i        i     -    ii
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_148882451_    748 CTAGAAACAAATCCATACACATACAGTGAACTCATTTTTGACAAAAGTGC 797
                          i     i   i       iv  ii  v  i v     i     ii    
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_148882451_    798 CAGAAGCATACGCTGAGGGAA-AAGAGTCTTTTCAATAATTGGTGCTGGG 846
                           ii v   v iv  i  i  -  v           i  v          
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_148882451_    847 AAAACTCAATAATCGTATGCAAAAGAATGAAACTAGACCCCTATCTCTCA 896
                          v    vi   ?i ii               ii i        i   v  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_148882451_    897 CCATAAACAAAAACCAAATCAAAATACATTAAAGACTTACATTTAAGACC 946
                              v       ii  v       iv  i ?    i  v  v     v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_148882451_    947 TCAAACTATGAAATTACTACAAGAAAACATTGGAGTAGCTGTCTAAGATA 996
                          v       i   i vi  v          v  ?   iv v iiiv  iv
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_148882451_    997 TTGATCTGGGCAAATATTTCTTGAGCAACACCCCATGAGCACAGGCAGCC 1046
                            ivi i     vvi      iiii vv  v   vi      i   i v
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_148882451_   1047 AAAGCAAAAATGGACAAGTGGGATCACATTAAG-TTAAAAAGCCTCTGCA 1095
                             v      i  i  i v   iiv   i  i-       - i i  ii
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTG 667

  chr2_148882451_   1096 CAGCAAAGGAAACAGTCAAGAAAGTGAAGAGACAACAAACAGAATGGGAG 1145
                          vv       v  vi             i       vv            
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_148882451_   1146 AAAATATTTGCAAACTACCTATCTGACAAAGGATTAATAACCAGAATATG 1195
                                       ii iv       i  i   i vi  v         i
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_148882451_   1196 TAAGGAGCTCATA-AACTTTACAGGAAAAATAATCTAACAATACAATTTA 1244
                            i  i   v  -    iv i iv     v -- v  i  iv     ? 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWA 815

  chr2_148882451_   1245 AAAATGGGCAAAAGATTTGATTCAATAGACATTTCTCAAAAGAAGACATA 1294
                                     i       ----             v        i   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGA----ATAGACATTTCTCCAAAGAAGATATA 861

  chr2_148882451_   1295 CAAATAGCAAACAGGTATATGAAAGGGTGTTCAATCATTAATCATCAG 1342
                              i  v  i i i i      i i  i    -   i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (138 / 73)
Gap_init rate = 0.01 (11 / 839), avg. gap size = 1.36 (15 / 11)  


2741 28.26 1.09 2.39  chr2_148899193_148905895.rev     5292  6211 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148899193_   5292 TGGAAAAGCATTCCACGTTCATGGATAGGAAGAATCAATATCGTGAAAAT 5341
                               iii  i   i          v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148899193_   5342 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGGTATCTCCACCAATC 5391
                            v     v      v i  i  i        i vv   i i i   vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148899193_   5392 TACCATTGACTTTCTTTGCAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5440
                          v   vivi i  i         v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_148899193_   5441 GTGGAACCAAAAAAGAGCCCATATAGCCAAGTCAATCCTTAGCAAAAAGA 5490
                         i     viiv  ii  v  viv        iv     i v iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_148899193_   5491 ACAAAGCTGTAGGCATCATGCTACTTGACTTCAAACTATACAACAAGGCT 5540
                               i  v   vv   ii  v iii i      viv   v    i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_148899193_   5541 ACAGCAACCAAAACAGCATGATACTGGTACCAAAACAGATATATAGACCA 5590
                             i  i   i    ii  i      i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_148899193_   5591 ATGAAACGGAACAGAGGCCTCAGAAATCATGCCACACATCTACAACTATC 5640
                            i  ii   iv   ivii       v vv   i    i  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_148899193_   5641 TGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5690
                             i  i     i v  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_148899193_   5691 TTTAATAAATGTTGTTAGGAAAACTGGCTAGCCATTTGCAGAAAACTGAA 5740
                           i  i     v  i i   v      v  ?   iv    i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_148899193_   5741 ACTGGACCCCTTCCTTACACTTTATAGAAAAATGAACTTAGGATGGATTA 5790
                         ii         v   i    iv    v      v    i ii      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_148899193_   5791 AAGACTTATATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5840
                         ?    i  v        v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_148899193_   5841 --TGCAATACCATTCAGGGCATAGGCATGGGCAAAGACTTCA-AGACTAA 5887
                         --? i  - i -   iv i v v  vv i     v ii   v-   -  v
  L1M4_orf2#LINE/    550 GGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TAT 596

  chr2_148899193_   5888 AATACCAAAAGCA-ATGCCAAAAAAGCCAAAATTGACAAACGGGGTCTAA 5936
                         i i          - v  v v     vv     v  i   iv  iii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_148899193_   5937 TTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTCTCATCAGAGTGAAC 5986
                          i   v v  i ii  i  ii vv    i  v   v   vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_148899193_   5987 AGCCCACCTACAGAACGCAAGAAAATGTTTGCAACCTATTCACCTGACAA 6036
                           v v   i      i vi       i       vii  vi i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_148899193_   6037 AGGGCTAATATCCAGAATCTACAGGGAACTT----AACCCCATCAAAAAA 6082
                         i  i  vi          v  i ii     i----   i v  -------
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT------- 789

  chr2_148899193_   6083 AAAAAAAAAAAAAAAAAAAAAGAAAGAACCCCATCAAAAAGTGGGAGAAG 6132
                         -----------  v     i v   v     v  i?    i    vi   
  L1M4_orf2#LINE/    790 -----------AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_148899193_   6133 TATATGAACAGACACTTCTCAAAAGAAGACATTTATGAGGTCAACAAACA 6182
                         v  v    i     i     v        i  vi viv  i   i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_148899193_   6183 TATGAAAAAA-ACTCATTATCACTGGTCAT 6211
                         i       i -i    vi    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (151 / 105)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.91 (32 / 11)  


1465 17.99 1.99 26.70  chr2_148909008_148912088.rev     1384  2589 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148909008_   1384 TGGAAAAACATCCTACGCTCATGGATTGGAAGAATCAGTATTGTTAAAAT 1433
                               i i    i i i               v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148909008_   1434 GACCAGACTGCCCAAAGCAATCTACAGATTCATTACAATCCCTATCAAAT 1483
                          i v v   v      vii             vii              v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148909008_   1484 TAGCAGCACCATTTTTCACAGAATTAGAAAAAACAATCCTAAAATTAATA 1533
                          vv    vv v     ii     v v  v  ivii           v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_148909008_   1534 TGGGTCTAAAAAATAAG--ACCCCAAATAGCCAAATCAATTGTAAGCAAA 1581
                            -----   vii   --    vi          v    iv i iv  i
  L1M4_orf2#LINE/    151 TGG-----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_148909008_   1582 AAGAATGAAGCTGGAGATGTCACATGACCTGACTCCGG--TTTACACTAC 1629
                              ii   i     ivv     ivv  ii i i ii--i    --   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TAC 243

  chr2_148909008_   1630 AAGGCTATAGTAACCAAAATAGCATGGTACTGGTATAAAAATAGATACAA 1679
                           i    i     i   i i  ii         i    ii     i i v
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_148909008_   1680 AGATTAATGGATCAGAATAGAGAACCCAGAAATAAAGCCATACACATATA 1729
                             i      vi     v    ii           v       iv   i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_148909008_   1730 ACCAACTGATCTCCAACAAAGTCAACAAAAATATACACTGAGAGGCTGGG 1779
                         ii   i    i i i    ----------------------------   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAA----------------------------GGG 365

  chr2_148909008_   1780 TGCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGACTAGC 1829
                            ------------------------------------- i    i --
  L1M4_orf2#LINE/    366 TGC-------------------------------------CAAGACCA-- 376

  chr2_148909008_   1830 AGATCACTTGAGGCCAGGAGTTCCACACTACCCTGGCCAACACAGTGAAA 1879
                         --------------------   ---------------------------
  L1M4_orf2#LINE/    377 --------------------TTC--------------------------- 379

  chr2_148909008_   1880 CCCTGTCTCTACTACAAATAAAAGAATTAGCCGGGCATGATGGCGCATGT 1929
                         ----------------   i------------------------------
  L1M4_orf2#LINE/    380 ----------------AATG------------------------------ 383

  chr2_148909008_   1930 CTGTAATCCCAGCTACTAGGGTGGCTGAGGCATGAGAACACTTGAACGCA 1979
                         --------------------------------------------------
  L1M4_orf2#LINE/    384 -------------------------------------------------- 383

  chr2_148909008_   1980 GGAGGCAGAGGTTGCAGTGAGCCGAAATTGCACCACTGCACTTCAGCCTG 2029
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    384 -------------------------------------------------G 384

  chr2_148909008_   2030 GGAAAGAGTGAGATTCTGTCTCAAGAAGAAACCAAAATACACTGGAGAAA 2079
                                i ---------------------------------------- 
  L1M4_orf2#LINE/    385 GGAAAGAAT----------------------------------------A 394

  chr2_148909008_   2080 GTACATCCTATTCAACAAGGGGTACTGGGAAAATTGGATAGCCATATGCG 2129
                           -----  v        iv   i      v  i      ?   i    i
  L1M4_orf2#LINE/    395 GT-----CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_148909008_   2130 TAAGAATT--TTTG------TATATCAC--CATATACAAAAATTAACTCA 2169
                         v      v--v   ------  iv    --                    
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_148909008_   2170 AGATGGATTAAATATCTAAATGTAAGATTGGGAACTATAAAA-TCCTAGA 2218
                          i      i ? v i            vivii          -  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_148909008_   2219 AGAAAACCGAGG---AAATCTCTTCTGAACATTGACCTAGACAAAGAATT 2265
                                vv   ---      - iv   v -   ivi   i   v iv  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCT-TCGTGACC-TTGGGTTAGGCAATGGTTT 587

  chr2_148909008_   2266 TATGAGTAAGTTCTCAAAGACAAATGCCAGAAAAAGAAAAATAGACAAAT 2315
                         iv iii  v vivi    ii  v v  v v    ii         i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_148909008_   2316 AGGACTAAATTAAACTAAAAAGATTCTGCACATCAAAAGAAACAATTAAC 2365
                         v     vv  i   v v    iv  i  ii v     i  v  v  i  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_148909008_   2366 AGAGAAAACAGACAATCTATAGAATGGGAAAAAAT-TTTGTAAACTCTGC 2414
                          i  vi  v      i i i         i     -    i   iiv ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_148909008_   2415 ATCCAAATAAAGGGCTAACATCCAGAATCTACAAGGAGCTCAAACAACTC 2464
                            ii -   i  i  vii         v  i  i  i   vv       
  L1M4_orf2#LINE/    738 ATCTGA-TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_148909008_   2465 ACAAGAAAAATAATTAAAAAA-AAA-AAC---ATTAAGAAGTAGGCAAAG 2509
                          --------     v    i -   -   ---   ? i  i i       
  L1M4_orf2#LINE/    787 A--------ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_148909008_   2510 TAAATGAGCAGACATTATTCAAAAGCAGATATACAAGTGGCTAACAAACA 2559
                         v vv   ii       vi  v    v          i    i  i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_148909008_   2560 CACGAAAAAATGCTCAACATCACTAATCAT 2589
                           i     i             ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (134 / 80)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 14.42 (346 / 24)  


3191 25.95 1.67 0.56  chr2_148914398_148920655.rev     4869  5766 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148914398_   4869 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATAAATATTGTGAAAAT 4918
                              ii i  i     i      i v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148914398_   4919 GGCCATACTGCCCAAGGTAATTTAGAGATTCAATGCCATCCCCATCAAGC 4968
                            v     v     iv i  i  v        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148914398_   4969 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5015
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_148914398_   5016 ATATGGAACCACAAAAGAGCCGG------CAAGTCAATCCTGAGCCAAAA 5059
                                 vii   ii  v  i ------   iv     i   ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_148914398_   5060 GAACAAAGCTAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5109
                                 i i    vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_148914398_   5110 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5159
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_148914398_   5160 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAAC 5207
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_148914398_   5208 TACCTGATCTTTGACAAACCTGAGAAAAAAAAGCAAAGGGTAAAGGATTC 5257
                         i vi    i  i     ivv  vv  i vv vv   v   v    i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_148914398_   5258 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAAAAAGC 5307
                         i  v  i  i              v      v  ?   i   i    iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_148914398_   5308 TGTAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5357
                           v ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_148914398_   5358 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAAAAGAAAA 5407
                           i ?    i    i  v   v       i      vi i  i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_148914398_   5408 CCTAGGCATTACCATTCAAGACATAGGCATGGGCAAGGACTTCCTGTCTA 5457
                          v    ?i v viv   iv   v v  vv i     v ii   i ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_148914398_   5458 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5507
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_148914398_   5508 ATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTACCATCAGAGTGAA 5557
                           i   v v  i i   i  ii vv    iv v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_148914398_   5558 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5607
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_148914398_   5608 AAGGGCTAATATCCACAATCTACAATGAACTC----AAATTTACAAGAAA 5653
                          i  i  vi      v   v  i  v      ----  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_148914398_   5654 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5703
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_148914398_   5704 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5753
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_148914398_   5754 CATCACTGGCCAT 5766
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (134 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


2978 24.26 0.84 5.06  chr2_148934327_148936545.rev      780  1727 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148934327_    780 TGAAAAAACATTACATGCTCATGGATTGGAAGAATCGATATTTTTAAAAG 829
                           i   i i  iv    i               v ii     v    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148934327_    830 GGCCATACTGCCCAAAGCAATCTACAGATTAAACGCTATTGCTATCAAAC 879
                            v     v      vii           v     v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148934327_    880 TACCAA-TGTCATTTTTCACAGAA-TTGGAAAAAAACTG-TTCTAAAATT 926
                          v   i-  i -     ii     -   --- v  i   - i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr2_148934327_    927 CATATGGAACCAAAAAAGAGCCTGAAGAGACAACGCAAATCCAAAGCAAA 976
                                  viiv  ii  v  v   v  v   vi   -  ivi iv  i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAG 195

  chr2_148934327_    977 AAGAACAAATCTGAAAGCATTACATTACCCAACTTCAAACTATACTATAA 1026
                                  vi  i i vv i   i v     i      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_148934327_   1027 TGCTTCTGTAACTAAAAGAGCATGGTACTGGTATAAAAACAGATGCATAG 1076
                         v   v v    ii  i v  ii         i    ii i   iii    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_148934327_   1077 ATCAATGGAACAGAATAAAGAACCCAGAAATAAAGTCACACACCTACAGC 1126
                                   i     vi   ii           vi  i   ii  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_148934327_   1127 CATCTAATCTTTGACAAAGTTGACAAAATTAAGCAATGGGGAAAGGACTC 1176
                           vi i  i  i     i v  v   i ii vv            i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_148934327_   1177 CCTATTCAATACATGGTGATGGAATAGCTTGGTAGCCACATGCAGTGCAG 1226
                         i  v     i v      v   i i i  v i  ?         i-----
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA----- 440

  chr2_148934327_   1227 AAGAATGAAATTGGACCACTACCTTTCACTATATACAAAAATTAACTAAA 1276
                                  i       v      iv   i                 v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_148934327_   1277 AATGGATTAAAGATTTCAATGTAAGAACTCAAACTATAAGAATGGTAGAA 1326
                                i ?   ii v         i  v         i v vv     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_148934327_   1327 GAAAACCCAG---TAAACACCGTTCTGGACATGGGCCTTAGGAAAGAATT 1373
                               vi  ---    i-- v iv  iv v    --     v  vii  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT--CTTCGTGACCTTGGG--TTAGGCAATGGTT 586

  chr2_148934327_   1374 TAT--GACTAAGTTCTCAAAAGCAATTGCAACAAAAACAAAAATTGGCAA 1421
                          v --  -  v vivi        vvv         iv      v ii  
  L1M4_orf2#LINE/    587 TCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_148934327_   1422 TTGGGACCTAATTAAACTAAATAGCTTCTGCACAGCGAAAGAAATTATCA 1471
                         v v    i v  i   v v  v i   i  ii -----------  ----
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGC-----------TT---- 670

  chr2_148934327_   1472 ACAAAGTAAACAGACAATCCACAGAAATTATCAACAGAGTAAATAGACAA 1521
                         -     ------    -----------i      v i   i  v      
  L1M4_orf2#LINE/    671 -CAAAG------GACA-----------CTATCAAGAAAGTGAAAAGACAA 702

  chr2_148934327_   1522 TCCACAGAATGGGTGAAAATATTTGCAAACTATGCAACCAACAATTGTCT 1571
                         i            v               ii  ii v ii i  vv v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_148934327_   1572 TATATCCAGAATCTATAAGGAACTTAAACAATTGAACAAGCAAAAAACCA 1621
                          i          v     i     ivv    i v  i  vv    i  v 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_148934327_   1622 ACAGCCCCATTAAAAATTGGGCAAAAGACATGAACAGACACTTTTCAAAA 1671
                          i i   v   ?    v        i  iv    i     i  i  v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_148934327_   1672 GAAGATATACAAGAGGCCAACAAACATAAGAAAAAGTGCTTATTATCACT 1721
                                     iv      i  i  i v     ii    i vi    ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_148934327_   1722 AATCAT 1727
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.36 (131 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.50 (56 / 16)  


2881 24.40 0.63 5.55  chr2_148945824_148947932.rev      663  1617 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148945824_    663 TGGAAAAACATTCCATACTCATAGATAGGAAAAACCAATATTGTGAAAAT 712
                               i i  i    ii    i   v    i vii        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148945824_    713 GGCCATACTGCCCAAAGTACTTTATAGATTCAATGCTATTGCAAAGTACT 762
                            v     v      v iv i  i        i  --------------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC-------------- 86

  chr2_148945824_    763 TTATAGATTCAATACTATTCAAATGCTATTCCCACCAAGCTACCATTGAC 812
                         -----i  i ----    -    ----  i  -----    i  ------
  L1M4_orf2#LINE/     87 -----AATCC----CTAT-CAAA----ATCCC-----AGCTGCC------ 111

  chr2_148945824_    813 TTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCATATG-AAATGT 860
                         -  i  ii     v v  v  i-  - iii    v        -     i
  L1M4_orf2#LINE/    112 -TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGC 159

  chr2_148945824_    861 AAAAAGAGCCTGTATAGCCAAGACAATCCTTAGCAAAAACAACAAAGCTG 910
                           ii-  v  v v        i      i v iv  i  v       i  
  L1M4_orf2#LINE/    160 AAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_148945824_    911 GAGGCATCACACTACTGGACTTCAAACTATATTACAAGGCTACAGTAATG 960
                             vv       v ivi i      viv  i     i           v
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_148945824_    961 AAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAATGGAACAG 1010
                           i    ii         i iv ii i   i       i        i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_148945824_   1011 AACAGAGACCTCAGAAATAATATCACACATCTACAACCATCAGATCTTTG 1060
                           iv    vii         vvi  i    i  iiii  viv   i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_148945824_   1061 ACAAAACTGGCAAAAACAAGCAATGGGGAAAGGATCCCCTATTTAATAA- 1109
                             iiv  v   i v  vv            i  vvi  v  i  i  -
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_148945824_   1110 TGCTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACAGAAACTGGATCC 1159
                           v  i     v      v  ?   i     i  i vv   ii    i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_148945824_   1160 CTTCCTTACACCTTATACAAAAATGAACTCAAGATGAATTAAAGACTTAA 1209
                           v   i     v           v       i   i  i ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_148945824_   1210 ATGTAAAACCTAAAACTATAAAAACCCTAGAAGAAAACCCGGGCA-ATAC 1258
                               i v              vi i           vii  ?i- v i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_148945824_   1259 CATTCAGGATATAGG--CAGGGACAAAGACTTCATGACTAAAACACCAAA 1306
                          -   iv  iv v  --i   --   v ii   v iiv  vi        
  L1M4_orf2#LINE/    559 C-TTCGTGACCTTGGGTTAGG--CAATGGTTTCTTAGATATGACACCAAA 605

  chr2_148945824_   1307 AGCAATGGCAAAAAAAAAAAAAAGCCAAAATCGACAAATGGGATCTAATT 1356
                             ----   iv  v    i  ---     v  i    v   ii v  i
  L1M4_orf2#LINE/    606 AGCA----CAAGCAACAAAAGAA---AAAATAGATAAATTGGACTTCATC 648

  chr2_148945824_   1357 AAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAATGAACAG 1406
                            v v  i i   i  iiivv    i  v       vv i i    v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_148945824_   1407 ACCACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAG 1456
                           v   i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_148945824_   1457 GTCTAATATCCAGCATCTACAAGGAACTTAAAAAAATTTACAAGAAAAAA 1506
                          v  vi       v  v  i  i     ivv v  v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_148945824_   1507 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 1556
                          -    i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_148945824_   1557 CAAAAGAAGACATTTATATGGCCAACAAACATATGAAAAAATGCGCATCA 1606
                          v        i  vi v        i  i  i       i    v  v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_148945824_   1607 TCATTGGTCAT 1617
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.49 (137 / 92)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.28 (59 / 18)  

 315 24.27 4.85 0.00  chr2_148945824_148947932.rev     1682  1784 (325)    L1M4_orf2#LINE/L1      801   908 (0)  

  chr2_148945824_   1682 AAAAAGTCCA-TCAAAAAGTGAGCAAAGGATATGAACAGACACTTCTCAA 1730
                            v ii   - i?    i  i         v    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_148945824_   1731 AAGAAGACATTTATGCAGCCAACAAACGTATGAAAAAAAGCTTA----CA 1776
                                i  vi viii     i  i ii       i v   i ----  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_148945824_   1777 GAGAAATG 1784
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 3.00 (18 / 6)
Gap_init rate = 0.02 (2 / 108), avg. gap size = 2.50 (5 / 2)  


3115 26.90 0.77 0.66  chr2_148952527_148959540     5616  6522 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148952527_   5616 TGGAAA-ACATTCCATGCTCATGGATAGGAAGAATCAGTATTGTGAAAAT 5664
                               - i  i     i        v      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148952527_   5665 GGGCCATAGTATGCAAAGTAATTTATAGATTCAATGTTATCCCCATTAAG 5714
                           - v   v viv    v i  i  i        i iv     i  i  i
  L1M4_orf2#LINE/     51 GG-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_148952527_   5715 CTACCATTGACTTTCCTCACAGAATTAGAAAAAACT-ACTTTAAATTTAA 5763
                         v v   vivi i  ii ii     v v  v  i-  - iii    v  v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_148952527_   5764 TATGGAAC--CAAAGAAGAGCCCATA-TAGCCAAGACAATTCTAAGCAAA 5810
                                v--   i i ---    v -       i     ii i iv  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_148952527_   5811 AAGAACAAAGCTGGAGGCTTCACACTACCTGACTTCAAATTATACTACAA 5860
                                   i      vi       v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_148952527_   5861 GGCTACAGTAATGAAAACAGCATGGTACTGGTATCAAAACAGATATATAG 5910
                         i           v  i    ii         i  v ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_148952527_   5911 ACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAC 5960
                          i        i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_148952527_   5961 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGATTC- 6009
                           vi    i  i     ivv  v   i v  vv             v v-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_148952527_   6010 CCTATTTAATAAATGGCGTTGGGAAAACCAGCTAGCCATATGCAGAAAAC 6059
                         i  v  i  i      i i     v   ii v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_148952527_   6060 AGAAACTGGACCCCTTCCTTACACCTTATACAAAAATGAACTCAAGATGG 6109
                         v   ii         v   i     v           v       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_148952527_   6110 ATTAAAGACTTAAACGTAAGACCCAAAACCATAAAAACCCTAGAAGAAAA 6159
                           i ?    i    i      v i     i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_148952527_   6160 CCTAGGCA-ATACCATTCAGGACATAGACATGGGCAAAGCCTTCATGACC 6208
                          v    ?i- v i -   iv   v v ivv i     v vi   v iivi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_148952527_   6209 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACAGGATCT 6258
                          vi            vvi          vv     v  i   iv   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_148952527_   6259 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGTCATCAGAGTGA 6308
                         v  i   v v  i i   i  ii vv    i  v   i   vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_148952527_   6309 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCTATCTGAC 6358
                          v  i     i                 v       vii  v       i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_148952527_   6359 AAAGGGCTAATATCCAGAATGTACAAGGAACTTAAGTAAATTTACAAGAA 6408
                           i  i  vi          i  i  i     ivvii  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_148952527_   6409 AAAAACAAACAACCCCATCAAAAAATGGGAGAAGTATATGAACAGATATT 6458
                            i     i     v  i?         vi   v  v    i   i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_148952527_   6459 TCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAACAAAAGCTCT 6508
                             v        i  vi viii     i  i  i     v i v    v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_148952527_   6509 TTATCACTGGTCAT 6522
                         vi    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3140 25.86 1.33 0.99  chr2_148971405_148977172     4372  5276 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_148971405_   4372 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATAAATATCGTGAAAAT 4421
                              ii i  i     i        v      v v     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_148971405_   4422 GGACATACTGCCTAAGGTAACTTATAGATTCAATGCCATCCCCATCAAGC 4471
                           vv     v  i  iv i ii  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_148971405_   4472 TACCAA-TGACTTTCTT-CATGGAATTGGAAAAAACT-ACTTGAAAGTTC 4518
                          v   i-  v    i  -  - i     -- v  i  - iiiv   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_148971405_   4519 ATATGGAACCACAAAAGAGTCCACATTGCCAAGTCAATCCTAAGCCAAAA 4568
                                 vii   ii  vi viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_148971405_   4569 GAACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATATTACAAGG 4618
                                 i      vv    v  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_148971405_   4619 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 4668
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_148971405_   4669 CAATGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCACATATCTACAAC 4716
                                 i    i--    i  --    i   vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_148971405_   4717 CATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 4766
                           vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_148971405_   4767 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 4816
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_148971405_   4817 TGAAACTGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 4866
                             ii  i i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_148971405_   4867 ATTAAAGGCTTACATGTTAGACCTAAAACCATCAAAAACCCTAGAAGAAA 4916
                           i ?  i i  v    v   v       i  -    vi i         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAA 544

  chr2_148971405_   4917 ACCTAGGCA-ATACCATTCAGGACATAGACATGGGCAAGGACTTCCTGTC 4965
                           v    ?i- v i -   iv   v v ivv i     v ii   i ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_148971405_   4966 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5015
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_148971405_   5016 TAATCAAACTAAAGAGCTTGTGCACAGCAAAAGAAACTACCATCAGAGTG 5065
                          v      v v  i i   v  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_148971405_   5066 AACAGGCAACCTACAGAATGGGAGAAAATTTTGGCAA--CGTACTCATCT 5113
                           v  i     i                 v  v    -- i  i--    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCT 741

  chr2_148971405_   5114 GACAAAGGGCTACTATCCAGAATCTACAATGAACTCAAACAAATTTACAA 5163
                           i  i  i  vv          v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_148971405_   5164 GAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 5209
                         v     i    ----   v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_148971405_   5210 ATTTCTCAAAAGAAGACATTCATGCAGCCAAAAGACACATGAAAAAATAC 5259
                                v        i  v  viii     v ii          i  i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_148971405_   5260 TCATCATCACTGGCCAT 5276
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (133 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


2221 22.64 2.58 12.41  chr2_149002410_149007934.rev     4027  5033 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_149002410_   4027 TGGAAGAAACTTCCATGCCCATGGAGAGGAAGAATCAATATCATTAAGAT 4076
                              ii vv i     ii      vv      v i     ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_149002410_   4077 GGCCATACTACCAGAAACAGTTTACAGATTCAATGCTATTCCTA-CAAAA 4125
                            v     v  vi  viii i           i  v  i    -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_149002410_   4126 CTACCAATGACAGTCTTCATGGAATTAGAAAAGACT-ATTTTAAAATTCA 4174
                         - v   iivi vv i  iiii   v v  v   -  -  ii         
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_149002410_   4175 TGTGAAAC--CAAAGAAGCACCCA-AACAGCCAAAGCAATCCTAAGTAAA 4221
                          i  i  v--   i i ---    -  i       i     i i iv  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_149002410_   4222 AGGAACAAAGGTGGAAACATCACATTATCCAACTCTCTCTCACTCTCTCT 4271
                          i        v    iivv     i -----------  i  v i  ---
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACT-----------TCCCAATTTC--- 231

  chr2_149002410_   4272 CTCTGTCTCTGTCTCTGTCTCTCTCTCTATATATATACATATATATATTC 4321
                         --------------------------------------------------
  L1M4_orf2#LINE/    232 -------------------------------------------------- 231

  chr2_149002410_   4322 TCTCTCTCTACACACACACACACACACACACACACACACAAAAAGTATAC 4371
                         ----------------------------------------    v -   
  L1M4_orf2#LINE/    232 ----------------------------------------AAAACT-TAC 240

  chr2_149002410_   4372 TACAAGGCTACAGTAACCAAAACAGTATGGTACTGGTACCAAGACAGAGA 4421
                              i          i   i     i         i iv i  i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_149002410_   4422 CATACACCAATGGAATAGAATAGAGAGCCCAGAAGTAAAGCTGCACACCT 4471
                         i   v i              v     i      i    v iii   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_149002410_   4472 ACAACCATTTGATCTTCAACAAAG---TCAAGACAAACAAGCAACGGGGA 4518
                          iiii  v     i   i    i ---i      ---  vv   i     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGA 387

  chr2_149002410_   4519 GAGGATTCCCCATTCAATAAATGTTGATGGGATAACTGGCTAGCCATATG 4568
                         i  i  vvi iv     i     v  v     i      v  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_149002410_   4569 CAGAAGATTGATATTGAGCCCCTTCTTTATACCATATAGAAAAACAAACT 4618
                           i    v   vi   ii     v i i i        v     iv    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_149002410_   4619 TAAGATAGATGAAAGACTTAAATGTAAAACTTTAAACTATAAAAACCCTG 4668
                         i  i  i   v ?    i         i vi v           vi i i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_149002410_   4669 GAAGATAACCAATAACCTTGGAAATATCGTTCTAGACATAGGCCCTGGGA 4718
                              v   --   i---- ?iv v   -   vv   v v  vi- i  v
  L1M4_orf2#LINE/    538 GAAGAAAAC--ATAG----GNGTAAATC-TTCGTGACCTTGGGT-TAGGC 579

  chr2_149002410_   4719 AATA-TTTCAT-GATGAAGATGCCAAAAGTAATTGTAACAAAAGCAAAAA 4766
                            i-    v -   - v  ii       i vvv i        -     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAG-AAAAA 627

  chr2_149002410_   4767 AGTGAGAAATGTGACTCAATATTAAAATAAAGAGCTTCTGCATAGTAAAA 4816
                          vv  v    vv    i--i  i     v  i i   i  iiivvi   i
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTT--CATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_149002410_   4817 GAAACTATCAAGA--GTAAACAGACAACCTACAGAATGCAAGAAAATATT 4864
                           v          --  i  v        i        vi          
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_149002410_   4865 TGCAAACTATTCATCTGAAAAAGTTCTAATATCCAGAATCTATAAGGAAC 4914
                               ii  vi      v  i vv  vi          v     i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_149002410_   4915 T--TA------AATGAACAAGAAACAAACACCCCA-TTAAAAAGTGGGCA 4955
                          --  ------   i vv  i i     i v    -  ?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_149002410_   4956 AAGGACATTAAGAGACATTTTGCAAAAGAAGACTTCCAAGGAACCAA--- 5002
                              iv v  v        iv v        iv v   ivii    ---
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_149002410_   5003 --GCATTAAAAAATGCTTAACATCACTAATCAT 5033
                         --i   v    i     i       ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (134 / 90)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 5.81 (151 / 26)  


2485 23.95 3.03 8.05  chr2_149290782_149293942.rev     1715  2670 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_149290782_   1715 TGCAGAGATATTCCATGTTCATGGACAGGAAGAC--ACTATT------AT 1756
                           v i      i             iv       -- v    ------  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_149290782_   1757 GTCAATTCTTCTCAAATGTGAT--ACAGATTCAACAACGTCTCAGTAAAA 1804
                          v    v  i i     -    --           ivvi  i vi v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_149290782_   1805 ATCCCAGTAAGTTATTTTGTTACAAT-GATGAATAGATTCTAG--TTCAT 1851
                                ivivi v     iviv   -  ii iiv   i   i--     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_149290782_   1852 ATAGAAAGACAAGTGCCCCCAAAGAGCCAATACAAGAGTAAAGAAGAAAA 1901
                           i    vi    v v   vi  v      v    --- -----------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA---T----------- 185

  chr2_149290782_   1902 AAGGCAGAGGACTTAGGTTCAGAGCAACTGGTGCTAAAAAAAAAAAAAAA 1951
                         -----------   i--------------------     i  i  v   
  L1M4_orf2#LINE/    186 -----------CTTG--------------------AAAAAGAAGAACAAA 204

  chr2_149290782_   1952 GTAAAAAGGGCAGAGGACTGACATTACTTGACTCCAAGACTTACTCTGAA 2001
                           --------ii       v   i v iii i i   i       vii  
  L1M4_orf2#LINE/    205 GT--------TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_149290782_   2002 GCTATTATAAACAAAACAGCAAGAATTTGACAAAAGAGTAAACAAGTAGA 2051
                             ivi   v   i    iiv ivvi  i  v   ii  i   vi    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_149290782_   2052 TCAATGGAACAGAAT--AGAGCCCAGATACAGATCCATACAAATATAGTT 2099
                                  i     --    i     v i i i       vv   i  -
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT- 345

  chr2_149290782_   2100 TTTGACAAAAGATCTTTGACAAAGGAGCAAAGGCAATTCAATGCGGGGCG 2149
                         -----   vv   i  i     i  v  v   i v        -------
  L1M4_orf2#LINE/    346 -----CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG------- 383

  chr2_149290782_   2150 GGGGGGAGGGGGGGAGTCTTTCCAACAACGAGTGCTAGAACGGT--GACA 2197
                         ---    ii iiv-       i      vvi     i i  iii--  i 
  L1M4_orf2#LINE/    384 ---GGGAAAGAAT-AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_149290782_   2198 TCCCATATGAAAAAAAATGAATCTAGATATAGAACTTATACCCTTCACAA 2247
                         ?  - i   v    i      vi i  ivivv v  i i   v vi    
  L1M4_orf2#LINE/    430 KCC-ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_149290782_   2248 AAATTAACTCAAAATGGATCACAGATCTACATATAAAATGC--AGTCTAC 2295
                                              ?   i   v  i   i -  -- iv   i
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTAT 527

  chr2_149290782_   2296 AAAACTTTTAGAAAATAACACTGGAGAAAATCTCAGGGACCTTGGGTTTG 2345
                               i      i v    iv  ? v      iv v           v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_149290782_   2346 ATGATGAGCTTTTAGAAATAATACCAAACACATAATTCATGAAAGTAAAA 2395
                         iii   ivi i     v  i i      vi  i  viv ii    --   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG--AAA 625

  chr2_149290782_   2396 AAATTGTTAAGCTGGACTTCATTAAAATTAAAAACTTTCACTCTGTGAAA 2445
                             v v   ii          i               iiiv  vii  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_149290782_   2446 GACACTGTTA-GTGAATGAAAAGACAAGGCACAGAGAGGAAGAAGATAT- 2493
                               i i - vi i           vv      iv  i    i    -
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_149290782_   2494 -GCAAAATACATATCTC-TACAGGACACGTATCTAAAATATATAAAGAAC 2541
                         -     vi i      v-  vi    vi     i i              
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_149290782_   2542 ACTTAAAACTCAACAATAAAA---CAAGCAATCCAATAAAGAAATGGGCA 2588
                         v    v       i       ---   ii  i     v? i         
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_149290782_   2589 AAAGATCTGAACAGACACCACACTAAAGAAGATATATAAATAATGTCAAT 2638
                           i   i    i     iiv v i            i    i-- i    
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG--GCCAAT 873

  chr2_149290782_   2639 ---CAAACAAAAAGGTGATCAACATCTTATGTTAT 2670
                         ---  v ii     i  v        v????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (141 / 84)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 4.24 (106 / 25)  


3054 27.11 0.77 1.10  chr2_149296259_149302061     4401  5311 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_149296259_   4401 TGGAAGAACATCCCATGCTCATGGATAGGAAGAATCAATATCGTAAAAAT 4450
                              ii i        i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_149296259_   4451 GGCCATACTGCCCAAGGTAATTTATAGATTAAATGCCATCCCCATCAAGC 4500
                            v     v     iv i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_149296259_   4501 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4548
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_149296259_   4549 TATGGAACCAAAAAAAGAGTCTGCATTGCCAAGACAATCCTAAGCCAAAA 4598
                                viiv  ii-  vi v v  v     i      i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_149296259_   4599 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGT 4648
                                 i      vv       v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_149296259_   4649 CTACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAAAC 4698
                                  i   i    ii    i    i iv ii i   v     i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_149296259_   4699 CAACAGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 4746
                            ii   i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_149296259_   4747 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAAGGATT 4796
                           vi    i  i     ivv  v   i v  vv           - i  v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATA 394

  chr2_149296259_   4797 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCCAGCCATGTATGGAAAG 4846
                         vi  v  i  i              v      vi ?   ii iiii  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_149296259_   4847 CTGAACCTGGATCCCTTCCTTACATCTTATACAAAAGTTAATTCAAGATG 4896
                         v    vi    i    v   i   i v         i    i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_149296259_   4897 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 4946
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_149296259_   4947 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGACAAGGAATTCATGAC 4995
                           v    ?i- v i -   iv   v v  vv i i   v iv   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_149296259_   4996 TAAAACACCAAAAGCAATGGCAAAAAAAGCCAAAATTGACAAATGGGATC 5045
                           vi            vvi    v     vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_149296259_   5046 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAGTACCATCAGATTG 5095
                          v  i   v v  i i   i  ii vv    i  v v  i  vv i v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_149296259_   5096 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5145
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_149296259_   5146 CAAAGGGGTAATATCCAGAATCTACAAAGAACT--TAATCAAATTTGCAA 5193
                         i  i  iv vi          v  i        --  --   v ivii  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAA 791

  chr2_149296259_   5194 GAAAAAAATCAAACAACACCATCAAAAAGTGGGCAAAGGATATGAACAGA 5243
                         v     i -    i   v v  i?    i            v    i   
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_149296259_   5244 CACTTTTCAAAAGAAGATATTTATGCAGCCAACAGACACATGAGAAAATG 5293
                           i  i  v           vi viii     i ii       i  i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_149296259_   5294 CTCATCATCACTGGTCAT 5311
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


2001 25.74 1.11 0.74  chr2_149305465_149311571.rev     4399  4938 (1169)    L1M4_orf2#LINE/L1        1   542 (366)  

  chr2_149305465_   4399 TGGAAAAACATTCCATGTTCATGGGTGGGAAGAATCAATATTGTGAAAAT 4448
                               i i  i            i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_149305465_   4449 GGTCACACTGCCCAAAACAATTTATAGATTCAATGCTATTCCCATTAAAC 4498
                           iv i   v      vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_149305465_   4499 TACCATTGACATTCTTCACAGAATTAGAAGAAACT-ATTTTAAAATTCAT 4547
                          v   vivi v  i  ii     v v - v  i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr2_149305465_   4548 ATGGAACCAAAAAAGAGCCCGAGTAGCCAAGACAATCCTAAGCAAAAAGA 4597
                               viiv  ii  v  v  i       i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_149305465_   4598 ACAAACATGAAGGCATCATACTACCTGACTTCAA--CTATGCTACAAGGC 4645
                              vv  i   vv   i   v  ii i     --  - i      i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_149305465_   4646 TATAGTAACCAAAACAGCATGATATTAGTACAAGAACAGACACACAGACG 4695
                           i     i   i    ii  i  i i i i   i i     i i   iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_149305465_   4696 AATGGAACAGAATAGAGAACCCAGAAATAAGATCACATACAT--ACAACC 4743
                                i     v    ii          - i -       -- iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAA-ACC-CATACATTTATGGTC 346

  chr2_149305465_   4744 ACCTGACCTCCAACAAACCTGACAAAAACAAGCAATGGGGAAAGAATTCC 4793
                          vi   ii i i    ivv  v   i v  vv               vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_149305465_   4794 CTATTTAATAAATGGTGCTCGGAAAACTGGCTAGCCATATGCAGAAAACT 4843
                           v  i  i          v   v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_149305465_   4844 GAAACTGGACCCCTTCCTTACACCAAAAACAAAAATCAATTCAAGATG-A 4892
                            ii         v   i      v v        i  i    i   - 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_149305465_   4893 TTAAAGACTTAAATGGAAAACCCAAAACTATAAAAACGCTAGAAGA 4938
                          i ?    i      v  i v i            vivi       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

Transitions / transversions = 1.85 (89 / 48)
Gap_init rate = 0.01 (8 / 542), avg. gap size = 1.25 (10 / 8)  

1071 25.13 3.21 1.34  chr2_149305465_149311571.rev     5242  5615 (492)    L1M4_orf2#LINE/L1      528   908 (0)  

  chr2_149305465_   5242 AAAACCCT-AGAAGAAAATCTAGGCG-ATACCATTCAGGATATAGGCATG 5289
                              i  -         iv    ? - v i -   iv  iv v  vv i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTA 576

  chr2_149305465_   5290 GGCGAAGATTTCATGACAAAGATGCCAAAAGCAACTGCAACAAAAGCAAA 5339
                            i v i    v iivv v  ii         vvv          v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_149305465_   5340 ACTTGACAAATGGAATCTAATTAAACTAAAGAGCTTATGCACAGCAAAAG 5389
                          v v  i    v i ii v  i   v v  i i   v  ii vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_149305465_   5390 AAACTCTCATCAGAGTAAACAGACAACCTACAGAATGGGAGAAACTTTTT 5439
                          v   v   vv i   i  v        i               v v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_149305465_   5440 GCAACTTACCCATCTGACAAAGA---TGTAATATTCCAGCATCTACAAGG 5486
                             v i ivi      i  i i---    ----     v  v  i  i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTA----TCCAGAATATATAAAG 772

  chr2_149305465_   5487 AACTTAAACAAATTTACAAGAAAAAAACAA----CCTGATT-AAAAGTGG 5531
                             ivv    v iv i  v     i    ----  ii   -    i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_149305465_   5532 TCAAAGGACATGAACAGACACTTCTCCAAAGAAGACATTCATGTGGCCAA 5581
                         v       iv    i     i              i  v  vi       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_149305465_   5582 CAA--ACATGAAAAGAAGCTCAACACCACTGATCAT 5615
                         i  --           v        i  ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.02 (47 / 46)
Gap_init rate = 0.02 (8 / 381), avg. gap size = 2.12 (17 / 8)  


2360 19.15 1.32 8.19  chr2_149317469_149319153.rev      502  1185 (500)    L1M4_orf2#LINE/L1      227   863 (45)  

  chr2_149317469_    502 ATTTTAAAACAAATTATAAAGCTATAGTGATTTAAACAGTATGGAATTGG 551
                             i     vv i  i       i   i  iv i     i   v i   
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_149317469_    552 CATAAAGACAGACATACAGACCAATGGAACAGAACAGAAACCCCAGAAAT 601
                              i  i       i   i        i    iv  i vi        
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_149317469_    602 AAACCCTGACATATATGGTCAAATGATT---GACAAGGATACCAAGACTA 648
                               vv    v         v     ---       i i       i 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_149317469_    649 CACAATGGGAAAAGGACAGTCTCTTCAATAAATGA-GCTGGTGA-AACTG 696
                         iv       i    i i     i     i     i-     -  -     
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG-GACAACTG 425

  chr2_149317469_    697 AATATTCACATGCAAAATAATGAAATTGGATCCTTACCTTATAGCATATA 746
                         i   ?i           v      i     i  i     i i v      
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_149317469_    747 TTTAAAAATCAACCCCAAATGGATTAAATACCTAAATGTAAGACACAAAA 796
                         i--      i   i v        i ? v              vvi    
  L1M4_orf2#LINE/    476 C--AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_149317469_    797 TTATAAAACTCCTAGAAGAAAATACAGGAAGAAAGACTTCATGACATTGA 846
                         i          i          i i   ?iv   v-    i    v   i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGG 572

  chr2_149317469_    847 ATTTGACAGTGATTTCTTGGATATGACATTAAA-GCACCAGTAACAAA-G 894
                         i  v i  i  i      i         ii   -    v  i      - 
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_149317469_    895 AAAAAACAGACAAATGGCATTACATCAAACTAAAAAACCTCTTCAGGGCA 944
                               i   i    v v i v       v v      i i viivvv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_149317469_    945 AAGGAAACAATCAACAGACTGCAAAGGCAACCTTATGGAAAGGGA-AAAA 993
                              v  v     v i v  v    i     i- ii   v    -    
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCC-ACAGAATGGGAGAAAA 721

  chr2_149317469_    994 TATCTGCAAACCATGTAGTGGATAAACAATTAATATCCA-AATATATAAA 1042
                            i      i   i  viv     ivi i vi      -          
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_149317469_   1043 GAACTCCTAAAACTCAAAAACAAAAAAACGCAAAAAAAAAAAAAACAAAA 1092
                               i  v       v  i     i  ---------------------
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGAC--------------------- 800

  chr2_149317469_   1093 AACAAAACAAAAAAAAAACCCAAAAGCAAAAATTTAAAGATTTTTTAAAT 1142
                         ------------   v       ---------  ?   ---------   
  L1M4_orf2#LINE/    801 ------------AAATAACCCAA---------TTWAAA---------AAT 820

  chr2_149317469_   1143 GGGCAAAGGATCTAAAGAGACAGGTCTTCAAAGAAGATATACA 1185
                                    i i  v     vv   i               
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.70 (80 / 47)
Gap_init rate = 0.02 (14 / 637), avg. gap size = 4.64 (65 / 14)  

 274  8.16 8.16 0.00  chr2_149317469_149319153.rev     1254  1302 (383)    L1M4_orf2#LINE/L1      856   908 (0)  

  chr2_149317469_   1254 GATATACAAATGGCC----GGCATACAAAAAGATGCTCAACATCAGTAAT 1299
                                        ----i   i ii                  ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_149317469_   1300 CAT 1302
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.00 (4 / 0)
Gap_init rate = 0.02 (1 / 53), avg. gap size = 4.00 (4 / 1)  


3047 28.06 1.22 0.11  chr2_149381565_149383486.rev      533  1430 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_149381565_    533 TGGAAAAACATTCCATACTCATGGATAGGAAGAATCAATATTGTGAAAAT 582
                               i i  i    ii        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_149381565_    583 GGCCATACTGCACAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 632
                            v     v v    v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_149381565_    633 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAACTACTTTAAATTTCAT 681
                          v   -   v    i  -i     v v  v  iviv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_149381565_    682 ATGGAACCAAAAAAGAGCCCATACAGCCAAGACAATCCTAAGCAAAAAGA 731
                               viiv  ii  v  viv i      i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_149381565_    732 ACAAAGCTGGAGGCATCATGCTAACTGACTTCGAACTACACTACAAGGCT 781
                               i      vv   ii  vv ii i   i  vivi       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_149381565_    782 ACAGTAACCAAAATAGCATGGTATTGGTACCAAAACAGATATATAAACCA 831
                                i   i i  ii     i   i iv ii i   i     i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_149381565_    832 ATAGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACTATC 881
                           i   i    iv   ivii         vv   i    i  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_149381565_    882 TGAACTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 931
                            vi  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_149381565_    932 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATTTGCAGAAAACTGAA 981
                           i  i        i     v      v  ?   iv    i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_149381565_    982 ACTGGATCCCTTCCTTACACCTTATATAAAAATTAACTCAAGGTGGATTA 1031
                         ii    i    v   i     v    i              ii     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_149381565_   1032 AAGAC-------TGAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 1074
                         ?    ------- i i v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_149381565_   1075 GGCAATACCTTTCAGGACACAGGCATGGGCAAAGACTTCGTGACTAAAAC 1124
                           ?ivv vii   iv   viv  vv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_149381565_   1125 ACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATAGGATCTAATTA 1174
                                   vvi          vv     v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_149381565_   1175 AACTAAAGAGCTTCTGCACAGCAAAAGAAACCATCATCAGAGTGAACAGG 1224
                           v v  i i   i  ii vv    i  v  i    vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_149381565_   1225 CAACCTATAGAATGGGAGAAAACTTTTGCAATCTATCTATCTGACAAAGG 1274
                              i i              iv       vii  v       i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_149381565_   1275 GCTAATATCCAGAATCTACAAGGAACCTAAACAAATTTACAACAACAA-- 1322
                         i  vi          v  i  i    iivv    v iv i  i  v  --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_149381565_   1323 CAAAAAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGATACCTCTC- 1371
                             v     v  i?    i            v    i   i ii    -
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_149381565_   1372 AAAAAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCTCATCATC 1421
                            i    i  vi vii      i  i  i       i v     v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_149381565_   1422 ACTAGTCAT 1430
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.40 (12 / 5)  


2744 12.62 2.85 24.37  chr2_149393997_149397366.rev     1727  2883 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_149393997_   1727 TGGAAAGACAACATGTGTTAATAAGTTGGAAAACTTAACATTGCTAAGAT 1776
                                 i v vii    v  iii      i      i    i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_149393997_   1777 TTCAATACAACCCAAATAAATCTACAGTTTTAATGCAATACTTA-CAAAA 1825
                         vv      vv       vi        v  i  i     v i  -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_149393997_   1826 TTCTATTTGCCTTTTT-GCAGATTTGGAAAAGCTGATCCCAAA-TTCATA 1873
                          i i vi         -     vv v  v          i   -      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_149393997_   1874 TG-AAATGCAAAGTCCCTA-AATTGCCAAAACA-TCTTGAAAAAGATGAA 1920
                           -        i vv  i -   v         -            v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_149393997_   1921 ---AGTTGGAGGACCCATACTTCCTAATTTTGAAACTTACTACAAAGCAA 1967
                         ---           i  i      i     ii                v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_149393997_   1968 TGGTAATTAAGACTGTGTGTTACTGGCATAGGAATAGACATATAGATCAA 2017
                         ii     i     v     v          i i                 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_149393997_   2018 TAGAATAGAATTCAGAGTCCAGAAATAAAACCCTACATCTATAGCCAATT 2067
                          i          v                v  v     i   i i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_149393997_   2068 GATTTTGTACA-GAATGCTGAGATCACTCAAAATGGGAAGAATAATCTCT 2116
                               vv   - ii   ii   i  i    viv  i       i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_149393997_   2117 CCAACAAATAGGGGCTGGGAAAATTAGATAGC-ACATGCAAAAGAATGAA 2165
                         i        -  v       v  i i    ? -                 
  L1M4_orf2#LINE/    401 TCAACAAAT-GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_149393997_   2166 GTTGTTCCCCTAACTCACACCTTACATAAAAATGAATTCAAAATGGATGA 2215
                             vv      v        v  i i      v  i           v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_149393997_   2216 ATGACT---ATGTATTAGAGCTAAAAAATCATAAAACTCTTGGTCAGGCG 2262
                         ?v   i---     --          --ii           i -------
  L1M4_orf2#LINE/    500 WAGACCTAAATGTA--AGAGCTAAAA--CTATAAAACTCTTAG------- 538

  chr2_149393997_   2263 TGGTGGCTCATACCTGCAATCCCAGCACTTTAGGAGGCCAAGGTGGGCGG 2312
                         ---------------------------------------   --------
  L1M4_orf2#LINE/    539 ---------------------------------------AAG-------- 541

  chr2_149393997_   2313 ATCACCTTAGGTCGGGAGTTCGAGACCAGCCTGACCAATATGGTGAAATC 2362
                         --------------------------------------------------
  L1M4_orf2#LINE/    542 -------------------------------------------------- 541

  chr2_149393997_   2363 CCATCTCTACTAAAAAAATAGAAAAATTAGCCGGGCGTGGTGGTGGGTGC 2412
                         ------------    v    ----------------------- ?  i-
  L1M4_orf2#LINE/    542 ------------AAAACATAG-----------------------GNGTA- 555

  chr2_149393997_   2413 CTACAATCTCAGCTACTCAGGAGGCTGAGGTGGGAGAATAGCTTGAACCC 2462
                         ----     -------  -----------   ------- v    -----
  L1M4_orf2#LINE/    556 ----AATCT-------TC-----------GTG-------ACCTTG----- 571

  chr2_149393997_   2463 AGGAGGTGGAGGTTGCAGTGAGCCGAGATCATGCCACTGCACTCCAGCCT 2512
                         ----------    i-----------------------------------
  L1M4_orf2#LINE/    572 ----------GGTTA----------------------------------- 576

  chr2_149393997_   2513 GGGCAACAGGCTCAAAAAAAAAATCATAAAATTCTTGTAAAAAATATAGA 2562
                         -     --------------------------------------------
  L1M4_orf2#LINE/    577 -GGCAA-------------------------------------------- 581

  chr2_149393997_   2563 ATTAAATACTCATGGATTCTTAGATATGACACCAAAAGCAT---TAACAA 2609
                         ------------   v                        i---i     
  L1M4_orf2#LINE/    582 ------------TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_149393997_   2610 AA----AAAT---TAAATTGAAGTTTACCAAAATTAAAAACTTTTATGCA 2652
                           ----    ---       i v  i i                 i   v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_149393997_   2653 TCAAAAAACATTGTCAGGAAAGTGAAAAGGCAAGCTACAAAATGGGAGAA 2702
                              ii   i i   i            i   v i   i          
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_149393997_   2703 AATCTTTGCAAATCGTAAAACTTATAAGGATCTAGTATGTAGAATATATA 2752
                            v          i  v v  v      iv  v    vi          
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_149393997_   2753 AGGAACTT---CAAC------ATAAAAAGGCTAACAACCCAATTGAAAAA 2793
                          i     i---    ------        i v  i         ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_149393997_   2794 TGGGCAAAGGATTTGAATAGACATTTCTCCAGAGAAGATGTACAAGTAGC 2843
                                                        i       i     i i  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_149393997_   2844 CAAATGTGCATATTAAAAGATAATTAATTTCTTCAGTCAT 2883
                            - iv   i  v       iv i  iv  v????????
  L1M4_orf2#LINE/    870 CAA-TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (85 / 57)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 10.86 (315 / 29)  


2469 18.64 0.94 1.88  chr2_149433673_149438833.rev     1455  1985 (3176)    L1M4_orf2#LINE/L1      209   734 (174)  

  chr2_149433673_   1455 GAGGACTTACACTTACTGATTCAAAAACTTACCATAAAGCTATAGTAATC 1504
                                i      v ii   iv         i i       i       
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_149433673_   1505 AAAACAGTGTGGTACTGGCATAAAGACA--CATGTTGTCCAATGGAATAG 1552
                           i                    i  i --   i v vi           
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_149433673_   1553 GATAGAGAGGCCAGAAATAAAGCCTTGCATATATGGTCAAATGATTGTCA 1602
                         i  v     v           v  v i   v         v     v  i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_149433673_   1603 ACA-GGCTGCCAAGAACATCCAATGTGGGAAAAGACAGTCTTTTCTACAA 1651
                            -  v        v   i     -      ii i         v    
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTTCAACAA 407

  chr2_149433673_   1652 ATGGGGTTGAGAAAACTGGATATCAACATGCAAAAGAATGAAGTTGGACC 1701
                             v i  i  v         ? v                         
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_149433673_   1702 CTTTCCTAACACCATGTGGAAAAATTAATTCAAAATGGATCTATGAGCTA 1751
                          i v   v       i iv         i            v?v  v   
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_149433673_   1752 AATGCAAGACCTAAAACTAAAAAACTCTTAGAAGAAAACAAAAAAGAAAA 1801
                             i    v         v                    v ii? v   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_149433673_   1802 GCTTCACAACATTGGATTTGGCAATGATTACCTGGACATAACACCAGAGA 1851
                         v    iii  v    i  v       i  v i i  i  i      i ii
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_149433673_   1852 CTCAGGCAACAAAAGAAAAAATAGACTTCATAAAATTTGACTACAT-AAT 1900
                          v  i                    i------     v    v   -  v
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGAT------AAATTGGACTTCATCAAA 651

  chr2_149433673_   1901 ATTAAAATATATATATATATATTAAAA-ACGCTATCAACAGAGTAAAAAG 1949
                                --- iv v i iiv i   i-  i       v i   i     
  L1M4_orf2#LINE/    652 ATTAAAA---ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_149433673_   1950 GCAACCCATAGAATGAAAGGAAATATTTGCAAGTCA 1985
                         i       i      ii  i            i   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

Transitions / transversions = 1.46 (57 / 39)
Gap_init rate = 0.01 (7 / 526), avg. gap size = 2.14 (15 / 7)  

 324 20.34 0.00 0.00  chr2_149433673_149438833.rev     3485  3543 (1618)    L1M4_orf2#LINE/L1        1    59 (849)  

  chr2_149433673_   3485 TGGAAAAATATTCCATGCTCATGGATTAGAAGAATCAGTATCATTAAAAT 3534
                               i    i     i         i     v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_149433673_   3535 GGCCCTACT 3543
                            vv    
  L1M4_orf2#LINE/     51 GGCAATACT 59

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  

2478 25.99 5.29 1.44  chr2_149433673_149438833.rev     3839  4669 (492)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr2_149433673_   3839 AAAAAGGCCCTACTGCCCAAAAAATAGCTATAGAGATTCAGTGCTATTCC 3888
                           i v   vv    v      --- v v v  v       ii  v  i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAA---TTGATCTACAGATTCAACGCAATCCC 92

  chr2_149433673_   3889 TATCAAAGTACTAG-TGTCAATTTTCACATGAATAGA-AA----ATTCTA 3932
                                i v i  -  i v-    ii  vi   v  -  ----  i   
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr2_149433673_   3933 AAATTCATATGGAACCAAAAAGAGCCCAGA-TAGGCAAAGCAATCCTAAG 3981
                                       viiv  i ii      -   v    i     i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_149433673_   3982 CAAAAAGAACAAAGCTGGAGGCATCACATTACCCAGCTG-GAAACTATGC 4030
                         v  i          i      vv     i v    ii v-i     - i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TAC 240

  chr2_149433673_   4031 TATAAGGCTACAGTAACCAAAACAGCATGGTACTGCTATGAAAACAGACA 4080
                           i  i          i   i    ii        vi  i ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_149433673_   4081 CAT----TAAC-----------------CCAGAAAGAAAGTCACACACCT 4109
                         i  ----i  i-----------------       v   vi  i   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_149433673_   4110 ACAGTCATCTGATCTTCAACAAAGTTGACAAAAATGAACAATGGGGAAAG 4159
                          ii    vi    i   i    i v  v   i viivv            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_149433673_   4160 AA----CTTCCTA-----TGGTGGTGGGAGAGCTGGCTAGCCATATGCAG 4200
                           ----   iii -----     v     v i    v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_149433673_   4201 AAGATTGAAACTGGACTGCTACCTTTCACCATATACCAAAATTAACTCAA 4250
                             v    ii     iv      iv          v             
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_149433673_   4251 GATGGATTAAATACTTAAATGTAAGACCTCAAACTACCAAAATCTCAGAA 4300
                         i      i ? v  i           v  v      iv   v   i    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_149433673_   4301 GAAAATCTAGAAAATACTATTC-TGGACATGGGCCTTGAGAAAGAATCTA 4349
                              iv   i?ivv v v   -  iv v    --  ii v  vii i v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTC 588

  chr2_149433673_   4350 TGCTAAAT----CCTCAAAAGCAGTTGCAACAAAAACAAAAATCGACAAC 4395
                          --  i  ---- vi        vvv         iv      v  i  v
  L1M4_orf2#LINE/    589 T--TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_149433673_   4396 TGGGACCTAATTAAACTAACAAGCTTCTGTACAGCAAAATAAACTATCAA 4445
                          v    i v  i   v v v  i   i   i vv    iv v        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_149433673_   4446 AAGAGTAAACAGAAAACCTACAAAATGAGAGGCCATATTTGTAAACTATG 4495
                         i i   i  v   v    i   i    i   ivv       i   ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_149433673_   4496 CGTCTCACAATAGTCTAATATCTAGAATCTATAAGGAACTCA-GCAATCC 4544
                         ii   v i  vi v  vi    i     v     i      v-i   ii 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_149433673_   4545 AACAAACAAAAAACAAATAACCCCATTTAAAAAACAGGCAAAAGACATGA 4594
                           i  vv    i           v   ?     -ii      i  iv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGA 835

  chr2_149433673_   4595 GCAGACACTTCCCAAAAGAAGATATATAAGCAGCCAACAAACATATATAC 4644
                         ii     i   i v            i  iii     i  i  i  i- -
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-A- 883

  chr2_149433673_   4645 AAAAATGCTAAACATCACTAATCAT 4669
                            i     v       ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (128 / 84)
Gap_init rate = 0.02 (20 / 863), avg. gap size = 2.80 (56 / 20)  


3326 14.76 1.89 17.88  chr2_149626424_149628751.rev      779  1835 (492)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr2_149626424_    779 ATTGATTGAAAGACTTAATATCATTAAGCTGTCAGTATTACCCAAAGCAA 828
                           v     i            ii     v  v  i  i v      vii 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr2_149626424_    829 TCTACAGATTCATGGCAATCTCTATCAAAATTTCAATGACATATTTTATA 878
                                     vv      i          ii  iivi v v    ii 
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr2_149626424_    879 GAAGCAGAAAAATCCATCCTAAAATTTATATGAAATCTCAAGGGATACCA 928
                            iiv  v  iiiv           i     i  viv       iv vi
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr2_149626424_    929 AATAGCCTAAACAATCTTGAAAAATAAGAACAGAGTTGAAGGTCTCACAC 978
                                v                v       i     i   v       
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_149626424_    979 TTCAACAATATAATGGACTTTGGGGACTTGAGGGGAAGGGTGGGAGTAGG 1028
                            -----------------------------------------------
  L1M4_orf2#LINE/    221 TTC----------------------------------------------- 223

  chr2_149626424_   1029 GTGAGGGATAAGAGACTACAAATAGGGTGCAGTGCATACAGTTCGGGTGA 1078
                         ------------------ v   ------------------   ------
  L1M4_orf2#LINE/    224 ------------------CCAAT------------------TTC------ 231

  chr2_149626424_   1079 TAGGTGCACCAAAACCTCACAAATTAGCACTAAAGAACTTACTCATGTAA 1128
                         ----------     -----------------------------------
  L1M4_orf2#LINE/    232 ----------AAAAC----------------------------------- 236

  chr2_149626424_   1129 CCAAATACCACCTGTACCCCAATAGCCTATGGAAAAATAAAAAATAAAAG 1178
                         --------------------------------------------------
  L1M4_orf2#LINE/    237 -------------------------------------------------- 236

  chr2_149626424_   1179 TTACTACAAAGCTACAGGAATCAAAACAGTGTGGTATTGACATAAAGACA 1228
                                          v      i           i  i     i  i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_149626424_   1229 GACATATAAATCAACAGAAGAGAATAAAGGGCCCAGAAATAAATCCTCAC 1278
                                 i     ii   v     vi  i i           i  vi  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_149626424_   1279 ATATATGGTTGAATAATTTTCAACAAGAGTGTCAAGACCATTTAATGTGG 1328
                           v      ii v i      i     i   i          i    v  
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_149626424_   1329 AAAGAACAGTCTTTTCAACAAATAGTGTTGGAAAAACTGGATAGCTACAT 1378
                               i                i   i   i v         ? i    
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_149626424_   1379 GCAAAAAATATATTAATGTTGGGCCCTTACCTTAGAGTACATGCAAAAAT 1428
                               i ---  v  -     i   i     i v vi i  i       
  L1M4_orf2#LINE/    437 GCAAAAGA---ATGAA-GTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_149626424_   1429 TTACTCCAAAAGGATCAAATACCTACATATAAAAACTAAAACTATAAAAC 1478
                          v    v   v      ? v     v  i   i i               
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_149626424_   1479 TCTTAGAAGAAAACACAGGAGAAAAGCTTCATGACATTGGACTTGGCAAT 1528
                                        i   ? v   v    i    v    ii v      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_149626424_   1529 AATTTCTTGGATATGACACCCAAAGCACAAGCAACAAAATAAAAA-TAGA 1577
                         ii      i           v                  v     -    
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_149626424_   1578 CA-------CTTCATCAAAATTAAAAACTTTTATA--TCAAAAGACACTA 1618
                         i -------                       i i--     i       
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_149626424_   1619 TCAATAGTGTAAAAAAGCAATCCATGGAATAGAAGAAAAT-TTTATAAAT 1667
                             v iv  i    ii   i   ii    i i       -   ii    
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_149626424_   1668 CATATATCTAATAAGGGATTGATGTCCAGAATACATAGAGAACTC---CA 1714
                                  i        i vi i         i   i       ---  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_149626424_   1715 AGTCAACAACAA-----CAAATTAACCTGATTAAAAAATAAATACAGACC 1759
                          v    i  i  -----     -    ii   ?      iiii v  ivi
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_149626424_   1760 TTGAATAGACATTCCTC-AAAGAAGATATACAAATGGCCTATAAGCACAT 1808
                                      i   -                     v          
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_149626424_   1809 GAAAAGATGCTGAACATCACTAATCAT 1835
                                    v       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (101 / 51)
Gap_init rate = 0.02 (14 / 888), avg. gap size = 14.93 (209 / 14)  


 849 25.99 13.89 5.75  chr2_149639957_149642016.rev      501  1004 (1056)    L1M4_orf2#LINE/L1       46   590 (318)  

  chr2_149639957_    501 AAGATGTTAATTCTCCTAAAATTGCTCTAGAGAATTAAAGTAATCCCCAC 550
                               vi   v    iv      v    v   v i  v i      i i
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_149639957_    551 CTTCCCCCAAAAAAACCCTAAGGGGTTTGTGTATGTGTATAGAAATTGGC 600
                          ----------    i  i i-----i  iv - v v ii        i 
  L1M4_orf2#LINE/     96 C----------AAAATCCCAG-----CTGCCT-TTTTTGCAGAAATTGAC 129

  chr2_149639957_    601 AAGCTGATTCTGAAATTTATAATAGAAATGAAAAAAAAA-AGAATAGCAA 649
                                 i  i     i   - i      v  iii vv-        v 
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATA-TGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr2_149639957_    650 GGACAGTTCTGAA------GATCAAAGTTAGAGGATTGA-ACATCATCAC 692
                         ii   i ii    ------  v       i     i v -  v  -i  v
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC-CCAA 227

  chr2_149639957_    693 TTTC--------TTATAAAGTAAAACTGATCAA-----------ATTGTC 723
                             --------i  i    iv v v i     ----------- i  v 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_149639957_    724 AGAAATCTTGGAATAAA----AACAGAATA-AATTG----TCCAGAAACA 764
                          v  ivv v iv   v ----  ii     -     ----        i 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_149639957_    765 GGCACTCAGA---TGACAGTCATCTGACTTATGACAAAAGTGTCCATAGA 811
                         i--  i  v --- v ii    vi   i  vi     ii   -   -   
  L1M4_orf2#LINE/    328 A--ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG-CCA-AGA 373

  chr2_149639957_    812 G-----AAGAGTGGAAAGGGCAGTCCTTTCAATACATGGCACTGAGG--- 853
                         v-----  vi -      iii    i      i v    ii   i i---
  L1M4_orf2#LINE/    374 CCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_149639957_    854 --GGA----------------AGTGGAACTTTATTCCTCACCCCCAATAC 885
                         --   ---------------- i  i ii vv ii   -   i -- i  
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT-ACCTC--ACAC 469

  chr2_149639957_    886 CATGTA-AAAAATTCTGTTCCAGAGAGATCCCAGACATAAATGTGAAAAG 934
                            i  -       v-ii  v i vi    v?    v       i i iv
  L1M4_orf2#LINE/    470 CATATACAAAAATTA-ACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_149639957_    935 TAAAACAATAAAGCTTCCACA-GAAAATATAGGACAGTA--TCTTCAAGA 981
                               v     i  iii v -     i     ?--   --     iv  
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGN--GTAAATCTTCGTGA 566

  chr2_149639957_    982 CCTTGGGGTAGGCAA-AGTTTTTT 1004
                                v       -i    i  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.74 (82 / 47)
Gap_init rate = 0.05 (29 / 545), avg. gap size = 3.41 (99 / 29)  

 659 18.98 22.99 2.55  chr2_149639957_149642016.rev     1295  1568 (492)    L1M4_orf2#LINE/L1      579   908 (0)  

  chr2_149639957_   1295 CAAAGATTTCTTAAATAGAACAT----------------AAAAGAAAAAA 1328
                            v i       i   vi   i----------------           
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_149639957_   1329 TA----AATTTGACTTCATTAAAATTAAAAACTTGTCTTCATTAGAAGCC 1374
                           ----    v        i              v v v v i i i v 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_149639957_   1375 ACCATTAAGACAGTTAAAAGGCAAGTTACAAGGTGGGAGAAGATATATA- 1423
                           i  i    v   v     i   vii   iii        i    v i-
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_149639957_   1424 AAATACATATACCTGACAAAGGACTT--ACCCAAAATA--------ACTG 1463
                             -      i    i  i      -- i   i    --------   -
  L1M4_orf2#LINE/    729 AAAT-CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT- 776

  chr2_149639957_   1464 CTT-TAAATCAATAAGAAAAA-AC-------------------TGGGCAA 1492
                            -i  v       v     -  -------------------       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_149639957_   1493 AGACTTGGAACAGGCACTTTATAAAAGAAG---------TG-CCAATAAA 1532
                           iv  v   i  i  i  iviv       ---------  -       i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_149639957_   1533 -ACACCTCCTGAAAAGGTGTTTAACATCATTAGCCTT 1568
                         -   -----       i  i i       ????????
  L1M4_orf2#LINE/    877 CACA-----TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (34 / 18)
Gap_init rate = 0.04 (14 / 330), avg. gap size = 5.00 (70 / 14)  


3271 16.98 4.21 0.93  chr2_149735870_149738456.rev      906  1547 (1040)    L1M4_orf2#LINE/L1        2   664 (244)  

  chr2_149735870_    906 GGAAAAGCATCCGGTTTTCATG-ACTGGAAGACTTA-CATTGTTAAGATG 953
                              iii    vi v      - i           -i            
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_149735870_    954 GCAATACTCTTCACATTGATTTACAAAATCAGTGCAACCTCTAGCACAAT 1003
                                  ii  v      i    i v   ii    i i   v  v   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_149735870_   1004 TCCAGCTGGCCTTTTTGGTAGAAATTAACAAGCTCATCC----------A 1043
                         i       -       v i       i       v    ---------- 
  L1M4_orf2#LINE/    102 CCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_149735870_   1044 TGGAAATGGAAGGGACCCAGAATAGCCAAAATAACACCGAACAAGAAGAA 1093
                                 v                      i  ivii   v        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_149735870_   1094 AAAAGCTGGAAGACTTATACTTCTCAATTTCAAAACTCTC-ACAAAGCAA 1142
                         v    i    i    i i     i             iv -       v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_149735870_   1143 CAATAATCAATATTTTGTGGTACTGCCAACAAGGACAGATGCACAAATCA 1192
                           i       v ivv          v  -i     i   iii i i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATCA 299

  chr2_149735870_   1193 ATGGAATAGAATTGAGAATCTAGAAATAAAGCCATGTATTTATGGTCAGT 1242
                                          i  i         v    ii           i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_149735870_   1243 TGACTTTTGACAAGGTTGCCAAAACAATTCAATGGCAGAAAGAACACTCT 1292
                            i   i       v      i  v         -i       i v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCT 398

  chr2_149735870_   1293 TGGCAACAAACAGTGCTGGGACAACTGGGAAGCCACATGCAACAGAATAA 1342
                          vv       ii                iv ?          v     i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_149735870_   1343 ATGTGGACTCCTAACTCATACTCTATACAGAA-TTGACTAAAAATAGATC 1391
                          vv     i    v    i  iv      i  -  i   v     i    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_149735870_   1392 AAATATCTACATGGAAGAGCTGAAATTATAAAATTCTTAGAAGAAA---- 1437
                          ? v i   v   v       i   i       i            ----
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_149735870_   1438 ---------CCTATGTGACCTTGGATTAAGCAATGGTTTCTTACATGTGA 1478
                         ---------i  vi          i   i              v  i   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_149735870_   1479 TGCCAAAAGCACAAGCGAAAAAAAGAAAAAAAATAGATAAATAGGACTTC 1528
                         ii              -  v           --         v       
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGC-AACAAAAGAAAAAA--TAGATAAATTGGACTTC 645

  chr2_149735870_   1529 ATCGAAACTAAAAACTTTT 1547
                            i   i           
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTT 664

Transitions / transversions = 1.82 (69 / 38)
Gap_init rate = 0.02 (11 / 663), avg. gap size = 3.00 (33 / 11)  

1077 16.98 1.89 3.02  chr2_149735870_149738456.rev     1831  2095 (492)    L1M4_orf2#LINE/L1      647   908 (0)  

  chr2_149735870_   1831 TCAAAATTAAAACCTTTCGTGTTTCATGTTTCAAAAGATACTACTAAGAG 1880
                                     v    i   i    -------  i  i    ii    i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCA-------AAGGACACTATCAAGAA 689

  chr2_149735870_   1881 AATGAAAAGACAGCTTACAGAATGCAATAAAATATTTGCAAATCTTATAT 1930
                          i          i ii        vi v                v     
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_149735870_   1931 CCAATAAGGGTCTACTATCCAGAATACGTAAAAACAAGATAATAACTCTA 1980
                          ii       v  vv           ii    i - vvv v i     v 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGA-ACTCTTACAACTCAA 788

  chr2_149735870_   1981 GAATAAAAAGACAAA-AA---AATCTTAAAATGG-CAAAGTATTTAAACA 2025
                         v              -  ---   i?v       -     v    i  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_149735870_   2026 GATATTTCTCCAAAGAAGATATACAAATGGCCAGTAAGCATATCAAAAAA 2075
                           i                              i      i  v    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_149735870_   2076 TTCCCAACAACATTAGTTAT 2095
                          v i     v  ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (26 / 18)
Gap_init rate = 0.02 (5 / 262), avg. gap size = 2.60 (13 / 5)  


1811 17.03 9.91 17.75  chr2_149786006_149791184.rev     3719  4687 (492)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_149786006_   3719 TGTTCATGGATTGGAAGACACATATTATTAT-ATTAAAATTGCAATTCTC 3767
                                            -----   v   -i    i  v     v   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGAC-----TTAATATTGTTAAGATGGCAATACTC 60

  chr2_149786006_   3768 CCTTAATCATTATATACA----CCATACAATC------AAAATCCCAGTG 3807
                           iv   -- v  v    ---- v ii     ------          iv
  L1M4_orf2#LINE/     61 CCCAAAT--TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_149786006_   3808 AGCTTTTTATTTTGTAGAAAGCAACAGGCTGATTCTTATTCCAAAATCCA 3857
                         -  i    ---   i     vii   i      i  ------     i  
  L1M4_orf2#LINE/    109 -GCCTTTT---TTGCAGAAATTGACAAGCTGATCCT------AAAATTCA 148

  chr2_149786006_   3858 TATCAAAATGCAAAAGGACCCAGAATAGCCAAATCAACC----------- 3896
                            vi        i-                  v   i -----------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_149786006_   3897 ---------------------ACTT---GATTTTAAGACTTATCACATAG 3922
                         ---------------------    ---i    i  i     ii   v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_149786006_   3923 CTGCAGTAATCAAGACA----------------AGGGTGG-CACATGGGT 3955
                           i              ----------------   i i -  i  i i 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_149786006_   3956 CCATGGAACAGAAT--AGGGTCAAGAAATAGACATATATTAACAAATATA 4003
                          v      i     --  i   v       i  vi   i------  v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC------ATTTA 341

  chr2_149786006_   4004 CAAATGACTGATTCTTGACAAATGTGCAATGGCCATTCAATGGAGAAAAG 4053
                         iiivii i     i i     iv    v v i           i    - 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-G 390

  chr2_149786006_   4054 GATAGACTTTTCAGCAA-TGGTGCTGGAGCAATTGGATGTATATTCACAA 4102
                         i    v       i   -         ii   i     ---- ?i    -
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT----AKCCACA- 435

  chr2_149786006_   4103 AAAGTTGAACCATTCAGAGGAATGATAATTGTTTAAAGTTATGGATATGA 4152
                         -----  -------  i i      -----------    --   i----
  L1M4_orf2#LINE/    436 -----TG-------CAAAAGAATGA-----------AGTT--GGAC---- 456

  chr2_149786006_   4153 TAATTATCCCAATTTGATCTTTACACTATATATACATGCATTGAAACATC 4202
                         -------   v ------ i i    i     ------------------
  L1M4_orf2#LINE/    457 -------CCCTA------CCTCACACCATATA------------------ 475

  chr2_149786006_   4203 ACATCGTACCCCATAAATATGCATAATTATGTGTCAATTATAAATTTTAA 4252
                         ----------------------------------   ----     ----
  L1M4_orf2#LINE/    476 ----------------------------------CAA----AAATT---- 483

  chr2_149786006_   4253 ACTTTCTTAATTAAATTCCAACTAAGAAAAACAATAAGTGAATATGGATC 4302
                         -------------  i  ---------    -------------      
  L1M4_orf2#LINE/    484 -------------AACTC---------AAAA-------------TGGATC 498

  chr2_149786006_   4303 ATAGACACAAAAGTAAAACCTGAAATTATAAAACTTCTGGAAGAAAATAT 4352
                          ?    vi   v    i v  i   i         ii i        i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_149786006_   4353 AGGAGAAAATCTTTATGACTTTGGGTTAGGCAAAGATTTCTTACATATAA 4402
                            ? v       ii    i             v i       v    i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_149786006_   4403 CACTAAAAGCAAGATC--CA---GTAAAAATTTTGATAAATT-----TCA 4442
                            i       vi v --  --- v      v--        -----   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTCA 646

  chr2_149786006_   4443 TCAATATTTAATTATTCACTTCTTTGAAAGACATTGTTAAGAGAATAAAA 4492
                             v   v  vvv  ivv v   ii  i    i i i    i i i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_149786006_   4493 AGACAAGCCACAGATTATAATAAAAGATTTGCAAAGTATCTATCTGATAG 4542
                               v       v ivi v    v         vi  v         i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_149786006_   4543 AGAATTTGCATACAGAATATATAA-GAATGCTCAAAAC-AAATAATGAGA 4590
                         i i i   i  v            -   iv  i v   -v      i i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_149786006_   4591 AAACAA-T--CCAAATTTTTAAATGGGCA-------------GACACCTC 4624
                          i    - --  v    ?vv         -------------    ii  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_149786006_   4625 ACCAAAGGAAATGGTATATAAATGATGAATAA-CACATAAAGA-ATGATT 4672
                         v      i i  ---   i     iiv     -     i  i -   v i
  L1M4_orf2#LINE/    847 TCCAAAGAAGAT---ATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_149786006_   4673 AACATCATTACTCAG 4687
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (104 / 57)
Gap_init rate = 0.05 (41 / 893), avg. gap size = 6.54 (268 / 41)  


2919 27.51 0.88 0.77  chr2_149933579_149935775.rev      801  1705 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_149933579_    801 GAAAAACATTCCATGCTCATGGATAGAAAGAATCAATATCATGAAAATGG 850
                             i i  i     i        v i    v i     ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_149933579_    851 CCATACTACCCAAAGTAATTTATAGATTTAATACTATGCCCATGAAGCTA 900
                          v     v      v i  i  i     i  ii v  v  i  v  iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_149933579_    901 CCA--TGGATTTTCTTCACAAAATTAGATAAAAACT-ACTTTAAATTTCA 947
                            --  vv    i v  -i     -  i  i--  - iii    v    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCA-GAAATT-GACAAG--CTGATCCTAAAATTCA 148

  chr2_149933579_    948 TATGGAAC--CAAAAAACAGCCCATATAGCCAAGGCAATCCTAAGCAAAA 995
                                v--   iii  --  viv        ii     i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_149933579_    996 AGAACAAAGCTGGAGGCATC-CAGGTACCTGACTTCAAACTACACTACCA 1044
                                  i      vv  -  vv -  ii i      vivi     v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAA 245

  chr2_149933579_   1045 GGCTACAGTAACCAAAACAGCATGGTACTGATACCAAAACAAATATATAG 1094
                         i          i   i    ii        ii iv ii i i i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_149933579_   1095 ACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAC 1144
                          i        i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_149933579_   1145 CACTTGATGTTTGACAAACCTGACAAAAACAAGCAATGGGAAAAGGATTC 1194
                           v     v  i     ivv  v   i v  vv       i    i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_149933579_   1195 CCTATTTAATAAATGGTATTGGGAAAACTGGCTAGCCATATGCAGAAAAC 1244
                         i  v  i  i       ii     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_149933579_   1245 TGAAACTGGACCCCTTCCTTACAACTTGCACAAAATTTAACCCAGCATGG 1294
                             ii         v   i   v v ii      v     i  iv    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_149933579_   1295 ATTAAAGATTTAACTGTAAGACCTAAAACCATAAAAGCCCTAGAAGAAAA 1344
                           i ?   ii   v       v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_149933579_   1345 CCTAGGCAATACTATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 1394
                          v    ?ivv v v   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_149933579_   1395 AAATACAAAAAGCAATAGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1444
                         vi i  v       vv           vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_149933579_   1445 ATTTAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 1494
                           iv  v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_149933579_   1495 CAGGCAACCTTCAGAAAAGGAGAAAATTTTTGCAATCTATCCATCTGACA 1544
                         v  i     iv     vi         v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_149933579_   1545 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 1594
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_149933579_   1595 AA-ATGAACAACCCTATCAAAAAGTGG-CAAAGGATATGAACAGACACTT 1642
                           - ii  i     v  i?    i   -        v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_149933579_   1643 CTTAAAAGAAGACATTTATGTGGGCAACAAACATATGAAACAAAGCTCAT 1692
                           iv        i  vi vi   v   i  i  i      vi v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_149933579_   1693 CATCACTGGTCAT 1705
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (140 / 105)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.36 (15 / 11)  


3157 28.05 0.22 0.33  chr2_150085004_150090806.rev     4403  5311 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150085004_   4403 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4452
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150085004_   4453 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4502
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150085004_   4503 TAACAATGATTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4550
                          vv  iiviii  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_150085004_   4551 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4600
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_150085004_   4601 AACAAAGCTGGAGGCATCACGCCACCTGACTTCAAACCATACTACAAGCC 4650
                                i      vv    i iv  ii i      v v        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_150085004_   4651 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4700
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_150085004_   4701 AATGGAACAGAACAGAGCCTTCAGAAATAATGGCGCATATCTACAACTAT 4750
                                i    iv   vv i         vvv ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_150085004_   4751 GTGATCTTTGACAAACCTGGGAAAAATAAGCAATAGGGAAAGGATTCCCT 4800
                         v    i  i     ivv  vv  i vi vv    i       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_150085004_   4801 ATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCATGTGTAGAAAGCTGA 4850
                         v  i  i              v      v  ?   ii  i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_150085004_   4851 AACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGATT 4900
                          ii    i    v   i    iv              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_150085004_   4901 AGAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 4950
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_150085004_   4951 AGGCATTACCATTCAGGACATAGGCAGGGGCAAGGACTTCATGTCTAAAA 5000
                            ?i v viv   iv   v v  vvvi     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_150085004_   5001 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5050
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_150085004_   5051 AAACTAAAGAGCTTCTGCACAGCAAGAGAAACTACCATCAGAGTGAACAG 5100
                            v v  i i   i  ii vv   ii  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_150085004_   5101 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 5150
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_150085004_   5151 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5200
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_150085004_   5201 AACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCT 5250
                          -    i     v  i?    i     i     iv    i     i    
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_150085004_   5251 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCA 5300
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_150085004_   5301 TCACTGGCCAT 5311
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (148 / 103)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.25 (5 / 4)  


3031 23.62 5.28 1.15  chr2_150142767_150145816     1687  2558 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150142767_   1687 TGGAAAGA----CCGTGTTCATAGATTGAAAGAC--AACATAGT-AAAAT 1729
                                 ----  i       i     i     --  i  v  -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150142767_   1730 GTCAGTTCTCTACAGATTGTTATATAGGTTTAACACAATTCCTGTCAAAA 1779
                          v  i v   iv  i    v v  i  i  i   i    i   i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150142767_   1780 TCCCAGGAAGATTTTTTTTTTTTTAGATATAGACAAAAGTG-TTCTACAG 1828
                               -----i vii      vi   v  v     iv-  - i   v i
  L1M4_orf2#LINE/    101 TCCCAG-----CTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAA 144

  chr2_150142767_   1829 TTTATATGGAAAGATAAGAAACT-GGTATAGCTAAAACGATTTTGAAAAA 1877
                           i         vii   ii  i-i v     i     i  i        
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_150142767_   1878 GAAGACTAAAGTAGAAGGAATCAAACTACCCTATTTCAGGATTTAATATA 1927
                              vi     v i    v   v   v   v      ii i   v  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_150142767_   1928 CAGCTGTAGTAATCAAGAC--TGCGGTACTGACAGAGAAATAGACATA-- 1973
                         v    ii            --  i       i  v iii         --
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_150142767_   1974 GATCAATTAAACAGAAT-----------AAATAGACCT-TAAAAATATGC 2011
                                vi  i     -----------     i   i-  v vv    v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_150142767_   2012 CCATCTAATTTTTAACAAAGGTGTAAAAGCAATTCAGTGGAGGAAAGACA 2061
                         i  vi i     ii    i    iv  ii v     i   i i  ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_150142767_   2062 GCCTTTTTAACAAATGGTACTGGAGGAACTGGACATTCACAGGCAAAA-A 2110
                          i     i          i    iiv       i ?i    v      - 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_150142767_   2111 ATGAATCTCAGCCTAAGTCTCACACTTTTTACAAAAGTTAA-----AGTG 2155
                              vi vii  ivvii       iv v       i    ----- i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_150142767_   2156 AATCACAGACTTAAATGTGAAATGTAAAAACATACAGCATTTAG--GAAA 2203
                         i    ?    i       i i vv     vi   v i vi    --    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_150142767_   2204 AAATAGAAGAAAATCTTCATAAATCTAGGGCTAGGTGA-GGTT-CTTAGA 2251
                          v    i? v        i i -i  v   i    ii -    -      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGA-CCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_150142767_   2252 CTTAATACCAAAAGCATGACTCATAAAAGAAAAAATA-ATAAATTAGACT 2300
                         iv i i          ii viv i             -       i    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_150142767_   2301 TCATCAAAATTTAAAACTTTTTTACCCGGCACAAGACCCTGTTAAGAGAA 2350
                                    v         v i ii--  v i   v  i i    i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAG 691

  chr2_150142767_   2351 TGCAAATGCAAGCTATGAAATGGGA-AAAATATTTGCAAATCACATATCT 2399
                           v   vi   v i iii       -                 i      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_150142767_   2400 GACAAAGAACTGCTATCTAGAATATATAAATAATTTTCAGAACACACCAG 2449
                           i  i i   vv    i            v  i i i v   v  vi i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_150142767_   2450 TAAACA---AAATACATC--ATTAGAAAATAGG--AAAAATATGAATAGA 2492
                             v ---     - i --   ?i     i  --  ii  v        
  L1M4_orf2#LINE/    792 TAAAAAGACAAATA-ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_150142767_   2493 CATTTCACCAAAGAAGATAACCAGATGGCAAATAAACACATGAAAACAT- 2541
                               v            vv  i     v     i          v  -
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_150142767_   2542 -TTAACATCATTAGCCAT 2558
                         - i       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (132 / 70)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.24 (56 / 25)  


2946 26.25 1.66 1.11  chr2_150176548_150183188.rev     5247  6149 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150176548_   5247 TGACAAAACATTCCATGTTCATTGATAGGAAGAATCAATAATGTGCAGAT 5296
                           iv  i i  i          v   v      v i    v   vv    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150176548_   5297 GGCTATACTGCCCAGAGTAATTTATGGATTCAATGCTATTCCCATCAAGC 5346
                            v     v    i v i  i  ii       i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150176548_   5347 TACCA-CTGACTTTCTT-CAGAGAATTAGAAAAAAACT-ACTTTAAATTT 5393
                          v   -   v    i  -    -    i--- v  i  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAGCTGATCCTAAAATT 146

  chr2_150176548_   5394 CATATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAA 5443
                                  viiv  ii  v  viv        i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_150176548_   5444 ACAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTGCAAG 5493
                          v       i      vv   ii  v  ii i      viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_150176548_   5494 TCTACCATAACCAAAACAGTATGGTACTGATACCAAAACAGATATATAGA 5543
                         v    vi   i   i     i        ii iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_150176548_   5544 CCAATGAAACAGAACAGAGGCCTCAGAAATAATGCCATACATCTATAACC 5593
                         i     i  i    iv   ivii         vv        i   iii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_150176548_   5594 ATCTGATCTTTGACAAACCTGACAAAGACAAGCAATAGGGAAAGGGT--T 5641
                          vi    i  i     ivv  v   iiv  vv    i       ii -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_150176548_   5642 CCATATTAAATAAACGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAA 5691
                          -- v  v  i   i    i     v      v  ?   i     i  i 
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_150176548_   5692 CTGAAATTGCACCCCTTCGTTATACCTTCTACAAAAATTAACTCAAGATG 5741
                         v    i   v      v v i i   v v                 i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_150176548_   5742 GATTA-AGACTTAAACATAAAACCCAAAACCATAAAAACTCT-AGAAGAA 5789
                            i -    i    ii   i v i     i      -    -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chr2_150176548_   5790 AACCTAGG--TAATACCATTCAGGACACAGGCATGGTCAAAGACTTCATG 5837
                            v    --   - i -   iv   viv  vv i v   v ii   v i
  L1M4_orf2#LINE/    544 AACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_150176548_   5838 ACTAAAACACCAAAAGCAGTGGCAACAATAGTTAAAATTGACAAATGGTA 5887
                         iv  vi            vvi       v  vv     v  i    v v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_150176548_   5888 TCTAATTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 5936
                         ii v  i   -     i -   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_150176548_   5937 GTGAAGAGGCAATCTACAGAATGAGAGAAAATTTGTGCAATCTATTCATC 5986
                              i  i   i i        i        v v     vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_150176548_   5987 TGACAAAGATCTAATATCCAGAATCTACAAGGAACTTGAACAAATTTACA 6036
                            i  i iv  vi          v  i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_150176548_   6037 AGAAAAA---AAA-AACCCA-TCTAAAAGTGGGCAAAGGATATGAACAGA 6081
                          v     ---   -      - i?    i            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_150176548_   6082 CACGTCTCAAAAGAAGATGTTTATGTGGCCAACAAACATACGAAAACAAG 6131
                           iv    v         i vi vi       i  i  i i     v v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_150176548_   6132 TTCATCATCATTGGTCAT 6149
                         i   v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.39 (25 / 18)  


3050 27.37 0.88 0.66  chr2_150183502_150189928.rev     5030  5935 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150183502_   5030 TGGAAGAACATTCTATTCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5079
                              ii i  i i  vi      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150183502_   5080 GGCCATACTTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5129
                            v     i     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150183502_   5130 TACCAATGACTTTCTTCACTGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5177
                          v   iivi i  i  ii v   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_150183502_   5178 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGACAAAAG 5227
                                viiv  ii  v  viv  vi    iv     i i i v i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_150183502_   5228 AACAAAGCCGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5277
                                ii     vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_150183502_   5278 TACAGTAAAAAAAAAAA-ATGGTACTGGTACCAAAACAGAGATATAGATC 5326
                                 vv  i v i-i         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_150183502_   5327 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5374
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_150183502_   5375 ATCTGATCTTTGACAAAGCTGACAGAAACAAGCAATGGGGAAAGGATTCC 5424
                          vi    i  i     i v  v  ii v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_150183502_   5425 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAAGTATAAAGCT 5474
                           v  i  i              v      v  ?   i v i v  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_150183502_   5475 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTAAAGATGGA 5524
                            ii    i    v   i     v              i v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_150183502_   5525 CTAAAGACTTACATGTTAGACCTAAAACCACCAAAACCCT-AGAAGAAAA 5573
                         ii ?    i  v    v   v       i i-     i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chr2_150183502_   5574 CCTAGGCA-ATACCATTCAGGACATAGGCAGGGGCAAGGACTTCATGTCT 5622
                          v    ?i- v i -   iv   v v  vvvi     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_150183502_   5623 AAAACACCAAAAGCA-AGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5671
                          vi            - i          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_150183502_   5672 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTGA 5721
                         v  i   v v  i i   i  ii vv    i  v   ii  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_150183502_   5722 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5771
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_150183502_   5772 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5821
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_150183502_   5822 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5871
                            i     i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_150183502_   5872 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5921
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_150183502_   5922 CCATCACTGGCCAC 5935
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3364 25.49 0.22 1.31  chr2_150199019_150201863     1436  2353 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150199019_   1436 TGGAAACACATCCCATGCTCATGGATAGGTAGAATCAGTAGTGTGAAAAT 1485
                               v i        i        v  v   v i i  v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150199019_   1486 GACCATACTGCCAAAAGCAATCTACAAATTCAGTGCAATCCCCATCAAA- 1534
                          i v     v  v   vii       i     ii        i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150199019_   1535 -TACAACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCAT 1583
                         -iv  i iii -  i  ii     v v  v  ivii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_150199019_   1584 ATGAAACTTAAAAAGAGCCTCCATAGCCAAAGCAAGACTAAGCAAAAAGA 1633
                            i  v vv  ii  v  vvv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_150199019_   1634 ACAAATTTGGAGGCATAACATTACCTGATTTCAAACTATACTATAAGGCC 1683
                              v       vv v   i v  ii        viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_150199019_   1684 ATAGTCACCAAAACAGCATGTTACTGGTATAAAAATAGGCACACAGACCA 1733
                          i   v i   i    ii  v      i    ii    i  i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_150199019_   1734 ATGGAACAGCATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAAC 1783
                               i  v  v    ii               v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_150199019_   1784 TGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTA 1833
                             i  i     i vviv   i v   vv i         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_150199019_   1834 TTCAACACATGGTGCTGGGATAATCGGCTAGCCACATGTAGGAGAATGAA 1883
                                v            i  ii  v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_150199019_   1884 ACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTA 1933
                         ii    i  ii i   v    v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_150199019_   1934 AGGACTTAAATCTAAGACCTGAAACTATAAAATTTCTAGAAGATAACATT 1983
                         ?i   i     v     v  i           i ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_150199019_   1984 GGAAAAACCCTTCTAGACAATGGCTTAGGTAAGGATTTCATGACCAAGAA 2033
                           ?iv  vi    vv   vv   v     i  v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_150199019_   2034 CCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATTA 2083
                         v         v v    i    iv   i   i   iv v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_150199019_   2084 AACTGAAGAGCTTTTGCACGACAAAAGGAACAGTCAGCAGAGTAAACAGA 2133
                           v v  i i      ii vv    i iv  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_150199019_   2134 CAACCCACAGAGTGGGAGAAAATCTTCACGATCTATACATCTGACAAAGG 2183
                                    i           v  ii i vii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_150199019_   2184 ACTAATATCCAGAATCTACAACGAACTCAAACAAATCAGTAAGAAAAAAA 2233
                            vi          v  i  v      vv    v   i   v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_150199019_   2234 AAACAAAACAAATAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGAC 2283
                         --------       i  v  i?    i     v     iv         
  L1M4_orf2#LINE/    800 --------CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_150199019_   2284 AATTCTCAAAAGAAGATACAAAAATGGCCAACAAACATATGGAAAAAAAA 2333
                          v     v          i v          i  i  i   ---    i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG---AAAAGA 888

  chr2_150199019_   2334 TGCTCAACATCACTAATGAT 2353
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (135 / 95)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 3.50 (14 / 4)  


3237 26.64 0.55 0.55  chr2_150227361_150233739.rev     4987  5887 (492)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_150227361_   4987 ACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAATGGCCATA 5036
                          i  i     i      i v      v i        v  i     v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_150227361_   5037 CTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAAT 5086
                           v     iv i  i  i        i  v     i     iv v   ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_150227361_   5087 GACTTTCTTCACTGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAA 5134
                         vi i  i  ii v   -   -- v  i  - iii    i           
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_150227361_   5135 CCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGAACAAAG 5184
                         viiv  ii  v  v v  vi    iv     i i ivv i          
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_150227361_   5185 CTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGGCTACAGTA 5234
                         i      vv   vi  v  ii i      viv        i         
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_150227361_   5235 ACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAA 5284
                          i   i    ii         i iv ii i   v                
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_150227361_   5285 CAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACTATCTGAT 5332
                         i    i--    i  --        vv iii i  i  iiiii vi    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_150227361_   5333 CTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCTATTTA 5382
                         i  i     ivv  vv  i v  vvv           i  vvi  v  i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_150227361_   5383 ATAATTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTG 5432
                          i  v           v      v  ?   i   i i  iiv    ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_150227361_   5433 GATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAAAGA 5482
                           i    v   i     v                   i      i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_150227361_   5483 CTTACATGTTAGACCTAAAACTATCAAAACCCT-AGAAGAAAACCTAGGC 5531
                          i  v    v   v          -     i  -          v    ?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAGGN 552

  chr2_150227361_   5532 ATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACC 5581
                         i v viv   iv   v v  vv i     v ii   v ivv  vi     
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_150227361_   5582 AAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAAC 5631
                                vvi          vv     v  i    v   ii v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_150227361_   5632 TAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAA 5681
                          v  i i   i  ii vv    i  v    i  vv i      v  i   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_150227361_   5682 CCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCT 5731
                           i   i             v  i    vii ivi      i  i  i  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_150227361_   5732 AATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAA 5781
                         vi          v  i  v      vv    v iv i  v     i    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_150227361_   5782 ACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCTCAAAA 5831
                          i     v  i?    i    ii      v    i     i     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_150227361_   5832 GAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACT 5881
                              i  vi viii     v  i          i       v     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_150227361_   5882 GGCCAT 5887
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.01 (7 / 901), avg. gap size = 1.43 (10 / 7)  


3048 27.64 0.55 0.55  chr2_150320149_150326513.rev     4966  5873 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150320149_   4966 TGGAAGACAATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5015
                              iivv  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150320149_   5016 GGCCATACTGCCCAAGGTAATTTACAGATTCAAGGCCATCCCCATCAAGC 5065
                            v     v     iv i  i           v  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150320149_   5066 TACTAATGACTTTCTTCACAGAATTAGAAAAATCTACTTTAAAGTTTATA 5115
                          v i iivi i  i  ii     v v  v  iiiv iii    i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_150320149_   5116 TGGGTCCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5165
                            ivviiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_150320149_   5166 CAAAGCTCGAGGCATCACGCTACCTGACTTCAAATTATACTACAAGGCTA 5215
                              i v    vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_150320149_   5216 CAGTAACCATAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5265
                               i  vi    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_150320149_   5266 TGGAACAGAAC--AGAGCCCTAAGAAATAATACTACACATCTACAACTAT 5313
                              i    i--    i  --        vv i i    i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_150320149_   5314 CTTATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACAATTCCCT 5363
                         i v  i  i     ivv  v   i v  vvv          v   vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_150320149_   5364 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGGCATATGAAGAAAGCTGA 5413
                         v  i  i              v      v  ?v  i   v i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_150320149_   5414 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5463
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_150320149_   5464 AAAGACTTAAATGTTAGACCTAAAACCATCAAAACCCT-AGAAGAAAACC 5512
                          ?    i       v   v       i  -     i  -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chr2_150320149_   5513 TAGGCA-ATACCATTCAGGATATAGGCATGGGCAAGGACTTCATGTCTAA 5561
                             ?i- v i -   iv  iv v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_150320149_   5562 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5611
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_150320149_   5612 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5661
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_150320149_   5662 AGGCAACCTACAAAATGGGAGACAATTTTTGCAATCTCCT-CATCTGACA 5710
                           i     i   i         v   v       -v  v -i      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATA 745

  chr2_150320149_   5711 AAGGGCTAATATCCAAAATCTACAATGAACTCAAACAAATTTACAAGAAA 5760
                          i  i  vi      i   v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_150320149_   5761 AAAACAAACAACCCCATCAACAAGTAGGTGAAGGATATGAACAGTCACTT 5810
                           i     i     v  i? v  i i  ii      v    i  v  i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_150320149_   5811 CTCAAAAGAAGATATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5860
                            v           vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_150320149_   5861 CATCACTGGCCAG 5873
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (139 / 108)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


1126 27.27 8.78 4.01  chr2_150444056_150445651.rev      458  1106 (489)    L1M4_orf2#LINE/L1      229   908 (0)  

  chr2_150444056_    458 TTCAATGAACTTAATGTAAAACAATAGAAATTGCT-CAAT------CTG- 499
                              --      v ii   i v i  v   iivv-  i ------   -
  L1M4_orf2#LINE/    229 TTCAA--AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_150444056_    500 ---AAGGACAGAGAGAAATAGACCTTAAAAAAAACAAAATAATCAGATAC 546
                         ---     i   v v --    i ---  vii  i i   -- v   -ii
  L1M4_orf2#LINE/    277 CATAAGGATAGACATA--TAGATC---AATGGAATAGAAT--TGAGA-GT 318

  chr2_150444056_    547 CCAGAAA----CCTATAGATCCATAAGAAATATCAAATATATGTATTATA 592
                                ----  i   v  ii  ii------    v i-  v viv i 
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGG------TCAATTG-ATTTTCGACA 361

  chr2_150444056_    593 AGGGTACCAAAAGTA------GAGGAGAAAAAGGGTGTGACTAACA---G 633
                              i    i vi ------ i   -  i  vi  v vvii    --- 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGA-AAGAATAGTCTTTTCAACAAATG 410

  chr2_150444056_    634 GTATTTGAAGAAACACTGGATATCCATTGGCAAAAACATGACTCTT--CA 681
                           ii v i v  ---       ?   ivv      iv    vvi v-- v
  L1M4_orf2#LINE/    411 GTGCTGGGACAA---CTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_150444056_    682 CCTAAATGACAACCTTATACCAAAATAAACTCTAAATGGATTATTGATTT 731
                             vv v   -  v     v     v     v        i ?v  ii 
  L1M4_orf2#LINE/    458 CCTACCTCACA-CCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_150444056_    732 AAATAGAAATTATAAAACTACAAA-CTTTTAGAATATAATGTAGGAGAAA 780
                             iv  ivvv        i   -  i      v v  ii    ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_150444056_    781 ATCTGTATGACCTT----TAG-CAGGGAGTTTTTAGACATGTTATCAATA 825
                             vii       ----   -  iv iv  i     i   vi i   v 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_150444056_    826 GCAAAATTTATTTTTTAAAAAATCAGTTGATTAGATTTCATCAAAGCTAA 875
                            v  viv ivvvvv       vii vi   i  i         ii   
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_150444056_    876 AAG--TTTGT--CTCAGGAAAGACACTGTTAAGAGTATGAAAACACAAAC 921
                           i--     --i   --  i      i i    ivi      v    v 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCA--AAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_150444056_    922 TAAAGACTAAGAGAAAATATCT------CAC-----------GAGACCTA 954
                         i v   v ii          i ------  i----------- i   i i
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_150444056_    955 TATCTAGAGCATGTAAAGAACTCTAACAAAACTTGAAGATTAAGAAA-AA 1003
                             i   ii  i           v    --  ii vi  v  i i -  
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAA--CTCAATAATAAAAAGACAA 802

  chr2_150444056_   1004 ATAA---AATTTTAAAATAGACAAAAGACACGATGAGATATTTCTTCAAA 1050
                             ---    ?v     i i    i  ivi  vv   i      i    
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_150444056_   1051 GAAGGTATACAGATGTCAAATAAGCACATGAAAAGATATTCATCACTAGC 1100
                             i      i   v v                   ii   v  ii ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_150444056_   1101 CATTAG 1106
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.37 (100 / 73)
Gap_init rate = 0.04 (28 / 680), avg. gap size = 2.96 (83 / 28)  


 965 26.03 1.59 0.63  chr2_150453565_150458398     3054  3368 (1466)  C L1M4_orf2#LINE/L1   (0)   908   591  

C chr2_150453565_   3368 AAAGATGACA---AAAGCAATCA--CAACAAAGGCAAAAATTGACAAATG 3324
                          i v      ---      --  --       i v      v  i    v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATT 638

C chr2_150453565_   3323 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACA 3274
                            ii v  i   v v  i i   i  ii vv    i  v        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

C chr2_150453565_   3273 GAGTAAACAATCAACCTACAGAATGGGAGAAAATTTTTGCAAACTATGCA 3224
                         i   i  v iv     i                 v        ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

C chr2_150453565_   3223 TCTGACAAAGGTTTACTATCTAGCATCTATAAGGAACTTAAACAAATCTA 3174
                              i  i  vi vv    i  v  v     i     ivv    v  v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

C chr2_150453565_   3173 CAAGAAAAAAACAAACAACCCCATTAAAAAGTGGGCAAAGACCACAAACA 3124
                         i  v     i     i     v   ?    i         ivivii  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

C chr2_150453565_   3123 GACACTTTTCAATAGATGACATACATGCAGCCAACAAACATACAAAAAAA 3074
                             i  i  v v   v  i     viii     i  i  i ii    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

C chr2_150453565_   3073 AGCTCAATATCTCTGATCAT 3054
                         v      i   v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (48 / 33)
Gap_init rate = 0.01 (3 / 318), avg. gap size = 2.33 (7 / 3)  

 930 30.97 11.32 3.98  chr2_150453565_150458398     3550  4353 (481)    L1M4_orf2#LINE/L1       36   898 (10)  

  chr2_150453565_   3550 TGATATTGTAAAGATGTCATTTCTTCTCAAAATGATCTATAGTATCTATG 3599
                          i       v      v  v v  i i    v       i  vv  v i 
  L1M4_orf2#LINE/     36 TAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACG 85

  chr2_150453565_   3600 TATTCCC-ATAAAATACTTCAATAATTTTTATGTTTGTATGTATGTTGTA 3648
                         i v    -  v   - iii  iiviii   ---    i vi---------
  L1M4_orf2#LINE/     86 CAATCCCTATCAAA-ATCCCAGCTGCCTTT---TTTGCAGA--------- 122

  chr2_150453565_   3649 TGTCACTTAACATGCTAATTCTAAAA--CATA--GAAACATACTGAACTA 3694
                         ---- v  i   v   i  i      --    --    iii vv i  iv
  L1M4_orf2#LINE/    123 ----AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr2_150453565_   3695 AAATTAGCTGACATA--CTTATATAGTGGAAAACAAGACAGAAGGACT-- 3740
                          i v    ii v i --   iv v i- i i     iiiv i      --
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAA-GAAGAACAAAGTTGGAGGACTCA 217

  chr2_150453565_   3741 ---TTCTGGTGAAGATATTAAGAATTAGTATACAATT-------TCAGGC 3780
                         ---   ivi-----  v i  i v   v  i v ii -------   i v
  L1M4_orf2#LINE/    218 CACTTCCCA-----ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_150453565_   3781 TAATGTGGTATTTATTCAAGTATTGATAAATAGGCTAGTAGAATAAAATA 3830
                         i i       i viivi   v  v  i v    iii i i     i   v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_150453565_   3831 GAGAGCCCAGAAACAGACTGAAACACAAATGCACACTTAATTCATTACAA 3880
                              i       i i  iv v   ivv   vv  v  i   iviv    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_150453565_   3881 ATTTGCTAGTGTAGAGCA--------GTACAGAGT-TTCTTTTCTATAAA 3921
                         ivv   i ----   v  -------- v v   i -v       v i   
  L1M4_orf2#LINE/    363 GGGTGCCA----AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_150453565_   3922 TGGTTTTGAGTAAATTGAATATCAATATAGAAAATA-TAAATTTG-ATCT 3969
                             vi  i vv  i  i   ? v i  iv    v - i  v   - i i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_150453565_   3970 TTACCATATACCATAAATGAACATTAATTTCAGAAAGATAGTAAACTTAA 4019
                         i    vi i      v ii  v     i iv i vi   vi? i  i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_150453565_   4020 TTGTAAAAAACAAA-TTATG---CTTCCAGAAGATAA--TAGGAAAAAGT 4063
                         v     i ivi   -i   i---  iii      v  --    ?iv  i 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_150453565_   4064 GCTTTATTCCCTTCAGT-AGAGAA---------AGATA----ACCA---- 4095
                         -   ii vv    vi  -  iv  ---------     ----    ----
  L1M4_orf2#LINE/    559 -CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_150453565_   4096 ---------CAAAGGAAAAGATTTATTAATT------TATCTAAATTAAA 4130
                         ---------    i     i  vv  v    ------i   v        
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_150453565_   4131 ATTATTTATTTATCAAAAAATAC-----AG-----GAAAAAGTAAGTTCT 4170
                          viv   i viv     ii i  -----  -----     iii  viivi
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_150453565_   4171 GAAAGGAGAAAAGATATTTCCCA--CAAGTATATCTGATAAGTGGCTTTT 4218
                         ii  v i  i  i      v v --  --             v i   --
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCA--TATATCTGATAAGGGACTT-- 753

  chr2_150453565_   4219 GTGTCCTGAATATATATAGAATGAATACAAATTGGTAAGCAAAATATAGA 4268
                           i   v         v    ivvv     v iii   vv    v i i 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_150453565_   4269 TAAC--AGTGAAAAAATTGG--AGCGACTTGAACAGACATTTCAC---AA 4311
                             -- i v?      v  -- iv  i     i         v --- i
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_150453565_   4312 AAGATGTACAAATGGCCAGCAAGGTTAGGAAA---TGGCCAATAT 4353
                              i            ii   vvi v    ---  vi   i  
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.04 (34 / 863), avg. gap size = 3.62 (123 / 34)  


3120 28.13 0.89 0.33  chr2_150472900_150479275.rev     4982  5884 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150472900_   4982 TGGAAGAGCATTCCATGCCCACGGATTGGAAGAATCAATATCATGAAAAT 5031
                              iiii  i     ii  i           v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150472900_   5032 GGCCATACTGCCTAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5081
                            v     v  i  iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150472900_   5082 TACCAATGACTTTCTTCACAGACCTGGAAAAAACT-ACTTGAAAGTTCAT 5130
                          v   iivi i  i  ii    vv v  v  i-  - iiiv   i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_150472900_   5131 ATGGAACCAAAAAAGAGCCCACATTGCCAAGTTACTCCTAAGCCAAAAGA 5180
                               viiv  ii  v  viv  v     ivi v  i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_150472900_   5181 ACAAAGCTGGAGGCATTATGCTACCTGACTTCAAACTATACTACAAGGCT 5230
                               i      vv i ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_150472900_   5231 ACAGTAACCATAACAGCATGGTACTGGTACCAAAACAGAGATACGGACCA 5280
                                i  vi    ii         i iv ii i   v   ii  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_150472900_   5281 ATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACTA 5328
                               i    i--    i  --        vv   i    i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_150472900_   5329 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5378
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_150472900_   5379 CTTTTAATAAATGGTGCTGAGAAAACTGGCTGGGCATATGTAGAAAGCTG 5428
                         i   i  i           i  v      v i?v  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_150472900_   5429 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 5478
                           ii    i    v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_150472900_   5479 TAAAAACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5528
                         i ? i  i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_150472900_   5529 TAGGCGATACCCTTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5578
                             ? vv vi    iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_150472900_   5579 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5628
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_150472900_   5629 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5678
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_150472900_   5679 GGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5728
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_150472900_   5729 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTA-CAAGAAAAA 5777
                           i  vi          v  i         vv    v i -i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_150472900_   5778 AACAA----CCCCATCAAAAAGTGGATGAAGGATATGAACAGACATTTCT 5823
                         i    ----   v  i?    i   iii      v    i          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_150472900_   5824 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5873
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_150472900_   5874 TCACTGGCCAT 5884
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.58 (153 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


3052 25.96 1.43 1.54  chr2_150516364_150522223.rev     4460  5368 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150516364_   4460 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4509
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150516364_   4510 GGCCATACTGCCCAAAGTAATTTATAGATTTAATGCTATCCCCATCAAGC 4559
                            v     v      v i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150516364_   4560 TACCC--TTGACTTTCTT-CACATAATTAGAAAAAAACTA--CTTTAAAT 4604
                          -   --i  v    i  -  v -    i--- v  i  i-- i v    
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAGCTGATCCTAAAAT 145

  chr2_150516364_   4605 T-ATATGCAAAACCATAAAAGAGCCCATATAGCCAAGACAATCCTAAGCA 4653
                          -     v   --iii  ii  v  viv        i      i i iv 
  L1M4_orf2#LINE/    146 TCATATGGAAA--TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_150516364_   4654 AAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTGTGCTAC 4703
                          i          i      vv    i  v  ii i      viv i    
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_150516364_   4704 AAGGCTACAGTAACCAAAACAGCATGGCACTGCTACCAAAACAGATATAT 4753
                           i          i   i    ii   i    vi iv ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_150516364_   4754 AGACCAATGGAACAGAACAGAGGCCTCAGAAATAACGGCACACATCTACA 4803
                            i        i    iv   ivii         vvv  i    i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_150516364_   4804 ACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT 4853
                         ii  vi    i  i     ivv  v   i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_150516364_   4854 TCCCTATTTAATGAATGGTGTTGGAA-AACTGGCTAGCCATATGCAGAAA 4902
                         vvi  v  i  ii       i   i -      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_150516364_   4903 ACTGAAACTGGATCCCTTCCCTTACACCTTATACAAAAATTAACTCAAGA 4952
                          v    ii    i    -v   i     v                   i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_150516364_   4953 TGGATTAAAGTCTTAAAGGTGTAAGACCTAAAAACCATAAAAACCCTAGA 5002
                              i ?  v i    --       v      - i      vi i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAA--TGTAAGAGCTAAAA-CTATAAAACTCTTAGA 539

  chr2_150516364_   5003 AGAAAACTCAGGCAATACAAT--TCAGGACACACGCATT-GGCAAAGACT 5049
                                vi   ?i-  -   --  iv   - vi vi  -     v ii 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNG-TA-AATCTTCGTGAC-CTTGGGTTAGGCAATGGTT 586

  chr2_150516364_   5050 TCATGAATAAAACACCAAAAGCAATTGCAACAAAAACCAAAATTGACAAA 5099
                           v ii   vi            vvv         ivv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_150516364_   5100 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAGCTATCAT 5149
                          v   ii v  i   v v  i i   i  ii vv       vi      v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_150516364_   5150 CAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGGAATCTATT 5199
                         v i      v  i     i                 v    v  vii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_150516364_   5200 CATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATT 5249
                         i      i  i  i  vi          v  i        ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_150516364_   5250 TACAAGAAAAAGA---ACAACTTCATCAATAAGTGGGGGAAGGATATGAA 5296
                         v i  v       --- i   iiv  i? v  i    vi      v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_150516364_   5297 CAGACACTTCTTAAAAGAAGACATTTATGTGGTCAACAAATATATGAAAA 5346
                         i     i    iv        i  vi vi   i   i  ii i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_150516364_   5347 ACAGTTCATCATCACTGGTCAT 5368
                         ivv i   v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (142 / 90)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.50 (27 / 18)  


3322 26.10 0.55 0.55  chr2_150531980_150538244     4866  5773 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150531980_   4866 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4915
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150531980_   4916 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4965
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150531980_   4966 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTGAAAGTTC 5012
                          v   i-       i  -i     -   -- v  i  - iiiv   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_150531980_   5013 ATATGGAACTAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5062
                                 v iv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_150531980_   5063 GTACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGC 5112
                          v      i      vv       v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_150531980_   5113 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5162
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_150531980_   5163 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCCTATCTACAAC 5210
                                 i    i--    i  --        vv  iivi  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_150531980_   5211 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5260
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_150531980_   5261 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5310
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_150531980_   5311 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5360
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_150531980_   5361 ATTAAAGACTTAAACGTTAGGCCTAAAACCATAAAAACCCTAGAAGAAAA 5410
                           i ?    i    i  v  iv       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_150531980_   5411 CCTAGGCATTACCCTTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5460
                          v    ?i v vi    iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_150531980_   5461 AAACACCAAAAGCAATGGCAACACAAGACAAAATTGACAAATGGGATCTA 5510
                         vi            vvi      v    v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_150531980_   5511 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5560
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_150531980_   5561 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACCCATCTGACA 5610
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_150531980_   5611 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5660
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_150531980_   5661 AAAACAAACAACCCCATCAAAAAGTGGACGAAGGATATGAACAGACACTT 5710
                           i     i     v  i?    i   i i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_150531980_   5711 CTCAAAAGAAGACATTTATGTAGCCAAAAAACACATGAAAAAATGCTCAT 5760
                            v        i  vi vi i     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_150531980_   5761 CATCACTGGCCAT 5773
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1893 23.96 7.51 5.31  chr2_150548559_150550301      482  1253 (489)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr2_150548559_    482 AGAAATGAATAATATAGTAGATT-TAAATTTTACCTGGAAAGGTAAAG-- 528
                               --- i i -  iv   i-    v  i iv      v i  i --
  L1M4_orf2#LINE/    120 AGAAAT---TGACA-AGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_150548559_    529 --TTGAATAGTTAAAACACTTCTCAGAAAGA-GAA--AAGTGGGAAGTAT 573
                         --iv      ii      v ii v i     -   --    v   i vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_150548559_    574 CATTCTACTCAGTTTGAAGAATTATTAGATAGCTGTAGGTAA-CAAGACT 622
                           iv  v i  i   v  i v   i  v v    ii  -   -      v
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG-TAATCAAGACA 264

  chr2_150548559_    623 GTGTAGCATTTGCAAAAGGATAGACATG--GGTCAATGGCACAGAATAGA 670
                             i i i v   v            i-- i       v i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_150548559_    671 GAACCCATAAACAGCTCCACACAAGTACAGCCAACTGATTTTTGATAAAA 720
                           ii   v   i ivi   i   vv  ii i   i       i  i  ii
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_150548559_    721 GTGCAAAAGCAATTTAAAGGATGAAGGATAATTTTGTCAATAAATGTTAA 770
                             v  ii v   i  v  ivi   i   i i  v    i     v iv
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_150548559_    771 TGGAAAAATTGGATATCCATA-GC-------TGTCTCCCCTCCCTGCTAA 812
                            i v  i      ?   i -  -------  ---------------  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATG---------------AA 449

  chr2_150548559_    813 CCTCCACAACCCTGCCTC-CACAAAAGGAATCTAAACCTCAGGAAAAATT 861
                         vi vv  --    i    -   v --------  v  ------       
  L1M4_orf2#LINE/    450 GTTGGAC--CCCTACCTCACACCA--------TATAC------AAAAATT 483

  chr2_150548559_    862 AACTCAAAATGGATCATAACTTTAAGTGTAA-------AACTATAAAGCT 904
                                         ? ivii   i     -------         i  
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_150548559_    905 TATAGAAGATACCATAGGA-TAAGCTCTTCAGGACTTATGTCTT-GGTGA 952
                         iv       v v      ?-   i-     iv   i -  vv  -  ii 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCT-TGGGTTAGGCAA 581

  chr2_150548559_    953 CAAGTTCTTAGACATGACATCAAATGCAAGATCTATAAAAGAAAAGTATT 1002
                         iiiv        i      i    v   vi v v i         i-  v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATA 630

  chr2_150548559_   1003 CATAAATTGTTCTTCATCAAAATTAAAAACTTCTGCTG-TGCAAAAGACT 1051
                         v        vv                     i  -  - v    i   -
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGAC- 678

  chr2_150548559_   1052 ATGGTGAGGAAGATGAAAGGACAGGG-ACAGACTAGGAGAAAATATATGC 1100
                          ivi v i   ii     i    ivv-     v i           v   
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_150548559_   1101 AAATCACATATGTG-T---GGAATTGT--CCAGA---------------- 1128
                               i    v  - ---   v    --     ----------------
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_150548559_   1129 -----CTCAACATTATGGCAATAAACAATCCAATTAGAAAATGAGCAAAA 1173
                         -----     i v  viivi i   i  i      ?i      i     i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_150548559_   1174 TATATAAAGGGATATTTCACCATAGAGGATACAAAAGTGTCAAATAAGTA 1223
                         v  v i  vi  i     v   v   i    i v  i  v v      i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_150548559_   1224 CATGAATAGATGTTCAACATGACTAGCCAT 1253
                               v     i       v ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (105 / 76)
Gap_init rate = 0.04 (30 / 789), avg. gap size = 3.30 (99 / 30)  

 233 24.10 3.61 3.61  chr2_150548559_150550301     1320  1402 (340)    L1M4_orf2#LINE/L1      787   869 (39)  

  chr2_150548559_   1320 AATAGTAGTAAAATGCTAATAACGTCATTTTTAAAACGGGCTAAAAGCTG 1369
                             i  --    vi v      -i  v  ?v    i    v  iiii v
  L1M4_orf2#LINE/    787 AATAATA--AAAAGACAAATAAC-CCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_150548559_   1370 AAATGGAAATTTCTCCAAAAAAGACATAC---TGGC 1402
                         i   i  v           i    i    ---    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 2.00 (6 / 3)  

 263 15.79 0.00 0.00  chr2_150548559_150550301     1686  1742 (0)    L1M4_orf2#LINE/L1      850   906 (2)  

  chr2_150548559_   1686 AAAAAAGACATACTAATGGCCATCCAATACATAAAAAGATGCTCAACATC 1735
                            i    i    v        viv ii    i                 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_150548559_   1736 ACTAATC 1742
                          ??????
  L1M4_orf2#LINE/    900 AZZZZZZ 906

Transitions / transversions = 2.00 (6 / 3)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.00 (0 / 0)  


 874 29.88 9.76 3.73  chr2_150572287_150574071      478  1307 (478)    L1M4_orf2#LINE/L1       29   908 (0)  

  chr2_150572287_    478 GAAGAGTTA----TGTCAAATTTTGAGAATTCTCTCCCAAATCTATCTAT 523
                              v   ----   i  iv -- iv   v   -       iv     i
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGAT--GGCAATACTC-CCCAAATTGATCTAC 75

  chr2_150572287_    524 GAAATTAATGAACCCCCTAC--AAATCTAAGCAGAATTATTTAATGAAAA 571
                         ii v i  i v vi     i--     iv   v vv  v   ivv    v
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr2_150572287_    572 TGAGTAAATGGATTCTAAAATGTATATGGAAA-ACAAAGAACCGAGAACA 620
                            -i  iiv   i       vi         -i   i i   v    i 
  L1M4_orf2#LINE/    126 TGA-CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr2_150572287_    621 GCAAAGATAATATTGAAGAAGA-GAATAAAAAATCAGGACTTAAA----- 664
                           v  i i   v     i    -   i   ivvvv      i v -----
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr2_150572287_    665 -AATAGATAAGC--AG-ATAAAGATATAATAATTAAACAAATATACTATT 710
                         -   vvvv  i -- v- i    v  i i    i  ivv i i iv  i 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr2_150572287_    711 AGTGTGAGAATAGACA-A-AGACCCAAAGGAACAGAATAGAGAGGATGAA 758
                         i ii i  i       - -   i -  v    i     v     vviii 
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATC-AATGGAATAGAATTGAGAGTCCAGA 323

  chr2_150572287_    759 AACTAACCCAAGCGTGCGTGAATACTTGGTTTATGACAAAATAGT-TCAG 807
                           iv      vi i vii  ivi v   i   vi     ii--  -i  -
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG--GTGCCA- 370

  chr2_150572287_    808 CAGAGCA----ATGAAGAAAGAA-AGTATTTTCAATAATAT--------- 843
                         -   v  ----   ii       -   v       i  -  ---------
  L1M4_orf2#LINE/    371 -AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA-ATGGTGCTGGG 418

  chr2_150572287_    844 -CATTTGGGTATTCAAATG--AAAAAATAAAATTTAACCATTGTTTCGTA 890
                         -  vi   i  ?i  v   --   i   i  i  vi   vi iii  ii 
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_150572287_    891 ACACTAGTTTGAAACTAATGTTTCAAACATTAGTTCTATTTAAACTCTAA 940
                         v  -  vvivi   i   i---     -  -i v  - ?-- i  -    
  L1M4_orf2#LINE/    469 CCA-TATACAAAAATTAAC---TCAAA-AT-GGATC-AW--AGAC-CTAA 508

  chr2_150572287_    941 CTGAGAAAGGTAAAAACAATGCAGACT-TTAAAAAGTTACTTAGGA-TAA 988
                         v  vi i  v     - v  i- i   -   i  iivv  v    ?-   
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAA-CTATA-AAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_150572287_    989 TATGTGTCTGTTGTTGGGATAAAAAAATG------CAAATATAATA---- 1028
                         -  v viv  viv     v  iiv  -  ------i i    i i ----
  L1M4_orf2#LINE/    557 -ATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAA 604

  chr2_150572287_   1029 -------ATCATCAAGGGAAGGACT-GACATTTTGTCAATATATTAAAAT 1070
                         ------- v  v   ii   ii v -  i vv   v- v vi  i     
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG-ACTTCATCAAAAT 653

  chr2_150572287_   1071 TAAGAACCTGTCTTTATCAAAAGATACCACTAAGAAGGTGAAAAAGTAAG 1120
                            i   i v v viv     i  i  i ii     i       iii  v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_150572287_   1121 TCAAAGAGGGGGAGAGAATATTTGTAG--CATATGTAATCTAAAAAAGGA 1168
                         i  v   iv      i        i i--     ---    i v  i   
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATAT---ATCTGATAAGGGA 750

  chr2_150572287_   1169 CTGTTCTTCAGAAT-----------TCCTTCAAATCAGTAA---GAAGGT 1204
                           vv v i      -----------  i v   v   i   ---i   ii
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_150572287_   1205 AGATAACCCAATAGAAAAATGGGCGAGAAACTTGACTA----TTGTT--- 1247
                          i          v?          i iii i    v  ----  vi ---
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_150572287_   1248 -AGAAGCTTATTCAAAAGGTCAACAAATATATGAAAAAAATCCCCCAACT 1296
                         -     v -  v    v  i   i  ii i       i --iv i    v
  L1M4_orf2#LINE/    851 AAGAAGAT-ATACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAACA 897

  chr2_150572287_   1297 TCTTTAATCAT 1307
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.05 (46 / 880), avg. gap size = 2.43 (112 / 46)  


 997 25.05 9.68 4.55  chr2_150591920_150596420      405   931 (3570)    L1M4_orf2#LINE/L1      178   731 (177)  

  chr2_150591920_    405 AAAACAA----AAAAACAAAAAAACAAAA--AAAAAACCCGCATACTTTA 448
                                ----i    - i  i      i--ii ii  i i  iviiii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAA-AGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_150591920_    449 AGAGAATTAAAAAC--AGTATAGGAATTA-AGTAA--AAGATAAATATAT 493
                          v----  v     -- v  i i- ii  -     --    i i----- 
  L1M4_orf2#LINE/    227 AT----TTCAAAACTTACTACAA-AGCTACAGTAATCAAGACAG-----T 266

  chr2_150591920_    494 GAGGAAATATTGGCAGTAGGAGAGGTATGTAGATCAATGTAACAGAATAA 543
                          v  ---  i     vv    v  ii  i          v  i     vi
  L1M4_orf2#LINE/    267 GTGG---TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_150591920_    544 TGACTCTAAAAATAGACCTAGA----------------AGTTTC----AG 573
                         v  v  i i     i   i v ---------------- v    ----  
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_150591920_    574 AGTG--------ATTCAATAGGGAAAAGAATAGTCTTT-CAATAAATGGT 614
                         i   --------       i      -           -   i       
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGT 412

  chr2_150591920_    615 GCTAGAATAATTGGACATTTGTATGGAAAATTACGACCTC---CCTTCTT 661
                            i i i  i    i ?iiii   v    vv i  vv i---  -- i 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC--CCT 460

  chr2_150591920_    662 ACCTGGTATCATATATAAAAATAAACTCAAAACGAAT--GAGACCACCAT 709
                             vii i      i      v         i i  --?     vvv  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_150591920_    710 ATAAGAATTAAAACAATAAAATTCCCTAAAAAAAATACACACAAAAAATT 759
                         i     ii      v      i  iivi  i    i i vi?iv   vi 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_150591920_    760 TTGTGATATTGG-TTAGGCAAACATTCCTTAGCAAGAAATGCTAAGAAAT 808
                          i    iv    -        vvi  i     ---- v   vi vv   v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAG----ATATGACACCAAAA 606

  chr2_150591920_    809 GAATGAACTACTAAAGAAAAAA--GATAATGTGGACTTCATCAAAATTAA 856
                          v ii i v  v          --     vv                   
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_150591920_    857 AA-CTTCAGCTCTTGAAAG-ACACTG-CAAGGAAATTTGAAAAGGCAAAC 903
                           -   iv iv   v    -     i-    i  i --      i   v 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT--GAAAAGACAACC 704

  chr2_150591920_    904 AACTAGAATTGCAGAAAATATTAGCAAA 931
                         v  -     v v          v     
  L1M4_orf2#LINE/    705 CAC-AGAATGGGAGAAAATATTTGCAAA 731

Transitions / transversions = 1.58 (79 / 50)
Gap_init rate = 0.05 (26 / 554), avg. gap size = 2.88 (75 / 26)  

3026 26.32 2.35 0.67  chr2_150591920_150596420     2271  3163 (1338)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150591920_   2271 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTAAAAAT 2320
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150591920_   2321 GGCCATACTGCCCAAAATAATTTATAGATTCAATGCTATTCCAATCAAGC 2370
                            v     v      v i  i  i        i  v  i  v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150591920_   2371 TACCAGTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 2419
                          v    ivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_150591920_   2420 GTGGAACCAAAAAAGAACCTGTATAGCCAAGACAATCCTAAGCAAAAAGA 2469
                         i     viiv  ii  v  v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_150591920_   2470 ACAAAGCTGGAGGCATCACACTACCTGACTT-AAAACTATACTACAACAA 2518
                               i      vv       v  ii i  -      -        viv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_150591920_   2519 TATAGTAACCAATACAGCATGGTACTGGTACCAAAACAGATATACAGAGC 2568
                           i     i   v    ii         i iv ii i   i   i   v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_150591920_   2569 AATGTAACAGAAC--AGAATCCTCAGAAATAACACCACACATCTACAACC 2616
                             v  i    i--   i   --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_150591920_   2617 ATCTGATCTTTGACAAACCTGACAAAAACAAGTGATGGGGAAAGGATTCC 2666
                          vi    i  i     ivv  v   i v  vvii          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_150591920_   2667 CTGTTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATGTGCAGAAAACT 2716
                           v  i  i        i     v      v  ?   ii    i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_150591920_   2717 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTA-CTCAGGATGGA 2765
                            ii         v   i     v             -    ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_150591920_   2766 TCAAAGACTTAAATGTAAGAACTAAAACCATAAAAACCCTAGAAGAAAAC 2815
                            ?    i           i       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_150591920_   2816 CTAGGCAATACAAT--TCAGGACATAGGCATGGGCAAAGACTTCATGACT 2863
                         v    ?i-  -   --  iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_150591920_   2864 AAAACACCAAAATCAATGGCAACAA---------CTGACAAATGGGATCT 2904
                          vi         v  vvi       ---------iv  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_150591920_   2905 AATCAAACTGAAGATCTTCTGCATAGTAAAATAAACAATTATCAGAGTGA 2954
                         v      v v  i v   i  iiivvi   iv v  v  i vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_150591920_   2955 ACATGTAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 3004
                          v vii    i                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_150591920_   3005 AAAAGGCTAATATCCAGAATCCACAAGGAACTTCAACAAATTTACAAGAA 3054
                           ii i  vi          vi i  i     iiv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_150591920_   3055 AAAAA-AAAT--CCCA-TCAAAAAGTGGGTGAAGGATACGAACAGACACT 3100
                            i -    --    - i?    i    ii      vi   i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_150591920_   3101 TCTCAAAAGAAGACATTTATGTGGCCAACAAATATATGAAAAAA-ACTCA 3149
                             v        i  vi vi       i  ii i       i -i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_150591920_   3150 TGATCACTGGTCAT 3163
                         vv    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (140 / 91)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.80 (27 / 15)  

 219 23.73 12.71 0.00  chr2_150591920_150596420     3899  4016 (485)    L1M4_orf2#LINE/L1      776   908 (0)  

  chr2_150591920_   3899 TCCCAGAACTTAA-AGTAAAATAACAA-----CAAAACAAAAAATGTGCA 3942
                           ii v    i  - i     vi    ----- v  vi?       v   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_150591920_   3943 AAAGATTT----AG---CTTCACAGAAGAAGATATAAGAATG-TGAATAA 3984
                           i     ----  ---i   v vi           vi    -iv     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_150591920_   3985 CCACTTGAAAAGTTGTT-AATGTTATTAGTCAT 4016
                         v   v       v  i -  ii i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.05 (6 / 133), avg. gap size = 2.50 (15 / 6)  


2806 26.27 2.76 2.54  chr2_150600424_150604598     2778  3683 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150600424_   2778 TGAAAAGATTTTCCATATTTATGGATTAACAGAATTAATTTTATCAAAAT 2827
                           i      v i    i  i       iiv   v     v  i i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150600424_   2828 ATCTATACTACCAAAAGTGGTCTACAGAGTCAATACAATCAATACCAAAA 2877
                         iv v     v  v   v  i        v    ii     vv  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150600424_   2878 TTCAAATGACAGTTTTCACAAAAATATTTTAAAC--ATATTAAAATTTGC 2925
                          i v iivi vv    ii  i    - vvi  i --  vi       iii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_150600424_   2926 ATGGAACCACAAAAGACCCTGAATATCTAAAGTAATCTTGAACAAGAA-- 2973
                               vii   ii     v     v i   ii         v     --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_150600424_   2974 -CAATGCTAGAAACATTATACTTCCTGATTT--AAATTACATTACAAAGC 3020
                         -   v i i  iivv i i      ii    --   i -i i        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_150600424_   3021 TATAGTAATCAAAATAGTATGATACTGACATAA----AAACACACAGACC 3066
                           i         i i   i  i     i     ---- i   i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_150600424_   3067 AATGCAACAGAATAGAAAGCTCAAAAATAAGTCCTCACATACATAGTCAA 3116
                             v  i     v  i  ii  i      ii  vi    vi  i     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_150600424_   3117 CTAATTTTTGACAAAGGGTCTGAGAATGCACAATGAGAAACGTAAGGTCT 3166
                         i i     i     i  vv ii   viiiv     i i  v v vi    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_150600424_   3167 CTTCAA-AAATGTTGGTGGAAAAACTAGATGTCCATATGCAAATAAATAA 3215
                         i     -     v  v   i v    i   i?   i       vi   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_150600424_   3216 ATAAATAAATTTGATCCTTATCTT---CTATACACAATAGTCAGCTCAAA 3262
                          -------i  v  i  i  i  i--- i   i    v i i i      
  L1M4_orf2#LINE/    449 A-------GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_150600424_   3263 ATTGATGAAAGATTTAAACATAGTACCTTAAACTATAAAACTCCTGGAAG 3312
                           v   v ?   ii    ii  iv v  v              i i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_150600424_   3313 AAAATATAGAGAAAAAGCTCTATGACATCTGTTT-GGCAAAGATTTTGGG 3361
                             i    i?iv   v  iii    v iv v  -     v i   ivvi
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_150600424_   3362 GGATATGACATTAAAAGCATAGGCAACAAAAACAAAAATAAGCGAGTAGA 3411
                          -        ii       i i         iv       iiii i v i
  L1M4_orf2#LINE/    592 G-ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_150600424_   3412 ATTGCATCAAACTAAAATATTTCTGTGTAGCAAAGGAAACAATCAGCAAA 3461
                          i v       v v   v i  i    ivv       v  v    iv   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_150600424_   3462 GTAAAAAATGAACCTACAGAA--GGAGAAAATATTTGCAAATTATACATT 3509
                           i    ivv    i      --                   i   i  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_150600424_   3510 GGCTGAGAGG--TATATCCAAAATATATAAGGA-CTGTATATAATTCAAT 3556
                         v v i  i i-- i      i         i  -  v -  i  i     
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAACTCAAT 789

  chr2_150600424_   3557 AGCAATAAACAACAAGAACAACAAATAACCTGAACTTAAAA-TGTTCAAG 3605
                          ---     ----    ----         i-  i ?    -  vv   i
  L1M4_orf2#LINE/    790 A---ATAAA----AAGA----CAAATAACCC-AATTWAAAAATGGGCAAA 827

  chr2_150600424_   3606 GGACCTGTATGAACATTTTTCCAAAGAAGTCATACACATGGCC--TGA-T 3652
                            ii  v  ii      i          vi     v      -- i -i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_150600424_   3653 ATATGAAAAGGTGACTAACATCACTAGTCAT 3683
                          i        i  vii       ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (156 / 78)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.18 (48 / 22)  


3248 27.20 0.44 0.44  chr2_150626788_150633065     4879  5786 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150626788_   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150626788_   4929 GGCCACACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v i   v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150626788_   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_150626788_   5027 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_150626788_   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_150626788_   5127 TACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                             i   i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_150626788_   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_150626788_   5225 ATCTGATCTTTGACGAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i   i ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_150626788_   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_150626788_   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_150626788_   5375 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_150626788_   5425 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_150626788_   5475 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5524
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_150626788_   5525 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5574
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_150626788_   5575 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5624
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_150626788_   5625 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_150626788_   5675 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_150626788_   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5774
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_150626788_   5775 TTCACTGGCCAT 5786
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2371 27.54 1.09 2.04  chr2_150640234_150644913.rev     2841  3577 (1103)    L1M4_orf2#LINE/L1        1   730 (178)  

  chr2_150640234_   2841 TGGTAAAATATTCCATCCTCGTGGATCGGAAGAATCAATATCATGAAAAT 2890
                            v  i    i    vi  i     i      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150640234_   2891 GGCCATATTGCC-AAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 2939
                            v   i v  -   v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150640234_   2940 TACCATTGATATTGTTCACAGAATTAGAAAAAACT-ACTTTAAAATTTAT 2988
                          v   viviiv  v  ii     v v  v  i-  - iii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_150640234_   2989 ATGGAACCAAAACAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAAAG 3038
                               viiv  vi  v  viv        i      i i i-   i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAG 198

  chr2_150640234_   3039 AACAAAGCTGGAGGCATTATGCTACCTGACTTCAAACTATACCACAAGGC 3088
                                i      vv i ii  v  ii i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_150640234_   3089 TACAGTAACCAAAACAGCATGGTAACCAAAACTGATGCCAAAACAGACAT 3138
                                 i   i    ii     -------   iiiiv ii i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTA-------CTGGCATAAGGATAGACAT 291

  chr2_150640234_   3139 ATAGACCAATGGAACAGAATAGAGATCTCAGAAATAAGACCACGTATCTA 3188
                              i        i     v    vii         iv   iii  i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_150640234_   3189 CAACCATCTGATCTTCAACAAACCTGACAAAAACAAGCAACAGGGAAATT 3238
                         iiii  vi    i   i    ivv  v   i v  vv   ii      vv
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_150640234_   3239 ATTTCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGA 3288
                           vvi  v  i  i              v      v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_150640234_   3289 AAACTGAAACTGGACCCCTTCCTTACATCTTATACAGAAATTAACTCAAG 3338
                          i v    ii         v   i   i v      i            i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_150640234_   3339 ATGGATTAAAGATTTAAATGTAAAACCAAAAACCATAAAAACCCTAGAAG 3388
                               i ?   ii         i v v     i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_150640234_   3389 AAAGCCTAGGC---AATTACATTTAGGACATAGGCATGGGCAAAGATTT- 3434
                            i v    ?---   i---  iiv   v v  vv i     v i   -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_150640234_   3435 -TAC-TATGAAATTGCCAAAATCAATGGCAACAAAAGCCAAAATTGATGA 3482
                         -  v-     v ---      v  vvi          vv     v   i 
  L1M4_orf2#LINE/    589 TTAGATATGACA---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_150640234_   3483 ATGGGATCTAATTAAACTAAAAAGCTTCTGCAGAGCAAAAGAAATTATCA 3532
                           v   ii v  i   v v    i   i  iivvv    i  v i     
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_150640234_   3533 TCAGGGTGAACAGGAAACCTACAGAATGAGAGAAAACTTTTATAA 3577
                         vv ii     v  iv    i        i       iv   ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

Transitions / transversions = 1.50 (120 / 80)
Gap_init rate = 0.01 (10 / 730), avg. gap size = 2.30 (23 / 10)  

 529 23.73 0.00 2.82  chr2_150640234_150644913.rev     4028  4204 (476)    L1M4_orf2#LINE/L1      737   908 (0)  

  chr2_150640234_   4028 TATCTGACAAAGTTCTAATATCCAGAATTTACAAGGAACTTAAGAAAAAT 4077
                                i  i vv  vi          v  i  i     iv-v v  v 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAACT 785

  chr2_150640234_   4078 TTACAAGAAAAAAACAAACAACCACATCAAAAAGTGGGCAAAGGATATGA 4127
                         iv i  v     i     i    vv  i?    i            v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_150640234_   4128 ACAGACACTTCTCAAAAGAAGAAATTTATGTGGCCGACAAACATATGAAA 4177
                          i     i     v        v  vi vi     i i  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_150640234_   4178 AAAAAAAAACTCAACATCTCTCATGAT 4204
                          i ----vi         v????????
  L1M4_orf2#LINE/    886 AGA----TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (22 / 19)
Gap_init rate = 0.01 (2 / 172), avg. gap size = 2.50 (5 / 2)  


3175 26.65 1.10 1.10  chr2_150647256_150653637     4983  5890 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150647256_   4983 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5032
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150647256_   5033 GGCCATACTGCCCAAGGTAATTTATAAATTCAATGCCATTCCCATCAAGC 5082
                            v     v     iv i  i  i i      i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150647256_   5083 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5130
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_150647256_   5131 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5180
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_150647256_   5181 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGGC 5230
                                i      vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_150647256_   5231 TACAGTAACCAAAACAGCATGGTAATGGTACAAAAACAGAGATATAGACC 5280
                                 i   i    ii     v   i i  ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_150647256_   5281 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCTCATATCTATAACT 5328
                                i    i--    i  --        vv  vi i  i   iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_150647256_   5329 ATCTGATCTTTGACAAACCTGTCAAAAACAAGAAATGGGGAAAGGATTCC 5378
                          vi    i  i     ivv  i   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_150647256_   5379 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5428
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_150647256_   5429 GAAACTGGATCCCTTTCTTACACCTTATACAAAAATTAATTCAAGATGGA 5478
                            ii    i    vi  i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_150647256_   5479 CTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5528
                         ii ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_150647256_   5529 CTAGGCACTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTGA 5578
                         v    ?iiv viv   iv   v v  vv i     v ii   v ivv iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_150647256_   5579 AACACCAAAAGCAATGGCAACACAAGACAAAATTGACAAATGGGATCTAA 5628
                         i            vvi      v    v     v  i    v   i----
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC---- 642

  chr2_150647256_   5629 TTCATC-----TAAAGAGTTCCTGCACAGTAAAAGAAACTA-CAATCAGA 5672
                               -----    i v  i-  ii vvi   i  v    -   v- i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAG-AAA 690

  chr2_150647256_   5673 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCGTC 5722
                              v  i     i                 v       vii ivii  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_150647256_   5723 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACACATTTACA 5772
                            i  i  i  vi          v  i  v      vv   vv iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_150647256_   5773 AGAAAAAAACAAACAACCCAATCAACAAGTGGGCAAAGGATATGAACAGA 5822
                          v     i     i        i? v  i            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_150647256_   5823 CACTTCTCAGAAGAAGACATTTGTGCAGCCAAAAGACACAGGAAAAAATG 5872
                           i     vi       i  viiviii     v ii    v     i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_150647256_   5873 CTCATCATCACTGGCCAT 5890
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2790 26.88 1.85 3.05  chr2_150661046_150665457     3003  3921 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150661046_   3003 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATTTTGTGACAGT 3052
                               i i  i     i        v      v i   v    v vii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150661046_   3053 GGCCATATTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 3102
                            v   i v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150661046_   3103 TACCATTGACTTTCTTCATAGAATTAGAAAAAAACTA--CTTAAAATTTC 3150
                          v   vivi i  i  iii    v v  v  i--  i-- i       - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT-C 147

  chr2_150661046_   3151 ATGTGGAACCAAAAAAGAGCCTGTATAGCCAAGACAGTCCTAAGCGAAAA 3200
                           i     viiv  ii  v  v v        i   i  i i ivi i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_150661046_   3201 GAACAAAGCCTGAGGCATCACGCTACCTGACTTCAAACTGTACTACAAGG 3250
                                 iiv    vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_150661046_   3251 CTACAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGCATTGTACTG 3300
                                  i   i    ii           --------------  ---
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCA--------------TA--- 280

  chr2_150661046_   3301 GCACCAAAACAGATATATAGACCAATGGAATAGAATGGAGGCCTCAGAAA 3350
                         ----- ii i   i       i              v   ivii      
  L1M4_orf2#LINE/    281 -----AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_150661046_   3351 TAACATCACACATCTAAAACCAACTGCTTGTTGACAAACCTGACAAAAAC 3400
                            vvi  i    i  viii   i  v  v i     ivv  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_150661046_   3401 AAGCAATGGGGAAATGATTCTCTATTTAATAAATTGTCTTGGGAAAACTG 3450
                          vv           vi  vv   v  i  i    v  vi     v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_150661046_   3451 GCTAGATATATGCAGGAAACTGAAACTGGAAACTTTCCTTACACCTTATA 3500
                          v  ?vi i     ii i v    ii    vv i v   i     v    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_150661046_   3501 CAAAAATTAACTCAAGATGGATTAAAGACTTAAAC-------CTAAAACC 3543
                                        i      i ?    i    i-------       i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_150661046_   3544 ATAAAAACCCTAGAAGAAAACCTAAGCA-ATACCATTCAGGACATAGGCA 3592
                               vi i           v  i ?i- v i -   iv   v v  vv
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT 574

  chr2_150661046_   3593 TGGGGAAAGACTTCATAACTA-AACACCAAAAGCAATGGCAACAAAAGCC 3641
                          i  v  v ii   v  iv  -i            vvi          vv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_150661046_   3642 AAAATTGACAAATGGGATCTAATTAAACCAAAGAGCTTCTGCACAGCAAA 3691
                              v  i    v   ii v  i   viv  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_150661046_   3692 GGAAACTATCATCAGAGTGGACAGGCAACCTACAGAATGGGAGAAAATTT 3741
                            v       vv i    i v  i     i                 v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_150661046_   3742 TTACAATCTGTCCATCTGACAAAGGGCTAATATCCAAGGTCTACAAACAA 3791
                           i   viii vi      i  i  i  vi      iii v  i   v  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_150661046_   3792 CTTAAACAAATTTACAAGAAAAAAGTAAATACCTGCC--TCAAAAAATAG 3839
                           ivv    v iv i  v     iii     v --  -- i?      i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAAC--CCAATTWAAAAATGG 822

  chr2_150661046_   3840 GCAAAGGATATGAACAGGCACTTATCAAAAGAAGACATGC---TG-CCAA 3885
                                  v    i  i  i  v  v        i  i ---  -    
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_150661046_   3886 GAAACTTATGAAGAAAAGCTCATCATCTCTGGTCAT 3921
                         v  i vi     i i v     v    v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.46 (45 / 13)  


2512 29.33 1.43 1.43  chr2_150753207_150755996     1392  2298 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_150753207_   1392 GAAAAAACATTCCATATTCATGGATTAAACGAATCAATATCATTAAAATG 1441
                          i   i i  i    i          ii v  v i     ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_150753207_   1442 GCCATACTGCCCACAGCAATCTACAGATTTAATACTATTCCTACCAAACT 1491
                           v     v    v vii           i  ii v  i    i    v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_150753207_   1492 ACCAA-TGTCATTCTTCATAGAA-TTAGGAAACACT-ATTCCAAAACTCA 1538
                         v   i-  i -  i  iii    -  --  v vi  -  i i    i   
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr2_150753207_   1539 T---GAAGAGCCAAAAAAGAGCCCA-AACAGCCAAAGAAATCCTAAGCAA 1584
                          ---   iv  ----  i ii    -  i       iv    i i iv  
  L1M4_orf2#LINE/    149 TATGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_150753207_   1585 AATAAACTAAGCCAGAGGCATCCCATTACCCAGCTTCAAATTATATTACA 1634
                         i vi   v   iii    vv  v  i v    ii      viv  i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_150753207_   1635 ATGCTGGAGTAACCAAACTGGCATGGTAATGGTACAAAAATAGAAACATC 1684
                          v   iv     i   ivii ii     v   i i  ii     v i  v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_150753207_   1685 AACAAATAGAACAGGATAGAGAACCCAGAAAGAAAGCCACACACCCAGAA 1734
                         i iv   i   i  i  v    ii       v   v   i   iii vii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_150753207_   1735 CCAACTGATTTTTAACAAAATTGACAAAAATAAGCAATGAGGGAAAGATT 1784
                         i   i       ii    iiv  v   i vi vv     i  i  ii  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_150753207_   1785 TTCTATTCAATAAACAGTGCTGGGACACTTATTTGGCTAGTCATATGAAG 1834
                         v   v     i   ii           --- i -  v  ?i  i   v i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACA---ACT-GGATAKCCACATGCAA 440

  chr2_150753207_   1835 ATGAATGAAACTGAACCCCTACACTT-CACCATATACGAAACTTTATTTA 1883
                          v       ii  i        -  i-          i   v  v i i 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTAC-CTCACACCATATACAAAAATTAACTCA 489

  chr2_150753207_   1884 AGATGGAATAAAGATTCAAATATAAGACCTCAAACTATAAGAATCATAGA 1933
                          i     vi ?   iii    i     v  v         i v  v    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_150753207_   1934 AGAAAACCTAGGAA-ACACCATGCTGGACATTGGCCTTGGGAAAGAATTT 1982
                                v    ?i- v i - v vv   v    vi v  v  v iv  i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_150753207_   1983 ATGACTAAGTTCTCAAAAGCAATTTCAACAAAAACAAAAATTGACAAGTG 2032
                         v iiv  v vivi        vvvv        iv      v  i  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_150753207_   2033 GGACCAAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACT--CAACA 2080
                             ivv  i   v v  i i   i  ii vv    i  v   --   v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_150753207_   2081 AAGTAAAGAGACAACCTATAGAATAGAAGAAAATATTTGCAAACTAAGCA 2130
                             i  i        i i     i i                ii vii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_150753207_   2131 TCCAACAAAGGTCTAATATCCAGAATCTATAAGGAACTTAAACAAATTAA 2180
                           ii i  i  v  vi          v     i     ivv    v i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_150753207_   2181 CAAGGAAAAAACAAACAACTTCATTGAAAAGTGGGGAAAGGCCATGAGCA 2230
                         i  vi    i     i   iiv   ?    i    v     viv   ii 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_150753207_   2231 GACCCTTTGCAGAAGAAGACATACAAGCAGCCAACAA--ATATGAAAAAA 2278
                            vi  iv vi       i      iii     i  -- i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_150753207_   2279 TGGTTAACATCACTAATCAT 2298
                           v i       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (164 / 98)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 1.62 (26 / 16)  


2899 26.82 2.01 0.56  chr2_150873963_150880379     5031  5925 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150873963_   5031 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATCAAAAT 5080
                               i i  i     i        v      v i     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150873963_   5081 GGCCATACAGCCCAAAGTAATTGATAGATTCAATGCTATCCCTATCAAGC 5130
                            v    vv      v i  iv i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150873963_   5131 TACCATTGACTTTCTTCACAGAATTAGAGAAAACT-ACTTTACATTTCAT 5179
                          v   vivi i  i  ii     v v  v  i-  - iii  v v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_150873963_   5180 ATGGAACCAAAAAAGAGCT-GTATAGCCAAGACAATCCTAAGCAAAAAGA 5228
                               viiv  ii  v i- v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_150873963_   5229 ACAATGCTAGAGGCATCACACCACCTGACTTCAAACTATACTACAAGGCT 5278
                             v i i    vv      iv  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_150873963_   5279 ACAATAACAAAAACAGCATGGTACTCGTACCAAAACAGATATATAGACCA 5328
                            i   iv  i    ii       v i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_150873963_   5329 AGGGAACAGAATAGAGGCCTCAGAAATAATGCTGCACATCTACAACCATC 5378
                          v    i     v   ivii         vv iii    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_150873963_   5379 TGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAACGAT--TCCT 5426
                             i  i     ivv  vv  i v  vv           vi  --  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_150873963_   5427 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAATCTG 5476
                          -- i  i        i     v      v  ?   i     i  ivv  
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_150873963_   5477 AAACTGGACTCCTTCCTTATACCTTGTAGAAAAGTTAACTCAAAATGGAT 5526
                           ii     i   v   i i   v i  v    i                
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_150873963_   5527 TAAAGACTTAAACATAAGATGTAAAGCCGTAAAAACCCTAGAAGAAAACC 5576
                         i ?    i    ii     vv    i ii     vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_150873963_   5577 TAGGCAGTACTATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA-A 5625
                             ?ivv v v   iv   v v  vv i     v ii   v iiv  -i
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_150873963_   5626 TCACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5675
                         v           vvv          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_150873963_   5676 TAAACTAAAAAGCTTCTGCACAGCAAAAGAAACTATCAG---AGTGAACA 5722
                         i   v v    i   i  ii vv    i  v       i---      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_150873963_   5723 GGCAACCTACAGAATGGGAGAAAATTTTTGCAA-TCAATCCATCTAACAA 5771
                          i     i                 v       -   - vi    i i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGATAA 746

  chr2_150873963_   5772 AGG-CTAATATCAAGAATCTACAAGGAACT--TA-AATTTA-CAAGAAAA 5816
                         i  -  vi    v     v  i  i     --  -  i i -i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_150873963_   5817 AAACAAACGACCCCATCAAAAAGTGG-CAGAAGGATATGAACAGAGACTT 5865
                          i     ii    v  i?    i   -  -      v    i   v i  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCA-AAGGATTTGAATAGACATTT 845

  chr2_150873963_   5866 -TCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAAGCTCAT 5912
                         -  v        i  vi viii     i  --         i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_150873963_   5913 CATCACTAGCCAT 5925
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.35 (23 / 17)  


3267 17.66 4.68 3.51  chr2_150931898_150934560.rev      955  1724 (939)    L1M4_orf2#LINE/L1        1   779 (129)  

  chr2_150931898_    955 TGAAAAGGCACCCTGTGTTCATGGATCAGAAGACTTAATATTGATAAGAT 1004
                           i    ii i  ii           ii               v      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150931898_   1005 GGCAATACTTTCCAAAT----CTACAGCATCAATGCAATTCCTATTGATA 1050
                                  ii      ----      vv    i     i     ii v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150931898_   1051 GCCCAATTGGCTTCTTTTGTTGAAAAAGACAAACTGATCTTAAAATTAAT 1100
                         v    ii  v   -     iv    vv     i      i       v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_150931898_   1101 GTACATATACAAGGAACCCAGAATAGACAAAATAATCTCAGAAAAGAG-- 1148
                         i iv v  i     i           v     i     iii      i--
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_150931898_   1149 -CAAAGTTGGAGGACTCACATTTCTAAGTTTTTAAACTTACTCCAAGGCT 1197
                         -                   i   iv i   iv         v   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_150931898_   1198 TACAGTAATCAACACAGTATATTACAGGCATAAGGATAGACATATATATC 1247
                         -           v     i iv   v                    v   
  L1M4_orf2#LINE/    250 -ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_150931898_   1248 AATAGAAAATAATTGAGATTCTAGAAATTAAGC---ACATTTATGGTCAT 1294
                            i   v v        v  i      v  v ---             v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_150931898_   1295 TTGATTTCC-AGAAGGGTGCCAAGACAATTAAATGCATAGGGGAAGGGTG 1343
                                i - v              v   v    -----     -----
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-----GGGAA----- 388

  chr2_150931898_   1344 TAGAGAATATTCTTTCCAACAACTATCCCTGGGACAACTGGATATCTACA 1393
                         ---      v     i      v iviv                ? i   
  L1M4_orf2#LINE/    389 ---AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_150931898_   1394 AACAAAAGAATAAATTTGGACAC--AACTCAC-CCATTTGCAAAAATTAA 1440
                         vi         i  v      v -- v     -    v i          
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_150931898_   1441 CTCTAAATGGA-CAATGATCTCAAACATAGAGGCTAAAACCATAAATCCA 1489
                            v       -  ?v  i  -   ii  iii        i     v i-
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCT-AAATGTAAGAGCTAAAACTATAAAACT- 533

  chr2_150931898_   1490 CATAGAAGAAAACATAGGCATAATTCATCATGACCTTGGGTTAGATTAGT 1539
                          v                ?i   v  v  i              ii----
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC---- 579

  chr2_150931898_   1540 TAGTTGATGATTTCTTAGTCACATCATCAAAAGAACAAGCAA------AA 1583
                         -----i   i        vi iiv  i      v        ------  
  L1M4_orf2#LINE/    580 -----AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_150931898_   1584 AAAATG------TGAGACT--ACCAAAAGTTAAAATCTTTTGCATTGCAA 1625
                              i------ vi    -- i     -      v      iii v   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAA-TTAAAAACTTTTGTGCTTCAA 673

  chr2_150931898_   1626 ATATGACCATCAAGAAAG-------ACTACCAATAGAATGTGAGAAAATA 1668
                          vivv  i          -------  v   v i      v         
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_150931898_   1669 TTTGCAAATTATATATTTGATCAGGCACTTGTATCCAGAATATATAAAGA 1718
                                  i      i    v   v                        
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_150931898_   1719 ACTGTT 1724
                            v  
  L1M4_orf2#LINE/    774 ACTCTT 779

Transitions / transversions = 1.25 (74 / 59)
Gap_init rate = 0.02 (19 / 779), avg. gap size = 3.32 (63 / 19)  

 558 17.02 3.55 2.13  chr2_150931898_150934560.rev     2040  2180 (483)    L1M4_orf2#LINE/L1      766   908 (0)  

  chr2_150931898_   2040 TATAAAGAACTGTTA-AACTCAATAATAAAAAGATGACTA-TCCAATTTT 2087
                                    v   -                  ii v  -i      ?v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_150931898_   2088 TAAATAGGCAAATATTTTGAATAGCTGTTTCTCCAAAGA---TATTCAAA 2134
                         v    i      viv         vii            ---   v    
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_150931898_   2135 TGGCTAATAAACATATGACACAATGCTCAGTAACCTTAGTCATTAG 2180
                             i     i  i    v vi       ---  v i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCA---ACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (12 / 11)
Gap_init rate = 0.03 (4 / 143), avg. gap size = 2.00 (8 / 4)  


2632 28.76 1.78 0.56  chr2_150993833_150998925     3705  4601 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_150993833_   3705 TGTAAAAACATTCCATGCTTACAGATAGGAAGAATCAATATAATGAAAAT 3754
                           v   i i  i     i i ii   v      v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_150993833_   3755 GCCCACATTGCCCAAAGCAATTTATAGATTCAATGCTATTCCCATTAAAC 3804
                          v v i i v      vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_150993833_   3805 TAGCA-CTGACATTCTTCACATCATTAGAAAAAACTG-TTTTAAAATTTA 3852
                          vv  -   v -  i  ii  vv v v  v  i-   - ii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_150993833_   3853 TATGAAAC--CAAAAAA----GAATAGCCAAGGAAATCCTAAGCAAAAAG 3896
                             i  v--   iii ----          iiv    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_150993833_   3897 AAAAAAGCTGGAGGCATCACACTACCCAACTTTAAACTATACTACAGTAC 3946
                           v    i      vv       v     i  i   viv       ivi 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_150993833_   3947 TACAATTGCCAAAATGGCATGGTACTG-TACCAAAACAGGCACACAGAGC 3995
                             i vii   i ii ii        -i iv ii i  i  i i   v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_150993833_   3996 AATGGAACAGAAAAGAGAACCCAGAAATAAGACCACACACATCTACAACC 4045
                                i    vv    ii          -   -  i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAA-ACC-CATACATTTATGGTC 346

  chr2_150993833_   4046 ATCTGATCTTCCACAAACCTTACAAAAACAAGCAATGGGGAAATGATTCC 4095
                          vi    i   v    ivv vv   i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_150993833_   4096 CTATTTAATAAATGGTGCTGGGAGAACTGGCTAGTGATATGCAGAAAATT 4145
                           v  i  i              v      v  ?iv i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_150993833_   4146 GAAACTGGACCTCTTCCATACACTATATACAAAAATGAATTTGAGATAGA 4195
                            ii      i  v  vi    i            v  i ii i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_150993833_   4196 GTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGAAAAC 4245
                         vi ?    i         i v i            vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_150993833_   4246 CTCGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTCATGACAA 4294
                         v v  ?i- v i -   iv   v v  vv i     v i    v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_150993833_   4295 AGATGTCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4344
                         v  iii        vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_150993833_   4345 ATTAAACTAAAGAGCTTCTGCACAGAAAAAGAAACTATCAACAGAGTAAC 4394
                           i   v v  i i   i  ii vvv   i  v        v i   i v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_150993833_   4395 TAGACAACCTACAGAGTGAAAGAAGATTTTTGCAATCTATTTATCTGACG 4444
                         v        i     i  ii    i  v       vii  v       ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_150993833_   4445 AAGG-CTAATATTCAGCATCTATCA-GAACCTAAACAAATTTACAAGACA 4492
                          i  -  vi   i   v  v   v -    iivv    v iv i  v v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_150993833_   4493 AAAACAA----CCCCATTAAAAAGTGGGCAAAAGACATGAACAGACACTT 4538
                           i    ----   v   ?    i        i  iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_150993833_   4539 TTCAAAAGAAGACATACATGCAGCCAAGAAACATGTGAAAAGAAGCTCAA 4588
                         i  v        i     viii     v  i  ii        v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_150993833_   4589 CATCACTGATCAT 4601
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (148 / 106)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  

 933 26.34 0.82 0.82  chr2_150993833_150998925     4799  5041 (52)  C L1M4_orf2#LINE/L1   (598)   310    68  

C chr2_150993833_   5041 TAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTC 4992
                          i  i  i        i  v     i     iv v   iivi i  i  i
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

C chr2_150993833_   4991 ACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAAGA 4944
                         i     -   -- v  i  - iii    i           viiv  ii  
  L1M4_orf2#LINE/    118 GCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

C chr2_150993833_   4943 GCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCAT 4894
                         v  v v  v     iv     i i ivv i          i      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

C chr2_150993833_   4893 CACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAG 4844
                               v  ii i      viv        i          i   i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

C chr2_150993833_   4843 CATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAA 4799
                         ii         i iv ii i   v                i    
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

Transitions / transversions = 2.05 (43 / 21)
Gap_init rate = 0.01 (3 / 243), avg. gap size = 1.33 (4 / 3)  


3455 19.97 1.72 1.19  chr2_151133223_151135907.rev      959  1714 (971)    L1M4_orf2#LINE/L1        5   764 (144)  

  chr2_151133223_    959 AAAATATGCACATGTTCATGGATTGGAAGAA--AAAATTGTTAAGATGAC 1006
                           i    v -                    v--  v            i 
  L1M4_orf2#LINE/      5 AAGATATCC-CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_151133223_   1007 CATATCATGTAAATCAATCTTCAGATTCAATGAGATCTCTATCAAAATTC 1056
                         v   iivivi    ii    v         i vi   i          - 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT-C 102

  chr2_151133223_   1057 CCA--TGCTATTTTTTGCAGAAATACAAAAATCCATCCTAATATTCATTT 1104
                            --   i-              vv v  iiiv       v      v 
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_151133223_   1105 GGAATAT-CAAGGAACCATAAGTGGTCAAAATAATCTTGGGGAAAAACAA 1153
                             -  -     i   vvi i i i     i       ---     v  
  L1M4_orf2#LINE/    152 GGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG---AAAAAGAA 197

  chr2_151133223_   1154 GAACAAAGTTGGAGGACTTATACTTCCTAATCTCAAAACTCACTACAAAA 1203
                                           i i      i   i        i        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_151133223_   1204 CTATAATAACCAAAACAGTGTGGTGTTGGCATAAGCTCAGACATATAGAC 1253
                            i i   i   i          ii         vvi           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_151133223_   1254 TAATGGAATAGAATAGAGAACTCAGACAAAAACCCCTTGCATATATGGTC 1303
                         i             v    iii    v v      v -i   v       
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGGTC 346

  chr2_151133223_   1304 AATTAATTTTTGGCAATAGTGCCAAAACCATTCAATAGGGAAAAGACAGT 1353
                             i     i i   vi       i          i      ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_151133223_   1354 CTTTTCAACATATGGCACTAGGATAACTAAATATTCACATGTAAAATAAA 1403
                                   v    ii  i   i    ii   ?i      i    v  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_151133223_   1404 GAAGTTGGACCTTTAATTTATGCTACATATAAGAATTAACTCAAAA-GGG 1452
                                    ii  vi i ii i i   i  i             -  i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_151133223_   1453 TCAACAACTTATATGTAAGGG-TGAAATTATAAAATGCTTAGAA-AAAAC 1500
                            ?vi  i  v       i - i   i       iv       -     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_151133223_   1501 CTAGGGGAAAATCTTCATGACATTGAAATTGGCAATGATTTCTTGAATGC 1550
                         v    ? v        i    v   iiv v       i      ii  ii
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_151133223_   1551 AACAGTATAAACACAAGTAAGAAAA----AAATAGGTAAATTGGACTTTA 1596
                         i   vi v  i      i  v    ----      i            i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_151133223_   1597 ATCAAAATTTCAAACATTTTAGCACCAAAGGATGTTATCAAGAGAGTGAA 1646
                         -        vv    v   vv  vi       iii        i      
  L1M4_orf2#LINE/    647 -TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_151133223_   1647 AAGACAACCCACAGAATGGGGAAAAATATTTGCAAAGCATATATCTGGTA 1696
                                             ii              v          i  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_151133223_   1697 AAA-AGTAATATCCAGAAT 1714
                          ii- v vi          
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAAT 764

Transitions / transversions = 2.02 (99 / 49)
Gap_init rate = 0.02 (15 / 760), avg. gap size = 1.47 (22 / 15)  

 789 12.50 1.32 0.00  chr2_151133223_151135907.rev     2042  2193 (492)    L1M4_orf2#LINE/L1      755   908 (0)  

  chr2_151133223_   2042 TATCCAGAATTTTTAAAAAAA-CTTATAAGTCAACAACAAAATAACAGAT 2090
                                   v v    i  v-    i  v    i  i    vi   i  
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_151133223_   2091 AAACCAATTCAAAAATGGGCAAAGGATTTAAATAGACATTTCTCCAAAGA 2140
                           v      ?                   i                    
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_151133223_   2141 AGATACACAAATGGCCAGTA-GCACATAAAAATATGTTCAACATCACTAG 2189
                              i           i  -      i    v   i         ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_151133223_   2190 CTAT 2193
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.57 (11 / 7)
Gap_init rate = 0.01 (2 / 154), avg. gap size = 1.00 (2 / 2)  


 232 27.18 16.41 7.05  chr2_151285567_151287523      690  1469 (488)    L1M4_orf2#LINE/L1       33   885 (23)  

  chr2_151285567_    690 ACTCAACATCATAAAGATGTGAATTCACCTTAAAATAATGTTGTA-ATTC 738
                            i  i  ii v      vv   v v  ii   v i  -i ii -    
  L1M4_orf2#LINE/     33 ACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGAT-CTACAGATTC 81

  chr2_151285567_    739 TTTGCAATCTTAATTAAAAGTAATCAAATTACCTTTT--ACAAAAAC--- 783
                         vvi      iiv  i    - --i v ii i      --i  i   i---
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAA-T--CCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chr2_151285567_    784 ---GCT-AT--TAAAATTTGTTTGAAGGAATGAATACACTTGTGTAAAGT 827
                         ---   -  --       ii v  i ------   i  ---------  v
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGA------AATGCA---------AGG 163

  chr2_151285567_    828 GAGGAAAAATA-TGAAAACA-TCT-AACAAGGGAGAA-AAAAT------A 867
                           vvv i    -iv      -   -i v  i i    -   i ------ 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_151285567_    868 TGCA-AC------ATATTAAAA--TGCTTCAAAAA-GCAATGTTCAAAAT 907
                         iv  -  ------  v i    -- i  v    iv-i  i iv    i i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_151285567_    908 GGCG--GTAC------AAGAATAGACAAGGAAATCAATGGAG--GAATCT 947
                         i i --    ------   i       viv i         i--    --
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT-- 311

  chr2_151285567_    948 ATAAGAG-CCAGAAATACATTCCTAGAAAAACTGAAAGTT--TTGTGTGT 994
                         - i    -         v ii v  v ----i v vi  i--   vv v 
  L1M4_orf2#LINE/    312 -TGAGAGTCCAGAAATAAACCCATACA----TTTATGGTCAATTGATTTT 356

  chr2_151285567_    995 TAAAATGGGGTTGTCAA-ACTGTT----GGGGAAAGATGTA--CTATTTA 1037
                         ii v v   --  i   -  ii  ----         -i  --  v  i 
  L1M4_orf2#LINE/    357 CGACAAGGG--TGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTTCA 403

  chr2_151285567_   1038 GTACATGTTGTTGGTTCATAC-GTGTAGCTATTTGGACAA-AACGCACTT 1085
                         ii v   v  i   vv  -  - vi  ? i iv  v v  -  i v v  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACA-ACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_151285567_   1086 --ACTCTTTACTTCATA--ATA----------AATTCTACACGGATTAAA 1121
                         --  i i -  i   i --   ----------  i  v v i    i ? 
  L1M4_orf2#LINE/    453 GGACCCCT-ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_151285567_   1122 GGTTTAAATAT--TTTTTAAA--TGTAAAATAACCA-AAGAAAA------ 1160
                          iii     i --vvvi    -- i     ivvii -       ------
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_151285567_   1161 ---AACTTTTTCGGTAATCTTGGACTAGGAAAGACATTTCTCAG-TATAA 1206
                         ---  v i  i--  i i     ii    v  vi-i     i  -   i 
  L1M4_orf2#LINE/    552 NGTAAATCTTC--GTGACCTTGGGTTAGGCAATG-GTTTCTTAGATATGA 598

  chr2_151285567_   1207 CA--AAAATCTGTAAGTAACAAACTAAAATCTAGACAAGTTTG-TTTCA- 1252
                           --    v -ii   i      vv    vv    i  i  v -i    -
  L1M4_orf2#LINE/    599 CACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_151285567_   1253 ----------AACACTTATGTTTAATGCAAAG--CATTATAAACAAAGTG 1290
                         ----------   vi  i  i  ----     --  i   v  v      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTT----CAAAGGACACTATCAAGAAAGTG 693

  chr2_151285567_   1291 AAACAATAATATCA----ATGGCAAAGAAAAAATAGAGTCG----TTACA 1332
                            vi i  i-i  ----    ----  i      v-- i ---- i i 
  L1M4_orf2#LINE/    694 AAAAGACAAC-CCACAGAATGG----GAGAAAATAT--TTGCAAATCATA 736

  chr2_151285567_   1333 TATATGACGGAAAAGATTAATTT----AATACACAAA-AACTTTCATGTA 1377
                            v   i--  ii  i vi v ----    i i   -    i i i-- 
  L1M4_orf2#LINE/    737 TATCTGAT--AAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC--A 782

  chr2_151285567_   1378 AATCAATAAGAATAAGGAAAATTACTC--TGTAGGAATTTGGGCAGAAGA 1425
                          v       v  v   iv    v  i -- v? ii   --     i i  
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT--GGGCAAAGGA 830

  chr2_151285567_   1426 TATGAGAATGGA----------AAGAA---ATACAAATCAACAAAAAAAC 1462
                          v   --  i  ----------     ---        -ii v  v  i 
  L1M4_orf2#LINE/    831 TTTGA--ATAGACATTTCTCCAAAGAAGATATACAAAT-GGCCAATAAGC 877

  chr2_151285567_   1463 AC-TAAAA 1469
                           - i   
  L1M4_orf2#LINE/    878 ACATGAAA 885

Transitions / transversions = 1.68 (131 / 78)
Gap_init rate = 0.08 (67 / 853), avg. gap size = 2.73 (183 / 67)  


3274 25.17 0.67 0.34  chr2_151349159_151353222     2679  3572 (492)    L1M4_orf2#LINE/L1       12   908 (0)  

  chr2_151349159_   2679 CCCATGCTCATGGATAGGTAGAATCAATATTGTGAAAATGACCCTACTGC 2728
                               i        v  v   v i        v  i   i vv    v 
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chr2_151349159_   2729 CAAAAGCAATCTATGAATTCAACACAATCCCTATCAAAATGCCACCATCA 2778
                          v   vii     iii       i                v   v vv v
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_151349159_   2779 TTCTTCACAGAATTAGAAAAAC-AATTCTAAAATTCATATGGAACTAAAA 2827
                           i  ii     v v  v  i -i  i                 v iv  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_151349159_   2828 AAGAGCCCACATAGCCAAAGCAAGACTAAGTGAAAGGAACAAATCTGGAG 2877
                         ii  v  viv         i   vvi i ivi i i       vi     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_151349159_   2878 GCATCACACTACCCAATTTCAAACTAAACTATAAGGCCATAGTTGCCCAA 2927
                          vv       v            vivv    i  i  i i   vii v i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_151349159_   2928 ACCGCATGGTACTGGTATAAAAATAAGCACATAGATCAGGGGAACAGAAT 2977
                           v ii         i    ii   ii  i        iv    i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_151349159_   2978 AGGGAACACAGAAATAAATTCAAACAATTACAGCCAACTGATCTTAGACA 3027
                         v i  iiv          ii  v   v   ii i   i    i  v    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_151349159_   3028 AAGCAAACAAAAAGATAAAGTGGGGAAAGGACACCCTTTTCAACAAGTGA 3077
                          i vviv   i vv  vv i         i i vi           i  i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_151349159_   3078 TGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAAACTGGATCCTCA 3127
                                 i  i   v  ?       i ii        ii    i  ii 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_151349159_   3128 TCTCTCACCTTATACAAAAATCAACTCAAGATGGATTAAGGACTTAAATC 3177
                         i   v    v           i       i      i ?i   i     v
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_151349159_   3178 TAATACCTGAAACTATAAAAATTCTAGAATATAACATTGGGAAAACCCTT 3227
                            v v  i           v ii     v v     v  ?iv  vi   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_151349159_   3228 CTAGACATTGGGTTAGGCAAGGATTTCAT-GATCAAAAAC-CCAAAAGCA 3275
                          vv   v             v i    v -   -- vi  -         
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGACACCAAAAGCA 609

  chr2_151349159_   3276 AATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATTAAACTAAACAG 3325
                         v v    i    iv   i   i   iv v      v  i   v v  v i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_151349159_   3326 CTTTTGCATGACAAGAGGA-ACAGTCAGCAGAGTAAACAGACAACCCACA 3374
                               iiivv   -    -  vi   iv i   i  v            
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAA-AGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_151349159_   3375 AAATGGGAGAAAATCTTCACAATCTATAAATCTGA-AAACAATGAATATG 3423
                         i             v  ii   vii   v      -  ivi ivvi   v
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_151349159_   3424 CAGAATTTACAATGAACTCAAACAAATCAGTAAGAAAAAAACAAATAATC 3473
                               v  i  v      vv    v   i   v     i        i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_151349159_   3474 CCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCAAAAGAAGAT 3523
                          v  i?    i     v     iv          v     v         
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_151349159_   3524 ATACAAATGGCCAACAAACATATGAAAA-ATGTTCAACATCACTAATGAT 3572
                                       i  i  i       -   i         ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (122 / 99)
Gap_init rate = 0.01 (8 / 897), avg. gap size = 1.12 (9 / 8)  


 305 27.34 2.16 6.47  chr2_151418346_151420962      876  1014 (1603)    L1M4_orf2#LINE/L1        3   135 (773)  

  chr2_151418346_    876 GAGAGGTA--CTTTGTTCCAGAATCAGATGATTTAGTGTTGTTACGATAT 923
                           i  i  -- iv     vv i  ii  v  i   i i      v   iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_151418346_    924 AAATTATGTTCAAATAGATCTATGAATTAAA-GTAATGCCAATCAAAATT 972
                         v   vv vii     v      iii   v  - i   v  v        i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_151418346_    973 CCAAGAGTATCTTTCTTGTTTTTTATAGAAAATTACAAGCTG 1014
                            i------  vi   ---    ii     v v        
  L1M4_orf2#LINE/    103 CCAG------CTGCCTT---TTTTGCAGAAATTGACAAGCTG 135

Transitions / transversions = 1.24 (21 / 17)
Gap_init rate = 0.03 (4 / 133), avg. gap size = 3.00 (12 / 4)  

2322 21.25 3.91 8.55  chr2_151418346_151420962     1307  2125 (492)    L1M4_orf2#LINE/L1      128   908 (0)  

  chr2_151418346_   1307 ACAAGCTGATTCTATAATCCTCATGGAAATGCAAAAAACCTAGAGTTATC 1356
                                   i   v   i vi            iii   i   i vii 
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_151418346_   1357 AAAACAATTTTGAAAACAAATAATAATGTTGGAGAACTCATTCTACCTGA 1406
                                 i       vi  v  i  v       i     iv  v  ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_151418346_   1407 TTCTAAGACTTAATATAAAAGTACAGCA-TCAAGACAGTATAATATTGGC 1455
                           ii  i     v  i   iv     i -          i ii  i    
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_151418346_   1456 ATATGACTAG---T-TAGTATCAATGGGGCAGAA--GAGAGTTTAGAAAT 1499
                            v iv   --- -   -        iii    --      ii      
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAG-ATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_151418346_   1500 AGACCCACATATATATATAGCCAGTTGATTTTCAACAAAGTTGTCAAGGG 1549
                          i     --  i  v   i i  i         i    i v  i    iv
  L1M4_orf2#LINE/    327 AAACCCA--TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_151418346_   1550 AACTTGATGTAGAAATGGGTA-TTTTTTCAATAAACTCTGCTGG-ATAAT 1597
                         v i ii   vi    - ii  - i       i   ivv      - i  i
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_151418346_   1598 TGGATATTCATATGCAAAATAGAAACAAAACCAAAACAGAATCTCAACTT 1647
                               ?i  i        --   -------ii  iiv i i i -----
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAA--GAA-------TGAAGTTGGACCCC----- 459

  chr2_151418346_   1648 TTTCTGCATTACCTTAAAATCATATA---AATTTAGCTCAAAATATATTA 1694
                         ---------     i v -i      ---  v   i        iv  i 
  L1M4_orf2#LINE/    460 ---------TACCTCACA-CCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_151418346_   1695 TATATCTAAATGTAATACCTAAAGCT--------TTGGGGAGAAATCAAA 1736
                         ? v i          v v     i  --------i vi i     v  v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_151418346_   1737 GGAGAAAACTGTTGTGACCTTGGGTTAGGCAAAGATTTCTTACATATGAC 1786
                           ? v   iiv i                   v i       v       
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_151418346_   1787 ACATACATATGTATCGTACATATGATACATAGAAAGTGCAAACCATAAAA 1836
                           -------------------------  ---    ii   i v i    
  L1M4_orf2#LINE/    600 AC-------------------------CA---AAAGCACAAGCAACAAAA 621

  chr2_151418346_   1837 GAAGACATTGGTAAATTATACTTCATTAAAATCAACAACTTCTGCTGTTT 1886
                            i v  v i      iv       i     i  v     i  -  i  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTT 670

  chr2_151418346_   1887 -ACAAGACAGTACTAGGAAAATGAAAATAGAAACAACAAAATGGAAATAA 1935
                         - v i    v  ii i    i      v v  v v   i     i iv  
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_151418346_   1936 ATATTTGCAAAACATTGATCTGATAAAAGACTT------AGAGTATATAT 1979
                                    v   vv         ii     ------   i      -
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA- 769

  chr2_151418346_   1980 TCAAAAACTCTTAAAACTCAATAAGAAAA---CAAGCAATTCAATT-AAA 2025
                         --  i        v          v    ---   ii  ii     -   
  L1M4_orf2#LINE/    770 --AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_151418346_   2026 ACTAGTCAA-TGATTTGAATAGACATGTTACCAAAGAGAAGTTATGACTG 2074
                          v i v   -v               v iv       --  v   i----
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA--AGATATA---- 861

  chr2_151418346_   2075 CAAATGATTACACATAAGTACATGGGAAAAATCTTCAACTTCATTAGCTA 2124
                               iii ---     i     i-   i  vi     v   ???????
  L1M4_orf2#LINE/    862 CAAATGGCCA---ATAAGCACATGA-AAAGATGCTCAACATCAZZZZZZZ 907

  chr2_151418346_   2125 A 2125
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.95 (113 / 58)
Gap_init rate = 0.04 (28 / 781), avg. gap size = 3.64 (102 / 28)  


3198 23.67 3.21 2.77  chr2_151425600_151428602     1608  2511 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_151425600_   1608 TGGAGAGTTATTCCATGTTCATAGATAAGAAGACTCAGTATTGTCAACCT 1657
                             i  v   i          i   vi       i i      i  vv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_151425600_   1658 GTCAGTTCTTTGCAATGTGGTCTATA------ATGCTATCCCAATCAAAA 1701
                          v  i v  iiv   vv  i    i ------ i  v     v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_151425600_   1702 TCCCTGAAAAGGAGTTATCTT----GTGGCTATCAACCC-CTGATTTTAA 1746
                             --------  i ii   ---- ii vv  ii  vv-     ii   
  L1M4_orf2#LINE/    101 TCCC--------AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr2_151425600_   1747 AGTTTATAGAAAGAGGCAAAAGACCGAGGATAGCCAACACAATGCTGAAG 1796
                          i  i   vii i v    ii    v  i        v     vi    i
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_151425600_   1797 GAGAAGAGCAAAGTTGAAGGACTAACACTACCTAATTTCAAGACTTACTG 1846
                         i      i        i      v     v  i        i       i
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_151425600_   1847 TAA-GCTATAGTAATCAAGATAGGGTGGTATTGGCA-AAG--TA-ACAAA 1891
                         i  -    i           i  v      i     -   --  -   v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_151425600_   1892 TAGATTAATAGAAAAGAATAGAGAGGTAAGAAATAGACCCACATAAATAT 1941
                              i   i   v     v     viv       i     i i vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_151425600_   1942 AGTCAGTTGATCTTTGACAAAGGAGCAAAGGCAATACAATGGAGCAAAGA 1991
                         i    i     i  i     i  v  v   i v  v      i v  ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_151425600_   1992 TGGTCTTTTCAACAAATGGTGCTAGAACAACTGGACATCCACATGTAAAA 2041
                          i                     i i         i ?       i    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_151425600_   2042 AAACTGAATCTATACAGAGACTTTACACTCTTTACAAAAATGAATTCAAA 2091
                         i  -    vi iv  vvvv  i i    iv v         v  i     
  L1M4_orf2#LINE/    443 GAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_151425600_   2092 ATGGATAACAGATCTAAATGTTTGA----AAACTATAAAGCTTCTAAAAG 2137
                               v ?   i        vv  ----          i  ii  i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_151425600_   2138 ATAACATCCCAGAC---AATCTAGATAACCCTAGGTTTGCTGATGACTTT 2184
                          v     ---  i?---     vvi i   i i    v vii   i-   
  L1M4_orf2#LINE/    542 AAAACAT---AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTT 587

  chr2_151425600_   2185 TTTAGCTACAACAACACTAAAGGCACAATTTATGAAAAAGAGAGTTTAAT 2234
                         i    v  ii   --- i   i      viv ii   i i i i v-i  
  L1M4_orf2#LINE/    588 CTTAGATATGACA---CCAAAAGCACAAGCAACAAAAGAAAAAATA-GAT 633

  chr2_151425600_   2235 GAAAAGAATTTTCATTAAAATTAAAA-CTTCTGCTCTACCAAG-ACACTG 2282
                         i  vv i i  -   i          -   i  iv  v v   -     i
  L1M4_orf2#LINE/    634 AAATTGGACTT-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_151425600_   2283 TCAAGAGAATGAAAAGACAAGCCACAGAATGGGAGAAAGTATTTGTGAAA 2332
                               i i           v                 i      ii  v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_151425600_   2333 GATATATCTGATAAAGAACTGTTGTTCAAAATATGGAAAGAACTCTTAAA 2382
                         v             i i   vv i i  i     iv            v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_151425600_   2383 ACTTAGCAATATGAAAACAA----CTTGTTTAAAAAATGAACCGATGACC 2428
                            i ii    vi  i    ---- iiiv  ?       ii vi v  ii
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_151425600_   2429 TTAACAGACACCTCACCAAAGAAGATACACAGATGGCAAAAAAAAAAAAA 2478
                          v  i     ii  v            i   i     v  v  -------
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA------- 875

  chr2_151425600_   2479 GCATATGAAAAGATGCTCTTCATCATATCTCAT 2511
                            i              vv     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (132 / 78)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.70 (54 / 20)  


3084 26.19 0.43 2.16  chr2_151519642_151523907.rev     2851  3774 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_151519642_   2851 TGGAAACATATCCCATGCTCATGGATGGGTAGAACGAATATTATGAAAAT 2900
                               v          i        v  v   viv      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_151519642_   2901 GACCATACTAGCAAAAGCAATCTACAAATCCAATGCAATCCCCATCAAAA 2950
                          i v     vv v   vii       i  i   i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_151519642_   2951 TATCACCATCATTCTTCACAGAATTAGAAAAGACAATTCTAAAATTCATA 3000
                          vi  v vv v  i  ii     v v  v   vii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_151519642_   3001 TGAAAC--CAAAGAACAACCGACATAGCCAAAACAAGACTAAGCAAAAAG 3048
                           i  v--   i i  --  iiv             vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_151519642_   3049 AACAAATCTTGAGGCATCACACTACCTGATTTCAAAGTATACTATACAGG 3098
                               vi v    vv       v  ii        iiv     i - i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA-AAG 247

  chr2_151519642_   3099 CCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGACACATAGAC 3148
                          i i   v i   i    ii         i    ii       i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_151519642_   3149 CAATGGAACAGTATAGGGAAACCAGAAATAAACCCAAGCACTGACAGCTA 3198
                                 i  v  v i  iv               vi  i v ii ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_151519642_   3199 ACCGATCTCTGACAAAGCAAAAAAGAAAAAGAAAAAAAAAAACCGTACAA 3248
                          ii   i ii     i vvivv    ----------------  i v   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGA----------------CCATTCAA 381

  chr2_151519642_   3249 TGGGGAAAGGACACCCTTTTCAACAAATGGTGCTGGAATGATTGGCAAGC 3298
                                  i i vi                     i ii i   vv ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_151519642_   3299 CACATGTAGGAGAATGAAACTGGATCCTCATCTCTCACCTTACACAAAAA 3348
                               i ii        ii    i  ii i   v    v  i       
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_151519642_   3349 TCAACTCAAGATGGATTAAGGACTTAAACCTAAGACCTGAAACTATAAAA 3398
                          i       i      i ?i   i    iv     v  i           
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_151519642_   3399 ATTCTT-GATAATAACGTTGGAAAAACCCTTCTAAACATTGGCTTAGACA 3447
                         -i    -  vi v   i v  ?iv  vi    vvi  v    v    i  
  L1M4_orf2#LINE/    532 -CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_151519642_   3448 AGGATTTCATGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATA 3497
                          v i    v iivi v  vv         v v    i    iv   i   
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_151519642_   3498 AATAGCTAGGACCTAATTAAACTAAAGTGCTTTTGCATGGTAAAAGGAAC 3547
                         i   iv v    i v  i   v v  ivi      iiivvi   i iv  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_151519642_   3548 AGTCAGCAGAGTAAACAGAAAACCCACAGAGTGGGAGAAAATCTTCACAA 3597
                         vi   iv i   i  v   v          i           v  ii   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_151519642_   3598 TCTATACATCTGACAAAGGACTAATAGCCAGAATCTACAGTGAACTCAAA 3647
                         vii   i      i  i     vi  v       v  i iv      vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_151519642_   3648 CAAATCAGTAA-AAAACCCCAAACAATCCCATTAAAAAGTGGGCTAAGGA 3696
                            v   i   -    vvv    i  i  v   ?    i     v     
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_151519642_   3697 CATGAATAGACAATTCCCAAAAGAAGATATACAAATGGACATCAAACCTA 3746
                         iv          v   i v                   v  vi  i vi 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_151519642_   3747 TGAAAAAATGCTCAGCATCACTAATGAT 3774
                               i       i     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.43 (24 / 7)  


2891 25.99 3.52 1.02  chr2_151669712_151673934     2851  3731 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_151669712_   2851 AGACATACCATGTTCATGGAGTAAAATAATTAATATTGTGAAAATGCCCA 2900
                            i  v             v ii  v v          v  i   v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_151669712_   2901 TCCTACAAAAAGTGATCTACAGATCCAGTGCAATCCCTATCAAG-TACCA 2949
                          v  v vv   v            i  ii              i- v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_151669712_   2950 CTAACATTCTTCACAGAAATAGAAAAA--AATCCTAAAATTCATAGAGTA 2997
                         vivi v  i  ii       v  v  i--i               vi v 
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_151669712_   2998 CCACAAAAGACCTCAAATAAC--------TC-----AAAGAAAAA---AT 3031
                         vii   ii    ivi    i --------  -----      i  --- v
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_151669712_   3032 CTGAAGGTATCACACTACCTGACTT-AAAATATAGTATAAAGCTAGATTA 3080
                         i  i   vv       v  ii i  -    iv  v  i       v v  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_151669712_   3081 ATCAAAATAGCATGGTACTGGCATAAAAACAGA-A---AGACCAATGGAA 3126
                              i i  ii              ii i   - ---   i        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_151669712_   3127 CAGAATAGAGAACCCAGAAATAAATCCACCTATTTGCAGCCAACTGACTT 3176
                         i     v    ii           i   ivi    iii i   i   i  
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_151669712_   3177 TCTACAAAGACTCTGTGAATGCTCATTAGGGGAAAGGACAGTCTTTTCAA 3226
                           v    i iiv iiv  viii   v -        i i           
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTTTTCAA 404

  chr2_151669712_   3227 TAAATGATGCTGGGAAAGCTGGATATCCATAAGCAGAAAAATGAAACTAG 3276
                         i     i        v i       ?   i v   i  i      ii i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_151669712_   3277 GCCTCTATCTCCCACCATATACAAAAGTCAACTCAAAATGCATTAAAGAC 3326
                         i  i   i   v              i i           v  i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_151669712_   3327 TTAAATGTAACACTCAAAACCATGAAGCTACTAGAAGAAAACAACAGGAG 3376
                         i         v vii     i  i  i  vi            -i   ? 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-TAGGNG 553

  chr2_151669712_   3377 -AAATGCTTTAGGACATTGATCTGGGCAAAGATTTTATGAA---GACCTC 3422
                         -    -   iiv   v   ivi i     v i   iv ii ---   vi 
  L1M4_orf2#LINE/    554 TAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_151669712_   3423 AAA-GCACAGGCAATAAAAGCAAAAATAGACTGATGAGATTATACCAAAC 3471
                            -     i    i     v         ivi  vi  i vi i    v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_151669712_   3472 TAAAAAGCTTCTTAACTGCAAAGGAAAA-ATTAAGAGAATGAAGAGACAA 3520
                          v    i   i vvi  v       v v-  i    i i    i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_151669712_   3521 CCTCCAGCACAAGGGAAAACATTTGAAAACTATTCATCCCACAAGGGATG 3570
                           iv   v iii i     i     v   ii  vi   iv i      iv
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_151669712_   3571 AATATTCAGAATATACAAGAAACTCAAATAACTCAACAACAACAACAAAT 3620
                         vi   i         i  ii     vv i       i  i  ----   v
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA----AAAG 798

  chr2_151669712_   3621 ATATATATATATAGGTTAAAAAGTGGGCCATGGGCT-GAACAGATATCTC 3669
                          i v   - ivi i-  ?    i     v v  ii -   i   i  i  
  L1M4_orf2#LINE/    799 ACAAATA-ACCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_151669712_   3670 TCAAAAGAAGATATACAAATAGCCAACAGGTATATTAAAAAATGCTGAAT 3719
                           v                 i     i i i i  v    i     v  i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_151669712_   3720 ACCACTAATCAT 3731
                          i  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (147 / 78)
Gap_init rate = 0.02 (19 / 903), avg. gap size = 2.11 (40 / 19)  


3338 21.42 0.70 4.54  chr2_151756792_151759017      501  1359 (867)    L1M4_orf2#LINE/L1        4   829 (79)  

  chr2_151756792_    501 AAAGACATCCCATGTTCATGGATTGGAATAATTAATATTGTTAAAATGTC 550
                              i                      v v             i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_151756792_    551 CATGCTACCCAAAGCAATCTACAGATTCAATGCGATCCCTATAAAAATTC 600
                         v  i  v      vii              i  i        v     i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_151756792_    601 CAA-TGACATTTTTACAGAAATTTTAAAAAC-AATTTTAAAATTAATATG 648
                           i-  v v     i        v- v  i -i  ii       v     
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCATATG 152

  chr2_151756792_    649 GAGGCACAAAAGACCCCAAATAGCAAAAACAATCTTGAGCAACAAAAACA 698
                           iiii   ii     vi      v             iv  v  i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_151756792_    699 AAGCTGAAAGCATCA-ATTACCCTATTTCAGAGTCTACTACAAAGCTATA 747
                            i  i i vv   - i v   v      i iii             i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_151756792_    748 GTAATCAATACAGCATGGTATTGGCATAAAAACAGACATATGGACTGATG 797
                                 v    ii     i        ii i        i  iii   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_151756792_    798 GAACAGAATAGAGAGCCCAGAAATAAGTCCACACATTTACAGTCAATAAC 847
                            i     v     i          ii   i       ii      ---
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT--- 349

  chr2_151756792_    848 TACAATAACTTGGGGATCTTCTATAATAATTTGGGGATCTTCAACAGATT 897
                         ----------  ---  i   v i  --------  i -------- ---
  L1M4_orf2#LINE/    350 ----------TG---ATTTTCGACAA--------GGGT--------G--- 367

  chr2_151756792_    898 CCCCAAGAACACAAAATGGAAAAAGTACAGTCTCTTCAATAAATGATGCT 947
                         --      v  ivv     ii    v i     i     i     i    
  L1M4_orf2#LINE/    368 --CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_151756792_    948 AGTAAAGCTAGATAGCCACATTCAGAAGAGTAAAATTAAACTTTTATCTC 997
                         i v v i  i    ?      v  i    i i  i  ii  iii  i   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_151756792_    998 ACACTGTACACAAAA-TCAACTCAAAATGTATTAAAAACTTAAATGTAAG 1046
                             ii  i      - i           v  i ? i  i          
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_151756792_   1047 ACCTGAAATT-TAAA-CTAATAGAAGAAAACATAGAGAGAAAGCTCTACA 1094
                          v  i   i -    -  vv               i?iv   v  iiiii
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_151756792_   1095 ACATTGGTCTTGGCAAAGAATTTTTGGATATGACCCCAAAAGCATAGGCA 1144
                           v    vi v     v iv  i  i        v         i i   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_151756792_   1145 ACAAAAGCAAAAATAAACAAATAGGATTGCGTCAAACTAAAAAGCTTATG 1194
                                v       i i    v   i v i     v v    i   v  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_151756792_   1195 TACAGCAAAGAAAACAATCAACCAAGTGAAGAGGCAACCTACAAAATGAA 1244
                          i vv     i v  v     vv       i  i     i   i    ii
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_151756792_   1245 AGAAATATATTTGCAAACCATACATCTGATAAAAGGTTGATATCCAAAAT 1294
                              -           i    i         ii ii vi      i   
  L1M4_orf2#LINE/    716 AGAAA-ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_151756792_   1295 ATATAAGGAACTCAAACAACTCAATAGCAAGATAACACATAACTCAATTA 1344
                               i      vv           ii  i vi   v     i     ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_151756792_   1345 AAAAATGGGCAAAGG 1359
                                        
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGG 829

Transitions / transversions = 2.05 (121 / 59)
Gap_init rate = 0.02 (13 / 826), avg. gap size = 3.46 (45 / 13)  

 216 15.49 32.39 0.00  chr2_151756792_151759017     1664  1734 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_151756792_   1664 AGAAATGGGCAAAGGACCTGAA--GACA---------------------A 1690
                          i              ii    --    --------------------- 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_151756792_   1691 ATGGCCAAAAGATATATGAAAACATGCTCAATGTCACTAATCAC 1734
                                 v iii i       v        ii   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 11.50 (23 / 2)  


2186 24.29 12.88 1.47  chr2_151805647_151808213     1261  2075 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_151805647_   1261 TAAAAAAACATTCCATGATCATGAATAGGAAGAATCAATATTGTTAAAAT 1310
                          ii   i i  i     v     i  v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_151805647_   1311 GGCCATACTGCCCAAAGCAATTTACAGATTTAATGCTATTTCTATCAAAC 1360
                            v     v      vii  i        i  i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_151805647_   1361 TACCAACATTATTTTTCACAGAA-TTGCAAAAACCTATT-TAAAATTCAT 1408
                          v   i vviv     ii     -   - v  i iv  i-          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr2_151805647_   1409 ATAGAAATAAAAAAGAGCCTAAATTACCAAAGCAATCCTAAGCAAACAGA 1458
                           i     iv  ii  v  vi   vi     i     i i iv  iv   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_151805647_   1459 ACAAAGCTGAAGGCATTACACTTCCTGACTACAAACTATACTACAAGGCT 1508
                               i  i   vv i        ii i v    viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_151805647_   1509 ATAGTAACCAAAGCATCATGGTACTAGTACAAAAACAGACACACAGGTCA 1558
                          i     i   ii  vii       i i i  ii i     i i  i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_151805647_   1559 ACCAAACAGGTTAGAGAA-CCAGAAATAAAGCCACACACCTA-------- 1599
                          ivi  i  iv v    i-           v   i   ii  --------
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_151805647_   1600 -------CAACTATGATG----GACCCCTTAA------------------ 1620
                         ------- i  v v i  ----    vi i  ------------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_151805647_   1621 ---------------------AACTGGAT--------------------- 1628
                         ---------------------        ---------------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_151805647_   1629 ------CCCTTCCCTT-CACCATATACAAAAATTAACTCAAGGTGGATTA 1671
                         ------   i v   i-                        ii     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_151805647_   1672 AAGACTTAAATGTAAGACCTAAAAACATAAAGATAAAATCTCTAGAAGAA 1721
                         ?    i           v      vi     ----- v   -        
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAA-----ACTCT-TAGAAGAA 543

  chr2_151805647_   1722 AACCTAGG---AAATACCATTCCTGATATTGGCTTTGGCAAAGAATTTAT 1768
                            v    ---    -- -   v   iv    v  v     v i-   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGG-TTTCT 589

  chr2_151805647_   1769 TAC-TAAGTCCCCAAAAGCAATTGCAACAAAACCAAAAATTGACAAGTGG 1817
                           v-  v v v         vvv         vv      v  i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_151805647_   1818 GAC--CAATTAAACTAAAGAGTTTCTGTACAGCAAAAGAAACTATCAACA 1865
                            --  viv   i    i v   -   i vv    i  v        v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGA 688

  chr2_151805647_   1866 GATTAAACAGACAATGTCCAGAATGGGAGAAAATATTCACAAACTATGCA 1915
                         i v i  v      iviv                   ii    ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_151805647_   1916 TCTGACAAAGG--TAATATCCAGACTCTATAAGGAACTT----AA---AA 1956
                              i  i  -- vi        v v     i     i----  ---  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_151805647_   1957 AAATCAAGCAAAAAACAACCCCAT-AAAAAATGGGCAGAGGACATGAACA 2005
                         v   v  ivi v   i     v  -?           i    iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_151805647_   2006 AAGACTTATCAAAAGAAGACATGCACACAGCCAACAAATACATGAAAACA 2055
                         i v i  v  v        i  i  v ii     i  ii         v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_151805647_   2056 TGTTCATCATCACTAATCAT 2075
                           i   v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (115 / 81)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 5.32 (117 / 22)  


1983 26.07 0.93 0.74  chr2_151998868_152004223     3644  4180 (1176)    L1M4_orf2#LINE/L1        1   538 (370)  

  chr2_151998868_   3644 TAGAAACACATCCCACGCTCATGGATGGGTAGAATCAATATTCTGAAAAT 3693
                          i    v i      i i        v  v   v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_151998868_   3694 AACCACACTGCCAAAAGCAATCTACATACAAATTCAATGCAATTCCCATC 3743
                         ii v i   v  v   vii       ----i      i     i  i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA----GATTCAACGCAATCCCTATC 96

  chr2_151998868_   3744 AAAATACCACCATCATTCTTCACAGAACCAGAAAAAC-GATCCTAAAATT 3792
                              v   v vv v  i  ii     viv  v  i -            
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_151998868_   3793 CATATGAAAACAAAAAAGCACCTGCATAGCCAAAACAAGACTAAGCAAAA 3842
                               i   iiv  ii vv  v v             vvi i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_151998868_   3843 AGAACAAATCTGGAGGCATCATATTACCTGACTTCAAACTATATTATAAG 3892
                                 vi      vv   i i v  ii i      viv  i  i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_151998868_   3893 GTCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGA 3942
                          ii i   v i   i    ii         i    ii    i  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_151998868_   3943 CCAATGAAACAGAATACAGAACCCAGAAATAAACCCAAATACTTACAGCC 3992
                         i     i  i     vv   ii               v i i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_151998868_   3993 AACTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGCA---- 4038
                           i    i   i    i vviv   i v   vv i         v ----
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_151998868_   4039 CCATTCAACAAATGGTGCTGGGATAACTAGCTAGCCACATGTAGGAGAAA 4088
                          iv                    i    i v  ?       i ii    v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_151998868_   4089 GAAACTGGATCCTCATCTCTCACCTTATGCAAAAATCAACTCAAGATGGA 4138
                            ii    i  ii i   v    v   i       i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_151998868_   4139 TCAAAAACTTAAATCTAAGACCTAAAACTATAAAAATTCTAG 4180
                            ? i  i     v     v              v ii   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

Transitions / transversions = 1.71 (87 / 51)
Gap_init rate = 0.01 (3 / 538), avg. gap size = 3.00 (9 / 3)  

1189 24.21 1.32 1.05  chr2_151998868_152004223     4485  4864 (492)    L1M4_orf2#LINE/L1      528   908 (0)  

  chr2_151998868_   4485 AAAATTCT-AGAAGATAACATTGGAAAAACCCTTCTAGACATTGGCTTAG 4533
                             i   -      v     v  ?iv  vi    vv   v    v    
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_151998868_   4534 GCAAGGATTTTGTGACCAAGAAAACAAAAGCAAATGCAGTAAAAACAAAG 4583
                             v i   iv iivi v  v v        v v   ii    iv   i
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_151998868_   4584 ATAAATAGCTAGGACCTAATTAAACTAAAGAGCTTTTGCATGGCAGAAGG 4633
                            i   iv v    i v  i   v v  i i      iiivv  -    
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGG 676

  chr2_151998868_   4634 A-ACAGTCATCAGACTAAACAGACAACCCACAGTGTGAGAGAAAATCTTC 4682
                          -  vi   vv i v i  v             vi  i        v  i
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_151998868_   4683 ACAATCATGATACATCCGACAAAGGACTAATATCCAGAATCTACAAAGAA 4732
                         i   --  v   i   i  i  i     vi          v  i      
  L1M4_orf2#LINE/    727 GCAA--ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_151998868_   4733 CTCAGACAAATTAGCAAGAAAAAAAAAAAT--CCCA-TCAAAAAGTGGGC 4779
                            vv    v i ii  v     i v    --    - i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_151998868_   4780 TAAGGACATGAATAGACAAATTCTCAAAAGAAGATAGATCAATGGCCAAT 4829
                         v     iv          v-     v          v iv          
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACAT-TTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_151998868_   4830 AAACATATGAAAAAATGCTCAACATCACTAATGAT 4864
                           i  i       i             ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (45 / 45)
Gap_init rate = 0.02 (7 / 381), avg. gap size = 1.29 (9 / 7)  


2327 26.05 5.26 0.79  chr2_152012908_152014659.rev      501  1260 (492)    L1M4_orf2#LINE/L1      115   908 (0)  

  chr2_152012908_    501 TTTGTAGACCTACGCAAGTTTATGCTAACATTGATATGGAAAGGCACGAG 550
                             i   vv vvi    i v  v    v   v         v   v i 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr2_152012908_    551 TTCTAAAATAGGCAGCACAATCTTGAAA-----GAACAGAGAAAGAAGAA 595
                         vi i i     v  iv            -----     i  vvi  i  v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_152012908_    596 TCACTCTACCTGATATTAAGGCATACTATATGGCGATAGTAATGAAGACA 645
                             v  v  ii  v i  ii v     i vi  v i      v      
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_152012908_    646 ATGTG-TCCTGGCAGAGGGATAGACACA--GATCAATAGAATAGATTTTA 692
                         i    - v      v i         i --       i       v  v 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_152012908_    693 AAATCCAGAAATAGATCCACACAAATATGCTCAACTAATTTTTGACACAG 742
                         i i          i i   i   vv    v    i i     i    vi 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_152012908_    743 GTG---AAAC-ATTTCAGGAGGAACAGACA-----TTCAACAAATGATGC 783
                            --- i  -   iv v i    vii i -----           i   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_152012908_    784 TGGAAAAATTAGGCATCCATAAGCAAAAAAATGA-GTCAGGACCTAAACC 832
                            i v  i i ii ?   i v      i     -  i-     ivv   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT-GGACCCCTACC 463

  chr2_152012908_    833 TCACACCTTATTCAAACATTAACTCAAAACAGATTATGAACTCAAAGGTA 882
                                v   v    v            ii   i ?ii  ii   v   
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_152012908_    883 AAATGTAAAATTATAGAAGT--TAGGGAAAAA---AGAAGAAAATATTAA 927
                          i vv     i    i  v --   iii    ---  i? v    v  vi
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_152012908_    928 GGATCTATGGCTAGGTAAAGAGTGCTTAGAT--GGTACCAAAAACACTAT 975
                         v  i  vv  i    i  v iv v       -- ii       i   v v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_152012908_    976 TCATAAAGGGAAAAATTAATAAATTGGACCTCATCGAAAGTTTTAAAACC 1025
                         iv i   i i      vi           i     i   --  v     i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA--TTAAAAACT 661

  chr2_152012908_   1026 TTTGCTCTCTGAAAGATCCTGTTAACAGGATGAAAAGACAAGCTACAGAC 1075
                             iv  iii  i  iv  i i  v iii           v i     v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_152012908_   1076 TAGGAGAAAGC-TTTG-AAATCCATATAGTTAACAAAGGACTAGTATCTG 1123
                          i       ii-    -     -     vi i i  i     v     ii
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGGGACTTGTATCCA 760

  chr2_152012908_   1124 GAATACATAAAGAATACTCAAAATGCAACAGCAAAATAACAAACAATCCA 1173
                              i        iv  i v  iv   i ii    vi     i  i   
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_152012908_   1174 ATCAGAAAATGGGCAAA--ACCC--ATAGACTGTATACACTAAAGAGG-T 1218
                           i?i            -- iii--      -i v - v i     i - 
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGAC-ATTT-CTCCAAAGAAGAT 858

  chr2_152012908_   1219 GTACA---GAC-----AGCAAATGAAAAGATATTCAACATCATTAGCCAT 1260
                         i    --- i -----    v          ii         ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (121 / 73)
Gap_init rate = 0.03 (22 / 794), avg. gap size = 2.09 (46 / 22)  

 881 14.81 13.76 0.00  chr2_152012908_152014659.rev     1449  1637 (115)    L1M4_orf2#LINE/L1      694   908 (0)  

  chr2_152012908_   1449 AAAAGACAGTTCTTAGAATGGGAGAAAAAACTTACAAACCATGTATCTGA 1498
                                 iii vi              v i  i    i   i       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_152012908_   1499 TAAGGGTCTAGTATCCAGAATATA--AAGGACTC----------ATAATA 1536
                               v  v              --   i    ----------      
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_152012908_   1537 AAAA--------------TTGAAAAATTGGCACAGGATCTGAATAGACAT 1572
                             --------------  ?      v    v     i           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_152012908_   1573 TTCTACAAAGAAGATATTCAGATGGTCAATGAGTGTGTGAAAAGATACTC 1622
                             v            v  i    i    i  iiii         i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_152012908_   1623 AACACCATTGGTCAT 1637
                             i  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (19 / 8)
Gap_init rate = 0.01 (3 / 215), avg. gap size = 8.67 (26 / 3)  


 624 23.30 5.68 1.70  chr2_152106676_152109624.rev      955  1130 (1819)    L1M4_orf2#LINE/L1        1   183 (725)  

  chr2_152106676_    955 TGGAAAGACATCT-GTGTTCATGGGTAGAAAGACTTAACATCAATGAAAT 1003
                                 i   i-i         i v i         i  iiv i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_152106676_   1004 GCTAA--CTACTCAAGGCATT-ATATGCAGATTCATCACAATCCCTACCA 1050
                          vi  --  v i   ---   -  v i        v i         i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA---ATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_152106676_   1051 TGATTCCAACTGTCTTTTTCACAGATA--AAGAAGTCGATCGTCAAATTC 1098
                         vi  i   i   i      ii    v --i v   ii    v v      
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_152106676_   1099 ACACGGAATTGCA---GTCTCAAAA-AGCCAAAACA 1130
                          i i    v    --- v i  i  -          
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

Transitions / transversions = 2.15 (28 / 13)
Gap_init rate = 0.04 (7 / 183), avg. gap size = 1.86 (13 / 7)  

 634 23.83 7.25 0.52  chr2_152106676_152109624.rev     1437  1629 (1320)    L1M4_orf2#LINE/L1      171   376 (532)  

  chr2_152106676_   1437 AAAAGCCAAAACAATCCTGAAAAATAA---TAAAACCAGA-----CAAAC 1478
                           v             i       v  ---i   iiii  -----  v  
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_152106676_   1479 T----GACTGCCAAACTTAGCATAAAGCTATAGTAATTAATACA-TATGA 1523
                          ----i i v v       vi i       i      i  v   - i  i
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_152106676_   1524 TAATGGCATAAGGACAGCCATACAGACCACAAGAATAGAATACTGAGCTT 1573
                           v           i  v    i   i  vvi         vvv   iii
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_152106676_   1574 GGATATAAATCTTTACACCTATGTTCAATTGATTTTCAA-AAGGGTACCA 1622
                         i  v     i iv    ii    v             i -      i   
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_152106676_   1623 CAGGCCA 1629
                         -  i   
  L1M4_orf2#LINE/    371 -AGACCA 376

Transitions / transversions = 1.71 (29 / 17)
Gap_init rate = 0.03 (6 / 206), avg. gap size = 2.50 (15 / 6)  

1799 22.82 6.58 0.58  chr2_152106676_152109624.rev     1941  2457 (492)    L1M4_orf2#LINE/L1      361   908 (0)  

  chr2_152106676_   1941 AAGGGTACCACAAGGATTTAAT-----AAAAACAACCTCTTCAGTAAAAG 1985
                               i   vi vv   i   -----  i  i ii  i    ii   v 
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_152106676_   1986 ATATTGAGGAATCTGAACATCTGCATGCAAAAGGATGAACGTGGACTCTC 2035
                         i ii  i iv v   i i ? ii          i     vv     i ii
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_152106676_   2036 ACCTTACACCATATCCAAATATTCACTCAAAATGGTTCAAAGATCTACAT 2085
                             i         v    v   v           v   ?   i   v  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_152106676_   2086 TCAAGATCTAAAACTGGAAAATTCTTAGACGAAAGCATTGGGAAACAAA- 2134
                         vi    v        iv    i       v    i   v  ?i--i   -
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG--TAAAT 558

  chr2_152106676_   2135 ---AATGACACTGGATTTGGCAACAACTTCATGAATATGATGTCAA--GT 2179
                         ---vi    vi   i  v     iiii   v ii      iii   -- i
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_152106676_   2180 ACTAGCAATAACA--AAAAATATATATATTATACTTCACCAAAATTAAAA 2227
                           v     i  v --       v   v   iv      i           
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_152106676_   2228 ACT------CTGCAATGGATATTACCAAGAAAGC-AAAAGAGAACCTACA 2270
                            ------  v   v   i i  i        i-      v    i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_152106676_   2271 GAACGGAATTAAATATTTGCAAATCACAAAACT---AAGGGATGCATATC 2317
                            i  i vv                i v v  ---      ivii    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_152106676_   2318 CAAAACATATAAAGAACT---ACAACTCAACAACAAAAATTCAAA----C 2360
                           i  i            ---         i  i     vv    ---- 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_152106676_   2361 CTACTCAAAAATGGGCCAAGGACTT----AGACATTTCTCCACAGACAAT 2406
                          v i ?          v     i  ----             v   vi  
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_152106676_   2407 GAAACAAACAGCCAAGAACCAAGTGAAAAGATGTTCAACATCACTAGTAA 2456
                         - v     ii     v  v  vi          i         ???????
  L1M4_orf2#LINE/    859 -ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_152106676_   2457 T 2457
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.53 (69 / 45)
Gap_init rate = 0.02 (12 / 548), avg. gap size = 3.08 (37 / 12)  


3342 26.65 0.44 0.44  chr2_152381136_152387411.rev     4877  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_152381136_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_152381136_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_152381136_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_152381136_   5025 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAGTCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  v     iv  i  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_152381136_   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_152381136_   5125 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_152381136_   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5222
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_152381136_   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_152381136_   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_152381136_   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_152381136_   5373 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_152381136_   5423 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCCTGTCTAA 5472
                         v    ?i v viv   iv   v v  vv i     v ii   i ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_152381136_   5473 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCGGATCTAA 5522
                         i            vvi          vv     v  i    i   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_152381136_   5523 TTAAACTAAAGAGCTTCTGCACAGCAAGAGAAACTACCATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv   ii  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_152381136_   5573 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5622
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_152381136_   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5672
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_152381136_   5673 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5722
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_152381136_   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5772
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_152381136_   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3166 26.87 0.66 0.66  chr2_152424893_152431262     4973  5880 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_152424893_   4973 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATAATGTGAAAAT 5022
                              ii i  i     i        v      v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_152424893_   5023 GGCCATACTGCCCAAGGTATATTATAGATTCAATGCCATCCCTATCAAGC 5072
                            v     v     iv ivvi  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_152424893_   5073 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTAAAATTCA 5120
                          v   iivi i  i  ii     -   -- v  i  - i i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_152424893_   5121 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5170
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_152424893_   5171 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTGTACTTCAAGGC 5220
                                i      vv       v  ii i      viv    v   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_152424893_   5221 TACACTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5270
                             v   i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_152424893_   5271 AATGAAACAGCAT--ACAGCCCTCAGAAATAATACCACACATCTGCAACT 5318
                             i  i  v  -- v  i  --        vv   i    i iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_152424893_   5319 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCT 5368
                          vi    i  i     ivv  v   i v  vvv           i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_152424893_   5369 CTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGTTATATGTAGAAAGCT 5418
                           v  i  i  i           v      v  ?ii i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_152424893_   5419 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5468
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_152424893_   5469 TTAAAGACTTAAATGTTACACCTAAAACCATAAAAACCCTAGAGAAAAAC 5518
                          i ?    i       v v v       i      vi i    ii     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_152424893_   5519 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGATTA 5567
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_152424893_   5568 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5617
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_152424893_   5618 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5667
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_152424893_   5668 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACA 5717
                         v  i     i                 v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_152424893_   5718 AAGGGCTAATATCCAGAATCCACAAAGAACTTAAACAAATTTACAAGAAA 5767
                          i  i  vi          vi i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_152424893_   5768 AAAACCAAACAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5817
                           i  -   i   i v  i?    i            v    i     i 
  L1M4_orf2#LINE/    796 AAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_152424893_   5818 TCTCAAAAGAAGACATTTAAGCAGCCAACAGACACATGAAAAAATGTTCA 5867
                             v        i  vi  iii     i ii          i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_152424893_   5868 TCA-CAACTGGCCA 5880
                         v  -  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


 310 32.35 9.19 3.31  chr2_152432617_152434365.rev      215   486 (1263)    L1M4_orf2#LINE/L1       22   309 (599)  

  chr2_152432617_    215 TGAATGGGAAGATT--ACATTATAAAACTACCAATTCTTGCGAAACAAAG 262
                           i  v      i -- i   i v  iv iv    v  iv v   ivi v
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGAT 71

  chr2_152432617_    263 CTATAAATTAAATGCAATTATTTTTTTAAATCCAAG--GATAATTTTAAT 310
                            i i   v  i     i-ii v iv      v  -- vivv    ivv
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATC-CCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr2_152432617_    311 GAAACATGATAGGCT-------AAAT--ATATCACAAATAACAAAAATAT 351
                             i-   i i   -------    --    vi-    ivv iii ivi
  L1M4_orf2#LINE/    121 GAAAT-TGACAAGCTGATCCTAAAATTCATATGG-AAATGCAAGGGACCC 168

  chr2_152432617_    352 AAAATATCCAAATGAATTTT-----AGAAGAA------TGGGGGCAGCTT 390
                          i    v     vv   i  -----       ------   i  --i  i
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG--ACTC 216

  chr2_152432617_    391 GCTCT-ACAGATATCAAAGCATACTAAAGAGCTGCAGTAGCTGAAACAGT 439
                         i v  -v vi  v     i v     v i    i     iiii i     
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_152432617_    440 GTGATACTGACTTAGGAACAATGAAACAGATTGATTGAGGAAAGAGA 486
                            i     i v  i i i i----   v  v   ii v i  v   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAG----ACATATAGATCAATGGAATAGA 309

Transitions / transversions = 1.44 (52 / 36)
Gap_init rate = 0.04 (12 / 288), avg. gap size = 2.83 (34 / 12)  

1801 27.37 6.87 2.85  chr2_152432617_152434365.rev      487  1257 (492)    L1M4_orf2#LINE/L1      107   908 (0)  

  chr2_152432617_    487 CTACACTTTTCAGGGAAATTGATAAGCTGGTTGTAAAATTTGTGTGGACT 536
                           i vi    iivi        i      i iv       ii i    v-
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA- 155

  chr2_152432617_    537 ATCCAAGA---CAGGAATAACCAAAACTCTGTTGAATATAAAGAATGAGG 583
                           v    i--- vi     i       vv v     v vi     ii i 
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_152432617_    584 TGAGAGGACTTGCTCTTCTAGAAATCAAGACATACCACAAAGCTACAG-A 632
                          vi       ii v    ivi vv    i  v   i            - 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_152432617_    633 ATTAAAATAGTGTGGTATTGGTGCAAGGCTAGACAAATAGACCAGTGGA- 681
                           i  i i         i   iii    v      v     i  i    -
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_152432617_    682 TATAACAGGGAGTTCAGAAA-GAACTCACA-ATTT-TGGTAACAGAAAAT 728
                           v  iv i    i      -i   i  i -    -    --  ------
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT--CA------ 347

  chr2_152432617_    729 ATTGAT----AGCAGAGG----AGGAACTTTATCCTGTTGGGAAATGATG 770
                               ----ii  ii  ---- i  v ---  i vi v      vi  i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACC---ATTCAATGGGGAAAGAATA 394

  chr2_152432617_    771 GAATTCTCAATAAA--ATG-TGAGACAATTGGCTATCTATATACTAAA-A 816
                          vv  i    i   --i  -  i     i   v  ? i i  i v   - 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_152432617_    817 ATAAAATTAAATCTCTCCTTCATA--ACATAGAAAAATAATTTCCAGGTA 864
                           i  i  ii i i  v i   i -- i   v      v vi  v ii i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_152432617_    865 GGTTAAAGACTTAAATGTAATACATAAAACTCTAAAGATTTTAGAAGAGT 914
                          i i ?    i         v vv       v    iv i        iv
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_152432617_    915 ATATAGGAACATATCTTCGTGACCTTGGGT-AAAAAGTATTTTTTTG--- 960
                          i     ?ii v                  - iiv i iv   i  i---
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_152432617_    961 ------TTGAAAGCAGTAGTCACAAAAAACAAGATTCATGAAGCTGACTA 1004
                         ------iii      vv  iv      i v  i  vv  i  viv    v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_152432617_   1005 CATGAAAATTAAAAACTTTT---CATCATATGTCAGTATGAAAATGATGA 1051
                            v                --- v   v v v  v   v  i vii   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_152432617_   1052 AAAGAAAAGCCA----ATGAGAGGCGAAGACATCTGCAGA--ATATGTGA 1095
                              v  v   ----   i   ---  i i  i    i --    i v-
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAG---AAAATATTTGCAAATCATATATC- 740

  chr2_152432617_   1096 TGATCAAAGGA----TATTCAGACTA----AAGAAGGTCTATAGATCAAT 1137
                             -  i   ----   i    v  ----     vvii  i iv     
  L1M4_orf2#LINE/    741 TGAT-AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_152432617_   1138 AAACAAAAGGTCAACAACTCAACAGAAAAATGGTTAAGAGACTC----AG 1183
                           vv     iiv  i   i   iv?        vi  ii  i i----  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_152432617_   1184 ACACTTCTCAAACAACAACAAAACATTGAATTGGCTAACAAACATATAAA 1233
                            i     ---   -- v  i i  vv  v    i  i  i  i  i  
  L1M4_orf2#LINE/    840 ACATTTCTC---CAA--AGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_152432617_   1234 AAGGAGTTCAGCCTCACCAGTAGT 1257
                            iv i   i v   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (129 / 78)
Gap_init rate = 0.04 (29 / 802), avg. gap size = 2.59 (75 / 29)  


2553 24.54 11.06 0.73  chr2_152591656_152597561.rev     4592  5414 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_152591656_   4592 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4641
                               i i  i    vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_152591656_   4642 GGCCATACTGTCCAAAGTAATTTATAGATTCAATGCTAGTCCCATCAAAC 4691
                            v     vi     v i  i  i        i  v vi  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_152591656_   4692 TACCATTGACATTCATCACAGAATTAGAAAAAAACT-ATTTTAAATTTCA 4740
                          v   vivi v  iv ii     v v  v  i--  -  ii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_152591656_   4741 TATGGAA-T-CAAAGAAGACCCCATATAGCCAAGACAATCTTAAGCAAAA 4788
                                - -   i --     viv        i        i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_152591656_   4789 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 4838
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_152591656_   4839 GCTACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGACGTATAGA 4888
                               i   i   i    ii         i iv ii i    i      
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_152591656_   4889 CTAATGGGGCA------AGAACCTCAGAAATAACACCACACATCTACAAC 4932
                         ii     iii ------   ii -         vv   i    i  iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chr2_152591656_   4933 CATCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGATCT 4982
                           vi    i   i    ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_152591656_   4983 CCTATTCAGTAAGTGGTGCTGGGAAAACTAGCTAGCCATATGCAGAAAAC 5032
                         i  v    ii  i           v    i v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_152591656_   5033 TGACACTGGACCCCTTCCTTATGCCTTACACAAAAATTAACTCAAGATGG 5082
                            vii         v   i ii  v  i                i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_152591656_   5083 ATTAAAGACATAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAA 5132
                           i ?    v         i v i     i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_152591656_   5133 C---------------------------CTAGGCA---GTTCC----AT- 5147
                          ---------------------------i      ---   i ----  -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_152591656_   5148 -----TCAGGA-CATAGGCA-------------TAGGTAA---------- 5168
                         -----i  ii -  i i   -------------   i   ----------
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_152591656_   5169 -------TTAAAGAGCTTCTGCACAACAAAAGAAACTATCATGAGAGTGA 5211
                         -------     i -   i  ii vv    i  v       v  i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_152591656_   5212 ACAGGCAACCTACAGAATGGGAGAAAATTGTTGCAATCTACCCATGTGAC 5261
                          v  i     i                 vv      vii ivi  v   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_152591656_   5262 AAAGGTCTAATGTCCAGAATTTACAAGGAACT--TA-AAC---ATATTTA 5305
                           i  v  vi i        v  i  i     --  -   ---   v v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_152591656_   5306 CAAGA-AAA--ACCCCACGAAAAAGTGGGCAAAGGATAGGAACAGACACT 5352
                         v    -   --    v iv?    i            vv   i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_152591656_   5353 TCTCAAAAGGACATTTATG--CGGCCAACAAACATATGAAAAAAAACACA 5400
                             v    i v  v  ii--i      i  i  i       i vi v  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_152591656_   5401 ACATCACTGATCAT 5414
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (125 / 74)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.62 (97 / 21)  


 816 28.64 11.69 5.49  chr2_152818897_152821082.rev      849  1686 (500)    L1M4_orf2#LINE/L1        3   892 (16)  

  chr2_152818897_    849 GGAGGATA--CCATGTTCATAG---GGAAGAAACCTTAATATTGCAAAGA 893
                          i i    --          i ---      ---          iv    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGA---CTTAATATTGTTAAGA 49

  chr2_152818897_    894 TTTCTTT-TTTCTTATATTATTGCATAATTTCAGTGCATTTCCAGTTCAA 942
                          vv vv -i i ii v   iv vi i iv    ii   v i  vi iv  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_152818897_    943 ATCCCAACAGGACTTTTTCCCCAGAGAACTTGAAAAG-TAATT-TAATAT 990
                               i v -- i    iiv    i --    v   - i  i-   v  
  L1M4_orf2#LINE/    100 ATCCCAGCTG--CCTTTTTTGCAGAAA--TTGACAAGCTGATCCTAAAAT 145

  chr2_152818897_    991 TAATGTGGAAATTTGAAGG-TGTGCAATA--------AAT---GAGAAAG 1028
                          v  i       vii i  -iviiv    --------   ---  i    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_152818897_   1029 AGTAACATAGAAAGGGTATT-----TTCCC--TGGCAGA---TATTA--- 1065
                          iv    v  vvi i v i -----     -- vv  i ---  i  ---
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_152818897_   1066 AGGTACATTAA-CAAGAT-GTGTGA-------------ACAGATACATGG 1100
                           v    v   -     i-     i------------- i   i i  i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_152818897_   1101 ACTATTGCAACAGAAT--GGAGTCTAGAAATAGGCTCATG-A---ATAG- 1143
                          ii v  v  i     --i     i       ii i   i- ---  i -
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_152818897_   1144 --ATTACTGTTTGAAAGGTAGGGTATTATAAATTACT------AGAAAAA 1185
                         --   iv v  i  v ---     iii - i ii i ------i    i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACA---AGGGTGCCA-AGACCATTCAATGGGGAAAGA 391

  chr2_152818897_   1186 ATGGTGGACTATTTAATAAATTTTGCTGTGATGAATGGCTCTTTTTATAC 1235
                           i  ---  v  i  i    vv     v  ii v   v v?iivi  i 
  L1M4_orf2#LINE/    392 ATAGT---CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_152818897_   1236 TACAGATAAAATTTTGATCAGT--TTCACATAGTACATTAAAATTTCATT 1283
                         v v   vvi  v  v  i vv --i     ivi  i iv      -v i 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AACT 487

  chr2_152818897_   1284 CCAAATGAATTAAAGACCTAAACATGGGAGAGGGAAAA--AAAAAAT--- 1328
                          v     i  i ?         --  vi    vv    -- v    i---
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAA--TGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_152818897_   1329 ---AAAAAAAC-------TAAAACTACA-G---TTAAGTATATAGGAGAA 1364
                         ---  i     -------    v  v i- ---  ii  ---    v-  
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT---TAGGC-AA 581

  chr2_152818897_   1365 TAGATTTAGGAGTTTAAGGGTAGAAAAGGGTAAAAGCATAAGCCATGAAA 1414
                          i -   -----i   -- i  vi v v--i       i    v ii   
  L1M4_orf2#LINE/    582 TGG-TTT-----CTTA--GATATGACAC--CAAAAGCACAAGCAACAAAA 621

  chr2_152818897_   1415 GAAAAGATTGCCAAATTTGATTGCAT-AGGGGAAAAAACCACTGTACAGT 1463
                              i  v vi     v  i v   - iiivv      ivi   i -v 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC-TT 670

  chr2_152818897_   1464 TAAAGAA-ACCATAAACATATGCTGAAAAGACAGCG-ACAGCCTAGAAGA 1511
                         i    i -  i  v  v v - -          i v-    vv i i   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAA-G-TGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_152818897_   1512 AGTTCTCTGCATAAT------TCAGACAAACAACTGCTGTCCAAAATGTG 1555
                          iv v i    -   ------  v  i  ivi   vv i    i   i i
  L1M4_orf2#LINE/    719 AAATATTTGCA-AATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_152818897_   1556 TAAAGAACTTCTACAGATCCATGA-AAAAAGACAAATGATCCAGTAGAAT 1604
                                  ii    iv  v  i -            i i   i ---- 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT----T 813

  chr2_152818897_   1605 AAGAAAAGTGGGCAAAA-ATACGAAAAAAAAGGCAGTT-TACAGAAAAGG 1652
                         ? i   --        i-  vi   v i ----  v  - v  i i   i
  L1M4_orf2#LINE/    814 WAAAAA--TGGGCAAAGGATTTGAATAGA----CATTTCTCCAAAGAAGA 857

  chr2_152818897_   1653 CAATCTGAATAGCTAGCAAGCACA--AGTAGATGCT 1686
                         i - vii   i  i ii       -- iv       
  L1M4_orf2#LINE/    858 TA-TACAAATGGCCAATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.06 (56 / 890), avg. gap size = 2.57 (144 / 56)  


3131 26.18 0.55 1.10  chr2_152874929_152880208     3876  4788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_152874929_   3876 TGGAAAAACATTCCATGCTCATGGATAAGAAGAATCAATATCATGAAAAT 3925
                               i i  i     i        vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_152874929_   3926 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCTCATCAAGC 3975
                            v     v      v i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_152874929_   3976 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 4023
                          v   -   v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_152874929_   4024 TATGGAACCAAAAAAGAACCCATATAGCCAAGACAATCCTAAGCAAAAAG 4073
                                viiv  ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_152874929_   4074 ACCAAAGCTGGAGGCATAACACTACCTGACTTCAAACTATACTACAAGGC 4123
                          v     i      vv v     v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_152874929_   4124 TACAGAAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAAACC 4173
                              v  i   i    ii         i iv ii i   i     i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_152874929_   4174 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCAT 4223
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_152874929_   4224 CTGATCTTAGACAAACCTTACAAAAACAAGCAATAGGGAAAGGATTCCCT 4273
                         i    i  v     ivv vv   i v  vv    i       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_152874929_   4274 ATTTAATAAATGGTGTTGGGAAAACAGGCTAACCATATTCAGAAAACTGA 4323
                         v  i  i        i     v   v  v  ?   i  v  i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_152874929_   4324 AACTGGGCCCCTGACTTACACTTTATACAAAACTTAACTCAAGATGGATT 4373
                          ii   i     iv  i    iv         v         i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_152874929_   4374 AAGGACTTAAACGTGAGACTTAAAAACATAAAAACCCTAGAAGAAAACCT 4423
                          ?i   i    i  i   vi     vi      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_152874929_   4424 AGACA-ATACCATTCAGGACATAGACATGGGCAAAGATTTCAT-GAT-TG 4470
                           i?i- v i -   iv   v v ivv i     v i    v -   -  
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_152874929_   4471 AAACACCAAAAGCAATAGCAACAAAAACCAAAATTGACAAATGGAATCTA 4520
                          --           vv          ivv     v  i    v i ii v
  L1M4_orf2#LINE/    598 A--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_152874929_   4521 ATTAAACTAAGGAGCTTTTGCACAGCAAAAGAAACTGTCATCAGAGTGAA 4570
                           i   v v ii i      ii vv    i  v   i   vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_152874929_   4571 CAGGCAACCTACTGAATGGGAGAAAATTTTTGCAATCTATTCATCTGACA 4620
                         v  i     i  v              v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_152874929_   4621 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 4670
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_152874929_   4671 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 4720
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_152874929_   4721 CTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAATCATAAAAAAG 4770
                            v        i  vi vi       i  i  i     -----  i v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-----AAGATG 890

  chr2_152874929_   4771 CTCATCATCACTGGTCAT 4788
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


 942 23.19 3.99 3.62  chr2_152887295_152889812      542   817 (1701)    L1M4_orf2#LINE/L1        1   277 (631)  

  chr2_152887295_    542 TGGAGAGATG--CCATGTTCATGG-TTGAAAGACTCAATATTGTAAAGAT 588
                             i    i--            -   i      i        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_152887295_    589 GCCATTTCTCCCCAAATTGCTCTATAGGTTTTATATAATTCCAATCAATA 638
                          v  v v            v    i  i  iv iii   i  v     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_152887295_    639 TCCCAGA-GTATTTACTTTGTTAAATTTGAACAAACTAATCCTAAACTTT 687
                               v- iv   --    ivi  v    -   i  i        v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT--TTTGCAGAAATTGA-CAAGCTGATCCTAAAATTC 147

  chr2_152887295_    688 ATGTGGAAGAGCAAAGG--CCAGTAATAACCAACACCCTCTTAAAGAAAA 735
                           i     iv    i  --    -    i    v  vv    i  i  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAG-AATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_152887295_    736 TAAATAA----GAAGGAG-CATACTTAACCTATCAGTTATAAAATTATTT 780
                         vi  i  ---- i    v-  i    --  ---  i  vi    i - vi
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTT--CC---CAATTTCAAAACT-TAC 240

  chr2_152887295_    781 TATAAAGTTGTAGCAATTAAAATGGTGTGGTGTTGGC 817
                           i    i ii  i   i  i ii       ii    
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

Transitions / transversions = 2.05 (43 / 21)
Gap_init rate = 0.04 (12 / 277), avg. gap size = 1.75 (21 / 12)  

 917 29.35 11.13 2.02  chr2_152887295_152889812     1111  1604 (914)    L1M4_orf2#LINE/L1      259   797 (111)  

  chr2_152887295_   1111 AAAATTATGTGGTGTTTGTATAGTGACAGGAAAAAAAGACTAA-GGGGCA 1159
                           i ivi      ii v i   iv  i  - v v v   ii  -  iii 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAG-ACATATAGATCAATGGAATA 307

  chr2_152887295_   1160 GAACTGAGAGCCTAGAAATAGACCCTTGCAAATACAGATATTTGAT---- 1205
                            i      i i       i    v i  vv  ii vi v     ----
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_152887295_   1206 -ACATGAATG---AAATTATCTTGCAAATGAACAAGGAAAGAGTGGTCTT 1251
                         -   v ii  --- i ii  ii----    i----       i i     
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTC----AATGG----GGAAAGAATAGTCTT 399

  chr2_152887295_   1252 -------------GCC---ACAAATAGATAAACATATGGGAAAAAAAGAA 1285
                         -------------  i---    v i    ?v  i   vi   i  v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_152887295_   1286 ATTGCACCCCT---TCACACCATACACACAAGA-------AAGACAGATT 1325
                         i   v      ---          i   -  i -------  i ii   i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACA-AAAATTAACTCAAAATGGATC 498

  chr2_152887295_   1326 AGAGACCTAA-TGGAATAAC-AATACAATTGAGTTTTCAGAAGGCAAAAT 1373
                          ?        -  v  v i -  v  v  vi ii i i     iv  v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_152887295_   1374 TGGT-TA--TCTTTATAACATCATAATGGGGAAAGATTTCTTAAA----A 1416
                         v  ?-  --    ii i  v iiviv i  v  v i       i ---- 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_152887295_   1417 CAG-AGAAGTGTAAAAAATAAGGGGAAAA-TGG-TGAATCA-ACTACATT 1462
                           v- i   iii  iv  i  ii i    - i - i   ii-   v   i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_152887295_   1463 TAAGTTTAGAGCTTTTATTCCTCAAAGGACACCATGAAGACAGTGAAAAG 1512
                         v  i  v i i     i v i           i  v    v         
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_152887295_   1513 ACAAACCATAAACTGGGAGAAGATAATTGCAGCACGTATAACCAATAAAG 1562
                             v   i i v        i   v     ivv i    v ii    i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_152887295_   1563 GATTAGT--CCAAAATGTATAGAGAATTTTTATGATTT-----TAAAAA 1604
                           i v  --   i   i    i    i i   ii i i-----      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

Transitions / transversions = 2.16 (97 / 45)
Gap_init rate = 0.04 (22 / 539), avg. gap size = 2.95 (65 / 22)  

 303 26.02 3.25 2.44  chr2_152887295_152889812     1896  2018 (500)    L1M4_orf2#LINE/L1      772   895 (13)  

  chr2_152887295_   1896 GAATTCCTGTGATTTTAATAAGAAAAATACAAACACTCCAATAGAAAGAC 1945
                            i  i iii i i-     v     v     i vi     v?   i i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTC-AATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_152887295_   1946 GGTCAAAAGAAATGACCAGAAATTTCACCAAACGGAA---ACAGAAATGG 1992
                           v    i  vv   vi   v     v     --   --- i v      
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAA--GAAGATATACAAATGG 868

  chr2_152887295_   1993 CCCATAAACCTATGAAAAG-TGTTTAA 2018
                           v    i vi        -  i i  
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.38 (18 / 13)
Gap_init rate = 0.03 (4 / 124), avg. gap size = 1.75 (7 / 4)  


 314 17.31 0.00 0.00  chr2_152892491_152897134.rev     1900  1951 (2693)    L1M4_orf2#LINE/L1        1    52 (856)  

  chr2_152892491_   1900 TGGAAAAACAACCCATATTCACGGATCAGGAGATTTAATATTGTTAAGAT 1949
                               i i v     i    i    ii i   i                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_152892491_   1950 GG 1951
                           
  L1M4_orf2#LINE/     51 GG 52

Transitions / transversions = 8.00 (8 / 1)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.00 (0 / 0)  

1231 14.60 4.42 0.88  chr2_152892491_152897134.rev     2383  2608 (2036)    L1M4_orf2#LINE/L1       46   279 (629)  

  chr2_152892491_   2383 AAAATGGCAATAATCTCCAAACCGATCTACAGATTTAATGCAATTACTCT 2432
                           i         v  i     ii            i  i     iv  v 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_152892491_   2433 CAGCATCC-AGCTGGCATCTTTGTGGAAATTAACAAACTGACCCTAAAAT 2481
                           iv    -     v v i    ii      i    i    i        
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_152892491_   2482 TTATATGGAAACTCAAGGGACCCAGAATAGCTGGAACAATCTTTTAA--G 2529
                          i         iv                  iii         vv  -- 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_152892491_   2530 AAGAACAAAGTTGGGGGACT------TCCCAATTTCAAAACTTACTACAA 2573
                                       i     ------                        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_152892491_   2574 AGCAACAGTAATCAAGACAACGTGCGGC-CAGGCAT 2608
                            v               --   i  i- v     
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACA--GTGTGGTACTGGCAT 279

Transitions / transversions = 2.00 (22 / 11)
Gap_init rate = 0.02 (5 / 234), avg. gap size = 2.40 (12 / 5)  

1146 22.01 2.24 0.00  chr2_152892491_152897134.rev     2879  3146 (1498)    L1M4_orf2#LINE/L1      258   531 (377)  

  chr2_152892491_   2879 CAAAA-AATGTGATGCTGGCATAAGGACAGACATAGAGATCAATGGAATA 2927
                            i - i    i i            i       v              
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_152892491_   2928 GAACTGAGAATTTACTC-TAAACCCTCTCATTTACAGTTA-TTACCTGCC 2975
                            i     i ii vvv-       viv      ii  i -  ivi vi 
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_152892491_   2976 TGCAAGGATCCCAAAACAATTTAATGGAGAAA-AATAGTCTTTTCAACAA 3024
                         vi     i v    i  v   i     i    -                 
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_152892491_   3025 ACAACAATGGGACAACTGTATAGCCACAGGCAAAAGAATTATTTTCGACT 3074
                          iiiiiv           v   ?     v          v vv  v   i
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_152892491_   3075 CCTACCTCATAC--TATACAAAACTTAACTAAAAATGGATCAAACACCTA 3122
                                  i  --         v      v           ? v     
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_152892491_   3123 AACATTAATGTCAAAATTATAAAA 3146
                           ii v iv ii    i       
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAA 531

Transitions / transversions = 1.48 (34 / 23)
Gap_init rate = 0.02 (5 / 274), avg. gap size = 1.20 (6 / 5)  

 853 17.86 1.02 3.57  chr2_152892491_152897134.rev     3456  3651 (993)    L1M4_orf2#LINE/L1      512   702 (206)  

  chr2_152892491_   3456 TAAGAGCTAAAATCTCCTAA--TCTTAGAGGAGAAGATAGGAGTAAATCT 3503
                                     -  viv  --       i  i  v     ?        
  L1M4_orf2#LINE/    512 TAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_152892491_   3504 TCATGACCTTGGATTCTGCAACATTTTCTTAGATACGACACTAAAGGCAT 3553
                           i         i  vv    iiv           i     i   i   i
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_152892491_   3554 GAGCAAGAAAAATAACAAAAATAGATAAATTGAGGTTTGTCAAAATTAAA 3603
                         i     v    i-  --               iiv  ii           
  L1M4_orf2#LINE/    611 AAGCAACAAAAG-AA--AAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_152892491_   3604 TACATTGGTGTGTCAAAGGATACTGTCAAGAAAGTGAGCCAAGGGCAA 3651
                         v  v  v   iv        i   i            ---  i i   
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA---AAAGACAA 702

Transitions / transversions = 1.83 (22 / 12)
Gap_init rate = 0.03 (5 / 191), avg. gap size = 1.80 (9 / 5)  

1123 15.45 0.81 5.28  chr2_152892491_152897134.rev     3907  4152 (492)    L1M4_orf2#LINE/L1      674   908 (0)  

  chr2_152892491_   3907 AAGACCCTGTCTCAAGAAAAAGTGCAAAGACAACTCACGGAATGGGAGAA 3956
                          i   v  i  --      --   v         i   i           
  L1M4_orf2#LINE/    674 AGGACACTATC--AAGAAA--GTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_152892491_   3957 AATACTAACAATTCATACATTGGACAAGATTGGACAAGGGCTTGTATCTA 4006
                             i vi   v     i  iv  i   ---------  i        i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAG---------GGACTTGTATCCA 760

  chr2_152892491_   4007 GAATATATAAAGTACTCCTACAATTAAATAATAAAAAGATAAGTAATCCA 4056
                                     v    i     i v             i  i   i   
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_152892491_   4057 ATTTAAAAATGGACAAAGGATCTTAA--GACAATTCTCCAAAGAGGATAT 4104
                            ?        i        i v  --    v           i     
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_152892491_   4105 ACAAACAACCAATAAACATTTGAAAAAATGCTTGACATCATTAGTTGG 4152
                              iii       i  iv      i     ii      ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.70 (27 / 10)
Gap_init rate = 0.02 (4 / 235), avg. gap size = 3.75 (15 / 4)  


3592 21.58 2.78 2.11  chr2_152947457_152952871     4025  4923 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_152947457_   4025 AAAGACATCCTGTGTTTATGGCTTGAAAGAC--AATATTGTTAAAACGTT 4072
                              i    ii    i    v   i     --           i i vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_152947457_   4073 CATACTATGCAAAGTGATCTACAGATTCAATGAAGTTCCTGTTAAAATCC 4122
                         v     viv    v                i v i i   i i       
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_152947457_   4123 CAACAGCATTCTTTGCAAAATTAGAAAAAAAGATT-TATAATTCATATGG 4171
                           i v  v  i      i  v v  v  ivv   i-  v           
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_152947457_   4172 AACCACAAAAGACCACAAACAGTCAAATCAATTTTGAG---GAAAAACAA 4218
                           vii   ii    vvi  i  i    v    i    i---   i     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_152947457_   4219 AGCTGGAGGCATCAGACTTCCTGATTTCAAAATATATTATAAATCTATTA 4268
                           i      vv   v      ii         iv  i  i   v   ivi
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_152947457_   4269 TCATCACAACAGTATGGTACTGGCATAAAGACAAACATATAGACCAATGG 4318
                          v    vi     i              i  i i         i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_152947457_   4319 GACAGAAAAGAGAGCCCACAAATAAACCCA--CATATACAGTAAACTGGT 4366
                         i i    vv     i   v           --   v  ii  v  i  i 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_152947457_   4367 TTTCAATAAGGGTGCCAAGAACAGGCAATGGAGAAAGAATAGTCTATTCA 4416
                             i i             v  vv      i             v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_152947457_   4417 GTGAATGTTGTTTTAAAAACTGGGTGTTCACATGCAAAAGAATGAAATTG 4466
                         iii    v  i vvi v      i i?i                  i   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_152947457_   4467 GACTCTTACTCCATACC-----CAAAAATCTACTGAAAATGGATGAAAGA 4511
                            i i   ii  i   -----       iv   v         v ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_152947457_   4512 TATAAATGTAAGACTTGAAACTCCAAAACTACTAGAAAAAAAAAGGAAGA 4561
                         iv           vi i     vi      vi     i    v ------
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA------ 547

  chr2_152947457_   4562 ATAGCAGAAAAGCTTCATGACATTGGTCTTGGCAATGATTTCATAGAAAC 4611
                         -   v? v   v    i    v    vi v       i    v    v i
  L1M4_orf2#LINE/    548 -TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_152947457_   4612 GATACCAAA-GCACAGACAACAAAAGCAAAAGTAAACAAATAGGACTAAA 4660
                           i      -     ii         v    i  i i    v     vv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_152947457_   4661 TCAAACT--AAAGTTTTTGCGCAGCAAAGAA-ACTATCAACATAGTGAAA 4707
                              v --   ii     i  vv     i -        v v       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_152947457_   4708 AGGCAACTT-CAGAATGG-------TTTTTGCTAGCCATATATCTGATAA 4749
                           i    ii-        ------- v     v ii              
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_152947457_   4750 GGAGTTTATCTCCAAAATATGTACAGAACTCATGCAACTGAGTAGTAAAA 4799
                           iii  i v    i     i  v       v i     v i  i     
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_152947457_   4800 AAAAAAAAAAAAAAAAAAACCATCAGATTTAAAAATGGGCTAAGGACTTG 4849
                          i v   v  ---------  --  -   ?          v     i   
  L1M4_orf2#LINE/    797 AGACAAATAA---------CC--CA-ATTWAAAAATGGGCAAAGGATTTG 834

  chr2_152947457_   4850 AACAGACACTTATCCAAAGAAGGCATACAAATGGCCAACAGGTATATGAA 4899
                           i     i  v          ii              i i i i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_152947457_   4900 AAAATGCTCAAGGTCACAAGTCAT 4923
                           i        vi   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (114 / 76)
Gap_init rate = 0.02 (14 / 905), avg. gap size = 3.14 (44 / 14)  


2202 24.33 3.63 3.48  chr2_152953182_152955215      501  1133 (901)    L1M4_orf2#LINE/L1      152   785 (123)  

  chr2_152953182_    501 GGAAATGCAAAGGACCAATAATAGCCCAAATAAACCAACCAAAAAATCTT 550
                                   i     v v       v   i  -------------    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAA-------------TCTT 188

  chr2_152953182_    551 TGAAAAAAAGGAACAAAGTTGAAGGATTTGCAATACCTGATGGTAAGATT 600
                         -      i i           i    i ii  v v  ii  vvi  i i 
  L1M4_orf2#LINE/    189 -GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_152953182_    601 TATTGTAAAGCTACAGCAATCAAGACAACGCAGTATTGACATAAAGATAT 650
                           i ii          i          ii ii   i  i     i    v
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_152953182_    651 TTTTAATAAATCAGTGGAACAGAATATAGAGTTTAGAAATAGACTGATAT 700
                         viv  -  i    i     i     vv     ii       i  iv   i
  L1M4_orf2#LINE/    288 ACATA-TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_152953182_    701 TTATATGTGTGGTCAGTTGACTTTTGACAAAGATGCAAAAGCATATTTAA 750
                         ----  v i      i    i   i     i i   v  ii -i   i  
  L1M4_orf2#LINE/    337 ----ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAA 381

  chr2_152953182_    751 ---GAAAACAAAAGTCTTTTCAACAAATGGTACTGGAACAACTGAACATC 797
                         --- i   v  v                   i    i       i i ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_152953182_    798 CATATGCAAAACAATGAACTTTAATTCATAACTTATACCATATATGAAAA 847
                           i        v      v  vi ii v  v  i i        ii    
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_152953182_    848 TTAATCCAAAATGGATAATAGGCCCAGAGGTAAAACTTAAAATGATAAAA 897
                             ii          v ?  i  i i v    i vi     iv      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_152953182_    898 ATTTTTAGAGAAATAC-CAGA---AAATGTTTGTAATCTTGAGTTAGGCA 943
                         -i i     ii  v  -i  i---    v  i  i i    i        
  L1M4_orf2#LINE/    532 -CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_152953182_    944 A----------ACTGTGAT--CTAAAGCATGATTCATAAAGGAAAAAATA 981
                          ----------iv i   i-- v      ii viv i   i         
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_152953182_    982 ----AATTAGATTTTACCAAAGTTAAAAAATTCTGCTTTTTAAAAGACAC 1027
                         ----    i  i  i i    i       v  i  ivi  i   i     
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_152953182_   1028 TCTTGAGAGAGTGAAAAGACAAGCCACAGACTGGTAAAAAATATTTGCAA 1077
                          v ii   i             v       v   v i             
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_152953182_   1078 ATCACAAGTTTTAAAAAAAGACTTGAACCCGGAATGTAAAAAAAGCTCTC 1127
                             i vi i -i v  ii      v i  i    i  v   i i    i
  L1M4_orf2#LINE/    731 ATCATATATCT-GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_152953182_   1128 GGAACT 1133
                         iv    
  L1M4_orf2#LINE/    780 ACAACT 785

Transitions / transversions = 2.53 (109 / 43)
Gap_init rate = 0.02 (13 / 634), avg. gap size = 3.46 (45 / 13)  

 235 20.51 9.40 3.42  chr2_152953182_152955215     1428  1544 (490)    L1M4_orf2#LINE/L1      785   908 (0)  

  chr2_152953182_   1428 TTAATAACCAAAAAAAC------CCCAATTTTTTAAATGGCTAAAACATT 1471
                          i     i-     i  ------       ?vv-      vi   iv   
  L1M4_orf2#LINE/    785 TCAATAAT-AAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATT 832

  chr2_152953182_   1472 -AAATAAAAA---CTTCATAAAAGATATGTATGGATAGTAAATAAGCACA 1517
                         -i    i v ---  i  v i       ii --i  i iv          
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACA--AATGGCCAATAAGCACA 880

  chr2_152953182_   1518 TGAAA-GATGCCCAACATAATTTTTCAT 1544
                              -     i      v ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.06 (7 / 124), avg. gap size = 2.14 (15 / 7)  


3388 24.67 2.09 2.09  chr2_152980674_152983246.rev     1174  2081 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_152980674_   1174 TAGAGAGATATTCCATTTTCATGGATAGAAAGACTCAACA-------GAT 1216
                          i  i      i    v         v i      i  i -------   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_152980674_   1217 GTCAGTTCTTTCCAACTTGATTTATAGGTTCCATGCATTCCTAATCAAAA 1266
                          v  i v  ii    v     i  i  i   v i   v   iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_152980674_   1267 TCCCAACAAATTATTTTACGACTATTGATAAACTGATTACAAAGTTCATA 1316
                              i vivi v    i iivv     i  i     ivi   i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_152980674_   1317 CAGAGAGGCAAAAGACCCAGAATAGCCAACACAGTATTAAAGGAGAAGAA 1366
                         ii  i v    ii                v   i v  i  ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_152980674_   1367 CA--GTCAGTGGACTGACATTACCCAATTTCAATACTTACTATACAGCTA 1414
                           --  ii v     v   i v           v        i v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_152980674_   1415 TAACAATCAAGACAGTGTGATATTAGTGAAAGAACAGACAAATAGATCA- 1463
                         i ii               i  i i iiv   i i     v        -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_152980674_   1464 TGGAACAGAATTGAGAGCCCATAAATAGTCCCATGTAAATATAGTCAACT 1513
                              i           i   v     iv     ii vv   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_152980674_   1514 GATTTTTGACAAAGAAGGAAAGGCAATACAATAAAGAACAGGTAGTCTTT 1563
                               i     i iv vv   i v  v    iii   viii        
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_152980674_   1564 TCAACAAATAGTGCTGGAACAACTGGACATCTGTATGCAATAGA-TAAAT 1612
                                  i       i         i ? iii      v   - i  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_152980674_   1613 ATAGACACAGACCTTATACCCTTTACAACAGTTAACTCAAAATTGGCACC 1662
                         v i   v vv    i i   v v     v i            -  - i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT-GG-ATC 498

  chr2_152980674_   1663 ATA--CTTAGATGTGAAACACAAAAGTTTCAAGCTCCTAGAAGATAACAT 1710
                          ? -- i  i    i i vvi    v v v  i   i       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_152980674_   1711 AGGAAAAAATATAGATGACCTTGGGTATGGCGGTGACTTTTTAGATGCAA 1760
                            ?iv    v vvi           vv   ii  ii  i      iii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_152980674_   1761 CACTAACGACATGATCCATGAAAGAAATAATTGATAAGCTGAACTTCGTT 1810
                            i  vii  ii v v ii       v   v     ii  i     i i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_152980674_   1811 CAAATTAAAAACTTCTGCTTTGTGAAAG-CA-----AAGAGAATAAGAAG 1854
                         v             i  ivi vii  i -  -----    i i i i   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_152980674_   1855 AGAAGCCACAGACTGGGAGAAAATATTTGCAAAAGATGTATCTGATAAAG 1904
                          v  v       v                    vv  i          i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_152980674_   1905 GAAGAACATAACTTGTATATGTTATCCAAGATATACAAAAAACTTGTAAA 1954
                           ---------       -------   ii     i   i    iv  v 
  L1M4_orf2#LINE/    749 GA---------CTTGTAT-------CCAGAATATATAAAGAACTCTTACA 782

  chr2_152980674_   1955 ACTCAGCAATAAGAAAATGAACAATTTGATTTTTAAACTGGGCAAAATAC 2004
                              ii     i  i ii  i  iiii   ?v-   v        iv i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGAT 831

  chr2_152980674_   2005 TTGAATAGACACCTCACCAAAGAAGGTATACAGATGGCAAGTAAGCATAT 2054
                                    ii  v         i      i     v i      i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_152980674_   2055 GAAAAGATAAACAACATCATATATCAT 2081
                                 ivv        ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (143 / 77)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.17 (38 / 12)  


3438 24.89 0.55 0.99  chr2_152994894_153000062.rev     3766  4677 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_152994894_   3766 TGAAAAGATATTCCATATTCATGGATTGGAAGAATGAATATTGTTAAAAT 3815
                           i        i    i                v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_152994894_   3816 GTCCATACTACCCAAAGCAATCTACAGATTCAATTAAATCCCTATCAAAA 3865
                          v v     v      vii              ivv              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_152994894_   3866 TACCAATGACATTCTTCACAGAAATAGAAAAAACAATTCAAATATTTATA 3915
                          v   iivi v  i  ii       v  v  ivii  i v  v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_152994894_   3916 TGGAAGCACAACAAAAGCAAAATATCCAAAGCTATTCTAAGCAAAAAGGA 3965
                              iii   vii vv  i    v     i v  ii i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_152994894_   3966 CAAAACTGGAGGAATCACATTACCTGACTTCAAA--TTATTTTACAGAGC 4013
                             ii       v     i v  ii i      --   i --   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT--ACAAAGC 248

  chr2_152994894_   4014 TATAGTAACCAAAACAGCATGGTACTGGCATAAAAACAAACACATGGACC 4063
                           i     i   i    ii              ii i i   i  i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_152994894_   4064 AACAGAACAGAATGGAGAATCCAGATATAAATCCACACACCTACAGTGAA 4113
                           ii   i     v    i      v     i   i   ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_152994894_   4114 CTTATTTTTGACAAGGTT-TCAAAAACATACACTGGGAAAAAAGACAATC 4162
                         i v     i       v -i   i v   v  v    i   i - i i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTC 397

  chr2_152994894_   4163 TGTTCAACACATGATGCTGGGAAAACTTAATATCCATATGCAGAAGAATG 4212
                          v       v   i        v    vi   ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_152994894_   4213 AAACAAGATCTTTATCTCTCACTATACATAAAAATCAAATTAAAATGGAT 4262
                           iivi  i ii  i   v   i   i i      i  v i         
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_152994894_   4263 TAAAGACTCAAATCTAAGACCTCAAACTATGAAACTACTATCAAAACACA 4312
                         i ?    ii    v     v  v       i     vi  vv i  v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_152994894_   4313 TTGGGGAAACTCTCCAGGACATTGGTCTGGGCCAAAATTTCTTGAATAAT 4362
                          v  ? v  v   i iv   v    vi i   v vii      ii   vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_152994894_   4363 ACCCCATAAGCACAGGCAACTAAAGCAAAAATGTATAAATGGGATCACTT 4412
                           v   v       i     v    v      iv      v   iiv v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_152994894_   4413 CAAG-TTAAAAACCTTCTGCACAGCAAAGGGAATGATTAACTAACTGAAG 4461
                            i-        i  -  ii vv      iv iv  i  vv  v    i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_152994894_   4462 AGACAACCCATAGAATGGGAGAAAATATTTGCAAACTACTCATGTGACAA 4511
                                   i                        ii ivi  v   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_152994894_   4512 GCGATTAATAACCAGAATATATAAGAGATGCAAACAACTTTACAGGAAAA 4561
                          v  i vi  v             iii iv vv      iv i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_152994894_   4562 AGTCTAATAATCTGATT-AAAAATGGACAAAAGATTTGAACAGACATTTC 4610
                           v v     i ii   -        i    i        i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_152994894_   4611 TCAAAAGAAGACATACAAATGGGAAACGTAAGAAACATATGAAAAAGTAC 4660
                           v        i          ---- -i  v  i  i       ii i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGG----C-CAATAAGCACATGAAAAGATGC 891

  chr2_152994894_   4661 TCAACATCACTGATCAT 4677
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


 681 23.61 2.31 5.09  chr2_153004549_153006984.rev      797  1012 (1424)    L1M4_orf2#LINE/L1       29   238 (670)  

  chr2_153004549_    797 GAAAACTTATTATTTTTAAGACATCAATTCCCTCCAAATAGATCTATAGA 846
                            i     v    v      iiv    v i i      v      i   
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chr2_153004549_    847 TTTCTTGTATTCCAAAATGAAATTCCATAAGACT--TTTTTTTGTAGAAA 894
                           ivvi i v   vv vii    i   ----i  --i       i     
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCA----GCTGCCTTTTTTGCAGAAA 124

  chr2_153004549_    895 TCGATAAGATAATTCTAAAATTCATGTGGAATTGCAAGG-ACCTAGAATA 943
                          i  i   v i  i           i     v       -   i      
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr2_153004549_    944 GGAAAAACAACTTGGAAAAAAAAAATACAAGGCCAGGCTTGGTGG-CTCA 992
                          vv       ii v      i  i -    i ------    v  -    
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGA-ACAAAG------TTGGAGGACTCA 217

  chr2_153004549_    993 CGCCTAT-AATCCCAGCACTT 1012
                          i i vi-   ii  iv    
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTT 238

Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.03 (7 / 210), avg. gap size = 2.29 (16 / 7)  

2355 21.96 7.76 2.49  chr2_153004549_153006984.rev     1262  1944 (492)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr2_153004549_   1262 AAAAAAAAGGACAAAATGGGAGGACAAATTCTACCTGATTTCAAGACTTA 1311
                              i   i     i v       vv iv  v  ii       i     
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_153004549_   1312 TTATAAAGCCACACTAATTAAGAGAGTATGCTATTGATATAAAGATAGA- 1360
                         i  i     i   v    i    v   i  v  i  ii    i      -
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_153004549_   1361 GT---GATCAATAGAATAGAATGGTGAGTCCAGAGGTGAGACCACAGATA 1407
                         i ---       i         v v         ii i iv   i v  v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_153004549_   1408 TATGGACAATGGGTTTT-GACAAAGGTGCAATGGCATTTCAGTGGAGAAA 1456
                              v    v i    -     i     v v i vv    i   i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_153004549_   1457 GGATAGTCTTTTCAGCAAATGATTGTAACAATAGTTGTACAGA-AATTGG 1505
                          i            i      i ---------- i  ---i  -  i   
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGT----------GCTG---GGACAACTGG 426

  chr2_153004549_   1506 ATATCCACATGCAACA-AATGAACGTTT-ATCTATACC-CACACCATTTA 1552
                            ?          v -      -   v- i iv    -        v  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAA-GTTGGACCCCTACCTCACACCATATA 475

  chr2_153004549_   1553 CAACA--CAACTCAAAGCA-ATTGTAGAAATAAGTGCAAATTCCAAAACT 1599
                            v --i        iii-  ii?   vv   i  i  ivv i      
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_153004549_   1600 ATACAACT-TCAGAAAAAAATATAGGAAAAAATCTTTGTTACCTTGGGTT 1648
                            v    - i    i    i     ?iv       i  v          
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_153004549_   1649 AGGCAAAGATGTCTTAGGTATG---CCAG------------CAAGAAAAA 1683
                               v i v      i    ---   i------------   i i   
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_153004549_   1684 AAAT-GATAAATTGGACTTCATCCAA-CTAAAAACATCTGCTATGCT--- 1728
                             -                  v  -i       v i  ---    ---
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG---TGCTTCA 672

  chr2_153004549_   1729 AAAGACATGGTTAATAGAATGAAAAGATCCACTGCAGACTAAGAAAAAGT 1778
                           i    ivi i  v i i        ivvv ii    v ii  i   i 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_153004549_   1779 ATTTACAAATTATATGTTTGATAAAGGACTTGTTCCCAGAATGCATAAAG 1828
                             i     i    i i      i        vi       ii      
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_153004549_   1829 AACTCTCAAAACTAAGTAA---------GAGTA---CAAC--------GG 1858
                               i v    v i   ---------i i  ---   i--------  
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_153004549_   1859 AAAAAAGACTTGAACAGATGCTTCGCCCAGGGAAATATATCCATGGCTAA 1908
                         iv   i  i     i   iii   v  v i i i     ivv     i  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_153004549_   1909 TAAACACATGAAAAGATGCTCCACATCATTCATCAT 1944
                            i                 v      ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (97 / 50)
Gap_init rate = 0.03 (22 / 719), avg. gap size = 3.18 (70 / 22)  


2163 22.83 6.06 8.80  chr2_153214033_153216433.rev      664  1504 (897)    L1M4_orf2#LINE/L1       13   830 (78)  

  chr2_153214033_    664 CCATGTTCATAGATCAGAAGAGTCAATATTGTATAAATGTCAATTCTACT 713
                                   i   ii     v i        vv i   v    v  v i
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_153214033_    714 GAAATTGATCTACAGAGCCAGTGCATCTTCTGCCAAACTCCTGGAAGGTT 763
                         v               vi  ii   viii  ii    v   i---  v v
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC---AGCTG 109

  chr2_153214033_    764 TTTTTTTCTTAGAAACTGACAAGCTGATTCTAAAATTTATATTAAAATGC 813
                         ii     ivi     i            i        i    vi      
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_153214033_    814 AAAGGAACTAGAATAGCCAAAATAATTTAGCAAAAAAAAAAAAAAAAAAA 863
                           i   v i             i   i v -------     i  i  v 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTG-------AAAAAGAAGAACA 202

  chr2_153214033_    864 AAGTTGGAGAATTGACACTACCTGATTTCAAGAC---------------A 898
                                  i i v     v  ii       i  --------------- 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_153214033_    899 GTAATCAAACCAGAGACATATTGGCGTAAGGATAAAAATATAGATGAGTA 948
                                 iv   v vvi  i    i        i v        v i i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_153214033_    949 GAACAGAATAGAGAACACAAAAATAGACCCACACGTTTATGGCCAATTGG 998
                            i     v    iiv  i     i     i  i       i      i
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_153214033_    999 TTTTC---AAAGATACCAAGGTAGTTCATGAAAAAAAGAGCAGTCTATTA 1045
                              ---  i i i     iivi    vviiii     ii     v  v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_153214033_   1046 AATAAATTGTGCTGAAACAGTTGGAGGTAAAGTTAGATAAATACAGAAGC 1095
                           i    v      ii   ii    --------  ?vi v  i  i   v
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGA--------TAKCCACATGCAAAAGA 444

  chr2_153214033_   1096 ATACATGGATGGATGGATAGA-CAGACAGATGATAGATAGACAGATGAGG 1144
                           iv -- v    ivvv  vv-  v  v--------   v   -------
  L1M4_orf2#LINE/    445 ATGAA--GTTGGACCCCTACCTCACACC--------ATATACA------- 477

  chr2_153214033_   1145 AAAAAGTACAACTCCACCCTTAACTCATCCCACATATCAAAATAGATTAT 1194
                         -    --------------        ------------    i   i ?
  L1M4_orf2#LINE/    478 -AAAA--------------TTAACTCA------------AAATGGATCAW 500

  chr2_153214033_   1195 AGACTAAAACATAAGAACCAAAACTGTAAAATTTCCAGAAGAAAACATAA 1244
                             iv   ii     i i      i     i iii             i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_153214033_   1245 GAGATAATCTCTGTGACCTGAAGGTAGACAAAAAATTTCTTAG----GAA 1290
                          ? vv     ii       vii v   i   vii-        ----  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGAC 599

  chr2_153214033_   1291 ACAAAATGCAAGAGCCACTTAAAAAA-------TAAATTCAATTTAATCA 1333
                           v   v   vi   v  vv  i   -------      vi i  v    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_153214033_   1334 GAA----AAACTTTTGTTCTTCAGAAAATACTATTATAAATACTAAAAAG 1379
                         i  ----          v     i ii i     i -------- i    
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--------AGAAAG 691

  chr2_153214033_   1380 TGAGACAAAAACT-----AATG-----AAATATTTGCAAAGTATCTGTTT 1419
                            i vi v   i-----    -----             vi  v i i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_153214033_   1420 GATAAAG-ACTTGTATCCAGAATATTGTTTAAAACTTCTGCAGCTCACTA 1468
                              i -                 -i vv i    ii i  i    v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATAT-ATAAAGAACTCTTACAACTCAATA 790

  chr2_153214033_   1469 A------GACAAATAACCCACTTTTTAAAAATAGGCAAAAGA 1504
                          ------             v  ?--      i      i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGA 830

Transitions / transversions = 1.69 (118 / 70)
Gap_init rate = 0.03 (22 / 818), avg. gap size = 5.68 (125 / 22)  

 397 16.91 4.41 2.21  chr2_153214033_153216433.rev     1774  1909 (492)    L1M4_orf2#LINE/L1      770   908 (0)  

  chr2_153214033_   1774 AAGA-CTC---CATCTCAAAAAAAAAAAAAATAAGAAAAAAAATT--AAA 1817
                             -   ---  v     v  v     i -i  iv  vvv    --   
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAA 818

  chr2_153214033_   1818 ATAGGCAAAAGATTTGAACAGAGCAGATCCTTCAACAAAGATATACAAAT 1867
                           i      i        i   -  v- i  i   vi             
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGA-CAT-TTCTCCAAAGAAGATATACAAAT 866

  chr2_153214033_   1868 GTCAAACAGGCACATAAAAAGATGCTCAACATCATTAGTCAT 1909
                          v v  i i      i                  ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (12 / 11)
Gap_init rate = 0.04 (6 / 139), avg. gap size = 1.50 (9 / 6)  


3401 22.17 5.03 1.26  chr2_153522334_153525766.rev     2067  2941 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153522334_   2067 TGGAAAGATATACCATGTTCATGAATTGGAAGAGTTGATATTATTAAAAT 2116
                                    v           i         v  i     i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153522334_   2117 GTCCATACTTTCCAAAGCAATATACAGATTCAATACAATCCTTACCAAAA 2166
                          v v     ii     vii  v           ii      i  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153522334_   2167 TTCCAATGGTATTTTTCACTGAAGTAGAAAAA--AATTCAAAAATTCATA 2214
                          i   iiv iv     ii v   i v  v  i--i  i v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_153522334_   2215 TGGAACCACAAAAGATCCCAAATAGTCAAAGTAATCCTGAGAAAGGAAAA 2264
                              vii   ii  i  vi     i    ii    i   i    i i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_153522334_   2265 CAAAGTTATAGGTAC-CACACTTAGTGACTTCAAA--TTACATTACAAAG 2311
                                iv   -  -       vvii i      --    --       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTAC--TACAAAG 247

  chr2_153522334_   2312 CTATAGTATTCAAAACAGTGTGACACTGTCATAGAAAAACACATAGAAAT 2361
                            i    v    i        ii    v    iii v v     v i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_153522334_   2362 --ATGGAACAGAA----AAGCTCAAAAATAAATCCAAACACATACAGACA 2405
                         --      i    ----i  ii  i       i   v   iv  ii v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_153522334_   2406 AAAAATTTTTGACAAGAGCACCAAGAAGACACAATGAGAAAAGGATAGTC 2455
                          vvi     i      i ii      vv iv     i i    i      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_153522334_   2456 TCTCTTTAACAAATGGTATTAGGGAAGCTGAATATCCACATGCAAAAGAA 2505
                          i -- i          ii i  iv i   i   ?               
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_153522334_   2506 TAAAATTGGACCCTTATCTTACATCACACACAAAAATCAACTCAAAGGGA 2555
                          i  i        i  i  i   i  i i        i        iv i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_153522334_   2556 ATTAAAGACATAAATATAAGACCTGAAACCATAAAACTCCTAAAAGAAAA 2605
                           i ?    v     i     v  i    i         i  i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_153522334_   2606 CATTGGGGAAAATTTT-----------------------------AGATG 2626
                            v  ? v    i  -----------------------------    i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_153522334_   2627 GGACACCAAAAACACAGGCAACAAAAGAAAAAACAAACAAATGGGACAAC 2676
                         v          i    i                i i i    v    vv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_153522334_   2677 ATCAAACTAAAACATTTCTACACAGCAAAGAAAACAATAAACAAAAAGAA 2726
                               v v   v i  i iii vv     i v  v  v  v   iv   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_153522334_   2727 AAGGCAGCCTAAAGATTGGGAGAAAATATTTGTGAACCGTATATCTGATA 2776
                            i  i  i v   v                ii  i i           
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_153522334_   2777 AGG----TGTCAAAATCCAAAACATCTAAGGAACTCACACAACTCAATGG 2822
                            ----   ----     i  i  v   i      vi          ii
  L1M4_orf2#LINE/    746 AGGGACTTGT----ATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_153522334_   2823 CAAAAAAAAAGATATAACACTATTTTAAAATGGGCAAATGATCTGAATAG 2872
                         i     i v i   --  v v   ?v            v   i       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATA--ACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_153522334_   2873 ACATTTCTCCAAAGAAGACATACAAATGGCCAACAGGTATATGAAAAGGC 2922
                                           i              i i i i        ii
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_153522334_   2923 ATTTAACATCATCCATCAT 2941
                         ii i       ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.22 (131 / 59)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 4.58 (55 / 12)  


3229 25.72 1.56 0.45  chr2_153577099_153583798     5311  6208 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153577099_   5311 TGGAAA-ATATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5359
                               -    i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153577099_   5360 GGCCATACTGCCCAAAGTAAT-TATAGATTCAATGCTATCCTCATCAAGC 5408
                            v     v      v i  -  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153577099_   5409 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5457
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_153577099_   5458 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATGCTAAGCAAAAAGA 5507
                               viiv  ii  v  viv        i     vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_153577099_   5508 ACAAAGCTGGAGGCGTCATGCTACCTGACTTCAAACTATACTACAAGGCT 5557
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_153577099_   5558 GCAGTAACCAAAACAGCATGGTACGTGTACCAAAACAGATATATAGACCA 5607
                         i      i   i    ii      vv i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_153577099_   5608 ATGGAACAGAAC--AGGGCCTCAGAAATAACACCACACATCTACAACCAT 5655
                               i    i--  i i -         vv   i    i  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_153577099_   5656 CTGATCTTTGGCAAACCTAACAAAAACAAGCAATGGGGAAAGGATTCCCT 5705
                         i    i  i i   ivv iv   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_153577099_   5706 ATTTAATAAGTGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5755
                         v  i  i  i     i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_153577099_   5756 AACTGGACCCTTTCCTTACACCTTATACAAAAATTAA-TGAAGATGGATT 5804
                          ii       i v   i     v              - v  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_153577099_   5805 AAAGACTTAAACATAGGACCTAAAGCCATAAAAACCCTAGAAGAAAACCT 5854
                          ?    i    ii  i  v     i i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_153577099_   5855 AGG--TAATACCATTCAGGACATAAGCATGGGCAAAGACTTCATGACTAA 5902
                            --   - i -   iv   v vi vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_153577099_   5903 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACATATGGGATCTAA 5952
                         i            vvi          vv     v  i v  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_153577099_   5953 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAG 6002
                          i   v v  i i   i  ii vv    i  v       vv i      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_153577099_   6003 AGGCAACCTACAGAATGGGAGAAAATTTTTGCGATCTATCCATCTGACAA 6052
                           i     i                 v     i vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_153577099_   6053 AGGGCTAATATCCAAAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 6102
                         i  i  vi      i   v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_153577099_   6103 AAACAA----CCCCATTGAAAAGTGGGCAAAGGATATGAATAGACACTTC 6148
                          i    ----   v   ?    i            v          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_153577099_   6149 TCAAAAGAAGACATTTATGTGGCCAACAA--ACATGAAAAAAAGCTCATT 6196
                           v        i  vi vi       i  --         i v     vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_153577099_   6197 ATCACTGGTCAT 6208
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (136 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


 937 23.13 6.05 0.71  chr2_153590091_153596842.rev     2278  2558 (4194)  C L1M4_orf2#LINE/L1   (0)   908   613  

C chr2_153590091_   2558 GCAACAACAGCAAATATTGACAAACGGGATCTAAGTAAACTAAAGAGCCT 2509
                                v  v   v  v  i   iv   ii v vi   v v  i i i 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

C chr2_153590091_   2508 CTGCACAGCAAAAGAAACTATCAACAAAGTAAACAGACAACCTACAGAAC 2459
                         i  ii vv    i  v        v     i  v        i      i
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

C chr2_153590091_   2458 GGGAGAAAATATTTGCA--TCCTATGCAGCTGACCAAGGTCTAATGTTTA 2411
                                          --  v   -- v    iv i  v  vi i ii 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATAT--ATCTGATAAGGGACTTGTATCCA 760

C chr2_153590091_   2410 GCATCTATAAGGAACTT---------AATAAGCAAAAAA-AAGCAACCCC 2371
                          v  v     i     i---------     vv    i -  ii     v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

C chr2_153590091_   2370 ATTAAAAAGTGGGCAAAGGACATGAACAGACATTTTTC---AAAAGACAT 2324
                            ?    i           iv    i        i  --- i    i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

C chr2_153590091_   2323 ACG--TAGCCAATAAGTATGTAAAAAAATGCTCAACATCACTAATTAT 2278
                           i-- i         i ii i    i             ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (39 / 25)
Gap_init rate = 0.02 (6 / 296), avg. gap size = 3.17 (19 / 6)  

1866 24.03 2.17 5.89  chr2_153590091_153596842.rev     2859  3503 (3249)  C L1M4_orf2#LINE/L1   (286)   622     2  

C chr2_153590091_   3503 GAAAAAACATTCCATGTTCATGGATAGAAAGAATCAAAATTGTTAAAATG 3454
                          i   i i  i              v i    v i  v        i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

C chr2_153590091_   3453 GACATACTGCCCAAA--GAATTTTAAATATTCAGTGCTATTCCTATCAAA 3406
                          vv     v      --  -- i  v v     ii  v  i         
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGA--TCTACAGATTCAACGCAATCCCTATCAAA 99

C chr2_153590091_   3405 CTACCAATGACATTCTTCACAGAATTAGAAAAAAAAAACT-ATTTTAAAA 3357
                         v v   iivi v  i  ii     v v  v  i-----  -  ii     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAA 144

C chr2_153590091_   3356 TTCACATTAACAAAAAAAAAGAGTTCA-AATAGCCAAAGCAATTCTAAGC 3308
                             i  vi --  viv  i iiii  -          i    ii i --
  L1M4_orf2#LINE/    145 TTCATATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-- 190

C chr2_153590091_   3307 AAAAAAAAAAAAAAATAAAATAAAATAAAGCCAGAGACATCACATTGCCT 3258
                         -----    i  i  i   i ---- ii  -----   -     i v  i
  L1M4_orf2#LINE/    191 -----AAAAGAAGAACAAAGT----TGGAG-----GAC-TCACACTTCCC 225

C chr2_153590091_   3257 GACTTCAAAG--TA-TACAAGGCTGCAGTAACCAAAACAGTACCATATGG 3211
                         i i      i--  -     i   i      i   i     i-----   
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG-----TGG 270

C chr2_153590091_   3210 TACTGCTCAAAAAACAGACATATAGACCAATGAAACAGAATAGAGAGCCC 3161
                              vivv  ii i           i     i  i     v     i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

C chr2_153590091_   3160 AGACATAAGGCCACACTCCTACAACCATCTAATCTTCAACAAAGTCAACA 3111
                            v    iv   i  vii  iiii  vi i  i   i    i viiv  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

C chr2_153590091_   3110 AAAACAAACAATGGGGAAAGGACTACCCATTCAATAAATGCTGCTGGGAT 3061
                          i v  vv            i ivii iv     i     v        i
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

C chr2_153590091_   3060 AACTGGCTAGCCATATGCAAAAGTTTGAAATGGGACCCCTTCCTTACATC 3011
                               v  ?   i         vv    i v        v   i   i 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

C chr2_153590091_   3010 ATATACAAAAATCAACTCAAGGTGGATTAAAGACCTAAATTTAAAACCTA 2961
                                     i       ii     i ?          v   i v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

C chr2_153590091_   2960 AAACTATACAAACCCT-GGAAGTTAACCTAGG---AAATACCATTCTGGA 2915
                                 -    i  -i    vv   v    ---    -- -   vv  
  L1M4_orf2#LINE/    521 AAACTATA-AAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGA 566

C chr2_153590091_   2914 CATAGGATCTGGTGACGATTTCATGACAGAGATG---CCAAAAGCAATTG 2868
                          v v  i iv  ii i i    v ---   v   ---         vvv 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTT---AGATATGACACCAAAAGCACAAG 613

C chr2_153590091_   2867 CAACAATAG 2859
                               v  
  L1M4_orf2#LINE/    614 CAACAAAAG 622

Transitions / transversions = 1.68 (96 / 57)
Gap_init rate = 0.03 (20 / 621), avg. gap size = 2.60 (52 / 20)  

 475 32.67 0.00 0.00  chr2_153590091_153596842.rev     4956  5105 (1647)    L1M4_orf2#LINE/L1        4   153 (755)  

  chr2_153590091_   4956 AGAGATATTCCATTATGATGAATAAAAAGACACAATATGGTCAAGGTATC 5005
                          i      i    vv v   i  vii     vi     v  i   i iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_153590091_   5006 AGGTCTTCCCAATTTGATCTATAAATTTGATGAAGTACCAATCAAAGTTC 5055
                          ivv  i     v        i i   ii i v i v  v      i i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_153590091_   5056 CAGCAAGTTACTTTGTGGATATAGACAAATTGATTCTAAGGTTTATGTGG 5105
                             vivi vi    ii  v  v     ii    i    ii  i  i   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

Transitions / transversions = 1.72 (31 / 18)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.00 (0 / 0)  

2089 27.73 1.75 1.48  chr2_153590091_153596842.rev     5510  6252 (500)    L1M4_orf2#LINE/L1      146   890 (18)  

  chr2_153590091_   5510 TCACGTGGAGGGG-AAAAGAGCCAGAATAGCCAATATAATATTAAAGGAG 5558
                            ii    iiv -  ii  v             v i   v  i  ii  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_153590091_   5559 AAGAACAAAGT-GGATGACTGAAACTATCCAACCCCAAGACTTAGTATA- 5606
                                    -   v    v v   vi    iii   i     v  i -
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_153590091_   5607 -GTTACAGTAATCAAGATAGTGTGATATTGGTGAAAGAATAAAT-TA--- 5651
                         - i              i      i  i   iiv   i   i i-  ---
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_153590091_   5652 ATCAATAGAACAGAATGGAGAATTGAGAG-TAGATACACATAAATATAGT 5700
                               i   i     v    i iv   i-  i iv  i i vv   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_153590091_   5701 CAACTGATCTTTGACAAAGGATCAAAGGCAATACAAAGGAGCAAAGACAA 5750
                            i    i  i     i  vv v   i v  v   v  i v  ii i i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_153590091_   5751 TCATTTCAATGAATGGTGCTGGAACAAGTGGATGTACACATGCAAAAAAT 5800
                           v      ii           i    v     i?v           i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_153590091_   5801 TTGAATGTAAATACAGATTTTACATCATTCAAAAAAAAAACAACTCAAAA 5850
                          -   vv ii iv vv ii i   i   -- v v     vi         
  L1M4_orf2#LINE/    446 T-GAAGTTGGACCCCTACCTCACACCAT--ATACAAAAATTAACTCAAAA 492

  chr2_153590091_   5851 TAGATAACAGAA-TAAATGTAAAATGC-AAGACTGTCACACTCCTAGAAG 5898
                          i   v ?   v-         i -  -  i   i v v    i      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAG 541

  chr2_153590091_   5899 ATAACATAGAAGAAAATTCAGATGACCTAGGGTATGGCAAAGACTTTTTA 5948
                          v       i? v    iivvi      v    vv     v ii  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_153590091_   5949 AATAT-AGAACAAAAGTCATAACCAATGAAA-AAAAGATTGATAAGCTAG 5996
                         i    - v v      -  i  v   ii   -    i  v     ii i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_153590091_   5997 ATTGCATCCTAGCTTATGTTTACGTCTTCTGATCTATAAAAGATAATGCC 6046
                          i v    v- iv   ----- viv   i  vv  vi   i  i v ii 
  L1M4_orf2#LINE/    641 ACTTCATCA-AAATTA-----AAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_153590091_   6047 AAGAGAATGAGAAAACAAGCTGGAGACTGGGAGAAAATAGTTGCTAGAGG 6096
                             i i   i  i    v iiv   v            v    v ivvi
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_153590091_   6097 CACAGCCAATAAAAGACAGTTATCCAAAATACACAAAGAACTCTCAAAAC 6146
                         i i v ii    ii   vvv      i    i i          i v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_153590091_   6147 TCAACAATAAGAAAATAAATGACCCAATTTAAAAATTGTCAAAAGACCTA 6196
                             i     i  i i    i        ?      v v    i  ii i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_153590091_   6197 AACAGAAACCTTACCAAAGAAGATATACAGATGAGGATTAAGTGTATGAA 6246
                           i   v ii iv                i   ivv v    iii     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_153590091_   6247 AATATG 6252
                           v   
  L1M4_orf2#LINE/    885 AAGATG 890

Transitions / transversions = 1.56 (123 / 79)
Gap_init rate = 0.02 (16 / 745), avg. gap size = 1.50 (24 / 16)  


3158 27.73 0.66 0.33  chr2_153677661_153683642     4586  5490 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153677661_   4586 TGGAAGAATATTCCATGGTCCTGGGTAGGAAGAATCAATATCATGAAAAT 4635
                              ii    i     v  v   i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153677661_   4636 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4685
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153677661_   4686 TACCAATGACTTTCTTCACAGAATTGGAAAAAAGTACTTTAAAGTTCATA 4735
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_153677661_   4736 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 4785
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_153677661_   4786 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 4835
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_153677661_   4836 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 4885
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_153677661_   4886 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATGTCTACAACTAT 4933
                              i    i--    i  --        vv iii ii i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_153677661_   4934 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 4983
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_153677661_   4984 ATTTAATAAATGGTACTGGGAAAACTGGCTAGCTATATGTAGAAAGCTGA 5033
                         v  i  i       i      v      v  ? i i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_153677661_   5034 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGCTT 5083
                          ii    i    v   i     v              i    i    v i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_153677661_   5084 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5133
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_153677661_   5134 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5183
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_153677661_   5184 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5233
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_153677661_   5234 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5283
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_153677661_   5284 GCAACCTACAATATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5333
                         i     i   iv            v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_153677661_   5334 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTGCAAGAAAAA- 5382
                          i  vi          v  i  v      vv    v ivii  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_153677661_   5383 ---AAGAACCCCATCAAAAACTGGGCGAAGGACATAAACAGACACTTCTC 5429
                         ---  v     v  i?    v     i     iv i  i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_153677661_   5430 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAAATGCTCACCA 5479
                         v        i  vi viii     v  i          i -      v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACA 897

  chr2_153677661_   5480 TCACTGGCCAT 5490
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.35 (142 / 105)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.25 (9 / 4)  


3233 27.75 0.22 0.22  chr2_153690041_153696318.rev     4879  5786 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153690041_   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATAGCGTGAAAAT 4928
                              ii i  i     i      i v      v i    vi  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153690041_   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153690041_   4979 TACCAATGACTTTCTTCACAGAATTGGAAAAAAGTACTTTAAAGTTCATA 5028
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_153690041_   5029 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5078
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_153690041_   5079 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5128
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_153690041_   5129 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5178
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_153690041_   5179 TGGGACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT 5226
                            i i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_153690041_   5227 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5276
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_153690041_   5277 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5326
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_153690041_   5327 AACTGGATCCCTTCCTTACACATTATACAAAAATCAATTCAAGATGGATT 5376
                          ii    i    v   i    vv           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_153690041_   5377 AAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5426
                          ?   ii    i  v i v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_153690041_   5427 AGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAA 5476
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_153690041_   5477 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5526
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_153690041_   5527 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5576
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_153690041_   5577 GCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5626
                         i     i   iv            v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_153690041_   5627 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5676
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_153690041_   5677 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5726
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_153690041_   5727 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCAT 5776
                         v        i  vi viii     v  i        i i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_153690041_   5777 CACTGGCCAT 5786
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


2372 25.42 2.84 7.46  chr2_153715151_153717976     1390  2341 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153715151_   1390 TGGAAAGAAATCCCATGCTTATGGATTAGAATAATTAATATTGTTAAAAT 1439
                                 v        i i       i   v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153715151_   1440 GACAATACTACCCAGAGCAATCTACAGATTCAATGCAGTACCCATCAAAA 1489
                          i       v    i vii              i   i v  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153715151_   1490 TACCAATGATATTTTTCACAGAAGTAGAAAGAACAATCTTAAATTTTGTA 1539
                          v   iiviiv     ii     i v  v iivii   i    v  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_153715151_   1540 TGGAACCACGAAATACCCA-AATAGCCAAA-CAACCCTGAGCCAAAACAA 1587
                              vii i iiv     -          -   i i   --------  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--------AA 192

  chr2_153715151_   1588 AATAAAAAACAACAACAACAACAACAAAAAACCCAAAGCTGAAGTTAC-C 1636
                           v  i  -------------------------     i  i  v-  - 
  L1M4_orf2#LINE/    193 AAGAAGAA-------------------------CAAAGTTGGAGG-ACTC 216

  chr2_153715151_   1637 ACACTACCTGACTTCAAGATATGCTGCAAAGTTATAGTAATCCTAAAGGC 1686
                              v  ii i     i iv i  i     i  i       ---   i 
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC---AAGAC 263

  chr2_153715151_   1687 A---TGATATTGGTATGAAAACAGATACATATAGACCAGTAGAACAGGAT 1733
                          ---  i  i   i  i ii i   --        i  i i   i  i  
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGA--CATATAGATCAATGGAATAGAAT 311

  chr2_153715151_   1734 AGAAAACCCAGAAATAAATTCACATATTTGCCGCCAACCAATTTTTGACA 1783
                         v  i ii           ii  i i    iiv i   iii     i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_153715151_   1784 AGG-TGCCAAGAATATACATTGGGGAAAAGGCAGTCTTTTCACTAAATGG 1832
                            -        vi  v  v        iiii          vi      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_153715151_   1833 TGCTAGAGAAACTGGGTATCTATATGCAGAAGAATGAAACTAGACCCCTA 1882
                             i iiv      i  ? i i     i         ii i        
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_153715151_   1883 TGTATTACCATATA--AAAATCAAATCAAAGTGGATTAGAAACTTACACA 1930
                         iv vvi        --     i  v     i     i ? i  i  v ii
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_153715151_   1931 CAAGACCCAAAAC-ATAAAATTAT-AGACAGAAACATTAGAGGAAATGCT 1978
                         i    v i     -      i v -   vii      vi ? v    vi 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_153715151_   1979 C----CC--AGGTCATCTAGGCAAAGATTTTATGTCTAAGGCTTCACAAA 2022
                          ----  --i   ----       v i   iv ivv  v i vi  v  i
  L1M4_orf2#LINE/    562 CGTGACCTTGGGT----TAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_153715151_   2023 TATAGTCAG-AAAAGACAAAAATATCCTAATGGGACTATATTAAGCTAAA 2071
                         i i iv  i-      -       vviv   v     vi  i  iv v  
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_153715151_   2072 AAGCTTCTACACAGCAAAGGAAATAAGCAACAGACTGAAGACACAATCTG 2121
                           i   i iii vv       v iv v   v i v    i v    i ii
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_153715151_   2122 TAAAATGACAGAAAATATTTACAAATTATCCATCTGACAAGTCACTGACA 2171
                         i i    iv           i     i  vi      -------------
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGA------------- 743

  chr2_153715151_   2172 TAAGGAACTCAACTCCACAGCAAAATTCGGCAATGCACATGTACTCCT-C 2220
                              i   iivv    -----i   ------  ii v - v    i - 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCA-----GAAT------ATATAAA-GAACTCTTAC 781

  chr2_153715151_   2221 AATTTAA-AATAAAA-GTTACATAA---AA---AAAAGTCGACAAAGGAT 2262
                           i i  -       - vi v    ---  ---    i v i        
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_153715151_   2263 ATGAATAATTTTCTTTTAAAAGAATACATACAAATGACCAAGAGTTATGT 2312
                         v      iviv i i iv      v i         i    v ivi ii 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_153715151_   2313 GAAAAAATATGCTCGCTATTACTAATCAT 2341
                              i  --    ivi  i ????????
  L1M4_orf2#LINE/    882 GAAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (162 / 77)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.50 (98 / 28)  


3408 20.11 2.92 4.76  chr2_153719413_153721610.rev      782  1706 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153719413_    782 TGGAAAGATATCCCATGCTCTCCAATTGGAAGAC--AGTACTTTTTAAAT 829
                                          i  vivi          -- i  i v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153719413_    830 GTCCATACTACCTAAAATGATCTATAGATTCAATATA-TCCTCATCAAA- 877
                          v v     v  i   v       i        iii -   ii      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153719413_    878 -CCCAA-TGGCATTTTTGCAAAAATAGAAAAA--AAATCTAAAATTCATA 923
                         -    i-  v v        i    v  v  i--i vi            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_153719413_    924 C--AAATTTTGATAGGATCTCAAATAGCCAAAACAAC--TAAGAAAGAAG 969
                         i--    vi-- vi   i ivi              i-- i i       
  L1M4_orf2#LINE/    151 TGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_153719413_    970 AATGAAGTTGGAAGCTTCACACTTTTTTATTTCAAAACACACTGCAA-GC 1018
                           ii        i vi        iiiv          vi   i   -  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_153719413_   1019 AACAGCAATCAAAACAGTA-GGTACTGACATA------GATATATATAAT 1061
                         v    i      i     i-       i    ------  i     v vi
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_153719413_   1062 AATGGAACAGAATAGGGAGCCCAGAAATAAACTCTTGCGTAGACGGCCAA 1111
                                i     v i   i            i v i i vv i  i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_153719413_   1112 ATGATTTTCAACAAGGACGCCAAAGCTGCACAAAGGGGAAACACCACTCT 1161
                         v        i      ii     ii iiiv   v       v vi v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_153719413_   1162 CTTCAA--AATGTTGTGAGAGGTGTTGGGAAAACCAGATATCCACAAGCA 1209
                         i     --    ---------   i     v   ii    ?     v   
  L1M4_orf2#LINE/    399 TTTCAACAAATG---------GTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_153719413_   1210 AAAGAATAAAGCTGGACCTCTACCTTATACCATATACAAAAATTAACTCA 1259
                                i   i      i      i i                      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_153719413_   1260 AAATGGATTAAAGACCTGAAGGTAAGACCAAAAACTATAAAACTCCTAGA 1309
                                 i ?      i  v      v v               i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_153719413_   1310 AGAAAACCTAGGGGGAAAGAATCAGGACATTTGAATTTGGCAATAATTTC 1359
                                v    ? v   vvv  iv   -i   ii  v      ii    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTC 588

  chr2_153719413_   1360 TTGAATATGACACCCAAAGTACATGCAACAAAAGAAAAAACAGAAAAACA 1409
                           ii          v    i   v                i   v   iv
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_153719413_   1410 GGACTACATCAAACAGAAAAACTTCCATGCATCAAAAAAAAACAGTCAAC 1459
                              v       vvv        iii   v     ii v vi -    v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAG 687

  chr2_153719413_   1460 AGAGTGAAAAGGCAACCTACAGAAGGGGAGAAAATACTTGCAAATTGTTT 1509
                          i         i     i      v           i        ii v 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_153719413_   1510 ATCTAATAAGCGGTTAATATACATATAAAAATTGTTACAAGTCAACATTT 1559
                             i     -  -------  ---------    -----------  ii
  L1M4_orf2#LINE/    738 ATCTGATAAG-GG-------AC---------TTGT-----------ATCC 759

  chr2_153719413_   1560 ATAGAATATATAGTGAACTTTTTCAAAGCAACAAGAAGAAAAACAAA--- 1606
                          --         iv     i  v   vv   i  v  -   i     ---
  L1M4_orf2#LINE/    760 A--GAATATATAAAGAACTCTTACAACTCAATAATAA-AAAGACAAATAA 806

  chr2_153719413_   1607 --CAATTTTTAAATGTACAAAGGACTTGAATAGACAATTCTTCAAACGAG 1654
                         --     ?vv     vi       i           v    i    vi  
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_153719413_   1655 ATATACAAATGGCCAAGAAACATATGAAAATGCGTTTGACATCACTACTA 1704
                                         v  i  i       vii i ii      ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_153719413_   1705 AT 1706
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.60 (112 / 70)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.23 (71 / 22)  


1822 27.15 4.05 0.84  chr2_153729745_153731337      501  1093 (500)    L1M4_orf2#LINE/L1      244   855 (53)  

  chr2_153729745_    501 AATGCTACAGTAACCAAAACGGCATGGTACTGGTACAAAAACAGACACAT 550
                           v          i   i  i ii         i i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_153729745_    551 AGACAGATGGAACATGTTACAGAACCCAGAAATAAAGCCTCACACCTACA 600
                            ivi      i viv vv   ii           v  vi   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_153729745_    601 GCCATCTGAGCTTCAGCAAATTTGACAAAAACAAGCAATGGGAAAAGGG- 649
                          i  vi   vi   ii   ivv  v   i v  vv       i    ii-
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_153729745_    650 -ATCCCCATTCAATAAATAGTGCTGAGATAGCTGGCTAGCCATATGCAGA 698
                         -i  ii--     i    i      i  i i    v  ?   i     i 
  L1M4_orf2#LINE/    394 AGTCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_153729745_    699 AGAATGAAACTGGACCCCTACCTTTCATCATATATATAAATTAACTCAAG 748
                                 ii             iv  i      i v            i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_153729745_    749 ATGAACTAAAGTTTTAAATGTAAGACCTCAAACTATAAGAATCCTACAAG 798
                            i ii ?  vii           v  v         i v  i  v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_153729745_    799 GGAAAGC-TAGGAA-ATATCATTCTCGACATTGGCCTTGGGAAAGAATTT 846
                         --   i -    ?i- v   -   vi   v    vi v  v  v iv  i
  L1M4_orf2#LINE/    542 --AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_153729745_    847 ATGGCTAAGTCTTCAAAAGCAATTGCAACAAAA-AAGAAATGGACAAATT 895
                         v i v  v v vi        vvv         -  i    i  i     
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_153729745_    896 GGACCTAATTAGACAAAAGAGCTTCTGCACAGCAAAAGAAATTAGCAG-- 943
                             i v  i i vvv  i i   i  ii vv    i  v i  v  i--
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_153729745_    944 -AGTAAACAGACAACCTACAGAATGGGAAAAAATATTCACAAACCATGCA 992
                         -   i  v        i           i        ii    i   ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_153729745_    993 TCTGACAAAGGTCTAATATT-ATAATCTATAAGGAACT--TA-------- 1031
                              i  i  v  vi   i- v   v     i     --  --------
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_153729745_   1032 -AGCAAAAAG-TAAATAACCCCATTAAAAAGCAGGCAAAAGACAT-AATA 1078
                         - ii      -i         v   ?    iii      i  iv -    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_153729745_   1079 GATGCTTC--CAAAAAA 1093
                           iii   --    i  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAA 855

Transitions / transversions = 1.85 (102 / 55)
Gap_init rate = 0.02 (14 / 612), avg. gap size = 2.07 (29 / 14)  


2982 25.69 1.33 0.78  chr2_153765019_153771526.rev     5119  6021 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153765019_   5119 TGGAAACACATTCCATACTCATGGATGAGTAGAATCAATATTGTGAAAAT 5168
                               v i  i    ii        vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153765019_   5169 GACCAAACTGCCAAAAGCAATCTACAGCTTCAATGCCATTCCCATCAAAA 5218
                          i v v   v  v   vii        v     i  v  i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153765019_   5219 ATACCATCATCATTCTTCACAGAACTAGAAAAAACT-ATCCTAAAATTCA 5267
                         - v   v vv v  i  ii     v v  v  i-  -             
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_153765019_   5268 TATTGAACCAAAAAAGAACCCACATAGCCAAAACAA----GACCAAGCAA 5313
                            v   viiv  ii  v  viv             ----  vv   ---
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG--- 195

  chr2_153765019_   5314 AGGAACAAGTCCGGAGGTATCACATTATCCAACTTCAAATTATACTATAA 5363
                          i      ivii     vv     i vi    i      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_153765019_   5364 CACTATAGTTACCAAAACAGCATAGTACTTGTATAAGAACAGGCTTGTAG 5413
                         vi   i   v i   i    ii i     v i     i i  i v i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_153765019_   5414 ACCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATTCTTACAGA 5463
                          i        i     v    ii           v   v ivi   ii v
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_153765019_   5464 CAACTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGAGAAACAACAC 5513
                            i    i   i    i vviv   i v   vv i   i    v  i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_153765019_   5514 CCTATACAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGAAGAA 5563
                         i  v v                  i  i   vv ?       i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_153765019_   5564 TGAAACTGGATCCTCATCTCTCACCTTATGCAAAAACCAACTCAAGATGG 5613
                             ii    i  ii i   v    v   i      ii       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_153765019_   5614 ATCAAATACTTAAATCTAAGACCTGAAAACATAAAAATTCTAGAGGATAA 5663
                             ? v  i     v     v  i   vi      v ii    i  v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_153765019_   5664 CATTGGAAAAACTCTTCAAGACATTGGCTTAGGCAAAGATTTCATGAGCA 5713
                            v  ?iv  v     iv   v    v        v i    v iiii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_153765019_   5714 AGA-ACTCAAAGCAAATGCAACAAAAACAAAGGTAAATAGATGGGACTTC 5762
                         v  -  iv      v v         iv   ii  i   i  v       
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_153765019_   5763 ATTAAA-TGAAAAAGCTTCTGCACAGCAATAGAAATAATCAGCACAGT-A 5810
                           i   - v     -   i  ii vv   vi  v iv    iv v   - 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_153765019_   5811 ACAGACAACCCACAAAGTGGGAGAAAATATTCACTAACCATACATCTGAC 5860
                          v            i i              ii v  i    i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_153765019_   5861 AAAGGACTAATATCCAGAATCTACAGGAAACTCAAACAAAGCAGCA-TGA 5909
                           i     vi          v  i iii     vv    vv  ii - i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_153765019_   5910 AAAAA-AAATAATACCA--TCAAAAGTGGGCAAGGGACATGAACAGATAA 5956
                            i -      i-   -- ?    i       i   iv    i   i v
  L1M4_orf2#LINE/    795 AAAGACAAATAAC-CCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_153765019_   5957 TTCTCAAAAGAAGCTATACAAATGGCCAACAAACATATTAAAAAATGCTC 6006
                              v       v               i  i  i  v    i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_153765019_   6007 AAATTCATTAATGAT 6021
                           vv   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (128 / 100)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


2805 28.07 1.29 0.70  chr2_153831781_153833724.rev      586  1440 (504)    L1M4_orf2#LINE/L1        1   860 (48)  

  chr2_153831781_    586 TGGAAGAACATTCCATGCTCTTGGGTAGGAAGAATCAATATCATGAAAAT 635
                              ii i  i     i  v   i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153831781_    636 GGCCATACTGCCCAAGGTAATTTAGAGATTCAATGCCATCCCCATCAAGC 685
                            v     v     iv i  i  v        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153831781_    686 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 730
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_153831781_    731 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 780
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_153831781_    781 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGGCTA 830
                              i      vv   ii  v  ii i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_153831781_    831 CAGTAACTAAAATAGCATGGTACTGATACCAAAACAGAGATATAAACCAA 880
                               ii  i i  ii        ii iv ii i   v     i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_153831781_    881 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACCAT 928
                              i    i--    i  --        vv  ii i  i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_153831781_    929 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAGCAATTCCCT 978
                         i    i  i     ivv  v   i v  vvv         iv   vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_153831781_    979 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1028
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_153831781_   1029 AACTGGATCCCTTCCTTACACATTATACAAAAATTAATTCAGGATGGATT 1078
                          ii    i    v   i    vv              i   ii      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_153831781_   1079 AAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1128
                          ?    i    ii v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_153831781_   1129 AGGC---AATGCCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTA 1175
                            ?---   -- -   iv   viv  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_153831781_   1176 AAACACCAAA-GCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1224
                         vi        -   vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_153831781_   1225 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1274
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_153831781_   1275 CAGGCAACCTACAGAATGGGAGAAAATTGTTGCAATCTACTCAACTGACA 1324
                         v  i     i                 vv      vii ivi v    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_153831781_   1325 AAGGGCTAATACCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 1374
                          i  i  vi  i       v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_153831781_   1375 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 1424
                           i -    i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_153831781_   1425 TCTCAAAAGAGGACAT 1440
                             v     i  i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATAT 860

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (9 / 860), avg. gap size = 1.89 (17 / 9)  


2105 26.18 1.22 3.35  chr2_153859982_153864114.rev     2392  3048 (1085)    L1M4_orf2#LINE/L1        1   643 (265)  

  chr2_153859982_   2392 TGGAAAGATACCTCGTGTTCATGGTATGGAAAAATTAATATTGTTAAAAT 2441
                                   i i i         vv     i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153859982_   2442 ATCCATCCTAGGCACAGTGATCAACAAATTCAATGCAATTTCCATCAAAA 2491
                         iv v  v  vvv  v v     v   i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153859982_   2492 TTTCAAC-GTCATTTTTCCTATAAATAGAAAAAATACAAACCTAAAATTC 2540
                          ii  i - i v     v - v    v  v  iv i-- v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGC-AGAAATTGACAAGCTG--ATCCTAAAATTC 147

  chr2_153859982_   2541 ATATGAAAGCACAAAA-ATCTTGAAAAACTAAGGCAATCATAAGCAAAAA 2589
                              i  iii   ii- i iv   v i i  ii     v i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_153859982_   2590 GAAGAAAGCTGGAAACATCACACTATTTGATTTCAAA--TTATATATGAA 2637
                            v    i    iivv       viiii        --   i-  ii  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC-TACAAA 246

  chr2_153859982_   2638 GTGAAAGTAATTTAAATAGCATGGTACTGGAATAAAAATAGGCTCATTAA 2687
                          iv v      iv i i  ii         v    ii    i vi  vi 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_153859982_   2688 CAAATGGAAAAGGATAGAGAATGCAGAAATGAACCCACTCATCTCTGATC 2737
                         iv       v  i  v    i v       i      iv   i v  i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_153859982_   2738 AATTGATTTTCAATAAAGGTGCCAAGAATTTTTAACAAATGTGCCTTTTA 2787
                                    i i  i          viv  i  ---------------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAA--------------- 381

  chr2_153859982_   2788 TGTTGTGAAAAGGA--GTCCCTTAAATAAATAGTGTTGAGTAAAC--AAT 2833
                         ---  v i    i --   ii  v  i    i   i  i vv   --i  
  L1M4_orf2#LINE/    382 ---TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_153859982_   2834 ATGGATATGCAAAAGAATGAAATTGGACCTTTATCTCACATCATATACTT 2883
                          ?vv i               i       ii  i      i       vv
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_153859982_   2884 AAATCAAGTCAATGTGGATGAAAGATTTAACCATAAGTACTGAAAGTTTA 2933
                             i  v    vi     v ?   ii   vii    vi  i   v v  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_153859982_   2934 AAACTACTAGAAGAAAACATATGAGAAAAACTATGTGACATTGGTCTGGG 2983
                              vi              v ? v   v  vi     v    vi i  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_153859982_   2984 CAATGATATTTTCGATTTGATCTCAAAAGCACAGGCAACAAAAGCAAAAA 3033
                              i v i  v   v   ivi          i          v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_153859982_   3034 CAGAAAAATGGGATT 3048
                         i   v    v   i 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACT 643

Transitions / transversions = 1.41 (99 / 70)
Gap_init rate = 0.01 (9 / 643), avg. gap size = 3.33 (30 / 9)  

 835 25.33 2.67 0.67  chr2_153859982_153864114.rev     3342  3641 (492)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr2_153859982_   3342 AAAAAAAAAAAAAAAAAAAGAAGAAG-AGAAAAATGGGATTGCATCAAAC 3390
                             iv v  iv  v       i  i-   v    v   i v       v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_153859982_   3391 TAAAAAGCTTCTGTACAAGAAATGAAAC-ATCACAA---TGAAGAGACAA 3436
                          v    i   i   i vvv   v  v  -    vi ---    i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_153859982_   3437 CCCATAGATTAGGATAAAATGTTTTCAAGCCATACATCCAATAAAGGGCT 3486
                             i   v i   v     i   v   ii    i   ii    i  i  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_153859982_   3487 AATATCCACAATATATATTAGGAATTCAAGCAACTTTATAGAAAGAAAAC 3536
                         vi      v        -- i   i  vvi     iv   iv  i  i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATA--AAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_153859982_   3537 AA-TA-TCTGATTTTAGAATGGGCAATGGACCTGAACAGATAGTTCTC-A 3583
                           -  -i ii   ?v i         v   ii    i   i v     - 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_153859982_   3584 AAGATAATTAAGAAATGGCCAATAGACATATGACAAAATATTCAACATCA 3633
                             vi  vv v            ii  i    v  i  ii         
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_153859982_   3634 CTTATCAT 3641
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.34 (43 / 32)
Gap_init rate = 0.02 (7 / 306), avg. gap size = 1.43 (10 / 7)  


2747 27.64 2.11 1.33  chr2_153864751_153869502.rev     3360  4260 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153864751_   3360 TGAAAAAGTATTCTACGCTCATGGACAGGAAGAATCAATATCATGAAAAC 3409
                           i   ii   i i i i       iv      v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153864751_   3410 GGCAATACTGTCCAAAGTAATTTATAAATTCAATTCAATTCCCATTAAAC 3459
                                  vi     v i  i  i i      iv    i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153864751_   3460 TACCA-CTGACATTCTTCACAGAATTAGATAAAAACT-ATTTTAAAATTC 3507
                          v   -   v -  i  ii     v v  i  i--  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_153864751_   3508 ATATGAAACAAAAAAAGAGCCCGCATAGCTGAGATAATCCAAAGCAAAAA 3557
                              i  vviv  ii  v  v v     ii i i    ivi iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_153864751_   3558 GAACAAAGCTGGAGGCATCAAGCCACCTGAATTCAAACTATATACTACAA 3607
                                 i      vv   vi iv  ii v      -- iv        
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAA 245

  chr2_153864751_   3608 GCCTACAGTAACCAAAACAGCATGGTACTGGTACAAGAACAGACACATAG 3657
                         iv         i   i    ii         i i   i i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_153864751_   3658 ACCAATGGAACAAAAGAGAGGACTCAGAAATAAGACCACATGCCCAGAAC 3707
                          i        i i  vv   iiii         iv   i iiiii viii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_153864751_   3708 CATCTTTTCTTTGACAAACCTGACAAAAACAAGCAATGGGGGAGAGACTG 3757
                           vi vv i  i     ivv  v   i v  vv        i iii iv 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_153864751_   3758 CCTCCTTAATAAATGGTGCTGCAAGAGCTGGCTAGCCATATGCAGAAAAC 3807
                         i  ii i  i           vi v i    v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_153864751_   3808 TGAAACTGGACCACTTTCTTACACCATGTGCAAAAATTAAC-CAAGATGG 3856
                             ii      v  vi  i       i i           -   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_153864751_   3857 ATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAAGCCTAGAAGAAAA 3906
                           i ?    i         i v i            vv i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_153864751_   3907 TCTAGGC---AATACTAATCAGGACATAGGCACAGGCAAAGATTTCAT-- 3951
                         iv    ?---   -  --  iv   v v  vvi      v i    v --
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_153864751_   3952 -TATGAAAATCCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGA 4000
                         -     v ---         vvv          v      v  i    vi
  L1M4_orf2#LINE/    593 ATATGACA---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_153864751_   4001 GATCTAATTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACTATCA-GAA 4049
                           ii v  i   v v  i i   i vii vv    i  v       -   
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_153864751_   4050 --TGAACAGACAACCCACAGAATGGGAGAAAAATTTTGCAATCTATCCAT 4097
                         --    v                         vv       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_153864751_   4098 CTGACAAAGGTCTAATACCTAGAGTCAACAAAGAACTTAAACAAATTTAT 4147
                             i  i  v  vi  i i   i vv i        ivv    v iv  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_153864751_   4148 GAGAAAAAAA------ACCCA-TTAAAAAGGAGGCAAAGAGCATTAACAG 4190
                         i v     i ------     -  ?    ivi       iiiv v  i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_153864751_   4191 ACACTTCTCAAAAGAAGACGTACACGTGGTTAACAAACATATGACAAAAA 4240
                            i     v        ii    vi   ii  i  i  i    -   i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGA 888

  chr2_153864751_   4241 AGTTTAACATTATGGATCAT 4260
                         v i i     i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (154 / 91)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.94 (31 / 16)  


2954 25.51 3.51 0.57  chr2_153871376_153875533.rev     2785  3666 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153871376_   2785 TGGAAAGATATCCCAGGCTCATAGATTGAGAGAATTAATATTTTTAAATT 2834
                                        v i    i     ii   v        v    iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153871376_   2835 AACCATATAACTCAAATCAACCTATAGATTCAATGCAGTCTCTATCAAAA 2884
                         ii v   ivv i     ii i   i        i   i  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153871376_   2885 TAGCAATCACATTTTTCACAGAAAT----AAGAAAATCCTAAAATTTGTA 2930
                          vv  iiii v     ii       ----   vvi           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_153871376_   2931 TGAAACCAAAAAAGAACCTGAATAGCCAAAGCAATACTGAGAAAAAAGAA 2980
                           i  viiv  ii  v  v           i    vi   i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_153871376_   2981 CAAAACTAGAGGCATCATACTACCTGACTTTAAAACATATTA-AAAGTCT 3029
                             ii i    vv   i   v  ii i  i     v  i  -    -  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG-CT 249

  chr2_153871376_   3030 TTATTAACCAAAACAACATGGTATTGGTATACAAACAGACACATAGACAA 3079
                         vi v   i   i   iii     i   i   vii i     i     iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_153871376_   3080 ATCAAACTGGATAGAGAACACAGAAATAAACTCCTGTATTGAAAGCCAAT 3129
                           vi  iv i  v    iiv           i v ii   v vi i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_153871376_   3130 TGATTTTTGACAAAGGTGCCAAGAGCATACTTTAGGGAAAGA-CACTCTC 3178
                                i     i          v   v vv i        -i v   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_153871376_   3179 TTCAATAAGTTGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAA 3228
                              i  i v         v         ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_153871376_   3229 ACTAGGCCCCTACTTCCCACCATATA-GAAAATTA-CTTAAAA------- 3269
                         ii i i       i  v         -i       -  i    -------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_153871376_   3270 ---ATTTAAATGTAATATCCAAAGCTATAAAACTATTAGAAGAAAACACA 3316
                         --- ii         v v i   i          v             i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_153871376_   3317 CGGGAAACACTATAGGACATTGGTCTAGACAAACATTTTATGGCTAAGAT 3366
                         v ? v  vv  viiv   v    vi   i   vvi   iv i v  v  i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_153871376_   3367 CCCAAAAGCACAAGCAACAGAAATACAGAATAAACGAATGGGACGTTATT 3416
                         v                  -   v v i    i ii   v    v i  i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_153871376_   3417 AAACTAAACAACTTCTGCAACAGCAAAAGAAATAATCAACAAAGTGAAGA 3466
                            v v  v     i  ii- vv    i  v iv     v        i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTG-CTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_153871376_   3467 GACAACCTGCTGAATGGAA-AAAATATTTGTCAAAT-ATTCATTCAAAAA 3514
                                ii v      i -          -     -  vi  iii v  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTG-CAAATCATATATCTGATAA 746

  chr2_153871376_   3515 GAGACTAATATTCAGATTATA-AAAGAAATCAGACAAC-----AGCATAA 3558
                          i    vi   i    v    -      v  vv     ----- ii v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_153871376_   3559 AAACG-----TTCCATTAAAAATTGGACAAATAATCTAAACAGACATTTC 3603
                          i  i-----ii v   ?    v   i    vi  i i  i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_153871376_   3604 TCAAAAGAAGGAATACAAATGGACAACAGATATATGAATCAAATGTTCAT 3653
                           v       iv          v   i iii i     -v i   i   v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGATGCTCAA 895

  chr2_153871376_   3654 CATCATTAATTAT 3666
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (136 / 86)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.25 (36 / 16)  


2242 22.02 5.11 2.49  chr2_153898086_153899825.rev      486  1248 (492)    L1M4_orf2#LINE/L1      126   908 (0)  

  chr2_153898086_    486 TGGCAAGTTTATGATAAA-TGCATATGTAAATTCAAA--ACCCAGAAGTA 532
                           i    i v  vv    - v      v    v   i--        -  
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA-TA 174

  chr2_153898086_    533 GTCAAAACA--CTTGGAAAAAGATGAAGAATGTTGGAGAGGAAACAATGT 580
                          i       --    -       v   v  v       iivvv   v vi
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTG-AAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chr2_153898086_    581 CTGATACCAGGTTTTGTTACAAAGATAGACTACTTAATACA-------AC 623
                          ii  vi  iivi  ii       v  v v  v i  v   -------  
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr2_153898086_    624 --AAATAAAAATAGACAAACAGATCAATGAAACAAAA--GAGACTCCAGA 669
                         --iv    ii       v i         i  i i  --    v      
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_153898086_    670 AATATACACATGTATATAAAAACAATGAACTTTGGTACAAGG-TACAAAG 718
                             v  v   ii  v  viiv    vi i   v -      - i v   
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCG-ACAAGGGTGCCAAG 372

  chr2_153898086_    719 ATAATTCAATGGAAAAAGA-TAGTCTCTTCAACAAATGTTGCTGAAACAA 767
                          iv         ii     -      i           v     ii    
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_153898086_    768 TTGGCTATTCATATGCACAAAAAAGAGAGGAAAAAATATGCAACCTCTAC 817
                         i   v  ?i  i     ----     ---- vi  i -  -i   i    
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCA----AAAGA----ATGAAGT-TG-GACCCCTAC 462

  chr2_153898086_    818 TTCACTCCATATATAAAAATTAACTCAAA-TGGATCATAGAACTAAATGT 866
                         i    v       i               -       ?   v        
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_153898086_    867 AAAACCTAAAACTATAAGATTTCTATAAGAAAATTTAAGGAAAAAATAAT 916
                           i v            i i ii  v       iv  -  ?iv    vv 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA-GGNGTAAATCTT 561

  chr2_153898086_    917 TGTGATCTTGGATCAGGCAAAATTTTCTTAGATATTACACCAAAA-CATG 965
                         i    i     i i      viv            v         -  ii
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_153898086_    966 ACCAACAAAAGAAAAAAATTGATAAATTGAACAT--TTAAAATTAAAACC 1013
                          v               - v         i  v -- i          v 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_153898086_   1014 TTTTTTCCATGAAAG-ACA-TACTAGGAGAATTTTTTAAAAATAAGCCAG 1061
                             v v v v    -   -  ii i  i i vv---   i i  v   v
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA---AAAGACAACCCAC 707

  chr2_153898086_   1062 AGACTTGGA-AAAATATTTACAAATCAAAAACCTTACAAGAGATTTTTAT 1110
                            v v   -         i       v v i  v i   i  i  v   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_153898086_   1111 CTAGAATATGTAAAGAACTCTCA-AAC---ACAATAGGAAAACAAA-AAT 1155
                          i       i           i -   --- i    ii  i     -  i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_153898086_   1156 CCAATATTAAAATGATGCAA-TTATTTG----GACATTTCACTGAAGAGG 1200
                              v?v      i-    -vv     ----        v ii    i 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGG-GCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_153898086_   1201 ACATGCAGGTGAC----AAGCTCATGAAAATATGTCCAACATCATTAGTC 1246
                          i  i  ii  i ----    v        v   ii        ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_153898086_   1247 AT 1248
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.28 (92 / 72)
Gap_init rate = 0.04 (31 / 783), avg. gap size = 1.87 (58 / 31)  


2805 27.27 1.10 1.64  chr2_153925874_153932815     5539  6451 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153925874_   5539 TGGGAAAAAATTTCATGCTCATTGATAGAAAGAATCAATATTGTGAAAAT 5588
                            i  i v  ii    i    v   v i    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153925874_   5589 AGCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATTCCCAT-AAAG 5637
                         i  v     v      v i  i           i  v  i  i  -   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153925874_   5638 TTACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 5686
                          iv vii  v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_153925874_   5687 TATGGTACCAAAAAAGAGCCCATATAACCAAGACAATGTTAAGCAAAAAG 5736
                              v viiv  ii  v  viv   i    i     v  i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_153925874_   5737 AACAAAACTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGTC 5786
                               ii      vv   i   v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_153925874_   5787 TACAGTAACCAAAACAGCAGGGTACTGATACCAAAACAGATATATAGACC 5836
                                 i   i    iiv       ii iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_153925874_   5837 AATGGAACAGAACAGAGACCTCAGAAATAACACCATACATCTACAACCAC 5886
                                i    iv    vii         vv        i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_153925874_   5887 AAGATCTTCAACAAAAATGACAAAAACAAGCAATGAGGAAAT--TATTCC 5934
                         vv   i   i    iii  v   i v  vv     i     v--  v  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chr2_153925874_   5935 ATATTTAATAAATCATGCTGGGGGAACTGGCTAGCCATACGCAGAAAACA 5984
                         - v  i  i    vi       iv      v  ?   i i   i  i vv
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_153925874_   5985 GAAACTGAACTCCCTCCTTACACCTTATACAAAAATTAATTCATGTTGGA 6034
                            ii  i  i  iv   i     v              i   viv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_153925874_   6035 TTAAAGACTTAAATGTGAAACCCAAAACCATAAAAAACCCTAGAAGAAAA 6084
                          i ?    i       i i v i     i      v-i i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chr2_153925874_   6085 CCTAGGCA-ATACCATTCAGGATATAGGCACGATCTCATAGTCATAAGAT 6133
                          v    ?i- v i -   iv  iv v  ----i ----   v  - v i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGG----GT----TAGGCA-ATGGT 585

  chr2_153925874_   6134 TTCATGAATAAAACACAAAAAGCAACTGCAACAGAAGCTAAAATTGACAA 6183
                            v ii   vi    v       vvv      i   vv     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_153925874_   6184 ATGGGATCTAATTAAGCTAAAGAGCTTCTGCACAGCGAAAGAAACTATCA 6233
                           v   ii v  i  iv v  i i   i  ii vv i  i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_153925874_   6234 TCAGAGTGAACAGACAACCCACAGAATGGGAGAAAATTTTTGCAATCCAT 6283
                         vv i      v                          v       vi   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_153925874_   6284 CCATCTGACAAAGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAAT 6333
                         vi      i  i  v  vi          v  i  i     ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_153925874_   6334 TTACAAGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGA 6379
                         iv i  v     i    ----   v  i?    i            v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_153925874_   6380 ACAGACACTTCCGAAAAGAAGACATTTATGTGGGCAACAAA-ATATGGAA 6428
                          i     i   ivv        i  vi vi   v   i  i- i   i  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_153925874_   6429 AAAAGCTCATCATCGCTGGTCAT 6451
                          i v     v    i????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.79 (25 / 14)  


3051 27.48 0.88 0.66  chr2_153933744_153939999.rev     4859  5764 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_153933744_   4859 TGGAAGAATATCCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4908
                              ii          i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153933744_   4909 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCACCATCAAGC 4958
                            v     v     iv i  i           i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153933744_   4959 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5006
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_153933744_   5007 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5056
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_153933744_   5057 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5106
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_153933744_   5107 TACAGTAACCAAAACAGCGTGGTGCTGGTACCAAAGCAGA--TACAGACC 5154
                                 i   i    i     i    i iv iiii   --  i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_153933744_   5155 AATGTAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5202
                             v  i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_153933744_   5203 ATCAGATCTTTGACAAACCTGACAAAAACCAG-AAGTGGGGAAAGGATTC 5251
                          viv   i  i     ivv  v   i -   v-v i         i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAG 395

  chr2_153933744_   5252 CCTATTTAGTAAATGGTGCTGAGAAAACTGGCTAGCCATATGGAGAAAGC 5301
                         i  v  i ii           i  v      v  ?   i   v i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_153933744_   5302 TGAAACTGGATCCCTTCCTTACACATTATACAAAAATTAATTCAAGATGG 5351
                             ii    i    v   i    vv              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_153933744_   5352 ATTAAAGACTTACAGGTTAGACCTAAAACCGTAAAAACCCTAGAAGAAAA 5401
                           i ?    i  v v  v   v       ii     vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_153933744_   5402 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCC 5450
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_153933744_   5451 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5500
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_153933744_   5501 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5550
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_153933744_   5551 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5600
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_153933744_   5601 AAAGGGCTAATATCCAGAATCTACAATGGACTCAAACAAATTTACAAGAA 5650
                           i  i  vi          v  i  v i    vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_153933744_   5651 AAAAGCAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5700
                            ii    i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_153933744_   5701 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5750
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_153933744_   5751 CCATCACTGGTCAT 5764
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2220 28.09 1.93 1.93  chr2_153959301_153964623.rev     3597  4372 (951)    L1M4_orf2#LINE/L1        1   776 (132)  

  chr2_153959301_   3597 TGGTAAATCATTCCATGCTCCTACATTAGAAGAATTACTATCATTAAAAT 3646
                            v  ivi  i     i  v iv   i     v   v   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_153959301_   3647 GGCCATATTGCCCAAAGTAACCTGCAGATTCAATACTATTTCTATCAAAC 3696
                            v   i v      v i i  i         ii v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_153959301_   3697 TACAAA-TGTCATTTTTCACAGAACTAGAAAAAAACTG-TTCTAAAACTC 3744
                          v v i-  i -     ii     v v  v  i--   - i      i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_153959301_   3745 GTATGGGACCAAAAAGGAGACAGAATAGTCAAAGCATTCCTAAGCAAAAA 3794
                         i     i viiv  i   vv        i    i  v  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_153959301_   3795 GAACAAAGCCAGAGGCATCACATTACCTGACTTCAAA--CTGTGACGGAA 3842
                                 iii    vv     i v  ii i      --i iiv  i-  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA-AA 246

  chr2_153959301_   3843 GCTGCAGTAAACAACAAAGCATGATACTTTGTTGTACAAAAAGAGACACA 3892
                            i      v   v v  ii  i    -- -- i i  ii v     i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACT--G--GCATAAGGATAGACATA 292

  chr2_153959301_   3893 TAGACCCATGGAACATAATAGAAACCCCAGAAATATAGCTGTACACCTAT 3942
                             i v      i v   v  i vi         v v ii    ii   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_153959301_   3943 AGCCA-T--ATTTTTGACAATGTTGACAAGAATAAGCAATGGAGAAAAGA 3989
                         i i  - --     i     v v  v     vi vv      i    -  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GA 391

  chr2_153959301_   3990 ATC-CCTATTCAATAAATGAGTCTGGGGTAACTGGCTGACCACAAGCAGA 4038
                           v-i  v     i     ivv     ii      v i?     v   i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_153959301_   4039 AGAATAAAACTGGATGACTGCCTTTCACTATATACGAAAATTCACTGCAA 4088
                              i  ii    ivv  i   iv   i      i      v   vv  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_153959301_   4089 ATGGATGCAAGATTTAAATGTAAGAACTCAAACTATAAGAATCCTTGAAG 4138
                               vv?   ii           i  v         i v  i v    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_153959301_   4139 AAAACCTGGGAA-ACACCACTCTGGACATTGGCCTTAGAAAAGAATTTAT 4187
                              v i  ?i- v i -i  vv   v    v-    iv  vii   -i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTT-C 588

  chr2_153959301_   4188 TTATAACTAAGTCCTCAAAAGCAATTGCAACAAAACCAAAAATGGACAAA 4237
                            v --  v v vi        vvv         vv      i  i   
  L1M4_orf2#LINE/    589 TTAGA--TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_153959301_   4238 TGGGGCCT------AATTAAACAGCTTGTGGATAGCAAAAGAAATCATCA 4281
                          v  i i ------       - i   v  viivv    i  v ii    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_153959301_   4282 GCAGAGTAAACAGACAACCTACAGAATGACAGAAAATATTTGCAAACTAT 4331
                         iv i   i  v        i        iv                ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_153959301_   4332 GCATCTGACAGAGGTTTAATACCCTGAAACTTTAAGAAACT 4372
                         ii      i ii  vi vi  i  v   vv v   ii    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.36 (124 / 91)
Gap_init rate = 0.02 (19 / 776), avg. gap size = 1.58 (30 / 19)  

 310 24.48 5.59 0.70  chr2_153959301_153964623.rev     4689  4831 (492)    L1M4_orf2#LINE/L1      759   908 (0)  

  chr2_153959301_   4689 CAAAAGAAAAAAGAAACTCAAGCAATTCAACAAGCAAAAACCAAAAAACT 4738
                           i  v v v  ii     vvi   i    i  vv    iv    v   i
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_153959301_   4739 GCATTTAAAAATGGGCAAAG------AACAGATACTTCTCAAAATAAGAC 4782
                         vv   ?              ------  i   i i     v   v    i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_153959301_   4783 ATACAAGCAGTCAGCAA--ACAAGAAAAAACTGCTGAACATCACTAGTCA 4830
                               iii i  ii  --   v     i -    v       ???????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZ 907

  chr2_153959301_   4831 T 4831
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.27 (19 / 15)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 3.00 (9 / 3)  


2699 26.47 2.15 2.04  chr2_154004771_154015042.rev     2618  3501 (6771)    L1M4_orf2#LINE/L1       24   908 (0)  

  chr2_154004771_   2618 GATTGGAAGAATTAATATCATGAAAATGGCCATACTGCCCAA--TGAAAT 2665
                                   v       ii v  i     v     v     --   -- 
  L1M4_orf2#LINE/     24 GATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA--T 71

  chr2_154004771_   2666 CTACAGATTCAATGCTATTCCTATCAAACTACCAACATCATTTTTCACAG 2715
                                     i  v  i         v v   i vv v     ii   
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAG 121

  chr2_154004771_   2716 AACTAGAAAAAGCT-ATTCTAAAACTCATATGGAACCAAAAAAGAGCCCA 2764
                           v v  v  -   -  i      i          viiv  ii  v  vi
  L1M4_orf2#LINE/    122 AAATTGACAA-GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr2_154004771_   2765 AATAGCCAAAGCAATCCTAAGCAAAAAGAACAAAGCCAGAGACATCACAT 2814
                                   i     i i iv  i          iii   ivv     i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_154004771_   2815 TACCTGACTTCAAACTATACTATAAGGCTACAGTAACCAAAAATGGCAGT 2864
                          v  ii i      viv     i  i          i   i ----    
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA----CAGT 266

  chr2_154004771_   2865 -TGG--CTGGTACAAAAACAGACTCATAGATGATTGGGACAGAATAGAGA 2911
                         -   --    i i  ii i    vi      v v   i i     v    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_154004771_   2912 AAATAGAATTAAAGCTTCACACCTACAACCATCTGAACTTTCACAAAG-C 2960
                         ivvi    v    v ivi   ii  iiii  vi   vi  iv    i -i
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_154004771_   2961 AATAAAAGTAAGCAGTGGGGAAAGGACTTTCTATTCAATAAATGGTGCTG 3010
                         ivi  i vi vv  i         i ivv   v     i           
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_154004771_   3011 GGATAGCTAGCTAGCCATATGCAGAAGAATGAAACTGGACTGCTGCCTTT 3060
                            i i  i v  ?   i     i         ii     iv  i   iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_154004771_   3061 CACTATATAGAAAAATTATCTCAAGATAAATTAAACATTCATACGTAAGA 3110
                            i     v        v     i  ii  i ? v iii v i      
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_154004771_   3111 CCTCAAACTGTAAGAATCTTAAAAGAAAACCCAGGAAACGCCATTCTGGA 3160
                         v  v     i   i v     i        vi   ?--- iv v   v--
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN---GTAAATCTT-- 561

  chr2_154004771_   3161 CGTTGACCTTGGG--AAGGAAT------TTATGACTAAGTCCTCAAAAGC 3202
                            -         -- i v   ------   -  -  v v vi       
  L1M4_orf2#LINE/    562 CGT-GACCTTGGGTTAGGCAATGGTTTCTTA-GA-TATGACACCAAAAGC 608

  chr2_154004771_   3203 AATTGCAACAAAAACAAAAATTGACAAATGGGGCCTTATTAAACTAAAGA 3252
                          vvv         iv      v  i    v  i i i  i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_154004771_   3253 GCTTCTTCACAGCAATATAAACTATCAACAGAGTAAACAGACATCCTACA 3302
                         i   i vii vv   viv v        v i   i  v     v  i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_154004771_   3303 AAATGGAAGGAAATATTCACAAACTATGTATC-AACAAGGGTATAATATC 3351
                         i     i  i       ii    ii  i    -i i     vv vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_154004771_   3352 CAGAGCCTATAAGGA--TATTAAACAATTGAACAAATAAAAACCAAATGC 3399
                             iiv     i  -- v   --   i v  i  vv    iv     iv
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTA--CAACTCAATAATAAAAAGACAAATAA 806

  chr2_154004771_   3400 CCATAATT-AAAAACAGTCAAAAGACATGAACAGACATTTCTCAAAAGAA 3448
                           -i    -     ii v    i  iv    i           v      
  L1M4_orf2#LINE/    807 CC-CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_154004771_   3449 GGCACACAAGTGGCCAACAGACATATGAAAAAATGTCCAGCATCAGTAAT 3498
                          ii i    i       i ii  i       i   ii  i     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_154004771_   3499 CAT 3501
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.57 (141 / 90)
Gap_init rate = 0.02 (20 / 885), avg. gap size = 1.85 (37 / 20)  

2996 27.38 1.55 0.89  chr2_154004771_154015042.rev     8879  9780 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154004771_   8879 TGGAAAAACATTATTCCATGCTCATGGATAAGAAGAATCAATATTGTGAA 8928
                               i ---   i     i        vi     v i        v  
  L1M4_orf2#LINE/      1 TGGAAAGA---TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chr2_154004771_   8929 AATGGCCATACTGCCCAAAGTAATTTATAAATTCAGTGCTATTTTCATCA 8978
                         i     v     v      v i  i  i i     ii  v  iiii    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_154004771_   8979 AGCTACCATTGACTTTCTTCACTGAATTAGAAAAAAACT-ACTTTAAATT 9027
                          iv v   vivi i  i  ii v   v v  v  i--  - iii    v 
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAAT 145

  chr2_154004771_   9028 TCATATGGAACCAAAAAAGAGACT--GTATAGCCAAGACAATCCTAAGCA 9075
                                   -- viv   i   i-- v        i      i i iv 
  L1M4_orf2#LINE/    146 TCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_154004771_   9076 AAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTTAAAATATACTAC 9125
                          i          i      vv   ii  v  ii i  i    iv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_154004771_   9126 AAGGTTACAGTAACCAAAACAGCATAGTACTGTTACCAAAATAGATATAT 9175
                           i i        i   i    ii i      vi iv ii     i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_154004771_   9176 AGACCAATGGAACAGAACAGAGGCCTCAGAAATAAGACCACACATCTACA 9225
                            i        i    iv   ivii         iv   i    i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_154004771_   9226 ACCATCTGATGTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT 9275
                         ii  vi    v  i     ivv  v   i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_154004771_   9276 TTCCCATTTACTAAATGGTGTTGGAAAAACTGCCTAGCCATATGCAGAAA 9325
                         vvi iv  i vi        i   i v     vv  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_154004771_   9326 ATTGAAACTGGACCCCTTCCTTACACCTTATACAATAATTAACTCAAGAT 9375
                          v    ii         v   i     v       v           i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_154004771_   9376 GGATTGAAGACTTAAATGTAAAACCTAAG-CCATAAAAACCCTAGAAGAA 9424
                             ii?    i         i v    i- i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_154004771_   9425 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 9473
                            v    ?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_154004771_   9474 CTAAAACACCAAAAGCAATGACAACAAAAGCCAAAACTGACAAATGGGAT 9523
                         v  vi            vvii         vv    iv  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_154004771_   9524 CTAATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAATTATCATCAGAGT 9573
                         i v  i   v v  i i   i  ii vv    i  v i     vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_154004771_   9574 GAACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTATTCATCTG 9623
                            v  i     i                vv       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_154004771_   9624 ACAAAGGGCTAATATTTGGAATCTACTAAGAACTTAAACAAATTTACAAG 9673
                          i  i  i  vi   iii    v  iv       ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_154004771_   9674 AAAAAAA-----AACCCTATCAAAAAGTGGGTGAAGGATATGAATGGACA 9718
                              i -----     v  i?    i    ii      v     i    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_154004771_   9719 CTTC--AAAAGGAGACATTTATGAGGCCAAAAA--ACATGAAAAAAAGCT 9764
                         i   --v    i   i  vi viv      v  --         i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_154004771_   9765 CATCATCACTGGTCAT 9780
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


3234 26.02 1.43 1.32  chr2_154033730_154036694.rev     1567  2473 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154033730_   1567 TGGAGAGATATTCCATTTATGGATCATGTATAGAAAGACTCAATAATGTC 1616
                             i      i    v -----     v  v i      i    v   i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGT-----TCATGGATTGGAAGACTTAATATTGTT 45

  chr2_154033730_   1617 AAGATGTCAGTTCTTCCTAAGTTGATCTATAGAATCAATACA-TCCCAAT 1665
                               v  i v  i  i  i        i   v    ii  -    v  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_154033730_   1666 CAAAATCCCAGCAAGTTATTTTGTGGATATCAACAAACTGATTCTATAGT 1715
                                     vivi v     ii  v  ii    i     i   v i 
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_154033730_   1716 TTATAGACAGAGGCAAAAGATTCAGGATAGCCAACACAATATTGAAAGAG 1765
                          i   viv i v    ii  ii   i        v     v      i  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_154033730_   1766 AAGAACAAAGTTGGCAGATTGACATTCTCCAACTTCAAGACGTACTACAA 1815
                                       vi  i v   i ii    i     i  v        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_154033730_   1816 AGCTATAGCCATTAAAACAGTGTAGTACTGATGAAAGAGCCGACAAAAAG 1865
                              i  iv  i  i       i      iiiv   iiiv    v v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_154033730_   1866 ATCAATGGAACAGAATAAAGAGCTCAGAAATAGACTGTTGTAAATATAGT 1915
                                   i     vi    ii        i  ivv ii vv   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_154033730_   1916 CAACAGGTCTTTGACA-GAGTA--AAGGCAATACAATGAAGAGAATATAG 1962
                            iv i i  i    - i  i--   i v  v     ii  i iv    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_154033730_   1963 CATTTTCAACAAATGGTGCTGGAACAACGGAACATTTACATGCAAATATA 2012
                         iv                    i     v i i ?ii         viv 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_154033730_   2013 TGATTCTAGATGCAGACCTTATAACCTTTACAAAAATTAACTCAAAA-GG 2061
                            vvi i  iv vv    i i v v v                   -  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_154033730_   2062 ATCACAGAACTAAATGTAAAATGAAAAACTATCAAACTCCTAGAAGATAA 2111
                             ?   v          i vvv        v      i       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_154033730_   2112 CACACAAGAAAACCTAAACGACTTTGGGATTGGTGATGACAATTATTCTT 2161
                           i vi? v   i  vvii   i     v v  ii   ii-----     
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-----TTCTT 590

  chr2_154033730_   2162 AGA-ATAACACTGAAGACATAATCCATGAGAGAAAGGATTAAGAGACTGA 2210
                            -  i    ii  ii  i  v v ii i     ii  vi v i i  i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_154033730_   2211 GCTTTATTAAATTTAAGA--TTTTCTGCTGTGTAAAAGACATGGTCAAAA 2258
                         i   i  i   v    i --    v    - -i   i    ivi    i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCT-T-CAAAGGACACTATCAAGA 688

  chr2_154033730_   2259 GAATAAAAAGAGG-----CAAACTGGAAGAAAATATTTGGAAAAGACATA 2303
                         i i i      vi-----  i v   i            v   vv i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_154033730_   2304 ACTGATAAAGAAGTGTTATCCAAAATATACAAAGAACTTTTAAAACTCAA 2353
                         v       i i v vv      i      i        i   v       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_154033730_   2354 CAATAAGAAAACAAACAACTCAATTTAAAAATAAGCTAAAGACCTTAACA 2403
                         i     i  i     i   i     ?      ii  v  i  ii v  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_154033730_   2404 GGCACCTCACTTAAGAAGATATACAGATGGCAAATAAGCATATCAAGAGA 2453
                          i  ii  v iv             i     v        i  v  i   
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_154033730_   2454 TGCCTTACATTATATGTCAC 2473
                            iiv    i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (149 / 83)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.27 (25 / 11)  


2937 26.56 0.98 1.75  chr2_154042604_154048177     4168  5082 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154042604_   4168 TGGAAAAACATTCCATGCTCACAGATAGGAAGAATCAATATCCTGAAAAT 4217
                               i i  i     i   ii   v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154042604_   4218 GGCCATACTGCCCAAAGTAATTTATGGATTCAATGCTAATCCC-ATCAAA 4266
                            v     v      v i  i  ii       i  -      -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAAA 99

  chr2_154042604_   4267 CTACCA-TTGACATTCTTGAAATGTCACATAATTAGAAAAAACT-ACTTT 4314
                         v v   -i  v v  i   ------  v -    i-- v  i  - iii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTG------CAGA-AATTG--ACAAGCTGATCCT 140

  chr2_154042604_   4315 AAATTTCCTATGGAACCAAAAAGAGCCCATGG-AGCCAAGACAAGCCTAA 4363
                            v   v       viiv  i ii    vii-      i    v i i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_154042604_   4364 GGAAAAAGAACAAAACTGGAGGCATCATGCTATCTGACTTCAAACTACAC 4413
                         ii  i         ii      vv   ii  vi ii i      vivi  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_154042604_   4414 TGGAAGCCTACAGTAACCAAAACAGCATGGTACTGGTCCCAAAACAGACA 4463
                          iv  iv         i   i    ii         iviv ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_154042604_   4464 TATAGATCAATGGAACAGAACAGAAACCTCAGAAATAACACCACACATCT 4513
                                        i    iv  i vii         vv   i    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_154042604_   4514 ACAACCATCTGATCTTTGACAAACCTGACGAAAACAAGCAATAGGTAAAG 4563
                          iiii  vi    i  i     ivv  v i i v  vv    i  v    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_154042604_   4564 GAT-TTCTTATTTAATGAATGGTGCTGGGAAAACTGGCTAGCCGTATGCA 4612
                         i  -v    -  i  ii             v      v  ?  ii     
  L1M4_orf2#LINE/    391 AATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_154042604_   4613 GAAAACTGAAACTGGACCCCTTCCTCACACCTTGTACAAAAATTAACTTA 4662
                         i  i v    ii         v         v i              i 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_154042604_   4663 AGGTATATTAAAGACTTAAATGTAAAACCCAAAACCATAAATCCCT-AGA 4711
                          ii iv  i ?    i         i v i     i     v i  -   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_154042604_   4712 AGAAAACTTAGGCA-ATATCACTCGGGACATAGGCATGGGCAAAGACTTC 4760
                                v    ?i- v   -i   v   v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_154042604_   4761 ATGAGTAAAACACCAAAA--ACAATTGCAACAAAAGCCAAAATTGACAAA 4808
                         v iii  vi         --    --          vv     v  i   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAA 636

  chr2_154042604_   4809 TGGGATCTAATCAAACTAAAGCACTTCTGCACAGCAATAGAAACTATCAT 4858
                          v   ii v      v v  iv    i  ii vv   vi  v       v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_154042604_   4859 CAGAGTGAACAGGCAACCTACAGAGTCGGAGAAAATTTTTTTGCAATCTA 4908
                         v i      v  i     i     i v         v   --    vii 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT--GCAAATCA 734

  chr2_154042604_   4909 CCCATCTGACAAAGGTCTAACATCCAGAGTCTACAAGGGACTTAAGCAAA 4958
                         ivi      i  i  v  vii       i v  i  i i   ivvi   v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_154042604_   4959 TTTACAAGAAAAAAACAAATGGCCCCATCAAAAAGTGGGCAAAGGATATG 5008
                          iv i  v     i      ii   v  i?    i            v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_154042604_   5009 AACAGACCCTTCTCAAAAGAAGACATTCATGTGGCCAAAACACATATGAA 5058
                           i    vi     v        i  v  vi       v vi  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_154042604_   5059 AAACAGCTCAACATCACTAGTCAT 5082
                           ivv           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.56 (25 / 16)  


3344 25.99 0.55 0.55  chr2_154080196_154086474.rev     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154080196_   4880 TGGAAGAACATCCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4929
                              ii i        i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154080196_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154080196_   4980 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5026
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_154080196_   5027 ATATGGAACTAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCGAAAA 5076
                                 v iv  ii  v  viv  vi    iv     i i ivi i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_154080196_   5077 GAACAAAGCTGGAGGTATCACACTACCTGACTTCAAACTATACTACAAGG 5126
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_154080196_   5127 CTACAGTAACCAAAACAGCGTGGTACTGCCACCAAAACAGAGATATAGAT 5176
                                  i   i    i         v  iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_154080196_   5177 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5224
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_154080196_   5225 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5274
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_154080196_   5275 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5324
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_154080196_   5325 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5374
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_154080196_   5375 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5424
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_154080196_   5425 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5474
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_154080196_   5475 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5524
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_154080196_   5525 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5574
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_154080196_   5575 CAGGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5624
                         v  i     i   iv            v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_154080196_   5625 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5674
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_154080196_   5675 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5724
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_154080196_   5725 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5774
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_154080196_   5775 CATCACTGGCCTT 5787
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3086 26.27 1.43 1.21  chr2_154116103_154122480.rev     4981  5886 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154116103_   4981 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5030
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154116103_   5031 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5080
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154116103_   5081 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5128
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_154116103_   5129 ATATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAA 5178
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_154116103_   5179 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATATTACAAGG 5228
                                 i      vv    i  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_154116103_   5229 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAGCAGA--TACAGAC 5276
                                  i   i    ii         i iv iiii   --  i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_154116103_   5277 CAATGTAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTA---- 5320
                              v  i    i--    i  --        vv  ii i  i  ----
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_154116103_   5321 CAACTATAAGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGG 5370
                            i ----   i  i     ivv  v   i v  vvv           i
  L1M4_orf2#LINE/    346 CAATT----GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_154116103_   5371 ATCCCCTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGTAGA 5420
                           vvi  v  i  i           i  v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_154116103_   5421 AAGCTGAAACTGGATCCCTTCCTTACACAGTATACAAAAATTAATTCAAG 5470
                          iiv    ii    i    v   i    vi              i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_154116103_   5471 ATGGATTAAAGACTTACAGGTTAGACCTAAAACCATAAAAACCCTAGAAG 5520
                               i ?    i  v v  v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_154116103_   5521 AAAATCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 5569
                             iv    ?i- v i -   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_154116103_   5570 GTCTAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGG 5619
                         ivv  vi            vvi           v     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_154116103_   5620 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 5669
                          ii v  i   v v  i i   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_154116103_   5670 GTGAACAGGCAACCTACAAAATGGGAGACAATTTTTGCAACCTACTTATC 5719
                              v  i     i   i         v   v       vii iv    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_154116103_   5720 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACA 5769
                            i  i  i  vi          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_154116103_   5770 AGAAAAAAACCAAACAACCCCATCAAAAAGTGGGCAAAGTATACGAACAG 5819
                          v     i  -   i     v  i?    i         v  vi   i  
  L1M4_orf2#LINE/    791 ATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_154116103_   5820 ACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAA- 5868
                            i     v        i  vi viii     v  i          i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_154116103_   5869 -CTCATCATCACTGGCCAT 5886
                         -    v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.00 (24 / 12)  


1769 26.48 10.69 2.85  chr2_154175558_154177504      615  1456 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154175558_    615 TAAAAAGATGTACCATGTTTACACATTTCCTTTCTTAGTATTGTTAAAAT 664
                          ii      i v       i iiv   vvvvvv    i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154175558_    665 TATAATTTTTCCCAA-TTGTGTGTATGTATTTTTCCCAACACAATTCCAA 713
                         vii   vi i     -   -i v  iiv   -----    i    i  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG-ATCTACAGATT-----CAACGCAATCCCTA 94

  chr2_154175558_    714 TCCAAATTTTCCA-CAGACTTTAAAAAAGTATAAATTTATCAGATGACTC 762
                           v    i--   - v v    vvviv  ---     v iv  v   ii 
  L1M4_orf2#LINE/     95 TCAAAATC--CCAGCTGCCTTTTTTGCAG---AAATTGACAAGCTGATCC 139

  chr2_154175558_    763 AAAAATGTATGTAGAAATCAAAATGACCTAGAATACTGC--GGGCAATTT 810
                         v     vi  i i     vv  iv    i      --  --iii    i 
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATA--GCCAAAACAATCT 187

  chr2_154175558_    811 --AGAGAGAA-AATTAATTTGGTGGACATGCACT-----ATTTTAAA--- 849
                         -- i i    -  iv  v    v    vii    -----    i   ---
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_154175558_    850 ----------------------------TGTGGT-TTGGCAACAAAAGGA 870
                         ----------------------------      -i     v---     
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT---AAGGA 284

  chr2_154175558_    871 TAGATATAAAGGTCAATATAATAGAATAGAGGGTCTAGAAATAAACTTAT 920
                             i   v  i     iv        v   i   i          ii  
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_154175558_    921 ACATATATGACCAATTGATTTTCAGCAAGTACCCCAAAACAATCCAATGG 970
                             v    ii            ii    viiv    i  v  i      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_154175558_    971 GGAAGGGAACATTTCTTTTAG---ATGTTGCTAGGATAACTAGATAAATA 1017
                             i -  i v ii   i i---   v    i   i    i    ?vi 
  L1M4_orf2#LINE/    385 GGAAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_154175558_   1018 CATGAGGAAAAGTGAACATTTACCCTTACCTCATACTGTGCTA-AAAAAC 1066
                             vii  i i    vv vv    i       i  ii i-  -     i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA-TACAAAAAT 482

  chr2_154175558_   1067 TAACAAGAAATGGATTATTAATATAAATGTAAAAAAGTAAAATTATAATA 1116
                             vvi        i ?vi iv         i iv-     i     v 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAA 531

  chr2_154175558_   1117 TTTCAACAAAGAAATAGAAGAG-AAACCTTTGTGACCTTAATGTAGGCAA 1165
                         i iiv v  ii   i v i ? -   i   i        iivv       
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_154175558_   1166 AGGTTTCT-----ATGAAAG-GAAAGTATAAGTAATCCAAGAAAAAAATG 1209
                         v       -----    v v-i    i i   i  ivv         vv 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_154175558_   1210 GTAACTTAGATTTCATCAGAATTTAACAACTTT-GCACTTTGAAAGAAAA 1258
                         i   v  i  i       i    -  v      - ii   i-    i v 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATT-AAAAACTTTTGTGCTTC-AAAGGACA 679

  chr2_154175558_   1259 CT-TTAGCAAAACAAAAGAAGTAAGCCACATAGTAGGAGAAAA------- 1300
                           - i iv   iii   ii -i  v     v i i        -------
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGA-CAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_154175558_   1301 ----CATACAT----------------ATCCAGAATATATATAATACTCT 1330
                         ----    i  ----------------              v iv     
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_154175558_   1331 TTTGAGTC--TA-TAAGAAGACCAGAGACCTAAT--AAAAATGAACAAAC 1375
                          vii v  --  -   i     v ivi   i   --       ii    v
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_154175558_   1376 TATTTGAATAGATACTTCTT-AAGAAAGATGTAAAAATGTCCAGTAAATA 1424
                         v           i i    i-  ii     i  v     v   i   ii 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_154175558_   1425 CAATGGAGAAGATTCACAATATCTCAATTGGG 1456
                           -  i -     v v   i   v????????
  L1M4_orf2#LINE/    879 CA-TGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (135 / 85)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 3.26 (114 / 35)  


 882 30.72 0.68 0.00  chr2_154184360_154188897.rev     2845  3137 (1401)    L1M4_orf2#LINE/L1        1   295 (613)  

  chr2_154184360_   2845 TGGAAACACATCCCATGCTTGTGGATGGGTAGAATCAATATTCTGAAAAT 2894
                               v i        i ii     v  v   v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154184360_   2895 GACCATACTGCCAAAAGCAATCTACAAATTCAACTCAATTCCCATCAATA 2944
                          i v     v  v   vii       i       v    i  i     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154184360_   2945 TACCACCATTATTCCTCATGTAACTAGAAAAAAAAATCCTAGAATTCATA 2994
                          v   v vviv  ii iiiiv  v v  v  ivvi      i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_154184360_   2995 TGCAA--CCAAAAAAGCCTGCAGAGCTAAAGCAAGACCAAGCAAAAAGAA 3042
                           v  --v   iii v  v v v   i   i   vviii iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_154184360_   3043 CAAATCTGGAGGCATCACATTACCCAACTTCAAACTATACTATAAGGCCA 3092
                             vi      vv     i v     i      viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_154184360_   3093 TAGTTGCCAAAACAGCATGGTACTTGTATAAAAATAGGCACATAG 3137
                         i   vii   i    ii       v i    ii    i  i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 1.25 (50 / 40)
Gap_init rate = 0.00 (1 / 295), avg. gap size = 2.00 (2 / 1)  

1882 25.41 4.79 0.99  chr2_154184360_154188897.rev     3441  4046 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_154184360_   3441 AAAAATAGGCACATAGACCAAATGGAACAGAATAGAGAACCCAGAAATGA 3490
                           ii    i  i     i   -     i     v    ii        i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAA-TGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_154184360_   3491 A--------------GCCAACTGATCTTTGACAAAGCAAACAAAAACATT 3526
                          -------------- i   i    i  i     i vviv   i v    
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_154184360_   3527 AAGTGGGGAAAGGGCACCCTATTCAACAAATGGTGCTAGGATAATTGGCA 3576
                         v i         iii vi  v                i   i  i   vv
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_154184360_   3577 ATCCAC-TGCAGGAGAATGAAACTGGATCCTCATCGTCTTACATTATACA 3625
                          ?    -    ii        ii    i  ii i -  vi  vv      
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACC-TCACACCATATACA 477

  chr2_154184360_   3626 AAAATCAACTCAAGATGGGTCAAATACTTCAATATAAGAACTGAAACCAT 3675
                              i       i    i   ? v  i v   i     i  i    i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_154184360_   3676 AAGGATTCTAGAAGATGACATTGAAA-AGATCATTTTAGACATTGGGTTA 3724
                           iiv ii       vi    v i?i- i   v iv -   v        
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACCTTGGGTTA 576

  chr2_154184360_   3725 GGCAAAGACTTCATGACCAAGAACCCCAAAGCAAATGCAACGAAAACAAA 3774
                              v ii   v iivi v  vv  v      v v     i   iv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_154184360_   3775 GATAAATAGATGAGAGTTAATTAAACTAAAAAGCTTC---ACAGCAAAAG 3821
                         i   i   i  vi  v  v  i   v v    i   i---i vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_154184360_   3822 AAATAATCAGCAGAGTTAACAGACAACCCACAGAGTGGAGGAAAATCTTC 3871
                          v iv    iv i   v  v              i   ii      v  i
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_154184360_   3872 ACAATCTACACATCTGACAAAGGATTAATATTCAGGATCTACAAAGAATT 3921
                         i   vii i i      i  i   i vi   i   i  v  i      i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_154184360_   3922 CAAACAAATCAGCAAGAAATTTAAAA-AAATCAC---ATC----AGTGGG 3963
                          vv    v   ii  v   ---  i -    v  ---  i---- i    
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAA---AAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_154184360_   3964 CTAAGGACATGAATAGACAATTCTCAAAAGAAGACATACAAATGGCCAAA 4013
                          v     iv          v     v        i              v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_154184360_   4014 AA--ACATGAAAAAATGCTCAACATCACTAATTAT 4046
                           --         i             ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (94 / 57)
Gap_init rate = 0.02 (12 / 629), avg. gap size = 2.92 (35 / 12)  


3089 22.61 6.99 1.75  chr2_154204136_154206856.rev     1373  2230 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_154204136_   1373 AGATGTTTTGTTTTTATGAAC-AAAAGACTCAATATTGTTAAGATGTCAG 1421
                             i iiii v  i   i i-ii      i               v  i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_154204136_   1422 TTCTTTCAAACTTGGTCCATAGATTCAATGCAATTCCAGTCAAAATTCCA 1471
                          v  ii v  v   i  i i        i     i  vi       i   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_154204136_   1472 GCAAGTTATTTTTGTAGATATCACCAGACTGATTCTAAAGTTCATATGGA 1521
                           vivi -      i   v  iiv  ii     i     i          
  L1M4_orf2#LINE/    106 GCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_154204136_   1522 GAAGTAAATGACTCAGA-TAGCCAATACAATAT---GTAAGAAGAACAAA 1567
                         i v i  iv   i    -       v     v ---iv            
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_154204136_   1568 GTTGGAGTATTGATATTGCCTGACTTTAAGATGTACTATAAAGCTACAGT 1617
                                v i v i i v  ii i  i  i iv     i           
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_154204136_   1618 AATCAGAAAAATTTGG-AT---CATCAAAAGAGA-ACATAGATC------ 1656
                              ii v i v   - i---   v ii v   - i       ------
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_154204136_   1657 --------------CCAGAAATAGACC------TGTATAGTCAATTGATC 1686
                         --------------         i   ------ v   i          i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_154204136_   1687 TTTGACAAAGGAGCAAAGCCAACGCAATTG--AAAGGAGAATCTTTTCAA 1734
                           i     i  v  v   v v iv    v --    i v i         
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_154204136_   1735 CAAATGGTGTTTGGAACAACTGGACACCCACATGCAAAAAAAAAAAAAAA 1784
                                  i -  i         i ?            i  vi  i---
  L1M4_orf2#LINE/    405 CAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGAATGAAG--- 450

  chr2_154204136_   1785 AAAAAAAATAGTAAACACAGACCTTGCATCCTTCACAAAAAATAACTCAA 1834
                         -------- -- ii  v vv    ii  i v vi       v        
  L1M4_orf2#LINE/    451 --------T--TGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_154204136_   1835 AATGGATCATAGACCTAAATGTAAAACACAAAACTGTCAACCTTTGAAGA 1884
                                  ?              i vvi      i v  v  i v ii 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_154204136_   1885 GATAACATA------------CATGTCCTTGGGTTTATCAATGACTTTTT 1922
                           v      ------------ i  v         viv     ii  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_154204136_   1923 AGATACAACACCAAAAGCACAATCCATGAAAGAAGGAATTGATAAATTGG 1972
                              ii               v v ii      ii   v          
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_154204136_   1973 ACTTCATTAAAACTACAAACTTTTGTTCTGCAAAAGACACTATGAAGAGA 2022
                                i    i  v          v  v    i        v    i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_154204136_   2023 ATCAAAA----AGCCACAGATTGGGAGAAAATATTTGGAAAAGACATATC 2068
                         i v    ---- v       v                v   vv i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_154204136_   2069 TATTAAAGCACCGTTATCCAAAATACACAAAGAACTCTTAAAATTCAAAA 2118
                          iv   i v  ivv      i    i i            v  i    v 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_154204136_   2119 ATAAGAAAACA-----TCCAATTAAAAAGGGGGCCAAATATCTCAATAGG 2163
                             i  i   -----i      ?    iv    v  iv  i v     i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_154204136_   2164 CACCACACGAAAGAAGATGTACACATGGAAAATAAGTACCTGAAAAGATG 2213
                           iiv v v         i    v    vv      i  v          
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_154204136_   2214 CTCCACAT-ATGTCTTCA 2230
                            v    - ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (113 / 78)
Gap_init rate = 0.02 (17 / 903), avg. gap size = 4.41 (75 / 17)  


3099 26.14 0.76 1.85  chr2_154251718_154253944.rev      818  1735 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154251718_    818 TGGAATAATATTCTACGTTCATGAACTGGAAGAATCAATATTGTTAAAAT 867
                              vi    i i i       i i       v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154251718_    868 GTCTATACTACCCAAGGCAATCTACAAATTCAATGCAATTCCTATCAAGA 917
                          v v     v     ivii       i      i     i        i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154251718_    918 TACCAATGACATTCTTCACAGAAATAGAAAAAAAAAAATACTAAAATGTA 967
                          v   iivi v  i  ii       v  v  ivvi -- v       vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chr2_154251718_    968 TATGGAACCACAAAAGTCTCAGAATAGCCAAAACTATCCTAAGCAAAAA- 1016
                                vii   ii v i               v   i i iv  i  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_154251718_   1017 -ACGAAACTGGAGGAATGGCATTACCTGACTTCAAATTATGTGACAGAGT 1065
                         -  i  ii       v vi  i v  ii i      viv iiv   i  i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_154251718_   1066 TATAGTAACTAAAACAACATGATACTGTCATAAAAACAGACACATAGAAC 1115
                           i     ii  i   iii  i     v     ii i     i     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_154251718_   1116 AATGGAACAGAATAGAGAACCCAGAAACAAATCCACATATCTACAATGAA 1165
                                i     v    ii       i   i   i i  i  iii v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_154251718_   1166 CTCATTTTCCACAAAGGTGCCAATAACCTGCACTGAAGAAAAGACAGTCT 1215
                         i v      v    i        v v v v  v  ii    ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_154251718_   1216 CTTTAATAAATGGTGCTGGGGAAACTAGATATCCATATGCAGAAGAATTA 1265
                         i  i  i             iv    i    ?   i     i      v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_154251718_   1266 AACAGGACCCC-ATCTCTCACCAAATTCAAAAATCAAATCAAAATGGATT 1314
                          iiv       - i   v     v  v       i  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_154251718_   1315 GAAGGCTTAAATTTATGACCTCAGCCTATGAAAGAACTACAAGAAAACAC 1364
                         i?  i i     v  v  v  v iv    i   vvvi  v         i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_154251718_   1365 TGGGGGAATATCTCCAGGACATTGGTCTGAGCAAAAATTTCTTGAGCAAT 1414
                         v  ? v  -    i iv   v    vi ii    vii      iiii vv
  L1M4_orf2#LINE/    549 AGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_154251718_   1415 ACTTCACAAGCATAGGCAACCAAAGCACAAATGAACAAATGGGATCACAT 1464
                           vi  v     i i     v    v v    ii i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_154251718_   1465 CACT-TTAAAAAGCTTCTGCACAGCAAAGGAAACAATAAACAAAGTTATT 1513
                           vv-       -   i  ii vv       v  v  v  v     v --
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA-- 694

  chr2_154251718_   1514 ATTTGCTTAAATA-AACCCACAGAATGGGGGAAAATATTCACAAACCATC 1562
                         --------   v -               i         ii    i   v
  L1M4_orf2#LINE/    695 --------AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_154251718_   1563 CATCTGACAAGGGATTGACAGCCAGAATATATAAACAGCTTAAACAACAC 1612
                         i      i      i vii v              v i  ivv     v 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_154251718_   1613 TATAGGGAAAAATTTAATAATCTGAT-AAAAAGTGGGCAAAG-ATTTGCA 1660
                         v   ivi    iviv     i ii  -?    i         -     v 
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_154251718_   1661 TAAACATTTATCAAGAGAAGAAGACATCCAAATGGCAAACAGGCATATAA 1710
                           i      v  v ---       i  v        v  i i   i  i 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCA---AAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_154251718_   1711 AAAGGTGCTCAACATCACTGATCAT 1735
                             i            ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.18 (24 / 11)  


1703 25.38 17.26 2.28  chr2_154266801_154274566     6539  7326 (440)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_154266801_   6539 GAAAAACATCCCAAACTCATGAGTCAGAAGAGTTAATATCATTAAAATGA 6588
                             i i      vii     ii ii     v       ii    i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_154266801_   6589 CCATAACATCCAAAGTAATCTATAGCTTCAATTCAGTCCCTATCAAAATA 6638
                          v   vivi     v i     i  v     iv  i             v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_154266801_   6639 CCA--TAATTTCCCT-CAGAATTAGAAAAATAGAATTGTAACATTTATAT 6685
                            -- ivi  iii -     v v  v  iiv  - iv   v   i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATAT 151

  chr2_154266801_   6686 GGAACCAAAAAGGACTCCAAATAGCCAAAAGAATTCTAAGCAAGAA---- 6731
                             viiv  i    i vi           v   ii i iv     ----
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_154266801_   6732 AAAGTTGGAGGCATTGCATTACCTGACTTCAAG--TTAGATTACAAAGCT 6779
                                    vv ii  i v  ii i     i--   --i         
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGCT 249

  chr2_154266801_   6780 ACAGTAACCAAAACAGCATGGTACTATTATAAA-ATAAACACATATATCA 6828
                                i   i    ii       ivi    i-   i   i   v    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_154266801_   6829 ACAGAACA---------------AAATAAATT------------GTCA-- 6849
                          ii   i ---------------       ii------------    --
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_154266801_   6850 --------------------------------TGGGGGAAGAATA----- 6862
                         --------------------------------     i       -----
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_154266801_   6863 ---AA--------GCT-----------ATATCTATAT------------- 6877
                         ---  --------   -----------   ? i i  -------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_154266801_   6878 -------------CTCTCACCATATACAAAAATCAACACAATATGGATTA 6914
                         -------------   v                i   v   v      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_154266801_   6915 GAGACTTAAATGTAAGACCCCAAACTGTAAAAACACTGGAAGTAAACACA 6964
                         ?    i           v iv     i     vivi i    v     i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_154266801_   6965 GGGAAAACTCTTCTGGAC-----ATTAGGCAAAAAATTTAT-GATGAAGA 7008
                           ?iv  v     vv   -----i        viiv  iv -   - v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGA 598

  chr2_154266801_   7009 TTTCAAAAGCACAGGCAATAAAAATAAAAACAGACAAATGGGACTTAAAT 7058
                         ivi          i    i    iv     i   i    v      v vi
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_154266801_   7059 AAACTAAAAAACTTCTGCAAAGCAAAAGAAATAATCAACAGGGTAAATAG 7108
                            v v        i  iivvv    i  v iv     v ii  i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_154266801_   7109 ATAACCTGCAGAATGAGATAAAATATTTGCAAACTGT---TCCCAAGATG 7155
                          i    ii       i  v              iii ---  i---   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT---GATA 745

  chr2_154266801_   7156 AGGGACGAATATCCAGAATTTACAAGAAACTCAAACAACTCAATAACAAC 7205
                               vvi          v  i  ii     vv            i  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_154266801_   7206 AAAAAATAATAGCC---TTAGAAAGTGGGCAAAGGACATGAACAGAATTT 7252
                           i v -    i  ---  ?i   i           iv    i   vv  
  L1M4_orf2#LINE/    796 AAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_154266801_   7253 TTTCAAAAGCAAACTGACAAATGGTTAACAGATTATATATATATATATAT 7302
                          i  v    v i ivv        ii  ---------  vii i  iv -
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAA---------TAAGCACATGAA- 884

  chr2_154266801_   7303 AAAATGCTCAAGATTACTAATTAC 7326
                           i        v  i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (122 / 74)
Gap_init rate = 0.03 (23 / 906), avg. gap size = 6.70 (154 / 23)  


3230 26.84 0.44 0.55  chr2_154328736_154333273.rev     3138  4046 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154328736_   3138 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 3187
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154328736_   3188 GGCCATAGCTCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3237
                            v   vii     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154328736_   3238 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3285
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_154328736_   3286 TATGGAACCAAAAAAGAGCCCACATTGCCAATTCAATCCTAAGCCAAAAG 3335
                                viiv  ii  v  viv  v     vv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_154328736_   3336 AACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTACACTACAAGGC 3385
                                i     ivv    i  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_154328736_   3386 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3435
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_154328736_   3436 AATGGAACAGAAC--AGAGCCCTCAGAAATAATAACACACATCTACAACT 3483
                                i    i--    i  --        vvv  i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_154328736_   3484 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 3533
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_154328736_   3534 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3583
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_154328736_   3584 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3633
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_154328736_   3634 TTAAAGACTTCAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3683
                          i ?    i v     v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_154328736_   3684 CTAGTCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTTTAA 3733
                         v   v?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_154328736_   3734 TACACCAAAAGCAATGGCAACATAAGCCAAAATTGACAAATGGGATCTAA 3783
                         v            vvi      v   vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_154328736_   3784 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3833
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_154328736_   3834 AGACAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 3883
                                 i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_154328736_   3884 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3933
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_154328736_   3934 AAAACAAATAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACACTT 3983
                          i -          v  i? v  i    ii      v    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_154328736_   3984 CTCAAAAGAAGACATTTATGCAGCCAACAGATACATGAAAAAATGCTCAT 4033
                            v        i  vi viii     i iii         i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_154328736_   4034 CATCACTGGCCAT 4046
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (138 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3014 27.41 1.11 0.33  chr2_154351082_154357478     5005  5905 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154351082_   5005 TGGAAGAACATTCTATGCTCATGGATAGGAAGAGTCATTATTGTGAAAAT 5054
                              ii i  i i   i        v      v i v      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154351082_   5055 GGCCATACTGTGCGAGGTAATTTATAGATTCAATGCTATCCCCAACAAAC 5104
                            v     viv i iv i  i  i        i  v     i v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154351082_   5105 TACCA-CTGACTTTCTTCACAGAATTGGAAAAAAGTAGTTTAAAGTTCAT 5153
                          v   -   v    i  -i     v v  v  ivvv vii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_154351082_   5154 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAGA 5203
                               viiv  ii  v  v v  v     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_154351082_   5204 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATATGACAAGCCT 5253
                               i      vv   ii  v  ii i      viv  iv    iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_154351082_   5254 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5303
                                i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_154351082_   5304 ATGGAACAGAACAGAG-GTCTAAGAAATAATACCATACATCTACAACCGT 5352
                               i    iv   -   i -       vv        i  iiii iv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATGGTCAA 348

  chr2_154351082_   5353 CTGATCTTTGACAAACCTGACAAAAAAAG-CAATGGAGAAAGGATTCCCT 5401
                         i    i  i     ivv  v   i vv v-      i     i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_154351082_   5402 ATCTAATCAATGGTGCTGGGAAAACTGGCTAGCCAAATGTAGAATTCTGA 5451
                         v ii  iv             v      v  ?   v   i i  vvv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_154351082_   5452 AATTGGATGCCTTCCTTACACCTTATA-AAAAATTAACTCATGATGGATT 5500
                          i     iv   v   i     v    -             vi      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_154351082_   5501 AAAGACTTAAATGTAAGACCTCAAACCTTAAAAACCCTAGAAGAAAACCT 5550
                          ?    i           v  v    iv     vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_154351082_   5551 AGGCA-ATACCATTCAGGAGATAGGCATAGGCAAAGACTTCATGACTAAA 5599
                            ?i- v i -   iv  vv v  vv       v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_154351082_   5600 ACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGGATCTAAT 5649
                             v       vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_154351082_   5650 TAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCATGAGAGTGAACG 5699
                         i   v v  i i   i  ii vv    i  v       v  i      vi
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_154351082_   5700 GGCAACCTACAGAATGGGAGAAAAATTTTACAATCTATCCATCTGACAAA 5749
                          i     i                vv   i   vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_154351082_   5750 GGGCTTATATCCATAATCTACAAAAAACTTACACAAATTTACAAGAAAAA 5799
                           i   i      v   v  i   i    ivi    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_154351082_   5800 AACAA----CCCCATGAAAAATTGAGCGAAGGATATGAACAGACACTTCT 5845
                         i    ----   v  v?    v  i  i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_154351082_   5846 C-AAAGAAGACATTTATGCATCCAACAGACATATGAAAAAATGCTCATTA 5894
                          -        i  vi viiiv    i ii  i       i       vi 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_154351082_   5895 TCACTGGTTAT 5905
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.25 (135 / 108)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2671 27.63 2.46 0.89  chr2_154379439_154384262     3439  4332 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154379439_   3439 TGGAAAAACATTCCATCCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 3488
                               i i  i    vi      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154379439_   3489 AACCATACTACCCAAAATAATTTATAGATTCAATGCTATTCTCATCAAAC 3538
                         ii v     v      v i  i  i        i  v  i ii      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154379439_   3539 TGCCATTGACATGCTTAACAGAATTAGAAAAAAAAACTTCTTTACATTTC 3588
                          v   vivi v vi  vi     v v  v  ivvi --  i v v   - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATT-C 147

  chr2_154379439_   3589 ATATGGAACAAATAAAAG-CCCATA-TAGGGAAGACAATCCTAAGCCAAA 3636
                                 - vii  ii -    v -   vv  i      i i ivv i 
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_154379439_   3637 TTAACAAAGCTAAAGGCATCATGCTGTCTCACTTCAACCTATACCTCAAG 3686
                         vv       i ii   vv   ii  vi iv i     vviv   iv   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_154379439_   3687 GCTACAGTAACCAAAACAGCATGATGCTGGTACCCAAACAGACATAAACA 3736
                                   i   i    ii  i i    i ivvii i       v v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_154379439_   3737 CCAATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACC 3786
                         i        i    iv    vii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_154379439_   3787 ATCTGATCTTCAACAAACTTGACAAAAACAAGCAATGGGGAAAGGATTCC 3836
                          vi    i   i    ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_154379439_   3837 CTATTTAATAAATGGTGCTGGAAAAACTGGCTAGCCATAAGCAGAAAACT 3886
                           v  i  i            i v      v  ?   i v   i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_154379439_   3887 GAAACTGGACCACTTCCTTACACTTTATACAAAATTTAATTCAAGATGGA 3936
                            ii      v  v   i    iv         v    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_154379439_   3937 TTAAAGACTTAAATGTAAAGCCCAAAACCATAAAAACCCTAGAAGAAAAC 3986
                          i ?    i         iiv i     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_154379439_   3987 CCAGGC---AATGCCATTCAGCACATAGGCATGGGCAAGGATTTCAT-GA 4032
                         vi   ?---   -- -   ivv  v v  vv i     v i    v -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_154379439_   4033 TGAAAATGCCAAA-GCAGTTGCAACAGAAGCTAAAATTGACAAATGGGAT 4081
                          - vi ii     -   vvv      i   vv     v  i    v   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_154379439_   4082 CTAAATAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGT 4131
                         i v vi   v v  i i   i  ii vv    i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_154379439_   4132 GAACAGGCAACCTACTGAATGAGAGAAAAGTTTTGCAA--------TCTG 4173
                            v  i     i  v     i       vv       --------    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_154379439_   4174 ACAAAGGTCTAATATCCAGAATCTACAAGGAACT--TA-AATTTA-TGAG 4219
                          i  i  v  vi          v  i  i     --  -  i i - i v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_154379439_   4220 AAAAGAACAAACAATCCCATCGAAAAATGGGCAAAGGATATGAACAGACA 4269
                             ii     i  i  v  i?                 v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_154379439_   4270 CTTTTC---AAAAGACACGTATATGGTCAATAGACACATGAAAAAAACCT 4316
                         i  i  --- i    i iii v    i     ii          i vv  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_154379439_   4317 CAACATCACTAATCAT 4332
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (139 / 104)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


2120 23.02 3.61 4.30  chr2_154390218_154391924      495  1215 (492)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr2_154390218_    495 AAAAACAACAAAGCTGGAGGCATCACACAACCTGATTTCAATCTACTGTA 544
                           i  v       i      vv      vv  ii       v--   ---
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACT--- 237

  chr2_154390218_    545 TACTACAAAGCAATAGTAATTAAAACAGCATGGTACTGCTGTTTTATAAA 594
                                    v i      i  i    ii        -- i---    i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG--GC---ATAAG 282

  chr2_154390218_    595 CATAGGCACATTGACCAATGGAATATAATAGAGAACCCAGAAATAAACCT 644
                         v    i  i  v  i          v   v    ii             i
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_154390218_    645 GTATATGTTCTG-TCCATTGATTTT-GACAAAGATGCCAAA--------- 683
                         i  i  -  v  -  v         -     i i      i---------
  L1M4_orf2#LINE/    333 ATACAT-TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_154390218_    684 -GGGGAAAGGACAATCTCTTCAATAATTGGTGTGGGAAAAACTGGATATC 732
                         -        i i i   i     i  v     iv  i v         ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_154390218_    733 CAAATGCAGAAGACTGAAATTGGGCCT-TATCATACACAATATGCAAAAA 781
                           v     i    v    i    i  i-  i vi    v    i      
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_154390218_    782 ATCAACCCAAAACGGATTAAAGACTTAA-CATAAAACTTGAACCTTTAAA 830
                         - i   i     i    i ?    i   -ii   i vi i  v  v    
  L1M4_orf2#LINE/    482 -TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_154390218_    831 GCTACTAGAAGAAATCA--GGGGAAAAATTACATGACATTGGTCTGCGCA 878
                         i  vi         v  --  ? v   vi v i    v    vi iv   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_154390218_    879 ATAATTTTTTAAATTTGACCCTGAAAGCACAGAGAATGAAAGGAAACCTA 928
                           ii   i   i  v    v ii        iiv  ii    i   vv  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_154390218_    929 GGAAAAATGGATTACAT-AAAACTAAAAAGATTTGTATAGCAAAGGAAAC 977
                          iv   v    i v   -    i      vv     iivv       v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_154390218_    978 -AGCAAG---GTCAAGAAACAATTTACAAATTGGGAGAAAATATTTTCTA 1023
                         - v    ---  v  i i    iii   i v               v v 
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_154390218_   1024 ACCACTTACAACTGAATGCAAAATATCTAAGGGACTCAAA--CAGATGAA 1071
                          i  --  i v    ------------         iiv --    --- 
  L1M4_orf2#LINE/    731 ATCA--TATATCTGA------------TAAGGGACTTGTATCCAGA---A 763

  chr2_154390218_   1072 TA-GCAAAAAACAACAACAAC--AAAAACAAAACAAACAAAAAAACCCAA 1118
                           -ii   i   vviv     --  v  i    - i     v  -     
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAA-AGACAAATAA-CCCAA 811

  chr2_154390218_   1119 CTAAAAGAAGGGCAAAAGACATGAATAGACTTTTCTCAAAAGAAAACATA 1168
                         i ?   i v       i  iv         v      v      i i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_154390218_   1169 TAAATGGCTAACAGATATATTAAAAAGTGTTCCACATCACTAATCAT 1215
                         i       i  i iii i  v    ii  i  v      ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (100 / 62)
Gap_init rate = 0.03 (23 / 716), avg. gap size = 2.48 (57 / 23)  


3202 26.98 0.66 0.66  chr2_154400969_154407238     4871  5778 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154400969_   4871 TGCAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4920
                           v  ii i  i   i i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154400969_   4921 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4970
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154400969_   4971 TACCAATGACTTTCTTCACAGAA-TTGAAAAAAACT-ACTTTAAAGTTCA 5018
                          v   iivi i  i  ii     -    v  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_154400969_   5019 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5068
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_154400969_   5069 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5118
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_154400969_   5119 TACTGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGATC 5168
                            v    i   i    ii         i iv ii i             
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_154400969_   5169 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATACCTACAACT 5216
                                i    i--    i  --        vv   i i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_154400969_   5217 ATCTGATCTTTGACAAACCGGAG--AAAAACAAGCAATGGGGAAAGGATT 5264
                          vi    i  i     i--  v --  i v  vv            i  v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAG--GGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_154400969_   5265 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5314
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_154400969_   5315 CTGAAACTGGATCCTTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5364
                         v    ii    i  i v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_154400969_   5365 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5414
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_154400969_   5415 ACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCC 5464
                           v    ?i v viv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_154400969_   5465 AAAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCT 5514
                          vi            vvi     v    vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_154400969_   5515 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5564
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_154400969_   5565 ACAGGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5614
                          v  i     i   iv            v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_154400969_   5615 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5664
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_154400969_   5665 AAAAACAAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGACACT 5714
                            i     i     v  i?    i     i i   iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_154400969_   5715 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5764
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_154400969_   5765 TCATCACTGGCCAT 5778
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


 632 26.05 9.93 4.22  chr2_154409945_154413322     1267  1669 (1709)  C L1M4_orf2#LINE/L1   (41)   867   442  

C chr2_154409945_   1669 AAAGTAAATTTTGACTCGAACCCTTACATCA-------AAATTGACTCCA 1627
                          i i i  v  v   i vv   - i   i  -------     i    v 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACC-TCACACCATATACAAAAATTAACTCAA 490

C chr2_154409945_   1626 GAGGGATTACAGATATAAATACAAAAG-TAACAGTAGAAAGCTTTTATTA 1578
                         i v    i ?   iv     ii  i  -   v v  v   i  i   vv 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

C chr2_154409945_   1577 AAAAACACAGCACAGTAA--CTTTGTGA---TGGAATAGGCAAGTATTTC 1533
                         i      i  v?--    --   i    ---   iv       vvi    
  L1M4_orf2#LINE/    541 GAAAACATAGGN--GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

C chr2_154409945_   1532 TTA-AGATGACACAATAATCA---GTAACCT--TAATTTTTTTAAAAT-G 1490
                            - v       v v  v  --- i   vv--v  -------     - 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAA-------AAAATAG 631

C chr2_154409945_   1489 ATAAATTAAACTATATTAAAATTAAAAGCCTGTGTTTGTTAACGTATAGC 1440
                                ii   vi  i          i i v   viv i  v v i vi
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

C chr2_154409945_   1439 ATTAAGAGACTGAACATTTAATCCACAGAA---GAAAAAATATATTAAAA 1393
                           i    i v    v vvi  i        ---  i       -  iv  
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT-TTGCAA 730

C chr2_154409945_   1392 ATATGTACATCTGAAAAGACATTTTTTCATATCTAAAATATCCAAATAAT 1343
                           -ii  i      v   iv i  ----i    i i     vi   v  i
  L1M4_orf2#LINE/    731 AT-CATATATCTGATAAGGGACTT----GTATCCAGAATATATAAAGAAC 775

C chr2_154409945_   1342 TTT--CAAATCAACAG----AAGTCAGA-AATCCAAT--------GGAAA 1308
                          i --   v    i i----   v  i -  i     --------  iv 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

C chr2_154409945_   1307 AAGGGTTTTAA-AGATACT-CTACATAAGAAGACATCTAAATG 1267
                             i   v  -   i i -  v  -       i  vi     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCA-AAGAAGATATACAAATG 867

Transitions / transversions = 1.29 (58 / 45)
Gap_init rate = 0.05 (22 / 426), avg. gap size = 2.59 (57 / 22)  

2503 25.64 7.38 1.41  chr2_154409945_154413322     2033  2886 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_154409945_   2033 AAAAAAATCCCATGTTCGTGGAATGGGAGAATCAATATTGTTAAAATAAC 2082
                            i v           i    v   i   v i           i  ii 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_154409945_   2083 CACACTGCCCAAAGCAATCTACAGATTCAGTGCAACACCTATCAAATTAC 2132
                         v i   v      vii             ii    iv         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_154409945_   2133 CAA-TGTCATTTTTCCCATGATTAGACAAAACAATTCTAAAATTCATATG 2181
                           i-  i v     v vivi   -     ivii  i              
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCATATG 152

  chr2_154409945_   2182 GAACCAGAAAAAAAAAGTCTGAATCATCAAAACAATCTTAAGCAGAAACA 2231
                            viiv  iii v---i v    vii            i iv ii  v 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_154409945_   2232 GCAAAGTGGGAGGCATCACATTACCTGACTTCAAATTATACTACAAGACT 2281
                         i      v     vv     i v  ii i      viv        ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_154409945_   2282 ATAGTA-CCGAAAGAGCATGGTACTGGTTTAAAAATAGATACATAGATCA 2330
                          i    -i i i v  ii         iv   ii     i i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_154409945_   2331 ATTG--CAGAGTAGGGAAACTAGAAATAAAGCCACACATCTACAACCAAC 2378
                           v --i   i v i  iv i         v   i    i  iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_154409945_   2379 TGATTTTTGACAAAATTGACAAAATAATACAAATATAACTGGAGAAAGGA 2428
                                i     iiv  v   i iv  v   -------   i     i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAA-------TGGGGAAAGAA 392

  chr2_154409945_   2429 CACTCTATTCAATAATTGGTACTAGAAAAATTGGATAGCTATAAGTAGAA 2478
                         i v   v     i  v    i  i i v  i      ? i i v i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_154409945_   2479 GACTGAA------CTGCTTTCTGTCACCATATACAAAAATCAACTCAAA- 2521
                           v    ------ iv  vi  vv                i        -
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_154409945_   2522 TGAATTAACAAGTTAAATATAAGACTTGAAACTTTAAAGGTCCTATAGGA 2571
                           i  i ?vi vi     i     vi i     v    iv  i  v i  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_154409945_   2572 AATCACAGGGATAA---TTTATGAC-------TA--------------AG 2597
                           v  i   ?i   ---  ii    -------  --------------  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_154409945_   2598 ATCT-----CAAAAGCAAATGTAACGAAA-------TAGACAAATGGGAT 2635
                           v -----        v v i   i   -------    i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_154409945_   2636 TT------AATTAAAAAGCTTCTTCACAACAAAAGAAATTATCAACAAA- 2678
                           ------         -   i vii vv    i  v i      v   -
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_154409945_   2679 TAAACATACAATCTACAGAA-GGGATAAAATATTTGTAAACTATGCATTT 2727
                          i  v v    i i      -    v          i   ii  ii  i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_154409945_   2728 GAAAAAGAACTGCTATCCAGAATCTACAGGGAACTCAAACAACTCAAGAA 2777
                           v  i i   vv          v  i ii      vv         v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_154409945_   2778 GAAAAAAA--AATAAGCCCATTAAAAAGTTGGCAAAAAACATAAACACAC 2825
                         v     i --     v  v   ?    i v      ii iv i  i v  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_154409945_   2826 ATTTCTCAAAAGAAGACATACAAGTGACTAACAA----ATAAAAA--TGC 2869
                                v        i      i  i i  i  ----  i    --   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_154409945_   2870 TCACCATCACTAATCAT 2886
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (134 / 81)
Gap_init rate = 0.02 (20 / 905), avg. gap size = 3.75 (75 / 20)  


2820 24.02 1.34 7.73  chr2_154430048_154434372.rev     2866  3835 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154430048_   2866 TGAAAATGTATTCCATGTTCATAGATTGGAAGAATGAATATTGTTAAAAT 2915
                           i   vi   i          i          v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154430048_   2916 GTCCATACTACGCAAAGCAATCAACAAATTCAATACAATCTCTATCAAAA 2965
                          v v     v v    vii   v   i      ii     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154430048_   2966 TATCAAGGACATTCTTCAAAGTAGAAA-----AAGC-AATGCCAAAATTT 3009
                          vi  ivvi v  i  i--- i     -----    -i  v i      i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_154430048_   3010 ATTTGAACCCATGAAAGACTCAGAATAATCTGAGTAAAAGCAATCAATGC 3059
                           v  i vviiii ii   i       ii ------   i     ----i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCC------AAAACAATC----T 187

  chr2_154430048_   3060 TGAGCAAAAAGAACAAAACTGGAGGAATTATATTACCTGAAGTCAGATTA 3109
                            iv  i         ii       v i i i v  ii vv   i viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_154430048_   3110 TGCTACAGAGTTATAGTCATCAACACAGTATGGCACTGTCATGAAAACAG 3159
                          i     i  i  i   v     v     i   i    v   i ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_154430048_   3160 ACACATAGACCAATGGAACATAATAAACAACTCAGAAAAAAATCCATACA 3209
                            i     i        i v   vi v iii      v   i       
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_154430048_   3210 CCCTACAGTCAACTCATTTTTGACCAAGGTGTCAAGAACATAAACTAGGG 3259
                         ii-  ii     i v     i   v i    i     v   vv v i   
  L1M4_orf2#LINE/    338 TT-TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_154430048_   3260 AAAAGTCAGTCTCTTCAATAAATAATGCTATAAAAACTGGATATTCATAT 3309
                            iivi     i     i    ii    ivi v         ?i  i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_154430048_   3310 GTAGAAGAATGAAACTAGAACCCTCCCCCTCACTATATACAAAAATCAAA 3359
                          i i         ii i  v    v  i v   i            i  v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_154430048_   3360 TCAAAATGAATTACAGCCTTAAGTCTAAGACTTCAAATGATGAAACTACT 3409
                                 i  i ?  v i   i v     vi v   iv  i     vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_154430048_   3410 ACAAGAAAACCCTGGGGAGAAAATC--CAGGACATTGGTCTTGGCAAACT 3457
                          v        vi--i  ? v     -- iv   v    vi v     ---
  L1M4_orf2#LINE/    537 AGAAGAAAACAT--AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA--- 581

  chr2_154430048_   3458 TTTCTTTCTTTCTTTCTTTTTTTTTCCAGGTATCATTATAATAAGGGTGG 3507
                         -----------------------------------------------   
  L1M4_orf2#LINE/    582 -----------------------------------------------TGG 584

  chr2_154430048_   3508 AAAAAGTTTCTTGAATAGTGCC-TCATGAGCATAGGCAACCAAAGCATAA 3556
                         ------      ii   -  v -i  vi    i i     v    v v  
  L1M4_orf2#LINE/    585 ------TTTCTTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_154430048_   3557 ATGGACAAATGGGATCATATCAAG-TTAAAAAGCTCTGCACAGCAAAGGA 3605
                           i  i    v   iivi     i-       vi i  ii vv       
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_154430048_   3606 TACACTCAACAAAGTGAAGAGACAACTCACAAAATGGGAGAAAATATTTG 3655
                         i  vv    v        i       i    i                  
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_154430048_   3656 CAAACTAGTCATCTGACAAGGGATTAACAACCAGAATATATAAGGAGCTC 3705
                             ii vvi      i      i vii v             i  i   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_154430048_   3706 AAACAACTCTATAGAAAAAAATCTAATAATCCAAT-ACAAAATTGGCAAA 3754
                         vv       v   iv     iv v     i     -?v     v      
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_154430048_   3755 ACATTTGAATAGACATTTCTCAAAAGAAGACATAAAAATATC--ATACTG 3802
                         iv                   v        i   v    iv --   --i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA--A 875

  chr2_154430048_   3803 GCATATGAAAAGGTACTCATCATTGATTATCAG 3835
                            i        i i    v   ii????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (142 / 87)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 5.50 (88 / 16)  


 295 21.88 0.00 0.00  chr2_154439255_154443778.rev     2808  2871 (1653)    L1M4_orf2#LINE/L1        1    64 (844)  

  chr2_154439255_   2808 TGTAAAGATATTTTATGTTCACAGGTTGGAAGAATTAATATTGTTAAAAT 2857
                           v        iii       ii i        v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154439255_   2858 GTCACTATTAGCCA 2871
                          v  v  i vv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCA 64

Transitions / transversions = 1.33 (8 / 6)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.00 (0 / 0)  

2408 28.59 1.75 2.22  chr2_154439255_154443778.rev     3177  4033 (491)    L1M4_orf2#LINE/L1       56   908 (0)  

  chr2_154439255_   3177 TATTTCTCAAAGTGATCTACATATT-GATGAAAATTCTACCGAAATGTAA 3225
                           i i i    v         v   -i i v  vii   i i    viv 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_154439255_   3226 ATT-CATTTTTCACAGAAATGGAAAAA-TAA--CTAAAATTTATATAAAA 3271
                         ii - v     ii       v  v  i- i --        i    ii  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_154439255_   3272 CCACAAAAAAGTACAAATTTCCAAGACAATCTTGCACCCTGAAACAAACA 3321
                         vii   iii vivvi   vv    i         v v---i i vi    
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA---AAGAAGAACA 202

  chr2_154439255_   3322 AAGCTGGAGGCATTACACTATCTGAATTCAAAATATATTACAAAATGATA 3371
                            i      vv i     vi ii v       iv  i      iiv i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_154439255_   3372 GTAATTAAAACAGCATGGTACTGGCATAAGAATAGACACATCCATCAACC 3421
                              i  i    ii               i       i  vv     --
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA-- 300

  chr2_154439255_   3422 AATGGAACAGAATAGAGAGCCAAAAAAAAAAAAACCCCATTTATTCACTG 3471
                         --     i     v     i v i   v   ----     vi   i iv 
  L1M4_orf2#LINE/    301 --TGGAATAGAATTGAGAGTCCAGAAATAAA----CCCATACATTTATGG 344

  chr2_154439255_   3472 TCAATTGATTTTTGATAAAGGTGTCTAAAACA--CAATATAGAAAAAAGA 3519
                                     i  i  i    i v i v  --    ivi    i  --
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-- 392

  chr2_154439255_   3520 CAGTCTCTTCAATAAAGGATATGGGGAAATTTGGGTATTCACATGCAAAA 3569
                         i     i     i   v i iiv    v vi   i  ?i           
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_154439255_   3570 GAATAAAATTGAACCCTCATCTCATGCCATATACAAAAGC-GACTCAAAC 3618
                             i  i   i    ii i    ii            ii-i       v
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_154439255_   3619 TGGGTTAAAAATT--GATGTAAAAAGTGAAACTGTAAAACTACTAAAAGA 3666
                            i i ? i ii--i      i iv i     i       vi  i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_154439255_   3667 GAAAAAGAACAGGGGAAAA-CTATACAACAATTGTCTGGACAATG---TT 3712
                         i  v ----i   ? v   -  viiii  vv v vi i i     --- i
  L1M4_orf2#LINE/    543 AAACA----TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_154439255_   3713 TTACGTTTGACCATGATAGCTCAGGGAACAAAACCAAAAATAGAGAAATA 3762
                            vi v    vvii v   v  i v       vv         v    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_154439255_   3763 GGATTATATCACACTTAAAA-CTTCTGTAGGGTAAAGAAAAAAATTAACA 3811
                            i vi    v v      -   i   ivvvi    i v vv  i  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_154439255_   3812 GAATGAAGATGCAGCCTATGAATTGAGAGAAAATATTTGCAAGCCATACA 3861
                         i i    i vi  i  i iii v  i                ii    i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_154439255_   3862 TCTAATAAGGAGTTAATATTCAAAATATATATGAAATGCAAACAATTCAA 3911
                            i      iii vi   i  i        vii  iv vv    i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_154439255_   3912 TAGAAAGCAAACAAATAACCTGATTTAAAAAATGGGCAAATGAGCAGAGC 3961
                           iv  iv i          ii   ?     -        v  viv  ii
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAAT 837

  chr2_154439255_   3962 AGATATTTCTTAAAAGAAGACATTCAAATGGCCGACAGATACATTTAAAA 4011
                            i      iv        i  v         i i iii    v-    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAA 886

  chr2_154439255_   4012 AATGTTCGACATCTCTAATCAT 4033
                         i   i  i     v????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (156 / 85)
Gap_init rate = 0.02 (17 / 853), avg. gap size = 2.00 (34 / 17)  


2271 28.40 2.67 1.56  chr2_154501707_154506548     3453  4350 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154501707_   3453 TGGAAAACCACTCCAAGCTCATGAATTGGAAAAATCAGTGTCTTTAAAAT 3502
                               ivi ii   v i     i       i v i i i iv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154501707_   3503 AGCCATATTGCCCAGGACAATATACAGATTCAAAGCTATTCCTATCAAGC 3552
                         i  v   i v    iivii  v           v  v  i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154501707_   3553 TACCAATATCATTTTTCACAGAAATAGA-AAACATATTCAAAAATTCATA 3601
                          v   iivv v     ii       v  -  i vv  i v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_154501707_   3602 TGGAACTCAAAAAGTGCCTGAATAGCCAAAGCAACCCAAAGTGAAAAGAC 3651
                              v vv  ii vv  v           i   i ivi ivi i    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_154501707_   3652 CGAAACCAGAGACAGCAGATTATCAAACTTCAAGCTATGCTACAAGGCTA 3701
                          i  iiii   ivvv  v i vi v  i     iviv i      i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_154501707_   3702 CAGTAACCAAAACAGCATGGTACTGGTACAAA-ACAGACGCATAGACCAG 3750
                               i   i    ii         i i  i- i    ii     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_154501707_   3751 TGGAAAAGGATAGTGAACCCAGATACAAACCCTCACAC----AACCATAT 3796
                              v  i  v v  ii     v i      vi   i----iii  vv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_154501707_   3797 GATCCTTGACAAAGTTGACAAAAGCAAACAATGGGGAAAGGACCCCCTAT 3846
                            ii i     i v  v   i v  vv            i ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_154501707_   3847 TCAATAAATGATGCTGGGATAACTGGCTAGCCATATGCAGAACAATCAAA 3896
                             i     i        i      v  ?   i     i  v   v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_154501707_   3897 TTAGACCCCCAACCTT-CACCATATACATAAATTAACAAAATATGGATTA 3945
                           i      i -   i-           v        vv  v      i 
  L1M4_orf2#LINE/    451 TTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_154501707_   3946 AATACTTAAATGTAAGACATACCACTGTAAAAACATTTTGA-GAATACTT 3994
                         ? v  i           vv  vv   i     - vi  v  -   v  v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr2_154501707_   3995 AGT--TAATATCATTCTGGACATTGGATTTGCCACAAATGTAT--GACTA 4040
                           v--   -   -   vv   v    i  v v  vvii v v --  -  
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TA 595

  chr2_154501707_   4041 AGCCCTCAAAAG---AAATTTTGACAAAAACAAAAATTGACAAGTGGGAT 4087
                         v v vi      ---  ii---i      iv      v  i  i v   i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGC---AACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_154501707_   4088 CTAATTAAACTAAAGAGCTTCTGTACAACCAAATAAATCATCAACAGAGT 4137
                         i v  i   v v  i i   i   i vv v  iv v ii     v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_154501707_   4138 AAATAGATGACCTATACCATTGTAGAAAAC-TTCACAAACTATGCTCCCA 4186
                         i  v   ii   i i vv  v v      i-  ii    ii  iivi ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_154501707_   4187 ACAAG---TTTTAATATCTTGAATCAATAA-GAAC-CTTAAACAATTCAA 4231
                          i   ---i  --i    iv    vv    -    -    --   i    
  L1M4_orf2#LINE/    743 ATAAGGGACTT--GTATCCAGAATATATAAAGAACTCTTA--CAACTCAA 788

  chr2_154501707_   4232 CCAACAAAAAC-CAAATAACCCCATTAAAATGTGGGCAAAGGATATAAAA 4280
                         i-  i     v-          v   ?   vi            v i  v
  L1M4_orf2#LINE/    789 T-AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_154501707_   4281 AGATACTTCTCAAAAGAAGGCATGCAAGTGAACAACAA--ACATGAAAAG 4328
                            i i     v       ii  i   i  iv   i  --          
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_154501707_   4329 AATGCTCCACATCACTAATCAT 4350
                          -     v      ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (143 / 109)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.58 (38 / 24)  


3027 22.74 3.16 5.11  chr2_154519539_154522077.rev     1135  2053 (486)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_154519539_   1135 ATATTC--TGTTAATAGATTAGAATAATTAATATTGTTAAAATGTCCATA 1182
                             i --    v  i    i   v v             i   v v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_154519539_   1183 TTACCTAAAGTTG-TCTAAAGATTCAATTCAATCTCTATCAAAACTTCAA 1231
                         i v  i   -   -    v        iv     i         iii  i
  L1M4_orf2#LINE/     58 CTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_154519539_   1232 AGACATTTTTCACAGACATAGAAAAAA-AATCCTAAAATTTGTGTGGAAG 1280
                         vvi v     ii    v  v  v  iv-i           ii i     i
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_154519539_   1281 CACAAGAGTTCCTGAATAGATCCCTGAGTAGACAAAAGACCAAAAGTAAT 1330
                         ii    i vi  v      --------------------      -i   
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAG--------------------CCAAAA-CAAT 185

  chr2_154519539_   1331 CTTGAACAAGAAGAACAAAACTGGATGCATCACACTACCTGATTTTAAAG 1380
                               v            ii    v vv       v  ii    i   i
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_154519539_   1381 TATTTTATAAAGCTATA----TCAAAACAGCATGGAACTGGCATTAAAAC 1426
                         iv vi  i       i ----    i    ii   v        v ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_154519539_   1427 AGACTTTTGCACCAATAGAGTAGAATTGAGAGCTCAAAATAAAGGAAAAT 1476
                             v v iv i    i  i            ii  i  ---------  
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA---------AT 326

  chr2_154519539_   1477 AAAAACTCATACA---A-ACTCAACTAATCTTCAATGAAGGCATCAAAAA 1522
                            -- i      --- -iv    i i  i   i ii i  iii   i v
  L1M4_orf2#LINE/    327 AAA--CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_154519539_   1523 TACACAATGGGGAAAGGGCCGTCCCTTCAATGAAGGG-GCTGGGAAAACT 1571
                         i iv            iiiv   ii     ii  v  -       v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_154519539_   1572 GGATATACCCAAAAATAAATTGGTTATATCCAATAAAATTGGACCCTTAT 1621
                              ?--   v vii   --i --------   i  i        i  i
  L1M4_orf2#LINE/    425 GGATAK--CCACATGCAAA--AG--------AATGAAGTTGGACCCCTAC 462

  chr2_154519539_   1622 CTTACACCACATACAAAAACTA-CTCAAAGTGAATTAAAGACTTAAATAT 1670
                           i      i         i  -      i  i  i ?    i     i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_154519539_   1671 AGGGTTTGAAACCATAAAAATCCTAGAAGAAA-TATAGGGGGAAAACCAC 1719
                          i ivi i    i      v  i         -i     ? v   v iv 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_154519539_   1720 ATGACATTGGTCTGGACAATGCTTTTTTGGATATCACACCAAAAGCACAA 1769
                         i    v    vi i i     v   i  i     v               
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_154519539_   1770 GCAACAAAAGCAAAAATAAACAAGTGGGACTACATCAAACTAAAAAGTTT 1819
                                   v       i i  i v     v       v v    ii  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_154519539_   1820 CTGCAGAGGAAAGGGAAAAATCAACAAAATGAAAAGGCCACCTATAGAAT 1869
                         i  iivvvv     iv vv     v   i       i v   i i     
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_154519539_   1870 GGGACAAAATATTTGCAAACTTTATATCTGACA-GTGTTTAACATTCGAA 1918
                             v              iiv         i - v vi vii  i ii 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_154519539_   1919 ATATATAAAGAACTCATACAACACAGTAGCAAAA------------TAGT 1956
                                        v      v  i  ii    ------------i i 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_154519539_   1957 T-AAAAATGGACAAAGGACCTGAATAGAGATTTATCCAAAGAAGATATAC 2005
                          -        i       ii        v    v                
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_154519539_   2006 AAATGTCCAACATGTATATGAAAAGGTGCTCAACTAATTATCAAAGAA 2053
                              v    i v i i        i        --  i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAAC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (135 / 71)
Gap_init rate = 0.02 (21 / 901), avg. gap size = 3.62 (76 / 21)  


2626 27.08 3.22 2.44  chr2_154589680_154595079.rev     4008  4908 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154589680_   4008 TAGAAAAACACTCCATGTTCATGGATCTCATGGATAGGAGGAATCAATAT 4057
                          i    i i ii              i---------   i  v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT---------GGAAGACTTAATAT 41

  chr2_154589680_   4058 CATTAAAATGGCCATACTGCCCAAAGCAATTTATAGATTCAATGCTATCC 4107
                         ii    i     v     v      vii  i  i        i  v    
  L1M4_orf2#LINE/     42 TGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chr2_154589680_   4108 CTATCAAACTATAAATAACATTATTGGCAGAACTAGAAAAATATATTTTA 4157
                                 v viv iivi v  v  v      v v  v  iivv  ii  
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr2_154589680_   4158 AAATTCATATGGAACCAAAAAAGAGCCCAAATATCCAAGGCAAGATATCT 4207
                                       viiv  ii  v  vi    v    ii   ----   
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA----TCT 187

  chr2_154589680_   4208 CAGCAAA-AAGAACAAAGTTGGACGCATTATG-TTACCAACTTCAAACTA 4255
                         iiiv   -               v vv i ii-  v    i      viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_154589680_   4256 TACTACAGAGCTACAATAA-AAAAATGGCATGGTACTGGTACAAAGGCAG 4304
                                i       i   -v  i ii ii         i i  i ii  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_154589680_   4305 ACATATAGGCCAATGGAATAGAATAGAGAGCCCAGAATTAAGGCTGCACA 4354
                                 ii              v     i      v   iv iii   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_154589680_   4355 CCTACAACCATCTGGTCTTCCACAAAGTCAACAAAAGAAAGCAATGAGGA 4404
                         ii  iiii  vi  i i   v    i viiv   i vv vv     i   
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_154589680_   4405 ATGGACTCCCTATTCAATGGGAGTGTGCTTGGATAACAGGCTAGCCATAT 4454
                          v i ivvi  v     iiiiv -     v   i   v  v  ?   i  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATG-GTGCTGGGACAACTGGATAKCCACAT 436

  chr2_154589680_   4455 GCAGAAGATTGAAACTGGACTCCTTCTTTATACCACATAGAAAAATCAAC 4504
                            i    v    ii     i   v i i i    i   v      i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_154589680_   4505 TCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACTCT 4554
                             i      i ?    i         i v i            -    
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCT 535

  chr2_154589680_   4555 -GGAAGACAACCTAGAAAATACCATTCTGGATGAAGAACCT---GTTAAA 4600
                         -i     v   v   i?i-  -- v   vvi   ----   ---    ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNG-TA--AATCTTCGTGA----CCTTGGGTTAGG 578

  chr2_154589680_   4601 ----GGTTTCACGACAAAAACACCAAAAGCAATTGCAACAAAAGCAAAAA 4646
                         ----      viiivv vi            vvv          v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_154589680_   4647 TTGACAAATGGGATCTAACTCAACTGAAGAGCTTCTGTGCAGAAAAAGAA 4696
                          v  i    v   ii v iiv  v v  i i   i     vvv   i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_154589680_   4697 ACTATCAACAGAGTAAGCAGACAACCTATAGAATGGGA-AATATATATGC 4745
                                 v i   i iv        i i         -  v    v   
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_154589680_   4746 AAACTATGCATCTGACAAAGCTCTAATATCCAGCATCTATAAGGAACT-- 4793
                            ii  ii      i  i vv  vi       v  v     i     --
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_154589680_   4794 TA-AATT--ACAATGAAAAAGTAAACAACCCCATTAAACAGTGGGCGGAG 4840
                           -  i -- i   i    iii   i     v   ?  v i     ii  
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_154589680_   4841 GACATGAACCAACACTTTTC----------ATAAATGTGGCAAACAATCA 4880
                           iv    ivi   i  i  ----------   v vi    v  i  v  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_154589680_   4881 CATGAAAAA--GCTCACTATCACTGATCAT 4908
                                 i--     vi    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.68 (51 / 19)  


2375 26.14 5.11 2.50  chr2_154611617_154616590.rev     3603  4482 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_154611617_   3603 AAACAGTCTATGCTCATGAGAAGGAAGAATCAATACTGATAAAATGGCTA 3652
                          i i vi i   i     iivv      v i    i  v   i     v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_154611617_   3653 TACTGCCCAAAGCCATTTACAGATTCAATACCATTCCTATCAAACTACCA 3702
                             v      viv  i           ii v  i         v v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_154611617_   3703 AGGACATTCATCACAGAATTAGAAAAAAACT-ATTCTAAAGTTCATATGG 3751
                         ivvi v  iv ii     v v  v  i--  -  i     i         
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATATGG 153

  chr2_154611617_   3752 CACCAAAT--AAGAG-CCCAGA-TAGCCAAAGCAATACTAAGCAAGAAAA 3797
                         ----    --   i -      -        i    vi i iv     i 
  L1M4_orf2#LINE/    154 ----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_154611617_   3798 ACAAAGCCAGAGGAATCACACTACCTGACTTCAAACTATACCACAAGACT 3847
                               iii     v       v  ii i      viv   i    ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_154611617_   3848 ACAGTAACCAACACAGCATGGTACTTACTGGTACAAAAACAGACATA--G 3895
                                i   v    ii       ----  i i  ii i       -- 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACT----GGCATAAGGATAGACATATAG 295

  chr2_154611617_   3896 ACCAGTGGAACAGAAGAAAGAACCCAGGAATAAAGCCATACACTTACAGC 3945
                          i  i     i    vvi   ii    i      v       i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_154611617_   3946 CATCTGATCTTCAACAAAGTAAAAAAAACTAG-CAATGAGGAACGGACTT 3994
                           vi    i   i    i vvivv  i  i v-     i    v i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_154611617_   3995 CCTATTCAATAAATGATGCTGAGATAACTGGCTAGTCATAGGCAGAAAAT 4044
                         i  v     i     i     i  i      v  ?i  i v   i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_154611617_   4045 TGAAATT---------CCTTTCACCATATGTAAAAGTCAACTCAAGATGG 4085
                             i  ---------   iv        ii    i i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_154611617_   4086 ACTATAGACTTAAATGCAAAACCTAAAACCATAAAAACTCT-AGGAGATA 4134
                          ii ?    i      i  i v       i      -    -  i   v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr2_154611617_   4135 ACCTAGG---AAATACCACTCTG-GACATAGGTCCCAGCAAAGATTTCAT 4180
                           v    ---    ----  ii -   v v  viivi    v i    v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_154611617_   4181 -GATGAAGATGCCAAAAGCAATTGCAACAAAAACAAAAATTCCCAAGTGG 4229
                         -   - v  ii         vvv         iv      vvvi  i v 
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_154611617_   4230 GACTTAATTAAA-TTAAAGAGCCTCTG-----CCAAG--CA-------GA 4264
                              v  i   -     i - i i  ----- v   --  -------  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_154611617_   4265 CAACAAACAGACAACCCTCACCTCAGAAAGGAAGAACGTATCTGCAAACT 4314
                         v iii  v         --  ---    v  i    vi   i      ii
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCC--AC---AGAATGGGAGAAAATATTTGCAAATC 733

  chr2_154611617_   4315 ATGCATCCATCAGAGGTCTAATATTCAGAATCTATAAGGAACTT----AA 4360
                           ii   iivi ii  v  vi   i      v     i     i----  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_154611617_   4361 ATAAACAAGCAAAAAACAAA---CCCCATTAAAAAGTGGACAAAAGACAT 4407
                         v v  i  vv    i     ---   v   ?    i   i    i  iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_154611617_   4408 GAACAGACACTTCTCAAAAGAAGGCATGCATGTGACCAACAAACATAAGG 4457
                            i     i     v       ii  i  vi  i    i  i  i v i
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_154611617_   4458 AAAAACGATAAACGTCACTAATAAT 4482
                            i i v v   i   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (145 / 82)
Gap_init rate = 0.03 (26 / 903), avg. gap size = 2.58 (67 / 26)  


2472 26.96 1.84 1.10  chr2_154628971_154630759.rev      498  1313 (476)    L1M4_orf2#LINE/L1       87   908 (0)  

  chr2_154628971_    498 AGTCCC-ATTAAATTGCCATTAACATTCTTCACAGAAATAGAAAAGACT- 545
                          i    -  i   v v   vivi v  i  ii       v  v   -  -
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTG 135

  chr2_154628971_    546 ATTTTAAAACTCATATGAAACCAAAAAAAGCCCAAAA--GTCAAAGCAAT 593
                           ii     i       i  viiv  iiii    i  -- i    i    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_154628971_    594 CCTAAGCAAAAAGAACAAAGCTAGAGGCATCATTCTACTTGACACCAAAC 643
                          i i iv  i          i i    vv   iv  v iii ivi    v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_154628971_    644 TATACTACAGGGCTACAGTAACCAAAACAGCATGGCACTGGTACAAAAAC 693
                         iv       ii          i   i    ii   i     i i  ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_154628971_    694 AGACATATAGACCAATGGAACAGAATACAGAACCCAGAAATAAGTTCACA 743
                                    i        i     vv   ii          iii  i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_154628971_    744 CACCTACAACTATCTGATCTTTGACAAACCTGACCAAAATAAG-CAATGG 792
                           ii  iiiii vi    i  i     ivv  -    i iv v-      
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGG 384

  chr2_154628971_    793 GGAAAGGATTCCCTATTCAATAAATGGTGCTAGGAGAACTGGCTAGGCAT 842
                               i  vvi  v     i          i   v      v  ?v  i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_154628971_    843 ATGCAGAAAATTGAAACTGGACCCCTTCCTTATACTATATG-GAAAATTA 891
                              i  i v    ii         v   i i  i    i-i       
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_154628971_    892 ACTCAAGATGGATTAAAGACTTGAATGTAAAACCCAAAACTATAATAACC 941
                               i      i ?    i i       i v i          -   i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACT 533

  chr2_154628971_    942 CT-GGAAGACAACCTAGGCA-ATACCATCCAGGACATGGGCACAGAAAAA 989
                           -i     v   v    ?i- v i - i iv   v v  vvi  iv  v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chr2_154628971_    990 GATTTCAT-GATGAAGACACCAAAAGCAATTTCAACAAAAGCAAAAATTG 1038
                          i    v -   - v             vvvv         v      v 
  L1M4_orf2#LINE/    583 GGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_154628971_   1039 ACAAATGGGATCTAATTAAACAAAAAAGCTTCTGCACAGCAAAAGAAACT 1088
                          i    v   ii v  i   vvv    i   i  ii vv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_154628971_   1089 AACAACAGAGTAAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAAT 1138
                          v   v i   i  v        i                 v       v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_154628971_   1139 CTATGCATCTGACAAAGGTCTAATATCCTGCATCTATAAGGGACT--TAA 1186
                         ii  ii      i  i  v  vi     v v  v     i i   --  v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_154628971_   1187 AAC-AAAT--TTACAAGAAAAAAAAACCA-CCAAAAAGTGGGCAAAAGAC 1232
                            -v   -- v v    v   v  v   -ii?    i        i  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_154628971_   1233 ATGAACAGACACTCCTCAAAAGAAGGCATATGTGCAGCCAACAATCATAT 1282
                         v    i     i i   v       ii   iiviii     i  v  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_154628971_   1283 GAAAAAAAAAAAACTCAACATCAGTGATCAT 1313
                              i vi----          ????????
  L1M4_orf2#LINE/    882 GAAAAGATG----CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (135 / 81)
Gap_init rate = 0.02 (18 / 822), avg. gap size = 1.33 (24 / 18)  


3276 26.54 0.77 0.77  chr2_154701972_154707741.rev     4371  5278 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154701972_   4371 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACTGTGAAAAT 4420
                              ii i  i     i      i v      v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154701972_   4421 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4470
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154701972_   4471 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTAATT-TAAAGTTCA 4518
                          v   iivi i  i  ii     -   -- v  i  i  i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_154701972_   4519 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4568
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_154701972_   4569 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4618
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_154701972_   4619 TACAGTAACCAAAACAGCATGGTACTGGTACGAAAACAGAGATATAGACC 4668
                                 i   i    ii         i ii ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_154701972_   4669 AATGGAGCAGAACAGAGGCGTCAGAAATAATGCCGCATATCTA----CAA 4714
                               ii    iv   ivvi         vv  ii i  i  ----   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_154701972_   4715 CTGTCGGATCTTTGACAAACCTCACAAAAACAAGCAATGGGGAAAGGATT 4764
                         i  ----  i  i     ivv vv   i v  vv            i  v
  L1M4_orf2#LINE/    349 TTG----ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_154701972_   4765 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 4814
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_154701972_   4815 CTGAAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 4864
                         v    ii    i i  v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_154701972_   4865 GATTAAAGACTTAAATGTTAGACTTAAAACCATAAAAACCCTAGAAGAAA 4914
                            i ?    i       v   vi      i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_154701972_   4915 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 4963
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_154701972_   4964 TAAAACACCAAAAGCAATGGCAATAAAAGCCAAAATTGACAAATGGGATC 5013
                           vi            vvi    i     vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_154701972_   5014 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5063
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_154701972_   5064 AACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGA 5113
                           v  i     i   i             v  ii   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_154701972_   5114 CAAAGGGCTGATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5163
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_154701972_   5164 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAAGATATGAACAGACAC 5213
                             i     i     v  i?    i     i  i   v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_154701972_   5214 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5263
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_154701972_   5264 ATCATCACTGGCCAT 5278
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  


1231 28.02 2.42 1.21  chr2_154780692_154784750.rev     2376  2789 (1270)    L1M4_orf2#LINE/L1        1   419 (489)  

  chr2_154780692_   2376 TGGATAAACATCCCATCCTCAAAGATTTCAAGAATCAATATT---AAAAT 2422
                             v i i       vi   vi    vv    v i      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154780692_   2423 GACCACACTGCCCAAAGAAATCTACAGATTCAATTAAATTCATATCCAAT 2472
                          i v i   v      vvi              ivv   i v    v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154780692_   2473 TACCAA-TGCCATTTTTCACAGAAGTTGGGAAAACAATCCTAAAATTCAT 2521
                          v   i-    -     ii     i   iv  ivii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_154780692_   2522 ATGGAACCAAAAATGTGCCCA-AATGGCCAAAGAAATTTTAAGAAAAAAG 2570
                               viiv  iv -i    -   i      iv   i  i i   i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_154780692_   2571 AAAAAAGCTAGAGG-CATATAATTCCTTGAGTT--AAAATTATATTTCAA 2617
                           v    i i    - vi i v    i-- i  --    i -  i v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCC--AATTTCAAAACT-TACTACAA 245

  chr2_154780692_   2618 GGCTATAGTTACCAAAACTGCATGGTATTGGTACAAAAAGAGACAGA--G 2665
                         i    i   v i   i  v ii     i   i i  ii v     v -- 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_154780692_   2666 ATCAATGAAATGGAATAAAGAACCCAGAAATAAAGCCACATAACTATAGC 2715
                                i   i    vi   ii           v   i i vi   i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_154780692_   2716 TAACTGCTCTTCAACAAAGTCAACAAAAATAAACAATGGGGCAAAAACTC 2765
                         i  i  v i   i    i viiv   i vi vv        v  i  ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_154780692_   2766 CCTTCTCAATTAATGGTGCTGGAA 2789
                         i   i    iv           i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGA 419

Transitions / transversions = 1.70 (73 / 43)
Gap_init rate = 0.02 (10 / 419), avg. gap size = 1.50 (15 / 10)  

1673 25.35 1.83 0.61  chr2_154780692_154784750.rev     3075  3567 (492)    L1M4_orf2#LINE/L1      410   908 (0)  

  chr2_154780692_   3075 GGTGCTGGGAAAATTGGCTAGCCATATGCAGAAGAACAAAAGTTGACCCC 3124
                                   v  i   v  ?   i     i     ii  iv v      
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_154780692_   3125 TGTTACTCACCATACACAAAAATTAAC-CAAGATGGATTAAGGGCTTAAT 3173
                          iiiv v       i            -   i      i ?i i i   v
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_154780692_   3174 GGTAAGACCTGAAACTA-AAAA-TCTTAGAAGAAAGCCTAGGAAAAACTC 3221
                         v      v  i      -    -            i v    ?iv  v  
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_154780692_   3222 TTCTGGGTGTTGGACTAGGTAAATAATTTAC--GATGAAGACCTTGATAG 3269
                            vv iiv    ii    i  - ii   vi--   - v   viii v  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT-ATGACACCAAAAG 607

  chr2_154780692_   3270 CACAAGCAACAAAAGCAGAAATAGACAGATGGGACTTAAGTAAACTAAAA 3319
                                        v i       i i  v      v vi   v v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_154780692_   3320 TGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTAAACTGACAATCTAC 3369
                         vi   i  ii vv    i  v iv    iv i   i  vv     i i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_154780692_   3370 AGAATAGGAGAAAATATTTGCAAATTATGCCTCTGACTAAAGAGTAATAT 3419
                              i                   i  iiv     iv ii  v vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_154780692_   3420 CCAGAATTTCCAAGCAACTAAAATAACTCAACAAGAAAAA-ACAAATAAT 3468
                                v vi  iv    vvv i       i  v     -        i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_154780692_   3469 CCCGTTAACAAGTAGGCAAAGAACATAAACCAACATTTCTC-AAAGTAAG 3517
                           vi  ? v  i i       i iv i  ivi         -    -   
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG-AAG 856

  chr2_154780692_   3518 ACATGCAAGCAGCCAATAA--AAATGAGAAAATGCTCAACATCACTAATT 3565
                          i  i   iii        -- v    i  i             ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_154780692_   3566 GT 3567
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.47 (72 / 49)
Gap_init rate = 0.02 (10 / 499), avg. gap size = 1.20 (12 / 10)  


1868 27.66 10.78 2.04  chr2_154789881_154792703.rev     1497  2331 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154789881_   1497 TGAAAACATATTCCATGTTCATGAATTGGAAGAGTTAATATTATTAAAAT 1546
                           i   v    i           i         v        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154789881_   1547 G-CACATACTACCCAAAGTGATCTAAACACTTAATGCGATCTCTATCAAA 1595
                          -  -     v      v       v v i i  i  i   i        
  L1M4_orf2#LINE/     51 GGCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_154789881_   1596 ATTCTAATATCATATTTCACATAAAT--ACAA-TTAAGCCTAA--TTTAC 1640
                           i i iivv v v   ii  v    --    -i i v     --  i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_154789881_   1641 ATAGGAAACCAATAAAACCCTCAAATAACCAAGGTAATCATGAGTTAAAA 1690
                           i i  vv   -iii    -vi    i    iii    v   ivv i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAA-GGGACCC-AGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_154789881_   1691 AAAGAAAGCTGAAGTTATTGTACTACATAATTACAAACTTCTGTATACCA 1740
                         i  v    i  i  vvv iii   v vi    v    vi -----   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-----TACTA 242

  chr2_154789881_   1741 CAGAGCTATGATAATTAAAACA---------------------------- 1762
                           i     iii    i  i   ----------------------------
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_154789881_   1763 --------------------------CCAGAAATGAACCCACACACGTAT 1786
                         --------------------------        i      i   iv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_154789881_   1787 GATCTATTGCCTTTCAATAAACATGCCAAGAATACTCAATGGAAAGAAAC 1836
                          i  v    vi    i i  ivi        vi i       ii i i v
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_154789881_   1837 T-GTTTCTTCAATAAATAGTGTTGGAAAAGCTGAATATCCACATGCAGAA 1885
                          -  i i     i    i   i   i v i   i   ?         i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_154789881_   1886 AAATGAAATTGGATCCTTACCTAATACTGTATACAAAACTCATACCCTAA 1935
                         i      i     i  i     v i  ii         v --  v ii  
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT--TAACTCAA 490

  chr2_154789881_   1936 AATGGATAGAAGATTTAAACATAAGACCAGAAATTGTTCAACTAAAAGAA 1985
                                vi?   ii    ii     v vi   i i vv    vvv    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_154789881_   1986 GAAAAAAAAATCACGGAATAA--TTACATAAGAAAGAGCTGGCCAATTAT 2033
                              v v -----  ?i   --i v i i vvvv i i i v    vi 
  L1M4_orf2#LINE/    541 GAAAACATA-----GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_154789881_   2034 TTTTCTTGGATTTGACCCCAAAAGCACAGGCAACCAAATAAAAA-TAGAC 2082
                           --   i   v    v           i     v   v     -    i
  L1M4_orf2#LINE/    586 TT--CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_154789881_   2083 AAATAGGATTACATCACATTTAAAAGCTACTGAACAGCATAGAAGACAAT 2132
                             v   i v     v v      i  vi  vi vv  v  i v  v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_154789881_   2133 TAACAGTGTGAAAA------TCACACTGTT------AATTTGTGCAAGGC 2170
                         i  v iv       ------i    vvi v------   v v     iv 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_154789881_   2171 ACACATCTGAGAAGGATTTAATATCTAAAATATGTAAGAAATTGAAAGAA 2220
                          i i      v    ivi vi    i i     i   ii  i vvv v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_154789881_   2221 CTCAACAGCACAAAAACAAA------------AAAATGGGCAAGAAAGTT 2258
                              i ii v   i     ------------           iii v  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_154789881_   2259 GAATTGACATCTC-ACAAAAAAGAAATAAAAATAGCAAACAGAAATATAA 2307
                             v     i  -v    i    v   v    i  v  i iiv i  i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_154789881_   2308 AAA-ATACTCAATATCATTAATCAT 2331
                            -  i     i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (137 / 91)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 5.35 (107 / 20)  


3077 28.08 0.55 0.55  chr2_154830198_154836602.rev     5006  5913 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154830198_   5006 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCATGAAAAT 5055
                              ii i  i     i      i v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154830198_   5056 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5105
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154830198_   5106 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTA--CTTAAAGTTCA 5152
                          v   iivi i  i  ii     -   -- v  i  i-- i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_154830198_   5153 TATGGAAGCAAAAAAGAGCCCGCACCACCAAGTCAATCCTAAGCCAAAAG 5202
                                iiiv  ii  v  v v ivi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_154830198_   5203 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5252
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_154830198_   5253 TACTGTAACGAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGATC 5302
                            v    iv  i    ii         i  v ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_154830198_   5303 AATGGAATAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5350
                                     i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_154830198_   5351 ATCTGATCTTTGATAAACCTGAGAAAAATAAGCAATGGGGAAAGGATTCC 5400
                          vi    i  i  i  ivv  vv  i vi vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_154830198_   5401 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5450
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_154830198_   5451 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATGCAAGATGGA 5500
                            ii    i    v   i     v              iv   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_154830198_   5501 TTAAAGACTTAAACTTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5550
                          i ?    i    iv v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_154830198_   5551 CTAGGCATTACCATTCAGCACATAGGCATGGGCAGGGACTTCATGTCTAA 5600
                         v    ?i v viv   ivv  v v  vv i    iv ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_154830198_   5601 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGTATCTAA 5650
                         i            vvi          vv    iv  i    v v ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_154830198_   5651 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5700
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_154830198_   5701 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5750
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_154830198_   5751 AGGGCTAATATCCACAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5800
                         i  i  vi      v   v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_154830198_   5801 AAACAAAACAACCCCATCAAAAACTGGGCGAAGGACATGAACAGACACTT 5850
                          i     -i     v  i?    v     i     iv    i     i  
  L1M4_orf2#LINE/    797 AGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_154830198_   5851 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAC 5900
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_154830198_   5901 CATCACTGGCTAT 5913
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (150 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


2679 23.01 3.11 9.22  chr2_154854295_154856315      565  1529 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_154854295_    565 GATAGATATTCTATGCTCGTGGATTGGAAGAATTAATATTGTTAAAATAA 614
                           v      i i   i  i            v             i  ii
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_154854295_    615 CAATACTACCCAAAGCAATTTATGGATTCACTGCAATCCCTATCAAAATA 664
                                v      vii  i  ii      vi                 v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_154854295_    665 CCAATGGCATTATTCACAGAAATAGAAAAA--AATCCTAAAATTTATATA 712
                            iiv  v  v  ii       v  v  i--i           i    i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_154854295_    713 GAACTACAGAAGACCCCAAATAGACAAAGCAATCATGAGCAAAAAAGAAC 762
                            v i  iii     vi     v    i     v   i-   i      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAAC 201

  chr2_154854295_    763 ATGAGTAAAGCTATAGGCATCACATTACTTGACTTCAAAAGTTACTGCGA 812
                          ------   i iv   vv     i v iii i       v     i i 
  L1M4_orf2#LINE/    202 A------AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_154854295_    813 AACTGTAGTAACCAAATCAGCATGGTATTGGCATTAAAACAGACATATGG 862
                          i  ii     i   iv   ii     i      v ii i        i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_154854295_    863 ACAAATTGAACAGAATAGAAGACCCAGATATAAATCCACGTATTTACAAC 912
                          iv   v   i     v  iiii     v     i   iii     iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_154854295_    913 CAACTTATTTTCAACAAAGATATTGAGAACATACACTGGGGAATGAACAG 962
                            i v      i    i i iiii   v   v  v       v   i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_154854295_    963 TCTCTTTGATAAATTGTGCTGGGGAAACTGGATAAC----TGTAGAAGAA 1008
                            i  ii i    v        iv         ? ----  i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_154854295_   1009 TGAAACTAGACCCCAATTTCTCACTATACACAAAAAAACAAATCATTTAA 1058
                             ii i      v ii  v   i   i       --------------
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAA-------------- 481

  chr2_154854295_   1059 TTTGATTTTTTAATTAAATTTAATTAATTAAATTTAAATTTTTAAATTAA 1108
                         --------------------------------------------------
  L1M4_orf2#LINE/    482 -------------------------------------------------- 481

  chr2_154854295_   1109 ATTAAATTAAATTAATAGATTGAATTAAAGACTTAAATCTAAGACCTGAA 1158
                         -    v i   ---  i   i----- ?    i     v     v  i  
  L1M4_orf2#LINE/    482 -TTAACTCAAA---ATGGATC-----AWAGACCTAAATGTAAGAGCTAAA 522

  chr2_154854295_   1159 ACAATGGAAGTTGAAAGTCTTA-AAGAAAACATTTGGG-AAATGATCCAG 1206
                           v  i-------   v     -          vv ? -    v- i iv
  L1M4_orf2#LINE/    523 ACTATA-------AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGT 564

  chr2_154854295_   1207 GATATTGTTCTGGAAAGTATTTTCTGTG-TAAGACTTTGGAAGCTCGAGT 1255
                           iv   vvi i iv i iv     vv -  v   viiii    v i  i
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_154854295_   1256 AACCAAAGAAAAA-TAGACAAATGAGAT---AACAAAGCTAAAAAGCTTC 1301
                            v         -    i    vi  i--- v    ii      -   i
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTT 663

  chr2_154854295_   1302 TGCACAGCAAATATAACAATCAACAAATTGAAGGGACAACCCACACAATG 1351
                           ii vv    vivv  v     v   v    ii           v    
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_154854295_   1352 GGAGAAACTGTTAGCAAACAATTCATCTGACAAGGAATTAATAACCAGAA 1401
                                v i  v     iv  vi      i    i i vi  v      
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_154854295_   1402 TATATAAGGAGCTCAAACAACTCAATAACAAAAA-----ATTATCT---- 1442
                                i  i   vv            i     -----  v i i----
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_154854295_   1443 --------GACAAAAGGTCTGAATAGACATTTCTCTAAAGAAGACATACA 1484
                         -------- i    i i i                i        i     
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_154854295_   1485 AAAGGCCCTCAAGTATATGAAAAAATGTTCAACATCACTAATCAT 1529
                           v    vvi   i i       i   i         ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (141 / 78)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 7.00 (119 / 17)  


 256 20.27 4.05 4.05  chr2_154945815_154950419     2841  2914 (1691)    L1M4_orf2#LINE/L1       16    89 (819)  

  chr2_154945815_   2841 TATTAATAG-TTAGTAGACTCAATATGATATTAAGATGACAATTCTCCCT 2889
                          i  v  i -  i v     i     -- i        i    v     -
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATAT--TGTTAAGATGGCAATACTCCC- 62

  chr2_154945815_   2890 CAGATCAAT--ATAGATTCACTGCAAT 2914
                           i  ii  -- i       vi     
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAAT 89

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.05 (4 / 74), avg. gap size = 1.50 (6 / 4)  

1394 25.98 9.77 1.76  chr2_154945815_154950419     3049  3560 (1045)    L1M4_orf2#LINE/L1      118   670 (238)  

  chr2_154945815_   3049 GTAGAAATTGACAAGTTGATTCTA---TCCATATAGATATACAAGGGATG 3095
                          i             i    i   --- i     i  v  i       iv
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_154945815_   3096 TATAATAGCTAAAAATGCA---TTAATAAAGAAAAA---AGTTAGAGAAT 3139
                         i v      i    ---  ---  i v      i  ---    i   i i
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAA---CAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_154945815_   3140 TAACAAAGTAGGATTT-AAAATGTATTATAAAGCTATAATAATCAAGACT 3188
                          v   vvvivvi    -    iv  i  i       i i          v
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_154945815_   3189 GTGTGTTATTAACATAAAGACAGACA--------AA-GGAACAGAACTGA 3229
                              v  i ii     i  i     --------  -    i    i   
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_154945815_   3230 AAATCTGGAAATAAACTTAACACATACGTGGACAACTGATTTCTAACAAA 3279
                         i i  ii         ii -i    vii   v   i      iii    i
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCA-TACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_154945815_   3280 TATGCAAAGGCTGTTTAGTAGAGAAAGAATAGTAGTTTCAA-AAATATTA 3328
                         vi   v   i ii  i i i i           vv      -    iv i
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_154945815_   3329 TTAGAACAACTGAATGTCTATGTGGGGGGGAAAAACAACTCCAATCCATA 3378
                         i i i       i  i? i ii  viiii   vi -- v ivi i  v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGA--AGTTGGACCCCTA 461

  chr2_154945815_   3379 ACTTATACCATG---AAAATATTAATTCAAAATG---------------- 3409
                         v  i i     i---    -     i        ----------------
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAA-ATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_154945815_   3410 --------TAAAAATATAAAATTAT-AAAAGAAAACATAGGAGAAGAACT 3450
                         --------     v       i v - i             ? v i v  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_154945815_   3451 TGTGTAACCATTGATTAGACAAATATTCCTTAGATATGACACCAAAAGTA 3500
                          -i  i   v v i    i   vvi  i                    i 
  L1M4_orf2#LINE/    561 T-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_154945815_   3501 TGAGTCATAAGAGAATGGATTGGTAAATTAGATATCATTAAAATTTAAAA 3550
                         ii  iv i  i    vii  v i      i  iv    i      -    
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT-AAAA 658

  chr2_154945815_   3551 ACTT--GTGCTT 3560
                             --      
  L1M4_orf2#LINE/    659 ACTTTTGTGCTT 670

Transitions / transversions = 2.45 (93 / 38)
Gap_init rate = 0.03 (17 / 553), avg. gap size = 3.47 (59 / 17)  

 808 20.32 3.98 2.79  chr2_154945815_154950419     3867  4117 (488)    L1M4_orf2#LINE/L1      655   908 (0)  

  chr2_154945815_   3867 AAAAACTTGTGCTTTTCAAAGC-CACTATTAAGAGAAAGAGAAGTGAAGG 3915
                                 v  ivi       v-      i    --   v   ---   i
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGA--AAGTGAA---AAGA 699

  chr2_154945815_   3916 CA-CTGACAGAAAAAAAGAAGTTA---GCAAATTATATATCTGATAATGG 3961
                           - iv      viii    iv  ---      i             v  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_154945815_   3962 ATTTGTATCTAGAA-A---AAAAAACTCTCAAAACTCAGTAATAAGAAAA 4007
                          i       i    - ---   i      i v      i      i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_154945815_   4008 CATTCAACTCAAT-AAAAAATGAGCAAAATAACTTGAATAGACACTTCAC 4056
                           vvi   i    -?       i     i-i i           i   v 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAG-GATTTGAATAGACATTTCTC 848

  chr2_154945815_   4057 TAAGAAAGGTCTACAAATGGCAAATAAGCAATTGAGTAAATCCTCAGCAG 4106
                         i  ii   i v          v        vv   iv i  v    i  -
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA- 897

  chr2_154945815_   4107 TTAGTGGGGAA 4117
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.78 (32 / 18)
Gap_init rate = 0.04 (10 / 254), avg. gap size = 1.70 (17 / 10)  


3057 25.65 3.75 0.68  chr2_154966501_154968979.rev     1107  1987 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_154966501_   1107 TAAAAATATATCCCATGGTCA-GG-----------TAATATTGGTAGAAT 1144
                          ii   v          v   -  -----------        v  ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_154966501_   1145 GTTCATATTACCTAAAGTAATCTACAGATTCCATGCAAAACCTATCAAAA 1194
                          viv   i v  i   v i            v i    vv          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_154966501_   1195 TTGCAA-TGTTATTTTCACAGAAATATAAAAAATAATCCTTAAGTTCATA 1243
                          iv  i-  iiv    ii       vv v  iv i     v  i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_154966501_   1244 TGGAAGCAGAAAAGACTCTGAATACCCAAAGAAATTTTGAACAAAAAGAG 1293
                              iiiv  ii   i v     v     iv   i     v  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_154966501_   1294 CAAAGCTTGAGCA-TCACATTTCCTGATTTCAAAATACACTATAAAGCTA 1342
                              i v   v -     i    ii         ivi    i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_154966501_   1343 TTATAAATCAAAAAAGCATGGGACTGGCATAAAAACAAACACATAGACCA 1392
                         ivi   -    i v  ii   v          ii i i   i     i  
  L1M4_orf2#LINE/    251 CAGTAA-TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_154966501_   1393 GTAAAACAGAATCAAAAGCCCAGAAATAAACCTAAGTATTTATA---AAT 1439
                         i ii  i     ii i  i             i vii      i---   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_154966501_   1440 TGATTTTCAACAGAGGTGGCAAGAACACATAATGAGGGAAAGAG-AATGT 1488
                                 i   ii    v     v  ivi    -        i- i v 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCT 398

  chr2_154966501_   1489 CTTTAATATGTGACATTGGGAAAACTTGATATCCACATGCAAAAGAATAA 1538
                         i  i  i vi  iiii     v    v    ?                i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_154966501_   1539 AACTGTAC---TATTTCACACCATATACAAACATCAACTCAAATTGGATA 1585
                          ii  v  ---  ii                v  i        v     -
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT- 497

  chr2_154966501_   1586 AAATATAGACTTAAATATAAGACTTGAAACTGTAAAGTTACTCAAATAAA 1635
                         ---i ?    i     i     vi i     i    ii vi vi  v   
  L1M4_orf2#LINE/    498 ---CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_154966501_   1636 ACATGGGGAAAAAACTCCATGATATTAGTCTGGGCAATGATATCTTGGCT 1685
                             i  ?iv   v  i i   iv  i vi i       i v    i v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_154966501_   1686 AGGACTCCAAAAGTATAGGCAACAAAAGCAAAAAGAGACAAATTAAATTG 1735
                          v   v       i i i          v     v   i     ii i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_154966501_   1736 TGTCAAACTAAAAAGCTCTTGCATAACAAAGGAAAC----AACAGAGTGA 1781
                         ii     v v    i  i   iiivv       v  ----  v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_154966501_   1782 GGAGACAACTCATGGACTGGGAGAAAATATATGCAAACCATATGTCTGAT 1831
                         ii       i  ii  v             v      i     i      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_154966501_   1832 AAAGAGCTAGTATC-AAAA---ACAAGGAATTCAAACAACTTAACAGCAA 1877
                           i ii  v     - i  --- i  i   i  vv      i  i ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_154966501_   1878 AAATATTAATAACCCAATTTCAAAATAGGCAAGTGATCTGAACAGATAAT 1927
                            v iv            ?v     i     iv   i    i   i v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_154966501_   1928 TCTCAAAAAAAGATATG--AATCACTAACA--TCTATGAAAAAATGTGAA 1973
                             v   i       i--   vi i  i --ivi       i   ivv 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_154966501_   1974 ACATCACTAATCAT 1987
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (147 / 75)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.60 (39 / 15)  


2066 21.20 3.44 6.59  chr2_155035671_155037325.rev      466  1163 (492)    L1M4_orf2#LINE/L1      233   908 (0)  

  chr2_155035671_    466 AAACTAAGGTTACAAA-TTATAATTTAAAATCACGA-AGTATGATGTCTG 513
                              v --i      -i  i i ----     v  -   i  i i-   
  L1M4_orf2#LINE/    233 AAACTTA--CTACAAAGCTACAGT----AATCAAGACAGTGTGGTA-CTG 275

  chr2_155035671_    514 GCAGATAAACAGAAACATCGACCGGTGGAATAGAA--GAGAACCTAGAAA 561
                            v vii i   v i  v  i ii          --    ii i     
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_155035671_    562 TAAATCCAAACATTTATGATCAGCTAATTTTCAACAAGGGCACCAAGAGA 611
                             i   v         i   ii i      i       ii      vv
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_155035671_    612 ACACAATGGGGAAAAGGGTGGTCTCTTCGATAAACGGTGCTTGCAGAAGT 661
                          iv           - ii i    i   i i   i      v v v  v 
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_155035671_    662 GAGTTTCCACATTCAAAAAAAAAAAAAGTGAGATTGAACCACCATTTCAC 711
                          ii v?      v     i  -------   ii   i   v i ii    
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAA-------TGAAGTTGGACCCCTACCTCAC 467

  chr2_155035671_    712 ACCATCCAGAAAGAATAACTCAAAATGAACAAAGGACTTAAATGTAAGAT 761
                              vi v   i v            i iv ?i   i           v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_155035671_    762 CTGAAACCATAAAAGTCTTAGAAGGGAACGTAGAGGAAAAACTGACATGG 811
                           i    i      v         ii   i   i? v   v  v- i  i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT-CGTGA 566

  chr2_155035671_    812 CCATGGC-----CAA-GATTTTTTAGATATCACACCAAAAGCTCAGCTAC 855
                           v   v-----   - i   i        v           ------  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC------AC 610

  chr2_155035671_    856 AACAGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGACT 905
                           --    v    i      v i v   vv---------------     
  L1M4_orf2#LINE/    611 AA--GCAACAAAAGAAAAAATAGATAAATT---------------GGACT 643

  chr2_155035671_    906 ACATCAAACTAAAAGGCATCTATCTGTCTGGCAAAGGAAA--A--AACAA 951
                         v       v v   ii v i i -- ii --       v -- --  v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGT--GCTT--CAAAGGACACTATCAAGAA 689

  chr2_155035671_    952 AATTAAAAGGCAACCTGTGGAGTGGGA-AAAATATTTGTAACCCACATAT 1000
                          i v     i     iiii  i     -          i  vi  i    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_155035671_   1001 CTGATAAGGGATTGATATTCAAAATTTA----AAACCCTCACAACTCAAT 1046
                                    i vi   i  i   v  ----i   i  i          
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_155035671_   1047 AGCAGAAAAACAA----CCCAATTAAAAAATGTGCAAAAGACCTGAACAG 1092
                          ii i   i    ----       ?       v     i  ii    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_155035671_   1093 AAATTTCTCCAAAGAAGATATAAAAATG-CCAACAGGTATATGAAAATGT 1141
                          v                    v     -    i i i i       - -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-G- 887

  chr2_155035671_   1142 ATGTTTAATCATCAGGGATATG 1163
                            i i  -     ????????
  L1M4_orf2#LINE/    888 ATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (97 / 47)
Gap_init rate = 0.04 (25 / 676), avg. gap size = 2.80 (70 / 25)  


2116 24.71 8.11 3.04  chr2_155179552_155181447      608  1396 (500)    L1M4_orf2#LINE/L1       32   860 (48)  

  chr2_155179552_    608 GACTCAATATTCTTAAGGTATCAGTTCTCCTCAAGTGGATCTGCAGATTC 657
                             i      v     i iv  i v    i   i v     i       
  L1M4_orf2#LINE/     32 GACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTC 81

  chr2_155179552_    658 AAAGCAATCTCAATTAAAATTCAAACAGACTTTTTTTTTGGTAGAAATTG 707
                           v      i v  i     i v i v v       ---- i        
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT----GCAGAAATTG 127

  chr2_155179552_    708 ACAAGTGGATTCTAAAATTTTTAT--AAAT--------TTTAGAGCATT- 746
                              iv   i        iv   --    --------iii   ii vi-
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_155179552_    747 -------TCTTTAAAAAGAATGATAAAGTTGGAGGATTGACCCTATCTGA 789
                         -------    v        vi i            i v  v  vi ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_155179552_    790 TTTCAAGACTTATTCTAAAATGACAGAAATCATGA--GTATGGT---GTC 834
                               i     i vi   iiv    v     v  --  i    --- v 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_155179552_    835 A--AGGCT-GACAAGTAGATTAATAAAACAGAATAGAGAATCTAGAAATA 881
                          --   v -    vi     i   ii  i     v    i  i       
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_155179552_    882 AATCCATATATATTTGGACAATTGATATTTGAC----GTTTCAAAGGCAG 927
                           i     i  v v   v        v  i   ----  vi   iiv  v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_155179552_    928 TTACTTGGAGAAAGAATATTTTTTTTAACAAATGGTGCAGCAACAATTGT 977
                          i v -  i         v i    i            v vi    i  v
  L1M4_orf2#LINE/    378 TCAAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_155179552_    978 AGCTCTATATGCAAAAAGAGGATAAAAAGCAAGAAAGAATCTTGATTCAC 1027
                          vv? i i        ----------------   v   vi v  ii vi
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAA----------------GAATGAAGTTGGACCCCT 460

  chr2_155179552_   1028 AGCCCACATCATTTACTAAAATTTAATTTAAAA--------AG---TGAA 1066
                          v i    i   v   v      -  i i    --------  --- i  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATT-AACTCAAAATGGATCAWAGACCTAAA 509

  chr2_155179552_   1067 -GT-----CTAAAACT-TAAATTTCT-AGGAATAAGCAAAGGAG-AAAGA 1107
                         -  -----        -    vi   -  i iv  i  v   ? -   vv
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_155179552_   1108 TTTGTGATCT-GGGCTAGGCAA-GATTTCTTAGCTGTGGCACTGAAAGTA 1155
                           i    i  -   i       - i        v i  i   ii    i 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_155179552_   1156 TAATTTACGAAAGAAAAAAT-GATGAATTGTACTTCATCCAAACTAAAAT 1204
                         i  viv  i           -   i     v        v   i     v
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_155179552_   1205 CTTCTGCTCTCAGAAAAACACTATTAAGAGAATCAAGAAACAAGAAACAG 1254
                            i  iv  ivi  ii       i    i i v  i i    vvv    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_155179552_   1255 ATTAGAAGAAAATATTTGCAAATTATAAAAC--AT----GAATTACATCC 1298
                          v i i                 i   v v --  ----  v  ii    
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_155179552_   1299 AGAATA---AAAGAAGATTGTTCCAACTCACAAATATGAAAATAAAAGGG 1345
                               ---      --i v  v       vv    vi  i i   viiv
  L1M4_orf2#LINE/    760 AGAATATATAAAGAA--CTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_155179552_   1346 ATAAT--AAAAATAAGCCAAAAACTTACACATACTTTTAACTAAAGAAGA 1393
                         vi   --      ii  v  ii i  iv i v  v   vv i        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_155179552_   1394 TAT 1396
                            
  L1M4_orf2#LINE/    858 TAT 860

Transitions / transversions = 1.38 (112 / 81)
Gap_init rate = 0.03 (27 / 829), avg. gap size = 3.26 (88 / 27)  


3418 24.42 1.44 0.67  chr2_155203056_155207305.rev     2858  3758 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_155203056_   2858 TGAAAAGATATTCCACGTTCATAGATTGGAAAA-TCAATATTGTTAAAAT 2906
                           i        i   i      i        i - i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_155203056_   2907 GTCCATATTACCCAAAGCAATTTCCAGATTCAATGTAATCCCTGTCAAAA 2956
                          v v   i v      vii  i v         i i       i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_155203056_   2957 TAGCAATGACATTATTCATAGAAATAGAAAAAACAATCCTAAAATTTATA 3006
                          vv  iivi v  v  iii      v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_155203056_   3007 TGAAGCCACAAAAAACTCAGCATAGCCAAAGCTATCCTAAACAAAAA-AA 3055
                           i ivii   iii  i   v         i v   i i  v  i  -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_155203056_   3056 CAAAACTGGAGGAATCACATTATCTCACTTCAAATTATACTCCAGGGCTA 3105
                             ii       v     i vi iv i      viv    v  ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_155203056_   3106 TATTAACTAAAGCAGCATGGTACTGGCATGAAAAGAGACACATAGAACAA 3155
                         i v   ii  ii   ii            i ii v     i     v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_155203056_   3156 TGGAACAGAATAGATAATCAACAAACAAATCCACACACCTACAATGAACT 3205
                              i     v  v i  v v   i   i   i   ii  iii v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_155203056_   3206 CATTTTTGACAAAGGTGCCAAGAACATACACGAGGGAAAAGATAGTCTCT 3255
                         v     i     i          v   v  vvi      ii       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_155203056_   3256 TCAATAAATGTTGCTGAGAAAACTGGATATCCATATGCAAAAGAATAAAA 3305
                             i     v     i  v         ?   i            i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_155203056_   3306 --------CTATCTCTCACTATATACAAAAATCAAATAAAAATAGATAAA 3347
                         --------   i   v   i            i  v v     i   v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_155203056_   3348 AGACTTAAATCTAAGACCTCAAAACTATGAAACTACTAAAAGAAAACATT 3397
                             i     v     v  -        i     vi  i          v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_155203056_   3398 GAGGAAACTCTCTAGGACACTGGTCTGTGCAAAAATTTCTTGAGTCAT-A 3446
                          i? v  v   iiiv   vi   vi iv    vii      -  vi  - 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chr2_155203056_   3447 CATCACAAGCACAGGCATCCAAAGCAAAAATGGACAAATGAAATCACATC 3496
                           i  v       i   v v    v      i  i    vii iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_155203056_   3497 AAG-TTAAAAAAGCTTCTGCACAGCAAAGGAAATAGTCAACAAAGTGAAG 3545
                           i-       --   i  ii vv       v ivi    v        i
  L1M4_orf2#LINE/    649 AAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_155203056_   3546 CAAAAACTCACAAAATGGGAGAAAATATGTGCAAACTACCCATGTGATAA 3595
                         vi v   i    i               v      ii ivi  v      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_155203056_   3596 GG-ATTAATCACCAGAATATATAAGGGGCTCAAACAACTCTGTAGGAAAA 3644
                           - i vi vv             i ii   vv       vi  iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_155203056_   3645 AACGTCTAATAATCTGATTTAAAAGTGGGCTAAAGATTTGAATAGACATT 3694
                          -- v v     i ii   ?    i     v  i                
  L1M4_orf2#LINE/    797 A--GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_155203056_   3695 TCTCAAAAGAAGACATACAAATGGCAAAGAGGCATATGAAAAGATGCTCA 3744
                             v        i           v  v i   i               
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_155203056_   3745 ACATCACTGATCAT 3758
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (133 / 83)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


2784 23.47 1.24 7.55  chr2_155242462_155246792.rev     2873  3839 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_155242462_   2873 GAAAGATATCCTATGCTCATGGATTGGAAGAGTTAATATTTTTTAAATGT 2922
                                    i   i               v        v  v i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_155242462_   2923 TCACACTATCCAGAGCAATCTGCAAACTCAATGCAGTGTCTGTCAGAAGA 2972
                         iv i   vi   i vii    i  i i    i   i vi  i   i  vv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_155242462_   2973 CCAATAACAATCTTAATAAATGTAGAAAAAAACAAACAGA-----AAATT 3017
                            iivi vv i  ------  i     vvi    i v  -----     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTT------TGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_155242462_   3018 CATATAGAAACGCAAAAGACCCAGAATAGCCAAAGCAATCCTGAGAAAAA 3067
                              i    i    ii                 i     i   i   i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_155242462_   3068 TGAACAAAGCTGGAGGTATCACATTTT--AGCTTCAAAATACACTAAAAA 3115
                         v        i      vv     i  i-- ii       ivi    v   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_155242462_   3116 GCTATAGTAACCAGAACAGTATGATACTGTTATAAAAGCAGATATATAGA 3165
                             i     i  ii     i  i     vi    iiii   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_155242462_   3166 CCAAAGGAACAAAATAGAGACTCCAGAACTAAATCCATGTATTTATGGCC 3215
                         i   v    i i   v    v       v    i    ii        i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_155242462_   3216 AATTCATTTTCAACAAAGGTGCAAACAACATACACTGGAAAAATGGCAAT 3265
                             v      i    i     v  v v   v  v   ii   viii i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_155242462_   3266 CTAATCCATACATGATGCTGGGAAACCTGACTATCCATATGCAGAAGAAT 3315
                           vv  v i v   i        v v   iv  ?   i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_155242462_   3316 GAAACTAGGCCCATATTTCTCAAAATATACCAAAAAATCACATCAAAATT 3365
                            ii i i   v  ii  v  vv      --      i vv       v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATAC--AAAAATTAACTCAAAATG 494

  chr2_155242462_   3366 CATTAAAGACTTAAACGTAAGACTTGAAGCTATGAAACTACTAGATAAAA 3415
                         v  i ?    i    i      vi i  i    i     vi    vi   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_155242462_   3416 ACTTTGGAG-AAATGCTTATGGACATGGTTCTGGTCAAAGATTTTTTTTT 3464
                           v v  ? -    vi ii  iv v   v iv  -   v i   i  ---
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG-CAATGGTTTCTT--- 590

  chr2_155242462_   3465 CAG-TAAGAACTTAAAAGCACAGACAACAAAAGTAAATATATACAAATAA 3513
                         -  -  v  vvii         ii         v   v   v i    vi
  L1M4_orf2#LINE/    591 -AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_155242462_   3514 GACTACATCAAGATAAAATGCTTCTGCACAGGAGGGAGGGCGGGAGGGAG 3563
                             v      i  v   vi   i  ii vvv -----------------
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCA----------------- 672

  chr2_155242462_   3564 GGAGGGAGGGAGGCAAGCAGGCAGGCAGGCAGGCAGTCCGGAGTGAGGA- 3612
                         ------ i   vi v v  i v ------------------     ii -
  L1M4_orf2#LINE/    673 ------AAGGACACTATCAAGAA------------------AGTGAAAAG 698

  chr2_155242462_   3613 ACAACCTAGAGCATGTAGAGAATGGGAGAAAATATTTGCAAACTATCCAT 3662
                               i ---  ------                       ii  vi  
  L1M4_orf2#LINE/    699 ACAACCCA---CA------GAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_155242462_   3663 -TGGCAAGGCATTAGTAACCAGAATATACAAGAAACTCAACTCCAAAACA 3711
                         -  ii    v i v   v          i  ii     --i v   vv  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCA 787

  chr2_155242462_   3712 A-AACAAAAAAAACCCAAATAATTTGATTTTAAAATGGGCAAATGATCTG 3760
                          -  i     i ---       iiii   ?v            v   i  
  L1M4_orf2#LINE/    788 ATAATAAAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_155242462_   3761 AATTGACATTTCTCAAAAGAAGACACACAAATGACCAACAAGAACATAAC 3810
                            v          v        i i       i    i   v    i -
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA- 883

  chr2_155242462_   3811 ATTTAACAATGCTCAACATCACTAATCAT 3839
                         ----  vi             ????????
  L1M4_orf2#LINE/    884 ----AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (134 / 89)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 4.72 (85 / 18)  


 700 27.97 7.07 2.25  chr2_155346009_155349922     2249  2559 (1355)    L1M4_orf2#LINE/L1        2   327 (581)  

  chr2_155346009_   2249 GGAAAGGGATATAC----TTTATGGACTGGAAGACTAAATATTGTGAAGA 2294
                               --    v ----  i     i         v        v    
  L1M4_orf2#LINE/      2 GGAAAG--ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_155346009_   2295 AGCCAAATCTCCCAAAATT-ATCAATATATTTGATAGTAGCCCAATATAA 2343
                         v v   vv     v     -   v i v   ii iivv v   v  vv  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_155346009_   2344 ATTACAACAGGTATTTT--CA-----TGGCAA-----TTCTAAAATTCAC 2381
                           iv  i v viv    --  -----  i   ----- i          i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_155346009_   2382 ATGGAAATGCAAAGG-TCAAGGATACCCAAGCCA-TCATGCAGAAGTGCA 2429
                                     i  -i v  i   v    iv  -  v  v i   viv 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_155346009_   2430 ACAAACCTGGAAGTGTTATACCAGCAAGATCCACGACATACTGTAAAGCT 2479
                              vi    i vv i i  ivv v iv i  vi  v    ii      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_155346009_   2480 ATAGTAATTAAGACAATTTGGTTTTGGTACAAGTTTGGGAGGGGCAAAT- 2528
                          i      i      i v    vi   i i   -----  vi i  v  -
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAG-----GATAGACATATA 294

  chr2_155346009_   2529 GACCAACAGAACAAAAC--AGAATCTAGAGACA 2559
                           i   ii   i i  i--   i  i   i i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

Transitions / transversions = 1.18 (47 / 40)
Gap_init rate = 0.03 (11 / 326), avg. gap size = 2.64 (29 / 11)  

1075 25.97 4.70 2.86  chr2_155346009_155349922     2960  3448 (466)    L1M4_orf2#LINE/L1      411   908 (0)  

  chr2_155346009_   2960 GTGCTGAATCAATTGGATATTTATCTGGAAAAAAAAGAATCTTAACTCCT 3009
                               iiv   i      ?ii iv  v    i  v   vi vi  i   
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_155346009_   3010 TCCTCGCACCACATACACAATTTAATTCTAGATGGATTACAGATGTAAAC 3059
                         v    i     i     v  v    i  v i      i ?   iv    i
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_155346009_   3060 ATAAAATATGAAACAATAAATATGATACAAAGGAAAACATAG---TAAAT 3106
                         i   i vv i    v     vv vv  v  --          ---     
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAA--GAAAACATAGGNGTAAAT 558

  chr2_155346009_   3107 CATCTTTGTGACCTTAGAATAGGCACAATAGACTTATTAAATAGAGCCTG 3156
                          ---  i        i iv      --  i -i  v   i   vii viv
  L1M4_orf2#LINE/    559 C---TTCGTGACCTTGGGTTAGGCA--ATGG-TTTCTTAGATATGACACC 602

  chr2_155346009_   3157 CAAATCACTGACTATAAAAGAAAAAATATTGATAAATTGGACTATATTAA 3206
                         v   v   vii v i             --             vi  i  
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTCATCAA 650

  chr2_155346009_   3207 AATTAAGGACTTCTGT-CATCAAAA------ATCACAAGAGTGAATTTAT 3249
                               ii    i   - v     i------    vi i      vvv i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_155346009_   3250 AACCCTCAGAGTAGCAGA---TATTT-----TC-TATTTCTGATAAAGGG 3290
                              v    i i v   ---     -----  -   v        i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_155346009_   3291 CACAAAACCAGAATATATAGACAGCTCTTTAAAAC-CAATAACAAAAAGA 3339
                          viiv v            i v i     - v   -      i       
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTT-ACAACTCAATAATAAAAAGA 799

  chr2_155346009_   3340 -AGGGACACACAAGAGAAAAATGAACAAAAGATCCTAACAGACAGTTCAT 3388
                         - iiv -  v   vv?       ii    i   iiv  i     v   vi
  L1M4_orf2#LINE/    800 CAAATA-ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_155346009_   3389 AAAAGAGTATTTTCAAATA-CAAATAAAGCTAC-TAAAATGCTTTTTAAT 3436
                         v     iv  v v     i- v     -  -  - i   v v vi i  i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAA-GC-ACATGAAAAGATGCTCAAC 896

  chr2_155346009_   3437 AGCGATTTAACT 3448
                          v i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.14 (66 / 58)
Gap_init rate = 0.04 (19 / 498), avg. gap size = 1.95 (37 / 19)  


4017 18.95 3.88 0.46  chr2_155424145_155428003.rev     2492  3367 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_155424145_   2492 GAAAGACATCCCATCTTCATAGACTGGAAGAC--AATATTGTTAAGATGT 2539
                               i       v     i  i        --               v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_155424145_   2540 CAATACTACTCAAAACTG-TTGACAGATTCTATCCAATCCCTATCAAGAC 2588
                                v i    -i  - iv        v iv             i i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_155424145_   2589 CTCGATGACATTTTTTGAAGAAATAGAAAAACTCATCTTAAAATTCATTT 2638
                          i iiivi v       v      v  v  i  v   i          v 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_155424145_   2639 GGAATTTCAAGAGACCCCAAATAGCCAAAACAAT--TGA----------- 2675
                             v v    i     vi               --   -----------
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_155424145_   2676 -----TGGAAGACTCATATTTCCTGATTTTAAAATTTACTATAAAGCTAC 2720
                         -----    i      i i    ii    i    i      i        
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_155424145_   2721 AGTAATAAAAACAGTGTGGTACTGGTATA--TACAGATATATAGACCAAT 2768
                               v  i               i   --v i   i       i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_155424145_   2769 GGAATAGAATAAAGAGCCCAGAAATAAACTCTTATGTATATGGTCAAATA 2818
                                   vi    i            i v  ii v         v i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_155424145_   2819 ATTTTTGACAAAGATGTCAAGACCATTTAATGAGGGAAAGGACAGTCTTT 2868
                              i     i i  i          i    -       i i       
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTT 400

  chr2_155424145_   2869 GCTACAAGTGGTGCTAAGAAAACCTGATATCCACATGTAAAAGAATGAAG 2918
                         v v    i       ii  v   iv    ?       i            
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_155424145_   2919 TTGAATTT-TATATAACACCATACACAAAAAATAA-TCAAAATGAATCAA 2966
                            i iii-  iv v        i       v   -        i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_155424145_   2967 AGACCTATATGTAAGAATTAAAACCATAAAACTCCTAGAAGAAAACACAT 3016
                                v        ii      i         i            i v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_155424145_   3017 G-GCAATAGCTT-ACAACATTGA-TTGGCCATTGATTTTTTGGCTATGAT 3063
                          - i  - v   -iii  v   i-  i v  v  i   i  i v     i
  L1M4_orf2#LINE/    551 GNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_155424145_   3064 ACAAAAGGTAAAGATAACTAAAATAAAA---GACAAATTGGACTTAATGA 3110
                           v   i i v iii   v   iv    ---  i           v  v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_155424145_   3111 AAACTTAAT-TTTTTTTGCTTCAAAAGACACTATCAATAAAGTAAAAAGG 3159
                            i v  v-i    v         i           v     i     i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_155424145_   3160 CCACCCACAGAATGAAAGAAAATATTTGCAAATCATATATCTGATAAAGA 3209
                          v            ii                               i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_155424145_   3210 ATTGACATCTGATGTATAGAGAGAATTCCTAAAACTCAACTATTAAAAAA 3259
                          i vii   iiivi    v i    i  i  v       iv  v    i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_155424145_   3260 CAAACAACCCAATTCAAACATGAGCAAAGAACTTGAATAGACATTTTTTC 3309
                             i         ?   v   i      i i              i - 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT-C 848

  chr2_155424145_   3310 CAAAGAAAATAAACAAATGGCCAATAAGCA--TGAAACGATGCTCAGTAT 3357
                                i   v                  --     v        ii  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_155424145_   3358 CAGTCATCAT 3367
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.91 (107 / 56)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 2.24 (38 / 17)  


3130 25.96 0.99 1.10  chr2_155521205_155526668.rev     4064  4972 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_155521205_   4064 TGGAAGAATATTCCATGCTCATGGATTGGAAGAATCAATATTGTGAAAAT 4113
                              ii    i     i               v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_155521205_   4114 GGCCATACTGCCCAAAGTAATTTATAGATTAAATGCCATCCCCATCAAGC 4163
                            v     v      v i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_155521205_   4164 TACCAA-TGACTTC---ACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4207
                          v   i-  v   i---i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_155521205_   4208 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 4257
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_155521205_   4258 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAAGTATACTACAAGGC 4307
                                i      vv   ii  v  ii i      iiv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_155521205_   4308 TACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGAGATATAGACC 4357
                                 i   i    ii        vi iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_155521205_   4358 AATGGAACAGAACAGAGCCCCCAGAAATAACACCACACATCTACAACCAT 4407
                                i    iv   vvi          vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_155521205_   4408 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAGGATTCCCTA 4457
                         i    i  i     ivv  v   i v  vvv         i  v v---i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA---G 395

  chr2_155521205_   4458 TTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 4507
                          i v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_155521205_   4508 TGAAACTGAATCCCTTCCTTACACCTTACATAAAAAGTAATTCAAGATGC 4557
                             ii  i i    v   i     v  i i     v   i    i   v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_155521205_   4558 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAA 4606
                           i ?    i       v   v       i      -    -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr2_155521205_   4607 ACCTAGGCA-ATACCATTCAGGACACAGGAATGGGCAAGAACTTAATGAC 4655
                           v    ?i- v i -   iv   viv  iv i     viii  vv iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_155521205_   4656 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 4705
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_155521205_   4706 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACGACCATCAGAGTG 4755
                          v  i   v v  i i   i  ii vv    i  v  v i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_155521205_   4756 AACAGGCAACCTACAGAATGAGGAGGAAATTTTTGCAA-TCTTCTCACCT 4804
                           v  i     i        -    i    v       -  v v - i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATG-GGAGAAAATATTTGCAAATCATAT-ATCT 741

  chr2_155521205_   4805 GGCAAAGGGCTAACATCCGGAATCTACAAAGAACTCAAACAAATTTACAA 4854
                          ii  i  i  vii    i    v  i         vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_155521205_   4855 GAAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGA 4904
                         v     i -    i     v  i?    i            v    i   
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_155521205_   4905 CACTTCTCAAAGGAAGACATTTATATGGCCAACAAACATATGAAAAAATG 4954
                           i     v  i     i  vi v        i  i  i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_155521205_   4955 CTCATCATCACTGATCAT 4972
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.36 (19 / 14)  


3010 27.88 1.22 0.77  chr2_155562532_155564611.rev      685  1588 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_155562532_    685 TGGAAGGATACTCCATTATCATAAATTGGA-GAAATAAAATAGTTAAAAT 733
                              i    ii    vv    ii      -  vv   v  v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_155562532_    734 GGCATTACTCCCCAAAGCAGCTTGCAGATTCAATGTAATCTTTATCAAAA 783
                             v           viiiii i         i i    ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_155562532_    784 -CGCAATGACATTCTTCACAAAAATAGAAAAACAAAACCCTACAATTTAT 832
                         - v  iivi v  i  ii  i    v  v  i vi -i    v    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_155562532_    833 ATGGGGCTACAAAAGATCTCAAATAACCGAAGCACTTCTGAACAAAATGA 882
                             iiv i   ii  i ivi    i  i  i  v ii    v  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_155562532_    883 ACAAAGCTAGAATTTTTACTCTGTTTGACTTCAAAATATACTACAAAGTT 932
                               i i  ivvi i  v  viiii i       iv          i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_155562532_    933 ATAGTAACCAAGTCAGCATGATATTGGCATAAAAATCAGACAAATAAACC 982
                          i     i    v   ii  i  i        ii  -     v   i i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGATC 298

  chr2_155562532_    983 AATGAAATAGAAATGAGAATCCAGATATAAATCCTTGCATTCACAGCCAA 1032
                             i       v     i      v     i  v i    i ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_155562532_   1033 CTAATTTTCCACAAAGGCACCAAGAACACTCA-TAGGGAAATGGACAATC 1081
                         i i      v    i  ii      v  i   - i      - i i i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTC 397

  chr2_155562532_   1082 TCTTCAATAGGCTGTGCTGGGAAATCTGGATAAGCATATGCAGAGGAATG 1131
                          i     i iiiv         v v       ?v  i     i i     
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_155562532_   1132 AAACTAGACCC-TATCTCTCACCATACACAAAACTCAAATCAAAATTTAT 1180
                           ii i     -  i   v       i      v i  v       vv  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_155562532_   1181 TAAAAACTTACATCTAATACTTGAAACAATGAAACTACCAGAAGGAAACC 1230
                         i ? i  i  v  v   v vi i    v  i     vii     i    v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_155562532_   1231 CTGGGGCAAAGCTCCAGGACTTTGGTCTGAGCAAGAATATTTCTTATATA 1280
                         iv  ? i   v  i iv   i    vi ii    vii --      v   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT--TTCTTAGATA 595

  chr2_155562532_   1281 AAACCTCAGAAGTACAGGCAATCAAAGCAAAAATTGAGAAATGGGATTAC 1330
                         vi  vi  i   i   i    iv    v      v  v    v   i v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_155562532_   1331 ATCAAGG--AAGGATCTTCA--CAGCAAAGGAAACAATTAACAAAGTGCA 1376
                              ii--  ii ii  ii-- vv       v  v  i  v      v 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_155562532_   1377 GAGTCAACATACAGAATGGGAGACTATATTCGCAAAACTCTT-CAGCTGA 1425
                         i  v    vi             vv     i     --  v -i v    
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAA--TCATATATCTGA 743

  chr2_155562532_   1426 CAACGGATTAATAATTGGAATATATAAGGAGCTCAAACAACTCAACAGCA 1475
                         i  v   i vi  viii          i  i   vv         i ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_155562532_   1476 GAAAAATAAATAATCTGCTTTAAAA-TTAGCAGTAGTTCTGAAGAGATAT 1524
                         i   i i      i iiv  ?    - vi   ivi v i    v   i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_155562532_   1525 TTCACAAAAGAAAATACACAAATGGCCAATGAGCATATTAAAA-ATGCTC 1573
                            v v      i   i             i    i  v    -      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_155562532_   1574 AACATTACTAATCAT 1588
                              i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (161 / 87)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.29 (18 / 14)  


1829 26.00 8.02 4.01  chr2_155602104_155604027      560  1432 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_155602104_    560 TGGAGACCTATACCACATTTGGGGATTGAAAGAAAAAAATATT-TTAAGA 608
                             i vv   v   ii  iiv      i    vvv  -    -      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAA-TATTGTTAAGA 49

  chr2_155602104_    609 TATCAAGTTTTCTTCACAATAATTTATAGAATCAACACAATCCCAACCAA 658
                          iv   - vi  ii  v v i  i  i   v     i       v i   
  L1M4_orf2#LINE/     50 TGGCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_155602104_    659 AATCCCATTT-TTTTTTTGGTAGAAATTGACCACTTAATTATACAATTTA 707
                                vi -ii     v i          v vi i  iv  v    i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_155602104_    708 TGTGGA----CAAA--------AAT---CAAAACACTTCTGAAAAAAAAG 742
                          i    ----   i--------   ---       v ii       i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_155602104_    743 AAATAAACTGTAGGACATGGACTATTGGATTTTAAGATTTCCTACAAATG 792
                           vv  ii  v     viiv   viivi    i  i i  v       --
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-- 246

  chr2_155602104_    793 AAGACATTTTCAGGAAAATAAAAGCTA-AGAAAATTCAAGGCAGTATTGT 841
                         -----------------------    -  v  --     i    i v  
  L1M4_orf2#LINE/    247 -----------------------GCTACAGTAA--TCAAGACAGTGTGGT 271

  chr2_155602104_    842 TTTGG-AGGAAAAGGGACAAAAACATCGACAAAA--GGATACAGAGTCCA 888
                         vi   - vi ii vi    v v v   i iii  -- i  vv        
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_155602104_    889 GAAGTTAACCCACATATCAAT--TTA-TTAATTTTTGA-AAATGTGCCAA 934
                            i v      i i  iv  -- i -  i     i  -  iv       
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_155602104_    935 AATAATTCAAAGTGGAAAGGATTGTCTTTTGAACAA-CAATGTCTGTAAT 983
                         i iv      v v      i  v       v     -iii  -   vi i
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG-CTGGGAC 420

  chr2_155602104_    984 AATTGAA-ATTCATATAAAAAAGAAT----CTTTACTCTTAATTCACGCT 1028
                           i  i - ?i  i  iv        ----i vv  i i  vi    i i
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_155602104_   1029 ATATACAAAATTTA-CTTGAA-TGAA--ATAGACCT----GCAATGAGAC 1070
                                   v   -  ii  -  i -- ?      ---- i  -   vi
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA-GAGCT 519

  chr2_155602104_   1071 AAAAGTGAAACAATTTTCGT-GAAGACATAAAAGAAAAATTATTGC-ATC 1118
                             v iv  v v i  v v-   i     ii? v   vi - i i- i 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT-TCGTGACC 568

  chr2_155602104_   1119 TTGAGTTAGGCAAATGTTTATTAGA-ACAACA--AAAAGCACAAAAACAT 1165
                            i         vv    v     - ii   --          iv - i
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA-AC 617

  chr2_155602104_   1166 AAAGGGGGAAATTAATAAATTAAACTTCATCGAAACTAAA--TGTCTAC- 1212
                            i iii    vi       ii        i   i    --iv i ii-
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_155602104_   1213 CTTTGAAAGGCACTAT----AAA---AAACCATAAGCCATATATTGACAG 1255
                            ii  i i      ----   ---   vv i  v   i v v  iv  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_155602104_   1256 AAAATACTTGCAAAACATCTATCTG-TAAAGGACTTGTAAACCAGACTAC 1304
                               i       v   v      -   i         v-     v  i
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT-CCAGAATAT 766

  chr2_155602104_   1305 AGGAAGAGCTCTTACAACTCAATAA---GAAGAAAAACATCCCA-CTAAA 1350
                          vi    i                 ---i    v   i v    -i ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_155602104_   1351 TTATAGGGCTAAAGATGTGAACA-----------AAAGAGTATGTGTAGA 1389
                         vv  -    v  i   v    i -----------     iv  i ii i 
  L1M4_orf2#LINE/    817 AAAT-GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_155602104_   1390 TAGCGAATAAACTCATGGAAAGATGCTGAGCATCATTAGAAAG 1432
                          i  v     i v    i         v i     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.04 (40 / 908), avg. gap size = 2.62 (105 / 40)  


2682 25.22 2.06 3.79  chr2_155745865_155750402.rev     3123  4046 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_155745865_   3123 TGGAAATACATGCTATGCTCATGGATTGGAGGAATCAATATCATGAAAAT 3172
                               v i  v i   i            i  v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_155745865_   3173 AACCATAGTGCCCAAGGCAATCTACAGATTCAATGCAATTCTTATGAAAA 3222
                         ii v   v v     ivii              i     i i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_155745865_   3223 TACCAACATCATTTTTCACA-AAATTAGAGAAAAAC-AACTCTAAAATTT 3270
                          v   i vv v     ii  -     ---  v  i -i ii        i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chr2_155745865_   3271 ATATGGAACCAAAAAGAAGCCCAGA-TAGCTAAAGCAATCCTAAAAAAAA 3319
                                 viiv  i i -      -    i   i     i i     i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_155745865_   3320 GTAACAAATCTGGAGGCATCATATTACCTGACTTCAAA--TTATTCTACA 3367
                         iv      vi      vv   i i v  ii i      --   --     
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACA 244

  chr2_155745865_   3368 GGGCTGTAGTAACCAAAACATAATGGTACCAATATAAAAACAGATACATA 3417
                         ii   ii     i   i   vvi      iiii    ii i   i i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_155745865_   3418 GAACAATGGAACAGAATAAAGAACCCCAAAATAAAGCAAAA----TATGA 3463
                           v        i     vi   ii  vi       v v v ----    i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_155745865_   3464 CCAACTGATCTTCCACAAAGCATACAAAAAT-ATAAATTGGGGAAAAAAA 3512
                         i   i    i   v    i -i i v  i i-  vv v        i  -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAA- 392

  chr2_155745865_   3513 CAACTTATTTGATAAATGGTCCTGGGAAAAATGGTTAGCCAGATGTAAAA 3562
                         i iii v  ii i       v      v  v   v  ?   v   i    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_155745865_   3563 GGATGAAACTGGATCCCTGTCTCTCACTATATATAAAAATTAACTGAAGA 3612
                          i     ii    i    ii   v   i     i           v  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_155745865_   3613 TAGATTAAAGACTTAAAAAATA-AAGACCTGAAACCATAAAAATTCTAGA 3661
                          i   i ?    i    --- i-    v  i    i      v ii    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAA---TGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_155745865_   3662 AGAAAACCTAGA---AAATACTTTCTGGGCCTTGGCTGAGGCAAATAATT 3708
                                v   i---    -   iv  i-      v v      - ii  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT-CTTCGTGA-CCTTGGGTTAGGCAA-TGGTT 586

  chr2_155745865_   3709 TATGA-ATAAGACCCCAAAAGTGAATGTAACAAA-AACAAAAATAAAAAT 3756
                          v v -   v   v       i-------    i-       iv      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGC-------ACAAGCAACAAAAGAAAAAAT 629

  chr2_155745865_   3757 AAATAAATTGGACCTAGTGAAACTAAAAAGCTTCTGCACAGCAAAAGAAA 3806
                          i           i vi v   v v    i   i  ii vv    i  --
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-- 677

  chr2_155745865_   3807 TACTTGTCAG---AGTAAATACACAACCTGCAGCATGGGAGAAGATACTT 3853
                         i   -i   i---   i  v v      ii   v         i   i  
  L1M4_orf2#LINE/    678 CACT-ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_155745865_   3854 GCAAGTTATGTATCCAACAAAGGTCTTATATCCAAAAATCTACAAGGAAC 3903
                             i i  i    ii i  i  v   i      i  - v  i  i    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAA-TATATAAAGAAC 775

  chr2_155745865_   3904 ACAAGTAAACCAGCAAGAAAAAATCCCTAATAAACCCATTAAATAGTGTG 3953
                         v vvii  vi  ii  v     iv v--     v  v   ?  v i  v 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACA--AATAACCCAATTWAAAAATGGG 823

  chr2_155745865_   3954 CAAATGAAACGAATAGACATTTCTCGAAATAGATATTTTTCATATATACA 4003
                             v  vvi               v   v ii--------     i v 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAG--------ATATACAAA 865

  chr2_155745865_   4004 TGACCAACAAACATATGAAAAAATGTTCAACGTCAGTAATCAT 4046
                           i    i  i  i       i   i     i   ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (149 / 81)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.08 (54 / 26)  


 423 27.56 0.79 1.57  chr2_155766494_155771047.rev     2879  3005 (1549)    L1M4_orf2#LINE/L1        1   126 (782)  

  chr2_155766494_   2879 TGGAAAAGTATTCCATCCTTCTGGATAGAAAGAATCAATATTGTTAAAAT 2928
                               ii   i    vi iv     v i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_155766494_   2929 GACCATACTACCCAAAC-AATGTACAGATTTAATACTATTTTTATCGAAC 2977
                          i v     v      i-i  v        i  ii v  iii    i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_155766494_   2978 TACCAACGACATTAATTTTTTAAAAATT 3005
                          v   i vi v  --    vi i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT--TTTTGCAGAAATT 126

Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.02 (2 / 126), avg. gap size = 1.50 (3 / 2)  

2412 26.72 1.87 1.25  chr2_155766494_155771047.rev     3262  4062 (492)    L1M4_orf2#LINE/L1      103   908 (0)  

  chr2_155766494_   3262 CCAATGGCTTTTCTT-CAGACAATTAGGAAAAAGT-ATTCTAAAATTCAT 3309
                            iiv  i   i  -    -    --  v  iv -  i           
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGA-AATT--GACAAGCTGATCCTAAAATTCAT 149

  chr2_155766494_   3310 ATGGGACCA-AAAAGACTCCAAATAACCAAAGCAATCTTAAGCAAAAAGA 3358
                             i vii-  ii   i vi    i     i       i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_155766494_   3359 ACAAAGCTGGCGGCATCACACTATTTGACATCAAACTATAATATAAGGCT 3408
                               i   v  vv       viiii iv     viv  v  i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_155766494_   3409 GCAGTAATTAGAACAGCATAGTGCTGGTACAAAAATAGCCACATAGACCA 3458
                         i       i ii    ii i  i    i i  ii    v  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_155766494_   3459 ATTGAACAGATTAGAGAACCCTGAAATAAAGCCAAGCACTTACAGCCATA 3508
                           v   i   v v    ii  v        v   vi  i   ii i  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_155766494_   3509 TGATTATTGATGAAGCTGATAA---TAAGGAATGGTGAAAGGACTTCCTT 3555
                              v i  ii i v  vi  ---i vvv     v     i ivvi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_155766494_   3556 TTCAATAAATGATGCTGTAATAACAGGCTAGCTACATACAGAAGAATAAA 3605
                              i     i     vi i   v  v  ? i    i  i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_155766494_   3606 ACTGGACAACATTCTTTCACCATATACAAAAAACAACTAAAGATGGATTG 3655
                         ii     vv vvi  iv               vi    v  i      ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_155766494_   3656 AAGATTTAAATGTAAAACCTAAAACTATAAAAACCCTAGAAGAAAATCTA 3705
                         ?   ii         i v              vi i          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_155766494_   3706 GG---AAATAGGATTCTGGATATTGGACCTGGCAAAGATTTCATGACAAG 3752
                           ---    v---   vv  iv    iiiv     v i    v iivv v
  L1M4_orf2#LINE/    550 GGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_155766494_   3753 GACTCCTGAAGCAACTACAACAAAAACAAAAATTGATACCAA--GGACCA 3800
                            v  vi     vvvi        iv      v    --  --    iv
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA--AATTGGACTT 644

  chr2_155766494_   3801 AAT-AAAACTAAAGAGCTTTGGCAAGACAAGAGAAACTATCAAGAAACTA 3849
                         v  -    i    i -    v iivvv   ii  v            v i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_155766494_   3850 AACAGAATACCTACA-AATGGGAGAAAACATTTGCGAACTATGTATCTGA 3898
                           v   vv   i   -            i      i  ii  i       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_155766494_   3899 CAATGGTCTAATATCCAGAATATATAAGGAACTTAAATATAC-CAACAAG 3947
                         i  v  v  vi                i     ivv i -  -   i  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCAATAAT 792

  chr2_155766494_   3948 CAAAAAACATATAACCCCATTAAAAAATGAGCAAAGGACACGAACAGACA 3997
                         v    i   v       v   ?       i        ivi   i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_155766494_   3998 ATTCTCAATAAAAGACATACATGTGATCAATAAGCATATGGAAA-ATGCT 4046
                         v     v v i    i     vi  ii         i   i   -     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_155766494_   4047 TACCATCATTAAACAT 4062
                         i v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (123 / 88)
Gap_init rate = 0.02 (16 / 806), avg. gap size = 1.56 (25 / 16)  


 343 20.00 0.00 0.00  chr2_155799510_155801352.rev       48   112 (1731)  C L1M4_orf2#LINE/L1   (843)    65     1  

C chr2_155799510_    112 TGGAAGAACATTCCATGCTCATGGGTTGGAAGAATCAATATAGTGAAAAT 63
                              ii i  i     i      i        v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_155799510_     62 GGCCATACTGCCCAA 48
                            v     v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA 65

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.00 (0 / 0)  

2926 26.56 1.06 0.82  chr2_155799510_155801352.rev      501  1351 (492)    L1M4_orf2#LINE/L1       56   908 (0)  

  chr2_155799510_    501 TGCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCA 550
                          i  v     iv i  i  i        i  v     i     iv v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_155799510_    551 ATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCATATGG 598
                         iivi i  i  ii     -   -- v  i   v i-    i         
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGG 153

  chr2_155799510_    599 AACCAAAAAAGAGCCTGCATTGCCAAGTTAATCCTAAGTCAAAAGAACAA 648
                           viiv  ii  v  v v  v     ivi    i i ivv i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_155799510_    649 AGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAG 698
                           i      vv    i  v  ii i      viv        i       
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_155799510_    699 TAACCAAAACAGCATGGTACTGGTACCA--ATCAGAGATATAGGCCAGTG 746
                            i   i    ii         i iv --  -   v      ii  i  
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGATCAATG 302

  chr2_155799510_    747 GAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACCATCT 794
                            i    i--    i  --        vv  ii i  i  iiii  vi 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_155799510_    795 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACGATTCCCTAT 844
                            i  i     ivv  v   i v  vvv          vi  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_155799510_    845 TTAATAAATGGTGCTGGGAAAACTGACTAGCCATATATAGAAAGCTGAAA 894
                          i  i              v     iv  ?   i  ii i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_155799510_    895 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTTGAGATGGATTAA 944
                         i    i    v   i     v              i ii i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_155799510_    945 AGACTTAAATGTTAGACCTGAAACCGTAAAAACCCTAGAAGAAAACCTAG 994
                             i       v   v  i    ii     vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_155799510_    995 G--TAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 1042
                          --   - i -   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    551 GNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_155799510_   1043 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACATATGGGATCTAATT 1092
                                    vvi          vv     v  i v  v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_155799510_   1093 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGAACAG 1142
                            v v  i i   i  ii vv    i  v    i  vv i v    v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_155799510_   1143 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACCAAG 1192
                         i     i                 v       vii ivi      iv i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_155799510_   1193 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTA-CAAGAAAAAA 1241
                          i  vi          v  i  v      vv    v i -i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_155799510_   1242 ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 1291
                              i     v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_155799510_   1292 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAACAT 1341
                         v        i  vi viii     v  i          i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_155799510_   1342 CACTGGCCAT 1351
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.45 (132 / 91)
Gap_init rate = 0.01 (11 / 853), avg. gap size = 1.45 (16 / 11)  


 414 11.11 0.00 0.00  chr2_155881316_155883251      501   563 (1372)    L1M4_orf2#LINE/L1      294   356 (552)  

  chr2_155881316_    501 AAATTAATGGAATAAAATTGAGAGTCCAGAAATAAACTGACACATCTATG 550
                          i  i         i                      iv i    i    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_155881316_    551 GTCAATTGATTTT 563
                                      
  L1M4_orf2#LINE/    344 GTCAATTGATTTT 356

Transitions / transversions = 6.00 (6 / 1)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.00 (0 / 0)  

1866 23.05 2.11 5.68  chr2_155881316_155883251      829  1444 (491)    L1M4_orf2#LINE/L1      315   908 (0)  

  chr2_155881316_    829 GATTCCAGGCATGAGCCATCGCACCCAGTGTATGGCCAATTGATATTTGA 878
                           v     iv  i i  ----  iv  v -     i        v  i  
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACC----CATACATT-TATGGTCAATTGATTTTCGA 359

  chr2_155881316_    879 AAAGGATGTTAATTCCATTCA-TTGAGAATACATAGTCTCTTTAGTAAAT 927
                         v    i  ii  vv       - v i   viv       i  i ii    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_155881316_    928 GGCAGTGGGACAACAAAATAGCCACATGCAAAGAATTGAAGATGAACCCC 977
                           iiv         vii   ?           ii v     v  i     
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_155881316_    978 TACCTCATATCATATACTAAAATTAACATAAAATGAATTTAAAACCTACA 1027
                                i i       v         vi      i  iv? i     v 
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_155881316_   1028 TGCAAGATCTAAAACTTTAAAACTCTTCAAAGGAAACACAGGTTTAAATT 1077
                           i    v        v          vi   i     i   ?v     i
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_155881316_   1078 TTCATAACCTTGGCTTTGAGGCAACAGTTTCTTAAATATAATATCCGAAG 1127
                            i i       v  --      ii        i    i i i vi   
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTT--AGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_155881316_   1128 CATAAGCTAAATAAATAAATACATAAAATCATTAGTTAATAAACTGTACT 1177
                           i    --  i   vi  -----     ----  ---     i  v   
  L1M4_orf2#LINE/    608 CACAAGC--AACAAAAGAA-----AAAAT----AG---ATAAATTGGACT 643

  chr2_155881316_   1178 TCA---AAATTAAATACTTGTATA--TCAACAGACACTATTAAGAGAGTG 1222
                            ---        v    v i i--    vi        i    i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_155881316_   1223 TACATGCAACCTACAGAATGAAAGAAAATATTTATGATT--TGTATCTAA 1270
                         v v vi     i        ii           iii v -- i     i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_155881316_   1271 TAAGATTTTTTATATGTCAGATATATCTGTTACATATAAAAAAA-CTTAC 1319
                             ivvi  -i   -i    ---------- i       i  v-     
  L1M4_orf2#LINE/    744 TAAGGGACTT-GTAT-CCAGA----------ATATATAAAGAACTCTTAC 781

  chr2_155881316_   1320 GACTCAGTAATGAAT-GAAAACTAGCCTA-CTCAAAATTAGGCAAAAAAA 1367
                         i     i    i  v-  v  v  i  i -i ?    v i      ii v
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_155881316_   1368 TGAGGTATATGTTTTATTTTAAA--AGATTAATAAATAGCCAATAAGCAG 1415
                          viii  v ii   i-- ii   --    vv i    i           v
  L1M4_orf2#LINE/    832 TTGAATAGACATTTC--TCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_155881316_   1416 ATGTAACATTTCTCAACATTAGTAGTCAT 1444
                            v  viv v        i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (87 / 51)
Gap_init rate = 0.03 (19 / 594), avg. gap size = 2.53 (48 / 19)  


3423 25.64 0.99 0.66  chr2_155956811_155961325.rev     3119  4023 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_155956811_   3119 TGAAAAAATACTCGATGTTCATAGATTGGAAGAATCAATATTATTAAAAT 3168
                           i   i   ii v        i          v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_155956811_   3169 GTCCATACTACCCAAAGCAATCTGCTGATTCAATGAAATCCCTATCAAAA 3218
                          v v     v      vii    i v       i v              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_155956811_   3219 TGCCAGTGATATTCTTTACAAAAATAGAAAAA--AAACCTGTAAAATTTG 3266
                          v    iviiv  i   i  i    v  v  i--i v   --      ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chr2_155956811_   3267 TATGGAAACACAAAAGACCCAGAATAGCCAAA-CATACCTTGAGCAAAAA 3315
                                 ii   ii                 -  - i     iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACA-ATCTTGAAAAAGAA 197

  chr2_155956811_   3316 TAGCAACACTGGAAGAATCACATTACCTAACTTCAAATTGTGCTACAGAG 3365
                         v i   vii    i  v     i v  i  i      viv i     i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_155956811_   3366 CTATATTAATGAAAACAGCATGGTAGTGGCATAAAAACAGACACATAAAC 3415
                            i v    v  i    ii     v        ii i     i   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_155956811_   3416 TGATGGAGCAGAATAGAGAACCCAGAAACAAATCCATGCATCTATAGTGA 3465
                         ii     ii     v    ii       i   i    i   i   i  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_155956811_   3466 ACTCATTTTTGACAAAA-TGCCAAGGCCATACATTGGGGAAAGGACAGTC 3514
                          i v     i     ii-       i    v  v         i i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_155956811_   3515 TCTTCAACAAATAGTGAGGAGGAAACTGGATATCCATGTGTAGAAGAATG 3564
                          i          i   vv i iv         ?   ii  i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_155956811_   3565 CAACTAGACCCCTATCTCTTGCCATATACAAAAATCAAATCAAAATGGAT 3614
                         v ii i        i   vii              i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_155956811_   3615 TAAAAACATAAATCTAAGACCTCAAACTATGCAATCACTGAAAGAAAATA 3664
                         i ? i  v     v     v  v       iv  iivi ii       i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_155956811_   3665 CTGAAGAAAGTCTCCACGACATTGGACTGTGCAAAAATATCTTGAGCAAT 3714
                         iv i? v  i   i ii   v    ii iv    vii v    iiii vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_155956811_   3715 TCCCCACAAGCACAGACAACCAAAACAAAAAGTGGACAAATGGGATCATA 3764
                         v v   v       ii    -    v     i i  i    v   iivi 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_155956811_   3765 TCAAG-TTAAAAAGCTTCTTCACAGCAAAGAAAACCATCAACAAAGTGAA 3813
                             i-       -   i vii vv     i v  i     v        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_155956811_   3814 GAGACAACCCACAGAATGGGAGAAAATATTTGTAATCTACTCATCTGTCA 3863
                         i                               i  vii ivi     vi 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_155956811_   3864 AGGGATTAACAACTGGAACATATAAGGAGCCCAAACAATTATATAGAAAA 3913
                              i vii v ii   i      i  i i vv    i vv   iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_155956811_   3914 ACGATCTAATAATCTGATTTAAAAATGGGCAAAAGATCTGAATAGACATA 3963
                          v  - v     i ii   ?             i   i           v
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_155956811_   3964 TCTC-AAAGGAGG---ACAAATAGTTAACAGGTATATAAAAAGGTGCTCA 4009
                             -    i  i---      i ii  i i i i  i     i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_155956811_   4010 ACATTATTGATCAT 4023
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (155 / 73)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2946 25.45 3.35 2.01  chr2_155972764_155975586.rev     1436  2331 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_155972764_   1436 TGGTAAAACATTCCATGCTTATGGATGGGAAGAATTAATAGCGTGAAAAT 1485
                            v  i i  i     i i      v      v      vi  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_155972764_   1486 GGCCATACTGTCCAAAGTAATTTATAGATTCAATGCTATCCCCATTGAGC 1535
                            v     vi     v i  i  i        i  v     i  ii iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_155972764_   1536 TACCA-TTGACTTTCTT-CAGAGAATTAGAAAAAACT-ACTTTAAATTTC 1582
                          v   -i  v    i  -    -    i-- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_155972764_   1583 ATATGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAA 1632
                                 viiv  ii  v  v v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_155972764_   1633 GAACAAAGCTGGAGGCATCATGTTACGTGACTTCAAACTATACTACAAGA 1682
                                 i      vv   iii v vii i      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_155972764_   1683 CTACAATAACCAAAGAAGCATGGTTTTGGGATACAAGGCTTCCAAAACAG 1732
                              i   i   iiv  ii    vi   v   --   -------- i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATA--AGG--------ATAG 287

  chr2_155972764_   1733 ATATATAGACCAATGGAGCAGAA--AAGAGGCCTCAGAAACAATGCCACA 1780
                          i       i       ii    --i    v  --     i  vv   i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATA 335

  chr2_155972764_   1781 CATCTACAGGCATCTGATCTTTGACACACATGACAAAAACAAGCAATGGG 1830
                            i  ii v  vi    i  i    vivi  v   i v  vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_155972764_   1831 AAAAGGATTCCCTATTTAATAAATGGTCTTGGGAAAACTGGCTAGCCATA 1880
                         i    i  vvi  v  i  i       vi     v      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_155972764_   1881 TGCAGAAAACTGAAACTAGACCCCTTCCTTACACCTTATACAAAAATTAA 1930
                             i  i v    ii i       v   i     v              
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_155972764_   1931 CTTAAGATGGATTAAAAACTTAAA-GTGAAGCCCTAAAACCATGAAAACC 1979
                           i  i      i ? i  i    -  -   vv       i  i   vi 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTC 534

  chr2_155972764_   1980 CTGGAGAAAAACCTAGGCA-ATACCATTCAGGACATAAGCATGGGCAAAG 2028
                         i i  ii     v    ?i- v i -   iv   v vi vv i     v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chr2_155972764_   2029 ACTTCATGACTAAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGAC 2078
                         ii   v iiv  vi            vvv          vv     v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_155972764_   2079 AAAGGGGA-TCCAATTAAATTAAGGAGCTTCTGCACATCAAAAGAAACTA 2127
                            vv   - i  viv       ii -   i  ii v     i  v    
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA 682

  chr2_155972764_   2128 TCATCAGAGTGAAAAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATC 2177
                            vv i         i     i                 v       vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_155972764_   2178 TATCCATCTGACAAAGGGCTAATATCCAGAATTTACAAGGAAC------- 2220
                         i  vi      i  i  i  vi          v  i  i    -------
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_155972764_   2221 -------------AAAACAAACAACCTTATCAAAAAGTGGGCAAAGGATA 2257
                         -------------  i     i    iv  i?    i            v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_155972764_   2258 TGAACAGACACTTCTCAAAAAAAGACATTTATGTGGCCAACAA--ACATG 2305
                             i     i     v   i    i  vi vi       i  --     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_155972764_   2306 AAAAAAAGCTCATCATCACTGGTCAT 2331
                             i v     v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (135 / 89)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.82 (48 / 17)  


2518 29.06 2.21 2.10  chr2_156009050_156011237      792  1696 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_156009050_    792 GAAAAACATGCCATCCTCATAGACTGAAAGAACCAATATCATGAAAATAA 841
                             i i  v    vi    i  i  i    vii     ii v  i  ii
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_156009050_    842 GTATACTACCCAAAGCGATCTGTAGATTTAATGCTATCTCTATCAAAATA 891
                         vv     v      vi     ii     i  i  v   i          v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_156009050_    892 TCAACATTATTTTTCACAGAATTAGAAGAAACT-ATTCTAAAATTCACAT 940
                         i  i vviv     ii     v v  v-  i  -  i          i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCATAT 151

  chr2_156009050_    941 GGAAACAAAAAAAAAGAGCTCA-AATAGCCAAAGTAATCCTAAGCAAAAA 989
                              iiv  iii ---- i  -          ii    i i iv  i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_156009050_    990 TAACAAAGCCAGAGCCATTATATTACTTGACTTCAAATTATACCATAAGG 1039
                         v       iii   vvv i i i v iii i      viv   i i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_156009050_   1040 CTACAGTAAACCAAACAGGTTTTTTCTTTACTAATATAAAAGTAGACACA 1089
                                  v v i    ----- vivv    iii    iii      i 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAG-----TGTGGTACTGGCATAAGGATAGACATA 292

  chr2_156009050_   1090 TAGAACAATGGAATAAGATATAGAACCCAGAAGTAAAGCCACACACCTAC 1139
                             v          ii  vv   ii      i    v   i   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_156009050_   1140 AGCCATCTGATCTTTGACAAAATTGACAAAA--AGTGAGCAATGGGGAAA 1187
                         i i  vi    i  i     iiv  v   i -- v ---           
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAA 389

  chr2_156009050_   1188 TTATTTCCTATTCATTAAATGGTGCTGGGATAGCTGGCTAGTCAAATGTA 1237
                         vv  vvi  v    vi              i i    v  ?i  v   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_156009050_   1238 GAGGAATGAAAGTGGATCTCCACTTTTAACTTTATACAAAAATTAACTCA 1287
                         i i       iv    i i i  i ivv  iv                  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_156009050_   1288 AGATGAATTAAAGATTTAAATGTAAGACTTCAATCTATAAGAATCCTAGA 1337
                          i   i  i ?   ii           vi v  v      i v  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_156009050_   1338 AGAAAACCTAGAAA-ATATCATTCTGGACATTGGCTTTGGGAAGGAATTT 1386
                                v   i?i- v   -   vv   v    v  v  v  v iv  i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_156009050_   1387 ATGACTAAGTTCTCAAAAG---AAATTTCAACAGAAACCAAAATCGACAA 1433
                         v iiv  v vivi      ---  i---     i  ivv     v  i  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAG---CAACAAAAGAAAAAATAGATAA 635

  chr2_156009050_   1434 ATGGGACCTAATGAATCTCAAGAGCTCTTGCACAGCAAGAGAAACTAT-- 1481
                           v    i v  v  vv i  i i  i   ii vv   ii  v     --
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_156009050_   1482 ACAGAGTAAACAGGCAACCTACAGAATGGAAGAAAAC----------TAT 1521
                          v i   i  v  i     i         i      i----------i  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_156009050_   1522 GCATCCCATAAAGGTCTAACATCCGGAATCTGTAAGAAACTTAAACGATT 1571
                         ii   iv    i  v  vii    i    v i   ii    ivv  i i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_156009050_   1572 CAACAAGCAAAAAAACAAATAAGCCCTTTAACAAGTGTACAAAAGGCATG 1621
                            i  -i     i        v  vv  ? v  i  vi    i iiv  
  L1M4_orf2#LINE/    786 CAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_156009050_   1622 AACAAACATTTCTCAAGAGAAAATATATAAGTGGCCAACAGACATGTGAA 1671
                           i i         v i    i     i  i       i ii  ii    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_156009050_   1672 AAAAATGTTCAACATCACTAATCAT 1696
                           i -  i         ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (164 / 95)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 2.60 (39 / 15)  


2786 27.32 1.33 1.22  chr2_156027784_156034506.rev     5328  6231 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_156027784_   5328 AAAAAAATTCCATGCTCATGGATAGGAAGAATCAATGTCACGAAAATGGT 5377
                            i v  i     i        v      v i   i iiiv  i    i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_156027784_   5378 CATACTGCCCAAAGTAGTTTGTAGATTCAGTGCTATTCCCATCAAGCTAC 5427
                         v     v      v ii i ii       ii  v  i  i     iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_156027784_   5428 CA-CTGACTTTATT-CAAATAATTAGAAAAAACTGCTT-TCAATTTCATA 5474
                           -   v    v  -  i -    i-- v  i   v i- v  v      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr2_156027784_   5475 TGAAACCAAAAAAGAACTCATATAGCCAAGACAATCCTAAGCAAAAAGAA 5524
                           i  viiv  ii  v iviv        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_156027784_   5525 CAAAGCTGAAGGTATCATGCTACTTTACTTCAAACTATACTACAAGGCTG 5574
                              i  i   vv   ii  v iiv i      viv        i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_156027784_   5575 CAGTAACCAAAACAGCATGGTACTGGTACCTAA--ACAGATATTTAGACC 5622
                               i   i    ii         i --   -- i   i  v    i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATAGATC 298

  chr2_156027784_   5623 AATAAAACAGAACAGAGGCCTCAGAAAAAAAAACACCACACATCTACAAC 5672
                            ii  i    iv   ivii      v   -- -   i    i  iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAA--C-CCATACATTTATGGT 345

  chr2_156027784_   5673 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAAAAGGATTC 5722
                           vi    i  i     ivv  v   i v  vv       i    i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_156027784_   5723 CCTGTTTAATAAAGGGTGCTGGGAAAACTGGCTAACCATATACAGAAAAC 5772
                         i  v  i  i   v          v      v  ?   i  i  i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_156027784_   5773 AGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGG 5822
                         v   ii         v   i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_156027784_   5823 ATTAAAGACTTAAAAGTAATACCTAAAATCATAAAAACTCT-AGAAGAAA 5871
                           i ?    i    v    v v      ii      -    -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr2_156027784_   5872 ACCTAGGCA-ATATCATTGAGGACATAAGCATGGGCAAAGACTTCGTGAC 5920
                           v    ?i- v   v i v iv v ii i- i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGA 593

  chr2_156027784_   5921 TAGAATACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGCATG 5970
                           vi i          vvv          vv     v  i    v v iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_156027784_   5971 CAATTAAACTAAAGAGCTTTTGCACAGCAACAGAAACTATCATCAGAGTG 6020
                         iv  i   v v  i i      ii vv   vi  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_156027784_   6021 AACAGGCAACCTACAGAATGGGAGAAAATTTTTG-AAATCTATCCATCTG 6069
                           v  i     i                 v    -     -  vi     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTG 742

  chr2_156027784_   6070 ACAAAGGTCTAATATCCCAAATCCACAAGGAACTTAAATAAATTTACAAG 6119
                          i  i  v  vi     vi   vi i  i     ivv i  v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_156027784_   6120 AAAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACA 6165
                              i    ----   v  i?    i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_156027784_   6166 CTTCTCAAAAGAAGACATTTATGCAGCCAAGAAACATAAGAAAAAAAGCT 6215
                         i     v        i  vi viii     v  i  i v     i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_156027784_   6216 CTTCATCACTGGCCAT 6231
                          vv     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 1.44 (23 / 16)  


2789 28.32 1.44 1.00  chr2_156105005_156108057.rev     1658  2561 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156105005_   1658 TGGAAAGACATCCCATGCTCTTCCTATGGATCTGAAGAAATAATACCATT 1707
                                 i        i  -----      iv     vv     iii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTC-----ATGGATTGGAAGACTTAATATTGTT 45

  chr2_156105005_   1708 AAAATGGCAATACTACCCAAAGCAGCCTACAGATTCAAGATAAGCCTTAT 1757
                           i           v      viiii            vii  v  i   
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_156105005_   1758 -GAAATACCAATAACATTCTTCACGGAAATAAAATAAACTG--TCTAAAA 1804
                         -i    v   iivi v  i  ii i     vi -i  i   --i      
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAA 144

  chr2_156105005_   1805 TTTTTGTGGAGTCACAAAAGACCCCAAAGAGCCAAAGCAATTCTCAGTGA 1854
                           iv i    ivii   ii     vi  v       i    ii v ivi 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_156105005_   1855 AAAGAACAAAGCTGAAGGTGTCACACTACCAGACTTCAAAATATACTGCA 1904
                         i          i  i   vv       v  vi i       iv    i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_156105005_   1905 AAGCTGAAGTAACCCA--CAGCTACACACTGACATAAAAATAGACATACA 1952
                              iv     i v --   ivvvii    i     ii         i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_156105005_   1953 GACCAGTGAAACAGGATAGCAAACCCAGAAATTAATCCAAATATCTCCAT 2002
                           i  i  i  i  i  v vi ii        v  i   v i  i viiv
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_156105005_   2003 CTAACTGATTTTTGACAAAAGTGCCAACAGCATTCACTGGGGCAAAGACA 2052
                         ii  i       i     ii       v v      v     v  ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_156105005_   2053 GTCTCTTCAATGAATGCTTCTGGGAAAAGAGGATAACTATACGCAAAACA 2102
                             i     ii    v v      v  vv     ? i i i      v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_156105005_   2103 ATGAAATTAGACTCCCACTTCTAACCCTATACAAAAAAACAACTCAAAAT 2152
                              i  i   i  i  i  vv   v          v-i          
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAACTCAAAAT 493

  chr2_156105005_   2153 GGATCAAATACCTAACTATAAGACCTGAAATGCTCAAACTAACAGACAAA 2202
                               ? v      v i     v  i   ivv v     vvi   vi  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_156105005_   2203 AATATATTGGAAACACTTCAGGACATTGGTCTGGGAAAAGATTTTATGAA 2252
                           i   vv? v  vv    iv   v    vi i  v  v i   iv ii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_156105005_   2253 TAAGACCTCGAAAACACAGGCAACAAAAGCAAAAATAAACAAATGGAATT 2302
                           v   vi i   i    i          v       i i    v i i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_156105005_   2303 ATGTCAAACTAAAAAGCTTCTGCACAGCAAAGGAAATAATCAACAGAGTG 2352
                         vii     v v    i   i  ii vv       v iv     v i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_156105005_   2353 AAAAGACAAAGTCTTGAATGGGAAAAAAATATTTTTAAACTACTCATTTA 2402
                                  vviviv        i    -     vi   ii ivi  i i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTG 742

  chr2_156105005_   2403 CCAGGGCATTAATGTCCAGAACGTACAAATAATTCAAACATTTCAACAGC 2452
                         vi i  v i vi i       ii  i   v  i  vv   vi    i ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_156105005_   2453 AAAAAATC------TCCGATTAAAAAATGGGCAAGTGATCTGAACACACA 2496
                              iv ------i  i   ?            iv   i    i v   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_156105005_   2497 TTTCTC--AACAAAATATATAAATGGCCAATAAATATATTTTAAAAATGC 2544
                               --  v  i     i             ii i  vv-   i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGC 891

  chr2_156105005_   2545 TAAACATCACTAATATT 2561
                          v       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (153 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.20 (22 / 10)  


1109 27.81 10.34 1.25  chr2_156114886_156116436.rev      499  1059 (492)    L1M4_orf2#LINE/L1      297   908 (0)  

  chr2_156114886_    499 TTAATGGGACAAAATAGAGAATCTAGATATCAACTCAGTATATTAA--AT 546
                          i     i i i   v    i  i   v  v   i  -  i   v --i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTATGGT 345

  chr2_156114886_    547 TAATCAATTTTCAACAAAGCTACAAAGGTAACTCAATAAGTAATGAATA- 595
                         i   ii      i    i v i v   iiv i     ii v  v     -
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_156114886_    596 --TTTTCAACATATGTTGTTAAAATAATTCTATATTT-C-TGTTAAAAAA 641
                         --         v   v  i iii i  i vv   ?ii- -  iv   i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_156114886_    642 TAAACTGTGACCCTTACCTCAG--TGTATACACCAAATTAAATCAAG-TG 688
                          i  v vv     i       v--ii      v-       v    i-  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAA-AAATTAACTCAAAATG 494

  chr2_156114886_    689 AAT-----------ATATCAAAACCAAAAACTGCAATCCTCCTGGAAGAA 727
                         i  -----------  i -  i v v      ii  vv   i i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_156114886_    728 A-TATAAAAAAGAGGCTAAGTGGCTTTAGGTT-GGCAAAATTATCTTTAA 775
                          -i   ii?ivi iv  vv   i i  i    -     viv v    - i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AG 592

  chr2_156114886_    776 AGAGAACTCAAAAAGCATGA-TAATAAAATAAGAGACTGATAAGTTGGAA 824
                          v vi  v v       ii -i  i    v  i i iv     i     v
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_156114886_    825 TTCATCCAAAT-AAAAA----------------GACAC------AAAAAT 851
                               v    -     ----------------     ------i   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_156114886_    852 GAAAAGACAAGCCACATTTTGGAAGAAAATATTTGGAAAACATACAATCT 901
                                   v     vvv   i            v   v    i -   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA-TCT 741

  chr2_156114886_    902 GTCAAAAGACCTTTAACTAGAATATGTAAAAAATGTTCACCATTTGATAT 951
                          vi  ii   i v  v i       i    i  ivi i  v i ii   -
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA- 790

  chr2_156114886_    952 GTAAACTAACAAA----CCATTGAAAAAATAGAACAAAGA--TTG----G 991
                         i    vvi     ----   v v?      i i-     i--   ---- 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGG-CAAAGGATTTGAATAG 839

  chr2_156114886_    992 ATACTTCACCAATGAAAATATAAAGATGACTAATAGCCACACGAAT-GAT 1040
                          i i   v    v   i     v i   i i    iv    i   v-   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_156114886_   1041 GCTTAACATTATTCAGCAT 1059
                            i     i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (94 / 59)
Gap_init rate = 0.04 (24 / 612), avg. gap size = 2.71 (65 / 24)  


3167 27.14 1.33 0.33  chr2_156148899_156155164.rev     4876  5774 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156148899_   4876 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCGTGAAAAT 4925
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156148899_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATACCCATCAAGC 4975
                            v     v     iv i  i           i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_156148899_   4976 TACCA----CTTTCTTCACAGAA-TTGGAAAATAGTACTTTAAAGTTCAT 5020
                          v   ---- i  i  ii     -   iv  iiv - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chr2_156148899_   5021 ATGGAACCAAAAAAGAGCCCACATTGCTAAGTCAATCCTAAGCCAAAA-A 5069
                               viiv  ii  v  viv  v  i  iv     i i ivv i  - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_156148899_   5070 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5119
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_156148899_   5120 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGATCA 5169
                                i   i    ii         i iv ii i              
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_156148899_   5170 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTA 5217
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_156148899_   5218 TCTGATCTTTGACAAGCCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5267
                         vi    i  i      vv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_156148899_   5268 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5317
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_156148899_   5318 AAACTGGATCCCTTCATTACACCTTATACAAAAATCAATTCAAGATGGAT 5367
                           ii    i    v v i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_156148899_   5368 TAAACACTTAAATGTTCGATCTAAAACCATAAAAACCCTAGAAGAAAACC 5417
                         i ? v  i       vv  v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_156148899_   5418 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5467
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_156148899_   5468 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5517
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_156148899_   5518 TAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5567
                         i   v    i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_156148899_   5568 GGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGACAAA 5617
                          i     i   iv            v  ii   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_156148899_   5618 GGGCTAATATCCAGAATCTACAATGAACCCAAACAAATTTACAAGAAAAA 5667
                           i  vi          v  i  v    i vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_156148899_   5668 AACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCT 5713
                         i    ----   v  i?    i     i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_156148899_   5714 CAGAAGAAGACATTTATGTAGCCAAAAGACACATGAAAAAATGCTCATCA 5763
                          vi       i  vi vi i     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_156148899_   5764 TCACTGGCCAT 5774
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.14 (15 / 7)  


2660 26.44 2.33 1.44  chr2_156184998_156190335     3947  4846 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156184998_   3947 TGGAAAAACATTCCATGCTCAAGGATAAGAAGAAC-AATATTGGTACAAT 3995
                               i i  i     i   v    vi     vi-       v  vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156184998_   3996 GGCCATACTGCTCAAAGTAATCTGCAGATTCAATGCTATTTCTATCACAA 4045
                            v     v i    v i    i         i  v  ii      v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_156184998_   4046 TACCAAAGACATTCTTCAGAGAATTAGAAAAAATCT-ATTCTGAAATCCC 4094
                          v   ivvi v  i  iiv    v v  v  i--  -  i  i    i v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_156184998_   4095 TATGTAAACAAAAAAGAGCCTGAATAGCCAACACAATCCAAAGCAAAAAG 4144
                             v   iiv  ii  v  v          v      ivi iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_156184998_   4145 AACAAAGTCAGAGGAATCACACTACCCAACTTCAAAATATACTAAATGGC 4194
                                 ii     v       v     i       iv     v vi  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_156184998_   4195 TACAGTTTCCAAAATGGCATGTGGCATGGGTACAAAAATAGACACATAGC 4244
                               vvi   i ii --     i iv  i i  ii       i    v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAG--TGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_156184998_   4245 CCAATGGAAAAGGATGGAGAACACAGAAATAATGACATCCACCTACAGCC 4294
                         i        v  i  v    iiv         vvv   v  ii  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_156184998_   4295 AACTGATCTTTG-CAAAGTTGACAATAACAAGCAATGGAGAAAGAACTCC 4343
                           i    i  i -   i v  v   v v  vv      i       ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_156184998_   4344 CCATTTAATAAACAATGCTGGGACAATTGGCTAGCCATGTGCAGAAGACT 4393
                          iv  i  i   iii           i   v  ?   ii    i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_156184998_   4394 GAAACTGGACTCCTTCCATTA-ACCATATACAAAAATTAACTCAAGATGC 4442
                            ii     i   v  - i -                       i   v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACC-TCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_156184998_   4443 ATTAGAGACTTAAGTATAAG-GCCAAAACCAATACAAAC-CATAGAAGAA 4490
                           i ?    i   i i    -  i     i -  -    - v        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTA-TA-AAACTCTTAGAAGAA 543

  chr2_156184998_   4491 AACCTAGG---AAATACCATTGTGAACATTGGCCTTGGAAATAATTTAT- 4536
                            v    ---    -- v i    v -    vi v  v   ii   v -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT--CTTCGTGACC-TTGGGTTAGGCAATGGTTTCTT 590

  chr2_156184998_   4537 -GACTAAGTCCCCAAAAGCAATTGCAACAAACACACAAATTGATAACTAG 4585
                         -  -  v v v         vvv        viv v    v     v v 
  L1M4_orf2#LINE/    591 AGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_156184998_   4586 GTACT-AATTAAT-TTAAGAGCTTCGGCATGGCAAAAGAAACTACTAACA 4633
                          -   -v  i  v-    i i   iv iiivv    i  v    ii  v 
  L1M4_orf2#LINE/    640 G-ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_156184998_   4634 AAGTAAACAAGCAACCTACAGAATGGGAGGAAGTATTTACAAACTATGCA 4683
                             i  v ii     i            i  i     i    ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_156184998_   4684 TCCAACAACTGTCTAATATCCAGAATCTATAAGGAAATTTTTAAAAATCA 4733
                           ii i  vv v  vi          v     i   -i i   v  v   
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCA 787

  chr2_156184998_   4734 ACAAGAAA----CAAATAACCCTATC-AAAAATGGGCAAAGAACATGGAC 4778
                          i  v   ----          v  i-              i iv  i i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_156184998_   4779 AATAACTTCTC-AAAGAAGGCATGCATGCAGCCCAAAA--ATATGAGGAA 4825
                          ivv i     -       ii  i  viii   v v  -- i    ii i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_156184998_   4826 GTGCTCATGGTCACTAATCAT 4846
                         i      vvi   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (136 / 100)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.42 (34 / 24)  


1867 27.33 3.18 6.99  chr2_156219171_156221527.rev      932  1875 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156219171_    932 TGGAGAGACATACAGTGTTAATGAATTGGAAAACTCAACAA-GTAAAAAT 980
                             i   i  v vi    v   i       i   i  i v-  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156219171_    981 GTCAATTATCT----ATTTATTCACAGGAAGATATAATACAATTTCTATC 1026
                          v    vv  i----   v  ii    ----  vi  ii    ii     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAG----ATTCAACGCAATCCCTATC 96

  chr2_156219171_   1027 AAAATTCCAGCAAAATATTTTTTAGATATAAACAGGTTTACTTTAATGCT 1076
                              i     vivv v    vi   v  vi   i i v iii   vii 
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_156219171_   1077 TACATGGCAAGGTAAAGGAACTAGAATAGCAAAAA-ATTTTTGAAAAAGG 1125
                         i i    v  v i  i   v i        v    - v i         i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_156219171_   1126 A---TAAAGATGAAGGGGTTATTATTCATTCTGATTTCAAATTTCTTATT 1172
                          ---i    v  i   iv i i- i -- i ii        v--    i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCAC-ACT--TCCCAATTTCAAAA--CTTACT 241

  chr2_156219171_   1173 ATAGAGCTATAGTAATCA-TACTGTGTGGTATTGGTAGAGAGAGAGTCGT 1221
                          i i     i        -v  v        i   i v ii  v  v i 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_156219171_   1222 ATAAATCAGTTGAACAGAAGAGAGAGCCCAGATAATAACCCCATACAAAT 1271
                            i    i v   i    vv     i     -     v        vv 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGA-AATAAACCCATACATTT 340

  chr2_156219171_   1272 ACAGACAACT-ATTATTGACAAATGTGCAAAGGG-GTTCAATGCAACAAA 1319
                          ii v   i -   v i     iv    v   iv-i       viiv  i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_156219171_   1320 GAT-GTCTTTTCAACAAATAGTGTTAGAACAATTTGATATCCATAGACAA 1368
                         i  -               i   i i i    i v    ?   i vi   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_156219171_   1369 AAAAGACAAAAAAAAAAAAAAAAAAAAACTCGAGCTGAATCTCATGCTTT 1418
                           i ------------------ vi  ii v  v ivv i    ii iv 
  L1M4_orf2#LINE/    441 AAGA------------------ATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_156219171_   1419 ATCTAAAAAAAAAAAAAAAACAACTAACTCAGAATGGATTGTTAATTTAA 1468
                           vi     --------------i       i       ii?vi ii   
  L1M4_orf2#LINE/    473 ATACAAAAA--------------TTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_156219171_   1469 CAGTAAAACATAAAGCTGAAAAACTTTTAAAAGATGCCATAGGAA-ATAT 1517
                         vv    i vv    i  iv      i   i    viv      ?i- v  
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_156219171_   1518 CTTTAAGACCTAGGATTTGCTAAAGAATTCTTGAATACTTTTGAGATCTT 1567
                            iiv     v  i  v vi  v iv     ii   ----   v ----
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA----TGACA---- 600

  chr2_156219171_   1568 GGGCTTCCAAAATAATGATCTACAAAAGAAAAAA-AAATCAAGAAATTGG 1616
                         ------      vv ii v v             - i  ----       
  L1M4_orf2#LINE/    601 ------CCAAAAGCACAAGCAACAAAAGAAAAAATAGAT----AAATTGG 640

  chr2_156219171_   1617 TCTTCATTAAGATTGAAATATTTTTCT-CTGTGAAAGACATGCTCTGTTA 1665
                         v      i  i   i   - i    v -  vii  i    ----  i i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACA----CTATCA 685

  chr2_156219171_   1666 AGATGGTGAAAATACAAGCAACA--ATGGGA-AAAATATTTGGAAACCAC 1712
                            vi       v    v v   --      -          v   i  i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_156219171_   1713 CTGTAAGACCAAGAAATCATATCCAGAATATGCAATAAAGTATCGAAACT 1762
                         v i vv  iv i i v ii            ii  vi  v v iiv    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_156219171_   1763 CAACACAAAGAGAATAAACAACTAACTTTCAAAAATAGACAAA-----TG 1807
                            i vv  i ii i   i   iv v  ?-      i i    -----  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTG 834

  chr2_156219171_   1808 A-CAGTTACTTCATCAAAGAA--TACGTAGATGACAAGTAATCACATGAA 1854
                          -i  vi i   vi       --  iii i   i v i   v        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_156219171_   1855 AAG---TTTTATATTATTTACCAT 1875
                            ---i iv i  i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (154 / 100)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 3.20 (96 / 30)  


3019 27.46 1.79 0.45  chr2_156252507_156257122.rev     3229  4124 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156252507_   3229 TGGAAGAACATTCCATGCTCACGGATAGGAAAAATCAATATCGTGAAAAT 3278
                              ii i  i     i   i    v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156252507_   3279 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3328
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_156252507_   3329 TACCAATCACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTGAAAGTTCA 3376
                          v   iiii i  i  ii     -   -- v  i  - iiiv   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_156252507_   3377 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 3426
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_156252507_   3427 AACAGAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3476
                             i  i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_156252507_   3477 TACAGTAACAAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGACC 3526
                                 iv  i    ii        vi iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_156252507_   3527 AATGGAACAGAACAGAGCTCTCAGTAATAATACCACACATCTACAACCA- 3575
                                i    iv   vvii   v     vv   i    i  iiii  -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_156252507_   3576 ------TCTGACAAACCTGACAAAAACAAGAAATGGGGAAAAGATTCCCT 3619
                         ------ ii     ivv  v   i v  vvv          ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_156252507_   3620 GTTTAATAAATGGTGCTGGGAAAACTTGCTAGTCATTTGTAGAAAGCTGA 3669
                         v  i  i              v    v v  ?i  iv  i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_156252507_   3670 AACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGATT 3719
                          ii    i    v   i   i v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_156252507_   3720 AAAGACTTAAATGTTAGATCAAAAACCATAAAAACCCTAGAAGAAAATCT 3769
                          ?    i       v   v v     i      vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_156252507_   3770 AGACA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 3818
                           i?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_156252507_   3819 ACACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATCTCAT 3868
                                     vvi          vv   i v  i    v   ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_156252507_   3869 TAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAACA 3918
                         i   v v  i i   i   i vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_156252507_   3919 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGATAAT 3968
                          i     i                 v       vii ivi         v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_156252507_   3969 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAACTTA-CAAGAAAA 4017
                           i  vi          v  i         vv    -  i -i  v    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAAA 796

  chr2_156252507_   4018 AAACAA----CCCCACCAAAAAGTGGGTGAAGGATATGAACAGACAATTC 4063
                          i    ----   v ii?    i    ii      v    i     v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_156252507_   4064 TCAAAAGAAGACATTTATGCAGCCAACAGACA-ATGAAAAAATGTTCATC 4112
                           v        i  vi viii     i ii  -       i   i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_156252507_   4113 ATCACTGGCCAT 4124
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


 506 22.50 0.83 3.33  chr2_156277303_156280646     1664  1783 (1561)    L1M4_orf2#LINE/L1        1   117 (791)  

  chr2_156277303_   1664 TGAAAATACATTCTGTGTTCATGGATTGGAA-ATGTAGTATTGTTAAAAT 1712
                           i   v i  i ii                - iv  i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156277303_   1713 GGCAATATCCCTTCACATTGATCTGAAAATTCAATACAATCTTGATCAGA 1762
                                - i ii  v        iv i      ii     iiv    i 
  L1M4_orf2#LINE/     51 GGCAATA-CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_156277303_   1763 TTTCCAGTTGATTTCTTTTTT 1783
                         v i    i  ---i       
  L1M4_orf2#LINE/    100 ATCCCAGCTG---CCTTTTTT 117

Transitions / transversions = 3.50 (21 / 6)
Gap_init rate = 0.03 (3 / 117), avg. gap size = 1.67 (5 / 3)  

3319 19.74 4.26 0.26  chr2_156277303_156280646     2078  2852 (492)    L1M4_orf2#LINE/L1      103   908 (0)  

  chr2_156277303_   2078 CCAGTTGACTTTTATGCAGAAACAGA---GTTGATCCTAAAATGAATAGG 2124
                             i  v     v        iv  --- i            vv   v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_156277303_   2125 GAAACGTATATGACCTAGAATAACCAAAATAATTCTGAAAA----GAACA 2170
                             i i viv    i      i      i   ii      ----     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_156277303_   2171 AAATAAGAAGACTAAAAATTCTCAATTTTAAAACTCAATACAAAGCTGCA 2220
                           i vi  i    v v v   i      i      i v         i  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_156277303_   2221 AGAATCAAAACAGAGTTGTACTAGCATAAGAATCAACATACAGAACAAAG 2270
                         iv      i    v  v     i       i  vi     i   v   v 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_156277303_   2271 GAACTGAATTT-GAGTCTAGATTGAAACCCAT-TATTT-TGATGAATTTA 2317
                            iv     v-     i   vvv        -i    -  i v    v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_156277303_   2318 TTTTCAACAAAAATGACAAGACAATCTAATGGAGAAAAAATAATCTTTTT 2367
                              i    iii  v      v  ii     i    i    i      -
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT- 401

  chr2_156277303_   2368 CCACAA-TGATGCTGAGTCAACTTGATACCCACATAAGAATGAATGAAGT 2416
                          v    -  i     i v     v    ?      ivi  v         
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_156277303_   2417 TAGAAAAATATCTCACATCATATACATAAATTAACTCAAAATTTATCAAA 2466
                          i  vvvv  i      i        v               vv    ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_156277303_   2467 GACCTAA-TGTAAAAGCTA------TAAAGTTCTTAGAAGAAAAATTAAG 2509
                                -     i     ------    ii             vv  i 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_156277303_   2510 CATAAATCTTAGTGACTTTGAATTAGGCTCTGGTTTCTTAGGTATGACTC 2559
                         ?i        v     i   ii      vv           i      v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_156277303_   2560 TAAAAACACAA-CAACAAAA------ATAGACAAATTGGAGCTTATCAAA 2602
                         i    i     -        ------     i        vi i      
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_156277303_   2603 TTTAAAA--TTTTGCTGAATTAAAAGATACCATCAGGAATATGAAAATGT 2650
                         v      --     -  vv i   i  i  i    i   vi      vii
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_156277303_   2651 AGCCCACAGAATAGGAAAAAATATTTACAAATTATATATTCA-----GGA 2695
                          i          i   i         i     i      iii-----   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_156277303_   2696 TTTGTCTTCAAAATATATAAAGAATTCTGATGACTCAATGGTAAAAGGAC 2745
                         i    v i  i             i   v ii       ii     i   
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_156277303_   2746 AAATAACCCAAATAAAAAATGGGCAAACGGTATGAATAGACATTTCTCTA 2795
                                    v ?             v i v                i 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_156277303_   2796 AGGAAGATATTCATATGAACAATA-GCACATGAAAAGATGCTCAGCATTA 2844
                          i        v  v   iv     -                   i   i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_156277303_   2845 CTAGTTAT 2852
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.48 (89 / 60)
Gap_init rate = 0.02 (15 / 806), avg. gap size = 2.33 (35 / 15)  


2631 25.59 3.95 1.58  chr2_156285215_156287457.rev      865  1751 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156285215_    865 TGGAAATATATCCCATACTCATGAATTAGAAGAGTCAA----ATAAAAAT 910
                               v         ii     i   i     v i  ----i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156285215_    911 GATTGTACTGCCCAAAGCAATCTATAGATTCAATGCAATTCCTATCAAAA 960
                          iivi    v      vii     i        i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_156285215_    961 TACCAACATAAGTATTCACAAAATTATTTAAAAAACT-ATTGTAAAATTC 1009
                          v   i vvvvv v  ii  i  --   -i v  i  -  iv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATT-GACAAGCTGATCCTAAAATTC 147

  chr2_156285215_   1010 ATATAGAACCAAAAAAGATCCCAGA-TAGCCAAAGCAACCCTAAGCAAAA 1058
                             i   viiv  ii  -      -        i   i i i ---   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGA---AAA 193

  chr2_156285215_   1059 AGAAAAA-AAAATTAGAGGCATTACATTACCTCACTT-AAAATTATACTA 1106
                             i  -   i  i    vv i   i v  iv i  -    i -     
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTA 242

  chr2_156285215_   1107 CAAAGCTATGGTAACCAAAAAAGCATGGTACTGGTATAAAAGTAAATGCA 1156
                                 ii    i   i v  ii         i    iii  i iii 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_156285215_   1157 TGGAACAATGGAACAGTA--GAGAACCCAGAAATAAAATCAAGTACTTAA 1204
                          i  v        i  v --    ii           vi  vii i   v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_156285215_   1205 AACCAACATATCTTTGACAAAGCATAC-AAAAC-AT--AAGTTGGAGAAA 1250
                         iii   ivv  i  i     i -i i -  i  -  --  --   i    
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAA--TGGGGAAA 389

  chr2_156285215_   1251 ----------TTCAATAAATGGTGCTAGAAAAATTGGATAGCCACAGGTA 1290
                         ----------     i          i i v  i      ?     v i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_156285215_   1291 GAAGAATAAAATTGGATCCCTATCTCTTACTATATACAAAAATTAACTCA 1340
                         i      i  i     i     i   vi  i                   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_156285215_   1341 ACATGGATTAAAGACTTAAATTTTAGACCTGAAGCCACAAAAAATTCTAG 1390
                          v      i ?    i     v v   v  i  i i i    v- ii   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAG 538

  chr2_156285215_   1391 AAGAAAACCTAAGAAATACTCTTCTGGATGTTGGCTGCGGGAAAAAATTT 1440
                                 v  i ?ivv v     vv  iv    v vv  v  viiv  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_156285215_   1441 ATGGCTAAGACCCCAAAAGCTAATTCAACAAAAAGAAAAATGAATAAATG 1490
                         v i v  v   v        vv vv        ii      ii      v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_156285215_   1491 GAAACTATAT--AAACTAAAAAGCCTCTG-----CACAGCAAATAATCAT 1533
                          i -  vi  --   i      - i i  -----  v  v v iv    v
  L1M4_orf2#LINE/    639 GGA-CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_156285215_   1534 CACAGTAAATAGACAACCTACAGAATGGGAGAATATATTTGCAAATTATG 1583
                         v v   i  v        i              v            i  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_156285215_   1584 CATGTGACAAAAAACTAATATCCAGAATCTACAAGAAACTC----AAATC 1629
                         i  v   i  iii   vi          v  i  ii     ----  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_156285215_   1630 AGCTAGAAAAAAACAAATGATCTCATCAAAAAGGGGGCAAAGGACATAAC 1679
                          iiv v     i      i i iv  i?    iv          iv i v
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_156285215_   1680 TAGGCATTTCTAAAAATAAGATATACAAGTGGACAAGAAACATATGAAAA 1729
                            i       vv   v           i   v   v  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_156285215_   1730 TATGCTCAATACCACTAATCAT 1751
                         v        i i  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (138 / 85)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.13 (49 / 23)  


1241 25.94 0.58 0.58  chr2_156352502_156355670.rev      147   493 (2676)  C L1M4_orf2#LINE/L1   (87)   821   475  

C chr2_156352502_    493 ACAAAAATTAACTCAAAATGGATTATAAACCTAAATGTAAAACACAAAAT 444
                                                i ? i            i vvi    i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

C chr2_156352502_    443 TATAAAATTCCTGGAAGATAACATGGGAGGAAATCTACATGACCCTGGGT 394
                                i  i i     v     i  ? v      v i     i     
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

C chr2_156352502_    393 ATTGCAATGATATTTTAAATACAACCTCAATGGCATGATTCATGAATGGA 344
                         vvv      i v i   i   ii  vi   vi   ii viv ii  -i  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA-AGA 623

C chr2_156352502_    343 AAAAAT-GATAAATTTGATTTAATTAAAATACAAAACTTCTTCTCTGTCA 295
                               -        v  i  v  i     vv       i viv  -   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT-TCA 672

C chr2_156352502_    294 AA-AACCCTGTCAAGAGAATAAAAAGACAAGCCACAGACTAGGAGAAAAT 246
                           -i  v  i      i i i         v       v i         
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

C chr2_156352502_    245 ATTTGTAAGAGACATATCTAATAAAGCACTGTTGTCTAATGTATTCTAAA 196
                              i  ivv i      i    i v   vv i  i ivi   viv  i
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

C chr2_156352502_    195 AACTCTTAAAGCTCAACAGTGAGAAAATGGACAACCCAATTTTAAAATG 147
                                 v i     i i i i  i iii i         ?v      
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

Transitions / transversions = 1.72 (55 / 32)
Gap_init rate = 0.01 (4 / 347), avg. gap size = 1.00 (4 / 4)  

2474 24.27 4.85 4.13  chr2_156352502_156355670.rev     1401  2224 (945)    L1M4_orf2#LINE/L1       16   845 (63)  

  chr2_156352502_   1401 TGTTCATTAATTGGAAAAATTAATATTGTTATATCCGTCTACCGAAAGTC 1450
                                vi       i v            ------------ii v v 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTA------------AGATGGC 53

  chr2_156352502_   1451 CATACTACCCAAAGCATCCATATTAAGGTGATCTGTAGATTAAGTGCAAT 1500
                         v     v      ---------  -----     ii     v ii     
  L1M4_orf2#LINE/     54 AATACTCCCCAAA---------TT-----GATCTACAGATTCAACGCAAT 89

  chr2_156352502_   1501 CCCTATCAAAATTCCAA-TGACGTTTTCACTGAGATAGAAAAAACAATCC 1549
                                     i   i-  v v    ii v  i  v  v  ivii    
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_156352502_   1550 TACA-TTCATATAGAA---CAAATGGTTGCCA-AATAGACAAG-CAATCT 1593
                           v -       i   ---   iv ii--   -     v   i-      
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCT 187

  chr2_156352502_   1594 TGAGAAA-AAGAACAAGACTAAAGGCATCATACT---------------- 1626
                            i   -        iii ii   vv   i   ----------------
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_156352502_   1627 -ACTACAAAGCTATAGTAGTCAAAACAACACGGTTCTGGCATGAAAA-AA 1674
                         -            i    i    i   iiii   v       i ii - i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_156352502_   1675 ACACATAGACCAATGGTTTAGTATAGAAATCCTAGTAATAAATCCAGGAA 1724
                            i     i      vv   v  v  i vi i  v      i   viv 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_156352502_   1725 TTTACAATCAATTGATTTTAGACAAAGATGCAAAACGACGCA--CAATAG 1772
                             iii            v     i i   v  --   -  --    i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAA--GAC-CATTCAATGG 384

  chr2_156352502_   1773 GACAAAGATTTTCTCCTCAGTAACTGCTGTTGGGAGAAC--GATATCCAC 1820
                          iv  ii  vv   ii   ii  v  v  i     v   --    ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_156352502_   1821 ATGTAGAAGAATGAAATCAGA----TACTT-ATATCAGTTGCAAAAATCA 1865
                            i i         i ii  ----   i - i i  vv i       i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_156352502_   1866 AATCAAAATGGATTAAAGACTTACATGTAAAACCTGAAATGGTAAAAATA 1915
                          v           i ?    i  v      i v  i   ivi     v v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_156352502_   1916 CTAGAATAAAGCATAGGGGAAAATCTTCATGACAATGGTCTGGGCAGTGA 1965
                         i     v   i      ? v        i    vv   vi i    i  i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_156352502_   1966 TTTTTTGAGATATGACCCCAAAAGCACAGACAACAAAAGCAAAAACAAAC 2015
                            i  -         v           ii         v     i i i
  L1M4_orf2#LINE/    585 TTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_156352502_   2016 A----GGATAACATCAAACTACAAAGCTTCTGCACAGCAAAGGAAATAAT 2061
                          ----   ivv       v vv   i   i  ii vv       v iv  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_156352502_   2062 TACCAAAACGAAGACATGATGCATGGAATGGGAAAATTTATTTGCAAAGC 2111
                         i vv   ii   i v ii iv  ii        i  vv          v 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_156352502_   2112 ATACATCTGATAAGGAGTTATTACTCAAAATATATAAGGAACTCAAACAA 2161
                            i           iii vv  ii  i         i      vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_156352502_   2162 CTCAATAGCAAGAAAACCAA-AATCCAAATTCAAAAAATAGGCAATAGAC 2210
                                ii  i  i  v  -  i    -- i?      i     vi  i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAA--TTWAAAAATGGGCAAAGGAT 831

  chr2_156352502_   2211 CGGAATAGACATTT 2224
                         iv            
  L1M4_orf2#LINE/    832 TTGAATAGACATTT 845

Transitions / transversions = 1.68 (123 / 73)
Gap_init rate = 0.03 (22 / 830), avg. gap size = 3.36 (74 / 22)  

 291 15.15 0.00 1.52  chr2_156352502_156355670.rev     2614  2679 (490)    L1M4_orf2#LINE/L1      844   908 (0)  

  chr2_156352502_   2614 TTCTTAAAATAAGACATAAAAATGGCCAATAAGTACATGAAAAAAATGCT 2663
                             iv   v    i   v              i         i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr2_156352502_   2664 CACCATTGCTAACCAT 2679
                           v   ii????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (6 / 4)
Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1)  


2263 26.48 9.14 1.31  chr2_156369136_156370995      527  1368 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156369136_    527 TGGAAAAGTGTATCAGGTTCATGAACTGGGTGACTCAATATT---AAAAC 573
                               ii i vi  v       i i   iv    i      ---  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156369136_    574 ATCATTTTTTTCCTTAAATTGATGTCTAGATCTAATGCAATCCAAACTAA 623
                         iv  v vi ii  --        v vi    ii  i       vv ii  
  L1M4_orf2#LINE/     51 GGCAATACTCCCC--AAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_156369136_    624 AATACCAGAAGACTTTTTTGTAGTATTTATTAAGTTGAATCTAAAATTAA 673
                            v    vv v        i  v v  ivi   i   vi        v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_156369136_    674 -ATAGAAATGCAAATAACCTAGAAAAGCCAAAAGCAATTTTGAAAGATAA 722
                         -  i         ivi   i    v        -    i      i v  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAA 197

  chr2_156369136_    723 ---CAATGTTGGAGCACTTA--------------------TACTATAAAG 749
                         ---   v       v   i --------------------     i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_156369136_    750 CTACAGTAATCAAAACAGTGTGTTTTTTGT-TAAG-ACACACATATGTGT 797
                                      i        v vi v i-    - i v      ivi 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_156369136_    798 CAATGGAACA-AATT-AGAGTCTAGAAAAAAACC---ACAATTATGAC-- 840
                                 i -    -      i     v     ---   v     ii--
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_156369136_    841 ----ACTTTTGACAAAAACGT--AGGCAATTCCATGGAGAAAAAGTAGTT 884
                         ---- i   i     iiii i--  i v    v    i    i i    i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_156369136_    885 TTTTCAACAAATAGCCTTAGAACAGCTGGATATGCATATG---------- 924
                                     i ivi i i   i       ?v  i   ----------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_156369136_    925 AACTTCAATTCTTAATTCACACAACAAACAAAATTTAGCATGAAATAGAA 974
                           v  vi ii i  vi      v i v      v   i vii    i  v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_156369136_    975 CATAGACCTAAAAATTAAAATTATAAATATAAAATTTCTAGAAGAGAACA 1024
                           ?         vi v i ii  v  v       i ii       i    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_156369136_   1025 CAGTAGGAAATCTTTGCACACTTGGACTACGCAATGATTTACTAGGCAAG 1074
                         i  v? v       i iivv     ii  v      i   vi   ii v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_156369136_   1075 CCACAAAAAGCTGAGTCCATAAAAGGAAAATATTGATACATTTTACTTTA 1124
                         v   v      vv iv v i     i    -  v    v   vv    i 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCA 646

  chr2_156369136_   1125 TCAAAATTTATCTAAGAATCTTT------CAG------CTCTTAAATAAA 1162
                                 -----  i  ii   ------  i------  v i  iv  i
  L1M4_orf2#LINE/    647 TCAAAATT-----AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_156369136_   1163 TGGAAAGGGAAGCCAAAAACTGGGAAAAAATATTCACAATGCATAAA-CT 1211
                           i    iv  v   v i v     i        ii   vv    v -  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_156369136_   1212 GATGAAAAGCTTATATTCAGAATATAAAAAGCATGTTTACATATCAGTTA 1261
                            i iiii   i   i         v    v ivi     vv   i v 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_156369136_   1262 CAAGAAGACAA----CTCAATT-AAAATTGGGAAAATGATTT-------T 1299
                         i  i       ---- i     -    v    v   v     -------i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_156369136_   1300 ATTTTTCACAAAGGATGGTACACAAATGAATGATGAATACAAGAAACAGT 1349
                             i  -     i - i  i       ivii  i ii   v    vii 
  L1M4_orf2#LINE/    842 ATTTCTC-CAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_156369136_   1350 GTTCAACGTCATTAGCAAT 1368
                          i     i   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (135 / 85)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.67 (88 / 24)  


1721 26.96 2.82 1.41  chr2_156426477_156428073      471  1108 (489)    L1M4_orf2#LINE/L1      262   908 (0)  

  chr2_156426477_    471 ATATTATGGTAATCACAAACAAAAAAGACACATAGACCAATGAAACGGAA 520
                          i v i     v vi  v - ii v     i     i     i  ii   
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATA-AGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_156426477_    521 CAGAAAGCACAGAAATAAATCCATTAAACTATTGTCAATTTATCTTTGTC 570
                         iv  i  iv          i    vv vi   v       v  i  i v 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_156426477_    571 AACAGTTCTGAGA--ATACAGACCGGAAATGGGATAGTCTCCT-AGTAAA 617
                           vi  v ii   --  v  ivvv     -- i       ii - ii   
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAA--GAATAGTCTTTTCAACAAA 408

  chr2_156426477_    618 TGTTATTGAGAAAACTGGATATCTATATGCAAAAAAAATTAAATTGGATC 667
                           v ii  i  v         ? i i        i  - v  i     i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACC 457

  chr2_156426477_    668 TTTATCTCA----GTATTAAAAAATCAACTTAAAATGAATTAAAAGCATA 713
                         ii  i    ----i   vv      i    i      i  i ? ii v  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_156426477_    714 ATCACTAAAGCTTAAAACTGTAAAACTACTAGAAAAAAACAGAGGG--AA 761
                          viiiv i    -      i       vi     i      v   ?--  
  L1M4_orf2#LINE/    508 AATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_156426477_    762 AACTATACAACATTAGTCTGGGCAATGAATTTTCCGATTTGACACCCATC 811
                          v  viiii  v  i vi i       iv  i iv   v       v -v
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA-A 605

  chr2_156426477_    812 AGAGCTGGCAACAAAAGTAAAAATAGATAAATGGGATTACATAACAAT-A 860
                           vi vi          v              v   i v   v v   - 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_156426477_    861 AAAAGTTCTACAGTACAAAAAAAAATA--AACAAAATGAATAGAAAACCT 908
                             v  i iiiv v    ii v v  --  v   i    v   v    i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_156426477_    909 GTGGAATTAAAGAAAGTATTTGCAAGACATACATCTGATAAGGAATTAAT 958
                         iii    vii     i         iv    i           i i vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_156426477_    959 ATCCAAAATATATAAGGAACT--TAATCAACTC--TA-TAGAAATACAA- 1002
                              i         i     --  --      --  -  i   v    -
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAAAAGACAAA 803

  chr2_156426477_   1003 CAACCTGATTAAGAAATAGTGAAAAAACCTGAATAGACATTTCTCAAAGG 1052
                         i    ii   ? i    i vv   ii ii                v  i 
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_156426477_   1053 AAAACATACAATTGGCTAACAGATATATGAAAAAAATGCTCAACAATATT 1102
                           i i      v    i  i iii i       i -         vi ??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZ 902

  chr2_156426477_   1103 AATCAT 1108
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.71 (106 / 62)
Gap_init rate = 0.03 (17 / 647), avg. gap size = 1.59 (27 / 17)  


2666 25.93 4.76 1.93  chr2_156503060_156505140      707  1589 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156503060_    707 TGAAAAAACATCCTGTGCTCAGGGGTTGGCAGAATCAATATTGTTAAAAT 756
                           i   i i    ii  i   v  i    v   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156503060_    757 GACCATACTCCCTAAAGCTAGAT--ACAGATTCAGTGAAATTGCTATCAA 804
                          i v        i   -- v   --         ii v   iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_156503060_    805 AATACCA------------------------AAG----TCAGAAAACTCA 826
                            v   ------------------------   ----  vv    i   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_156503060_    827 CCTGGAACCTACAAG--ACCCTGAATAGCCAACCCAAGTCTAAATGAAAA 874
                         iv     v- i    --    v          vv   vii i  vi i  
  L1M4_orf2#LINE/    149 TATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_156503060_    875 GAATAAAACTGGAGACAACACATTAGCTGACTTTAAATTATACGATAAGT 924
                            i   ii     ivvv    i vv ii i  i   viv   v i  iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_156503060_    925 TCATAGTAACCAAAATAGCACGGTACTGGTATAAAAATAGACACATAGAT 974
                         ii i     i   i i  iii        i    ii       i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_156503060_    975 CAATGGACCAAAATAGGGAACCCAGAAATAAAGCCATATACCTATGACCA 1024
                                vi i   v i  ii           v     i ii    ii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_156503060_   1025 ACTGCTCTTTGACGAAGTCAACTAAAAACGTACACTGGGGAAACAATACC 1074
                          i  v i  i   i i vii- i  i v i v  v        v    vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_156503060_   1075 CTATTCAACAAATTGTGCTAGGAAAATTGGATTGTCATATGCAGAAAAAT 1124
                           v          v     i   v  i     v?i  i     i  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_156503060_   1125 GAAACTGGACCCCTATTTCTCACCATATACAAAAATTAACTCAAGGTG-A 1173
                            ii          ii  v                        ii  - 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_156503060_   1174 TTAGACATTTAAA-ATTAAACCTGAAACTATGAAATTCCTAAAATAAAAC 1222
                          i ? v ii    -i v i v  i       i   i  i  i  v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_156503060_   1223 CTAGGAG-AAA-CTTCTGGACATTGACCTAGGCCAAGAATTTATGACCAA 1270
                         v    ? -   -    vv   v   ivi     v v iv  iv iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_156503060_   1271 AACTTCAAAAGCACAAGCAACAACAACAACAAAAGTAGACAAATGGGACT 1320
                         i  vi                  -  v  --   i    i    v     
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAA-AAGAA--AAAATAGATAAATTGGACT 643

  chr2_156503060_   1321 TCCTCAAG--TGAAAATGCTTCTGCACAGCAAAAGAAATAATCAGCAGAG 1368
                           v    i-- i    --   i  ii vv    i  v iv    iv i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_156503060_   1369 TAAATAGGTAATCTACAGAATGGGAGAAGATATTTCCAAACTATGCATCT 1418
                          i  v  ii  i i              i      v    ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_156503060_   1419 GACAAAGAACAAATACCCAGATTCTCCAAGGAAGTCAAACAACTCAAGAA 1468
                           i  i i  vvi  i     v v vi  i   v  vv         v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_156503060_   1469 GAAAAAACAAAACAAATAACTTCATTTAAAAATGAGTAAAAAAACATGAA 1518
                         v     i----         iiv   ?       i i   ii vi-    
  L1M4_orf2#LINE/    792 TAAAAAG----ACAAATAACCCAATTWAAAAATGGGCAAAGGATT-TGAA 836

  chr2_156503060_   1519 --GACACTTCTTAAAAGAAGACATACACATTGCCAACAA--ACATGAAAA 1564
                         --    i    iv        i     v  v     i  --         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_156503060_   1565 AACTTTAAACAACATCAATGATAGA 1589
                         i ivi ---        ????????
  L1M4_orf2#LINE/    887 GATGCT---CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (142 / 83)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.95 (59 / 20)  


1295 30.34 10.25 1.26  chr2_156509135_156510838.rev      501  1212 (492)    L1M4_orf2#LINE/L1      133   908 (0)  

  chr2_156509135_    501 CTGATTCTAAACTT-ATATTAAAATATAAATGACCAGAAATAGCCATAGC 549
                              i     v  -    vi    ii  iv    vii        v i 
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_156509135_    550 AACCTT---AAATAAAAACAAAGATGAAGGATATACATTACCAGATTTCA 596
                           i   ---   v  i       v  i    ivi   i v  vi      
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_156509135_    597 TAGTGTATTGTAAAGCTTTAGTAGTTAAGACAGTGTGGT-TTGATGTAGT 645
                         v iiv  i ii      vi    i i             -i  iii  iv
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_156509135_    646 TATAG---TTTAAAACACCAAAGCA--ACTAAGAATTAAGAGATAGGCC- 689
                         v    --- v  i v  viii ii -- i i   i iv   i   ii  -
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_156509135_    690 ---------TGCTTA------------------TGCCATGACAATTTTGT 712
                         ---------  v i ------------------     v   v   ivi 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_156509135_    713 GAGCATAAGA-----TTGTTTAATAAATAATGCTGGACAAATTCTATATC 757
                          i v -    -----i v  i  i    ii      ivv  i vv   ? 
  L1M4_orf2#LINE/    383 GGGGA-AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_156509135_    758 CATATGAATAAAAATGGACTTTAAAATAGATTGTATAC--TAGACATAGA 805
                           i   v v  i    i v  vi vvivv iivi i  --  v   v i 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_156509135_    806 GTAATTTAGGATAGTTTATAGTTGCAAATGTGAAATGTAAAACTATTATG 855
                         v   i i ii  i v i ?  vivi      i i vv         v vi
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_156509135_    856 TTTCCAGAAAAAAATATAAGACAATATATTTATGACCTTGGTGGAGACAA 905
                         i iii    i    i   i ?vv v  v  ii         vvv  i   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_156509135_    906 ATATTTCTTTAAAAGGGCACAAAAA--ATTAGCTCTAAAAGAAAAGGTTG 953
                         vvi      vi v v i   v    -- iv   vvi         ii v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_156509135_    954 CTACATTGGAATTCATTTTAAAAT-AAATAATTTTGTTCATCAGAAGATA 1002
                         v  v      v     i--     -   v v      v v   i i  i 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATC--AAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_156509135_   1003 TAATAAAAAGAGTGAAGAGGTAGGCCACAGATTAGGAGAAGATAT--GCA 1050
                         iv  v  i i      i  ii iv       v i      i    --   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_156509135_   1051 ATGCATATATCTAA---------------CATAATATATAAAGAACTCCT 1085
                          vv         i ---------------  v                i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_156509135_   1086 AAAAATAAAATAGAAAAAGACAGCCAAACCAGTTTTTTTAAAAAATGGGC 1135
                          v  v v  vv v         ivi  v   i  ?-----          
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTW-----AAAAATGGGC 824

  chr2_156509135_   1136 AAAGAACTCAAAATGGCAC----CCAAAAAACACTATTCATTTGGCCAA- 1180
                             i i ii  vv i  i----     i  v -   v  vv       -
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGA-TATACAAATGGCCAAT 873

  chr2_156509135_   1181 ---CATATGGAAAGATACTTAACATCATTAGTTAT 1212
                         ---  i   i      i  i       ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (119 / 93)
Gap_init rate = 0.02 (19 / 776), avg. gap size = 4.32 (82 / 19)  


 357 28.83 0.00 3.60  chr2_156541099_156542785      376   486 (1201)    L1M4_orf2#LINE/L1        1   107 (801)  

  chr2_156541099_    376 TGTAGAGATATGCCATGAGCATAGGTTGGAATGCTCAACATACTAAAGGT 425
                           v i      v     vv   i i      vi  i  i  vv v   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156541099_    426 GTCAGTTCTATCTAAATTGATCTGTAGGTTTACTGCATGCAGGTCTTATT 475
                          v  i v  vi i          ii  i  i ---- i   ivi i   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCA----ACGCAATCCCTATC 96

  chr2_156541099_    476 AAAATTCCAGC 486
                              i     
  L1M4_orf2#LINE/     97 AAAATCCCAGC 107

Transitions / transversions = 1.67 (20 / 12)
Gap_init rate = 0.01 (1 / 107), avg. gap size = 4.00 (4 / 1)  

1656 26.26 4.45 3.73  chr2_156541099_156542785      501  1197 (490)    L1M4_orf2#LINE/L1      207   908 (0)  

  chr2_156541099_    501 TAGAGTGAATCACTCTACCAGATATAAGGGCCTACTAGATAGCTA--ATA 548
                          i   -  v    v  v  vi  v v iii i     v v     --i  
  L1M4_orf2#LINE/    207 TGGAG-GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_156541099_    549 ATCAATGTTATGTGGTATTGACAGAGGGGCAGACACACAGATCAATGGGA 598
                              viivi       i  i  v i  ii     i i          i 
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_156541099_    599 CAGAATAAAGAGCCCAGAAGCAGACTAATATAAATATGCTAAACTGATTT 648
                         i     vi    i      ii i  iv   i vv    v v  i      
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_156541099_    649 T-AACAAAGGTGCAAAAGCAATCCAATGGAGAAAAGTAAGCCTTTTCAAC 697
                          -i    i     v  ii v  i      i    iivv  i         
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_156541099_    698 AAATTGGGCTGGAACAACTGTATATCGATAGTCGAAAAAATGACACCCAA 747
                             v v     i       v   ? v i vv i   i     viiivi 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_156541099_    748 CTTAAATCTCACATTTTATATGAAAATTAACTCATAATGGATTACAGATT 797
                          iivv i      iiv    ii            v       i ?   ii
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_156541099_    798 TAAAACTTTAGAAAAAGTTAAGAAAAAAATACTTCCAGAAAAAAA-ACAG 846
                             -- v  --- i  i   i vv v  v   iii    i    - i  
  L1M4_orf2#LINE/    506 TAAA--TGTA---AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_156541099_    847 GATAAAAATATTTGGGATCT-AGGCCAGGCAAAAATTT-TTAGA-ATGAC 893
                          ?-iv    v  i v  i  -i  ii      vii   -     -     
  L1M4_orf2#LINE/    551 GN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_156541099_    894 AACAAAAGCATAAATTATAAGAGAAAA------CAAACTGGACGTTATCA 937
                          v        i  iiv i  i      ------i   i     v i    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_156541099_    938 AAATTAAAATCTTTGAT-CTGTAAAAGCTCATGTGAAGA---TGAAAAGA 983
                                  v    vi -  vi   i vivv i v    ---        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_156541099_    984 CAGACTAGAGACTGGGAGAAAATACATGCAAACCACATAACAGACCAAAA 1033
                           iv i v   v            iv      i  i   v v  i-----
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT----- 744

  chr2_156541099_   1034 AAAAAAAAAAAAAGACA-GTATCTGGAATATACAAA-AACTCTCAAAACT 1081
                         ---------  ii   v-     ii       i   -      i v    
  L1M4_orf2#LINE/    745 ---------AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_156541099_   1082 GAAGAATTTTTAAAAA----------TTAATTACAAATTAGGAAAAATAC 1121
                         v  v   ----     ----------ii    ?v   v i  v   iv i
  L1M4_orf2#LINE/    786 CAATAAT----AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_156541099_   1122 ATGGAAAGATATTTGCCTGAAAGAA--TAGACAAATGCAAAATAAGCAAA 1169
                         v  i v   i    vi i-      --  v       vvv        v 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCC-AAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_156541099_   1170 TGAAAAGATGCTCAACATAATTAGCCAT 1197
                                           v ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (104 / 75)
Gap_init rate = 0.03 (20 / 702), avg. gap size = 2.85 (57 / 20)  


2868 27.80 0.70 0.47  chr2_156561987_156570603     4754  5609 (3008)    L1M4_orf2#LINE/L1        3   860 (48)  

  chr2_156561987_   4754 GAAAAACATTTCATGCTCATGGATAGGAAGAATCAATATTGTGAA-ATGG 4802
                             i i  ii    i        v      v i        v  -    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_156561987_   4803 CCATACTGCCCAAAGTAATTTATAGATTAAGTGCTATTTCCATCAAGCTA 4852
                          v     v      v i  i  i     v ii  v  ii i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_156561987_   4853 CCATTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTTATA 4901
                            vivi i  i  ii     v v  v  i--  - iii    v  i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chr2_156561987_   4902 TGAAACCA-AAAAGAGCTTGTATAGCCAAGACAATCCTAAGCCAAAATAA 4950
                           i  vii-  ii  v iv v        i      i i ivv i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_156561987_   4951 CAAAGCTGGAGGCATCACAATACCTGACTTCAAACTATACTACAAGACTA 5000
                              i      vv     v v  ii i      viv        ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_156561987_   5001 CAGTAACCAAAACAGCATGGTACTGTCC--AAAACAGAGATATAGACCAA 5048
                               i   i    ii        v v-- ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_156561987_   5049 TGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTGCCAACATCC 5098
                              i    iv   ivii         vv   i    i iiviv  vii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_156561987_   5099 GATCTTTGATAAACCTGGCAAAAACTAGCAATGGGGAAAGGATTCCCTAT 5148
                            i  i  i  ivv  v   i v vvv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_156561987_   5149 TTAACAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAA 5198
                          i           i     v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_156561987_   5199 CTGGATCCCTTCCTTACTCCTTATACAAAAATTAACTCGAGATGGATTGA 5248
                         i    i    v   i  v  v                 i i      ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_156561987_   5249 AGACTTAAACATAAGACCTAAAACCATAAAAACCTTAGAAGAAAACCTAG 5298
                             i    ii     v       i      vi             v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_156561987_   5299 GCA-ATACCATTCAGGACATATACATGGGCAAAGACTTCATGACTAAAAC 5347
                          ?i- v i -   iv   v vvivv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_156561987_   5348 ACCAAAAGCAACAGCAACAAAAGCCAAAATTGACAAATGGCATGCAATTA 5397
                                   vv           vv     v  i    v v iviv  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_156561987_   5398 AACTAAAGAGCTTCTGCACAGCAAAGGAAACTATCATCAGAGTGAACAGG 5447
                           v v  i i   i  ii vv       v       vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_156561987_   5448 CAACCTACAGAATGGGAGAAAAGTTTTGCAATCTGTCCATCTGACAAAGG 5497
                              i                vv       viii vi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_156561987_   5498 GCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAA 5547
                         i  vi          v  i  i     ivv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_156561987_   5548 TCATACAACCCCATCACAAAGTGGGCAAAGGATATGAACAGGCACTTCTC 5597
                         -  v i     v  i?v   i            v    i  i  i     
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_156561987_   5598 AAAAGAAGACAT 5609
                         v        i  
  L1M4_orf2#LINE/    849 CAAAGAAGATAT 860

Transitions / transversions = 1.29 (132 / 102)
Gap_init rate = 0.01 (8 / 858), avg. gap size = 1.25 (10 / 8)  

 225 20.34 0.00 0.00  chr2_156561987_156570603     5913  5971 (2646)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr2_156561987_   5913 AAAGAAGACATTGATGTGACCAAAAAACATATGAAAAAAGGCTCATCATC 5962
                                 i  vv vi  i    v  i  i       i v     v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_156561987_   5963 ACTGGTCAT 5971
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.00 (6 / 6)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  

2464 25.93 7.18 2.43  chr2_156561987_156570603     7262  8125 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_156561987_   7262 AAAGACACTCTATGTTCATG-ACTGGAAGACTTTATATTATTAAAGTGAC 7310
                              i ii i         - i          v     i    ii  i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_156561987_   7311 CATACTGCCCAAAACAATCAACAAATTCAATATAAATCTTAGCAAAATAC 7360
                         v     v      vii   v   i      iii  vi i  v      v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_156561987_   7361 CAA-TGTCATTTTTCACAGACATTTTTAA----ATCCTAAAATTTGCATG 7405
                           i-  i -     ii    v   vvi  ----           iii   
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_156561987_   7406 GAACCAAAAGAGAGCCTGAATAGCAAAAATAATTCTGAGAAAGAGGAACA 7455
                            viiv   i  v  v       v    i   ii   i     i     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_156561987_   7456 AAGCTACAGGTGTCACATTACCTGACTTCAAAAGTACATTAAAAGGCTAT 7505
                            i iv   vv     i v  ii i       v -i i  v  i    i
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTAC 251

  chr2_156561987_   7506 AGTAACCCAAACAGCATGGTTTTGTTATTAAGAAAAATAAAAGAAACATA 7555
                              i v i    ii    vi  vi  ----  ii   ---  v i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCAT----AAGGATA---GACATATA 294

  chr2_156561987_   7556 GATCAATGTAACAGAATAGAGAATCCAAAAATCAATTCATGCATATA--- 7602
                                 v  i     v    i    i    v  ii   i   v  ---
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_156561987_   7603 ----------------------------------CACTGAGGAAAGGCAT 7618
                         ----------------------------------  v  i      i-  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-AT 393

  chr2_156561987_   7619 A--CTCTTCAATAAATGGTACTAGGGAAGCTTGATATCCACATGCAGAAG 7666
                          --  i     i       i  i  iv i  v    ?         i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_156561987_   7667 AATGAAACTAGGACTCTATTTCTCACTATATGTAAAAGTGAAGTCAAGAT 7716
                               ii i iv i   ii  v   i    ii    i v  v    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_156561987_   7717 GGATAAAAGACTTACGTGTTCAACCTGAAACTATGAAATTAATACAAGAA 7766
                             v ?    i  vi   vvi v  i       i   i vv  v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_156561987_   7767 AACATAGGGA-AAACATTTGAGGACATTAACCTAGGAAAAGACTTTATAG 7815
                                 ?i-   iv  i -v   v  iivi    v  v ii  iv   
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_156561987_   7816 CTAAGACCTCATAAAGCACAGACAACTAAAACAAAAATAGACAAATGGGA 7865
                         v  v   vi  -        ii    v   iv         i    v   
  L1M4_orf2#LINE/    593 ATATGACACCA-AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_156561987_   7866 CTACAGTACT-CTAAAAACTTCTGCAAAGCAAAGGA-AC-------AGAG 7906
                           v  vi vv-i         i  iivvv       -  ------- i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_156561987_   7907 TAAAGAGACAACCTGTTGAATGGGAGAAAATATTTGCCCACTATTCATCT 7956
                          i  i        iiiv                    vv ii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_156561987_   7957 AGTAAGGAATTAATATCTGGAATATATAAGAAATT--TA-AAC--AGTAG 8001
                         ii     i i vi    ii          ii  i --  -   -- i  i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_156561987_   8002 CCTAAAGCCAAATGATCACATTCAAAAGTGGGCAAGGACAAGAATATTTC 8051
                         ivv    v     i i vv   ?    i       i i-------    v
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG-------ATTTG 834

  chr2_156561987_   8052 TCAAAAGA-ATTTTTCAAAAGAAGGCATA-AAATGGCCAGCAGGCATATG 8099
                         --  v   -    i  v       ii   -         ii i   i   
  L1M4_orf2#LINE/    835 --AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_156561987_   8100 AGATAATGCTCAATATCATTAATCAT 8125
                          i vi        i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (141 / 79)
Gap_init rate = 0.03 (23 / 905), avg. gap size = 3.61 (83 / 23)  


3215 26.40 0.66 0.77  chr2_156647408_156655575     4873  5781 (2387)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156647408_   4873 TGGAAGAACATTCCATGCTCATGGGTAGGAGGAATCAATATCGTGAAAAT 4922
                              ii i  i     i      i v   i  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156647408_   4923 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCACCAAGC 4972
                            v     v     iv i  i           i  v     i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_156647408_   4973 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5019
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_156647408_   5020 ATATGGCACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5069
                               v viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_156647408_   5070 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5119
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_156647408_   5120 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5169
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_156647408_   5170 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5217
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_156647408_   5218 TACCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5267
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_156647408_   5268 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5317
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_156647408_   5318 TGAAACTGGATCCCTTCCTTAACACCTTACACAAAAATCAATTCAAGATG 5367
                             ii    i    v   i -    v  i        i  i    i   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATG 494

  chr2_156647408_   5368 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5417
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_156647408_   5418 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5467
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_156647408_   5468 AAAACACCAAA-GCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5516
                          vi        -   vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_156647408_   5517 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5566
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_156647408_   5567 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5616
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_156647408_   5617 AAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAA 5666
                           i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_156647408_   5667 AAAAAACAAACGACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAC 5716
                            i -    ii    v  i?    i     i     iv    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_156647408_   5717 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5766
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_156647408_   5767 ATCATCACTGGCCAT 5781
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  

2233 22.10 9.86 4.37  chr2_156647408_156655575     6876  7676 (492)    L1M4_orf2#LINE/L1       64   908 (0)  

  chr2_156647408_   6876 AAACTGATTTATAGATTCAATGTAGCTTCAATCAAAATCCAAATAGGCCT 6925
                            i    i  i        i i iiii v          v ii-v    
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCT 112

  chr2_156647408_   6926 TTT--GTAGATATTG-CAAGATGATTCTAAAATGTATGTG-AAATGCA-G 6970
                            -- i   v    -    v    i       vi  i  -       - 
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_156647408_   6971 TGACCTGTGTAATAACCAAAATAATCTTTAAAATGAAGAACAAATCTGGA 7020
                         v    ii- -    i      i      v    v          vi    
  L1M4_orf2#LINE/    163 GGACCCA-G-AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_156647408_   7021 GAACTTACACTGTCCTATTTCAAGAATTACAACAAAGCTACAGTAATCAA 7070
                          i   i     vi  v       i v    v                   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_156647408_   7071 GACATTGTGATACTGACA-AAGAATAGACATTCAAATCAACGGAATGGAA 7119
                             v    i     i  -   i        vi i     i     i   
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_156647408_   7120 ---ATAATTCAGAAATAAAAGTAATACATGTGTCATAAACTGATTTTTGA 7166
                         --- v i i          vvi -     v i vi v  i       i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCA-TACATTTATGGTCAATTGATTTTCGA 359

  chr2_156647408_   7167 CAAAGGTGTCAGGGTAATTCAACAGAGTAA-AATAGTCTTTTCAACAA-T 7214
                            i    i  i iiv      ii i v  -                 - 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_156647408_   7215 GGTTCTGGAACAGCTGGATATGTTTATACAAGAAAAAAAATAAACCTTGA 7264
                            v    i   i       ?vi----   v v    i   i  vi v  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCC----ACATGCAAAAGAATGAAGTTGGA 455

  chr2_156647408_   7265 CCCTTACTACACATCATTTGCAAAAATTAACTCAAAATCAGCCATAGAGC 7314
                            i   iv    i   v i                  viii  ?   v 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_156647408_   7315 TAAATGTAGCAGTTAAACCTATAAAACTTCTAGAAAAAAAAAAAAAAGAA 7364
                                 iv  i    v          ii     i    v --------
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-------- 547

  chr2_156647408_   7365 AAACAGGAGAAATTCTTTGTGACTTTATGATAGTTAA-AGTTTTTTTGAT 7413
                         ---i   ? v  v    i     i  iv v   vi  -i    i  v   
  L1M4_orf2#LINE/    548 ---TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_156647408_   7414 ATTATTCCAAAACCTAGATTCATATAAGAAAAAAATAAAGGTACATTGTA 7463
                           v iv      v vvi viv i v         -  i --  v    v 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGA--TAAATTGGA 641

  chr2_156647408_   7464 CTTCTCCCAAAATGAAAAACTTTT------------ACTCTGTTAAAAAA 7501
                             -vi      v          ------------  v  i i  i   
  L1M4_orf2#LINE/    642 CTTC-ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_156647408_   7502 A-AAAAAAA----------------AGAAAAACTTTG-AGA----ATATG 7529
                         i-i    i ----------------      vv    - i ----    v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_156647408_   7530 TGAC---GGATC---ATCT----------------TCTTACAACTCAATA 7557
                            i---   ii---   i----------------               
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_156647408_   7558 ATTGGAAAACAATCAATCTCATTTAAAAGTTGAGCAAAAATGGGCTAAAG 7607
                           vii  i    vi  i iv   ?    -----------      v  i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAA-----------ATGGGCAAAGG 829

  chr2_156647408_   7608 ACTTGAGTAAATAGTTTCCT------GATG----AATTGCAAACAAGCAC 7647
                          i    i  i i v  ii i------   i----   v  v  i      
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_156647408_   7648 ATTAAAAAAATG-TCAACACCATTGTTTAT 7676
                           -i    i   -      i  ????????
  L1M4_orf2#LINE/    880 AT-GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (107 / 66)
Gap_init rate = 0.04 (31 / 845), avg. gap size = 3.68 (114 / 31)  


 383 31.94 10.43 3.37  chr2_156665468_156667090      509  1131 (492)    L1M4_orf2#LINE/L1      242   908 (0)  

  chr2_156665468_    509 ATAAAGCTATACAAATT----CTTAGTGTGA-ATTTGTTGAAGAAATATA 553
                          i       i vv   i---- --      i- i v ivv   i -  v 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGAC--AGTGTGGTACTGGCATAAGGA-TAGA 288

  chr2_156665468_    554 CACATAAATCAGTGAAATAGAATAAAGAGTCCAGGGAGATAAATGCCTAT 603
                           i   i    i  i        vi         -- i     iv v  i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAG--AAATAAACCCATAC 336

  chr2_156665468_    604 -------GTCAGC--ACTT---AAAAATTTG----AATCATTTA-----G 632
                         -------    ii-- i  --- v  ivv  ----i i    i ----- 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_156665468_    633 AAAAAATTGACTATTTTATAAACGGCCATATAATAATTGACTATT----T 678
                            i   v v  v  iv i   i  ivv ivi i  i  iv  ?i---- 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_156665468_    679 GGAAAATA-TGAAGTTCAATTCCATATATGCATGCAACATACCTAAAAGT 727
                          v    v -       vi ii  -  iv -  ii v i    --    i 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCC-TACCT-CACACCATATAC--AAAAAT 482

  chr2_156665468_    728 ATATTTCAGAGAGGTATAAAGAC--AAATGTAAAAAATTTAAAGATACAA 775
                         -  vi   i iv  vvi ?    --        i i--i    iv  i  
  L1M4_orf2#LINE/    483 -TAACTCAAAATGGATCAWAGACCTAAATGTAAGAG--CTAAAACTATAA 529

  chr2_156665468_    776 CAC-ATTAGA-GAAAAAATTGAAATA--TTTTAATAGTCTTGAAATTAA- 820
                         v  -v     -     v  v i?i  -- i  vi iii    ii-   i-
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGG 578

  chr2_156665468_    821 -AAAGCCTTTTTAAATAAATTGCAATCTGAAATCCA-----TAAAGAAAA 864
                         -  v vi  i   i   ---  vv i vi  iiv  -----i   ii   
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATA---TGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_156665468_    865 CATTTGACAGATTTGGCT------AATTTTTATACTTTGGTATTTTCAAA 908
                         v v v  i i   v i  ------  v  vv v     v  ii  iv  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_156665468_    909 GATCTTATGGCCAAAGATAAAAAACAAGGCACAAACTAGAA-AAAATATT 957
                           ivi   vivv    vv    i    vv    i v i i -        
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_156665468_    958 TTCAA--CATATGT--AATAGTAAAAATTTTTATAATCAAAATATATATC 1003
                          v   --     i --i   -- iii i  v   --i  i        vv
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATA--AGGGACTTGTAT--CCAGAATATATAAA 771

  chr2_156665468_   1004 TACCTCCTACAA------AGCAAAAAGAATAAACAATGTAAC-AGAAAAT 1046
                         v v   i     ------ ii       -i   i  ivi  i-?i     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAAT 820

  chr2_156665468_   1047 GAGAAAAGAATAAGAGAAAGCAACTC---AGAGAAGAAATATGATTAGCC 1093
                          i v    i  vv  iv ii  vi  --- i      v   ii v i   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_156665468_   1094 AATAAATACACAGAAATGTCATCAACCTCACTAAGATC 1131
                              ii   iii   vi vv     v   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (117 / 78)
Gap_init rate = 0.05 (35 / 667), avg. gap size = 2.46 (86 / 35)  


2782 26.48 1.40 3.66  chr2_156671990_156674466.rev     1059  1987 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156671990_   1059 TGGAAAAACTTTCCATGTTAGTGGATAGGAATAATTAGTATTATTAAACT 1108
                               i iv i       vi     v    v v   i    i    iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156671990_   1109 GGTCATACTGCCCAAAGCAATTTACAGATTTGAAGCTATTCCTATTAAAC 1158
                           iv     v      vii  i        ii v  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_156671990_   1159 TACCAACATTATTTTTCACAGAATTAGAAAAACACATTCTTAAATTTATA 1208
                          v   i vviv     ii     v v  v  i vv  i  v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_156671990_   1209 CAGAACCAAAAAAAGAGCCTGAATAGTCAAAGTATTCCTAAGCAGAAAAA 1258
                         ii   viiv  ii-  v  v      i    ii v  i i iv ii  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_156671990_   1259 ACAAAGCCAGAGG-CATACACTACTGGACTTCAAACTATGTCACAAGGTT 1307
                               iii    - vi     v ivi i      viv iii    i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_156671990_   1308 ACAGTAACCAAAACAGAATGGTACTGGTACAAAAATAGACACATAGACCA 1357
                                i   i    vi         i i  ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_156671990_   1358 ATGGAACAAGTTAGAGAACTCAGAAATAAAGCTACACACCTAAAACCATC 1407
                               i iiv v    iii          v i i   ii  viii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_156671990_   1408 TAATCTTCAACAAAGTTGAACAATAACAAAGTTGTCAACAAAGTTGACAA 1457
                          i  i   i    i ---------------  - i   -------   v 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG---------------GT-GCCAA-------GACCA 376

  chr2_156671990_   1458 TAACAAAAAAATGGGGAAAGGAC--TCATTATTCAATAAATGGTGCTGGG 1505
                          v-   -----         i i--  -  -     i             
  L1M4_orf2#LINE/    377 TT-CAA-----TGGGGAAAGAATAGTC-TT-TTCAACAAATGGTGCTGGG 418

  chr2_156671990_   1506 ATATCAGGCTTGCCATATACAGAACATTGAAACTGGACCCCTTACTTTCA 1555
                          i v v  v v?   i  i  i  v v    ii         vv  iv  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_156671990_   1556 CCATATACAAAAACCTACTTAAAATGGATTGAAGACTTACATGTAAGACC 1605
                                      iiv   i         ii?    i  v        v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_156671990_   1606 TAAAGCTATAAAATTCCTAGAAGAAAACCTAGGAAATACTCTTCTGAATA 1655
                             i        i  i           v    ?ivv v     vvi iv
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_156671990_   1656 TCTGCCTTGGCAAAAATTTCAT-GATG-GAGTCTCCAAAAGCAATTGCAA 1703
                          iv vi v     vii    v -   i-  -- v         vvv    
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGA--CACCAAAAGCACAAGCAA 616

  chr2_156671990_   1704 CAAAAATAAAAATTGACAAGTGGGATCT-ATTAAACTAAGCAGCTTCTGC 1752
                              iv      v  i  i v   ii -  i   v v iv i   i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_156671990_   1753 CAAGCAAAAGAAACTATCAACAGAGTAAGCAGACAACCTACAGAATGGGA 1802
                         vvvv    i  v        v i   i iv        i           
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_156671990_   1803 GTCAATATTTGCAAACTATGCATCCAACAAAGGTCTAATATTCAGAATCT 1852
                          vv            ii  ii   ii i  i  v  vi   i      v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_156671990_   1853 ATAAGGAATTTAAACAAATCAATAA----AAACCAACTGACCCCATT-AA 1897
                             i   i ivv    v       ----  iv   v i    v   -  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_156671990_   1898 AAGTAGGCAAAGGACCTGAACAGGCACTTCTCAAAAGAACATATACAGGT 1947
                           i i         ii    i  i  i     v      v       ii 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_156671990_   1948 GGCCAACAA--ACATGAAAAAATGCTCAACATTCCTAATCAT 1987
                               i  --         i           iv????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.76 (47 / 17)  


1345 27.76 0.94 2.35  chr2_156723888_156727814      908  1332 (2595)    L1M4_orf2#LINE/L1        4   422 (486)  

  chr2_156723888_    908 AAAAACATTCCATGCTCATAGATTGTAAGAATCAATATTGTTAAAATAGC 957
                            i i  i     i    i     v    v i           i  i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_156723888_    958 CATCCCGTCCAAAGCAATCTACAGATTCAACATTATTCCTATCAAACTAC 1007
                         v  v ivi     vii               iiv  i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_156723888_   1008 CAA-TGTCATTTTTCACAGAACTGGAGAAAACACATTCTAAAGTTCATAT 1056
                           i-  i -     ii     v v  v  i- vv  i     i       
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr2_156723888_   1057 GGAACCAAAAAAGAGCCCAAAGAGCCAAAGCAATCCTCAGCAAAAAGAAC 1106
                             viiv  ii  v  vi  v       i     i v iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_156723888_   1107 AAAGCTGGAGGAATCACATTACTTGACTTCAAACTGTATTATAAGGCTAC 1156
                             i       v     i v iii i      viv  i  i  i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_156723888_   1157 AGTAAACAAAACAGCATGATACTGGTTTGAAAAAAGCCCAGACACATAGA 1206
                              v   i    ii  i      iv i ii -----i     i     
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGA-----TAGACATATAGA 296

  chr2_156723888_   1207 CCAATGAAACAGGATAGAAAGCCCAGAAATAAAGCTGCACACCTACAA-C 1255
                         i     i  i  i  v  i  i           v iii   ii  iii- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_156723888_   1256 AATTTGAACTTTGGCAGAGTCAACAAAAATAAGCAATAGACAAAGAAC-- 1303
                             -  vi  i i  ii viiv   i vi vv    i iv      i--
  L1M4_orf2#LINE/    347 AATT-GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_156723888_   1304 TCCTTATTCAAAAAATGGTGCTGAAAAAA 1332
                           i  --    v           ii v  
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAA 422

Transitions / transversions = 2.11 (80 / 38)
Gap_init rate = 0.02 (8 / 419), avg. gap size = 1.75 (14 / 8)  

1810 26.36 1.98 1.48  chr2_156723888_156727814     1371  1977 (1950)    L1M4_orf2#LINE/L1      239   848 (60)  

  chr2_156723888_   1371 ACTACAGGGCTACAGTAACCAAAACAGCATGGTACTGGTACTAAAAAACA 1420
                               ii          i   i    ii         i i--  ii i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATA 286

  chr2_156723888_   1421 GACACATAGACCAGTGCAACAGAATAGAGAGCCCAGAAATAAGGCTGCAC 1470
                             i     i  i  v  i     v     i          iv iii  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_156723888_   1471 ACCTACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATAGGG 1520
                          ii  iiii  vi    i  i     ivv  v   i v  vv    i   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_156723888_   1521 AAGGACT---CTTTATTCAATAAATGATGCTCGGATAACTTGTTAGCCAT 1567
                           i  v ---    --    i     i    v   i    v v  ?   i
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_156723888_   1568 ATGCAGAAGATTGAAAGTGGACTCCTTCCTCATACCATGTACAAAAATCA 1617
                              i    v    iv     i   v     i     i         i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_156723888_   1618 ACTCAACATGAATTAAAAACTTAAAAGTAAAACCCAAAACTATAAAAACC 1667
                               v   i  i ? i  i    v    i v i            vi 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_156723888_   1668 CTGGAAGATAACCTAGGCAATACCATCTT-G-GACATAGGAACTGGCAAA 1715
                         i i     v   v    ?i-  v-     - -   v v  iviv     v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNG-TAA-ATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_156723888_   1716 GATTTCATGG-CAGGAAGCCAAAAGC-CATCACAACTAAAACAAAATTTG 1763
                          i    v i -i v  vi        -  -vi    v   iv    v v 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAG 631

  chr2_156723888_   1764 ACAAACGGGATATAATTAAA-TTAAAGAGCTTCTGCACAGGAAAA-ACAA 1811
                          i   iv   iv v  i   -     i -   i  ii vvv   i-   v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACAC 680

  chr2_156723888_   1812 TAATCAATCAAGTAAACAGAAAACCTACAGTATAGGAGAAAATTTCTGCA 1861
                           -    vv    i  v   v    i    v  i         v i    
  L1M4_orf2#LINE/    681 TA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_156723888_   1862 AACTATGCATCTGACAAAGGTCTAATATCCAGCATCTATAAGAAACTGAA 1911
                           ii  ii      i  i  v  vi       v  v     ii    vvv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_156723888_   1912 ACAAATCTGCAA-GAAAAG-CAAACAAACCCATT-AAAAGTGGACAAAAG 1958
                             v  vii  -i     -    i  v  v   -    i   i    i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_156723888_   1959 GCATGAACAGACACTTTTC 1977
                         iiv    i     i  i  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTC 848

Transitions / transversions = 1.53 (95 / 62)
Gap_init rate = 0.03 (17 / 610), avg. gap size = 1.24 (21 / 17)  

1806 28.57 2.49 0.00  chr2_156723888_156727814     2759  3360 (567)  C L1M4_orf2#LINE/L1   (0)   908   292  

C chr2_156723888_   3360 ATAGACCAATGGAACAGAATAGAGATCTCAGAAATAAGACCACACATCTT 3311
                              i        i     v    vii         iv   i    i v
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

C chr2_156723888_   3310 CAACCATCTGATCTTCGACAAACCTGATGAAAACAAGCAGTTGGGTAAAG 3261
                         iiii  vi    i        ivv  vii i v  vv  i v   v  ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

C chr2_156723888_   3260 ATTCTCTATTTAATAAATGGTTCTGGGTAAACTGGCTAGCCATATGCAGA 3211
                           vv   v  i  i       v     vv      v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

C chr2_156723888_   3210 AAATTGATACTGTACCCCTTCCTTACACATTATACAACAACTAACTCAAG 3161
                          i v   vii  v      v   i    vv       v  i        i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

C chr2_156723888_   3160 ATGGATTAAAGACTTAAATGTAAAACCCAAAACTGTAAAAACCCTAGAAG 3111
                               i ?    i         i v i      i     vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

C chr2_156723888_   3110 AAAATCTAGGCAATAACATTCAGGACATAGGCATGGGCAAAGATTTTGTG 3061
                             iv    ?ivv  iv   iv   v v  vv i     v i   iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

C chr2_156723888_   3060 ACAAAAATATCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGA 3011
                         ivv vi i i        vvv          v      v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

C chr2_156723888_   3010 TATAATTAACCTAAAGAGCTTCTACACAGCAAAAGAAACTCTCATTAGAG 2961
                         iv v  i  vv v  i i   i iii vv    i  v   v   vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

C chr2_156723888_   2960 TGAACAGACAACCTATGGAATGGGAGAAAATTTTTGCAATCTATCCATCT 2911
                             v        i ii              v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

C chr2_156723888_   2910 GACAAAAAGCTAATATCTAGAATCTACAAGGAACT--TA-AATTTA-CAA 2865
                           i  iiii  vi    i     v  i  i     --  -  i i -i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

C chr2_156723888_   2864 GAAAAAAACCA----CCCCATCAAAAAGTGGG-----GATGTAAACAGAC 2824
                         v     i  v ----   v  i?    i    -----   v i  i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chr2_156723888_   2823 ATGTCTCAAAAGAAGACATTTATGCAACCCACAA--ACATGAATAAAAGC 2776
                           v    v        i  vi viiii  v i  --       v i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

C chr2_156723888_   2775 TCAACATCATTGATCAT 2759
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (91 / 77)
Gap_init rate = 0.01 (6 / 617), avg. gap size = 2.50 (15 / 6)  

 264 12.33 5.48 4.11  chr2_156723888_156727814     3363  3435 (492)    L1M4_orf2#LINE/L1      835   908 (0)  

  chr2_156723888_   3363 AACAGACATTTTTCAAAAGAAGACATA--ATTGCAGCCAACAAGCATATG 3410
                           i        i  v        i   -- v  --     i     i   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATG 882

  chr2_156723888_   3411 AAACAAAT--TCAATATCACTGATCAT 3435
                            - i  --    i    ????????
  L1M4_orf2#LINE/    883 AAA-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.05 (4 / 74), avg. gap size = 1.75 (7 / 4)  


1781 24.93 1.40 7.00  chr2_156733379_156735083      501  1214 (491)    L1M4_orf2#LINE/L1      235   908 (0)  

  chr2_156733379_    501 ACTTACTATAAAA-TAGAGTAATTAAGACAGTGTGGTATGGGTGAAAGAA 549
                                 i   i-  v      i              iv  iiv   i 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_156733379_    550 TACAGAAATCAATCAACAGAGCAGAATACAGAACCCAGAAACAGACCTAT 599
                           v v v  vi     ii  ii     vv   ii       i i   i  
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_156733379_    600 ATGTAAACAAAGTCAACTGATCTTTGACAAAGGAACAAAGGCAATAAAAT 649
                          ii vv ii--     i    i  i     i  vi v   i v  vv   
  L1M4_orf2#LINE/    335 ACATTTATG--GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_156733379_    650 GGAGCAAAGACAGT-TTTTCAGCAA-TAGTG-TGGAAAAACCA-ACATCC 695
                           i v  ii i   -      i   - i   -   i v   ii- i ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_156733379_    696 ACATGCAAAAAAGAAAAAAAGAATCTAGACACAGACCTTGGATCCTTTAC 745
                                   i ------ v   vi i   v vv    iiv i v v   
  L1M4_orf2#LINE/    433 ACATGCAAAAGA------ATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_156733379_    746 AAAAAAATAATTATAAGTGAACATAGACTCATAGACCTAAATATAAAATG 795
                              -----   -- v v  v  i  -   ?          i   i - 
  L1M4_orf2#LINE/    477 AAAAA-----TTA--ACTCAAAATGGA-TCAWAGACCTAAATGTAAGA-G 517

  chr2_156733379_    796 CAAAAACCATAGAAGACAATATTTTTTAAAGTCCTAAATTACCT-GGTGT 844
                          v     i   i  -------i i  vi   ----   --  v -  ?  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAA-------CTCTTAGAAG----AAA--ACATAGGNGT 554

  chr2_156733379_    845 ATTTTTTTATATTTTTAATGGACCTGACATTGCAAACATAGGCAAATCAC 894
                          vv i  ii ----------     vivi  --------      - vii
  L1M4_orf2#LINE/    555 AAATCTTCGT----------GACCTTGGGTT--------AGGCAA-TGGT 585

  chr2_156733379_    895 TTTTTAGATACAACACCAAAGGCATGATCCATGAAAGAAAGAATTGATAA 944
                           i       ii        i   ii v v ii       i   v     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_156733379_    945 ACTAGATTTCACTAAAATTAAAA-CCTCTACTCTGTGAAAGACAATGTTA 993
                          i i  i    ii          - i i iiv  vii  i    v i i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_156733379_    994 ACAGAATGAGAAAACAAGCCA--GATTAGGAAAAAACATTTGCAAAAGAA 1041
                          v i i   i  i    v   --  v i   i    i         vv v
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_156733379_   1042 ATGTCTAATAACAGAATATTATTCAAAACATACAAAGAACTCTTAAAACT 1091
                           i   i    vi  v vv   i  i  i   i            v    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_156733379_   1092 CAACAATAAGAAAATGGACAACCCAACTATAAAATAGGCCAAAGACCTTA 1141
                            i     i  i iii i       i ?v     i   v  i  ii v 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_156733379_   1142 ACAGACTTCTCACCAAAGAAGATATACAGATG-CCAATTAAACTTATGAA 1190
                          i    v i  v                i   -     -  i vi     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCACATGAA 884

  chr2_156733379_   1191 AAGATGTTCAACATCGTATGTCCT 1214
                               i        i????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (114 / 60)
Gap_init rate = 0.03 (22 / 674), avg. gap size = 2.73 (60 / 22)  


2916 27.31 4.00 0.23  chr2_156771666_156773750.rev      719  1593 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156771666_    719 TGGAGAGAGATGCCATGTTCATGGGTAGGAAGACTCAACATTGCTAAGAA 768
                             i   v  v            i v        i  i    i     v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156771666_    769 GTCCATTCCTCCCAACTTGATCTATAGTTTCAATGCAATCCCAATCAAAA 818
                          v v  v ii     v        i  v     i        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_156771666_    819 CCCAAGCAACATGTTATGGTGGTATCAATAAACTGACTCAAAAGTTTATA 868
                         i  v   vi v v  v  vv iv  ii i  i    ii v   i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_156771666_    869 TGGAGAGGCAAAAGACCCAGAAAAGTCAACAGAATATTGAAGGAAAACAG 918
                             i v    ii         v  i   v v   v     ii i  v i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_156771666_    919 GAAAGTCAGAGGACGAACACCACCAAACCTTAAACCTTACTATAAAGCGA 968
                         v     ii      vv    iv  v  ii i   v       i     v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_156771666_    969 CATTAATCATGACAGTGTGGTATTGGT-CAGAGA---ACGGATTGATTAA 1014
                           v      v            i   i-i ii  ---  iv  v   i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_156771666_   1015 TGGAACAGAATAGAGAGCCCAGAAATAGACCCACATAAATATAGTTAATT 1064
                              i     v     i         i     i i vv   i  i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_156771666_   1065 GACATTTGATAAAACAGCAAAGGCGACACAATGGAGAGAAGATAGTCTTT 1114
                           iv  i  i  iivv  v   i v iv      i  i ii         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_156771666_   1115 TCAGGAAATGGTGCTGGAACAACTGGACAGTCACATGCAAAAAAAAAAAA 1164
                            iv            i         i ?i           i  vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_156771666_   1165 TGTAGACACCGACCTTACTTTTCCTCCAAA---TAAATCTAAATGTCTCA 1211
                          - i   v  v    i  viiviv v    ---   v  v     vv   
  L1M4_orf2#LINE/    451 T-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_156771666_   1212 TAGACCTACATGGAAAA--------TGCAAAACTCTTAAAAGGTAATATA 1253
                         ?       v   v  i -------- ii          i   iv  i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_156771666_   1254 GAAAACCAACTAAATGACGTTGGGCATGGTAATGACTTTTTAGATACAAC 1303
                          i?ivvv v  vvi    v     ivv  i    ii  i       ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_156771666_   1304 ATCAAATGCATGGTTCAT----TAAAAAATTGATAAGTTGGACTTCATTA 1349
                          i    v   iiiviv i----v       v     i           i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_156771666_   1350 TAAATAAAAATGTCTGCTCTGGAAAAGTCACTGTCAAGAGAATGAAAAGA 1399
                         v  v      iv i  iv  vv   i v    i      i i        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_156771666_   1400 TAAACCACAGACCGGGACAAAATATCCTCAAAGGGCATTTCTGATAAAAG 1449
                         i  v       vi    v       iiv    vvii  v        ii 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_156771666_   1450 ACTGTTGTGCAAAATATACATAAAAATCCTTACAACTCAACAATAAG--- 1496
                            vv i v  i      i -  i  ii            i     i---
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATA-AAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_156771666_   1497 -------------TTAAAAAATAGACCAAAGACATTAATAGATACGTCAC 1533
                         -------------  ?      i i v  i  iv v      i iv  v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_156771666_   1534 AAAAGAAGATATACCGATGAGTAATAAAGATATGAGAACATATTCAATAT 1583
                         v             vi   ivi     iv i    i  v  ii    i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_156771666_   1584 CATGTGTCAT 1593
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.33 (134 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 4.62 (37 / 8)  


 208 10.00 2.00 4.00  chr2_156852614_156854207.rev      459   508 (1086)  C L1M4_orf2#LINE/L1   (0)   908   860 *

C chr2_156852614_    508 TACAA-TGCAGCCAACAATCATATGAAAAAAAGCTCAACATCACTGATTA 460
                              -  --     i  v  i       i v           ???????
  L1M4_orf2#LINE/    860 TACAAATG--GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

C chr2_156852614_    459 G 459
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.50 (3 / 2)
Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.50 (3 / 2)  

1933 27.58 2.71 0.34  chr2_156852614_156854207.rev      506  1096 (498)    L1M4_orf2#LINE/L1      270   874 (34)  

  chr2_156852614_    506 GTACTGGTACAAAAACAGATACATAGACCAATGGAACAGAATAGAGAACC 555
                                i i  ii i   i i     i        i     v    ii 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_156852614_    556 CAGAAATAAGACCACACACCTACAACTATCTGATCTTCAGCAAATCTGAC 605
                                  iv   i   ii  iiiii vi    i   ii   ivv  v 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_156852614_    606 AAAAAC------TGGC-----AATTTTGTGTTCCATAAATGGTGCTGGGA 644
                           i v ------   v-----   vv v v   v i              
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_156852614_    645 TAACTGGTTAGCCGTATGCAGAAGTTTGAAACTGGATCCCTTCTTTATAC 694
                         i      v  ?  ii     i   vv    ii    i    v i i i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_156852614_    695 CATATGCAAAAATTAACTCAAAATGAATTAAAGACTTAAATATAAAACCC 744
                              i                   i  i ?    i     i   i v i
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_156852614_    745 AAAACTATAAAAACCCTGGAAGACAATGTAGT--TAATACCATTCAGGAC 792
                                     vi i i     v  ii   v--   - i -   iv   
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATC-TTCGTGAC 567

  chr2_156852614_    793 ATAGACATGGGCAAAGGTTTCATGACAAAGACACCAAAAGCAATTGCAGC 842
                         v v ivv i     v      v iivv v             vvv   i 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_156852614_    843 AAAAGCAAAAATGGACAAATGGGATATAATTAAACTAAGGAGCTTCTGTA 892
                              v      i  i    v   iv v  i   v v ii i   i   i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_156852614_    893 AG-CAAAAGAAACTATCAACAGAGTAAACAGACAATCTACAGAATGGGAA 941
                         vv-    i  v        v i   i  v      i i           i
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_156852614_    942 AAAAT-TTTACAAACTATGCATCCAACAAAGGTCTAATATCCAACATCTA 990
                              -   i    ii  ii   ii i  i  v  vi      iv  v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_156852614_    991 TGAGGAACTTGAACAAACGTACAGGAAAAAAACAA-CAACCATATTTGAA 1039
                          i i     ivv    vivv i iv     i    -i    vv   ?i  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_156852614_   1040 AGTGGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACATGCAGACA 1089
                          i           iv    i     i  i  v        i  i  i ii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_156852614_   1090 GCCAATA 1096
                                
  L1M4_orf2#LINE/    868 GCCAATA 874

Transitions / transversions = 1.71 (101 / 59)
Gap_init rate = 0.01 (8 / 605), avg. gap size = 2.25 (18 / 8)  


 331 31.61 1.29 1.94  chr2_156891715_156897047.rev      161   315 (5018)    L1M4_orf2#LINE/L1      682   835 (73)  

  chr2_156891715_    161 ATCTAGAAAATATTGAGAAAACAAGCCATGGTTTAAAAGTAGATGTTTGC 210
                            v     i ---  i  i    v   ii vv iii  v i  i     
  L1M4_orf2#LINE/    682 ATCAAGAAAGT---GAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_156891715_    211 AATGAATATATCTAACAGAAGACCAATGTCTG--ACATATACTGAGCTCC 258
                           vvv        i i iii   ivi i  ii-- i     vv  i   i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_156891715_    259 TATAAATCAATATGTAAAAGATAAAATATATAATGGAAAAATGGGTAAAA 308
                           i  v      vvv      i   vv ivi   v?         i   i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_156891715_    309 GATTTGA 315
                                
  L1M4_orf2#LINE/    829 GATTTGA 835

Transitions / transversions = 1.53 (29 / 19)
Gap_init rate = 0.01 (2 / 154), avg. gap size = 2.50 (5 / 2)  

2615 27.23 2.09 1.98  chr2_156891715_156897047.rev     3935  4841 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156891715_   3935 TGGAACAACATTCCATACGCATGTATAGGAAGAATCAATTATTGTTAAAA 3984
                              vi i  i    iiv    v  v      v i   -        i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT-ATTGTTAAGA 49

  chr2_156891715_   3985 TGGACATACTGCCCAATGCAATGTATAGATTCTATCTTATTTTTATCTAA 4034
                            vv     v     vvii  v  i      v iviv  iii    v  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_156891715_   4035 CTACCAATGACATTCTTCACAGAACTAGAGAAATCTAGTTTAAAATTCAT 4084
                         v v   iivi v  i  ii     v v  v  iiiv vii          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_156891715_   4085 ATAGAACCACAAAAGAGCCCGCATAGCCAAGAAAATCTTAAGTAAAAAGA 4134
                           i   vii   ii  v  v v        i v      i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_156891715_   4135 ACA--GCTGGAGGCATCATACTACCTGACTTCAAACAATACTACAGGG-T 4181
                            -- i      vv   i   v  ii i      vvv       ii - 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_156891715_   4182 ACAGTAACCAAAACAGCATGATACTGGTACAAAAACAGACACAAAGACCT 4231
                                i   i    ii  i      i i  ii i     i v   i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_156891715_   4232 ATGCAACAGAATAGAGAGCCTAGAAATAATGCTGCACACCTACAACCCTC 4281
                            v  i     v     i i        vv iii   ii  iiii vvi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_156891715_   4282 TGATCTTTCACAAAGCTGACAAAAATAAGTAATAGGGAAAGGAC--TCCA 4329
                             i  iv    i v  v   i vi vvi   i       i i--  --
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-- 397

  chr2_156891715_   4330 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAGATTG 4379
                          v  i  i              v      v  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_156891715_   4380 AAACTGAACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGAT 4429
                           ii  i      v   i                 i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_156891715_   4430 TAAAGACTTAAATATAAAATGTAAAACTATAAAAACCCTT-GAAGACAAC 4478
                         i ?    i     i   i vv             - i   -     v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr2_156891715_   4479 CCAGG---AAATACCATTCTGGATATAGGTCCTGGCAAAGACTGTAT-GA 4524
                         vi   ---    -- -   vv  iv v  viiv     v ii viv -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_156891715_   4525 TGAAT-ACACCAAAAGTGATTGCAACCAAAACTAAAACTGACAAATGGGA 4573
                          --  -          iivvv     v   ivv    iv  i    v   
  L1M4_orf2#LINE/    594 T--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_156891715_   4574 TCTAATTAAACTAAAGACCTTCTACACAGCAAAGGAAACTATCAACAGAG 4623
                         ii v  i   v v  i v   i iii vv       v        v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_156891715_   4624 TACACAGGCAACCTGTAGAAAGGGAGAAAATATTTGCAAACTATACCTCT 4673
                          iv v  i     iii    v                   ii   iv   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_156891715_   4674 GACAAAGGTCTAATAACTAATCTAAAATAAATCTAAAAGAAA-CTTA--A 4720
                           i  i  v  vi  -----  i i    v  ---      v-    -- 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTA-----TCCAGAATATAT---AAAGAACTCTTACAA 783

  chr2_156891715_   4721 TTTTACAAGCAAAAACCAAACAATCCCATTATAAAGTGGACAAAGGACAT 4770
                         i iv i  vv    iv    i  i  v   ?v   i   i       iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_156891715_   4771 GAAAAGACA---CTTCAAAAAAACACATACATATGGCCAACA-GCATATG 4816
                            v     ---  i    i  i- i     v        i -   i   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAGCACATG 882

  chr2_156891715_   4817 AAAA-ATGTTCAGTATCACTAATCAT 4841
                             -   i   ii    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.76 (37 / 21)  


2873 25.65 1.19 2.92  chr2_156902651_156907610     3545  4468 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156902651_   3545 TGGAAAAATATCTCATGCTCATGGAGAGGAATAATTAATATGATGAAAAT 3594
                               i     i    i       vv    v v       vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156902651_   3595 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGACATACCCATTAAAC 3644
                            v     v      v i  i  i        i vv  v  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_156902651_   3645 TACT-GTTGACATTCTTCACAGAATTAGAAAAAAGCT-ATTTTAAAATTC 3692
                          v i- i  v -  i  ii     v v  v  --   -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTC 147

  chr2_156902651_   3693 ATTTGAAAACAAAAAAGGACCTACGAATAGCCAAGACAATTCTAAGCAAA 3742
                           v  i   iiv  i-     i -          i     ii i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAG-GGACCCA-GAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_156902651_   3743 GAGAACAAAGCTGGAGGCATCACACTACCCAACTTCAAACTATACTACAA 3792
                         i         i      vv       v     i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_156902651_   3793 GGCTACATTAATCAAAACAGCATGGTACTGGTTCAAGAACAGTCACATAG 3842
                         i      v       i    ii         ivi   i i  v  i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_156902651_   3843 ACCAATGGAACTGAATAGAGAACTCAGAAATAAGACTG-ACAAATAAAAC 3891
                          i        iv    v    iii         iv ii-   vv  viii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_156902651_   3892 CATCTGAGCTTTGACAAACCTGACAAACCTGAGAAAAACAAGCATTAGGG 3941
                           vi   vi  i     ivv  -----  ----  i v  vv  v i   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTG-----CC----AAGACCATTCAATGGGG 386

  chr2_156902651_   3942 AAATGATTCCCTATTCAATAAATGGTTCTGGGATAACTGGCTAGCAATAT 3991
                            vi  vvi  v     i       v      i      v  ? v i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_156902651_   3992 GCAGAAGATTAAAACTAGACCCTTTCCTTACACCATATATAAAAATCAGC 4041
                            i    v i  ii i     i v   i          i      i i 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_156902651_   4042 TCAAGATGGATTAAAGACTTAAATGTAAAACTCAAAACTATAAAAA---- 4087
                             i      i ?    i         i vii            v----
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_156902651_   4088 AAAAAAAAACCTAGGAGAAGATCTAGGCAATACCATTCAGGACATAGGCA 4137
                          i  i     v    ? v i    ------------  iv   v v  vv
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCT------------TCGTGACCTTGGGT 574

  chr2_156902651_   4138 TGGGCAAAGATTTCAT-GATGAAGACACTAAAAGCAATTGCAACAAAAGC 4186
                          i     v i    v -   - v     i       vvv          v
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_156902651_   4187 AAAAATTGACATATGGGATCTAATTAAACTAAAGAGCTTCTGAACAACAA 4236
                               v  i v  v   ii v  i   v v  i i   i  vi vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_156902651_   4237 AAGAAACTATTATCAGAGTAAACGGACAACCTACAGAATGGGAGAAAATG 4286
                          i  v     i vv i   i  vi       i                 i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_156902651_   4287 TTTGCAATCTATCCATCTGACAAACATCTAATATCCAGAGTCTACAATGA 4336
                                vii  vi      i  iviv  vi        i v  i  v  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_156902651_   4337 ACTTGGACAAATTTACAAGAAAAA---AAACAATTTCATTAAATAGTGGG 4383
                            ivv    v iv i  v     ---   i  iiiv   ?  v i    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_156902651_   4384 CAAAGGACATGAAAATACACTTCTCAAAAGAATATATACCTCCAGCCAAC 4433
                                iv    v v   i     v      v      vvvii     i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_156902651_   4434 AAACATAAGAAAAAAAGCTCAGCATCACTGATCAT 4468
                           i  i v     i v     i     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (128 / 105)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.71 (38 / 14)  


2883 24.89 2.44 1.56  chr2_156913355_156917659     2914  3813 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156913355_   2914 TGGAAACACATCCCATGCTCATGGATGGGAAGAATCAATATC------AT 2957
                               v i        i        v      v i     i------  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156913355_   2958 GACAAT-CACCATAGGGCCAAAAAAATCTACAAATTCAATATAATGCTCA 3006
                          i    - v  ------     vvi       i      iii   v ii 
  L1M4_orf2#LINE/     51 GGCAATACTCC------CCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_156913355_   3007 TCAAAATACCATCACCATTCTTCACAGAACTAGAAAAAAACAATCCTAAA 3056
                                v   v vv v  i  ii     v v  v  iv-ii        
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAA 143

  chr2_156913355_   3057 AGTCATATGAAACAAAAAAAAGAGTCCACA-TAGCCAAAGAAAGACTAAG 3105
                          v       i  -- viv  i iii   v -        iv  vvi i i
  L1M4_orf2#LINE/    144 ATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_156913355_   3106 CAAAAAGAACAAACCTGGAAGCATCACATTACCCAACTTCAAACTATACT 3155
                         v  i         vi    i vv     i v     i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_156913355_   3156 ACAAGTCCAGAGTTACCAAAGCAGCACATGACTGGTATAAAAATAGACAC 3205
                             iv i v   v i   ii   iiiivv     i    ii       i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_156913355_   3206 ATAGACCAATGGAACAGAATAGAGAACTCAGAAATAAACTCACGTACTTA 3255
                              i        i     v    iii           i  iii i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_156913355_   3256 CAGCCAAGTGATCTTTGACAAAGCAAACCAAAACAA---AAAGTGGGGAA 3302
                         ii i   v    i  i     i -ivi    i  v ---  --       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAA--TGGGGAA 388

  chr2_156913355_   3303 AGGACATCCTATTCAA-AAATGGTGCTAGGATAATTGGCAAGCCACATGT 3351
                           i i vi  v     -          i   i  i   vv ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_156913355_   3352 AGAAGAATGAAACTGGATCTTCCTCTCTCACCTTATACAAAAACCAACTC 3401
                          i         ii    i iiivi   v    v          ii     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_156913355_   3402 AAGATTGATCAAAGACTTAAATCTAAGACCTGAGACTATTAAAATTCT-A 3450
                           i  v     ?    i     v     v  i i     -    i   - 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTA 537

  chr2_156913355_   3451 GAAGATAACATCAGAAGAAACTTTTCTAGACATTGGCTTAGGCAAAGAGT 3500
                              v     -  i? v  v i   vv   v    v        v iv 
  L1M4_orf2#LINE/    538 GAAGAAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_156913355_   3501 TCACGACCAAGAACCCAAAAGCAAATGCAACAAAATAAAAA-TAAACAGA 3549
                           viiivi v  vv         v v         v     -  i i i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_156913355_   3550 TGGGACTTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAA 3599
                          v      v  i   v v    i   i  ii vv    i  v iv     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_156913355_   3600 CAGAATAAACAGACAACCCACAGAGTGGGAGAAAATATTTGCAAACTATG 3649
                         v i i i  v              i                    ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_156913355_   3650 CAT----TAAAGAACTAATATCCAGAATCTACAAGAAACTCAAACAATTC 3695
                         i  ----   i i   vi          v  i  ii     vv    i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_156913355_   3696 AGCAAGAAAAAAA-AAAT---CCTATCAAAAAGTGGGCTAAGGACATGAA 3741
                          ii  v     i -    ---  v  i?    i     v     iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_156913355_   3742 CAGAAAATTCTCAAAAGAAGATGTACAAATGGCCAATAAACATATGAAAA 3791
                         i   v v     v         i                i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_156913355_   3792 AATGTTCACCATCACTAATGAT 3813
                         i   i   v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (132 / 88)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


1349 25.52 3.91 1.15  chr2_156936039_156942313       64   498 (5777)    L1M4_orf2#LINE/L1      376   822 (86)  

  chr2_156936039_     64 ATTGAATGGGGAAAAGATTTTCCATTCAATAAATAATGCTGGGATAACCG 113
                            v          ii  vv  iv     i    ii        i   i 
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_156936039_    114 GCTAGCCATATGCCAAAGTTTAAAACTGGACCCCTTCCTTACACATTATA 163
                          v  ?   i    v    vv i  ii         v   i    vv    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_156936039_    164 CAAAAATTTACTCAAGATGGATTAAAGGCTTAATTACAAAACCCAAAACT 213
                                 v      i      i ?  i i   v ii  i v i      
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_156936039_    214 ATAAAAACCC-AGAAGACAACCTAGACA-ATATCATTCAGGACATAGGCA 261
                               vi i-      v   v   i?i- v   -   iv   v v  vv
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT 574

  chr2_156936039_    262 TGGGCAAAGATTTCATGACAAAGACACCAAAAGCAATTGCAACAAAAGCA 311
                          i     v i    v iivv v             vvv          v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_156936039_    312 AAAATTGACAAATGGGATCT------AATTAAAGAGCTTCTGCACATCAA 355
                              v  i    v   ii ------       i -   i  ii v    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chr2_156936039_    356 AAGAAACAATCAACAGACTAAACAGACAACT-ACAGAATGGGAGAAAAAT 404
                          i  v  v     v i v i  v       i-                - 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-T 722

  chr2_156936039_    405 TTTTGCAACCTATGCATCCTACAAAGGGCTAATGTTCAGCATCTACAAGG 454
                         v       vii  ii   iv i  i  i  vi i i   v  v  i  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_156936039_    455 AACTTTAACAATTTCCAA----GAAAAAACAA----CCCCATTAAAAACT 496
                             i v    i --   ----i    i    ----   v   ?    v 
  L1M4_orf2#LINE/    773 AACTCTTACAACT--CAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_156936039_    497 GG 498
                           
  L1M4_orf2#LINE/    821 GG 822

Transitions / transversions = 1.18 (58 / 49)
Gap_init rate = 0.02 (10 / 447), avg. gap size = 2.20 (22 / 10)  

3222 27.64 0.22 0.22  chr2_156936039_156942313     4876  5783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156936039_   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATAGTGAAAAT 4925
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156936039_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_156936039_   4976 TACCAATCACTTTCTTCACAGAATTGGAAAAAAATACTTTAAAGTTCATA 5025
                          v   iiii i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_156936039_   5026 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5075
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_156936039_   5076 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTG 5125
                              i      vv   ii  v  ii i      viv        i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_156936039_   5126 TGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATTGATCAA 5175
                         ii    i   i    ii         i iv ii i   v    v      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_156936039_   5176 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACTAT 5223
                              i    i--    i  --        vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_156936039_   5224 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5273
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_156936039_   5274 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5323
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_156936039_   5324 AACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAGATGGATT 5373
                          ii    i    v   i     v  i        i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_156936039_   5374 AAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5423
                          ?    i    ii v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_156936039_   5424 AGGCGTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5473
                            ?  v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_156936039_   5474 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5523
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_156936039_   5524 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5573
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_156936039_   5574 AAAACCTACAAAATGGGAGAAAATTTTCGCAACCCACTCATCTGACAAAG 5623
                          v    i   i             v  i    vi  ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_156936039_   5624 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5673
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_156936039_   5674 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTGTC 5723
                              i     v  i?    i     i     iv    i     i  v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_156936039_   5724 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5773
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_156936039_   5774 CACTGGCCAT 5783
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (144 / 103)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


2056 15.31 1.56 26.83  chr2_156970929_156973412.rev      778  1992 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_156970929_    778 TAAAAAGA----CCAT-TTAATGGATTGTAAGACTCAGTATTGTTAAGAT 822
                          ii     ----    -  v        v      i i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_156970929_    823 GGCATCA-TCCTCAAATTGGTTTATAGATATAACACAATCACTGTCAAAA 871
                             vi -   i       i i  i    vi   i     v  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_156970929_    872 TCCCAGAAAGTTTTTTTCTGTAAAAATTGAAAAACGAATACCCCAAATTT 921
                               vv- ii     -  i i       v  i vi  -  iv     i
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTT-TGCAGAAATTGACAAGCTGAT-CCTAAAATTC 147

  chr2_156970929_    922 ATATAGAACTGCAAAGAACTTGAAATAACCAAAACAATTTTGAAAAA--A 969
                             i   v     i i  iiii    i          i        -- 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_156970929_    970 TAA-AAAGATGGAGGACTTAGAGCACCCAATTTTAAAACTTTTTCTAAAG 1018
                         v  -    v         i v viv        i       vi vi    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_156970929_   1019 CAACAGTAATCAAGACAGCATGGTGTTGGTGAAAGGATAAACATATATAT 1068
                          v                ii    ii   iiv       i       v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_156970929_   1069 CAATGGAGCAGCATGGATAGTCTAGAAGT----CCTTACATTTATAGTCA 1114
                                ii  v  v  v    i    i ----  v         i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_156970929_   1115 GTTGATTTTTAACAAAAATGCCAAGCTAATTCAAGGGAGAAAGGATAGCC 1164
                         i        ii    iii       viv      v  i     i    i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_156970929_   1165 TTTTCAACAAATTGTGCTGGGACAATGGTATATCCATATGTACAAAGCAA 1214
                                     v            iv v   ?   i   i -    ---
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAG--- 443

  chr2_156970929_   1215 GCATAAACCCTTAACTCACATACACAATGAAATAAAAATGAATCATGGGC 1264
                         -------------------------      i -----------------
  L1M4_orf2#LINE/    444 -------------------------AATGAAGT----------------- 451

  chr2_156970929_   1265 TGGCATGGTGGCTCACGCTTGTAATCCAAGCACTTTGGGAGGCTGAGGCA 1314
                         -----------------------------------   ------------
  L1M4_orf2#LINE/    452 -----------------------------------TGG------------ 454

  chr2_156970929_   1315 GGCAGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGACCAACATGGTG 1364
                         -----------------------------   --   -   ---------
  L1M4_orf2#LINE/    455 -----------------------------ACC--CCT-ACC--------- 463

  chr2_156970929_   1365 AAATCCCACCTTTGCTAAAAATACAAAAATTAGATGGGTGTGGTGGTGTG 1414
                         ---  v    v --------            ------------------
  L1M4_orf2#LINE/    464 ---TCACACCAT--------ATACAAAAATTA------------------ 484

  chr2_156970929_   1415 CACCTGTAATCCCAACTACTCAAGAGGCTGAGGCAGGAGAATCGCTTGAA 1464
                         -----------------      ----------------   --------
  L1M4_orf2#LINE/    485 -----------------ACTCAA----------------AAT-------- 493

  chr2_156970929_   1465 CCCGGGAGGCAGAGCCTGCAGTGAGTTGAGATGGCACCACTGCACTCCAG 1514
                         ----------------------------i   ------------------
  L1M4_orf2#LINE/    494 ----------------------------GGAT------------------ 497

  chr2_156970929_   1515 CCTGACTGACAGAGTGAGACTCCACCTAAAAACAACAACAACAACAACAA 1564
                         ---------  ?  ---------       --------------------
  L1M4_orf2#LINE/    498 ---------CAWAG---------ACCTAAA-------------------- 509

  chr2_156970929_   1565 CAACAACAACAACAACAAACCATAAACGTAATGTACAAGATAACATAATA 1614
                         -------------------------------    vi  v   v iv   
  L1M4_orf2#LINE/    510 -------------------------------TGTAAGAGCTAAAACTATA 528

  chr2_156970929_   1615 CAACTTGTAGAAGACAAAAAAGTAGAGAATCTTTGTGCAACCTTGGGTTA 1664
                         v    iv       v  v v  v? vi      i   --           
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG--ACCTTGGGTTA 576

  chr2_156970929_   1665 GACAAACATTTCTTAGATGTGATGCCAAGAGCAGGATCCATAAAAGAAAA 1714
                          i   vvi          i   ii    i    vi v v i         
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_156970929_   1715 AATATTGATAGACTGGACTTTATAAAAA--GAAAATTTTAGCTCCTCAAA 1762
                             --    i i       i  v    --i    i   v iv i     
  L1M4_orf2#LINE/    627 AATA--GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_156970929_   1763 AGACACCTTTAAAAGAATGAAAAGACAAGACAATAACTGGGAGAAAATAT 1812
                         i     iv i  i i i           vv  vvi v             
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_156970929_   1813 TTGGAAAGCTTGTGTCTAAGAAAGCATTTGCATCCAGAATATATAAATAA 1862
                            v   v v i i   i v  i v i   i                v  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_156970929_   1863 CTCCTACAATTCAAAGATAA---GACAGACAACCCAAATAAAAAATGGGT 1909
                            i     i    vi    ---    i i       v ?         i
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_156970929_   1910 GCAATATCTGAATAGATGTTTCTCCAAGGAAGATATCCAAA-AGTTAATA 1958
                         iv iv  i        ii         i        v    -i ii    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_156970929_   1959 AGCAGGTGAAAAGATTCTCAAAATCATGACTCAT 1992
                             vi         v     v    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (110 / 72)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 12.32 (345 / 28)  


 307 15.87 1.59 1.59  chr2_156987412_156989525      238   300 (1814)    L1M4_orf2#LINE/L1       63   125 (783)  

  chr2_156987412_    238 CAAAGCTATCTATAGATTCAATGCAATCCCTATTAAAATCCCAA-TACCA 286
                             viv     i        i           i         i- i  -
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC- 111

  chr2_156987412_    287 TTTCTTACAGAAAT 300
                            i  i       
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAAT 125

Transitions / transversions = 4.00 (8 / 2)
Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2)  

 443 22.81 1.17 13.45  chr2_156987412_156989525      486   656 (1458)    L1M4_orf2#LINE/L1      119   268 (640)  

  chr2_156987412_    486 CAAAAAATAACACAC--ATTCTAAAATTCACATGGAACCACAAAAGGCCT 533
                           i   v i   vi --  i          i      vii   ii i  i
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr2_156987412_    534 TGAATAGCCAAAAAAAAATTTTTTTGAGAAAGGAGAGAAAGAGGAGAAGA 583
                         v            v  ----- i    i    i   --------------
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAA-----TCTTGAAAAAGAAGA-------------- 199

  chr2_156987412_    584 GAAGAGAAAGCTGGAGACATCACAATTCCTGATTTCAAAACATATTGTGA 633
                         ---- v    i     ivv     v    ii          v  i iii 
  L1M4_orf2#LINE/    200 ----ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_156987412_    634 AGTTATAGTAATTAAAGTAGTAT 656
                           i  i      i  iii   i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGT 268

Transitions / transversions = 2.90 (29 / 10)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 8.33 (25 / 3)  

2337 21.86 5.02 3.69  chr2_156987412_156989525      953  1629 (485)    L1M4_orf2#LINE/L1      223   908 (0)  

  chr2_156987412_    953 CTCCATCTCAAAA------ATAAAA----AATAAACAAAAGTAGCATAGT 992
                          i v  i      ------ i   i---- i   v   i -i  ii i  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGT 271

  chr2_156987412_    993 ACTGGCATAAAGACAGACATACAGACCAATGGAACAGAATAGGGATCCCA 1042
                                   i  i       i   i        i     v i  vi   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_156987412_   1043 GAAATAAATCTACACATACATATATA--CAACTCATCTTCCACAAGGGCA 1090
                                 i ----       v   i--   i v  i   v       ii
  L1M4_orf2#LINE/    322 GAAATAAACC----CATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_156987412_   1091 CCAAGAATACTCAGTAGTAAAAGGACAGTCTCTTCAACAAATGGTGTTAG 1140
                               vi i   i i vi    i i     i              i i 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_156987412_   1141 GAAAACTAGATCTCCACATGCAAAAA-------TTGGACCCTTATCTTAC 1183
                           v    i   v?            i-------        i  i  i  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_156987412_   1184 ACTGTACACAAAAATCA-CTATAAATGGATTAAATATTTCAACATAAGAC 1232
                           ii  i        i -  vv        i ? v ii v  ii     v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_156987412_   1233 CTGAAAGTATAAAACTTCTAGGAAAAAATTTAGAGGAAAAGCTTCATGAT 1282
                           i   v         ii   i i    iv   i? v   v    i   i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_156987412_   1283 ACTGATCTTGGCAATTTTTTCATGGATATGACCCCAAAACCTCAGGCAAC 1332
                         vi  ivi v      vv    v i        v      v v  i     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_156987412_   1333 AAAAGTGAAGATAGACAAATGGGACTAAATCAAACTAAAAAGCTTCTATA 1382
                              vi  i     i    v     vv      v v    i   i i i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_156987412_   1383 CAGCAAAGCAAAAAACCAACAGAGTGAAAAGGCAACCCACAGAACAAGGG 1432
                          vv     v v vv i   v i         i            iii i 
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_156987412_   1433 AAAGTATTTGCAAACATATACCTCATATACCTGATACAGGGTTAATTTCC 1482
                            i          --------       i      vi  ii vi v   
  L1M4_orf2#LINE/    718 AAAATATTTGCAAA--------TCATATATCTGATAAGGGACTTGTATCC 759

  chr2_156987412_   1483 AAAATATATAAGGAACTCTTACAATGCAATAGCAAAAGAAAAAAAAAAGA 1532
                          i         i            iv     ---------- v       
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATA----------ATAAAAAGA 799

  chr2_156987412_   1533 CTGACAACCCAATT-AAAAATGAGCTGAAGACTTGAATAGACATT---CC 1578
                          vi i         -       i  vi i  i             ---  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_156987412_   1579 AAAGA---CATACAAATGGCC------TACA-GAAAAGATATTCAAGGTA 1618
                              ---i            ------i   -        ii    --i 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA--CA 897

  chr2_156987412_   1619 TTAATCATCAG 1629
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.96 (96 / 49)
Gap_init rate = 0.02 (15 / 686), avg. gap size = 3.93 (59 / 15)  


3226 26.96 0.88 0.55  chr2_157052537_157058916.rev     4984  5888 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_157052537_   4984 TGGAAGAAGATTCCATGCTCATGGATAGGAAGAACCAATATCGTGAAAAT 5033
                              ii v  i     i        v      vii     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157052537_   5034 GGCCATACTGCCCAAGGTTAATTTGTAGATTCAATGTTATCCCCGTCAAG 5083
                            v     v     i-  i  i ii        i iv     ii    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_157052537_   5084 CTACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCA 5132
                         v v   iivi i  i  ii     v v  v  i-  - iii    i    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_157052537_   5133 TACAGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5182
                           ii   viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_157052537_   5183 AACAAAGCTGGAGGCATCACGCCACCTGACCTCAAACTATACTACAAGGC 5232
                                i      vv    i iv  ii ii     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_157052537_   5233 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGACC 5282
                                 i   i    ii         i iv ii i   v v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_157052537_   5283 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5330
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_157052537_   5331 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5380
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_157052537_   5381 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5430
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_157052537_   5431 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 5480
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_157052537_   5481 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5530
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_157052537_   5531 CTAGGAA-ATATCATTGAGGACATAGGCATGGGCAAGGACTTCATGACTA 5579
                         v    ?i- v   v i v iv v i  i- i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr2_157052537_   5580 AAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTA 5629
                         vi            vvi      i   vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_157052537_   5630 ATTAAACAGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5679
                           i   vvv  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_157052537_   5680 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATTTACCTATCTGACA 5729
                         v  i     i                 v   i   v i iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_157052537_   5730 AAGGGCTAATATCCAGAATCTATAAAGAACTTAAACAAATTTACAAGAAA 5779
                          i  i  vi          v           ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_157052537_   5780 AAATCAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5825
                           iv   ----   v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_157052537_   5826 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5875
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_157052537_   5876 CATCACTGGCCAT 5888
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (147 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


 575 22.94 5.88 2.35  chr2_157323783_157328869     2843  3012 (2075)    L1M4_orf2#LINE/L1        1   176 (732)  

  chr2_157323783_   2843 TGGAAAGGCGTTCTGTGTTCATGAATTGGAAGAATTATTA--GTTACAAT 2890
                                iii i ii        i         v   v  --    vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157323783_   2891 GTCCATACTACCTGAAATAATCTACAGGGTCAATGCAAACCCTAACGAAA 2940
                          v v     v  ii  v i        iv    i    v     v i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157323783_   2941 CACCAATGACATTATTTACAGAAATATTTTAAAAAC----CCTAAAATTC 2986
                         iv   iivi v  v   i       --- v v  i ----          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT---TGACAAGCTGATCCTAAAATTC 147

  chr2_157323783_   2987 ATATGGAACTG--AGAGAC--AGGACTAGC 3012
                                 v  --  i   --  i -    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAA-TAGC 176

Transitions / transversions = 1.29 (22 / 17)
Gap_init rate = 0.03 (6 / 176), avg. gap size = 2.33 (14 / 6)  

2259 24.91 0.74 7.52  chr2_157323783_157328869     3785  4595 (492)    L1M4_orf2#LINE/L1      153   908 (0)  

  chr2_157323783_   3785 GAACCGTGAAAGACCCTGAGTAGCAAAAACAAACAAACAAAAAATCCTGA 3834
                            vi ii ii     v  i    v       ------------  i   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAA------------TCTTGA 190

  chr2_157323783_   3835 ACAAAAAGAACAAAGCTGGAAATATTACACTACACGACCACAAATTATAC 3884
                          v  i          i    iivv i     v v i iiv    viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_157323783_   3885 TACAAAGCTAGAGTAACCAAAACAAGATTTTGGCAAATGCACACTCTCTC 3934
                                   v     i   i   i--- v   i ---------------
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAG---TGTGGTA--------------- 272

  chr2_157323783_   3935 ACGCTCTCTCTCACACACACACACGCACGCACACATAGACTAATGGAACA 3984
                         ---------  vi  i viv i ----- -   i     ii       i 
  L1M4_orf2#LINE/    273 ---------CTGGCATAAGGATA-----G-ACATATAGATCAATGGAATA 307

  chr2_157323783_   3985 GAATAGGTAACTCAGAAATAAATCCACACAC----AGCCAACTGATTTTC 4030
                             v iv iii          i   i   i----i i   i        
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_157323783_   4031 AACAAAAGTATTAAGAACAGATATTGGGGAAAGGATGGTCTCTTCAATAA 4080
                         i    ii  iii    v  vvi v         i  i    i     i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_157323783_   4081 ATGGTGCTGGAAAAACCACTTATCC-CAGTGCAGAAGAATGAAACTAAGC 4129
                                   i v   iivv  ?  -  -    i         ii iii 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGAATGAAGTTGGAC 456

  chr2_157323783_   4130 CACCATCTCTCATCATATACAAAAATCAACTAAAAATGGGTTAAAGACTT 4179
                          v i i   v  i             i    v       i i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_157323783_   4180 AAACATAAGCCCCGAAACTATAAAACTACTAGAAGAAAACAAAGGAGAAA 4229
                            ii    vv ii             vi            v   ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_157323783_   4230 CACTTCAGGATATTGGTATGGGCAGGGATTTTTTTGATAAGAACTTAAAA 4279
                         vv    iv  iv    vv i    iv i   i  v    v  vvii    
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_157323783_   4280 GCACAGGCAACACAAGCAAAAACAGACAAATGAGATTACATTGAACTAAA 4329
                              i      v   v     i   i    vi  i v   ii  v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_157323783_   4330 AAGCTTACATATAACAAAGGAAACAATCCACTGAGTGAAGAGACAACTTA 4379
                           i   vii iivv       v  v   v vvi      i       ii 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_157323783_   4380 CAGAATGGAAGAATATACTTTTAAATTATGCATCTGACAAGGGGTTAATA 4429
                                 i    v   i  vi    i  ii      i     ii vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_157323783_   4430 TCCTGAATGTATATGGAACTCAAACAATTCAACAGCAAAATTCAAACAAA 4479
                            v    i    vi      vv    i    i ii    ----------
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA---------- 796

  chr2_157323783_   4480 CAAAAACAAATAATTTGATTTAAAAAATGAGCAAAAGACCT-AATAGACT 4528
                         --- i        iiii   ?     -  i     i  ii -       v
  L1M4_orf2#LINE/    797 ---AGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chr2_157323783_   4529 TTTCTTAAAGAAAGACATAAAAAGAGCCAATAGGTATATGAAATATATGC 4578
                              iv  ii    i   v   vi       i i i      - v    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATGC 891

  chr2_157323783_   4579 TCAATATCACTAATTGT 4595
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (128 / 70)
Gap_init rate = 0.02 (12 / 756), avg. gap size = 5.58 (67 / 12)  


1119 22.97 1.74 7.27  chr2_157348285_157351965.rev     1935  2278 (1403)    L1M4_orf2#LINE/L1        3   327 (581)  

  chr2_157348285_   1935 GAGAGATAGTCCATGTTCATAGATAGAAAGATTCAGAT-TTATTAA-ATG 1982
                           i     vi          i   v i    i i -  -  i    -   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTA-ATATTGTTAAGATG 51

  chr2_157348285_   1983 TCAGTTATTCACAATTTGAACTATAGATTCAAAGCCATCCCAACCAAAAT 2032
                         v  i vv i v   v    v   i        v  v     v i      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_157348285_   2033 CCCAGACAGTTATTTTGTGTACATTGACAAATTGATTCTAGAGTTCCTAT 2082
                              viivi v     iiv v        ii    i   i i   v   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_157348285_   2083 CAAAAGATGAAAGAGCTAGAATTGCTAATATAATAATGAAGAAGAA---- 2128
                         vi   viii ii  v i     v  i  v i   vv    i     ----
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_157348285_   2129 AAAGTCAGAGAGTTGACACTAACCAACTTCAAGACTTACTACAGAGCTAC 2178
                              ii   iii v     vv    i     i          i      
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_157348285_   2179 AGTGAATAAGACAGTGTGGTACTGGTAGAAGAACAGACAAATAGATCAAT 2228
                            i vi                  i v   i i     v          
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_157348285_   2229 TGACCAATTGGTCAACAGAGCAATGGAACAGAATAAAGAACCCAGAAATA 2278
                         ------------------------    i     vi   ii         
  L1M4_orf2#LINE/    302 ------------------------GGAATAGAATTGAGAGTCCAGAAATA 327

Transitions / transversions = 1.55 (48 / 31)
Gap_init rate = 0.02 (5 / 325), avg. gap size = 6.20 (31 / 5)  

2140 19.90 3.51 4.85  chr2_157348285_157351965.rev     2592  3189 (492)    L1M4_orf2#LINE/L1      319   908 (0)  

  chr2_157348285_   2592 CCAGAAATATACC-ACACAAATATTGTCAACTCATCTTTGGCAAAGG--- 2637
                                  v   - i   vv   v     i v  i  i i   i  ---
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_157348285_   2638 -AA---CA--CAGTGGAGAAAGGATGGTCTTTTCAGCAAACAGGAATGGA 2681
                         -  ---  --  i   i     i  i         i    ii viv   i
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_157348285_   2682 ACAACTGGACATCTACATACAAAA-AATTAATCTGGATACATACCCTATA 2730
                                  i ? i    i     -   v  vi    iv v    ii i 
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_157348285_   2731 CCTCTCACAAAAAT-AACTTAAAAGGGGTCTTAGACCTAAATGCAAATGC 2779
                           vivi        -    i    v  i  v?           i  i---
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG--- 515

  chr2_157348285_   2780 AAAACCGAAGCAAAATGCAAAACTATAAAACTCCTAGAAGATAAAACG-A 2828
                         --------   ------i               i       --    i- 
  L1M4_orf2#LINE/    516 --------AGC------TAAAACTATAAAACTCTTAGAAGA--AAACATA 549

  chr2_157348285_   2829 GAAAAAAAAATTCTAGGTGACCTTGGGTTTGGCAATGATTTTTCAGATGT 2878
                          i?iv   vv   ---             v       i   i i    i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTC---GTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_157348285_   2879 AATACCAAAAGTGCAATTCATGAAAGAAAAAAAATGGATAACTTGAAC-- 2926
                         i i        ii   viv ii          -- i     v   i  --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAAATTGGACTT 644

  chr2_157348285_   2927 -ATTAAAATTAAAACCTTCTG--CTCCACCAAAGACATTGTTTAGATAAT 2973
                         -  i          v   i  --  i  --  i    i i iv   v i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAAAGT 692

  chr2_157348285_   2974 GAAAAGACAAGCCACAGACTGGGAGAAAAAAATCTTTGCAAAACACATAT 3023
                                   v       v          --- v        v  i    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAA---TATTTGCAAATCATATAT 739

  chr2_157348285_   3024 CTGATAAAGGACTCATAATCAAAATAGCTAAAGAATACTTAAAACTCAAC 3073
                                i     ii  vi  i    vv       iv    v       i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_157348285_   3074 AACAAGCAAACAAACAACCCAATTAAAAAATGGGCAAAAGATCTGAACAG 3123
                           i  iv i     i         ?             i   i    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_157348285_   3124 ATACTTCACCAAAGA---TATACAGATGGCAGATAAGCATATGAAAATAT 3170
                          i i   v       ---      i     vi       i       v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_157348285_   3171 GTTCAACATTATATATCAT 3189
                          i       i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (77 / 38)
Gap_init rate = 0.03 (17 / 590), avg. gap size = 2.94 (50 / 17)  


3578 20.50 3.51 1.70  chr2_157361364_157363390.rev      653  1535 (492)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_157361364_    653 ATCTCATGCTCATGGATTGCAAGATTTAATATTATTAAAATGTCTATACT 702
                            i    i          v    i        i    i   v v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_157361364_    703 ACCCACAGCTACCTAAAATTTCAATGTAATCCCTATAAAAATCCCAATGA 752
                         v    v viv i   v iv     i i         v         iivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_157361364_    753 CAATTTTTGTAAAAATAGAAAAAAAATTCCTAATATTCATATGGAT-TGT 801
                          vv      i i    v  v  ivviv      v           v-  i
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_157361364_    802 TAAGGGACCCCAAATAACTAAAACAATCT-GGAAAAGAAGGAAAATGT-G 849
                         -         vi    i i          - i        i v  v  - 
  L1M4_orf2#LINE/    160 -AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_157361364_    850 GAGGCCTCACCCTTCCTGATTTCAAAACATACAACAAAGCAACAGTAATC 899
                             v     v     ii          v   v       v         
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_157361364_    900 CAGATGATGTAATACTGGCATAAAGTCAAATATCTGGATCAATGGAACAG 949
                         v   iii   ii           i vi i i  v i           i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_157361364_    950 AATAGAGAGGCCAGAAACAAACCCTTATATATATGGCCAAATGATATTCA 999
                            v     v       i      v  i  v     i   v    v   i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_157361364_   1000 ACAAGGATGCCAACACTACACAATGGGGAAAGGACAGTGTCTTTGACGAG 1049
                               i      v  i iv            i i   v i  ii  i i
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_157361364_   1050 TAGTATTGGAAAAACTGGATATCCATTTGCAAAATAATTATTTCGGACCC 1099
                          i  ii   i v         ?   iv       v   v vv i      
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_157361364_   1100 TTA----ACATTATACACAAAAATTAACTCAAAATGAGT----GA----A 1137
                         i  ----   ii   i                    ii ----  ---- 
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_157361364_   1138 ATATAAGC-CGAAAAGCTACAAAACTCCTAAAGCAAAACATAGAG---AG 1183
                           i    v- v    -   i       i  i iv         i?--- i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_157361364_   1184 TCT-CAAGACATTGGATGTGACA-TAATTTTTTGGATATGACACATATGA 1231
                            - iv   v    i vv i  - ii   i  i          ------
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC------ 601

  chr2_157361364_   1232 CAAAATCACAGGCAGTAAAAGAAAAAAAAAACAGATAAATGGGACTATAT 1281
                              v    i   ii           ----i        v     vi  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAA----TAGATAAATTGGACTTCAT 647

  chr2_157361364_   1282 CAAA-CTAAAA--------GCTATCAAAGGAAACAATCAGTGAAG-AAAA 1321
                             -i     --------   -        v  v    ivi   -i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_157361364_   1322 AGAGCAACCTATGGAATGCGAAAAAATATTTGCAAGTCATGTATTTGTTA 1371
                            -     i ii     v  i             i    i   i  v  
  L1M4_orf2#LINE/    697 AGA-CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_157361364_   1372 TAGGGTTAATACCCAGAATATATAAGGAACTTCTACAACTCAACCACAAA 1421
                         vi  ii vi  i             i     ii          iv i   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_157361364_   1422 AAAAACAAATCACCCAATTTAAAAATGGGCTAAGGACGTGAATAGACAAT 1471
                           i -     v        ?          v     iv          v 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_157361364_   1472 TCTCCAAAGAAGACATGCAAATGGCCAATAAGCCTATAAAAAGATGCTCA 1521
                                      i  i                vi  i            
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_157361364_   1522 GCATCACTAATAAT 1535
                         i     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (109 / 69)
Gap_init rate = 0.02 (20 / 899), avg. gap size = 2.30 (46 / 20)  


1793 24.47 6.04 2.77  chr2_157443234_157444817      480  1092 (492)    L1M4_orf2#LINE/L1      276   908 (0)  

  chr2_157443234_    480 GCATGAGAATGGACTAATACATAGACCAATGGAACAGAATAGAGAACCCA 529
                             i  i  i   ---- i     i        i     v    ii   
  L1M4_orf2#LINE/    276 GCATAAGGATAGAC----ATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_157443234_    530 GAATTAAGCCAA-ATACTTACAACCAAGTGATCTTGGACAAAGCAAATAA 578
                            v   i  v - i i   iiii   v    i  v     i vvivi  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_157443234_    579 AAACATAAAGTGAGGAAAG--------------------GTGCTGGGCCA 608
                         i v   vv i  i      --------------------        v  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_157443234_    609 ATTTGTCAGCCATATGTAGA-GAATGAAACTGGATCTTCATCTCTCACCT 657
                          i v vi ?   i   i i -       ii    i iii i   v    v
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_157443234_    658 TATACAAAAATCAACTCAAGGTAGATCAAAGACTTAAATATAAGACCTGA 707
                                    i       ii i     ?    i     i     v  i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_157443234_    708 AACCTTAAAAATTCTAAAAGATAACATTGGAAAAACCCTTCTAGACATTG 757
                            iv     v ii  i    v     v  ?iv  vi    vv   v   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_157443234_    758 TCTTAGGCAAAGACTTCATGACCAAGAACCCAGAAGCAAATGCAATAAAA 807
                         vv        v ii   v iivi v  vv   i     v v    i    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_157443234_    808 ACAAAGATAAATAGATGGAACTTAATTAAACTAATTAA--------GTAC 849
                         iv   i   i   i  v i    v  i   ---     --------  i 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAA---ATTAAAAACTTTTGTGC 668

  chr2_157443234_    850 AGCAAAAGAAATAATCAGCAGAGTAAACAGACAACCTACAGAGTGGGAGA 899
                         vv    i  v iv    iv i   i  v        i     i       
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_157443234_    900 AAATCTTGGCAA-TC-TATACTTAGATTGCCAACAAAGCTCTAATATCCA 947
                             v  v    -  -    ii -   -------  i vv  vi      
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCT-GAT-------AAGGGACTTGTATCCA 760

  chr2_157443234_    948 GAATCTACAAAGAACTCAAACAAATCAGCAAGGAAAAAAACCAAACAATC 997
                             v  i         vv    v   ii  vi    i --    i  i 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CAAATAACC 808

  chr2_157443234_    998 CCATCAAAAAGTGGGCAA-GGAC----ATAGACAATTTTCAAAAGATGAT 1042
                          v  i?    i       -   i----       v  i  v     v   
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_157443234_   1043 ATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCACTAACGAT 1092
                                       i  i  i       i             ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (87 / 59)
Gap_init rate = 0.02 (13 / 633), avg. gap size = 4.15 (54 / 13)  


3275 26.35 0.66 0.55  chr2_157453644_157459095.rev     4054  4960 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_157453644_   4054 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAACCAATATCGTGAAAAT 4103
                              ii i  i     i      i v      vii     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157453644_   4104 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4153
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157453644_   4154 TACCAATCACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4201
                          v   iiii i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_157453644_   4202 TATGGAACCAAAAAAGAGCCCGGATAGCCAAGTCAATCCTAAGCCAAAAG 4251
                                viiv  ii  v  v i        iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_157453644_   4252 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4301
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_157453644_   4302 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGATC 4351
                                 i   i    ii         i iv ii i   v v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_157453644_   4352 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 4399
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_157453644_   4400 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4449
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_157453644_   4450 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4499
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_157453644_   4500 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4549
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_157453644_   4550 TTAAAGACTTCAACGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 4598
                          i ?    i v  i  v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr2_157453644_   4599 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4648
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_157453644_   4649 AAACACCAAAAGCAATGGCAACAAAACCAAAATT-GACAAATGGGATCTA 4697
                         vi            vvi         vv    v -  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_157453644_   4698 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4747
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_157453644_   4748 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 4797
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_157453644_   4798 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4847
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_157453644_   4848 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 4897
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_157453644_   4898 CTCAAAAGAAGACATTTATACAGCCAAAAAACACATGAAAAAATGCTCAC 4947
                            v        i  vi v ii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_157453644_   4948 CATCACTGGCCCT 4960
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1780 26.06 4.13 5.86  chr2_157496742_157498846      695  1615 (490)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_157496742_    695 AGAGATATATCATGAT-ACAGATTGCAACA--TAATGTTCTCAAGA--AC 739
                          i      vi    v - ii     v  v --    i  v i    --i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_157496742_    740 TAAATTTTCTTCAAATCAATCTATTGGTTCAATGCAATCAATCTCAGTCA 789
                         --   vi  ii     ii     iv i     i      --- ii -   
  L1M4_orf2#LINE/     54 --AATACTCCCCAAATTGATCTACAGATTCAACGCAATC---CCTA-TCA 97

  chr2_157496742_    790 AAATCT-AGAAAGGGTTTTGGTAGAAATTGACATGATGATTGTAAAATCT 838
                              i-  vvivvv    v i           v v    iv      ii
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_157496742_    839 GTATGGACTTTCAAGGAACCTAGAATAGCCAAA-CAATTTTGAAAAAGAA 887
                         i      vv v     i   i            -    i           
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_157496742_    888 GAGCTGAGTTTGAACATTTAAACTATTAATACACAATCTCAAGACTTAAT 937
                           i vi    v  iv i i v   ----- v -    i    i     v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACT-----TCC-CAATTTCAAAACTTACT 241

  chr2_157496742_    938 GTAATGAAACTCCAGTAATCAAGAC----TGAT--TTATATCAAGATAGC 981
                         ii  --- i  v             ----  i -- vii  v i     v
  L1M4_orf2#LINE/    242 ACAA---AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_157496742_    982 TATAAAGATTTTTTAAAACTGTCAGAA-AGAATACAGAGTCCAGACA-AA 1029
                         i   v    i------  -  ---   -     vv          v -  
  L1M4_orf2#LINE/    289 CATATAGATC------AA-TG---GAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_157496742_   1030 GACTACACTTCTATAGTCAA--AAATTTTAATGAAGGAACTGGAACAATT 1077
                         iv i i  v i   i     --i v   ii ii i  vi iiii  v   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_157496742_   1078 AAATGGAGAAAGACAAATCTTTTCAATATATGGTTCTGGAAAAACTG--- 1124
                         v     i      vv i         i v     v    i v     ---
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_157496742_   1125 -CCTATGTGGGGGAAAAAATAAGCCTTCAATCATATCTCAGATCATATAT 1173
                         -? i ii  vi--   i   i ivi vv vi v  i    v i      i
  L1M4_orf2#LINE/    429 AKCCACATGCA--AAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_157496742_   1174 AACAATTAATTCAAGACAAATCATAGACCTAAACATAA-AGTATAATACT 1222
                           v      i    i iii    ?         ii   -  i-   v   
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACT 525

  chr2_157496742_   1223 CTACAGTTTCTTGTAGAAAGCA--AGAGAAAATCTTCATGACCACGTGGT 1270
                         v  v ii ii v v     i  --i ? v        i     vi -   
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG-GGT 574

  chr2_157496742_   1271 GTAGAAAAAAATTTA--AGAACTGGATCCAAAATCCTTATTTATGAAAGA 1318
                         -   iv  vii   v--   vv  ivv      v viv viv ii     
  L1M4_orf2#LINE/    575 -TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_157496742_   1319 AAAA-TAGATTAAATGTATGTAATCCCAGTTTAAGA------TGCCAATT 1361
                             -     v  v  v iv v   vv i  v  i ------   i-- i
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT--TC 671

  chr2_157496742_   1362 AAAAGATACCACTAAGAAAATGATAAATAAGCAAGTCTCAGATTGTGAGG 1411
                            i  i  i ii      i   -   v --   vi v    v  v   i
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGA-AAAGA--CAACCCACAGAATGGGAGA 718

  chr2_157496742_   1412 AAATGTTCATGATATGTTTATGAAATAATGTTATATTTCA-AAAGGACTT 1460
                             i  -------  i-----    v  ---    i v -  i      
  L1M4_orf2#LINE/    719 AAATATT-------TGC-----AAATCAT---ATATCTGATAAGGGACTT 753

  chr2_157496742_   1461 CCGTCCAGAACACATATACAAATCTTACAATCCAATACTAAAA-TATAAA 1509
                         vii       i i   v v  v        ii     v     -v i   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_157496742_   1510 TGAACCCA--CAAAAATAATAGACAAAAGACTTGAACAGGAAATTTATA- 1556
                          -      --i?    --  i i    i  i     i  - v    v v-
  L1M4_orf2#LINE/    804 T-AACCCAATTWAAAA--ATGGGCAAAGGATTTGAATAG-ACATTTCTCC 849

  chr2_157496742_   1557 AAGGAAGATATAGAAATGGTCAATAGAAACCTTTAAAAATGTTCAACATG 1606
                           i         v      i     iiv  v vv   i   i       v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_157496742_   1607 ATTAAAGAA 1615
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.34 (135 / 101)
Gap_init rate = 0.05 (42 / 905), avg. gap size = 2.19 (92 / 42)  

1969 18.61 4.22 0.25  chr2_157496742_157498846     1687  2089 (16)    L1M4_orf2#LINE/L1      379   797 (111)  

  chr2_157496742_   1687 CAATGGGAAAAGGTCAGTTTTATCAACAAAAGATGCTGGAAAAACTGGAT 1736
                                i    ivi   i  v        v i      i v        
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_157496742_   1737 ATCTACATG-AAAAGAAGAAAGTTAGACCCTTAGCCTGA-ACCTTATATA 1784
                          ? i     -       vi     i     i  -   v -   v    i 
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTA-CCTCACACCATATACA 477

  chr2_157496742_   1785 AAAATTCATTTAAA-TGGACCAAAGACCTTAATGTAAGTGCTAAAACTGT 1833
                               v i i   -    i  ?      v        v         i 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_157496742_   1834 AAAACTCTTAACAGAAAACGTAGGGGAAGATCTTCATGACATTGAATTTG 1883
                                   iv       i    ? v i      i    v   ii  v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_157496742_   1884 GCAATGATTTCTTGCGCATGACACCAAAAG--------------AAAAAA 1919
                               i      ivii             --------------i     
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_157496742_   1920 GTAGATAACTTGGACTTCACCAAAATTTAAAACTTTTGTGTATGAAAGGA 1969
                         i       v          i       v            iv v      
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_157496742_   1970 CACCATCAAGGGAATGAAAAGACAACCCACAGAATGGGATTAAATATTTG 2019
                            i      ii i                         vv         
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_157496742_   2020 CCAATCATGTATCTGATGAGAGGTTAACATTCAGACCATATAAAGAACTC 2069
                          v      i        i  i ii vii  i    vi             
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_157496742_   2070 CTATCACTCAACAACAATAA 2089
                         i  iv      i  i  v  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAA 797

Transitions / transversions = 1.77 (46 / 26)
Gap_init rate = 0.01 (5 / 419), avg. gap size = 3.60 (18 / 5)  


2758 21.46 6.15 0.14  chr2_157594783_157596469.rev      501  1199 (488)    L1M4_orf2#LINE/L1      168   908 (0)  

  chr2_157594783_    501 CAGAA--GCCAAGTCAATTTTTAAAAAGAAGAACAATGTTGAAGGACTTC 548
                              --     iv    i  v              v    i      iv
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_157594783_    549 CACTACTCAATTTTAAAATGCACCATAAAGCTACAGGAATCAAGGCAGAG 598
                             v i      i    ivi  i i          v       i   v 
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_157594783_    599 TGTTATTGGCATAAAGATAGGAATGTAGAT-----AAACAGAATTGAGAG 643
                           v  i        i     iv  i     -----i  i           
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_157594783_    644 TTAAGAAATGAA-----------ATG--------ATTTTTTACAAAGGTA 674
                          iv      i  -----------   --------     iv    i   i
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_157594783_    675 CTCAGGCAATTCAATTGAAGAAAGGATGGTGTTTTTGACAGATAGTGCTA 724
                          iv  i v       - ii     i  i  v    ii   i  i     i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_157594783_    725 GGACAATTAGTTATCCATTTGTAAA-GAATTAGCTTAGTCTCTTCTCTCA 773
                               i i v  ?   iv  i   -    v iv  i v i i vi    
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_157594783_    774 CACTAT-CAAGAAAATTATCTCAAAATGGTTCACAGGTCTAAATATAAGA 822
                            i  -i vi       v          v   ?  ii      i     
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_157594783_    823 GTTTAAACAATAAAACTTCTGAAAGAAAATATAGGAGAAAACCTTTGTGA 872
                          i v    v        ii ii       i     ? v   i   i    
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_157594783_    873 ACTTGAGTTAGGCA--GAGTTCTCAGATATGACATCAAAAGCACA-GTG- 918
                         v    i        -- iv    i          i          - ii-
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_157594783_    919 CATAAAATAAAAT-GATAAATTAAATTTCATTAAAATTAAAA-TATTTGC 966
                           v  i v     -        ii i     i          -iv    i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_157594783_    967 ACTTCAAGAGATACT-TTAAGAAAATAAAAACACAA---A-AGACTGTGA 1011
                         i      ii  i   - i      i i    v    --- -   v  v  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_157594783_   1012 AAAAATATTTGCAAATTACATGCCTCATAAAAGTATTGTATCCAGAATAA 1061
                         i               i i  ii  v    ii vv              v
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_157594783_   1062 ATAAAGAAGTCTCACAAGTCA-TAATAATAACACAAA-ACCCCGATATAA 1109
                                 v   i    v   -      v  v     - v   i  v?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_157594783_   1110 AAATGGGTAAA--ACTTAAATGAACATTTCGCCAAAAAAGACATAAGAAT 1157
                                i   -- i  i   ii       v     i    i   vi   
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_157594783_   1158 CGCTAATAAGCACATGAAAAGATACTTAACTTTATTAGGCAT 1199
                         v  i                   i  i   v i ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (97 / 49)
Gap_init rate = 0.02 (18 / 741), avg. gap size = 2.44 (44 / 18)  


2624 27.70 2.89 1.89  chr2_157632819_157636745.rev     2537  3435 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_157632819_   2537 TGGAAGACCATTCCATGTTTATGGATTAACAGAATTGATACCATTAAAAT 2586
                              iivi  i       i       iiv   v  i   iii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157632819_   2587 AGCCATACTGCCCAAAGCAATTTACAGATTCAATGTTATTTCTATCAAAC 2636
                         i  v     v      vii  i           i iv  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157632819_   2637 TACCAA-TGTCATTTTTCATAGAA-TTGGAAAAAGCT-ATGCTAAAATTT 2683
                          v   i-  i -     iii    -   -- v     -  v        i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_157632819_   2684 ATATGGAACCAAAAAAGAATCCAAATAACCAAAACAATCCTCAGCAGAAA 2733
                                 viiv  ii  vi vi    i           i v iv ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_157632819_   2734 GATTAAATCTGGAGGCATTACATAACCTGACTTCAAACTATACTGTAAGG 2783
                           vi   vi      vv i   ivv  ii i      viv    ii  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_157632819_   2784 CTAGAGTAAGCAAAATAGCATGGTAGTGGTACAAAAACAGATACATAGAC 2833
                            v     v   i i  ii     v   i i  ii i   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_157632819_   2834 CAATGGAGCAGAATAGAGAACTGAGAAATAAAGCCACACACCTACAGCTA 2883
                                ii     v    iiiv         v   i   ii  ii ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_157632819_   2884 TCTACTCTTCAACAAAGTTGACAAAAATAAGCAATGGGGAATGGACTCCC 2933
                         vi iv i   i    i v  v   i vi vv          v i i----
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT---- 393

  chr2_157632819_   2934 AGACTCCCTATTCAATAAATGGTCCTGGCATAACTGGCTAGCCATATATA 2983
                           v  i----     i       v    v i      v  ?   i  ii 
  L1M4_orf2#LINE/    394 AGTCTT----TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_157632819_   2984 GAAGAATAAAACTGGACTCCTACTTTTCACCATATACAAAACTTAACTTG 3033
                         i      i  ii     i     i iv              v      ii
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_157632819_   3034 AGGTAGACTCA-AGATTTAACTGTAAGACCTCACGCTATGAGAATCCAAG 3082
                          ii i  -   -   ii   v       v  v vi    i i v  iv  
  L1M4_orf2#LINE/    490 AAATGGA-TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_157632819_   3083 AGGAAAACCTAGGAAACACTATTCTTGACATCTGTGTTGGAAAATAATGT 3132
                          i      v    ?ivv v v   v    v -  v   i iv   ii v 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTT 587

  chr2_157632819_   3133 AT--GATTAAGTTCTCAAAAGCAATTGAAACAAAAATAGAAATTGACAAA 3180
                         v --   - v vivi        vvv v       iv i    v  i   
  L1M4_orf2#LINE/    588 CTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_157632819_   3181 TGAGACCTAATTAAA-TTAAAGAGCTTTTGCACAGCAAAAGAAACTATCA 3229
                          vi   i v  i   -     i -      ii vv    i  v       
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_157632819_   3230 CCAGAGTAGACAGACAA---AAGGAGAATGGGAGAAACTAT--------- 3267
                         vv i   ii v      --- v--             v   ---------
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCAC--AGAATGGGAGAAAATATTTGCAAATC 733

  chr2_157632819_   3268 --ATATCCAACTAAGGTCTGATATCCAGAATCTGTAATGAACTTAAACAA 3315
                         --     ii iv i  v  vi          v i   v     ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_157632819_   3316 TTAAACAAGCAAAAAAC---TATCT--ATTACAAAATGGGCAAAAGACAT 3360
                         i v  i  vv    i  ---  v i--   ?v            i  iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_157632819_   3361 GAACAGACACTTTTCAAAGGAAGATACACAATTGGCCAACAAACATATGA 3410
                            i     i  i  v  i       i    v       i  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_157632819_   3411 AAAGCTGTTCATCATCACTAATCAT 3435
                             v  i   v     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.26 (43 / 19)  


3203 26.43 0.66 0.66  chr2_157644610_157651003.rev     4995  5902 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_157644610_   4995 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5044
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157644610_   5045 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5094
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157644610_   5095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5142
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_157644610_   5143 TATGGAACCAAAAAGAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAA 5192
                                viiv  i -  v  v v  v     i      i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_157644610_   5193 GAACAAAGCTGGCGGCATCACGCTACCTGACCTCAAACTATACTACAAGG 5242
                                 i   v  vv    i  v  ii ii     viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_157644610_   5243 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGAC 5292
                                  i   i    ii         i iv ii i   v v     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_157644610_   5293 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5340
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_157644610_   5341 CATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5390
                           vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_157644610_   5391 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5440
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_157644610_   5441 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5490
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_157644610_   5491 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAA 5539
                           i ?    i       v   v       i      -    -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr2_157644610_   5540 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5589
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_157644610_   5590 AAAACACCAAAAGCAATGGCAACAACAGCCAAAATTGACAAACGGGACC- 5638
                          vi            vvi       v  vv     v  i   iv    i-
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_157644610_   5639 AATTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGA 5688
                         v  i   v v  i i   i iii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_157644610_   5689 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5738
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_157644610_   5739 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5788
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_157644610_   5789 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGATCAGACACT 5838
                            i     i     v  i?    i     i     iv   vi     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_157644610_   5839 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5888
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_157644610_   5889 CCATCACTGGCCAT 5902
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3139 27.97 0.33 0.33  chr2_157751956_157755532     2180  3087 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_157751956_   2180 TGGAAGAACATTCCATTCTCATGGATAGGAAGAATCAATATCATGAAAAT 2229
                              ii i  i    vi        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157751956_   2230 GGCCATATGGCCCATGGTAATTTACAGATTGAATGCCAACCCCATCAAGC 2279
                            v   ivv    viv i  i        v  i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157751956_   2280 TACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTCAAAGTTCATA 2329
                          v   iivi i  i  ii     v v  v  iv v iiii   i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_157751956_   2330 TGGAACCAAAAAAGAGCCCTCATAGCAAAGACAATCCTAAGCATAAAGAA 2379
                              viiv  ii  v  vvv     v  i      i i iv vi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_157751956_   2380 CAAAGCCAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGTTA 2429
                              iii    vv   ii  v  ii i      viv        i i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_157751956_   2430 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 2479
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_157751956_   2480 TGGAACAGAAC--AGAGCCCTCAGAAATAACATCACACATCTACAACCAT 2527
                              i    i--    i  --        vvi  i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_157751956_   2528 CTGGTCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCT 2577
                         i  i i  i     ivv  vv  i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_157751956_   2578 ATTTAATAAATGGTGCTGGGAAAACTGGCCAGCCATATGTAGAAAGCTGA 2627
                         v  i  i              v      vi ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_157751956_   2628 AATGGGATCCCTTCCTTACTCCTTATACAAAAATTAATTCAAGATGGATT 2677
                          i v   i    v   i  v  v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_157751956_   2678 AAAGACTTAAAGGTAAGATCTAAAACCATAAAAACCCTAGAAGAAAACCT 2727
                          ?    i    v      v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_157751956_   2728 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 2776
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_157751956_   2777 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATTTAAT 2826
                                     vvi          vv     v  i    v   i  v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_157751956_   2827 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGCGTGAACA 2876
                         i   v v  i i   i  ii vv    i  v    i  vv iv     v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_157751956_   2877 GGCAACCTGCAGAATGGGAGAAAATGTTTGCAATCTACCCATCTGACAAA 2926
                          i     ii                i       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_157751956_   2927 GGGCTAATATCCAGAATCTATAAAGAACTTAAACAAATTTATAAGAGAAA 2976
                           i  vi          v           ivv    v iv    v i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_157751956_   2977 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAGCAGACACTTCT 3026
                         i     i     v  i?    i            v   ii     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_157751956_   3027 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 3076
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_157751956_   3077 TAACTGGTCAT 3087
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (147 / 103)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


2993 26.65 0.86 2.91  chr2_157779526_157785323.rev     4380  5306 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_157779526_   4380 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4429
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157779526_   4430 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCAACCCCATCCAGC 4479
                            v   i v     iv i  i  i        i  v v   i   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157779526_   4480 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4527
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_157779526_   4528 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 4577
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_157779526_   4578 AACAAAGCTGGAGGCATTATGCTACCTGACTTCAAACTATACTACAAGGC 4627
                                i      vv i ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_157779526_   4628 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGCATGGTACTGG 4677
                                 i   i    ii         i --------------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA-------------------- 278

  chr2_157779526_   4678 TACCAAAACAGAAATATACACCAATGGAACAGAAC--AGAGCCCTCAGAA 4725
                           -- ii i   v     v i        i    i--    i  --    
  L1M4_orf2#LINE/    279 TA--AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAA 324

  chr2_157779526_   4726 ATAATACCACACATGTACAACCATCTGATCTTT---AAACCTGACAAAAA 4772
                             vv   i    v  iiii  vi    i  i---  ivv  v   i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_157779526_   4773 CAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACT 4822
                           vvv           i  vvi  v  i  i              v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_157779526_   4823 GGCTAACCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTATGCCTTAT 4872
                           v  ?   i   i i  iiv    ii    i    v   i ii  v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_157779526_   4873 ACAAAAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAAC 4922
                                    i    i      i ?    i       v   v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_157779526_   4923 CATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGC 4971
                         i      vi i           v    ?i- v i -   iv   v v  v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

  chr2_157779526_   4972 ATGGGCAAGGACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGC 5021
                         v i     v ii   v iiv  vi            vvi          v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_157779526_   5022 CAAAATTGGCAAATGGGATTTAATTAAACTAAAGAGCTTCTGCACAGCAA 5071
                         v     v ii    v   i  v  i   v v  i i   i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_157779526_   5072 AACAAACTACCATCAGAGTGAACAGACCACCTACCGAATGGGAGAAAATG 5121
                          iv v    i  vv i      v    v   i  v              i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_157779526_   5122 TTTGCAATCTACCTATCTGACAAAGGGCTAATATCCAGAATCTACAAAGA 5171
                                vii iv       i  i  i  vi          v  i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_157779526_   5172 ACTTAAACAAATTTACAAGAAAAAATCAAACAACCCCATCAAAAAGTGAG 5221
                            ivv    v iv i  v     iv    i     v  i?    i  i 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_157779526_   5222 CGAAGTATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAGC 5271
                          i   v  v    i     i     v        i  vi viii    ii
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_157779526_   5272 AGATACATGAAAAAATGCTCATCATCACTGGCCAT 5306
                          iii         i       v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.50 (35 / 10)  


2655 25.51 4.20 1.25  chr2_157790974_157796458     4112  4993 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_157790974_   4112 TGGAAACACATCTCATGCTCATGGATTAGAAGAATCAATATTGT------ 4155
                               v i   i    i         i     v i        ------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157790974_   4156 ---GATACTGCCCAAAGCAATCTACAGATTCAATGTGATTCCTATTAAAA 4202
                         ---i     v      vii              i ii  i     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157790974_   4203 TACCAA-TACCATTTTTCACAGAA-TTAAAAAA--AATACTAAAATGCAT 4248
                          v   i- i  -     ii     -  i v  i--i  v       v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_157790974_   4249 ATGGAACCAAAAAAGAGCCTAAATAGCCAAAGCAATCCTAAGCAGAAAGA 4298
                               viiv  ii  v  vi          i     i i iv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_157790974_   4299 ACAAATTTGGAGGCATTACATTACCAGATGTCAAATTATACTACAAGGAT 4348
                              v       vv i   i v  vi  v     viv        i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_157790974_   4349 ATAGTTACCAAAACAGCATGGTACTGATATAAAAAGGAGATGCATCGACT 4398
                          i   v i   i    ii        ii    ii v-   iii  v  ii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGATC 298

  chr2_157790974_   4399 A---GAACAGAATAGAGAACTCAGGTATAAAGCCAAATAATTACAACCAA 4445
                          ---   i     v    iii   iv     v   v i v   iiii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_157790974_   4446 CTGATCTTTGACAAAGCATATAAAAAC-ATAAATTGGGGAAATGATACCC 4494
                         i    i  i     i -i iiv  i  -  vv v        vi   vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_157790974_   4495 TATTAAATAAACGGTTTTGGGAAAACTGGCTAGCCACAAGTAGAAAAACG 4544
                          v  v  i   i   vi     v      v  ?     v i i  i  i 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_157790974_   4545 AAACTGGATCC-TGTCTCTCACCTTGTAAAAAAATCAACTCAAGAGGGAT 4593
                           ii    i  - ii   v    v i  v      i       i v    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_157790974_   4594 CAAATACTTAAATCTAATAGACAAAAACATAAAATTTCTAGGAGATGACC 4643
                           ? v  i     v   v  vi    vi      i ii   i   vi  v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_157790974_   4644 TAGAAAAAACTCTCTG-GACATTGGCTTAGGCAAAGAATTCATGACTAAG 4692
                            i?iv  v   ii -   v    v        v iv   v iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_157790974_   4693 ACCTCTAAAGCAAATGCAACAAAAATTTAAAAAATA-ATAAATGAGACCT 4741
                           vi v      v v         i---        -      vi   i 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAG---AAAAAATAGATAAATTGGACTT 644

  chr2_157790974_   4742 ------AATTAAAAAGCGTCTGAACAGCAAGAGAAATAATCA------TC 4779
                         ------         - v i  vi vv   ii  v iv    ------ v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_157790974_   4780 AAACATACAACTCACAGAATGGGAGAAAATATTTGCAAACTATGCATCTG 4829
                            - v     i                           ii  ii     
  L1M4_orf2#LINE/    694 AAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_157790974_   4830 ACAAAGGA-TAATATAGAGAAACTACAAAGAACTCAAACAAATCAACTAA 4878
                          i  i   - vi   vv    vv  i         vv    v    -   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA-TAA 791

  chr2_157790974_   4879 GAAAAAAACAA----TCTCATCAAAAAGTGAGAAAATGACATGAATAGAC 4924
                         v     i    ----i iv  i?    i  i v   v  iv         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_157790974_   4925 ATTTCTCAAAAAAATATATATACAGATGGCCAATGAACATATGAAAAGAT 4974
                                v   i  v     --  i         i i  i          
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATA--CAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_157790974_   4975 GCTCAATATCACTTATCAT 4993
                               i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (131 / 90)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.29 (48 / 21)  


2112 22.83 2.20 15.47  chr2_157801181_157803711.rev      994  2040 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_157801181_    994 TGGAAACACATCCCATGCTCATGAATGGGTAGAATCAATATTGTGAAAAT 1043
                               v i        i     i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157801181_   1044 GACCATATTCCTAAAAGCAATCTACAAATTCAACACAATCCCCATCAAAA 1093
                          i v   i   iv   vii       i       i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157801181_   1094 TACCACCATCATTCTTCACGGAATTAGAAAAAAACAG-TTCTAAAATTCA 1142
                          v   v vv v  i  ii i   v v  v  i-- v - i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_157801181_   1143 TATGGAACCAAAAAAAGAGCCTGCATAGGCAAAACAAGACTAAGCAAAAA 1192
                                viiv  ii-  v  v v    v        vvi i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_157801181_   1193 GAACAAATCTGGAGGTATCACATTACCTGATTTCAAACTATACTATAAGT 1242
                                vi      vv     i v  ii        viv     i  iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_157801181_   1243 CCATAGTCACCAAAAAAGCATGGTACTGGTATAAAAATAGGCACATAGAC 1292
                          i i   v i   i v  ii         i    ii    i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_157801181_   1293 CATTGGAACAGAATAGAGAACCCAAAAATAAACCCAAATACTTATATCTA 1342
                           v     i     v    ii   i           v i i    ivii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_157801181_   1343 ACTGAACTTTGACAAAGCAAACAAAAACATAAAGTGGCGGAAAGGACACC 1392
                          i   vi  i     i vviv   i v   vv i   -      i i vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGT 396

  chr2_157801181_   1393 CTTTTCAACAAATGGTGCTGGGATAATTGGGTGGCCACATATAGGAGGAT 1442
                                                i  i   i i?      ii ii  i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_157801181_   1443 GAAACTGGAGTCTCATCTGTCACATTATACAAAAATCAACTCAGGTAGCC 1492
                            ii    vi ii i  --    ii   ---------------------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCT--CACACCATA--------------------- 473

  chr2_157801181_   1493 AGGTGTGGCAGCATGCGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCA 1542
                         -------------------------------   ----------------
  L1M4_orf2#LINE/    474 -------------------------------TAC---------------- 476

  chr2_157801181_   1543 GGAGAATTGCTTGAACCCAGGAGGCGGAGGTTGCAGTGAGCCGAGATTGC 1592
                         --------------------------------------------------
  L1M4_orf2#LINE/    477 -------------------------------------------------- 476

  chr2_157801181_   1593 ACCACTGCACTCCAGCCTGGGCGACAGACTCAGTCTCAAAAAATCAACTC 1642
                         --------------------------------------      i     
  L1M4_orf2#LINE/    477 --------------------------------------AAAAATTAACTC 488

  chr2_157801181_   1643 AAGATTGATTAAGTACTTAAATCTAAGACCTAAAACTATGAAAATTCTAG 1692
                           i  v   i ?iv  i     v     v          i   v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_157801181_   1693 AAGATAACATTGGAGAAACCCTTCTAGACATTGGCTTAGGCAAGGAGTTC 1742
                             v     v  ? v  vi    vv   v    v        v iv   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_157801181_   1743 ATGACCAAGAACCCAAAAGCAAATGCAGTAAAAACAAAGATAAATAGCTG 1792
                         v iivi v  vv         v v   ii    iv   i   i   iv v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_157801181_   1793 GTACTTAATTAAACTAAAAAGCTTTTGCATGGCAAAAGGAACAGTCAGGA 1842
                          v    v  i   v v    i      iiivv    i iv  vi   i  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_157801181_   1843 GAGTAAACAGACAACCCACAGAATAGGAAAAAATCTTCACAATCTACACA 1892
                         i   i  v                i   i     v  ii   vii i i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_157801181_   1893 CCTGACAAAGGACTAATATCCAGAATCTACAATGACCTCAAACA--CCAA 1940
                         i    i  i     vi          v  i  v  v   vv   --i   
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_157801181_   1941 CAAGAAAAGAACAA----TCCCATCAAAAAGTAG--------------TA 1972
                         i  v    ii    ----i  v  i?    i i --------------  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_157801181_   1973 --CAATTCTCAAAAGAAAATATACAAATGGCCAACAAACATAAGAAAAAA 2020
                         --  v     v      i                i  i  i v     i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_157801181_   2021 TGCTCCACATCGCTAATGAT 2040
                              v     i????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 16.82 (185 / 11)  


1450 30.11 1.54 0.44  chr2_157809213_157814962     3959  4413 (1337)    L1M4_orf2#LINE/L1        1   460 (448)  

  chr2_157809213_   3959 TGGAAAAATATTCCATGCTCATGGATAGGAAGCATCAAAATTGTTAAAAT 4008
                               i    i     i        v     vv i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157809213_   4009 GGCCATGCTACTCAAAGCAATCTACAGACTCAATGCTATTTCTATCGAAC 4058
                            v  i  v i    vii         i    i  v  ii     i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157809213_   4059 TATCAATATCATTTTATTCAGAAGTAGAAAGAACT-ATTTTAAACTTCAC 4107
                          vi  iivv v    v v     i v  v - i  -  ii    v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr2_157809213_   4108 ATGGAACCCGAAATGAGATGAAATAGCCAAGGCAATTCTAAGCATAAAGA 4157
                               vivv  iv  vviii         ii    ii i iv vi    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_157809213_   4158 AAAAAG-----GCA-TCATGTTACCTGACTTCAAACTGTACTACAAGTCT 4201
                          v    ----- v -   iii v  ii i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_157809213_   4202 GCAGTAACCAAAACAGCATGGTATCGGTACAAAAACAGACACATACACCA 4251
                         i      i   i    ii     ii  i i  ii i     i   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_157809213_   4252 ATGGAACAGAATAGAGAGCCCAGAAATAATGCTGCACACCTACAACCATC 4301
                               i     v     i          vv iii   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_157809213_   4302 TGATATTCAACAAAGCCAACAAAAACAAGCAATGGGGGAAAGGACCCCCT 4351
                             v   i    i viiv   i v  vv        -    i ivvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCT 398

  chr2_157809213_   4352 ATTCAGTAAATGGTGCTGGGATAACCAGCTAGCCATCTGCAGAAGATTAA 4401
                         v    ii              i   ii v  ?   iv    i    v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_157809213_   4402 AACTGGACCACT 4413
                          ii      v  
  L1M4_orf2#LINE/    449 AGTTGGACCCCT 460

Transitions / transversions = 1.72 (86 / 50)
Gap_init rate = 0.01 (5 / 460), avg. gap size = 1.80 (9 / 5)  

1237 24.50 3.34 2.23  chr2_157809213_157814962     4810  5258 (492)    L1M4_orf2#LINE/L1      455   908 (0)  

  chr2_157809213_   4810 ACACCTTTCTTACCTCACTTGCAAAAATCAACTCAACATGGATTAAAGAC 4859
                           v   vi  i  vi  iv i       i       v      i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_157809213_   4860 ATAAATGTAGAACCTAAAACTATAAAAGCCTTGGAAGAAAACCTAGG--- 4906
                         v        ii v              vi   i         v    ---
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_157809213_   4907 AAATACCATTCTGGATATAGGACCTGACAAAGATTTCA-AGACCAAGATG 4955
                             -- -   vv  iv v  iiiv i   v i    v-   i- v  ii
  L1M4_orf2#LINE/    555 AAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACA 600

  chr2_157809213_   4956 TCAAAAAAGCAATTGCAACAAAAACAAAAATTGGCAAATGTAG-CATAAT 5004
                         i     ivi   --         iv      v ii    - i - v v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAAT-TGGACTTCAT 647

  chr2_157809213_   5005 -AAAACTAAAGAGCTTCTGCGCATCAAAAGAAATGATCAACA----GAAT 5049
                         -    i    i -   i  i  v     i  v iv     v ----   v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_157809213_   5050 AAACAGCCTATAGAATGGGAGAAAATATTTTCTAATTATGTATTGGACAA 5099
                          i   i  i i                   v v   i  i   iv  i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_157809213_   5100 TGGTTTAATATCCAGAATCTATAAATAAATTAGACAA----ATAGGGCAA 5145
                         v  vi vi          v      v  v ivv    ----   i--i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA--TAA 794

  chr2_157809213_   5146 GCAAA-AAACAACCCCATTAAAAAGTGGGCAAAGGACATAAACAGACAAC 5194
                         iv i -   i     v   ?    i           iv i  i     vi
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_157809213_   5195 TTTCAAAAGAAGACATACATGTGCCCAACAAGCATATGAAAGAATACTCA 5244
                          i  v        i     vi  v    i     i      ii  i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_157809213_   5245 ATATCACTAATCAT 5258
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (63 / 45)
Gap_init rate = 0.03 (14 / 454), avg. gap size = 1.79 (25 / 14)  


2997 26.51 1.21 1.32  chr2_157820605_157824879.rev     2875  3783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_157820605_   2875 TGGAAACATATCCCATGCTCATGGATGAGTAGAATCAATATTGTGAAAAT 2924
                               v          i        vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157820605_   2925 GGCCATATTGCCAAAAGCAATCTATGAATTCAACACAATCCCCATCAAAA 2974
                            v   i v  v   vii     iii       i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157820605_   2975 TACCA-CCATCATTCTT-CAAAGAATTACAATAAAC-AATTCTAAAATTC 3021
                          v   - iii v  i  -  i -    i-- i  i -i  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_157820605_   3022 ATATGGAACCA-AAAAGAGCCTGCATAGCCAAAGCAAGAGTAAGCAAAAA 3070
                                 vii-  ii  v  v v         i   vvv i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_157820605_   3071 TAACAAATCTGGAGACATCATTCTACCTGATTTCATACTATGCTATGAGG 3120
                         v      vi     ivv   iv  v  ii      v viv i   ii i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_157820605_   3121 CCTCAGTCACCAAAACATCATGATACTAGTATAAAAATAGGCACATGCAC 3170
                          iv    v i   i   vii  i    i i    ii    i  i  iv i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_157820605_   3171 CAATGGAAGAGAACAGAGAACCCAGAAATAAACCAAAATACTAACAGCCA 3220
                                 v    iv    ii             v v i i v ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_157820605_   3221 ACTGATCTTCCACAAAGCAAACAAAAACATAGCGTGGGGAAAGA-CACCC 3269
                          i    i   v    i vviv   i v   vvvi          -i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_157820605_   3270 TTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGCAGGAGAGTG 3319
                                               i  i   v  ?         ii   i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_157820605_   3320 AAACTGGATCCTCATCTCTCACCTCACCCAAAAATCAACTCAAGATGGAT 3369
                           ii    i  ii i   v    vi iv       i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_157820605_   3370 TAAGGACTTAAATCTAAGACCTGAAACTATGAAAATTCTAGAAGATAGCA 3419
                         i ?i   i     v     v  i       i   v ii       v i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_157820605_   3420 TTGATAATATTGGAAAAACCCTCCTAGACACTGGCTTAGGCAAGGATTTC 3469
                          v -------- ?iv   i i  v -   vi   v        v i    
  L1M4_orf2#LINE/    548 TAG--------GNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTC 588

  chr2_157820605_   3470 ATGACCAAGAGCCCAAAAGCAATTGCAATAAAAACAATGATAAATAGTTG 3519
                         v iivi v  vv         vvv    i    iv  vi   i   iv v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_157820605_   3520 GAACTTAATTAAACTAAAGAGCTTTTTCATGGCAAAAGAAACAGTCAGCA 3569
                          i    v  i   v v  i i     viiivv    i  v  vi   iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_157820605_   3570 GAGTAAACAGACAACCCACAGAGTGGGCGAAATTCTTTACAATCTATACA 3619
                         i   i  v              i    v    v v   i   vii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_157820605_   3620 TCTGACAAAGGACTAATATCCAGAATCTACAATGAATTCAAACAAATCAG 3669
                              i  i     vi          v  i  v   i  vv    v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_157820605_   3670 TAAGAAAAA---AAACAATCCCAT-AAAAAGTGGGCTAAGGACATCAATA 3715
                            v     ---   i  i  v  -?    i     v     iv v    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_157820605_   3716 GACAATTCTCAAAAGAAAATATGCAAATGGCCAACAA--ACATGAAAAAA 3763
                             v     v      i    i           i  --         i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_157820605_   3764 TGCTCAGCATCACTAATAAT 3783
                               i     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


2482 24.05 6.26 4.70  chr2_157888647_157890319.rev      288  1181 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_157888647_    288 TGGAGAGAAATACTGTTTTTATGGATCAGAAGATTCAATACTGATATAAT 337
                             i   v  v ii v  i      ii     i i    i  v  vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_157888647_    338 GCCAATTATCTCC----------------------TAATCC--ATCAAAC 363
                          v    vv  i  ----------------------i     --      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_157888647_    364 TTC-AATTGGGCATTTTCTTGGTAGAAATTGACAAGATGATTCCAAAATT 412
                          i - ii  -- v    i -- i             v    i i      
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_157888647_    413 AATATGAAAAT-TAAAGGACCTAGATTATCCCAAATAATTTTAAATAT-- 459
                         v     i    -i  i     i   v  v  v   i   i  i  v v--
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_157888647_    460 ---ACAAAATTTAGAGGTCTCACACTATCTGATTTCAAAACTTGCTGTAA 506
                         ---     i  -i    v        vi ii            i  ii  
  L1M4_orf2#LINE/    197 AGAACAAAGTT-GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_157888647_    507 AGTTAACCTAAATGAAACAGAGAAGTATTGATTTAAGGATAAATGTATTG 556
                           i  vvv   vii i    v vi   i  iiv        i ii   v 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_157888647_    557 AGTAATGGAATAGAATTGA-AG-CCAGAAGTAGATCCACACATGTATGGT 604
                          vi                -  -      i  i i   i    v      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_157888647_    605 TAACTGGTTCTTTATAAAGGTGCCAAAGTAATTTATTGGAAAATGAATAG 654
                         i  i  i  i iv i  i        iiiv   i v   ii  v      
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_157888647_    655 CTTTTTTTTTTAACACATAGGATTGAAATAACTGGA-ATCTAGATGCTAC 703
                         ---- i    i    v  i vii  ii i       - ? i v    v v
  L1M4_orf2#LINE/    396 ----TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_157888647_    704 ATAATGAAATTCAACACCTATCTCACACCATATTAAGAAAATGAGATTGA 753
                          v      i  vi  v    i            - vi     v iv ii 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAA 490

  chr2_157888647_    754 AATAGATTATAAGCCTTAATGAAAATTCTAAAACTTAAAAAAAAACTCTA 803
                            i   i ? ii   v    v  ivv        ---- v        -
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACT----ATAAAACTCT- 535

  chr2_157888647_    804 CATAAGAAAACATAGGAGAAAATCTTTTCTGCCTTAAGTTCATCAGAGAT 853
                         i v             ? v       ivivi    ii   viv  iv i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_157888647_    854 TTCCTAGATAGGACACACACACACACACACACACACACACACACACACAC 903
                            i      v     ---------------------  v vi    vi 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACAC---------------------CAAAAGCACAAGC 614

  chr2_157888647_    904 ACACAACCATAAAGGAAAATTAATAAGTTGGACTTTA-CATAAT-GAAAA 951
                          -    ----  iii     vi    i        i -  v   -i    
  L1M4_orf2#LINE/    615 A-ACAA----AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_157888647_    952 CATTTGTTTTTTGAATGACACTATTTAAACAGTGAAAATTCATGCTATAG 1001
                          v     vi  ii  v        iv i v        vv  vv i i  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_157888647_   1002 ATTGGG-GAAAATATTTGCAAAACACATCTTT--TGAAAGACTTGTATCC 1048
                          v    -               v  i  v i -- i ii           
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_157888647_   1049 AGAATACATAATACAATCTTACAACTCAATAATAA---GACAAACATCCC 1095
                               i    viv v                   ---      i v   
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_157888647_   1096 A--TAAAAAA---GCAAAAAGACTTGA-----CATTTCATCAAAGAAAAT 1135
                          -- ?     ---     i-  i    -----      vi       i  
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAG-GATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_157888647_   1136 ATACAACTGTC----AAGCTCGTGAAAGGGGACTGAACATTATTATTCAT 1181
                               v  v ----    v i     i ivi  v     i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (127 / 84)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.50 (98 / 28)  


3095 27.04 0.99 0.99  chr2_157956100_157962470.rev     4974  5879 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_157956100_   4974 GAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATAGTGAAAATGG 5023
                            ii    i     i        v      v i     v  v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_157956100_   5024 CCATACTGCCCATAGTAATTTATAGATTCAGTGCCATCCCTATCAAGCTA 5073
                          v     v    v v i  i  i       ii  v           iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_157956100_   5074 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT---CCTTTAAAGTTCA 5119
                            iivi i  i  ii     -   -- v  i  ---   --   i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCT--AAAATTCA 148

  chr2_157956100_   5120 TATGGAACCAAAAAAAGAGCCTGCATTGCCAAGACAATCCCAAGCGAAAA 5169
                                viiv  ii-  v  v v  v     i      iii ivi i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_157956100_   5170 GAACAAAGCTGGCGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5219
                                 i   v  vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_157956100_   5220 CCGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATGGAC 5269
                          ii      i   i    ii         i iv ii i   i    i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_157956100_   5270 GAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5319
                         v       i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_157956100_   5320 TCTGATCTTCGACAAACCTGACAAAAACAAGAAATGGAGAAAGGAC--CC 5367
                         vi    i        ivv  v   i v  vvv     i     i i--i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_157956100_   5368 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5417
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_157956100_   5418 AAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGAT 5467
                           ii    i    v   i    iv              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_157956100_   5468 TAAAGACTTAAACGTTAGACCTAAAACCGTAAAAACCCTAGAAGTAAATC 5517
                         i ?    i    i  v   v       ii     vi i      v   iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_157956100_   5518 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTAATGACTAA 5566
                             ?i- v i -   iv   v v  vv i     v ii  vv iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_157956100_   5567 AACACCAAAAGCAATGGCAACAAAAGCCAAAACAGACAAATGGGATCTAA 5616
                         i            vvi          vv    i   i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_157956100_   5617 TTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAGTGAAC 5666
                          i   v v  i i   i  iiivv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_157956100_   5667 AGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 5716
                           i  i  i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_157956100_   5717 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATGTACAAGAA-- 5764
                         i  i  vi          v  i         vv    v ---   v  --
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATA 793

  chr2_157956100_   5765 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGAATATCAACAGACGC 5814
                             i     i     v  i?    i         i  v v  i    ii
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_157956100_   5815 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAGAAATACTC 5864
                              v        i  vi viii     i ii        i i  i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_157956100_   5865 ATCATCACTGGTCAT 5879
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.80 (18 / 10)  


3196 27.42 0.44 0.44  chr2_158050056_158056335     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158050056_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158050056_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158050056_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_158050056_   5029 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_158050056_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_158050056_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_158050056_   5179 AATGGAACACAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5226
                                i v  i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_158050056_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_158050056_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_158050056_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_158050056_   5377 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAATCCCTAGAAGAAAAC 5426
                          i ?   ii    i  v i v       i      ii i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_158050056_   5427 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_158050056_   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_158050056_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_158050056_   5577 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_158050056_   5627 AGCGCTAATATCCAGAATCTACAATTAACTCAAACAAATTTACAAGAAAA 5676
                         i vi  vi          v  i  vv     vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_158050056_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_158050056_   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCTTC 5776
                           v        i  vi viii     v  i          i      vv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_158050056_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 975 28.47 1.07 1.07  chr2_158070633_158075256.rev     2871  3151 (1473)    L1M4_orf2#LINE/L1        1   281 (627)  

  chr2_158070633_   2871 TGAAAAAACATCCTATGATCATGGATAGGAAGAATCAATATCATTAAAAT 2920
                           i   i i    i   v        v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158070633_   2921 GGCCATACTCTCCAAAGCAATTTACAGTTTCAATGTTATTCCTATCAAAC 2970
                            v      i     vii  i     v     i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158070633_   2971 TAACAATGACATCCTTCACACAAA--GACAAAAGACT-ATTTTAAAATTT 3017
                          vv  iivi v ii  ii  v   --     i---  -  ii       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_158070633_   3018 ATATGGAACCAAAAAAGAGCCCAAATAGCAAAGGCAATCCTAAGCAAAAA 3067
                                 viiv  ii  v  vi      v  ii     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_158070633_   3068 GAAGAAAGATGGAGGCATCATGTTACCTGACTTCAAACTATACTACAGGG 3117
                            v    v      vv   iii v  ii i      viv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_158070633_   3118 CTACAGTAACCAAAACAGCATGATGCTGGTACAA 3151
                                  i   i    ii  i i    i i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

Transitions / transversions = 2.08 (54 / 26)
Gap_init rate = 0.01 (3 / 281), avg. gap size = 2.00 (6 / 3)  

1855 26.50 3.44 2.10  chr2_158070633_158075256.rev     3465  4132 (492)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_158070633_   3465 AAAACTTA-----AAG-TATAATAATAATAATAATAATAATAATAACAGG 3508
                                 -----   -  i i    v vi i i i- ii  v ----  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTG-TGGTACT----GG 276

  chr2_158070633_   3509 CACATGGA---ACAGA---ACCAATAGAACAGAATAGAGAGCGCTGAAAT 3552
                           i v   ---   v --- i    i   i     v     iv v     
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_158070633_   3553 AAGGCCACACACCTACAACCACCTGATCTTCAACAAAGCTGAAAAAACAA 3602
                           iv   i   ii  iiii  vi    i   i    i v  vv  i  v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_158070633_   3603 G-CAATGTAGAAA--ATACTCCTTATTCAGTAAATGATGCTCGGATAACT 3649
                         v-     vi    --   v  i  --   ii     i    v   i    
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACT 424

  chr2_158070633_   3650 TGCTAGCCATATACAGAAGCCTGAAGCTCAACCCTTTTTTTTACACCACG 3699
                         v v  ?   i  i  i   vv     i vi    i vii i-      ii
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC-ACACCATA 473

  chr2_158070633_   3700 TACAAAAATCAACTCAAGATGGATTGAAGACTTAAATATAAAACACAAAA 3749
                                  i       i      ii?    i     i   i vvi    
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_158070633_   3750 CTATAAAAACCCTGGAAGACAACGTAGGCAATAACATCCT-GT-ACATAG 3797
                                 vi i i     v   i    ?i-   -   i -  -  v v 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNG-TAA-ATCTTCGTGACCTTG 571

  chr2_158070633_   3798 AAACGGGAAAAGATTTCAT-GACGAAACGCCAAAATCAATCA--CAACAA 3844
                         iivii  v  v i    v -  iivi  i      v  --  --      
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA--CAAGCAACAA 619

  chr2_158070633_   3845 AAGCAAAAATTGATATATGGGATGTAATTGAACTAATGAGCTTCTGCACA 3894
                            v      v    v  v   iv v  ii  v v vi i   i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_158070633_   3895 GCAAAAGAAACTATCAACAGAGTAAACAGACAACCTACAGAATGGGAGAA 3944
                         v    i  v        v i   i  v        i              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_158070633_   3945 AATATTTACAAATTATGCATCTGACCAAAGTCTAATATCCAGCATCTATA 3994
                                i     i  ii      iv ii v  vi       v  v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_158070633_   3995 AGAAACT--TAACCAATTTA-CAAGAGAAAAACAAGCAACCCTGTTAAAA 4041
                          ii    --  --   i i -i  v i   i    ii     vi  ?   
  L1M4_orf2#LINE/    770 AAGAACTCTTA--CAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_158070633_   4042 AGTGGGCAAAGGACGTGAACTGACACTTTTCAAAGGAAGGCATGCATGTG 4091
                          i           iv    iv    i  i  v  i    ii  i  vi  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_158070633_   4092 GCCAACAAGCAAATGAAAAAAAGCTCAGTATCACTGATCAT 4132
                              i     v       i v     ii    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (110 / 63)
Gap_init rate = 0.03 (20 / 677), avg. gap size = 1.85 (37 / 20)  


3095 27.64 0.55 0.55  chr2_158079869_158086222.rev     4955  5862 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158079869_   4955 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCGTAAAAAT 5004
                              ii    i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158079869_   5005 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5054
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158079869_   5055 TACCAATGACTTTCTTCACAGCA-TTGGGAAAAACT-ACTTTAAAGTTCA 5102
                          v   iivi i  i  ii   v -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_158079869_   5103 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTCAGCCAAAAG 5152
                                viiv  ii  v  viv  v     iv     i v ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_158079869_   5153 AACAAAGCTGGAGGCATCACGCTACCTGATTTCAAACTATACTACAAGGC 5202
                                i      vv    i  v  ii        viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_158079869_   5203 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5252
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_158079869_   5253 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5300
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_158079869_   5301 ATCTGATCTTTGACAAACCTGATGAAAACAAGAAATGGGGAAAGGATTCC 5350
                          vi    i  i     ivv  vii i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_158079869_   5351 CTATTTAATAAATGGTGCTGGGAAAACTGGTTAGTCACATGTAGAAAGCT 5400
                           v  i  i              v      v  ?i      i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_158079869_   5401 GAAACTGGATACCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGA 5450
                            ii    iv   v   i     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_158079869_   5451 TTAAAGACTTGCATGTCAGACCTAAAACCACAAAAACCCTGGAAGAAAAC 5500
                          i ?    i iv    v   v       i i    vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_158079869_   5501 CTAAGCA-ATACCACTCAGGACATAGGCATGGGCAAGGACTTCATATCTA 5549
                         v  i ?i- v i -i  iv   v v  vv i     v ii   v  vv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_158079869_   5550 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTA 5599
                         vi            vvi          vv     v  i    v i ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_158079869_   5600 ATTAAACTAAAGAGCTTCTGCACAGCAAAACAAACTACCATCAGAGTGAA 5649
                           i   v v  i i   i  ii vv    iv v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_158079869_   5650 CAGGCAACCTACAGAACGGAAGAAAATTTTTGCAATGTACTCATCTGATA 5699
                         v  i     i      i  i       v       vvi ivi        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_158079869_   5700 AAGCGCTAATATCTGGAATCTACAATGTACTCCAACAAATTTACAAGAAA 5749
                          i vi  vi    ii    v  i  v v    iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_158079869_   5750 AAAACAAACAACCCCATCAAAAAGTGGGAGAAGGATATGAACAGACACTT 5799
                           i     i     v  i?    i    vi      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_158079869_   5800 CTCAAAAGAAGACATTTATGCAGCCAACAGACAAATGAAAAAATGCTCAT 5849
                            v        i  vi viii     i ii  v       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_158079869_   5850 CATCACTGGCCAT 5862
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (145 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3234 27.01 0.55 0.44  chr2_158196664_158202938     4877  5783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158196664_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158196664_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158196664_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_158196664_   5025 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_158196664_   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_158196664_   5125 TACAGTAACCAAAACAGCACGGTACTGGCACCAAAACAGAGATATAGATC 5174
                                 i   i    iii          iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_158196664_   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5222
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_158196664_   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_158196664_   5273 CTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i  i           v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_158196664_   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5372
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_158196664_   5373 TTAAAGACTTCAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?    i v  i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_158196664_   5423 CTAAGCATTA-CATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5471
                         v  i ?i v -iv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_158196664_   5472 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5521
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_158196664_   5522 TTAACCTAAAGAGCTTCTGCACAGCAGAAGAAACTACCATCAGAGTGAAC 5571
                          i  vv v  i i   i  ii vv  i i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_158196664_   5572 CGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5621
                         v i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_158196664_   5622 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5671
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_158196664_   5672 AAACAAACAACCCCATCAAAAATTGGGCGAAGGACATGAACAGACGCTTC 5721
                          i     i     v  i?    v     i     iv    i    ii   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_158196664_   5722 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5771
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_158196664_   5772 ATCACTGGCCAT 5783
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3287 26.43 0.55 0.55  chr2_158251956_158254147      793  1700 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158251956_    793 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 842
                              ii i  i   i i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158251956_    843 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 892
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158251956_    893 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 939
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_158251956_    940 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 989
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_158251956_    990 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 1039
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_158251956_   1040 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 1089
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_158251956_   1090 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 1137
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_158251956_   1138 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 1187
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_158251956_   1188 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1237
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_158251956_   1238 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 1287
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_158251956_   1288 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1337
                           i ?   ii    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_158251956_   1338 CCTAGGCATTACCATTGAGGACATAGGCATGGGCAAGGACTTCATGTCCA 1387
                          v    ?i v viv  viv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_158251956_   1388 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 1437
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_158251956_   1438 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1487
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_158251956_   1488 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 1537
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_158251956_   1538 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1587
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_158251956_   1588 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 1637
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_158251956_   1638 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCAT 1687
                            v        i  vi viii     v  i        i i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_158251956_   1688 CATCACTGGCCAT 1700
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2471 24.52 3.94 1.91  chr2_158263925_158267021     1489  2275 (822)    L1M4_orf2#LINE/L1        4   806 (102)  

  chr2_158263925_   1489 AAAAAAATACTATGTTCATGGATTAAAAG-TTCAATATTGTGAACATGAT 1537
                            i v  v i             ii   -i i        v  v   ii
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_158263925_   1538 TATTCTCTGCAAATTAATCTATATATTCAACTCAGTTTA-ATCAAAATCT 1586
                         v  v   iv      i     i v       v  i iiv-         i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_158263925_   1587 CAGCGTGTGTTTTT-GTAGAAATTGTCAAGTGGATTATAAAATTTAAATA 1635
                             -  iv     - i        v    iv   iv       i v  i
  L1M4_orf2#LINE/    104 CAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_158263925_   1636 AAAATGCAAAGGACTTATAATAGGCAAATCAAT-TTG-----GAAAAACA 1679
                         i        i    ii v     v    v    -   -----   i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_158263925_   1680 AAGTTGGAGAATTCACAAAACCTGATTTCAATACTTACTATAAAACTACA 1729
                                  i i     vvv  ii       v        i   i     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_158263925_   1730 ATAATCAAAACAGTTTGACGATAGTATAAGG-----CATATAGAACAACT 1774
                         i       i     v  iiiv i i      -----        v   iv
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_158263925_   1775 GAACAGAAGAAAGAGGCCAGAAATATACCCACATATATAAAGTTACTTTA 1824
                            i    vvi    v         v     i i  v  vi  i v  v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_158263925_   1825 TTTTCAACCAAAGTGCCACCATAACTCAATGAGTAAAGAATAGACTTT-C 1873
                              i  v ii      vv iv i      i v         v    - 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_158263925_   1874 AATAAATGATGCTAGAAGAACTTCAAATCCATATGGAAAA-AATAAAACT 1922
                           i     i    i i v    vv v ?   i   v    -   i  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_158263925_   1923 CCACCTTAACCTCACATAATA-ACACAAATTAAGTTGAAACTGAATGCAA 1971
                         vv   iiv        iv   -   v       v ii   -  i  -  ?
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGAT-CAW 500

  chr2_158263925_   1972 AGATTGAAACTAATTGTAAAAACTGAAATATTAAAACTTCTGGAAGAAAA 2021
                            i-----    v     i i  i   ivv       ii i        
  L1M4_orf2#LINE/    501 AGAC-----CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_158263925_   2022 CATAAAAACACAT----ATGAATTTTGGGTAGACAAAAA---CTCAGGAC 2064
                             ii?ii v  ----i   vi  v  v   i   vii---  i  - i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-AT 594

  chr2_158263925_   2065 ATGAAACTA---GTA-AACTATCATAATTTTTTTAAAAA---GATAAATC 2107
                             v  i --- i -  vi v  v  v------     ---       i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAG------AAAAAATAGATAAATT 638

  chr2_158263925_   2108 AGACTTCATCAAAATTTCAACCTTGTGCTCTGTAAAAAATACCTTCAAGA 2157
                         i               vv  v   v  iv  vi   ii i  iv      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_158263925_   2158 AAACAAAATGGCAAACCACAGAATGGAAGAAAATAGTCACAATTTATCTA 2207
                           iii   v i   v           i        v ii   v i  v  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_158263925_   2208 TCTGATAAAGGACTTGTATTCAGAATATATAAAGAACTCTTCCAATTCAA 2257
                                 i          i                     v   i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_158263925_   2258 CCAGAAGAAGATAAAAAA 2275
                         iv v  i    i   v  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAA 806

Transitions / transversions = 1.38 (110 / 80)
Gap_init rate = 0.02 (20 / 803), avg. gap size = 2.30 (46 / 20)  


2311 22.52 8.00 5.74  chr2_158362915_158364853      560  1447 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158362915_    560 TAAAAAGAGATTTATACCATGTTCATGGAGAGGAGGACTCAATCTTTTTA 609
                          ii     ----   v             vv   i    i   v  v   
  L1M4_orf2#LINE/      1 TGGAAAGA----TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chr2_158362915_    610 AGATATCCATTCTCCCTAGAT--------AGATTTGATGCAATTCTGATC 651
                             iv v  v     i i  --------     ii i     i iv   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_158362915_    652 AAAATCACAGTGGGCATTTTTGTAGAAATTGGCAAGCAGATTTTAAAATT 701
                               v   iv v v      i        i     v   ii       
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_158362915_    702 AATATGAAAGTGCAATGGACCTAGAGTAGCCAAAATACTATACTAGAAAA 751
                         v     i  i     v     i   i         i --  -  v     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA--AT-CTTGAAAA 193

  chr2_158362915_    752 ACAAAAACAGGATTTAAGGGCTTTCACACTT---GATT------------ 786
                          v  i    iii  vi   i  --       ---i   ------------
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACT--CACACTTCCCAATTTCAAAACTTACT 241

  chr2_158362915_    787 ---AAGCCACAAGAATCAAGAGAGCTTGTTATTGGCATAAGGATAGACAT 833
                         ---    i   iv        v  iv  v  i                  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_158362915_    834 ACAGAT-AACAGAATACAGATAA----CAAAAAATAGATTCCATAAAT-- 876
                          i    -  ii     v iv i ---- v i     i i-     v  --
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTT 340

  chr2_158362915_    877 AAGGTCAGATGACTTT-GACAAAGGTGCCAAAGTAATTCAATGCGAGACA 925
                          v     iv   i   -     i        iiiv        - i  - 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGA-A 388

  chr2_158362915_    926 AGAA-AGAGTTTGCAACAGCTGGTACTAG---AAGTAAGCATCTTTATGG 971
                             -  vv   v     iv    i  i ---  v iiii ? ivi   v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_158362915_    972 AAAA--ATGA-----GATTCGTGCCTCATATCCT-T-CAAAATCATTAAC 1012
                             --    -----  ii v i     i i v - -     --      
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA--ATTAAC 486

  chr2_158362915_   1013 TCAAAATGGATTATGGGCCTAAATGCGAAACCTAAAACACTGAATGCTTC 1062
                                    i ?i i        ii i v       vv i  -i  ii
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCT 535

  chr2_158362915_   1063 TAGACAAAAAAAAAAAAAAAAAAAAAAAAAAAATTGAGTGAAGTATGAGG 1112
                             --------------------- i    v  -------  --- ? v
  L1M4_orf2#LINE/    536 TAGA---------------------AGAAAACAT-------AG---GNGT 554

  chr2_158362915_   1113 AAGTCTTTGCCACCTTAGAATAGGCAAAGTTTTCTCAG----GACACAAA 1158
                           i    i iv     i iv       v v     i  ----     v  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_158362915_   1159 GAGGATGGATGATAAAAGCAAAAATA-ATAAATCGGTTGTCTTCATCAAA 1207
                         i  v iiiiii i     v       -      i  v---          
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA---CTTCATCAAA 651

  chr2_158362915_   1208 ATTTAAAACTTTTA--CTTCAAAAGTGAC-CTA--AAGAAAAT---AAGG 1249
                            v         i--       i --  -   --      i ---   i
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGG--ACACTATCAAGAAAGTGAAAAGA 699

  chr2_158362915_   1250 CAAGACACAAATCAGGAGAAAATATTCACAGTACATATACCTAAGAAACA 1299
                            vv    i vii            ii  ivv      i  i v  ivi
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_158362915_   1300 ACTTGTATCTAAAATATATACCAAACTTACGCAACTCAAAACTAAGAAAA 1349
                                  i i        vvi    ivii        v v   i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_158362915_   1350 CAA----CTCAATT--AAAATAAGCAAATATTTTAACAAAAC----CTTC 1389
                            ---- i     --     ii     viv   i vv i  ----  i 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_158362915_   1390 ACAAAAAATATACAAAATGCCATTAAGT-CATGAAATGATGCTTAATATT 1438
                          v i  i         vv    v    i-       v      i  i  i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_158362915_   1439 ATTAGTCAT 1447
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.66 (123 / 74)
Gap_init rate = 0.04 (37 / 908), avg. gap size = 3.30 (122 / 37)  


2891 27.41 3.17 0.34  chr2_158388323_158393746     2690  3572 (1852)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158388323_   2690 TGGAAAAACATTCCATGCTCATGGAGAGGAAGAATCAATATCATGAAAAT 2739
                               i i  i     i       vv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158388323_   2740 GGCCATACCGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 2789
                            v    iv      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158388323_   2790 TACCATTGACTTTCTTCACAGAATCAGAAAAAAACT-ACTTTAAATTTCA 2838
                          v   vivi i  i  ii     -- vvi v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr2_158388323_   2839 TATGGAACCAAAAAAGAGGCTGTATAGCCAAGACAATCCTAAGCAAAAAG 2888
                                viiv  ii  vv v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_158388323_   2889 AACAAA--------------------------CAAACTATAATAGAAGGC 2912
                               --------------------------    viv  v  v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_158388323_   2913 TACAGTAACCAAAACAGCATGGAACTGGTACCAAAACAGATATATAGACC 2962
                                 i   i    ii   v     i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_158388323_   2963 AATGCAACAGAACAGAGGCCTCAGAAATAATGCCACATGTCTACAACCAT 3012
                             v  i    iv   ivii         vv   i ii i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_158388323_   3013 CTGATCTTTGACAAACCTGACAAAAACAAACAATGGGGAAAGGATTCCCT 3062
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_158388323_   3063 ATTTAATAAATGGTGGTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 3112
                         v  i  i        v     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_158388323_   3113 AACTGCACCCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGGACT 3162
                          ii  v      v   i     v  i                i     ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_158388323_   3163 AAAGACTTAAACGGAAGATCTAAAACCATAAAAACCCTAGAAGAAAATCT 3212
                          ?    i    i v    v       i      vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_158388323_   3213 AGGCA-ATACCATTCAGGACATAGGCATGAGCAAAGACTTCATGACTAAA 3261
                            ?i- v i -   iv   v v  vv ii    v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_158388323_   3262 ACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAAT 3311
                                     vvi      i   vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_158388323_   3312 TAAACTAAAAAGCTTCTGCACAGCAAAAGAAACCATCATCAGAGTGGACA 3361
                         i   v v    i   i  ii vv    i  v  i    vv i    i v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_158388323_   3362 GGCAATCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 3411
                          i   i i                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_158388323_   3412 GGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 3461
                           i  vi          v  i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_158388323_   3462 AACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 3511
                         i     i     v  i?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_158388323_   3512 CAAAAGAAGACATTTATGTGGCCAACAAACAGATGAAAAAAACCTCATCA 3561
                          v        i  vi vi       i  i  v       i vv    v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_158388323_   3562 TCACCGGTCAT 3572
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 6.20 (31 / 5)  

2052 25.56 2.41 1.29  chr2_158388323_158393746     4311  4932 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_158388323_   4311 AAAAATAGATACATAGATCAATGAAATAGGATAGAGAACTCAGAAACAAA 4360
                           ii     i i           i     i  v    iii      i   
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_158388323_   4361 GCCACATATTTACAGCCAACTGATCTTTGACAAAGGTACTAGGAACATTC 4410
                         v   i i     ii i   i    i  i     i   i i i  v     
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_158388323_   4411 ATTTGAGAAAGGACACCCTTTTCAATAAATGGTGCTGGAAAAATTAGATA 4460
                          v v i     i i vi        i            i v  i i    
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_158388323_   4461 GTTGTACACAGAAAAGTGAAACTGGATCCCTG-TTCTCACCATATATTAA 4509
                         ?iiii ii  i  i i    ii    i    i-i  v         ----
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA---- 475

  chr2_158388323_   4510 TACAAAAGTCATCTCAGA-TGGATTAAAGACTTAAACATTAGATATAAAA 4558
                         --     i i v    i -     i ?    i    ii v   vv     
  L1M4_orf2#LINE/    476 --CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_158388323_   4559 ACTATAAAAATACTATAAGAAAACCTAGGAAAAACTCTTCTGGACATTGG 4608
                         -        v vi  v        v    ?iv  v     vv   v    
  L1M4_orf2#LINE/    524 -CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_158388323_   4609 TCTAGGCAAAGAATTTACGACTATGACCACAAAAACACAGGAAACAAAA- 4657
                         vi       v iv  iviiiv      vv     i    i v       -
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_158388323_   4658 ACAAAATCAACAAATGGGACTT-----AAACTAAAAAGTGGTTGCACATC 4702
                          v     vi i    v      -----   i      v -v   ii v  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT-TTTGTGCTTC 671

  chr2_158388323_   4703 AAAAGAAACAATCAACAGAGTGAAGAGACAACCTGTTGAATAGGATAAAA 4752
                            i  v  v     v i      i        iiiv    i   v    
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_158388323_   4753 TATTTGCAAACTATTCATCTGACA-GGGACTAACATCCAGAATATAGAAG 4801
                                   ii  vi      i -      vii            v  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_158388323_   4802 GAACTCAAACAACTCCACAA--AACTCCCAAATAATCCCATTAAAATGTG 4849
                               vv       v i  --  vvvv       i  v   ?   vi  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_158388323_   4850 GGCGAAGGAAACAAATGGACATTTTGCAAAAGAAGACATAAAAATGACCG 4899
                            i     vvii   i       iv v        i   v     i  i
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_158388323_   4900 ATA----TATTCAACTCTGCTCAATATCACTAATCAT 4932
                            ----i  vv  vvv       i    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (93 / 62)
Gap_init rate = 0.02 (10 / 629), avg. gap size = 2.30 (23 / 10)  


2829 27.62 1.78 0.67  chr2_158434456_158439086     3243  4140 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158434456_   3243 TGGAAACATATCCCATGCTCATGGATAGGTAGAATCAATATTGTGAAAGT 3292
                               v          i        v  v   v i        v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158434456_   3293 AACCATAATGCCAAAAGCAGTCTACAAATTCAATGAAATTCCCATAAAAA 3342
                         ii v   v v  v   viii      i      i v   i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158434456_   3343 TACCA-CCGTCATTCTTCACAGAACTAGAAAAAGCAATCCTAAAATGTAT 3391
                          v   - i i -  i  ii     v v  v  ivii          vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_158434456_   3392 ATGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAGGA 3441
                               viiv  ii  v  v v         i   vvi i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_158434456_   3442 AAAAATCTGGAAATAATACATTACCTGACTTCAAACTATACTGTAAGGCC 3491
                          v   vi    iivvvi   i v  ii i      viv    ii  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_158434456_   3492 ACAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACACAGACCA 3541
                              v i   i    ii         i    ii    i  i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_158434456_   3542 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTAACATCCAA 3591
                               i     v    ii               v i i   vvi  -  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC-AA 348

  chr2_158434456_   3592 CTGATCTTTGACACAGCAAAAAAAAACATAAAGTGGGGAAGGA-T-GTCC 3639
                         i    i  i    vi vvivv  i v   vv i       i  - -   i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_158434456_   3640 TATTCAACAAATGGTGCTGGGATAACTGACAAGCCACATGTAGGAGAATG 3689
                          -                    i     ivv ?       i ii      
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_158434456_   3690 AAACTGGATCCTCATCCTTCACCTTATATAAAAATCAACTTAAGATGGAT 3739
                           ii    i  ii i iiv    v    i      i    i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_158434456_   3740 CAAGGACTTAAATCTAAGATCTGAAAC-ATAAACATTCT-AGAAGATAAC 3787
                           ?i   i     v     v  i    -     - i   -      v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chr2_158434456_   3788 ACTGGAAAAACCCTTTA-GACATTGGCTTAGGAAAAGACTTCATCACCAA 3836
                          iv  ?iv  vi   ii-   v    v     v  v ii   v vivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_158434456_   3837 GAACCCAGAAGCAAAAGCAATAAAAGCGAAGATAAATAGGTGGGACTT-- 3884
                           vv   i     v      i     vi  i   i   ii v      --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_158434456_   3885 ----AATTAAAGAGCTTCTGCACAGCAAAAGGAACAGTCAGCAGGGTAAA 3930
                         ----       i -   i  ii vv    i iv  vi   iv ii  i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_158434456_   3931 CTGACACCCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCCGACA 3980
                         vv    v        i           v  ii   vii   i   i  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_158434456_   3981 AAGGAATATTATTCAGAATCTACAAGGGACTCAAGCAAATTAGCAAGAAA 4030
                          i   v vv   i      v  i  i i    vvi   v i ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_158434456_   4031 AAAACAA----CTTCATCAAAAAGTGGGCCAAGGACATGAATAGACAATT 4076
                           i    ---- iiv  i?    i     v     iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_158434456_   4077 CTCAAAAGAAGATATACAAATGGTCAACAAACATATTTTAAAAATACTCA 4126
                            v                   i   i  i  i  vv-   i  i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTCA 894

  chr2_158434456_   4127 ACATCTCTAATGAT 4140
                              v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.57 (22 / 14)  


 240 19.23 1.92 0.00  chr2_158646336_158652523.rev     4528  4579 (1609)    L1M4_orf2#LINE/L1        1    53 (855)  

  chr2_158646336_   4528 TGGAAACACATTTCATGCTCATGGATAGGTAGAATCAATATTGTGAA-AT 4576
                               v i  ii    i        v  v   v i        v  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158646336_   4577 GGC 4579
                            
  L1M4_orf2#LINE/     51 GGC 53

Transitions / transversions = 1.00 (5 / 5)
Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1)  

2504 26.18 6.03 0.84  chr2_158646336_158652523.rev     4868  5696 (492)    L1M4_orf2#LINE/L1       37   908 (0)  

  chr2_158646336_   4868 AAAATTGTGAAAATGACCATGCTGCCAAAATCAATCTACAAATTCAATGC 4917
                           v     v  i   i v  i  v  v    ii       i      i  
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chr2_158646336_   4918 AATTCCCATAAAAATACCATC-G--TTCTTCACAGAATTAGAAAAAACAA 4964
                            i  i  v     v   v - --  i  ii     v v  v  ivii 
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr2_158646336_   4965 TTATAAAATTCGTATGCAACCAAATAAGAGCCTCC--ATAGCCAAAGCAA 5012
                          iv        i    v  -- vii   i v i v--         i   
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_158646336_   5013 GACTAAGCAAAAAGAACATATCTAGAGGCATCACATTACCTGATTTCAAA 5062
                         vvi i iv  i       v vi i    vv     i v  ii        
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_158646336_   5063 CTATAGTATAAGACCATAGTCACCAAAACAGCGTGGTACTGGCATAAAAA 5112
                         viv  v  i  ii i i   v i   i    i               ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_158646336_   5113 TAGGAACATAGACCAATGGAACAGAATAGAGAACCCAGAAATGAA----- 5157
                            iv i     i        i     v    ii        i  -----
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_158646336_   5158 ---------GCCAACTGATCTTTGACAAAGCAAACAAAAATATAAAGTGG 5198
                         --------- i   i    i  i     i vviv   i vi  vv i   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_158646336_   5199 GGAAAGGACACACCCTATTCAACAAATGGTGCTGGGAAGATTGGCAAGCC 5248
                               i i -ii i -                    vi i   vv ?  
  L1M4_orf2#LINE/    385 GGAAAGAATA-GTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_158646336_   5249 ACACGTAGGAGAATGAAACTGGCTCCTTATCTCTCACCTTATACAAAAAT 5298
                            i i ii        ii   vi  i  i   v    v           
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_158646336_   5299 CAACTCAAGATGGATCAAGGACTTAAATCTAAGACATAAAACTATAAAAA 5348
                         i       i        ?i   i     v     vv             v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_158646336_   5349 TTCTAGAAGATAACTTTGGAAAAACCCTTTTAGACATTGGCTTAGGCAAG 5398
                          ii       v   v v  ?iv  vi   ivv   v    v        v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_158646336_   5399 GATTTCATGACCAAAAACCCAAAAGCAAATGTAACAAAACAAAGA-CATA 5447
                          i    v iivi vi vv         v v i       v   i -i v 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_158646336_   5448 TAGCTGGGACTTAAT--AAACTAAAGAGTTTT-TGCATGGCAAAAGGAAC 5494
                           iv v      v  --   i    i v    -   v --    i iv  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACAC 680

  chr2_158646336_   5495 AGTCAGCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTCTGCAA 5544
                         vi   iv i   i  v              i           v i     
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_158646336_   5545 TCTGTACATATGACAAAAGACTAATACCCAGGATCTACAA---------- 5584
                         viii  i  v   i  ii    vi  i    i  v  i  ----------
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_158646336_   5585 CAAATTAGCAAGGAAAAAAACAAACAATCCCATCAAAAATTGGGC----- 5629
                            v i ii  v-     i     i  i  v  i?    v     -----
  L1M4_orf2#LINE/    781 CAACTCAATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_158646336_   5630 -------TA-----TTCTCAAAAGAAAATATACAAAAGGTCAACAAACAT 5667
                         -------  -----     v      i         v  i   i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_158646336_   5668 ATGAAAAAATGCTCAACGTCACTAATGAT 5696
                                i         i   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (127 / 86)
Gap_init rate = 0.02 (15 / 872), avg. gap size = 3.80 (57 / 15)  


3050 25.03 1.00 0.38  chr2_158657903_158661712.rev     2125  2923 (887)    L1M4_orf2#LINE/L1        1   804 (104)  

  chr2_158657903_   2125 TGGAAAGATATTTCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 2174
                                    ii                    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158657903_   2175 GTCCATACTACCCAAAGCAATCTATAGATTCAATGCAATCCCTATCAAAA 2224
                          v v     v      vii     i        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158657903_   2225 TGCCAATGACATTATTCACAGAAATAGAAAAAAAAATCCTAAAATTTATA 2274
                          v   iivi v  v  ii       v  v  ivvi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_158657903_   2275 TGGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAACAAAAAGAA 2324
                              vii   ii                 i v   i i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_158657903_   2325 CAAAACTGGAGGAAGCACATTATCTGGCATCAAATTATACTTCACGACTA 2374
                             ii       vv    i vi iiiiv     viv    v  vii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_158657903_   2375 TAGTAACCAAAACATCATGGTACTAGAATAAAAACAGACACACAGACCAA 2424
                         i     i   i   vii       i v    ii i     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_158657903_   2425 TGGGATAGAATAGAGAACCCAGAAACAAATCCACACACCTACAGTGAGCT 2474
                            i       v    ii       i   i   i   ii  ii  v ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_158657903_   2475 CATGTTCGACAAAGGTACCAAGAAGATACACTAGGGAAAAGACAGTCTCT 2524
                         v  v        i   i      vv  v  v i      ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_158657903_   2525 TCCATAAATGATGCTGGGAAAACTGGACATTCATATGCAGAAGAAAGAGA 2574
                           v i     i        v       i ?i  i     i     v  ii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_158657903_   2575 CTAGACCCCTATCTCTCATCATATACAAAAATCAAATCCAAATGGATTAA 2624
                         i i        i   v  i             i  v  v        i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_158657903_   2625 AGACTTAAA-----GACCTCAAACTATGAAACTACTACAAGAAAACATTG 2669
                             i    -----  v  v       i     vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_158657903_   2670 GGG-AAACTTCCAGGACATTGGACTGCACTAAGATTTCTTGAGTAATACC 2718
                          ? -   ii i iv   v    ii ivi v v i      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_158657903_   2719 CCACAAGCACAGGCAACCAAAGCAAAAA-AGCATAAATGGGATCACATCA 2767
                            v       i     v    v     -  -      v   iiv     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAG-ATAAATTGGACTTCATCA 649

  chr2_158657903_   2768 A-GTTAAAAAGCTTTTGTATAGCAAAGGAAACAACCCAAAAAGGAAAGAG 2816
                          -i       -       iivv       v  v i v i    vi  i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_158657903_   2817 GCAACCCACAGAATGGGAAAAATTATTCACAAACTACCTATCTAACAAGG 2866
                         i                 i   v    ii    ii iv     i i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_158657903_   2867 GATTAATAACAAGTATATATAAGTAGCTCAACCAACTCTGTCAAAAAAAA 2916
                           i vi  v v  v        iv i   vvv      vi -  v     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-AATAAAAA 797

  chr2_158657903_   2917 AAAAAAT 2923
                         i v    
  L1M4_orf2#LINE/    798 GACAAAT 804

Transitions / transversions = 1.56 (120 / 77)
Gap_init rate = 0.01 (7 / 804), avg. gap size = 1.57 (11 / 7)  

 496 15.93 2.65 0.00  chr2_158657903_158661712.rev     3210  3322 (488)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr2_158657903_   3210 AAAAAAACTAATAATCCAATTTTAAA-TGGGCAAAAGATTTGAAAAGACA 3258
                              i  v     i      ?v   -        i        v     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_158657903_   3259 TTTCTCAAAAGAAGAGATACAAATGGCAAACGGACCTATGAAA-GATGCT 3307
                               v        v           v  iiii vi      -      
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_158657903_   3308 CAATGT-AGTGATCAT 3322
                            ii - ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (10 / 7)
Gap_init rate = 0.03 (3 / 116), avg. gap size = 1.00 (3 / 3)  


3324 22.92 4.33 0.80  chr2_158756264_158760563     2932  3808 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158756264_   2932 TGGAAAAATATTCCGT-TTCATAGATCGGAAGAATCAATATTGTTAA-AT 2979
                               i    i  i -     i   i      v i           -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158756264_   2980 GTCCATACT----------ATCTA-------AA-GCAATCCCTATCAAAA 3011
                          v v     ----------     -------  -                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158756264_   3012 TACCAATGACATTCTTCACATAAATAGAAAAAAACAATCCTAGAACTTAT 3061
                          v   iivi v  i  ii  v    v  v  iv-ii      i  i i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_158756264_   3062 ATGAAACCACAAAAGACTCAAAACAGCCAAGGCTATCCTGAACAAAAAGA 3111
                            i  vii   ii   i  i  i      ii v   i    v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_158756264_   3112 ACAAAACTGGAGGAATCACATTACCCGACTTCAAATTATACTACAGAGCT 3161
                              ii       v     i v   i i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_158756264_   3162 ATCATAACCAAAACAGCATGGTACTGCCATAAAAACAGACACATAGACCA 3211
                          ivi   i   i    ii        v     ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_158756264_   3212 ATGGAACAGAATAAAGAACCCAGAAACTAATCCATACACTTACAGTGAAC 3261
                               i     vi   ii       iv  i       i   ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_158756264_   3262 TCATTTTCGACAAAGGTGCCAAGAACGTACATTGATGACAAGACAGTCTC 3311
                          v           i          v i v  v  iv  v ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_158756264_   3312 TTTAA-----GGTGCTGGGAAAACTGGATATCCATAGGCAGAAGAATAAA 3356
                           i  -----          v         ?   i v   i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_158756264_   3357 ACTAGACCCTTATGTCTCACCATATATAAAAATCAAATCAAAATGGATTA 3406
                         ii i     i  iv  v         i      i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_158756264_   3407 AAGACTTAAATCGAAGACCTAAAACTATAAAACTGCTACAAGAAAACATT 3456
                         ?    i     vv    v                vi  v          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_158756264_   3457 GGG--AAA---------CATTGGATTGGCTAAAAATTTCTTGAGTAATAA 3495
                           ?--   --------- v    i  i vi  vii      iii  vv v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_158756264_   3496 ACTACAAGCACAGGCAACCAAAGCAAAAATGGACAAATGGGATCACATCA 3545
                           i v       i     v    v      i  i    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_158756264_   3546 AG-TTAAAA-CTTCTGCACAACAAAGGAAACAATCAACAAAGTGCATGAG 3593
                          i-      -   i  ii vv       v  v     v      v -i  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA-AAG 698

  chr2_158756264_   3594 ACAACCCACAGAATAAGAGGGAGAAAATACTTATAAACTACCTATCTGAC 3643
                                       ----           i  ii   ii iv       i
  L1M4_orf2#LINE/    699 ACAACCCACAGAAT----GGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_158756264_   3644 AAGGGATTAATAACCAGAATGCATAAAGAGCTCAAAACAGCTCTATAGGA 3693
                               i vi  v       ii       i   vv -  i   v   iv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATA 793

  chr2_158756264_   3694 AGAAATCTAGTATTCCAATGAAAACATGGGCAAAAGATCTAAATGGACAT 3743
                          i  iv v i  vi     v?   v         i   i i   i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_158756264_   3744 TTCGCAAAAGAAGAGATACAAATAGCAAACAGGCATATGAAAAAATGCTC 3793
                            v v        v        i  v  i i   i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_158756264_   3794 AACATCATTGATCAT 3808
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (125 / 72)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.21 (45 / 14)  


2976 26.24 2.59 0.34  chr2_158765781_158770714.rev     3555  4442 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158765781_   3555 TGGAAACATATCCCATGCTCATGAATGGGTAGAATCAATAATGTAAAAAT 3604
                               v          i     i  v  v   v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158765781_   3605 AACCA-ACTGCCAAAAGCAATCTTCAAACTCATTGCAATTCCCATCAAAA 3653
                         ii v -   v  v   vii    v  i i   vi     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158765781_   3654 TACCACCATCATTCTTCACAGAACTAGAAAAA--AATTCTAAAATTCATA 3701
                          v   v vv v  i  ii     v v  v  i--i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_158765781_   3702 TGTAACAAAAAAAGAGTCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 3751
                           v  vviv  ii  vi v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_158765781_   3752 CAAATCTGGAGGCATCACATTACCCAACTTCAAACTATATTATAAGGCCA 3801
                             vi      vv     i v     i      viv  i  i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_158765781_   3802 TAGTCACCAAAACAGCATGGTACTAGTATAAAAATAGGCATACAGACCAA 3851
                         i   v i   i    ii       i i    ii    i    i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_158765781_   3852 TGGAATAGAATAGAGAACCCAGAAATAAACCCAAATACTTACACCAAACT 3901
                                    v    ii               v i i   iiviv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_158765781_   3902 GATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGTATATCCTAT 3951
                            i   i    i vviv   i v   vv i         v   vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_158765781_   3952 TCAAAAAATTGTGCAGGGATAATTGGCAAGCCACATGTAGGAGAATGAAA 4001
                             v    v    v    i  i   vv ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_158765781_   4002 CTGGATCCTCATCTCTCACCTTATTCAAAAGTCAACTCGAGGTGTATCAA 4051
                         i    i  ii i   v    v   v     i i     i ii  v    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_158765781_   4052 ATACTTAAATCTGAAACCTGAAACTGTAAAAATTCTAGAAGATAACATCA 4101
                          v  i     v i i v  i     i     v ii       v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_158765781_   4102 GAA-AAACCTTTGTCGATATTGGCTTAGGCAAAGACTTCTTGACCAAGAA 4150
                          ?i-   i   i  -  iv    v        v ii     iivi v  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_158765781_   4151 CCCGAAAGCAAATGCAACATAAACAAAGATAAATAGATGGGACTTAATTA 4200
                         v  i      v v      v  iv   i   i   i  v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_158765781_   4201 AA-TGAAAAAGCTTCTGCACAGCAAAAGAAACAATCA-----GCAAACAG 4244
                           - v     -   i  ii vv    i  v  v    ----- ii  v  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_158765781_   4245 ACAACCTACAGAATGGGAGAAAATCTTTGCAATTTATATATCCAACAAAG 4294
                               i                 v       v i       ii i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_158765781_   4295 GACTAATTTCCTGAATCTATAAAGAACTC----AAATCAGCAAGAAAAAA 4340
                             vi v   v    v            ----  v   ii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_158765781_   4341 A-----AATCCCATCAAAAAGTGGTCTAAGGACATGAATAGACAATTCTA 4385
                          -----  i  v  i?    i   v v     iv          v    -
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT- 847

  chr2_158765781_   4386 TTCAAGAAGGTATACAAATGGC----AAACATATGAAAAAATGTTCAATG 4431
                         iiv      i            ----  i  i       i   i    ii
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_158765781_   4432 TCACTAATTAT 4442
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.34 (131 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.36 (26 / 11)  


3182 26.05 1.00 0.33  chr2_158827841_158833188     3955  4856 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158827841_   3955 TGCAAACACATCCCATGCCCATGGATGGGTAGA-TCAATATTGTGAAAAT 4003
                           v   v i        ii       v  v   - i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158827841_   4004 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAAA 4053
                          i v     v  v   vii       i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158827841_   4054 TACCATCATTCTTCT---CAGAATTAGAAAAAACAATTCTAAAATTCATA 4100
                          v   v vvi   i ---     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_158827841_   4101 TGGAACCAAAAAAGAGCCTACATAGCCAAAGCAAGACTAAGCAAAAAGAA 4150
                              viiv  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_158827841_   4151 CAAATCTTGAGGCATCACATTACCTGATTTCAAACTATACTATACGGCCA 4200
                             vi v    vv     i v  ii        viv     i vi  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_158827841_   4201 TAGTCACCAAAACAGCATGGTACTGGTATAAATATAGGCACGTAGATCAA 4250
                         i   v i   i    ii         i    iv    i  ii        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_158827841_   4251 TGGAACAGAATAGAGAACCCCAAAATAAACTCAAATACTTACAGCCAAGT 4300
                              i     v    ii  vi        i  v i i   ii i   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_158827841_   4301 GATCTTTGACAAAGCAAACAAAAACATAAAATGGGGAAAGGACACTCTTT 4350
                            i  i     i vviv   i v   vv           i i v     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_158827841_   4351 TCCAAACAAATGGTGCAGAAATAATTGGCTAGCCACATGTGGGACAATGA 4400
                           --            v ii i  i   v  ?       iiii v     
  L1M4_orf2#LINE/    401 TC--AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_158827841_   4401 AACTGGATCCTCACCTCTCACCTTATA-AAAAATCAACTTAAGATGGATT 4449
                          ii    i  ii     v    v    -      i    i  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_158827841_   4450 AAGGACTTAAATATAAGACCTGAAACTATAAAAATTCTAGGAGATAACAT 4499
                          ?i   i     i     v  i           v ii   i   v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_158827841_   4500 TGGAAAAGCCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGA 4549
                         v  ?iv ivi    vv   v    v        v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_158827841_   4550 GCCCAAAAGCAAATGCAATAAAAACAAAAATAAATTGTTGGGACTTAATT 4599
                         vv         v v    i    iv       i  viv v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_158827841_   4600 AAACTAAAGAGTTTTTGCACAGCAAAGAA-ACAGTCAGCAGAGTAAACAG 4648
                            v v  i ii     ii vv     i -  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_158827841_   4649 ACAACCCACAGAGTGGGAAAAAATCTTCACAATCTATACATCTGACAAAG 4698
                                     i     i     v  ii   vii   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_158827841_   4699 GTCTA--ATCCAGAATCTACAACAAACTCAAACAAATTAGTAAGGAAAAA 4746
                          v  v--         v  i  vi     vv    v i i   v-     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAAAA 797

  chr2_158827841_   4747 AACAAACAATCCCAGCAACAAGTAGGCTAAGGACATGAATAGACAATTCT 4796
                         i     i  i  v vi? v  i i   v     iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_158827841_   4797 AAAAAGAAGATATACAAATGGCCAACAAACATATAAAAA-ATGCTCAACA 4845
                         vv                       i  i  i  i    -          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_158827841_   4846 TCACTAATGAT 4856
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.33 (132 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3786 17.24 4.97 4.64  chr2_158843806_158846381     1180  2084 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158843806_   1180 TGGAAAGATATCCTATGTTCATAGATTGGAAGACTTAATATTTTTAAGAT 1229
                                      i        i                   v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158843806_   1230 GTCTATATTACCCAAAGCCATCTAAAGATTTAATGCACTCCCCATTAAAA 1279
                          v v   i v      viv     v     i  i   v    i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158843806_   1280 TCCCAATGGTGTTGTTTTGCAGAAATATTTTTTAA----ATTCTAAAATT 1325
                              iiv iv  -            --- vvi  ----  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAAT---TGACAAGCTGATCCTAAAATT 146

  chr2_158843806_   1326 TGTATGGAA-TTCAACAAACCCTGACTAGCCAAAAAAA-CTTGAAAAAAT 1373
                         ii       - v   vii    v  v         v  -         i-
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG- 195

  chr2_158843806_   1374 AAGAACAAAACAATAGTGAAAAAGATCAAAGTTGAAGGACT------TCC 1417
                                  ---------------------    i      ------   
  L1M4_orf2#LINE/    196 AAGAACAAA---------------------GTTGGAGGACTCACACTTCC 224

  chr2_158843806_   1418 TGATTTCAAAACGTACTACAAAGTTACAGTGATCACACTAATGTCTTTAG 1467
                         ii          v          i      i    -------------  
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCA-------------AG 261

  chr2_158843806_   1468 GTTAGTGTGGTACTAGTCTAAAGACAGACA----GACCAATGGAATAGAA 1513
                         ii-           i iv   i  i     ----  i             
  L1M4_orf2#LINE/    262 AC-AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_158843806_   1514 TAGAGAGCTCAGAAACAAGCCCTCGCATATATGGTCAACTGATTTTCAAC 1563
                          v     ii      i  i   vii   v         i        i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_158843806_   1564 AAGGGTGACAAGACCATTCAATTA--AAAGGACAGTCTTTTAAACAAACA 1611
                                v              vi--    i i        v      ii
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_158843806_   1612 GTGCTGAGAAAAC--AATATCCACATGCAAAAGGATGAAATTGGATTCTT 1659
                               i  v   --i   ?             i     i     ii i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_158843806_   1660 ACT-------GTATACAAAAAATAA-----AGTGGATGAAAGCTCTAAAT 1697
                           i-------i          v   ----- i     v ?  vi      
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_158843806_   1698 GTAGGTACTAAAACTATAAAACTCTTATAAGAAAACATGGAGGAAAAGCT 1747
                            i vi                    v          i i? v   v  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_158843806_   1748 TCATGACATTGGGTTTGGCAATGAATCTTTGGATATGACAGTAAAAACAC 1797
                           i    v       v       iv ii  i         vi    i   
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_158843806_   1798 A-GCAATAAAAGAAAAAATA----AATTGGAC---ACTGATATTAAAAAC 1839
                          -    i             ----        --- iii v         
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_158843806_   1840 TTTTGTACATCAGAGGATACTATCAACAGGATAAAAAGGCAACCTACAGA 1889
                               i v   i    i        v iii i     i     i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_158843806_   1890 ATAGGAGAAAATATTTGGAAATGATATATATCTGATAAGGCATGAATTTC 1939
                           i              v    --i               v ivvi v  
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAAT--CATATATCTGATAAGGGACTTGTATC 758

  chr2_158843806_   1940 TGGAATATGCGGAGCTCCCCTACAACACAACAACAACAA-ACCAAT---C 1985
                         ii      iiii  vv i i      v   i  i  v  -  v   --- 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_158843806_   1986 CAATTCAAAAATGGGCAAAGGGCTTGAATAGACATTCCTCCAAAGAAGAT 2035
                              ?               ii             i             
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_158843806_   2036 ATACAAATGACCAAAAAGCACCTAAAAA-ATTCTCACCAACACTAATCAT 2084
                                  i    v      v i    -  v    v  v  ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (97 / 55)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.95 (87 / 22)  


3232 26.98 0.55 0.55  chr2_158904353_158910739     4988  5895 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158904353_   4988 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5037
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158904353_   5038 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5087
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158904353_   5088 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTCA 5135
                          v   iivi i  i  ii     -   -- v  i  - iii i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_158904353_   5136 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5185
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_158904353_   5186 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5235
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_158904353_   5236 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGATC 5285
                                 i   i    ii  i      i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_158904353_   5286 AGTGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5333
                          i     i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_158904353_   5334 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATTCC 5383
                          vi    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_158904353_   5384 CTATTTAATAAATCGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGCT 5433
                           v  i  i    v         v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_158904353_   5434 GAAACTGGATCCCTTCCTTATGCCTTATACAAAAATTAGTTCAAGATTGA 5483
                            ii    i    v   i ii  v             ii    i  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_158904353_   5484 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5533
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_158904353_   5534 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5582
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_158904353_   5583 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5632
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_158904353_   5633 ATTAAAATAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAGGGAA 5682
                           i     v  i i   i  iiivv    i  v       vv i  v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_158904353_   5683 CAGACAACCTACAGAATGGGAGAAAAATTTTGCAATCTACTTATCTGACA 5732
                         v        i                vv       vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_158904353_   5733 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5782
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_158904353_   5783 AAAACAAACAACCCCATCAAAAAGTGGGCAAAAGATATGAACAGACACTT 5832
                           i     i     v  i?    i        i   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_158904353_   5833 CTCAAAATAAGACATTTATGCAGCCAAAAGACACAGGAAAAAATGCTCAT 5882
                            v   v    i  vi viii     v ii    v     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_158904353_   5883 CATCACTGGGCAT 5895
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3127 27.77 0.88 0.44  chr2_158959659_158966057     5004  5907 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_158959659_   5004 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5053
                               i i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_158959659_   5054 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5103
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_158959659_   5104 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5151
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_158959659_   5152 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5201
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_158959659_   5202 AACAAAGCTGGAGGCGTCACGCTACTTGACTTTAAACTACACTACAAGGC 5251
                                i      vv    i  v iii i  i   vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_158959659_   5252 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 5301
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_158959659_   5302 AATGGAACAGAAC--AGAGCCCTCGGAAATAACGCTGCATATCTACAACT 5349
                                i    i--    i  --i       vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_158959659_   5350 ATGTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5399
                          vv    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_158959659_   5400 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5449
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_158959659_   5450 GAAACCGGATCCCTTCCTCACACCTTATACAAAAATCAATTCAAGATGGA 5499
                            iii   i    v         v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_158959659_   5500 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGACGAAAAC 5549
                          i ?    i    i  v   v       i      vi i    v      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_158959659_   5550 CTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAA 5599
                         v    ?i v viv   iv   viv  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_158959659_   5600 AACATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5649
                         i   i        vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_158959659_   5650 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5699
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_158959659_   5700 AGGCAACCTACAACATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5749
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_158959659_   5750 AGAGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGTGAA 5799
                         i ii  vi          v  i         vv    v iv i  vvi  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_158959659_   5800 AAACAA----CGCCATCAAAAAGTGGGCAAAGGATATGAATAGACACTTC 5845
                          i    ---- v v  i?    i            v          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_158959659_   5846 TCAAAAGAAGACATTTATGCAGCCAAAAGACACAGGAAAAAATGCTCATC 5895
                           v        i  vi viii     v ii    v     i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_158959659_   5896 ATCACTGGCCAT 5907
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3162 26.80 1.33 0.78  chr2_159010285_159015022.rev     3344  4246 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_159010285_   3344 TGGAAGAACATTCCATGCTCTTGGGTAGGAAGAATCAATATCGTGAAAAT 3393
                              ii i  i     i  v   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_159010285_   3394 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3443
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_159010285_   3444 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3491
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_159010285_   3492 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 3541
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_159010285_   3542 AACAAAGCTGGAGGCATCAC-CTGGCC----TCAAACTATACTACAAGGC 3586
                                i      vv    -  vv  ----     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_159010285_   3587 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATGCATC 3636
                                 i   i    ii         i iv ii i   v    iv   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_159010285_   3637 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 3684
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_159010285_   3685 ATCTGATCTTTGACAAATCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3734
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_159010285_   3735 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3784
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_159010285_   3785 GAAACTGGATCCCTTCCTTACACCATGTACAAAAATTGATTCAAGATGGC 3834
                            ii    i    v   i       i          i i    i    v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_159010285_   3835 TTAAAGACTTAAATGTTTGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3884
                          i ?    i       vv  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_159010285_   3885 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 3933
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_159010285_   3934 AAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTA 3983
                         vi            vvi          vv    iv  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_159010285_   3984 GTTAAAATAAAGAGCTTCTGCACAGCGAAAGAAACTACCATCAGAGTGAA 4033
                         i i     v  i i   i  ii vv i  i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_159010285_   4034 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCA--TTCTACTCATCTGA 4081
                         v  i     i                 v      -- iv  i--      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chr2_159010285_   4082 CAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGA 4131
                         i  i  i  vi          v  i  v      iv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_159010285_   4132 AAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 4181
                             i     i     v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_159010285_   4182 TTCTCAAAAGAAGACATTTATGCAGTCAGCAGACACATGAAAAAATGCTC 4231
                              v        i  vi viii i  ii ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_159010285_   4232 ATCATCACTGGCCAT 4246
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


3402 25.66 0.55 0.55  chr2_159032752_159039012     4862  5769 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_159032752_   4862 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4911
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_159032752_   4912 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4961
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_159032752_   4962 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5008
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_159032752_   5009 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5058
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_159032752_   5059 GAACAAAGCTGGAGGCATCACACTACTTGACTTCAAACTATACTACAAGG 5108
                                 i      vv       v iii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_159032752_   5109 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5158
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_159032752_   5159 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5206
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_159032752_   5207 TATCTGATCTTTGACAAGCCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5256
                         i vi    i  i      vv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_159032752_   5257 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5306
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_159032752_   5307 TGAAACTGGATCCCTTCCTTACAGCTTATACAAAAATCAATTCAAGATGG 5356
                             ii    i    v   i   v v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_159032752_   5357 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5406
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_159032752_   5407 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5456
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_159032752_   5457 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5506
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_159032752_   5507 ATTAAAATAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5556
                           i     v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_159032752_   5557 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5606
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_159032752_   5607 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTATAAGAAA 5656
                          i  i  vi          v  i  v      vv    v iv    v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_159032752_   5657 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5706
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_159032752_   5707 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5756
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_159032752_   5757 CATCACTGGCCAT 5769
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3176 25.83 1.55 0.89  chr2_159040910_159047586     5285  6186 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_159040910_   5285 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATGAATATCGTGAAAAT 5334
                               i    i     i        v      v v     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_159040910_   5335 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCTATCAAGC 5384
                            v     v      v i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_159040910_   5385 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTT 5431
                          v   -   v    i  -i     -   -- v  i  - iii    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_159040910_   5432 ATATGGAACCAAAAAAGAGCCTGCATAGTCAAGACAATCCTAGGCAAGAA 5481
                                 viiv  ii  v  v v    i   i      i iiiv     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_159040910_   5482 GAACAAAGCTGGAGGCATCATGCTACCTGACCTCAAACTATACTAAAAGG 5531
                                 i      vv   ii  v  ii ii     viv     v  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_159040910_   5532 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATACAGAC 5581
                                  i   i    ii         i iv ii i   i   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_159040910_   5582 AAACAGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTAAAACCA 5631
                         v  ii   i    iv   ivii         vv   i    i  viii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_159040910_   5632 TCTGATCTTTGACAAACCTGTCAAAAACAAGCAAATGGGGAAAGGAT--T 5679
                         vi    i  i     ivv  i   i v  vv   -         i  -- 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGT 396

  chr2_159040910_   5680 CCTTATTTAATAAATGGTGTTGGGAAAATTGGCTAGCCATATGCAGAAAA 5729
                          i  -- i  i        i     v  i   v  ?   i     i  i 
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_159040910_   5730 CTGAAACTGGATCCCTTCCTTACACCTTATAGAAAAATTAATTCAAGATG 5779
                         v    ii    i    v   i     v    v         i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_159040910_   5780 GATTAAAGACTTAAATATAAGACCTAAAACCGTAACAGTCCTAGAAGAAA 5829
                            i ?    i     i     v       ii   v v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_159040910_   5830 ACCTAGG--TAATACCATTCAGGACATAGGCATGGGCAAAGGCTTCATGA 5877
                           v    --   - i -   iv   v v  vv i     v  i   v ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_159040910_   5878 CTAAAGCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5927
                         v  vii           vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_159040910_   5928 CTAATTAAAATAAAGAGCTTCTACACAGCAAAAGAAACTATCATCAGAGT 5977
                         i v  i     v  i i   i iii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_159040910_   5978 GAACAGGCAATCTACAGAATGGGAAAAAAATTTTGCAATTTATCCATCTG 6027
                            v  i   i i           i    vv       v i  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_159040910_   6028 ACAAACAGCTAATATCCTGAATCTACAAAGAACTTAAACAAATTTACAAG 6077
                          i  ivii  vi     v    v  i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_159040910_   6078 AAAAA-----ACAACCCCATCAAAAAGTGGGTGAAGGATACGAACAGACA 6122
                              ----- i     v  i?    i    ii      vi   i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_159040910_   6123 CTTCTGAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAATGCT 6170
                         i    vv        i  vi viii     i  --         i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_159040910_   6171 CATCATCTCTGGTCAT 6186
                           v    v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


2153 27.45 4.21 3.08  chr2_159062039_159063895      492  1369 (488)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr2_159062039_    492 ATGG--TGGAAAAGACTCAGTATTGTAAAAATGTCAA--CTCTTCCAAAT 537
                             --     --    i i      v  i   v   --   i-      
  L1M4_orf2#LINE/     21 ATGGATTGGAA--GACTTAATATTGTTAAGATGGCAATACTCC-CCAAAT 67

  chr2_159062039_    538 TGATTTATA---------CAATCTCAACTGAAATCCTAGAAAGTTTTTTT 578
                             i  i ---------     i v iii      i  vv- ii     
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT-GCCTTTTT 116

  chr2_159062039_    579 GTGCATATGAAAATTGGCAAGCTGGTTTAAAAATATGTATAGAAATGCAA 628
                         -    ----i      i       i iiv     vii   i         
  L1M4_orf2#LINE/    117 -TGCA----GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_159062039_    629 AGGACA-AGGATAGCCAAGAGAATCTTGATGAA-AAGAGTAAAGCTGGAG 676
                         i    v-  i        i v        vi  -    ii    i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_159062039_    677 GATTTATAGTACCATATACCAAGATCCATTATGAAGTTCTAATAATCAAG 726
                           i i i v v  vv  vi   i iii i  ii   i vi i        
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_159062039_    727 AC--TGT--TATTGGAGCAAGGATGGGCAAATAGGTCAATG-AACAGTAT 771
                           --   --  i   vii      i i  v    i      -  i  v  
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_159062039_    772 AAAGAGCCTCAAGAAACAGTTCCATACATACATGATCACCTGATTTATGA 821
                         vi    --  v     i ivi        vi   i   vi      vi  
  L1M4_orf2#LINE/    312 TGAGAG--TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_159062039_    822 AGAAGTGAGTCATACTGCTGTGCAGTATGGAAAGAACAGTCTTT--AATA 869
                         v-   v v i  vi--i ii v  i iv        i       --  i 
  L1M4_orf2#LINE/    360 C-AAGGGTGCCAAG--ACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_159062039_    870 AATGGTCCTGGTTCTGTTGGATACCCACATGGAAAA-AGTGATTCTTGAT 918
                               v    vv vii      ?       v    - i   vv-   iv
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG-TTGGA 455

  chr2_159062039_    919 CTCCTACTTCCCAACAGTCACATAGATCAAATCCAGATGTACTGCAGATC 968
                          i     i  v  v  vvi   v i  i  v  v i   v iii?   i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_159062039_    969 TAAATGTGAAAGATAAAA--ATGAGCATTTTGGAAGAAAACAAAGGAGAA 1016
                                i i  v     --  i ivv i  i          v   ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_159062039_   1017 CATATTCATGACCTTGGAATTGGCAAAGATTTCTT---TTTAAAA--AAA 1061
                         v  v   i         iv v     v i      --- v i v --   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_159062039_   1062 TGTTCATCTTA-AATGGAAAACATA-ATAAGTTGGGAAATACTAAAATTA 1109
                         v iv  vviv -  vi     v   -    i    ivvvi ii       
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_159062039_   1110 AGACCATCTATTCATCCAAAGACACCATTAAGGGAGTGAAAAGGGAGCCT 1159
                          i v v i i v v  v  i     i  i   ii         iv i  i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_159062039_   1160 GAAGAGCAGGAAAATCCATTTGC----CATATATCTCTTCAAAATATTTG 1205
                         iv   iii   i  vvi      ----         vv -  iiv i   
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT-AAGGGACTTG 754

  chr2_159062039_   1206 AATCCAGAATACATATGTATATATTAAAGCACATACAAATTAATGAGAAA 1255
                         v          i   ------- -- i i v v     v i   i v   
  L1M4_orf2#LINE/    755 TATCCAGAATATATA-------A--AGAACTCTTACAACTCAATAATAAA 795

  chr2_159062039_   1256 AAGGCAGACGACCCAAT-AAAAAATGGGGCAGAAGACCTCAACAGACACT 1304
                            i  i ii       -?         -  i i  ii v  i     i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGG-CAAAGGATTTGAATAGACATT 844

  chr2_159062039_   1305 CCACAATAAAAGGATACCCAAGTGGCCAATAAACATATTACAATGCGCTC 1354
                         i v v -  i i    iv   i          i  i  v v  vii    
  L1M4_orf2#LINE/    845 TCTCCA-AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_159062039_   1355 AACTTTATCCATTAG 1369
                            v i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.03 (31 / 888), avg. gap size = 2.06 (64 / 31)  


3150 26.17 1.56 0.56  chr2_159078751_159083481     3343  4240 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_159078751_   3343 GGAAGAACATTCCATGTCCATGGATAGGAAGAATCAATATCGTGAAAATG 3392
                             ii i  i      i       v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_159078751_   3393 GCCATACCACCCAAGGTAACTTGTAGATGCAATGCCATCCCCATCAAGCT 3442
                           v    iv     iv i ii ii    v   i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_159078751_   3443 ACCA-CTGACTTTCTTCACAGAATTCGAATAAACTACTTC-AAAGTTCAT 3490
                         v   -   v    i  -i     v i  -i  i  iv i -   i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT-GCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr2_159078751_   3491 ATGAAACCAAAAAAGAGCCCACATAGCCAAGAAAATCCTAAGCAAAAAGA 3540
                            i  viiv  ii  v  viv        i v    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_159078751_   3541 ACGAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 3590
                           i   i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_159078751_   3591 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACCA 3640
                                i   i    ii         i iv ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_159078751_   3641 ATGGAACAGAACAGAG-GTCTCAGAAATAATGCCACACATCTACAACCAT 3689
                               i    iv   -   -         vv   i    i  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_159078751_   3690 CTGATCTTTGACAAACCTGACAAAAACAAGAAAGGGAGAAAGGATC-CCT 3738
                         i    i  i     ivv  v   i v  vvv  v  i     i  v-i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_159078751_   3739 ATTTAATCAATGGTGCTGGGAAAACCGGCTAACCATATGCAGAAAGCTGA 3788
                         v  i  iv             v   i  v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_159078751_   3789 AACTGGATCCTTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 3838
                          ii    i  i v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_159078751_   3839 AAAGATTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAACC 3887
                          ?   ii       v   v       i      -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr2_159078751_   3888 TAGGCA-ATACCATTCAGGACATAGGTATGGGGAAAGACTTCATGACTAA 3936
                             ?i- v i -   iv   v v  vv i  v  v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_159078751_   3937 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3986
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_159078751_   3987 TTAAAATAAAGAGCTTCTGCACAGCAAGAGAAACCATCATCAGAGTGAAC 4036
                          i     v  i i   i  ii vv   ii  v  i    vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_159078751_   4037 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 4086
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_159078751_   4087 AGGGCTAATATCCAGAAGCTACAAAGAACTTAAACAAATTTACAAGAAAA 4136
                         i  i  vi         vv  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_159078751_   4137 A--------ACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 4178
                          --------    v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_159078751_   4179 TCAAAAGAAGACATTTATGTAGCCAACAGACATATGAAAATATGCTCATC 4228
                           v        i  vi vi i     i ii  i       v       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_159078751_   4229 ATCCCTGGTCAT 4240
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 1.58 (19 / 12)  


3116 26.09 2.35 0.67  chr2_159101652_159106498     3463  4355 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_159101652_   3463 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3512
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_159101652_   3513 GGCCACACTGCCCAAAGTAATTTATACATTCAATGCCATCCCCATCAAGC 3562
                            v i   v      v i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_159101652_   3563 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3610
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_159101652_   3611 TATGGAACCAAGAAAGAG-CCCACATT-GCCAAGACAATCCTAAGCCAAA 3658
                                -- v v   i -    v v -     i      i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_159101652_   3659 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 3708
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_159101652_   3709 GCTACAGTAACCAAAACAGCAGGGTACTGGTACTAAAACAGAGATATAGA 3758
                                   i   i    iiv        i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_159101652_   3759 CCAATGGAATAGAAAT-----------AATA---CCACACATCTACAACC 3794
                         i             v -----------    ---   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_159101652_   3795 ACCTGATCTTTGACAAACCTGACAAAAACGAGCAATGGGGAAAGGATC-C 3843
                          vi    i  i     ivv  v   i v ivv            i  v-i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_159101652_   3844 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3893
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_159101652_   3894 GAAACTGGATCCCTTCCTTACACCTTACACAAAACTTAATTCAAGATGGA 3943
                            ii    i    v   i     v  i      v    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_159101652_   3944 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCTTAGAAAAAAAC 3993
                          i ?    i       v   v       i      vi       i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_159101652_   3994 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 4042
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_159101652_   4043 AAACACCAAAAGCAATGGCAACACAAGCCACAATTGACAAATGGGATCTA 4092
                         vi            vvi      v   vv v   v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_159101652_   4093 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4142
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_159101652_   4143 CAGGCAACCTACAGAATGGGAGAAAATTTTTGTAATCTACTCATCTGACA 4192
                         v  i     i                 v    i  vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_159101652_   4193 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 4242
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_159101652_   4243 AAAATCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 4292
                           i -    i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_159101652_   4293 TCTCAAAAGAAGACATTTACGCAGTCAGCAGAC-CATGAAAAAATGCTCA 4341
                             v        i  vi viii i  ii ii -        i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_159101652_   4342 TCATCACTGGCCAT 4355
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.08 (27 / 13)  


3131 27.97 0.55 0.55  chr2_159115593_159121407     4416  5323 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_159115593_   4416 TGGAAGAACATTCCATGCCCATGGGTAGGAAGAATCAATATCGTGAAAAT 4465
                              ii i  i     ii     i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_159115593_   4466 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4515
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_159115593_   4516 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACGTTAAAGTTCA 4563
                          v   iivi i  i  ii     -   -- v  i  - ivi    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_159115593_   4564 TGTGGAACCAAAAAAGAGCCCGCGTTGCCAAGACAATCCTAAGCCAAAAG 4613
                          i     viiv  ii  v  v vi v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_159115593_   4614 AACAAAGCTGGAGGCATCATGTTACCTGACTTCAAACTATACTACAAGGC 4663
                                i      vv   iii v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_159115593_   4664 CTCAGTAACCAAAATAGCATGGTACTGGTACCAAAACCGAGATATAGACC 4713
                         iv      i   i i  ii         i iv ii iv  v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_159115593_   4714 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 4761
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_159115593_   4762 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATTCC 4811
                          vi    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_159115593_   4812 CTATTTAATAAATGGTGCTGCAAAAACTGGCTAGCCATATGTAGAAAGCT 4861
                           v  i  i           vi v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_159115593_   4862 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGA 4911
                            ii    i    v   i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_159115593_   4912 TTAAAGACTTGAAGGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4961
                          i ?    i i  v  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_159115593_   4962 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5010
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_159115593_   5011 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5060
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_159115593_   5061 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5110
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_159115593_   5111 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACG 5160
                         v  i     i                 v       vii ivi      ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_159115593_   5161 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5210
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_159115593_   5211 AAAACGAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5260
                           i  i  i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_159115593_   5261 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5310
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_159115593_   5311 CATCACTGGCCAT 5323
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (154 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 313 28.09 6.74 0.00  chr2_159129174_159131250.rev      501   589 (1488)    L1M4_orf2#LINE/L1       68   162 (746)  

  chr2_159129174_    501 TAATCTATAGATTAAATGTCATCTCTATCAATATCTTAGCAAGCATTTTT 550
                          i     i     v  i iv   i       v   ii   viv v     
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chr2_159129174_    551 ATAGGAATTGAGAAGTCAATTTTAAAAT------GGAAATACAGG 589
                         ii  i      v   iii  ii      ------      i  i 
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.01 (1 / 95), avg. gap size = 6.00 (6 / 1)  

2044 22.80 9.35 0.57  chr2_159129174_159131250.rev      881  1586 (491)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr2_159129174_    881 AAAAATAAAATGGAAATACA------------TATCAAAAACAATCTTGT 918
                             v v v        i  ------------  v v            -
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG- 189

  chr2_159129174_    919 AAAAAAAAGGTAAGAGTTA------TTACAAT-ACTAATTTCAAAACTTA 961
                              i   ivv i    i------ i   v -v i              
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_159129174_    962 T---AAAGCTATAATAAT-AGGA---TGTAATATTGGCATAATGATAGAC 1004
                         i---       i i    - i  ---   ii  i        v       
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_159129174_   1005 ACTTAGATCAATGAAATAGAA-----GGTACAGAAATTAA----TATATT 1045
                          iv          i       -----i  v       v  ----  i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_159129174_   1046 TACAATCAGTTGGTTTTCAGCAAAGATGACAAGGCAGAGCAATAGTGAAA 1095
                           iii   i   i     ii   i i  v    i vivv    i v    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_159129174_   1096 GGGAT-TTTTTTTAAAGAAATACTACTGGAATAATTGCATATTCATATGC 1144
                          i-  -v i    v  v    iv i    i i  i  v   ?i  i    
  L1M4_orf2#LINE/    390 GA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_159129174_   1145 AAAATACTGAACTTAAATTCTTACCAAACACCATACAGAAAAA--AATTT 1192
                             v v    v  ii ii i    vv        i v     --  i i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_159129174_   1193 ATA-TATATCACAGACCTACCTGTAAGAGCTAAAATTATA----TCT--- 1234
                          v - iv    ?       vv              i    ----   ---
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_159129174_   1235 --GAAAACAGTAGA---AAATCTCTGCAACCTTGCTTTTGGAAA-GGTTT 1278
                         --       -   i---      ii ii      vv  v  v  -     
  L1M4_orf2#LINE/    539 AAGAAAACA-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_159129174_   1279 CTTTAGATACAATACCAAAATTGTGATCCATTAAAGAAGAAATTGATAAA 1328
                            -     ii i       viiii v v iv      i    v      
  L1M4_orf2#LINE/    588 CTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_159129174_   1329 TTGCATTTTATAAAAATGAAAAG-TTTTGCCCTCCAAAAGATACTGGTAA 1377
                            v i  i  v     v    i-     iv  i    i  i   ivi  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_159129174_   1378 GAAAGTGAAAAGACAAATAACAGCCTGTGAAAAAAT--TCCTAGGTCAAA 1425
                                         viv    vv  v  i     -- ivi ii   v 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_159129174_   1426 TATCTGATAAAGTACTTGTATCTAGAATATATAAAGCATGCT-AAATGTG 1474
                                   i v         i             v iv  - v vv v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_159129174_   1475 AAAAATAA---GATAAGCAATTCAATT-AAAAAT----AAAATGTTTTAA 1516
                           v     ---  i  ii  ii     -      ----   ivi   v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_159129174_   1517 TAGAGATTTCACCAAA-AAGGTATACAAATGATTAATAAGCACATGAAAA 1565
                             v     v     -   i          iii                
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_159129174_   1566 GATGTTCAACAT-ATTAGGGAA 1586
                             i       - ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (93 / 66)
Gap_init rate = 0.04 (27 / 768), avg. gap size = 2.59 (70 / 27)  


3222 27.09 0.55 0.55  chr2_159206501_159210418     2519  3426 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_159206501_   2519 TGGAAGAACATTCCATGCTCGTGGGTAGGAAGAATCAATATCGTGAAAAT 2568
                              ii i  i     i  i   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_159206501_   2569 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2618
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_159206501_   2619 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2665
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_159206501_   2666 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 2715
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_159206501_   2716 GGACAAAGCTGGAAGCATCACACTACCTGACTTCAAACTATACTACAAGG 2765
                          i      i    i vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_159206501_   2766 CTACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 2815
                                  i v i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_159206501_   2816 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATACCTACAAC 2863
                                 i    i--    i  --        vv iii i ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_159206501_   2864 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 2913
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_159206501_   2914 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2963
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_159206501_   2964 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 3013
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_159206501_   3014 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3063
                           i ?   ii    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_159206501_   3064 CCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCA 3113
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_159206501_   3114 AAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTA 3163
                         vi            vvi      i   vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_159206501_   3164 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3213
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_159206501_   3214 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 3263
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_159206501_   3264 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 3313
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_159206501_   3314 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 3363
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_159206501_   3364 CTCAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTCAT 3413
                            v        i  vi viii     v  ii         i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_159206501_   3414 CATCACTGGCCAT 3426
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 575 26.07 18.01 0.47  chr2_159926079_159928629      974  1184 (1367)    L1M4_orf2#LINE/L1        1   248 (660)  

  chr2_159926079_    974 TGCAAAGTGATACCATGTTCATGGATTAGAGCA---------GTT----- 1009
                           v    vv  v               i  iv ---------   -----
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_159926079_   1010 --CAA----CTCCAAACTAATCTATAGATTAAACACCATCCCAGTGAAAA 1053
                         --   ---- i     i i     i     v   i v     vi v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_159926079_   1054 TCCGGGC----------AAGGAAACTGAGAAAGTGTTTCTAAGATCTATG 1093
                            vi  ----------ivi    i   v  iv  v i    i  ii  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_159926079_   1094 TGGAAATGCAAAAGGAGCAAGAATAATCAAAACAGT--------AAAAGA 1135
                                    i-   v v      ii       i -------- i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_159926079_   1136 ACTAAGTCATGTGATTTTCACTATCTGACTTCAAGACTTACTATAAAGC 1184
                           v    iiviv  i iv    vi ii i     i        i     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

Transitions / transversions = 1.62 (34 / 21)
Gap_init rate = 0.02 (6 / 248), avg. gap size = 6.50 (39 / 6)  

1198 25.17 18.71 1.57  chr2_159926079_159928629     1488  2059 (492)    L1M4_orf2#LINE/L1      239   908 (0)  

  chr2_159926079_   1488 ACTATAAAGCTACAGTAATCGAAGCACTGTGGTAACCGGCCCCCAGATAG 1537
                             i               i ii  v       - i   vivvi     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTA-CTGGCATAAGGATAG 287

  chr2_159926079_   1538 ACATAAAAATCAATCAAACATCATACAAAGTCTAGAAATGGA-------- 1579
                              v i      vi  i vv  vv i    i      ii --------
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_159926079_   1580 ------------TGATTT-CAACAAACATGCCAGG-TAATTCATTAATAA 1615
                         ------------      - i    ivi     i -iv     v iivi 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_159926079_   1616 AATGAT----TTCTCAATAAGTGATGCTGGAACAACTGGATATTCATTTA 1661
                           vi  ----  i    i  i  i      i           ?i  iv i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_159926079_   1662 GGAAAG-------------------------CCATAAACAAAAATG---- 1682
                         vi    -------------------------     v        v----
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_159926079_   1683 TGAAATAAGTCCTAGACCTAAACCTAAAATTTAAAACCTTAAATTGTCTA 1732
                         ii    iii  v?         iv   i vi      iv    vivii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_159926079_   1733 GAAGAAAA---AAGGATAAAAGATCTCTGAAACCTTGGGGTAGACA--GA 1777
                                 --- i ?i    ---   ii vi        v   i  -- i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_159926079_   1778 TTTCTTAG----GACTC--AAAGTATGA-----AAGTGAAAAA-----TA 1811
                                 ----   v --    i ii -----  iv      -----  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_159926079_   1812 A----GATTTCATCAAAATTAAAAACGTT-GTCTCTATAAGAGACATCAT 1856
                          ----  i                  v  -  v-  vi  ii    ii  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTG-CTTCAAAGGACACTAT 683

  chr2_159926079_   1857 TATGAAAGTGATGAGGCAGGCTACAAGACCAAGAGAAACTATGTGCAATA 1906
                         i v        vi  i  iv i   -  viii      v   v     vv
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACA-GAATGGGAGAAAATATTTGCAAAT 732

  chr2_159926079_   1907 CAT-TACCTTACAAAAGACTTGCATC---------TAAAGAACTC--ACA 1944
                            -  i  v i  ii      i   ---------          --   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_159926079_   1945 ACACAGTAA----------GATAATCCAACATGAAA-TGGGGAAAAAACT 1983
                           v  i   ----------i    i    iv?i   -    v   ii i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_159926079_   1984 TGAAGATATAAATT---ACAGAAATGATATATGACTGGATAAATAAGCTC 2030
                             --  v v   ---v  i i v      ii v   vi  -     v 
  L1M4_orf2#LINE/    833 TGAA--TAGACATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCAC 879

  chr2_159926079_   2031 AGAAAAAGATGCTCAACATCATTAGTCAA 2059
                          vi                  ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (88 / 52)
Gap_init rate = 0.04 (26 / 670), avg. gap size = 4.46 (116 / 26)  


 634 21.51 4.84 3.76  chr2_160024104_160026175      100   285 (1787)    L1M4_orf2#LINE/L1        1   188 (720)  

  chr2_160024104_    100 TGGAAAAA-ATCCCATGGTCATAGATAGGAAGACTAAATATCATTAAAAT 148
                               i -        v    i   v        v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_160024104_    149 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATAAAAC 198
                            v     v      vii  i           i  v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_160024104_    199 TACCAA-TGAAATTCTTCTTTGAACTAGAAA-----AAACT-ATTGAAAA 241
                          v   i-  ----i   i    ---i     -----  i  -  ivv   
  L1M4_orf2#LINE/    101 TCCCAGCTG----CCTTTTTTG---CAGAAATTGACAAGCTGATCCTAAA 143

  chr2_160024104_    242 GTTCATATAGAACCAAAAGAGAGCCCAAATAGCCAAGGCAA-CTT 285
                         i       i   viiv   i  v  vi         ii   -   
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

Transitions / transversions = 1.50 (24 / 16)
Gap_init rate = 0.04 (7 / 188), avg. gap size = 2.29 (16 / 7)  

3246 24.11 3.10 0.34  chr2_160024104_160026175      710  1580 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_160024104_    710 CATGCTTATGGATCAGAAGAATCAATATTGTTAAAATGATAATACTACCC 759
                             i i      ii     v i           i   ii      v   
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_160024104_    760 AATGCGATCTACAGATTCAACACAATCCCTATCAAAACACTAATGATATT 809
                           vvi                i               iv i iiviiv  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_160024104_    810 CTTCACAGAAATAAAGAAAA-AATATTAAACTTTGTGTGGAATTACAAAA 858
                         i  ii       vi v  iv-i  vi    v  ii i     v i   ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_160024104_    859 GACT--GAATAGCTAAAGCAATCCTGAGTAACAAGAACAAAGCTGGAGGT 906
                            i--       i   i     i   iv  v          i      v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_160024104_    907 ATCAGACTACTAAGACTTCAAAATAAACTACAAAGCTGTAGTAATCAGAA 956
                         v   v   v iv - i       ivv           ii        ii 
  L1M4_orf2#LINE/    214 CTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_160024104_    957 CAGCATGGTACAGGCATAAAAACTGACACATAAACCAATGGGATAGAATA 1006
                            ii      v       ii iv    i   i i      i       v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_160024104_   1007 GAAAACCCAGAAATTAATCCACACCTCTACAATCAACTGCTTTTTAACAA 1056
                           i ii        v  i   i  v i  iii    i  v    ii    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_160024104_   1057 AGCTGCCAAGAATGCTCATTGTGAAAAGAATAGTCTCTTCAATAAATGGT 1106
                         i v        viii   v  v i            i     i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_160024104_   1107 GCCAGGAAAACTGGATATCCATATGCAGAGGAATTAAACTAGACCCCCAC 1156
                           ii   v         ?   i     i i    v  ii i      i  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_160024104_   1157 CTCTTATCCTATACAAAAAT-AACTCAAAATAGATGAAAGACTTAA-TGT 1204
                            vi i v           -          i   v ?    i   -   
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_160024104_   1205 AAGACCCCAAATGATAAAACTAC-AGAAGAAA-----------------C 1236
                             v iv   iv        vi-        ----------------- 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_160024104_   1237 AGGACACTGGTCTGGGAAA--ATATTTTATATATAAAACTTCAAAAGCAC 1284
                         iv   vi   vi i  v  --i v i   v    i v  --         
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC--CAAAAGCAC 610

  chr2_160024104_   1285 AGGTAACAGAAGCAAAAATAAACAAATGCAACTACATCAAATGAAAAAAC 1334
                          i i    i   v       i i    vvi   v       vvv      
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_160024104_   1335 TTCTGTACAGCAAAAGAAAAAGTCAACAGAGTGAAAAGAAAATCCTCAAA 1384
                           i   i vv    i  v vvi    v i          v  i  v  i 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_160024104_   1385 ATGGGCTAAAATATTTGCAAATAATACATCTGAAAGGAGATTAATA-CCA 1433
                              vv               v   i      v i i  i vi  -   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_160024104_   1434 GGATATACAAGGAACTCAAACATCTCAACAGCAAAAAACCAAACAATCTG 1483
                          i     i  i      vv   v     i ii     iv    i  i ii
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_160024104_   1484 ATT-AAAAATGGGCAAATAATCTGAACAGACATTTCTCAAAAGAAGACAT 1532
                            -             vi  i    i           v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_160024104_   1533 ATACATGGCCAACAAATATATGAAAAAATGCTGAACATCACCACTCAT 1580
                          i v        i  ii i       i     v       ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (132 / 76)
Gap_init rate = 0.01 (11 / 895), avg. gap size = 2.73 (30 / 11)  


3245 26.27 1.00 0.55  chr2_160037212_160043880     5276  6177 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_160037212_   5276 GAAAAACATTCCATGCTCATGGAT-AGAAGAATCAATATTGTGAAAATGG 5324
                             i i  i     i        -i     v i        v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_160037212_   5325 CCATATTGCCCAAAGTAATTTATAGATTCAATGCTGTCCCCATCAAGCTA 5374
                          v   i v      v i  i  i        i  vi    i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_160037212_   5375 CCA----CTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTCATA 5419
                            ---- i  i  ii     v v  v  i--  - iii    v      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chr2_160037212_   5420 TGGAACCAAAAAAAGGTCCCATA-TAGCCAAGACAACCCTAAGCAGAAAG 5468
                              -- viv  i  v    v -       i    i i i iv ii   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_160037212_   5469 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATGCTACAAGGC 5518
                                i      vv       v  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_160037212_   5519 TACAGTAACTAAAACAGTATGGTACTGGTACCAAAACAGATATATAGAAC 5568
                                 ii  i     i         i iv ii i   i       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_160037212_   5569 AGTGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCAT 5618
                          i     i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_160037212_   5619 GTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5668
                         v    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_160037212_   5669 GTTTAATAAATGGTGTTGGGAAAACTGGCTAGTCATATGCAGAAAACTGA 5718
                         v  i  i        i     v      v  ?i  i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_160037212_   5719 AACTGGACCCCTTCCTTACACCTTATACGAAAATTAACTCAAGATGGATT 5768
                          ii         v   i     v     i             i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_160037212_   5769 GAAGACTTAAACGTCAGACCTAAAACCATAAAAACCCTAGAACAAAACCT 5818
                         i?    i    i  v   v       i      vi i     v     v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_160037212_   5819 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTGGTAACTAAA 5867
                            ?i- v i -   iv   v v  vv i     v ii  vv  iv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_160037212_   5868 ACACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5917
                             i       vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_160037212_   5918 TAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 5967
                         i   v v  i     i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_160037212_   5968 GGCAGCTTACAGAATGGGAGAAGATTTTTGCAATCTAGCCATCTGACAAA 6017
                          i  i ii              i  v       vii vvi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_160037212_   6018 GCGCTAGTATCCAGAATCTACAAAGAACTTAAACAAATTTACAA-GAAAA 6066
                          vi  v           v  i        ivv    v iv i  -i    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_160037212_   6067 TATAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAATAGACACTTCT 6116
                         v i   i     v  i?    i    ii      v          i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_160037212_   6117 CAAAAGAAGACATTGATGCAGCCAACAAACATATGAAAAAAAGCTCATCA 6166
                          v        i  vv viii     i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_160037212_   6167 TCATGGGTCAT 6177
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 1.56 (14 / 9)  


2590 26.02 6.88 0.93  chr2_160103258_160105472      868  1724 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_160103258_    868 TGGAAAAACGTTCCATGCTCATGGATAGGAAGAATCAATATTGTCAAAAT 917
                               i ii i     i        v      v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_160103258_    918 GGCCATATTGCCCAAAGTAATTTACAGATTCAATGCTTATTCCTATCAAA 967
                            v   i v      v i  i           i  v-  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA-ATCCCTATCAAA 99

  chr2_160103258_    968 CCATCAACGTAATGTTTCACAGAAACAGAAAAAACT-ATTCTAAAATTCA 1016
                         vivi  i vvvv v   ii      iv  v  i-  -  i          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_160103258_   1017 TATG-AAACCTAAAGAGCCTA-AATTGCCAAAGCAATCT-AAGCTAAAAG 1063
                             -   ivi  i ii  i -   v      i      -i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_160103258_   1064 AACAAAGCTGGAGGCATCACACTTACCTGACTTCCAACTATACTACAAGG 1113
                                i      vv        -  ii i   v  viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAAG 247

  chr2_160103258_   1114 CTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACACAGAC 1163
                                  i   i    ii         i i  ii i     i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_160103258_   1164 CAATGGAACAGGACAGAGAACTCAGAAATAAGACTGCACATCCATGACCA 1213
                                 i  i iv    iii         iv iii    ii   ii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_160103258_   1214 CCTGATTTTTGACAAAGTCAACAATAACAAGCAATGGAGAAAGAAATCCC 1263
                         vi       i     i viiv   v v  vv      i       - vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGT 396

  chr2_160103258_   1264 CTATTCAATAAATAGTTCTGGGATAACTGGCTAGACATATGCAGAATATT 1313
                           v     i    i  v      i      v  ?v  i     i  v v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_160103258_   1314 GAAACTGGACCTCTTCCTTTCACCATATACAAAAATTAACTCTACATGTA 1363
                            ii      i  v   iv                      v v   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_160103258_   1364 TTAAAGACTTAAAT----------------------TCCTAGGAACAAAC 1391
                          i ?    i     ----------------------  i   i iv    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_160103258_   1392 CTAGG---AAATACCATTCTGAACATCAGCCTTGGCAAAGAATTTATTAC 1438
                         v    ---    -- -   vvi  v ii vi v     v i-   v   v
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAG 592

  chr2_160103258_   1439 -TAAGTCCCTAAAAGCAACTGCAAAAAAAATAAAAATTGACAAGTGAGAC 1487
                         -  v v v i       vvv    v    iv      v  i  i vi   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_160103258_   1488 CTAATTAAACT--AGAGCTTCTGTACAGCAAAAGAAACTATCAC------ 1529
                         i v  i   v -- i i   i   i vv    i  v       v------
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_160103258_   1530 ----AGACAACCTACAGAATGGGAGCAAATATTCACAAACTATATATCTG 1575
                         ----        i            v       ii    ii         
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_160103258_   1576 ACAAAGGTGCAATATCTAGACTCTGTAAGAAACTT----AATTCAACAA- 1620
                          i  i  vvivi    i   v v i   ii    i----  i    i  -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_160103258_   1621 ACAAA---AAATAACCCCATTAAAAAATGGACA-------TGAACAAACA 1660
                          v   ---         v   ?        i  -------    i i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_160103258_   1661 CTCCTGAAAAAAAGATACATGGA--GCCAACAAATATACACAGAAATGCT 1708
                         i i  vv   i      i iii --     i  ii i iiv i i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_160103258_   1709 CAACACCCTTAATCAT 1724
                              i v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (136 / 84)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.19 (67 / 21)  


3288 14.15 4.02 1.77  chr2_160254710_160256787      501  1122 (956)    L1M4_orf2#LINE/L1      167   802 (106)  

  chr2_160254710_    501 CCAGGATTGCCAAAATAATCTTGAAAAGGAAGAATAAAGTTGGAAGGCTC 550
                             i  v       i           i      i         i i   
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr2_160254710_    551 ACACTTTCTGATTTCAA--TTTACTACAAAGCTATAGTAATCAAAGCAGA 598
                               i ii       --i              i         ii   v
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_160254710_    599 GTAGCA-TGGCTTAATGCTAGACCTTTAGATCAACAGAATAGAATTGAGA 647
                           i i -    v   v v     v v        ii              
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_160254710_    648 TTCAAGAAACAAACCCTTGCTTACATGTACAGTCAAATGATATTTGACAA 697
                         v  v     i      ----v     v  ii     v    v  i     
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCC----ATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_160254710_    698 GGGTGCCAAAACAATTCAATGGGGAAAGAATA-TCTTTTCAACAAAAGGT 746
                                  i  v                   -             v   
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_160254710_    747 GCTGGAACAACTGAATATCCACATGTAAAAGAAGGAAACTGGACCCCTAC 796
                              i       i   ?       i       v   ii           
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_160254710_    797 CTCACACCATACACAAAAAGGAACTAAGAATGAATCAATGACCCAAACGT 846
                                    i       vv    v i    i    ?v    i   i  
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_160254710_    847 AAGAGGTAAAAACGTAAAATTCCTGGAAGAAAATAAAGGCGTAAATCTTC 896
                              v     vii     i  i i        i v   ?          
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_160254710_    897 TTGACCTTGGATTAGGCAATGTTTACTTAGATATGGCATCAAAAGCACAA 946
                         v         i          v  v          i  i           
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_160254710_    947 GCAATCAAAGGAAAAATAGATAACGTGGACTT------------------ 978
                             iv    i            vv       ------------------
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_160254710_    979 TTGTCCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCTACAGAAT 1028
                             v                                     i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_160254710_   1029 GGAAGAAAATATTTGTATATCATATATCTGA--AGACAGTTGTATCCAAA 1076
                           i            i v             --  iv v         i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_160254710_   1077 ATATATTTTTAAAAAACACTTATAACTACTCAATAATTAAAA-ACAA 1122
                               ----   i   v    i    ---       v    -    
  L1M4_orf2#LINE/    763 ATATAT----AAAGAACTCTTACAACT---CAATAATAAAAAGACAA 802

Transitions / transversions = 1.43 (50 / 35)
Gap_init rate = 0.01 (9 / 636), avg. gap size = 4.00 (36 / 9)  

 607 12.61 0.00 0.90  chr2_160254710_160256787     1476  1586 (492)    L1M4_orf2#LINE/L1      799   908 (0)  

  chr2_160254710_   1476 ACACACAGCACAATTTTAAAATGGGCAAAGGGTTTGAATAGATATTTTAT 1525
                            v i i v     ?v              i          i    i- 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC-T 847

  chr2_160254710_   1526 CAAAAGAAGATACACAAATGGCCAATAAGCATAAGAAAAGATGCTCAATA 1575
                          v          i                  i v              i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_160254710_   1576 TCATTAGTCAT 1586
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.01 (1 / 110), avg. gap size = 1.00 (1 / 1)  


 212 24.68 14.94 8.44  chr2_160303058_160305248      340   647 (1544)    L1M4_orf2#LINE/L1       88   415 (493)  

  chr2_160303058_    340 ATCCCTGATTAAGAACACGGCTG-----TAAGCACAAATTT----GTTAA 380
                               -  i  i v v i    ----- vv   v     v---- i i 
  L1M4_orf2#LINE/     88 ATCCCT-ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr2_160303058_    381 ----AAAATTCAGTTGGAAA---AAGAAATA-AGAAAAACACAGGA-AAT 421
                         ----        vv      ---   ii iv-    v i -  ii -   
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC-CAAAACAAT 185

  chr2_160303058_    422 CTTGAAAAAGA-GAGCTTTGCCAGGGGTGGAGGGGACAATCATAACAGAT 470
                                    -  i ------ ii v      --  --   ---  vv 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAAC------AAAGTTGGAGG--AC--TCA---CACTT 222

  chr2_160303058_    471 ACTAAAGCATTATAAAAC---CTTTAAAGCT----TAAT------AGT-T 506
                         v i  ----  vi     ---  vi      ----    ------   - 
  L1M4_orf2#LINE/    223 CCCAA----TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_160303058_    507 GGCACTGGCACATGAATAAA-----AAACCAATAAAACATAATAGGAAAA 551
                           i       i v i   i ----- i i    ii  i v   v ii iv
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_160303058_    552 TGAGAAATTGACCCAAGTACAT--ATGG-AAATTTAGTATAGATAAAAGC 598
                         iv      vi     --     --    -v    v v v v  i  ii -
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCA--TACATTTATGGTCAATTGATTTTCGACAAGGG- 365

  chr2_160303058_    599 TGTATCTCAAAGC-----AGTGAGGAAGAGATGGACTTTTTGATAATTGG 643
                           i----   ii ----- i  i    iii  i v     ii i  v   
  L1M4_orf2#LINE/    366 TGC----CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_160303058_    644 TGTT 647
                           i 
  L1M4_orf2#LINE/    412 TGCT 415

Transitions / transversions = 1.62 (47 / 29)
Gap_init rate = 0.08 (25 / 328), avg. gap size = 2.88 (72 / 25)  

 359 30.87 10.51 4.25  chr2_160303058_160305248     1256  1702 (489)    L1M4_orf2#LINE/L1      406   880 (28)  

  chr2_160303058_   1256 AAGTGGTATTCAAATAACTGGGTATTCGTAAGAAAAAGGATAAACTTGGA 1305
                           i    ii vii i      i  ?i ii v v     i  i  v     
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_160303058_   1306 TCTG---CTC----------CAAAAATAAAACTGAAAA-AGATCAGATAT 1341
                         i iv---   ----------       v  -  v    -i     ? v i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAA-CTCAAAATGGATCAWAGAC 504

  chr2_160303058_   1342 TTAAACATGAAGATTTGAACCTATACAAGTACTAAAAAAAATTATGGGAG 1391
                         i    ii -    vi i  v     v  v vi  i  i   vi  i  ? 
  L1M4_orf2#LINE/    505 CTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_160303058_   1392 -GATTCCCCAATAATTAGAGCCTAAAGAAAACTTTCCCAGCAATGGT--C 1438
                         -i v  ii i- i iivvi vi  iiv  viv    ii  vv   ii-- 
  L1M4_orf2#LINE/    554 TAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_160303058_   1439 AAAACCAGATACAATAAAGGGAAATACTGGTAAATCTTACTACAT-AAAA 1487
                             v  v vi   i   i i   v iv i     ivv   v   -    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_160303058_   1488 T----AGCTTTTCTATAGC--CAAAACAAAAACACCA-CAAGCAAACTAT 1530
                          ---- i     v ---  --    i----i    i -    -   v iv
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGT---GCTTCAAAG----GACACTATCAAG-AAAGTGA 694

  chr2_160303058_   1531 AAAGACAAATGACAAACTGTAAAGAAATATTTGCAACTTATAT------- 1573
                                 viv   i v  vi ii            v i    -------
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_160303058_   1574 --GAGACAGTTGAAT--AAACTTATATGTAAAGCCTGCCTAAAAACAGAG 1619
                         -- i   --   v  -- i ---    i     vviv i  v  vivi v
  L1M4_orf2#LINE/    745 AAGGGAC--TTGTATCCAGA---ATATATAAAGAACTCTTACAACTCAAT 789

  chr2_160303058_   1620 AAGAAAAAGACTAACAACCTGATAGCAAAATGACTAGAGAGAT--AAGCA 1667
                           v        v  i    ii  v?v      ivi i  -   --i ii 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG-GATTTGAATA 838

  chr2_160303058_   1668 GTCATTTT---AGAGAAAA---AGAAATGGGGCCAG---GCACA 1702
                          v     i--- i    i --- v      --   i---     
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGG--CCAATAAGCACA 880

Transitions / transversions = 1.48 (80 / 54)
Gap_init rate = 0.05 (25 / 475), avg. gap size = 2.64 (66 / 25)  


3119 27.22 0.44 0.77  chr2_160305477_160311603     4725  5635 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_160305477_   4725 TGGAAAAACATTCTATGCTCATGGATAGGAAGAGTCAATATTGTGAAAAT 4774
                               i i  i i   i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_160305477_   4775 GGCCATACTGCCCAAAGTAATTTATACATTCAATGCTATCCCCATCAAGC 4824
                            v     v      v i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_160305477_   4825 TACCAGTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 4873
                          v    ivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_160305477_   4874 ATGGAACCAAAAATGAGCCCGCATGGCCAAGACAATCCTAAGCAAAAAGA 4923
                               viiv  iv  v  v v  i     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_160305477_   4924 ACAAAGCTGTAGGCGTCACGCTACCTGACTTCAAACTATACTACAAGGCT 4973
                               i  v   vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_160305477_   4974 ACAGTAATCAAAACAGCACAGTACTGGTACCGAAACAGATATATAGACCA 5023
                                    i    iiii       i iviii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_160305477_   5024 ATGAAACAGAACAGAAACCTGAGAAATAACACCACACATCTACAACCATG 5073
                            i  i    iv  i viiv        vv   i    i  iiii  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_160305477_   5074 TGATCTTTGACAAACCTGAGAAAAAGAAGCAATGGGGAAAGGATTCCCTA 5123
                             i  i     ivv  vv  i vv vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_160305477_   5124 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 5173
                           i  i        i     v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_160305477_   5174 ACTGGACCACTTCCTTACACCTTATACAAAAATTAACTCAAGACGGATTA 5223
                         ii      v  v   i     v                   i i    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_160305477_   5224 AAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5273
                         ?    i    i      v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_160305477_   5274 GGCA-ATACCATTCAGGACATAGGCAAGGGCTAAGACTTCATGAGTAAAA 5322
                           ?i- v i -   iv   v v  vvvi   v v ii   v iii  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_160305477_   5323 CACCAGAAGTAATGGCAACAAAAGCCAAAATTGACAAATGGGACT-AATT 5371
                              i   i vvi          vv     v  i    v     -v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_160305477_   5372 AAACTAAGGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 5421
                            v v ii i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_160305477_   5422 GAAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATGTGACAAAG 5471
                         iv    i                 v       vii  vi  v   i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_160305477_   5472 AGCTAATATCCAGAATCTACAAAGAGCTTAAACAAATTTACAAGAAAAA- 5520
                         ii  vi          v  i     i  ivv    v iv i  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_160305477_   5521 ACAAACAACCCCATCAAAAAGTGGGGTGGGTGAAGGATGTGAACAGGCAC 5570
                              i     v  i?    i    -----ii      v    i  i  i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGG-----CAAAGGATTTGAATAGACAT 843

  chr2_160305477_   5571 TTCTCAAAAGAAGACATTTATGCAGCAAACAAACATATGAAAAAAAGCTC 5620
                              v        i  vi viii  v  i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_160305477_   5621 ATCATCACTGGTCAT 5635
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


2991 22.48 6.26 1.62  chr2_160338270_160341667.rev     2045  2907 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_160338270_   2045 AGATATTCCATGTACATGGATAGGAAGAGTCTATTAT-GTCAAGATGTCA 2093
                               i      v       v      v -  v   -  i      v  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACT-TAATATTGTTAAGATGGCA 54

  chr2_160338270_   2094 GCACTTTCCAACTTGATTTATAGATTTAACAGAATCTCAATCAAAGTCAT 2143
                         ii   ii    v     i  i     i   iv    i v      i  --
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC-- 102

  chr2_160338270_   2144 TGCCAATTA---TTTTTG-GGACATCAACAAGCTGATTCTGAAGTTTATA 2189
                         --   ii i---      -i  v  ii          i  i  i  i   
  L1M4_orf2#LINE/    103 --CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_160338270_   2190 CGTAAAGACAAAAGATGCAGAAAAGCCAAGACGATATTGAA------GAA 2233
                         i v   vi   ii  iv     v      i  i  v     ------   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_160338270_   2234 CAAGGTTAGAGGA-TGACACTCCCCAATTTCATGGCTTACTGTAAAGCTA 2282
                            i   i     - v     i          vii      ii       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_160338270_   2283 CAGTAATCAACACGGTGTGGTACTGATA-AAAGA---ACAAATTGAT--A 2326
                                   v  i           ii -  i  ---   v  v   -- 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_160338270_   2327 CAGAACA------------CAGAAATAGACCTACGCAAAGAATAGTCAAT 2364
                         ii   i ------------        i   i ii  vvv - i      
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAAT 349

  chr2_160338270_   2365 GGATCTTTGACAAAAGAGCAAAGACAATTTAATGTAGAAAGGATAGTCCT 2414
                         v   i  i     ii v  v     v   i    vi     i      i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_160338270_   2415 TTCAATAAATGGTTCTGG---AACTGGACATCTACATGCAAAAAAAGAAA 2461
                              i       v    ---       i ? i          i  vi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_160338270_   2462 GAATATAAACATAGGACTTACAGCTTTCAGAAAAATTAATTAAGCATGGA 2511
                          -- - ii  vivviv  i   v v vi v         i v iv     
  L1M4_orf2#LINE/    450 G--T-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_160338270_   2512 T---AGACCTAAATGTAAAACTGC-AAAACTGTAAAACTCCTGGATGATA 2557
                          ---              i --  -      i        i i  v  v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGA--GCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_160338270_   2558 ACACTGGAGAACGTCTAAGTGACCTAGAGTT-TGCAGGGAATTTTTAGAT 2606
                            iv  ? v vi   vv       v i   -v   iv iv  i      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_160338270_   2607 ACAATACCAAAAGCATATACTCCATAAAAGAAAAAAATTGGTAAGTTGTA 2656
                          ii i          i vi --v i           - v i   i   v 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGC--AACAAAAGAAAAAA-TAGATAAATTGGA 641

  chr2_160338270_   2657 CAAGATTAAAATTTAAAACTTCTCTGC---AAAAGACACCATTAAGAGAA 2703
                          vvv  i      v       i v   ---   i     i  i    i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_160338270_   2704 TGAAAAAACAAGCCACAGAGTGGGAGAAAATATTTGCAAAATACGTATCT 2753
                               i    v       i                    vi ii     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_160338270_   2754 GAT----GACTGTTATTCA-AACATGCAGAGTACTATTTAAATTCAAAAA 2798
                            ----    vv   i  -  i  ii i  v   v  vv  i    v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_160338270_   2799 TAAGAAAACAGACAACCTGATTAAAAAATGAGCAAAGGATCTAAA----C 2844
                            i  i   i i    ii   ?       i         i i  ---- 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_160338270_   2845 ATAT----AAAGAAAAGATACGTATGGCAAATAAGCATATGAAAAGATGC 2890
                           v ----      i v    iv     v        i            
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_160338270_   2891 TCAGCATCGTATGCCAT 2907
                            i    i????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (119 / 72)
Gap_init rate = 0.03 (26 / 903), avg. gap size = 2.62 (68 / 26)  


 967 28.79 4.63 2.83  chr2_160347484_160351069.rev     1022  1410 (2176)    L1M4_orf2#LINE/L1        6   401 (507)  

  chr2_160347484_   1022 AGATATACCATGTTCATGAATTACAACACTTAAGATTGTTGACATGTTGC 1071
                               v           i   iv  v      v      i v   viiv
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_160347484_   1072 TTCTAATGAAATTGATTAATAAAACTAATATAATTTCAATTAAAATTTCA 1121
                          v  vviv        iv i i vii  iii   ii v  i     ii  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_160347484_   1122 GTAGACCATTTTGAGAGAACCTGAAAAGCTGATGGTAAAATCAATGTGAA 1171
                          iv -  v    viv    vi   v        vv      iv  i  i 
  L1M4_orf2#LINE/    106 GCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_160347484_   1172 AATGCATAAAAACAAGCAATAATAGACAATGCAGTTTTTAAAATGA---- 1217
                               - iii  --- v v     v   vi  i i  v    v  ----
  L1M4_orf2#LINE/    155 AATGCA-AGGGAC---CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_160347484_   1218 TAAAATTGGAGAACCTA----TCCAGATTTCAAGACTT----CAA-GTTA 1258
                         i   i      i  ii ----   vi       i    ----   - i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_160347484_   1259 ---TAATCATAACTATTTGTTATTGGCAAAATGAAAAGCCCGTGGACCAA 1305
                         ---      vi  vi v  v  i     v  v  v ii vii i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_160347484_   1306 TGGAACAGAATCAAA--TCTTAAAATAGGCCTGGGACATACATATATAAT 1353
                              i     ii i--  ivi     ii  -----       v   ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACC-----CATACATTTATGGT 345

  chr2_160347484_   1354 TAACTGATTTTCACCAAGGATGCTAAGGTAATTTAGTGAGGGAATGGAGA 1403
                         i  i        iv     i   i   iiv   i i  -     v i v 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATA 394

  chr2_160347484_   1404 GTCTTTT 1410
                                
  L1M4_orf2#LINE/    395 GTCTTTT 401

Transitions / transversions = 1.55 (68 / 44)
Gap_init rate = 0.03 (11 / 396), avg. gap size = 2.64 (29 / 11)  

 236 30.54 5.91 7.88  chr2_160347484_160351069.rev     1743  1945 (1641)    L1M4_orf2#LINE/L1      394   592 (316)  

  chr2_160347484_   1743 AGTCCTTTCAATAAAT--TGTTGATATAATTGACTGCCAAAATG--GGGG 1788
                             i      i    --  i  iv i  i  iv i? v v   --iii 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_160347484_   1789 A--GAAATTATTAATCCTATCTTATAT--TGAAGAAAAA--AACTCAAAA 1832
                          --   i  iv- vi    i  i i i-- iv v     --         
  L1M4_orf2#LINE/    444 AATGAAGTTGG-ACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_160347484_   1833 TTAACTATAAACTTAAATCTAAAGCCTTGCACTGTAAATCGCTGAGAAAA 1882
                          vi ii ? i  i     v   iiv  viv   i    v v  v    i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_160347484_   1883 AAATTAAAAAAAAAAAACAGGAGAAAAATCTTTGCAATCTAGAAATGGGA 1932
                            i------------ i   ? v   -    i ii i  v iiv i  v
  L1M4_orf2#LINE/    543 AAAC------------ATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGC 579

  chr2_160347484_   1933 AA--ATTATTCTTAG 1945
                           --i  --      
  L1M4_orf2#LINE/    580 AATGGTT--TCTTAG 592

Transitions / transversions = 1.95 (39 / 20)
Gap_init rate = 0.05 (10 / 199), avg. gap size = 2.80 (28 / 10)  

 780 22.26 2.90 4.19  chr2_160347484_160351069.rev     2785  3094 (492)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr2_160347484_   2785 AAAAAAAAAAGAATCATAAAAAAATATA-ATAAATTGGCCTTTTTTTAAA 2833
                             iv v   v v  v  i    v   -         v   i-------
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC------- 645

  chr2_160347484_   2834 GATCAAAATTTAAAACTTTTGCTCTTTGAAA-ACACACTTAATAAAATGA 2882
                         -         v          iv   ii  i-    vv i  v   i   
  L1M4_orf2#LINE/    646 -ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_160347484_   2883 AAATGCAGTGCAT-GCATGGAGGAACAATATT-GTAAAT-ATATATCAAA 2929
                            vi  iiv  i- v    ii   -      - i    -       vi 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCATATATCTGA 743

  chr2_160347484_   2930 GGACTGGGACTTGCTTGCAGGATAT-TAACAGAACTTTTACAACTCAATA 2978
                         vi --        iv v   i    -   -      i             
  L1M4_orf2#LINE/    744 TAA--GGGACTTGTATCCAGAATATATAA-AGAACTCTTACAACTCAATA 790

  chr2_160347484_   2979 ACAAGAAGA-ACGTGACCCATTTAACAAATGAACAAAAGTTTTGCCTAGG 3027
                          i  i    - vi i     v  ? v     ii    i v    vv   i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_160347484_   3028 TACATCATAAAAG--GATACATGAATGTGAAAATAACCACATGAAAATAT 3075
                         i iv  viv    --    i ii    - vv     v          v  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATG-GCCAATAAGCACATGAAAAGAT 889

  chr2_160347484_   3076 GCCCAACATCATTAGTCAA 3094
                           i        ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (36 / 32)
Gap_init rate = 0.04 (13 / 306), avg. gap size = 1.69 (22 / 13)  

1273 26.45 1.16 1.45  chr2_160347484_160351069.rev     3243  3586 (0)  C L1M4_orf2#LINE/L1   (314)   594   252  

C chr2_160347484_   3586 AGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAAT 3537
                              i   i    ii         i iv ii i   v            
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

C chr2_160347484_   3536 GGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTATC 3489
                             i    i--    i  --        vv  ii i  i  iiiii vi
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAAT 349

C chr2_160347484_   3488 TGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTA 3439
                             i  i     ivv  vv  i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

C chr2_160347484_   3438 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 3389
                           i  i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chr2_160347484_   3388 ACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTA 3339
                         ii    i    v   i     v           i  i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chr2_160347484_   3338 AAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 3289
                         ?   ii    i  v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

C chr2_160347484_   3288 GGCATTACCATTCAGGACATAGGCGTGTCAAACCAT--TTTCTAAGGT 3243
                           ?i v viv   iv   v v  ---  i ii v  --     v  i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGG---GTTAGGCAATGGTTTCTTAGAT 594

Transitions / transversions = 1.75 (56 / 32)
Gap_init rate = 0.01 (4 / 343), avg. gap size = 2.25 (9 / 4)  


2570 17.42 1.02 9.43  chr2_160376618_160378597.rev      828  1516 (464)    L1M4_orf2#LINE/L1      278   908 (0)  

  chr2_160376618_    828 ATAAAAAAAGATATATAGATCAATGGAATAGAACTGAGACTTTATAACTA 877
                             ii v   i                     i     v ii v  v  
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_160376618_    878 GACCCTTATATTTATGGTCAATTCATTTTCTTCAAGAATGCCAAGGTAAT 927
                         i    v  i              v      vv    ii       iiv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_160376618_    928 TCAATGGGGGAAGAAAAACCTCTCTAACAAATGATGCTGGGATAAATGGA 977
                                  i     v ii  i ii        i        i  v    
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_160376618_    978 AATTGACATGCAGA-GAATGAAGTTGGACCCCTACCTCACACCATGCACA 1026
                         v ?iv       i -                              ii   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_160376618_   1027 AAAATTCATTTAAAAATGGATTAAAGATCTAACTTTAAGTACTAAAACTA 1076
                               v i i    -     i ?   i    v v    vi         
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAA-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_160376618_   1077 TACAACTTGTAGAAAAAATTGTAATGTGAATATTACATGTAAGTATTCTT 1126
                           v    iv     i   ----------- i  - vi?    i v   v 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAA-----------ACAT-AGGNGTAAATCTTCGT 564

  chr2_160376618_   1127 GACCTCAGACTTACTAGTGGTTTTTTTTTTTAGATATGACACCTTCAAGT 1176
                              ii ii vivi i      i  -----            v-v   i
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTT-----AGATATGACACCA-AAAGC 608

  chr2_160376618_   1177 ATAAGCAACCAAAGAAAAC-TAGATAAATTGGACCTCATAAAGTAAAACA 1225
                          i       v        v-              i    ----i    i-
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT----CAAAAT- 653

  chr2_160376618_   1226 AACAAAAACCTTT-TGCTTCAAAGGATACCACTAAGCAAGCGAAAAGACA 1274
                         --i      i   -            i  i ii   v   i         
  L1M4_orf2#LINE/    654 --TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_160376618_   1275 ACACATAGAATGTGAGAAAAAGGTTGTAAATCCTATATATGACAAGGCAC 1324
                           v  i      v       viv   i     v     v   i    v  
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_160376618_   1325 CTGTATCCAGAATA----AAGAACCTCTTAAAACTCAACAATAAAAACAC 1370
                         i             ----      -     v       i        v  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAAC-TCTTACAACTCAATAATAAAAAGAC 800

  chr2_160376618_   1371 AAATAATCTAATTGTAAAATAGCTTACAATCATTATTGTAAAATTGGCAA 1420
                               i i    ?v     i ------------------------    
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGG------------------------GCAA 826

  chr2_160376618_   1421 AGGATTTAAATAGATATTTTTCTAAAGAAGATATAAAAATAGTCAATAAA 1470
                                i      i    i  i            v    i i      i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_160376618_   1471 TGCATAAAAAATAGACAATAAATATATGCTCAGCCTCAGCAGTCAT 1516
                         ii   i    i--------------       i v   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAG--------------ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (75 / 41)
Gap_init rate = 0.02 (14 / 631), avg. gap size = 5.14 (72 / 14)  


 368 20.93 5.81 0.00  chr2_160503264_160509888        4    89 (6536)    L1M4_orf2#LINE/L1      463   553 (355)  

  chr2_160503264_      4 CTTTCACCACACACAAAAATTAA-----AGTAGATCACAGACATAAATAT 48
                           iv     i i           ----- i i     ?    v     i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_160503264_     49 AAGCGCTACAGCTATAAAATCTTTAGAAGAAAACATGGAAG 89
                            v    v i        iii              i i? 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

Transitions / transversions = 3.00 (12 / 4)
Gap_init rate = 0.01 (1 / 91), avg. gap size = 5.00 (5 / 1)  

 363 17.72 12.66 0.00  chr2_160503264_160509888      400   478 (6147)    L1M4_orf2#LINE/L1      539   627 (281)  

  chr2_160503264_    400 AAGAAAACATAGGAGTAAGTCTTCATAACCCTGGGGTAAGCAAAGCCTTC 449
                                      ?    i     i i   i    v  i    v vi   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_160503264_    450 TTACATATG----------CACAAATGACAAAAGAAAAA 478
                            v     ----------     iii            
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.01 (1 / 89), avg. gap size = 10.00 (10 / 1)  

3224 26.40 0.44 0.55  chr2_160503264_160509888     5225  6133 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_160503264_   5225 TGGAAAAACATTCCATGCTCATGGATAGGTAGAATCAATATCGTGAAAAT 5274
                               i i  i     i        v  v   v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_160503264_   5275 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATGAAGC 5324
                            v     v      v i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_160503264_   5325 TACCA-CTGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAACTTCA 5372
                          v   -   v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_160503264_   5373 TATGGAACCAAAAAAGAGCCCGGATAGCCAAGACAATCCTGGACAAGAAG 5422
                                viiv  ii  v  v i        i      i  i v      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_160503264_   5423 AACAAAGATGGAGGCATCATGCTACCTGACTTCAAACTATACTATGAGGC 5472
                                v      vv   ii  v  ii i      viv     ii i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_160503264_   5473 TACAGTAACCAAAACATCATGGTACTGGTACCAAAACAGAGATATAGACC 5522
                                 i   i   vii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_160503264_   5523 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5572
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_160503264_   5573 CTGATCTTTGACAAATCTGACACAAACAAGCACTGGGTAAAATATTCCCT 5622
                         i    i  i     ivv  v  vi v  vv  v    v   iv  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_160503264_   5623 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5672
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_160503264_   5673 AACTGGACCCCCCTTCCTCACACCTTATACAAAAATAAACTCAAGATGGA 5722
                          ii        -- v         v           v       i     
  L1M4_orf2#LINE/    449 AGTTGGACCCC--TACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_160503264_   5723 TCAAAGACTTAAATGTAAGACCTATGACCATAAAAATCCTAGAAGGAAAC 5772
                            ?    i           v   vi  i      v  i      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_160503264_   5773 CTGGGCA-ATACCATCCAGGACATAGGCATGGGCAAAGACTTCATGTCTA 5821
                         v i  ?i- v i - i iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_160503264_   5822 AAACACCAAAAGCAACGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5871
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_160503264_   5872 ATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAGTCAA 5921
                           i   v v  i i   i  iiivv    i  v       vv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_160503264_   5922 CAGGCAACATACAAAATGAGAGAAAATTTTTGCAGTCTATCCATTTGACA 5971
                         v  i    vi   i    i        v      ivii  vi  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_160503264_   5972 AAGGGCTAATATCCAGAATCTACAAGAAACTTCAACAAATTTACAAGAAA 6021
                          i  i  vi          v  i  ii    iiv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_160503264_   6022 AAAACAAACAACCCCATC-AAAATTGGGCAAAGGATATGAACAGACACTT 6070
                           i     i     v  i-    v            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_160503264_   6071 CTCAAGAGAAGACATTTATACAGCCAACAGACACATGAAAAAATGCTCAT 6120
                            v i      i  vi v ii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_160503264_   6121 CATCACTCGTCAT 6133
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (135 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


1481 14.44 2.17 1.08  chr2_160689110_160691478      663   939 (1430)    L1M4_orf2#LINE/L1        1   280 (628)  

  chr2_160689110_    663 TGGAAATAAATCCCGTGTTCATGCCTTGGAAGACTTAATATTGTTAAGAT 712
                               v v     i        vv                         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_160689110_    713 GCTCATACTACCTAAAGTGATGTATACATTCAATGCAATCCCTATCAAAA 762
                          viv     v  i   v    v  i v      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_160689110_    763 TCCCAATGATATCTTTTT--CAAAAATAGAAAAGTTCATCCTAAAATCCA 810
                              -- v ii      --  i    v  v   i v          i  
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_160689110_    811 TATGGAAATTCAAGGAACCCTGAATAGCCAATATAATCGTGAAAA-GAA- 858
                                  v     i    v          v i    v      -   -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_160689110_    859 -ACCAAGTTAGAGGTCTGACACTTTTTGATTTCCAAACTTACTACAAAGC 907
                         -  v     i    v  v      iiii     v                
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_160689110_    908 TACAGTAATCAAGACAGTGTGG-GCTGGGCATA 939
                                               -i    -    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGG-CATA 280

Transitions / transversions = 0.82 (18 / 22)
Gap_init rate = 0.02 (6 / 280), avg. gap size = 1.50 (9 / 6)  

3263 18.15 2.68 0.60  chr2_160689110_160691478     1206  1877 (492)    L1M4_orf2#LINE/L1      223   908 (0)  

  chr2_160689110_   1206 CCCTGTCTCAAAA---ACAACAAAA--ACA--AAACAAAAAACCAGTGTG 1248
                            vi i      ---  v     i--   --  v   i ---       
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA---CAGTGTG 269

  chr2_160689110_   1249 GTACTAGCATAAACACTAACGCATAGGCCAGTGGAATAGA---------C 1289
                              i      iv ivi  ii    ii  i         --------- 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_160689110_   1290 TAGGAATAAACCCTTGCATATATG-TCAAATGATTATCAAGAATGGTGCC 1338
                         i  i         v i   v    -    v     v  i v  v      
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_160689110_   1339 AAGACTGTTCAGTGCAGAAAGGACAGTCTTCTCAATAAACTGTGCAGGGA 1388
                              ii    i  vi     i i      i    i   iv    v    
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_160689110_   1389 AAACTAGACAACCACTTGCAACAGAATGAAGTTAGACCCTTACCTTATAC 1438
                         v    i  i ?    v     v           i     i     i i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_160689110_   1439 TATGCACAAAAATGAACTCAAAGTAGATTAAAGACCTAAACATGAGAGCT 1488
                         i  ii        v        i i   i ?         ii i      
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_160689110_   1489 AAAACTATAAAACTCTTACAAGGAAACACAGGAAAAAGACTTCATAACAT 1538
                                           v   i     i   ?iv  iv    i i  v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_160689110_   1539 TGTATTTGGCAATGATTTCTTGTATATGATACCAAAAGCACAGGCAACGG 1588
                           vi  v       i      iv      i            i     ii
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_160689110_   1589 AATAAGAAATTAATAAATTGGACTTTATAAAAATTAAAAACTTT-GCACA 1637
                           v  i    vi             i  v               - ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_160689110_   1638 TCAAAGGACACTATCAACAGAATGAAAAGGCAACCCACAAAATGGGAGAA 1687
                                          v i i       i         i          
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_160689110_   1688 AGTATTTGCAAGTTGTACATCAGATAAGGGATTAATATCCAGAATATATT 1737
                          i         i ii  i   v         i vi              v
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_160689110_   1738 AAAAATTCCTATAACTAAACAATAGAAAAGACAAACATCCCAATTAAAAA 1787
                           i  i  i  i    v  i    -          i v       ?    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATA-AAAAGACAAATAACCCAATTWAAAA 818

  chr2_160689110_   1788 ATGGACAAAGGACTTGAATAGACATTTCTCCAAAGAAGATACACAGATAG 1837
                             i       i                            i   i  i 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_160689110_   1838 CCAATAAGCACGTGAAAAGATGTTCAACATCATCAATCAC 1877
                                    i          i         ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.37 (83 / 35)
Gap_init rate = 0.01 (8 / 686), avg. gap size = 2.75 (22 / 8)  


3164 27.64 0.55 0.55  chr2_160797411_160802446     3637  4544 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_160797411_   3637 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3686
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_160797411_   3687 GGCCATACTGTCCAAGGTAATTTATAGATTCAGTGCCATCCCCCTCAAGC 3736
                            v     vi    iv i  i  i       ii  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_160797411_   3737 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3784
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_160797411_   3785 TATGGAACCAAAAAAGAGCCCGCGTCACCAAGTCAATCCTAAGCCAAAAG 3834
                                viiv  ii  v  v vi vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_160797411_   3835 AACAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3884
                                i i    vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_160797411_   3885 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3934
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_160797411_   3935 AATGGGATAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3982
                              i      i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_160797411_   3983 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4032
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_160797411_   4033 CTGTTTAATAAATGGTGATGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4082
                           v  i  i        v     v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_160797411_   4083 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4132
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_160797411_   4133 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4182
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_160797411_   4183 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4231
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_160797411_   4232 AAACACCAAAAGCAATGGCAACAAAAGTCAAAATTAACAAATGGGATCTA 4281
                         vi            vvi          vv     vi i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_160797411_   4282 ATTAAACTAAAGGGCTTCTGCACAGCAAAAGAAACCACCATCAGAATGAA 4331
                           i   v v  iii   i  ii vv    i  v  i i  vv i i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_160797411_   4332 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 4381
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_160797411_   4382 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4431
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_160797411_   4432 AAAACAAACAACCCCATCAAAAAGTGGGCCAAGGATATGAACAGACACTT 4481
                           i     i     v  i?    i     v      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_160797411_   4482 GTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 4531
                         v  v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_160797411_   4532 CATCACGGGCCAT 4544
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3133 26.77 1.22 0.77  chr2_160814614_160818830     2822  3725 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_160814614_   2822 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2871
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_160814614_   2872 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2921
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_160814614_   2922 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTATAGTTCAT 2970
                          v   iivi i  i  ii     v v  v  i-  - iii  v i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_160814614_   2971 ATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGA 3020
                               viiv  ii  v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_160814614_   3021 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 3070
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_160814614_   3071 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 3120
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_160814614_   3121 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTA 3168
                               i    i--    i  --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_160814614_   3169 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 3218
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_160814614_   3219 TATTTAATAAATGGTGATGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 3268
                          v  i  i        v     v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_160814614_   3269 AAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGAT 3318
                           ii    i    v   i     v     v        i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_160814614_   3319 TAAAGATTTAAATATTAGACCTAAAACAATAAAAACTCT-AGAAGAAAAC 3367
                         i ?   ii     i v   v       v      -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr2_160814614_   3368 CTAGGC---AATGCCATTCGGGACATAGGCATGAGCAAGGACTTCATGTC 3414
                         v    ?---   -- -    v   v v  vv ii    v ii   v ivv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_160814614_   3415 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATC 3464
                           vi            vvi          vv    iv  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_160814614_   3465 TAATTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTACCATCAGAGTG 3514
                          v  i   v v  i i   i  ii vvi   i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_160814614_   3515 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 3564
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_160814614_   3565 CAAAGGGCTAACATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 3614
                         i  i  i  vii         v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_160814614_   3615 AAAAAACAA----CCCCATCAACAAGTGGACAAAGGATATGAACAGACAC 3660
                             i    ----   v  i? v  i   i        v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_160814614_   3661 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 3710
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_160814614_   3711 ATCATCACTGGCCAT 3725
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


 255 28.57 5.36 0.89  chr2_160828930_160836362      385   496 (6937)    L1M4_orf2#LINE/L1      540   656 (252)  

  chr2_160828930_    385 AGAAGTCAGGGGAGT-TATCTTCACAGCCTTATGGTTA-ACAAGAATATC 432
                             iv  vi  ?  -v      iiii    i-     -i   vii v  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTG-GGTTAGGCAATGGTTTC 588

  chr2_160828930_    433 TTAAGTAGGATAGAAAAAGCACTACCCATAAAGGAAAAGATTAATAAATA 482
                            ii  v  i vv        v v v i   i     i  vi      v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_160828930_    483 AGACTT----AAAATTAA 496
                         i     ----        
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAA 656

Transitions / transversions = 1.38 (18 / 13)
Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.75 (7 / 4)  

2935 24.97 3.79 0.37  chr2_160828930_160836362      498  1314 (6119)    L1M4_orf2#LINE/L1       64   908 (0)  

  chr2_160828930_    498 AATTTCATTTATAGATTTAATGCAATGCCAATCAAAATGCCATCAAATTA 547
                           v  v  i  i     i  i     v  v        v   v vivi v
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_160828930_    548 TTTTGTGGATATGAACAAACTGATTCTAAAGTTTCTATGGAAAGGCAAAT 597
                              ii  v  vi    i     i     i  iv        v    iv
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_160828930_    598 GATCCAGAATAGCCAACTCAACACTGAA---GATGAACAAAGTTGGAGGA 644
                           i             vv   ivi    ---  v                
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_160828930_    645 TTGACACTATCTGACTTCAAGACTTACTATAAAGCTGAAGCAATCCAAAG 694
                         i v     vi ii i     i        i      iv  i    v i v
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_160828930_    695 AGTGTGGTATTGACAAAAGAATAGTCA----GACAAATGTAACAGAATAG 740
                                  i  i  v   i    v  ----  iv    v  i     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_160828930_    741 AGAGCCCAGAAATAGACCTACATAAATATAGTCAACTGATCCTTGACAAA 790
                             i         i   i i i vv   i     i    ii i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_160828930_    791 GGAGCAAAGGCAACACAATGGAGCAAGGGTAGTCTTTTCAACAAACGGTG 840
                           v  v   i v iv      i v   ii                i    
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_160828930_    841 CTTGAACAACTGGACATTCACATG-AAAAAAA--AATCTAGACACATTA- 886
                           v i         i ?i      -    i  --  vi i   v -i  -
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC-CTAC 462

  chr2_160828930_    887 -TTACACCCTTCACAAACATTAGCTCAAAATG-ATCACAGACCTAAATGT 934
                         - i     v vi     v    i         -    ?            
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_160828930_    935 AAAATGC-AAAACCATAAAACTCCAAAAAGATAATGGTAGAA--AAATCT 981
                           i -  -     i         iv i    v  ii-   i?--      
  L1M4_orf2#LINE/    513 AAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACA-TAGGNGTAAATCT 560

  chr2_160828930_    982 AGATTATCTTGAGTATGTTGATGACTTTTTAGATATAACACCAAAGGCAC 1031
                         vvi v i    i  vv vii   ii  i        i        i    
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_160828930_   1032 AATCCATGAAAGAAAAAATTGGTAAGCTGGACTT----AAAATTAAAATC 1077
                           v v ii           v i   ii       ----          v 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_160828930_   1078 TTCTACTCCGTGAAAGATGATGTCAAAAGAACAAGAAAACAAGTCATGGA 1127
                           i iiv ivii  i  iiv i    i i iii i  i    vi  ii  
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_160828930_   1128 CTGGAAGAAAATATTTGCAAAATACACATCTACTACAAGACTATTA-CCA 1176
                         v   i                vi i i    iv  vii    vv  -   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_160828930_   1177 AAATATACAAAGAACTCTTA----------ACAAGAAAACAAACATTTCA 1216
                         i      i            ---------- i  i  i     i vii  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_160828930_   1217 ATTAAAAAATGATCCAAAGACCCTAACAGACATATTACCAAAGAAGATAC 1266
                            ?       iv v  i  iiiv  i      v iv            i
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_160828930_   1267 AGAGATGGCAAATAGGCATATGAAAAGATGCTCCACATTAAATGTCAG 1314
                          v i     v    i   i              v    i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (128 / 72)
Gap_init rate = 0.02 (14 / 845), avg. gap size = 2.43 (34 / 14)  

3171 27.61 1.00 0.33  chr2_160828930_160836362     6040  6941 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_160828930_   6040 TGGAAGAACATTCCATGCTCATAGATAGGAAGAATCAATATTGTGAAAAT 6089
                              ii i  i     i    i   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_160828930_   6090 GGTCATACTGCCCAAGGTAATTTATAAGTTCAATGCCATCCCTATTAAGC 6139
                           iv     v     iv i  i  i ii     i  v        i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_160828930_   6140 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTGA 6187
                          v   iivi i  i  ii     -   -- v  i  - iii    i  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_160828930_   6188 TATGGAATCAAAAAAGAGCCCGCACTGCCAAGACAATCTTAAGCAAAAAG 6237
                                viiv  ii  v  v v iv     i        i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_160828930_   6238 AACAAAGCTGGAGAGATCACGCTACCTGACTTCAAACTATGCTACAAGGC 6287
                                i     iiv    i  v  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_160828930_   6288 TACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAGATATAGACC 6337
                                 i   ii   ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_160828930_   6338 AATGGAACTGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 6387
                                iv   iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_160828930_   6388 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCCCT 6437
                         i    i  i     ivv  v   i v  vv       i    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_160828930_   6438 ATTTAATAAATGGTGATGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 6487
                         v  i  i        v     v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_160828930_   6488 AATTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATAGATT 6537
                          i     i    v   i     v              i    i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_160828930_   6538 AAAGACTTAAATATTAAACCTAAAACCATAAAAACCCTAGAAGAAAACCT 6587
                          ?    i     i v i v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_160828930_   6588 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 6636
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_160828930_   6637 ACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTAAT 6686
                                     vvi          vv    iv  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_160828930_   6687 TAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTACCATCAGAGTGAACA 6736
                         i   v v  i i   i  ii vvi   i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_160828930_   6737 GGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 6786
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_160828930_   6787 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAA 6836
                           i  vi          v  i         vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_160828930_   6837 AA-----AACCCA-TCAACAAGTGGACAAAGGATATGAACAGACACTTCT 6880
                         i -----      - i? v  i   i        v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_160828930_   6881 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAATCGCTCGTCA 6930
                          v        i  vi viii     i ii          ivi    iv  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_160828930_   6931 TCACTGGCCAT 6941
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.66 (153 / 92)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


3197 25.00 1.78 0.89  chr2_160862216_160868895     5289  6188 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_160862216_   5289 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5338
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_160862216_   5339 AGCCATACTGCCTAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5388
                         i  v     v  i   v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_160862216_   5389 TACCA-TTGACTTTCTT-CACAGATTTAGAAAAAACT-ACTTTAAATTTC 5435
                          v   -i  v    i  -  v i   ---i v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chr2_160862216_   5436 ATATGGAATCAAAAAGGAGCCCATTTAGCAAAGACAATCCTAAGCAA-AA 5484
                                 viiv  i   v  vivv    v  i      i i iv  -  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_160862216_   5485 GAACAAAGCTGGAGGCATCATGCCACCTGACTTCAAACTATACTACAAAG 5534
                                 i      vv   ii iv  ii i      viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_160862216_   5535 CTACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGATATATAGAC 5584
                                  i   i    ii         i  v ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_160862216_   5585 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCA 5634
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_160862216_   5635 TCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5684
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_160862216_   5685 TACTTAATAAATGGTGTTGGGAAAACTGACTAGCCATATGCAAAAAACTG 5734
                          vi i  i        i     v     iv  ?   i        i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_160862216_   5735 AA-CTGGACCCCTTCCTTACACCTTATATAAAAATTAACTCAAGATGGAT 5783
                           -i         v   i     v    i              i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_160862216_   5784 TAAAGACATAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAATC 5833
                         i ?    v    ii     v       i      vi i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_160862216_   5834 TAGGCAATACAAT--TCAGAACATAGGCATGGGCAAAGACTTCATGATTA 5881
                             ?i-  -   --  ivi  v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_160862216_   5882 AAACACCAAAAGC-CATGGCAATAAAAGTCAAAATTGACAAATGGGATCT 5930
                         vi           -  -i    i     vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_160862216_   5931 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTATCAGAGTGA 5980
                         v  i   v v  i i   i  ii vv    i  v     i vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_160862216_   5981 ACAGGCAACCTACAGAATGGGAGAAAATTTCTGCAATCTATCCATCTGAC 6030
                          v  i     i                 v i     vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_160862216_   6031 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTC-----C 6075
                           i  i  vi          v  i        ivv    --i  -----i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CTCAATAAT 792

  chr2_160862216_   6076 AAAAAAAAAAAAAAC---ATCAAAAAGTCGGCAAAGGATATGAACAGACA 6122
                              i v   v   ---  i?    i v          v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_160862216_   6123 CTTCTCAAAAGAAGACATTTATACGGCCAAGAAACATATGAAAAAAAGCT 6172
                         i     v        i  vi v i      v  i  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_160862216_   6173 CATCATCACTGGTCAT 6188
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (132 / 89)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.71 (24 / 14)  


2915 21.88 4.49 5.14  chr2_160872971_160875415     1040  1953 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_160872971_   1040 TGAAGATATATGTCATGTAAAATGATTGGAAAATTCAATATGTGT-AAGA 1088
                           i i v    vi     vv vv        i i i     -   -    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-TGTTAAGA 49

  chr2_160872971_   1089 TGTTCAATATCCCCACAAATTGATCTATGGTTTCAATGTTGTCTCAATAA 1138
                           v-     ii   -            ii v     i ivi  i v  v 
  L1M4_orf2#LINE/     50 TGG-CAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_160872971_   1139 AAATCTCAGC-ATATTTTTTGAAGAAATTGACAAGTTGATTCTAAAATTT 1187
                              i    -iiv       v             i    i        i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_160872971_   1188 ATATGGAAATGCAAAGGATCTAGGATAAACAAAA------TGAAA----- 1226
                                       i   i i  i   iv     ------     -----
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_160872971_   1227 GAACAAAGTTGGAGGATTTATGCT-CCTGATTTCAAGACTTTTTATAAAG 1275
                                         i i ii  -  ii       i    vi  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_160872971_   1276 CT-CTGTAAGGGGGGTAGTGAGGCATTAGTGGTTACATGGGTATATGCA- 1323
                           - v    vvii ii    v  i i i ------   ii v   vi  -
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGG------CATAAGGATAGACAT 291

  chr2_160872971_   1324 ATGGATCAATGAAACAGAAT--AGTGTCCAGAATTAGACTCACACATATA 1371
                           i        i  i     --  v        v  i  i  i    v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_160872971_   1372 TGGTCAATTGCTTGTCAACAAAGACATTAAGATAACTCAATGTGGAAAAG 1421
                                   v  v  i    i iiiii    iv i      -  i    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAG 390

  chr2_160872971_   1422 AA-ATTCTTGTGTAACAAATAGTGCTTGAACAACTAGATATCTCTGTGGA 1470
                           - v    v -i       i     v i      i    ? ivii  --
  L1M4_orf2#LINE/    391 AATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATG-- 437

  chr2_160872971_   1471 AACAAAAGA-TGAACCTAGACCTTCCT-TCTCATTCCAAATACAAAAACT 1518
                         --       -    vi i    --   -i    iv   v         i 
  L1M4_orf2#LINE/    438 --CAAAAGAATGAAGTTGGACC--CCTACCTCACACCATATACAAAAATT 483

  chr2_160872971_   1519 AATCTGA----GATCAGAAGCCTAAATGTAAGCATGTTAAG--CATAAAG 1562
                           iiii ----     ? ii            - - i   i--i     i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAG-A-GCTAAAACTATAAAA 531

  chr2_160872971_   1563 CTTCTAGAAGAAAATATAGGAA-GAGTCTTTGTGATCTTTACAGTAAGCA 1611
                           ii          i     ?i-i i    i    i   vi-iv  i   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCA 580

  chr2_160872971_   1612 AAAATTTCTTAG----GACATACAACACACCAACCATAAAATTAAAAATT 1657
                          vii        ----    ivv  vi   v i v i    vv      v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_160872971_   1658 AATAAGCTGGACTTCATCAAAATTACAAACTTTTG--CTTGACCAAAGG- 1704
                         i    ii                  v         --   ---      -
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT---CAAAGGA 677

  chr2_160872971_   1705 TATCGCCAGAAAAATTAAAACACAAGCTATAAACTGGGAGAGAATATTTT 1754
                         i iiii  ii   i v    v    v i i i v       i       -
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT- 726

  chr2_160872971_   1755 TGACTAAAATATCTATTTTTTGGCAAA--ATATATTTGACAAAAAACTTG 1802
                         ----------------------     --      i   i  iii     
  L1M4_orf2#LINE/    727 ----------------------GCAAATCATATATCTGATAAGGGACTTG 754

  chr2_160872971_   1803 TATCCAGCATATATAAAGTACTCTTACCACACAATATTGGAAAGACAGTC 1852
                                v          v        v  v     v ii       i-v
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA-A 803

  chr2_160872971_   1853 TAATCTTA--AAAAAATGGGCAAAAGATTTGAAAAGAAAC--CACAAAAT 1898
                            i iv --?             i        v   v i-- v v   v
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_160872971_   1899 AAGAAATAAGAATGGCAAATAAACACAGGAAAAGGAGCTCAACATCATTC 1948
                             v   vi      v     i    v      iv           ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_160872971_   1949 ATTAT 1953
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.93 (129 / 67)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 2.59 (88 / 34)  


2098 14.11 2.09 25.03  chr2_161201026_161204155      962  1868 (1262)    L1M4_orf2#LINE/L1        1   699 (209)  

  chr2_161201026_    962 TGAAAAGATATAACATGTTCATGAATTAGAAGATTTAATATTGGTAAGAT 1011
                           i        vv          i   i     i         v      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161201026_   1012 GTCGATACT----AAAGCAATCTAAACATTCAATACGGAGTCTATCAAAA 1057
                          v i     ----   vii     v v      ii iivvi         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161201026_   1058 TTCCAACAGCCTCTTTATTTTTTTTTTGGCAGAAATGGAAAAACCAAACT 1107
                          i   i v    ----------      -       v  v  i ii v i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT----------TTTTTG-CAGAAATTGACAAGCTGATCC 139

  chr2_161201026_   1108 TCAAATTCATATGGAATTGCA-GGGCCCCTAAAAAGCCAAAACAATATTG 1156
                          v              v    -   v   vi  v            v   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_161201026_   1157 AAAAAAGAACAACAAAATTGGAGAGCTCACATTTCCTGATTTCAAAAGCT 1206
                              -   v      i      ii      i    ii         vi 
  L1M4_orf2#LINE/    190 AAAAA-GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_161201026_   1207 ACTGCAAAGCTATAGTAATTAAAACACCGTGATACTGGCACAAGGATAAA 1256
                            i        i      i  i   vi   i        i       i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_161201026_   1257 CATATAGAT-----GAATAAAAGCATGAGTCCAGAAAT-----CACAGAT 1296
                                  -----     i  viiv            -----  i v  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_161201026_   1297 CTGTGGCAAACTGATTT-CAACAAGGGTGCCAAGACCATTCAATGAGGAA 1345
                         i i   iv  i      - i                         i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_161201026_   1346 -GAGTAGCCTCTTAACTAAATGATGCTGGGACAATTGGATATCCCCATGT 1394
                         -  i   i  i  v vi     i           i      ?  v    i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_161201026_   1395 AAAGGAATTAATTTGGATCTTTACTCCATATACAAAAATTAAAGACCAGC 1444
                            i    v  v     i ii   ii  ----------------------
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCA---------------------- 466

  chr2_161201026_   1445 CTGGGCAACATGGTGAAACCTTATGTCTACAAAAAATATAAAAATTAGCT 1494
                         -----  v   ------------------------   i        ---
  L1M4_orf2#LINE/    467 -----CACCAT------------------------ATACAAAAATTA--- 484

  chr2_161201026_   1495 GGGCATGGTGGCACATGCCTGTAGTCCCAGCTACTCAGGAGGCTGAAATG 1544
                         --------------------------------     --------     
  L1M4_orf2#LINE/    485 --------------------------------ACTCA--------AAATG 494

  chr2_161201026_   1545 GGAGGATTGCTTGAGCATGGGAGATTAAAGCTGCAGTGAGCCATGTTCAC 1594
                          ----------------------  i ?  --------------------
  L1M4_orf2#LINE/    495 G----------------------ATCAWAG-------------------- 502

  chr2_161201026_   1595 ACCACTGCGTTCCAGCCTGGCTGAGAGAATGAGACCCTGTCTCAAAAAGA 1644
                         --------------------------------------------------
  L1M4_orf2#LINE/    503 -------------------------------------------------- 502

  chr2_161201026_   1645 CAAATAAAACATAAAACCTCAGAATGGATCAAAGACCTAAGAGTTAAAAC 1694
                         ---------------    --i    -----------      i      
  L1M4_orf2#LINE/    503 ---------------ACCT--AAATG-----------TAAGAGCTAAAAC 524

  chr2_161201026_   1695 TATAAAACTTTCAGAAGGAAGTATAGGAGTAAATCTTGATGATATTTAGA 1744
                                  i i     i  ii     ?         vi   i-i  i i
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC-CTTGGG 573

  chr2_161201026_   1745 TTTGGCAATGGTTTCTTAGATATGACCCCAAAAACACAAGTAGCAAAAGA 1794
                           v                       v      i      i i       
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_161201026_   1795 AAA--TAGAGAAATGAAATTTCACTGAAATTAAAAACTACTATGCATCAA 1842
                            --    v    vii i    iii            vi i   v    
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_161201026_   1843 AAAACACTATCAAGGGAGTGAAAAGA 1868
                          ii           ii          
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGA 699

Transitions / transversions = 2.21 (86 / 39)
Gap_init rate = 0.03 (19 / 699), avg. gap size = 12.95 (246 / 19)  

 972 19.09 2.73 0.00  chr2_161201026_161204155     2419  2638 (492)    L1M4_orf2#LINE/L1      683   908 (0)  

  chr2_161201026_   2419 TTAAAAAAGTGAAA---CAAACCATGGAAGGGGAAAACATATTTGCAAAT 2465
                          i  i         ---   v   ii   v    i  v            
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_161201026_   2466 CATATATATGATAAGT--CTGATATCTAGAATATATGAAGAGTTATTACA 2513
                                v       v--  vi    i         i    ii v     
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_161201026_   2514 AATCAACAACAGCAAAATAAATA-CCCAGTTTAAAAATAGGCAAAAACCT 2562
                          v    i  i iv  i i     -    i  ?      i      iivi 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_161201026_   2563 TGAATAGACATTTATTTAAAGAAGATATACTAGTGGCTAACAAATACATA 2612
                                      v ii             v i    i  i  ii    i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_161201026_   2613 AAAAGATGGTCAACATCATCAGCCAG 2638
                                 v         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (28 / 13)
Gap_init rate = 0.01 (3 / 226), avg. gap size = 2.00 (6 / 3)  


2314 20.16 5.74 1.97  chr2_161220939_161222549.rev      510  1119 (492)    L1M4_orf2#LINE/L1      276   908 (0)  

  chr2_161220939_    510 GCATAAGAAGAGACATATAAATAACTGAAACAGAATAGTGTGTCCAGAAA 559
                                i v         i  v v  i  i     v v v         
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_161220939_    560 TAGACCCACGCATACATAGAGAATTGATTTTTGACAAAGGTGCCAAGGTA 609
                           i     ii   vi  i vv          i     i         iiv
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_161220939_    610 ACTCAATGTGAAAAGGATAGTCTTTTCAACAAATGGTGCTGGAACAACTG 659
                          i      v i    i                          i       
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_161220939_    660 GATATCCATATAAAGAAAAATCGATCTTGGTATTTCT---TCACACAATA 706
                             ?   i  iv i  i   -  vv    - iii  ---      v   
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAAT-GAAGTTGG-ACCCCTACCTCACACCATA 473

  chr2_161220939_    707 CACCCCCACACAAAAAT---CTCTAAATGGATCATAGACCAAAACATAAA 753
                         i  --------      ---   v          ?     v   ii   i
  L1M4_orf2#LINE/    474 TAC--------AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_161220939_    754 AGCTAAAATTATTAAACTTCTAGGTGAAAACATA-----AAATCTTCACA 798
                                 i   v     ii   iv         -----        iii
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_161220939_    799 ACCTTGGGCTAAGCAGAGATTTCTTAG----GACACAAAAATCATAA--- 841
                                 i  i   iv i        ----     v    v  i  ---
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_161220939_    842 ----AAGAAAAACTTGATAAACTGAAATTCATCAAAATTAAAA-CTTTTG 886
                         ----        v v      i  i v                -      
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_161220939_    887 CTCTTTGAGAGATACTATTAAAAAA-TAAAAAAGCAAGTCACAGACTGGG 935
                         iv   ii ii  i     i  i   - i    ii   vi      v    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_161220939_    936 A-AAAATATTTGCAATACATTCACCTGAAAAAGGTCTTATATCTAAAATA 984
                          -             vv   vi i    v  i  v   i    i i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_161220939_    985 TATAAAAATATCTCATAACTCAATTTTTAAAATG----TAATCCAATTGT 1030
                               i vv   i i        vv v    vi----   i      ?v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_161220939_   1031 TTAATGGGCAAAAGACTTGAACAGCTA---CTTCAAAAAGCAGATATATA 1077
                         vv          i  i     i  vi ---  i    i --       i 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA--AGATATACA 863

  chr2_161220939_   1078 AATGGACATTAAGCACATGAAT---TAGTCAACATCATTAGTTTC 1119
                              v  v            v--- iv         ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (73 / 47)
Gap_init rate = 0.02 (15 / 633), avg. gap size = 3.13 (47 / 15)  


3429 15.27 11.81 3.70  chr2_161274279_161278177.rev     2570  3407 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_161274279_   2570 GAGAGATATCTCATGTTCATGGACTAGAAAACTTAATATTAT---GATGG 2616
                           i       i            i i   i          i ---     
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_161274279_   2617 CAATACTCTCCAAATTGATCCACAGTTTCAATGTGCTTTCTATTATAATC 2666
                                 i           i    v     i iiv ii    i v    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_161274279_   2667 TCAGCTGACATCTTTTG-AGAAATTGGTAACCTGATACCAAAATTCATAT 2715
                         i      v - i     -        ii  v     v i           
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_161274279_   2716 GACAATTCAAGGGACCTA---T--------CAATCTTGAAAAA--ATAAC 2752
                          iv   v         i --- --------             -- v   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_161274279_   2753 AAAGTTGCAGGAATTTCACATCTCAATTTCAAAACTT------------- 2789
                                v    v iv   v  i              -------------
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_161274279_   2790 -GTAA----GATAGTGTGGTATTTGCAAGAGGA----CAAGTAGGTAAAT 2830
                         -    ----  i         i v   vi    ----  vi   i v   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_161274279_   2831 GGAATAGAATTGAGACTCCAAAAATAA-TTCATACATCAATGACCAACTG 2879
                                        v    i      -ii       iv   ii   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_161274279_   2880 AGTTTTGACTAGAGTTCCA-GAC------------AAA------TCTTTT 2910
                          v   i   v  i  v   -   ------------   ------      
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_161274279_   2911 CAACAAATGGTGGTGGGAAAACTGGAAATCTACATGCAAAAAATAAATAA 2960
                                     v     v       v ? i          i -------
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA------- 444

  chr2_161274279_   2961 ATAAATAAATAAATAAATAATGAATTTGGAGCCTTACCTCACTCCATA-- 3008
                         -------------------     v     v  i        v     --
  L1M4_orf2#LINE/    445 -------------------ATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_161274279_   3009 --AAAATTAACAAAAAATGGATCA---------------------AAACC 3035
                         --         vv           ---------------------    i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_161274279_   3036 ATAAAAGCTTTAGAAGAAAA-ACAGGAGGTATATT---G-GA--TTAGAT 3078
                               vii           - i   ? -  v  i--- -  --  i i 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGT 574

  chr2_161274279_   3079 TAAGCAATGGTTCCTTTAAGATGACACCAAAAGCATAAACAACAAAAGAA 3128
                           i         i   vi v               i  i           
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_161274279_   3129 AAAATAGGTAATCTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 3178
                                i   vi                                     
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_161274279_   3179 GAACACCATAAAATAAGTGAAAAGGCAACCCATAGTATGGGAGCAAATAA 3228
                          i    i  v  iv          i       i  v       v     v
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_161274279_   3229 TTGCAAGTCATATAT---ATAACAGATTTGTATCTAGAATGTATATTTAT 3275
                               i        ---    vi  i       i     i    --- v
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA---AA 771

  chr2_161274279_   3276 AAACTTTTACAACTCAAACATAAAAAGA-AAATAACCAAGTTGAAAACTG 3324
                         i    i           vv         -        v i  ?    v  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_161274279_   3325 GGCAGACTATATGAATAGATGTTTCTGCAAAGAAGATATACAA----CCA 3370
                             i vv  v        ii     v                ----   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_161274279_   3371 ATACACATATAAAAAGATGTTCAACATCATTAGCCAT 3407
                            vi  i  i        i         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (74 / 51)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 5.20 (130 / 25)  


3062 26.97 1.33 0.55  chr2_161304866_161311233.rev     4976  5876 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161304866_   4976 TGGAAAAACATTCCACACTCATGGAT-AGAAGAATCAATATCGTGAAAAT 5024
                               i i  i   iii        -i     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161304866_   5025 GGCC-TACTGCCTAAAGTAATTTATAGGTTCAATTCTATCTCCATCAAGC 5073
                            v-    v  i   v i  i  i  i     iv v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161304866_   5074 TACCA-CTGACTTTCTT-CATGGAATTGGAAAAAACT-ACTTTAAACTTC 5120
                          v   -   v    i  -  - i     -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_161304866_   5121 ATCTGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTGGGCAAGAA 5170
                           v     viiv  ii  v  v v  v     i      i  iiv     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_161304866_   5171 GAACAAAGCTGGAGGCATCACGCTACATGACTTCAAACTATACTACAAGG 5220
                                 i      vv    i  v vii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_161304866_   5221 CTACAGTAACTAAAACAGCATGGTACTGGTACCAAAACAGATATATAGGC 5270
                                  ii  i    ii         i iv ii i   i      ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_161304866_   5271 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACTCATCTACCACCA 5320
                                 i    iv   ivii         vv   iv   i  ivii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_161304866_   5321 TCTGATCTTTGACAAACCTGACACTCACAAGCAATGGGGGGAAGATTCCC 5370
                         vi    i  i     ivv  v  vvvv  vv        ii ii  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_161304866_   5371 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAACCTG 5420
                          v  i  i        i     v      v  ?   i     i  ivv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_161304866_   5421 AAATTGGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGATGGAT 5470
                           i          v   i     v           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_161304866_   5471 TAAAGACTTAAACATAAGACCTAAAACCATAAAAAGCCTAGAAGAAAACC 5520
                         i ?    i    ii     v       i      vv i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_161304866_   5521 TGGGCAATAGCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAAA 5570
                          i  ?ivv iiv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_161304866_   5571 ACACCAGAAGCAATGGCAACAAAAGCCAAAATTGGCAAATGGGATCTAAT 5620
                               i     vvi          vv     v ii    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_161304866_   5621 TAAACTAAAGAGCTGCTGCACGGCAAAAGAAACTATCATCAGAGTGAACA 5670
                         i   v v  i i  vi  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_161304866_   5671 GGCAACCTACAGAATGGGAGAAAAGTTTTGCAATCTATCCATCTGACAAA 5720
                          i     i                vv       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_161304866_   5721 GGGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTA-CAAGAAAAA 5766
                           i  vi          v  i        --  -  i i -i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_161304866_   5767 ---AAACAACCCCATCAGAAAGTGGGCAAAGGATATGAACAGACACTTCT 5813
                         ---   i     v  i?i   i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_161304866_   5814 CAAAAGAAGACATTCATGCAGCCAACAAACATATGAAAAAAAAAACTCAT 5863
                          v        i  v  viii     i  i  i       i vi--    v
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG--CTCAA 895

  chr2_161304866_   5864 CATCACTGGTCAT 5876
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


2497 23.53 10.92 1.92  chr2_161340598_161344673     2752  3584 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161340598_   2752 TGAAGAGAAAGGTCATGTTTACAGATTAGAAGACTTAATATT---AAAAT 2798
                           i i   v vvi      i ii    i              ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161340598_   2799 GTCAGTTTTTCTCTAATTGATCTATGATTTCACCATGATACCAATCAATA 2848
                          v  i vi i i v          iiiv    v iii  v  v     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161340598_   2849 TTTCAGC-ACTATT----CAGGAAATTGGCAAGTTGATTCTAAAATGTGC 2893
                          ii    -i iv  ----   -      i    i    i       viii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG-AAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_161340598_   2894 ATGGAAATAAAAAAGACCCAGAATAACCAATATGATTTTGAAAAATAA-- 2941
                                 iv  ii           i    v ii  i        v  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_161340598_   2942 -CAAAATTATAAGACTTCTACAATCTGAGTT-AAGACTAATTATAAAGTC 2989
                         -    i  iv i    ivi  vvi ii v  -  i   v i  i    ii
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_161340598_   2990 AC--TAGT----GCAATGCAATATTGATGTCAAGGTAGACATATAGATTA 3033
                           --  i ----i  i  iii  i  iii v i i             i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_161340598_   3034 ACACAATAGAA-----AGCTCAGAAATAGACGTAGACACATATTACATGA 3078
                          iiv       -----  ii        i  v----  i i   -i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACC----CATACATT-TATGG 344

  chr2_161340598_   3079 TTATGTGATTTTTGACAAAGGTTTCAAAGTAATTCAATTGGGTAAGTATG 3128
                          i vv       i     i   vi   iiiv       v   v   v  i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_161340598_   3129 GTCTTGTCAACAAATAG-GC--------------ATCCATA--------- 3154
                              v         i -  -------------- ?   i ---------
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_161340598_   3155 ----AGT-----CCTTACCTCACATCATGCTTAAAAATTAACTCAAAATG 3195
                         ----   -----  i         i   iivi                  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_161340598_   3196 GATTATAGAATTA----TAAAAG-TGAAACTATTAAACTTTTAGAAGAAA 3240
                            i ?   vi  ----   i  - i       v     i          
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_161340598_   3241 GTATGTGAAGAAATCTTTGTGACCTTGG-TTAG-CAAAGATTTGCTAGAT 3288
                         ii  iv ?iv       i          -    -   v i   vi     
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_161340598_   3289 AGAAAACCAAAAACACAAACTATAAACTAATAAGTTGTTATGCTAGATTT 3338
                          vi v       i     i v i   vv  v  i v v  vii i  i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_161340598_   3339 CATTAAAATACAAAATTAGAATCTTTTGCTTTTCAAAAGACTCTTTTATG 3388
                            -------        i  v      ivi      i   v  v i v 
  L1M4_orf2#LINE/    645 CAT-------CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_161340598_   3389 AAAATGGAAGG-TAAGCCATAGTCTGAAAGAAAATATTTGTAAA--ATAT 3435
                            i  i  i -i  v   i  vv  ii            i   --    
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_161340598_   3436 AGTTCTAA-AATAGACCT-TAACTGGAAGATATAA-GAACACTTA-AACT 3481
                          --   i -  vi   i -  v ii   v      -    v    -    
  L1M4_orf2#LINE/    738 A--TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_161340598_   3482 CAATAATTAAAAAAACTAATAA----AT-----------------ATTTG 3510
                                -     i  v     ----  -----------------     
  L1M4_orf2#LINE/    786 CAATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_161340598_   3511 AATAGACACTTCACCAAAGAAGATATATAAATGGCAAGTAAGCACATGAA 3560
                                 i   v              i       v i            
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_161340598_   3561 AGGATGCTCAACATCATTAGTCTG 3584
                          i              ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (129 / 64)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 3.57 (107 / 30)  


3444 23.79 2.13 0.56  chr2_161373141_161376801.rev     2278  3168 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_161373141_   2278 AAAAATATTCCATGTTCATGAATTGGAAGAATCAATACTGTTAAAATGTC 2327
                            i    i           i         v i    i      i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_161373141_   2328 CATACTACCCAAAGCAATATACAGATTCAATGCAATCCCTGCCAAAATAC 2377
                         v     v      vii  v           i         ii      v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_161373141_   2378 CAATGACTTTTTTTGCAAAAATAGAAAAAA-AATTCTAAAATTTATATGG 2426
                           iivi i         i    v  v  iv-i  i        i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_161373141_   2427 AATTATAAAAGACCCAGTATAGCCAAAGCTATCCTGAGCCAAAAAAAAAA 2476
                           v ii  ii       v         i v   i   ivv i  i  v  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_161373141_   2477 ACCTGGAGCAATCACATTCTCTGACTTCAAATTATACTACAGAGCTATAG 2526
                          vi     v v     i ii ii i      viv       i     i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_161373141_   2527 TAATCAAAACACCATGTTACTAGCATAAAAACAGACACATAGACCAATGG 2576
                                i   vii  v    i      ii i     i     i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_161373141_   2577 AACAGA-----GAGTCCAGAAACAAATCCATATAGCTATAGTGAACTCAT 2621
                           i   -----           i   i     i vi   i  v  i v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_161373141_   2622 TTTCAACAAAACTGCCAAGAACAT---ATTGGCAAAGGACAGTCTCTTCA 2668
                             i    iiv        v   ---  v  v    i i     i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_161373141_   2669 ATAAATGATGCTGGAAAAACTGGGTATCCAAATGCAGAAGGATGAAACTT 2718
                          i     i      i v      i  ?   v     i   i     ii v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_161373141_   2719 GACTCCTATCTTTCTCCACATTCAAAAATCAGATCAAAATGGATTA--GA 2766
                            i    i  iv v   i  v       i iv           i --  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_161373141_   2767 CTTAAAGCTAAGACCTCAAACTATGAAACTACTACAAGAAAACATTGAGG 2816
                          i    vv     v  v       i     vi  v          v i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_161373141_   2817 AAACTCT--AGGACACCGGTCTGCACAAAAATTTCTTGAATAATACCCCA 2864
                         v  v   --iv   vii  vi ivi   vii      ii   vv  v   
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_161373141_   2865 CAAGCTCAGGCAATCCAAAGCAAAAGCGGACAAATGGGA---TATC-AAG 2910
                         v    v  i    - v    v    iii  i    v   ---i   -  i
  L1M4_orf2#LINE/    604 AAAGCACAAGCAA-CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_161373141_   2911 TTAAAAAGCTTCTGCACAGTGAAGCAAACAAGCAACAAAGTGAAGAGACA 2960
                                -   i  ii vvii   v v  v v   v        i     
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_161373141_   2961 ACACACGAAATGGGAGAAAATATTTGCAAACTAC-CATCTGACAAGGGAT 3009
                           v   ii                      ii i-i      i      i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_161373141_   3010 TAATAACCAGAATATATAAGAAGCTTAAACAACTCCACAGGAAAAAGAAA 3059
                          vi  v             ii i  ivv       v i iv       --
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-- 799

  chr2_161373141_   3060 TCCAATAATCCAATTAAAGAACGGGCAAGAGATTTGAATAGACATTTCTC 3109
                         - v     i      ?  i  i      ii                    
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_161373141_   3110 AAATGAAGACATACAA-TGGCAAATAGAAATATAAAAAGGTGTTCAACAT 3158
                         v  v     i      -    v    iiv i  i     i  i       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_161373141_   3159 CATTGATAAT 3168
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.65 (130 / 79)
Gap_init rate = 0.01 (12 / 905), avg. gap size = 2.00 (24 / 12)  


2006 18.61 14.13 0.67  chr2_161388761_161392401.rev       60   505 (3135)    L1M4_orf2#LINE/L1        3   508 (400)  

  chr2_161388761_     60 GGAAGACACTCCAAGTTCATGGATAAGAAGATTTAATATTGTTAAGATGG 109
                          i    i ii   v          vi     i                  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_161388761_    110 TAATATGCCCCAAATTAATCTACAGATTCCATGCAATTCATATCAAATTT 159
                         i    iv         i            v i     i v       v i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_161388761_    160 TCAGCTAGGC---TTTTACAGATATAGACAAGCTGATCTTGAAAATCATA 206
                         i     --  ---    i    v  v            i i   v     
  L1M4_orf2#LINE/    103 CCAGCT--GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_161388761_    207 TGGAAACTCAAAGAACCTGGAATAGCCAAAAACAATCTAGAAAAGAATAA 256
                               iv   i i   ii            -      v     ii vi 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGA 199

  chr2_161388761_    257 ACAAAATTGGAGAACTCTGATTTTCCAATTTCCAAATGTCATACAAAGCC 306
                              i      i    vv i  i        v   iv vv        i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_161388761_    307 ACAGTAATCAAAACTGAATGGCACTGACACAAGGGTAG------------ 344
                                    i  v vi   i    i  i    i   ------------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_161388761_    345 -TGAAAT------------------------------------------- 350
                         -  i   -------------------------------------------
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_161388761_    351 -GATTTTCATCAAGAGTGCCAAGACAATTCAATGGTGAAAGAATAGTCTT 399
                         -       iv    i          v         v              
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_161388761_    400 TTCAACAAATGATACTAGGACAACTGGAGAGTCATATGCAAAACA-TAAA 448
                                    i i  i           v ?i  i        v - i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_161388761_    449 GTTGAATCCCTTCTTCATATTATACACAAAAATTAATTCAAAATAGATCA 498
                             i i    v i   i ii   i           i       i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_161388761_    499 TA--TCTAA 505
                         ? --i    
  L1M4_orf2#LINE/    500 WAGACCTAA 508

Transitions / transversions = 2.12 (55 / 26)
Gap_init rate = 0.01 (7 / 506), avg. gap size = 9.43 (66 / 7)  

2928 24.78 3.59 1.79  chr2_161388761_161392401.rev     2257  3148 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161388761_   2257 TGGAAAAAACTTCCATGCTTCTGGATTGGAAGAATCAAT---GTTCAAAT 2303
                               i vv i     i iv            v i   ---   v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161388761_   2304 GGCCATACTGTCCAAAGCAAACTACAGATTCGATGCTATTCCTATCAAAT 2353
                            v     vi     vii v          i i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161388761_   2354 TACCAACATCATTTTTCACAGCA-TTAGGAAAAACT-ACTATAAAATTCA 2401
                          v   i vv v     ii   v -  --  v  i  - iiv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr2_161388761_   2402 TA--GAAACCAAAAAAAGAGTGTGACTAGCCAAAGCAATCCTAAGCAAAA 2449
                           --    i--iv  ii  vivv  v        i     i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAAT--GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_161388761_   2450 AGAACAAAGCTAGAGGCATCACATTTCTCAACTT-AAAACTATACTGCAA 2498
                                  i i    vv     i   i   i  -      -    i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chr2_161388761_   2499 GGCTATAGTAACAAAAACAGCATGGTATCTATA-AAAAATCAGACACATA 2547
                         i    i     iv  i    ii     iivii -  ii  -     i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATA 294

  chr2_161388761_   2548 GACCAATGGAACAGAATAGAGAATCCAGAAATAAAGCTGCACAGCTGCAG 2597
                           i        i     v    i            v iii   vi iii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_161388761_   2598 CC---TGATCTTTGACAAAG-TGCACAAGA--ATTAGCAATGAGAAAAGG 2641
                         i ---    i  i     i -   -     --   --     i i    i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGC-CAAGACCATT--CAATGGGGAAAGA 391

  chr2_161388761_   2642 ACTCCCTATTCAATAAATGGTTCTGGGATAGCTGGCTAGGCTTATGCAGA 2691
                          ivvi  v     i       v      i i    v  ?v vi     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_161388761_   2692 AAAATGAAACTCGACCCCTACCTTTTACTATATACAAAACTTAACTCCAG 2741
                          i      ii v           ivi  i          v       v i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_161388761_   2742 GTGGATTAAAGGCTTAAATGTAGGACTTCAAACTATAAAAACCCTAGAAG 2791
                         i     i ?  i i        i  vi v           vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_161388761_   2792 AAACTCTAGG---AAATACCATTCTGAACATCAGCCTTGGGAAATAATTT 2838
                            viv    ---    -- v iv   v v vi --  i  v   ii   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT--CTTCGTGACCTTGGG--TTAGGCAATGGTTT 587

  chr2_161388761_   2839 AT-AACTAAGTCCTTAAAAGCAACTGCAACAAAAAGAAAAACTGACAA-T 2886
                         v - iv  v v vii       vvv         ii     iv  i  - 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_161388761_   2887 TGAGAACT-------AATTAAAGAGCTTCTGTACAGCAAAAGAAACTATG 2929
                           i--   -------       i -   i   i vv    i  v     v
  L1M4_orf2#LINE/    638 TGG--ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chr2_161388761_   2930 AATAGAGTACACTGACAACCTACAGAATAGAAGAAAGTATTCACAAACTA 2979
                           v i   iv vv       i       i i     i    ii    ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_161388761_   2980 TGCATCTGACAAAGGTTTAATATCCACGATCTATGAGGAACTT----AAT 3025
                          ii      i  i  vi vi      vi  v   i i     i----  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_161388761_   3026 TCAACAAGCAAAAAACAAATAACCCCATTAAAAAGTAGGCAAAAGACATG 3075
                             i  vv    i           v   ?    i i      i  iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_161388761_   3076 AACAGACACTTCTTCAAAGAAGACATATAAATGACCAACAAACATATGAA 3125
                           i     i    i         i   i     i    i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_161388761_   3126 AA-ATGCTCAACATCACTAATCAT 3148
                           -             ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (140 / 78)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 1.92 (48 / 25)  


2549 28.91 2.34 1.00  chr2_161407477_161410723     1860  2755 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161407477_   1860 TGGAAAAACCTGCTATGCTTATGTATTGGAAGAATCAATACTGTTAAAAT 1909
                               i iv v i   i i   v         v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161407477_   1910 GGCTATATTGCCCAAAGCAAACTGTAAATTCACTGCTATTCCTATCCAGT 1959
                            v   i v      vii v  ii i     vi  v  i      v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161407477_   1960 TATCAA-TGTTATTCTTCACAGAATTAGAAAAAAACT-ATTTTAAAATTT 2007
                          vi  i-  ii-  i  ii     v v  v  i--  -  ii       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_161407477_   2008 ATATAGAATCAAAAAAGAGCCTGAACAGACAAAGAAACCCAAAGCAAAAA 2057
                             i   viiv  ii  v  v   i  v    iv  i ivi iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_161407477_   2058 GAACAAAGCTGGAGGGACCACATTACTCAACTTCACACTATACTGTGAGG 2107
                                 i      ivi    i v i   i    v viv    iii i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_161407477_   2108 CTATAGTAACCAAACCAGCATGGAACTGGTACAAAAATAGACACATAGGC 2157
                            i     i   iv   ii   v     i i  ii       i    ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_161407477_   2158 CAATGGAACAGAATAAAGAACAAAGAAATAAAGCTGCACATCTACAACCA 2207
                                 i     vi   iivv         v iii    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_161407477_   2208 ACTGATCTTTGACTCAGTTGACAAAAATAAGCAATGTGGAGAGGACACCC 2257
                          i    i  i   vvi v  v   i vi vv     v   i  i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_161407477_   2258 TATTCAATAAACAGTTTTGGGAAAGTTGGCCAACCATAAGCAAAAGAATG 2307
                          v     i   ii  vi     v ii   vi ?   i v           
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_161407477_   2308 AAACCAG-CCCCTACCTTGCACCATATA-AAAAATTAACTCAAGATGGAT 2355
                           iiii -         ii         -              i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_161407477_   2356 TAATGACTTAAATGTAAGACCTCAAACTATAAAAATCCTAGAAGTAAACC 2405
                         i ?v   i           v  v           v  i      v    v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_161407477_   2406 TAGAAAATATTCTTCTGAACATTGGCGTAGGCAA---------AGA-ATG 2445
                            i?ivv v     vvi  v    vv       ---------   -   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_161407477_   2446 TCCTGAAAAACAAATACAACAAAAACAAAAATTAACAATTGGGACCTAAT 2495
                         v viv    i  v vi        iv      vi i  v v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_161407477_   2496 TACACTAAAGAGACCCTGCACAGTAAAAGAAACTATCAACAGAGTAAA-- 2543
                         i v v v  i iviii  ii vvi   i  v        v i   i  --
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_161407477_   2544 --CAGCCTACTGAATGAGAGGCAATATCTGCAAACAATGTATCCAACAAA 2591
                         --  i  i  v     i   iv     i      iv  i    ii i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_161407477_   2592 CAACTGATACCCAGAACTAATACCCAGAA-TCTATAAGGAACTTAA-ATC 2639
                         vi   vi  i      i--   ivv    -   -  v--    i  - vi
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAAT--ATATAAAGAACTCT-TAC--AACTCAATAAT 792

  chr2_161407477_   2640 AACAAGCATAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAATGGAC 2689
                           v   - i   i     v   ?    i           iv     i   
  L1M4_orf2#LINE/    793 AAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_161407477_   2690 ACTTCTTAAAAGAAGACATAGAAGCAGCCAACAAACACATAAAAA-ATGT 2738
                          i    iv        i   v  iii     i  i     i    -   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_161407477_   2739 TCCATATCATCATCATT 2755
                           v i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (159 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


3225 27.09 0.44 0.44  chr2_161439188_161445608.rev     5022  5929 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161439188_   5022 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5071
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161439188_   5072 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5121
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161439188_   5122 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5169
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_161439188_   5170 TATGGAACCAAAAAAGAGCCCTCATTGCCAAATCAATCCTAAGCCAAAAG 5219
                                viiv  ii  v  vvv  v      v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_161439188_   5220 AACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGAC 5269
                                i      vv    v  v  ii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_161439188_   5270 TACAGTAACTAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5319
                                 ii  i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_161439188_   5320 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATAACTACAACT 5367
                                i    i--    i  --        vv   i i vi  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_161439188_   5368 ATCTGATCTTTGAGAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5417
                          vi    i  i  v  ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_161439188_   5418 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5467
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_161439188_   5468 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGA 5517
                            ii    i    v   i     v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_161439188_   5518 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5567
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_161439188_   5568 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATATCTAA 5617
                         v    ?i v viv   iv   v v  vv i     v ii   v  vv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_161439188_   5618 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTAA 5667
                         i            vvi          vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_161439188_   5668 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5717
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_161439188_   5718 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5767
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_161439188_   5768 AGGGCTAATATCCAGAACCTACAATGAACTCAAACAAATTTACAAGAAAA 5817
                         i  i  vi         iv  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_161439188_   5818 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5867
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_161439188_   5868 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5917
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_161439188_   5918 ATCACTGGCCAT 5929
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3212 26.99 0.88 0.44  chr2_161448018_161454385     4973  5876 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161448018_   4973 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5022
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161448018_   5023 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5072
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161448018_   5073 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5120
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_161448018_   5121 TATGGAACCAAAAAAGAGCCCTCATTGCCAAATCAATCCTAAGCCAAAAG 5170
                                viiv  ii  v  vvv  v      v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_161448018_   5171 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGAC 5220
                                i      vv       v  ii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_161448018_   5221 TACAGTAACTAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5270
                                 ii  i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_161448018_   5271 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATAACTACAACT 5318
                                i    i--    i  --        vv   i i vi  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_161448018_   5319 ATCTGATCTTTGAGAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5368
                          vi    i  i  v  ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_161448018_   5369 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5418
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_161448018_   5419 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGA 5468
                            ii    i    v   i     v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_161448018_   5469 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5518
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_161448018_   5519 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5568
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_161448018_   5569 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTAA 5618
                         i            vvi          vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_161448018_   5619 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5668
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_161448018_   5669 AGGCAACCTACGGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5718
                           i     i  i              v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_161448018_   5719 AGGGCCAGTATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5768
                         i  i iv           v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_161448018_   5769 AAACAA----CCCCATCAAAAAGTAGGCAAAGGATATGAACAGACACTTC 5814
                          i    ----   v  i?    i i          v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_161448018_   5815 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGTAAAAGTGCTCATC 5864
                           v        i  vi viii     v  i      v   ii      v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_161448018_   5865 ATCACTGGCCAT 5876
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2730 28.86 1.33 0.55  chr2_161459439_161464332     3510  4410 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161459439_   3510 TGGAAAAACATTCCATGCTCATGCATAGGAAGCATCAATACTGTTAAAAT 3559
                               i i  i     i     v  v     vv i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161459439_   3560 GGCCATACTGCCCACAGCAATTTACAGACTCAATGCTATTCCTATCAAAC 3609
                            v     v    v vii  i      i    i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161459439_   3610 TACAAACAACATTTTTCACAGAATTAGAAAAAACT-ATTCTAAAATTCAA 3658
                          v v i vi v     ii     v v  v  i-  -  i          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_161459439_   3659 CTGGAACCAAGAAAAATCCCCAATAGCCAAAGCAATCAGAAGCAAAAAGA 3708
                         v     viivi iii i  vv          i     vvi iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_161459439_   3709 ACAAAGCTAGAGGCATCGTACTACCTGTCTTCAAACTATACTACAAATGT 3758
                               i i    vv  ii   v  iivi      viv         vv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_161459439_   3759 ACAGTTACCCAAACAGCATGGTACTGGTACTAAAACAGACATATAGACAA 3808
                              v i v i    ii         i iv ii i           iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_161459439_   3809 ACGAAACA-AGTTATAGAACCCAGAAATAAACCTGTACTCCTACAACCAA 3857
                          i i  i - i  i-   ii             ii   vii  iiii   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTG-AGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_161459439_   3858 CTTATCTTCAACTAAGTAAACAATAGCAAGCAACAGGGGAAAAACTTCCT 3907
                         i v  i   i  v i vviv   v v  vv   ii   i  i  ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_161459439_   3908 ATTCAATAAATGGTGCTGGGATAACTAGCTAGACATAGGCAAAAGATTGA 3957
                         v     i              i    i v  ?v  i v        v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_161459439_   3958 AACTAAACACCTTGCTTTCACTGCATACAAAAATCAACTCAAGATGGATT 4007
                          ii ii  v   vv  iv   iii          i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_161459439_   4008 AAAGACTTAAATATAAAACCTAAAACTATAAAGATCCTAGAAAAAAAGCT 4057
                          ?    i     i   i v             iv  i     i    vv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_161459439_   4058 AGG---AAATACCATTCTGGACATCAGCCCTGGCAAAAATTTTGTGAA-- 4102
                            ---    -- -   vv   v ii viiv     vii   iv ii --
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_161459439_   4103 -GACTCCAAAAGGAATTGCAACAAAAACAAAAATTAGCAAGTGGGGCCTA 4151
                         -   v       v vvv         iv      viii  i v  i i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_161459439_   4152 ATTAGACCAAAGAGCTTTTGCACAACAAAATAAACTATCAACAGAGTAAA 4201
                           i i viv  i i      ii vv    iv v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_161459439_   4202 CAGACAATCTACTGAATGAGAGACAATATTTGTGAACTATACATCCAATG 4251
                         v      i i  v     i    v        ii  ii   i   ii  i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_161459439_   4252 AAGAACTAATATCGAGAATCTATAGGGAACTTAAAAAAATCAACAAGAAA 4301
                          i i   vi    v     v    ii     ivv v  v    i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_161459439_   4302 ----CAAACAACCCTGTTAAAAAATGGGCAGAGGACATGAACAGACACTT 4347
                         ----    i     vi  ?           i    iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_161459439_   4348 TCCTAAAGAAAACATACACAAGGCCAACAAGCATATGAAAAAATGCTAAA 4397
                         ii i      i i     v v      i     i       i     v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_161459439_   4398 TGTCACTAATTAT 4410
                         ii   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (155 / 102)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


3149 27.51 0.99 0.66  chr2_161479231_161485251     4625  5529 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161479231_   4625 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAGTCAATATCGTGAAAAT 4674
                              ii i  i     i i    i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161479231_   4675 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4724
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161479231_   4725 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4772
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_161479231_   4773 TATGGAACCAAAAAAAGAGCCC-GCATCGCCAAGTCAATCCTAAGCCAAA 4821
                                -- viv  i ii   - v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_161479231_   4822 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 4871
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_161479231_   4872 ACTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 4921
                         i         i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_161479231_   4922 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAA 4969
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_161479231_   4970 CTATCTGATCTTTGACAAACCTGAGGAAAACAAGCAATGGGGAAAGGATT 5019
                         ii vi    i  i     ivv  vvi i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_161479231_   5020 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5069
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_161479231_   5070 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5119
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_161479231_   5120 TATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5169
                         v  i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_161479231_   5170 ACCTAGGTGTTACCATTCAGGACATAGGCATGGGCTAGGACTTCATGTCT 5219
                           v    ?  v viv   iv   v v  vv i   v v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_161479231_   5220 AAAACGTCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5269
                          vi  ii        vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_161479231_   5270 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGGGTGA 5319
                         v  i   v v  i i   i  ii vv    i  v    i  vv ii    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_161479231_   5320 ACAGGCAACCTGTAAAATGGGAGAAAATTTTCGCAACCTGCTCATCTGAC 5369
                          v  i     iii i             v  i    viiiivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_161479231_   5370 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5419
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_161479231_   5420 A----TAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5465
                          ----i   i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_161479231_   5466 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATAAAAAAATGCTCA 5515
                             v        i  vi viii     v  i     i    i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_161479231_   5516 CCATCACTGGCCAT 5529
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (150 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


3178 24.43 3.51 0.79  chr2_161501003_161503249.rev      872  1755 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161501003_    872 TGAAGAGATAGTCTGTGTTCAGAGACAGGAAGACTCAATATTGTCAAGAC 921
                           i i     vi ii      vi  iv        i        i    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161501003_    922 ATCAATTCTTCTCAACTTGACCTATAGATTCAATGCAGTCCCACTTAAAT 971
                         iv    v  i i   v    i   i        i   i    vv i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161501003_    972 TCTCAGCAGT-TATTTTAAGGATATTGGCAAACTAAATCTGAAGTTTAAA 1020
                           i    v i- v    ivi  v    i   i  i vi  i  i  i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_161501003_   1021 TAGAGAAGCAATG-ACCCAGAATAACCAACATGATATTGTAGGAAAATAA 1069
                          i  i v    v -          i    v ii  v   v ii i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_161501003_   1070 GAAAGTTGGA-------CACTACCAAACTTAAAGACATACTATATAGCTA 1112
                         v         -------    v  v  i  v  i  v     i v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_161501003_   1113 CAGTAATCAAGACAGTGTGGTATTGGTAGAAGAATAAACAAAAAGATGAG 1162
                                               i   i v   i   i   v v    v i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_161501003_   1163 TGGAACTGAATAGAGAATCCAGAA-TGGACCCAGACAAGTATAGTGAACT 1211
                              iv    v    i       - ii     v   vv   i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_161501003_   1212 GATATTTGACAAAGAAGCAAAGGCAATAGAATGGAACAGAGATAGTCTTT 1261
                            v  i     i iv  v   i v  vv     iiv iii         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_161501003_   1262 TCAACAAATGGTTCTGGAACAACTGGACATCCACATGCAAACAA------ 1305
                                     v    i         i ?           vi ------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_161501003_   1306 TTGAATCCATATGAGATTTTATGCCCTTCACAAAAATTAGCTCAAAGTG- 1354
                            i i  v  i-----i i ii  v vi          i      i  -
  L1M4_orf2#LINE/    451 TTGGACCCCTAC-----CTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_161501003_   1355 ATTATAAATCTAAATGTAAAATGC-AACACTATAAAACTCCTTGAAATAA 1403
                           i ? i i          i -  -  v            i v   iv  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_161501003_   1404 A-ATGGGAGAAAATTGAGGTAACCTTGAGTATGGCAATGATGTTTTAGAT 1452
                          -  i  ? v    ivvv  i      i  vv       i v i      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_161501003_   1453 ATACCACCAAGA-CATGATCTATGAAA---AAAATA-ATAAGCTAGACTT 1497
                           iv      i -  ii v v ii   ---      -    ii i     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_161501003_   1498 CACTAGAACTAAAAACTTCTACTCTGGAAAAGACACTGTCAAGAGAATGA 1547
                           ii i  i         i iiv  vv   i      i      i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_161501003_   1548 GAACAGAAACCACAGAATGGGAGAAGATATTTGCAAAAGACACATTTGGT 1597
                         i  v v  v                i           vv i i  i  i 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_161501003_   1598 TAAGGGTTCTTATC-AAAA-ATATAAATA----TTAAAACTCAACAGCAA 1641
                         v i  ii iv    - i  -       v ----   v       i ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_161501003_   1642 GAAAACTAATAAATCAATTTTAAAAATGGACAAAAGACCTGAACAGACAC 1691
                         i  i  v     vi     ?-        i    i  ii    i     i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_161501003_   1692 TTCACTAAAGAAGATATACAGGTGGCGAA-AAGCATATGAAAAGATGTTG 1740
                            v i              ii    v  -     i           i v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_161501003_   1741 AACATCACATACCAT 1755
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (133 / 79)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.11 (38 / 18)  


3072 25.19 1.66 0.89  chr2_161525396_161530651     3864  4764 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161525396_   3864 TGGAAACACATCCCATGATTATGGATGGGTAGAATCAATATCGTAAAAAT 3913
                               v i        v i      v  v   v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161525396_   3914 GACTATACTTGCCAAAAGCGATCTACAAATTCAACACAATTCCCATCAAA 3963
                          i v     iv     -vi        i       i    i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_161525396_   3964 ATACCATCATCATTCTTCACAGAATTAGAAAAAAAAATCCTAAAATTCTT 4013
                           v   v vv v  i  ii     v v  v  ivvi            v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_161525396_   4014 ATGGAACAAAAAAGAGCCCACA-TAGCCAAAGCAAGACTGAGAAAAAAGA 4062
                               vviv  i ii    v -        i   vvi   i   i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_161525396_   4063 ACAAATTTGAAGGCATCATATTACCAAACTTCAAAATATACTACAAGGCT 4112
                              v   i   vv   i i v  v  i       iv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_161525396_   4113 ACAGTTACCAAAACATCATGGTACTGGTATAAAAATAGGCATGTAGACCA 4162
                              v i   i   vii         i    ii    i   i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_161525396_   4163 ATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATATTTACAGCCAAC 4212
                               i     v    ii           v   v i     ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_161525396_   4213 TGATCTTTGACAAAGCAAACAAAAACATAGAGTGGA-AAAGGACAACCTC 4261
                             i  i     i vviv   i v   vv i   i-    i i ii  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_161525396_   4262 TTCAACAAATGGCGCTGGGATAATTGGCAAGCCACATGTAGAAGAATGAA 4311
                                     i       i  i   vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_161525396_   4312 ACTGGATTCTCATGTCTCACCTTCTACAAAAAT-----CAAGAAGGATCA 4356
                         ii    ii ii iv  v    v v         -----   i v      
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_161525396_   4357 AAGACTTCAATCTAAGACCTGAAACCATAAAAAATCTAGAAGATAACACT 4406
                         ?    i v   v     v  i    i      vvii       v    iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_161525396_   4407 GGAAAAACTCTTCTAGACATTGGCTTAGGCAAAGACTTTATGACCAAGAA 4456
                           ?iv  v     vv   v    v        v ii  iv iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_161525396_   4457 CCCAAAAGCAAATGCAACAAAAACAAGGATGGG-AG---GGACCTAATTA 4502
                         v         v v         iv  ii  i i- i---    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_161525396_   4503 AACTAAAAACCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTAAATAGA 4552
                           v v    v   i  ii vv    i  v iv    iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_161525396_   4553 CAACCCACAGAGTGTGAGAAAATTTTGACAACCTATGCATCTGACAAAGG 4602
                                    i  v        v  vi   vii  ii      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_161525396_   4603 ACTAATATCCAGAATCTACAAAGAACCC----AAATCAGCAAGAAAAAAA 4648
                            vi          v  i       i ----  v   ii  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_161525396_   4649 ACAAACAATCTCATCAAAAATTGGGCAAAGGACAGGAACAGACAATTCTC 4698
                         -    i  i iv  i?    v           ivv   i     v     
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_161525396_   4699 AAAAGAAGATATACAAATGGCCAAAATATGAAACATATGAAAAAAATGCT 4748
                         v                       --  --- i  i       i -    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAA--TA---AGCACATGAAAAGA-TGCT 892

  chr2_161525396_   4749 TAACATCACTAATTAT 4764
                         i       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (127 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


3241 27.20 0.44 0.44  chr2_161532990_161539266.rev     4878  5785 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161532990_   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4927
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161532990_   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161532990_   4978 TACCAATGACTTTCTTCACGGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi i  i  ii i   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_161532990_   5026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_161532990_   5076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5125
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_161532990_   5126 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_161532990_   5176 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5223
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_161532990_   5224 ATCTGATCTTTGACAAACCTCACAAAAACAAGCAATGGGGAAAGGATTCC 5273
                          vi    i  i     ivv vv   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_161532990_   5274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_161532990_   5324 GAAAGTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5373
                            iv    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_161532990_   5374 TTAAAGATTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?   ii    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_161532990_   5424 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGAACTTCATGTCCAA 5473
                         v    ?i v viv   iv   v v  vv i     viii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_161532990_   5474 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5523
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_161532990_   5524 TTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGAAC 5573
                          i   v v  i i   i  iiivv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_161532990_   5574 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5623
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_161532990_   5624 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5673
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_161532990_   5674 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5723
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_161532990_   5724 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5773
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_161532990_   5774 ATCACTGGCCAT 5785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3755 16.15 8.39 0.38  chr2_161663817_161665594      488  1286 (492)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr2_161663817_    488 AGGAAAACAATGTCTCCCCAACGTAATCTATAGATTCAATGCAATCCCTA 537
                          i  vii    i-        vv i     i        i          
  L1M4_orf2#LINE/     46 AAGATGGCAATA-CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_161663817_    538 TCAAAGTCCCAGCAGTCTTTTTTTTGCAGATATGGAAAAG---GTCCTAA 584
                              i       v i       --     v  v  v   ---i      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAA 142

  chr2_161663817_    585 AATTCCAATGGAATT---------CCA--ATAGCCAAAACAATCTTCAAA 623
                              vv      v ---------   --                 v   
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_161663817_    624 CAGAAAAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-ACTA 672
                         v    i                                       -    
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_161663817_    673 CAAAACTTCAGTAATCAAAACAG-----------------------CATA 699
                             i  v          i    -----------------------    
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_161663817_    700 TCAATCAATGGAATAGAATTGAGAATGAAGAA-TAAACTCATACATATAT 748
                          vi                     i vv    -     i       v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_161663817_    749 AGTCAATTGATTT-CAAAAAGGATAACAAGAC-ATTCAATGGAGAAATAA 796
                         i            - i v    i iv      -         i    v  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_161663817_    797 TAATCTCTTAAAGATATGAGACTAG-AGAACTAGATATCCATATGCAAAA 845
                           i   i  v  v v   ivi  i - v    i    ?   i        
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_161663817_    846 CAATGAAGTTAGACTCTTGCCTCACACCATATATAAAAATTAACTGAAAA 895
                         v         i   i i i              i           v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_161663817_    896 TGGGTTAAAGACCTAAATGTATGAGGTAAAACTATAAAATTTTTAGAAGA 945
                            i i ?             v   v             i i        
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_161663817_    946 AAATATAGGGATAAATCTAAATAAACATGGATTTGGCAAGGAT--CTTAG 993
                            i     ?i       vvi i v v   i  v     v i --     
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_161663817_    994 ATATGACACCAAAAGCACAAGCAACAACA---AAAGTAGATAAGCTGGAC 1040
                                                    v ---   i       ii     
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_161663817_   1041 TTTATTAACACTAACA---TTTGTGCATCAAAGGACACTATCAAGAGAGT 1087
                           i  i  v i   v ---       v                   i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_161663817_   1088 GAAAAGATAACCCACAGAATGGGAGGAAATATTTACAATTCCCACATGTG 1137
                                i                 i        i   v  vi i  v  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_161663817_   1138 ATAAGAGGCT---------AACA----AAGAACTTCTACAACTCAACAAC 1174
                              i i  ---------  i ----       ii          i  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_161663817_   1175 AAATAGACAA----TTCAATTTAAGAATAGGTAAATAATTTGAATAGATA 1220
                            v      ----ii     ?  i   i  i   vi           i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_161663817_   1221 TTTCTTCAAAGAAGGCATAAAAATGGACAACAAGTATATAAAAAGTTATT 1270
                              i        ii   v      v   i   i i  i     v ii 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_161663817_   1271 CAACATCAGCAATCAT 1286
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (78 / 47)
Gap_init rate = 0.02 (17 / 863), avg. gap size = 4.12 (70 / 17)  


3278 26.35 0.66 0.55  chr2_161679767_161684691.rev     3527  4433 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161679767_   3527 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3576
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161679767_   3577 GGCCATACGGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3626
                            v    vv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161679767_   3627 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3674
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_161679767_   3675 TATGGAACCAAAAAGGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3724
                                viiv  i   v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_161679767_   3725 AACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGGC 3774
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_161679767_   3775 TATAGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3824
                           i     i   i v  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_161679767_   3825 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 3872
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_161679767_   3873 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3922
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_161679767_   3923 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3972
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_161679767_   3973 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4022
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_161679767_   4023 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCATAGAAGAAAAC 4072
                          i ?    i       v   v       i      vi v           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_161679767_   4073 CTAGGCA-ATACCATTCAGGACCTAGGCATGGGCAAGGACTTCATGTCTA 4121
                         v    ?i- v i -   iv     v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_161679767_   4122 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4171
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_161679767_   4172 ATTAAACTAAAGAGCTTCTGCGCAGCAAAAGAAACTACCATCAGAGTGAA 4221
                           i   v v  i i   i  i  vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_161679767_   4222 CAGACA-CCTACAAAATGGGAGAAAATTTTCGCAACCTGCTCATCTGACA 4270
                         v     -  i   i             v  i    viiiivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_161679767_   4271 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4320
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_161679767_   4321 AAAACAAAAAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 4370
                           i     v     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_161679767_   4371 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAGATGGTCAT 4420
                            v        i  vi viii     v ii              v   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_161679767_   4421 CATCACTGGCCAT 4433
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2945 28.46 0.78 0.22  chr2_161691524_161698217     5300  6202 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161691524_   5300 TGGAAAAACATTCCATGCTCATAGATAGGAAGAATCAATATTGGGAAAAT 5349
                               i i  i     i    i   v      v i       vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161691524_   5350 GGTGATACTGCCCAAAGTAATTTATAGGTTCAATGCTATTCCCATCAAGC 5399
                           ii     v      v i  i  i  i     i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161691524_   5400 TACCATTGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAATTTCATA 5448
                          v   vivi i  i  ii     v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_161691524_   5449 TGGAACCAAAATAGAGCTCACATAGCCAAGACATTCCTAAGCAAAAAGAA 5498
                              viiv  vi  v iviv        i   v  i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_161691524_   5499 CAAAGCTGGAGGCATCATGCTATCTGACTTCAAACCATACTACAAAGCTA 5548
                              i      vv   ii  vi ii i      v v             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_161691524_   5549 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5598
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_161691524_   5599 CGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCATCT 5648
                         i    i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_161691524_   5649 GATCTTTGACAAACCTGAGAAAAACAAGGAACAGGGAAAGGATTCCCTAT 5698
                            i  i     ivv  vv  i v  vvv  ii       i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_161691524_   5699 TTAATAAATGGTGCTGGGAAAACTCACTAGCCATATGCAGAAAGCTGAAA 5748
                          i  i              v    viv  ?   i     i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_161691524_   5749 CTAGATCCCTTCCTTACACCTTCTACAAAAATTAACTCAAGATGGATTAA 5798
                         i i  i    v   i     v v                 i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_161691524_   5799 AGACTTAAACTTAACACCTGAAACCATAAAAACCCTAAAAGAAAACCTAG 5848
                             i    iv   v v  i    i      vi i  i        v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_161691524_   5849 GCG-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAAC 5897
                          ? - v i -   iv   v v  vv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_161691524_   5898 ACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATAAGATCTAATTA 5947
                                   vvi         ivv     v  i    vi  ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_161691524_   5948 AACTAAAGAGCT---GCGCAGCAAAAGAAACTATCATCCGTGTGAAAAGG 5994
                           v v  i i  --- i  vv    i  v       vvviv        i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_161691524_   5995 CAACCTACAGAATCGGAAAAAATTTTTGCAATCTATCCATCTGACAAACG 6044
                              i       v   i     v       vii  vi      i  iv 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_161691524_   6045 GCTAATATCGAGAGTCTACAAAGAACTTAAAGAAATTTACAAGAAAAAAA 6094
                         i  vi    v   i v  i        ivv v  v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_161691524_   6095 ACAAACGACCCCATCAAAAACTGGTCGAAAGATATGAACAGACATTTTTC 6144
                         -    ii    v  i?    v   v i  i   v    i        i  
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_161691524_   6145 AAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAAGCTCATCAT 6192
                         v        i  vi viii     i  --         i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_161691524_   6193 CACTGGTCAT 6202
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.36 (146 / 107)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2972 25.25 3.25 1.35  chr2_161706501_161709369     1487  2377 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161706501_   1487 TGGAAAAACATTTCATGCACATGGATAGAAAGAATCAGTGTTGTCAAAAC 1536
                               i i  ii    iv       v i    v i i i    i  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161706501_   1537 AGCCATACTGCCGAAAGCAATTTATAGATTCAATGTTATTCCTATTAAAC 1586
                         i  v     v  v   vii  i  i        i iv  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161706501_   1587 TACCAATGGCATCCTTCACAGAA-TTAAAAGAAAAACT-ATTTTAAAATT 1634
                          v   iiv  v ii  ii     -  ----  v  i  -  ii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT----GACAAGCTGATCCTAAAATT 146

  chr2_161706501_   1635 CATATGGAATCAAAAAAGAACCCAAATAGCCAAAGCAATTCTAAGCAAAA 1684
                                  viiv  ii  v  vi          i    ii i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_161706501_   1685 AGTACAAAACTGGAGGTATCAC----CGCAACTTCAGA--CTA-TACAAT 1727
                           v     ii      vv    ---- v   i    i --i  -     v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_161706501_   1728 GCTACAGTA-CCAAAACAGCATGGTACTGGTACAAAAGAAAACACATAGA 1776
                                  -i   i    ii         i i  iiiv i   i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_161706501_   1777 CCAATGGAACAGAATGAAGAGCCCACAAATAAAGCTGCACACCTACAACC 1826
                         i        i     vi    i   v       v iii   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_161706501_   1827 ATCTGATCTTT--CATGAATTCAACAAAAACAAGCAATGGGGAAAGGATT 1874
                          vi    i  i--  v ii v --   i v  vv            i  v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGC--CAAGACCATTCAATGGGGAAAGAATA 394

  chr2_161706501_   1875 CTCTGTTCAATAAATGGTGCTGGGATAACTGGCTAACCATATGCAGAAGA 1924
                         v   v     i              i      v  ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_161706501_   1925 TTGAAACTGGACCCCTTCCATACGCTATATACAAAAATAAAGTCTAGATG 1974
                         v    ii         v  vi  i i            v  v  v i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_161706501_   1975 GATTAAAGGCTTAAATGTAAAACCTAAAACTATAAAAAACTCT-AGAAGA 2023
                            i ?  i i         i v              --    -      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA--CTCTTAGAAGA 542

  chr2_161706501_   2024 TTGCCCAGG---AAATACCATTCTGGACATAGGCTTTGGCAAAGATTTCA 2070
                         vvi vi   ---    -- -   vv   v v  v  v     v i    v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_161706501_   2071 TGGCAAAGACACCAAAAGCAATTATAACAAAAATCAAATTTGACAAATGG 2120
                          i vv v             vvvii       ivv   v v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_161706501_   2121 GACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAG 2170
                            i v  i   v v  i i   i  ii vv    i  v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_161706501_   2171 AGTAAACAGACAGCCTACAGAATGGGAGAAAATATTTGCAAACTATGTAT 2220
                            i  v     i  i                          ii  i   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_161706501_   2221 CTGACAAAGGTCTAATAGCCAGCATCTAAAAGGAACTT----AATTCAAC 2266
                             i  i  v  vi  v    v  v  v  i     i----  i    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_161706501_   2267 AAGTAAAAAAA--AATAA-------GGAAAGTAGGCAAAGGACAAGAACA 2307
                           -      i --     -------?i   i i         ivv   i 
  L1M4_orf2#LINE/    790 AA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_161706501_   2308 GACACTTTTCAAAAGAAGACACATACACAGCCAACAAGCATATGAAAAAA 2357
                             i  i  v        i i i v ii     i     i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_161706501_   2358 TGCTCAGCATCACTAATTAT 2377
                               i     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (138 / 84)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.28 (41 / 18)  


3109 26.61 1.44 0.78  chr2_161823598_161829457.rev     4467  5368 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161823598_   4467 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAACATCATGAAAAT 4516
                               i i  i     i        v      v i  i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161823598_   4517 GGCCATACCGCCTAAAGTAATTTATAGACTCAATGCTATTTCCATCAAAC 4566
                            v    iv  i   v i  i  i   i    i  v  ii i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161823598_   4567 TACCA-CTGACATTTTTCACAGAATTAGAAAAAAAACT-ACTTTATATTT 4614
                          v   -   v -     ii     v v  v  i---  - iii  v v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chr2_161823598_   4615 CATATGGAAACCCCAAAAGAGTCCATA-TAGCCAAGACAATCCTAAGCAA 4663
                                   iv --  i iii   v -       i      i i iv  
  L1M4_orf2#LINE/    147 CATATGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_161823598_   4664 AAAGAACAAC-CTGGAGGCATCACGCTACCTGACTTCAAAATATACTATA 4712
                         i        v-i      vv    i  v  ii i       iv     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_161823598_   4713 AGGCTACAGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGACATATA 4762
                          i          i   i v  ii         i iv ii i         
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_161823598_   4763 GACCAATGGAGCAGAACAGAGACCTCAGAAATAACACCACACATCTACAA 4812
                           i       ii    iv    vii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_161823598_   4813 CCATCTGATCTTTGACAAATGGGACAAAAACAAGCAATGGGGAAAGGATT 4862
                         i  vi    i  i     iv v v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_161823598_   4863 CCCCATTTAATAAATGGTGTCGGGAAAAGTGGCTAGCCATATGCAGAAAA 4912
                         vi iv  i  i        ii    v  v   v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_161823598_   4913 CTGAAACTGCACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATG 4962
                         v    ii  v      v   i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_161823598_   4963 GATTAAAGACTTAAACATAAGACCTAAAACCATAAAATCCTTGGAAGAAA 5012
                            i ?    i    ii     v       i      ii   i       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_161823598_   5013 ACCTAGGTA-AGACCATTCAGGACATAGGCATGGGCAAAGATTTCATGAC 5061
                           v    ?i- i i -   iv   v v  vv i     v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_161823598_   5062 GAAAATGCCAAAAGCA-ATGCAACAAAAGCCAAAATTGACAAATCAGATC 5110
                         v vi ii         - v          vv     v  i    ii  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_161823598_   5111 TAATTAAACT--AGAGTTTCTGCACAGCAAAAGAAATTATCATTAGAGTG 5158
                          v  i   v -- i ii  i  ii vv    i  v i     vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_161823598_   5159 AGCAT-CAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 5207
                          iv v-  i  i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_161823598_   5208 AAAAGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGA 5257
                         v  i  v  vi          v  i  i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_161823598_   5258 AAAAAACAA----CCCCATCAAAGAGTGGGCACAGGATATGAATAGACAC 5303
                             i    ----   v  i?  i i      v     v          i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_161823598_   5304 TTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGGAAAAAAGCTC 5353
                              v        i  vi viii     i  i  i   i   i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_161823598_   5354 AACATCATTGATCAT 5368
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (146 / 90)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


4201 16.57 5.52 1.04  chr2_161829797_161834326.rev     3170  4038 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161829797_   3170 TAGAAAGACATCCTATGTCCATGGATTGGAAGACTTAATATTATTAAGAT 3219
                          i      i    i    i                       i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161829797_   3220 GGCAGTACTCCACAAATTGATCTCCAGATTCAATGCAATTGCTATTGAAA 3269
                             i      v           v         i     iv    ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161829797_   3270 TTTCAATAGCCTATTTTTTTTTGTAGAAATTGAAAAGCTGATTCTGAAAT 3319
                          ii  iiv    -----      i         v        i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-----TTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_161829797_   3320 TCATATTAAATTGCAAGTG--------TAGCCAGAAGAATATTGCAAAGG 3361
                               vi  v      v --------      i  v   v   v   i 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_161829797_   3362 AAAAACAAAGTTGGAAGACTCACGCTTCCCAATTTCAACACTGACTACAA 3411
                           i            i       i              v   v       
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_161829797_   3412 AGCTACAGTAATCAAAACAGCATGGCACTAGCATAAAGATACACATATGG 3461
                                        i    ii   i   i      i    v      i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_161829797_   3462 ACCAAAGGAATAGAACTGAGAGTACAAAAATAAAC------ACTTAT--- 3502
                          i   v         i       v  i        ------ i    ---
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_161829797_   3503 ---------------AAGGGTGCCAAGACCATTTAATGGAGAAAAAATAG 3537
                         ---------------                  i     i    i     
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_161829797_   3538 TCTCTTCAACAAATGATGCTGGGACAAGTG-ATAACCACATGCAAAAGAA 3586
                            i           i           v  -   ?               
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_161829797_   3587 AGAAGGTGGACCCCTACCTCACACCACATACAAAAATTAACTCCCAATCG 3636
                         v    v                    i                vv   v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_161829797_   3637 ATCAATTACCTAAATATAAGAGATAAAACCATAATAGCACACTTAGACAA 3686
                             ?vv        i      v      i    - --  v      vi 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-A--ACTCTTAGAAGA 542

  chr2_161829797_   3687 ACACA-AGTGGGTAAGTCATCATGACATTGGATTTGGCAATGGATT-TTA 3734
                          v   -  - ?    i  v  i    v    i  v        v  -   
  L1M4_orf2#LINE/    543 AAACATAG-GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_161829797_   3735 GATATGATACCAAAA-------TAACAAACAAGAAAACAAACCAATTTGA 3777
                                i       -------i      vi i    i i iv    v  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_161829797_   3778 CTTAATAATTTTTTAAAACTTTAA-ACATTGAAAGA---TGTCAAGACAC 3823
                            v  v vvv  v        vi-i v ii  i  --- i      v v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_161829797_   3824 TGAAAAGACAGTCTATAGAAAAGGAGAAAATATTTGCAAATCACATATCT 3873
                                   ii i i    vi                     i      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_161829797_   3874 GATAAGGGGCTAGAATCTAGAATATATAAAAAACTC--ATGACTCAACAA 3921
                                 i  v v   i            i     -- ii      i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_161829797_   3922 CAAAAAGACAAACAATCCAATTAAAACGTGGGTAACTGACTTGAATAGAC 3971
                         i           i  i      ?   vi    i  vv  i          
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_161829797_   3972 ATTTATCTAAAGAGGATCTACACATGGTCAACAAACACATGAAAAAATGC 4021
                             v  i     i   v    v    i   i  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_161829797_   4022 TTGACATTATTAGTCTT 4038
                          ii    i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (86 / 54)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.07 (57 / 14)  


3095 27.14 1.33 0.33  chr2_161967714_161974105     5002  5900 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_161967714_   5002 TGGAAGAACATTC-ATGCTCACGGATAGGAAGAATCAATATTGTGAAAAT 5050
                              ii i  i -   i   i    v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_161967714_   5051 GGCCATACTGCCCAAGGTAGTTTATAGATTCAATGCCATCCCCATCAACC 5100
                            v     v     iv ii i  i        i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_161967714_   5101 TACCAA-TGACTTTCTT-CATGGAATTGGAAAAAACT-ACTTTAAAGTTC 5147
                          v   i-  v    i  -  - i     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_161967714_   5148 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAA 5197
                                 viiv  ii  v  viv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_161967714_   5198 GAACAAAGCTGGAGGCATCATGCTGCCTGACTTCAAACTATACTACAAGG 5247
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_161967714_   5248 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5297
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_161967714_   5298 CAATGGAACAGACCAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5347
                                 i   viv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_161967714_   5348 TCTGATCTTCGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5397
                         vi    i        ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_161967714_   5398 TATTTAATAAATGGCGTTGGGAAAACTAGCTAGCCATATGTAGAAAGCTG 5447
                          v  i  i      i i     v    i v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_161967714_   5448 CAACAGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGAT 5497
                         v iiv   i    v   i     v  i           i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_161967714_   5498 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5547
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_161967714_   5548 TAGAC-TA----TTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 5592
                            i?-  ----   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_161967714_   5593 ACATCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAAC 5642
                            i        vvi          vv        i    v   ii v i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_161967714_   5643 TAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5692
                         i  iv v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_161967714_   5693 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5742
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_161967714_   5743 GGGCTAATATCCACAAATTATAAAGAAGTTAAAGAAATTTACAAGAAAAA 5792
                           i  vi      v  vv         v ivv v  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_161967714_   5793 AAT---CAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5839
                         i i---i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_161967714_   5840 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5889
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_161967714_   5890 TCACTGGCCAT 5900
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2686 26.21 0.72 0.97  chr2_162116836_162118653.rev      501  1328 (490)    L1M4_orf2#LINE/L1       83   908 (0)  

  chr2_162116836_    501 ATGCTACTCCTATCAAACTACCAACATCATTTTTTCACAGAATTAGAAAA 550
                          i  v ii         v v   i vv v      -i     v v  v  
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT-GCAGAAATTGACAA 131

  chr2_162116836_    551 AAT-ATTTTAAAATTCATATGGAACCAAAAAAAAGCCCCCAA-AGCCAGT 598
                         iv -  ii                viiv  iii -   vv  -     iv
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAA 180

  chr2_162116836_    599 GCAATCCTAAGCAAAAAGAATAAAGCCAGAGGCAGCAGGCTACCTGACTT 648
                         i     i i iv  i     i    iii    vvv  vi  v  ii i  
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr2_162116836_    649 CAAACTATACTACAAGGCTACAGTAGCCAAAACAGCATGGTACTGATACA 698
                             viv        i         ii   i    ii        ii i 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_162116836_    699 AAAACAGACACATAGACCAATGGTACAGGTTACAGAACCCAAAAATAAAG 748
                          ii i     i     i      v i  iv vv   ii   i       v
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr2_162116836_    749 CTGCACACCTACAACCATCTGATATTTGACAAAGTCGACAACAACAAGCA 798
                          iii   ii  iiii  vi    v  i     i vi v   v v  vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_162116836_    799 ATGCAGAAAGGACTGCCTGTTCAATAAATGGTGCTGGGTTAACAGGCTAG 848
                            vi     i iv i  v     i             vi   v  v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_162116836_    849 CCATATGCAGCAGATTGAAGCTGGACCCCT-TCTTATACCATACACAAAA 897
                            i     iv   v     i         -i  i i      i      
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_162116836_    898 ATCAACTCAATATGGATTAAACACTTCAATGTAAGACCTAAAACTACAAC 947
                           i       v      i ? v  i v         v         i  -
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA- 529

  chr2_162116836_    948 AACCCT-AGAAGAAAACCTAGGAA-ATACCATTCTGGACATAGACCTTGG 995
                            i  -          v    ?i- v i -   vv   v v ivi v  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGG 578

  chr2_162116836_    996 CAAAGAGTTCATGACAATGTCTCCAAAAGCAAATGCAACAAAACCAAAAA 1045
                            v iv   v iivv   v v         v v         vv     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_162116836_   1046 TACACAAATGGGACCTAATGAAACTAAAGAGCTCCTGCACAGCTAAAGAA 1095
                           v i    v    i v  v   v v  i i  ii  ii vv v  i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_162116836_   1096 ACTATCAACAGAGTAAACAGACATCCTACAGAATGGGTGAAAATATTTGC 1145
                                 v i   i  v     v  i          v            
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_162116836_   1146 AAACTATTCATCTGACAAAATTCTAATATCCAGAATCTATAAGGAATTTA 1195
                            ii  vi      i  iivv  vi          v     i   i iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_162116836_   1196 AACAAAACTCAACAACAAAAAG-CAAACAACCCCATTAAAAAATGGGCAA 1244
                         v    --     i  i      -    i     v   ?            
  L1M4_orf2#LINE/    779 TACAA--CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_162116836_   1245 AGGACATGAACAGACACTTCTCAAAAGAAGACATACAAGTAGCCAACAAG 1294
                             iv    i     i     v        i      i i     i   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_162116836_   1295 CATATAAAAAAAAATGCTCAGCATGACAAATTAT 1328
                           i  i    i --      i   v ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (121 / 92)
Gap_init rate = 0.01 (12 / 826), avg. gap size = 1.17 (14 / 12)  


3414 24.53 0.66 1.20  chr2_162164355_162168833     3075  3987 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_162164355_   3075 TGGAGAAACATCCCATGCTTAGGCCCATCAATTGGAAGAATTAATATTGT 3124
                             i i i        i ------   vi         v          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTT------CATGGATTGGAAGACTTAATATTGT 44

  chr2_162164355_   3125 TAAAATGGCCATACTGCCCAAAGCAATCTACAGGTTCAATGTAATCCCTA 3174
                            i     v     v      vii        i     i i        
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_162164355_   3175 TAAAAATATGAATGACATTCTTTACAGAAATAGAAAAAAAAAATCTTAAA 3224
                          v     viv iivi v  i   i       v  v  ivvi -  i    
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAA 143

  chr2_162164355_   3225 ATTTGTACAGAACCACAAAAGACTCCAAATAGCCAAAGGAATCCTGAGCA 3274
                            ii  ii   vii   ii   i vi          iv    i   iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_162164355_   3275 AAATAAACAAAGCTGGAGGCATCATACTACTAGACTTTAAAATGTACTAC 3324
                          i vi       i      vv   i   v ivi i  i    iv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_162164355_   3325 AAAGTTATACAAACCAAAATA-CATGGTACTGGCATAAAAACAGAAACAC 3373
                             i  i vv  i   i i -ii              ii i   v i i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_162164355_   3374 AGACCAACTGAACAGAATAGAGAATCCAGATATCAATTCATA--TCCAAA 3421
                            i   iv   i     v    i      v  v  ii    -- ii vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_162164355_   3422 GCCAACTGATTTTTGACAAAAGTGCCAAGAACATACACTGGGGAAAGGGC 3471
                          i   i       i     ii         v   v  v         iii
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_162164355_   3472 AGTCTATTCAATAAATGGTGCTGGGAAAACTGGTTATTCCTATGCAGAAG 3521
                              v     i              v      v  ?i vi     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_162164355_   3522 AA-GAAACTAGACTCCCACCTCTCACCCTATACAAAAATCAATTCAAAAT 3570
                           -   ii i   i  i     v    v           i  i       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_162164355_   3571 AGATCAAAGACCTAAATGTAAGACCTAAAACTATAAAACTACTGGAATCA 3620
                         i     ?                v                vi i   vv 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_162164355_   3621 AACATAGGGGAAAATGCTTCAGGACATTAGTCTGGGAAAAGATTTTATGA 3670
                                 ? v    -    iv   v  i vi i  v  v i   iv ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_162164355_   3671 ATAGGACCTGAAAATCACAGGCAACCAAAGCAGAAACTAATAAATATGAT 3720
                            v   viv    v    i     v    v i   ivi      vv  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_162164355_   3721 TATATCAAACTAAAAAGCTTCCACACAGCAAAGGAAACAGTCAACAGAGG 3770
                          vi      v v    i   iiiii vv       v  vi    v i  v
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_162164355_   3771 GAAAAGACATCCTGCAGAATGGGAGAAAATATTTGCAAACCATTTATCTG 3820
                                  v  ii                         i   v      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_162164355_   3821 ACAGGGGATTAATATCTAGAATATAAAAGGAACTCAAACATCTCAACAGC 3870
                          i i    i vi    i        v  i      vv   v     i ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_162164355_   3871 AAAACCCCCAGATAATCCTATTTTAAAAAGGGCAAATGATGTGAACAGTC 3920
                             vvv - i    i  v   ?v    v       v   v    i  v 
  L1M4_orf2#LINE/    793 AAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_162164355_   3921 ATTTCTCTATTCAGAAGTCATACAAATGGCCAA-AAATATATTTCAAAAT 3969
                                i --v     vi              -  ii i  vvv  i  
  L1M4_orf2#LINE/    842 ATTTCTCCA--AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_162164355_   3970 GC-CAACATCACTAGTCAT 3987
                           -        ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (129 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


4859 17.10 0.90 0.22  chr2_162179006_162180886.rev      493  1381 (500)    L1M4_orf2#LINE/L1        2   896 (12)  

  chr2_162179006_    493 GAAAAGGCATTCTGTGCTTGTGAATTGGAAGATTTAATATTATTAAGATG 542
                          i    ii  i ii  i ii  i         i        i        
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_162179006_    543 ACAATACTCCCCTAAAATAATCTACAGATTCGATGTGATCCCTATCAAAA 592
                         i           -   v i            i i ii             
  L1M4_orf2#LINE/     52 GCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_162179006_    593 TCCCAACAGCCTTTACTGCAGAAATGGAAAAGCTCTTCCCAAA-TTTATA 641
                              i v      vi         v  v     vv   i   -  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_162179006_    642 TGAAATCCCAAGGAACCCCAAACAGCCAAAACAATCTTGAAAAAGAAAAA 691
                           i  viv     i    vi  i                        i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_162179006_    692 GAAAGTTGGGGGACTCAAGTTTCCTGATTTCAAAACT----ATGAAATTA 737
                         v        i       vii    ii           ---- ii  ii  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_162179006_    738 CCATAATCAAAACAGTG--GTACAGGTAGGAAAACAGACATACACATCAA 785
                          vi       i      --    v  i vi ii i       i v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_162179006_    786 TGAAATTGAATTGATGGGTGCATAGATAAACCCATGTATCTATGGTCAAC 835
                           i   v       - i  v  v i          ii  i         i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_162179006_    836 CGATTTTTGACAAGGGTACCAGAACCACTCAATGGGGAAAGTGTAGTCTC 885
                         i      i         i   ii    i             vi      i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_162179006_    886 TTCAACAAATGGTGCTGAGACAATTAGATACCCACATGCAAAAGAACAAT 935
                                          i     i i    ?               ii v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_162179006_    936 GTTGGAACCTAACCTCACACCATATACAAAAATTAACTCAAAATGTATCA 985
                               v  iv                                  v    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_162179006_    986 AAGACCTAAATATAGGAGCTAAAATTACAAA-CTCTTAGAAGAAAACATA 1034
                         ?          i  i         i  i   -                  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_162179006_   1035 AGGACAAATCTTCATGGTCTTGAATTTGGCAATAGATTCTTAGATATGAC 1084
                         i ?ii        i  ii    ii  v      i v              
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_162179006_   1085 ACCAAAAACACAAGAAACTAAAGAAATAATAGATAAATTGGACTTTATAA 1134
                                i      v   v       v                  i  v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_162179006_   1135 AAATTTTAAATGTGTGTGTATTAAAGGACATTATCAACAGAGTGGAAAGA 1184
                              vv   iv v    iv i        i      v i    i     
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_162179006_   1185 CAACTCACGGAATGGGAGAAAATATTTGAAAATCATATATCTGATAAGAG 1234
                             i   i                   v                   i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_162179006_   1235 TCTAACACCCAGAATATTTAAAGAACTCTTAAAACTCAACAACAATAAGA 1284
                         v  vii i         v             v       i  i  v    
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_162179006_   1285 CACAAAACTCAATTACAAAATGGGCAAAGGACTTGGATAGACATTTCTTC 1334
                           v v   i     ?v               i   i            i 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_162179006_   1335 AAAGAAAATATACAAATGACCAACAAACACATGAAAAGATGCTCAAC 1381
                               i           i    i  i                    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

Transitions / transversions = 2.29 (103 / 45)
Gap_init rate = 0.01 (6 / 895), avg. gap size = 1.67 (10 / 6)  


3200 24.75 2.91 1.34  chr2_162190404_162195417      493  1385 (3629)  C L1M4_orf2#LINE/L1   (0)   908     2  

C chr2_162190404_   1385 GGAAAAATATCT-ATGATCAT-------AAGAACCAATACCAT-AAAATA 1345
                              i     i-   v    -------    vii    iii -  i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

C chr2_162190404_   1344 TCCATACTACCCAAAATAATCTAATCTACAGATTCAA-----------TC 1306
                         v v     v      -----i i              -----------  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAA-----TTGATCTACAGATTCAACGCAATCCCTATC 96

C chr2_162190404_   1305 AAAATTCCAA-TGTAATTTTTCACAGCAATATAAAAACAAA-CCTAGAAT 1258
                              i   i-  iv-     ii   v   vv v  i vi -    i   
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

C chr2_162190404_   1257 TCATATAGAACCATAAAAGACTCC-AACAGTCAAAGCAATCTTGAGCAAA 1209
                               i   viii  ii   i v-  i  i    i         iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

C chr2_162190404_   1208 AAGAACAAAGCTGAAGGCATCACACTTGCTGATTTCAAATTATATTACAA 1159
                                   i  i   vv        v ii        viv  i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

C chr2_162190404_   1158 AGCTATAGTAATCAAAACACTATGTACGGTCTTGGTATAAAAACAGACAC 1109
                              i         i   ----  ii   vi   i    ii i     i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACA----GTGTGGTACTGGCATAAGGATAGACAT 291

C chr2_162190404_   1108 ATACTCTAATGGAACAGAATAGAAAGCCCAGAAATAAACCCATGCATATA 1059
                            vvii       i     v  i  i                i   v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

C chr2_162190404_   1058 CACTCAAATATTCTTCTACAGAGGCAGCAATAATAAACAATGGGAAAAGG 1009
                         iiv    v iv i   v   ii  iiv   v vi vv       i    i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

C chr2_162190404_   1008 ATAATCTGTTCAATTAATTAGGTTTGGAAAACTGGGTATTCACATGCAAA 959
                            i   v     iv   viv i v   v      i  ?i          
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

C chr2_162190404_    958 AAAAAAGAAATTGGATCCTTATCTTACACCATACACAAAAATCAACCCAA 909
                          i  v-   i     i  i  i  i        i        i   i   
  L1M4_orf2#LINE/    442 AGAAT-GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

C chr2_162190404_    908 AATAGATTACAGATTTAACTGTAAGACCTGAAACTGTAAAACTACTAGGA 859
                            i   i ?   ii   v       v  i     i       vi   i 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

C chr2_162190404_    858 GAAAATAT-GGTGGGAAGCTCCATGACATTGGTATTGGCAATGAGTTTTT 810
                              i  -  ? vi  v  i i    v    vv v       iv  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

C chr2_162190404_    809 GGATATCACACCAAAAACACAGTTAATGAAAGCAAAAATAAGCTAGTGCA 760
                         i     v         i    ivi  ii    v       iiiv i vvi
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

C chr2_162190404_    759 ACTACATCAAAAGAAAAAGTTTTTCCACAGCAAAGGGAATAATCAACAAA 710
                            v        vv    ii    vii vv      iv iv     v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

C chr2_162190404_    709 ATGAAAAGGTAACATGCATAATAGGAGAAAATATTTTCAAACTACATATC 660
                         i       ii   vii  v   i             v    ii i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

C chr2_162190404_    659 TGATAAGGGCTTAATATCCAAAATATATAAGGAACTCATACAACTCAATT 610
                                  vi vi      i         i      v           v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

C chr2_162190404_    609 GCAAGAAAACAAATAACTCAGTATTTTCAATGGACAAAGAACTTGAATAG 560
                         ii  i  i         i  i - ?vvv     i     i i        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAG 839

C chr2_162190404_    559 ACATTGTTTCAAAGAAGACATA--AATGGCCAATAGGTATATGAAAAGGT 512
                              vi i         i   --           i i i        i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

C chr2_162190404_    511 GCCTAACATCACTAGTCAT 493
                           ii       ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (141 / 76)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 2.71 (38 / 14)  

2853 24.67 3.22 0.60  chr2_162190404_162195417     3677  4515 (499)    L1M4_orf2#LINE/L1        1   861 (47)  

  chr2_162190404_   3677 TGGAAAAACATTCCATGCTCATGTATAGGAAGAATCAATATCATTAAAAT 3726
                               i i  i     i     v  v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_162190404_   3727 GTCCATACTGACCAAAGCAATTTACAGATTCAAT-CATATTCCTATCAAA 3775
                          v v     vv     vii  i           i-  -  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA-ATCCCTATCAAA 99

  chr2_162190404_   3776 CTACCAAGCACATTCTTCGTAGAGCTAGAAAAAACT-ATTTTAAAAT-CA 3823
                         v v   ivii v  i  i i   iv v  v  i-  -  ii      -  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_162190404_   3824 TATGGAACCAAATAAAGAGCCT-GAATAGCCAAGATAATCCTTAACAA-A 3871
                                -- vii  i ii  i-          i i    i v  v  - 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_162190404_   3872 AGAATAAAGATGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 3921
                             i    v      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_162190404_   3922 GCTACAGTAATCAAAACAGT----TAC------AAAAACAGACATA--GA 3959
                                       i     ----   ------  ii i       --  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_162190404_   3960 CAAATGGAACAGAATAGAGGGCCCAGACATAATGCCACACATCTACAACC 4009
                         iv       i     v   i i     v    vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_162190404_   4010 ATTTGATCATTGACAAAGTTGACACAAACAAGCAATGGGGAGAGGACTCC 4059
                          v     iv i     i v  v  vi v  vv         i  i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_162190404_   4060 CTATTCAATAAATGGTGCTGGGATAGCTGGCTAGCCATATACAGAAGATT 4109
                           v     i              i i    v  ?   i  i  i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_162190404_   4110 AAAACTGGACCCCT-TCTTACACCATATACAAAAATTAACTCAAGCTGGA 4158
                         i  ii         -i  i                         iv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_162190404_   4159 TTAAAGACTTAAATGTAAAATCTAAAACTACAAGAACTCTGA-AAGAAAA 4207
                          i ?    i         i v         i  -      v -       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAA 545

  chr2_162190404_   4208 CCTAGG---AAAT----AGGACATAGGACCTGGCACAGATTTCATGACAA 4250
                          v    ---    ----iv   v v  iiiv    vv i    v iivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_162190404_   4251 AGACATCAAAAGCAATTGCAACAAAAACAAAACTTGACAAATGGGAACTA 4300
                         v    i        vvv         iv    v v  i    v   vi v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_162190404_   4301 AATAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTGAA 4350
                          vi   v v  i i   i  ii vv    i  v        v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_162190404_   4351 CAGACAACCTACAGAATGGCAGAAAATATTTGCAAACTATATAACTGACA 4400
                         v        i         v                ii     v    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_162190404_   4401 AAGGTCTAATATCCAGAATCTATAAGGCACTTAAACAAATTTATAAGCAA 4450
                          i  v  vi          v     i v   ivv    v iv    vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_162190404_   4451 AAC-CAAACAACCCTGTTAAAAAATGGGCAAAGGACATGAACAGGCACAT 4499
                           v-    i     vi  ?                iv    i  i  iv 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_162190404_   4500 TTCAAAAGAAGACATA 4515
                         i  v        i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATA 861

Transitions / transversions = 1.27 (114 / 90)
Gap_init rate = 0.02 (17 / 861), avg. gap size = 1.88 (32 / 17)  


3302 26.65 0.44 0.44  chr2_162217766_162223459     4295  5202 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_162217766_   4295 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4344
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_162217766_   4345 GGCCATAGGGTCCAAGGTAATTTACAGATACAATGCCATCCCCATCAAGC 4394
                            v   vvvi    iv i  i       v   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_162217766_   4395 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4442
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_162217766_   4443 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 4492
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_162217766_   4493 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4542
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_162217766_   4543 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4592
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_162217766_   4593 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 4640
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_162217766_   4641 ATCTGATCTTTGACAAACCTGAGAAAAACAAGTAATGGGGAAAGGATTCC 4690
                          vi    i  i     ivv  vv  i v  vvi           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_162217766_   4691 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4740
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_162217766_   4741 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4790
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_162217766_   4791 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4840
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_162217766_   4841 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4890
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_162217766_   4891 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4940
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_162217766_   4941 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4990
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_162217766_   4991 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5040
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_162217766_   5041 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5090
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_162217766_   5091 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACATTTC 5140
                          i     i     v  i?    i           iv    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_162217766_   5141 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAGAAAATGCTCATC 5190
                           v        i  vi viii     v  i       i  i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_162217766_   5191 ATCACTGGCCAT 5202
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2359 24.44 8.26 1.42  chr2_162255777_162257628.rev      514  1360 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_162255777_    514 AAAACTATC--ATGTTCATGAATTGAAATACTCAATATATTAAAGATGTT 561
                            iv    --         i    i  v   i     vv v      vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_162255777_    562 AATTCTCCCCAAATTGATGCATAGGTTTAATGCAATTCTTATCAGAATCT 611
                            v              vi i  i  i  i     i i     i    i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_162255777_    612 CAGTAGGTTTGCTTTTATATTTAT--ACAAGATTATTTTACTATGTATAT 659
                            iv vi  --    ii vvv  --     v v  ii  vv  vi    
  L1M4_orf2#LINE/    104 CAGCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_162255777_    660 GAATAAT-CAAAGAACT-AGAATAGCTAAAACAATTTTTTAAAAGAAGAA 707
                          i -   -   i i  i-        i        i  vv          
  L1M4_orf2#LINE/    152 GGA-AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_162255777_    708 TGAAG----AATAATCAATATACCTAATTTCAGGACTATCTATATAACAA 753
                         ii   ---- iv v   vvv v  i       ii   vv   i v i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_162255777_    754 CAGTAGTCAAGACTAAGTGATATTGGTCTA----CAGACACATACACCAA 799
                              i       viv   i  i   iv  ----i     i   v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_162255777_    800 TGGAATAGAACAGAGAACACAGAAATAGAACCATATAAATATGCCCAAAT 849
                                   iv    iiv        i v     i vv    vi   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_162255777_    850 GATTTTTGACAGAAGTACAAAAGCAATTCA-TGGACGAAAGA-TAGACTT 897
                               i    iii  i v  ii v     -   i-      -   v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTT 399

  chr2_162255777_    898 TTCAACAAAC--TGTTGGAGCAACTGGACACCCATAGGCAATAAAATGAA 945
                                  i--  i   ii        i ?   i v    v i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_162255777_    946 CTTCAACCTAAATCTCACACTTTATATAAAAATTAACTAAAAATGAGTTA 995
                         v  vi   ivv i       iv    i           v      ii i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_162255777_    996 TATACATTAAAATAA-AGTATAAAATAGTAAAACTTTTAGAAAAAAAACC 1044
                         ? v  v v  vi   -  i-     ivi       i      i    -- 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAA--C 546

  chr2_162255777_   1045 ATAGTAGAAAATC---AGGATCTAGGGTTAAGCAAAAAGGTTCTAAGATT 1091
                             v? v     ---iv  i  v      i    vi- v    v    v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTAGATA 595

  chr2_162255777_   1092 TGACACCAAAAGCATAATCGATAAAAGGAAAAAAATGACAAACTGGACTT 1141
                                       i  v i i     i     v -  i   i       
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTT 644

  chr2_162255777_   1142 CAACCAAATTAAAAACTTTCTCTCTTT----------------------- 1168
                           v v              iviv   i-----------------------
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_162255777_   1169 ---GACAGCATACAAAATGGGAGAAACAT-TTTGCAAACTATGCATCCAA 1214
                         ---    i vi   i           -  -        ii  ii   ii 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAA-ATATTTGCAAATCATATATCTGA 743

  chr2_162255777_   1215 CAAATGTCAAGTACCCAGAA-----------------CAAATTAATAAGT 1247
                         i  iv v vv   i      -----------------   v i     - 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-T 792

  chr2_162255777_   1248 AAAAA---AAAAAACCCA-TTAAAAAATGGACAAAGTACATGTACTGGAA 1293
                              ---   v      -  ?        i     v iv  - v i  v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG-AATAGAC 841

  chr2_162255777_   1294 AGTTCTCAAAGGAAGTCATACACACAGCAAACAGGCATATGAAAAAATGT 1343
                          v     v  i    vi     v ii  v  i i   i       i   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_162255777_   1344 TCAACATCACTAATCAT 1360
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (116 / 87)
Gap_init rate = 0.03 (26 / 905), avg. gap size = 3.15 (82 / 26)  


2716 25.75 3.66 2.89  chr2_162278666_162281303     1246  2146 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_162278666_   1246 TGGAAAAACATTCCATGCTCATGGATTGGCAGAGTCAATATCACTAAAAT 1295
                               i i  i     i           v   v i     iii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_162278666_   1296 GCCA-CACTACCTAAAGCAGTTTACAGATTCAATGCTATTCCTCTCTAAC 1344
                          v  -i   v  i   viii i           i  v  i   v  v  -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr2_162278666_   1345 TATTATACAAATGTCGTTCTTCACAGAATTAGAAAAAACTG-TTCTAAAA 1393
                         -  iv--  iv  i -  i  ii     v v  v  i-   - i      
  L1M4_orf2#LINE/    100 -ATCC--CAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAA 144

  chr2_162278666_   1394 TTCTTATGGAATCAAAAAAGGTCCCCAG--TAGGCAAAGCAATCCTAAGC 1441
                            v       -- viv    vv     --   v    i     i i iv
  L1M4_orf2#LINE/    145 TTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_162278666_   1442 CAAAAGAACAAAGCTGGAAGAATAACACTATCTGACTTTA-----TACTA 1486
                         v i          i    i  v v     vi ii i  i -----     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_162278666_   1487 TAAGGCTACAGTAACCAAAACAGCATAAT---GGTACAAAAACAGACACA 1533
                         i  i          i   i    ii ii ---  i i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_162278666_   1534 TAGACCAGTGGAGCAGAGT---------ATAAATAAAGCCACACACTTAT 1574
                             i  i    ii   i --------- v       v   i   i    
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_162278666_   1575 ACAACCAACTGATTTTCGACAGGGCTGATAAACACATGCAATGGGGAAAG 1624
                         i--ii   i            i  v  vi  ivv   v            
  L1M4_orf2#LINE/    343 G--GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_162278666_   1625 GATTCCCTATTTAATAAATGGTGCTGGAATAACTGGCGAGCCTTATGCCG 1674
                         i  vvi  v  i  i            i i      vv ?  vi    vi
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_162278666_   1675 AAGAATGAAGCTGGACCCTCACCTTCCACTATATACAAAAATTAACTCGA 1724
                                   i       ii    iv   i                  i 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_162278666_   1725 GATGGATTAAAGATTTAAATGTAAGCCCTCAAATTATAAAAATCCTAGAA 1774
                         i      i ?   ii          vv  v   i       v  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_162278666_   1775 AAAAACCTAGGGAATACCCTTCCCCACATTGGTCTTAGTAAAGAATTTTT 1824
                         i     v    ?ivv vi    viv  v    vi vi i  v iv  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_162278666_   1825 GGCTAATTTTG----CAAAA--ACAATTGCAACAAAAACAAAAATTAACA 1868
                         i v  ----  ----     --    --         iv      vi i 
  L1M4_orf2#LINE/    591 AGATA----TGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATA 634

  chr2_162278666_   1869 AGTGGGACCCAATTAAA-TGAAAGAGATTCTCTACAGCAAAAAAGAAAAA 1917
                          i v    iiv  i   - v   i v-  i v i vv    ii ------
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGA------ 677

  chr2_162278666_   1918 CAAAACTATCAATAGAGTAAACAGA--ACCTACATAATAGGAGAAAATAT 1965
                           ---       v i   i  v   --   i   v   i           
  L1M4_orf2#LINE/    678 CA---CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_162278666_   1966 TTACAAACTGTGCATCTGATAAAGGTCTAATATCCAGAA-GCAACAGGAA 2014
                           i    iii ii         i  v  vi         -ii vv i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_162278666_   2015 TTTAAACAAATCGATAAGCCAAA-ACCAATAACCCCATC-AAAAATGAGC 2062
                         i ivv    v  i    vvv   -  v        v  i-       i  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_162278666_   2063 AAAGGACAAGAATAGGCCCTTTTCAAAAGGAGACATACAAGCAGCCAACA 2112
                               ivv      i vi  i  v    i   i      iii     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_162278666_   2113 AACATATGAAAAAATGTTTGTCATTAATCATCAG 2146
                          i  i       i   i iiv   i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (145 / 84)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.46 (59 / 24)  


2305 21.53 0.92 13.27  chr2_162288630_162292316.rev      494  1473 (2214)    L1M4_orf2#LINE/L1       50   908 (0)  

  chr2_162288630_    494 TGGCATACATACTGTCCAAAGCAATTTATAGATTCAATGCTATCTCTATC 543
                              ---     vi     vii  i  i        i  v   i     
  L1M4_orf2#LINE/     50 TGGCA---ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_162288630_    544 AAACTACCAATTCCATTCTTCACAAAAACTAGAAAAAAACTAATT-TAAA 592
                            v v   ii v v  i  ii  i   i i--- v  i  i  i-    
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAA 143

  chr2_162288630_    593 ATTCACTTGGAAACAAAAAAGAGCCCAAATAACCAAGACAATCCTAAGCG 642
                              iv      iiv  ii  v  vi    i    i      i i ivi
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_162288630_    643 AAAAAAACAAAGCTGGTAGCATCACACTACCTGACTTCAAACTGTACTAC 692
                          i  i       i   vi vv       v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_162288630_    693 AAGGCTGCAGTAACCAAAATAGCATGGTACTAGTATAAAAACAAACACAT 742
                           i   i      i   i i  ii       i i    ii i i   i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_162288630_    743 AGACCAATGGAAAAAAATAAAGAGCCCAGAAATAAGGCCACACACCTTCT 792
                            i        v i   vi    i          iv   i   ----- 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA-----T 338

  chr2_162288630_    793 TCAACAAAGCTGAAAATCAATCTGATCTTCAACAAAGCTGAAAAAAAAAA 842
                          i -------  i---     -    i   i    i v  vv  i v---
  L1M4_orf2#LINE/    339 TTA-------TGG---TCAAT-TGATTTTCGACAAGGGTGCCAAGAC--- 374

  chr2_162288630_    843 AAAACAAGGAAGGGGGAAAGGACTCCCTGTTAAGCAAATGGTGCTGGGAT 892
                         ----  vvv  v        i ivvi  v  v i               i
  L1M4_orf2#LINE/    375 ----CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_162288630_    893 AACTGGCTAGCCATATGGAGAAGATTGAAACTGGATCCCTCCCTTACATA 942
                               v  ?   i   v i    v    ii    i    v   i   iv
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_162288630_    943 ATATACAAATGTTAACTCAAGATGGATTAAAGACTTAAATGTAAAACTCA 992
                                  vi         i      i ?    i         i vii 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_162288630_    993 AAACTATAAAAACCATGGAAGACAACCTAGGTAATATCATTCTGGACATA 1042
                                    vi v i     ----------  -----------     
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGA----------AA-----------ACATA 549

  chr2_162288630_   1043 GGAAAGGGCAAATATTTCATGACAAAGACACCAAAAGCAATTGTGACAAA 1092
                           ?---- i    -i   i    -------------- --   v vi --
  L1M4_orf2#LINE/    550 GGN----GTAAAT-CTTCGTGAC--------------C--TTGGGTTA-- 576

  chr2_162288630_   1093 AGCAAAAAATGGCAAATAGTATCTAATTAAAC-TGAAGAGCTTCTTCACA 1141
                         ----------     - i  v   ---  i i-   ----------   -
  L1M4_orf2#LINE/    577 ----------GGCAA-TGGTTTCT---TAGATATGA----------CAC- 601

  chr2_162288630_   1142 GCAAAAGAAACTATCAGCAGAGTAAAAAGACAACCTACAGAATGCAACAA 1191
                         -      ----------  -----------   ----------       
  L1M4_orf2#LINE/    602 -CAAAAG----------CA-----------CAA----------GCAACAA 619

  chr2_162288630_   1192 AAGCAAAACTTGACAAATGGAATCTAATTAAAGCAGAGAGCTTCTGCACA 1241
                            v    v v  i    v i ii v  i   iivi i i   i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_162288630_   1242 GCAAAAGAAACTATCAACAGAGTAAAAAGACAACTTACAGAATGGGAGAA 1291
                         v    i  v        v i   i          ii              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_162288630_   1292 AAATTTTGCAAACTCCACATCTAACAAAGGTCTAGTATCCAGCACCCATA 1341
                           vv        iivi i    i i  i  v  v        v ivi   
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_162288630_   1342 AGGAACT--TA-AATTTA-CAAGGGAAAAAAAAAAAAC---ATTAAAAAG 1384
                          i     --  -  i i -i  vii   i v   v   ---   ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_162288630_   1385 TGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATACATGTGGC 1434
                                    iv    i     i     v        i     vi    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_162288630_   1435 CAACAATCATATGAAAAAAAGTTCAACATCACTGACCAT 1473
                            i  v  i       i v i         ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (136 / 71)
Gap_init rate = 0.03 (27 / 859), avg. gap size = 5.15 (139 / 27)  

2972 17.55 6.17 11.39  chr2_162288630_162292316.rev     2240  3196 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_162288630_   2240 GGAAGAGACATTCCATGTTCATGAATCAGAAGACTTTGTTAAGATATCTT 2289
                             -   i  i           i  ii        ------i    ---
  L1M4_orf2#LINE/      2 GGAA-AGATATCCCATGTTCATGGATTGGAAGACTT------AATAT--- 41

  chr2_162288630_   2290 CTTGTTAAGATGGTAATATTACATCTTATAAATCTAAGGCAATAAATCTA 2339
                         --           i    i v ----------- i  -------------
  L1M4_orf2#LINE/     42 --TGTTAAGATGGCAATACTCC-----------CCAA------------- 65

  chr2_162288630_   2340 ATTGACTTCTTTTAGATAGAAATTTTAAGGCAATTTCTATCAAACTCCCA 2389
                              --   ----- i   ---  i  v     ii        v     
  L1M4_orf2#LINE/     66 ATTGA--TCT-----ACAGA---TTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_162288630_   2390 GGAGGCTTTTTTTTGGCAGAAATTGACAAGGCAAACCTAAAATTCATATG 2439
                          vv v       ---               vii v               
  L1M4_orf2#LINE/    106 GCTGCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_162288630_   2440 AAAATTCAAAGGAAACAGAATATCTAAAACAGAATATCT---AAAATAA- 2485
                         i    v   i   vv       v i      ----    ---    v  -
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACA----ATCTTGAAAAAGAAG 198

  chr2_162288630_   2486 AACAAGTAGTTTGGGGTACTTACACATCTTAATCTCAAAGCTCACTCTAA 2535
                              --    v i  -   i    v  ii   i     i  i   vi  
  L1M4_orf2#LINE/    199 AACAA--AGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_162288630_   2536 AGCTACAATAATCAAGATAATGTGGTACTGGCATAGGAAGATAGATAGAT 2585
                                i         i i               i -------------
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG------------- 282

  chr2_162288630_   2586 AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAAAATA 2635
                         -------------------------      i v      vi  ii    
  L1M4_orf2#LINE/    283 -------------------------GATAGACATATAGATCAATGGAATA 307

  chr2_162288630_   2636 GAATTGAAAGTCCAGGAATAAAGTTAACTTTCATATTATATACGA--AAC 2683
                                i       i      -------ii    i-  v  i i--  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAA-------CCCATAC-ATTTATGGTCAAT 349

  chr2_162288630_   2684 ATACTTCTTAA--AAGGTGC-AAGACAGTTCAATGGGGAAGACAGGGTCT 2730
                         - iv  i ii -- i     -     vi            iiv vi    
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_162288630_   2731 TTTCAACAACTCATTCTAAAACAATTAGATATCTACATGCAAAAGGACTA 2780
                                  v vi v  iii    i i    ? i           i iv 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_162288630_   2781 ATTTGAACCCTTGCCTTATGCCATACACGAAAATTAATGAAAAATAAATC 2830
                          v   i    i i   i ii     i  i        ivv     ii   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_162288630_   2831 ATGGACCTGTGTGTAAGAACTGAAACCACAAAACTTCTTAGAAGAAAACA 2880
                          ?i     ivi       i  i    i i      -              
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACA 547

  chr2_162288630_   2881 TAAGGGCAAATCTTCATGACTTTTGGTTAAGCAACGATTT-TTAGATAGG 2929
                           i ? i        i    i  v     i    i i   -       v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_162288630_   2930 ACACCAAAAGAACAAATAATAAAAGAAAAAA---ATAATGTAGACTT--- 2973
                                   v    ii  i           ---    vv i     ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_162288630_   2974 --------------TTTGTGTTCCAAAAGACACTATCAAGCAAATAAAAA 3009
                         --------------      i i    i            v  i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_162288630_   3010 GACATGATCTAGACA--GACAGAAAACATTTGCAAATTATAGATCTTATA 3057
                             -- i i v v -- iv      i          i   v    v   
  L1M4_orf2#LINE/    698 GACA--ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_162288630_   3058 AGGGACTC--ATCTATAATCTATAAAGAACTCCTAAAACTCAATAAGAAA 3105
                                i--   i v   v            i  v          v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_162288630_   3106 -------------------------GGACAAAATATTTGAATCGATATAT 3130
                         -------------------------  i    iv        v  i  - 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT-T 844

  chr2_162288630_   3131 TCCCCCCAGAAAAGATATGTTAATAGCCAGTAAGCACATTAAAAGATGTC 3180
                           i  -- i i       iiv   i    i         v        ii
  L1M4_orf2#LINE/    845 TCTCC--AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_162288630_   3181 CAACATCCCTAGTCAT 3196
                                v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (114 / 51)
Gap_init rate = 0.03 (31 / 907), avg. gap size = 5.42 (168 / 31)  


3102 24.73 1.74 3.25  chr2_162319374_162321388.rev      602  1523 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_162319374_    602 TGAAAAGATATCCCATGATGATGATTTGGAAGAATTAATATTGTTAAAAC 651
                           i              v v   iv        v             i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_162319374_    652 ACTCATACTACTCAAAGCAATCTACAGAATTAATGTAATCCCTATCAAAA 701
                         iviv     v i    vii         v i  i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_162319374_    702 TACCAATGACAGTCTTCACAAAAACAGAAAAA---ATCTTAAATTTTGTA 748
                          v   iivi vv i  ii  i   iv  v  i---   i    v  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_162319374_    749 TGGAAGCCCAAAAGACCCTAAATAGACAAAGATATCT-GAGCAAAAAGAA 797
                              iiv   ii     vi     v    ivv    -  iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_162319374_    798 GAAAACTAGAGGTATCACACTACCTGACTTCAAAATACACTGCAAAACAA 847
                         v   ii i    vv       v  ii i       ivi   i    i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_162319374_    848 TAGTAACCAAACTATCATGGTGCTGGTATAAAAACAGACTCATAAATCAA 897
                         i     i   ivi vii    i    i    ii i    vi   i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_162319374_    898 TGAAACAGAATAGAAAACCCAGAAACAAATCCACGTATTTACAGCCAAAT 947
                           i  i     v  i ii       i   i   iii     ii i   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_162319374_    948 GATTTTTGACAAAAGCATCATGAGCA--CATATTGGAAAA----AGCCTT 991
                               i     ii iii  v  v  --  -  v  i   ----  i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAGAATAGTCTT 399

  chr2_162319374_    992 GTCAATAAATGATGCTGGGAAAACT--ATGTCCACATGCATAAGAATGAA 1039
                         v    i     i        v    --  i?         v         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_162319374_   1040 ACTAGAACCCTATGGATCACCATATACAAAAATCAACTCAAAATGGATTA 1089
                         ii i  v     ivvvv                i              i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_162319374_   1090 AATACTTAAATGTAAGACCTGAAACTATAAAACTACTAGAAGAAAACATG 1139
                         ? v  i           v  i             vi             i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_162319374_   1140 TAGAGGAAATGCTTCATGATATTGGTCTGGGCAAGGATTTTCTGGATAAG 1189
                         -i ? v    -    i   iv    vi i     v i   ii i    v 
  L1M4_orf2#LINE/    550 -GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_162319374_   1190 ACCTCAAAAGCACAGGCAACAAAAGCAAAAACAGACAAATGGGATTACAT 1239
                           vi          i          v     i   i    v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_162319374_   1240 TAAGCTGAAAAGCTTCTGCTCAGTAAAGGAAACAATAAACAGAGCAAAAA 1289
                         i  iv v    i   i  iv vvi      v  v  v  v i  ii    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_162319374_   1290 GACAACTTA----ATTGGAGAAAACACTTGCAAACCTTGCATCTGACAAA 1335
                               ii ----  v        i i       i v ii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_162319374_   1336 AGGTAAATATCCAGAATTTATAAGAAACTCAAACAATTAAATAGCAAAAA 1385
                         i iivvi          v     ii     vv    i v    ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_162319374_   1386 ATTAAATCAGAAACTCAAATAGCAAAAATTAAATCACCTAATTTAAAAAT 1435
                         ---------  ----      --------------   i    ?      
  L1M4_orf2#LINE/    798 ---------GA----CAAATA--------------ACCCAATTWAAAAAT 820

  chr2_162319374_   1436 GGGTGAAAGATCTGATTAGGCATTCATCAAAATAAGACATTCAAGTGACT 1485
                            ii  i   i   v   i    iv  v   v    i  v   i  i i
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_162319374_   1486 AACTAGCATATGAAAAACTGCTCAACATCACTAACAAT 1523
                           iv    i       iv            ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (144 / 80)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.83 (46 / 12)  


3579 22.56 2.00 1.11  chr2_162335655_162338041.rev     1002  1901 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_162335655_   1002 TGGAAAGATATCCTGTGTTCATGAATTCGAAGATTTAATATTGTTTAAAT 1051
                                      ii        i   v     i           v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_162335655_   1052 ATTCATACTAGCCAAAACCACCCACAGATTCAATTCAGTCTCCATCAAAA 1101
                         iviv     vv     viv i i          iv  i  i i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_162335655_   1102 TCCCAATGGCATTTTTT-TACAAATAGAAAAAC-AATTCTGCAATTCATA 1149
                              iiv  v      -i v    v  v  i -i  i  iv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_162335655_   1150 TGAGACCACAAAGAACCCCAAATAGCTAAATCAATCTTGAGAAAAAAGAG 1199
                           ii vii   i i    vi      i   v         i   i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_162335655_   1200 CAAAACTGGAGGCAC-CACACTCCCTGATTTCAAAATATATCATAAATCT 1248
                             ii      -  -      i  ii         iv  ii i   v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_162335655_   1249 ACAATAATTAAAATAGCATGGTAATGGAATAAAGATAAACATACAGACCA 1298
                            i    i  i i  ii     v   v    i    i     i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_162335655_   1299 ATGAAACAGAATAGAGAGCCCAGAAATAAACCCATGCATATAAGGTCAAC 1348
                            i  i     v     i                i   v  v      i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_162335655_   1349 TAACCTTTGACAAGGGTGCCAAGA--ATACACACAGGGAAAGAATAGCCT 1396
                          i ii  i                --  v  - ii            i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAGAATAGTCT 398

  chr2_162335655_   1397 CTTCAACAAATGGTGATGGAAAAACTGGATATTCACATACAAAAGAATGA 1446
                         i              v   i v         ?i     i           
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_162335655_   1447 AATTTGTCCCGTAT-----ACCATTTACAAAAAATTTACTCAAAATGGAT 1491
                          i  v v   v  i-----     v        -  v             
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGAT 497

  chr2_162335655_   1492 GTAAGACTTAAACATAAGACTGGAAAC----AAACTCCTAGAAAAACAAC 1537
                         vv?    i    ii     vivi    ----      i     i  -   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA-AAC 546

  chr2_162335655_   1538 ATAGAGGAAAAGCTTCATGACACTGGTCTTGACAATGATTTCACGACTAT 1587
                             i? v   v    i    vi   vi v i     i    viiiv   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_162335655_   1588 AATAACAAAAGCACAGGCAACAAAAGCAAAAATATACAAATGCAACTACA 1637
                         i i v          i          v       v i    vvi   v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_162335655_   1638 ACAAA--CAAAAATTATTCTGCCCAGCAAAGAGTGAAAAGGCTCCACAGA 1685
                         v    --i     i v  v   ii--     iiiivv ----  v v i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTA----TCAAGAAA 690

  chr2_162335655_   1686 GTGAAAACGCAACCTACACAAAGGGAGAAAATATTTGCAAGCCATATATC 1735
                                vi     i   v  v                  ii        
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_162335655_   1736 AAATAAAGGTTTAATTTCCAAAATATATAAGGAACTCCTATAACTCAGTA 1785
                         vi    i  vi vi v    i         i      i  i      i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_162335655_   1786 GCAAAACT-CTAATAACCCAATTTAAAAATGGGCTAAAGACTTGAAGAGG 1834
                         ii    vv- v            ?          v  i  i     v  i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_162335655_   1835 TACTTCTCCAAAGAAGACATACAAATGGCCAGTG-TTATATGAAAAGACG 1883
                         i i              i             i i-vi i         i 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_162335655_   1884 GTCATTGTCACTAATCAT 1901
                         v   vii   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (127 / 72)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.87 (28 / 15)  


3340 22.69 1.95 3.37  chr2_162429533_162433761.rev     2817  3737 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_162429533_   2817 TGGAAAGACATCGCATGTTCATGGATTGGAAACATTAATATTCTTAAAAT 2866
                                 i   v                  ivv        v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_162429533_   2867 GCCTATACTACCCAAAGCAATATACAGATTCAACACAACCCCTATCAAAA 2916
                          v v     v      vii  v            i   i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_162429533_   2917 TTCCAGTGGCATTTTTCATACACATAGAAAAAC-AATTCTAAAATTCATA 2965
                          i    iv  v     iii v v  v  v  i -i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_162429533_   2966 TGGAACCACAAGAGACCACAAATAGCCAAGGAAATCTTGAGAAAGAAAAA 3015
                              vii    i    vvi         iiv        i      i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_162429533_   3016 CACAGTTGGGGGCATCACAATTCTTGGATTTTAAGTTATATTACAAAACT 3065
                           v      i  vv     v   iii-    i  iviv  i      i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCT 249

  chr2_162429533_   3066 ACAGTAATCAAAACCATATGGTATTTGCACAAAAACAGACATGTA--TCA 3113
                                    i  vi i     i v   i  ii i      i  --   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_162429533_   3114 ATGGAACAGAGTGTAAAGTCCAGAAATAAGCCCAGACATACACATTCAAC 3163
                               i   i vv i             i    v    vi iiv    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_162429533_   3164 TGACTTTTGACAAAGCAACCAAGAAGATACCATGTGGAAAGAACAGTCTT 3213
                            i   i     i vvi      vv  v v   v        i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_162429533_   3214 TTCAACAAATGGTA-----------GAATATCCACATGCAAAAGAATAAA 3252
                                      i----------- i   ?                i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_162429533_   3253 ACTGGAACCATATCTTACACCACACACACACACACACACACACACACACA 3302
                         ii    v  v  i  i      i i   v --------------------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAA-------------------- 479

  chr2_162429533_   3303 CACACAAACTCAAAATGGCTTA-AGACATAGACGTAAGATTTAAAATTGC 3351
                         - - iv            v i -    v  i i      vi     i ii
  L1M4_orf2#LINE/    480 -A-ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_162429533_   3352 AAAACTTTTGGAAGAAAACAAAGAGGAAAATCTCCTTGACATTGGGCTTG 3401
                               i  i          v  i? v      i v    v     i v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_162429533_   3402 GTGATA--TTTTTAGATATCAAACCAAAAGCTTAGGCAA-GAAAGCAAAA 3448
                          ii  i--  i        v v         vi i    -i    v    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_162429533_   3449 ATGAACAGGTAGACCTACATGAAACTAAGAAGTTTCTGCACAGCAAAGGA 3498
                           ii i ii v iv  v   v   v v i  ii  i  ii vv       
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_162429533_   3499 AACAATCCACACAATAAAAAAGGCAGGCCACAGGATGGGAGAAAATATTT 3548
                         v  v   v v v i i    - i  iv      i                
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAA-GACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_162429533_   3549 GAAAATCATATGTCTCATCATAAGAGATTGGTTTCCAAAATATATAAGGA 3598
                          v         i   v  ---   i  i v  v    i         i  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGAT---AAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_162429533_   3599 ACTTACACAACTCAATAGCAAAAACCCCCCAAATAACTCAATTTTAAAAT 3648
                            ivi           ii     vv ---       i     ?v     
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGAC---AAATAACCCAATTWAAAAAT 820

  chr2_162429533_   3649 GAGCAAATAATTTGAAATTACATTTTTTCCAAAGAAGACATAAAAATGAC 3698
                          i     vi       vvv      i -          i   v     i 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCT-CCAAAGAAGATATACAAATGGC 869

  chr2_162429533_   3699 GAGCAGATATATGAAAAGGTGCTCATCATCAGAAAAATG 3737
                         v ii iii i        i      v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (122 / 84)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.77 (49 / 13)  


 994 26.33 2.67 1.00  chr2_162518519_162521250      959  1258 (1474)    L1M4_orf2#LINE/L1        5   309 (599)  

  chr2_162518519_    959 AAGATA-CACATAGTTTCCATGGGTTGGAAAAATCATTACACTTAAGGTA 1007
                               - v   -   --     i      i v i v  ivv     i i
  L1M4_orf2#LINE/      5 AAGATATCCCAT-GTT--CATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_162518519_   1008 -CTATTCTCCCTAAATTGATCCATAGATTTAGTGCAATATCAATCAAATT 1056
                         - v  v     i         i i     i ii     vi v      v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_162518519_   1057 CCAAGCAGGAATTTT-GTAGATACAGAAAAACTTGTTCTAAAATGTATAT 1105
                           v   v vvv    - i   v iv  v  i  vi i       vi    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_162518519_   1106 CAAAAGGCAAAAAGATTAGAATAGCCAAA-CAGTTTTGAAAAAGAAGAGC 1154
                         vi   v    iiiivii            -  i i             i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_162518519_   1155 AAAGTTGGGAGACTCATACCATCTGACTTTAAGAATTACTCTAAAGCTAT 1204
                                 ii      i  ivi ii i  i  i v     vi       i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_162518519_   1205 AGTAATCAAAAAAGTGTGGTATTGTCAAAGGAATAGACA----AAGCAAT 1250
                                  i v         i  v  v i i       ----i v    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_162518519_   1251 GAACTAAA 1258
                          i v  i 
  L1M4_orf2#LINE/    302 GGAATAGA 309

Transitions / transversions = 1.55 (48 / 31)
Gap_init rate = 0.02 (7 / 305), avg. gap size = 1.57 (11 / 7)  

1498 24.24 4.88 7.16  chr2_162518519_162521250     1588  2243 (489)    L1M4_orf2#LINE/L1      268   908 (0)  

  chr2_162518519_   1588 TGG-ACTGACTGAAATATAGGCCTA--GATCAATGGGACATTTTAGAAAG 1634
                            -    i vv  iv    i v  --         i i vvv v  i  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_162518519_   1635 TCCAGAAAAACAGTCCAAACAAATATAACTAATTGATTTTTGAAAACGGC 1684
                                 v - ii   v   vv   iiii          i  v  v  i
  L1M4_orf2#LINE/    318 TCCAGAAATA-AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_162518519_   1685 AC--AAACCAT---------GAAGAATATACTTTTTCTGTGTCTTTTATT 1723
                         i -- i     ---------i       ----------------------
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATA---------------------- 394

  chr2_162518519_   1724 TGGGTCTTTTCCATAAATGGTATGATATTGGAACAATTTAACATCCATAT 1773
                         ---        v i       ii-----   i    i vi i ?   i  
  L1M4_orf2#LINE/    395 ---GTCTTTTCAACAAATGGTGC-----TGGGACAACTGGATAKCCACAT 436

  chr2_162518519_   1774 GCAAAA-AATAAAAAAAAACCCTTGAATTAAACCTCATATCTTATACCAA 1822
                               -   i  ivvii    i -------      i i v     v  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCT-------ACCTCACACCATATACAAA 479

  chr2_162518519_   1823 AATTAACTCAAAATGGACCATAGCTTCAAGATGTAAAATATAATA-TATG 1871
                                          i  ?  viii  -      i vv   v -   i
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAA-ATGTAAGAGCTAAAACTATA 528

  chr2_162518519_   1872 AAACT-TTAGAAGAAAACATAAAAGAAAATCTTTGTGACCTT----TAGG 1916
                              -               ii? v       i        ----    
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_162518519_   1917 CAGAGAGTTTTCAAATTTGATACCAAA-GCATAATTTATAACACACA--- 1962
                           iv iv  i i i  v   i      -   i  viv i  v v v ---
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_162518519_   1963 CACACAAATCAGAATTTATCAAAATTTAAAACTTTT---CCTCAGTGAAA 2009
                         i v i    ii  v  i         v         --- i   ---  i
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA---AAG 675

  chr2_162518519_   2010 GACACTGCTAAAAGAATATAAAGTCAAACTATAAATGGGGAGAAAAGACA 2059
                               iii  i i i iv    v   v i i i vv         v i-
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT- 724

  chr2_162518519_   2060 AATATTGCAAATCATATGTTCAAAAAATGTCGTGTATCCAGAATGTATAA 2109
                         ----             i iii v  iv v v            i     
  L1M4_orf2#LINE/    725 ----TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_162518519_   2110 AGAAGTCTCAAAACTCGACAGTAAGGA-ACAGACAACCCAAT--AAAAAT 2156
                             v   i v     i i i   ii -   i i        --      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_162518519_   2157 AAGCAAAATGTTTTCATAAACACTTTGCCAGAGAATAAATATGGATGTCA 2206
                         ii     ivi   vv   i   i  iv   i    v v   iii   v v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_162518519_   2207 AATAAACTCAGGAAAAATTG-TCAACAATAACCATTAT 2243
                              i v  v     iv  -      vi ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (96 / 60)
Gap_init rate = 0.03 (21 / 641), avg. gap size = 3.76 (79 / 21)  


1971 28.43 2.29 0.49  chr2_162527146_162528749      501  1112 (492)    L1M4_orf2#LINE/L1      286   908 (0)  

  chr2_162527146_    501 AGACACATAAATCACTGGAACGGAATAGAGAACTAAGAAATAGACCAGCA 550
                              i   i    v     ii    v    iiiv       i   vii 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_162527146_    551 CAAGTAAAGCTTACTGATTTTTGACAAAAG-ACAAAAACTATTAAATGAA 599
                           vv  vi iiv i       i     ii -i v  i  i   v    ii
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_162527146_    600 GGAAAAATAATCTTTTTGAAAAATAATGTTGGAGCAATTAGACACCTACA 649
                          i  i    i      ii v    ii  i   ii   i i  i ? i   
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_162527146_    650 GGCAAAA-AATTAGCCTTGATATAAACCTCAC--CATGTACATAAAAATT 696
                         v      -   v ivi v  ivivv       --   i    --      
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA--AAAATT 483

  chr2_162527146_    697 AATTTAAAATAGTTTATAGATTTAAATTTGAAACATAAAGCCATGAAATT 746
                           i i     i v i ?   ii     v i i vv    i i  i   i 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_162527146_    747 TTTAGAAGAAAATATTAGATAAAATCTTCAGGACCTAGGGCTAGGTGGCA 796
                         i           i  vi ?vv        iv     v   i    iiiii
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_162527146_    797 AGTTTTTAGACATAACACCAAAAGCGCAATTCGTAAAAGGAAATATTTAT 846
                         iv  i     i  i           i   vivii     i   v  vv  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_162527146_    847 AGATTGAACTTTACCAAAATTAAAA-TGTTTGTGCTGTGAAAGATTCTGT 895
                          i    i    i i           -iv        vii  i  iv  i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_162527146_    896 TAAGTGGATGAAAAGGCAAGCTACAGAC----AGAAAGTATTTGTAAACC 941
                         i   viii       i   v i     v----     i      i   i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_162527146_    942 AGATATTCAACAAAAGTGTTATATGTAGAACATATAAAGAACTCTCAAAG 991
                          v    iii i  ii vv  i   vi    i              i v i
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_162527146_    992 TTCAACAGTATGAAAATAAAT----CAACTAGAAAAGTGGGCAAAAGGCA 1037
                         i    i i  vi  i i    ----   i ?i    -        i iiv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATT 832

  chr2_162527146_   1038 CAAACAGACATTTCACCAAAGAAGAGATACATATGGCGAATA-GCACATG 1086
                         ii  i         v          v     v     v    -       
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_162527146_   1087 GAAAAATGTTCAATATCATTAGTCAT 1112
                         i   i   i    i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (120 / 50)
Gap_init rate = 0.01 (9 / 623), avg. gap size = 1.89 (17 / 9)  


2930 24.30 1.82 4.60  chr2_162529644_162534053.rev     2985  3918 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_162529644_   2985 TGGAAAAACATTCCATGCTCATGGATAGGAAAAAAATCAAAATT---AAA 3031
                               i i  i     i        v    i v-- i  v   ---  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC--TTAATATTGTTAAG 48

  chr2_162529644_   3032 ATGGCA-TACTGCCCAAAGCAATTTACAGATTCAGTGCTATTCCTATCAA 3080
                               -    v      vii  i          ii  v  i        
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_162529644_   3081 CCTACCAATAACATTTTTACAAAATTAGAAAAAAGTGCACATTTTTCAAA 3130
                         vv v   iivi v     -----------------    --------i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTT-----------------TGCA--------GAA 123

  chr2_162529644_   3131 ATTAGAAAAA--AATTCTAAAATTCATATGGAACCAAAAAAGATCCCAAA 3178
                            -  v  i--i  i                 viiv  ii  i  vi  
  L1M4_orf2#LINE/    124 ATT-GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr2_162529644_   3179 TAGCCAAAGTGATCCTGAACAAAAAGAATGAAGCTGGAGGCATCACACTA 3228
                                 iii   i    v  i     ii   i      vv       v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr2_162529644_   3229 CCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTA 3278
                           ii i      viv        i          i   i    ii     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_162529644_   3279 TCAGTATAAAAACAGACACATAGACCAATGGAACAGGTTAAAGGACCCAG 3328
                         iii i    ii i     i     i        i  iv vi  iii    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_162529644_   3329 AAATAGAGCCACATATGTAGAACCATCTGATCTTCAACAAAGCCAATAAA 3378
                              i v   i i  v  viii  vi    i   i    i viivi  i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_162529644_   3379 AATAAGCAATGAGGAAAGGACTCCCTACTCAATAAATGCTGCTGGGATAA 3428
                          vi vv     i      i ivvi  vi    i     v        i  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_162529644_   3429 CTGGCTAGCCATATGCAGAAGATTGAAACGGGACCCCTACATTTCACCAT 3478
                             v  ?   i     i    v    iiv          v iv      
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_162529644_   3479 ATACAAAAGTCAACTCAAGATGAATTAAAGACTTAAATGTAAG-GCCAAA 3527
                                 i i       i   i  i ?    i          -  i   
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_162529644_   3528 AACACTATAAAAACTCT-AGAAGAAAATCCAGG---AAATACCATTCTGG 3573
                          ---        -    -         ivi   ---    -- -   vv 
  L1M4_orf2#LINE/    523 A---CTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTG 565

  chr2_162529644_   3574 ACATCAGCCAAAGAAAAGACTTCAT-GATGAAGATGCCAAAAGCAATTGC 3622
                           v ii viv i v  v ii   v -   - v  ii         vvv  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGC 614

  chr2_162529644_   3623 AACAAAAACAAAAATTGACAAGTGGAATTTAATTGACCTAAAGAGCTTTT 3672
                                iv      v  i  i v i i  v  ii vv v  i i     
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_162529644_   3673 GCACAGTAAAAGAAACTATCAACAGAGTAAA----CAACCTACAGAGTAG 3718
                          ii vvi   i  v        v i   i  ----     i     i i 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_162529644_   3719 GAGAAAATGTTTGCAAACTATGCATCTGACTAAGGTTTAATATCCAGAAT 3768
                                 i        ii  ii      iv i  vi vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_162529644_   3769 CTTTAAGGAACTCAAATAAATCAACAAGCAAAAAACAAACAACCCTATTT 3818
                         v v   i      vv i  v    i  vv    i     i     v   ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_162529644_   3819 AAAAAGTGGGCAAAAGATATTAACAGACACTTCTCAAAAGAAGACATACT 3868
                              -        i   v v  i     i     v        i    -
  L1M4_orf2#LINE/    815 AAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC- 862

  chr2_162529644_   3869 AATACAAGTAGC-AACAAGCATATGAAAAAATGCTCAGTATCACTAATCA 3917
                         -----  i i  -  i     i       i       ii    ???????
  L1M4_orf2#LINE/    863 -----AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_162529644_   3918 T 3918
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.84 (145 / 79)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.00 (60 / 20)  


3030 26.29 2.36 0.34  chr2_162569078_162572140.rev     1682  2571 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_162569078_   1682 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 1731
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_162569078_   1732 GGCCATACTGCCCAAAGTAGTTTATAGATTCAATGCTATCCCCATCAAGC 1781
                            v     v      v ii i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_162569078_   1782 TACCA-TTGACTGTCTTCGCAGAATTGGAAAAAACGACTTTAAATTTCAT 1830
                          v   -i  v  - i  i      v v  v  ivi  iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_162569078_   1831 ATGGAACCAAAAATAGAGCCTGTATGGCCATGACAATCCTAAGCAA-AGG 1879
                               viiv  i-i  v  v v  i    vi      i i iv  - i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_162569078_   1880 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACATGG- 1928
                                i      vv       v  ii i      viv       vi -
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_162569078_   1929 ---AAAAACCA---CAG---GGCACTTGTATCCAAACCAATATTTAGACC 1969
                         --- iv  i  ---   ---  i   v i  vvii ivi i  v    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_162569078_   1970 AATGGAACAGAACAGAGACCTCAGAAATAATGCCATTTATCTACAACCAC 2019
                                i    iv    vii         vv    vi  i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_162569078_   2020 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAGGATT--CCT 2067
                         i    i  i     ivv  v   i v  vv          i  v --i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_162569078_   2068 ATTTAATAAATGGTGTTGGGAAAACTAGCTAGCCATATGCAGAAAACAGA 2117
                         v  i  i        i     v    i v  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_162569078_   2118 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 2167
                          ii         v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_162569078_   2168 AAAGACTTAAATGTAAGACCTAAAGCCCTAAAAACCCTAGAAGAAAACCT 2217
                          ?    i           v     i iv     vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_162569078_   2218 AGGCA-ATACCATTCAGGACATAGGCATAGGCAAAGACTTCATGACTAAA 2266
                            ?i- v i -   iv   v v  vv       v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_162569078_   2267 ACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGAGCTAAT 2316
                                     vvi          vv    iv  i    v   vi v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_162569078_   2317 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAATGAACA 2366
                         i   v v  i i   i  ii vv    i  v        v i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_162569078_   2367 AGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATACATCTGACAAA 2416
                         ii     i                 v       vii   i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_162569078_   2417 GGACTCATGTCCAGAATCTACAAGGAACTTCAACAAATTTACAAGAAAAA 2466
                              ii i        v  i  i     iiv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_162569078_   2467 AACAA----CCCCAGCAAAAAGTGGGTAAAGGATATGAACAGAAATTTCT 2512
                         i    ----   v vi?    i    i       v    i   v      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_162569078_   2513 CAAAAGAAGACATTTATGTGGCCAAGAA--ACATGAAAAAAAGCTCATCA 2560
                          v        i  vi vi       v  --         i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_162569078_   2561 TCACTGGTCAT 2571
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.30 (130 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.00 (24 / 12)  


2806 23.80 8.97 0.48  chr2_162616214_162619736.rev     2196  3031 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_162616214_   2196 GGAAAAATATCCTGTGTTTATGGATTGGAAGAACTGATATT--TAAAATA 2243
                              i      ii    i             vi i     --   i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_162616214_   2244 TCCATACTAACAAAAGCTATCAACAGATTCAATATAATCCCTGCCAAAAT 2293
                         v v     vv v   viv   v          iii       ii      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_162616214_   2294 GCCAATGACATTTTTTACAAAAATAGAAAAAAGC-AATCCTAAACTTTGT 2342
                         v   iivi v      i  i    v  v  --  -i        v  ii 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCAT 149

  chr2_162616214_   2343 AT--AACCACAAAAAAC---AAATAACCAAATAAATCTTGAGCAAAAAGA 2387
                           --  vii   iii  ---i    i     vv        iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_162616214_   2388 ACAAACCTGGAAGTATCACAATATCAAACTTCAAAATACACCACAAAGCT 2437
                              vi    i vv     v vi v  i       ivi  i        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_162616214_   2438 GTATTA--CAAGGCAGCATGGCACTGGCATAAAAATAGACACAGAGGCCA 2485
                         ii v  --    i   ii   i          ii       i v  ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_162616214_   2486 GTG-AACAGAATAGACAACCC-GAAATAAATCCATGTATTTAAGGTCAAA 2533
                         i  -  i     v  v ii  -        i    ii     v      v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_162616214_   2534 TGATTTTCGACAAAGATGCTGAGAGCACACAGTGGGGAAAGGACAGTCTC 2583
                                      i i   ii   v  iv  i         i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_162616214_   2584 TTCAACAAATGGTGTTGGGACAACTGAATATCCACATGTGGAAGAATGAA 2633
                                       i           i   ?       iii         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_162616214_   2634 ATCAGACCCTTATCTCACACCATAT-------TTAA---AAAA-GGATTA 2672
                         i ii     i  i            -------    ---    -    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_162616214_   2673 AATACCTAAA------ACC----ACTATAA-----------GAAAACATT 2701
                         ? v       ------ v ----       -----------        v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_162616214_   2702 GCCATTTGTCTGCATAATTTT---------------TTTTTGGATTTAAC 2736
                          v?i vvi   v i i ii  ---------------  i  i   v i  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_162616214_   2737 CCCAAA-TCACAGACTGGGAAAGCAAAGATAGACAAATGAGATTACATCA 2785
                         v     -v    ii vivi    v   i     i    vi  i v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_162616214_   2786 AACTAAAAAGCT-----GCATAGCCAAGAAAATAATCAGCAGAGTGAATA 2830
                           v v    i  -----  v -- v   i v iv    iv i      v 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_162616214_   2831 TACAACCTATGGAATGAGATAAAATATTTACAAACCATAAATCTGATAAG 2880
                         v      i ii     i  v         i    i    v          
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_162616214_   2881 AGATTAATGTTTAAAATATACGAGGAACTC----AACACAACTGTAAGAA 2926
                         i  i vi i ii i      ii i      ----   v   ivi   i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_162616214_   2927 AAAAAACAA----GGTTAAAAATGGGCAAAGTATCTGAATAGACATTTCT 2972
                         i v   i  ----iv ?              v  i               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_162616214_   2973 CAAAAGAAGACATACAAATAGCCAATG-GTATGTGAAAAAATGCTCAA-A 3020
                          v        i        i      i- i ii      i        - 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_162616214_   3021 TCACCAATGAT 3031
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.91 (128 / 67)
Gap_init rate = 0.02 (22 / 907), avg. gap size = 3.59 (79 / 22)  


4593 15.71 3.03 1.12  chr2_162914999_162917158.rev      786  1676 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_162914999_    786 TGGAAAGACATCCCATGTTTATGGATCATAAAAC--AATATTTTTAAGAT 833
                                 i          i      iiv  i  --      v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_162914999_    834 GGCAATACTGCCTAAATTTATCAACAGATTAAATGTAATCTCTATCCAAA 883
                                  v  i     v   v       v  i i    i     v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_162914999_    884 TCCTGGATAGCTTTCTTTTTTTGCAGAAAGTGACTAGCTGATCCTAAAAT 933
                            i----    vi       -       v    v               
  L1M4_orf2#LINE/    101 TCCC----AGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_162914999_    934 TCATACAAAAATGCAAGGGACCCAAAATAGCTAAAACAATATTGAAAAAG 983
                              iii                i      i        v         
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_162914999_    984 AATAATAAACTTAGAGGAATCACACTTCCTTATTTTAAAACTTACTACAA 1033
                           v  i   v  i     v          iv    i              
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_162914999_   1034 AGCTCC-GTAGTCAAGACAGTGTGTTACTGGCATAAGGATAGATATATAG 1082
                             v -   i             v                  i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_162914999_   1083 ATCAATGGAATAGAATTGAGTGTCCAGAAATAAAGTCTTTTACTTA--GT 1130
                                             v             vi v vi i   --  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_162914999_   1131 TAATTGATTTTTGATGAGGATGCCAAGACAATTCAACGGGAAAAG----- 1175
                         i          i  ii   i         v      i   i    -----
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_162914999_   1176 TCTTTTCAACAAATGATGGTGAAACAATTGGATATCTATGTGCAAAAAAA 1225
                                        i  v  ii    i      ? i ii       i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_162914999_   1226 -GATGTTGGACCCAATTCCTCACACCACACACAAAAATTAACTCAAAATG 1274
                         -  v         v- v          i i                    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_162914999_   1275 GATCAAAGACTTAAATGTAAGAGCTAAAAACTATAAAACTCTTA-----A 1319
                              ?    i                  -              ----- 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAA 543

  chr2_162914999_   1320 AACATACAGATACATTTTTATGTTTTTGAGTTAGGCAA-ATTTTCTAAGA 1368
                               vi?i  v  i  ii  vii   i         -iv     v   
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_162914999_   1369 TATGAC--CAAAAATGCAAGAAACAAAAGAAAACATACATAAATTGGACT 1416
                               --     iii    v            v   v            
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_162914999_   1417 TCATCAAAATTTAACATTTTAGGGTGGCCAAGAATACCATTTAAAGAGTG 1466
                                    v  v i   v v ivv v   i i  i  iv i i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_162914999_   1467 AAAAGACTACCTAGAAAATGAGAAAAAATATTTGCAAAT-ATATATTCGA 1515
                                v   i v i    i  i               -      ii  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_162914999_   1516 TAAAGGCCATGCATCTAGAATATACAAAGAATTCTGGCAGCTCAATAATA 1565
                            i  v v  i   i        i      i   vi  i          
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_162914999_   1566 AAAAGATAAATAACTCCATTAAAAAATGGACAAAGGAC------AGACAT 1609
                               i       i v   ?        i       i------      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_162914999_   1610 TTTGCTAAGGAAGATATACAAATGACTAATAAGCACATGAAT-GATGCTC 1658
                           iv i  i               i i              v-       
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_162914999_   1659 AATGCTATCAGTCACTGC 1676
                           i---    ????????
  L1M4_orf2#LINE/    894 AAC---ATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (86 / 50)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.31 (37 / 16)  


2686 26.11 1.52 3.36  chr2_163091092_163093377      872  1794 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_163091092_    872 GAAAAACATTTCATGCTCATGGATAGGAAGTATAAATATTGTTAAAATGA 921
                             i i  ii    i        v     vv v           i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_163091092_    922 CCACACGGCCCAAAGCAATGTACAGATTCAATGCCATTCCTGTCAATGTA 971
                          v i  vv      vii  v           i  v  i   i    vi v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_163091092_    972 CCAAAGTCAC--TTTTCACAGAATTAGAAAAAATTATTCTAAAAT-CATA 1018
                            -- iii --    ii     v v  v  iv v  i       -    
  L1M4_orf2#LINE/    103 CCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_163091092_   1019 TGAAACCAGAAATACTCCTGAATTGCCAAAGGAAT-TCGAGGCAAAAAGA 1067
                           i  viiv  ivivi  v    v      iv   - i  ii-  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGAAGA 199

  chr2_163091092_   1068 ACAAAGCTGGAGCCATCACACTACCCAACTTCAAACTATACTACAAGGTT 1117
                               i     vvv       v     i      viv        i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_163091092_   1118 ACAGTAACCAAAACAATGTGGAACTGGTACAAAAACAAACATA--GACTA 1165
                                i   i   i     v     i i  ii i i     --  ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_163091092_   1166 ATGGAATAGCATAGAGAAACCAGAAATAAAGCCACACACATACAGCCACC 1215
                                  v  v    iv           v   i   iv  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_163091092_   1216 TGATTTTCAACAAAGCTGACAATAACAAACAATGAAGAAAAGAT--TCCT 1263
                                 i    i v  v   v v  vv     ii    ii  --  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_163091092_   1264 TATTCAATAAATGATGTTTGGATAACTGGCTAGCCATATGCAGAAGATTG 1313
                          --    i     i  i v   i      v  ?   i     i    v  
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_163091092_   1314 AAACTGGACCCTTATGTTTTTCCATCAACAAAAATTAGCTCAAGATGGAT 1363
                           ii       i  iv iviv    vv          i     i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_163091092_   1364 TAAAGACTTAAATACAAGACCTAAAAACAATAAAAACTCT-AGAAGAAAG 1412
                         i ?    i     ii    v      - v      -    -        i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAA-CTCTTAGAAGAAAA 545

  chr2_163091092_   1413 CCTATGAAATGACATTCCAGGCCATATCATTACCAACACCTCTTCAACCT 1462
                          v  - i?i i -  ii---------  i v   --------- iiivi 
  L1M4_orf2#LINE/    546 CATA-GGNGTAA-ATCT---------TCGTGACC---------TTGGGTT 575

  chr2_163091092_   1463 TGGCAAAAATTTATGACTAAAT----CCCCAAAAGCAATTGCAACCAAAA 1508
                         v     vii   v ---  i  ---- v         vvv     v   i
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCT---TAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_163091092_   1509 CCACAATTGAGAAGTGGAACCTAATTAAA-TGAAAGAGATTCTGCACAGC 1557
                         vv v   v  v  i v i  i v  i   - v   i v-  i  ii vv 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTC 671

  chr2_163091092_   1558 AAAAGAAACTACCAACAGAGTAAACAGAAAACCTACAGAATGGGAGAAAA 1607
                            i  v    i   v i   i  v   v    i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_163091092_   1608 TATTTGCACACTGTGCATCTGATAAAGATCCAATAACCAGAATCCATAAG 1657
                                 v iii ii         i iv ivi  v       vi    i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_163091092_   1658 GAACTTAAGCAAACCAACAAGCAAAAATCAAAGAACTCCAATAAAAAGTG 1707
                              ivvi   vi   i  vv    iv    v   i v v ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_163091092_   1708 GGCAAAGGACATGAACAGATACTTCTCAAAAAAAGGCATACCAGTGGCCA 1757
                                  iv    i   i i     v   i   ii    v i      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_163091092_   1758 AGAAACATATGAAAAAATGTTTATCATCAATAATTAT 1794
                          v  i  i       i   i i v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 2.37 (45 / 19)  


2495 27.21 4.59 2.07  chr2_163321148_163323456      947  1817 (492)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_163321148_    947 TGTTCATGGATTGGAAGACTCAATA--GTAACTATTTCAATTCTCCCCAA 994
                                             i    --  v vv  vv    v        
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_163321148_    995 ATTGCTATACCGGTTTAACACAATTCTTATCAAGATCCCAGCAAAATATT 1044
                             v v   v i  i   i    i i      i        ---- iii
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC----TGCC 111

  chr2_163321148_   1045 TTTTATGTAGACATAGACAATATTG--CATGAATTTTTATATTGAAAAGC 1092
                             v  i   v  v     -ii  -- v i  v  i-    v    v  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTC-ATATGGAAATGC 159

  chr2_163321148_   1093 AAAGGAAGTAGAATAGTTTTAGAGCAAT-TTGAAAGAGAT---TAAAATG 1138
                           i   vvi       ii-- i i    -      i   v---i   i v
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCC--AAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_163321148_   1139 GAAGTAATTAGCCTATATGATTTCAAGACTTATAACATAGCTACCCTAAT 1188
                          i  v v i vv  vivii       i     iv   v      vv    
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_163321148_   1189 CAAGATTGCATGTTATTAGTGGAAGCATAGATGCATAGATCCATGGAATA 1238
                              iv ii  v  i i iiv   v     iii       v        
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_163321148_   1239 TAACACAGTACCTAGAAATAGACCCACATAAATATGCCTGCCTATTTTTT 1288
                         v  ivv  vii i       i     i i vv    --- i v   vv  
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATG---GTCAATTGATT 354

  chr2_163321148_   1289 TT-----AAGTTATAAAAATGATTCAGTGGAAGAAGGATACCTTTTTCAC 1333
                           ----- i v iiv  i iv     i   iii   i   vii      v
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_163321148_   1334 CAAATGAAGTGGGAGCAATTGGACATCCCATATACATTAAAAAAAAATGA 1383
                               iv iv  ii   i    i ?  - i  i  -----   i     
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCC-ACATGCA-----AAAGAATGA 448

  chr2_163321148_   1384 AATTTGACCCAAGTCTCAAACCTTGTGCAAAAACTAACTCAAAATGTATC 1433
                          i  v     vvii    v   v i i      i            v   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_163321148_   1434 ACAGGCTTAAATGTAAAATGTACATCTACAAAACTTTTAGAACCAAACAT 1483
                          ?  i i         i vv  v v   i      i      vv      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_163321148_   1484 GGAAGAAAATCTTCAGGATCTAGAAT-AGGCAATAATT-CTTAGACTTGA 1531
                         i i? v        iv  i  v ii -       ii  -      iv   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_163321148_   1532 CACCCAAAAGATGATACGTGGAAGGAAAAATTGACAATTTGGATTTTGTT 1581
                             v   iv ii vvviiii   i      v  i  v     i  ii i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_163321148_   1582 AATATCAAAA-CTTTT-TACTGCAAA--------------------AAGG 1609
                           v  i    -     - i  v    --------------------  i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_163321148_   1610 ACAAGATATAGTGTGGGAGAAAATATTCGCAA-TGACATACCCAGTAAAG 1658
                             vvi i  vi              i    - v i   i iii   i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_163321148_   1659 GACTGGTATCTAGAATATGTAAAGACCTCTCAAAGCTCACTAGTGAAAGA 1708
                             v     i       i      v    i v i    v  i i   - 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA-A 797

  chr2_163321148_   1709 AACAAACAACCCAACTAGAAAATAGATAAAAGTCATGAAGAGAT-TTTCA 1757
                         i     i       i ?i     i ii   i viv    v   i-    v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_163321148_   1758 CTGAAAACTATATTCAGATGGCAAATAATCACATGAAAAAA-GTTCCACC 1806
                          ii  i vv    v  i     v     v          i - i  v  v
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_163321148_   1807 TCATTAGCCAT 1817
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.02 (21 / 893), avg. gap size = 2.76 (58 / 21)  


 408 26.76 0.00 6.34  chr2_163409770_163412009.rev      501   642 (1598)    L1M4_orf2#LINE/L1      123   255 (653)  

  chr2_163409770_    501 AATTGACAAGCTGATTCTAAGATGTATATGGGAATAGAAAAGATGTAGCT 550
                                        i    i  vi      i   iv  ii  ivi  vv
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr2_163409770_    551 TAACTAAAACAACTATGGAAAAAGAAAAAAAGAAAAACAAAATTGGGGGA 600
                           i i       iiv  ---------        i      i    i   
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTG---------AAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_163409770_    601 CATATATTACTTGATTTCAAATTTGACTAAAAAGTCAAAATA 642
                          vi i i v iii        vi v    v    ii v i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

Transitions / transversions = 2.17 (26 / 12)
Gap_init rate = 0.01 (1 / 133), avg. gap size = 9.00 (9 / 1)  

 822 27.96 9.68 3.23  chr2_163409770_163412009.rev      824  1195 (1045)    L1M4_orf2#LINE/L1      259   654 (254)  

  chr2_163409770_    824 AAAAAAATTTGGGTATATTGACAAAATGACAATCATATAGATCGATGAAA 873
                           i v i v   ---  i  i  v  v  i iv          i   i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGG---TACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_163409770_    874 CAGTAT--AGAGTCGAGAGACAGATGTACATATATATGG----------- 910
                         i  v  --      v   i i i ivi i i  v     -----------
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_163409770_    911 -----------GCCAAGGTAATGTAATAGGGGAAGGGCAGTCTTTTAAAC 949
                         -----------      iiv  vi   i   i   iii        v   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_163409770_    950 AAATGGCGCTGTAACAGTTACATATCTTTGTTTAAAAAAATAAAAAAAAA 999
                               i    vi   ii iv   ? ivii vi    i   i  i-----
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG----- 450

  chr2_163409770_   1000 ACTTGAACCT-TACTTCACATCATGTACA----CTAACTCAAAATAGATC 1044
                         --   i   i-   i     i   i    ----i           i    
  L1M4_orf2#LINE/    451 --TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_163409770_   1045 ATTGATCTAAGTATGACAGGTAAAACTATAAA--TTTTACATGAAATCTT 1092
                          ?v  i    i i i v  v            -- i   v v    v v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_163409770_   1093 -GGAG-AAATTTTCATACTTTTGCATTAAGCAAAGATGT-TCAAA-ATAA 1138
                         -  ? -    i   i ivii   vi   i    v i v - i i -  i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_163409770_   1139 GACCAAAATTACCATGAATTTTAAAATAATATTTGATAACTTGG-CTTCA 1187
                         v       vi  v vv  iv--   iv  v v v     v    -     
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACA--AAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_163409770_   1188 TCAAAGTT 1195
                              i  
  L1M4_orf2#LINE/    647 TCAAAATT 654

Transitions / transversions = 1.66 (63 / 38)
Gap_init rate = 0.03 (13 / 396), avg. gap size = 3.69 (48 / 13)  

 728 20.31 7.42 2.34  chr2_163409770_163412009.rev     1493  1748 (492)    L1M4_orf2#LINE/L1      640   908 (0)  

  chr2_163409770_   1493 GGCCTCATCAAAGTTTTAAACTTCTGCTCTTCTGAAAGACACTATCAAGA 1542
                          i i        i  vv      i  iv    -i  i             
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTC-AAAGGACACTATCAAGA 688

  chr2_163409770_   1543 AAATAAAAAGACAAGACACCTACTGGGA-AAAATATTTGGAAAACATATT 1591
                           i i         vv   vv v     -          v   v     v
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_163409770_   1592 TCTAATAAA--ACTTGAACCCAAAATATATAAAGAA------------AA 1627
                            i    i--     v i   i             ------------  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_163409770_   1628 TATAAAAAACACCACTCAAACAGCTTCATTTTACA---GGCAAAATCTTT 1674
                           vv     v  -----   i i iiv   ?v v ---      ivv   
  L1M4_orf2#LINE/    789 TAATAAAAAGAC-----AAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_163409770_   1675 GTAGAGACATTTCACCAAAGAAGA-ATACAAATGGTAAAACAGCACATAA 1723
                          v v         v          -          iv  vv       i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_163409770_   1724 AAAATTTATCAAGATCATTAGTCAT 1748
                            iv vv    v    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.70 (21 / 30)
Gap_init rate = 0.03 (7 / 269), avg. gap size = 3.57 (25 / 7)  


1709 27.18 6.91 4.65  chr2_163531946_163535323     2040  2878 (500)    L1M4_orf2#LINE/L1        1   858 (50)  

  chr2_163531946_   2040 TAGAAAGATATATAATGTTCACAGATCTAAAGACTTAATATTGTTAAAAT 2089
                          i         viv       ii   ivi                  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_163531946_   2090 TTCAATTATCCCTATAACTGGTCTATGGATTCAATATAATTATAATGAAA 2139
                         vv    vv    i -  i  i    ii       iii   iviv  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCA-AATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_163531946_   2140 ATCCAAAGAGT-TTTATTAAAGAAATTAACCGGCCAGTTACAAAATTTAT 2188
                             v ivv i-   v  iv       i  vi  iii ivi      i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_163531946_   2189 ATAAAATTTATAAAAAATTTATATAAAATTAAATGGTCCAAAAAATTAAT 2238
                           ii  v -ii  iii iii ---------i   i -      ---i   
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCA---------GAATAG-CCAAAA---CAAT 185

  chr2_163531946_   2239 GTGTACTTAACAGTGAATGTTAAAAGAGAAGTGAGAGGACTTACATTATC 2288
                         -----   i v iv   -----i  v -    vi       i   i vi 
  L1M4_orf2#LINE/    186 -----CTTGAAAAAGAA-----GAACA-AAGTTGGAGGACTCACACTTCC 224

  chr2_163531946_   2289 TGATTTCAATACTCAGCATAGAGCTACATTAATCAAGACCATGTGGCATT 2338
                         ii       v   i vi i i       v          vi     i i 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr2_163531946_   2339 GTGCA--AAAACAGAAATATAGAT-AATGGAAGCAAAGGAAGAGTTCAAA 2385
                          -   -- ii i   v        -       vvi  vvi     i  i 
  L1M4_orf2#LINE/    275 G-GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_163531946_   2386 AGTAGACCCAGACATATATGAGTAATAAATAATGATTTTCAATAAATGAG 2435
                          i  i     v    v    ivi   ------        i i  iv v 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAAT------TGATTTTCGACAAGGGTG 367

  chr2_163531946_   2436 CCTAGGTAATTCAATGGAGAAGTAATGCTCTTTAATAATAATTGGTGCTA 2485
                           v  iiv         i   iv   iv     v-i  i  v       i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTT-CAACAAATGGTGCTG 416

  chr2_163531946_   2486 GAGCAATTGGA-AGCCATATGAAATAAAATGAGACACCTCAACCCTTATG 2534
                          ii   i    - ?   i   v  v i     --- vi vi    i  iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGA---AGTTGGACCCCTACC 463

  chr2_163531946_   2535 TTACCGCCATATACAAAT-TTATCTCAAAATACATGATAACCCTAAATAT 2583
                          i  -i           v-   v        iv  v ? iv       i 
  L1M4_orf2#LINE/    464 TCAC-ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_163531946_   2584 AAGAACTAAAAGTATAAAATTTCTAGAAGAAAGCATAATCG--AATC--- 2628
                             i      v       i ii         i    iv? --    ---
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_163531946_   2629 --AAA---AGACTACACAA---------AAATAT----CC-----CATA- 2654
                         --i v---i ii  vi   --------- i    ----  -----  i -
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_163531946_   2655 -TTATAAAAGAAAGAAT-GATAATTTGGAATTCAATATAATTAAA---TT 2699
                         -iv i        i   -     v     v    vi v       ---  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_163531946_   2700 TTTTATT----------CTGTTAAGAAAATACAACAGCAAGGCAAAGATT 2739
                           v ii ----------  i i      i iv  vii   vv  v   v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_163531946_   2740 GTGGGAAACTATTTGCAAAGCATCTGTCCAATAAAGAACCTATATTCAGA 2789
                          v i    v          v   v i  ii    i i  i i   i    
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_163531946_   2790 AAAC-TAAGC--CTGCTTGAAAGTCAATAATAAGACAACAAA-AATT-AA 2834
                          v i-   iv--  -   iv  v          i vi     -  ii-  
  L1M4_orf2#LINE/    763 ATATATAAAGAACT-CTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_163531946_   2835 TTTCA---TGAGTGATATATTGGAATAGACATTACATTAAAGAAGAT 2878
                           ?v ---  i ii viv   v           v vii         
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

Transitions / transversions = 1.67 (140 / 84)
Gap_init rate = 0.04 (34 / 858), avg. gap size = 2.85 (97 / 34)  

 224 15.79 1.75 0.00  chr2_163531946_163535323     3092  3148 (230)    L1M4_orf2#LINE/L1      851   908 (0)  

  chr2_163531946_   3092 AAGAAGATATAAGAATGG-TAATAAGTACTTGAAAATATGGTCAACATTT 3140
                                    vi     -i      i  v      v   v       iv
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_163531946_   3141 TTTTCTCA 3148
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 0.80 (4 / 5)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1)  


2122 24.73 1.88 2.03  chr2_163630937_163632528      501  1139 (453)    L1M4_orf2#LINE/L1      271   908 (0)  

  chr2_163630937_    501 TACTGGCATAAAACTAGACACATAGACCAATGGAACAGAATAGACAGCCC 550
                                    iiv      i     i        i     v  v  i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_163630937_    551 CAGAATAAATGCATAAATCTACG-TGAATTCATTTTTGACAGAGGTGCTG 599
                         vii      iv    v  i  i - v    v     i    ii     ii
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_163630937_    600 AGAACATAGATTGGAGAATAGACAGTCTCTTCAACAAATGGTGCTGGAA- 648
                            v   vv v   i   vii i     i                  i -
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_163630937_    649 AACTGAATATCCATATGCAGAAGAATGATATTAGACCCCTATCTCTTGCA 698
                              i   ?   i     i        vi  i        i   vii v
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_163630937_    699 ATGTACAAAAATAAAATCAAAATTTATTGAAAACTTAAATATAAGACCTT 748
                           i         v  v       vv  ii? i  i     i     v  v
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_163630937_    749 AAACTATGAAACTACTATAAAAA----TTGGAGAAACACTCTAGGATATA 794
                                i     vi  v  i  ---- v  ? v  vv  iiiv  iv v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_163630937_    795 GGTCTGTGTAGAGATTTATTGAGTAAGACCTCAAAAGGGCAGGCAACCAA 844
                           vi iv i iv i   v  iii  v   vi      vi  i     v  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_163630937_    845 AGCAAAAGTGGATAAATGAGATCACATGAAGCTAAAAAGCTTCTGCACGG 894
                           v    i i       vi  iiv   v  iv v    i   i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_163630937_    895 TAAAGGAAACAATCAACAAAGTGAAGAAACAACCCACAGAATAGGAGAAA 944
                         i      v  v     v        i i              i       
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_163630937_    945 ATATTTGTAGACTATCTATATGACAAGGGATTAATAACCAGAATATAGAA 994
                                i i ii  v   v   i      i vi  v          v  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_163630937_    995 GGAACTC----AACTCAATAGAAAGAAAACAAATTATCCAATTATTAAAA 1040
                         i      ----         iv  i  i      v i      ?v-    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAA 819

  chr2_163630937_   1041 TGGGAAAAGG-TCTGAATAGATATTTCTTGAAAGAA-AGGTACAAATGTC 1088
                             v     - i        i      iv      - vi        v 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_163630937_   1089 CAACCAACATCACTAATCATCAGAGAAATGCAAATCAAAATGACAATGAG 1138
                            iv i  --------   v i - i    ---    v  v ???????
  L1M4_orf2#LINE/    870 CAATAAGCA--------CATGAAA-AGATGC---TCAACATCAZZZZZZZ 907

  chr2_163630937_   1139 A 1139
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.33 (88 / 66)
Gap_init rate = 0.02 (10 / 638), avg. gap size = 2.50 (25 / 10)  


1553 16.88 4.37 26.56  chr2_163682091_163684469      733  1899 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_163682091_    733 TAGACAGAT-TCTCACATTCACAGATTGGAAGAATTAATA---------- 771
                          i  v    -  i  ii    ii          v      ----------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_163682091_    772 ---AAT------------GATCTACAGATTCAATTCAGTCCCTATCAAAA 806
                         ---   ------------               iv  i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_163682091_    807 TTTCAA-TGACTGTTTTTCAGAAA-----AAAATAATTCTAGAGTTCATA 850
                          ii  i-  v  v    v      -----  iv i  i   i i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_163682091_    851 TGAAACCACAAA--ATCACTGAATAGCTAAAGCAACCTCGAGCAAAAAGA 898
                           i  vii   i-- i - v       i   i   i  i  iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_163682091_    899 ACAAAGCTGGAGGTATCACACTTCCTGATTTCAAAAAATATTACAAACCT 948
                               i      vv          ii         vv  i      v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_163682091_    949 ATACTAATCAAAATAGCATGGTACTGCCATAAAAGCAGACACATAGACCA 998
                          i v       i i  ii        v     iiii     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_163682091_    999 ATGAAACAAAATAGAGAGTTCAGAAATAAATCCACGCATATATGGTTAAC 1048
                            i  i i   v      i          i   ii   v      i  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_163682091_   1049 TAATTATCAACAAAGATGCCAAAAATACACAACAGGACAATAATAGACTC 1098
                          i   v  i    i i      i vi iv   ii  iv  v     v  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_163682091_   1099 TTCAATAAATGGTGTTGGGAAAACTGGATATCCACATGCAAAAATAAAAA 1148
                              i        i     v         ?            i----  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG----AA 445

  chr2_163682091_   1149 TAAAAATTAGGCCGGGCACAGTGGCTCATGGTTGTAATCCCAGCACTTTG 1198
                          i  --------------------------    ----------------
  L1M4_orf2#LINE/    446 TGAA--------------------------GTTG---------------- 453

  chr2_163682091_   1199 GGAGGCCAAGGCAGGTGGATCACAAGGTCAGGAGTTCAAGACCAGCCTGG 1248
                         ---------------------------------------    -------
  L1M4_orf2#LINE/    454 ---------------------------------------GACC------- 457

  chr2_163682091_   1249 CCAATACAGTGAAACCCTGTCTCTACTAAAAATACAAAAATCAGCTAGGT 1298
                         ---------------   ii   ---------------------------
  L1M4_orf2#LINE/    458 ---------------CCTACCTC--------------------------- 465

  chr2_163682091_   1299 GTGGTGGTGGGCACCTGTAATCCCAGCTACTAGGGAGGCTGAGGCAGGAG 1348
                         --------------------------------------------------
  L1M4_orf2#LINE/    466 -------------------------------------------------- 465

  chr2_163682091_   1349 AATCACTTGAACCCAGGAGGCAGAGGTTGCAGTGAGCCAAGATCATGCCA 1398
                         --------------------------------------------------
  L1M4_orf2#LINE/    466 -------------------------------------------------- 465

  chr2_163682091_   1399 CTGCACTCCAGCCTGGGCAACAGAGCAAGACTCCATCTCAAAAAAAAAAA 1448
                         -------------------   ----------    --------------
  L1M4_orf2#LINE/    466 -------------------ACA----------CCAT-------------- 472

  chr2_163682091_   1449 TTAAATTGGACTCTTAAGTCAGATATAAAAGTAAACTAAAAATGTATTAA 1498
                         ----------------------   i    i v    v      v  i ?
  L1M4_orf2#LINE/    473 ----------------------ATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_163682091_   1499 AGACTTAATCTTAAGA-CCGGAACTGTAAAACTGCCAGAAGAAGAATATA 1547
                             i   viv     - iii    i       vii       -  i   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA-AACATA 549

  chr2_163682091_   1548 CAAGATAAACTCTT--TGACATTGGTCTTGGCTATGATTTTTGGGGTTTC 1595
                         vi? -    -    --    v    vi v   v   i   i vi i v v
  L1M4_orf2#LINE/    550 GGNG-TAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_163682091_   1596 ATAACAAAAGCAGAGACAAGAAAAGTAAAAATAAACAAGTGGGGCTTCAT 1645
                          i v        v ii   v     v       i i  i v  i      
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_163682091_   1646 CAAACTAAAACATTTTTGCACAGAAAAGAGAAATAACAATAAA----AAA 1691
                             v v   v i     ii vvv    iiv v  v   v   ----   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_163682091_   1692 GGCAGCCTATGTAATGAGAGTAAATATTTT--AATTATATATCTGATAAG 1739
                          i  i  i iiv    i   v        v--   i              
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_163682091_   1740 GG-TTAATACCCAAAATACATAAAGAACTC----AACTCAATAGCAAAAT 1784
                           -i vi  i   i    i           ----         ii    v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_163682091_   1785 GA---GTAACCCAATTAAAAAATGAGTAAAGGACCAACATAAACAGTTTT 1831
                           ---i          ?       i i      iiviv   i   v  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_163682091_   1832 CCAAAATAGACATACAAGTGGCCAATGCGTAAATAAAAAGATGCTCAATG 1881
                              iv   i      i        iv i v  i             i-
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC- 896

  chr2_163682091_   1882 AGACTAATCACCAGGGAA 1899
                         ------    ????????
  L1M4_orf2#LINE/    897 ------ATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (127 / 66)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 14.44 (361 / 25)  


3030 26.77 1.22 0.77  chr2_163693382_163700595.rev     5819  6722 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_163693382_   5819 TGGAAAAATATTCTATGCTCATGGATAGGAAAAATCAATATTGTGAAAAT 5868
                               i    i i   i        v    i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_163693382_   5869 TGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCCTCAAGC 5918
                         v  v     v      v i  i  i        i  v  i  iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_163693382_   5919 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5967
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_163693382_   5968 ATGGAACCAAAAAGAGCCCATA-TAGCCAAGACAATTCTGAGCAAAAAGA 6016
                               viiv  i ii    v -       i     ii   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_163693382_   6017 ACAAAGCTGGAGGCATCACGCTACCTGACTTTAAACTATGCTACAAGTCT 6066
                               i      vv    i  v  ii i  i   viv i      iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_163693382_   6067 ACAGTAACCAAAACAGCATGGTACTGGTACTAAAAGAGATATATAGACCA 6116
                                i   i    ii         i iv ii v   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_163693382_   6117 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 6166
                               i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_163693382_   6167 TGATCTTCGACAAATCTGACAAAAACAAGCAATGGGGAAAGGAT--TCCT 6214
                             i        ivv  v   i v  vv            i  --  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_163693382_   6215 TATATAATAAAGTTGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACT 6264
                          - -i  i   - v         v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    400 T-T-CAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_163693382_   6265 GAAATTGGACCCCTTCCTTACACCTTACGTAAATATTAACTAAAGATGGA 6314
                            i          v   i     v  iii   v       v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_163693382_   6315 TTAAAGACTTAAATGTAAGACCTGAAACCAGAAAAACCCTAGAAGAAAAC 6364
                          i ?    i           v  i    i v    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_163693382_   6365 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATCGCTT 6413
                         v    ?i- v i -   iv   v v  vv i     v ii   v v v v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_163693382_   6414 AAACACCAAAAGCAATTGCAACGAAAGCCAAAATTGACAAACGGGATCTA 6463
                         vi            vvv     i    vv     v  i   iv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_163693382_   6464 GTTAAACTAAAGACCTTCTGCACAGCAAAAGAAACTATTGTCAGAGTGAA 6513
                         i i   v v  i v   i  ii vv    i  v     iivv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_163693382_   6514 CAAGCAACCTACAGAATGGGCAAAAATTTTTTCAATCTATCCATCTGACA 6563
                         v ii     i          vi     v   v   vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_163693382_   6564 ACGGGCTAATATCCAGTATCTACAAGGA--TCTTA-AAC-CAGTTTACAA 6609
                          v  i  vi       v  v  i  i  --     -   -  i v- i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAA 794

  chr2_163693382_   6610 GAAAAAAAACCAACTCCGTTAAAAAGTGGACAAAGGATATGAACAGATAC 6659
                         i  i v   i-   i vi  ?    i   i        v    i   i i
  L1M4_orf2#LINE/    795 AAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_163693382_   6660 TTCTCAAAAGAAGACATTTATGCGGCCAACAA--ACATGAAAAAAAGCTC 6707
                              v        i  vi vii      i  --         i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_163693382_   6708 ATCATCACCAGTCAT 6722
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.20 (18 / 15)  


2424 24.32 4.94 3.64  chr2_163738556_163740768.rev      590  1358 (855)    L1M4_orf2#LINE/L1        1   779 (129)  

  chr2_163738556_    590 TGGAGAAATATTCCATGTTCATGGATAGGAAGATTCAATATTAT------ 633
                             i i    i              v      i i      i ------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_163738556_    634 --CAGTTTTTCCTAACTTGATCTATAGACTCAAAACAATCACAA-CAAAA 680
                         --  i vi i  i  v        i   i    vi     v v -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_163738556_    681 TCCCAGCAAATTATTTTTTAAAGTATAGAAAAACTGATTTAAAAGTTTAT 730
                                vivi v    vi i i-  v  v  i     iiv   i  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_163738556_    731 ATGGAGAAACAAAAGACCCAGGAGGGC-------------------AGGA 761
                              i vi   ii       i vi  ------------------- i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_163738556_    762 ACAAAGTTGGAAGACTGATGCTACCTGACTTTAAGACTTACTATAAAGCT 811
                                    i    v ii  v  ii i  i  i        i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_163738556_    812 ATAGTTATAAAGATAGTGTAGTATTGGCAACAGAATAGACAAATAGATCA 861
                          i   v  v    i     i   i     vv  i       v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_163738556_    862 ATGGAACAGAAACAGACTAGGGAACCCAGAAATGGACCCACATAAATATA 911
                               i    ------ v i  ii        ii     i i vv   i
  L1M4_orf2#LINE/    300 ATGGAATAGAA------TTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_163738556_    912 GTCAACTGATCTCTTACAAGGAAGCAAAGGCAATACAATAGGGAAACACT 961
                              i    i iiv      iv  v   i v  v    i      v v 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_163738556_    962 ACTCTTTTCAACAAATGGTGCCCAAACAACTGGACATC-ATATGCAAAAC 1010
                          v                   ivii         i ? - i        -
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA- 442

  chr2_163738556_   1011 ATAAAATAAAATAAAATAAACTTAGAAACAGACCTTATACATTTCACAGA 1060
                         -------------i   i  v  i  vv vv    i i  ----  i v 
  L1M4_orf2#LINE/    443 -------------GAATGAAGTTGGACCCCTACCTCACAC----CATATA 475

  chr2_163738556_   1061 AAAAAGT---CTCAAAATGGATTACAGACCTAAATGTAAAACACAAAACT 1107
                         v    i ---            i ?              i vvi      
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_163738556_   1108 ATAAAACTCCTAAAAGATAACATAGGAGAAAATCGAGATGACCTTGGGTT 1157
                                  i  i    v        ? v     vvvi            
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_163738556_   1158 TAGCAATGACTAAACCCA-ATGTTTCAGACAAAAACATGATCTACGAA-G 1205
                         vi      ii v-- ii -  i vv  v-     i  ii v v  i  - 
  L1M4_orf2#LINE/    576 AGGCAATGGTTT--CTTAGATATGACAC-CAAAAGCACAAGCAACAAAAG 622

  chr2_163738556_   1206 AAAAATTA-ATAAGCTAGACTTCATTGACATTAAAAATTTTGGATCTGCA 1254
                              v  -    ii i        ii v        i   v vv  v  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_163738556_   1255 AAAATAACTG--AAGAGAATAAAAAGACAAGCCAAAGACTGA-AGAGAAT 1301
                           iivv   i--    i i i         v   v   v  i-   i   
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_163738556_   1302 ATTTGCAAAAGACATATTTGATAAAGGGCTGTTATTAAAAACGTACAAGG 1351
                                  vv i    i      i  i  vv   iv i  ii  i  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_163738556_   1352 GACTCTT 1358
                         i      
  L1M4_orf2#LINE/    773 AACTCTT 779

Transitions / transversions = 1.59 (113 / 71)
Gap_init rate = 0.02 (16 / 779), avg. gap size = 4.12 (66 / 16)  

 452 25.55 0.00 0.00  chr2_163738556_163740768.rev     1585  1721 (492)    L1M4_orf2#LINE/L1      772   908 (0)  

  chr2_163738556_   1585 GAACTCTTAAAACTCAATACTAGGAACACAAACAATACAATATACAAATA 1634
                                  v         v  ii  v     i  iv    v? v    i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_163738556_   1635 AGCTGAAGATCTTCACAGTCATCTCACTAAAAAAGACATACAGATAGCAA 1684
                         i  vi i   i vv i  v   i  v i   i    i     i  i  v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_163738556_   1685 ATAAGGCTATGAAAATATGCTCCACATTATATGTCAT 1721
                              vvi       v      v    i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (18 / 16)
Gap_init rate = 0.00 (0 / 137), avg. gap size = 0.00 (0 / 0)  


3201 24.72 2.22 1.55  chr2_163877722_163879804.rev      690  1591 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_163877722_    690 TGGAAATATATTCTGAGTTGATGAGTAGGAAGAATTAATATTGTTAAAAT 739
                               v    i iiv   v   ii v      v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_163877722_    740 GTCCATACTACTCAAAGCAATATGCAGATTTAACACAATCCCTATCAAAA 789
                          v v     v i    vii  v i      i   i               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_163877722_    790 TTCCCATGGCATTCTTTACAGAAATAGAAAAAAAAAG---AAAATTCACC 836
                          i  viiv  v  i   i       v  v  ivvi v---        iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_163877722_    837 TGAAACCACAAAAATTAAAAAAAATATATAGAATAGCTAAAACAATACCG 886
                           i  vii   iii----------- ivi        i        vii 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-----------ACCCAGAATAGCCAAAACAATCTTG 189

  chr2_163877722_    887 AGAAAGAA---CAAAGGTGAAGGCATCACACTTCTTGATTT-AAAATTAT 932
                          i      ---     v  i   vv         iii    -    i - 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-T 238

  chr2_163877722_    933 ATTTCAATACTATGATAACCAAAACAGTATGGTACTGGCATTAA-ACAGA 981
                          i v   vi   iii   i   i     i            v i- i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_163877722_    982 AACATAGACCTATGGAACAAAATAAAGAGCCCAGAAATAAGTCCAAACAT 1031
                         v i     i v      i i   vi    i          ii   v    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_163877722_   1032 ATATGGTCAACTAATTTTCAACAAGGATACCAACAGGAAATAATAGGGGA 1081
                         v         i i      i      i i    v vv vvi   i   i 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_163877722_   1082 AAAACAGTTTATTTCATAAATGGTGCTGGGAAAACTGGATTTCCACAAGC 1131
                          i  i   i v  iv i              v        v?     v  
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_163877722_   1132 AAAAGGATAAAATGAAACCCTCATCTTACACCATACACAAAAATCAACTT 1181
                              i  i  i vii    ii i  i        i        i    i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_163877722_   1182 GAAATGGATAAAATACCTAAAT-TAAGACCTGAAACCATGAAATTCCTAG 1230
                         i        v ? v        -     v  i    i  i   i  i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_163877722_   1231 AAAAGAACATAGGAAAAAAGCT--G-AACCTTGGCTTTGGCA-TGATTTT 1276
                           i i        ?iv   v  -- -i       v  v    -  i   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_163877722_   1277 TTTAAAATTTCACACCAAAAGCCCATACGACATAAGTGAAAATAAGTAAA 1326
                           -- i  v v           v  vi i   v   vi      ii    
  L1M4_orf2#LINE/    589 TT--AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_163877722_   1327 TGGGACTGCATCAAACTAAAAAGCTTCCACAAG-CAAAAGAAAC----AA 1371
                          v     v       v v    i   iiiiivv-    i  v  ----  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_163877722_   1372 CAAAATGAAAAAGCAATCTACA-ACTGGGA-AAACTACTTGCAATCCACA 1419
                         v   i      ii   i i   - v     -   v  i      vi  i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_163877722_   1420 TATCGGATAAGGGGTTAATATCCAAAATTCATAAAGAACAATTACAATTC 1469
                             v        ii vi      i   vi         vv      i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_163877722_   1470 AATAGCAGAAAAATAAATAACCTGATTAAAAAACGGGCAAAGAATCCGAA 1519
                             ii i   i i        ii   ?     i        i  ii   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_163877722_   1520 CAGATATTTCTCCAAAATATATATATATATGATCAACAGGTATATGGAAA 1569
                         i   i           iv v     i v   ii   i i i i   i   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_163877722_   1570 GGTGCTCAATATCACTAATCAT 1591
                          i       i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (143 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.27 (34 / 15)  


3583 18.11 3.22 8.68  chr2_163914407_163917077.rev     1247  2179 (492)    L1M4_orf2#LINE/L1       27   908 (0)  

  chr2_163914407_   1247 TAGAAGGCTTAAAATTTTTAAGATGGCAATACTACTCAAAACAAACTACA 1296
                          i    i     v   v                v i    vii v     
  L1M4_orf2#LINE/     27 TGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACA 76

  chr2_163914407_   1297 GATTCAATGCAATCCCAATCAAAATTCCAACAGCCTATTCTGCAGAAATG 1346
                                i        v        i   i v    v  i         v
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

  chr2_163914407_   1347 CAAATGCCAGTCCTCAAATTTATGTGGAATTAAAAAGGGCCCTGAAATGC 1396
                         v v v  iii    v     i  i     v iv  i  i   v   vv  
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr2_163914407_   1397 TAAAACAATCTTGAGTAAAA----------TGGAGGACTCATACTTTTTC 1436
                         i             iv  i ----------           i    iiiv
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_163914407_   1437 ATTTCAAAAATTACTTAAAAACTACAGTAATCACAATATTCTGGTACTAG 1486
                                  v     vv   i            vi i v v       i 
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_163914407_   1487 AATA----CAGACATATAAACAAATGGAATACAATTGAGAACTTCTTTGA 1532
                         v   ----i         i iv         v        ----------
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA---------- 316

  chr2_163914407_   1533 AAAGAAGTTGCTTCTTTGAAAAGATCAGCAAAGAAATGATTCAAATTACT 1582
                         --------------------------------------------------
  L1M4_orf2#LINE/    317 -------------------------------------------------- 316

  chr2_163914407_   1583 AAAGTAAGAAATTAAACATGCCCAGAAATTGAACCCATACATCTATGTAC 1632
                         ------------------- i        -i           i    vv 
  L1M4_orf2#LINE/    317 -------------------GTCCAGAAAT-AAACCCATACATTTATGGTC 346

  chr2_163914407_   1633 AATTAACTTTCTATAAGGGTTCCAAGACCATTCAGTGCAGGTAAGAATGG 1682
                             i i    v i      v             i  -i  v      i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAG 395

  chr2_163914407_   1683 TCTCTTCAATGAATGGTTCAGGGCCAACCAGATATTCACATGTAAAAGAA 1732
                            i     ii      v v   v    ii    ?i      i       
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_163914407_   1733 TGAAGTTAGAGCCCCACCTTACACCGTATACAAAAGCTAATTCAGAATGT 1782
                                i  v   i    i     i         ii   i   i    v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_163914407_   1783 ACTAGAGACCTAAATGCAAGAGCTAAAACTGTAGAATTTTTAGAAGAAAA 1832
                          ii ?           i             i  i  i i           
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_163914407_   1833 CACAGGTGTAAATCTTTATAAACTTGGATTTGGTAATGGATTCTTAGATA 1882
                           i   ?         ii i v     i  v  i     v          
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_163914407_   1883 TGACACCAAAAACATGAGCAACAACAAAAAA------TTAATTAGTATTC 1926
                                    i  ii        v i    ------ v    i vv   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_163914407_   1927 ATCAAAATTTAAAACTTCGGTACATCAAAAAATATTATCAAGAAAGTGAA 1976
                                  v       iv  i v     ii i i               
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_163914407_   1977 AACACAACCCATAGAATGGGAGAAAATACTTGGAAATCATATCTCTAATA 2026
                           v        i                i   v         v   i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_163914407_   2027 AGGTAATAGTATCCAATATATATGAAAAACTCTTACAACTCAACAGTAAA 2076
                            v v v       iv      i  i                i i    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_163914407_   2077 A-GACA-----CCCCATTAATAAATAGGTAAAGGACTC----AGATACTT 2116
                          -    -----   v   ? v    i  i      i i----   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_163914407_   2117 CTCTAAAAAAGATACGAAAACGGCCAACAAGTACACAAAAAGATGCATAA 2166
                            i   i      iiv   i      i   i   ii         vi  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_163914407_   2167 CGTTATTAATAAC 2179
                          i i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (105 / 60)
Gap_init rate = 0.01 (9 / 882), avg. gap size = 12.33 (111 / 9)  


2011 20.74 8.58 3.86  chr2_163948626_163950315.rev      501  1199 (491)    L1M4_orf2#LINE/L1      177   908 (0)  

  chr2_163948626_    501 CAAAATAACTTTTAAAAAGAA---CAAAGTTAGAAAAC-AACAATACCTG 546
                              i  ii  v        ---       i  ii  -v   v v  ii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_163948626_    547 GTTTAAAAACTTATTA--AAACCATA-----TAAGACAGTGTAGTACTGG 589
                         i   v        i  --  i i i -----i          i       
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_163948626_    590 CACAAGGAAAGGAAGATAGAT-AATGCAACAGAATTTAGAGTTTACAAAT 638
                           i     v  iv v      -    v  i      v     ii v    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_163948626_    639 AAA--------------GAGAACT------CAATAAAGATGACAAAAAGA 668
                            -------------- vv  i ------ i i  i i  v   i vv 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_163948626_    669 GTCAATGGGAAAAGGATAGCCTTTTAAAAAAGTAGTGCTGGGACAATTGG 718
                         v        i    i    i     v  v  i i            i   
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_163948626_    719 ATATCCACATGTGTTAATTAATAACTTAAAAAAACTTTGACTCCT-TCTA 767
                            ?       i---  --  v  -- i  i----  v   i   -i  v
  L1M4_orf2#LINE/    427 ATAKCCACATGC---AA--AAGAA--TGAAG----TTGGACCCCTACCTC 465

  chr2_163948626_    768 ACACCA----CCACAATTAATTAAAAATAGACTTCAGATCTAAATG---- 809
                               ---- v v      i v     i  iiv?   i       ----
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_163948626_    810 AGTAAAAACTATAAAACCTCTAAAAAAATAGAAAAAAATAT-GGAACAAA 858
                           iv             -   -------     i    i  -  ?ii   
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAAC-TCT-------TAGAAGAAAACATAGGNGTAAA 557

  chr2_163948626_    859 CACCCTCATAACTTTGGGTTATGCA-----TCCTTAGATATG-CA--AAA 900
                         i-- i  i i  i        v   ----- i          -  --   
  L1M4_orf2#LINE/    558 T--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_163948626_    901 AGCATGATCCATAATAAAATAAAATAATGATATATTGAAAT-CACCAAAG 949
                             ii v v i  v i  -      --    v    i v -  i    i
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAA-AAAATA--GATAAATTGGACTTCATCAAAA 652

  chr2_163948626_    950 TTCAAAACT---GTGTTTCAAAAAACATGATTAAGAAAATAAAAAGACAA 996
                           v      ---   i      ii   iv  i      i i         
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_163948626_    997 GTCACAGACCGGGAGATAAT-TTGGCAAGTCATGTGCCTGATAAAGTAAT 1045
                         vi      vi      v   -  v    i    i ii       i v v 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_163948626_   1046 TGTATCTAGAATATGTAAAGAACTCTTACAACTCAATTAAAGGAAGACAT 1095
                               i       i                      v v ii      v
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_163948626_   1096 ACAACACAATTTTTAAAA---GGCAAAATATATTAATAGAAATTCCACCA 1142
                          i   v     ?--    ---      iv  v v      v   i v   
  L1M4_orf2#LINE/    803 ATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_163948626_   1143 AAGAAAACATGTGAATAGC--ATACATTACATCAAAAGATGCTCAACATC 1190
                              i i  iii   i  --   - vi    v                 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATA-AGCACATGAAAAGATGCTCAACATC 899

  chr2_163948626_   1191 TTTAGTCAT 1199
                         v????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.66 (88 / 53)
Gap_init rate = 0.04 (30 / 732), avg. gap size = 2.90 (87 / 30)  


2194 24.16 15.12 2.60  chr2_164042764_164046879.rev     2819  3625 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164042764_   2819 TGGAGAGATATTCCATTTTCATGGATAGAAAAAC-----ATTGTCAAAAT 2863
                             i      i    v         v i  i  -----     i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_164042764_   2864 GTCATTGTTTTTTCAACATCATCTGTAGATTCAATGTAATCTCAATAAAA 2913
                          v  v ii iii-   vv v    ii        i i    i v  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_164042764_   2914 ATTTCAACAAGTCATTGAGTAACAAGTCATTCTGTGGATATTAACAAACT 2963
                           ii  i v- i -  -------------  i  ii  v   i    i  
  L1M4_orf2#LINE/    100 ATCCCAGCT-GCC-TT-------------TTTTGCAGAAATTGACAAGCT 134

  chr2_164042764_   2964 GATTCTAATGTTTATTCAGATAAGCAAAAGACTCAGAATAGCCAACACAA 3013
                            i    vi  i  vii  v v    ii   i            v    
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_164042764_   3014 TATTAAAGGAAAAGAGCAGAGTCAGAGGATTTCCACTGCTTCACTTCAAA 3063
                          v  i  ii i    i  i   ii     i iv    v iiv i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_164042764_   3064 AC--AATATAAAGCTACAGAAATCAAGACAGTGTGG------CAAAAGGG 3105
                           -- v  i          v                ------  v    i
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_164042764_   3106 AAGACAAATAGATAAATTGAACAGAATGGAG----CAAA----------- 3140
                         v     v      v   v   i     v   ----  i -----------
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_164042764_   3141 -----TATAGT--------------------------------------- 3146
                         -----   i  ---------------------------------------
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_164042764_   3147 -------------TTTTCAGCAAATAGTGCTGGAACAACTGGGCATCCAC 3183
                         -------------      i     i       i        ii ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_164042764_   3184 ATGCAAGAAAAAAATGAATCTAGATTCAGACTTTATACTCTTTACAACAA 3233
                               ---  i      vi i  ii vv  i i i  iv v     v  
  L1M4_orf2#LINE/    435 ATGCAA---AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_164042764_   3234 TTAACTCAAAAGAGACCACAGAACTACACATAA-AGTGAAAAACTATAAA 3282
                                    vi  i  ?   v   v ii   -  iv    -       
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAA 530

  chr2_164042764_   3283 ACTCTTAGAAGATATCATTGGAAAAAAGTCTGATGCCCTTGAATATGGCA 3332
                                     v v   v  ?iv   vii vi  v     ii vv    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_164042764_   3333 ATGCCTTTTTATATTGAACACCAAAGTCTCGACCCAGGAAATAATAAATT 3382
                            vi  i   v  vvi        iv v i v v vi   v  v    v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_164042764_   3383 GATAA-CTAAACTTTATTAAAATAAAAAACTTATGCTCTGTAAAAGACAC 3431
                              -i ii    i  i     v        v  iv  vi   i     
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_164042764_   3432 TGCCAAGAGAATGAAAAGACAAGTCACC--ATGGGGAGAATATATTTGCA 3479
                          ii     i i           vi   v--     -    v         
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGG-AGAAAATATTTGCA 729

  chr2_164042764_   3480 AAAGATATATCCGATAAAGGACTGTTATTTAAAATATACAG--------- 3520
                           vv       i     i     vv   ii i      i i---------
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_164042764_   3521 ------TAACAATAAGAAAACTAGCAACCCAATT---------ACAAA-- 3553
                         ------i  i     i  i  v ii         ---------i    --
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_164042764_   3554 ------ACAGACACCTCAGTGAAGAAGGTATACAGAAGGCCAATAAGCAT 3597
                         ------ i     ii  vvii      i      i v            i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_164042764_   3598 ATCAAAAGATGCTCAACAT-ATGTCACTA 3625
                           v                - ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (117 / 75)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 7.15 (143 / 20)  


2651 27.91 2.47 0.67  chr2_164177009_164185619      933  1824 (6787)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164177009_    933 TGGAAAAACATTCCATGCTCATAGATAGAAATAACCAACACCGTGAAAAT 982
                               i i  i     i    i   v i  v vii  i ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_164177009_    983 TGCCATACTGCCCAAAGTAATTTGTAGATTCAATGCTATTACCATTAAAC 1032
                         v  v     v      v i  i ii        i  v  iv i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_164177009_   1033 TACCATTGACAGTCTTCATAGAATTAGAAAACACT-ACTTTAGAATTCAT 1081
                          v   vivi vv i  iii    v v  v  -i  - iii  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_164177009_   1082 GTAGAACCAAAAAAAGAACCT-GTATAGCCAAGACAATCCTAAA------ 1124
                         i i   -- viv  i i   i- v        i      i i  ------
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_164177009_   1125 ---CAAAGCTTGAGGCATCAGGCTACCCGACTTCAAACTGTACTACAAGC 1171
                         ---     i v    vv   vi  v   i i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_164177009_   1172 CTACAGTAACCAAAACAGCATGATACTGGTATAAAAACAGACACATAGAC 1221
                                  i   i    ii  i      i    ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_164177009_   1222 CAATGCAACAGAATAGAGATCTCAGAAATAAGACCACACATCTACAACCA 1271
                              v  i     v    vii         iv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_164177009_   1272 TCTGATCTTTGACCCACCTGACAAAAACAAGCAATGGGAAAATGATTCCC 1321
                         vi    i  i   vvivv  v   i v  vv       i   vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_164177009_   1322 TATTTAATAAACGATGCTGGTAAAACTGGCTAGCCATACGCAGAACATTG 1371
                          v  i  i   i i      v v      v  ?   i i   i  v v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_164177009_   1372 AAACTGGACCATTCCCTTACACCTTATACAAAATTTAACTCAAGATGGAT 1421
                           ii      vi v   i     v         v         i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_164177009_   1422 TAAAGACTTAAATTTAAAACAGAAAAGTATAAAAACCCTAGAAGAAAATC 1471
                         i ?    i     v   i vvv    v       vi i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_164177009_   1472 TAGGCA-ATACCATTCAGGATATGGGCACAGGTAAAGGTTTCAT-GATGA 1519
                             ?i- v i -   iv  iv v  vvi   i  v      v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr2_164177009_   1520 AAATGTCAAAAGCAACTGCAACAAAAGGAAGAATTGACAAATGGGATCTA 1569
                         vi iii        vvv          i  i   v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_164177009_   1570 ATTACA-TTAAATAGCTTCTGCACAGTAAAAGAAACGATCGTCAGAGTGA 1618
                           i v -     - i   i  ii vvi   i  v  v   ivv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_164177009_   1619 ACAGACATTCTACAGAATGGGAGAACATTTTTGCAATCTATACAACTGAC 1668
                          v     vi i              v  v       vii   i v    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_164177009_   1669 AAAGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAA-AA 1717
                           i  v  vi          v  i  i     ivv    v iv i  -  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_164177009_   1718 AAAAAAAAA-AA---AATTTAAAAGTGGGCAAAGGACATGAAGAGACACT 1763
                            i v   -  ---    ?    i           iv    v     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_164177009_   1764 TCTC--AAGAAGACATTTATGTGACCAA-AAACATATGAAAAAAAGCTCA 1810
                             --       i  vi vi  i    -  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_164177009_   1811 ACATCACTGATCAT 1824
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.75 (28 / 16)  

2914 27.87 0.77 1.53  chr2_164177009_164185619     7205  8119 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164177009_   7205 TGGAAAAATATTCCAAGTTCATGGAGAGAAAGAATTAATATCTTGAAAAT 7254
                               i    i   v         vv i    v       iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_164177009_   7255 GGTCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 7304
                           iv     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_164177009_   7305 TACCATTGACTTTCTTCACAGAATTAGAGCAAACT-ACTTTAAATTTCAT 7353
                          v   vivi i  i  ii     v v  -   i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr2_164177009_   7354 ATGGAATCAAAAAAGAGTCCATATAGCCAAGACAATCCTAAACAAAAAGA 7403
                               viiv  ii  vi viv        i      i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_164177009_   7404 ACAAAGCTGGAAGCATCATGCTACCTGACTTCAAACTGTACTACAAGGCT 7453
                               i    i vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_164177009_   7454 ACAGTAACCAAAACAGGACTGTTTTGGTACCAGTACTGGTACCAAAACAG 7503
                                i   i    ---   ---------i       i iv ii i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAG---TGT---------GGTACTGGCATAAGGATAG 287

  chr2_164177009_   7504 ATATATAGAACAATGAAACCGAACAAAGGCCTCAGAAATAATGCCACACA 7553
                          i       v     i  iv   ivi  ivii         vv   i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_164177009_   7554 TCTACAACCATCTGATCTTTGACAAACCTGATAGAAACAAGCAATGGGGA 7603
                          i  iiii  vi    i  i     ivv  vi ii v  vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_164177009_   7604 AAGGATTCCCTATTTAATAAATGGTGTTGAGAAAACTGGCTAGCCATGTG 7653
                            i  vvi  v  i  i        i  i  v      v  ?   ii  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_164177009_   7654 CAGAAAACTGAAACTGGACCCCTTCCTTAGACCTTATACAAAAATTAACT 7703
                           i  i v    ii         v   i v   v                
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_164177009_   7704 CAAGATGGATTAAAGACTAAAACCTAAGACCTATAGCCATAAAAACCCTA 7753
                            i      i ?    iv   iv     v   v i i      vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_164177009_   7754 AAAGAAAAGCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAAGACT 7802
                         i       vv    ?i- v   -   iv   v v  vv i     v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_164177009_   7803 TCATGACTAAAATACCAAAAGCAATGGCATCAAAAACCAAAATTGACAAA 7852
                           v iiv  vi i          vvi   v     ivv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_164177009_   7853 TGGGATCTGATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAT 7902
                          v   ii v  i   v v  i i   i  ii vv    i  v       v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_164177009_   7903 CAGAGTGAACAGGCAACCTCAAGAATGGGAGAAAAATTTTGCAATCTATC 7952
                         v i      v  i     ivv              vv       vii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_164177009_   7953 CACTTGTAAAAGGGCTAATATCCAGAATCTACAAAGAACTTCAACAAATT 8002
                         i ii  vv  i  i  vi          v  i        iiv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_164177009_   8003 CACAAGAAAAAAACAA----CCCA-TCAAAAAGTGAGTGAAGGATATGAA 8047
                         v i  v     i    ----    - i?    i  i ii      v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_164177009_   8048 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAGAAAAATATGAAAA 8097
                         i     i     v        i  vi viii     v  iv i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_164177009_   8098 AAAGCTCATCATCACTGGTCAT 8119
                         i v     v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (145 / 106)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.62 (21 / 8)  


1442 21.29 5.88 0.56  chr2_164224252_164226756.rev      496   852 (1653)    L1M4_orf2#LINE/L1      114   489 (419)  

  chr2_164224252_    496 TTTTA-AGAAATTGGCAAGCTGATCCTAAA-TTTATGAGGAAATTCAAAT 543
                             i-        i               -  i  iv      v   iv
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_164224252_    544 GACCTAGAATATCCAAAAACTATTTTGAGAAAGAGAATCAAGGTTGGAGG 593
                             i      v      - v  i    i     ii v   i        
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_164224252_    594 CCTTATACTACCTGATTTCAAGCCTTATTATAAAGCTACATTAATCAAGA 643
                         v  i i   v  ii       iv    i  i         v         
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_164224252_    644 CAG--------------GAAGAT---CA-ATGAAAAAATGGAACAGAATT 675
                            --------------i i   ---  -  ii vv       i      
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_164224252_    676 GAGAGTCCAGAAATAAACCCTTATTTGTACATTTAATTGGTTTTCAACAA 725
                                             v  iv v  iiv i     i     i    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_164224252_    726 AGTTGAAAAGGCAATTTAATGGAAAACTAAAAGTCTTTTTAAGATATGGT 775
                         i v  vv   i v   i     ii  vv  v        i  v v     
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_164224252_    776 TCTAGGAAAATTGAATATCCATATGCAAAATGAATGAACTTAGATCATTA 825
                         v  i   v  i  i   ?   i        -       v  i  i vi  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAAGTTGGACCCCTA 461

  chr2_164224252_    826 CTTCACACAATACA-AAAAATTAATTCA 852
                          i      v   i -         i   
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCA 489

Transitions / transversions = 1.50 (45 / 30)
Gap_init rate = 0.02 (8 / 376), avg. gap size = 2.88 (23 / 8)  

 870 23.85 13.76 0.61  chr2_164224252_164226756.rev     1121  1447 (1058)    L1M4_orf2#LINE/L1      454   823 (85)  

  chr2_164224252_   1121 GACTCC-ATCTCAAA--AAAAAAAAAAATTAACTCAAAATAAATCATAGA 1167
                            i  - i    v -- v v v                 ii    ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_164224252_   1168 CCTAAATGTAATAGCTAAAACTATAAAAGTTTTAGAAGAAATCATAGGAA 1217
                                    v                v i          v      ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_164224252_   1218 -AAATATTTTATGA----AATTTAAGTAATGATTTCCTGGATAAACCACT 1262
                         -    -i  ii   ----iiv   i i    i    i i    viv   i
  L1M4_orf2#LINE/    554 TAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_164224252_   1263 CCATGCAAGATTTATAACAGAAAAAAAATGATGAATTGGGCTTCATCAAA 1312
                         vv v   vi viv i  v        v -   i      i          
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTCATCAAA 651

  chr2_164224252_   1313 TTTAAAA-CTTTTACTCTTTAGAAGACACCCTTAAGAATG-AAAAAGATG 1360
                         v      -     iiv   i i i     iv i     v -i      ii
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_164224252_   1361 AGTT-CAGGCTAGGAAAAAA-ATTTTCAATTAATGTATCTAACATAGG-- 1406
                          vii-   iv i   i    -    v   v v  i     i i vi  --
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_164224252_   1407 ------------------------CCTTACAACTCAGTAATAA---GACA 1429
                         ------------------------i           i      ---    
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_164224252_   1430 A----CCTAATTAAAGAATAGG 1447
                          ----  i    ?  i   i  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGG 823

Transitions / transversions = 1.68 (47 / 28)
Gap_init rate = 0.04 (13 / 370), avg. gap size = 3.62 (47 / 13)  

 458 18.68 0.00 0.00  chr2_164224252_164226756.rev     1924  2014 (491)    L1M4_orf2#LINE/L1      818   908 (0)  

  chr2_164224252_   1924 AATAGAGAAAAGATTTGAATGGATTTTTCTCCAAAGAAGATCTATGAATG 1973
                            i iv   i         i  iv                v  ii    
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_164224252_   1974 GCTAATAAGTCCATAGAAAGATGCTTAACATCTGTAGTCAT 2014
                           i      iv   ii         i      v????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.00 (0 / 0)  


2473 18.20 2.36 0.00  chr2_164324266_164326856      653  1119 (1472)    L1M4_orf2#LINE/L1        2   479 (429)  

  chr2_164324266_    653 GAAAAAATATCTCATGCTCCTGGATTGAAAGACTCAATATTGTTAAGATG 702
                          i   i     i    i  v       i      i               
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_164324266_    703 GCAATAATCTTCAAATTAATGTGTAGATTCAGTGCAATCCCTATCAGAAT 752
                               v  ii      i  v ii       ii             i   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_164324266_    753 CCCAAATTACTTATTTGTAGAAATTGATACACTGATTCTAAAATTCATAC 802
                             iv vv   v    i         i vi     i            i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_164324266_    803 GAAATTGCCAGGG-CCCAAAATAGTAAAAACAATCTTATTTAAAAAAAGC 851
                          i  v   v    -    i     iv           ivvv  i  i i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_164324266_    852 A-----GGAGGAGTCACAGTTCTCAATTTCAAAACTTACTACAAAGCAAC 896
                          -----      v     v   i                        v  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_164324266_    897 AGTGATCAAGTCAGGGTGATGCTGGCATAAGGACAGACCTATAGATCAAT 946
                            i      v   v   i i            i    v           
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_164324266_    947 GGAATAGAACTGAGAGTCTAGAAATAAATGCATG--TTTATGGGCAACTG 994
                                  i        i         iv   i--       v   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_164324266_    995 ATTTTCTACCAGAACATGAAGAC--TTCAATCGAGCAAAAACAGTCTTTT 1042
                               v  v  iiiiiv     --      v i v  i  i        
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_164324266_   1043 CAACAAATGGTGATAGGACAAGTAGGTAGCAACATACAAAAGAACGAAGT 1092
                                     v i      v i i  ? v    i        i     
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_164324266_   1093 TGGACTCC-ACTTTACACAATATACAAA 1119
                              i  -  i i    v         
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAA 479

Transitions / transversions = 1.71 (53 / 31)
Gap_init rate = 0.01 (5 / 478), avg. gap size = 2.20 (11 / 5)  

1684 14.43 10.45 2.99  chr2_164324266_164326856     1704  2105 (486)    L1M4_orf2#LINE/L1      477   908 (0)  

  chr2_164324266_   1704 AAAAA--AAGTCAGAATGGATCACAAACCTAAACGTGAGACCTAAACCTA 1751
                              --  v   i         ? i       i  i   v     v   
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_164324266_   1752 -AAGGTAGGCGCTTCTCTTAGAAGAAAACACAGG---------------- 1784
                         -  ii---------                i   ----------------
  L1M4_orf2#LINE/    527 TAAAA---------CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_164324266_   1785 ----GATTTGGCGAAGAATTCTTAGATATGAC-CCAAAAGCATGAGCACC 1829
                         ---- i  v   i v iv              -         ii    v 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_164324266_   1830 AAAAGAAAAA-TAGATAAATTAGACTTTACTGAAATTAAAAACGTTT-TG 1877
                                   -          i     i iii           v   -  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_164324266_   1878 CTTCAAATGA----------AAGGTGGAAAGACAACTCACAA-----GAG 1912
                                v  ----------  i   i         i    i-----   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_164324266_   1913 AAAATATTTACAAATCATATATCTGATTAAGGACTTGTATTTAGAATATA 1962
                                  i                 v i          ii        
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_164324266_   1963 TAAAGATTACTTAAAGCTGAATTTTAAAAAGACAAATACCCCAATTAAAC 2012
                               viv    v i  v   vv              v       ?  v
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_164324266_   2013 AATTGGCAT-TAATTTGAATAGACATTTCTCCAAGGAAGACATCTAAATA 2061
                            v    v-vi                      i     i  vi    i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_164324266_   2062 GCCAATAAGCACATGAAAAGATGCTGGACAACCTTAGTCATCAT 2105
                                                  ---    v i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCT---CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (33 / 23)
Gap_init rate = 0.03 (11 / 432), avg. gap size = 4.91 (54 / 11)  


3489 23.58 2.79 1.34  chr2_164503466_164507879.rev     3028  3922 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164503466_   3028 TGAAAAAATATTCCATGTTTCTGGATTGGAAGAATCAATATTGTTAAAAT 3077
                           i   i    i       iv            v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_164503466_   3078 GTCCATACTATCAAAAGCAATCTACAGATTCAATGCAATCTTTATCAAAA 3127
                          v v     vi v   vii              i      ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_164503466_   3128 TACCAATGACATTCTTCACAGATATAGAAAAAACAATCTTAAAATGCATA 3177
                          v   iivi v  i  ii    v  v  v  ivii   i      v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_164503466_   3178 TGGAACCACAAAAGACCCAAA---GCTAA--------TAAGCAAAAAGAA 3216
                              vii   ii      i ---  i  -------- i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_164503466_   3217 CAAAACTAGAGGAATCACATTACTTTACTTCAAGTTATACTACAGAGCTA 3266
                             ii i     v     i v iiv i     iviv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_164503466_   3267 TTGTAACCATGACAGTGTGATGCTGGCATAAAAACAGACACACAGACCAT 3316
                         iv    i  v         i i         ii i     i i   i  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_164503466_   3317 TGAAACAGAATAGAGAACCCAGAAACAAATCTACACACTTAGAGTGGACT 3366
                           i  i     v    ii       i   i i i   i   vi  vi i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_164503466_   3367 CATTTTTGACAAAAGTGCCAGGAACATACACTGGGGAAAAGGCAGTCTCT 3416
                         v     i     ii      i  v   v  v        iiii     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_164503466_   3417 CCAATAAATGGTGCTGGGAAAACTGGATATTCATAGGCAGAAGAATGAAA 3466
                         i   i              v         ?i  i v   i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_164503466_   3467 TTAGACTCCTGTCTCTTGCCATATATAAAAA--AAAGCAAAAAAAAATGG 3514
                           i   i   ii   vii       i     --  vv     -----   
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-----TGG 495

  chr2_164503466_   3515 ATTAAAGACTTAAATATAAGACCTCAGACTATAAAACTACTACAAGAAAA 3564
                           i ?    i     i     v  v i           vi  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_164503466_   3565 CATTGGGGAAAATCTACAGGACTTTGGTCTTGGCAAAGATTTCTTGAGCA 3614
                            v  ? v      v iv   i    vi v     v i      -  vv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGAT 594

  chr2_164503466_   3615 ATAACCCCA----------CAATCAAAGTAAAAATAAACAAATGGGATCA 3654
                           i  v   ----------   iv    v       i i    v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_164503466_   3655 CATTGAA-TTAAAAAGCTTCTGCACAGCAAAGGATACCATCAACAAAATA 3703
                            ii  -       -   i  ii vv       i  i     v   i i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_164503466_   3704 AAGAGATAACCCACAGAATGGGAGAAAATATTGACAAACTGTCCATCTGA 3753
                           i   i                         vi    iii vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_164503466_   3754 CATAGGATTAATTAATAACCAGAATACATAAAGAGTTCAAACAACTCTAT 3803
                         i vi   i vi --  --        i       ii  vv       v  
  L1M4_orf2#LINE/    744 TAAGGGACTTGT--AT--CCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_164503466_   3804 AGGAAAAA-ACAGAGTAATCTGATCAATAAATGGGTAAAAGATTTGAATA 3852
                          iv     -   i -   i ii  i? v       i   i          
  L1M4_orf2#LINE/    790 AATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_164503466_   3853 GACATTTCTCAAAAGAAGACATACAAATGCCAAAGAGGCATATGAAAATG 3902
                                   v        i         v v  v i   i       vi
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_164503466_   3903 TGCTCAACATCACTGACCAT 3922
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (135 / 72)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.08 (37 / 12)  


 937 26.48 7.80 8.02  chr2_164545769_164548158.rev      989  1898 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164545769_    989 TAGAAA-ATA--CCATCTTCGTGAATTGGAGTGCTACTAGATTCAGTTTT 1035
                          i    -   --    v   i  i      --------   i i i v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGA--------AGACTTAATATT 42

  chr2_164545769_   1036 GTAAAAATGTCAGTTTTCCCTAA-TTGATCTATTTATTTAATATAATTGC 1084
                           v  i   v  i vi    i  -        ivv   i  iii   iv 
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chr2_164545769_   1085 AATCAAAATTTCAGAAGGCTTTTGTTTTCATAAA-----AAGTCAATTCA 1129
                         v        ii   vv v     --  v  v   -----   iii  i v
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTT--TTGCAGAAATTGACAAGCTGATCCT 140

  chr2_164545769_   1130 AAAATATATATGAAAATTC-------CAAGAATATTCAAGACAAACTAGA 1172
                              vi     i    v ------- v      vi   i    v  v  
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_164545769_   1173 AGAAGGAGTACAATGTTAGGGGATGTTCACT-ACCAGTTATAAAGATACA 1221
                          i   i  v    v   i i   iviv    -v   i  vi   - ivi 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-ACTTA 239

  chr2_164545769_   1222 TTGCAA-GCTAGAGTAATTAAAACAGT-TAGTATTGCTGAAAAAGATAGA 1269
                         i i   -    v      i  i     - i   i  vi- v  i      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGA 288

  chr2_164545769_   1270 CAAAAAAAATCAATAAAACAAAACAGAAAGTATAGAAACAGACCT---CC 1316
                           v v i -     ii  i i  iv  i   vi     i i   i--- v
  L1M4_orf2#LINE/    289 CATATAGA-TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_164545769_   1317 TATATGGCGAATTGATTTACATAAGTAGCATTGATTACAAAAGTAGCATG 1366
                          v     iv         ------------ i  ---   ii  iv  v 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTT------------TCGA---CAAGGGTGCCAAG 372

  chr2_164545769_   1367 GCAGTGCA--GGGCATAAAAGGTTATATTTTTTAGGAAATGATGATGGAT 1414
                         i vi v  --   ---i    iv  vvi    i iv     i  v   iv
  L1M4_orf2#LINE/    373 ACCATTCAATGGG---GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_164545769_   1415 CAATTAGATGTGCATATGGAAAAAAGTGAGTCTT--CACCTACTTCATAC 1462
                            i i   i?v  i   v    i i   ivi v-- v     i   i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_164545769_   1463 TG-------AAGT--ATTCCAACTATTTTGTAGATCTAA-TGTGAAAAGT 1502
                         ii-------  i -- i  v  v ivv ii?   i    -   -  i  i
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGC 518

  chr2_164545769_   1503 TTAAAAAAAAAATCTCCTTAGATGGAAGAATGTAAACAGGACAGCAAATG 1552
                          v   vv v   v   -     ----    ----    viiv? i    v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTC-TTAGA----AGAA----AACATAGGNGTAAATC 559

  chr2_164545769_   1553 --CATGAACCATAAATTAAA-AATTGTTAAATCTAATTATATTACAATTA 1599
                         -- i   -  v iii   ii-   v   ---   v v-    v   -ii 
  L1M4_orf2#LINE/    560 TTCGTGA-CCTTGGGTTAGGCAATGGTT---TCTTAG-ATATGACA-CCA 603

  chr2_164545769_   1600 AAGGTTTATTTTTAATCAATAGGAAAAATTAAA-AGAGTAAAAAGGCAAA 1648
                           i i-- i----  v   i ii i   --   -   -    vv  - vv
  L1M4_orf2#LINE/    604 AAAGC--AC----AAGCAACAAAAGAAA--AAATAGA-TAAATTGG-ACT 643

  chr2_164545769_   1649 TC--CAAGAGTAGGAAAA------TACTTCAGA--------TTGAGAAAG 1682
                           --   i v  --    ------ i     i -------- ii      
  L1M4_orf2#LINE/    644 TCATCAAAATTA--AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_164545769_   1683 AGAGAGAGAGA---CACAGTGGTTAGGAGAGAGAGAGAGAGATAGACATA 1729
                         v  i -   v ---     vi-- i     i ----- v vv iv v  v
  L1M4_orf2#LINE/    692 TGAAA-AGACAACCCACAGAA--TGGGAGAAA-----ATATTTGCAAATC 733

  chr2_164545769_   1730 AGTGTATCTCACAATGCATTTGTATACAGAATACATAAAGAACTTCTATA 1779
                          - i     v i  v v i      v       i          ii  i 
  L1M4_orf2#LINE/    734 A-TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_164545769_   1780 AGTCAATAAGAAAGTAGA-----AACCCAGTT-AAAAATGG--AAAAACT 1821
                          v       v   i-   -----      i  -        --   iiv 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_164545769_   1822 TGCTGATTAGGCACTGATCAAAAGA-GAAAAACTAAAATG-CTACCAAAC 1869
                          --   v   i  i vv  v     -  v v  --     - i vi  i 
  L1M4_orf2#LINE/    832 T--TGAATAGACATTTCTCCAAAGAAGATATAC--AAATGGCCAATAAGC 877

  chr2_164545769_   1870 AC--GACAATGTGCTTCACCTCATTAGTCAA 1898
                           --  v  vi    iv  v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (135 / 103)
Gap_init rate = 0.06 (56 / 908), avg. gap size = 2.57 (144 / 56)  


2608 26.89 2.52 2.85  chr2_164581456_164586152     2292  3202 (1495)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164581456_   2292 TAGAAAAACCTTTCATGCTCCTGGATTGGAA----CAAAACAATTAAAAT 2337
                          i    i iv ii    i  v          ----i  v ivi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_164581456_   2338 GACCATACTGTCCAAAGAAATGAGTAGATTCAATGCAATCCCTTTTAAAA 2387
                          i v     vi     vvi  vvii        i         v i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_164581456_   2388 ---CA-CTGTTATTTTTCACA-AAATTAGGGAAAAA--AATCCTAAAATT 2430
                         ---  -   ii-     ii  -     ---  v  i--i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATT 146

  chr2_164581456_   2431 CACATGGAACCAAAAAAGAGCCCAAACATCCAAAGCAATCCTGAGG--GG 2478
                           i      viiv  ii  v  vi  i v     i     i   ii-- i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_164581456_   2479 TGAA-AAAGCTGGAGGTGTGACATTACCTGACTG-AAAATTATATTACAA 2526
                         v   -    i      vv v   i v  ii i v-    i -  i     
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chr2_164581456_   2527 AGCTATTATAACCAAAACAGAATTATAAGAGTATTAAAACAGACATAGAG 2576
                              ivi   i   i    vi vi  vvi i  v ii i       v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_164581456_   2577 ATCAATGGAACAGAATAGAAAAGAATAGAGAACCCAGAAATAAAGCTACA 2626
                                   i     --------- -    ii           v i i 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAAT---------T-GAGAGTCCAGAAATAAACCCATA 335

  chr2_164581456_   2627 TATTTACAGACAACTGATATTTGACAAAGCCAACAAGAACATACATTGGG 2676
                         i     ii v   i    v  i     i viiv     v   v  v    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_164581456_   2677 AAACGAACACCCTTTTCAATGAATAGTACTGGGGAAATTGGATAGCCATA 2726
                         i  v   i vi        ii   i  i     iv  i      ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_164581456_   2727 TGCAGAAGAATCAATCTGAACCTCGGTCTCCCACCATACACAAAGATTAA 2776
                             i      v  vi  i   i vii   v       i     i     
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_164581456_   2777 TTCAAGGTGGATTGATCAATTGACC-AAACACTATAAACTATATAGAAAC 2825
                         i    ii     i----- ?v    -   ii-  vi i   -----    
  L1M4_orf2#LINE/    486 CTCAAAATGGATC-----AWAGACCTAAATG-TAAGAGCTA-----AAAC 524

  chr2_164581456_   2826 TATAAAAATATGAGAAGGAAACCCATGGA-ACCTCTTCTGGACAATAGCC 2874
                                v v v     i    vi v ?i- vv     vv   vv i vi
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_164581456_   2875 TAGGCAAAGAATTTATGACTAAGACCTCAAAAGTAGAGGCAACAAAAACA 2924
                                v iv  iv iiv  v   vi      i v i         iv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_164581456_   2925 AAAATAGATAAATGAGACTT----ACACTTAAAAGTTTCTACACAGCAAA 2970
                                      vi     ---- v v      ii  i iii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_164581456_   2971 AGAAATAATCAACAGTGCGAAGAGGCAACCTGTTGAATGGAAGACAATAT 3020
                         i  v iv     v iv i   i  i     iiiv      i   v     
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_164581456_   3021 GTGCAAACTATTCATCTATTAGGGAACTCATATCTAGAATATGCAAGGAA 3070
                         v      ii  vi    iv  i  i   ii    i       ii  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_164581456_   3071 CTCAAACAACTCAACAACAAGAAAA-AAATAATCTTATTAAAAAATGAAC 3119
                            vv         i  i  i  i -      i iv   ?       ii 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_164581456_   3120 AAAGGACATGAACAGATATTTTCCAAAAGAAAATATACAAATGGCCAATT 3169
                               iv    i   i    ii v      i                 v
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_164581456_   3170 AGTG-ATGAAAAAAAGTTAAACATCACTAATTGT 3202
                           ii-       i v i v       ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (152 / 89)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.33 (49 / 21)  

2052 23.60 7.09 3.41  chr2_164581456_164586152     3473  4205 (492)    L1M4_orf2#LINE/L1      149   908 (0)  

  chr2_164581456_   3473 TATAAACATA-AAAGGATGTAAAATAGACGAAACATCTTTGAAAAAGAA- 3520
                            ii v  i-  i   ivi i     v i     vii           -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_164581456_   3521 --CAAAGTTGG--GAATCAAACACTGCCTGATTTCAAAGCTTATTGTAAA 3566
                         --         --  v   --    v  ii        i    i ii   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCA--CACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_164581456_   3567 GCTACATCAATCAAGATAATGCAGTATTGATGTAAAGATAG---T-TAGA 3612
                               vi        i i  ii   i  iii   i     --- -    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_164581456_   3613 TTGGTAGA-CAAAA--GAGAGTACAGCAACAGATCCACATATGTACGGTC 3659
                          iii i  -i i  --      v   v  i i i   i i  v  i    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_164581456_   3660 AATTGTTTTATTATAAATATGCCAAGGCATTTCAATGGGGAAA--ATAAT 3707
                              v   viv i  ivi       i vv             --   i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_164581456_   3708 CTTCTTA-CAAATTATGCTAGGATCATTGGATAGTCCTTTTTAAAAAATA 3756
                            i i -     vi    i   iv i      ?i viv vi    i - 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-A 445

  chr2_164581456_   3757 TGTACCTTGACCTTTACTTCACACCATTTATAAAAATTAACTCAAA-TGG 3805
                           v vi v    ii   i         v  i               -   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_164581456_   3806 ATCAGAGAATAAAATTTAAGAACTAAAACTACAGG-CTTCCAGAAGAACT 3854
                             ?   viv    v     i         i ii-  iii       vv
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_164581456_   3855 CATAAGAATAAATCTTAGTG----TAAGTGCTTGGCAAGTATGTCTTAAC 3900
                             i ?i        v   ---- ii  -- v     vvi v     iv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGT--TAGGCAATGGTTTCTTAGA 593

  chr2_164581456_   3901 TATAA----AAAGGTATGAAATATAAAATTAGAAATAG-TACTTTAAACT 3945
                            i ----   i i ii ivv i    vv i      -  vv  ii   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_164581456_   3946 TCA---AAATTAATAGTTTTTGTGTTTCAGAAGACACT--TAGGAAAATG 3990
                            ---       v ii       i    i i      --i i    i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_164581456_   3991 AAAA--CA---CACAGACTGGTAAACAATCTTTGCAAAT-ATATATTAGG 4034
                             --  ---      v   v i v   v         -      iv i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_164581456_   4035 TAAAGAACTTGAATCTAGAAAATATGAATAACTC----AACTAAATGATA 4080
                            i i     v   i    v    i  v     ----    v   i   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_164581456_   4081 AGAAAACAAGTCTCATTCTCATCTTCACCCAA----AAAATTGGCAAAAA 4126
                          i  i    i --------- -----      ----     v      ii
  L1M4_orf2#LINE/    794 AAAAGACAAAT---------A-----ACCCAATTWAAAAATGGGCAAAGG 829

  chr2_164581456_   4127 ATTTGAGCAGA-ATTTTTTCAACCAAAGAAAATGTG--GATGG--AA-AA 4170
                               ii   -    i ----        i  i i--i    --  -  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCT----CCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_164581456_   4171 GTAGACATGAAAATATCTTCAATATTATTTGCTAC 4205
                          i --        v  vi    i  i ????????
  L1M4_orf2#LINE/    876 GCA--CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (115 / 55)
Gap_init rate = 0.04 (32 / 760), avg. gap size = 2.41 (77 / 32)  


4229 20.27 2.02 0.45  chr2_164586631_164588967      960  1852 (485)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_164586631_    960 GGAGGGACATCCCATGTTCATGGATCAGAAAGCTTAATATTGAAGAGACA 1009
                            ii  i                 ii   ii          vvi   ii
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_164586631_   1010 GTAATAGTTCCCAAATTGTCCTGCAGAGTTGATGCCATTTCTACCAAAAC 1059
                          i    v i         vi  i    v ii i  v  ii   i     i
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_164586631_   1060 CTCAGCTGCCTTTTTCTAAGCATAAATTGACACAACCAATCCTAAAATTC 1109
                          i             i---   v         - i ii            
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT---GCAGAAATTGACA-AGCTGATCCTAAAATTC 147

  chr2_164586631_   1110 ACATAGAATTGCATGTGACCCTAAATAGCTAAAATAATCTTAAAGAGGAA 1159
                          i  i   v    v v     vi      i    i      i  i i   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_164586631_   1160 AAACATAGCTGAGGCACTCACAATTCCTAATTTCAATACTTACTACAAAT 1209
                         i    v  i  ii v       v    i        v            v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_164586631_   1210 CTATAGTAAACATTACAGTATGGTACTGGCATAAGCATAGA--TATAGAG 1257
                            i     v  vv     i               v     --      v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_164586631_   1258 CAATGGAATAAAATTGAGAGTCTATAAAGAAAT------ATTTATGGTCA 1301
                                   i           i v   v   i------           
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_164586631_   1302 CTTAATTTTACATAAGGGTCCCAAAACTATTCAATGAAAAAAGAATAGTC 1351
                         v  i     vv i      v    i  i        iii           
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_164586631_   1352 TTTTCAACAAATGGTGTTGGGAAAACTGAATATCCACATGCTAAAGA--- 1398
                                         i     v     i   ?        v     ---
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_164586631_   1399 --GCTGGATACTTCCCTCACATCATACATAAAAATAAACCCAAAATAGAT 1446
                         -- i    iv i v       i    i i      v   i      i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_164586631_   1447 GAAAGACCTAAATGTAAAAGTTAAAAATATAAGACTCCAAGAAGAAAACA 1496
                         v ?              i  i     v     i    iv           
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_164586631_   1497 TAAGAATATATCCTTCCAGCCTTTCATTGAGCAATAGCTTCTCAGATAGG 1546
                           i ?i  v   i iviii    vvi  ii     i i    i     v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_164586631_   1547 ACAAAAAAAGCATAAGTGACAAAAGTGAAAATAGATGAATTGGACTTCAT 1596
                            vv       i   ii       vi         i             
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_164586631_   1597 CAAAATTAAAAACTTTTATGCTTCAA-TGATATCGTCATGAAAATGTAAT 1645
                                          i        -v  i iii   v    i  v  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_164586631_   1646 AACATCTCACAGAATTGAAGAAAATATTTGCAAATTATGTATCTGTTAAG 1695
                         i   v i        v i                 i  i      v    
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_164586631_   1696 AATGTAGCATTTGAAATATATAAAGAACTCTTACAATTCAATAATAAAAA 1745
                         iivv v i  iiii                      i             
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_164586631_   1746 GACAA----TCCAATTAAAAATCGAGGGAAGAATGTTAGTAGATATTTTT 1791
                              ----i      ?    vi i vi   i  v v i    i    i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_164586631_   1792 CCAAAGAAAATATAAAAATGGCCACTAGTCACATAAAAAGATGCCCCTCA 1841
                                 i     v         v  iv     i         i vv  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_164586631_   1842 TAATTAGTCAT 1852
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.81 (114 / 63)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 3.14 (22 / 7)  


2482 25.92 0.84 5.56  chr2_164603669_164608253.rev     3141  4093 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164603669_   3141 TGGAAAGATGTACTCTGTTCCTCATTCAAAAGATTCAGTACTCTTAATAT 3190
                                  i v iv     v viv iii    i i i  i v    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_164603669_   3191 GTAAATTCTCCTCAAATTGATCTATAGCTTAATAAATATCATCACATTCA 3240
                          vv   v    i            i  v  v --- iiiv   v vv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCA---ACGCAATCCCTATCA 97

  chr2_164603669_   3241 AAATTCAATGTGGCGTTTTTTGTAGAAATGGATACGCTGATTTGGAAATT 3290
                             i v - iv  v       i      v  i v      iivi     
  L1M4_orf2#LINE/     98 AAATCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_164603669_   3291 CATATAGAAATGCAAAAAAACCTAGTACATCCAGAATAATTTT-AAAAAG 3339
                              i         iii -  i  v i v   i  i   i  -      
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_164603669_   3340 AGAAACAAAGTTGTTTTACT-GTACTACTTGATTTCAAGATTTATTATAA 3388
                          ii          vvvv   -ii   v iii       i i   i  i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_164603669_   3389 AGCTACATTAATTAAGATAATGTGGCATTGGAACAAATGA-AGAGATATA 3437
                                v    i    i i     i i   v i  i-  -   v     
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATATA 294

  chr2_164603669_   3438 GATCAATGGAACAAAGTAGAATGTTCAGAAATATATCAATACATACATTG 3487
                                    i i i v  iv  i        v i v      vi  v 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_164603669_   3488 AAAACTGAATTTTGACAGTGGTTTGAAAACAATTCAGTAGAAAAAATTAT 3537
                         vv  i   v   i    iv   viv  i  v     i i ii   iv-  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-AT 393

  chr2_164603669_   3538 AGTCTTTTCCAAAGATGGTGCTAGAAAAATTTCATGTCTACAAATTAGAA 3587
                                  v v i        i i v  i vv  i? i   -- vvi  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA--TGCAAA 441

  chr2_164603669_   3588 AAAAT-AACTTTAATACATAGTTCACAGAATATATAAATATTAACCTTAA 3636
                          i   -  v  vi iv v  vi     vv     i   v      iiv  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_164603669_   3637 ACGGATCATAGACCTAAATGAAAAACCTAAAATAACAAAAAGCTTGAAAG 3686
                          i      ?           v  i v      iv i    vv   ii   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_164603669_   3687 ACCATGTAGGAAAAAGTCTT-GTGGCCTTAAGATTCAAGCAAATGTTCCT 3735
                          vv ii    ?iv  i    -   i    ii -- i i    vv   i  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCT 589

  chr2_164603669_   3736 TAAATATAACACCAAT-GCATTATCTATAACAGAAAATATTAAGAGTTCA 3784
                           i    i       v-   iv v v i  v      ----  v  --- 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA----AATAG---A 632

  chr2_164603669_   3785 TAAAATTTTAAAATCTAACATTCTTCCGTTGGAATTTTAAAATTTATTTA 3834
                             ---  ii ----------    -i iii    v-    i  --  i
  L1M4_orf2#LINE/    633 TAAA---TTGGA----------CTTC-ATCAAAATTA-AAAACTT--TTG 665

  chr2_164603669_   3835 AATTTTAAAAATCTTTTTGGACAATAATATTAAGACAGTGAAGCCATAGA 3884
                         vii  i   ---------     v  --- i    v      i----   
  L1M4_orf2#LINE/    666 TGCTTCAAA---------GGACACTA---TCAAGAAAGTGAAA----AGA 699

  chr2_164603669_   3885 GAAACCTCAGATTGGGGTAAAATATTTGCAAATCATATACTTGATAAAGG 3934
                         v  v  v    v    iv                     ii      i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_164603669_   3935 ATCTGTATTTGCAGTATATAAAGAATCCTCAAAATTCAGTAATATGGAGA 3984
                          ii     iiiv i           ii  i v  i   i     vii   
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_164603669_   3985 CAAGCAATCTAATTTTTTAAATAGGAGAAAGATTTGAAAAGATATTTCAC 4034
                            ii  i i    ?vv-    i  vi  i        v   i     v 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_164603669_   4035 CAAAAAGAGATATATGGATGGCCAATAAACATATAAAAT--TGCCTAACA 4082
                             i -       iii           i  i  i   v--   ii    
  L1M4_orf2#LINE/    849 CAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_164603669_   4083 TCATATAAGTC 4093
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.35 (61 / 26)  


 301 25.84 1.12 0.00  chr2_164822958_164824996.rev      501   589 (1450)    L1M4_orf2#LINE/L1      120   209 (699)  

  chr2_164822958_    501 AAAAATAGAAAAAA-AATCCTAAAATTCATATGAAACCATGAAAGACCCT 549
                          i    v  v  iv-i                 i  viiii ii     v
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_164822958_    550 GAGTGGCCAAAGCAATCATGAGCAAAAAGAACAAAGCTGG 589
                           i i      i     v   iv  i          i   
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1)  

2248 25.96 3.40 1.42  chr2_164822958_164824996.rev      875  1579 (460)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr2_164822958_    875 AAAAAAAAGAACAAAGCTGGAGGTATCACACTATGTGACTTCAAAGTATA 924
                              i          i      vv       vivii i      iiv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_164822958_    925 CTATAAACCTATACTAACCAAAACAGCGTAGTTTTGCCATTAAAAACAAA 974
                            i   v   i v   i   i    i  i  vi  v   -  ii i i 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGA 288

  chr2_164822958_    975 TGCATAGACAAATGGAATAAAAT----AGCTGAAAATTAAATTCATGCAG 1020
                         iii     iv         i   ----  iiv i  v    ii   i  v
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_164822958_   1021 GTCTAGCCAACCTATTTCCAACAAAAGTGCCATTAACACACACTGGGGAA 1070
                         v v i i   iiv    i i    ii      vv v  iv  v       
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_164822958_   1071 GAGACAGTCTTTTCAATACATG-TCCTGAGAAAACTGGATAGCTACATAC 1119
                         iii i           i v   - v   i  v         ? i    i 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_164822958_   1120 ACAAAAATATGACTAGACCCCTACCTCTCACCATATTTAAAAAATCAGCT 1169
                          v  i   iviii i            v        vi     - i i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACT 487

  chr2_164822958_   1170 CAAAATGGATTAAAGACTTAAATGTAAAACCCACGGCTATGAAGCTACTG 1219
                                   i ?    i         i v i vii    i  i  vi i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_164822958_   1220 GAAGAAAACTTAGGA-TAAATGCTTTATGATACTGGTCTGGGCAA-GGAT 1267
                                  v    ?-     -   ii   ivi   vi i     -  v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_164822958_   1268 TCTTAAAATAGGACCTTAAAAACACAAGCAACAGAAGCAAAAATA-ACAA 1316
                              i -  v   vii    i           i   v       - i  
  L1M4_orf2#LINE/    587 TCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_164822958_   1317 ATGGGATTACATCAAACTAAAAAGTTTTTGCACAGCAAAGGAAAC----A 1362
                           v   i v       v v    ii     ii vv       v  ---- 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_164822958_   1363 ATAGAGTGCAGTGGCAGCCTACACAATGGGAGAAAGTATTTGGAAACTAT 1412
                          v i    v iv i  i  i   v           i      v   ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_164822958_   1413 ACATTTGGCAAAAGACTAAAATCCAGAATATGTAAGGAACTT-------- 1454
                          i  i  ii  ii    viv           i   i     i--------
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_164822958_   1455 -AAT--TGAAAAAAAAAAAAACCTGATTTAAAAATGTTCAAAGACTTT-A 1500
                         -   -- i    i v   v    ii   ?       vv     iv   - 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_164822958_   1501 GTAGACGTTTCTCAAAAGAAGACATAAACATGTTCAACATCCCTATCAGA 1550
                         i     i      v        i   v v   vi   i vv vi  --  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT--GA 883

  chr2_164822958_   1551 GAAAAATGCAGTTCAAAACCACAGTGAGA 1579
                         -   i    ---    v i  ????????
  L1M4_orf2#LINE/    884 -AAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (114 / 65)
Gap_init rate = 0.02 (16 / 719), avg. gap size = 2.12 (34 / 16)  


3686 20.95 3.38 1.24  chr2_164843334_164845292.rev      580  1467 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_164843334_    580 GGAAAGAG--CCAGTGTTTATATGTTGGAGGAATTAAAGTTGTTAAGATG 627
                                v--  vi    i  ivi     i  v    vi           
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_164843334_    628 GCAATATTCCCCAAATTGATTCATGAATTCAGTGCAATCCCCATCAAA-T 676
                               i             ii iii     ii        i      - 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_164843334_    677 CTCAGCCGTCTTCTTTACAGAAACTGACAAGTTTATCTTAAAATTTATAT 726
                          i    i i   i   i      i       i v   i       i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_164843334_    727 AAAGAT--AAGAGACCCAGAAT--TCAAAACAATCT--AAAAAG--GATC 768
                         ii i  --   i          --i           --      --  v 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_164843334_    769 ATGTTTGGTATATTCACACTTCCTA-CTTCAAAATTTAGTGCAAAGCTAT 817
                          viv    viv i          i -i       i   v i        i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_164843334_    818 AGTAATCAAGAGAGTCAGCTGTGGTGCTGGCGTAAGGATGGACATACAGA 867
                                    ----   -      i     i       i      i   
  L1M4_orf2#LINE/    252 AGTAATCAAGA----CAG-TGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_164843334_    868 TTAATAGAACAGAAGTGAAA-TCATAGTGATAAACCCTTATATTTAT--T 914
                          i   i   i    v   i -  -i  vi        v  i      -- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chr2_164843334_    915 TAATTGTTTTTTGACAAGAGTGTCAA-ACAATTTAGTGTCTT--GAATTG 961
                         i     v    i      i   i   -  v   i i  vvvv--    v 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_164843334_    962 TCTTTTCAGCAAATGGTGCCAATGCAATTAGATGTCTCTATGCACAAGAT 1011
                                 i          iiivi   i i   i? ivi     v    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_164843334_   1012 CAAAGTTGGGCATCTATTTTTACACTATACAAAAAAATTAACTCAAAATG 1061
                         ii       i vi   ii i-    i   i v                  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTC-ACACCATATACAAAAATTAACTCAAAATG 494

  chr2_164843334_   1062 GATCCTGGACCTAAATGTAAAGGTTACAACTATAAAACTGT-AGAAGAAA 1110
                             v?i             ii i  v            v -        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_164843334_   1111 ACAGAGGAATAAATGTTTGTGGCCTTTGATTGGGCAATGATTTCTCTATC 1160
                            v   ?i     v  i   i    v i  i       i     ivivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_164843334_   1161 ATAACAACAAAAGCACAAATGACAAAAGAAACA-TAAATAAATCA-ACTG 1208
                           i   v           iii          v -  i      ii-   v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_164843334_   1209 CACAAAAAGTAAAA-CTTTTG--CTGTAAATAATACCACTAAGAAAACGA 1255
                           iv    v     -      --  vi   vi i  i ii      ii  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_164843334_   1256 AAAAACAGCCTACAGTATGGGTGCAAATATTT-CAAAGCTTTCCTCTAAT 1304
                            i   i  i    v     v v        -    v v viv   i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_164843334_   1305 AACAGTCTTGTATTCGCATTATATAAAAAAACTGTTACTACTCAGTAATA 1354
                           vi v       i iv v        i  -  v    v     i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATAATA 793

  chr2_164843334_   1355 AAA-GACAA----CTTCATTAAATTATGGGCAAAGGATTTGAATAAACAT 1399
                            -     ---- iiv   ?  vv                    i    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_164843334_   1400 TTTGCTCCAAAGAAGCTATATGAATCGTCAATAAGCACATGAAAAGATTT 1449
                           --           v    ii   v i                    v-
  L1M4_orf2#LINE/    844 TT--CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG- 890

  chr2_164843334_   1450 CTCAAAATTATTAGTCAT 1467
                              v  i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (119 / 63)
Gap_init rate = 0.03 (26 / 907), avg. gap size = 1.58 (41 / 26)  


3137 26.44 1.22 0.77  chr2_164942765_164948912     4753  5656 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164942765_   4753 TGGAAGAACATTCCATGCTCATTGGTAGGAAGAATCAATAT-G--AAAAT 4799
                              ii i  i     i    v i v      v i     - --  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_164942765_   4800 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4849
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_164942765_   4850 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4897
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_164942765_   4898 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 4947
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_164942765_   4948 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAATTATACTACAAGGC 4997
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_164942765_   4998 TACAGTAACCAAAACAGCATGGTACTGGTACCAACACAGAGATATAAATC 5047
                                 i   i    ii         i iv iv i   v     i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_164942765_   5048 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATATACAACT 5095
                                i    i--    i  --        vv   i i  v  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_164942765_   5096 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5145
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_164942765_   5146 CTTTTTAG-AAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5194
                              i i-              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_164942765_   5195 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5244
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_164942765_   5245 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCATAGAAGAAAAG 5294
                          i ?    i       v   v       i      vi v          v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_164942765_   5295 CTAGGCAATACCAATC---AGGGCATAGGCATGGACAAGGACTTCATGTC 5341
                         v    ?i-  --    ---iv i v v  vv i i   v ii   v ivv
  L1M4_orf2#LINE/    547 ATAGGNG-TA--AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_164942765_   5342 TAAAACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATC 5391
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_164942765_   5392 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5441
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_164942765_   5442 AACAGGCAACCTACAGAATGGGAGAAAATTTGTGCAACCTACTCATCTGA 5491
                           v  i     i                 v v     vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_164942765_   5492 CAAAGGGCTAATATCCAGAATCTACAATGAATTCAAACAAATTTACAAGA 5541
                         i  i  i  vi          v  i  v   i  vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_164942765_   5542 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 5591
                             i     i     v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_164942765_   5592 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5641
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_164942765_   5642 ATCATCACTGGCCAT 5656
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


 564 26.44 12.02 0.00  chr2_164951773_164953765.rev      298   505 (1488)  C L1M4_orf2#LINE/L1   (0)   908   676  

C chr2_164951773_    505 GATATCATTGTAAAAATGAAAGGGCAAACCACAAATTGTGAGAAAACATT 456
                           i ii  iivi   i     i i   v     i v  v       i   
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

C chr2_164951773_    455 CAAAACACATATATTAGACAAAAGCCTTGTATCTAGAATATATGAAGAAT 406
                         iiv  vv       iv  i  ii v        i         i     i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

C chr2_164951773_    405 TCTTATAATCCAATAATAAGAAAATAAAAAATCCAAT--AAAAAT----- 363
                              i  ii         i  i i   v  i     --      -----
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

C chr2_164951773_    362 -----------TAAGCA-------AAAGAATATATATGAATGCCTGATAA 331
                         -----------  ii  -------      v     ii    v ii    
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

C chr2_164951773_    330 GTATATGAAAATACATTCAATGTTGTTATTCAT 298
                          i i       v iii    ii ii????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.23 (42 / 13)
Gap_init rate = 0.01 (3 / 233), avg. gap size = 8.33 (25 / 3)  

2547 28.29 1.99 1.66  chr2_164951773_164953765.rev      598  1502 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164951773_    598 TGGAAAAACATTCCACGTTCATGGACTGCAAGAATCAGTATCTCTAAAAT 647
                               i i  i   i         i  v    v i i   ivi   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_164951773_    648 GGC---------CAAAGCAATCTATAGATTCAACATTATTCCTATCAAAC 688
                            ---------    vii     i         iiv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_164951773_    689 TACCAACATAATTTTTCACAGAACTGGAAAAAATTATTCTAAATATCGTA 738
                          v   i vvvv     ii     v v  v  iv v  i     vv  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_164951773_    739 TGCAACCAAAAAAGAACCCAAATAGTCAAATAAATCCTAAGCAAAACAAC 788
                           v  viiv  ii  v  vi     i    vv    i i --    v  -
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAA- 197

  chr2_164951773_    789 AAATAAGAAAAGCCAAAGGCATTC-CATTCGCCAAAT--GAAACTATACT 835
                         i  i  ----  iiii   - i  -  i iv    v --i     -    
  L1M4_orf2#LINE/    198 GAACAA----AGTTGGAGG-ACTCACACTTCCCAATTTCAAAACT-TACT 241

  chr2_164951773_    836 GTAAGGCTACAGGAACCAAAACGACATGGTACTGGTATAAAAACGGACAC 885
                         ii  i       v  i   i  iiii         i    ii ii    i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_164951773_    886 ATAGACCAAGGGAACAGAATAGAAAACCCAGAAATAAAGCCACATACCTA 935
                              i   v    i     v  i ii           v   i i ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_164951773_    936 TAGCTATCTAATCCTCAACAAAGTTGGCCAAAATAAG-CAATAGAGAAAG 984
                          i ii vi i  ii  i    i v  -    i iv v-    i i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAG 390

  chr2_164951773_    985 AACTCCCTGTTAAATAAATGGTGCTGGAATAGCTGCCTAGCTATATGCAG 1034
                           ivvi  v  v  i            i i i   vv  ? i i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_164951773_   1035 AAGAATGAAGCTGGACCCCTATCTTTCACCATACACAATAATTAACACAA 1084
                                   i          i  iv       i    v       v   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_164951773_   1085 GATGAGTTAAGGATTTAAATGTCAGACCTCAAGCTGTAAGAATCCTAGCA 1134
                         i   ii i ?i  ii       v   v  v  i  i   i v  i   v 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_164951773_   1135 GAAAACCTAGGAA-ACACCATGCTGGATATTGGCCTTGGGAAAGAATTTA 1183
                               v    ?i- v i - v vv  iv    vi v  v  v iv  iv
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_164951773_   1184 TGACTAAGCCCTCATAAGCAATTGCAATAAAAACAAAAATTGACAAGTGG 1233
                          iiv  v v vi  v     vvv    i    iv      v  i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_164951773_   1234 GACCTAATTAAA--TAAAAAACCTTCTGCACAGCAAAAGAAACTATCAAC 1281
                            i v  i   --      --   i  ii vv    i  v        v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_164951773_   1282 ATAGTAAACATACAACTTACAGAATGAGA-AAAATATTTTCAAAATATGC 1330
                          v   i  v v     ii        i  -         v    vi  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_164951773_   1331 ATCTGACAAAAGGTCTAATGTCTAGAATCTATAAGGAACTTAAACAACTG 1380
                               i  i-  v  vi i  i     v     i     ivv      v
  L1M4_orf2#LINE/    738 ATCTGATAAG-GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_164951773_   1381 AACAAGAAAAA-ACAAATACTCCCGTGAAAAAATGAGGAAGATACATGAG 1429
                           i  v     -       vi  vi v?       i v  iiv iv   i
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_164951773_   1430 CAGACACTTCTCAAAAGAAGACATGCAAGCAGCCAACAAACATATGAAAA 1479
                         i     i     v        i  i   iii     i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_164951773_   1480 AAATGCTCATCATCTCCAATAAT 1502
                         i -      v    v????????
  L1M4_orf2#LINE/    887 GA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (153 / 99)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.83 (33 / 18)  


3202 25.76 2.24 0.56  chr2_164960155_164964617.rev     3092  3984 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164960155_   3092 TGGTAAGATATTCTGTGTTCATGGATTGGAAGAACTAACATTGTTAAAAT 3141
                            v       i ii                  vi   i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_164960155_   3142 GGCCCTACTACCCAAAGTGATCTACAGATGTAACGCAGTCCCTATCAAAA 3191
                            vv    v      v            vi      i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_164960155_   3192 TACAAATGACATTCTTCATAGAAATAGAAAACACAATTCTAAAATTCCTT 3241
                          v v iivi v  i  iii      v  v  vvii  i         v v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_164960155_   3242 TGGAACCACAAAGGACCCTGAATAGCCAAAGCAATACTGAACAAAAAGAA 3291
                              vii   i      v           i    vi    v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_164960155_   3292 AAAAGCTGGTGGCATCATACTACCTAACTTTAAAATATATTACAAAACTG 3341
                         v    i   v  vv   i   v  i  i  i    iv  i      i  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_164960155_   3342 TAGTAACCAAAATAGCATGGTTTTGGCTTAAAAACAAACAGACAAA--AA 3389
                         i     i   i i  ii    vi    v   ii i i   v i i --  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_164960155_   3390 --GAACAGAATAGAGAGCTCAAAAATAAATTCATGCACCTATAGCCAACT 3437
                         --   i     v     ii  i       ii   i  ii   i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_164960155_   3438 AAGTTTCAACAAAGGTGCCAAAAACACACATTGGAGAAGAGACAGTCTCT 3487
                         i v    i    i        i v  iv  v   i   iii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_164960155_   3488 TCAGTGAATGTTCCTGGGAAAATGGAATATCCACATGCACAAAAATGAGA 3537
                            iii    v v      v  iv i   ?         v  i     ii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_164960155_   3538 CAAAACCTTCACCTCTCAACATATACAAAAATCAACTCAAAATGG-TTAA 3586
                         ivii   iii     v  v             i            - i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_164960155_   3587 GGACTTAAATGTAAAGCCCAAAACTATGAAATTACTATAAGAAAACATAG 3636
                         i   i         iiv i        i   i vi  v            
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_164960155_   3637 -CATAAACACTTTATGACATTGGCCTAGGCAATGAATT-TTAAATTAAAT 3684
                         -?i    i-   ii    v    vi         iv  -   i  vvi i
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_164960155_   3685 CTTAAAAGCTCAGGCA-CTGAAGAAAAAATAGACAAACAGGATTTCATCA 3733
                         vii      v  i   - vi             i   iv   i       
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_164960155_   3734 AACTAAAAAGACTTTGCACTGCAAAAAA----AGCAACAAAGTGAAGGGA 3779
                           v v    ivi    ii  v    ii ---- v   v        ii  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_164960155_   3780 CAACCTGCAGAGTGGGAGAAAATATTTGCAAACTATACATTCAACAAAAG 3829
                              ii    i                    ii   i  iii i  ii 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_164960155_   3830 GTTAATATCCAGAATGTACAGGGAACTTAATAGCAAC--AACAACAACAA 3877
                         ii vi          i  i ii     i-- vi    --  i  i  v  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCAATAATAAAAA 797

  chr2_164960155_   3878 CACCCAAATGACTCATTTTAAAA-TGAGCCAAAGACATCTACAGACATTT 3926
                         v  --    i  i  v  ?    -  i  v  i  iv vv i        
  L1M4_orf2#LINE/    798 GAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_164960155_   3927 CTCAAAATAAGACATTCAAATGGCCAATATGAA----AAAAAAAGCTTGA 3972
                            v   v    i  v             v v ----    i v   ii 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_164960155_   3973 CA-CATTAATTAT 3984
                           -  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (150 / 76)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.79 (25 / 14)  


3592 18.31 2.93 4.55  chr2_164986132_164988606     1062  1984 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_164986132_   1062 TGGAAAGATATGGTATCTTCATCCATTCAACATATTTAAAATCATTAAAA 1111
                                    vvi  v     vv   vi - v i    v  ii    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGA-AGACTTAATATTGTTAAGA 49

  chr2_164986132_   1112 TGTAAATATTCCCCAAATTTATCTTCAGATTCAACAAAATTCCTATCAAA 1161
                           vv    i          v    v          iv   i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_164986132_   1162 ATCTCAATT-TGTTTGTTGCAAGCTGACAAGCAAACTGAAAAGCTCATGC 1210
                            i  ii -iv   v     i----------   i   v     v  v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAG----------AAATTGACAAGCTGATCC 139

  chr2_164986132_   1211 TAAAATTCATATGTAAATGCAAGGGACTCAGAGTAGCCAGAACTGTCTTC 1260
                                      v             i    i      i   vi    v
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_164986132_   1261 AAAAAGAAGAATAAAGTTGGAGGAATCACCCTTCTTGATTTCATAATGTG 1310
                                    i            v    v    iii      v  iv i
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_164986132_   1311 CTACAA-GATACGGTAATCAAGACAGTATAGTAAGCCAGTAAGAGAAGGA 1359
                               - v   i              i i   -- ii i ---v     
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTA--CTGGCA---TAAGGA 284

  chr2_164986132_   1360 TATAGTACATTGCAGTACAGTGTAAGAAGACATCAATAAAATGGAATTGA 1409
                           -- -    ------ i  -----------      ii   i       
  L1M4_orf2#LINE/    285 TA--G-ACAT------ATAG-----------ATCAATGGAATAGAATTGA 314

  chr2_164986132_   1410 GAATCCAAAAGTCAACCCTAACATTTATAGTCAATTGATTT-CAGCAAGG 1458
                           i    i  i v     vv        i            - ii     
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_164986132_   1459 GTGCCAAGACATTTCAATGCAGAAAAAA-AATCTTTTCAATCAATAGGGC 1507
                                   vv       vi    i  - i         iv   i v  
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_164986132_   1508 TGGGACAACAGGATATCCA------AAAGAATGATGAATGTGCAGAATAA 1551
                                  v     ?   ------         -- i -  --  vivv
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGA--AGT-TG--GACCCC 459

  chr2_164986132_   1552 TACAAAATTCCATATA---AAAT-AACTTAAA-----TCATAGACATAAG 1592
                            vvv iv       ---    -    i   -----   ?    v   i
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_164986132_   1593 TGTAAGAGCTGAAACTATAGCATATTTGGTAGAAAACATAGGCCTAAATC 1642
                                   i        iv ivi  i v            ?v      
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_164986132_   1643 ATCATGACCTTGGAGTAGACAATGGTTTCTTAAACATGACATTAAAAGGA 1692
                         v  i         iv   i             i i      ii     v 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_164986132_   1693 TAAGCAACAAAA-AATAAATAAATACACTGGAATTCATCCAACTTTGAGA 1741
                         i           -  v     i   v i    v      v  v  vi i 
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_164986132_   1742 CATTTTTTCTTCAACAAACACTGTCAAGAAAGTGAAAAGACAAAACACAG 1791
                          v   v v      vii     i                    vv     
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_164986132_   1792 AATGAGAGAAGATATTTGTAAATCATATATCTGCCAAAGC-CTTGTATAT 1840
                             i     i       i              vi  i v-       vi
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_164986132_   1841 AAAATAAATAAAGAGCTCTTGCAATTCAATAATAAAAA---AGACAACCC 1887
                          i    v       i     i   i             --- i i     
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_164986132_   1888 AATTTTTTAAATGAGCAAAGGGTCTGAATGGACATTCATTGAAAGAAGAT 1937
                             ?vv-     i       i i     i      iv iv         
  L1M4_orf2#LINE/    810 AATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_164986132_   1938 ATACAAATGGCCAATA--CATAGGAAAACATAGTCAACAT-AGTTAGCTG 1984
                                         --  i v     v  iv       - ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (91 / 74)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.76 (69 / 25)  


2647 25.54 2.38 4.11  chr2_165006214_165008582.rev      954  1877 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_165006214_    954 TGGAAAGACATTCCATGCTCAGGGATTAGACGAATCAATAGTATTAAAAT 1003
                                 i  i     i   v     i  v  v i    v i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_165006214_   1004 AAATAAACACTAAAATGACCATATTGCCCAAAGCAGTCTACTGAATCAAT 1053
                         ---------------- i v   i v      viii     v  v    i
  L1M4_orf2#LINE/     51 ----------------GGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr2_165006214_   1054 GTAACTCCTATCAAACTACCAA-TGTCATTTTTCACAAAATTTTAAAAG- 1101
                          i  ii         v v   i-  i -     ii  i  v  v v   -
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC 133

  chr2_165006214_   1102 -AATCCTAAAATTAATATG-AAATCCAAAAAGAGCCCA-AATAGCCAAAG 1148
                         -i           v     -    v   i-- ii    -          i
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAG--GGACCCAGAATAGCCAAAA 181

  chr2_165006214_   1149 CCATCATAAGCAAAAAGAATAATACTGGAGGCTTCATATTACTTGACTTC 1198
                          v   v i iv  i     i  vii      vi   i i v iii i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_165006214_   1199 AAATTACACTAAAAGGCTATAGTAACCAAAATAGCATGGTACCAAGATAA 1248
                            vivi    v  i    i     i   i i  ii      iiiv    
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_165006214_   1249 AAATAGACACATAGATCAACCTGGAACAGAATTGACACATATCGTAGAAA 1298
                         ii       i         --     i        v ---i  -i     
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAA--TGGAATAGAATTGAGA---GTC-CAGAAA 325

  chr2_165006214_   1299 TAAAGCCACCTACCTGCAACCAGCTGATTTTC-ACAAAGTCAACAAAAAT 1347
                             v   ivi ii iiiii  ii        -    i viiv   i vi
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_165006214_   1348 ATACACTGGGAAAAGGACACTCTCTTCAATAAATGGTGCTGGAATAATTG 1397
                           v  v    i    i i v   i     i            i i  i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_165006214_   1398 GAAAGCCATATGCAGAAGAATGAAACAGTATACCTGTCTCTCAGCATATA 1447
                           v ?   i     i         iiv v iv   ii   v  v      
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_165006214_   1448 CAAAAATTAACTCAAGGTGGATTAAATACTTAAATGTCAGAAGTGAAACT 1497
                                        ii     i ? v  i       v   iv i     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_165006214_   1498 ACAAAACTCATAGAAGAAAACCTAAGAAAAACTCTTCTGGACATTGGTCT 1547
                          i       v           v  i ?iv  v     vv   v    vi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_165006214_   1548 AGAGAAATAATTT-------ATGCTAC-AAAAACAAAATGCTACAAAAAC 1589
                           - v   ii   -------   vi  -    i  v  -  v      iv
  L1M4_orf2#LINE/    576 AG-GCAATGGTTTCTTAGATATGACACCAAAAGCACAA-GCAACAAAAGA 623

  chr2_165006214_   1590 AAAAATAAACAAATTAGATTGCATTAAACTAAAAAGCTTCTTCACAGCAA 1639
                                i i     i  i v   i   v v    i   i vii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_165006214_   1640 AAGAAATAATCAACAGAGTAAACGGAAAACATGCAGAATGGGAAAAAAAA 1689
                          i  v iv     v i   i  vi  v   vii          i    v 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_165006214_   1690 ATTTGTAAACAATGCATCCAACAAAGGGCTAATATTCAGTATCTACAAGG 1739
                         -    i   iv  ii   ii i  i  i  vi   i   v  v  i  i 
  L1M4_orf2#LINE/    724 -TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_165006214_   1740 AAATC----AACTCAACAAGGAAAAAACGTATAAAAGTGAGCAAATGACA 1785
                           v  ----       i  vi    i  ------  i i v v   ----
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGAC------AAATAACCCAAT---- 812

  chr2_165006214_   1786 TAAAAAGTGAGCAAATGACATAAACTGACATTT-TCAAAAGAAGACATAC 1834
                          ?    i  i     v  iv i  iv       -  v        i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_165006214_   1835 ATGTGGCCAAAAACCA---AAAAAAATGCTCAACATCACTAGTCAT 1877
                          vi       v  v  ---i    i             ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (147 / 85)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.86 (60 / 21)  


2784 25.00 4.19 1.47  chr2_165086068_165088077      637  1520 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_165086068_    637 TGGAAAGATATTCCACGTTCAGAGGTTAGAAGACTCAATATTGTTAAGAT 686
                                    i   i     vi i  i       i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_165086068_    687 GTCA---TTCTTCAAAACTTGATTTGTAGGGTCATCAAAATCCCCGT-AA 732
                          v  ---i  ii    --     i ii  iv   v iv      ii -  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_165086068_    733 TATTCCAAGGATGA-TATTTTGTAGATATCAATAAACTGACTTTTAATTT 781
                         v  i   -- v  v- v     i   v  ii i  i    iii v  v  
  L1M4_orf2#LINE/     99 AATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_165086068_    782 CATATGTAAAGACAAAAGACCGAGAATAGCTAATAAAATACCGAA---GC 828
                               v   vi   ii    v        i  v v   vii   --- v
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_165086068_    829 AAAAAAAA--TG--------ACACTTACCAATTTCAATATTTACTGTAAA 868
                          i  v   --  --------      v          v i     ii   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_165086068_    869 GC-AAAGTAATCAATACAACATGGTATTGGCAAAATTATAAACATAGAG- 916
                           - v         v   iii     i     v  vv   i     v  -
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_165086068_    917 -CAATATAACAGAATGTAGGACATAGAAGTAGACCCCC-CAAATATAGTC 964
                         -    iv  i     vv  iiivi    i  i    vi-  vv   i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_165086068_    965 AACTGATTTTTTATAAAGGCTCAACAACAGTTCAATGAAGAAATGATAGA 1014
                           i       iv i  i  iv v vi  vi       ii    vi    v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_165086068_   1015 CTTTTCAACAAATTATACTGAAAGAATTAGACATCCATACGCAAAAAAAT 1064
                                      vi i   ii v  i i  i ?   i i      i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_165086068_   1065 GAATTCAGACACAGACCTTACACTA-------AAGCTAACTCAAAATGGA 1107
                            v ii   v vv    i    i -------  ii              
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_165086068_   1108 TTTTACAGCTAAATGTAAAGTGAAAGACAAACAACCAAAAACCTACAAGA 1157
                          iv? v v          i-----  vi   --  i v   v  viv   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAG-----AGCTAAA--ACTATAAAACTCTTAGA 539

  chr2_165086068_   1158 AGAAAGCATAGGAGAAAATTTATGTGACCTTAGTTT-GGTGATAAGTTCA 1206
                              i      ? v    i vi        i v  -  ii  iiv   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_165086068_   1207 TAGCCACTATGCCAAAATCATGACCTATGAAGGAAAAATATTGATAAATT 1256
                            vi iv ii      v  ii v v ii  i      -  v        
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATT 638

  chr2_165086068_   1257 CGACTTAATTAAA-TGAAAATCTTCTACTCTACAAAG-ACAGTGTTAAGA 1304
                         v     v  i   - v    v   i iiv  v     -   v i i    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_165086068_   1305 GGAATATAAAG-CAAGCCATGGC-TGGGAGAAAATATTTGTAAAATACTT 1352
                         i- i iv    -   v   ii v-                i   vi iv 
  L1M4_orf2#LINE/    689 A-AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_165086068_   1353 ATCTAATGAAGGAATTGTATCCAAAATAT-TAAAGAACCCTTAAAACCCA 1401
                             i  i i   v         i     -        i    v   i  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_165086068_   1402 ACAATAAGAACACAAACAACCCAATT-AAAAATGAGCAAAATATCTGGAC 1450
                          i     i  v     i         -       i     iv  i  i i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_165086068_   1451 AGATACTTG-CCAAAGGAGATATACAGATGGCAAAGAAGCATATGAAAAG 1499
                            i i  v-      i         i     v  v     i        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_165086068_   1500 ATGCTCAACATGATTTCTCAT 1520
                                    v ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (131 / 87)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.08 (50 / 24)  


2892 26.94 1.22 0.55  chr2_165198026_165203287     3869  4770 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_165198026_   3869 TGGAAACACAGCCCATGCTCATGGATGGGCAGAATCAATATTTTGAAAAT 3918
                               v i v      i        v  v   v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_165198026_   3919 GACCATACTGCCAAAAGCAATCTAGAAATTCAATGCAATTCTCATCAAAA 3968
                          i v     v  v   vii     v i      i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_165198026_   3969 TACCATCATCGTTCTTCACAGAACTAGAAAAAAAAATCCTAAAATTTGTA 4018
                          v   v vv v  i  ii     v v  v  ivvi           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_165198026_   4019 TGGAACCAAAAAAGAGCCTGCATAACCAAAGCAAGACTAAGCAGAAAGAA 4068
                              viiv  ii  v  v v   i     i   vvi i iv ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_165198026_   4069 CAAACCTGGAGGCATCACATTACCCGACTTCAAACTATACTACAAGGCCA 4118
                             vi      vv     i v   i i      viv        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_165198026_   4119 TAGTCACCCAAACAGTAAAGTACTGGTATAAAAATAGGCACATAGACGAA 4168
                         i   v i v i     ivi       i    ii    i  i     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_165198026_   4169 TGGAACAGAAT--A-----CAGAAATAAAGCCAGATACTTAACAGCCAAC 4211
                              i     -- -----          v   v i i   -ii i   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAAT 349

  chr2_165198026_   4212 TGGTCTTTGACAAAGCAAACAAAAAAA---AGTGGGAAAAAGGACACTCT 4258
                           i i  i     i vviv   i vv --- i    i   - i i v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCT 398

  chr2_165198026_   4259 AGTCAACAAATGGTGCTGGGATAATTGGCAAGTCACATGTAGAAGAATGA 4308
                         vv                   i  i   vv ?i      i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_165198026_   4309 AAGTGGATCCTTATCTCTGACCTTATACAAAAATCAACTCAAGATGGATC 4358
                          iv    i  i  i   vv   v           i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_165198026_   4359 AAAGGCTTAAATCTAAGACCTGAAGCCACAAAAGTTTCTAGAAGATAACA 4408
                          ?  i i     v     v  i  i i i    v i -       v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAACA 547

  chr2_165198026_   4409 TCAGAAAAACCCTTCTAGATATTGGCTTAGGGAAAGACTTCCCGACTAAG 4458
                          vi ?iv  vi    vv  iv    v     v  v ii   iiiiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_165198026_   4459 AACCCAAAATCAAATGAAACAAAAATAAAGATAAATAGATAGGACTTAAT 4508
                          vv      v  v v v       iv   i   i   i  v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_165198026_   4509 TAAA-CTAAAAGCTTCTGCACAGCAAAAGAAACACTCATCAGAGTAAACA 4557
                         i   -i     i   i  ii vv    i  v  vv   vv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_165198026_   4558 GACAACTCACAGAGCAGGAGAAAATATTTGCAATTTCTACATCTGACAAA 4607
                               i      iii                 v iv  i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_165198026_   4608 GGACTAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAAGAAAAA 4657
                              vi          v  i  i      vv    v   ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_165198026_   4658 AAACAAAGAATCCCATCAAAAAGTACGCTGAAGACATCAATAAAAAACTC 4707
                         i -    v  i  v  i?    i iv  vi i  iv v    i v vi  
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_165198026_   4708 TCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAAATACTCAA 4757
                           v                       i  i  i       i - i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

  chr2_165198026_   4758 CATCACCAAAGAT 4770
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (134 / 105)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


2286 24.72 6.50 0.71  chr2_165223456_165225169      515  1222 (492)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr2_165223456_    515 AAGAGACCAAG--TAGTCAAAGTAATCCTGAGCAAAGAA--ACAAAGCTG 560
                            i    v  --   i    ii    i   i-      --      i  
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAACAAAGTTG 208

  chr2_165223456_    561 GAGGGGTCACATTACCCCACTTCAAACCATATTATAATCCTACAGTAATC 610
                             iv     i v   v i      v v  i  i  vv           
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_165223456_    611 AAAACAGCATGATACTTGTACAAAAACAGACATATTGACCAATGGAACAC 660
                           i    ii  i    v i i  ii i        v  i        i v
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_165223456_    661 AACAGAGAACCCAGAAATAAAGCCATACTCCTACAGCCATCTGAGCTTTG 710
                           iv    ii           v      vii  ii i  vi   vi  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_165223456_    711 ACAAAGTTGACAAAAATAATCAATGAGGAGGGGACTCCCTATTCAATAAA 760
                             i v  v   i vi v      i   ii i ivvi  v     i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_165223456_    761 TGGTATTGGGAAAACTGGCTAGCCAAATACAGAAGAATGAAAGTGGACCC 810
                             ii     v      v  ?   v  i  i         iv       
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_165223456_    811 CTACCTTGCACCACATACAAAAATTAGCTCAGGACGGATTAAAGATTTAA 860
                               ii     i            i    ii i    i ?   ii   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_165223456_    861 A----AGA-TTAAAACC----------TAGGAAACACCAT---------T 886
                          ----   -i      i----------   i i v v   --------- 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_165223456_    887 CTGGACAACAGCCTTG----AGG-AAGAATTTAT--GACTATGTCCTCAA 929
                           vviii  ---    ----   -  vii   v --  -    v vi   
  L1M4_orf2#LINE/    559 CTTCGTGAC---CTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAA 604

  chr2_165223456_    930 AAGCAATTGCAACAAAAACAAAAATAGACAAGTGGAACCTAATTAAACTA 979
                              vvv         iv         i  i v i  i v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_165223456_    980 AAGAGCTTCTGAACAGCAAAGGAAACTATCAACAGATTAAACAGACAACC 1029
                           i i   i  vi vv       v        v i v i  v        
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_165223456_   1030 TACAGAATGGGAGAAAATATTTGCAAACTATGCATCCAACAAAGGTCTAA 1079
                         i                          ii  ii   ii i  i  v  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_165223456_   1080 TATCTAGAATCTATAATGAAC-CT---AATTCAACAAACAAAAAACAA-- 1123
                             i     v     v    -  ---  i    i  vv    i    --
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_165223456_   1124 --CCCCATTATAAAGTGG-TGAAGGACACGAATCAACACTTCTTGAAAGA 1170
                         --   v   ?v   i   -ii     ivi    vi   i    iv     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_165223456_   1171 AGACATACAAGTAGCCAACAA--ACATGAAAAATTCCTCCACATCACTAA 1218
                            i      i i     i  --         iv v   v      ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_165223456_   1219 TCAT 1222
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.69 (108 / 64)
Gap_init rate = 0.02 (17 / 749), avg. gap size = 3.00 (51 / 17)  


1194 16.51 5.50 0.00  chr2_165312545_165315325.rev     1093  1310 (1471)    L1M4_orf2#LINE/L1        1   230 (678)  

  chr2_165312545_   1093 TGGAAAGGTAATCCATGTTCAT----TGGAAAACTTAATATGGTTAAGAG 1138
                                i  vi          ----     i         v       v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_165312545_   1139 GGCAATGCTCCCGAACTTGAACCCCAGATTCAATGCAATCCCTACCAAAA 1188
                               i     v  v    v iv         i          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_165312545_   1189 TCCCAGCTGGCTCCTCTGCA----TT----AGCTGATCTGAAAATTCATG 1230
                                  v  ii i    ----  ----        iv         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_165312545_   1231 CAGAAATTCAAGGGACTCAGAATAGCTTAAATAATCTTAAAAAAGAAAAA 1280
                         ii     v        i         iv   i      i        i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_165312545_   1281 CAAAGTTGGGGGACTCACAGTTTCTGATCT 1310
                                  i         v  i ii  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTT 230

Transitions / transversions = 2.00 (24 / 12)
Gap_init rate = 0.01 (3 / 230), avg. gap size = 4.00 (12 / 3)  

3151 17.69 3.15 0.00  chr2_165312545_165315325.rev     1623  2289 (492)    L1M4_orf2#LINE/L1      221   908 (0)  

  chr2_165312545_   1623 TTTCAAAATTTAAAGTTTACTACAAAGCTACAATAATAAAAATAGTGTGG 1672
                           i v  v  i   ii                i    v  i i       
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_165312545_   1673 TTC-GGCATAAGAATAGACA----AATCAATGGACTAGATTTGAGAACTC 1717
                          v -        i       ----i         v    v      iii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_165312545_   1718 AGAAATAAACTCTCATATTTATGGTCAATTGATTTTTGACAAGGGTGCCA 1767
                                   i vi i                    i             
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_165312545_   1768 AGACAATTCAATGGAAAAATAATAGTGTTTTTACTGATCGATGCTGG-AC 1816
                             v         ii   v      v    i vii vi i      -  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_165312545_   1817 AACTGGATATATACATG-AAAAGAAATAAGTTGGACTCCTTCCTCATACC 1865
                                  ?vi     -       vv         i   v     i   
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_165312545_   1866 ATACACGAATATTAACTCAAAATT-ATCACA-ATGTACATGTAAGGACTA 1913
                            i  i  v             v-    ? - iv  v       ii   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_165312545_   1914 AAACTATAAAACTCTTAGAAACAAATATAGGAGTAAATCTTTGTGACCTT 1963
                                             iv   i     ?         i        
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_165312545_   1964 CGCATAGGAAAAGTTTTCATAG----GATCACAAAATCAAAAGTGTCCAA 2009
                         v vv    v  v v    v   ----  ivv     v  v   iiv v  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_165312545_   2010 AGGAAAA-TA--TAAATTGTACTTCATCATAATTAAAAGCATTTTTGGTT 2056
                           i    -  --       v         v        i v   v  v  
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_165312545_   2057 CAAAG-ATATCATCAAAAAAGTGAAAAGTCAACTCCCCATATGAGAGAAA 2105
                              - i ii     i           v    i v viv   i      
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_165312545_   2106 A-ATTTGCAAATCATAAATCTGATAAGCGATTTGTACCTAGAATATGTAC 2154
                          -              v          v  i     i i       i  v
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_165312545_   2155 AGAACAATTA-AGGTCAATAATAAAAAGACAAATGGCTCAATTAAAAAGC 2203
                              vv   - iv                    ii i     ?    ii
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_165312545_   2204 AGGCA--GGATCTGAACAGACATTTCTCCAAAGACAATATGCAAATGGCC 2251
                         i    --    i    i                 vi    i         
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_165312545_   2252 AATAGGCACATGAAAATATACTCAACATCATTAGCCAT 2289
                             i           v  i          ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (63 / 51)
Gap_init rate = 0.02 (13 / 688), avg. gap size = 1.62 (21 / 13)  


 617 23.03 2.42 1.82  chr2_165330292_165332787.rev     1276  1440 (1056)    L1M4_orf2#LINE/L1        1   166 (742)  

  chr2_165330292_   1276 TGGAAATGCATC--ATGTTTGTGGATTGCAAAAC--AATATTGTTAAAAT 1321
                               vii   --     ii       v  i  --           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_165330292_   1322 ATCTACCCTACCCAGATCAATCAATGAATTCAACGCAATCACTGTCAAAA 1371
                         iv v iv  v    i  ii   v iii             v  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_165330292_   1372 TCCTAATGGCATATTTTTTGTAGAAATAGAAAAAAAGAATCCTAAAATTC 1421
                            i iiv  v --      i      v  v  ivv  -           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT--TTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTC 147

  chr2_165330292_   1422 ATATGGAATCTCAAAGGAC 1440
                                 viv   i    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC 166

Transitions / transversions = 1.38 (22 / 16)
Gap_init rate = 0.02 (4 / 166), avg. gap size = 1.75 (7 / 4)  

2598 21.14 1.07 0.18  chr2_165330292_165332787.rev     1442  2004 (492)    L1M4_orf2#LINE/L1      341   908 (0)  

  chr2_165330292_   1442 ATGATGAAATGATCTTCTACAAAGGCACCAAGGCTATATAAGAGAGAAAA 1491
                            i v  v    i   v    i  ii     i i  vi  vi i    i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_165330292_   1492 GACAGTCTCTTCAGCGAATGATGTTGGGAAAACCGTGTATCTATATCCAA 1541
                         i i     i    i i    i  i     v   i vi  ? i i  v   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_165330292_   1542 AAGAATGAAATTCAACCCCTACCTTATGCCATATACAAAA-----CTTAA 1586
                                  i  vi          i ii            -----  i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_165330292_   1587 AATGGATTAAAGACCTAAATGTAAGATCTAAAACTATAAAACTCCTAAAA 1636
                                i ?                v                 i  i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_165330292_   1637 GAAAACACAGGAAAAAATCTTCATGGCATCGGATTTGGCAATGATTTCTT 1686
                                i   ?iv        i  i v i  i  v       i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_165330292_   1687 GGATTTGACACTGAAAGCACAAGCAACAATAGCAAAAACAGACAAATCGG 1736
                         i   v      ii                v  v     i   i    i  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_165330292_   1737 ACT-AATGTAACTTGAAAACTTCTGCACAGCAAATAAAACAATCAACAGA 1785
                            -v  vv  v  i       i  ii vv    vi v  v     v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_165330292_   1786 GTGAAAAGGTAACTTATGAAATAGGAGAAAATATTTGCCAACTATATATC 1835
                                 ii   ii iii   i               v  ii       
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_165330292_   1836 TTATAAGGGGTAAATATCCAGAATGCATAAAAAACTACTAAAACTCAACA 1885
                          v       iivvi          ii     i    vi  v       i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_165330292_   1886 AGAAAAAGAAAAGCAACCCAATTTAAAAAATGGGCAAAAGACTTGAATAG 1935
                          v       v  ii         ?     -        i  i        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAG 839

  chr2_165330292_   1936 ATATTTCTCCAAAGAAGATGTAGAAATAGCCAACAAGCCTATGAGAAGAT 1985
                          i                 i  v    i     i    vi    i     
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_165330292_   1986 GCTAAACATCAGTAATCAT 2004
                            v       ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (78 / 37)
Gap_init rate = 0.01 (3 / 568), avg. gap size = 2.33 (7 / 3)  


2647 24.45 5.82 0.93  chr2_165480894_165482850      607  1465 (492)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_165480894_    607 ATATCC--TGTTCATGGATTAGAAGACTCAGTACAGTGAAGAT-----T- 648
                               --            i       i i  iv  v     ----- -
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_165480894_    649 CTTTTCAAATTTATCTGTATTTTTAACACAATTCCAGTCAAAACTCCAG- 697
                           iii      v    ii vv  i   i    i  vi      ii    -
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_165480894_    698 TGGGATTTCTGTAGATATAGACAAGCACATATTAAAAT--ATACAGTATA 745
                           vvv   i  i   v  v       vv  vi      --   ii v vv
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_165480894_    746 ATAAAGGAACTAGAAT-TTTAAAAAAGGC--AAAAAAGAATAGCAA-GCT 791
                         ii  i   v i     -vii    v iv --i        v i   - i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_165480894_    792 GGAGAACTGATACAATTCAATTTCAAGACATTATAAAGAAAGCTACAGTA 841
                             i   v i  vvii         i  -   iv v-            
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAAC-TTACTAC-AAAGCTACAGTA 255

  chr2_165480894_    842 ATCAAAACAATGTGGTATTGACA--AG--TAGACACA--GATCAATGGAA 885
                              i   i       i  i  --  --      i --           
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_165480894_    886 CAAAATAGACAATCTAGAAATAGAGCCACACAAACATGAACAACTTGTTT 935
                         i i   v  v i  i       i v   i   vvi   iv   i vi   
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_165480894_    936 TTGACAAAGGTGCAAAGGCAATTCATTAGAGAAAGGATAGTCCTTTCAAC 985
                          i     i     v   i v     v i i     i      i       
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_165480894_    986 AAATAATAGTGGAATAATTGGA---CTGTATGCTAAAAATATGAATCCAG 1032
                             ii iv   i i  i    --- iii    v   i -     viii 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-ATGAAGTTGG 454

  chr2_165480894_   1033 AGCTAAAGCTTATACCTTTAACAAAAATTAACTCAAAATGATTAATACAT 1082
                          v ivv v  i i   v vv                    iv v ? v i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_165480894_   1083 CTAAATACAAAATGAAAAGCTGTAAAACTTT----AAAAAACAAAAATAC 1128
                               ii  i vvv   i  i       i ---- i      v ii?ii
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_165480894_   1129 A----TTCATGATCTGGATTTAGGCAACAAGTTCTTAA----GACACCAA 1170
                          ----   i   i  v iv        iiiv      i----        
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_165480894_   1171 A-GCATA-GTA-CATTTTTAAGAATTGGTAAATTGGATTTTATCAAAATT 1217
                          -   i - i -  vvvvv  i   v i         i  i         
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_165480894_   1218 AAAAACTTTTG--CTCTAAAAATACACAATTAAGAGAATAAAAAAGACAA 1265
                                    --  ii   ii-    v  i    i i i    -     
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGG-ACACTATCAAGAAAGTGAAAA-GACAA 702

  chr2_165480894_   1266 GCAACAGTCTAGGAGAAAATATTTCCAAATCACATATCAGACAAATAACT 1315
                         v v    vv i             v       i     v  i  ivi   
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_165480894_   1316 TGTATCCAGAATATATAAAGAACT--TAGAATATTCTGCAGTAAGAAAAC 1363
                                                 --  v  i--  vii i   i  i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAAC--TCAATAATAAAAAGAC 800

  chr2_165480894_   1364 AG----CCCAAATTAAAAATTGGCCAGGGACTTAAACAG---TTGTCTCA 1406
                          i----     v ?      v   v i   i  i  i  ---  -    v
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT-TCTCC 849

  chr2_165480894_   1407 AAAAAGGATATACAAATGGCAAATAAGCACATGAAAAGCTTTTCAACATC 1456
                            i i              v                 v vi        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_165480894_   1457 AAGTGCCTT 1465
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.59 (127 / 80)
Gap_init rate = 0.03 (29 / 901), avg. gap size = 2.00 (58 / 29)  


3131 22.44 7.76 1.06  chr2_165582069_165584538.rev     1128  1978 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_165582069_   1128 TGGAAAGATATCC--TGT----GGAT-GGAA---TTAATATTGTTAAAAT 1167
                                      --   ----    -    ---             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_165582069_   1168 GGCCATACTACCCAAAGCAATATACAAATTCAACATAATTCCTATCAAAA 1217
                            v     v      vii  v    i       ii   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_165582069_   1218 TTCTAACGGCATTCTTCACAGAAAT------------------------- 1242
                          i i i v  v  i  ii       -------------------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_165582069_   1243 ------------------AGAA-----AAAACAATCAGTATTGAAAA-GA 1268
                         ------------------    -----         ----       -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC----TTGAAAAAGA 196

  chr2_165582069_   1269 AAAATAAAGTTGAAGGCATCACACTTTCTGATTTCAAATGATATTACAAA 1318
                          i  i       i   vv        i ii        vvv  i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_165582069_   1319 GCTGCAGTAATCAAAACGGTATGATACTGGCATAAAAACACAAATATAGA 1368
                            i          i  i  i  i           ii i v v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_165582069_   1369 CCGATGGAACATAAAAGAGAGCCAAGAAATAAATCCAAACATATAGGGTC 1418
                         i i      i v  vv     i v         i   v    v  v    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_165582069_   1419 AACTAATTTTCTACAAGATCACCAAGAGGACACAATGGGGAAAGGATAGT 1468
                           i i      v     ivii      vv iv            i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_165582069_   1469 CTT--CAATAA-TGATGCTGGGAAAAATGGATTCTCAAATGCAAAAGAGT 1515
                            --   i  -  i        v  v     v?i  v          i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_165582069_   1516 GAAATTGGACCCTGATCTTACACCATACACAAAAATCAATTCCAAATGGA 1565
                            i        iv i  i        i        i  i  v       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_165582069_   1566 TAAGATACCTAAATGTAAGGCCCAAAACTGTAAAATTCCTAGAAGAGAAC 1615
                          v ? v             iv i      i     i  i       i   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_165582069_   1616 ATAGAATAAAAGCTCCTTGACATTAGCCTTGGAAATGATTTTTTTGAATA 1665
                             i?vv   v  i v    v  i vi v  v    i   i  v  -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TA 595

  chr2_165582069_   1666 TCACACTAAAAGCTCAGACTATAAAACTAAAAATAAATAAATAGGACTAC 1715
                          v    i      v  ii v i    vv       i      v     v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_165582069_   1716 ATCAAACTAAAAGGCCTCTGCAGTGGGGAGGGGGTGCAGGG-CGGGAA-- 1762
                               v v   ii i i  iiv vvii   i----  vvi- ii   --
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGA----CACTATCAAGAAAG 691

  chr2_165582069_   1763 -GAAAAGACAACGTACAGATTGGGAAAAAATATTTGCAAACCATCTAACT 1811
                         -           vi     v     i              i   v  v  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_165582069_   1812 GATAAAGGGTCACTACAAAAAGTTTACAAATAATTCTAATAACTCAATAG 1861
                              i  iiivv  ivv i i v  i   v  i   v i         i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_165582069_   1862 CAGAAAAATGATTAACTTGATTAAAAAATGGGCAAAGGACCTTAGCAGAT 1911
                         i i   i ii v    iii   ?                ii v ii   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_165582069_   1912 ATTTCTCCAAAGAAGACATGAAAATGGCCAACAGGTATACGAAAAAGTGC 1961
                                         i  iv          i i i i i     ii   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_165582069_   1962 TCAACATCATTAATCAT 1978
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (116 / 71)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 5.36 (75 / 14)  


3030 26.59 2.68 1.34  chr2_165604106_165606002      511  1405 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_165604106_    511 GGAAAAGCAGTCTTCGCTTGCGGATTGGAAGAATCAATATCATTAAAAGA 560
                              iii vi ivi i iii           v i     ii    i vi
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_165604106_    561 ACTATACTACCCAAAGCAATCTACAGATTCAACACTATTCCTATC----- 605
                         i v     v      vii               i v  i      -----
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_165604106_    606 --CAACATCATTTTTT----AAATTTAGAAAAAAACT-ATTATGAAATTC 648
                         --  i vv v      ----     ----i v  i  -  iv i      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATT----GACAAGCTGATCCTAAAATTC 147

  chr2_165604106_    649 GTATGGAATGAGAAAAGCCCCAT--TAGCTAAAACAACCCTGAATAAAAA 696
                         i       vviv  ii v    v--    i       i i    v  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_165604106_    697 GAACAAAGCCAGAGGCATCACATTATCTGACTTCAAACTATATTATGAGG 746
                                 iii    vv     i vi ii i      viv  i  ii i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_165604106_    747 CTACAGTAACCAAAGAAGCATCATACTAGTACACAAACAGACACATAGAC 796
                                  i   iiv  ii vi    i i i vii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_165604106_    797 CAATGGAACAGAATAGAGAATCCAGAAATAAAGCCACACACCTACAACCA 846
                                 i     v    i            v   i   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_165604106_    847 TCTGGTCTTTGACAAAGTCGACAAAAATAAGCAATGGGGAGAGGATTCCC 896
                         vi  i i  i     i vi v   i vi vv         i  i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_165604106_    897 TAGCCAATAAGTGGTGCTGAGATAACTGGCTAACCATATGCAGAAGAATG 946
                          vvi   i  i        i  i      v  ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_165604106_    947 AAACTAGACCCCTACCTTTTTCCATATACAAAAACTAACTTGAGATGGAT 996
                           ii i           iviv             i     ii i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_165604106_    997 TAGAGATTTAAATGTAAGACCTCAAACTATAAAAATCCTAGA-GAAAACC 1045
                         i ?   ii           v  v           v  i    -      v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_165604106_   1046 TAGG---AAATACCCTTCCCGACATTGGCCTTGGCGAGGAATTTATGGCT 1092
                             ---    ---    vi   v    vi v   i v iv  iv i v 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_165604106_   1093 AAGGCCTCAAAAGCAATCA--CAACAAAAACAAAGACTGACAAGTGGGAC 1140
                          v i vi        --  --        iv   i iv  i  i v    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_165604106_   1141 CTAATTAAACTAAAAAGCTTCAGCACAGCAAAAGAAACTATCAACAGAAT 1190
                         i v  i   v v    i   iv ii vv    i  v        v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_165604106_   1191 AAACAGACAACCTACAGAATGGGAGAAGATATTTACAAACTCTGTATATG 1240
                         i  v        i              i      i    iiv i   v  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_165604106_   1241 ACAAAGTTCCAATATCCAGAATCTGTAAGGAACTT----AATTTGACAAG 1286
                          i  i vv ivi          v i   i     i----  i ii i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_165604106_   1287 CAAAAACCAAATAACTCCATTAAAAGGTGGGCAAAGGATATGAACAGACA 1336
                         v    iv        i v   ?   ii            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_165604106_   1337 TTTCCCAAAAGAAGAAGACAAACAAATAGCCAATGAACATATGAAGAAAT 1386
                             i v        ---i v      i      i i  i     i i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGA---TATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_165604106_   1387 GCTCAACATTACTAATTAT 1405
                                  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (154 / 81)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 3.00 (36 / 12)  


2319 27.13 3.62 0.65  chr2_165719486_165721253.rev      503  1276 (492)    L1M4_orf2#LINE/L1      112   908 (0)  

  chr2_165719486_    503 TTCTTCACAGAACTTGAAAAAGCAATCTGAAATTTCATATGGAA---CAA 549
                           i  ii     v    v  ivii   iv   v           ---   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_165719486_    550 AACAGAGCCCACA-TAGCCAAAGCAAGACTAAGCAA-AAGAACAAATCTG 597
                         i--- ii    v -        i   vvi i iv  -         vi  
  L1M4_orf2#LINE/    162 G---GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_165719486_    598 GAGGCATCACATTACCCAACTTCAAACTATACTGTAAGGCTATACTCACC 647
                             vv     i v     i      viv    ii  i    i v v i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_165719486_    648 AAAACAGCATG-TACTGTTTTACAG-TATGCAGTATG---CAA---AACA 689
                           i    ii  -     viv  vi -  vi  -   i---   ---  i 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACA-TATAGATCAATGGAATA 307

  chr2_165719486_    690 ------------CAGAAATAAAGCCAAATACTTACAGCCAACTGACCTTC 727
                         ------------          v   v i i   ii i   i   ii   
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_165719486_    728 GACAAAGCAAACAAAAACATAAAGTGGAGAAAGGACACCCTATTCAACAA 777
                              i vviv   i v   vv i   i     i i vi  v        
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_165719486_    778 ATGGTGCTGGGATAATTGGCAAGCCACATGTGGAAGAATGAAACTGGATC 827
                                     i  i   vv ?       iii         ii    i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_165719486_    828 GTCATCGCTCACCTTATACAAAC-TCAACTCAAGATGGAGCAAATACTTA 876
                         vii i v v    v        v- i       i     v  ? v  i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_165719486_    877 AATTTAAGCCCTGAAGCCACAAAAATTCTAGAAGATAACATTGGAAAAAA 926
                            v    vv  i  i i i    v ii       v     v  ?iv   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_165719486_    927 CCTTTCTAGACATTGCCTTAGGCAAAAACTTCATGACCAAGAACCCAAAA 976
                         i   iv -   v   vv        viii   v iivi v  vv      
  L1M4_orf2#LINE/    558 TCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_165719486_    977 GTAAATGCGACAAAAACAAAGATAAACAGATGAGACTTAATTAAACTAAA 1026
                          i v v  i      iv   i   i i i  vi     v  i   v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_165719486_   1027 AAGCTTCCGCACAGCAAAATAAATTATCAGCAGAGTAAACAGACAACCCA 1076
                           i   ii ii vv    iv v i     iv i   i  v          
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_165719486_   1077 CAGAGTGGGAGAAAATATTCACAAACTATGCATCTGACAAAGGACAAATA 1126
                             i              ii    ii  ii      i  i    vvi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_165719486_   1127 TCCAGAATCTATAAGGAACTCAAACAGATCAGCAAGAAAAAAGCAAATAA 1176
                                 v     i      vv   iv   ii  v     ii       
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_165719486_   1177 TCCCATCAAAAACTGAGCTAAGAACATGAATGGACAGTTCTCAAAAGAAG 1226
                         i  v  i?    v  i  v   i iv     i    v     v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_165719486_   1227 ATATATAAATGGCCAACAAACATATAAAAA--TGCTCAATATCACTAATT 1274
                              i          i  i  i  i    --       i    ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_165719486_   1275 AT 1276
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.48 (123 / 83)
Gap_init rate = 0.02 (13 / 797), avg. gap size = 2.54 (33 / 13)  


 968 28.23 0.00 0.00  chr2_165732041_165736566     2886  3133 (1393)    L1M4_orf2#LINE/L1        1   248 (660)  

  chr2_165732041_   2886 TGGATAGATATTCCATGGTTATGTACAGGAAGACTCAATAGTGACAAGAT 2935
                             v      i     v i   v iv        i    v  vi     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_165732041_   2936 TTCAGTTCTTCCCAGCTTGATGTATAGATTCAACACAATCTCAGTCAAAA 2985
                         vv  i v  i    iv     v  i         i     i vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_165732041_   2986 TCCCTGCGAGTTATTTTGTGGGTACAGACAAACTAATTCTGAAGTTTATA 3035
                             v  vivi v     ii iv iv     i  i  i  i  i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_165732041_   3036 TAGAGAGGCAAAATATCCAGAATAGCCAATAGAATATTGATGTAGAAGAA 3085
                          i  i v    iiv i             v v   v    viv       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_165732041_   3086 CAAAACCAGAGGACTGCCACTATCTGACTTCAAGACTTACCCTAAAGC 3133
                             iiii       vv    vi ii i     i      ivi     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

Transitions / transversions = 1.41 (41 / 29)
Gap_init rate = 0.00 (0 / 248), avg. gap size = 0.00 (0 / 0)  

2198 24.31 1.89 3.49  chr2_165732041_165736566     3348  4034 (492)    L1M4_orf2#LINE/L1      233   908 (0)  

  chr2_165732041_   3348 AAGCTTGCTTTAAAGCTATAGTAATTAAGACATCATGGTATTAGAAAAAT 3397
                           i   i  vi       i      i      vii     i i v v  v
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_165732041_   3398 AATAGACAAATAGATCAATGGAACAGAAAAAGAGAGCCCAGAAATAG-CC 3446
                         i       v              i    vv-     i         i-  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATT-GAGAGTCCAGAAATAAACC 331

  chr2_165732041_   3447 C-TACATGAATATAGTCAACTGATCTTTGATAAAAGGGTGA-AAGAA-AT 3493
                          -     v--   i     i    i  i  i  --     v-    v-  
  L1M4_orf2#LINE/    332 CATACATT--TATGGTCAATTGATTTTCGACAA--GGGTGCCAAGACCAT 377

  chr2_165732041_   3494 GCAATGGAACAAAGATAGTCTTTTAAACAAATGGTACTGGAAGAACAGGA 3543
                         v      iiv  ii          v          i    i v   v   
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_165732041_   3544 CATACATATATAAAAAAAAAAAAAAAAAAAAAAAGAATTTACACACAGAC 3593
                         i ?v  i  ii    i  v---------------   v  iv  v vv  
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAAT---------------GAAGTTGGACCCCTAC 462

  chr2_165732041_   3594 CTTACACCCTTCAGGGAAATTAACTCAAAATGGTTCATGGACCTAAATGT 3643
                           i     v vi vii                 v   ?i           
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_165732041_   3644 AAAATGC-AAAACTATGAAATTCCTAGAATATAACAAAGACG---ACCTA 3689
                           i -  -        i   i  i     v v    v  i? --- i  v
  L1M4_orf2#LINE/    513 AAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_165732041_   3690 GATGACCTTGGGTATAGTAATAACTCTTTAGATACAACAAGAAGGGCATG 3739
                         vi           vvi i   iii ii       ii   vv  ii   ii
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_165732041_   3740 ATT--CAAGGAATAAATTATTAATAAGCTGGACTTTATTAAATTTAAAA- 3786
                          vi--   iii v   v  --i    ii       i  i   v      -
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATA--GATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_165732041_   3787 CTTCTGCTTTGTATAAGACAGTATCAAGAGACTGAA--GACAAACCGCCC 3834
                            i  ivi vi v i    v        i v    --     v  i vv
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_165732041_   3835 ACTAGGAGAAAATATTTGCAAAACACACATCTGATATAGGATTATTATCC 3884
                          v i                  v  i i        vi   i vv     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_165732041_   3885 TAAATATGCCAAAAACTCTTAAAACTAAACAATAAGAAAATGAACAACCC 3934
                         vi     iiv  i        v    v  i     i  i ii  i     
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_165732041_   3935 AATTTAAAAAATGGGCAAAAGATCTGAACAGAAATCTTACTAAAGAAGAT 3984
                             ?     -        i   i    i   v  i iv i         
  L1M4_orf2#LINE/    810 AATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_165732041_   3985 ATATAGGTGGTGAGTAAGCATATGAACCGATATTCAACATTATATATCCT 4034
                            i ii   iv i      i     vv   ii       i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (101 / 62)
Gap_init rate = 0.02 (16 / 676), avg. gap size = 2.31 (37 / 16)  


3159 27.97 0.44 0.44  chr2_165813553_165815560      609  1516 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_165813553_    609 TGGAAGAACATTCGATGTTCATGGGTAGGAAGAATCAATATCGTGAAAAT 658
                              ii i  i v          i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_165813553_    659 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGGCATCCCCATCAAGC 708
                            v     v     iv i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_165813553_    709 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 756
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_165813553_    757 TATGGAACCAAAAAAGAGCCTGCATCGCCCAGTCAATCCTAAGCCAAAAG 806
                                viiv  ii  v  v v  v   v iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_165813553_    807 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 856
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_165813553_    857 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 906
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_165813553_    907 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACGTATCTACAACT 954
                                i    i--    i  --        vv   iii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_165813553_    955 GTCTAATCTTTGACAAATCTGAGAAAAACAAGCAATGGGAAAAGGATTCC 1004
                         ivi i  i  i     ivv  vv  i v  vv       i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_165813553_   1005 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1054
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_165813553_   1055 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1104
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_165813553_   1105 TTAAAGACTTAAAAGTTAGACCTAAAGCCATAAAAACCCTAGAAGAAAAC 1154
                          i ?    i    v  v   v     i i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_165813553_   1155 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCACGTCTAA 1204
                         v    ?i v viv   iv   v v  vv i     v ii   viivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_165813553_   1205 AACACCAAAAGCAATGGCGACAAAAGCCAAAATTGACAAATGGGATCTAA 1254
                         i            vvi  i       vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_165813553_   1255 TTAAACTAAAGAGCTTCTGCACAGCAAAAGATACTACCGTCAGAGTGAAC 1304
                          i   v v  i i   i  ii vv    i  i    i ivv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_165813553_   1305 AGGCAACCTACAAAATGGGAGGAAATTTTCGCAACCTACTCATCTGACAA 1354
                           i     i   i        i    v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_165813553_   1355 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1404
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_165813553_   1405 AAACAAACAACCCCATCAACAAGTGGGTGAAAGACATGAACAGACACTTC 1454
                          i     i     v  i? v  i    ii  i  iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_165813553_   1455 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 1504
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_165813553_   1505 ATCACTGGCCAT 1516
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (150 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1495 24.57 13.43 3.71  chr2_165834468_165836159      501  1200 (492)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr2_165834468_    501 AAAACTCATACAGAACTACAAGGGACATAAAACAGCCAAAACAGCTTTGA 550
                             i     ii   v i        vi i  i          iii    
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_165834468_    551 AAAAAAAAAAAAAGAACAAAAAGTTGG-GGACCTGCACTATGTTATTTCA 599
                             i  ------       --     -    iii    viviv      
  L1M4_orf2#LINE/    191 AAAAGAA------GAACAAA--GTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_165834468_    600 AGACTCGTCATAAAAGGTACAGGAATTAAGAGAGTGTGGTACTGGTATAA 649
                          i   iiii i   - v     v   i    v             i    
  L1M4_orf2#LINE/    233 AAACTTACTACAAA-GCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_165834468_    650 AAAT-GACAAATAAACTAA----ACAGAAT--AGAGTTCAGAAATAGACA 692
                         ii  -    v   i ii  ---- i     --     i        i  v
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_165834468_    693 AACTCACCTATGGACAACTAATAATTGACAAAAGTTCAAAGGCAATGCAG 742
                         v iv  ii     v   i i  vv i     ii  v v   i v  v  i
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_165834468_    743 TGGAGAATGAATATTTTGTTTTTA-----TGCAGTTGGAATAATTAGATA 787
                            i   v     v i --   i -----  vv i   i i  i i    
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCT--TTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_165834468_    788 CTCAT-TTTAAAAAAGTGAATCTCAACATATCACTCATATGTTATACAAA 836
                         ?i  i- vi    i i    vi vi  viv vv    i ivv        
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_165834468_    837 AATTAACT-AAAATGGGTTATTTACCTAAATATAA-AGCATAAAACTA-- 882
                                 -       i i ?vv        i   -   -        --
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATA 528

  chr2_165834468_    883 --ACT-TAAGAAGAAAATTTAGAAGAAAATACTCATGGTGTTGACTT-GG 928
                         --   - v         iv   i? v    vi  i  iiv   iv  -  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_165834468_    929 CAAAAATTTCTTAGAT------CCAAAAGAATGATTTAAACAA-AAAAGC 971
                            vii          ------       v i-----  i   -     -
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCAC-----AAGCAACAAAAG- 622

  chr2_165834468_    972 TAAGAAATA-ATACTCTGGAT--------------AAACT---GCACTTT 1003
                         -  i     -   vvi    i--------------     --- ii   i
  L1M4_orf2#LINE/    623 -AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_165834468_   1004 AAA----------------------------------------------- 1006
                            -----------------------------------------------
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_165834468_   1007 TATTTGAGAAGCATATATGTGATATAGGACTTACATCCCAAAGAGTCAAA 1056
                               vi  v       v     vi      ii    vi  v vvi   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_165834468_   1057 GAATGCTCAAAACTCAATAATATGAAATCAAACAACCTAACTAAAAAAAA 1106
                            iv  i v            vi  iv    i    i  i ?     v-
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT- 820

  chr2_165834468_   1107 AGGAGGGGATTAAAGATTTGAACAACCACTTCATAAAAGAAGCTATACAG 1156
                         ----   v --  i        i iv  i   viv       v      i
  L1M4_orf2#LINE/    821 ----GGGCA--AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_165834468_   1157 ATGGAAAATAAGAACAGAAAAAGGTGCTCAACATTAGTAATTAG 1200
                             vv      v   vi     i          i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (102 / 66)
Gap_init rate = 0.03 (26 / 768), avg. gap size = 4.62 (120 / 26)  


2428 27.01 4.40 0.38  chr2_165944511_165946722.rev      925  1720 (492)    L1M4_orf2#LINE/L1       81   908 (0)  

  chr2_165944511_    925 CAACA-AATTCCCATAAAAATACCACCATTATTCTTCATAGAACTAGAAA 973
                             i-   i  i  v     v   v vviv  i  iii    v v  v 
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA 130

  chr2_165944511_    974 AAATAATCTTAAAATTCATATGAAAATAAAAAGAGCCC-GCATAGTCAGA 1022
                          iv i   i             i    iv  i ii   - v    i  i 
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr2_165944511_   1023 GCAAGACTAAACAGAAAGAACAAATTTGGAGGCATCACATTACCTGAATT 1072
                         i   vvi i  v ii         v       vv     i v  ii v  
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr2_165944511_   1073 CAAA-----CTATAGGGCTATAGTCACCAAAACAGCA-GGTACTGGCATA 1116
                             -----   i ii    i   v i   i    ii-            
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr2_165944511_   1117 AAAGTCAGCATATAGACCAATGGGACAGAATACAGGATTCAGAAATAAAG 1166
                          iii vii        i      i i     vv  ii i          -
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA- 329

  chr2_165944511_   1167 CCCA-ATGTTTACAGC---------TTTGACAAAGCAAACAAAAAAATAA 1206
                             - ii    ii i---------  i     i vviv   i vv  vv
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_165944511_   1207 AGTAGGGAAAAGACTCCCTATTCAATAAATGGTGCTGGGATAATTGGCAA 1256
                          i i      ii ivvi  v     i              i  i   vv 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_165944511_   1257 ACCACATGTAGGAGAATGAAACTGGATCCTCATATTTCACCTTATACAAA 1306
                         ?       i ii        ii    i  ii iv iv    v        
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_165944511_   1307 ACTCAATTCAAGAGGGATCAAGAACTTAAAT-TAAGACCTGAAGCCATAA 1355
                          v i  i    i v      ?ii  i     -     v  i  i i    
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_165944511_   1356 AACTTCTAGAA-----CATCAGAAAAACCCTTCTAGACATTGGCTTGGGC 1400
                             ii     -----   vi ?iv  vi    vv   v    v  i   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_165944511_   1401 AAAGACTTC--AAA----AC-CCAAAAGCAAGTGCAACAAAAACAACAAT 1443
                           v ii   -- i ----  -         viv         iv  v   
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_165944511_   1444 AAATAGATGAGACTT-ATTAAACTAAAAAGCTTCTGACCAGCAAAATAAA 1492
                          i   i  vi     -  i   v v    i   i  vv vv    i--i 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG--GA 677

  chr2_165944511_   1493 TACT--TGGCAGAGTAAACAGACAACCCACAGAGTGGGATAAAATATTCA 1540
                         i   --iiiv i   i  v              i     v        ii
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_165944511_   1541 CAATCTATACATCTGACAAAAGACTAATATCCAGAGTCTACAATGAACTC 1590
                            vii   i      i  ii    vi        i v  i  v      
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_165944511_   1591 AAACAAATCAGCCAGAAAAAAACAAACAATCTCATC-AAAAGTGGGCTAA 1639
                         vv    v   iiv v     i     i  i iv  i-    i     v  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_165944511_   1640 GGACGTGAATAGACAATTCTCAAAAGAAGATATATAAATGGGCAACAAAC 1689
                            iv          v     v            i      v   i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_165944511_   1690 ATATGAAAAAATGCTCAACATCACTAATTAT 1720
                          i       i             ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (133 / 79)
Gap_init rate = 0.02 (16 / 828), avg. gap size = 2.38 (38 / 16)  


3914 19.08 3.03 1.35  chr2_166014857_166018522     2284  3174 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_166014857_   2284 GAAAGCACATTTTATATTCATAGATTAGAGGAA--AATATTGTTAAGATG 2331
                              - i  iii  i     i    i  i  v--               
  L1M4_orf2#LINE/      3 GAAAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_166014857_   2332 GCAATACTCACCAAATTAATCTACAAATTTAACGCTATTCATATCAAAAT 2381
                                  v       i       i   i     v  i v         
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_166014857_   2382 CCCAGCTACCTATTTTGCAGAAAGTGATAAATTGACTGTAAATTTTATAT 2431
                                i   v           v   i  ii   iiv    v  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_166014857_   2432 GAAAATGCAAGAGACT----ATATGCCACA-CAATCTTAACTAGAAAAAA 2476
                          i         i   i----   -    v -       i -- i  i  i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATA-GCCAAAACAATCTTGA--AAAAGAAG 198

  chr2_166014857_   2477 AATAAAGTTGGAGAACTCAAACTTCCAAATTTTAAAACTTACTACAAAGC 2526
                           i          i     v      v     i                 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_166014857_   2527 AAAAGTAAGCAAGATAGTTTGGTACTGGCATAAGGATAGCTATATACATC 2576
                         v v     v     i   v                    vi     v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_166014857_   2577 AATGGAATAAAATTGAAATTCCAACAGTAAGTCTTCATATTTATGTTAAA 2626
                                  i      i v    iv i   ii ivi i       v v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_166014857_   2627 TTAATTTTCAACAAGA---CCACTAGACAATTTTATTAAGGAAAGAA--G 2671
                           i      i     i---   --    v   iv  -ii        -- 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCA--AGACCATTCAAT-GGGGAAAGAATAG 395

  chr2_166014857_   2672 CCTTTTCAACAAATGGTGCTTGGACAAGTGAATATCCACATATGAAAGAA 2721
                         i                   v      v  i   ?      iii      
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_166014857_   2722 TGGAATTGAACCCTTACTTAATAACATATATAAAAATTAA-----GATAG 2766
                           i i   i    i   i v i v      i         -----i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_166014857_   2767 GTCATAGGCCTAAAGGTA-GAGCTAAAACTATGAA-CTGTTAGAAGGAAA 2814
                         i   ?  i      v   -             i  -  v       i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_166014857_   2815 TTTAGAAGTAAATCTTCATGACCTATTATTAAGCAATGATTTCTTAGATA 2864
                         iv   i?          i      vvvi   i      i           
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_166014857_   2865 TGATACCAAAAGCACACACAATAGCAATAAGAAAAAAAAGGTTCATTGGA 2914
                            i            vi   ---   -         v  i vv      
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAA---CAA-AAGAAAAAATAGATAAATTGGA 641

  chr2_166014857_   2915 CTTTATCAAAATTAGAAACTTTCATACTGCAAACAATATCATCAAG---- 2960
                            i          i       ii i  v    vi i ii      ----
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_166014857_   2961 TAAAAAGACAACTTAAAGAATGGAAGAAGACATTTGCAACCCAGATATCT 3010
                          i          ii v       i    i i        vi  v      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_166014857_   3011 GATCATG-ATTTGTATCTAATATATGTAAAGGATTATTATAACTCCACAA 3059
                            v v - i       i iv    i     i i v   i     v i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_166014857_   3060 CAAATAAAATAGATAACTCACT--AAAAATGATCAAAATATTTGAATAGA 3107
                         i   -  i i i     i  v --       iv    iv           
  L1M4_orf2#LINE/    792 TAAA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_166014857_   3108 CATATTGAAAAAGGAGTTAGACAAAAGGCCAATAAGCACAT-AAAAGATG 3156
                            v ivvv    i  v  v     v               -        
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_166014857_   3157 GTCAGCGTCACTGGCTAA 3174
                         v   i i   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (108 / 59)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 1.95 (39 / 20)  


2889 26.17 1.41 2.82  chr2_166096382_166098663.rev      870  1790 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_166096382_    870 TGGAAATGCATCTCATGCTCATAGACGGGTAGAATCAATATTGTAAAAAT 919
                               vii   i    i    i  iv  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166096382_    920 GACCATATCTCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 969
                          i v   iii  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166096382_    970 TACCACCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTTATA 1019
                          v   v vv v  i  ii     v v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_166096382_   1020 TGGGAGCAAAAAAGAGCCCACATAGGCAAAGCAAGATTAACCAAAAAGAA 1069
                            i iiiv  ii  v  viv    v    i   vv  i vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_166096382_   1070 CAAATCTGGAGGCATCACATTGCCTGACTT-AAAACTATACTATAAGGAT 1118
                             vi      vv     i v  ii i  -      -     i  i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr2_166096382_   1119 ATAGTCATCAA-ACAGCATAGTACTGGTAAAAAAAAAAAAAAAAAAAAAA 1167
                          i   v     -    ii i       i v  ii v i -----------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA----------- 288

  chr2_166096382_   1168 AAAAGCACATAGACTGATGGAACAGAATAGAGAACCTAGAAATAAAGCCA 1217
                         -----  i     iii      i     v    ii i         v   
  L1M4_orf2#LINE/    289 -----CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_166096382_   1218 AATACTTACAGCCAACTGATCTTCAACAAAGCAAACAAAAACATAAAATG 1267
                         v i i   ii i   i    i   i    i vviv   i v   vv    
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_166096382_   1268 GGGAAAGGACATCCTATTCAACAAATTGTGCTGAGATAATTGGCAAGCCA 1317
                                i i vi  v          v      i  i  i   vv ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_166096382_   1318 CCTGTAGAATTATAAAACTGGACCTTCATCTCTCACGTTATACAAAAATC 1367
                          v  i i  vv  i  ii      iii i   v   vv           i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_166096382_   1368 AACTCAAGATGGATCAAAGACTTAAATCTGAGACCTGAGACCATATAAAT 1417
                                i        ?    i     v i   v  i i  i   v  v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_166096382_   1418 CCTAGAAGATAACATCAGAAGAAAACCTTCTATACATTGGCTTAGGCAAA 1467
                          i       v     -  i? v   i    vvv  v    v        v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_166096382_   1468 GACTT------TATGACCAAGAACCAAAAAGCAAATGCAATGAAAACAAA 1511
                          ii  ------      -----       -   v v    ii   iv   
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGAC-----ACCAAAA-GCACAAGCAACAAAAGAAAA 626

  chr2_166096382_   1512 TATGAATAGATGGGACTTAATTAAA-TGAAAAAGCTTCTGTGCAGCAAAA 1560
                         v  ii   i  v      v  i   - v     -   i     vv    i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAG 675

  chr2_166096382_   1561 GAAATAATCAGCAGAGTAAATAGACAACCCACAGAGTGGGAGAAAATCTT 1610
                           v iv    iv i   i  v              i           v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_166096382_   1611 CTCAAACTATGCATCCAACAGAGTACTAATATCCAGAATTTACAAGGAAC 1660
                         iv    ii  ii   ii i ii v   vi          v  i  i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_166096382_   1661 TC----AAATCAGCAAGAAAGAAACAAAACAATCCCATCAAAAGGTGGAC 1706
                           ----  v   ii  v   i i     -i  i  v  i?   ii   i 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGC 824

  chr2_166096382_   1707 TAAGGACATGGATAGACAGTTCTCGAAAGAAGATATAAAAATGGCTAACA 1756
                         v     iv  i       v     v            v       i  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_166096382_   1757 AACATAAGGAAAAATGCTCAGTGTCACTAATGAT 1790
                          i  i v i   i       iii   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.25 (39 / 12)  


2726 25.22 4.20 3.76  chr2_166140761_166142703.rev      551  1454 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_166140761_    551 TGGAAAAACACTCCATATTCATAGATTAGAAGAATCAATGTCATTAAAAT 600
                               i i ii    i     i    i     v i   i ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166140761_    601 GACTGTTCTGCCCAAAGCAATCTACAGATTCAATGGAATTCCTATCAAAT 650
                          i vi v  v      vii              i v   i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166140761_    651 TACCAA-TGTCATCTTTCACAGAGTTACAAAAAAGT--ATTCTAAAATTC 697
                          v   i-  i - i   ii    i-- ivi v   i--  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chr2_166140761_    698 ACATGGAGCCACGAAAAAGCCCAAATAGCCAAAGCAATCCTAAGCAAAAA 747
                          i     ivii i iii v  vi          i     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_166140761_    748 GAACAAAACCAGAGGTATTACATTGCCTGACTTTAAACGATACTACAAGG 797
                                iiii    vv i   i v  ii i  i   vvv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_166140761_    798 CTGTAGTAACCAAATCAGCATGGTACTAGTACAAAAATAGACACAGAGAT 847
                           ii     i   iv   ii       i i i  ii       i v    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_166140761_    848 CAATGTAACAGAATAGAGAACACAGAAATAAAGCTGCACATCTACAATCA 897
                              v  i     v    iiv          v iii    i  iii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_166140761_    898 ACTGATCTTCAACAAAGTTGACAAAAAGAAACAATGGGGAAAGGACACCC 947
                          i    i   i    i v  v   i vv vv            i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_166140761_    948 CACTCAATAAATTGTGCTGGGAAAGCTGGCTAGCCATATGCAGAAGAATG 997
                         ivi    i    v         v i    v  ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_166140761_    998 AAACTGTACCTCTACCTCTCACCATAAACAAAAATTAAC--AAGATGGAT 1045
                           ii  v   i       v       v            --  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_166140761_   1046 TAAAGACTTAAAT-TAAGGCCTCAGACTGT--------TAAAAAAAATTC 1086
                         i ?    i     -    iv  v i   i --------  i  i   viv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_166140761_   1087 TAGAAGTAAACCTCTTCTGGACATTGGAAATGCCCAGAATTTGGGCAAGA 1136
                            i?     --     vv   v    i------------  i     vi
  L1M4_orf2#LINE/    548 TAGGNGTAAA--TCTTCGTGACCTTGGG------------TTAGGCAATG 583

  chr2_166140761_   1137 ATTTTGGCAAAAAATTTATGACTAAGCCCTTAGAAGCAAATGCATCAAAA 1186
                         i   --- vv i ---      ---i  --- i     v v   v     
  L1M4_orf2#LINE/    584 GTTT---CTTAGA---TATGAC---ACC---AAAAGCACAAGCAACAAAA 621

  chr2_166140761_   1187 ACAAAAATTGACAATTGAGACTT------ACTTAAGATATTCTGCATAGC 1230
                         iv      v  i  v vi     ------ v    i vv  i  iiivv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_166140761_   1231 AAAAAAAAAAAAAAAATCAACAGATTAAACAAACAACCTACATAATGGGA 1280
                            ii v vv -----    v i v i  v i      i   v       
  L1M4_orf2#LINE/    672 AAAGGACACTA-----TCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_166140761_   1281 GAAGATATTTTCAAACTATGCATCTGACAAAGGACTACTATCTAGAATCT 1330
                            i      v    ii  ii      i  i     vv    i     v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_166140761_   1331 ATAAAGAACTT----AAATCAATAAGAAAAA-------AACTCA-CTAAA 1368
                                   i----  v       v     -------   i  -i ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_166140761_   1369 AAGTGGGCAAAGGACATAAACAGACACTTCTTAAAAGAAGATATACAAGT 1418
                           i           iv i  i     i    iv               i 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_166140761_   1419 GGCCAA------CATGAGAAAATGCTTATCACTAATCTTCAG 1454
                               ------     i  i     i v  ii ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (146 / 78)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.79 (72 / 19)  


3142 27.42 0.55 0.55  chr2_166167452_166173728     4878  5785 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_166167452_   4878 TGGAAGAAAATTCCATGCTCATGGGTAGGAAGAATCAATATCTTGAAAAT 4927
                              ii v  i     i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166167452_   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166167452_   4978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_166167452_   5026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_166167452_   5076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5125
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_166167452_   5126 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_166167452_   5176 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5223
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_166167452_   5224 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5273
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_166167452_   5274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_166167452_   5324 GAAACTGGATCCCTTCCTTACACTTTATACAAAAATCAATTCAAGATGGA 5373
                            ii    i    v   i    iv           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_166167452_   5374 TTAAAGATTTAAACGTTAGACCCAAAAGCATAAAAACCCTAGAAGAAAAC 5423
                          i ?   ii    i  v   v i    vi      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_166167452_   5424 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5473
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_166167452_   5474 AACACCAAAACCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT-A 5522
                         i         v  vvi          vv     v  i    v   ii - 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_166167452_   5523 TTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5572
                          iv   i    i -   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_166167452_   5573 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCGTCTGACA 5622
                         v  i     i   iv            v  i    vii ivii     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_166167452_   5623 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5672
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_166167452_   5673 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5722
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_166167452_   5723 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5772
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_166167452_   5773 CATCACTGGCCAT 5785
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1735 25.25 4.21 1.00  chr2_166206686_166208802.rev      501   999 (1118)    L1M4_orf2#LINE/L1       89   603 (305)  

  chr2_166206686_    501 TTCCGATCAAAATCTCAGCAGGCTTTTTTGTAGATATCTACAAGCTAACT 550
                          i  v         i    v v        i   v  iv       i ii
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chr2_166206686_    551 CTAAAATTCACAGTGTAATACAAAGGAATTAGAATA-CCAAAGCAATTTT 599
                                   i vv v   i   i   vii      -     i    i  
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr2_166206686_    600 GTAAAAGAAGA-----------GGATTCACACTATATGATTTCAAGACTT 638
                          v         -----------   i       vivii       i    
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_166206686_    639 ACTGTAAAGCTACTGTAATAAAGACAGTGTGATAATAGAAAAAGTATAAA 688
                            ii        v     v           i  v i v v   v   i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_166206686_    689 TACATACGTCAGTCGGACACAATAGAGA--CTAGAAATATACCTGCACAA 736
                         i i   vi   i v i i v   v    -- i       v   iii   v
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_166206686_    737 ATGTG----ATTGATTTTCTGACAAAAATGCAAAGTCAATTTAGTGGATA 782
                         v i  ----          -     iii   v   v v   i i   iv 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_166206686_    783 AAAAATAGTCTTTTATAAAAAA--GTGATGAAACTATTGGATGTCCGTAA 830
                           i           -i  v   --   v  ii  v i     i?  ii v
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_166206686_    831 GCACATAAGTAAAATTGTGAACTTCAATCTTTCATAACATGCAAAAATTA 880
                            v vi i i  i   --i  ii v i  iv  iv i  i         
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTG--GACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_166206686_    881 ACCCCAAACAGATCATATGAC-TAAATACAAAACATAAAATTATAATACA 929
                           i v   ii     ? -   -     ii  i vv     i     v  v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWA-GACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_166206686_    930 TTTAGAAGAAAACATAGTTGAAAATCATTGTGACCTTGGGTTAAGCAAAG 979
                         i                v? v     v i              i    v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_166206686_    980 ACCTCTTAGATATAACATCA 999
                         iii          i   i  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCA 603

Transitions / transversions = 1.62 (76 / 47)
Gap_init rate = 0.02 (10 / 515), avg. gap size = 2.60 (26 / 10)  

 817 23.28 5.57 1.97  chr2_166206686_166208802.rev     1321  1625 (492)    L1M4_orf2#LINE/L1      593   908 (0)  

  chr2_166206686_   1321 ATATAAACATCAAAATCATAATCCACAGAAGAAAAAAACTGATATCAT-- 1368
                             i -  i     v  i  v v   i         -iv    -v  --
  L1M4_orf2#LINE/    593 ATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATA-AATTG 639

  chr2_166206686_   1369 GACTTTACCAAATTTAAAA-CTCT-------AAAAGGATGTGGTCAAGAA 1410
                              i i    v      -  i -------v      iiivi       
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_166206686_   1411 AACAAAAAAGCATGCCACAGACAGAGAGAAAATGTTTGCAAATCACCTAT 1460
                          iii    ii  vv       vv i        i           iv   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_166206686_   1461 TTCCTACAGGATTTTTATGCAGAATATTTATAAAGAACTCTCAAAACTCA 1510
                         i vv  vi   i  v   v        --            i v      
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATAT--ATAAAGAACTCTTACAACTCA 787

  chr2_166206686_   1511 AAAATAGAAA-ACAACTTAGTATAATT------TGGGCAAAATGTATGAA 1553
                          v    i   -    v - iivi    ------        ivi v    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_166206686_   1554 CAAACACTTCACAAAAGAAAACAAACAGATGGCGAATAAGCAGAAGAAAA 1603
                         i i   i   v v      i i v   i     v        v v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_166206686_   1604 CATGTTCAATGTTATTATCCAT 1625
                         v   i    ii i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (40 / 31)
Gap_init rate = 0.03 (10 / 316), avg. gap size = 2.30 (23 / 10)  


1935 26.12 3.34 3.05  chr2_166209612_166211274.rev      499  1187 (476)    L1M4_orf2#LINE/L1      218   908 (0)  

  chr2_166209612_    499 CACTACCTGACTTCAAAGTATATTACAAAGAAATAATAGTAAAAACAGTA 548
                             v  ii i      iiv  i       vv i i  i v  i     i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_166209612_    549 TGGTACTGACATAAAAATGGAAAAATTGACCAATAGAATAAAATAGAGAA 598
                                 i     ii  i  v v  v  i    i     i   v    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_166209612_    599 ACCAGAAATGAACTTAAAAATCCATGGTCAATTAATATTTCACAAAGCTG 648
                         v        i   ii v v  ii          i  v  iv    i v  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_166209612_    649 CCAAGAGCACACAATGGGGAATAGACAGTCTCTTTAATAAAGAGTGTTGA 698
                               v  iv          vii i     i  i  i   vi   i  i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_166209612_    699 GAAAACTGGATATCCACATGCAGAAACATGAAAC--AACCTTTATCCTTT 746
                           v         ?         i  iv     ii--i   ii  i --- 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC---T 464

  chr2_166209612_    747 TATCTCATATTCGTTACAAAAGTCAACTCAAAATGGATTAAAGTCTTAAA 796
                         i ivi     -----      i i              i ?  v i    
  L1M4_orf2#LINE/    465 CACACCATAT-----ACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_166209612_    797 CCTAAGACCTGAAACAGTAA--CTGCACTAGAAGAAAGCATAGGA--AAA 842
                         iv     v  i    vi   --  - -i         i      ?--   
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACT-C-TTAGAAGAAAACATAGGNGTAAA 557

  chr2_166209612_    843 CACCACATGACACTGGTCTGGGCAATTATTTTTTTGGATTTGATTCTAAA 892
                         i- iv i    vi   vi i      vi   i  -i   v   iv i   
  L1M4_orf2#LINE/    558 T-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAA 605

  chr2_166209612_    893 AGATCAAGCAACAAAAGCAAAAATAGACAAAGGGAATTATATCAAACTTA 942
                           vv             v         i   vv i i vi      v   
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_166209612_    943 CAAG-TTTTGCACAGCAAAGGAAGCAGTTAATAGGATGAAGAAATAATAT 991
                         v  i-     ii vv       vi vi i  v iii    i i i  ivi
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_166209612_    992 GCAAATTAGGATAAAATATTTGCAA-TCAAAACATCTGATAGGGAGTTAA 1040
                         i  i v i   v             -   v -i        i  iii vi
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATA-TATCTGATAAGGGACTTG 754

  chr2_166209612_   1041 TATCCAAAATATGTAAGGAACTCAAAAAACTCAATAGCTAAAAAACAA-- 1088
                               i     i   i      vv v         iiv    i    --
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_166209612_   1089 --CCTGATTAAAAGATAGGCAAAGGACTCAA-----CATTTCTATCAACA 1131
                         --  ii   ?   i  i         i ii -----       -i   - 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT-CCAA-A 852

  chr2_166209612_   1132 G----TATATGACTGGGAAACAAATATGTAATAAAAAAACTTTGCT-AAT 1176
                          ----    ii v   vv  i  ii i---  i    i ---    -  i
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCAC---ATGAAAAGA---TGCTCAAC 896

  chr2_166209612_   1177 -TTATAGACATA 1187
                         - i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (119 / 57)
Gap_init rate = 0.03 (21 / 691), avg. gap size = 2.10 (44 / 21)  


3251 24.60 3.74 0.79  chr2_166294690_166297266.rev     1204  2085 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_166294690_   1204 TAGTAAGACATCC-ATGCTCACAGATTGGAAGAATTCATATTGTTAAAAC 1252
                          i v    i    -   i   ii          v  v          i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166294690_   1253 GACCATACTACTCAAAGCAATTTACAAAT-CTACGCAATCTCTATCAAA- 1300
                          i v     v i    vii  i    i  - v        i        -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166294690_   1301 CACCAATGACATTCTTCACAGAATAAAAAAAAAAAC--ACTCTAAAAGTC 1348
                         iv   iivi v  i  ii     --- vvi v  i -- ii      v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA---ATTGACAAGCTGATCCTAAAATTC 147

  chr2_166294690_   1349 ATATGGAACTACAAAAGACCCTGAATAGCCAAAGCAATTCTCAGCAAAAA 1398
                                 v i   ii     v           i    ii v iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_166294690_   1399 GAACAAAGCTGGAGGCATCACATTACCTGACTTCAAAATCCACTACAAAG 1448
                                 i      vv     i v  ii i       iii         
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_166294690_   1449 CTGTAGTAACCAAAATAGTGTGGTACTGGCATCAAAACACACACATAGAC 1498
                           ii     i   i i                v ii i v   i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_166294690_   1499 CACTGGAACAGAACAGAAGACCCAAATAGAAATCCATGCATTTACAGCCA 1548
                           v     i    iv  iiii   i v v   i    i      ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_166294690_   1549 ACCTGTTTTCAACAGAGCTGGCAAGAACATACAATGGGGGAAGGATAAGT 1598
                          iivi     i   ii v  v     v   v        i   i   -  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-GT 396

  chr2_166294690_   1599 CTTTTCAATAAGTGGT-TTGGTGAGAACTGAATATCTATATGCAGAAAAA 1647
                                 i  i    -i   -  v     i   ? i i     i  i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGG-GACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_166294690_   1648 GTAAACCAGACTCCTATCTCTCACTGTATACAAAAATCAATTCCAAATGA 1697
                         vv  iiii   i    i   v   ii           i  i  v     i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_166294690_   1698 ATTAAAGACTTAAACATAAG-GCTCAAAACCATAAAACTCTCAGAAGAAA 1746
                           i ?    i    ii    -   -     i          i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAA 544

  chr2_166294690_   1747 ACACAGGGGAAATTCTTCATCTCATTGGTCTAAGGAAAGAGTTCATGGGT 1796
                            i   ? v  v     i vv v    vi  i v  v iv   v i i 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_166294690_   1797 AAGACTTCAAAAATGTAGGCAACAGAAACAAAAATAGATACATGGGACTA 1846
                          v   vi     iiii i      i  iv           v  v     v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_166294690_   1847 TATCAGGATAAAAAGCTTGTGCACAACAAAGGAAACAATCAACAGAGTGA 1896
                         i    ii  v    i   v  ii vv       v  v     v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_166294690_   1897 A---------------------GAAAATATTTTCAAACTATTCATCTGAC 1925
                          ---------------------          v    ii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_166294690_   1926 AAGAGACTAATATCCAGACTATATGAGGAATTCAAACAACTCAAGAACAA 1975
                            i    vi        v     i i   i  vv         v  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_166294690_   1976 AAA-ACCAAT---CCAATT-AAAAATGGTCAGAGGATCTGAACAGTTATT 2020
                            -  v   ---      -        v  i     i    i  vi   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_166294690_   2021 TTTCTAAAGAAGACATATAAATAGCCAACAAGTATTATTAAAAAATGCTC 2070
                          i  i        i   i    i     i   i i-  v    i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCAC-ATGAAAAGATGCTC 893

  chr2_166294690_   2071 GGCATCACTAATCAT 2085
                         ii     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (143 / 71)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  


3789 17.65 7.76 0.94  chr2_166410465_166412665      864  1713 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_166410465_    864 TGGAAAAACATCCCATGTTCATGGATCAGAAGACTTAATATTGTTAAAAT 913
                               i i                 ii                   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166410465_    914 GGCAAT---------------------------------CTCTATTAGAA 930
                               --------------------------------- i    i i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166410465_    931 TCCCAGATATCATT---GTGGAAATTGACAAGCTGATACTAAAGTTCATA 977
                               v ii v  --- ii                 v     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_166410465_    978 TAAAATCGCAAAGGGTACATAAGAGCTAAAACAATCTTGAAAACACAGAA 1027
                          ii  vi    i  iiv  v  v   i                viv    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_166410465_   1028 AGCAAAGTAGAAAAAAATCACACCTCTCAATTTCAAAATTTACTCCAAAA 1077
                         --      v i ii v-      i  i           i     v    i
  L1M4_orf2#LINE/    201 --CAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_166410465_   1078 TGATGGCAACCAAAATAGTGTGGTGCTAGCACAAGGACAGA-ATATAGGT 1126
                         iv ii i  i   i i        i  i   i     i   -      i 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_166410465_   1127 GAAAGGAACTGAATTGAGAG-----------ACC-ATGTTTCTATGGTCA 1164
                         v  v    iv          -----------   -  iiv i        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_166410465_   1165 ACTGATTTT-GACAAGAATGCCACAACCATTCAGTGAGGAGAAGAATAGT 1213
                          i       -      ii     vi        i  i   -         
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATAGT 396

  chr2_166410465_   1214 CTTTTCAACAAATGGGGCTGGAACTATTGGATATCCACATGCAAAATAAT 1263
                                        v     i  v i      ?            v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_166410465_   1264 GAGGCTGAACCCTTACCTCATACCATATACAAAAATAAACTTAAAATGTA 1313
                           i i  i    i       i               v    i      v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_166410465_   1314 TCAAAGACCTAAATTTAAAACGGAAAACCATAAAAACTCATTGAAGAAAA 1363
                            ?          v   i vvv     i      -   v v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr2_166410465_   1364 CATAGACATAAATCTTCATGACCTCAGATTTGGCAAAGGATTCTTACATA 1413
                              i?i         i      ii i  v     v  v      v   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_166410465_   1414 TGGCATGAAACGTATGAACAACAAAAGAAAAAAAATTGATAATTTGAACT 1463
                           i  iv   v i ii i               v --     v   i   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACT 643

  chr2_166410465_   1464 TGATAAAAATTAAAACCTT--GTCCTTCAAAGGAAACCACCAATAAAGTG 1511
                          v  v          v   --  v          v  i i   v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_166410465_   1512 AAATAACAATTTCACAGAATGGGAGAAAATATTTGCAAATCATATCTCTT 1561
                            vi    ii-                                 v   v
  L1M4_orf2#LINE/    694 AAAAGACAACC-CACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_166410465_   1562 ATATGGGACTT---TCCAAAATATATAAATAAC----ACAACTTACTAAG 1604
                            v       ---    i          v   ----      i v   v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_166410465_   1605 AAAAA---AGACAGCCCAAATTAAAAATAGGCAAACCAC---AATAAACA 1648
                              --- i i i     v ?      i      vv i---    i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_166410465_   1649 TTTCTTCAAGGAAAATATACAAATGGCCAATAAGCACATGAAA-GATGTT 1697
                              i   i   i                             -    i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_166410465_   1698 TAACGTAATTATTTAT 1713
                         i   i v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (92 / 54)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.11 (74 / 18)  


 326 26.32 9.21 0.66  chr2_166413933_166420211.rev        2   153 (6126)  C L1M4_orf2#LINE/L1   (376)   532   368  

C chr2_166413933_    153 CCATAACAATTCCTTTGGGAAAGCA-AGT---TCC--CAAATGGTGTTTG 110
                            vi  v    vv v       v -   --- i --         i v 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

C chr2_166413933_    109 AACAAC-GGA-----AAAT-TAAATTAGTAAATCTCAACCTCCTACATCA 67
                         i     -   ----- v  -i   vv i i  vi vi   -     v   
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC-CCTACCTCA 466

C chr2_166413933_     66 CTCTATGTACAAAAATTATTTCAAGATTAATCATTGACTTAAA-ATAAAA 18
                          v i  i           vi    i  vi    ?v   i    -i   i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

C chr2_166413933_     17 GTTAGAAAAATAAAGC 2
                          i  i  vv     i 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAAC 532

Transitions / transversions = 1.05 (20 / 19)
Gap_init rate = 0.05 (8 / 165), avg. gap size = 1.88 (15 / 8)  

3191 27.34 0.55 0.44  chr2_166413933_166420211.rev     4881  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_166413933_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166413933_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCGCCATCAAGC 4980
                            v     v     iv i  i           i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166413933_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_166413933_   5029 TGTGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                          i     viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_166413933_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTTTACTACAAGGC 5128
                                i      vv       v  ii i      vi         i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_166413933_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_166413933_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACGACATACCTACAACT 5226
                                i    i--    i  --        vv v i i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_166413933_   5227 GTCTGATCTTTGACAAATCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5276
                         ivi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_166413933_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_166413933_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_166413933_   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_166413933_   5427 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_166413933_   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_166413933_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAGAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv   ii  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_166413933_   5577 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_166413933_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAACCAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vvv   v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_166413933_   5677 AAA-AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i -   i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_166413933_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5775
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_166413933_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


1128 26.65 1.88 1.25  chr2_166530237_166534764.rev     2828  3146 (1382)    L1M4_orf2#LINE/L1        1   321 (587)  

  chr2_166530237_   2828 TGGAAAGTCACCTCATGCTCATGGATTGGAAGAATTAATATTGTTAAAAT 2877
                                vi i i    i               v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166530237_   2878 GACCATGCAACCCAAATCAATTTACAGATTCAATGCAATCCCTATTAAGA 2927
                          i v  i vv       ii  i           i           i  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166530237_   2928 TATCAA-TGTTATTTTTCACTAGAATAGAAAAAAACAACTCTAAAATTGT 2976
                          vi  i-  ii-     ii vii   v  v  iv-ii ii        vv
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chr2_166530237_   2977 TACAGA--TCAAAAAAACAGCTCTAATGGCCAAAGCAATACTGAGAAAAA 3024
                           ii  -- vv  iii  -- ivv   i      i    vi   i   i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_166530237_   3025 AAAGCAAAGCTGGACGTATCACACTACCTGACTTCAAAATATATTACAAG 3074
                          i i     i    v vv       v  ii i       iv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_166530237_   3075 GCTATAGTAATCAAAACAGCATGGTATTGGTACAAAAACAGACACA--GG 3122
                             i         i    ii     i   i i  ii i     i -- i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_166530237_   3123 CCAATGGAACA-AATAGAGAACCCA 3146
                         i        i -   v    ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCA 321

Transitions / transversions = 2.70 (62 / 23)
Gap_init rate = 0.02 (7 / 321), avg. gap size = 1.43 (10 / 7)  

2188 25.70 0.83 1.00  chr2_166530237_166534764.rev     3436  4038 (490)    L1M4_orf2#LINE/L1      307   908 (0)  

  chr2_166530237_   3436 AAAATAGAGAACCCAGAAATAAACCCACATTTTTATAGCCAACTGATTTT 3485
                          i   v    ii               i iv     i i   i       
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_166530237_   3486 CAACAAAGGCTCCAAGAACACACATTGGGGAAAGGATATCCACTCCAATA 3535
                          i    i  iv      v  iv  v         i   vi vi i   i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_166530237_   3536 CGTGGTGCTGGTAAAACTGGATCTTCATATGCAGAAGAATAAAACTAGAC 3585
                         vi         v v        v?i  i     i      i  ii i   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_166530237_   3586 AGCTATCTCTCATCATATAAAAATATCAATTCAAAATGGATTAAAGTCCT 3635
                         vv   i   v  i      v   v  i  i           i ?  v   
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_166530237_   3636 AAACATAAGACCCAAAACTATAAAACTGCTAGGAGAAAACATAGAGGAAA 3685
                            ii     v i              vi   i           i? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_166530237_   3686 CACCACAGGATATTGGCCTAGGCATAGATTTTATGGCTAAGATCTCAAAA 3735
                         vv iv iv  iv    vi      vv i   iv i v  v  ivi     
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_166530237_   3736 GTGCAGGCAACAAATACAAGAATGGA--GATGGGACTATGTTAAACTAAA 3783
                          ii  i        viv  i   i  --i  v     vii i   v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_166530237_   3784 AATCTTCTGCACAGCAAAGGAGATCATCAATAGAGTGAAGAGACAACCTG 3833
                           v   i  ii vv       v ii     v i      i        ii
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_166530237_   3834 TTGAATAGGATAAAATATTTGCAAATTATTCATCTGATA-GAAACTAATA 3882
                         iv    i   v               i  vi        - ii   vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_166530237_   3883 TCCAGAATATGCAAGGAACTCAAACAGTTCAACAGCCAAAAAAAACTTAA 3932
                                   ii  i      vv   ii    i ii--     i  v-  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAAT--AAAAAGACA-AA 803

  chr2_166530237_   3933 TAATCCTACTAAAATATGGGCAAAGTACATAAATAGACATTTCTCTAAAG 3982
                            i  v i ?   v          v iv i              i    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_166530237_   3983 AAGACATACAAATGGCCAACAGTTATATTTTTAAAA--TGCTCAGTATTT 4030
                             i              i ivi i  v---    --      ii  iv
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATG---AAAAGATGCTCAACATCA 900

  chr2_166530237_   4031 CTAATCAT 4038
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.60 (93 / 58)
Gap_init rate = 0.01 (6 / 602), avg. gap size = 1.83 (11 / 6)  


2939 24.69 4.66 1.48  chr2_166617023_166619219      827  1705 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_166617023_    827 GGAGAGATATTCCATGT-CATGGATGCAAAGAC--AATAC----AAGATG 869
                            i      i      -       vvi     --    i----      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_166617023_    870 TTAGTTCTTCCCAATTTGATCTGTAAACTAACTCAATGCAATCCCAATCA 919
                         vi i v  i     v       ----  vi i    i        v    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCT----ACAGATTCAACGCAATCCCTATCA 97

  chr2_166617023_    920 AAATCCCAGCAAGTTATTTTGAGGATATTGACAAACTCATCCTAAAGTTT 969
                                   vivi v     vi  v        i  v        i  i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_166617023_    970 ATACAGATTAGCAAAAAAACACAGAATAGC-AACATACTATGGAAGGAAA 1018
                            ii  vvv    iii v -         -  v i v v v   ii i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_166617023_   1019 AGAGCAAAGTTAGAGGTCTGACATTAGTTGACCTCAAGACTTACTATAAA 1068
                            i       i    v  v   i vviii ii    i        i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_166617023_   1069 GCTTCAGTAATCAAGAGAGTAGTGTGGTATTGGTGAAAGAACAAACA--- 1115
                            v            ---i         i   iiv   i i i   ---
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGA---CAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_166617023_   1116 -GGTCAATGGAACAGGGTGGAAA-TCACAGAAATAGACCCA--CATAGAT 1161
                         - i         i  ii v  i -  -        i     --   vv  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTAT 342

  chr2_166617023_   1162 AGTAAACTGATCTTTGACAAAAGAGCAAGGACAATGCAGTGGAGAAAAGA 1211
                         i  v  i    i  i     ii v  v i   v  v  i   i    ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_166617023_   1212 CACTCTTTTCAATAAATGGCACTGGAAAAACTGGACATCCACATGGAAAA 1261
                         i v         i      ii    i v       i ?       v    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_166617023_   1262 -AATGAATATAGATACAGACCTCACCTTCTTCACAAAAATTAATCTGAAA 1310
                         -      vv i  iv vv       viiv vi           iiii   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_166617023_   1311 TAGATCACAGAGCTAAATGTAAAACATAAAACTATAAAATTCCTAGAAGA 1360
                          i     ?   v          i vv             i  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_166617023_   1361 TAATACAGGAGAAAATCTG-ACGGCCTATGGTTTGATGATGACATTTTAG 1409
                         v  i i   ? v      v-ii i   vv    v iii   iiv i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_166617023_   1410 ATAATACACAAAAGGCATAATTCATGAAAGAAAGAGTTGATAAGCTGGAC 1459
                            vv    v   i   i  viv ii       i i v     ii     
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_166617023_   1460 TTCATTAAAATTAAAAATTTCTGCTCT---------------------GT 1488
                              i           i  i  iv  ---------------------  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_166617023_   1489 GAAC-GACAAGCCACAGACTGGGAGAAAATATTTATCAGATATAGATATA 1537
                            v-     v       v               i-  i  v---     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTG-CAAATC---ATATA 738

  chr2_166617023_   1538 TCTGATAAAGGACTGTTTTACAAAATATACAGAGAGCTCTTCAAACCCAA 1587
                                 i     vv v v  i      i i   i     vv   i   
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_166617023_   1588 CAATAAGAAAACAATCAATC-AATTAAAAGATGGGCCAAAGACCTTAACA 1636
                         i     i  i    vi  i -    ?   i      v  i  ii v  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_166617023_   1637 AACACATA-ACAAGCAAGATACACAGACTGCAAATAAGCATATTTAAAAA 1685
                         i   iv v-v   iv      i   i iv  v        i  vv   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_166617023_   1686 TGCTCCACATCATGTCATCA 1705
                              v      ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (128 / 85)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 2.84 (54 / 19)  


2933 25.61 2.54 2.32  chr2_166641463_166646368.rev     3512  4417 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_166641463_   3512 TGGAAGGATATTGCATGCTCATAGATTGGAAGAAT-AATATTGTTAAAAT 3560
                              i     iv    i    i          v -           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166641463_   3561 GGCAATCCTATTCAAAGCAATTTACAGATTCAATGCAATCCTTATCAAAA 3610
                               v  vii    vii  i           i       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166641463_   3611 TAAGAATAAAATTCTTCATAGAAATTGAAAAAAATAATCTTAAAACTTAT 3660
                          vvv iivivv  i  iii         v  iv- i   i     i i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_166641463_   3661 CTGGAACCACAAAAGACCCCTAATAGACAAAACAATCCTGAACAAAAAGA 3710
                         v     vii   ii     vv     v          i    v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_166641463_   3711 ACAAAGCTAGAGGCATCACATTATCTCACTTCAAAATTTATGACAAAGCT 3760
                               i i    vv     i vi iv i       i   iv        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_166641463_   3761 ATAGTA-CCAAAACAGCATTGTGTGGGCATAGACCATACAATGTGTACAG 3809
                          i    -i   i    ii v  iiv      -----------------  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATA-----------------AG 282

  chr2_166641463_   3810 GAAAGACACATAGACCAACGGACCAGAACAAAGAACCCAGATGTAAAGCC 3859
                           v     i     i   i   vi    ivi   ii     vi    v  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_166641463_   3860 ATGCCTTTACAGTCAACCTATTTTTGACAAAGGCTCCAAGAACA--CCAT 3907
                           i v    ii     iiv     i     i  iv      v  -- v  
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_166641463_   3908 GGGGAAAGGATAGTCTCTTCAATAAAGGGTGCTGGGAAAACTGTGTAACC 3957
                                 i       i     i   v          v     vi  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_166641463_   3958 GAATGTAGAAGAATGAAACTAGGCCCCAAATTCCCACCATATACAAAAAT 4007
                         iv   i i         ii i i    v vi  v                
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_166641463_   4008 CAAATCAAAAT-----AAAGACTT-----TAAGACCTGAAACTTTGAAAC 4047
                         i  v       ----- ?    i -----     v  i     v i    
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_166641463_   4048 TACTAGAAGAAAACATTGAGG-AAATGCTCCAGGACATTGATACAGGAAA 4096
                          vi             v i? -    -  i iv   v   ivvi   v  
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAA 581

  chr2_166641463_   4097 AAATTG--TATGTGTCAGACCTCAACAGCATAGGCAATCAAAGCAAAAAC 4144
                         vii  v--  vi i --   vi   v    i i    iv    v     i
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATAT--GACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_166641463_   4145 AGATAAATGGGATTACATCAAGCTAAATATCCTCTGGACAGCAAAGGAAA 4194
                                 v   i v      iv v  v v i i  vi vv       v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_166641463_   4195 CAATCATCACAGTGAAGAGATAACCCATAGAATAGGAGAAAATATTTATA 4244
                          v    vv v      i   i      i     i             ii 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_166641463_   4245 AGCTCTCCATCTGAGAAGAGATTAAAAACCAGAATACATAAGGAGCTCAA 4294
                          iiiv vi      v   i  i viv v        i    i  i   vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_166641463_   4295 ACCACTCAATAGGAAAAAAATA-----TCTGATTTAAAAATGAACATAAG 4339
                           v        iv     i i -----i ii   ?       ii  v i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_166641463_   4340 CTCTCAACACACTTTTCTCAAAAGAAGACATACACATGCCTAACAGGGAT 4389
                         v i v  i v  v      v        i     v   v i  i i v i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_166641463_   4390 AGGAAAAT-TGCTCATCAATAATAATCAG 4417
                          v     v-      v  vi ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (131 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.38 (44 / 13)  


2810 27.38 2.58 0.67  chr2_166653022_166659748     5345  6235 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_166653022_   5345 TGGAAAAACATTCTATACTGATGGATAGGAAGAATCAATATCATGAA-AT 5393
                               i i  i i  ii v      v      v i     ii v  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166653022_   5394 GGCCATACTGCCCAAAGTGATTTATAGATTCAATGCTATTCCCATCAAGC 5443
                            v     v      v    i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166653022_   5444 TACCATTGACTTTCTTCATAGAACTAGAAAAAACT-ACTTTAAATTTCAC 5492
                          v   vivi i  i  iii    v v  v  i-  - iii    v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_166653022_   5493 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 5542
                               viiv  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_166653022_   5543 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5592
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_166653022_   5593 ACAGTAACCAAAACAGCATGGTACTGGAAACCAAAACAGAAATATAGACC 5642
                                i   i    ii         v -iv ii i   v       i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATC 298

  chr2_166653022_   5643 AATGGAACAGAAC--AGAGCCCTCAGAAACA---CCACACATCTACAGCC 5687
                                i    i--    i  --     i ---   i    i  ii i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_166653022_   5688 ATCTAATCTTTGACAAACCTGACAGAAACCAG-CAATGGGGAAAGGATTC 5736
                          vi i  i  i     ivv  v  - i    v-            i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAG 395

  chr2_166653022_   5737 CCTATTTAATCAATGATGCTGGGAAAACTGGCTAGCCATATGCGGAAAAC 5786
                         i  v  i  iv    i        v      v  ?   i    ii  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_166653022_   5787 TGAAACTGGATCCCTTCCTTACAACTTGTACAAAAATTAACTAGAGATGG 5836
                             ii    i    v   i   v v i              vi i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_166653022_   5837 ATTAGAGATTTCAACATAAATCCTAAAACCATAAAAACCCTAGAAGAAAA 5886
                           i ?   ii v  ii   ivv       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_166653022_   5887 CCTAGGCA-ATACCATTCAGGACATAGGCATGGACAAAGACTTCATGACT 5935
                          v    ?i- v i -   iv   v v  vv i i   v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_166653022_   5936 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGTATCT 5985
                          vi            vvi          vv     v  i    v v ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_166653022_   5986 AATTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTGTCATTATAGTGA 6035
                         v  i   v v  i i   i  ii vvi   i  v   i   vv v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_166653022_   6036 AAAAGCAACCTACAGAATGGGAGAAAAT-T---CAATCTATACATCTTAC 6081
                            ii     i                 - ---   vii   i    v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_166653022_   6082 AAAGGTCTAATATCCAGAATCTACTAAGAACTTAAGCAAATTTACAAGAA 6131
                           i  v  vi          v  iv       ivvi   v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_166653022_   6132 AAAAACAA----CCCCATGAAAAGGTGGGTGAAGTATATGAACAGACACT 6177
                            i    ----   v  v?   ii    ii   v  v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_166653022_   6178 TCTTGAAAGAAGACATTTATATGGCCAACAAACATA-GAA-----GCTCA 6221
                            iv        i  vi v        i  i  i -   -----     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_166653022_   6222 TCATCACTGGTCAT 6235
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.81 (29 / 16)  


1021 25.81 3.23 0.36  chr2_166779555_166784648     1337  1615 (3479)    L1M4_orf2#LINE/L1        1   287 (621)  

  chr2_166779555_   1337 TAGAAAAACATTCCATGCTCATGGGTAGGAAGAATTAATATTGTTAAAAT 1386
                          i    i i  i     i      i v      v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166779555_   1387 GACTATGCCACCCAAAGCAATTTACAGATTCAATGCTATTTCTATCAAAC 1436
                          i v  i iv      vii  i           i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166779555_   1437 TACCAA-TGTCATTTTTCACAGAATTAGAAAAACT-ATTTGAAAATTCAT 1484
                          v   i-  i -     ii     v v  v  i  -  iiv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_166779555_   1485 ATAAAACCCAAAAAGATCCTGACTAGCCAAAGCAATCCTAAACAAAAAGA 1534
                           ii  vivv  ii  i  v  v        i     i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_166779555_   1535 ACAATGTCTGAGGCATCACACCACCCAACTATAA-------TACAAGTCT 1577
                             v  iv    vv      iv     i vi  -------     iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_166779555_   1578 ACAGTAACCAAAACAGCATAGTACTGGCACAAAAACAG 1615
                                i   i    ii i         i  ii i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

Transitions / transversions = 1.88 (47 / 25)
Gap_init rate = 0.01 (4 / 287), avg. gap size = 2.50 (10 / 4)  

3281 25.91 1.11 0.55  chr2_166779555_166784648     2339  3241 (1853)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_166779555_   2339 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCGTGAAAAT 2388
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166779555_   2389 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2438
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166779555_   2439 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2485
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_166779555_   2486 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAA 2535
                                 viiv  ii  v  v v  v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_166779555_   2536 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 2585
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_166779555_   2586 CTACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 2635
                                  i v i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_166779555_   2636 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAAC 2683
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_166779555_   2684 CATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 2733
                           vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_166779555_   2734 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2783
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_166779555_   2784 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 2833
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_166779555_   2834 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2883
                           i ?   ii    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_166779555_   2884 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACCTCATGTCCA 2933
                          v    ?i v viv   iv   v v  vv i     v iii  v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_166779555_   2934 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 2983
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_166779555_   2984 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGA-ACTACCATCAGAGTGAA 3032
                           i   v v  i i   i  ii vv    i  -    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_166779555_   3033 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 3082
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_166779555_   3083 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 3132
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_166779555_   3133 AAAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 3178
                           i    ----   v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_166779555_   3179 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 3228
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_166779555_   3229 CATCACTGGCCAT 3241
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  

2020 22.78 4.04 2.42  chr2_166779555_166784648     3984  4602 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_166779555_   3984 AAAAACAGACACATAGACCAATGAAACAGAAGAGAGAACCCAGAAATAAA 4033
                           ii i     i     i     i  i    vv    ii           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_166779555_   4034 GTCACACACATACGACGTT--CTGATCTTGAACACAATCGATAATAGCAA 4081
                         vi  i   iv  i --  i--i    i  vi   viivi vi  v v  v
  L1M4_orf2#LINE/    330 CCCATACATTTATG--GTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_166779555_   4082 GCAAGGCAGAAAAGACTCCCTGTTAAATAAACTGTGCTGGGATAACTGGC 4131
                         v   v vi    ii ivvi  v  v  i   iv         i      v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_166779555_   4132 TAACCATACGCAGAAGATTGAAACTGGACCCCTTCCTTTCACCATATACA 4181
                           ?   i i   i    v    ii         v   iv           
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_166779555_   4182 AAAATCAGTTCAAGATGGATTAAAGACTTAAATGTAAGACCTAAAACTCT 4231
                              i ii    i      i ?    i           v        v 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_166779555_   4232 AAA--CCCTAGAAGAAAAC-TAAG---AAATACCTCGATTAAGGCCTTGG 4275
                            --i i           -  i ---    - i   -- i --      
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCG--TGA--CCTTGG 572

  chr2_166779555_   4276 ------CAAAGATTTC------ATGACAAAGTCTCCAAAAGCAATTGCAA 4313
                         ------   v i    ------      ------         vvv    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAA 616

  chr2_166779555_   4314 CAAAACCAAAAATAGACAAGTGGGACCTAATTAAAATAAAGAGCATCTGC 4363
                              vv         i  i v    i v  i     v  i i v i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_166779555_   4364 ACAACAAAAACAAAACTATCAATAGAGTAAACAGACAACCAGCAGAATGG 4413
                         i vv    ii-- v        v i   i  v        vi        
  L1M4_orf2#LINE/    667 GCTTCAAAGG--ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_166779555_   4414 GAGAAAATATTTGCAAACCATGCATATGATGAAGGTCTAATATCCAGTAT 4463
                                          i   ii  v    i i  v  vi       v  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_166779555_   4464 CTATAAGGAACTTACATAAATCAACAAGTGAAAAACAA----CCCCATTT 4509
                         v     i     ivi i  v    i  vvi   i    ----   v   ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_166779555_   4510 AAAAATGGGCAAAGAATTAAAA-AGACAGTTCTCAAAAGAATACATACAC 4558
                                       i   vi  -     v     v      v i     v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_166779555_   4559 GTGACCAACAAGCATATGAAAAAATGCTCAACATCATGAATCAT 4602
                         i  i    i     i       i             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (82 / 56)
Gap_init rate = 0.02 (14 / 629), avg. gap size = 2.86 (40 / 14)  


2678 25.11 2.97 2.97  chr2_166849845_166852097      854  1761 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_166849845_    854 TGGAAAAATGTTCCATGCTCATGGATTAGAAAAATTAATATTGTTAAAAT 903
                               i  i i     i         i   i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_166849845_    904 GCCCATACTGCCCAAATAAATTTAAAGATTCAACATTATTCCTATCAAAT 953
                          v v     v       vi  i  v         iiv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_166849845_    954 TAACAA-TGTCATTCTTCACATAATTAGAAAAAAAAGACTCTAAAATTCA 1002
                          vv  i-  i -  i  ii  v  v v  v  ivv-  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCT-GATCCTAAAATTCA 148

  chr2_166849845_   1003 TACGAAACCAAAAAAGAGCCAAATTAGCCAAAGCAATACAAAGCAAAAAG 1052
                           i i  viiv  ii  v   i v        i    vivi iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_166849845_   1053 AACAAAGCCAGAGGCATCACACTAGCCAACTTCAAACTATACTATAAGGC 1102
                                iii    vv       vv    i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_166849845_   1103 TACCATAAGTAATCAAAACAGCACGGTACTGG-ACAAAAACAGATATATA 1151
                            ----         i    iii        - i  ii i   i     
  L1M4_orf2#LINE/    249 TAC----AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_166849845_   1152 GACCAATGGAACAGAATATAAAACTCAGAAATAAAGCAACACACCTACAA 1201
                           i        i     vv i iii          v v i   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_166849845_   1202 CCATGTGATCCTGAACAAGG-T-CCAACAAAAATGAGAACAAGCAATGGG 1249
                         i  vv    ii vi      - -    ---------  v  vv       
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAA---------GACCATTCAATGGG 385

  chr2_166849845_   1250 GGAAAAACTCTCTATGCAATAAATGGTGCTGGGCTAACTGGCTAGTCATA 1299
                          i  i  ivv   v v   i             vi      v  ?i  i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_166849845_   1300 TGCAGAAGAATGAAACTGGACACTTACCTTTCACCACATACAAAAATTAA 1349
                             i         ii     v i     iv     i             
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_166849845_   1350 CACAATAGCGGTTGAAGATTTAAATGTAAGA-CTAAAATTATAAAAAATC 1398
                          v   v vv i ii?   ii           -      i       v-  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TC 534

  chr2_166849845_   1399 CTAGAAGAAAACCTAGA---AAATGCCCTTCCTGACATCAGCCTTGGTGA 1445
                         i           v   i---    ---    v    v ii vi v  i- 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGC-A 580

  chr2_166849845_   1446 AGAATTTAT--GAT-TAAGTTCAC-GAAAGCAATTGCAACAAAAACAGAA 1491
                          vii   v --   - i ---   -i      vvv         iv i  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGA---CACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_166849845_   1492 CTTGACGAGTGGGACCT------AATTAAAGAGTTTCTGCACAGCAAAAG 1535
                         v v  ii i v    i ------       i v   -  ii vv    i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGG 676

  chr2_166849845_   1536 AAACTACCAACAGAATAAACAAACAACCTACAGAATGGTAGAAAATAGGC 1585
                          v    i   v i i i  v i      i         v        vvi
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_166849845_   1586 ACAAACTGTGCATCAGACCAAGGTCTAACATCCAGAATCTATAAGGAACT 1635
                         i    iii ii   v  iv i  v  vii         v     i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_166849845_   1636 T----AAATCAATCA---ACAGGCAAAAATTAACCCCATTAAAAAGTGGG 1678
                         i----  v     v --- v  i    ---      v   ?    i    
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAA---TAACCCAATTWAAAAATGGG 823

  chr2_166849845_   1679 CAAAATAGATGAACAGACACTTCTCAAGAGAAGACATATAAGTGGCTAAC 1728
                             iv vv    i     i     v i      i   i  i    i  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_166849845_   1729 AA--ACGTGAAAAAATGCTCATGATCACTAATCAT 1761
                           --  i      i       vv    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.35 (54 / 23)  


3052 24.23 4.21 1.37  chr2_166896440_166900139     2331  3209 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_166896440_   2331 AATATATTTCATGTTCATGTGTTGGAAGAATTAATATTGTTAAAATGTCC 2380
                           v    ii          vi        v             i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_166896440_   2381 ATACTACCCAAAATAATCTACAGATTCAATGCAATCCCTATCAAAATTCT 2430
                              v      v i              i                 i i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_166896440_   2431 AA-TGTCAGTTTTCACAGAAATAGTAAAA--AATCCTAACATTTGAATA- 2476
                          i-  i -v    ii       v vv  i--i       v   iiv  i-
  L1M4_orf2#LINE/    105 AGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_166896440_   2477 AAATAAAAAAGATGCTAAATGGCCAAAGCAATCT-GAGCAAAAAGAACAA 2525
                             iv  ii  iv vi   i      i      -  iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_166896440_   2526 AGCTAGAGGTGCAATACTCTGTCATTTCAAAA-----TATAAAGCTA--- 2567
                           i i    vviv i   iiviv         -----  i       ---
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_166896440_   2568 --------------TGCTATTGGCATAAACACAGATATATTGGCTAATGG 2603
                         --------------  v  i        iv i   i    v iii     
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_166896440_   2604 AAAAGGATAAAAAGCCCAGAAATAAACCCAATTATTTATAGTCAATTGAT 2653
                           v  i  vi i  i               vvi      i          
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_166896440_   2654 TTTCAGCAAAGGTGCAAAGAATAAACAATGGGGGAAAGGACGATCTCTTC 2703
                             ii   i     v    vi vv        -    i iii   i   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTC 402

  chr2_166896440_   2704 AATAAATGGTGTTGGGAAAACTGAATATTCCTTATGCAAAAGAATGAAAT 2753
                           i        i     v     i   ?-  vi               i 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAK-CCACATGCAAAAGAATGAAGT 451

  chr2_166896440_   2754 TGGGCCCTT-TCTCATACCATATGTTTATAAAA-------CCAAACAAGT 2795
                            i   i -i    i       ---- i    ------- v   iiii 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATAT----ACAAAAATTAACTCAAAATGGAT 497

  chr2_166896440_   2796 AAAAGACTTAAATATAAGAAATGAAACTATAAAGCTACTAGAAGAAAACA 2845
                         v ?    i     i     iv i          i  vi            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_166896440_   2846 TAAAAGAAAAGCTGTATGACATTTATCTGGGCAAGGATTTCTTGGCTAGG 2895
                           ii? v   v  vii    v  vivi i     v i      i v  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_166896440_   2896 ACTCTAAAAGCACAGGTAACAAAAGACAATAAGAGACAAGTTGGATTAGA 2945
                           v i         i i         v  -  v   i  i     i vv 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCA 646

  chr2_166896440_   2946 TCAAA-CTAAAAATGTTCTTTACAGCAAACGAAGCAAT-AACAGAGTGGA 2993
                              -i      i-  i v i vv    v  vi v  -  v i    i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_166896440_   2994 GAGAGAGATCATGGATTGAAATAAAATATCTGCAAACCATACATCTGATA 3043
                         i   v ivi  ii  v  ii v       i      i    i        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_166896440_   3044 AAGGGCTAATATCCAACATTATACATAAAAAGCTCAAGCAACTCAACACC 3093
                          i  i  vi      i- --   i     i i   vvi        i vi
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAG-A--ATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_166896440_   3094 TAGAAAATCAATAAACCAATTGTAGAATGGGCAAATAATCTGAACAGACA 3143
                         v i  i iv     v      ?v i          vi  i    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_166896440_   3144 TTTCTCAAAAGAAGAGATATGAATGGCCAATAGATATATTAAAAAATGCT 3193
                               v        v   ii           iii i  v    i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_166896440_   3194 CAACATCTCTAATCAT 3209
                                v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (132 / 77)
Gap_init rate = 0.02 (18 / 904), avg. gap size = 2.72 (49 / 18)  


3498 19.04 5.85 2.06  chr2_167080750_167082623      513  1384 (490)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_167080750_    513 AAATACATACCATATTAATGAATAAGGAAA---AATAAGGCAAAAATACC 559
                            v i  v    i  v   i  vi i i ---    vv iv  i  iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_167080750_    560 CAAACGATTCTCAAAACAATTTGGTAGGGTTTTGATGGCAA-CCCTATCA 608
                         v v  -- i i    vii  i i-i  i--  ii i -   -        
  L1M4_orf2#LINE/     54 AATAC--TCCCCAAATTGATCTA-CAGA--TTCAACG-CAATCCCTATCA 97

  chr2_167080750_    609 AAATCCCAACTTGGC--TTTTTGTAGAAGTTAACAAGCTTATCATAAAAT 656
                                 i  --  --      i    i  i       v   v      
  L1M4_orf2#LINE/     98 AAATCCCAGCT--GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_167080750_    657 TTATGTAGGAACAGGACAGGGCCCTAGAATAACCTAA-CTATCTTGAAAA 705
                          i  i i i  i- v -    v  i      i  v  - v          
  L1M4_orf2#LINE/    146 TCATATGGAAAT-GCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_167080750_    706 AAATTTAGAACAAAGTTGAAGGAGTCGTATCTTCTTATTTCCAAGCTTAC 755
                          i ---            i    v  ii ii i iv     v  i     
  L1M4_orf2#LINE/    194 AGA---AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_167080750_    756 TACACAGCTACTGCAATCAAAACAGTCTGGTGATGGAAAAAGAATAGATA 805
                             v      v i      i     v    iv   v v   i     i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_167080750_    806 TATAGGTCAAAGGAATAGA-----GAATCCAGAAATAAATGT-TACATTT 849
                              i    v        -----  i            ivi-       
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_167080750_    850 ATGGTCAATTGATTT-CAACAAGAGTGTCAAGACAATTGAATGGGGAAAG 898
                                        - i     i   i      v   v           
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_167080750_    899 AACAATACT--CAATAAATGG------GACGGCTGGATAGCAATATGCAA 940
                           i i vi --   i      ------   ii       ? v i      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_167080750_    941 AAGCATGATCTTAGACCCCTTTCTTAAACCATAGACACACAAAAATTAAC 990
                            v    vv  i       vi  i v      ----i            
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATA----TACAAAAATTAAC 486

  chr2_167080750_    991 TCA----GAAGCATAAACTTAAATATGAGAGCTAAAAGCACAAAACTCTT 1036
                            ---- i v  ? i  i     i i          vi i         
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_167080750_   1037 AGAAGAAAACATGGGAGTAAATCATCGTAAGCTTGGATTAGGCAATAGTT 1086
                                     i  ?       v    i v     i         i   
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_167080750_   1087 TCTCAAATAT--C-CTAAAAGTACAAGCAA--------AAGTTTGATAAA 1125
                            i i    -- - i     i        --------  iv v      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_167080750_   1126 TTAGACTTCAACAAAATTAAAG-CTTTTGTGTATCAAAGGACACAATCAA 1174
                           i       v          i-        iv           v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_167080750_   1175 GAAAGTAAAAAGACAACTCACATAACATGATAAAAATATTTGCAAATCAT 1224
                               i          i    v  iiv  -i                  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGA-GAAAATATTTGCAAATCAT 735

  chr2_167080750_   1225 ATATCTAATAAAGAACTGCTATCTAAAATATAGGAAGAAC---------- 1264
                               i    i i   vv    i i      vi      ----------
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_167080750_   1265 -AGCAATAAAA-GATAAATAACCCAATT-AAAAATGGGCAATGGATTTGA 1311
                         - ii       -  i             -            v        
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_167080750_   1312 ATAGGCATCCCTCCAAAGAAGACATACAGATATCCAGTAAACTCACGAAA 1361
                             i   ii            i     i  iv   i   i v  i    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_167080750_   1362 ACGTTCTCAACATAATTAGCCAT 1384
                          vi v        v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (106 / 57)
Gap_init rate = 0.03 (27 / 905), avg. gap size = 2.56 (69 / 27)  


2981 27.56 1.22 0.67  chr2_167187866_167194519.rev     5263  6162 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_167187866_   5263 AAAAAAATTCCATGCTTATGGATAGGAAGAATCAATATCATGAAAATGGC 5312
                            i v  i     i i      v      v i     ii v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_167187866_   5313 CATACTGCCCAAAGTAATTTATAGATTCAATGCCATTCCCATCAAGGTAC 5362
                         v     v      v i  i  i        i  v  i  i     ii v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_167187866_   5363 CA-TTGACTATTTTTGCAGAATTAGAAAAAAAACT-ACTTTAAATTTCAT 5410
                           -i  v  -           v v  v  i---  - iii    v     
  L1M4_orf2#LINE/    104 CAGCTGCCT-TTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCAT 149

  chr2_167187866_   5411 ATGGAACCAAAAAAGAGCCTGTATAACCAACACAATCCTAAGCAAAAACA 5460
                               viiv  ii  v  v v   i    v      i i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_167187866_   5461 ACAAAGGTGGAGGCATCACGCTACCTGACTTCAAACTGTGCTACAGGGCT 5510
                               v      vv    i  v  ii i      viv i     ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_167187866_   5511 ACAGTAACCAAAACAGCATGTTACTAGTACCAAAACAGATATATAAACCA 5560
                                i   i    ii  v    i i iv ii i   i     i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_167187866_   5561 ATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTATAACCATC 5610
                               i    iv    vii         vv   i    i   iii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_167187866_   5611 TGTTCTTCGACAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCCCTA 5660
                           v i        ivv  v   i v  vv       i    i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_167187866_   5661 TTTAGTAAATGATGTTGGGAAAACTGGGTAGCCATATGCAGAAAACAGAA 5710
                           i ii     i  i     v      i  ?   i     i  i vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_167187866_   5711 ACTGGACCCCTTTCCTTATACCATATACAAAAATTAACTCAAGATGGATT 5760
                         ii         v-   i i                       i      i
  L1M4_orf2#LINE/    450 GTTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_167187866_   5761 AAAGACTTAAATGTGAAACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5810
                          ?    i       i i v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_167187866_   5811 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTGAA 5859
                            ?i- v i -   iv   v v  vv i     v ii   v iiv ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_167187866_   5860 ACACCAAAAGCAATTGCAACAAAAGCCAACATTGGCAAATGAGATCTAAT 5909
                                     vvv          vv  v  v ii    vi  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_167187866_   5910 TAAACTAAAGAGCTTCTGCACAGCAAAAGGAACTACCATCAGAGTGAACA 5959
                         i   v v  i i   i  ii vv    i iv    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_167187866_   5960 GGCAGCCTGCAGAATGGGAGAAAAGTTTTACAGTCTATCCATCTGACAAA 6009
                          i  i  ii               vv   i  ivii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_167187866_   6010 GATCTAATGTCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 6059
                          iv  vi i        v  i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_167187866_   6060 AACAA----CCCCATCAAAAAGTGAGCAATGGATATGAACAGACACTTCT 6105
                         i    ----   v  i?    i  i    v    v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_167187866_   6106 CAAAAGAAGACACTTATGCGGCCAACAAACATAT-AAAAGAT---CATCA 6151
                          v        i ivi vii      i  i  i  -       ---  v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_167187866_   6152 TCACTGGTCAT 6162
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (10 / 905), avg. gap size = 1.70 (17 / 10)  


1411 33.00 2.13 4.92  chr2_167210140_167212029      511  1404 (486)    L1M4_orf2#LINE/L1       40   908 (0)  

  chr2_167210140_    511 ATTTTAAATATATCATTTTTCTCCAAACTGATTTATAAAGGCAATGCAAT 560
                            v v  v  iv  v vi  i     i    i  i i vv   i     
  L1M4_orf2#LINE/     40 ATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

  chr2_167210140_    561 TCCAATTGAAGTCTCTGCAAATCTGTTT----AAATTGAAAAGCCAATTT 606
                         i  v  ii  i  i v  vivii v   ----       v    ii  ii
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_167210140_    607 TGAAGTCGATATGGCACTATAAATAGCCAAAATTAGTGGACATAATACTC 656
                          i  i iv      v v ii  ivii  v i v   i---  v  i v  
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC---CAAAACAATC 186

  chr2_167210140_    657 TTGACAAGAAAGAATATGGTTAGAGGATTTATGCTATCAGAAGTGAAGAC 706
                             v  ii     i vi   i     i i ii  vi vi vv v  i  
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_167210140_    707 TTATTATAAAG-TACAATAATTAAGGCAGTGTGGTATTGGCATAAAGATA 755
                            i  i    -    i    i   i          i        i    
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_167210140_    756 GACAAATCAAACAGTATATTAGAATGGAAAGCCCCAACACATATAGACAC 805
                             v  vi v  i iv v      v  i  i  vi v i v ivv i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_167210140_    806 ATGT-TGATTCATAATAATTTATAATGAAGTTGATACAAAAATGCTTTTG 854
                           v -  i iv  -- i    vii i-   -- i i v  i i- v  ii
  L1M4_orf2#LINE/    337 ATTTATGGTCAAT--TGATTTTCGAC-AAG--GGTGCCAAGAC-CATTCA 380

  chr2_167210140_    855 AT----AAAAAATGATCTATTACATAACTAGTGCTGGGTTAATTGAATAA 900
                           ----   i   ii   v  vv i  v i        vi  i  i   ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_167210140_    901 CCATATAGAAATTTATAGATTATCCTTACATAGATTTTCTAAAAATATAT 950
                            i  iv   -----   ----------  i----------  i --- 
  L1M4_orf2#LINE/    431 CCACATGCAAA-----AGA----------ATG----------AAGT---T 452

  chr2_167210140_    951 TAATCTTGACTCTATACCATCCATAAAAATCCCTTCTATGAGTATGATAG 1000
                         vi i iiv  iii i     vi i      ivvi  v viv v  v ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_167210140_   1001 ACCAAAATATAAAA-CTTACATCATAAAATGTCTAGAGGATATTGTAAGA 1049
                            v    i   i -  v v ii      ivii    i  v vii  i ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_167210140_   1050 AGCTATTTTTCATGATCTTGGTGTAGAAAAGGATTTCTTAAAGAGGATAG 1099
                         - iv v i   i   i     vv   iv  v i       i v v  i v
  L1M4_orf2#LINE/    553 -GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_167210140_   1100 -AACAGTACTAATCCTAAACAGGCAGATCTGCAAATTGAACGCTATTAAA 1148
                         -  v  i  v iivvi   viiiv i  vvii      i  vii  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_167210140_   1149 ATTTAAAACACTCTTAA---TCAAAAGACACCACTAAGAGAGTAAAACTG 1195
                            -    -   i  iv---     i     i ii    i   i   vvi
  L1M4_orf2#LINE/    652 ATT-AAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_167210140_   1196 CAAGCCACACACAGAGAGCAAGTATTTGCAACACATATACCCAAGAAAGA 1245
                            v     v vv i   v  i         vv      i ii v  i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_167210140_   1246 ACTAATATCTGGAATATATAAAAGA-TCATGTAAATCACTAGGAGAAGGG 1294
                            vi    ii           ii -  v ii  v   v  iv i  ---
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA--- 796

  chr2_167210140_   1295 TAGACAAGCAACTTTTTTTAAA---GGACAAATAATTATAACAAGAATAT 1341
                         -      ii   iivv  ?   ---  i    vi   vv  i iiv  v 
  L1M4_orf2#LINE/    797 -AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_167210140_   1342 CAAAAAAGAGGCTATCTAAATTATCAGTAAATATATGAAATGTTACTCAG 1391
                          vvv     i v   vi    vii  i   ii i      v v i    i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_167210140_   1392 TTTCATCTGTCAT 1404
                         iv   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (174 / 117)
Gap_init rate = 0.03 (22 / 869), avg. gap size = 2.86 (63 / 22)  


2517 26.72 5.85 1.72  chr2_167247556_167249432      514  1385 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167247556_    514 TGGAAAGATACTCAGTTTCCATGGATTGGAAGA-------------AGGT 550
                                   ii vi v i              -------------  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167247556_    551 --CCATACTACTCAAAGAAGTCTATAGATCCAAAGCAA----------AA 588
                         -- v     v i    vvii    i    i   v    ----------  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167247556_    589 TTCCAATGACATTTTTT-CAGAAATGGAAGAAACAATCCTAAAATGTGTA 637
                          i   iivi v      -       v  vi ivii          vii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_167247556_    638 CAAAGCCATGAAAGG--TTAGGAATACCTGAAGAAATCTTGAGCAA-AAG 684
                         iii i--   v    --iivi     v ii  iv        iv  -   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_167247556_    685 AACAA-GCTGGAGGCATCACACTACCTAATATCAGAATCAGTTACAA-GC 732
                              - i      vv       v  i   v   i  iivii     -  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_167247556_    733 TGTAATAATCAAAACAGCAAGGTACTGGCACAAAACCAGACATATAGACC 782
                          ii i       i    iiv          i  iivi           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_167247556_    783 AATGAAACAGAATAGAGGCTCCAGAAATAAATC--------TATG--CAA 822
                             i  i     v   iv            i --------    --   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_167247556_    823 TTCTCTTTTGATAATGATATTAAAAATACATATTGGAGAAAAGATAAAAT 872
                           vvi   i  i  v i iii  i vi ivi v   i    ii   ivv 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_167247556_    873 TTTTAA-AAGTGGTATTGGGAAAACTGGATG------TGAAGAAAAAGAA 915
                            i  -  i    ii     v        i------  v i  i  vi 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_167247556_    916 AATTAGACCCTTATCTCATACCATATTAAAAAAATCAATGGAAAATGAAT 965
                          i  i     i  i    i       - v      i  ivv      i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGAT 497

  chr2_167247556_    966 TAAGGACTAAAATTTAAGGTCTGAAACTGTAAAATAACTGGAAGAAAACA 1015
                         i ?i   iv    v    iv  i     i     ivvi i          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_167247556_   1016 CATAGGAAAAGCTTTATGACATTGGTCTAAGCAATGAGTTTTTGGCAATG 1065
                         i vi? v   v   ii    v    vi  i      iv  i  i vv   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_167247556_   1066 ACCATAAAAGCCCAGGCAACAAAATCAAAAATAGAAAAATGAAATTACAT 1115
                           vvi      v  i         vv         v    vii i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_167247556_   1116 CAAACTAAAAACCTTTTTCACTGCCAAGGAAACAATCAACAGAATGCAGA 1165
                             v v    v     vii  v v     v  v     v i i  v i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_167247556_   1166 GACAACTTAAAAAAATGG---ACAATATTTATAAACCATATTTCTAATAA 1212
                               ii v i  -   --- v       ii   i     v   i    
  L1M4_orf2#LINE/    698 GACAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_167247556_   1213 GGGGTTAATATCCAAAATGTGTAAGGAATTCAAACAACTGAATAGCAAAC 1262
                            ii vi      i   i i   i   i  vv      v    ii   v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_167247556_   1263 AAACAAACAACAACAAAAAAAAAACACTTAAAAATGCGCAAAGGTTGTGA 1312
                          i     i   -- v  ---------i ?       v       v v   
  L1M4_orf2#LINE/    797 AGACAAATAAC--CCAA---------TTWAAAAATGGGCAAAGGATTTGA 835

  chr2_167247556_   1313 GTAGACATTTCTCCAAAGAAGACATGTAAATAGCCAACAAATATATAGAA 1362
                         i                     i  ii    i     i  ii i  ii  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_167247556_   1363 AGATGCACGACCTCACTAATCAT 1385
                               v i  v   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (144 / 86)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.67 (66 / 18)  


3297 27.53 0.22 0.22  chr2_167262734_167269147     5015  5922 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167262734_   5015 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5064
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167262734_   5065 GGCCATACTCCCCAAGGTTATTTATAGATTCAATGCCATTCCCATCAAGC 5114
                            v           iv v  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167262734_   5115 TAACAA-TGTCTTTCTTCACAGAATTGGAAAACACT-ACTTTAAAGTTCA 5162
                          vv  i-  i    i  -i     v v  v  -i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr2_167262734_   5163 TATGGAACGAAAAAAGAGCCCACATTGCCAAAGCAATCCTAAGCACAAGG 5212
                                vviv  ii  v  viv  v      i     i i iv vi i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_167262734_   5213 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATACTACAAGGC 5262
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_167262734_   5263 CACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5312
                         i       i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_167262734_   5313 AATGGATCAGCACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5362
                               vi  v iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_167262734_   5363 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5412
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_167262734_   5413 ATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCTGA 5462
                         v  i  i              v     iv  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_167262734_   5463 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCGAGATGGGTT 5512
                          ii    i    v   i     v              i  i i    i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_167262734_   5513 AAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGGAAACCT 5562
                          ?    i     i v   v       i      vi i      i    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_167262734_   5563 AGGCAATACCTTTCAGGACACAGGCATGGGCAAGGACTTCATGATTAAAA 5612
                            ?ivv vii   iv   viv  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_167262734_   5613 CACCAAAAACAATGGCAACAAAAGCCAAAATAGACCAATGGGATCTAATT 5662
                                 i  vvi          vv        iv   v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_167262734_   5663 AAAGTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAACAGAGTGAAGAG 5712
                            i v  i i   i  ii vv    i  v    i   v i      i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_167262734_   5713 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACACATCTGACAAAG 5762
                         i     i                 v       vii i i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_167262734_   5763 GGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAA 5812
                          i  vi          v  i        ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_167262734_   5813 TCAAACAACCCCATCAAAAAGTGGGCACAGGATATGAACAGACACTTCTC 5862
                         v    i     v  i?    i      v     v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_167262734_   5863 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 5912
                         v        i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_167262734_   5913 CACTGGTCAT 5922
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.59 (151 / 95)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.00 (4 / 4)  


3085 24.62 5.09 0.12  chr2_167303130_167306052.rev     1567  2431 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167303130_   1567 TGGAAAAATACTTCATGTTCCTGGATTGGAAAA----ATATTGTTCCAAT 1612
                               i   iii       v          i ----        vvi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167303130_   1613 GTCCATACTA---AAAGCAATCTACAAATTCAACGCAGTCTCTATCAAAA 1659
                          v v     v---   vii       i          i  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167303130_   1660 TACCAATGACATTCTTCACAGAAAGAGAAAAAA-AATCCTCAAATTTATA 1708
                          v   iivi v  i  ii      vv  v  iv-i     v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_167303130_   1709 TGGAACCACAGAAGACATGGAATAACCAGAACCATTCTGAGCAA-AAGAA 1757
                              vii  iii   vii     i   i   v  ii   iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_167303130_   1758 CAAAACTGGAGGAATCACATTACCTGACTTCAAATTGTACTACAGAACTA 1807
                             ii       v     i v  ii i      viv       i i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_167303130_   1808 CAGTAACCAAAACAGTATAGTACTGACATATAAACAGACACATAGGTCAG 1857
                               i   i     i i      i    vii i     i    i   i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_167303130_   1858 TGGAACAGAATAGAGAACCCAGAAACAAATTCATACATCTACAGTGAACT 1907
                              i     v    ii       i   ii       i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_167303130_   1908 CATTTTCAACAAAGGTGCCAAGAACATACATCAGGGAAAGTACTGTCTCT 1957
                         v      i    i          v   v  vii       v iv    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_167303130_   1958 TCAATAAATGGTGCTGGAAAACCTGGATATCCATATGCAAAAAAATGAAA 2007
                             i            i v v       ?   i        i      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_167303130_   2008 CTAGACTTCTATCTCTCACTATAT-CAAAAATCAAATCAAAATGGA---- 2052
                         i i   ii   i   v   i    -       i  v          ----
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_167303130_   2053 ----CTAAA------AACTAAAA-TCTAAGAC-------ATAAAACATGC 2084
                         ----     ------ i      - v   i  ------- v       iv
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_167303130_   2085 TGGAAAATCTCTAGTACATTGGTCCAGGCAAAGATTTCTTGAGTAATACC 2134
                         v? v      iiivv  v    vii      v i      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_167303130_   2135 CCAAAAGCACATGAAACCAAAGCAAAAATGAACAACTGAGGTGACACCAA 2184
                                    v v   v    v      ii i  v vi iivv  i   
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_167303130_   2185 G-TTAAAAAGCTTCTGCACAGCAAA---------CAACAAAGTGAAGACA 2224
                         i-       -   i  ii vv    ---------   v        i v 
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_167303130_   2225 CAATGCACAATATGGGAGAAAATGTGTACAAACTATCCATCAGACAAGGG 2274
                            iv    iv            i v i    ii  vi   v  i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_167303130_   2275 ATTAAAGATCAGAATATATAAGGAGCTCAAAAAACTCAATAGGAAAAATA 2324
                          i vivivi            i  i   vv v         iv     v 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_167303130_   2325 TAA-TAAACCTATT-AAAAATGGACAAAAGATCTGAATAGACATTTCCCA 2372
                         i  -   v  v   -        i    i   i              i v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_167303130_   2373 AAAGAAGACATGCAAACGGCAAACAGGTATATGAAATGGTGCTCAACATC 2422
                                 i  i    i   v  i i i i      v i           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_167303130_   2423 ATTAATCAT 2431
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.67 (132 / 79)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.21 (45 / 14)  


2955 26.38 3.11 0.58  chr2_167335472_167337450.rev      612  1479 (500)    L1M4_orf2#LINE/L1        1   890 (18)  

  chr2_167335472_    612 TGGAAAGACATCC-ATGTTTCTGGATTCGAAGAATTAACATTGTTAAG-T 659
                                 i    -     iv      v     v    i         - 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167335472_    660 GTCTATGCTACTCAAAGCAATCTACAGCTTCAATACAATTTACATCAAAA 709
                          v v  i  v i    vii        v     ii    iivi       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167335472_    710 TTCCAATGACATTTTTCATAGAAGTAGAATAA----ATCTTAAAATTCAT 755
                          i   iivi v     iii    i v  -i  ----   i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr2_167335472_    756 ATGGAACCACAAAAGGCCTGGTATAGCCAAAGCAGTCCTGAGGAAAAGGA 805
                               vii   ii i  ii v         i  i  i   ii  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_167335472_    806 ACAAAACTGGAAGCATCACACTACCTGATCT-AA-------TATAGAGCT 847
                              ii    i vv       v  ii  i -  -------  i i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_167335472_    848 ACAGTAATTAACAAAGGAAGGCACTGG-ATTGAAAAAAGGAC-CATAGTG 895
                                 i  v v  viv  i     -  --  ii vi   -i    vv
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGAT 297

  chr2_167335472_    896 CAATGGAACAACATAGAGAGTCCAGAAATAAGCCCATGCATTTATGGTCA 945
                                 i iv  v                i     i            
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_167335472_    946 CTTAATTTTTGGCAGAGATGCAAAGAACACAAAATAGGGAAACAGCAATC 995
                         v  i     i i  ii i   v    v  ivv   i      v ii i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_167335472_    996 TCTCTAATAAATAGTGCTAGGAAAACTGGATATTCACATGCAGAATAATG 1045
                          i ii  i    i     i   v         ?i        i  v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_167335472_   1046 AATTTATACAATTATCTCACACCATAGACAAAA-TCAACCCAAAATT-AT 1093
                           v  iv  vvi  i           v      - i   i      v-  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_167335472_   1094 TGAAGTCTTAAATATAATACCTGAATCTGTAAA-CTACCAAAATAAAACA 1142
                         ii?  v i     i   v v  i  v  i    -  vii i  v      
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_167335472_   1143 -AAAAGGAGATGCTCCGTGACATTTGTCTAGGCAATGATTTTTCAGATAG 1191
                         - ii? v i  -  i      v  v vi         i   i i     v
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_167335472_   1192 GACCCCAAG-GCATGGACAGTTAAAGCAAAAATAGAAAAACAGAATTGCA 1240
                            v    i-   iiii  iiv    v         v   iv i i v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_167335472_   1241 TCAAACCAAAAAGTTTCTGCACAGCCAATGAAAC-ATCAACAGAGTGAAG 1289
                              viv    ii  i  ii vv v  v  v  -     v i      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_167335472_   1290 AGATGGTCTACAGAATGTGAGAAAATATTTGCAGATCATACATGCT-ATA 1338
                            iiii i        v               i      i  -  -   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT-CTGATA 745

  chr2_167335472_   1339 AGAGGTTAATATCCAAAATATATAAGGACCTCAAACAACTTAATAGTAAG 1388
                           i ii vi      i         i  v   vv      i    i   i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_167335472_   1389 AAAACAAATCATCTGATTAAAAAATGG-CAAGAGATCTAGATAAACATTT 1437
                           i      v i ii   ?        -   ii   i ii   i      
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_167335472_   1438 CTCAAAAGAACTTATAT---TGGTTAACAGTTAAAAGAACACATG 1479
                            v      vv    i---   ii  i ivi v v   v v   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

Transitions / transversions = 1.85 (146 / 79)
Gap_init rate = 0.02 (20 / 890), avg. gap size = 1.60 (32 / 20)  


 889 27.24 3.11 0.78  chr2_167343729_167345716.rev      500   756 (1232)    L1M4_orf2#LINE/L1      195   457 (451)  

  chr2_167343729_    500 GAAGCGCAAAGCTAGGAGCAC-CATAGTCCCTGATTTTACAATGTATTA- 547
                             vi     i -    v  -  i v i  ii    i v  iv  i  -
  L1M4_orf2#LINE/    195 GAAGAACAAAGTT-GGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_167343729_    548 AGAGCTAAAGTAATTAAAACAGAATGACACTATTATAAAGGCAGACATAT 597
                          i     v      i  i    vi  ii   ivi    i ii        
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_167343729_    598 AGACCAAATGGAACAGACTAGAAAGCCCAAAAGTAAATCCACATAAATAT 647
                            i   -     i   v v  i  i   i  i    i   i i vv   
  L1M4_orf2#LINE/    294 AGATCAA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_167343729_    648 GATCAACTGATCTTTGGCAAGAATATGAAAAATACACAAAGGGGAAAAGA 697
                          i    i    i  i i    ii iiv  i vi iv   v       ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_167343729_    698 GAGTCTCTTCAAAAGATGCTGCTGGGAAAATTGGA------CATACAAAA 741
                         v     i     v i   v        v  i    ------   i     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_167343729_    742 GAATGAAATTAGGCC 756
                                i  i i  
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACC 457

Transitions / transversions = 2.50 (50 / 20)
Gap_init rate = 0.02 (5 / 263), avg. gap size = 2.00 (10 / 5)  

1483 25.22 1.99 2.43  chr2_167343729_167345716.rev     1040  1491 (497)    L1M4_orf2#LINE/L1      439   888 (20)  

  chr2_167343729_   1040 AAAAAAATGAAATTAGATTC--ATCTTACACCATACACA-----TAAATG 1082
                             i      i  i  ii -- i  i        i   -----   v v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_167343729_   1083 AGAATGGACTAAACACTTAAATGTAAGACCTGAGATTGTGTAACTCCTGG 1132
                          i      ii ? v  i           v  i i i i iv     i i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_167343729_   1133 AACAAAACATAGGGG--AATCGCTTTCTGACTTTGGTCTTGGCAATGATT 1180
                           v          ? --    --  iv    i    vi v       i  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_167343729_   1181 TCGTGCATATGACACAAAAGATACAGGCAATAAAATCAAAGATAGATAAA 1230
                           v iv         v   iii   i    i    vv   i         
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_167343729_   1231 TGGGACTACATCAAACTGAGAAGCTTCTGTACAGCAAAGAAAACAGTTAA 1280
                          v     v       v v i  i   i   i vv     i v  vi i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_167343729_   1281 CAGAGTGAAATGTCAACCTATGAAATGAGAGATAACATTGGCAAACAATA 1330
                         v i       v v     i iii    i    v  i   v     iv   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_167343729_   1331 TATCAGATAATTATTTAATTTACAAAACAAATATGGAACTCCTACAACTC 1380
                             v     vvivi vi v v  i  i v   vi      i        
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_167343729_   1381 AACAGCAAAAAAAACAACAACAACAATATTATGATTCAAACATAGACTAA 1430
                           i ii     i -   -- i   ----ii --   ?   v  i i v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGA-CAA--ATAAC----CCA--ATTWAAAAATGGGCAAA 827

  chr2_167343729_   1431 TGACTTGAATAGACATTTCTCCAATGAAGACATACAAATGGCTAACAGGT 1480
                         v  i                    v     i           i  i i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_167343729_   1481 ATTTGAAATGA 1491
                          iv     v  
  L1M4_orf2#LINE/    878 ACATGAAAAGA 888

Transitions / transversions = 1.58 (68 / 43)
Gap_init rate = 0.02 (8 / 450), avg. gap size = 2.50 (20 / 8)  


3196 27.30 1.11 0.33  chr2_167367356_167373709     4962  5862 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167367356_   4962 TGGAAGAACATTCCATGCTCATGGATAGGAATAATCAATATCATGAAAAT 5011
                              ii i  i     i        v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167367356_   5012 GGCCATACTGCCTAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5061
                            v     v  i  iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167367356_   5062 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5109
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_167367356_   5110 TATGGAACCAAAGAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5159
                                viiv iii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_167367356_   5160 AAGAAAGCTGGAGACATCATGCTACCTGACTTCTAACTATACTACAAGGC 5209
                           v    i     ivv   ii  v  ii i   v  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_167367356_   5210 TACAGTAACCAAAACAGCATGGTACTGGTACCAACACAGAGATATAGACC 5259
                                 i   i    ii         i iv iv i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_167367356_   5260 AATGGAACAGGACAGAGGCCTCATAAATAATACCACACATCTACAACCAT 5309
                                i  i iv   ivii  v      vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_167367356_   5310 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5359
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_167367356_   5360 ATTTAATAAATGGTTCTGGGAAAACTGGCTAGCCATATGTAGAAAGTTGG 5409
                         v  i  i       v      v      v  ?   i   i i  iiv  i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_167367356_   5410 AACTGGATCCCTTCCT-------TATACAAAAATTAATTCAAGATGGATT 5452
                          ii    i    v   -------              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_167367356_   5453 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAGGAAAACCT 5502
                          ?    i       v   v       i      vi i    i      v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_167367356_   5503 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5551
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_167367356_   5552 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5601
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_167367356_   5602 TAAACTAAAGAGCTTCTGCACATCAAAAGAAACTACCATCAGAATGAACA 5651
                         i   v v  i i   i  ii v     i  v    i  vv i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_167367356_   5652 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5701
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_167367356_   5702 GGGCTCATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 5751
                           i  ii          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_167367356_   5752 ATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCT 5801
                         iv    i     v  i?    i     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_167367356_   5802 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5851
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_167367356_   5852 TCACTAGCCAT 5862
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.17 (13 / 6)  


3242 27.20 0.44 0.44  chr2_167384995_167390319.rev     3926  4833 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167384995_   3926 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3975
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167384995_   3976 GGCCATACTGCCCAAGGTAATTTTGAGATTCAATGCCATCCCCATCAAGC 4025
                            v     v     iv i  i vv        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167384995_   4026 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4073
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_167384995_   4074 TAGGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4123
                           v    viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_167384995_   4124 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTTTACTACAAGGC 4173
                                i      vv       v  ii i      vi         i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_167384995_   4174 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4223
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_167384995_   4224 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTGCAACT 4271
                                i    i--    i  --        vv  ii i  i iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_167384995_   4272 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4321
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_167384995_   4322 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4371
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_167384995_   4372 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4421
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_167384995_   4422 TTAAAGACTTCAATTTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4471
                          i ?    i v   v v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_167384995_   4472 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 4521
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_167384995_   4522 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4571
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_167384995_   4572 TTAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTACCATCAGAGTGAAC 4621
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_167384995_   4622 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 4671
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_167384995_   4672 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 4721
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_167384995_   4722 AAACAAAGAACCCCATCAAAAAGTGGGTGAAGGAAATGAACAGACACTTC 4771
                          i     v     v  i?    i    ii     vv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_167384995_   4772 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 4821
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_167384995_   4822 ATCACTGGCCAT 4833
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2275 24.23 4.04 0.16  chr2_167391442_167393051.rev      499  1117 (492)    L1M4_orf2#LINE/L1      266   908 (0)  

  chr2_167391442_    499 TATAGTACTGATATAAACACAGACATATAGACCAATGGAACATAATAGAA 548
                          i i      ii    iv i           i        i v   v  i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_167391442_    549 ATCTCAGAAATAAATTTACACATAAACAGTCAACTCATCTTTGACAAGTA 598
                          vii          iii i    vv ii     i v  i  i      vi
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_167391442_    599 TGCCAAGG------AA-AAACAAATGATAGTTCCTTCAATAAATGGTGGT 641
                                i------  -iiiv   vi     iii     i        v 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_167391442_    642 GATAGTACTGGATATTCTCATGTAAAAGGATGAAGTGTGATCCTTATCTT 691
                          iv vv        ?i v    i     i       vv  i  i  i  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_167391442_    692 ACACTGTACCCAAAAATCAACTCAAAATGAATTGAAGACTCAAA----AG 737
                             ii  iv       i           i  ii?    ii   ----  
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_167391442_    738 ---TGAAACTGTAAAACTCCTAGAAGAAAACATAGGAGAAAAGCTTCATC 784
                         --- i     i        i                ? v   v    i v
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_167391442_    785 ATATTGGTTT-GGCAATGATT-CTTAAATATGACACCAAA-GCACAGACA 831
                          iv    v  -       i  -    i             -     ii  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_167391442_    832 ATAAAAGCAAAAAATAAATAAATGGGATTACAGCAAACTAAAGAGTTTAT 881
                          i     -        i      v   i v  v    v v  i ii  v 
  L1M4_orf2#LINE/    616 ACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_167391442_    882 GCACAGCAAAAGA----ATCAAGAGACCAAAATGGCAATCTATAGAATGA 927
                          ii vv    i  ----       i vii   v i   i i i      i
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_167391442_    928 GAGAAAATATT-GCAAACTATTTATCTGATAAGG-AGTTAAAGCTAAAAT 975
                                    -     ii  v            - v  iv v i i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_167391442_    976 ATATGAGGAACTCCTACAATTCAATAGCAATAA-ACTAATAATCCTAAGA 1024
                             i i      i     i      ii  v  -  v     i  v vv?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_167391442_   1025 AAAAAGGGTTAAACTATCT-AATAGACATTTCTTCAAAGAAGACATACAA 1073
                              v  vi   vv  i -             i         i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_167391442_   1074 ATGGTCATCAGGTACATGACAAAATGTTCTATGTCACTAGCCAC 1117
                             i  vi i i      v  i   i  v ii   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (97 / 49)
Gap_init rate = 0.02 (13 / 643), avg. gap size = 2.00 (26 / 13)  


2967 25.43 1.30 3.03  chr2_167471873_167475378     2091  3014 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167471873_   2091 TGGAAAAATGTCCCATTCTCATGTACAGGAAGACCCAATATCATTAAAAT 2140
                               i  i      vi     v iv       ii     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167471873_   2141 GACTATATTGACCAAAACAATTTACAGATTCAATGCTATTACTATCAAAC 2190
                          i v   i vv     vii  i           i  v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167471873_   2191 TACTAATGACATTCTTCACAGAACTAGAAAAACGTATTCCAAAAATAATA 2240
                          v i iivi v  i  ii     v v  v  i vv  i i    v v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_167471873_   2241 TGGAACCAAAAAAGCCCCAAAA-AGCCAAAGCAATCCTAAACCA-AAGAA 2288
                              viiv  ii v    i  -       i     i i  vv -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_167471873_   2289 CAAAGCTGGAGGCATCACGTTACTCAACTTCAAACTACACTACAAGGCTA 2338
                              i      vv    ii v i   i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_167471873_   2339 CAGTAACCAAAACAGCATGGTAATGGTACAAAAACAGGCACAAAGACCAA 2388
                               i   i    ii     v   i i  ii i  i  i v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_167471873_   2389 TGGAACAAAATGGACAGCCCAGAAGTAAGGTTGTACATCTAAGATCATCT 2438
                              i i   v  v  i      i   iviii     i  v i   vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_167471873_   2439 GATCTTTGACAAAGCTGACCAAAGACAA--CAATGGGGAAAAGACTGT-T 2485
                            i  i     i v  -    -   v --           ii iv  - 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG-CCAA-GACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_167471873_   2486 ATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGATGACTGA 2535
                         v     i              i      v  ?   i     i v  v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_167471873_   2536 AGCTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGGTGAATT 2585
                           i         v   i                 i       ii  i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_167471873_   2586 AAAGACTTAAATGTAAAACCCAAAATTATAAAAACCCTGGAAGACAACCT 2635
                          ?    i         i v i    i       vi i i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_167471873_   2636 AGGCA-ATACCATCCTGGACATAGGAACAGTCAAAGATTTTATGACAAAG 2684
                            ?i- v i v  v  -  v v  ivi  v   v i   iv iivv v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_167471873_   2685 GCACCAAAAGCAATCA--CAACAAAGGCAAAAATTGACAAGTGGGATCTA 2732
                         i           --  --       i v      v  i  i v   ii v
  L1M4_orf2#LINE/    598 ACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_167471873_   2733 ATTAAACTTAAGAGCTTCTGCACAGCAAAACCAAAACAAAAAACAAAATG 2782
                           i   v    i i   i  ii vv    i-----------i   vv  -
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAG-----------GACACTAT- 683

  chr2_167471873_   2783 AACAAACAAAAAACTATCAACAGTAAACAACCTACAGAATGGGAGAAAAT 2832
                         ------   i   v i--  v  ---      i                 
  L1M4_orf2#LINE/    684 ------CAAGAAAGTG--AAAAG---ACAACCCACAGAATGGGAGAAAAT 722

  chr2_167471873_   2833 ATTTGCAAACCATGCATCTGACAAAGGTCTAATATCCAGCATCTATAAGG 2882
                                  i   ii      i  i  v  vi       v  v     i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_167471873_   2883 AACTTAAGCAAATTTACAAGCGAAAAACAA----TCCTGTTACAAAGTGG 2928
                             ivvi   v iv i  vvi   i    ----i  vi  ?v   i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_167471873_   2929 GCAAAGGAAATGAACAGGCACTTCTCAAAAGAAGACATACATGCAGCCAA 2978
                                 vv    i  i  i     v        i     viii     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_167471873_   2979 CATGCACATGAAAAAGAGCTCAATATCACTGATCAT 3014
                         i v           iiv      i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (141 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  

 270 20.91 7.27 3.64  chr2_167471873_167475378     3357  3466 (40)    L1M4_orf2#LINE/L1      795   908 (0)  

  chr2_167471873_   3357 AATGACAGATTGGCCAATTTTTTTAATAATGG-CAAAAGATT--AATAGG 3403
                           v    i  viv      ?----  v     -    i    --     i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTW----AAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_167471873_   3404 CATTTC-CCAAATAAGGTATCTAAATTGTTA-CAAGTATATAAAT---TA 3448
                               -     v   i   vi    v ii -i   i i  i  v--- i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_167471873_   3449 TTCAACATCATTATTCAT 3466
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.05 (6 / 114), avg. gap size = 2.00 (12 / 6)  


1731 27.20 10.53 0.93  chr2_167512213_167513954.rev      501  1250 (492)    L1M4_orf2#LINE/L1       87   908 (0)  

  chr2_167512213_    501 AGTTCCAATCAAAATCATAGAAGATCGTTTCAAAGAAATTGAAAACTTGA 550
                          i i  v         vi  vv viiv   iiv         v  vi   
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr2_167512213_    551 TTCTAAAACATACACGGACATGCAAAAAATCTAAAATATCTAAA-CAATT 599
                          i      ivi i i   v      iii i i i    v i   -    i
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_167512213_    600 TT--AAAAGA-GAACAAATTTG------T-----------ATTTCAAGGT 629
                           --      -       v   ------ -----------       iii
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_167512213_    630 TTGCTGTAAAACTAAAGGAATAAAAATAGTGCATCTTTGACAAAA----A 675
                           i  ii   i   v  v   v  i i    iivivi  i  v  ---- 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_167512213_    676 GACATATAGATAAAT----TTTAA--GAGAATTTAGAAATAGCCTCATGT 719
                                    v   ---- vv  --    i ii       iv i   ii
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_167512213_    720 TTATATGGTAAATTAATTTTTGACAAAGGTACCAAAGTAATTTGATGGGG 769
                         v v      v    i     i     i   i    iiiv   ii      
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_167512213_    770 AAAGGACAGCAATTTCAATAAAAATTACTAGGACAACTAGATAGTCACAT 819
                             i i  ivv      i   viv i  i        i    ?i     
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_167512213_    820 ATAAA----TGAAATTCTATACTTATCTATTACTACAAACAAAAACTAAA 865
                         ii   ----    i  vv iv i  i  vvi  i i v       i   v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_167512213_    866 TGAAGGTAGATAATAGATCTAAACATAAAGACT-----TCTAAAGTTAT- 909
                          v  ii i   v ?   i     ii   iii  ----- v    ii v -
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_167512213_    910 ATAAGAAAACGTA-----AAATGTCTTTGCATCTTTAGAGTAAGTAA-AA 953
                          v        i  -----    --   i iiv i  i iv  i i  -ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_167512213_    954 TTTATTTCATA-GACAC--AAAGCAAAATCCATACAA------ATTGATC 994
                            v  vv   -     --      v  v v i v  ------  v   -
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT- 633

  chr2_167512213_    995 AAATTAGGA--TCATAAAAATTAAAA-CTTTTGTTGTCCAAAAGACAACA 1041
                              -   --    v          -       vv i    i    vi 
  L1M4_orf2#LINE/    634 AAATT-GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_167512213_   1042 TTATTAAAATGAGGGGGAAACCCATAGATTGGAAAACAAATACTTGCAGT 1091
                          i vv   i   iii iv      i   v   i i -     i     iv
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA-AAATATTTGCAAA 731

  chr2_167512213_   1092 GAATATACCTGTCAAAAAACCTCTATCCAAAATATATAAAGAACTCTTAC 1141
                         vv     i   vi  iii  i v      i                    
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_167512213_   1142 AACT---------GAAGACTAACCATCCAATTTCTTAAACAGGCAAAAGA 1182
                             ---------i     v  iv i      ?vv-   ii      i  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGA 830

  chr2_167512213_   1183 CTTAAATAGGCACTTTCACAAAAGGATATGTAAGAATGGCCAATAAG--- 1229
                         i  i     i  -    v v    i v  i  vi             ---
  L1M4_orf2#LINE/    831 TTTGAATAGACA-TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_167512213_   1230 --------ATGCTTAACATCATTAGGAAA 1250
                         --------     i       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (127 / 74)
Gap_init rate = 0.03 (26 / 822), avg. gap size = 3.31 (86 / 26)  


3099 26.12 0.98 1.75  chr2_167529165_167531544      974  1888 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167529165_    974 TGCAAAAACATTTCATGCTCATGGATAGAAAGAATCATTATTATGAAAAT 1023
                           v   i i  ii    i        v i    v i v    i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167529165_   1024 AGCCATACTGCCCCAAGTAATTTAGAGATTCAATGTTATCCCCATCAAGC 1073
                         i  v     v   v  v i  i  v        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167529165_   1074 TACCA-TTGACTTCCTT-CAGAGAATTAGAAAAAACT-ACTTTAAATTTC 1120
                          v   -i  v   ii  -    -    i-- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_167529165_   1121 ATATGGAACCAAAAAAGAGCCCGAATAGCCAAGAAAATCCCAAGCAAAAA 1170
                                 viiv  ii  v  v          i v    iii iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_167529165_   1171 GAACAAAATTGGATGCATCACGCTTCCTGACTTTAAACTATACTGCAAGG 1220
                                i     v vv    i     ii i  i   viv    i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_167529165_   1221 CTACAGTAACCAAAACAGCATGGTACCGGTACCAAAATAGACATGTAGAC 1270
                                  i   i    ii      i  i iv ii        i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_167529165_   1271 CAATGGAACAGAATGGAACAGAACAGAGGCCTCAGAAATAACACTACACA 1320
                                 i     v  --------   v  --        vv i i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGA--------GAGTCC--AGAAATAAACCCATACA 337

  chr2_167529165_   1321 TCTACAACCATCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGA 1370
                          i  iiii  vi    i  i     ivv  v   i v  vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_167529165_   1371 AAGGATTCCCCTATTTAATAAATGGTTTTGGGAAAACTGGGTAGCCATAT 1420
                            i  vvi i -  i  i       vi     v      i  ?   i  
  L1M4_orf2#LINE/    388 AAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_167529165_   1421 GCAGAAATCTGAAACTGGACCCCTTCCTTACACCTTATACAAACATTAAC 1470
                            i  ivv    ii         v   i     v        v      
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_167529165_   1471 TCAAGATAGATTAAAGATTTAAATGTGAGACCTAAAACTATAAAAACCCT 1520
                             i  i   i ?   ii       i   v              vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_167529165_   1521 AGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGAC 1569
                                   v    ?i- v i -   iv   v v  vv i     v ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_167529165_   1570 TTCATGGCTAAAACACCAAAACCAATGGCAACAAAAGCCAAAATTGGCAA 1619
                            v i v  vi         v  vvi          vv     v ii  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_167529165_   1620 AT-GCATTCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATC 1668
                           - v i - v  i   v v  i i   i  ii vv    i  v      
  L1M4_orf2#LINE/    636 ATTGGACT-TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_167529165_   1669 ATCAGAGTGAACAGGCAACCTACAGAATGGGAAAAAGTGTTTGCAGTCTA 1718
                          vv i      v  i     i           i   i i      ivii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_167529165_   1719 TCCATGTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAA 1768
                          vi  v   i  i  i  vi          v  i        ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_167529165_   1769 TTTACAAGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGTATATA 1814
                          iv i  v     i    ----   v  i?    i         v  v i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_167529165_   1815 AATAGACGCTTTTCAAAAGAAAACATTTATGTGGCCAACAAACATATGAA 1864
                                ii  i  v      i i  vi vi       i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_167529165_   1865 AAAAAGCTCATCATCACTGATCAT 1888
                           i v     v     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.92 (25 / 13)  


1205 22.66 2.27 1.98  chr2_167535229_167541616        2   354 (6034)    L1M4_orf2#LINE/L1      555   908 (0)  

  chr2_167535229_      2 AAAACTTTATAACATTTGCCTGTGCAAGTGATTTTTTGGATATCATCCCA 51
                            v   ii i  v  v vi iv    -  i   i  i     v iv   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCA 603

  chr2_167535229_     52 AAAGCACACAGTCAACAAAAGCAAAAAAATAGACAAATGAGATTATATCA 101
                                 -  -         --          i    vi  i vi    
  L1M4_orf2#LINE/    604 AAAGCACA-AG-CAACAAAAG--AAAAAATAGATAAATTGGACTTCATCA 649

  chr2_167535229_    102 AA-TTAAAATGCTTTGG-----CAAAGGGAACAATCAACACAGTAAAGAG 145
                           -      -i    v -----      iv  v     v v   i  i  
  L1M4_orf2#LINE/    650 AAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_167535229_    146 ACAACCTGTGGAGTGGGAGAATATATTTGCAAACCATACAGCAGATAGGT 195
                               iiii  i        v           i    i v v    i v
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_167535229_    196 GTCA-ATGTCCAAAACATATAAGAAACTCAAGCAACTTAATAGTAAGAAG 244
                          v v-i i    i  i      ii     vvi     i    i   i   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_167535229_    245 ACAAATATTCTGATTTAAAAGTGAACAAAGGAACTGAATAGACATTTCTC 294
                                vi ii   ?    i  ii       vi                
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_167535229_    295 AAAAGAAGGAATATGAATGGCCAGCAGCTATATAGAAAAGA-GTTAAACA 343
                         v       iv   ii        ii ivi i  -       - i v    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACAT-GAAAAGATGCTCAACA 897

  chr2_167535229_    344 TCACTAATCAT 354
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.82 (51 / 28)
Gap_init rate = 0.03 (10 / 354), avg. gap size = 1.50 (15 / 10)  

3191 27.21 0.88 0.44  chr2_167535229_167541616     4993  5896 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167535229_   4993 TGGAAGAACATTCCATGGCCATGGGTAGGAAGAATCAATATCATGAAAAT 5042
                              ii i  i     vi     i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167535229_   5043 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5092
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167535229_   5093 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5140
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_167535229_   5141 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5190
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_167535229_   5191 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5240
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_167535229_   5241 TACAGTAACAAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5290
                                 iv  i i  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_167535229_   5291 AATGGAACAAAAC--AGAGCCCTCAGAAATAATGCCGTATATCTACTACT 5338
                                i i  i--    i  --        vv  i  i  i  iviii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_167535229_   5339 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5388
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_167535229_   5389 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5438
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_167535229_   5439 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5488
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_167535229_   5489 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5538
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_167535229_   5539 CTAGGCATTACCATTCAGGACATAGGCATGAGCAAGGACTTCATGTCTAA 5588
                         v    ?i v viv   iv   v v  vv ii    v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_167535229_   5589 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAGTGGGATCTAA 5638
                         i            vvi          vv     v  i  i v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_167535229_   5639 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCGAAGTGAAC 5688
                          i   v v  i i   i  ii vv    i  v    i  vvi       v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_167535229_   5689 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5738
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_167535229_   5739 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5788
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_167535229_   5789 AAACAA----CCCCATTAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5834
                          i    ----   v   ?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_167535229_   5835 TCAAAAGAAGAAATTTATGCAGCCAAAAAACACATGAAAAAATTCTCACC 5884
                           v        v  vi viii     v  i          i  v    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_167535229_   5885 ATCACTGGCCAT 5896
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3127 26.21 0.99 0.99  chr2_167589883_167595972.rev     4691  5598 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167589883_   4691 TGGAAGAACATTCCATGCTCGTGGATAGGAAGAATCAATATCATGAAAAT 4740
                              ii i  i     i  i     v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167589883_   4741 CCCA-TACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4789
                         vv  -    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167589883_   4790 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 4837
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_167589883_   4838 TATGGAACCAAAAAAGGG-CCCACATT-GCCAAGACAATCCTAAGCCAAA 4885
                                -- viv     -    v v -     i      i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_167589883_   4886 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 4935
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_167589883_   4936 ACTATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 4985
                         i   i     i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_167589883_   4986 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATAGCACACATCTACAA 5033
                         i        i    i--    i  --        vvv  i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_167589883_   5034 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 5083
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_167589883_   5084 CCCTATTTAATAAATGGTGCTAGGAAAACTAGCCAGTCATATGTAGAAAT 5133
                         vi  v  i  i          i   v    i vi ?i  i   i i  iv
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_167589883_   5134 CTGAAACTGGATCCCTTCCCTACACCTTATATGAAAAATTAATTCAAGAT 5183
                         v    ii    i    v  ii     v    i-         i    i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAAAT 493

  chr2_167589883_   5184 GGATTAAAGAGTTAAATGTCAGACCTAAAGCCATAAAAACCCTAGAAGAA 5233
                             i ?   vi       v   v     i i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_167589883_   5234 AACCTAGGC-TATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 5282
                            v    ?-  v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_167589883_   5283 CTAAAACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGAT 5332
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_167589883_   5333 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5382
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_167589883_   5383 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTG 5432
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_167589883_   5433 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAACTTA-CAA 5481
                          i  i  i  vi          v  i         vv    -  i -i  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAA 791

  chr2_167589883_   5482 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGGC 5531
                         v     i     i     v  i?    i     i      v    i  i 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_167589883_   5532 ACTTCTCAAAAGAAGACATTTATGCAGCCAACACACACATGAAAAAATGC 5581
                          i     v        i  vi viii     i vi          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_167589883_   5582 TCATCATCACTGGCCAT 5598
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.29 (18 / 14)  


 480 26.73 3.69 6.45  chr2_167613528_167616041.rev      221   437 (2077)  C L1M4_orf2#LINE/L1   (634)   274    64  

C chr2_167613528_    437 AAATTGATATATAAGTTTAATTCA-TTCCAATTAAAATTCCAGAAGGTGC 389
                                 v  i ii  i  iv  - i  v  i     i    v---   
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC---TGC 110

C chr2_167613528_    388 ATGTTTGTGTGTGTGTGTGTAGATTAACAAAATAATTCTATAAAGTTAAA 339
                         v v   ---------  iiv i   i    iv i  i   -   v i v 
  L1M4_orf2#LINE/    111 CTTTTT---------TGCAGAAATTGACAAGCTGATCCTA-AAATTCATA 150

C chr2_167613528_    338 TGCAAACAGGAAGGAATAAATATAGCCAAGACAATCCTGAA---GAAGAA 292
                           v   iivi i   viv iv        i      i    ---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chr2_167613528_    291 CTAGGGTTGAGGAAGTTA-AC---CAGATTTTACTATTTATTACAAAGCT 246
                          - ii    ii i v i -  --- vi    i vv i   i         
  L1M4_orf2#LINE/    201 C-AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

C chr2_167613528_    245 ACAATAATGAAGATAGTGTGATATT 221
                            i    v    i      i  i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACT 274

Transitions / transversions = 1.90 (38 / 20)
Gap_init rate = 0.04 (8 / 211), avg. gap size = 2.75 (22 / 8)  

 246 25.23 3.60 9.91  chr2_167613528_167616041.rev      501   611 (1903)    L1M4_orf2#LINE/L1        4   107 (801)  

  chr2_167613528_    501 AGAGACATTTTATGTTAAAGAATTAAGAGATTTAATATT-TTGAGATGTA 549
                          i   i  iii     v v i   iii   i        -  i     vv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_167613528_    550 AATTCCTCTTAAATTGATATATAAGTTGGCCGGGCACAGTGGCTCATGCC 599
                            v ii ii        v  i ii  viv  ----  -------  v  
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACG----CA-------ATCCC 92

  chr2_167613528_    600 TAT---AATCCCAGC 611
                            ---         
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGC 107

Transitions / transversions = 2.11 (19 / 9)
Gap_init rate = 0.04 (4 / 104), avg. gap size = 3.75 (15 / 4)  

1051 30.43 7.43 2.90  chr2_167613528_167616041.rev      955  1506 (1008)    L1M4_orf2#LINE/L1      117   693 (215)  

  chr2_167613528_    955 TGTAGA--TTAACAAAATAATTTTATAAAGTTAAATGCAAACAGGAAGGA 1002
                           i   --  i    iv i  ii  -   v i v   v   iivi i   
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTA-AAATTCATATGGAAATGCAAGGGA 165

  chr2_167613528_   1003 ATAAATACAGCCAAGACAATCCTGAA---GAAGAACTAGGGTTGAGGA-- 1047
                         viv iv i      i      i    ---       v i v v     --
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_167613528_   1048 ---AGTTCACCAGGTTTTAATATTTATTACAAAGCTACAATAATGAAGAT 1094
                         --- v   -   i-   i  v i   i            i    v    i
  L1M4_orf2#LINE/    216 CACACTTC-CCAA-TTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_167613528_   1095 AGTGCGATATTGGTTTCCAAATGGACAAACAGACCAAATGAATAGAATAG 1144
                             i i  i   iv vvii  i    v i   i   vv         v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_167613528_   1145 TTGGTTCAAAAATAGATCCAGATATAGA-GGTAAACTTATTTTTGACAAA 1193
                         vvi  i  i     i i   v i  vv -   v  i v     i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_167613528_   1194 CATGTCATGGCAATGCAGTGTATGTCAGGGGCTGTGGTTGGTCTTTTCAA 1243
                         vi  i  v i v  v  i  -------   i--iv iv i          
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATG-------GGGA--AAGAATAGTCTTTTCAA 404

  chr2_167613528_   1244 GCGGTGGTGTTGCAGCAAATAGATA-CTACACATATGGAAACAAAATCTG 1292
                         vvii     i  vii   v i    - i   iii viii  ii  i -  
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT-TG 453

  chr2_167613528_   1293 GATCCCTACCTCACACCAGACACACAAAA--AGTTTAAATTGAACTACCA 1340
                           i               v i   -    -- ii i   v  i ii ?- 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACA-AAAATTAACTCAAAATGGATCAW-A 501

  chr2_167613528_   1341 GAACTAAATGTGA-----AAAATAGTAAAGATTCTAAAAGAAAATATAGA 1385
                           v        i -----    ivi    iv ii  i       i    i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_167613528_   1386 AATA--TTATTATAATACCGGAGTAAGCAAGTATTTCTTACACAGAACAT 1433
                         ?i  -- iv ii i ivii  iv  i    vvi       v i vi   i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_167613528_   1434 TATA-------GTAACA----------TTTATAAATTAGACTT-ATTAAA 1465
                         i v ------- i    ---------- vv       i     -  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_167613528_   1466 ACAAAACACTTCTGATGAG-CAAAAAATA-TATTAAGAGAGCG 1506
                          iv   v    i  -  vv-    ii i -   i    i  i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTG 693

Transitions / transversions = 1.86 (108 / 58)
Gap_init rate = 0.04 (22 / 577), avg. gap size = 2.59 (57 / 22)  

 335 26.32 6.43 1.17  chr2_167613528_167616041.rev     1852  2022 (492)    L1M4_orf2#LINE/L1      729   908 (0)  

  chr2_167613528_   1852 AGATGATA-ATCTGGGAAATGACTCATATCTAGCATCTATATA----CCC 1896
                          i  v   -     iv  iv    ii    i  v  v    v ----i i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_167613528_   1897 AACAAATCCAGAA---AAATACAAA-AACC-AATTTAATATGATGGACAA 1941
                         v    v  v v  ---   v     -    -    ?  v --    i   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA--ATGGGCAA 826

  chr2_167613528_   1942 AAGATTTGAACAAGTGATACATAAAAGAAGATATCCATATGTGCGATAAA 1991
                          i        i iiiiv v viv           v  v   vv i    i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_167613528_   1992 CAT-TGACAAAGTGGTTAACATCATTAGTTAC 2022
                           i-   v  ii  v i       ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (22 / 22)
Gap_init rate = 0.04 (7 / 180), avg. gap size = 1.86 (13 / 7)  


3335 27.09 0.22 0.22  chr2_167669972_167676255     4885  5792 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167669972_   4885 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4934
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167669972_   4935 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4984
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167669972_   4985 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5032
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_167669972_   5033 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5082
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_167669972_   5083 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACATGGC 5132
                                i      vv       v  ii i      viv       vi  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_167669972_   5133 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5182
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_167669972_   5183 AATGGAACAGAACAGAGCTCTCAGAAATAATGCCACATATCTACAACTAT 5232
                                i    iv   vvii         vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_167669972_   5233 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5282
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_167669972_   5283 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5332
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_167669972_   5333 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5382
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_167669972_   5383 AAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5432
                          ?   ii    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_167669972_   5433 AGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAA 5482
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_167669972_   5483 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5532
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_167669972_   5533 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5582
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_167669972_   5583 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5632
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_167669972_   5633 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5682
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_167669972_   5683 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5732
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_167669972_   5733 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCAT 5782
                         v        i  vi viii     v  i        i i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_167669972_   5783 CACTGGCCAT 5792
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


3151 27.75 0.44 0.44  chr2_167704723_167708499.rev     2378  3285 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167704723_   2378 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2427
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167704723_   2428 GGCCATACTGCACAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2477
                            v     v v   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167704723_   2478 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTAATT-TAAAGTTCA 2525
                          v   iivi i  i  ii     -   -- v  i  i  i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_167704723_   2526 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 2575
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_167704723_   2576 AACACAGCCAGAGGCATCACGCTACCTGACTTCAAATTATACTACAAGGC 2625
                             v  iii    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_167704723_   2626 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2675
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_167704723_   2676 AATGGAACAGAAC--AGATCCCTCAGAAATAATGCCGCATATCTACAACC 2723
                                i    i--   vi  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_167704723_   2724 ATCTGATCTTTGACAAACCCGAGAAAATCAAGCAATGGGGAAAGGATTCC 2773
                          vi    i  i     ivvi vv  i i  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_167704723_   2774 CTATTTAATAAATGGTGCTGGGAAAACTGGCTGGCCATAAGTAGAAAGCT 2823
                           v  i  i              v      v i?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_167704723_   2824 GAAACCAGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2873
                            iiii  i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_167704723_   2874 TTAAAGACTTACATGTTTGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2923
                          i ?    i  v    vv  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_167704723_   2924 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2973
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_167704723_   2974 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 3023
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_167704723_   3024 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3073
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_167704723_   3074 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 3123
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_167704723_   3124 AGGGCTAATATCCAGAATCTATAATGAACTCAAACAAATTTACAAGAAAA 3173
                         i  i  vi          v     v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_167704723_   3174 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 3223
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_167704723_   3224 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTAACC 3273
                           v        i  vi viii     v  i          i     v v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_167704723_   3274 GTCAATGGCCAT 3285
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2557 27.22 3.60 1.46  chr2_167722706_167728162     4077  4965 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167722706_   4077 TGGAAAAATATTCCATGCTCATTGACTGGAAGAATCAATATCATCAAAAT 4126
                               i    i     i    v  i       v i     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167722706_   4127 AGCCATACAGCCCAAAGTGATGTACAGATTCGATGCTATTCCTATCAAAC 4176
                         i  v    vv      v    v         i i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167722706_   4177 CACCAA-TGTCATTTTTCACAGAATTAGAAAAGCC--TCTTACAAAATTC 4223
                         iv   i-  i -     ii     v v  v    i--  i  --      
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTA--AAATTC 147

  chr2_167722706_   4224 ATATGGAATCAAAAAGAACTCA-AATGCCTAAAGAAATTCTAAGAAAAAA 4272
                                 viiv  i i  i  -   iv i   iv   ii i i   i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_167722706_   4273 AAA---AGCCAGAGGCATCACAATTCCTCATTTCAAACTATACTGAATGG 4319
                         i  ---  iii    vv     v    iv        viv    iv vi 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_167722706_   4320 CTACAGTAACAAAAACAGCATACTATTGGAAAAAAAAGAAAAAAACAGGT 4369
                                  iv  i    ii iv  i   v v  ii v i ----  vi 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA----CATAT 293

  chr2_167722706_   4370 GGACCAATGGAACATGTTAGATAAGCTAGAAATATAGCTGCACACCTACA 4419
                         i  i        i viv v  v iv i       v v iii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_167722706_   4420 ACCATGTGATCGTGGACAAAGTTGACAAAAGTAAGCAATGGGAAAAGGAT 4469
                         ii  vv    iv v     i v  v   i vi vv       i    i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_167722706_   4470 TTCCTAATCAATAAATGGTGCTGGGATAGTTGGCTAGCCATATGCAAAAG 4519
                         vvi  vv    i              i ii   v  ?   i         
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_167722706_   4520 ATTGAAACTAGACCTCCTCCTTTCACCATACAGAAAAATTAACTCAAGAT 4569
                          v    ii i    i iv   iv       i v              i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_167722706_   4570 GACTTAAAGACTTAAGCATAAAACCTAAAACTATAAAAAATCTTAGAAGA 4619
                          iv i ?    i   iii   i v              v-          
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGA 542

  chr2_167722706_   4620 AACCCTAGA---AAATACCATTCTGGATATTGGCCTAAGCAAACATTTTA 4666
                           v v   i---    -- -   vv  iv    vi  i    vvi   iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_167722706_   4667 TGACAAAGACTCCAAAAGCAATTGCAACAAAAACAAAAACTGACAAATGG 4716
                          iivv v   v         vvv         iv     iv  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_167722706_   4717 GACT-AATTAAA-CTAAAGAGTTCTGCACAGCAAAAGAAACTATCATGAC 4764
                             -v  i   -i    i v  i  ii vv    i  v       v  -
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA- 688

  chr2_167722706_   4765 CGAGTAAACAGACAACCTATTGAATGGGAGAAAATATTTGCAACCTATGC 4814
                         -i   i  v        i iv                      vii  ii
  L1M4_orf2#LINE/    689 -AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_167722706_   4815 ATCCAACAAAGGCCTAATATTCGGAATCTATAAGGAACT--TAAAGCACA 4862
                            ii i  i  v  vi   i i    v     i     --  v i v  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_167722706_   4863 A----------ACAAA-AAC---AGTAAAAAATGGGCAAAGGACATGAA- 4897
                          ----------     -   --- v ?                iv    -
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_167722706_   4898 ---CAATTTTTAAAAGAAAACATAGATGTGGCTAACAAGCATATGATAAA 4944
                         ---  v  i iv      i i   v vi    i  i     i    v  i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_167722706_   4945 CTGCTCAACACCATTAATCAT 4965
                         v         i  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.37 (45 / 19)  


3166 27.07 0.88 0.55  chr2_167764214_167770484.rev     4875  5779 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167764214_   4875 TGGAAGAACATTCCATGGCCATGGGTAGGAAGAATCAATATCATGAAAAT 4924
                              ii i  i     vi     i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167764214_   4925 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4974
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167764214_   4975 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTATAATGTTCA 5022
                          v   iivi i  i  ii     -   -- v  i  - iiv   vi    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_167764214_   5023 TATGGAACCGAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCAAAAAG 5072
                                vi v  ii  v  v v  v     ii     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_167764214_   5073 AACAAAGCTGGAGGCATCACACTACCTGACTTCAATCTATACTACAAGGC 5122
                                i      vv       v  ii i     vviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_167764214_   5123 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5172
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_167764214_   5173 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5220
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_167764214_   5221 ATCTGATCTTTGACAAACCTGAGAAAAGCAAGCAATGGGGAAAGGATTCC 5270
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_167764214_   5271 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5320
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_167764214_   5321 GAAACTGGATCCCTTCCTTACACCTTATACAAAA-TCAATTCAAGATGGA 5369
                            ii    i    v   i     v         - i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_167764214_   5370 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAAACCCTAGAAGAAAA 5419
                          i ?    i       v   v       i      v-i i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chr2_167764214_   5420 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5469
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_167764214_   5470 AAACACCAAAAGCAATGGCAACAAATGACAAAATTGACAAACGGGATCTA 5519
                         vi            vvi        v  v     v  i   iv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_167764214_   5520 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5569
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_167764214_   5570 CAGGCAACCTACAAAATGGGAGAAAATGTTCACAACCTACTCATCTGACA 5619
                         v  i     i   i             i  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_167764214_   5620 AAGGGCTAATATCCAGAATCTACAATGAACTGAAACAGATTTACAAGAAA 5669
                          i  i  vi          v  i  v     vvv   iv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_167764214_   5670 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5719
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_167764214_   5720 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA- 5768
                            v        i  vi viii     v  i          i       -
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_167764214_   5769 --TCAGTGGCCAT 5779
                         --   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3183 27.45 0.44 0.33  chr2_167775585_167782481.rev     5499  6405 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167775585_   5499 TGGAAAAACATTCCATAGTCATGGATAGGAAGAAACAATATAGTGAAAAT 5548
                               i i  i    iv        v      vvi     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167775585_   5549 GGCCATACTGCCCAAAGTAATTTGTAGATTCAATGCTATCCCCATCAAGC 5598
                            v     v      v i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167775585_   5599 TACAATTGGCTTCCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 5647
                          v v viv  i ii  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_167775585_   5648 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAGA 5697
                               viiv  ii  v  v v  v     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_167775585_   5698 ATAAAGCTGGAGGCATCACGTTACCTGACTTCAAACTATACTACAAGGCC 5747
                          i    i      vv    ii v  ii i      viv        i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_167775585_   5748 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATGTAGACCA 5797
                                i   i    ii         i iv ii i   i  i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_167775585_   5798 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACATATCTACAACCGTC 5847
                               i    iv   ivii         vv   i i  i  iiii ivi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_167775585_   5848 TGATCTTTGACAAACCTGACAAAAACAAGCAATAGGGAAAGGATTCCCTA 5897
                             i  i     ivv  v   i v  vv    i       i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_167775585_   5898 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5947
                         -  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    400 -TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_167775585_   5948 AACTAGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 5997
                          ii i       v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_167775585_   5998 AAAGACTTAAATGTAAGACCTAAATCCATAAAAACCCTAGAAGAAAACCT 6047
                          ?    i           v     v i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_167775585_   6048 AGGCA-ATACCATTCAGGTCCTAGGGATGGGCAAAGACTTCATGACTGAA 6096
                            ?i- v i -   iv v   v   v i     v ii   v iiv ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_167775585_   6097 ACACCAAAAGCAACTGCAACAAAAGCCAAAATTGACAAACGGGATCTAAT 6146
                                     vvv          vv     v  i   iv   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_167775585_   6147 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCA--GTGAACA 6194
                         i   v v  i i   i  ii vv    i  v       vv --     v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_167775585_   6195 GACAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCACCTGACAAA 6244
                                i                 v       vii  vi i    i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_167775585_   6245 GGGCTAATATCCAGAATCTACAAGGAACTTAAACATATTTACAAGAAAAA 6294
                           i  vi          v  i  i     ivv   vv iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_167775585_   6295 AACAAACAACCCCATCAAGTAGTGAGCATAGTATATGAACAGACACTTTT 6344
                         i     i     v  i? iv i  i   v  v  v    i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_167775585_   6345 CGAAAGAAGACATTTATGTGGCCAACACATATATGAAAAAAAGCTCATCA 6394
                          v        i  vi vi       i vii i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_167775585_   6395 TCACTGATCAT 6405
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


1910 25.57 4.53 6.58  chr2_167787423_167790502.rev     1662  2588 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_167787423_   1662 TGGAGAGAAATACTGTGTTCAGGGATTA----ACTCAACAAAGTAAAGAT 1707
                             i   v  v ii      v     i----   i  i vv  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_167787423_   1708 GCCAATTCTAGTTAAATTAATATATAGATACGACA-AATTCCTATAAAAG 1756
                          v    v  vvii     i  v  i    v i  i-   i     v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_167787423_   1757 ----AGCAAGACTTTTTGTAGATAAAGACAACACTT-TTATAGAATTCAT 1801
                         ----   vivvi      i   v vv     -i  v- iv  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_167787423_   1802 ATGGAAA-GCAAAGAAAGTACA-TAGCTAAAACTTTTTTTGTAAAAAATA 1849
                                -    i i vvi v -    i     vv i  - v    i vi
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT-GAAAAAGAAG 198

  chr2_167787423_   1850 AAGTAATTGGGAGGAATTTTAAGATTTTAAGATTTATTTTAAGAATTTTT 1899
                           vv  v v      v i--- v i  i----iiv    i  i v  vi 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTC---ACACTTC----CCAATTTCAAAACTTACT 241

  chr2_167787423_   1900 ATATAGCTATAGTAATCAAGACTGCAGGGGAATTAGCA----GATAGACA 1945
                          i v     i            v i- v  v i i   ----        
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGT-GTGGTACTGGCATAAGGATAGACA 290

  chr2_167787423_   1946 TATATTATAGATTAATGAAAGAGTATATGTATATAGAACCCGGAAA-AAG 1994
                             -----   i    i  v  v  -  -----   ii  i    -  i
  L1M4_orf2#LINE/    291 TATA-----GATCAATGGAATAGAAT-TG-----AGAGTCCAGAAATAAA 329

  chr2_167787423_   1995 GTCACATAAATATGCCTAACTGATTTTTGAAAAAGGTACAAAAAGCAGTT 2044
                         vi  i i vv    vii  i       i  v  i   i v  i v  -  
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TT 378

  chr2_167787423_   2045 CAATGAAGAAGGGATCGACTTTTAACCTTTTCAGTAA-T--TGCTGGAAC 2091
                              ii   i i  -------- ii       ii  - --      i  
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAAT--------AGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_167787423_   2092 AACTGGATATCAATAGGCAGAAACAAACAAACTCTAGTTAAACTTC--CC 2139
                                  ? v i v   i  i--  ii  -----   ii  ii --  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAG--AATGAA-----GTTGGACCCCTACC 463

  chr2_167787423_   2140 T------------AAAAATTAACTAAGAATTGATCACAGACTTAAATGTA 2177
                          ------------           v i   v     ?    i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_167787423_   2178 ACATGTAAAAATATAAAACTTTTAGGAATAAACATATAAG-AATCCTTCA 2226
                          v vv     v         i    i iv       vi? -  vi    i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_167787423_   2227 GAATCCAGGGTGAGGAGAAGAGTTCTTAGCCTTGACTTCAAAATCATGAC 2276
                         vi i iv    v   vi v iv       viv    vi     v  ii v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_167787423_   2277 CCATAAAATGAACATT-GATACTTTTGACTCCATCAATATTAAAAACTTT 2325
                          v i    vi  v v -    vv  v    i      v            
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_167787423_   2326 TA-G--TCAGGTAAATACCTTAATAAGATGACAAAAAGAGGAGCAGCAAA 2372
                          i- --   ---  iv  vi  vi    viiii      vi v vi  i 
  L1M4_orf2#LINE/    664 TGTGCTTCA---AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_167787423_   2373 GTGG-AGAAAATATTTGCAAATCACATATGTGTCAAGTGACTAGTATCTG 2421
                         i   -                   i    v  vi   v    v     ii
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_167787423_   2422 GAACGTACAAATAACTCTCAAAACTCATAACTCTCAAAACTCAATAGCAA 2471
                            ii  i   v      i --------------   --       ii  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTA--------------CAA--CTCAATAATAA 794

  chr2_167787423_   2472 AATCAAAACAAAAACAATCCAAGCAGAAAGTGGGCAAAAG-TCTTAAGAG 2520
                           --- i     --i  i    vi?i   i        i - i v  v  
  L1M4_orf2#LINE/    795 AA---AGACAAA--TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_167787423_   2521 GCATTTAACCTCAGAGAATATACAGATGGT-AATGACTACATGAAAAGAT 2569
                         i     vv  vv   ii       i    i-   i vi            
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_167787423_   2570 GTTCAACGTCATTAGCTAT 2588
                          i     i   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (133 / 100)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 2.86 (103 / 36)  


1924 23.72 3.88 2.95  chr2_167844934_167849884.rev     1639  2283 (2668)    L1M4_orf2#LINE/L1      258   908 (0)  

  chr2_167844934_   1639 CAAGAAAGTGTGACAT--GCATCAAAGAAAAAAAACCTCAAGATATTTAA 1686
                              v      ii i--    --   i v i v iv --    vvv ii
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCAT--AAGGATAGACATAT--AGATCAATGG 303

  chr2_167844934_   1687 AATATTTTGAGCTAAATGAAAAT--AGAAATACAACTTATCAAAATTTGT 1734
                             ----  ---- v   i i --       -   ii  -- v    i 
  L1M4_orf2#LINE/    304 AATA----GA----ATTGAGAGTCCAGAAATA-AACCCAT--ACATTTAT 342

  chr2_167844934_   1735 AGCCAACTGATTTTAGACAAACAAGCATAGGCAATACAATGGAGAGTGA- 1783
                         i i   i       v     iviv  vv  i v  v      i  iv  -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_167844934_   1784 ----CTTTTCAACAAATGGTATTGGAACAAGTGGACATCCATATACAAAA 1829
                         ----                ii   i    v    i ?   i  i     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_167844934_   1830 --ATTAAGCTAGACATAAACCTAACATGTTTTATAAAAA--AATTCTAA- 1874
                         --  v   i i   vivv    v   ivv v  i     --  i  v  -
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_167844934_   1875 TGGATCACGGACCTAAATGTAAAGTGC-AAAACTACAAAACTCCTAGAAG 1923
                                ?i             - v  -       i       i      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAA-GAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_167844934_   1924 GTAAGATAATACAAAATCTAGATGACCTAGGGTTTGGTGACGACTTTTTA 1973
                         iv  v   iv?vv      vvi      v     v  ii i ii  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_167844934_   1974 GATACAACATCAATAACATAATCCATGAGAGAACAAATA----AGCTGGA 2019
                             ii   i   v i  i  v v ii i    v     ---- ii    
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_167844934_   2020 ATTCATTAAAATTAGAAA--TTTCTGCTCCATGAAAGACAGCATCAAGAG 2067
                         v     i       i   --   v    i  --  i    vi       i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAA 689

  chr2_167844934_   2068 AATAAAAAGGCAAGCCATGGCCTGGGAGAAAATAATTTGCAAAAGACTTA 2117
                          i i     i   v   ii vv            -        vv iv  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATA-TTTGCAAATCATATA 738

  chr2_167844934_   2118 TCTGATAAGGGACTGTTATCCAAAATATACAAAGAATGCCTACAACTCAA 2167
                                       vv      i      i      iv i          
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_167844934_   2168 CAATAAGAAAACAA----CCCAATTAAACAACAGGCCAAACATTTTAACA 2213
                         i     i  i    ----       ?  v  ii   v  iv    v  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_167844934_   2214 GACACCTCACCAAAAAGGACATGCAGATAGCAAATAAGCACTTAAAAAGA 2263
                             ii  v     i i  i  i  i  i  v         v i      
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_167844934_   2264 GGCTCCACATCATCGTCAAA 2283
                         v    v      ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (87 / 62)
Gap_init rate = 0.03 (19 / 651), avg. gap size = 2.32 (44 / 19)  

 371 27.21 4.41 2.21  chr2_167844934_167849884.rev     3263  3398 (1553)    L1M4_orf2#LINE/L1        2   140 (768)  

  chr2_167844934_   3263 GAGAAGATACACCATGTTAAAATATTGGAGGACTTAATGTTGCTATGATG 3312
                          ii      iv       v viv      i        i   i  v    
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_167844934_   3313 TCAATTCTCCTCAAATTGATC-ATAATATTACAATAACAA-CTCTGGTAA 3360
                         v    v    i          - i i-   -   ii-   - i  ivi  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAG-ATT-CAACG-CAATCCCTATCAA 98

  chr2_167844934_   3361 GATTTC--TTGT-TTTCCTA-AAAAACTCACAAGTTAATTCT 3398
                         i  ii --i  i-   ii i- i   i v     i i  i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 3.11 (28 / 9)
Gap_init rate = 0.06 (8 / 139), avg. gap size = 1.12 (9 / 8)  

1923 26.40 6.80 2.00  chr2_167844934_167849884.rev     3710  4459 (492)    L1M4_orf2#LINE/L1      123   908 (0)  

  chr2_167844934_   3710 AATTCACAAGTTAATTCTAAAGGA---ATATGGAAA-ACAATATATTCTT 3755
                             v     i i  i     -- ---         -i   viv ii --
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAA--ATTCATATGGAAATGCAAGGGACCC-- 168

  chr2_167844934_   3756 TTGGCACTGTAGCCAAGAGGACTTTGGAAAAGGAGATCACACTTGGAAGA 3805
                         --i v ---       i vi ii   i     i   v  v v     i  
  L1M4_orf2#LINE/    169 --AGAA---TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_167844934_   3806 C--ATAC--CCTAAATGGCTTTAATGTTTACTATAAAGCTATAGTAACCA 3851
                          -- i  --  i  ----i  i  vii      i       i     i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAA----TTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_167844934_   3852 AGACAATGTGATACTGGTGAAAGAATAAA-ACATAGGTCAATAAAACAGA 3900
                              i    i      iiv   i   i - i    i     ii  i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_167844934_   3901 AT-------------ACAA-----TGTATT-ATGTTGAAATTATTTT-GA 3930
                           ------------- i  ----- ii   -   v v  v v     -  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_167844934_   3931 CAACAGCACCAAAGCAATTCTTTAAGAAAA----AGTCCTTTCAAAAAAT 3976
                            vi ii    ii v    vv ii i   ----    i      v    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_167844934_   3977 GGTACTGGAACAAGTGGTCATCCACACGGAAATAAAAGAACCTTGACTTT 4026
                            i    i    v   vi ?     i v   vi  v   vi v   iii
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_167844934_   4027 TACATTACACTATAAATACAAATGAATTCAACATAGATCATAGATTTACA 4076
                            v i    i   v i v    v  i    v  i     ?   ii  v 
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_167844934_   4077 TGTAAAACCTAAAACTATAACACTTCAAGAGGAAAGCACAGAAATA--TC 4124
                              i v            v   iiv   i    i  i  i?i  --  
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_167844934_   4125 TTTGCAATTCTAGAGTAGAAAGAGGTTC---AGAGAT--CATAGAAAGTC 4169
                           i ii iii i iv   iv iv    i---   v  --  ivi    iv
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_167844934_   4170 TTAACCATAAAAGACAACAT-GATAAATTAGATTTGATAAAAATTAACAA 4218
                         iv i v i      v  v  -        i  i  v  v        v  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_167844934_   4219 CTTCTGCTCATTAAACAAGACTAATAAAAA--TAAATGGGCAAATCTTAG 4266
                            i  iv v i   vi v    vi  i  -- i  vi i   vi vi  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_167844934_   4267 ACTAGAAAGAAATATTTGCAGCGCATAAA-CTGACAAAGGATTTTTATGC 4315
                          v i i ii           ivv    v -    i  i   i  v   --
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT-- 757

  chr2_167844934_   4316 CTTTGATATGTAAAGAACACCTACAACAAGATAATAAAAAGACAAGCA-T 4364
                          ivvi    i        v i      vvi               ii -i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_167844934_   4365 CCAATTAAAAAATGGGCAA-GTAGTTGAATAGACACTTCTT--AAGA-GA 4410
                               ?            - v v           i    i--    -  
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_167844934_   4411 GATAAATATGCCCAA-AAACACATGAAAA-ATGTTCAATATCATCAGTCA 4458
                         v   v v   v    -  i          -   i    i    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_167844934_   4459 T 4459
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.69 (122 / 72)
Gap_init rate = 0.03 (27 / 786), avg. gap size = 2.44 (66 / 27)  


2658 25.59 3.95 1.58  chr2_168056127_168061122.rev     3618  4504 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_168056127_   3618 TGGAAAAACACTCCATACTCATGAATTGGAAGAATCA-CATCATTAAAAT 3666
                               i i ii    ii     i         v i -i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_168056127_   3667 GGCCATACTTCCCAAAGCAATCTATAGATTCAACGCTATTCCTATCAAAC 3716
                            v     i      vii     i           v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_168056127_   3717 TACCAA-TGCCATTTTTCACAGAA-TTGGAAAAAAAACT-ATGCTAAAAT 3763
                          v   i-    -     ii     -   ---- v  i  -  v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAAT 145

  chr2_168056127_   3764 TCATATGGAACTAAAAAAGAGCCCAAATAGCCACAAAAATCCTAAGCAA- 3812
                                   v iv  ii  v  vi        v  v    i i iv  -
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_168056127_   3813 AAGACCAAAGCCAGACATAC---CATTTTACCTGACTTCAAACTATACTA 3859
                             v     iii  vi-  ---  i  --  ii i      viv     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGG-ACTCACACTT--CCCAATTTCAAAACTTACTA 242

  chr2_168056127_   3860 TAAGTCGACAGTAACCAAAACAGCATGGTTCTGGCACAAAAACAGATACC 3909
                         i  iv v       i   i    ii    v      i  ii i   i iv
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_168056127_   3910 TAGACTAATGGACTAGAATAGTGAACCCAGAGAAGTAAAGCCACACACCT 3959
                             ii      v      v v  ii     i --    v   i   ii 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAA--TAAACCCATACATTT 340

  chr2_168056127_   3960 CCAGGCATCTAATCTTCAACAAAGTTGACAAAAAAATAAGCAATGGGGAA 4009
                         vii v  vi i  i   i    i v  v   i vv  --v          
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAA 388

  chr2_168056127_   4010 AGGATTCTCTATTCAATAAATGGAGCTGGGATAGCTGGCAAGCCATATGC 4059
                           i  vv   v     i      v       i i    vv ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_168056127_   4060 AGTAGAATGAAACTGGACCCCTATCTTTCGCCATATCCAAAAATGAACTC 4109
                          iv        ii          i  iv i      v       v     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_168056127_   4110 AAGATGAATTAAAGATTTAAATTTAAGACCTCAAACTATAAGAATTCTAG 4159
                           i   i  i ?   ii     v     v  v         i v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_168056127_   4160 AAGAAAACACTATTCTAGACATT---GGCCTTG----AGGAAACAATTTA 4202
                                  iviv?v  i iv  --- i     ----   v  iii   v
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_168056127_   4203 T--GAC-TAACTCCTCAAAAGCAATTGCAACAAAAAAAAATATTTACAAG 4249
                          --  i- i  v  --       vvv         i    v  vv i  i
  L1M4_orf2#LINE/    589 TTAGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_168056127_   4250 AGGAACCTAATTAAACTAAAGTGCTCCTACACAGCAAAAGAAACTATCAA 4299
                         vv i  i v  i   v v  ivi  ii iii vv    i  v        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_168056127_   4300 TAGAGTAAACAGACAACCTACAGAATGTGAGAAAATATTTGCAAACTATG 4349
                         v i   i  v        i        v                 ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_168056127_   4350 CATCCAACAAAG---TT----CTAAGATCTATAACAAACTTAAACATTTA 4392
                         i   ii i  i ---  ---- i ii  v     vi    ivv   vi v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_168056127_   4393 AACAAGCAAAA-ACTAATAACCCCACT-AAAAATGGGCAAAAGAC----A 4436
                           i  vv    -  v        v i -             i  i---- 
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_168056127_   4437 TAAAC--TGCTCAAAAGAAGACACACAAGCAGCCAACAA--ACATGAAAA 4482
                           i  -- v   v        i i    iii     i  --         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_168056127_   4483 AATGCTCCACATCACTAACCAT 4504
                         i      v      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (137 / 87)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.04 (49 / 24)  


2518 27.30 3.69 0.92  chr2_168124147_168132938.rev     1683  2550 (6242)    L1M4_orf2#LINE/L1        1   892 (16)  

  chr2_168124147_   1683 TGAAAACACATCCCATG------GATGGGTAGAATCACTACTGTGAAAAT 1726
                           i   v i        ------   v  v   v i v  i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_168124147_   1727 GACCATATTGCCAAAAGCAATCTACAGATTCAATGCAATTCCCATCAAAA 1776
                          i v   i v  v   vii              i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_168124147_   1777 TGCCATCATCATTCTTCACAGAACTAGAAAAAA-AATCCTAAAATTCATA 1825
                          v   v vv v  i  ii     v v  v  iv-i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_168124147_   1826 TGGAA---CAAAAAAATAGCCCTCAGAA---CCAAAGGAAGACTAAGCAA 1869
                              ---   iii ------ i     ---     iv  vvi i iv  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA------CCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_168124147_   1870 AAATAACAAATCTGAAGGCATCACATTACCCAACTTTAAACTATACCATA 1919
                         i  v      vi  i   vv     i v     i  i   viv   i i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_168124147_   1920 AGCCCATAGTCACCAAAAGAGCATGGTACTGGTATAAA-ATGG-CATACA 1967
                          iv i i   v i   i v  ii         i    i-  i -    i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_168124147_   1968 AACCAATAAAATGGAATAGGGAATCCAGAAATAAAGCCAAACACTTATAG 2017
                         i i    ii   i    v i  i            v   v   i    i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_168124147_   2018 CCAACTGATCTTAGAAAAAGCCAACAAAAACAAAAAGTGGAGAAAGCACA 2067
                         i   i    i  v  v  i viiv   i v  vvv i   i     v i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_168124147_   2068 CCCTATTCAACAAATGGTCCTGGGATAATTGGCAAGCCACATGTAGGAGA 2117
                         vi  v             v      i  i   vv ?       i ii   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_168124147_   2118 ATGAAACTGAATCCTAATCTCAT--CTTACATGAAAATCAACTCAAAATG 2165
                              ii  i i  iv i    i-- v  i ii     i           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_168124147_   2166 AATGAAGGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATA 2215
                         i  v ?i   i     v     v  i    i      v ii       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_168124147_   2216 CCATCAGAAAAACCCTTCTAGACATTGGCTTAGGCAA----------GA- 2254
                         v   vi ?iv  vi    vv   v    v        ----------  -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_168124147_   2255 ---AC-CTAAAAGCAAATACAACAAAAACAAAAAGATAAATAGGTGGGAC 2300
                         ---  - i       v vi        i--    i   i   ii v    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAG--AAAAAATAGATAAATTGGAC 642

  chr2_168124147_   2301 TTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGT 2350
                           v  i   v v    i   i  ii vv    i  v iv    iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_168124147_   2351 AAACAGACAAACCACAGAGTGAGAGAAAATCTTCACAATCTATACATCTG 2400
                         i  v      v       i  i        v  ii   vii   i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_168124147_   2401 ACAAAGGACGGGTATCCAGAATCTACAAGAAACTCAAACAAATCAGCAAC 2450
                          i  i    vv           v  i  ii     vv    v   ii  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_168124147_   2451 AAAAAAACCAACAATCCCATCAAAAATTGAGCTAAGGACATTAATAGATA 2500
                              i  v  i  i  v  i?    v  i  v     iv v      i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_168124147_   2501 ATTCTCAAAAGAAAATATACAAATGTACAACAAACATATTAAAAAAAGCT 2550
                         v     v      i           vv   i  i  i  v    i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.38 (135 / 98)
Gap_init rate = 0.01 (12 / 892), avg. gap size = 3.33 (40 / 12)  

3190 27.24 1.00 0.44  chr2_168124147_168132938.rev     7398  8300 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_168124147_   7398 TGGAAGAATATTCCATGCTCATGGATAGGAACAATCAATATCACGAAAAT 7447
                              ii    i     i        v    v v i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_168124147_   7448 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATTCCCATCAAGC 7497
                            v     v     iv i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_168124147_   7498 TTCCGATGACTTTCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCA 7545
                          i  iiivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_168124147_   7546 TATGGAACCAAAAAAGAGTCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 7595
                                viiv  ii  vi v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_168124147_   7596 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 7645
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_168124147_   7646 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGATC 7695
                                 i   i i  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_168124147_   7696 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 7743
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_168124147_   7744 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 7793
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_168124147_   7794 CTATTTAATAGATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 7843
                           v  i  i i            v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_168124147_   7844 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 7893
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_168124147_   7894 TTAAAGACTTAAACTTA-GACCTAAAACCATAAAAACCCTAGAAGAAAAC 7942
                          i ?    i    iv  -  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_168124147_   7943 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 7992
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_168124147_   7993 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 8042
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_168124147_   8043 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 8092
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_168124147_   8093 AGGCAACCCACAAAATGGAAGAAAATTTTCGCAACCTACTCATCTGACAA 8142
                           i         i     i       v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_168124147_   8143 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 8192
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_168124147_   8193 AAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 8238
                          i    ----   v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_168124147_   8239 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 8288
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_168124147_   8289 ATCACTGGCCAT 8300
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2746 24.74 6.21 1.73  chr2_168250003_168252964.rev     1602  2470 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_168250003_   1602 TGGAGAGATATTTCATGTAAATAACCAGGAAGA--TAG----G--AAGAT 1643
                             i      ii     vv  iiviv      --  i---- --     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_168250003_   1644 G---------------TTGATGTATTGATTCAATACAGACTCAATCAAAA 1678
                          ---------------     v  iv       ii  iv i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_168250003_   1679 CCCTAGCAACTTATTTTATGGCTGTAGACAAACTGATTTTACTATTTATA 1728
                         i  i   vi i v    iii vvi v     i     ii  vv   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_168250003_   1729 TGGGGAGGCAAAAAATCCAGAATAACAAATATAATACTGAA---GAAGAA 1775
                            ii v    iii i        i v  v i   vi    ---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_168250003_   1776 CAAAGTTGGAGAACTGACATTATCTGACTTTAAGACTTACTGTAAAGCTA 1825
                                    i   v   i vi ii i  i  i       ii       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_168250003_   1826 CAGTAATCAAGATAATGTGGTATTAGTAAAAGCAAAGACAAATAGATCAG 1875
                                     i i       i i i v   v v     v        i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_168250003_   1876 TGGAACAGAATAAAGAACCCAGAAA-AAGCCCACATAAATATGGTCAATG 1924
                              i     vi   ii       -  i    i i vv          v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_168250003_   1925 GATCTTTGAAAAAGGAACGATGAAAATACAAATGGAACAATGATGGTCTT 1974
                            i  i  v  i  vi v v  vv  v   -   iiv  vi  i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTT 399

  chr2_168250003_   1975 TTCAACAAATGGTGCTAGAACAACTGCACATCCACGTGCAAAACAATGAA 2024
                                         i i       v i ?    i       v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_168250003_   2025 TCTAAACACATACCTTATGGTACCTTTCCCCAAAATTAA-----GATGGA 2069
                         vi ii  v v     i i---   v viv v        -----i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCAC---ACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_168250003_   2070 TTATAGATCTAAA----ACA--TAAAACTATAAAAATCCTCAAAAATAAC 2113
                          i ?   i     ---- v --             v  i vi  i v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_168250003_   2114 ACAGGAGAAAGAAAATCTTGATGATCTTGGGTATGGCAATGACTCTTTAG 2163
                          i   ? v  ----     vi   i       vv       ii ii    
  L1M4_orf2#LINE/    547 ATAGGNGTAA----ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_168250003_   2164 ATAAAAAAAAAATCAAAGACATGATTCATGAAAGAAATACT-GATAAGCT 2212
                            vi v ----i    ii  ii viv ii       v v -     ii 
  L1M4_orf2#LINE/    593 ATATGACA----CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_168250003_   2213 GGACTTCATGAAAATTTAAAACTTCCCTG-----AAATACAATGTCAAGA 2257
                                  v      v       iiv  -----  iv   v i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_168250003_   2258 GAATGAGAAGACAAGTCACAGACTGGGAGAAAATATTTGCAGAAGATGCA 2307
                         i i   i       vi      v                  i vv  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_168250003_   2308 TCTGATAAAATATTGTTATCTAAAATATATATTAAAAA--------ACTA 2349
                                 iiv i vv    i i        --  i  --------   v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATA--AAGAACTCTTACAACTC 786

  chr2_168250003_   2350 AACAATAAGAAAACAAACAACCCAATTAAAAAATGGGTCAAAGTCCTT-A 2398
                           i     i  i     i         ?         -     vvi  - 
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGG-CAAAGGATTTGA 835

  chr2_168250003_   2399 ACAGGTAACTCACTAAAGAAGACATTCAAG-AGCAATTAAGCATATGAAA 2447
                          i  ii vi  v i        i  v   i-i  v v      i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_168250003_   2448 AGATGCTCCACATCATGTGTCAT 2470
                                 v      ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (129 / 82)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.45 (69 / 20)  


3244 26.98 0.44 0.44  chr2_168345229_168351491.rev     4864  5771 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_168345229_   4864 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4913
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_168345229_   4914 GGTCATACTGCCCAAGGTAATTCACAGATTCAATGCCATCCCCATCAAGC 4963
                           iv     v     iv i  ii          i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_168345229_   4964 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5011
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_168345229_   5012 TATAGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5061
                            i   viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_168345229_   5062 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAAGC 5111
                                i      vv   ii  v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_168345229_   5112 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAGAGATC 5161
                                 i   i    ii         i iv ii i   v   v     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_168345229_   5162 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACACATCTACAACT 5209
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_168345229_   5210 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5259
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_168345229_   5260 CTATTTAATAAATGGTGCTTGGAAAACTGGCTAGCCATATGTAGAAAGCT 5309
                           v  i  i          v   v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_168345229_   5310 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5359
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_168345229_   5360 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTACAAGAAAAC 5409
                          i ?    i    i  v   v       i      vi i  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_168345229_   5410 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5459
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_168345229_   5460 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5509
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_168345229_   5510 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5559
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_168345229_   5560 AGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5609
                           i         i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_168345229_   5610 AGGGCTAACATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5659
                         i  i  vii         v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_168345229_   5660 AAACAAAGAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGAGACTTC 5709
                          i     v     v  i?    i     i     iv    i   v i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_168345229_   5710 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5759
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_168345229_   5760 ATCACTGGCCAT 5771
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2363 26.09 2.00 3.12  chr2_168479566_168481230.rev      379  1179 (486)    L1M4_orf2#LINE/L1      117   908 (0)  

  chr2_168479566_    379 TGAAAAAATTGCCAAAACT-ATCCTTTACTTCATGGCCTCTTGAAAATGT 427
                           v i      v   i-  -     vv v     i------  i     i
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAG-CTGATCCTAAAATTCATA------TGGAAATGC 159

  chr2_168479566_    428 TCCTGCAAACCAAAAAAGAGCTTCAATAGCCAAGACAATTCTAAGCAAAA 477
                         -------------  ii  v ivv         i     ii i iv  i 
  L1M4_orf2#LINE/    160 -------------AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_168479566_    478 AGAACAAAGTTGGAGGCATCATGCTACCTGATTTCAAACTATACTACACG 527
                                         vv   ii  v  ii        viv       vi
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_168479566_    528 GCTACAGTAACCAAAACAGCATGGAACTGGTATAAAAATAGACACGTAGA 577
                                   i   i    ii   v     i    ii       ii    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_168479566_    578 CCAATAGAACATAATAGAGAACTCAGAAATAAGACCCACAC--CTACAGC 625
                         i    i   i v   v    iii         -     i  --i  ii i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGT 345

  chr2_168479566_    626 CA-TCTATCTTCAACTAAGCCAGCAAAAACAAGCAATGGGGAAAGGATTC 674
                           - iv  i   i  v i viiv   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_168479566_    675 CCTATTTCATAAATGGTGCAGGGAGAACTGGCTAGCCATGTGCAGAAAAT 724
                         i  v  iv i         v    v      v  ?   ii    i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_168479566_    725 AAAAATTGGACCCCTCCCTTATACCTTGTACAAAAATTAACTCAAGATGG 774
                         vi  i          v   i i   v i                 i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_168479566_    775 ATTAAAGACTTAAAGGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAG 824
                           i ?    i    v    i v i     i      vi i         i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_168479566_    825 CCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAAGATTTCAT-GAT 872
                          v    ?i- v i -   iv   viv  vv i     v i    v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_168479566_    873 GAAAACACCAAAAGCGATGGCAACAGAAGCTAAAAAT-GACAAATGGGAT 921
                         - vi           ivvi      i   v-      -  i    v   i
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGAC 642

  chr2_168479566_    922 TTAATTAAACCAAAGAGCTTCTTCACAGCAAAAGAAACTATTATCAGAGC 971
                           v  i   viv  i i   i vii vv    i  v     i vv i  i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_168479566_    972 AAACAGACAACCTACAGAATGG---AAAATTTTTGTAATCTATCCATCTG 1018
                         i  v        i         ---     v    i  vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_168479566_   1019 ACAAAGGTCTAATATCCAGAGTCTACAAGAAACTT----AAAGAAAT--T 1062
                          i  i  v  vi        i v  i  ii    i----  vvv   -- 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_168479566_   1063 TACAAGATAAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGAC 1112
                         v v    i   -i     v   ?    i           iv    i    
  L1M4_orf2#LINE/    793 AAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_168479566_   1113 ACTTTTCAAAAGAAGACATTCATGCAACCAACAAACATATGATAAAAAGC 1162
                          i  i  v        i  v  viiii    i  i  i    v  i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_168479566_   1163 TCAATGTCATAGATCAT 1179
                             ii   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (124 / 81)
Gap_init rate = 0.02 (17 / 792), avg. gap size = 2.41 (41 / 17)  


3247 26.76 0.55 0.55  chr2_168486595_168492943.rev     4950  5857 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_168486595_   4950 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4999
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_168486595_   5000 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCTATCAAGC 5049
                            v     v     iv i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_168486595_   5050 TACCAATGACTTTCTTCACACAA-TTGGAAGAAACT-ACTTTAAAGTTCA 5097
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_168486595_   5098 TAGGGAACCAAAAAAGAGCCTGCATTGCCAAGTGAATCCTAAGCCAAAAG 5147
                           v    viiv  ii  v  v v  v     ivv    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_168486595_   5148 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATATTACAAGGC 5197
                                i      vv       v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_168486595_   5198 TACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5247
                                     i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_168486595_   5248 AAAGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACGTATCTACAACC 5295
                           v    i    i--    i  --        vv   iii  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_168486595_   5296 ATCTGATCTTTGACAAACCTGACAAAAATGAGAAATGGGGAAAGGATTCC 5345
                          vi    i  i     ivv  v   i viivvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_168486595_   5346 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5395
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_168486595_   5396 GAAACTGGATCTCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5445
                            ii    i i  v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_168486595_   5446 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTACAAGAAAAC 5495
                          i ?    i       v   v       i      vi i  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_168486595_   5496 ATAGGCA-ATACCATTCAGGACATAGGCAGGGGCAAGGACTTCATGTCTA 5544
                              ?i- v i -   iv   v v  vvvi     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_168486595_   5545 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5594
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_168486595_   5595 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5644
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_168486595_   5645 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5694
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_168486595_   5695 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATCTACAAGGAA 5744
                          i  i  vi          v  i  v      vv    v  v i  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_168486595_   5745 AAAACAAACAGCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5794
                           i     i i   v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_168486595_   5795 CTCACAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5844
                            vv       i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_168486595_   5845 CATCACTGGCCAT 5857
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3203 26.99 0.88 0.44  chr2_168516560_168522954     5000  5903 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_168516560_   5000 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5049
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_168516560_   5050 GGCCATACTGCCCAAGGTAATTTTTAGATTCAATGCCATCCCCATCAAGC 5099
                            v     v     iv i  i vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_168516560_   5100 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5147
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_168516560_   5148 TATGGAACCAAAAAAGAGCCCGCCTTGTCAAGTCAATCCTAAGCCAAAAG 5197
                                viiv  ii  v  v vv v i   iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_168516560_   5198 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5247
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_168516560_   5248 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5297
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_168516560_   5298 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTGCAACT 5345
                                i    i--    i  --        vv  ii i  i iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_168516560_   5346 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5395
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_168516560_   5396 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5445
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_168516560_   5446 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5495
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_168516560_   5496 TTAAAGACTTCAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5545
                          i ?    i v     v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_168516560_   5546 CTAGGCATTACCATTCAGGACATAGGCAGGGGCAAGGACTTCATGTCTAA 5595
                         v    ?i v viv   iv   v v  vvvi     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_168516560_   5596 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5645
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_168516560_   5646 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5695
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_168516560_   5696 AGGCAACCCACAAAATGGGAGAAAATTTTTGCCACCTACTCATCTGACAA 5745
                           i         i             v     v vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_168516560_   5746 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5795
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_168516560_   5796 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5841
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_168516560_   5842 TCAAAAGAAGACATTTTTGCAGCCAAAAAACACATGAAAAAATGCTCACC 5891
                           v        i  vivviii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_168516560_   5892 ATCACTGGCCAT 5903
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (139 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


1866 26.97 0.98 0.98  chr2_168527568_168532822     3545  4052 (1203)    L1M4_orf2#LINE/L1        2   509 (399)  

  chr2_168527568_   3545 GGAAACATATCTCATGATCATGGATGGGTAGAATCAATATTGTGAAAATG 3594
                              v     i    v        v  v   v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_168527568_   3595 ATCATACTGACAAAAGCAATCTACAAATTCAATAGAATCCCCATCAAAAT 3644
                         iiv     vv v   vii       i      iiv      i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_168527568_   3645 ACCACCATCATTCTTCATAGAA-TTAGGAAAAAC-AATTCTAAAATTCAT 3692
                         v   v vv v  i  iii    -  --  v  i -i  i           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCAT 149

  chr2_168527568_   3693 ATGGAA---CAAAAGATGAGCCTGCATAGTCAAAGCAAGACTAAGCAAAA 3739
                               ---   ii  i---  v v    i    i   vvi i iv  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_168527568_   3740 AGAACAAATCTGGAGGCATCACACGACCTGATTTTAAACTATACTATAAG 3789
                                 vi      vv      vv  ii    i   viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_168527568_   3790 GCCATAGTCACCAAAACAGCATGGTGCTGGTATAAAAATAGGCACATAGA 3839
                           i i   v i   i    ii    i    i    ii    i  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_168527568_   3840 CCGATGGAACAGAATAGACAACCCAGAAATACACCCAAATACTTACAGCC 3889
                         i i      i     v  v ii         v     v i i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_168527568_   3890 AACTGATCTTCAACAAAGCAAACAAAAATATGAAGTGAGGAAAGGACACC 3939
                           i    i   i    i vviv   i vi  vv i  i      i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_168527568_   3940 CTTTTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAAAAC 3989
                                                i  i   vv ?       i ii i  i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_168527568_   3990 AAAACTGGATACTCATCTCTCACCTTATACAAAAATCAGCTCAAGATGGA 4039
                         i  ii    iv ii i   v    v           i i     i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_168527568_   4040 TTAAGGACTTAAA 4052
                          i ?i   i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAA 509

Transitions / transversions = 1.87 (88 / 47)
Gap_init rate = 0.01 (5 / 508), avg. gap size = 2.00 (10 / 5)  

1323 25.93 0.74 0.25  chr2_168527568_168532822     4359  4763 (492)    L1M4_orf2#LINE/L1      502   908 (0)  

  chr2_168527568_   4359 GACTTAAACCTAAGACCTGAAACTGCAACAATTCT--GAAGATAACATTG 4406
                            i    iv     v  i     ii  -  i   --     v     v 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACATAG 550

  chr2_168527568_   4407 GAAAAACTCTTCTAAACATTGGCTTAGGCAAGGATTTCATAACCAAGAAC 4456
                          ?iv  v     vvi  v    v        v i    v  ivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_168527568_   4457 CCAAAAGCAAATTCAATAAAAACAAAGATAAATCACTGGGACCTAATTAA 4506
                                  v vv   i    iv   i   i  v v v    i v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_168527568_   4507 ACTAAAGAGCTTTTGCACAGCAAAAGAAACAGTCAGCAGAGTAAACTGAC 4556
                          v v  i i      ii vv    i  v  vi   iv i   i  vv   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_168527568_   4557 AACCCACAGGGTGGGAGAAAATCTTCACAATCTGTACATCTGACAAAGGA 4606
                                  ii           v  ii   viii  i      i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_168527568_   4607 CTAATATCCAGAATCTACGACAAACTCAAACAAATCAGTAAGTCAAAAAC 4656
                           vi          v  ii vi     vv    v   i   vvv   i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_168527568_   4657 AAACAATCCCA-CAAAAAGTGGGCTTAGGACATGCATAGACAGTTCTCAA 4705
                            i  i  v -i?    i     vv    iv  v       v     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_168527568_   4706 AAGAGGATATCCAAATGGCCAACAAGCATATGAAAAAATGCTCAACATCA 4755
                             i     v           i     i       i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_168527568_   4756 CTAATGAT 4763
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 0.98 (51 / 52)
Gap_init rate = 0.01 (3 / 407), avg. gap size = 1.33 (4 / 3)  


3054 24.39 2.33 1.66  chr2_168568044_168570400.rev      964  1865 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_168568044_    964 TGGAAACACATCCCATGATCATGGATGGGTAGAATCAATATTGCGAAAAT 1013
                               v i        v        v  v   v i       iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_168568044_   1014 GACCATACTGACAAAAGCAATCTACAAATTCAACACTATTCCCGTCAAAA 1063
                          i v     vv v   vii       i       i v  i  ii      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_168568044_   1064 TACTACCATCATTCTTCACAGAATTAGAAAAAAAAACCCCTAGAAATTCA 1113
                          v i v vv v  i  ii     v v  v  ivvi i  -  -       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC-TA-AAATTCA 148

  chr2_168568044_   1114 TATGGACCCAAAAAAGAGTCTGCACAGTCAAAGCAA----GACAAAGCAA 1159
                               vviiv  ii  vi v v i  i    i   ----  v    ---
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG--- 195

  chr2_168568044_   1160 AAAGAACAATTCTGGAGGCAC-CACATTACCTGATTACAAACTATACTAT 1208
                         -        vvi      -  -    i v  ii   v    viv     i
  L1M4_orf2#LINE/    196 -AAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_168568044_   1209 AAGACCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACAT 1258
                           ii i i   v i   i    ii         i    ii    i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_168568044_   1259 AGACCAATGGAACAGAATAGAGAACCCAGAAAGAAACCCAAATACTTACA 1308
                            i        i     v    ii       v       v i i   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_168568044_   1309 GCCAACTGATCTTCAGCAAAGCAAACAAAAACATAAAGTGGGGAAAAGAC 1358
                          i   i    i   ii   i vviv   i v   vv i        ii i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_168568044_   1359 ACTCTTTTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAG 1408
                          v                        i  i   vv ?       i ii  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_168568044_   1409 AATGAAACTGGATCCTCATCTCTCACATTATACAAAAATCAACTCAAGAT 1458
                               ii    i  ii i   v   vv           i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_168568044_   1459 GGATGAAGGACTT-----TAAGACCTGAAACTATAAAAATTCTAGAAGAT 1503
                             v ?i   i -----     v  i           v ii       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_168568044_   1504 AACATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTC----- 1548
                              v  ?iv  vi    vv   v    v        v i    -----
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_168568044_   1549 -ATGAC--CAAGAACCCAAAAGATAAAGATAAAAACAAAGATAAATTGCT 1595
                         -     --   i i v   ivi i   iiv     i --         --
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTG-- 639

  chr2_168568044_   1596 GGGATTTAATTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGC 1645
                         --  i  v  i   v v  i i      iiivv    i iv  vi   iv
  L1M4_orf2#LINE/    640 --GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_168568044_   1646 AGAGTAAACAGACAACCCACAGAATGGGAAAAAA-ATCTCCACAATCTAT 1694
                          i   i  v                    i    -  i v  -    -  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-AT 735

  chr2_168568044_   1695 ACATCTGACAAAGGAGTAGTATCCAGAATCTACAATGTACTCAAACAAAT 1744
                          i      i  i   v v           v  i  v v    vv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_168568044_   1745 CAACAAGAAAAAAATAAACAACCCCATCAAAAAGTGGGCTAAGGATATGA 1794
                            i  v     i i   i     v  i?    i     v      v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_168568044_   1795 ATAGACAGTTCTCAAAAGAAGATAACTGAATGGCCAACAA--ACATGAAA 1842
                                v     v          vvii         i  --        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_168568044_   1843 AAATGCTCAACATCACTAATGAT 1865
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (124 / 92)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.40 (36 / 15)  


2848 19.05 4.31 9.18  chr2_168633673_168635553.rev      508  1389 (492)    L1M4_orf2#LINE/L1       70   908 (0)  

  chr2_168633673_    508 ATCTACAAATTCAGTATAATCCTTATCAAAATTTTTAAATTGTATTACCC 557
                                i     iiii     i         iii-- ii  iv  viii
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCC--AGCTGCCTTTTTT 117

  chr2_168633673_    558 ACAGAAATATGAAAAAC-AATCCTAACATTTGTATGGAACCACAAAAGAC 606
                         i       -   v  i -i       v   ii       vii   ii   
  L1M4_orf2#LINE/    118 GCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr2_168633673_    607 CCTGAATAGCCAAAGCAATCTTGACGAAAAAGAACAAAACTGAAAGCAC- 655
                           v           i         vi  i         ii  i i -  -
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-ACT 215

  chr2_168633673_    656 CACACTTCCTGATTTTAAA--TTACATTATAAAGTTATAGTAATCAAAAT 703
                                  ii    i   --    --  i    i  i         i i
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTAC--TACAAAGCTACAGTAATCAAGAC 263

  chr2_168633673_    704 AGCATGGTACTGGTATAAAAACAGAC--------CAGTAGAACAGACT-- 743
                           ii         i    ii i    --------  i i   i   v --
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_168633673_    744 AGAGTCCAGAAATAAACCCATACATGTATGG-CAATT----TTTGACATG 788
                                                  v     -     ----  i    v 
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_168633673_    789 AGTGCCAAAAATATACAATGGGAAAAGGACAGTCTCTTCAGCAAATTTTG 838
                         i       i vi  v       i    i i     i    i     vv  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_168633673_    839 TTGGGAAAACTGTATATCCACTTGCAAAACAATGAAATTGGACCTTTATC 888
                         i     v     v   ?    v       v      i       ii  i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_168633673_    889 TTACAACTTA-----AAATCAACTCAAAATGGATTAAAGACAT---TATA 930
                          i   v v  -----    i              i ?    v --- i  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_168633673_    931 AGACATGAAACTCTAAAACTCCTGGAAGAAAACA--GGAAGAAATCTCCT 978
                            vv i     v        i i          --  ?iv      i v
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_168633673_    979 TGGCATTGGTCTTATCAATGACTTTTTTGGATATGACACCAAAAGCACAG 1028
                           i v    vi viv     i-   i  i                    i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_168633673_   1029 GCAACAAAAGCAAAAATA---AAGTGGGATTATATGACACTAAAAAGCTT 1075
                                   v       ---  i v   i vi  v v v v    i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_168633673_   1076 CTGCACAGCAAAGGAAATAGTAGACAAAGAGCAAAAGCAAAAATAAAATG 1125
                         i  ii vv       -----------------------------------
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGA----------------------------------- 677

  chr2_168633673_   1126 GGATTATATGACACTAAAAAGCTTCTGCACAGCAAAG-GAAATAGTAGAC 1174
                         -----------     vv   ------------    -    ----    
  L1M4_orf2#LINE/    678 -----------CACTATCAAG------------AAAGTGAAA----AGAC 700

  chr2_168633673_   1175 AAAGAGCAAAAGCAATCTATGGACTTAGGAAATATTTTTAAACTATATAT 1224
                           vvvi  i  --------   i---  i        vi   ii      
  L1M4_orf2#LINE/    701 AACCCACAGAA--------TGGG---AGAAAATATTTGCAAATCATATAT 739

  chr2_168633673_   1225 CTGATAAGGGGTTAATATCCAAAGTGCATAAAGAACTCATATAACTCAAG 1274
                                   ii vi      i i ii           v  i       v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_168633673_   1275 AGCAAACA-ACAACAAAAC---ATT-AAAAATAGGCAAAGGACTTGAATA 1319
                          ii   v -    - v   ---   -      i         i       
  L1M4_orf2#LINE/    790 AATAAAAAGACAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_168633673_   1320 GATATTTTCCCAAAGAAGACATATAGTTGGCCAATAAGCATATGAAAATG 1369
                           i    ii          i   i iv             i       vi
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_168633673_   1370 TACTCAACATCATTTAATCA 1389
                          i          ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (113 / 52)
Gap_init rate = 0.03 (26 / 839), avg. gap size = 4.58 (119 / 26)  


3399 25.83 0.33 0.11  chr2_169066041_169071016     3579  4484 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_169066041_   3579 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTTTGAAAAT 3628
                               v i        i        v  v   v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_169066041_   3629 GACCATACTGCCAAAAGCAATCTGCATATTCAATGCAATCCCCATCAAAA 3678
                          i v     v  v   vii    i  v      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_169066041_   3679 TACCACCATCATTCTTCACAGAATTAGAAAAAATAATCCTAAAATTCATA 3728
                          v   v vv v  i  ii     v v  v  iv i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_169066041_   3729 TGGAACCAAAAAAGGGCCTGCATAGCCAA-GTAAGACTAAGCAAAAAGAA 3777
                              viiv  ii iv  v v        -ii  vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_169066041_   3778 CAAATCTGGAGGCATCACATTACCTGATTTCACACTACACTATAAGGCCA 3827
                             vi      vv     i v  ii      v vivi    i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_169066041_   3828 TAGTCACCAAAACAGCATGGTAGTGGTATAAAAATAGGCACATAGACCAA 3877
                         i   v i   i    ii     v   i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_169066041_   3878 TGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACGGCCAACT 3927
                              i     v    ii               v i i   i  i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_169066041_   3928 GATCTTCGAGAAAGCAAACAAAAACATGAAGTGGGGAAAGGACACCCTTT 3977
                            i     v  i vviv   i v   vv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_169066041_   3978 TCAACAAATGATGCTGGGATAACTGGCTAGCCACATGTAGGGGAATGAAA 4027
                                   i        i      v  ?       i iii       i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_169066041_   4028 CTGGACCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGAATTAA 4077
                         i       ii i   v    v           i       i   i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_169066041_   4078 AGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATTG 4127
                             i    iv     v  i           v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_169066041_   4128 GAAAAACCCTTCTAGACATTAGCTTAGGCAAGGATTTCATGACCAAGAAC 4177
                          ?iv  vi    vv   v  i v        v i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_169066041_   4178 CCAAAAGTAAATGCAATAAAAACAAAGATAAATAGTTGGGACGTAATTCA 4227
                                i v v    i    iv   i   i   iv v    v v  iv 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_169066041_   4228 ACTAAAAAGCTTTCGTCTGGCAAAAGGAACAATCAGCAAAGTAAACAGAC 4277
                          v v    i    i  vivv    i iv  v    iv     i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_169066041_   4278 AACCCACAGAGTGGGAAAAAATCTTCACAATCTATATATCTGACAAAGGA 4327
                                   i     i     v  ii   vii          i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_169066041_   4328 CTAATATCCAGAATCTACAACGAACTCAAATAGATCAGCAAGTAAAA--C 4375
                           vi          v  i  v      vv i iv   ii  -     --v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAGA 799

  chr2_169066041_   4376 CAAACAATTCCATCAAAACGTGAGCCAAGGACATGAATAGACAATTCTTA 4425
                             i  ii v  i?   vi  i  v     iv          v    iv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_169066041_   4426 AAAGAAGATATCTAAATGGCCAACAAACATATGAAAAAATGCTCAACATC 4475
                                    vi          i  i  i       i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_169066041_   4476 ACTAATAAT 4484
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.30 (130 / 100)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


2973 23.78 4.30 1.47  chr2_169297411_169302135     3351  4233 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_169297411_   3351 TGGAAACACATCTCATGCTCATGGGTGGGTAGAATAAATATTGTGAAAAT 3400
                               v i   i    i      i v  v   v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_169297411_   3401 GACCATACTGCCAAAAGCAATCTACAAATTCAGTGCAATTTCCATCAAAA 3450
                          i v     v  v   vii       i     ii     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_169297411_   3451 TACTACCATCATTCTTAACAGAACTAGAAAAGC-AATCCTAAAATTTATA 3499
                          v i v vv v  i  vi     v v  v    -i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_169297411_   3500 TGGAACCAAAAAAGAGCCTACATAGCCAAAGCAAGACTATGCAAAAGAA- 3548
                              viiv  ii  v  viv         i   v-  -  v       -
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGAAG 198

  chr2_169297411_   3549 --CAAATCTGGAGG-------CTTC---------AAACTATACTATAAGG 3580
                         --    vi      -------    ---------     -     i  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_169297411_   3581 CCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGATACATAGAC 3630
                          i i   v i   i    ii         i    ii     i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_169297411_   3631 CAATGGAACAGAACAGAGAA-CCAGAAATAAAGCCAAATACTTACAGCCA 3679
                                 i    iv    i-           v   v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_169297411_   3680 ACTTATCTTCAACAAAGGAAACAAAAACATAAAGTGGGGAAAGGACACCC 3729
                          i v  i   i    i  viv   i v   vv i         i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_169297411_   3730 TATTCAACAAATAGTGCTGGGATAATTGGGAAGCCACATGTAGGAGAATG 3779
                          v          i         i  i   iv ?       i ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_169297411_   3780 AAACTGGATCCTCATCTCTCATC---TACAAAACTCAATTCAAGATGGAT 3826
                           ii    i  ii i   v  i ---       v i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_169297411_   3827 GAAGGACTTAAATCTAAGACCTGAAACT-TAAAAATTCCAGAAGATAACA 3875
                         v ?i   i     v     v  i     -     v iii      v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_169297411_   3876 TTGGAAAAACCCTTCTAGACATTGGCTTAAGCAA--GTTTTTCA----TG 3919
                          v  ?iv  vi    vv   v    v   i    --    i i ----  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_169297411_   3920 AC--CAAGAACCTAAA-AGCAAATGCAGAAAAAACAGAGAAATGGCTGGG 3966
                           --   i i vi  i- i    ---        i   v    ---   -
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAA---AGAAAAAATAGATAAAT---TGG- 640

  chr2_169297411_   3967 ACTTAATTAAACTAAAGAACTTTTGCATGGCAAAAGGAA--GTCAGCAGA 4014
                             v  i   v v  i        iiivv    i iv --i   iv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_169297411_   4015 GTAAATAGAGCACCCACAGAGTGGGAGAAAATCTTCGCAATCTATACATC 4064
                           i  v   vv         i           v  i    vii   i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_169297411_   4065 TGACAAAGGACTAACATCCAGAATCTAAAAAGAACTCAAACAAATCAGCA 4114
                            i  i     vii         v  v         vv    v   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_169297411_   4115 AGAAAAAAAAATCAAACAATCCCATCAAAAAGTGGGTTAAGGACATTAAT 4164
                          v     i ---    i  i  v  i?    i    iv     iv v   
  L1M4_orf2#LINE/    791 ATAAAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_169297411_   4165 AGAGAATTCTCAAAAGAAGATATACAAATGGCCAACAA--ACAGGAAAAA 4212
                            v v     v                       i  --   v     i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_169297411_   4213 ATGCTCAACATCACTAATGAT 4233
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (123 / 83)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.55 (51 / 20)  


3171 25.58 1.32 1.21  chr2_169547004_169553135     1000  1906 (4226)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_169547004_   1000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATTGTGAAAAT 1049
                              ii i  i     i      i v      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_169547004_   1050 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1099
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_169547004_   1100 TACCAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTTCA 1147
                          v   iivi i  i  ii  -      -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_169547004_   1148 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 1197
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_169547004_   1198 AACAAAGCCAGAGGCATCACGCTACCTGACTTCAAACTATCCTACAAGGC 1247
                                iii    vv    i  v  ii i      viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_169547004_   1248 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATAGATATA 1297
                                 i   i    ii         ---  v  -   v v v     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGG---CATAA-GGATAGACATATA 294

  chr2_169547004_   1298 GACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATCCCGCATATCTAC 1345
                           i        i    i--    i  --        v   ii i  i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chr2_169547004_   1346 AACTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGA 1395
                         iiii vi    i  i     ivv  v   i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_169547004_   1396 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 1445
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_169547004_   1446 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 1495
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_169547004_   1496 TGGATTAAAGACTTACATGTCAGACCTAAAACCATAAAAACCCTAGAAGA 1545
                              i ?    i  v    v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_169547004_   1546 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGATTTCATG 1594
                             v    ?i- v i -   iv   v v  vv i     v i    v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_169547004_   1595 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 1644
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_169547004_   1645 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAAAG 1694
                         ii v  i   v v  i i   i  ii vv    i  v  i i  vv    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_169547004_   1695 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCCA--CCTACCATC 1742
                             v  i     i                 v     v -- v  i-   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATC 740

  chr2_169547004_   1743 TGACAAAGGGCTAATATCCAGAATCTACAACGAACTCAAACAAATTTACA 1792
                            i  i  i  vi          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_169547004_   1793 AGAAAAAAACAA-----CCACATCAAAAAGTGGGCGAAGGATATGAACAG 1837
                          v     i    -----   -  i?    i     i      v    i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_169547004_   1838 ACACTTGTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAAT 1887
                            i  v  v        i  vi viii     v  i          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_169547004_   1888 GCTCATCATCACTGGCCAT 1906
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  

3250 26.35 0.77 0.66  chr2_169547004_169553135     4734  5640 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_169547004_   4734 TGGAAGAACATTCCATGCTCCTGGGTAGGAAGAATCAATATCATGAAAAT 4783
                              ii i  i     i  v   i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_169547004_   4784 GGCCATGTTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4833
                            v  ii v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_169547004_   4834 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4881
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_169547004_   4882 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4931
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_169547004_   4932 AACAAAGCCAGAGGCATCACGCTACCTGACTTCAAACTATCCTACAAGGC 4981
                                iii    vv    i  v  ii i      viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_169547004_   4982 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5031
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_169547004_   5032 AATGGAACAGAAC--AGAGCCCTCAGAAATAATCCCACATATCTACAACC 5079
                                i    i--    i  --        v    i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_169547004_   5080 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5129
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_169547004_   5130 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5179
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_169547004_   5180 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5229
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_169547004_   5230 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5279
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_169547004_   5280 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGATTTCATGTCTA 5328
                         v    ?i- v i -   iv   v v  vv i     v i    v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_169547004_   5329 AAACACCAAAAGCA-ATGTCAACAAAAGCCGAAATTGACAAATGGGATCT 5377
                         vi            - v -         vvi    v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_169547004_   5378 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGA 5427
                         v  i   v v  i i   i  ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_169547004_   5428 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5477
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_169547004_   5478 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5527
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_169547004_   5528 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 5577
                            i     i     v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_169547004_   5578 TGTCAAAAGAAGACATTTATGCAGCCAA-AATCACATGAAAAAATGCTCA 5626
                          v  v        i  vi viii     -  v          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_169547004_   5627 TCATCACTGGCCAT 5640
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2547 26.66 4.81 1.03  chr2_169632053_169636678.rev     3261  4134 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_169632053_   3261 GGAAAAACATCCCATGCTCATGGATTGGAAGAATTAATAACATTAAAATG 3310
                              i i        i               v      vii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_169632053_   3311 ACCATACTTCCCAAACCAATCCACTGATTCAATGCAATCACTATCAAATT 3360
                         i v     i      iii   i  v       i      v        v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_169632053_   3361 ACCAA-TGTCATTTTTCACAGAATTAGAAAAAAACAATTTTAAAATTCAC 3409
                         v   i-  i -     ii     v v  v  iv-ii  ii         i
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_169632053_   3410 ATGGAACTAAAAAAAAGAGCCCTAATAGCCAAAGCAATCCTAAGCAAAAG 3459
                               v iv  ii--  v  vv          i     i i iv  i i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_169632053_   3460 GAACAAAGCTAAAGGTATCATATT-----ATTT---GGCTGACTA---AA 3498
                                 i ii   vv   i i -----    ---ii  v    --- i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_169632053_   3499 TTATTCTA-CCAAG--------------GTATACAAATAGACACATAGAT 3533
                         i  ivv  -i    -------------- i   vii       i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_169632053_   3534 CAATGGAACAGAATAGAGAACCCAGAAACAAAGCCACATACCTAAAACCA 3583
                                 i     v    ii       i   v   i i ii  viii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_169632053_   3584 AGTTATCTTTGAAAAAGTCAACAAAAATATTCATTGAAGAAGTGACACCC 3633
                          v v  i  i  v  i viiv   i vi     v  ii   ivi i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_169632053_   3634 TACTCAATAAAAGGTGCTGGAAAAATTGGATAGCAGTATGCAGAAGAAAG 3683
                          vi    i   v        i v  i      ? vii     i     v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_169632053_   3684 AAATTAGACCCATACCTCTCACCACTTACAAAA-TTAACACAAGATAGAT 3732
                           i  i     v      v     iv       -     v   i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_169632053_   3733 AGAACACCTAAACATA-GACCTGAAACTATAAAAATACTAGAAGAAAACC 3781
                         vi? v       ii  -  v  i           v vi           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_169632053_   3782 TAGGAAAAACTCTTCTGGACATTTGCTTAGGCAAAGAATTTAATTCAAA- 3830
                             ?iv  v     vv   v  v v        v i-   --i i i -
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTT--CTTAGAT 594

  chr2_169632053_   3831 --GTCCTCAAAAGCAAACACAACCAAAACAAAAATAGACAAATGGGAATA 3878
                         -- v vi        v vi    v   iv         i    v   v v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_169632053_   3879 AATTAAGCTAAAAAGCTTTTGCACAGCAAAAGAAGCAGTCAACAGAGTAA 3928
                         v  i  iv v    i      ii vv    i  vi vi    v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_169632053_   3929 ACAAACAACTTACACAATTGGAGAAAATATTTACAAA-CATTACATCCAA 3977
                          v i     ii   v   v             i    -   - i   ii 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-ATATCTGA 743

  chr2_169632053_   3978 CAAAGGGCTAATATTCAGAATCTATAGGGAACTC----AACTCAAGCAAC 4023
                         i  i  i  vi   i      v    ii      ----       -i  i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA-TAAT 792

  chr2_169632053_   4024 AAC----CAAATAATTTCATTAAAAGGTAGGTGAAGGACATGAGCAGATA 4069
                           v----       iiiv   ?   ii i  ii     iv   ii   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_169632053_   4070 TTTTTCAAAAGAAGACATACAAGCAGCCAACAAACAT-TAAAAAAATGCT 4118
                            i  v        i      iii     i  i  i- i    i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_169632053_   4119 CAACATCACTAATCAT 4134
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (145 / 84)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 2.55 (51 / 20)  


2964 20.48 2.04 6.62  chr2_169670434_169672164.rev      506  1291 (440)    L1M4_orf2#LINE/L1      159   908 (0)  

  chr2_169670434_    506 CAAAAGACCTTGAATAGC-AAAA--ATCCTGAACAAGAAGAACAAAGCTG 552
                            ii    iv       -    --   i    v             i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_169670434_    553 GAGGCATCACGTTACCTGATCTCAAAATCTACTACAAAGTAATAGATCAT 602
                             vv    ii v  ii  i      ii          -----------
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG----------- 247

  chr2_169670434_    603 TATTAGATTATTTGATTACTATAGTAATAAAAACAGCATGGTACTGGCAT 652
                         ------------------   i      v  i    ii            
  L1M4_orf2#LINE/    248 ------------------CTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_169670434_    653 AGAAACAGACACATAGACCAGTGAAAAAGAATGGAGAGCCCAGAAAGAAG 702
                          iii i     i     i  i  i  v     v     i       v  i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_169670434_    703 TCCATGCATTTATAGTCCATTGATTTTCAATAAAGAGACCAACAACACAC 752
                         i    i       i   v          i i  i ivi    v v  iv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_169670434_    753 CATGAGGAAAGGGCAGTCTCTTCAATAAACGATGTTGGGGAAACTGGATA 802
                         v   i      iii     i     i   i i  i    iv         
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_169670434_    803 TCCACATGCAGAAGAATGAAATTTGATCCTTACCTCACACTATACACAAA 852
                         ?         i         i  v  i  i          i   i     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_169670434_    853 TATCAACTCAAAATGGATTAAAGTTTTAAATGTAGGATATAAAACTGAAA 902
                         v  i              i ?  vii        i  vv       iv  
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_169670434_    903 AACTACTAGAAGAAAGCATAGGGAAGAAGCTCTATGACATTGGTCTAGGC 952
                             vi         i      ?ivi  v  iii    v    vi     
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_169670434_    953 AATGATTTTTTTGACACAACCCCAAAAGGACAGGTAACAAAAGCAAAAAT 1002
                             i   i  v  i ii  v       v   i i        v      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_169670434_   1003 AGACAGATGGGATTACATCAAA-CTAAAAA-------GCTTCAAAAAGGA 1044
                            i i  v   i v       -i      -------        --   
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA--GGA 677

  chr2_169670434_   1045 AGCAATCAACAGAGTGAAGAGGCAATTTATAGAATGAGAGAAAATATTTG 1094
                         vi v     v i      i  i   iii i      i             
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_169670434_   1095 TAACCCATACATCTGATAAGGGGTTAATATCCAATACATATAAGAAACAC 1144
                         i  vi    i            ii vi      iv i      ii   v 
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_169670434_   1145 AAACAACTCAATGACAAGAAAACAA----CCTGATTAAAAAGTGGTCAAA 1190
                         vv          i i  i  i    ----  ii   ?    i   v    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_169670434_   1191 AGACCTGAATAGACATTTCTCAGAAGAAAACATACAAATAGAAACGTACA 1240
                         i  ii                vi     i i        i ---------
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG--------- 868

  chr2_169670434_   1241 AAAAGAAACATACAACAGGCATGTGAAAAGATG-TCACACATCACTAATC 1289
                         -------- ---   i i   ii          -   -      ??????
  L1M4_orf2#LINE/    869 --------C---CAATAAGCACATGAAAAGATGCTCA-ACATCAZZZZZZ 906

  chr2_169670434_   1290 AT 1291
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.57 (113 / 44)
Gap_init rate = 0.01 (11 / 750), avg. gap size = 6.18 (68 / 11)  


2513 22.28 8.03 2.33  chr2_169681585_169683329.rev      482  1253 (492)    L1M4_orf2#LINE/L1       93   908 (0)  

  chr2_169681585_    482 TATCAAAATATAAGCAAGATTTTTTGTAGATATAGAAAAGATTACCCTAA 531
                                  viv   vivv       i   v  v  v   v v i     
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr2_169681585_    532 AATGTTTATGAAAATGTAAAAAAACTGGAATAGCTAAAATAATTTTGAAA 581
                            viv    i     i  iii v ii       i    i   i      
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_169681585_    582 AAGAATAATAAAGTGAGAAGAATCAATCTACCCAATTTCAAGACATATTA 631
                              v  i     vi  i  v   vv  v           i  v  i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_169681585_    632 TATAGCTAATGCAGTCAAGGCTGTGTGGCATTGACA-GAGGACAGATATA 680
                         i v     vv i i     i v      i i  i  -i    i   i   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_169681585_    681 TAGACCAATGGAACAGAATGGAGAACTCAGAAATAGACCCACACAAATAT 730
                             i        i     v    iii        i     i   vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_169681585_    731 GTCCAATTGATTTTTGACAAAAGTGGAAAAACAATTCAGTGGGGGAAAGA 780
                          vi           i     ii   vv  i  v     i     i  ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_169681585_    781 TAAGCTTTTTATCAAATGGCTG-TGGAGCAGCTGGACATCCATAGGGCAA 829
                           iv     i v       -  -   ii  i     i ?   i v -   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGG-TGCTGGGACAACTGGATAKCCACATG-CAA 440

  chr2_169681585_    830 AAAAATGAAATT--------------------ACACAAAAATTTTCTTAA 859
                           i      i  -------------------- i         vv  i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_169681585_    860 A-TGAATCATGGACTTATATGTAACAAATAAAACTA---AACTTTTAGAA 905
                          -  i    ?i   i  v      v iv        ---    i      
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_169681585_    906 --AAATATGGAAGAGACCATTTTCATGTTCTAGGGCTGGACAGAGCATG- 952
                         --   i  i i? vi --  i   i  vi  v   i i i  ----   -
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCA----ATGG 584

  chr2_169681585_    953 -----TAGAT--GACACCAAAAGCACAATTCATAAAGGGAAAATTTGATA 995
                         -----     --                viv i   i i    v v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_169681585_    996 AATTGGACTTCAATAAAATTAAAAACTTT-GT-----AAAAGATCCTGTT 1039
                                     vi               -  -----   i  iv  i i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_169681585_   1040 AAGAGAATGAAAAGACAAGCTACTGACTGGGAGAACATATTTGCAACTTG 1089
                             i i           v i  v  v        v          v ii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_169681585_   1090 TATATCCAAAAAAGGACTAGGATCCCGAATATATAAAAAATTCTCAAAAC 1139
                               ii v  i     v v    v           i  i   i v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_169681585_   1140 TCAGTGTTAAAATAACAA-TAGCAAATTTCAGTTCAAAGATGGGAAAAAG 1188
                            i iv     vi    -  i -----i  i  ?   i     v   i 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAAC-----CCAATTWAAAAATGGGCAAAGG 829

  chr2_169681585_   1189 ACATGAGTAAGGACA-------AAAGA-----------TGGCAAATGAGC 1220
                          iv   i  --    -------     -----------    v   i   
  L1M4_orf2#LINE/    830 ATTTGAATA--GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_169681585_   1221 ACATGAAA-TATGTTAAACAACATCAATAGAGAA 1253
                                 -v   i ---        ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCT---CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (104 / 64)
Gap_init rate = 0.03 (21 / 816), avg. gap size = 3.81 (80 / 21)  


2938 27.94 1.44 0.78  chr2_169735751_169740731     3588  4489 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_169735751_   3588 TAGAAAAATATTCCATGTTCATGGATAGGAAGAATCAATATCGTAAAAAT 3637
                          i    i    i              v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_169735751_   3638 GGCCATACTGTCCGAAGTAATTTATAGATTCAATGTTGTTCCCATTAAAT 3687
                            v     vi  i  v i  i  i        i ivi i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_169735751_   3688 TACTATTGACGTTCTTTACAGAATTAGAAAAAAATACTTTAAAATTCATA 3737
                          v i vivi v  i   i     v v  v  ivvv iii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_169735751_   3738 TGGAAATAAAAAAGAGCCCGTATAGCAAAGACAATCCTAAGCCAAAAGAA 3787
                                iv  ii  v  v v     v  i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_169735751_   3788 CAAAGCTGGAAGCATCATGTTCCAGGGCTTCAAGCTATACTACAAGGCTA 3837
                              i    i vv   iii i vviii     iviv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_169735751_   3838 CAGTAAACAAAACAGTATGGCACTGGCACAAAAACAGACACATAGACCAA 3887
                               v   i     i   i       i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_169735751_   3888 CGGAACAGAATAGATATCTCAGAAATAAGACTGCACATCTACAACTGTCT 3937
                         i    i     v  v vii         iv iii    i  iiiiiivi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_169735751_   3938 GATCTTCAACCCAGA---CAAAAACAAGCAATGAGAAAAGGATTCCCTAT 3984
                            i   i  vvi i---   i v  vv     i i    i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_169735751_   3985 TTAATAAATGGTGCCAGGAAAACTGGCTAGCTATATGCAGAAAATTGAAA 4034
                          i  i         ii   v      v  ? i i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_169735751_   4035 CTGGACCCCTTCCTTACACCTTATACAAAAATTACCTCAAGAGGGATAAA 4084
                         i         v   i     v             v     i v    v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_169735751_   4085 AGACTTAAGTGTAAAACCCAAAACTATGAAAACCCTAGAAGAAAATCAAG 4134
                             i   i     i v i        i   vi i          ivv  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_169735751_   4135 GCA-ATACCATTCAGGACATGGGCACACACAAAGATTTCAT-GATGAAAA 4182
                          ?i- v i -   iv   v v  vvi vi   v i    v -   - vi 
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGA 598

  chr2_169735751_   4183 TGTCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGA-----TC 4227
                         iii        vvv          v      v  i    v   -----  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_169735751_   4228 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGCAAACA 4277
                         v   i    i -   i  ii vv    i  v       vv i  ii  v 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_169735751_   4278 AGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 4327
                         ii  i  i                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_169735751_   4328 GGTCTAATATCCAGAATCTACAAGGAACT--TA-AACTTATTTACAAGAA 4374
                           v  vi          v  i  i     --  -    i v v i  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_169735751_   4375 AACAACAAAACAACTCCATTAAAAAGTGGACAAAGGACATGAGCAGACAC 4424
                         i    ---- i   i v   ?    i   i       iv   ii     i
  L1M4_orf2#LINE/    798 GACAA----ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_169735751_   4425 TTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGGAAAAAAGCTC 4474
                              v        i  vi viii     i  i  i   i   i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_169735751_   4475 AACATCACTGATCAT 4489
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (154 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


3295 26.98 0.44 0.44  chr2_169933776_169936421     1247  2154 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_169933776_   1247 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1296
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_169933776_   1297 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1346
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_169933776_   1347 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1394
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_169933776_   1395 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1444
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_169933776_   1445 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1494
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_169933776_   1495 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1544
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_169933776_   1545 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1592
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_169933776_   1593 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1642
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_169933776_   1643 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1692
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_169933776_   1693 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1742
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_169933776_   1743 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 1792
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_169933776_   1793 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 1842
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_169933776_   1843 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 1892
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_169933776_   1893 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1942
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_169933776_   1943 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 1992
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_169933776_   1993 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2042
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_169933776_   2043 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 2092
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_169933776_   2093 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 2142
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_169933776_   2143 ATCACTGGCCAT 2154
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3219 27.31 0.55 0.55  chr2_169990491_169996252.rev     4363  5270 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_169990491_   4363 TGAAGGAACATTCTATGCTTATGGATAGGAAGAATCAATATCATGGAAAT 4412
                           i iii i  i i   i i      v      v i     ii vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_169990491_   4413 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4462
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_169990491_   4463 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4510
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_169990491_   4511 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 4560
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_169990491_   4561 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4610
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_169990491_   4611 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACACAGATATAGACC 4660
                                 i   i    ii         i iv ii i v v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_169990491_   4661 AATGGAACAGAAT--AGAGCCCTCAGAAATAATACCACACATCTACAACC 4708
                                i     --    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_169990491_   4709 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAACGGGAAAAGGATTCC 4758
                          vi    i  i     ivv  v   i v  vvv  i   i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_169990491_   4759 CTATTTAATACATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4808
                           v  i  i v      i     v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_169990491_   4809 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4858
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_169990491_   4859 TTAAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4908
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_169990491_   4909 CTAGGCA-ATACCATTCAGGACATAGACATGGGCAAGGACTTCATGTCTA 4957
                         v    ?i- v i -   iv   v v ivv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_169990491_   4958 AAACACCAAAAGCAATGGTAACAAAAGCCAAAATTGATAAATGGGATCTC 5007
                         vi            vvi i        vv     v       v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_169990491_   5008 ATTAAACTAAAGAGTTTCTGCACAGCAATAGAAACTACCATCAGAGTGAA 5057
                           i   v v  i ii  i  ii vv   vi  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_169990491_   5058 CAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5107
                         v  i     i i               v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_169990491_   5108 AAGGGCTGATATCCAGAATCTACAAAGAACTTAAACAAATGTACAAGAAA 5157
                          i  i  vi          v  i        ivv    v vv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_169990491_   5158 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5207
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_169990491_   5208 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTGAT 5257
                            v        i  vi viii     i ii          i     v v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_169990491_   5258 CATCACTGAGCAT 5270
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (150 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 236 19.51 0.00 0.00  chr2_170062043_170065852     1644  1684 (2126)    L1M4_orf2#LINE/L1        1    41 (867)  

  chr2_170062043_   1644 TGGAAAAACATTCTGTGTTCACGGATTACAAGACTTAATAT 1684
                               i i  i ii      i     iv            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT 41

Transitions / transversions = 7.00 (7 / 1)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  

3815 17.99 3.85 1.36  chr2_170062043_170065852     2124  2929 (881)    L1M4_orf2#LINE/L1       10   835 (73)  

  chr2_170062043_   2124 ATTCCAT-CTCAAAAA--GAAAGAC--AATATGGTTAAGATGACAATACT 2168
                           i    -i   vii -- i     --     v         i       
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_170062043_   2169 TCCCAAAGTAATCCTCAGATTCCATGTAAACCCTATCAAA-TGACATTT- 2216
                         i      v i   iv       v i i  v          - vv  vi -
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_170062043_   2217 TTTGTTTTGCAGAAATACAAAAGCCAATCTTAAATTTCATAT-----TGC 2261
                         ii v            vv v    ii   i    v       -----   
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_170062043_   2262 AAAGGGACCCCAAATAGCCAAAACAATCTTGGAAAAGAA---CAAAATTG 2308
                           -       vi                   i       ---    i   
  L1M4_orf2#LINE/    160 AA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_170062043_   2309 GAGGATTCACATTTCCTGATTTCAGAATTTACTACAAAGCTACAGTAATC 2358
                              i     i    ii      i  i                      
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_170062043_   2359 CAAACTGCGT----TTGGCATAAGTATAGACATACAGATCCATGGAAAAG 2404
                         v i  v i  ----i         v         i     v      v  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_170062043_   2405 CATTGGGAGTTCAGAAAGAAACCCATGCATCTATGGTCAATCAGTTTTCA 2454
                         v    i    i      v        i   i          iii     i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_170062043_   2455 ACAACGGTACCATGACCATCCAATGAAGAAAGAAAAGTCTTCTCAACATA 2504
                             v   i   v      i     ii       v      i      v 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_170062043_   2505 TGATGATGAGACAATAATATATCTATATACAAAACAATAAAGTTGGATCC 2554
                           i  v  i     iviv   ? i i  i     v   i        i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_170062043_   2555 TTACTTCACGACTTCGCACCATATATGAAAATT----TAAAATCGATCAA 2600
                         i   i    --------        ii      ----i     v     ?
  L1M4_orf2#LINE/    459 CTACCTCAC--------ACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_170062043_   2601 AGACCTAA-CATA-----TAAAACTATAAAACTCTTAGGAAAAAACAGAG 2644
                                 -ii  -----                    i i      v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_170062043_   2645 GGGCAAATCTCTATTACTTTGAATTTGGCAATGGTTTCTAAAATATGACA 2694
                          ? i      iii v  i   ii  v             v i        
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_170062043_   2695 CCAAGAGCACAGGCAACAAAAGAAAAAAATAGATAAACTGGACTTCATCA 2744
                             i      i                -        i            
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCA 649

  chr2_170062043_   2745 AAATTTTAAAACTTTTGTGTATCTAAGGGCACACTCAATAGAATGAACAG 2794
                              v-            iv  v    i   vv    v i i    v  
  L1M4_orf2#LINE/    650 AAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_170062043_   2795 TTAACCCACAGAATGGGAGAAAATATTTGTAAATCATATATGTGATAAAG 2844
                         vi                           i           v      i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_170062043_   2845 CTCTAGTATCCAGAAAATATAAAGAACTCCTACAACCTGACAACAAAAAG 2894
                         vv  v          v             i      iii i  i      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_170062043_   2895 ACAAA--ACCCAATTTAAAAGTGGACGAGAAAGCTGA 2929
                              --        ?    i   i i iii vi   
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

Transitions / transversions = 1.88 (92 / 49)
Gap_init rate = 0.02 (16 / 826), avg. gap size = 2.62 (42 / 16)  

 413 16.10 8.47 0.00  chr2_170062043_170065852     3202  3319 (491)    L1M4_orf2#LINE/L1      781   908 (0)  

  chr2_170062043_   3202 CAACTCAAAAAAAAAAAAAAAAAAAA--------AAAAA--GACAAAGAA 3241
                                 v  v     i v   v  --------     -- i     i 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_170062043_   3242 TTTGAACAGACATTTATCCAAAGAAGGTATATAAATAGCCAAAAAGTACA 3291
                               i        v          i    i    i     v   i   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_170062043_   3292 TGAAAATATACTCAATGTCGTTAGTCAT 3319
                               v  i     ii  i????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.02 (2 / 128), avg. gap size = 5.00 (10 / 2)  


3120 27.86 0.44 0.44  chr2_170080723_170087065     4944  5851 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_170080723_   4944 TGGGAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4993
                            i ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_170080723_   4994 GGCCATACTACCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5043
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_170080723_   5044 TACCAATGACTTTCTTCACAGAATTCAAAAAAACT-ACTTTGAAGTTCAT 5092
                          v   iivi i  i  ii     v ii v  i-  - iii i  i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_170080723_   5093 ATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGTCAAAAGA 5142
                               viiv  ii  v  viv  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_170080723_   5143 ACAAAGCTGGAAGCATCACACTACCTGACTTCAAA-CTAACCTACAAGTC 5191
                               i    i vv       v  ii i      -  v  -     iv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC-TACAAAGC 248

  chr2_170080723_   5192 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACACAGATATAGACC 5241
                                 i   i    ii         i iv ii i v v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_170080723_   5242 AATGGAACAGAAC--AGAGCCCTCAGAAATAATCCCACATATCTACAACC 5289
                                i    i--    i  --        v    i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_170080723_   5290 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5339
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_170080723_   5340 CTATTTCATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5389
                           v  iv i       i      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_170080723_   5390 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5439
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_170080723_   5440 TTGATGACTTAAATGTTAGACTGAAAACCATAAAAACCCTAGAAGAAAAC 5489
                          ii?v   i       v   viv     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_170080723_   5490 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5539
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_170080723_   5540 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATCTAA 5589
                         i            vvi          vv     v  i i  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_170080723_   5590 TTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAATGAAC 5639
                          i   v v  i ii  i  ii vv    i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_170080723_   5640 AGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5689
                           i     i i               v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_170080723_   5690 AGGGCTAATATCCAGAATCTACAATGAACTAAAACAAATTTACAAGAAAA 5739
                         i  i  vi          v  i  v     vvv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_170080723_   5740 AAACAAACAATCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTTC 5789
                          i     i  i  v  i? v  i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_170080723_   5790 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5839
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_170080723_   5840 ATCACTGGCCAT 5851
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (149 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2416 20.83 3.49 13.09  chr2_170124081_170128805     2937  3853 (872)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr2_170124081_   2937 TAGAGAGACATACCATGTTCAAGTACTGAAAGACTCAACATAATAAAGAT 2986
                          i  i   i  v         v v i  i      i  i  vi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_170124081_   2987 G-------TC----AATTGATCCATATGTTTAATGCA-TTCCAATCATAA 3024
                          -------  ----        i i vi  i  i   - i  v    v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_170124081_   3025 TCCCAGCAACATATTTGGCAGATATAGACAATCTGATTCTAATATTTATA 3074
                                vi v v   v     v  v     v     i    v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_170124081_   3075 TGCAAAAGCAAAGGAACTAAAATAGCCTAAATAATTTTGAAAAGGGGGAA 3124
                           v   v    i   v i i       v   i   i       i ii   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_170124081_   3125 TAAAGTTGGAAGAATCACACTACTGTATTTTAAGATGTACTACAAAGCTA 3174
                         i         i  v       v ivv    i  i iv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_170124081_   3175 CACCAGCATGGCACATGTATACATATGTAACTAACCTGCACATTGTGCAC 3224
                           ------------------------------------------------
  L1M4_orf2#LINE/    251 CA------------------------------------------------ 252

  chr2_170124081_   3225 ATGTACCCTAAAACTTAAAGTATAATAATAATAAAATTAAATTAAATTTA 3274
                         --------------------------------------------------
  L1M4_orf2#LINE/    253 -------------------------------------------------- 252

  chr2_170124081_   3275 AAAAAAACAAAGCTACAATAATCAAGAGAATGTAGTATTGGCAAAGGAAC 3324
                         -----------------i         v i   i   i     v i i i
  L1M4_orf2#LINE/    253 -----------------GTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_170124081_   3325 AGACACATAAATCAATGAAACATAAT--AGAGTCCAGAAACAAAACCATA 3372
                              i   i       i  i v   --            i   v     
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_170124081_   3373 CAT--AT-----ATTAATTTT-GACACACATGC-AAAAGCATTTCAGTGG 3413
                            --  -----   i     -    vivi   -  i v    -  i   
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGG 384

  chr2_170124081_   3414 AGAAAGGATAGTCTTTTCAACAAATAGTGTTGGAAACATTGAGTATCCAT 3463
                         i     i                  i   i   i vv i  ii  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_170124081_   3464 GTGCAAGACAATGACACTCGACTCATAACTTGCACCATATATAAAAATTA 3513
                         i     i v     vii v   i v  v  ii         i        
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_170124081_   3514 ACTCAAAATGGGTTATAAATCTAAATGTAAAACCCAAAGTGATACAATCT 3563
                                    i i ? i i          i v i   iiv   v  iii
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_170124081_   3564 TTAGAA--ATATATATAAATAGAACTTCATGACCTGGGTTTAGGCAAAAA 3611
                               -- v i   vi?i  i v    i      v  v        vii
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_170124081_   3612 GTTCTTTGATAGGACACTAAAAATGTAATCTATGAAGGAAAATATTAATA 3661
                         v     v    v     i    iiii  v v ii  i     v  vi   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_170124081_   3662 AATTGGACTTCAAACAAATTTAAAACTTTTACTCTGCAAAAGATGTTCAC 3711
                                     vvv     v         iiv  v    i  ----   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA----CAC 680

  chr2_170124081_   3712 TGTTAAGAGAATGAAAAAA-AAGCTACAAACTGGGAGAAATTATTTGTAA 3760
                          i i    i i      i -  v i   i v         v      i  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_170124081_   3761 ATCGTATGTCTGGTAAAGGACTTCTATCCAGAATTTTTTT-TAACTCTCA 3809
                            i   i    i   i      v          v v vv-v      i 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_170124081_   3810 AAATTCATTAGTAAAAAAACAAA-----CAGTTAAAAGATGGAAAAAGG 3853
                         v  i   v  i      i     -----  i  ?   i    iv     
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.56 (114 / 73)
Gap_init rate = 0.02 (15 / 829), avg. gap size = 10.13 (152 / 15)  

 221 22.43 7.48 0.00  chr2_170124081_170128805     4145  4251 (474)    L1M4_orf2#LINE/L1      794   908 (0)  

  chr2_170124081_   4145 AAAAAATAAATAA----AT-AAAAGATGGA-AAAAGATGTGTACAGATAT 4188
                             i i      ----  -?   i    i-   i   v  v i   i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_170124081_   4189 TTCACCAAAAAGGATACACAGAAAGCAAATTAGCACAGTACAACAT-CT- 4236
                            v     i i    i   i vi  v   v      vv v  v  -  -
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_170124081_   4237 AACATCTTCAGCAAT 4251
                               v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (12 / 11)
Gap_init rate = 0.04 (5 / 115), avg. gap size = 1.60 (8 / 5)  


3110 27.06 0.66 0.77  chr2_170134299_170140693     4995  5903 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_170134299_   4995 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5044
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_170134299_   5045 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5094
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_170134299_   5095 TACCTA--TGACTATCCT-CACGGAATTGGGAAAAACT-ACTTTAAAGTT 5140
                          -  i --  v  v ii -  - i     -- v  i  - iii    i  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATT 146

  chr2_170134299_   5141 CATATGCAATCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAA 5190
                               v  viiv  ii  v  viv  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_170134299_   5191 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5240
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_170134299_   5241 GCTACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAAAGATATGGA 5290
                                   iv  i    ii         i iv ii i i v    i  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_170134299_   5291 CCAATGGTACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 5338
                         i      v i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_170134299_   5339 CCATCTGATCTTTGACAAACCTGATAAAAACAAGCAATGGGGAAAGGATT 5388
                         i  vi    i  i     ivv  vi  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_170134299_   5389 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5438
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_170134299_   5439 CTGAAACTGGATCCCTTCTTTACACCTTATACAAAAATTAATTCAAGATG 5488
                         v    ii    i    v i i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_170134299_   5489 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5538
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_170134299_   5539 ACCTAGGCATTACCATTCAGGACACAGACATGGGCAAGGACTTCATGTCT 5588
                           v    ?i v viv   iv   viv ivv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_170134299_   5589 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5638
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_170134299_   5639 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGA 5688
                         v  i   v v  i i   i  ii vv    i  v    i  vv i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_170134299_   5689 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5738
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_170134299_   5739 AAAGGGCTAATATCCAGAATCTACAATGAACTAAAACAAATTTACGAGAA 5788
                           i  i  vi          v  i  v     vvv    -i i vv iv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chr2_170134299_   5789 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAAACAC 5838
                             i     i     v  i?    i            v    i i   i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_170134299_   5839 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5888
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_170134299_   5889 ATCATCACTGGCCAT 5903
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


1210 22.91 1.24 0.93  chr2_170298113_170302165.rev        2   324 (3729)    L1M4_orf2#LINE/L1      585   908 (0)  

  chr2_170298113_      2 TTTTCTGGATATGACCCCAAAACCACAGGCAACAAAAAGCAAAAATAAGA 51
                            ii i        v      v    i         - v       -  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA-GAAAAAATA-GA 632

  chr2_170298113_     52 CAAATGGGATAACATCAAACTAACAGGGTTCTGCACAGCCAAAGAAACAA 101
                         i    v   ivv       v v v iiv  i  ii vv v  i  v  v 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_170298113_    102 TCAACAGAGTGAAGATACAACCTCTGGAATGGGAGAAAATATTTGCAAAC 151
                             v i      i v      ivii                       i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_170298113_    152 CATACATCTGACAACGGGTTAATATCCAAAATATATAAGGAATGCAAACA 201
                             i      i  v  ii vi      i         i   iv vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_170298113_    202 ACTCATCAGCAAGAAAACAA----CCTGATTTAAAAATGGGAAAAGAATC 247
                              vi ii  i  i    ----  ii   ?         v    i  i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_170298113_    248 TGAAGAGATATTTCTCAAACGAAGACATACAAATGGCCAACAGGTATATG 297
                             v   i       v  v     i              i i i i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_170298113_    298 GCAAAAATGCTCAATGTCACTAAACAT 324
                         i-   i        ii   ????????
  L1M4_orf2#LINE/    883 A-AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (45 / 28)
Gap_init rate = 0.01 (4 / 324), avg. gap size = 1.75 (7 / 4)  

3168 25.03 0.87 2.49  chr2_170298113_170302165.rev     2639  3561 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_170298113_   2639 TGGAAAAACATTCCATGCTCATGGATAGGGAGAATCAATATCGTAAAAAT 2688
                               i i  i     i        v  i   v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_170298113_   2689 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCTCCATCAAGC 2738
                            v     v      v i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_170298113_   2739 TAC-AACTGACTTTCTTCACAGAATCAGAAAAAAACTGCTT-TAAATTTC 2786
                          v - i   v    i  -i     -- vvi v  i   v i-    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chr2_170298113_   2787 ATATGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGGAAAAG 2836
                                 viiv  ii  v  v v        i      i i ii  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_170298113_   2837 GAACAAAGTTGGAGGCATCATACTACCTGACTTCAAACTATACTGCAAGG 2886
                                        vv   i   v  ii i      viv    i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_170298113_   2887 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAATGGATATATAGAC 2936
                                  i   i    ii         i iv ii  i  i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_170298113_   2937 CAATGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACAACCA 2986
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_170298113_   2987 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATAGGGAAAGGAT--TC 3034
                         vi    i  i     ivv  v   i v  vvv   i       i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_170298113_   3035 CTATTTAGTAAATGGTGTTAGGA-AACTGGCTAGCCATATGCAGAAAACT 3083
                         i -  i ii        i i   -      v  ?   i     i  i v 
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_170298113_   3084 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACACAAAAATTA 3133
                            ii         v   i     v               v     ----
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA---- 492

  chr2_170298113_   3134 ACTCAAGAGATAGATTAAAGACTTAAACATAAGACCTAAAACCATAAAAA 3183
                         ---------- i   i ?    i    ii     v       i      v
  L1M4_orf2#LINE/    493 ----------TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_170298113_   3184 CCCTAGAATAAAACCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAA 3232
                         i i     v     v    ?i- v i -   iv   viv  vv i     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA 581

  chr2_170298113_   3233 AGAATTCATGACTAAAACACCAAAAACAATGGCAACAAAAGCCAAAATTG 3282
                         v iv   v iiv  vi         i  vvi          vv     v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_170298113_   3283 ACAAATGGGATTTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACT 3332
                          i    v   i  v  i   v v  i i   i  ii vv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_170298113_   3333 ATCATCAGAGTGAACAGGCAACCTATAGAATGGGAGAACATTTTTGCTAT 3382
                             vv i      v  i     i i            v  v     v v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_170298113_   3383 CTATCCATCTGACAAAGGGCTAATATCCAGAATCTATAAAGAACTTAAAC 3432
                         ii  vi      i  i  i  vi          v           ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_170298113_   3433 AAATTTACAAGAAAAAAACAAACCACCCCATCAAAAAGCGGGCAAAGGAT 3482
                           v iv i  v     i     iv    v  i?    ii           
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_170298113_   3483 ACGAACAGACACTTCTCAAAAGAAGACATTTATGTGGCCAACAA--ACAT 3530
                         vi   i     i     v        i  vi vi       i  --    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_170298113_   3531 GAAAAGAAAAAAGCTCATCATCACTGGTCAT 3561
                                v----     v     ????????
  L1M4_orf2#LINE/    882 GAAAAGAT----GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (134 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


 261 16.13 0.00 9.68  chr2_170366877_170372511.rev     3633  3694 (1941)    L1M4_orf2#LINE/L1        8    63 (845)  

  chr2_170366877_   3633 ATATTTCATGTTAATGGGCTGGGAGATTTAGTATTGTTAAGATGGTTTGA 3682
                             ii      v    ii   i   i   i              i--- 
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC---A 54

  chr2_170366877_   3683 ATATTTGTCCCC 3694
                            i ---    
  L1M4_orf2#LINE/     55 ATACT---CCCC 63

Transitions / transversions = 9.00 (9 / 1)
Gap_init rate = 0.04 (2 / 56), avg. gap size = 3.00 (6 / 2)  

3114 12.83 2.47 20.53  chr2_170366877_170372511.rev     4092  5143 (492)    L1M4_orf2#LINE/L1       47   908 (0)  

  chr2_170366877_   4092 AGATGGCAATACTTCCCAAATTGATCTACACATTCAACACAATTCCTATC 4141
                                      i                v       i    i      
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_170366877_   4142 AAAATTCTACTTGGCTTTTTTGTTGATATTGACAAGCTGATCTTAGAATT 4191
                              i i vi  v        iv  v               i  i    
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_170366877_   4192 CATATGGAAATGAAAAGGACAATAGAATAGCTAAAACAATTTTGAATCTG 4241
                                     v  i    v-i        i        i     ---i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAA---A 192

  chr2_170366877_   4242 AAGAAATATTAATAA-GTAGGAGGACTCACGCTTCATGATATTAAGACTT 4290
                              i----  i  -  v           i    vii  v i  i    
  L1M4_orf2#LINE/    193 AAGAAG----AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_170366877_   4291 ACTACAAAGCTACACTCATTGGCTGGACATGGGAATGTGCACCTATAGTC 4340
                                       ------------------------------------
  L1M4_orf2#LINE/    239 ACTACAAAGCTACA------------------------------------ 252

  chr2_170366877_   4341 CCAGCTACTCAGGTGGTTGTGGCCAGAAGGATCACTTGAGACCGGGAGTT 4390
                         --------------------------------------------------
  L1M4_orf2#LINE/    253 -------------------------------------------------- 252

  chr2_170366877_   4391 CGAGGGTGTAGTGCACAATGGTTGTGCTTATGAATAGCCACTGCACTCCA 4440
                         -------   i --------------------------------------
  L1M4_orf2#LINE/    253 -------GTAAT-------------------------------------- 257

  chr2_170366877_   4441 GCCAGGGCTACATAGAGAGACCCTGTTTCTAAAAACAATAAAAAAAACTA 4490
                         --------------------------------------------------
  L1M4_orf2#LINE/    258 -------------------------------------------------- 257

  chr2_170366877_   4491 CAGTCACCAAGAGATTGTGGTGTTGGCTTAAGGAAAGACATATAGATGAG 4540
                         -------     v v      ii    v      v            v i
  L1M4_orf2#LINE/    258 -------CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_170366877_   4541 TGTAATAGAA---ATAAT---GAAATAAACCCATACATCTATACT-AAGT 4583
                           v       --- v i ---                 i   iv -  v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_170366877_   4584 GGGTTTTGACAAGAATGTTAA-----TGCAATGGGGAAAGAGTAGAATTT 4628
                          iv   i      ii  ii  ----- v             i   vv   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_170366877_   4629 TTAACAAATGGTGCTGGGATAAGTGGATATCCATATGCAAAATAATGAAT 4678
                          i                 i  v      ?   i        v      v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_170366877_   4679 TTTGACTCCCAAATTTATAGACACCTCACACCACATACAAATATTAGTTT 4728
                           v   i  i ------------          i       v    ii i
  L1M4_orf2#LINE/    451 TTGGACCCCTA------------CCTCACACCATATACAAAAATTAACTC 488

  chr2_170366877_   4729 GAAATGAATCATATAACTAAATATAAAAGCTAGAACTATAAAACTATTAG 4778
                         i     i    ? v v      i   i     i            v    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_170366877_   4779 AAGAAAACTTATACATACATCTTTATTATCTTGGATTAGGCAACAATTTC 4828
                                 v  vi?i  v     ii v i     i        iii    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_170366877_   4829 TTAGATATGACACCAAAAGCACAATCAACCCAAGAAAAA-CAGAT---TT 4874
                                                 v    vv        -i    ---  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_170366877_   4875 GGCCTTCCTCAAAATTAAAAACTTTAGTATTAATACATCAAAGAACACTA 4924
                           v    v                 v  ii ------      i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCT------TCAAAGGACACTA 682

  chr2_170366877_   4925 TCAA-AAAGTGCAAATACA-TCCACCGAATGGGAGAAGATATTTGTAAAT 4972
                             -      v   v   -i    v           i       i    
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_170366877_   4973 TATATATATGCTAAGG-ATCTATAATCCAGA-T-TATAAAGAATTCTTAC 5019
                         i      v  v     - ii i  -      - -         i      
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTA-TCCAGAATATATAAAGAACTCTTAC 781

  chr2_170366877_   5020 AACTCAACAATAAAAAGACAG----CCCATTTTTAAAAAGGGACAAATGA 5065
                                i            i----    v  ?-     v  i    v  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGA 830

  chr2_170366877_   5066 TTTGAACTGATATTTCTCCAAACAAGATGTATAAATAGCCAATAAGCACA 5115
                               iv  i           v     i  i    i             
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_170366877_   5116 TGAAATGATGCTCAACTTCATTAGCTAT 5143
                              v          v   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (78 / 53)
Gap_init rate = 0.03 (22 / 862), avg. gap size = 11.00 (242 / 22)  


 455 26.30 18.34 2.08  chr2_170518266_170520661.rev      498   786 (1610)    L1M4_orf2#LINE/L1       75   410 (498)  

  chr2_170518266_    498 CATATTTAATGTGATGCCAGTCAACATCTTAACAGAAGTTTTCCAGAGAA 547
                           v   i  i ii  v  vi    v   ii i v vv-    iiiv    
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAA 123

  chr2_170518266_    548 CTTGACAAGCT---CCTGAAATTCAAATGAAAAC---AGGAACCAAGAAC 591
                         v          ---   i       v   i   i---   i   v    i
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chr2_170518266_    592 AGCCAAAAACCCTTTTGAAGACTAATAATAA----GGAAA--TC---CTG 632
                                 - vv i     i vv  v  i  ----   ii--  ---  v
  L1M4_orf2#LINE/    174 AGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr2_170518266_    633 CC--ATATCAAAATACATTTTAATGTT-C--TAATAAAG-TAGTATGGTA 676
                           --  v      ivi i vi  v i - --    v   -i   i     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_170518266_    677 TTGTTATAAG---AGACATAT----CAATACAATAGA-----GAACTTAG 714
                         i  vi     ---        ----    iv      -----  iiii  
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_170518266_    715 GA-------CACACAT--A-GGT---TTGGTCTGTGATAGAGGTGACATT 751
                         i -------  i    -- -   ---   i i vi  i ii    v  --
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA-- 370

  chr2_170518266_    752 ATAGA----TCAATGGAGGAAAAAAA---TGTTCAATAAGTG 786
                         --   ----       i i  i  v --- v     i  i  
  L1M4_orf2#LINE/    371 --AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

Transitions / transversions = 1.71 (48 / 28)
Gap_init rate = 0.06 (21 / 336), avg. gap size = 2.81 (59 / 21)  

 714 30.07 9.31 0.72  chr2_170518266_170520661.rev     1490  1908 (488)    L1M4_orf2#LINE/L1      454   908 (0)  

  chr2_170518266_   1490 GACCTCAATCTCATACTACATGTAAAAATAAATTCCAGATGGACAAAAGA 1539
                             i v i    i  i i  ii      v  i  v i     iv ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_170518266_   1540 CCTAAGTGTACAATGAAAAACCTTAAATCTTTCAGTAGAAAACATATAAG 1589
                              i    vi vvv     iv    v  i i  v          vi? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_170518266_   1590 CA--TTTTTTTAAACCAAGGTGAAG-AA-GATTTCTTTAACAAGATACAA 1635
                         i -- i  iv i v ivi   v i -  - i      vi i v  i  v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_170518266_   1636 ATAATACAAACTGTAGAAGAAAAACTACAT---TT----TTAAT-----T 1673
                          v ii    i vii i        v  v  ---  ----  v  ----- 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_170518266_   1674 TAAAATCGTTTA--CAACAAAATTATATATT-TCAAG---GTAAAAAGAC 1717
                              v v   i-- vv    iv--- i i -     ---  i       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGG---ACACTATCAAGAAAGTGAAAAGAC 700

  chr2_170518266_   1718 AAGACACAAACTAGAAGATGAAATT----AAGTATTTATACAACAAAGGA 1763
                           vv    i v i i   vi v   ----  vi  v   vii i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_170518266_   1764 TCAGCATCTAGAGTATGTACAGCATTCTTAAAACTCAGTAA--AACAGAA 1811
                         iiv i   i   i   i  v  v i     v      i   --  v   v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_170518266_   1812 AAACAA-----------AACAGGCAAATAATATGAACCAGCAGTTCACCA 1850
                            i  -----------  ii      vi  v    ivii  v   v   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_170518266_   1851 AGAAAGAAGCCCAAATGGCCCCAAAACATATGAAAAGATGTTCAACTTTA 1900
                          ii    viiv         vvv  i  i           i     v i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_170518266_   1901 CTAGTCAA 1908
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.30 (70 / 54)
Gap_init rate = 0.03 (13 / 455), avg. gap size = 3.23 (42 / 13)  


 284 30.16 16.73 1.75  chr2_170551294_170553150.rev      844  1357 (500)    L1M4_orf2#LINE/L1      303   893 (15)  

  chr2_170551294_    844 GAACAATAATGA-AGTCCAGAAAAAGAACATACAAATTTGTGATAAAT-G 891
                            i iv v   -          v -   vi i v    i  i v   - 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATA-AACCCATACATTTATGGTCAATTG 351

  chr2_170551294_    892 -----TGACA----TCTCAA-ATCAAT--ATAGTGGAAAGAAGA--CTT- 926
                         -----i    ---- vi   - i  v --  i -        v --   -
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTT 400

  chr2_170551294_    927 --AATAAACTACTTTAGAACAAAATTTACTAT-TATTTAAATGCAG--GA 971
                         --  i   iviivi i i    ------  iv-  ?ii v     i--  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAA------CTGGATAKCCACATGCAAAAGA 444

  chr2_170551294_    972 AGCAAATTTGATTCCTATCTTATACTATATACGAAATATATTCTGGAATA 1021
                          vv  i  v  ii    i  i i  i      i   vv  viiiii   i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_170551294_   1022 CATTAAAAATC-AAATGTAAGAA--------ATGGAGCC--TGGAAGATA 1060
                         v  i ? i i -          i--------  ii i i-- i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_170551294_   1061 AT-TAACTATTTTCCTACATTATCTCAGAATATAGAAAG---CCTAAGTT 1106
                          i-  iv?i vvvi  v i v i  ii iv  viv  v ---i  v  v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_170551294_   1107 AAGAC-TTAAAACCAAAAGCCACAAAAGAAAAAA------AACTG-ACT- 1147
                          v   -ii    v  v    v             ------  i  -   -
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_170551294_   1148 -ATGTAAATCAAAAGCTT-----CTACACAG---------AAGACAGTAA 1182
                         -  vv    i    i   -----  v  v  ---------    v   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_170551294_   1183 -----CAAACT--------GGAAAAAATATTTACAATTTATAAATGAGAT 1219
                         -----   v i--------   i         i   v i   v  vv   
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_170551294_   1220 AAAAGATTAATAGCTATGAT-TACAAA---CTCTCAAAAATGGATAAGAA 1265
                           ii  i vi  v i vi  -  i   ---    i v  v vi    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_170551294_   1266 AAATA-AAGGAATTCAACAGAAAAATCAAGCAAGG--TC---ATGAACAA 1309
                            v -  iv  ii   iv?      -ii    i -- i---  ii   v
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAAT-GGGCAAAGGATTTGAATAGACAT 843

  chr2_170551294_   1310 TTCACAAAACAAG-TAC-CAAACAGCCAATAAACAAATGGAAAGATGCTC 1357
                            v v   v   -  i-    ii        i  v   i          
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.44 (89 / 62)
Gap_init rate = 0.06 (34 / 591), avg. gap size = 2.79 (95 / 34)  


 207 22.73 6.82 1.14  chr2_170716446_170718772.rev       72   159 (2168)    L1M4_orf2#LINE/L1      816   908 (0)  

  chr2_170716446_     72 AAAATGGACAGAGGTCCAGAATATATCATTCA--CAAAGAATGTATACAA 119
                                i  i   viiv     v -    iv--       vi       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGA-CATTTCTCCAAAGAAGATATACAA 864

  chr2_170716446_    120 ATAGCTAATAA--ATATAAAAA--TACTTAACTTTGCTAGAAAT 159
                           i  i     -- i  i    -- i  i   v ii????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.04 (4 / 93), avg. gap size = 1.75 (7 / 4)  

3573 22.37 2.80 1.45  chr2_170716446_170718772.rev      949  1842 (485)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_170716446_    949 GAGAGATAGTCCATGTTCATGAGTAGGAAGACTCAATATTGTCAAGATGT 998
                           i     vi           ii v        i        i      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_170716446_    999 CAGTTCTTTGCTACTTGACCTAGAGATTCAATGCAATCTCAATCAAAATC 1048
                           i v  iiv v v    i   v        i      i v         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_170716446_   1049 CCAGCAAGTTATTTTGTAGATGTTGACAAACTGATTTTAAAATTTATATA 1098
                              vivi v     i   vi       i     ii       i    i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_170716446_   1099 GAGAGGCAAAACAGCTGGAATAGCTAACACAAAATCGAA---GAAGAACA 1145
                           i v    iiv v ii       i  v    vv i   ---        
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_170716446_   1146 AAATTAGATGACTGACACTACCTGACTTCAAGACTTATCATAAAGCTACA 1195
                           i  i  v    v     v  ii i     i     ii i         
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_170716446_   1196 GTAATCAAGACAATATGGTACTAGCAAAAAAGCACACAAATAAGATCAAT 1245
                                     i i       i   v  iiii v   v   -       
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA-GATCAAT 301

  chr2_170716446_   1246 GGAACAGAACAGAGAGCCCAGAAATAGATTCACATAATTATAGTCAACTG 1295
                             i    iv     i         i ii  i i v    i     i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_170716446_   1296 ACTTT-AACAAAGGAGTAAAGGCAATACAGTGGAAAAAACACAGTCTTTT 1344
                          i   -i    i  v iv   i v  v  i   ii   iv i        
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_170716446_   1345 CAACAAATGGTGCTAGAACAACTGGACATTCACATGCACAAAAATGAATT 1394
                                       i i         i ?i        v  i      v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_170716446_   1395 TAGACAAAGACCT-ATGCCCTTCACAAAAATTAACTAAAAATGGATTACA 1443
                          i   vvvv    - ii  v vi             v         i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_170716446_   1444 GACCTAAATGTAAAACACAAAACAATAAAATTCTTA----------TAGG 1483
                                      i vvi     v      i     ----------    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_170716446_   1484 AGAAAACCTAGATAACCTTGGGTATGGCAATGACTTTTTAGATATAACAC 1533
                         ? v   i  vvi i         vv       ii  i        i    
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_170716446_   1534 CAAAAGCATAATTCATGAAATAAATAACTGATAAGCTGAACTTCATTAAA 1583
                                 i  viv ii   v   v  iv     ii  i       i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_170716446_   1584 ATTAAAATCTTCTATTTGGCAAAAGACAATGTCAAGACAATGAGAAGACA 1633
                                v   i i vivv    i    v i      v i   i      
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_170716446_   1634 AGCCACAGTCCTGGAGAAAACATTTGCAAAAGACACATCTGATAAAGGAC 1683
                          v      vviv        i         vv i i         i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_170716446_   1684 TGATATGTAAAATACTCGTATAAATATAAAGAACTCTTAAAACT-AATAG 1732
                          vi   vi i    ----------               v    -    i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATA----------TATAAAGAACTCTTACAACTCAATAA 791

  chr2_170716446_   1733 GAAAAA-------AACCCAATTAAAAAATGGTACCACGGCATT--AACAG 1773
                         v     -------         ?        -i v v  -   --  i  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGG-GCAAAGG-ATTTGAATAG 839

  chr2_170716446_   1774 ATACCTCACCAAAGAAGATATACAGATGCTTAATAAGCATATGAAAAGAT 1823
                          i ii  v                i   vii        i          
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_170716446_   1824 GCTCCAGACCGTATGTCAT 1842
                             v v i i????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (120 / 76)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 3.45 (38 / 11)  


3222 25.28 1.55 0.89  chr2_170807127_170813839     5320  6221 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_170807127_   5320 TGGAAGAACATTCCATGCTCATGGATAGGAAGA----ATATCGTGAAAAT 5365
                              ii i  i     i        v      ----    i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_170807127_   5366 GGCCATACTGCCCAAAGTAATTTATAGTTTCAATGGTATCTCCATCAAGC 5415
                            v     v      v i  i  i  v     i vv   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_170807127_   5416 TACTATTGACTTTCTTCACAGAA--TGGAAAAAAACT-ACTTTAAACTTC 5462
                          v i vivi i  i  ii     --  --- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_170807127_   5463 ATGTGGAACCAAAGAAAGGG--CCTGTATAGCTAAGACAATCCTAAGCAA 5510
                           i     --- v v     --  v v     i  i      i i iv  
  L1M4_orf2#LINE/    148 ATATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_170807127_   5511 AAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACA 5560
                         i          i      vv    i  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_170807127_   5561 AGGCTACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 5610
                          i          iv  i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_170807127_   5611 GACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAA 5660
                           i        i    iv   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_170807127_   5661 TCACTTGATCTTTGACAAATCCGACAAAAACAAGAAATGGGGAAAGGATT 5710
                            v     i  i     ivvi v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_170807127_   5711 CACTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAA 5760
                         vv  v  i  i              v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_170807127_   5761 CTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATG 5810
                         v    ii         v   i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_170807127_   5811 GATTAAAGACTTAAACATAAGACCTAAAACCATAAAAATCCTAGAAGAAA 5860
                            i ?    i    ii     v       i      v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_170807127_   5861 TCCTAGGC--AATTCCATTCAGGACATAGGCATGGGAAAAGACTTCATGT 5908
                         v v    ?--  v  --   iv   v v  vv i  v  v ii   v iv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_170807127_   5909 CTAAAACTCCAGAAGCAATGACAACAAAAGCCAAAATTGACAAAAGGGAT 5958
                         v  vi  v   i     vvii         vv     v  i   vv   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_170807127_   5959 CTAATTAAACT--AGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 6006
                         i v  i   v -- i i   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_170807127_   6007 GAATAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTAAGCATCTG 6056
                            v  i     i                 v       vii vii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_170807127_   6057 ACAAAGGGCTAATATCCAGAATCTACAAAGAATTAA-ACAAATTTACAAG 6105
                          i  i  i  vi          v  i      i vv-    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_170807127_   6106 AAAAAAACAAACGACCCCATTAAAAAGTGGGCAAAGGATATGAACAGACA 6155
                              i     ii    v   ?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_170807127_   6156 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAGCACATGAAAAAAAGCT 6205
                         i     v        i  vi viii     v             i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_170807127_   6206 CATCATCACTCATCAT 6221
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (126 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.20 (22 / 10)  


3021 24.62 5.69 0.35  chr2_170866456_170870995.rev     3188  4048 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_170866456_   3188 GGAAAGATATTCTATGTTCATAGTTTGAAAGAAGCAATATTGTTAAAACG 3237
                                   i i        i v   i    vvi           i i 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_170866456_   3238 TCCATACTACCCAAAGCAATCTACAGATTCAATGCATTCCCTATCAAAAT 3287
                         v v     v      vii              i   v             
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_170866456_   3288 ACCAA-TGTCATTCCTCACATAAATAGAAAAAAC-ATCATAAAATGTATA 3335
                         v   i-  i -  ii ii  v    v  v  ivi-   v      vi   
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_170866456_   3336 TGGAGCCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAGCAAA 3385
                             ivii   ii                 i v   i   iv  iivi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_170866456_   3386 CAAAACTAGAAGAATCACTTTACCTAACTTCAAATTATACTACAGAGCTA 3435
                             ii i  i  v    vi v  i  i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_170866456_   3436 TAGTAACCAAAACAGCATGGCACTGGCATAAAAACAGTTATATAGACCAA 3485
                         i     i   i    ii   i          ii i  vi       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_170866456_   3486 TAGGACAGAATAGAGAACACAGAAACAAATCAATGCATTCACAGTGAACT 3535
                          i i i     v    iiv      i   i v  i    i ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_170866456_   3536 CTTATTTGACAAAGCTGCCACAAACATACATTGAGGAAAGGACAGGCTCC 3585
                         vv v  i     i v     vi v   v  v  i      i i  v  ii
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_170866456_   3586 TCAATAAATGGTGCTGGGAAAATTGGTTATCCATATGCAAATGAATGAAA 3635
                             i              v  i   v  ?   i       v       i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_170866456_   3636 T--------------------------AAAAT---CT--AAATGGATTAA 3654
                          --------------------------     ---  --        i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_170866456_   3655 AGACTTAAGTCTAAGACCTCAAACTATGAAACTACTCAAAGAAAACAATG 3704
                             i   i v     v  v       i     vi vi         vv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_170866456_   3705 GAGAAACTCTCCAGGACGTTGGTCTGGGCAATGATTTCTT-GA-GTGATA 3752
                          ? v  v   i iv   v    vi i       i      -  -i   i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_170866456_   3753 CCCTACAGGCACAGGCAGCCACAGCAAACATGGACAAATGGGATTACATC 3802
                           -- v i     i   i v v  v   v  i  i    v   i v    
  L1M4_orf2#LINE/    601 CC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_170866456_   3803 AAGTTTAAAA-CTTCTGAACAGCAAAGGAAACAATAAACAAAGTGAGGAG 3851
                           iv      -   i  vi vv       v  v  v  v       ii  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_170866456_   3852 ACAACCCACAGAATGAGAGAAAATATTTGCAAACTATCCATCTGACAAGT 3901
                                        i                 ii  vi      i   v
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_170866456_   3902 TATTAATAATGAGAATATATAAGGAGATCAAACAACTCTATAAGAAAAAT 3951
                         v i vi  viv           i  iv  vv       v    v     v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_170866456_   3952 -CTAATAATCTGATTTTAAAATGAACAAATGACCTAAACAGATATTTCTC 4000
                         - v     i ii   ?v      ii    v  ii i  i   i       
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_170866456_   4001 -AAA-----------AATGGCAAATAGGTTTATGAAAAGGTGCTCAAAAT 4038
                         -   -----------      v    i ivi        i       v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_170866456_   4039 CAATAATCAG 4048
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (122 / 86)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 4.00 (52 / 13)  


2491 25.76 3.71 4.59  chr2_170937602_170942500     3492  4407 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_170937602_   3492 TGGAAAAACATTCCATGCTCATGGACTGGAAAAATCAGTGTTGTTAAAAA 3541
                               i i  i     i       i     i v i i i       i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_170937602_   3542 GGCCATTCTGTCCCTTAGCAATCTATAGATTCAACACTATTCCTATGAAA 3591
                            v  v  -i   vv vii     i         i v  i     v   
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_170937602_   3592 CTACC-GATGTCATTTTTCATAGAATTATAAAAAACT-ATTCTAACATTT 3639
                         v v  - v  i -     iii    v - i v  i  -  i    v   i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTC 147

  chr2_170937602_   3640 ATATGGAACAAAAAAAGAGCCCA-AATAGCTGAAGCAATCCTAAGCAAAA 3688
                                 - viv  i ii    -      ii  i     i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_170937602_   3689 AGAACACAGCCAGAGGCATCACGTCACTCAACTTCAAACTATACTGCAAG 3738
                               v  iii    vv    iiiv i   i      viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_170937602_   3739 GTTACAGTAGCCAAAA-AGCATGGTACTGGTATAAAAACAGTCACATACA 3787
                          i       ii   i -  ii         i    ii i  v  i   v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_170937602_   3788 CCAATGGAACAGAATAGATTACCCAGAAATAAAGCCAC-----TATAACC 3832
                         i        i     v  vvii           v   i-----   iii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_170937602_   3833 ATCTAATCTTCAACAAAG---TCAACACAAATAAGCAATGGGGAAAGGAC 3879
                          vi i  i   i    i ---i   v  v v ---            i i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAAGAAT 393

  chr2_170937602_   3880 TCCCTTTTCAATAAATCGTGCTTGGATAACTGGCTATCCTTTTGCAGAAG 3929
                         vvi        i    v     v   i      v  ?  viv    i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_170937602_   3930 AATGAAGCTAGACTCCTACCTATTACCATATACAAAAATTAACTCAGGAT 3979
                                i i   i       vvi                      ii  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_170937602_   3980 GGATTAAAAACTTAG------GACCTAAAACTATAAAAATCC-AACTGGA 4022
                             i ? i  i  i------  v              v  i- ivv i 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_170937602_   4023 AGCCTAGG---AAATGCTATTATGGACATTGGCCTTGGCAAAGAATT--- 4066
                          i v    ---    -  - ii  -  v    vi v     v iv  ---
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CT-TCGTG-ACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_170937602_   4067 ---TATGACAAAGTCCTCAAAAGTAGTTGCAATGAAAACACAAATAGACA 4113
                         ---       ------i      i vvv    ii   iv v       i 
  L1M4_orf2#LINE/    591 AGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_170937602_   4114 AGTGGGACATAATTAAACACAAATTGATAAGTGGGACACATTAAGCTTTT 4163
                          i v    v v  i   -----   i ---------------  i     
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAA-----ATTAA---------------AAACTTTT 664

  chr2_170937602_   4164 GCATAGCAAAATAAAATATCAATAAA-TG----GATAACTTACAGAATGG 4208
                          iiivv    iv v v      v   -  ----  i   ii         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_170937602_   4209 GAGAATATATTCACCAACTATGCATCC-ACAAAGGTCAAATATCCAGAAT 4257
                              v     ii v  ii  ii   i- i  i  v vvi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_170937602_   4258 GTGTAAGGAACTTAAATAATCTAACAAGCAAAAAACATATAACCCCCTTA 4307
                         i i   i     ivv i  iii  i  vv    i   v       vv  ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_170937602_   4308 AAAAGTGGGCAAAGGACATGAAGAGATAGATACATCTCAGAAGAAGACAC 4357
                             i           iv    ----    i iv    vi       i i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAA----TAGACATTTCTCCAAAGAAGATAT 860

  chr2_170937602_   4358 ACAAGCAGCCAACAAACATGAAAAAAAAAAAGCTCAACACCACTAATCAT 4407
                             iii     i  i  i-- vi    i v        i  ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCAC--ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (149 / 84)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.92 (76 / 26)  


3415 24.69 1.67 0.67  chr2_170969000_170973229.rev     2840  3738 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_170969000_   2840 TGGAAAGATACTCCCTGCTCATGGATTGGAATAATTAATATTGTCAAAAT 2889
                                   ii  v  i             v v          i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_170969000_   2890 GACAACACTACTCAAAGCAATTTACAGATTCAATGAAGTCCCTATTAGAA 2939
                          i   i   v i    vii  i           i v i       i i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_170969000_   2940 TACCAATGACATTCTTCACAGAAATAGAAAAAAAAAAAACCTAAAATTTA 2989
                          v   iivi v  i  ii       v  v  --ivvi v         i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr2_170969000_   2990 TGTGAAACCACAAAAGACCCCAAAAAGACAAATCAGTCCTGAGCAAAAAG 3039
                          i  i  vii   ii     vi  v  v    v  i  i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_170969000_   3040 AGCGAAGCTGGAGGCACCACACTCTCTGACTTCAAAATTTACTACAAATC 3089
                          i i   i      vvi      ii ii i       i          v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_170969000_   3090 TATAGCAACCAAAACAGTACGGTACTGGCATAAAAATGGACACATAGACA 3139
                           i  i  i   i     ii             ii  i    i     iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_170969000_   3140 AATGGAACAGAATAGAGAACCCAAATATAAATCAATGTATTTACAATCAG 3189
                                i     v    ii   i v     i v  ii     iii   i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_170969000_   3190 CTCATCTTTGACAAAGGTACCAAGAACATACAATGGGGAAAGGACGGTCT 3239
                         i v  i  i     i   i      v   v            i ii    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_170969000_   3240 TTTCAA---ATGGTGCAGGGAAAACAGGATAACTATATGTAGAAGAATGA 3286
                               ---       v    v   v     ? i i   i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_170969000_   3287 AACTAGACCCCAGTCTCTCTCCATACACAAAAGTCAAATCAAAATGGATT 3336
                          ii i      vii   v v     i      i i  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_170969000_   3337 GAATAATTAAATCTGAGACTTGAAACAATGAAACTACTAGAAGAAAACAT 3386
                         i? v vi     v i   vi i    v  i     vi             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_170969000_   3387 TGGGA-AAATTGCTCTAGGACATTAATCTGGGCAAAGTTTTTTTTTATGT 3435
                         v  ?i-    --  iiiv   v  iivi i     -- vv   i   vi 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAA--TGGTTTCTTAGAT 594

  chr2_170969000_   3436 AAGACATCATAAGCACAGGCAACCAAAGCAAAAATAAACAAATGGGATTA 3485
                          v    i  v       i     v    v       i i    v   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_170969000_   3486 TATCAAGCTAAAAATCTTCTGCAAATCAAAGGA-----------AATTGA 3524
                         i     iv v    v   i  iivv        -----------  v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_170969000_   3525 AGAAACAACCCACATAATAGGAGAAAATATTTGTAAACTATTCATCTGAA 3574
                          i i          v   i              i   ii  vi      v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_170969000_   3575 AAAGAATTAATAACCAGAATATATAAGGAGCTCAAACAAATCAATAGCAA 3624
                           i i i vi  v             i  i   vv    v      ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_170969000_   3625 AAAACCAAATACTACAATTTAAAAATGGAGAAAACATATGAAGAGACACT 3674
                            iv      viv     ?        iv   iv  v    v     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_170969000_   3675 TCTCAAAATAAGACATACAAATGGCCAAGAAGCATATGAAAACATGCTCA 3724
                             v   v    i              v     i       v       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_170969000_   3725 ACATCAGTAATCAA 3738
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (137 / 81)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 3.50 (21 / 6)  


3501 16.32 3.66 0.84  chr2_170992887_170994583.rev      501  1211 (486)    L1M4_orf2#LINE/L1      178   908 (0)  

  chr2_170992887_    501 AAAGCAATATTGAAAAATAAGAA--AAG----AGCACTCACACTTTCTTA 544
                            i    v        v     --   ----  v          i iv 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_170992887_    545 TTTCAACACCTACTACAAAGCAACAGCAATCAAAGTAGTGTGATTACCGG 594
                               v  i           v    i      iii      i -  i  
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT-ACTGG 276

  chr2_170992887_    595 CATAAGAAGCGACGTACAGATCAATGGGATAGAATGGAGGGTCCAGAAAT 644
                               i vv   i  i          i       v   i          
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_170992887_    645 AAACCCATATATTTG------ATTGATTTTCGACAATGTTGCCAAGACCA 688
                                  i    i------               v v           
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_170992887_    689 TTCAATGGAGAAAGAATAGTCTCTTTAACAAACGGTGCCGGGAAAACTGC 738
                                 i             i  i      i     i    v     v
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_170992887_    739 ATATACAGACACAAAAGA-CGAAGTTGGACCCACACATTACAACAAATGT 787
                            ?v  v ii       -i            vi  v i   v  v  ii
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_170992887_    788 AAAA-TTAACTCAAAATGGATCAACAACCTAAATATAAGAAATAAAACCA 836
                             -                  ?vi        i     iv      i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_170992887_    837 TAAAACTCTTAGAAGAACGCATAGAGGTAAATCTTCATGACCTTGGACTT 886
                                          vi     i?          i         ii v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_170992887_    887 GGCAATGGATTCTTAGGTATGACACACCAAAAGCACAAGCAACAAAAGAA 936
                                 v       i        --                       
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACAC--CAAAAGCACAAGCAACAAAAGAA 624

  chr2_170992887_    937 AAAA-----AAACTGGATGTCATCACAATTTAAAGCTTTTATGTTTCAAA 981
                             -----   i    iv      v    v   i     i  i      
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_170992887_    982 GGACATCACCAAGAAAGTAAAAAGACAACCCACAAAACAGGAAAAAATAT 1031
                              ii i         i               i  ii   i       
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_170992887_   1032 TTGTAAATCATATATCTGATAAGGATCTAGTATCCAGAATATATTAGAAA 1081
                            i                    iv  v               --i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT--AAAG 772

  chr2_170992887_   1082 AAATCTTAAAACTCAGCAACA------CAAACAGTTAAATTTTTAAGTGG 1125
                           v     v      ii  i ------    i iiiv    ?vv  i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_170992887_   1126 CCAAAAAACATGAATAGACATT-CTTCAAAGTAGGTATACAAATAGCCAA 1174
                         v    ii iv            -  i     v  i         i     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_170992887_   1175 GAAGCACATGAAAACATGTTAAAACACCATTAGTCAT 1211
                         v             v   i v  -  i  ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (72 / 40)
Gap_init rate = 0.02 (12 / 731), avg. gap size = 2.67 (32 / 12)  


1527 22.12 18.51 0.68  chr2_171120508_171123104.rev      667  1109 (1488)    L1M4_orf2#LINE/L1        7   528 (380)  

  chr2_171120508_    667 GACATCAC-TGTTCATGGGTTGGAAGACTTAACATTGTTAAAATGTTCAT 715
                           i   v -         i             i        i   viv  
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_171120508_    716 ACTATCCCAAGCATTCTACAGATTCAGTGTAATCCCTATTAAG-TCCCAA 764
                            vi  v  viiv            ii i         i  i-     i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_171120508_    765 TGGCATCTTTTGCAGATA--GAAAAAAT-ATCCTAAAATTCATATAGAAC 811
                         iv  v i         v --  v  iv -                i   v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_171120508_    812 CACAAAGGACCCAGAATAGCCAAAACAACAGTGAGAAA-AAGAATAAAGC 860
                         ii   i                      ivv   i   -     i    i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_171120508_    861 TGGAGGACTCACATTTCCTGAATTCAAAAC-------------------- 890
                                      i    ii v        --------------------
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_171120508_    891 -------------------------------------------------- 890
                         --------------------------------------------------
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_171120508_    891 AGAGT-----GCCCAGAAATAAACACACAACAGATGCATGATCAAATGAT 935
                            i ----- i            v  i -  -- vi   i    v    
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATA-CA--TTTATGGTCAATTGAT 353

  chr2_171120508_    936 CTTTGATAAAATCACCAAGAGTATACAATGGGGTAA-AATAATCTCTTCA 984
                         i  i  i  iivii      vi  v        v  -    i   i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_171120508_    985 ACAAACAGTGTTAGGAAAAGTGAATATCCACATACAAAAGAATAAAATTT 1034
                              ii   i i   v  v  i   ?      i         i  i  v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_171120508_   1035 AACTGTTACCTTATACCATACACAAAAATCATATCAAAATGGCTTGAAGA 1084
                         i  ivi     i i      i        i vv         v ii?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_171120508_   1085 TTAAAATGCAAGAACTGAAACTATA 1109
                         iiv     i    i  i        
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATA 528

Transitions / transversions = 2.10 (65 / 31)
Gap_init rate = 0.02 (10 / 522), avg. gap size = 8.50 (85 / 10)  

1012 24.23 1.37 0.68  chr2_171120508_171123104.rev     1395  1687 (910)    L1M4_orf2#LINE/L1      513   807 (101)  

  chr2_171120508_   1395 AAGAACTGAAACTATAAAACTGCTAGAAGAAAACATAGGAGAAAAGCTTC 1444
                             i  i             vi                ? v   v    
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_171120508_   1445 ATAACATTAGTCTTGGCAACAATTTTTTTGGATATGAAACCAAAA-CATG 1493
                         i i  v  i vi v     iii   i  -i       v       -  ii
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCACA 611

  chr2_171120508_   1494 GGCTATAAAAGCAAATATAGACAA-TGGGACTACAT-AAAACTAGAA-CT 1540
                         i  v i     v   v     i  - v     v   -    i  i  -  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_171120508_   1541 TCTACTCAACCAAGGAAACAATCAACGAATTGTAGAGATAAGCTATGGAA 1590
                          i iiv vv v     v  v     vi  v  v i   i  v i ii   
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_171120508_   1591 TAGGAGAAACTTTTTTCAAACTATATAGCTAATAAAGGATTAATGTGTAA 1640
                          i       v v   v    ii     v  i    i   i vi i vi i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_171120508_   1641 AATATATAAGGAACTCCTACAACTCAATAGTAAAAAAGCCAAATAAC 1687
                                  i      i            i      - v        
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAA-GACAAATAAC 807

Transitions / transversions = 1.41 (41 / 29)
Gap_init rate = 0.02 (6 / 295), avg. gap size = 1.00 (6 / 6)  

 363 20.56 8.41 0.00  chr2_171120508_171123104.rev     1999  2105 (492)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr2_171120508_   1999 AAAAAAAAAAAAAAC--AATTTAAATATGGAC-------TTGACTACACA 2039
                              i v   v   --    ?   v    i -------    v  v   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_171120508_   2040 TATCGCCAAAGAAGGCATACAAATGGCTAACCGGTATATGAAGAGATACT 2089
                          v  v         ii           i  ivi i i     i    i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_171120508_   2090 CAGTATCACTAAACAT 2105
                           ii    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 4.50 (9 / 2)  


 281 11.59 7.25 1.45  chr2_171152343_171154601.rev      500   568 (1690)    L1M4_orf2#LINE/L1      281   353 (555)  

  chr2_171152343_    500 AGAAAAGATATAGAGA--AA-AGAATAGAA--GAGAGTCCAGAAATAAAC 544
                           i v   i   v   --  -i        --                  
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr2_171152343_    545 CCTTAAATTTATGGTCAAGTTGGT 568
                           v  v            -   i 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAA-TTGAT 353

Transitions / transversions = 1.00 (4 / 4)
Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.50 (6 / 4)  

1846 15.60 3.06 1.39  chr2_171152343_171154601.rev      876  1234 (1024)    L1M4_orf2#LINE/L1      342   706 (202)  

  chr2_171152343_    876 TGGTCAAGTGATTTTCAACAAGAAT-CCAAGGACAATTCAATGGGAGGAA 924
                                v        i     ii -     -  v          --   
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAG-ACCATTCAATGGG--GAA 388

  chr2_171152343_    925 ATAACAGTATTTTCAACAAAATGGTGTTGAAACTGCTGGATATCCGCATA 974
                          v  i   v           -     i  ii  vi       ?  i   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_171152343_    975 CAAAAGAATGATGTTAGACTTCTACCTTACACCATACA-AAAAATTAAAT 1023
                                    v   i   ii      i        i -         v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_171152343_   1024 CCAAATGGACCATAGATCTAAAATATAAGAGGTAAAACTACAAAACTCCC 1073
                          v       i  ?   i     - i      v        i       ii
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_171152343_   1074 AGAATAATG-ATAGGAGTAAATCTTTGTCACATTGGATTAGATGATAGCT 1122
                             v  vi-     ?         i  v  v    i    iii  i i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_171152343_   1123 TCTTAGGTAGAATACCAAAAGTACGAGCAACAAAAGAAAACATACATAAA 1172
                               i  vi i        i  i               v   v     
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_171152343_   1173 TTGAACTTCATCAAAATTAAAAAATTTTGTGCTTCAAAGGACACCATCAA 1222
                            i                   v                    i     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_171152343_   1223 GAA--------GACAACCCA 1234
                            --------         
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCA 706

Transitions / transversions = 2.12 (36 / 17)
Gap_init rate = 0.02 (8 / 365), avg. gap size = 2.00 (16 / 8)  

 701 13.98 22.04 0.00  chr2_171152343_171154601.rev     1581  1766 (492)    L1M4_orf2#LINE/L1      682   908 (0)  

  chr2_171152343_   1581 ATTAAAAAA---AAAAGAGAG-----AGAGAGAGAGAAAATATTTGCAAA 1622
                           i  i   ---      v i-----   iv i                 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_171152343_   1623 TTATCTATGTGATAAGGGACTAATATTTGGAATACATAAA---------C 1663
                          i  v   v            vi   iii     i     --------- 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_171152343_   1664 A--TCAACAATATAAAG---------------------TGGGCAAAGGAT 1690
                          --    i    v    ---------------------            
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_171152343_   1691 TTGAATAAACATTTCTCCAAAGAAGGTATACACATAACCAAGAAACACA- 1739
                                i                 i      v  ii    v  i    -
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_171152343_   1740 GAAAAGCTGCTCAACATCATTAGTCAT 1766
                               v            ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.03 (6 / 227), avg. gap size = 6.83 (41 / 6)  


3112 27.23 0.55 0.44  chr2_171304841_171311188.rev     4950  5856 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_171304841_   4950 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4999
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_171304841_   5000 GACCATACTGCCCTAGGTAATTTATAGATGCAATGCCATCCCCATCAAGC 5049
                          i v     v   v iv i  i  i    v   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_171304841_   5050 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5097
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_171304841_   5098 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCTGAAGCCAAAAG 5147
                                viiv  ii  v  viv  v     iv      vi ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_171304841_   5148 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACGAGGC 5197
                                i      vv       v  ii i      viv      i i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_171304841_   5198 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAAATATAGACC 5247
                                 i   i i  ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_171304841_   5248 AATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATCTACACT-AC 5296
                                i    iv   ivii         vv   i    i  iiv - v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_171304841_   5297 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGAAAAGGATTCCCT 5346
                         i    i  i     ivv  v   i v  vvv      i    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_171304841_   5347 ATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGATGA 5396
                         v  i                 v      v  ?   i   i i  ii    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_171304841_   5397 AACTGGATCCCTTTGTTACACATTATACAAAAATTAATTCAAGATGGATT 5446
                          ii    i    viv i    vv              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_171304841_   5447 AAAAACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAACC 5495
                          ? i  i       v   v       i      -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr2_171304841_   5496 TAGGCA-ATACCATTCAGGATAGAGGCATGGGCAAAGACTTCATGTCTAA 5544
                             ?i- v i -   iv  ivvv  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_171304841_   5545 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5594
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_171304841_   5595 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5644
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_171304841_   5645 AGGCAACCTACAGAATAGGAGAAAATTTTTGCAGTCTACCCATCTGACAA 5694
                           i     i       i         v      ivii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_171304841_   5695 AGGGCTAAAATCCAGAATCGACAAAGAACTCAAACAAATTTACAAGAAAA 5744
                         i  i  viv         vv i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_171304841_   5745 AATCAAACAACCCCATCAAAAAATGTGCAAAGTATATGAACAGACACTTT 5794
                          iv    i     v  i?       v      v  v    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_171304841_   5795 TCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAATGCTCATC 5844
                           v        i  vi viii     i  i  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_171304841_   5845 ATCACTGGCCAT 5856
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


 636 23.32 13.07 4.24  chr2_171591951_171594465.rev        2   284 (2231)    L1M4_orf2#LINE/L1      432   739 (169)  

  chr2_171591951_      2 CAAATGCAAAATA-TAAACCTCAACTCTT--CCCACACCATATA--AAAA 46
                           v        v - i  vi vi  i i -- i           --    
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_171591951_     47 TTAACTTGAAATGGGTCCTAGACCATTTTCTTACCCAAGTGTAAAAACAA 96
                               ii      i  v?     -----------i  i     i i v 
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACC-----------TAAATGTAAGAGCTA 520

  chr2_171591951_     97 ACATTATAAAACTGCAAGAAAAAAAAATAGAAG-AAATCTTAGCAAT-TT 144
                          v i         viv    i    v    i? -       v ii i-  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_171591951_    145 GGATTTGGCACAGAATTAT-AAATA-GGTTTCAAAAACACAG-------- 184
                           i  v    vv iv  v - i   - iivi     i    i--------
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_171591951_    185 ------------TAAATTGGACTT-ACCAAAATTTAATGCTTTTGCTCTT 221
                         ------------            - i       v  vi      iv   
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_171591951_    222 CAAAAGAGAATTGTTAAAAA--TGGAAAG-----TCACAGAATGGGAGGA 264
                             i  v -i i i  i  --  i    -----i             i 
  L1M4_orf2#LINE/    671 CAAAGGACA-CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_171591951_    265 AATATTCTCAATACATATAT 284
                               iv   vv       
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATAT 739

Transitions / transversions = 1.67 (40 / 24)
Gap_init rate = 0.04 (13 / 308), avg. gap size = 3.77 (49 / 13)  

 732 19.80 2.03 3.05  chr2_171591951_171594465.rev      551   747 (1768)    L1M4_orf2#LINE/L1        3   197 (711)  

  chr2_171591951_    551 GAAAAAAATACCATGTTCATAGCTTGGAAGAC--AATATTGTTAAGATAG 598
                             i v  v          i v         --              i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_171591951_    599 CGACACTACTCAAAGCAATCTAAAGATTCACTGCAATACCTATCAAAATT 648
                          i i   v i    vii     v       vi     v           i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_171591951_    649 CCAACAACCTTTTATTGCAGAAATGGAAAAGCTGATATTCAA-TTCGTAT 697
                            i vi      -          v  v        vi v  -   i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_171591951_    698 GCAT-TGCATATCCCACCTCCCACAATAGCCAAATAATTCTTGAGAAAAA 746
                          v v-    vivv--   ---  v          vv v      i   i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGG--ACC---CAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_171591951_    747 A 747
                          
  L1M4_orf2#LINE/    197 A 197

Transitions / transversions = 0.77 (17 / 22)
Gap_init rate = 0.03 (6 / 195), avg. gap size = 1.67 (10 / 6)  

2849 16.05 2.51 0.19  chr2_171591951_171594465.rev     1014  1530 (985)    L1M4_orf2#LINE/L1      194   722 (186)  

  chr2_171591951_   1014 AGAGAGAACAAAATCAGAGGACTCATACTTCTTGATTTCAAAACTTACTA 1063
                            -        i ii         i     iii                
  L1M4_orf2#LINE/    194 AGA-AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_171591951_   1064 CAAAAATACATTAATCAA-ACAATGTGATACTAACATAAGGATAGACATA 1112
                             iv    v       -   i    i    ii                
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_171591951_   1113 TAAACCAATGGAATATAATTGAGACTCCCTAAAAAAACCCATACATCTAT 1162
                           i i          v        v   vv   v            i   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_171591951_   1163 AGCCAGTTGATTTTTGATAAGGATGCCAAGTTCATTCAATGGCAAAGGAA 1212
                         i i  i        i  i    i       vi          vi  i   
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_171591951_   1213 TAGTCTT--CAACAAATTGTGCTGGGACAACTGGATAACTACATGCAAAA 1260
                                --        v                   ? i          
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_171591951_   1261 GAATGAAGTTGGATTCTTACCACACTCTATATATGAAAATTAACTCAAAA 1310
                                      ii i    v   v i     ii               
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_171591951_   1311 TAGATTAATAACCTAAGTATAAGAGTTAAAACCATAAAGCTCTTAGAAAA 1360
                          i   i ?vi      i i      i      i     i         i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_171591951_   1361 AAACATATGGGGAAACCTTCATGACTTTGGATTTGGAAATAGATTCTTAG 1410
                                v ? v   i    i    i    i  v  v   i v       
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_171591951_   1411 ATATGACACCAAAAGCACAGGCAACAAAAAAAA-------TAAATTGCAC 1453
                                            i         i   -------       v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_171591951_   1454 TTTGTCAAAATGAAAAACTTTTGCACCTCAAAGGACGTTATAAAAAAAGT 1503
                           ii       v           ii i         ii   v  i     
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_171591951_   1504 GAAAA---AACCTATAAAATAGGAGAAAAT 1530
                              ---    i i i   i         
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAAT 722

Transitions / transversions = 2.81 (59 / 21)
Gap_init rate = 0.01 (5 / 529), avg. gap size = 2.80 (14 / 5)  

 852 18.97 3.08 0.00  chr2_171591951_171594465.rev     1829  2023 (492)    L1M4_orf2#LINE/L1      708   908 (0)  

  chr2_171591951_   1829 AAAAAGAGAGAAAACA-----AAATAATATATCTGATAAAAGTTTAACAT 1873
                          i  v i       i -----    v             ii vi vii  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_171591951_   1874 CCAGAATATATAGAGAACTCCTGCAACTCAATCACAAAAAGACAAACAAC 1923
                                     i       i i         v i           i   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_171591951_   1924 CCAAT-AAAAAATAGACGAAGAATTTAAACAGACAGTTCTCTAAAGAAGG 1972
                              -?      i i i   i    i  i     v     i       i
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_171591951_   1973 TAAACAAATGGCCAAAATGCATGTGAAAAGGTGTTCCGCATCATTAGTCA 2022
                           v            v v   ii       i  i  vi     ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_171591951_   2023 T 2023
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.60 (26 / 10)
Gap_init rate = 0.01 (2 / 201), avg. gap size = 3.00 (6 / 2)  


 218 14.29 2.86 0.00  chr2_171714158_171716545      466   500 (1888)    L1M4_orf2#LINE/L1        1    36 (872)  

  chr2_171714158_    466 TGAAAAGATATCCTATGTCCACAGATTGGA-GACTT 500
                           i          i    i  ii       -     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTT 36

Transitions / transversions = 1.00 (5 / 0)
Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1)  

1485 17.13 3.85 0.00  chr2_171714158_171716545      501   786 (1602)    L1M4_orf2#LINE/L1      257   553 (355)  

  chr2_171714158_    501 TCAAAA-AGTATGGTACTGCCATAAGAATACACATATATACCTATGAAAT 549
                             i -   i        v      i   v       v i v   i   
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_171714158_    550 AGATCTGA--ATTCAGAAATAAACCCAAAAATCTACGGCCAGTTGATTTT 597
                            vi   --i i              v v  i  i  i  i        
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_171714158_    598 TGACAAGAGTACCAAGACCACTCAATGAGGAAAGAATAATCTCTTCAACA 647
                         i      i  i         i      i          i   i       
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_171714158_    648 AATGATGCTGGGACAACTAGGGAACCACATGCAAAATAATGAAGTAGGAC 697
                             i             i iv ?            v        v    
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_171714158_    698 CCCTACCTCACTCTATGTACAAAAATTAACTAAAAATGAATGAATGACCT 747
                                    v i  i              v      i  v ?v     
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_171714158_    748 AAATATAGTAACTAAAACTAT--------TAGAAGACAATACAGGAG 786
                             i  iv i          --------       v  i i   ? 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

Transitions / transversions = 1.88 (30 / 16)
Gap_init rate = 0.01 (3 / 297), avg. gap size = 3.67 (11 / 3)  

 463 21.71 0.00 2.33  chr2_171714158_171716545     1091  1219 (1169)    L1M4_orf2#LINE/L1      538   663 (245)  

  chr2_171714158_   1091 GAAGATAACACAGGGGTAAATCTTCATGACTACAAATTTGGCAATAAATT 1140
                              v    i   ?          i    iviiii  v      iiv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_171714158_   1141 CTTAGATTTGTCACCAAAAGCATAAACAACAACAGTAACAAAAATCAACA 1190
                                v  v           i  i      v  -- -      vi i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAG--A-AAAAATAGATA 634

  chr2_171714158_   1191 AAATACATTTCATAAAAATTAAAAACATT 1219
                           v iv i     v            v  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTT 663

Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.02 (2 / 126), avg. gap size = 1.50 (3 / 2)  

1039 17.36 3.40 3.77  chr2_171714158_171716545     1632  1896 (492)    L1M4_orf2#LINE/L1      645   908 (0)  

  chr2_171714158_   1632 CATAAAAATAAAAAACTTCTGTACATCAAAGGATATTATCAAAAAAGT-A 1680
                            v     v        i   i v        i i      i     - 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_171714158_   1681 AAAGACAACTTACAGAATAGCAGAAAATATCTGCAAATCATATATGT--T 1728
                                  ii       i v         i              v -- 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_171714158_   1729 AAGGGTTTAGTATCCAGATTTTTTAAAAAAAAAAAAAAACCTCCCACAAC 1778
                              vi v         v v v    i  ----------   ii     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAA----------CTCTTACAAC 784

  chr2_171714158_   1779 -----AACAAAACAACAAACAGTCTGGTGAAAAAATGAGCAAAAGACTTG 1823
                         -----  i    vi     i ii iii v?       i     i  i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_171714158_   1824 AATAGACATTTCTCCAAACAAGATATATAAA-GACCAGCAAACACATTAA 1872
                                           v        i   - i   ii  i     v  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_171714158_   1873 AAGATGTTCAACAACATTAAGTCA 1896
                               i      v  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (30 / 15)
Gap_init rate = 0.02 (5 / 264), avg. gap size = 3.80 (19 / 5)  


2577 22.73 0.76 3.79  chr2_171752541_171755812.rev     1551  2210 (1062)    L1M4_orf2#LINE/L1        1   640 (268)  

  chr2_171752541_   1551 TGGAAGGATATTCCATGGTCATGGAATGGAAGCATCAATACTTTTAAAAT 1600
                              i     i     v       v      vv i    i v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_171752541_   1601 GTCCATTGTACCCAGAGCAATCTATAGGTTTAATGTAATCCCTGTCAAAA 1650
                          v v  vv v    i vii     i  i  i  i i       i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_171752541_   1651 TACCAATGGCATTCTTCACAGAAATAGAAAAAATAATTCTAAAATTTGTA 1700
                          v   iiv  v  i  ii       v  v  iv i  i        ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_171752541_   1701 TAGAACCACAAAAGACCCAGAATAGCCAGAGCTATCCTGAGCAA--AGAA 1748
                          i   vii   ii               i i v   i   iv  --    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_171752541_   1749 CAAAACCAGACGAATCACATTACCTGACTTCAAATTATACTACAAAGCTA 1798
                             iiii  v  v     i v  ii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_171752541_   1799 TAGTAATCAAAACAGCATTGTACTGGCATAAAAACAGACACATAGATCAG 1848
                         i         i    ii v            ii i     i        i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_171752541_   1849 TGAAACACATAGACCAGTGGAACAGAACAGAGAATCCAGATAGCAATCCA 1898
                           -----------------   i    iv    i      v vv  i   
  L1M4_orf2#LINE/    301 TG-----------------GAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_171752541_   1899 TATATCTACAGTGAAGTTG-TTTTTGACAAAGGTGCCAAGAACAAACATT 1947
                           i  i  ii  v  -   -    i     i          v  vv  v 
  L1M4_orf2#LINE/    334 TACATTTATGGTCAA-TTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_171752541_   1948 GGGGAAAGGACAGTCTGTTCAATAAATGGTGCAGGGAAAACTGGATATTC 1997
                                 i i     v     i         v    v         ?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_171752541_   1998 ATATGCAGAAGAATGAAACTAGATCCCCTATCTCTCACCATATACAAAAA 2047
                          i     i         ii i  -      i   v               
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGA-CCCCTACCTCACACCATATACAAAAA 481

  chr2_171752541_   2048 TCAAATCAAAATGGGTTAAAGACTGAAATCTAAAAAGACCTCAAACTGTG 2097
                          i  v         i i ?    iv    v   ---  v  v     i i
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAA---GAGCTAAAACTATA 528

  chr2_171752541_   2098 AAACTACTATAAGAAAACACTGGGGAAACTCTCCAGGACATTGGTCTGGG 2147
                              vi  v         iv  ? v  v   i iv   v    vi i  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_171752541_   2148 CAAAGATTTCTTAAGTA--ATACCCGACAAGCACAGGCAACCAAAGGTAA 2195
                            v i       ii  -- i   -- v       i     v    i-  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACC--AAAAGCACAAGCAACAAAAGA-AA 625

  chr2_171752541_   2196 AAATGGACAAATGGG 2210
                             i  i    v  
  L1M4_orf2#LINE/    626 AAATAGATAAATTGG 640

Transitions / transversions = 1.62 (91 / 56)
Gap_init rate = 0.01 (9 / 640), avg. gap size = 3.33 (30 / 9)  

1125 21.31 1.03 0.69  chr2_171752541_171755812.rev     2490  2780 (492)    L1M4_orf2#LINE/L1      617   908 (0)  

  chr2_171752541_   2490 CAAAAAAAAAAA-GGACAAATGGGATCACATCAAA-TTAAAAAGCTTCTG 2537
                              i      -i  i    v   iiv       -       -   i  
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTG 665

  chr2_171752541_   2538 CACAGCAAAGAAAACAATCAACAAAGCGAGGAGATAACCCACAGAGTAGG 2587
                         ii vv     i v  v     v    i  ii   i          i i  
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_171752541_   2588 AGAAAATATTTGCAAACTATCCATCTGACAAGGAATAAATAACTAGAATA 2637
                                         ii  vi      i    i ivvi  v i      
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_171752541_   2638 TATGAGGAGCTCAAACAACTCTGTAG-GAAAACATATGATAATCCAATCT 2686
                            i i  i   vv       vi  i-i    v i -i    i     i?
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACA-AATAACCCAATTW 814

  chr2_171752541_   2687 AAAAATGGGCAAAAGATTTGAAGAGACATTTCTCAAAAGAAGACATACAA 2736
                                      i        v           v        i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_171752541_   2737 ATGGCAAACAACTTGATGAAAAGGTGCCCAATATCATTGTTTAT 2780
                              v  i  vivv        i   i   i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (40 / 21)
Gap_init rate = 0.02 (5 / 292), avg. gap size = 1.00 (5 / 5)  


1916 21.04 6.13 15.02  chr2_171785354_171787919     1088  2066 (500)    L1M4_orf2#LINE/L1        1   892 (16)  

  chr2_171785354_   1088 TAGAAAGACACCCCACGTTCATGAATTGGAAGA----ATACTGTGAAAAT 1133
                          i      i i    i       i         ----   i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_171785354_   1134 GACA-TACTACCAAAAGTGATCTACAGATTCAATGCAATTCCTATCAAAA 1182
                          i  -    v  v   v                i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_171785354_   1183 TACCAATGACATTCCTCACAGAAAGAGAAAAAAC-ATCCTAAAATTCATA 1231
                          v   iivi v  ii ii      vv  v  ivi-               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_171785354_   1232 TGAAACCACAGAAGACTCTGAATAGCCAAAGCAATACAGAGCTAAAAGAA 1281
                           i  vii  iii   i v           i    viv  ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_171785354_   1282 TAAAACTGGAGGCATCACACTACTGGACTTCAAAATACACTACAATGTTC 1331
                         i   ii      vv       v ivi i       ivi       v i -
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT- 249

  chr2_171785354_   1332 ACCATGTTGGCCAGGCTGGTCTCAAACTCCTGGCCTCAAGTGATCCTCCC 1381
                           vi -------------------  ---------     ----------
  L1M4_orf2#LINE/    250 ACAGT-------------------AA---------TCAAG---------- 261

  chr2_171785354_   1382 AAAGTGCTGGGATTACAGACATAAGCCACTGCTCCCAGCCAGGGATTGCT 1431
                          v    -   ---   v i      -------------------------
  L1M4_orf2#LINE/    262 ACAGTG-TGG---TACTGGCATAAG------------------------- 282

  chr2_171785354_   1432 TTCTTGATTTCTTTTTCTGCTAGTTCATTGTTGGTGTATAGAAATGCTAC 1481
                         -----   -------------------------------   v  -----
  L1M4_orf2#LINE/    283 -----GAT-------------------------------AGACAT----- 291

  chr2_171785354_   1482 TACTTTTTGTATGTTGATTTTGTGTAACAGACACAGATCAATGGAACAGA 1531
                         -------------------------------- i            i   
  L1M4_orf2#LINE/    292 --------------------------------ATAGATCAATGGAATAGA 309

  chr2_171785354_   1532 AT--AGAACCCAGAAATAAATCTATGCATTTATGGCCAACTAATCTTCGA 1579
                           --   ii           i i  i         i   i i  i     
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_171785354_   1580 CAAAGG-------------CACTGGGAA--------------CATTAAA- 1601
                            i  -------------  v    i --------------  vi   -
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_171785354_   1602 -----------AACTGGATATCCATAGGCAGAAAAATGAAACTAG-CCCC 1639
                         -----------         ?   i v   i  i      ii i -    
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_171785354_   1640 TATCTCTCACTGTATACAAAAATCAACTCAAAATGGGTTAAAGATTTAAA 1689
                           i   v   ii           i            i i ?   ii    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_171785354_   1690 TGTAAGATCCCAAACTATGAAACTACTAGAAGAAACCTTAGAGGAAACAC 1739
                                v iv       i     vi         v v   i? v  vv 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_171785354_   1740 TTCAGGGCATTGGTCTAGGTTAAGATTTTATGAAGAAGATCTCAAAAGCA 1789
                            iv i v    vi    iv v i   iv ii v v  ivi        
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_171785354_   1790 CAGGCAACAAAAGCAAAAACAGACAAACT--ATTATCTCAAACTAAAAAG 1837
                           i          v     i   i   i -- i viv     v v    i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_171785354_   1838 CTTCTTCACAGCAAAGGAAACAATCA-TAGAGTGAAGATACAACCTGCA- 1885
                            i vii vv       v  v    -v i      i v      ii  -
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_171785354_   1886 ------AGAAAGTGATTTGTAAACTATTCATCTGAGAAGGGATTAATATC 1929
                         ------     i -     i   ii  vi      v      i vi    
  L1M4_orf2#LINE/    710 AATGGGAGAAAAT-ATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_171785354_   1930 CAGAATTTACAAGGAACTCAAACAACTCAACAGCAAAACAATAAATAATC 1979
                               v  i  i      vv         i ii    vi i      i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_171785354_   1980 CAATCTAAAAATGGGCAAAGACATCTCTTGAA-AGAAGTAACCATACAAA 2028
                             i?              i-  ---     -   vi vv ivi v i 
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGG-AT---TTGAATAGACATTTCTCCAAAGA 854

  chr2_171785354_   2029 AACCATACAAATT-TTAACAGGTATATTTAAAAAATGCT 2066
                          ivi        v-ii  i i i i  v-    i     
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATG-AAAAGATGCT 892

Transitions / transversions = 1.69 (127 / 75)
Gap_init rate = 0.03 (26 / 892), avg. gap size = 7.96 (207 / 26)  


1729 10.21 1.56 34.38  chr2_171801117_171803068      501  1460 (492)    L1M4_orf2#LINE/L1      264   908 (0)  

  chr2_171801117_    501 AATATGGTACTGGCATAAAGACAGACATATATATAGAGCAATGGGATAAA 550
                          i i              i  i         ----  v      i   i 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATA----GATCAATGGAATAGA 309

  chr2_171801117_    551 ACAGGGAGACCAGAAAATAAACCCTCAC-------GTGAAATGATTTTCA 593
                          iv i   v       -       vi  -------  v  v        i
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_171801117_    594 GTAAGAACACCAACACCATTTAGTGGAGAAAGATCAGTCTTTTCAACAAA 643
                         ii   iiii    v      i i   i      vi               
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_171801117_    644 TGGTGCAGGGAAAACTGGATATCCACATGCAAATAAATTGAGTTGGATCC 693
                               v    v         ?           vi   vi       i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_171801117_    694 TTACTTTA-ACCATATAAAAAAATTAACTCAAAATGGATCAAATGCCTGA 742
                         i   i i -        v                       ? vi   i 
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_171801117_    743 ATATAAGACCTAAAACTTTCTAACTCTTAGAAGAAAACATATGGATAAAG 792
                           i     v        v vv                    v ?i    v
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_171801117_    793 CTTCATGGCACTGAATTTAGCAATGGTTTCTTTGATCTAACACCAAAAGC 842
                             i  i vi  ii  vi             v   v i           
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_171801117_    843 ACAGGCAACTAAAGAAAAAATAGGGCCAGGTGCAGTGGCTCATGCCTGAA 892
                            i     v             i--------------------------
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGA-------------------------- 632

  chr2_171801117_    893 ATCCCAGCACTTTGGGAGGCCAAGGCCGGCAGATCACTTGAGGTCAGCAG 942
                         --------------------------------------------------
  L1M4_orf2#LINE/    633 -------------------------------------------------- 632

  chr2_171801117_    943 TTCGAGACTAGCCTGGCCAACATCTCTACTAAACGTCTCTACTAAAAATA 992
                         --------------------------------------------------
  L1M4_orf2#LINE/    633 -------------------------------------------------- 632

  chr2_171801117_    993 CAAAAAAATTAGCCGAGCGTGGTGGTGTGTGCCTGTAATCTCAGCTACTC 1042
                         --------------------------------------------------
  L1M4_orf2#LINE/    633 -------------------------------------------------- 632

  chr2_171801117_   1043 AGGAGGCTGAGGCAAGAGAATCACCTGAACCCAGGAGGCAAAGGCTGCAG 1092
                         --------------------------------------------------
  L1M4_orf2#LINE/    633 -------------------------------------------------- 632

  chr2_171801117_   1093 TGAATCGAGGTCGTACCACTGCACTCCAGCCTGGGCGACAGAGTGAGACT 1142
                         --------------------------------------------------
  L1M4_orf2#LINE/    633 -------------------------------------------------- 632

  chr2_171801117_   1143 CCGTCAGAAAAAAAAAAAAAAAAAAAAAAAAGGAAGGAAGGAAAATAGGT 1192
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    633 -------------------------------------------------T 633

  chr2_171801117_   1193 AAGTTGGACTTCATCAAAATTAAAAACTTTTGTGCCTAAAAGGACACAAT 1242
                           i                                i v         v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_171801117_   1243 CAACAGAGTGAGACGGCAACCCACAGAATGGAA-AAAATATCTGAAAATT 1291
                            v i     i v i               i -       i  v    i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_171801117_   1292 ATATATCTGATAAAGGATTGATATCCAGAATATATAAAGAACTTCTACAA 1341
                                      i   i vi                      ii     
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_171801117_   1342 CTCAATAACAAAAAAA------ACCCAATTAAAAAATGGGCAAAAGACTG 1385
                                 i     i ------        ?             i  i v
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_171801117_   1386 GAATACAAATTTTTCCAAAGAAGATATGCAAATGACCAATAAGCACATGA 1435
                              v v    i              i      i               
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_171801117_   1436 AAAGATGCTCAACATTAATCATGAG 1460
                                        i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (60 / 34)
Gap_init rate = 0.01 (7 / 645), avg. gap size = 49.29 (345 / 7)  


 373 16.67 1.04 3.12  chr2_171904917_171907908      493   588 (2404)  C L1M4_orf2#LINE/L1   (0)   908   815  

C chr2_171904917_    588 AAAAAAGTGCAAAATACCTGAATAGACATTTATCAAAAGAAGACATA-AA 540
                              v v     iv ii             v  v        i   -  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

C chr2_171904917_    539 ATGGCCAACAGGTATGTGAAAGAAAAATGCTCAACCTCATTAATCAT 493
                                 i i i ii     --- i         v   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAA---AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 2.00 (4 / 2)  

2305 24.66 5.48 0.96  chr2_171904917_171907908      882  1611 (1381)  C L1M4_orf2#LINE/L1   (83)   825    63  

C chr2_171904917_   1611 CAAAGCAGTCTAAAGTTTCAATGCAATCCCTATCAAAATACCAGTGGCAT 1562
                             viii    v  v     i                 v    iv  v 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

C chr2_171904917_   1561 TTTTCTTGGAGAAA-----AAA--------AAAATT---ATG-AAATTTA 1529
                             --  v     -----  i--------      ---   -    vi 
  L1M4_orf2#LINE/    113 TTTT--TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

C chr2_171904917_   1528 AAG-ACCCAGAATAATCAAAGCAACCCTGAGCAAAAAGAACAAAACTTTA 1480
                          i -          ii    i   i i   iv  i         ii vv 
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

C chr2_171904917_   1479 GCA-TCACATTACCTGACTT--AAATTATACTACAAAGCTATAGTAA-CA 1434
                          v -     i v  ii i  --   i -             i     -  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCA 259

C chr2_171904917_   1433 CAAACAGCACAGGGCTGACATAA----AAACATC--AACCAATGGAACAG 1390
                         - i    iiii vi   i     ---- i    v--i i        i  
  L1M4_orf2#LINE/    260 -AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

C chr2_171904917_   1389 AATAGATAACTCAGAAATAAGTCTACACATGTATAGCCAACTGATTTTTT 1340
                            v  v iii         ii i i    v   i i   i       iv
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

C chr2_171904917_   1339 ACAACAGTGCCAAGATCATATATTGAGGAAAAGACAGTCTGTTCAAAAAA 1290
                             vi         i   vi v  i     ii i     v     v   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

C chr2_171904917_   1289 TGGTGCTAGAAAAACTGGATAGCCATATGTGGAAGAATGAAACCAAGTCC 1240
                                i i v         ?   i   iii         iiiiiii  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

C chr2_171904917_   1239 CTATCTCTCAT-ATATACAAAAATCAAATCAAAATGGAGTAAAGACTTAA 1191
                            i   v  i-            i  v          vi ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

C chr2_171904917_   1190 ATCTAAGACCTCAAAGTATAAAACTACTAGAAAAAAAT---GGGG-AAAT 1145
                           v     v  v   v         vi     i    i---  ? -    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

C chr2_171904917_   1144 GCTCCATAGCATTGGTCGGGGCAAAGACTTCTTGAGTAAGACCTCAAAAG 1095
                         -  i i ii v    vivi     v ii     iii  v   vi      
  L1M4_orf2#LINE/    559 -CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

C chr2_171904917_   1094 CACAGGCAACAAAAGCAAAAATAGACAGATAAGATCACATCAAACTAAAA 1045
                             i          v         i i  vi  iiv       v v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

C chr2_171904917_   1044 AGCTTTTGGACAGCAAAGAAAAAAATCAACAAAGTGAAGAGACAAC--AC 997
                          i      vi vv     i v vv     v        i       --  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

C chr2_171904917_    996 AGAATGGGAAAACATAT-----AACTACCCATCTAACAAGCGATGAATAA 952
                                  i  v    -----  ii ivi    i i   v  ivvi  v
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

C chr2_171904917_    951 CCAGAATATACAAGGAGCTCAAACAACTCAATAGCAAAAAAAAAAAAAAA 902
                                   i  i  i   vv           -- v     i v   v 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATA--ATAAAAAGACAAATA 805

C chr2_171904917_    901 AATTGATTTTAAAATGTGCA 882
                          viii   ?v      v   
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 1.71 (111 / 65)
Gap_init rate = 0.03 (20 / 763), avg. gap size = 2.35 (47 / 20)  

3934 14.97 11.02 2.28  chr2_171904917_171907908     1666  2500 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_171904917_   1666 TGGACAGATATCCCATGTTCATGGATCTGAAGTCTTAATATCATTAAGGT 1715
                             v                     iv    v        ii     i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_171904917_   1716 GGCAATATTCCCCAAGTTGATCTACAGATTCAACAAAATCCCTATAAAAA 1765
                                i       i                  iv         v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_171904917_   1766 TCCCAGCTACTTTTTTAATTTTTGCAAAATTTGACAAACTCATCCTAAAA 1815
                                 i i     ------    i  v       i  v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT------TGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_171904917_   1816 TTTATATGGAAATGCAAGAGACCCAGAAGAGCCAAAACAATCTTAAA--- 1862
                           i               i         v               i  ---
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_171904917_   1863 ---GAACAAAACTGTGGAAGAGTCACATTTCTTAGTTTCAAAACTCACTA 1909
                         ---       ii  --  i  v     i   ii i          i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTG--GAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_171904917_   1910 TAAAGCTATAGCAATCAAGACAGTG--ATACTGGCTTAGTGATAGACATA 1957
                         i       i  i             --i       v  iv          
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_171904917_   1958 TGTGTATATCAATGAAATATAATTGATAATTCAGAAATAAATCCTCACAT 2007
                          ---- v       i    v      v i i          i  vi    
  L1M4_orf2#LINE/    293 T----AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_171904917_   2008 TTACAGTTAATTGATTTTTTCAACAAGGGTTTCATGACAATTCAATGAGG 2057
                            ii  i          -- i        vi  v   v        i  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTT--CGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_171904917_   2058 AAAGAATAGTCTTT--AAAAAATGTTTCTGGAACAACTGGATATTCATAT 2105
                                       --  v     v v    i           ?i  i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_171904917_   2106 ACAAAGGAATGAATTTATTATAGACCCCTACCTCACATCATATATAAAAA 2155
                         i    i       v  i-----               i      i     
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTG-----GACCCCTACCTCACACCATATACAAAAA 481

  chr2_171904917_   2156 TTAACTCAAAATGAATCAAATATCT------------------------- 2180
                                      i    ? v i  -------------------------
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_171904917_   2181 --------------CA-AGGC-----------------------AGGCA- 2191
                         --------------  -   ?-----------------------     -
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_171904917_   2192 -------CTAAATATGACCCTAAAAGCACAGGTAATGATAAAAAAAATAC 2234
                         -------i  i       v i         i i  ii v i        v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_171904917_   2235 AC----TGGGTATCATCACAATTAAAAACTTTTCTGCTTCAAAGGACATC 2280
                          i----   iiv      v              v              ii
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_171904917_   2281 AGTGAGAAAGTGAGAAG-CAACCCACAAATTGGGAGAAAATACTTGCAAA 2329
                          vii         i   -         i v            i       
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_171904917_   2330 TCATATGTATAATAAGGGTCTTGTATGCAGAATATATAA-TAACTCTTAC 2378
                               i v i       v       v            -v         
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_171904917_   2379 AATTCAACAATGTAAAGA-AAA---CCCAATTTAAAAACAGGCAAAGGAT 2424
                           i    i   iv     -   ---       ?     ii          
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_171904917_   2425 CTGCACAAACATTTCCCCAAAGAAGACACACAAATGGCCAATAAGCATAC 2474
                         i  v i i       i          i i                  i i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_171904917_   2475 TAAA-GATGCCTAACATCATTAGTCAT 2500
                         v   -     ii       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.18 (83 / 38)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 6.17 (111 / 18)  


3244 26.79 0.66 0.55  chr2_172032231_172041787      493  1399 (8158)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_172032231_   1399 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATAGCATGAAAAT 1350
                              ii i  i     i        v      v i    vii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_172032231_   1349 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1300
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_172032231_   1299 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTGAAAGTTCA 1252
                          v   iivi i  i  ii     -   -- v  i  - iiiv   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chr2_172032231_   1251 TATGGAAACAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCAAAAAG 1202
                                 iiv  ii  v  viv  v     iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr2_172032231_   1201 AGCAAACCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGCC 1152
                          i    vi      vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr2_172032231_   1151 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1102
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr2_172032231_   1101 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTATAACC 1054
                                i    i--    i  --        vv   i    i   iii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chr2_172032231_   1053 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 1004
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chr2_172032231_   1003 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAT-TAGAAAGCT 955
                           v  i  i              v      v  ?   i  -i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chr2_172032231_    954 GGAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 905
                          i ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chr2_172032231_    904 TTAAAGACTTAAATGTTAGTCCTAAAACCATAAAAACCCTAGAAGAAAAC 855
                          i ?    i       v  vv       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chr2_172032231_    854 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 806
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chr2_172032231_    805 AAACACCAAAAGCAATGACAACAAAAGCCAAAGTTGACAAATGTGATCTA 756
                         vi            vvii         vv   i v  i    vv  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chr2_172032231_    755 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 706
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chr2_172032231_    705 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 656
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chr2_172032231_    655 AAGGGCTAATATCCAGAATCTGTGAAGAACTTAAACAAATTTACAAGAAA 606
                          i  i  vi          v i i       ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chr2_172032231_    605 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATAGACACTT 556
                           iv    i     v  i?    i            v          i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chr2_172032231_    555 CTCAAAAGAAGACATTTATGTAGCCAACAGACATATGAAAAAATGCTCAT 506
                            v        i  vi vi i     i ii  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chr2_172032231_    505 CATCACTGGCCGT 493
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  

 525 25.34 2.05 2.05  chr2_172032231_172041787     7332  7477 (2080)    L1M4_orf2#LINE/L1        1   146 (762)  

  chr2_172032231_   7332 TGGGAAGATATTCCATGCTGATGAGTCCAAATAATTAATATTGTTAAAAT 7381
                            i       i     i v   ii ivi  v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_172032231_   7382 GACAATTCTACCCAAAGCAATTTATAGATTCAATGGAATCCCAGTCAAAA 7431
                          i    v  v      vii  i  i        i v      vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_172032231_   7432 TACCTATGACATTCTTCACAGAAATAGAGCACAAA---ATCCTGAAATT 7477
                          v  viivi v  i  ii       v  ---   i---     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA---CAAGCTGATCCTAAAATT 146

Transitions / transversions = 1.64 (23 / 14)
Gap_init rate = 0.01 (2 / 146), avg. gap size = 3.00 (6 / 2)  

 327 22.97 1.35 0.00  chr2_172032231_172041787     7784  7857 (1700)    L1M4_orf2#LINE/L1      138   212 (696)  

  chr2_172032231_   7784 CCTAAAGTTTTTATAGAACCCCAAAAGATCCAGAATAGCCAAAGCAATCC 7833
                               i  iv   i   viv   ii  i              i     i
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_172032231_   7834 TGAGGAAAATGAACAAAGCTG-AGG 7857
                            ii  i v        i  -   
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGG 212

Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1)  

2383 24.11 0.93 2.16  chr2_172032231_172041787     8150  8796 (761)    L1M4_orf2#LINE/L1      190   828 (80)  

  chr2_172032231_   8150 AAAAAAAAGAACAAAGTTGGAGGCATCATACTACCTGACTTCAAAACATA 8199
                              i                 vv   i   v  ii i        v  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_172032231_   8200 CTACAAAGCTACAGCAACCAAATTGGCATGGTACTGGCATAAAAACAGAC 8249
                                       i  i   ivii ii              ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_172032231_   8250 ACATTGACTGATGGAAGAGAATAGAGAACCCAAATATAAATCCATGCATT 8299
                          i  v  iii      v     v    ii   i v     i    i    
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_172032231_   8300 TACAACCAACTCATTTTTGACAAAGGTGTCAAGTACATATGATGGGGAAA 8349
                           iiii   i v     i     i    i    vv   vii         
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_172032231_   8350 GGACAGTCTCTTCAATAAATGGTGCTGGGATAACTGGAAAACTGTAAGCA 8399
                          i i     i     i              i       v ? iii v   
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_172032231_   8400 GAAGAATGAAACTAGATTCTTATTT---ACTATATATAAAAATCAAATCA 8446
                         i         ii i  ii i  ii ---  i     i      i  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_172032231_   8447 AAATGGACTAAAGACTTAAATCTATGACCTGAAACTATGAAATTACTAGA 8496
                                ii ?    i     v  v  v  i       i   i vi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_172032231_   8497 AGAAAACATTGGGGGAAATGCTCCAGGACATTGGAGCATTTTTATTTGTC 8546
                                  v  ? v    -  i iv   v    i------   --- v 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGG------TTA---GGC 579

  chr2_172032231_   8547 TATTTTGTCATTTGTCAAAAGATTTCAAAAGCACAAGCAACCAAAGCGAA 8596
                         v  vv v  -  v -- v v  ivi                v    vi  
  L1M4_orf2#LINE/    580 AATGGTTTC-TTAG--ATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_172032231_   8597 AATAGA-AAATGGGATTATATCATGCTAACAAGCACCTGTACAGCAAAGA 8645
                               -    v   i vi    viv v v  i vii   i vv     i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_172032231_   8646 A-ACAATCAACAAAGTGAAGAGACAACCCACAGAATGGAAGAATATATTT 8694
                          -  v     v        i                  i    v      
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_172032231_   8695 GCAAACTACCCATTTGACAAGGGATTAATAATGGGAATATATTAAGGAGC 8744
                              ii ivi  i   i      i vi  vivi        -  i  i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT-AAAGAAC 775

  chr2_172032231_   8745 TCAAACAACTCAATAGGAAGAAAAAGAA-AATCAGATTAAAAAATGGGCA 8793
                           vv           iv  i  i vi  -  i vi   ?           
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_172032231_   8794 AGG 8796
                          i 
  L1M4_orf2#LINE/    826 AAG 828

Transitions / transversions = 1.71 (96 / 56)
Gap_init rate = 0.02 (10 / 639), avg. gap size = 2.00 (20 / 10)  

 479 15.05 1.08 0.00  chr2_172032231_172041787     8973  9065 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_172032231_   8973 AAAAAT-GGCAAAAGATCTGAATAGATATTTCTCAAAAGAAGGCATACAA 9021
                               -      i   i        i       v       ii      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_172032231_   9022 ATGGCCAACAGCTATACGAAAAAATGCTCAATATCACTAATCAT 9065
                                 i ivi i i     i        i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 6.00 (12 / 2)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


2923 24.65 1.28 4.78  chr2_172057887_172064177      846  1786 (4505)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_172057887_    846 TGGAAACACATTCCATGCTCATGGATGGGTACAATCAATATTGTAAAAAT 895
                               v i  i     i        v  v v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_172057887_    896 TACCGTACTGCCAAAAGCAATCTATAGATTCAATGCAATTTCCATCAAAA 945
                         vi vi    v  v   vii     i        i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_172057887_    946 CACCATCATCATTCTTCAAAGAAA-----AAAC-ATTCCTAACATTTATA 989
                         iv   v vv v  i  iiv     -----  i -iv      v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_172057887_    990 TAGAACCAAAAAAGAGCCCATAG-AGCCAAAGCAACAATAAGCAGAAAGA 1038
                          i   viiv  ii  -    v i-       i   ivv i iv ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_172057887_   1039 ATAAATCTGGAGGTGTCACATTACCCAACTTCAAACTATACTATCAGGCT 1088
                          i   vi      vv     i v     i      viv     iv i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_172057887_   1089 TTAGTTACCAAAACAGCATGGTACTGGTATAAAAATAGGCATATAGACCA 1138
                         vi   v i   i    ii         i    ii    i        i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_172057887_   1139 ATGGAACAGAATATAGAACTCAGAAATAAAGCCAAATACTTACAGCCAAC 1188
                               i     vv   iii          v   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_172057887_   1189 TAATCTTCAACAAAACATACAAAAAC-ATGAACCAGGGAAAGGATACTCT 1237
                          i  i   i    ii-i i v  i  -  vv vii       i   v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_172057887_   1238 ATTCAATAAATGGTGCTGGGATAACTGACAAGCCACATAACAGAAGAATG 1287
                         v     i              i     ivv ?      i-  i       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAATG 447

  chr2_172057887_   1288 AAACTGGATGCTCATCTCTCACCTTAAGCAAAAATCAACCCAAGATGGAT 1337
                           ii    iv ii i   v    v  vi       i   i   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_172057887_   1338 CAAAGATTTAAATCTAAGACTTGAAACCATAAAAATTCTAGAAGATAACA 1387
                           ?   ii     v     vi i    i      v ii       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_172057887_   1388 TCGGAAAAACTCTTCTAGACATTGGCTTAGGCAAAGAATTCATGACTAAG 1437
                          v  ?iv  v     vv   v    v        v iv   v iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_172057887_   1438 ACCCCAAAAGCAAAACAAAATAAAACAAAAATAAATATAACAACAAAAAA 1487
                           v         -------------   i-----------        i 
  L1M4_orf2#LINE/    598 ACACCAAAAGCA-------------CAAG-----------CAACAAAAGA 623

  chr2_172057887_   1488 TAAATATAACAAAAACAAAAATAAATAAATCAGACCTAGTTAAGCTGAAA 1537
                         ----------------       i      ii   i vi i  iv v   
  L1M4_orf2#LINE/    624 ----------------AAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_172057887_   1538 AGCTTCTGCAAAGCAAAAGAAATAATCAGCAGAGTAAACAGACAACCCAC 1587
                          i   i  iivvv    i  v iv    iv i   i  v           
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_172057887_   1588 AGAGTGGGAGAAAATATTCTCAAACTATGTATCTGACAAAGGACTAATAT 1637
                            i              iv    ii  i       i  i     vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_172057887_   1638 CCAGAATCTACAAGGAACTC----AAATCAGCAAGAAATAAAACAAATAA 1683
                                v  i  i      ----  v   ii  v   -  i        
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAAATAA 806

  chr2_172057887_   1684 TCCTGTCAAAAAGTGAGCAAAGGACATGAATAGGCAATTCTCAAAAGAAG 1733
                         i  vi i?    i  i        iv       i  v     v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_172057887_   1734 ATGTACAAACAGCCAACAAACATATGAAAAAAATGCTCAACATCACTAGT 1783
                           i      ii     i  i  i       i -            ?????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZ 905

  chr2_172057887_   1784 TAT 1786
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.65 (142 / 86)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.38 (57 / 13)  

2901 27.01 1.65 1.54  chr2_172057887_172064177     4893  5799 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_172057887_   4893 TGGAAGAACATTCCATGCTCACAGATAGGAACACTCAATATCGTGAAAAT 4942
                              ii i  i     i   ii   v    v   i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_172057887_   4943 GCCCATACTGCCCAAAGTAATTTATAGATTCAATGTTATTCCCATCAAAC 4992
                          v v     v      v i  i  i        i iv  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_172057887_   4993 TACT-GTTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 5040
                          v i- i  v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_172057887_   5041 TATGGAACTAAAAAAGAGCCCATATAGCTAAGACAATCCTAACCAAAAAG 5090
                                v iv  ii  v  viv     i  i      i i vv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_172057887_   5091 AATAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAGGGC 5140
                           i    i      vv   ii  v  ii i      viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_172057887_   5141 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGACATATAGACC 5190
                                 i   i    ii         i  v ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_172057887_   5191 AACGGAACAGAACACAGACCTCCATTAAACAGAGAAATAAGTCCACACAT 5240
                           i    i    ivv   v-    ---------       ii   i    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAG-TCCA---------GAAATAAACCCATACAT 338

  chr2_172057887_   5241 CTACAACTATCTGATCTTCAACAAACCTGACAAAAACCAG-CAATGGGGA 5289
                         i  iiiii vi    i   i    ivv  v   i -   v-         
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGA 387

  chr2_172057887_   5290 AAGGAT--TCCCTATA-TAAATGGTGCTGGGAAAACTGGCTAGCCATATG 5336
                            i  --  ii vi -i              v      v  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_172057887_   5337 CAGAAAACTGAAACCGGACTCCTTCCTTAGACCTTATTCAAAAATTAGCT 5386
                           i  i v    iii    i   v   i v   v   v         i  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_172057887_   5387 CAAGGTGGATTTAAGACTTAAATGTAAAACCAAAAAACATAAAAACCCTA 5436
                            ii     iv?    i         i v v    vi      vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_172057887_   5437 GAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACT 5485
                                  v    ?i- v i -   iv   v v  vv i     v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_172057887_   5486 TCACGACAAAAACACCAAAAGCAACTGCAACAAAAGCCAAAGTTGACAAA 5535
                           viiivv vi            vvv          vv   i v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_172057887_   5536 TGGGATCTAATTAAACTAAAGGGCTTCTGCACAGCCAAAGAAATTAGCAT 5585
                          v   ii v  i   v v  iii   i  ii vv v  i  v i  v  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_172057887_   5586 CAAAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACC 5635
                         v        v  i     i                 v       vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_172057887_   5636 CATCTGACAAAGGGCTAATATCCAGAATCTACAAGGTATTTAAACAAATT 5685
                         i      i  i  i  vi          v  i  i v i ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_172057887_   5686 TACAAGAAAAAAA-----AAC---ATCAAAAAGTGGGCAAAGGATATGAA 5727
                         v i  v     i -----   ---  i?    i            v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_172057887_   5728 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAATAAACATATGAAAA 5777
                         i     i     v        i  vi viii        i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_172057887_   5778 AAGGCTCATAATCACTGATCTT 5799
                         i v     vv    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.07 (29 / 14)  


1485 27.87 7.85 4.66  chr2_172102239_172105238     1634  2512 (488)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_172102239_   1634 GGAAAGAC--TCTATAGTCTTCATAGATAGGATTATTTGATATTGTAAAG 1681
                                i--i i  i---     i   v   vv i  i       v   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATG---TTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_172102239_   1682 ATGTCAGTTCTCTTCAAACTGATATACAGATTTAATGCCATCCCAATCAA 1731
                            v  i v   ii    i    v        i  i  v     v     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_172102239_   1732 AATTTCAATAAGGC---TTTTG-GGAAGCC--CAAGCTGATTTTAAAAGG 1775
                            ii  ii--v  ---     -i   iii--         ii     vv
  L1M4_orf2#LINE/     99 AATCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_172102239_   1776 TATATGAAAGTGTCAATGG-CAAAAAAGAAATAAGACACTCCTAAAGAAG 1824
                         i     i  i  -   v  - vv i  v ivi  i   v  i i  i   
  L1M4_orf2#LINE/    147 CATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_172102239_   1825 AGGAGTAA-GATGGAACAGTTCCCCTACCAGCTCTCAAGCCTTATGATAA 1873
                          i  ii  - v    iv v iv v  v  viv i    iv    iv i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_172102239_   1874 AACTGCAGTGAATAAG------TGGTCACTTATCACCCCAGGGACAGAAA 1917
                          i  i    i vi   ------    -   vi-  i--- i   i   v 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGT-ACTGG-CAT---AAGGATAGACA 290

  chr2_172102239_   1918 AATAAGAT-AATGGAACAGAAAACAGAGCACAGAAATAGACTTGACCAGA 1966
                         v   -   -       i    vvv    iv        i  ----   v 
  L1M4_orf2#LINE/    291 TATA-GATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC----CCATA 335

  chr2_172102239_   1967 TA-----GGTAACTTGATCTACAACA---GAACTAGCACCACAGATCTGT 2008
                         i -----   v v     i v i   --- vi i iv    i---  vi 
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT---TCAAT 382

  chr2_172102239_   2009 GAAGAAATGAAGAGACTATTCAATAAGTGGGTCTGGAACAAGTGATTATT 2058
                          ii    -   v  v  v     i  i   vv    i    v  iv  ?i
  L1M4_orf2#LINE/    383 GGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_172102239_   2059 CATATACAAAAAATAATAATAATGAAA--GGATCTCTAATTTATACCATA 2106
                           i  i     i --------     i--   i i   vi i i      
  L1M4_orf2#LINE/    432 CACATGCAAAAGA--------ATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_172102239_   2107 CTCTCAAATCAATTTCATCACTGACTGAAGACTTAAGTGGGAAAGTTAAA 2156
                         iv vv    i  i -  vv iv  iii?    i   i  vi i  i    
  L1M4_orf2#LINE/    474 TACAAAAATTAACT-CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_172102239_   2157 ACTTTAAAACC--TAGAAAAAGA-ATAAGAGGATATCTTTATGACCTCAA 2203
                            v      i--     i  i -   i ? v v     ii      iii
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_172102239_   2204 GTTAAGCAAT----TCTTAAACA--ATAGTCAAATTATAACCA-TAAAAG 2246
                             i     ----     i i -- i viv   vi i  v  -i     
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_172102239_   2247 GAAATACTGACTACTT-----TTACCACATTTAATGTGAGCTTCTTT-TT 2290
                         i   v iv  iv v  ----- i i  v v    ---i i   i v -i 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAA---AAACTTTTGTGCT 669

  chr2_172102239_   2291 TTA---TATAGTATCAAATAAG------------CCACATATTGGGAGAA 2325
                          i ---v i v      iv   ------------     v v        
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_172102239_   2326 GACATTTGTAA--CACATATTATGATGAAGAATTGTTACGGAGAA-ACAT 2372
                         i i     i  --  i    i-    i i i i vv  ivv    - i  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATC-TGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_172102239_   2373 GCAGAAACATTCTA-AACTCAAGAAGAAAAAGACACACAATCTAAT-AGA 2420
                         iv    - - ii  -       v  v         v i  i i   -?i 
  L1M4_orf2#LINE/    769 AAAGAA-C-TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_172102239_   2421 AAATGGGCAAAAGTCATGATCAGGCTTTGCAC--AAGAATGAAA-ACAGG 2467
                                    i viv   vi  i v  v v --     -  v -   --
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-GATATACA-- 863

  chr2_172102239_   2468 AATGCCTAGTGA---CATTAAAAATAGATGCTCAACTGTATTTATAAT 2512
                             v i i i ---   v    ---          vvi ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAA---GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.05 (46 / 907), avg. gap size = 2.39 (110 / 46)  


2198 18.03 0.72 0.96  chr2_172118061_172120015.rev      501   916 (1039)    L1M4_orf2#LINE/L1      242   656 (252)  

  chr2_172118061_    501 ACACAGCAGCAGTGATCAAGACAATGTGGTATTGACATAAGGACAGACAT 550
                            v   vi    i         i       i  i        i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_172118061_    551 ACAGATCAGTGGAACAGACTTGAACGTCCGGAAATAAATCCAAAAGTGTC 600
                          i      i     i   v    iv    i        i   v --ii i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA--CATT 339

  chr2_172118061_    601 TATGGTCAATTGATTTTTGACAAGGGTGGCAAGGCCTTGCAATGAAGAAA 650
                                          i          v    i  v v     ii    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_172118061_    651 GAAAAGTCTTTCTAATAAATGGTGCTAGGACAAATGTATAGCTGCATGTT 700
                            v       ii  i          i      v  v   ? ii    i-
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC- 438

  chr2_172118061_    701 AAAAAAAATGGAGTTGGATACCTACCTTATACCCTATACTAAAATTAACT 750
                         -    i    i       iv       i i   v     v          
  L1M4_orf2#LINE/    439 -AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_172118061_    751 CAAAGTGGATCAACCACCTAAATAT--GAGCTAAAACTATAAACCCTTTA 798
                             i       ?vv        i --                v ii   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_172118061_    799 GAAAAAAACCTAGGAGCAAATCTTAATGACCTCAAATTTTGCAATGGATT 848
                            i     v    ? i       vi      iiii  vv       v  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_172118061_    849 CTTAGATATGGCACCAAAAGCATGAGTAATGAAA-AAAATTTAGATAAAT 897
                                   i           ii  i  ii   -    vv         
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_172118061_    898 TGGACTTCATCAAAATTAA 916
                                            
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAA 656

Transitions / transversions = 2.00 (48 / 24)
Gap_init rate = 0.01 (4 / 415), avg. gap size = 1.75 (7 / 4)  

1021 17.70 7.41 0.41  chr2_172118061_172120015.rev     1221  1463 (492)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr2_172118061_   1221 AAAATTAA---CCTCTCTGTTTCAAACAATAACATCAGGAAAGTAAAAAG 1267
                                 --- i i v  i      vi i vi    i      i     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_172118061_   1268 ACAATCTACACAATGGGAGAAAGTATTTG-AAATCATATATCTGATAAGG 1316
                             i i   v           i      -                    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_172118061_   1317 GACTTGTATCTAAAATATGTAAGGA-TTTTTGTAA---AA----AAAAAA 1358
                                   i i     i   i  -i i  ii  ---  ----     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_172118061_   1359 AAAAA------AATTTACAAGTGGGCAAAATATCTAACCAAACATTTCTC 1402
                          v   ------    ? v  i        iv  i i vi i         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_172118061_   1403 CAAAGAATAACATACAAATGGCTAATATGCACAAGAAAAGATGCCTGACA 1452
                                -i i           i    v     v          iii   
  L1M4_orf2#LINE/    849 CAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_172118061_   1453 TCACTAGTCAT 1463
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 3.20 (32 / 10)
Gap_init rate = 0.03 (7 / 260), avg. gap size = 2.71 (19 / 7)  


 360 26.98 5.56 0.00  chr2_172184326_172188360.rev       14   139 (3896)    L1M4_orf2#LINE/L1      557   689 (219)  

  chr2_172184326_     14 ATCTTCAT-ATTCAGAGATAGGTAAAAAGTCCTTAGATAAGACACAGAAA 62
                               i - iiiv i v    i  viiv i        v     vi   
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_172184326_     63 GCAATCGCCATATAAGAAAAGAT-GATAAA-----CTTCATCAAAATTAA 106
                            vvv  v i v       i  -      -----               
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_172184326_    107 AAACTTTGGCTCACCAAAAGGCACCATTGAAAA 139
                                v iv vi    i i   i  ii i  
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

Transitions / transversions = 1.43 (20 / 14)
Gap_init rate = 0.02 (3 / 133), avg. gap size = 2.33 (7 / 3)  

2261 15.74 10.86 0.89  chr2_172184326_172188360.rev     1975  2425 (1610)    L1M4_orf2#LINE/L1        4   499 (409)  

  chr2_172184326_   1975 AAAGATAATCTGTGTTCATGGATTGGAAAAC--AATGTTGTTAAGACGGC 2022
                                vi ii                i  --   i         i   
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_172184326_   2023 AATACTATCTAAGC-AATCTGTAGATTCGATGGAATCCCTATCAAAATGC 2071
                               vi i  ii-i    ii      i i v               v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_172184326_   2072 CAA-TACCTTTCTTTTTGCTGAAATGGAAAAATTGATCC----------- 2109
                           i- i     ---     v     v  v  ii      -----------
  L1M4_orf2#LINE/    104 CAGCTGCCTTT---TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_172184326_   2110 -----------------------------AATAATAT---AAAAGAAGAA 2127
                         -----------------------------  i   v ---          
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_172184326_   2128 AAAGGTTGGAAGACTTACACTCTCTGATTTCAAAACTTACTACAAAGCTA 2177
                         v  i      i    i     ii ii                        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_172184326_   2178 CAGTAATTAAAAGAGTGTGGTACTGGCATAAGGATAGACACATAAACCAA 2227
                                i  i v                           i   i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_172184326_   2228 TTAAATAGAATTGAGAGTCCAGAACTAAACTCATCCATCTATGGCAAATT 2277
                          vi                     v     i   v   i     iv    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_172184326_   2278 GATTTTTAACAAGGTTGGTAAGACCATTCTAGGAGGGAAAGAATAGTCTT 2327
                               ii      v  vi          v v -                
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTT 399

  chr2_172184326_   2328 TTCAAAGAATAGTGC-ATGACAACTAAATATCCACATGCGTAAGAATGAA 2376
                              vi   i    -iv       ii   ?        iv         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_172184326_   2377 ATTGAACCTCTACCTCACACCATATACAAAA-TTAACTCAAAATAGATCA 2425
                         i   i   i                      -            i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

Transitions / transversions = 2.33 (49 / 21)
Gap_init rate = 0.02 (9 / 496), avg. gap size = 5.89 (53 / 9)  

 564 19.23 3.08 0.00  chr2_172184326_172188360.rev     2827  2956 (1079)    L1M4_orf2#LINE/L1      503   636 (272)  

  chr2_172184326_   2827 ACCTAAAT---AGAACTAAAACCATAAAATTCTTGGGATAAAACATTGAA 2873
                                 ---   i       i      i    i i v       v i?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_172184326_   2874 GGAAATCTTTATTACCTTGGATTTGGCAATGGAGTCTTAGATATGACACC 2923
                          v       ii v       i  v        vv                
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_172184326_   2924 AAA-GCAAGAGAAACAACAACAAAAATAAATTAA 2956
                            -   vi  v     v iv       i  v  
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

Transitions / transversions = 1.00 (12 / 12)
Gap_init rate = 0.01 (2 / 134), avg. gap size = 2.00 (4 / 2)  

1411 11.04 2.34 4.01  chr2_172184326_172188360.rev     3246  3544 (491)    L1M4_orf2#LINE/L1      615   908 (0)  

  chr2_172184326_   3246 AATAAATAAATAAAAATAAAATAAATTGGACTTTATCCAAATTAAAAACT 3295
                           i   - i -       i -            i   v            
  L1M4_orf2#LINE/    615 AACAAA-AGA-AAAAATAGA-TAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_172184326_   3296 TTTGTACATCAAAGAACACTATCAAGAACAGTGAAAAGACAACTTACAGA 3345
                              i v      i             -              ii     
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAA-AGTGAAAAGACAACCCACAGA 710

  chr2_172184326_   3346 ATGGGAGAAGGGAGAAAATATTTGCAAATCATACATCTGATAAAGGTCTA 3395
                                  -------                 i         i  v  v
  L1M4_orf2#LINE/    711 ATGGGAGAA-------AATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_172184326_   3396 ACATCCAGAA-----AAAGAACTCTTAATCACTCAACAACAAAAATACAA 3440
                         ii        -----            -iv      i  i     v    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATAAAAAGACAA 802

  chr2_172184326_   3441 ACAATCCAATTTAAAAATGGGGAAAGGACTTGAAAAGATATTTCTC-AAA 3489
                          i  i      ?         v      i     v   i       -   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_172184326_   3490 GAAGATA-AAAAATGGCCAAGAAGCACATGAAAAGACGATCAACATCGTT 3538
                                - v          v               i v        i??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_172184326_   3539 AGTCTT 3544
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.91 (21 / 11)
Gap_init rate = 0.03 (9 / 294), avg. gap size = 2.11 (19 / 9)  


 737 28.65 11.99 5.81  chr2_172269735_172272768     1455  1988 (1046)    L1M4_orf2#LINE/L1       46   612 (296)  

  chr2_172269735_   1455 AAGATACAAATAGTATTTCCCTAAAATAAGCTGTAGATTTAATG-ACTTT 1503
                              ivv    ----i    i   v i v  ii     i  i - v ii
  L1M4_orf2#LINE/     46 AAGATGGCAATA----CTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chr2_172269735_   1504 CTAT--------------------TCACAGAACTTGACAAGCTGACCCTA 1533
                             -------------------- ii     v            i    
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr2_172269735_   1534 AAATTTATATATTTTATATAGCAAAGCAAAGGGCCAAAGATAGCCAAAAT 1583
                              i    i--------- v  v    i  i  v ii          i
  L1M4_orf2#LINE/    142 AAATTCATATG---------GAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_172269735_   1584 AATCCTGAA---GAAGAACAA-GTGTCAGTAATTACACTACTACCAGGTA 1629
                             i    ---         -  vvv  v v i     v --   iv -
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC--CCAATT- 229

  chr2_172269735_   1630 TTAAGAATTGATATAAAATCATCATAATTAAGAC--TGTGATA------T 1671
                          i  i v  iv  i   iii ivi    i     --    i  ------ 
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_172269735_   1672 AAGTTCAGAGATA--GATCCATGGACCAAAAC--AGAATCTAGAA-TAAG 1716
                            vvi   v   --    v     vi i  i--   i  i    -   -
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA- 328

  chr2_172269735_   1717 ACTTGTGAATAGATGAATAAACAGAAACCTCACCTATGACAAAACTGGCA 1766
                           iii iv  vv   ivi  --------i v ii vi     iiv  v  
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAA--------TTGATTTTCGACAAGGGTGCCA 370

  chr2_172269735_   1767 TTGCACATT--AGGGGGAGGGAGGA--CTATTTAATAAA-AAT------- 1804
                         vvi -    -- v     ii  iv --  v  i  i   -ii -------
  L1M4_orf2#LINE/    371 AGAC-CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_172269735_   1805 TAATTGATTAGCCATAT--AAGGGAA--AAGCTAAACTGACTCCAACTTT 1850
                         i  i  iv  ?   i  --  ii   --   i i----   i  v  i i
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTG----GACCCCTACCTC 465

  chr2_172269735_   1851 ACACTATACACAAAAGTCAATTTTAGATGGATAGATGACTTAAA-----G 1895
                             i   i      i i  i iv i      vi?v   i    ----- 
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_172269735_   1896 GG--AAAATTTTTTAACT-TTAGAAGAAAATGTAGAA-TATCATCTTTTT 1941
                         i --    i v vv    -           ii   i?-  -v     iv 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA-AATCTTCGT 564

  chr2_172269735_   1942 AACCTTGAGGGAAGGAAGGATTTCTTA-ATGCAAAACTGGAAACATAA 1988
                         i      i vv i v  v i       -  iii v  iii  i  i  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

Transitions / transversions = 1.88 (98 / 52)
Gap_init rate = 0.05 (29 / 567), avg. gap size = 3.28 (95 / 29)  

 305 25.31 12.65 6.53  chr2_172269735_172272768     2298  2542 (492)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr2_172269735_   2298 AAAAT---AAACTATGGCTTCTCCAAAGACATCAAGATACCAAGAGAGTG 2344
                              ---     v v ivii  v  i    i-----  i     i    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACAC-----TATCAAGAAAGTG 693

  chr2_172269735_   2345 AAAACATAAGCTAAAAACTAGAGGAAGATACTCAC----CACACAT---A 2387
                             v i  v i v i v i ii   i   i ii ----  i i  --- 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_172269735_   2388 TAATGGCCTTGGGGTTAGAACTGAGACTATAT---GAGCTCCTTTGAATC 2434
                            v  v    vivii    -------     ---  i   i vii v  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAA-------TATATAAAGAACTCTTACAACTC 786

  chr2_172269735_   2435 AATAA-AAAAA--------ATTTAATAGAAAAATAGAAAAACAACATGAA 2475
                              -     -------- iii   v?      i iv   vi iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_172269735_   2476 TAG-CATTTCAC---AGAAGA---ACAATTCTATG--TGGTACACATTTG 2516
                            -      v ---      ---    ----   --iii  vi  iv  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAA----ATGGCCAATAAGCACATG 882

  chr2_172269735_   2517 AAAATATGCTCAACCTCATTAACCAT 2542
                             v         v   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (38 / 23)
Gap_init rate = 0.05 (13 / 260), avg. gap size = 3.62 (47 / 13)  


 440 23.64 1.82 0.91  chr2_172321655_172329936.rev       62   171 (8111)    L1M4_orf2#LINE/L1       21   131 (777)  

  chr2_172321655_     62 ACGGTTTGGAAGGATCAATATTGCTAAAATGTTCCTACTCCTCGAAGCAA 111
                          i  v       iv i       i   i   vivv      i i  vii 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr2_172321655_    112 TCTACAGATTCAATGCAATCCCTACCAAAATATCA--TGACATTCTTCAC 159
                                      i          i      vi  --  v -  i  ii 
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGC 119

  chr2_172321655_    160 AGAAATAGAAAA 171
                               v  v  
  L1M4_orf2#LINE/    120 AGAAATTGACAA 131

Transitions / transversions = 1.60 (16 / 10)
Gap_init rate = 0.02 (2 / 111), avg. gap size = 1.50 (3 / 2)  

3221 26.77 1.00 0.55  chr2_172321655_172329936.rev     4992  5895 (2387)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_172321655_   4992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATGTCGTGAAAAT 5041
                              ii i  i     i      i v      v i   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_172321655_   5042 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5091
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_172321655_   5092 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5139
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_172321655_   5140 TGTGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCAAAAAG 5189
                          i     viiv  ii  v  v v  v     iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_172321655_   5190 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTATAAGGC 5239
                                i      vv       v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_172321655_   5240 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5289
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_172321655_   5290 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5337
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_172321655_   5338 ATCTGATCTTTGACAAACCTGAGAAGAACAAGCAATGGGGAAAGGATTCC 5387
                          vi    i  i     ivv  vv    v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_172321655_   5388 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCT 5437
                           v  i  i              v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_172321655_   5438 GAACCTGGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAGATGGA 5487
                            vi    i    v   i     v    i         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_172321655_   5488 TTAAAGACTTACATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAAC 5537
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_172321655_   5538 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5586
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_172321655_   5587 AAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5636
                         vi    v       vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_172321655_   5637 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5686
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_172321655_   5687 CAGGCAACCTACAGAATTGGAGAAAATTTTTGCAATCTACTCATCTGACA 5736
                         v  i     i       v         v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_172321655_   5737 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5786
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_172321655_   5787 AAAACAA----CCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTT 5832
                           i    ----   v  i? v  i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_172321655_   5833 TTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5882
                         i  v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_172321655_   5883 CATCACTGGCCAT 5895
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  

1085 20.58 1.33 17.70  chr2_172321655_172329936.rev     6630  7081 (1201)    L1M4_orf2#LINE/L1      120   497 (411)  

  chr2_172321655_   6630 AAAAATTAAAAAA--AATCCTAAAATTTATAAGGAACCACAAAAAAACCA 6677
                          i     i v  i--i           i   v    vii   iii v   
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_172321655_   6678 -AATAGCCAAAGCTATTCTGAGCAAAGGGAATAAAACTGGAGGAATCACA 6726
                         -          i v  ii   iv  iii   i   ii       v     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_172321655_   6727 TTACCTGACTTTGAATTATACTACAGAGCTATAGTAACCAATACAGCAGC 6776
                         i v  ii i  ii  viv       i     i     i   v    ----
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG---- 265

  chr2_172321655_   6777 ACTATCTACAACAGCCAAGATTTGGAAGCAACCTAAGTGTCCATCAACAG 6826
                         --------------------------------------------------
  L1M4_orf2#LINE/    266 -------------------------------------------------- 265

  chr2_172321655_   6827 AGGAATGGATAAAGAAAATGTGCTACATATACACTAACATGAAAACAGAC 6876
                         ------------------    v   -------- ii   i ii i    
  L1M4_orf2#LINE/    266 ------------------TGTGGTAC--------TGGCATAAGGATAGAC 289

  chr2_172321655_   6877 ACATAGACCAAGAGAACAGAATAGAGAACCAAGAAAGGAATTCATGCATC 6926
                          i     i   vi   i     v    ii v     vi  ii   i   i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_172321655_   6927 TACAGT-AATTCATTTTCAACAAAGGTGCCAAGAACATACACTGGGGAAA 6975
                           ii  -    v      i    i          v   v  v        
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_172321655_   6976 GGACAGTCTCATCAATAAATGGTGCTGGGGAAACTGGATATCTATGTGCA 7025
                          i i     iv    i             iv         ? i ii    
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_172321655_   7026 GAAGAATGAAACTAGATCCCTATCTCA-AC-ATATACAACAATCACATCA 7073
                         i         ii i  i     i    -  -        v   i vv   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_172321655_   7074 GAATGGAT 7081
                         i       
  L1M4_orf2#LINE/    490 AAATGGAT 497

Transitions / transversions = 2.68 (67 / 25)
Gap_init rate = 0.02 (7 / 378), avg. gap size = 12.29 (86 / 7)  

1556 22.81 2.76 0.69  chr2_172321655_172329936.rev     7357  7790 (492)    L1M4_orf2#LINE/L1      466   908 (0)  

  chr2_172321655_   7357 ACTTCATCTAAAAAAAAAAAATCAGAATGGATTAAAGACTTAAGTCTAAG 7406
                           vi   v  v     vv  v   i       i ?    i   i v    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_172321655_   7407 ACCTCAAACTATGAAACTACTAAAAGAAAACTTCGGGGAAACTCTCCAGG 7456
                          v  v       i     vi  i        v v  ? v  v   i iv 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_172321655_   7457 ACATTGGTCTGGGCAAAGATTTCTTAAGTAATGCC-CCACAAGCATAGGC 7505
                           v    vi i     v i       ii -   v -   v     i i  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGC 614

  chr2_172321655_   7506 AACCAAAGTGAAAATGGAGAAATGGAATCACAT-AAAGTTAAAAAGCTTC 7554
                            v    vi     i  v    v i iiv   -   i       -   i
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTT 663

  chr2_172321655_   7555 TGCACAGCAAAGGAAACAATCAACAATGTGAGAAGATAACCCATACAATG 7604
                           ii vv       v  v     v  v    i    i      i v    
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_172321655_   7605 GGAGAGAATATTTGCAAATTATCCATCTGACAAGGGGTTAATAACCAGAA 7654
                              i             i  vi      i     ii vi  v      
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_172321655_   7655 TATATAACAAGCTCAAACAACTCTATAGGAAAGAAATCTGAGAATCTGAT 7704
                                vi i   vv       v   iv   i i - vi v  i ii  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAAT 812

  chr2_172321655_   7705 TTTAAAAT---------ATGTGAATA-ACATTTCTCAAAAGAAGACATAC 7744
                          ?v     ---------  v      -         v        i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_172321655_   7745 AAATGGCAAAGAGGCATATGAAAAGGTGCTCAACATCATTGGTCAT 7790
                                v  v i   i        i            ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.04 (49 / 47)
Gap_init rate = 0.02 (7 / 443), avg. gap size = 2.14 (15 / 7)  


1283 25.55 8.15 2.42  chr2_172339807_172342522.rev     1013  1466 (1250)    L1M4_orf2#LINE/L1        4   483 (425)  

  chr2_172339807_   1013 AAAGAAGTATGATATTCATAGGAAGAGAGAATCAGTAT-GATAAGAGTGT 1061
                              vi viv  i     i ivv ii   v i i   - v     -  v
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-TGG 52

  chr2_172339807_   1062 GAATATTCTCCAAATTGATCTAAAGAGTCCATGTAACTTCAATTAAAATC 1111
                         v    i  i             v   v  v i i  iii v  i      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_172339807_   1112 TCAACAGAGCTTGTCACAGAA-CTGGCAAGCTGACTCTAAAATTACATAT 1160
                         i  i v vvi  v ii     -i  i        ii        -     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT-CATAT 151

  chr2_172339807_   1161 ACAACAGCAAAGG-TCAAGAATAGCCAAGACACTCTTGAA------GAAT 1203
                         iv  vv    i  -i v           i   v       ------   i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_172339807_   1204 A-----GGAG-ACTTGCTCTACCCAGATATCAAAACTTAATAGAAAGCCA 1247
                          -----    -   ii v  v    -  v          v  v     i 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTA 250

  chr2_172339807_   1248 CAGTAATTAAGCCATTATGATACTGACATAGAGGCAGACA---------- 1287
                                i   v  v i  i     i    ii ii     ----------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_172339807_   1288 -------GAATGGAGAGCCCAGAAACAGACTCACACATATGTGAAAACTT 1330
                         -------    v     i       i i  i  i    v i  ivv v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_172339807_   1331 GCTCTGTCACACATCTGGTATTACAGATCATTTA----GGAAAGAAGGGT 1376
                          v i viv   vi---   iii -   i    i ----        vi  
  L1M4_orf2#LINE/    351 GATTTTCGACAAG---GGTGCCA-AGACCATTCAATGGGGAAAGAATAGT 396

  chr2_172339807_   1377 CTAAACAAGAAATAGTACTGGAA-AATTGGATATCCATATAGGAAAAAAA 1425
                           vvv   v    i  i    i -  i      ?   i  -- v    i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT--GCAAAAGA 444

  chr2_172339807_   1426 AAGTGGAATTGGACTCCTACCTCACACCATACCCCAAATTT 1466
                          --  i i      i                iv v   v  
  L1M4_orf2#LINE/    445 A--TGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

Transitions / transversions = 1.45 (68 / 47)
Gap_init rate = 0.03 (16 / 480), avg. gap size = 3.00 (48 / 16)  

 959 27.05 8.86 1.36  chr2_172339807_172342522.rev     1789  2228 (488)    L1M4_orf2#LINE/L1      436   908 (0)  

  chr2_172339807_   1789 TGCAAAAGACATGA--TCTCATTCTTTTTT---ACTATACACCAAATTTC 1833
                                  -    -- ivv ii i vii ---  i   i  v   v  -
  L1M4_orf2#LINE/    436 TGCAAAAGA-ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT- 483

  chr2_172339807_   1834 AATTCCAGTTTAAATTAAAGATACAAACGTGAAAAGCTAAA--------- 1874
                           i  v iv -ii  i ?   ivi   i  -  i       ---------
  L1M4_orf2#LINE/    484 AACTCAAAAT-GGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAA 531

  chr2_172339807_   1875 TTTTTAGAATAAGTTATGAGAAAATATTTTTATGACCTTAGGTT------ 1918
                         i i      v  ivi  ii ?iv v  i  ii       i    ------
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_172339807_   1919 -----TCTTAAATAAGATACACAAAGTTC---TAACTGAGGAAG---TGT 1957
                         -----     i   v  i  vv    iv ---i   vi i   i--- i-
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA- 630

  chr2_172339807_   1958 GATGAATTTTACTTCATTAAAATTAAGAACTCCTGATCATCAAAAGACTA 2007
                            i    vv       i        i    ii  vv v     i   - 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC-A 679

  chr2_172339807_   2008 CCATCAAGAAAATGAAAAGACAAGTCATAATCTGGAAGAAGATATTTGCA 2057
                          i         i           vi  i ivv   i    i         
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_172339807_   2058 ACACACATAACCAACAAATCACTGGCATCTAGAATTTATGAAAA--TTTT 2105
                          vv  i   v ii i  ivv   v i   i     v   i  i -- i  
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_172339807_   2106 ACAAATCAATA-TAAAAAGA-AAA-AACGTGATAGAAAAATGAGCAGAAA 2152
                             v      -        -   -   vii  v?       i   i ii
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_172339807_   2153 GCATGAACAAACATTTC-ACAGACAAGAAACAGGAATGACCAATAA--AC 2199
                         iiv    i i       -v  i v    v i vi    i       --  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_172339807_   2200 ATGAAAAGATGCTTAACCTTATTAGTAAT 2228
                                      i   v i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (75 / 41)
Gap_init rate = 0.04 (18 / 473), avg. gap size = 2.50 (45 / 18)  


 833 26.90 8.81 2.38  chr2_172377470_172379403.rev      496   915 (1019)    L1M4_orf2#LINE/L1      176   622 (286)  

  chr2_172377470_    496 CTAGGACTATTTTGTAAAAG--GAACAAAG--GGGGTGATTTTCTGTATC 541
                          i ii  v  i   v     --        --  i -  i iv vv -  
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG-GACTCACACT-TC 223

  chr2_172377470_    542 AGAAATT-AGAATATAATACAAAGGTGCAGTAATTAAAACTGGGTTGTG- 589
                         vv  v  - i  iv  v       v i       i  i  v v  v  i-
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr2_172377470_    590 -----TAGAACCAAACAAATAGATTCATAGTG-AAAATAGAGAGCCCAGA 633
                         -----  iiivi i   v      iv  i vi- i   v     i     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_172377470_    634 AATG--CCCATAAATATATGGG-AATTTACTGTATGACAAAGTTGGCATC 680
                            i--      v  v     v-    v i v -i     i v  v  --
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTT-CGACAAGGGTGCCA-- 370

  chr2_172377470_    681 GGAC--TTCAGTGGGGGAAAAGATAGACT----AACAAATGGCACTGAGA 724
                         i   --    i     i  i -    v  ----         ii   i  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_172377470_    725 AAATTAGCTACCTATATAGAGAAAAATTAGGTTGGATCCCTACCTCATAC 774
                         v  i i v  ? i i  iv i  i   v i      i          i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_172377470_    775 TATTTTTAAAAATATAACCCAAA-T---------ATCTACATGTGAAGGG 814
                         i  v vi      -    i    - --------- i   v    i ii v
  L1M4_orf2#LINE/    470 CATATACAAAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_172377470_    815 TAAAACTATAAAATTAATAGGA-AAAACATAGAAGAATATATTTGCATCC 863
                                      i vv   i -         i? v v  v  i iiv  
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_172377470_    864 ACAATGTAGGAAACAATTTCTTTTTAAAAAAGAC--CAAAAGCACA--CA 909
                         viiivv    v  iii      --- i v v   --          --  
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTT---AGATATGACACCAAAAGCACAAGCA 615

  chr2_172377470_    910 A-AAAAG 915
                          -     
  L1M4_orf2#LINE/    616 ACAAAAG 622

Transitions / transversions = 1.36 (64 / 47)
Gap_init rate = 0.05 (22 / 447), avg. gap size = 2.14 (47 / 22)  

 225 30.72 4.10 7.85  chr2_172377470_172379403.rev     1150  1442 (492)    L1M4_orf2#LINE/L1      627   908 (0)  

  chr2_172377470_   1150 AATTGCTAGATTTGATCATATCAAAATGAAGGATTTGATCATA--TCAAA 1197
                            v v  i   v  iivi        v  ii i  -- ii i--     
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTT--TTGTGCTTCAAA 674

  chr2_172377470_   1198 ATAGAGGATTCTGTTCAATGAAGAATATTATAAG-CAGTTAACAGATTAG 1246
                         -----   iv  -----  v     vi v v   -  iiiv     v i 
  L1M4_orf2#LINE/    675 -----GGACACT-----ATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_172377470_   1247 AAGGG--TTTTTAAAAAGACTAAAACAGACAAAAGTCCTCCCTAAAATAT 1294
                         i  ii-- v   iv   vvv  v v v  i  ii v i -------i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT-------GTAT 757

  chr2_172377470_   1295 ACAAAATACACAAAGAATGCCTATA---CA----TCAGAAGATAAAGAAC 1337
                         v  i    i i      iv i  i ---  ---- v i    i   v   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_172377470_   1338 CTCAATCATAGTAAATGGGGAGAAGGACATGAATATGCAGTTCACAGAAG 1387
                          -    i?v --       v -     iv      vi  v   v vi   
  L1M4_orf2#LINE/    808 C-CAATTWAA--AAATGGGCA-AAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_172377470_   1388 GGAAAACTTGAATGGTTAAAAGATATATAAAGAGGTGGTCAACCTCACTG 1437
                         iii v ivii     ii  v iii i  i  i  i  v     v   ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_172377470_   1438 TAATC 1442
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.41 (52 / 37)
Gap_init rate = 0.04 (12 / 282), avg. gap size = 2.92 (35 / 12)  


3009 25.98 2.56 1.34  chr2_172437514_172444505.rev     5604  6500 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_172437514_   5604 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 5653
                               i i  i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_172437514_   5654 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCTCCATCAAGC 5703
                            v     v      v i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_172437514_   5704 TACCATTGACTTTCTTCACAGAATTAGAAAAAACGACTTTAAATTTTATA 5753
                          v   vivi i  i  ii     v v  v  ivi  iii    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_172437514_   5754 TGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAAAAGAA 5803
                              viiv  ii  v  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_172437514_   5804 CAAAGTTGGCGGCATCACACTATCTGACTTCAAACTATACTACAAGGCTG 5853
                                  v  vv       vi ii i      viv        i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_172437514_   5854 CAGTAACCAC-ATGGCATGGTACTGGTACCAAAAAAGATATATATATATA 5902
                               i  v- ii ii         i i----  i    v i     v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCAT----AAGGATAGACATATAGA 296

  chr2_172437514_   5903 TATATCAATG-AACAGA--TCAGAGCCTTCAGAAATAACACCACACATCT 5949
                          ----     -  i   -- v    -- i         vv   i    i 
  L1M4_orf2#LINE/    297 T----CAATGGAATAGAATTGAGAG--TCCAGAAATAAACCCATACATTT 340

  chr2_172437514_   5950 ACAATCATCTGATCTTTGACAAACCTGACAGAAACAAGCAACAGGGAAAG 5999
                          iii   vi    i  i     ivv  v  ii v  vv   ii       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_172437514_   6000 GATTCCCTGTTTCATAAATGGTGCTGGGAAAACTGGCTAACCATATGCAG 6049
                         i  vvi  v  iv i              v      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_172437514_   6050 AAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAA 6099
                           i v    ii         v   i     v                   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_172437514_   6100 GATGGATGAAAGACTTAAACATAAGACCTAAAACCATAAAAACCGTAGAA 6149
                         i      v ?    i    ii     v       i      vi v     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_172437514_   6150 GAAAACCTAGGCAATACTATTCTAGACAGAGGCATGAGCAAAGACTTCAT 6199
                               v    ?ivv v v   vv   vvv  vv ii    v ii   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_172437514_   6200 GACTGAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 6249
                         iiv ivi            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_172437514_   6250 ATCTAATTAAACTACAGAGCTTCTGCAAAGCAAAAGAAACTGTCATGCAA 6299
                          ii v  i   v vv i i   i  iivvv    i  v   i   v v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_172437514_   6300 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATC 6349
                              v  i     i                 v       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_172437514_   6350 TGACAAGGGGCTAATATCCAGAATCTACGAAGAACT--TA---------A 6388
                            i     i  vi          v  ii       --  --------- 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_172437514_   6389 ACAAAAAAACAAA---CCTCATCAAAAAGTGGGCAAATGTTATGAACAGA 6435
                          i     i     ---  iv  i?    i        v v v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_172437514_   6436 CACTTCTCAAAAGAAGACA--CTGATGCAGCCAGCAAACATGTGAAAAAA 6483
                           i     v        i -- vi   --    ii  i  ii      i 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGA 888

  chr2_172437514_   6484 AGCTCA---TCACTGGTCAT 6500
                         v     ---   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (130 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.92 (35 / 12)  


2781 14.81 9.05 16.15  chr2_172460973_172464777      994  1965 (1840)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_172460973_    994 AGAGATCCCCAGTGTGTGGATTGGAAAACTAAGGATTGTTAAGATGGCAG 1043
                            v     vv  vii          i   v iv               i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_172460973_   1044 TTCTTCCCAAATTGATCTATAAATTCAGCAAAATCCCTATCAAAAAAAGA 1093
                          v  i              i i     i iv              ---vv
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA---TC 102

  chr2_172460973_   1094 ACAGCTGGTTTTTTTGAAGAAATTGACAAGCTAATCCTAAAGTTTATATG 1143
                         v      vi       v               i        i  i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_172460973_   1144 GAAATACAAAAGATCCAACATAAGCACAACAGTTTTGAAAAAGAA---CA 1190
                              i   ii  i   iv   iv  v    i i           ---  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_172460973_   1191 AAGTTAGAGGATTTACACTTCCCTATTTCAAAACTTAATGTGAAGCTACA 1240
                              i     i i         v             v iii        
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_172460973_   1241 ATAATCAAGAT--TGTGATACTGGCATAAGTATAGTGATATAGATTAATG 1288
                         i         i--    i            v    vv        i    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_172460973_   1289 GAACAGAAATGAGGGTCTACAAATAAACTCTTACAGGTATTGTCAATTTA 1338
                            i    v    i   i v        i v    vv   v       v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_172460973_   1339 TTGTTGATTAAAGAACACCAAGGCAATTCACTGAGGAAAGGATTGCCTTT 1388
                           v i  i--   iiii     i v     v  i      i  v i    
  L1M4_orf2#LINE/    353 TTTTCGAC--AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_172460973_   1389 -CAA-GAATGGTGCTGAGGTTGGACATAGTGGCTCACACCTGTAATCCCA 1436
                         -   -i          i --------------------------------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGG-------------------------------- 418

  chr2_172460973_   1437 GCACCTTGGGAGGCCAAGGCAGGAGGATTGCTTGAGGCCAGGAATTTGAG 1486
                         --------------------------------------------------
  L1M4_orf2#LINE/    419 -------------------------------------------------- 418

  chr2_172460973_   1487 ACCAGCCTGGGCAACATAGTAAGACCTCATCTCCACAAAAAGTAAAAATA 1536
                         --------------------------------------------------
  L1M4_orf2#LINE/    419 -------------------------------------------------- 418

  chr2_172460973_   1537 AAATAAAAATAGTAATTAGACAATCGGATATTCACATACAGAATA-TGAA 1585
                         -------------------    ii     ?i     i  i  v -    
  L1M4_orf2#LINE/    419 -------------------ACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_172460973_   1586 TTTAAATCCTTACTTCATACCATATACAAAAATTAACTCAAAATA-ATCA 1634
                         v  ii i  i   i   i                          i-    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_172460973_   1635 TAGACCTAAATGTAATAACTAAAA-TACTAAACTTTTCAAGGAAAACAGA 1683
                         ?              v i      -  iv     i  vi i       v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_172460973_   1684 -----AAATCTTCATGACCTTAGTTTAACCA---GTTT-TTAGAT--GAC 1722
                         -----        i       i v   iv  ---    -      --   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_172460973_   1723 ACCAAAA--ACAGG--------------------AAATTGAACTTAATAA 1750
                                --   i --------------------      i    v  v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_172460973_   1751 AAATGTTAAGCTTTTGTGCTTCAAAAGACACCAATAAGAAA--------- 1791
                             vvv  i               i     i vi      ---------
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_172460973_   1792 ------ACAGACTGGGAGAAAATATTTGCAAATC-------TGATATAGG 1828
                         ------     v                      -------     vi  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_172460973_   1829 ACTCACATCCAGAACATATAAATAACTACTT-CAACTCAATAATAAAAAG 1877
                            iii        i       v    -   -                  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACT-CTTACAACTCAATAATAAAAAG 798

  chr2_172460973_   1878 ACAAAC--TCCAATTAAAAAATAGATAAAAGATTTGAAGAAACAT----- 1920
                              i--i      ?      i ii   i        v i    -----
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_172460973_   1921 ------AGAT---------GTCTATAAGCACATGAAAAAATGCTCGACAT 1955
                         ------    --------- i v               i      i    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_172460973_   1956 TAGTTATTAG 1965
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.76 (90 / 51)
Gap_init rate = 0.03 (23 / 903), avg. gap size = 10.65 (245 / 23)  

1011 25.36 15.29 5.95  chr2_172460973_172464777     2490  3313 (492)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_172460973_   2490 ATATATCATGTTCATGGATTGAAAGGCCCACTAT------GATATAAATT 2533
                             vi               i   i ii v   ------   ivv   v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_172460973_   2534 CTCCCAAAATAGCT-TATAGATTCATCGCAACTCCAATCAAATTTTCAAT 2582
                              v    v v -  i       v     ii  v      v ii  --
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA-- 105

  chr2_172460973_   2583 GTGTTCGGCTTTTTTTAGTGAAACGTGATAAGCTATTTCTAAAATATATA 2632
                         -- i --  i      ivv    i-   i     iv i       vi   
  L1M4_orf2#LINE/    106 --GCT--GCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATA 150

  chr2_172460973_   2633 AAGAAGAGCAGAGAACCAAGAAGAGCCACAAGC--TGTTGATGAATAACA 2680
                         vi   iv   ii i   v    v     -  i -- v    vi  v  v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCA-AAACAATCTTGAAAAAGAAGA 199

  chr2_172460973_   2681 AGGATGTGAAAGGACTTTGATATTAT---ATATCAAAAATTTTTTTGAAG 2727
                          vi v  vii      i-- i i vi---  v      v  vi vii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTC--ACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_172460973_   2728 ATCATGAAGTAATGAAGAGAGTGTA-CATTAGCACAGGAAAAAA------ 2770
                         v - i--      v    v     i-i i i   i i i v i ------
  L1M4_orf2#LINE/    248 CT-AC--AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_172460973_   2771 -ACCAATATAATAAA-----GAGCCCATAAA-AGATCTTTGCATATATTG 2813
                         - i    iv    i -----   i   v   - i i iv i   v   v 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_172460973_   2814 ACAAT--ATA--CAACAGAAAAGGCACTTCAAAGC-----AATAGGAAAA 2854
                         v    --  v-- i   --- i  ii --   ii -----   i  i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACA---AGGGTGC--CAAGACCATTCAATGGGGAAA 389

  chr2_172460973_   2855 GGAAGGTTTTTTGTTTTTGTTTTTTTTCAATAAACAGTGCTGGCACAACA 2904
                          i vi  i    ---------------   i   ii       v     v
  L1M4_orf2#LINE/    390 GAATAGTCTTTT---------------CAACAAATGGTGCTGGGACAACT 424

  chr2_172460973_   2905 GACTAGCCCTATAGCAGCAAAAAAAT-------------TACCTCATACT 2941
                          iv  ?  vi  ----      i   -------------       i  i
  L1M4_orf2#LINE/    425 GGATAKCCACAT----GCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_172460973_   2942 ATATGTTGAAGATTG-TTCCAAGTGGGAT--GAAACCAAAATGTGAGAGG 2988
                             ii-i  i   i-i  v  i   -  --? i   v      i    v
  L1M4_orf2#LINE/    471 ATATAC-AAAAATTAACTCAAAATGG-ATCAWAGACCTAAATGTAAGAGC 518

  chr2_172460973_   2989 CAAAACTACAAAGCATGTAACAAGAGAATAT-----TAA--CT------- 3024
                         i       i   i viv  i-    i  i  -----   --  -------
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAG-AAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_172460973_   3025 -------------ATA--TTTTTA-ACATAACCATAAAAAAAACCGAGCT 3058
                         -------------  i--  i   - i  i  - iv    iv  -i   -
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGAC-ACCAAAAGCAC-AAGC- 614

  chr2_172460973_   3059 AACCATAAAGGAAAACTA--TTATTTGAAGAT-ATTAAAATTAAAATGTT 3105
                            - -    i    v  -- v v   i vv -  i          vv  
  L1M4_orf2#LINE/    615 AAC-A-AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_172460973_   3106 ACTATATTT--ATAAACATT---------GTGAAAAGACAAACCACAAAG 3144
                         -i i ii  -- vii   i ---------            v     i i
  L1M4_orf2#LINE/    663 -TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_172460973_   3145 TGGGAAAAGAT-TCTGCAA----CACAACTCATAAAGGAGTAGTAGCCAG 3189
                              i  i  - i     ----i i v  v    i   v v   v    
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_172460973_   3190 AATATATAAAGAACCACCTGCAAATTCATGA------GA----------- 3222
                                       i- i i   v iv  i ------  -----------
  L1M4_orf2#LINE/    762 AATATATAAAGAACT-CTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_172460973_   3223 -----AAAATGGG---AGAACTTTAACACACTTCATTCACCAAAGATGAA 3264
                         -----        ---  i i  v  i v  v --   v       v  v
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACAT--TTCTCCAAAGAAGAT 858

  chr2_172460973_   3265 ATCCAAATGGTCAAAAAATATATGAAATG-TGATCAGCCTCATGAACACC 3313
                           v       i   v  ii i      v -  v   i v   ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (126 / 81)
Gap_init rate = 0.06 (51 / 901), avg. gap size = 3.43 (175 / 51)  


 740 22.02 2.29 5.05  chr2_172579416_172583757      505   722 (3620)    L1M4_orf2#LINE/L1      140   351 (557)  

  chr2_172579416_    505 TAAAAATTGTGTGGGAGAAAAGCAAAGGTCCCAAAATAGCCAAAGCAAAT 554
                              v ii i   ---   v    i  v    i          i   vi
  L1M4_orf2#LINE/    140 TAAAATTCATATGG---AAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_172579416_    555 TTGAGAAGGAA---CAAAGTTGGAGGACTTAGACTACCTGGCTCCAAGAC 601
                             i  i   ---               i v   v  iiii i   i  
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_172579416_    602 TTACTATAAAGCTTAAGAAATTGCTACAGCATAGTGCTGCTGGCTGGCAT 651
                               i      vv  v   iivv    ii i  i   -------    
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG-------GCAT 279

  chr2_172579416_    652 ATGAATTGATAAACAGATCAATGGAACAGAATAGAGAGCCCAGAAATAGA 701
                          v i  v  i v i            i     v     i         i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_172579416_    702 TCCA-AAATTATAAAGTCA-TTG 722
                         i   - v   -  vi    -   
  L1M4_orf2#LINE/    330 CCCATACATT-TATGGTCAATTG 351

Transitions / transversions = 1.82 (31 / 17)
Gap_init rate = 0.03 (6 / 212), avg. gap size = 2.67 (16 / 6)  

 825 24.61 1.05 1.57  chr2_172579416_172583757     1148  1338 (3004)    L1M4_orf2#LINE/L1      344   533 (375)  

  chr2_172579416_   1148 GTCATTTGATTTCTAACAAAGTTGCCAAAGCAATTCAGTGGGGGCAAGGA 1197
                             v       iii    i v      ii v     i     i-   i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAA 392

  chr2_172579416_   1198 AA--CTTTTCAACAATTGATGCTAGAATAACTAGATATCAGTGTGGGAAA 1245
                         v --           v  i    i i i    i    ? viii  vi   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_172579416_   1246 ATTAATGAACCTAAATCCCTACCTCACACCATATACTAAATTTGATTTGA 1295
                         i--      vi ii i                    v   v  i i ii 
  L1M4_orf2#LINE/    443 G--AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_172579416_   1296 GATGAATCATAGACCTAAATGCAAAAGCTGAAGTTATAAAGCT 1338
                         i   i    ?           i  i    i  ii      i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

Transitions / transversions = 3.50 (35 / 10)
Gap_init rate = 0.02 (3 / 190), avg. gap size = 1.67 (5 / 3)  

 802 25.41 4.56 0.98  chr2_172579416_172583757     3544  3850 (492)    L1M4_orf2#LINE/L1      591   908 (0)  

  chr2_172579416_   3544 AGA-ATGATCAATAAAAA---AAAAAAAAGAAAAAGAAATTGATAAATTA 3589
                            -    -  vi    i---  iv  v i  i  i    v        i
  L1M4_orf2#LINE/    591 AGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_172579416_   3590 GATTTCACTAAAGATAAAAATGTCTTTTCCTCAAAATATAGCATTAAGAA 3639
                           i    ii   iv      iv i v v i     iv i vi  i     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_172579416_   3640 AATGAATAGGCAAGGTATTAACTGGGAGAGAATATTAGCAAAACATATAC 3689
                          i    v  i   vvi ivi v       i      v     v      i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_172579416_   3690 ACAACAAAGGACTAATATCCAGGATATAT--------CCTAAATCTCAAT 3731
                         vii i  i     vi       i      -------- i  v v      
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_172579416_   3732 GACATCAATGATAAACAACCTAGTCCTAAAAATTGGCAAAAGACTGGAAC 3781
                         i i vv  -  i   i    i i i-?      v      i  i v   i
  L1M4_orf2#LINE/    790 AATAAAAA-GACAAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAAT 837

  chr2_172579416_   3782 AGA-ACTTCACAAAATAAGGTATACAAATGGTCAATAA-CACATGAAAAA 3829
                            - i   v v   v   i           i      -          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_172579416_   3830 GTGTACAACATCATTAGTCAT 3850
                         i  iv        ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (48 / 29)
Gap_init rate = 0.03 (8 / 318), avg. gap size = 2.12 (17 / 8)  


2060 23.70 10.26 3.54  chr2_172610754_172613443.rev     1367  2214 (476)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_172610754_   1367 AGAAATACATCATGTTCATATACTGGAAGGCTCAATGTTATTAAGATAGC 1416
                          i i   ivi         iv i      i  i   i  i       i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_172610754_   1417 AATTCTCCCCACATTCAATTTTAGATTCAATGTAATC----TTAAGATTA 1462
                            v       v   v vi vi        i i    ---- i  i  i-
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC- 102

  chr2_172610754_   1463 GTCAGA-ACTTTTTAAATAGAAATTAACCACCTGATTCCAAAATGTATAC 1511
                         -i   v-i i    vvii       i  v v     i i     vi   i
  L1M4_orf2#LINE/    103 -CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_172610754_   1512 AGAAAT--AAGG--TCAAGAATAATCGAAACAATCTTTAAAAA-----AT 1552
                         i     --    --i v      ii i          v     ----- i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_172610754_   1553 AAAGATGTGGGACTCACACTACC-------AGGAATCAATAGAAAGTTAC 1595
                             v  vi           v  ------- ii v i v  v    i   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_172610754_   1596 ACTAATCCAGACAGTACGATATTGACAGAAAAACAGACA-----ATGAAT 1640
                          v     v       ii i  i  i  v  ii i     -----  v   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_172610754_   1641 G----AGAA----AAGTCCAGATGTAGATCCACACGTGTAAGTTCAATAT 1682
                          ----    ----i        vi  i i   i  i v  v v     vv
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_172610754_   1683 TTTTTTGTTAAAAACGCACCAAGGC-ATTCA------------------- 1712
                         v    i -- v  iv ii     i -     -------------------
  L1M4_orf2#LINE/    352 ATTTTCG--ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_172610754_   1713 --CA-CAAATTATACTGAAACAAGTGGATATCCACATG--GAACAACAAA 1757
                         --  -     vi i   ii    v      ?       --i  v  ii  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_172610754_   1758 CCTTAATCCCTTTCCTCATATTGGACATGAAAAATAACATGAGATGGATC 1807
                         v-  iiv   i v     i iiiv i ii    v    vii i       
  L1M4_orf2#LINE/    450 G-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_172610754_   1808 ATGGACATAATTTTAATAAGCTAAAACTAAAAACCTTCCAGAAGAAAACA 1857
                          ?i   v   v v   -i           v   v  iii           
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAA-GAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_172610754_   1858 TTAGGAG---AGCTTCATGATCTCCTTGGGGTAGACAAAGAT--ATTAGG 1902
                          -   ? --- v    i   ---       v   i   v i --v    i
  L1M4_orf2#LINE/    548 T-AGGNGTAAATCTTCGTGA---CCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_172610754_   1903 CATGA-ACCAGAA-----AACACTAATAGAAATTTTTAAAATTAATAAAC 1946
                         i    -    i  ----- i  vi  v     ------    vi     i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAA------AAATAGATAAAT 637

  chr2_172610754_   1947 TGGACATGATTAAAACTAAAAACTTCCAGTTATACAAAAAA-A--GTTGA 1993
                              v v  i    i         ii-  vv v    ii - --i ii 
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAA 686

  chr2_172610754_   1994 GAATATGAACAGGCAAACCACAAACTGAGAGAAAA-ATGTGCACAAAACA 2042
                            vi    v  i   v     i v  i       -  v    --  v  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA--AATCA 734

  chr2_172610754_   2043 TGTAATCTGCATAAAGGACTC--ATCCAGAATATGTAGGTAAATAACACC 2090
                          i  -    -    i     i--           i  ----  v   v i
  L1M4_orf2#LINE/    735 TATA-TCTG-ATAAGGGACTTGTATCCAGAATATATA----AAGAACTCT 778

  chr2_172610754_   2091 TACAACT-AATAACAAAAAGACAAATAACCTAATTTTAAAATGGGCAAAA 2139
                                -     i                i    ?v            i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_172610754_   2140 GATGTGAATA--CATGAGTCCAAAAGGAGATA--------GTCGATAACC 2179
                            v      --   vvv      - i     -------- i i    v 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGC 877

  chr2_172610754_   2180 ACATTAAAAAAACAATCCTTAATAGCATTAGTTAT 2214
                             v    i ---- v  i  i v  ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGA----TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (120 / 77)
Gap_init rate = 0.04 (38 / 905), avg. gap size = 3.08 (117 / 38)  


 294 10.71 0.00 0.00  chr2_172663720_172665772.rev      497   552 (1501)    L1M4_orf2#LINE/L1      141   196 (712)  

  chr2_172663720_    497 AAAATTCATAAAGAAAGACAAAGGACCCAGAATAGCCAAAACAATATTGA 546
                                   vi    vi   i                       v    
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_172663720_    547 AAAAGA 552
                               
  L1M4_orf2#LINE/    191 AAAAGA 196

Transitions / transversions = 1.00 (3 / 3)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.00 (0 / 0)  

3352 16.14 1.66 2.62  chr2_172663720_172665772.rev      843  1567 (486)    L1M4_orf2#LINE/L1      191   908 (0)  

  chr2_172663720_    843 AAAAAAAGAACAAAACTTGAAGGACTCAACACGTTCTGATTTCAAAACTT 892
                             i         i-   i        -   v i ii            
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAG-TTGGAGGACTCA-CACTTCCCAATTTCAAAACTT 238

  chr2_172663720_    893 ACTTCAAACCTATGATAATCAAGACCATGTGACACTAGCATAAGGACAGA 942
                            v    v   iii          vi    ii   i         i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_172663720_    943 CATACACATGAATGGAACTGAACTGATAGTCCAGAAATAAAACCATAGAT 992
                             i v  v       iv   i   v              v     v  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_172663720_    993 TTA-GGTCAGTTAATCTTGGAGAAGGTTGCAAAGACAATTCAATGGGGGA 1041
                            -     i  i  i  v  v    v   v     v           - 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-A 387

  chr2_172663720_   1042 AAGAAGAGTCTTTTCAACAAATGGTGATGGGACAACTGGATCTCTATCAT 1091
                              v                    v              v? i -   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA-CAT 436

  chr2_172663720_   1092 -CAAAAGAATAAAGTGGGATCCCCTTTCCTCACACCATACATAAAAATTA 1140
                         -         i    v   i   -- v            i i        
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCC--TACCTCACACCATATACAAAAATTA 484

  chr2_172663720_   1141 AC-CAAAATTGATCACAGTCCCAAATTTAAGAGGTAAAACTACAAAACTC 1189
                           -      v     ?  v  i    v      v        i       
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_172663720_   1190 TTAGAAGAAAACACAGGAGTAAATCTTCATGACCTTTGGTTAGACAATGG 1239
                                      i   ?          i       v      i      
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_172663720_   1240 TTTCTTAGATAATGAGACCAAA-GCATAAGCAACAAAAGAAAAAACAAAT 1288
                                    -   v      -   i                  i i  
  L1M4_orf2#LINE/    585 TTTCTTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_172663720_   1289 AAACTAGGTGACA--AAAATTTTAAAACTCTTGTGTTTCAAATGACACCA 1336
                            i i iivv  --      v-      i     i      v     i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_172663720_   1337 GTAAAAAAATGAAAAAAATAACATACAGAATGGGAGAC--TATTTGCAAA 1384
                         vi  i   i      i -i   vi             v--          
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGA-CAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_172663720_   1385 TCATGTATCTAATAAAGCACCTGTATCCAGATTCATATAAATTGGTGTAC 1434
                             i     i    i v  i          v -       ---------
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAAT-ATATAAA--------- 771

  chr2_172663720_   1435 AAACTCTTATAATT---TGGTAAAAAAAAAAA-GACCCAACTAAAAAATG 1480
                         i        i  i --- ii      i v   -i      i ?       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_172663720_   1481 GGCAAAGGATCTAAGTTGACATTTATCAATAAGATATATACAAGTGGATA 1530
                                   i i i v       v  v v ii v        i   vi 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_172663720_   1531 ATAAACACATGAAAAGATGCACAGTCTCCCTAGCCAC 1567
                             i               v  iiv  v????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (68 / 45)
Gap_init rate = 0.03 (18 / 718), avg. gap size = 1.72 (31 / 18)  


2774 19.04 1.48 10.38  chr2_172850069_172851869.rev      501  1309 (492)    L1M4_orf2#LINE/L1      172   908 (0)  

  chr2_172850069_    501 ATAGCCATATCAATCCTGAGAAAGAAGAACAAAGCTGAAGGCATCATGCT 550
                                v v     i   i              i  i   vv   ii  
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_172850069_    551 TCCTGATTTCAAAATACGTTATGAAGCTACAGTAATCAAAACAGTATGGT 600
                            ii         iviii  ii                i     i    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_172850069_    601 ACTGGCATGAAGACAGACATATAC-TCAATGGCACAAAAAAGAGAGCCCA 649
                                 i i  i         v-       v i i  vv     i   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_172850069_    650 GAAATAAATCCA--CATATATCAGTCAGTTGATCTTCAATAAGGGTGCCA 697
                                 i   --   v   -i    i     i   i i          
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTAT-GGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_172850069_    698 AGAATACACAATGGGGAAAGGATAATCTCTTCAATAAATGGTGTGGGGAA 747
                            vi iv            i   i   i     i        iv    v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_172850069_    748 AATTGGATATCCACAGACAAAAAAATGAAATTGGATCCTTAT-----ATC 792
                           i      ?     vi     i      i     i  i  i----- i 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_172850069_    793 ATACACAAAAATCAACTCAAAATGACTTAAAGACTTAAATTTAAGACCTG 842
                            i        i           iv i ?    i     v     v  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_172850069_    843 AAACTATAAAACTCCCAGAAGAAAACAT-GGGGAAAAACTTCATGACATT 891
                                       ii            -  ? v   v    i    v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_172850069_    892 GGTGTTAG-CAAAGATTTTATTTATATATATTCATATAATATATTCATAA 940
                           -     -   v i   i-------------------------------
  L1M4_orf2#LINE/    571 GG-GTTAGGCAATGGTTTC------------------------------- 588

  chr2_172850069_    941 AATCATAAAATATTTATATTCATATTTATATTAGGAATATAAAATATTTT 990
                         ------------------------------    --    i --------
  L1M4_orf2#LINE/    589 ------------------------------TTAG--ATATGA-------- 598

  chr2_172850069_    991 ATGAATATACCCCAAAAGCACAGGTAACAAAACCAAAAATAAACAAGTGG 1040
                         --------- v           i i       vv       i i  i v 
  L1M4_orf2#LINE/    599 ---------CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_172850069_   1041 GATTACACTGC--CTAAAAAGCTTCTGCACTGCAAAGAAAAAAAATCATT 1088
                           i v  iiiv--i      -   i  ii  v     i v vv -   vv
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA-TCAAG 687

  chr2_172850069_   1089 GGAATGAAAAGACAACCTATGCAATGGTAAATAACATTTGCAAGCAATAT 1138
                         ii i             i iiv     v i v  i        iiv    
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_172850069_   1139 TACTGATAAGGGGTTAATCTTCAAAATATATAAGGAACCCCTACAACTCA 1188
                         vv          ii vi v i  i         i    i i         
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_172850069_   1189 ATAACACAAAAAGTAATTATGCAATTTAAAAATAGGCTAAGAACTTGAAT 1238
                             i v   i vv   v iv     ?      i   v   i i      
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_172850069_   1239 AGACAGTTCTCCAAAGAAGATATACAAATGACCAACAGGCATATGAAAAA 1288
                              v                        i    i i   i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_172850069_   1289 ATGCTCATTGTCACTGAGGGC 1309
                                vii   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (100 / 50)
Gap_init rate = 0.02 (13 / 737), avg. gap size = 7.38 (96 / 13)  


3250 26.98 0.55 0.55  chr2_172877752_172884149.rev     4999  5906 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_172877752_   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5048
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_172877752_   5049 GGCCATACTTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCCAGC 5098
                            v     i     iv i  i  i        i  v     i   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_172877752_   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_172877752_   5147 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5196
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_172877752_   5197 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAAGC 5246
                                i      vv   ii  v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_172877752_   5247 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGGTC 5296
                                 i   i    ii         i iv ii i   v      i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_172877752_   5297 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5344
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_172877752_   5345 ATCTGATCTTTGACAAACCTGAGAAAAACGAGAAATGGGGAAAGGATTCC 5394
                          vi    i  i     ivv  vv  i v ivvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_172877752_   5395 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5444
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_172877752_   5445 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5494
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_172877752_   5495 TTAAAGACTTACATGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAT 5544
                          i ?    i  v    v i v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_172877752_   5545 CTAGGCATTACCATTCAGGACATAGGCATGGGCAA-GGTCTTCATGTCTA 5593
                         v    ?i v viv   iv   v v  vv i     -   -   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATA 595

  chr2_172877752_   5594 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTA 5643
                         vi            vvi          vv     v  i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_172877752_   5644 ATTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5693
                           i   v v  i i      ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_172877752_   5694 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5743
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_172877752_   5744 AAGGGCTAATATCCAGAATCTGCAATGAACTCAAACAAATTTACAAGAAA 5793
                          i  i  vi          v ii  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_172877752_   5794 AAAACAAATAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5843
                           i           v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_172877752_   5844 CTCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5893
                            v           vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_172877752_   5894 CATCACTGGCCAT 5906
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3240 26.60 0.66 0.44  chr2_172955191_172961598.rev     5011  5916 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_172955191_   5011 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5060
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_172955191_   5061 GGCCATACTTTCCCAAGGCAATTTATAGATTCAATGCCATCCCCATCAAG 5110
                            v     i-     ivii  i  i        i  v     i     i
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_172955191_   5111 CTACCAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTTC 5158
                         v v   iivi i  i  ii  -      -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_172955191_   5159 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAA 5208
                                 viiv  ii  v  v v  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_172955191_   5209 GAACAAAGCTGGAGGCGTTACGCTACCTGACTTCAAACTATACTACAAGG 5258
                                 i      vv i  i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_172955191_   5259 TTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5308
                         i        i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_172955191_   5309 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5358
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_172955191_   5359 TCTGATCTTTGACAAACCTGACAAAAACAA-CAATGGG-AAAGAATTCCC 5406
                         vi    i  i     ivv  v   i v  v-       -       vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_172955191_   5407 TATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5456
                          v  i  i          i   v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_172955191_   5457 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATCCAAGATGGAT 5506
                           ii    i    v   i     v              ii   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_172955191_   5507 CAAAGACTTAAATGTTAGCCCTAAAACCATAAAAACCCTAGAAGAAAACC 5556
                           ?    i       v  vv       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_172955191_   5557 TAAGCA-ATACCATTCAGGACATAAGCATGGGCAAAGGCTTCATGACTAA 5605
                           i ?i- v i -   iv   v vi vv i     v  i   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_172955191_   5606 AACACCAAAAGCAACGGCAACTAAAGCCAAAATTGACAAATGGGATTTAA 5655
                         i            vvi     v    vv     v  i    v   i  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_172955191_   5656 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAGAGTGAGC 5705
                          i   v v  i i   i  ii vv    i  v    v  vv i     iv
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_172955191_   5706 AGGCAACC-AGAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 5754
                           i     - v               v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_172955191_   5755 AGGGCTAATATGCAGAATCTGCAAAGAAGTTAAACAAATTTACAAGAAAA 5804
                         i  i  vi   v      v ii      v ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_172955191_   5805 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5854
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_172955191_   5855 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCCCATC 5904
                           v        i  vi viii     i ii          i    i  v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_172955191_   5905 ATCACTGGTCAT 5916
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


 375 25.74 0.00 0.00  chr2_172962210_172964358.rev      501   601 (1548)    L1M4_orf2#LINE/L1       40   140 (768)  

  chr2_172962210_    501 ATTGTTAAAGTGACCATACTGTCCAAAGCAATCTACAGATTCAATGCAAT 550
                                 ii  i v     vi     vii              i     
  L1M4_orf2#LINE/     40 ATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

  chr2_172962210_    551 CCCTAACAAATTACCAACATCATTTTTCACAGAATTAGAAAAAAGAATCC 600
                              v    v v   i vv v     ii     v v  v  ivvi    
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chr2_172962210_    601 T 601
                          
  L1M4_orf2#LINE/    140 T 140

Transitions / transversions = 0.86 (12 / 14)
Gap_init rate = 0.00 (0 / 101), avg. gap size = 0.00 (0 / 0)  

2503 25.69 4.48 0.53  chr2_172962210_172964358.rev      900  1658 (491)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr2_172962210_    900 AGAAA--GAAAAAGGAATCCTCATATTCATATGGAAACAAAAAAGAACTC 947
                              --  v  ivvi     v v             iiv  ii  v iv
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_172962210_    948 AAATAGCTCCTAAGCAATCCTAAGAAAAAGGAGTAAAGCTGGAGGCATCA 997
                         i      -- v  i     i i i   i i  ii    i      vv   
  L1M4_orf2#LINE/    170 GAATAGC--CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_172962210_    998 AATTACCTGATTTCAAATTATATTACAAGGTTATAGTAACCAAAACAGCA 1047
                         v i v  ii        viv  i     i i  i     i   i    ii
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_172962210_   1048 TGGTACTGGTATAAGAATAGACACATAGATCAATGGAACAGAACAGAGAA 1097
                                  i     i       i              i    iv    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_172962210_   1098 CCCAGAAATAAAGCCACATACCTACAACCAACTGATCTTCGACAAAGTCA 1147
                         i           v   i i ii  iiii   i    i        i vii
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_172962210_   1148 ACAAAAATATACACTGGAAAAAGGACACCCTATTCAACAGATGTTGCTAG 1197
                         v   i vi  v  v   ii    i i vi  v       i   v    i 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_172962210_   1198 GAAGATTGGATAGCCATATGCAGAAGAATGAAACCGGACCCATACCTCTC 1247
                           vi i      ?   i     i         iii      v      v 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_172962210_   1248 ACCATAGACAAAAATTAACTC----TAGA----AGA-----ATTTAAGGC 1284
                               v              ---- i  ----   -----  v    iv
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_172962210_   1285 CCAAAACTA--AAATTCCCAGACAAAAGCTTAGGAAAAACTCTTCTGGAC 1332
                          i       --   i  ii   vi   i v    ?iv  v     vv   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_172962210_   1333 ATTGGCTCTAGGCAAAGAATTTATGACTAAGTCCTCAAAAGCAAACACAA 1382
                         v    v -       v iv  iv iiv  v v vi        v vi   
  L1M4_orf2#LINE/    568 CTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_172962210_   1383 CAAAAACAAAAATAGGCAAATGAGACTTAATTAAA-TTAAAAAGCTTCCG 1431
                              iv        ii    vi     v  i   -       -   ii 
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTG 665

  chr2_172962210_   1432 CACAGCAAAAGAAGCAATCAGCAGAATAAACAGACAACCTACAAAATGGG 1481
                         ii vv    i  vi v    iv i i i  v        i   i      
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_172962210_   1482 AAAAAATATTTGCAAACTATGCATCCAACAAAGGGCTAATATCCAGAATC 1531
                          i              ii  ii   ii i  i  i  vi          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_172962210_   1532 TACAAGGAACTC---------AACAAGAAAAA-ACAAATAGCACCACTAA 1571
                           i  i      ---------  i  v     -       i v v i ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_172962210_   1572 AAGGTGGGCAGAGGACATGAA----CATTTTTCAAAAGAAGGCATATAAG 1617
                           ii      i    iv    ----     i  v       ii   i  i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_172962210_   1618 CAGCCAACAA--ACATGAAGAAATGCTCAACATCGCTAATCAT 1658
                         ii     i  --       i i            i????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (128 / 64)
Gap_init rate = 0.02 (13 / 789), avg. gap size = 2.92 (38 / 13)  


3288 26.98 0.44 0.44  chr2_173005006_173011281     4877  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_173005006_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_173005006_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_173005006_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_173005006_   5025 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_173005006_   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_173005006_   5125 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_173005006_   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5222
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_173005006_   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_173005006_   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_173005006_   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_173005006_   5373 TTAAAGATTTAAACGTTAGACCTCAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?   ii    i  v   v  v    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_173005006_   5423 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5472
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_173005006_   5473 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5522
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_173005006_   5523 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5572
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_173005006_   5573 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5622
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_173005006_   5623 AGGGCTAATATCCAGAATCTACAATTAACTCAAACAAATTTACAAGAAAA 5672
                         i  i  vi          v  i  vv     vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_173005006_   5673 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5722
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_173005006_   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5772
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_173005006_   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1582 20.25 0.59 25.77  chr2_173338108_173344764     4962  6156 (501)    L1M4_orf2#LINE/L1        1   894 (14)  

  chr2_173338108_   4962 TGGAAGGACATTCCATGCTCATGGATAGGAAGAATCAAGATCGTGAAAAT 5011
                              i  i  i     i        v      v i  v  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_173338108_   5012 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGGCATCCCCATCAAGC 5061
                            v     v     iv i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_173338108_   5062 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5109
                          v    ivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_173338108_   5110 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5159
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_173338108_   5160 AACAAAACTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5209
                               ii      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_173338108_   5210 TATGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5259
                           ii    i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_173338108_   5260 AATGGAACAGAAC--AGAGCCCTCGGAAATAATACCACACATCTACAACC 5307
                                i    i--    i  --i       vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_173338108_   5308 ATCTGATCTTTCACAAACCTGACAAAAACAAGGAATAGGGAAAGGATTCC 5357
                          vi    i  iv    ivv  v   i v  vvv   i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_173338108_   5358 CTATTTAATAAATGGTGCTGTGAAAACTGGCTAGCCATATGTAGAAAGCT 5407
                           v  i  i           v  v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_173338108_   5408 GAAACTGGATCCCTTCCTTACATCTAATACAAAAATTAATTCACCAGGCG 5457
                            ii    i    v   i   ----------------------------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACA---------------------------- 468

  chr2_173338108_   5458 CAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTAAGGTGCGTGG 5507
                         --------------------------------------------------
  L1M4_orf2#LINE/    469 -------------------------------------------------- 468

  chr2_173338108_   5508 ATCACCTGAGGTAAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACT 5557
                         --------------------------------------------------
  L1M4_orf2#LINE/    469 -------------------------------------------------- 468

  chr2_173338108_   5558 CCATCTCTACTAAAAATACAAATGTCAGCCGGGCATGGTCGTGGGCACCT 5607
                             -----------       ----------------------------
  L1M4_orf2#LINE/    469 CCAT-----------ATACAAA---------------------------- 479

  chr2_173338108_   5608 GTAATCCTGGCTACTTGGGCAGCTAAGTAACAAAAATTGCTTGAACCTGG 5657
                         --------------------------------------------------
  L1M4_orf2#LINE/    480 -------------------------------------------------- 479

  chr2_173338108_   5658 GAAGCGGAGGTTGCAGTAAGCCAAGATCGTGCCACTGCACTCCTGCCTAG 5707
                         --------------------------------------------------
  L1M4_orf2#LINE/    480 -------------------------------------------------- 479

  chr2_173338108_   5708 GCGACAAGAGCGAGACTCCATCTCAAAAAAAAAAAAAATTAATTCAAGAT 5757
                         ------------------------------------      i    i  
  L1M4_orf2#LINE/    480 ------------------------------------AATTAACTCAAAAT 493

  chr2_173338108_   5758 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5807
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_173338108_   5808 AACTTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCCTGA 5856
                            v    ?i- v i -   iv   v v  vv i     v ii   i ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_173338108_   5857 CTAAAACACCAAAAGCAATGGCAATAAAAGCCAAAATTGAGAAATGGGAT 5906
                         v  vi            vvi    i     vv     v  v    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_173338108_   5907 CTAATTAAACTAAAGAGCTTCTGCACAGCGAAAGAAACTACCATCAGAGT 5956
                         i v  i   v v  i i   i  ii vv i  i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_173338108_   5957 GAACAGGCAACCTACAGAACGGGAGAAAATTTTTACAATCTACCCATCTG 6006
                            v  i     i      i          v   i   vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_173338108_   6007 ACAAAGGG-TAATATCCAGAAT-CACAAAGAACTTAAACAAATTTACAAG 6054
                          i  i  i- vi          -i i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_173338108_   6055 AAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 6104
                              i     i     v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_173338108_   6105 CCTCTCAAAAGAAAACATTTATGCAGCCAATAGACACATGAAAAAATGCT 6154
                         ii    v      i i  vi viii       ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_173338108_   6155 CA 6156
                           
  L1M4_orf2#LINE/    893 CA 894

Transitions / transversions = 1.64 (148 / 90)
Gap_init rate = 0.01 (12 / 894), avg. gap size = 26.25 (315 / 12)  


 210 17.86 12.50 0.00  chr2_173629143_173630772.rev      239   294 (1336)    L1M4_orf2#LINE/L1      171   233 (675)  

  chr2_173629143_    239 AATAGTCAACACAAC------ACAGAAGAAAAAAGT-GGAGAACTCATGC 281
                              i   v    i------ v       v     -    i     ii 
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_173629143_    282 TACCTAATTTCAA 294
                          v  i        
  L1M4_orf2#LINE/    221 TTCCCAATTTCAA 233

Transitions / transversions = 1.50 (6 / 4)
Gap_init rate = 0.03 (2 / 63), avg. gap size = 3.50 (7 / 2)  

2046 22.57 7.05 1.72  chr2_173629143_173630772.rev      501  1138 (492)    L1M4_orf2#LINE/L1      237   908 (0)  

  chr2_173629143_    501 TTATAATAAAGCTA--GCAATTAAGACAGTGAAATATTGGTGAATGAACA 548
                            iv i       -- i   i         vii  i   iiv v i i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_173629143_    549 GACATGTAGATGAATGGAACAGAATGTGA-AGTCCAAAAATAGACCCACA 597
                              i     v       i     -   -      i     i     i 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATA 335

  chr2_173629143_    598 TAAACATAGTCAACTGATCTTTTACAAAGGAACAAAGACAATTCAATGGA 647
                         i vvi  i     i    i  iv    i  vi v     v         i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_173629143_    648 GAGAAGACAGTCTTTTCAAGAAATGGAGCTGGAAAAACTGGATGGCCCAT 697
                           i ii i           v      v     i v        i?  - i
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC-AC 434

  chr2_173629143_    698 ATGCTAAAAAAAATGAATCTACACACAGACCTTATGCCTTATACACACAT 747
                             --    i      vi iv  v vv    i ii  v      v v  
  L1M4_orf2#LINE/    435 ATGC--AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_173629143_    748 CTGTACCTCAGAAATG-ATTATAAACCTAAATGTAAAACACAAAACTATA 796
                         ---  v    -     -  i ? i            i vvi         
  L1M4_orf2#LINE/    483 ---TAACTCA-AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_173629143_    797 AAATTTCTAGAAGAAAATACAGGGGAAAATCTAAATGACATTTAGTTTGG 846
                            i ii          i i   ? v      vvi    v  vi   v  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_173629143_    847 TGATAAGTT---AGATACAACAACAAAAGCATAATCCATGAAAGAAAAAA 893
                         ii  iiv  ---     ii   v        i  v v ii          
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_173629143_    894 --AATGAATGTTGGACTAGACTGAAATTAAAAACTTCTTCTCTACTAAGG 941
                         --i  i   --      vv iii             i viv  v v    
  L1M4_orf2#LINE/    629 TAGATAAAT--TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_173629143_    942 ACACTGTTAAGA---TGAAAAGCAAAACCACAGACTGGA---------CT 979
                              i i    ---       vv  v       v   i---------i 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_173629143_    980 GCAAAACTCATATCTGATAAAGGACTTGTATCTAAAATATGCAAAGAATT 1029
                              v vi           i           i i     ii      i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_173629143_   1030 CTC-CAAA-CAATAAGAAAAGAACCAAAT-------TTTTTAAATGGGCA 1070
                           i-   v-      v    ii  -    -------  ?vv         
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCA 825

  chr2_173629143_   1071 AA----------AGACACCTCAACAAAGAAGA----CAGATGGCAAACA- 1105
                           ----------     ii  vv         ----  i     v  i -
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_173629143_   1106 GCATATGAAAAGATACTCAATATCATCTGTCAT 1138
                            i          i     i    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (86 / 54)
Gap_init rate = 0.03 (20 / 672), avg. gap size = 2.80 (56 / 20)  


3201 25.45 2.36 0.11  chr2_173800918_173805160.rev     2864  3751 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_173800918_   2864 TGGAAACACATCCCATGCTCACGGATGGGTAGAATCAATATTGTGAAAAT 2913
                               v i        i   i    v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_173800918_   2914 GACCATAATGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAAA 2963
                          i v   v v  v   vii       i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_173800918_   2964 TAC-AACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCAC 3012
                          v - i iii -  i  ii     v v  v  ivii  i          i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_173800918_   3013 ATGAAACCAAAAAAGAGCATGCATAGCTAA---------GCAAAA--AGA 3051
                            i  viiv  ii  v vv v     i  --------- v    --   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_173800918_   3052 ATAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACAATAAAGCC 3101
                          i   vi      vv       v  ii        viv   v i     i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_173800918_   3102 ATAGTCACCAAAACAGCATGACACTGGTCCAAAAATAGGCACATAGACCA 3151
                          i   v i   i    ii  ii     ivi  ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_173800918_   3152 ATGGAACAGAATAGAGGACCCAGAAATAAATCCAAATACTTACAGCCAAC 3201
                               i     v   iii           i   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_173800918_   3202 TGATCGTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTT 3251
                             iv  i    i vviv   i v   vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_173800918_   3252 TTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAA 3301
                                             i  i   v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_173800918_   3302 ACTGGATCCTCATCTCTCACCTTATATAAAAATCAACTGAACATGGATTA 3351
                         ii    i  ii i   v    v    i      i    v  v      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_173800918_   3352 AGGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGGTAACATT 3401
                         ?i   i    iv     v  i           v ii      iv     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_173800918_   3402 GGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAA 3451
                           ?iv  vi    vv   v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_173800918_   3452 CCCAAAAGCAAATGCAATAAAAACAAAGATGAATAGTTGGGACTTAATTA 3501
                         v         v v    i    iv   i  ii   iv v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_173800918_   3502 AACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAGA 3551
                           v v  i i      ii vv    i iv  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_173800918_   3552 CAACCCCCAGAGTGGGAGAAAATCTTCACAATCTATACATCTCACAAAGG 3601
                               v    i           v  ii   vii   i    v i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_173800918_   3602 ACTAATATCCAGAATCTACAACAAACTC--ACA--TCAATAAGAAAAAAA 3647
                            vi          v  i  vi     --   --       v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_173800918_   3648 CAA-T--CCCA--TAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCA 3692
                            - --    -- ?    i     v     iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_173800918_   3693 AAAGAAGATATGCAAATGGCCAACAACCATATGAAAACATGCTCAACATC 3742
                                    i           i  v  i       v            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_173800918_   3743 ACTAATGAT 3751
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.44 (131 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.44 (22 / 9)  


1888 23.35 4.32 7.83  chr2_173834534_173836261      501  1241 (487)    L1M4_orf2#LINE/L1      194   908 (0)  

  chr2_173834534_    501 AGAAAAATCAAATTGGAGGATTCACATTACCTGATTTCAAGACTTAATCC 550
                             i  iv  i        i     i v  ii       i     v v 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_173834534_    551 AAAGCTCTGGTAATTAAAACAGTATAGTATTGGTATAAAGACAAAAATAT 600
                               vii     i  i     i i   i   i    i  i i v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_173834534_    601 AGAT----GCAACAGAATT------TCATATTTAGACCCAGACATATTAT 640
                             ---- v  i      ------i  v vv  i     v    -    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-TTAT 342

  chr2_173834534_    641 AATCCATTGAGTTTTAACAAACATGCCAATGTAATTAAATGCAGAAAAGA 690
                         ii  v     v   ii    ivi      viiv   v    -i i     
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGA 391

  chr2_173834534_    691 AAAATCTTTTTAATAAATAGTGCTGGAGGAGTAGGATATGCATATGAAAA 740
                          v i      i  i    i       iiv iiv     ?v  i   v   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_173834534_    741 AAAGGGAACCTTGACTTCT---TTATACCAAATGCAAAAATTAATTCAAG 787
                          i iv   vi v   ii  --- i i    v  i          i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_173834534_    788 ATCCAGGGT---AAACCTAAATGTAAAAGCGAAAACTATAGTACTTCTAT 834
                           ---  i --- i            i   v         iv   ii  v
  L1M4_orf2#LINE/    492 AT---GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_173834534_    835 AAGAAAGCAAAGGT---AATCTCTTGTGACCTTTGAT-AGCCAGATA-TT 879
                               i  v   ?---     - i        v i -  v  -  i-  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCA-ATGGTT 586

  chr2_173834534_    880 CCTTAGACAAACCATAACAGGTACTAAAAATAAAATTCCAGCCTGGGTGA 929
                         i      i ----- i   ---- i    -----------  ------- 
  L1M4_orf2#LINE/    587 TCTTAGATA-----TGACA----CCAAAA-----------GC-------A 609

  chr2_173834534_    930 CAGAGCAAGACTCCGTCTCAAAAAAAAAGAAAAAAAAATTGGTAACTAGA 979
                           -     ----------     i    i v i v       --------
  L1M4_orf2#LINE/    610 CA-AGCAA----------CAAAAGAAAAAATAGATAAATTGG-------- 640

  chr2_173834534_    980 GCTTCATCAAA--TCCAAACTCT-GTGCTTACATAAAGAAATTGTTTGAA 1026
                         i          -- vv     i -      -  -  i  v i i ivii 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTT-CA-AAGGACACTATCAAGA 688

  chr2_173834534_   1027 AAACAAAGATGCAATCTACTGACTGGGAGAGCATGTTTATAATGAGATAT 1076
                           iii  i vi   i i  v  v       iv  i   ii  -ivv    
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATAT 737

  chr2_173834534_   1077 ATCTGTCAAAGCACTTGCTTTCAGAATATTTAAAGAACTCCTGCAAGTCA 1126
                              vi  i v     iv i        v          i i   v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_173834534_   1127 ATATTAAAAAGATAA------CGATTTTCAAAAATAGGTAGAGGATTAGA 1170
                            v        i  ------ i   ?--      i  i i      v  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGA 835

  chr2_173834534_   1171 ATAGTCATCTCAC--AAAAAGTTATATGAATAATCAATAAGCATGTGTGA 1218
                             v   i  v --  i   v    ii   iii         ii  vi 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_173834534_   1219 AAGTGTTCAATGACAGTGGTTAA 1241
                          ii  i    iiv  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (114 / 56)
Gap_init rate = 0.04 (27 / 715), avg. gap size = 3.33 (90 / 27)  


2128 15.68 2.40 25.02  chr2_173866406_173871872     3813  4979 (488)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_173866406_   3813 AGACATTTACATATTTATGGTTTAGAAGATTCAGTGTTGTCAAGAGGGCA 3862
                            i  ii-   i  i    v  i     i i i i    i    v    
  L1M4_orf2#LINE/      6 AGATATCC-CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_173866406_   3863 GTTCTCCCCAAAATGATCTATAAATTCCACACAATTCCTATCCAAATCCC 3912
                         i v         v       i i    v  i    i      v       
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_173866406_   3913 AGCAGACTTTTTTTTAGAAATTAACAAGCCAATCCTAAAATTTACGTGGT 3962
                            v v       vi       i      ii           i ii   v
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_173866406_   3963 AATGCAAAAGACCTAGAAATAGCCAAACCAATTTTGAGAAAGAA---CTA 4009
                                ii    i    -        v    i    i      --- v 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAA-TAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_173866406_   4010 ACTTTGAGGACTTAGACTGCCTCATTTCAAAACTTAT---AAATCTGTAG 4056
                          v  v       i v   v  iv             i---   v  ii  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_173866406_   4057 TAATCAACATAATACAATATTGGCACAATATCTACAGGGATATAGACCAA 4106
                                v i i iiii  i     i  vi--- i  iv       i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGG---ATAGACATATAGATCAA 300

  chr2_173866406_   4107 AGGAACACAATTAAAATTCTAGGGAAAAAGCCTCACATTGATTGGCAATG 4156
                         v    i v    i i v  i  ii v   v  vi     v  v v    v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_173866406_   4157 GATTTTCAACAAAGATGCCAAGACAGCCTTTGATTGCTGAGACAATTAGA 4206
                                i    i i         --- ----   -------    ----
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGAC---C----ATT-------CAAT---- 382

  chr2_173866406_   4207 AATTGATATGCCAGGGCCGGGTGTGGTGGCTCACACCTGTAATTCCAGCA 4256
                         ------------------   -----------------------------
  L1M4_orf2#LINE/    383 ------------------GGG----------------------------- 385

  chr2_173866406_   4257 CTGTAGAAGGCTGAGGTGAGAGGATCG-CTTGAGCCCAGGAGTTCAAGAC 4305
                         -----------------  i  i  v -   -----------     ---
  L1M4_orf2#LINE/    386 -----------------GAAAGAATAGTCTT-----------TTCAA--- 404

  chr2_173866406_   4306 CAGCCTGAGCAACATGACAAAATCCCATCTGTACAAAAAATACAAATAAA 4355
                         ------------------------------------------     i--
  L1M4_orf2#LINE/    405 ------------------------------------------CAAATG-- 410

  chr2_173866406_   4356 AATTAGCCAGCGTGGTGATGTGCACCTGTAGTCCCAGCTACTAGAAAGGC 4405
                         -------------------    ---------------------------
  L1M4_orf2#LINE/    411 -------------------GTGC--------------------------- 414

  chr2_173866406_   4406 TGAGGTGGGAGGATTGCTTAAACCCAGGAGGTTGAGGCTGCAGGGAGCCA 4455
                         -----     ----------------------------------------
  L1M4_orf2#LINE/    415 -----TGGGA---------------------------------------- 419

  chr2_173866406_   4456 AGAGTGTGCCACTGCACTCAAGCCTGGGCAACAGAGTGAGACCTTGTCTC 4505
                         ------------------   --    -----------------------
  L1M4_orf2#LINE/    420 ------------------CAA--CTGG----------------------- 426

  chr2_173866406_   4506 AAAAATAAATCCATATGCCAAAAAAAAAAATTAGAGCCACACCTCAGACC 4555
                         ----   --?   i    v   i  vi  i  i  v  vi      v   
  L1M4_orf2#LINE/    427 ----ATA--KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_173866406_   4556 ATACATAAAAATGAAATGAACTCAAAATGGATCATAAGCCTAAGTATAAG 4605
                            i i      ---- -                ? ii     i i    
  L1M4_orf2#LINE/    471 ATATACAAAAAT----T-AACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_173866406_   4606 GGTTAAA-CTATAAA-CTCTCAAAAGAAAA-ATAGA---AAATCTTCATG 4649
                         i i    -       -    i i       -    i---        i  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_173866406_   4650 CTTTGGGGTTAAGCAAAGAGTTCTTAGAAATGATACCAAAAGCACA-GCC 4698
                         vii v      i    v iv        v    i            -  v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_173866406_   4699 ATAATAGAAAAATT-GAGAAATTGGAATTTATAAAAATTAACAATTTCTG 4747
                          i  v       v -  v        v  i  v        v  i  i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_173866406_   4748 CTCTTTGAA--ACATGATCTTAAGAGAATGAAAAGACAAATGACAAACTG 4795
                         iv   ii  --   iv   --    i i           viv   i v  
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATC--AAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_173866406_   4796 GGAAAAAATATTTGCAAATCATATATATGACAAAGGACTTGTATCTAGAA 4845
                            i                      v   i  i           i    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_173866406_   4846 C-TAAAAAAAATTATTAGAACTCAATAA----------AACAACCCAGTG 4884
                         i-  v   i  i v   v          ----------  i      i v
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_173866406_   4885 TAAAAGTGGACAAAAGATTTGAATAGATATTTTGCTTAAGAATATATAAA 4934
                         ?    i   i    i            i    iv iv     v     v 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_173866406_   4935 AGGGGCTAATAGGCACATAAAAAGATGCCCAACTTTGTTAGTCAC 4979
                          iv   i    i      i         i    v ii????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (115 / 65)
Gap_init rate = 0.03 (31 / 903), avg. gap size = 10.32 (320 / 31)  


3264 26.87 0.44 0.44  chr2_174217777_174224052.rev     4877  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_174217777_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4926
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_174217777_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_174217777_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_174217777_   5025 TATGGAACCAAAAAAGAGCCCTCATCACCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  vvv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_174217777_   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_174217777_   5125 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_174217777_   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCTTACCTACAACT 5222
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_174217777_   5223 ATCTGATATTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    v  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_174217777_   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_174217777_   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_174217777_   5373 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_174217777_   5423 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5472
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_174217777_   5473 AACACCAAAAGCAATGGCAACACAAGACAAAATTGACAAATGGGATCTAA 5522
                         i            vvi      v    v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_174217777_   5523 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_174217777_   5573 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5622
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_174217777_   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAGAA 5672
                         i  i  vi          v  i  v      vv    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_174217777_   5673 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAAACACTTC 5722
                          i     i     v  i?    i           iv    i i   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_174217777_   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5772
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_174217777_   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2900 27.56 2.59 0.45  chr2_174251957_174256044     2708  3596 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_174251957_   2708 TGGAAAAACATTTCAGGCTCATGGATAGGAAGAATCAATAATGTGAAAAT 2757
                               i i  ii  v i        v      v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_174251957_   2758 GGCCATACTGCCCAAAGTAATTTTTAGATTCAATGCTATCCCCATCAAGC 2807
                            v     v      v i  i vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_174251957_   2808 CACCATTGACTTTCTTCACA-AAATTAGAAAAAACT-ACTTTAAATTTCA 2855
                         iv   vivi i  i  ii  -     --i v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr2_174251957_   2856 TATGGAACCAAAAAAGAGCCCACGTAGCCAAGACAATCCTAAGCAAAAAG 2905
                                viiv  ii  v  vivi       i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_174251957_   2906 AACAAACCTGGAGGCATCATGCTACCTGGCATCAAACTATACTACAAGGC 2955
                               vi      vv   ii  v  iiiiv     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_174251957_   2956 TACAGTAACCAAAACAGCATAGTACTTGTACCAAAACAGATACATAGACC 3005
                                 i   i    ii i     v i iv ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_174251957_   3006 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 3055
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_174251957_   3056 CTGCTCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 3105
                         i  v i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_174251957_   3106 ATTTAATAAACGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 3155
                         v  i  i   i    i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_174251957_   3156 AACTGGACCCCTTCATTACACCTTATACAAAAATTCACTCAAGTTGGATT 3205
                          ii         v v i     v            v      iv     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_174251957_   3206 AAAGACTTAA------GATCTAAAACCATAAAA-------------ACCT 3236
                          ?    i   ------  v       i      -------------  v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_174251957_   3237 AGGC-TATGCCATTCAGGACATAGGCATGGGCAAAGACTTCA-AGACTAA 3284
                            ?-  vii -   iv   v v  vv i     v ii   v-   -  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TAT 596

  chr2_174251957_   3285 AATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGGATCTAA 3334
                         i i          vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_174251957_   3335 TTAAACTAAAGACCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 3384
                          i   v v  i v   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_174251957_   3385 AGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTACCCATCTGACAA 3434
                           i     i              v  v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_174251957_   3435 AGGACTAATATGCAGAATCTACAAGGAACTTCAACAAATTTACAAGAAGA 3484
                         i     vi   v      v  i  i     iiv    v iv i  v  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_174251957_   3485 AAACAAACAACGCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 3534
                          i     i   v v  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_174251957_   3535 TCAAAAGAAAACATTTGTATGGCCAACAAACATATGAAAAAAAGCTCATC 3584
                           v      i i  viiv        i  i  i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_174251957_   3585 ATCACTGGTCAT 3596
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.00 (27 / 9)  


3107 24.44 1.60 1.23  chr2_174284498_174286281      487  1296 (488)    L1M4_orf2#LINE/L1       96   908 (0)  

  chr2_174284498_    487 CAAAGTT--AGCCGATCATTTTCACAGAAATAGGAAAACCAATCCTAAAA 534
                             i i--   i -i v    ii       v iv  i ii         
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_174284498_    535 TTTGTGTAAAACCACAAAGGTCCCTGAATAGGCAAAGAAATCTTTGGTAA 584
                           ii i ii  vii   i  v   v      v    iv      viiv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_174284498_    585 AAAGAGCAAAGCTGAAGGCATCACACTACCTAACTCCAAAATGTATTACA 634
                         i    i     i  i   vv       v  i  i i     iv  i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_174284498_    635 AAACTATAGAAACCAAAACAGCAAAACACTGGCATAAAAACAGACA-A-A 682
                           i   i  v  i   i    iiviii          ii i     - - 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_174284498_    683 AACCAATGAAACAGGATAGAGAGCCCAGAAATAAACCCACATGTTTATGG 732
                         i i     i  i  i  v     i               i ii       
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_174284498_    733 TCAATTGATTTTCAACAAGGCTGCCAAGAACGCACAATAGAGAAAGGACA 782
                                      i      v        v iiv    i i     i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_174284498_    783 ATCTCTTTAATAAATGATGTTGGGAACATTGGATAT--GCATGCAGAAGA 830
                         i   i  i  i     i  i     vv i      ?--i      i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_174284498_    831 ATGAAATTGAACCCTTACCTCACATGATACACAGAAATGAACTCAAAATG 880
                              i   i    i         iv   i   i    v           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_174284498_    881 AATTAAAGACTTAAATGTGACACTTGAAACTGTAAAACTACTAGAAGAAA 930
                         i  i ?    i       i v vi i     i       vi         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_174284498_    931 ACGTAAAGGGAATGCTCCACAATATTGTTCTGG--GGGCAAACATTTCTT 978
                           i  ii? v  vv  i iii iv   ----  --i     vvi      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTG----GGTTAGGCAATGGTTTCTT 590

  chr2_174284498_    979 GGATGTGACCCCCAAAGCACAGGCAACAAAAGCAAAAAATAAACAAAAAG 1028
                         i   i    v  v        i          -        i i   vv 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTG 639

  chr2_174284498_   1029 TATGTCATCAAACTGAAAAGCTTCTGCATGGCAAAAGA----AGCAATAG 1074
                         v iv        v v    i   i  iiivv    i  ---- v   v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_174284498_   1075 AATGAAGAGACAACTCATGGATTGGGAGAAAATATTTGCAAGCCACATAT 1124
                          i    i       i  ii  v                   ii  i    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_174284498_   1125 CTGATAAGGGGCTAATATCCAAAATATATAAGAAACTCAAATAACTCAAT 1174
                                   i  vi      i         ii     vv i        
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_174284498_   1175 TGCAAGAAAATAAAGAACCCAATTTAAAAAATGGGCAAGAGACTTAAATA 1224
                         vii  i  i i   v         ?     -       ii  i  i    
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATA 838

  chr2_174284498_   1225 GACATTTCTTAAAAAAAAAAGACATGTAAATGGTCAACAGATATATGAAA 1274
                                  iv   i  ---  i  ii      i   i iii i      
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAA---GATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_174284498_   1275 A-ATCATCATCTTCACTAATTAT 1296
                          -  vv   v v   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.46 (138 / 56)
Gap_init rate = 0.01 (12 / 813), avg. gap size = 1.92 (23 / 12)  


1731 23.96 5.27 5.91  chr2_174288689_174290305.rev      500  1125 (492)    L1M4_orf2#LINE/L1      287   908 (0)  

  chr2_174288689_    500 GACAAATAAATGA--GGCATAGCA--GAGAATCTAAAAATAAACTCACAT 545
                             v   i  v --  v    v --    i  i i        i  i i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_174288689_    546 ATATGTGGTCAACTGCTTTTCAACAAAGATTCCAAGGTAATTCAATGGGG 595
                           v i       i  v     i    i i v     iiv           
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_174288689_    596 AAGAGGATAATATTTCCAACAATTATCCAACAATTTAAAAATTGTTTAAA 645
                           -  i   i v   i      ----------  ------iv  i vii 
  L1M4_orf2#LINE/    387 AA-AGAATAGTCTTTTCAACAA----------AT------GGTGCTGGGA 419

  chr2_174288689_    646 TATATCCAACAATTTAAAAATTGCATATCTATGTGTGTAAAAA-GACCCT 694
                         ------    -----------  v   ? i ii  iiv  i  -  vvi 
  L1M4_orf2#LINE/    420 ------CAAC-----------TGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_174288689_    695 GAGCCATCACCTCATAACATATAAAATAATTCATT-GAAATGTATCATGG 743
                          ii  vii      i v      v  v    v i -i     v    ?i 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_174288689_    744 ACCTAAATTTGAGGGCTAGAAATA-AAAATTTTCTGATGAAAATATAGAA 792
                                 v i  i    i  v  -    i i iv  v     i    i?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_174288689_    793 GAAAATATTAGCAATCTTGGGATTGACAAAGATGTGCTTTAAGTAGGATA 842
                          v    v  v ii i      v v i   v i v --i   ii  v  i 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT--CTTAGATATGACA 600

  chr2_174288689_    843 CAGAGAGCACAAACTACAAAATACAAAAGTA--TTAATTGGACTT----- 885
                          vi i       i v      v -    i  -- v          -----
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCA 649

  chr2_174288689_    886 ------------TCTGCACTTTAAAAAATTCTGTTAAGAAAATAAAAAGA 923
                         ------------ i  ii   i   ii iv  i i      i i      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_174288689_    924 CAAGCCTCAGGCTGGGAGAAAATGTTTGTAAAACATAAATCTGACAAAGG 973
                            v  v   iv           i    i   v    v      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_174288689_    974 AC--GTATCCAGGATACGTAAAGAACTCTTCCAACTCAACAATATGAAGA 1021
                           --        i   ii            v        i    vi    
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_174288689_   1022 TAAA---CTT--TTTTCTAATAGGCAAAAGATATGAATAAATACTTTACC 1066
                         i   --- ii--  ?vvv   i      i   v      i i i  iv  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_174288689_   1067 AAAAAAAGCACACAAATGGCAAATATGCACATGAAAAGATGCTCATTATC 1116
                            i  iii i         v    v                   vi   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_174288689_   1117 ATTAGTTAT 1125
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.75 (93 / 53)
Gap_init rate = 0.03 (17 / 622), avg. gap size = 4.12 (70 / 17)  


3219 27.31 0.44 0.44  chr2_174389865_174396145.rev     4882  5789 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_174389865_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 4931
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_174389865_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_174389865_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_174389865_   5030 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_174389865_   5080 AACAAAGCTGGAGACATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i     ivv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_174389865_   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_174389865_   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCTTACCTACAACT 5227
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_174389865_   5228 ATCTGATCTTTGACAAACTTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_174389865_   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_174389865_   5328 GAAAGTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            iv    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_174389865_   5378 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_174389865_   5428 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_174389865_   5478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5527
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_174389865_   5528 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_174389865_   5578 AGGCAACCTACAACATGGGAGACAATTTTCGCAACCTACTCATCTGACAA 5627
                           i     i   iv        v   v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_174389865_   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_174389865_   5678 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_174389865_   5728 TCAAAAGAAGACATTTATGCAGCCAAAAACCACATGAAAAAATGCTCATC 5777
                           v        i  vi viii     v  v          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_174389865_   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 571 28.09 3.37 0.56  chr2_174414336_174416241      501   678 (1228)    L1M4_orf2#LINE/L1      247   429 (479)  

  chr2_174414336_    501 GCAACAATTATCAAGACAAAGTGAATTTTGTTCAAGGATAGATGAATAGA 550
                           v   i v         iv   ivvi v ivi         iiv     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_174414336_    551 TCAATGGAATATAAT--AGAGTTCAGAATCAGACCTAGACATGAACAATC 598
                                    v   --     i     vi i   i v    vv iii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_174414336_    599 ACTTGATTTATGACAAAAGTGCT----CCAGCGCAGTGGGGAAATTATGA 644
                          v       vi     ii    i----   vi-  i        vv  ii
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAG 395

  chr2_174414336_    645 TCTTTTCAATAAATGATACATGGCCAGCAGGGTA 678
                                  i     i i vv  v  i v  i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

Transitions / transversions = 1.27 (28 / 22)
Gap_init rate = 0.02 (3 / 183), avg. gap size = 2.33 (7 / 3)  

1037 23.09 9.69 5.36  chr2_174414336_174416241      930  1414 (492)    L1M4_orf2#LINE/L1      403   908 (0)  

  chr2_174414336_    930 AAAAAAAGATACATGGCCAACTAGAAAGCCATACAGAAAAACAAATTAAT 979
                           v   v i i vv  v     i  v ?   i iiv    i------   
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG------AAT 446

  chr2_174414336_    980 ATTTAATTTTGACTCCTACCTCACACCTCACATACACAAA----CTTCAG 1025
                         i---  v  v   i             -- i     v   ----  iv i
  L1M4_orf2#LINE/    447 G---AAGTTGGACCCCTACCTCACACC--ATATACAAAAATTAACTCAAA 491

  chr2_174414336_   1026 ACAGATTTTAGAGCTAAACGTAAAAA-TCAATCAATAAAATTTAATCTAA 1074
                          ii   iv?   v     i    i i- v  v v      i i---i  i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC---TTAG 538

  chr2_174414336_   1075 AAGAAGACAGCATAGTAGGATATCTTCGTGCTCTTG---TAGACACCATG 1121
                              i   ---   v? v v         vi    ---   i  --   
  L1M4_orf2#LINE/    539 AAGAAAACA---TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA--ATG 583

  chr2_174414336_   1122 GT-----AGACATGA-ACAAAAAA-ACAAATTA-AAAAGAAAAAGACCGA 1163
                           -----   i    -  v    i-    iiv -          - iv  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGA 632

  chr2_174414336_   1164 CAAATTGGAGTACATTCCAATTAAAAACCTCTGT----TAA--------- 1200
                         i        v v   ivv          i i   ----i  ---------
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_174414336_   1201 ---------TGAAAAGACA---CTTAGAAAGGGAGAAGATACTTACAGCA 1238
                         ---------          --- vi    v       i   i  i  -- 
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA--A 730

  chr2_174414336_   1239 A--AAATATCTAAT---GGTCTCATATCTAAAATATATAAAGAAGTTCTA 1283
                          -- v      i  ---  v  ii    i i             v ii  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_174414336_   1284 CAAATTAACAGGAAAAAGACAGACTACTCAATTTTAAAAAGCAAGGGTGA 1333
                            v i  i iv         i iv  i     ?-     v---   ii 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAAT---GGGCAA 826

  chr2_174414336_   1334 GAGACTTGTACAGGTACTT-TCCAAAGAGGTTATCCAAATGGCTAATAAG 1382
                         ii  i   v i  ii i  -        i v   v        i      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_174414336_   1383 CATATGAAAAATTACCCAACCTCAATAGTCAT 1414
                           i       iv i i    v   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (67 / 41)
Gap_init rate = 0.05 (23 / 506), avg. gap size = 3.17 (73 / 23)  


1019 31.38 13.78 3.06  chr2_174475550_174477515      683  1466 (500)    L1M4_orf2#LINE/L1       29   896 (12)  

  chr2_174475550_    683 GAAGACTAGATAT-ATAAAGATGATGATTCTCCCCAAATCATTCTATATA 731
                                vi    -i v      iii  v          iiv    i --
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACA-- 76

  chr2_174475550_    732 GATTCAATGTACTTCTCATCAAAATCCTAAAGGAACATTTCACATAGCTT 781
                                i i v i ii          i ivv vviv   ii  v iv  
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

  chr2_174475550_    782 GACAAGGTGATCTTGAAATTCAGGAAGAAGAGTAAAGAACAAAAAATAGC 831
                               v     i i       vivi   iv i  i i  vv i      
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr2_174475550_    832 CAAGAAAAATTTGACTAAGAAG------GTTAG-----TTTCACCCTGCA 870
                            i v  vi    vv      ------   i ----- iv   iiiv  
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_174475550_    871 GG---AAAGATTATTATAAAATCGCATTTAAATCAATGCAG--------- 908
                         iv---   iv   i  i   iiii  v --      vi   ---------
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGT--AATCAAGACAGTGTGGTACT 274

  chr2_174475550_    909 ---ATAAAGACAAACAAAAAGAT---------AGAA-----AGTCTAGAA 941
                         ---    i  i i   v v    ---------    -----    i    
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr2_174475550_    942 ACAGACCCACGTATGAA-GAAGAACGTGGTATAGACCCAAAGTGGCACTA 990
                          i i     iii  vv - ivv  i-  i v vviv v ii   v  vv 
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGA 373

  chr2_174475550_    991 CGAGTCAGTGGGAACAGGATGGACTGCTCTATAAATGATGCTGG----AC 1036
                          v v   i    i v  i  i v  vi  v i     i      ----  
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_174475550_   1037 TG--TGGTC---TACAAAA--------CTAGATTCTTACCTCATCCCATA 1073
                           -- i?i --- i     --------i i  ii i       iv     
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_174475550_   1074 ------GATGCACTCCAAG------------------GTAAAAAACAAAA 1099
                         ------i  vv    v  i------------------    i ivi    
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_174475550_   1100 CCG--GAACTTTTAGACGCAAACCT----TTGATTCGTTTATGACATCAG 1143
                          ii--i    i     v v    v ----v i v  -  ii    v ii 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGG 572

  chr2_174475550_   1144 GATAGGGAAAGATTTTTTAAATGTAAAGCCAGA-TCGCAATTCATAAAAA 1192
                          v    v  v i   i   i  i i vi   i -v i   viv i    i
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_174475550_   1193 GAGATATTGTTATATTTGACTACCTT----TT-----CTATTTCTATTTC 1233
                         i i v  v v  v   v    v v i----  -----  -   v ii   
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT-TTTGTGCTTC 671

  chr2_174475550_   1234 TATAGCCAAAAAAAAAAATACCAT-AAGCAATGTGAAAAAATAAGCCACA 1282
                         ------------   ii i  i  -   v  -       i i  v     
  L1M4_orf2#LINE/    672 ------------AAAGGACACTATCAAGAAA-GTGAAAAGACAACCCACA 708

  chr2_174475550_   1283 GAACAGAAAAAGACATTTGTCTCCCATACACAACTAACAAAGTATTAATG 1332
                            ii i i  i i     ivvvi    i i--  i i  i v i vi i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATAT--CTGATAAGGGACTTGTA 756

  chr2_174475550_   1333 TCCAGAATACGTACAGAATTTCTACAAATCACT--TAGCAAACACAA--- 1377
                                  ii  v    i ii     v   v --  i-   v    ---
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AAAGACAAATA 805

  chr2_174475550_   1378 ---CAATTAAAAAAATAGACACTGGAGATGAACAGGAAATTCACAGAAGA 1424
                         ---     ?     - i i  vv   vv    i  iv v   v vi    
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_174475550_   1425 GGATGTCCAGATGCCCAGTAAACATAAGAAAATGTGCCTAAC 1466
                         i   i v  i   v   i   i  i v     vi   ii   
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.04 (32 / 868), avg. gap size = 4.12 (132 / 32)  


2146 24.97 8.45 3.15  chr2_174864289_174866230      661  1453 (489)    L1M4_orf2#LINE/L1       74   908 (0)  

  chr2_174864289_    661 ACAGTTTCAATACAAAGTCAAAAATCAATGAAATTCCAGCAAGCTTTTTT 710
                             v     ii   vvi v ---    ---   i     v-  i     
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTA---TCAA---AATCCCAGCT-GCCTTTTT 116

  chr2_174864289_    711 TTCAGG--------------TTCTTAAATTTATACAGAAATGCAAAGGAA 746
                          v   i-------------- i  v     i   ii         i   v
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr2_174864289_    747 CTAGAAAAGCTAAAGCAATCTTAAAAAATAGGAAAAGGGTCAGAAGACCT 796
                          i    v   i   i       i     v i   v ii  ii  i   ii
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr2_174864289_    797 ACACTATCTAATTTTAAGACTTACTCTAAAGCTATAATAATCAAGACAGT 846
                              vi i     i  i       vi       i i             
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_174864289_    847 ATGGTATTGCCA-------AAACAAATAGATCAATGGAACAGAAT--AGA 887
                         i     i  v  ------- i   v              i     --   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_174864289_    888 GTGTGTAAACTGACC--TGCACTTGACCTCCTAAACAGTTATTTGATTTT 935
                           viiv   ivi   -- i  i  ---------- ii  i v        
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTT----------ATGGTCAATTGATTTT 356

  chr2_174864289_    936 TGACACGG-TGCCAGGTTAATTCAGTGAGAGAAAAGATA-----TTCAAC 979
                         i    v  -     i viv     i  i -    ii   -----      
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTTTTCAAC 405

  chr2_174864289_    980 AAATAATTCTGGAAAAACTATGCATCTGTATG-----GAAGAAAATTAAC 1024
                             ii v    i v    ivii ? iii   -----   vi  i  iiv
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_174864289_   1025 ACCTTACCTCATGCCATATGCAAAA-TTAACTAGAAA--GATGACAGGCC 1071
                         v  i       ii      i     -      vi   --   v ?  i  
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_174864289_   1072 CGAATGTAAGAGCTAAAGTTAT-------TTAAAATTAAACTTTAACAGA 1114
                         ii               ii   -------   i  vv    ---- i  i
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC----ATAGG 551

  chr2_174864289_   1115 AGAAAATATCTGTAACACAGCGCTGGGTAAAGATTTCTGA-ACCGGACAC 1163
                         ? v    v ii  i  viv v i i  i  v i     v - ivv     
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_174864289_   1164 AAAAAACACAAATATCAGA-GAAAATCAACTGATAAAATGAACATCCT-- 1210
                         v    i     ii v  i -     --  iv      v  i  v  v --
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAA--AATAGATAAATTGGACTTCATCA 649

  chr2_174864289_   1211 -AATGAAAAA-TTTTGTTCTTTTAAAGACAGAATTAAAAAAAAAAAAAAG 1258
                         -   v     -      v   iv  i    vv  i  i   ivi    ii
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_174864289_   1259 CCAGCCACAGACTAGGAGAAAAT-TTCATATAACATATACTTGACAAAGA 1307
                          v v       v i         -  iii v v      ii   i  i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_174864289_   1308 ACTTGTATCCAG-------------TTCTTTGATACTGGATCAAAATAAG 1344
                                     -------------i    vv -   vi  v v  v   
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCAATAATAAAAAG 798

  chr2_174864289_   1345 ACAAACAATCCAATT-AAAAATGGACAAAAGATTTAGACAGATACTTCAC 1393
                              i  i      -        i    i     ii i   i i   v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_174864289_   1394 CAAAGAAGATATACAGTTTGGAAGTAAGCAAATGAAAAGATGGTCATCAC 1443
                                        iv v vv i      v           v   v  i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_174864289_   1444 TAATAGGCTG 1453
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.71 (123 / 72)
Gap_init rate = 0.03 (25 / 835), avg. gap size = 3.68 (92 / 25)  


3325 26.87 0.33 0.33  chr2_174959201_174964447     3848  4755 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_174959201_   3848 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3897
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_174959201_   3898 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3947
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_174959201_   3948 TACCAATGACTTTCTTCACAGAATTGGAAAACACT-ACTTTAAAGTTCAT 3996
                          v   iivi i  i  ii     v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_174959201_   3997 ATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAGA 4046
                               viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_174959201_   4047 ACAAAGCTGGAGGAATCACACTACCTGACTTCAAACTATACTACAAGGCT 4096
                               i       v       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_174959201_   4097 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 4146
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_174959201_   4147 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACTA 4194
                               i    i--    i  --        vv  ii i ii  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_174959201_   4195 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 4244
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_174959201_   4245 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4294
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_174959201_   4295 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 4344
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_174959201_   4345 CAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4394
                           ?   ii    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_174959201_   4395 TAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAA 4444
                             ?i v viv   iv   v v  vv i     v ii   v ivvi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_174959201_   4445 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 4494
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_174959201_   4495 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 4544
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_174959201_   4545 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 4594
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_174959201_   4595 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAGAAA 4644
                           i  vi          v  i  v      vv    v iv i  v i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_174959201_   4645 AACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCT 4694
                         i     i     v  i?    i     i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_174959201_   4695 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 4744
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_174959201_   4745 TCACTGGCCAT 4755
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3187 26.76 0.77 0.77  chr2_174979231_174982093     1464  2371 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_174979231_   1464 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 1513
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_174979231_   1514 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 1563
                            v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_174979231_   1564 TACCAATGACTTTCTTCACAGAAGTGGAAAAAACT-ACTTTAAAGTTCAC 1612
                          v   iivi i  i  ii     i v  v  i-  - iii    i    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_174979231_   1613 ATGAAACAAAAAAAGAGCCCCC--ATTGCCAAGACAATCCTAAGCCAAAA 1660
                            i  -- viv   i v   v--  v     i      i i ivv i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_174979231_   1661 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 1710
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_174979231_   1711 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 1760
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_174979231_   1761 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTATAAC 1808
                                 i    i--    i  --        vv   i    i   iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_174979231_   1809 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 1858
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_174979231_   1859 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1908
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_174979231_   1909 TGAAAGTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGG 1958
                             iv    i    v   i i   v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_174979231_   1959 ATTAAAGACTTAAGTGTTAGACCTAAAGCCACAAAAACCCTAGAAGAAAA 2008
                           i ?    i   i   v   v     i i i    vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_174979231_   2009 CCTAAGCA-ATACCATTTAAGGCATAGGCATGGGCAAGAACTTCATGTCT 2057
                          v  i ?i- v i -  iiv i v v  vv i     viii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_174979231_   2058 AAAACACCAAAAGCAATGACAACAACAGTCAAAATTGACAAATGAGATCT 2107
                          vi            vvii      v  vv     v  i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_174979231_   2108 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 2157
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_174979231_   2158 ACAGGCAACCTACAGAATGGGAAAAAATTTTTTGCAATCTATTCATCTGA 2207
                          v  i     i           i     v   -    vii  vi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGA 743

  chr2_174979231_   2208 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 2257
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_174979231_   2258 AAAA-ACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 2306
                             -     i     v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_174979231_   2307 TTCTCAGAAGAAGACATTTATACAGCCAACAGACATATGAAAAAATGCTC 2356
                              vi       i  vi v ii     i ii  i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_174979231_   2357 ATCATCACTGGCTAT 2371
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (147 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


1964 24.38 1.65 2.27  chr2_174993830_174996732.rev      876  1359 (1544)    L1M4_orf2#LINE/L1        1   481 (427)  

  chr2_174993830_    876 TGGAAAGACATCCCATGTTCATGTTTCCAATATTCTTGGAAGA----ATA 921
                                 i              -----i  -----       ----   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATG-----GAT-----TGGAAGACTTAATA 40

  chr2_174993830_    922 TTGTGAAAATGACCATACTATTAAAAGTGATCTACAGATTAAATACCATC 971
                             v  i   i v     viiv   v             v  ii v   
  L1M4_orf2#LINE/     41 TTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chr2_174993830_    972 CCTATCAAAATATTAATGACTCTCTTCACAGAAATAGAAAAAA-AACCTT 1020
                                    vii iivi ii i  ii       v  v  iv-i i i 
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_174993830_   1021 AAAATTTCTATGGAACCACAAGAAGCCATGAATGGCCAAAGCAATCTTGA 1070
                               iv       vii    iii  vv    i      i         
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_174993830_   1071 GCAAAAAGAACAAAATTGGAGGCATCACACTACTGGAATTCAAAATATAC 1120
                         iv  i         i       vv       v ivi v       iv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_174993830_   1121 TACAAGAGCTATAGTAA-CAAAACAACATGGCACTGGCACAAAAGCAGGC 1169
                              -     i     -   i   iii   i       i  iiii  i 
  L1M4_orf2#LINE/    241 TACAA-AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_174993830_   1170 ACACAGATGAATGGGACAGAATAGAGAGCCCAAAAATAAATCCACATATT 1219
                          i i    v     i i     v     i   i       i   i i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_174993830_   1220 TGCAGTTAGCTTATTTTCAACAAAGATGCCAAGAACATTTATTGGGGAAG 1269
                          iii  i ii v      i    i i        v    i v       i
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_174993830_   1270 GGGCAGTCTTTTCAATAAATGGTGCTGGAA-AACTGAATATTTGTATGTG 1318
                          iii           i            i -     i   ?iiii   ii
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_174993830_   1319 AAAAAATAAAACTAGACCCCTGTCTCTCACCATAT-TAAAAA 1359
                            i   i  ii i       ii   v        -i     
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

Transitions / transversions = 3.03 (88 / 29)
Gap_init rate = 0.02 (8 / 481), avg. gap size = 2.38 (19 / 8)  

1129 24.14 5.82 4.09  chr2_174993830_174996732.rev     1948  2411 (492)    L1M4_orf2#LINE/L1      437   908 (0)  

  chr2_174993830_   1948 GCAACAAGAGTGAAACTCTTTGAAACTCCATCTCAAAAAAAAGAAAAAAA 1997
                             -    i    i----   i v i i i    v vv v v v     
  L1M4_orf2#LINE/    437 GCAA-AAGAATGAAG----TTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_174993830_   1998 --AACAAAAAACAAA-AAAAGATTTAAATGTAAGACCAAAAACTATAAAG 2044
                         --   vv    iii -v ?   ii           v v           i
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_174993830_   2045 ---------------ACAGGAG-AAATGCTTCAGGACATTGC-CTGGTCA 2077
                         --------------- i   ? -    -    iv   v   v-i i v  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCA 580

  chr2_174993830_   2078 AAGATTTTTATGGAAAAGACCTCATAAGTATAGGCAATAAAGGCAAAAAC 2127
                          v i   i - i  v v   vi  v   i i i    i   i v     i
  L1M4_orf2#LINE/    581 ATGGTTTCT-TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_174993830_   2128 AGACAAATGGAATTCTGTCAAA-TGAAAAAGCTTCTGCACAGCAAAGAAA 2176
                            i    v i i iii     - v     -   i  ii vv     i v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chr2_174993830_   2177 ACAATCAACAGAGTGAAGAGACGACTTACAGAATGTTAGAAAATATTTGC 2226
                           v     v i      i    i  ii        vv             
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_174993830_   2227 AAGCTATTTATCCAGCCAGGGATTAATATCCAGAGTATACAAGGAACTCA 2276
                           iii  v    iiiiv     i vi        i    i  i      -
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC- 777

  chr2_174993830_   2277 AGGAATGCAAACAACTCAACAG-AAAAAAATAAATAA----AT-GAAAAA 2320
                         ----- v---         i i-     i i      ----  -?     
  L1M4_orf2#LINE/    778 -----TT---ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_174993830_   2321 TAGGCAAATGAGCTGAACTGATATCTCTCATTCAAGAAGATATACAAATG 2370
                          i      v  vi    iv  i  i    --iv                 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTC--CAAAGAAGATATACAAATG 867

  chr2_174993830_   2371 GCCCACAGGTATATGAAAAGATGTTCAACATTACTAATCAT 2411
                            v i i i i           i       i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (69 / 40)
Gap_init rate = 0.04 (17 / 472), avg. gap size = 2.71 (46 / 17)  


3323 26.43 0.44 0.44  chr2_175094943_175101217.rev     4876  5783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_175094943_   4876 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATTGTGAAAAT 4925
                              ii i  i     i i    i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_175094943_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_175094943_   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_175094943_   5024 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_175094943_   5074 AACAAAGCTGGAGGAATCACACTACCTGACTTCAAACTATACTACAAGGC 5123
                                i       v       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_175094943_   5124 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5173
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_175094943_   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATAACTACAACT 5221
                                i    i--    i  --        vv   i i vi  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_175094943_   5222 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5271
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_175094943_   5272 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 5321
                           v  i  i              v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_175094943_   5322 GAAACTGGATCCCTCCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5371
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_175094943_   5372 TTAAAGACTTAAACTTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5421
                          i ?    i    iv v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_175094943_   5422 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5471
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_175094943_   5472 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5521
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_175094943_   5522 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5571
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_175094943_   5572 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5621
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_175094943_   5622 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATGTACAAGAAAA 5671
                         i  i  vi          v  i  v      vv    v vv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_175094943_   5672 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5721
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_175094943_   5722 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5771
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_175094943_   5772 ATCACTGGCCAT 5783
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2710 25.19 2.93 4.34  chr2_175541473_175544091     1207  2127 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_175541473_   1207 TGGAAAAATATCACATGCTCATAGATTGGAAGAATCAAT-TCATAAAAAT 1255
                               i     v    i    i          v i   - ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_175541473_   1256 GGCCATAATGCCCAAAGCAATTTATAGATTCAACACTATTCCTGTCAGAT 1305
                            v   v v      vii  i  i         i v  i   i   i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_175541473_   1306 TACCAACATCATTCTTTACAGAATTAGAAAAACCTATTCTAAAATTCATA 1355
                          v   i vv v  i   i     v v  v  i iv  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_175541473_   1356 TGAAACCAAAAAAAGAGCCTGGCTAGACAAAGCAATCCTAAGCAAAAAGA 1405
                           i  viiv  ii-  v  v iv   v    i     i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_175541473_   1406 ACAAAGCTGGAGGTATCACACTACCTGACTTCAAA-CTAAGTTATAACGT 1454
                               i      vv       v  ii i      -  v -i  i  v i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAAAGC 248

  chr2_175541473_   1455 TATAGTAACCAAGACAGCAAGGTACTGGTACAAAAACAGACACACAGACC 1504
                           i     i        iiv        i i  ii i     i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_175541473_   1505 AATGGAAGAGAGCAGAATACCAAGAAATAAAGCCTCACACTTAAAA-CAA 1553
                                v   iiv  ivii v         v  vi   i   vii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_175541473_   1554 TCTGATCTTCGACAAGGCTGACAAAAATAAGTAATGGAGAAAGGACTCCC 1603
                          -    i          v  v   i vi vvi     i     i i----
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT---- 393

  chr2_175541473_   1604 TAAGAAACAAGTAATGGGAAAAGGATTCAATAAATAGTGCTGGGATAACT 1653
                         ---------   vv ----------     i    i         i    
  L1M4_orf2#LINE/    394 ---------AGTCTT----------TTCAACAAATGGTGCTGGGACAACT 424

  chr2_175541473_   1654 GGCTAGTCATATGCAGAAGAATGAAAATTGGATCCTTACCTTTCACCATA 1703
                           v  ?i  i     i         i-     i  i     iv       
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAG-TTGGACCCCTACCTCACACCATA 473

  chr2_175541473_   1704 TACAAAACTTAAC-----ATGGATTAAAGATTTAAA-----GATCTCAAA 1743
                                v     -----      i ?   ii    -----  v  v   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_175541473_   1744 CTATAAAAATCCTAGAGGAGAACCTAGG---AAATACCCTTTTTCGTATC 1790
                                 v  i    i  i   v    ---    ------i     i--
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT------CTTCGTG-- 565

  chr2_175541473_   1791 AACTTTGGG------AAAGAATTTTTG--TGTAATCCCTAAAAGCAACTG 1832
                         -  i     ------  v iv  i  i-- i i iv  -       vvv 
  L1M4_orf2#LINE/    566 -ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC-AAAAGCACAAG 613

  chr2_175541473_   1833 CAACAAAAACAAAAATGGACAAGT-GGGCCTAATTCAACCGAAGAGCTTG 1881
                                 iv      i  i  i -  i i v  iv  viv  i i   v
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_175541473_   1882 TGCACAGCAAAAGAAACTATCAATAGAGTAAGCAGACAATTTACAGAATG 1931
                           ii vv    i  v        v i   i iv      iii        
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_175541473_   1932 GGA-AAAATATTTGCAAACTATGCACCCGGCAAAGGTCGAATAACTGAAG 1980
                            -              ii  ii i i ii  i  v vvi  v iii i
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_175541473_   1981 TCTATAACAATCTATAACAAACTTAAATCAACAAGCAAA-AAACAACCCC 2029
                          v     vi v  v v    -  i  --i  i  iv i -   i     v
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAA-CTCAA--TAATAAAAAGACAAATAACCCA 810

  chr2_175541473_   2030 AATAAAAAATGGGCAAAGGACATGAACAAACACTTCTCAAAGGAAGACAT 2079
                          v ?                iv    i i   i     v  i     i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_175541473_   2080 ATAAATGGCTGACAAACATATGAAAAAATGCTTATCATCACTAATCAT 2127
                          i       ii i  i  i       i     i v     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (146 / 83)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.05 (67 / 22)  


3333 21.39 3.86 4.19  chr2_175579789_175585117     3931  4837 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_175579789_   3931 AAGATA-CTCATGTTTACAGGTTAGAAAACTTAATACTGTTAAAAATGTC 3979
                               - i      i ii i  i   i        i      i -  v 
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-TGGC 53

  chr2_175579789_   3980 CATACTATCCAAAGCAATCTAGACACTAAAGCAATCTAGACACTAAAGCA 4029
                         v     vi     vii     v v i ----   i------------   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATT----CAAC------------GCA 87

  chr2_175579789_   4030 ATCCCTACTAAAACCTCCA--TAGAATTTTTGCAGAAGTAGAAAAAA-GA 4076
                                ii    i -   -- ivvv           i v  v  iv-  
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATC-CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chr2_175579789_   4077 TTCTGAAATTCATATGAAATCTCAAAAGACCACAAATGGCCAAAACGATC 4126
                          i  i           i  viv   ii    vvi   i        i   
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr2_175579789_   4127 TTGGGAAAGACAAACAAGGCTGGATGCCTCAAATATCCTCATTTCAAAGC 4176
                            ii     vi     i i    v v    v iv   iv        i 
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr2_175579789_   4177 ATATAACAAAGCTACAAAGCTACAGTAATCAAAGTTGTATGGTTTTGG-- 4224
                         v  --------                     iiiv  i    vi   --
  L1M4_orf2#LINE/    237 TTA--------CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_175579789_   4225 -----------ACATAGACCAATGAAAGAGAACAGAGAGCTCAGATATAA 4263
                         ----------- i     i     i  v    iv     ii    v    
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_175579789_   4264 ACTGTCATGTGTATGGTCAAATGATCTTTAACAAGAGTACCAAGACTACA 4313
                           ivvi ii v         v    i  ii     i  i       i iv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_175579789_   4314 CAACAGGAAAAGGATAGTCTCTTCAACAAACAGTGTTGGGAAATCTAGAT 4363
                            ii  i    i       i         ii   i     v v  i   
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_175579789_   4364 ATCTATATGCAAAGGAATCA-------TCTGTAT---ACACCATGTACAA 4403
                          ? i i       i    v -------i iv  i---       i     
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_175579789_   4404 ACATCAACTCAAAATGGATTAAAGACCTAAATAGAAGACCTGAAACAACA 4453
                          v  i              i ?          iv    v  i    v i 
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_175579789_   4454 CAACTCCTAGAAGAAAACATAGGGGAAAAACATCATGACATTGGAATGGG 4503
                         v     i                ? v   v v  i    v    iv i  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_175579789_   4504 CAGTAATTTCTTGGATATGACACCAAAAGCACAAGTAACAAGAGCAAAAA 4553
                           i ii      i                      i     i  v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_175579789_   4554 CAGACAAATGGCACGACAGCACAA---AAAACTTCTGCACAATGAAGGCA 4600
                         i   i    v v  vv  v  v  ---       i  ii vvii    vv
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_175579789_   4601 ACAATCAACAGAGTGAAAAGGTAACCTAGGGAATGGGAGGAAATATTTAT 4650
                           v     v i         ii    i vi         i        ii
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_175579789_   4651 AAGCCATATTATCAGATATGGGGCTAATATCCAGAATATATAAAATATAT 4700
                           ii     -   v    v   i  vi                 ------
  L1M4_orf2#LINE/    729 AAATCATAT-ATCTGATAAGGGACTTGTATCCAGAATATATAAA------ 771

  chr2_175579789_   4701 AAAGAACCCCTATAACTCAATAACCAAAAAGTAGTAATAACCCAATTAAA 4750
                         ---    i i  i          iv    iii --            ?  
  L1M4_orf2#LINE/    772 ---GAACTCTTACAACTCAATAATAAAAAGACA--AATAACCCAATTWAA 816

  chr2_175579789_   4751 AACTGGCCAAAGGA-----ACAGACATTTCTCCAAAGAAGATATACAAAT 4795
                           v   v       ----- i                             
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_175579789_   4796 GACAAACAAGCATATGAAAAGATGTCCAACATCACTAATCAT 4837
                          i v  i     i           ii        ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (122 / 68)
Gap_init rate = 0.02 (16 / 904), avg. gap size = 4.56 (73 / 16)  


3040 26.82 0.88 0.66  chr2_175643177_175645438      865  1770 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_175643177_    865 TGGAAACACATCCCATGCTCACGGATGCATAGCATCAATATTGTGAAAAT 914
                               v i        i   i    vviv  vv i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_175643177_    915 GACCATACTACCAAAAGTAATCTGCAAATTCAATGCAACTCCCATCAAAA 964
                          i v     v  v   v i    i  i      i    ii  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_175643177_    965 TACCACCATTATTCTTCACAGAACTAGAAAACACAATCCTAAAATTCATA 1014
                          v   v vviv  i  ii     v v  v  vvii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_175643177_   1015 TGGAACCAAAAGAGAGCCTGCACAGCCATAGCAAGACTATGCAAAAAGAA 1064
                              viiv   i  v  v v i     v i   vvi iviv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_175643177_   1065 CAAATCTGAAGGCATTACATTACCCAGTTTCAAACTATACTATAAGGCCA 1114
                             vi  i   vv i   i v    i       viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_175643177_   1115 TAGTTACCAAAACAGCATAGTACTGGTATCAAAATAAGGATATGGACCAG 1164
                         i   v i   i    ii i       i  v ii   iiv    i  i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_175643177_   1165 TGAAACAGAATAGAGAATCCAGAAATAAAGCCAAATACTTACAGCCAACT 1214
                           i  i     v    i            v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_175643177_   1215 GACCTTCAACAAAGCAAACAAAAACATTAAGTGGGGAAAGGATACCCTAA 1264
                           ii   i    i vviv   i v    v i         i   vi  -v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT-T 399

  chr2_175643177_   1265 TTCAACAAATGGTGCTGGGAAAATTGGCAAGCCACATGTAGAAGAACAAA 1314
                                             v  i   vv ?       i i     ii  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_175643177_   1315 AGTGGATCCTCGTTTCTCACCCTATACAAAAATCAACTCAAGATGGATCA 1364
                         iv    i  iiiii  v    v           i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_175643177_   1365 AAGACTTAAATTTAAGACCTGAAATCATAAAAATTCTAGAAGATAACATT 1414
                         ?    i     v     v  i   ii      v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_175643177_   1415 GGAAAACCCCTTCTAGATACTGGCTTAGGCAAAGACTTCATGACCAAGAA 1464
                           ?iv vvi    vv  ivi   v        v ii   v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_175643177_   1465 CCCAAAAGCAAACGGAACAAAAGCAAAGATAAATAGATGGAACTTAATTA 1514
                         v         v v v        v   i   i   i  v i    v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_175643177_   1515 AA-TGAAAAAGTTT----CTTCATAGCAAAAGAAATAATCAGCAAAGCAA 1559
                           - v     v   ----     -----  i  v iv    iv    ii 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCA-----AAGGACACTATCAAGAAAGTGA 694

  chr2_175643177_   1560 ACAGACAACCCACAGAATAGGAGAAA-TCTTCACAATCTATACATCCGAC 1608
                          v                i       - v  ii   vii   i   i  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_175643177_   1609 AAAGGACTAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAAGAA 1658
                           i     vi          v  i  i      vv    v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_175643177_   1659 CAAAACAAGCAATCCCATCAAAAAGTGGGCTAAGGACATGAATAAACAAT 1708
                         v  i    ii  i  v  i?    i     v     iv      i   v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_175643177_   1709 TTTTAAAAGATGATATACAAATAGTCAACAA--ACATGAAAAAATGTTCA 1756
                          i iv     v           i i   i  --         i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_175643177_   1757 ACATCACTAATTAT 1770
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (138 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.33 (14 / 6)  


2828 27.97 1.66 0.89  chr2_175732536_175735913.rev     1994  2894 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_175732536_   1994 TGGAAAAAGATTCCATCCTCATGGATAGGAAGAATCAATATCATGAAAAC 2043
                               i v  i    vi        v      v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_175732536_   2044 GACCATATTGCCCAAGGTAATTTATGGATTCAATGCCATTTCCATCAAA- 2092
                          i v   i v     iv i  i  ii       i  v  ii i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_175732536_   2093 --CCATTGACATTCTTCGCAGAA-TTAAAAAAAAACT-ATTTTAAATTTT 2138
                         --   vivi v  i  i      -  i v  i---  -  ii    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_175732536_   2139 ATATGGAA-T-CAAAGAAGACCCCATATAGCCAAGACAATCCTAAGCAAA 2186
                                 - -   i --     viv        i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_175732536_   2187 AAGAACAAAGCTGGGGGCATCACACTATCTGACTTCAAACTATACTACAG 2236
                                   i   i  vv       vi ii i      viv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_175732536_   2237 GACAACAGTAACCAAACCAGGATGGTACTGGTACCAAAACAGATATGTAG 2286
                         ii v       i   iv   vi         i iv ii i   i  i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_175732536_   2287 ACCAACAGAGCAGAACAGAGACTTCAGAAGTAACACCACACATCTACAAC 2336
                          i   ii  ii    iv    v i     i   vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_175732536_   2337 CATCTGATCTTCAACAAACCTTACAAAAACAAGCAATGGGGAAAGGATCT 2386
                           vi    i   i    ivv vv   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_175732536_   2387 CCTATTCAGTATATGATACTGGGAAAACTGGCTAACCATATGCAGAAAAC 2436
                         i  v    ii v   i i      v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_175732536_   2437 TGAAACTGGACCCCTTCCTTACACCTTATGCAAAAATTAACTCAAGATGG 2486
                             ii         v   i     v   i               i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_175732536_   2487 ATTAAAGGTTTAAATGTAAAACCCAAAACCGTAAAAATCCTAGAAAAAAA 2536
                           i ?  iii         i v i     ii     v  i     i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_175732536_   2537 TCCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGCCTTCATGAC 2585
                         - v    ?i- v i -   iv   v v  vv i     v vi   v iiv
  L1M4_orf2#LINE/    546 -CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_175732536_   2586 AAAAACGCCAAAAGCAACTGCAACAAAAGCCAAAATTGACAAATGGGATC 2635
                         v vi  i         vvv          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_175732536_   2636 CAATTAAACTAAAGAGCTTCTGCACAGCAAAAAAAGCTATCATCAGAGTG 2685
                         iv  i   v v  i i   i  ii vv    ii vi      vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_175732536_   2686 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCAATCTGA 2735
                           v  i     i                 v       vii ivv      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_175732536_   2736 CAAAGGTCTAATATCCAGAATTTACAAGGAACTTAAACATATTCA-CAAG 2784
                         i  i  v  vi          v  i  i     ivv   - i   -i  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCAATAAT 792

  chr2_175732536_   2785 AAAAAAACAA----CCCCATCAGAAAGTGGGCAAAGGATATGAATAGAGA 2830
                              i    ----   v  i?i   i            v        v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_175732536_   2831 CTTCTTAAAAGAAGACATTTACACAGCCAACAAACATATCAAACAGTGA- 2879
                         i    iv        i  vi v ii     i  i  i  v   vii  v-
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_175732536_   2880 -GATATCATCTTATGG 2894
                         -i i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (151 / 97)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


 940 28.57 0.00 0.00  chr2_175817665_175819664      501   759 (1241)    L1M4_orf2#LINE/L1      169   427 (481)  

  chr2_175817665_    501 AGACTAACCAAAAATATCTTGAAAAATGAGGACTAAATTGGAGAATTTAC 550
                            v  i      vv           vi  i  v  i      i i i  
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_175817665_    551 CCTAACTGACTGGAACACTAACTGTAAAGCTAGAGTAATCAAAATGGTGT 600
                         v  vv ii i vv  v   v   ii       v         i ii    
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_175817665_    601 GGTACTAGCATAAAAGTTGACAGAGTGATGAATGGAACAGAATATAATGC 650
                               i      iii v    v vv   v       i     vv iv i
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_175817665_    651 CCAGAAACAGACCCACACTTACACAATCATTTGATTTTCATTAAAGGAGC 700
                                i i     i  v vi iii   v         ivi  i  v  
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_175817665_    701 CAAAGCAGTTTAATGAGGAAAGAAAAATCTTTTCAGGAAATTATGCTGGG 750
                            ii vi  i    i        v i        iv    vi       
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_175817665_    751 ATATCTAAA 759
                          i v  ii 
  L1M4_orf2#LINE/    419 ACAACTGGA 427

Transitions / transversions = 1.39 (43 / 31)
Gap_init rate = 0.00 (0 / 259), avg. gap size = 0.00 (0 / 0)  

1220 21.88 8.47 2.59  chr2_175817665_175819664     1076  1500 (500)    L1M4_orf2#LINE/L1      439   888 (20)  

  chr2_175817665_   1076 AAAAAAAAAAAGTTAGCTTCAACCCCTATCTCACACCATACACAAAAATT 1125
                             i  vi     i -----       i           i         
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGG-----ACCCCTACCTCACACCATATACAAAAATT 483

  chr2_175817665_   1126 AATTCAAGATTAAAGAGAAATCTAAATG---------AAACAGTAAG--T 1164
                           i    i  vi vv ? i i       ---------    vi   i-- 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_175817665_   1165 TTTAGAGGAAAACAAAGGAGAATACCTTCATAATCTAAAGGCAAGCAAAA 1214
                         i     i       v   ? v v i    i i i  vii vi i    vi
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_175817665_   1215 ATTTCT--GACAAGTCACAGAAAGCAACAACCATAAGAGGAAAAAAATTA 1262
                         i     --  i v v   vi      vv i v i  i  --       vi
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG--AAAAAATAG 631

  chr2_175817665_   1263 ATACATTAGGATTCATTAAAATTAGAAACATCTGCTCATCAAAAGATATT 1312
                            v   i iv     i       i    v i  iv v     i  i i 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_175817665_   1313 ATTACGAAAATTAAGATGCAAACCACAGAA--AAAGAA-------GC--- 1350
                           i v    i v  i vi   v        --ii    -------  ---
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_175817665_   1351 -C-----TCTGACAAGG-ACTGGTATCCAGGATATATAAAGAACTCCTAC 1393
                         - -----     i    -   v        i               i   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_175817665_   1394 AACTCAATAATAAAAAGACAA----CCCAATTTTTTAAAATGAGCAAAAG 1439
                                              ----       ?v--      i     i 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWA--AAAATGGGCAAAGG 829

  chr2_175817665_   1440 ATTTAAAAAGATACTTCACAAAATGTAAGGGATACAAATGGCCAACAAAC 1489
                             i  v   i i   v v   - -   iv              i  i 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAA-G-AAGATATACAAATGGCCAATAAGC 877

  chr2_175817665_   1490 ACATGAAAAAA 1500
                                  i 
  L1M4_orf2#LINE/    878 ACATGAAAAGA 888

Transitions / transversions = 1.73 (57 / 33)
Gap_init rate = 0.03 (14 / 450), avg. gap size = 3.36 (47 / 14)  


4599 15.75 4.11 0.46  chr2_175905796_175909243     2081  2956 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_175905796_   2081 TAGAAAGACATCATCCATGCACATAGATTGGAACACTTTCTATTGTTGAG 2130
                          i      i   --     iv   i        v    vv       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATC--CCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_175905796_   2131 ATGGCAGTACTCCCCAAATTCATCTACAGATGCAACACAATTCCTATAAA 2180
                               i             v          v    i    i     v  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_175905796_   2181 AATCCCAGCTGGCTTTTT-GCAGAAATTGACAATCTGATCCTAAAATTCA 2229
                                    v      -              v                
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_175905796_   2230 TATGAAAATTGAAGGGACATAGAATAGCCATAGTAATTTTAAGAAAAAGG 2279
                             i    vv       vi          v ii   i  i i   i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_175905796_   2280 AATAAAGTTGGATTTTTCACATTTCCTGATTTC-----------CAA-GC 2317
                           i         vvvi     i    ii     -----------   -  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_175905796_   2318 TACGGTAATCAAGACATTGTAGTACCAACATCAGGATAGACATAGAGATC 2367
                            i            v   i    iii   v            v     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_175905796_   2368 AATGAAATAGAATTGAGAGTCTAGAAACAAATCCTTACATTTCTGGT-AA 2416
                             i                i     i   i  v       v    -  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_175905796_   2417 TTTTTGTTTTTG-CAAGAGTGACAAGACAATTCAACGGGAGATGGGTATT 2465
                           v--i    i -    i   v      v      i   ii v ii  v 
  L1M4_orf2#LINE/    349 TTG--ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_175905796_   2466 AATTTCAACAAATGGTGCTAGGACAACTGAATATTCACTTGCAAAATAAT 2515
                         vv                 i         i   ?i   v       v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_175905796_   2516 GAATTTGGATCCATACCTCACATTATACCCAAAACTTAACTAAAAAAGGA 2565
                            v     i  v         ii   iv     v      v    v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_175905796_   2566 TCAAAGACCCAAATATAAGAGATAAAACTATGCAATTCTTAGAGGAAAAC 2615
                            ?     i    i      v         iv  i       i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_175905796_   2616 ATAGGCATAAATCTTCATGGCCTTGAATTAGTCAACAGTTTCTTAGACTT 2665
                              ?i         i  i     ii    v   ii          iv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_175905796_   2666 ATCAACAAAAGCATAAGTAACAAAAGAAAAAATAGATAAATTGAACTTCA 2715
                         iv  v        i   i                         i      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_175905796_   2716 TCGAGATGAAAAACTGTTGTGTTTCAAAGGGCACTAT-AAAAAAGTGAA- 2763
                           i i  v       v     i        i      -  i        -
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_175905796_   2764 -GACAGCCCACAGAATGGAAGAACATATTTGCAAGTCATATATCTGATAA 2812
                         -    i            i    v          i               
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_175905796_   2813 GAG-------CCCAGAATATGTAAAGAACTC--ACAGCTGAAGAATAAAA 2853
                          i -------i         i          --   i  v  v       
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_175905796_   2854 AGACAA-TAGCTTAATCACAAAACGAACAAAA-ATTTGAATAAACATTTC 2901
                               -  i ii   i?v    i ii    i-         i       
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_175905796_   2902 TCCAAAGGAGACATACAAATG-------AGCACATGAAAAGATGCTCAAC 2944
                                i   i         -------                      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_175905796_   2945 ATCATTAACCAT 2956
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (86 / 48)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.86 (40 / 14)  


2462 14.90 5.37 11.18  chr2_175914071_175915731.rev      499  1169 (492)    L1M4_orf2#LINE/L1      277   908 (0)  

  chr2_175914071_    499 CGTAAGGATAGACATACGAATTAAAGAGAATAGAATCGAGAGTCCAGAGA 548
                          i              iii  i  v -         i           i 
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATG-GAATAGAATTGAGAGTCCAGAAA 325

  chr2_175914071_    549 TACACTATTACATTCAAGTTCAGTCAATTTTTGACAAAGGTGCCTAGACA 598
                           v  ivv      i v v   i ii     i     i      v    v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_175914071_    599 ATTCAATGGGGAA-GAACAGTCTTTTCAAAAAATAGTTCTGGGACAACTG 647
                                      -   i           v    i  v            
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_175914071_    648 GATAGCCACAGGCAAAAGAATC---TT----CCTTCTCTTATACCATATA 690
                             ?     v          v---  ----  i vi  i i        
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_175914071_    691 CAAAAATTAACTCCAAATGGATCATAGAGCTAAATGTAAGAGGTAAAACT 740
                                      v          ?   v             v       
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_175914071_    741 ATAAGACTCCTAGAAGAAAATATAGGATTCAGTCTTTGTGACCTGGGGCT 790
                             i    i          i     ?v v i    i       v   i 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_175914071_    791 A-------------TA----------CAAAGGCACAAATAACAAAGGACA 817
                          -------------  ----------    i      ii      i  - 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-A 624

  chr2_175914071_    818 AAAATAGATAAA-----CTTTCTCAAAATTTACCACTGTAATGCTCCAAG 862
                                     -----   iv        v vv   v vi    i   i
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_175914071_    863 GGAGAATATCAAGAAAGTGAAAAGACAACCTACAAAATGCAAAAAAGTAT 912
                            v v                        i   i    vi i   i   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_175914071_    913 TTACAAATCATATATCTGATGTGTGACTTGTATTTAAATTCTATTTTAAA 962
                           i                 iv v         ii i v v   ---   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT---AAA 771

  chr2_175914071_    963 AAACTCTTACAACCAGTAATAAAAAAATGAAAAGCCCACTCAATTTTTCT 1012
                         i            --------------------------     ------
  L1M4_orf2#LINE/    772 GAACTCTTACAAC--------------------------TCAAT------ 789

  chr2_175914071_   1013 GTATATCTAAAACTGTTCAAAAAATAAAGTCTATTCATTTTTAAAAGACA 1062
                         ----------------------      ----------------      
  L1M4_orf2#LINE/    790 ----------------------AATAAA----------------AAGACA 801

  chr2_175914071_   1063 AATAACTAAATTTTAAAATAGACAAATGATCTGCGTAGAAACCTTTCCAA 1112
                               iv    ?v     i i    v   i  vi    v ii i     
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_175914071_   1113 AGAAAATATACAAATCGCCAATAAGCAGCTGAAAGGATGTTCAACATCAT 1162
                             i          v           vv     i    i         ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_175914071_   1163 TAGCCAT 1169
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.40 (56 / 40)
Gap_init rate = 0.02 (12 / 632), avg. gap size = 9.25 (111 / 12)  


3043 18.80 7.43 0.58  chr2_176048437_176050114      501  1186 (492)    L1M4_orf2#LINE/L1      176   908 (0)  

  chr2_176048437_    501 CCAAAACAATCTTGATAAAGAAAAGTAAAGCTGAAGACCTCACATTTTTT 550
                                        v      i ii    i  i  iv      i  iii
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_176048437_    551 GATTTTAAAGTATATTACAAAGTTATAGTGATCAAAATAGTGTGTTACTG 600
                         i    i   iiv  i       i  i   i     i i      v     
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_176048437_    601 GCATAATGATAGACATATAGACCAATGGAACAGAATAGAAAGTCCA-AAA 649
                               v              i        i     v  i      -   
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_176048437_    650 TAAACCCTCATGCAT--ATGGTCAA---AT------------------GA 676
                                --  i   --        ---  ------------------  
  L1M4_orf2#LINE/    326 TAAACCC--ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr2_176048437_    677 CC------------------------TTCAACAAATATTGTTGGAA-AAC 701
                           ------------------------          iv  i   i -   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_176048437_    702 TGGATATCCACATGCAAAACAATGATGTTGGACTCCTACGTTATACCACA 751
                               ?            v     v       i     v i i    i 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_176048437_    752 TACAGAAATTAATTAAAAGTAGATTAAAGACTTAAACATAAGACCTTTAA 801
                             i       i v   i i   i ?    i    ii     v  vv  
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_176048437_    802 CTAGAAAACTCTTAGAAGAAAACATAAAGGAGAAGTTTTATGACATCGGA 851
                            v                      ii? vi  vi  ii    v i  i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_176048437_    852 TTTGGCAATGATTTCTCAAATATGACACCAAAAACACAGGCGAGAAAAGC 901
                           v       i     i i              i    i  i v     v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_176048437_    902 AAAAA-AGACAAATAGGATTACACCAAGTTTAAAAACTTATGCACAGCAA 950
                              -   i    v   i v  i   iv          v  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_176048437_    951 AGGAAACAATCAACAGAGTGAAAAGGCAACCAATGAAATGGGAGAAAACA 1000
                             v  v     v i         i     v iii            i 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_176048437_   1001 TTTGCAAACCATCTATCTGATAAGAGGTTAATACTCA-AATATATAAAGG 1049
                                 i   v           i ii vi  ii  -           i
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_176048437_   1050 ACTCCTACACTTCAATAACAAAAAACCCCAAATAATCAAATTTAAAAGCG 1099
                             i    vi       i     iv --      i v    ?    ii 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGAC--AAATAACCCAATTWAAAAATG 821

  chr2_176048437_   1100 GGCCAAGGATTTGAAGAGACATTTCTCCAAAGAGGACATACAAATGACCA 1149
                            v           v                 i  i         i   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_176048437_   1150 AAATGTACATGAAAAGAAGCTCAACATCACCAATCAT 1186
                          v v i           v           ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (84 / 41)
Gap_init rate = 0.01 (10 / 733), avg. gap size = 5.50 (55 / 10)  


3339 26.65 0.44 0.44  chr2_176172453_176178729.rev     4878  5785 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_176172453_   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4927
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176172453_   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176172453_   4978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_176172453_   5026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_176172453_   5076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5125
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_176172453_   5126 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGATC 5175
                                 i   i    ii         i i  ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_176172453_   5176 AATGGAACAGAAC--AAAGCCCTCAGAAATAATGCCGCATATCTACAACT 5223
                                i    i-- i  i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_176172453_   5224 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5273
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_176172453_   5274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_176172453_   5324 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5373
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_176172453_   5374 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_176172453_   5424 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5473
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_176172453_   5474 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5523
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_176172453_   5524 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5573
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_176172453_   5574 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5623
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_176172453_   5624 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5673
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_176172453_   5674 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5723
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_176172453_   5724 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5773
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_176172453_   5774 ATCACTGGCCAT 5785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3459 24.39 1.33 0.67  chr2_176186447_176189723.rev     1884  2785 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_176186447_   1884 TGGCAATATATTCCATGTTCATGAATTGGAAGAATCAATATTGGTAAAAT 1933
                            v  v    i           i         v i       v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176186447_   1934 GTCCATACTACCCAAAGCAAACTACAGATTCAATGCAATGCCTATCAAAA 1983
                          v v     v      vii v            i     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176186447_   1984 CATCAATGACATTCTTCACAGAAATAAAACAAAATG---CTAAAATGTAT 2030
                         ivi  iivi v  i  ii       vi -   iv  ---       vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr2_176186447_   2031 ACAGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAGAAAAAAGA 2080
                          ii   vii   ii                 i v   i   i   i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_176186447_   2081 A---AATTGGAGGGATCACATTACCTGACTTCAAATTATACTACAGAACT 2127
                          --- i       iv     i v  ii i      viv       i i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_176186447_   2128 ATAGTAAACAAAACACAATGGTACTGGCATAAAAACAGGCACATAAACCA 2177
                          i     v   i   vvi              ii i  i  i   i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_176186447_   2178 ATGAAACAGAATCGAGAATTGAGAAACAAATTCATGGACTTACAGTGAAA 2227
                            i  i     i    i iv     i   ii   iv i   ii  v  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_176186447_   2228 TTACTTTTGACAAAGGTGCCAAGAACCTACATTGGGGAAAAAAACCATCT 2277
                          v i   i     i          v v v  v        i  -ivi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCT 398

  chr2_176186447_   2278 CTTCAATAAATGATGTTCGGGA-AACTGGATATCGATATGCAGAAGAATG 2326
                         i     i     i  i -    -         ? v i     i       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_176186447_   2327 AAACTTGACCCTTCTCTCTCACCATATGCAAAAATCAAATCAAAATGGAT 2376
                           ii v     i vi   v        i       i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_176186447_   2377 TAAAGACTTAAGTCTAAGACCTCAAACTG--AAACTACTGCAAGAAAACA 2424
                         i ?    i   i v     v  v     i--     vi iv         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_176186447_   2425 CTGGGGAAACTCTCCGCAATACTGGTCTGAGCAAAAATTTCTTGAGTAAT 2474
                         iv  ? v  v   i  ii ivi   vi ii    vii      iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_176186447_   2475 AC-CCAACAAGCACAGGCAACCAAAGCAAAAATGGACACATGGAATCACA 2523
                           -    -       i     v    v      i  i v  v i iiv  
  L1M4_orf2#LINE/    598 ACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_176186447_   2524 TCAAG-TTAAAAGCCTTCTACACAGCAAAGGAAACAACCAACAAAGTGAA 2572
                             i-      i i  - iii vv       v  v i   v        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_176186447_   2573 GAGACAACACATAGGATGGGAGAAAATATTTGCTAATGGCCCATCTGACA 2622
                         i       v  i  i                  v   viivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_176186447_   2623 AGTGATTCATAACCAGAATATATAAGGAGTTCAAACAACTCTACAGGAAA 2672
                           v  i ii  v             i  ii  vv       v i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_176186447_   2673 AAAGTCTAATAATGCAATTTAAAAGTGGGCAAAAGTTCTGAATAGACATT 2722
                           - v v     iv     ?    i        i v i            
  L1M4_orf2#LINE/    796 AA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_176186447_   2723 TCTCAAAAGGAGACATACAAATGGCAAACAGGCATGTGAAAGG-TGCTCA 2771
                             v    i   i           v  i i   ii     i -      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_176186447_   2772 AAATCATTGATCAT 2785
                          v    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (136 / 80)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.38 (18 / 13)  


2882 26.74 4.46 0.69  chr2_176195395_176199578     2818  3692 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_176195395_   2818 TGGAAGAACATTCCATGCTCATGGATAGGAA-------TAT-----AGGT 2855
                              ii i  i     i        v    -------   -----  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176195395_   2856 --------------AATT----TATAGATTCAATGCCACCCTCATCAAAC 2887
                         --------------    ----  i        i  v i  ii      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176195395_   2888 TACCAATGACTTTCTTCACAGAA-TTGGAGAAAAACT-ACTTTAAAGTTC 2935
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_176195395_   2936 ATATGGAACCAAAAAAGAAGCCC-GCATTGCCAAGACAATCCTAAGCCAA 2984
                                 viiv  ii  --   - v  v     i      i i ivv i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_176195395_   2985 AAGATCAAAGCTGGAGGCTTCATGCTACCTGACTTCAAACTATACTTCAA 3034
                             v     i      vi   ii  v  ii i      viv    v   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_176195395_   3035 GGCTACAGTAATCAAAACAGCATGGTACTGGTACCAAAATAGAGATATAG 3084
                         i              i    ii         i iv ii     v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_176195395_   3085 ACCAATGGAAAAGAACAGAGGCCTCAGAAATAACACCACACATCTACAGC 3134
                          i        v    iv   ivii         vv   i    i  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_176195395_   3135 CATGTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 3184
                           vv    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_176195395_   3185 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3234
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_176195395_   3235 TGAAACTGGATTCCTTCTTTACACCTTATACAAAAAATAATTCAAGATGG 3284
                             ii    ii   v i i     v          v   i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_176195395_   3285 ATTAAAGATTTAAATATTAGACCTAAAACCATAAGCACTCA-AGAAGAAA 3333
                           i ?   ii     i v   v       i    i-    v-        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAA 544

  chr2_176195395_   3334 ACCTAGGCATTACCATTCAGGACATAGGCTTGGGCAAGGACTTCATGACT 3383
                           v    ?i v viv   iv   v v  v  i     v ii   v iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_176195395_   3384 AAAACACCAAAAGCAATGGCAACAAAAGTCAAAACAGACAAATGGGATCT 3433
                          vi            vvi          vv    i   i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_176195395_   3434 AATTAAACTAAAGAGCCTCTGCATGGCAAAAGAAGCTACCATCAGAGTGA 3483
                         v  i   v v  i i i i  iiivv    i  vi   i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_176195395_   3484 ACCGGCAGCTTACAGAATTGGGGAAAATTTTTGCAATCTACCCATCTGAC 3533
                          vv i  i ii       v  i      v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_176195395_   3534 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 3583
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_176195395_   3584 AAAAACAA----CCCCAT-AAAAAGTGGGCAAAGGATATGAACAGGCACT 3628
                            i    ----   v  -?    i            v    i  i  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_176195395_   3629 TCTCAAAAGAAGACATTTACATAGCCAACAGACACATGAAAAAATGCACA 3678
                             v        i  vi v  i     i ii          i    v  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_176195395_   3679 TCATCACTGGTCAT 3692
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.46 (45 / 13)  


 989 26.78 0.00 2.37  chr2_176221501_176223067      152   446 (1121)  C L1M4_orf2#LINE/L1   (620)   288     1  

C chr2_176221501_    446 TGGGAAAACATTCCATGCTCATGGACTGGAAGAAACAATGTGTGGTTCAG 397
                            i  i i  i     i       i       vvi   i -  -  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-TG-TTAAG 48

C chr2_176221501_    396 CTGGTTCAAATATGGTTCAAAAGCAATCTACAGATTCAATACTATTTCTA 347
                         v   i---    ivvii    -vii              ii v  ii   
  L1M4_orf2#LINE/     49 ATGGC---AATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTA 94

C chr2_176221501_    346 TCAAATTACCAACATCATTTGTCACAGAATTAGAAAAACACAATTCTAAA 297
                              v v   i vv v   v ii     v v  v  i -ii  i     
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAA 143

C chr2_176221501_    296 ATTCATGTAGAACCAAAAAAGAGCCTGAATAGCCAAAGCAATCCTAAGCA 247
                               i i   viiv  ii  v  v           i     i i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

C chr2_176221501_    246 AAAAGAACAAACCTGAAGGAATCACACTACCTGACTTCAAACTATACTAT 197
                          i         vi  i    v       v  ii i      viv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

C chr2_176221501_    196 AAAGCTACAGTAATCAAAACAGGATAGTACTGGTCCAACCATAGA 152
                                          i    vi i       ivi  vv     
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

Transitions / transversions = 1.55 (48 / 31)
Gap_init rate = 0.02 (5 / 288), avg. gap size = 1.40 (7 / 5)  

1511 28.00 8.70 1.74  chr2_176221501_176223067      501  1075 (492)    L1M4_orf2#LINE/L1      294   908 (0)  

  chr2_176221501_    501 AGACCAATGAAACAGAATAGGGAACTCTGAAATAAAGTTGCACACCTACA 550
                            i     i  i     v i  iii v        viiii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_176221501_    551 GCTATCTGATTTTTGACAAAATAGACAAAAATAAGCAATATGGAAAGGAC 600
                          ii vi       i     iivv v   i vi vv    iv      i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_176221501_    601 TCCCTATTTAATAAATGGTGCTGAAATAGCTAGCTAGCCATATGCAGAAG 650
                         vvi  v  i  i           ii i i  i v  ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_176221501_    651 AATGAAACTGGACTCCTATCTTTCACCATATACGAAAACTAACTCAAGAC 700
                               ii     i    i  iv          i    i        i i
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_176221501_    701 GGAGTAAAGATTTAAATCTAAGGTCTCAGACTATAAGAATGCTAGAAGAA 750
                            vi ?   ii     v    iv  v i       i v vi        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_176221501_    751 AACCTAAAAA-ACACCACTCTAGACATCAGCCTTGGGAAAGAATT----- 794
                            v  ii?i- v i -i  vv   v ii vi v  v  v iv  -----
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_176221501_    795 -TATGACTCAGTCCTCAAAAGCAACTGCAACAAAAACAACAATTGACAAG 843
                         -      v ------        vvv         iv  v   v  i  i
  L1M4_orf2#LINE/    593 ATATGACAC------CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_176221501_    844 TGGGAACTAATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAAGTACCAA 893
                          v   vi v  i   v v  i i   i   i vv    i  v v  i   
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_176221501_    894 TAGAGTAAACAGACAACAACTTGCAGAAGGGGAGAAAATATTTGTAAATT 943
                         v i   i  v       ---iii     v               i    i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAAC---CCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_176221501_    944 ACACATCTGAAAAGGGGCTAATACGCAGAATCTATAAGGTACTTATAAAA 993
                          i i      v     i  vi  iv      v     i v   iv  v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_176221501_    994 TTCAAT-------------------------------GAGCAAA------ 1006
                         i     ------------------------------- i     ------
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_176221501_   1007 -AACGGACATAC-----AAGAAGACATACAAGTGGCCAAGAAACATATGA 1050
                         -  ii     vi-----       i      i       v  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_176221501_   1051 AAAAATACTCCACATCACTAGTCAT 1075
                            i  i   v      ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (97 / 61)
Gap_init rate = 0.01 (8 / 615), avg. gap size = 7.50 (60 / 8)  


3238 26.43 0.88 0.88  chr2_176279037_176285298.rev     4863  5770 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_176279037_   4863 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4912
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176279037_   4913 GGCCATACTGCCCAAGGTAATTTACAGATTCAGTGCCATCCCCATCAAGC 4962
                            v     v     iv i  i          ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176279037_   4963 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5010
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_176279037_   5011 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5060
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_176279037_   5061 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5110
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_176279037_   5111 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5160
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_176279037_   5161 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5208
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_176279037_   5209 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5258
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_176279037_   5259 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5308
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_176279037_   5309 GAAAGTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5358
                            iv    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_176279037_   5359 TTAAAGACTTAAACTTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5408
                          i ?    i    iv v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_176279037_   5409 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGCCTTCATGTCTAA 5458
                         v    ?i v viv   iv   v v  vv i     v vi   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_176279037_   5459 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5508
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_176279037_   5509 TTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGAAC 5558
                          i   v v  i i   i  iiivv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_176279037_   5559 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCTTCTGACAA 5608
                           i     i   i             v  i    vii iviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_176279037_   5609 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5658
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_176279037_   5659 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5708
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_176279037_   5709 TCAAAAGAAGACTTTTATGCA----GCCAAAAAACACATGTAAAAATGTT 5754
                           v        ----   i  ----     v  i      v   i   i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_176279037_   5755 CATCATCACTGGCCAT 5770
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


3700 21.59 2.24 1.23  chr2_176307724_176309743.rev      635  1528 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_176307724_    635 AGATTTTCCATGTTTATTGATTGGAAGAATTAATATTGTTAAAATGTCCA 684
                             v i       i  v          v             i   v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_176307724_    685 TACTACCCAAAGCAATCCATAAAGTCAGTGCAATCCCTATTAAAATTCAA 734
                             v      vii   i i i v   ii           i     i v 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_176307724_    735 ATGACCATTTTTTTGTAGAAATAGAGAAAATGATACTAAAAGTCTTATGG 784
                         iivi  --       i      v  v  iv    v      v  v     
  L1M4_orf2#LINE/    106 GCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_176307724_    785 AACCACAAAAGATCTCAAATAGCCAAAGGAATCTTTCAGCAAAAAGAACA 834
                           vii   ii  i ivi          iv      vv i-  i       
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGAAGAACA 202

  chr2_176307724_    835 AAGCTGGAG-----ACA--------TCTCAAAATTTGCTACAAAACTATA 871
                            i     -----   -------- i      i  i       i   i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_176307724_    872 ATAATCAAAACAGGATGATACTGGCA-AAAAACAGACATAGAGACCAGTG 920
                         i       i    vi  i        -  ii i       v   i  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_176307724_    921 GAACAGAATAGAGAATCTAGAAATAAATCTACACAACAACAGTCAACTAC 970
                            i     v    i  i         i i i   viv ii     i i-
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG- 351

  chr2_176307724_    971 AAGCAACTTTGACAAAGGTGACAAGAACAAATT--ATGAGGAAAGGATAA 1018
                         ---- vi  i     i    v     v  --  --   i      i   i
  L1M4_orf2#LINE/    352 ----ATTTTCGACAAGGGTGCCAAGACCA--TTCAATGGGGAAAGAATAG 395

  chr2_176307724_   1019 CACCTTCAATAAATGGTGCTGGAAAAATTGGATA-CCACATGCAAAAGAA 1067
                         ivii     i            i v  i      -               
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_176307724_   1068 TAAAATAGGACCCTTATCTCACCCCATA-AGAAACACAAACTTAAAATGG 1116
                          i  i v      i  i     v     - v   v iv    i       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_176307724_   1117 ATTAAAGACTTAAAGTTAAGACCTGAAACTGTAAAACTACTAGAAGAAAA 1166
                           i ?    i    vv     v  i     i       vi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_176307724_   1167 CATAGGGA-AAGTCTCCATGACATTGGTCTGGGCAATAATTTGTCGGTTG 1215
                               ?i-  i   i i    v    vi i      ii   v ii v i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_176307724_   1216 TGACCACAAAAGCATAGGCACCAAAAGCAAAAATAGACAAATAGGATTGC 1265
                             vv        i i   v      v         i    v   i v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_176307724_   1266 ATCAAACTAAAAAGCTTCTGCACTGCCAAAGAAACAATCAACAGAGTGAG 1315
                               v v    i   i  ii  v v  i  v  v     v i     i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_176307724_   1316 GAGACATCCTATGGAATGGGAGAAAATATTTGCAAACCATACATCTGATA 1365
                         i     v  i ii                       i    i        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_176307724_   1366 AGGGACTAATATCAAAAATATATATGGAACTTGAACAACTCAATAACAAG 1415
                                vi    v i        vi     ivv            i  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_176307724_   1416 AAAACAAATAGCCCAATTTTAAAAATGGACAAAGGATCTGAATAGACTTT 1465
                           i       i       ?-        i        i         v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_176307724_   1466 TCTCAAAAGAAGACATAACAATGATCAATAGGTAAATTAAAA-ATGTTCA 1514
                             v        i   vv    ii     i i v  v    -   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_176307724_   1515 ACATTACTAATCAT 1528
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (121 / 69)
Gap_init rate = 0.01 (13 / 903), avg. gap size = 2.38 (31 / 13)  


1135 21.96 8.63 0.39  chr2_176333955_176336737.rev     1118  1372 (1411)    L1M4_orf2#LINE/L1        1   276 (632)  

  chr2_176333955_   1118 TGGAGTGATATTCCGTGTTCATGGATAGGAAGACACAATATTGTCAAAAC 1167
                             iv     i  i           v       vi        i  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176333955_   1168 GTCATTTCTTCCCAACTTGCTCTATAGATTCAGTGCAATCCCAATCAAAA 1217
                          v  v v  i     v   v    i       ii        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176333955_   1218 TCCCAGCAGGTTATTTTGTAAACATCAACAAACTAATTCTGAAGTTTAAA 1267
                                v vi v     i i v  ii    i  i  i  i  i  i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_176333955_   1268 TGGAGAGGCAAAAAATCCCCAAATAGTCAACACAATATTGAAGGAGAAAA 1317
                             i v    iii -   vi     i   v     v     ii    i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_176333955_   1318 ACAAAGTTGGAGGACT----------------------TACTATAAAATT 1345
                                         ----------------------     i   ii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_176333955_   1346 GCAGTAATCAAGACAGTGTGTGGCTGG 1372
                         i                   vvi    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGG 276

Transitions / transversions = 1.80 (36 / 20)
Gap_init rate = 0.01 (2 / 276), avg. gap size = 11.50 (23 / 2)  

2158 24.96 3.50 0.16  chr2_176333955_176336737.rev     1671  2299 (484)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr2_176333955_   1671 AAGACAGTGAGGTATGGGCAAAAGAATAGACAAATAGATCAATAGAAGAG 1720
                                  v    iv    v   i       v          i   v  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_176333955_   1721 AATAGGGAGCCCAGAAATAAACCTACATAAATACAGTCAACTTATCTTTG 1770
                            v i   i             i i i vv  ii     i v  i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_176333955_   1771 GCAAGAAAGCAAAGGCAATACAATGAAACAAAGATAGTCTTTTCAACAAA 1820
                         i    iiv  v   i v  v     iiiv  ii                 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_176333955_   1821 TGGTGCTGGAACAACTGGACATCCACAAGTGAAAAAA-GAATCTAGGCAT 1869
                                  i         i ?     v ii   i  -   vi i i vi
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_176333955_   1870 AGACCTTAAACCCTTCACAAAAATTAATTAAAAAT-------AGACCTAA 1912
                         vv    i v   v vi           i v     -------        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_176333955_   1913 ATGTAAAATGTAGAAGTATAAAACTCCTGGAAAATAACA--AGAGAAAAC 1960
                               i vv  i  v          i i   i v    --i ? v   i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_176333955_   1961 CTAGATAACCTTGGGTATGGAAATGACTT--TGGCTACAACACTAAAAGC 2008
                           vvi i         vv  v    ii  -- i v  ii    i      
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_176333955_   2009 ACAATCTATGAA-GAAACAGTTGATAAGCTGGACATTATTAAAATTAGAC 2057
                             v v ii  -    v i v     ii     v i  i       i v
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_176333955_   2058 ACTGATTCT-CTGTAAAAGACAATGTCAAGAGAATGAGAATATAAACCAC 2106
                            v-  v -  vi   i    v i      i i   i  v i  v    
  L1M4_orf2#LINE/    659 ACTT-TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_176333955_   2107 AGACTGGGGGAAAGTATTTGCAAAAGACACACCTAATAAAGAACTCTTAT 2156
                            v    i    i          vv i i i  i    i i   iv   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_176333955_   2157 CCAAAATATACAAAGATCCCTTAAAACT---TAATGAGAAAACAAATGAC 2203
                            i      i     v i    v    ---    i i  i      i  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_176333955_   2204 ATAATTAAAAAATGTGTCAAAGACTTTAAC-GACACTTCATCAAAGA--- 2249
                         vi    ?       v iv  i  i  v  i-    i   vi      ---
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_176333955_   2250 TATATAGATGGCAAATAAGCATATAAAAA-ATGCTTTAGGCCAGGCATAG 2298
                             i i     v        i  i    -     iv vii  ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_176333955_   2299 T 2299
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.57 (94 / 60)
Gap_init rate = 0.02 (11 / 650), avg. gap size = 2.09 (23 / 11)  


2931 26.19 0.75 3.12  chr2_176339566_176344074     3090  4017 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_176339566_   3090 GAAACATATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAATGA 3139
                             v          i        v  v   v i        v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_176339566_   3140 CTATGCTGCCAAAAGCAATCTACAAATGCAATGCAATTCTCATCAAAATA 3189
                          v  i  v  v   vii       i  v   i     i ii        -
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT- 101

  chr2_176339566_   3190 CCC--CCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCATA 3237
                            -- iii -  i  ii     v v  v  ivii               
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_176339566_   3238 TGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAAACTGAGCAAAAAGAA 3287
                              viiv  ii  v  viv         i   vvi   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_176339566_   3288 CAAATCTGGAGGCATCACATTACCTGACTTCAAGCTGGACTCTAAGGCCA 3337
                             vi      vv     i v  ii i     ivivv   vi  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_176339566_   3338 TAGTCACCATAACAGCATGGTACTGGTATAAACATAGGCACATAGACCAA 3387
                         i   v i  vi    ii         i    iv    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_176339566_   3388 TAGAAAAGAATAGAGAACCCAGAAATAAAGCCAAATACTTAAAGCCAACT 3437
                          i   v     v    ii           v   v i i   vi i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_176339566_   3438 GATCTTCAACAAAGCGAACAAAAGCATAAAGTGAGGAAAGGGCATCCTAT 3487
                            i   i    i vviv   i v   vv i  i      iii vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_176339566_   3488 TCAACAAATGGTGCTGGAATGATTGGCAAGCCACATGTAGAACAGTGAAA 3537
                                          i ii i   vv ?       i i  v i    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_176339566_   3538 CTGGATCCTCATGTCTCACCTTATACAAAAATCAACTCAAGATGGATCAA 3587
                         i    i  ii iv  v    v           i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_176339566_   3588 AGACTTAAATCTAAGACTGGAAACCATAAAAATTCTAGAAGTTAGATGTC 3637
                             i     v     vivi    i      v ii      ---------
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG--------- 541

  chr2_176339566_   3638 AGGAAAACCCTTCTAGACAATGGCTTAAGAAAACCCTTCTAGACATTGGC 3687
                         ---     -----------  i ---i? v   i -   vv   v    v
  L1M4_orf2#LINE/    542 ---AAAAC-----------ATAG---GNGTAAATC-TTCGTGACCTTGGG 573

  chr2_176339566_   3688 TCAGGCAAAGACTTCGTGACCAAGAAGCCAAAACCAAATGCAACAAAAAC 3737
                          i      v ii   v iivi v  vi      v  v v         iv
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_176339566_   3738 AAAGATAAATAGATGGGACTTAATTAAACTAAAGAGTCTCTGCACAGCAA 3787
                            i   i   i  v      v  i   v v  i iii i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_176339566_   3788 AAGAAACAATCAGCAGAGTAAACAGAAAACCCACAGAGTGGGAGAGAATC 3837
                          i  v  v    iv i   i  v   v          i       i   v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_176339566_   3838 TTCACAATCTATACATCTGACAAAGGACTAATGTCAAGAATCTACAAGGA 3887
                           ii   vii   i      i  i     vi i  v     v  i  i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_176339566_   3888 ATTCAGACAAATCAGCAAGAAAAAAACAATT---CTA--TCAAAAATGGG 3932
                          i  vv    v   ii  v     i    v --- i -- ?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_176339566_   3933 TTAAGGACATGAATAGACAATTTTCACAAGAAGATATACAAATGGCTAAC 3982
                         iv     iv          v  i  vv                   i  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_176339566_   3983 AAACATATGAAAAAATGCTGAACATCACTAATGAT 4017
                           i  i       i     v       ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 4.00 (36 / 9)  


3198 27.34 0.44 0.33  chr2_176357766_176364787     5624  6530 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_176357766_   5624 TGGAAAAACATTCTATGCTCATGGATAGGA-GAATCAATATTGTGAAAAT 5672
                               i i  i i   i        v   -  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176357766_   5673 GGCCATACTGCCAAAAGTGATTTATAGATTCAATGCTATCCCCATCAAGC 5722
                            v     v  v   v    i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176357766_   5723 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCTC 5771
                          v   vivi i  i  ii     v v  v  i-  - iii    v   vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_176357766_   5772 ATGGAACCAAAAAAGAGACT--GTATAGCCAAGATAATCCTAATCGAAAA 5819
                               -- viv   i   i-- v        i i    i i vvi i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_176357766_   5820 GAACAAAGCTGGAGGGATCACGCTACCTGACTTCAAACTATACTACAAGG 5869
                                 i      iv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_176357766_   5870 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACACATATATAGAC 5919
                                  i   i    ii         i iv ii i v i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_176357766_   5920 CAATGGAACAGAACAGAGGCCTCATAAATAACGCCACACATCTACAACCA 5969
                                 i    iv   ivii  v      vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_176357766_   5970 TCTGATCTTTCACAAACCTGATAAAAACAAGCAATGCAGAAAGGATTCCC 6019
                         vi    i  iv    ivv  vi  i v  vv     vi     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_176357766_   6020 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATACAGAAAACTG 6069
                          v  i  i        i     v      v  ?   i  i  i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_176357766_   6070 AAACTGGACCCCTTCCTTACACCTTATACAGAAATTAACTCAAGATGGAT 6119
                           ii         v   i     v      i            i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_176357766_   6120 TAAAGACTTATACATAAAACCTAAAACCATAAAAACCCTAGAAGAAAACC 6169
                         i ?    i  v ii   i v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_176357766_   6170 TAGGCAATATTATTCAGGACATAGGCATGGGCAAAGACTTTATGAGTAAA 6219
                             ?ivv v v   iv   v v  vv i     v ii  iv iii  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_176357766_   6220 ACACCAAAAGCAATGGAAACAAAAGCCAAAATTTACAAATGGGATCTAAT 6269
                                     vvi v        vv     vv i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_176357766_   6270 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 6319
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_176357766_   6320 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 6369
                          i     i                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_176357766_   6370 GGGCAAATATCCAGCATCTACAAGGAACTTTAACAAATTTACAGGAAAAA 6419
                           i vvi       v  v  i  i     i v    v iv i iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_176357766_   6420 AACAAACAACTCCATCAAAAAGTGGGCAAAGGGTATAAACAGACACTTCT 6469
                         i     i   i v  i?    i          i v i  i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_176357766_   6470 CAAAAGAAGACATTTATGTGGCCAATAAACATATGAAAAAAAGCTCATCA 6519
                          v        i  vi vi          i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_176357766_   6520 TCACTGGTCAT 6530
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


3276 26.19 0.88 0.55  chr2_176398555_176405257     5307  6211 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_176398555_   5307 TGGAAAAACATTCTATGCTCATTAATAGGAAGAATCAGTATTGTGAAAAT 5356
                               i i  i i   i    vi  v      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176398555_   5357 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAAC 5406
                            v     v      v i  i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176398555_   5407 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTCAT 5455
                          v   vivi i  i  ii     v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_176398555_   5456 ATGGAACAAAAAAAGAGCCCATA-TAGCCAAGACAATCCTAAGCAAAAAG 5504
                               - viv  i ii    v -       i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_176398555_   5505 AACAAAGCTGGAGGGTTCATGCTACCTGACTTCAAACTATACTACAAGGC 5554
                                i      ii   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_176398555_   5555 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATGTATAGACC 5604
                                 i   i    ii         i iv ii i   ii      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_176398555_   5605 AATGGAACAGAAC--AGAGTCCTCAGAAATAACACCACATATCTACAACC 5652
                                i    i--       --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_176398555_   5653 ATCTGATCTTTGACAAATCTGAGAAAAACAAGCAATGCAGAAAGGATTCC 5702
                          vi    i  i     ivv  vv  i v  vv     vi     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_176398555_   5703 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5752
                           v  i  i        i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_176398555_   5753 GAAATTGGATGCCTTCCTTACACT-TACACAAAAATTAACTCAATATGAA 5801
                            i     iv   v   i    i-  i                v   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_176398555_   5802 TTGAAGATTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5851
                          ii?   ii           v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_176398555_   5852 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5900
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_176398555_   5901 AAACACAAAAAGCAATGGCAATAAAAGCCAAAATTGACAAATGGGATCTC 5950
                         vi    v       vvi    i     vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_176398555_   5951 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 6000
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_176398555_   6001 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACA 6050
                         v  i     i                 v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_176398555_   6051 AAGGGCAAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 6100
                          i  i vvi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_176398555_   6101 AAAA--AACAGTCTCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 6148
                           i --  i ii iv  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_176398555_   6149 CTCAACAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCTCAT 6198
                            v v      i  vi vii      i  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_176398555_   6199 CATCACTGGTCAT 6211
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3090 27.01 0.88 0.77  chr2_176406940_176412711     4374  5280 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_176406940_   4374 TGGAAGAACCTTCCATGCTCATGGGTAGGAAGAACCAATATCATGAAAAT 4423
                              ii iv i     i      i v      vii     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176406940_   4424 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4473
                           iv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176406940_   4474 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4521
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_176406940_   4522 CATGGAACCAAAAAGGAACCCACATTGTCAAGTCAATCCTAAGCCAAAAG 4571
                         i      viiv  i   v  viv  v i   iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_176406940_   4572 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGCC 4621
                                i      vv   ii  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_176406940_   4622 TACAGTAACAAAAACAGCATGGTACT--CATACCAAAACAGAGATATAGA 4669
                                 iv  i    ii       --    -- ii i   v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATATAGA 296

  chr2_176406940_   4670 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAA 4717
                         i        i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_176406940_   4718 CTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 4767
                         ii vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_176406940_   4768 CCCTATTTAATAAATGATTCTGGGAAAACTGGCTAGCCATATGTAGAAAG 4817
                         vi  v  i  i     i v      v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_176406940_   4818 CTGAAACTGGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAGATA 4867
                         v    ii    i    v   i     v    i         i    i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_176406940_   4868 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 4917
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_176406940_   4918 ACCTAGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCATGTC 4966
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_176406940_   4967 CAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5016
                         i vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_176406940_   5017 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5066
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_176406940_   5067 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTGCTCATCTGA 5116
                           v  i     i                 v       viiiivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_176406940_   5117 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 5166
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_176406940_   5167 AAAA-ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5215
                             -     i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_176406940_   5216 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5265
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_176406940_   5266 ATCATCACTGGCCAT 5280
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3371 25.77 0.55 0.55  chr2_176449331_176455611     4882  5789 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_176449331_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176449331_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCTATCAAGC 4981
                            v     v     iv i  i           i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176449331_   4982 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5028
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_176449331_   5029 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5078
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_176449331_   5079 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5128
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_176449331_   5129 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5178
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_176449331_   5179 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5226
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_176449331_   5227 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5276
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_176449331_   5277 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5326
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_176449331_   5327 TGAAAGTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5376
                             iv    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_176449331_   5377 ATTAAAGACTTAAACTTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5426
                           i ?    i    iv v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_176449331_   5427 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5476
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_176449331_   5477 AAACACCAAAAGCAATGGCAATAAAAGCCAAAATTGACAAATGGGATCTA 5526
                         vi            vvi    i     vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_176449331_   5527 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5576
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_176449331_   5577 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5626
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_176449331_   5627 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5676
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_176449331_   5677 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5726
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_176449331_   5727 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5776
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_176449331_   5777 CATCACTGGCCAT 5789
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3300 26.65 0.33 0.33  chr2_176647326_176653701     4977  5884 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_176647326_   4977 TAGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5026
                          i   ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176647326_   5027 GGACATACTGCCTAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5076
                           vv     v  i  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176647326_   5077 TACCAGTGACTTTCTTCGCAGAA-TTGGAAAAAACT-ATTTTAAAGTTCA 5124
                          v    ivi i  i  i      -   -- v  i  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_176647326_   5125 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAG 5174
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_176647326_   5175 AACAAAGCTGGAGGCATCACACTTCCTGACTTCAAACTATACTACAAGGC 5224
                                i      vv          ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_176647326_   5225 TACAGTAACCAAAACAGCATGGTACTCGTACCACAACAGATATATAGACC 5274
                                 i   i    ii       v i iv vi i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_176647326_   5275 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5324
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_176647326_   5325 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAAGATTCCCT 5374
                         i    i  i     ivv  v   i v  vvv          ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_176647326_   5375 GTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCTGA 5424
                         v  i  i              v      v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_176647326_   5425 AACTGCATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGTATT 5474
                          ii  v i    v   i     v              i    i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_176647326_   5475 AAAGACTTAAATGTTAGACCTAAAACCATAAAAAACCTAGAAGAAAACCT 5524
                          ?    i       v   v       i      vv i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_176647326_   5525 AGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAAA 5573
                            ?i- v i -   iv   viv  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_176647326_   5574 ACACTAAAAGCAATGGCAACAAAAGCCACAATAGACAAATGGGATCTAAT 5623
                             i       vvi          vv v      i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_176647326_   5624 TAAACTAAAGAGCTTCTGCACAGCAGAAGAAACTACCATCAGACTGAACA 5673
                         i   v v  i i   i  ii vv  i i  v    i  vv i v    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_176647326_   5674 CGCAATCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5723
                         vi   i i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_176647326_   5724 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5773
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_176647326_   5774 AACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCT 5823
                         i     i     v  i?    i     i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_176647326_   5824 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5873
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_176647326_   5874 TCACTGGCCAT 5884
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


3128 26.78 1.33 0.44  chr2_176996396_177002767.rev     4981  5880 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_176996396_   4981 TGGAAGAACATTCCATGCTCATGGATAGGAAAAATCAATATCGTGAAAAT 5030
                              ii i  i     i        v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_176996396_   5031 GGCCATACTGCCTGAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5080
                            v     v  ii  v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_176996396_   5081 TACCAATGACTTTTTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 5125
                          v   iivi i     ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_176996396_   5126 TGGAACCAAAAAAGAGTCTGCATTGCCAAGACAATCCTAAGCAAAAAGAA 5175
                              viiv  ii  vi v v  v     i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_176996396_   5176 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGCTA 5225
                              i      vv       v  ii i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_176996396_   5226 CAGTAACAAAAACAGCATGGTACTGGTACCAAAACACAGATATAGACCAA 5275
                               iv  i    ii         i iv ii i v v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_176996396_   5276 TGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACCAT 5323
                              i    i--    i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_176996396_   5324 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGTGAAAAGGATTCCCT 5373
                         i    i  i     ivv  v   i v  vvv    v i    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_176996396_   5374 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5423
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_176996396_   5424 AACTGGATCCCTTCCTTACACCTTATACAGAAATTAATTCAAGATGCATT 5473
                          ii    i    v   i     v      i       i    i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_176996396_   5474 AAAGACTTAAATGTTAGACCTAAAACCATAAAAAATCTAGAAGAAAACCT 5523
                          ?    i       v   v       i      vvii           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_176996396_   5524 AGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAAA 5572
                            ?i- v i -   iv   viv  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_176996396_   5573 ACACCAAAAACAATGGCAACAAAAGCCAAAATAGGCAAATGGGATCTAAT 5622
                                  i  vvi          vv       ii    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_176996396_   5623 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5672
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_176996396_   5673 GGCAACCTACAGAATGGGAGAAAATTTTTGCAAACTACCCATCCGACAAA 5722
                          i     i                 v        ii ivi   i  i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_176996396_   5723 GGGCTAATATCCAGAATCTACAAAGAACTCAAAAAAATTTACAAGAAAAA 5772
                           i  vi          v  i         vv v  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_176996396_   5773 AACAA----CCCCATCAAAAAGTGAGCAAAGGATATGAACAGACACTTCT 5818
                         i    ----   v  i?    i  i         v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_176996396_   5819 CAAAAGAAGACATCTACGCAGCCAATAGACACGTGAAAAAAATACTCATC 5868
                          v        i  vi viii       ii   i      i - i    v 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAAC 896

  chr2_176996396_   5869 ATCACTGGTCAT 5880
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


1825 27.17 11.29 1.86  chr2_177065932_177068002.rev      774  1579 (492)    L1M4_orf2#LINE/L1       27   908 (0)  

  chr2_177065932_    774 TAGAGGAAACAATACTGTTGAGGTATTGATTCTCCCTAAATTCTCCCTAT 823
                          i  i  vvi    i    i  i ivii  v     i     v-vi   i
  L1M4_orf2#LINE/     27 TGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG-ATCTAC 75

  chr2_177065932_    824 TGATTCTCTCTAAGTTGTACTGAAAAAAAAAAATCCCAGC-AAGTTTTTG 872
                         v     vvivi  viiv  ii--------           -ivv     v
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATC--------AAAATCCCAGCTGCCTTTTTT 117

  chr2_177065932_    873 ATAAAAATAGGCAAG-------TAAAATTTATATAGAAATGTAAAGAACC 915
                         ii i    v i    -------       i    i      i  i i   
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr2_177065932_    916 TACGATAGCCAAAAATACTTTGCTAAAGAAGGATAATATAGGAGGACTT- 964
                         i vi          vv ii   vv       i i  vi v        i-
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_177065932_    965 ---TGCCTGATTTCAAGACTAACTATAAAACTACTGCAATCTACATAGAT 1011
                         --- v  ii       i   v    i   i    v i    v v i  --
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG-- 265

  chr2_177065932_   1012 TATTCTTACTGGCATAAGAAGAGATGTATAGATTAATGGAACAGAACAAA 1061
                          i vv -           i v   ii       i       i    ivi 
  L1M4_orf2#LINE/    266 TGTGGT-ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_177065932_   1062 GTATGTAGAAACAAACTGATTAATATGTGATCAATTAGTTTTCCACAAAG 1111
                          vi vi     i    iv  vv  v i  i      ii     v    i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_177065932_   1112 ATGCCAAAGTAATTCAATGTGGGAAAAAAT-GTCTTTTCAACAAATGGTG 1160
                         i      iiiv        -      i   -                   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_177065932_   1161 CTTCAATAACTGAAAATAAATATTTTAAA-AATATATATG-ACC------ 1202
                           vvi i     i v ?vv i  viv   -   iv vv  -   ------
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_177065932_   1203 --ACACTGTACACAAAAAT------------------------AAATGTA 1226
                         --    ii  i        ------------------------       
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_177065932_   1227 AAAGTTAAGACTCTAAAACT--TAAAA------ATAGTAGAATATCTTTG 1268
                          i  i   i   v       --  i  ------    v? v v     i 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_177065932_   1269 TGACCCTGGGGTAGGGGAAGATTTTTTTAAATGGAACAC----AGCACAA 1314
                              i    v    vi v i   i  - i  ivi    ----       
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAA 612

  chr2_177065932_   1315 ACCTAGAAATAAAAAAAAAATAAATCAAATTTCTTCAAAATGTACAGCAT 1364
                         i vvvi   v      v i      iii i   v       vv v i - 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC-T 661

  chr2_177065932_   1365 TTTCTATTTCAGAG-ACATTCTTCATAAAATGAACAGGCAAGCCACAATC 1413
                            v ii    i  -   i v iv v   i    v  i   v     ivv
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_177065932_   1414 TGGGAGAATACATTCATAA----TATG---GACAAAAAACTTCTGTCCAA 1456
                                 v i   iii  ----   i---  i  iii    v i    i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_177065932_   1457 AATAT-TAAAAAA----TA-AACTC--T--TGGAA-----------TCAA 1485
                              -    i  ----  -     -- -- ii  -----------i   
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_177065932_   1486 ATTAAAACTGAGCAAAAGATTTAAGTAGATACTTCATAAAAGAAGACATG 1535
                         v ?    v  i     i     i i    i i   viv        i  i
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_177065932_   1536 --GTTAGTCAATAAGCCTAT-AATAGATGCCCAATATCAATGTCAAC 1579
                         --iv i i        vi  -  v      i   i    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (132 / 84)
Gap_init rate = 0.03 (29 / 882), avg. gap size = 3.66 (106 / 29)  


3193 26.91 1.00 0.44  chr2_177486158_177492410     4859  5761 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_177486158_   4859 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4908
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_177486158_   4909 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4958
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_177486158_   4959 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5006
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_177486158_   5007 TATGGAACCAAAAAAGAGCCTGCATCTCCAAGTCAATCCTAAGCCAAGAG 5056
                                viiv  ii  v  v v  vv    iv     i i ivv ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_177486158_   5057 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5106
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_177486158_   5107 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5156
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_177486158_   5157 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCTCATATCTACAACT 5204
                                i    i--    i  --        vv  vi i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_177486158_   5205 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5254
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_177486158_   5255 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCCTATGTGGAAGC-T 5303
                           v  i  i              v      v  ?  vi   iii   v- 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_177486158_   5304 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5353
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_177486158_   5354 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5403
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_177486158_   5404 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5453
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_177486158_   5454 AACACCAAAAGCAATGGCAACAGAAGTCAAAATTGACAAATGGGATCTAA 5503
                         i            vvi      i   vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_177486158_   5504 TTAAACTAAAGAGCTGCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5553
                          i   v v  i i  vi  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_177486158_   5554 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5603
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_177486158_   5604 AGGGCTAATATCTAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5653
                         i  i  vi    i     v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_177486158_   5654 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACGTGAACAGACACGTC 5699
                          i    ----   v  i?    i           iv    i     iv  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_177486158_   5700 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5749
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_177486158_   5750 ATCACTGGCCAT 5761
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2501 25.12 6.10 1.59  chr2_177588264_177590152.rev      569  1388 (501)    L1M4_orf2#LINE/L1        1   857 (51)  

  chr2_177588264_    569 TGGAAAAACATCCCATGTTCATGGATCAGAAGAATTAATATCATTAAAAT 618
                               i i                 ii     v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_177588264_    619 GACCATACTGCCCA------TCTACAGATTCAATACAATTTCTGTTATAT 662
                          i v     v    ------             ii    ii  i i v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_177588264_    663 TACCAAAGTCATTCTTCACAGAATTAGAAAAAA-AATCCTAAAGTTCATG 711
                          v   ivvv v  i  ii     v v  v  iv-i        i     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_177588264_    712 TGGAA-CAAAAAAGAGCCTGAATAGCCAAAGCAATACTAAGTAAAAAGAA 760
                              -iiv  ii  v  v           i    vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_177588264_    761 TAAATCTGGAGGTATCACATTACCTGACTTCAAA--TTAGACTACAAGGC 808
                         i   vi      vv     i v  ii i      --   --      i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGC 248

  chr2_177588264_    809 TATAGTAACCAAAACAGCATGGTACTGGTATAAAAATGGACACATAGATC 858
                           i     i   i    ii         i    ii  i    i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_177588264_    859 AATGGAACAGAATAGAGAACCCAGAAATAAAGCCACCAATCT----TTAA 904
                                i     v    ii           v   ivv  i ---- i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_177588264_    905 CAAATT--CAACAAAAATAT-------ATGC--TAGAGAAAGGATGCTCT 943
                         ivi   -- i    iii ii-------  v -- i i     i  iv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_177588264_    944 ATTCAATAAATGGTGCTTGGAAAATTGGAAAGCCACATGCAAAAGAACAA 993
                         v     i          v   v  i    v ?               ii 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_177588264_    994 AACTGGACCCATACC--ACTC----TACAAAAATTAA-----GATGGATT 1032
                          ii       v    --  v ----            -----i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_177588264_   1033 AAAGACTTAAATGTGAGACCTCAATCTGTAAAAATCCTATAAGAAAACCT 1082
                          ?    i       i   v  v  v  i     v  i  v        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_177588264_   1083 AGGA--AAAACT------CATTGGCCTAGGCAAAGAATTTGTGACTAAGT 1124
                            ?--   v  ------ v    vi       v iv  iv iiv  v v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_177588264_   1125 CCTCAAAAGGAAATGCAACAACAACAATAGCAACAACAAAAAAACGAATG 1174
                          vi      v v v       ----------  v  v   v i ii   v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAA----------AAGAAAAAATAGATAAATT 638

  chr2_177588264_   1175 GGACTTAATTAAACTAAAAAGTTTCTACATAGCAAAATAAA-TAACATAG 1223
                               v  i   v v    ii  i iiiivv    iv v -  v  -  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA-AG 687

  chr2_177588264_   1224 AAA----ACAGACAACCTACAGAATGGGAGCAA-TATTTATGAACAATGC 1268
                            ---- v        i            v  -     iii  iv  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_177588264_   1269 ATCCAACAAAGGGCTAATATCCAGAATCTACAAGGTATTCAAACAGCTTA 1318
                            ii i  i  i  vi          v  i  i v i  vv   i  i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_177588264_   1319 ACAAGAAAAAAACAAGTAACCCCATTAACAAGTGGGCAAAGTACATGAAC 1368
                          i  v     i    i      v   ? v  i         v iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_177588264_   1369 AGACATTTTTCAAAAGAAGA 1388
                                 i  v        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGA 857

Transitions / transversions = 1.49 (121 / 81)
Gap_init rate = 0.02 (19 / 857), avg. gap size = 3.32 (63 / 19)  


2625 22.52 8.32 1.10  chr2_177619877_177621668      484  1300 (492)    L1M4_orf2#LINE/L1       33   908 (0)  

  chr2_177619877_    484 ATTTAAT-TTTTTAA-ATA--AATTCTTCCTAAATTGATTTGTAAATTCA 529
                          i     -  v    -  i--   v  i  i        i ii i     
  L1M4_orf2#LINE/     33 ACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCA 82

  chr2_177619877_    530 ATGCAATCTCAATCAAAATCCTAGCAGGTTTCTTTGAAGAAATTGAAAAG 579
                          i      i v          i   v vi  i    v         v   
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG 132

  chr2_177619877_    580 CAGATGCTAAAATGTATATGGAAATGGAAAGGACCTAGAATAGCCAAAAT 629
                          v   v       vi           v  i     i             i
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_177619877_    630 AAT-TAGAAAAAGAATAATAAAG------GATTTATTATCCTACTTGATT 672
                            - v         v  i    ------  i i i- --  v iii   
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC-A--CTTCCCAATT 229

  chr2_177619877_    673 CTAAGACTTACAAGAAAGCTACGATCGTCAAGACAGTGCGGCACTGAGGC 722
                         ii  i      v v        ii vi           i  i    ivii
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_177619877_    723 AAGGATAGACCTATAGATTCATGGAACAGAATAGAGAGTCCAGAAATAAA 772
                                   v       iv      i     v                 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_177619877_    773 TCCAAAGTTATATGGT----TGATTTTTGACAAAGATGTGAACATAACTA 818
                         i   v vv v      ----       i     i i  iv  v iv i v
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_177619877_    819 AATTGGAAAA-----------TCAGCAAAATAGTGCTGCAACAACTAAAT 857
                            v  i   -----------   i    - i      vi      ii  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAA-TGGTGCTGGGACAACTGGAT 428

  chr2_177619877_    858 ATCTAGAGGGGAAAAAA---------ACA---ACCTTACAACATATTTTA 895
                          ? i v v vi   i  ---------  v---    i   v     vi- 
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC-A 477

  chr2_177619877_    896 AAAGCTAACACAAAATACATCATAGGCCTAAACAGTAAGAGCTAACACTA 945
                            ii    v      iv    ?  i      i-           v    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAAT-GTAAGAGCTAAAACTA 526

  chr2_177619877_    946 TTACATTTCTGGAAGAAAATATAAGAGAAAATATTTGTAACAAC---AGT 992
                          v v i ii i        i   i ? v    v  i  i  -- ---i  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC--CTTGGGT 574

  chr2_177619877_    993 TAGGAAAGGCATTTTTAAACAGGACACCAAAAGTACAACT--CATAAGGA 1040
                             v  v vv  i   i i v           i    vi--  v   i 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_177619877_   1041 AAAATATTTA---TAAACATTTTCAAAAGTAAAAGCTTTTGCTCTTCAGA 1087
                               vv  --- ii  v iv      v     i      iv     i 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_177619877_   1088 AAAAAGTGTTAA-------AAAAGGCAAGCCG--GACTGAAATAATAGAT 1128
                         ii v v i i  -------     i   v  i--  v  ii v  v v  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_177619877_   1129 ATGAAAA--ACATATCTGACAAAAAGGCTTGTATCCAGAATATATAAAAG 1176
                         v  v   -- i        i  ii- i                     ii
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGG-GACTTGTATCCAGAATATATAAAGA 773

  chr2_177619877_   1177 ATATTTACAACT------TAAGAAGGCAAG-AGCCCAAT---AAAATGGG 1216
                          ivi        ------   i   i   i- i      ---        
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_177619877_   1217 GAAAAGATTTGAAGAGACTCTTTACAAAAGAAGTTATACAAATT-CCAAT 1265
                         v   i        v    vi  iv v       v         v-     
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_177619877_   1266 AAGCACATGAAAAGATGATCTACATCACAAATTAT 1300
                                          v  v      ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (105 / 76)
Gap_init rate = 0.03 (26 / 876), avg. gap size = 2.96 (77 / 26)  


3157 25.44 1.31 2.18  chr2_178058696_178064528.rev     4426  5341 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_178058696_   4426 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTCTTCCTAT 4475
                               i i  i     i        v      v i      --------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-------- 42

  chr2_178058696_   4476 GGGCAGTGATAATGCCCATACTGCCCAAAGCAATTTATGGATTCAATGCT 4525
                         -----  v vi   v v     v      vii  i  ii       i  v
  L1M4_orf2#LINE/     43 -----GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chr2_178058696_   4526 ATTCTGATCAAGCTACCATTGACTTTCTTCACAGAATTAGAAAAAACT-A 4574
                           i iv     iv v   vivi i  i  ii     v v  v  i-  - 
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGA 136

  chr2_178058696_   4575 CTTTAAATTTCATATGGAACC-CAAGAAGAACCCATA-TAGCCAAGACAA 4622
                         iii    v           vi-    -- i     v -       i    
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAA 184

  chr2_178058696_   4623 TCCTAAGCAAAAAGAACAAAGCTGGATGTATCATGCTACCTGACTTCAAA 4672
                           i i iv  i          i    v vv   ii  v  ii i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_178058696_   4673 CTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACTAAAA 4722
                         viv        i          i   i    ii         i iv ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_178058696_   4723 CAGATATACAGACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCAC 4772
                         i   i   i   i        i    iv   ivii         vv   i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_178058696_   4773 ACATCTACAACCATCTGATCTTCGACAAAACTGACAAAAACAAGCAATGG 4822
                             i  iiii  vi    i        iiv  v   i v  vv      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_178058696_   4823 GGAAAGGAT--TCCTTATTTAATAAATGGTATTGGGAAAACTGGCTAGCC 4870
                               i  --  i  -- i  i       ii     v      v  ?  
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_178058696_   4871 ATATGCAGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAAT 4920
                          i     i  i v    ii         v   i     v           
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_178058696_   4921 TAAATCGAGATGGATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAA 4970
                            v  i i      i ?    i           v       i      v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_178058696_   4971 CCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAA 5019
                         i i           v    ?i- v i -   iv   v v  vv i     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA 581

  chr2_178058696_   5020 AGACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTG 5069
                         v ii   v iiv  vi            vvi          vv     v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_178058696_   5070 ACAAATGGGATCTAATTAAACTAAAGGGCTTCTGCACAGCAAAAGATACT 5119
                          i    v   ii v  i   v v  iii   i  ii vv    i  i   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_178058696_   5120 ATCACCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAAT 5169
                             vv i      v  i     i                 v       v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_178058696_   5170 CTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAAC 5219
                         ii  vi      i  i  i  vi          v  i  i     ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_178058696_   5220 AAATTTACAAGATAAAAACAA----CCCCATCAAAAAGCAGGCTAAGGAT 5265
                           v iv i  v v   i    ----   v  i?    iii   v      
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_178058696_   5266 ATGAACAGACACTTCTCAAAAGAAGACATTTA--TGCACCAGCAAACATA 5313
                         v    i     i     v        i  vi --  -i   ii  i  i 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATG-GCCAATAAGCACA 880

  chr2_178058696_   5314 TGAAAAAAAGCTCCTCATCACTATTCAT 5341
                               i v    vv     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (139 / 90)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.46 (32 / 13)  


1422 27.94 3.53 6.47  chr2_178076302_178077973      501  1180 (492)    L1M4_orf2#LINE/L1      249   908 (0)  

  chr2_178076302_    501 TATAATAGTTAAGATAGTGTGATACTGATACAAAGTT-GATAGATAAACC 549
                           i i  i i    i      i     ii i  i v -  i v   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_178076302_    550 AATGGAACAGAATAGAGAGCCCAGCAATACATCAGTGCTTATATGGACAC 599
                                i     v     i    v    v i vi i v v     v  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_178076302_    600 TCGATCTATGACAGAGGTGGCAATGTCA-----------AACAAGAG-CT 637
                          i   i vi    ii    v   vii  -----------  v  v  -  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_178076302_    638 TTTCAACAAGTGGTGCTGAGACAACCCCCCATACCAATGTGGGGGAAAAA 687
                                  i        i      ivv--   ? v ii  v---    i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGG--ATAKCCACATGC---AAAAG 443

  chr2_178076302_    688 AAAAAAACTTGACCTCTACT-----CCATAAACACCAAAATCAATTCCAG 732
                           vi  ii v    i    i-----     v   --     i  i  v i
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACA--AAAATTAACTCAAA 491

  chr2_178076302_    733 GTGAACTATAGATATAAATATGAAAGGCAAATCGATATAGATATGAAAGT 782
                         i  i ii ?   iv     i --   ---------------------  i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGT--AAG---------------------AGC 518

  chr2_178076302_    783 CAAAAAAGCCTTATAAAAATAAGGCTTCTAGAAGATAATACAGGAG-AAT 831
                         i    -----i       ------  ii       v  i i   ? -  -
  L1M4_orf2#LINE/    519 TAAAA-----CTATAAAA------CTCTTAGAAGAAAACATAGGNGTAA- 556

  chr2_178076302_    832 TACCTTCACTACCTCAAAGCAGAAAAAGATATCTTAAACAGAACACAAAA 881
                         - i    iiv    iiiivi  iv  v i v     i i vi    v   
  L1M4_orf2#LINE/    557 -ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_178076302_    882 AATGTCA--AATAAAGGAAAAGGTTGGTAAATTTGGTCACAATGAAAGTT 929
                          iiiiv --  i   i     ii v i      -  v viv  v   i  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATT-GGACTTCATCAAAATT 654

  chr2_178076302_    930 AGAT-CTATTGCTCTTCAAATATCACTATTAGGCAAATAAAAAGGCAAAT 978
                          i v-  v   iv       viv      i i v  i i     i   vi
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_178076302_    979 CACATAATGAAATTAGAAATTTGCAATACATCTATCTGAAAAAGG-CTCA 1027
                             v    ii vv i v        vv   v       v  i  -  ii
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_178076302_   1028 TATCTGAAATATATAAATAATTCTTACAAATCAATAAGACGATGACAGGT 1077
                             iii          v  i        v       v vi v    ii 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_178076302_   1078 AACC-AACTGAAAGATGAATAAGAGCCTTGAACAGGAGTTTCACAAATAA 1126
                             -  i ?   i   iii  ii vi     i  ivi    v v  vi 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_178076302_   1127 CGACATCCAAATAGTCAACAAACACATAAAAAGGTGCTTGATCTCATTAG 1176
                         v  i  v     i i   i  i     i     i    ii iv   ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_178076302_   1177 TAAT 1180
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.82 (120 / 66)
Gap_init rate = 0.03 (18 / 660), avg. gap size = 3.78 (68 / 18)  


1640 18.98 0.74 26.13  chr2_178114568_178116590.rev      315  1531 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_178114568_    315 TGGAAAAACATTCTATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 364
                               i i  i i   i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_178114568_    365 GGCCATACTACCCAAAGTAATTTATAGATTCAATGCTATTCCCATTAAAC 414
                            v     v      v i  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_178114568_    415 TATCATTGACATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 463
                          vi  vivi v  i  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_178114568_    464 ATGGAATCAAAAAAGAGCCTGTATAGCCAAGACAATCCTACACAAAAAGA 513
                               viiv  ii  v  v v        i      i iv v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_178114568_    514 ACAAAGCTGGAGGCATCACACTACCCAAGTTCCAACTATACTACAAGCCT 563
                               i      vv       v     v   v  viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_178114568_    564 ACAGTAACCAAAACATCATGGTACTGGCACAAAAACAGACACATAGACCA 613
                                i   i   vii           i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_178114568_    614 ATGGAAAAGAATAGAGATCCCAGAAATAAGACTGCACACCTACAACCATC 663
                               v     v    vi          iv iii   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_178114568_    664 TGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTTCCTT 713
                             i   i    ivv  v   i v  vv            i  ------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT------ 393

  chr2_178114568_    714 TTTTTTTTTTTTTTTTTTTTCTAGGCAGAGTTTCACTCTTGTTGCCCAGG 763
                         --------------------------------------------------
  L1M4_orf2#LINE/    394 -------------------------------------------------- 393

  chr2_178114568_    764 CTGGAGTGCAATGGCGTGATCTTGGCTCACCGCAACCTCCACCTCCCGGG 813
                         --------------------------------------------------
  L1M4_orf2#LINE/    394 -------------------------------------------------- 393

  chr2_178114568_    814 TTCAAGCGAGTCTCCTGCCTCAGCCTCATGAGTAGCTGGGATTATAGGCA 863
                         --------     -------------------------------------
  L1M4_orf2#LINE/    394 --------AGTCT------------------------------------- 398

  chr2_178114568_    864 TGCGCCACCATGCCCTGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTT 913
                         -----------------------------------------------   
  L1M4_orf2#LINE/    399 -----------------------------------------------TTT 401

  chr2_178114568_    914 CTCCATGTTGGTCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACC 963
                          -------------------------------------------------
  L1M4_orf2#LINE/    402 C------------------------------------------------- 402

  chr2_178114568_    964 CGCCTCAGCCTCCCAAAGTGCTGGGATTACGGGTGTGAGCCACTGCGCCC 1013
                         --------------------------------------------------
  L1M4_orf2#LINE/    403 -------------------------------------------------- 402

  chr2_178114568_   1014 GGCCAGGATTCCCTATTTAATAAATGGTGCTGGGAGAACTGGGTAGGCAT 1063
                         ------------------  i              v      i  ?v  i
  L1M4_orf2#LINE/    403 ------------------AACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_178114568_   1064 ATGCAGAAAATTGAAACTATATCCCTTCCTTACATCTTACACAAAAATTA 1113
                              i  i v    ii iv i    v   i   i v  i          
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_178114568_   1114 ACTCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACC 1163
                               i      i ?    i         i v i            vi 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_178114568_   1164 CCAGAAAAAAATCTAGGCA-ATACCATTCAGAACATAGGCATGGGCAAAG 1212
                         ii    i    iv    ?i- v i -   ivi  v v  vv i     v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chr2_178114568_   1213 ATTTCACGACAAAAACGCCAAAAGCAATTGCAGCAAAAGCCAAAATTGAC 1262
                         i    viiivv vi  i         vvv   i      vv     v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_178114568_   1263 AAATGAGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAT 1312
                             vi  ii v  i   v v  i i   i  ii vv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_178114568_   1313 CATCAGAGTGAACAGACAACCTACAGAACGGGAGAAAATTTTTGCAA-TC 1361
                           vv i      v        i      i          v       -  
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_178114568_   1362 GGAGCATCTGACAAAGGTCTAATATCCAGAGTCTACAAGGAACTTAAACA 1411
                         iv -i      i  i  v  vi        i v  i  i     ivv   
  L1M4_orf2#LINE/    734 ATA-TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_178114568_   1412 AATTTACAAGAAAAAACCAA----CCCCATTAAAAAGTGGGCAAAGGACA 1457
                          v iv i  v     iv   ----   v   ?    i           iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_178114568_   1458 TGAACAGACACTTCTCAAAAGAAGACATTCATGCAGCCAACAA--ACATG 1505
                             i     i     v        i  v  viii     i  --     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_178114568_   1506 AAAAAAAGCTCAGCATCACTCATCAT 1531
                             i v     i     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 29.73 (327 / 11)  


2222 20.50 13.14 4.86  chr2_178139499_178142470.rev     1337  2097 (875)    L1M4_orf2#LINE/L1        4   827 (81)  

  chr2_178139499_   1337 AAAGATATACCATGTTCATGGGTCAGGTCAGAAGAATCAAAACTGTTAAG 1386
                                 v            i ii -----    v i  v i       
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGG-----AAGACTTAATATTGTTAAG 48

  chr2_178139499_   1387 CTGTCAGT-CTCCTCAAACTGATATATAGAGTCAATGCAATCCCAATCAA 1435
                         v  v  i -    i    i    v  i   v    i        v     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_178139499_   1436 AATCCCAATGGGACTTTTTCTTTTTTTAACAGAAACTGACATTTCCATAT 1485
                                iiv -------- i      i-      i     ----- vv 
  L1M4_orf2#LINE/     99 AATCCCAGCTG--------CCTTTTTTG-CAGAAATTGACA-----AGCT 134

  chr2_178139499_   1486 GAACATGAAGTTCATATAGAAATACAAAGAACCTAGAATAGCCAAAACAA 1535
                           v v i  i       i     i   i i   i                
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_178139499_   1536 CTTTGAAAAAGA-----------------CTCGTG--------------- 1553
                         ii          -----------------   iii---------------
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_178139499_   1554 -------ATAAAGCTATAGTAATCCAAACAGTATAGTATTAGCACAG--- 1593
                         ------- i       i       v i     i i   i i   i i---
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_178139499_   1594 -AGACATATA-----------TAGA-------GTCCAGAACTAGAAGCAG 1624
                         -         -----------    -------        v  i vv  v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_178139499_   1625 ACATATATAGACAACAGATTTTTTTAAATGATGGTGCAAAGTCAACTCAG 1674
                             v   i v   iv      i---i ii v     v   v v i   i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTC---GACAAGGGTGCCAAGACCATTCAA 381

  chr2_178139499_   1675 TGAAGAAAGGATAATCTTTTCCAATAAATGGTGCTGA-ACAATTGGATAT 1723
                           ii     i   i       -  i           i-    i      ?
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTC-AACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_178139499_   1724 CCATGTGCAAAAATCATTAACTTCAATCCA-ATTTTATACCATATACAAA 1772
                            ii       i-v  v  v  vi i  v- ii i i            
  L1M4_orf2#LINE/    431 CCACATGCAAAAG-AATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_178139499_   1773 TAATAACTCAGAAATCTTCAAAACTGATTAGAGACCTAAATCTAAGACTA 1822
                         v v       ----------   iv   i ?          v     viv
  L1M4_orf2#LINE/    480 AATTAACTCA----------AAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_178139499_   1823 AAAATTATAAAACTC-------AAA---TGGGAGAAAATCTCTATAACCT 1862
                             i          -------   --- i  ? v      iii i    
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_178139499_   1863 TGCATTA-------------------TGACAC-AACAGCAGAAGCATGAT 1892
                           vi   -------------------      -  v    v     -- i
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA--AC 617

  chr2_178139499_   1893 AGAAAGACAAATTAATACACTGGGCTTCATAAAAATTAAACACAGCTGGT 1942
                          i  ii v    vi   v i   i      v         v  vvi  vv
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_178139499_   1943 CTTCAAAAGATAGTGT-AAGAAAATGAAAAGAGAAACCACAGACTGAAAG 1991
                                i  i v i -      i        v  v       v  ii  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_178139499_   1992 AAAATATTTGCAAAGCATATATCTGAAAAAAGACTTATTCCCAGAATAAA 2041
                                       v           v  ii     i vi        v 
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_178139499_   2042 TAAAGAATTCC-AAAACTCAATAATAAGAAAACAA----CCCAATCTTAA 2086
                                i  i- v             i  i    ----      - ?  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT-TWAA 816

  chr2_178139499_   2087 AATTGGGCAAA 2097
                           v        
  L1M4_orf2#LINE/    817 AAATGGGCAAA 827

Transitions / transversions = 1.58 (93 / 59)
Gap_init rate = 0.03 (25 / 824), avg. gap size = 5.48 (137 / 25)  

 406 16.30 2.17 0.00  chr2_178139499_178142470.rev     2389  2480 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_178139499_   2389 AAAATTGGGCAAATAATTTAAGGAGA-ACTTCACCAATAAAGA-ATATGG 2436
                             v        vi    i iv   - i   v    vi    -   iii
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_178139499_   2437 ATGGCAAATAAGCACATGAAAAGATGTTCAACATCACTAGTCAT 2480
                              v                    i         ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.00 (2 / 2)  


2705 26.46 5.04 1.03  chr2_178220922_178223106      822  1694 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_178220922_    822 TGAAGAGACATACAGTATTCATGGTTTGGTAGAAAACTCAACATAGTAAA 871
                           i i   i  v vi i       v    ---  i   i  i  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGG---AAGACTTAATATTGTTAA 47

  chr2_178220922_    872 GCTGTCAGTTCTTTCCAAATTGATCTATCTGTTTAGTGCATTTTCTGCCA 921
                          v  v  i v  ii             ivvi  i ii   v ii  ii  
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_178220922_    922 AAATTTCAGCAAGATG---TTTAAATAGATATAGAAAATATTATTCTAAA 968
                             ii    ----  ---   vvii   v  v  v  vv v  i     
  L1M4_orf2#LINE/     98 AAATCCCAGC----TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_178220922_    969 ATTTATATGGTAAGGAGAAGGAACTAGA-CAGCTAAAACAAATTTGAAAA 1017
                            i      v  v vi i   v i   -i   i       vi       
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_178220922_   1018 A-ATGAATAAAGTAAAAGCAGTCAATCTACCTTATTTCAAGACTTACTAT 1066
                          - v   i     vii  v v   vv  v  iv       i        i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_178220922_   1067 ATAGTTACAGTAGTCATGACTGTGTGTTATTGG----AGGA-GGACACAT 1111
                          v  i       i   v   v     v  i   ----    -i    i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_178220922_   1112 AGATCAGTGGAACAGAATAGAGAACCCAGAAATAGAGC-ACACAAATATG 1160
                               i     i     v    ii         i v - i   vv    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_178220922_   1161 -CCAAGCTGAGTTT-GACGAAAGTACAAAAGCAATCTAGCGGAGGAAGCA 1208
                         -i   -i   v   -   i ii  i v  ii v  ii ii  i i   v 
  L1M4_orf2#LINE/    344 GTCAA-TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_178220922_   1209 TAGCTTTTTCAACAAATAGTACTGGGCGGAGGGG----------GCGGGG 1248
                            ii            i  i     vvi vv  ----------  iiii
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_178220922_   1249 GGAAGAACTCTGACCTAAATCTCATACC-TATACAAAAATTTAACTCAAA 1297
                          i v   v iv    ivv i    i   -            -        
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AACTCAAA 491

  chr2_178220922_   1298 ATGAATAATGAACTTAAAAGTAAAA--CAAAACTATAAAACCTTTAGAAA 1345
                            i  v ?ii  i    v    i --i             ii      i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_178220922_   1346 AATTTA-AAGAATA--TCTTCAGGATCTAGAGCCAGGCAAAGAATTCTTA 1392
                           vvi - i ?i  --     iv  i  v i ii      v iv      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_178220922_   1393 GACCGGACACTAAAAGTACAATTTATAAAA-----AATTGATAAACTGGA 1437
                           ivv     i     i    viv i    -----   v      i    
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_178220922_   1438 TTTTATCAAAATTAGAAACTTTTGCTCTATGAAGGACTCTGTTAGGA--- 1484
                         i  i          i         iv  vii      v  i i i  ---
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_178220922_   1485 TAAAAAGATAGGTTATAGAGTAGGAGAAAATATGTGCAAACCTTATATCC 1534
                          i      i ivii i   i i           v      i v      i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_178220922_   1535 AAGAAAAGAC--ATATCTATTATATATAAA----TCTCATAGCTCATTAG 1578
                         i v  ii   --i    i vv         ----   i i i    v  i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_178220922_   1579 TAAAAAG-CAAATACTTTAATTAGAAAATAGGCAAGAGACATGAAGAAAA 1627
                                -      viii    ?i     i     ii  iv    v i v
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_178220922_   1628 ATTTCACTGAAGAAGATATACAGATGGCACATAATCACATGAAAAAATGT 1677
                              v ii             i     vv    v          i   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_178220922_   1678 TCAACATCGTTAGCTAT 1694
                                 i????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (144 / 84)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.41 (53 / 22)  


3220 26.66 1.00 0.55  chr2_178479233_178481533      906  1809 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_178479233_    906 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 955
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_178479233_    956 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCGCCATCAAGC 1005
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_178479233_   1006 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1053
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_178479233_   1054 TATGGAACCAAAAAGAGCCC-GCATCACCAAGTCAGTCCTAAGCCAAAAG 1102
                                viiv  i ii   - v  vi    iv  i  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_178479233_   1103 AACAAAGTTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1152
                                       vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_178479233_   1153 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1202
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_178479233_   1203 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 1250
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_178479233_   1251 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1300
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_178479233_   1301 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGACATATGTAGAAAGCT 1350
                           v  i  i              v      v  ?v  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_178479233_   1351 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1400
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_178479233_   1401 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1450
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_178479233_   1451 CTAGGCATTACCATTCAGGACATAGGCAAGGGCAAGGACTTCATGTCCAA 1500
                         v    ?i v viv   iv   v v  vvvi     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_178479233_   1501 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1550
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_178479233_   1551 TTAAACTAAAGGGCTTCTGCACAGCAAAAGAAACTACTATCAGAATGAAC 1600
                          i   v v  iii   i  ii vv    i  v    ii vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_178479233_   1601 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 1650
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_178479233_   1651 AGGGCTAATATCCAGAATCTACAATAAACTCAAACAAATTTACAAGAAAA 1700
                         i  i  vi          v  i  vi     vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_178479233_   1701 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 1750
                          i     i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_178479233_   1751 TCAAAAGACATTTATGCA----GCCAAAAGACGCATGAAAAAATGCTCAT 1796
                           v     - vv   i  ----     v ii i        i       v
  L1M4_orf2#LINE/    847 TCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_178479233_   1797 CATCACTGGCCAT 1809
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2524 27.56 2.81 2.25  chr2_178511578_178513748.rev      791  1679 (492)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_178511578_    791 ATATTTATGGATTGAAAGACTCAGTTTTGTAAAGGTGTCAATTCTCCCCC 840
                           i  i        i      i i v    v   i  v    v      -
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC- 63

  chr2_178511578_    841 AAACAGAT----AGATTCAAAA-AATACCGATAAAAATCCCAGGAATGTA 885
                            iv   ----        vi-   v  v  v          v--  iv
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC--TGCC 111

  chr2_178511578_    886 TATGTATGTGTATAAACTG-CAAATTGATTCTAAAATTTATATGTAAATG 934
                          v v ---  i v   i  -   ii    i        i     v     
  L1M4_orf2#LINE/    112 TTTTT---TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_178511578_    935 CCAGAGGTCAAAAATAGTCAAGACAATCTTGAAGAAG--GAA-AAAGTTG 981
                          v  i ii v i     i   i           i   --   -       
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_178511578_    982 GAGGATTTGCACTACCAGATACTGAGCCTTATCATACAACTGTATTATTT 1031
                              i ii    v  vi  viii iv    ii i v i  ii v  v i
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_178511578_   1032 AAGACAGTGTGGTATTGGCATAAGGATAGATACCTAGATCAATGGAATAG 1081
                                       i               i iv                
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_178511578_   1082 AATAGAGAGTCCAGAAACAGATCCAAATATATATGGACAGTTGATTAATG 1131
                            v             i i i   v i  v     v  i      vvi 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_178511578_   1132 AAAATGATGGCACAGTAGAGTG----ATGGGGAGAGGTATTGCTTTTTCC 1177
                          v  v i  v  ----   vii----       i  i-  v ii     v
  L1M4_orf2#LINE/    359 ACAAGGGTGCCA----AGACCATTCAATGGGGAAAGA-ATAGTCTTTTCA 403

  chr2_178511578_   1178 CTCAAAACAGTGCTGGATCAACTGAATATCCAT-TTCAAAAAAA-AAAGA 1225
                         vi--   ii       iv      i   ?   i- v     i  -i   -
  L1M4_orf2#LINE/    404 AC--AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG- 450

  chr2_178511578_   1226 AATTTTGACTCCTAGCTCATATTATACATGAAAATCATTTTCAGTTGGAT 1275
                         ---  v   i    v    i ii   i ii     i vi iv iv     
  L1M4_orf2#LINE/    451 ---TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_178511578_   1276 TATAAATTTAAATGTGAAAGTTAAAACAGTAAGGATTCTAGGA-AAAGCA 1324
                         i ? i ii       i i  i      vi   iiv ii   i -   i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_178511578_   1325 CAGAAGAATATCTTCATGAGGTTGGAATACAGAAAGATCTCTTGAACA-- 1372
                         i  i? v v      i   vv    iv  viv  v i i    ii i --
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_178511578_   1373 AAACCAAAAAAATACTGACCATAAATTTAAAAATTGAAATATTTGCCTAT 1422
                          v       iv i --ii v i   vvv      v  v v   v v  vi
  L1M4_orf2#LINE/    598 ACACCAAAAGCACA--AGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_178511578_   1423 ATCATA-TTAGGGACCTCTGAA--TCAAAAGACACCATTAAAAGAGTGGA 1469
                             v -   iii  i i  vi--     i     i  i  i i    i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_178511578_   1470 AAAACAAGCCATGGAATAAGA-AAAATATTTGTAATACATATATCTTGCA 1518
                           i    v   ii    ii  -          i  vv         vii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_178511578_   1519 GAGGGCTCTTATCCAGAATATAGAAGATACTTTTACGAGCCAATTTTTAA 1568
                         ii  i  iv             v  iiv   i    i vi    vv v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_178511578_   1569 AAATCAGACAACCCAACAGGACAAAAGACCAAAGTTCTGAACAGGCA--- 1615
                           iv  i i       iv?i v  vi i v  i v i    i  i  ---
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_178511578_   1616 CTTCATGGAAGAGAGTAGAAATAGATGATAAGTATATGAAAAGTTGCTCA 1665
                           i  vi     v -  v    i vii     i i        v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATA-TACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_178511578_   1666 ACTTCATTAATCAT 1679
                           v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.03 (23 / 894), avg. gap size = 1.96 (45 / 23)  


4216 18.96 2.82 0.45  chr2_178549148_178554327     2526  3411 (1769)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_178549148_   2526 GGAAAGACAACTTATATACAGGAGTTGGAATA--TAATCTTGTTAAGATT 2573
                                i v ii  i v  v ii      v --    v          v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_178549148_   2574 GCAATACTCTCCAAATTGATTGACAGAGTCAATGCAATCCCTAAAATAAA 2623
                                  i          iv     v    i          vv v  v
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_178549148_   2624 CTCAGCTACTAATTTTGGAGAGATTGACAAGTTGATTCTAAAATTAATAT 2673
                          i     i ivv     v   i         i    i        v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_178549148_   2674 GGACATACAAGAGACCTAAAATAGTCAAAATGATCTTCAAGATGAAAAAC 2723
                            v  i    i    i i     i     ii     v  i v   i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_178549148_   2724 AAAAAGTCAAAGGACTCACACTTTTAGATTTTAAAACTTACTTCAAAGAT 2773
                            --  iii             iivi    i          v     v 
  L1M4_orf2#LINE/    202 AAA--GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_178549148_   2774 ACAGTAACCAAGACAATGTGATACTGGCATGA----AGACATACAGATTA 2819
                                i       i    i         i ----       i    i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_178549148_   2820 ATGGAGTAGAGTTGAGAGTCTC---ATAAACCTATATATCTATGGTCAAT 2866
                              i    i         iv---       i   i  i          
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_178549148_   2867 TGACTTTCCACATGGGTGGCAAGACAAATAAATTGGGAAGGAATAGTCTT 2916
                            i    v   v     v      v v v   v     i          
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_178549148_   2917 TTCAACAAATGGTGCTGGAATA-CTGGATGTCCCTGTACAAATGAATGAT 2965
                                           i i -      i?  vii i    v      v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_178549148_   2966 ATTGGACCCCTTATCTCACACCATGTACAAAAATTTAACTTAAAGTGGAT 3015
                         i          - i          i          -    i   i     
  L1M4_orf2#LINE/    450 GTTGGACCCCT-ACCTCACACCATATACAAAAATT-AACTCAAAATGGAT 497

  chr2_178549148_   3016 CAAGGGCCTAGATGCAAAAGCTAAAATAATCAG-CTCTTAGAAGAACACA 3064
                           ?i i    i   i  i        iv  v i-            v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_178549148_   3065 TGGGCATATGTATTCATGCGCTTAGATTAAACAATCACTTCTTAGATATA 3114
                          i  ?i  vi v   i  vv   i i   ii    vii           i
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_178549148_   3115 ATACCAAAAGCACAAGTAACAAAA----AAAT-TATAAATTGAAT---AT 3156
                          i              i       ----    -v        i i---  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_178549148_   3157 CAAAATCTAAAACTTTTGTGCTTCAATAGACACCATCAAGAAAGTGAGAA 3206
                               iv                  vi     i             i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_178549148_   3207 GACAACTCA--GAATGAAGGCAAATATACATAAATCATAAATCTGATAAG 3254
                               i  --     iii v      viii        v          
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_178549148_   3255 GGACCTGTATACAAAGTATACCAAAAACTCC-AAGACTCAGCAATAAAAA 3303
                             i     v  i i    iv  i     i- vi     ii        
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_178549148_   3304 GACCATTAACACAATT-GAAAATGA-TAAAGGACCTGAATAGACGTTTC- 3350
                            v v    v     -i      i-i      ii         i    -
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_178549148_   3351 CTAAATAAGACATACAAATGGCCAATAATCACATGAAAAGATGCATAACA 3400
                          i   v    i                 v               vi    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_178549148_   3401 TTGTTAGCCAT 3411
                          ii????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.95 (109 / 56)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 1.81 (29 / 16)  

3599 23.45 0.77 0.33  chr2_178549148_178554327     3785  4688 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_178549148_   3785 TGGAAAGATATCCTATGCTCCTGGATTGGAAGAAGTAATATTGTTAAAAT 3834
                                      i   i  v            vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_178549148_   3835 GTCCATACTACCTAAAGC-ATATCCAGATTCAGTACAATACCTATCAAAA 3883
                          v v     v  i   vi-  v v        iii    v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_178549148_   3884 TTCCA-CTGGCATTCTTACAGAAACAGAAAAAACCATCCTAATATTTGTA 3932
                          i   -   v v  i  i      iv  v  iviv       v   ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_178549148_   3933 TAAAACCATAAAAGACCCCAAATAGCCAAAACAATACTGAGAAAGACAAA 3982
                          ii  viii  ii     vi               vi   i     vi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_178549148_   3983 CAAAATTGGAGGCATCACACTTCCTGATTTCAAATTATATTACAAAGCTA 4032
                             i       vv          ii        viv  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_178549148_   4033 TAGTAAT-AAAACAGTAAGATATTGACATAAAAACTGACACACAAGCCAG 4081
                         i      -  i     iv i  i  i     ii iv    i i iii  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_178549148_   4082 TGGAACAGAATATAGAGCCCAGAAATAAATCCAAACCATGTATGGTCAAC 4131
                              i     vv    i           i   v  -  v         i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC-ATTTATGGTCAAT 349

  chr2_178549148_   4132 TAATTTATGATGAAAGCACCAACAGGACACAACAGGAAAATAATGGTCTC 4181
                          i    vi  ii ii ii    v vv iv   ii  i   v   i    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_178549148_   4182 TTAAATTAATGGTTCTGGGAAAACTGGATTTCCAAATGCAAAAGAAGGAT 4231
                           v  iv      v      v        v?   v           v  v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_178549148_   4232 ATTGGACCATTATCTTACACCATACACAAAAATCAACTCAAAATGAA--A 4279
                         i       vi  i  i        i        i           i -- 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_178549148_   4280 AAGACCTAAATATAAGACCAAAAACTATAAAATTCCTAGAGGATAACATA 4329
                         ?          i     v v            i  i    i  v      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_178549148_   4330 GGGAGAAAAGTCCTGGACAATGCCTT-GGTCATGATTTTTTGAATATCAC 4378
                           ?iv   vv i vv   vv  vv  -  iv   i   i  ii    v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_178549148_   4379 ACCAAAAGCTCAGTCCACAAAAGCAAAAGTAAATAAATGGGACTACATCA 4428
                                  v  iv v       v    i  i      v     v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_178549148_   4429 AA-TGAAAAAGCTTCTGTACACCAAAGGAAACAACCAACAAAATGAAATA 4477
                           - v     -   i   i vi       v  v i   v   i     vi
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_178549148_   4478 GCAAACTATGTATTGGGAACAAATATTTGCAAACTATATATCTGACAAGG 4527
                         i   v i iiv v     iv             ii          i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_178549148_   4528 GGTTAACCATTCAAAATTTATAAAGAACTCATACAACTCAAAAGTGGAAA 4577
                          ii vii-  i  i   v            v          v i ii   
  L1M4_orf2#LINE/    749 GACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_178549148_   4578 AACAAACAGCCCAATCCAAAAATGGGCAAAAAATCAGAATAGACATTTCT 4627
                         i     i i      i?             ii  iv              
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_178549148_   4628 CCAATGAAGACATTAAAATGGCCAACAGGTACATCAAAAGGTGCTCAACA 4677
                             v     i  vv          i i i    v     i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_178549148_   4678 TTATCAACATC 4688
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (123 / 85)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


3220 26.96 1.79 0.22  chr2_178662808_178669071     4879  5772 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_178662808_   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_178662808_   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_178662808_   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_178662808_   5027 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_178662808_   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_178662808_   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_178662808_   5177 AATGGAA--------------CAGAAATAATGCCGCATATCTACAACTAT 5212
                                --------------         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_178662808_   5213 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5262
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_178662808_   5263 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5312
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_178662808_   5313 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5362
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_178662808_   5363 AAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5412
                          ?   ii    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_178662808_   5413 AGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAA 5462
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_178662808_   5463 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5512
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_178662808_   5513 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5562
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_178662808_   5563 GCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5612
                         i     i   iv            v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_178662808_   5613 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5662
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_178662808_   5663 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5712
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_178662808_   5713 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCAT 5762
                         v        i  vi viii     v  i        i i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_178662808_   5763 CACTGGCCAT 5772
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 4.50 (18 / 4)  


 280 33.22 9.49 3.73  chr2_178722274_178728016        2   296 (5447)    L1M4_orf2#LINE/L1      351   662 (246)  

  chr2_178722274_      2 GATTTATGGCAAAGCAGTCATCACAGATCAT------GAGAAAAGATGAA 45
                              vi i   i vv i  ----   i   ------ i    ii  iiv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGAAAGAATAGT 396

  chr2_178722274_     46 CTTCTCAATAAATGACCCTAGGTCAATTGCTTATTCAAATAGAAAAGAAA 95
                            i    i     iiv  i  v   i  vv  ?i  v  iv       -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA- 445

  chr2_178722274_     96 TAAAATTGTATTCATATCCTACACCCTAACACAAAAAAGGAATTACAATT 145
                          i  i   v ii v  i ii     v  -i       vvi v i v   -
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATA-TACAAAAATTAACTCAAAAT- 493

  chr2_178722274_    146 AAACTAAATACTTAA-TATGAAAAC-AAATTTATAAAAATTTCCAAAGAC 193
                         ii ii ? v  i   - i i i i -   vi       v i ivi    v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_178722274_    194 ACTATAGGAGAATATTTTTCTTCATACCCT--------------GTTTCA 229
                          vi     ? v v  ----    i iv   --------------     v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_178722274_    230 -AGA-ATAAGAACAAAAATGCAAATTTCTATAAGATCAATAAATCAAGTA 277
                         -   -  i v v     iii   iivv v v ii vv    i  v  v i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_178722274_    278 G----TATTAAAATTAAGAGCTT 296
                          ----i  i        i i   
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTT 662

Transitions / transversions = 1.57 (58 / 37)
Gap_init rate = 0.04 (12 / 312), avg. gap size = 3.25 (39 / 12)  

2965 27.07 1.10 0.77  chr2_178722274_178728016     4347  5251 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_178722274_   4347 TGGAAAAAAATTCCATGCTCATGGATAGGGAGAATCAG-ATCATGAAAAT 4395
                               i v  i     i        v  i   v i i-  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_178722274_   4396 GGTCATACTGCCCAAAGTAACGTATAGAGCCAATGCTATTCGCATCAAGC 4445
                           iv     v      v i iv  i   vi   i  v  i vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_178722274_   4446 TACCATTAACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTCA 4494
                          v   vivi i  i  ii     v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_178722274_   4495 TATGGAACCAAAAAAGAACCTGTATAGCCAAGACAATCCTAAGAAAAAAG 4544
                                viiv  ii  v  v v        i      i i i   i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_178722274_   4545 AACAAAGCTGGACATGTCATGCTACCTGACTTTAAACTATACTACAAGTC 4594
                                i    vivv   ii  v  ii i  i   viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_178722274_   4595 TACAGAAACCAAAACAGCATGGTACTGGTACCAAAACAGATACATAGACC 4644
                              v  i   i    ii         i iv ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_178722274_   4645 AACGGAAC-GAAAGGAGACCTCAGAAATAACACCACACATCTACAATCAT 4693
                           i    i-   vv    vii         vv   i    i  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_178722274_   4694 CTGATTTTCAACAAACCTGACAAAAACAAGCAGTGGAGAAAGGAT--TCC 4741
                         i        i    ivv  v   i v  vv  i   i     i  --  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chr2_178722274_   4742 ATATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACA 4791
                         - v  i  i              v      v  ?   i     i  i vv
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_178722274_   4792 GAAACTGGACCCCTTCCTTACACCTTATAGAAAAATTAACTCAAGATGGA 4841
                            ii         v   i     v    v              i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_178722274_   4842 TTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAAC 4891
                          i ?    i         i v i     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_178722274_   4892 CCAGGC---AATACGATTCAGGACATAGGCATGGGCAAAGACTTCATGAC 4938
                         vi   ?---   - --   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-C--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_178722274_   4939 TAAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGAGATC 4988
                           vi            vvv          vv     v  i    vi  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_178722274_   4989 TAGTCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 5038
                          vi     v v  i i   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_178722274_   5039 AACAGGCAACCTACAGAATGGGAAAAAATGTTTGCAATCTATCCATCTGA 5088
                           v  i     i           i     i       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_178722274_   5089 CAAAGGTCTAATATCCAGAATCTACCAGGAACTTAAACAAATTTACAAGA 5138
                         i  i  v  vi          v  iv i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_178722274_   5139 AAAAAACAAACAACACCATGAAACAGTGGGCAAAGGCTATGAACAGATAC 5188
                             i     i   v v  v?  v i          v v    i   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_178722274_   5189 TTCTCAAAAGAAGACATTTATGTGGCCAACAA--ACGTGAAAAAAAGCTC 5236
                              v        i  vi vi       i  --  i      i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_178722274_   5237 ATCATCACTGGTCAT 5251
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (138 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


2992 26.54 2.35 0.67  chr2_178739099_178745493     5011  5903 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_178739099_   5011 TGGAAAAAAATTCCATGCTCATGGATAGGGAGAATCAG-ATCACGAAAAT 5059
                               i v  i     i        v  i   v i i-  iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_178739099_   5060 GGCCATACTGCCCAAAGTAATGTATAGAGTCAATGCCATCCCCATCAAGC 5109
                            v     v      v i  v  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_178739099_   5110 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5157
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_178739099_   5158 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5207
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_178739099_   5208 AACAAAGCTGGAGGCGTCGCGCT-------------ACTGTACTACAAGG 5244
                                i      vv  i i  -------------   -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_178739099_   5245 CTACAGGAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5294
                               v  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_178739099_   5295 CAATGGAACAGAAC--AGAGCCCTCAGAA-TAATACCACACATCTACAAC 5341
                                 i    i--    i  --    -   vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_178739099_   5342 CATCTGATCTTTGACAAGCCTGACAAAAACAAGAAATGGGGAAAGGATTC 5391
                           vi    i  i      vv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_178739099_   5392 CCTATTTAGCAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5441
                         i  v  i i               v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_178739099_   5442 TGAAATTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCCAGATAG 5491
                             i     i    v   i     v  i           i  v i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_178739099_   5492 AGTAAAGACTTAAATGTTTGACCTAAAACCATAAAAACCCTAGAAGAAAA 5541
                          vi ?    i       vv  v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_178739099_   5542 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5590
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_178739099_   5591 AAAATACCAAAAGCAATGGTAACAAAAGCCAAAATTGACAGATAGGATCT 5640
                          vi i          vvi i        vv     v  i i  v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_178739099_   5641 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGA 5690
                         v  i   v v  i i   i  ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_178739099_   5691 ACAGGCAACCTAAAGAATGGGAGAAAATTTTTACAATCTACCCATCTGAT 5740
                          v  i     i v               v   i   vii ivi       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_178739099_   5741 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTATAAGAA 5790
                           i  i  vi          v  i        ivv    v iv    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_178739099_   5791 AAAT-CAAACAACCTCATAAAAAACTGGGCAAAGGATATGAACAGACACT 5839
                            v-    i    iv  v?    v            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_178739099_   5840 TCTCCAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5889
                                      i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_178739099_   5890 TCATCACTGGTCAT 5903
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (134 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.25 (27 / 12)  


3980 20.60 2.34 1.22  chr2_178874381_178876446      677  1574 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_178874381_    677 TGGAAAGATATCCTGTGTTCATGGATTGGAAGAATTAACATTGTTAAAAT 726
                                      ii                  v    i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_178874381_    727 GTCCATGCTACCCAAAGCAATCTACAGATTCAATGCAATTCCTATCAAAA 776
                          v v  i  v      vii              i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_178874381_    777 TCCCAATGACATTTTTCACAGAAATAGAAAAA---GTCCTCAAATTTGTA 823
                              iivi v     ii       v  v  i---i    v     ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_178874381_    824 TGAAACCACAAAAGATCCTGAATAGCCAAAGGAACACTGAGCAAAAAGAA 873
                           i  vii   ii  i  v           iv  ivi   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_178874381_    874 CAAAGCTGGAAGCAC-CACACCACCCGACTTGAAAACATATTTAAAAGTT 922
                              i    i -  -     iv   i i  v     v  i vv    i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_178874381_    923 GTAGTAGTCAAAACAGCATGATACCGGCATAAAAACAGACATGTAGACCA 972
                         ii    i    i    ii  i   i       ii i      i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_178874381_    973 ATGAATGGAACAGAACAGAGAACCCAGAAATAAACCCACACTTTTATAGT 1022
                            ----   i    iv    ii               i  v     i  
  L1M4_orf2#LINE/    300 ATG----GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_178874381_   1023 CAATTGATTTTTGACAAGGGTGCCAAGAGCACACAGTGGGGAAAGGACAT 1072
                                    i                v  iv  i         i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_178874381_   1073 TCTCTTTAATAAATGGTGTTGAGACAACTGGATAGCCACATGCAGAAGAA 1122
                            i  i  i        i  i            ?         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_178874381_   1123 TGAAATTAGACCGTTATCTCTCACCAGAAACAAAAATCAACTCAAAATGT 1172
                             i  i    vi  i   v     v v        i           v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_178874381_   1173 GTTAAAGGCTTATATGTAAGACCTAAGACTGTAAAATTCCTAGAAGAAAA 1222
                         i i ?  i i  v        v    i   i     i  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_178874381_   1223 CATAGAAAAAAAGCTCCATAATATTGGTTTAGGCAAGGATTTTTTTTAAT 1272
                              i?iv   v  i i i iv    v        v i   i  v-i  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GAT 594

  chr2_178874381_   1273 ACGTACCCCAAAA---TAGACAACAAAAGCAAAG-TAGACAAATGGGATT 1318
                          i -  v      ---i ii         v   i-    i    v   i 
  L1M4_orf2#LINE/    595 ATG-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_178874381_   1319 ACATCAAAATAAAAAGCTTCTGTACAGCCAAGGA-A--ATCAACAGAATT 1365
                         v         v    i   i   i vv v     - --     v i i v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_178874381_   1366 AAGAGGCAGTCTACAGATTGGGAGAAAATATTTGGAAACCATACATCTGA 1415
                           i  i  ii i     v                v   i    i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_178874381_   1416 TAGGAGATGTTAGTATCCAAAATATATAAGGAACTC---------AATAG 1456
                           i i  i-  -       i         i      ---------    i
  L1M4_orf2#LINE/    744 TAAGGGAC-TT-GTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_178874381_   1457 TAAGAAAACAAATAACCCAATTAAAAAATGGTCAAAAGATCTGAATAGAC 1506
                            i  i               ?        v    i   i         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_178874381_   1507 ATT-ATCAAAAGAAGACATTTACAGATGGCCAACAGGTGTATGAGAAAAT 1555
                            -v  v        i  --   i        i i iii    i  i  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_178874381_   1556 GCTAAAAATCACTACTTAT 1574
                            v  v    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (126 / 55)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.13 (32 / 15)  


 222 34.34 0.00 0.00  chr2_179041854_179048229      392   490 (5886)    L1M4_orf2#LINE/L1       55   153 (755)  

  chr2_179041854_    392 ATACTACCTAAAGAAATATACAGATTCAATATAATTCTTATCAAAATGCT 441
                              v  i   vvi  v           iii   i i         v i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_179041854_    442 AATGGCACTCTTCCAAGATATAGGAAAAACAATAATAAAATTTACATGG 490
                          iiv  vi i  ivv   v  v iv  ivii  vv       i i    
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

Transitions / transversions = 1.27 (19 / 15)
Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.00 (0 / 0)  

3324 26.39 1.11 0.44  chr2_179041854_179048229     4983  5884 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_179041854_   4983 TGGAAGAACATTCCATGCTCATAGATAGGAAGAATCAATATTGTGAAAAT 5032
                              ii i  i     i    i   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179041854_   5033 GGCTATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5082
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_179041854_   5083 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 5130
                          v   iivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_179041854_   5131 TGTGGAAACAAAAAAGAGCCTACATTGCCAAGACAATCTTAAGCAAAAAG 5180
                          i      iiv  ii  v  viv  v     i        i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_179041854_   5181 AACAAAGCTGGAGGCATCACGCTACCTGATTTCAAACTATACTACAAGGC 5230
                                i      vv    i  v  ii        viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_179041854_   5231 TACAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGATACATAGACC 5280
                                 i   i    ii       i i iv ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_179041854_   5281 AATGGAACAGAACAGAGGCCTCAGAAACAACACCACACATCTACAACCAT 5330
                                i    iv   ivii      i  vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_179041854_   5331 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATTCCCT 5380
                         i    i  i     ivv  v   i v  vv      i     i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_179041854_   5381 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5430
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_179041854_   5431 AACTGGACCCTT-CCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5479
                          ii       i -   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_179041854_   5480 AAAGACTTAAACGTTAGACCTAAAACTGTAAAAACTCT-AGAAGAAAACC 5528
                          ?    i    i  v   v        i     -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr2_179041854_   5529 TTAGCAATAC-TATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5577
                          -  v?i  v- v   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 T-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_179041854_   5578 AACACTAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 5627
                         i    i       vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_179041854_   5628 TGAAACTAAAGAGCTTCTGCACAGCGAAAGAAACTACCATCAGAATGAAC 5677
                          v   v v  i i   i  ii vv i  i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_179041854_   5678 AGGCAACCTACAGAATGGGAGAAGATTTTTGCAATCTACCCATCTGACAA 5727
                           i     i              i  v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_179041854_   5728 AGGGCTAGTATTCAGAATCTACGAAGAACTCAAACAAATT-----TAGAA 5772
                         i  i  v    i      v  ii        vv    v i-----  i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_179041854_   5773 GCAAAAACAATCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5822
                         iv v   i  i  v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_179041854_   5823 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5872
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_179041854_   5873 ATCACTGGTGAT 5884
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (147 / 87)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2744 27.01 0.88 0.38  chr2_179655066_179662065     5303  6098 (902)    L1M4_orf2#LINE/L1        1   800 (108)  

  chr2_179655066_   5303 TGGAAAAACATCCCATGCTCACGGATAGGAAGAATCAATATTGTGAAAAT 5352
                               i i        i   i    v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179655066_   5353 GACCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCTCATCAAGC 5402
                          i v     v      v i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_179655066_   5403 TACCA-CTGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCAT 5450
                          v   -   v    i  -i     v v  v  i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_179655066_   5451 ATGGAACAAAAAAAGAGCCCACA-TAGCCAAGACAATCCTGGGCAAGAAG 5499
                               - viv  i ii    v -       i      i  iiv      
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_179655066_   5500 AACAAAGCTGGAGGCATCCCACTACCTGACTTCAAACTATCCTACAACGC 5549
                                i      vv  v    v  ii i      viv v      v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_179655066_   5550 TACGGTAAACAAAACAGCGTGATACTGGTACCAAAACAGATATATAGACC 5599
                            i    v   i    i   i      i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_179655066_   5600 AATGGAACAGAACACAGGCCTCAGAAATAACACCACACATCTACAACCAT 5649
                                i    ivv  ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_179655066_   5650 CTGATCTTTGACAAACCTGATACAAACATGCAATGGGGAAAATATTCCCT 5699
                         i    i  i     ivv  vi vi v   v           iv  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_179655066_   5700 ATTTAATAAATGGTGTTGGGA-AACCTACTAGCCATATGCAGAAAACAGA 5748
                         v  i  i        i     -   iviv  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_179655066_   5749 AACTGGACCCCGTCCTTACACCTTATATGAAAATCAACTCAAGATGAATC 5798
                          ii        vv   i     v    ii     i       i   i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_179655066_   5799 AAAGACTTAAATGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAACCT 5848
                          ?    i           v   ii  i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_179655066_   5849 GGGCA-ATACCATTCAAGACACAGGCATGGGAAAAGACTTCATGTCTAAA 5897
                         i  ?i- v i -   iv   viv  vv i  v  v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_179655066_   5898 ACACCAAAAGCAATGGCAACAAAAGCCAAAATACACAAATGGGATCTAAT 5947
                                     vvi          vv      v i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_179655066_   5948 TAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCA--GTGAACA 5995
                         i   v v  i     i  ii vv    i  v       vv --     v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_179655066_   5996 GGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTATCCATCTGACAAA 6045
                          i     i                 i       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_179655066_   6046 GGGCTAATATCCAGAATCTACAAATAATTTAAACAAATTTACAAGACAAA 6095
                           i  vi          v  i   v  i ivv    v iv i  v v   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_179655066_   6096 GGC 6098
                          i 
  L1M4_orf2#LINE/    798 GAC 800

Transitions / transversions = 1.33 (121 / 91)
Gap_init rate = 0.01 (9 / 800), avg. gap size = 1.11 (10 / 9)  

 487 21.37 0.85 0.00  chr2_179655066_179662065     6392  6508 (492)    L1M4_orf2#LINE/L1      791   908 (0)  

  chr2_179655066_   6392 ATAAGAAAA-AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGA 6440
                             i  i -   i     v  i?    i            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_179655066_   6441 TACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAATG 6490
                         i i     v        i  vi viii     i  i  i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_179655066_   6491 CTCGTCATCACTGGTCAT 6508
                            iv     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (18 / 6)
Gap_init rate = 0.01 (1 / 118), avg. gap size = 1.00 (1 / 1)  


3229 26.98 0.44 0.44  chr2_179672185_179680485     4880  5787 (2514)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_179672185_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179672185_   4930 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_179672185_   4980 TACAAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTACAGTTCA 5027
                          v v iivi i  i  ii     -   -- v  i  - iii  v i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_179672185_   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCAAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     ivi ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_179672185_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_179672185_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_179672185_   5178 AATGGAACAGAAC--ACAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i-- v  i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_179672185_   5226 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_179672185_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_179672185_   5326 GAACCTGGATCCCTTCCTTACACCATATACAAAAATCAATTCAAGATGGA 5375
                            vi    i    v   i                 i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_179672185_   5376 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_179672185_   5426 CTAGGCATTACCATTCAGGACATAGGCATGTGCAAGGACTTCATGTCTAA 5475
                         v    ?i v viv   iv   v v  vv iv    v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_179672185_   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAACTCA 5525
                         i            vvi          vv     v  i    v   vi   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_179672185_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_179672185_   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_179672185_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_179672185_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_179672185_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5775
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_179672185_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

3841 18.96 1.77 0.88  chr2_179672185_179680485     6569  7359 (942)    L1M4_orf2#LINE/L1        1   798 (110)  

  chr2_179672185_   6569 TGGAAAGAGAACCCACGTTTATGAGTTGGAAGACTTAGTGTTGTTAAAA- 6617
                                 v v    i   i   ii            i i       i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179672185_   6618 AGCAATACTGTCTAAAGTAATCCACAGATTCAATGTAATCAATATAAAAA 6667
                         i        vi i   v i   i          i i    vv   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_179672185_   6668 TTTTATTTCACAGGCTTTTTGACAGAAATTGAAGAGATAATCCTCATATT 6717
                          iii vi ---- v      vi          vi  v i     v v   
  L1M4_orf2#LINE/    101 TCCCAGCT----GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_179672185_   6718 TATGTGGACTTGTAAGGGGATCATAATAGTCAAAACAATCTTGAAAAAGA 6767
                         i  i    vv  i     ivi  v     i                    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_179672185_   6768 A---CAAATTCGGAGGACTCACACTTCTAAACTTCAAAACTTACTACAAA 6814
                          ---    v i                iv  i                  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_179672185_   6815 GCAACAGTAATCAAAATGGTGT---ATTGACATAAGGATAGACATATAGG 6861
                           v           i ii    --- i  i                   i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_179672185_   6862 GTAATGGCCTAGAATTGAGAGTTCAGAAATGTACCTATATGTCTATGGCC 6911
                         vi     vv             i       iv   i   ii i     i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_179672185_   6912 AATTGATTTTCAACAATGGTGTCAGGACCATTCAATTAGGAAAGAATAGT 6961
                                    i    v    i  i           vi            
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_179672185_   6962 CTC--AAACTAGTGGAACTAGAAGTACTAGATATTCACATGTAAAAGAAT 7009
                           i--v   v i   vi  i i vv   i    ?i      i        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_179672185_   7010 AAAATTGAATTATTACCTTTCATACCATATA--AAAATTAACTCAAAATG 7057
                         i  i   i iivi     --  i        --                 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCT--CACACCATATACAAAAATTAACTCAAAATG 494

  chr2_179672185_   7058 TATCAGTGATCTCAATGTAAAAGCTAAAACTATAAAATTTTTAGAAGAAT 7107
                         v    ?v  i  v       i                i i         v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_179672185_   7108 TT-TGTAAGTAAATTTTCATCACCTTGAATTTGGCAATAGTTTTTTAGAT 7156
                         vi- ivi?      i   i v      ii  v      i    i      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_179672185_   7157 ACGACACCAGTAGCATAAGCAACAACAACAACAAACAGATAAATTGGACT 7206
                          i       iv    i         -  v  v   i              
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAA-AAGAAAAAATAGATAAATTGGACT 643

  chr2_179672185_   7207 TCATCAAAATTAAGA-CTTTTGTG-TACAAAGGACATTATCAAAGAAGTA 7254
                                      i -        - v         i      ii    i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_179672185_   7255 AAAAGAAAATCCTTAGAATGGGAGAAAATGTTTGCAAATGATATATCTGA 7304
                               v  i  vi               i         v          
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_179672185_   7305 TAAGCATCTAGTATTCAGAATATACAAAGAGCTCTTTCAACTTAACAATA 7354
                             viv  v    i         i     i     v     i  i    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_179672185_   7355 GAAAG 7359
                         i    
  L1M4_orf2#LINE/    794 AAAAG 798

Transitions / transversions = 1.83 (95 / 52)
Gap_init rate = 0.01 (11 / 798), avg. gap size = 1.91 (21 / 11)  

 438 18.12 7.25 0.72  chr2_179672185_179680485     7676  7813 (488)    L1M4_orf2#LINE/L1      762   908 (0)  

  chr2_179672185_   7676 AATAAATAAATAA-----ATAA---AACAATAGAAAGGACAA-CAATACA 7716
                             v     v  ----- i  ---  i    i    -    -i  iv  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAG-ACAAATAACCCA 810

  chr2_179672185_   7717 ATCATAAAATGGGCAACGGACTTGAAAAGACATTTCTCCAACAAAGATAT 7766
                           i?v           v   i     v              vi       
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_179672185_   7767 ATAAATGGCAAACAAGTGCACACAAAGATGCTCAA-ATGATTAGTCTT 7813
                          i       v  i   ii  iiv            -  v ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (14 / 10)
Gap_init rate = 0.03 (5 / 147), avg. gap size = 2.20 (11 / 5)  


 665 30.00 0.00 0.00  chr2_179699832_179705414     3880  4089 (1494)    L1M4_orf2#LINE/L1        1   210 (698)  

  chr2_179699832_   3880 TGGACACACATCCCATACTCATGGATGGGTAGAATCAATATTGTGAAAAT 3929
                             v v i       ii        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179699832_   3930 GATCATACTGTCAAAAGAAGTCTACAAATTTAACGCAGTTCCCATCAAAA 3979
                          iiv     vi v   vvii      i   i      i i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_179699832_   3980 TACCAGCATCATTCTTTACAGAATTAGAAAAAACAATTCTAAAATTCACA 4029
                          v     vv v  i   i     v v  v  ivii  i          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_179699832_   4030 TGAAACCAAAAAGGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 4079
                           i  viiv  i   v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_179699832_   4080 TAAATCTAGA 4089
                         i   vi i  
  L1M4_orf2#LINE/    201 CAAAGTTGGA 210

Transitions / transversions = 1.25 (35 / 28)
Gap_init rate = 0.00 (0 / 210), avg. gap size = 0.00 (0 / 0)  

2486 25.77 1.41 0.14  chr2_179699832_179705414     4382  5091 (492)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr2_179699832_   4382 AAAAAAAAGGACAAATCTAGAGGCATCACACTACCTCATTTCAAACTATA 4431
                              i   i     vi i    vv       v  iv        viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_179699832_   4432 CTATAAGGCCATAGTCACCAAAACAGCATGATACTGGTATAAAAATAGAC 4481
                            i  i  i i   v i   i    ii  i      i    ii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_179699832_   4482 A-ATAGA-CACATGGAACAGA---GAAA--CCACAAATAAACCCAAATAC 4524
                          -     -  -      i   ---  i --   v           v i i
  L1M4_orf2#LINE/    290 ATATAGATCA-ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_179699832_   4525 TCACAGCCAACTGATCTTCGACAAAGCAAACAAAAATGTAAAGCAGGGAA 4574
                          i ii i   i    i        i vviv   i vii vv iii     
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_179699832_   4575 AGGACACCCTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCA-ATGT 4623
                           i i vi                       i  i   v  ?   -   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_179699832_   4624 AGGAGAATGAAACTGGATCCTCATCTCTCACCTTATACAAAAACCAACTC 4673
                          ii        ii    i  ii i   v    v          ii     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_179699832_   4674 GAGATGGATTAAGGACTTAAACCTAAGGTCTGAAACTATAAAAATTCTAG 4723
                         i i      i ?i   i    iv    iv  i           v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_179699832_   4724 AAGATAACACTGGAAAAACCCTTCTAGACATTTGCTTACGTAAGGATTTC 4773
                             v    iv  ?iv  vi    vv   v  v v   v i  v i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_179699832_   4774 ATGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAACATAAATAGCTG 4823
                         v iivi v  vv         v v    i    iv   v   i   iv v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_179699832_   4824 GGACCTAATGAAACTTAAGAGCTTTTGCACGGCAAAAGGAACAGTCAGCA 4873
                             i v  v   v    i i      ii vv    i iv  vi   iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_179699832_   4874 AAGTAAACAGACAACCCACAGAGGGGGAGAAAATCTTCACAATCTATACA 4923
                             i  v              iv          v  ii   vii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_179699832_   4924 TCTGACAAAGGACTAATATCCAGAATCTACAATGAACTCAAACAAATCAG 4973
                              i  i     vi          v  i  v      vv    v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_179699832_   4974 CAAGAAAAAAACAAACAATCCCATCAAAAAGTAGGCTAAGGACATGCATA 5023
                         i  v     i     i  i  v  i?    i i   v     iv  v   
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_179699832_   5024 CACAATTCTCAAAAGAAGATATCAAAATGGCCAAGAA--ACATGAAAAAA 5071
                         v   v     v           vv          v  --         i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_179699832_   5072 TGCTCAGCATCACTAATGAT 5091
                               i     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (105 / 74)
Gap_init rate = 0.01 (7 / 719), avg. gap size = 1.57 (11 / 7)  


3258 27.09 0.44 0.44  chr2_179751667_179753955.rev      890  1797 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_179751667_    890 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 939
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179751667_    940 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 989
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_179751667_    990 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1037
                          v i iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_179751667_   1038 TATGGAACCAAAAAAGAGCCCGCATCAGCAAGTCAATCCTAAGCCAAAAG 1087
                                viiv  ii  v  v v  viv   iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_179751667_   1088 AACAACACTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGTC 1137
                              vii      vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_179751667_   1138 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1187
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_179751667_   1188 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGTGTATCTACAACT 1235
                                i    i--    i  --        vv  i ii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_179751667_   1236 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCA 1285
                          vi    i  i     ivv  v   i v  vv            i  vvv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_179751667_   1286 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1335
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_179751667_   1336 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 1385
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_179751667_   1386 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1435
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_179751667_   1436 CTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1485
                         v    ?v v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_179751667_   1486 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1535
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_179751667_   1536 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1585
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_179751667_   1586 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 1635
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_179751667_   1636 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1685
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_179751667_   1686 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 1735
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_179751667_   1736 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 1785
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_179751667_   1786 ATCACTGGCCAT 1797
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3229 27.20 0.55 0.55  chr2_179774297_179784293.rev     5025  5932 (4065)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_179774297_   5025 TGGTAGAATATTCCATGCTCATGGGTAGGGCGAATCAATATCGTGAAAAT 5074
                            v ii    i     i      i v  iv  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179774297_   5075 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 5124
                            v     v     iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_179774297_   5125 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5172
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_179774297_   5173 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5222
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_179774297_   5223 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5272
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_179774297_   5273 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5322
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_179774297_   5323 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5370
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_179774297_   5371 ATCTGATCTTTGACAAACATGACAAAAACAAGCAATGGGGAAAGGATTCA 5420
                          vi    i  i     ivi  v   i v  vv            i  vvv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_179774297_   5421 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGACATATGTAGAAAGCT 5470
                           v  i  i              v      v  ?v  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_179774297_   5471 GAAACTGGATCCCCTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5520
                            ii    i   iv   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_179774297_   5521 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5570
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_179774297_   5571 CTAGGCA-ATACCATTCAGGACATAGGCATGCGCAAGGACTTCATGTCTA 5619
                         v    ?i- v i -   iv   v v  vv iv    v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_179774297_   5620 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5669
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_179774297_   5670 ATTAAAGTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGCAAA 5719
                           i   i v  i i   i  ii vv    i  v       vv i  ii  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_179774297_   5720 CAGGCAACCCATATAATGGGAGAAAATTTTCACGACCTATTCATCTGACA 5769
                         v  i       i v             v  ii i vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_179774297_   5770 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5819
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_179774297_   5820 AAAACAAACAACCCCATCGAAAAGTGGGTGAAGGATATGAACAGACACTT 5869
                           i     i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_179774297_   5870 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5919
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_179774297_   5920 CATCGCTGGCCAT 5932
                             i????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

3227 24.89 1.55 1.44  chr2_179774297_179784293.rev     8602  9505 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_179774297_   8602 AAAGATATTCTATGTTCATGAATTGGAAGCATAAACATTGTTAAAATGTC 8651
                                 i i         i        vv v  i        i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_179774297_   8652 CATACTACCCAGAGCAATCTACAGATTTAATGAAATGCCTATCAAAATAC 8701
                         v     v    i vii           i  i v   v           v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_179774297_   8702 CAATGATATTCTTCACAGAAATAGAAAAAAAACT-ATGCTAAAATGTATA 8750
                           iiviiv  i  ii       v  v  i---  -  v       vi   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCATA 150

  chr2_179774297_   8751 TGGAACAACAAAAGATCCAGAATAACCAAAGTTATCCTAAGCAA-AAGGA 8799
                              vvi   ii  i        i     iiv   i i iv  -   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_179774297_   8800 CAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTACGGAGCTA 8849
                             ii       v     i v  ii i      viv      ii     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_179774297_   8850 TTGTAACCAAAAACCAAAACAGCATAGTAATGGCATGAAAACAGGCACAT 8899
                         iv    i   i -------   ii i   v      i ii i  i  i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGA-------CAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_179774297_   8900 AGACCAATGAAACAGAATACAGAACCCAGAAATAAATCCACACACCTACA 8949
                            i     i  i     vv   ii           i   i   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_179774297_   8950 GTGAACTCATTTTCGACAAAGTTGCCAAGAACATACATTGGGAAAAAGAT 8999
                           v  i v           i v        v   v  v    i   ii  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_179774297_   9000 ----TCTTCAATAAATAGTGCTGGGAAAACTGGATATCCATATGCAGAAG 9045
                         ---- i     i    i         v         ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_179774297_   9046 AAGGAAACTAGTCCCCTATCTCTTGTCATACACAAAAATCAAATCAAAGT 9095
                           v   ii i v      i   viii    i        i  v     i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_179774297_   9096 GGATTAAAGACTTAAACCTAAGACCTCAAATTATGAAACTAACACAAGAA 9145
                             i ?    i    iv     v  v   i   i     vvi v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_179774297_   9146 AACATTGGGGAAACTCTCCAGGCCATCAGTCTTGGCAAAGATTTCTTGAG 9195
                              v  ? v  v   i iv v v ii vi v     v i      iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_179774297_   9196 TA--ATATCCAACAAACATAGGCAACCAAAGCAAAAATGGACAAATGGAA 9243
                           -- i -    -  i  i i     v    v      i  i    v i 
  L1M4_orf2#LINE/    594 TATGACA-CCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_179774297_   9244 TTGCATCAAG-TTAGAAAGCTTCTGCACAGCAAAAGAAACAATCAACAAA 9292
                         i v      i-   i   -   i  ii vv    i  v  v     v   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_179774297_   9293 GTAAAGATACAACCCACAGAATGAGAGAAAATATTAGCAAACTACTCATC 9342
                           i  i v               i           v     ii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_179774297_   9343 TGACAAGGGATTAAAAACTAGAATATTTAAGAAAATC--AC--CCCTACA 9388
                            i      i viv v i       v   ii  v  --  -- i v i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_179774297_   9389 GGAAAATATCTAAAAATCTGATT-AAAAATGGAGAAAAGACTTGAATAGA 9437
                         iv    viv v  v  i ii   -        iv   i  i         
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_179774297_   9438 CATTTCTCAAAAGAAGACTTACAAATGGCAAACAGGCATATGAAAATGTG 9487
                                 v        iv          v  i i   i       vi  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_179774297_   9488 TTCAACATCACTGATCAC 9505
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (140 / 82)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 2.08 (27 / 13)  


2562 25.65 4.96 1.18  chr2_179876604_179881508     3560  4405 (500)    L1M4_orf2#LINE/L1        1   878 (30)  

  chr2_179876604_   3560 TGGAAAAACATTCCATCGTCAT----------ATTTAAAAT-GTTAAAAT 3598
                               i i  i    vv    ---------- i    v  -     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179876604_   3599 GGCCATACAGCCCAAAGCAATCTACAAATTCAATGCTATTCATATCAAAC 3648
                            v    vv      vii       i      i  v  i v       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_179876604_   3649 TACCAA-TGTCAATTTTCACAGAA-TAGAAAAA--AA--CTAAAGTTCAT 3692
                          v   i-  i v-    ii     - v  v  i--i --     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_179876604_   3693 ATGGAAACAAAAAAAAGCCCAATTAGCTACAGCAATTCTAAGCAAAAAGA 3742
                                iiv  iii v  vi v    i v i    ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_179876604_   3743 AAAAATCCAGAGATACT-ACATTACCTGTCTTCAAACTACACTACAAGGC 3791
                          v   viii   i-   -   i v  iivi      vivi       i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_179876604_   3792 TGCAGTAAACAAAACAGCATGGTACTAGTACAGAAACAGACACATGGACC 3841
                          i      v   i    ii       i i i iii i     i  i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_179876604_   3842 AATGGAACAGAATAGAGATTCCAGAAATAAGGTCACATACCTATAGCCTT 3891
                                i     v    v           ivi  i i ii   i i vv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_179876604_   3892 CTGATCTTCAACAAAA----------CACGCAATGGGGAAAGAACTACCT 3931
                         i    i   i    ii----------  iv              ivii  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_179876604_   3932 ATTTAATAAATGATGCTAGGATAACTTGCTAGCCATATGCAGAAGAATGA 3981
                         v  i  i     i    i   i    v v  ?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_179876604_   3982 AACTGAACCA-TACCTTTCACCATATACAAAAATTAACTCAAGATGAATT 4030
                          ii  i   v-     iv                        i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_179876604_   4031 AAAGACTTAAACCTAAGGCCTAAAACTATAAAAATCCTAGAAGAAAACCT 4080
                          ?    i    iv    iv              v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_179876604_   4081 AGG---AAATACAATTC-TGAGTATCGGCCTCAGAAAAAAAATTAT--GA 4124
                            ---    - --   -   viv v  -- i  iv  viiv  v --  
  L1M4_orf2#LINE/    549 AGGNGTAAAT-C--TTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGA 593

  chr2_179876604_   4125 CTAAGTCCTCAAAAGTAACTGCAACTAACACAAAAATTGAAAAGTAGGAC 4174
                         -  v v vi      i vvv     v  viv      v  v  i v    
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_179876604_   4175 GTAATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCAA-----T 4219
                         v v  i   v v  i i   i  ii vv    i  v        ----- 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_179876604_   4220 AAACAGACAACCTACAAAATGGGAGAAAATATTCACAAACTATGCCTCCA 4269
                         i  v        i   i                ii    ii  iiv  ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_179876604_   4270 ACAAAGGCCTAATACCAAGAATCCATAATGAACT--TAATCAATTCAACA 4317
                          i  i  v  vi  i v     vi    v     --  --   i    i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATA 790

  chr2_179876604_   4318 AGGAAAAAACAAATAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGA 4367
                          vi    i           v   ?    i           iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_179876604_   4368 CATTTCTCAAAAGAAGACACACAAGTGGCCAACAAGCA 4405
                                 v        i i    i       i     
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

Transitions / transversions = 1.68 (134 / 80)
Gap_init rate = 0.02 (21 / 878), avg. gap size = 2.48 (52 / 21)  


3187 27.64 0.44 0.44  chr2_179888321_179891916     2198  3105 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_179888321_   2198 TGGTAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2247
                            v ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179888321_   2248 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2297
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_179888321_   2298 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2345
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_179888321_   2346 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 2395
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_179888321_   2396 AACAAAGCTGGAGGCATCACATTACCTGACTTTAAACTATACTACAAGGC 2445
                                i      vv     i v  ii i  i   viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_179888321_   2446 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2495
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_179888321_   2496 AATGGAACCGAATAGAGCTCTCAGAAATAACGCTGGATATCTACAACTAT 2545
                                iv    v   vvii         vv iiv i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_179888321_   2546 CTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAATGATTCACT 2595
                         i    i  i     ivv  vv  i v  vvv          vi  vvv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_179888321_   2596 ATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 2645
                         v  i  i   i          v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_179888321_   2646 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 2695
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_179888321_   2696 AAAGACTTAAACATTAGACTGAAAACCATAAAAACCCTAGAAGAAAACCT 2745
                          ?    i    ii v   viv     i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_179888321_   2746 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 2795
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_179888321_   2796 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 2845
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_179888321_   2846 AAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 2895
                            v i  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_179888321_   2896 GCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATTTGACAAAG 2945
                         i     i                 v  i    vii ivi  i   i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_179888321_   2946 GGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAAAA 2995
                          i  vi          v  i  v      iv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_179888321_   2996 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 3045
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_179888321_   3046 AAAAGAAGACATT--AATGCAGCCAAAAAACACATGAAAAAATGCTCTCC 3093
                         v        i  v--    --     v  i          i      vv 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_179888321_   3094 ATCGCTGGCCAT 3105
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (145 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3171 26.93 0.88 0.66  chr2_179901763_179908124     4965  5870 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_179901763_   4965 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5014
                              ii    i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179901763_   5015 GGCCATACTGCCCAAGGTTAATTTATAGATTCAATGCCATCCCCATCAAG 5064
                            v     v     i-  i  i  i        i  v     i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_179901763_   5065 CTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5112
                         v v   iivi i  i  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_179901763_   5113 ATATGCAACCAAAAAAGGAGTCCACATT-GCCAAGACAATCCTACGCAAA 5161
                              v  -- viv    iii   v v -     i      i iviv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_179901763_   5162 AAGAACAAGGCTGTAGGCATCATGTTACCAGACTTCAAACTATACTACAA 5211
                                 i i  v   vv   iii v  vi i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_179901763_   5212 GTCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATACAG 5261
                         iv         i   i    ii         i iv ii i       i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_179901763_   5262 ACCAGTGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAC 5311
                          i  i     i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_179901763_   5312 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5361
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_179901763_   5362 CCTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTTGAAAGC 5411
                         i  v  i  i              v     iv  ?   i   ivi  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_179901763_   5412 TGAAACTGGATCCCTTCCTTAAACCTTATATAAAAATTAATTCAAGATGG 5461
                             ii    i    v   i v   v    i         i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_179901763_   5462 ATTAAAGACTTAAATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAA 5511
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_179901763_   5512 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 5560
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_179901763_   5561 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5610
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_179901763_   5611 AATTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAGTGA 5660
                         v  i   v v  i i   i  iiivv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_179901763_   5661 ACAGGCAAACTACAGAATGGGAGAAAATTTCTGCAATCTACCCATCTGAC 5710
                          v  i   v i                 v i     vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_179901763_   5711 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5760
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_179901763_   5761 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATAAATAGACACT 5806
                            i    ----   v  i?    i            v i        i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_179901763_   5807 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACCTGAAAATATGCTCA 5856
                             v        i  vi viii     i ii   v      v       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_179901763_   5857 TCATCACTGGCCAT 5870
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2740 24.54 5.28 1.15  chr2_179931689_179933924      873  1744 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_179931689_    873 TGGAAAAACATTACATGTTCATGAATTGGAAGAATCAACATCATTAAAAT 922
                               i i  iv          i         v i  i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_179931689_    923 GGCCATACTGCCCAAAGCAATCTACAGATTTAATGCAATTCCTATCAAAC 972
                            v     v      vii           i  i     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_179931689_    973 AACCAA-TGTCATTTTTCACAGAATTAGAAAAAACT-ATTCTAAAATTCA 1020
                         vv   i-  i -     ii     v v  v  i-  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_179931689_   1021 TCTGGAACCAAAAAACGACCCA-AGTACCCAAAGCAATTCTAAGCAAAAA 1069
                          v     viiv  ii-      - i  v     i    ii i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_179931689_   1070 GAACAAAGCCAGAGGTATTACATTACTCAACTTCAAACAATACTATAAGG 1119
                                 iii    vv i   i v i   i      vvv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_179931689_   1120 CTACAGTAACCAACACAGCATGGTACTGGTACAAAAACAGACACATGGAC 1169
                                  i   v    ii         i i  ii i     i  i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_179931689_   1170 AAATGGAACAGAAAAGTGAACCCCAAAATAAAGACAAACCTC---AGCCA 1216
                         v       i    vv v  ii  vi       vv  v  v i---i i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_179931689_   1217 TCTGCTCTTCAACAA---TAC-AAG------CAATGGGAAAGGACTC-CC 1255
                         vi  v i   i    --- i -   ------       i  i  v v-i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_179931689_   1256 TATTCAAATAAATGGTGCTGGGATAATTGGCTAGCCACGTGCAGAAGAAT 1305
                          v     -i              i  i   v  ?    i    i      
  L1M4_orf2#LINE/    398 TTTTCAA-CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_179931689_   1306 GAAACCGGACAG-TACCTTTTACCACATACAAAAATTAACTCAAGATGAA 1354
                            iii    vv-     ivi    i                  i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_179931689_   1355 TTAAAGACTTAAATGTAAGACCTAAAAGCATAGAAATCCTAAAAGAAAAC 1404
                          i ?    i           v      vi   i  v  i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_179931689_   1405 CTAGG---AAATACCATTCTAGACATCAGCCTTGGCAAACAATTCATGAC 1451
                         v    ---    -- -   vv   v ii vi v     vviv   v iiv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_179931689_   1452 TAAGTCCTAAAAAGCAAGTGCAACAAAAACAAAAATTGACAAGTGGTACC 1501
                           v v viv       viv         iv      v  i  i v v  i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_179931689_   1502 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACACAGTA 1551
                          v  i   v v  i i   i  ii vv    i  v        v v   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_179931689_   1552 AACAGACAACCTACAAAATGGAAGAAAACATTCACAAATTATGTATCTGA 1601
                           v        i   i     i      i   ii     i  i       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_179931689_   1602 CAAAGGTCTAATATCCAGAATCTATAAGGAACT--TAATCAATTCAACAA 1649
                         i  i  v  vi          v     i     --  --   i    i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAA 791

  chr2_179931689_   1650 GCAAAAAACAA----CCCTATTAAAAAGTGGGCAA----------TAGAC 1685
                         vv    i    ----   v   ?    i       ----------     
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_179931689_   1686 AT-------GAACAGACATACAAGCAGCCAACAA--ACTTGAAAAAAATG 1726
                           -------i iv   i      iii     i  --  v      i -  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chr2_179931689_   1727 CTCAATATCACTAGTCAT 1744
                              i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (129 / 82)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.43 (56 / 23)  


1374 25.49 20.78 2.35  chr2_179939478_179941018      285  1049 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_179939478_    285 GAGAGACATAACATGTTCATGGATTTGCAGACTCACTATAGA-AACGTGT 333
                           i   i  vv              v v     i v   v v-  vi  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_179939478_    334 CAATTCTCTCTGAATTTAT--ATGAGTTAAATGCAATTCCTAGCATAATT 381
                             v   i ii    v  -- iiii  v  i     i    v  v   i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_179939478_    382 CTATCAAAATTCTTTGTAAATACAGAAAAAAATTATCCTAAAAGTTACGT 431
                          i v vivv  i    i i v iv  v  iv- v         v i ii 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATAT 151

  chr2_179939478_    432 ACAGAGGCAAAAAA---AGAATACCTAAAACAATTTTGGAAAATAA---T 475
                         iv i v    iii ---      v i        i   i    v  ---i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_179939478_    476 GCAGTAGAAGGAATCA-----------------------------GTTA- 495
                         iv   v i    v   ----------------------------- i  -
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_179939478_    496 ----ACC----CA---------------------------ATAAATGAAT 510
                         ---- i ----  ---------------------------   i  v   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_179939478_    511 AAAACAGAAGAGAGAACTCAGAAATAGAAACACACAAATATGCCCAACTG 560
                         ii  i    vv    iii        i vv  i   vv    vi   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_179939478_    561 CTTTTTGACAAAGGTACAAAAACAACTCGATGGAGAAAGACT-GCCTTTC 609
                         v    i     i   i v  i  v i  i    i      v - i    i
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_179939478_    610 CTACAAATGGTGGTAGAGCAACTGAATATCCACAGGCAAAAAAAAAAAAA 659
                          v          v i ii      i   ?     v      i  vi  iv
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_179939478_    660 AAGAACCTTGACCTAAGTCTCACACCTTACACAAAA------TC------ 697
                         vi  -  ----    --i        v  i      ------  ------
  L1M4_orf2#LINE/    452 TGGA-CC----CCTA--CCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_179939478_    698 GATCATGGACTTAAATG-AAAAGTGAAAAACTGTAAAACTTTTAGAATAA 746
                              ?i   i      -  i  iv    -  i       i      v  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAA 543

  chr2_179939478_    747 AA-----------GTCTTC-TAA-------------AAT--TTTC--AGG 767
                           -----------i     - i -------------   --    --  i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_179939478_    768 ------ATCTAGAGC------------------------TGAA----ATT 783
                         ------ i v i   ------------------------ i  ---- i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_179939478_    784 TCATCAAAATTAAAAATATTTGCTCTGTGAACAACA-TGTTAAAACAATG 832
                                         iv    iv  vii  vi   - i i  i v i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_179939478_    833 AAAAGACAAGCTACAGAGTGGAATAAATTACTTAACAAACCACATATTCA 882
                                  v i     i   i v   v  i  i-    i  i    iii
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTG-CAAATCATATATCTG 742

  chr2_179939478_    883 ATAAAGAACTAGTTTCTAGAATACATAGAGAAGGCTTGAAACCCAACAGT 932
                             i i   v  v  i      i   i    vv   iv   i   i i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_179939478_    933 TAAAAAAAAAAT---CCAAATAGAAAATGGGCAGAAGGGCAGAAGTCACA 979
                         v    i v    ---    v ?i          -    ----- v ii--
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCA-AAGG-----ATTTG-- 834

  chr2_179939478_    980 AACAGACAACTCATCAAAGAGGATATACCGATGAC----AAGCACATGAA 1025
                           i     vi  vi      i       vi   i ----           
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_179939478_   1026 AAGATGTTCAACATCATCAGCCAC 1049
                               i         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (119 / 73)
Gap_init rate = 0.04 (32 / 906), avg. gap size = 5.53 (177 / 32)  


3083 27.48 0.77 0.55  chr2_180075490_180081889     5003  5908 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_180075490_   5003 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATAGTGAAAAT 5052
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_180075490_   5053 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 5102
                            v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_180075490_   5103 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5150
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_180075490_   5151 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5200
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_180075490_   5201 AACAAAGCTGGAGGCATCATGCCACCTGACTTCAAACTATACTACAAGGC 5250
                                i      vv   ii iv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_180075490_   5251 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5300
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_180075490_   5301 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACGTATCTACAA-C 5347
                                i    i--    i  --        vv   iii  i  iii- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_180075490_   5348 GATCTGATTTTTGAGAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5397
                         i  -       i  v  ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_180075490_   5398 CCTATTTAATAAATG-TGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5446
                         i  v  i  i     -        v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_180075490_   5447 TGAAACTGTATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5496
                             ii  v i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_180075490_   5497 ATTAAAGACTTAAACTTTGGC-CTAAAACCATAAAAACCCTGGAAGAAAA 5545
                           i ?    i    iv vi v-       i      vi i i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_180075490_   5546 CCTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTGCATGACTA 5595
                          v    ?i v viv   iv   v v  vvii     v ii v v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_180075490_   5596 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5645
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_180075490_   5646 ATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGTGAA 5695
                           i   v v  i i   i  ii vv       v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_180075490_   5696 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5745
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_180075490_   5746 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5795
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_180075490_   5796 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5845
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_180075490_   5846 CTCAAAAGAAGACATTTATGCAGCCAAAAGACAAATGAAAAAATGCTAGT 5895
                            v        i  vi viii     v ii  v       i     viv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_180075490_   5896 CATCACTGGCCGT 5908
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3765 20.38 4.20 0.72  chr2_180091042_180092971.rev      605  1438 (492)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr2_180091042_    605 AAGATGGCTGTACTCCCCAAATTAGTCTACAGATTCAACATCATCCTTGT 654
                                 vi             ii              iiv    i i 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_180091042_    655 CAGACTCTGGGCTGC-TTCTTTGTAGAAGGTGACAAGCTGAATCTAAAGT 703
                           i v  ivi     -  i    i    iv           vi     i 
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_180091042_    704 TCACATTGAACTTCAAGGAACCCAGAAGGGTCAAATCAATCTTAAAATAG 753
                            i  v   v v     i        vi i    v       i   v  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_180091042_    754 ACTAACAAAGTAGGAGGATTTATTCCTTCTAATTTCAAAGCTTACTACAA 803
                          vv        v      i i iv i i i         i          
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_180091042_    804 AGCAACAGTAATCAAGACAGAGTGGTACTGGCACTAGGATAGACATACAA 853
                            v                v            iv            i i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_180091042_    854 ATCAATGGAATAGAATTCTGAGTTCATAAATAGACCTGTGTGTCTGTGAT 903
                                          vv    i  v     i   ii iii i i  i 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_180091042_    904 CAACTGATTTTTGACAATGATGCCAAGAGTATTGAATGAGAAAATAATAG 953
                            i       i     v i        vi   v    i i   v     
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_180091042_    954 TCTTTTCAACAATTGGTGCCAGTGCCATTCAATAGCTACATGCAGAAGTA 1003
                                     v      ii vi v i vi   ? i       i   v 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_180091042_   1004 TGAAGTTAGACCCTTACTTTACATCTT---TAAAAA--AATCCAAAATGG 1048
                                i     i   i i   i v ---i     --  ii        
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_180091042_   1049 ACCAAAGACTTAAACATAAGAGCTAAAACT--------CCTAGAGGTAAA 1090
                          i  ?    i    ii              -------- i    i v   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_180091042_   1091 AATAGGCATAAATTTTCATGACCTTTTATTTAGCAGTGATTTCTCA--TA 1138
                         v     ?i     i   i       vvi  vi   i  i     i --  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_180091042_   1139 T--CACCAAAAGCACAAGAAATTAAAGAGAAAAAAGATAAATTTGAATTC 1186
                          --               v  iv     i    v         v  v   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_180091042_   1187 CTAAAAATTAAAA-CTCTTGTATATCAAAGGACACTATCAAGAAA-TGAA 1234
                         v v          -  i    iiv                     -    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_180091042_   1235 AAAACAATCTCCAGAATTGAAGAAAACATTTGCAAATTGTATGTCTAATA 1284
                           i    i iv      v i      i          ii   i   i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_180091042_   1285 AGGATGTAGTACCAATAATACATATTTTAAAATCTCTTATAACTCAACAA 1334
                            ivv v   i v v    i   ----  i v      i       i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATA----AAGAACTCTTACAACTCAATAA 791

  chr2_180091042_   1335 AAAAAAGAAACAGGAC---------------GCAAAGGACATAAATAGAT 1369
                         v       v v vi  ---------------        iv i      i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_180091042_   1370 ATCTTTTCAAGGAAGACATGCAAATGTCCAACAAGCACATAAAAAAAGAT 1419
                           i i i   i     i  i      v    i        i    --   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA--GAT 889

  chr2_180091042_   1420 GCTCATCATCATTAATGAT 1438
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (107 / 60)
Gap_init rate = 0.01 (11 / 863), avg. gap size = 3.73 (41 / 11)  


 228 16.92 0.00 4.62  chr2_180103552_180107211      231   295 (3365)  C L1M4_orf2#LINE/L1   (0)   908   847  

C chr2_180103552_    295 TTCAGAGAAAATAATACTTGAATGGCCAATAAGCATATGAAAATATGCTA 246
                          i  i    i   -   --i               i       v     v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATA-TAC--AAATGGCCAATAAGCACATGAAAAGATGCTC 893

C chr2_180103552_    245 TATATTTCTTCATAA 231
                         v i  iv????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.50 (3 / 2)  

2329 27.18 1.98 1.72  chr2_180103552_180107211     1964  2721 (939)    L1M4_orf2#LINE/L1        1   760 (148)  

  chr2_180103552_   1964 TAGAAAAA-ATCCCATGCTTATGGATTAGAATAATCAATATTTTTAAAAT 2012
                          i    i -        i i       i   v v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_180103552_   2013 GTCTATACTACCCAAAGCAATTTATGAATTTGGTGCTATCCCCAACATAT 2062
                          v v     v      vii  i  iii   iiii  v     i v  v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_180103552_   2063 TACCAAA-GTCATTTTT--AGAAA-----AAACT-ATTCTAAAATTCATA 2103
                          v   iv- i v     --     -----  i  -  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_180103552_   2104 TGGAACCCCAAAAGAGCCCAAATAGCCAAGGCAATCCTAAACAAACACAA 2153
                              viv   ii  v  vi         ii     i i  v  iv v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_180103552_   2154 CAAAGCTGGAGACATCACTCTACCTGACTTCAAATCATACTACAAGGCTA 2203
                              i     ivv    v  v  ii i      v v        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_180103552_   2204 CAGTAACCAAAACAACATGGCACTGGCACAAAAATAGACACATAAAACAA 2253
                               i   i   iii   i       i  ii       i   i v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_180103552_   2254 TGGAACAGAGTCGAGA-TCACTGAAATAAAGC--TGCATTCCTACAACCA 2300
                              i   i i    -  - v        v -- i    --  iiii  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATT--TATGGTCA 347

  chr2_180103552_   2301 ACTGATCTTTGACAAAGTTGACAAAAATAAACAATGGGGAAAGGATATTC 2350
                          i    i  i     i v  v   i vi vv            i   v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_180103552_   2351 TATTCAATAAATGGTGGTGGGAAAACCAGCTAACTGTATGCAGAAGAATG 2400
                          v     i        v     v   ii v  ? iii     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_180103552_   2401 AAACTGGACCTCTACCTATCACTGTATAAAAAAAAATTAACCCGAGCTGG 2450
                           ii      i      vv   ii    v     --     i i iv   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAATGG 495

  chr2_180103552_   2451 AATAAAGATTTAAATATAAAACCTAAAACTGTAAAAATTCTAGAAAAAAG 2500
                          vi ?   ii     i   i v        i     v ii     i   i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_180103552_   2501 TAGGAAGTAGGAAATACTCTTCTAGACACTGGCCTAGGCAAAAAATTTTT 2550
                         i -----    ?ivv v     vv   vi   vi       viiv  i  
  L1M4_orf2#LINE/    546 CA-----TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_180103552_   2551 GACTAAGTCCTCAAAAGCAAATGCAACAAAAACAAAAATTGA-AAATTGG 2599
                         iiv  v v vi        v v         iv      v  -       
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_180103552_   2600 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAATGAAATTATCAATAG 2649
                         - ii v  i   v v  i i   i  ii vv    v  v i      v i
  L1M4_orf2#LINE/    641 -ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_180103552_   2650 CATAGACAGACAACCTACAGAATCGGAAAAAAAATATTTACGAAGTATGC 2699
                         vi ii v        i       v   i    --     i i  vi  ii
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAA--TATTTGCAAATCATAT 737

  chr2_180103552_   2700 ACCCCACAAAGT-CTAATATCCA 2721
                          i iv i  i v-  vi      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCA 760

Transitions / transversions = 1.57 (124 / 79)
Gap_init rate = 0.02 (15 / 760), avg. gap size = 1.87 (28 / 15)  

 469 22.64 3.77 0.63  chr2_180103552_180107211     3023  3181 (479)    L1M4_orf2#LINE/L1      745   908 (0)  

  chr2_180103552_   3023 AAAAGCCTAATATCAAGAATCTATAAGGAACTTAAACAAATCAACAAGAA 3072
                           ii v  vi    v     v     i     ivv    v    i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_180103552_   3073 A----CAAACAACCCTATTAAAAAGTGGGCAAAGGACATGAACAGATATT 3118
                          ----    i     v   ?    i           iv    i   i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_180103552_   3119 TTTCAAAAGCAGACATATAAGTGGCCAAGAA--ATATGAAAAAAATAGAG 3166
                          i  v    v   i   i  i       v  -- i       i - ivvv
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chr2_180103552_   3167 ACCATCACTAATCAT 3181
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.06 (18 / 17)
Gap_init rate = 0.02 (3 / 164), avg. gap size = 2.33 (7 / 3)  


2863 21.21 0.44 2.50  chr2_180107484_180109151      498  1176 (491)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr2_180107484_    498 AAAGTTATAATAATTAACACAGCATGGTACTGACATAAAAGCAGACACA- 546
                             i  i i    i  v    ii        i     iiii     i -
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_180107484_    547 -GATTAATGGAACTGAATAGAGAGCCTAGAAATAAATCCATGCATTTATG 595
                         -   i       iv    v     i i         i    i        
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_180107484_    596 GTCAATTGATTTTTGACAAAGATGCCAAGAACACACAATGGGGAAAGAAC 645
                                      i     i i        v  iv              i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_180107484_    646 AGTTTATTCAATAAACAGTCCGAGGAAAACTAGATATCCACATGCAGAAG 695
                            i v     i   ii  v vi   v    i    ?         i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_180107484_    696 AATGAAACTAGATCCTTATCTCACACCATATGCAAAAATCAGCTCAAAAC 745
                               ii i  i  i  i            i       i i       i
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_180107484_    746 AGATTAAGGATTTAAATGTAAGACCTGAAACTGTAAAGCTATTAGAAGTA 795
                         i   i ?i  ii           v  i     i    i  v       v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_180107484_    796 AACATAGGGGAAAAGCTCCATGACCTTGGTCTAGACAGATT-TTTTTTGG 844
                                 ? v   v  i i         vi   i  -  v-   i  i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAG 592

  chr2_180107484_    845 ATATGATCCCTAACATGTAACATGTTTGCACAGATAACAAAAGCAAAAAT 894
                               iv  -  -----  -------     iii        v      
  L1M4_orf2#LINE/    593 ATATGACACC-AA-----AA-------GCACAAGCAACAAAAGAAAAAAT 629

  chr2_180107484_    895 AGACTGTTGGGGGTTGCATCAAACCAAAAAATCTTCTGTGCAGCAAAGGA 944
                            iviv v  iv  -       viv     -   i     vv       
  L1M4_orf2#LINE/    630 AGATAAATTGGACTT-CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

  chr2_180107484_    945 AACAATCAACAGAGTGAAGAGAGAACTTACAGAATGGGAAAAAATATTTG 994
                         v  v     v i      i   v   ii           i          
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_180107484_    995 TAAACGATAAATCCGTTAAGGGGTTAATATCCAAAATATATAAGGAACTC 1044
                         i   iv   v   i v      ii vi      i         i      
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_180107484_   1045 AAACAGATCAATAGCAAGAAAATGAAAAATCCAATTAAAAAATGGGCTAA 1094
                         vv   iv      ii  i  i ii  v  i      ?          v  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_180107484_   1095 GCACCTGAATAGAAATTTCTCAAAGAAAGACATATGAAAGACCAACAAGT 1144
                          v ii        v       v  ii    i   ii  v i    i   i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_180107484_   1145 ATATGAAAAAAATGCTCAACATTACTAATCAT 1176
                          i       i -          i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.26 (97 / 43)
Gap_init rate = 0.01 (9 / 665), avg. gap size = 2.22 (20 / 9)  


3401 23.41 5.07 0.35  chr2_180187432_180191736     2947  3813 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_180187432_   2947 TGAAAGGATATTCCATGTTCATGGATTGGAAGAATTAATATTGTTAAAGT 2996
                           i  i     i                     v             ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_180187432_   2997 GTCCATACTACCCAAAGCAATCTACAGATTCATTGCAATC---------- 3036
                          v v     v      vii             vi      ----------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_180187432_   3037 --------ACATTTTTCACAGAAATAAAAAAAACTATCCTAACATTTATA 3078
                         --------i v     ii       vi v  iviv       v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_180187432_   3079 TGCAATCACAAAAGACCCAGAATCACCAAAGCTATCCTACACCAAAAGAA 3128
                           v  vii   ii          vi     i v   i iv vv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_180187432_   3129 CAAAACTGGAGGAATCACATTATCTAACTTCAAATTATATACTACAGAGC 3178
                             ii       v     i vi i  i      -- iv       i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAGC 248

  chr2_180187432_   3179 TGC-------------------TACTGGCATACAAGCAGATATATAGACT 3209
                          i -------------------          viiii   i       ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_180187432_   3210 AATGTGACAGACTAGAGAACCCAGAAACAAACTCAGATATCTACAGTGAA 3259
                             vi i   v v    ii       i    i  v i  i  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_180187432_   3260 CTCATTTTTAACAAAGGTGCCAATAACATACACCAGGGAAAAGGGAGTCT 3309
                         i v     ii    i        v v   v  vii      iiiv     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_180187432_   3310 CTTCAGTAAATGGTGTTGGGAAAACTCGTTATCCATATGCAGAAGAATGA 3359
                         i    ii        i     v    v v  ?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_180187432_   3360 AACCAGACCCC-ATCTCTTGCCATATATAAAAATGAAATCAAAATGGATT 3408
                          iiii      - i   vii       i      v  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_180187432_   3409 AAAGACTTAAATCTAAGACCTCAAACTATAAAACTGCTACAAGACTAACA 3458
                          ?    i     v     v  v             vi  v    v-    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA-AACA 547

  chr2_180187432_   3459 ATGGGGAAAATCTCCAGGACATTGGTCTTGGCAAAGATTTGTTGAACAAT 3508
                         vv  ? v      i iv   v    vi v     v i   v  ii i vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_180187432_   3509 ACCCCACAAGCACAGGCAACCAAAGCAAAAATGGACAAATGGGATCACAT 3558
                           v   v       i     v    v      i  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_180187432_   3559 CAA-GTTAA--GCTTCTGCAC---AGAAGAAACAATCAATAAAGTGAAGA 3602
                            -i    --i   i  ii --- i i  v  v     v        i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_180187432_   3603 GACAACCCATAGAATGGGATAAAACATCTGCAAACTACCTATCTGACAAG 3652
                                  i         v    i  i      ii iv       i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_180187432_   3653 GGATTAATAACTAGAATACATAAGGATCTCAAACAACTCTATAGGAAGAA 3702
                            i vi  v i      i    i  v   vv       v   iv  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_180187432_   3703 ATCAAATAACCCAATCAAAAAATGGGCAAAAGATTTGAATAGACATTTCT 3752
                         iv             i?             i                   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_180187432_   3753 TAAAAGAAGACTTACAAATGGCAAACAGGCATATGAAAAGGTGTTCAACA 3802
                         iv        iv          v  i i   i        i  i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_180187432_   3803 TCATTGATCAT 3813
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.52 (120 / 79)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 5.88 (47 / 8)  


2583 23.66 7.34 2.91  chr2_180206266_180208136.rev      514  1371 (500)    L1M4_orf2#LINE/L1        3   898 (10)  

  chr2_180206266_    514 GAGAAATATACAGTGTTAATTCATTTGAAGTCTTAATATTGTTAAGATGT 563
                           i i    v vi    v  vv   v    v                  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_180206266_    564 TAGTTCTTCCCCAATTGATCTATAGATCCAGCACAATCCTGATCAAAATC 613
                         i i v  i   v          i    i  i i      iv         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_180206266_    614 TCAAAATGTTTTTTTATTATGGAAAATGGCAAGCTGTTTCTTAAATATAC 663
                         i  iv-  ii     -- iii    v  i       v i  v    vi i
  L1M4_orf2#LINE/    103 CCAGC-TGCCTTTTT--TGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_180206266_    664 ATAGAAAAG-AAAAGCCCTAGAATAGTCAAAACATTTTTTTAAAGGT--- 709
                           i    v -  ii v  i       i       v i  vv   i v---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_180206266_    710 -CAAATTTTGAAGACTTAATGCTTCCTGATTTTAATACTTACTCTAAAAT 758
                         -    v  v  i    i -ii     ii    i  v       vi   i-
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAG- 247

  chr2_180206266_    759 CTACAATAATCAAGAC--TGTGAAACTGGTGAAAGAATGGTAGACACATG 806
                              i          --    iv     iiv   i  ---     i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT---AGACATATA 294

  chr2_180206266_    807 GATCAATGGAACAGAAC--AGAGTCCAGAAATAGACTCACACCAATATAG 854
                                    i    i--              i  i  i  vvv   i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_180206266_    855 TCAGTTGATTTTCAACAAAGTTGCAGAGTGAATTCAATGAAGAAAGGCTA 904
                            i         i    i v   vi  vvv        ii     iv  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_180206266_    905 ATCTTTTCAACAAACAGTGCTAGAAGAAGTACGTATTCATATGTAAATTC 954
                         i             ii     i i v  v ivi  ?i  i   i   ---
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA--- 441

  chr2_180206266_    955 AAAA-AACGCCTTGACTACTACCTGATACAAAACATAAAAATTAATTCAA 1003
                          i  -i v i- v   iv      v i  v v i i         i    
  L1M4_orf2#LINE/    442 AGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_180206266_   1004 TA-GGATCATT--CATAAA-ATAAAAACTTTAAAAAAACTATTAAACTTC 1049
                         v -      ?v-- v    -i   i i  -----        v     ii
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCT-----AAAACTATAAAACTCT 535

  chr2_180206266_   1050 TAGATGAAAACAGTAGA---AAATCTATTTGGCTTTGCATTAGGCAAAGA 1096
                             v       -   i---      viv  i i   vi        v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACA-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_180206266_   1097 TTTCTTAGA-----------AAATA-AAG----AAGTGTGAATATTGATA 1130
                                  -----------  ii -   ----  iv vi  v  v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_180206266_   1131 TATTGGACTTTATCAAAATTTAAAACTTCTACTCTTTAGAGACACTTTTA 1180
                         v         i         v       i iiv   i i  i------- 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG-------A 677

  chr2_180206266_   1181 CACTGTTCAGAAAATGAAAAAACAAGCTATAGACTACTAGAAAGTATTTG 1230
                             i iv     i      i    v i i   v ivv     i      
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_180206266_   1231 ---------TATCTGCTTAAGAAATTGCATACAGA---TATAAATAATT- 1267
                         ---------      v v i i v   i  v    ---      v  i -
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_180206266_   1268 -TATAACTCAATAATAAA--------TGAT--------AAAATGGGAAAA 1300
                         -  i              -------- i i--------        v   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_180206266_   1301 CAATTTTAACAGGCATTTTACCAAAGAAGAAATATGAATGATGAATAAGC 1350
                         vi    v  i  i     iv          v   ii    iiv       
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_180206266_   1351 ACATAAAAAAATGCTCAACAT 1371
                             i    i           
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACAT 898

Transitions / transversions = 1.58 (123 / 78)
Gap_init rate = 0.03 (27 / 896), avg. gap size = 3.26 (88 / 27)  


 825 29.83 10.50 4.01  chr2_180411974_180413699      511  1234 (492)    L1M4_orf2#LINE/L1      138   908 (0)  

  chr2_180411974_    511 CTCAACATTTGCATGGAAAAGCAAATGGCCAAGA-TAG--ATATCATTCC 557
                          ii  v   iii       v    iv i  v   -   -- v v  v  i
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_180411974_    558 TAAAGAAGAAAAACAATGT-GTAGTGCTT----TGCTCAGTCAGCTGTGA 602
                          i  i     i     v  - v  vi  i---- v i  i i----- v 
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT-----TCA 232

  chr2_180411974_    603 AGAATTTTTATACATTCACAGATATTAACATATTATGACATTGGTGTAGA 652
                          i v  vi  i v vii    vv  i  v i v i  ii i   ii  ii
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_180411974_    653 GACAAACA-AT---TCAATGGAATGGAAT--AGAGTATAAAAAGAAACTT 696
                           i i   -  ---          i    --     vi i   v    ii
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_180411974_    697 GCACATACACAGAAACTTGGTTTTTGGTACAGTGAATACTGAAAGC---C 743
                         ii    vi ii vv v   i    i --   i- ii i ii i v --- 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCG--ACAA-GGGTGCCAAGACCATTC 379

  chr2_180411974_    744 AGAGGGGAA-GAAGAAACTATTCACTAAATGACTCTGGAACAACTGGTTA 792
                          iv      -   v iv  v    vi     iiv    i        v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_180411974_    793 TCTATA--CAGAAGAAAGAA---------------------AAATGCATA 819
                         ? i i --  i     v   --------------------- v  i  - 
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA-A 478

  chr2_180411974_    820 AAATTGACTGCACAAAAACAGTTACTGG--TAAATTCAAGATTTAAAGCC 867
                              i   ---     vvii i ?v i--     vi    vi    ---
  L1M4_orf2#LINE/    479 AAATTAACT---CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA--- 522

  chr2_180411974_    868 AAATTATAGCAATTGTAGATTAATATATTTGGG---ATCCATATAATCTC 914
                         -- i    iv v iv    vv  v i  vv ? ---   ivii i i  i
  L1M4_orf2#LINE/    523 --ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_180411974_    915 AAGGTAGAGAAACACTTCTTAAATGGAGTATTAAAAAGCACAATTCATAA 964
                         ii v   iv  vvii      i  iviii ii    -      viv i  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA-GCACAAGCAACAA 619

  chr2_180411974_    965 AAGCAATAA-AAATA--CTTGATTATATTAAAATTAAAGATTAATTT-TA 1010
                            v  v  - i   --i v  i vi  i         i i --   - i
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT--TTTGTG 667

  chr2_180411974_   1011 CT--AAGAGTCAC---CAAAAATAATAAAAACCCAAGCCATTCCACGTGA 1055
                           --  ii v   ---   i  - i i    vv   v   ivvv i v  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAA-AGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_180411974_   1056 GAATTTATCTGCAA--CATAGAAAACTGAAAAAGAATTAGC-TCTAC--T 1100
                            vv   i     --    v v--    v  i i i v i-  i v-- 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATAT--CTGATAAGGGACTTGTATCCAGAAT 764

  chr2_180411974_   1101 ATATGA----CTACTACAA----ATAATTTTTTTAAA----TTAGTGATT 1138
                             i ----  vi     ----     ------   ----iv i i ii
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAAT------AAAAAGACAAATAACC 808

  chr2_180411974_   1139 CTATT--AAAATGGTCACATGATATGAATAGGAATTTCACCAAAGAGGAA 1186
                          v   --       v  v v   v       iv     v       i  v
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_180411974_   1187 ACACAAATGGCCAAAAA--ACATGAAAAGATGCTCAGCCTCATTAGTTAC 1234
                          i            v  --                 i v   ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (125 / 88)
Gap_init rate = 0.05 (37 / 771), avg. gap size = 2.84 (105 / 37)  


3056 26.02 1.43 1.54  chr2_180442419_180448832.rev     5016  5922 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_180442419_   5016 GGAAGA-ATTCCATGGTCATGGATAGGAATAATAAATATCGTGACAATGG 5064
                          i    -  i     v        v    v v v     i  v vi    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_180442419_   5065 CCATAAAGCCCAAGGTAATTTATAGATTTAATGCTATCCCTATCAAGCTA 5114
                          v   vvv     iv i  i  i     i  i  v           iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_180442419_   5115 CCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 5162
                             ivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr2_180442419_   5163 TGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAGAG 5212
                              viiv  ii  v  viv  v     i      i i ivv i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_180442419_   5213 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCCA 5262
                              i      vv    i  v  ii i      viv        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_180442419_   5263 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATATATAGA 5312
                               i   i    ii         i iv ii i   ----i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA----CATATAGA 296

  chr2_180442419_   5313 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACAACACATTTACAA 5360
                         i        i    i--    i  --        vv v i       iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_180442419_   5361 CTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATT 5410
                         ii vi    i  i     ivv  v   i v  vvv          vi  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_180442419_   5411 CCCTATTTAACAAATGGTGCTGGGCAAATTGGCTAACCATATGTAGAAAG 5460
                         vi  v  i                vv  i   v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_180442419_   5461 CTGAAACTAGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATA 5510
                         v    ii i  i    v   i     v              i    i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_180442419_   5511 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5560
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_180442419_   5561 ACCTAGGCA-ATACCATTCAGGACATAGGCTTGGGCAAAGACTTCATGAC 5609
                           v    ?i- v i -   iv   v v  v  i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_180442419_   5610 TAAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATC 5659
                           vi            vvi          vv i   v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_180442419_   5660 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5709
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_180442419_   5710 AATAGGCAACCCACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5759
                           v  i                       v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_180442419_   5760 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCCCAACAAATTTACAAG 5809
                         i  i  i  vi          v  i         ii -   v iv i  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAAT 792

  chr2_180442419_   5810 AAAAAAACAAACAACCCCATCACAAAGTGGGTGAAGTATATGAACAGACA 5859
                              i     i     v  i?v   i    ii   v  v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_180442419_   5860 CTTCTCAAAAGAAGACAATTATGCA----GCCAG---ACAAATGAAAAAA 5902
                         i     v        ----   i  ----    i---i  v       i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_180442419_   5903 TGCTCATCATCACTGGACAT 5922
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 2.08 (27 / 13)  


1246 28.96 8.25 3.37  chr2_180470800_180475437      498  1091 (3547)    L1M4_orf2#LINE/L1       55   677 (231)  

  chr2_180470800_    498 ATTCTCCCCAA-TTAATCTGTAGATTCAATGCAATCTTAACCAAAGTCCT 546
                           v        -  i    ii        i      iiv i    i   i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_180470800_    547 GGCAGGTTTACTTTTTG--GAAACTGACAACATGATTCTGAAATGTATAT 594
                         i  v vi  ---     --    i      vv    i  i    vi    
  L1M4_orf2#LINE/    105 AGCTGCCTT---TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_180470800_    595 A-AAAGGTAAAGGAACCAAGAATAGCCAGGGCAATTCTGAA---GAACAA 640
                         i-   v i  i   v   -         iii    ii    ---   v  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_180470800_    641 TGAAGATGCAGGACTTACACTAAGAGACATCACAGCATATTATGAGGCTC 690
                         ii   v  v      i     vvvvi iv   v i v  i  ii i   v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_180470800_    691 TATTAATTAAGACAGTCTGGTTTTGGCCCAAGGAAAAGTAACCTGACCAA 740
                         i v    i        v    vi    vi     v iii vviv  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_180470800_    741 TGGAACAGAAGGAAGAGTCCAAACACACACACACACCGACATACATATAT 790
                              i    vvi        i v i ----- -   --       v   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATA-----A-ACC--CATACATTTAT 342

  chr2_180470800_    791 --TCACCTGATTTATGACAATACTGACAAAGGTAACTTACGACAAAGTGG 838
                         --   vi      vi     viv  v   iivi --  ----   --   
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCA--TT----CAA--TGG 384

  chr2_180470800_    839 TAAAAGGATAGTAATTTCAATGAATGGAG-TAAGTTGCTTGAATATACAT 887
                         vi    i     vv      ii     v - ii viivi  i   ?v  i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_180470800_    888 AT-TGGACAAATTATCTTG-ATCTTTACCTT-CACTGTATG------TCA 928
                           -iii vi   v vv   - i ii     i-   ii   i------ i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_180470800_    929 ATTCCAGAAGGATTGCAAATCTAAATGTTAAAGAAAAAATAATAAAGTTT 978
                          i  v i v    ii? i i        v i  vv    iv     ii i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_180470800_    979 TTAAAGGAAAA-----GAGAACATCTTCATGACTCTGGAGTAGGCAA--- 1020
                            i i     ----- ? v v      i    ii   iv       ---
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_180470800_   1021 ------AGACATAG-----AAAGTATTAACTATAAGAGAAAAAAT----- 1054
                         ------   i  ii-----    i iv i v i  i         -----
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_180470800_   1055 ---TGGGATACACTAAAATTAAAATTGTTT---CTTCAAAGAA 1091
                         ---   iv v  ii          viv   ---        i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

Transitions / transversions = 1.64 (105 / 64)
Gap_init rate = 0.04 (23 / 623), avg. gap size = 3.00 (69 / 23)  

3049 26.19 1.78 1.00  chr2_180470800_180475437     2280  3180 (1458)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_180470800_   2280 TGGAAAAACATCCCATGCTCATGGATAGGAAGAATCAGTATCATTCAAAT 2329
                               i i        i        v      v i i   ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_180470800_   2330 GGCTATACTGCCCAAAGCAATTTACAGATTCAACGCTATTCCTATCAAAC 2379
                            v     v      vii  i              v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_180470800_   2380 TACGAATGACATTCTTCAGAGAACTAGA-AAAC-AATCTTTTAAAATTCA 2427
                          v v iivi v  i  iiv    v v  -  i -i   i --        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chr2_180470800_   2428 TATGGAACCAAAAAATAGCCCGAATGGCCAAGGCAATCTTAAGCAAAAAG 2477
                                viiv  iiv v  v    i     ii       i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_180470800_   2478 AGCAAAGCTGGAAGCATCACATTACCCAACTTCAAA--TTATCCTACAGG 2525
                          i     i    i vv     i v     i      --   --     ii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAA 246

  chr2_180470800_   2526 ACTACAGTAACCAA-ATAGCATAGGACTGGTACAAAAACAGGTGCTTTGA 2574
                         i         i   - i  ii i v     i i  ii i  iiiiv v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_180470800_   2575 CCAATGGACCAGAATATAGAGCCCAGAAATAAGGCCGTACACCTACAACC 2624
                         i       vi     vv    i          iv  i    ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_180470800_   2625 ATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGA--GTAGAGT 2672
                          vi    i  i     i v  v   i v  vv         -- v v   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_180470800_   2673 CCCTATTCGATAAATTGTGCTGCGATAACTTGCTAGCCATATGTAGAAGA 2722
                          -- v   i i    v      v  i    v v  ?   i   i i    
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_180470800_   2723 TTGAAGCTGGATCCCTTCCTTATACCATCAACAAAAATCAACCCAAGATG 2772
                         v     i    i    v   i i     vv        i   i   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_180470800_   2773 GATTAAAGACTTAAATGTAAAAGCAAAGACTATAAAAACCCTGGAAGACA 2822
                            i ?    i         i   v  i         vi i i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_180470800_   2823 ACCTAGGCA-ATACCATCCTGGACATAGGAACTGGCAAAGATTTCATGAC 2871
                           v    ?i- v i v  v  -  v v  iviv     v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_180470800_   2872 AATGACATCAAAAGCAATCA--CAACAAAAACAAAAATTGCCAAGTGGGA 2919
                         v      i        --  --        iv      v vi  i v   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_180470800_   2920 TCTAATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAG 2969
                         ii v  i   v v  i i   i  ii vv    i  v        v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_180470800_   2970 TAAACAGACAACCTACAGTATGGGAGAAAATATCTGCAAACTATACATCT 3019
                          i  v        i    v              i      ii   i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_180470800_   3020 GACAAAGGTCTAGTATCTAGCATCTATAAGGAATTTAAACAAATTTACAA 3069
                           i  i  v  v     i  v  v     i   i ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_180470800_   3070 GAGAAAAACAA----CTCCATT-AAAAGTGGGCAAAGGACAT-ACCAGTC 3113
                         v i   i    ---- i v   -    i           iv - vi  v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_180470800_   3114 ACTTCTCAAAAGAAGACATACATGCAGCCAAGAAGCATATGAAAAAAAGC 3163
                          i     v        i     viii     v     i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_180470800_   3164 TCAATGTGACTGGTCAT 3180
                             ii v ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  

 463 24.89 14.85 1.31  chr2_180470800_180475437     3918  4146 (492)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr2_180470800_   3918 AAAA--AAAAACTGTTG--CTTCATCTGAATACACCATTCAGATATTTAA 3963
                             --       v   --     ---i iv    i  iv   v v v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCA---AAGGACACTATCAAGAAAGTGAA 695

  chr2_180470800_   3964 GAGACAACTCCCAGAGTGGAAAAAGATATTTGCAATACATATATACAACA 4013
                         i       i v    i   i i  i          vv       vii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_180470800_   4014 AATTACTC---TC------ATATGAA-AACTTT---AAATCAACAA---- 4046
                          ivv   i---  ------    i  -    i ---  v    i  ----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_180470800_   4047 ---GCAGAAAACCCAACAGAAAAATGAACAAAAACTGTGAAT-------- 4085
                         ---i  i v       iv?       ii    iiv v     --------
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_180470800_   4086 --TCAGAAAAGACATCCCAATGGCAAATAAGCATGTGAAAAGGCACTCCA 4133
                         --i  i i    i  v v      v        ii       iii   v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_180470800_   4134 CCTCATTTGTCAT 4146
                          v   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (34 / 22)
Gap_init rate = 0.03 (9 / 260), avg. gap size = 4.11 (37 / 9)  


2649 27.33 3.26 1.12  chr2_180500576_180502783      828  1716 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_180500576_    828 TGGAAAAATATTCCATGATCATGGGTTAGAAGAATTAATATTGTTAAAAT 877
                               i    i     v      i  i     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_180500576_    878 AACCATATCACCCAAAACAATCTGCAGAGTCAACATTAATTCTATCCCAC 927
                         ii v   iiv      vii    i    v     iiv vii     vv v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_180500576_    928 TACCAGCATCATTTTTCACAGAA-CTAAAAAGAACT-ATTATTAAATTCA 975
                          v     vv v     ii     -i i v   --  -  iv v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_180500576_    976 TATAGAACCAAAAAAGAGCCCAAATATTGAAAGCAATCCTAAGCAAAAAG 1025
                            i   viiv  ii  v  vi    viv   i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_180500576_   1026 AACAAAGTCATAGATATTGCATTACCTGACTTCAAACTATACTATATGGC 1075
                                 iiv  ivv ii  i v  ii i      viv     i vi  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_180500576_   1076 TGTAATAACCAAAACAGTGTGGTAC------AAAAACAGATTCACAGATC 1119
                          ii i   i   i            ------  ii i   ivi i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_180500576_   1120 AATGTAACTGAATAGAGAACCCAGAAATAAAGCTCCACACCTACAGCCTT 1169
                             v  iv    v    ii           v ivi   ii  ii i vv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_180500576_   1170 TTGATCTTTGACAAAGTTGACAAAAATAAGCAATGGGAAAAGGACTCCCT 1219
                              i  i     i v  v   i vi vv       i    i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_180500576_   1220 ATTCAGTAAATGGTGCTGAGATAGCTGGCTAGCCATATGAAGAAGAATAA 1269
                         v    ii           i  i i    v  ?   i   v i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_180500576_   1270 AACTAGACCTCTACATTTTAACATGTACAAAAATTAACACAACATGGATT 1319
                          ii i    i    v ivi v   i             v   v      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_180500576_   1320 A----TTTAAATGTAAGACCTCAAACGATAAGAATCCTAGAAAAAAACCT 1365
                          ----ii           v  v    v    i v  i     i     v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_180500576_   1366 AGGAA-ACACCATCCTGGACATTGGCCTTGGGAAAAAATTTAT--GACTA 1412
                            ?i- v i v  v  -  v    v-  i  v  vii   v --  -  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTG-ACCTTGGG-TTAGGCAATGGTTTCTTAGA-TA 595

  chr2_180500576_   1413 AAACCTCAAAAGCAACTGCCACACA-CACAAAAAAAAATTGACGAGTGGG 1461
                         vi  vi        -----  vi  -  v  i       v  ii i v  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCA-----CAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_180500576_   1462 ACCTAATTAAAATAAAGACCTTCCACACAGCAAAAGAAACTATCAACAGA 1511
                           i v  i     v  i v   iiiii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_180500576_   1512 ATAAACAGACAACCTACAAAAGGGAAGAACTTATTTATAAACTATGCATC 1561
                         i i  v        i   i  v  i    vv     ii   ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_180500576_   1562 TGACAAATGTCTAATATCCAG--TCTATAGGGAACTT----AATTGAACA 1605
                            i  iv v  vi       -- v    ii     i----  i v  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_180500576_   1606 AGCAAAAAACAA----CCCA-TTTAAAAATGGGCAAAAGACATGAACAGA 1650
                          vv    i    ----    -  ?             i  iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_180500576_   1651 CATTTCTCAAAAGAAGACATACAAGTGGCCAATAAAC-TATGAAAA-ATG 1698
                                 v        i      i          i -i       -   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_180500576_   1699 CTCAATATCACTAATCAT 1716
                              i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.17 (39 / 18)  


2563 25.76 5.08 2.49  chr2_180593975_180596217.rev      867  1751 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_180593975_    867 TGGAAAAATATGCCATGCTCATAGATTGAAAGAATCAACATCATTAGAAT 916
                               i    v     i    i     i    v i  i  ii   ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_180593975_    917 GGCCAAATTGCCCAAAGTAATCTACAGATTTAAAAATGTTTCTATCAAGC 966
                            v v i v      v i           i  vivvi ii       iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_180593975_    967 TACCAAC-ACTATTTTTACAAAGCTAGAAAAAGCT-ATTCTAAAATTCAT 1014
                          v   i -i iv     i  i iv v  v  -   -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_180593975_   1015 ATGGAGGCAAAAAAAATAAAAGAG-CCCA-AATATCGAAAGCAATCCTAA 1062
                              ---------   iv   i -    -    v v   i     i i 
  L1M4_orf2#LINE/    150 ATGGA---------AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_180593975_   1063 GCAAAAGGAACAAAGCTGGAAGAATTACACTACCTGACTT-GAAGCTATA 1111
                         iv  i i        i    i  v i     v  ii i  -i  i  -  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TA 239

  chr2_180593975_   1112 CTATAAGGCTACAATAACCAAAACAGCATGATAC-------AAAACAGAC 1154
                            i  i      i   i   i    ii  i   ------- ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_180593975_   1155 ACATAGGCCAGCAGAACAGAATAGAGAACCCAGAAATAAATC-ACACACC 1203
                          i    ii  iii   i     v    ii           i - i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_180593975_   1204 TGTGGCCACTTGATCACTGATAAAA----TAAG------CAATGGGAAAG 1243
                          i   i  v     ivii  i  ii----i   ------       i  i
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_180593975_   1244 GACC--CCTTATTTAATAAATGGTTCTGTGAAAGCTGGCTAGCCATAGGT 1291
                           vi--i   -  i  i       v   v  v i    v  ?   i v i
  L1M4_orf2#LINE/    390 GAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_180593975_   1292 GGAAGAATGAAACTGGACCCCTATATTTCACTAAATATAAAAAGTAACTC 1341
                         ii         ii          iv iv   i v   i     v      
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_180593975_   1342 AACATGGATTAAAGACTTGTATGTAAGACCTCAAAACTATAAGAATCTTA 1391
                           v      i ?    i iv        v  -          i v     
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTA 537

  chr2_180593975_   1392 GAGGAAAACCTAGGAA-ACATCATTCTGGACATCAGCCTTGGGGAAAAGT 1440
                           i      v    ?i- v   -   vv   v ii v-  i  v  vi  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGT 585

  chr2_180593975_   1441 T-----GATGACCAAGTCCTCAAAAGCAATTGCAACAAAAACAAAAATTG 1485
                          -----   ---- v v vi        vvv         iv      v 
  L1M4_orf2#LINE/    586 TTCTTAGAT----ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_180593975_   1486 ACAAATAAAATCTAATTTAACTAAAGAGCTTCTGCACAGAAAAAGAAACT 1535
                          i    vii ii v  iv  v v  i i   i  ii vvv   i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_180593975_   1536 ATCAACAGAGTA-----------CACAGAATGGGA-AAAATATTTGCAAA 1573
                              v i   i-----------            -              
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_180593975_   1574 CTATGCATCC-ATCAGAGGTCTAATTATCCAGAATCTATAAAGAAATTAA 1622
                         ii  ii   i-  v  i iii i--          v         v ivv
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTG--TATCCAGAATATATAAAGAACTCTT 779

  chr2_180593975_   1623 ACCAATCAACAAGCAAAAGACAAATAACCCCATTCAAAAGTGGGCAAAAG 1672
                           v v    i  vv                v   ?    i        i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_180593975_   1673 ACATGAACAGACACTTCTCAGAAGAGGACATGCAAGTTTCCAACAAACAT 1722
                          iv    i     i     vi    i  i  i   i vv    i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_180593975_   1723 GGGAAAAAAATGTTCA-CATCAGTGATCAT 1751
                         iv     i -  i   -     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (145 / 79)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.58 (67 / 26)  


3211 25.55 0.76 1.64  chr2_180718007_180722266.rev     2861  3776 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_180718007_   2861 TGGAAAGATATTCCATGTTCCCGGATGGGAAGAATTAATATTGCTAAAAT 2910
                                    i        vi    v      v         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_180718007_   2911 GTCCATACTACCCAAAGCAATCTACAGATTAAATGCAATCCCTATCAAAA 2960
                          v v     v      vii           v  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_180718007_   2961 TACCAACAACATTCTTCAGATAAAAAGAAAAACCAATCCTAAAATTTATA 3010
                          v   i vi v  i  iiv v   vv  v  i ii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_180718007_   3011 CAGAGTCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAGGATAAAGAA 3060
                         ii  ivii   ii                 i v   i i ii vi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_180718007_   3061 CAAAACTGGAGGAATCACATTACCTGACCTTGAATTACACCACAAAGGTA 3110
                             ii       v     i v  ii ii ii  vivi  i      v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_180718007_   3111 TAGTAACTAAAACAGTGTGGTACAGGCATAAAAATGGACACGCAGACCAA 3160
                         i     ii  i            v       ii  i    iii   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_180718007_   3161 TGGAATAGA-CAGAGAACCAAGAAACAAATCCACACACCTACAGTAAACT 3209
                                  -iv    ii v     i   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_180718007_   3210 CATTTTTAATAAAGGTGCTAAGAACCTACATTAGAAAAAAGACAGTGTCA 3259
                         v     ii i  i     i    v v v  v i ii   ii i   v iv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_180718007_   3260 TCAACAAATGATGCTGGGAAAACTGGATATTCATATGCAGAAGAATTAAA 3309
                                   i        v         ?i  i     i      v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_180718007_   3310 TGTGATCCCTATCTCTCGCCCTGTACAAAAACCAAATCAAAATTGATTAA 3359
                          vv  i     i   v i  v i        ii  v       v   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_180718007_   3360 AAACTTAAATCTGAGACTTCAAACTATGAAACTACCACATGAAAACTTTG 3409
                          i  i     v i   vi v       i     vii v v      v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_180718007_   3410 GGGAAACTCTCCAGGACATTGATCTGGGTAAAAATTTTCTGGGAAATATC 3459
                          ? v  v   i iv   v   ivi i  i  vii   -  vi  v  iv 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-CTTAGATATGAC 599

  chr2_180718007_   3460 -CCATAAGTATAGG-AACCAAAGGTGAAATTGACAAATGGGATGACATCC 3507
                         -   v   i i i -   v    ivi    v  i    v   ivv    v
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_180718007_   3508 AG-TTAAAAAGCTTCTGTGCCACAAAGGAAACAATCACCAAATT-AAGAG 3555
                          i-       -   i     iv       v  v    vv   v -  i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_180718007_   3556 ACAACCCAGAGAATGGGAGAAAATATTTGCAAACTACACATTTTACAAGG 3605
                                 v                        ii i i  i v i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_180718007_   3606 G--TTATATAATAACCAGCTCCTTATATATTATAAGGAGCTCAAACAACT 3653
                          --  i   -----    ------ -    -    i  i   vv      
  L1M4_orf2#LINE/    749 GACTTGTAT-----CCAG------A-ATAT-ATAAAGAACTCTTACAACT 785

  chr2_180718007_   3654 CTATAGGAAAAACTCTAAAAATCCTATTTTAAAATGGGCAAAAAATCTGA 3703
                          v   iv     vv v  v  i  v   ?v            ii  i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_180718007_   3704 ATAGACATTTCTCAAAAGAAGACATACAACTGGCAAACAGGCATATGAAA 3753
                                      v        i      v    v  i i   i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_180718007_   3754 AAGTCCTTGTCATTGATCATCAG 3776
                          ii v  iiv   ii????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


2865 19.88 2.48 1.55  chr2_180726007_180727624      483  1126 (492)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr2_180726007_    483 AAAACCAAGTGTGGCATTGGCA-AA-----------TAGATCAATGGAAT 520
                           i  --       i i     -  -----------              
  L1M4_orf2#LINE/    259 AAGAC--AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_180726007_    521 AGAATAGAGAACCCAGAAATAAACCC-TGGTTATATAGTTGAT-GATCTT 568
                              v    ii              - ivv v   i  ii  -   i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_180726007_    569 CAACAAGGGTGCCTAGACTACTCAGTGGGAAAAGGACAGTTTCTTCAACA 618
                          i           v    i i   i    i    i i   i i       
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_180726007_    619 AATAGTGTTGGGAAAACTGGGTATCTATGTGCAAAATAATGAAGTTGGAC 668
                            i   i     v      i  ? i ii       v             
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_180726007_    669 TCCTCTTTTACATTATATACAAAAGTTAATGGAAAATGGACTACAGACCT 718
                         i   vii i   ii          i    ivv        ii ?      
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_180726007_    719 AAATGTAAAATCCCAAACTATAAAACTCTTATAAGATAATGTAGAGAAAA 768
                                 i v iv                 v    v  ii   i?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_180726007_    769 AGCTTTGTAACATAACACTGGACTTGGCAATGATTTCTTGGATATGTCCC 818
                          v   i  i  v -----   ii v       i      i      v v 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCT-----TGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_180726007_    819 CTACAAAGCACAGACAACAAAAGAAAAC-TAGGCAAATAGCACTGTATGA 867
                          - -        ii             v-   ii    v v   vi  v 
  L1M4_orf2#LINE/    602 C-A-AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_180726007_    868 AACTTAAAAACTTTTGTGCATCAAAGCACACAATCAACTGAGTAAAAAGG 917
                           v                v      v    v     vvi   i     i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_180726007_    918 CAACTGGCAAAATGGGAGAAAATATTTGCAAGTTTTATGACTGTTAAGAG 967
                             ivi  i                     i iv   iv   v    i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_180726007_    968 GTTAATATCCAGAATATATAAAGAACTCCTACAACTCAACAACAAAAAT- 1016
                         ii vi                       i          i  i     v-
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_180726007_   1017 CAAATAATCTGATTAAAAATTGGGCAAAGATCTTGAGCAGATATTTCTTC 1066
                                i ii   ?    v         ivi    ii   i      i 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_180726007_   1067 GAAGAAGAAATAAAAATGGCCAACATTCATATGAAAAGATGCTCAATTAT 1116
                         i       v   v          i vv  i                i-  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC-AT 898

  chr2_180726007_   1117 CACTAATCAT 1126
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.88 (81 / 43)
Gap_init rate = 0.02 (11 / 650), avg. gap size = 2.36 (26 / 11)  


4087 17.59 5.44 0.46  chr2_180730139_180732431.rev      938  1801 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_180730139_    938 GAAAAGGT-TCACAT---CATGGATTCGAAGAC--AATAGTGTTATAATG 981
                          i    i -  v   ---        v      --    v     vi   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_180730139_    982 GCAATATTCCCCAAATTGATCTTCCAACTTTTAACACAATCTGCATAATA 1031
                               i               v vi --  i   i     ivi  v v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGA--TTCAACGCAATCCCTATCAAA 99

  chr2_180730139_   1032 ATCCCAGCTGATATTTTTTTAGAAATTGACCAACCAATTTTAAAAATTCA 1081
                                   viv     vi          v i ii  ii     -    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCA 148

  chr2_180730139_   1082 TATGGAATTACATAGGGTCCAGAATAGACAAAAGAATCTTGAA------- 1124
                                v i  vi  ii         v     v         -------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_180730139_   1125 --CAA-GTAGGAGCTCTCACATGACCCAGTTTCAAAACTTACTACCAAGC 1171
                         --   -  v    vv      ivv    i                v    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_180730139_   1172 AATGTTAATCAA----------CACTGGCAAAAGGACAGACATACACATG 1211
                         v iiv       ----------i       v     i       i v  v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_180730139_   1212 AATGGAATCGAAACGGGAGTTCAGAA-TAAAATCATGCATCTATGGTCAA 1260
                                 v   vi i    i     -    vi   i   i         
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_180730139_   1261 CTGATTTTCAACAAGGATGCCAAGACCATTTAATGTG--------AGTAT 1302
                         i        i      i             i    v --------   v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_180730139_   1303 TTTCAAAAGAGAGTGCTGGATTTACCAGACAGCTACACAGAAAAGAATCA 1352
                               v i vi       iviv  ii  i ? i   iiv        v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_180730139_   1353 GGCTGGACCCTTTCCTCACACCATATGCAAAAACTAACTCAAAAT----- 1397
                         i i       i v             i      i           -----
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_180730139_   1398 AAAGACCTCAAAATAAGAGCTAAAACTACAAAGCCATTAGAAGAAACCA- 1446
                          ?      v  vi               i   i iv          v  -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_180730139_   1447 AAGAGTAAACCT-CATGACCTTGGATTTGGCAAAGATT-CTTGGAATATG 1494
                          i ?     i  - i         i  v     v i  -   i  -    
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATG 597

  chr2_180730139_   1495 ACATCAAAAGCATAAGCAACAAAAGGAAAAATA----AAGTGGACTTCAT 1540
                            i        i            i       ----  v          
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_180730139_   1541 TAAAATTAGAAACATTTGTGCTTCAAAGGATACCATTGAGAAAATGAAAA 1590
                         i       i    v                i  i  ii     i      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_180730139_   1591 GACAAACCACAGGATGTGAAAAATTATTTGCAAATCATATACCCGATAAG 1640
                              v      i   v  i   v                 i i      
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_180730139_   1641 GAACTTGTATACCAAATATACAATGGACTTTTACAACTCAATAGTAAAAT 1690
                          i        v vi      i  v i   i             i     v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_180730139_   1691 GACAAATAGCTCAATTTAAAAATTGGCAAAAGATTTGAATAGGCATTTCT 1740
                                 i i     ?      v      i           i       
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_180730139_   1741 CCAAGGAAGATGTACAAATGGCCAAAAAGCACTTGAAAAGTTGCTCAACA 1790
                             i      i             v      v       v         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_180730139_   1791 ACATTACTCAT 1801
                         v  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (88 / 60)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 3.19 (51 / 16)  


2308 27.30 8.63 1.30  chr2_180763293_180765593      964  1809 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_180763293_    964 TGGACAAACATTCCATGCTCACGAATTAGAA---TCAATATTATTAAAAT 1010
                             v i i  i     i   i i   i   --- i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_180763293_   1011 GGCCATACTGCCCAAAGCAATCTATAGATTCAAACATAATT--------- 1051
                            v     v      vii     i        - ii   i---------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAA 99

  chr2_180763293_   1052 ------------TTTTTTACAGAACTAGAAAAAACT-ATTCCAAAGTTCA 1088
                         ------------      i     v v  v  i-  -  i i   i    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_180763293_   1089 TATGGAACCAAAAAGGAACCCTAATATTGGAAGCAATCCT---AAGCAAA 1135
                                viiv  i   v  vv    vivi  i     i ---  iv  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_180763293_   1136 AACAAAGC-AGAGGTATCACATTACCTGACTTCAAATTATACTATAAGGC 1184
                                i-i    vv     i v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_180763293_   1185 TACAATACCCCAAACAGCATGATACTGGTATCAAAACAGACACATACACT 1234
                             i  vi v i    ii  i      i  v ii i     i   v ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_180763293_   1235 AATGGAACAGAATGGAAAACTCAAAGATGAAGCCGTACACCTACAACCAT 1284
                                i     v  i iii  i i  i  v  i    ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_180763293_   1285 CTCATCTTTGACAAAATTGACAAAAATAAGCAATGGGAAAGGACTC-CCT 1333
                         i v  i  i     iiv  v   i vi vv       i  i  v v-i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_180763293_   1334 AATCAATAGATGGTGCTGGGATATCTGGCTAGCCACATGCAGAAGAATGA 1383
                         vv    i i            i v    v  ?         i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_180763293_   1384 AACTGGACCCCTACCTGTCACCATATTCAAAA-TTAGC-----ATGGATT 1427
                          ii             vv        v     -   i -----      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_180763293_   1428 AAATATTTAAATGTAAG--CTCAATATATAGGAATTGTAGAAGAAAACCT 1475
                          ? v ii          --  v  vv    ii v iv           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_180763293_   1476 AGGAA-ACACCATTCTGGACGTTGGCCTTGGGAAATAATTT-------AT 1517
                            ?i- v i -   vv   v    v-  i  v   ii   -------  
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATAT 596

  chr2_180763293_   1518 GAC--CAAGTTCTCAAGCAATTGCAACAAAAACAAAAATTGACAAGTGGG 1565
                            --   ------     vvv         iv      v  i  i v  
  L1M4_orf2#LINE/    597 GACACCAA------AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_180763293_   1566 ATCTAATTAGA-TGAAAGAGCTACTGTACAGCAAAAGAAGCTATTAGGAG 1614
                          ii v  i i - v   i -  vi   i vv    i  vi    i i  i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_180763293_   1615 A-----------ACCTACAGAATAGGAAAAAATATTCGCAAACTATGCAT 1653
                          -----------   i       i   i        i     ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_180763293_   1654 CTGACAGAGGTCTAATATCCAGAATCTATAAGAAATGTAAACAACTCAA- 1702
                             i ii  v  vi          v     ii  ivivv         -
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_180763293_   1703 ----ACAAATCAAACAATCCCATT-AAAGACAGGCAAAAGACT-GAAC-- 1744
                         ---- v  iv    i  i  v   -   i ii      i  i -   i--
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_180763293_   1745 ----TTCTTAAAGGAAGACATACAAGCAGCCAATGCCCATGTGAAAAAAT 1790
                         ----    iv  i     i      iii      ivv  ii      i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_180763293_   1791 ATTCTACATTACTAATCAG 1809
                         ii  v    i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (148 / 80)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.50 (84 / 24)  


1795 24.78 2.62 1.05  chr2_180787318_180792711.rev     1774  2346 (3048)    L1M4_orf2#LINE/L1      327   908 (0)  

  chr2_180787318_   1774 AAATCAGTATATCCA--ACCATTTGATCTTTTACAAGC-TGACGAAAACA 1820
                            i vi  i  ii --ii  v     i  iv     v-  v i i v  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_180787318_   1821 AGCAATAAAGGAAAGAACTCCCTATTCAATAAATGGTGCTGGG-TAACTG 1869
                         vv    ii-        ivvi  v     i             -i     
  L1M4_orf2#LINE/    377 TTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_180787318_   1870 GTTAGCCACATGCAAAT---TTAAACTGGACCCCTACCTGTCACTACA-G 1915
                          v  ?           v--- v  ii             vv   i i -i
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_180787318_   1916 CAAAAATCAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACT 1965
                                i       i      i ?    i         i v i      
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_180787318_   1966 ATACAAACCCT-GGAAGACAACCTAGGCA-ATACCATCCTGGACATAGGA 2013
                            -    i  -i     v   v    ?i- v i v  v  -  v v  i
  L1M4_orf2#LINE/    526 ATA-AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGG 573

  chr2_180787318_   2014 ATGGGCAAAGATTTCATGAAAAAGATGCCAAAAGCA-AACCCCCAAAAAG 2062
                         v i     v i    v ii v v  ii         -  v vv     - 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA-G 622

  chr2_180787318_   2063 CAAAAATTGACAAATAGAATCTAATTAAACTTAGGAGCTTCTGCACAGCA 2112
                         v      v  i    v i ii v  i   v   ii i   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_180787318_   2113 GAAGAAACTATCAACAGAGTGAATAGACAACCTACAGAATGGGAGAAAAT 2162
                         i i  v        v i      v        i                 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_180787318_   2163 ATTTCTGCAAACTGTACACCCAAAAAAGGTCTACTATCCAGCATCTTTAA 2212
                             --     iii  i i ii v  i  v  vv       v  v v   
  L1M4_orf2#LINE/    723 ATTT--GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_180787318_   2213 GGAACT--TA-AATTTA-CAAGAAAAAAATAAACAACCCCATAGAAAAGT 2258
                         i     --  -  i i -i  v     i i   i     v  v?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_180787318_   2259 GTATAAAGGACATGAACAGACATTTTTCAAAAGAAGACATACATGTGGCC 2308
                          vii      iv    i        i  v        i     vi     
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_180787318_   2309 AAAAAGCATATGAAAAAAAGTTCAACATCACTGATCAT 2346
                           v     i       i v i         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (80 / 58)
Gap_init rate = 0.03 (16 / 582), avg. gap size = 1.31 (21 / 16)  

1160 26.00 5.44 11.00  chr2_180787318_180792711.rev     4005  4904 (490)    L1M4_orf2#LINE/L1       59   908 (0)  

  chr2_180787318_   4005 TCTCCAAATTACTCCACAGAGTCAAGGCAATTACAATTAAAATCGTAGAA 4054
                           i       iv  i     v    v     iv v  i      vi  vv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_180787318_   4055 GTATTTTTAG-AGAAATTGATAAGTAGAATCTCAAGTTTATATGGACATC 4103
                          iv     v -         i   iv  vi  v  i  i       v  v
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_180787318_   4104 CGAAAGATCAAGTATGACTAAGATAAACTTGAAAAAGAATGAA-ACAGCT 4152
                          i ii  i v  v  ii i  i i  v            -   - v  i 
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GAACAAAGTT 207

  chr2_180787318_   4153 AGAGACCTTATATTTTCAGATATCAAGACATATCTAAAGAAATTTTTCAA 4202
                         i   iv  i i i  i vi  v    i  v  -   -----------   
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTA-CTA-----------CAA 245

  chr2_180787318_   4203 ATTCTTAAAATTAAGGAATAGAGATATTCTTAAAAATTAAGTAATAGAGA 4252
                          --------------------- v  i------------      -----
  L1M4_orf2#LINE/    246 A---------------------GCTAC------------AGTAAT----- 257

  chr2_180787318_   4253 TAAATAGAATTTATCTAATTATTAACTAAGCCAATGTGAAGTTGGTGCAA 4302
                         --------------------------i   v  i    ivii   iii  
  L1M4_orf2#LINE/    258 --------------------------CAAGACAGTGTGGTACTGGCATAA 281

  chr2_180787318_   4303 AAATAGAGAAATAAA-CAAAAGTACAGACTAGATAGTCCAGAACCAGGAG 4351
                         ii     v v   i -   vi v i   v v  v         vi iivv
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_180787318_   4352 CATATAA--ACCATCACTCAATTTGTGAC--------TAAGATTGT---- 4387
                             i v-- ivi   v ii    vi   --------i    iii ----
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_180787318_   4388 -GAGGAAAGAATGGTCTTTTCAATTAGTGATGCTGGGACAATGTGACATC 4436
                         - i         i          iv i  i           ivv  i ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_180787318_   4437 TGCATTTTTTAAAAAATGAATCTTGATGACTAACTCACATCACATCCAAA 4486
                         ii   viv--   i      vi v  ivv   v      i  i  v    
  L1M4_orf2#LINE/    432 CACATGCA--AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_180787318_   4487 AAT--ATTACAACTGGATTCCAGATTTAAATGTGAAAAG--GAAACTATA 4532
                            -- i vv  v     iv?   ii       -  i  --i        
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATA 528

  chr2_180787318_   4533 AAACTCCTGGAATAAAGCACGAGAGAAATTCATCATTAACTTGGGATAGG 4582
                               i i   v   i  iii ? v  v  v  i v v      v    
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_180787318_   4583 CAAAAGTTTCTTAAACAGGACTCAAAGTGCTAACCATAAGTA-TAAAATG 4631
                            vi        i i v   v v  -----  v  i   i -i    vi
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAA-----AAGCACAAGCAACAAAAGA 623

  chr2_180787318_   4632 GAGAGTAGA---GTTGTATAT-ATTAAGCTGTATTAACTTCCAT---TCA 4674
                         i i i    ---i   v iv -  i  iv -  vv     iii ---   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTTTGTGCTTCA 672

  chr2_180787318_   4675 ACTTAATCCACCAA-AAAGAGAAAAGGACAAACCACAAAGTGTT-GAAGA 4722
                          vvv vv i i   -    v      -    v     i i  vv-   i 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAG-ACAACCCACAGAATGGGAGAAAA 721

  chr2_180787318_   4723 TAATTGTCATAT-ATATTTCTAACAAAGAATTTGTATCCAAAGTATGAAT 4771
                           v   -  v  -    v   i i  i i i         ------    
  L1M4_orf2#LINE/    722 TATTTG-CAAATCATATATCTGATAAGGGACTTGTATCCA------GAAT 764

  chr2_180787318_   4772 CTATACCAGTAACTATATCAATTCATTAAAATTAATACAAAGATAACTCA 4821
                         v    -- iv    v vv   i   v   v vv  v     --    i  
  L1M4_orf2#LINE/    765 ATATA--AAGAACTCTTACAACTCAATAATAAAAAGACAAA--TAACCCA 810

  chr2_180787318_   4822 --TGTAAAATAAACCAAAAA---------AC-TTTAT--AAAAGAGGTAT 4857
                         -- ?v     iii v  ii ---------  -   v --   ii  i   
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_180787318_   4858 TTAAATTGCCAATAA--ACATGAAAAAATATGTCAACGTTTGGTTTCAT 4904
                         vi    v        --         i  ii-     i iv????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGC-TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (129 / 101)
Gap_init rate = 0.04 (36 / 850), avg. gap size = 4.11 (148 / 36)  

 852 27.27 13.43 2.48  chr2_180787318_180792711.rev     4911  5394 (0)  C L1M4_orf2#LINE/L1   (299)   609    73  

C chr2_180787318_   5394 TACAGATTCACCACTATTTTTATCAAAGTACCAATTATATTCTTTACAGA 5345
                                   v i v  iii       i v   ii iiv  i   i    
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

C chr2_180787318_   5344 ACTAAAAAAAAAACT-ACTTTAAAATTCATGTAGAAACCAAAAAAAGAGC 5296
                          v vi v  i---  - iii          i i    i---iv  i ii 
  L1M4_orf2#LINE/    123 AATTGACAAG---CTGATCCTAAAATTCATATGGAAAT---GCAAGGGAC 166

C chr2_180787318_   5295 CCA-AATAGCTAAGGCAATCCT-AAGCAGCAGCAACAA------------ 5260
                            -      i  ii     i -  iv  v  -     ------------
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAG-AACAAAGTTGGAGGACT 215

C chr2_180787318_   5259 CA-AC-----AA---CAAAACAAAA-ACAAA----CAA-AA--AAAACA- 5228
                           -  -----  ---      vv v-     ----  i-  --  i   -
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

C chr2_180787318_   5227 ------ACT--CACAAAACTGGA-----GGCCTCATG--------TTG-- 5201
                         ------   --  i  iiv i  -----i viiv   --------   --
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

C chr2_180787318_   5200 ---CCTGATTTCAAACTATACTACCTACAACCATCTGATCCTTGACAAAA 5154
                         ---  v  vv v  v i    - ii  iiii  vi    ii i     ii
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATAC-ATTTATGGTCAATTGATTTTCGACAAGG 364

C chr2_180787318_   5153 TTGACAAATATAAACAATGGATTAAGGATTCCCCATTCAATAAATGGTGC 5104
                         v  v   ivvi vv      ivv   i  vvi iv     i         
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

C chr2_180787318_   5103 TGGGATAACTGGCTAGCCATATGCAGAAGATTGAAAGTGGACCCCTTCCG 5054
                              i      v  ?   i     i    v    iv         v  v
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

C chr2_180787318_   5053 TACACCATATACAATAACCAACTCAAAATGGATTAAAAACTTAAATGTAA 5004
                         i             v  ii              i ? i  i         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

C chr2_180787318_   5003 AAAATAAAACTATAAGGACCCTGGAAGATAATCTTAGG---AAATACCAT 4957
                         i iv           iivi i i     v  - v    ---    -- - 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGTAAAT--C-T 560

C chr2_180787318_   4956 TCTGGACATAGGACCCGGCAAAGATTTCATGAA---GACACCAAAAGCA 4911
                           vv   v v  iiiv     v i    v ii ---             
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

Transitions / transversions = 1.60 (80 / 50)
Gap_init rate = 0.05 (25 / 537), avg. gap size = 3.08 (77 / 25)  


2314 26.93 7.02 2.53  chr2_180897653_180899486.rev      510  1378 (456)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_180897653_    510 TGGAAAAACATTCCACGCTGAATGATAGGAAGAATCAATATCATTAGAGT 559
                               i i  i   i i v vv   v      v i     ii   iii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_180897653_    560 GGCCATATTGCCCTAAGCAATTTACAGATTCAATGCTATTCCTGTCAAAC 609
                            v   i v   v  vii  i           i  v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_180897653_    610 TGCTAA-TGTCATTCTTTGCAAAACCAGAAAACACT-ATTTTAAAATACA 657
                          v i i-  i -  i      i  viv  v  -i  -  ii      v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr2_180897653_    658 TATGGAATCAAAAAAGAGCCCAAATAACCACAACAATCCTAAGCAAAAAG 707
                                viiv  ii  v  vi    i   v       i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_180897653_    708 AACAAAACGGGAGGCATCACATTATCTAATTTCAAA--CTACAGTACAGG 755
                               iiv     vv     i vi i         --i   --    ii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAA 246

  chr2_180897653_    756 GCTACACTAATCAAAACAGCATTGTACTGATACAGAAACCGCCACATAGA 805
                               v       i    ii v      ii i iii iv v  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_180897653_    806 CCAATGGAA----AT------------AATA------------------- 820
                         i        ----  ------------    -------------------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_180897653_    821 ----GATCTTTAACAAAGTAGACAAAAACAAGCACTAGAGAAAGAACTCC 866
                         ----   i  ii    i vv v   i v  vv  v i i       ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_180897653_    867 CTATTTAATAAGTGATGCTGGGATAACTGGCTAGCCATATGCAAAAGATT 916
                           v  i  i  i  i        i      v  ?   i          v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_180897653_    917 GAAACTGGACCCTTTCCTTACACCATATACAAAAATCAACTCAAGATGGA 966
                            ii       i v   i                 i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_180897653_    967 TTAAATACTTAAGTGTAAAACCTAAAACTATAAAAATCCTGGAAGACAAC 1016
                          i ? v  i   i     i v              v  i i     v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_180897653_   1017 CTAGAGAATACCATTCCG-GACATAGGAACAGGCAAAGATTTCATGACCA 1065
                         v   - ?i  vvvi i  -   v v  ivi      v i    v iivi 
  L1M4_orf2#LINE/    547 ATAG-GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_180897653_   1066 AGATGCCAAAAGCAATTGCAACGAAAACAACACTTGACAAGTGGGACCTA 1115
                         v  ii         vvv     i   iv  v v v  i  i v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_180897653_   1116 ATTAAAATAAACAACTTCTGCACAGCAAAATAAACTATCAACAAAGT--A 1163
                           i     v  v     i  ii vv    iv v        v     -- 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_180897653_   1164 AACACAACCTACAGAAAGGGAGAAAATATTTGCAAACTATGCATCTGGTA 1213
                           v      i      v                   ii  ii     -- 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG--A 743

  chr2_180897653_   1214 TACGTATAATATCTGGATAGGCATAATATCCGGAATGTGTAAGGAACTTA 1263
                           v ----------   i----- vi     i    i i   i     iv
  L1M4_orf2#LINE/    744 TAAG----------GGAC-----TTGTATCCAGAATATATAAAGAACTCT 778

  chr2_180897653_   1264 AACAAGT------TGAGAAG-CAAA-AATTCCATTAAAAAGTAGGCAAAG 1305
                         v    v ------ i i   -    -  ii v   ?    i i       
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_180897653_   1306 GAAATGAACAAACACTTTGTAAATGAAGA---GC---TTTTCAGTA-GCA 1348
                           vv    i i   i  iviv  v     ---i --- vvi  i  -   
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_180897653_   1349 TACTAAGACGTGTCCAACACTAGAATGGGT 1378
                         i iv  i vi  ii     ii ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.95 (83 / 21)  


2545 25.62 4.47 2.91  chr2_180904774_180909251     3093  3986 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_180904774_   3093 TGAAAAAACATTTCATACTCATGGATAGGAAGAATCAAGATTGTTAA-AT 3141
                           i   i i  ii   ii        v      v i  v        -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_180904774_   3142 GGGCATACTGATGAAAACAGTTTACAGATTCAATACTATTCCTATCAAAC 3191
                           vv     vviv   viii i           ii v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_180904774_   3192 TATCAATGACATTCCTCACA-AAATTGGAAAAATACTATACTAAAATTAA 3240
                          vi  iivi v  ii ii  -      iv  iv i--  v        v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCA 148

  chr2_180904774_   3241 TATGGAACCAAAAAGAATA-AAAATAGCCAAAGAAATCCT-------AAG 3282
                                viiv  i i iv- i          iv    i -------   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_180904774_   3283 ATCAAAGCTGGAGACATTATATTACTTGACTTCAAACTATACTACAAAGT 3332
                          v     i     ivv i i i v iii i      ----   -------
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACT------- 237

  chr2_180904774_   3333 ATACTACAAAGCTACCATAACCAAAACAGTATGCTACTGGTACAAAAACA 3382
                         -              vi   i   i     i  v      i i  ii i 
  L1M4_orf2#LINE/    238 -TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_180904774_   3383 GACACACAGACCAATGGAACAGAA--AAGAGCCCAGAAATAAAGCTACAC 3430
                             i i   i        i    --i    i           v i i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_180904774_   3431 ACCTACAACCATGTGATATTTGACAAGGTCAACAAAAACAAGCAATGGAA 3480
                          ii  iiii  vv    v  i       viiv   i v  vv      ii
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_180904774_   3481 AAAGGAC--TCCATATTTAATAAATGGTGCTGGGATAATTGGATGGCCAT 3528
                             i i--  -- v  i  i              i  i     i?   i
  L1M4_orf2#LINE/    387 AAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_180904774_   3529 ATACAGAAGATTGAAACTGGACCCCT-TCTTACACTGTGTACAGAAATCA 3577
                           i  i    v    ii         -i  i    ii i    i    i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_180904774_   3578 ACTCAACATGTATTAAAGAATTAAAAGTAAAACTTACAAGTAGGCAAACT 3627
                               v   v  i ?   vi    v    i vi  v  v  vi-     
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACT 533

  chr2_180904774_   3628 CT-AGGATATAGCTTAGA---AAATACCATTCTGGAAAAGGCCCTGG--- 3670
                           -  i v v i v   i---    -- -   vv  -----  i   ---
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGA-----CCTTGGGTT 575

  chr2_180904774_   3671 ---CAAAGATGCCAT-GATGAAGACTCCAAAAGCAATTGTAACAAAAACA 3716
                         ---   v i vi v -   - v   v         vvv i       iv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_180904774_   3717 AGAATTGACAAATGGGATCTACTTAAGCTAAAGAGCTTTTGTACA-CAAA 3765
                          i   v  i    v   ii vv i  iv v  i i       i v-    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_180904774_   3766 AGAAACTATCAAAAGATTAAATAGACAACCTACAGAATGGGAGAAAATAT 3815
                         i  v        i i v i  v        i                   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_180904774_   3816 TTGCAAACTATTCATCCAACAA--------TATCCAGAATCTATATGGAG 3857
                                ii  vi   ii i  --------          v    vi  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_180904774_   3858 CTTAAACAAATTAATAAGCAAAAATCAA----CCCCATTAACAAGTGGGC 3903
                           ivv    v i     vv    iv   ----   v   ? v  i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_180904774_   3904 AAAGGACATGAACAGATAGTTTTC-AAAAAAGACATACACATGGCCAACA 3952
                               iv    i   i v  i  -   i    i     v        i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_180904774_   3953 AGCATATGAAAAAATTCTCAACATCACTAATCAT 3986
                             i       i  v          ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (140 / 86)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.75 (66 / 24)  


1552 25.67 5.67 3.67  chr2_180975548_180977138      500  1099 (492)    L1M4_orf2#LINE/L1      297   908 (0)  

  chr2_180975548_    500 TCAAGGGAAGAGACTAGAGAACCCAGAAATAAAGGTGCATAC--CTACAG 547
                             v    v   v v    ii           --iv     --i  ii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACATTTATGG 344

  chr2_180975548_    548 CCATCTGATTTTTTACAAAGTTGACAAAAATGAGCAATAGGGAAAGGTTT 597
                         i  vi       iv    i v  v   i viivv    i       iv v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_180975548_    598 CCCTATTCAATAAATAGTGCTGGGATTGCTGGCTGGCCATATGCTGAAGA 647
                         vi  v     i    i         ivi    v i?   i    vi    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_180975548_    648 ATGAAAACTGGACTTTT------CACTACATGCAAAAACTTACTCAAGAT 691
                              i-i     iii ------   i i  i      i v      i  
  L1M4_orf2#LINE/    445 ATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_180975548_    692 GGATGAAAGATTTAAATGTAAGACCTCAAACTATAAGAATCCTAGAAGGT 741
                             v ?   ii           v  v         i v  i      iv
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_180975548_    742 AACCTAG----AAAGC---ATGATTCTGGA-----CATCAGTCTCGGGAA 779
                            v   ----   v ---i   iii   i-----  vii  i  -----
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC----- 588

  chr2_180975548_    780 ATAAGTTATGAT--TAAGTCCTCAA--AACAATTCCAAAAAAATTTGACA 825
                         - v  v     i--i  ivv v   --     ---v i     v v  i 
  L1M4_orf2#LINE/    589 -TTAGATATGACACCAAAAGCACAAGCAACAA---AAGAAAAAATAGATA 634

  chr2_180975548_    826 AGTGAAACCTAATTAAATTGAAGAGCTTCTGCACTGCCAAAGAAATTGTC 875
                          i vii  i v  i   v v  i i   i  ii  v v  i  v i i  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_180975548_    876 AGTGGAGTAAACAGACAACATAGCGGATGGGAGAAAATATTTGCAAACTG 925
                          ivii   i  v       vi vv i                     iii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_180975548_    926 TCCATCCAGCATCCAGCAAAGGTCTAATATCCAGAATCTATAA-GAA-TC 973
                          --  -----   iiii  i  v  vi          v     -   -  
  L1M4_orf2#LINE/    735 T--AT-----ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_180975548_    974 TTAAACAATTGAACACGCCAAAAG-CAAATAACTTCATTAAAAAA-GGAC 1021
                            --   i v  i -iiv     -        iiv   ?     -  i 
  L1M4_orf2#LINE/    778 TTA--CAACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_180975548_   1022 AAAATACATGAACAGACATTTCTC---AGAAGACATACAAGTGGCCAA-A 1067
                            iv iv    i           ---      i      i       - 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_180975548_   1068 A--ATATGAAACAATGCTCCACATCACTAATTAT 1099
                          -- i      vi      v      ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (93 / 58)
Gap_init rate = 0.04 (22 / 612), avg. gap size = 2.55 (56 / 22)  


2664 24.51 1.55 7.76  chr2_181019889_181024169     2825  3791 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_181019889_   2825 GGAAAGATATTTCATGTTCATGGATGGAAATAATCAATATTGTTAATATG 2874
                                   ii             v i  v v i           v   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_181019889_   2875 CCCAAAATCCTCAAAT----CTACAAATTTAATACAATTTTTATGAAAA- 2919
                         v v v v   i     ----     i   i  ii    iii   v    -
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_181019889_   2920 ATCAATTACATTCTTCACAGAAATATAAAAGAAAAATCCTAAAATTAATG 2969
                         vi  ii i v  i  ii       - i v iivvi           v  i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATA 150

  chr2_181019889_   2970 TGAAGCCACAAAAGACTTAATATAGTCAAAGCTATCCTAAGCAAAAAAAA 3019
                           i ivii   ii   ii iv    i    i v   i i iv  i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_181019889_   3020 CAAAACTGGAGGAAACTCATTACCTGACTGCAAATTTTACCACAGAGCTA 3069
                             ii       vv v  i v  ii i v    vi    i   i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_181019889_   3070 TAGTAGCCAAAACAGCATGGTACTCGCATAAAAGCAGACATGTAGACCAA 3119
                         i    ii   i    ii       v      iiii      i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_181019889_   3120 TGGAACAGAATAGAGATCCCAGAAACAAATCCACACACCTACAGTTAACT 3169
                              i     v    vi       i   i   i   ii  ii  i  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_181019889_   3170 CATTTTTTATAAAGAACATGCCCTGAGGAAGAACACACCGTGAGGAAAAG 3219
                         v     i-------------------------------------  v   
  L1M4_orf2#LINE/    351 GATTTTC-------------------------------------GACAAG 363

  chr2_181019889_   3220 GGTATGAGGAAGAACATACCCCGAGGAAAAGGTATGCCAAAAACATACCC 3269
                            --------------------------------     i v   v vv
  L1M4_orf2#LINE/    364 GGT--------------------------------GCCAAGACCATTCAA 381

  chr2_181019889_   3270 TGAGGAAAAGACAGTCTCTTCAATAAATGGTACTGGGAAAACTGGATATT 3319
                           i     ii i     i     i       i      v         ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_181019889_   3320 GATATGCAGAAAAATGAAACTAGGCTCCTCTCTATTATCTTATACAAAAA 3369
                         v i     i  i      ii i i i   vi  vvi i v          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_181019889_   3370 AATCAAATGAAAATTGACTAAAGA--TAAATCTAAGACCTCAAACTATGA 3417
                         -- i  v v     v  ii ?   --     v     v  v       i 
  L1M4_orf2#LINE/    482 --TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_181019889_   3418 AAATACTATAAGAAAATACTGGGGAAAACCTCCAAGACATTGATCTGGAC 3467
                           v vi  v       i iv  ? v   i  i iv   v   ivi i i 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_181019889_   3468 CAAACTTTCTTGAGTAATAC-CCAACAAGCACAGGCAACCAAAGCAAAAA 3516
                         v viv      iii  vv  -    -       i     v    v     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAA-AAGCACAAGCAACAAAAGAAAAAA 628

  chr2_181019889_   3517 TGGACAAATGGGATCACATCAAG-TGAAAAAGCTTCTGCACAGCAAA--A 3563
                          i  i    v   iiv      i- v     -   i  ii vv    -- 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

  chr2_181019889_   3564 CA--ACCAACAAAGTGAAGAGACAATCCACAGAATGGAAGAAAATATGTG 3611
                           -- i   v        i      i           i         v  
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_181019889_   3612 CAAACTACCCATTTGACAAGGAATTAATAACCAGAATATATAAAGAGCTC 3661
                             ii ivi  i   i    i i vi  v                i   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_181019889_   3662 A-AAAACCCTGTAGGAATAAATTCTAATAATCTAATGAAAAAATGCGCAA 3710
                         v- v   i vi  iv  -   vv v     i i   v?       v    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_181019889_   3711 AAGACTTGCATAGACATTTCTCAAAAGAAGACAAACAAACGGCAAACAGG 3760
                          i  i   v             v        i v     i   v  i i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_181019889_   3761 CATACTAAAAGGTGCTCAACA-CAGTTGATCA 3791
                           i iv     i         -  ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (148 / 85)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 5.62 (90 / 16)  


2512 28.76 1.44 1.00  chr2_181043774_181048089.rev     2921  3824 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_181043774_   2921 TGGAAACACATTTCATAGTCATTAATGAGAAGAATCAATATTGGGAAAAA 2970
                               v i  ii   iv    vi  vi     v i       vv  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr2_181043774_   2971 TGATTATACTACCCAAAGCGACCTACAGATTCAGTGCAATTTCAATTAAA 3020
                           iiv     v      vi  i           ii     ii v  i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_181043774_   3021 CTGC-AATCATCATTTTC-CAGAGAATTAGAAAAAAAATCCGAAAATTCA 3068
                         v v - iiiii v    i-    -    iiv  ivvi    v        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCA 148

  chr2_181043774_   3069 TGCAGAA-CAAAAAGAGCCCA-AATAGCCAAAGCAATCCTTAGTAAAATA 3116
                          iii   -iiv  i ii    -          i     i v iv  i vi
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_181043774_   3117 AACAAATCTGGAGGCATCACGTTGCCTGACTTCAAATTATACAACAAGAT 3166
                               vi      vv    ii v  ii i      viv   v    iii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_181043774_   3167 TA---TTACCATAACAGCTTGGTAGTGGTATAAAAGTAGGCATG--GACC 3211
                           --- v i  vi    iv     v   i    iii   i   i--  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_181043774_   3212 AATGAAACAGAATAATAAAGAACCCAGAAATAAAGCCAAATACTTACAAC 3261
                             i  i     -- i -  ii           v   v i i   iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAAT--TGA-GAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_181043774_   3262 CAACTGATTTTCAACAAAGCATACAAAAAT-ATAAATTAGGGAAACGAGA 3310
                            i        i    i -i i v  i i-  vv v i      vi v 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_181043774_   3311 CCCTATTCAATAAATGGTGCTGGGGAAACTGGCTAGCTACATAGAAAAGA 3360
                         vi  v     i             iv      v  ? i    iv      
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_181043774_   3361 ATGATACTGGGTCCCTATCTCTCACCTTATACAAAAATCAACTTAGGATG 3410
                             vii   ii     i   v    v           i    i ii   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_181043774_   3411 GATTAAAGATTTAAACATAAGACCTGAAACCATAAAAATTCTACAAGATA 3460
                            i ?   ii    ii     v  i    i      v ii  v    v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_181043774_   3461 ACCTTGGAAAAACTCTTTCGGACATTGGCATAGGCAAAAAATGTATGACT 3510
                           v v  ?iv  v    ivv   v    vv       viiv viv iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_181043774_   3511 AAAACTTCAAAAGAAAATGCAACAAAACAAATAAATAAACAAGTGGGACC 3560
                          vi  vi      v v v         v   -     i i  i v    i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACT 643

  chr2_181043774_   3561 TACTTAAACT--AAAACTCTTCTGCACAGCAAAAGAAATAATCAACAAAG 3608
                          vv i   v --      i  v   vi--    i  v iv     v    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAG 691

  chr2_181043774_   3609 CAAACAGACAACCCACAGAATAAAACAAAATATTTACAAAGTATGCATCC 3658
                         ii  v                iii v         i    vi  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_181043774_   3659 AACGAAGGACTACAATACAAAATCTACAAGAAACTCAAATAAGTCAACAA 3708
                         i ii i     vvv  v  i   v  i  ii     vv i  v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_181043774_   3709 GATAAAAA-AGATAATCCCATTAAAAAGTGAGCAAAGGACATGAATAAGC 3757
                         v v   i - i    i  v   ?    i  i        iv      ii 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_181043774_   3758 ATTTGTCAAAAGAACGTATACAAACGACCAACAGGCAAATGAAAAAATGC 3807
                             v  v      vi        i i    i i   v       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_181043774_   3808 TCAACATCACTAATCAT 3824
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (155 / 101)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.38 (22 / 16)  


3558 18.56 6.95 3.53  chr2_181075928_181077833.rev      537  1414 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_181075928_    537 TGGAAAAACATTTCATTTTCATGAATCAGTAGA---------ATGAAGAT 577
                               i i  ii   v      i  ii v   ---------i v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_181075928_    578 GGCAATACTCCACAAATGTATCTACAGATTCAGCATAATCTTTCTCAAAA 627
                                    v     vv             i ii    ii v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_181075928_    628 TTCCATCTGGCTTATTTGTAAAAGTTGATAACCTGATTGCAACACTTATG 677
                          i   v   v   v    i i  i    i  v     ivi  v i i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_181075928_    678 TAGAACTTTAAGGGACA-AGGATAGCCAAAA--ATCTTGAAGTA-AAGAA 723
                          i   v vi       v-  i          --        iv -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_181075928_    724 TGAAGTTGGAGGACTCACACTGCCTAATTTAAAATCTTATTACAAAAGCT 773
                         ii                   v  i     v   v    i      -   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-GCT 249

  chr2_181075928_    774 ACAGTAATCAAGACAGCATGGTACTGGCATAAAGCTAGACACACAGATCA 823
                                         ii              i v      i i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_181075928_    824 ATGGAAGATAGTCGAGAATCCAGAAACAAACCCTTACATT-ATGATCAAC 872
                               v v i i    i        i      v      -   i    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_181075928_    873 TGATTTTTGAAAAAAGTG---------------GGGGAAAGAATCGACTT 907
                                i  v  ii   ---------------           v v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_181075928_    908 TTCAACAAATGGTGCTGGGACAACTAGATATCCACATGCACACACACACA 957
                                                  i    ?         v --------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-------- 441

  chr2_181075928_    958 CACACACACACACACACACACACACTGTAGACTTCTACCTCATAACACAT 1007
                         --------------- v - iiv v - i   ii        i v  i  
  L1M4_orf2#LINE/    442 ---------------AGA-ATGAAGT-TGGACCCCTACCTCACACCATAT 474

  chr2_181075928_   1008 ACAAAAATTCACTCAGAATGAATCAC---TCTAAATGTAAGAGTTCAAAT 1054
                                  v     i    i    ?---i             i v   i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_181075928_   1055 TACAAAACTCTCAGAGGAAAACATAAAAGTAAATTTTTGTGATCTCAAAT 1104
                           i        i   i         ii?      i  i    i  iiii 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_181075928_   1105 TAGGCA-TTTTTTCTTA--TATAATTCAAAAATCTCAGGCAACTAAAAAA 1151
                               - vv       --   i iv v    v v  i     v   i  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_181075928_   1152 G-----GACAAATTACTCTCCATCGAAGGTAAAAATTTGTGTGCTTCAAA 1196
                         i-----  i     ivv  i    i  iv      i  v           
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_181075928_   1197 TGACTC-ATTAGGAAAGAGAGGAGACAACCCACATAATGGAAAACAAAC- 1244
                         v   v -  i i     v  ii            v     i i -   i-
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA-AAATA 723

  chr2_181075928_   1245 --TACAAATCATATGTCTGATAAGGCACTTGTATCCACAA-ATGTAAATA 1291
                         -- i          i          v           v  -  i    v 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_181075928_   1292 CCTCTTTAAAACAACT--ATTTTAGAAA---------CCCAATAAAAAGG 1330
                         v     ----      --  vv  i   ---------      v?   ii
  L1M4_orf2#LINE/    774 ACTCTT----ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_181075928_   1331 TGGGCAAATGATTTGAATAGGCATTTCTCCAAAGA---TATATAAACAGC 1377
                                 v           i              ---    i   ii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_181075928_   1378 CAATGA--ACATGTAAAAATGTTCAACATCATTATTCAT 1414
                             i --     v   i   i         ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (101 / 58)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 4.00 (92 / 23)  


 229 21.74 0.00 0.00  chr2_181158028_181160074      600   645 (1402)    L1M4_orf2#LINE/L1        2    47 (861)  

  chr2_181158028_    600 GAAAAAAAATCCTGTGTTCTTGGACTGAAAGCCTTAATATTATTAA 645
                          i   i v    ii     v    i  i   v         i    
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.00 (0 / 0)  

3666 20.13 0.99 3.74  chr2_181158028_181160074      647  1555 (492)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr2_181158028_    647 ATTTAAAGTCTTAATATTATTAAAATGGCCATACTACACAGAATT-ATCT 695
                            vi   v         i    i     v     v v  -    -    
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA-AATTGATCT 73

  chr2_181158028_    696 CCAGATTCAATGCAATCACTATTTAAATACCAATGGCATTATTTACAGAA 745
                         v         i      v    iv    v   iiv  v  v   i     
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAA 123

  chr2_181158028_    746 AGAGAAAAATCTATCCTAAAATTCATTTAGAGCCATTAAGGACCTTAAAT 795
                          vv  v  iiiv              v i  iviiiv i     ivi   
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chr2_181158028_    796 AGTCAACACAATCTCAAGAAAGAA---CAAAGCTGTAGGCAC-CACATGT 841
                           i   v       ii i      ---     i  v   -  -    iv 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-ACTCACACTT 222

  chr2_181158028_    842 TCTGATTTCAAAATATATTACAAAGCTACAGTAATTTAAAAAGTATGGTA 891
                         i ii         iv  i                 iv i v   i     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_181158028_    892 CTAGCATAAAGACAGACATGTAAAACAATGGAATAAAATAGAAAGCCCAG 941
                           i      i  i      i  i v          i   v  i  i    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_181158028_    942 AAATAAATCCATGCATATACAGGCAATTGATCAATTGATCTTTGACAAGG 991
                                i    i   v  --------  i         i  i       
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTA--------TGGTCAATTGATTTTCGACAAGG 364

  chr2_181158028_    992 GTTCCAAGAACACATGATGGGAAAAGGCTAGTCTCTTCAAAAAAATGCTG 1041
                           v      v  ivii     i    iv      i     v   -  v  
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA-TGGTG 413

  chr2_181158028_   1042 TTGGGAAAACTGGATATCCACATGAAGAAAAAATGAAAATATACTTTAAT 1091
                         i     v         ?       v -   i      iv iv  iiiv i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCA-AAAGAATGAAGTTGGACCCCTAC 462

  chr2_181158028_   1092 CTCACACATTA-ATAAAACTCCACTCACAATAGATTAAAGACTCAAATGT 1140
                                vv  - i    v iv     v   i   i ?    ii      
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_181158028_   1141 AAGGCCTGAAACTATAAAACTCCCAGAAGAAAACACAGGGGAAAAGCCTC 1190
                            iv  i              ii           i   ? v   v i  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_181158028_   1191 ATGACATTAGCCTTGGAAATGATTAATTGGATATGACATTAAAAGCACAG 1240
                         i    v  i vi v  v    i  vv  i         ii         i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_181158028_   1241 GCAACAAAAGCAAAATTAGACAAGGGGAACTACATCAAACTCAAAAGCAT 1290
                                   v    v    i  ivv i   v       v i    i v 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_181158028_   1291 CTGTACAGCAAAGGAAACAATCAATAAAGCGAAAAGAGAACATATAGAAT 1340
                         i   i vv       v  v     v    i       v   vi i     
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_181158028_   1341 GGGAGAAAATATT--CAAACCATATATCTTATAAGGAATTAATATCCAAA 1388
                                      --    i         v      i i vi      i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_181158028_   1389 ATATACAAGGAACTCCTACAACCCAGTAGCAAAAAAAAAAAAACCAAATA 1438
                              i  i      i      i  ----------------------   
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCA----------------------ATA 790

  chr2_181158028_   1439 ATAAAAAAATAA-TAACCCATTTAAAAAATGGGCTAAGGATTTGAATAGA 1487
                                i i  -       v  ?          v               
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_181158028_   1488 CATTTCTCCAAAGGAGACATACAAATGGCCAATAGGCATATGAAAAAATG 1537
                                      i   i                i   i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_181158028_   1538 CTCAGCATCACTAATAAT 1555
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (107 / 72)
Gap_init rate = 0.01 (12 / 884), avg. gap size = 3.58 (43 / 12)  


3174 25.00 1.44 1.00  chr2_181178596_181182753.rev     2763  3666 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_181178596_   2763 TGGAAATACATTCTATGCTCATGAACTGGAAGAATCAATATTGTTTAAAT 2812
                               v i  i i   i     i i       v i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_181178596_   2813 AACCATACTGCCCAAAACTATCTACAGGTTTAATACAATCCTTATGATAT 2862
                         ii v     v      viv        i  i  ii      i   v v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_181178596_   2863 TACCAACATCATTTTTCACAGAATTAGAAAAAACAATTCTAAAATTTATA 2912
                          v   i vv v     ii     v v  v  ivii  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_181178596_   2913 TGGAACTAAAAGAAGAAGTGAAATAGCCAAAGCAATCT-AAGCAAGAAGA 2961
                              v iv   i-  vviii          i      -i iv       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_181178596_   2962 ACAAAGTTGGAGGCATCACATTCCGCAACTTCAAATTATACTACTAGGTT 3011
                                      vv     i i v   i      viv      v i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_181178596_   3012 AGAGTAACCAAAACAGTATGGTACTGGTATAGAAATAGGCA-ATAGATTA 3060
                          v     i   i     i         i   iii    i  -      i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_181178596_   3061 ATGGAACAGAATAGAGAA-CCAGAAATAAAGTCATGTACCTACAACCAAA 3109
                               i     v    i-           vi   ii ii  iiii   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_181178596_   3110 TGATGTTTGACAAAGTCAACAAAA--ATACAAACTGGAGAAAAGATACCC 3157
                             v  i     i viiv   i --  v   --   i    ii   vi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTC 397

  chr2_181178596_   3158 TATTCAATAAACGGTGCTGGGAAAATTAG----CCATATGCAGAAGAATG 3203
                          v     i   i          v  i i ----   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_181178596_   3204 AAACAACTGGACCCATACCTCTCACTATACACAAAAATTAACTCAAAATG 3253
                           ii---       v      v   i   i                    
  L1M4_orf2#LINE/    448 AAGT---TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_181178596_   3254 GATTAAAGATCTAAACATAACACCTGAAACTATAAAATTCCTGGAAGAAA 3303
                            i ?   i     ii   v v  i           i  i i       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_181178596_   3304 ACCTAGGGAAAACCCTTCTGGATATTGGCCTGGGCAAAGAATTTATGACC 3353
                           v    ?iv  vi    vv  iv    vi i     v iv  iv iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_181178596_   3354 AAGTCTTCAACAGCAAATGTAACAAAAACAAAAATAAGCAAATGGGACTT 3403
                          v v vi   v    v v i       iv       iii    v      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_181178596_   3404 AATTAAACCAAAAAGCTTCTGTGCAGCAAAGGACACTAACGACATAGTAA 3453
                         v  i   viv    i   i     vv            v i v v   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_181178596_   3454 ACAGGAAACCTACAAAACGGGAAAAAATATTTGCAAACTATACATCAGAT 3503
                          v  iv    i   i  i    i              ii   i   v   
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_181178596_   3504 AAATGACCAATATCCAGAATCTATAAGAAACTCAAGCAGCTCAACAAGAA 3553
                           iv   ivi          v     ii     vvi  i     i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_181178596_   3554 AAAAA-AAA-AACTTATTTAAAAAAAATGCCAAAGGACATGAACAGACAT 3601
                            i -   -   ii v  ?     viv  -      iv    i      
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGC-AAAGGATTTGAATAGACAT 843

  chr2_181178596_   3602 TTTTCAAAAGAAGACATGCAAGTATCCAACAA--ACATGAATAAAAATGG 3649
                           i  v        i  i   i iv    i  --       --  i   v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA--AAGATGC 891

  chr2_181178596_   3650 TCAACATCACTAATAAT 3666
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (136 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


3057 26.93 0.88 0.66  chr2_181217200_181223461.rev     4865  5770 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_181217200_   4865 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATAAATACGGTGAAAAT 4914
                              ii i  i     i       iv      v v    iv  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_181217200_   4915 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGGCATCCCCATCAAGC 4964
                            v     v      v i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_181217200_   4965 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5012
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_181217200_   5013 TATGGAATCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5062
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_181217200_   5063 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5112
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_181217200_   5113 TACAGTAACCAAAACACCATGGTACTGGTACCAAAACAGAGATATAGACC 5162
                                 i   i   vii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_181217200_   5163 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 5210
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_181217200_   5211 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5260
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_181217200_   5261 CTATTTAATAAATGGTGCTGGGAAAACTAGCTAGCCATACGTAGAAAGCT 5310
                           v  i  i              v    i v  ?   i i i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_181217200_   5311 AAAACTGGATCCCTTCCT-GCACTTTCTACAAAAATTAATTGAAGATGGA 5359
                         i  ii    i    v   -i   iv v            i v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_181217200_   5360 TTAAAGACTTAAATGTTCGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5409
                          i ?    i       vv  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_181217200_   5410 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5458
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_181217200_   5459 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 5508
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_181217200_   5509 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGA-ACTACCATCAGAGTGAA 5557
                           i   v v  i i   i  ii vv    i  -    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_181217200_   5558 CAGGCAACCTGCAAAATTGGAGAAAATTTTTACAATCTACCCATCTGAAA 5607
                         v  i     ii  i   v         v   i   vii ivi      v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_181217200_   5608 AAGGGCTAATATCCACAATCTA-AAAGAACTCAAACAAATTTACAAGAAA 5656
                          i  i  vi      v   v  -         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_181217200_   5657 AACATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACATT 5706
                           v -    i     v  i?    i     i      v    i       
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_181217200_   5707 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5756
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_181217200_   5757 TCATCACTGGCCAT 5770
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3148 27.13 0.44 1.09  chr2_181276104_181282450.rev     4942  5855 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_181276104_   4942 TGGCAGAACATTCCATGCTCATGGATAAGAAGAATCAATATCATGAAAAT 4991
                            v ii i  i     i        vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_181276104_   4992 GGCCATACTGCCCGAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 5041
                            v     v   i iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_181276104_   5042 TACCAATGACTTTCTTCACAGAACTGGAAAAATAAAAACT-ACTTTAAAG 5090
                          v   iivi i  i  ii     v v  v  i------  - iii    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG------CTGATCCTAAAA 144

  chr2_181276104_   5091 TTCATATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCA 5140
                                    viiv  ii  v  v v  v     i      i i ivv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_181276104_   5141 AAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACG 5190
                         i          i      vv    i  v  ii i      viv      i
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_181276104_   5191 AGGCTACAGTAACCAAAACAGCATGGTACTAGTATCAAAACAGAGATATA 5240
                          i          i   i    ii       i i  v ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_181276104_   5241 GACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTAC 5288
                           i        i    i--    i  --        vv   i    i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chr2_181276104_   5289 AACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGA 5338
                         iii  vi    i  i     ivv  v   i v  vvv           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_181276104_   5339 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 5388
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_181276104_   5389 AGCTGAAAATGGATCCCTTCCTTACAGCTTATACAAAAATTAATTCAAGA 5438
                         iiv    iv    i    v   i   v v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_181276104_   5439 TGGATTAAAGACTTAAACGTTAGACTTAAAATCATAAAAACCCTAGAAGA 5488
                              i ?    i    i  v   vi     ii      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_181276104_   5489 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAACGACTTCATG 5537
                             v    ?i- v i -   iv   v v  vv i     i ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_181276104_   5538 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5587
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_181276104_   5588 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5637
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_181276104_   5638 TGAACAGGCAACCTACACAATGGGAGAAAATTTTTGCAACCTACTCATCT 5687
                             v  i     i   v             v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_181276104_   5688 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 5737
                           i  i  i  vi          v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_181276104_   5738 GAAAAACATCAAACAACCCCATCAAAAAGTAGGCAAAGGATATGAACAGA 5787
                         v     v -    i     v  i?    i i          v    i   
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_181276104_   5788 CACTTCTTAAAAAAAGACATTTATGCAGCCAAAAGACACATGAAAAAATG 5837
                           i    iv   i    i  vi viii     v ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_181276104_   5838 TTCATCATCACTGGCCAT 5855
                         i   v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  


 593 26.37 1.10 1.65  chr2_181354404_181357316     1047  1228 (1685)    L1M4_orf2#LINE/L1        3   183 (725)  

  chr2_181354404_   1047 GAAAAATATTCCAGGCACATGGGTTGAAAAAATTAATATTGTTAAAATGG 1096
                             i    i   v iv     i   i  i v             i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_181354404_   1097 CCATGGTGCCCAAAGCAATTTATAGAACCAATGTTATTCTTATCAAAATA 1146
                          v  iv v      vii  i  i   vi   i iv  i i         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_181354404_   1147 CTAACATCATTTTTCACA-AAATTAGTACAAAACT-ATTCTAAAATTCAT 1194
                          i i vv v     ii  -     i--    i-  -  i           
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAG-CTGATCCTAAAATTCAT 149

  chr2_181354404_   1195 AGAGAACCAAAAAAGAGCCCAAATAGCCAAAACA 1228
                          vi   viiv  ii  v  vi             
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

Transitions / transversions = 1.67 (30 / 18)
Gap_init rate = 0.02 (4 / 181), avg. gap size = 1.25 (5 / 4)  

1728 21.76 0.90 17.02  chr2_181354404_181357316     1535  2421 (492)    L1M4_orf2#LINE/L1      165   908 (0)  

  chr2_181354404_   1535 ACCCAGC----CCAAAGCAATCTTAAGCAATAAGAACAAAGCCAGAGGAA 1580
                               v----     i       i iv  v          iii     v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_181354404_   1581 TCACCTTATCCAATTTCAAACTATACTGGAATGCTACAGTAACCATAACA 1630
                             vi vi           viv    iv  v          i  vi   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_181354404_   1631 GTATGGTACTGGTACAAAAACAAACATATAGACCAATGGAACAGAATAGA 1680
                           i         i i  ii i i         i        i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_181354404_   1681 GAATCCAGAAGAAATGACACACAGCTACAACCATATGATCTTTGACAAAG 1730
                           i       iv  vvv  i   vi  iiii  vv    i  i     i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_181354404_   1731 TCAACAAAAATAAGCAATGGGAAAAGGACTCCCTATTGAATAAATGATGC 1780
                         viiv   i vi vv       i    i ivvi  v  v  i     i   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_181354404_   1781 TGGGATAGCTGGTGAGCCACATGCAGAAGAATGAAACTGGACTTCTACCG 1830
                              i i    vv ?         i         ii     ii     v
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_181354404_   1831 TTCACCATACACAAAAATTAACCCAAATTAGATTAAAGATTTAAATGTAA 1880
                         iv       i            i    v i   i ?   ii         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_181354404_   1881 GTCCTCAAACTGTAAAAATTCTAAGGGGCCAGGTGTGGTGGCTCACGCCT 1930
                          vv  v     i     ---------------------------------
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAA--------------------------------- 531

  chr2_181354404_   1931 GTAATCCCAGCACTTTGAGAGGCCGAGGCCAGGCTCCACTATAGCCTTGG 1980
                         ------------  i ----------------------------------
  L1M4_orf2#LINE/    532 ------------CTCT---------------------------------- 535

  chr2_181354404_   1981 TGACAGAGCAAGACTGTGTCTTGGAAAAATATATATATATATATTCTAGA 2030
                         ----------------------------------------------    
  L1M4_orf2#LINE/    536 ----------------------------------------------TAGA 539

  chr2_181354404_   2031 AGGAAACATAGGAATCTTTTTTGACATTGACCCTTTTTGACATTGACCCT 2080
                           i         ?i -------- v  -----   iv    v   iviiv
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGT--------AAAT-----CTTCGTGACCTTGGGTTA 576

  chr2_181354404_   2081 GGCAAAGAATT--TAAGGCTAATCCTCAAAAGCA-AAGCAAAAAAAAAAA 2127
                              v iv  --  iivv i iv -        -      v    i   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACAC-CAAAAGCACAAGCAACAAAAGAAA 625

  chr2_181354404_   2128 ACAAAAAACAAAATATGACTTGA-CAAGTGGAACCTAATTGAAGCGTTTC 2176
                          -  v i i   v i-     v -   ---------    i  i-ii  i
  L1M4_orf2#LINE/    626 A-AATAGATAAATTG-GACTTCATCAA---------AATTAAAA-ACTTT 663

  chr2_181354404_   2177 TGTACAGCAACAGAAACTATCAACAGAGTAAACAGACAACCTACAGAATG 2226
                            i vv   vi  v        v i   i  v        i        
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_181354404_   2227 GGAAAAAGTATTCTCAAACTATGCATCTCACAAAAGCCTAATATCCAGAA 2276
                            i   i    iv    ii  ii    v i  ii v  vi         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_181354404_   2277 TCTATAAGAGACTTAAACACATCAATGAACAAAAAACAAACAACTCAATT 2326
                          v     iii   ivv   vv     i vv    i     i   i     
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_181354404_   2327 AAAAGGCAGGTGAAGGATATGAATAGACACTTCTCAAAATAAGATATACA 2376
                         ?   iiii  ii      v          i     v   v          
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_181354404_   2377 AGCAGCCCACAAGAATATGAAAAAATTCTCATCATCACTAATCAT 2421
                          iii   v i   v i       i  v    v     ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (115 / 74)
Gap_init rate = 0.02 (13 / 744), avg. gap size = 12.23 (159 / 13)  


1997 26.91 3.45 3.17  chr2_181361186_181362858.rev      487  1181 (492)    L1M4_orf2#LINE/L1      212   908 (0)  

  chr2_181361186_    487 GACACACACTT----ATTT--ACACTT----TAAGTTTACAGTAACCAAA 526
                            v       ----    -- v    ----i  ivi        i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_181361186_    527 ATGGCATGTTACTGGTTCAAAAAGAGGCACATAGACCGATGGAACAGAAT 576
                          ii ii  v      ivi  ii v  i  i     i i      i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_181361186_    577 AAAGAACCTAGAAATAAAGCTGCACACCTACAGCCATATGATCTTCTAAA 626
                         vi   ii i         v iii   ii  ii i  vv    i   v v 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_181361186_    627 AAGTCAACAAAAACAAGCAATGTGAGAAGGACTGTCTATCTCATAAATGG 676
                          i viiv   i v  vv     v ii   i iv    v iiv i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_181361186_    677 TGCTGGAATAGCTGGCGATCCATATGCAGAAGAATGACACTGGACTCCTA 726
                               i i i    vv ?   i     i        vii     i    
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_181361186_    727 CCTTTTACCATATACAAAAATTAACTCAAGATGGATTAAAGATTTAAATG 776
                            ivi                       i      i ?   ii      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_181361186_    777 TAAATCCTCAAACTATAAAATTCCTAGAA---AACCTAGG---AAACACC 820
                            ivv  v           i  i     ---   v    ---   ----
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA---- 557

  chr2_181361186_    821 CTTTTTCATATGGGCCTTGG--CAAGGAATG-----TAAGGCTAAGTCCT 863
                         -- i   i --- i      --i i v    ----- v  i-  v v vi
  L1M4_orf2#LINE/    558 --TCTTCGT---GACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACAC 601

  chr2_181361186_    864 CAAAATCAACTGCAATGAAAACAAAAGTTGACAAGTGGGACCCAATTAGA 913
                              v  vvv    ii   iv    i v  i  i v    iiv  i i 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_181361186_    914 -TGAAAGAGATTCTATACAGCAATGAAAACTATCAACAGAGTAAACAGAC 962
                         - v   i v-  i i i vv   v i v        v i   i  v    
  L1M4_orf2#LINE/    652 ATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_181361186_    963 AACCTGTAGAACGGAAGAAAATATTCTTAAACTATGCATCCAACAAAGGT 1012
                             iii    i  i          ivi   ii  ii   ii i  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_181361186_   1013 CTAATATCCAGAATCTAAAAGAAACTGAAACAAATCAATAAGCAAAAAAC 1062
                           vi          v  v  ii    vvv    v       vv    i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_181361186_   1063 AAATAACTCCATTAGAAGGTGGGCTAAGGACATGAACAGACACTTCTCAA 1112
                                i v   ?i  ii     v     iv    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_181361186_   1113 AAAAAAAAAAAAAGAAGACATAGAAGCAGCCAACAAACACATGAAAAACT 1162
                           -----------     i   v  iii     i  i          iv 
  L1M4_orf2#LINE/    851 AA-----------GAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_181361186_   1163 GCTCCACATCACTAATCGT 1181
                             v      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (116 / 68)
Gap_init rate = 0.02 (13 / 697), avg. gap size = 3.54 (46 / 13)  


1935 20.61 3.48 10.03  chr2_181388378_181391726.rev      504  1221 (2128)    L1M4_orf2#LINE/L1      238   908 (0)  

  chr2_181388378_    504 TATTATAAAACTACAGGTATCATAATAG-ACAGTACTGGCATAAAAACAG 552
                           i  i   i      vv    vi i  -iii            ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_181388378_    553 ACATATCTGCCAACAGTTTAGA-----GAGCCCAGAAATAAACCCACACA 597
                               vvii   ii vv    -----   i               i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_181388378_    598 TATACAGTCAATTGATTTTATGTTTTCTTTTCTTATTTTACATGTTATGT 647
                          -------------------------------------------     -
  L1M4_orf2#LINE/    338 T-------------------------------------------TTATG- 343

  chr2_181388378_    648 GACATGGCAAAAGTCAATTAATTTTCTACAAAGGTGCCAATAGCATACAA 697
                         ------------       i      v    i        v v   v   
  L1M4_orf2#LINE/    344 ------------GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_181388378_    698 TGGGGAAAGGACCATCTTTTCAATAAATAGTATTGGGA-AACTGGATGTC 746
                                  i ivi         i    i  ii     -        i? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_181388378_    747 TACATGAAGAAGAATCAAAATGGTCCCCTGTGTCAC-CCATTACACTAGA 795
                         i     v i      v  iv   v     iiv    -    - i  v i 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT-ATACAAAA 480

  chr2_181388378_    796 ATCAAGTCAATATGGATTAAAGACTTAATTGTAAAAGCTGTAACTATAAA 845
                           i  v    v      i ?    i   v     i    iv         
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_181388378_    846 ACTACTAGAAGAAAACAGAAGA--AAAGCTCCATGACATTTGTCTTAG-- 891
                            vi            v i ?--   v  i i    ------   i --
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC------CTTGGGT 574

  chr2_181388378_    892 TAGGTA----TTTCTTGGATATGACCCCAAACACGTAAGCAATGACAGCA 937
                             i ----      i        v     vi ii      ii v  v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_181388378_    938 AAATTAGACAAATGGGATTGCATCAAACTGGAAACCTTTTGCACAGCAAG 987
                            v    i    v   i v       v vi   v      ii vv   i
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_181388378_    988 GGAAACAATTAATAAAG-----AGAGAATCCACAGATTGGGAGAAAAATA 1032
                            v  v  i  v    -----   v  i       v          -  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TA 723

  chr2_181388378_   1033 TTGACAAATCATACATTGGATAAAGGGCTAATATCCAAAAATATGCAAGA 1082
                           vi         i  iv     i  i  vi      i  -   ii  ii
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA-TATATAAAG 772

  chr2_181388378_   1083 AACTCA-ACATACTCAATAAGAAGAAAACAAATCACCTGATTTTAAAAAT 1131
                              v-   -         v  i  i      v   ii   ?-      
  L1M4_orf2#LINE/    773 AACTCTTACA-ACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAAT 820

  chr2_181388378_   1132 AC-TGAAGGATGTGAATAGACATTTCTCAAAAAAACAAAAACAAAATAA- 1179
                         iv-ii      v                v   i  v v v     - ii-
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGC 869

  chr2_181388378_   1180 -AACAAACAAACAAAAATACAAATGGCCAAAATGATGGCAACA 1221
                         -  i  i  v ii    ----i   vi   v  v ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAA----GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (86 / 58)
Gap_init rate = 0.03 (21 / 671), avg. gap size = 4.62 (97 / 21)  


3240 27.31 0.44 0.44  chr2_181524145_181526685.rev     1142  2049 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_181524145_   1142 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1191
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_181524145_   1192 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1241
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_181524145_   1242 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1289
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_181524145_   1290 TATGGAACCAAAAAAGAGCCCCCATCACCAAGTCAATCCTAAGCCAAAAG 1339
                                viiv  ii  v  vvv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_181524145_   1340 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1389
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_181524145_   1390 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1439
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_181524145_   1440 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 1487
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_181524145_   1488 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1537
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_181524145_   1538 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1587
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_181524145_   1588 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1637
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_181524145_   1638 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1687
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_181524145_   1688 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 1737
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_181524145_   1738 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1787
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_181524145_   1788 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1837
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_181524145_   1838 AGGCAACCTACAACGTGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 1887
                           i     i   ivi           v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_181524145_   1888 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1937
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_181524145_   1938 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 1987
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_181524145_   1988 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 2037
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_181524145_   2038 ATCACTGGCCAT 2049
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3231 25.61 2.12 1.45  chr2_181564463_181569045     3196  4093 (490)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_181564463_   3196 AAAACATC--GTGTTCATGAATTAGAAGAATCACTATTGTTAAAATGTCC 3243
                           i i   --i        i   i     v i v         i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_181564463_   3244 ATACTACTAAAATCAATCTACAGATTCCATGCAATCCCTGTCAAAATAAT 3293
                              v iv    ii            v i         i       vvi
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_181564463_   3294 AATGACATTCTTCACAGAAGTAGAAAAAACAATTCTAAAATTTATATGGA 3343
                          iivi v  i  ii     i v  v  ivii  i        i       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_181564463_   3344 AACACAAAAGACCCAGAATAGCTGTAGCTATCCTGAGCAAAAGGAACAAA 3393
                           ii   ii             iiv i v   i   iv  i i       
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_181564463_   3394 ACTGAAAGAATCACATTACCTGACTTCAAATTATACTACAAAACTATAGT 3443
                         ii  i i  v     i v  ii i      viv         i   i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_181564463_   3444 AACCAAAACATCATGGCATTGTTGTAAAAACAGACACATAGATGAATGAA 3493
                           i   i   vii   i i  vii   ii i     i      v    i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_181564463_   3494 ACAGAATAGAGA-CCTAGAAATAAATCCATACATGTGCAGTGAACTCATT 3542
                          i     v    -i i         i        v iii  v  i v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_181564463_   3543 TTTGACAAAGATGCCAAGAACATAGGTATTGGAAAGGGACGGTACAGTCT 3592
                           i     i i        v   --vi v   ii ii  ---- i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGA----ATAGTCT 398

  chr2_181564463_   3593 T--CAATACATGGTGCTGGGAAAACTACATGTCTATATTCAGAAGAATGA 3640
                          --   i v            v    iv  i? i i  v  i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_181564463_   3641 AACTAAACTCCTATTTCTTTCCATATACAAAAATCAAATCAAAGTGGATT 3690
                          ii ii  i    ii  viv              i  v     i     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_181564463_   3691 AAAGACTTAAACCTAAGACCTCAAACTGTAAAACTACTATAAGGAAACTT 3740
                          ?    i    iv     v  v     i       vi  v   i    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_181564463_   3741 TAAGGAAACTCTCCAGGACATCGGATTGGGGAATGATTTCTTGAGTAGTA 3790
                         vii? v  v   i iv   v i  i  i  v    i      iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_181564463_   3791 CCTCACAAGCACAGCCAACCAAAGCAAAAATGGACAAATGGGATCACATC 3840
                          vi  v       iv    v    v      i  i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_181564463_   3841 AAG-TTAAAAAGTTT----CTTCTCAGTAAAAGAAACAATCAACAAAGTG 3885
                           i-       v   ----    -----   i  v  v     v      
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTC-----AAAGGACACTATCAAGAAAGTG 693

  chr2_181564463_   3886 A-----CATCCCACAGAGTGGGAGAAAATACTTGCAAACTACCTATCTGA 3930
                          -----  v        i            i       ii iv       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_181564463_   3931 CAAGGGATTAAAAACCAGAATATACAAGGAGCTATCAAACAATTCTATAG 3980
                         i      i viv v          i  i  i  v i --   i  v   i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAA 791

  chr2_181564463_   3981 GAAAAACTCTAATAATCTGATTTTAAAATGAGCAAAATATCTGAATAGAC 4030
                         v     vv v     i ii   ?v      i     iv  i         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_181564463_   4031 AATTTTCAAAAGAAGA----CAAATGGCAAACAGGTATATGAAAAGGTTC 4076
                          v  i  v        ----        v  i i i i        i v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_181564463_   4077 TCAACATTGTTGATCAT 4093
                                ii????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (146 / 80)
Gap_init rate = 0.01 (11 / 904), avg. gap size = 2.91 (32 / 11)  


2851 26.01 3.38 1.13  chr2_181574229_181578919     3312  4199 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_181574229_   3312 TGGAATTACATCCCATGCTCATAAATC--AACAATGTATACAGTTAAAGT 3359
                              vv i        i    ii  i--  v v vv   iv     ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_181574229_   3360 GACCATACTGCACAAAGCAATCTACAGATTCAATGCAATCCCTATCAAA- 3408
                          i v     v v    vii              i               -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_181574229_   3409 TACCAATGTTG--TTTTTCACAAAAATAGAAAAAATAATAGTAAAATTTG 3456
                          v   -- i  --     ii  i    v  v  iv i  vv       ii
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_181574229_   3457 TATGGAACCAAAAAGTCTCCTGAATAGCTAAAGCAATTCTGAGTGAAAAG 3506
                                viiv  i vvi  v       i   i    ii   ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_181574229_   3507 AGCAAAGCTGGAGGCATCACACTATCTGACATCAAAGTATATTACAAGCC 3556
                          i     i      vv       vi ii iv     iiv  i     iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_181574229_   3557 TATAGTA-TCCAAACAGGATGATACTGATGTGAAAACAGACACATACACC 3605
                           i    -  v i    vi  i     iii i ii i     i   v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_181574229_   3606 AATGGAACAGAAATGAGGATCCAGAAATGAATCCATGTATTTACATCCAA 3655
                                i    v    ii         i  i    ii     iivi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_181574229_   3656 CTGATTTTCAACAAAGGTGCCAAAAACACACACTAGGAAAAGGAC--TCT 3703
                         i        i    i        i v  iv  v i  i    i i--   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_181574229_   3704 CTTAAATAAATGGTGCTGAGAAAAATGGATATCCATATGTAAAAGAATGA 3753
                         i  v  i           i  v  v      ?   i   i          
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_181574229_   3754 AACTGAATCCATTTGTCT-AC-CCATAT-CAAAAATCAACTCAAGATGTA 3800
                          ii  i i  --i ii  -  -      -       i       i   v 
  L1M4_orf2#LINE/    449 AGTTGGACCC--CTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_181574229_   3801 CTAAAGACTTAAATGTAAGACTCAAAATTGTAAAACAACTAGAAAAAAG- 3849
                         ii ?    i           vii    i i      vvi     i   i-
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_181574229_   3850 -TAGGGA-ACATACTTTAAGATC--GGTCTAGGCAAAGATTTCATGGCTA 3895
                         -    ?i- v  -   iiv  i --  vi       v i    v i v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_181574229_   3896 AGAGCTCAAACGCACAAAAAACTATAATAAAAATAAATAAATGGGACTAT 3945
                         v  vvi    v      iv   v v iv       i      v     vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_181574229_   3946 ATTAAACTAAAAAACTTCTATACAGCCAAGGAAACATTCAAGAGAGTGAC 3995
                           i   v v        i i i vv v     v  vv      i     v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_181574229_   3996 ----CAGTTTT----ATGGGAGAAAATATTTGTAAACTATTCATCTGACA 4037
                         ----  iiiiv----                 i   ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_181574229_   4038 AAGAATGAATATCCAGAATAACCAAGGAACTCAAACAACTCAACAATAAA 4087
                          i i ivvi           vvi  i      vv         i      
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_181574229_   4088 AA---AAAT--CTCA-TTTAAAAGTGGTCTGTGGACATGAATATAAATTT 4131
                           ---    -- i  -  ?    i   v viv   iv      v v    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_181574229_   4132 TTCAAAAGGAGACAGACAAATGGCCACCAGGCATATGAAAAAAAAAAATG 4181
                         i  v    i   i v           vi i   i       i -----  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-----TG 890

  chr2_181574229_   4182 CTCAACATCAGGAAAATG 4199
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (141 / 86)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.00 (40 / 20)  


 760 28.99 16.86 2.68  chr2_181718380_181720285.rev      632  1414 (492)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_181718380_    632 ATGTTTATGAAAAAGAAAATTCAACATTTTTAAGA-----ATTCTACTTC 676
                              i   i vvi   i i i  i   v      -----  v  - ii 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT-CCCC 63

  chr2_181718380_    677 TAATT--TCT-CAAATTCAATAAAATTCTAATTAAAACCACAAGAATACT 723
                         v    --   -  i      iiv   i iv  i    i v  ivvii-  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC-CT 112

  chr2_181718380_    724 TTTCCAAGGAATTTGATAAGCTGATTCTCAT-TTTATATG--AATGCG-- 768
                            iiivi   v    i        i  v v-  i     --     i--
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_181718380_    769 ----TCAGG-CAGC--------TCCT---AATGAA-AATACAGAT----- 796
                         ----i   i-i   --------  i ---  v   -  i v  v -----
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_181718380_    797 ACTTGTCCTACTAGATATCAAGACTCATTAGAA--TTATAGTAATTAAAA 844
                            iiiv  v ivi  v    i   i i  v  --i  i      i  i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_181718380_    845 CTATATCATGTACTATTTGTGCAGAGATAGACAACTTGATGAATAGAATG 894
                          vi i v--     i--- iii ii        vv v   v   i    i
  L1M4_orf2#LINE/    263 CAGTGTG--GTACTG---GCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_181718380_    895 GAA----GAGCCCA-ACACAGAACTAGGCAAAAAAAGAATCA--TGAAAT 937
                            ----   i   - v i i v i vi  vvv vi --   --   vv 
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGG--TCAATTGATTT 355

  chr2_181718380_    938 --GACAGATGGCACT----CTAGCCACTGGA-----------CTATTCAA 970
                         --    - v  ii i---- i vi  v   i-----------  v     
  L1M4_orf2#LINE/    356 TCGACA-AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_181718380_    971 TAAA-GTTACTAAAACAAATAGTTATCCATATGGAGAAAAATGAAATTGG 1019
                         i   - v i  iii    v i v  ?   i   v i  i      i    
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_181718380_   1020 ACTACTACCTTAC-CCTTTT-CAAAGAATCAATTCCAAATAAATT-TGGA 1066
                           iv      i  -  v v -    -   i  i  v    ii  i-?i  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAA-AATTAACTCAAAATGGATCAWAGA 503

  chr2_181718380_   1067 AC---AC-TAAGGGC--AAGC---------CTTTGAAAAAAAAATAAAGA 1101
                         v --- i-    i  --  i ---------   v   i    v   ii?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_181718380_   1102 TA--TCCTCGAGACCTTGGGACAGAAAGTAATTTCTTAACCATGACACAA 1149
                           --  i   v         vi  iv i ii       ivi       v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_181718380_   1150 AAAGTGCTAATCATATAAGAGA---CTGATAAATTTAACTACCATTTAAA 1196
                             ii v iiv i v    i ---iv        vi   -i   iv   
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT-TCATCAAAA 652

  chr2_181718380_   1197 TTCAGTTCTTTT-CACT----AATATACCATAAAAGAACC---AAGTCA- 1237
                           v ivv     -ii  ---- iv i  i  v  ii  vi---   v  -
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_181718380_   1238 TTAACAGA----GAGAAGATTTTTGCAA--CATATATGTACAAAAGGCAT 1281
                         iiv     ----     i  v       --       v i- v    v i
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG-ATAAGGGAC 751

  chr2_181718380_   1282 CTGTATCCACAATACATAAGAACCCCTAATAAAACAA-AATTGGGGGCAG 1330
                         i        v    i    ii v i  v i  vv   -   ------- i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-------AA 794

  chr2_181718380_   1331 GGGGACAAATAAC-------AAAAA-----AAAGG-----------CATT 1357
                         iii          -------     -----     -----------    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_181718380_   1358 TCAC---AGAA---ATGAGAATGGAAGATAA--ACATAAAAAAATTGTTC 1399
                           v ---    ---  ivi     vvi    --    i    i  - i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTC 893

  chr2_181718380_   1400 AACCTCATTATTAGG 1414
                            v   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.06 (52 / 894), avg. gap size = 2.94 (153 / 52)  


1012 26.29 3.59 0.80  chr2_181725847_181729549      501   751 (2952)    L1M4_orf2#LINE/L1      185   442 (466)  

  chr2_181725847_    501 TTTTGCAAAGAAAGAACGAAGTTGGAGGACTCATACTACTTGATTCTGA- 549
                          i   v   ii      i               i   v iii   iii -
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr2_181725847_    550 -CGTACTAGGTAAACATAGAGTAATCAAAATAGTGTGGTATTGGCATG-G 597
                         - v     --i   vv  v         i i         i      i- 
  L1M4_orf2#LINE/    235 ACTTACTA--CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_181725847_    598 GTTGGGCATATAGATCAGTGAAACAGAATAAGGAGCCCAGAAGTAGATCC 647
                          v i i           i  i  i     vii   i      i  i i  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_181725847_    648 ACACATAAATGGTCAGTTGATTTTCAGCAGAAATGCCAAGGTAATTCAGT 697
                          i    vv       i         ii  iiii       iiv     i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_181725847_    698 AGGGAAAGGAT------TTCGACATAAAGTGTTAGAATAACTGAGTATCT 741
                         i       i  ------   i   v vi   i i i i     ii  ? i
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_181725847_    742 ATACACAAAA 751
                          i ii     
  L1M4_orf2#LINE/    433 ACATGCAAAA 442

Transitions / transversions = 4.00 (52 / 13)
Gap_init rate = 0.02 (4 / 258), avg. gap size = 2.75 (11 / 4)  

1082 20.83 16.67 3.12  chr2_181725847_181729549     2846  3229 (474)    L1M4_orf2#LINE/L1      473   908 (0)  

  chr2_181725847_   2846 ATACAAAAATTAATTCAAAATGGGTCATTGACCTAAATGTAGGAGCTAAA 2895
                                      i         i   ?v            i        
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_181725847_   2896 GCTATAA--CTTCTAGAATATAATGTAAGAGCAAAATTTTATGCCCTTGG 2943
                         i      --  ii     v v  ii  i ? i   vi  ii  v      
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_181725847_   2944 ATTAAGTAAAAATCTCTTAG----GACA---AAAGCA--AGAAATAAAAT 2984
                         i   i i  vii i      ----    ---      --  v  i    v
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_181725847_   2985 AA----TTGGCAGGTGGAACTT-----AAAGTAAAA-------------- 3011
                           ---- v ii ii v i    -----   v     --------------
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_181725847_   3012 ---GACACTGTTGAGAAGATGAAAAGGCAAATCACAGAAAGGGAGAAAAT 3058
                         ---      i ii    ii       i   vi       v          
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_181725847_   3059 AATTTGAAAACC-TCTGTCTGATAAAAGACTTGTATCCAGAACATGCAAG 3107
                          -    v   i - v i        ii               i  ii  -
  L1M4_orf2#LINE/    723 A-TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA- 770

  chr2_181725847_   3108 TCTTAACATACAAGTCTTATATCTTAATA-------GACAAA----CCAA 3146
                         --------- v  v     i v  i    -------      ----    
  L1M4_orf2#LINE/    771 ---------AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_181725847_   3147 TTTAAAA-TGGACAAAAGATTTGAATAGAGATGTTACTGATGAAGCTGTA 3195
                           ?    -   i    i            v  v iv ii v    v i  
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_181725847_   3196 TGAATAAC-----AGT---------GGTGCTTACACATCATTAGTCGT 3229
                         ii   ii -----  i--------- i    i -      ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 2.35 (54 / 23)
Gap_init rate = 0.04 (16 / 436), avg. gap size = 4.75 (76 / 16)  


3298 25.83 1.11 0.44  chr2_181778663_181785361     5306  6207 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_181778663_   5306 TGGAAAAACATTCCATGCTCATGGTTATGAAGAATCAATATCATGAAAAT 5355
                               i i  i     i      v vv     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_181778663_   5356 GGCCATACTGCCAAAAGGAATTTATAGATTCGATGCTATTCCCATCAAGC 5405
                            v     v  v   vvi  i  i      i i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_181778663_   5406 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5452
                          v   -   v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_181778663_   5453 ATATGGAACTAAAAAGGAGCCCATACAGCCAAAACAATTCTAAGCAAAAA 5502
                                 v iv  i   v  viv i            ii i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_181778663_   5503 GAACAAAGCTGGAAGCATCACACTACCTGACTTCAAACTATACTACAAGG 5552
                                 i    i vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_181778663_   5553 CTACATTAACTAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5602
                              v   ii  i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_181778663_   5603 CAATGGAACAGAACAGAGGCCTCAGAAATAACATCACACATCTACAACCA 5652
                                 i    iv   ivii         vvi  i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_181778663_   5653 TCTGTTCTTTGACAAACCTGACAAAAGCA----ATGGGGAAAAGATTCCC 5698
                         vi  v i  i     ivv  v   i v  ----         ii  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_181778663_   5699 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGCAGAAAACTG 5748
                          v  i  i              v      v  ?   i i   i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_181778663_   5749 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTTAAGATGGAT 5798
                           ii         v   i     v                i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_181778663_   5799 TAAAGATTTAAACATAAGACCTAAAACCATAAAAATCCTAGAAGAAAACC 5848
                         i ?   ii    ii     v       i      v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_181778663_   5849 TAGCAATACCAC-TCAGGACATAGGCATGGGCAAAGACTTCATGAGTAAA 5897
                            v?i  vvv -  iv   v v  vv i     v ii   v iii  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_181778663_   5898 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGATCTTAT 5947
                                     vvi          vv     v       v   ii i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_181778663_   5948 CAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 5996
                             -     i -   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_181778663_   5997 AGGTAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 6046
                           ii    i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_181778663_   6047 AGGGCTAATATCCAGAATCTACAAGGAACTTACACAAATTTACAAGAAAA 6096
                         i  i  vi          v  i  i     ivi    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_181778663_   6097 ACACAAACAACCCA-TCAAAATGTGGGCAAAGGATATGAACAGACACTTC 6145
                          v     i      - i?   vi            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_181778663_   6146 TCAAAAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCTCATG 6195
                           v        i  vi vii      i  i  i       i v     vv
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_181778663_   6196 ATCACTGGTCGT 6207
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2459 25.14 1.68 1.54  chr2_181823464_181825517.rev      847  1562 (492)    L1M4_orf2#LINE/L1      192   908 (0)  

  chr2_181823464_    847 AAAAAAGAAAATAGTTGGAACACTAATACTACCTAATTTCAAGATGGA-T 895
                            i     v v       iv   v i   v  i        i ivv - 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_181823464_    896 ATAA-TTTATAGTAATCAAAGCAGCATAGTTTTGACATCAAAATACCCAA 944
                          i  -vi  i         ii   ii i  vi  i   v ii   vv  v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_181823464_    945 ATAGATAAATGGAATAGAACAGAGTGTACAGAAATAGGCCTACATATACA 994
                               v            iv   v  v        ii  i i i  vi 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_181823464_    995 TAGACAACTGCTGTTTTGGCAAAGGTCAAAAGGCAATTCAATTGAGAAAG 1044
                          i v   i  v -   i i   i   vvv   i v       v i     
  L1M4_orf2#LINE/    342 TGGTCAATTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_181823464_   1045 AATAGT-TTTTCAAAAAATGGTTTTGGAACAATTATATATCCATATGTGG 1093
                               -       v       vi   i    i iv   ?   i   iii
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_181823464_   1094 GAAAATAAACT--GATCTATACCTCATACCATACATGAAAATTAATTTAA 1141
                         i i   i  v --  i iv       i      i ii        i i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_181823464_   1142 AATGGATTGTAGGCCTAAATGCA-GAGCATAAAACTATAAAACTTCTGTA 1190
                                ii?  i        i -    -               ii iv 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGA 539

  chr2_181823464_   1191 AGAAAATATAGAGA-AAATCTTTTTGACCCTGGTTTAGACAAACAATTTT 1239
                               i    i?i-       iv     i   v    i   vviv  i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_181823464_   1240 TAAATATTACACCAAA-GCATGATACAGCAAAC-AGAAAATTGGTAAATT 1287
                           i    v        -   ii -i  i    v- i     v i      
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATT 638

  chr2_181823464_   1288 GTACTTCAGCAAAATTGAATATGCCTGCTCTTTTAAAGACACGGTTAAGC 1337
                          v      v       i  v ivii  iv   iv  i     vi i   v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_181823464_   1338 AAATAAACGAACAGGCCACAGACTGGAAGAAAATATTTACAAAGTATATA 1387
                           i i  vii   iv       v   i           i    vi     
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_181823464_   1388 TCTGCCAAAGAACTTGTATCTCCCCAAAAAAACTATATTACATATTCTCA 1437
                             vi  i i         ----  i  ----     v viv i   i 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATC----CAGAA----TATATAAAGAACTCTTA 780

  chr2_181823464_   1438 AAACTCAATATTAGGAA-ACAACCAACCCAATTTAAAAACAGGGAGATGA 1486
                         v         v  ii  -    vi         ?     ii  v i v  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_181823464_   1487 TTTGAGCAAATACTTCTCCAAAAATGA-ATACAGATAGCAAATAAGCACA 1535
                              ii i i i         i v  -     i  i  v          
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_181823464_   1536 -GGTAAGATACTCAACATCATTTGTTAT 1562
                         - iv     i          ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (113 / 63)
Gap_init rate = 0.02 (16 / 717), avg. gap size = 1.44 (23 / 16)  


3480 24.18 2.94 0.34  chr2_181911215_181913241.rev      651  1535 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_181911215_    651 TGGAAAGAGAGCCCGTGTTCATGGATTAGAAGAATTAATAAGGCTAAAAT 700
                                 v v   i            i     v      vv i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_181911215_    701 GTCCAGAGGAGCCAAAGCGATCTACAGATTCAATGCAATCTCTAACAAAA 750
                          v v v vvvv     vi               i      i   v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_181911215_    751 TTCCAATTGCATTTTTTACAGAAATAGAAAAATCAATCCTAGAATTCATA 800
                          i   ii   v      i       v  v  iiii      i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_181911215_    801 TGAAGTCACAAAGGACCTCAAATAGACAAAA-AATCTTGAGCAA-AAGAA 848
                           i ivii   i     ivi     v     -        iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_181911215_    849 TGAAGTTGGAAGCCTTACACTACCTGATTTCAAAA--TATTACAAAACTA 896
                         ii        i v  i     v  ii         --  i      i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_181911215_    897 TAGTAGTGAAAATAGCATGGTACTGTCATAAAAACAGACACATAAACCAA 946
                         i    i v  i i  ii        v     ii i     i   i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_181911215_    947 TGGAACAGAATAGAGGGCCGAGAAATAAACTTATACCAACATAGCCAAAG 996
                              i     v   i i v          ii    vvvi  i i   vv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_181911215_    997 AATCTCCAACAAGAATACGAAGAATACACAATGGGGAAATGGCAGTCTTT 1046
                         i  i i i     ii i v    vi iv           viii       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_181911215_   1047 TCAAGAAATGGTGCTGGGAAAACTGGATCTCCATATGCAGAAGAATAAAA 1096
                             v              v        v?   i     i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_181911215_   1097 GTAGACTCTTATCTCATATCATATATAAAAAT-----CAAAATAGATTAA 1141
                         v i   i i  i    i i      i      -----      i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_181911215_   1142 AGACTTAACCCTAAGATGTGAAACTCTAAAAT-----GAGGAAAACA--G 1184
                             i   viv     vv i     v     i-----  i       -- 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_181911215_   1185 GGAGAAAGTTTCAGGATATTGGACTGGGCAATAATTATTTTGGATATAAC 1234
                          ?iv   vi   iv  iv    ii i      ii  - i  i     i  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAGATATGAC 599

  chr2_181911215_   1235 CCCAAA-GTGCAAGCAATAAAGGCAAAAATAGACAAATAAGATTGTATCA 1283
                         v     - ii       i   i v         i    vi  i vi    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_181911215_   1284 CA-CTACAAAGCTTTGCACAGCAAAGGAAAAAATCAACAGAGGGAAGAGA 1332
                         v -i  v   vi    ii vv       v vv     v i  v   i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_181911215_   1333 CCAACCTACATAATGGGAGAAAATATTTGCAAGCCATGTATCTGAGAAAG 1382
                          -    i   v                     ii   i       v  i 
  L1M4_orf2#LINE/    700 C-AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_181911215_   1383 GGTTAATGTCTAAAATATATAAGGAACTC----AACTTGATAGCAAGAAA 1428
                          ii vi i  i i         i      ----    ii   ii  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_181911215_   1429 ACAA----TCCAATTAAAAAATAGACGAAAGACTTGAATAAACATTTCTC 1474
                             ----i      ?      i i i  i  i       i         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_181911215_   1475 ACAAAAACACATACAAATGGCCAACAGATACATGAGAAAAATGCTCAATA 1524
                         vv  i  v i              i iii      -   i        i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTCAACA 897

  chr2_181911215_   1525 TCACTAATTTC 1535
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.04 (141 / 69)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.23 (29 / 13)  


3625 18.21 4.02 3.13  chr2_182075219_182078157     1553  2447 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_182075219_   1553 AGATTTTTCATATTTATGGATTGGAAGACCTAATATTGTTAAGGTGGCAC 1602
                             v ii   i  i              i             i     v
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_182075219_   1603 TACTCTTCAAAGTGATCTACAGATTCAATATAACCC--GTCAAAATCCCT 1650
                              ii    v                iii  i  --i          v
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_182075219_   1651 GCTGCCTTTTTTCCAGAACTTGACAGGCTGACGCTAAAATTCCAATGAAA 1700
                                     v     v      i     iv         vv   i  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_182075219_   1701 ATATAAAGGAAGCAGAATAGCTAAAACAATTTTGAAAAA--AGAACTAAG 1748
                           ii  i   vv         i        i        --     v   
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_182075219_   1749 CTAGAGGTCACACATGTCCCAGTTGCAAAGTTTATCCTAAAACTACATTA 1798
                         i i    v v    iv     i  v    ii   iivi   i     v  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_182075219_   1799 ATCAAGATTATATGGGACTGGTATGAAGATATACATACATACATCAGTAG 1848
                                ivi i   v     i  i i    v     --  v    i i 
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA--TAGATCAATGG 303

  chr2_182075219_   1849 AATCAAAATAAAAG-CCAGA------------TATGTATAGTCAGTTGAT 1885
                            vi  v i i  -     ------------i  v   i    i     
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_182075219_   1886 TTTTTACATGGATGCCATGACAACTTAATGCAGAAAGGATAGTCTTT-CA 1934
                            iv   v  i     v   v i i    vi     i         -  
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_182075219_   1935 AGAAATTTGGCTGCGACAACTGAATATCCAGTTGCAAATGATAGAAATTG 1984
                          v    vvv    v        i   ?   vv      v  vv   i   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_182075219_   1985 GACCCTTTCTTCATTTCCTAGTAAAAAAAAAAAATTAACTCAAAATGAAT 2034
                              i v i   ivi v  -  v     -----             i  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATA-TACAAAAA-----TTAACTCAAAATGGAT 497

  chr2_182075219_   2035 CATATTAATGGCTAACTATAAGAGCTAAAACTATGA--CTCTTGGAATTA 2082
                           ? --i i--    v i                i --     i   vv 
  L1M4_orf2#LINE/    498 CAWA--GAC--CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_182075219_   2083 AACATAGGTGTATATCTTAATGACCTTGAATTAGGCAATGTTTTCTTATG 2132
                                 ?   v     vi        ii          v       - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-G 592

  chr2_182075219_   2133 A-ATGACAAGTAAAGCACAAGCAACTTTATAAAGAATAAATAGATAAATT 2181
                          -      vvv              --- -      v             
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAAC---A-AAAGAAAAAATAGATAAATT 638

  chr2_182075219_   2182 GGACTTCATCAACAATGAAAATGTTCGTGTTTTAC-GTACACTGTCAAAA 2230
                                     v v i    iv  i   i  i v- v     i    i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_182075219_   2231 AAATGAAAAGGCAATTCACAGAATGGGAGAAA-TATTTGCAAATCATCTA 2279
                           i       i   ii                -              v  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_182075219_   2280 CCAGATATATT-CTAGCATCCAG--TATATAAA--ACTATTACATGCAAC 2324
                         i v    vivv-  v i      --        --   v     ----  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA----AC 784

  chr2_182075219_   2325 T--ATTTAAATAAAAGAAACAAA--ACCACACTAATAAAAAAAGGG-AAA 2369
                          --  ---       - i     --   -  v -- ?     v   -   
  L1M4_orf2#LINE/    785 TCAAT---AATAAAA-AGACAAATAACC-CAAT--TWAAAAATGGGCAAA 827

  chr2_182075219_   2370 AGATTTGAATAGACGTTTCTCCAGAGA---TCTGCAAATGGCTAAGAAGC 2416
                         i             i        i   --- v i        i  v    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_182075219_   2417 ACAGTAAAAGAAGCTCAACATCATTAGCTTT 2447
                            vv      v           ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (86 / 73)
Gap_init rate = 0.03 (29 / 903), avg. gap size = 2.21 (64 / 29)  


3096 25.58 1.66 1.11  chr2_182101364_182107271     4514  5416 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_182101364_   4514 TGGAAAAACATTCCATTCTCATGGATAGGAAGACTCAATATCATAAAAAT 4563
                               i i  i    vi        v        i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182101364_   4564 GGCCATACCGCCCAAAGTAATTTACAGATTCAATGCTATTCCCATCAAAT 4613
                            v    iv      v i  i           i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_182101364_   4614 TACCATTGACACTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTCAT 4662
                          v   vivi vi i  ii     v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_182101364_   4663 ACGGAA-T-CAAGAAGACCCTGTATAGCCAAGATAATCCTAAGCAAAATG 4710
                          i    - -    i-     v v        i i    i i iv  i v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_182101364_   4711 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4760
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_182101364_   4761 TATAGTAACCAAAACAGCATGGTACTGGTTTCAAAACAGACATATAAACC 4810
                           i     i   i    ii         iv v ii i         i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_182101364_   4811 AATGGAGAAGAACAGAGACCCCAGAAATAACACCACATATCTGTAACCAT 4860
                               iv    iv    vi          vv   i i  i i iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_182101364_   4861 CTGATCTTTGGCAAACCTGACAAAAATAAACAATGGGGAAGGGATC-TCG 4909
                         i    i  i i   ivv  v   i vi vv          i i  v-  v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_182101364_   4910 TATTCAGTAAATGGTGTTGGGAAAACTGGCTAGCCATATGCTGAAAATTG 4959
                          -    ii        i     v      v  ?   i    vi  i v  
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_182101364_   4960 AAACTGGACCCCTTCCTTAAACCTTATACAAAAATTAACTCAAGATGGAT 5009
                           ii         v   i v   v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_182101364_   5010 TAAAGACTTAAATATAAAACCCAAAACCATAAAAACCTTAGAAGAAAACC 5059
                         i ?    i     i   i v i     i      vi             v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_182101364_   5060 TAGGC---AATGCTATTCAGGACATAGGCATGGGCAAAGACTTCATGACA 5106
                             ?---   -  --  iv   v v  vv i     v ii   v --- 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CT--TCGTGACCTTGGGTTAGGCAATGGTTTCTT---A 591

  chr2_182101364_   5107 GAAATG---CCAAAAGCAATTGTAACAAAAGCCAAAATTGGCAAACGGGA 5153
                           v   ---         vvv i        vv     v ii   iv   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_182101364_   5154 TCTAATTAAA-TTAAAGAGCTTCTTCACAGCAAAAGAAACTAGCATCAGA 5202
                         ii v  i   -     i -   i vii vv    i  v    v  vv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_182101364_   5203 GTGAACAGGCAACCTACAGAACGGGAGAAAATTTTTGCAATCTACCCTTC 5252
                              v  i     i      i          v       vii iviv  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_182101364_   5253 TGACAAAGGGCTAATATCCAGAATTTATGAGGAATTTAAACATATTTACA 5302
                            i  i  i  vi          v   i i   i ivv   vv iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_182101364_   5303 AGAAAAAGACAA----CCGCATCAAAAAGTGGGCAAAGGATATGAACAAA 5348
                          v          ----  vv  i?    i            v    i i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_182101364_   5349 CACTTCTCAAAAAAAGACACTGACATGGCCAAGAAACATATGAAAAAAAG 5398
                           i     v   i    i ivv v        v  i  i       i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_182101364_   5399 CTCAACATCACTGATCAT 5416
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (131 / 96)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


3148 25.33 1.55 1.11  chr2_182124164_182126768     1210  2113 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_182124164_   1210 TGGTAAAACATCCCATGCTCATGGATAAGAAGAATTA---TTATTAAAAT 1256
                            v  i i        i        vi     v   ---  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182124164_   1257 GACTATACTTTCTAAAGCAATCAACAGATTCAACACAATCCCTATCAAAT 1306
                          i v     ii i   vii   v           i              v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_182124164_   1307 TAACAATTTCCTTTTTCACAGAATTAGAAAAAGTAATTCTAAAATTCATA 1356
                          vv  ii v       ii     v v  v  iv i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_182124164_   1357 TGGAAGCAAAAAGAGCCTA-AATAGCCAAAGCAATCCTAAGCAAAAAGAA 1405
                              iiiv  i ii  i -          i     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_182124164_   1406 CAAAGCCAGAGGCATCACATTACCCAACTTCAAACTATACTACAAGCCTA 1455
                              iii    vv     i v     i      viv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_182124164_   1456 TAGTAACCAAAACAGCATGTTATTGATACAAAAATAGACATACAGATCAA 1505
                         i     i   i    ii  v  i  ii i  ii         i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_182124164_   1506 TGGTATAGAATAGAGTACCCAGAAATAAAGCCACATAGCTACAATCCACT 1555
                            v       v   vii           v   i i vi  iii  v i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_182124164_   1556 TATCTTTGACAAAGGCAGCTAACATAAA-CAATAGGGAAAGGACACCCTA 1604
                         v  i  i     i  i-  i  v iv v-    i       i i vi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_182124164_   1605 CTCAATAAATAGCGC-AAGAAAACTGGCTAACCACATGCAGGAGAATAAA 1653
                         i    i    i i  -ii  v      v  ?         ii     i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_182124164_   1654 ACTGGACCCCTACTTGTCATCCTATACAAAAATTAACTCAGTATGTATTA 1703
                         ii           i vv  i v                  iv   v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_182124164_   1704 AAGACTTAAATGTAAGACCTCAAAAAATAAAAATCCTAGAAGAAAACCTG 1753
                         ?    i           v  v   vv      v  i           v i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_182124164_   1754 GGTATAC-TCTTCTGGACATGGGCTGAGGCAAAGAATTTATGACTGAGAC 1802
                           ?i  v-     vv   v v  v v      v iv  iv iiv iv   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_182124164_   1803 CTCAAAAGCAAACAAG--ACCAAAGCAAAATT-GACAACTGGAACCTAAT 1849
                         vi        --    --  v    v    v -  i  v v i  i v  
  L1M4_orf2#LINE/    600 ACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_182124164_   1850 TAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCAACAGAGTAAGCA 1899
                         i   v v  i i   i  iiivv    i  v        v i   i iv 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_182124164_   1900 GACAACCTACAGAATGAGAGAAAATATTTGCGAACTACGTAAATATTTTT 1949
                                i        i              i  ii ii  ------- i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA-------TC 740

  chr2_182124164_   1950 TGACAAAGAACTAATATCCAGAATATATAAGTAACTTAAACAAATCCACA 1999
                            i  i i   vi                iv    ivv    v  v i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_182124164_   2000 AGAAAAA-ATAAATAACCGGATTAAAAAGTGAGCAATGGACATGTACAGA 2048
                          v     - i        vi   ?    i  i    v   iv  v i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_182124164_   2049 TACTTTTCAAAAGAAGGCATACAAATATCCAA-AA--ACATGAAAAAGTG 2095
                         i i  i  v       ii        iv    -  --         ii  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_182124164_   2096 CTCAACATCACTAATCAT 2113
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (138 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


1780 17.93 1.26 25.00  chr2_182142297_182145110.rev     1135  2322 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_182142297_   1135 GAAATATACTCCGTG---ATAGACTGGAAGAACTAATATTGTTAAAATTA 1181
                             v   ii  i  ---  i  i       vi            i  vi
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_182142297_   1182 CAATACTACCTAAAGCAATTTACAGATTCAATGCAATTCCTATCAAAATA 1231
                                v  i   vii  i           i     i           v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_182142297_   1232 CAAATGACATTCTTCAC-GAAACAGAAAAATT---CCTAAAATTTATAAG 1277
                          v iivi v  i  ii -    iv  v  ii ---         i   v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_182142297_   1278 AAACCACAAAAGACCCTGAATAGCCAAAGCAATCCTGAGCAAAAAGAACA 1327
                         i  vii   ii     v           i     i   iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_182142297_   1328 AAGCTGGAGGCATCACACTACCTAACTTCAAAATTTACTACAAAGCTATA 1377
                            i      vv       v  i  i       i              i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_182142297_   1378 GTAACCAAAACAGCACAGTATTGGCATAGAAACAGACACATAGACCAATG 1427
                             i   i    iiii   i       iii i     i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_182142297_   1428 GAGCAGAATAGAGAATCCACATATAAATCCATGCACTTACAACCAACTAA 1477
                           ii     v    i    v v     i    i  i   iiii   i i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_182142297_   1478 TCTGTGACAAAGCTGTAAAGAACATACAATGGAAAAA-AACAGTCTCTTT 1526
                          i vi     i v  iv    v   v      ii   -  i     i  i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_182142297_   1527 AATAAATGGTGCTAGGAAAACTTAATAACTACATGCAAAAAAATAAAATT 1576
                           i          i   v    vi   ? i          i   i  i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_182142297_   1577 AAAACTTTCTCACCACTTCTTCCTTTCCAGTTTGGATACCCTTCCTTTCT 1626
                         ---------------------------------   i-    v   ----
  L1M4_orf2#LINE/    453 ---------------------------------GGAC-CCCTACCT---- 464

  chr2_182142297_   1627 TCCTCTTGCCTGATAGCTCTGGCCAGGACTTTCTGCACTATGTAGAATAA 1676
                         -----------------------  ----------   i  i  v  ---
  L1M4_orf2#LINE/    465 -----------------------CA----------CACCATATACAA--- 478

  chr2_182142297_   1677 CAGTGGTAAGAGGGGGTATCCTTGTCTGTTTCAGTCCTTGGAGGAAAGGC 1726
                         --------------------------------------------   ---
  L1M4_orf2#LINE/    479 --------------------------------------------AAA--- 481

  chr2_182142297_   1727 CTTCATTTTTTCTGTGTTCAGTATGATGTTGACTGTAGGTTTGTCATATA 1776
                         ----------------------------  i   ----------  v - 
  L1M4_orf2#LINE/    482 ----------------------------TTAACT----------CAAA-A 492

  chr2_182142297_   1777 TGGCCTTCATTATTTTGAAGTATGTTCCTTCTATATCCATTTTGGTGAGA 1826
                            -----------------------------------------------
  L1M4_orf2#LINE/    493 TGG----------------------------------------------- 495

  chr2_182142297_   1827 ATTTTTATCATAAAGGAATGTTGAATTTTATCAAATGCTATCTCAGCATC 1876
                         ------    ? i ----------------------------------i 
  L1M4_orf2#LINE/    496 ------ATCAWAGA----------------------------------CC 505

  chr2_182142297_   1877 TATTGAAATAACCAATACACCAAAACCAAATCAAAATGAATTATAGACCT 1926
                           --------------------------------    ---  -   v  
  L1M4_orf2#LINE/    506 TA--------------------------------AATG---TA-AGAGCT 519

  chr2_182142297_   1927 GAAATTATGAAATTACTAAAAGAAAACATTGGGG-AAATGCTCTAAGATA 1975
                         i   i   i   i vi  i          v  ? -    -  iiiv  iv
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACC 568

  chr2_182142297_   1976 TTGGTCTGGGCAAAGATTTTTTTG-TGTAAGACCTAAAAAGCACAGGCAA 2024
                             vi i     v i   i  v - i i v   --         i    
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACC--AAAAGCACAAGCAA 616

  chr2_182142297_   2025 CCTGAACAAAAATAGACAAATGAGATTACATCAAGCTAAAAAGCTTCTGC 2074
                          vvi iv         i    vi  i v      iv v    i   i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_182142297_   2075 ACAGCAAAGAAAAC-ATCAACTAAATGTAGAGAGAACCCACATAATGAGA 2123
                         i vv     i v  -     vv  i  v i   v        v    i  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_182142297_   2124 GAAAACATTGGCA---CAC-TATCTGATGAGGGATTAATAACCAGAATAT 2169
                              i   v   ---  i-        i     i vi  v         
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_182142297_   2170 ATAAGGAGCTCAAACAACTCAATAGCAACAAAACTAAAACCTAACAAAGA 2219
                             i  i   vv           ii  -------   i----     v 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAA-------AAAG----ACAAATA 805

  chr2_182142297_   2220 ATGTAATTTCAAAATTGGCAAAAGATCTCGACAGATATTTCTCAAAAGAA 2269
                          ivi    ?v     v      i   i vi i   i       v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_182142297_   2270 GATATACAAATGGCAAACGGGTATAAGAAAACATGTACAACATCACTAAT 2319
                                       v  iii i i v     v   iv        ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_182142297_   2320 CAT 2322
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.99 (139 / 70)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 12.00 (312 / 26)  


2408 24.80 7.26 1.45  chr2_182339918_182343903     2334  3091 (895)    L1M4_orf2#LINE/L1        1   802 (106)  

  chr2_182339918_   2334 TGGGAAGATAGTACATGTTCATGGATTGAAATAATTA-TATTGTTAAAAT 2382
                            i      viv               i  v v   -         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182339918_   2383 GGCCATACTACCCAAAGTGATCTATGGATTTAATGCAATTGCTATCAGAA 2432
                            v     v      v       ii    i  i     iv      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_182339918_   2433 TACCAACACCATTCTTTACAGAAATGTTACAATCTGA-----AAATTCAT 2477
                          v   i vv v  i   i       - v    v    -----        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_182339918_   2478 GCAGAACCACAAAAAAAACCCCAAATAGCCAAAGCAACCCTGAGCAAAAA 2527
                         iii   vii   iii --   vi          i   i i   iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_182339918_   2528 GAACAAAACTGGAAGTATCATACTACCTGACTTCGAAATATACGATAAAA 2577
                                ii    i vv   i   v  ii i   i   iv   v i   i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_182339918_   2578 CTATA----TCAACACAGCATGGTACTAGCATAAAACCAGACA----GAC 2619
                            i ----    v    ii       i      iivi     ----  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_182339918_   2620 CCATGAAATAAAATGGAAAGCCCAGAAATAAATTTTTGCACCTACAACAG 2669
                          v   i    i   v  i  i           iiiv i  ii  ii--- 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG---G 344

  chr2_182339918_   2670 CCAACTGAATTTTTAA----GATGTCAAGAACATGCACTGGGAAAAAGAC 2715
                         i   i   -    ii ---- i  i     v   v  v    i   ii i
  L1M4_orf2#LINE/    345 TCAATTGA-TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_182339918_   2716 AGTCTCTTCAACAAATGGTACTAGGAAAATCAGATATTCACATGCAGAAG 2765
                              i             i  i   v  iii    ?i        i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_182339918_   2766 AATGAGATTAAACCCCTCCCTCTCACCATATACAAAAAT-AA----AAAT 2810
                              ii  ii      v    v                -  ----    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_182339918_   2811 AGATTAAAGATTTAAAATGTAAAACTTGAAAACTATGAAA---TTACAAG 2857
                         i   i ?   ii    -     i vi -        i   ---   v   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAA-TGTAAGAGCT-AAAACTATAAAACTCTTAGAAG 541

  chr2_182339918_   2858 AAAA---AAGGGAAATTATTCTCGACACTGACCTGAGCAAGGATTTTTAA 2904
                             --- i ? v  v v   vi   vi  ivi ii    v i   i v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_182339918_   2905 AATAAGACCTCAAAAGCATA----------GACAAAATAA--------GA 2936
                         i   v   vi        i ----------  v      i--------  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_182339918_   2937 TTACATCAAACTAAAAAACTTT-GCACCTTGAAGAAAACTATTAACAAAG 2985
                         i v       v v         - ii i ii   i v     i  v    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_182339918_   2986 TGAAAA--CAGCT-GCAGAATGGGAGAAAAATATTTGCAATCTATACATG 3032
                               --  i i-i               -         vii   i  v
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATC 740

  chr2_182339918_   3033 CGACAAAGGGATAAAATCCAAAATATATAAGAAAATT----AATTCAACA 3078
                         i  i  i  iv viv     i         ii  v i----  i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_182339918_   3079 GATAAAATAATAA 3091
                         -      vi i  
  L1M4_orf2#LINE/    791 -ATAAAAAGACAA 802

Transitions / transversions = 2.19 (127 / 58)
Gap_init rate = 0.03 (23 / 802), avg. gap size = 2.87 (66 / 23)  

 371 21.51 0.00 1.08  chr2_182339918_182343903     3402  3494 (492)    L1M4_orf2#LINE/L1      817   908 (0)  

  chr2_182339918_   3402 AAATGGGCAAACGACTTTAATTGATAGGTCTCAAAAGAAGACATATAAAT 3451
                                    v  i  v   v  i vv    v        i   i    
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_182339918_   3452 GATCAACAGGTGCATTTAAAAGATACTTGACATCACTAATCAT 3494
                          ii   i i ii   -v       i  ii      ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACAT-GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1)  


3102 27.51 1.10 0.77  chr2_182421389_182427810     5026  5930 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_182421389_   5026 TGGAAGAACATTCCATGGTTATGGATCGCAAGAATCAATCTCATGAAAAT 5075
                              ii i  i     v i      i v    v i   v ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182421389_   5076 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCGTCAAGC 5125
                            v     v     iv i  i ii        i  v     ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_182421389_   5126 TACCAATGGCTTTCTTCACGGAATTGGGAAAAACGACTTTGAAGTTCATA 5175
                          v   iiv  i  i  ii i   v v iv  ivi  iii i  i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_182421389_   5176 TGGAACCAAAAAAGAGCCCACA----TCAAGACAATCCTAAGCAAAAAGA 5221
                              viiv  ii  -    v ----i   i      i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_182421389_   5222 ACAAAACTGGAGG---CATGCTACCTGATTTCAAACTATACTACAAGACT 5268
                              ii      ---  ii  v  ii        viv        ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_182421389_   5269 ACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGACCA 5318
                                i   i    iii        i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_182421389_   5319 ATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCA 5366
                               i    i--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_182421389_   5367 TTTGACATTTGACAAATCTGACAAAAACAAGAAATGGGGAAAGGATTACC 5416
                         v    iv  i     ivv  v   i v  vvv           i  vii 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_182421389_   5417 TATTTAATAAATGGTGCTGGGAAAACTGGTTAGTCATATGCAGAAAGCTG 5466
                          v  i  i              v      v  ?i  i     i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_182421389_   5467 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGTT 5516
                           ii    i    v   i     v              i    i    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_182421389_   5517 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5566
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_182421389_   5567 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5615
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_182421389_   5616 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATGTAA 5665
                         i            vvi          vv     v  i    v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_182421389_   5666 TTAAACTAAAGAACTTCTGCACAGCAAAAAAAAAAACTACCATCAGAGTG 5715
                          i   v v  i     i  ii vv    ii v ---   i  vv i    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACA---CTATCAAGAAAGTG 693

  chr2_182421389_   5716 AACAGGTAACCTACAGAATGTGAGAAATTTTTTGCAATCTATCCTTCTGA 5765
                           v  ii    i        v      v v       vii  viv     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_182421389_   5766 CAAAGGGTTAAAATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 5815
                         i  i  ii viv         v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_182421389_   5816 AAAAAACAAACAACCCCATCAAAAAGTGGGTAAAGGATATGAACAGACAC 5865
                             i     i     v  i?    i    i       v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_182421389_   5866 TTCTTAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 5915
                             iv        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_182421389_   5916 ATCATCACTGATCAT 5930
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


3123 26.76 0.66 0.66  chr2_182489039_182495434.rev     4997  5904 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_182489039_   4997 TGAAAAAACATTCCATGCTCATGGATAGGAAGAATCTATATCATGAAAAT 5046
                           i   i i  i     i        v      v iv    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182489039_   5047 GGCCATACAGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v    vv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_182489039_   5097 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 5144
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_182489039_   5145 TATGGAATCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5194
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_182489039_   5195 AACAAAGCTGGAGGCATCACACTACCTGACGTCAAACTATACTACAAGCC 5244
                                i      vv       v  ii iv     viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_182489039_   5245 TAGAGTAACGAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 5294
                           v     iv  i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_182489039_   5295 ACTGCAACAGAAC--ACAGCCCTCAGAAATAATACCACACATCCACAATC 5342
                          v  v  i    i-- v  i  --        vv   i    ii iii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_182489039_   5343 ATCTGATCTTTGACAAACCTGACAAAAATAAGAAATGGGGAAAGGATTCC 5392
                          vi    i  i     ivv  v   i vi vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_182489039_   5393 CTATTGAATAAATGGTGCTGGGAAAACTGGCTAGACATATGCAGAAAGCT 5442
                           v  v  i              v      v  ?v  i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_182489039_   5443 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5492
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_182489039_   5493 TTAAAGACTTAAATGTTAGACGTAAAACCATAAAAATCCTAGAAGAAAAC 5542
                          i ?    i       v   vv      i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_182489039_   5543 CTAGGCAGTACAAT--TCAGGACATAGGCATGGTCAAGGACTTCATGACT 5590
                         v    ?-   -   --  iv   v v  vv i v   v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGN-GTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_182489039_   5591 AAAACACCAAAAGCAATGGCAACGAAAGCCAAAATAGACAAATGGAATCT 5640
                          vi            vvi     i    vv        i    v i ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_182489039_   5641 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5690
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_182489039_   5691 ACAGGCAACTTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5740
                          v  i    ii                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_182489039_   5741 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACATATTTACAAGAA 5790
                           i  i  vi          v  i        ivv   vv iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_182489039_   5791 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATAAAGAGACACT 5840
                            i     i     v  i?    i            v i  v     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_182489039_   5841 TCTCAAAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAATGCTCA 5890
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_182489039_   5891 TCATCACTGGTCAT 5904
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (136 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3464 24.23 1.10 1.54  chr2_182654782_182658329.rev     2145  3056 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_182654782_   2145 TGCAAAAATATTTCATCTTCATGGATTGGAAGAGTTAATATTGTTAAAAT 2194
                           v   i    ii   v                v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182654782_   2195 GTCCATACTCCCTAAAGCAATCTACAGATTCAGTGCAAGCCCCATCCAAA 2244
                          v v        i   vii             ii    v   i   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_182654782_   2245 TACCAATGACATTCTTCATGGAAATAGAAAAAACT-ATCCCAAAATTTAT 2293
                          v   iivi v  i  iiii     v  v  i-  -    i      i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_182654782_   2294 ATGGAACCACCAAAGATCCAGAATAGCCAAAGCTATCCCGAGCAAAAAGA 2343
                               vii v ii  i              i v   ii  iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_182654782_   2344 ACAAAACTGAAGGGATCACATTACCTGACTTCAAATTATACTTTAAAGCT 2393
                              ii  i   iv     i v  ii i      viv    vi      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_182654782_   2394 GTAGTAACCAAAACAGCATGGTTTTGGTTACTGGCATAAAAACAGACACA 2443
                         ii     i   i    ii    -------          ii i     i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGT-------ACTGGCATAAGGATAGACATA 292

  chr2_182654782_   2444 --GACCAATGGAACCAAACTGAGAACCCGGAAACAAATATACACAGCTAC 2491
                         --  i        ivi  i     ii  i    i   ivi i   vi  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_182654782_   2492 AGTGAACTCATTTTCAACAAAGATGTCAAGAACATACATTGAGGAAAAGA 2541
                         i  v  i v      i    i i  i     v   v  v  i     ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_182654782_   2542 CAGTTTCTTCAATAAATGGTGCCAGGAAAACTGAATATTTATATGCAGAA 2591
                         i   i i     i         ii   v     i   ?ii i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_182654782_   2592 GAATGAAACTTGACCCCTATCTCTTGCCATGTACAAAAATCAAATCAAAA 2641
                                ii v        i   vii    i         i  v      
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_182654782_   2642 TGGATTAAAGACTTAAAT-CAAGAACCCCAAACTATGAAACCATTAAAAG 2690
                              i ?    i     -i    i iv-       i    iv   i   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAG 541

  chr2_182654782_   2691 AAAACATTGATG-AAATCCTTCAGGACATTGGAGTGGGCAAAGATTTCTT 2739
                                v i? -     -   iv   v    iv i     v i      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_182654782_   2740 GAGTA--ATATCTGACAAGCACAGGCAACTAAAGCAAAAATGGATAAATA 2787
                         iii  -- i i -- v       i     v    v      i       v
  L1M4_orf2#LINE/    591 AGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_182654782_   2788 GGATCACATCAAG-TTAAAAAGATTCTGCATAGCAGAGGAAACAATCAAC 2836
                            iiv      i-       v-  i  iiivv  i    v  v     v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_182654782_   2837 AAAGTAAAAAGACACTCCATAAAATGGCAGAAAATGTTTGCAAACTATTC 2886
                              i        vi   i i     v       i        ii  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_182654782_   2887 TTATGACAAGGGATTAATA-ACAAAA-ATATAAGGAGCTCAAACAACTCT 2934
                         v v   i      i vi  -v  i  -      i  i   vv       v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_182654782_   2935 ATAGGAAAAAAATCTAATAATCCAATTTAAAAATGGAGAAAAGATCTGAA 2984
                            iv     i - v     i      ?        iv   i   i    
  L1M4_orf2#LINE/    788 ATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_182654782_   2985 TACAGATTTATCAAAAGAAGATATATAAATGGCAAACAGGTATATGAAAA 3034
                           v v    v  v            i       v  i i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_182654782_   3035 GGCACTCAACATCATTGATCAT 3056
                          iii          ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (147 / 70)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.60 (24 / 15)  


3197 24.16 2.67 1.56  chr2_182699115_182703374.rev     2871  3768 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_182699115_   2871 TGCAAAAATATTTCATGTTCATGAATTGGAAGAACAAATATTGTTAAAAT 2920
                           v   i    ii          i         viv           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182699115_   2921 ATCCATAGTACCCAAAACAGTCTAGAAATTCAATGTAATCCCCATAAAAA 2970
                         iv v   v v      viii    v i      i i      i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_182699115_   2971 TACCAATGACACTTTTCACAGAAATAGAAAAAAAAAACT-ATCCTAAAAT 3019
                          v   iivi vi    ii       v  v  i-----  -          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAAT 145

  chr2_182699115_   3020 TTACA-GGAATCACAAAAGAGCTAGAATAGCCCAAACAATCCTGAGCAAA 3068
                          i i -    vii   ii  v i         v        i   iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_182699115_   3069 AAGAACAAAACTGGAGGAATCACATTACCTGACTTTA-----TACTACAG 3113
                                  ii       v     i v  ii i  i -----       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_182699115_   3114 AGCTATAGTAACCAAAACAGCATGATCCTAGCATAAAAACAGACACACAG 3163
                              i     i   i    ii  i v  i      ii i     i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_182699115_   3164 ACCAATGGAACAGAATTGAGAACCCAGAAACAAATCCACACACCTACAGT 3213
                          i        i          ii       i   i   i   ii  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_182699115_   3214 GAATTCATTTTTGACCAAAGTGAAAAAAACGTATAACAAGGGAAGGACAG 3263
                         v    v     i   v ii   vv  i v i vi  iii  i   i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_182699115_   3264 TCTCTTTAATAAATTAGTTCTGGAAAAACTGGATATCCATATGCAGAAGA 3313
                            i  i  i    -i  v    i v         ?   i     i    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAAT-GGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_182699115_   3314 ATAAAACTAGACCCCTATCTCTCACCATAAACAAAAATCCAATCAAAATA 3363
                           i  ii i        i   v       v        iv v       i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_182699115_   3364 GATTAAAGACTTAAATCTAAGACCTCAAATTATGAAACT---AAGAGAAA 3410
                            i ?    i     v     v  v   i   i     --- ii     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_182699115_   3411 ACATTGGGGAAACTCTCCAGGAT-TTGGTCTTAGCAAATATTTCTT-GA- 3457
                             v  ? v  v   i iv  i-    vi vi    vvi      -  -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_182699115_   3458 ATGATACCTCACAAGCACAGGCAACTAA-GCAAAAATGGACAAATAGAAT 3506
                             i   -- v       i     v  - v      i  i    v i i
  L1M4_orf2#LINE/    595 ATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_182699115_   3507 CATATCCAG-TTAGAAAGCTTCTGCACAGCAAAGGATACAACAAACAAAG 3555
                         ivi   v i-   i   -   i  ii vv       i  v iv  v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_182699115_   3556 TGAATAGACACCCCCACCGAATGGGAGAAAATATTCA-AAACTACTCATA 3604
                             v     v   -  v                 ii-   ii ivi  v
  L1M4_orf2#LINE/    692 TGAAAAGACAACCC-ACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_182699115_   3605 TGACAAAGGGATAATAACCAGAATATATAAGGAACTCAAGCAAC--AGTA 3652
                            i  i  iv vi  v             i      vvi    -- i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_182699115_   3653 -TAGGCAAACACCATAATAATCTGATTTAAAAATGGGCGAAAGATCTGAA 3701
                         -  iiv i   ----     i ii   ?          i  i   i    
  L1M4_orf2#LINE/    791 ATAAAAAGACA----AATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_182699115_   3702 TAGACATTTCT-----GAAGAGATACAAATGGCAAATAGGTATATGAAAA 3746
                                    -----     v           v    i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_182699115_   3747 GGTGCTCAAAGTCATTGATCAT 3768
                          i       vi   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (142 / 71)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.00 (38 / 19)  


3244 27.31 0.33 0.33  chr2_182715693_182721972.rev     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_182715693_   4881 TGGAAGAACATTCTATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i i   i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182715693_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_182715693_   4981 TACCAATGACTTTCTTCACAGAATTGTAAAAAACT-ACTTTAAAGTTCAT 5029
                          v   iivi i  i  ii     v - i v  i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_182715693_   5030 ATGGAGCCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5079
                              iviiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_182715693_   5080 ACGAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGCCT 5129
                           i   i      vv       v  ii i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_182715693_   5130 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5179
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_182715693_   5180 ATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATCTACAACTA 5227
                               i    i-- v  i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_182715693_   5228 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5277
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_182715693_   5278 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGACATATGTAGAAAGCTG 5327
                          v  i  i              v      v  ?v  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_182715693_   5328 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5377
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_182715693_   5378 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCGAGAAGAAAACC 5427
                         i ?    i    i  v   v       i      vi iv          v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_182715693_   5428 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAA 5477
                             ?i v viv   iv   v v  vv i     v ii   v ivvi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_182715693_   5478 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5527
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_182715693_   5528 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5577
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_182715693_   5578 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5627
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_182715693_   5628 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5677
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_182715693_   5678 AACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCT 5727
                         i     i     v  i?    i     i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_182715693_   5728 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5777
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_182715693_   5778 TCACTGGCCAG 5788
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


2483 27.21 2.56 0.93  chr2_182730137_182731960.rev      473  1332 (492)    L1M4_orf2#LINE/L1       35   908 (0)  

  chr2_182730137_    473 TTAAAATTGTGAAGA----AA-----CTTAGATTAAA--ACACATCCAAT 511
                             v     v    ----  ----- ii i   i v--   v  i   i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr2_182730137_    512 GCAATTCCTATAAAGATATCAACATCATTTTTCACAGAATTAGA-AAACA 560
                              i     v  i  vi  i vv v     ii     v v  -  i -
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC- 133

  chr2_182730137_    561 ACAACCCTAAAATTCAAATGGAACCAAAAAGGAGCCTGAAGAGC-AAAGC 609
                         -ii i           v      viiv  i   v  v   v   -   i 
  L1M4_orf2#LINE/    134 -TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_182730137_    610 AATCCTATGCAAAATGAACAAATCTGGACGTATCGCATTACAGGAATT-A 658
                             i iviv  i v       vi    v vv  i  i v vvi v  - 
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_182730137_    659 AAATTATTCTACAAGGCTATAGCTACCAAAACAACATGGTACTGGTATAA 708
                            i - v      i    i  iv i   i   iii         i    
  L1M4_orf2#LINE/    233 AAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_182730137_    709 AAGTAGACACCTAGACCAATGGAACAGAATAGAGAACCCAGAAATAAAGC 758
                         iii      iv    i        i     v    ii           v 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_182730137_    759 CAGTTACTTACAACTAAATAATCTTTGACAAAGCATACAAAAAC-ATAAA 807
                           vvi i   iiiii  v i  i  i     i -i i v  i  -  vv 
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCA 380

  chr2_182730137_    808 CTAGGGACAAGACACCCTATTCAATAAATGGTGCTAGGAAAACTGGCAAG 857
                         v i    v ii i vi  v     i          i   v      vv ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_182730137_    858 CCACATGTAGA-GAA---AACTGGGTCCCTACCTCTCACTATATATAAAA 903
                                i i -   --- ii   ii         v   i     i    
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_182730137_    904 ATCAAGTCAAGATGGATCAGAGTCTTAAATCTAAGACCTGAAGCCATAAA 953
                           i  v    i        ?  v i     v     v  i  i i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_182730137_    954 AATTCTATAAGATAACCTAGGAAAAACTCTGTAAGACATTGGCCTAGGCA 1003
                          v ii  v    v   v    ?iv  v   viiv   v    vi      
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_182730137_   1004 AAGAATTCATGACTAAGACCTCAAAAGCAAATGCAACAAAAACAAAAATA 1053
                          v iv   v iiv  v   vi        v v         iv       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_182730137_   1054 TATAAATGGGATTT-ATTTAAACCAAAAAGCTT-GTACATGGCAAAATA- 1100
                         v      v   i  -  iv   ii     vi  -  i v --    iv -
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGAC 678

  chr2_182730137_   1101 ATAATCATTGGAATAAACAGAAAACCCATGAAATGGGAGAAAATATTTGC 1150
                          iv    vvii i i  v   v      iii                   
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_182730137_   1151 AAACTATGCATCCAACAAAGGACCAATATCCAGAATCTACAAGCAACTCA 1200
                            ii  ii   ii i  i    ivi          v  i  iv     v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_182730137_   1201 AACAAATCTGCAAGAAAAAAAATAAATAATCCCATTAAAAAGTGGGCAAA 1250
                         v    v  vii  v     i -i      i  v   ?    i        
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_182730137_   1251 TGACATGAATAGGCAGCTCTCAAAAGAAGATATACCGATGGCCAATAAAT 1300
                         v  iv       i  vi    v             vi           ii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_182730137_   1301 GTATGAAGAAAATGCTCAATATCACTAATCAT 1332
                         ii     -  i        i    ????????
  L1M4_orf2#LINE/    878 ACATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (135 / 95)
Gap_init rate = 0.02 (18 / 874), avg. gap size = 1.67 (30 / 18)  


2862 26.23 2.01 0.67  chr2_182773749_182776020.rev      885  1780 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_182773749_    885 TGGAAATACATCTCATGCTCATGAATTAGAAGAATCAATATTGTGAA-AT 933
                               v i   i    i     i   i     v i        v  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182773749_    934 GGCCATACTACCCAAAGCAATCTATAGACTCAATGCAATTCCTATCAAAA 983
                            v     v      vii     i   i    i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_182773749_    984 CATCAACATCATTTTTTCACAGAA-TTAAGAAAACAATCCTTAAATTAAT 1032
                         ivi  i vv v      -i     -  i v  ivii     v     v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_182773749_   1033 A-AGAA---CAAAA-AT---GAATAGCCAAAGTAACTCTGTGTAAGATGA 1074
                          -i   ---   ii- i---           ii  iii  viv    v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_182773749_   1075 ACAAATCTGGTGGCATCACATTAGCCAACTTCAAATTATACTACAAGGCT 1124
                              vi   v  vv     i vv    i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_182773749_   1125 ATAGTAACCAAAACAGCATGGTATTGGCATAAAAGTAGATGCATAGACCA 1174
                          i     i   i    ii     i        iii    iii     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_182773749_   1175 ATAAAACAGAATAGGTAACCCAGAAATAAAACCAAA----TACAGCCAGC 1220
                           ii  i     v iv ii           v   v ----  ii i  ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_182773749_   1221 TGATCTTAAATGAAGCATACAAAAAC-ATAAAATGGGGAAAGGACACCCT 1269
                             i  vi i-   vi i v  i  -  vv           i i vi  
  L1M4_orf2#LINE/    350 TGATTTTCGAC-AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_182773749_   1270 ACTTAATAAATGGCGCTGAGAAAACTGGATAGCCACATGTAGAAGAATGA 1319
                         vi i  i      i    i  v         ?       i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_182773749_   1320 AACAGGGTCCTTCTCTCTCACCACATACAAAAATCAACTCAAATTGGATT 1369
                          iiv  ii  i vi   v     i          i        v     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_182773749_   1370 AAAGACTTACATCTAACAGTTGAAATCATAAAAATCTTAAAATAAAACCT 1419
                          ?    i  v  v   v  i i   ii      v     i  v     v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_182773749_   1420 AGGAAAAACTCTTCTGGACATTGG-CTAGGCAAAGAATTTATGACTAAGA 1468
                            ?iv  v     vv   v    -i       v iv  iv iiv  v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_182773749_   1469 CACTTAAAGCAAATGCAACAAAAACAAAAATAAATAAACGGGACCTAATT 1518
                            iv      v v         iv       i     iv    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_182773749_   1519 AAACTAAAAAGCTCCTGCACAGAAAAAGAAATAATTATCAGAGTAAACAG 1568
                            v v    i  ii  ii vvv   i  v iv  i vv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_182773749_   1569 ACAACCCACAGAATGGGAGAAAATACTTGCAAACTGTGCTTCCAACAAAG 1618
                                                  i       iii iiv  ii i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_182773749_   1619 GACTAGTAACAAGACTCTGCAAGAAATTCAAACAAATAAAATAAAAAAAA 1668
                             v   v v   v v ii  ii  i  vv    v v  -   v     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA-TAATAAAAA 797

  chr2_182773749_   1669 ACACAAATAATCCCATTAAAAATTAGGCAAATGACATGAATAGATAGCTC 1718
                         i-        i  v   ?    v i      v  iv        i vi  
  L1M4_orf2#LINE/    798 G-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_182773749_   1719 TCAATAGAAGATATACATAAATGACCAACAAACATTTTAAAA--TGTTCA 1766
                           v v            --    i    i  i  iv v    --  i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACA--AATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_182773749_   1767 ACATCACTAATAAT 1780
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.60 (24 / 15)  


2118 27.05 3.02 1.58  chr2_182798835_182800521.rev      501  1195 (492)    L1M4_orf2#LINE/L1      204   908 (0)  

  chr2_182798835_    501 AGGTGGGGAACTGATGCTACTTTAGTTTAAGACTTACTATAAAACTACAG 550
                           v   i i   v ii  v iiv v  i  i        i   i      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_182798835_    551 TAATCAAGAGAGTGTG----TGGTGAAAAAACAGACAAAGAGAACAATGG 596
                                  v      ----   iiv  ii i     v v   v      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_182798835_    597 AACAGCATAGAGAGTCCAGAAACTGACTCATGTAAATGTAGTCAACTAAT 646
                           i  v  v             ivi  i   ii vv i i     i i  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_182798835_    647 CTTTGACAAAGGAGAAAAGGGAATACAATGGAGCAAAGACAGTCTTTCCA 696
                         i  i     i  v vv   ivv  v      i v  ii i       i  
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_182798835_    697 ACAAACGGGAACTTGAACAACTGGACATCCACATGCAAAAAAATATAATA 746
                              i  vi-  v i         i ?            i   iv i -
  L1M4_orf2#LINE/    404 ACAAATGGTG-CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT- 451

  chr2_182798835_    747 ATCTAGATTCAGACACTACACTCTTCACCAAAAA--AACCCAAA-TTGAT 793
                         --- i  ii vv  vii    iv vi  -     --   i    - v   
  L1M4_orf2#LINE/    452 ---TGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAAATGGAT 497

  chr2_182798835_    794 C-CAGACTTCAATGTAAAACACACATTTATGATACTCCTAGAAAATAACA 842
                          -?    i v       i vvi v vi   i v    i     i v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_182798835_    843 TAGGAGAATACCTGGGTAGCCTTAAATATGGGGATGGCTTTTTAGGTTCA 892
                             ? v v i  vv  ii    iii vv  vi    i  i    i vii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_182798835_    893 ACACCAAAGACATAATCCATGAAAGAAAAGAAACAGGTAAGCTGTTCTTC 942
                                 ii  i  v v ii        --  i  i   ii  vv    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAA--AATAGATAAATTGGACTTC 645

  chr2_182798835_    943 ATTAAAATTAAAA-CATCTGCTCTGTGAAAAACAATGTAAAGGATGCGAA 991
                           i          - v i  iv  vii  ii   v i v   i v i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_182798835_    992 --TACAAGCCATAGACTGAGAGAAAATGTTTGCAAAAGACACACCTGATA 1039
                         --v    v   i   v  i        i        vv i i i      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_182798835_   1040 AAAGGGCTACTATCCAAAACATACAAAGGACTCTTAAAACTCAACAGTAA 1089
                          i-  i  vv      i  i   i    i       v       i i   
  L1M4_orf2#LINE/    746 AG-GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_182798835_   1090 GGAAACAAACAATCCAATT-AAGAATGGAAAAAAAAGGTCTGAACAG--- 1135
                         ii i     i  i      -  i     iv   ii -- i    i  ---
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA--TTTGAATAGACA 842

  chr2_182798835_   1136 -----CCAAGGA-GATACATAGATGGCAAGTAAGCATATGAAAAGATGTT 1179
                         -----    i  -    i i i     v i      i           i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_182798835_   1180 CAACATCATCTTTCAT 1195
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (119 / 66)
Gap_init rate = 0.02 (15 / 705), avg. gap size = 2.13 (32 / 15)  


2478 26.36 5.43 2.08  chr2_182886915_182890275.rev     1997  2861 (500)    L1M4_orf2#LINE/L1        1   894 (14)  

  chr2_182886915_   1997 TGGAGAGATAT-----GTTAATG-ACTGAAAGACTCAATATTTCTAAGAT 2040
                             i      -----   v   - i  i      i      vi      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182886915_   2041 GTCAATTCTTAC-AAATT--TTTAATAAATTTAGCATAATCTTTATCAGA 2087
                          v    v  iv -     -- i  -i i   i i ii    ii     - 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTA-CAGATTCAACGCAATCCCTATCA-A 98

  chr2_182886915_   2088 AATTGTAACAGGCTTATTTGTAGAAGTTGAAAGGCTGATTCTAAAATCTG 2137
                            ivi i v v   v    i    i    v i      i       iii
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_182886915_   2138 TATAGAAATATAAGAG-TCTAAGGCAGCTAAAACAATTTTGAAAAAGATT 2186
                            i     ii   i -i i iiii   i        i          vv
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_182886915_   2187 AAAGAAGTTGGAGGACTTACACTTCCTCCTTATGTGAGTTAGTATAAAGC 2236
                           vi             i        ivv  viivi v   v  i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_182886915_   2237 TACAGTGATCAAGGCACTGTGTTATTGGCATAGGGCATAGGGCTAGGCAA 2286
                               i      i  v    v  i       i  -    i------  v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAGA------CAT 291

  chr2_182886915_   2287 ATAGATCATTAAAATAGAGGAGTGATTTCAGAAACAGGCTCATATATATA 2336
                                 v ii      ivv v  v i      i ii i    i  v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_182886915_   2337 ATGTCATGTGATCTTT-ACAAAGGCACCAAAACAACTACATGGGGAAAGG 2385
                         vv    vv    i  i-    i  ii    i  v i vv          i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_182886915_   2386 AAAGTCTTTCCA-CAAAAGGAAATGGAACAGCAATTAGTGAATGT----A 2430
                          v       i  -    v  viv   i   i ------  i  i?---- 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAAC------TGGATAKCCACA 435

  chr2_182886915_   2431 TGGGAAGAAAAGGAAACTTGTCCCCTACCT-ACACCTTAACACAAAAACT 2479
                           vi  - i  v   ii v v         -     v  -i       i 
  L1M4_orf2#LINE/    436 TGCAAA-AGAATGAAGTTGGACCCCTACCTCACACCATA-TACAAAAATT 483

  chr2_182886915_   2480 AATTCAAAAT----TAAGGAGTTTAAGACAAAACCTAAAACTATAAAGAT 2525
                           i       ----i ?i  vi v  vii  i v             iv 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_182886915_   2526 CTTAGAGGAAAACGCAAGAGAAGATCTCTCTAATCTCGGGGGTAGGTAAA 2575
                               i      ii i ? v i    iiv i i  i   v-    i  v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAAT 582

  chr2_182886915_   2576 TATTTCTTAGAGAAGACACATAAAGCATTACCCATAAAAGAAAAAAAAAA 2625
                         vi         v v     vv      iv v v i           v i 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_182886915_   2626 TGAAGTGGAAAAAAGCAAAACTCAAAACTTCTGATCTTCCAAAGGCACTA 2675
                          i  v    vvvv v     i v       i  vv    v  i i     
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_182886915_   2676 CTAAGAAAATG------CAAACCATAGACTGAGAGAAAATATTTGTACTA 2719
                         ii      i  ------   v   i   v  i             i vvv
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_182886915_   2720 CAAATATCTGTCCAAGGACTTGTGTCCA-ATTGCATATAGAACTCCAACA 2768
                           v       viv i        i    - v ii   v       iv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_182886915_   2769 AATCAATAGTAAAAAGA-AAAT----CA----------GGCCAA----TT 2799
                          v      i        -    ----  ----------  v   ----  
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_182886915_   2800 TGAATGGATATTTTATAAAAGGAAATGTACAAGTAGGTAATACTTACATA 2849
                              i  i    iviv    i i  i     i i vi    vvi    i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_182886915_   2850 CAAGTATGTTCA 2861
                         v  iv   i   
  L1M4_orf2#LINE/    883 AAAAGATGCTCA 894

Transitions / transversions = 1.45 (133 / 92)
Gap_init rate = 0.03 (24 / 894), avg. gap size = 2.71 (65 / 24)  


1913 15.34 1.03 29.33  chr2_182900137_182908413      493  1757 (6520)  C L1M4_orf2#LINE/L1   (0)   908     2  

C chr2_182900137_   1757 GGACAGATATTTCATGTTCATAGAT----AGACTCAAAATTGTCAGGATG 1712
                            v      ii         i   ----     i  v     i i    
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

C chr2_182900137_   1711 TCAGTTCTTCGCAACTTCATCTATAGATATAATCCAATCCCAATGAAAAT 1662
                         v  i v  i v   v  v     i    vi  iv       v  v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

C chr2_182900137_   1661 ACCAGCAAGTTATTTTAT-GATTCTGACAAAGTGATTCTAAAGTTTGTAT 1613
                         v     vivi v    ii-  vvi      iv    i     i  ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

C chr2_182900137_   1612 GGAGAGGCAAAAGACTCATAATAGCTAACACAGTTTTAAAGGAGAAGCAC 1563
                            i v    ii   i  v      i  v   i i  i  ii     v  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

C chr2_182900137_   1562 AAAGTTGGAGGACTGACACTACCTAACTTTAAGACTTGCTACAAAACCAC 1513
                                       v     v  i  i  i  i    i       i i  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

C chr2_182900137_   1512 AGTAATCAAGACAGTGTAGTATTGATAAAAGGACAGACAAATAGATCAAT 1463
                                          i   i  ii v     i     v          
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

C chr2_182900137_   1462 GAAAAAGAGTAGAGAGCCCAGTAATGAACCTACAAAAAATATAGTCAACT 1413
                          i  v   i v     i    v   i    i i v vv-   i     i 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGGTCAATT 350

C chr2_182900137_   1412 GATCTTTGACAAAGGAGTAAAAGCAATACAGTGAAGCAAAAATAATCTTT 1363
                            i  i     i  v iv  ii v  v  i  ii v  i    i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

C chr2_182900137_   1362 TCAATAAATGGTGCTAACACGACTGAACATCCACATGCAAAAGCAAAAAG 1313
                             i          iiv  i    i i ?             -------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG------- 443

C chr2_182900137_   1312 CAAAGAAGAATCTAGACACAAACTGCTATGGTTTGAATGTGTTTCCCAGA 1263
                         -----------------------------------    -----------
  L1M4_orf2#LINE/    444 -----------------------------------AATG----------- 447

C chr2_182900137_   1262 ATTCATGTGTTGCAAACATAACTCCCAATGTGACAGGGTTGGAAGGTATT 1213
                         --------------------------  ---------      -------
  L1M4_orf2#LINE/    448 --------------------------AA---------GTTGGA------- 455

C chr2_182900137_   1212 GAGGTCAGGAGTGTTCTATCCTGATAAATAAATTAATGCCATTATAAAAT 1163
                         --------------------------------------------------
  L1M4_orf2#LINE/    456 -------------------------------------------------- 455

C chr2_182900137_   1162 GGGGCTTGCCAGAGAGGGTTTGCTCTCTTGCACTCTCTGCCTTTCTACTA 1113
                         --------------------------------------------------
  L1M4_orf2#LINE/    456 -------------------------------------------------- 455

C chr2_182900137_   1112 TGTGATGCTTTCCACCATTTGATGATACAGCAAGAAGGCCCTCCTGAGAT 1063
                         ---------------------------------------- i   -----
  L1M4_orf2#LINE/    456 ----------------------------------------CCCCT----- 460

C chr2_182900137_   1062 GATGGTATGTTGATCTTTGACTTTCCAGTTAAGAACTGTGATAAATAAAT 1013
                         --------------------------------------------------
  L1M4_orf2#LINE/    461 -------------------------------------------------- 460

C chr2_182900137_   1012 TTCTTTTTTTTTTTTGATAAATTACCCAGCCTCAGGTATTCTGTCACATC 963
                         -----------------------   -----------------     i 
  L1M4_orf2#LINE/    461 -----------------------ACC-----------------TCACACC 470

C chr2_182900137_    962 AGCATAAAACACACTAAGACACAGGCCTTATACCCTTTACAAAATTAACT 913
                          ---------------------------     ----- -          
  L1M4_orf2#LINE/    471 A---------------------------TATAC-----A-AAAATTAACT 487

C chr2_182900137_    912 CAAAATGGATCACAGACCTAAATTTAAAA-CAAAAATCTATAAAATTCCT 864
                                     ?          v   i - v    -        i  i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTT 536

C chr2_182900137_    863 AGAAGATTACATAGAAGAAAAATCTAGATGACCTTAGATTTGGTGATGAC 814
                               vv      i? v   -   vvi       i i  v  ii   ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGT 585

C chr2_182900137_    813 TTTTTAAATATAATATCAAAGGCACAATATATGAAATAATAAATTGATAA 764
                           i   i    i i i    i      vvv ii   v  v    v     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

C chr2_182900137_    763 GTTGGATTTCATTAAAATTAAAAA--TTTATGCTCTACCAAAGACACTAT 716
                         i     i     i           --   i    ii --  i        
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTAT 683

C chr2_182900137_    715 CAAGAGACTAAAAAGACAAGCCACAGACTGGAAGAAAATATTTGCAAA-- 668
                              i v i         v       v   i                --
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

C chr2_182900137_    667 GAACATCTGATAAAGCACTGTTATCCAAAATATACAAAGAATGCTTAAAA 618
                         iv i         i v   vv      i      i      iv    v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

C chr2_182900137_    617 CTCAACAATAAGAAAACTAACAACCTAATTTAAAAATGAACCAAAAACTT 568
                              i     i  i  v  i    i    ?       ii v  ii i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

C chr2_182900137_    567 TACCAGTCA---CTCCAGCTAGGAAGATATACAAATGGCAAATAGGCATA 521
                         v vi  v  ---     --- i                 v    i   i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCA---AAGAAGATATACAAATGGCCAATAAGCACA 880

C chr2_182900137_    520 TGAAAAGATATTCCATATCATGTCATCA 493
                                  ii  v i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (122 / 68)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 19.20 (384 / 20)  

3324 26.54 0.44 0.44  chr2_182900137_182908413     6878  7785 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_182900137_   6878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 6927
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_182900137_   6928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 6977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_182900137_   6978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 7025
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_182900137_   7026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 7075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_182900137_   7076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 7125
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_182900137_   7126 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 7175
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_182900137_   7176 AATGGAACAGAAC--ACAGCCCTCAGAAATAATGCCGCATATCTACAACT 7223
                                i    i-- v  i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_182900137_   7224 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 7273
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_182900137_   7274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 7323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_182900137_   7324 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATCAATTCAAGATGGA 7373
                            ii    i    v   i i   v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_182900137_   7374 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 7423
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_182900137_   7424 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 7473
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_182900137_   7474 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 7523
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_182900137_   7524 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 7573
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_182900137_   7574 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 7623
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_182900137_   7624 AGGGCTAATATCCAGACTCTACAATGAACTCAAACAAATTTACAAGAAAA 7673
                         i  i  vi        v v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_182900137_   7674 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 7723
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_182900137_   7724 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 7773
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_182900137_   7774 ATCACTGGCCAT 7785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2617 23.08 4.29 2.52  chr2_182996155_182997942      504  1296 (492)    L1M4_orf2#LINE/L1      102   908 (0)  

  chr2_182996155_    504 CCCA--TGTCATTTTTCACAGAAATAGGAAAA--AATCCAAAAATTCATA 549
                             --  i -     ii       v iv  i--i    v          
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_182996155_    550 TGGAACCACACACACACACACACACACACAAAAGC-AAGGCAATATTGAG 598
                              -------- ii  - viv  v  v  v   -  ii    v    i
  L1M4_orf2#LINE/    151 TGGAA--------ATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_182996155_    599 CAAAAAGAACAAATCTGAAGACAC-CATACTACCTGATTCCAAACTATAA 647
                         v  i         vi  i  i-  -  i   v  ii   i    viv  v
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_182996155_    648 TATAAATCTATAGTAATTAAAACAGCATGGGACTGGCATAAAAATAGACA 697
                           i   v   i      i  i    ii   v          ii       
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_182996155_    698 CATTTGCCAATGGAATAGAAGAAAGAACCAAGAAATGAACTCAAACATTT 747
                         i  vvii             vvi   ii v      i   i  v      
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_182996155_    748 ACAGTCAATTGATTTTTGATGAAAGTGC-AAGA--ATACAATGGGAAGAA 794
                          ii             i  ii ii    -    --  v       i -  
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AA 389

  chr2_182996155_    795 GAA-AGTCTCTTCAATAAAAAGTATTG--ACAA----------ACATGAA 831
                            -     i     i   vi  ii  --    ----------     v 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_182996155_    832 GAAAAAGAATGACATTGGATCCTTATCTCACTCTTTATA---GAATAAAC 878
                         ---         vi     i  i  i     v iv    ---i   v   
  L1M4_orf2#LINE/    440 ---AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_182996155_    879 TCAAAATGGATTAAAGACTTAAATGTATGACCCGAAACTGTGAAACTACA 928
                                    i ?    i        v  v ii     i i     ---
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT--- 533

  chr2_182996155_    929 CT-----GAAAACACAGGGGTGACACTATACAACAT-GGGTCTGGGTATT 972
                           -----       i   ?  i vv  viiii  v -    - i  i v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAAT 582

  chr2_182996155_    973 GATTTTTTAGATATGACCCCAAAAGCTCATGCAACAAAAGCAAAAGTAGA 1022
                          i   i           v        v  v          v    i    
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_182996155_   1023 TAAACGGGATTACATCAAACTAAAAAGTTTCTGCACAGCAAAGC-TACAA 1071
                             iv   i v       v v    ii  i  ii vv     v-i  v 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_182996155_   1072 TTAGCAGAGTGAAGAGAGAACCTACCAACTGGGAGAAA-TATTTACAAG- 1119
                          i iv i      i   v    i  vi v         -     i   i-
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_182996155_   1120 CATATTATCTGTTAAGTGGTTAATATGTATAATATAAAAGGAAATTAAAC 1169
                              -     v    v ii vi   vi v      v  i   v ivv  
  L1M4_orf2#LINE/    733 CATAT-ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_182996155_   1170 AACTCAATAGCAAGAAAACAAATAACCTGATTAAAACATGGGCAAGGGGC 1219
                                  ii  i  i          ii   ?   v        i  ii
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_182996155_   1220 CTGAATAGATATTTCTCAAAAGAAGACATACAAATTACCAACAGATATAT 1269
                         i        i       v        i        vi    i iii i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_182996155_   1270 GAAAAAATGCTCAACATTACTGCTATG 1296
                              i           i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (115 / 65)
Gap_init rate = 0.03 (24 / 807), avg. gap size = 2.25 (54 / 24)  


3004 21.85 3.70 5.00  chr2_183001768_183003799.rev      621  1540 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_183001768_    621 TAGAGAGATATACTATGTTTATGG-TC--AAGACTCAA---------GAT 658
                          i  i      v i     i    - i--      i  ---------   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183001768_    659 GTCAGTTCACACTAAATTGTTCTATAGGTTCAATTTCAATATAACCCCAG 708
                          v  i v v v i      v    i  i     i------ii  i   vi
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAAC------GCAATCCCTA 94

  chr2_183001768_    709 TCATAATCCCAGCAGGTTTTTTTTTTTGGTAAAACATAAAAAGTTTATTC 758
                            v         v vi      ----- i i  vv i v   i v  i 
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTT-----GCAGAAATTGACAAGCTGATCC 139

  chr2_183001768_    759 TAAAATCCATATGAAAATGCCAAGAACCTGTAATAGCCAAAATAAATTTG 808
                               i      i      v i i   iiv           i  vi   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_183001768_    809 TAAAAGAAGAACGAAGTTAGAAGACTGACACTACCCGATTTCAAGATTGA 858
                         v           i     i  i    v     v   i       i i v 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_183001768_    859 TTA-AAAGCTACAGTAATCAAGATAGTGTGGCATCACTGGTA----GATA 903
                         i  -                   i       i ---    i ----    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTA---CTGGCATAAGGATA 286

  chr2_183001768_    904 G---TAGAGA--AATGTAATAAAGT--GGAGTCCACAAATTAACCCACAT 946
                          ---  v   --    v    i i --i       v    v      i i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_183001768_    947 ATATATGGACAATCTATTTTTTACACAGAGGTACAAAGGCAATTCAGTGG 996
                           v     v    iv     iv   -  -   i v   i v     i   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACA-AG-GGTGCCAAGACCATTCAATGG 384

  chr2_183001768_    997 AGAGATAATAGCTTTTTCAACAAATGGTGCTCTCAATAATTGGATGTCTA 1046
                         i  i v     ii                  vv-i i  i     i? i 
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGG-GACAACTGGATAKCCA 433

  chr2_183001768_   1047 --TGTATAGAAATAAAAT-AAACTGCTAGGAGTATCTCACATCATATGTA 1093
                         --  i v ii   i  i -ii  iv   ------i      i     ii 
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTA------CCTCACACCATATACA 477

  chr2_183001768_   1094 AAATATTAACTCAAAATGAATTATAGGTCTAAATGTAAAGCCTAAAACTA 1143
                            -              i  i ?  ii          iiv         
  L1M4_orf2#LINE/    478 AAA-ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_183001768_   1144 TAAAACATCTAGGAGAAATTATAAGAGAAGAGCCTTGTGATCTTGAGTTA 1193
                               vii   i     vi   i ? v i v i i    i    i    
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_183001768_   1194 GGCAAATATTGTTTAGATATAACACAAAACATATAATCTACAAAATTAAA 1243
                              vvi  vi        i    v   vii i  v v      vv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_183001768_   1244 AAAACATGA--TGGACTTCATTAACTATTTAAAAACCACAAAGGTTTGCT 1291
                           v v  i --          i  -- v        i-------    iv
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAA--AATTAAAAACT-------TTTGTG 667

  chr2_183001768_   1292 CCTTGAAAGACATTGTACAGAGAATGAAAAGATG--CCATGGACAGGGA- 1338
                          i ii  i    i i vv   i i        ii--   ii  vv    -
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_183001768_   1339 AATATATTTGCAAACCATATATCTGAAAAAGGACTTACATCAAGAATATA 1388
                           v           i           v  i      ii   v        
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_183001768_   1389 TAAAGAACTCTCAAAATTCTATAAAAGGAAAAAGGATAATAAAAATAATT 1438
                                    i v  i  v    ---v      ------ v      ii
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAA---TAAAAAG------ACAAATAACC 808

  chr2_183001768_   1439 CAACT-AAAAATGGGAAAAAAATTTAAA-AGACACTTCCATCAAAGAGGA 1486
                            i -         v   ii    i  -     i   i-i      i  
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT-CCAAAGAAGA 857

  chr2_183001768_   1487 TACATGAATAGCAAGTAAGCACATGAAAAGATAACTCATAGCATCAGAAG 1536
                           i ii   i  v i                 i-    --i     ????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATG-CTCA--ACATCAZZZZ 904

  chr2_183001768_   1537 CATT 1540
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.96 (131 / 67)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.67 (80 / 30)  


3121 27.53 0.44 0.44  chr2_183024686_183026762      678  1585 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_183024686_    678 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 727
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183024686_    728 GGCCATACTGCCCTAGGTAATTTATAAGTTCAATGCTATCCCCATCAAGC 777
                            v     v   v iv i  i  i ii     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_183024686_    778 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAATGACTTTAAATTTCAT 826
                          v   -   v    i  -i     v v  v  iv   iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_183024686_    827 ATTGAACCAAAAAGGAGCCCATACAGCCAAGACAATCCTAAGCAAAAAGA 876
                           v   viiv  i   v  viv i      i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_183024686_    877 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGTT 926
                               i      vv    i  v  ii i      viv        i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_183024686_    927 ACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGATTTATAGACCA 976
                                i   i    ii        ii iv ii i   iv      i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_183024686_    977 ATGGAACAGAACAGAGGCCTCAGAAATAACGCCAACACATCTACTAACTT 1026
                               i    iv   ivii         -i  v i    i  iviv vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCAA 348

  chr2_183024686_   1027 CTGATCTTTGACAACCCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 1076
                         i    i  i     vvv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_183024686_   1077 ATTTAATAAATGGTGTTGGGAAAACTGGCTGGCCATATGCAGAAAACAGA 1126
                         v  i  i        i     v      v i?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_183024686_   1127 AACTGGATCCCTTCCTTACACCTTATACAAAAGTTAACTCAAGATGGATT 1176
                          ii    i    v   i     v         i         i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_183024686_   1177 AAAGACTTAAACGTAAGACCTTAAATCATAAAAACCCTAGAAGAAAACCT 1226
                          ?    i    i      v  v   ii      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_183024686_   1227 AGGCA-ATACCATTGAGGACATAGGCATGGGCAA-ATCTTCATGAGTAAA 1274
                            ?i- v i v i v iv v i  i- i     -ivi   v iii  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chr2_183024686_   1275 ACATCAAAAGCAATGGCGACAAAAGCCAAAATTGACAAGTGGGATATAAT 1324
                            i        vvi  i       vv     v  i  i v   iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_183024686_   1325 TAAA-TTAAAGAGCTGCTGCATAGCAAAAGAAACTATCATCAGCATGAAC 1373
                         i   -     i -  vi  iiivv    i  v       vv ivi    v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_183024686_   1374 AGGCAACCTATAGAATGGGAGAAAATTTTTGCAATTTATCCACCTGACAA 1423
                           i     i i               v       v i  vi i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_183024686_   1424 TGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 1473
                         v  i  vi          v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_183024686_   1474 AAATAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTA 1523
                          i i   i     v  i?    i            v    i     i  v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_183024686_   1524 TCAAAAGTAGACATTTATCTGGCCAACAAACATATGAAAAAAAGCTCATC 1573
                           v    v   i  vi vv       i  i  i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_183024686_   1574 ATCACTGGTCAT 1585
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.00 (8 / 8)  


1286 23.97 2.05 2.28  chr2_183172568_183177909     2014  2451 (2891)    L1M4_orf2#LINE/L1      472   908 (0)  

  chr2_183172568_   2014 TATATAAAAATCAACTCAAGATGGATTACAGACATAAATGTAAAACCCAA 2063
                             i      i       i      i ?    v         i v i  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_183172568_   2064 AACTATAAAAACTCT-GGAAGATAATCTAGGCA-ATACCATCCTGGATAC 2111
                                   -    -i     v  iv    ?i- v i v  v  - ivi
  L1M4_orf2#LINE/    522 AACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCT 569

  chr2_183172568_   2112 AGGAACAGGCGAAGACTTCAT-GATAAAGATACCAAAAGCAATCGCAACA 2160
                         v  ivi    i v ii   v -    v-  i          vvv      
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAACA 618

  chr2_183172568_   2161 AAACAAAAATT-GACAAGTGGGATCTAATTAAATTGAAAAGCTTCTTCAC 2209
                            v     v -  i  i v   ii v  i   v v    i   i vii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_183172568_   2210 AGCCAAAGGA-ACTATTGACAGAGTAAACAGACAACCTAGAAAATGGAAG 2258
                         -vi       -     ii v i   i  v        i v i     i  
  L1M4_orf2#LINE/    669 -TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_183172568_   2259 AAAATATTTGCAAACTATGCATCTGACAAAGGACTAACATCCAGCTTCTA 2308
                                       ii  ii      i  i     vii      vv v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_183172568_   2309 TAAGGAACT--TA-AACT-AATTTGCAGGAGAAAAACAAACAACCCCATT 2354
                            i     --  -    -   ---- iv i   i     i     v   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAAT----AATAAAAAGACAAATAACCCAATT 813

  chr2_183172568_   2355 AAAAAGTGGGCAAAAGACATGAACAAATACTTTTCAAAAGAAGACATACA 2404
                         ?    i        i  iv    i i i i  i  v        i     
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_183172568_   2405 TGCAGCCAACAAGCATGTGAAAAAAAAAGCTCAAAATCACTGATTAT 2451
                         viii     i     ii      i v--      v    ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (64 / 38)
Gap_init rate = 0.03 (14 / 437), avg. gap size = 1.36 (19 / 14)  

3534 20.90 4.71 0.46  chr2_183172568_183177909     3980  4850 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_183172568_   3980 TAGATGGACATTATATGTTTATG-AT--GAAGACTTAATATTGGTTAACA 4026
                          i  vi  i  ivi     i   -  --               -    v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTG-TTAAGA 49

  chr2_183172568_   4027 AGAAAAT--TCCCAAGAATTGATCTACAGAAACAATAATATTTCTATCAA 4074
                         v iv   --    v -              vv   iivv  ii       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCA-AATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_183172568_   4075 AACCCCACCAGGCTTTTTTTGTAGAAGTTGGAAATATGCTTCTAAACTTG 4124
                           i    v -v  i       i    i   iv  vv  v i     v  v
  L1M4_orf2#LINE/     99 AATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_183172568_   4125 AGAGGGAATTATAAAGGATCTAGAATAGCCAGAACAATTTTTTAAAAGAA 4174
                          v v    v ii  i   i i          i      i  vv       
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_183172568_   4175 ---CAAAGTTGGAGGATTTACACTTTGAAGTTACAAA-CTTACTATAAAG 4220
                         ---             i i      ivv i  v    -       i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_183172568_   4221 CTACAGTAATCAAGACAGT-TGGTACTAGCATAA--ATTGACATATAGAC 4267
                                            -       i      --  v          i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_183172568_   4268 AAACAGAACAGAATTGAAAGACCAGAAATAAATCCTTAGATTTTTGATCA 4317
                         v  ii   i        i  v           i  v  v    v  i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_183172568_   4318 ATTCATTTTTAACAAAGCT------ACCATT----GGGAAATGGATGATC 4357
                            v     ii    i v ------      ----   i  v i  ii  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_183172568_   4358 TTTTCAACAAATGTTTCCAGGTCAATTAGATATCCATATGCAAAAATATG 4407
                                      v v ii  v   i i    ?   i        iv   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_183172568_   4408 ACTTTCGGCCCTTACCTCAAACCATACACAAAGATTAACTCAAATAGGAT 4457
                          vv  v i   i       v      i     i           vv    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_183172568_   4458 TATAGACCTAGATGTAAGAGCTAATATTACAAAGACTTCTAGTAGAAAAC 4507
                         i ?       i             v i  i   -   ii   v       
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chr2_183172568_   4508 A--GGAGAGAATTTTTGTGACCTTAGATTAGGCAAAGATT--------AA 4547
                          --  ? vi   i  i        i i        v i  -------- v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_183172568_   4548 GACACTAAAAGCATAATC--CATAAGGGAAAAT-GATAAATTTGACTTCA 4594
                              i       i  v --  v   ii     -        v       
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_183172568_   4595 TTAAAATTAAAAACCTTTATTCTTCAAAAGATGCCATTAAGAAAATGAAG 4644
                          i            i   i v       i  ii i  i      i    i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_183172568_   4645 -GACAAGTAATAAACTGAGAAAAAATATTTGTAAATCATCTATTGGACAA 4693
                         -     viv i i v  i  i          i       v   iv  i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_183172568_   4694 AGCACTTGTGACCAGAATTGATAAAGGACTCTTAAAACTCAA-AATATG- 4741
                         i v      iv       vv      i       v       -    vi-
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_183172568_   4742 -GATT--TAATTCATCTTAAAAATTGGCAAAAGAATTGAATAGATATTCT 4788
                         -  iv--   ii  vi ?      v      i  v         i   ii
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_183172568_   4789 ATCAAAGAGGCTATACAAAGGACAAATAAGCACATGAAAAGATGTTCACC 4838
                         vi      i v        v i v                    i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_183172568_   4839 ATCATCGGTCAT 4850
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (104 / 74)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.14 (45 / 21)  


3085 26.59 1.67 0.67  chr2_183250548_183253955.rev     2018  2916 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_183250548_   2018 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2067
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183250548_   2068 GGCCATACTGCCCAAGGTAATTTATAGATTCAATAGCATTCCC-ATCAAG 2116
                            v     v     iv i  i  i        i-   v    -     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAAC-GCAATCCCTATCAAA 99

  chr2_183250548_   2117 CTACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 2163
                         v v   i-       i  -i     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chr2_183250548_   2164 CATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAA 2213
                                  viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_183250548_   2214 AGAACAAAGCTGGAGGCATCATGCTGCCTGACTTCAAACTATACTACCAG 2263
                                  i      vv   ii  v  ii i      viv      v i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_183250548_   2264 ACTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 2313
                         i         i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_183250548_   2314 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCTCATATCTACAA 2361
                                  i    i--    i  --        vv  vi i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_183250548_   2362 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 2411
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_183250548_   2412 CCCTATTTAATAAATGGTGCTGGGAAGACTGGCTACCCATATGTGGAAAG 2461
                         vi  v  i  i              vi     v  ?   i   iii  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_183250548_   2462 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 2511
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_183250548_   2512 GAT-AAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAA 2560
                            - ?    i    ii v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_183250548_   2561 ACCTAGGCATTACCATTCAGGACATAGGCTTGGGCAAGGACTTCATGTCT 2610
                           v    ?i v viv   iv   v v  v  i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_183250548_   2611 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 2660
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_183250548_   2661 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 2710
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_183250548_   2711 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCAACTCATCTGAC 2760
                          v  i     i   i             v  i    viv ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_183250548_   2761 CAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 2810
                         v i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_183250548_   2811 AAA-----ACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACT 2855
                            ----- i     v  i?    i    ii     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_183250548_   2856 TCTC---AGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 2902
                             ---      i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_183250548_   2903 CCATCACTGGCCAT 2916
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


3075 26.64 1.55 0.78  chr2_183376288_183382668     4989  5889 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_183376288_   4989 TGGAAGAACATTCCATGCTCATGGGTAGGAAGACTCAATATTGTGAAAAT 5038
                              ii i  i     i      i v        i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183376288_   5039 GGCCATACAGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5088
                            v    vv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_183376288_   5089 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5136
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_183376288_   5137 TATGGGACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5186
                              i viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_183376288_   5187 AACAAAGCTGGACGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5236
                                i    v vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_183376288_   5237 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGACC 5286
                                 i   i    iii        i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_183376288_   5287 AATGGAACAGAAC--AAAGCCCTCAGAAATAATACCACACATCTACAACC 5334
                                i    i-- i  i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_183376288_   5335 GTCTGATCTTTGACAAACCTGACAAAAACAAGAAATAGGGAAAG--TATT 5382
                         ivi    i  i     ivv  v   i v  vvv   i       --  v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_183376288_   5383 CTCTAGTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5432
                           i -- i                 v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_183376288_   5433 CTGAAACTGGATCCCTTCCTTGCACCTTATACAAAAATTAATTAAAGATG 5482
                         v    ii    i    v   ii    v              i v  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_183376288_   5483 GATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5532
                            i ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_183376288_   5533 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5581
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_183376288_   5582 TAAAACACCAAAAGCAATGGCAACAAAAGCCATAATTGACAAATGGGATC 5631
                           vi            vvi          vv v   v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_183376288_   5632 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTA 5681
                          v  i   v v  i i   i  ii vv    i  v    i  vv i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_183376288_   5682 GACAGGCAACCTACAGAATGGGAGAAAATTTTTACAAACTACTCATGTGA 5731
                         i v  i     i                 v   i    ii ivi  v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_183376288_   5732 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAA----ATTACA 5777
                         i  i  i  vi          v  i         vv    ----  v i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_183376288_   5778 AGAAAAAAAA-AACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 5826
                          i  i v   -     v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_183376288_   5827 TTCTCAAAAGAAGACATTTATGTAACCAACAGACAC--GAAAAAATGCTC 5874
                              v        i  vi vi ii    i ii   --     i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_183376288_   5875 ATCATCACTGGCAAT 5889
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


1899 17.69 5.19 3.07  chr2_183383157_183385100.rev      498   921 (1023)    L1M4_orf2#LINE/L1      256   688 (220)  

  chr2_183383157_    498 ATCAAGACTCTGCAGTACTGGCA-AA--ACAGACATATGTATCAATATAT 544
                                 vv  ii         -  -- i        iv      iv -
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA- 304

  chr2_183383157_    545 CTCAATAGAACTAAGAGCCCAGAAACAAACCCATACATTTGTGGTCAATT 594
                         ----      i i    i       i              i         
  L1M4_orf2#LINE/    305 ----ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_183383157_    595 GATTTTCAACAAAGAAGCCAAAACAATTTAGTGGG-AAAGAA--GTGTTT 641
                                i    i iv     i  v   i i    -      --  v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_183383157_    642 TCAACAAATGGTGCTAGGACACCTGGATATCCACATGGTAAAGAATGAAT 691
                                        i     v       ?       vv          v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_183383157_    692 TTGGGTCTCTAT-TCACACCACATACAAAAATTAAGTCAGAATGAATCAA 740
                             ii i   i-        i             v   i    i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_183383157_    741 CGACATAAATATA-----T----CTAT------CTAAGAAGAAAATATAG 775
                         v   v     i  ----- ----    ------  v         i    
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_183383157_    776 GTGCAAATCTTCATGATTTTGGATTAGGCAATGGTCTCTTAGATATTTAG 825
                          ? i        i   ii    i            i          ----
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT---- 596

  chr2_183383157_    826 ATATAATACCAAAGATAGAAACAACCAAAGAAGAAATAAATAAAACAGGC 875
                         ----i i      iii v  i    v      i     i     vii i 
  L1M4_orf2#LINE/    597 ----GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_183383157_    876 TTCATCAGAATTAAACAGCTTTGTTTTTATAAAAACACTGTCAAGA 921
                                i       v vi     vi  vv  ii     i      
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

Transitions / transversions = 2.13 (49 / 23)
Gap_init rate = 0.02 (10 / 433), avg. gap size = 3.50 (35 / 10)  

 870 18.67 6.67 1.33  chr2_183383157_183385100.rev     1228  1452 (492)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr2_183383157_   1228 AAAGAACACTATCAAGAAAGTGACCAGACAACACACCGAAAAGAAAAAAA 1277
                             i                  vv       v   v   vi i i    
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_183383157_   1278 TACTTGAAAAACATATGTCTGATAAGGGTCTAGTGTCCAGAATATATTTA 1327
                           i   v   v     i           v  v  i            v- 
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA-A 770

  chr2_183383157_   1328 AAAACCCTTATAATTCAACATCAAC----CAAGTAACCCAATTGTTAAAA 1373
                          i   i    i  i    i vi  v----   i          --?    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT--WAAAA 818

  chr2_183383157_   1374 ATGGCCAAAG-----------ACATTTATGCAAAGAAGTTATGCAAATGA 1412
                             v     -----------      v v        v   i      i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_183383157_   1413 CCTGCAAGCACATAAAAGGCTGCTGCACATTATTAGCTGC 1452
                           vii        i   i v    vv    i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.05 (21 / 20)
Gap_init rate = 0.02 (4 / 237), avg. gap size = 4.50 (18 / 4)  


3136 26.66 1.00 0.55  chr2_183436218_183439512.rev     1900  2803 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_183436218_   1900 TGGAAGAACATTCCATGCTCATGGGTAGGAAGACTCAATATTGTGACAAT 1949
                              ii i  i     i      i v        i        v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183436218_   1950 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1999
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_183436218_   2000 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2046
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_183436218_   2047 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 2096
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_183436218_   2097 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 2146
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_183436218_   2147 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 2196
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_183436218_   2197 CAATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATATACAAC 2244
                                 i    i-- v  i  --        vv  ii i  v  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_183436218_   2245 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 2294
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_183436218_   2295 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2344
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_183436218_   2345 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 2394
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_183436218_   2395 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2444
                           i ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_183436218_   2445 CCTAGGCATTACCATTCAGGACACAGGCATGGGAAAGGACTTCATGTCTA 2494
                          v    ?i v viv   iv   viv  vv i  v  v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_183436218_   2495 AAACAACAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2544
                         vi   v        vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_183436218_   2545 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAGTACCATCAGAGTGAA 2594
                           i   v v  i i   i  ii vv    i  v v  i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_183436218_   2595 CAGGCAACCTAAAGAATGGCAGAAAATTTTCGCAACCTACTCATCTGAGA 2644
                         v  i     i v       v       v  i    vii ivi      v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_183436218_   2645 AAGGGCTAATATGCAGAATCTACAATGAACTCACACAAATTTACAAGAAA 2694
                          i  i  vi   v      v  i  v      vi    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_183436218_   2695 AAAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 2740
                           i    ----   v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_183436218_   2741 CTCAAAAGAAGACATTTATGCAGCCAAAAAACAAATGAAAAAATGCTCAC 2790
                            v        i  vi viii     v  i  v       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_183436218_   2791 CATCACTGGCCAT 2803
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (134 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3306 25.11 1.90 0.56  chr2_183459310_183465725.rev     5029  5924 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_183459310_   5029 TGGAAGAATATTCCATGCTAATGGATAGGAAGAATCAATAATGTGAAAAT 5078
                              ii    i     i v      v      v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183459310_   5079 GGCCATACTGCCCAAAGTAATTTATAGATTCAATTCCATCCCCATCAAGC 5128
                            v     v      v i  i  i        iv v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_183459310_   5129 TACCAATGACTTTCCTTACAGAA-TTGAAAAAAACT-ACTTTAAATTTCA 5176
                          v   iivi i  ii  i     -    v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_183459310_   5177 TATGGAACCAAAAAAGAGCCCGTATTGCCAAGACAATCCTAAGCAAAAAG 5226
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_183459310_   5227 AACAAAGGTGGAGGCATCACAGTACCTTTCTTCAAACTATACTACAAGGC 5276
                                v      vv     v v  ivvi      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_183459310_   5277 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5326
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_183459310_   5327 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 5374
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_183459310_   5375 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGA-----TACC 5419
                          vi    i  i     ivv  v   i v  vv         -----  vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_183459310_   5420 CTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGTAGAAAGGT 5469
                           v  i  i           i  v      v  ?   i   i i  iii 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_183459310_   5470 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5519
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_183459310_   5520 TTAAAGACCTAAACGTAAGATCTAAAACCATAAAAACCCTAGAAGAAAAC 5569
                          i ?         i      v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_183459310_   5570 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACGA 5618
                         v    ?i- v i -   iv   v v  vv i     v ii   v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_183459310_   5619 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 5668
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_183459310_   5669 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5718
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_183459310_   5719 AGG-CAACCTACAGAATGGGAGAAAATGTTGGCAATCTACCCATCTGACA 5767
                          i -     i                 i  v    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_183459310_   5768 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAATAAA 5817
                          i  i  vi          v  i         vv    v iv i      
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_183459310_   5818 AAAA-----AACCCA-TCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5861
                           i -----      - i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_183459310_   5862 CTCAAAAGAAGACATCTATGCAGCCAACAGATGCATGAAAAAATGCTCAT 5911
                            v        i  vi viii     i iiii        i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_183459310_   5912 CATCACTGGTCAT 5924
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


2480 27.32 0.14 0.14  chr2_183563710_183570610      752  1450 (5451)    L1M4_orf2#LINE/L1      210   908 (0)  

  chr2_183563710_    752 AGGCATCATGCTACCGGACTTCAAACTATACTACAAGACTACAGTAACCA 801
                            vv   ii  v  vi i      viv        ii         i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_183563710_    802 AAACAGCATGGTACTGGTACCAAAACAGAGATATACACCAATGGAACAGA 851
                          i    ii         i iv ii i   v     v i        i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_183563710_    852 ACGGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCTGATCTTTGA 901
                          iv   vvii         vv  ii i  i  iiiii vi    i  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_183563710_    902 CAAACTTGACAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAAT 951
                            ivv  v   i v  vv            i  vvi  v  i  i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_183563710_    952 GGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCC 1001
                                   v      v  ?   i   i i  iiv    ii    i   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_183563710_   1002 TTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAA 1051
                          v   i     v              i    i      i ?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_183563710_   1052 CATTAAACCTAAAACCATAAAAATCCTAGAAGAAAACCTAGGCA-ATACC 1100
                         ii v i v       i      v  i           v    ?i- v i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_183563710_   1101 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGC 1150
                         -   iv   v v  vv i     v ii   v ivv  vi           
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_183563710_   1151 AATGGCAATAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTGAAGA 1200
                          vvi    i     vv     v  i    v   ii v  i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_183563710_   1201 GCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACA 1250
                         i   i  ii vv    i  v    i  vv i      v  i     i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_183563710_   1251 AAATGGGAGAAAATTTTCGCAACCTACTTATCTGACAAAGGGCTAATATC 1300
                         i             v  i    vii iv       i  i  i  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_183563710_   1301 CAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACC 1350
                               v  i  v      vv    v iv i  v     i     i    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_183563710_   1351 CCATCAAAAAGTGGGTGAAGTATATGAACAGACACTTCTCAAAAGAAGAC 1400
                          v  i?    i    ii   v  v    i     i     v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_183563710_   1401 ATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATGATCACTGGCCAT 1450
                           vi viii     v  i          i       vv    ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (108 / 79)
Gap_init rate = 0.00 (2 / 699), avg. gap size = 1.00 (2 / 2)  

3178 26.92 1.33 0.33  chr2_183563710_183570610     5511  6409 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_183563710_   5511 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5560
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183563710_   5561 GGCCATACTGCCCAAACGAATTTATAGATTCAGTGCTATCCCCATCAAGC 5610
                            v     v      ivi  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_183563710_   5611 TACCA-CTGACTTTCTTCACAGAATTAGAAAAACT-ACTTTAAATTTCAT 5658
                          v   -   v    i  -i     v v  v  i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_183563710_   5659 ATGGAACCAAAAAAGAGCCCATATAGCCAAGATAACCCTAAGCAAAAAGA 5708
                               viiv  ii  v  viv        i i  i i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_183563710_   5709 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTATAAGGCT 5758
                               i      vv   ii  v  ii i      vivi    i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_183563710_   5759 CCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5808
                         v      i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_183563710_   5809 ATGGAACAGAA--AAGAGGCCTCAGAAATAACGCCACACATCTACAACCG 5856
                               i    --i    v  --        vv   i    i  iiii i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_183563710_   5857 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5906
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_183563710_   5907 TATTTAATAAATGATGTTGGGAAAACTGGCTAGCTACATGCAGAAAACTG 5956
                          v  i  i     i  i     v      v  ? i       i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_183563710_   5957 GAACTGGACCCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGGAT 6006
                         i ii         v   i     v  i                i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_183563710_   6007 TAAAGACTTAAACCTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 6056
                         i ?    i    iv     v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_183563710_   6057 TAGGCATTACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 6106
                             ?i v viv   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_183563710_   6107 ACACGAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTGAT 6156
                             v       vvi      i   vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_183563710_   6157 TAAACTAAAGAACTTCTGCAGAGCAAAAGAAACTATCAG---AGCGAACA 6203
                         i   v v  i     i  iivvv    i  v       i---  i   v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_183563710_   6204 AGCAACCTACAGAATGGGAGAAAATTTTTCCAATCTATCCATCTGACAAA 6253
                         ii     i                 v   v   vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_183563710_   6254 GAGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 6303
                          ii  vi          v  i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_183563710_   6304 AA-----AACTCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCT 6348
                         i -----   i v  i?    i     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_183563710_   6349 CAAAAGAAGACATTTATGTGGCCAGCAAACATATGAAGAAAAGCTCATCA 6398
                          v        i  vi vi      ii  i  i     i i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_183563710_   6399 TCACTAGTCAT 6409
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.14 (15 / 7)  


 215 13.33 23.33 5.00  chr2_183574114_183576054.rev      501   560 (1381)    L1M4_orf2#LINE/L1      286   356 (552)  

  chr2_183574114_    501 AGATATCTAGGGAATTAATGGAATGGAATTGAAAGTCCAAAAATA----- 545
                            i  v   ---  i        i       i      i     -----
  L1M4_orf2#LINE/    286 AGACATATAG---ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_183574114_    546 ---------TGTTCAACTGATTTT 560
                         ---------  v    i       
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.03 (2 / 71), avg. gap size = 8.50 (17 / 2)  

2482 16.09 3.61 8.37  chr2_183574114_183576054.rev      841  1449 (492)    L1M4_orf2#LINE/L1      329   908 (0)  

  chr2_183574114_    841 ATCCAC-CATTCCTGGCCTGTAAACTGATTTTTGACAATGGTGCCAAGAC 889
                          i   i-    iv   i ----  i       i     v           
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTC----AATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_183574114_    890 AATGAAATAAGGGAAACAATA----TTTGAACAAGTAAGTGCTGAGACAA 935
                         v  vv   i-      v    ----   v     i i-      i     
  L1M4_orf2#LINE/    375 CATTCAATG-GGGAAAGAATAGTCTTTTCAACAAATG-GTGCTGGGACAA 422

  chr2_183574114_    936 CAAGATAGTAGCATGTAAAAGAATGAAGTGGAATCACTTCCGTACATCAT 985
                          vi    ?ivi    i             v i i v  v  vi   i   
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_183574114_    986 GCATAAAAACTCACCCAGAACGGATTATAGACCTAAAGATAAGAGCTGAA 1035
                         ii i     i v  i  i  i    i ?         vi        i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_183574114_   1036 ACTATTAAGAATTCTTAGAAGAAAACAAAGGAGCCAATCTTTGTGACCTT 1085
                              -- i  i               v   ? iv      i        
  L1M4_orf2#LINE/    523 ACTAT--AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_183574114_   1086 GG------------CTTCTTAGATATGACACTAAAAGCACAAGAGACAAA 1123
                           ------------i                i           vi     
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_183574114_   1124 AGAAAAAA--GATAAATTGAACTTCATCCATATTAAAAACTTTTGTGCTT 1171
                                 --         i        v v                   
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_183574114_   1172 CAAAAGATACCATTAATAAAATGAAAAGACAATCCATAAAATGATAAAAT 1221
                             i  i  i  i  v   i           i   i i    iv i  v
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_183574114_   1222 ATATTTTCTAATCATATATCTAATAAGGGACTTGTATGTGGAATATATAA 1271
                               v v            i               vii          
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_183574114_   1272 AGAACTCTTAAAACTCAAAAACAA---GACAAGTAACTCAATTAAAAAGT 1318
                                   v       v  i  ---     i    i     ?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_183574114_   1319 GGCAAAGGTATTAGCAATAACACAGACCAAAAAGAAAAAAAAGTGGCAAA 1368
                           -------------------------------------------     
  L1M4_orf2#LINE/    821 GG-------------------------------------------GCAAA 827

  chr2_183574114_   1369 GGATTTGAATAGCAATTTCCCCAAGGAAGTTGTACAAATAGCCAATGAGC 1418
                                     vv     i    i    v i       i      i   
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_183574114_   1419 ATTTGAAAAGATATTCAACGTCATCAGTCAT 1449
                          iv         ii     i   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (62 / 32)
Gap_init rate = 0.02 (10 / 580), avg. gap size = 7.30 (73 / 10)  


3074 23.19 1.06 4.79  chr2_183659261_183663045     2388  3327 (458)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_183659261_   2388 AAAGATATCTCATGTTCATGAATTGGAAGAATTGATATTGCTAAA----C 2433
                                  i          i         v  i      i   i---- 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_183659261_   2434 A-TACCACCCAAAGTGATCTACAGATTCAATAAACTATCTATCTAAATAC 2482
                          -   iv      v                iiv v vi     v    v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_183659261_   2483 CAATGACATTCTTTACAGAAACAGAAAAAATAAATCCTAAAATTCATATG 2532
                           iivi v  i   i      iv  v  iv i -                
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATATG 152

  chr2_183659261_   2533 GAACAAACAACAACAAAAAAAAAACTAGAAGAGCCAAATCAATCCTGAAA 2582
                            - vi   ---------iii v i    v       v     i     
  L1M4_orf2#LINE/    153 GAA-ATGCAA---------GGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_183659261_   2583 AGTACAATCCAAAAAGTACAAAGCAGGAGGAATCACA-TTACTGATCGCA 2631
                          ---------- i   v      iv      v     -  v ii  iv  
  L1M4_orf2#LINE/    193 A----------AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr2_183659261_   2632 AAATCTACTACAAAGCTATAGTAATCAAAACAGTATGGTGTTGGCATAAA 2681
                            ii             i         i     i    ii        i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_183659261_   2682 AGCAGATACAAATATCAATGAAACGGAACACAGAACCCAGAAATAAATCC 2731
                         iii   i i v v       i  ii   ivv   ii           i  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chr2_183659261_   2732 ACACATTTACTATTAGCTCATTTCCAACAAAAGTGCCAAGAATATACATT 2781
                          i       ivi i ii v    i i    ii         vi  v  v 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_183659261_   2782 GGGGAAAGGACAGTCTCTTCAATAAATTGTGCTGAGAAAACTGGATATCC 2831
                                 i i     i     i    v      i  v         ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_183659261_   2832 ACATGTAAAGGAATGAAACTAGACCTCTATCTCTCATCATACAAAAAAAA 2881
                              i   i       ii i    i   i   v  i    i v     -
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA- 481

  chr2_183659261_   2882 TCAAATCAAAATGAATTAAAGACTTAAATGTAAGACCTGAAACTATGACA 2931
                          i  v        i  i ?    i           v  i       i v 
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_183659261_   2932 CTACTAGAAGAAAACACTGGTG-AAACATGCCAGAATATTGGTCTGGTCA 2980
                           vi            iv  ? -   iv -i ivi iv    vi i v  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCA 580

  chr2_183659261_   2981 AAGATTTCTTGAGTTA-GACCTCAAAAGCCACAGTGAACAAAAGCAAAAA 3029
                          v i      -  v  -   vi       -   ivv        --    
  L1M4_orf2#LINE/    581 ATGGTTTCTT-AGATATGACACCAAAAGC-ACAAGCAACAAAAG--AAAA 626

  chr2_183659261_   3030 AATGGATAAATAGGATCACATTAAGCTAAAAAGCTCCTGCACAACAAAGA 3079
                            i       v   iiv   i  iv v    i  ii  ii vv     -
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG- 675

  chr2_183659261_   3080 AGGAAACAATCAGCACAGTGAAGAGACAACCTATAGAATGAGAGAAAATA 3129
                         --  v  v    iv v      i        i i      i         
  L1M4_orf2#LINE/    676 --GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_183659261_   3130 TCTACGAACTATTCAACAGACAAGGCATTAACAATCAGAATATATAAGGA 3179
                          i i i  ii  vi v v  i    v i vii vi            i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_183659261_   3180 ACTCAAACAGCTTAATAGCAAAAAAAAAAAAAAAAAAAAACAAAACTGAT 3229
                             vv   i  i    ii     i v   v  ------------ iv v
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAA------------CCCAA 811

  chr2_183659261_   3230 TTTAAAAATGGGCAAAAGAGCTAAACAGACATTTCTCAAAAGAAGACATA 3279
                           ?             i  vi i  i           v        i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_183659261_   3280 CAGGTGGCCAACAGATATATTTTTAAAC--TGCTCCCCATCAGAGAAATG 3327
                           ii       i iii i  v---   v--     vv     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATG---AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (136 / 78)
Gap_init rate = 0.02 (18 / 905), avg. gap size = 3.06 (55 / 18)  


1589 25.57 4.55 4.17  chr2_183799477_183803516     2338  2865 (1175)    L1M4_orf2#LINE/L1       16   545 (363)  

  chr2_183799477_   2338 TGTTAATGTATTGAAAAATTAAGTGTAGTAAAGGTATCAATTTACCTCAA 2387
                             v   v    i  i i v i i v  v   i iv    viv  i   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_183799477_   2388 ATTGATACACAGCTTTAATCAAATTCCTATGAAAACCTCAGCAAGACTTT 2437
                               vi    v  i  ivv   i     v    i i    vivvi   
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_183799477_   2438 TTACAGATACAGACAAGATTATTCTAAAATGTATACGGAAAGGCAAGAAA 2487
                           i    v iv      v v  i       vi   i     v     ii 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_183799477_   2488 CA-AAAATAGCTACAACAATTTTGAAAAAGAAGAATAAAGT-----AAT- 2530
                          v- i      i v      i              i     -----i i-
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_183799477_   2531 --------CTGGTTTCAAGACTGGTTATATAGCTACAGTAAACAGGACTG 2572
                         -------- iii      i   vii  i v           v  i   v 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_183799477_   2573 TGTAGTATTGGCAAAGAGACAGACACTTAAATCAATGGAACAGAACAAAA 2622
                            i   i     v ii  i     iv  i          i    ivi i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_183799477_   2623 AAATCCAGAAGTAGACCCATATAAATATGTTCAAGTGATCTTTGACAAAG 2672
                          i-       i  i       i vv    v    v    i  i     i 
  L1M4_orf2#LINE/    316 AG-TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_183799477_   2673 GTGCAAAAGCAATTCAATGAAGGAAAGGTAGCCTTTTTAACAAATGATGC 2722
                             v  ii v        ii i  iii   i     i        i   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_183799477_   2723 TGGAGCAATTGGACATCTGTATTTCCATAGGCCAAAAAAAAAAAAAAAGA 2772
                            ii   i    i ? --------  i v  --------    i  v  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKC--------CACATGC--------AAAAGAATGA 448

  chr2_183799477_   2773 AA--GAAATTCTATGTAATCCCATACCTTCAACAAAAATTAACCAAAAAT 2820
                          i-- i vii   iv v iv     i-----            iv     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATAT-----ACAAAAATTAACTCAAAAT 493

  chr2_183799477_   2821 GGAGTATAGACTTAAAAGGAAAA-CTAAAAC------ACTTTTAGGAGAA 2863
                            vi ?    i    v v  i -       ------   i    i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_183799477_   2864 AA 2865
                           
  L1M4_orf2#LINE/    544 AA 545

Transitions / transversions = 1.83 (86 / 47)
Gap_init rate = 0.02 (10 / 530), avg. gap size = 4.60 (46 / 10)  

1075 23.47 4.53 5.33  chr2_183799477_183803516     3174  3548 (492)    L1M4_orf2#LINE/L1      537   908 (0)  

  chr2_183799477_   3174 AAAAAAAAAAAGAAGGA-AAATCACTGGGTTCCAGGGCTAGTCAAAATG- 3221
                          i  i    v v i ?i-     vii v vi iv   i   v   --  -
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA--TGG 584

  chr2_183799477_   3222 -TCCTTAGACTTGACACCAAACTTGTGACCCACAAAAGCAAAAATTTATA 3270
                         - i      iv          vviiii v v       -     ---   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAA---ATA 630

  chr2_183799477_   3271 AATTGGAAATTTATAAATTGGACCTCATCAAAATTAAAAACTTTGCTATT 3320
                         i  -----------         i                    vv ii 
  L1M4_orf2#LINE/    631 GAT-----------AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_183799477_   3321 T-GAAGGACCTTGTTAAGAAGATGAAAA-------------ATGGAAGAA 3356
                          -i      vi i i     ii      -------------    i    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_183799477_   3357 CATATTTGCAAACCGTGTATTTGACAAAAGATTAGCATCTAGAATATATT 3406
                         v           i i i   i   i  ii  i v i   i         -
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT- 768

  chr2_183799477_   3407 TAAAAAATTCTCAAAATTCAACAGTCAGAAAAAAAATCAACCCAATTAGG 3456
                         -   i  i   i v  i    i i v i  i v    -         ?ii
  L1M4_orf2#LINE/    769 -AAAGAACTCTTACAACTCAATAATAAAAAGACAAAT-AACCCAATTWAA 816

  chr2_183799477_   3457 AAATGGACAAAATGTATGAAGAGACACTTTACTGAAGAGGATATACAGAT 3506
                               i    ivi v    v     i  iv ii    i        i  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_183799477_   3507 GACAAATAAGCACATAATAAAATGTTCGACATCATAGCTACT 3548
                          i v           i v  i   i  i      ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (60 / 26)
Gap_init rate = 0.03 (10 / 372), avg. gap size = 3.70 (37 / 10)  


2462 25.95 8.41 0.83  chr2_183836719_183838751.rev      697  1540 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_183836719_    697 TGGAAAAACATTCCACGCTCATAGATTAGAAGAATCAGCATCATTAAAAT 746
                               i i  i   i i    i    i     v i ii  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183836719_    747 GACCATATTGCCCAAAG-GA-------ATTCAACACAATTCCTATCAAAT 788
                          i v   i v      v-  -------       i    i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_183836719_    789 AACCAACATCATTTTTCACAGAATTATAAAAAACT-ATTCTAAAATTCAC 837
                         vv   i vv v     ii     v - i v  i  -  i          i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_183836719_    838 AGGGAA--GCAAGAAGAGCCCA-AATAGCCAAAGCAATCCTAAGCAAAAA 884
                          v    --     -- ii    -          i     i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_183836719_    885 GAACAAAGCCAGCAGCATCATATTACCTGACTTCAAA-----CTATGGGA 929
                                 iii vi vv   i i v  ii i      -----   iiiii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_183836719_    930 CTACAGTAACCAAAACAGTATGGTACTGGTACAAAAATAGGTACACAGAC 979
                                  i   i     i         i i  ii    ii i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_183836719_    980 CAATGAAACAGAATGGAGAACCCAGAAACAAAGTCACACACCTACAAACA 1029
                              i  i     v    ii       i   vi  i   ii  iiiv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_183836719_   1030 ATGGATCTTTGACAAAGTTGGCAAAAATAAAAAATGGATAAAGGAT-GCC 1078
                           v   i  i     i v  v   i vi vvv     iv    i  - i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_183836719_   1079 TTACTCAATAGATGGTGCAAGGAAAACTAGCTAACCATATGCAG------ 1122
                           -i    i i       vi   v    i v  ?   i     i------
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_183836719_   1123 -----------CCTGCCTCTCACCATATAAAAAAAATTAAC-CAAGATGA 1160
                         -----------   i    v         v     -     -   i   i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGG 495

  chr2_183836719_   1161 ATTGAAGACTTAAATGTAAGACCTCAAACTACAAAAATTCTAAAAGAAAA 1210
                           ii?    i           v  v      i    v ii  i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_183836719_   1211 CCTTGAAAAACCTCTTCTGGACATTGGCCTAGGCAAAGACTTTACAACTC 1260
                          v v i?iv vv     vv   v    vi       v ii  ivi iv -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr2_183836719_   1261 ATATCGC-AAAAGCAAATACAACAAAAACAAAGATTGACAAGTTGGACCT 1309
                           iv i -       v vi        iv   i  v  i  i      i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_183836719_   1310 AATTAAA-CTAATGACTTCCTGCACA-CAAAAGAAACTATCAAAAGAATA 1357
                         v  i   -i   vi    i-  ii v-    i  v        i i i i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_183836719_   1358 AATCGACAACCTACAGAATAGGAGAAAACATGTGCAAAGTATGCATCCAA 1407
                           vv       i       i        i  v      vi  ii   ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_183836719_   1408 CAAAGG-----CATC-------TGTAAAGAACT---------------TA 1430
                         i  i  -----i   ------- i         ---------------  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_183836719_   1431 ACAAGAAAAAAAAC---ATTAAAAAGTGGGCAAAGGACATGAACAGGCAC 1477
                          v    v   v   ---   ?    i           iv    i  i  i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_183836719_   1478 TTCTCAAAAGAAGACATGCAGGTGACCAACAA--ACATGAAAAAATGTTC 1525
                              v        i  i  ii  i    i  --         i   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_183836719_   1526 AATGTCACTAATCAA 1540
                           ii   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (148 / 67)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.39 (78 / 23)  


 706 24.00 8.00 1.78  chr2_183871155_183873984.rev      273   497 (2333)    L1M4_orf2#LINE/L1      313   551 (357)  

  chr2_183871155_    273 GAGCATCAAAAAAAGAACTTAGGAATAAATTAAGAGTCAGTTGATTTTTC 322
                            vi  v i   vi   ii ----  v   v vi    i        iv
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCA----TACATTTATGGTCAATTGATTTTCG 358

  chr2_183871155_    323 ACAAAAGGACCAAGAACACATAATGGA-AAAGGACGGTCTCTTCAACAAA 371
                             ii vi      v  ivi     i-    i ii    i         
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_183871155_    372 TAGTGTTGGGAAAACTGCATAATCACAAGCAGAAGAATGAAATTGGAACC 421
                          i   i     v     v   ?i    v   i         i     v  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_183871155_    422 TTAACTCATACCATATATAAAAATCAACTAAAAAC--------------- 456
                         i  v    i        i      i    v    i---------------
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_183871155_    457 ATATAAGATTTCAA-CTTTAAACCTACTAGAAGAAA-CACAGG 497
                           i     vi v  -  v    v  vi         -  i   
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

Transitions / transversions = 1.52 (32 / 21)
Gap_init rate = 0.02 (5 / 239), avg. gap size = 4.40 (22 / 5)  

2865 23.88 4.26 2.96  chr2_183871155_183873984.rev     1484  2329 (501)    L1M4_orf2#LINE/L1        1   857 (51)  

  chr2_183871155_   1484 TGTAAATACATCCTGTGTTGCTGAATTGGAAAACTTACTATTGTTCAAAT 1533
                           v   v i    ii    vv  i       i     v       v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183871155_   1534 GTCTATACTACTCAAAGCAATTTTCAGATTCAATGCAATCCCT-TCAAAA 1582
                          v v     v i    vii  i v         i         -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_183871155_   1583 TTTCAAAGACATGTTTTACAGAAATAGAAAAAA-GGTTATATACTTCATA 1631
                          ii  ivvi v v    i       v  v  iv- i iv  v v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_183871155_   1632 TAGAA---CAAAAGATTATGAA---CCAAATCAATCCTGACAAAGAA--- 1672
                          i   ---   ii  iivv   ---     v     i   v      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_183871155_   1673 CAAAGCTAGAGGCACT-GCATTTCCTGATTTCAAAATATTTTATGAAGCT 1721
                              i i    -   -i  i    ii         iv vi  ii     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_183871155_   1722 ACAGTAATCAAAAAACAGTATGGTACATGGTACTGGCATAAGGACAGCCA 1771
                                    i --    i      -------           i  v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGA--CAGTGTGGTAC-------TGGCATAAGGATAGACA 290

  chr2_183871155_   1772 TATAGACCAATGGAA--AAATAGAGAACTCCAAAGTAAACCTACACATAT 1819
                               i        --i   v    iii vi  i      i i    v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_183871155_   1820 ATGATCA-CTGACCTTTGGCAAGGATGCAAAGAATACATGTTGGAACAAT 1868
                            i   -i   ii  i i     i   v    vi iviiv   iiv  v
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_183871155_   1869 GATAGTCTTTTTCAACAAATG-TGGTGAGGAAAACTGAATATTCACATGT 1917
                         i          -         -  v  -   v     i   ?i      i
  L1M4_orf2#LINE/    391 AATAGTCTTTT-CAACAAATGGTGCTG-GGACAACTGGATAKCCACATGC 438

  chr2_183871155_   1918 ACAAGAATAAAATTGAGCCCTTATCTTACCCTGTATACAAAA-TCAACTC 1966
                          v      i  i   ii   i  i  i  v ii         - i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_183871155_   1967 AAAATGGATTAAAGACTTAAACCTAAGACCTGAAACTATAAAACTCCTAG 2016
                                  i ?    i    iv     v  i              i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_183871155_   2017 AAGAAAACATGGGATCAGGACTCCTTGACTTTGGTCTTGGTGGTGATTTT 2066
                                   i  ?vi iiv  i v    i    vi v  iii  i   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_183871155_   2067 ATGGATGTGAACCCAAAAGCA----------------AAATAAATAAGTA 2100
                         v i   i   vv         ----------------     i    i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_183871155_   2101 GGACTATATCAAACTAAAAATCTTCTGCACAGCAAAAGAAAC-ACTGACA 2149
                              vi      v v    v   i  ii vv    i  v  - iii v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_183871155_   2150 GAGTGAAAACGCAACCTACACAATGGGAGAAAATATTCATGAAAACAACA 2199
                         i        vi     i   v                --  v   iv i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT--TGCAAATCATA 736

  chr2_183871155_   2200 TATCTGATAAGTG-CTAATCCCCAGAATGTACAAGGAATTAATAGAGCTC 2248
                                    v -  vi vi       i  i  i   i vv  v i   
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_183871155_   2249 AA-AGCAAAAAAACTAATATAAGCCAACAACAACAACAAAAAAATGGGCT 2297
                           - ii     i  v    ---i  --------   iv?          v
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATA---ACC--------CAATTWAAAAATGGGCA 825

  chr2_183871155_   2298 AAGGGCTTGACTAGACATTTCTCCTGAGAAGA 2329
                             ii    v             vi      
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

Transitions / transversions = 1.64 (123 / 75)
Gap_init rate = 0.03 (22 / 857), avg. gap size = 2.77 (61 / 22)  


3238 23.04 5.99 1.38  chr2_183888485_183890500      657  1524 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_183888485_    657 TGGAAAGATATTCCATGTTCATGGATTGGAAGAATTAATGTTGTTAAAAT 706
                                    i                     v     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183888485_    707 GTTCATATTTACCCAAAGTGATATGTAGATATAATGCAATTCCTATCAAA 756
                          viv   i i-      v    v ii    vi  i     i         
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_183888485_    757 ATCC-AATGACAGTTTTCATAGAAATAGAAAAAAAAATTCTAAAATTCAT 805
                             - iivi vv    iii      v  v  ivvi  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_183888485_    806 ATGGAA-----------CCA-------CAAAA-------------GAGG- 823
                               -----------   -------     -------------  i -
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_183888485_    824 ---------GAGGCATTATATTACCTGCTCTCAATATTGACTACAAAGCT 864
                         ---------    vv i i i v  iiv i    v i v           
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_183888485_    865 ATGGTAATTAAAACAGTATGGTAGTGGCATAAAAACAGACACACAGACCA 914
                          ii     i  i     i     v        ii i     i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_183888485_    915 ATGGA---GAATAGAGAGTCCAGAAGTAAACCCAAACGCATACAGTCAAC 961
                              ---    v            i        v  iiv  ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_183888485_    962 TAATTTTTGACAATGGCACCAATGAG-ATGGCATGGGGAAAGGTTAGTCT 1010
                          i     i     v  ii    -  v-  vvv          iv      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_183888485_   1011 CTTCAGTAAATGGTGCTGGGAGAA---AATATCCACAGGCAAAATAATAA 1057
                         i    ii              v  ---i   ?     v      v   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_183888485_   1058 AATCAGACCCTTATATTAAGGAATGCAAAAAAACAAAAACAAAAACCTCA 1107
                          i ii     i  iv i vivv  ------ v       iv  ---    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCAT------ATACAAAAATTAA---CTCA 489

  chr2_183888485_   1108 AAATGGCTTAAAGACCTGCACATAAGACCTGAAACTACAAAACCCCGACA 1157
                               v i ?      iv ii     v  i      i     i iv v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_183888485_   1158 AGAAAACATAGGTGCAGAGCTCCTTGACTTTGGCCTTGGCAATGATTTTT 1207
                                     ? i i v  i v    i    vi v       i   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_183888485_   1208 TGCTTATAGCTCCAAAAGCACATGCAATAGAAGCAAAAATAAACAAGAGG 1257
                          ivv   ii v           v    i i   v       i i  ivv 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_183888485_   1258 GACTACATCAAACTAAAAAGCTTCTGCACAGCAAAGGAAACAATCATCAA 1307
                             v       v v    i   i  ii vv       v  v    vv  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_183888485_   1308 AATGAAAAGGTAGCCTACAGATTGGGTGAAAATATTTGCAAACCATACAT 1357
                          i       ii i  i     v    v               i    i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_183888485_   1358 CTAATAAGGGGCTAATATCCAAAATATATAAGGAACTCACACAACTCAAT 1407
                           i       i  vi      i         i      vi          
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_183888485_   1408 AGCAAAAAAAATGAATAACCTGATTAAAAAATGGGCAAAGAACCTTAATA 1457
                          ii     i -ii       ii   ?              i ii v    
  L1M4_orf2#LINE/    790 AATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_183888485_   1458 AA--TTTTTCCAAAGGAGACATAAAAACAGC-AACAGGTATCTGAAAAGG 1504
                         i --   i       i   i   v   ii  -  i i i iv       i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_183888485_   1505 TTCTCAACATTACTAATCAT 1524
                          v        i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (125 / 71)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.27 (64 / 15)  


2311 25.74 1.34 0.89  chr2_183952006_183953666      498  1169 (492)    L1M4_orf2#LINE/L1      234   908 (0)  

  chr2_183952006_    498 AACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTTCTGGTACCAA 547
                             -        i          i   i    ii    v    i iv i
  L1M4_orf2#LINE/    234 AACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chr2_183952006_    548 AACAGAGATATAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATA 595
                         i i   v       i        i    i--    i  --        vv
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAAC 330

  chr2_183952006_    596 CCACACATCTACAACCATCTGATCTTGGACAAACCTGACAAAAACAAGAA 645
                            i    i  iiii  vi    i  v     ivv  v   i v  vvv 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_183952006_    646 ATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAG 695
                                   i  vvi  v  i  i              v      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_183952006_    696 CCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTATACCTTATACAAAA 745
                            i   i i  iiv    ii    i    v   i i   v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_183952006_    746 ATTAATTCA----GGATTAAAGACTTAAATATTAGACCTACAACCATAAA 791
                              i   ----    i ?    i     i v   v   v   i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_183952006_    792 AACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGC 840
                          vi i           v    ?i- v i -   iv   v v  vv i   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGC 579

  chr2_183952006_    841 AAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAGCAAAAGCCAAAAT 890
                           v ii   v ivv  vi            vvi   i      vv     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_183952006_    891 TGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAA 940
                         v  i    v   ii v  i   v v  i i   i  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_183952006_    941 CTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCA 990
                            i  vv i      v  i     i                 v      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_183952006_    991 GTCTACCCATCTGACAAATGGCTAATATCCAGAATCTACAAAGAACTTAA 1040
                         ivii ivi      i  iv i  vi          v  i        ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_183952006_   1041 ACACATTTACAAGAAAAAATCAAACAACCTCATCAACAAGTGGGCGAAGG 1090
                            vv iv i  v     iv    i    iv  i? v  i     i    
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_183952006_   1091 ATATGAACAGACACGTCTCAAAAGAAGACATTTATGAA--GCCAACAGAC 1138
                           v    i     iv    v        i  -- ii  --     i ii 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATAT--ACAAATGGCCAATAAGC 877

  chr2_183952006_   1139 ACATGAAAAAATGCTCATCATCACTGGCCAT 1169
                                  i       v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (97 / 72)
Gap_init rate = 0.01 (8 / 675), avg. gap size = 1.88 (15 / 8)  


 506 30.81 3.54 0.00  chr2_183958284_183960922.rev      950  1147 (1492)    L1M4_orf2#LINE/L1        1   205 (703)  

  chr2_183958284_    950 TGGGAAAACATTCCATGCTGATGGATTGGAAGAATTAATATCATTATAAT 999
                            i  i i  i     i v             v       ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_183958284_   1000 GTCCATACTACCCAAAGCAATCTAGAGATTAAACATTACTCCTATCAAGC 1049
                          v v     v      vii     v     v   iiv ii        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_183958284_   1050 TACCAACATTATTTCCCACAGAATTAGAAAAACC-ATTCTAAAATTAATA 1098
                          v   i vviv   iiii     v v  v  i i-  i        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_183958284_   1099 TTGAACCAAAAAGAGGCTTGAAT--CTGAAGCAAAT----AAAAAAACAA 1142
                          v   viiv  i iiv iv    -- ii  i   vi----    i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_183958284_   1143 CAAAG 1147
                              
  L1M4_orf2#LINE/    201 CAAAG 205

Transitions / transversions = 1.35 (35 / 26)
Gap_init rate = 0.01 (3 / 205), avg. gap size = 2.33 (7 / 3)  

2026 27.62 4.46 0.70  chr2_183958284_183960922.rev     1431  2147 (492)    L1M4_orf2#LINE/L1      165   908 (0)  

  chr2_183958284_   1431 ATCCAAAAAAA--AAAAAAA----AAAAAAAAAGAACAAATCCAGAGTAA 1474
                          i   i  v i--    v  ----i     i         viii   v v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_183958284_   1475 TCACATTACCCAACTTCAAACTATACTACAAAGCTACAGTAACCAAAACG 1524
                              i v     i      viv                   i   i  i
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_183958284_   1525 GCATGATACTAGTATAAAAACAGACACGTAGAACAATGGAACAGCAGGGA 1574
                          ii  i    i i    ii i     ii    v        i  v vv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_183958284_   1575 AAACCCAGGAATAAAGCTGCACACCTACAACCAACTAATCTTTGACGAAG 1624
                         i ii    i      v iii   ii  iiii   i i  i  i   i i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_183958284_   1625 TCAACAAAATAAG-CAGCAGGGAAAGGACTCCCTATTCAA--AATGGTGC 1671
                         viiv   i iv v-  iii       i ivvi  v     --        
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_183958284_   1672 TAGGATAACTGGCTAACCATATATAGA-GATTGAAGCTAGACCTCTACCT 1720
                          i   i      v  ?   i  ii i -  v     i i    i      
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_183958284_   1721 ATAATCATATATAAAAATTAACTCAAGATGGATTAAAGACTTAAATGTAA 1770
                         vvv i      i              i      i ?    i         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_183958284_   1771 AACTTCAAATTATAAAAATCCTAAAAGAAATTGTAGA---AAATACCCTT 1817
                         i vi v   i       v  i  i      vii   i---    ---   
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTT 561

  chr2_183958284_   1818 CTGGACACTGGCATTGGTAAAAATTTAT--GACTAAGTCCTCAAAAGTAA 1865
                          vv   vi   vv v  i  vii   v --  -  v v vi      i v
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCAC 610

  chr2_183958284_   1866 TTGCAAGAAAACAAAAATT-GAAAGATGGGACCT------AATTAAAGAG 1908
                         vv    v    v     v -  v i  v    i ------       i -
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA- 659

  chr2_183958284_   1909 CTGCTACACAGCAAAAGAAACTATCAACAGAGT--AAAGAGAGCCTACAG 1956
                           vi iii vv    i  v        v i   --     v i  i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_183958284_   1957 AATAGGAGAAAATATTCTCAAACTATGCATCCAACAAAGGTCTCATATCT 2006
                            i            iv    ii  ii   ii i  i  v  ii    i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_183958284_   2007 AGAATCTCTAAGGAACTT----AAATCAACAAGCAAAAAACAA----CCC 2048
                              v v   i     i----  v    i  vv    i    ----   
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_183958284_   2049 TATTAAAAAGAGGGCAAAGAACATGAACAGATACTTCTCAAAAGAAGACA 2098
                         v   ?    iv        i iv    i   i i     v        i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_183958284_   2099 TATGAGAAGCCAACAAACATATGCAAAAGTGTTCAACCTCACTAATCAG 2147
                           ii ivi     i  i  i   v   ii  i     v   ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (127 / 68)
Gap_init rate = 0.02 (15 / 744), avg. gap size = 2.47 (37 / 15)  


2895 23.45 6.77 1.17  chr2_184023438_184026679.rev     1910  2766 (476)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_184023438_   1910 AAAGATATCCTGTGTCCATGGATTGGAAGAATTAATGTTGTGAATATATC 1959
                                   ii   i              v     i    v  v  iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_184023438_   1960 CATACTACCCAAAGTAACCTACAGACTCAATGTAACTACTATCAAA-TTT 2008
                         v     v      v i i       i    i i  iiv        - ii
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_184023438_   2009 CAA-TGTCATTTTTCACAGAAACAGAAAAAAATAATCATTAA-TTTGTAT 2056
                           i-  i -     ii      iv  v  iv- i   v v  -  ii   
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATAT 151

  chr2_184023438_   2057 GGAACCACAAAAGACCCCAAATAACCAAAACAGTCTTGAGCAAAAAGAAC 2106
                             vii   ii     vi    i        i      iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_184023438_   2107 AAAGCTGGAGGCATCACACTTTATGATTT-GAAAC--ATTATAAAGTAAC 2153
                             i      vv        ivii    -i    -- i  i    iv  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_184023438_   2154 AGTAATCAAAACAGCATGGTACTGGCATAAAAACAGAAACACTGACCACT 2203
                                  i    ii              ii i   v i iv  i  v 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_184023438_   2204 GAAATTAGACAGAAACTTCAGAAATAAACTCACCCATTTATAGTCCATTG 2253
                          i   vii iv  i v i           i  iv       i   v    
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_184023438_   2254 ATTTTTGAAAAAGGTGCAAAATACACACAATTAGGAGAGGACAGTGTCAT 2303
                              i  v  i     v  ivv  iv    vi   i  i i   v iv 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_184023438_   2304 CAATAAATAGGGTCTGGA-AACTGGTTCTACAAAGGCAGAAGAATAAAAT 2352
                            i    i v iiv   -      v v?v  v v   i      i  i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_184023438_   2353 TAGACTCTTA----A-ACCATATACAAAAATAAACTCAAAATAGATAAAA 2397
                          i   i i  ---- -               v          i   v ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_184023438_   2398 GACTTAA------GATCTGAAACTATGAAACTACAAGAAGAAAACA---- 2437
                            i   ------  v  i       i     viv           ----
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_184023438_   2438 --------------------GGTCAGAACAATGATTTATTTGGATATGAC 2467
                         --------------------   i  i-     i   -i  i        
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGG-CAATGGTTT-CTTAGATATGAC 599

  chr2_184023438_   2468 CCCAACGGCACAGGCAATAAAATCAAAAATAGACAAATGAGATGGCATTA 2517
                         v    vi     i    i    vv         i    vi  ivv   i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_184023438_   2518 AA-CTAAAAGCTACTGCACAGCAAAGGA-------AAAAAAGGGAAGAGA 2559
                           -i     i  vi  ii vv       -------  i    v   i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_184023438_   2560 CAACTTACAGAATGCAAGAA--TATT-GAAAAGTATATATCTGATAAGGG 2606
                             ii        vi    --    - v   vi                
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_184023438_   2607 ATTAATGTCCAAAATATAAAAGGGACTC----AACTCAATAGCAAGGAAA 2652
                          i vi i    i      v  i i    ----         ii  ii i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_184023438_   2653 CAAATAGCTCAATTAAAAGATGGGCAAAGGACCTGAACAAATATTTCTTA 2702
                               i i     ?   i            ii    i i i      iv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_184023438_   2703 AAAGAAGATATATATGAATGACAAATAAGTACATGATAA-ATATCCATTA 2751
                                     i --    i v      i      v  -  iii  -- 
  L1M4_orf2#LINE/    850 AAAGAAGATATACA--AATGGCCAATAAGCACATGAAAAGATGCTCA--A 895

  chr2_184023438_   2752 CTAATCATTAGGGAA 2766
                          --    ????????
  L1M4_orf2#LINE/    896 C--ATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (131 / 67)
Gap_init rate = 0.03 (23 / 905), avg. gap size = 2.96 (68 / 23)  


3113 25.64 2.23 1.34  chr2_184055164_184057397.rev      846  1742 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_184055164_    846 AAAGACATCC-ACACTCATGGATCAGAAGGGTTATTAACAATTAAAATGA 894
                              i    - iii        ii    iv   v  vii-    i   i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTG-TTAAGATGG 52

  chr2_184055164_    895 CCCTACTACCCAGACCAATCTACAGATTTAATGCGAAACTTATCAAAATA 944
                          vv    v    i iii           i  i  i vv i         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_184055164_    945 CCAA-TGTCATTTTTCACAGAATTAGAAAAAA-AATCCTAAAATTTGTAT 992
                            i-  i -     ii     v v  v  iv-i           ii   
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_184055164_    993 GGAAC--CAAAAAACAGCCAGAACAGCCAGAGCAATCCTGATCAATAAGA 1040
                             v--   iii  --      i     i i     i   vv  v    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_184055164_   1041 GGAAAACTGAAGTTATCACACTATCTGACTTCAAAATATATCACAAAGCT 1090
                         iv   ii  i  vvv       vi ii i       iv  ii        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_184055164_   1091 CTAGTAACCAAAACAACTTGGTATTGGTATAAAAATTGACACATGGACCA 1140
                         vi     i   i   iiv     i   i    ii  v    i  i  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_184055164_   1141 GTGAAACAGAATAGAGAGTCC-GAAATTAGTCCATGTATTTACAACCAAC 1189
                         i  i  i     v        -     v ii    ii     iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_184055164_   1190 TGGTTTTTGACAACAGTGCCGAGAATATATATTCAGGAAAGGACACCCTC 1239
                           i    i     vi     i   vi  vi v vi      i i vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_184055164_   1240 TTCAATAAATGGTGCTAGAAAAAATTGGATATCTGTATGCAAAAGAAGGA 1289
                              i          i i v  -i      ? iii           v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGA 448

  chr2_184055164_   1290 AACTGGACCCCTATCTCTCACCATCTACAAAAATCAACTCAAGATGGATT 1339
                          ii          i   v      v         i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_184055164_   1340 AAAGACTTAAACATAATACACAGAACTATAAAACTAGTAGAAAAAAAACA 1389
                          ?    i    ii   v vvi i            vv     i    -  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CA 547

  chr2_184055164_   1390 TAGAGG-AAATACTTCAAGACCTCAGTCTAGGCAAAGATTTTGTGGCTAA 1438
                            i? -    -    iv     ii vi       v i   iv i v  v
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_184055164_   1439 GACCTCAAAAGTACAGATAACTATTTTTATAAATAGACAAATGGGACTAT 1488
                            vi      i   iii   v vvvvv -       i    v     vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTC 645

  chr2_184055164_   1489 ATTAAACTAAAAAGCTTCTATACCACAAAAAATTGTTCATCAACAGAATA 1538
                           i   v v    i   i i i iv    ii i-ii -     v i i i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC-ACT-ATCAAGAAAGTG 693

  chr2_184055164_   1539 AAGAGACAACCTGTTGAATGGGAGAAAATATTTGCAAACTATTCACCTAA 1588
                           i        iiiv                       ii  vi i  i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_184055164_   1589 TAAGGGACTAATATCCAAAATATAGAAGGAACTC----AACTCAACAA-- 1632
                                  vi      i      v  i      ----       i  --
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_184055164_   1633 --AAAACAAATAATCCCATTTAAAAGTGGACTAAAGACATAAATAGGCAT 1680
                         --  i        i  v   ?    i   i v  i  iv i     i   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_184055164_   1681 TTC-CCATAAGAAGA----CAAATGGCCAACAGATATGTGGAAAAAATGC 1725
                            -   -       ----           i iii ii  -    i    
  L1M4_orf2#LINE/    844 TTCTCCA-AAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGC 891

  chr2_184055164_   1726 TCAGCATCACAGATCAT 1742
                            i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.28 (157 / 69)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 1.52 (32 / 21)  


1822 25.48 3.39 5.01  chr2_184076945_184078615.rev      501  1179 (492)    L1M4_orf2#LINE/L1      241   908 (0)  

  chr2_184076945_    501 TATAGGACTACAATCACCAAAACCGCATGGTACTGGTATAAATCAATCAA 550
                           i iii     i v i   i  v ii         i    i--------
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-------- 282

  chr2_184076945_    551 TCAATCAATCAACAAATCACCAGATACATTGACCAATGGAACAGAATAGA 600
                         --------------i  ----   i i  v  i        i     v  
  L1M4_orf2#LINE/    283 --------------GAT----AGACATATAGATCAATGGAATAGAATTGA 314

  chr2_184076945_    601 GAACCCAGAAACAAGACAACACGTATACAACCATCTAATCTTCAACTAAG 650
                           ii       i  iv v i  i v  iiii  vi i  i   i  v i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_184076945_    651 CCAACAAAAGCAAGCAATGGAGAAAGGACTACCTATTCAATAAATGGTGC 700
                         viiv   i v  vv      i     i ivii  v     i         
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_184076945_    701 TGGGATAACTGGCTAGCCATGTGCAGAAGATTGAAACTAGATCCCTTCCT 750
                              i      v  ?   ii    i    v    ii i  i    v   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_184076945_    751 CACACCACATACAAAAATCAACTCAAGATGAA-CA---ACTTCAATGTAG 796
                                i          i       i   i -  ---  i v      i
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_184076945_    797 CACCCAAAACTATAAACACCCT-GGAAGACAACATAGGCAGTAACATTCT 845
                         v v i           -  i  -i     v        ?ivv  iv   v
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_184076945_    846 AGATATTGGAACTGGCAAAGATTTCAT-GATGAAGACACCAAAAGCAAGT 894
                         v  iv    iviv     v i    v -   - v             viv
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAA 612

  chr2_184076945_    895 GCAACAAAAGCAAAAATTGACAAATGGAATCTCATTGAA-CTAACAAGTT 943
                                   v      v  i    v i ii    ii  -i   v  v  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_184076945_    944 C----CTTCAGAGCAAAAGAAATGATGAACAGAGTAAAAAGAGAGTCTAC 989
                         i----     -----  i  v iv  v  v i   i      v ii i  
  L1M4_orf2#LINE/    663 TTGTGCTTCA-----AAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_184076945_    990 AGAATGGGAGAAAATTTTTGCTAATCTATGCATCTGACAAATGTCTAATA 1039
                                        v     v    -  ii      i  iv v  vi  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGGGACTTGTA 756

  chr2_184076945_   1040 TCGAGCATTTATAAGGAACTTAAACAAATT-----TACATGCACAAA-AG 1083
                           v  v  v     i     ivv    v i-----  v viv     - i
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_184076945_   1084 CC--ATAGAAAAGTGGACAAAAGACACGAACAG----TTTTCAAATGAAG 1127
                           --  v?    i   i    i  ivi   i  ----  i  v  v    
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_184076945_   1128 ACGTACTTGTGGCTAACAAGCATGTGAAAAAATGCTCAACATCACTGATC 1177
                          ii   vvi    i  i     ii      i             ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_184076945_   1178 AT 1179
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.58 (104 / 66)
Gap_init rate = 0.02 (16 / 668), avg. gap size = 3.56 (57 / 16)  


1524 26.29 4.60 2.76  chr2_184135394_184137741.rev      722  1265 (1083)    L1M4_orf2#LINE/L1        3   556 (352)  

  chr2_184135394_    722 GAAAAATATACCA-----AT--ATCAGAAGAGCCAATATTTTTAAGATGG 764
                             i    v   -----  --  ii     vii      v         
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_184135394_    765 TAATTTTCTCCATTTTCTCCACACTGATTCATGGGTTCAAGGTATTTACA 814
                         i   v--    -------   v i    ii ii i     v i v iv v
  L1M4_orf2#LINE/     53 CAATA--CTCC-------CCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr2_184135394_    815 AATAAAATCACAGCAGGCTTTTAAATT----AAATTTTTAAACTGACTCT 860
                          vi      v    v v     ---  ----     vvi  i    ii  
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTT---TTGCAGAAATTGACAAGCTGATCCT 140

  chr2_184135394_    861 AAAATTCATATGGAAAAGCAAAGGACCTAAAACAGTTAAAACTA-CTTGG 909
                                         v    i     i i  i  ii     v -    i
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_184135394_    910 CAAAGA-GAACGATAATTTGGAGAATTTATAATACCTAATTTTAAAACTT 958
                         v     -    i -- v      i i i i v v  i     i       
  L1M4_orf2#LINE/    191 AAAAGAAGAACAA--AGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_184135394_    959 ATTTTAAAACCACAATAATCATGACAGTGTGGTTTTAGCACAAATAACAG 1008
                          i vi   i i   i      v           vi i   i  i-i i  
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAG 287

  chr2_184135394_   1009 AAAAACAGATCAATGGAACAG---------TCCATAAATAGAGCCTCATA 1049
                          v v i            i  ---------    v     i v  vi i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_184135394_   1050 TACATGAGCAACTGATTATCAACAAAGATGTAAAG-TAATTCAGTGGAAA 1098
                          vi   iv   i     v  i    i i  iv   -iv     i   ii 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_184135394_   1099 AAGGGTAATATTTTCAACAAATGACACAAGAAATATTGGATATTCAGATA 1148
                            ii  i v             iii vi i vv i      ?i  v  i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_184135394_   1149 -AAGACATTGAACTTTGACTTATACTTTGTACCATTTACAAAAATTATAT 1197
                         -  i v v    v  v   iiv   i iii     v           vv 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_184135394_   1198 CAAG-TTCATCGCAAACCTAAATGTAAAACCAAAAACAATAAAACATATA 1246
                            i- vv   i? i            i v v     v       viv  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_184135394_   1247 GAAGGAAACATAGAAGAAA 1265
                             i        i? v  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAA 556

Transitions / transversions = 1.55 (85 / 55)
Gap_init rate = 0.03 (14 / 554), avg. gap size = 2.86 (40 / 14)  

 986 22.12 5.45 1.28  chr2_184135394_184137741.rev     1545  1856 (492)    L1M4_orf2#LINE/L1      584   908 (0)  

  chr2_184135394_   1545 GTTTCTTAATTACAACAAGAAAAGTACAATTCATAAAAGAACAAATTGAT 1594
                                 iv  ii   vv     i    viv i       v    v   
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_184135394_   1595 AAAT-GGACTTCATCA----------TTTTTGTTCTTTGAAATAACATTG 1633
                             -           ----------i      v   i-   vi   i i
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC-AAAGGACACTA 682

  chr2_184135394_   1634 TTTAAAAA-TGAAAAGGGAAGCTATATACTGGGAGAAGATAATTTCAAAT 1682
                          iv i   -       iv  v i i v v        i   v  v     
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_184135394_   1683 CATACAGCTAATAAAGCACTTG-ATCCAGAGTATATCAAGAACTTCCAAA 1731
                             i v  i    i v     -       i     v       iii v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_184135394_   1732 ACTCAATTAGAAGAAAACAAAAAA---AATCAATACATCATAGGTAAAAG 1778
                                v v  i  i     v  ---   i? - v --  i  i   i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWA-AAA--ATGGGCAAAGG 829

  chr2_184135394_   1779 ATTT-AATAGACATTTTACCAACGGAAAAATACACATGACAAATAAACCC 1827
                             -           iv    v i i v     v   i v     i v 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_184135394_   1828 ATGAAAAGATGTCCAACGTCATTTGTCAT 1856
                                    ii    i   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (38 / 30)
Gap_init rate = 0.03 (9 / 325), avg. gap size = 2.33 (21 / 9)  


3137 26.46 0.88 0.77  chr2_184138792_184145210.rev     5021  5927 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184138792_   5021 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5070
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184138792_   5071 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCAATCAAGC 5120
                            v     v     iv i  i           i  v     v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184138792_   5121 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5168
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_184138792_   5169 TATGGAACCAAAACAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5218
                                viiv  vi  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_184138792_   5219 AACAAAGCTGGAGGCATCACACTACCTGACTC--AAACTACACTACAAGG 5266
                                i      vv       v  ii i i--     -i       i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_184138792_   5267 CTACAGTAACCAAAACAGCATGGAACTGGTACCAAAACAGCGATATAGAT 5316
                                  i   i    ii   v     i iv ii i  vv        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_184138792_   5317 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTGCAAC 5364
                                 i    i--    i  --        vv  ii i  i iiiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_184138792_   5365 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5414
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_184138792_   5415 CCTATTTAATAAATGGTTCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5464
                         i  v  i  i       v      v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_184138792_   5465 TGAAACTGGATCCCTTCCTTTCACCTTACACAAAAATTAATTCAAGATGG 5514
                             ii    i    v   iv    v  i           i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_184138792_   5515 ATTA-AGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5563
                           i -    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_184138792_   5564 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5612
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_184138792_   5613 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5662
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_184138792_   5663 CATTAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5712
                            i   v v  i i  ii  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_184138792_   5713 ACAGGCAACCTACACAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5762
                          v  i     i   v             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_184138792_   5763 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5812
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_184138792_   5813 AAAAACAAACAACCCCATCAAAAAGTGAGCAAAGGATATGAACAGACACT 5862
                            i     i     v  i?    i  i         v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_184138792_   5863 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAAATGCTC 5912
                             v        i  vi viii     v  i          i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chr2_184138792_   5913 ATCATCACTGGCCAT 5927
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2596 19.53 6.65 9.23  chr2_184224345_184227012.rev     1245  2176 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184224345_   1245 TGGGGAGATCCATCACTTGTTTA--GATTGA------TAATAATGT-AAT 1285
                            ii    --   v v    i --     i------     v   -  v
  L1M4_orf2#LINE/      1 TGGAAAGAT--ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_184224345_   1286 TTGCCA------CCCAAATTAATCTATCAATTTAGTACACTTCTTGTTAA 1329
                         v  v  ------        i     ivi   i iii  v i i i i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_184224345_   1330 AATCCCAGTAGCCATTTTTGTAGAACTTGACAATCTGAACTTAAAACTTG 1379
                                 iv   v      i    v       v    v i     i ii
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_184224345_   1380 TATAAAAATGTAAAGGACTTAGAATAGCTAAAACAATTTTTTAAAAAAGA 1429
                            ii     i  i    ii        i        i  --i       
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--GAAAAAGA 196

  chr2_184224345_   1430 A-AACAA---TGG--GACTTACATTGCCTGATTTACACACTTATTACAAA 1473
                          -     ---   --    i   i v  ii    vv v     i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_184224345_   1474 GTTACAGTAATC--TACAGTGTGATATTGGCATAA------ATATATAGA 1515
                          i          --v        i  i        ------ i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_184224345_   1516 TCCATGGAACATAAT--AAATCCCAAAAGTAAACCCTTAAATATATGATC 1563
                           v      i v   -- i vi   i  i       v  v  v    i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_184224345_   1564 AGTTAATTTT-ATCAAAGGT-CCA-GACAATTCAATGGAGAAACAATAGT 1610
                          i  i     -iv   i   -   -   v         i    v      
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_184224345_   1611 GTTTTTATCAAACGTATGATGGG-CAAC-GTCTACCTATATGCCAAATAT 1658
                         v    i v    i -i  v    -    - vv  ? i i    -   ---
  L1M4_orf2#LINE/    397 CTTTTCAACAAATG-GTGCTGGGACAACTGGATAKCCACATGC-AAA--- 441

  chr2_184224345_   1659 AGATATAATTTTTGTGTATGCTATGAGGTAAACTAATTTATGCATATAGG 1708
                            -------------------    i  ----------------- i -
  L1M4_orf2#LINE/    442 AGA-------------------ATGAAGT-----------------TGG- 454

  chr2_184224345_   1709 TATAACTACCTCACATATTTTATATATAATTATCTCACATCATACACAGA 1758
                         -------   i ------------------  i      i    i   i 
  L1M4_orf2#LINE/    455 -------ACCCC------------------TACCTCACACCATATACAAA 479

  chr2_184224345_   1759 AATTAATTCAAAATGAATCACAGACTTAAAT---------AAAAATCTAA 1799
                               i        i    ?    i     ---------    v v   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_184224345_   1800 TACTTTTAGAAGAAAGCATAAGA--AAATTTTTGTGATATTGGGTTAAGC 1847
                         v   i          i    i ?--    i  i    iv        i  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_184224345_   1848 ATAAGATTTTTGTTACATGTGGCACTAAAAATAGGATCTATAAAA----- 1892
                          - v i   i --  v  i  i   i    ii vi v v i    -----
  L1M4_orf2#LINE/    580 A-ATGGTTTCT--TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_184224345_   1893 -ACTGATAAGCTGAACATTTTAATAATTAAAA-CTGTCGCTCTTCAAAAG 1940
                         - iv     ii  i  v iv v v        -  v i iv       i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_184224345_   1941 AAAAGCAAAGAAGAAAATGAAAAGACAAGCCACAATCTAGGAGAAATTAC 1990
                          v -- v vv      i           v     ivv i       v  i
  L1M4_orf2#LINE/    677 ACA--CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_184224345_   1991 TTGCAAATCATATATCATCATCTATCTGATAAAGGACTTCTATATAGAAA 2040
                                         ----------      i      v   vi    v
  L1M4_orf2#LINE/    725 TTGCAAATCATATATC----------TGATAAGGGACTTGTATCCAGAAT 764

  chr2_184224345_   2041 ATATAAAGAACCCTTACAAGTCAATAAGAAAA---CA-----CCCAGTTA 2082
                                    i       v       v    ---  -----    i  ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_184224345_   2083 AAAAACAGGCAAAAGGTCTACATAAACATTTCACCAAATAAGATATACAA 2132
                              ii      i i i iv   i       v     v           
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_184224345_   2133 GTATTTAATAAACACATGAAAGGATATTAAACATCATTAGTCAT 2176
                         i ivii     i         i   ii v       ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (112 / 66)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 4.35 (148 / 34)  


2975 27.61 0.88 0.99  chr2_184232970_184241124     6757  7665 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184232970_   6757 TGGAAAAACATTCCATGTTCATGGATAAGAAGA----ATATCATGAAAAT 6802
                               i i  i              vi     ----    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184232970_   6803 GGCCATAATGCCCAAAGGAATTTATAGATTCAATGCTATCCCCATCAAGC 6852
                            v   v v      vvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184232970_   6853 TACCATTCACTTTCTTCACGGAGTTAGAAAAAACT-ACTTTAAATTTCAT 6901
                          v   viii i  i  ii i  iv v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_184232970_   6902 ATCGAACCAAAAAAGAGCATGTACAGCAAAGACAATCCTAAGCAAAAGGA 6951
                           v   viiv  ii  v vv v i   v  i      i i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_184232970_   6952 ACAAAGCTGGAGGCATCACACTACTTGACTTCAAATTATACTACAAGGCT 7001
                               i      vv       v iii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_184232970_   7002 ACAGTAACCAAAACAGCATGGTACTGGTATGGTACCAAAATAGATATATA 7051
                                i   i    ii         i  i----- ii     i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATA-----AGGATAGACATATA 294

  chr2_184232970_   7052 GACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCATACATCTACAA 7101
                           i        i    iv   ivii         vv        i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_184232970_   7102 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 7151
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_184232970_   7152 CCCTATTTAATAAATGGTGTTGGGAGAACTGGCTAGCCCTTTGCAGAAAA 7201
                         vi  v  i  i        i     v      v  ?  viv    i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_184232970_   7202 CTGAAACTGGACCCCTTCTTTACACTTTATATAAAAATTAACTCAAGATG 7251
                         v    ii         v i i    iv    i              i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_184232970_   7252 GATTAAAGACTTAAACATAAGATCTAAAACCATAAAAACCCTAGAAGAAA 7301
                            i ?    i    ii     v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_184232970_   7302 ACCTAGGCAATACAAT--TCAGGACATAGGCATGGGCAAGGACTTCATCA 7349
                           v    ?i-  -   --  iv   v v  vv i     v ii   v vi
  L1M4_orf2#LINE/    545 ACATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_184232970_   7350 CTAAAACACCAAAAGCAATGGCAACAAAACACAGAATTGACAAATGGGAT 7399
                         v  vi            vvi         v v i   v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_184232970_   7400 CTAATTAATCTAAAGAGGTTCTGCACAGCACAACAAACTATCATCAGAGT 7449
                         i v  i  vv v  i iv  i  ii vv  v iv v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_184232970_   7450 GAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTG 7499
                            v        i                 v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_184232970_   7500 ACAAAGGGCTAATATCCAGAATCTACAA-GAACTTAAACAAATTTACCAG 7548
                          i  i  i  vi          v  i  -     ivv    -i i vi i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAA 791

  chr2_184232970_   7549 AAAAAAAACAAACCATCCCATCAAAAAGTAGGCATAGGATATGAACAGTC 7598
                         v     i     iv i  v  i?    i i    v     v    i  v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_184232970_   7599 ATTTCTCAAAAGAAGATGTTTATGCAGCCAACAAACATATTTTAAAAAGC 7648
                                v         i vi viii     i  i  i  vvv  i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_184232970_   7649 TCATCATAACTGGTCAT 7665
                            v   v ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (141 / 106)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


 984 29.53 5.96 1.04  chr2_184275930_184282323        1   386 (6008)  C L1M4_orf2#LINE/L1   (482)   426    22  

C chr2_184275930_    386 TAAATTCAAACACCTAATATT---AAAATGTCGATTCACCCCAAATTGGC 340
                          ii   vi  v  i       ---  i   v i  v v          --
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG-- 69

C chr2_184275930_    339 ATGTATTTGTTCAATGTAATCTCAGTGGAAATCCTATCATATTTTTCGGT 290
                           v  ivvi     i i    i vi vi      i v vvvi    iv i
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

C chr2_184275930_    289 AGAAATTGGCAAAGTGCCTATAAAATTCATGTAGAAATTCAAAGTGTCTA 240
                                 i   iv  viiv          i i     v   i vii i 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

C chr2_184275930_    239 GGGTAGC-AAAACA---TTAAAAAA----AATAAATTTGAAGGGTTTTTG 198
                          ii    -      ---  i     ----  i   v   i   ii ivii
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

C chr2_184275930_    197 CTACTCAATTTTAAGACTTAATAAAAAGCCATCCTAATCAATATAGTCTG 148
                           v i      i  i     v  v     i ivv       v i   v  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

C chr2_184275930_    147 GTATTTACCTAAGAATAGACAAGTAGCTCAGTCTAACAGAACCGAGAGCA 98
                            i vi v    i       vi   v   i vv  i    ii     iv
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

C chr2_184275930_     97 CAGAATTAGAACCATACATT-------AA--AATTT--GACTAAGGAGCA 59
                              v  i v         -------  --i    --   v i  v  v
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

C chr2_184275930_     58 AAG-CAATTTAGGAAATAAATGATTGCCTTTTCAACAATTTGTATGTCAG 10
                            - v   i iviiiv   vi  v i           v v  -- iii 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT--GCTGG 417

C chr2_184275930_      9 AACAACTGG 1
                         i        
  L1M4_orf2#LINE/    418 GACAACTGG 426

Transitions / transversions = 1.38 (66 / 48)
Gap_init rate = 0.02 (10 / 405), avg. gap size = 2.70 (27 / 10)  

3171 27.53 0.55 0.55  chr2_184275930_184282323     4995  5902 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184275930_   4995 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5044
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184275930_   5045 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5094
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184275930_   5095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5142
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_184275930_   5143 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAGTCCTAGCCAA-AAG 5191
                                viiv  ii  v  v v  v     iv  i  i iivv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_184275930_   5192 AACAAAGCTGGAGGCATCACGCTACCTGACTTTAAACTATACTACAAGGT 5241
                                i      vv    i  v  ii i  i   viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_184275930_   5242 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5291
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_184275930_   5292 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5339
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_184275930_   5340 ATCTGATCTTTGACAAACCTGAGAGAAACAAGCAATGGGGAAAGGATTCC 5389
                          vi    i  i     ivv  vv ii v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_184275930_   5390 CTGTTTAATAAATGGTGGTGGGAAAACTGGCTACCCATATGTAGAAAGCT 5439
                           v  i  i        v     v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_184275930_   5440 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5489
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_184275930_   5490 TTAAAGACTTACACGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAAC 5539
                          i ?    i  v i  v   v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_184275930_   5540 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTGTAA 5589
                         v    ?i v viv   iv   v v  vv i     v ii   v ivi  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_184275930_   5590 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5639
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_184275930_   5640 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5689
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_184275930_   5690 AGGCGACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCCTCTGACAA 5739
                           i i       i             v  i    vii iviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_184275930_   5740 AGGGATAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5789
                         i  iv vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_184275930_   5790 AAACAAACAACCCCAATTAAAAAGTGGGCGAAGGACATGAACAGACACTT 5839
                          i     i     -    ?    i     i     iv    i     i  
  L1M4_orf2#LINE/    797 AGACAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_184275930_   5840 CTCAAGAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5889
                            v i      i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_184275930_   5890 CATCACTTGCCAT 5902
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2794 26.29 2.46 0.89  chr2_184306491_184313144.rev     5269  6162 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184306491_   5269 TGGAAAAACATTCCATGCACAAGGATAGGAAGAATCAATATTGTGAAAAT 5318
                               i i  i     iv  v    v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184306491_   5319 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATTCCCATCAAGC 5368
                            v     v      v i  i           i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184306491_   5369 TACCA-TTGACTTTCTT-CACCAAATTAGAAAAATCTACTTTAAATTTCA 5416
                          v   -i  v    i  -  v-     -  v  iiiv iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG-AAATT-GACAAGCTGATCCTAAAATTCA 148

  chr2_184306491_   5417 TGTGAAAGCAAAAAAGAGCCTGCAGAGCCAAGACAATCATAAGCAAAAAG 5466
                          i  i  iiiv  ii  v  v v v      i      v i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_184306491_   5467 AACAAAGCTGGAGGCACTAA-GCTACCTGACTTCAAACTATATTACAAAG 5515
                                i      -   v -i  v  ii i      viv  i       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_184306491_   5516 CTACAGTAACCAAAACACCTTGGT-CTGATACCAAAACAGATATATAGAC 5564
                                  i   i   viv    -   ii iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_184306491_   5565 CAACAGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAGGA 5614
                            ii   i    iv   ivii         vv   i    i  iiivv 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_184306491_   5615 TCTGATCTTTGACAAACCTGACAAAAACAAGAAACGGGGAAAGGATTCCC 5664
                         vi    i  i     ivv  v   i v  vvv  i        i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_184306491_   5665 TATTTAATAAATGGTGTTGCAAAAACTGGCTAGCCATATGCAGAAAACTG 5714
                          v  i  i        i  vi v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_184306491_   5715 AAACTGGACCCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGGAT 5764
                           ii         v   i     v  i                i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_184306491_   5765 TACAGATTTAAACATAAGATCTAAAACCATAAAAACCCTGGAAGAAAACC 5814
                         i ?   ii    ii     v       i      vi i i         v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_184306491_   5815 TAGGCA-ATACCATTCAGGACATAGGCAT-GGCAA--ATTCTTCATGACT 5860
                             ?i- v i -   iv   v v  vv -     --i  ii i -  - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GA-T 594

  chr2_184306491_   5861 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGGTCT 5910
                          vi            vvi          vv    iv  i    v  iii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_184306491_   5911 -AGCTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 5959
                         - v v   i      -   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_184306491_   5960 AACAGGCAACCTTCAGAATAGGAGAAAATTTTTGCAGTCTACCCATCTGA 6009
                           v  i     iv      i         v      ivii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_184306491_   6010 CAAAGGGCTAATATCCAGAATCTACAAGAAACTTAAACAA----AT--TT 6053
                         i  i  i  vi          v  i  ii    ivv    ----  -- v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_184306491_   6054 ACAAGA-AAACAACCCCATCAAAAAGTGGGTAAAGGATATGAACAGACAT 6102
                          v    -   i     v  i?    i    i       v    i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_184306491_   6103 TTTTCAAAAGAAGACATTTCTGTGGCCAAACAA--ACATGAAAAAA-GCC 6149
                           i  v        i  vivvi       -i  --         i -  i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGATGCT 892

  chr2_184306491_   6150 CA---TCACTGGTTAT 6162
                           ---   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.36 (30 / 22)  


3306 25.83 1.22 0.55  chr2_184375828_184380002.rev     2782  3683 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184375828_   2782 TGGAAATATATTCCATGTTTGTGGATTGGAAGAGTCAATGTTGTTACAAT 2831
                               v    i       ii            v i   i      vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184375828_   2832 ATTCATACTACCCAAAGCAATCTGCAGATTCAATGCAACCCCTATCAAAA 2881
                         iviv     v      vii    i         i    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184375828_   2882 TACCAATGACGTGCTTCACAGAAATAGAAAAAGCT-ATCCTAAATTTTAT 2930
                          v   iivi v vi  ii       v  v  -   -        v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_184375828_   2931 ATGGAGCCACAAAAGACCAAGAATAGCCAAAGCAATCCTGAGAAA-AAGA 2979
                              ivii   ii    v            i     i   i   -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_184375828_   2980 ACAAAACTGGAGTTATCACATTACCTGACTTCAATTTGTACTGAAGATAT 3029
                              ii     vvv     i v  ii i     vviv    iv i vv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_184375828_   3030 ATAGTAAATACAGCAATTATGGTACTAGCATAAAGACAGACACATAGACC 3079
                          i     vi vii  i -i       i      i  i     i     i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGT-GTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_184375828_   3080 AGTGGAACAGAATATAGAATCCAGAAATAAATTCATTCATCTACAATGAA 3129
                          i     i     vv   i            ii   v   i  iii v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_184375828_   3130 CTCATCTTCAACAAAGGTGCAAAGAACATTCATTGGGAAAAAAAACAGAC 3179
                         i v  i   i    i     v    v      v    i   i  -i  v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTC 397

  chr2_184375828_   3180 TTT--AATAAATAGTGCTGGGAAAACTGAATATACATATGCAGAAGAA-- 3225
                            --  i    i         v     i   ?v  i     i     --
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_184375828_   3226 --ACTAGACCCCTATCTCTCACCATATA-GAAAATCAAATCAAAATGGAT 3272
                         --ii i        i   v         -i     i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_184375828_   3273 TGTAGACTTAAATCTAAGACCTCAAAGAATGAAACTACAAAAAGAAAATA 3322
                         ii?    i     v     v  v   vv  i     viv i       i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_184375828_   3323 TTGGGGAAACTCTCCAGGACATTGGACTTAGCAAAAATTTCTTTAGTAAT 3372
                          v  ? v  v   i iv   v    ii vi    vii      vii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_184375828_   3373 ACCTCCAAAGCACTGGCAACCAAAGCGTAAATGAACAAATGGGATCATGT 3422
                           vi v       vi     v    viv    ii i    v   iivii 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_184375828_   3423 CAAG--TAAGAAACCTTCTAGACATCAAAGGAAACAATCGACAAAGTGAA 3470
                            i--   i  --   i ivi v        v  v   i v        
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_184375828_   3471 GAGACAACCCACAGAATGGAAGAACATATTTGCAAACTAGCCACGTGACA 3520
                         i                  i    v           ii vvi iv   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_184375828_   3521 AGGGATTAATAACCAGAATACAGAAGGAGTTCAAACGGCTCTGTAGAAAA 3570
                              i vi  v        i v  i  ii  vv  ii   vi  iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_184375828_   3571 AATCCAAATGATCTGATTTAAAAATGGGCCAAAGATTTGCATAGACATTT 3620
                           vv     i i ii   ?          v  i      v          
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_184375828_   3621 ATCAAAATAAGACATATGAATGGTGAACAGGCATGTGAAAAGGTGCCCAA 3670
                         v  v   v    i   ii     iv  i i   ii       i   i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_184375828_   3671 CATCATCAGAGAA 3683
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (139 / 90)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2119 26.37 9.31 1.31  chr2_184392097_184394731     1306  2143 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_184392097_   1306 AAAAAGATTTCATGTTCATGGATCAGAAGAACCAACATT---AAAATGAC 1352
                            i v  ii             ii     vii  i   ---  i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_184392097_   1353 CATACTGTCCAAAGCAATCTACAGATTCAATGCAATTTCTATCAAATT-- 1400
                         v     vi     vii              i     ii        v --
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_184392097_   1401 --ACTGTAATTTTTCACAGAATTTTTAAAGAATTTAAAATTCTAAAATTA 1448
                         --i   iv-     ii     v  ---i v  vi i -- i        v
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATT---GACAAGCTGA--TCCTAAAATTC 147

  chr2_184392097_   1449 ATATGGCATCAAAAGAGACCCTAAAAAGCCAAAGCAATTCTGAGGGAAAA 1498
                               v viiv   i     vi  v       i    ii   iii i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_184392097_   1499 AACCAAAGTGGGATGCATCATATTATCCAATGTCAAATTATACTCCAGGG 1548
                         i v      v   v vv   i i vi     v     viv    v  ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_184392097_   1549 GTATAGTAACCAA-ACGGAATGGTACTGGTATAAAAATAGACACAAGGAC 1597
                         v  i     i   -  i vi         i    ii       i vi  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_184392097_   1598 TCATAGAACAGAACAGAGGACCCAGAAATAAAGCCACATACCTAAAATCA 1647
                         iv  i   i    iv   iii           v   i i ii  vii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_184392097_   1648 G---------GACA------CC----TTATTCAA---------------- 1662
                         i---------    ------  ----ii      ----------------
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_184392097_   1663 --------AAATGGTGCTTGGAAAACTGGATGGCTATACGCAGAAGAAAA 1704
                         --------          v   v        i? i i i   i     vi
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_184392097_   1705 AAATGGGACCCATATATCAC--CGTATACAAAAAATAACTCAAGATAAAT 1752
                           i v      v  iv    -- i          v        i  ii  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_184392097_   1753 TG-AGACTTAAATGAAAGACCTCAAACTATCAAAATCT-AGACAAAAACA 1800
                         ii-    i      v    v  v       v   v   -   vi      
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_184392097_   1801 TAGGAAAAACTCTTCTGGACATTGGTCTAGGCAA--ATTATTTATAATTA 1848
                             ?iv  v     vv   v    vi       --i  vi   v --  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA--TA 595

  chr2_184392097_   1849 AGACTTTAAAAGCAAATGCAACAAAACCAGAAATAGACAAACGAGACATA 1898
                         v   vii       v v         vv i       i   ivi   v v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_184392097_   1899 ATTGAACTAAAGAGCTTCTGCACAACAGAAAAAAAAATCTACAAAAT--A 1946
                           ii  v v  i i   i  ii vv  i ii v vv   v v   i -- 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_184392097_   1947 AAGACAACCTACAGAATGGAAGGAAATATTTACAAACTATGCATCTGACA 1996
                                  i         i  i        i    ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_184392097_   1997 AAGGACCAATAGATTCGGAATCTACAAACAA-----AGAAGTAAACAA-G 2040
                          i    i-- iv  i i    v  i   v  ----- v  v v  i  -i
  L1M4_orf2#LINE/    746 AGGGACT--TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_184392097_   2041 AAAATACAA-----CCA-TTAAAAAGTGAACAAAGGATATGAA----CAT 2080
                             v    -----   -  ?    i  ii        v    ----   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_184392097_   2081 TTT---AAACAAGAAATGTAAGTAGAAAACGAAACACATGAAAAAATGTT 2127
                           i---   v    v  ii  i i vv  i-  i          i   i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCACATGAAAAGATGCT 892

  chr2_184392097_   2128 CAACATCAGTAATCAA 2143
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (134 / 84)
Gap_init rate = 0.03 (24 / 905), avg. gap size = 3.71 (89 / 24)  


1917 26.15 6.12 1.68  chr2_184422542_184424641      510  1163 (937)    L1M4_orf2#LINE/L1      112   794 (114)  

  chr2_184422542_    510 TTTTGTGTAGACATAGCCAAACTCATTCTAAAATTTATTGTAGAAAGGCA 559
                             v  i   v  v v   i  v  i        i  -i i    v   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT-ATGGAAATGCA 160

  chr2_184422542_    560 CAGGACCTACACTAGCTTGAATAATTTTGAAAAATAAGCATAAAGTGGGA 609
                         vi     i v v    ivi  i   i        v   v i     v   
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_184422542_    610 AGAATCACTTTACTCAAAACTAGGGCTAACTATATAGCTATAGTAATCGA 659
                         i  v    vi v i   vvii iii  v    i v     i       i 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_184422542_    660 AACAGCATGATATTGGCAGAGAAACAGACACACAGATCAATGAAACAGAA 709
                         i    ii  i  i     v iii i     i i         i  i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_184422542_    710 TAGAAAACCCAAAAATAAAGCCACACAAATATATCCAACTGATTTTTGAC 759
                          v  i ii   i       v   i   vv   ivi   i       i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_184422542_    760 AAAGGTACAAAGGTAATTCAATAGAGAAAGGCTAGTCTCTT------AT- 802
                           i   i v   iiv       i i     iv      i  ------  -
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_184422542_    803 ----TGGAGCAATTGGACATTCATAGGTTTAAAAAAGCACAAAGAAAGTA 848
                         ----   ii   i    i ?i  i v i----     ---  v   iv i
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGC----AAAAG---AATGAAGTTG 453

  chr2_184422542_    849 GACATAAACCTCACACCTTATACAAAACTAAACTCAAAGTGAATCCCAGG 898
                            vivv          v         v v        i  i   v?  i
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_184422542_    899 TTTAAATTTAA-AGTATAAAACTATAAAACT-TTAGAAAATTAAATA--- 943
                         ii     v   -  i-               -      i --   i ---
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGA--AAACATAG 550

  chr2_184422542_    944 ----AAATATTTA-GTCCTTAGG----GCTAAGAGTTCTTACATTTGACA 984
                         ----    v  ii- v    i  ----  v v iv      v  v     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_184422542_    985 ATAAA-TTACAATTTATAAAAGAAAAAATGTATCA---------CATCAA 1024
                         vi   -vi    viv i            iv  v ---------      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_184422542_   1025 AATTTAAAACTTTTGC-TTTCCAAAGATCCTGTAAAAAGGATAAAAAGAT 1073
                             v          i-i   v  i  iv  i v  i iii i      i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_184422542_   1074 TAGTTACAAAC----AGAAAATATTTATAAACCATATATTCAACAAAGGA 1119
                         v vii   i v----           ii   i       iii i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_184422542_   1120 CTTGTAGCTAGAATATATAAAGAACTCTCAAAACTCAACCATAA 1163
                               v i                   i v       iv    
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

Transitions / transversions = 1.68 (106 / 63)
Gap_init rate = 0.02 (16 / 683), avg. gap size = 3.19 (51 / 16)  

 373 21.26 3.94 3.94  chr2_184422542_184424641     1482  1608 (492)    L1M4_orf2#LINE/L1      782   908 (0)  

  chr2_184422542_   1482 AACTCAACGGTAAAATG-CAAATAAAATAGTTGAGTTATAAAATGGGCAA 1530
                                iii     v -       vvi i  ? -----           
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWA-----AAAATGGGCAA 826

  chr2_184422542_   1531 AAGACATAAACAGACATTTA-CTGAAGAGGACGTATAGATGGCAAATGAT 1579
                          i  iv i  i        v- ii    i  ii  i i     v   i v
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_184422542_   1580 CACATGAAAAG---TTCAATATCATTAACCAT 1608
                                    ---i    i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.71 (19 / 7)
Gap_init rate = 0.03 (4 / 127), avg. gap size = 2.50 (10 / 4)  


2319 27.65 4.55 1.25  chr2_184444876_184447561     1316  2194 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184444876_   1316 TGGAAACACATCCCAATGT-CTTGGGTGGGTAGAATT----TTACGAAAA 1360
                               v i      -   - v   i v  v   v  ----  iiv  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCA-TGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_184444876_   1361 TGACCATATT------AT-GA---AAAG---CAATCCAATTCCCATCAAA 1397
                           i v   i ------  -  --- v  ---   iv    i  i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_184444876_   1398 ATACCATCACCATTCTTCACAGAAGC--ACAAAAAAATCCCCAAATTCAC 1445
                           v   v vv v  i  ii     ii--    ivvi    iv       i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_184444876_   1446 GTGGAACCCAAAAAGAGCGCACATAGCCAAAGCCAGACTAAGCAAAAAGA 1495
                         i     vivv  ii  v vviv         i v vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_184444876_   1496 ACAAA-TTGCGGCA-TCTCAATACCCACCTTCCCACTATACTACAAGGCT 1543
                              -   vi v -  v  v v    vi   vv viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_184444876_   1544 ATAGTTACCAAAACAGCATGGTACTGATATGAAAATAGGCACACAGACCA 1593
                          i   v i   i    ii        ii  i ii    i  i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_184444876_   1594 ATGGAACAGAATAGAGAGCCCAAACAAAGAGAGAATGTTTTTCTCTATTT 1643
                               i     v     i   i --  v i -------iiiv vi    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGA--AATAAA-------CCCATACATTT 340

  chr2_184444876_   1644 -TG-TCAACTCATCTTTGACAAAGTAAACAAAAACATGAAGTGGGGAGAA 1691
                         -  -    i v  i  i     i vviv   i v   vv i      i i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_184444876_   1692 GACACCCTATTCAAAAAATGGTGCTATTACAATTGGCAAGCCACATGTAG 1741
                         i i vi  v     v          ivv    i   vv ?       i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_184444876_   1742 AAGAATGAAACTGGATCCTCATCTCTCACCTT---CAAAAATCAACTCGA 1788
                                  ii    i  ii i   v    v ---       i     i 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_184444876_   1789 GATGGATCAAATACTTAAATCTAAGGTCTGAGACCATAAAAATTATGGAA 1838
                         i        ? v  i     v    iv  i i  i      v iv i   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_184444876_   1839 GATAACATCAGAA-AATTCTTCTAGGCATTGA--TAGGCAAAGAATTCAT 1885
                           v     vi ?i-  v     vv i v   i--       v iv   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_184444876_   1886 -GACGTGGAACCCAAAAGCAAATGCAACAAAAACAAAAATAAATGAATGG 1934
                         -  ii  iv   -       v v         iv       i  i   v 
  L1M4_orf2#LINE/    591 AGATATGACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_184444876_   1935 GACTTAATTAAACTAAATAGCTTCTGCACAGCAAAAGAAATAATCAGCAG 1984
                              v  i   v v  v i   i  ii vv    i  v iv    iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_184444876_   1985 AGTAAACAGACAACCCACAG--TGGGATAAAATATTCAAAAACTATGCAT 2032
                            i  v             --     v        iiv   ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_184444876_   2033 CCAACAAAGGACTAATATACAGAATCTACAAGGAACTG----AGATCAGT 2078
                          ii i  i     vi   v      v  i  i     v---- iv   i 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_184444876_   2079 AAGAAAA---CAAATAATCCCATCAAAAAGTGGGCAAATGATATGAATAA 2125
                           v    ---       i  v  i?    i        v   v      i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_184444876_   2126 ACAATTCTCAAAAGAAAATATACAAACAGCCAACAAACATATGAAAAAAT 2175
                            v     v      i         ii     i  i  i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_184444876_   2176 TCTCAGTGTCACTAATCAT 2194
                         v    iii   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (137 / 102)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.32 (51 / 22)  


2881 27.73 1.96 0.58  chr2_184483050_184487528     3111  3979 (500)    L1M4_orf2#LINE/L1        1   881 (27)  

  chr2_184483050_   3111 TGGAAGAACATTCCATGCTCTTGGGTAGGAAGAATCAATATCGTGAAAAT 3160
                              ii i  i     i  v   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184483050_   3161 GGCCATACTGCCCAAGGTAATTTATAGACTCAATGCCATCCCCATCAAGC 3210
                            v     v     iv i  i  i   i    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184483050_   3211 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACCTTAAAGTTCA 3258
                          v   iivi i  i  ii     -   -- v     - i i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_184483050_   3259 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 3308
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_184483050_   3309 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATTCTACAAGGC 3358
                                i      vv    i  v  ii i      viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_184483050_   3359 TGCAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATACAGACC 3408
                          i      i   i    ii i       i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_184483050_   3409 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 3456
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_184483050_   3457 TTCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGAAAAGGGTTCC 3506
                         vvi    i  i     ivv  v   i v  vvv      i    ii vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_184483050_   3507 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3556
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_184483050_   3557 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3606
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_184483050_   3607 TTAAAGACTTAAGTGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3656
                          i ?    i   i   v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_184483050_   3657 CTAGGCA-ATACCATTCAGGACATAGGCATAGGCAAGAACTTCATGTCTA 3705
                         v    ?i- v i -   iv   v v  vv       viii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_184483050_   3706 AAACACCAAACGCA-AAGCAA----------AATTGACAAATGGGATCTA 3744
                         vi        v   -      ----------   v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_184483050_   3745 ATTAAACTAAAGAGCTTATTCACAGCAAAAGAAACTACCATCAGATTGAA 3794
                           i   v v  i i   v vii vv    i  v    i  vv i v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_184483050_   3795 CAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACTCATCTGACA 3844
                         v  i     i                vv       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_184483050_   3845 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 3894
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_184483050_   3895 AAAACACACAACCCCATCAACATGTGGGCGAAGGATATGAACAGACACTT 3944
                           i   v i     v  i? v vi     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_184483050_   3945 CTCAAAAGAAGACAT-TATGCAGTCAGAAGACACAT 3979
                            v        i  -i viii i  iv ii     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (10 / 881), avg. gap size = 2.20 (22 / 10)  


3020 27.27 0.78 0.11  chr2_184507152_184511786.rev     3243  4144 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184507152_   3243 TGGAAACATATCCCATGCTCATGGATGAGTGGAATCAATACTGTGAAAAT 3292
                               v          i        vi vi  v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184507152_   3293 GACCATACTGCCAAAAGCAATCTACAAATTTAATGCAATTCCCATAAAAA 3342
                          i v     v  v   vii       i   i  i     i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184507152_   3343 TACCATCATCATTCTTCATGGAACTAGAAAAA--AATCTTAAAATTTATA 3390
                          v   v vv v  i  iiii   v v  v  i--i   i       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_184507152_   3391 TG-AAACAAAAAAGAGCCTGCATAGACAAAGCAAGACTAAGCAAAAAGAA 3439
                           -   iiv  ii  v  v v    v    i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_184507152_   3440 TAAATTTGGAGGAATCAAATTACTTGATGGCAAAGTATACTACAAGGTTA 3489
                         i   v        v   v i v iii  vv    iiv        i i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_184507152_   3490 TAATTACCAAAATAGCATGGTTCTAGTATAAAAATAGGCAGGTAGACCAA 3539
                         i i v i   i i  ii    v  i i    ii    i  vi    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_184507152_   3540 TGAAACAGAAATAGAGAACCCAGAAGTAAAGCCAAATACTTACACCCAAC 3589
                           i  i    v -    ii      i    v   v i i   iivi   i
  L1M4_orf2#LINE/    301 TGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_184507152_   3590 TGATTCTTGACAAGGCAAATAAAAACATAAAGTGGGAAAAGGACACCCTA 3639
                              i i       vvivi  i v   vv i    i    i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_184507152_   3640 TTCAACAAATGGTGCTGGAATAACTGGCAAGCCACATGTAGAAGAATGAA 3689
                                           i i      vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_184507152_   3690 GCTGGATCCTAATCCCTCAACTTATATAAAAATCAACTCAATATGGATCA 3739
                          i    i  iv i i v  v v    i      i       v        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_184507152_   3740 AAGACATAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACATC 3789
                         ?    v     v     v  i    i      v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_184507152_   3790 AGAAAAATTATTCTAGACATTGGCTTAGGCAAAGAATTCATGACCAAGAA 3839
                         i ?iv  v v   vv   v    v        v iv   v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_184507152_   3840 CCCAAAAGCAAATGCAACAAAAACAAAGATTAATAGATTGGACCTAATTA 3889
                         v         v v         iv   i  vi   i       i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_184507152_   3890 AACTAAAAAGCTTCTGCACAGCAAAAGAAATAATTGGAAGAGTAAATAGA 3939
                           v v    i   i  ii vv    i  v iv  iiii i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_184507152_   3940 CAACCCACAGAGTGGGAGAGAATATTCACAAATTA-GCATCTGACAAAGG 3988
                                    i       i      ii     i -ii      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_184507152_   3989 ACTC--ATCCAGAACCTACAAGGAACTCAAACAAATCAGCAAGAAAAAAA 4036
                            i--        iv  i  i      vv    v   ii  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_184507152_   4037 TAA-TAATCCCATCAAAAAGTTGGCAAAGGGCATGAATAGACAATTCTCA 4085
                         i  -   i  v  i?    i v        iiv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_184507152_   4086 AAAGAAGACATACAAATGGCAAACAAACATATGAAAAAATGCTCAAAATC 4135
                                 i           v  i  i  i       i        v   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_184507152_   4136 CCTAATTAT 4144
                         v????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


3175 23.39 1.50 4.08  chr2_184511987_184516566     3157  4088 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184511987_   3157 TAAAAAAAT---TCATGTTCATGAATCAGAAGAATCAATATTGTTAAAAT 3203
                          ii   i  ---i          i  ii     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184511987_   3204 GTCCATACTACTCAAAGCAGTCTACAGATTTAATGCAATCCATATGAAAA 3253
                          v v     v i    viii          i  i       v   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184511987_   3254 TAGCAATGACATTCTTCACAGAAATAAAACAAA--AATC-TAAAATTCAT 3300
                          vv  iivi v  i  ii       vi -   i--i   -          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr2_184511987_   3301 ATATAATCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAGTAAAAATA 3350
                           iv  vii   ii                 i v   i i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_184511987_   3351 ACAAAACTGGAGAAATCACATTACCTGACTTCAGATTATACTATAGAACT 3400
                              ii     i v     i v  ii i    i viv     i i i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_184511987_   3401 ATAATA-TCCAAACAGAATGGTATTGTCATTAAAACAGACACATAGACCA 3449
                          i i  -  v i    vi     i  v   v ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_184511987_   3450 ATGGAAAAGAATAGAGAACCCTGAAATAAATCCACACAACTATAGCTATA 3499
                               v     v    ii  v        i   i   vi   i i----
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT---- 345

  chr2_184511987_   3500 AGTGCCAACATAAAAATAAGTGCCAACTCATTTTTGACAAAGGTGCCAAC 3549
                         -----------------------   i v     i     i        v
  L1M4_orf2#LINE/    346 -----------------------CAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_184511987_   3550 AACATACCCTGGGGAAAAGGCAGTCTCTTCAATAAATGGTGCTGGGAAAA 3599
                          v   v vv        iiii     i     i              v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_184511987_   3600 CTGGATATCCATCTGCAGAAGAGTGAAACTAGGCCTATATTTCTCACCAT 3649
                                ?   iv    i    i    ii i i  iv  ii  v      
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_184511987_   3650 ATACAAAAATCAAATGAAAATTACATTAATGACTTAAATCTAA---CTCC 3696
                                   i  v v     vi-  i ?v   i     v   ---  v-
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGG-ATCAWAGACCTAAATGTAAGAGCTA- 520

  chr2_184511987_   3697 AAACTATTAATCTACTACAAGAAAACATTGGAG-AAACCACCATGGCATT 3745
                                v  v  vi  v          v  ? -   i vi i  i v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_184511987_   3746 GATTTGGGCAAAAATTTCTT-GATCACTAAAT-ACCCCACAAGTACAGGC 3793
                          iv  i     vii      -   ------  -  v   v   i   i  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGAT------ATGACACCAAAAGCACAAGC 614

  chr2_184511987_   3794 AACCAAAGCAAAAATGGACAAATGGGATCACATCAAG-TTAAAAAGCTTC 3842
                            v    v      i  i    v   iiv      i-       -   i
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTT 663

  chr2_184511987_   3843 TGCACAGCAAGAGACACAATTAACAAAATGAAGAAACAACCCACAAAATG 3892
                           ii vv   ii     v  i  v   i    i i          i    
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_184511987_   3893 GGAGAAAATATTTACGAACTGCTCATCTGACAAGTGATTAATAACCAGAA 3942
                                      i i  iiiivi      i   v  i vi  v      
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_184511987_   3943 TATATAAGGATCCCAAACAACTCTATAGAAAAAAAAATGAATAATCCCAT 3992
                                i  v i vv       v   - v     i ii     i  v  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATA-ATAAAAAGACAAATAACCCAAT 812

  chr2_184511987_   3993 CGAAAAATGGACAAAAAATTTGAATAGACATTGCTCAAAAGAAGACATAC 4042
                         i?        i    ii               v   v        i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_184511987_   4043 AAATGGCAAACAGGCATATGAAAAGATGCTCAACGTCATGGATCAT 4088
                                v  i i   i                 i   ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (137 / 77)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.25 (52 / 16)  


2839 27.08 1.89 1.11  chr2_184531281_184537966     5294  6194 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184531281_   5294 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAACAT 5343
                               i i  i     i        v      v i        v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184531281_   5344 GGCCATACTGCCCAAAGGAATTTATAGATTCAATGCTATATCCATCAAGC 5393
                            v     v      vvi  i  i        i  v  vi i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184531281_   5394 TACCAATGACTTTCTTCACAGAATTAGAAAAAAT-ACTTTAAATTTCATA 5442
                          v   iivi i  i  ii     v v  v  iv - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_184531281_   5443 TTGAATCTAAAACAAGCTTCT----ATAGCCAAGACAATTCTAAGCAAAA 5488
                          v   ---- vi    vvv i----        i     ii i iv  i 
  L1M4_orf2#LINE/    151 TGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_184531281_   5489 AGAACAAAGCTGGCAGCATTATGCTACCTGACTTCAAACTATACTACAAG 5538
                                  i   vi vv i ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_184531281_   5539 GCTCCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGA 5588
                            v      i   i    ii         i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_184531281_   5589 CCAATGGAACAGAACAGA-AGCCTCAGAAATAAAGCCACACATCTACAAT 5637
                         i        i    iv  -  i -          v   i    i  iii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chr2_184531281_   5638 CATCAGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAATGATTC 5687
                           viv   i  i     ivv  v   i v  vv           vi  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_184531281_   5688 CCTATTTAATAAATGGTGTTGGGA-AACTGACTAGCCATATGCAGAAAAC 5736
                         i  v  i  i        i     -     iv  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_184531281_   5737 TGAAGCTGGATCCCTTCCTTACACCTTTTACAAAAAT-AACTCAAGAGGA 5785
                              i    i    v   i     v v         -       i v i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_184531281_   5786 ATTAAAGAATTAAACATAAGACCTAAAGGCATTAACATCCTAGAAGAAAA 5835
                           i ?   vi    ii     v     ivi  v  vv  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_184531281_   5836 CCTAGGCA-ATACCACTCAGGACATAGGCATTGGCAAAGACTTCATGACT 5884
                          v    ?i- v i -i  iv   v v  vv v     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_184531281_   5885 AAAACACCAAAACCAATGGCAACAAAAGCCAAGATTGACAAATGGGA--- 5931
                          vi         v  vvi          vv  i  v  i    v   ---
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_184531281_   5932 --TCTAAATAAAGAGCTCCTGCACAGCAAAATAAACTCTCATCGGAGTGA 5979
                         --  v    v  i i  ii  ii vv    iv v   v   vvii     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_184531281_   5980 ACAGGCAACTTTACAGGATGGGAGAAATTTTTTGCAATCTATTCATCTGA 6029
                          v  i    ii-    i          v v       vii  vi      
  L1M4_orf2#LINE/    695 AAAGACAACCC-ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_184531281_   6030 CAAAGGGTGAATAATATCCAGAATCTACAAAGAACTCAAACAAATTTACA 6079
                         i  i  --- v vi          v  i         vv    v iv i 
  L1M4_orf2#LINE/    744 TAAGGG---ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_184531281_   6080 AGAAAAA---AAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGA 6126
                          v     ---   i     v  i?    i    ii      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_184531281_   6127 CACTTCTCAAAAGAAGACATTTATACAGCCAACAAACATATGAAAAAATG 6176
                           i     v        i  vi v ii     i  i  i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_184531281_   6177 CTCATCATCACTGGTCAT 6194
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (135 / 105)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.08 (27 / 13)  


3211 27.06 0.55 0.66  chr2_184539257_184548185     4877  5785 (3144)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184539257_   4877 TGGAAGAACATTCCACACTTATGGGTAGGAAGAATCAATATTGTGAAAAT 4926
                              ii i  i   iii i    i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184539257_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184539257_   4977 TACTAAC-GCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTT 5023
                          v i i -      i  -i     -   -- v  i  - iii    i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_184539257_   5024 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCACTCCTAAGCCAAAA 5073
                                 viiv  ii  v  v v  v     iv  v  i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_184539257_   5074 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5123
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_184539257_   5124 CTACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATGTAGAT 5173
                                  i   i    ii        ii iv ii i   v  i     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_184539257_   5174 CAATGGAACAGAAC--AAAGCCCTCAGAAATAACGCCACATATCTACAAC 5221
                                 i    i-- i  i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_184539257_   5222 TCTCTGATCTTTGACAAACCTGAGAAAAACAACCAATGGGGAAAGGATTC 5271
                         ivvi    i  i     ivv  vv  i v  vi            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_184539257_   5272 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5321
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_184539257_   5322 TGAAACTGGATCCCTTCCTTACATCTTATACAAAAATCAATTCAAGATGG 5371
                             ii    i    v   i   i v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_184539257_   5372 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5421
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_184539257_   5422 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5471
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_184539257_   5472 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTC 5521
                         vi            vvi          vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_184539257_   5522 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5571
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_184539257_   5572 CAGGCAACCTACAAAATGGTAGAAAATTTTTGCAACCTACTCATCTGACA 5621
                         v  i     i   i     v       v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_184539257_   5622 AAGGGCTAATATCCAGAATCTACAATGAGCTCAAACAAATTTACAAGAAA 5671
                          i  i  vi          v  i  v  i   vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_184539257_   5672 AAAACAAACAACCCCATCAAAAGGTGGGTGAAGGACATGAACAGACACTT 5721
                           i     i     v  i?   ii    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_184539257_   5722 CTCAAAAGAAGACATTTACGCAGCCAAAAAAACACATGAAAAAATGCTCA 5771
                            v        i  vi viii     v  i-          i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCA 894

  chr2_184539257_   5772 CCATCACTGGCCAT 5785
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  

2855 28.27 1.79 0.34  chr2_184539257_184548185     7543  8437 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184539257_   7543 TGGAAACTTACCCCATGATGATGGATGGGTAGAATCAATATTGTGAAAAT 7592
                               vv  i      v v      v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184539257_   7593 GACCATACTCACAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAAA 7642
                          i v      v v   vii       i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184539257_   7643 TACCACCATCATTCTTCACAGAATTAGAAAAAGCAATTCTAAAATTCATA 7692
                          v   v vv v  i  ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_184539257_   7693 TGGAAGCAAAAATGAGCCTGCATAGCCAAAACAAGACTAAGCAAAAAGGA 7742
                              iiiv  iv  v  v v             vvi i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_184539257_   7743 TAAATCTGGAGGCATCCCATTATCTGCTTTTAAACTACC--CTGTAAGGT 7790
                         i   vi      vv  v  i vi iiv   i   --  i--  ii  i i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAGC 248

  chr2_184539257_   7791 CATAGTCACCAAAACAGCATGGTAGTGATATACAAATAGACACATAGACC 7840
                         i i   v i   i    ii     v  ii   vii       i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_184539257_   7841 AATGGAACAGAATAGAGAACCCAGAAGTAAACCCAAATACTCACAGCCAA 7890
                                i     v    ii      i        v i i i ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_184539257_   7891 CTGATCTTCAACAAAGCAAACAAAAACAAAAAGTGCAGAAAGGACATTCT 7940
                         i    i   i    i vviv   i v  vvv i  vi     i i v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_184539257_   7941 ATTCAACAAATGATGCTGGGATAATTGGCTAGCCACATGTAGGAGAATAA 7990
                         v           i        i  i   v  ?       i ii     i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_184539257_   7991 AACTGGATCCTCATCTCTTATCTTATACAAAAATCAACTCAAGATGGATT 8040
                          ii    i  ii i   vi i v           i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_184539257_   8041 AAGGACTTAAATCAGAGACCTGAAACTTTAAACGTTCTGTAAGATAACAT 8090
                          ?i   i     vvi   v  i     v    vv ii iv    v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_184539257_   8091 TGGAA-AAACCTTTCTAGACATTGTCTTAGGAAAGGATTTAATGGCCAAG 8139
                         v  ?i-   i   iv -   v   vv     v  v i   vv i vi v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_184539257_   8140 AACCTAAAAGCAAATGCAATAAAAACAAACATAAATAGCTAAAACTTAAT 8189
                          vv i       v v    i    iv   v   i   iv vii    v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_184539257_   8190 TAAACTAAAGAGCTTTTGTGGGGCAAAAG----TAACAGCAGAGTAAACA 8235
                         i   v v  i i        vvv    i ----  v  iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_184539257_   8236 GGCAACTTACAGAGTAGGAGAAAATCTTCACTATCTATACGTCTGACAAA 8285
                          i    ii     i i         v  ii v vii   ii     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_184539257_   8286 GGACA-GTATCCAGGATCTAAAACAAACTC----AAATCAGCAAGAATAA 8330
                             v-        i  v  v  vi     ----  v   ii  v  v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_184539257_   8331 AACAA----TCCCATCTATAAGTGGGCTAAGGACATGAATAGACAACTCT 8376
                         i    ----i  v  i? v  i     v     iv          vi   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_184539257_   8377 CAAAAGAAGACATACAAATGGCCAACGAACATATGAAAAAATACTCAACA 8426
                          v        i              ii i  i       i  i       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_184539257_   8427 TCACTAATGAT 8437
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.37 (144 / 105)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  


2885 23.39 2.54 6.56  chr2_184628711_184634056     3910  4854 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_184628711_   3910 GAAAATACATCCCATGCTCATGTATTGGAAGAATTAATATTGTTAAAATG 3959
                          i   v i        i     v         v             i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_184628711_   3960 ACCATACTACCTAAAATAATTTACAGATTCAATGCAATCCCCACTAAAAT 4009
                         i v     v  i   v i  i           i        i ii     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_184628711_   4010 ACCAGTGACATTTATCGTAGAAATAGAAACAATAATCCTAAAATTTGTAT 4059
                         v    ivi v   v i i      v  v viv i           ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_184628711_   4060 GGAAGCACAGAAGACTCTGAATAGTTGAAGTAATAATGAACAAAAAGAAC 4109
                             iii  iii   i v      iii  ii   vv    v  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_184628711_   4110 AAAAGTGGAGGCATCACACTATTGGACTTCAAAATATACTACAGAACTAT 4159
                            iv      vv       viivi i       iv       i i   i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_184628711_   4160 AGTAACCAAAGCAACATGGTACTAGCATAAAAACAGACACAAAAACCAAT 4209
                              i   ii  iii       i      ii i     i v i i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_184628711_   4210 ACCATGGAAGTATAGTAATGAAAGCAGCATGGTACCAGCATAAAAGCACA 4259
                         -----    ---   v v   i  i-------------------------
  L1M4_orf2#LINE/    302 -----GGAA---TAGAATTGAGAGT------------------------- 318

  chr2_184628711_   4260 CACACAGTCCAAAGGAACAGGACAACCCAGAAATGAATCCATGTATTTAC 4309
                         --------------------------        i  i    ii     i
  L1M4_orf2#LINE/    319 --------------------------CCAGAAATAAACCCATACATTTAT 342

  chr2_184628711_   4310 AGCCAACTTGAGTTTTGACAAAGGAGCCAAGAACATTCAGTGGGGAAAGG 4359
                         i i   -    v   i     i  v       v      i         i
  L1M4_orf2#LINE/    343 GGTCAA-TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_184628711_   4360 ACAGTTTCTTCAATAAATGGTGTTGGGAAAAGTGGATATCCATACGCAGG 4409
                          i   i i     i        i     v  v      ?   i i   ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_184628711_   4410 AGAATGAACCTAGACCCCTATATCTCAACATCTA-AAAAATCCAACTCAA 4458
                                 vi i        iv  v  v   v  -      i-       
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AACTCAA 490

  chr2_184628711_   4459 AATCGTTTAAAGAGTTAAATGTAAGACCAAAAACTTAAAAAACACT-ATA 4507
                            v v i ?   vi           v v      - v     v  - v 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTTAGA 539

  chr2_184628711_   4508 AGAAAACATAGAGGACAAGCTTTAAAAAATTGGTCTAGGCAAAGATTTTT 4557
                                    i? vv  v   iivi vv    vi       v i   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_184628711_   4558 T-----TGGC--TAAAA-CATAGGCAATAAAA--ATTAATGGATGA---- 4593
                          -----  i --i    -  i i    i    -- vv   i   i ----
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_184628711_   4594 GACTATATTAA--TGAAAATCTTCTGTACAGCAAATAAAACAGTCAACTG 4641
                             vi  i  -- v    v   i   i vv    vi v  vi    vvi
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_184628711_   4642 AATGGAGAGATAACCAA-AAATTGGCAGAAAATATTTGCAAACTATTCAT 4690
                          i  i i   i    v - i v   v                ii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_184628711_   4691 CTGACATTGTATTAATATCCAGAATACACAAGGAGCTCAGACAGTGCAAT 4740
                             i vv v i vi           i i  i  i   vv   iiv    
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_184628711_   4741 AGCAAAAAAA-AAATG---CA-TTAAACAGTGTGCAAAGGATCTGAATAG 4785
                          ii     i -    i---  -  ?  v i  v         i       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_184628711_   4786 ACATTTCTCAAAAGAGGACTTACGGATGGCCAACAGGTACATGAAAAAAT 4835
                                  v     i  iv   ii        i i i         i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_184628711_   4836 GCTCAGTATCACCAATCAT 4854
                              ii    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (137 / 80)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 4.78 (86 / 18)  


2079 25.50 3.07 7.20  chr2_184678176_184681789.rev     2178  3122 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_184678176_   2178 GAATAATACTCCATGCTCATGAATTGAAAGAATCAGTATCATTAAAATGA 2227
                            vi   ii     i     i    i    v i i   ii    i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_184678176_   2228 CCACACTGCTCAAAGCAATTTACAGATTCAATGCTATTTCTATCAAATTA 2277
                          v i   v i    vii  i           i  v  ii        v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_184678176_   2278 CCAA-TGACATTTTTCAAGGAATTAGAAAAAAACTG-TTCTGACATTCAT 2325
                            i-  v v     vv  i    i--- v  i   - i  i v      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCAT 149

  chr2_184678176_   2326 ATGGAAC--CAAAAAAATAGCCCA--ATAGCCAAATCAATCCTAAGCAAA 2371
                               v--   iii ----    --         v     i i --   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGA--AAA 193

  chr2_184678176_   2372 AAAACAAAACAAAACAAAACAAAACAAAAAGCTGTAGGCATCACAGTACC 2421
                          i  -----------------i      -- i  v   vv     v v  
  L1M4_orf2#LINE/    194 AGAA-----------------GAACAAA--GTTGGAGGACTCACACTTCC 224

  chr2_184678176_   2422 CATCTTCAAACTATACTACCAGGCTACAGTAACTAAAATGTCATGGTACT 2471
                           vi      viv      v i          ii  i iivii       
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr2_184678176_   2472 AGTTCAAAAACAGACACAGAGACCAATGAAATAGTATAGAGAACCCAGAA 2521
                         i ivi  ii i     i v   i     i     v  v    ii      
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr2_184678176_   2522 ATAAAGTAGCATAC--CTGCAACCATCTGATCTTTGGCAAAGTTGACAAA 2569
                              vi--     --i iiiii  vi    i  i i   i v  v   i
  L1M4_orf2#LINE/    325 ATAAACC--CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_184678176_   2570 AATAAGCAATGGGAAGAAGACT--TCCTATTCAATAAATGGTTCTGG--C 2615
                          vi vv       i -    v --  i -     i       v    -- 
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGA-AAGAATAGTCTT-TTCAACAAATGGTGCTGGGAC 420

  chr2_184678176_   2616 TAGTGGGCTATGCATATACAGAATAATGAAACTAGACTTCTACC-CATCA 2664
                         v v   i-  ?v  i  i  i  v      ii i   ii     -  -  
  L1M4_orf2#LINE/    421 AACTGGA-TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA-CA 468

  chr2_184678176_   2665 CCATGTACCAAAATTAACTCAAGATGGATTAAAGACATAAATGTAATGCC 2714
                             i   v             i      i ?    v         viv 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_184678176_   2715 TCAAACTATAAAACTTCTGTGAGAAAACCAAGAAATAT-CCTTCTCAATA 2763
                          v             ii ivi       vv  i?i  v-i    vii iv
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_184678176_   2764 TCAGCATTGGCAAATAATTTAT-GGCTAAGTCCTCAGA-GCAATTGAGCA 2811
                          ii vv v     - ii   v -i v  v v vi  i -   --ii    
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCA--CAAGCA 615

  chr2_184678176_   2812 A---AAATAAGAATTGTTGAATGAGACCTGATTAAACTAAAGAAC----- 2853
                          ---  iv  i   v v i   vi   i v  i   v v  i   -----
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_184678176_   2854 -ACAGCAAAAAGAAAGAAAAAAAAAAAAACTATCCACCGAGTAAGCAAAA 2902
                         -i vv    ii--------------- v      v vvi   i iv i v
  L1M4_orf2#LINE/    666 TGCTTCAAAGG---------------ACACTATCAAGAAAGTGAAAAGAC 700

  chr2_184678176_   2903 AACCTACATAACAGCAGAAAATATTTACAAAC--TGTATCTGACAAAGGT 2950
                             i   v  ii v           i    i-- i       i  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_184678176_   2951 CTAATGTCCAGAACATGTAAGGAGCTTAAACAAATCAATAAGCAAAAAAA 3000
                           vi i       i  i   i  i  ivv    v       -i     i 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAGA 799

  chr2_184678176_   3001 AAAAAAAAAAAAAAAAAAATACGCTATTAAAAAGAGAGCAAAAGACATGA 3050
                         v   v  -------------- v v   ?    iv i     i  iv   
  L1M4_orf2#LINE/    800 CAAATAA--------------CCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_184678176_   3051 AAAGACACTGCTCAAAAGAAGATATATAAATGGCCAACAA--ACTTGAAA 3098
                          v     i v   v            i          i  --  v     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_184678176_   3099 AAAGTGCTCAACATCACTAATCAT 3122
                          i -            ????????
  L1M4_orf2#LINE/    886 AGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.03 (31 / 906), avg. gap size = 3.13 (97 / 31)  


2698 29.44 1.22 0.33  chr2_184750611_184753955.rev     1954  2853 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184750611_   1954 TGGAAAAAAATTTCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2003
                               i v  ii    i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184750611_   2004 GGCCATACTGACCAAAGAAATTTATAAATTCAATGCTATTCCTATCAAGG 2053
                            v     vv     vvi  i  i i      i  v  i        ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184750611_   2054 TACTATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 2102
                          v i vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_184750611_   2103 TTCAAACAACAGAAAAGCCCGTATAGCCAAGACAATCCTAACCAAAAATA 2152
                         v vi  vvi  iiii v  v v        i      i i vv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_184750611_   2153 ACAAAGCTGGAGGTATCATGCTACCTGACTTCAAACTGTACTACAAGCCT 2202
                               i      vv   ii  v  ii i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_184750611_   2203 ACAGTAACCAAAACAGCATAGTACTGGTACTCAAACAGATATATAAGCCA 2252
                                i   i    ii i       i ivvii i   i     iii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_184750611_   2253 ATAGAAAAGAACAGAGGCCTCACAAATAACACCACACATCTACAACCATC 2302
                           i   v    iv   ivii  v      vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_184750611_   2303 TGATT---GGCAAACCTGATAAAAACAAGCAATGGAGGAAGGATCCTCTA 2349
                              --- i   ivv  vi  i v  vv      i i   i  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_184750611_   2350 TTTAATTAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACAGAA 2399
                           i  iv             v      v  ?   i     i  i vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_184750611_   2400 ACTGGGCCTCTTCCT-ACACCTTATACAAAAATGAACTCAAGATGGATTA 2448
                         ii   i  i  v   -     v           v       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_184750611_   2449 AAGACTTAAATGTAAAACCGAAAACGATTAAAACCCT-AGAAGAAACCCT 2497
                         ?    i         i v v     v  -     i  -        v v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chr2_184750611_   2498 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 2546
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_184750611_   2547 ACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTAAT 2596
                                     vvii         vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_184750611_   2597 TAAACTAAAGGGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGAACA 2646
                         i   v v  iii   i  ii vv    iv v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_184750611_   2647 GGCAAACTACAGAATGGAAGAAAATTTTTGCAATCTATCCATCTGACAAA 2696
                          i   v i         i       v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_184750611_   2697 GGTCTAATATCAAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 2746
                           v  vi    v     v  i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_184750611_   2747 AACAA----CCCCATCAAAAAGTAGGTGAAGGATATGAACAGACACTTCT 2792
                         i    ----   v  i?    i i  ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_184750611_   2793 CAAAAGAAGACATTTATGCGGCCAAGAAACATGCAAATAAAAGCTCATTA 2842
                          v        i  vi vii      v  i  iiii  v i v     vi 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_184750611_   2843 TCACTGGTCAT 2853
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.33 (149 / 112)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2705 27.86 1.10 1.10  chr2_184783904_184788191.rev     2889  3796 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184783904_   2889 TGGAAATACATCCCATGCTTACAGATGGATAAAATCAATATTGTGAAAAT 2938
                               v i        i i ii   v iv i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184783904_   2939 GACCATACTGCCAAAAGAAATCTATAAATTAAACGTAATTTCTATCAGAA 2988
                          i v     v  v   vvi     i i   v    i   ii      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184783904_   2989 AACCACCATCATTCTTCACAAAACT--ATAAAAAAAAACTAAAATTCATA 3036
                         vv   v vv v  i  ii  i  v -- i  ivvi vv            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_184783904_   3037 TGGAACCAAAAATAAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGGA 3086
                              viiv  ivi v  v v         i   vvi i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_184783904_   3087 CAAATCTGGCA---TTACATTACCTGCTACAAACTATGAAATATACTATA 3133
                             vi   vi--- i   i v  i------  i vii   iv     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCC------AATTTCAAAACTTACTACA 244

  chr2_184783904_   3134 AGGCCATAGTCATCAAAACAACATGGTATTCGTATTAAAACAGGCATATA 3183
                          i  i i   v     i   iii     i v i  v ii i  i      
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_184783904_   3184 GACCAATGGA-CAGAATAGAGAAACCAGAAATAAAGTCAAATCCTCACAG 3232
                           i       -i     v    iv           vi  v ivi i ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_184783904_   3233 TCAACTGATCTTTGACAAAGCAAACAAAACCATAAAGTGGGGAAAGGAAC 3282
                             i    i  i     i vviv   i     vv i         -  i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AAT 393

  chr2_184783904_   3283 ACCCTATTCAACAAAGGGTGCTGGGCTAATTGGCAAGCCACATATAGAAG 3332
                          vi  v         v         vi  i   vv ?      ii i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_184783904_   3333 AAGGAAACTGGATCCTCACTTCTCACCTTATACAAAAATCAACTCAAGAT 3382
                           v   ii    i  ii  i  v    v           i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_184783904_   3383 GGATCAAAAACTTAAATCTCAGACCTAAAACAATAAACATTCT-AGAACA 3431
                               ? i  i     v v   v       v     - i   -    v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGA 542

  chr2_184783904_   3432 CAACATTGGAA-AAACCTCTGTAGACAATGGGTTAGGCAAAGCCTTCATG 3480
                         v     v  ?i-   i  ii  -   vv            v vi   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_184783904_   3481 ACCAAGAACCCAAAAGCAAATGCAACAAAAACAAAATTTAATAAATGGGA 3530
                         ivi v  vv         v v         iv    v vi      v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_184783904_   3531 CTCAATTAAGCTAAAAAGCTTATGCACATCAAAAGAAATAAT-AAGCAGA 3579
                           iv  i  iv v    i   v  ii v     i  v iv  -   - i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAA 690

  chr2_184783904_   3580 GCAAACAGACAACCCACAGAGCGGGAGAAAATCTTCACAATCCATACATC 3629
                          ii  v              ii          v  ii   vi    i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_184783904_   3630 TGACGAAGGGCTAATATCTGGAATTTATAAGGAAGTCAAACCA-TCAGCA 3678
                            ii i  i  vi    ii    v     i   v  vv  v -   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_184783904_   3679 AGAACAAAACTTACAATCTCATCAAAAAGTGGGCTAAAGACATGAATAGA 3728
                          v  v  i  vv i  i iv  i?    i     v  i  iv        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_184783904_   3729 CTATTTTGTAAGGAAGATATACAAATGACCAACAAACATATGAAAAGATG 3778
                          vv  i vi  i               i    i  i  i           
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_184783904_   3779 CTCAACATCATTAATAAT 3796
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (143 / 106)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


1279 24.27 2.15 9.39  chr2_184822523_184828542.rev     3869  4379 (1641)    L1M4_orf2#LINE/L1        1   474 (434)  

  chr2_184822523_   3869 TGGAAAAACATTCCATACTCATAGATAGGAAGCACA-AATATGGTAAAAA 3917
                               i i  i    ii    i   v     -  v-     v  v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGA 49

  chr2_184822523_   3918 TGGCTATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCTTATCAAA 3967
                             v     v      vii  i  i        i  v  i i       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_184822523_   3968 CTAGTAATGACATTCTTCACAGAACTAAAAAAAAACAAAAAAAGCCAAAA 4017
                         v vvi iivi v  i  ii     v vi ------   -----  ii --
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGA------CAA-----GCTGA-- 136

  chr2_184822523_   4018 AAACCCTATTTTAAAATTCGTATAAAAACGTTTCAAGAAGCCTA-AATAG 4066
                         -------- ii        i   ii   i ---    iii  i -     
  L1M4_orf2#LINE/    137 --------TCCTAAAATTCATATGGAAATG---CAAGGGACCCAGAATAG 175

  chr2_184822523_   4067 CCAAGGCAATGCTAAGCAGAAAGAACAAACCTGGAGGCATCACA-TTACC 4115
                             ii    vi i iv ii         vi      vv     -  v  
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_184822523_   4116 AGTCTTCAAACTATCCTATAGGGCTACACTCACCAAAACAGCATGGTACT 4165
                          i i iv     - v   i ii      v v i   i    ii       
  L1M4_orf2#LINE/    226 AATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr2_184822523_   4166 GGTACAAAAATAGTCATATAGACCAAAGGAACAGAATAGAGAGTCTAGAA 4215
                           i i  ii    v        i   v    i     v       i    
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr2_184822523_   4216 ATAAGACCACACACTTATGAACATGTGATGTTTGACAAAGCTGACAAAAA 4265
                             iv   i   i     iv  vv    v  i     i v  v   i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_184822523_   4266 CAAGCAATGGGGAAAGAACTCCTGTATCAGTCTGTTTTCACACTGCTATA 4315
                           vv              i---------     --     ------- i 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAAT---------AGTCT--TTTCA-------ACA 406

  chr2_184822523_   4316 AAGAACTGCTGGAG--ACTGGGTA---ATTTATAAAGGAAAGAAGTTTAA 4360
                           vii-      ii--     i  --- iv ii   i   v      vi 
  L1M4_orf2#LINE/    407 AATGG-TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_184822523_   4361 T---TGACTCACAGTTCCACAT 4379
                         i--- iv      ---   i  
  L1M4_orf2#LINE/    456 CCCCTACCTCACA---CCATAT 474

Transitions / transversions = 1.88 (81 / 43)
Gap_init rate = 0.04 (17 / 474), avg. gap size = 3.47 (59 / 17)  

1076 26.63 2.49 4.41  chr2_184822523_184828542.rev     5007  5528 (492)    L1M4_orf2#LINE/L1      397   908 (0)  

  chr2_184822523_   5007 CTATTCAATAAATAATGCTGGAATAACTGGCTAGAAATATGCAAAAGTTT 5056
                           v     i    ii      i i      v  ?vv i         vv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_184822523_   5057 GATACTGGACCCCTTCCTTACACCATACACAAATATCAACTCAAGATGGA 5106
                           vii         v   i        i     v  i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_184822523_   5107 TTAAAGACTTAAATGTAAACCCCAAAACTATAAAAACTCT----GGAAGA 5152
                          i ?    i         ivv i            -    ----i   i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr2_184822523_   5153 CATCTAAGCAATACCATTCTAGACATAGAAAGT--GGCAAAGATTTCACG 5200
                            vvi? i  - i -   vv   v v i--  --     v i    vii
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATC-TTCGTGACCTTGG--GTTAGGCAATGGTTTCTTA 591

  chr2_184822523_   5201 ACAAAAACACCAAAAGCAATTGCAATGAAAGCAAAAGTTGACAAATGGAA 5250
                         ivv vi            vvv    ii    v    i v  i    v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_184822523_   5251 TCTAATTAAACTAAAGAGCTTCTGCAAAACAAAAGAAACTATCAACAGTG 5300
                         ii v  i   v v  i i   i  iivvv    i  v        v iv 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_184822523_   5301 TTAACAGACAATGTACACAATGGGATAA--T-TTTGCAAACTATTCATCT 5347
                          v  v      ivi   v       v  -- -        ii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_184822523_   5348 GACAAAGGTCATTAGACAAAGGTCTAATG-ACAAAGGTCATTAGATATTA 5396
                           i  i  v -  iv ivv  ----   i- i    iv vi ---  i- 
  L1M4_orf2#LINE/    742 GATAAGGGAC-TTGTATCCAG----AATATATAAAGAACTCT---TAC-A 782

  chr2_184822523_   5397 ATCTGGTATCTATAAAGA-ACTTAAATTTACACACAA--AACAATTCGTC 5443
                          iiiii  ---     i -  --    -- -  v   --? v  v v v 
  L1M4_orf2#LINE/    783 ACTCAATA---ATAAAAAGAC--AAAT--A-ACCCAATTWAAAAATGGGC 824

  chr2_184822523_   5444 CAAGGACATAAATAGACACTGTTCAAAAGATGACCTACATGCCGCCAAGA 5493
                         v     iv i        i vi  v     v  iv    viiv     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_184822523_   5494 AGCATATGAAGAAAAAGCTCAACATCACTGATTAT 5528
                             i     -  i v           ????????
  L1M4_orf2#LINE/    875 AGCACATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (71 / 64)
Gap_init rate = 0.04 (20 / 512), avg. gap size = 1.80 (36 / 20)  


3028 24.60 0.96 4.47  chr2_184848405_184851867.rev     2033  2971 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_184848405_   2033 GAAAAATATTTTGTGTTCACAGATCGGAGGACACAATATTGTTAAAATGC 2082
                             i    iiii      ii   i   i   vi           i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_184848405_   2083 CCATAACACCCAAATCGAGCTACAGATTTAAAGCAATCCCTATCAGAATA 2132
                          v   viv       i  v         i  v             i   v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_184848405_   2133 CCAA-TGACATCCTCACAGAAATAGATGAAACAATCCTGAAAGTTATATG 2181
                            i-  v v ii ii       v  ii ivii     i   v i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_184848405_   2182 GAACCACAAAAGATCCAGAATAGCCAAAACTATCCTAAGCAAAAGTAGTA 2231
                            vii   ii  i                v   i i iv  i iv ii 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_184848405_   2232 AAACTGAAAGAATCATG-TTACTGACTTTAAATTATACTATAGAACTATA 2280
                           ii  i i  v   ii-  v ii i  i   viv     i i i   i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_184848405_   2281 GTAATCAAAATAGCATCCTATTGGCATAAAACACACACACACACACACAC 2330
                                 i i  ii vv  i        ii-------------------
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGG------------------- 283

  chr2_184848405_   2331 ACACACACACACACACACACACACCCCAATGGGACAGAAAAGACAACCCA 2380
                         ---------- i v   i i v i --     i i    vv  v ii   
  L1M4_orf2#LINE/    284 ----------ATAGACATATAGATC--AATGGAATAGAATTGAGAGTCCA 321

  chr2_184848405_   2381 TAAATAAATCCACACACTTAACATTGAACTTATTTTTGACAAATATGCCA 2430
                         v       i   i   i   vvi i-  i v     i     ivi     
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTC-AATTGATTTTCGACAAGGGTGCCA 370

  chr2_184848405_   2431 AGGACATACACTGGGGAAAGC-TAGTCTCTTCAATAAATGTTGCTGGGAA 2479
                           iv   v  v         v-      i     i     v        v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_184848405_   2480 AACTGGATATCCATATGCAGAAGAATGAAATTAGACACCTGTCTCTCACC 2529
                                  ?   i     i         i  i   v   ii   v    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_184848405_   2530 ATATTACAAAA-TCAAATCAAAATGGATTAAAGACTTAAGTCTAAGACCT 2578
                             -      - i  v           i ?    i   i v     v  
  L1M4_orf2#LINE/    471 ATAT-ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_184848405_   2579 CAAACTATGAAACTCCTCCAAGAAAACATTGGAGAAAATCTCCAAGACAT 2628
                         v       i      i vv          v  ? v      i iv   v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_184848405_   2629 TGGTCTGGGCAGAAATTTATTGAGCAATACTCCACAAGCACAGGAAACCA 2678
                            vi i    ivii   v  iiii vv  v   v       i v   v 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_184848405_   2679 AAGCAAAAATAGACAAACGAGATCACATCAAG-TTAAAAAGCCTCTGCAC 2727
                            v         i   ivi  iiv      i-       - i i  ii 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGC 668

  chr2_184848405_   2728 ATCAAAGGAAACAATCAACTAAATGAGGAGTCGGGCCACAGACCGGGATA 2777
                         v        v  v     vv  i   ii  v iiv       vi    v 
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_184848405_   2778 AAATATTAGCAATCTACCCAT-TGATCAGGGGC--GTAACCAAAACAGAA 2824
                                v    vii ivi  -    v    i --   v   -----   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA-----GAA 763

  chr2_184848405_   2825 TATATAAGGAGCTCATACAATCCTATAGAAAAAAAAAATCTAATAATCTG 2874
                                i  i   v     ii v   iv     i v ---     i ii
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACA---AATAACCCA 810

  chr2_184848405_   2875 ATTAAAACATAA-CAAAAGATTTGAATAGACATTTCTCAAAAGAAGATAT 2923
                            ?   v  ii-    i                    v           
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_184848405_   2924 ACAACTGGCCAACAGACATATGAAAAGGTGCTCAACATCATTATCAGA 2971
                             v       i ii  i        i            ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (143 / 84)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 3.40 (51 / 15)  


2310 23.19 13.74 2.58  chr2_184871973_184873636      360  1174 (490)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_184871973_    360 GAAAGATATTCTGTATTCATAAATTGGAAAAATTAATATTGTTAAAATGC 409
                                  i ii i     ii       i v             i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_184871973_    410 CCATACTACTTAAGT-GATCTAGGGATTTAGTATAATCTTT-TCAAAAT- 456
                          v     v ii  i -      vi    i iiii    ii -       -
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_184871973_    457 --AG-------------------TGATAA--TAGTCCTCAAA-------- 475
                         --  -------------------   i  -- ii    v   --------
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_184871973_    476 GAAAT-----------AGAA-----AAAAAAATCCTAAAA---------- 499
                              -----------    -----    v    i i   ----------
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_184871973_    500 -----------TTCACATTATCTGACTTCAAAATATACTACAAAGCAATA 538
                         -----------i     i vi ii i       iv           v i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_184871973_    539 GTAATCAAAACAGCATGGAACTGACATAAAAACAGACA-GCAGACCAATG 587
                                 i    ii   v    i     ii i     -ii   i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_184871973_    588 GAACAGAAAAGAGAGACCAGAAATAAATCCACACACTTTCAGGCAACTGA 637
                            i    vv     v           i   i   i  vii v   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_184871973_    638 ATTCTGGAAAAAGTGCTAAGAACACACAATGGGGAAG--ACAGTCTCTTC 685
                         v  ii iv  ii    i    v  iv          i-- i     i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_184871973_    686 AATAAATGGTGTTGGGAAAACTAAATAGTTACATGCAGAAGAATGACATT 735
                           i        i     v    ii   ?ii       i        vi  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_184871973_    736 AGACCCTTTAATCTCAC--TATATATAAAAATCAACT-AAAATGGATTAA 782
                         i     i -- i     --i     i      i    -         i ?
  L1M4_orf2#LINE/    453 GGACCCCT--ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_184871973_    783 AGACTTAAATGTAAGAGCCAAAAGTATGAGATTGCTAGAATAAAATGCAG 832
                             i             i    v   i i i vi     v    iii  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_184871973_    833 GGG-AAATGCTTTATCATATTGGTCTTCAGAAGTA-TTTTTTGGATATCA 880
                          ? -    -   ii v iv    v-  vi v i i-   i  i     v 
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGA 598

  chr2_184871973_    881 TCTCAAAAGCATAAG---------------TAGATAAGTGGG--TTGATT 913
                         ivi        i   ---------------       i v  --  v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_184871973_    914 TAAAATTTAAAAATTTCACACAGCAAAAGAAAC------AACAGTGAAGA 957
                         -      v    v   iiii vv    i  v  ------i v      i 
  L1M4_orf2#LINE/    649 -AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_184871973_    958 GGCAACCTAAGGAATGGGAGAAAATATTTGCAAACTCTATAGCCAATAAA 1007
                          i     i vi                       iiv    v ii    i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_184871973_   1008 GGGATAATATTCAAATTACATGAGGAATTC--ACAACGCTA-AAGAAACA 1054
                           iv vi   i  i v  i  i i   i  --     v v -  v   v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_184871973_   1055 GGTAAACAAATAAACTAATTTAAAAGTGGGCAAAGGATCTGAA----CAT 1100
                          ----        v i    ?    i            i    ----   
  L1M4_orf2#LINE/    798 G----ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_184871973_   1101 TCCTAAAAAAAAAAAAAAGAGACATACAAATGGCCAACCAGTATATTTTT 1150
                          i  vv   i  --------  i              iv  i i  v---
  L1M4_orf2#LINE/    844 TTCTCCAAAGAA--------GATATACAAATGGCCAATAAGCACATG--- 882

  chr2_184871973_   1151 TAAA---TGCTCAATATAATTAATCAT 1174
                         -   ---       i  v ????????
  L1M4_orf2#LINE/    883 -AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.30 (129 / 56)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 4.59 (133 / 29)  


 826 31.32 0.00 0.00  chr2_184901546_184910339.rev     2896  3160 (5634)    L1M4_orf2#LINE/L1        1   265 (643)  

  chr2_184901546_   2896 TGGAAAAATACTCCATGCTCATCAATAGGAAGACTCAATATCGTGAAAAT 2945
                               i   ii     i    vi  v        i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184901546_   2946 GGCCATACAGCCCAAAGTAATTTATAAATTCAATGCTATTCCCATTAAAC 2995
                            v    vv      v i  i  i i      i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184901546_   2996 TACCATTGACATTCTTCATAGAACTAGAGAAAACTACTTTAAAATTCATA 3045
                          v   vivi v  i  iii    v v  v  iviv iii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_184901546_   3046 TGGAACCAAAACAGAGCCCACATACTCAAGGCAATTCAAAGCAAAAAGAA 3095
                              viiv  vi  v  viv   vi   ii    iivi iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_184901546_   3096 CACAGCTGAAGGCCTCACACTACCTGACTTCTAACTATACTACAAGGCTA 3145
                           v  i  i   v        v  ii i   v  viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_184901546_   3146 CAGAGAGCAAAACAG 3160
                            vi v   i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAG 265

Transitions / transversions = 1.37 (48 / 35)
Gap_init rate = 0.00 (0 / 265), avg. gap size = 0.00 (0 / 0)  

1891 27.71 2.17 0.46  chr2_184901546_184910339.rev     3473  4118 (4676)    L1M4_orf2#LINE/L1      252   908 (0)  

  chr2_184901546_   3473 AGAAAGCCAAACAGCA-GATACTGGTACAAAAACACAAACATAAACCAAT 3521
                           v  v v i    ii- i      i i  ii i v v i   i i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_184901546_   3522 GAAATGGAATAGAGAACTCAGAAATAAGACTGCACACCTATAACCATCTT 3571
                          i   i    v    iii         iv iii   ii   iii  vi v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_184901546_   3572 ATCTTTGACAAATTTGACAACAACAAGCAATGAGGAAATGAT--TCCCGT 3619
                           i  i     ivv  v   v v  vv     i     vi  --  ii- 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-T 400

  chr2_184901546_   3620 TTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAATTTAAA 3669
                          i  i              v      v  ?   i     i  i v v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_184901546_   3670 CGGAACCTCTTTCTTACACCTTATATAAAAATTAACTCAAGATGGATTAA 3719
                         iv i   i  vi  i     v    i              i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_184901546_   3720 AGACTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAACAAAATCTAA 3769
                             i         i v i            vi i i   v    iv  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_184901546_   3770 GCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTCATGAGGAAAAC 3818
                          ?i- v i -   iv   v v  vv i     v i    v iiiv vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_184901546_   3819 ACCAAAAGCAATTGCAAGAAAAGCAAAAATTGACAAATGGGATCTAATTA 3868
                                   vvv    v     v      v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_184901546_   3869 AACTAAAGAGCTTCTGCACAGCATAATAAACTATCATCAGAGTGAACAGA 3918
                           v v  i i   i  ii vv  v iv v       vv i      v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_184901546_   3919 CAACC-GCAGAAAGGTAGAAAATATTTGCAACCTATCTATCTGACAAAAG 3967
                              -i     v  v               vii  v       i  ii 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_184901546_   3968 TCTAATATCCAG--TCTATAAGGAACTT----AACTAAATTTACAAAAAA 4011
                         v  vi       -- v     i     i----    v   v- i     i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAAAAG 798

  chr2_184901546_   4012 A-ACCCAACCCCATTAAAATGTGGGCAAAGC-CATGAACAGACATTCCTC 4059
                          - vvi     v   ?   vi         v-iv    i       i   
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_184901546_   4060 AAAAGAAGACATTCATGCAGCCAATAAACATATGAAGAAAGG-TCAACAT 4108
                         v        i  v  viii        i  i     i i v -       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_184901546_   4109 CACTCATCAT 4118
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.33 (100 / 75)
Gap_init rate = 0.02 (12 / 657), avg. gap size = 1.42 (17 / 12)  

2299 25.36 1.56 5.14  chr2_184901546_184910339.rev     7040  7875 (919)    L1M4_orf2#LINE/L1       35   840 (68)  

  chr2_184901546_   7040 TCAATATTGTAAAAATGACCATATTGCCAAAAGCAATCTACAGATTCAAT 7089
                          i        v  i   i v   i v  v   vii              i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr2_184901546_   7090 GCAATTCCCATAAAAATACCA--TATCATTTTTCACAGAATTGGAAAAAA 7137
                              i  i  v     v   -- ii -     ii     v v  v  iv
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC 133

  chr2_184901546_   7138 CAATCCTAAAATTCATATGGAAACACTAAAGAGCCTAAATAGACAAAGCA 7187
                         ii                     ii v ii  v  vi     v    i  
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr2_184901546_   7188 ATCCTAAGGAAAAAGAACAAATCTGGAGGCATCACATTACCAGATTTCAA 7237
                            i i ii  i         vi      vv     i v  vi       
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_184901546_   7238 ACTATACTACAAGGCAATAGTTACCAGAGCAGCATGGTCCTGGTATGAAA 7287
                          viv        i  v i   v i  iii   ii    v    i  i --
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA-- 281

  chr2_184901546_   7288 GTAGGCACACAGACCAATGGAAAAGTAGGCACATGGACCAATGGAGCAGA 7337
                         ------------------   ----   i  i  i  i       ii   
  L1M4_orf2#LINE/    282 ------------------GGA----TAGACATATAGATCAATGGAATAGA 309

  chr2_184901546_   7338 ATAGAAAACCCAGAAATAAAGCCAAATACATACAGCCAACTGACCTTCAA 7387
                           v  i ii           v   v i iv  ii i   i   ii   i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_184901546_   7388 CAAAGCATACAAAAACATAAATTGGATAATGGACACAATA-----TTTAA 7432
                            i -i i v  i  v---   vi  ii-   v v    -----  i  
  L1M4_orf2#LINE/    360 CAAGG-GTGCCAAGACC---ATTCAATGG-GGAAAGAATAGTCTTTTCAA 404

  chr2_184901546_   7433 TAAACAGTGCTGGGAAAACTGG-TACGCCACATGCAGAAGAAAAAAAACT 7481
                         i   ii         v      -  -?         i     vi  i-i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATA-KCCACATGCAAAAGAATGAAG-TT 452

  chr2_184901546_   7482 AGATCACTATCTCTCACCATATACAAAAATTAATTCAAGATGGATCAAAG 7531
                         i  i v   i   v                   i    i        ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_184901546_   7532 ACTTAAATATAAGGCCTGACACCAAAAAAATTCTAGATGACAACATTGG- 7580
                           i     i    iv  i v  i v    v ii    v  v     v  -
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_184901546_   7581 --AAATGTCTTC-TAAACAAGGGCCAGGGCAAAGAATTCATGACTAAGAC 7627
                         --    --    - i v vv   ii   -   v iv   v iiv  v   
  L1M4_orf2#LINE/    553 GTAAAT--CTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTAGATATGAC 599

  chr2_184901546_   7628 ACTAAAGTCA-ATGCAACAAAAACAAAAATAAATAAGTGGGACCTAATTA 7676
                           i   iv  - v         iv       i    i v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_184901546_   7677 AACTAAAAAGCTTCTGTACAATGAAAAAAATAATCAACCAAATGAAAGTA 7726
                           v v    i   i   i vvii  ii v iv     vv  i     iv 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_184901546_   7727 CACCCTACAGAATGGAGGAAAATATTTGCAAGCTATGTATCGAACAAAGG 7776
                           v  i         ii              iii  i    vi i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_184901546_   7777 ACTAGTATCCAGAATCTATAAGGAATTTAAACAAATCACCAGGAAAAAAT 7826
                            v           v     i   i ivv    v   ------- v   
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-------ATAAT 792

  chr2_184901546_   7827 AAATAAATAAAATAACCCCATCCAAAAGTAGGCAAAATACATAAATAGA 7875
                            v i i   -      v  i?    i i      iv iv i      
  L1M4_orf2#LINE/    793 AAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

Transitions / transversions = 1.65 (130 / 79)
Gap_init rate = 0.02 (18 / 806), avg. gap size = 3.11 (56 / 18)  

 324 16.30 0.00 7.61  chr2_184901546_184910339.rev     8211  8302 (492)    L1M4_orf2#LINE/L1      824   908 (0)  

  chr2_184901546_   8211 CAAACCATATCAATAGCTATTTCTCAAAAGAAGATATACAGATGTGTGAT 8260
                             vv  v v     vi       v              i   vvii  
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_184901546_   8261 AAACACATCTGTTCTGAAGAAATGCTCAACATCACTAATCAT 8302
                           i     -------   i i             ????????
  L1M4_orf2#LINE/    874 AAGCACAT-------GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.88 (7 / 8)
Gap_init rate = 0.01 (1 / 85), avg. gap size = 7.00 (7 / 1)  


3104 26.62 0.99 1.10  chr2_184920437_184925462.rev     3626  4534 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184920437_   3626 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3675
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184920437_   3676 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3725
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184920437_   3726 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3773
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_184920437_   3774 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 3823
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_184920437_   3824 AACAGGTAGCTGGAGGCATCACGCTACCTGACTTTAAACTATACTACAAG 3873
                             i--  i      vv    i  v  ii i  i   viv        i
  L1M4_orf2#LINE/    199 AACAA--AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_184920437_   3874 ACTACAGTAATCAAAAGAGCATGGTACTGGTACCAAAACAGAGATATAGA 3923
                         i             i v  ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_184920437_   3924 TCAATGGAACAGAAC--AGAGCCCTCAGAAAAAATGCTGCATATCTACAA 3971
                                  i    i--    i  --     v  vv iii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_184920437_   3972 CTATCTGATCTTTGACAAATCTGACAAAAACAAGAAATGGGGAAAGGA-- 4019
                         ii vi    i  i     ivv  v   i v  vvv           i --
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_184920437_   4020 GTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 4069
                            -- v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    395 GTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_184920437_   4070 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 4119
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_184920437_   4120 TGGATTAAAGACTTACACATTAGACCTAAAACCATAAAAATCCTAGAAGA 4169
                              i ?    i  v ii v   v       i      v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_184920437_   4170 AAACCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATG 4218
                             v    ?i- v i -   iv   viv  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_184920437_   4219 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 4268
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_184920437_   4269 TCTAAT-AAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 4317
                         ii v  -    i    i -   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_184920437_   4318 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCACAACCTACTCATC 4367
                              v  i     i                 v  ii   vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_184920437_   4368 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACA 4417
                            i  i  i  vi          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_184920437_   4418 AGAAAAAG-CAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGA 4466
                          v      -    i     v  i?    i    ii     iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_184920437_   4467 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATG 4516
                           i     v        i  vi viii     v  i          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_184920437_   4517 CTCACCATCACTGGCCAT 4534
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (146 / 92)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


3205 26.77 1.00 0.55  chr2_184933776_184936744     1574  2477 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_184933776_   1574 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1623
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_184933776_   1624 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1673
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_184933776_   1674 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 1721
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_184933776_   1722 TACGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1771
                           i    viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_184933776_   1772 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1821
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_184933776_   1822 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1871
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_184933776_   1872 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 1919
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_184933776_   1920 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 1969
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_184933776_   1970 CTATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGCT 2019
                           v  i  i          i   v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_184933776_   2020 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2069
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_184933776_   2070 TTAAAGACTTACATGTTAGCCCTAAAACCATAAAAATCCTAGAAGAAAAC 2119
                          i ?    i  v    v  vv       i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_184933776_   2120 CTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTA 2168
                         v    ?i- v i -   iv   viv  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_184933776_   2169 AAACAACAAAAGCAATGGCAACATAAGCCAAAATTGACAAATGGGATCTA 2218
                         vi   v        vvi      v   vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_184933776_   2219 ATTAAACTTAAGAGCTTCTGCACAGGAAAAGAAACTACCATCAGAGTGAA 2268
                           i   v    i i   i  ii vvv   i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_184933776_   2269 CAGACAACCTACAGAATGGCAGAAAATTTTTGCAATCTACTCATCTGACA 2318
                         v        i         v       v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_184933776_   2319 AAGGGCTAATATCCAGAATCTACAATAAACTCCAACAAATTTATAAGAAA 2368
                          i  i  vi          v  i  vi     iv    v iv    v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_184933776_   2369 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 2414
                           i    ----   v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_184933776_   2415 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 2464
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_184933776_   2465 CATCACTGTCCAT 2477
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


 940 30.16 7.82 5.67  chr2_184981216_184983250      662  1543 (492)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_184981216_    662 ATATACCATAACCATGGGTTGGAA-ACTCAATA--GT--AGA----AATA 702
                             v    ivi     i      -   i    --  --   ----    
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_184981216_    703 TT----AAATTGACCTATATACT-AATACAATCTCATACAAAGTCAATAA 747
                         i ----       i   i v i -  ii     i -  -----    -- 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCC-TA-----TCAA--A 99

  chr2_184981216_    748 ATTTTAATTTATTGTTCTTTTTTGTGAAAATATATAAGCTGATTCTAAAA 797
                           iii ii ---- i-        iii    vv i        i      
  L1M4_orf2#LINE/    100 ATCCCAGCT----GC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_184981216_    798 ATTGTATGTAAAAGAATAGGGCCAATAGTAAGTAAAATAATGTGAAATTA 847
                         v ii    v   v v vi  i  v v i  ivi    i   v vi  vv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_184981216_    848 GAATAAT----TTTGAATACATACTCTTATTAGATGTTAAGAC--AATAA 891
                            v  i----  v  iv  vi  v   vii -  v i  i  -- v  v
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTAC 243

  chr2_184981216_    892 AATATTATAATAATTAAAACAATGTGGTATTATTGAAAGGCTTAATATAC 941
                           vii  i i    i  i   i       i iviiv    v vi i   i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_184981216_    942 AGACTAACAGAAAAAAAT--AGAGTCCAGAAATCAACTTACACATATATG 989
                            ii  ii   v i   --             v   ii i    v    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_184981216_    990 TTTTCCTCACTAT-GACAATT-TGGCACTACAGTGCTGTGGAGACAAAAA 1037
                         v ivvi v i v -     vv-  v  vv  vi v vi   i  --  i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA--AAGA 391

  chr2_184981216_   1038 ACA-TCTTTTCAACACACTTTGCTAGATCAGTTGAAT--CCATAAGTCAG 1084
                          i -           v ivv    i iv  ii  i  --   i v iv i
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_184981216_   1085 AGTAACAAATTTAACCCTCTGCCTCATAGCCTTATACTATATGCAAACAA 1134
                           -  ii  v  iiv  i  i     i -------- i    i    -  
  L1M4_orf2#LINE/    442 AG-AATGAAGTTGGACCCCTACCTCACA--------CCATATACAAA-AA 481

  chr2_184981216_   1135 TAAATCCTAGATG--TGAAGGGAATAATAATATATGCAGACACACGCACA 1182
                          v  ii v i   -- v ?i ivv   --  i  ---   -----  ---
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAA--ATGTA---AGA-----GC--- 518

  chr2_184981216_   1183 TAAAG--ATGAACACACATTTTTCCCAGAAGAATATGTACAAATCTGTCT 1230
                             i--  i  ----- i i  ---       v ii  vi?i vvi   
  L1M4_orf2#LINE/    519 TAAAACTATAAA-----ACTCTT---AGAAGAAAACATAGGNGTAAATCT 560

  chr2_184981216_   1231 TC-TGAATTTCTGTAAGAC------TTCTTAAATAGGACAGAAAATTCAC 1273
                           -   vi  vv  v  i ------      i   v    vv   vv   
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_184981216_   1274 TAACCATAAAGAAACAAACTCATATATTATACGGTACTAAAATTAAGAAC 1323
                         v i v i   ii  v   ivv   v   iv  vvi ii        i   
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_184981216_   1324 ATCTGTTACTT-AAAAGAGAC-ATTAAACATGGGAAAATTCAAATCATAA 1371
                         v i   -i   -   i  v  -  i  iv v v     vv   vi  i i
  L1M4_orf2#LINE/    661 TTTTGT-GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_184981216_   1372 AGGTAGGAGAAGACATTTGGCATA-CACATATTTAACAAAATATTCATAT 1420
                          i- i      i i     -  v -  i    i i i  iiv i ii   
  L1M4_orf2#LINE/    710 AA-TGGGAGAAAATATTTG-CAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_184981216_   1421 CCAGAA------AAGAGTTATTAAGAC----------AAAGACAGC--AC 1452
                               ------    ii v   vi  ----------       iv--  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_184981216_   1453 TTA-TT----AATGAGCCAGAGACTTGGACATGCACTT----AAATGTG- 1492
                         ii -  ----    i  v ii  i   i i vi  i  ----   viv -
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_184981216_   1493 CATGTAGATACCCAATAGTTACATTAAAGGATTCCCGACTTCATTGATCA 1542
                         i  ii i  iv      ivi    v   i   v i i  v   ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_184981216_   1543 T 1543
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.54 (160 / 104)
Gap_init rate = 0.05 (46 / 901), avg. gap size = 2.59 (119 / 46)  


2563 26.17 1.91 5.64  chr2_184996676_184999290.rev     1184  2123 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_184996676_   1184 AAAAACATTCCATGCTTATGGATAGGAAGAAACAATATTGTTAATATGAC 1233
                            i i  i     i i      v      vvi           v   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_184996676_   1234 CATACTGTCCAAATGTATTTATAGATTCAATGCTATTCCTAGCAAACTAC 1283
                         v     vi      vv  i  i        i  v  i    v    v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_184996676_   1284 CAACAACATTTTCCACAGAATTAGAAAAAAC-ATTCCAAAATTCATTTAG 1332
                           i vi v    iii     v v  v  ivi-  i i         v i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_184996676_   1333 AACCACAAAATAGCCTGAATAGCCAAAGTAATCCTAAGCAAAATGAACAA 1382
                           vii   iiv v  v           ii    i i iv  i v      
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_184996676_   1383 AGCTGGAGGCATCACATTATTTGACTTCAAACTATACTATAAGGCTACAG 1432
                           i      vv     i viiii i      viv     i  i       
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_184996676_   1433 TTAACTAAAACAGCATGGTACTGATATATCTATCTATCTATAGATAGATT 1482
                          -  ii  i    ii        ii   ----------------------
  L1M4_orf2#LINE/    254 T-AATCAAGACAGTGTGGTACTGGCATA---------------------- 280

  chr2_184996676_   1483 AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATGCCAATGGAA 1532
                         --------------------  ---      i v      --        
  L1M4_orf2#LINE/    281 --------------------AG---GATAGACATATAGAT--CAATGGAA 305

  chr2_184996676_   1533 CAAGTTAGAGAACTCAGAAATAAAGCTGCACACCTACAACTGTCTGATCT 1582
                         i iiv v    iii          v iii   ii  iiiiiivi    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_184996676_   1583 TTGACAAAGCCAACAAAAATAAGCAATGGAGAAAGGACTGTATTG--AAT 1630
                          i     i viiv   i vi vv      i     i iv  v  v--  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_184996676_   1631 AAATG-TACTGGGATAACTATCAAGCCATATGCAGAAGATTGAAACTGGA 1679
                              - i      i    ivvv ?   i     i    v    ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_184996676_   1680 CCTTCACACCTCACTATATATAAAAATCAACTCAAGATGGATTAAAGACT 1729
                           iii  vi v   i     i      i       i      i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_184996676_   1730 TAAACATAAAACCTAAAACCATAAAAGGCCTTAGAAGAAAGTCTGGG--- 1776
                             ii   i v       i      v-i           iiv i  ---
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACATAGGNGT 554

  chr2_184996676_   1777 AAATACCATTCTAGACGTTAC-CCAGGCAAAGTCTTCGTAACAAAGTCTC 1825
                             -- -   vv   v  iv-ii      v vi   v  ivv v v v 
  L1M4_orf2#LINE/    555 AAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_184996676_   1826 CAAAAGCAATTGCAACAAAAACAAAAAAT-GACAAGTGGGACCT----AA 1870
                                 vvv         i-       -  i  i v    i ----  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_184996676_   1871 AG-----AGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTAAACAGAC 1915
                          i----- i   i  ii vv    i  v        v i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_184996676_   1916 AAATTATGGAATGGGATAAAATATTTGCAAACTATGCATCTGACAAAGGT 1965
                           vii ii        v              ii  ii      i  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_184996676_   1966 CTAACATCCAGAATTTATAAGGAACTGAAATAAATTAACAAGCAAAAAAC 2015
                           vii         v     i     vvv i  v i  i  vv    i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_184996676_   2016 AAATGACCCTATTAAAAAATAGGCAAAGGACACACACAGACATTTCTCAA 2065
                             i    v   ?      i         iviiv i           v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_184996676_   2066 AAGAAGACATATATGGAGCCAACAAGCATATTAAAATATGCTCAATATCA 2115
                                i   i vivi     i     i  v    v        i    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_184996676_   2116 CTAATCAT 2123
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.64 (151 / 92)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 4.44 (71 / 16)  


1618 28.92 4.07 2.03  chr2_185059579_185061254      489  1176 (500)    L1M4_orf2#LINE/L1      178   879 (29)  

  chr2_185059579_    489 AAAAAAAGCTTGA----GAAGAACAAAATTTAAGGACTCATACTATCCAA 534
                             v  v     ----          i  vi        i   vi    
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_185059579_    535 TTTCAAGACTTACTATAAAGCTACAG-AATTAGAAGCTGCAGAATATTAG 583
                               i        i          -   i ii - v iivii  i i 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGG 276

  chr2_185059579_    584 TAGAAAAGTAGACACATAAATCAATGGAATAGAGATGTAATAGAGACCCC 633
                         i v  iii      i   i              ------  v    vi  
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGA------ATTGAGAGTCC 320

  chr2_185059579_    634 AGACATGAAGCTGAACAAATATAGTCAAGTAGTTTTTAACAAAGTCACAG 683
                            v  i  v iiv   vv   i     v ii    ii    i vii vi
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_185059579_    684 AAGCAATTCAATGAAGGAAGGATACTTTTTTTCAATAAATGATGCTAAAG 733
                          ii v        ii i   i   v i    -   i     i    iiii
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTT-CAACAAATGGTGCTGGGA 419

  chr2_185059579_    734 CAATTAGACTTCTGTGTGGAAAAAAAAAGAATCTCG--CCTGATCTTATA 781
                            i i  iv? iiii  v    i  v-   vi v --  iv i  i i 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAAT-GAAGTTGGACCCCTACCTCACA 468

  chr2_185059579_    782 AATTACACAAAAATTAACTTGAAATAGACTGTAGGCTTAAATTTAAAATC 831
                         vvv  i             ii    i  iii?  i i     v   i v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_185059579_    832 CAAAACTAGAAAATTCTAAGAAAAAAATAAACATAAGTAAAAATTGGTGT 881
                         i       v    i   v    i    ----    i ?iv    ivvi  
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAA----CATAGGNGTAAATCTTCGT 564

  chr2_185059579_    882 GATAATGAGTTTGGCAATTAGTTGCT-GGATTCAACATCAAAAACAAAAT 930
                           ivv  i   v      -i   v  -i   vii   i     i  v  v
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAAT-GGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr2_185059579_    931 TCATGAAAGAAAAAA---ATAACTGATAGTTTATCAATTTTAAAA-CTTA 976
                         iv ii          ---    v viv v  i     vv      -   v
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_185059579_    977 TCTGG---GAATGACATTGTGAAGAGTATCAATAGACGAGGCCCAATATC 1023
                          v  v---i  v    i i v    ivi v  v    i vv v  iv  v
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_185059579_   1024 AGAGAATATATTTGGGAAAC-----TC--ATAAGG-ACATGTATACAAAA 1065
                         i     v       vi  v -----  --      -  v     v  i  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_185059579_   1066 TA----AAGAAGTCCTAAAACTTAACAATAACAAAACAAAGCACCCAAGA 1111
                           ----     v  i  v    i  i     v  i     vv      vv
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_185059579_   1112 AAAAACTGGGCAAAAGCTCTGAACAGACACATCACTAGAGAAGAAACACA 1161
                         ?    v        i v i    i     iv  v i i      v i   
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_185059579_   1162 GGTAGA-AATAATCAC 1176
                         ii i v-     v   
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCAC 879

Transitions / transversions = 1.41 (114 / 81)
Gap_init rate = 0.03 (18 / 702), avg. gap size = 2.33 (42 / 18)  


3120 20.31 3.93 0.66  chr2_185087802_185089556.rev      501  1263 (492)    L1M4_orf2#LINE/L1      121   908 (0)  

  chr2_185087802_    501 GAAATTGAAAAGCCAATCTTTAAATTCATATGAAATTTAAATTGGCCCCC 550
                                 v    ii   i v           i  v vv  vv i   vv
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr2_185087802_    551 AATAACCAAAACAATTTTGGAAAAGAAGAACAATGTTGGAAGCCTCATAC 600
                             i          i   i             v      i v    i  
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_185087802_    601 TTCTCAGGTTTGATGCCTACTACAAAGCTACAATAATCAAAAAAGTGTTG 650
                            i  iv  ii vi i               i       i v     v 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_185087802_    651 TATTGGCATAAGGATAGACATATAGACCAGTGGAACAGAATTGAGAGTCC 700
                           i                       i  i     i              
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_185087802_    701 AGATATAAATCCATACATGAATGAGCAGTCGATTTGTGTCAAGG-TGCCA 749
                            v     i        vv   iv  i i     vi v     -     
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_185087802_    750 AGTCTACTTAGTTGAAAAAGAATAGCATCTTTGACAAATGGTGGTGAGA- 798
                           v i i i i v ii         iv i  ii          v  i  -
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_185087802_    799 AACTGGCTTTACATATGTAAAATAATAAAATTAGAC-------TCACATT 841
                               v v?v  i   i    v   i  i  i   -------     ii
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_185087802_    842 ATGTA--AAAATTAATT-GAAATGGAACAACAGCCTAACGACAAAAGCTG 888
                           i  --        i -i       v  ?vii     vvii  i    i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_185087802_    889 AAAGCATAAAACTCTCAGAAGAAAACGTAGGGGTTAATCTTCTTGACCTT 938
                            vi          i          i    ?  v       v       
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_185087802_    939 GGATATGGCAAGAGAATTATAAA-GTGACACCAAAAGCACAA--AATACA 985
                           i vv     vi vv iv  i -i                 --  i - 
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA-A 619

  chr2_185087802_    986 AAGAAAAAATGTATA--TTGAACTTCATCAAAATTTAAAAATGTTTGTGG 1033
                                   iv   --   i              -     iv      v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATT-AAAAACTTTTGTGC 668

  chr2_185087802_   1034 ATCAAACAATATTAACAAGAAAGTGAAAA-----CTGGCGGAATGAGAGA 1078
                         v     vi i i  v              ----- ivi i     i    
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_185087802_   1079 AAACATTTGCAAATTATATA-CTAA-AATCAGAATTTAATATCCACATTA 1126
                            i          i     -  i -  --i i i  i-      v v  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAA--GGGACTTG-TATCCAGAATA 765

  chr2_185087802_   1127 TATAAAAAACTGTTA-AACTCAACAACACA----CAAACTACCGTATTTT 1171
                               i    v   -       i  i v ----    iv   vv   ?v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_185087802_   1172 AAAATGGGTAAAGAAATTAAATAAACTTTTCTCCAAATAAGATATACAAA 1221
                                 i    i v  i    i  v          v            
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_185087802_   1222 TGGCCAA-AAGAACATGAAAAGATGTTCATCATCATTAGTTAT 1263
                                -   v             i   v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (89 / 62)
Gap_init rate = 0.02 (18 / 788), avg. gap size = 1.94 (35 / 18)  


2544 23.81 0.79 10.71  chr2_185303419_185305530      613  1620 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185303419_    613 TGGAAAAATATTCCATATTCATGGACAGGAAGAATCAATATCATGAAAAC 662
                               i    i    i        iv      v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185303419_    663 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 712
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185303419_    713 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ATGTTAAATTTAAT 761
                          v   vivi i  i  ii     v v  v  i-  -  vi    v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_185303419_    762 ATGGAACCAAAAAAGAGCTGGTATAGCCAAGACAATCCTAAGTAAAAAGA 811
                               viiv  ii  v ii v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_185303419_    812 ACAAAGCTGGAGGCATCATGCTATCTGACTTCAAACTATACTACAAGACT 861
                               i      vv   ii  vi ii i      viv        ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_185303419_    862 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACTA 911
                                i   i    ii         i iv ii i   i       ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_185303419_    912 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 961
                               i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_185303419_    962 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT--TCCC 1009
                             i  i     ivv  v   i v  vvv           i  --  ii
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_185303419_   1010 AATTTAATAAA-GGTGTTGGGAAAACTGGCTAGCCATAGGCAGAAAACGG 1058
                         --  i  i   -    i     v      v  ?   i v   i  i vv 
  L1M4_orf2#LINE/    400 --TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_185303419_   1059 AAACTGGACCCCTTTCTTACACCTTATACAAAAATTAACTCAATATAGAT 1108
                           ii         vi  i     v                   v  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_185303419_   1109 TAAAGATTTAAACATAAGACCTAAAACCATAAAAAACCCTGTAAGAAAAC 1158
                         i ?   ii    ii     v       i      v-i i iv        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAAC 546

  chr2_185303419_   1159 CTAGGCAGTA--CCATTCAGGACATAGGTATGGGCAAAGACTTCATGTCT 1206
                         v    ?-   --i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_185303419_   1207 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAAGATCT 1256
                          vi            vvi          vv     v  i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_185303419_   1257 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 1306
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_185303419_   1307 ACAGGCAATCTACAGAATGGGAGAAATTTTATACAATCTATCCATCTGAC 1356
                          v  i   i i               v v v i   vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_185303419_   1357 AAAGAGCTAATATCCAGAATCTCCTGGCATTATTAATAATGACACTGCCT 1406
                           i ii  vi          -----------  --    v  --------
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAAT-----------AT--ATAAAGA-------- 773

  chr2_185303419_   1407 TTAACTCTCACAATTAATTTGGATGATAACTTATGTGGTAACCCTGCTAA 1456
                         ---     i    ---------------------------------  v 
  L1M4_orf2#LINE/    774 ---ACTCTTACAA---------------------------------CTCA 787

  chr2_185303419_   1457 ATAAAAAATAAAAATTACCATAGTAACAGGAACTTAAACAAATTCACAAG 1506
                             ----      ------------------------------------
  L1M4_orf2#LINE/    788 ATAA----TAAAAA------------------------------------ 797

  chr2_185303419_   1507 AAAAAAACAAACATCCCAATCAAAAAGTCGGCAGAGGATGTGAACAGACA 1556
                         -----i     i v      i?    i v    i     v    i     
  L1M4_orf2#LINE/    798 -----GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_185303419_   1557 CTTCTGAAAAGAAGACATTTATGTGACCAACAA--ACATGAAAAAAAGCT 1604
                         i    vv        i  vi vi  i    i  --         i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_185303419_   1605 CATTATCACTGGTCAT 1620
                           vi    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 7.25 (116 / 16)  


2721 28.36 1.67 0.67  chr2_185337436_185342427     3609  4507 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185337436_   3609 TGGAAAAACATTTTATGATCATGGATTGGAAGAATCAGTATTGTTAAAA- 3657
                               i i  iii   v               v i i         i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185337436_   3658 ----ACACTGCCCAA-TTAAGCTACACATTCAATGCTTTTCTTATCAAAC 3702
                         ---- i   v     -  i v     v      i  vv i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185337436_   3703 TACTAA-TGTCATTTTTCACAAAACTAGAAAAATATATTCTAAAATGTGT 3751
                          v i i-  i -     ii  i  v v  v  iivv  i       vii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_185337436_   3752 ATGGTA-TCAAAAAGAGCCTGAATAGCCAAAGCAATCCTGAGCAAAAAGA 3800
                             v - vv  ii  v  v           i     i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_185337436_   3801 GCAAAGACAGATATATCATATTACCCAACTTCAAATTATACTATAAGGCT 3850
                         i     vii  vivv   i i v     i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_185337436_   3851 ATTATTATAGCCAAAACAGCATGGTACTGGTATGAATTCAGATACATAGA 3900
                          ivi v  ---   i    ii         i  i ivvi   i i     
  L1M4_orf2#LINE/    250 ACAGTAAT---CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_185337436_   3901 CCAATGGAATACAATAGAGAACACAGAAAAAAAGCCATACACCTACAACC 3950
                         i          v   v    iiv      v   v       ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_185337436_   3951 ATGTGATCCTTGA-AAAGGTGACAAAAACAAGCAATGGGGAAAGGACTCC 3999
                          vv    ii i  -  i    v   i v  vv            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_185337436_   4000 CTATTCAGTAAATGGTGTTGGGATAACTGGCTAGCCATATACAGAAGGTG 4049
                           v    ii        i     i      v  ?   i  i  i   ivv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_185337436_   4050 GAAACTAGAGCCTTACCTTTCACCGTACACAAAA-TTAACTCAAAATGGA 4098
                            ii i  v  i     iv    i  i      -               
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_185337436_   4099 TTAAAGATTTAAATGTAAGACCTCAAATTTTAAGAAGCCTA-ATTAAAAT 4147
                          i ?   ii           v  v   i v   i vv i  - vv    i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_185337436_   4148 CTAGGAA-ACAGCATCCTGAACATTGGCCTTGGGAAAGAATTTATGACTA 4196
                         v    ?i- v v v  v   v -    vi v  v  v iv  iv iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_185337436_   4197 AGTCCTCAAAAGCAATTGCAACAAAAACAAAAATTGGCAAATGAGACCTA 4246
                         v v vi        vvv         iv      v ii    vi   i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_185337436_   4247 ATTAAACTAAAAAGCTTCTGAACAGCAAAAAA-ATTATCAATAGAATAAA 4295
                           i   v v    i   i  vi vv    ii - i      v i i i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_185337436_   4296 CAGACAACCTACACAATGGGAGAAAATATTCACAAACTACACATCTGACA 4345
                         v        i   v                ii    ii i i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_185337436_   4346 AACATATCTATATCTGGAATCTATAAGGAAACTAAACATTTTAATAAGCA 4395
                          ivi- ii i    ii    v     i   viivv   vi i     vv 
  L1M4_orf2#LINE/    746 AGGG-ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_185337436_   4396 AGAAACAAACAACTTTATTTAAAAGTAGGCAAAAAATAGGAACAGACACT 4445
                          i i     i   iiv   ?    i i      ii  vv   i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_185337436_   4446 ACTCAAAAGAAGATATACAAGTGGCCAACAA--ACATGAAAAAATGTTCC 4493
                         v   v               i       i  --         i   i  v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_185337436_   4494 ATATCACTAATCAT 4507
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (148 / 103)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


3219 23.15 5.56 0.46  chr2_185400991_185402953.rev      608  1471 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185400991_    608 TAAAAAGACATCCCATGTTTGTGGACTGGATGACTTAATATTGGTAAAGT 657
                          ii     i          ii    i    v            v   ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185400991_    658 GTCCTCATTACTCAAGAAGACTTACAGATTCAATGAAATCCCTATCAAAA 707
                          v vvi i v i   ivv  ii           i v              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185400991_    708 TACTAA-TGCATTTCTTACAGAAAAAGATT-ATAA--TTATACTAATATT 753
                          v i i-   v   i  i      ----  - i  -- v  v    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA----TTGACAAGCTGATCCTAAAATT 146

  chr2_185400991_    754 CATAAGGA--TTCA-------CAAAAT--CCAAATCAATCTT----AAGA 788
                             v   -- v  -------  i   --     v       ----    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_185400991_    789 ACAACAAAACTGGACGCATTACAATTCCGAATTTCAAAATACACTACAAT 838
                          v      ii    v vv i   v    v          ivi       v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_185400991_    839 GCTATAGTAATCAAAACAGTATAATAATGAAATTAAAATAGACAGACAGA 888
                             i         i     i ii  v  iv  v ii       v i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_185400991_    889 ATAATGGAACAGAATAGAAAGCCCAGAAATAAACCCATATATGTATGGTC 938
                         vi       i     v  i  i                 i  v       
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_185400991_    939 AACTGATCTTTGACAAGGGTGCCAATAACACAAAAAGGAGAAAGGACAGT 988
                           i    i  i              v v  ivv  v  i     i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_185400991_    989 CTCTTCAATAAATGGTGTTGAGAAAACTGAGGATTCATATGAAAAACAAT 1038
                           i     i        i  i  v     iiv ?i  i   v    v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_185400991_   1039 AAAATTGGATGCTTCTCTTACACCATACACAAAA-------TAAAATGGA 1081
                         i  i     iv i vi  i        i      -------i        
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_185400991_   1082 TTAAAGATT--AAT----------------TAAAAATCATAAAAGAAAAC 1113
                          i ?   ii--   ----------------     v  v  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_185400991_   1114 ATAGAAGGAGAGATTCATGGCATTAGACTAAGCAAT--TTTTTAAAATAT 1161
                             i? v i vv   i  i v  i ii  i     --   i v i    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_185400991_   1162 G-CATAAAAAGTGCAAGCAACAAAAGCAAAAATAGACAAGTAGTACTCCA 1210
                          -  iv     ii             v         i  i v v   i  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_185400991_   1211 TCTAACTTAAAAGCTTCTGCACAGCAAAGGAAACAACCAACAGAGTGCAG 1260
                           v  v      i   i  ii vv       v  v i   v i    v i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_185400991_   1261 AGGCAACATACAGTATGGGAGAAAATATTTGCAAAACATATATCTGAAAA 1310
                           i    vi    v                     v           v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_185400991_   1311 AGGATCAATATCTAAAATATGCAGGTAACTTCTACAACTTGATAACAAAA 1360
                         i   iivi    i i     ii iiv    ii       ii    i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_185400991_   1361 AAGCAAGTATCCCAGTTAAAATATGGACAAAGAATGTGAGAAAACAGTTC 1410
                          ii   i  v    i  ?   v    i     i  v   iv i   v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_185400991_   1411 TCCAAAGTA-ATATATAAATGGTCAACAGATATATGAAAAGATGCTCAAC 1459
                                v -     i      i   i iii i                 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_185400991_   1460 ATCACTAATCCT 1471
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (122 / 74)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.71 (52 / 14)  


2944 26.87 3.51 0.57  chr2_185407595_185412227     3260  4141 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185407595_   3260 TGGAAAGATGTCTTATAATCATGGATCAGAAGAAATAAAACCATTAAAAT 3309
                                  i  ii  iv        ii     vv   v iii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185407595_   3310 GACGATACTACCCAAAGCAATATACAGATTCAGTGCAATCTCTATCAAAG 3359
                          i i     v      vii  v          ii      i        i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185407595_   3360 TACC-GATGTCATTTTTCACAGAGATAGAACAAAAAAATTCTAAAATCTG 3408
                          v  - v  i -     ii    i  v  -   ivvi  i       iii
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chr2_185407595_   3409 TATGGTA-TCAAAAAGACCTCAAATAGCCAAAGCAATCCTGACTAGAAAG 3457
                              v - vv  ii    ivi          i     i   vv ii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_185407595_   3458 AACA------------TCACATTACCTGACTTTAAGATATAGTACAAGGC 3495
                             ------------     i v  ii i  i  i iv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_185407595_   3496 TATAGTAACCAA-ACAGCATAATACTGATACAAAAACAGATACATAAAGC 3544
                           i     i   -    ii ii     ii i  ii i   i i   i v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_185407595_   3545 AATGCAATAGAATAGAGAACCCATAAATAAGTCCATATATTTGCAGCCAA 3594
                             v        v    ii   v      ii     i    iii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_185407595_   3595 CTGAATTTTGACAAAGGTGCCAAGAACATACACTGAGGATAGGACACTTT 3644
                         i   v   i     i          v   v  v  i   v  i i v i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_185407595_   3645 CTTCAATAAATGATATTGGGAAAATTTGATACCCATATACAGAATAATAA 3694
                         i     i     i ii     v  i v    ?   i  i  i  v   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_185407595_   3695 ATCTGGACTCCTATTTCTGATCATATACAAATATCAACTCAAGATGAATG 3744
                          vi     i    ii  vv i          v  i       i   i  v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_185407595_   3745 AAAGACTTAAACATAAGACTCAAAACTATTAAAATCCTAGAAGAAGACAT 3794
                          ?    i    ii     vii        v   v  i        i    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_185407595_   3795 AGGGGAAACACTTCTGGAAATTTGCCTAGGCAAAGATTTTGTGGCTAAGA 3844
                            ? v  vv    vv  vv  v vi       v i   iv i v  v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_185407595_   3845 CCTCAAAAACACAGTCAATAAAAACAAAAATTAGACAAATGAGACTATAT 3894
                          vi     i    iv   i    iv      -   i    vi    vi  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAATTGGACTTCAT 647

  chr2_185407595_   3895 TAAACCAAAAAGTTTCTGCACAGCAAAGAAAGCAATCAACAGAGTGAAAA 3944
                         i   viv    ii  i  ii vv     i vi v     v i        
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_185407595_   3945 GACAACCTGTTAAATGGGA-AAAATATGTGCAAACTATTCATCTAACAAG 3993
                                iiivi       -       v      ii  vi    i i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_185407595_   3994 GGACTAATGCCTAGAATATACAATGAGCTGAAACAAC-----AGTAAAAA 4038
                              vi ii i        i  v  i  vvv     ----- i      
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_185407595_   4039 AATAAATAA----------AAGTGAGCAAAGGACATTCATAGATATTTCT 4078
                         i i      ----------  i  i        iv vv     i      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_185407595_   4079 CAAAATAAGACATACAAACGTCCAACAGGTATATAAAAAAAAATGCTTAA 4128
                          v   v    i       i v    i i i i  i    i --    i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAA 895

  chr2_185407595_   4129 CATCACTAGTCAT 4141
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (153 / 81)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.27 (36 / 11)  


2664 24.50 4.23 1.12  chr2_185421218_185424802.rev     1893  2696 (889)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr2_185421218_   1893 TAGAAATATATTCCATGTTCATGGATGGGAAATCTCAATATATTTGAGAT 1942
                          i    v    i              v    iv  i     vv  i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185421218_   1943 GTCACTACTTCCCAAGTTGATTTACAGATTAAATGAAATTCCAGTAAAAA 1992
                          v  v    i     i     i        v  i v   i  vi v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185421218_   1993 TATCTGCAAGTTATTTTGAAGATATTGACAAAGC-------AAAATTTAT 2035
                          vi v  vivi v     v   v        -  -------      i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_185421218_   2036 AGGGAGAGGGAAAAGACACAGAATAGCCAACACAGT---AATAAAGAAGA 2082
                          v   i v v  ii   v            v   i ---i v        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_185421218_   2083 ACAAAGTTGAAGAACTGACATTACCCAACTTTAAGACTTATTCTTAGTCT 2132
                                  i  i   v   i v     i  i  i     i viv iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_185421218_   2133 ACAGTAATCAAGACAGTGTAGTATTGGTGAAAAAATAGACAAATAGATCA 2182
                                            i   i   iiv  ii       v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_185421218_   2183 ATGAAACATGATAGAAGGTCCAGAAGTAAACCCACACA------------ 2220
                            i  i vi  v  ii        i        i   ------------
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_185421218_   2221 -AATTTTTAGCAAAAGAGAAAAGACAATACAATGGC-AAAGAAGAGTATT 2268
                         -i     iii   ii v vv     v  v      v-      v   v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_185421218_   2269 TTCAACAAAGTATGCTAGTACAACTGGATATTGACATGCAAAAAAAAAAT 2318
                                  vvi    i v           ?iv          i  --- 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA---T 446

  chr2_185421218_   2319 GAGTTTAAACACAAACCTTACACCCTTCACAAAAATTAAATCAAA-TAGA 2367
                           iv  ii  v vv    i     v vi           v     - i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_185421218_   2368 GTCCAGACCTAAATATGAAACACAAAACTATAAAATTCT-AGAAGATAAC 2416
                         viv?          i i i vvi            i   -      v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_185421218_   2417 ATAGAAAGAAA-CTTAGATGA---TGAGTTTGGCAA-GATATTTTTGGAC 2461
                             i?iv   -   v -   ---  i   v     - i -  i  i  i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGT-TTCTTAGAT 594

  chr2_185421218_   2462 ATAACACCAAATAAAACA-TCCACAAAGGAAAGAACTGATAAGCTAGACC 2510
                           i        - iv   -v v     i    i  iv     ii i   i
  L1M4_orf2#LINE/    595 ATGACACCAAA-AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_185421218_   2511 TCTCCCAAATTAAACATTTCTGACCCATGAAAGACACTGTCAAGAGGATA 2560
                           vi v        v i  i  vv ivii  i      i      iii i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_185421218_   2561 AAAATACAATTCAAAGACTAGGA-AAAATATTTGCAAATTGCATCTCTGA 2609
                             v    ii  v   v i   -               iii  v     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_185421218_   2610 TAATGGCCTGTTATC-AAAATATACAAAGAAACATTAACAGTTTATTAAT 2658
                            v  v  vv    - i      i      - vi v   ii i v    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATAAT 792

  chr2_185421218_   2659 AAGGATACAAACGACCCAATTAAGAAATGGGTTAAAAG 2696
                           ii v     ii        ? i       i-   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGC-AAAGG 829

Transitions / transversions = 1.35 (111 / 82)
Gap_init rate = 0.02 (19 / 829), avg. gap size = 2.26 (43 / 19)  

 273 24.56 9.65 0.00  chr2_185421218_185424802.rev     2980  3093 (492)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr2_185421218_   2980 CTCAAAAAAAAAAAAAAAAA-----------AAAAAAGCGTTAAAGACCT 3018
                              v  v     i v   -----------     v v iv  i  ii 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_185421218_   3019 TAACAGACATCTCACTGAGGAAGATATGCAAATGAAAAATGAGCATAGAA 3068
                         v  i      i  v ii i        i      ivv   i    i vi 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_185421218_   3069 AAAGATGTTCCACATCATACGTTAC 3093
                                i  v      ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (16 / 12)
Gap_init rate = 0.01 (1 / 125), avg. gap size = 11.00 (11 / 1)  


2210 27.84 7.49 1.29  chr2_185438112_185440338.rev      881  1735 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185438112_    881 TGGAAAAACATCCCATTTTCATGGATTGGA-GAATCAATATCATTAAAAT 929
                               i i       v             -  v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185438112_    930 GGTCATACTTCTCATAGCAATTTACAGATTCTTATAAAACTACCCATAT- 978
                           iv     i i  v vii  i         ----  vi v i  v   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTC----AACGCAATCCCTATC 96

  chr2_185438112_    979 --AATTCC-----------TCACA-AAATTAGAAAAAAACT-ATTCTAAA 1013
                         --   i  ----------- ii  -     i--- v  i  -  i     
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAA 143

  chr2_185438112_   1014 ATCCATATCGAACCAAAAAGGAGCCCAAATAGCAAAGGCAATTATAAGCA 1063
                           i     v   viiv  i   v  vi      v  ii    iv i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_185438112_   1064 AAAAGATCAAAGCCAGAAGCATCACACTACCTGATTTCAAACTATGCCAT 1113
                          i    v     iii  i vv       v  ii        viv i i i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_185438112_   1114 AAAGCTACAGTAACCAAAACAGCATGTTATTAGTACAAAAACAGACACAC 1163
                                      i   i    ii  v  i i i i  ii i     i i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_185438112_   1164 AGACCAATGGAACAGACTAGAAAACTCAGAAATAAAGCCGCACACCTACA 1213
                            i        i   v v  i iii          v  ii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_185438112_   1214 A-CATGCTGATATTCAACAAGTTCAACAAAAAGAAGCAATGAGGAAAGGA 1262
                         i-  -ii    v   i     vviiv   i vv vv     i      i 
  L1M4_orf2#LINE/    344 GTCA-ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_185438112_   1263 CTCCCTATTCAATCAATGGTGCTAAAATAACTGGCTAACCATATGCAGAA 1312
                         ivvi  v     iv         iii i      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_185438112_   1313 GAACGAAACTAGACACTTACCTTTCACCATATAAAAAAATTAACTCAAA- 1361
                            i   ii i   v i     iv         v               -
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_185438112_   1362 TTGATAAAACATTTAAATTTAAGACCTCAAACAATAAAAATCCTAGAAGA 1411
                          v   v ? v ii     v     v  v    v      v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_185438112_   1412 AAATCTAGG---AAAT------AACCTTCAG--AAGC-------TATT-- 1441
                            iv    ---    ------i     vi -- i  ------- v  --
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_185438112_   1442 --------------------GCAACAAAAACAGAAATTGACAAATAGGGC 1471
                         --------------------         iv i    v  i    v  i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_185438112_   1472 CTAATTAAAAT-AAGAACTTCTGCATAGCCTAAAAA---ACTATCAGTGG 1517
                         i v  i     -  i     i  i---  i v   i---       ivii
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGT---GCTTCAAAGGACACTATCAAGAA 689

  chr2_185438112_   1518 AATAAAGAGACAATCTGTAGGGTGGGAGAAAATATTGACAAGCTATGCAA 1567
                          i i  i      i iii  ii              vi   iii  ii v
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_185438112_   1568 CTGTCAAAAGTCCAACATCTAGAATCTAAAAGGAACTTAAACAAATAAAC 1617
                            vi  ii v ivii   i     v  v  i     ivv    v v  i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_185438112_   1618 AAACTGGACACAAATAATCTCATT-AAAATTGGGTAGAAGACATGAACAG 1666
                           vvvii v        i iv   -    v    i i i  iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_185438112_   1667 ACACTTCTCAAAAGAAGACATTCAAGGGGCCAATAAATGTATGAAAACAC 1716
                            i     v        i  v   iv         iiii       v i
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_185438112_   1717 TCTCAACATCACTAATCAT 1735
                         v          ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (153 / 83)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.95 (75 / 19)  


2434 28.01 2.92 0.79  chr2_185477338_185481230.rev     2513  3401 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185477338_   2513 TGCAAAATTGTCTCAAGCTCATGGATTTACATAATCAATATTGTTCAAAT 2562
                           v   iv i  i  v i         viv v v i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185477338_   2563 TACCATTCTACCCGAAGTAATCTA--GATT-AACACAACTTTTATCAAAT 2609
                         vi v  v  v   i  v i     --    -   i   iiii       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185477338_   2610 TGCCAGCATCATTTTCTTACAGAG-TTGAAAAAAATATCCTTAAGTTCAT 2658
                          v     vv v    -  i    i-    v  ivvv     v  i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_185477338_   2659 ATAAAACTGAAAAGAAGCCAGACCACCTACAGCATTCCAAAGCAAAAAGA 2708
                           ii  v  v  i i v     vi v i v i  v  ivi iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_185477338_   2709 ACAAATTTGAAGGTATCACATTGTTTAACTTCAAATTATACTATAAGGCT 2758
                              v   i   vv     i viii  i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_185477338_   2759 ATAGTAACAAAAACAGCGTGGTACTGGTACAAAAATAGACACATAGATCA 2808
                          i     iv  i    i          i i  ii       i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_185477338_   2809 TTGGAACAAAATAGATAACCCAGAAATAAAACCACATACCTAAAACAAAA 2858
                         v     i i   v  v ii           v   i i ii  viiiv  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_185477338_   2859 TGATCTTGGATAAGTTTGACAAAAATAAACAATGGGAAAATGACACCGTA 2908
                             i  v  i   vv  v   i vi vv       i   vi i viv v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_185477338_   2909 CTCAATAAATGGTGTTGGGAAAATTAGCTAGCAACATGCAGGAGAATGAA 2958
                         i    i        i     v  i i v  ? v       ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_185477338_   2959 ACTA---TCCTATCTCTCATTATGTACAAAAATTAATTCAAGAAGGATTA 3005
                         ii i---i    i   v  ii  i            i    i v    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_185477338_   3006 AAGGCCTAAACCTAGGACATGAAGCCATAAAAATGTTAAAATAAAACCTA 3055
                         ?  i      iv  i  vv i  i i      v v   i  v     v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_185477338_   3056 AGAAAAAGCTCTCCTTGACATTTGCCTAGGCAAATAATTTATGACAAA-G 3104
                         i ?iv  i-   i v    v  v vi       - ii   v v v v - 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATG 597

  chr2_185477338_   3105 ACCTCAAAAGCAAATGTAACAAAAACAAATATAGACAAATGGGACTTAAT 3154
                           vi        v v i       iv   v     i    v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_185477338_   3155 TAAA-CTAAAAA------------AAAAAACAGCA-AAAGAAATAATAAA 3190
                         i   -i      ------------   ii   vi -v      --i i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA--GTGAA 695

  chr2_185477338_   3191 CAGACAACCTACAGAATGGGAGAAAATATTTACAAATTATGTCTCCAATA 3240
                         v        i                     i     i  i v  ii   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_185477338_   3241 AAGGTCAAATATACAAAAACTACAAGGAACTAAAAGAAGTCAACGAGAAA 3290
                          i  v vvi   v  i  vv  i  i     vvv v  v    ii v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_185477338_   3291 GGCACCAAAAAAC----TTAAAAGCTGGACAAAGGACATGAACAGATATC 3336
                         iiv  -   v   ----  ?   iv   i       iv    i   i  i
  L1M4_orf2#LINE/    796 AAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_185477338_   3337 TCTCAAAAGAAGAAATACAAGTGGCCAACGAAACACATAAAGAAATGCTT 3386
                             v        v      i       i-  i     i  i i     i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAAT-AAGCACATGAAAAGATGCTC 893

  chr2_185477338_   3387 AACATCACTAATCAC 3401
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (138 / 107)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


2691 28.44 1.44 0.78  chr2_185506895_185512556     4271  5170 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_185506895_   4271 GGAAGACATTCGATGCTCATGGATAGGAAGAATCAATATGGCAAAAATTG 4320
                          i    i  i v   i        v      v i     v iv  i  v 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_185506895_   4321 CCATATTGCCCAAAGTAACTTATAGATTAAATGCTATTTGTATTAAATTA 4370
                          v   i v      v i ii  i     v  i  v  iiv   i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_185506895_   4371 TCA-TTGACAGTCTTAAAAGAATTAGAATAAATT-ATTTTAAAATTCATA 4418
                         i  -i  v vv i  iv ii    i-- i  ii -  ii           
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr2_185506895_   4419 TGGAACCAAGAAAGAG-CCCA-AATAGCCAAGACAATCCTAAGCAA-AAG 4465
                              -- v v   i -    -         i      i i iv  -   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_185506895_   4466 AACAAAGCTGGAGGCATCATGCT-ACTGACTTCAAAGTATACTACAAGGC 4514
                                i      vv   ii  -v ii i      iiv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_185506895_   4515 TGCAGTAACCAA-ACAGCATGGTACTGGTACAAAGACAGACACATAGACC 4563
                          i      i   -    ii         i i  i  i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_185506895_   4564 AATGGAACAAAATAGATAACTCAGAAATAAAACTGCACACCTACAACCGT 4613
                                i i   v  v iii          v iii   ii  iiii iv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_185506895_   4614 CTGAGCTGTGACAAACCTGACAAAAACAAGCAATGGGGAAATGATTTTCT 4663
                         i   vi vi     ivv  v   i v  vv           vi  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_185506895_   4664 ATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAATTTA 4713
                         v  i  i              v      v  ?   i     i  i v v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_185506895_   4714 AACTAGACCCCTTTCTTACACTTTATACAAAAATTAACCCAAGGTGGATT 4763
                          ii i       vi  i    iv               i   ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_185506895_   4764 AAAGATTTAAATGTAAAACTCCAAACCATAAAAACCCTAGAACAAAATCT 4813
                          ?   ii         i viiv    i      vi i     v    iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_185506895_   4814 A--CGCAATGCCATTCAGGATGTAGGCATAGGTAAATATTTCATGAGGAA 4861
                          --? i  vv --   iv  iv v  vv    i  vvi    v iiiv v
  L1M4_orf2#LINE/    549 AGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_185506895_   4862 AACAC-AAAAGCAATGGCAACAAAAATGAAAATTGAGAAATAGGATCTAA 4910
                         i    -       vvi         ivi     v  v    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_185506895_   4911 TTAAACTAAAGAGTTTCTGCACAGCAAAGGAAACTGTCATCAGAGTGAAC 4960
                          i   v v  i ii  i  ii vv       v   i   vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_185506895_   4961 AGACAACCTACATAATTAGAGACACT-TTTGCAATCTATCCATCTGATAA 5009
                                 i   v   vi    v v -       vii  vi         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_185506895_   5010 AAGTCTAGTATCCAGATTCTACAAGGAACTTAAACAGATTTACAAGGAAA 5059
                         ii v  v         v v  i  i     ivv   iv iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_185506895_   5060 AGACAAACAACCATATTAAAAAGTGGGCAAGAGTACATAAGCATATACTT 5109
                                i    vv   ?    i       -  v iv i ii v i i  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAA-AGGATTTGAATAGACATTT 845

  chr2_185506895_   5110 CTCAAAAGAAGACATTTATGCGGCCAACAA--ACATGAAAAAAAGCACAA 5157
                            v        i  vi vii      i  --         i v  v   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_185506895_   5158 CATCACTGATCAT 5170
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (148 / 104)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 1.33 (20 / 15)  


1794 27.15 14.82 1.74  chr2_185570947_185575839     3599  4401 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185570947_   3599 TGGAAAAATATTTCATTCTCATGGGTAGGAAGAATTGATGTTGTTAAAAT 3648
                               i    ii   vi      i v      v  i  i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185570947_   3649 TGCCATACTTTCCAAAGCAACTTACAGATTTAGTGCAATTCCTACCAAAC 3698
                         v  v     ii     vii ii        i ii     i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185570947_   3699 TACCAATGATAGTCTTCATAGAATTAGAAAAAAAACT-ACTATAAAATTC 3747
                          v   iiviivv i  iii    v v  v  i---  - iiv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_185570947_   3748 ATATGGAGCCAAACAAGAG-CCCA-AATAGCCAAGGCAACCCTACTTAAA 3795
                                i-- vi    i -    -         ii   i i i---   
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG---AAA 192

  chr2_185570947_   3796 AAAAAAATCAAAGCTGGAGACATCACATTACCCCTTTTTAAACTACACTG 3845
                           i  i v     i     ivv     i v   vv   i   vivi   i
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_185570947_   3846 TAAAACTATGGTAACCAGAGCACCATGGTACTGATACAAAAACAGAACCA 3895
                         i   i   ii    i  iii  vii        ii i  ii i   vvi 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_185570947_   3896 TAGACCAATGGAACAGAATAGAGAACCCAGAAATAA-------------- 3931
                             i        i     v    ii          --------------
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_185570947_   3932 -------------------------------------------------- 3931
                         --------------------------------------------------
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_185570947_   3932 -------------------TGCTG---------------CACATGTACAA 3947
                         -------------------     ---------------      i v  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_185570947_   3948 ---TCAA--------TCTTCTTTATACTGTATACAAAAATTAACTCAAGA 3986
                         --- v  --------i  v i i i  ii                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_185570947_   3987 TGTATTAAAGACTTAAATGTATAACCTAAAGACATAAAAACCCTGGAAGA 4036
                           v  i ?    i        vi v     ivi      vi i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_185570947_   4037 TAACCAAGGAAATAAATATAATTCTGTACATAGGCCCTGGCAAAGTTTTC 4086
                         v   vv   ?i-     v -- iv  -  v v  viiv     v v    
  L1M4_orf2#LINE/    543 AAACATAGGNG-TAAATCT--TCGTG-ACCTTGGGTTAGGCAATGGTTTC 588

  chr2_185570947_   4087 AT-GATAAAGACCCCAAAAGCAAGTGTAACTGAACCAAAAATTGACAAAT 4135
                         v -    v-   v         viv i   vi  vv      v  i    
  L1M4_orf2#LINE/    589 TTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_185570947_   4136 GGGATCTAATTAAA-TGAAAGAGCTTTGTACAGCAAAAGAAATTGTCAAC 4184
                         v   ii v  i   - v   i vi     i vv    i  v i i    v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_185570947_   4185 AAAG-AAACAGACAACCTGCAGAATAGAAGAAAACACTTGCAAACTATGC 4233
                             -i  v        ii      i i      i i       ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_185570947_   4234 ATCTGAAAACAGTCTAATATCCAGAATCTGTAAGGGAGTTAAACAAATTT 4283
                               v  vi v  vi          v i   i i v ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_185570947_   4284 ATAAGAACAAAAGCAAACAACCCCATTAAAAAGTAGGCAAAAGACACGAA 4333
                             v  -   ii    i     v   ?    i i      i  ivi   
  L1M4_orf2#LINE/    788 ATAATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_185570947_   4334 CAGACACTTTGCAAAAGAAGATATACACATGGCCACCAAGCATATAAAAA 4383
                         i     i  iv v              v       vi     i  i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_185570947_   4384 -ATG---AACATCACTAATCAT 4401
                         -   ---       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (133 / 82)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 6.65 (133 / 20)  


2741 26.91 1.99 1.44  chr2_185600460_185602524.rev      671  1573 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185600460_    671 TAAAAAAAAATTCCATGCTCATGAATTAGAAAA-TCAATATGGGTAAAAT 719
                          ii   i v  i     i     i   i   i - i     v v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185600460_    720 GACCATACTGCTCAAAGTAATCTATAGATTAAATGCTATTACTATCAAAT 769
                          i v     v i    v i     i     v  i  v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185600460_    770 TACCTACTAATGTCATTCTTTGCAAAATTAGAAATACT-ATTCTAAAATG 818
                          v  vi  --- i -  i      i  v v  v vi  -  i       v
  L1M4_orf2#LINE/    101 TCCCAGCT---GCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_185600460_    819 GATAAGGAACCAAAAAAGAGCCCGAATAGCCAAAACAATCTTAAGCAAAA 868
                         v   v    viiv  ii  v  v                   i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_185600460_    869 TGTATGAAGCCAGAAGTATCATGTTACTAGACTTCAAACGATACTGTAAG 918
                         v v ii   iii  i vv   iii v ivi i      vvv    ii  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_185600460_    919 GGCTTCAGTAACCAA-ACAACATGGTACTGGTACAAAAACAAACACATAG 967
                          -  v      i   -   iii         i i  ii i i   i    
  L1M4_orf2#LINE/    247 G-CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_185600460_    968 ACAAATGGAACCGAA--GAGCAAACCCAGGAATAAAGCTGCACACCTGCA 1015
                          iv       iv   --   -- ii    i      v iii   ii iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAG--AGTCCAGAAATAAACCCATACATTTATG 343

  chr2_185600460_   1016 GTCATCTGACCTTTGACAAAGTTGACAAAAATAAACAATGGGGAAAGGAC 1065
                             vi   ii  i     i v  v   i vi vv            i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_185600460_   1066 TCCCTATTCAATTAATAGTGCTGAGATAGCTGGCTAGCTATATGCAGAAG 1115
                         vvi  v     iv   i      i  i i    v  ? i i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_185600460_   1116 AATGAATCTGGACCCCTAACTCTCACCAAATACAAAAATTAATTCAAGAT 1165
                               vi          v   v     v             i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_185600460_   1166 TTATTAAAGA------TGTAAGACTTCAAACTATAAGAATCGTAGAAGAA 1209
                         vv  i ?   ------       vi v         i v  v        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_185600460_   1210 AACCT-GGTAAACACCATTCTGGACATTGATGTTGGGAAAGAATTTAT-- 1256
                            v -  ?iv v i -   vv   v   i-   i  v  vii   v --
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGG-GTTAGGCAATGGTTTCTTA 591

  chr2_185600460_   1257 GACTAAGTCCTCAAAA--ATAATTTCAATAAAAACAAAAATTGACAAGT- 1303
                           -  v v vi     -- i  v--   i    iv      v  i  i -
  L1M4_orf2#LINE/    592 GA-TATGACACCAAAAGCACAAG--CAACAAAAGAAAAAATAGATAAATT 638

  chr2_185600460_   1304 GGACCTAATTAAAATAAAGAGCTTCTGCACATCAAAAGAAACTATCAACA 1353
                             i v  i     v  i i   i  ii v     i  v        -i
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA-G 687

  chr2_185600460_   1354 AAAGTAAGCAGAGAACCTGCAGAATGGGAGAAAATATTTACAAATTATAC 1403
                              i iv   v    ii                    i     i   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_185600460_   1404 ATCTGATAAAGGTCTAATATCATGAATCTATTAGGAACTTGAACACCTGA 1453
                                  i  v  vi    vv    v   v i     ivv   v  v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_185600460_   1454 ACAAGCAAAAAGCAAATAATCTTATTAAAAAGTGTGCAAAAGACACATCC 1503
                          i  vv    ii       i iv   ?    i  v     i  iviivvi
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_185600460_   1504 AGACACATCTCAAAAGAAGATATACAAGTGGCCAACAAACACATGAAAA- 1552
                              iv    v               i       i  i          -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_185600460_   1553 ATGCCCAACATTACTAATCAT 1573
                             i      i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.63 (31 / 19)  


2811 24.91 6.67 0.47  chr2_185612086_185616309.rev     2878  3732 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185612086_   2878 TAGAAATGTATTCCATTTTCATGGATTGAAAGAACCAATATTGTTAAAAT 2927
                          i    vi   i    v           i    vii           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185612086_   2928 GTACATACTACCCAAAGTAATCTACAGATTTAATGCAATTCATATTAAAA 2977
                          vvv     v      v i           i  i     i v   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185612086_   2978 TACCAATGATATTATTCACATAAAT----AAA--AATCATAAAATGTATA 3021
                          v   iiviiv  v  ii  v    ----  i--i   v      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_185612086_   3022 TGGAACCACAAAAGACCCAGAATAACCAAAGTTGTCTAAAGCAAAAGGAA 3071
                              vii   ii           i     iivi   vi iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_185612086_   3072 CAAAACTGGAGGAATCACATTACTTGGCTT--AAATTATAATACAGAGCT 3119
                             ii       v     i v iiiii  --   i -  v    i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr2_185612086_   3120 AAAGTAACCAAAATGGCATGGTATTGGCATAAAAA-AGACA----GACCA 3164
                          v     i   i ii ii     i        ii -     ----  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_185612086_   3165 ATGGAATAGAATGGGGAACCCAGAAATAAATCCATACATCTACAGTGAAC 3214
                                     v i  ii           i        i  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_185612086_   3215 TCACTTTCAACAAAGTTTCAAAGAACATACATTGGGGAAATGACAGTCTC 3264
                          v i    i    i v v v    v   v  v        vi i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_185612086_   3265 TTCAATAAATTGCACTGAGAAAACTAGGTATCCATATGCAGAAGAAAGAA 3314
                              i    v ii   i  v    i i  ?   i     i     v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_185612086_   3315 ATTAGACTCCTATTTTTTGCCATATGCAAAAAT---CCCA---------- 3351
                         i  i   i    ii ivii      i       --- i  ----------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_185612086_   3352 -----CCAAAT---------AAAACTA-----------AAAGAAAACACT 3376
                         ----- i    ---------       -----------i         iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_185612086_   3377 GGGGAAACTCTTCAGGACATTGGAGTAGGCAAAGACTTCTTGAGCAATAA 3426
                           ? v  v     iv   v    iv       v ii     -  vv  i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chr2_185612086_   3427 C-TCACAGACCCAGACAATCAAAGGAAACATGGACAAATAGGGCCACATC 3475
                          -i  v ii v  ii   iv    i   v  i  i    v  i iv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_185612086_   3476 AAA-TTAAAAAGCTTCTGCACAGCAAAGAAAACAATTAACAAACTGAAGA 3524
                            -       -   i  ii vv     i v  v  i  v   v    i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_185612086_   3525 GACAACTCACAGAATGGCAGAAAACATTTGCAAACTACCCATCTGACAAG 3574
                               i          v      i         ii ivi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_185612086_   3575 GCATTAATAACCAAAATATAAAAGGAGCTCAAACAACTCTATAAGAAAAA 3624
                          v i vi  v   i      v  i  i   vv       v    v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_185612086_   3625 AATCAAATAATCAGATTAAAAAATAGGCAAAATATCTAAATAGACATTTC 3674
                         i -       i vi   ?      i      iv  i i            
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_185612086_   3675 -CCAAA--AGACATAAAAATGACAAACAGGAA-GTGAAAATGTGCTCAAC 3720
                         -     --   i   v     i v  i i v -i      vi        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_185612086_   3721 ATCATTGACTAT 3732
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (135 / 75)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.39 (61 / 18)  


1724 26.60 1.00 1.20  chr2_185665192_185667768        1   500 (2077)  C L1M4_orf2#LINE/L1   (291)   617   119  

C chr2_185665192_    500 CAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAAGAG 453
                              -   -- v  i  - iii    i           viiv  ii  v
  L1M4_orf2#LINE/    119 CAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

C chr2_185665192_    452 CCCTCATCGCCAAGTCAATCCTAAGTCAAAAGAACAAAGCTGGAGGCATC 403
                           vvv  v     iv     i i ivv i          i      vv  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

C chr2_185665192_    402 ACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGC 353
                           i  v  ii i      viv        i          i   i    i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

C chr2_185665192_    352 GTGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGA 305
                                   i iv ii i   v                i    i--   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

C chr2_185665192_    304 GCCCTCAGAAATAATGCCACATATCTACAACTATCTGATCTTTGACAAAC 255
                          i  --        vv   i i  i  iiiii vi    i  i     iv
  L1M4_orf2#LINE/    317 GTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

C chr2_185665192_    254 CTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGC 205
                         v  vv  i v  vv            i  vvi  v  i  i         
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

C chr2_185665192_    204 TGGGAAAACTGGCTAACCATATGTAGAAAGCTGAAACTGGATCCCTTCCT 155
                              v      v  ?   i   i i  iiv    ii    i    v   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

C chr2_185665192_    154 TACATCTTGTACAAAAATTAATTCAAGATGGATTAAAGACTTAAAACGTT 105
                         i   i v i            i    i      i ?    i    -i  v
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA-TGTA 513

C chr2_185665192_    104 AGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGGA-ATACCATTC 56
                            v       i      vi i           v    ?i- v i -   
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC 562

C chr2_185665192_     55 AGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATG 6
                         iv   v v  vv i     v ii   v ivv  vi            vvi
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

C chr2_185665192_      5 GCAAC 1
                              
  L1M4_orf2#LINE/    613 GCAAC 617

Transitions / transversions = 1.45 (77 / 53)
Gap_init rate = 0.02 (8 / 499), avg. gap size = 1.38 (11 / 8)  

3232 27.29 0.66 0.33  chr2_185665192_185667768     1181  2085 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185665192_   1181 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 1230
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185665192_   1231 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1280
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185665192_   1281 TACCAATGACTTTCTTCACAGAATTGGAAAAA---ACTTTAAAGTTCATA 1327
                          v   iivi i  i  ii     v v  v  i--- iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_185665192_   1328 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 1377
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_185665192_   1378 CAAAGGTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 1427
                              v      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_185665192_   1428 CAGTAACCAAAACAGCATGGTACTGGTAACAAAACAGAGATATAGACTAA 1477
                               i   i    ii         i vv ii i   v       ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_185665192_   1478 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT 1525
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_185665192_   1526 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 1575
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_185665192_   1576 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1625
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_185665192_   1626 AATTGGATCCCTTCCTTACACCTTATACAAAAATGAATTCAAGATGGATT 1675
                          i     i    v   i     v           v  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_185665192_   1676 AAAGACTTAAATCTTAGACTTAAAACCATAAAAACCCTAGAAGAAAACCT 1725
                          ?    i     v v   vi      i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_185665192_   1726 AGGCA-ATACCATTCAGGACAGAGGCATGGGCAAGGACTTCATGTCTAAA 1774
                            ?i- v i -   iv   vvv  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_185665192_   1775 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1824
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_185665192_   1825 TAAACTAAGGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1874
                         i   v v ii i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_185665192_   1875 GGCAACCTACAGAATGGGAGAAAATTTCTGCAATCTACTCATCTGACAAA 1924
                          i     i                 v i     vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_185665192_   1925 GGGCTAATATCCAGAATCTACAATGAATTCAAACAAATTTACAAGAAAAA 1974
                           i  vi          v  i  v   i  vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_185665192_   1975 AACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTTCT 2024
                         i     i     v  i? v  i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_185665192_   2025 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAGTGCTCATCA 2074
                          v        i  vi viii     v ii          ii      v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_185665192_   2075 TCACTGGCCAT 2085
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.80 (9 / 5)  


3028 26.64 1.49 1.26  chr2_185680638_185682500      501  1371 (492)    L1M4_orf2#LINE/L1       36   908 (0)  

  chr2_185680638_    501 TAAAACTGTTAGAACA-CACTCATTGCCCAAAGCAATCTACAGATTTAAT 549
                            v i     ii ii-  v - i v      vii           i  i
  L1M4_orf2#LINE/     36 TAATATTGTTAAGATGGCAAT-ACTCCCCAAATTGATCTACAGATTCAAC 84

  chr2_185680638_    550 GCAATCCTTATCAAAATATCAATGACTTTTCTCATAGAAACAGAAAAACA 599
                                i         vi  iivi i   i iii     iv  v  i v
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr2_185680638_    600 AAATCCTAAAGTTCATATGCAACCACAAAAGATCCTGAATATCCAAAGCA 649
                         i -       i        v  vii   ii  i  v     v     i  
  L1M4_orf2#LINE/    135 GA-TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr2_185680638_    650 ATCTGGAGCAAAAAGAACAAAGCTGGAGGAATTATATTTCCTGATTTTGA 699
                             v  iv  i          i       v i i i    ii    ii 
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_185680638_    700 AATATACTACAAAGCAATAATAACCAAAACAGCATGGTACTGTCATAAAG 749
                           iv           v i i   i   i    ii        v     i 
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_185680638_    750 -CAGACACATG--TGAATAGAACTGAATT-AGAACTTAGAAACAAATCCA 795
                         -i     i  i-- v   i   iv     -   iiii     i   i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_185680638_    796 TGCATTTGCAGCCAACTGATTTTTGATAAAAGTGCCAAGAACACACATTG 845
                          i     iii i   i       i  i  ii         v  iv  v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_185680638_    846 GATAAAGGACAGTCTCTTCAATAAACAGTGCTAGGAAAACTGGATATCCA 895
                          iv    i i     i     i   ii     i   v         ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_185680638_    896 CAGGCAGAATAATAAAATGAAATCTTTATTTCTCACTACTTACAAAAATC 945
                           v   i  v   i  i vii i ii  ii  v   i iv         i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_185680638_    946 AATGCAAAATGGATTGAAGACTTTAGCATTAGACTTGAAACTATGAAACT 995
                           iv          ii?    i v iii v   vi i       i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_185680638_    996 ACTAGAATAAAACATAGGAA-AAATACTTCATGATAGTGGTCTGTGGAAT 1044
                         vi     v          ?i-    -    i   ivv   vi iv v   
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_185680638_   1045 AATTTTTTG--TATAACA---GAAGCATGGGTAACCAAAGCAAAAATAGA 1089
                         ii   i  i--   i   ---i     iii i   v    v         
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_185680638_   1090 CAAATGAGATTTCATCAAACTAAAAAGTTTCTGTACAACAAAGGACATAA 1139
                         i    vi  i         v v    ii  i   i vv         iv 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_185680638_   1140 TCCATAGAGTGAAGAGAAAACCTACAGAGTAGGAGAAAATACTTAAAAAC 1189
                           v v i      i   v    i     i i          i  iv   i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_185680638_   1190 TCTGCATCTAACAAGAGGTTAATATCCAGAATATAAAAGAAACACAAACA 1239
                         iv ii    i i   i ii vi             v  ii   v vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_185680638_   1240 ACTCAGTGACAACTCCCCCCCACCCCAAAGAATCCAATTAAAAAATGTGC 1289
                              i i i  v-------- vvv    v  i      ?       v  
  L1M4_orf2#LINE/    783 ACTCAATAATAAA--------AAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_185680638_   1290 AAAG-ATTTGAATAGACGGTTTTCAAATGAAGACATACAAATCGCAAATG 1338
                             -            iv  i  v  v     i        v  v   i
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_185680638_   1339 GGTATAC-AAAACATGCTCAACATCACAAATCAT 1371
                         i i i i-    v             ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (156 / 72)
Gap_init rate = 0.01 (13 / 873), avg. gap size = 1.85 (24 / 13)  


2098 23.40 2.23 11.38  chr2_185721255_185724485.rev     1792  2731 (500)    L1M4_orf2#LINE/L1        1   854 (54)  

  chr2_185721255_   1792 TGAAACAATATTGTATGTTTATGGATTAAAACAATTAATATTGTTAAAAT 1841
                           i  vi    ivi     i       ii  v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185721255_   1842 GACTATACTACCCAAAGCTTA--CTACAAATTCAATGCAATCTTTATTCA 1889
                          i v     v      --  i--     i      i      ii   iv 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_185721255_   1890 AACTCCAA-TGTCATTTTTCATAGCTATAGAAAATATCATATATAAATAT 1938
                           ii   i-  i v     ----  ---     -----------------
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTT----GC---AGAAA----------------- 124

  chr2_185721255_   1939 CATTTATAAATCATATATAAAAATATCATATATAAAGGTATAGATATATC 1988
                         --  v i  iiii-  viv     -      iv   v i ----------
  L1M4_orf2#LINE/    125 --TTGACAAGCTG-ATCCTAAAAT-TCATATGGAAATGCA---------- 160

  chr2_185721255_   1989 ATTTTTCATAGGTATAGATATAGATTGATTTCATATGGATCCACACACAC 2038
                         ---------   -------------------------  i   -------
  L1M4_orf2#LINE/    161 ---------AGG-------------------------GACCCA------- 169

  chr2_185721255_   2039 ACAAAAACAAATAGCCAAGGC--TCTCATTCAAAAAGAACAAAGCTGGAG 2086
                         --------i         ii --   iivvv  i          i     
  L1M4_orf2#LINE/    170 --------GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_185721255_   2087 GTATCACACTATTTTGTTGCAAACTATATTACAAAGTAATAGTAATTACA 2136
                          vv       viiivi  v    viv  i       iv i      i vi
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_185721255_   2137 GCAGCATGGTACTGGCATAAAAACAGACACATTGACAAATAAAATAGAAT 2186
                         i   ii              ii i     i  v  iv   ii        
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_185721255_   2187 AAAGAGTCCACAAGTGAGATTCTAAC---TATGGTCAATTAATTTTAAAC 2233
                         vi        v  i i - ii vv  ---           i     vi  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_185721255_   2234 AAATGTGTCAAGAATATGCAATGGGAAAAGGACAGTTTCTTCAATAAATG 2283
                           iv   i     vi  v       i    i i   i i     i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_185721255_   2284 GAGTTGGAAAAATGGGATATTTCAATAGAGAAGAATGAAATTGAAACCCT 2333
                          v i   i v  iv     ?iivv  iv i         i   i v    
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_185721255_   2334 ATCTCATACCATATA--AAAATCAAATCAAAATGGATTGGAGACTTAAAC 2381
                          i    i        --     i  v           ii?    i    i
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_185721255_   2382 ATAAGATCTGAAGC-ATAAAAACTATAAGAATAAAACAGAGG---AAAAC 2427
                         i     v  i  i -      -  v v    v      v   ---   v 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_185721255_   2428 CACATGACATTGGTTTAGGCAAAATTTTTTTAGAT----C-CCAAAACTG 2472
                         iv i    v    v        viv   i      ---- -      vii
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_185721255_   2473 CAGGCAACAAAAGCAAAA-TAGACAAATGAAATTACGTCAAAATAAAAAG 2521
                           i          v    -    i    vii i v i       v    i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_185721255_   2522 GATTCTGCACACCAAAGGAAACAAGTAACAGGGTGAGGAGACAACTTATA 2571
                         v-  i  ii vi       v  v vi  v ii    ii       ii i 
  L1M4_orf2#LINE/    660 C-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_185721255_   2572 GGTGGGGAGAAAATATTTGCAAACTAAAGTACTAATATGTACAAGATAAA 2621
                          ivv                   ii ------  -   v ----     i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCA------TA-TATCT----GATAAG 747

  chr2_185721255_   2622 GTATTAATATATAAGATATATAAGAAATTCAAAGAACTCTGCAGAAAGAA 2671
                          v i vi   vi ii        ii  i  vv v     vii iv  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_185721255_   2672 AACAAATATCCTAATTGATTAAGAAATGG-CAAAAGACCTGAACAGACAT 2720
                         i       v  i    ----? i      -    i  ii    i      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATT----WAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_185721255_   2721 TTCTCAAAAAA 2731
                              v   i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGA 854

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.03 (27 / 854), avg. gap size = 4.74 (128 / 27)  

1067 26.64 1.64 2.96  chr2_185721255_185724485.rev     2749  3052 (179)  C L1M4_orf2#LINE/L1   (608)   300     1  

C chr2_185721255_   3052 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAATATCGTGAAAAT 3003
                              ii i  i     i    i i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_185721255_   3002 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2953
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_185721255_   2952 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAAACT-ACTTTAAAGT 2905
                          v   iivi i  i  ii     -   ----- v  i  - iii    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-----ACAAGCTGATCCTAAAAT 145

C chr2_185721255_   2904 TCATATGGA---GCCAAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAG 2858
                                  ---  ----  ii  v  v v  v     iv     i i i
  L1M4_orf2#LINE/    146 TCATATGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

C chr2_185721255_   2857 CTAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACT 2808
                         vv i          i      vv   ii  v  ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

C chr2_185721255_   2807 ACAAGGCTGCAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGAT 2758
                             i   i      i   i    ii        vi iv ii i   v  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

C chr2_185721255_   2757 ATAGACCAA 2749
                              i   
  L1M4_orf2#LINE/    292 ATAGATCAA 300

Transitions / transversions = 2.12 (55 / 26)
Gap_init rate = 0.02 (5 / 300), avg. gap size = 2.80 (14 / 5)  

 201 33.64 1.87 1.87  chr2_185721255_185724485.rev     3125  3231 (0)    L1M4_orf2#LINE/L1      301   407 (501)  

  chr2_185721255_   3125 TGTAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT 3172
                           v  i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_185721255_   3173 CTGATCTTTGAAAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 3222
                         i    i  i  v  ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_185721255_   3223 ATTTAATAA 3231
                         v  i  i  
  L1M4_orf2#LINE/    399 TTTCAACAA 407

Transitions / transversions = 1.40 (21 / 15)
Gap_init rate = 0.02 (2 / 107), avg. gap size = 2.00 (4 / 2)  


1699 26.41 13.46 2.95  chr2_185742125_185743963      567  1346 (493)    L1M4_orf2#LINE/L1        4   865 (43)  

  chr2_185742125_    567 AAAGATATCTCATGTTTATAGATTAGAAAAATTGA-ATTTTT--GATGTT 613
                                  i      i  i    i   i v  i -   v  --    vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_185742125_    614 TACACTACCCAAAGCAATCTACAAATTCAATGCAATCTTTATCAAAATTC 663
                         v i   v      vii       i      i      ii         i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_185742125_    664 CAA-TGTCATTCTTTATAGAAACAGA--AGTTA-----------CA---- 695
                           i-  i -  i   ii     iv  --  i i-----------  ----
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_185742125_    696 -------AAAAAACCC-TAATAGCTAAAGCAAACTTGA----GAAAAAGA 733
                         -------  iii    -v      i   i   v     ----   i  v 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_185742125_    734 AATCTGAAGGCATCACACTATTAGATTACATTACAAAGATTTCAG--TTT 781
                           vi  i   vv       ----------- iv   ---     i--i  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACT-----------TCCCAA---TTTCAAAACTT 238

  chr2_185742125_    782 ACATTACAAAGCTATATTTATCATAA-AGCATAATATTCGCATAAAAACA 830
                           --          i v v    vi -  ii ii  i v      ii i 
  L1M4_orf2#LINE/    239 AC--TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_185742125_    831 GATAAATTGACCAATGGAACAGGACAGAGAGCCCA-AAATAAACCCACAT 879
                           i v  v  i        i  i iv     i   -           i i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_185742125_    880 GCCTATAGTAAGTTGATTTTCAACAAAAGTGTGAGGAACACATGAGGAGA 929
                         iii   i  v i         i    ii   iv i  v  ivii v i i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_185742125_    930 AAAGGACAGTCCCT-CAATAAATGATGTTGGGAAAACTGAGTATCTA-AT 977
                             i i    ii -   i     i  i     v     ii  ? i -  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_185742125_    978 ACAAAAAAATAAAAATGGGCCTTTGTCTCAGTTCCTACACAAGAATCACC 1027
                         i     i   i  iv   i  ii ii    vvi v  i    i   i v 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_185742125_   1028 TTAAAATGAATTAAAAAGTTGAATGCAA---------------------T 1056
                          i      i  i ? i vi i    i  --------------------- 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_185742125_   1057 AGGAGCAAA----------AGTCTACG--ACATTGGTCT-GGAAAGAGTT 1093
                           i  v   ---------- i   v  --  v    vi -  v  vi   
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_185742125_   1094 T--TAG--------------------GGAA-AAAAGTGAAAATAGACAAA 1120
                          --   -------------------- v  -     vi        i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_185742125_   1121 TGGGATTTTATGAAACTATAATAAAAACGTTCTACGTAGCAAAGAAAACA 1170
                          v   i  i  v   --  --       -  i ii ivv     i v  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAA--AT--TAAAAAC-TTTTGTGCTTCAAAGGACACT 681

  chr2_185742125_   1171 ATTAA-----TTGAGAGACAGCCCATGGATTCGGATGAAATATTTGCAGA 1215
                           i  ----- vi i     i    ii  v v   vi           i 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_185742125_   1216 TCACGTAACTGATAAGGAACAAATATCTAAAATATACAAGGAACCCAAAC 1265
                            ii  v         i  vvi    i i      i  i    i vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_185742125_   1266 TACTCAATAACAAGAAAA-AAA-AATCTA--TGAAAAGTGAACAGAAGAC 1311
                         v         i  i  i -   -  i i -- ?    i  ii  i i  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_185742125_   1312 TTGAACATAAATTTATACAAAAAAGACACTAAAAA 1346
                              i v v    v v    i    i -  v   
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATA-TACAAA 865

Transitions / transversions = 2.27 (141 / 62)
Gap_init rate = 0.04 (32 / 862), avg. gap size = 4.00 (128 / 32)  

 307 25.74 8.09 1.47  chr2_185742125_185743963     1429  1564 (275)  C L1M4_orf2#LINE/L1   (0)   908   764  

C chr2_185742125_   1564 TATATAAAGAATTGTCAAAACTCACAATTTTAAAAAGCCAAGTAA----- 1520
                                    i v i v      --  vv       v   i   -----
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCA--ATAATAAAAAGACAAATAACCCAA 811

C chr2_185742125_   1519 -----AAATGGGTAAAAGACAGAAACCCATATTTTACTGAAAAGGATATA 1475
                         -----       i   i  ivvi  ivv i    iv ii  i i      
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

C chr2_185742125_   1474 CAGAAGGCAAGTAAGAACAT-AAAGCCTGTTTCACATCATCAGCCAT 1429
                           i v   v i    v    -   ivv  i iv      ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (19 / 16)
Gap_init rate = 0.02 (3 / 145), avg. gap size = 4.33 (13 / 3)  


2870 26.54 3.99 0.57  chr2_185768070_185770069      631  1508 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185768070_    631 TGGAAAGATATTATCTGCCCATGGGTTGAAATAATTGAGATTGTTAAAA- 679
                                    iviv  ii     i   i  v v  i v        i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185768070_    680 ATCCAT-CTATCCAAAGTCATCTATAGACTGTATGTAATCCCTATCAAAG 728
                         iv v  -  vi     v v     i   i vv i i             i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185768070_    729 TTA-AACTAGCGTTTTTCATAGAAATTAACAA-----TTTCAAAAGTTAA 772
                          iv- i  -  v     iii       i    ----- iii    v i v
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_185768070_    773 ATGGGAA---AAAAGGCCATGAATAGCCAAAACAATGTTGAGAAAAAAAC 819
                             i  ---  ii i  vv                v    i   i  iv
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_185768070_    820 ACATATTTGGCTGAATCACAGTTCTTGATTT-AAAAT--------AGGTT 860
                            v v    vv  v     v   iii    -    i-------- i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_185768070_    861 AATTAGTAATCAAAACAGCACAGTACTGGCATGAAG-TAGGAATGTAAGT 909
                          --i         i    iiii          i i -   iv  i  ii 
  L1M4_orf2#LINE/    250 A--CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_185768070_    910 AAATGCAACATAATAGAGCACCCAGAAATAAACTCCAACATGTAAAGTCA 959
                         v    v  i v   v   vii            i vv    v  vi    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_185768070_    960 ACCAATTTTCAACAAGCCTACCAAGGGGACACAATGGGGAAAGAATAGTC 1009
                          iii      i     vv i     ivv iv                   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_185768070_   1010 TCTTCAATTAATGATGTTAGGAAAACTGAATTTTCACATACAAAAGAATC 1059
                          i     iv    i  i i   v     i  v?i     i         v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_185768070_   1060 AAATTGGGCCCATATCTTATGCCA-ACCCAAAAATCAGCTCAAAATGGAT 1108
                           i    i   v  i  i ii   - iv       i i            
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_185768070_   1109 TAAATCCCTAAATGTAAGACCTGAAACTGTAAAACTTCTAGAAGAAAACA 1158
                         i ? vv             v  i     i       ii            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_185768070_   1159 TGGGAC--AAGCTTTTTGACATTGGCCTTGGCAATAATGTTTTTAGATAT 1206
                          i  ?v--  v   iv    v    vi v      ii -  i        
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATAT 596

  chr2_185768070_   1207 --CAAAAAAAATTTGAGCAACAAAAGCAAAAACAAACAAATGGGACTACA 1254
                         --  vv    iivii           v     i i i    v     v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_185768070_   1255 GCAAACTAAAAGAAATCCACATAACAAAGGAAAAAATTAACAAAACGAAA 1304
                         v    v v   i vv iiiiiivv       v vv  i  v   ii    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_185768070_   1305 AGGTAACCTGTAAATTGGAAGCAAATATTTGCAAACCATAAATCTGACAA 1354
                           ii    iii i v   i  v             i    v      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_185768070_   1355 GGTGTTAATATCCAAAATATACAAGGAACTCAAACAGCTCAATACAAAAA 1404
                           vii vi      i      i  i      vv   i       vv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_185768070_   1405 ACAACAAATAACTTGATTAAAAAATGGTCAAAAGACCCGAACAGACATTT 1454
                          -i         iii   ?        v    i  iii   i        
  L1M4_orf2#LINE/    797 A-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_185768070_   1455 CTCTGAAGAA---------ATGCTTAACAGGTATATGATTAGATGCTCAG 1495
                            ii     ---------   vii  i i i i    vv         i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_185768070_   1496 TCTCACTAATCAT 1508
                         iv   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (142 / 87)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.50 (40 / 16)  


 797 22.79 0.93 3.72  chr2_185782381_185784789      688   902 (1507)    L1M4_orf2#LINE/L1        4   212 (696)  

  chr2_185782381_    688 AAAGATATACTATGGTCATTAATTGGAGGAACAT-ATATTGTTAAAGTGT 736
                                 v i   v    vi      i  - v -          ii  v
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGA-CTTAATATTGTTAAGATGG 52

  chr2_185782381_    737 CTATACAACCCAAAGTGTATAGGTATTT-CAGACTCAATGCAATCCCTGT 785
                          v    vv      v  -------  i -    i    i         i 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTG-------ATCTACAGATTCAACGCAATCCCTAT 95

  chr2_185782381_    786 CAAAACACCAATGGCACTCTTCACAGAAATAGAAAAAAAAATGCTAAAAT 835
                              iv   iiv  vi i  ii       v  v  ivvi  v       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_185782381_    836 TTGTATGGAACTGCCAAAGACCCTGAATAGTCAAAACAATTTTGAGGAAA 885
                          ii       v   v ii     v      i         i    ii  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_185782381_    886 AAGAACAAAGCTGAAGG 902
                                   i  i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGG 212

Transitions / transversions = 1.45 (29 / 20)
Gap_init rate = 0.02 (4 / 209), avg. gap size = 2.50 (10 / 4)  

2769 23.24 1.35 2.43  chr2_185782381_185784789     1178  1917 (492)    L1M4_orf2#LINE/L1      177   908 (0)  

  chr2_185782381_   1178 CAAAAAAA----AAAAAAAAAGGAGAAAACTGTAGGCATCATACTACCTG 1223
                              v  ----i     i   i v   ii  v   vv   i   v  ii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_185782381_   1224 ACTTCAAAATAAAAATATAGTAGACAATTATAGTAAACAAAATAGCATGA 1273
                          i       i----- -  v  v v ii  i     v   i i  ii  i
  L1M4_orf2#LINE/    227 ATTTCAAAAC-----T-TACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_185782381_   1274 TATTGGCATACAAACAGACATGTAGGCTGTTGGAAAATAAATAAATAAAG 1323
                           i       vii i      i   iiiiv     --  i ---  vi  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAA--TAGA---ATTGAG 315

  chr2_185782381_   1324 AGCCCAGAAATAAATCCACACATTTATGGCCAATGGATTTTTGACAAAGG 1373
                           i           i   i          i    v      i     i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_185782381_   1374 TGCCAAGAGCATTCATTGGGGAAAGTATAATCTTTTCCACAAATGATGTT 1423
                                 v      v         v   i       v       i  i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_185782381_   1424 AGGAAAACTGCAACATCTACATA-AAAAAAATTAAATTAGACCTTTATCT 1472
                         i   v     -i i ? i    i-    i   v  i  i    ii  i  
  L1M4_orf2#LINE/    416 GGGACAACTG-GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_185782381_   1473 CTCACCCTATA--AAAATCAGCTCAAAATTGATTAAAGACTTAAATATAA 1520
                          v    v    --     i i        v   i ?    i     i   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_185782381_   1521 GAACCAAAACTGTAAAACCATTGGGATAAAACATAAAGGAAGTTCTTTAT 1570
                           i i      i      iv  i i v        ii? v iv    ii 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_185782381_   1571 GACATTGG--TAGGGATAAGGATTTTTTAGATAAGACCTTGAAAGCACAG 1618
                            v    --    --i  v i   i       v   viii        i
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGG--CAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_185782381_   1619 GCCACAAAAGCCAAAATGGACCAATGGGATTACA-CTGAATTAAAACACT 1667
                           v       vv     i  iv   v   i v  - vi        -   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA-ACT 661

  chr2_185782381_   1668 TCTGCACAGAAGAGGAAACAACCAACAGAGTGCAGAGACAACCTACAGAA 1717
                          i  ii vvv i    v  v i   v i    v i        i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_185782381_   1718 TGGAAAAAGATATTTGCAAATCATACATCTGCCAAGGGATTAGTATCCAA 1767
                            i i  i                i     vi      i v       i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_185782381_   1768 AATATATAAGAAACTCAAACAACTCAATAACAAAAAAAGCCCAAATAATT 1817
                                  ii     vv            i     i ---       ii
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGA---CAAATAACC 808

  chr2_185782381_   1818 TGATTAAAAAGTGGGCAAACTACCAGAATTGATATTTCTTAAAAGAAGGC 1867
                         ii   ?    i        vv iiv    v  i      iv       ii
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_185782381_   1868 GTACAAATGGCCAACAGGTATACTAAAAAATGCTCAACATCACTAAACAT 1917
                         i             i i i i iv    i             ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (113 / 55)
Gap_init rate = 0.02 (13 / 732), avg. gap size = 2.15 (28 / 13)  

1178 25.94 1.01 1.26  chr2_185782381_185784789     1958  2354 (55)    L1M4_orf2#LINE/L1      513   908 (0)  

  chr2_185782381_   1958 AAAACCCAAAAGTATAAAAACCCTGGAAGACAACCTAGGCA-ATATCATT 2006
                           i v i    v       vi i i     v   v    ?i- v   -  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TT 561

  chr2_185782381_   2007 CATGACGTAGGCATGGGCAAATAATTCAT--GATTGAAGGTGCCAAAAGC 2054
                          i    v v  vv i     - ii  iv --   -- v iii        
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT--ATGACACCAAAAGC 608

  chr2_185782381_   2055 TTTTGCAACAAAAATGAAAATTGACAAATGGTATCTAATTAAACTAAAGA 2104
                         vivv         ivi     v  i    v v ii v  i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_185782381_   2105 GCTTTTGCACAGCAAAAGAAACTATCAACAGAGTAAACAGACAACCTCCA 2154
                         i      ii vv    i  v        v i   i  v        iv  
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_185782381_   2155 GAATGAGAGAAAATTTTTGAAAACTATATATCTGACAGGGGTCTAATATC 2204
                              i        v    v   ii          i i   v  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_185782381_   2205 CAGCATCTATAAAGAACTGAAACAAATTTACAAGATAAAAAACAAACAAC 2254
                            v  v           vvv    v iv i  v -    i     i   
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATA-AAAAGACAAATAAC 807

  chr2_185782381_   2255 CCCATCAAAAAGTGAGCAAAGAACATGAACAGACACTTTTCAGAAGAAGA 2304
                           v  i?    i  i      i iv    i     i  i  vi       
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_185782381_   2305 CATACATGTTGCCAACTATCATATGAAAAAA-GCTCAATATCACTGATTA 2353
                         i     vi v     iv v  i       i -      i    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_185782381_   2354 G 2354
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.15 (54 / 47)
Gap_init rate = 0.02 (7 / 396), avg. gap size = 1.29 (9 / 7)  


2565 26.95 1.89 2.90  chr2_185797427_185800843     2028  2925 (492)    L1M4_orf2#LINE/L1       20   908 (0)  

  chr2_185797427_   2028 CATGGATGGGAAGAATTGGT--CATAAAAATAGCCATACTGCCCAAAGCC 2075
                                v      v  ii --ii v  i  i  v     v      viv
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chr2_185797427_   2076 ATTTACAAATTCAACACTACTCCTATCAAACTACCAA-TGTCATTTTTCA 2124
                           i    i       i v ii         v v   i-  i -     ii
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTG 118

  chr2_185797427_   2125 CAGAAGTTCCAAAAACACT-ATTCTAAAATTCATATGGAACCAAAAAGAA 2173
                              i  --i v  -i  -  i                 viiv  i i 
  L1M4_orf2#LINE/    119 CAGAAATT--GACAA-GCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_185797427_   2174 CCCA-AATAACCACAGCAATTCTAAGTAAAAAGTACAAGGCTGAAGGCAT 2222
                             -    i   v i    ii i iv  i   v    i i  i   vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_185797427_   2223 CACAGTACCCAACTT-AAAACTATACTATAAAGCTACAGTAACAGAAATA 2271
                             v v     i  -      -     i             ivi i i 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACA 264

  chr2_185797427_   2272 GCATGGTACTTGACACGGTATAAAAACAGACACATAAAACAATGAAACAG 2321
                          ii       ------  i    ii i     i   i v     i  i  
  L1M4_orf2#LINE/    265 GTGTGGTACT------GGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_185797427_   2322 AGTAGAAAAATTCAGAAACATATCTGCACACCTACAACCATCTGATCTTT 2371
                          i v  i i- i      i v i iii   ii  iiii  vi    i  i
  L1M4_orf2#LINE/    309 AATTGAGAG-TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_185797427_   2372 GATAAGGCCAACAAAAACAAAAAATGGGGAATGGACCCCCTGTTCAATAA 2421
                           i    viiv   i v  vvv         v i ivvi  v     i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_185797427_   2422 GTGGTGCTAAGATAACTGGCAAGCCATATGGAGAAGAATGAAACTAAACC 2471
                         i       ii  i      vv ?   i   v i         ii ii   
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_185797427_   2472 CTTACTTTTGAGCATATACAAAAATTAATTTAAGACGGATCAAAGGTTTA 2521
                          i   i ivv v                i i  i i      ?  iii  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_185797427_   2522 AACGTAAGACACCAAACTATCAAAATCCTGAAAGAAAACCTAGGAA-ATA 2570
                           i      vviv       v   v  i ii        v    ?i- v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_185797427_   2571 TCATTATCAACCTCAGCCT---TAATAGAACTTTTGTCTAAAT----CCC 2613
                           v ii -i    ii vi ---i   i ----   v -  i  ---- v 
  L1M4_orf2#LINE/    558 TCTTCGT-GACCTTGGGTTAGGCAATGG----TTTCT-TAGATATGACAC 601

  chr2_185797427_   2614 CAAAAGCAATCA--CAACAAAACCAAAAATTGACAAGTGAGACCTAATTA 2661
                                 --  --        vv      v  i  i vi   i v  i 
  L1M4_orf2#LINE/    602 CAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_185797427_   2662 AACTAAAGAGCTTCTGCACAGCAATAGAAACTATCAACAGAGTAAACAAG 2711
                           v v  i i   i  ii vv   vi  v        v i   i  v ii
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_185797427_   2712 CAGCCTACAGAATGGGCAAAAATATTCACAAACTGTGCATCTGATAAAGG 2761
                           i  i          vi        ii    iii ii         i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_185797427_   2762 TCTAATATCCATATCCAGAACCTAGAAGGAACTTAAACAAATCAACAAGC 2811
                         v  ------ii         iv  v  i     ivv    v    i  vv
  L1M4_orf2#LINE/    750 ACT------TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_185797427_   2812 AAAAAACAAATTACACGATT-AAAAATAGTCAAAAGACACGAACAGATAT 2860
                             i      v  v i   -      i v    i  ivi   i   i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_185797427_   2861 TTCTCAAAAGAAGACATACAAGTGGTGAACAAACAAATGAAAAAATGCTC 2910
                              v        i      i   iv  i  i  v       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_185797427_   2911 ATCATCACTAATCAG 2925
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (157 / 82)
Gap_init rate = 0.02 (21 / 889), avg. gap size = 2.05 (43 / 21)  


2445 25.63 0.74 1.03  chr2_185875582_185877218.rev      467  1145 (492)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_185875582_    467 AAAGCTTATT-CAAATGGAAAATAACTGAGAAGCAAGGATGGTACTGGCA 515
                            i    i -    vvv v i   iii   --  iv -           
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGA--CAGTG-TGGTACTGGCA 278

  chr2_185875582_    516 TGAAAATAGACACGTAGAACAATGTAACTGAATAGAGAGAACCCAGAAAC 565
                          i ii       ii    v     v  iv    v     --i       i
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG--TCCAGAAAT 326

  chr2_185875582_    566 AAATCCGCACACCTCCAGTGAACTCATTTTTGACAAAGGTGTAAAGAATA 615
                            i  ii   ii vii  v  i v     i     i    iv    vi 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_185875582_    616 TACACTGAGGAAAAGACAGTTTCTTCAATTAATGGTTCTGGGAAAACCGG 665
                          v  v  i     ii i   i i     iv      v      v   i  
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_185875582_    666 ATATCCATTTAAAGAAGAATGAAACTAGCCCTTTATCTCTTGCCATATAC 715
                            ?   iv iv i         ii i v  ii  i   vii        
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_185875582_    716 AAAAATAAAATTCAAATAGATTAAAGACTTAAATCTAAG-GTTCAAACTG 764
                               v  v iv    i   i ?    i     v    - i v     i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_185875582_    765 TGAACGTACTATAAGAAAACACCGGGGAAAATCTCCAGGATACTGGTCTG 814
                          i  vv vi  v         iv  ? v      i iv  ivi   vi i
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_185875582_    815 GGCAAAAATTTCTTGAGCA--ATACCATACAAGCACAGGCAACCAAAGCA 862
                              vii      iiii -- i    - -       i     v    v 
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCA-A-AAGCACAAGCAACAAAAGAA 624

  chr2_185875582_    863 AAAATGAACAAATCAGATTACATCAAGTTCAAAAGTTTCTGCATAGCAAA 912
                              ii i    ii  i v      iv i    ii  i  iiivv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_185875582_    913 GGAAGCAATCAACAAAATGAAAAGACAAGCCACAGAATGGGAGAAAATAT 962
                            vi v     v   i           v                     
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_185875582_    963 TTGCAAATTACCCATCTGACAAGGGATTCATAACCAGAATATATAAAGAG 1012
                                 i ivi      i      i ii  v                i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_185875582_   1013 CTCAAACAACTCTATAGGAAAAAT-CTAATAATCCAATCAAAAAGTGGGC 1061
                            vv       v   iv     v- v     i     i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_185875582_   1062 AAAATATTTGAATAGACAACTCTCAGAAGAAGGGATACAAATAGCAAAGA 1111
                            iv             vi    vi      iv        i  v  v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_185875582_   1112 GGCATATAATAAGGTGCTCAATATCATTGATCGT 1145
                         i   i  i v   i       i    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (107 / 63)
Gap_init rate = 0.01 (9 / 677), avg. gap size = 1.33 (12 / 9)  


3292 25.84 1.90 0.34  chr2_185925063_185928558     2111  3004 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185925063_   2111 TGAAAAGATATCCTGTTCTCATGGGTTGGAAGAATTAATATTGTTAAAAT 2160
                           i          ii vi      i        v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185925063_   2161 ATCCATGTTTCCTAAAGCAATCTACAAACTCAATGCAATTTCTATCAATA 2210
                         iv v  ii i  i   vii       i i    i     ii       v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185925063_   2211 TTCCAGTGGTACTTTTCACAGAGATAGAAAAAAACAATCCTAACGTTTAT 2260
                          i    iv ivi    ii    i  v  v  iv-ii       vi  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_185925063_   2261 GTGGAACTATAAAAGACTCTGAATTGTGAAAGCA-TCTTGATCAAGA-GA 2308
                         i     v ii  ii   i v    v iv   i  -      vv    -  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_185925063_   2309 ACAAAGCTGGAG-ACATACATCTGTTGATTTCAAAAAATATTACAAAGCC 2357
                               i     -  vi   ii viii         vv  i        i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_185925063_   2358 ACAGTAATAAAAACAGTATGGTACT--TAAAAAAACAGAC-TAGTAGACA 2404
                                 v  i     i       --i v  ii i    -  -    iv
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGATC 298

  chr2_185925063_   2405 AATGGAACAGAATAGAGACCCTTGAAATAAACCCATGCATTTAAGGGCAG 2454
                                i     v    vi iv             i      v  v  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_185925063_   2455 TTGGTTTT-AATCGGGGTGCCAGGAACATACAGCAGGGAAAGA---GTCT 2500
                            i    -i ivi        i  v   v  iii        ---    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_185925063_   2501 CTTCAATAAATGGTGTTGGTAAAACTCAGTATCCATATATCAAAGAGTCC 2550
                         i     i        i   v v    vii  ?   i  iiv     i vv
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_185925063_   2551 AATTAGACTT-TATCTCACACAATATAGAAAAGTCAACACAAA-TGGATT 2598
                          i  i   ii-  i       v     v    i i   v    -     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_185925063_   2599 AAAGACCTAAATGTAACACCTGAAACTATTAAATTCCTAAAAAGAAGAAT 2648
                          ?              v v  i       v   i  i  i  ii  iv  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_185925063_   2649 AA----AAACCTTATTGACATTGGTATGGGAAATTATTATTTTGCTTATA 2694
                          i----   i   vv    v    vv i  v   vi  - i  ivv   i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAGATATG 597

  chr2_185925063_   2695 ATCCCAAAAGTACAGTCAAAAAAAGCAAAAATAGACAAGTAGGGGTATGT 2744
                          iv       i   iv   v     v         i  i v  iv vii 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_185925063_   2745 CAAATGTAAGGGCTCCTGCACTGCAAAGAAAATAATCAACAGAATAAAAA 2794
                             vv   iii  ii  ii  v     i v iv     v i i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_185925063_   2795 GACAACCTACAAAATGGGAAAAAACATTTTCAAACCATTTGTCTGATAAG 2844
                                i   i       i    i    v    i   v i         
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_185925063_   2845 GGGTTAATATCCAAGATACATGAAGAACTCA-AAAACTTAAGAGCAAAAA 2893
                           ii vi      ii   i  i        v- v    i  v ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_185925063_   2894 ACCAAATTACCCAATTAAAAAATGGGCAGTGGACCTAAACAGACATTTCT 2943
                         iv     v        ?           iv   ii i  i          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_185925063_   2944 ACAAAGCAGAAATACAGATGGTCAATAGGTGTATGAAAAGGTGCTCAACA 2993
                         v     v   v     i    i     i iii        i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_185925063_   2994 TTACTAATTAT 3004
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.85 (148 / 80)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.43 (20 / 14)  


2175 26.31 4.21 4.67  chr2_185928841_185931540     1323  2200 (500)    L1M4_orf2#LINE/L1        6   879 (29)  

  chr2_185928841_   1323 AGCTATATCATGCTCCTGGGTTGAGATATTCAATATTGTTAAAATGCCAA 1372
                           v   vi    i  v   i   ii v i i           i   v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_185928841_   1373 TTCTTCCCAA-TAGATTTATAGTTTTAACATGATCTCTATCAAAATCCCA 1421
                          v  i     - v   i  i  v  i   iii   i              
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_185928841_   1422 TCAGGCTTCATTATAGAAGTAGAAAAATTGATTGTAAAACTCACATGGAA 1471
                         v v v   iv  ii    i v  v  ii    iv     i   i      
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_185928841_   1472 ATGCAAAGGATCTAGACCAGCCAAAACAACTTTGAAAAATAG---CAGAC 1518
                               i   i i   vi           ii        v i---  i v
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_185928841_   1519 TTGGAGGAGTATCACT----GGTTTCTAGAATCACTCTCAAGCTACAATA 1564
                                 v vv    ----ii    v i v i   viv        i  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_185928841_   1565 ATCAAGAAAAAGAGATGGTAGCATAACGATATACACTTTGATCAATC-AA 1613
                                v iv v i iv i      v    v   iv v       v-  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_185928841_   1614 TACAGCAGAGAATCCAGGAATAGGTCAACAAAGAAATGAAAAAATGCATG 1663
                           v iiv    i     i    iii v i v vvv   ivv  v  ---i
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG---A 352

  chr2_185928841_   1664 TTTTAGCACCTTTGTTGAAGAAGATCCTCTCTTCCCAGATCCTTCGCATC 1713
                             v -  --------   ii--------- v  v   i v   i-  v
  L1M4_orf2#LINE/    353 TTTTCG-AC--------AAGGG---------TGCCAAGACCATTCA-ATG 383

  chr2_185928841_   1714 TTTAGAAAGGTTATTCTA--CAACAAAGGATGATAAAACAATTGGATACC 1761
                         v--i     iv  v   v--       v i  v iii    i      ? 
  L1M4_orf2#LINE/    384 G--GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_185928841_   1762 CATATGTGAAAAAA--AATTTGTTGTA----TACCTTACAACAT-TA-AA 1803
                           i   ii   i  --  ---    v ----     i   v   -  -  
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAA---GTTGGACCCCTACCTCACACCATATACAA 478

  chr2_185928841_   1804 CAATCTTCTGAAACTGGCTTGTGGACCGAAATGTAAGATATAACACTATT 1853
                         v   ivv  v   v   v ii?i    v          vv   v     v
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_185928841_   1854 TAACTTCTAAAAGAAAACACAGGAGAAAAACTTTGTGACCTTGG-TCAGG 1902
                         v    ii  i         i   ? v   v   i          - i   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_185928841_   1903 TA--GATATCTTAAATATTGTGCAAATATGCACCAAAAATATAGTCTATA 1950
                         i -- i v     i    ------i ----        ii i iv v i 
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATAT------GA----CACCAAAAGCACAAGCAACA 618

  chr2_185928841_   1951 AAAGACTAAGTTGTTAAATTAAATGTTAGCAGAATTAAAACCTTCTGCTC 2000
                              vv  i v v      ii iv i v  i        v   i  iv 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_185928841_   2001 TTCAAAAGACACTCCTAAAAGAACAAAAAGATCAGCCACAGACTTGGAGA 2050
                               i      vii  i i iii      iv v       v v     
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_185928841_   2051 AAACACTTGAAAATAACATATCTGATAAAAGTCTTTTGTCCAGAACATAT 2100
                            i i   v    v i           ii v   v i       i    
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_185928841_   2101 AAAAATATAATTTTCA-AACTGAATAATTAAAAAA-AAA----------- 2137
                            i ---- i i i -    v      v    i -   -----------
  L1M4_orf2#LINE/    769 AAAGA----ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_185928841_   2138 -GAAGTGGG-AAAGGTTTTGAGCACTCACTTTACCAAAAAAGATATAAAG 2185
                         -i  i    -     v     ii vv  i  iv     i        v i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_185928841_   2186 ATGACAAATAGACAC 2200
                            i v    ii   
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCAC 879

Transitions / transversions = 1.30 (129 / 99)
Gap_init rate = 0.03 (25 / 874), avg. gap size = 3.12 (78 / 25)  


 543 21.30 2.96 1.78  chr2_185974790_185979135      274   442 (3904)  C L1M4_orf2#LINE/L1   (0)   908   738  

C chr2_185974790_    442 ATATGATAAGGGAGTTGTATCCAAAATATAGGAAGAGTGCTTAAAATTCC 393
                           v          v         i      vi    iiv    v  i  v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

C chr2_185974790_    392 ACAATAAGAAAGCAA----CCCAGTGAAAACAATAGATAA-GGATATTAA 348
                          i     i  ii   ----    i v?   -   i ii  -    -  i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGAT-TTGA 835

C chr2_185974790_    347 AAAAACACCTCACCACAAAAAGATATACAGATGCCAAATATGCACATGGA 298
                          v i   ii  v   -  i          i   v v    v       i 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCA-AAGAAGATATACAAATGGCCAATAAGCACATGAA 884

C chr2_185974790_    297 AATATGCTAAAGATCATATGTCAC 274
                           v     v  v    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (20 / 15)
Gap_init rate = 0.03 (5 / 171), avg. gap size = 1.60 (8 / 5)  

 758 23.78 1.62 0.00  chr2_185974790_185979135     2661  2845 (1501)    L1M4_orf2#LINE/L1        1   188 (720)  

  chr2_185974790_   2661 TGGAAAGAAATATTGTCGTTGTAAACTGAAAGACTTATTAGTGTTAAGAT 2710
                                 v  viii vv ii ii i  i        v  v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185974790_   2711 GGCAATATACCCCATATTTTTCCACAGAGTCA---CAAACCATATCAAAA 2757
                                iv     v   vv  i     v   ---   v  v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185974790_   2758 CCCCAGCTTCCTTTTCTGCTGAAATTGACAAGCTGTTCTTAAAATTCATG 2807
                         i       v      i   v               v  i          i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_185974790_   2808 CAGAATTGCTGGGGCCACTGTAAAGGCAAAAAAATTTT 2845
                         ii   v   vi   v v v v v  v     v   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

Transitions / transversions = 0.76 (19 / 25)
Gap_init rate = 0.01 (1 / 188), avg. gap size = 3.00 (3 / 1)  

2556 21.24 4.78 1.97  chr2_185974790_185979135     3144  3854 (492)    L1M4_orf2#LINE/L1      178   908 (0)  

  chr2_185974790_   3144 AAAACAATCTTGAAAAAGAA---CAAAGTTGAAGGCGTCATACATCCTGA 3190
                                             ---        i   vv   i  v   ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_185974790_   3191 TTTTAAACCTTAATACAAATCTACCATAAACAAAAGTTTGTGTTGTTGTC 3240
                            i   v    v      v    vi   v   i vvv    v ii  v 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_185974790_   3241 ATATGGATAGGCATATAAATCAACAGAATGCAGTTGATATTTCATAAATA 3290
                            v      i      i     ii    iv i    v v i  v     
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_185974790_   3291 CACCCTTATATTTATCATCACTTGACTTT-AACTATGATGGGAAAACTAT 3339
                         v    v  i      vi   v    i   -i  v v i  vv  i  i  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_185974790_   3340 TCAA--GGGGAAGTACAGACTTCTCAGTAAAAGGTACTGTGCCAACTA-A 3386
                             --   i   v i  v   i   ii   v   i   v v     i- 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_185974790_   3387 TAGTCACATGCAAAATAATCAATCTAGACCCATACTTCACAACATTCGTT 3436
                           ?i           v   v  vi i     v   i     v   -----
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT----- 472

  chr2_185974790_   3437 AAGAGAAAAAAAT---CTCAAAACAAATTAAAGACATAAAGGTAAGATAT 3483
                         --- v v      ---       iii  i ?    v    v      vv 
  L1M4_orf2#LINE/    473 ---ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_185974790_   3484 AAATCTATAAAATTTGTATAAGAAAAAATAGGTCTAAGTATTTGTGACCT 3533
                            v        i iv  v       v     ?v   i v  i       
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_185974790_   3534 TAA-TTAGGCAACGATTTCGTGGATATAAAACCAAAAGCA-GAGCAACAA 3581
                          ii-        i i    v i     i v          -i        
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_185974790_   3582 AA----AAATACATAAATTGGACTT------AAT-AAAA---TTTGTCCT 3617
                           ----     v             ------   -    ---     v  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_185974790_   3618 TTAAAGTATACTATCAAGAAAGCAAAATGTTAACCCATAGAGTGAAAAAA 3667
                          i    v i             ii   v vi      i   i  ii i  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_185974790_   3668 A----TTCCAA-TCACATATCTGATAAAGGACTTTTATTAAGAATGTATA 3712
                          ----  v   -   i           i      v   iv     i    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_185974790_   3713 AATA-CTTCTACTCCTCAATAATAAAATGATAAATATTTCAATC--AGAA 3759
                           v -  ii   vv             v  i     vii    i-- i  
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_185974790_   3760 TACACAAAGGGTTTGAATGAACATTACTCTAAAGAAGAGATATTAATAGA 3809
                          ivi      i       ii     v   i        v   i------ 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC------A 863

  chr2_185974790_   3810 AATAGCCAATAAGCATATGAAAAGATGTTCAGTATCATTAGTCAT 3854
                            i           i           i   ii    ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (82 / 66)
Gap_init rate = 0.02 (17 / 731), avg. gap size = 2.82 (48 / 17)  


2944 26.54 4.10 0.68  chr2_185981670_185987049     4011  4888 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_185981670_   4011 TGGAAGAACATTCCATGTTCATGCATAGGAAGAATCAATATCATGAAAAT 4060
                              ii i  i           v  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_185981670_   4061 GGCCATAGTGCCCAAGGTAATTTATGGATTCAATGCCATCCCCATCAAGC 4110
                            v   v v     iv i  i  ii       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_185981670_   4111 TACCAAGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 4158
                          v   ivvi i  i  ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_185981670_   4159 TATGGAAGAAAAAAGGA---------GCCAAAACAATCCTAAGCATAAAG 4199
                                iviv  i   ---------            i i iv vi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_185981670_   4200 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4249
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_185981670_   4250 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGATATATAAACC 4299
                                 i   i i  ii         i iv ii i   i     i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_185981670_   4300 AACGGAACAGAACAGAGACCTCAGAAATAACATCACACATCTACAACCAT 4349
                           i    i    iv    vii         vvi  i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_185981670_   4350 CTGATTTT-GACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 4398
                         i       -     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_185981670_   4399 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 4448
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_185981670_   4449 AACTGGATCCCTTCCTT--------------------CTCAAAATGGATT 4478
                          ii    i    v   i--------------------            i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_185981670_   4479 AAAGACTTAAGTGTAATACCTAAAACCATAAAAACCCTAGAAGAAAACAT 4528
                          ?    i   i     v v       i      vi i             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_185981670_   4529 AGG---AAATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 4575
                            ---    -- -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_185981670_   4576 AAACACAAAAAGCAATGGCAAGAAAAGCCAAAATAGACACAT-GGGCTCT 4624
                         vi    v       vvi    v     vv        i v  -  i  ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_185981670_   4625 AATTAAACTAATGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGA 4674
                          viv   i   -i i   i iii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_185981670_   4675 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 4724
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_185981670_   4725 AAAGGGCTAATATCCAGAATATACAAAGAACTTAAACAAATTTACAATAA 4774
                           i  i  vi             i        ivv    v iv i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_185981670_   4775 AAAATCAAACAACCTCACCAAAAAGTGGGCAAAGGATATGAACAGACACT 4824
                            iv    i    iv ii?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_185981670_   4825 TCTCAAAAGAAGACATTTGTGCAGCCAACAGACATATGAAAAAAGGCTCA 4874
                             v        i  viiviii     i ii  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_185981670_   4875 TCATCACTGGTCAT 4888
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (144 / 86)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.82 (42 / 11)  


2670 26.58 4.52 2.04  chr2_186018614_186020685.rev      699  1582 (490)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_186018614_    699 GAAAGACACCCCATGCTCATAGATTGGAGAAATTAATATTTTTAA-ATGG 747
                               i i      i    i       ii v        v    -    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_186018614_    748 CTATACTACTCAAAGAAATCTATAGATTCCTCGCAATCTCTATCAACATC 797
                          v     v i    vvi     i      vv       i       v   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_186018614_    798 CCAATGACAATCCTTGCATAAATTTTTAAAAAGT--ATCCTAAAATGTGT 845
                            iivi vv ii     v     ---i v   i--          vii 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTCAT 149

  chr2_186018614_    846 GTAAAACCAGAAAAGACCCTGGATAGTCAAAGCAATTCTGAGCAAAAAGA 895
                         i ii  viiv  ii     v i    i    i    ii   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_186018614_    896 AGAAAACTGGAGG---CAGACTACCTGACAA----AAAATATACTGCAAA 938
                          v   ii      ---  v   v  ---   ----    iv    i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCC---CAATTTCAAAACTTACTACAAA 246

  chr2_186018614_    939 AC----------AAAACAGCATGGTATTGGTATAAGTAAAGACACACAGA 978
                         i ----------  i    ii     i   i     v v     i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_186018614_    979 CTAATAAAATAGAAGAGAGAACCCAGAAACAAAGCAACA-GTTTACATCC 1027
                         ii   ii       vv    ii       i   v v i -i    iivi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_186018614_   1028 AACTGATTTTTTTAAATGGCATCAAGAACATATATTGCAAAAGGGAATAG 1077
                           i       ivvv  v  iii     v   vi v  vii  i -     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAG 395

  chr2_186018614_   1078 TCTCTTTAATAAACGGTGCTGGGAAAATTGGATATTTATATGCAGAAGTA 1127
                            i  i  i   i          v  i      ?ii i     i   v 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_186018614_   1128 TAAAAGTAGACCACTATTTTTCACCATTTACAAAAATCAACTCAAAAAGG 1177
                          i  iv i    v   ii iv      v         i         v  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_186018614_   1178 ATTAAAGGCATAAACATAAGACTAAAAACTCTAAAGCTGCTAGAAAAAAA 1227
                           i ?  i v    ii     viv      v    i  vi     i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_186018614_   1228 T---GGAGAAATTCTTCAGGACATTGGTCTAGGCAAAGATTGTATAGCTA 1274
                         i---  ? v  v     iv   v    vi       v i  viv   v  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_186018614_   1275 GGACTTTAAAAGCACAGGTGA----AGCATGTATAGACAAATGGTACTAT 1320
                         v   vii         i ii ----  v viv     i    v v   vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_186018614_   1321 ATTAAACTAAAAAGCTTCTGCACATTGAAGAA-ACAATTAGCAGAGTGAA 1369
                           i   v v    i   i  ii v ii   i -  v  i iv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_186018614_   1370 AAG-CAGCCTGTTGAATGAGAAAAAGTATTTGCAAACTATTCATCTGACA 1418
                            -  i  iiiv     i  i   i          ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_186018614_   1419 AGGGACTATTAACCTGAAAATACAT---GAATTCATGCATCT-AATGGTA 1464
                                vv  v  -- i    i  ---   i  v i  v  -   ii  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCC--AGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_186018614_   1465 AAAGGAAAAATAAGACAAATAATCCCAGTAAAACATGGGCAAAAGAC--- 1511
                            ---------          i  v v ?   v         i  i---
  L1M4_orf2#LINE/    794 AAA---------AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_186018614_   1512 ---AGACATTTTTCAAATGAAGACATACAAATGGCCAAAAAACCTTTGAA 1558
                         ---        i  v  v     i              v  i viv    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_186018614_   1559 GAAATGTTCAGCATTTCTAATCAT 1582
                         i i   i   i   iv????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (143 / 88)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 3.22 (58 / 18)  


3274 26.57 0.55 0.44  chr2_186109918_186116195.rev     4880  5786 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186109918_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186109918_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186109918_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_186109918_   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186109918_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186109918_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5177
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_186109918_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_186109918_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_186109918_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_186109918_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_186109918_   5376 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_186109918_   5426 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAA 5475
                         v    ?i v viv   iv   v v  vvii     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_186109918_   5476 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGAACTAA 5525
                         i            vvi           v     v  i    v   vi v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_186109918_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_186109918_   5576 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_186109918_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_186109918_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_186109918_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAA-ATGCTCATC 5774
                           v        i  vi viii     v  i          -       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_186109918_   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2742 25.54 2.51 1.94  chr2_186135985_186138037      688  1564 (489)    L1M4_orf2#LINE/L1       27   908 (0)  

  chr2_186135985_    688 TGGAAAAATTAATATAGTTAATATGACTATACTGCCCAAAGCAATCTACA 737
                              i v       v     v   i v     v      vii       
  L1M4_orf2#LINE/     27 TGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACA 76

  chr2_186135985_    738 TATTCAATGCAATCTTTATCAAAATACCAATGTCATCTTTCGTGGAATTA 787
                         v      i      ii         v   -- iiii    iv  ----i 
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCA--GCTGCCTTTTTTG----CA 120

  chr2_186135985_    788 GAAAATAAAAAAAAACAG-TCCTAAATTTCATATGGAACAAAAAAAGAGC 836
                             v i v  i--- v -       v           - viv  i ii 
  L1M4_orf2#LINE/    121 GAAATTGACAAG---CTGATCCTAAAATTCATATGGAA-ATGCAAGGGAC 166

  chr2_186135985_    837 CCA-ACTAGTCAAAGCAATCCTATGCAAAATGAACAAAGTTGGAGG--TC 883
                            - v   i    i     i iviv  i v               --  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr2_186135985_    884 ACATTATCTGACGTTAAATTATGCTACAGGACTATCATAACCAAAACAGC 933
                            i vi ii iv i   viv i     iii   ivi   i   i    i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_186135985_    934 ATAGTACTAGCATA-GAA-------ATAGATTAAAGGAACAGATTAGAGA 975
                         i i     i     - i -------      i  v    i   v v    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_186135985_    976 ACCCAGAAATAAAGCCACATATCTATAATCAAATGATTTTTTAAAAAGCC 1025
                         ii           v   i i  i   ii    v       iv v  i vi
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_186135985_   1026 AGCAAAAGCATACACTGTGGAAAGGACACCCTTTTCAACAAATGTTGCTG 1075
                         iv   i v   v  v  v      i i vi              v     
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_186135985_   1076 G---AATTGGATTGGCATATGCAGAAGAATGAAACTGGACCCATATCTCT 1122
                          ---  i     v?v  i     i         ii       v  i   v
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_186135985_   1123 CACCCTATAAAGAAATAAACT-AAAATGGATTAAAATCTCAAAT-TATTA 1170
                             v    v i    v    -         i ? iv ii    -  vv 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_186135985_   1171 CCTAAAGCTATAAAAATCCTAGGATAAAACCTGGG---AAATCTCTCTTG 1217
                         v     i        v  i   i v     v i  ---      -  v  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT-TCGTG 565

  chr2_186135985_   1218 AAAATTGGTGTAGGTGAAGAATTTATGACTAAGACTTCAAAAGCAAGTGC 1267
                          vv-    vv    ii v iv  iv iiv  v   vi        viv  
  L1M4_orf2#LINE/    566 ACC-TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_186135985_   1268 AACAAAACCAAAAACAGACAAATAAGATTTAATTAAACTAAGAAGCTTCT 1317
                                vv     i   i    vi  i  v  i   v v i  i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_186135985_   1318 GCACTGCCAAAGAAGTTGTCAACAGAGTGAACAGACAATCTAGAGAATAG 1367
                          ii  v v  i  vii i    v i      v      i i v     i 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_186135985_   1368 GGAAAAATATTTGCAAACTATGCATTTGACATGGGACTAATATC-AGAAG 1416
                          ii              ii  ii  i   i v      vi    -    v
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_186135985_   1417 TTACAAGGAATTCAAACAACTCAACAACAACAAAAAAATCAAATAACCTA 1466
                         v  i  i   i  vv         i  i  ---   i -         i 
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAA---AAAGA-CAAATAACCCA 810

  chr2_186135985_   1467 ATTAAAAATTGGACAAAGTATATAAATAGGTATTTTTC-AAAGAAGATAT 1515
                            ?    v   i     v  v i     ii    i  -           
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_186135985_   1516 ACAAATGACTAATAAGCATGCCAAAAAAATGCTCATCACTAATCATCAG 1564
                                i i        iii-i    i       v  ii ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACAT-GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.02 (20 / 882), avg. gap size = 1.95 (39 / 20)  


 242 28.68 3.10 3.10  chr2_186206469_186209237.rev      861   989 (1780)  C L1M4_orf2#LINE/L1   (706)   202    74  

C chr2_186206469_    989 ATAGATTTAATGCTAGTCCCATCAAGCTGCCA-TTGACTTTGTTCACAGA 941
                          i     i  i  v vi  i     iv v   -i  v    -  ii    
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT-TTTGCAGA 122

C chr2_186206469_    940 ACTAGAAACAACTAGTT-TAAATGTCATATGCAACCAAAAAAGGG-CCCA 893
                          v v  v - i  ii i-    vv       v  -- viv     -    
  L1M4_orf2#LINE/    123 AATTGACA-AGCTGATCCTAAAATTCATATGGAA--ATGCAAGGGACCCA 169

C chr2_186206469_    892 TA-TAACCAAGAAAATCCTAGGCAAAAAGAACA 861
                         v -  i    i v    i iiiv  i       
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

Transitions / transversions = 1.31 (21 / 16)
Gap_init rate = 0.05 (7 / 129), avg. gap size = 1.14 (8 / 7)  

3021 26.93 0.55 0.55  chr2_186206469_186209237.rev     1372  2277 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_186206469_   1372 GAAAAACATTCCATTCTCATAGATAGGAAGAATCAATATTGTGAAAATGG 1421
                             i i  i    vi    i   v      v i        v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_186206469_   1422 CCATACTGCCCAAAGTAATTTATAGATTTAATGCTAGTCCCATCAAGCTG 1471
                          v     v      v i  i  i     i  i  v vi  i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_186206469_   1472 CCA-TTGACTTTGTTCACAGAACTAGAAACAACTAGTT-TAAATGTCATA 1519
                            -i  v    -  ii     v v  v - i  ii i-    vv     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTT-TTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATA 150

  chr2_186206469_   1520 TGCAACCAAAAAAGGG-CCCATA-TAACCAAGAAAATCCTAGGCAAAAAG 1567
                           v  -- viv     -    v -  i    i v    i iiiv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186206469_   1568 AACAAAACTGGAGGCATCATGCTACCTGACTTTGAACTATACTACGAGCC 1617
                               ii      vv   ii  v  ii i  ii  viv      i iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186206469_   1618 TACAGTAATCAAAACAACAAGGTACTGGTACCAAAACAAATATATAGAGC 1667
                                     i   iiiv        i iv ii i i i       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_186206469_   1668 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATTTACAACCAT 1717
                                i    iv   ivii         vv   i       iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_186206469_   1718 TTGATCTTCAACAAACCTGATAAAAACAAGCAACGGGGAAAGGATTCCCT 1767
                              i   i    ivv  vi  i v  vv   i        i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_186206469_   1768 ATTTAAGAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAAAAAACAGA 1817
                         v  i  v              v      v  ?   i        i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_186206469_   1818 AACTGGACCTCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGATT 1867
                          ii      i  v   i    iv                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_186206469_   1868 AAAGACTTAAATGTAAAACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1917
                          ?    i         i v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_186206469_   1918 AGGCA-ATACCATTTAGGACATAGGCATGGGCAAAGGCTTCATGGTTAAA 1966
                            ?i- v i -  iiv   v v  vv i     v  i   v i v  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_186206469_   1967 ACACCAAAAGCAATTGCAACAAAAGCCACAATTGACAAATGGGATATAAT 2016
                                     vvv          vv v   v  i    v   iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_186206469_   2017 AAATCTGAAGAGCTTCTGTTCAGCAAAAGAAACAATCATCAGAGTGAACA 2066
                         v  vv v  i i   i   v vv    i  v  v    vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_186206469_   2067 GACAACCTACAGAATGGGAGACAATTTTTGCAATCTATCAATCTGACAAA 2116
                                i             v   v       vii  vv      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_186206469_   2117 GGTCTAATATCCAAAATATACAAGGAACTTAAATAAATTAACAGGAAAAA 2166
                           v  vi      i      i  i     ivv i  v i  i iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_186206469_   2167 AACAAAGAATCCCATCAAAAAGTGAACGAAGTATATGAACAGACATTTGT 2216
                         i     v  i  v  i?    i  ii i   v  v    i        v 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_186206469_   2217 CAAAATAAGACATTTATGTGGCCAAGAAACATATGAAAAAAAGCTCATCA 2266
                          v   v    i  vi vi       v  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_186206469_   2267 TCACTGTCATT 2277
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.16 (129 / 111)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 1.11 (10 / 9)  


2521 25.67 3.30 1.83  chr2_186251956_186256144     2530  3347 (842)    L1M4_orf2#LINE/L1        1   830 (78)  

  chr2_186251956_   2530 TGGCAAGACATCCCATGTTCATAGATTGGAAGAATTAATGTTGTTAAAAT 2579
                            v    i             i          v     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186251956_   2580 GTCCCATACTACTCAACACAATTTACACAATTTA-------CCTTATCAG 2622
                          v v-     v i   vvii  i    -i   i -------  i     i
  L1M4_orf2#LINE/     51 GGCA-ATACTCCCCAAATTGATCTACA-GATTCAACGCAATCCCTATCAA 98

  chr2_186251956_   2623 AATACCAATGACATACTTCGCTAAAATAGAAAAAAAAAAACACTAAAATT 2672
                            v   iivi v vi  i  vi    v  v  ivvi --iv        
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATT 146

  chr2_186251956_   2673 TGTATGGAACCATGAAAGACACC---AAAAGTGAAAGAAATATTGAGCAA 2719
                         ii       --   v   iv   ---  v  iv   iv   v    iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_186251956_   2720 AAAGAACAAAGCTAAAGGCATCACACTATTTTACATCAAAATATACTACA 2769
                         i          i ii   vv       viiiv iv      iv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_186251956_   2770 AAGCAATAGTAAACAAAACAGATTGATACTGGCATAAAAATAGACACATA 2819
                             v i     v   i    vv  i           ii       i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_186251956_   2820 GATCAATAAAAGAGAATACAGAACCCAGAAATAAACTTATGAACTTATAG 2869
                                ii  v     vv   ii            ii  iv i    i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_186251956_   2870 ACAAATGATTTTTGACAAAAGCACCAAGTATATATACTGGGGATATGACA 2919
                         v   v       i     ii ii     vvi  vi v      v vi i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_186251956_   2920 GTCTCTTCCACAAATGATTCTGGGAAAACTGGATTTTTAACACATGTAGA 2969
                             i   v       i v      v        v?i---      i i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC---CACATGCAAA 441

  chr2_186251956_   2970 AGAATGAGACTAGACCCCTATCTCTCACCATATAAAATAATTCAACTCAA 3019
                                iii i        i   v         v  v    -       
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AACTCAA 490

  chr2_186251956_   3020 GAT-----AAAGACTTAAAGGTAAAACCTGAAACTATAAAACTACTAGAA 3064
                         i  ----- ?    i    v    i v  i             vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_186251956_   3065 GGAAACACAGGGG-AAATCCTTCATGACATTGATCTGGGCAAGAATTTTT 3113
                          i     i   ? -     -   i    v   ivi i     vii   i 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_186251956_   3114 TGGATAAGAACTCAAAAGCACAGTCAACAAAAGCATA--TAGACGAAATG 3161
                          i    v  vvi          iv         v v --    ii  v  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_186251956_   3162 ----TTATCAAACTAAAATGCCTCTGCACAGCAAAGAAAATAATCAACAG 3207
                         ---- i      v v   vi i i  ii vv     i v iv     v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_186251956_   3208 AAGGAAGAGAACACTTACAGAAT---AGAAGATGTTTGCAAACTGTACAT 3254
                          iv   i   vv  ii       ---    i  i        iii  i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_186251956_   3255 CTGACAAGGG--TTAAATATCCAGAATCTATAACAAACCCAAAAAACTCA 3302
                             i     --  i--          v     vi   i vv v      
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTG--TATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_186251956_   3303 ATAGCGAAAAAAAACAAGTAATCTGATTTAAAAATAAAATAAGGA 3347
                            ii--     i    i   i ii   ?      iiivv     
  L1M4_orf2#LINE/    788 ATAAT--AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.45 (122 / 84)
Gap_init rate = 0.02 (17 / 830), avg. gap size = 2.47 (42 / 17)  

 286 20.91 4.55 1.82  chr2_186251956_186256144     3588  3697 (492)    L1M4_orf2#LINE/L1      796   908 (0)  

  chr2_186251956_   3588 AAAATAAATAAATAAAT---AAAATATGATAAA--ATCTGAATAGACATT 3632
                           i i      viv   ---     i- ii   --  i            
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATG-GGCAAAGGATTTGAATAGACATT 844

  chr2_186251956_   3633 TCTCAAAAGTATACATACTAATGACTACTAAGTACATTTAAAAAATGTTT 3682
                             v    v v i    v    i i v    i    v-    i   i i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTC 893

  chr2_186251956_   3683 GACATCATTGATCAT 3697
                         i      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.75 (7 / 4)  


2826 26.04 1.17 4.68  chr2_186276371_186284797.rev     1094  2034 (6393)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186276371_   1094 TGGAAGAACATTCCATGCTTATGGATAGGAAGAATCAATACCGTGAAAAT 1143
                              ii i  i     i i      v      v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186276371_   1144 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 1193
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186276371_   1194 TACCGATGACTTTCTTCACAGAA-TTGGAAGGAACT-ACTTTAAAGTTCA 1241
                          v  iiivi i  i  ii     -   iv -- i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA--AGCTGATCCTAAAATTCA 148

  chr2_186276371_   1242 TATGGAACCAAAAGAGAGCCCACATTGACAAGACAATCCTAAGCCAAAAG 1291
                                viiv   i  v  viv  v v   i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186276371_   1292 AACAAAGCTGCAGGCATCATGCTACCTGACTTCAATCTATACTACAAGGA 1341
                                i  v   vv   ii  v  ii i     vviv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186276371_   1342 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1391
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_186276371_   1392 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 1439
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_186276371_   1440 ATCTGATCTTTGACAAACCTGACAAAAACA---AAACTGGGGAAAGGATT 1486
                          vi    i  i     ivv  v   i v  ---  --         i  v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATA 394

  chr2_186276371_   1487 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 1536
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_186276371_   1537 CTGAAACTGGATCCCTTCCTTACAGCTTATACAAAAATTAATTCAAGATG 1586
                         v    ii    i    v   i   v v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_186276371_   1587 GATTGAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 1636
                            ii?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_186276371_   1637 ATCTAGGCA-ATACCATTTAGGACATAGGCATGGGCAAGTACTTCATGAT 1685
                          iv    ?i- v i -  iiv   v v  vv i     vvii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_186276371_   1686 TAAAACAACAAAAACAATGGCAACAAAAGCAATA-TAGACAAATGGGATC 1734
                           vi   v     i  vvi          v  v -    i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_186276371_   1735 TAATTAAACTAAAGAGCTTCTGCACAGCAAAACAAACAAACAAAACAAAA 1784
                          v  i   v v  i i   i  ii vv    i------------------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAG------------------ 675

  chr2_186276371_   1785 CAAAACAACAACAAAAAAAACTACCATCAGAGTGAACAGGCAACCTACAG 1834
                         ---i   vi v   i   -------------     v  i     i    
  L1M4_orf2#LINE/    676 ---GACACTATCAAGAAA-------------GTGAAAAGACAACCCACAG 709

  chr2_186276371_   1835 AATGGGAGAAAATTTTTACAATCTACCCATCTGACAGGG--CTAATATCC 1882
                                      v   i   vii ivi      i i  --  vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_186276371_   1883 AGAATCTACAAATAACTTAAACAAATTTACAAGAAAAAAAAATCATACAA 1932
                              v  i   v    ivv    v ---   v  v     iv  v i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACT---CAATAATAAAAAGACAAATAA 806

  chr2_186276371_   1933 TTCCATCAAAAAGTGGGCAAAGGATATGAACAGATACTTCTCAAAAGAAG 1982
                         ii v  i?    i            v    i   i i     v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_186276371_   1983 ATATTTATGCAGCCAACAGGCACATGAAAAAATGCTCATCATCACTGGCC 2032
                             vi viii     i i           i       v     ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_186276371_   2033 AT 2034
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.93 (55 / 14)  

3204 27.01 0.66 0.55  chr2_186276371_186284797.rev     7029  7935 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186276371_   7029 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 7078
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186276371_   7079 GGCCATACTGCCCAAGGGAATTTACAGATTCAATGCCATTCCCATCAAGC 7128
                            v     v     ivvi  i           i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186276371_   7129 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 7176
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_186276371_   7177 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 7226
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186276371_   7227 AACAAAGCTGGAGGCATCACACTGCCTGCCTTCAAACTATACTACAAGGC 7276
                                i      vv       v  iivi      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186276371_   7277 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 7326
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_186276371_   7327 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 7374
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_186276371_   7375 ATCTGATCTTTGACAAACCTGAGAGAAACAAGCAATGGGGAAAGGATTCC 7424
                          vi    i  i     ivv  vv ii v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_186276371_   7425 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 7474
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_186276371_   7475 GAAACTGGATCCCTTCCTTACAGCTTATACAAAAATCAATTCAAGATGGA 7524
                            ii    i    v   i   v v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_186276371_   7525 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 7573
                          i ?    i    ii v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr2_186276371_   7574 TCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 7623
                         iv    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_186276371_   7624 AAACACCAAAAGCAATGGCAACAAAAGACAAATT-GACAAATGGGATCTA 7672
                         vi            vvi           v   v -  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_186276371_   7673 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTGAA 7722
                           i   v v  i i   i  ii vv    i  v   ii  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_186276371_   7723 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 7772
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_186276371_   7773 AAGGGCTAATATTCAGAATCTACAATGAACTCTAACAAATTTACAAGAGA 7822
                          i  i  vi   i      v  i  v       v    v iv i  v i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_186276371_   7823 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 7872
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_186276371_   7873 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 7922
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_186276371_   7923 CATCACTGGCCAT 7935
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1357 25.28 9.38 4.61  chr2_186285309_186288235      501  1129 (1798)    L1M4_orf2#LINE/L1      250   908 (0)  

  chr2_186285309_    501 ACAGTGACCAAAACAGCATGGTCCTGGTACAAAAACAGACAAATAGACCA 550
                              i i   i    ii    v    i i  ii i     v     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_186285309_    551 A-GAAAAACCAAATCGAAAGCCCAGAAATAAAGCCACATGCTTACAGCCA 599
                          - i  v --i   i  i  i           v   i iii   ii i  
  L1M4_orf2#LINE/    300 ATGGAATA--GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_186285309_    600 TCTGATCTTTGACAA---TGTCAA-------CAA----AAAAAAGCAGT- 634
                         vi    i  i     ---  i   -------   ----i   i ii   -
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_186285309_    635 ---------------------------GGATAAACATCTGTAGATGACTA 657
                         ---------------------------     ?v  iv  i i v  v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_186285309_    658 AAACAGGACACCGTACCTTTCACCATGTACAAAAATCAACTCAAGATAGA 707
                           iiv    v  -     iv      i         i       i  i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_186285309_    708 TTAAGAGCTTAAAGATAAACCCTAATACCATAAAACTTCTTA-AAGAAAA 756
                          i ?iii i    vi   ivv    v  i        -    -       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAA 545

  chr2_186285309_    757 CCTAGAAAATACCATTTTAGACATATGCCCT-------GGCAAAGATTTC 799
                          v   i?i-  v-  i  v -----  v   -------     v i    
  L1M4_orf2#LINE/    546 CATAGGNG-TAA-ATCTTCG-----TGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_186285309_    800 ATAATGAAGATCACAAAAGCACTTGCAACAACAACAAAAAAATGGACAAA 849
                         v  ivv v  ivv         vv       -  -i       i  i   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAA-AA-GAAAAAATAGATAAA 636

  chr2_186285309_    850 TGGGATTTACTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAGCTACCAA 899
                          v   i  vv i   v v  i i   i  ii vv    i  vi   i   
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_186285309_    900 CAGAGTGAAAAAGACAACCTACAGAATGGGA-AAAATATTTTCAAACTAT 948
                         v i        -       i           -         v    ii  
  L1M4_orf2#LINE/    687 GAAAGTGAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_186285309_    949 GCATCTGACAAAAGTCTAATATTTAAACTATATTAGG--CGTCTATAAGG 996
                         ii      i  ii v  vi   ii i v     v i -- vii  i  --
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-- 783

  chr2_186285309_    997 AACATAAAAATTTTTCAAAAAAAAGCCCCCAAACAACCCCACTCAAAAAT 1046
                         -- vi  v   ------     i -----    i     v i ?      
  L1M4_orf2#LINE/    784 --CTCAATAAT------AAAAAGA-----CAAATAACCCAATTWAAAAAT 820

  chr2_186285309_   1047 GGCCAAAGGAC----ATGGACACTTTTCAAAAGAAAACATACATGGGGCC 1092
                           v       i----  i    i  i  v      i i     viv    
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_186285309_   1093 AGCA-GCATATGAATAAAAGCTCAATATCACTGATGGA 1129
                          ii -   i     v i v      i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (102 / 53)
Gap_init rate = 0.03 (23 / 659), avg. gap size = 3.83 (88 / 23)  

1802 23.49 5.40 3.65  chr2_186285309_186288235     1806  2435 (492)    L1M4_orf2#LINE/L1      268   908 (0)  

  chr2_186285309_   1806 TAGCAATGACATAAAAACAGACACATAGACCAATGAAACAGAATAGAGGA 1855
                          i i v  i     ii i     i     i     i  i     v   ii
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_186285309_   1856 CCCATAAATAAATCCACACATTTACAGTAAACTAATTTTTGATAAAAATG 1905
                         i   v       i   i       ii  v  i i     i  i  iii  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_186285309_   1906 CCAAAAGACAAAAATGCCAAAATGCTACATTGGGGAAAGAACAATCTT-- 1953
                             i ----------   ------ v  v           i i    --
  L1M4_orf2#LINE/    368 CCAAGA----------CCA------TTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_186285309_   1954 CCATAAATGGTGCTGGGAAAACTGAATATCTACATGCAGAAGAATAAAAC 2003
                          v i              v     i   ? i       i      i  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_186285309_   2004 TAGACTCCTATTTCTCACCATATACAAAAACCAAACCAAAATGAATAAAA 2053
                          i   i    ii  v               ii  vi       i  v ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_186285309_   2054 TACTTACA---AATACCTGAAACTATAAAAC----AGAAGGAAAC-TGTT 2095
                         v  i  v ---  v v  i            ----     i    - ivv
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_186285309_   2096 AGAAAACACTCTAGGACATTGGTTTAGGCAGAGATTTCTTGAGTAAGACT 2145
                         ? v   i-  iiiv   v    v       iv i      iii  v   -
  L1M4_orf2#LINE/    552 NGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC- 599

  chr2_186285309_   2146 ACAAAAGCAAAAGCACAGGCAAATGAAGTAAAAATAGAATAACCGAACCA 2195
                           -----          i    vvi   v         vv  ii i  iv
  L1M4_orf2#LINE/    600 AC-----CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_186285309_   2196 TATCAAACTTAAAAGCTTCTGAACAGCAAAGTAAAC----AAGAAATTGA 2241
                         i      v      i   i  vi vv     v v  ----      v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_186285309_   2242 AA-GACAACCCTCATATTGGGA-AAAATATTTGCAAACAATCCATCTGA- 2288
                           -        v  v v     -              iv  vi      -
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_186285309_   2289 AATGAATTAATAATGAGAATATATAAAGTGCTCAAACAACTCAATAGGAA 2338
                           v i i vi  viv             vi   vv           iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_186285309_   2339 AAA-----AT--TTTGATTTAAAAATGTGCAAA----------ACACACT 2371
                            -----  --iiii   ?       v     ---------- v   i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_186285309_   2372 TCTCAAAAGAGGACATACAAATGCCTAACAGATATACGAAAAAATAATAA 2421
                             v     i  i         v i  i iii i i     i  iv v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_186285309_   2422 ACATCACTAATCAT 2435
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (89 / 55)
Gap_init rate = 0.02 (16 / 641), avg. gap size = 3.56 (57 / 16)  


2748 22.20 10.38 2.27  chr2_186303789_186308177.rev     3060  3897 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_186303789_   3060 GAAAGACCCAGCCCATGTTTATGGATTGCAATACTTGTTATTGGAAAAAT 3109
                               i-- v        i        v  v    iv     vv  i  
  L1M4_orf2#LINE/      3 GAAAGAT--ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186303789_   3110 G---------TCCAAAGCAGTGTACAAATTTAGCACAATCCCT------- 3143
                          ---------i     viii v    i   i i i        -------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186303789_   3144 ---------------------------------------TAAAATTCATA 3154
                         ---------------------------------------           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_186303789_   3155 TGAAACCACAAAGGACTGCTAAGAATCAAAATAATTTT-ATACAGAAGAA 3203
                           i  vii   i    ivvv  v ii     i   i  - v v       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_186303789_   3204 CAAATCTAGAGGTATCATTTTCTCTAATTTTTAAGCATATTACAAAGCTA 3253
                             vi i    vv   ivi ii i     iv  i v  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_186303789_   3254 CAGTAATCAAAACAGCATGCTGCTGACA--AAGACAGACATATAGAAAAA 3301
                                   i    ii  v i   i  -- i  i           vv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_186303789_   3302 TGGAACACAATAAGGAGCTCATAAATAAACCCCCACATGTATGGTCAACT 3351
                              i v   vii   ii  v          vi    v         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_186303789_   3352 GGTTTTTAACAAG--TGTCAAGAACA--CAAGTGTCAAGAAAAGGCAGCT 3397
                          i    ii     --  i     v  --   -  --ii    iiii  ii
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA-TG--GGGAAAGAATAGTC 397

  chr2_186303789_   3398 TCTTCAACAAATGGTGTTTGGAAAACTGAATATCCACATGCAAA-TAATA 3446
                          i              i v   v     i   ?           -v   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_186303789_   3447 AAATTGGACCCTTATCCTAGACCATCCACAAAAGTCAACTCAAAATGCAT 3496
                           i        i  i ii v     vi      i i           v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_186303789_   3497 TAAGCACTTAAATGTAAGACCTCAGAAACTATAATGCTACTGGAAGAAAA 3546
                         i ?iv  i           v  --i         vi  vi i        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCT--AAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_186303789_   3547 CATAGAA--AAAACTTCATTATGGTAATCTCGA-TCA--CA-TG--TTCT 3588
                              i?--   v    ------  i i  i i- i --  -  --    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTC------GTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_186303789_   3589 TGGCTATCACACCAAAAGCAGAGGCAACAAAAGACAAAAATAGACAAGTT 3638
                          i v   v            v i           -         i  i  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATT 638

  chr2_186303789_   3639 TGGACTACATCAGA-CTAAAAA-----GT-----AAAGGAAACAATCAAC 3677
                         -     v     i -i      -----  -----      v  v     v
  L1M4_orf2#LINE/    639 -GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_186303789_   3678 AGAGTAAAAAAGCATCCTATGAAATGGAAGAAAATATTTGTTTGTGAGAC 3727
                          i   i    ii  v  i iii     i            i----i iv 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC----AAATC 733

  chr2_186303789_   3728 ATATATCTGGTAAGGTATTAATATCCAAATTACATAAGGGACTTCTACAA 3777
                                  i     v i vi      i v  i    i i   ii     
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_186303789_   3778 CTGAATAGCAAAAGAAAAAAT---CTAATT-AAAAATGGGCAAAGGACCT 3823
                           v    ii    ii v    --- i    -                ii 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_186303789_   3824 GAACAGACATTTTTCCAAA-AAGACATAAAAATGGTTAACATGTATATGA 3872
                            i        i      -    i   v      ii  i v i i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_186303789_   3873 AAAGTTGCTCAACATTACTAATCAT 3897
                             v          i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (125 / 58)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 4.08 (106 / 26)  


2828 28.04 2.59 0.34  chr2_186372859_186379215.rev     4979  5866 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186372859_   4979 TGGAAGAACATTCTGTGCTCATGAATAGGAAAAATCAATATCGTGAAAAT 5028
                              ii i  i ii  i     i  v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186372859_   5029 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTACCCCCATCAAGC 5078
                            v     v     iv i  i  i        i  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186372859_   5079 TACCA-CTGACTTTCTTCACAGAA-TTGAAAAAAACTA--CTTTAAATTC 5124
                          v   -   v    i  -i     -    v  i--  i-- i v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_186372859_   5125 TAATGGAACCAAAAAAGAGCTCACATAGCCAAGACAATCCTAACCAAAAA 5174
                         vv      viiv  ii  v iviv        i      i i vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_186372859_   5175 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACCACAGGA 5224
                                 i      vv   ii  v  ii i      viv   i   iii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_186372859_   5225 CTATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATA--- 5271
                            i     i   i    ii         i iv ii i   i     ---
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_186372859_   5272 -AATGGAACAGAACAGAGGCCTCAGAA---------CACATCTACAACTA 5311
                         -       i    iv   ivii     ---------i    i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_186372859_   5312 TCTAATATTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATTCCC 5361
                         vi i  v  i     ivv  v   i v  vv      i     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_186372859_   5362 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCTG 5411
                          v  i  i              v      v  ?   i     i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_186372859_   5412 AAACTGGATCCCTTCCATATACCATATACAAAAACTAACTCAAGATGGAT 5461
                           ii    i    v  vi i              i        i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_186372859_   5462 TAAACACTTAAATGAAAGACCTAAAACAATAAAAACCCTAGAAGAAAACC 5511
                         i ? v  i      v    v       v      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_186372859_   5512 TAGGCAATACTCTTCAGGACACAGGCATGGGCAAAGACATTATGACTAAA 5561
                             ?ivv v     iv   viv  vv i     v iiv iv iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_186372859_   5562 GCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5611
                         i           vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_186372859_   5612 TAAACGAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5661
                         i   vvv  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_186372859_   5662 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 5711
                          i     i                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_186372859_   5712 GG-CTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAGGAAAAA 5760
                           -  vi          v  i   v    ivv    v iv i iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_186372859_   5761 AACAA-T--CCCA--TCAAAATTGGGCAAAGGGTATGAACAGACACTTTT 5805
                         i    - --    -- ?    v          i v    i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_186372859_   5806 CAAAAGAGGACATTTATGCAGCCAACAGACATATGAAAAAATGCTCATCA 5855
                          v     i  i  vi viii     i ii  i       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_186372859_   5856 TCCCTGGTCAT 5866
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.36 (26 / 11)  


2457 25.12 8.84 1.77  chr2_186394986_186397167.rev      843  1690 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186394986_    843 TAGAAAAATACTCCATGCTCACAGATTGGAAAAGTCAATATCAATAAAAT 892
                          i    i   ii     i   ii        i v i     iiv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186394986_    893 GGTCATACTGCCTAAAGCAATTTACAGAGACAATGCTATTTCTGTCAAAT 942
                           iv     v  i   vii  i      vv   i  v  ii  i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186394986_    943 TACCAGTGATAATGTTCACAGAACTGGAAAAAAAAACT-ATGCAAAAATT 991
                          v    iviivv v  ii     v v  v  i----  -  v v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chr2_186394986_    992 CATATGGAAAGAAGAAGGAGCCCAAGTAGCCAAGGCAATCTTAAGCAAAA 1041
                                   vivi i   v  vi i       ii       i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_186394986_   1042 AGAACAAAACCATAGGCATCACACTATCCAACTTTAAAGTACACTAAAAG 1091
                                 iiiiv   vv       vi    i  i   iivi    v  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_186394986_   1092 GCTACAGTAACCAAAACAGCATAGTGTTGGTTCAGAAACAGACATATAGA 1141
                                   i   i    ii i  ii   ivi iii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_186394986_   1142 CCAATGGAACTTAATAGAGAGCCAAGAAATAAAGTCACACACCT----TC 1187
                         i        ivv   v     i v         vi  i   ii ----  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_186394986_   1188 AATCTGATTTTTGACAAGGCCAACAAAAACAAGCAATGGGGAAAAGAAT- 1236
                            -       i       viiv   i v  vv           -    -
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATA 394

  chr2_186394986_   1237 -TCCTATTCAATAAATGGTGCTGCAATAACTGGTTA-------------- 1271
                         -  i -     i           vi i      v  --------------
  L1M4_orf2#LINE/    395 GTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_186394986_   1272 ------------------------ACCATATACAAAAATTAACTCAAGGT 1297
                         ------------------------                       ii 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_186394986_   1298 GGATTCAAGACTTAAATGTAACACCTAAAACTATAAAAACTCT-AGAAGA 1346
                             iv?    i         v v              -    -      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGA 542

  chr2_186394986_   1347 AACCCTAGG---AAATACCCTTCTTGGCAATGACCATT--GCAAAGAATT 1391
                           v v    ---    ---    v  i vv  i--i  --    v iv  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT---CTTCGTGACCTTGG--GTTAGGCAATGGTTT 587

  chr2_186394986_   1392 TCTGGCCAAGTTCCCAAAAGTAATTGCAACAAAACCAAAAAATGGATAAG 1441
                         ii i vi v viv       i vvv         v-       i     i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAA 636

  chr2_186394986_   1442 TGGAACCTAATTAAA-CTAAAAACCTTGTGCACAGCAAAAGAAAGTATCA 1490
                          v i  i v  i   -i       i  -  ii vv    i  v v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCA 685

  chr2_186394986_   1491 ACAGAGTAAAGAGACATTTTACAGAATGAAAGAAAATATTCACAAACTAT 1540
                          v i   i  i     viii        ii          ii    ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_186394986_   1541 GCATCTGAAAATGGTCTAATATCCAGA----------------------T 1568
                         ii      v  v  v  vi        ---------------------- 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_186394986_   1569 CAACAAGCAAAAACCAAATAACCCCATTATAAAATGGGCAAAGGACATGA 1618
                            i  vv    iv          v   ?v               iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_186394986_   1619 ATAGACACTTGTCAAAAGCAGATATACAAGCAACTAACGAGCATATGAAA 1668
                                i  v  v    v          iiii i  ii    i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_186394986_   1669 A-ATGGTCATCATCACTAATCAT 1690
                          -   v   v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (127 / 84)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 4.74 (90 / 19)  


2017 26.76 3.11 1.49  chr2_186404023_186406084.rev      475  1214 (848)    L1M4_orf2#LINE/L1      120   871 (37)  

  chr2_186404023_    475 AGAGATTGAAAACCTGAATAGACCAATAAAATTTAGATGGAACCAAAAAA 524
                            i     v  v    - ---  --       i v      viiv  ii
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGA-T---CC--TAAAATTCATATGGAAATGCAAGG 163

  chr2_186404023_    525 CACGCCAAATAGCCACAGCAATTGTAAGCAAAAAGAATAAAGCCAGAGGC 574
                         v  v vi        v i    iv i iv  i     i    iii    v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_186404023_    575 ATCACACTAACCAACTTCAAACTATACTATAAAGCGACCATAACCAAAAC 624
                         v       vv    i      viv     i     v  vi   i   i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_186404023_    625 AACTTGGGACTGGTACAAAAACAGACACATAGACCAATGGAAAGGAATAG 674
                          iiv   v     i i  ii i     i     i        vi    v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_186404023_    675 AAAACTCAGAAATAAAGCTACACATTTACAACCATCTGACTTTCAACAAG 724
                          i iii          v i i       iiii  vi   i    i     
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_186404023_    725 ATCAACAAAAATAAGCAATGGGTAAAGGCATC-TCTATTCAATAAATGGT 773
                         iviiv   i vi vv       v    i-  v-   v     i       
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACAAATGGT 412

  chr2_186404023_    774 GCAGTGATAACTGGCTAACCATATGCAGA-GAATGAAACTAGACTGCTAT 822
                           v v  i      v  ?   i     i -       ii i   iv   i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_186404023_    823 CTTTCACTATACACGAAAACTAACTCAAGAAGGATTCCAGACTTAAATGT 872
                           iv   i   i  i    i        i v    iv?    i       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_186404023_    873 AAACACTAAAGCTATAAAAACTCT-AGAAGAAAACCCAAGAA-ATATCTC 920
                           ivi     i        -    -          vi i ?i- v    -
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCT- 560

  chr2_186404023_    921 TCTCGACATCAACCCTGGCAAAGATTTCA-AGACAAAGACACCAAAGGCA 969
                           vi   v iiiviiv     v i    v-   i v-         i   
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCA 609

  chr2_186404023_    970 ACTGTAACAAAACCAAAAATTGACAAGTAAGACCTAATTAAA-TTACAGA 1018
                         vvv i       vv      v  i  i vi   i v  i   -   - i 
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA-AAA 658

  chr2_186404023_   1019 GCTTCTGCACAGCAAAAGAAACAATCAA-----TAAACAAACAACTTACA 1063
                         i   i  ii vv    i  v  v     ----- i  v i     ii   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_186404023_   1064 AAATGGGAGAAAATATTTGCAAAC--TGCATCT---AAGAGAA----ATC 1104
                         i                      i-- ii    ---   i  v----   
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_186404023_   1105 TAACATCTGTAAGAAATTTAAACAAATCAAAAAGAGAACAACAAATAACC 1154
                         i iv  v i   ii  i ivv    v    v  v i  vi          
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_186404023_   1155 CCATT-AAAAATGGGCAAAAGACATAAACAGACCCTTCTCAAAAGAAGAC 1203
                          v   -             i  iv i  i    vi     v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_186404023_   1204 ATACAA--GGCCA 1214
                               --     
  L1M4_orf2#LINE/    859 ATACAAATGGCCA 871

Transitions / transversions = 1.57 (119 / 76)
Gap_init rate = 0.03 (20 / 752), avg. gap size = 1.70 (34 / 20)  

 329 10.34 0.00 0.00  chr2_186404023_186406084.rev     1513  1570 (492)    L1M4_orf2#LINE/L1      851   908 (0)  

  chr2_186404023_   1513 AAGAAGACATACAAGTAGCCAACAAGCATATGAAAAAATGCTCAACATCA 1562
                                i      i i     i     i       i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_186404023_   1563 CTAATCAT 1570
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.00 (6 / 0)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.00 (0 / 0)  


2461 27.04 7.67 0.47  chr2_186459116_186461093.rev      640  1486 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186459116_    640 TAGAAAAAGGTACTATGCTCATAGATAGGAAGAATTAATATTGTTAAAAT 689
                          i    i vi v i   i    i   v      v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186459116_    690 GACCATGCTGCCCAAAGCAATTTACAGATTCAATGCCATTCCTATCAAAC 739
                          i v  i  v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186459116_    740 TACCAATGGCATTCTTCACACAACAAGAAAACATTATTTTAAAATTTGTA 789
                          v   iiv  v  i  ii  v  vvv  v  vv v  ii       ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_186459116_    790 TGGAACCAAAAGAAAGAGCCTGAATAGCCAAGGCAATCCTAAACAAAAAG 839
                              viiv   i--  v  v          ii     i i  v  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186459116_    840 AACAAAGCAGGAGGCATCAAGCTACCTGAATTCAAAGTATACTACAGGTC 889
                                iv     vv   vi  v  ii v      iiv       iiv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186459116_    890 TACAGTAACCAA-ACAGCATGGTATTGGTACAAAAATAGATATATAGGCC 938
                                 i   -    ii     i   i i  ii     i      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_186459116_    939 --TGCAA-------------------------CCAT-------------- 947
                         --  v  -------------------------    --------------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_186459116_    948 CTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 997
                         i    i  i     i v  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_186459116_    998 ATTCAATAAATGGTTCTGGAATAACTGGCTAGCCATATGCGGAAGATCAA 1047
                         v     i       v    i i      v  ?   i    ii    vii 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_186459116_   1048 AACTGGGCCCCT-CCT--------ATACAGAAATCAACACAAGATGGATT 1088
                          ii   i     -   --------     i    i   v   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_186459116_   1089 AAAGACTGAAATGTAAAA-CTCTATTTATAAAAACCTTGGAAGACAACAT 1137
                          ?    iv        i -  vv vi       vi   i     v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_186459116_   1138 AGGCA-ATACCATTCAGGACATAGGAACTGACGAAGGTTTCATGAAGAAG 1186
                            ?i- v i -   iv   v v  iviv i i v      v ii v v 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_186459116_   1187 ATGCCAAAAGCAATTGCAACAAAGGCAAAAATTGACAAATGGGATCT-AC 1235
                          ii         vvv        i v      v  i    v   ii - i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_186459116_   1236 TGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGTAATACAGTAAAC 1285
                         ii   i    i -   i  ii vv    i  v    vi  v v   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_186459116_   1286 AGACAACCTAGAAAATGGGAAAAAATATTTGCAAACTATGCATCTGGCAA 1335
                                 i v i       i              ii  ii     ii  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_186459116_   1336 GAGTCTAATATTCAGCATCTGTAAGTAACT--TA-AATTTA-TAAGAAAA 1381
                          i v  vi   i   v  v i   iv    --  -  i i -   v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_186459116_   1382 A---AAAT--TCCA-TTAAAAAGAGGGCAAAGGATATGAACAGACACTTT 1425
                          ---    --i   -  ?    iv           v    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_186459116_   1426 TCAAAATAAGATAAACATGCAGTCAGCA-GCATATTTAAAAAAGCCCAAT 1474
                           v   v      v   viii i  ii -   i  vv   i v  i   i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_186459116_   1475 ATCACTGATCAT 1486
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (134 / 91)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.63 (69 / 19)  


3783 19.89 2.89 2.00  chr2_186509052_186514195     3756  4655 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186509052_   3756 TAGAAAGACACCTCATGTTTATAGATTGGAAGACTTAATATTATTAAAAT 3805
                          i      i i i      i  i                   i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186509052_   3806 GTTAATTCTACTCAAAGTAATTCATAGAATCAATGGAATCCTTATCAAAA 3855
                          vi   v  v i    v i  ii i   v    i v     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186509052_   3856 TACCAATAATTTTTTTTTGCAGAAATAGA-AAATTTATCCTAAAGTTCAT 3904
                          v   iiviii      -        v  -  ii v        i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_186509052_   3905 -TAGTTTCTCAAGAGACTCTTAATAGG-AAAACAATCTTAAAATAGAATA 3952
                         - i vvviv    i   i vv     v-           i   v    v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_186509052_   3953 A-AAA--TGCAGATGTCTTATTTACTGATTTCAAATCTTACTACAAAGCT 3999
                          -   --  v  ivv  vi i  v ii        v              
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_186509052_   4000 ACCGTAATCAA-ACAGTGTGATACTGATATAAAGACAGACTTATAAAGCA 4048
                           v        -        i     ii    i  i    v    i v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_186509052_   4049 AAGACATGGAATAAAGAGCCCAGAGATAAACTCTTCCATACATGATCAAA 4098
                          v iv  i    vi    i     i      i v v   vi   i    v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_186509052_   4099 TGATTTTTACCAAGGGTACCAAGACCATTTAATGAGGGAAGGGATGGCCT 4148
                                iiv       i           i    -     i i  i i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCT 398

  chr2_186509052_   4149 TTTCCACAAGTGGTGATGGGA-A--TAGATACTCACATGCAAAAAACAAA 4195
                             v    i     v     - -- i    ?i           i ----
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA---- 444

  chr2_186509052_   4196 CAAAAATGAAGGTGAACCCTTACCTTACACCATATACAAAAATTAACTCA 4245
                         -----      v  i    i     i                        
  L1M4_orf2#LINE/    445 -----ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_186509052_   4246 AAATGAGTCAGAGATCTAAACATAAGAACTAAAA-----AAACTTTTGTT 4290
                              ii   ?   i     ii     i      -----     i  ivv
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_186509052_   4291 GGAAGACATGGGAAAAAGGCTTCTTGACATTGGATTTAAAAATTTTTTTT 4340
                         i   i    i  ?iv  iv    v    v    i  viiv   vv   --
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-- 587

  chr2_186509052_   4341 GTTCTTGTTGTTATGATACCAAA-GCACAAGCAAGAAAAGAAAAA-TAGA 4388
                         ---   i-- v     i      -          v          -    
  L1M4_orf2#LINE/    588 ---CTTA--GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_186509052_   4389 TATATTGTGCTTCATTATAATTAAAAA-TTTTGTGCTTCAAAGGACGCCA 4437
                           v    vi      i v         -                  i i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_186509052_   4438 TCAACAAAGTGAAAAGTCAACCCATGGAATGGGAGAAAATATTTGCAAAT 4487
                             v           v       ii                        
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_186509052_   4488 TATACATCTAGTAAATAATTAATATTCAGAATATGTAAATAATTCTTATG 4537
                         i   i    ii   ivi i vi   i        i    v  i     ii
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_186509052_   4538 ACTCAACAATGATAAAACAA----CCCAATT-AAAAATGTGCAAAGGACT 4582
                               i   i v  i    ----       -       v        i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_186509052_   4583 TGAATAGGCAGTTCTCTAA-GAAAATATACAAATGGCTAACAGGCACATA 4631
                                i  v     i  -   i             i  i i      i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_186509052_   4632 AAATGATTTTCAA--TCATTTCCCTA 4655
                            v   vi    --   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (112 / 64)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.10 (44 / 21)  


3037 28.34 0.55 0.44  chr2_186532213_186539925.rev      614  1520 (6193)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186532213_    614 TGGAAAAACATTCCATGCTCATGGATAGGAAGAAGCAACATCATGAAAAT 663
                               i i  i     i        v      vvi  i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186532213_    664 GGCTATACTGCCCTAAGTAATTTATAGACTCAATGCTATCCCCATCAAGC 713
                            v     v   v  v i  i  i   i    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186532213_    714 TACCATTGACTTTCTTCACCGAATTGGAAAAA--GACACTTCAAATTTCA 761
                          v   vivi i  i  ii v   v v  v  i--  iv  --   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chr2_186532213_    762 TATAGAGCCAAAAAAGAGCCCGCATAGCCAAGACAATCCTAAGCAAAAAG 811
                            i  iviiv  ii  v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186532213_    812 AGCAAAACTGGAGGCATCACGCTACCTGACTTCTAACTATACTACAAGGC 861
                          i    ii      vv    i  v  ii i   v  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186532213_    862 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 911
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_186532213_    912 AATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAT 961
                                i    iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_186532213_    962 TTGATCTTTAACAAACCTGACAAAAACGAGCAATGGGGAACGGATTTCCT 1011
                              i  ii    ivv  v   i v ivv          v i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_186532213_   1012 ATTTAATAAATGGTGTTGGGAAGACTGGCTAGCCATATACAGAAAGCTGA 1061
                         v  i  i        i     vi     v  ?   i  i  i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_186532213_   1062 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATC 1111
                          ii    i    v   i     v                   i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_186532213_   1112 AAAGACTTAAATGTAAGACCTAAAACCACAAAAAACCCTAGAAGAAAACC 1161
                          ?    i           v       i i    v-i i           v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACA 547

  chr2_186532213_   1162 TAGGCA-ATACCATTCAGGACATAGGCATGGGAAAAGACTTCATGACTAA 1210
                             ?i- v i -   iv   v v  vv i  v  v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_186532213_   1211 AACACTGAAAGCAATGGCAACAAATGCCAAGATAGACAAATGGGATCTAA 1260
                         i    ii      vvi        v vv  i     i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_186532213_   1261 TTAATCCAAAGAGCTTCTGTATAGCAAAAGAAACTATCATCAGAGTGAAC 1310
                          i  vviv  i i   i   iivv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_186532213_   1311 ATGCAGCTTACAGAATGGGAGAAATTTTTTGCAGTCTATCCATCTGACAA 1360
                          vi  i ii               v v      ivii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_186532213_   1361 AGGGCTAATATCTAGAATCTACAAAGAACTTAAACAAATTTATAAGAAAA 1410
                         i  i  vi    i     v  i        ivv    v iv    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_186532213_   1411 AAAGAAACACCCCTATCAAAAAGTGGGTGAAGGATATGAACAGACACTCC 1460
                          i v   i v   v  i?    i    ii      v    i     i i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_186532213_   1461 TCAAAAGAAGACATTTATGCAGCCAACAG--ACATGAAAAAAGGCTCATC 1508
                           v        i  vi viii     i i--         i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_186532213_   1509 ATCACTGGTCAT 1520
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (149 / 104)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  

3221 27.64 0.33 0.33  chr2_186532213_186539925.rev     6314  7221 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186532213_   6314 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 6363
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186532213_   6364 GGCCATACTGCCCACTGTAATTTATAGATTCAATGCCATCCTCATCAAGC 6413
                            v     v    vvv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186532213_   6414 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 6462
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_186532213_   6463 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAGA 6512
                               viiv  ii  v  v v  v     ii     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_186532213_   6513 ACAAAGCTGGAGGCATCACACTACCTGACCTCAAACTATACTACAAGGCT 6562
                               i      vv       v  ii ii     viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_186532213_   6563 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 6612
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_186532213_   6613 ATGGAACATAAC--AGAGCCCTCAGAAATAACGTCGCATATCTACAGCTA 6660
                               i v  i--    i  --        vvi ii i  i  ii ii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_186532213_   6661 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 6710
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_186532213_   6711 TATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCTG 6760
                          v  i  i              v     iv  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_186532213_   6761 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAGTTCAAGATGGAT 6810
                           ii    i    v   i     v           i ii    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_186532213_   6811 TAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 6860
                         i ?   ii    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_186532213_   6861 TAGGCGTTACCATTCAGGATACAGGCATGGGCAAGGACTTCATGTCCAAA 6910
                             ?  v viv   iv  iviv  vv i     v ii   v ivvi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_186532213_   6911 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 6960
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_186532213_   6961 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 7010
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_186532213_   7011 GGCAACCTACAAAATGGGAGAAAATTTTCACAACCCACTCATCTGACAAA 7060
                          i     i   i             v  ii   vi  ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_186532213_   7061 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 7110
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_186532213_   7111 AACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACATTTCT 7160
                         i     i     v  i?    i     i     iv    i          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_186532213_   7161 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 7210
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_186532213_   7211 TCACTGGCCAT 7221
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3157 27.75 0.44 0.44  chr2_186554331_186560608     4879  5786 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186554331_   4879 TGGAAGAACATTCTATGCTCATGGGAAGGAAGAATCAATATTGTGAAAAT 4928
                              ii i  i i   i      ivv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186554331_   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186554331_   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_186554331_   5027 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186554331_   5077 ATTGAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                          vii   i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186554331_   5127 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                           i     i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_186554331_   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCTTACCTACAACT 5224
                                i    i--    i  --        vv iiivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_186554331_   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_186554331_   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_186554331_   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_186554331_   5375 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_186554331_   5425 CTAGGCATCACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCCAA 5474
                         v    ?i v viv   iv   v v  vv i i   v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_186554331_   5475 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5524
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_186554331_   5525 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGATTCAAC 5574
                          i   v v  i i   i  ii vv    i  v    i  vv i v v  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_186554331_   5575 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5624
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_186554331_   5625 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_186554331_   5675 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_186554331_   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5774
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_186554331_   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3203 26.51 0.77 0.88  chr2_186572877_186575714     1438  2346 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186572877_   1438 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 1487
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186572877_   1488 GGCCATACTGCCCAACTTAATTTATAGATTCAATGCCATCCCCATCAAGC 1537
                            v     v     v  i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186572877_   1538 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTCA 1585
                          v   iivi i  i  ii     -   -- v  i  - iii i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_186572877_   1586 TACGGAACGAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 1635
                           i    vviv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186572877_   1636 AACAAAGCTGGAGGCATCACGCTACCTGACTTCTAACTATACTACAAGGC 1685
                                i      vv    i  v  ii i   v  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186572877_   1686 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1735
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_186572877_   1736 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTATAACC 1783
                                i    i--    i  --        vv   i    i   iii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_186572877_   1784 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 1833
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_186572877_   1834 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAAGTAGAAAGCT 1883
                           v  i  i              v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_186572877_   1884 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAACATGGA 1933
                            ii    i    v   i     v  i           i    v     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_186572877_   1934 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1983
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_186572877_   1984 CTAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGTCT 2031
                         v    ?i- v i -   i- i  v i  i- i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_186572877_   2032 AAAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCT 2081
                          vi            vvi      i   vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_186572877_   2082 AACTAAACTAAAGAGCTTCTGCACAGCAGAGAA-ACTACCATCAGAGTGA 2130
                         v ii   v v  i i   i  ii vv  i  i -    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_186572877_   2131 AGAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGAC 2180
                          i  i     i                 v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_186572877_   2181 AAAGGGCTAATATCCAGAATCTACAAAAGAACTTAAACAAATTTACAAGA 2230
                           i  i  vi          v  i   -     ivv    v iv i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAA-GAACTCTTACAACTCAATAATA 793

  chr2_186572877_   2231 AAAAAATCAAACAACTCCATCAAAAAGTGGGCGAAGGACATGAACAGACA 2280
                             i -    i   i v  i?    i     i     iv    i     
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_186572877_   2281 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAACGCT 2330
                         i     v        i  vi viii     i ii          i i   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_186572877_   2331 CATCATCACTGGCCAT 2346
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (148 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


 618 30.08 2.44 2.03  chr2_186626783_186631677.rev     3205  3450 (1445)    L1M4_orf2#LINE/L1        1   247 (661)  

  chr2_186626783_   3205 TGAAAAAAAATCTCATGCTCATAGATCAGAAGAATTAATATCATTATAAT 3254
                           i   i v   i    i    i   ii     v       ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186626783_   3255 GACCATACTACCGAAAGCAATATAAATATATATAGAATGAAATCTCTA-C 3303
                          i v     v  v   vii  v  v v  vi ---- i v    i   - 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCA----ACGCAATCCCTATC 96

  chr2_186626783_   3304 ATAGTTTCAG-TGTTATTTTTCACAAAAATAGAAAAAC----CATAAAAT 3348
                          v i ii   -  ii-     ii  i    v  v  i ---- v      
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_186626783_   3349 TCATATGAAACCAAAAAAGAGTCAGAATAGTCAATCTAATCCTAAGCAAA 3398
                                i  viiv  ii  vi        i   vvi    i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_186626783_   3399 GTGAACAAAGCTGGAGGCATCACACTACTTGACTTCAATATATATTACAA 3448
                         iv        i      vv       v iii i     v iv  i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_186626783_   3449 GG 3450
                         i 
  L1M4_orf2#LINE/    246 AG 247

Transitions / transversions = 1.64 (46 / 28)
Gap_init rate = 0.02 (5 / 247), avg. gap size = 2.20 (11 / 5)  

1284 28.15 21.94 0.18  chr2_186626783_186631677.rev     3857  4403 (492)    L1M4_orf2#LINE/L1      243   908 (0)  

  chr2_186626783_   3857 CAAGGCTATAGTAACCAGAACAGCATGGTATTGGTATGAAAATAGAAACA 3906
                            i    i     i  ii    ii     i   i  i ii     v i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_186626783_   3907 CAGACCGAGGGAACAGAATAGAGTACCCAGGAATAAATCCACATAGTTAT 3956
                         i   i i v    i     v   vii    i      i   i i v    
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_186626783_   3957 AGTTAATTGTTTTTCAGCAAGG-CACCAAGAACATACACTGGGGAAAGCA 4005
                         i  i     v     ii     -ii      v   v  v         v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_186626783_   4006 CA-TTTCTCCAACAAGTGGTGCTGGGAACATTGGATATCCATATGCGGAA 4054
                         i - i i i      i           vv i      ?   i    ii  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_186626783_   4055 GAATAAAACTG--------------------------------------A 4066
                             i  ii  -------------------------------------- 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_186626783_   4067 TGG-------------------------------------TCT------- 4072
                            -------------------------------------   -------
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_186626783_   4073 ---------------------------------GGGCAACGATTTTATGG 4089
                         ---------------------------------i     i i   iv i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_186626783_   4090 TTAAGACCTCAAAAGCACAGACAACTAAAACAAAAGTAAACAAACAGTTC 4139
                         v  v   vi          ii    v   iv    i  i i   iv vv 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_186626783_   4140 TATATTAAACTAAAAGGCTTCTACATAGCAGATGAAACAACCAACAGAGC 4189
                          vi  i   v v   ii   i iiiivv  i v  v  v i   v i  i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_186626783_   4190 GAAGAGGCAACCTGTTGAATAGGAGAAAATATCTGCAAACTATTCATCCT 4239
                            i  i     iiiv    i           i      ii  vi   - 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC-T 741

  chr2_186626783_   4240 GACAAAAGACTAACATCCAGAATATACAAGAAACTCAAACAACTCGACAG 4289
                           i  ii    vii            i  ii     vv       i i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_186626783_   4290 TATAGAAGCAAACAATTGCATTAAAAAGTGGGCAAAAAAAT-GAATAGAT 4338
                           v i ii    i  iivv   ?    i        ii v -       i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_186626783_   4339 AATTTTCAAAAGAGGAT-TACAAATATTTAACG-GTATATGAAAAAATGA 4386
                          v  i  v     i   -       ivii  ii- i i       i   v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_186626783_   4387 TCAATATCAAAGCATCA 4403
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.53 (109 / 43)
Gap_init rate = 0.01 (9 / 666), avg. gap size = 13.44 (121 / 9)  


1992 28.31 0.30 0.46  chr2_186648683_186650333.rev      503  1159 (492)    L1M4_orf2#LINE/L1      253   908 (0)  

  chr2_186648683_    503 GTCACCAAAACAGCATGATACTGGTATAAAAAATAGACACATAGACCAAT 552
                           v i   i    ii  i      i    ii -      i     i    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAAT 301

  chr2_186648683_    553 GAAACAGAATAGAGAAACCTAGAAATAAAGCCAAATACTTAGAGTCAACT 602
                          i  i     v    iv  -         v   v i i   vi     i 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCC-AGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_186648683_    603 GATCTTCAACAAAGCAAACAAAAACATAAAGTGGGTAAAGGACACCTTAC 652
                            i   i    i vviv   i v   vv i    v    i i vii vi
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_186648683_    653 TCAACAAATGGTGCTGGAGTAATTGGCAAGCCACATGTAGAAGAATTAAA 702
                                          iii  i   vv ?       i i      v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_186648683_    703 CTAGATCTTCATCTCCCACCTTATACAAAAATCAACTCAAGATGGATCAA 752
                         i i  i iii i   v    v           i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_186648683_    753 ATACTTAAATCTAAGAGCTGAAACCATGAAAATTTTAGAAGATAACATCA 802
                          v  i     v        i    i  i   v i        v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_186648683_    803 GAAAAGCCCTTCTAGATATTAGCTTAAGGAGAGACTTCATGGCCAAGA-A 851
                          ?iv ivi    vv  iv  i v   i v iv ii   v i vi v  - 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_186648683_    852 CCGAAAAGCAAATGTAACAAAAACAAAGATAAATAGATGAGACTTAATTA 901
                           -       v v i       iv   i   i   i  vi     v  i 
  L1M4_orf2#LINE/    601 CC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_186648683_    902 AACTAAAAAAATTCTACACAGAAAAATAAATAATAAGCAGAGTTAACAGA 951
                           v v     v  i iii vvv   iv v iv  v iv i   v  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_186648683_    952 CAACACACAGAGTGGGAGAAAATCTTCACAATCTGCACATCCAACAAAGG 1001
                             v      i           v  ii   viiii i   ii i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_186648683_   1002 AC-AACATCCAGAATCTACCAAGAACTCAAACAAATCATCAGGAAAAAAT 1050
                           -vii         v  iv        vv    v   vi iv     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_186648683_   1051 TAAACAATCCTACCAAAAAGCAGACTAAAGACATGAATAGACAATTCTCA 1100
                         i   i  i  v ii?    iii i v  i  iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_186648683_   1101 AAAGAAGATATACAAATGGGCAACAAGTATATGGAAAAATGCTCAACATC 1150
                                            v   i   i i   i   i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_186648683_   1151 ACTAATTAT 1159
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.53 (110 / 72)
Gap_init rate = 0.01 (5 / 656), avg. gap size = 1.00 (5 / 5)  


 320 27.63 0.00 0.00  chr2_186655896_186659010     1305  1380 (1735)    L1M4_orf2#LINE/L1        1    76 (832)  

  chr2_186655896_   1305 TGGAGAAATATTCTGTATTCATGGATTGGAAGATTCAACATAGTAAGGAT 1354
                             i i    i ii i                i i  i  v  v i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186655896_   1355 GTCAGTATTCTCCAAAATAACATATA 1380
                          v  i  i  i     v i iv  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA 76

Transitions / transversions = 3.20 (16 / 5)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.00 (0 / 0)  

 681 26.96 4.35 1.30  chr2_186655896_186659010     1382  1611 (1504)    L1M4_orf2#LINE/L1      145   381 (527)  

  chr2_186655896_   1382 TTGATATGGAAAAGCAGAGGAACTAAAATAGCTAAAACAAATTCTGGGGG 1431
                           v         v   ii   v i i      i       - ii  iiii
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAA 193

  chr2_186655896_   1432 AGAA-----AAGTAGGAGGAA--ACATTTTACCTAATTTCAAGTCTTAT- 1473
                             -----    v      v--   i  --  i        iv    i-
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTT--CCCAATTTCAAAACTTACT 241

  chr2_186655896_   1474 -CAACACCACAGTAATCAAGACTCTAAGGTGTTGGCAGAGGGATAGAAAC 1522
                         -   vi i              vv iv   ii     v i       v i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_186655896_   1523 ATAG-TCAATAGAATAAAATAGGGAACTCAGAAACAGTGCCACAAAAGTA 1571
                             -     i     i   v i  iii      i ivv   i v vv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_186655896_   1572 CAGCCAACAGATTTGTGACAAAGGTGCAAAATCAATTTAA 1611
                         ii i   iv     vi     i     v  iv v   i  
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

Transitions / transversions = 1.70 (39 / 23)
Gap_init rate = 0.03 (6 / 237), avg. gap size = 2.17 (13 / 6)  

1177 27.05 3.81 4.57  chr2_186655896_186659010     2101  2625 (490)    L1M4_orf2#LINE/L1      388   908 (0)  

  chr2_186655896_   2101 AAGGATAGTATTTTCAACAAATGGTGCTGGAGCAACTGAATAGCCATAGA 2150
                            i     v                    ii      i   ?   i vi
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_186655896_   2151 CAACAAAAAAAACAAACTAACAAAAAAACCCAAATTTTGATTTAGGTCTC 2200
                            ---  i  vv  ii ii-------    ----------i  --i   
  L1M4_orf2#LINE/    438 CAA---AAGAATGAAGTTGG-------ACCC----------CTA--CCTC 465

  chr2_186655896_   2201 ACACTTTGTGCAAATATCAACTCAAAATAGATCATAGTCTTCAATGTAAA 2250
                             iv i i    v  i          i     ?  v i v       i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_186655896_   2251 A--CAAAACTAAAATAACT-TTGTAAGATAATGTAAGAAAAAATCTTTGA 2297
                          --i       v  -    -  iv    v  ii  i ?iv       i v
  L1M4_orf2#LINE/    516 AGCTAAAACTATAA-AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_186655896_   2298 GACATAGGGCTTGGTGAAGAGTCCTTTAAAATGATATCAAA-GTACAATT 2346
                            v v   i v  ii v iv i   vi v    i i    - i    vi
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_186655896_   2347 CTTTAAA---AATATTGCTAAATTGAACTTCTTTTATATTAAAA-CTTTT 2392
                         vviv   ---  v  v v       i     v iv v       -     
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_186655896_   2393 GTTCCATGAAAAACCCT---------GTTAAAAGACAAACTACAGATTTG 2433
                           v ivii  ii  v  ---------  v         v i     v v 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_186655896_   2434 GAGCAAACATTTTTATATCTATATATTTAACAAAGAATTCATA-AAAGAA 2482
                            v   i    vi v   -      i i i  i i i ii  -vv    
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATC-ATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_186655896_   2483 TATATAAATAATTCTCAAAACTCAACTGTGAAACAA--AACTATTTAATT 2530
                                 v  i   i v       ivi i   vi --  iv iii    
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_186655896_   2531 TTAAAATGTGTAAAGGATATAAAAAGACATTTCACAGAAGTGAATATGTG 2580
                         ?v      v i       v i  v         v vi   vii    iii
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_186655896_   2581 GATTGAAAACAAGCATAGGAAAAGATGTTCAACATTGCTAGCCAT 2625
                         i  v vv  i     i v         i       ii????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (80 / 58)
Gap_init rate = 0.03 (14 / 521), avg. gap size = 3.14 (44 / 14)  


2149 27.20 2.84 0.60  chr2_186678904_186680532      471  1139 (490)    L1M4_orf2#LINE/L1      225   908 (0)  

  chr2_186678904_    471 CAATCTCAG--CTCACTGCAA--CCTCCGCCTCCAAAACAGCACGGTACT 516
                             i   i--  i   i   -- iv v ivvi   i    iii      
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chr2_186678904_    517 GGTACCAAAACAGAGATATAGACCAGTGGAACAGAAC--AGAGCCCTCAG 564
                           i iv ii i   v       i  i     i    i--    i  --  
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AG 322

  chr2_186678904_    565 AAATAATGCCGCATATCTACAACCATCTGATCTTTGACAAACCTGACAAA 614
                               vv  ii i  i  iiii  vi    i  i     ivv  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_186678904_    615 AACA------------AGATTC-CCTATTTAATGAATGGTGCTGGGAAAA 651
                          v  ------------   v v-i  v  i  ii             v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_186678904_    652 CTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTT 701
                             v  ?   i   i i  iiv    ii    i    v   i     v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr2_186678904_    702 ATACAAAAATTAATTCAACATGGATTAAAGACTTAAATGTTAGACCTGAA 751
                                      i    v      i ?    i       v   v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_186678904_    752 ACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGG 801
                           i      vi i           v    ?i v viv   iv   v v  
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_186678904_    802 CATGGGCAAAGACTTCATGTCTAAAACACCAAATGCAATGGCAACAAAAG 851
                         vv i     v ii   v ivv  vi        v   vvi          
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_186678904_    852 CCAAAATTGACAAATGGGATCTCATTAAACTAAAGAGCTTCTGCACAGCA 901
                         vv     v  i    v   ii    i   v v  i i   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_186678904_    902 AAAGAAACTACCATCAGAGTCAACAGGCAACCTACAAAATGGGAGAAAAT 951
                           i  v    i  vv i   v  v  i     i   i             
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_186678904_    952 TTTTGCAATCTACTCATCTGACAGAGGGCTAATATCCAGAATCTACAATG 1001
                         v       vii ivi      i ii  i  vi          v  i  v 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_186678904_   1002 AACTCAAACAAATTTACAAGAAAAAAAATCAAACAACCCCATCAAAAAGT 1051
                              vv    v iv i  v     i --    i     v  i?    i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAAT 820

  chr2_186678904_   1052 GGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGATATTTATGCAGCC 1101
                             i      v    i     i     v           vi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_186678904_   1102 AAAAGACACATGAAAAAATGCTCATCATAACTGGCCAT 1139
                           v ii          i       v   v ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (104 / 74)
Gap_init rate = 0.01 (7 / 684), avg. gap size = 3.29 (23 / 7)  


2446 26.87 5.86 1.61  chr2_186699320_186704880     4201  5071 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186699320_   4201 TGGTAAAACATTTCGT-CTCATGGATAAGAAGAATAAATATCGTGAAAAT 4249
                            v  i i  ii i -i        vi     v v     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186699320_   4250 GGCCATAGTGCCCAAGGTAATTTATAGATTCATTGCTATTCCCATTAAAA 4299
                            v   v v     iv i  i  i       vi  v  i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186699320_   4300 TACCATTGACATTCTTCACAGAATTAGAAAAAAAATACTTTTAAA-TTCA 4348
                          v   vivi v  i  ii     v v  v  iv-- iv ii    -    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chr2_186699320_   4349 TGTAGAACCAAAAAAGACCCTTTATAGCCAAAACAATTCTAAGCAAAAAG 4398
                          i i   viiv  ii     vvv              ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186699320_   4399 AATAAAGCTGCAGGCATCACACTACCTGACTTCAAACTATACTACAAAGC 4448
                           i    i  v   vv       v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186699320_   4449 TACAGTAACCAA-ACAGCATGGTACCAGTAAAAAAAAAACAGATACATAG 4497
                                 i   -    ii      ii i v  ii ---i   i i    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA---TAGACATATAG 295

  chr2_186699320_   4498 ACCAATGAAACAGAATAGAGATCTCAGAAATAAGACTGTGCATCTACAAG 4547
                          i     i  i     v    vii         iv ii i   i  iiiv
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_186699320_   4548 CATTTGATCTTCAACAAACCCGAAAAAAGCAAGCAATGGGGAAAGGAT-- 4595
                           v     i   i    ivvi vv  i v  vv            i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_186699320_   4596 ---TCTCAA----------------AACTGGA--------------AAAT 4612
                         --- i    ----------------       -------------- i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_186699320_   4613 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATAG 4662
                             ii    i    v   i     v                   i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_186699320_   4663 ATTAAAGACTTAAATGTAAAACTCTAAACTATAAAAACCCTAGAAGAAAA 4712
                           i ?    i         i viiv           vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_186699320_   4713 TCTAGGG---AAT----ATGATTTAGGAATAGGCACAGGCAAATATTTCA 4755
                         iv    ?---   ----i   ii v  iv      vv  ------    v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG------TTTCT 589

  chr2_186699320_   4756 TGACGAAAACACCCAAAGTGATTGCAAAAAAAGCAAAAATTTACAAATGG 4805
                          iivv vi     v    iivvv    v     v      vv i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_186699320_   4806 GATCTCATTAAACTAAAGAGCTTCTGGACAGAAAAACAAAACTATCATCA 4855
                           ii    i   v v  i i   i  vi vvv   i-i v       vv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGA 688

  chr2_186699320_   4856 GAGTAAACAGACAATCTACAGAATGAGAGATAATTTTTGCAATCTATCCA 4905
                         i   i  v      i i        i    v   v       vii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_186699320_   4906 TCTGATAAAAGTCTAATATCCAGAATCTACAGGGAACT--TA-AAC-CAA 4951
                                 ii v  vi          v  i ii     --  -   -   
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_186699320_   4952 T--TTACAAGAAAAATACAACCTCATTAAAAAGTGGACAAAGGACATGAA 4999
                          -- v v    v     --   iv   ?    i   i       iv    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATA--ACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_186699320_   5000 CAGACACTTCTCAAAAGAAGACATTCATGTGGCCAACAAACATATGAAAA 5049
                         i     i     v        i  v  vi       i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_186699320_   5050 AAAGTTCAACATAACTGGTCAT 5071
                         i v i       v ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (135 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.82 (65 / 17)  


3032 25.75 1.88 1.77  chr2_186710349_186714089.rev     2345  3249 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_186710349_   2345 GAAAAGTATCTCATGCTCATGGACTGGAAGAATTGCATATTTTTATAATA 2394
                             ii    i    i       i       v  i-     v   -----
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTA-ATATTGTTA----- 46

  chr2_186710349_   2395 AAATGTCTGTACAATCCAAAGAGATCTACAGATTCAGTGCAGTGCTTATC 2444
                          i   v vi   vvi     vv              ii   i v i    
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_186710349_   2445 CAAATTCCAG-TGTAATTTTTCATAGCTATAGAAAAAAACAACCGTAAAA 2493
                         v    i    -  iv-     iii  vv  v  v  iv-ii i v     
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGATCCTAAAA 144

  chr2_186710349_   2494 TTCACATGGAACT---AAAAATCCGTGAATAAAGAAGGCAACCATGAGCA 2540
                             i      v --- iii i  i-     ivv  ii   i v   iv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAA 193

  chr2_186710349_   2541 AGAAGAACAAAGCTGGAGGCATTACACTATCTAATTTCAAACTATACTAC 2590
                                     i      vv i     vi i         viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_186710349_   2591 AAAGCTGAAGCAATTAAAACAGCATGGTACTGGCAAAAAAAAAAAATAGA 2640
                               iv  i   i  i    ii           v  ii -----    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-----TAGA 288

  chr2_186710349_   2641 TATATTAACCAATTGAACAAAATAGTGACCCCAGAAATAAACCCATGTAT 2690
                         i    vi i    v   i i   v v  vi                ii  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_186710349_   2691 GTACAGTCAATTAATTTTTAACAAAGATGCCAAGAATATGCAAAGGGAAA 2740
                         v  ii       i     ii    i i        vi  v   v   i  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_186710349_   2741 AAGACAGTCTCTTCAATAAATGGTCTTGGGAACACTAAATATCCACATGC 2790
                          ii i     i     i       vi     vv   ii   ?        
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_186710349_   2791 AGGAGAATAAAATTGGATCCTCATCTCACACCATATACAAAAAACAAACC 2840
                          ii     i  i     i  ii i                   vi  vi 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_186710349_   2841 AAAATGGATTAAACACTTAAACATGGCACCGGAACCTTTAAAGCTAATAG 2890
                                  i ? v  i    ii iiv v vi  v  v    i  vv   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_186710349_   2891 AGGAAAACATCAGTGAAAATTCACACAACTTTGGGCCATGAAATTATTT- 2939
                          i        vi ? v    iiv iii  i     ii v v   vi   -
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_186710349_   2940 TTGGATATCAC-CCAAAACACGCATGCAACAAAAGGATAAATAGACAAAT 2988
                           i     v  -      -i i  v          i v       i    
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_186710349_   2989 AGGATTACATCAAACT--AAAATTTCTGCACACCAAAGGAAAC----AAC 3032
                         v   i v       v --    i  i  ii vi       v  ----  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_186710349_   3033 AACATTCAAAGACAGCCTGTGGATTGTCAGAAAATATGTGTAAGCCATTC 3082
                           vi vv       i  iiii  v  vv         v  i  ii   vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_186710349_   3083 ATATGATAAGGGGTTAATGTGCAAAAAAATGCAAGTAACTC----AACTC 3128
                           v         ii vi i v  i  v - ii  iv     ----     
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATA-TATAAAGAACTCTTACAACTC 786

  chr2_186710349_   3129 AACAGCAAAAA-ACAAAAAACCCAATTAAGAAAGGGGCAAAAGACTCGAA 3177
                           i ii     -     v         ? i   v       i  i i   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_186710349_   3178 CAGACATTTCTCAAAGGAAGACATACAAATGGCCAACAAATATATACAAA 3227
                         i           v  i     i              i  ii i  iv   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_186710349_   3228 AATGTTCAACATCACTAATCAC 3249
                         i   i         ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (146 / 83)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 2.06 (33 / 16)  


3283 23.81 3.72 1.24  chr2_186799064_186803514.rev     3074  3959 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186799064_   3074 TGGAACATTATTTTGTAATCATGAATTGGAAGAATTCATATTGT-AAAA- 3121
                              viv   iiii iv     i         v  v       -  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186799064_   3122 -----------CCAAAGTGATTCACAAACTCAATACAAGCGCTATCAAAA 3160
                         -----------     v    ii   i i    ii   v v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186799064_   3161 TTCC-GATGTCATTTTTCACAGAAATAGGAAAAATGATCTTTAAATTCAT 3209
                          i  - v  i -     ii       v iv  iv     i v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_186799064_   3210 ATGGAACCATAAAAGACCCC-AATAGTCAAAACAGTCTTAGGCAAAAAGA 3258
                               viii  ii     v-     i       i    iiiv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_186799064_   3259 ACAAAGCTGGAGGCATCACACTCCCTTATTTCAAAACATATTATAAAGCA 3308
                               i      vv       i  iv          v  i  i     v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_186799064_   3309 ACTGTAAATAAAACTGCTTCATGTTACCGGCATAAAACTAGATATATTAA 3358
                           v    vi  i  v i---i  v   i       iiv    i    vi 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGT---GTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_186799064_   3359 CCAATGAAACAGAATACAAGACCCAGAGGTAAACCCATACATTAACGGTC 3408
                         i     i  i     vv iiii     ii              v i    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_186799064_   3409 AATTGATTTTTGACAAAGTTGCCAAGAACACACAATGAGAAAAGGACAAT 3458
                                   i     i v        v  iv     i i    i i i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_186799064_   3459 TTCTTTAATAAATGTTATTGGGA-AATTGGATATTTACATGCAGAAAAAT 3507
                         i i  i  i     v ii     -  i      ?ii       i  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_186799064_   3508 TAAATTAGACTCTTATCTTACACCATATACAAATATCA-CTCAAAATGAA 3556
                         v  i  i   i i  i  i              v  i -         i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_186799064_   3557 ATAAAATTTTGAATGTAAGACGTGAAACTGTAAAACAACTAGAA-----T 3601
                         vi ? ivii i         vv i     i      vvi     -----i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_186799064_   3602 TTAGG-GTAAATACTCTGTGACTCCACTGGTCTGGGCAATGATTTTTTTG 3650
                         v    -      -  ii     ii---   vi i       i   i  -i
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCT---TGGGTTAGGCAATGGTTTCTT-A 591

  chr2_186799064_   3651 GATATGACTGTAAAAACATAGCCAACAAAATCAAAAATAGACAAATTGGA 3700
                                 vvi    i  i iv        vv         i        
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_186799064_   3701 --TGAT--AAACTACAAAACTTCTGTGCAGTGAAGAAAGCAATTAACAAA 3746
                         -- v  --   i  -       i     vvii   i vi v  i  v   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_186799064_   3747 GTGAAGAGACCAACCGTGGAGTGGGAGAAAATATTTGCAAAGCATACATC 3796
                              i    v v  iii  i                    v    i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_186799064_   3797 TGATAAGGGG-TTAAGT---GAGTA-ATAAAAAAATGCCAACAATTAAAT 3841
                                  i-  ivi ---  i  -     i  v - iv    i v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACT-CTTACAACTCAAT 789

  chr2_186799064_   3842 AGCAAGAAAACAAATAACCTGATTTAAAAATGAGCAAAGGACCTGACTAG 3891
                          ii  i  i          ii   ?       i        ii   v   
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_186799064_   3892 ACACTTCTC-AGAGAAGACATACAAATGACCAATAGGTACATGAGAAAAT 3940
                            i     - i      i         i      i i      i  i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_186799064_   3941 GCTGAGCATCAGTAATCAT 3959
                            v i     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (144 / 64)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.10 (44 / 21)  


3138 25.11 1.10 1.10  chr2_186834018_186838450     3034  3941 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186834018_   3034 TGTAAAAACATTCCATGCTCATGGATGCAAAGAATCAATATCATGAAAAT 3083
                           v   i i  i     i        vvi    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186834018_   3084 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATTCCCATCAAAC 3133
                            v     v      v i  i           i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186834018_   3134 TGCCA-TTGACTTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTCAT 3181
                          v   -i  v   i  ii     v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_186834018_   3182 ATGGAA-T-CAAAGAAGACCCTGTATAGCCAAGACAATTCTAAGCAAAAA 3229
                               - -   i --     v v        i     ii i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_186834018_   3230 ACACAAAGCTAAAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 3279
                         iv      i ii   vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_186834018_   3280 CTACAGTAATCAAAACAGCATGGTACGGGCACCAAAATAGACATATAGAT 3329
                                      i    ii      v    iv ii              
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_186834018_   3330 GAATGGAGCAGAACAGAGACTTCAGAAATAACATCATGCATCTACAACCA 3379
                         v      ii    iv    v i         vvi   i   i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_186834018_   3380 TCTAATCATTGACAAATCTGACAAAAACAAGCAATGGGGAAAGGATCTCC 3429
                         vi i  iv i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_186834018_   3430 TATCCAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 3479
                          v i  ii              v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_186834018_   3480 AAACTGGACCCCTTCCTTACACCTTATACAAATATTAACTCAAGATGGAT 3529
                           ii         v   i     v        v          i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_186834018_   3530 TAAAGACATAAATGTAAAACCCCAAACCATAAAAACCCTAGAAGAAAACC 3579
                         i ?    v         i v iv    i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_186834018_   3580 TAAGCAGTACAAT--TCAGGACATAGGTGTGGGCAAAGGCTTCATGACAA 3627
                           i ?-   -   --  iv   v v  vv i     v  i   v iivv 
  L1M4_orf2#LINE/    548 TAGGN-GTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_186834018_   3628 AAACGCCAAAAGCAATCGCAACAAAAGCCAAAATTGACAAATGGGAACTC 3677
                         vi  i         vvv          vv     v  i    v   vi  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_186834018_   3678 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 3727
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_186834018_   3728 CAGGCAACCTACATTATGGGAGAAAATTTTTGCAA--TATACCCATCTGA 3775
                         v  i     i   vv            v       --i   i--      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chr2_186834018_   3776 CAAAGGTCTAATATCCAGAATTTACAAAAAAA-CTTA-AACATGTTTACA 3823
                         i  i  v  vi          v  i   i  v-    -   --- iv i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC---TCAATA 790

  chr2_186834018_   3824 AGAAAAAAACAACCAACCACATCAAAAAGTGGGCAAAGGATATGAACAAA 3873
                          v     i    vi    vv  i?    i            v    i i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_186834018_   3874 CACTTATCAAAGGAAGACATTAAAGTGGCCAAAAAACATATAAGAAAAAG 3923
                           i  v  v  i     i  vv  i       v  i  i  i i  i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_186834018_   3924 CCCAACATCATTGATCAT 3941
                          i        ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (125 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.43 (20 / 14)  


1072 30.05 1.86 1.86  chr2_186846088_186853371     3569  3944 (3340)    L1M4_orf2#LINE/L1        1   376 (532)  

  chr2_186846088_   3569 TGAAAAGCT-TTCCATATTCATGGACAGAAAGAGTCAATATTGTTAAAAT 3617
                           i    v - i    i        iv i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186846088_   3618 GATAATACTTCTCAAAGCAATTTATAGATTCAGTGGTATTCCTGTCAAGC 3667
                          ii      i i    vii  i  i       ii vv  i   i    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186846088_   3668 TACCAATGACATACTTCACAGAATTAGAAAAAAAAAAACGATTTTAAAAG 3717
                          v   iivi v vi  ii     v v  v  iv-----i   ii     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-----TGATCCTAAAAT 145

  chr2_186846088_   3718 CCATATGGAACAAAAAAAGGCCTA-AATAGCCAAAGAAATACTAAGCAAA 3766
                         i         vviv  ii i  i -          iv   vi i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_186846088_   3767 AAGAACAAAGCTGGAGATATCACTTTGCCCAACTTCAAACTATGCTACAA 3816
                                   i     ivv    vi v     i      viv i      
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_186846088_   3817 GGCTATGGTAACCAAAACAGAATGATACGGATATAAAAACAGATACACAG 3866
                         i    ii    i   i    vi  i   v ii    ii i   i i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_186846088_   3867 ATCAATGTAACAAAAC----AGCCCAGAAATAAGGCCACACACCTACAAT 3912
                                v  i i  i----  i          iv   i   ii  iii 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_186846088_   3913 -AATCTGATCTTCAACAAAGACAACAAAAACCA 3944
                         -   -    i   i    i iiiv   i -   
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGA-CCA 376

Transitions / transversions = 2.42 (80 / 33)
Gap_init rate = 0.02 (7 / 376), avg. gap size = 2.00 (14 / 7)  

1465 24.28 4.82 2.70  chr2_186846088_186853371     6280  6798 (486)    L1M4_orf2#LINE/L1      379   908 (0)  

  chr2_186846088_   6280 CAACGGGGAAAGGAATCACCATT-CAATAAATGGCGCTGG-ATAACTGGC 6327
                            i        -   vii v  -   i      i     - i      v
  L1M4_orf2#LINE/    379 CAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_186846088_   6328 TAACTGGCTATATGCAGAAGATTGAACCTGAACTCCTTCCTTACATCATA 6377
                           ----? i i     i    v    vi  i  i   v   i   i    
  L1M4_orf2#LINE/    428 TA----KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_186846088_   6378 CACAAAAATCAACTCGAGATAGATTAAAGACTTAAATGTAAAACCTAAAA 6427
                         i        i     i i  i   i ?    i         i v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_186846088_   6428 CTTGCAAAATCCCTGACAGATAACTTAGG---AAATACCATTCTAGACAT 6474
                           -ii    ii i iiv   v   v    ---    -- -   vv   v 
  L1M4_orf2#LINE/    524 CT-ATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCT 569

  chr2_186846088_   6475 AGGAACTTGGTAA-GATTT--TACGATGAATATC-CCAAAAGCAATTGCA 6520
                         v  i-i v  i  - i   --  -   --  iv -         vvv   
  L1M4_orf2#LINE/    570 TGGG-TTAGGCAATGGTTTCTTA-GAT--ATGACACCAAAAGCACAAGCA 615

  chr2_186846088_   6521 ACAAAAATAATAATTGACAAATGGGACTTAATTAAACTAAAGAGCTTCTG 6570
                               iv  v   v  i    v      v  i   v v  i i   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_186846088_   6571 GAC-----AG--CA-TATCAACAGATTAAAGAG----TGTACAGAATGAG 6608
                         vi -----  --  -      v i v i  i  ----ivi        i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_186846088_   6609 AGAAAACATTTGCAAACTATGCATCTGACAAAAGTCTAATATCTGAAATC 6658
                               i         ii  ii      i  ii v  vi    iii   v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_186846088_   6659 TATAAGGAAATTAAACAAAT---TAACAAAGA-ACAAACAACCCCATTAA 6704
                              i   v ivv    v ---   i   i -     i     v   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_186846088_   6705 AAAGTAGGCAAAGAACGTGAACAGACACTTTTCGAAGAGAAGATATACAC 6754
                            i i       i iv    i     i  i  v  -            v
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA-AGAAGATATACAA 864

  chr2_186846088_   6755 ACAGCCAACAAGAATATGAAACAATTCTCAGTGTCACTAATTAT 6798
                          ii     i   v i      vi  v    iii   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (79 / 44)
Gap_init rate = 0.04 (21 / 530), avg. gap size = 1.86 (39 / 21)  


2875 25.92 4.95 0.35  chr2_186892660_186895491     1473  2340 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186892660_   1473 TGGAATGATATTCTATGCTTGTAGATTGAAAGA----ATATTGTTAAAAT 1518
                              v     i i   i ii i     i    ----          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186892660_   1519 GAACAACACTAACAAAAGCAAAATATAGATTCAATGCAATCCCTAT-AAA 1567
                          i-   i   vv v   vii vv  i        i           -   
  L1M4_orf2#LINE/     51 GG-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_186892660_   1568 AT---A-----TTTCTTCACAGAAACAGAAATAAC-AATTTTAAAATTTA 1608
                           --- -----i  i  ii      iv  v - i -i  ii       i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chr2_186892660_   1609 TATGAAACCACAAAAGACTCCTAATAGTCAAG-CAATCCTGAGCAAAAAG 1657
                             i  vii   ii   i vv     i   i-     i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186892660_   1658 AACAAAGCTAGAGTCATCGCACTACCTGACTTCAAAATATACTACGAATC 1707
                                i i   vvv  i    v  ii i       iv      i  v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186892660_   1708 TATAGTAACCAGGTAAGCATGGCACTGGTACAAAAACAGACATGT-GACC 1756
                           i     i  i vv  ii   i     i i  ii i      i -  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_186892660_   1757 AATGGAACAGAATACAGAACTTAGATATAAATGCATGCATTTACAGCCAA 1806
                                i     vv   iiii   v     iv   i      ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_186892660_   1807 CGCATTTTTGACAAAGTTGCCAAGAACATACAATAGGAAAAGGACAATCT 1856
                         ivv     i     i v        v   v    i  i    i i i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_186892660_   1857 CTTCAATGAATTGTGCTAGCAAAACTGTATAACCATCTGCAGAAGAATAA 1906
                         i     ii   v     i v v     v   ?   iv    i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_186892660_   1907 AACCAGATGCCTACCTCTCATCATACATAAAAATCAAATCAAAATGAATT 1956
                          iiii  iv        v  i    i i      i  v        i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_186892660_   1957 AAAAACTCAAATCTAAGATCTGAAAATACAAAGC-CATAGGAGAAAATAT 2005
                          ? i  ii    v     v  i   v  i   i - v   i      i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_186892660_   2006 -TGAGTAAATGCTTGAGGACATTAGTCTGGGCAAAGATACTTTGTGTAAG 2054
                         -v ?      -   viv   v  i vi i     v i vii  ivi  v 
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_186892660_   2055 ACTTCAAAAGTACAGGCAACTACAGCAAAAATAGACAAATGGGATTATAT 2104
                           vi      i   i     v v  v         i    v   i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_186892660_   2105 TCAGCTAAAAAGCTTCTGCATAGCAAAGGAAACAATCAATGGAGTGAAGA 2154
                         iv iv v    i   i  iiivv       v  v     vii      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_186892660_   2155 GACAACCCACGAAATGAAAGAAAATATTTATAAAC----TATCTGACAAT 2200
                                   ii    ii           ii   i----       i  v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_186892660_   2201 --ATTAATAACCAGAATATATAAGGAGCTCAAACAACT------TAAAA- 2241
                         -- i vi  v             i  i   vv      ------     -
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_186892660_   2242 --CAA-TAATCTGCTTTTAAAATGGGCAAAAGATCTGAATAGACATTTCT 2288
                         --   -   i iiv  ?v            i   i               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_186892660_   2289 C--AAGA-------CAAATAGCCAACAGTGACATGAAAAACTGCTCAACA 2329
                          --    -------     i     i ivv         iv         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_186892660_   2330 TCACAAGCTGA 2340
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.95 (146 / 75)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.42 (46 / 19)  


2740 25.58 3.11 2.11  chr2_186898942_186901394.rev     1076  1974 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186898942_   1076 TGGAGAGATATTACATGTTAACGGAGTGGAAGACTCAATTTTATCAAGAT 1125
                             i      iv      v i   v         i   v  i i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186898942_   1126 TTCAGTTAATTCC--AACTTGATTTCTAGATTCAATGCAATCCCATTCAA 1173
                         vv  i -- i   --  v     i vi        i        vv    
  L1M4_orf2#LINE/     51 GGCAAT--ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_186898942_   1174 AATCTCAGTGAGTTATTTTATGGATATTGACAAACTGATTCTAAAGTTTG 1223
                             i   ivivi v    iii  v        i     i     i  ii
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_186898942_   1224 GTATAAAAAGGCAAAGGCCACAGAATAATGAACACAATTATGTAGGAGAA 1273
                         -   ii   v    i  v v       iiv  v     iv  v ii    
  L1M4_orf2#LINE/    149 -TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_186898942_   1274 GAAAAAAGTTGGAGGACTGACAG----CA----TAGGACTTTTATGATAA 1315
                            v              v   v----  ----i ii    -- iv i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT--ACTACAA 245

  chr2_186898942_   1316 AGGTACAGTAATCAAGGCCGCGTGATATTGGTGAAAGAATGCAAAAATAG 1365
                           v             i v i   i  i   iiv   i  iv v v    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_186898942_   1366 AACAGTGGAACAGAACAGAGAGCCCAGAAACAGGCCCAGATCAATATAAC 1415
                          v  i     i    iv     i       i ii    v ivvv   iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_186898942_   1416 CAACTGATCTTTGACAAAGGAGCAAAGGCCTTACAAGGGAGCAAAGACAG 1465
                            i    i  i     i  v  v   i  v v   v  i v  ii i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_186898942_   1466 TTTTTTCGATAAATTGTGTTGGAATAATCGGACATTCACTCCCTGCCCAA 1515
                          i     i i    v   i   i i  ii   i ?i   ---v   --  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC---ATGC--AA 440

  chr2_186898942_   1516 AACGAATCTAGATAGAG----ACTTTACACTCCTGACAAAACTTA-CTCA 1560
                           -    vv  v i  v----  i i    ivivv      v   -    
  L1M4_orf2#LINE/    441 AA-GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_186898942_   1561 AAAATGGATCACAGACCTAAATGTAAAACAAAACTAAAACAAAAAAAAAC 1610
                            -       ?              i ----i       v v    vv 
  L1M4_orf2#LINE/    490 AAA-TGGATCAWAGACCTAAATGTAAGA----GCTAAAACTATAAAACTC 534

  chr2_186898942_   1611 TTAGTATATAATATTGGGG-AAATCTAGATGACTTTGGGTTTGACTATAC 1659
                             v v v  i  v  ? -      vvi    i       v i v  iv
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_186898942_   1660 CCTCCTAGTTACAATAGCAAAAGCATAATCAATGAAAGAAAAAATA-AT- 1707
                         ii  i   v  ii i v        i  v   ii            -  -
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_186898942_   1708 --TTGGATATCATTAAAATAAAAAAATCT-GTGCTGGGAAATACATTGTC 1754
                         --     iv    i     v     v i -     vvi  iv   i i  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_186898942_   1755 AAGAGAATGAAAAGACAAGCAACAGACTGGGAGAAAATATTTGCAAAAGA 1804
                             i i           v v     v                    vv 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_186898942_   1805 TATATCTGGTAAAAGACAGTTATTTAAAATATAAAAAGAACTTTTAAAAT 1854
                                 i   ii   vvv   ii i      v        i   v  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_186898942_   1855 TCAACAATAAGAA---AAATATGTGATTTAAAAAATTGGTCAAAGACCTT 1901
                             i     i  ---     vviv v  ?      v  iv  i  ii v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_186898942_   1902 AATGTACACCTCATCAAAGAAGATATAAAGATGACAAATATGCATTTGAA 1951
                            iv   ii  vi             v i   i v    v   iv    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_186898942_   1952 AATTATATGT----CATCAGAGAAAAG 1974
                           v---   i----     ????????
  L1M4_orf2#LINE/    885 AAG---ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (127 / 99)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.35 (47 / 20)  


3067 27.61 0.55 0.66  chr2_186920057_186926446     4990  5898 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_186920057_   4990 TGGAAGAACACTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5039
                              ii i ii     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_186920057_   5040 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5089
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_186920057_   5090 TACCAATGACTTTCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCA 5137
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_186920057_   5138 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5187
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_186920057_   5188 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAAATATACTATAAGGC 5237
                                i      vv    i  v  ii i       iv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_186920057_   5238 TACAGTAACCAAAACAGCATGGAACTGGCACCAAAACAGAGATATAGATT 5287
                                 i   i    ii   v       iv ii i   v        i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_186920057_   5288 AATAGAACAGAA--GAGAACCCTCAGAAATAATGCCACATATCTACAACT 5335
                            i   i    --    ii  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_186920057_   5336 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAATGACTCC 5385
                          vi    i  i     ivv  vv  i v  vv   i       vi ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_186920057_   5386 CTATTTAACAAATAGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAGCT 5435
                           v  i       i         v      v  ?   i   iii  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_186920057_   5436 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5485
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_186920057_   5486 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAACAC 5535
                          i ?    i       v   v       i      vi i        v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_186920057_   5536 CTAGCCA-ATACCATTCAGGACATAGGCATGGGCAAGTACTTCATGTCTA 5584
                         v   v?i- v i -   iv   v v  vv i     vvii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_186920057_   5585 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5634
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_186920057_   5635 ATTAAACCAAAGAGCTTCCGCACAGCAAAAGAAACTACCATCAGAGTCAA 5684
                           i   viv  i i   ii ii vv    i  v    i  vv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_186920057_   5685 CAGGCAACCTACAGAATGGGAGAAAATTTTTTGCAACCTACTCATCTGAC 5734
                         v  i     i                 v   -    vii ivi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGAT 744

  chr2_186920057_   5735 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5784
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_186920057_   5785 AACAACAAACAACCCCATCAAAAACTGGGTGAAGGATATGAACAGACACT 5834
                           vi     i     v  i?    v    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_186920057_   5835 TCTCACAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5884
                             vv       i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_186920057_   5885 CCATCACTGGCCAT 5898
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (147 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3096 27.54 1.00 0.55  chr2_187002809_187008932     4729  5632 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_187002809_   4729 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAATATCGTGAAAAT 4778
                              ii i  i     i    i i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_187002809_   4779 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 4828
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_187002809_   4829 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4876
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_187002809_   4877 TATGGAATCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 4926
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_187002809_   4927 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTGCAAGGC 4976
                                i      vv   ii  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_187002809_   4977 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATGGACG 5026
                                 i   i    ii         i iv ii i   v    i  iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_187002809_   5027 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATATACAACT 5074
                                i    i--    i  --        vv   i i  v  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_187002809_   5075 ACCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5124
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_187002809_   5125 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5174
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_187002809_   5175 GAAACTGGATCCCTTCTTTACACCCTATACAAAAACTAATTCAAGATGGA 5224
                            ii    i    v i i     v          i   i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_187002809_   5225 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAACAC 5274
                          i ?    i       v   v       i      vi i        v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_187002809_   5275 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGAACTTCATGTCTA 5323
                         v    ?i- v i -   iv   v v  vv i     viii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_187002809_   5324 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTAACAAATGGGATCTA 5373
                         vi            vvi          vv     vi i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_187002809_   5374 ATTAAACTAAAGAGCTTCTGCAGAGCAAAAGAAACTACCATCAGAGTGAA 5423
                           i   v v  i i   i  iivvv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_187002809_   5424 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5473
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_187002809_   5474 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5523
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_187002809_   5524 AAAACAA----CTCCATCAAAAAGTGTGCAAATGATATGAACAGACACTT 5569
                           i    ---- i v  i?    i  v     v   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_187002809_   5570 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5619
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_187002809_   5620 CATCACTGGCCAT 5632
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2113 24.97 11.88 1.82  chr2_187027793_187030513.rev     1411  2235 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_187027793_   1411 TGGAAAAACACTCCATGCTCATGGATAAGAAGAATCAATATTGTTAAAAT 1460
                               i i ii     i        vi     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_187027793_   1461 GGCCATACTGCCCAAAGCAAAATACAAATTCAATGCTATTCCTATCAAAC 1510
                            v     v      vii vv    i      i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_187027793_   1511 TACCAATGACATTCTTCACAGAATTAGAAAAAAAATTATTTTAAAATTCG 1560
                          v   iivi v  i  ii     v v  v  iv-- v  ii        i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chr2_187027793_   1561 TATGGAACCAAAAAAGAGCCCCAG--TAGCCAAGATTAGCCTAAGCAAAG 1608
                                -- viv   i v     --       i iv v i i iv  ii
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_187027793_   1609 AGAACAAAGCAGGAGGCAACATGTTACCTGACTTCAAACTATACTGCAAG 1658
                                  iv     vvv  iii v  ii i      viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_187027793_   1659 GCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAAGAGACACATAGA 1708
                                   i   i    ii         i i  ii v     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_187027793_   1709 TTAATGGAACAGAATAGAGAGCCCAGCAGTAA-----TGC-----TG--C 1746
                          i       i     v     i    v i   ----- i -----  -- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_187027793_   1747 AA---ACCT------------CCAA--CCATCT----------GAAC--- 1766
                           --- ii ------------    --    ii----------   i---
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_187027793_   1767 ---TTCAACAAA----GTTGA--------------------CAAAAAAAC 1789
                         ---         ---- i  i--------------------     i  i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_187027793_   1790 -----TGGACTCCTTCCTTTTACCATATA--AAAACCAATTCAAGATGGA 1832
                         -----     i   v   ivi        --    ii  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_187027793_   1833 TTGTAGACTTAAATATAAAACCTAAAAC-----AATTCT-GGAAGATAAT 1876
                          ii?    i     i   i v       -----  i   -i     v  i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_187027793_   1877 CTAGG---AAATACCATTCTGGACATAAGCCCTGGCAAAGATTTCAT-GA 1922
                         v    ---    -- -   vv   v vi viiv     v i    v -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_187027793_   1923 TGAAGGCACCAAAAGCAACAGCAACAAAACCAAAAATTGACAAATTAGAC 1972
                          - v i           vv          vv      v  i     i   
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_187027793_   1973 CTAACTAAA--CAAAAGCTTCTGCACAACAAAAGA-ACT-TCAACAGAGT 2018
                         i v ii   --i    i   i  ii vv    i  -   -    v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_187027793_   2019 CAACAGAAAACCTGTAGAATGGGAGAAAATATTTGCAAACTATGCATCTG 2068
                         v  v   v    iii                        ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_187027793_   2069 ACAAAGG--TAGAATATACAGAATCTATAAGAAACTT----AATTCAACA 2112
                          i  i  -- v --   v      v     ii    i----  i    i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTG--TATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_187027793_   2113 AGCAAAAAAAACCCAGCCTCATTAAAAAGTGGGCAAAGGACAGAAACAGA 2162
                          vv    i v vvi i  iv   ?    i           ivvi  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_187027793_   2163 CACTTTTCAAGAGAAGACATATATGTACATGGATGACAAGCATATGAAAA 2212
                           i  i  v i      i   i --- -    vii i     i       
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACA---A-ATGGCCAATAAGCACATGAAAA 886

  chr2_187027793_   2213 AAATGCTTAATATTATTAATCAT 2235
                         i -    i  i  i ????????
  L1M4_orf2#LINE/    887 GA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (132 / 72)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 3.65 (113 / 31)  


2556 26.50 0.28 0.28  chr2_187092009_187093901.rev      700  1401 (491)    L1M4_orf2#LINE/L1      207   908 (0)  

  chr2_187092009_    700 TGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAA 749
                               vv       v  ii i      viv        i          
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_187092009_    750 CCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAAC 799
                         i   i    ii         i iv ii i   v                i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_187092009_    800 AGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTATCTGATC 847
                             i--    i  --        vv  ii i  i  iiiii vi    i
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_187092009_    848 TTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAA 897
                           i     ivv  vv  i v  vv            i  vvi  v  i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_187092009_    898 TAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGG 947
                         i              v      v  ?   i   i i  iiv    ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_187092009_    948 ATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGAC 997
                          i    v   i     v           i  i    i      i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_187092009_    998 TTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCAT 1047
                         i    i  v   v       i      vi i           v    ?i 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_187092009_   1048 TACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAA 1097
                         v viv   iv   v v  vv i     v ii   v ivv  vi       
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_187092009_   1098 AAGCAATGGCAACGAAAGACAAAATTGACAAATGGGATCTAATTTAACTA 1147
                              vvi     i     v     v  i    v   ii v  iv  v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_187092009_   1148 AAGAGCTTCTGCAGAGCAAAAGAAACTACCATCAGAGTGGACAGGCAACC 1197
                           i i   i  iivvv    i  v    i  vv i    i v  i     
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_187092009_   1198 TACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAA 1247
                         i   i             v  i    vii ivi      i  i  i  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_187092009_   1248 TATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAAC 1297
                                   v  i  v      vv    v iv i  v     i     i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_187092009_   1298 AACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGA 1347
                              v  i?    i           iv    i     i     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_187092009_   1348 AGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCCCTGG 1397
                            i  vi viii     v  i          i       v    v????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_187092009_   1398 CCAT 1401
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.36 (105 / 77)
Gap_init rate = 0.00 (2 / 702), avg. gap size = 2.00 (4 / 2)  


 485 22.08 4.55 3.90  chr2_187217145_187219877.rev     1214  1367 (1366)    L1M4_orf2#LINE/L1        1   155 (753)  

  chr2_187217145_   1214 TGGAGAGACATCC-ATGCACGTGGATTGAAAAACTTTAATTTTGTTAAAA 1262
                             i   i    -   iv i       i  i    -   v       i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTT-AATATTGTTAAGA 49

  chr2_187217145_   1263 TGTCCATACTATCCAAAGCCATTTACAGATTCAATGCAGTATTTATCATA 1312
                           v v     vi     viv  i           i   i vii     v 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_187217145_   1313 ATCCCAGTGGCAAGTTGGGTGTTGTAGCATTTGCC---TTAGTCCTAAA- 1358
                                iv  v--  --- v   i  v v   v ---i ii       -
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC--TT---TTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_187217145_   1359 TTC-T-TGGAA 1367
                            - -     
  L1M4_orf2#LINE/    145 TTCATATGGAA 155

Transitions / transversions = 1.27 (19 / 15)
Gap_init rate = 0.05 (8 / 155), avg. gap size = 1.62 (13 / 8)  

3630 18.79 2.65 0.25  chr2_187217145_187219877.rev     1449  2241 (492)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr2_187217145_   1449 AAAATCCCAAAGGAATATTTTTGAAGAAACAGAAAAAAAAAATCTTAAAA 1498
                                  ivv vv -      v     iv  v  ivvi -  i     
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGA-TCCTAAAA 144

  chr2_187217145_   1499 TTCATATGGAATCTCAAGGGACCCCAAATAGCCAAAATAATCTTGAAAAA 1548
                                    viv          vi           i            
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_187217145_   1549 GAA---CAAATTTGGAGGA-TCCCACTTCCAGATTTTAAAACCTACTTCA 1594
                            ---    v        -  v       vi    i     i    v  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_187217145_   1595 AAGCAACAGTAATCAAGATGATGTGGTACTGGCATAA--ACAGATATATA 1642
                             v             iii                -- i   i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_187217145_   1643 GACCAATGGAACATAAT----AGCCCAGAAATAAACCCTTGTGTATATGG 1688
                           i        i v   ----  i              v iii v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_187217145_   1689 CCAAATGATTTTTGACAACGGTGCCAAGACTACATAATGGGGAAAGGACA 1738
                         i   v       i     v           i ivi           i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_187217145_   1739 GTCTCTTCAACAAATGGTGTTGGGAGGACTGGATAACCATATGCAAA-GA 1787
                             i              i     vi        ?   i       -  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_187217145_   1788 ATGAAGTTGGACCCTTACCTTACACTATATGCAAAAATTAATTCAAAAGC 1837
                                       i     i    i    i          i      vv
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_187217145_   1838 GATTAAAGACCTACAT--AAGACCTAAAACTATACAACTCCTAGAAGAAA 1885
                            i ?       v  --    v           v     i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_187217145_   1886 ACATAGGTGAGAAGCTTCAGGACACTGGATTTGGCAAAGATTTCTTGGAT 1935
                                ? vi  v    iv   vi   i  v     v i      i   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_187217145_   1936 ATGACATCCAAAGCATACATAAAAAAACCAAAAACAGACAAATGTGTCTA 1985
                               i v      i vii  v    vv     i   i    vv v  v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_187217145_   1986 TATCAAATGTAAAAAAATT-GTGCATCAAAGGAAATAACTGAGA--GCAA 2032
                         i      vv      vv  -    v        v iv iii   -- ii 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_187217145_   2033 AAAGGCAAGCTATGGAATGGGAGAAAATATT-GCAAATCATATATTGGAT 2081
                             i   v i ii                 -             iv   
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_187217145_   2082 AATGGGCTGATATACAGAAAATAAAAGGAATGTTTACAACTCAACAACAA 2131
                           v  i  vi   v     v   v  i   ivi           i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_187217145_   2132 AAAC-CAAATAACTCAATTAAAACATGGGCAAAAGACTTGAATAGGCAAT 2180
                            v-        i     ?   v         i  i        i  v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_187217145_   2181 TCTCTAAAGA---TATATAAATGACCAACAAGCATATGAAAATATGCTTG 2227
                             i     ---    i     i    i     i       v     ii
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_187217145_   2228 ACATCACTAATTGA 2241
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (82 / 63)
Gap_init rate = 0.02 (13 / 812), avg. gap size = 1.77 (23 / 13)  


4102 17.51 5.41 1.04  chr2_187362418_187365725.rev     1949  2816 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_187362418_   1949 GAAAGACATACCATGTTCATGAACTGAACTATGTAAT---GTTAAGATAG 1995
                               i  v           i i  i vv iv    ---        i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_187362418_   1996 CAATACTCCCTAGGTTG---------CTCAAGAAAATTGCTACCAAAATT 2036
                                   i ii   ---------i    viv   iv   i      i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_187362418_   2037 CCAACTACCTTGTCTGCAGAAATGGACAAGCTGATCCTAAAATCCACATG 2086
                            i  i    v i         v                   i  i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_187362418_   2087 GAATCGCAAGGGACTC----TAACCAAAATAATCTT--AAAAG--GAATA 2128
                            vi         i ----  i      i      --     --   i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_187362418_   2129 AAAT----GTATTCATATTTCCCTATTTCAAAACCTGAACTCCAGAGCTA 2174
                           i ---- v i   i i     v          i --   v  i     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT--ACTACAAAGCTA 250

  chr2_187362418_   2175 TGGTAATCAAAACAATTTGTTACTTGTATTAAGGATATACATATAGGTCA 2224
                         ii        i   i v  v    v i  -       v        i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATCA 299

  chr2_187362418_   2225 ACTGAATAGAACTGAATGTCTAGAAATAAATCCATATATTTATAATCAAT 2274
                          iv        i   iv   i         i     i      ii     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_187362418_   2275 TCATCTCCAACAAGACTGCCAAGACCATTTAA-GGGGAAAGAATAATTTC 2323
                          v  i i i     iv             i  -            i i i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_187362418_   2324 TTCAACAAATGTTGCTCAGACAGGTGGATAGCCACACACAAAAGAATCAA 2373
                                    v    vi    iv      ?     ii         v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_187362418_   2374 TCTGGACCCCTACCTCACACCATACACATAAATTAACCCAAAATGAATCA 2423
                         vi                      i   v        i       i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_187362418_   2424 GGGATGTAAATGTAAGAGCTGTAAGTGTAAAACTTATAAAACCAAAAAGC 2473
                         ?i  iv              iv  v i       iv  i  ---i   i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA---GAAAAC 546

  chr2_187362418_   2474 CTAGGTATGAATCTTCATGACCTTGTATTGGGCAATGGTTTTAAAAATAT 2523
                         v    ?i i       i        vi  i           ivv i    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_187362418_   2524 GATGACAAAATTACAAGCAACAAAAGAAGACATAGATAAATTGAACTTCA 2573
                           iiv     vi                i v            i      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_187362418_   2574 ---GATTTAAAAATTTTTGTGCATTAAAGGACACCATCAAGAAAGTAAAA 2620
                         ---i v       i        v i         i           i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_187362418_   2621 AGACAGTTCACACAGAATGAGACAAAACCTGTGCAA-TCATATATCTAAT 2669
                              i-- v         i  v    iv v     -          i  
  L1M4_orf2#LINE/    697 AGACAA--CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_187362418_   2670 GAAGG--TAGTATCCAGAATATATAAATAACTCTTTGCAACTCAACAATA 2717
                         i i  -- v                  v       -i        i    
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTT-ACAACTCAATAATA 793

  chr2_187362418_   2718 AAAGG-CAAATAACCCAATTTAAAAATGGGCAAAAAATTTGAATAGACAT 2766
                            i -              ?             ii              
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_187362418_   2767 TTGTCTAAAAAAGATACACAA----C-----------TGAAAAGATGCTG 2801
                           v  i   i      i    ---- -----------            v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_187362418_   2802 AATATCATCAGTCTA 2816
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (100 / 48)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 3.11 (56 / 18)  


3172 24.42 1.17 1.40  chr2_187389111_187390962.rev      505  1360 (492)    L1M4_orf2#LINE/L1       55   908 (0)  

  chr2_187389111_    505 ATACTACCCGAAGCAGTTTACAGATTCAATGGAATCTCTATCAAAATACC 554
                              v   i  viii i           i v    i          v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_187389111_    555 AATGGCATACTTCACAGAAATAGAAAAA--AATAACCTAAAATTTACATG 602
                          iiv  v vi  ii       v  v  i--i  --         i i   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT--CCTAAAATTCATATG 152

  chr2_187389111_    603 GAACCACAAAAGGCTCCAAATAGCCAAAGCCACCCTGAGCTAAAAAAAAA 652
                            vii   ii i i vi          i v i i   ------    i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------AAAAGA 196

  chr2_187389111_    653 ACAACAAAATTGGAGAAATCAAATTACCTGACTTGACATTATACTGCAGA 702
                          v      i      i v   v i v  ii i  v v viv    i  i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_187389111_    703 GCCATAGTAACCAAAACAGCATTGTAACTGGCATAAAAACAGACAAAGAG 752
                           i i     i   i    ii v   -         ii i     v v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTA-CTGGCATAAGGATAGACATATAG 295

  chr2_187389111_    753 ACCAATGGAACAGAATAGAGAACCCAAAAATAAATCTATTCATCTACAGT 802
                          i        i     v    ii   i       i i  v   i  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_187389111_    803 GAACTCATTTTCAACCAAGTTGCCAAGAACATACATTAGGGGAAGGACAG 852
                         v  i v      i  v i v        v   v  v i   i   i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_187389111_    853 TCTATTCAATAAATAGTGCTGGGAAAACTGGATATCCTTATGCAGAAGAA 902
                            v     i    i         v         ?  vi     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_187389111_    903 TAAAACTAGACCCCTATCCCTCACCATATACAAAAATCAAATCAAAATGG 952
                          i  ii i        i i v                i  v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_187389111_    953 ATTAAAGATTTAAATCTAAGACCTCAAACTATGAAACTACCACAAAAAAA 1002
                           i ?   ii     v     v  v       i     vii v  i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_187389111_   1003 CACTGGGG-AAATTTTCCAGGACATTGGTCTGCACAAAGATTTATTGAGT 1051
                           iv  ? -    i   -iv   v    vi ivi   v i   v  iii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_187389111_   1052 AATACCCTACAAGCACAGGCAACCAAAGCAAAAATGGTTAAATGGGATCA 1101
                          vv  v i v       i     v    v      i v     v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_187389111_   1102 CATCAAAAGCA------TCTGCAGAGCAAAGGAAACAATCAACAAAGTGA 1145
                                 vi ------ i  iivvv       v  v     v       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_187389111_   1146 AGAGATAACCCATAGAATGGGAGAAAGTATCTGCCAACTATCCATCTGAC 1195
                          i   i      i             i   i   v  ii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_187389111_   1196 AAGGGATTAATAACCAGAATATATAAGGAACTCAAACAATTCAATAGGCA 1245
                               i vi  v             i      vv    i      i-i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TA 793

  chr2_187389111_   1246 AAAAAACCCAATAATCCTATTTAAAAGTAGGCAAAAGATCTGCATAGATA 1295
                             i  v-     i  v   ?    i i      i   i  v     i 
  L1M4_orf2#LINE/    794 AAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_187389111_   1296 TTTCTCAAAAGAAAACACACAAATGGCAAACAGGTATATGAAAAGGT-CT 1344
                               v      i i i         v  i i i i        i -  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_187389111_   1345 CAACATCACTGATCAT 1360
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (129 / 76)
Gap_init rate = 0.01 (10 / 854), avg. gap size = 2.20 (22 / 10)  


3004 25.40 4.35 0.46  chr2_187464090_187468462     3010  3883 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_187464090_   3010 TGGAAAGATATCT-ATGTACAGGGATTCGGAA-----AATATTGTTATAA 3053
                                     i-    v  v     -    -----          vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT-GGAAGACTTAATATTGTTAAGA 49

  chr2_187464090_   3054 TGTCTATATCACCCAAAGAAATCTACAAATTCAATACAATCCTTATCAAA 3103
                           v v   iiv      vvi       i      ii      i       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_187464090_   3104 ATTCCAATAACATTTTTTACCAAAATTT-TAAA--AATTCTAAAATTTGT 3150
                           i   iivi v      i vi     v-i  i--i  i        ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_187464090_   3151 AAAGAAGCACAAAAGACCCTGAATAGCCAAAGCAATTCTGAGCAAAAA-- 3198
                          vi   iii   ii     v           i    ii   iv  i  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_187464090_   3199 -CAAAGCTGAAGC-CACATACTACCCAACTTCAAAATATACTGCAAAGCT 3246
                         -     i  i  v- v  i   v     i       iv    i       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_187464090_   3247 GTGGTAATCAATAGAGCATGGTGCCAGCATAA------ATACACAGACAA 3290
                         iii        v v  ii    i ii      ------ i i i   iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_187464090_   3291 ATGGAAAAAAAATGAAAAGTTCAGAGATAAATCCA-ATATTTACAGTCAA 3339
                               v i  v   i -  i    i     i   - i     ii     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGA-GTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_187464090_   3340 CTGATTTTTTACAAAGGCACCAAGAATAAACAGTGAGGAAAGA-CAGTTT 3388
                         i       iv    i  ii      vi vv  i  i       -i   i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_187464090_   3389 CTTCAGTAAGTGGTGTTGGGACTACTGGATAGAAACATGCAGAAGAATAA 3438
                         i    ii  i     i      v        ?vv       i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_187464090_   3439 AATTAGATGC-TATTTTATATCAGA---AAAAATTAACTCAAGATTAATT 3484
                          i  i  iv -  ii i i i  v ---              i  vi  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_187464090_   3485 AAAGACTTAAATGTAAGATCTGCAACTGTAAAATTACTAGAGGAAAATAT 3534
                          ?    i           v  iv    i     i vi    i     i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_187464090_   3535 AGGAGAAAAACTCTATGACATTGGTCTTGGCAATGATTTTTTGGAT--GA 3582
                            ? v   v  iii    v    vi v       i   i  i   --  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_187464090_   3583 CTCCAAAAGCACAGGCATCAATAGCAAAAATAGACAAATGGGATTGCATC 3632
                          v           i   v   v  v         i    v   i v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_187464090_   3633 AAACTAAAAGGCTTCTA------ACAGTAAGCAATCAACACAGTAAAGAA 3676
                            v v   ii   i i------ v  v vi v     v v   i  i i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_187464090_   3677 ATAACTTATGTTAATGGG-GAAAATATTTGCAAACCACACATCTTACAAG 3725
                          i   ii iiv-      -               i  i i    v i   
  L1M4_orf2#LINE/    699 ACAACCCACAG-AATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_187464090_   3726 GGGTTAATATCTA-AATACATAAGGGATACAAAGAACTCAATAGTGAGTA 3774
                           ii vi    i -    i    i i iv vv v         i i iv 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_187464090_   3775 AACAAATAACCAGATTTGAAAACTGGGCAAATGACCTGAAGAGAAGTTTT 3824
                         i          vi   ?i    -        v  ii    v   vi   i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_187464090_   3825 TCTCAAGAAGACATACAA-TTGCCAAAAGGTATATAAAAA--TACTCAGC 3871
                           iv       i      - v     v i i i  i    -- i    i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_187464090_   3872 ATAAATAATCAT 3883
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (146 / 72)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.00 (42 / 21)  


2515 27.66 3.85 0.91  chr2_187479231_187481446      843  1724 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_187479231_    843 TGAAAAAACATTCTATGCTCACAGATAGAAAGAATCAACATTGTAAAAAT 892
                           i   i i  i i   i   ii   v i    v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_187479231_    893 GGCCATACTGCCCAAAGTAATTTATAGATTCAATTCTATTCCTATTAAAC 942
                            v     v      v i  i  i        iv v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_187479231_    943 TACCATTGAAATTCTTCACAGAATTAGAAAAAACT-ATTTTAAAATTCAT 991
                          v   vivivv  i  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_187479231_    992 ATGGAACAAAAAAAGAGCTCA-AATAGCTAAGGCAATCCTAAGCAAAAAG 1040
                               - viv  i ii i  -      i  ii     i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_187479231_   1041 AACAAAGCTGAAGGCGTTACACTACCTGACTTCAATCTATACTACAAGGC 1090
                                i  i   vv i     v  ii i     vviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_187479231_   1091 TACAGTTATCAAAACAGCATGGTAC------------AGACACACAGA-C 1127
                               v     i    ii      ------------     i i   - 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_187479231_   1128 ATTGGAACAGAATAGAGAACTCAGAAATAAGATCACACACCTACAACCAT 1177
                          v     i     v    iii         ivi  i   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_187479231_   1178 CTGATCTTCAATAAACCTGACAAAA--AATAGCAATGGGAAAAGGATTCT 1225
                         i    i   i i  ivv  v   i -- v --       i    i  vv 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATT--CAATGGGGAAAGAATAGT 396

  chr2_187479231_   1226 CTATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCAAATGCAGAAAATT 1275
                           v  i  i              v      v  ?   v     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_187479231_   1276 GAAACTGGACTCCTTCCTTACGCCTTATAAAAAAATTAACTGAAGAGGAA 1325
                            ii     i   v   i  i  v    v           v  i v i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_187479231_   1326 TTAAACACTTAAATGTAAAACCCCAAACTATAAAAACCCTAAAAGAAAAT 1375
                          i ? v  i         i v iv           vi i  i       i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_187479231_   1376 CTAGCAGTA--CCATTCAGGACACAGGCACGGGAAAAGATTTCAT-GATG 1422
                         v   v?   --i -   iv   viv  vvii  v  v i    v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr2_187479231_   1423 AAAATGCCGAAAGTAATTGTGCCAAAAATCAAAATTGACAAAT-GAATTA 1471
                          vi ii  i    i vvv iiv     ivv     v  i    - i i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_187479231_   1472 TAGTTAAACTAAAGAGCTACTGCACAGCGAAAGAAACTATCATTAGAGTG 1521
                         i viv   i    i -  vi  ii vv i  i  v       vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_187479231_   1522 AACAAAAAAATCTACAGAATGGGAGAAAAATTTTGCAATCTGTTCATCTG 1571
                           -  i v  i i                vv       viii vi     
  L1M4_orf2#LINE/    694 AA-AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_187479231_   1572 ACAAAGGTCTAATATCCAGGTTTTACAAGAAATT--TA-AATTTA-TAAG 1617
                          i  i  v  vi       iv v  i  ii  i --  -  i i -   v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_187479231_   1618 AAAAA--------ACCCCATTAAAAAGTGGGCAAAGGAAT-AAATAGACC 1658
                              --------    v   ?    i           v -i       v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_187479231_   1659 CTTCTCAAAAGAAGACATTCGTGTGGCCAATAAACAGATGAAAAAAAGCT 1708
                         i     v        i  v ivi          i  v       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_187479231_   1709 AAACATCACTGATCAT 1724
                         v       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.10 (42 / 20)  


2883 27.99 1.33 0.88  chr2_187482455_187489111     5262  6165 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_187482455_   5262 TGGAAAAACATTCCATGCTCATGGACAGGAAAAATCAGTAC-ATGAAAAC 5310
                               i i  i     i       iv    i v i i  i-i v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_187482455_   5311 GGCCATACTCTTCAAAGTAATTTACAGATTCAATGATGTCCCCATTAAGC 5360
                            v      ii    v i  i           i vvi    i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_187482455_   5361 TAACATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAACTTCAT 5409
                          vv  vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_187482455_   5410 ACAGAA-TGAAAAAAGAGCCCACA-TATCCAAGAAAATCCTACGAAAAAA 5457
                          ii   -  v  i-- ii    v -  v    i v    i ivi   i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_187482455_   5458 GAACAATGGTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5507
                               v v      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_187482455_   5508 CTGCAGTAACCGAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5557
                           i      i i i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_187482455_   5558 TGATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5607
                         ii      i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_187482455_   5608 TCTGATCTTTGATAAACCTGACAAAAACAAGCAATGGGGAAAGGATCCCC 5657
                         vi    i  i  i  ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_187482455_   5658 TATTTAATAAATAATGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5707
                          v  i  i    ii  i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_187482455_   5708 AAACTGG-CCCCTTCCTTACACCTTATACAAAAATTAACTCAATATGGAT 5756
                           ii   -     v   i     v                   v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_187482455_   5757 TAAATACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACT 5806
                         i ? v  i    ii     v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_187482455_   5807 TAGGCA-ACACCATTCAGGACATAGGCATGAGCAAAGACTTCATGACTAA 5855
                             ?i- v i -   iv   v v  vv ii    v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_187482455_   5856 AACACCAAA-GCAATGGCAACAAAAGCCAAAATTAACAAATGGAATCTAA 5904
                         i        -   vvi          vv     vi i    v i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_187482455_   5905 TTAAACTAAAGAGCTTCTGCACAGCAAAAGATACCATCAACAGAGTGAAC 5954
                          i   v v  i i   i  ii vv    i  i  i     v i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_187482455_   5955 AGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATTTGACAA 6004
                           i  i  i                 v       vii  vi  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_187482455_   6005 AGGGCTAATATCCAGAATCTACAAAGAACTTAATTA-AATTTACAACAA- 6052
                         i  i  vi          v  i        i--   -  i --   i  -
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTC--TTACAACT--CAATAAT 792

  chr2_187482455_   6053 AAAAAACCAAACCAC---ATCAAAAAGTGGGCAAATGATATGAACAGGCA 6099
                              iv    iv  ---  i?    i        v   v    i  i  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_187482455_   6100 CTTCTCAAAAGAAGACGTTTATACAGCTAACAAATATATGAAAAAAAGCT 6149
                         i     v        ii vi v ii  i  i  ii i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_187482455_   6150 CATCATCACTGGCCAT 6165
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (159 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.33 (20 / 15)  


2833 25.06 3.95 1.47  chr2_187490219_187495426.rev     3831  4716 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_187490219_   3831 TGGAAAAACATTTCATGTTCATGGATAGGAATAATTGACATCATTAAAAT 3880
                               i i  ii             v    v v  i i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_187490219_   3881 GGCCATGCTGCCCAAAGCAACGTACAGACCCAATGCTATTTCTATCAAAC 3930
                            v  i  v      vii iv      ii   i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_187490219_   3931 TACCAATGACATTCTTCACAGAATTAGAAAAACACTATTCTAAAATTTCA 3980
                          v   iivi v  i  ii     v v  v  i -iv  i        -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATT-CA 148

  chr2_187490219_   3981 TATGAAACCAATAAAAGAG-CCCA-AACAACCAAAACAATCCTAAGCAAA 4028
                             i  ---  iv   i -    -  i i           i i iv  i
  L1M4_orf2#LINE/    149 TATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_187490219_   4029 AAGAACAAAGCTAGAGGCATTACATTACCTGACTTTA-----TACTACAA 4073
                                   i i    vv i   i v  ii i  i -----        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_187490219_   4074 GGATACAGTAACCAA-ACGGCATGGTAGTGGCACAAAAATAGACACATAG 4122
                         i v        i   -  i ii     v     i  ii       i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_187490219_   4123 ACAAATGGAACAGAATGGAGAG-CCAGAAATAAAGCTACACAGCTA---- 4167
                          iv       i     v     -           v i i   vi  ----
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_187490219_   4168 CAACTTTGTGATTTTTGAAAAGTAGACAAAAAAAAACAAACAATTGGGAA 4217
                            i ----      i  v   vivi v  i v---  vv    v     
  L1M4_orf2#LINE/    346 CAATT----GATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAA 388

  chr2_187490219_   4218 AGGACTTCCTATTCAACAAATGGTGCTGGGATAACTGGCTAGCCATATGC 4267
                           i ivvi  v                    i      v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_187490219_   4268 ACAAGATTGAAACTGGACCCATTCTTTATACCATATACAAAAATCAACTC 4317
                          v    v    ii       v v i i i               i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_187490219_   4318 AAGATGAATTGAAGACTTAAATGTAAAACCTAAAACTTTAAAAATCCTTG 4367
                           i   i  ii?    i         i v        v     v  i v 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_187490219_   4368 AAGAAAGCCTAGGAAATATTATTCTAGACATAGGCCCTGGCAAAGATTTT 4417
                               i v    ?ivv v v   vv   v v  viiv     v i   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_187490219_   4418 GTTGCAAAAACTCCAAAAGCAATTGCTACAAAA--AAAAGTTGACAAATG 4465
                         v v vv vi  v         vvv  v      --    i v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_187490219_   4466 GAACCTAATTAAGCTAAAGAGCTTCAGCACAGCAAAAGAAACTATCAACA 4515
                          i  i v  i  iv v  i i   iv ii vv    i  v        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_187490219_   4516 GACTAAACAGACAATCCACAGAATTAGAGAAAGTATTTGCAAACCATGCA 4565
                         i v i  v      i         vi      i          i   ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_187490219_   4566 TCTGACAAAAGTCTAATATCCAGAATCTATAAGGAACT------------ 4603
                              i  ii v  vi          v     i     ------------
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_187490219_   4604 TAAGCAAAAAA-AAATA------TTAAAAAGGGGGCAAAGTATATGAACA 4646
                            vv    i -     ------  ?    iv        v  v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_187490219_   4647 GACACTTTTC-AAAGAAGATATACATGTGACCTAAAAGCATATGAAAAAA 4695
                             i  i  -              vi  i  v v     i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_187490219_   4696 ATGTTTATCATCACTAATCAT 4716
                         -  i i v     ????????
  L1M4_orf2#LINE/    889 -TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (124 / 94)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.82 (48 / 17)  


2865 26.16 3.23 0.48  chr2_187501508_187508256     5056  5892 (857)    L1M4_orf2#LINE/L1        1   860 (48)  

  chr2_187501508_   5056 TGGAAAAACATTCCATGCTCATGGACAGGAAGAATCAGTAC-GTGAAAAT 5104
                               i i  i     i       iv      v i i  i-  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_187501508_   5105 GGCCATACTGCCCAAACTAATTTACAGATTCAATGCTATCCCCATCAAGC 5154
                            v     v      i i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_187501508_   5155 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5203
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_187501508_   5204 ATGGAACCAAAAAAGAGCCCACACAGCCAAGAAAATCCTAAGCAAAAAGT 5253
                               viiv  ii  v  viv i      i v    i i iv  i   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_187501508_   5254 ACAAAGCTGGAGGCATCACACT----GACTTCAAACTATACTACAAGGCT 5299
                               i      vv       ----i i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_187501508_   5300 ACAGTAACCAAAACGGTATGGTACTGGTACCAAAACAGATATATAGACCA 5349
                                i   i  i  i         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_187501508_   5350 ATGGAACAGAACAGAG-GTCTCAGAAATAGCACCACACACCTACAACCAT 5398
                               i    iv   -   -        ivv   i   ii  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_187501508_   5399 CTGATCTTTGACAAACCTGACAAAAACAAGCAATAGGGAAAGGATCCCCT 5448
                         i    i  i     ivv  v   i v  vv    i       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_187501508_   5449 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5498
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_187501508_   5499 AACTAGACCCTT-CCTTACACCTTATACAAAAATTAACTTGATATGGATT 5547
                          ii i     i -   i     v                ii v      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_187501508_   5548 AAAGACTTAAACATAAGACATAAAACCATAGAAACTCT-AGAAGAAATCC 5596
                          ?    i    ii     vv      i   -       -        v v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACA 547

  chr2_187501508_   5597 TGGCAATA--CCATTCAGGACATAGGCATGAGCAAAGGCTTCATGACTAA 5644
                          i v?i  --i -   iv   v v  vv ii    v  i   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_187501508_   5645 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5694
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_187501508_   5695 TTAAACTAAAGAGCTTCTGCACAGCAAAAGATACTATCATCAGAGTGAA- 5743
                          i   v v  i i   i  ii vv    i  i       vv i      -
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_187501508_   5744 ----------CAGAATGGGAGAAAATTTTTGCAATCTATCCATCCGAGAA 5783
                         ----------                v       vii  vi   i  v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_187501508_   5784 GGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAGAA 5833
                            i  vi          v  i        ivv    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_187501508_   5834 AAACAA----CCCA-TCAAAAAGTGGGCAAAGGATATGAACGGGCACTTC 5878
                          i    ----    - i?    i            v    ii i  i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_187501508_   5879 TCAAAAGAATACAT 5892
                           v      v i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATAT 860

Transitions / transversions = 1.53 (130 / 85)
Gap_init rate = 0.02 (14 / 860), avg. gap size = 2.21 (31 / 14)  


3217 27.29 0.66 0.33  chr2_187586563_187593006.rev     5048  5952 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_187586563_   5048 TGGAAGAATATTCCATGCTCAGGGGTAGGAAGAATCAATGTCGTGAAAAT 5097
                              ii    i     i   v  i v      v i   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_187586563_   5098 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5147
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_187586563_   5148 TACCAATGACTTTCTTCACAGAATTGGAAAAAACCACTTTAAAGTTCATA 5197
                          v   iivi i  i  ii     v v  v  iviv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_187586563_   5198 TGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAGAA 5247
                              viiv  ii  v  v v  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_187586563_   5248 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5297
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_187586563_   5298 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGCTCAA 5347
                               i   i    ii         i iv ii i   v      v    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_187586563_   5348 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5397
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_187586563_   5398 GATCTTTGATAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 5447
                            i  i  i  ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_187586563_   5448 TTAATAAATGCTGCTGGGAAAACTGGCTATTCACATGTAGAAAGCTGAAA 5497
                          i  i     v        v      v  ?i      i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_187586563_   5498 CTGGATCCCTTCCTTACACCTTATACAAAAATTACTTCAAGATGGATTAA 5547
                         i    i    v   i     v             vi    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_187586563_   5548 AGACTTAAATGTTAAGCCTAAAAACCATAAAAACCCTAGAAGAAAACCTA 5597
                             i       v iiv      - i      vi i           v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACATA 549

  chr2_187586563_   5598 GGCA-ATACCATTCAGGACATATGCATGGGTAAGGACTTCATGACTAAAA 5646
                           ?i- v i -   iv   v vv vv i  i  v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_187586563_   5647 CACCAAAAGCAATAGCAACAAAAGCCAAAATAGACAAATGGGGTCTAATT 5696
                                    vv           vv        i    v  iii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_187586563_   5697 AAACTAAAGAGCTTCTGTACAGCAAAATAAATTACCATCAGAGTGAACAG 5746
                            v v  i i   i   i vv    iv v i  i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_187586563_   5747 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAG 5796
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_187586563_   5797 GGCTAATATCCAGAATCTACAAAGAACTCAAACAAATT-----TACAAAA 5841
                          i  vi          v  i         vv    v i-----  v   i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_187586563_   5842 ACAAACAACCCCATCAAAAAAATGGGCAAAGGATATGAACAGACGCTTCT 5891
                              i     v  i?     -            v    i    ii    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_187586563_   5892 CAAAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5941
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_187586563_   5942 TCACTGGCCAT 5952
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.80 (9 / 5)  


2138 27.91 1.73 0.86  chr2_187738833_187744033.rev     3503  4197 (1004)    L1M4_orf2#LINE/L1        1   701 (207)  

  chr2_187738833_   3503 TGGAAAAACATGCCATGTTCATAGATTGGAAAAATTAATAA-ATTAAAAT 3551
                               i i  v          i        i v      v-i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_187738833_   3552 GATCATACTGCCCAAGGCAATCCACAGATTCAATGCAATTTTTGT-AAAA 3600
                          iiv     v     ivii   i          i     iii i -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_187738833_   3601 TTACCAAGGT-CATTTATCACA-AAATTGGAAAACACAATTCTAAAATTC 3648
                          --  v  v - v   v ii  -      iv  i -ii  i         
  L1M4_orf2#LINE/    101 T--CCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTC 147

  chr2_187738833_   3649 ATTTGAAACCAAAAGAAGAGTGTGAATAGCCAAAGCAATCCTAAGCAAAA 3698
                           v  i  viiv   i-  vivv           i     i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_187738833_   3699 AGGACAAAGCCAGGGGCATCACATTACCTGACTTCCAACGCTACTACAAG 3748
                           i      iii i  vv     i v  ii i   v  vvi        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_187738833_   3749 GCTATAGTAACAAAAACAGCTTGGTACTAGTACAAAAATAGGCATATAGA 3798
                             i     iv  i    iv       i i i  ii    i        
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_187738833_   3799 TCAATAATATAGAATAAAGAACCCCAAAATAAAGCTAAATACCTACAATC 3848
                              iiv       vi   ii  vi       v i v i ii  iii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_187738833_   3849 GCCTTATCTTTGACAAAACTGACAAAAATAAATAATGGGGAAAAGGATAC 3898
                         ivi v  i  i     iiv  v   i vi vvi          - i   v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAG 395

  chr2_187738833_   3899 CCTATTCAATAAATGGTGCTGGGTAAACTGATTAGCCATATGCA---GAA 3945
                         i  v     i             vv     iv  ?   i     ---   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_187738833_   3946 TGAAACTGGATCCCTACCTCTAACCATATACAAAAATTCATGCAAAATGG 3995
                             ii    i         vv                v iv        
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_187738833_   3996 ATTAAAGACTTAAATTTAAGACCTGAAAATGTAAAAATTCTAGCATGAAA 4045
                           i ?    i     v     v  i   v i     v ii   v vi   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_187738833_   4046 CCTAAGAAAAACTCTTCTGGACATTGTCCTAGGCAAAGAATTTATGACTA 4095
                          v  i ?iv  v     vv   v   vvi       v iv  iv iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_187738833_   4096 AGACCATAAAAGCAAAGGCAACACAAACAAAAATAGACAAATAGGAGTTA 4145
                         v   vvi       v i      v  iv         i    v   v  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_187738833_   4146 ATTAAA-TTAAAGAGCTTCTGCACAGCATAAGAAATTATCAATA----GA 4190
                           i   -     i -   i  ii vv  v i  v i      v ----  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_187738833_   4191 AAAAACA 4197
                            i   
  L1M4_orf2#LINE/    695 AAAGACA 701

Transitions / transversions = 1.42 (112 / 79)
Gap_init rate = 0.02 (12 / 701), avg. gap size = 1.50 (18 / 12)  

 759 19.72 5.63 0.94  chr2_187738833_187744033.rev     4497  4709 (492)    L1M4_orf2#LINE/L1      686   908 (0)  

  chr2_187738833_   4497 AGAGAGAGAAAACAAACAACCTACAGAATGGGAGAAAACATTTGTAAATT 4546
                            i  v     --i      i                i     i    i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAA--GACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_187738833_   4547 ATGCATCCAACAAAAAACTAATATCCAAAATCGAGAAGGAACT--TAAAG 4594
                           ii   ii i  iii   vi      i   vv v  i     --  v i
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_187738833_   4595 C--------AACAAGAAAAATAACC--ATTAAAATATGGGCAAAGTACAT 4634
                          --------  v    v        --   ?   v          v iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_187738833_   4635 GAACAGACACTTCTCCAAAGAAGACATACACATGGCCAAAAAACTTATGA 4684
                            i     i              i     v        v  i vi    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_187738833_   4685 AAAAAAGTTCAACATCACTAATCAT 4709
                            i v i         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (26 / 15)
Gap_init rate = 0.02 (4 / 223), avg. gap size = 3.50 (14 / 4)  


2631 26.36 1.89 1.00  chr2_187959380_187961591.rev      822  1720 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_187959380_    822 GGAAA-ACATTCCATGCTCATGGGTTGGAAGAATTGATATCATTAAAATG 870
                              - i  i     i      i        v  i    ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_187959380_    871 ATAACACTGCCCAAAATAATCCACAGAGTCAACACAATCCCTATCAAATT 920
                         ii  i   v      v i   i     v     i              v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_187959380_    921 ACCAACATCATTTTTCATGGAATTAGAAAAAAACAG-TCCTAAAGTTCAT 969
                         v   i vv v     iiii   v v  v  i-- v -       i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCAT 149

  chr2_187959380_    970 ACAAAACCAAAAAAGAGCCCAAAGAGCCAAAGAATTACTAAACAAGAAAA 1019
                          iii  viiv  ii  v  vi  v       iv v vi i  v     i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_187959380_   1020 ACACATCCAGAGGCATCATATTGCCTGACTTCAAATTACACTACAAGGAT 1069
                            v viii    vv   i i v  ii i      vivi       i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_187959380_   1070 TTAGTAACTAAAACAATGTGGTACTGGTACAAAAAGAGACACATAGATCA 1119
                         vi     ii  i   i           i i  ii v     i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_187959380_   1120 GTGGAACAGAATAAAGAACCCAGAAATAAAGCCACATACCTACAACCAAC 1169
                         i     i     vi   ii           v   i i ii  iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_187959380_   1170 TGATCATCAGTAAAGTTGACAAAAATAACAAATTTGAAAAGGGCATCCTA 1219
                             iv  iii  i v  v   i vi viv   vv i    iii vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_187959380_   1220 TTCAAAAAATGTTGTTGGGAAAATTGGCTAGCCATATGCAGAAGAATGAA 1269
                              v     v  i     v  i   v  ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_187959380_   1270 AACCGACCCTTATCTCTCACATTATATAAAAATTAAGTCAATATGGATGA 1319
                         iviv     i  i   v   vv    i         v    v      v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_187959380_   1320 AAGACTTAAAAGTAAGACCTGAAGCTATACAAATTCT-AGAAGAAAGC-T 1367
                         ?    i    v      v  i  i     -   i   -        i - 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACAT 548

  chr2_187959380_   1368 AGAAAAAAACTCCTCTGGAGATTGGTCTAGGCAA--ATAACTTATGATGA 1415
                           i?iv   -  i  vv  vv    vi       --i vv    -   --
  L1M4_orf2#LINE/    549 AGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GAT-- 594

  chr2_187959380_   1416 AT-ACCCCAAAATCAAATGAAACAAAAATAAAAATAGACA--TGGGATTT 1462
                           -  v      v  v v v       iv         i -- v   i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_187959380_   1463 AATTAAACTAAAAGCCTTCTGTACAACAAAAGAAATAATCAACAGAGTAA 1512
                         v  i   v v   iv   i   i vv    i  v iv     v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_187959380_   1513 ACAGACAACCTACAGAATGGGAGAAA-TATTTGCAAATTATGCCTCTCAC 1561
                          v        i               -           i  iiv   v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_187959380_   1562 AAAGGACTAATATCCAGAATCTATAAGGAATTC--AAAATCTCAATAAGA 1609
                           i     vi          v     i   i  -- v  -        v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chr2_187959380_   1610 TACAAACAACAAACCCTATTAAAAACTAG-CAAAG-ACATGAACAGATAT 1657
                         v v i    vv     v   ?    v i -     - iv    i   i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_187959380_   1658 TTATCAAAAGAAGAAATAATAAGTGTAAAACAA--ACATAAAAAT-TGTT 1704
                           v  v        v   -i  i  vvv  i  --    i    v-  i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATA-CAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_187959380_   1705 CAACATCATTAAACAT 1720
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (130 / 103)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 1.30 (26 / 20)  


 551 32.66 1.01 0.00  chr2_187962208_187967557.rev        6   204 (5146)  C L1M4_orf2#LINE/L1   (707)   201     1  

C chr2_187962208_    204 TGGAAAAAGATTTGATGCTCATGTTTTAGAATAATTAATATCAATAAAAT 155
                               i v  iiv   i     vv  i   v v       iiv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_187962208_    154 GACCATATTGCCCAAAGCAATCTATGGATTTAATGCAATCTTTGTCAAAA 105
                          i v   i v      vii     ii    i  i      ii i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_187962208_    104 TACCAACATCATTCTTCACAAAATCAGAAAAA--AATCCTGAAATTCATA 57
                          v   i vv v  i  ii  i  viv  v  i--i     i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr2_187962208_     56 TCGAATCATAAAAGAGCCTGAATCATCAAAGCAGTTCTAAACAAAAATAA 7
                          v   viii  ii  v  v    vii    i  i ii i  v  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chr2_187962208_      6 C 6
                          
  L1M4_orf2#LINE/    201 C 201

Transitions / transversions = 1.71 (41 / 24)
Gap_init rate = 0.00 (1 / 201), avg. gap size = 2.00 (2 / 1)  

1805 27.15 4.59 0.19  chr2_187962208_187967557.rev     1719  2241 (3109)    L1M4_orf2#LINE/L1        1   546 (362)  

  chr2_187962208_   1719 TGGAAACACATTTCATTCTCATAGATAAAAAGAATCAGTATCATTAAAAT 1768
                               v i  ii   vi    i   vii    v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_187962208_   1769 GGCCATACTTCCCAAAGCAATGTACAGATTCAATGCTATACCTA-CAACA 1817
                            v     i      vii  v           i  v  v    -   - 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-A 99

  chr2_187962208_   1818 ATACTGATTACATTTTTCACA-AAATT------------CTAAAATGCAT 1854
                           v iiii i v     ii  -     ------------       v   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_187962208_   1855 ATAGAACCACAAAAGAGCCTGAATAGTCAAAGCAATTCTAAGCAAAAAGA 1904
                           i   vii   ii  v  v      i    i    ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_187962208_   1905 ACAAAGCTAAACCA-TCACATTACCTGATTTCAAGCTATAATAAAAGGAT 1953
                               i ii vv -     i v  ii       iviv  v  v  i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_187962208_   1954 AGAGAAACCAAAACAGCATGGTACTAGTACAAGAACAGACACATAGACCA 2003
                          v  v  i   i    ii       i i i   i i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_187962208_   2004 ATGGAATAGACTAGAGAAGCTAGAAATAATGCTGTACACCTACAGCTGTC 2053
                                   v v    iv i        vv ii    ii  ii iiivi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_187962208_   2054 TGATCTTTGACAAACCTGACAAAAATAAGCAATGGAGAAAGGACTCTGTA 2103
                             i  i     ivv  v   i vi vv      i     i ivv v v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_187962208_   2104 TTTAATAAATGGTGCTGCGATAACTGGCCAGTCATATGCAAAAGATTGAA 2153
                           i  i           v  i      vi ?i  i          v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_187962208_   2154 ACTGGACCCCTTCCTTATACCATATACAATAATTAACTCAAGATAGATTG 2203
                         ii         v   i i           v           i  i   ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_187962208_   2204 AAGACTTAAA-------GTTAAAACTA-AAAACCCTT-GAAGACAAC 2241
                         ?    i    ------- i        -     i   -     v   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

Transitions / transversions = 1.92 (92 / 48)
Gap_init rate = 0.01 (8 / 546), avg. gap size = 3.12 (25 / 8)  

 799 23.20 7.21 3.13  chr2_187962208_187967557.rev     2655  2973 (2377)    L1M4_orf2#LINE/L1      577   908 (0)  

  chr2_187962208_   2655 GGCAAAAATTTTAT-GATGAAGATACTAAA--CATAATTGCAACAAGAAA 2701
                              vii   iv -   - v  i  i   --  i  --       i i 
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAA--GCAACAAAAGA 623

  chr2_187962208_   2702 GAAAATTGACCAAT-G----TTACCTAAAT--AAAGTTTCCGCACATCAA 2744
                         i     v  iv   - ---- i i v    --   ii  ii ii v    
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_187962208_   2745 AATATAAACTATCAATAGAGTAAACAGACAACTTACAGAATGGGAGAAAA 2794
                          iv i --       v i   i  v       ii                
  L1M4_orf2#LINE/    674 AGGACA--CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_187962208_   2795 TATTTTGCAAACTGTGCATCTGACAAAGGTCTAATATCCAGAATGTATAA 2844
                              -     iii ii      i  i  v  vi          i     
  L1M4_orf2#LINE/    722 TATTT-GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_187962208_   2845 GGAACTTTAACAAAT---TTACAAGCAGA-AAACAACCCCTTTATTAAAA 2890
                         i     i v    v --- v i  iv   -   i     v---   ?   
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA---ATTWAAA 817

  chr2_187962208_   2891 AA---AAAAAGGACATGAACAGACACTTCTCAAGAGAAGGCA--CATGTG 2935
                           ---iv      iv    i     i     v i     ii --  vi  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_187962208_   2936 GCCAAAATGCATTATGAG----TGCTCAGCATTACTAATCAT 2973
                              v v   i-    i----      i   i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCAC-ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (50 / 23)
Gap_init rate = 0.05 (16 / 332), avg. gap size = 2.06 (33 / 16)  

3030 23.78 5.92 0.58  chr2_187962208_187967557.rev     3997  4858 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_187962208_   3997 TGGAAGGACATACTGTGTTTGTGGCTTGGAAGATTTAATATTGCTAAAAT 4046
                              i  i  v ii    ii   v        i         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_187962208_   4047 GTTCTTATTACATAAAGCAATGTACAATGTCAATGCAACCCCTATCAAAA 4096
                          vivv  i v vi   vii  v    ivv    i    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_187962208_   4097 TCTCAGTGACTTTTTGTTCAGAAATAGAAAAAA-AATACTAAATTTAATA 4145
                           i   ivi i    v v       v  v  iv-i  v     v  v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_187962208_   4146 TGGAAA--CAAAGAATCCCATAGAGCCAAAACAATCTTGAGAAAGAA--- 4190
                               --   i i i  viv v                 i      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_187962208_   4191 CAATCCTGGACGCCCCACACTTCTGAAATTCAATACATATGACAAGACTA 4240
                            vvi    v v i        iv  v     v  v  iv    ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_187962208_   4241 TAGTAATCAAGAGAATA--GTACTGGCATAAAGATAGACATGTAATCCAA 4288
                         i           v i i--            i         i  ivi   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_187962208_   4289 TCAAATAGAATAGAGAGCCCAGAAATAAACCCACACATGTATAGTCAAAT 4338
                          vi        v     i               i    v   i     v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_187962208_   4339 GATCTCCAACAAAGATACCAAGAATACACAATGGGGAAAGGATAGTCTTT 4388
                            i i i    i i i      vi iv            i         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_187962208_   4389 TCCATAAATAGATTTGGTAAAGTTGAATATCTACATGCAAAA--ATAAAA 4436
                           v i    i vvi   v v ii  i   ? i          --  i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_187962208_   4437 ATGGAATTTTATCGTATGCTATATGCAAAAATCAAGTCTAAGTGGATTAA 4486
                         v    viii  i vi ii i    i       i  v  v  i     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_187962208_   4487 AGAC------ATAAGACCTAAAGCCATAAAACTCCTAAAAGAACACATGA 4530
                             ------i     v     i i         i  i     v    ii
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_187962208_   4531 AGGCAAATCTTTATAACACTATATT-GGCATCAAAAAGTT----GGATAT 4575
                         i? i       ii i  vi ivi  -    ---- vi   ----i     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCA----ATGGTTTCTTAGATAT 596

  chr2_187962208_   4576 AACATCAAAACCACAAGCAACAAACACAAAAATAGACAATTTGGAATATG 4625
                         i   i     v             viv         i  v     v vii
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_187962208_   4626 TCAAT-CTAAAAGTTTATGTGCAACAAAGGAAACAATCAACAGAGTGAAA 4674
                             v-i     ii  v     vv       v  v     v i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_187962208_   4675 AGGCAACCTACAGAATGAGAGAAGATATTTCTAAA--------CTGTATA 4716
                           i     i        i     i      vi   --------   -   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG-ATA 745

  chr2_187962208_   4717 AGTGGTTAATATCCAAAATATACAAGAAAACCATAAAACTTAAT--TAAA 4764
                           v ii vi      i      i  ii  vi v  v    i   --    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_187962208_   4765 AATATA-------CAA------AAT-----AAGTATATGAATAGACATTT 4796
                           v i -------   ------   -----   v  v             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_187962208_   4797 CTTCAAAGAAGACATACAAATGGC-AACATGTATATGAAAAGATTCTCAA 4845
                           i         i           -  i v i i          v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_187962208_   4846 TATCACTTATCAA 4858
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (123 / 79)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.29 (56 / 17)  


2900 23.23 1.83 4.52  chr2_187971235_187974090.rev     1435  2364 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_187971235_   1435 AAAGATATTCCATGTTCATGGATTGGAAGATTCAATATCATCAAAATGTC 1484
                                 i                     i i     ii i  i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_187971235_   1485 CATACTACCCAAAGTAATCTACAGTTTCAGTATAATCCTTATCAAAATAC 1534
                         v     v      v i        v    iiii     i         v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_187971235_   1535 CAAGGACATTCTTCACAGAAATTCAAAAAAAAATCCTAAAATTTATATGT 1584
                           ivvi v  i  ii        v v  ivvi           i     v
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_187971235_   1585 AATAT-CAAAAGACCCAGAATAACCAAAGCTATTTTGAGCAAAAGGAACA 1633
                           -  -   ii           i     i v  i    iv  i i     
  L1M4_orf2#LINE/    154 AA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_187971235_   1634 AAGCTGGATGAATCACATTACCTGACTTCAAATCTGGTGCTACAGCAACC 1683
                            i    v  v     i v  ii i      v  -- i     i- i i
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACT--TACTACAA-AGCT 249

  chr2_187971235_   1684 AGAACAGGAGGGTATTGGCATAAAAACAGTTACACG-GGTACCAGCATGA 1732
                          ---   -----  -----  v  i     ----- -     ii    i 
  L1M4_orf2#LINE/    250 A---CAG-----TA-----ATCAAGACAGT-----GTGGTACTGGCATAA 281

  chr2_187971235_   1733 AAATTAAAAACACACCAAAAAATAATATAAAAAACCAAAGAAATAGAATG 1782
                         ii  --- i   -------------    i ---i   v i        v
  L1M4_orf2#LINE/    282 GGAT---AGACA-------------TATAGA---TCAATGGAATAGAATT 312

  chr2_187971235_   1783 GAAAACCCATAAACAAATCCATACAGCTACAGTGAACTCATATTTAACAA 1832
                           i ii   v   i   i       vi  ii  v  i v  v  ii    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_187971235_   1833 TGGTGCCAAGAATATACATTGAAGAAAAGATAGTCTCTTCAATAAATGGT 1882
                         v          vi  v  v  ii    ii       i     i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_187971235_   1883 ACTGAGAAAACTAGATATCAATATGTAGAAGAATTAAACTTGACCCCACT 1932
                         i   i  v    i    ? v i   i i      v  ii v      vvi
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_187971235_   1933 CTTTCACCATATACAAAAATCATATTAAAATGGATTAAAGATGTAAATAT 1982
                           iv                i vv i         i ?   iv     i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_187971235_   1983 AAGATCTCACATTATAAAACTACTATAAGAAAACATTGGGGAAAATCTCT 2032
                             v  v v i         vi  v          v  ? v      ii
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_187971235_   2033 AGCACATTGGTCTGGGCAAAAATTTCCTGAATAATACCCCACAAGCACAG 2082
                         ivv  v    vi i     vii    i ii   vv  v   v       i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_187971235_   2083 GGAACCAAAGCAAAAATGGAAAAATGAGATCACA-CTAAGTTAAAAA--- 2128
                          v   v    v      i  v    vi  iiv  - v  i       ---
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_187971235_   2129 ----GCTTCT--GGACAGCA--AAGGAAGTGAAGAGACAACCCATAAAAT 2170
                         ----     v--     vi --   i       i          i i   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_187971235_   2171 GGGAGAAAAAAATTTCAAACTACCCATCTGACAAGGGACTAGTA-ACAGA 2219
                                  v v  v    ii ivi      i        v   -v    
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_187971235_   2220 ATACA-AAAGAAGCACAAACAACTCTATAGGTAAAAATCTAATATTCCAA 2268
                            i -      - v vv       v   ivv    iv v    vi    
  L1M4_orf2#LINE/    763 ATATATAAAGAA-CTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_187971235_   2269 TC-AAAAATGGGCAAAAAAAGTGAATAGGCATTTGTCAAATGAAGACATA 2317
                          i-             ii vv       i     v  v  v     i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_187971235_   2318 CACATGACAAACAGGCACATGAAATGATGCTCAAAGTCACTGAACAC 2364
                           v   i v  i i          v         vi   ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (122 / 91)
Gap_init rate = 0.02 (20 / 905), avg. gap size = 2.95 (59 / 20)  


2461 16.88 5.29 10.58  chr2_188030702_188032476      501  1294 (481)    L1M4_orf2#LINE/L1      157   908 (0)  

  chr2_188030702_    501 TGCAAGAGATCCAGAATAGCAAAAACAATTGTGAAAAAGAAGAATAAAAC 550
                               i  i          v        iv             i   ii
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_188030702_    551 ---AGAATTCATACTTTCTGATTTCAAA-CTCACTACAAA-CAAAGGTAA 595
                         ---  i i   i    i ii        -  i        - v vi    
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_188030702_    596 TAATGACAGTGTGGTTTGAGCACAAGGACAGACATATATATATATATATA 645
                          v v           vivi   i     i         v  vv  iv --
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA-- 304

  chr2_188030702_    646 TATATATATATATATATATATATATATATATATATATATATATATGAAAT 695
                         -----------------------------------   v -  -   ---
  L1M4_orf2#LINE/    305 -----------------------------------ATAGA-AT-TGA--- 314

  chr2_188030702_    696 AGAATTTTAAAATAAACCCATGAATCTATGGCTGATTGCTTTTTGATAAG 745
                         -  i iivi            iv  i     iii    v    i  i   
  L1M4_orf2#LINE/    315 -GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_188030702_    746 GATGCCAAGACCTTTCAATGGGGAAA--ATGGTCTTTTCAACAAATGATC 793
                          i          v             --  i                i v
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_188030702_    794 CTAGAACAA----ATAGCCACATTCAAAAATATATGAAGCTAGACCCTTA 839
                           i i    ----   ?      v     i- -      i i     i  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAG-A-ATGAAGTTGGACCCCTA 461

  chr2_188030702_    840 CCTCACACCACATACAAAAATTAACTCAAAATGGATCAATGACCTATAAT 889
                                   i                           ?v      -   
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA-AAT 510

  chr2_188030702_    890 TT------T----CTATAAATTTCTTAGAAGATTTTATAGGAGTAAATCT 929
                         v ------ ----       vi          vvvi     ?        
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_188030702_    930 TCATGATTTTGAATTTGGCTAAGGATTCTTAGATGTGACACTAAAAGCAT 979
                           i   ii   ii  v   v v  v         i      i       i
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_188030702_    980 GACCAACAAAAGAAAAAA---AT-----GTACTTAATAAATAATTGTTAC 1021
                         i v               ---  ----- v    v  v  -    ivv v
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA-AATTAAAAA 659

  chr2_188030702_   1022 CTTTTATGCATCAAAGGACACAATTAAGAAAGGGACAAGACAATTCACAG 1071
                              i   v           v  i       v  v       ii     
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_188030702_   1072 AATGGGAGAAAGTATTTGCAAAT----TATCTGAAAAGAGACCTATACAT 1117
                                    i           ----       v   i   i i  ---
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA--- 756

  chr2_188030702_   1118 ATATATTTGCAGATGTGAGTGTGTGAGACTATATATATATACATATTGAT 1167
                         ------- v    -------------------       v v - i vv 
  L1M4_orf2#LINE/    757 -------TCCAGA-------------------ATATATAAAGA-ACTCTT 779

  chr2_188030702_   1168 ATATATATATATCAATAATAAAAAGACAA-----CCAAATTAATAATGGA 1212
                          i ----- i-                  -----    v ?  v     i
  L1M4_orf2#LINE/    780 ACA-----AC-TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_188030702_   1213 CCAATAATCTGAATAAATATTCCTCCAAAAAAGAT-TACACATGGCCAAT 1261
                          v  vi  i      i i   i       i     -    v         
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_188030702_   1262 AGATGCTTGACA---TCTTTAACCATCAGAGAAATG 1294
                          iiii v   v --- vi i   -    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (76 / 54)
Gap_init rate = 0.04 (27 / 752), avg. gap size = 4.67 (126 / 27)  


2753 28.27 0.99 1.10  chr2_188045405_188047645      843  1751 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_188045405_    843 TGAAAAAACATTCCATGCTCATACAT-AGAAGAATCAATATCGTGAAAAT 891
                           i   i i  i     i    iv  -i     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188045405_    892 GGCCATACTACCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 941
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_188045405_    942 TACTATTGACTTTCTTCACAGAA-TTAGGAAAAACT-ACTTTACGTTTCA 989
                          v i vivi i  i  ii     -  --  v  i  - iii  viv    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chr2_188045405_    990 TATGGAACCAAAAAAAGAGCCTGTATAGCCAAGACTAAGCAATCCTAAAC 1039
                                viiv  ii-  v  v v        i  -----    i i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAAC-----AATCTTGAAA 192

  chr2_188045405_   1040 AAAAAGAACAAAGCTGGAGGCGTCACGCTACCTGACTTCAAACCATACTA 1089
                           i          i      vv    i  v  ii i      v v     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_188045405_   1090 CAAGGCCACATTAGCCAAAACAGCATGGTACTGGTACCAAAACAGATACA 1139
                            i  i   v  ii   i    ii         i iv ii i   i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_188045405_   1140 TAGACCAATTAAACAGAACAGAGGCCTTAGAAATAACACCACACTTCTAC 1189
                             i    vi  i    iv   iviii        vv   i  v i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_188045405_   1190 AACCATCTGATCTTTCACAAACCTGACAAAAACCAG-CAATGGGGAAAGG 1238
                         iii  vi    i  iv    ivv  v   i -   v-            i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGA 391

  chr2_188045405_   1239 ATTCCCTATAAAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGA 1288
                           vvi  v vv  i        i     v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_188045405_   1289 AAACTGAAACTGGACCCTTTCTTTATACCTTATACAAAAAATAACTCAAG 1338
                          i v    ii       i v i i i   v          v        i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_188045405_   1339 ATGCATGAAAGACTTAAAAGTAAGACCTAAAACCATAAAAACCCTAGAAG 1388
                            v  v ?    i    v      v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_188045405_   1389 AAAAGCGAGGCA-ATATCATTCAGGACATAGGCATGGGCAAAGACTTCAT 1437
                             vvv   ?i- v   -   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_188045405_   1438 GACTAAAACACTAAGAGCAATGGCAACAAAAGCCAAAATTGACAAACGGG 1487
                         iiv  vi    i  i    vvi          vv     v  i   iv  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_188045405_   1488 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAA--ACA--ATCACCAGA 1533
                          ii v  i   v v  i i   i  ii vv    --   --    vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_188045405_   1534 GTGAACAGGCTACCTACAGAATGGGAGAAATTTTTTGCAATCTACCCATG 1583
                              v  i v   i               v v       vii ivi  v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_188045405_   1584 TGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACA 1633
                            i  i  i  vi          v  i        ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_188045405_   1634 AGAAATAAACAATCAACGCCATCAAAAAGTGGGCAAATGATATGAACAGG 1683
                          v   v i    vi   v v  i?    i        v   v    i  i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_188045405_   1684 CACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAG 1733
                           i     v        i  vi viii     i  i  i       i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_188045405_   1734 CTAATCATGACTGGTCAT 1751
                           v v   v ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (145 / 108)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


1286 25.69 15.16 1.48  chr2_188144147_188145675      497  1037 (492)    L1M4_orf2#LINE/L1      294   908 (0)  

  chr2_188144147_    497 AGTTCAATGGACAAAAATAGAGAACCCAGAAATATATTTACATATCAAAC 546
                           v        vv i   v    ii         v iii i i  i----
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT---- 339

  chr2_188144147_    547 TACCATC---TAGTTTTCAACGAAGGC------ACCATTCAATA------ 581
                           ivi  --- ii     i  i i  i------          i------
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_188144147_    582 -AATAGT------ACCA----GTATCCAGAAAACTGGATTACCATATGCA 620
                         -      ------ v  ----  iiivi  v        v?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_188144147_    621 GAAGAATAAAACTAGACCCCTATCTCGTATCATATATAAAAGTCAACTCA 670
                         i      i  ii i        i   ii i      i    i i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_188144147_    671 AAGTGGATTAGAGACCAAAATATAAGTCTCAAAACTGTAAAACTACTAGA 720
                           i     i ?     v    i    vvii      i       vi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_188144147_    721 AAAAAA--TAGGAGACACAT-----TGATCT--AGTTAAA----GATTT- 756
                          i    --    ? -i v  -----   i  --i    ii---- i   -
  L1M4_orf2#LINE/    540 AGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_188144147_    757 -TATGTATAA----GAAGGCAGAGGCAATAAAACAAAAA-TAAACAAATG 800
                         -  vi   i ----i  i   v i    i    v     -  i i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_188144147_    801 ATACTATA-CTAAATTAAAAACTTCTGTATAGCAAAGGCAACAATCAACA 849
                         iv   vi - v             i   iivv      vv  v     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_188144147_    850 GAATAAAGAAATAACCTGTTGAATGGGGGAAAATATTTGCTACCTTTTCA 899
                         i i i  i i i    iiiv       i            v viiv vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_188144147_    900 TCTGACAAGGGACT---------AATA--------------ACAGC---- 922
                              i        ---------    --------------   i ----
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_188144147_    923 ------AAAAACTAATAACTCAATTAACAAGTAGGCAAAGAACATGAATA 966
                         ------   i  v      i     ? v  i i       i iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_188144147_    967 GACATTTTTCAATAGATGACATACAAATAGTCAACAGATATATTTTTAAA 1016
                                i  v v   v  i        i i   i iii i  v---   
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG---AAA 885

  chr2_188144147_   1017 A--TGCTTATTATCACTGATCAT 1037
                          --    i vi    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (94 / 41)
Gap_init rate = 0.03 (20 / 615), avg. gap size = 4.50 (90 / 20)  


2956 27.59 1.21 0.99  chr2_188222018_188228729     5315  6220 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_188222018_   5315 TGGAAAAACAGTTCATGCTCATGGATAAGAAAAATCAATATCATGAAAAT 5364
                               i i vii    i        vi   i v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188222018_   5365 AGCCATACTGTCCTAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5414
                         i  v     vi  v  v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_188222018_   5415 TACCATTTACTTTCTTCACATATTAGAAAAAG-CAAACT-ACTTTAAATT 5462
                          v   vi i i  i  ii  -----    vv -   i  - iii    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-----GAAATTGACAAGCTGATCCTAAAAT 145

  chr2_188222018_   5463 TCATATGGAAC--CAAAAAACAGTCTATATAGCCAAGACAATCCTAAGCA 5510
                                   v--   iii  --i viv        i      i i iv 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_188222018_   5511 AAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTAC 5560
                          i          i      vv    i  v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_188222018_   5561 AAGGCTACAGTAACCAAAACAGCACGGTACTGGTACAAAAGCAGATATAA 5610
                           i          i   i    iii        i i  iiii   i   v
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_188222018_   5611 AGACCAATGGAACAGAACAGAGGCCTCAGAGATAACGCCACACATCTACA 5660
                            i        i    iv   ivii    i    vv   i    i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_188222018_   5661 TCCATCTGATCTTTGACACACCTGACAAAAACCAG-CAATGGGGAAAGGA 5709
                         vi  vi    i  i    vivv  v   i -   v-            i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAA 392

  chr2_188222018_   5710 TTCCCTATTTAATAAATCGTGTTGGGAAAACTGGCTAGCCATATGCAGAA 5759
                          vvi  v  i  i    v   i     v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_188222018_   5760 AACAGGAACTGGACCCCTTCCTTATACCTTACACAAAAATTAACTCAAGA 5809
                         i vv i ii         v   i i   v  i                i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_188222018_   5810 TGCATTAAATACTTAAATGTAAGTCCTAAAACCATAAAACCCT-AGAATA 5858
                           v  i ? v  i          vv       i       i  -    v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_188222018_   5859 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGCCGAAGACTTCATC 5907
                             v    ?i- v i -   iv   v v  vv i v i v ii   v v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_188222018_   5908 ACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5957
                         iv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_188222018_   5958 TCTAATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTATCTTCAGAG 6007
                         ii v  i   v v  i ii  i  ii vv    i  v      vvv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_188222018_   6008 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 6057
                             v  i     i                 v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_188222018_   6058 GACAAAGGGCTAATATTCAGAATCTACAAAGAACTTAAACAAATTTACAA 6107
                           i  i  i  vi   i      v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_188222018_   6108 GAAAAAAACAA----CCCCATCAAAAAGTGGACAAAGGATATGAACAGAC 6153
                         v     i    ----   v  i?    i   i        v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_188222018_   6154 ACTTCTCAAAAGAAGACATTTATGCAATCAACAAACATATGAATAAAAGC 6203
                          i     v        i  vi viiiii   i  i  i     v i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_188222018_   6204 TCATTATCACTGGTCAT 6220
                            vi    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


1369 24.13 5.88 13.54  chr2_188355113_188357438      879  1831 (495)    L1M4_orf2#LINE/L1        1   880 (28)  

  chr2_188355113_    879 TGGAGAGGTAGTCTATGTTTCTGAATTGGAGAACTCAATATTGTTA---T 925
                             i  i  vi i     iv  i      ii   i          --- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188355113_    926 CTCATTCATTCTTCACAAATTGGTCAATAGAATCAATGCGATACCAGTCA 975
                         vv  ---  v  i v       i  v i   v    i  i  v  vi   
  L1M4_orf2#LINE/     51 GGCA---ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_188355113_    976 AAACCACATCCAACTCAACTGTAGAAAT-GTCCAGGTGATTCTTAA-TTT 1023
                            i v  v iiv  ivvi  i      - v v  v    i  v  -  i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_188355113_   1024 ATATAAAAATGCAAAGGTCCTAGAATAGCTAAATCCACATTGAAAAATAA 1073
                             ii        i  v  i        i   v v iv        v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_188355113_   1074 GG-CAAAACTGGAAGAATAACAACATCTGATTTTAGTACT-ATTAGCAA- 1120
                          i-    ii    i  v v   vivi ii    i iv   - i  -   -
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA-CAAA 246

  chr2_188355113_   1121 --TACAGGAATTCAAG-CAGGGTAATATTAATGTGAGGATAGACAAATAC 1167
                         --     v   -    -   v  ii  i iiii i          v   v
  L1M4_orf2#LINE/    247 GCTACAGTAAT-CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_188355113_   1168 AACAGTGGAG-GGAGTAGAGAGCCTAGAAACAGAATCACCAATTTGTG-- 1214
                          v  i    i-i  i v     i i     i i vi  ivv    i  --
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_188355113_   1215 ---------TTTGACAAGGGCACCTGAAAA--ATTCAATAGGAAAAATTC 1253
                         ---------  i        ii  --  i --       i  i   i---
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCC--AAGACCATTCAATGGGGAAAG--- 390

  chr2_188355113_   1254 AATGAGAAATAGTGCTGGAGGCTGCTCTGCCTATGGAGTAGCCATTCTTT 1303
                         -------      ---------------------------------    
  L1M4_orf2#LINE/    391 -------AATAGT---------------------------------CTTT 400

  chr2_188355113_   1304 TATTTCTTTACTTTCTCAATAAACATGCTTTCAGTTAAAAAAAAAAAGAA 1353
                          ---------------   i   ---------------------------
  L1M4_orf2#LINE/    401 T---------------CAACAAA--------------------------- 408

  chr2_188355113_   1354 AGAAATAGTGTTAGAATAAGTAGATATT-ACATGAAAAATATTGAA--TA 1400
                         ----- i   i i i i  v i    ?i-     v    v v    -- i
  L1M4_orf2#LINE/    409 -----TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_188355113_   1401 AACCTTGAAAAACCTACCTTAGACCATACACAAACATTATTTTGTGATGT 1450
                         i   --------       i v      i     v    vi iivi   v
  L1M4_orf2#LINE/    454 GACC--------CCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_188355113_   1451 TTTATAGACCTAAATATTACATCTTAACCTAGAAAATT-TTGGAAGAAAA 1499
                         v i ?          i v v v  v  v   v    i -  i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_188355113_   1500 TATAAAAGACTATCCTCATGAC--TGGAGTAGGCAAAATTATCTTAGAAA 1547
                         i   ii? vvv   i  i    --   iv       viv v       v 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_188355113_   1548 GGAAAGGAAATCTTTGAGCA-TATTAGAAAT--TGGTTAAGTAGGACTTT 1594
                         v  v vv   vvivii    -i vv     v-- i v   i v      i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_188355113_   1595 ATCAAA-TTAAAA-CTTACGTTCTTCAGAAGACTGGTTTTAGAAAATGAT 1642
                               -      -   vi  v     i i   vvvv iv     i   v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_188355113_   1643 GG-------CATGGATTTGGAGAAGATATTAGATGTGTGTGTGTGTGTGT 1685
                         ii-------  ii  v v      i     -----------------  i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATT-----------------TGC 728

  chr2_188355113_   1686 GTGTGTGTGTGTTTGAGAGAGAGATCATTTATATTTAGAATATATAATGA 1735
                         ivi -ii i i i   v -  i  i---  i   ii           v  
  L1M4_orf2#LINE/    729 AAAT-CATATATCTGATA-AGGGAC---TTGTATCCAGAATATATAAAGA 773

  chr2_188355113_   1736 ACTCTTACAACTC-----TAAAAAGACA--CCACCAAAT--AAAAATGTA 1776
                                      -----          --iv   v   --       vi
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_188355113_   1777 TGAAA-AGTTGAACACAGATCTCAGACCAAA--AGATATACAAATAGCCC 1823
                         ii  i- v     i v v  i  v--     --            i   v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCT--CCAAAGAAGATATACAAATGGCCA 871

  chr2_188355113_   1824 ATA-GTACA 1831
                            - i   
  L1M4_orf2#LINE/    872 ATAAGCACA 880

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.04 (39 / 880), avg. gap size = 4.74 (185 / 39)  


2605 24.47 3.80 2.35  chr2_188391911_188396600     3304  4198 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_188391911_   3304 TGGAAACACATCCTATGCTCATGGACTGGAAGAATTGATATTGTGAAAAT 3353
                               v i    i   i       i       v  i       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188391911_   3354 GACCAAACTCTC-AAAGCAATCTACAGATTCAATGCAATTCCCAGAAAAA 3402
                          i v v    i -   vii              i     i  i vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_188391911_   3403 TACCAACATAATTTTTAACAGAATTAGAAAAAA-AATACTAAAATTCATA 3451
                          v   i vvvv     vi     v v  v  iv-i  v            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_188391911_   3452 TGGAA-T-CAAAAAACAGCCCAAATGTCCAAAGCAATCCTAAGCAAAAGG 3499
                              - -   iii  --  vi   iv     i     i i iv  i i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_188391911_   3500 AAGAAATCTGGAGGCAC-CATATAACTAGACTTCAAATGAC--ACTATAA 3546
                           v   vi      -  -  i ivv ivi i      --  --    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAA--ACTTACTACAA 245

  chr2_188391911_   3547 GGCTGTAGTTACCAAAACAGTATGGTACTGCTATAAAAATAGAC------ 3590
                         i   ii   v i   i     i        vi    ii      ------
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_188391911_   3591 --CAGTGGAACAGGATACAGAACCCAGAAATAAAGCCAAATATGTACAGT 3638
                         --  i     i  i  vv   ii           v   v i  v  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_188391911_   3639 GAATTGATCTTTGACAAGACATACAAAAAC-ATAAATTGGGGAATGGATA 3687
                         v       i  i      i-i i v  i  -  vv v       v i   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_188391911_   3688 CCCTATTTAATAAATGGTGCTGGGAAAACTAGCAAGCCACATGTA---GA 3734
                         vi  v  i  i              v    i vv ?       i ---  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_188391911_   3735 ATGAAACTGGATCCCTGTCTCTCATCTTATACAAAAATTAACTTGAGATG 3784
                              ii    i    ii   v  i v                ii i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_188391911_   3785 GATCAAAGCCTTAACTATAAGACCTGAAACTA-AAAGTTAT----GGAAA 3829
                              ?  v i   v i     v  i      -   ii v ----i    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_188391911_   3830 ACGTCAGAAAAACTCTTCTAGACTTCCGCCCAGGCAAAGAATTAATGACA 3879
                           i vi ?iv  v     vv   i iv vii      v iv  vv iivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_188391911_   3880 AAGACCCCAAAAGCAAATGCAATAAAAACAAAAATAAATGAATGGGACCA 3929
                          v   v         v v    i    iv       i  i   v    iv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_188391911_   3930 AATTAAACTAAAAAGCTTCTGCATAACAATTG-CAGTGATCAAGA----G 3974
                         v  i   v v    i   i  iiivv   vv -  v -       ---- 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGAAAGTG 693

  chr2_188391911_   3975 AAAA--CAA---AAAAAAAGGGAGAAAATATTTGAAAAGTATACATCTGA 4019
                             --   --- v i  v               v   vi   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_188391911_   4020 CAAAGGACTAGTATCCACAATCTACAATGAACTAAAAAAAAAAAAACAAC 4069
                         i  i     v       v   v  i  v     vvv ---------    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA---------CAAC 784

  chr2_188391911_   4070 AACAACAAAAAAGAGAAAAGCAAATAATCCCATTAAAAAGTCTGCAAAGG 4119
                         v-   i  v   i   ----       i  v   ?    i vv       
  L1M4_orf2#LINE/    785 T-CAATAATAAAAAGA----CAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_188391911_   4120 ATATAAATAAACATTTCTCAAAAGAAGATTTACAAATGGCCAACAAACAT 4169
                           v i    i         v         v             i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_188391911_   4170 ATGAAAAAATGTTCAACATCACTAATCAT 4198
                                i   i         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (117 / 98)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.39 (55 / 23)  


2604 23.71 8.97 0.49  chr2_188482884_188487924      493  1306 (3735)  C L1M4_orf2#LINE/L1   (0)   908    26  

C chr2_188482884_   1306 TTTGATAACTTAATATTGTTGAGATGGTAAAGATCCTGAAATTTATCTAC 1257
                           v  vi             i      i  viv   iv     v      
  L1M4_orf2#LINE/     26 TTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

C chr2_188482884_   1256 A--TTCAATATGATTATTATCTAAATACCAGTTTACCTTTTAACAGAAAT 1209
                          --     iiii  ivi    v    v    i vv i    vi       
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

C chr2_188482884_   1208 TGACAA-CTGATCTTAAAACTCATATA-AAATGCAAGAAAACTAAAATAG 1161
                               -      i     i      i-         ii v i i     
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

C chr2_188482884_   1160 GCTAACAAATCTTGAAAAAGAA---CAAAGTTGGAGGACTCACATTTGTG 1114
                         v v  vv               ---                   i  viv
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

C chr2_188482884_   1113 GATTTCAAAATTTAGTACATAGCTGCAGTAATAAATGCATCGTGATACTG 1064
                         i         i   v    v    i       v  vi  vi   i     
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

C chr2_188482884_   1063 ACACAAATATAAA--TATAGATCAGTGGAACAAAGTTTAACATACAAAAT 1016
                         i  i  iv   i --         i     i i i  v ivi v  i  v
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

C chr2_188482884_   1015 TAAACTCATA--TTTATGGTGAACTTAT-----------GTATTTAAAAT 979
                              i    --        v  i v  -----------  iii-  i i
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC-AAGAC 374

C chr2_188482884_    978 TATT--ATGA-------------TTTTAAATAAA-GATACCTTGATAATT 945
                         i   --   i-------------    v  i   - i i ivv  i  i 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

C chr2_188482884_    944 GAGTA-------AGAAAAGA--GCAATTG--------TTTCA----ACAT 916
                          ii  -------iv      -- v i   --------ii   ---- i  
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

C chr2_188482884_    915 GCGG----TGCTGGGAAGTGAATTAGAGAC-TAAATGTAAGACCTAAAAC 871
                         i ii---- ivivvi  i  i  i ?    -           v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

C chr2_188482884_    870 TATAAAACTCTTAGAAAAAAAGATAAGAGTGAATCTTTGTGAACTTGCAT 821
                                         i    v   i ?  i      i    v    vi 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

C chr2_188482884_    820 TAGGCAGCTGTTTCTTTGATATGATATTGAAAGCATAAGAGGCTAGAGAT 771
                               iiv       v       i iii      i   vii v i   v
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

C chr2_188482884_    770 ATAATAGATAAATTGGACTTCTTCAATATTAAAA-CCTTTATATTGCA-- 724
                          v                   v    v       - i   i ii v  --
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

C chr2_188482884_    723 TGATACTAT-AATAAAATG----GATAAACCACAGAATAGGAGAAAATAT 679
                         v  i     -  v   i  ----  i  v         i           
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

C chr2_188482884_    678 TTATAAATTGCATATCTGATAAGAGACTGATATCCAGACTACAAAAAGAA 629
                           ii    iii            i    vi        v  i v      
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

C chr2_188482884_    628 CATCCT-TAACTCAATAATAAAAAGGCATGTAAACCAAATTCCAAAATCA 580
                          -  i -i                 i  vi   v    -  ?v     vi
  L1M4_orf2#LINE/    775 C-TCTTACAACTCAATAATAAAAAGACAAATAACCCAA-TTWAAAAATGG 822

C chr2_188482884_    579 GTAATGAATTTGAATAGAAATTTCTCAAAAGGGGAAAAACAGATGACAAA 530
                          i  v i           v       v    ii  v v   i   i v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

C chr2_188482884_    529 TAAGCATGGGGCAAAGATTCCTAATACCATTAGTCAT 493
                               iiv i-      v ii  i i  ????????
  L1M4_orf2#LINE/    873 TAAGCACATGA-AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (120 / 70)
Gap_init rate = 0.03 (25 / 883), avg. gap size = 3.08 (77 / 25)  

2246 24.17 0.83 1.16  chr2_188482884_188487924     1320  1923 (3118)    L1M4_orf2#LINE/L1      307   908 (0)  

  chr2_188482884_   1320 AGAAGAGAGATCCCAGAAATAAAAGCAAACATTTATGGTCAGCTGATATT 1369
                             vv    vi           vv  v             ii    v  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_188482884_   1370 TGACAAGGATGCTGAGAACA--CAAAGAAAAGAAAAGATAATCTGATCCA 1417
                         i       i   ii   v  --   v ii--    ii   i   vv  v 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGG--GAAAGAATAGTCTTTTCAA 404

  chr2_188482884_   1418 TAAATAATGTTCAAAAAATTGTCTATCCATATGCTGAAGAATAAA-TTAT 1466
                         i    ii  i vii v  i  vv  ?   i    vi      i  -  iv
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_188482884_   1467 ACCCTTATCTCACACCACATGCAAAAATCAACTAAAAATGGATTACAGAC 1516
                             i  i         i  i       i    v         i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_188482884_   1517 TTAAACATAAAAACTGAAGCTATAAAGCTACTAAGAGAAAACATACGGGT 1566
                         i    ii   i i  i  i       i  vi  ii          v ?  
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_188482884_   1567 AAAGCTCCTTGACATTGGTCTGGGAAATAATTTTTTGGTAATCACATCAA 1616
                            v  i v    v    vi i  v   ii   i  i vv  v   i   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_188482884_   1617 AAACACAGGCAACAATAGCAAAAAACAGATAAGTAAGATCATGTCAAACT 1666
                           i    i       v  -      i      i vi  iivii     v 
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_188482884_   1667 AAAAAGTTTCTGCACAGCAAAGGAAACAATCAAAATAGTGAAAGGGAAAC 1716
                         v    ii  i  ii vv       v  v     i v       i iv   
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_188482884_   1717 CTACAGAATGGAAGAAAATATGTGCAAACCATATATCTAATGTGGAGCTA 1766
                          i         i         v      i         i  iv  ii  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_188482884_   1767 GTATTCAAAATATATAATCAACTCATATAACTCAATAACAAAAAATTCAA 1816
                             i  i         vv     v  i          i     iv-   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAA 802

  chr2_188482884_   1817 ATAACCCAGCTTAAAAATGAGGAAAGAAGATCCTGAA--GATATTTCACT 1864
                                 ii ?       i v    --   i-    --  i     v i
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAG--GATT-TGAATAGACATTTCTCC 849

  chr2_188482884_   1865 AAGGAAAGCATACAAATGACCAATAGGTATATGAAAAGGTGCTGAACATC 1914
                           i   iii         i      i i i        i    v      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_188482884_   1915 ACTAATCAT 1923
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.84 (92 / 50)
Gap_init rate = 0.01 (8 / 602), avg. gap size = 1.50 (12 / 8)  

 338 19.35 0.00 0.00  chr2_188482884_188487924     3215  3276 (1765)    L1M4_orf2#LINE/L1        1    62 (846)  

  chr2_188482884_   3215 TGGCAAGGTATTCCATATCCATGGATTGGAAGAATCAGTATTGTTAAAAT 3264
                            v   i   i    i i              v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188482884_   3265 GTCCATACTACC 3276
                          v v     v  
  L1M4_orf2#LINE/     51 GGCAATACTCCC 62

Transitions / transversions = 1.40 (7 / 5)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.00 (0 / 0)  

3125 25.90 0.70 1.28  chr2_188482884_188487924     3693  4549 (492)    L1M4_orf2#LINE/L1       57   908 (0)  

  chr2_188482884_   3693 ACTACCCAAAGCAAACTACAAATTCAATGCAATCCTTATCAAAATACCAA 3742
                            v      vii v     i      i       i         v   i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_188482884_   3743 GAACATTCTTCACAGAAATAGAAGAAATAATCCTAAAATTTGCATGGAAC 3792
                         vvi v  i  ii       v  vi iv i           iii      v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_188482884_   3793 CACAAAAGACCCAGAATAGCCAAAGCTATCCTAAGCAAAAAGAACGAAAC 3842
                         ii   ii                 i v   i i iv  i      i  ii
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_188482884_   3843 TGGGGGAATCAATCACATTATGTGACTTCAAATTATAAAACAGAGCCATA 3892
                            i   -- --     i vivii i      viv  vv   i   i i 
  L1M4_orf2#LINE/    207 TGGAGGA--C--TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_188482884_   3893 GTAATCAAAACAACAAGGTACTGGCATAAAAACAGACACATAGAACAGTG 3942
                                 i   iiiv             ii i     i     v  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_188482884_   3943 GAACAAGATTAAAAAAAAACCCAGAAACAAATCTTTACATCTATAATGAA 3992
                            i ii   i i i----i       i   i iv     i   ii v  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAG----TCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_188482884_   3993 CTCATTTTTGCCAAAGTTGCCAAGAACCTACACTGGGGAAAGGACAGTCT 4042
                         i v     i v   i v        v v v  v         i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_188482884_   4043 CTTCCATAGATGGTGCTGGGGAAACTAGATATCTATATGTAGCAGAAAGA 4092
                         i   v i i           iv    i    ? i i   i iv    v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_188482884_   4093 AACTAGACCCCTCTCTC----CATAGACAAAAATCGTATCAAAGTGGGTT 4138
                          ii i       vi   ----    v        iivv     i   i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_188482884_   4139 AAAGATTTAAATGTAAGACCTCAAATTATGAAGCAACAGCAAAAGAAAA- 4187
                          ?   ii           v  v   i   i  i --ivvi i       -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAAC--TCTTAGAAGAAAAC 546

  chr2_188482884_   4188 ATTGAGGAAAATCTCCAAGACATTGGACTTGGCAAATATTTCTTGAGTAA 4237
                           v i? v      i iv   v    ii v     vvi      iii  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_188482884_   4238 TACCCCACAAGCACAGTCAATCAAAGCAAAAATGGACAAATGGGATTACA 4287
                         v  v   v       iv   iv    v      i  i    v   i v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_188482884_   4288 TCAAG-TTAAAAAGCTTTTGCACAACAAAGAAAATAATCAATAAAGTGAG 4336
                             i-       -      ii vv     i v iv     v       i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_188482884_   4337 GAGACAATCCACAAAATGGGAGAAAATATTTACAAACTACCCATCAGACA 4386
                         i      i     i                 i    ii ivi   v  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_188482884_   4387 AGAGATTAATAATCAGAGTATATAAGAAGCTCGAACAACTTTATAAGAAA 4436
                           i  i vi  vi    i       ii i   vv      iv    v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_188482884_   4437 AAAAGGAATAATCCAATTACAAAATTGGCAAAAGACTTGAATGAGCATTT 4486
                           i vi     i      ?v     v      i  i      iii     
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_188482884_   4487 CTCAAAAGAAGACATACAAATTGCCAATAAGTATATGAAAAGGTGCTCAA 4536
                            v        i        v         i i        i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_188482884_   4537 CATTATTGTTTGT 4549
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (142 / 76)
Gap_init rate = 0.01 (8 / 852), avg. gap size = 2.12 (17 / 8)  


2581 26.32 1.90 0.27  chr2_188501376_188503112      509  1245 (492)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr2_188501376_    509 AAAGAGCCCACAA-AGCCAAAGCAAGACTGAGCAAACGGAACAAATCTGG 557
                           i ii    v  -       i   vvi   iv  ivi       vi   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_188501376_    558 AGGCATCATATTACCTGATTTCAAACTATACTATAAGTCCATAGTCACCA 607
                            vv   i i v  ii        viv     i  iv i i   v i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_188501376_    608 AAACAGCATGGCACTGGGATAAAAATAGGCACA----------GAACAGA 647
                          i    ii   i     v    ii    i  i ----------   i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_188501376_    648 ATAGAGAACTCAGAAATAAACCCAAATACTTATAGCAAACTGATCATCGA 697
                           v    iii              v i i    i iv  i    iv    
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_188501376_    698 CAAAACAAACAAAAACAT--AAGTTGGGGAAAGGCCACTCTATTCGACAA 745
                            iivviv   i v   --  --         ivi v   v   i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_188501376_    746 ATGGTGCTGG-ATAATTGGCAAGCCACATGTAAGAGAATGAAACTGGATC 794
                                   - i  i   vv ?       i  i        ii    i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_188501376_    795 CTCATCTCTCACCTTACACAAAAATCAACTCAAGATGGATCAAGGGCTTA 844
                          ii i   v    v  i        i       i        ?i i i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_188501376_    845 AATCTAAGACCTGAAACTATAAAAATTCTAGACGATAACATCGGGAAAAG 894
                            v     v  i           v ii    v  v     v  ?iv  i
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_188501376_    895 CCTTCTAGACATTCCTTTAGGTAAGGATTTCATGACCAAGAACCCAAAAG 944
                         i    vv   v  vvv     i  v i    v iivi v  vv       
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_188501376_    945 CAAATGCAATAAAAACAAAGATAAATAGTTGGGACTTAATTAAACTGAAG 994
                           v v    i    iv   i   i   iv v      v  i   v v  i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_188501376_    995 AGCTTTTGCATGGCAAAAGGAGCAATCAGCAGAGTAAACAGACAACCCAC 1044
                          i      iiivv    i ivi v    iv i   i  v           
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_188501376_   1045 AGAATGAGAGAAAATCTTCACAATCTATACATCTGACAAAGGACTAATAT 1094
                               i        v  ii   vii   i      i  i     vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_188501376_   1095 CCAGAATATACAATGAACTCAAACAAATTAGCAAGAAAAAAACCAACAAT 1144
                                   i  v      vv    v i ii  v     i  v  i  i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_188501376_   1145 CCCATCCAAAAGTGGGCTAAGGACATGAATAGACAATTCTCGAAAGAAGA 1194
                           v  i?    i     v     iv          v     v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_188501376_   1195 TATACAAATGACCAACAAACATATGAAGAAATGTTCAACATCACTAATTA 1244
                                   i    i  i  i     i i   i         ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_188501376_   1245 C 1245
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.50 (114 / 76)
Gap_init rate = 0.01 (5 / 749), avg. gap size = 3.20 (16 / 5)  


2700 26.25 2.06 3.58  chr2_188517595_188520319     1349  2270 (455)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_188517595_   1349 TGGAAAAACATTCCATGCTCATAGAC---AAGAATCAACACAGTTAAAAT 1395
                               i i  i     i    i  i---    v i  i iv     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188517595_   1396 AGGCATACTGACCAAAGCAATTTATAGATTCAATGCTATTCCCATTGAAC 1445
                         i vv     vv     vii  i  i        i  v  i  i  ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_188517595_   1446 TACCATTGGGATTTTTCACAGAACTAGAAAAAAACT-ATTTTAAAATTCA 1494
                          v   viv vv     ii     v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_188517595_   1495 TACAGAAGCAAAAAGAACCT-GAATAGCCAAGGCAGTT----ACAAAAAG 1539
                           ii   iiiv  i i   i-          ii  i i---- v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_188517595_   1540 GACAAAGCTGGAGGCATTGCTCTATCTGACTTCAAAATATACTACAGGGC 1589
                         i      i      vv ii v  vi ii i       iv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_188517595_   1590 TACAGTAATCAAAACAGCATGGTACTGGTACAATAACAGACACATAATGG 1639
                                     i    ii         i i  vi i     i   ----
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA---- 294

  chr2_188517595_   1640 TACTGGTACATAACAGACCAATGGAACAGAATAGAGAACCCAGAAATAAG 1689
                         ---------------  i        i     v    ii          i
  L1M4_orf2#LINE/    295 ---------------GATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_188517595_   1690 GCTTCACACCTTCTACTATC---TGATCTTCACCAAACCTGACAAAAACA 1736
                         v --  i  v  -  ivi  ---    i   iv   ivv  v   i v  
  L1M4_orf2#LINE/    330 CC--CATACATT-TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_188517595_   1737 AGCAATGGGGAAAGGATTCTCTATTCAGTAAATGGCACTGGGAGAACTGG 1786
                         vv            i  vv   v    ii      ii      v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_188517595_   1787 CTAGCCATATGCAGAAGATTGAAAATGGACCCCCTTCCTTACAACATATA 1836
                         v  ?   i     i    v    iv        - v   i   v      
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCC-TACCTCACACCATATA 475

  chr2_188517595_   1837 CAAAAATTAACTCAACATGGATCAAACACTTAAACATAAAACCCAAAATT 1886
                                        v        ? v  i    ii   i v i    i 
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_188517595_   1887 ATAAAAATTCTGGAAGACAACCAAGGCA-ATACCATTCAGGACATAGGCA 1935
                               v ii i     v   vv   ?i- v i -   iv   v v  vv
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT 574

  chr2_188517595_   1936 TGGGCAAAAATTTCATGACAAAGACACCAAAAGCATTTGCAATAAAAACA 1985
                          i     vii    v iivv v             ivv    i    iv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_188517595_   1986 AAAATGGACAAGTGGAATTTAATTAAACTAAAATGCTTCTGCACAGCAAA 2035
                              i  i  i v i i  v  i   v v   vi   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_188517595_   2036 AGAAACTGTCAGCAGAGTAAACAGACAACCTACAGAATGGGAGAAAATTT 2085
                         i  v   i   iv i   i  v        i                 v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_188517595_   2086 TTACAAACTATGCATCTGACAGAGGTCTAATATTCAGCATCTATAAGGAA 2135
                           i    ii  ii      i ii  v  vi   i   v  v     i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_188517595_   2136 CTTAAACAAATTTATAAGAAAAAAACTAACAGCCCCAT-AAAAATTGGGC 2184
                           ivv    v iv    v     i  v  i i   v  -?    v     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_188517595_   2185 AAAGGACATGAACAGACACTTTTCAAAAGAATTCGATATTTTAAAAATAG 2234
                               iv    i     i  i  v      ---     --- v    i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAA---GATAT---ACAAATGG 868

  chr2_188517595_   2235 CTAAATAAATTTGTAAAAAA-----CAAAACCAAAAGTATT 2270
                          i  -   iivii i    i-----   v i  ????????
  L1M4_orf2#LINE/    869 CCAA-TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.06 (52 / 17)  


2832 27.46 1.88 1.33  chr2_188640030_188646092     4669  5571 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_188640030_   4669 TGGAAAAACATTCTGTGCTCATGGACAGGAAGCATCAATATTGTGAAAAT 4718
                               i i  i ii  i       iv     vv i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188640030_   4719 GGCCATACTGCCCAAAGCAATTTATAGATTCAATGTTATTCCCATCAAGC 4768
                            v     v      vii  i  i        i iv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_188640030_   4769 TACCATTGACTTTCTTCACAGAATTAGTAAAAACT-ACTTTAAATTTTAT 4817
                          v   vivi i  i  ii     v v - v  i  - iii    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr2_188640030_   4818 ATGGAA-T-CAAAAAACAGCCCGTATAGCCAGGACAATCCT----AAGCA 4861
                               - -   iii  --  v v       ii      i ----   v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_188640030_   4862 GAACAAAGCTGGAAGCAAGCATCACGCTACCTGACTTCAAATTATACTAC 4911
                                 i    i ---i -    i  v  ii i      viv      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG---AC-TCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_188640030_   4912 AAGGCTACAGTAACCAAAACAGTAAGGTACTGCTACCAAAACAGATATAT 4961
                           i          i   i     iv       vi iv ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_188640030_   4962 AGACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCAACA 5011
                            i        i    iv   ivii         vv   i    iv ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_188640030_   5012 ACCATCTGATCTTTGACAAACCTGACAAAAGCA----ATGGGGAAACGAT 5057
                         ii  vi    i  i     ivv  v   i v  ----         vi  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_188640030_   5058 TCCCTATTTAATAAATAATGTTGGGAAAACTGGCTAGCCATATGCAGAAA 5107
                         vvi  v  i  i    ii  i     v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_188640030_   5108 ACTGAAACTGTACCCCTTCCATACACCTTATACAAAAATTAACTCAAAAT 5157
                          v    ii  v      v  vi     v                      
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_188640030_   5158 GGATTAAAGATTTAAATGTAAGACCTAAAACCATTAAAAATCCTAGAAGA 5207
                             i ?   ii           v       i  -    v  i       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGA 542

  chr2_188640030_   5208 ATACCTAAGCA-ATACCATTCAGGATGTAGGCATGAGCAAAGACTTCATG 5256
                          v  v  i ?i- v i -   iv  iv v  vv ii    v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_188640030_   5257 ACTAAAACACCAAAAGCAATTGCAGCAAAAGCCAAAATTGATGAATGGGA 5306
                         iv  vi            vvv   i      vv     v   i   v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_188640030_   5307 TCTAATTAAACTAAAGAGCTTCTGCATAGCAAAAGGAAACAACATCAC-- 5354
                         ii v  i   v v  i i   i  iiivv    i ---   vi    v--
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG---ACACTATCAAGA 688

  chr2_188640030_   5355 -AGTAAACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTATCAG 5403
                         -   i  v  i     i                vv       vii  vvi
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_188640030_   5404 TCTGACAAAGGGCTAATATCCAGAAGCTATAAGGAACTTAAACAAATTTA 5453
                              i  i  i  vi         vv     i     ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_188640030_   5454 CAG-AAAAAAACAA-CAACCCCATCATAAAGTGGGTGAATGATATGAACA 5501
                         i i-     i    -i     v  i?v   i    ii  v   v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_188640030_   5502 GATGCTTTTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAA 5551
                           iii  i  v        i  vi viii     i  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_188640030_   5552 AGCTCATCATCACCGGTCAT 5571
                         v     v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.81 (29 / 16)  


2633 27.85 2.68 1.12  chr2_188686898_188692158     3876  4769 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_188686898_   3876 TGGAAATACATCTTGTTCTTATGGATTGGAAGAGTCAATGTCATGAAAAT 3925
                               v i   iii vi i             v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188686898_   3926 GACCATACTGCCCAAAGCAATCTACACATTCAATGTAATTCCTATCAAAA 3975
                          i v     v      vii       v      i i   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_188686898_   3976 TATCAGC-ACTTTTTTTCACAGAACTAGAAAAA--AAATCTCAAATTCAT 4022
                          vi    -i i      -i     v v  v  i--i vi  v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_188686898_   4023 GTGGAATGAAAAAAGAGCCTGAATGGCCAAAGCAGTCTTAAGCGAAAAGA 4072
                         i     vviv  ii  v  v    i      i  i    i ivi i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_188686898_   4073 ACAAATCTGGAGACAC-CACATTACCCGACTTTGCATGA--TACTACAAG 4119
                              vi     i-  -    i v   i i  --  vi --        i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTT--CAAAACTTACTACAAA 246

  chr2_188686898_   4120 CCTATCGTAACCAAAGCAGCATAGTTCTGGTATAAAAGTAGATACATAGA 4169
                         v   iv    i   ii   ii i  v    i    iii    i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_188686898_   4170 CAAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAGATACTTACAACC 4219
                         iv       i     v    ii           v   v i i   iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_188686898_   4220 AACTTGTCTTTGA--AGGAAGCATAGAAAAAATAAATAAACTGGGGGAAA 4267
                           i vi i  i  --   iv  v-----  i iv v v  -     i  i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCC-----AAGACCATTCAA-TGGGGAAAG 390

  chr2_188686898_   4268 GGCACCCTATTCAATAAATGGTGCTGGAAAAACTGGATAAACACATGTAG 4317
                         iii vi  v     i            i v         ?v      i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_188686898_   4318 AAAAATGAAACTGGATCTCTATCTCTCATCATATACAAAAATCAACACCA 4367
                           i      ii    i i   i   v  i             i   v v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_188686898_   4368 GATGTATTAAAGACTTAAATCTAAGACCCTAAATTATAAAAATTCTAGAA 4417
                         i   v  i ?    i     v     v iv   i       v ii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_188686898_   4418 AAAAATCT----GAAAAACTTCTGAATATTGTCCTATTCAAAGAATGTAT 4463
                         i    iv ---- v   v    vvi iv   vvi  vv   v iv viv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_188686898_   4464 GACTAAGACCCCAAAACCAAATTCAATGAGAACAAAAATGAATCA-TGGG 4512
                         iiv  v   v      v  v vv   ii i iv      ii  v - v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_188686898_   4513 ACCTAATTAAACTAAAAAGCTTCTGCGCAGAAAAAGAAATAATCATCAGA 4562
                           i v  i   v v    i   i  i  vvv   i  v iv    vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_188686898_   4563 GTAAACAGACAACCCACAGAATCGGGGGAAATATTTGCAAACTATGTACC 4612
                           i  v                v  i i             ii  i  i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_188686898_   4613 CTACAAAGGACTAATATCCAGAATCTACAAGAAATTCAAATAAATCAGCA 4662
                         iv i  i     vi          v  i  ii  i  vv i  v   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_188686898_   4663 AGAAAAAAA------ACTCA-CTAAAAGGTGAGCAAATGACATGAATG-- 4703
                          v     i ------  i  -i ?   ii  i     v  iv     i--
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_188686898_   4704 CATTTCTCAAAAAGAGATATACAAATGGCTAACAA--ACATGAAAAAAAG 4751
                                 v   ii               i  i  --         i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_188686898_   4752 CTCAACATCACTAATCAT 4769
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (151 / 95)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.12 (34 / 16)  


2438 28.21 4.28 1.16  chr2_188759922_188764191.rev     2914  3778 (492)    L1M4_orf2#LINE/L1       17   908 (0)  

  chr2_188759922_   2914 GTTCACA-ATAGGAAGAATCAATATTGTTAAAATGGCCAGACTGTTTAAA 2962
                              ii-  v      v i           i     v v   viii   
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chr2_188759922_   2963 ACAATTTATAGATTCATTGCTAGCCCTATCAAATTACCAACATTATTTTT 3012
                         vii  i  i       vi  v v          v v   i vviv     
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTT 116

  chr2_188759922_   3013 CACAGAACTAGAGAAAACT-ATTCTAAAATTCACATAGAA---CAAAAGA 3058
                         ii     v v  v  i-  -  i          i  i   ---   ii  
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_188759922_   3059 TCT-GAATAGCCAAAGCAATCCT----AAGAAAAAAAAGGCTGGAAGCAT 3103
                         i i-           i     i ----     i  v  i i    i vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_188759922_   3104 CACACTATCCAACTT-GAAACTATATTACAA-------GTAATCAAAATA 3145
                               vi    i  -i     -  i     -------        i i 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACA 264

  chr2_188759922_   3146 GCATGGTACTGGTAAAAAAAAAAAATAGACACATAGACAAATGGAATAGG 3195
                          ii         i v  ii -----      i     iv          i
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGA-----TAGACATATAGATCAATGGAATAGA 309

  chr2_188759922_   3196 TTAGAGAACCCAGAAATAAAGCTGCACATCTACAACCATCTGATCTTCAA 3245
                         v v    ii           v iii    i  iiii  vi    i   i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_188759922_   3246 TAAAGTCAACAAAAACAAGCAATGGGAAAAGGACTCCCTATTCAATAAAT 3295
                         i  i viiv   i v  vv       i    i ivvi  v     i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_188759922_   3296 GGTGCTAGGATAACTAGTTAGCCATATGCA---GATTGAAACTGAATCCC 3342
                               i   i    i v  ?   i     ---  v    ii  i i   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_188759922_   3343 TTCCTTATATTATATACAGTGATCAACTCAAGATAGAATAAAGATTTGAA 3392
                          v   i i ii       ivi  i       i  i  vi ?   ii i  
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_188759922_   3393 TGTAAAACGTAAAACTATAAAAACTGTAGAGGAAAACCTTGG---ACACA 3439
                              i vv             viiv    i      v v  --- v iv
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_188759922_   3440 TTCTGGATATAGGCCTTGGCAAAGAGTGCC-GGACA-GATTCTCCTAAAG 3487
                            vv  iv v  vi v     v iv v i-i  i -  -- v  v    
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA--CACCAAAAG 607

  chr2_188759922_   3488 CAATTGAAACTAAAACAAAAATG------CTGGATCTAATTAAACTAAAG 3531
                           vvv v   v   iv      i------i    ii v  i   v v  i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_188759922_   3532 AGCTTCTGCACAGCAAAAGAAACTATCAACAGAATAAACAAATAACCTAG 3581
                          i   i  ii vv    i  v        v i i i  v i i    i v
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_188759922_   3582 TGAATGGGAGGAACTACTTGCAAACTGTGCATCTGACAAAGGTCTAATAT 3631
                         v         i  v  i       iii ii      i  i  v  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_188759922_   3632 TCAGGATCTGTAAGAAACTTAAACAAATTTATGAGCAAAAATCAAA---- 3677
                         i   i  v i   ii    ivv    v iv  i vv    iv    ----
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_188759922_   3678 CCA-TTAAAAAATGGGCAAAGGACATGAACAGGTATTTCTCAAAATAAAA 3726
                            -  ?                iv    i  ii       v   v  i 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_188759922_   3727 CATACATGTGGTGAACAAGCATATGAAAAAAATACTTCACATCACTAATC 3776
                         i     vi   iv  i     i       i - i  iv      ??????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZ 906

  chr2_188759922_   3777 AA 3778
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.02 (19 / 892), avg. gap size = 2.47 (47 / 19)  


2087 27.97 5.21 2.38  chr2_188776348_188779286     1581  2463 (476)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_188776348_   1581 TGTAGGGATACACCATGATCATTGATTGGAAGATGCAACATGATCAATAA 1630
                           v ii    iv     v    v          ivi  i  vi i  v v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188776348_   1631 TACAATTCTCTCAAAACTAACCTATAGTATTCTAT-CAATTTGTATCAAA 1679
                         vi    v   i v   i i i   i  -    v i-    iiv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAG-ATTCAACGCAATCCCTATCAAA 99

  chr2_188776348_   1680 AACTTAG--GATATTTTTGTAGATATATACAAAGTAATTCTGAAATTTAT 1727
                          v ii  -- viv      i   v  vv    iv i  i  i     i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_188776348_   1728 ATAAAAA-GCAAAGGAACTATAGAAGAGTTAAAACAAT-TTGAAAATGAA 1775
                           ii   -    i   v i --   v  ii        -       v   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCA--GAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_188776348_   1776 TAATAAGGTTTGAGAAATCACATTACTGGATTTTAAGACTTTCTACATAC 1825
                         v  i  i   v   i v     i v ivi    i  i    v     - v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA-AA 246

  chr2_188776348_   1826 TTTACAGTAAGTGTAAAAGAAGCATGAGTA--GG----GGGACTGACACA 1869
                         vi        --- v  iiv  ii  -   --  ----i   iv    i 
  L1M4_orf2#LINE/    247 GCTACAGTAA---TCAAGACAGTGTG-GTACTGGCATAAGGATAGACATA 292

  chr2_188776348_   1870 AATACCAGTGGAGCAAAATAGGAAGTTCAGTAATAGGCAAACCAAAGTAC 1919
                         v v i  i    ii i   v ii   i   v    ----    v vii i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATA----AACCCATACAT 338

  chr2_188776348_   1920 TCA----CAACTGATTTTTGACAATGATTCAAAAGCAATTCAATGTAAAA 1965
                          i ----   i       i     v i v v  ii v        vii  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_188776348_   1966 AGGATAGTTTTCT-AACAAATGA------AATAATTGGACATCCCTAGGC 2008
                           i     i  i -        i------i i  i    i ?  vi v  
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_188776348_   2009 AGAA-AAT-AAGCCTCAGTCTAAACTTACAAATTGTATAAAATATTAACT 2056
                          i  -   -   iivv vi iv v  i   vvv i  i    -       
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTAACT 487

  chr2_188776348_   2057 CAAAATAAATTAGAGATATAAATA----ACCTAACACTA--AAATTTTTA 2100
                               ii  i ?   iv     i---- v    v    --   i i   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_188776348_   2101 GACAAAAACACAGGAGAAAATCTTTGTTACTTTGGGCTAGGTGACACATT 2150
                           vi      i   ? v       i  v  i     i    ii iivv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_188776348_   2151 CTTAGACATGATGCCAAATGTACAATTTACAAAAGAAAATATTTATTAAT 2200
                               i    ii     v i    viv           v  vv  v   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_188776348_   2201 TAAACTTCACTAAAATTGAAACACTTT-GTTCTGTAAAATATCCTGTTAA 2249
                          ii      ii      i   -     -  v  vi   iv iv  i i  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_188776348_   2250 TAGGTTGAAAAGACTAGCCACAGACTGGCAGAAAATATATTGCAAATTGC 2299
                         v iiv         v v       v   v         -        iii
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT-TTGCAAATCAT 735

  chr2_188776348_   2300 TTATGTTACAAAGGGCTTGTTTCTGGAATATGTAAGGAA----TATG--- 2342
                         v   v v i  i  i     v  ii      i   i   ----  ii---
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_188776348_   2343 ------TAAGGA-ACTCATA-TTCAATCAGAAAATGGGCAGAAGTCTTAA 2384
                         ------   ii -  vv   -ii    i?i          i i vi  i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_188776348_   2385 ACAGACATTTAATCATAGAAGATACATAAAAGGCAAAAAAAATCGCATGA 2434
                          i        vvi  v        i i   v   v  v  i-- i     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG--CACATGA 883

  chr2_188776348_   2435 AAAGAAAAATACTAGCCATTAAGGAAATG 2463
                              ---- i  viv   i ????????
  L1M4_orf2#LINE/    884 AAAGA----TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.31 (67 / 29)  


2659 26.26 1.82 4.50  chr2_188794471_188798994     3100  4032 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_188794471_   3100 TAGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTCAAAAT 3149
                          i    i i  i     i        v      v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188794471_   3150 GGCCACACTGCCCAAAGCAATCTACGGATTACATGCTATTTCTGTCAAAC 3199
                            v i   v      vii      i    vv i  v  ii  i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_188794471_   3200 TACCAATGACATTCTTCACAGAATTAGAAAAAAATAACTATTTTAAAATT 3249
                          v   iivi v  i  ii     v --------- i  ------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT---------TGAC------------ 129

  chr2_188794471_   3250 TAAATTTAATTTAAAATTCATATGAAACCAAACAAGAG-CCCA-AATAGC 3297
                         -  ii v vii             i  -- vi    i -    -      
  L1M4_orf2#LINE/    130 -AAGCTGATCCTAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGC 176

  chr2_188794471_   3298 CAAGGCAATCCTAAACAGAAAGAACAAAGCTGGAGG-----CATTACCCT 3342
                            ii     i i  v ii          i      -----  i v   v
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_188794471_   3343 ACTTCGAACTATACTACAAGACTGCAGTAACCAACACATGATGGCACTGA 3392
                          i   i  viv        ii  i      i   v   vvi   i    i
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_188794471_   3393 TGTGAAAACAGACACATAAACCAATGAAAAAGAATAGAGAACACTAAAAT 3442
                         ii i ii i     i   i i     i  v     v    iiv vi    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_188794471_   3443 AGTGCCACATATCTACAACCATCTGATCTTCAACAAAATTGACAA-AGCA 3491
                          ivv   i i  i  iiii  vi    i   i    iiv  v   - v  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_188794471_   3492 AGCAATGGGGAAAGAACTCCCTATTCAATAAATGGTGCTGGGATAATTTG 3541
                         vv              ivvi  v     i              i  i v 
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_188794471_   3542 CTAGCCATAGGCAGAAAACTGATGA-GGACTCCTTCCTTGTGCCATGTGC 3590
                         v  ?   i v   i  i v   v v-    i   v   iiii    i i 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_188794471_   3591 AAAAATTAACTCAAG-TGCACTAAAGACTTAAATATAAAACCAAAAACTT 3639
                                       i-  v ii ?    i     i   i v v      -
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT- 525

  chr2_188794471_   3640 TTTTATAGGGTTTTTATCCCTGGAAGACAACCTAGG---AAATACCATTC 3686
                         ----   iiii i   ------     v   v    ---    -- -   
  L1M4_orf2#LINE/    526 ----ATAAAACTCTTA------GAAGAAAACATAGGNGTAAAT--C-TTC 562

  chr2_188794471_   3687 TGGACATAGGACCTGACAAAGACTGCATGACAAAGATGCCAAAAGCAATT 3736
                         vv   v v  iiiv i   v ii v v iivv v  ii         vvv
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_188794471_   3737 GCAACAAAAACAAAAAATAACTAC-TGGGACCTAATTAAACGAT--AGAG 3783
                                  i-        iv  v- v    i v  i   --  -- i i
  L1M4_orf2#LINE/    613 GCAACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAA--ATTAAAAA 659

  chr2_188794471_   3784 CTTCTGCACAGCAAAAGAAACTATCATCAGAGTAAACAGACAACCTACAG 3833
                            i  ii vv    i  v       vv i   i  v        i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_188794471_   3834 AATGGGAGAAAATATGTTTAAGCTATGCATCTGACAAAGGTCTAATATCC 3883
                                        v vi  iii  ii      i  i  v  vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_188794471_   3884 AAAATCTGTAAAGAACTTAAACAAATTTAAAAGCAAACA-ACAAATAACC 3932
                          i   v i         ivv    -i i  v ii   v -          
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAA-CTCAATAATAAAAAGACAAATAACC 808

  chr2_188794471_   3933 CCATTAAAAAGTGGGCAATGGACATGAACAGACACTTTTCAAAAGAAGCC 3982
                          v   ?    i       v   iv    i     i  i  v       vi
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_188794471_   3983 ATTCATGTGGCCAATGAGCATGTGAAAAAATGCTCGACATCACTCATAAA 4032
                           v  vi        i    ii      i      i      ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (151 / 91)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.95 (59 / 20)  


3393 25.88 0.55 0.55  chr2_188813295_188819518     4825  5732 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_188813295_   4825 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4874
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188813295_   4875 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4924
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_188813295_   4925 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4972
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_188813295_   4973 TAGGGAACCAACAAAGAGCCCA-CATCGCCAAGTCAATCCTAAGCCAAAA 5021
                           v    vi-i   i ii    -v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_188813295_   5022 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5071
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_188813295_   5072 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5121
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_188813295_   5122 CAATGGAACAGAAT--AGAGCCCTCAGAAATAACGCCACATATCTACAAC 5169
                                 i     --    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_188813295_   5170 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5219
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_188813295_   5220 CCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGC 5269
                         i  v  i  i              v      v  ?i  i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_188813295_   5270 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5319
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_188813295_   5320 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5369
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_188813295_   5370 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5419
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_188813295_   5420 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5469
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_188813295_   5470 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5519
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_188813295_   5520 CAGGCAACCTACAAAATTGGAGAAAATTTTTGCAACCTACTTATCTGACA 5569
                         v  i     i   i   v         v       vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_188813295_   5570 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5619
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_188813295_   5620 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5669
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_188813295_   5670 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAC 5719
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_188813295_   5720 CATCACTGGCCAT 5732
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 346 24.80 10.40 0.80  chr2_188931489_188933604      501   625 (1491)    L1M4_orf2#LINE/L1       61   197 (711)  

  chr2_188931489_    501 CCTGAATTAATCTACAAATTTAATGCACTCCTAATTAAAATCTCGGCAGA 550
                           ii    i       i   i  i   v   iv  i      i i  v v
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr2_188931489_    551 GCTTTTCTG-GGAGCTTGATGGGTTGATT-TAAAA--CATAT---ATTGC 593
                         -     i  -i  iv    iii i    i-     --     --- v   
  L1M4_orf2#LINE/    111 -CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_188931489_    594 A--GAAC--AAAACGGCCAAAAAAAG--TGAAAAAAAA 625
                          -- i  -- i  ii       v  v--       i  
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

Transitions / transversions = 2.88 (23 / 8)
Gap_init rate = 0.06 (8 / 137), avg. gap size = 1.75 (14 / 8)  

 442 33.54 9.96 2.24  chr2_188931489_188933604     1138  1629 (487)    L1M4_orf2#LINE/L1      379   908 (0)  

  chr2_188931489_   1138 CAAAAGTAAAATGATGAACTATTTTATAAATAGTGCTAGAAAAATCAGTA 1187
                            vi vi   vi  iiv  v  iv i    i     i i v  iii vv
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_188931489_   1188 ATTCATATGAAACAAAATGATCTCATTTTTCTATGTTATTTTATGTACAA 1237
                          ?i  i   v  v i     vv iivviii   iv i ivii  i     
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_188931489_   1238 AAATAAATTCCAAGTGAGT-AAATATCTTAATATAAAAA-TCAACTTTTA 1285
                             v  i  v  i  ii - ? v i  v   i   i i- v  vi v  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_188931489_   1286 TCCCTTCTGGAAGTAAGGGTAGTGGCCTGTATTTAGGACTCCAGGTCA-- 1333
                         vvv  ii i    v  ivi   v? ivvi v  iiv   iiii   i --
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_188931489_   1334 -AATGAATTTATTAAACA-AACATAAAATGTGTAATCTCCAATAAAAAAG 1381
                         -    i-   v   i i -i   iv   v iii  v vv   v i    i
  L1M4_orf2#LINE/    579 CAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_188931489_   1382 ATGGGTAACTTTGACTACATTAGAATTTAAAACTTTACTACT-AAAAGTG 1430
                           i i   v  v    v   i i    v        vv i  -v    - 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-G 676

  chr2_188931489_   1431 ACCTTAT--AAAATGTGAAAAG------------------GAAAGTCT-- 1458
                           vi   -- i  v        ------------------    i v --
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_188931489_   1459 ---AACCAT-TA-CTAATA-----TTTG------GAAAATATGAAGGTTA 1492
                         ---  i   -  -  i   -----i   ------   v    i   iviv
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_188931489_   1493 CCTACAAATCAATAAGAAAGAGA-AAAT---CTAATTAAAGCAAAAACAA 1538
                          i     v       v   i   -    --- i    ?  ----   iii
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA----AAATGG 822

  chr2_188931489_   1539 CCATCAAAAAGGCTAGGAACAGGCAAACTGCAAAAGGAGAAACTCAAGTA 1588
                         v  -----    v vv   i  i  vviiv v    i   v iv   i i
  L1M4_orf2#LINE/    823 GCA-----AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_188931489_   1589 CCTAATAAGCAGATGAAAAGCTGCTCAATCTCTAGTAATTA 1629
                         v i        v        v       iv  v????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (90 / 71)
Gap_init rate = 0.03 (18 / 530), avg. gap size = 3.33 (60 / 18)  


 852 26.36 1.36 0.45  chr2_188952285_188955411     1421  1640 (1487)    L1M4_orf2#LINE/L1        1   222 (686)  

  chr2_188952285_   1421 TGAAAAGATATTTCATGTTCATAAATTAGAAGAAATAATATTGTTAAAAT 1470
                           i        ii         ii   i     vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_188952285_   1471 GTCCATACTACTCAAGGCAATCTACAGATTCAATATAACCCTTATTAAAA 1520
                          v v     v i   ivii              iii  i  i   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_188952285_   1521 TTCCAATGACATTTTTTACAGAAATAGAAAAA--AATCTTAAAATTCATA 1568
                          i   iivi v      i       v  v  i--i   i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_188952285_   1569 TAGAACCGTAAGAGATCCCAAATAGTCAAATCAATATTAAGTAAGACGAG 1618
                          i   vi i   i  i  vi     i    v    v  i iv    v  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_188952285_   1619 CCGGGT-GCAGTGGCTCTCACCT 1640
                          vii  - v  - i   v   i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAG-GACTCACACTT 222

Transitions / transversions = 2.05 (39 / 19)
Gap_init rate = 0.01 (3 / 222), avg. gap size = 1.33 (4 / 3)  

2714 23.59 2.07 1.24  chr2_188952285_188955411     1911  2635 (492)    L1M4_orf2#LINE/L1      178   908 (0)  

  chr2_188952285_   1911 AAAAAAAT---GAGTAAAAAGAACAAAGCTAGAGGCATCACACTACCAGA 1957
                             v   ---  iv  i          i i    vv       v  vi 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_188952285_   1958 CTTTAAAATGTACTGCAAATCTATAGTAATCAAAACAGCATGTTACTATT 2007
                         i  i    iv    i    v   i         i    ii  v    i--
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG-- 275

  chr2_188952285_   2008 ATAGCATATGGACA--CATACAGA--AATGAAACTTAATAGAGAGCTCAT 2053
                         ---     v   i --    i   --    i  ivv   v     ii  v
  L1M4_orf2#LINE/    276 ---GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_188952285_   2054 AAATAAATCCATGCATTTGAAATCAACTGATTTTTGACAAAGGCACCAAT 2103
                                i    i     ivii    i       i     i  ii    v
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr2_188952285_   2104 AACACACAATAGGGAAAAGAC--TTTCTTCAGTAAATAACGTTGGGACAA 2151
                          v  iv    i      ii i-- i i    ii    iii i        
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_188952285_   2152 CTGGATATCCATATGTAGAAGAATGAAACTAGACCTTTTTTTCCACACCA 2201
                                ?   i   i i         ii i    ii vii  -      
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC-ACACCA 471

  chr2_188952285_   2202 AATACAAAAATCAACTCAAAATTGATTAAAGACTTAAATGTAAGATCTGA 2251
                         v          i          v   i ?    i           v  i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_188952285_   2252 AACTGTAAAACTACTAGAAAGGAACAT-GGGGAACAGCTCCATGACATTG 2300
                             i       vi     iii     -  ? v v v  i i    v   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr2_188952285_   2301 GTATGGGAAATACATTTTTGGATATGA-ACGCAAAAGCACAGGGAACAAA 2349
                          vv i  v   ivv  i  i       -  -          i v      
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACAC-CAAAAGCACAAGCAACAAA 620

  chr2_188952285_   2350 AACAAAAATAGGCAAATGGGATTATATCAAACTAAAAAACTTCTGCACAC 2399
                          iv        ii    v   i vi      v v        i  ii vi
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_188952285_   2400 TCAAGGAAAATATCAACAGAGTGAAGAGGCAACATACAGATTGAGAGAAA 2449
                         iv     v v      v i      i  i    vi     v  i      
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_188952285_   2450 CTATTTGCAAACCATACCTCTGATAAGAGATTAATATCCAAAATATATAA 2499
                         v          i    iv         i  i vi      i         
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_188952285_   2500 GAAACTCAATATTACTT--T--TAGAAAACCAAATAATTAATTTTTAAAA 2545
                         ii     v-  iv   i-- --  i   iv       iiv v  ?v    
  L1M4_orf2#LINE/    771 AGAACTCT-TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_188952285_   2546 TGGGCAAAGGTCTTGAGTAGACATTTCTCAAAAGAAGACATACAAATGGG 2595
                                   vi    i            v        i          v
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_188952285_   2596 CAGCAGGTATACGAAAAATATGCTAAACACCACTAATCAT 2635
                           ii i i i i     i-     v    i  ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (109 / 58)
Gap_init rate = 0.02 (13 / 731), avg. gap size = 1.85 (24 / 13)  


3991 18.08 6.03 0.81  chr2_189039226_189041402.rev      823  1685 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189039226_    823 TGGCAAATATACCCTAGGCTTATACACTGTA-GACTTAATATTGTTAAAA 871
                            -   v   i  i v i i  iv i  v -                i 
  L1M4_orf2#LINE/      1 TGG-AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_189039226_    872 TGGCAATATTTTCCAACTTAACCTACAGATCTAATGCAATCCTTATCAAA 921
                                 i ii    v  i i        ii  i       i       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_189039226_    922 ATTTCAGCTGCCTTTCTTGAAGAAATTGATAATCTGATCCCAAAATTCAT 971
                           ii           i   v         i  v       i         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_189039226_    972 ATAGAAATACAAGGAACCCAGAATGGACAAAATAATACTAAAAAA----- 1016
                           i     i     i         i v     i   vi i     -----
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_189039226_   1017 ----AGTTGGAAGAT--ATGCTTCCCAATTTTAAAATGTACTACAAAGCT 1060
                         ----       i  i-- ii           i    iv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_189039226_   1061 AAAGTAATTAAGACAGTGTGGTCCTGGCATAAATCTAGGCCTATACATCA 1110
                          v      i             v         ivv   i v    v    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_189039226_   1111 ATGGAGTAGAATTGAAAATCCAGAAATAAACCCTTATATGTATAGCCAAT 1160
                              i         i i               v  i  v   i i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_189039226_   1161 TGATTTTTTGCAAAGGTGCCAAGACAAATCATTGGGGAAATAATAGTCTT 1210
                                ivi   i           v v   v        v         
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_189039226_   1211 TTAAACAAATGGTGCTGGCACAACTGGGGATCCAGATGTAAAATAATGAA 1260
                           v               v        iv ?   v   i    v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_189039226_   1261 GTTGGACCCCCTATGTCATATTATACACAAAATTTCACTGACAATAGTTT 1310
                                   -  iv   i ii   i      v  v   v v   i v i
  L1M4_orf2#LINE/    450 GTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_189039226_   1311 ATAGAGCTTACTGAAACAGCTACAACTGTAAAACTCTTAGAAGAAGACAT 1360
                          ?   v  v v  v  v     v    i                 i    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_189039226_   1361 AGCCATAA-TTTTCATGATCTTGATTTAGGCAATAGTTTCCCACATATGA 1409
                           v?i   - i   i   i    iv         i     ii v      
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_189039226_   1410 AATCAAACAGAAAAACAATAAAATAAAATATATACATCATCAAATATTTT 1459
                         v i    viv v  i   i    v    v   v i -v  iii i---  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA-AATTGGAC---TT 644

  chr2_189039226_   1460 CATCAAAATATAAAAGTTTTGT--TTCACAGGACCAC-ATCAAGAAAGTG 1506
                                  vv    v      --    v     -  -            
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC-ACTATCAAGAAAGTG 693

  chr2_189039226_   1507 AA--GACAATCCACAGAATTGCAGAAAATATTTGCAAATCATACATCTGA 1554
                           --     i         v v                     i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_189039226_   1555 TA-GAGA-----------------------------ACAACTCAACAATA 1574
                           - i  -----------------------------         i    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_189039226_   1575 AAAAGACAA----CTCAATTAAAAACTGAGCAAAATATCTGAGTACACAT 1620
                                  ---- i     ?    v  i     iv  i   i  v    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_189039226_   1621 TTCTCTAAAGAAGATATACAGATGATTAATAAGCACATGAAAAGATATCC 1670
                              i              i   iii                   iii 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_189039226_   1671 AATATCATTAGCCAT 1685
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (92 / 60)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.93 (59 / 15)  


2847 26.81 1.89 0.89  chr2_189080098_189084343.rev     2856  3754 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189080098_   2856 TGGAAACACATTCCATGCTCATGGATTGGAAGAATAAATAATGTGAAAAT 2905
                               v i  i     i               v v    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189080098_   2906 GACCATACTGTCCAAGGCAATTTACAGATTCAATGCAATTCC-ATCAAAA 2954
                          i v     vi    ivii  i           i     i  -       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189080098_   2955 TAGCAAC-ATCATTTTCACAGAATTAGAAAAAA-AATCCTGAAATTCATA 3002
                          vv  i -ii v    ii     v v  v  iv-i     i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_189080098_   3003 TG-AAATGAAAAAAAGTGCTCA-AACAGCCAAAGCAATCCTAAGCAA-AA 3049
                           -     v  iii --- i  -  i       i     i i iv  -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_189080098_   3050 GAACAAATCTAGAGGCATTACATTTTC-AATT--A-----TATTATATGT 3091
                                vi i    vv i   i  i -    -- -----  i  i viv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_189080098_   3092 TTACAGTTACCAAAACAGCATGGTACTGGCATAAAAGTAAACACATAGAC 3141
                         i      v i   i    ii              iii  i   i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_189080098_   3142 CAATGGACCATAATAGAGAAGACAGAAATAGAGTCAAATACTTATAACCA 3191
                                vi v   v    ivv        i vi  v i i    iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_189080098_   3192 ACTGATCTTTGACAAAGCATATATAAACATAACT---TGGGGAAAGGACA 3238
                          i    i  i     i ---i iiv  v iv i ---         i i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG---GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_189080098_   3239 CCCTACTTAATAAATGGTTCTGGGAAAACTGGATAGCTACATGTAGAAGA 3288
                         vi  vi i  i       v      v         ? i     i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_189080098_   3289 GTGAAACTGGATCCCTATCTCTCATCTTATTTTAAAAAAACAACTCAAGA 3338
                         i    ii    i     i   v  i v   vi--     vi       i 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATAC--AAAAATTAACTCAAAA 492

  chr2_189080098_   3339 TGGGTCAAATCCTTAAATCTAAGACCTGAAACCATAAAAAACCTAGAAGA 3388
                            i   ? vv i     v     v  i    i      vv i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_189080098_   3389 TAACCCAGGAAAAACTCTTCTGAACTTCAGCCTAGGCAAAGAATTTATGA 3438
                         v   vi   ?iv  v     vvi  i ii vi       v iv  iv ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_189080098_   3439 CTAAGACCACAAAAGCAAATGCAACAAAAACAAATATAAATAAATGGGAC 3488
                         v  v   vv        v v         iv   v   i      v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_189080098_   3489 CTAATTAAACTAAGAATCTTCCATACAGCAAAAGAAATAATCAACAGAAT 3538
                         i v  i   v v i  v   iii i vv    i  v iv     v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_189080098_   3539 AAACAGACAACACATAGAATGGGAGAAAATATTTGCAAACTATGCATCCG 3588
                         i  v       v  i                        ii  ii   i 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_189080098_   3589 ACAATGGACAAATATCCAAAATCCACAAGGTACTTAAATAAATCAGCAAG 3638
                          i  v    vvi      i   vi i  i v   ivv i  v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_189080098_   3639 AAAAAAACAAATAATCCCATCTAAAAGTGGACAAATGACATAAATAGATA 3688
                              i        i  v  i?    i   i    v  iv i      i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_189080098_   3689 TTTCTCAAAAGCAGATAAACAAATACCCAACAAACATTTGAAAAAATGCT 3738
                               v    v     v      iv    i  i  iv      i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_189080098_   3739 CAACATCACTAATCAT 3754
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.92 (25 / 13)  


2883 24.31 2.37 1.31  chr2_189099586_189101329      499  1259 (485)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr2_189099586_    499 TGAAATCCCTATGAAAACAGCAAAAGACCTTGAATAGCCAAAGCAATCTA 548
                          i    i v    i   i-    ii    iv           i      v
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr2_189099586_    549 GAGCAAAATGAACAAAGCTGGAAGCATCACACTACCTGATTTCAAAATAT 598
                           iv  i v        i    i vv       v  ii         iv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_189099586_    599 ACTACAAAGTTACA-------AAACAGGATGGTTCTGGCATAAAAGAACA 641
                                  i    ------- i    vi    v         -- i i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA--GGATA 286

  chr2_189099586_    642 GACACATAAGCCAATGAAGCAGGATAAAGTGCCCAGAAATAAATTCCCAC 691
                             i   iii     i ii  i  vi  v i           ii vi  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_189099586_    692 ATTTACAGTTAATTGATTTTCAACAAAGATTCCAAGAACACACAGTGGAG 741
                              ii  i           i    i i v      v  iv  i   i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_189099586_    742 AAAGGACAGTATCTTCAATAAACAGTGCTGGAAAAACTGGACAGTTGCAT 791
                             i i   v i     i   ii       i v       i ?iii   
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_189099586_    792 GGAGAAGAATGAAATTAGACTGTCATTTCATGTCACATACAAAAATAAAA 841
                          v i         i  i   ivii ii   iii  i          v  -
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA- 485

  chr2_189099586_    842 AAAAACTCAAAATGATTTAAAGACTCAAACATAAGACCTCAGACTATAAA 891
                         -----         iv i ?    ii   ii     v  v i        
  L1M4_orf2#LINE/    486 -----CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_189099586_    892 ACTACTAGAAGAAAACAAAGGGGAAAAGCCCTGTGACATTGGTTTGGGTA 941
                            vi            v   ? v   v iii     v    v  i  i 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_189099586_    942 AAGATTTATTAGATAT---ATT-----CACA-GAAGCAAAGGCAAGAGTA 982
                          v i   v        --- ii-----    - v i    i v  i i  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_189099586_    983 GGCAAATGGTATTACATCAAAAATAAAAGGCTTCTGGATAGCCAAGGAAA 1032
                          ii    v v i v        v     i-   i  viivv v     v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA 679

  chr2_189099586_   1033 CAATCAACAAAGTGAAGAGACAACCTATGGAACGGGAGAATGTATTTGCA 1082
                          v     v        i        i ii   i       vi        
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_189099586_   1083 AACCATAAATCTGATAAGGGGTTAATAGCCA-AATATATAAGAAATTCAA 1131
                           i    v            ii vi  v   -         ii  i  vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_189099586_   1132 AAAACTCAATGGCAAAGAAACAAATAACCCAATTAAAGAATGAGCAAATG 1181
                          v        iii   i i               ?  i    i     v 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_189099586_   1182 ACCTGAATAGACATTTCTCAGAAGAAAACATACAGATGACCAACAGGTAT 1231
                          ii                vi     i i     i   i    i i i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_189099586_   1232 ATGAAAAGATGCTTTCC-TCATGACTAAT 1259
                                      ivv -   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.18 (124 / 57)
Gap_init rate = 0.01 (10 / 769), avg. gap size = 2.80 (28 / 10)  


3270 21.66 4.65 1.70  chr2_189109186_189111166.rev      608  1489 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189109186_    608 TGGAAAAACATCCTGTATTTAT----TGAAAGAC--AATATTGTTAAAAT 651
                               i i    ii i  i  ----  i     --           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189109186_    652 ATTCATACTACTCAAAGTAATCTACACATTCAACGCAATTCTGATTAAAA 701
                         iviv     v i    v i       v            i iv  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189109186_    702 TCCCAATAGTAGTTTTTGCA-AAATTAGAACAAAT--ATC-TAAAATTCA 747
                              iiv ivv        -     i--    ii--   -         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_189109186_    748 TATGAAACCACAAAAACCCCA-AATAGCCAAAACAATCCAGAAAAA---- 792
                             i  vii   iiiv    -                iv      ----
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_189109186_    793 -ACAAAGCTGGAGGCATCACATTTCTTGATACCAAAATGTATTA----AT 837
                         -      i      vv     i   iii  vi     iv  i  ----ii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_189109186_    838 TACAAAACACCAAAACAGTATGGAGCCAGAGCAAAGACAGATATATAGAC 887
                             iv - i   i     i   vi ii vii  i  i   i       i
  L1M4_orf2#LINE/    249 TACAGTA-ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_189109186_    888 CAGTGGAACAGAACACAGAACCCAGAAATAAGCCCATACAAATATAGTCA 937
                           i     i    ivv   ii          i        vv   i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_189109186_    938 ATTGATCT-------GGGTGCTAAGAACATACAATGAAGAAAGGATACTC 980
                               i -------      i    v   v     ii     i   v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_189109186_    981 TCTTCAACAAATGGTGTTGAGAAAACTGGATAGCCACATGCAAAAAAAGT 1030
                          i              i  i  v         ?            i  - 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-T 446

  chr2_189109186_   1031 GACATTGTACCCTTATCTTACAACGTACACTAAACTCAACTCAAAATAGA 1080
                           vi   v    i  i  i   v i  i  v   v i          i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_189109186_   1081 TTAAGGACTTAAACATACGACTCAAAATTGTTAAACTCCTAAAAGAAAAC 1130
                          i ?i   i    ii  v  vii    i i v      i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_189109186_   1131 CTAAGAGAAAAGCTTCATTACATTGGTCTTGGCAATGATGT--TACAGAT 1178
                         v  i ? v   v    i v  v    vi v       i v --  v v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_189109186_   1179 GACACCAAAAGGACAAGCAACAAAA-------TAAACATGTGGGACTACA 1221
                                    v             -------  i i vi v     v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_189109186_   1222 TCAAACTAAAAAGCTCTTGCACAGCAAAGAAAACAATCAACAATGCGTGA 1271
                              v v    i  i   ii vv     i v  v     v  --v    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA--AGTGA 694

  chr2_189109186_   1272 AAA-ACAAGCACTATAGAATGGGAGGAAATACT-GCAAGACACATATATT 1319
                            -    - - i i          i     i -    iv  i    v v
  L1M4_orf2#LINE/    695 AAAGACAA-C-CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_189109186_   1320 ATGAGGA--TAATCTCCAAAATATA-AAAGAACTCCTATAACTCAATATT 1366
                           i   i-- vi v    i      -         i  i         v 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_189109186_   1367 AAAAAAAAAAACACAAATGGCCCAATTAAAAAATGGGCAAAGAATCTGAA 1416
                              i ------     ii       ?              i  i    
  L1M4_orf2#LINE/    793 AAAAAGA------CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_189109186_   1417 TAGACATTTTTTCCAAAAAAGATATGCAAATGGCCAACAGGAACATGAAA 1466
                                  i -     i       i           i i v        
  L1M4_orf2#LINE/    837 TAGACATTTCT-CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_189109186_   1467 AGGTTCTCAGCATCACTAATCCA 1489
                           i v    i     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (122 / 65)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.43 (56 / 23)  


1480 24.97 4.22 12.32  chr2_189235446_189240141     3282  4206 (490)    L1M4_orf2#LINE/L1       59   908 (0)  

  chr2_189235446_   3282 TCTTCATACTGATGTATAGATTTAACACAATTCCTGTCAAAATTATAGCA 3331
                           ii  v i    v  i     i   i    i   i       ivi   v
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_189235446_   3332 AGGTTGTTTGTAGATATAGACAAGACAAGATTATTCTAAACTTTATATGG 3381
                         ivv  v    i   v  v      - ---- v  i     v  i      
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAG-C----TGATCCTAAAATTCATATGG 153

  chr2_189235446_   3382 AAAAGCAGAGGAACTGGAATCACTAAAACAATTTCAAAAAAAGAGCAGTG 3431
                            v   ii   v ii    vi i        i ii     ii  - iii
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG-AACA 202

  chr2_189235446_   3432 AAGTGAAAGTAATTCAT-CTACCCTGTTTCAAGACTTATTAGATACCTTT 3480
                             vii  -i i   i-  v   vi      i     i  v v v  vi
  L1M4_orf2#LINE/    203 AAGTTGGAG-GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_189235446_   3481 ACTAATGAAGAC--TTTAGTTTTGGTGGAGGGAAAGACA-ATAGGTCAAT 3527
                          v    v     -- v i  vi   iiv i   v     -    i     
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_189235446_   3528 GGAAGAG---TGAACAT--ATAAATTAACACACAGAAATATGCCCAGCTA 3572
                             v  ---   ivi -- v    v   v  i v vv    vi  ii i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_189235446_   3573 ATGTTTGTCAATGCTGCAAAAGCAGTGCAATAGGGGAAAGAAGGTTTTGT 3622
                           v  i v   v v   v  ii vi v    -          --------
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAA-------- 392

  chr2_189235446_   3623 TTTGTTTTGTTTTGTTTTGTTTTGTTTTATTTTGTTTTCAGACAGTGCTG 3672
                         ---------------- v  i  --  i v--------  i ii      
  L1M4_orf2#LINE/    393 ----------------TAGTCTT--TTCAA--------CAAATGGTGCTG 416

  chr2_189235446_   3673 GTGCAATTGGACTTTCATAGGCAAATAAAATGCACCTTGACCTAAACCTC 3722
                          vi   i    iv?i  i v     - i    v vi v    ivv     
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAA-AGAATGAAGTTGGACCCCTACCTC 465

  chr2_189235446_   3723 ACACTCTATCTAAAAATTAACTGAAAATTCATCATGGACTTAGATATAAA 3772
                             iv   vi           v     vv    ?i   i  i  i   i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_189235446_   3773 AA-TACAACTATAAAACATTTAGAAAAAAAACACATGGG-AAATCTTCAG 3820
                          i-  v           vi      i    -  i v ? -        iv
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGTAAATCTTCGT 564

  chr2_189235446_   3821 GATGTAGGGCTAGGAAAAGAGTTCTTAGAATTGACATCCATAGCAGGATT 3870
                           iv v   i    v  v iv        vv     i v v    vi vi
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_189235446_   3871 --TAAAATGGGGGAAAAT-GATATACTGAACTT--------TTGAAAACA 3909
                         --i    --- ii     -    v i  i    --------  i     -
  L1M4_orf2#LINE/    615 AACAAAA---GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC- 660

  chr2_189235446_   3910 TTTTTCTATGTATAAGTGCTTTGTTCCATGTCTTAGGAAAGCATTCTTTT 3959
                         -    ----------      i---------------    v iv  ---
  L1M4_orf2#LINE/    661 -TTTT----------GTGCTTC---------------AAAGGACACT--- 681

  chr2_189235446_   3960 TTTATCA-TAAAGTAAAATATCTGTATTTTGTTTAGATGCTCCTTATCAA 4008
                         ---    -v     i   ----------------   iivi  -- ivi 
  L1M4_orf2#LINE/    682 ---ATCAAGAAAGTGAAA----------------AGACAACCC--ACAGA 710

  chr2_189235446_   4009 ATTAGGGATGAAAAGACGGGGAGAAAGTATTAGCAAACCACATATCAGAC 4058
                           ----------------        i    v     i  i     v  i
  L1M4_orf2#LINE/    711 AT----------------GGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_189235446_   4059 AAATAACTAGTA------------AAAAATCATTCAACACTCAACAATAT 4096
                           ivi   v   ------------   i v vi i vv      i    v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_189235446_   4097 GAAAACAA-TGA---AATTAGAACATGAACAAAAGACAACAAGATGCATT 4142
                         i  i    - i ---    ?i  v   ii    i  ivvv  v vi    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_189235446_   4143 TCATTGAAGAGGATATACAGATGGAAAGTAAGCACGTGAAAAGATGTCAA 4192
                           viii    i        i    vv i       i          iiv 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_189235446_   4193 ACATTGGTGTCCAT 4206
                             ii????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (129 / 98)
Gap_init rate = 0.04 (32 / 850), avg. gap size = 4.78 (153 / 32)  


2401 26.86 7.89 0.94  chr2_189241656_189246430.rev     3435  4283 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189241656_   3435 TAGAAAAATATCCTATATTCATGGATCATAAGAAATAATATCATTTAAAT 3484
                          i    i      i  i         iiv    vv      ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189241656_   3485 GAC--TACCATCCAAAGCAACCTGTAGATTCAATGCAATGCCTATCAAAA 3532
                          i --   ivi     vii i  ii        i     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189241656_   3533 T----------------------ACTGACA------TC-----ATTCATC 3549
                          ---------------------- i     ------  -----      -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT- 149

  chr2_189241656_   3550 ACAGAA---TAAGAAAC--GGCAAACTTAAAGCAATTCTGAGCAAAAAGA 3594
                          ii   ---i   ii  --i v v vii   i    ii   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_189241656_   3595 GCCAAGCTGGAGGCATCACATTACCCGACTTCAAAA--TA-TACAAGGTA 3641
                         i v   i      vv     i v   i i       --  -     i iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_189241656_   3642 ACAGTAACCAAAGCAGTATGGTATTGGTATAAAAACAGACACACAGAATA 3691
                                i   ii    i     i   i    ii i     i i   vi 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_189241656_   3692 ATGGAATAGAATAAAGAACTCAGAAATAAAACCACTTATTTACAGTCAAC 3741
                                     vi   iii          v   ivi     ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_189241656_   3742 TGAGGTTTGACAAAG---CCAAAAAGAAGTTACACTGGAGAAAGAACATC 3788
                            vv  i     i ---    i vv --  -  v   i       i vi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCA--TT-CAATGGGGAAAGAATAGT 396

  chr2_189241656_   3789 CTCTTCAATTAATGGTGCTGGGAAAATTGAAT-------TG-AATAGAAT 3830
                           i     iv             v  i  i  -------  -  v     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_189241656_   3831 GAAACTGGACCCCTATC----ACCATATATAAAAATCAACTCAAAGTGGC 3876
                            ii          i ----        i      i        i   v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_189241656_   3877 CTAAAAACTTAAATGTAATATCTGGAACTGTAAAAATATTAAAAGAAAAT 3926
                         ii ? i  i         v v  ii    i     v v   i       i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_189241656_   3927 CTAAGG--AAAACTACTGAACATTGGGCTAGGCAGAGAATTTATGACTAA 3974
                         v  i ?--   v  v vvi  v     i      iv iv  iv iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_189241656_   3975 GATCTCAAAAGTACTGGCAACACAAACAAAAATGGACAAATGGTACTTAA 4024
                           ivi      i  vi      v  iv      i  i    v v    v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_189241656_   4025 TTACACTAAAAAGCATCTACACAGAAAAATAAATAATCAACAGAATGAAG 4074
                          i v v v    i v i iii vvv   iv v iv     v i i    i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_189241656_   4075 AAACAACTTTT-GAATTGGAGAAAATATTTTCGGATTATTCATCTGACAG 4123
                          i     iivi-    v             v ii  i  vi      i i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_189241656_   4124 AGGACTAACTTCCAGAATATACAAGGAACTCAAACAACTTAG----AAAA 4169
                         i     viiv           i  i      vv      i i----    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_189241656_   4170 AAA-AAATGTTCCCATTTAAAAAAAAATGGG-AAAGAACATGAATAGACA 4217
                          i -    ivi  v   ?     ----    -    i iv          
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAA----TGGGCAAAGGATTTGAATAGACA 842

  chr2_189241656_   4218 TTTCCCGGAGGAAGACACACATTCAGCCAGCAAGTATATTAAAACATGCT 4267
                             i vi i     i i   vvii    ii   i i  v    v     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_189241656_   4268 CAATATTATAATCATC 4283
                            i  i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (146 / 79)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.57 (75 / 21)  


1897 27.84 6.64 2.86  chr2_189252268_189256170     2552  3424 (479)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_189252268_   2552 GAAAGATA--CCATGTTTATAGATTGGAAGGCTCAGTTTAATTG---TGG 2596
                                 --       i  i         i  i i v vi  i---   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_189252268_   2597 TTAATTCTACCAAATTGATCGATCCATGGATTCAATACAATTCTGATTAA 2646
                         i-   v  v  v  ---  i    i ii       ii    i iv  i  
  L1M4_orf2#LINE/     53 C-AATACTCCCCAA---ATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_189252268_   2647 AATCACAATGGGATTGTTAGTAAAAACTGAAAAGTTATTTCTAA------ 2690
                             v  iiv vv  v  v i i   i   v   i iv i    ------
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_189252268_   2691 TAAGGTAATGTAAATTACCTAGAACAAAAACAAATTAATTTTGAGAGAGA 2740
                           v  v    i  ivv   i    i iv--    vi   i    i i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGC--CAAAACAATCTTGAAAAAGA 196

  chr2_189252268_   2741 AGACCAAAATCTGGGCAAGCATAC---CTGATGTCAGAACTTACCTTAAA 2787
                            v    i iv i v vv  i  --- ii  v   i       ivi   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_189252268_   2788 -CT-C--TTATCAAGTCAGGGTGATATTAATGTAATAATA-----ATAAA 2828
                         -  - -- v      v   v   i  i iiii   vi   -----   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_189252268_   2829 T-----GAACTGTATTGTAGAGTTTAGAAATA--TCCATACATACATGGT 2871
                          -----   iv v    -     ii       --i        vi     
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTG-AGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_189252268_   2872 TAATTTTTTTTCCCACAAATGTGACAAAAA-ATTCAATGGAAAAAAGAAA 2920
                         i    vv     v-    iv   v   i v-         ii   ii v 
  L1M4_orf2#LINE/    346 CAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_189252268_   2921 GTCTTTTTGACAAATGGTTTTGAAATAACTAGCTAAATATATGGGAAAAA 2970
                                ii         vi  ii i    i v  ?vi i   vi   i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_189252268_   2971 ATTATGAAAATTATCTCCTACTT-ACGCTACATA---AAACTA-TTTGAG 3015
                           ---   iv viv i     i -  i i i   ---   i  -i ii i
  L1M4_orf2#LINE/    445 AT---GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_189252268_   3016 GTGGATCATAGACATAAAAGTAGAAGCTTTTGTAATCTTATACGTAACTT 3065
                         i       ?    v    v   ii    -----  vvi    v--    i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCT-----AAAACTATAA--AACTC 534

  chr2_189252268_   3066 TCATTAAAAAACATAGA---ATGTCATTATGAACTTTGGATGGATAGTGA 3112
                          i vv i         i--- vi  v ii   v   v  v i ii i  i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_189252268_   3113 TTTCCTGGAAATGACCCCAAAAGCACTA-CACATGAACAAAAAAA-GGAT 3160
                             i i  v     v          v -  - ii  vi      -i   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCA-ACAAAAGAAAAAATAGAT 633

  chr2_189252268_   3161 ACAATGGACTTTATCAAAAATAAAACATTTTCTGTTAATCTATAAACACT 3210
                          v v       i       v     vv    v  i --  v vii     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGGACACT 681

  chr2_189252268_   3211 ATCAGCAAACTGAAAAAGCAA--------GTGGCT----ATATTCCCAAT 3248
                             iv   v      ii   --------i   vv----     iv   v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_189252268_   3249 ACGTGTATCTGAAAAAGGATCTGTATCCAGACTATATAAAAAACTCCTAA 3298
                         v i i       v  i   ii          v        i     i  v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_189252268_   3299 AAATCACAAATAAAAAGACAAAACACCTAAT--AAAAGTGGGCAGTAGAC 3346
                           v   vv              vv   i   --    i      ivi  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_189252268_   3347 TTCTACAGGGAGTTAGTTTATTAAAGAGAACATA-AAAGAGGCAATGAAC 3395
                           vv i  i----i v  ivii     ii i   -   vi v    i i 
  L1M4_orf2#LINE/    832 TTGAATAGA----CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_189252268_   3396 ACACGAAAC--TGAGCAATATTATTATTCAA 3424
                            i    v--  vv   i  i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.04 (33 / 906), avg. gap size = 2.52 (83 / 33)  


2136 27.82 1.11 0.48  chr2_189339098_189340726      501  1129 (500)    L1M4_orf2#LINE/L1      249   881 (27)  

  chr2_189339098_    501 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 550
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_189339098_    551 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 598
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_189339098_    599 ATCTGATCTTTGACAAACCTGACAAAAACAGGAAATGGGGAAAGGATTCC 648
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_189339098_    649 CTATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTGGAAAGCT 698
                           v  i  i       i      v      v  ?   i   iii  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_189339098_    699 GAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGA 748
                            ii    i    v   i     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_189339098_    749 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 798
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_189339098_    799 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 847
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_189339098_    848 AAACACCAAAAGCAATGGCAACAAAAGCCACAATTGACAAATGGGATCTA 897
                         vi            vvi          vv v   v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_189339098_    898 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGATTGAA 947
                           i   v v  i i   i  ii vv    i  v    i  vv i v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_189339098_    948 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACTCATCTGACA 997
                         v  i     i                 v      ivii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_189339098_    998 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 1047
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_189339098_   1048 AAAACAA----CCCCATCAACAAGTGGGTGAAGGACATGAACAGACACTT 1093
                           i    ----   v  i? v  i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_189339098_   1094 CTCAAAAGAAGACATTTATGGAGCCAAAAGATACAT 1129
                            v        i  vi vivi     v iii    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 1.44 (101 / 70)
Gap_init rate = 0.01 (5 / 633), avg. gap size = 2.00 (10 / 5)  


3112 27.02 1.22 0.66  chr2_189370703_189372708      612  1514 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189370703_    612 TGGAAGAACATTCCATGCTCTTGGATAGGAAGAATCAATATCATGAAAAT 661
                              ii i  i     i  v     v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189370703_    662 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCTGTCAAGC 711
                            v     v     iv i  i  i       ii  v      i    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189370703_    712 TACCAA-TGTCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 758
                          v   i-  i    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_189370703_    759 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAA 808
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_189370703_    809 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 858
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_189370703_    859 CTATAGTAACCAAAACAGCATGGTGCTAGTACCAAAACAGAGATATAGAC 908
                            i     i   i    ii    i  i i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_189370703_    909 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 956
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_189370703_    957 CATATGCTGTTTGATAAACCTGACAAAAACAAGAAATGGGGAAGGATTC- 1005
                           vv  v v  i  i  ivv  v   i v  vvv         i  v v-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_189370703_   1006 CCTATTTAATCTATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1055
                         i  v  i  ivv            v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_189370703_   1056 CAAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 1105
                         ii  ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_189370703_   1106 ATTAAAGACTTAAATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAA 1155
                           i ?    i       v   v  i    i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_189370703_   1156 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 1204
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_189370703_   1205 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 1254
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_189370703_   1255 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAAAGTGA 1304
                         v  i   v v  i i   i  ii vv    i  v    i  vv       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_189370703_   1305 AAAGGTAACCTACAGAACGGGAGAAAATTTTTGCAATCTACTCATCTGAC 1354
                             ii    i      i          v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_189370703_   1355 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 1404
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_189370703_   1405 AAAAACAA----CCCCATCAACAAGTGGGTGAAGGATATGAACAGACACT 1450
                            i    ----   v  i? v  i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_189370703_   1451 TCTCAAAAGAAGACATTTATGCAGCCAGCAGACACATGAAAAAATGCTCA 1500
                             v        i  vi viii    ii ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_189370703_   1501 TCATCACTGGCCAT 1514
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


2763 27.13 2.55 1.99  chr2_189372835_189376378.rev     2156  3058 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189372835_   2156 TAGAAAAACCTTCCATGCTCCTGGATTGGAACAATCAATATCATTAAAAT 2205
                          i    i iv i     i  v          v v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189372835_   2206 GGCCACACTGCCCAAAGCAGTTTTCAGATTCAATGTTATTCCTATCAAAC 2255
                            v i   v      viii i v         i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189372835_   2256 TACCAG-TGTCATTTTTCACAGAATTAGAAAAAAATATTCTAAAATTCAT 2304
                          v    -  i -     ii     v v  v  ivvv  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_189372835_   2305 ATGGA-----------TCCTGAATAGCCAAAGCAGTCCTGAGCAAAAAGA 2343
                              -----------i  v           i  i  i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_189372835_   2344 ACAAAGCCAGAGGCATTGCATTATCTGACTT-GAAACTATACTATAAGGT 2392
                               iii    vv ii  i vi ii i  -i     -     i  i i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_189372835_   2393 TACAGTAAATAAAACAACATGGTACTGGTACAAAGACAGACATATAGAGT 2442
                                 vi  i   iii         i i  i  i           vi
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_189372835_   2443 AATGTGTAGGACAGGTAGGAGAACCCAGATATACAACTGCACACCTACAG 2492
                             ---- i i  ivvv    ii     v   v v iii   ii  ii 
  L1M4_orf2#LINE/    299 AATG----GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_189372835_   2493 CCATCTGATGT-CGATAAAGTCAAATAAAAATTAAGCAGTGGGGAAA--- 2538
                         i  vi    v -   i  i --iviiv  i ii vv  i        ---
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGG--GTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_189372835_   2539 -AGTCTTCCCTTTTTTATAAATTGTTGTGGGATAGCTGGCTGGCCACACA 2587
                         -      -----  iv i    v  vv     i i    v i?     ii
  L1M4_orf2#LINE/    393 TAGTCTT-----TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_189372835_   2588 CAGAAGAATGAAACTGAATCCCCACCTTTCACCATATACAAAAATTAACT 2637
                           i         ii  i i   i    iv                     
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_189372835_   2638 CAACATGCATTAAACATTTAAATGTAAGATGTCAAATTATAAGAATCCTG 2687
                            v   v  i ? v ii           vv v   i     i v  i i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_189372835_   2688 GAAGAAAATCTAGGAA-AAACCATTCTTGACATTGGTCTTAGGACAGAAT 2736
                                 iv    ?i-   i -   v    v    v-     vv vii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGT 585

  chr2_189372835_   2737 TTAT--GACTAAGTCCTCAGAAGCAATTGCAACAAAACAGAAGTT-GACA 2783
                           v --  -  v v vi  i     vvv         v i  iv -  i 
  L1M4_orf2#LINE/    586 TTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_189372835_   2784 AATGGGGCTTAATTAAACTAAAGAACTTCTGAATAGCAAAATAAACTATC 2833
                            v  i   v  i   v v  i     i  viivv    iv v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_189372835_   2834 AACAGAGAAAACAGATGATGTAGAGAACGGGAGAAAATATTTGCAAACTA 2883
                           v i  vi  v   ii ivi v    i                   ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_189372835_   2884 TGCATCTGACAAAGGTCTAATATCCAGAATCTATTACAAACTTAAACAAA 2933
                          ii      i  i  v  vi          v   v vi    ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_189372835_   2934 TCAACAAGCAAAA-ACAAAAAACCCTATTTAAAAAATGAGCAAAGGATCT 2982
                             i  vv    -     v     v   ?     -  i         i 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTT 833

  chr2_189372835_   2983 AAACGGATGCTTCTCAAAAGAGGACATAAAAGTGGCCAATAAACATATGA 3032
                         i  ii  iii     v     i  i   v  i          i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_189372835_   3033 AAAAAATGCTTATTGTCACTAATGAT 3058
                            i -    i vii   ????????
  L1M4_orf2#LINE/    884 AAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.16 (41 / 19)  


1714 22.82 2.32 14.51  chr2_189377777_189383569.rev     4275  5308 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189377777_   4275 TGAAAAAACATTCCATGCTCATGGATAAAAAGAATCACTATAATTAAAAT 4324
                           i   i i  i     i        vii    v i v   vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189377777_   4325 GACCATACTGCCCAGAGGAATTTATGGATTTAATGTCATTTCTATCAAAC 4374
                          i v     v    i vvi  i  ii    i  i iv  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189377777_   4375 TACACA--TGACTTCTCTACAAAACTAGAAAAAAAAAACCCACT-ATTTT 4421
                          v -  --  v   i i i  i  v v  v  i---------  -  ii 
  L1M4_orf2#LINE/    101 TCC-CAGCTGCCTTTTTTGCAGAAATTGACAAG---------CTGATCCT 140

  chr2_189377777_   4422 AAAATTCATATGGAGCCAAGAAAGAGCCTGAATAGCCAAGCCAATCCTAA 4471
                                       iviivi ii  v  v          iv     i i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_189377777_   4472 GCAA-AAGAACAAATCTGGAGGCATCACGCTACCTGACTTCAAACTATAC 4520
                         iv  -         vi      vv    i  v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_189377777_   4521 TAACAGGGCTACAGTAATCAAAACAGCATGGTACCAGTACGGAAACAGAC 4570
                           -  ii              i    ii      ii i iiiii i    
  L1M4_orf2#LINE/    241 TA-CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_189377777_   4571 ATATAGACCAATGAAACAGAATAGAGAG-CCAAAAATAAGCCTGCACACC 4619
                                i     i  i     v     -   i      i  iii   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_189377777_   4620 TACAACCACCTCATCTGTGACAAAACTGACAAAAACAAACAATGGGAAAA 4669
                           iiii  vi v  i vi     iiv  v   i v  vv       i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_189377777_   4670 GATTC-CCTCTTCAGTAAATGGTGCTGGGATAACTGGGCCCCTTCCTTAC 4718
                           v v-i  i    ii              i      i---------  ?
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA---------TAK 430

  chr2_189377777_   4719 ACCATATACAAAACAAAAACAAGAACAAAAAACACCTCAAAATGAATTAA 4768
                         -   i  i     --------------------------i      ----
  L1M4_orf2#LINE/    431 -CCACATGCAAAA--------------------------GAATGAA---- 449

  chr2_189377777_   4769 AGACTTAAATTGGAAAACCCATAACTATAAAAACCCTGGAAGACAACCTA 4818
                         --------i     ---   ----   -------   -----------i 
  L1M4_orf2#LINE/    450 --------GTTGGA---CCC----CTA-------CCT-----------CA 466

  chr2_189377777_   4819 CGCAATACCATTCTGGACATAGAAATAGGCAAAGATTTCATGATGAAGAT 4868
                          -----     ----- i i i    ---i  ----i   vi   --   
  L1M4_orf2#LINE/    467 C-----ACCAT-----ATACAAAAAT---TAA----CTCAAAATG--GAT 497

  chr2_189377777_   4869 GCCAAAAGCAGTGAAAAAAAAAAAAGCAAAAATTGACAAATGGGGTCTAA 4918
                         --  ? ii v- ---   viv  i   v    i --------------- 
  L1M4_orf2#LINE/    498 --CAWAGACC-T---AAATGTAAGAGCTAAAACT---------------A 526

  chr2_189377777_   4919 TTAAACTAAAGATCTTCTGCACAGCAAAAGAAACTACGATAGTAGGAAAT 4968
                          v     ------   --------- i      --  -    v? v    
  L1M4_orf2#LINE/    527 TAAAACT------CTT---------AGAAGAAA--AC-ATAGGNGTAAAT 558

  chr2_189377777_   4969 AACATTCTGGACATAGGAATGGGCAAAGATTTCA-AGATGAAGATGCCAA 5017
                         -- -   vv   v v  iv i     v i    v-    - v  ii    
  L1M4_orf2#LINE/    559 --C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAA 604

  chr2_189377777_   5018 AAGCAATTACAACAAAAAGAAAAATTGACAAATCGGACTTAATTAAACCA 5067
                              vvvi        ii      v  i    i      v  i   viv
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_189377777_   5068 AAGAGCTTCTGCACAGGAAAAGAAACTATCTATCATCAGAGTAAACAGAC 5117
                           i i   i  ii vvv   i  v      v v---- i   i  v    
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAG----AAAGTGAAAAGAC 700

  chr2_189377777_   5118 AACCTACAGAATGAGAGAAAATATTTGCAAACTATGCATTTGACAAAGTC 5167
                             i        i                 ii  ii  i   i  i vv
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_189377777_   5168 CTAATATTCAGCATCTATAAGGAACT--TA-AATTTAC-------AAGAA 5207
                           vi   i   v  v     i     --  -  i i v-------    v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_189377777_   5208 AAAAAACCTCATTAAAAAGTGGGCAAATGACATGAA----CACTTC--AA 5251
                            v    iv   ?    i        v  iv    ----  i   --v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_189377777_   5252 AAGAAGACATACACGCAGCCAACAAGCATATGAAAATA-GTGCAACCACA 5300
                                i     viii     i     i       v - iv    vv  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_189377777_   5301 CTGATAGA 5308
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.73 (147 / 85)
Gap_init rate = 0.04 (40 / 908), avg. gap size = 4.35 (174 / 40)  


 947 25.25 3.22 2.72  chr2_189399296_189401343       77   480 (1568)  C L1M4_orf2#LINE/L1   (0)   908   503  

C chr2_189399296_    480 ACCATATATGTGACACCATAAACCATAAAAATCCTAAAATGAAATGTCAA 431
                            -  v    i v v vv    i      v  i  i  vi   ii - i
  L1M4_orf2#LINE/    503 ACC-TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AG 550

C chr2_189399296_    430 AAATACCGTTCTCAATATCAACCTTGG--TA---AAGAGTTT-TTGGCTA 387
                         i?i  --iv   ivi i---       --  ---  vi    -  i v  
  L1M4_orf2#LINE/    551 GNGTA--AATCTTCGTG---ACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chr2_189399296_    386 AGTCCTCAAAGGTAATTGTAACAAAAACTAAAGAT-GACAAATGGGGTCT 338
                         v v vi    i i vvv i       iv-   i  -  i    v  iii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTT 644

C chr2_189399296_    337 CATTAAAGTAAAGAGCTTCTGCACAGCAAAAGAAAGTATCAACAAAGAAA 288
                            i   i v  i i   i  ii vv    i  v v      v    vi 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

C chr2_189399296_    287 ACAGACAACCTACAGAGTGGTAGAAAATATTGGCAAACTATGCATCTGAC 238
                          v        i     i   v          v     ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

C chr2_189399296_    237 AAAGGTCCAATATACAGAATCTATAAGGAACT--TA-AAC-CAACAAACA 192
                           i  v ivi   v      v     i     --  -   -   i  -i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TA 793

C chr2_189399296_    191 AAAAAACAAATAACCCCATT-AAAAATGGGCAAAAAAAACATGAACAGAA 143
                             i           v   -             ii --iv    i   v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA--TTTGAATAGAC 841

C chr2_189399296_    142 ACTTCTCAAAAGAAGATATAGAAGTGGCCAAAAAATATATTAAAAAA-GT 94
                          i     v            v  i       v  ii i  v    i - i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

C chr2_189399296_     93 TCATCATCACTAATTAT 77
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (60 / 41)
Gap_init rate = 0.04 (16 / 406), avg. gap size = 1.50 (24 / 16)  

3532 24.26 0.44 1.20  chr2_189399296_189401343      642  1556 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189399296_    642 TGGAAAAATATTTCATGTTTATGTATCAGAATAATTAATATTGTTAAAAT 691
                               i    ii      i   v  ii   v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189399296_    692 GTCCATCCTACCCAAAACAATTTACAGATTCAATGCAATCCCTATAAAAA 741
                          v v  v  v      vii  i           i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189399296_    742 TACCAATGACACTCTTCACAGAAATGGAAAAAAACAATCCTAAGATTTAT 791
                          v   iivi vi i  ii       v  v  iv-ii       i   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_189399296_    792 ATGGAACCACAAAAGACCAAGAATAGCCTATCCAAAGGCATTCTAAGCAA 841
                               vii   ii    v         -----   ivv  ii i iv  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCC-----AAAACAATCTTGAAAAA 194

  chr2_189399296_    842 AAAGAACCAAACTGGAGGAATCACATTACCTCACTTCAAAATGTACTACA 891
                         i      v  ii       v     i v  iv i       iv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_189399296_    892 GAGCTATAGTAACCAAAACAGCATGGTACTGGCATAAAAACAAACATGTA 941
                         i     i     i   i    ii              ii i i    i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_189399296_    942 GACCAATGGAACAGAATAGAGAACCCAAAAACAAATCTGCACACCTGCAG 991
                           i        i     v    ii   i   i   i iii   ii iii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_189399296_    992 TGATCTCATTTTCAACAAAAGTGCCAAGACCATACACTGGAGGAAAGATA 1041
                          v vi v      i    ii             v  v   i i  ii   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_189399296_   1042 ATATCTTCAATAAATGGTGGTGGGGAAACTGAATATTCATATGCAGAAGT 1091
                         i v i     i        v    iv     i   ?i  i     i   v
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_189399296_   1092 ATGAAACTAGACCCCTATCTCTCACCATATACAGAAATCATATCAAAATG 1141
                              ii i        i   v           i    i vv        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_189399296_   1142 GGTTAAAGATTTAAATCTAAGACCACAAACTATGAAACTACTACAAGAAA 1191
                          i i ?   ii     v     v vv       i     vi  v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_189399296_   1192 ACATTGGGGAAAATCTCCAGAACACTTGC-CTGGGCAAAAATTTATTAAG 1240
                             v  ? v      i ivi  -    v-i i     vii   v   ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_189399296_   1241 CAATACCCTACAAGCACAGGCCACCAAAGAAAAA-TGGACAAATGGGATT 1289
                         i vv  v i v       i  v  v         - i  i    v   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_189399296_   1290 ACATCAAGTTAAAAAACATCTGCACAATAAAGGAAACAAACAACAAAGCA 1339
                         v      iv v      v i  ii vvi      v  v v   v    ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_189399296_   1340 AAAAGACAACCCACAGAATGGAAGAAAATATTTGCAAACTCT-CATCTGA 1388
                                              i                iiv -i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_189399296_   1389 CAAAGGATTAATAACCTGAATATATAAGGAGCTCATACATGTTTATTAGG 1438
                         i  i   i vi  v  v          i  i   v    -ii i v  iv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCAATAAT 792

  chr2_189399296_   1439 AAAAAAAATCTAATAATT-GATTAAAATTATGGGCAAAAGATTTGAATGG 1487
                              i -- v     ii-i   ?   v-         i         i 
  L1M4_orf2#LINE/    793 AAAAAGA--CAAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAG 839

  chr2_189399296_   1488 ACATTTCTCGAAAGAAGATATACAAATGGCAAACAGGCATATGAAAAGGA 1537
                                  v                    v  i i   i        iv
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_189399296_   1538 GCTCAACATCATTAATCAT 1556
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (139 / 79)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


 617 26.79 5.80 3.12  chr2_189404048_189406227.rev      501   724 (1456)    L1M4_orf2#LINE/L1        1   230 (678)  

  chr2_189404048_    501 TAGAAAGATATTCCATGTTCATGAATTGGAAAACCCAAT-TTGTTAAGAT 549
                          i         i           i       i  ii   -          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189404048_    550 GTTAATTTCTCCCAACTTGATCTACATATACATTCATCTTCATCAATACA 599
                          vi   viii     v          v  ----   v viv   vv  --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGAT----TCAACGCAATCCCTA-- 94

  chr2_189404048_    600 ATCAAAATTTTAGCAAACTATATTGTAGCTATCAACCAAC--ATTCCAAG 647
                         -       iii   viv  v v   i  vv  ii  v i --  i i  i
  L1M4_orf2#LINE/     95 -TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_189404048_    648 GTGTATTTATAAAGGCAAAAAACCTCAAATAGC----ACAATTCTAAAAA 693
                         i vi  v iv   v    iii   ivi      ----     ii i    
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_189404048_    694 AGAA----AAAGGTGGGGAACTCAT--TACCTAATTT 724
                             ----    v   i i     i-- v  i     
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

Transitions / transversions = 1.61 (37 / 23)
Gap_init rate = 0.03 (7 / 230), avg. gap size = 2.86 (20 / 7)  

1833 26.36 5.45 0.76  chr2_189404048_189406227.rev     1030  1689 (491)    L1M4_orf2#LINE/L1      218   908 (0)  

  chr2_189404048_   1030 CATTACCTAATTTCAAGGCTTTCTGTAAAGCTACAGTAATCAAAATAGTG 1079
                           i v  i        ii   v  ii                 i i    
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_189404048_   1080 TGATCTTGGTAAAAAG-TAGACACATTAATCAATGGATCAGACCTG---- 1124
                           i vi   i v  i -      i  vi         vi   vi  ----
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_189404048_   1125 --CA----TAAATGCA---ATT-------AACTGATCTTTGACAAAAACA 1158
                         --  ----    iv  ---   -------  i    i  i     iiiii
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_189404048_   1159 CAAAAACAATTCAACAAAGAGAGGTTAATGTTTTCAATAAATTGTGCTGA 1208
                          v  i  v      iiii  i  iv  i v       i    v      i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_189404048_   1209 AAAAATTGGATATCCAT-TTCAAAA-ATTGAGTCTAGGCACAGGACTTAT 1256
                         i v  i      ?   i- v     - v   ivi i i v vviv  i i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_189404048_   1257 ACTTTTCACAAAAATTAATTCAAAATGGATGACAAAATTAAGTGTAAATA 1306
                           iv vi           i           v ? i vi   i     ivi
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_189404048_   1307 C-AATGCTATAAAAATTCTAGCAGAAAACA-AGGAGAAAATCTTTGTTAG 1354
                          -  vi        v ii   v        -   ? v       i  v v
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_189404048_   1355 TTTGGATGTGATAATAAATGTTTGCATGTCATACCAAAAACATGACCATG 1404
                         i    i vv ii   iiv vi  iv  i v i       i  ii v  --
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA-- 615

  chr2_189404048_   1405 AACAACAATAAAAAATAGG---AT-GGACTTTATTAAAATTAAAAAATTC 1450
                         -    -  v         i---  -      i  i           v  i
  L1M4_orf2#LINE/    616 -ACAA-AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_189404048_   1451 TGTTAAACAAAATCTACTTTTAAGAAAATGAAAATACAAACAACAAAATG 1500
                            vvvv    ivvi   v i      i      v    v v   i    
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_189404048_   1501 AGAGAAGTTATTTGAAAA--ACGTATCTGATAAAATACTTATATCTAAAA 1548
                         i     iv      v   -- ii          iiv    i    i i  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_189404048_   1549 TATACAAAGAACTCTTAAAATTCAATAATAATAAAACAA----CCCAATT 1594
                             i            v  i          v  i    ----       
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_189404048_   1595 TTAAA-TAGACAAAAGATTTATAAAGGGATCTCACCAAACAAGTTATACA 1643
                         ?v   - i i    i     iv v  iv  i  v     v   v      
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_189404048_   1644 TATATCAAATAAGCATATTGGAAAGATGACCAATATCTTTTTTCAT 1689
                         v  iv v        i  - i       vi   i   v????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACAT-GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (102 / 68)
Gap_init rate = 0.02 (17 / 691), avg. gap size = 2.41 (41 / 17)  


2601 25.08 2.05 3.89  chr2_189444799_189448306.rev     2092  3016 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189444799_   2092 TGAAAAAACATGTCATGCCCATGGATAGGAGGAATCAATATTTTTAAAAT 2141
                           i   i i  vi    ii       v   i  v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189444799_   2142 GGTCACACTGCCCAAAGCAGTTTACAGATTCAATGCTGTTCTTATCAAAC 2191
                           iv i   v      viii i           i  vi i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189444799_   2192 TACCAATATCATTTTTCATAGAATTAGAAGAAACT-ATTATAAAATCCAT 2240
                          v   iivv v     iii    v v  v-  i  -  iv      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chr2_189444799_   2241 ATGGAACCACAGAAGAGTCCAGG-TAGCCAATGTAATCTGAAGAAAAAAA 2289
                               vii  iii  -i    i-       vii     v--      i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTT--GAAAAAGA 196

  chr2_189444799_   2290 AAAACAAAGCCAGAGGCATCATACCACCTGACTTTAAACTATACTACGAA 2339
                          i       iii    vv   i  iv  ii i  i   viv      i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_189444799_   2340 GCTACAGTAACAAAAATTGCAGTGT---ACTGGTGCAAAAACAGACATAC 2386
                                   iv  i ---      ---     iii  ii i       i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGA---CAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_189444799_   2387 AGACCAATGGAACAGGTTAGAGAACCCAGAAATAAAGCTAAACACCTACA 2436
                            i        i  iv v    ii           v i v   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_189444799_   2437 ACCATCTGATTTTTGACAAAGTCAACAATAACAACCAATGGGGAAAGAAC 2486
                         ii  vi       i     i viiv   v v  vi              i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_189444799_   2487 --TCCTTGCTCAATAAATGGCTCTGGTATAGCTGGCTAGCCATATGCAGA 2534
                         --  i  --    i      iv    v i i    v  ?   i     i 
  L1M4_orf2#LINE/    394 AGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_189444799_   2535 GGATTGAAACTAGACCCCTTCCTTTCAGCACACACAAAAATCAACTCAAG 2584
                         i  v    ii i       v   iv  v  i i        i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_189444799_   2585 AGGGATTAACAACTTAAATATAATATCTAAAACGATAAAAACTCT-AGAA 2633
                          v    i ?vi  i     i   v v       v      -    -    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAA 540

  chr2_189444799_   2634 GAAAATCTAGGAAATACCAATC--CA-GACCTAGGCCTTGGCAAAGATTT 2680
                              iv    ?i-  --    -- i-     v  vi v     v i   
  L1M4_orf2#LINE/    541 GAAAACATAGGNG-TA--AATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_189444799_   2681 CAT-GATGAAGTTTCCAAAAGCTATTA-CAACAAAACCAAAAATAGACAA 2728
                          v -   - v viv        - iv -        vv         i  
  L1M4_orf2#LINE/    588 CTTAGAT-ATGACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_189444799_   2729 GTGGGACCT-ATTTAAACTAAAGAGCTTCTATAAAGCAAAACAAACAAAG 2777
                         i v    i -  iv   i    i -   i i ---  vv------     
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGT---GCTT------CAAAG 675

  chr2_189444799_   2778 CAAGCAAGCAAAACTATCAACAGAGTAAACTGACAATGTACAGAATGGGA 2827
                         ---------i v        v i   i  vv     ivi           
  L1M4_orf2#LINE/    676 ---------GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_189444799_   2828 GAAAACATTTGCAAAACATGCCTCTGACAAAGCCCTAATATACAGAATTT 2877
                              i         v   iiv     i  i vv  vi   v      v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_189444799_   2878 ATAAGGAACATAAACAAATCAACAAGCAAAAAACAAACAACCTCATTTAA 2927
                             i    vivv    v    i  vv    i     i    iv   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_189444799_   2928 AAAAATGGTCAAAGAACATGAATAAAAACATTTCAAAAGTAGACATAC-- 2975
                            --   v     i iv      i v iv i  v    v   i    --
  L1M4_orf2#LINE/    817 AAA--TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_189444799_   2976 -TG-CCAA-AAGCATATGAATAAATACTCAACATCACTAATTAT 3016
                         -  -    -     i     v i  i          ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (138 / 90)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 1.96 (55 / 28)  


3057 25.20 1.73 1.27  chr2_189532743_189536072     1970  2838 (492)    L1M4_orf2#LINE/L1        1   873 (35)  

  chr2_189532743_   1970 TAGAAAGATATCCCATACTT-TGAATGAGAAGACTTAATATTGTTAAAAT 2018
                          i              ii i-  i  vi                   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189532743_   2019 GTCCATAATACCCAAAGCAATATACAGATCCAACACAATCCCCATAAAAA 2068
                          v v   v v      vii  v       i    i       i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189532743_   2069 TCCCAGTAGCATTCTTCACATAAGCAGAAAAA-TAATCCTAAAATATATA 2117
                               iv  v  i  ii  v  iiv  v  i- i          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_189532743_   2118 TAGAACCATAAAAGACCCCAAACAGCCAAACCAATTCTGAGAAAGAA--- 2164
                          i   viii  ii     vi  i       v    ii   i      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_189532743_   2165 CAAACTTAGAGACATCACACTTTCTG-TTTTAAAATTATTTTACAAAGCT 2213
                             v  i   ivv        i ii-   i    i - vi         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chr2_189532743_   2214 ATAGTAATGAAAACAGTATGATACTGACATAAATACAGATATACAGACCA 2263
                          i      v  i     i  i     i     iv i   i   i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_189532743_   2264 GTGGAACAGAATAGACAGCCCAGAAATAAATGCAAGCATTTACAGTTAAC 2313
                         i     i     v  v  i           iv  vi      ii  i  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_189532743_   2314 TAATTTTTGAGAAGGGAGTCAAGAGGACTCAA-GGGGAAAGAACAGCATC 2362
                          i     i  v     v i     vv i    -          i  iv i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_189532743_   2363 TTCACTAAATGGTTCCAGGAAAATTGGATTTCCACATGCAAAGGAATGAA 2412
                             vi       v ii   v  i     v?           i       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_189532743_   2413 ATTGGGCCCTTAGCTTACATTA-----AAAAATCAAATAAAAATGGTTAA 2457
                         i    i   i  v  i   ii -----      i  v v       v v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_189532743_   2458 AAGACCTAAATATAAGACCAAAAACTAAAAAATCTCCTAGAAAGCAACAT 2507
                         ?          i     v v       v    -   i     iiv     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr2_189532743_   2508 ATTA--AAAGCTCCTAGACGTTGGCCTTGGCAATGATTTTTTTGAATATC 2555
                          vv?--   v  i vv   v    vi v       i   i  v  -   v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATG 597

  chr2_189532743_   2556 ACATCAGAAGTTCAGGCCACAAAAGAAAAAATGAATAAGCAGGACTATAT 2605
                            i  i   iv  i  v              ii    iiv     vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_189532743_   2606 CGAA-CCAAAAACATTTTTCACAGCAAAGGAAACAATCAACAAAATGAAA 2654
                          i  -ii      -    vii vv       v  v     v   i     
  L1M4_orf2#LINE/    648 CAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_189532743_   2655 TGGTAGCTTACATAATATGATAAAAACATAGTCACAAATCACATAACTGA 2704
                         v ii i ii   v   iv  v    ---  v ii       i   v    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAA---TATTTGCAAATCATATATCTGA 743

  chr2_189532743_   2705 TAAAGGGTTAATATTCAGTATTCGTAAAGAACTCTTACCACTCAATAGTG 2754
                            i  ii vi   i   v  vii              v        i i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_189532743_   2755 GAAAAACAAGTAACCTCATTAAAAAAAAAATGGTCAGAAGGCCTCAATAC 2804
                         i   i    i     iv   ?     ----   v  i i iii v    v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA----TGGGCAAAGGATTTGAATAG 839

  chr2_189532743_   2805 ACATTTCTCCCAAGAAGAGACAGAAAAAACAAAT 2838
                                   v       v i v   vii v   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

Transitions / transversions = 1.56 (131 / 84)
Gap_init rate = 0.02 (14 / 873), avg. gap size = 1.86 (26 / 14)  


3559 20.23 3.89 1.14  chr2_189549888_189558406     1389  2263 (6256)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_189549888_   1389 ATCCCAGGTTTCTGTACTG-AAG--TTATTAGATTGTTAGGATGTCCAGT 1435
                               v   iv  v i  -   --   -- v       i    v - i 
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTA--ATATTGTTAAGATGGC-AAT 56

  chr2_189549888_   1436 ATTTTCCCAAACTGATATACAGATTCAATGCTATCCCTATGAGAATCCCA 1485
                          i i-      i    v           i  v        v i       
  L1M4_orf2#LINE/     57 ACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_189549888_   1486 GCTAAATTATCTGTAGGAACTGAGAAGCTGATTTTTAAATCCATGTAGAA 1535
                            ivv  v i  i  i  i   v        ii v    i   i i   
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_189549888_   1536 TTGCCAGAAGCTCAGAATACTCAAAACCAACTTGATAAAGAG---CAAAG 1582
                         v   v  iii i       vi      v v     v     i---     
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr2_189549888_   1583 AAAGAAAACTCACACTTCCTGAATTCAAAACCGAATACAAAGAAACACTC 1632
                         vvi  ii            ii v        iv v       vv   v v
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_189549888_   1633 TTCAGGACTGTGTGGTACTAGCTTAAGTATAAA-------GTTAATGGAA 1675
                         v   i   v          i  v    v   i -------i i       
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_189549888_   1676 CAGAACTGACAGCTCAGAAATTAATCCATATATCTATGGTCAACTAATTT 1725
                         i    i   v  ii       v  i     i  i         i i    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_189549888_   1726 ATGACATGGATGCTGAGACAAACCAATGGGAAAATAATCAA------CAA 1769
                         vi    v  i   ii    v vi       i   v   - i------   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT-AGTCTTTTCAA 404

  chr2_189549888_   1770 AAAATTGTGCTTAGACAACTATGCAGGTAAATTCAAAAGAATGAAGTTTG 1819
                         v    v     vi       ivii ?vi v  v               v 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_189549888_   1820 AACCTTATCTCATACCACATA--AAAATTAACTCATAATTGATCAAAGAC 1867
                          v  i  i    i    i   --            v   v     ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_189549888_   1868 CTAACTATAAAAGTTAAA-CTATAAAACTCATAAGATAAAATTATAGA-- 1914
                             v i   i  i    -           v  ii v    i-    i--
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC-ATAGGNG 553

  chr2_189549888_   1915 TAAATCTTCATGATCTTGGATTTAGCAAAGATTTTTTTACTATGACACCA 1964
                                  i   i     i  vi    v i   i  viv          
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_189549888_   1965 AA-GCATGAGGAACAAA-GAAAAAACTGATAATTTGGACTTCAGCAAAAT 2012
                           -   ii  v      -       iv     v          v      
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_189549888_   2013 TAAAAACTTCTGTGCTTCAAAGGACACTATCCAGAAAGTTAAAAGACAAA 2062
                                  i                     v       v         v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_189549888_   2063 CCCCAAAATATGATAAAATATTTGTAAATCATACATCTGATAAGAGACTT 2112
                           v  i   iv  v          i        i          i     
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_189549888_   2113 GTGTCTGAAATAGATTAAGAAATATTTCAACTTAATAA-AAAAAGACAA- 2160
                           i  iii    v  v     v v  v     i     -          -
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_189549888_   2161 ---CCCAATTTAAA---GGGCAAAGGACCTCAAAATATATTTCTACAAAG 2204
                         ---       ?   ---          ii v  v v i      v     
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_189549888_   2205 AAGATATACAAATAGCCATCAAGCACATGTGAAAAAAATGCTCAATAATT 2254
                                      i    vi         ---    i        i - i
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATG---AAAAGATGCTCAACA-TC 899

  chr2_189549888_   2255 AGTCATCAG 2263
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.26 (97 / 77)
Gap_init rate = 0.02 (20 / 899), avg. gap size = 2.20 (44 / 20)  

2822 26.80 1.88 1.33  chr2_189549888_189558406     7125  8027 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189549888_   7125 TGAAAA---ATTCCAACCTCATAAGTAGGAAGAATCAGTATCATGAAAAT 7171
                           i   ---  i   vvi    iii v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189549888_   7172 TGCCATACTGCCCAAAGTAATTTATAGATTCAATGTTACTCCCATCAAAC 7221
                         v  v     v      v i  i  i        i iv ii  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189549888_   7222 TACCATTGATATTCTTCACAGA--TTTAGAAAAAAACT--TCTTTAAATT 7267
                          v   viviiv  i  ii    --  ----i v  i  --  i v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT----GACAAGCTGATCCTAAAATT 146

  chr2_189549888_   7268 TCATACAGA--TCCAAAGAAGATCCCA----AGCCAAGACAATCCTAAGC 7311
                         -    ii  -- v   i i ---    ----      i      i i iv
  L1M4_orf2#LINE/    147 -CATATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_189549888_   7312 AAAAAGAACAAAAGCTGGAGGCATCATGCAACCTGACCTCAAACTATACT 7361
                           i         - i      vv   ii vv  ii ii     viv    
  L1M4_orf2#LINE/    193 AAGAAGAACAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_189549888_   7362 ACAAGACTACAGTAATCAAAACAGCATGGCACTGGTACCAAAACAGACGT 7411
                             ii             i    ii   i     i iv ii i    i 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_189549888_   7412 ATAGAGCAAGAGAACAGAACAGAGACCTCAGAATTAATGTTACACATCTA 7461
                              v   vi   i    iv    vii     v   vvii i    i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_189549888_   7462 CAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGA 7511
                         iiii  vi    i  i     ivv  v   i v  vv             
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_189549888_   7512 ATCCCCTATTCAATAAATGGTGCTGGGAAAACTGGCTAGCCGTATGCAGA 7561
                           vvi  v     i              v      v  ?  ii     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_189549888_   7562 AAACTGAAACTGGACACCCT-CCTTACACCTTATACAAAAATTAACTCAA 7610
                          i v    ii     -    -   i     v                   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_189549888_   7611 GAGGGATTAAAGACTTAAATGTAAAACTCAAAACCATAAAAAACTGTAGA 7660
                         i v    i ?    i         i vii     i      vv  -    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGA 539

  chr2_189549888_   7661 AGAAAAGCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTC 7709
                               vv    ?i- v i -   iv   v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_189549888_   7710 ATAGAGCAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATG 7759
                         v    vvvi            vvv          vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_189549888_   7760 GGATCTAAATAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCA 7809
                            ii v vi   v v  i     i  ii vv    i  v       vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_189549888_   7810 GAGTAAATAGGCATCCTACAGAATGGGAGAAAATGTTTGCAATCTATGCA 7859
                         i   i  v  i  v  i                 i       vii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_189549888_   7860 TCTGACAAAGGGCTAATATTCAGAATCTAAAAGGAACTTAAACAACTTTA 7909
                              i  i  i  vi   i      v  v  i     ivv      iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_189549888_   7910 CAAGAAAAAAA-AAA-AACCCCATCAAAAAGTGGGCAAAGGATATGAACA 7957
                         i  v     i -   -     v  i?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_189549888_   7958 GGCACTTCTCAAAAGAAGATATTTATGCAGCTAAGAAACATATGATAAAA 8007
                          i  i     v           vi viii  i  v  i  i    v  i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_189549888_   8008 AGTTCAACATCACTTATCAT 8027
                         v i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.81 (29 / 16)  


2143 27.52 7.73 1.41  chr2_189641607_189643685.rev      734  1587 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189641607_    734 TGAAAAGGCATATCTTCTTTATAAATTGAAACACATAATAATATTAAGAT 783
                           i    ii  vi v v  i  ii    i  v  v     v i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189641607_    784 ATCTGTTCTCCTCAAGTTGAACTATAGATTTAATGCCGTCTCAATCAAAA 833
                         iv vi v    i   i    v   i     i  i  vi  i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189641607_    834 TCTTAGCATGATTTGTTTTCAGAAATTGGCGAGCTCATTCTAAGGTTCAT 883
                           ii   -  vi  v   v         i i    v  i    ii     
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_189641607_    884 ATAAAAACACAAAGCACTTAGAATAGACAAAAGAA-CTTGAAAAA-AAGA 931
                           ii   ii   i v  ii       v     v  -         -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_189641607_    932 TTCAAGTTGGAAGAC--AAACTATCTGGCTTCAGGACTTATTTTAAAGTT 979
                         viv        i   -- v   vi iiii    ii     i vi    i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_189641607_    980 AAGGTATTCAACACAAATTGATAATGGTTTATGTATAAACAAGTAGATTA 1029
                          vi   v    v   ivv  i  v   iv  v v   i   vi     i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_189641607_   1030 ATCGAACAG--TTA------------------CATAT--------TCAAT 1051
                           v   i  --  i------------------    i--------     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_189641607_   1052 TGATATTCAACAAAAGTGTGAAGTTAATTCCATGAAAAAGAATATAATTG 1101
                             v   i    ii   iv   viv    v   iii  ii -   i iv
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCT 398

  chr2_189641607_   1102 TTT-----AATTGTTCTGG----ATTGGATATTCATTTAAAAAACA--GA 1140
                            -----   v  v    ---- i      ?i  iv iv    v --  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_189641607_   1141 ACCTTTCTTCATACCTACCTCCAGATACAAAAAAATAGACTCAAAATAAG 1190
                          vi vvvii v     vv v   v         -- vi         iii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAATGGA 496

  chr2_189641607_   1191 TCATAGACCTAAATGTAACACCCCAGACCATAAA-CTCACTAGAGGAAAA 1239
                            ?              v v iv i  i     -   -i    i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC-TTAGAAGAAAA 545

  chr2_189641607_   1240 TATGAGAACACATTGTTTTAACCTTGGGTTGACTAAA-------TAGACA 1282
                         i  ii ?ii v  iv iv i          iivi  v-------    i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_189641607_   1283 --ACACCAGAATCATAATACATAAAAGAAAGTGTTGTAAAATGGAAGGTT 1330
                         --      i  v  i  vvv i        ivi v vv    v i vv i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_189641607_   1331 ATCTAAGTAAAAAACT---G-GCTCTTGAACAACATTGTTAAGGAATTGA 1376
                            v  i v       --- -   - ii  vi   i i i   i  v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAAGTGA 694

  chr2_189641607_   1377 AAAGAGAAGTCACACATCGAAAGAAAATATTTGCAAATTGTATATCTAAT 1426
                              v  vi    v vi ii                 ii       i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_189641607_   1427 AAAAAAAACCCTTGTATCCAGAGTATATATAGAACTCTCAAAACTCAGTA 1476
                           iii ----            i      v        i v      i  
  L1M4_orf2#LINE/    745 AAGGGA----CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_189641607_   1477 AGACAA---CAAAGAGCCCAATTAAAAAA-AAGCAAAATATTTGAA---- 1518
                          v v  ---    v i       ?     -ii     iv       ----
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_189641607_   1519 CACTTTTATTAAAGAATATAAATTGATGGT-AATAAGTATATTGAAATGA 1567
                           i  i -ii      v   v ivi    i-      i i  -    v  
  L1M4_orf2#LINE/    841 CATTTCT-CCAAAGAAGATATACAAATGGCCAATAAGCACAT-GAAAAGA 888

  chr2_189641607_   1568 TCTTCAACATCATTAATCAC 1587
                          vi         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (137 / 94)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.00 (78 / 26)  


2814 26.47 2.34 1.45  chr2_189884676_189886934      885  1783 (476)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_189884676_    885 GGAAAAACATTCCATCTTCATGGATAGGAAGAATTAATATCGTGAAAATG 934
                              i i  i    v         v      v       i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_189884676_    935 GCCATGCTGCCCAAAGTAATTCATAGATTCACTGCTATTCCCATCAAACT 984
                           v  i  v      v i  ii i       vi  v  i  i      v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_189884676_    985 ACGATTGACATTCTTCACAGAATTAGAAAAAAATTACTTTAAACTTCATA 1034
                         v v vivi v  i  ii     v v  v  iv- v iii    v      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATA 150

  chr2_189884676_   1035 TGGAACCAAAAAAGAGCTCGTATAGCCAAGACAATCCTAAGCAAAAAGAA 1084
                              viiv  ii  v iv v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_189884676_   1085 CAAACCTGGAGGCATCACCCTACCTGACTTCAAAGTATACTACAAGTCTA 1134
                             vi      vv    v  v  ii i      iiv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_189884676_   1135 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACCAA 1184
                               i   i    ii         i iv ii i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_189884676_   1185 TGGATCAGAACAGAGACCTCAGAAATAACACCACGTATCTACAGCCATCT 1234
                             vi    iv    vii         vv   iii  i  ii i  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_189884676_   1235 GATCTTCCACAAACCTGACAAAAACAAGCAATGGGGGAAGGATTGCCTAT 1284
                            i   v    ivv  v   i v  vv        i   i  v i  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_189884676_   1285 TTAATAAATGGTGCTGAGAAAACTGGCTAGCCATA--CAAAGAAAGCTGA 1332
                          i  i           i  v      v  ?   i --    ii  --   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--TGA 448

  chr2_189884676_   1333 AACTGGACCCCTTCCTTATGCCCTATACAAAAATTAACTCTCGATAGAT- 1381
                          ii         v   i ii  v                 vvi  i   -
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_189884676_   1382 -------TAAATGTAAAACCCAAAACCATAAAA-TCCTAGAATAAAGCCT 1423
                         -------         i v i     i      -  i     v   i v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_189884676_   1424 AGG---AAATACCATTCAGGACATAGGCATGGGCAAAGACTTTAT-GATG 1469
                            ---    -- -   iv   v v  vv i     v ii  iv -   -
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr2_189884676_   1470 AAAATGCCAAAA--ACAATTGCGACAAAAGCAAAAATTGACAAATGGTAT 1517
                          vi ii      --    --  i       v      v  i    v v i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_189884676_   1518 CTAATTAAACTAAAGATCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 1567
                         i v  i   v v  i v   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_189884676_   1568 GAACAGGCAATCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTG 1617
                            v  i   i i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_189884676_   1618 ACAAATGTCTAATATACAGAATCTACAAGGAACTTAAACAAATTTACAAG 1667
                          i  iv v  vi   v      v  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_189884676_   1668 AAAAAAACAA----CCCCATCAAGAAATGGGCAAAGGATGTGAACAGACA 1713
                              i    ----   v  i? i               v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_189884676_   1714 CTTCTCAAAAGAAGACATTTATGCAACCAACAAACATATGAAAAAAGTAT 1763
                         i     v        i  vi viiii    i  i  i       i - ii
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chr2_189884676_   1764 TTCAGTACTTCAAAGGTGGT 1783
                          -  --  v   ????????
  L1M4_orf2#LINE/    892 T-CA--ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (136 / 100)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 2.12 (34 / 16)  


3133 25.25 2.20 2.52  chr2_189917104_189921322     2824  3734 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_189917104_   2824 TGAAAACATATTCTATGTTCATGCATTGAAAGAGTTAAGATTATTAAAAT 2873
                           i   v    i i         v    i    v    v   i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_189917104_   2874 GTCCATACAACTGAAAGCCATCTACAGATTTAATACAATCTCTATCAAAA 2923
                          v v    vv iv   viv           i  ii     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_189917104_   2924 TCTTAATGACAATTTTTACAGAAATAGAAAAA--AATTCTAAAATACACA 2971
                           ii iivi vv     i       v  v  i--i  i       v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_189917104_   2972 TAAAGCCACAAAGACCCCA-ACTGGCCAAAATAACTTTGGGAAAGAA--- 3017
                          ii ivii   i iv    - v i       i  ii   ii      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_189917104_   3018 CAAAGCTGAAGATATTATACTTCCTGATTTTAAAACAAATCGGCTGTATT 3067
                              i  i  ivv i i      ii    i     -------- -  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC--------T-TACT 241

  chr2_189917104_   3068 ACAAAGCTACAATAATCAATAGAGTATGGTACTGCCATAAACACAGACAT 3117
                                    i       v v   i        v     iv i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_189917104_   3118 ATAGGCCAATGGACTAAAATAGACAACCCCAAAATAACATTAGACATTTA 3167
                             ii       v  i   v  v ii  vi      vvii v       
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_189917104_   3168 TGGTCAAGTGATCTTTGAGAAGGGTGCCAAGAATACATAAGGGGATAAAG 3217
                                v    i  i  v             vi ivi  v   iv  ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_189917104_   3218 ATAGTGTGTTTAACAAGTTATGTTGAAAAAACTGGATATTTTCATGCAAA 3267
                              v v  i     i vi  i  ii v         ?iiv        
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_189917104_   3268 AGAATGAAATTGGACCTTTATCTAATACCATACCCAAAAATCAATGAAAA 3317
                                 i       ii  i  v i      iv       i  ivv   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_189917104_   3318 ATTGAT--------TAAACACAATACCTGAAACTATAAAATTCCTAGACA 3359
                           v   --------    iii  v v  i           i  i    vi
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_189917104_   3360 AAAACATAGATAAAAGGTTTCATGACATTGGTTTTTGCCATGATTTGATG 3409
                                  i?iv  ivi   i    v    v  vv  v   i   vv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_189917104_   3410 GATATGACCCTAAAAACACAGGCAACGAAAGCAAAAATTAA-AAATGGGA 3458
                                 v i    i    i     i    v      vi -    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_189917104_   3459 ATACATCAAACTAAAAAACTTCTGCCCAGCAAAGGAAAC----AAGAGAG 3504
                         v v       v v        i  iv vv       v  ----    i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_189917104_   3505 TCAAAAGGCAGCCCACAGAATGGAAGACAATATTTGCAAATTATATATCT 3554
                          v     i  i            i   v             i        
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_189917104_   3555 GATCAAGTATTCATACCCAAAATATATAAAGGATTACATATAAAGGATTC 3604
                            v i v i ii  i   i           i i -------------- 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACT--------------C 777

  chr2_189917104_   3605 CTATAGCTCAACAGCAAGAAAATAAATGACCCAATTTTAAA-TGGACAAA 3653
                         i  i i     i ii  i  i i    i        ?v   -   i    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_189917104_   3654 TGACTTAAATAGATATATATTCTAAGAAAATTTCAAAACAGCTAACAGGT 3703
                         v  i  i      i  v v i v     i  v vv   ii  i  i i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_189917104_   3704 ACATGAAAAAATACTCCTCACTAATTATCAG 3734
                                  i  i   vv  ii ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (140 / 87)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 4.30 (43 / 10)  


3094 26.97 1.44 0.67  chr2_190008923_190015309     4995  5895 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_190008923_   4995 TGGAAGAACATTCCATGCTCATGGATAGCAAGAATCAATATTGTGAAAAT 5044
                              ii i  i     i        v v    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190008923_   5045 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5094
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190008923_   5095 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5141
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_190008923_   5142 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATACTAAGCCAAAA 5191
                                 viiv  ii  v  v v  v     iv    vi i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_190008923_   5192 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5241
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_190008923_   5242 CTACAGTAACTAAAACAGCATGATACTAGTACCAAAACAGAGATACAGAC 5291
                                  ii  i    ii  i    i i iv ii i   v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_190008923_   5292 CAGTGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5339
                           i     i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_190008923_   5340 TATCTGATCTTTGGCAAACCTGACAAAAACAAGAAATGGGCAAAGGATTC 5389
                         i vi    i  i i   ivv  v   i v  vvv      v    i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_190008923_   5390 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAAGTAGAAAGC 5439
                         i  v  i  i              v      v  ?   i v i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_190008923_   5440 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTCATTCAAGATGG 5489
                             ii    i    v   i     v            v i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_190008923_   5490 ATTAAAGACTTA-------GACCTAAAACCATAAAAACCCTAGAAGAAAA 5532
                           i ?    i  -------  v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_190008923_   5533 TCTAGGCA-ATACCACTCAAGACATAAGCATGGGCAAGGATTTCATGTCT 5581
                         iv    ?i- v i -i  iv   v vi vv i     v i    v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_190008923_   5582 AAAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCT 5631
                          vi            vvi      i   vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_190008923_   5632 AATTAAACTAAATAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGA 5681
                         v  i   v v  v i   i  iiivv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_190008923_   5682 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5731
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_190008923_   5732 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 5781
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_190008923_   5782 AAAAACAAACAACCCCATCAAGAAGTGGGTGAAGGATATGAGCAGACATT 5831
                            i     i     v  i? i  i    ii      v   ii       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_190008923_   5832 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5881
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_190008923_   5882 TCATCACTGGCCAT 5895
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


 743 28.17 1.98 1.98  chr2_190042281_190048907.rev        8   259 (6368)    L1M4_orf2#LINE/L1       55   306 (602)  

  chr2_190042281_      8 ACACTATCCAAAGCAATCTACAGATTCATTGTAATATTTGTCAAAACACC 57
                          i   vi     vii             vi i   vii i      iv  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_190042281_     58 TAAGATG--TTCTTCACAGAAGTAGAAAAA--AATTCCTAAAATTTATAT 103
                         --  v  --  i  ii     i v  v  i--i  -         i    
  L1M4_orf2#LINE/    105 --AGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCATAT 151

  chr2_190042281_    104 GGAACCACAGAAGACTCCAAATAGCCAAAGCAACTATGAGCAAAAAGAAC 153
                             vii  iii   i vi          i   iiv   iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_190042281_    154 AAAGCTGGGGGCATCACACTACTTAATTTCAAAATATCCTACAAGGCTAT 203
                             i   i  vv       v ii          iv v      i    i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_190042281_    204 AGCAACCCAAACAGCATGAAAATGTCATAAATACAG-CAGCTATAGCCTT 252
                           i  i v i    ii  iv v  v     iv i  -  --     viiv
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA--TATAGATCA 299

  chr2_190042281_    253 ATGAAAT 259
                            i   
  L1M4_orf2#LINE/    300 ATGGAAT 306

Transitions / transversions = 1.96 (47 / 24)
Gap_init rate = 0.02 (6 / 252), avg. gap size = 1.67 (10 / 6)  

2901 28.03 1.67 0.67  chr2_190042281_190048907.rev     5237  6135 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_190042281_   5237 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5286
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190042281_   5287 GGCCACGTTGCCCAAAGTAATTTATAGATTCTTTGCTATCTCCGTAAAGC 5336
                            v iii v      v i  i  i      vvi  v   i ii v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190042281_   5337 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAAATTACTTTAAATTTCA 5385
                          v   vivi i  i  ii     -   -- v  iv v iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_190042281_   5386 TATGGAACCAAAAAAGAGCCCACATAGCTAAGACATTCCTAAGCAAAAAG 5435
                                viiv  ii  v  viv     i  i   v  i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_190042281_   5436 AACAAAGCTGGAGGCATCACGCTACCTGACTTTGAA--CTACAATACAAG 5483
                                i      vv    i  v  ii i  ii  --i   --     i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAA 246

  chr2_190042281_   5484 GCTACAGCAACCAAAACAGCTTGGTACTGGTACCAACACAGATATATACA 5533
                                i  i   i    iv         i iv iv i   i     v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_190042281_   5534 CCAATGGAACAGAACAGAGGCCTCAGAAATAGCACCACACATCTACAACC 5583
                         i        i    iv   ivii        ivv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_190042281_   5584 ATCTGATCTTTGACAAACATGATAAAAACAAGCAATGGGGAAAGGATTCC 5633
                          vi    i  i     ivi  vi  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_190042281_   5634 CTATTTAATAAATGGCGTTGGGAAAACTGGCTAGCCATATGCCAGAAACT 5683
                           v  i  i      i i     v      v  ?   i    v i i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_190042281_   5684 GAAACTGGACCCCTTCCTTACAACTTGTACAAAAATTAACTCAAGATGGA 5733
                            ii         v   i   v v i                 i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_190042281_   5734 TTAAAGACTTAAACGTAAGACCTAAAACTATAAAAACCCCAGAAGAAAAC 5783
                          i ?    i    i      v              vi ii          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_190042281_   5784 CTAGGCAGTG--CCATTCAGAACATAGCCGTGGGCAAAGACTTCATGACT 5831
                         v    ?-  i--i -   ivi  v v vvv i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_190042281_   5832 AAAACACCAAAAGCAATGGCAACAGAAGCCAACATTGACAAATGGGATCT 5881
                          vi            vvi      i   vv  v  v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_190042281_   5882 AATTAAACTACAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5931
                         v  i   v vv i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_190042281_   5932 ACAGGCAACCTACAGAATGAGAGAAAATTTTCTCAATCTATCCATCTGAC 5981
                          v  i     i        i        v  iv   vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_190042281_   5982 AAAGGGCT---A---AGAATCTACAAAGAACT--TA-AACACATTTACAA 6022
                           i  i  --- ---     v  i        --  -   v  v v i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_190042281_   6023 GAAAA-AAGCAACCCCGTCAAAAAGTGGGCAAAGGATATGAACAGACTCT 6071
                         i  i -  ii     vi i?    i            v    i    vi 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_190042281_   6072 TCTCAAAAGAAGACATTTATGCGGCCAACAAACATACGAAAAAAAGCTTA 6121
                             v        i  vi vii      i  i  i i     i v   i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_190042281_   6122 CCATCACTGGTCAT 6135
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


3191 27.45 0.55 0.44  chr2_190120112_190126320     4811  5717 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_190120112_   4811 TGGAAAACCTTTCCACGCTCATGGAGAGGAAGAATCAATATTGTGAAAAT 4860
                               iviv i   i i       vv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190120112_   4861 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4910
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190120112_   4911 TACCAATGATTTTCTTCACAGAA--TGAGAAAAAACT-ACTTTAAAGTTC 4957
                          v   iiviii  i  ii     --   v  i---  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_190120112_   4958 ATATGGAACCAAAAAAGAGCCCTCATTGCCAAGACAATCCTAAGCCAAAA 5007
                                 viiv  ii  v  vvv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_190120112_   5008 GAACAAAGCTGGGGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5057
                                 i   i  vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_190120112_   5058 CTACAGTAACTAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGAC 5107
                                  ii  i    ii        vi iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_190120112_   5108 CAACGGAACAGAACAGAG-GCTCAGAAATAACACCACATGTCTACAACCA 5156
                            i    i    iv   - ii         vv   i ii i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_190120112_   5157 TCTGATCTTTGACAAACCTGACAGAAACAAGAAATGGGGAAAGGATTCCC 5206
                         vi    i  i     ivv  v  ii v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_190120112_   5207 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5256
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_190120112_   5257 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTCATTCAAGATGGAT 5306
                           ii    i    v   i     v            v i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_190120112_   5307 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5356
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_190120112_   5357 TAGGCA-ATACCATTCACGACATAGGCATGGGCAAGGACTTCATGATTAA 5405
                             ?i- v i -   ii   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_190120112_   5406 AACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGGGATCTAA 5455
                         i            vvi         ivv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_190120112_   5456 TTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACGACCATCAGAGTGAAC 5505
                          i   v v  i i   i  iiivv    i  v  v i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_190120112_   5506 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 5555
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_190120112_   5556 AGGGCTAATATTCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5605
                         i  i  vi   i      v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_190120112_   5606 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5655
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_190120112_   5656 TCAAAAGAAGACATTTATGCAGCCAACACACACATGAAAAAATGATCACC 5705
                           v        i  vi viii     i vi          i   v   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_190120112_   5706 ATCACTGGCCAT 5717
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3276 26.55 1.00 0.55  chr2_190401362_190408080     5324  6227 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_190401362_   5324 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5373
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190401362_   5374 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5423
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190401362_   5424 TACCAATGACTTTCTTCACAGAA-TTGGTAAAAACT-ACTTTAAAGTTCA 5471
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_190401362_   5472 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAGGCAAAAAG 5521
                                viiv  ii  v  viv  v     i      i iiiv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_190401362_   5522 AACAAAGCTGGAGCAATCACGCTACCTGACTCCAAACTATACTACAAAGC 5571
                                i     v v    i  v  ii i i    viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_190401362_   5572 TACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGAGATATAGACC 5621
                                 i   i   iii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_190401362_   5622 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 5669
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_190401362_   5670 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5719
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_190401362_   5720 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5769
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_190401362_   5770 GAAACTGGATCCCTTCCTTATACCTTATATAAAAATTAATTCAAGATGGA 5819
                            ii    i    v   i i   v    i         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_190401362_   5820 TTAAAGACTTAAATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAAC 5869
                          i ?    i       v   v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_190401362_   5870 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5918
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_190401362_   5919 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 5968
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_190401362_   5969 ATTAACCTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGATTGAA 6018
                           i  vv v  i i   i  ii vv    i  v    i  vv i v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_190401362_   6019 CAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 6068
                         v  i  i  i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_190401362_   6069 AAGGGCTAATATCCAGAATCTACGGAGAACTTAAACAAATTTACAAGAAA 6118
                          i  i  vi          v  iii      ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_190401362_   6119 AAAACAA----CCCCATCAAAAAGCGGGCAAAGGATATGAACAGACACTT 6164
                           i    ----   v  i?    ii           v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_190401362_   6165 CTCAAAAGAAGACATTTATGTAGACAACAGACACATGAAAAAACGCTCAT 6214
                            v        i  vi vi i v   i ii          i i     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_190401362_   6215 CATCACTGGCCAT 6227
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (147 / 89)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2989 25.40 3.87 0.46  chr2_190577453_190584405.rev     5584  6461 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_190577453_   5584 TGGAAAAACATTCCATGCTCATGAATAGGAAGAATCAATATCATGAAAAT 5633
                               i i  i     i     i  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190577453_   5634 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5683
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190577453_   5684 TACCA-TTGAGTTTCTT-CACAGATTTACAAAAAACT-ACTTTAAATTTC 5730
                          v   -i  vv   i  -  v i   v    i---  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr2_190577453_   5731 A-----AAA---AAGAG--CCTGAAAAGCCAAGACAATCCTAAGCAAAAA 5770
                          -----   ---   i --  v   v      i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_190577453_   5771 GAACAAAGCTGGAAGCATCATACTACCTGACTTCAAACTATACTACAAGG 5820
                                 i    i vv   i   v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_190577453_   5821 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAATAGATATATAGAC 5870
                                  i   i    ii         i iv ii     i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_190577453_   5871 CAATGGAATAGAAC--AGGCCTCAGAAATAATCCCGCCTATCTACAACCA 5918
                                      i--  ivii         v   iivi  i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_190577453_   5919 TTTGATCTTTGATAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCCC 5968
                         v     i  i  i  ivv  v   i v  vv       i    i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_190577453_   5969 TATTTAAAAAATGGTGTTTGGAAAACTGGCTAGCCAGATGCAGC----TA 6014
                          v  i  v        i v   v      v  ?   v     iv---- i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_190577453_   6015 AAACTGGACCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGGAT 6064
                           ii         v   i i   v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_190577453_   6065 TAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 6114
                         i ?    i    ii     v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_190577453_   6115 TAGGCA-ATACCATTAAGGACACAGGCAGGGGCAAAGACTTCATGACTAA 6163
                             ?i- v i -  viv   viv  vvvi     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_190577453_   6164 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATTGGATCTAA 6213
                         i            vvi          vv     v  i i      ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_190577453_   6214 TTAAACTAAAGAGCTTCTGCAGGGCAAAAGAAACTATCATCAGAGTGAAC 6263
                          i   v v  i i   i  iivvv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_190577453_   6264 AGGCAACCTACACAATGGGAGAAAATTTTTGCAATCTATCCATCTGAGAA 6313
                           i     i   v             v       vii  vi      v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_190577453_   6314 AGGGCTAATATCCAGAATCTACAAATAA-----ACAAATTTACAAGAAAA 6358
                         i  i  vi          v  i   v  -----    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_190577453_   6359 AAA-----AACC--ATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 6401
                          i -----    --  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_190577453_   6402 TCAAAAGAAGACATTTATGTGGCCAAGAA--ACATGAAAAAAAGCTCATC 6449
                           v        i  vi vi       v  --         i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_190577453_   6450 ATCACTGGTCAT 6461
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (127 / 92)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.53 (38 / 15)  


3175 26.30 0.99 0.66  chr2_190661467_190667857.rev     4995  5899 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_190661467_   4995 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 5044
                              ii    i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190661467_   5045 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5094
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190661467_   5095 TACCAATGACTTTCTTTGCAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 5142
                          v   iivi i  i         -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_190661467_   5143 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5192
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_190661467_   5193 AACAGAGCTGGATGCATCATGCTACCTGACTTCAAACTATACTACAAGAC 5242
                             i  i    v vv   ii  v  ii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_190661467_   5243 TACAGCAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5292
                              i      i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_190661467_   5293 AATGGAACCGAAC--AGAACCCTCAGAAATAATACCACACATCTACAACC 5340
                                iv   i--   ii  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_190661467_   5341 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAAAGGGGAAAGGATTCC 5390
                          vi    i  i     ivv  v   i v  vvv  v        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_190661467_   5391 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5440
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_190661467_   5441 GAAACTGGATCCCTTCTTTACACCTTATACAAAAATTAATTCAAGATGGA 5490
                            ii    i    v i i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_190661467_   5491 TTAAAGACTTAAATGTTAGACATAAAACCATAAAAACCCTAGAAGAAAAC 5540
                          i ?    i       v   vv      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_190661467_   5541 CTAGGCAATACTATTCAGGACATAGGAATGGGCAAGGACTTCAT-GTCAA 5589
                         v    ?ivv v v   iv   v v  iv i     v ii   v - vi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_190661467_   5590 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5639
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_190661467_   5640 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5689
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_190661467_   5690 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTGATCTGACAA 5739
                           i     i                 v       vii ivv      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_190661467_   5740 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAAAAAA 5789
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_190661467_   5790 AAATCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5839
                          i -    i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_190661467_   5840 CTCAAAAGAAGACATTTATGCAGCCAA-AAGTCACAATAAAAAATGCTCA 5888
                            v        i  vi viii     -   -    vv    i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCA 894

  chr2_190661467_   5889 ---TCACTGGCCAT 5899
                         ---   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2827 27.18 2.35 0.78  chr2_190668498_190670562      680  1573 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_190668498_    680 TAGAAAAACATTCAATGCTTATAG-TTGAAAGAATCAATATCATTAAAAT 728
                          i    i i  i v   i i  i -   i    v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190668498_    729 GACCATACCACCCAAAGCAATCTATAGATTCAATGTCATTCCTATAAAAT 778
                          i v    iv      vii     i        i iv  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190668498_    779 TACCAAAGTCATTTTTCACAGAAGTAAAAAAAAAAAATTCTAAAACCCAT 828
                          v   ivvv v     ii     i vi v  ivvi - i      ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_190668498_    829 GTGAAACCAAAAAAGAGCTCAAATAGCCAAAGCAAATCTAAGCAAAAAGA 878
                         i  i  viiv  ii  v ivi          i   vii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_190668498_    879 ACAAAGCTGGAGGCATCATATTACCTAACTTCAATCTATACTACAAGGCT 928
                               i      vv   i i v  i  i     vviv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_190668498_    929 ATAGTAACCAAAACAACATGGTACTGGCACAAAAATAGATGCATGTATTA 978
                          i     i   i   iii           i  ii     iii  iv  i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_190668498_    979 ATGAAACAGAA--GAGAACCCAGAAATAAAGCC-CACACCTACAACCAAC 1025
                            i  i    --    ii           v  -i   ii  iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_190668498_   1026 TGATCTTAAACAAAGTCAACAAAAATATACAATGGGGAAAGAACACCCTA 1075
                             i  vi    i viiv   i vi  v              i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_190668498_   1076 TTCAATAAATGGTGCTGGGAAAACTAGCCAGGCATATGCAGAAGTATGAA 1125
                              i              v    i vi ?v  i     i   v     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_190668498_   1126 ACTTGATTCCTACCTCTCATCATATACAATAATTAACTCAAGATGGATTA 1175
                         ii v  ii        v  i         v           i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_190668498_   1176 AAAACTTAAATATAAGACCTCAAACTATAAATGTCCTAAAAGAAAAAGTA 1225
                         ? i  i     i     v  v          vv  i  i       vi  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_190668498_   1226 GGAAAAACTCTTCTGGACATTGGCCTAGACAAAAA------AATTATGAC 1269
                           ?iv  v     vv   v    vi   i   vii------ iv      
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_190668498_   1270 TAAAATCTTAAAAGCAAATTCAACAGAAACCAAAATAGATACATGAGACT 1319
                         ---- i --       v vv     i  ivv          v  vi    
  L1M4_orf2#LINE/    600 ----ACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_190668498_   1320 TAATTAAACTAAGGCATCTCTGTATAGCAGA-------ATCAACAGAGTA 1362
                          v  i   v v iiv ii i   iivv  i -------     v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_190668498_   1363 AACAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTATACACTTGA 1412
                           v        i                          ii   i ii   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_190668498_   1413 CATAGGAGTAATACTTAGAATCTATAAGAAACTTAAACAAATCAACAAGA 1462
                         i vi   v vi  iii     v     ii    ivv    v    i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_190668498_   1463 AAAA-ACTAATAACCCC-TTCAAAAGTGAGCCAAGGACATGAACAGACAC 1510
                             -  v        v-  ?    i  i  v     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_190668498_   1511 TTCTCAAAAGAAGACATAAAAGCAGCCAATAA--ACATGAAAAAATGCTC 1558
                              v        i   v  iii        --         i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_190668498_   1559 CACATCACTAACCAT 1573
                         v      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (151 / 88)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.55 (28 / 11)  


 859 28.78 1.48 0.37  chr2_190681180_190686384.rev     3483  3753 (1452)    L1M4_orf2#LINE/L1        1   274 (634)  

  chr2_190681180_   3483 TGGAAACACATCCCATGCTCATGGATGAGTAGAATCAGTATTGTGAAAAT 3532
                               v i        i        vi v   v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190681180_   3533 GACCATATTGCCAAAAGCAATCTAAAGATTTAATGCAATTATCATCAAAA 3582
                          i v   i v  v   vii     v     i  i     ivii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190681180_   3583 TACTATCATCATTTTTCACAGAACT--ACAAAAAAAATCCTAAAATTTAT 3630
                          v i v vv v     ii     v --    ivvi -          i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_190681180_   3631 ATGGAACCAAAAAGAGCCCACA-TAGCTAAAGCAAGACTAAGCAAAAAGA 3679
                               viiv  i ii    v -    i   i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_190681180_   3680 ATACA-CTGGAGGCATCACATTACCTGACTTCAAATTATATTACAAGGCT 3728
                          i v -i      vv     i v  ii i      viv  i     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_190681180_   3729 ACAGTTACCAAAACAGCATGGTATT 3753
                              v i   i    ii     i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACT 274

Transitions / transversions = 1.44 (46 / 32)
Gap_init rate = 0.01 (4 / 274), avg. gap size = 1.25 (5 / 4)  

1986 25.31 1.70 1.85  chr2_190681180_190686384.rev     4066  4713 (492)    L1M4_orf2#LINE/L1      262   908 (0)  

  chr2_190681180_   4066 ACAAAGTGGGACTC-CATCTCAAAAAAAAAAAAAAAAATCTATTTAATAG 4114
                            iv    v   v-   ---  ii v i v v v i   v  vv     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCAT---AAGGATAGACATATAGATCAATGGAATAG 308

  chr2_190681180_   4115 ----GTGAGTATAAAAATTCATCTATT--TTTATAGACTCAGCCAATTGA 4158
                         ---- v    vi i    vv i i  v--     i ------i       
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGG------TCAATTGA 352

  chr2_190681180_   4159 TCTTCAACAAAGCAAATAAAAATATAAACTGGGCAAAGGACACCCTATTC 4208
                          i   i    i vvivi  i vi  vv v    v    i i vi  v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_190681180_   4209 AACAAATGGTGCTGGGATAATTGGCAAGCTACATGTAGAAGAATGAAGCT 4258
                                          i  i   vv ? i     i i          i 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_190681180_   4259 GGATCCTCATCTCTTACCTTATACAAAAATCAACTCAACATGGATCAAAC 4308
                            i  ii i   vi   v           i       v        ? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_190681180_   4309 ACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACTTCAAA 4358
                           i     v     v  i    i      v ii       v   v vii?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_190681180_   4359 --AAATCTTTTCTAGACATTGGCTTAGGCAAAGAATTCATGACCAAGAAC 4406
                         --       -- vv   v    v        v iv   v iivi v  vv
  L1M4_orf2#LINE/    553 GTAAATCTT--CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_190681180_   4407 CCGAAAGCAAATGTGACAAAAACAAAGATAAATAGATGGGACCTAGTTAA 4456
                           i      v v ii      iv   i   i   i  v    i vi i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_190681180_   4457 ACTAAAAAGCTTCTGCACATCAAAAGAAATAATCAGCAGAGTAAACAGAC 4506
                          v v    i   i  ii v     i  v iv    iv i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_190681180_   4507 AACC-ACAGAGTGGGAGAAAATACTCACAAACTATACTTCCAACAAAGGA 4555
                             -     i            i ii    ii   iv  ii i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_190681180_   4556 CTAATAACCAGAATCTATAAAGAATTCAAACAAATCAGCAAGAAAGAAAA 4605
                           vi  v       v         i  vv    v   ii  v   -  i 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGA 799

  chr2_190681180_   4606 CAAATAATCCCATCAAAAAGTGGGCAAAGGACATGAATAGACAGTTCTCA 4655
                                i  v  i?    i           iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_190681180_   4656 AAAGA-GATATACAAATGGCCAACAAACATATGAAAAAATTCTCAACATC 4704
                              -                 i  i  i       i  v         
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_190681180_   4705 ACTAATTAC 4713
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.19 (87 / 73)
Gap_init rate = 0.02 (10 / 647), avg. gap size = 2.30 (23 / 10)  


2742 26.77 1.12 0.87  chr2_190791307_190795630     2627  3433 (891)    L1M4_orf2#LINE/L1        1   809 (99)  

  chr2_190791307_   2627 TGGAAAAATATTCCATACTCATAAATTGGTAGAATAAATACTATTAAAAT 2676
                               i    i    ii    ii     v   v v    i i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190791307_   2677 GGCCACACTGCCGAAAGCAATCTACAGATTCAAT---ATTCCTATCAAAC 2723
                            v i   v  v   vii              i---  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190791307_   2724 TACCAA-TGTCATTTTTCACAGAATTAGAAAAA--AATTCTAAAATTCAT 2770
                          v   i-  i -     ii     v v  v  i--i  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_190791307_   2771 ATGCAACAGAAAAGTGCCCA-AATAGCCAAAGCAATCCTAAGCAAAAACA 2819
                            v  vv v  i vi    -          i     i i ---    v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGA 196

  chr2_190791307_   2820 AAAACAAAAAGCCAAAGGAATCACATTACCTGACTTCAAACTATACTATA 2869
                          i      -- iiii    v     i v  ii i      viv     i 
  L1M4_orf2#LINE/    197 AGAACAAA--GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_190791307_   2870 AGGTCACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATA 2919
                          i ii       i   i    ii         i i  ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_190791307_   2920 GACCAATGGAACAGAATAGAGACCCCAGAAATAAAGCCTCACACCTACAG 2969
                           i        i     v    vi           v  vi   ii  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_190791307_   2970 CCATCTGATCTTTGACAAAGTTGACGAAAATAAGCAATGAGGAAAGGACT 3019
                         i  vi    i  i     i v  v i i vi vv     i      i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_190791307_   3020 CCCTATTCAACAAATGATGCTAGGATAGCTGGCTAGCCATATGCGGAGGA 3069
                         vi  v           i    i   i i    v  ?   i    ii i  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_190791307_   3070 ATGAAACTATACCCCCACATTTCACCATATACAAAAATTAACTCAAGATA 3119
                              ii iv     i  v iv                        i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_190791307_   3120 GAGTAAAGATTTAAATGTAAGACCTCAAACTGTAAGAATCTTAGAAGAAA 3169
                           vi ?   ii           v  v     i   i v            
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_190791307_   3170 ACCTAGGAA-ACACCATTCTGGACATTGGCCTTGGGAAAGAATTTATAAC 3218
                           v    ?i- v i -   vv   v    vi v  v  v iv  iv  iv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_190791307_   3219 TCAGTCCTCCAA-GCAATTGCAACAAAACCAAAAATTGACAAGTAGGATG 3267
                          vv v vi v  -   vvv         vv      v  i  i v   iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_190791307_   3268 TAATTAAACCAAAGAGCTTCTATAGAGCAAAAGAAACTATTAACAGAGTA 3317
                          v  i   viv  i i   i i ivvv    i  v     i  v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_190791307_   3318 AACAGGCAACCAACAGAATGGGAGAAAATATTCACAAACTATGCATCAGA 3367
                           v  i     v                    ii    ii  ii   v  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_190791307_   3368 CAAGGGTCTAATATCCAGAATCTATAAGGAATTTGAATAGTTCAATAAGC 3417
                         i     v  vi          v     i   i ivv i ii       vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_190791307_   3418 AAAAAACAAATAACCC 3433
                             i           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCC 809

Transitions / transversions = 1.48 (127 / 86)
Gap_init rate = 0.01 (10 / 809), avg. gap size = 1.60 (16 / 10)  

 347 20.83 4.17 0.00  chr2_190791307_190795630     3713  3832 (492)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr2_190791307_   3713 CTCAGACACAACAAAACAAA--ACCTA-TTAAAAAGTGAGAAAAGAACAT 3759
                             ivv i  v  i     --   i -  ?    i  i v    i iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_190791307_   3760 GAACAGACACGTCTCAAAAGAAGACAAACAAGTGGCCAACAA--ACATGA 3807
                            i     iv    v        i v    i       i  --      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_190791307_   3808 AAAAATGCCCCACATCACTAATCAT 3832
                            i    i v      ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (15 / 9)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 1.67 (5 / 3)  


3442 22.51 2.34 0.62  chr2_190821642_190824080      753  1565 (874)    L1M4_orf2#LINE/L1        3   829 (79)  

  chr2_190821642_    753 GAAAGATATCTTGTGTTCATGGATTAGGAGAACTGATATTGTTAA-ATGT 801
                                   iii            i i   vi i          -   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_190821642_    802 CCATATTAC--AAAGCGATCTACAGGTTCAACATAATCCCTATCAAAATT 849
                          v   i v --   vi         i      ii               i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_190821642_    850 CCAATGACAATTTTCACAGAAATAGAAAAAATAATACTAAAATTTGTATG 899
                            iivi vv    ii       v  v  iv i  v        ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_190821642_    900 GAACCACAAGAGACCCTGAATAGCGAATGCAATCTTGAGCAAAAAGAACA 949
                            vii    i     v       v  vi         iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_190821642_    950 AAGCTGGAGGCATCACACTGTCTGATTTCAAAATATAAGGCAAGGCTACA 999
                            i      vv       vi ii         iv  vvi   i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_190821642_   1000 GTAATCAAAACAGCATGGTACTGACATTAAAAACAGACACACAGA----- 1044
                                 i    ii        i   -  ii i     i i   -----
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATCAAT 301

  chr2_190821642_   1045 ---ATAGA-----GAGCCCAGAAATAAATCCACGCTTTTACAGTTAATTT 1086
                         ---     -----   i           i   ii v    ii  i    v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_190821642_   1087 ATTTTTGGCAAAGATGTCAAGCATATACAATGGGAGAAAGAACAATCTCT 1136
                              i i   i i  i    vvi  v       -       i i   i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTTT 400

  chr2_190821642_   1137 TCAATAAATAGTGTAGGGAAAACTGAATATCCACATGCAGAAGAATGAAA 1186
                             i    i   iv    v     i   ?         i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_190821642_   1187 TCAGACCCTTATATCACACCATATA-AAAAATCAACTCAAAATAGATGAA 1235
                          ii     i  iv            -      i          i   v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_190821642_   1236 ACACACTTAAACATAAGACCTGAAACTGTAAAACTACTAGGAAAAAACAC 1285
                          v  --i    ii     v  i     i       vi   i i      i
  L1M4_orf2#LINE/    501 AGAC--CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_190821642_   1286 AGGGGGAAAGCTCTATGACATTACTTTGGGGGATGTTTTTTTTGGAGATG 1335
                            ? v   v  iii    v  ivv  i  vi   v   i  -i  v   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chr2_190821642_   1336 ACTCCAAAAGCACAAGCAACAAAAGCAAAAATAAACAAATGAGATTACAT 1385
                           v                      v       i i    vi  i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_190821642_   1386 CAAA-CTAAAAAGCTCTGCACAT-AAAGGAAATAATCAACAGAGTGAAAA 1433
                             -i      vi i  ii v -      v iv     v i        
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_190821642_   1434 GACAACTTACAGAATGGGTGAAGATATTTGCAAACCATGCATCTGATAAG 1483
                               ii          v   i           i   ii          
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_190821642_   1484 GGGTCAATATCTAAAATATATAAGCAACTCAAACAATTCAATAGCAAGAA 1533
                           iiivi    i i         iv     vv    i      ii  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_190821642_   1534 AGCAAATAAGCCAATTTAAAAATGTGCAAAAG 1565
                         ii       v      ?       v     i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 2.03 (120 / 59)
Gap_init rate = 0.01 (11 / 827), avg. gap size = 2.18 (24 / 11)  

 250 18.03 4.92 4.10  chr2_190821642_190824080     1826  1947 (492)    L1M4_orf2#LINE/L1      786   908 (0)  

  chr2_190821642_   1826 CAAAAAAAAAAAAAAAAAAAA---AA---AAAAAAGTGCAAAAGAACCTG 1869
                            v  v     i v   v  ---  ---     v v     i  -ii  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA-TTTG 834

  chr2_190821642_   1870 AATAGATATTTCTCAAAAAAACACATATAAATGACCAAACAGGTATATGA 1919
                               i       v   i  v i   i     i    -i i i i    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGA 883

  chr2_190821642_   1920 AAAAAACATGCTCAACATCATTAATCAT 1947
                            i ---            ????????
  L1M4_orf2#LINE/    884 AAAGA---TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.04 (5 / 123), avg. gap size = 2.20 (11 / 5)  


 352 23.64 20.00 0.00  chr2_190881449_190884003.rev     1123  1232 (1323)    L1M4_orf2#LINE/L1       16   147 (761)  

  chr2_190881449_   1123 TGTTCATGATCTGAAAGAC--AATATTCTTAG--------TCCTCCCCAA 1162
                                 ivi  i     --      v   i-------- v        
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_190881449_   1163 ATTAACATGTATATTCGGC------------AAAATTCCAGCAGGCTTTT 1200
                            i iv ii v    ii ------------     i     v v     
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_190881449_   1201 CTGTAGACATTGACAAATGGATTCTAAAAGTC 1232
                         i  i   v        iiv   i      v  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

Transitions / transversions = 1.60 (16 / 10)
Gap_init rate = 0.02 (3 / 132), avg. gap size = 7.33 (22 / 3)  

2006 24.10 7.32 3.33  chr2_190881449_190884003.rev     1313  2063 (492)    L1M4_orf2#LINE/L1      128   908 (0)  

  chr2_190881449_   1313 ACACACAGATTCTGAATTATACATGGAAACACAAA----CTAGAATGGCC 1358
                            vi v   i  i  v vi i       ii   i---- i     i   
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_190881449_   1359 AAAACAATTTTGAGAAAGAACAATAA-TTTGGAGTACTCCTATTATCTAA 1407
                                 i    i      v  i  -v      v    vi i vi i  
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_190881449_   1408 TGTTAAGAATGACTATAAAGCTACAGTAATTA-----GTGCTATATTGAC 1452
                          v i  i v v    i              i -----   ivi  i  i 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_190881449_   1453 AAAAGGCTAGCCACA--AACCTATGAAACAGAA--ACAAGTCCAGAGATA 1498
                          v    v   v  i --i i v   i  i    --ivi        i   
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_190881449_   1499 CACCCATAAAAATATGGTAAACTGATACTTGACA----TGTCCAAAAACA 1544
                         v       v vv      v  i    vi i    ----  -    i v  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG-CCAAGACCA 376

  chr2_190881449_   1545 ATGAATGCAAAAAGGATAATCTTTTCAACAAATGGGATTGGAACAATTGG 1594
                         v v    vii    i   i                vii   i    i   
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_190881449_   1595 ACATTCACATACTCTCCCCCCACCAAAAT----CT--ACTTATACCTTAT 1638
                          i ?i     i --------- vv i   ----i --  iiv     i i
  L1M4_orf2#LINE/    427 ATAKCCACATGC---------AAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_190881449_   1639 ACTTTATAGAAAAATTAACTCAAAAGGGATCATAGTTTTAAATGTAAAAT 1688
                           iv    v                v      ?  vii         i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_190881449_   1689 GTAAAACTATAAAAC------AAGAAGACA-------AAACATTTGCGAT 1725
                         v              ------     i   -------   iv  i i  i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_190881449_   1726 CTTGGGTTAGGAAAAGAGTTCTTAGATGTGATACCAAAAGCATGAACCAT 1775
                                    v  v iv         i   i          ii i v i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_190881449_   1776 GAAAGAAAAAAACTGGTAAACTAGACTGAATCAAAATGAAAAAGATTTGC 1825
                         i          -iv i    i i    vv        v     vv    i
  L1M4_orf2#LINE/    618 AAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_190881449_   1826 TCTGGAAAAAAAAACACAGTTAAAAGATTGAAAAAAAAACA-GCAAATAT 1874
                         v  vv   ii ---   vi i  i i v      i v   v-i  i -  
  L1M4_orf2#LINE/    667 GCTTCAAAGGA---CACTATCAAGAAAGTGAAAAGACAACCCACAGA-AT 712

  chr2_190881449_   1875 ---AAAAAATATTTGCAAGTCATCATCTAGCCAATAAATGACTTGAATCC 1921
                         --- i             ---     v  v ii    iv      v    
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAA---ATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_190881449_   1922 AGAATATATAAGTA----TCAAAACTCAATAGCAA---GACAA-CAACCC 1963
                                    iv ---- i v         ii  ---     -i     
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_190881449_   1964 AGTTTAGAAA---ACGA--GATTTGAAAGATTTAGGCAGTTCACTTGGTA 2008
                          i  ? i   ---i i --        -----   i  v   v iviiv 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAA-----TAGACATTTCTCCAAAGA 854

  chr2_190881449_   2009 CCACCTATAGATAGCAAATATAAGTACATGAAA-GATGCTCAATATCATT 2057
                         vv iv  i i  i  v    --  i        -         i    ??
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATA--AGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_190881449_   2058 AGCCAT 2063
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.54 (108 / 70)
Gap_init rate = 0.03 (26 / 781), avg. gap size = 3.08 (80 / 26)  


3014 25.99 3.50 0.90  chr2_190914068_190918548     3107  3991 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_190914068_   3107 TGGAAGAACATTCCATGCTCATGGATGGGAAGAATCAATATCATGAAAAT 3156
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190914068_   3157 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3206
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190914068_   3207 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3254
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_190914068_   3255 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 3304
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_190914068_   3305 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3354
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_190914068_   3355 TACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3404
                                 i v i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_190914068_   3405 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 3452
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_190914068_   3453 ---------TTGACAAACGTGACAAAAAGAAGAAATGGGGAAATGATTCC 3493
                         --------- i     iv   v   i vv vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_190914068_   3494 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3543
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_190914068_   3544 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3593
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_190914068_   3594 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3643
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_190914068_   3644 CTAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGACT 3691
                         v    ?i- v i -   i- i  v i  i- i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_190914068_   3692 AAATCACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3741
                          viv        i  vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_190914068_   3742 ------AATTAAACA-------GC---AAAAGAAACTACCATCGGAGTGA 3775
                         ------       v -------  ---   i  v    i  vvii     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_190914068_   3776 ACAGGCAACCTACAGAATGGGAGAGAATTTTTACAATCTACCCATCTGAC 3825
                          v  i     i             i   v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_190914068_   3826 AAAGGGCTAATATCCAGAATCTACAAAGAACCTAAACAAATTTACAAGAA 3875
                           i  i  vi          v  i       iivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_190914068_   3876 AAAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGCCA 3925
                            i --    i     v  i?    i            v    i  v  
  L1M4_orf2#LINE/    795 AAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_190914068_   3926 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCT 3975
                         i     v        i  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_190914068_   3976 CATCATTGGCCATCAG 3991
                           v   ii????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (141 / 85)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.79 (39 / 14)  


2612 28.49 2.98 0.83  chr2_190928156_190930379.rev      540  1378 (846)    L1M4_orf2#LINE/L1        1   857 (51)  

  chr2_190928156_    540 TGGATAAACATTCTATGCTTATGGATAGGAAGAATCAATATCATGAAAAT 589
                             v i i  i i   i i      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_190928156_    590 GGCCATACTGCCCAAAGTAATTTTTAGATTCAGTGCTATTCCTATCAAGC 639
                            v     v      v i  i vi       ii  v  i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_190928156_    640 TACCATTGACTTTTTTCACAGATCTAGAAAAAACAAT-------TTCATA 682
                          v   vivi i     ii    vv v  v  ivii  -------      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_190928156_    683 TGGAACCAAAATAGAGCCCGTGTACTCTAGAGAATCCTAAGCAAAAAGAA 732
                              viiv  vi  v  v vi  vi v i v    i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_190928156_    733 CAAAGTTGGAGGCATCATGCTACCTGACTTCAAATTATACTACAAGGCTA 782
                                     vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_190928156_    783 GAGTAACCAAAACAGCATGGTATAGTGGTACCAAAACAGATATATAGACC 832
                         v     i   i    ii     i--   i iv ii i   i       i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTAC--TGGCATAAGGATAGACATATAGATC 298

  chr2_190928156_    833 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACACCTACAACCAT 882
                                i    iv   ivii         vv   i   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_190928156_    883 CTGATCTTTGACAAACCTGACAAAAACAATCAATGGGGAAAGGAT--TCC 930
                         i    i  i     ivv  v   i v  v             i  --  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chr2_190928156_    931 GTATTTAATAAATGTTGTTGGGAAACTTGGCTAGCCATATGCAGAAAACT 980
                         - v  i  i     v  i     v vi   v  ?   i     i  i v 
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_190928156_    981 GAAACTGGACCCCTTCCTTACACTTTAGGTGAAAATTAATTCAAGATGGA 1030
                            ii         v   i    iv  viii        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_190928156_   1031 TTA--GACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAGAAC 1078
                          i --   i    ii     v       i      vi i       i   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_190928156_   1079 CTAGGCA-ATACCACTCAGGACAT--AGTCATGGGCAAAGACTTCATGAC 1125
                         v    ?i- v i -i  iv   v --i  i --     v ii   v iiv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGA 593

  chr2_190928156_   1126 TAAACCACCAAAAGCAATTGCAACAAAAGCCAGAATTGAGAAATAGGATC 1175
                           viv           vvv          vv i   v  v    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_190928156_   1176 TAATTAAACTAAAGAGCTTCTGTACAGCAGAAGAAATTCTCATCAGAGTG 1225
                          v  i   v v  i i   i   i vv  i i  v i v   vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_190928156_   1226 AACAGGCAACTCACGGAATGGGAGAAAAATTTTGCAACCTATCCATCT-- 1273
                           v  i    i   i             vv       vii  vi    --
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_190928156_   1274 -AAAGGTCTAATATCCAGAGTCTACAAGGTACT--TA-AATTTA-CGAGA 1318
                         -  i  v  vi        i v  i  i v   --  -  i i -ii v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_190928156_   1319 AAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATGTGAACAGACAC 1364
                             i    ----   v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_190928156_   1365 TTCTCAAAAGAAGA 1378
                              v        
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGA 857

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.02 (14 / 857), avg. gap size = 2.29 (32 / 14)  


1186 22.82 15.21 1.13  chr2_191113621_191116558.rev     1343  1697 (1241)    L1M4_orf2#LINE/L1       53   457 (451)  

  chr2_191113621_   1343 CAATTCTCCTCAAATTGATATACAGGTTTAACACAACTCCTATCAAAATC 1392
                             v    i         v     i  i   i   ii            
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_191113621_   1393 TCAGCAACATATTTTTGTAGATATAGACAAG---ATTTTAAAATTTATAC 1439
                         i    vi v -      i   v  v      ---  ii       i   i
  L1M4_orf2#LINE/    103 CCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_191113621_   1440 AGAAAAGGAAAGAAAC--GAATAGCTAAAGCAGTTTTGAAAAAGA----- 1482
                         i    v v  i i v --       i   i  i i          -----
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_191113621_   1483 -------------TCATAT-------------------------AGCT-- 1492
                         -------------   i i-------------------------    --
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_191113621_   1493 -GTGCATTAAGACCGTGTGGTATTAGCAGAAGGACAGACACATAGATCAA 1541
                         -  i-  i     v        i i   v     i     i         
  L1M4_orf2#LINE/    252 AGTA-ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_191113621_   1542 TGTAACAGAATACAGAACCCAGAA-CAAATCCACCCAAATATGCCCAACT 1590
                           v  i     vv   ii      -i   i   iv  vv    vi   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_191113621_   1591 GTTTTTTAACAAAGATGCAAAAAAAATTCAATGGTGGAAAGG-TAACCTT 1639
                          v    ii    i i   v  i vv         -      i-  ii   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTT 399

  chr2_191113621_   1640 T-CAACAAATGGTGCTGAGGTAATTAGACATCCATGGGCAAAAATAATGA 1688
                          -               i ii  i i  i ?   iiv      i-     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AATGA 448

  chr2_191113621_   1689 AACTCGGCC 1697
                          ii v i  
  L1M4_orf2#LINE/    449 AGTTGGACC 457

Transitions / transversions = 2.33 (56 / 24)
Gap_init rate = 0.03 (12 / 405), avg. gap size = 4.83 (58 / 12)  

1341 23.01 5.69 4.10  chr2_191113621_191116558.rev     2008  2446 (492)    L1M4_orf2#LINE/L1      463   908 (0)  

  chr2_191113621_   2008 CTTATACCTTATACAAATATTAACTCAAAATGGATCA-----TTAACTAT 2052
                           i i   v        v                   -----i   v i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_191113621_   2053 ACAATTTGAAACTATAAAACATTTAGAAAAAAAAAAAAAGAAGAAGAAAA 2102
                          vi vi i            vi      i    v v ----- i? v   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA-----GGNGTAAA 557

  chr2_191113621_   2103 TCTT--TAGCCTCTAGTGCTAGGCA--GAGTTTTTAGACTTGACACCGAT 2148
                             -- ii   - i - i      -- iv  i     iv       i v
  L1M4_orf2#LINE/    558 TCTTCGTGACCT-TGG-GTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_191113621_   2149 ACCATGATCCATAAAAGGAAAAACTAATG--TTAGACTTCATTAAAATTT 2196
                          v  ii v v i     i     ivi  i--  i        i      v
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_191113621_   2197 AAAACTTTTGCTCTTTAAAAGACTCTGCAAAGAGGATGAAAACACAAGCT 2246
                                   iv   i   i   v  iiv    iii      v    v i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_191113621_   2247 ACAGACTGTGAGAAAATACTTGGAAACCACAAATCCAGCGAAGGATTAGT 2296
                              v  v         i   v   i  i v   iiiii i   i v  
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_191113621_   2297 TTCTAGAATATGTAAAGAATTCTCCAAACTCAA-----------CAAACA 2335
                         v  i       i       i   ivv       -----------    i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_191113621_   2336 ATCCAATTAGAAAATGGACAAAAAACGTGAAGGGACATTTCACTGAAGAG 2385
                          i      ?i       i    ii iv    vi        v ii    i
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_191113621_   2386 GATAGACAGGATATATAAATG--CA-TAGATACAAATGAAAAGATGTTCA 2432
                             ---------  i     --  -  iii   --          i   
  L1M4_orf2#LINE/    856 GATA---------TACAAATGGCCAATAAGCACA--TGAAAAGATGCTCA 894

  chr2_191113621_   2433 ACATCATTAATGAT 2446
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (66 / 33)
Gap_init rate = 0.03 (12 / 446), avg. gap size = 3.58 (43 / 12)  


3196 26.14 1.67 0.67  chr2_191161046_191167197     4762  5660 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_191161046_   4762 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4811
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_191161046_   4812 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATGAAGC 4861
                            v     v     iv i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_191161046_   4862 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4909
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_191161046_   4910 TACGGAACCAAAAAAGAGCCCGCATTGCCAAGTGAATCCTAAGCCAAAAG 4959
                           i    viiv  ii  v  v v  v     ivv    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_191161046_   4960 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGCC 5009
                                i      vv       v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_191161046_   5010 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5059
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_191161046_   5060 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5107
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_191161046_   5108 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATAGGGAAAGGATTCC 5157
                          vi    i  i     ivv  v   i v  vvv   i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_191161046_   5158 CTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATATAGAAAGCT 5207
                           v  i  i           i  v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_191161046_   5208 GAAACTGGATCCCTTCCTTACACCTTATACAGAAATTAATTCAAGATGGA 5257
                            ii    i    v   i     v      i       i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_191161046_   5258 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5307
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_191161046_   5308 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5356
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_191161046_   5357 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT- 5405
                         vi            vvi          vv     v  i    v   ii -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_191161046_   5406 -----AATTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5450
                         -----       i -   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_191161046_   5451 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5500
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_191161046_   5501 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTATAAGAA 5550
                           i  i  vi          v  i         vv    v iv    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_191161046_   5551 AAAAACAA----CCCCATCAACAAGTGGGCAAAGGATATGAACAGACTCT 5596
                            i    ----   v  i? v  i            v    i    vi 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_191161046_   5597 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5646
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_191161046_   5647 TCATCACTGGCCAT 5660
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


3083 26.18 2.02 0.00  chr2_191181754_191186975     3841  4730 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_191181754_   3841 TGGAAACATATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3890
                               v          i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_191181754_   3891 GACCATACTGCTAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAA- 3939
                          i v     v iv   vii       i      i     i  i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_191181754_   3940 TACCACCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAATTTCATA 3989
                          v   v vv v  i  ii     v v  v  ivii        v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_191181754_   3990 TGGAGCCAAAAAAGAGCCTGCATAGCCAAAGTGAGACTAAGCAAAAAGAA 4039
                             iviiv  ii  v  v v         iii vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_191181754_   4040 CAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGCCA 4089
                             vi      vv       v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_191181754_   4090 TAGTCACCAAAACAGCATGGTACTGGTATAAAAACTGGCCCATGGACCAA 4139
                         i   v i   i    ii         i    ii iv i vi  i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_191181754_   4140 TGAAACAGAATAGAAAACCCATAAATAAAGCCAAA----TACAGCCAACT 4185
                           i  i     v  i ii   v       v   v ----  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_191181754_   4186 GATATTTGACAAAGCAAACAGAAACAT-AAAGGGGGAAAGGATACTCTAT 4234
                            v  i     i vviv  ii v   -v  v        i   v   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_191181754_   4235 TCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAGAATGAAA 4284
                                            i  i   vv ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_191181754_   4285 CTGGATCCTCATTTCTCACCGTATAAAAAAATCAACTCAAGATGGATCAA 4334
                         i    i  ii ii  v    i    v      i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_191181754_   4335 GGACTTAAATCTAAGACCTGAAACT-TAAAATTCT-AGAAGATAACATCA 4382
                         i   i     v     v  i     -     i   -      v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_191181754_   4383 GAAAAACCCTTCTAGACATTGGCTTAGGCAGAGATTTCGTGACCAAGAAC 4432
                          ?iv  vi    vv   v    v       iv i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_191181754_   4433 CCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGACTTAATTAA 4482
                                  v v         iv   i   i   i  v      v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_191181754_   4483 ACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAGAC 4532
                          v v  i i      ii vv    i iv  vi   iv i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_191181754_   4533 AACCCACAGAGTGGGAGAAAATCTT--CAGTCTATATATCCGACAAAGGA 4580
                                   i           v  --  ivii       i  i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_191181754_   4581 CTAATATCCAGAATCTATGACGAACTCAAACAAATTAGCAAGAAAAAAAA 4630
                           vi          v   i v      vv    v i ii  v     i v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_191181754_   4631 AAACA--CCAA----AGAGTGGACTAAGGACATGCATAAACAATTCTCAA 4674
                            i --    ---- i i   i v     iv  v   i   v     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_191181754_   4675 GCAAAGATACACAAATGGCCAACAA--ACATGAAACAATGGTCAACATCA 4722
                         ivi      i            i  --        vi   v         
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_191181754_   4723 CTAGTGAT 4730
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.30 (130 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


3432 24.41 2.02 0.56  chr2_191228444_191232275.rev     2449  3341 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_191228444_   2449 GAAAGAAATTTAAGATTTCATGGATTGGAATAATTAATATTATTAAAATG 2498
                               v  iiv vi  -            v v        i    i   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTT-CATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_191228444_   2499 TCCATACTGCCCAAAGTGATCTACAAATTCAATACAACCCCTATCAAAAT 2548
                         v v     v      v         i      ii   i            
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_191228444_   2549 ACCAATGACATTCTTCACAGAAATAAAAAAA--AATCCTAAAATTTGTAT 2596
                         v   iivi v  i  ii       vi v  i--i           ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_191228444_   2597 GAAGCCATTCAAG--ATTCAAAATAGCCAGAGCAATCCTGGGCGAAAAGA 2644
                          i i--  v    -- ii  i        i i     i  iivi i    
  L1M4_orf2#LINE/    152 GGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_191228444_   2645 ACAAAGCTGGAGACATCATACTACTTGATTTCAAAATATATTACAAAGCT 2694
                               i     ivv   i   v iii         iv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_191228444_   2695 ATAGTAACCAAAACAGAAGGGTACTGGCATAACAAAAGACACATAGACCA 2744
                          i     i   i    viv             vi v     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_191228444_   2745 ATGGCACAGAATACAGAACCCAGAAATAAATCCACATGTTTAGAGCCAAC 2794
                             v i     vv   ii           i   i ii    vi i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_191228444_   2795 TCATTTTCAACAGAAGTACCAAGGACATACAATGGGGAGAAGAGAGTCTC 2844
                          v      i   iii  i     iv   v         i ii v     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_191228444_   2845 TTCAATAAAATGTGCTGGGAAAAATGGATAACCATATGCAGAAGGATGAA 2894
                              i   vv         v  v      ?   i     i   i     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_191228444_   2895 GCTA-ACCTCTATATCTTACCATATAGAAACATCAACTCAAGATGAATTA 2943
                          i i-   i   iv  vi        v   v  i       i   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_191228444_   2944 AAGGCTTAAATCTAAGACCTGAAACTATGAAACTACTAGAAGAAAACGT- 2992
                         ?  i i     v     v  i       i     vi           i -
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_191228444_   2993 ----------TTCAGGACATTGATTTGGGCAAAGATTTTTTGG-TAAGAC 3031
                         ----------   iv   v   iv  i     v i   i  i -  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_191228444_   3032 CACAAAAGTACAGGGAACCAAAGAAAAAATAGGCAAACAGAATTACATCG 3081
                         vv      i   i v   v             ii   iv i i v    i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_191228444_   3082 AGCTAACAAGCTTCTGCATAGCAAAGGAAATACTCAACAAACGGAAGAGA 3131
                          iv v v  i   i  iiivv       v ivv    v   vv   i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_191228444_   3132 CAACCCATAGAATGAGAGAAAATATTTGCAAACTACTTGTCTGACC-GAG 3180
                                i      i                 ii iv i     iv- i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_191228444_   3181 ATTAATAACCAGAATATATCAGGAACTCAAACAATTGAATAGCAAAAAAC 3230
                          i vi  v           v i      vv    i v    ii     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_191228444_   3231 CCCAAATAATCCAATTTTAAAATAAGCAAAAGATCTGAATAGACATTTCT 3280
                          --      i      ?v     ii     i   i               
  L1M4_orf2#LINE/    800 C--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_191228444_   3281 CAAAAGAAGACATACAAATAGCTAACAGGTATACGAAAAAATGTTCAACA 3330
                          v        i        i  i  i i i i i     i   i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_191228444_   3331 TCCAAAATAAT 3341
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.79 (138 / 77)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 2.56 (23 / 9)  


1429 17.72 15.34 1.32  chr2_191312539_191314942      136   513 (1891)    L1M4_orf2#LINE/L1      413   843 (65)  

  chr2_191312539_    136 GCTAAGACATCTAGATATTTGCATGCAAAAGAAAGAAGTTGGATTCTGAC 185
                            ii    v  i    ?iii            v         ii iv  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_191312539_    186 CTTTCATCTTATAGAATAATTAGCTCAAAATAAATCAAAGGCCTAAATGT 235
                           iv  i v    v  v     i        ii    ?  i         
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_191312539_    236 AAGGGTAAAAATTATAAAACTCTTGGAAGAAAACATTAGAGTAAACCTTT 285
                            i iv    i            i           vi ?     i   i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_191312539_    286 GTGACTTGGGATTGGGCAGTGGTTTCTTAGATATGACACCAAA-GCACGA 334
                              i v  i  i    i                        -    i 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_191312539_    335 -CAACAAAA--------------ATCGGACATCATCACCATAAAAAACTT 369
                         -        --------------  i    v      vv  v        
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_191312539_    370 TTGTGCTTCAA-------TA--AAG-----GGAAAGACACACCACGGA-- 403
                                    -------  --   ----- i       vv    i  --
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_191312539_    404 -------------------CCCT-TATCTAATAAGGAATTTGTATC-AGA 432
                         -------------------i v -     i      i i       -   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_191312539_    433 ATATATAAAGAATTCTTAAAAGTCAA-AATAAGATCAAAAATTAAAAAAC 481
                                     i     v  v    -     ----   i i-   v   
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAA----AAAGAC-AAATAAC 807

  chr2_191312539_    482 --AATTTAAA--TGGCCAAAGAATTTTATTCAACAT 513
                         --    ?   --   v     i    v v vi    
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

Transitions / transversions = 1.62 (39 / 24)
Gap_init rate = 0.03 (14 / 431), avg. gap size = 4.50 (63 / 14)  

2998 24.33 2.19 1.58  chr2_191312539_191314942      876  1697 (707)    L1M4_orf2#LINE/L1        2   828 (80)  

  chr2_191312539_    876 GGAAAAATGTTCCATGCTCATGGATTGGAAGAATTAATATCATTAAAATG 925
                              i  i i     i               v       ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_191312539_    926 ACCATACCGCCCAAAGCAATCTGCAGATTCAATACAATCTCTATCAAAAT 975
                         i v    iv      vii    i         ii     i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_191312539_    976 ACCAATGACATTCATCACAGAAATAGAAAAAAAAACCCTAAAATTCTAAT 1025
                         v   iivi v  iv ii       v  v  ivvi i          vv  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_191312539_   1026 GGGACCACTCAAGACCCCAAATAGCCAAACCATTCCTGAGCAAAAAGAAC 1075
                           i vii vvii     vi          v  v  i   iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_191312539_   1076 AAAGCTGGAGGCATCACACTACCTGACTTTGAAATACACTACAAAGCTAT 1125
                             i      vv       v  ii i  ii   ivi            i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_191312539_   1126 AGTAGCCAATAGAAAG---GCTACTGGCATAAAAACAGACACACTGACCA 1172
                             ii   --  v  --- v           ii i     i iv  i  
  L1M4_orf2#LINE/    252 AGTAATCAA--GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_191312539_   1173 ATGGCACAGAGTAGAGACTC-AGAAATAAATCCATGCATTTACAGCTAAC 1221
                             v i   i v    v  -         i    i      ii ii  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_191312539_   1222 CCATTTTCAACATAGGTGCCAAGAACATATATCAGAGACAAGATGGCCTC 1271
                         iv      i   vi          v   vi vii i  v ii  i i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_191312539_   1272 TTCAATAAATGGTGGTGGGAAAACTGAATAACCAGATGCAGAAGAATGAA 1321
                              i        v     v     i   ?   v     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_191312539_   1322 GCTA-ACCTCTATATCTCATCATAT-CAAAAATTAAATCAAAGTAGATTA 1369
                          i i-   i   iv  v  i     -          v     i i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_191312539_   1370 AAGAC--AAATCTAAGACCTAAAACTATGAAACAACTAGAAGAAAACATT 1417
                         ?    --    v     v          i    vvi             v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_191312539_   1418 GGGGGAAATGCTTCGGGACACTGGTCTAGGCAAAGATTTTTTGGAAAAGA 1467
                           ? v    -     v   vi   vi       v i   i  i  v v  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_191312539_   1468 CCTCAAAAGCACAGGCAGCCAAAACAAAAATAGACAAATGGGGTTATATC 1517
                          vi          i   i v   iv         i    v  ii vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_191312539_   1518 AAGTTTTAAAAAAACACAAAACCTCTGCAGAGCAAAGGAAACAATCAGCA 1567
                           iv  ---      -------i i  iivvv       v  v    iv 
  L1M4_orf2#LINE/    649 AAAATT---AAAAAC-------TTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_191312539_   1568 AAGTGAAGATACAACCTACAGAACGGGAGAAAATATTTGCAAACTATCCA 1617
                                i v      i      i                   ii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_191312539_   1618 TCTCACAAGGAATTAATAAGCAGAATATAGAAAGA----TT-CAACTCTA 1662
                            v i    i i vi  vv         v     ----  -      v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_191312539_   1663 TAGCAAAAA-----ACAATCTGATTAAAGAATGGGCAGAG 1697
                           ii     ----- i  i ii   ?  i        i  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.61 (121 / 75)
Gap_init rate = 0.01 (12 / 827), avg. gap size = 2.58 (31 / 12)  

 425 17.24 1.15 0.00  chr2_191312539_191314942     1826  1912 (492)    L1M4_orf2#LINE/L1      821   908 (0)  

  chr2_191312539_   1826 GGGCAAAAGACCCAAATAGATATTTCTCAAAAGAAGACATACAAATGGCC 1875
                                i  iiii      i       v        i            
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_191312539_   1876 AACAGGTAT-TAAAAAAATGGTCAACATCAGTAATCAT 1912
                           i i i i- i    i   v         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 6.50 (13 / 2)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)  


2687 27.25 0.99 1.11  chr2_191439055_191442063     1302  2112 (897)    L1M4_orf2#LINE/L1        1   810 (98)  

  chr2_191439055_   1302 TGGAAAAACATTCCATGCTCATGGACAGGAAGAATCAATATTGTGAAAAT 1351
                               i i  i     i       iv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_191439055_   1352 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATCCCCATCAAGC 1401
                            v     v      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_191439055_   1402 TACCATTGACTTTCTTCACAGAATTAGAAAAA--AATGCTTTAAATTTCA 1449
                          v   vivi i  i  ii     v v  v  i--i  v  --   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chr2_191439055_   1450 TATGGAACCAAAAAAGAGTCCAT--TAGCCAAGACACTCCTAAGCAAAAA 1497
                                viiv  ii  -i   v--       i   v  i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_191439055_   1498 GAACAAAGCTGGAGGCATCACGCTACCTGATTTCAAACTATGCTATAAGG 1547
                                 i      vv    i  v  ii        viv i   i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_191439055_   1548 CTACAGTAACCAAAACAGCTTGGTACTGGTACCAAAACAGATATATAGAC 1597
                                  i   i    iv         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_191439055_   1598 CAATGGAA-AGAACACAGGCCTCAGAAATAATGCCACACATCTACAACCA 1646
                                 -    ivv  ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_191439055_   1647 TCTGATCTTTGACAAATCTGACAAAAATAAGCAATGGGGAAAGGATTCCC 1696
                         vi    i  i     ivv  v   i vi vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_191439055_   1697 TGCTTAATAAATGGCGTTGGGAAAACCGGCTAGCCCTATGCAGAAAACTG 1746
                          vi i  i      i i     v   i  v  ?  vi     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_191439055_   1747 AAACTGGGCCCCTTCCTTATATCCTATACAAAAATTAACTCAAGATGGAT 1796
                           ii   i     v   i i i v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_191439055_   1797 TAAAGACTTAAACGCAAGATGTAAAATCATAAAAACCCTAGAAGAAAACC 1846
                         i ?    i    i i    vv     ii      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_191439055_   1847 TAGG--TAATACCATTCAGGGCATAGGCACGGGCAAAGACTTCATGACTA 1894
                             --   - i -   iv i v v  vvii     v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_191439055_   1895 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1944
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_191439055_   1945 ATTAAACTAAAGAGGTTCTGCAGAGCAAAAGAAACTATCATCAGAGTGAA 1994
                           i   v v  i iv  i  iivvv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_191439055_   1995 CAGGCAGTCTATAGAATGGGAGAAAATCTTGGCAATCTATCCATCTGACT 2044
                         v  i  ii i i               v  v    vii  vi      - 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA-T 744

  chr2_191439055_   2045 AAGGG-CTAATATCCAGAATCTACAAGGGACTTAAACAAATTTACAAGAA 2093
                              -  vi          v  i  i i   ivv    v ---   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAA 791

  chr2_191439055_   2094 AAAAAATACAAACAGGCCA 2112
                         v     v     i iv   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCA 810

Transitions / transversions = 1.38 (127 / 92)
Gap_init rate = 0.01 (11 / 810), avg. gap size = 1.55 (17 / 11)  

 411 21.85 2.52 0.00  chr2_191439055_191442063     2399  2517 (492)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr2_191439055_   2399 AAGAAAAAAAATACAAA---CCCCACCAAAAAGTGGGCAAAGGATATGAA 2445
                           v  v     v     ---   v ii?    i            v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_191439055_   2446 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAA 2495
                         i     i     v        i  vi viii     i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_191439055_   2496 AAAGCTCATCATTACTGATCAT 2517
                         i v     v   i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 3.00 (3 / 1)  


2510 18.55 3.02 0.81  chr2_191462734_191469133.rev        3   498 (5902)    L1M4_orf2#LINE/L1      237   743 (165)  

  chr2_191462734_      3 TTACTATAAAGCTACAGTAATCAAAACAGTGTGGTACTGGTATAAAGATA 52
                               i                 i               i    i    
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_191462734_     53 GACACACATAGACCAATGGAGTAGAATTTAGGGTCCAAGTGGAAACCTGT 102
                             i --    i       i       v  i     iiviv     ii 
  L1M4_orf2#LINE/    287 GACATA--TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_191462734_    103 ATTTCTATGGCCAAATGATTTTTGACTAGGGTGCCAAGTCCAGTCAATGG 152
                          iv i     i   v       i   v           v   v       
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_191462734_    153 AAAAACAGCAGTCTTTTCAGCAAATGGTGTTGGGACAGCTGGATTTTCAC 202
                         ii   v ii          i         i       i      v?i   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_191462734_    203 ATGCAAAAGAATGAAGTGTGACCCCAACCCCACATCGTATAAAAACATTA 252
                                          vv      v   i    i i    v   v    
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_191462734_    253 ACTCAAAATGGATCAACAATCTAAATATAAGAGCTGAAACCACGAAAGTC 302
                                        ?vi i      i        i    i ii   v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_191462734_    303 TTAGAAGACAACATAGGGGTAAATCTTCATTACTCTGGATT--------- 343
                                 v        ?          i v  ii   i  ---------
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_191462734_    344 -----TGGATATAACCCTGAAAGTATGAGCAACAAAAGAAAAAATAGATA 388
                         ----- i     i  v ii    i ii                       
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_191462734_    389 AGTTGGACATTCTCAAAACTAAAATGCTTCT-TGCATTAAAGGATGATAT 437
                          i      v iv      i     -i   i -   v i      iiv   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_191462734_    438 CAAGAAATTAAAAAGACAACTTATAGAATTAGAGAAAATATTTATAAATA 487
                                v i          ii i     vi            ii    -
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT- 732

  chr2_191462734_    488 AAAATATCTGA 498
                         v v        
  L1M4_orf2#LINE/    733 CATATATCTGA 743

Transitions / transversions = 2.18 (61 / 28)
Gap_init rate = 0.01 (5 / 507), avg. gap size = 3.80 (19 / 5)  

3175 27.53 0.55 0.55  chr2_191462734_191469133.rev     5001  5908 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_191462734_   5001 TGGAAGAACATTCCATGCTCACAGATAGGAAGAATCAATATCATGAAAAT 5050
                              ii i  i     i   ii   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_191462734_   5051 GGCCATACTGCCTAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5100
                            v     v  i  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_191462734_   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5148
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_191462734_   5149 TATGGAAGGAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGACAAAAG 5198
                                iviv  ii  v  v v  v     iv     i i i v i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_191462734_   5199 AACAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTATACGACAAGGC 5248
                                i i    vv   ii  v  ii i      viv   v    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_191462734_   5249 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGACC 5298
                                 i   i    iii        i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_191462734_   5299 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTACATATCTACAACT 5346
                                i    i--    i  --        vv i i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_191462734_   5347 ATCTGATCTTTGGCAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5396
                          vi    i  i i   ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_191462734_   5397 CTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATATAGAAAGCT 5446
                           v  i  i           i  v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_191462734_   5447 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5496
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_191462734_   5497 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5546
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_191462734_   5547 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTGCATGTCTA 5595
                         v    ?i- v i -   iv   v v  vv i     v ii v v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_191462734_   5596 AGACACCAAAAGCAATGGCATCAAAAGCCAAAATTGACAAATGGGATCTA 5645
                         v             vvi   v      vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_191462734_   5646 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTGAA 5695
                           i   v v  i i   i  ii vv    i  v   ii  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_191462734_   5696 CAGGAAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5745
                         v  iv    i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_191462734_   5746 AGGGGCTAATATCCAGAATCTACCAAGAACTCAAACAAATTTACAAGAAA 5795
                             i  vi          v  iv        vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_191462734_   5796 AAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACATTT 5845
                           i     i     v  i? v  i    ii      v    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_191462734_   5846 CTCAAAAGAAGACATTTATGCAGCCAAAAGACATATGAAAAAATGCTCAT 5895
                            v        i  vi viii     v ii  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_191462734_   5896 CATCACTGGCCAT 5908
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2838 27.80 3.16 0.56  chr2_191645608_191650288.rev     3305  4189 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_191645608_   3305 TGGAAAAACATTCCATGCTCGTGGCTAGAAAGAATCAATATCATGAAAAT 3354
                               i i  i     i  i   v v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_191645608_   3355 GGCCATACAACCCAAAGTAATTTATAGGTTCTATGCTATCCCCATAAAGC 3404
                            v    vv      v i  i  i  i   v i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_191645608_   3405 TACCATTGACTTTCTTCACAGAATTAGAAAAAAAATACCTTAAATTTCAT 3454
                          v   vivi i  i  ii     v v  v  ivvi- i i    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chr2_191645608_   3455 ATATAACCAAAAAAGAGCCCACATAGCCAAGACGATCCTAAGCAAAAAGA 3504
                           iv  viiv  ii  v  viv        i  i   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_191645608_   3505 AGAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 3554
                          v    i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_191645608_   3555 ACAGTAATCAAAACAGTATGGTACTGATACCAAAATAGATACACAGAGCA 3604
                                    i     i        ii iv ii     i i i   v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_191645608_   3605 ATGGAAAAGAACTGAGGCCTCAGAAATAACAGCACACATCTACAACCATC 3654
                               v    i    ivii         vvv  i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_191645608_   3655 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAG--------- 3695
                             i  i     ivv  v   i v  vv            ---------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_191645608_   3696 -----------GTATTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 3734
                         -----------  ii     v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_191645608_   3735 CCTGGACCCCTTCCTTTCACCTTATACAAAAATTAACTCAAGATGGATTA 3784
                         vi         v   iv    v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_191645608_   3785 AAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 3834
                         ?    i    ii     v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_191645608_   3835 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACCAAAA 3883
                           ?i- v i -   iv   v v  vv i     v ii   v iivi vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_191645608_   3884 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGATCTAATT 3933
                                    vvi          vv     v       v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_191645608_   3934 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGGGCGAACAG 3983
                            v v  i i   i  ii vv    i  v       vv ii i   v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_191645608_   3984 GCAACCTACAGAATGGGAGAAAATTTTTGCGATCTATCCATCTGACAAAG 4033
                         i     i                 v     i vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_191645608_   4034 GGCTAATATCCAGAATCTACAAGGAAGTTAAGCAAATTTACAACAACAAA 4083
                          i  vi          v  i  i   v ivvi   v ---   i  i   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAAA 795

  chr2_191645608_   4084 AA-------AACCCCATCAAAAAGTGGGTGAAGGATGTGAACAGACACTT 4126
                           -------     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_191645608_   4127 CTCAAAAGAAGACATTTATGCAGCCAACAAACATGTGAAAAAAATATCAT 4176
                            v        i  vi viii     i  i  ii      i vvv   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_191645608_   4177 CATCACTGGTCAT 4189
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (141 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 5.50 (33 / 6)  


2556 23.89 5.89 5.00  chr2_191777577_191780049     1082  1981 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_191777577_   1082 TGAAAAGATATTTCATATTCACTTTAGGCAGAAATAAGCAGAATAAAGAC 1131
                           i        ii   i    --- i ------  vi v   v v  ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCA---TGG------ATTGGAAGACTTAA--- 38

  chr2_191777577_   1132 TGTATTGTCAAGATGTCAGTTATTCCCCA--CTTATCTATAGATTCAATG 1179
                         --      i      v  i - i      --i v     i        i 
  L1M4_orf2#LINE/     39 --TATTGTTAAGATGGCAAT-ACTCCCCAAATTGATCTACAGATTCAACG 85

  chr2_191777577_   1180 GAATTATCTACAGATTCCAATCAAAATACTAGCAAGTTATTTTCTGGATA 1229
                         ----------  -  i  v        v i   vivi v    vii  v 
  L1M4_orf2#LINE/     86 ----------CA-ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr2_191777577_   1230 ATGAC----TAATTTTAAAGTTTATATGGAGAGGCTAAAGAGCCAGA-TA 1274
                         v    ---- i  ii    i  i       i v  v ii  v     -  
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr2_191777577_   1275 GCAATGACA---TTGAAAGAGAAAACCAAAGTTGAAGTGACTC-CACT-- 1318
                           v vi   ---      i    i v        i  -     -    --
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG-GACTCACACTTC 223

  chr2_191777577_   1319 -CAACTTTGGGACTTAGTATAAACCTATAGTAATCAAGACAGTGTGGTAC 1367
                         -   i  iiii     v  i   v   i                      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr2_191777577_   1368 AGGTAAAAGAATGGACAGATAGATCAATGGAACAGAATAGACAGTTCTGA 1417
                         v  i v   i  i    v              i     v  v   i v  
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_191777577_   1418 AATGGATCCACGTAAATGTACTTAACTGACTTTTGACAAAAGGGCAAATG 1467
                            ii i   iii vv i iv i  i   i   i     ii v  v  vi
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr2_191777577_   1468 CGACACAACAGAACAAAGGTGGTCTTTTCAACAAGTGGTGCTGGAATAGC 1517
                          v iv   ii iiv  iii i             i         i i i 
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_191777577_   1518 TGGATATTCAGCTGGATATGCAAAA-AGTGAATCTAGACACTGACCTTTC 1566
                               ?i  ------i        - i    vi i   -----  i --
  L1M4_orf2#LINE/    424 TGGATAKCCA------CATGCAAAAGAATGAAGTTGGAC-----CCCT-- 460

  chr2_191777577_   1567 ACCTCCCACAAAAAATAAGTGAAATTAACTCAAAGTGAACCACAGACTTA 1616
                              v   v v v i  ---             i  i i  ?    i  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAA---AAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_191777577_   1617 AATGTAAAATGC-AAAACTATAAACGTCTTAGAAGATAACAGAAAA-TAA 1664
                                i -  -           vv          v    v ii?-   
  L1M4_orf2#LINE/    508 AATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_191777577_   1665 -TCTAGATGACCTTGGATTTAGTGATGACTTTTTAGATACAACACTAAAG 1713
                         -   vvi         i  vi ii   ii  i       ii    i   i
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_191777577_   1714 GCAAAATTCATGAAACGACAGATTGATTAGT-GGA--------------A 1748
                            v  viv ii   vi v i  v   v i -   -------------- 
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_191777577_   1749 AAATTTCTGCTCTGTGAAAGACACTGTTAAGAAA-TGAAAATGA-AAGTC 1796
                            i  i  iv  vii  i      i i      -      -  -  vi 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GACAACCC 705

  chr2_191777577_   1797 ACAGGCTAGGAGAGAATATTGGCAAAAAACATATCTGATAATGAATTATT 1846
                             iv i     i      v     vv i           v i i vv 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_191777577_   1847 ATCTAAAATAT---------TTTTAAAA------AGCAAGAAAACAAA-- 1879
                            i i     --------- i   v  ------ ii  i  i     --
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_191777577_   1880 -CTCAATTTAAAAATGGGCCAAATACCATAATAGATGTCTCACCAAAGAA 1928
                         - i     ?          v  iv iivv      ii i  v        
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_191777577_   1929 GATATATAGATGAAAAATAGGCATATGAAAAGATGCTCCACATCATACGT 1978
                               i i   ivv    i   i              v      ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_191777577_   1979 GGT 1981
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.81 (136 / 75)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 3.27 (98 / 30)  


3121 27.25 1.33 0.33  chr2_191782306_191788756     5061  5959 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_191782306_   5061 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5110
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_191782306_   5111 GGCCATACTGCCCAATATAATTTATAGATTCAATGCCATCCCCATCAAGC 5160
                            v     v     vv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_191782306_   5161 TACCAAAGACTTTTTTCACAGAATTGGAAAAACT-ACTTTGAAGTTTTTA 5209
                          v   ivvi i     ii     v v  v  i  - iii i  i  iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_191782306_   5210 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAACAAAAAGAA 5259
                              viiv  ii  v  v v  v     iv     i i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_191782306_   5260 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5309
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_191782306_   5310 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5359
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_191782306_   5360 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5409
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_191782306_   5410 GATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCTAT 5459
                            i  i     ivv  vv  i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_191782306_   5460 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACTAAAG 5509
                          i  i              v      v  ?   i   i i  i v i   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_191782306_   5510 CTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGATTAA 5559
                         i    i    v   i     v  i           i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_191782306_   5560 AGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5609
                             i       v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_191782306_   5610 GCAATACTATTCAGGACATAGGCATGAGCAAGTACTTCATGACTCAAACA 5659
                          ?ivv v v   iv   v v  vv ii    vvii   v iiv vvi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_191782306_   5660 CCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAATTAA 5709
                                  vvi          vv        i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_191782306_   5710 A-CTACAGGCTTCAGCACAGCAAAAGACACTACCATCAGAGTGAACAGGC 5758
                          -i  v ii   iv ii vv    i       i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_191782306_   5759 AA---------TGGGAGAAAAGTTTTGCAATCTACCCATCTGACAAAGGG 5799
                           ---------          vv       vii ivi      i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_191782306_   5800 CTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAAAA 5849
                           vi          v  i        ivv    v ---   v  v     
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAAAAA 797

  chr2_191782306_   5850 ACCAACCAACCTA-TCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5898
                         iv   vi    i - i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_191782306_   5899 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATTA 5948
                          v        i  vi viii     i ii          i       vi 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_191782306_   5949 TCACTAGTTGT 5959
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 3.00 (15 / 5)  


3207 22.85 2.65 2.43  chr2_191824406_191832037     3196  4101 (3531)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_191824406_   3196 TGGAAAGACATCTCTATGTTCATGGATTGGAAGAATTAATATCATTAAAA 3245
                                 i   i -                   v       ii    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_191824406_   3246 TGATCATACTGCCCAAAGCAATCTACAGAATCAAAGCAATCCCTATTAAA 3295
                           iiv     v      vii         v    v           i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_191824406_   3296 ATACCAA-TGTCGTTTTTCACAGAAATAGAAAAAACAAAATAGTAAAATA 3344
                           v   i-  i -     ii       v  -----   iv ii vv--  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGA-----CAAGCTGATCC--TA 141

  chr2_191824406_   3345 GAAAAAAAATTTGTATGG---TACCAAAAAGAGCCTGAAGAGCCAAAGCA 3391
                         ------     ii     --- i --  ii  v  v   v       i  
  L1M4_orf2#LINE/    142 ------AAATTCATATGGAAATGC--AAGGGACCCAGAATAGCCAAAACA 183

  chr2_191824406_   3392 ATCT-GAGCAAAAAGAACAAAGCTGGAAGCATCATACTACCTGACTTCAA 3440
                             -  iv  i          i    i vv   i   v  ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_191824406_   3441 AGTATATTATAAGACTATAGTAACCAAAACAGCATGTTACTGGTATAAAA 3490
                          iiv  i  i  ii   i     i   i    ii  v      i    ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_191824406_   3491 ACAGACACATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAATCCA 3540
                          i     i     i        i     v    ii           i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_191824406_   3541 CATATTTACAGCCAACTAATTTTTGACAAAGGTGCCAGGAACCTACACTC 3590
                         i i     ii i   i i     i     i       i  v v v  v v
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_191824406_   3591 GGGCAAAAACATCCTCTTCAATAAATCGTGGTGGGA--------TATCCC 3632
                            v  i  i vi  i     i    v   v     --------  ?  v
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_191824406_   3633 TACACCGAAGAATAGAACTGGACCC-TATCTCTCACCATATATAAAAATC 3681
                         i ii vi      ii ii       -  i   v         i      i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_191824406_   3682 AACTCAAGATGGATTAAAGATTTAAATGTAACACCTAAAATTATAAA-CT 3730
                                i      i ?   ii         v v      i      -  
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_191824406_   3731 GCTACAAGATAACATAAGGA-AAATGCTTCAGGACATTGGTCTAGGCAAA 3779
                         vi  v    v      i ?i-    -    iv   v    vi       v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_191824406_   3780 GATTTTATGCTTATGACCTCAAATGCACAGAAAACAAAAACAAAAATAGA 3829
                          i   iv ivv      vi    v     iiv       iv         
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_191824406_   3830 TAAATAGAACTACATTAAACTAAAAAGCTTCTGCACAGCAAAGGAAACAA 3879
                              v i   v   i   v v    i   i  ii vv       v  v 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_191824406_   3880 TCAGCAGAGTGAAGAGACAATCTGCTGAATGGGAGAAAATATTTGCAAAC 3929
                            iv i      i      i ii v                       i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_191824406_   3930 TATTCATCTGACAAAAGGCTAATATCCAGACTATAAAAGGAACTCAAACT 3979
                         i  vi      i  ii i  vi        v    v  i      vv  v
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_191824406_   3980 ATTCAACAGTAAAAAC-CAAATAATCCCATTAAAAAGTGGGCAAAA-ATA 4027
                          i    i i      v-       i  v   ?    i        i-  v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_191824406_   4028 TGAATAGACATTTCTCAAAAAAAACTAAATCCAAAC--CCAGCATAA-CA 4074
                                         v   i  iv  -- v    i--   --    -  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATA--TACAAATGGCCA--ATAAGCA 878

  chr2_191824406_   4075 CAAGAAATAACA---AAGATCAGAGAACTA 4101
                           v    vi ii---  v    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (128 / 75)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.19 (46 / 21)  

3088 24.86 2.35 0.67  chr2_191824406_191832037     5444  6336 (1296)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_191824406_   5444 TGGAAACACATTTCATGCTCATGAATGGGAAGAATCAATATTGTGAAAAT 5493
                               v i  ii    i     i  v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_191824406_   5494 GACCACTCTGCCCAAATCAGTCTACAGATTCAATGCAATTTCCATCAAAA 5543
                          i v iv  v       iii             i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_191824406_   5544 TACCATCATCATTCTTCATAGATTTAGAAAAAACAATCCTAAAATTCATA 5593
                          v   v vv v  i  iii   vv v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_191824406_   5594 TGAAAC--CAAAAAACAACCTGCATAGCCAAAGCAATACTAAGCAAAAAG 5641
                           i  v--   iii  --  v v         i    vi i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_191824406_   5642 AACAAATCTGGAGACATCATATTACCCAACTTCAAATTATATTAGAAGGC 5691
                               vi     ivv   i i v     i      viv  i  v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_191824406_   5692 TATAGTTACCAAAACAGCATGGTACTGGCATAAAAGTAGGCAGGTAGACA 5741
                           i   v i   i    ii              iii   i  vi    iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_191824406_   5742 AATGGAACAGAATAGAGAACCCAGAAACAAAGGCAAATATTTACAGCCAA 5791
                                i     v    ii       i   vv  v i     ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_191824406_   5792 CTGATCTTCGACAAAGCATGCAAAAAT-AT-AAATCAGGGAAAAGACACC 5839
                         i    i        i -i   v  i i-  -v   -i      ii i vi
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAAT-GGGGAAAGAATAGT 396

  chr2_191824406_   5840 CTATTCAATATATGG-GCTGGGAAAACTGGCAAGCCACATGTAGAAGAAT 5888
                           v     i v    -       v      vv ?       i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_191824406_   5889 GAAACTG-------ATTTCTCAGCCTATACAAAAATCAACTCAACATGGA 5931
                            ii  ------- ii  v  v v           i       v     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_191824406_   5932 TCAAAGATTTAAATCTAAGACCTGAAGCCATAAAAATTCTAGAACATAAC 5981
                            ?   ii     v     v  i  i i      v ii     v v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_191824406_   5982 ATTGGAA-AAATACTTCTAGGCATTGGCTTAGGCAAAGAATTCATGGCTA 6030
                           v  ?i-    -    vv i v    v        v iv   v i v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_191824406_   6031 AGACCCCACAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGACCTA 6080
                         v   v   v     v v         iv   i   i   i  v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_191824406_   6081 ATTAA--CTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCCAAGTAA 6128
                           i  --i      -   i  ii vv    i  v iv    ivv    i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_191824406_   6129 ACAGACAACCCACAGCGTGGGAGAAAATATTTGCAAGCTATGTATCTGAC 6178
                          v             vi                   iii  i       i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_191824406_   6179 AAAGGACTAATATCCATAATCTGCAAGGAACTCAAACAAATCAGCAAAAA 6228
                           i     vi      v   v ii  i      vv    v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_191824406_   6229 AACTAATAATAATCCCATCAAAAAGCGGGCAAAGGACTTGAATACACAAT 6278
                           vv vv     i  v  i?    ii          i       v   v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_191824406_   6279 TCTCAAAAGAAGATATACA----GTCAACAA--ACATGTAAAAATGCTCA 6322
                             v              ---- i   i  --     v   i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_191824406_   6323 ACATCACTAATTGT 6336
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (124 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.93 (27 / 14)  

 218 17.57 13.51 0.00  chr2_191824406_191832037     7067  7140 (492)    L1M4_orf2#LINE/L1      825   908 (0)  

  chr2_191824406_   7067 AAAGAATTTAAA-A---ATTT------AAAAGACATACAAATAGTCAACA 7106
                             i    i  - ---    ------ i    i        i i   i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_191824406_   7107 GATATAAGAAAAAATGCTCAACATCACTAATCAG 7140
                         iii i v     i             ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 12.00 (12 / 1)
Gap_init rate = 0.04 (3 / 84), avg. gap size = 3.33 (10 / 3)  


2807 23.59 3.97 1.20  chr2_192141087_192142909.rev      501  1331 (492)    L1M4_orf2#LINE/L1       55   908 (0)  

  chr2_192141087_    501 ATAATACCTAAATTGATCCACAGATGTAAATGCAATTCCAATCAAAATCC 550
                            v v  i         i      - v  i     i  v          
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGAT-TCAACGCAATCCCTATCAAAATCC 103

  chr2_192141087_    551 C-TCTAGATTGTTTTCTAGAAATAGGTAAGTTGATTATAAAATATATA-G 598
                          -v  - vi v    vi      v ii   i    iv      vi   - 
  L1M4_orf2#LINE/    104 CAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_192141087_    599 GAAATGTGAAAGACCTAGAAGAGCCAAAATAATCTTCAAAAATAGAAGCA 648
                               ii ii    i    v        i      v     v ii i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_192141087_    649 AACATAGAGGACACACACAATCTAATTTCTAATCTAACTCTAAAACAAAA 698
                           vv i      v     vvi i      v  v  v   vi   i v v 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_192141087_    699 G-AATCAAGCAAGTATGATGTTGGCTTAAG-ATAAA--TATGGA---ATG 741
                          -       vv   i  i ii    v    -   i --   i  ---   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_192141087_    742 GAACAGAATAGAGAATCCAGAAATAAACCC---CATTT--GGTGAACTGA 786
                            i     v    i               ---     --   v  i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_192141087_    787 TTTTTGACATGGGCACCAATATGCCAATTTAATGGAAAAAGGAAAGTCTT 836
                             i    v   ii    v --   -  i     ii    i v      
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGA--CCA-TTCAATGGGGAAAGAATAGTCTT 399

  chr2_192141087_    837 TTCAACACATAGTGCTGGTACAATTGAATAAATATATAGAAAAAAAT-AA 885
                                v  i       v    i  i   ?vi i  iv    i   -  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_192141087_    886 TTTCAACTTCTACTTTATACCATACACAAAAATTAATTTGGGATGAATTA 935
                         v  vi  ii    i i i      i           i iiii   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_192141087_    936 TGGACCTACATGTAAGGGTTAATACTAGAAAGTTTTTAGAAAAAAACAAA 985
                         ?i      v       i i   v    v   ii i      i      v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_192141087_    986 ATAGAATATCT--GCAAACTTAGAGTAGGTAAAGATATCTTAGAGAGGAT 1033
                         iv? v v    -- ii v   i iv    i  v i v       v v  i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_192141087_   1034 AT--AAAATGCAATAAACATAAAAAGAAATACTGATAAATTGAATTTCAT 1081
                          i--   iii   vv    v  i  i     --         i i     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTCAT 647

  chr2_192141087_   1082 TAAAGTTAAAAACTTCT---CACCAAAAAATAGCATTAAGAAAATAAAAA 1128
                         i   i          i --- vi    ii i vi  i      i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_192141087_   1129 GGCAAGCCATCAAAA----AGAAAATATTTGCAATACATACATCCAACAA 1174
                          i   v   -  i  ----               vv    i   ii i  
  L1M4_orf2#LINE/    698 GACAACCCA-CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_192141087_   1175 AGGACTTATATCCAGAATATACAGA-AGCTTCTATAGATCAATAATAAAA 1223
                         i      i             i i - i  ii  i iv            
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_192141087_   1224 ACACACACAACTCAGTAAAAATAGTGGGCAAAATATCTGAACAGACTATT 1273
                          v   v i   i  i v?   - i        iv  i    i    -   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGAC-ATT 844

  chr2_192141087_   1274 ------ATAAAAATATACCAATGGCCAACAGGCACATGAAAAGATGATTA 1317
                         ------ vi  i      v         i i               v i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_192141087_   1318 ACAGCATTTGTCAT 1331
                            v  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (123 / 69)
Gap_init rate = 0.03 (23 / 854), avg. gap size = 1.87 (43 / 23)  


2628 24.88 7.06 1.97  chr2_192181914_192184001.rev      735  1598 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_192181914_    735 TGAAGAGAGATGCTGTGCTCAGAGATTCAAAGACTCAACGTTGTTAC--- 781
                           i i   v  v ii  i   vi    vi      i  ii      v---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_192181914_    782 --TAATTATCCACAAATTAATCTAATGATTCAACTAAA-----ATCAAAA 824
                         --i   vv   v      i     vv        vv  -----       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_192181914_    825 TCACAACAGGATATTTTATAGAAACAGACAAGCTGATACTAAAATGTATA 874
                           v  i v vv v    ii     iv           v       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_192181914_    875 CAGAAAAGCCAAGAAGGTAGAATAGCCAACACAATTTTGAAAAAGGA--- 921
                         ii    v  v i i vvi           v     i         i ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_192181914_    922 CAAAGTTGTAAGGTCTTACATTACTTGATTTTTAAGACTTCCTATGAAAC 971
                                 -i   v  i   i v iii    i-  i    v   ii  i 
  L1M4_orf2#LINE/    201 CAAAGTTG-GAGGACTCACACTTCCCAATTTC-AAAACTTACTACAAAGC 248

  chr2_192181914_    972 AACACTAATCTAAACTATGTTATATTAGTAAAAGGAGAGAC--------C 1013
                         v   v     v i  vi   vi  i i i v     v    -------- 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_192181914_   1014 ACTAGAACAGAAGAGAGAGTCCAGAAACACAGCCACATATACATGGTCAA 1063
                          v i   i    vv             i v v   i i  vi        
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_192181914_   1064 TTGATTGTAATTGACCATAGTA--------ATTTCATAGGGAAAGAATCA 1105
                               - -- i   v vi  i--------   iv  i          vi
  L1M4_orf2#LINE/    349 TTGATT-T--TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_192181914_   1106 TATTTTCAATAAATTGTGGTGGGACAATCTGACATTCATACAGGAATGTA 1155
                          v       i    v   v        iiv  i ?i  i iivi  v v 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_192181914_   1156 TGAA-TTGG-CACATACCTCACATCACACACAAAAATAGATTTAAA---- 1199
                             -    - v v         i  i i        vi i i   ----
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_192181914_   1200 ---------TTAAATGTTAAAACAAAAACTATAAAATTTATAGAAGAAAA 1240
                         ---------i       v i i v            i iv          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_192181914_   1241 ------------TTTTTGTGACCTTGAGTTAGGCAA-AACGTCTTCAGAT 1277
                         ------------ i  i         i         -iiiv    -    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGAT 594

  chr2_192181914_   1278 ATCACACTAAAAGCACAATCCATAAAAGAAAATATTGATTAATTAGAACT 1327
                           v    i          v v i         v  v   v    i  vi 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_192181914_   1328 AATCAAAATGTAAAACTTCTACTCTTTGAAAGACACAATTAAGGAAATGA 1377
                         v        vv       i iiv   ii  i     v  i   i  i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_192181914_   1378 ATAGACAAGGCACAGAATGGGA-AAAATAGCTATAAAATTAAAATACATG 1426
                          v      vv            -      vi ii   - i -----i  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCA-----TATA 738

  chr2_192181914_   1427 TCCGATGAAATGTTTATACCTAGAATTTACAAAGAATCTTCAAAACTCAA 1476
                           i   i iivii  i  i i     v  i      iii i v       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_192181914_   1477 TAATAAGAAAACAAAGCACCCAATTTATTTTAAAAATGGGTGAAAGATTT 1526
                               i  i     vv        ? -----        ii  i     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWA-----AAAATGGGCAAAGGATTT 833

  chr2_192181914_   1527 GAACAAACACTTCACCAAAGA---TACATGGGTGGCATATAAGCACATGA 1573
                            i i   i   v       ---  i iiii    vv            
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_192181914_   1574 AAAGATTTGCAACACTATTAGTCAG 1598
                               viv     ii ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (128 / 85)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.90 (78 / 20)  


 340 30.65 7.04 3.52  chr2_192451582_192457857      286   484 (5792)  C L1M4_orf2#LINE/L1   (581)   327   122  

C chr2_192451582_    484 AACTTGTCTAAGTGATTCTAAGATTCATCTAGAAAAATAAAACATTGAGA 435
                           v   v v iv    i    i      v i    vii  iiv iiv   
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

C chr2_192451582_    434 CCAGC--------TTTTAAAAAATTAAAGAAAAGAGTAATGAATAAGGAT 393
                         vi   -------- i  i     --i     v i   --  i ---   i
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAA--GAAGAACAAAGT--TGGA---GGAC 214

C chr2_192451582_    392 TTA-GCTACTAGACATAAAAACTT-TTATGAAACTACAATAATTTAGATG 345
                          i -i  v ivi iv v       -i  ii  i     i    iv   ii
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

C chr2_192451582_    344 ATGTGGTAATAGCACAGGCCTTGACA----GATTAATAGGAAAGACTAGA 299
                         i       v i   i i vv v    ----   i   i i v   v v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

C chr2_192451582_    298 TAGTCCTGAAATA 286
                         v     v      
  L1M4_orf2#LINE/    315 GAGTCCAGAAATA 327

Transitions / transversions = 1.54 (37 / 24)
Gap_init rate = 0.03 (7 / 206), avg. gap size = 3.00 (21 / 7)  

3272 25.94 0.88 0.66  chr2_192451582_192457857     4879  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_192451582_   4879 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAATATCGTGAAAAC 4928
                              ii i  i     i    i i v      v i     i  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_192451582_   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCTATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_192451582_   4979 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5025
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_192451582_   5026 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5075
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_192451582_   5076 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5125
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_192451582_   5126 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5175
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_192451582_   5176 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAA- 5222
                                 i    i--    i  --        vv iii i  i  iii-
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_192451582_   5223 CAATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5272
                             -    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_192451582_   5273 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5322
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_192451582_   5323 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAACCAATTCAAGATG 5372
                         v    ii    i    v   i     v          ii  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_192451582_   5373 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5422
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_192451582_   5423 ACCTAGGCATTACCTTTCAGGACATAGGCATGGGAAAGGACTTCATGTCT 5472
                           v    ?i v vii   iv   v v  vv i  v  v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_192451582_   5473 AAAACACCAAAAGCAATGGCAACAA--GCCAAAATTGACAAATGGGATCT 5520
                          vi            vvi       -- vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_192451582_   5521 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5570
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_192451582_   5571 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5620
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_192451582_   5621 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5670
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_192451582_   5671 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5720
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_192451582_   5721 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5770
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_192451582_   5771 TCTTCACTGGCCAT 5784
                         v v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (137 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2717 19.55 2.88 1.12  chr2_192730494_192732109      501  1124 (492)    L1M4_orf2#LINE/L1      274   908 (0)  

  chr2_192730494_    501 TAGCATAAGAATAGATACATAGATCACCGGAATAGAAT-GAGACTAGAGA 549
                          i       i     i i        vi          -    v vv   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_192730494_    550 AATAAATCTTTGTATACAGGGTCAATTGATTT-CAATAAGGGTGTCCAAA 598
                               i iv ii  vi v             - i i       i v i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr2_192730494_    599 AAATTTGATGATGAAAGGCTAGTCTTTTCAACAAATGGTGTAGAAACAAC 648
                         vv   ii   iv     iv                     iv ii     
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_192730494_    649 TGGATATCTACATGTAACA-AATGAATTTGGACCCCTTCCTCACTCCATC 697
                               ? i     i  v -      v          v      v    v
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_192730494_    698 TGCAAAAAATACCACAAAATGGATCACAGACCTAAATATA-GAGCTAAAA 746
                          i      v  v v            ?          i  -         
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_192730494_    747 CTATAAATCCCTTAGAAGAAAATATTGGAATAAATATTTGCTCCCTTGGG 796
                                v i            i  v  ?i     v  i ivv       
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_192730494_    797 TTGAGCAAAACCTTCTTAGATATAACAACAAA--CACAAGCAACAACAAA 844
                           ii    vivi           i   v    --            v i 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_192730494_    845 G--------TAAATTGGAGTTCATCAAAATTAAAAAGTTT-GTGTTTCAA 885
                         i--------         v                 v   -   i     
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_192730494_    886 AGGATACGGTCAAGAGAGTGAAAGG-CAATTCCACAAAATAG-AGAAACT 933
                             i  vi      i       i -   i-     i   i -     v 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAAC-CCACAGAATGGGAGAAAAT 722

  chr2_192730494_    934 ACCTGCAAACCATATATCTGCCAGGGAACTTATATTTAGATTATATATAT 983
                          ii      i          vi i  i    i   ii   --       v
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA--ATATATAA 770

  chr2_192730494_    984 TTTTAAAACTCTTACAGCTCAATAACAAATAGACAAATCGCTGAATTTAA 1033
                         ---- i          i        i   v        vi iv    ?  
  L1M4_orf2#LINE/    771 ----AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_192730494_   1034 GAATAGACAAATGATCTGAATGGATATTTCTTCTAAAAAGATAAACAAAT 1083
                         i   i i    v   i     i  i      i v  i      v      
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_192730494_   1084 GTTCAATATACAAATAAAAAGAGAC-CAACACCATTAGACCT 1124
                          vi     vi  v  i      vi -     i  ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (72 / 46)
Gap_init rate = 0.02 (13 / 635), avg. gap size = 1.92 (25 / 13)  


1919 23.65 16.20 3.60  chr2_192804115_192806484     1101  1878 (492)    L1M4_orf2#LINE/L1       33   908 (0)  

  chr2_192804115_   1101 ACTAAATATTTTTTTAAAGTCCATACTACCCAAAGTGATCTACAGATTCA 1150
                            v      v  vvi v v v     v      v               
  L1M4_orf2#LINE/     33 ACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCA 82

  chr2_192804115_   1151 ATGCAATCCCTATCAAAATTTGAATGGCATTTTTCTCACAGGTAAAAAAA 1200
                          i                 iiv iiv  v     iv  v ii vi v  i
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG 132

  chr2_192804115_   1201 TT---CCTAAAATCCATATGGAGCCACAAAAGTTTCTAATTAGCTAAAGC 1247
                         i ---        i        ivii   ii vii vi v    i   i 
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_192804115_   1248 AACCTTGAGTAAGAAAAAATGAAACTGAAGGCATCATATTACCTGACTTC 1297
                           i     iv     i  -ii  ii  i   vv   i i v  ii i   
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAA-CAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_192804115_   1298 AAAGTATACTACAAAGCTATGGTAATCAAAACAACATGGTAGTGGCATAA 1347
                            iiv             ii        i   iii     v        
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_192804115_   1348 AAAGAGACATATAGATCAATAGAACAGAATAGAAAGCCAAGAAATAAACC 1397
                         ii v                i   i     v  i  i v           
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_192804115_   1398 TATGTAT--AT---------------------------AAGAC------- 1411
                         i  ii  --  ---------------------------     -------
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_192804115_   1412 -------AAACTAATCTT--CA---------------------------- 1424
                         ------- i v  i    --  ----------------------------
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_192804115_   1425 -----GCAAAAG-------------------CTC----------CAAGAA 1440
                         -----       -------------------   ----------   i  
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_192804115_   1441 T--ACACAAAATGGATTAAAGACTTAGACATAAGACCTGAAACAGTAAAA 1488
                          --  v          i ?    i  i ii     v  i    vi     
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_192804115_   1489 TTCCTACAAGAAAACATCAGGGAACAGCTGTATGACATCAATCTTGGCAT 1538
                         i  i  v          vi ? v v v  vii    ------     -i 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC------CTTGG-GT 574

  chr2_192804115_   1539 CTTGGCAATTATTTTTTGGATAGAACACCAAAAGCACAGGCAACAAAAGT 1588
                         - v      vi   i  i    vi              i          v
  L1M4_orf2#LINE/    575 -TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_192804115_   1589 -----CAGATAAACACGTGGAATTACATCAAACAAAAAAGTTTCTACAGA 1633
                         -----i       i---    v  -       vvv    ii  i iiivv
  L1M4_orf2#LINE/    624 AAAAATAGATAAAT---TGGACTT-CATCAAAATTAAAAACTTTTGTGCT 669

  chr2_192804115_   1634 GCAAATGAAACAATCAACAAAGTGAAAAG-CAACATATGGAGTGGGAGAA 1682
                         v    v  v  v     v           -    vi ii  i        
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_192804115_   1683 AATATTTGCCAGCCACGTATATGAGAAGGGGTTAATATTCAAAATATATA 1732
                                  v ii  ii   v   v     ii vi   i  i        
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_192804115_   1733 AGGAACTCT-ACAACTCAATAGCAAAAATCAAAAACAAACCCCCCAAAAA 1781
                          i       -           ii     -----i     i--------- 
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAA-----GACAAAT---------A 805

  chr2_192804115_   1782 ACTCAATCAAAATATGGGCAAAGGCC----AT---CATTTATTCGAAAGC 1824
                           i    i?   v           vi----  ---     v i -    v
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC-AAAGA 854

  chr2_192804115_   1825 TTACATCTAAATGGTCAACAGTTATATGAAAAGGTGATTAACATCACTAA 1874
                         vv i  vi      i   i ivi i        i  v i       ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr2_192804115_   1875 TCAG 1878
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.66 (113 / 68)
Gap_init rate = 0.03 (23 / 876), avg. gap size = 6.70 (154 / 23)  


2438 25.03 9.02 1.30  chr2_192945701_192949057.rev     2023  2865 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_192945701_   2023 TGAAGAGACATACCATGTCTAGGGATTAGAAGACTTAACATAAT-AAAA- 2070
                           i i   i  v      ii v     i          i  vi -  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_192945701_   2071 GACAAATCTTCCCCAAATTGATC---------AATGACCTTCTTGTCAAA 2111
                          i   - vi              ---------  i vvv i i i     
  L1M4_orf2#LINE/     51 GGCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_192945701_   2112 A-CTGAGAAGAATTTTTTATAGATATAGACAAGCTGACTCTAAAATTTAT 2160
                          - iv  vv vv      ii   v  v          ii        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_192945701_   2161 ATGGAAAATCAAAAGAATTAGAATAG-----ACAATTTTGAATAATGAAA 2205
                                vv   ii  vii       -----     i     v  vi i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_192945701_   2206 GTAAGCATGGAGAAATCACACTACCTAACTTTAAGACTT----------- 2244
                         ii  ivv     i v       v  i  i  i  i    -----------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_192945701_   2245 -TAGTAATTAA--CAGTGTGGTATTGGCAGAAGGATAGATGCATAGATCA 2291
                         -i      i  --          i     v         iii        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_192945701_   2292 ATGGACCAGAATAACAAGTGCAGAAATAGAATGACAAAAATATGGCCATT 2341
                              vi     vivi   v        i viv i v vv     i  v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_192945701_   2342 TGGTCTTTTACAAGATTGTAAAAGCAATTCAATGGGGAAAAGATAATCTT 2391
                           i i  iv     iv  iv  ii v              ii   i    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_192945701_   2392 TTCAACAAAT--TGC--------------------ATACAAAAAAAT--- 2416
                                   --   --------------------  i     i   ---
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_192945701_   2417 -CTCAACCTAAATCTCACATCTTATACTAAAAATAACTCAAAATTGATTA 2465
                         -i vi   ivv i      i v     v    v           v   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_192945701_   2466 TATATGTAAATTTAAAATATAAAACTTTAAAACTTTTAGGAAAAAATGTA 2515
                         ? v iv     v   i vv       v       i    i i    ii  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_192945701_   2516 AGAGAATATCTTCATAACCTGAGATCAGGCAAA----TCTTAGACGTAGC 2561
                         i ? v v      i i    vi i i      v----       ii ii 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_192945701_   2562 ACTAAAAGCACAATCCACAAAATAAAAAATTGTTAAAATT--ACTT-ATC 2608
                           i          v v      v       v v    -  --    -   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA-TTGGACTTCATC 648

  chr2_192945701_   2609 AAAATAACAAACTTTTGCTCTATGAAATACAT-----AGA---CGAAAAT 2650
                              v v         iv  vii  iv   i-----   ---i     v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_192945701_   2651 ACAAGCTATAGATTGAGAGAAA-TATTTGCAAATTACATATCTATCAAAG 2699
                             v i i   v  i      -           i i      ivi  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_192945701_   2700 AACCTGTGTC-AAACTATATATGCGACTTTCAAGAAAGCAAAAACTCAA- 2747
                         i  i   i  - i v      vivi   i i ------   ---     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTA------CAA---CTCAAT 789

  chr2_192945701_   2748 AATAAGAAAGCACATAACCTAATTAAAAAATGAGCAAAGGACTTGAGCAG 2797
                              i  ii  v      i    ?       i        i    ii  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_192945701_   2798 ATACTTCATGTAAGTGATTATATGGATGGCAAATAAGCATGTGGAT-GTT 2846
                          i i   vivv   viiv    iii     v        ii  i v- v 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_192945701_   2847 GTTCAACATCATAAAATAT 2865
                          i         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (127 / 81)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.78 (87 / 23)  


3258 27.09 0.44 0.44  chr2_192958910_192965182.rev     4874  5781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_192958910_   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4923
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_192958910_   4924 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4973
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_192958910_   4974 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5021
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_192958910_   5022 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5071
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_192958910_   5072 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5121
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_192958910_   5122 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5171
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_192958910_   5172 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5219
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_192958910_   5220 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5269
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_192958910_   5270 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5319
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_192958910_   5320 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAGATGGA 5369
                            ii    i    v   i     v  i        i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_192958910_   5370 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5419
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_192958910_   5420 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5469
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_192958910_   5470 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5519
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_192958910_   5520 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5569
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_192958910_   5570 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5619
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_192958910_   5620 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5669
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_192958910_   5670 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 5719
                          i     i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_192958910_   5720 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5769
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_192958910_   5770 ATCACTGGCCAT 5781
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1719 26.82 14.22 2.10  chr2_193008140_193010091      652  1460 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_193008140_    652 GGGGAGATGTACCATACATATGGATTGGAAGACCCAATATTGTCAAGATG 701
                           ii    i v    iivi              ii        i      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_193008140_    702 AAAAATTTGGCCAAAATGATCTATAGATTCAGTGCAATCTCAGTTGAAAT 751
                         iv  vvi vv     v       i       ii      i vi ii    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_193008140_    752 TACAGCAGTACTTGTTTTCTAGAAATTGAAAAGCTGATTCTAAAAATTAT 801
                         iv    -- i i v    vi         v        i      v i  
  L1M4_orf2#LINE/    102 CCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_193008140_    802 ATAAGAATGCAACATGTCTTTAATA-CTAATGCAATTTTTACAAAGAGGA 850
                           iii       vivii ivv    - i  vi    i  v v     i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_193008140_    851 GCGAATTTGTGGGCCTTATCCTATCTGATTTTAGGTTTTA---------- 890
                         i i  v   vi  v  i iv  vi ii    i iivi   ----------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_193008140_    891 ---------------------TATTTGTATTTAGATAGAAATGTAGAT-- 917
                         ---------------------  i v i  vvi      v  i     --
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_193008140_    918 ---------------------------AGACTCAAACATATATGGTATAT 940
                         --------------------------- i  i  v    v      vv  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_193008140_    941 TAATTTTTGATAAAGG---------CACTTAATTGGGAAAGAAAAATCTT 981
                          i     i  i  i  ---------  i i   v         v i    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_193008140_    982 CAAAATGAATGATG--GAGAATGAACTCAATAGCTA--TGCAGGAACAAA 1027
                         ivv  ii    i  -- i  v--    vi   ? i --    --  - i 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGAC--AACTGGATAKCCACATGCA--AA-AGA 444

  chr2_193008140_   1028 ATGAACATCCATCCTTACCTCACAGTATATA---ATGTTAAATCAAAATG 1074
                              vv vv i  i         vi     --- vi    v        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_193008140_   1075 GACAATAGATCTAAACATAAAACCTAGAATTGTAAAAATTCTAGAAGATA 1124
                           iv ?   i     ii   i v   i  i i     v ii       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_193008140_   1125 ACATAGAATAAAAATTTTGTGACTTTCATCAGAGTCAA-CATGTTGTATT 1173
                               i?vv   vi  i     i  ----- i  i i-  -i v  v i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTT-----GGGTTAGGCA-ATGGTTTC 588

  chr2_193008140_   1174 TTGG--------TCAAAA---CAAG----GAAAGAAAAATT-GATAACCT 1207
                           i --------i     ---    ----i         v -     vi 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_193008140_   1208 GGACATCATTCAAATTTTCAAACTTT---GCTTTTCAAGTCACTACTAAG 1254
                             v    -    v  vv       ---    ivv i v     ii   
  L1M4_orf2#LINE/    639 GGACTTCAT-CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_193008140_   1255 AAGACAGAAAGACTGCAACACAC----TTGAAGAAAATATTCACTACACA 1300
                           iiiii      ---   v   ---- v i          ii v vv  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGAC---AACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_193008140_   1301 TAAAT----TAAAGGACATGTAATATGAATGTATAAAAAACT--TGCATC 1344
                           v  ----   i    v    vivv    i      i    -- i  v 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_193008140_   1345 TCAATAATAAAA---CTAACAAACCAATTAACAAATGGAGAAGCAATTTG 1391
                                     --- v  i  v      ? v      iv  ivi     
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_193008140_   1392 AACAGACA---CTTCATAG--GATATATTCATAGCAAATAAACATATAAA 1436
                           i     ---  i  v  --      ivv  i  v     i  i  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_193008140_   1437 ATGATGCCCACTATCACCACTCAG 1460
                          v     i  vi    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (125 / 88)
Gap_init rate = 0.03 (27 / 907), avg. gap size = 4.89 (132 / 27)  

 978 25.67 0.67 0.67  chr2_193008140_193010091     1512  1811 (141)  C L1M4_orf2#LINE/L1   (131)   777   478  

C chr2_193008140_   1811 AAAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCAT 1762
                                 i    i      i ?    i       v   v       i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

C chr2_193008140_   1761 AAAAAGGCTAGAAGAAAACGTAGGCA-ATACCATTCAGGACATAGGCATG 1713
                             vvvi           i    ?i- v i -   iv   v v  vv i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTA 576

C chr2_193008140_   1712 GGCAAGGGCTTCACATCTAAAACACCAAAAGCAATGGCAACAAAAGCCAA 1663
                              v  i   vi vv  vi            vvi          vv  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

C chr2_193008140_   1662 AATTGACAA-TTGGAATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAA 1614
                            v  i  -     v - v  i   v v  i i   i  ii vv    i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACT-TCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

C chr2_193008140_   1613 GAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTAC 1564
                           v    i  vv i      v  i     i                 vvi
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

C chr2_193008140_   1563 TGCAATCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAAC 1514
                              vii ivi      i  i  i  vi          v  i  v    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

C chr2_193008140_   1513 TC 1512
                           
  L1M4_orf2#LINE/    776 TC 777

Transitions / transversions = 0.97 (37 / 38)
Gap_init rate = 0.01 (4 / 300), avg. gap size = 1.00 (4 / 4)  

 482 21.01 0.00 0.00  chr2_193008140_193010091     1823  1941 (11)    L1M4_orf2#LINE/L1      790   908 (0)  

  chr2_193008140_   1823 AAGAAAAAAACAAACAACCCCATCAAAAAGTAGGCGAAGGATATGAACAG 1872
                           v     i     i     v  i?    i i   i      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_193008140_   1873 ACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAAT 1922
                            i     v        i  vi viii     v ii          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_193008140_   1923 GCTCATCATCACTGGCCAT 1941
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.00 (0 / 0)  


3023 23.05 1.98 3.95  chr2_193031684_193033897.rev      825  1735 (479)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_193031684_    825 TGTTCATG-ATAGGAAGAC--AATATTGTCAAGAAGTCAGTTTCTCTCAA 871
                                 -  v       --        i    v v  i viii i   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_193031684_    872 CTTGGTCTATAGATTCAATGCAATCTCAGTGAAAACCCCAGAAAGTTATT 921
                         v   i    i        i      i vi v    i     vvivi v  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_193031684_    922 TTGTGGATATACACAACGACTCAAAAGTTTCTATGAAGAGGAAAATGACT 971
                            ii  v  vv    --i  v ----- i   ---------    --- 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAA--GCTGA-----TCCTA---------AAAT---T 146

  chr2_193031684_    972 CAGAAGTTTCTATGAAGAGGTAAAAGACCCAGAATAGCCAACACAATATT 1021
                           --------    i i v i  ii                v     v  
  L1M4_orf2#LINE/    147 CA--------TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr2_193031684_   1022 GAAGGAGAAGAACACAGTTGGAGGACTGATGCAACTCAACTTCAAGATT- 1070
                            ii         v            v ii vv i   i     i i -
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_193031684_   1071 ---ATAAAGCTGCAGTACTTAAGA-AGTGTGGTATTAGTG-AAGGA-AAA 1114
                         --- i      i     v i    -         i i ii-     - i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_193031684_   1115 AATGAGTAAATCTATGAAATAGAATACAGATACCAGAAATAGACCCATAT 1164
                         v  i--  i   v   i        vv   vv         i       i
  L1M4_orf2#LINE/    289 CATA--TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_193031684_   1165 AAATATAGTCAACTGATCTTTGAAAAAGGAGCAAAGACAATTCAGTGAAA 1214
                          vv   i     i    i  i  v  i  v  v     v     i  iii
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_193031684_   1215 CAAAAATAGTCTTTTAAACAAACAGTGCTTGGATAATTGGATATCCACAT 1264
                         v  i           v      ii     v   i  i      ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_193031684_   1265 GTAAGAAAAAAAATGAATGTAGACACAAACCTTACACC-TATCACAAAAA 1313
                          i  ----  i      vv i   v vv    i     -   -       
  L1M4_orf2#LINE/    437 GCAA----AAGAATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAA 481

  chr2_193031684_   1314 TTCACTCAAAAATGGATCATAGACCTAAATATAAAATGGAAATCTATAAA 1363
                           v        -       ?          i   i vvv   v       
  L1M4_orf2#LINE/    482 TTAACTCAAAA-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_193031684_   1364 ACTCCTAGAAAATAACACAGGA-TAAAACTGAGATGGTCTTGGGTATGGC 1412
                             i     i v    i   ?-    v  vv -  ii       vv   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGC 579

  chr2_193031684_   1413 AATGATTATTTAGATACAATACCAAAGGAATGATCCATGAAAGAAATAAT 1462
                             i  vi       ii i      i v ii v v ii       v   
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_193031684_   1463 TGATAAG-----CTACATTAAGATTAAAAACTTCTGCTTTGTGAAAAACA 1507
                         v     i-----  v   i  i           i  ivi vii  ii   
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_193031684_   1508 ATGTGAAGAGAATGAGAAGACAAGCCACAGACTGGGAAAAAATATTTGCA 1557
                         v i v    i i   i       v       v     i            
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_193031684_   1558 AAAGACACATCTAATAAAGAACTGTTATCCAAAATCTATAAAGAACACTT 1607
                           vv i i    i    i i   vv      i   v          v   
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_193031684_   1608 AAAACTCAACAATAAGAAAACAAGCAATCCAATTTCAAAATGGGCCAAAA 1657
                          v       i     i  i    ii  i      ?v         v  ii
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_193031684_   1658 ATCTTACTATGCACCTCACCAAAGAAGATACAGAGCTGTCAAATAAGCAT 1707
                           i v v  vi  ii  v            i v iv  v v        i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_193031684_   1708 ATAAAGA-ATTCTTCATATGATACGTTAT 1735
                           i  i -  v  iv i  v ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (119 / 87)
Gap_init rate = 0.02 (20 / 893), avg. gap size = 2.70 (54 / 20)  


3163 26.67 1.56 0.67  chr2_193119308_193121420.rev      722  1621 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193119308_    722 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 771
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193119308_    772 GGCCATATTGCCCAAGGTAATTTATAGATTCAACACCATCCCTATCAAGC 821
                            v   i v     iv i  i  i         i v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193119308_    822 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 869
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_193119308_    870 TATGGAACCAAAAAAGAGGCCGCATTGCCAAGTCAATCCTAAGACAAAAG 919
                                viiv  ii  vv v v  v     iv     i i i v i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_193119308_    920 AACAAAGCTGGAGGCATCTCACTACCTGACTTCGAACTATACTACAAGGC 969
                                i      vv  v    v  ii i   i  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_193119308_    970 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAGCAGAGATATAGACC 1019
                          i      i   i    ii         i iv iiii   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_193119308_   1020 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 1067
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_193119308_   1068 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1117
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_193119308_   1118 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGAT 1167
                           v  i  i              v      v  ?   i   i i  ii  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_193119308_   1168 GAAACTGGATCCCTTCTTTACACCTTATACAAAAATTAATTCAGGATGGA 1217
                            ii    i    v i i     v              i   ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_193119308_   1218 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1267
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_193119308_   1268 CTAGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTA 1316
                         v    ?i- v i -   iv   v v  vv i i   v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_193119308_   1317 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTC 1366
                         vi            vvi          vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_193119308_   1367 ATTAAAG-----AGCTTCTGCAACAGCAAAAGAAACCACCATCAGAGTGA 1411
                           i   i----- i   i  ii- vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTG-CTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_193119308_   1412 ACAGGCAACCTACAGAATGGGAGAAAATTTGTGCAACTTACTCATCTGAC 1461
                          v  i     i                 v v     v i ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_193119308_   1462 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1511
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_193119308_   1512 AAA----AATAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACT 1557
                            ----        v  i? v  i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_193119308_   1558 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 1607
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_193119308_   1608 TCATCACTGGCCAT 1621
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2659 23.68 1.84 4.14  chr2_193144749_193146597      488  1357 (492)    L1M4_orf2#LINE/L1       59   908 (0)  

  chr2_193144749_    488 TCTTTAAATTATCATCTAGAGAACCAAGGCAATTTTTATCATAATTCCAA 537
                           iii     i--     v   vi   v     iii     v   i   i
  L1M4_orf2#LINE/     59 TCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_193144749_    538 TGGAAGTTTGTTACAGAAAAAGAAAAAAGC-AATCCTAAAATTCTTATGG 586
                         iv vvv   -  i      vv  v  --  -i            v     
  L1M4_orf2#LINE/    107 CTGCCTTTT-TTGCAGAAATTGACAA--GCTGATCCTAAAATTCATATGG 153

  chr2_193144749_    587 AACCACAGAAGACTCCAAATAGTCAAAGCAATCTTGAGAAAGAA-ATGAA 635
                           vii  iii   i vi     i    i         i      - vv  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_193144749_    636 AGTTGG-GGTCATCATGTTTCCTGTTTTCAAATTATATCACAAATCTATA 684
                               -  v -   iii    iiv       viv  ii     v   i 
  L1M4_orf2#LINE/    204 AGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_193144749_    685 GTAATCAAAAGGGTAGAATACTGTCATAAAAACAGATACATAGATGAATG 734
                                 i vi  ivii     v     ii i   i i      v    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_193144749_    735 GGACAGAATATATAGCACAGAAATAAACCCATGTATATACAGTCAAATTT 784
                          i i     vv v  iv               ii  v  ii     --  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA--TT 350

  chr2_193144749_    785 CATATATATATATGTGTATATATATATATGAATATATATGAATGTGTATA 834
                         v  v - vv i v v  ii-------i v  vi  --- v    v ----
  L1M4_orf2#LINE/    351 GATTT-TCGACAAGGGTGC-------CAAGACCAT---TCAATGGG---- 385

  chr2_193144749_    835 TATATATGAAATAATAGTCTCTTAAATAATAAAGAATCCTGGGAAAACTG 884
                         -------    v        i  ---i  i   vii v      v     
  L1M4_orf2#LINE/    386 -------GAAAGAATAGTCTTTT---CAACAAATGGTGCTGGGACAACTG 425

  chr2_193144749_    885 GATATCCACATGCAAAA-AATGAAATTTGACCCTTATCTTATACAACACA 933
                             ?            -      i  v     i  i  i i  v i i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_193144749_    934 GAAAAGTTAACTGAAAATGTATTAAAGAGTTAAA-GTAAGGCCTAAAACC 982
                         v    i      v      v  i ?   vi    -     iv       i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_193144749_    983 ATAAAACTTCTAGAA-AAAATATTAGACAACAAACATTT-TGACATTGGT 1030
                                 ii     -    i  -  i?i-i   iv  i-    v    v
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACAT-AGGNG-TAAATCTTCGTGACCTTGGG 573

  chr2_193144749_   1031 CTTGGAAATGATATCATGGATATGACACCAAAAGCACAGGCAACAAATGC 1080
                         i v  v    i v  v i                    i        v v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_193144749_   1081 AAAAATAAACAAGTGGGACTACATTAAACTAAAGAGCTCTGTTACAACAA 1130
                                i i  i v     v   i   v v  i i  i vv i vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_193144749_   1131 AATAAATAATCAATAAATAGAAAAGGCAACCTACAGAATGGGAGAAAATA 1180
                          iv v iv     v   vv      i     i                  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_193144749_   1181 TTTGTAAACCATGTATATGACAAAGGGTTAATATTCAAAATATATAAGAA 1230
                             i   i   i   v   i  i  ii vi   i  i         ii 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_193144749_   1231 ATGCATACAGTAGCAA-AATAAATACATAAATAA--------AAACATGG 1271
                          iv v    ii-v   -      v v i      --------   v    
  L1M4_orf2#LINE/    774 ACTCTTACAAC-TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_193144749_   1272 GCAAATGACTTGAATACACATTTCTCCAAAGAAGATATACAGATGGCCAA 1321
                              v  i       v                        i        
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_193144749_   1322 TAGGGATATGTAAAAATGCTCAACGTCACTAATCAT 1357
                           i v i   v   i         i   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (117 / 86)
Gap_init rate = 0.03 (22 / 850), avg. gap size = 2.36 (52 / 22)  


2990 28.37 0.77 0.55  chr2_193213912_193220638     5330  6235 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193213912_   5330 TGAAAAAACATTCCATTCTCTTGGATAGGAAGAATCAATATCATGAAAAT 5379
                           i   i i  i    vi  v     v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193213912_   5380 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 5429
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193213912_   5430 TACCATTGACTTTCTTCACAGAATTAGAAAAA--AATCCTTTAAATTTCA 5477
                          v   vivi i  i  ii     v v  v  i--i     --   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chr2_193213912_   5478 TATGGAACCAAAAAAGAGACT--GTATAGCCAAGACAATCCTAAGCAAAA 5525
                                -- viv   i   i-- v        i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_193213912_   5526 AGAACAAAGCTGGAGGCATCATGCTACTTGACTTCAAACTATACTAAAAG 5575
                                  i      vv   ii  v iii i      viv     v  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_193213912_   5576 GTTACAGTAACCAAAA-AACATGGCACTG-TACCAAGACAGATATACAGA 5623
                          i        i   i - iii   i    -i iv i  i   i   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_193213912_   5624 CCAATGGAACAGAACAGA-AGCCTCGGAAATAATGCTACGCATCTACAAC 5672
                         i        i    iv  -  i - i       vv i ii   i  iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chr2_193213912_   5673 CATTTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5722
                           v     i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_193213912_   5723 CCTATTTAATAAATGGTGATGGGAAAACTGGCTAGCCATATGCGGAAAAC 5772
                         i  v  i  i        v     v      v  ?   i    ii  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_193213912_   5773 TGAAACAGAACCCCTTCCTTACACTTTAGGCAAAAATTAACTCAAGATTG 5822
                             iiv i      v   i    iv  vi               i  v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_193213912_   5823 ATTAAAGACTTACATGTAAGACCTGAAGCCATAAAACCTCTAGAAGAAAA 5872
                           i ?    i  v        v  i  i i       iii          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_193213912_   5873 CCTAGGCAATACTATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5922
                          v    ?ivv v v   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_193213912_   5923 AAACTCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCAGATCTC 5972
                         vi  v         vvi          vv     v  i    ii  ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_193213912_   5973 GTTAAACCAAAGAGCTTCTGCACAGCAGAAGAAACTATCATCAGAGTGAT 6022
                         i i   viv  i i   i  ii vv  i i  v       vv i     v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_193213912_   6023 CAGGCAACCTACAGAATGGGAGAAAACTTTTACAATCTATCCATCTGACA 6072
                         v  i     i                iv   i   vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_193213912_   6073 AAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGGAA 6122
                          i  i  vi          v  i  i     ivv    v iv i  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_193213912_   6123 AAAACAAACAACTCCATCAAAAAGTGGGCAAGGTATATGAGTAGACACTT 6172
                           i     i   i v  i?    i       i v  v   i      i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_193213912_   6173 CTCAAAAGAAGACATTTATGGAGCCAACAAACATATGAAAAAAAGCTCAT 6222
                            v        i  vi vivi     i  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_193213912_   6223 CATCACTGGTCAT 6235
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (153 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


 844 21.59 5.29 1.32  chr2_193428716_193430786      501   727 (1344)    L1M4_orf2#LINE/L1      121   356 (552)  

  chr2_193428716_    501 GAAAATGACAAGCAGATACTAAATTTTATATTGATATGAAAGAGTCTTGG 550
                             v        v   v     v  i    v  v   v   i v iii 
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr2_193428716_    551 AATTTCTAAAGAAGTCTTGAAAAAAAAG------TTTGGAGTACTTAAAC 594
                            vv i   iv i          i   ------v      v   i v  
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_193428716_    595 CTCTCCAATTTTAAAACTTACTACTTACAGCTACAGT------GATGGTG 638
                         i  -       i            -- v         ------  ii   
  L1M4_orf2#LINE/    221 TTC-CCAATTTCAAAACTTACTAC--AAAGCTACAGTAATCAAGACAGTG 267

  chr2_193428716_    639 TGGTGGTGGCATTAGGATAGGCTTATAGATCAATAGAATACATTTGAAGT 688
                             iv      v       i v           i     v v    iiv
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_193428716_    689 TTCAGAAATATACTCATCTAGTTATGGTGAATTTTTTTT 727
                          i        v  i   vi v       v    vv    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 0.81 (22 / 27)
Gap_init rate = 0.02 (4 / 236), avg. gap size = 3.75 (15 / 4)  

2630 20.50 2.14 0.00  chr2_193428716_193430786     1021  1581 (490)    L1M4_orf2#LINE/L1      336   908 (0)  

  chr2_193428716_   1021 CAGTTACGGTGAATTT-TTTTAAACAAGGTTGCTGCCACAATTCAATGGG 1069
                           v   i   v    v-    vi      v   iivv  v          
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_193428716_   1070 GAAAAAAC--TTTTTTTATCAAATGATGCTCAGATAACTGGATAGCCACG 1117
                             i  i-- i    i v      i    vi  i         ?    i
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_193428716_   1118 TGCCAAAGCATGAAATTGGAACCTTCCCTTACACCATCTATATACATTTG 1167
                            v    v     i     v  i v   i       v  i v v   vi
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_193428716_   1168 CTCAAAATGGATTATGAGCCTAAATTTAAGAGCTAAAGCTATGGAATACT 1217
                                     i ?iii       v           i    ii  iv  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_193428716_   1218 TAGAAGAAAATACAAGAGCAACTCTTTGTGACCTTAGGTTAGGCAATAGT 1267
                                   i i i ? i  v    i        i           i  
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_193428716_   1268 TTCTTAGATATGACACCAAAAGCACGAGTGACAAAAGAAAAAA---ATGA 1314
                                                  i  ii             ---  i 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_193428716_   1315 ATTGAACTACATCAAAATTGAAAACTTTTGTGCTTTAAGTGATATCATCA 1364
                             i   v          i               i  iv  i ii    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_193428716_   1365 AGCAAATAAAAGGACAACCAACAGAATAGGAATAAATATTTGCAAATCAT 1414
                           v  i i   i       v       i   iv                 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_193428716_   1415 ATGTTAGATAAAG---CTGT--CCAGATCACA-AAAACACTCTTAGAGCT 1458
                           i iv     i ---i   --     vi i -   iv       v i  
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_193428716_   1459 CAATGGTAAATAAAGAAATAATCCAATTAAAAAGTGGACAAAGAATTTGA 1508
                             ii    v i v      i      ?    i   i     i      
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_193428716_   1509 ATAGATATTTCTCTGAAGTGCTTACACAAATGACCTACAATCACAGGAAA 1558
                              i       ii   vivv  i       i  v i  v    v    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_193428716_   1559 ATATGCTCAAAATAATTATTCAC 1581
                          v        v  v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (70 / 41)
Gap_init rate = 0.01 (6 / 573), avg. gap size = 2.00 (12 / 6)  


 483 26.47 13.61 8.11  chr2_193483911_193486047.rev      850  1650 (487)    L1M4_orf2#LINE/L1       64   908 (0)  

  chr2_193483911_    850 AAATTGTTCTCTAGTTTGGATGCAATCTGAATTAAAATTTCAAGAAACTA 899
                               v   vi  v  vi i      ivv  i     ii  i----  i
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG----CTG 109

  chr2_193483911_    900 TTTTTCTGGCA---ATTAAAAAGCCAAGTCTAAAATTTATGTATGAAA-G 945
                         ii   i v   ---   i v    ii vi        i  i i-    - 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG-GAAATG 158

  chr2_193483911_    946 CAAAATACCAAGAATAACAAAAAT--TGTTGAAGAAATAATATAAGGAGA 993
                            iiv   v      i v    i-- v     i  --------- i   
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA---------GAAGA 199

  chr2_193483911_    994 ATAAAGAGAATGAAAAAATGAGGGAGGACTTGCTACTTTGGATAACAAAT 1043
                          i    v---  i ii v v v-----    v i v   ---i  --  i
  L1M4_orf2#LINE/    200 ACAAAGT---TGGAGGACTCAC-----ACTTCCCAATTT---CAA--AAC 236

  chr2_193483911_   1044 ATATTGCTATGTTAAACTAATGGAGACAGTGTAGTCTTGCCATA-GAAAA 1092
                         v  i i v v i  v v    vi         i  vi  v    - i v 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_193483911_   1093 GACATATACATCAATGGAACTCCATAAATAATCTAAAAGGGTCCTATGTA 1142
                                 v          -----  i --  i---i  i    - - v 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAA-----TAGA--ATT---GAGAGTCC-A-GAA 324

  chr2_193483911_   1143 ATA---TCA-ACATTTTATGACAAATATTGACCATC-ATAGTAGTGTC-- 1185
                            ---i  -      -   iiv   --   iiv  - i ivi   i --
  L1M4_orf2#LINE/    325 ATAAACCCATACATTT-ATGGTCAAT--TGATTTTCGACAAGGGTGCCAA 371

  chr2_193483911_   1186 ---CA---AATAAAGCCAAAGAGAGGTATTTTCATTAAAATATTATGAGT 1229
                         ---  ---   iii --     ivi  v      vi   vvi vv  i v
  L1M4_orf2#LINE/    372 GACCATTCAATGGGG--AAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_193483911_   1230 CAATTGCAATATC-AC-TATAAAA-AATGTTTAAGCAAACTATACCACTG 1276
                            i  -i   ? -  - ii    -    -------  ii iv   v  i
  L1M4_orf2#LINE/    420 CAACTG-GATAKCCACATGCAAAAGAATG-------AAGTTGGACCCCTA 461

  chr2_193483911_   1277 TTTCACATCATGTATAAAA-TTACTTCCGGGTGAATTTTATATTTTATTG 1325
                         ii     i   i  i    -   vi  viii  i  iv? v ii v v  
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_193483911_   1326 TT-GAATTAAAG--ATAAAACT--------------TGGGCCTA------ 1352
                          v-  ii    i--        -------------- i  ?v  ------
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_193483911_   1353 --TGA--------TAAGAAAT---TTTTTAGTTA-AATAGAAAGAGAAAA 1388
                         --   --------  i v   ---  i    v  -i i vv  i  v v 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_193483911_   1389 AATTCTACCACAAAATGAAAATATTGGTACATT--------TTAATGTTA 1430
                          i----- v      -     v  v i  v   -------- i  vi   
  L1M4_orf2#LINE/    612 AG-----CAACAAAA-GAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_193483911_   1431 AAA--TTT----------AG--CACTACTAA-AAAG-AAAAATATATATA 1464
                            --   ----------  --     ii  -    -i    v i - iv
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA-ACC 704

  chr2_193483911_   1465 TGTCAAAATTAGAGCATTAATAATAG--ATTCATAT-TCT---------- 1501
                         ii-  i   vi   v --    v v -- v      -   ----------
  L1M4_orf2#LINE/    705 CA-CAGAATGGGAGAA--AATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_193483911_   1502 ---TATCTGAAA---ATAAAGGAAATTTTTATA---CATCAAAGAAAAGA 1542
                         ---    iii  ---      --  i i   i ---  vi  vi      
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAG--AACTCTTACAACTCAATAATAAAAAGA 799

  chr2_193483911_   1543 CAGGTAATCTGTTTCAAAAATGGTTAAGAGATTTGAACAGGCATTTC-AT 1591
                           ii   i iiv  ?        vi  ii        i  i      -vi
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_193483911_   1592 AAAGGGGTTATTCAAA-GGCCTATAAAAATATGAAAAGTTGTTCAACTGT 1640
                             ii v   v    -    v    iv i        v  i     -i 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC-AT 898

  chr2_193483911_   1641 TATCCACAAG 1650
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.63 (129 / 79)
Gap_init rate = 0.07 (57 / 845), avg. gap size = 3.05 (174 / 57)  


1957 25.11 5.28 7.44  chr2_193493134_193495156      610  1537 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193493134_    610 TGGTGATATATACCATGCCCATAGATTTGAAAAATCAATGTGGTTAAGGT 659
                            vi v    v     ii   i    v   i v i   i v      i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193493134_    660 GTCATTTCTCTCCAGTTGGAACTATTGACTCATAATAATCCTAATCAAAA 709
                          v  v v   i   iv v  v   iv  i   vvii     iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193493134_    710 CCTCAGTAAGCTTATTCTTTCTTTTGGTAGACATTGGAAATTTAACTTTA 759
                         i i   i------- v i  i   -- i   v    iv  vi i iii  
  L1M4_orf2#LINE/    101 TCCCAGC-------TGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTA 141

  chr2_193493134_    760 AAATTTACACAGAAAGGTAAAGGATCTAAAATAGTTTAAAGAATTTTAAG 809
                              i i ii    v i  i   i i i     iiv   v   i  i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_193493134_    810 GAAAAATAACAAAGTTGAA--ATTCGCATTATACAATTTCAAGACTTATT 857
                         i  i  v          i -- i  i  i viv         i     i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_193493134_    858 TTAAAGAAACAGTA--TAA-AC----TTATAC----ATAAAAAAAGTGAT 896
                         vi    vv      --i  -  ---- vi   ----    ii v  vv  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_193493134_    897 AT-------TGAAACAGAATAGAGCACCCAGA------TTCATGCACATA 933
                           -------  i  i     v   vii     ------ii   i  iv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_193493134_    934 TAGTCAACTATTTTTTTTTAATG-TGGCAATGACAACCTAA-GGTGAAAA 981
                          i     i iv    ivvi  v -  v   -   v iii  -  v    i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAG 390

  chr2_193493134_    982 AATAGTCTTTTCAATACATGTTGTGAGAACAAAACTGGAACCCCATATG- 1030
                                       i v   v  ivi i    --     vv?   i   -
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAA--CTGGATAKCCACATGC 438

  chr2_193493134_   1031 AAAAAAA---AATTGAACCATGTCACATATCTCAGGATC-TACATAAAAA 1076
                             i  --- i   i   ------ v  i    v- i -  i i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACC------CCTACCTCAC-ACCATATACAAAAA 481

  chr2_193493134_   1077 TGAACTCAAAATGAATTAGACTATAAATGCAAAATATAAATATAATTCTT 1126
                          v           i  i ------------? i iv     i   -----
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCA------------WAGACCTAAATGTAA----- 514

  chr2_193493134_   1127 AATATAAATGTAAATTTCATTCAAAATTTTAAAAATCTGA-AAGAAATTA 1175
                         -----------i ii ------    i v     v   v -      vi 
  L1M4_orf2#LINE/    515 -----------GAGCT------AAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_193493134_   1176 TAGAAGAAAATCTACATGACCTAAGGTTTGATTATGAATTTTTA-ATATG 1224
                            i? v      v i      vi    v iiv   iv  i   -     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_193493134_   1225 ACACAAAACACATGATGCATGAGATGAGAGGAAAAAATGGTTAAATTAGA 1274
                             v   vi  ii -   ---- ii i  -       i v      i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA-GCA----ACAAAAG-AAAAAATAGATAAATTGGA 641

  chr2_193493134_   1275 CTTCATTAAAATTGTTATA---TTTGTTCTGTGAAAGACACTGTTATAAG 1321
                               i      i-- v ---     v  vii  i      i i vi i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTA--AAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_193493134_   1322 AATGAAAAG-CAAGCAACAGACTGAGGGAATATATT-GCTAATCACATAT 1369
                          i       -   v v     v  i i   v     -  v     i    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_193493134_   1370 CTGATAAAAAAGACTTGCATCCAAACTATAGAAAGAATACTTAAATCTCA 1419
                                ii--      i     i v    v      iv    v v    
  L1M4_orf2#LINE/    740 CTGATAAGG--GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_193493134_   1420 ATAACAAGAAAATGAACAACCCAAGTTAAAAAATGGGTCAAATATCTTAA 1469
                             i  i  i ii  i       -  ?         iv  iv  i v  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_193493134_   1470 CAAAGAAGATAT-----CAAAGGGGATATATAAATGGC----AGACACAT 1510
                         i -----  i  -----     ii      i       ---- ii     
  L1M4_orf2#LINE/    837 TA-----GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_193493134_   1511 GAAAAAATGCTCATTTTCATTTGTCAT 1537
                              i       viv   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (145 / 84)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 3.37 (118 / 35)  


2853 27.24 3.63 0.57  chr2_193510563_193515631     3697  4577 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193510563_   3697 TGGAAAGATATTTCATGTTTATGGATTGGAAGAATTAACATTGTTAAAAT 3746
                                    ii      i             v    i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193510563_   3747 AACAATA----------TG-------GATTCAATGCAATCTCTATCAAAA 3779
                         ii     ----------  -------       i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193510563_   3780 CATCAATGACATTCCTCACAGAAATAGAGGAAACAACACTAAAATTTATA 3829
                         ivi  iivi v  ii ii       v  vi ivii iv        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_193510563_   3830 TGGAACCACAGAAGACCCTAAATGGCCAAAGCAATCCTGAGCAAAAGGAA 3879
                              vii  iii     vi   i      i     i   iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_193510563_   3880 CAAAACTGGAGGCAGCCCACCAGCTGACATCAAGACATATTACAAATCTA 3929
                             ii      vvv v   ivv ii iv    i  v  i      v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_193510563_   3930 TAATAACCAAATCAGCACGGTACTAGTATAAAAACAGACATATAGACCAT 3979
                         i i   i   iv   iii      i i    ii i           i  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_193510563_   3980 TGAAACAAAATAGCAAACTCAGATATAAATCCACATATTTACAACCAACT 4029
                           i  i i   v vi iii    v     i   i i     iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_193510563_   4030 CCTTTTTGACAAAGGGGTCAAGACTGCACTGAA--GTGAAAGGACAGTCT 4077
                         vv    i     i  v i      --  i v  -- v     i i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGAC--CATTCAATGGGGAAAGAATAGTCT 398

  chr2_193510563_   4078 CTTCAATTAATCATGCTGAGA-ACCTGGAGAACCATAGGCAGAAGAATTA 4126
                         i     iv   vi     i  - v     v ?   i v   i      v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_193510563_   4127 AAATAGATCCAAATCTCTCATTATGTACAAAAATAAAATCCGAATGGATT 4176
                          iv i  i  vv i   v  ii  i         v  v  vi       i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_193510563_   4177 AAAGACTTAAATTTAAGACTTGAAACAATAAAACTCCTAGGAGAAAACAT 4226
                          ?    i     v     vi i    v         i   i         
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_193510563_   4227 TGGAGAAACACTGCAGGATATTGGTCTGGGCATAGATATATTATGTGTAA 4276
                         v  ? v  vv  v iv  iv    vi i    vv i v v   vi i --
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-- 596

  chr2_193510563_   4277 GACCTCAAAAGCACAGGCAACCAAAACAAAATTAGACAAATATCATTACA 4326
                            vi          i     v   iv    v    i    vvv i v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_193510563_   4327 TCAATCTAAAAAGCTTCTGCACAGAATAGAAAAC----AACAAAGTGGAG 4372
                             vv v    i   i  ii vvv v  i v  ----  v      i i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_193510563_   4373 AGAAAAACTCACAGAATGGGAGCAAATATTTGTAAACTACCTTTCTGACA 4422
                            v  - i             v         i   ii iv v     i 
  L1M4_orf2#LINE/    697 AGACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_193510563_   4423 AGGGTTTAATAACCACAGTACATAA-GAGCTCAAGCAACTCAGTAG-AAA 4470
                             vi vi  v   v i  i    -  i   vvi       i  i-   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_193510563_   4471 AAAA-----AATCCAATTAGAAAATAGGCAAAG-ACCTGAATAGACATTT 4514
                           i -----  i      ?i     i       - ii             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_193510563_   4515 CTCAAAGGAAGACATACAAATGATCAACAGGCATGTGGAAAAATGATCAA 4564
                            v  i     i         ii   i i   ii  i   i   v    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_193510563_   4565 TATCACTAATCAT 4577
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (148 / 88)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.08 (37 / 12)  


3279 26.98 0.44 0.44  chr2_193524423_193526685.rev      864  1771 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193524423_    864 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 913
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193524423_    914 GGCCATACTGCCCAAGGTAATTTAGAGATTCAGTGCCATCCCCATCAAGC 963
                            v     v     iv i  i  v       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193524423_    964 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1011
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_193524423_   1012 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTGAGCCAAAAG 1061
                                viiv  ii  v  v v  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_193524423_   1062 AACAAAGCTGGAGGCATCACACTACCTGACTTCAGACTATACTACAAGGC 1111
                                i      vv       v  ii i    i viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_193524423_   1112 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1161
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_193524423_   1162 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 1209
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_193524423_   1210 ATCTGATCTTTGACAAACCTGACAAAAACAAGGAATGGGGAAAGGATTCC 1259
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_193524423_   1260 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1309
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_193524423_   1310 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1359
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_193524423_   1360 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCTTAGAAGAAAAC 1409
                          i ?    i    i  v   v       i      vi             
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_193524423_   1410 CGAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1459
                         vv   ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_193524423_   1460 AACACCAAAAGCAACGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1509
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_193524423_   1510 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAGCTACCATCAGAGTGAAC 1559
                          i   v v  i i   i  ii vv    i  vi   i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_193524423_   1560 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAG 1609
                           i     i                 v  i    vii ivi      i i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_193524423_   1610 AGGGTTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGTAAA 1659
                         i  ii vi          v  i  v      vv    v iv i  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_193524423_   1660 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 1709
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_193524423_   1710 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 1759
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_193524423_   1760 ATCACTGGCCAT 1771
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1877 26.37 2.09 0.96  chr2_193562504_193564117      501  1122 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr2_193562504_    501 AAAAATAGACAAATAGATCAAATAAACAATATAGCGACCCCAGAAATAGA 550
                           ii       v         vvi  i iv  v v  vi         i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_193562504_    551 CCTAGATAAATATAG-CTACTGATCTTTGACAAAGGAGAAAAGACAATGT 599
                           i v i vv   i - v i    i  i     i  v vv     v  vi
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_193562504_    600 AATGGAAAAAATACAGTCTTTTCAACAAATAATGCTGGAACAACTGGACA 649
                              ii   iv i                ii      i         i 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_193562504_    650 TCCACATGCAAAAAAAAAAAAGATATAACCCT----TACATCTTTCACAA 695
                         ?            i  vi  - v iv v    ----i   i v vi    
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAA-GTTGGACCCCTACCTCACACCATATACAA 478

  chr2_193562504_    696 AAAGTAATTCAAAATAAATAATAGATCCAACTGTAAATTGC-ATAACTAC 744
                            v   i       ii  v ?   i i  v     iv-  - v     i
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTAT 527

  chr2_193562504_    745 ACAACTTTTAGAAAATTACATAGTAGAAAACCTACATAACCTTGGGTTTG 794
                          v    i      i vv      v? v   i  v i i          v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_193562504_    795 GCACTTAGTTT--TAGATAGGACATCAAAGTCACAATTCATGAAAGAAAG 842
                            v -i    --      v    i    iv     viv ii       i
  L1M4_orf2#LINE/    578 GCAAT-GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_193562504_    843 AATTGATATGCTGGATTTCATTAAAATTTAAAACT-----ACTCTAGAAT 887
                            v    vii    i     i      v      -----i  ii -  v
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAG 675

  chr2_193562504_    888 GAAAATGCCCAGAGAATGAGAAGACAAGCCACAGACTGAGAGAAAATATT 937
                           v v ii v   i i   i       v       v  i           
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_193562504_    938 TGCAAAGAACATATTTGTTAAAAGACTATTACCCAAAATATACAAAGAAC 987
                               vv i    i  v   ii    vv  i   i      i       
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_193562504_    988 CATTAAAACACAACAATTAAAGAATGAACAATCCATTTAAAAAAAATGAG 1037
                         iv   v   v   i   v   ii ii  i  i   v  ?     --  i 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA--TGGG 823

  chr2_193562504_   1038 TTAAAGCTACGAACACATACTTCACCCAAGATGATATGCAGATAACAAAG 1087
                         iv  i v vi   i v i i   v  v    v     i  i  ii v  v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_193562504_   1088 AAACATACAAAAAGATGCTCCACATCACAGGCCAT 1122
                           i  i ii           v      ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (91 / 69)
Gap_init rate = 0.02 (10 / 629), avg. gap size = 1.90 (19 / 10)  


1995 27.79 6.26 2.85  chr2_193585272_193587290      658  1535 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193585272_    658 TGAAGAGATACTCCATGTTCATA------AAGGCTAAACATT---AAGAA 698
                           i i     ii          i------   i  v  i   ---    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193585272_    699 GTCAA--CTCTTCTAACTTGTTCTATATGTTAAATGCAATACCAACTGAC 746
                          v   --   ii -  v   v    i vi  v  i     v  v iii v
  L1M4_orf2#LINE/     51 GGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_193585272_    747 ATCCCAGCAAGTTATTTTGCAGATATTCATAA-CTGATTCTAAAGTTTAT 795
                                 vivi v         v   v i  -     i     i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_193585272_    796 ACGAAAAGACAAAAGTCACAGATTAGTCAAAACAAAACTGA----GAAGG 841
                          i i   vi   ii v v    v   i        vvi   ----    i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_193585272_    842 ACAAACTCAGAGGACTTACATCACCTAACTTCAAGATATATTATAAAATT 891
                              v ii       i   iiv  i  i     i iv  i  i   i--
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG-- 247

  chr2_193585272_    892 GTAGACTTCAGTAATCAAGCTAGTAT---ATTGATGAAAAAGTAGACAAA 938
                         -----  v           vi   i --- i  iiiv  iii      v 
  L1M4_orf2#LINE/    248 -----CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_193585272_    939 TTGACCAAGTGAACAGAATAGATAACTCAGAAAGAGCCTCACTCAAATAT 988
                          v  i   vv   i     v  v iii      v iv i  iv  vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_193585272_    989 AGTTAACTAATACATGATGAGGAGGGAGCAAAGGCATTTCAACAGAGAAT 1038
                         i  i  i i  --- vvi  vi    v  v   i vv     ii i   v
  L1M4_orf2#LINE/    343 GGTCAATTGAT---TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_193585272_   1039 TCATAATCTGTCTAGCAAATGCTTCTGGAACAATTGGATATCCATATGCA 1088
                         vv   i   v ii i      v v    i    i      ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_193585272_   1089 AAAAGAAAAAATATTCAAACACAGACCTTACACC-TCTGACAAAAATTAA 1137
                            -   vi  -i  -ii  v vv    i     - v -           
  L1M4_orf2#LINE/    440 AAA-GAATGAA-GTT-GGACCCCTACCTCACACCATAT-ACAAAAATTAA 485

  chr2_193585272_   1138 CTCAAAATTA--CGTAAACACAAA-GT----GC-AAAACTATAAAATATC 1179
                                 vi-- i? i  vi   -  ----  -            i-  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TC 534

  chr2_193585272_   1180 TACAGACCTTTAAAAAA-----GAGTGTACCTAAGTGATCTTGGGTTTGG 1224
                          -i   ----- i    ----- ?  iv i  vv    i        v  
  L1M4_orf2#LINE/    535 T-TAGA-----AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_193585272_   1225 CAATGAGTTTTTAGATTTCACATTAAAGATAAGATTAATAAAAGGAGAAA 1274
                              iv  i      v v   ii   iii vi vi  i     i -   
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA-AAA 627

  chr2_193585272_   1275 ATGG-TAATTTAGACTTTAT-AAAATCACAAGTTTCTATGC---AAA--A 1317
                           i -   v  i     i  -     i v  ii  i i   ---   -- 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_193585272_   1318 CATTGTTAAAAGAATAAGGAAGGAAGTCATGGACTTGGAGAACAATGTTT 1367
                           i i i  i i i i ii iiv  vi  ii  v v      -   i   
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA-AATATTT 726

  chr2_193585272_   1368 ACAAA-AATATATTTGATAA----TTTATATCTAAAATATAAAAAGAAC- 1411
                         i    -v      i      ----i  i    i i      v       -
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_193585272_   1412 CT--------AATAATAGGAAAGCAAACAACATAATTTTTTAAATGGGCA 1453
                           --------       ii  ii    i   vi    ?vv-         
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCA 825

  chr2_193585272_   1454 AGATATCTAAACAAACACCTTGTCAAACAGGATAAACAG-TGGTGAACAA 1502
                          iiv  i i  i i   ii ivi    v i    v   i-   iv  i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_193585272_   1503 GCATATGAGAATATGCTGTACTGCATTTGTCAT 1535
                            i    i  v     vv  vv  ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (152 / 88)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 2.35 (80 / 34)  


3133 28.11 0.66 0.55  chr2_193615651_193622023.rev     4975  5881 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193615651_   4975 TGGAAGAATATTCCATGCTCATTAATAGGAAGAATCAGTATCGTGAAAAT 5024
                              ii    i     i    vi  v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193615651_   5025 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5074
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193615651_   5075 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 5122
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_193615651_   5123 TATGGAACCAAAAAGGAGTCCATATAGCCAAGTCAATCCTAAGCCAAAAG 5172
                                viiv  i   vi viv        iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_193615651_   5173 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATGCTACAAGGC 5222
                                i      vv   ii  v  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_193615651_   5223 TACAGTAACCAAAACAGCATGGTATTGGTACGAAAACAGATTTATAGATG 5272
                                 i   i    ii     i   i ii ii i   iv       v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_193615651_   5273 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5322
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_193615651_   5323 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAGGATTC-CCT 5371
                         i    i  i     ivv  v   i v  vvv         i  v v-i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_193615651_   5372 ATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTTGA 5421
                         v  i  i     i        v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_193615651_   5422 AACTGGATCTCTTCCTTACACTTTATACAAAAATTAATTCAAGGTGGATT 5471
                          ii    i i  v   i    iv              i    ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_193615651_   5472 AAACACTTAAAAGTTAGACCTAAAATCATAAAAACCCTAGAAGAAAATCT 5521
                          ? v  i    v  v   v      ii      vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_193615651_   5522 AGGCA-ATACCATTCAGGATATAGGAACAGGCAAGGACTTCATCACTAAA 5570
                            ?i- v i -   iv  iv v  ivi      v ii   v viv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_193615651_   5571 ACACCAAAAGTAATGGCAACAAAAGCCAAAATAGACAAATAGGATCTAAT 5620
                                   i vvi          vv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_193615651_   5621 TAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5670
                         i   v v  i ii  i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_193615651_   5671 GGCAATTTACAGAATGGGAGAAAATTTTTGCAA--TATACCCACCTGACA 5718
                          i   iii                 v       --i   i-- i    i 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGATA 745

  chr2_193615651_   5719 AAGGGCTAATATCTAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5768
                          i  i  vi    i     v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_193615651_   5769 GAAACAAACAATCCCATCAAAAAGTGGGCAAAGAATATGAACAGACACTT 5818
                         i i     i  i  v  i?    i         i  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_193615651_   5819 CTCAAAAGAGGACACCTAAGCAGCCAACAGACACATGAAAAAATGCTCAT 5868
                            v     i  i ivi  iii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_193615651_   5869 TATCACTGGTCAT 5881
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (160 / 91)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2804 27.04 3.17 0.90  chr2_193623821_193626096.rev      902  1785 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_193623821_    902 AAGATATACCATGTTCATGTATTGGAAGAATCAATATTGTTAAAATGTCT 951
                                v           v         v i           i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_193623821_    952 GTACTACTCAAAGCAGTCTACAGATGCAATGAAGTTTCTATCAAAATACC 1001
                         i    v i    viii         v   i v i ii          v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_193623821_   1002 AATGACATTCTTCTCAGAAATAGAAAAGC-AATCCTAAAATTTAAATGGA 1050
                          iivi v  i  iv       v  v    -i           i v     
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_193623821_   1051 ACTACAGAAGACCCAGAATAACCAAAGCTGTCCTGGAAACAAAGCACAAA 1100
                          v i  iii           i     i vi  i  i   vi   v     
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_193623821_   1101 ACTGGAAGAATCGCTTTACCTGCCTTCAAATTGTACTACAGAGCTATGGT 1150
                         ii    i  v  i vi v  iivi      viv       i     ii  
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_193623821_   1151 AATTCAAAGAGCATGGTACTAGCATAAAGACAGACACATAGACAAATGGA 1200
                            iv i v  ii       i      i  i     i     iv      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_193623821_   1201 ACAGAAT-AAAAACACAGAAATGAATGCAGATATCTACAGTGAACACATT 1249
                          i     -i i iiv       i  iv  v i  i  ii  v  ivv   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_193623821_   1250 TTTGACAAAGGTGGCAAGAACATACACATTGGGGAA--ACAGTCTCATCA 1297
                           i     i    v     v   v  -  v   i  -- i     iv   
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAGAATAGTCTTTTCA 403

  chr2_193623821_   1298 ATAAATTGTGCTGGGA-AACATAAATATCCTCAAGCAGAAGAAAGAAGCT 1346
                          i    v         -   - ii   ?  v  v   i     v    i 
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAAC-TGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_193623821_   1347 AAAACT-TATCTCAC--TATATACAAGAATCAAATCAAAATGAATTGAAG 1393
                         ii v i-  i     --i        i   i  v        i  ii?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_193623821_   1394 ATATAATTATAAGACTTCAGACTATGAAACTACTAAAAGAAAACATTGCT 1443
                          iv   v i     vi v i     i     vi  i          v v?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_193623821_   1444 GAAACTCTCCAGGATGTTGGACTGGACAAAGATTTTTGAGCAAT-ACCCT 1492
                          v  v   i iv  iv    ii i i   v i   i v  vv  -  v i
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_193623821_   1493 ACAA--ATGGGCAACCAAAGCAAAAATGGACACATGAGATCACATCAAG- 1539
                          v  -- iii     v    v      i  i v  vi  iiv      i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_193623821_   1540 TTAAGAAGCTTCTGCACA-AAAAAGAAACAATCAACAAAGTAAAGAGACA 1588
                             i  -   i  ii v-v   i  v  v     v     i  i     
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_193623821_   1589 AACCACACAACGGAAGAAGTTATTTGCAAACTACACATCTGACAAGAGAT 1638
                          v     v  i  i    iv          ii i i      i   i  i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_193623821_   1639 TAATAGCCAGAATATTTAAGGAGCTCAAAAAACTTCATAGAAAAAAAAAA 1688
                          vi  v         v   i  i   vv v    iv   iv     i v 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_193623821_   1689 CCTCTACTGATCCAACTTAAAAAT---------------ATGGGCATTTT 1723
                         ----- v i i    i ?      ---------------  i i     i
  L1M4_orf2#LINE/    802 -----AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_193623821_   1724 TTAAAAGAAGACATACAAATGGCAAGCAGATATATGAAAAGGTGTTCAAC 1773
                          iv        i           v ii iii i        i  i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_193623821_   1774 ATCCTTGATCAT 1785
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (146 / 89)
Gap_init rate = 0.02 (15 / 904), avg. gap size = 2.40 (36 / 15)  


1334 27.39 11.11 3.75  chr2_193645607_193647774.rev      538  1311 (857)    L1M4_orf2#LINE/L1        1   831 (77)  

  chr2_193645607_    538 TGGAGAAATATGCTACATTCATGAATCAGAAGACACCATATCCACCAATC 587
                             i i    v i ii      i  ii      viv    i--------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-------- 42

  chr2_193645607_    588 AGAAGAATCAGAAGATGATAATTCTTTCCAAACCAAACTATAGATTCACT 637
                         ------i i --     ii   v  ii     iii v   i       vi
  L1M4_orf2#LINE/     43 ------GTTA--AGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr2_193645607_    638 ACACTTCCAATAAAAACCATAGCAGGATTTTTAAAATAAAAATTTGA-AA 686
                         i  v i  v  v    i vi   v vv     vi--i i     -  -  
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG--CAGAAATT-GACAA 131

  chr2_193645607_    687 TCTGGTTCTAAAAGTTATATGATTACTCAGCAGACCTAAAGTAACTAAAA 736
                         v   i i      v i     ivv iv  ivi    i i i  i i    
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr2_193645607_    737 CAAAATTGAAAGATA----TAATGT----AAATTTATATT---------- 768
                            vv      i v ----i  v  ----ii i i i i ----------
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_193645607_    769 -AAAC--------AAGTGATAGTT-TCAAAACAG--------------AA 794
                         -    --------   iv i   v-    i    --------------  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_193645607_    795 --------ATATAGAACA-T--AACAGAAT-----ATTCAGAAATAGACC 828
                         --------       v  - --  i     -----i i        i   
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_193645607_    829 CATATACATATGGT-AACTGATTTTTTACAAAAGTGC-AAAACAATTAAG 876
                             i iv      -  i       iv    ii    -  i  v   v i
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_193645607_    877 TAGAAAAAAATGATAGTCTTTTCAACATACGTT-TTA--ATGATTGAATA 923
                          i ii   i --               v i v -i i-- ii i  i   
  L1M4_orf2#LINE/    382 TGGGGAAAGA--ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_193645607_    924 TCCATATGCAAAAATTATAA-GATATTTGATCCATAATTTGCATCATATA 972
                         ?   i        i----  -  vi  v  i  v  vi ii  i      
  L1M4_orf2#LINE/    430 KCCACATGCAAAAG----AATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_193645607_    973 -----AGTCACTTAAAATGACTCATAGCTCTAAATG--AAAATGAAAAAT 1015
                         ----- v v   i      iv   ?  vi       -- i iiv    v 
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_193645607_   1016 ATAAAATGTCTAGAA-AAAATATAACAA-AAACGTTTGCTAACCTTGG-T 1062
                               ivii     -    i   iv?i-   iv  i - i       - 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGT 574

  chr2_193645607_   1063 TATGAAAAAAATTTCT-AGATATG-CACTAAAAATATGATCTATGAAAGT 1110
                           - iv  vii     -       -   i    ii ii v v ii    v
  L1M4_orf2#LINE/    575 TA-GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_193645607_   1111 GA---CTGAAAAATTATACTCAATTCAAAATAAGAACTTCTGCTCTTCAA 1157
                         i ---iv  v     iv   iv  iv   v   i     i  iv      
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_193645607_   1158 AAGACACTGTTAACCGAGTGAAGATATAAGCCACAGACTAGGTGAATATA 1207
                          i      i i  vvi      i v i  v       v i  v   v   
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_193645607_   1208 GTTACAAATCATATACTTGACAAAAGACTTTTGTCCAAAGAATATA-AAA 1256
                         v  i           ii   i  ii     v i    --       -   
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCA--GAATATATAAA 771

  chr2_193645607_   1257 GAA-TCTCAAAATTTAATAATATACA-ACAAA---CCCAATAAAAATATT 1301
                            -   i v  i i       v v -     ---      v?   v  v
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_193645607_   1302 AGTGAAGGAT 1311
                         i ii      
  L1M4_orf2#LINE/    822 GGCAAAGGAT 831

Transitions / transversions = 1.85 (135 / 73)
Gap_init rate = 0.04 (37 / 831), avg. gap size = 3.11 (115 / 37)  

 280 24.68 0.00 0.00  chr2_193645607_193647774.rev     1592  1668 (500)    L1M4_orf2#LINE/L1      815   891 (17)  

  chr2_193645607_   1592 AAAAAAAAGCAAAGGATTTCAATAAGCAGTCCAACAAAGGGGATATATAG 1641
                              vii           v    ii  v i vv     ii      i i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_193645607_   1642 ATGGTAAATAAGTACATGAAAATATAC 1668
                             iv      i         v  i 
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGC 891

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.00 (0 / 0)  


2634 27.73 2.35 1.29  chr2_193695598_193697661.rev      713  1563 (501)    L1M4_orf2#LINE/L1        1   860 (48)  

  chr2_193695598_    713 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATGTTGTGAAAGT 762
                               i i  i     i        v      v i   i    v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193695598_    763 GGCCATACTGCCAGAAGAAATTTATAGATTAAATGCTATTCCCATCAAGC 812
                            v     v  vi  vvi  i  i     v  i  v  i  i     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-- 98

  chr2_193695598_    813 AA--CCATTGACTTTCTCCACA-AAATTAGAAAAAAAACT-ACTTTAAAT 858
                           --   vivi i  i iii  -     i---- v  i  - iii    v
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAA 144

  chr2_193695598_    859 TTCATATGGAACCAAAGAAGAACCTGCATAGCCAAGACAATCCTAGGCAA 908
                                    viiv iii  v  v v        i      i iiiv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_193695598_    909 AAAGAATAGAGCTGGAGGCATCATGCTACCTGACTTCAAACTAAACTACA 958
                         i     i i  i      vv   ii  v  ii i      vivv      
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_193695598_    959 AGTCTACAGTAACCAAAACAACATGGTACTGGTACCAAAATAGATATATA 1008
                          iv         i   i   iii         i iv ii     i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_193695598_   1009 CACCAATGGCAAAGAACAGAGACCTCAGAAATAACACCACACATCTACAA 1058
                         v i      v v    iv    vii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_193695598_   1059 CCATCTGATCTTCGACAAC----CCAA---CGTGTAATGGGGAAAGGATT 1101
                         i  vi    i        v----    --- i vi           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_193695598_   1102 CCCTATTTAATAAATGGTGCTGGGAAAACAGGCTAGCCGTATGCAGAAAA 1151
                         vi  v  i  i              v   v  v  ?  ii     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_193695598_   1152 CTGAAACTGGATGCCTTCCTTACACTTTATACAAAAATTAACTCAAGATG 1201
                         v    ii    iv   v   i    iv                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_193695598_   1202 AATTAAAGACTTAAGTGTAAAACCCAAAACCATAAAAACCCTGGAAGAAA 1251
                         i  i ?    i   i     i v i     i      vi i i       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_193695598_   1252 ACCTAG---TCAATACCATTCAGGACAAAGGCATGGGCAAAGACTTCATG 1298
                           v   --- v   -- -   iv   vvv  vv i     v ii   v i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_193695598_   1299 ACTGAAACACCAAAA--ATAATTGCAACAAAAGCCAAAATTGACAAATGG 1346
                         iv ivi         -- i  --          vv     v  i    v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_193695598_   1347 GATCTAATTAAACTAAAGATCTTCTGCACAGCAAAAGAAACTATTGTCAG 1396
                           ii v  i   v v  i v   i  ii vv    i  v     iivv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_193695598_   1397 AATGAACAGGCAACTTACAGAATGGGAGAAAATTTTTGCAATCTACCCAT 1446
                          i    v  i    ii                 v       vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_193695598_   1447 CTGACAAAGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTAT 1496
                             i  i  v  vi          v  i  i     ivv    v iv  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_193695598_   1497 GAGAAAAAAACAAA---CCCA-TCAAAAAGTGGGTGAAGGATATGAGTAG 1542
                         i v     i     ---    - i?    i    ii      v   i   
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_193695598_   1543 AAACTTCTCAAAACAACACAT 1563
                          v i     v   v  v i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.02 (14 / 860), avg. gap size = 2.21 (31 / 14)  


2830 26.72 4.40 2.03  chr2_193714710_193720670     4583  5469 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193714710_   4583 TGAAAAGATATTATAGATTCATTGATTAGATGAATCAACATCGTTAAAAT 4632
                           i        ivi vi     v    i  v  v i  i  i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193714710_   4633 GTCCATATTACACAAAGAAATCTACAGATGCAATTGTGATCTCTATCAAA 4682
                          v v   i v v    vvi          v   i- ii   i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAAC-GCAATCCCTATCAAA 99

  chr2_193714710_   4683 ATGCCAATGGCATTCTTCACAGAAATAGAAAAA-TAATCATAAAATTCAT 4731
                           v   iiv  v  i  ii       v  v  i- i   v          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_193714710_   4732 AGGGAACCACAAAAGACTCA---TGGCCAAA------------------- 4759
                          v    vii   ii   i  --- i      -------------------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_193714710_   4760 ------CTGAAGGAACCATATTATCTGACTTCAAATTACACTACAGAGCT 4803
                         ------i  i    vi  i i vi ii i      vivi      i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_193714710_   4804 ATAGTAACCAAAACATCATAGTACTGGCATAAAAACACACACATAGATCA 4853
                          i     i   i   vii i            ii i v   i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_193714710_   4854 ATGGAACAGAATAGAGAACCCAGAAACAAATCCATAAACTCACAGTGAAC 4903
                               i     v    ii       i   i     v i i ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_193714710_   4904 TCATTTTTGACAAATATGCCAAGAGCATACATTGGAGACAGGACAGTCTC 4953
                          v     i     ivi        v   v  v   i  v  i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_193714710_   4954 T--AATAAATGGTGCTCAGATAAATGAATATGTATATGCAGAGGAATAAA 5001
                          --  i          vi  i  v  i   ?vi i     i i    i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_193714710_   5002 TCTTGATTCCTATTACTTGCCATATAAAACAATAAAATCAAAATGGATTA 5051
                         vi v  ii    iiv vii       v  v   v  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_193714710_   5052 AGGACTTAAACCGAAGACCTTGAACTATGAAACTACTACAAGGATACATT 5101
                         ?i   i    ivv    v  vi      i     vi  v   i v    v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_193714710_   5102 GGAGAAACTCTCCAGGATATTGGTCTGGACACAAATTCCTTGACTAATAT 5151
                           ? v  v   i iv  iv    vi i i  vvii  i   ii---    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG---ATAT 596

  chr2_193714710_   5152 TCACAC---GATCACAGGTGACCAAAGCAAAAGTGGAAAAATGGTATCTC 5198
                         v-    ---i v    i ii  v    v    i i  v    v v ii  
  L1M4_orf2#LINE/    597 G-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_193714710_   5199 ATCAAG-TTAAAAGGCTTCTGTTCAGTGAAGGAAGCAATCAACAAAGTGA 5247
                              i-      i-   i   v vvii     vi v     v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_193714710_   5248 AGAGACAACCCATAGGATGGGAGACAATATTTACAAACTACCCATCTGAC 5297
                          i          i  i        v       i    ii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_193714710_   5298 AAGGGATTAATAACCAGGATGCGTAAGCAGCTCAAACAACTCCACAGGTA 5347
                               i vi  v    i  iii   iv i   vv       v i ----
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA---- 790

  chr2_193714710_   5348 TATATATATTTAAAAGTCTAATGATCTGATTTAAAAATGGGCAAAAGATT 5397
                         -----   ---     v v   i i ii   ?             i    
  L1M4_orf2#LINE/    791 -----ATA---AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_193714710_   5398 TGAATAGATGTTTCTCAAAAGAAGACATATAAATGGC----AGACATATG 5443
                                 ii      v        i   i       ---- ii  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_193714710_   5444 AAAAGGTACTCAACATCATTGATTGT 5469
                              i i          ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (148 / 85)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.38 (57 / 13)  


3241 27.09 0.44 0.44  chr2_193722994_193728676.rev     4284  5191 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193722994_   4284 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4333
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193722994_   4334 GCCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4383
                          v v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193722994_   4384 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4431
                          v i iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_193722994_   4432 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4481
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_193722994_   4482 AACAAAGCCGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4531
                                ii     vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_193722994_   4532 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4581
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_193722994_   4582 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 4629
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_193722994_   4630 ATCTGATCTTTGACAAACCTGACAAAAACAAGGAATGGGGAAAGGATTCC 4679
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_193722994_   4680 CTATTTATTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4729
                           v  i vi              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_193722994_   4730 GAAACTGGATCCCTTCCTTACACCTGATACAAAAATCAATTCAAGATGGA 4779
                            ii    i    v   i     vv          i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_193722994_   4780 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4829
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_193722994_   4830 CTAGGCGTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4879
                         v    ?  v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_193722994_   4880 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGGATCTCA 4929
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_193722994_   4930 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4979
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_193722994_   4980 AGGGAATCTACAAAATGGGAGAAAATTTTCTCAACCTACTCATCTGACAA 5029
                           iv  i i   i             v  iv   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_193722994_   5030 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5079
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_193722994_   5080 AAACAAACAACCACATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5129
                          i     i    vv  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_193722994_   5130 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5179
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_193722994_   5180 ATCACTGGCCAT 5191
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1983 30.00 0.97 1.11  chr2_193754314_193756022.rev      498  1217 (492)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr2_193754314_    498 AAAAAAAAAAACAAAGCTGGAAGCATTACATTAGCTGACTTGAAAGAATA 547
                              i  i       i    i vv i   i vv ii i  v   ivv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_193754314_    548 TCACAAGGCTACAGCAACAAAAACAGCATAGTATTGGCATAAAAACAGGC 597
                         ii    i       i  iv  i    ii i   i        ii i  i 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_193754314_    598 AATTTGACCAATGAAATGG----GACAGTTATCACAGAAATAAAGTCATC 643
                          vv v  i     i   i ----  v   i----          vi   v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTC----CAGAAATAAACCCATA 335

  chr2_193754314_    644 TATTTACAGCCAACTGATCCTTCATAAAGTGAACAAGAACTTACATTGGG 693
                         i     ii i   i    ii iv i  i vviv     v v v  v    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_193754314_    694 GAGAGTACATCCTGTTCAATAAATGGTGCTGGAAAAAATGGATAGCTATA 743
                           i  v i vi  v     i            i v  v      ? i i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_193754314_    744 TGCAAAATAATAAGATTTGACTTCTATCTCTCAACATAAGAAAAATATCA 793
                                v   i ii  v   ii   i   v  v    viv    -  i 
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTA 484

  chr2_193754314_    794 ACTAAAACTGGATTAACAACTGAAACATCAGATCTAAAATTCTAAATATC 843
                            v   v     i ?vi  iv   ii v   v      i v    vv  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_193754314_    844 CTAGAAAAAAAATCTAGGGAAAACTCTACTGGACATTGGGCTAGATAAAG 893
                         i     i    -iv    ?iv  v   v vv   v     i   ii  v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAA-CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_193754314_    894 GATTTATGACTAAGATCTCAAAAGCACAGGCAACCAAAATGAAAATAGAC 943
                          v  iv iiv  v  ivi          i     v   ivi        i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_193754314_    944 AAATGGGACTATATTAAGCTAAAAAGCTTCTGCACAGCAAATGAAACAAT 993
                             v     vi  i  iv v    i   i  ii vv    v  v  v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_193754314_    994 CAGCAGAGTGAAGAGACAACTTGTTGAATTGGGGAAAGTATTAACAAAAT 1043
                           iv i      i       iiiiv    v  i    i    vi    vi
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_193754314_   1044 GTTTATGTGACAGAGGATTCCTGTGTAGAATATGTAAGAAATTCA-ACAA 1092
                         i v   v   i ii   i iv i vi       i   ii  i  v-    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_193754314_   1093 GTCAATGGTCAAAAGAACCAAATAACTGTATTAAAAAGTGAGCAAAG-AC 1141
                         v     ii v      --        ivv   ?    i  i      - i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_193754314_   1142 ATGAACATACATTTTTCAAAAGAGGATGTACAAGTATTGGACAAAC-TAT 1190
                         v    i v      i  v     i   i     i ivivi i  i -i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_193754314_   1191 GAAAAAATGCACATCATCAATAAAATG 1217
                              i    v  v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (125 / 87)
Gap_init rate = 0.01 (8 / 719), avg. gap size = 1.88 (15 / 8)  


3247 23.13 4.95 0.46  chr2_193780353_193782636      924  1792 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193780353_    924 TAAAAGGACATATCATGTTTTCAGATTACAGGACTTAATATT-TTAAGAT 972
                          ii  i  i  vi      ivii    iv i           -       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193780353_    973 GGTAATATTCCTCAAGGC-ATCTATAGATTTAATTCAATAACCATCAACA 1021
                           i    i   i   ivi-     i     i  iv    vv i     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193780353_   1022 TCCTTATAGCCTTTTATTCAGAAATGGAAAAGCTGATCCTTGCAAATTCA 1071
                            iviiv       v v       v  v           --v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chr2_193780353_   1072 TA--AAATTACAGGTGACTCTTAATAG--AAAA--ATCTAGAAAAA-AGG 1114
                           --i  v i  i v   i vv     --    --    v      - i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_193780353_   1115 AGCAAAGTTGGAGAATTCACACATCCTGATTACAAAAGTCACTATAAACT 1164
                          i           i i      v   ii   v     v i    i   vi
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_193780353_   1165 TACAGTAATTGAAATAATCTAGTACTGGCATAAGAATAGATGTTGAGAAT 1214
                                  ii i i i v i             i     ii vv   vi
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_193780353_   1215 AATGGAATTGAATGTAGATTTCTGGAGTAAATTAATACATCTACAGTCAA 1264
                                 v    vv   v i v i i    iiv      i  ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_193780353_   1265 TTGATTTTCAAAAAGGGAGTGAAGATTATTCAATGGGAAAATAATAGTCT 1314
                                  i v     v iv    ii          i   v        
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_193780353_   1315 CTTCAACAAATGATGCTAGTACAACTAGATTTCTACATGCAAAAGAATGA 1364
                         i           i    i v      i   v? i                
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_193780353_   1365 AAATAA---CTTGTCTCACAGCATGCACAAAAAT--------AATAA--C 1401
                          iv ii--- i ii      v   ii        --------   ii-- 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_193780353_   1402 A---ACTGAAATGTAAGAGAGAAAACTA--AACCTCTTAGAACAAAAATA 1446
                          ---  iv           vv       --  v         -i    i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA-GAAAACA 547

  chr2_193780353_   1447 TAAGGCTAAGTGTATGTGACCTTGGATTTGGTAATGGAGTTTTAGATATG 1496
                           i ?v   i v vi          i  v  i     vv i         
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_193780353_   1497 ACACTAAA-GTACAACCAACA---GAGAAAACCTATAAATTGGACAACAT 1542
                             i   - i    v     ---  i    ivv           vv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_193780353_   1543 CTAAATTAAAAATGTTTGTGAATCAAATAACTCTATCAATAGAG----AA 1588
                          v          iv      vv     vi  v       v i  ----  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_193780353_   1589 GATGACTCACAAAATGAGAGAAAATATTTGCAAATCATATAGCTGACCGG 1638
                           ii  i    i    i                        v    ivi 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_193780353_   1639 ATTCTACTATCTAGAATACATGAAGAACGCCTGCAACTCAACAACAAAAA 1688
                         ivv  vv    i      i  i      v i i        i  i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_193780353_   1689 GATGAGCAACCTAATCGGTAAATGGTCGAAGGACTTTGAAT------TTC 1732
                           ii ii    i   i?iv      v i     -       ------   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGA-TTTGAATAGACATTTC 846

  chr2_193780353_   1733 TACAAGAAAAAAATGCAACTGTCTAGCAAGCATATGAA--GATGGTCAAC 1780
                          v   ii  i v  i   v  v i ii     i     --    v     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_193780353_   1781 ATCATTAATAAT 1792
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (120 / 78)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.47 (47 / 19)  


2840 25.85 4.67 1.25  chr2_193788451_193791085.rev     1266  2143 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193788451_   1266 TGGAAAGATAGCCTATGTTCATGGGTCCGAAGAATTCAT---GTTAAAGT 1312
                                   v  i          i iv     v  v  ---     ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193788451_   1313 GAACATACTACCGAAAGTGATCTACAGATTCAATCTAATCTGTATCAAAA 1362
                          ivv     v  v   v                ivi    iv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193788451_   1363 TTCGAAC-GACACTTTCACAGAAACAGGAAAATATTATCCCAAAATTTGT 1411
                          i v i - v vi   ii      iv iv  ii- v    i      ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_193788451_   1412 ATAGAACCACATAAGATGCAGAATACTGAAAGCAATTTTGATTACAAAGA 1461
                           i   vii  vii  iv       viv   i    i    vv vi    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_193788451_   1462 ATAAAACTGGAAACATCACACTACCTGACTTCAAAATCTATTACAAAGCT 1511
                          i   ii    iivv       v  ii i       ii  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_193788451_   1512 ATAGTAATAAAAATAGCATGGTACTGGCGTAAAAACAGAAACCTAGATCA 1561
                          i      v  i i  ii          i   ii i   v iv       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_193788451_   1562 ATGGAGCAGAATAAACAGTCCAGAAAAAAATTTATGTATTTATGCTTAAT 1611
                              ii     vi v          v   iii  ii       v i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_193788451_   1612 TATTTTTTGTCAGAGGTGCCAAGAATAAACAATGGGTGAGGAATAATTTT 1661
                          iv    i v  ii          vi vv       vi i     i i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_193788451_   1662 TGCAATAAATGGTACTGAGAAAACTGCACATCCACATGCAGAAATCTGCA 1711
                          v   i       i   i  v     v i ?         i  ivv  v 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_193788451_   1712 ATTAAACTC--ATCTAATATCATATACAAAAAGTAACTCAAAATGAATTA 1759
                         i  ii  i -- i  v i i            v            i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_193788451_   1760 AAGACTTAAATGTGAGACCTTATACTATGAAACTACTCAG---------T 1800
                         ?    i       i   v  v v     i     -  i  --------- 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACAT 548

  chr2_193788451_   1801 A-----AAATGCTCCATGACATTGGCCTAAGCAATTATTTTTTGGATATG 1845
                          -----    -  i i    v    vi  i     vi   i  i      
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_193788451_   1846 ACCCTAAAATCACAAGTAACAAAAACAAAAATAGACAAATGAGATTACAT 1895
                           v i    v      i       iv         i    vi  i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_193788451_   1896 CAAACTAAAAATCTTCTACAGAACAAAGGAAACAAACAAACAAAAAACAG 1945
                             v v    v   i iiivvv       v  v v   i-------- i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG--------AA 689

  chr2_193788451_   1946 AGTAAAGAGACAACCTAAGAAATGTAAGAAAATATTTGAAAACAATACAT 1995
                            i  i        i vii    vi            v   iv   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_193788451_   1996 CATACAAAAAA---AAATCCAAAA-ATGTGAGGAACTT---------AAT 2032
                          vv i  iii ---iv     i  -  i i i     i---------   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_193788451_   2033 AGCAAGAAAACAA-TA-------TAAATAATGGTCAAAGGACATGAGTAG 2074
                          ii  i  i    -  ------- ?  v     v       iv   i   
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_193788451_   2075 ACATTTCCCAAAAGAAGACATACAAAGAGCCAACAGATATGTGAAATAAT 2124
                                i v        i       vi     i iii ii     vi  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_193788451_   2125 GCTCAACATCAGTAAAAAT 2143
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (142 / 82)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.71 (52 / 14)  


 217 13.10 39.29 2.38  chr2_193807479_193809774      614   697 (1599)    L1M4_orf2#LINE/L1       13   127 (781)  

  chr2_193807479_    614 CCATATTCATGGATTGGAAAATTTAACA--G--AAGATG----------- 648
                             i              i i    i -- --      -----------
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_193807479_    649 ----TTGATTCTGC--------TGCAATTCCTACCAA--TCACCAG-TGC 683
                         ----     -  i --------i     i    i   --  -    -   
  L1M4_orf2#LINE/     63 CAAATTGAT-CTACAGATTCAACGCAATCCCTATCAAAATC-CCAGCTGC 110

  chr2_193807479_    684 ---TTTTGTAGACACTG 697
                         ---     i   v i  
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTG 127

Transitions / transversions = 10.00 (10 / 1)
Gap_init rate = 0.08 (9 / 115), avg. gap size = 3.89 (35 / 9)  

 881 28.57 15.13 4.06  chr2_193807479_193809774     1091  1804 (492)    L1M4_orf2#LINE/L1      116   908 (0)  

  chr2_193807479_   1091 TTACAGACGTAGAGAGACTTATCTTAAAA--CATATGTGAA--------- 1129
                           i    vi v  v ii  v   i     --      vi  ---------
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_193807479_   1130 ---AAAACAG-------AATTTTGAAATGAAAGACTAAAGTTGGAAAAAT 1169
                         --- i  i  -------   i      vii    vi         ii v 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_193807479_   1170 CATCCTAACTAATACTAGCACTTATTATACAGCTATGGT---CAAGA--G 1214
                           iv  vv i   vii iv     i  i v     ii  ---     -- 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_193807479_   1215 TGTGGTGTTCTTGGAGGGACAGACATATTGATTAAC---ATA-------- 1253
                               ii vviiv i   i        v   i  i---   --------
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_193807479_   1254 --CTCATAAGTAGACACAAA----TATGTCCAACTGATTTGTTTTACAAA 1297
                         --ii  v  i  i  v  v ----    vi   i      -- iv    i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT--TCGACAAG 363

  chr2_193807479_   1298 -----CA----CATTCAGTATAGATCAGGTGGCATTTTCAACAAAATGCA 1338
                         -----  ----      i ivi  vviii i iv           vv ii
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_193807479_   1339 CTACAGCAATTCATTATCCATAGGCAAATACATAAATCAATAGGAGTGTA 1388
                           ivii   i viv  ?   i v     ----- i ---  - i   - i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAA-----AGA---AT-GAAGT-TG 453

  chr2_193807479_   1389 TACATATATATCAC-TCATGTAAAAATTTTATGAATCATGGATTCAAA-- 1435
                         v  viv  iv    -i   i  v   -------   i --- i     --
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAA-------AATTA---ACTCAAAAT 493

  chr2_193807479_   1436 -GATTATTGATTTAAATATAAGACATAAAGCTATAATATTTTTAAGAGGA 1484
                         -   i ?v  ii     i     vv    i      v i i   -  i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA-GAAGA 542

  chr2_193807479_   1485 AAAAATAGGAGAAAATCTTGG-GAACTAGGCCTAGATAAAGAGTTCTTGT 1533
                            v     ? v       v -  v  v  vi   ii  v iv     iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_193807479_   1534 ACATGACACTAAAAATGTGATTCACAAGAAATCAAATTTATAAATCTGAC 1583
                          i       i    iiiii viv    i i vv    vv      iv   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_193807479_   1584 CTCATCAATATTAAAAATTTT---GCTGTCAATAGACCTGGTTAATAAAA 1630
                         i       v        i   ---   -    vi   vivi i  v   i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAAG 691

  chr2_193807479_   1631 C-AAAAGACAAGC-ACAAAA-GTAAGAA---------------------- 1655
                         i-         v -   i  - vi    ----------------------
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_193807479_   1656 --TAA------TGTG----GAATATACAAAGTACTCTCAAGATTCCACAG 1693
                         --   ------   i----       i    v     i vi i  v i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_193807479_   1694 TAAAAA----------TCATTTGAAAAAGAAACTTATCAAAAGACATGAA 1733
                               ----------i  v  ?     viii -----   i  iv    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGC-----AAAGGATTTGAA 836

  chr2_193807479_   1734 GAGACATTATGCATAAGAACATGTAAAGATGGCAAATAAATACATAAAAT 1783
                         v       viv vv     v  i  v i     v     ii    i   v
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_193807479_   1784 G-TGTTTAACATTATTAGCCAT 1804
                          -  i i     i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (120 / 80)
Gap_init rate = 0.04 (32 / 793), avg. gap size = 4.28 (137 / 32)  


3003 28.01 2.14 0.00  chr2_193826933_193829485     1175  2063 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193826933_   1175 TGGAAAAACATCCTATGCTCATGGATCAGAAGAATTA---TTGTTGAAAT 1221
                               i i    i   i        ii     v   ---     i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193826933_   1222 AACTATACTTTCTAAAGCAATCTACAGATTCATTATAATCTCTATCAAAA 1271
                         ii v     ii i   vii             viii    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193826933_   1272 TACCAAAGGCATTTTTCACAGAAATAGAAATAATAATCTTAAAATTTGTA 1321
                          v   ivv  v     ii       v  v viv i   i       ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_193826933_   1322 TGGAAGTACAAAAGACCCCGAGTAGCCAAAACAATAATGACCAAACAGAA 1371
                              i i   ii     v  i             vv   vv  iv    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_193826933_   1372 CAAAGCTGGAGACATCACACTACCTGGATTCAAAATATGCTACAAAGTGA 1421
                              i     ivv       v  iiiv       iv i        iv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_193826933_   1422 CAGTATCCAAAACAGCATAGTAATTGTATAAAAATAGACACAAATACCAA 1471
                              vi   i    ii i   v v i    ii       i v v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_193826933_   1472 TAGAACAGAATAGATAACCTAGAAATAAGTCTACATATTTACAGCCAACT 1521
                          i   i     v  v ii i        ii i i i     ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_193826933_   1522 GATTTTTTACCAAGGCACCAAAAACATGCAATGGAGAAATGATACTGTCT 1571
                               iv  v i  ii    i v   v      i    vi   v v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_193826933_   1572 TCAATAAATGTTGCTGGGAAAGCTGGATGTCCATCTTCAGAAGAGTTAAA 1621
                             i     v        v i      i?   iv v  i    i v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_193826933_   1622 CTAAAATATTATTTCTCACCATATACAAAAA-GGACTCAAAATTGATTAA 1670
                         i ii vivi  ii  v               -vi         v   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_193826933_   1671 AGACTTAAACCTAAAACTCCAAACTATGAAACTATTAATAGAAAACAT-- 1718
                             i    iv   i viiv       i     v   iv         --
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_193826933_   1719 -------TCTTCAGCACATTGGTCTAGACAATGATTTTATGGCTATGACA 1761
                         -------     ivv  v    vi   i     i   iv i v       
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_193826933_   1762 TCAAAACCA-AGGCAACAAAAATGAAAATAGAAAAATGTGACTATATTAA 1810
                         i     v  - i         ivi        v    vv    vi  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_193826933_   1811 ACAAAACAGTTTCTGCACAGCAAAGGAAACAGTAAACAAAGTCAAGGGAT 1860
                          vvv  v ii  i  ii vv       v  vi v  v     v  ii  i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_193826933_   1861 AACTTGTAGAGTGGGAGAATATATTTGCAAACTATTCATCTAACAAGGGA 1910
                            iiii   i        v           ii  vi    i i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_193826933_   1911 CTAATATCCAGAATACACAAA-AGCTC----AACTCAACAGCCAGAATAC 1955
                           vi           i i   - i   ----       i iiv i  v  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_193826933_   1956 AAATATTTGTATTAAAAAGTTGGAAAGGGACATGAATAAACATTTATAAA 2005
                              viivv   ?    i v  v  i   iv      i      v vv 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_193826933_   2006 AAGAAGACGTGTAAATAGCCAACAAATACATTTTAAAATGCTCAATATTG 2055
                                ii ii    i     i  ii    vvv  i        i  ii
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_193826933_   2056 CTAATCAT 2063
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.65 (153 / 93)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 3.17 (19 / 6)  


3263 27.09 0.44 0.44  chr2_193902901_193909180.rev     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193902901_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4930
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193902901_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193902901_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_193902901_   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_193902901_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_193902901_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_193902901_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5226
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_193902901_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_193902901_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_193902901_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAGTCAATTCAAGATGGA 5376
                            ii    i    v   i     v         i i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_193902901_   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_193902901_   5427 CTAGGCATTACCATTCAGGACATAGGTGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_193902901_   5477 AACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvv          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_193902901_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_193902901_   5577 AGGCAACCTACAACATGGGAAAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   iv      i     v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_193902901_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_193902901_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_193902901_   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_193902901_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2762 20.25 2.93 2.79  chr2_193914354_193916058.rev      500  1215 (490)    L1M4_orf2#LINE/L1      192   908 (0)  

  chr2_193914354_    500 AAAGCACAACAAAATTGGAGGATTCACACTTTCTGATTTCAAAACTTACT 549
                             v v      i        i        i ii               
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_193914354_    550 ACAAAGTAACAATAA---AGACAGTGTGGTTTTGACATAAGGATGTACCC 596
                               iv   i   ---            vi  i         iv  vi
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_193914354_    597 ATCAGTCAGTGAAATAGAATTTGATAATCTAAATATAAGTTCTCACATTA 646
                           vii   i  i         -  v i  i i v    iii vi     v
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_193914354_    647 ATTGTCAGCTGATTTTTGATAAGATTGACAAGACAATTCAATGGTGAAA- 695
                           v    ii       i  i   iv  v      v         v    -
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_193914354_    696 ATTAGTATTTTCAGCAATTGGTATTGGGACAACTGGATATCCAAATGCAA 745
                          v    v      i   v    ii               ?   v      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_193914354_    746 AAGAATAAAGTTAAACATCTATCTCATATTATATATAAAAATTAACTTAA 795
                               i     ii  vi   i    i ii     i           i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_193914354_    796 AATATATCACAAACCTAAATGTAACACCCTAAATAATAAAACTCTTAGAA 845
                            iv    ? i            v v iv   iv               
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_193914354_    846 GAAAACAGAGATACTA--TTTCTCAACTTCT--TTAGGCAATTGTTTCTT 891
                                v  i?iiv --i   vii  i iv--         v       
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_193914354_    892 AGATAAGACACTGAGACCAGAAGTGACAAAGAAAACAATAGATAAATTCA 941
                              v     ii i v  v   ii     ii   v            vi
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_193914354_    942 A-TTCATCAAAATCAAAAAACTTTT-TGCCATAAACAATACTACCAAGAA 989
                          -           i     -     -   ivi   vi i    i      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_193914354_    990 AGTGAAAAGAAAAACCACAGAATGAGATTAATATATTTGCAAATGAAATA 1039
                                   v  v          i  -------------i  ---    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGA-------------GAA---AATA 723

  chr2_193914354_   1040 TCTGTAAATCATTTATCTAATAAACTACTTGCATATAGAATACATAGAGA 1089
                          i  i       v     i    ivv     i  vi      i   i   
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_193914354_   1090 ATTGTTA------AATAATAAATAAA-AGATATCTCA--TTCAAAATGAG 1130
                          i v   ------         v i - i   v i  -- ?v      i 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_193914354_   1131 CAAATGAGATCTGAACCAACTTTTCTCCAACGAAGATATA-AAGTGGCCA 1179
                             --i   i    ivi  v         v         -  i      
  L1M4_orf2#LINE/    824 CAAA--GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_193914354_   1180 CTAAGTACATGAAAACATGTTCAACA-CAAATAATTA 1215
                         v    i         v   i      -  ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (88 / 53)
Gap_init rate = 0.02 (16 / 717), avg. gap size = 2.56 (41 / 16)  


2437 25.61 2.32 2.70  chr2_193922762_193924539      510  1286 (492)    L1M4_orf2#LINE/L1      135   908 (0)  

  chr2_193922762_    510 GATCCTAAAATGCACATG--AATCCACAAAGACCCTTAATAGTCGAAGCA 557
                                    v  i   --   v  - ii     vv     i i  i  
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCA-AGGGACCCAGAATAGCCAAAACA 183

  chr2_193922762_    558 ATATTGAGTAAGAAAAA--ACTTTGAAGTA-TCAAACTTACTGACTTCAA 604
                           v    iv     i  -- vv   i  v -   v    v ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_193922762_    605 A--TTAAATCCCAAAGGGATACCAATACAAAT-GTATGATGTTAGTTTAA 651
                          --   --iiv     vv i vi   vv i i-  i  i ii i iv   
  L1M4_orf2#LINE/    234 AACTTA--CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_193922762_    652 AAACAGACAAACAGACTAATGGAACAAAGTGGAGAGCCCAGAAATAGTCT 701
                         ii i     v i   ii       i i i v     i         iv i
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_193922762_    702 CACATAAATATGGCCAAATAATTTTCAACAAGAGTTCCAAAAGTACACAA 751
                           i i vv     i   v i      i     i  v    i vi iv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_193922762_    752 TGGGTAAA----AGCCTCTTCAATAAATGGTGTTATAAAAGCTGGATAGT 797
                             v   ----  i  i     i        i ivi v i       ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_193922762_    798 CACATGCAAAATAATAAAAGTGGACCCTTATCTTACTCCATATA--AAAA 845
                                    v   i  iv       i  i  i  v       --    
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_193922762_    846 TCAACTCAAAAAGGATTAATGACTTAAATATGAGGCCCAAAGCTGTAAAA 895
                          i         v    i ?v   i     i i  iv i   i  i     
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_193922762_    896 CTCTTAGGAGAAAACATCGTAGTTAAGCTCCTTAACATTGATCTTGGCAA 945
                                i         v v?  v  v  i v i  v   ivi v     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_193922762_    946 TGATTTTATTTGGACATGACACCAAAAGCACAGGCAATTAAAGCAAATAC 995
                           i   i--  i  i                 i    iv    v   v i
  L1M4_orf2#LINE/    582 TGGTTTC--TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_193922762_    996 AGATGAATTATATTACATCAAACAAGAAAGCTTCTGCACAGCCATGGAAA 1045
                             i    iv i v       vvvi   i   i  ii vv v v   v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_193922762_   1046 TAGTCAACGAAATGAAAAGGTAACCTACCGAATGGGGTGAAATATTTGCA 1095
                         ivi    vi  i       ii    i  v       ivi           
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_193922762_   1096 AACTATATACCTAATTAAGG-TTAATATTCAAATTATGTAAGAAGCACAC 1144
                           ii     i  i  v i  -i vi   i  i v   i   ii i v vi
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_193922762_   1145 AAAACTCAGTGACGAAAACAAAACAAAATAAACAAAAAAACCCATGATTT 1194
                          v      i -----------  i    - i     v  -    --   ?
  L1M4_orf2#LINE/    780 ACAACTCAAT-----------AATAAAA-AGACAAATAA-CCCA--ATTW 814

  chr2_193922762_   1195 TTTAAATGAGCAAAGGAATTGAATAGACATTTCTTAACAGAA---ATACA 1241
                         vv-     i        v                iv v    ---     
  L1M4_orf2#LINE/    815 AA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_193922762_   1242 AATGGCCAACAGGTATATGAAAAGGTGCTCCACACCACTAATCAT 1286
                                  i i i i        i     v   i  ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (121 / 74)
Gap_init rate = 0.02 (17 / 774), avg. gap size = 2.29 (39 / 17)  


3140 26.56 1.67 0.33  chr2_193975048_193979310.rev     2876  3771 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_193975048_   2876 TGGGAACACATCCCATGCTCATGGATGGGTAGAATCAATTTTGTGAAAAT 2925
                            i  v i        i        v  v   v i   v    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_193975048_   2926 AATCATACTGCCAAAAGTAATCTACAAATTTAGTGCAATCCCCATCAGAA 2975
                         iiiv     v  v   v i       i   i ii        i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_193975048_   2976 TACCACCATCATTCCTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 3025
                          v   v vv v  ii ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_193975048_   3026 TGGAATCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAG 3075
                              viiv  ii  v  viv         i   vvi i iv  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_193975048_   3076 AAAATCTGGAAGCATCACACTACCTGATTTCAAACTATACTATAAGGCCA 3125
                         v   vi    i vv       v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_193975048_   3126 TAGTCACCAAAACAGCATGGTACTGGTATGAAAATAGGCACATAGACCAA 3175
                         i   v i   i    ii         i  i ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_193975048_   3176 TGGAACAGAATAGAGAACCCAGAAATAAACCCGAATACTTACAGACAACT 3225
                              i     v    ii              iv i i   ii v   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_193975048_   3226 GATCTTCAACAAAGCAAAGAAAAATATAAAGTGGGGAAAGA-CACCCTTT 3274
                            i   i    i vvivv  i vi  vv i          -i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_193975048_   3275 TAAACAAATGGTGCTACGATAATTGGCTAGCCACATGTAGGAGAATGAAA 3324
                          v             iv  i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_193975048_   3325 CTGGATCCTCATCTTTCACCTTATACAAAAATCAACTCCAGATGAATTAA 3374
                         i    i  ii i  iv    v           i     v i   i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_193975048_   3375 GGACTTAAACCTAAGACCTAAAACTGTAAAAGTTCTAGAAGATAACTTTG 3424
                         i   i    iv     v        i     v ii       v   v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_193975048_   3425 GAA-AAATACTTTTAGACATTGGCATATTCAAGGATTTCAT-GACCAATG 3472
                          ?i-    -   ivv   v    vv  vv   v i    v -  i--   
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATG 597

  chr2_193975048_   3473 AC-CCATAAGCAAATTCAATAAAA------ATAAACAGCTGGGACCTAAT 3515
                           -   v     v vv   i    ------   i i iv v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_193975048_   3516 TAAACTAAAGAGCTTTTGCACTGCAAAAGGAACAGTCAGCAGAGTAAACA 3565
                         i   v v  i i      ii  v    i iv  vi   iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_193975048_   3566 GACAACCCACAGAGTGGAAGAAAATCTTCACAATCTATACTTTTGACAGA 3615
                                      i   i       v  ii   vii   iv i   i ii
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_193975048_   3616 GGACTAATATCCAGAATCTATAACGAACTGAAACAAGTCAGTAAGAAAAA 3665
                              vi          v     v     vvv    v   i   v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_193975048_   3666 -----ATAATCCCATCAAAAACTGGGCTAAGGACATGAATAGACAGTTCT 3710
                         -----    i  v  i?    v     v     iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_193975048_   3711 CAAAAGAAGATATACAAATGGTCGACAAACATATGAAAAGATGCTCAACA 3760
                          v                   i i i  i  i                  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_193975048_   3761 TCACTAATGAT 3771
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.25 (18 / 8)  


1174 25.10 11.96 6.18  chr2_193980507_193984323     2573  3333 (484)    L1M4_orf2#LINE/L1      104   908 (0)  

  chr2_193980507_   2573 CAGCTTAACCTTCTTTTGTGGAAATTGGTATGCTGATTCTAAAACT-ATG 2621
                              --i    -     ii       ii v      i      i -  i
  L1M4_orf2#LINE/    104 CAGCT--GCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_193980507_   2622 TGAAAATGTAATGGATATAGATTAGCCAAAATAACCTTGTAAAAGAGAAA 2671
                           i     i  v   ivi   v         i  i    v      ii  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_193980507_   2672 CAACACAGT----GGACTTTTACTATCTGACTTCAAGA---A-TACAAGC 2713
                            ---   ----     ivi   vi ii i     i --- -     i-
  L1M4_orf2#LINE/    201 CAA---AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA- 246

  chr2_193980507_   2714 TTTGTTACTATAGTCAA----------TATTGGTATACGGAT-----TAA 2748
                         --- i   vi  i    ----------  i   i   v    -----  v
  L1M4_orf2#LINE/    247 ---GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_193980507_   2749 AAAAGAAGGGAACAAAAA-GATAATCCAAAAATGA-TGTGTGCATTTATA 2796
                          i vv  v    i i  v-  v i    i    i -ivii i       i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_193980507_   2797 ATCAATTGAATGTTGAC-------------CTAGTCAATGTGAAGGAGAA 2833
                         i        v v i   ------------- i v      ---i   i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG---GGGAAAG 390

  chr2_193980507_   2834 GATATATCTTTTCAATAAATGGTTCTGGAACAACTGGATATAT-TAGTCA 2882
                         i   -i         i       v    i           ?vi-i vv  
  L1M4_orf2#LINE/    391 AATA-GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_193980507_   2883 AAGGTATTTTTAAGAAACTTTTTATTATTTTTATATAAACTCTTATATCA 2932
                           i v  ------   ii -----------------ii  i i  iv   
  L1M4_orf2#LINE/    440 AAAGAAT------GAAGTT-----------------GGACCCCTACCTCA 466

  chr2_193980507_   2933 CAGCTCA---AAAAATCAGTTTAAGATGAGTTTTAGACCTAATTATAAGC 2979
                           v vi ---      i ii i  i   ii iv?        v i    v
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_193980507_   2980 ACTAC--CCATAAAACTTCTAGAAGAA--CA-AAGATTA--CCATTATGG 3022
                         i   v-- i        ii        --  - i ?v  --i v ii  i
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_193980507_   3023 C-TAAGGTTAAGCA-----------GAAATGCATTCGAAAAAAGAAAACT 3060
                          - vi     i   -----------  v   - iv v    iviv  i v
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATG-ACACCAAAAGCACAAGCA 615

  chr2_193980507_   3061 ATAAAAGAAAAAAATGATAA-TTTGACTTAATATAAAAT---AAACATTT 3106
                          i           vv     -  v     v  -i     ---    v   
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCAT-CAAAATTAAAAACTTTT 664

  chr2_193980507_   3107 GTTCTCATCTAA-------AT--AGAAAATCAGAAGAAAAGCCACAGACT 3147
                           v  --  v  -------  --     i v i    v  v       --
  L1M4_orf2#LINE/    665 GTGCT--TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA-- 710

  chr2_193980507_   3148 ACAGGAGGGAAAACACTTAAAAAGCATATATATGGCAATTCACTAACATC 3197
                          ii    --    i i  iv   v       v  ii  vvv   vii   
  L1M4_orf2#LINE/    711 ATGGGAG--AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_193980507_   3198 AAGAATACATAAAATGTAC----ACAAGTCAATAGTAAAAATATAAATAA 3243
                         v      i     -- v  ----    v      i      v i      
  L1M4_orf2#LINE/    759 CAGAATATATAAA--GAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_193980507_   3244 GCCAATT--AAAATTGGCACAAACTTTAAAAAGGAA---CTTTAAGTAGG 3288
                         v      --     v    v iiv   i  v  iv ---  ii  iv i 
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_193980507_   3289 A---ATAAAT--TTAAAAAGCATGTGAAAATATGT--GATGTCACTTTGA 3331
                          --- i    --ii  v     ii      v   i--i ii   ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_193980507_   3332 AT 3333
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.69 (118 / 70)
Gap_init rate = 0.05 (41 / 805), avg. gap size = 3.37 (138 / 41)  


 940 25.40 12.30 10.11  chr2_194015122_194017171.rev      689  1558 (492)    L1M4_orf2#LINE/L1       20   908 (0)  

  chr2_194015122_    689 CATAAATGTATAAAAAATTTGATATA--TAAGATGACGATTCTTCCCAAA 736
                            ii  --- ii  i i  i    v--       i i  v  i      
  L1M4_orf2#LINE/     20 CATGGAT---TGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chr2_194015122_    737 TTGAAGTATATGTTAAAGGCAATCCCAATCAAAATTAATCACATGAGGCT 786
                             vv  i vi  v  v        v        i--i  vv  v--  
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATC--CCAGCTGC--CT 112

  chr2_194015122_    787 TTAATATAAAAAT----AAATCAATAACAAAATTTATATGAAAATCCAAA 832
                           vv ii i    ----  iiii  vvi      i     i    v   i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_194015122_    833 AAATATTGCATAGTCAAAACA----------------------------- 853
                         ii iviv v    i       -----------------------------
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_194015122_    854 --------TTTCTGATTTCAAGATTTATTATTGTCCTATAGTAATCAAGA 895
                         --------  i ii       i i   i  ivivv   i           
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_194015122_    896 CAGTTTGGTGTTGAATTAAGGTTAGA-A-ACAGATTGATAAAACAAAAT- 942
                             v    ii  ivv     v    - - i    ii  ii  i i   -
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_194015122_    943 -AGACTCTA-AAATAGGCCCACGTATACATGA-CAA------------AA 977
                         -   v  i -     ii    iii  vi   i-   ------------  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_194015122_    978 GGGTGT--AGTTAAGTCAGTGGTCAAA-ATTAGTCTTTTCAACAAATAGT 1024
                              i--  viv v   i   vv   - v                 i  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_194015122_   1025 GCTGAAATTTCGAGATAGTCCAATGACAAAGGACTTTAACTTAACCTTTA 1074
                             ii ivv vi    ?i vv   -    i  v vv ii vi   ii  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATG-CAAAAGAATGAAGTTGGACCCCTA 461

  chr2_194015122_   1075 TCTCTCACTATGCATACACACACACACACTCTCTGTCTCTCCCTTTCTCT 1124
                         i   v   i  --     v v ----------------------------
  L1M4_orf2#LINE/    462 CCTCACACCAT--ATACAAAAA---------------------------- 481

  chr2_194015122_   1125 TTTTTCTCTCTCACCCCAAATAGTCAAAATGGAACATAAAACTAGGATAA 1174
                         ---  -------------  i--          v  ? i v   i-  i-
  L1M4_orf2#LINE/    482 ---TT-------------AAC--TCAAAATGGATCAWAGACCTAA-ATG- 511

  chr2_194015122_   1175 AACTAAGGATAAACTCTAAAACTACTATATTTCTAAAAGGCAACATAGGG 1224
                         ---    ii------         iv v i ii  i   iv        ?
  L1M4_orf2#LINE/    512 ---TAAGAG------CTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_194015122_   1225 AACAAATATTGATGATGTCGGGGTAAGCCAAAAA------AGAAATAACA 1268
                         i-i    v  vi   iv i   v  i  -  vii------   v  i   
  L1M4_orf2#LINE/    553 G-TAAATCTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTAGATATGACA 600

  chr2_194015122_   1269 TTAAAGACAGCAAAAAAAAATTCCAAACAGTGTGAGAAGAAATATAAAGA 1318
                         ii   ---    v  iv  ----    -------    i     v v i 
  L1M4_orf2#LINE/    601 CCAAA---AGCACAAGCAA----CAAA-------AGAAAAAATAGATAAA 636

  chr2_194015122_   1319 TTGTAGTTCATCAATACTAAAACGTTTTGCAATGAAGAAGACAA-ATTAA 1367
                            v v        v i     vv     iiv vv i i    v-  i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_194015122_   1368 GGAAATAAAAATTTAAGTCACATAATATGTGAAATCATT----AATTATA 1413
                          i  i i    vvi  vi    v   iv v    vi   ----   i   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_194015122_   1414 TATGTATCTCAATAAATTACTAGTATCCA-AATCCATGAA--ACTCT-AC 1459
                            ----  -i    ivv   v       -   vi  i  --     -  
  L1M4_orf2#LINE/    737 TAT----CT-GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_194015122_   1460 AATTTCATAATAAAAAGGCAA----CCCAATC------------------ 1487
                           i iv           i   ----      i------------------
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_194015122_   1488 -TGAATAGATGTTTT-----ATAAAATATACAGCTAACCAACAAGGACAT 1531
                         -        ii   i----- v  i       iv ii    i   v    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_194015122_   1532 GAAAATAGGCTCAACAACATTAGTCAT 1558
                              v v        v  ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (130 / 88)
Gap_init rate = 0.04 (38 / 889), avg. gap size = 5.13 (195 / 38)  


2426 26.39 6.37 1.27  chr2_194063194_194067602.rev     3054  3917 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194063194_   3054 TGGAGAGACATATCATGCTCATATATTAGAAGGGTCAACAT-ATTATAGA 3102
                             i   i  vi    i    iv   i    iv i  i  -i   -   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGA 49

  chr2_194063194_   3103 TGTCGGTGTTCCCCAAATTGATGTACTAGTTTAACTAAACTTCTATCTAT 3152
                           v ii ii             v   vii  i   vv  iii     v v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_194063194_   3153 GTCCCAGTAACAAGTTCTGTAGATAGTAATAA--TG-TTCTAAAATTTAT 3199
                         i      ivi vvv  i  i   v v i i  --  - i        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_194063194_   3200 AAAGAAAGTCAAAGGAACTAGAAAAGCTAAGACAATTTTGAAAAGGAAGA 3249
                          vi    vv   i   v i    v   i  i     i       i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_194063194_   3250 ATAAAATGGGAGAAATCTCTCTATCCAATCTCATGATTTATTACATAGCT 3299
                          i   i v    i v  v v  vi     i   vi i   i    v    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_194063194_   3300 ACCATTATCAAGAC--TGAAGTATTGGCAGAGATACAGACAAATAGATCC 3347
                           vi v        --  vi   i     v iiv i     v       v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_194063194_   3348 ACAGAACTGAAGAGGGAATCCAGAAAGAGAC--A-AAATTT--GCCCAAT 3392
                          ii   iv   vv i  i        v i  -- - v    -- vi    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_194063194_   3393 TATTTTTTGATATAGGTACACAAGA--ATTTAAATTGAATAAAGA-TAGC 3439
                          iv    i  i vi   i -     --   i  --  iiv     -   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGC-CAAGACCATTCAA--TGGGGAAAGAATAGT 396

  chr2_194063194_   3440 CTTTTCAACAAATGATGTTGGAGAAAGTAGACATCCTGAAGAAAAAATAT 3489
                                       i  i   iiv  v i  i ?  vv v v    iv  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_194063194_   3490 GAACCTTGACCTAAGTCTCACACTTTTATTATACAAAAATTAATTTAAAA 3539
                            vi v    ivvii       i---  -             i i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACC---AT-ATACAAAAATTAACTCAAAA 492

  chr2_194063194_   3540 TGAGTCATAGACTTAAGTGTAA-------AACTATAAAACTTGTAGGAAA 3582
                           ii   ?    i   i     -------            iv   i i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_194063194_   3583 AAACAGGGGAG--AACAATTATGATATGGAGTT------------CTTAA 3618
                              vi  ? --  ivv ii   iv v i   ------------    i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_194063194_   3619 ACGTGACAGCAAAAGCTCAAAATATAAAAGGAAAAATTGATAAATTGGAC 3668
                          ii     v       v   ivv i     i      v            
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_194063194_   3669 TTCATCAAATTTAAAT-TTTTTTCACTTTAAAATAAGTTGTTAAGAGGAT 3717
                                  v     v-i    vii   i   iv vii i i    iii 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_194063194_   3718 AAAAAGTCA-TCTACAGACTTGGAGAAAATGTATGCAAACTACGTATCTG 3766
                         i     v  -i i     v v         i v      ii ii      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_194063194_   3767 ACAAAGGATTAGTATTTAGAATACATAA-TAATTCTCAAAATGCAA--AT 3813
                          i  i   i v    ii      i    -v  i   i v  iv   --  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_194063194_   3814 AAAAA---------TTGAATTAGAAAATGATCAAATGAGATTGA---GAC 3851
                              ---------iiv    ?i      iv    v  v-    ---   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGAC 841

  chr2_194063194_   3852 ATTTC---AATGAAGATAATACCACATCGCAAATAAACATATGAAAAGAT 3898
                              ---  v       -   v -  v  v     i  i          
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATA-TACAA-ATGGCCAATAAGCACATGAAAAGAT 889

  chr2_194063194_   3899 GTTCAATGTCATTAGCCAT 3917
                          i    ii   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (137 / 87)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.44 (66 / 27)  


2478 27.63 4.51 2.77  chr2_194091294_194093689.rev     1032  1896 (500)    L1M4_orf2#LINE/L1        2   881 (27)  

  chr2_194091294_   1032 GAAAAAACATTCCATCCTCATGGATAGGAAGAATCAATATCGTGAAAATG 1081
                          i   i i  i    vi        v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_194091294_   1082 GCTATACTGCCGGAAGTAATTTATATATTCAATGCTATTTCCATCAAACT 1131
                           v     v  vi  v i  i  i v      i  v  ii i      v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_194091294_   1132 ACCA-CTGATATTCTTCACAGAATTAGAAAAAAAAACT-ATTTTAAATTT 1179
                         v   -   vi-  i  ii     v v  v  i----  -  ii    v  
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chr2_194091294_   1180 CATATGGAA-T-CAAAGAAGAACCTGTATAGCCAAGACAATCCTAAGCAA 1227
                                  - -   i --  v  v v        i      i i iv  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_194091294_   1228 AAAGAACAAAGCTGAAGGCATCACATTATCTGACTTCAAACTATACCACA 1277
                         i          i  i   vv     i vi ii i      viv   i   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_194091294_   1278 AAGTTACAGTGACCAAAACAGCATGGTGCTGGTCCCAAAACAGACATATA 1327
                            i      i i   i    ii    i    iviv ii i         
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_194091294_   1328 GACCAATGGAACAGAGCAGAGATCTCAGAAATGACACCACACATCTACAA 1377
                           i        i   iiv    vii       i vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_194091294_   1378 CCATCTGATCTTCGACAAACCTGC-------------------------- 1401
                         i  vi    i        ivv   --------------------------
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_194091294_   1402 ------TCAGTAAATGGTGCTGGGAAAACTGGGTAGCCATATGCAGAAAA 1445
                         ------   ii              v      i  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_194091294_   1446 CTATAACTGGACCCCTTCCTTACACTTTATGAAAAAAAAAACACAAGATA 1495
                         v iv ii         v   i    iv   iv     vv   v   i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_194091294_   1496 CATTAAAGACTTAAATGTAAAACCCAAAACCATAGGAACCCTAGAAAAAA 1545
                         v  i ?    i         i v i     i   ii vi i     i   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_194091294_   1546 ACATAGGC-TATACCATTCA-GATCATAGGCATGGGCAAAGACTTCATGA 1593
                                ?-  v i -   i-  i v i  i- i     v ii   v ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAG 592

  chr2_194091294_   1594 CGAAAACGCCAAAAGCAATGACAAAACGCCAATTTGTAACAAAAGCCAAA 1643
                         vv vi  i         ------------   --- i        vv   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCA------------CAA---GCAACAAAAGAAAAA 627

  chr2_194091294_   1644 ATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCAGAACAAAAGA 1693
                           v  i    v   ii v  i   v v  i i   i  iivvv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_194091294_   1694 AACTATCATCAGAGTAAACAGGCAACCTTCAGAATGGGAGAAACTTTTTG 1743
                         v       vv i   i  v  i     iv              v v    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_194091294_   1744 CAATGTATTCACCTGACAAAGATCTAATGTCCAGAATTCACAAGGAGTTT 1793
                            vvi  vi i    i  i iv  vi i        vi i  i  ii i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_194091294_   1794 AAACAAATTTACAAGAAAAA-ACAAGCAACTCCATCAAAAGGTAGGCAAA 1842
                         vv    v iv i  v     -    ii   i v  i?   ii i      
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_194091294_   1843 GGATGTGAACAGACACTTCTCAAAAGAAGGCATTTACATGGCCAACAAAC 1892
                             v    i     i     v       ii  vi v        i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_194091294_   1893 ATAT 1896
                          i  
  L1M4_orf2#LINE/    878 ACAT 881

Transitions / transversions = 1.70 (148 / 87)
Gap_init rate = 0.02 (15 / 880), avg. gap size = 4.20 (63 / 15)  


2703 27.14 3.04 0.90  chr2_194096550_194099554     1626  2513 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_194096550_   1626 GAAAAAACATTCCATCCTCATGGATACGAAGAATCAATATCGTGAAAATG 1675
                          i   i i  i    vi        vv     v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_194096550_   1676 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAACT 1725
                           v     v      v i  i  i        i  v  i  i      v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_194096550_   1726 ACCATTGAAATTCTTCACAGAATTAGAAAAAAAACT-ATTTAAAATTTTA 1774
                         v   vivivv  i  ii     v v  v  i---  -  iiv   v  i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCA 148

  chr2_194096550_   1775 TATGGAA-TCAAAGAAGAACCC-GTATAGCCAAGACAATCCTAAGCAAAA 1822
                                - vv   -- i    - v        i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_194096550_   1823 AAAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTATAAG 1872
                          i       i      vv    i  v  ii i      viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_194096550_   1873 GCTACAGTGACCAAAACAGCATGGTACTGGTCCCAAAACAGACATATAGC 1922
                                 i i   i    ii         iviv ii i          v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_194096550_   1923 CCAATGGAACAGAAT-GAGACCTCAGAAATAATGCCACACTACTACAATT 1971
                         i        i     -    vii         vv   i  vvi  iii i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_194096550_   1972 GCCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAA------- 2014
                         ivi    i  i     ivv  v   i v  vv           -------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_194096550_   2015 -----------ATGGTCCTAGAAAAACTGACTAACCATATATAGAAAATT 2053
                         -----------     v  i i v     iv  ?   i  ii i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_194096550_   2054 GTAACTGGACCCCTTCCTTAGACCTTATACAAAAATTAACTCAAGATGGA 2103
                          v ii         v   i v   v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_194096550_   2104 TTAAATACTTAAAGGTAAAACCCCAAAGCATAAAAATCCTAGAAGAAAAC 2153
                          i ? v  i    v    i v iv   vi      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_194096550_   2154 CTAGGCA-ATACCATTCAGGACAT--AGTCATGTGCAAAGACTTCATGAC 2200
                         v    ?i- v i -   iv   v --i  i - -    v ii   v iiv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTA-G-GCAATGGTTTCTTAGA 593

  chr2_194096550_   2201 GAAAATGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATC 2250
                         v vi ii         vvv          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_194096550_   2251 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 2300
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_194096550_   2301 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 2350
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_194096550_   2351 CAAAAGCCTAATATCCACAATTTACAATGAACTTAAACAAATTTACAAGA 2400
                         i  ii v  vi      v   v  i  v     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_194096550_   2401 AAAAAA--AACAACTCCATCAAAAAGTGGTCAAAGGACATGAACAGACAC 2448
                             i --  i   i v  i?    i   v       iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_194096550_   2449 TTCTCAAAAGAAGAAATTTACATGGCCAACAAATATATGAAAAGAAGCTC 2498
                              v        v  vi v        i  ii i         v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_194096550_   2499 AACATCATTGATCAT 2513
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (133 / 104)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 2.69 (35 / 13)  


 441 28.49 3.23 2.69  chr2_194136532_194138875.rev      502   687 (1657)    L1M4_orf2#LINE/L1       35   221 (687)  

  chr2_194136532_    502 TCAATATCATTAAAAGGACCATACAGCCCAAAGCAATCTACAGTTTTAAT 551
                          i     ii    i v i v    vv      vii        v  i  i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr2_194136532_    552 GTAACTCCTATCAAAATACTAA-TGTTATTTTTTCACAAAATTAGTGAAA 600
                          i  ii           v i i-  iiv     v  -i     iii-  i
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA-GAAATTGAC-AAG 132

  chr2_194136532_    601 ACAATCATAAAATTTACATGAAA--GCAAAAAAGAACCCTGT-TAGCCAA 647
                         vii   v       i i   i  --    i--- i    v v-       
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAG---GGACCCAGAATAGCCAA 179

  chr2_194136532_    648 AGCAATTCTCACCAAAAA--ACAAAGCTTGAGGCATCACATT 687
                          i    ii v vv  i  --      i v    vv     i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

Transitions / transversions = 1.79 (34 / 19)
Gap_init rate = 0.04 (7 / 187), avg. gap size = 1.57 (11 / 7)  

1754 26.17 9.97 1.87  chr2_194136532_194138875.rev     1211  1852 (492)    L1M4_orf2#LINE/L1      215   908 (0)  

  chr2_194136532_   1211 TCACATTATCCAAATTCAAG--TTAGATTACAAGTCTATAATAACCGGAA 1258
                              i vi    v     i--   --i     iv   i i   i iii 
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTA--CTACAAAGCTACAGTAATCAAGA 262

  chr2_194136532_   1259 CGGCATAGTACAGGCATAAAAAT-GATACATACATTAATGGAACAGAATA 1307
                          i ii i    v       ii  -  i i   v  i       i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_194136532_   1308 GAGAATGCCA-------ACCTATAC------------------------- 1325
                             i -   -------   i    -------------------------
  L1M4_orf2#LINE/    313 GAGAGT-CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_194136532_   1326 --------------------TGGGGAAAGGACCCCCTATTCAATAAATGG 1355
                         --------------------         i ivvi  v     i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_194136532_   1356 TGCTGAGAAAATCAGTTCGTCATATGCAGATGAATGAAACTGGACTCTT- 1404
                              i  v  iii v v?i  i     i v       ii     i i -
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_194136532_   1405 -CTCAC--CATAAACAAAAACTAGCTTAAGATGAATTCAAGACTTAAGTG 1451
                         -     --    v       i  i  i  i   i  iv?    i   i  
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_194136532_   1452 TGAGATCTGAAACTACAAAAACACCAGAAGAAAACTGAGGG--AACTCTT 1499
                          i   v  i      i    vivii          vv   ?--  v    
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_194136532_   1500 TTCTGGACATTGACGTAGGCAAACAATTCATGACTAAGACCTCAAAAGGA 1549
                         -- vv   v   ivv       vviv   v iiv  v   vi      v 
  L1M4_orf2#LINE/    562 --CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_194136532_   1550 AATGCAACAAAAACAAAATTAGACAAATGAGACTTACTTAGTAACTAAAC 1599
                         v v         iv    v    i    vi     vv i i-  i    -
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA-AATTAAA- 657

  chr2_194136532_   1600 AGCTTCTGCACAGAAAAAGAAATAATTAACAGAGTGAACAGACAACCTGA 1649
                          i   i  ii vvv   i  v iv  i  v i      v        iiv
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_194136532_   1650 AGATTGGGAGAAAATATTTGTAAACTATGCATCCAACAAAAGACTAATAT 1699
                            v                i   ii  ii   ii i  ii    vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_194136532_   1700 CCAGAATCTACAAGGAACTCAAACAACTCAACAAAAACACAACAACAAAA 1749
                                v  i  i      vv         i  v  ---  vi     -
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAA---AAAGACAAA- 803

  chr2_194136532_   1750 GTTGCCTCATTAAAAGGGGGGCAAGGGACATGAATAGATGTTTTTC---A 1796
                         - vi  iv   ?   iiv      i   iv        ii   i  --- 
  L1M4_orf2#LINE/    804 -TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_194136532_   1797 GAAGACATGCAAATGGTCAACAAGCACATGAAGAAATGCTTAACATCACT 1846
                              i  i       i   i           i i     i       ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_194136532_   1847 AATCAT 1852
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.73 (104 / 60)
Gap_init rate = 0.02 (15 / 694), avg. gap size = 5.07 (76 / 15)  


1159 24.07 13.82 3.25  chr2_194166413_194168019      501  1115 (492)    L1M4_orf2#LINE/L1      229   908 (0)  

  chr2_194166413_    501 TTCAAGACTTAAAAATAAATCCCTAATATTTAAGACAATATGGTATTGGT 550
                              i     vv -i   v ivi i  v i      i i     i   i
  L1M4_orf2#LINE/    229 TTCAAAACTTACTA-CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_194166413_    551 ATAAATATCAGCAACAAATTAATCAAGGAACTA--ATT-AGAGTC-AAAA 596
                             iv  -  --   v  vi     v i v  --   -      - i  
  L1M4_orf2#LINE/    278 ATAAGGAT-AG--ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr2_194166413_    597 ATAAAGCTATATATATATGTTCAATTGATTTTTCACAATGTT--CATAGG 644
                              v i   i  v    v            iv    v v --  -  i
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA-AGA 373

  chr2_194166413_    645 CAATCTGGTAGAAAAAATGTAGAATTTTCAACAAATAATGTTGGAA-AAT 693
                          v  iiii i ii   ivi   vv            ii  i   i -  i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_194166413_    694 TTATTGTCCATACAGTATTGAATAAAAAGAAC-AACTGGGATTGATATAT 742
                          viv i?   i ------  v ---      i-  v v   iivv  iv 
  L1M4_orf2#LINE/    424 TGGATAKCCACA------TGCA---AAAGAATGAAGTTGGACCCCTACCT 464

  chr2_194166413_    743 TATACCATATA--AAAAT-AACTAAAAGT---TCAGAAACC--------- 777
                         i i        --     -    v   i ---   ? i   ---------
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_194166413_    778 ---CCAAA-TTCCAAAACT--TCAAAGAAAA--TAATTTTTAAAATATTT 819
                         --- i   -i vi      -- vi       --  iv?v --    v  i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT--AAATCTTC 562

  chr2_194166413_    820 AT--CCTTGGATTAGGCAAAGATTTCTTATATCTCATACCAAAAGGATGA 867
                         i --      i        v i       v  v v i        v ii 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_194166413_    868 CTTATTAAGGTATAAATAG-----TTAAACTTCATCAAAATGAAGAAC-- 910
                         viv iv  i v v      -----  ii             v  i   --
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_194166413_    911 -----ATCCAAAGG-CACCATTAAGAGAATCAGAA-ACAAGCTACAAACT 953
                         -----v i      -   i  i    i i v i  -    v i   i --
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA-- 710

  chr2_194166413_    954 ATGAGA-AAAATATCTGAAAATCACATATTTGTTTAAGTACT-ATATTCA 1001
                            i  -       i  v      i    i  v v i v   -i   i  
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_194166413_   1002 GAATGTATAA-GAACTCTTATTAACCTCAGTAATAAAAA-------AACC 1043
                             i     -         i-   -   i         -------    
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTAC-AAC-TCAATAATAAAAAGACAAATAACC 808

  chr2_194166413_   1044 --------------------------AACAGACTTTTCATTGAAGAAGAT 1067
                         --------------------------  i    v    viii        
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_194166413_   1068 GCACAGATGGCAAATAGACACATAAAAA--TGCTCAGCATCATTATTCAT 1115
                         ii   i     v    ii     i    --      i     ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (90 / 55)
Gap_init rate = 0.05 (34 / 680), avg. gap size = 3.09 (105 / 34)  


2687 23.49 0.82 8.07  chr2_194233417_194238498     3612  4590 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194233417_   3612 TGGAAACACCTCCCATGCTCAGGGATGGATAGAATCAATATTGTGAAAAT 3661
                               v iv       i   v    v iv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_194233417_   3662 GACCATATTGCCAAAAGTAATCTACAAATTCAATGCAATTCTCATCAAAA 3711
                          i v   i v  v   v i       i      i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_194233417_   3712 TACCATCATCATTCTTCACAGAACTAGAAAAAAC-ATCCTAAAATTCATG 3760
                          v   v vv v  i  ii     v v  v  ivi-              i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_194233417_   3761 TGGAACCACCAAAGAGCCCACA-TAGCCAAAGCAAGACTAAGCAAAAAGT 3809
                              vii -  i ii    v -        i   vvi i ---     -
  L1M4_orf2#LINE/    151 TGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAG- 195

  chr2_194233417_   3810 ACTAATCTGGAGGTACAAACAGTTTTGGTGACTATGGCCTTATAGTATAG 3859
                         ---------- i v     ------------------------------ 
  L1M4_orf2#LINE/    196 ----------AAGAACAAA------------------------------G 205

  chr2_194233417_   3860 TTGGAAATCAGATAATGTAATTTGTACAAATTGCAAATCACAATTACATG 3909
                              ------------------ v  ----------     v  v -ii
  L1M4_orf2#LINE/    206 TTGGA------------------GGAC----------TCACACTTCC-CA 226

  chr2_194233417_   3910 ATTTCCAACTATACTATAAGGCCATAGTCACCAAAACAGCATGGTACTGG 3959
                              v  viv     i  i  i i   v i   i    ii         
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_194233417_   3960 TATAAAAATAGGCACATAGACCAATGGAACAGAATAGAGAACCCAGAAAT 4009
                         i    ii    i  i     i        i     v    ii        
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_194233417_   4010 AAACCTAAATATTTACAGTCAACTGCTCTTCAACAAGGTAAACAAAAACA 4059
                              i v i     ii     i  v i   i      vviv   i v  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_194233417_   4060 TAAAGTAGGGAAAGGACACCCTATTCAACAAATTCTGTTGGCATCATTGG 4109
                          vv i i       i i vi  v          vv  i   v iv i   
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_194233417_   4110 CAAACCACATGAAGGAGAATGAATCTGGATTTTCCTCTCTCACCTTATAC 4159
                         vv ?       v ii        vi    iiiiivi   v    v     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_194233417_   4160 AAAAATCAACTCAAGATGGATCAAGGACTTAAATATGCAGTGG-GAAACT 4208
                               i       i        ?i   i     i i-  v v-i     
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA-AGAGCTAAAACT 525

  chr2_194233417_   4209 ATAAAAATTCTGGAAGATAAAATTGAAAAAACCCTTCTGGACATTGGCTT 4258
                               v ii i     v  v  v i?iv  vi    vv   v    v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_194233417_   4259 AGGCAAAGATTTCATGACCAAGA-ACCCAAAAAACAGATGCAATAAAAAC 4307
                               v i    v iivi v  -   --    i  v v    i    iv
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACC--AAAAGCACAAGCAACAAAAGA 623

  chr2_194233417_   4308 AAAGATAAATAGCTGGGACTTCATTAAAGTAAAAACCTTTTGCATGGCAT 4357
                            i   i   iv v         i   i v    v      iiivv  -
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA- 672

  chr2_194233417_   4358 AAGGA-ACAGTCAACAGAGTAAACAGAAAACCCACAGAGTGGGAGAAAAT 4406
                              -  vi    v i   i  v   v          i           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_194233417_   4407 CTTCACCATCTATACATCTGACAAAGGACTAATGTCCAGAATCTACAATG 4456
                         v  ii v vii   i      i  i     vi i        v  i  v 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_194233417_   4457 AACTCAAACAAATTAGCAAGGAAAAAAACAAACAATCCTATC-AAAAGTG 4505
                              vv    v i ii  v-     i     i  i  v  i-    i  
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAAT-AAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_194233417_   4506 GACTAAGGACATGAATAGACAATTATCAAAAGAAGATATACAAATGGCCA 4555
                          i v     iv          v  v  v                      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_194233417_   4556 ACAA--ACATGAAAAAATGCTCAACATCACTAATGAT 4590
                          i  --         i             ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (128 / 99)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.83 (87 / 18)  


 461 23.57 5.00 2.86  chr2_194276803_194279301       47   186 (2312)  C L1M4_orf2#LINE/L1   (765)   143     1  

C chr2_194276803_    186 TGGAAAAAGTATCTCATGATCATGGATCAGAAGAATCAGTATCTTTAAAT 137
                               i -    i    v        ii     v i i   iv    iv
  L1M4_orf2#LINE/      1 TGGAAAGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

C chr2_194276803_    136 TG----TACTGCCCAAAGCGATCCACAGGTTCGATGCAATTCCTATCAAA 91
                           ----    v      vi    i    i   i i     i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

C chr2_194276803_     90 CTACCAAGGTGATTCTT---CAGAGAATTATGTAAAACAATCCTAAA 47
                         v v   - v  vi i  ---    -    i-ii  ivii        
  L1M4_orf2#LINE/    100 ATCCCA-GCTGCCTTTTTTGCAGA-AATTG-ACAAGCTGATCCTAAA 143

Transitions / transversions = 2.00 (22 / 11)
Gap_init rate = 0.04 (6 / 143), avg. gap size = 1.83 (11 / 6)  

2279 27.39 5.64 1.15  chr2_194276803_194279301     1139  2007 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194276803_   1139 TGGAAAAAGTATGTAATGCTCATGGATCAGAAGAATCAGTATCATTAAAT 1188
                               i -   viv   i        ii     v i i   ii    iv
  L1M4_orf2#LINE/      1 TGGAAAGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_194276803_   1189 TG----TACTGCC-AAAGCAACCTACAGGTTCAATGCAATTCCTGTCAAA 1233
                           ----    v  -   vii i      i     i     i   i     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_194276803_   1234 GTACCAAG-GTCATTCTC-CAGAGAATTATGTAAAACAATCCAAAAAATT 1281
                         i v   iv- i v  i i-    -    i-ii  ivii    v    -  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGA-AATTG-ACAAGCTGATCCTAAAA-TT 146

  chr2_194276803_   1282 CATCTGCAAAGAAAAAAAGCCCA-AATAGTCAAAGTAATCTCAAGCAAAA 1330
                            v  v   viv  iiii    -     i    ii     ii iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_194276803_   1331 TGAAAAAAGCTCTAGGCATCACATTACCTGACTTCAAATAATATTATAAG 1380
                         v   v    i vv   vv     i v  ii i      vvv  i  i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_194276803_   1381 GTTATAGTAACCAAAACAGCACAGTACTGGTATAAAAATAGACACATCAA 1430
                          i  i     i   i    iiii       i    ii       i  vi 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_194276803_   1431 TTAATGGAACAGAATAGAGAA-CTAGAAATAAAGACATA--TCTACAACC 1477
                          i       i     v    i- i         vv    -- i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_194276803_   1478 ATATGATTTTTGACAAAG-T-CCATGAAAATACGCACTAGTAAAAGAACA 1525
                          vv       i     i - -   -- i vi iv  v i vi      i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCA--AGACCATTCAATGGGGAAAGAATA 394

  chr2_194276803_   1526 TGCTATAAAATAAATGGTGGTGGAAAAAACGGATACTCACATGCTGAGGA 1575
                         vv  v vv  i        v   i v  vi     ?i       vi i  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_194276803_   1576 ATGAAGCTGGACTCCTATCTTACACCATATACAAA--CTAACTCAAGATG 1623
                               i     i    i  i              --i        i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_194276803_   1624 AATTAAAG-TTTAAA-----GA----------TAAAATTTCTAGTAGAAA 1657
                         i  i ?  -ii    -----  ----------     i ii   v     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_194276803_   1658 ACCTAGGA--AAAACT--ATGGCCATTTCTCTAGGCAAACAATTTATGA- 1702
                           v    ?--   v  --i  i  -  vvvi       -iii   v v -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAA-TGGTTTCTTAG 592

  chr2_194276803_   1703 ATAAGTTCTCAGAAGGACACACAACGAAAACAAAAATAAACAATTGGGAT 1752
                            v vivi  i   v   vi    i   iv       i i  v v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_194276803_   1753 TT-----AAAT---AAACT---AAGCATGCAAAAGAAATAGTCAACAAAG 1791
                           -----    ---     ---iv  - v    i  v ivi    v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAG 691

  chr2_194276803_   1792 TAAACAGACAGCCTACACA-TGTGAGAACATATTTGCAAACGGTACCTCC 1840
                          i  v     i  i   v -  v     v           ivi  iv  i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_194276803_   1841 AACAGAGTGTTAATATCCAGAATTTACTGGGAACTCAAACTACTCAACAA 1890
                         i i ii vii vi          v  ivii      vv  v      i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_194276803_   1891 CAAAAAAAACAAA-AACTTCATTAAAAAGTGGGCAAAGGACATGAACAGA 1939
                         i     i -    -   iiv   ?    i           iv    i   
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_194276803_   1940 CATTTTACAAAGGAAGACATACAAGTGGCCAGCAAACATATTAAAAGATG 1989
                              iv v  i     i      i      ii  i  i  v        
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_194276803_   1990 CTTAACATCACTTATCAT 2007
                           i       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (150 / 84)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 1.97 (59 / 30)  


2958 27.22 1.44 0.67  chr2_194287428_194291051     2233  3132 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_194287428_   2233 GGAAAAATATTTCATGTTCATGGATTGGAAGATTCAATATTGTTAAAATG 2282
                              i    ii                    i i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_194287428_   2283 TCCACACTACCCAAA--GAACTCTACAGATTGAATGCAATTCCAATCAAA 2330
                         v v i   v      --  --          v  i     i  v      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGA--TCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_194287428_   2331 ATACCAATTACATTCTTCATAGAAATTGAAAAA-TG-TCCTAAAATTTAT 2378
                           v   ii i v  i  iii         v  i-  -          i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_194287428_   2379 GTGGAATCACA-GAAATGCAGAATAGTCAAAGCTCTTCTGTGCAA-AAGA 2426
                         i     vii  - ii iv        i    i vv ii  viv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_194287428_   2427 ACAAAATTTGAGGAATTATATTATCTGGCTTCAAATTATACTGCCTAGCT 2476
                              i  v     v i i i vi iiii      viv    i vv    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_194287428_   2477 ATA-TAAACAAAACAGCATAGTACTTGTATAAAAACGGGCACATAGACAA 2525
                          i -   v   i    ii i     v i    ii ii i  i     iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_194287428_   2526 ATGGAACAGAATAGAGAACTCAGGAACAAATCCACACACCTTCAATAAAC 2575
                               i     v    iii   i  i   i   i   ii viii v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_194287428_   2576 TCATTTTAGACAAAGGTGCCCTGAACATACACTGGGGGAAAGAGAGTCTA 2625
                          v     v     i      vv  v   v  v     i  ii v     v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_194287428_   2626 TTCGTTAA-TGGTGCTGGAAAAACTGAATATCCATATGCAGAAGA-TGAA 2673
                            ivi  -         i v     i   ?   i     i    -    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_194287428_   2674 ACTAGACCTCTCTCTCTTTCCATACACAAAAAATAAAATCAAAGTGGATG 2723
                         ii i    i  vi   viv     i       v   v-     i     v
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAAC-TCAAAATGGATC 498

  chr2_194287428_   2724 AAAAAATGTAAATCTAATATCTCAAACTATGAAACAACTATAAGAAAACA 2773
                          ? i vi-     v   v v  v       i    vvi  v         
  L1M4_orf2#LINE/    499 AWAGACC-TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_194287428_   2774 TTGGAGAAAATCTTCAGGCCATTGGTCTGGGTAAACATTTTTTGAATAAT 2823
                          v  ? v        iv v v    vi i  i  vvi   i  ii   vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_194287428_   2824 ACCCCACCAACACAGGCAACCAAAGCAGAAATGTACAAATGGGATCACAT 2873
                           v   vv i    i     v    v i    iv i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_194287428_   2874 CAAGTTAAAAAACTTCTGCACAGCAA-GGAAACAATAAACAAAGTGAAGA 2922
                            iv v        i  ii vv   -   v  v  v  v        i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_194287428_   2923 GACAAACCACAGAATGGAAGAGAGTATTTCCAAACTACTCATCTCACAAG 2972
                              v           i   i i     v    ii ivi    v i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_194287428_   2973 GAATTAAGAACTAAAATATGTAAGGAGCTCAAACAACTCTGTAGGAAAAA 3022
                          i i viv v i i     i   i  i   vv       vi  iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_194287428_   3023 AAAATTAATAATTTGACATAAAAATGGACAAAATACATGAATAGATGTTT 3072
                         i v --     iiii iv?        i    iv iv        ii   
  L1M4_orf2#LINE/    798 GACA--AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_194287428_   3073 CTC---AAAAGACATACAAATGGCAAACAGGCATACAAAAAGGTTCTCAA 3119
                            --- i    i           v  i i   i ii     i v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_194287428_   3120 CATCACTGATCAT 3132
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 1.36 (19 / 14)  


2625 24.77 5.34 2.16  chr2_194328641_194332887.rev     2876  3755 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194328641_   2876 TGAAAAAATAATACCCAATAGTCTCAGATTTGAAAAATTAATATTGTTAA 2925
                           i   i   ---i  v  iv  vii    v   i v             
  L1M4_orf2#LINE/      1 TGGAAAGATA---TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chr2_194328641_   2926 AATGTCTATAC-CCTTATAGTAATCTATAGATTCAATGCAATCCTTACCA 2974
                         i   v v    -  ii v v i     i        i       i  i  
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_194328641_   2975 ATATTCCCA--TGTCATTTTTCACAGAGACAGAAAAAATCAATTGTAAAA 3022
                          v  -    --  i -     ii    i iv  v  iv -i  iv     
  L1M4_orf2#LINE/     98 AAAT-CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCT-GATCCTAAAA 144

  chr2_194328641_   3023 TT-GTATGGAACTACAAAAGACCTCAAATAGCAAAAGCAATCTTGAGTAA 3071
                           -i       v i   ii    ivi      v   i         iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_194328641_   3072 AATGAACAAAACTGGAGGCATTACACCTCTCGTAATTTCATATTACAAAG 3121
                         i v       ii      vv i    i  i --       ------   v
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCC--AATTTCA------AAAC 236

  chr2_194328641_   3122 CTATAGCAAAGCTACAGTAATCGAAACAGTATGGACCTAGCATAAAAAGA 3171
                         i  ivi                i i     i   vv  i      ii v 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_194328641_   3172 GACACATAGACAAATAAAACAGATTAGAGAGCCCAGAAATTAACCCAGGT 3221
                             i     iv   ii  i   v v     i        v      -- 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--T 334

  chr2_194328641_   3222 TCAT--ATGGCCAACTAATTTTTGGCAAGATCTCTAAGAACACACAAACA 3269
                         v   --    i   i i     i i    iviv i    v  iv   vvi
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_194328641_   3270 GTAACGTATA--CTCATCATTAAATGATGCTGAAAAACCTGGATGTGCAC 3317
                          v  v v   --  iv   vi     i     ii v v      i?v   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_194328641_   3318 AGCCAGAAGAATGACATTAGACACCTACCT---------TACAAAAATTA 3358
                          vv  i        vi  i   v       ---------           
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_194328641_   3359 TATTGAAATTAATTAAAGACTTAAATATAAGACCTGAAACCATAAAATAC 3408
                         vv ii    vi  i ?    i     i     v  i    i      iv 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_194328641_   3409 TTAGAAAAAAA-----GGATAAA-CTT---GACTTTGGTGGT--GCCAAT 3447
                               i    ----- ?i    -   ---   i    --  -- v    
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG--GTTAGGCAAT 582

  chr2_194328641_   3448 GATTTTTTTGGAAGTGACACCAAA-GTATTGGCAATGAAAGCAAAAATAA 3496
                          i   i  -i  vi          - i ivi    ii    v       i
  L1M4_orf2#LINE/    583 GGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_194328641_   3497 ACAAGTGAGGCAT-ATTAAACTAAAAAGTTTCTTCGCACCACAGGAAATA 3545
                          i  i vi i v -  i   v v    ii  i vi  vi  v    v iv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_194328641_   3546 ATCATTAAAATGAAAAGGCAACCTTTGGAATGAGAAAAAA-AT--GTAAA 3592
                             vv   i       i     ivii     i  i    -  -- i   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_194328641_   3593 TCATATATATGTTAACGGGTTCATATCCAGACCAAATAAA---TTCATAG 3639
                                 v  v   v  ii ii        vi v     ---i  v  v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_194328641_   3640 AAATCAATAG--------CAAGTAAC--AAC-AACAAATAGGCAAAGGAC 3678
                           v      i--------   i    --  i-? v    i         i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_194328641_   3679 ATGAATAGACATTTTTTGAAAGAAGACATACAAATGTCTAACAGTTACAT 3728
                         v             i iv        i         v i  i ivi    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_194328641_   3729 GAAAAGGTGCTCAACATCACTAATCAT 3755
                               i            ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (131 / 83)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.44 (66 / 27)  


2454 27.32 1.75 2.51  chr2_194371647_194374580.rev     1535  2449 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194371647_   1535 TGGAAAAATATCCTGTGCTCATAAATCAGAAGAATCAGTATCATTAAAAT 1584
                               i      ii  i    ii  ii     v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_194371647_   1585 GATCACACGGCCCAATGCAATCTACAAATTCAATGCAATTCCTATTCAAA 1634
                          iiv i  vv     vvii       i      i     i     iv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_194371647_   1635 TACCAAAGGCATTTTTCACAGAACTAGAAAAAAAAAAATCCTAAAATTTA 1684
                          v   ivv  v     ii     v v  v  ivvi --          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chr2_194371647_   1685 TATGGAACAAAAAGGTGCCCA-AGTAGCCAAAGAAATCCAAAGCAAAATT 1733
                                vviv    vi    - i        iv    ----------  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC----------TT 188

  chr2_194371647_   1734 AAAAAAAAAAAAAAGAAGGTGGAGGCATCACATTATCGGATTTGAAATTA 1783
                         i     i  i  v -   v      vv     i vi vi    v   viv
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACA-AAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_194371647_   1784 CACTGTGAGGCTATAGAAACCCAAACAGCATTGTACTGAAAAAAAAAATA 1833
                         i   iii i    i  v  i v i    ii v      iv v  ii -  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TA 286

  chr2_194371647_   1834 GTCAAACACATCAATGAAACTAGA-TGGAAAATCCAAAAATAAAGCCACA 1882
                          v  v i v       i  -    - v  i i    i       v   i 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAA-TAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_194371647_   1883 GACC-ACAGCCAACTTATCTTTGACAAAGCTGACAAAAACATACACGGAG 1931
                         v ii- ii i   i v  i  i     i v  v   i v   v  vv i 
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_194371647_   1932 GAAAGGACACTCTATTCAACAG-TGGTGCTGAGAAAATTGGATTGCCAAA 1980
                              i i v   v       i-        i  v  i     v?   v 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_194371647_   1981 TACATAAGAATGAAACTGGACTTCTATTTCTCACTCTATACAAAAATTAA 2030
                          i  v         ii     ii   ii  v   iv              
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_194371647_   2031 C-----ATGGATTAAATACTTAAATCTGAGACCTGAAACCAGAAAAGCCC 2075
                          -----      i ? v  i     v i   v  i    i v    vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_194371647_   2076 TGTAAGAAGACCTAGAAA-AACTCTATTG-GACATTGGCCTTGGCAAAGC 2123
                          iv     i  v   i?i-  v   - i -   v    vi v     v v
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGG 584

  chr2_194371647_   2124 ATTCTTGACTAAGACCTCAAAAGCAAATACAACAAAAATATAAGTAGACA 2173
                         v     iiv  v   vi        v vi        iv v  i    i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_194371647_   2174 AATGGGATTTAATTAAAACTAAAAAGTTTTTGCACAGAAAAAGAAATATT 2223
                            v   i  v  i    i      -i     ii vvv   i  v ivv 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chr2_194371647_   2224 CAACAGAATGAACAGACATCCTGCAGAATGAGAGAAAATATTTGCAAACT 2273
                            v i i    v     v  ii       i                 ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_194371647_   2274 ATGCATTTGATAAAAAAACTAATATCCACAATCTCCAAGAAATTCAAATA 2323
                           ii  i      iii -  vi      v   v vi  ii  i  vv i 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGA-CTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_194371647_   2324 TCTCTAAAAAATCAAAACAAACAAAATAACACCATGAAAAAATGGGCCAA 2373
                         v   --  v   -    - i     -    v v  v?          v  
  L1M4_orf2#LINE/    783 ACTC--AATAAT-AAAA-AGACAAA-TAACCCAATTWAAAAATGGGCAAA 827

  chr2_194371647_   2374 GGACATGAGCTAATATTTTTCAAAAGAAGACATACAAGTGGTCAACAAGC 2423
                            iv   iivi i    i  v        i      i   i   i    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_194371647_   2424 ACGTGAAAAAA-----AAAATCAAGCACCAA 2449
                           i      i -----  v    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (142 / 104)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.95 (39 / 20)  


3262 27.09 0.55 0.55  chr2_194395384_194401664.rev     4882  5789 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194395384_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_194395384_   4932 GGCCATACTGCCCAAGGTAACTTACAGATTCAGTGCCATCCCCATCAAGC 4981
                            v     v     iv i ii          ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_194395384_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_194395384_   5030 TATGGAACCAAAAAAGAGCCCAAGTCGCCAAGTCAATCCTGTGCCAAAAG 5079
                                viiv  ii  v  vi i v     iv     i  vivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_194395384_   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_194395384_   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_194395384_   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTGCAACT 5227
                                i    i--    i  --        vv  ii i  i iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_194395384_   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_194395384_   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_194395384_   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGGTGGA 5377
                            ii    i    v   i     v           i  i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_194395384_   5378 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5427
                          i ?    i       v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_194395384_   5428 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5476
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_194395384_   5477 AAACACCGAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTA 5526
                         vi     i      vvi   i      vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_194395384_   5527 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5576
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_194395384_   5577 CAGGCAACCTACAAAGTGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5626
                         v  i     i   i i           v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_194395384_   5627 GAGGGTTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5676
                         ii  ii vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_194395384_   5677 AAAACAAATAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5726
                           i           v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_194395384_   5727 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5776
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_194395384_   5777 CATCACTGGCCAT 5789
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2440 23.64 3.18 0.61  chr2_194407464_194409109      501  1160 (486)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr2_194407464_    501 AAAATTCACCTTGAAATGACAGTAATCAAAATAGTGTGGTACTGGTATAA 550
                             i i  ivii  iiv           i i             i    
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_194407464_    551 TGAGAGGCATGTAAACCAATGAAAAAGAATATATAGCTCAGAAATAAAAC 600
                         v  v  i   i  i i     i  v     vv v  ii          v 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_194407464_    601 CTTCTATATAGGTTCACATT-ATTTTCAACACAAATGCCAAGGCCATGCA 649
                          v vi  v  v v   -   -      i   viii       i    v  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCA-ATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_194407464_    650 ATGGAGAAAGATTACTCTTCTAAACAAATTATGTTGGGAAAACTGGATGA 699
                             i      v  v    i v       vi  i     v        i?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_194407464_    700 CTACATGCAAATGAATGAAATTGGACCCTTGCCTTGTGACTTATACAAAA 749
                          i         v       i        i i   iiiiv v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_194407464_    750 ACCAACTCAAAATGAATTAAAGACCTAAACATAAGAGCTAAATGTCTACA 799
                          ii           i  i ?         ii           vv v  v 
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_194407464_    800 GCTCTTAGAAGAAAACACAGCAGAAAAGATTCATGACACTGGATTTGGCA 849
                         i                i  v? v   vv   i    vi   i  v    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_194407464_    850 ATTATTTGTTGGATATAACATCAAAAACTCA-----CAAAAGAAAAAAAT 894
                           vi   v  i     i   i     i v  -----            - 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-T 629

  chr2_194407464_    895 GGGTAAATTGTACTTGATAAAAATTAAAAACATCTGTTTATCGAAGGACA 944
                         i i       v    v  v            v i   viv  i       
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_194407464_    945 TTCTCAACAGATTAAAAA-----TTTAAGGAATGA---AAAATAATTGCA 986
                         i v    v i v i    -----iii vi     i---      v     
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_194407464_    987 AATAATGTATCTAATATGAAATTAATATCCAGATTATATAAAGAATTCCT 1036
                            v  i     i   v ii i vi        v           i  i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_194407464_   1037 ATGACTCAACTACAAAAA-------AAGTTGATTCAAAAATAAACAAAAT 1079
                          ii      iv i     -------  viii   ?      iii    iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_194407464_   1080 ACTTGAATATACATTTCTCTCCAAAGCAGATAAACAAATAGCCAATAAAC 1129
                          i       v         --     v     v      i        i 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTC--CAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_194407464_   1130 ACTTGAAAAAAAGCTCAGAATTTGTAATCAT 1160
                           v      i v     iv  iv????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (90 / 62)
Gap_init rate = 0.01 (8 / 677), avg. gap size = 3.12 (25 / 8)  


2099 25.56 7.82 3.21  chr2_194463239_194464949      504  1219 (492)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr2_194463239_    504 AAAAGACTCAGAATAGCCAAAGCCACCCTGAGCAAAAA-AACAAAACTAG 552
                           ii   i             i v i i   iv  i  -      ii i 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_194463239_    553 AGGAATCACATTACCTGACTTCAAATTATACT-ATTATGAAGCTGTAGTA 601
                             v     i v  ii i      ----   - i  ii     ii    
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAA----ACTTACTACAAAGCTACAGTA 255

  chr2_194463239_    602 ACCAAAACAGCATTGTACTGGCATAAAAACAGACACATAGACCAAAGAAA 651
                          i   i    ii v            ii i     i     i   v i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_194463239_    652 CAGAATAGACAGCCTAGAACCAAATTTCTGTATGT---GTCAACTCATTT 698
                         i     v  v  i i    vi   iiiv ii  v ---     i v    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_194463239_    699 TTGATAAAGGTGCAAAGAATATACATTGGGTGAAAGAAGACTCTCCTCAG 748
                          i  i  i     v    vi  v  v    -       v v   ii   i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTTTTCAA 404

  chr2_194463239_    749 TAAATGGTACTGTGATAACTGGATATACATGTGAAGAAAAATAAAACTAG 798
                         i       i   v  i         ?v  ii  v i  i   i  ii i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_194463239_    799 ACCCCCATCT---------------------------------------- 808
                              i i  ----------------------------------------
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_194463239_    809 -TAAATATAAGACCTGAAACTATGGAATTACTT-GAAGAAAACATTGGGG 856
                         -     i     v  i       ii  i -   -           v  ? 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNG 553

  chr2_194463239_    857 ACACACTCCATAACACTGTTCTGGGTAACAATATCTTGAGTAATATCTCA 906
                         vv vv  i i i  vi  vvi i  i  iii v    iii  vv ivi  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_194463239_    907 AAAGCATAGGCAACTAAAGCAAAAATGGACAAATGGGATCACATCAAGCC 956
                               i i     v    v      i  i    v   iiv      ivi
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_194463239_    957 TAAAAGTTTCTGTACGACAAAGCCAACA--ATCAGCAAAATGAAGAGACA 1004
                              ii  i   i vv     --i   --    iv   i    i     
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAG--GACACTATCAAGAAAGTGAAAAGACA 701

  chr2_194463239_   1005 GCCCAGCCCACGGAATGAGAGAAAATATTTGCAAATTACCCATCTCACAA 1054
                         i    ----- i     i                  i ivi    v i  
  L1M4_orf2#LINE/    702 ACCCA-----CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_194463239_   1055 AGGATTAGTA-CCAGAATATATAAAACATATTAAAGAGGTCAAACAGATC 1103
                         i   i v   -              ----------  iv  vv   iv  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAA----------GAACTCTTACAACTC 786

  chr2_194463239_   1104 AGGAATAAAA---CAAATCATCAAATTTTAAAATGGGCAAAATATCAGAA 1150
                          iv       ---     v i v    ?v            iv  iv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_194463239_   1151 TAGACATTTCTTAAAGGAAGACATACAGATGACCTACATGTATATGAAA- 1199
                                    iv  i     i     i   i  v i v i i      -
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_194463239_   1200 --CACTTAACATCAATAGTACT 1219
                         --ii  i       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (122 / 58)
Gap_init rate = 0.02 (15 / 749), avg. gap size = 5.27 (79 / 15)  


2896 26.37 2.57 1.12  chr2_194475005_194478882     2492  3386 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194475005_   2492 TGGAGATATAGTCCATGTTCATAAATAGGAAAAATCAACATTACTATTAT 2541
                             i v   vi          ii  v    i v i  i   ii  vv  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_194475005_   2542 ATTGGTTCTTCCCAAACTGACATATAGATTCAATGCAATCCTAATCAAAA 2591
                         iviii v  i      i   iv  i        i       iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_194475005_   2592 TGCCAGCAAATTATTTT-TAGATATCAACAAACTGATTCTAAAGTTTATA 2640
                          v     vivi v    -i   v  ii    i     i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_194475005_   2641 TGGAG-TGTCAGAAGATACAGAATTGCCAAAACAACATTGAACGAAAAGA 2689
                             i-  -  iii  iv      v          iv     vi i    
  L1M4_orf2#LINE/    151 TGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_194475005_   2690 AAAATGTTGGAAGATTGACTCTTTCTGACTTCAAGACATGTCA---AGCT 2736
                          v  v      i  i v  v   i ii i     i  v iii ---    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_194475005_   2737 TCAGTATGAAAGACAGTGTGGGATTTATGAAATAATAGGCAAACAAACC- 2785
                         v     vvv            v i viiiv  vi    i  v i i i -
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_194475005_   2786 -TGAAATAAAAT----AGCCCGGAAACAGTTAAAAATGTATATAGTATAT 2830
                         -  i    i   ----  i  i    i ------  ivi   i v -   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATA------AACCCATACATT-TAT 342

  chr2_194475005_   2831 AGTCTATTGATCTTTGACAAAGAAGCAAAGGCAATACACAATGCAGCAAA 2880
                         i   v      i  i     i iv  v   i v  v  --   vi v  i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAG 390

  chr2_194475005_   2881 GATAGCCTTTTCAACAAATAGTACTAGAACAACTGAATGTCCACATGCGA 2930
                         i    i             i  i  i i       i  i?        i 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_194475005_   2931 AAAAATAAATCTAGACACATACTACACAC--TTCACAAAAATTAACTCAA 2978
                           i   i  vi i   v v   iv     -- vi                
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_194475005_   2979 AATGGATCATAGACTT---TGTAAAAGGCAAATCTATAAAACTTTGAGAT 3025
                                  ?    i ---     i  vi   v          i v   v
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_194475005_   3026 GATATCATAGGAGAGAACCTAGATGTTCATGTGTATGACAATGAATTTCT 3075
                           v v      ? vi  i  vvi  vi v  v  vv i     iv  ii 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_194475005_   3076 AGATACAACACAAAAGGCACTACCCATAAAAGAAATAATTCATGAG--AA 3123
                              ii    v   i    v v v i        v   vv  i i--ii
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_194475005_   3124 ACTTCATTGAAATTAAAGATTTCTACTCTGTGAAAGATACTGTTATGAGA 3173
                                ii        i i  i iiv  vii  i  i   i i v  i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_194475005_   3174 ATAAAAAGACAAGCCATAGACTGGGAGAAAATATTTGCAAAAGACATATC 3223
                         i i         v   i   v                    vv i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_194475005_   3224 TGATAAAGGATTATTAACCAAAATATACAAAGAACGCTTAAGACTCAAAA 3273
                               i   i vv  v   i      i       v    vi      v 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_194475005_   3274 ATAAGAA-ATGAATAG---AATT-AAAAATGGGTCAAAGACCTTAACAGA 3318
                             i  - ii    i---    -         iv  i  ii v  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_194475005_   3319 CACATCAAAAAAGAATATATACAAATGGTAAACAAGCACATGAAAAGTTG 3368
                           iv  vvv      v            iv  i              v  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_194475005_   3369 CTCCACATCAGAAGTCAA 3386
                            v      ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


3153 26.60 0.77 0.77  chr2_194521351_194526685.rev     3938  4843 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_194521351_   3938 GAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAATGG 3987
                            ii i  i     i        v      v i i   ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_194521351_   3988 CCATACTGCC-AAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 4036
                          v     v  -  iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_194521351_   4037 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCATA 4084
                            iivi i  i  ii     -   -- v  i  - iii    v      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr2_194521351_   4085 TGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGAA 4134
                              viiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_194521351_   4135 CAAAGCTGGAGGCATCACACTACCTGACTTCAAAATATACTACAAGGCTA 4184
                              i      vv       v  ii i       iv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_194521351_   4185 CAATAACCAAAACACCATGGTACTGGTACCAAAACAGAGATATAGACCAA 4234
                           i   i   i   vii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_194521351_   4235 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCAT 4282
                              i    i--    i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_194521351_   4283 CTGATCTTTAACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT-TTCT 4331
                         i    i  ii    ivv  v   i v  vv            i  -v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_194521351_   4332 TATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4381
                          -  i  i       i      v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_194521351_   4382 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 4431
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_194521351_   4432 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4481
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_194521351_   4482 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTGA 4530
                             ?i- v i -   iv   v v  vv i     v ii   v ivv iv
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_194521351_   4531 AACACCAAAAGCAATGGCCACAAAAGCCGAAATTGACAAATGGGATCTAA 4580
                         i            vvi  v       vvi    v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_194521351_   4581 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAAC 4630
                          i   v v  i i   i  ii vv    i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_194521351_   4631 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 4680
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_194521351_   4681 AGGGCTAATATCCAGAATCTACAAAGAACTTAAAAAAATTTACAGAAAAA 4730
                         i  i  vi          v  i        ivv v  v iv i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_194521351_   4731 AAATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 4780
                          i -    i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_194521351_   4781 CTCAAAAGAAGACATTTATGCAGCCAACACACAAATGAAAAAATGCTCAT 4830
                            v        i  vi viii     i vi  v       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_194521351_   4831 TATCACTGGCCAT 4843
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.27 (14 / 11)  


2421 26.38 5.65 1.04  chr2_194563486_194566446.rev     1602  2469 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194563486_   1602 TAGAGAAATATTTTA-GTACATGGATAGGAAGACTCAATATTATCAA-AT 1649
                          i  i i    iii -  v       v        i      i i  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_194563486_   1650 GTCAGTTTTTCCCAACTCGATCTTTAGATTCACTGAAATCTTAATGAAAA 1699
                          v  i vi i     v i     vi       vi v    iiv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_194563486_   1700 TA--AGTTA--TTTTTTGTATA--CTGACAAAATGTTTCCAACATTTATG 1743
                          v--  i i--       i v --i      iv  v i i  v   i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_194563486_   1744 TGGAAAAGCAAAAGACTTAGAATGACCACAGTAATATTGCAGG-GAAGAA 1792
                               v    ii   ii     ii   v ii   v   v ii-      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_194563486_   1793 CAAAGATGGAGAACTGATACTACCTAACTTCAAGACTT-TTG---AATTA 1838
                              v     i   v i   v  i  i     i    -i i--- ii  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_194563486_   1839 CGGTAATGAAGAC--TGTGGTATTGGCAAGAAAATAGACAAATATATCAA 1886
                          i     v     --       i     vi ii       v   v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_194563486_   1887 -GAAACAGATATATT-----CCCTGAAATACACCCACACAAATACAATTA 1930
                         - i  i   ---   -----i  v      v     i   vv  iii i 
  L1M4_orf2#LINE/    301 TGGAATAGA---ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_194563486_   1931 ACTGGCTTTTAAAAAAGAAGCAAATGGA--ATTCAATT----AAGTATAG 1974
                          i  ii   ii v  i iv  v  --  --       v----   v    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAA--GACCATTCAATGGGGAAAGAATAG 395

  chr2_194563486_   1975 TCTTTCCAAAACAGTGTACTGAAACAA-TGGAAATTCAGAGGCAGAAAAA 2023
                              i   v v vv  i   ii    -    v ?i  v v   i  i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_194563486_   2024 TGAATAATGA--CATGACTTTATACCATTCACAAAAATTAAATTGCAAT- 2070
                             -iv  i-- viv  i i i     vi           v iiv   -
  L1M4_orf2#LINE/    446 TGAA-GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_194563486_   2071 ---TATA----TAAATGTAAAATGAAAAATTATAAAACTCCTAGAAAATA 2113
                         ---i ? ----         i vvv    i          i     i v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_194563486_   2114 ACAGAAGAGAAAATCTAGATAACTTTGGGTTTGATGATGACATTTTAGAT 2163
                            v i ? v      vvi i  i       v iii   iiv i      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_194563486_   2164 ACAACATCAAAAGCATAATCTATTATAGAATAATTTTATAAATTGAACTT 2213
                          ii   i        i  v v iv v    v  v vv        i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_194563486_   2214 TATTAAAATTAAAAACCT--GCTCTACAAAAAGCACTGTCAGGAGACTAA 2261
                         i  i            i -- iv  v    iii    i   i  i v i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_194563486_   2262 AAAGACAAGCCAGAGACTGTGAGAAAATATTTATAAAGCACATATTTCTC 2311
                                 v   v   v  v            ii   v  i    --  v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT--CTG 742

  chr2_194563486_   2312 AAAAATGA----TATTTGAAATATACAAAGAAGTCTTAAAAGTCAACA-T 2356
                          v  iv  ----   iiii      i      v     v  v    i - 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_194563486_   2357 AAAGATAGCAAACAACCCAATTTAAAAATTGGCAGTAGATGTGAGCAGAC 2406
                            i v -    i         ?      v    ivi   v   ii    
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_194563486_   2407 ATCTGTCCAAAGAAGACATG-AAATAACAAATAATCATATGA---GATAC 2452
                           i v           i  i-    ii v     v  i    ---   i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_194563486_   2453 TCCATATCAGACGTCAG 2469
                           v i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (137 / 88)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.15 (58 / 27)  


2632 27.11 2.11 1.22  chr2_194720684_194725027     2955  3854 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194720684_   2955 TGGAAACACATCCCGTCTTCATGGATGGGTAGAATAAATATTGTGAAAAT 3004
                               v i     i v         v  v   v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_194720684_   3005 GACCATATTGCCAACAACAATCTACAGATTAAATTCAATTTCCATCAAAA 3054
                          i v   i v  v v vii           v  iv    ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_194720684_   3055 TGCCTTCATTATTCTTCACAGAACTAGAAAAAACT-ATCCTAAAATTTAT 3103
                          v  vv vviv  i  ii     v v  v  i-  -           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_194720684_   3104 ATGGAGCCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTGAGCAAAAGGA 3153
                              iviiv  ii  v  v v         i   vvi   iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_194720684_   3154 ACAAATCTAGAGGTATCACATGGCCTGACTTCAAAGTATACTATGAGTCT 3203
                              vi i    vv     ivv  ii i      iiv     ii iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_194720684_   3204 GTAGTTAACAAAACAACATG-CAGTGGTATAAAAATAGACACACAGACCA 3252
                         ii   v v   i   iii  -i v   i    ii       i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_194720684_   3253 ATGGAACAGAATAGAGAACCCAGACATAAAGCCAAATACTTACAGTCAAT 3302
                               i     v    ii     v     v   v i i   ii      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_194720684_   3303 TGATCTTCAACAAAGCAAACAAAAC-ATAAGGTGGACAAAGGACACCCTA 3351
                             i   i    i vviv   i  -  vvii   iv    i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_194720684_   3352 TTCAACAAATGGTGTCGGAATTATTGGCAAGCCATAGGTAGAATAATGAA 3401
                                       ii  i iv i   vv ?   i v i i  v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_194720684_   3402 GCTGGATTCTAATCTCTCACCTTATATAAAAATCCACTCAAGATGGATCA 3451
                          i    ii iv i   v    v    i      iv      i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_194720684_   3452 AGGACTTAAGTCTAAGACCTAAAACCATGAAAATTCTAGAAGATAACATA 3501
                         ?i   i   i v     v       i  i   v ii       v      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_194720684_   3502 TAGAAAACACTTCTAGA--TTGACTTAGGCAAAGAGTTAATAAGA-AGGA 3548
                         vi?iv  vv    vv  --   iv        v -   vv v   - v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTAGATATGA 598

  chr2_194720684_   3549 ACCCTAAAACAAATGCAAGAAAAACAAAAGTAAATAGATGGGACTTAATT 3598
                         vv  v   i  v v    v    iv    i  i   i  v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_194720684_   3599 AATCTATTAATCAAAAAAGCTTCTGCACAG-AAATGAAA--ATCAGCAGC 3645
                           ------   i     --   i  ii vv-   v  v --    iv iv
  L1M4_orf2#LINE/    649 AA------AATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_194720684_   3646 GTAAACAGACATCCCACAGAATTGGAGAAAATATTCACAAAATATGCATC 3695
                           i  v     v          v            ii    vi  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_194720684_   3696 CAACTAAGGG-CTAATATCCAGAATCTACAAGAAACTCAAACAAATCAGC 3744
                         ii -      -  vi          v  i  ii     vv    v   ii
  L1M4_orf2#LINE/    741 TGA-TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_194720684_   3745 AAGAAAAA----AATGTC---ATCAAAAAGTGAGCAAAGAACATGAATAG 3787
                           v     ----   iv ---  i?    i  i      i iv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_194720684_   3788 ACAGTTCTCAAAAGAAGGTATACAAATGGCCCACAA--ACATGAAAAAAT 3835
                            v     v       i             v i  --         i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_194720684_   3836 GCTCAACATTGCTAATTAT 3854
                                  ii????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (132 / 108)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


2203 26.97 7.87 1.29  chr2_194727607_194729360      496  1270 (484)    L1M4_orf2#LINE/L1       83   908 (0)  

  chr2_194727607_    496 ATGCAAATCCCCATCAAAATCCAAGCAAGTTATTTTGCAGACATTGACAA 545
                          i    -    i          v   vivi v         v        
  L1M4_orf2#LINE/     83 ACGCAA-TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

  chr2_194727607_    546 ATTGATTATAAAGCTTACATGTAGAGGCAAAAAACCCAGAATAGCAAACA 595
                         ii    iv    ii i i   v i v    iii            v  v 
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr2_194727607_    596 CAATATTAAAGGAGAAGAACAAAG----AAGACTGATATTGTCCTATTTA 641
                             v  i  ii            ---- i    v i i vi  v    v
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_194727607_    642 AAGGCTTAGTGTAGCGCTGTAGTAATCAAAACAGTGTGGCTTTGACAAAG 691
                           ii    v ii iv   ii         i         ivi  i  v i
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_194727607_    692 AAATAGACAAATAGATCAATGAAACAGAATAGAGAGTCCAGTAATAGTCC 741
                         ii       v           i  i     v          v    iv  
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_194727607_    742 ACATAAAT--AGAGCCAACTAATCTTTGACAAAGGAGTAAAGGC------ 783
                         -    v  -- vi i   i i  i  i     i  v iv   i ------
  L1M4_orf2#LINE/    332 -CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr2_194727607_    784 -------------AGT----------------------ACAACTTTATAT 798
                         -------------   ----------------------      vv   ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_194727607_    799 CCACATGCAAAAAACAAAAAGAATCTAGATACAGACTTTATAATTTTCAC 848
                                     i ---- v   vi i  iv vv  i i i viv vi  
  L1M4_orf2#LINE/    431 CCACATGCAAAAGA----ATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_194727607_    849 AAAAATGAACTCATAATGGATCACAGACCCAAATGTAAAGAGC-AAAATA 897
                               v      v         ?     i        -    -    iv
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA-GAGCTAAAACT 525

  chr2_194727607_    898 ATAGAACTCCTGGAAGATAACA--GGAGTACATGCAGATGGCCTGAGGTT 945
                            i     i i     v    --  ?   v  vivvi  i   vi    
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_194727607_    946 TAGGATTGACTTTTTAGCTATAACATCAAAGGCATA-GTATGTGAAAGAA 994
                         vi v v  ii  i    v   i   i    i   i - i -iii      
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA-ACAAAAGAA 624

  chr2_194727607_    995 A-------TAAGCTAAACTTTATTAAAATTTAAAAGTTTTCCTCTATGAA 1037
                          -------   ii ii    i  i      v    v    viv  vii  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_194727607_   1038 ACACATTATCAGGAGAATAAAAAGACAAGCCATGATCTGGGAGAAGAGAT 1087
                         iv   i     i  i i i         v   iiivv        i v  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_194727607_   1088 TTGCAAAATACTTTTCAGATAAAGGATAATTATA--CAAAATATTCAAAG 1135
                                vi iv v  v     i   i--  i  --  i     vi    
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGAC--TTGTATCCAGAATATATAAAG 772

  chr2_194727607_   1136 AACTCTTAAGATTCAATATTAAGCAAACAAACAACTCCGTGTAAAAATGC 1185
                                 vi i      v   iv i     i   i vi v?       v
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_194727607_   1186 ACCAATGATGCTAACAAACACCTCACCAAAGAAGACATACTGACAGC-AG 1234
                         i v  v   viv  i i   ii  v          i    vi ii  - i
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_194727607_   1235 TAAGCATATGAAAAGATACTTTAAATTATAGGTAAT 1270
                               i          i  iv v  i ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (126 / 79)
Gap_init rate = 0.02 (16 / 826), avg. gap size = 4.44 (71 / 16)  


2405 29.90 2.04 0.79  chr2_194740310_194742181      501  1383 (489)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_194740310_    501 ATGCTGACAGATTAAAATAATCAATAAGACAAAAATGACCATACTGCCCA 550
                            i v ii    ii  v v i    vviiv  i   i v     v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_194740310_    551 AAGCAATTTACAGATTTAATGCTGTTCCTAACAAACTTCCAA-TGTCATT 599
                           vii  i        i  i  vi i    v    v i   i-  i -  
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TT 113

  chr2_194740310_    600 TTCTACAGAATTCAAAAAAAAAATTCTAAATTTTATGTGGAACCAAAAAA 649
                           i i     v ii v  ivvi  i     v  i  i     viiv  ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_194740310_    650 GAGCCTGAATGGCCAAAGCAATCCTAAGTAAAAAGAACAAAACTGGGGGC 699
                           v  v    i      i     i i iv  i         ii   i  v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_194740310_    700 ATCATACTACCTTACTTCATATTATAGTAAAAAACTATAGTAACCAAAAA 749
                         v   i   v  iv i    v viv  v  v   i   i     i   i v
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_194740310_    750 AACTTGGTACTGGTACAAAAACAGACACATGGACCAATGGAACAGAATAG 799
                          iiv         i i  ii i     i  i  i        i     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_194740310_    800 AACACCCAGAAATAAAGGTGCATAC--CTACAAGCATCTGATATTTGACA 847
                          ivii           --iv     --i  iiiv  vi    v  i    
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAA--CCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_194740310_    848 AG----CCAACAAAAAAGCAATGGGGAAAGGAATC-CCTTTTCAATAAAT 892
                           ----    -i vv vv            -   v-i        i    
  L1M4_orf2#LINE/    362 AGGGTGCCAA-GACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAAAT 409

  chr2_194740310_    893 GGTTCTGGGATAGCTGGCTAGTCATTTGCAGAAGATTAAAGCTGGATTCC 942
                            v      i i    v  ?i  iv    i    v i   i    ii  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_194740310_    943 TACCTTTCACCATGCACAAAAACTAACTCAAAATGGATTAAAGATTCAAA 992
                              iv      ii       i               i ?   iii   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_194740310_    993 TGTAAGACCACAAACTTTAAAAATCCTGGAAGACAACCTAGGAAATACTT 1042
                                v vv     v     v  i i     v   v    ?ivv v i
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_194740310_   1043 TTCTCAACAGTGGCCTTGGCAAAGAATTTTTGACTGTGTCTCCAAAAGCA 1092
                            vii  vv   vi v     v iv  i  iiv i  v v         
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_194740310_   1093 GTTGCAGCAAAA--AAGAATTGACAAGTGAGACTTGGTTAGACTAAAGTG 1140
                         vvv   i     --  i   v  i  i vi     vi i i v v  ivi
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_194740310_   1141 CTTTTGCACAGCAAAATAAACTATCAACAGAGCAAACTAATAACTAATAG 1190
                               ii vv    iv v        v i  ii  vvi i   iv i  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_194740310_   1191 AATGGGAGAAGATATTCACAAACTATACATCTGACAAAGGCTTAATATCC 1240
                                   i     ii    ii   i      i  i  vi vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_194740310_   1241 AGAACCTAGAGATAAATT----AAATGAATAAGCAAAAAAAAAAAAACCC 1286
                             iv  v i v  v i----  v v     vv    i v   v     
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_194740310_   1287 TATT-AAAAGTCAGCAAATGACATAAACAGACAC--CTCTAAAATTAAGA 1333
                         v   -    i vi     v  iv i  i     i--   i   i--    
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG--AAGA 857

  chr2_194740310_   1334 CATACAAGTAGCCAACAAACATACACAAA-ATGTGCATCACTAATCAAAA 1382
                         i      i i     i  i  i iiv   -   iv  v  ii ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_194740310_   1383 G 1383
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.49 (156 / 105)
Gap_init rate = 0.02 (14 / 894), avg. gap size = 1.79 (25 / 14)  


 373 20.89 3.80 3.16  chr2_194758935_194764668.rev      171   328 (5406)    L1M4_orf2#LINE/L1      750   908 (0)  

  chr2_194758935_    171 ACTCTTATCCAGAATACATAAAAAACT--TACCAAATCAATAAGAAAAAT 218
                            iv           i     i    --   -  v       v     v
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTAC-AACTCAATAATAAAAAG 798

  chr2_194758935_    219 -TATATA--TCACTTTAGAAATACCGGGAAAAGAATGTGAGCAGACATTT 265
                         -i v   --i  v  ? i    ---   v    i  v   ii        
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAAT---GGGCAAAGGATTTGAATAGACATTT 845

  chr2_194758935_    266 -TACAAAGAAAATAAGCTAAATGCACTGTAAACATATGAAAACGTTCTCA 314
                         - v       i   vi -     vv vi   i  i       vi v    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATAC-AAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_194758935_    315 ACCTAAGAAATCAT 328
                           v v ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 0.88 (15 / 17)
Gap_init rate = 0.04 (7 / 159), avg. gap size = 1.57 (11 / 7)  

3281 26.43 0.77 0.77  chr2_194758935_194764668.rev     4335  5242 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194758935_   4335 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATCGATATTGTGAAAAT 4384
                              ii i  i     i       iv      v ii       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_194758935_   4385 GGCCATACTGCCCAAGGTAGTTTATAGATTCAATGCCATCCCCATCAAGC 4434
                            v     v     iv ii i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_194758935_   4435 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 4482
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_194758935_   4483 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAA 4532
                                 viiv  ii  v  viv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_194758935_   4533 GAACAAAGCTGGAGGCATCGTGCTACCTGACTTCAAACTATACTACAAGG 4582
                                 i      vv  iii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_194758935_   4583 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 4632
                                  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_194758935_   4633 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 4680
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_194758935_   4681 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 4730
                           vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_194758935_   4731 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTGTATGTAGAAAGC 4780
                         i  v  i  i              v      v  ? iii   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_194758935_   4781 TGAAAATGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 4830
                             iv    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_194758935_   4831 ATCAAAGACTTAAATGTTAGGCCTAAAACC-TAAAAACCCTAGAAGAAAA 4879
                             ?    i       v  iv       i-     vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_194758935_   4880 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 4928
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_194758935_   4929 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATCT 4978
                          vi            vvi          vv   i v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_194758935_   4979 AAGTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5028
                         v vi   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_194758935_   5029 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5078
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_194758935_   5079 AAAGGGCTGACATCCAGAATGTACAAAGAACTCAAACAAATTTACAAGAA 5128
                           i  i  vii         i  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_194758935_   5129 AAAAAACAAACAACTCCATC-AAAAATGGGCAAAGGATATGAGCAGACAC 5177
                            i -    i   i v  i-                 v   ii     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_194758935_   5178 TTCTCAAAAGAAGACATTTATGCAGCCAACAGGCACATGAAAAAATGCTC 5227
                              v        i  vi viii     i i           i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_194758935_   5228 ACCATCACTGGCCAT 5242
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (148 / 89)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


 887 25.42 0.85 1.69  chr2_194812825_194817861     3271  3506 (1531)    L1M4_orf2#LINE/L1        1   234 (674)  

  chr2_194812825_   3271 TGGAAAGATATCTCATGTTCATGGATTGGAATAATTAATTTTGTTAAAAT 3320
                                     i                  v v     v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_194812825_   3321 GTCCATTCTTAACCCAATGCAATCTACAGGTTCGACACAATCTTTATCAA 3370
                          v v  v  i--     vvii        i   i  i     ii      
  L1M4_orf2#LINE/     51 GGCAATACTC--CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_194812825_   3371 AATATCAATGACATTCTTCACAGAAATAGAAAAAAGC-AATCCTAAAATT 3419
                            vi  iivi v  i  ii       v  v  --  -i           
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATT 146

  chr2_194812825_   3420 TGTACAGAGCCATGAAAGACCCTGAATAGCCAAATCAATACAGAGCAAAA 3469
                         ii  ii  iviiii ii     v           v    viv  iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_194812825_   3470 AGAACAAAGCTGGGGCA-TCATGCAACCTGATTTCAAA 3506
                                  i   i v -   ii vv  ii        
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

Transitions / transversions = 1.73 (38 / 22)
Gap_init rate = 0.02 (4 / 234), avg. gap size = 1.50 (6 / 4)  

1853 28.95 2.35 2.19  chr2_194812825_194817861     3898  4536 (501)    L1M4_orf2#LINE/L1      239   878 (30)  

  chr2_194812825_   3898 ACTACAAAGGTATAGTAGCCAAAACGATATGGTACTGACATGAAAATAGA 3947
                                  v  i    ii   i  ii i        i   i ii     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_194812825_   3948 TACATAGACCAAAGAAACAGAATAGAGAACTTAGAAATAGATCTGCACAT 3997
                         i i     i   v i  i     v    iiii       i i iii    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_194812825_   3998 TTACAGCGAACTCATTTTTGACAAAGTCAGCAATAATATATATCGGGGAA 4047
                            ii iv  i v     i     i viiv   v vi  vi vi      
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_194812825_   4048 GGGACAGTCTCCTTAA----TGGTGTTGGGAAAACTAGATCTCCTTATGG 4093
                         i i i     ii i  ----     i     v    i   v?  vi   v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_194812825_   4094 AGAGCAATTAAACTAGACTTTTATCTTTCCCTATGCACAAAAATCAAAT- 4142
                          i iv   v  ii i   iii  i  iv v i  ii        i  v -
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_194812825_   4143 -GGATACATTAAAGACTTAAATGTAAGACCACAAACTATGAAACTACTGG 4191
                         -ii  iv  i ?    i           v vv       i     vi i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_194812825_   4192 AAGAAATCATTAAGA--AAACACTTCAGGACATCAATTGTTCTGAGCAAA 4239
                               v   - i ?--   i-    iv   -- --   vvi ii    v
  L1M4_orf2#LINE/    539 AAGAAAACAT-AGGNGTAAAT-CTTCGTGAC--C--TTGGGTTAGGCAAT 582

  chr2_194812825_   4240 GATTTTTGTGGTAAGACCTCAAAAGCACAGGCAACAAAAGTGAAAGTAGA 4289
                          i   i vv i  v   vi          i          vi   i    
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_194812825_   4290 CAAATGAGATTATA-CTAAGCTAATCAAACTTCTGCACAGCAAAGGAAAC 4338
                         i    vi  i vi - v  ii   --      i  ii vv       v  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAA--AAACTTTTGTGCTTCAAAGGACAC 680

  chr2_194812825_   4339 AATCAACAGAGTGAAGAAACGTCCTCCAGAAGATGAGAAAATATTTGCAA 4388
                         v     v i      i i  iv  iv     viv                
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_194812825_   4389 AT----TGTCTGACAAGAAATCAATAACCAGGATATATAAGGACCTCAAA 4434
                           ---- i     i   ii iivi  v    i        i  v   vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_194812825_   4435 CAACTCAATAGCGACTCCCCAAAAA-AAA-AATCTGATTCAAAAGTGAGC 4482
                                   iii ------   i -   -  i ii   ?    i  i  
  L1M4_orf2#LINE/    781 CAACTCAATAATAA------AAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_194812825_   4483 ACATGATCTGCACAGACATCTCTCAAAAGAAGGCACACCATTGGTCAACA 4532
                          v v   i  v i      i    v       ii i  v v   i   i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_194812825_   4533 GGTA 4536
                         i i 
  L1M4_orf2#LINE/    875 AGCA 878

Transitions / transversions = 2.12 (123 / 58)
Gap_init rate = 0.02 (13 / 640), avg. gap size = 2.23 (29 / 13)  

 407 30.19 10.06 2.60  chr2_194812825_194817861     4546  4853 (184)    L1M4_orf2#LINE/L1      300   630 (278)  

  chr2_194812825_   4546 ATGTAATCAATTGGAGAGTC-AGAAGTAGATTTGCACAC--ATGATAAAA 4592
                            v   vi v v       -    i  i iiiii   i--   i v  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_194812825_   4593 AAAATTTAGATAAAAGTATCAAAACAGCTTAATGAGAAGAGGA-AACATT 4641
                         vi v   v  i  ii  ii   i  vii i    i i i  i - iiv  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_194812825_   4642 TTCTAACAAATGTTGCTGGAAATACTGGGTAAAACTATG-AATCAATAAT 4690
                            -        v      i vv     i  ?vvvi   -  --  v   
  L1M4_orf2#LINE/    400 TTC-AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA--AAGAAT 446

  chr2_194812825_   4691 GAATTTCAATCCCT----TACACCAT-TA-------TAATTTGAGTTGGA 4728
                            v  vi i    ----i       -  -------   i ii iv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_194812825_   4729 AAATAGACC-AAGTGTTAATAGTTATAACCATATAACTTCTAGCATAAA- 4776
                         vv ?     -  i   -  v  i  v   i   v    ii   v v   -
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_194812825_   4777 CACAGGA--AACTATAATTGTAATCCTGGGAAAAGCAAATACTTCTTAGG 4824
                           i   ?--  v v -- i  i i i    vv i    vvii       i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_194812825_   4825 ------ACCAAA----TAAGTAATGTGATAGACAAAATA 4853
                         ------      ----i   i  ii-- v   v      
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACA--AAAGAAAAAATA 630

Transitions / transversions = 1.50 (54 / 36)
Gap_init rate = 0.05 (17 / 331), avg. gap size = 2.29 (39 / 17)  


2475 26.06 4.01 2.90  chr2_194892482_194896639.rev     2775  3672 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_194892482_   2775 TGGATAAAACATCTACTGCTCATGGATTAGAAGAATCAATATTGTCAAAA 2824
                             -  i i   ivv  i         i     v i        i  i 
  L1M4_orf2#LINE/      1 TGGA-AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_194892482_   2825 TGGCCACACTGTCCAAAGCAATCTCCTGATTTAATGCGATTCCTATCAAG 2874
                             v i   vi     vii    v v    i  i  i  i        i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_194892482_   2875 CTATATAAGTCAT-TTTTTCACAGAATTTGAAAAAAAAAACCTATTCTAA 2923
                         --  viv  iiii-     ii     v    v  i----- iv  i    
  L1M4_orf2#LINE/    100 --ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAA 142

  chr2_194892482_   2924 AATTCATA--GAAGAACAAAATTATCCA-AACAGCCTTAGCAATCTTAAG 2970
                                 --   ivi   iiv- i   -  i    vv i       i -
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGA- 190

  chr2_194892482_   2971 TAAAAAAAAAAGAAACAGCTGGAGG-CTTAC--TTC--AACCT----AC- 3010
                         -    i  i  v   -- i      -  i  --   --  ii ----  -
  L1M4_orf2#LINE/    191 -AAAAGAAGAACAAA--GTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_194892482_   3011 -ACTACAAGACTAAAGTAACTAAAACAGCATGGTATTGTGGCAAAAACAG 3059
                         -       ii   v     ii  i    ii     i  vvii  ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_194892482_   3060 ACACATAGACTAATGGAACAGGTTTGAGAATCCAGGAATAAAACCACACA 3109
                            i     ii       i  iv      i     i      v   i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_194892482_   3110 CCTACAGTCAAA-GATTTTCAACTAAGTCATCAATAACAAGCAATGAAAA 3158
                         ii  ii     v-       i  v i viii   v v  vv     iii 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_194892482_   3159 AATGATTCCCTGTTCAATAAATGATGCTTGAATAACTGGCTAGCCATACG 3208
                           vi  vvi  v     i     i    v i i      v  ?   i i 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_194892482_   3209 CAGAAGAATGAAACAGCATTCTTACATTTTACCGTATACAAAAATTAACT 3258
                           i         iiv v ii i   v ivi   i                
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_194892482_   3259 TAAAATGCATTAAAGACTTAAATGTTAGACCTTAAACTATAAAAATTCTA 3308
                         i      v  i ?    i       v   v  v           v ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_194892482_   3309 AAAGAAAACCTAGG---AAATAGTATTTTGT-ACATCAGCCTTGGCAAAG 3354
                         i        v    ---    ----i  i  -  v ii vi v     v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_194892482_   3355 A------ATATATGACTAAGTCTCCAAAAGCAATTGCAACAAAAACAAAA 3398
                         i------ v       -- ----         vvv         iv    
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGAC--A----CCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_194892482_   3399 ATTGGCAAGTGGGACTTACTTAAACTAAAAAAAGTTTCCGCACAGCAAAA 3448
                           v ii  i v      vv i   v v     --i  ii ii vv    i
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAG 675

  chr2_194892482_   3449 GAAACCATCAGCAGAGTAAATAGATAACCTACACAGTGAAAGAAAATATT 3498
                           v  i    iv i   i  v   i    i   v i  ii          
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_194892482_   3499 TGCAAGCTATGCACCC-ACAAAAGGTCTATCATCCA-AATCTATAAGGAA 3546
                              iii  ii i i- i  ii iii i -     -   v     i   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGT-ATCCAGAATATATAAAGAA 774

  chr2_194892482_   3547 CT-TAACAATACAACAAAGAAAAGA-AAA-AATCCA-TTAAAAAATGGAC 3592
                           - v    iv   i  vi      -   -  i   -  ?        i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_194892482_   3593 AATGGACATGAACAAACACTTCTCAAAAGAAGACATACCAGTGACCAA-- 3640
                           v   iv    i i   i     v        i    v i  i    --
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_194892482_   3641 --CATATAAAAAGATGCTCATTTTTACTGATTAT 3672
                         --  i  i            viv i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (154 / 77)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.07 (62 / 30)  


3061 25.20 3.41 0.34  chr2_195004568_195008082.rev     2143  3023 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195004568_   2143 TGGAAAGCCATCCCAGGTTCATAGATTGGAAGACTAGATATTGTTAAAAT 2192
                                vi      v      i            vi          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195004568_   2193 ATCCATGTGTGCCAAAGTAATCTACAGAGGCAATGTAGCATCTGTTAGAA 2242
                         iv v  iiviv     v i         vv   i i iivi  i i i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195004568_   2243 TCACAA-TGGCATTTTTACAGAAATAGGAAAA-TAATTTCTAAATTCAGA 2290
                           v  i-  v v     i       v iv  i- i  iiiv       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_195004568_   2291 TAGAATCACAAG-----CATGAATAATCAAAGAAATCTTGAGAAAGAA-- 2333
                          i   vii    -----  -     ii    iv        i      --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_195004568_   2334 -TAAAGGTGAAGGCATCACATTTCCTGATTTCAAAATATGTAACAAAGCT 2382
                         -i    v  i   vv     i    ii         iv iiv        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_195004568_   2383 ATAGTAATAAAAACAATATAGTACTGGCA-AAGAACAGACATACAGACCA 2431
                          i      v  i   i i i         -   i i       i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_195004568_   2432 GTGAAACAGAATACAAAACACAGAAATAAATCCATGCATATATGGCCAAT 2481
                         i  i  i     vv i iiv          i    i   v     i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_195004568_   2482 -GATTTTTAAC--GGG-GCTAATGGAATATACGATGGAAAAATGATTGTT 2527
                         -      ii  --   -  i  --  vi  v i    ii   vi  v  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAA--GACCATTCAATGGGGAAAGAATAGTC 397

  chr2_195004568_   2528 TCTTCAACAAATGATTATGATAAAACT--ATATCTCTATGCAAAACTATG 2575
                          i           i vv  iv v    --   ? ivi        vv   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_195004568_   2576 AAATTGCACCTCTGTCTTATAGCATATGCAAGTATTAATTCAAAATGGAT 2625
                           i   v   i  ii  i i v     i   iv     i           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_195004568_   2626 TA--GACTTAAACACAAAACCTGCACCTGTACAAAGACTAGAAGAAAATA 2673
                         i --   i    iii  i v  iv v  i  v  vvvi          i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_195004568_   2674 TAGAGGAAAACCTTCATGACATTGGCCTTGGCAATTATTTTATTGCTATG 2723
                            i? v   i    i    v    vi v      vi   iv v v    
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_195004568_   2724 ACACCAAAAGCACAGACAACAAAACCAAAAATAAACAAGTAAAACTATAT 2773
                                       ii        vv       i i  i vii   vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_195004568_   2774 -GAAACTAAAAAGCTCTGCACAGCAAAAGAAAC-----AGAA--TGAAAA 2815
                         -i   i      vi i  ii vv    i  v  -----    --      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_195004568_   2816 GGGAACCTACAGATGGGGAGAAAACATTTGTAAACCATTTATTTGATAAG 2865
                          iv    i     vv         i     i   i   v   i       
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_195004568_   2866 GAGTTAATCTTCAAAAAATATAAGAAACTCTTACAACTGAAAAACAAATA 2915
                          iii vi v i  i  v      ii             v  v  i   v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_195004568_   2916 -ACAAATAACCTAATTTAAAAATAGTTTAATGACTTGAATAGACATTTGT 2964
                         -          i    ?      i viv  v  i              v 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_195004568_   2965 C-AAAGAAGATATACAAATGGCTTATAGATATATGAAAA-ATGTTCAACA 3012
                          -                    iv   iii i       -   i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_195004568_   3013 TCATTAATCAT 3023
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.67 (137 / 82)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.83 (33 / 18)  


3232 26.99 0.88 0.44  chr2_195080571_195084838     2873  3776 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195080571_   2873 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2922
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195080571_   2923 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGCCGTCCCCATCAAGC 2972
                            v     v i   iv i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195080571_   2973 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3020
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_195080571_   3021 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 3070
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_195080571_   3071 AACAAAGCTGGAGGCATCACGCCACCTGACTTCAAACTATACTACAAGGC 3120
                                i      vv    i iv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_195080571_   3121 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 3170
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_195080571_   3171 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3218
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_195080571_   3219 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3268
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_195080571_   3269 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 3318
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_195080571_   3319 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3368
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_195080571_   3369 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3418
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_195080571_   3419 CTAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAA 3468
                         v    ?i v viv   iv   v v  vv i i   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_195080571_   3469 AACACCAAAAGCAATGGCAAGAAAAGCCAAAATTGACAAATGGGATCTAA 3518
                         i            vvi    v     vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_195080571_   3519 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3568
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_195080571_   3569 AGGCAACCTACAGAATGGGAGAAAATTTTCACAACCTACTTATCTGACAA 3618
                           i     i                 v  ii   vii iv       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_195080571_   3619 AGGGCTAATATCCAGAATCTACAATGAACTTAAACAAATTTACAAGAAAA 3668
                         i  i  vi          v  i  v     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_195080571_   3669 AAACAA----CCCCATCAAAAAGCGGGCAAAGGATATGAACAGACACTTC 3714
                          i    ----   v  i?    ii           v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_195080571_   3715 TCAAAAGAAGACATTTATACAGCCAAAAGACACACGAAAAAATGCTCATC 3764
                           v        i  vi v ii     v ii    i     i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_195080571_   3765 ATCACTGGCCAT 3776
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2995 27.78 1.33 0.44  chr2_195151087_195153743     1266  2165 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195151087_   1266 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1315
                               i i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195151087_   1316 GGCCATACCGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 1365
                            v    iv     iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195151087_   1366 TACCAATGACTTTCTTCACAGAATTAGAGAAAACT-ACTTTAAAATTCAT 1414
                          v   iivi i  i  ii     v v  v  i-  - iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_195151087_   1415 ATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGA 1464
                               viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_195151087_   1465 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATTACAAGGCT 1514
                               i      vv   ii  v  ii i      viv  i     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_195151087_   1515 ACAGTAACCAAAACAGCATGGTACCGGTACCAAAACAGAGATATAGACCA 1564
                                i   i    ii      i  i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_195151087_   1565 ATGGAACAGACC--AGAGCCCTCAGAAATAATGTTGCATATCTACAACCA 1612
                               i   vi--    i  --        vviiii i  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_195151087_   1613 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGCAAAATGATTCCC 1662
                         vi    i  i     ivv  v   i v  vvv     vi   vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_195151087_   1663 TATTTAATAAATGGTGCTGGGAAAACTGGAGAGCCATAGGCAGAAAGCTG 1712
                          v  i  i              v       v ?   i v   i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_195151087_   1713 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTTATTCAAGATGGAT 1762
                           ii    i    v   i     v            v i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_195151087_   1763 TAAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1812
                         i ?    i     i v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_195151087_   1813 TAGGCA-ATACCATTCAGGACATGGGCATGGGCAGGGACTTCATGTCTAA 1861
                             ?i- v i -   iv   v v  vv i    iv ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_195151087_   1862 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAAAAATGGGATGTAA 1911
                         i            vvi          vv     v  v    v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_195151087_   1912 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1961
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_195151087_   1962 AGGCAACCCACAGAATGGGAGAAAAATTTTGCAATCTACTCATCTGACAA 2011
                           i                      vv       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_195151087_   2012 AGGGCTAATAACCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2061
                         i  i  vi  v       v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_195151087_   2062 A---AAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 2108
                          ---   i     v  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_195151087_   2109 TCAAAAGAAGACAT-----TTATCAAAAGACACATGAAAAAGTGCTCATC 2153
                           v        i  ----- vii   v ii          ii      v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_195151087_   2154 ATCACTGGCCAT 2165
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (143 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


1918 26.98 2.22 0.79  chr2_195213489_195215103      494  1123 (492)    L1M4_orf2#LINE/L1      270   908 (0)  

  chr2_195213489_    494 GTACTGG--TAACAAAACATATATAGACCAGTGGAACAGAA--GAGAGGC 539
                                --   vi v v i       i  i     i    --     v 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_195213489_    540 CTCAGAAATAACACCACACATCTACAACCATCTCATCTTCAAAAAACCTG 589
                          --        vv   i    i  iiii  vi v  i   i v  ivv  
  L1M4_orf2#LINE/    320 C--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_195213489_    590 ACAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAGTAAATGGTGCTGG 639
                         v   i v  vv            i  vvi  v  i ii            
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_195213489_    640 GAAAACTGGCTAGCCATATGCGGCAAACTGAAACTGGACCCCTTCGTTAT 689
                           v      v  ?   i    iiv i v    ii         v v i i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_195213489_    690 ACCTTATACAAAAATTAACTCAAGATGGATTAAAGACTTAAATATAAGAC 739
                            v                   i      i ?    i     i     v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_195213489_    740 CTAAAAGCATAAAAACCCTAGAATAAAGCCTAGGC---AATGCCATTCAG 786
                               vi      vi i     v   i v    ?---   -- -   iv
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGT 564

  chr2_195213489_    787 GACACAGGCATGGGAACAGACATCATGACTAAAACACCAAAAACAATGGC 836
                            viv  vv i  v vv iiv  v iiv  vi         i  vvi  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_195213489_    837 AACAAAAGCCAAAATTGACAAATAGAATCTAATTAAACTAAAGAGCTTCT 886
                                 vv     v  i    v i ii v  i   v v  i i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_195213489_    887 GCACAGCAAAAGAAACTATCATCAAAGTGAACAGGCAACCTACAGAATGG 936
                          ii vv    i  v       vv        v  i     i         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_195213489_    937 GAGAAAATTTTTGAAAGCTATCCATCTGGCAAAGGTCTAATTTCCAGAAT 986
                                 v    v  iii  vi     ii  i  v  vi v        
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_195213489_    987 CTATAAGGAACTTAAACAAATTTACAA--GAAAGA-----AACCCCATCA 1029
                         v     i     ivv    v iv i  --i     -----     v  i?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_195213489_   1030 AAAAGTGGGCAAAGAATATGAACAGATACTTCTCAAAATAAGACATTTAT 1079
                             i         i  v    i   i i     v   v    i  vi v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_195213489_   1080 ACCGCCAACAGAAATATGAAAAAATATTCATCATCACTGGTCAT 1123
                          iv     i iiv i       i  ii   v     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (89 / 77)
Gap_init rate = 0.01 (8 / 639), avg. gap size = 2.38 (19 / 8)  


 434 30.59 9.02 4.97  chr2_195282079_195283835.rev      501  1265 (492)    L1M4_orf2#LINE/L1      113   908 (0)  

  chr2_195282079_    501 TTTTTGTGGAAATCAACAAAGCTGATTTAAAAATTTACACAAAAATTAAA 550
                               ii     ii    -      iiv      i i iii    vv  
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_195282079_    551 ATGGTCAAGAAGAAACATA-CA--CTTCAA------GATTTGAATTATGG 591
                         iv ii v    v iv  v -  --   v  ------  vivi i  ivi 
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_195282079_    592 G--TCACACTTTTACAGATTTCAAAGCTTACATTTAAGAATCTA---TAA 636
                          --        ii-  -        i     ---  vi  v   ---   
  L1M4_orf2#LINE/    212 GACTCACACTTCC-CA-ATTTCAAAACTTAC---TACAAAGCTACAGTAA 256

  chr2_195282079_    637 TTGTGGGAATATAATATTGGTACACAGATAAACAAAAAGGCCAATAAAA- 685
                          iiv iv i i ii  i   i i vi    i   v v  ii    ii  -
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_195282079_    686 AATATCGAGATGCTAGAAAGAGACCCGTATGCACAAGACCACTTAATTTA 735
                          iv  i    vv i     v i    i  iiivi v ii  v  i    v
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_195282079_    736 GAACAAAGGAGTAATATAGACCA--------GTAAAGAAAGGTCTATTTG 777
                         vi    i  v iv ---      -------- v      vi    v  ii
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCA---AGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_195282079_    778 TTAACTATTTCTTGGGTGCATCACTAGCGATATAGAAAATA-TAAA-TCA 825
                         vi  v iv v  v  iiivv viv  ? v i  iv    v - i  - ii
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_195282079_    826 CATCATTA--TTATACAATATACAAAAATCAATTCTTAAAGG-TTAT-GA 871
                         v i vi  -- i i  v            i  i  vv  v  - i ?-  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_195282079_    872 ---AAATATTATAGATAAAATAATATGATTTCTAGACTATATTAAAGAAG 918
                         ---    i v v  v     iv   vi i ii    vv v vi v  i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_195282079_    919 ATATTTTTCCTGA---TAACATAGACAA-GATTTTTTAAAATATTAGTTT 964
                         vv v i   v   --- iivv   i   - i   i   i -   v vvii
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACC 602

  chr2_195282079_    965 AAAA-----AACATTAAATATATAGACAATTTTTGACTAATTGGGCTTC- 1008
                             ----- i  vi   --- v i v   v---  iv      i    -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAA---AGAAAAAATA---GATAAATTGGACTTCA 646

  chr2_195282079_   1009 CCAAAATTTAGGAACTTCTTT-TTATAAAAATACCACATTA-CATGAGAA 1056
                         i       - ii     i v -i vi   ii----   i  -  --    
  L1M4_orf2#LINE/    647 TCAAAATT-AAAAACTTTTGTGCTTCAAAGG----ACACTATCA--AGAA 689

  chr2_195282079_   1057 A---AAAAGAGAGCC---AGAA---GAGATAAT--TAGACAATTAAATAT 1095
                          ---      v i  ---    ---    v   -- v vv   i v    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_195282079_   1096 ATAATTTCCTTAATAAATTTCTAAATC---AATG-ATAAAACAC----AC 1137
                         v i  ------  vii i  v  --  ---   i-     iv  ----  
  L1M4_orf2#LINE/    740 CTGAT------AAGGGACTTGTA--TCCAGAATATATAAAGAACTCTTAC 781

  chr2_195282079_   1138 AAGCCAAAAA-AAAAAAAAAAATAGGCAAA---GAAGATGGAAGGAGCCA 1183
                           vi   v  -     i v     iv v  ---i  i    i------  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG------CA 825

  chr2_195282079_   1184 GAGAAGTGGACTA-ACACTTCAGAAAAGATGGTATA-AAATTGCATGATA 1231
                         i  i v v  v  -   i   vvv     v i    -    v  -ii   
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC-CAATA 874

  chr2_195282079_   1232 AGCACATGTGAAATTGCTCAACATCATTTGGAAC 1265
                                 vi  iv            ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (129 / 102)
Gap_init rate = 0.06 (45 / 796), avg. gap size = 2.38 (107 / 45)  


2904 20.70 10.94 0.91  chr2_195290346_195292409.rev      807  1574 (490)    L1M4_orf2#LINE/L1       64   908 (0)  

  chr2_195290346_    807 AAATTTTTCTATAGGTTTAATTTTATTTTTATCAAAAGCTCAACTTTCAT 856
                              vv    i  i  i  iviv  iii        v i  i  vi - 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-T 112

  chr2_195290346_    857 CTTTTGCAGAAATAGACAAGCTAATCCTAAAATTAATATTGAAATAAATG 906
                         i            v        i           v    v     ---- 
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT----G 158

  chr2_195290346_    907 CAAGGGACTTAGAA-AGCCCAAAGCAGTATTGAAAAAGAA---CAAATTT 952
                                 ii    -    -   i  i v           ---    v  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCC-AAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_195290346_    953 GGAAGGCTCACACTTACAGATTTAAAAATTTACTGCACAGGTACAGTAAA 1002
                            i i         v vi    v    i     i  v  v        v
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_195290346_   1003 AAAGACA------TACTG--------ATAGATGCATAGATCAATAGAATA 1038
                         v      ------     --------     iii          i     
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_195290346_   1039 CAATTGAAAATCCAAAAATTAACCCAAACATCTTTAATCAATTGCTTTCT 1088
                         v      i i    i    v      v    i v ii       v   ii
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_195290346_   1089 GACAAGAGTGCTAAAGCCATTCAATGGGAAAAGAGTTGTCTTTTTAACAA 1138
                               i    i  ii            i     i v       i     
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_195290346_   1139 ATGGTGCTGGAACATTTGGATAGCCATATGCAAAAGAATACATTT----- 1183
                                   i   vi      ?   i            iv v  -----
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_195290346_   1184 TTTATTTTCACACCATATACAAAAATGAACTCAAAATTGATCAAAGAACT 1233
                         ii  ii -                  v          v     ?   v  
  L1M4_orf2#LINE/    458 CCTACCT-CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_195290346_   1234 AGATGTATCAGTTAATACTATAAAACT--TAAAGAACAACACAGGATTTC 1281
                          i     vv  i   v           --  i ii v    i   ?v vv
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_195290346_   1282 ATATTTATGACTTT--------------------AGATATAATGCCAAAA 1311
                           v  ii    i  --------------------      i ii      
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_195290346_   1312 GCACAAG--------AAAAAAATAGA---ATT------CATCAACATTAA 1344
                                --------i          ---   ------      v     
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_195290346_   1345 AAGATT--GAACTGCAAACCACATCACCTAGAAAGTGAAAACACAGCCCA 1392
                           iv  -- vi  v    vv   ii i v            v   i    
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_195290346_   1393 CAGAATGGGAGACAGTATTTTTAGATTATATATCAAAAAAGAAATTTGTA 1442
                                     v i     vi i  i       vi v   ii i     
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_195290346_   1443 TCCATTATATATATACAATCTTTACAGCTCAAT----------------- 1475
                             vv       v v  iii     i      -----------------
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_195290346_   1476 TTTTTTTAAAGTTTAGACAGAGGATCTGAACAGATATTTCTCCAAAAA-- 1523
                         iiivv  ?  ivv i i  i     i    i   i           i --
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_195290346_   1524 -TATACAAATAGCCAATAAACATATGAAAAGATGCTCAGCATTGTTAGCC 1572
                         -         i        i  i               i   ii??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_195290346_   1573 AT 1574
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.67 (97 / 58)
Gap_init rate = 0.02 (17 / 845), avg. gap size = 5.35 (91 / 17)  


1619 26.40 5.28 0.99  chr2_195326688_195334888     1077  1682 (6519)    L1M4_orf2#LINE/L1      277   908 (0)  

  chr2_195326688_   1077 CACAAAAAAAGACATATAGACTAATGGAACTGAATAGAAAACTCAGAAAT 1126
                           i  ii v           ii       iv    v  i iii       
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_195326688_   1127 AAAGCCTCACACCTACAATCGTCTGATCTTAAACAAAGAGAATGAAAGCA 1176
                            v  vi   ii  iii  ivi    i  vi    i ivivii i v  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_195326688_   1177 AGCAATAGTGTAAGGAC--TCTATTTAATAAATGGTTCTGGAATAACTGG 1224
                         vv    i v v   i i--   v  i  i       v    i i      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_195326688_   1225 CTAGCCATAAGCAGATAAATAAAACTAGACACTTACCTTTCATCAT-TAC 1273
                         v  ?   i v   i vi   i  ii i   v i     iv  i   -   
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_195326688_   1274 AAGCATTAACTCAAGATGGATTA-AAATGTAAATGAAAGACCCCAAACAA 1322
                           iv          i      i - i iv      v    v iv    v 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_195326688_   1323 TTAAAATCCTAGAAGAAAACAT---TGAAAATGCCCTCTCAACATTGGCC 1369
                          v   v  i             ---? v    -- i  vii  v    vi
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGT 574

  chr2_195326688_   1370 TTGGCAAAGAATTTCT--GACTAAGTCCCCGAAAGCAATTGCAA-AAAAA 1416
                          v     v i-     --  -  v v v  i      vvv    -    i
  L1M4_orf2#LINE/    575 TAGGCAATGG-TTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_195326688_   1417 CAAAAATTGAGAAGGGGAACCTAATTAAACTAAAAAGCTTCTCCACAGCA 1466
                         v      v  v  ivv i  i v  i   v v    i   i vii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_195326688_   1467 AGATAAACTATCAGCAGAGTAAACAGACAACCTACAGAATGTGATAAAAT 1516
                          iiv v       iv i   i  v        i        v  v     
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_195326688_   1517 ACTCACAAAT------------AGAGGCCTAATATCCAGAATCTACAGGG 1554
                          i ii     ------------ ii  v  vi          v  i ii 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_195326688_   1555 AACTTAAACAAATCAACAAGCCAAAAAG-CAA-TAACCCC-TTTAAAAAT 1601
                             ivv    v    i  --i      -   -      v-  ?      
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAA--TAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_195326688_   1602 GGGCAAAGGACATGAATAGACACTTCTC---AAAAGACGTGCAAATGGCC 1648
                                   iv          i     --- i    ii i         
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_195326688_   1649 AA-AA---CATGAAAAAATGTTCAACATCACTAATCAT 1682
                           -  ---        i   i         ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (91 / 66)
Gap_init rate = 0.03 (17 / 632), avg. gap size = 2.24 (38 / 17)  

3001 25.03 3.62 0.79  chr2_195326688_195334888     6827  7709 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195326688_   6827 TGTAAGAACATTCCATGTTCATGGATAGGAAGAATCAGTATCGTGAAAAT 6876
                           v  ii i  i              v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195326688_   6877 GGCCATACTGCCCAAGGTAATTTATAGATTCAACGCCATCCCCATCAAGC 6926
                            v     v     iv i  i  i           v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195326688_   6927 TACCAACGACTTTCTTCACAGAA-TTGGAAAAAACT-ACGTTAAAATTCA 6974
                          v   i vi i  i  ii     -   -- v  i  - ivi         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_195326688_   6975 TATGGACCAA---AAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCAAGA 7021
                               --  ---  ii  v  v v  v     iv     i i iv    
  L1M4_orf2#LINE/    149 TATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_195326688_   7022 AGAACAAAGCTGGGGCA-TCACGCTACCTGACTTCAAGCTATACTACAA- 7069
                                  i   i v -    i  v  ii i     iviv        -
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_195326688_   7070 GCTACCATAACCAAAACAG--------------------AGACACA--GA 7097
                              vi   i   i    --------------------     i --  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_195326688_   7098 ACAATGGAACAGAACACAGGCCTCAGAAATAACAGCATACATCTACAACC 7147
                         v        i    ivv  ivii         vvv       i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_195326688_   7148 ACCTGATCTTTGACAAACCTGACAAAAACAAGAGATGGGGAAAGGATTCC 7197
                          vi    i  i     ivv  v   i v  vvvi          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_195326688_   7198 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 7247
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_195326688_   7248 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 7297
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_195326688_   7298 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 7347
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_195326688_   7348 CTAGGCA-ATACCATTCAGGACATAGGCATTAG-CAAGGACTTCAT-GAT 7394
                         v    ?i- v i -   iv   v v  -i    -   v ii   v -   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGAT 594

  chr2_195326688_   7395 CAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATCGACAAATGGTATC 7444
                         - vi            vvi          vv     v  i    v v ii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_195326688_   7445 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATGATCAAAGTG 7494
                          v  i   v v  i i   i  ii vv    i  v     v vv      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_195326688_   7495 AACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTATCCATATGA 7544
                           v  i     i                 v   i   vii  vi  v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_195326688_   7545 CAAAGGGCTAATATCCAGAATCTTCAAAGAACTTAAACAAATTTAAAAGA 7594
                         i  i  i  vi          v vi        ivv    v iv v  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_195326688_   7595 AAAAATCAAACAACCCCATCAAAAAGTGGACAAAGGATATGAATAGACAC 7644
                             iv    i     v  i?    i   i        v          i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_195326688_   7645 TTCTCAAAAGAAGACATTTAAGCAGCCAACAGACACATGAAAAAATGCTC 7694
                              v        i  vi  iii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_195326688_   7695 ATCATCACTGGTCAT 7709
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (123 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.60 (39 / 15)  


 848 30.18 2.07 1.78  chr2_195367018_195369305      615   952 (1336)    L1M4_orf2#LINE/L1        5   343 (565)  

  chr2_195367018_    615 AGGATATACAATGGTCATTAACTAGAAGA--TAATATTGTTAAAATTTTC 662
                          i     v v   v    vi i i     --            i  vvi-
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC- 53

  chr2_195367018_    663 TAATTCTCCCCAAAGTAATATATACATTCAATAAAA-CCTAATCAAAATC 711
                         -   v         v i  v  i v      iiv  -  iv         
  L1M4_orf2#LINE/     54 -AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_195367018_    712 CTA-CAAACTTCTATTTAGAAATTGAGATGTTGATTTTTTAAGTTCCATA 760
                          i - viv   i v vi         v v i    ii --  iv i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCATA 150

  chr2_195367018_    761 TGGAAAAGTGAAAGACCTAGAATAAACAAATTAACTTTAAGAAATAA--- 807
                               v ii ii    i      iv    vi  ii  i i   v  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_195367018_    808 TACGTTTAGTGAATTTGCACTACCTGATTTTAAGGCTTACTATAAAGTTA 857
                         i viv  i v i i ii    v  ii    i  ii       i    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_195367018_    858 TAGCAATCAACACAGTCTGAAATTAAAATCAGAATAGATACATAGGTAAA 907
                         i  i      v     v  iv i iiv  v  i     i i    i v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_195367018_    908 CACTGCAAAATGGAGAATCCAGAAATAGACAAGCAAATATATATG 952
                         iivvii i   v    i          i  v--  v i  v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATG 343

Transitions / transversions = 1.62 (63 / 39)
Gap_init rate = 0.02 (7 / 339), avg. gap size = 1.86 (13 / 7)  

1491 26.34 5.71 1.29  chr2_195367018_195369305     1263  1805 (483)    L1M4_orf2#LINE/L1      342   908 (0)  

  chr2_195367018_   1263 TGGCCAAATTTATTTTTTATATAGGTGCAAAGGTAATTCAATAGAGAAAA 1312
                            i   -  v     iv i vi     v   iiv       i i    i
  L1M4_orf2#LINE/    342 TGGTCAA-TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_195367018_   1313 GAGAACCC--------AGTGGTGCTATAACAATTAAACAACCATATGCAA 1354
                         i v ii i-------- i       ivi    i ii i ?   i      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_195367018_   1355 AAA-------TTGAATCCCTTACTTCACATCATAGACAGAAATTAACCAG 1397
                           i-------   i i    -  i     i    v   i        ivi
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCA 489

  chr2_195367018_   1398 AAATGGAACATA-ACCTACATTTCTGAGCCACTTCTACAAAGCTACTAGA 1446
                                v  ? -     v  v vv    i vvv   i   i  vi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_195367018_   1447 AGAAAACATAGGATAAAATCCTTGTAACCTACAGTCAAGCATAAATTTCT 1496
                                     ?vv     i i  i    vvi  i i   vvii     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_195367018_   1497 TAGATAAGGTA--AAAAGCACAAACA-TAAAAGAAAAAA---ATGAAATA 1540
                               v ii --          i  -i           ---  i  v i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_195367018_   1541 AACTTTATCAAAACCTAAAGGCT---GCTCTTCAAAAGACACTACTAAGA 1587
                         i    i       i-    ii  --- iv       i       ii    
  L1M4_orf2#LINE/    640 GACTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_195367018_   1588 AAATAAAAAGACGAATTATAGACTTGGAAGCAATATTTGAATAACACTTG 1637
                           i i       i vii i   v v   iiv        v v v  iv i
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_195367018_   1638 CATGATAAAG-ACTTTCATTCAGAAATTATAAACTACTCTTAAAATTCAA 1686
                         iv      i -    vi  i     vv      vv       v  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_195367018_   1687 CAATAAAAA-ACAAACATTCCAATTAATAAATTGCCAAAAGATTTGAA-- 1733
                         i        -     i vi      ? v    v v    i        --
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_195367018_   1734 --CACTTTATCAAAGAAACTATATTGTTAGCAAATAAGACTATGAGAAGA 1781
                         --  i  ivi       iv    iviv i  v      vvi    i    
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_195367018_   1782 TTCTCAAAAAGCATTAATCTTTAG 1805
                          v     ----   i ????????
  L1M4_orf2#LINE/    889 TGCTCAA----CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (85 / 54)
Gap_init rate = 0.02 (14 / 567), avg. gap size = 2.71 (38 / 14)  


1715 27.03 5.54 3.38  chr2_195489572_195491303.rev      501  1240 (492)    L1M4_orf2#LINE/L1      153   908 (0)  

  chr2_195489572_    501 GAAATAATCAAAGGAATTGGAATAGGTAAAACAATGG-GAAAAGGCAGAA 549
                              i--   i   viii      vi        vv-     i v    
  L1M4_orf2#LINE/    153 GAAATG--CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_195489572_    550 TGAAGTGGGAGGAAT-GCATCTTCTGATTCCAAAAGTCATTATGTAGCTA 598
                         ii    v      v -i  ii i ii   i     v i i  iiv     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_195489572_    599 CAGTGATCAAGACTATGTTATATTGGAA-AAGTGATAGACAC-----TTA 642
                             i        vi   vi  i   v -   -        i----- i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATATAGATCA 299

  chr2_195489572_    643 ATAAAACAAGCTAGAAAACACAGAATTATACAAATATGAGTATATTTGTA 692
                           ii  i iiv v  i iiv     v  v  vv   i------    -- 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC------ATTT--A 341

  chr2_195489572_    693 TGCCCAACTTATTTTTGACAAAGGT-CAAAAGTAATTCAATGGAGAGAAG 741
                           vi   i v     i     i   - v  iiiv         i  i ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_195489572_    742 ATAGACTTTTTAACAAATAATGCTGTAGCAATTGGACATCAATAGAAAAA 791
                             v     i       ii     vii   i    i ? v i viv   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_195489572_    792 CAAATAAGCTTCAATGTAAGTCTGATACCTTATGCAAAAATTAAATCACA 841
                         vi   i iv  vi ivivvii  v i   v   i          v   v 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_195489572_    842 ATATGTCATGGACTTAAAATG-AAGA---AA---TATAAA-CATTTAGAA 883
                           ivi   ?i   i    -  -    ---  ---      - vi      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_195489572_    884 AAAAACAATATGGGAGAAAATCTTCAGGATCTAGGACTAGGCAAATAGTT 933
                         i      --- i  ? v        iv  i  v  ii       - i   
  L1M4_orf2#LINE/    541 GAAAACA---TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTT 586

  chr2_195489572_    934 -CTTAGTTTTTTTTTTTTTTTTTTAAAAAGCACGATTTTCTTG-GAAAAA 981
                         -     v v vvivii---------        i vivv vvi-      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACC---------AAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_195489572_    982 AT-GATAACTTTGATCCAACTAAAATTTAAAACTATTGCTCTATGAAATA 1030
                           -     v  v  iiiv ii      v      v   iv  vii  iv 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_195489572_   1031 CCCTGTTAAGAGATTGGAAAGACAAGCTACATACAGGGAGAAAATA---- 1076
                          v  i i    i v  i        v i   v vv           ----
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_195489572_   1077 --------ATGTGGAACAAAGGACTAGTATCTAGAATATATAAAGAACTC 1118
                         --------  i vvi i  i     v     i                  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_195489572_   1119 TCAGAATT-------AAAAAGTTAAA--ATCCAGTCAAAACATGAACAAA 1159
                          i v  i -------      vi   -- i   i i?   v   ii    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_195489572_   1160 AGACATGAAGAGAGATTTCACATATGAAGATATATAAATGGCAAATAAGC 1209
                         i  iv    v   v     v vv v         i       v       
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_195489572_   1210 ACATGAAATGATGTTCAACATCATTTAACTA 1240
                                 v    i         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (114 / 82)
Gap_init rate = 0.03 (23 / 756), avg. gap size = 2.87 (66 / 23)  


3164 26.76 0.77 0.77  chr2_195525071_195526685.rev      216  1123 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195525071_    216 TGGAAGAACATTCCATGTTCATGGGTGGGAAGAATCAATATCATGAAAAT 265
                              ii i  i            i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195525071_    266 GGCCATACTTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 315
                            v     i     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195525071_    316 TACCAATGACTTTCTTCACAGCA-TTGGAAAAAACT-ACTTTAAAGTTCA 363
                          v   iivi i  i  ii   v -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_195525071_    364 TATGGAACCAAAAAATAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 413
                                viiv  iiv v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_195525071_    414 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 463
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_195525071_    464 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 513
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_195525071_    514 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGGCGCATATCTACAACT 561
                                i    i--    i  --        vvv ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_195525071_    562 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 611
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_195525071_    612 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 661
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_195525071_    662 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 711
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_195525071_    712 TTAAAGATTTAAACGTTAGACCTAAAACCATAAATACCCT-AGAAGAAAA 760
                          i ?   ii    i  v   v       i     -  i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chr2_195525071_    761 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 809
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_195525071_    810 AAAACACCAAAAGCAATGGCATCAAAAGCCAAAATTGACAAATGGGATCT 859
                          vi            vvi   v      vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_195525071_    860 -ATTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 908
                         -  iv   i    i -   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_195525071_    909 AACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGA 958
                           v  i     i                 v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_195525071_    959 CAAAGGGCTAATATCAAGAATCTACAATGAACTCAAACAAATTCACAAGA 1008
                         i  i  i  vi    v     v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_195525071_   1009 AAAAAACAAACAACGCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 1058
                             i     i   v v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_195525071_   1059 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 1108
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_195525071_   1109 ACCATCACTGACCAT 1123
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3202 26.93 0.77 0.55  chr2_195541040_195545410.rev     2974  3879 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195541040_   2974 TGGAAGAACATTCCAAGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3023
                              ii i  i   v i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195541040_   3024 GGCCATACTGCCCAAGGTAATTTATAGAATCAATGCCGTCCCCGTCAAGC 3073
                            v     v     iv i  i  i   v    i  vi    ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195541040_   3074 TACCAATGACTTTCTTCACAGAATTGGAAAAA--AAT--TAAAGTTCATA 3119
                          v   iivi i  i  ii     v v  v  i--i  --    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_195541040_   3120 TGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGAA 3169
                              viiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_195541040_   3170 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 3219
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_195541040_   3220 CAGTAACCAAAACAGCATGGTACTGGCTCCAAAACAGAGATATAGACCAA 3269
                               i   i    ii          viv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_195541040_   3270 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAGCCAT 3317
                              i    i--    i  --        vv   i    i  ii i  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_195541040_   3318 CTGATCTTTGACAAACCTGACAAACACAAGAAATGGGGAAAGGATTCCCT 3367
                         i    i  i     ivv  v   ivv  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_195541040_   3368 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3417
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_195541040_   3418 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3467
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_195541040_   3468 AAAGACTTAAAGGTTAGACCTAAAACCATAAAATCCCTAGAAGAAAACCT 3517
                          ?    i    v  v   v       i      ii i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_195541040_   3518 AGGCA-ATACCATTCAGGACGTAGGCATAGGCAAGGACTTCATGACTAAA 3566
                            ?i- v i -   iv   v v  vv       v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_195541040_   3567 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCCAAT 3616
                                     vvi          vv     v  i    v   iiiv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_195541040_   3617 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAACA 3666
                         i   v v  i i   i  ii vv    i  v    i  vv i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_195541040_   3667 GGCAACCTACAGAATGGGAGAAATTTTTTATAATCTACCCATCTGACAAA 3716
                          i     i               v v   ii  vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_195541040_   3717 GGGCTAATATTCAGAATCTACAAAGGACTTAAACAGATTTACAAAAAAAA 3766
                           i  vi   i      v  i    i   ivv   iv iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_195541040_   3767 AAATCCAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 3816
                         i -- v  i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    798 GA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_195541040_   3817 CTCAAAAGAAGACATGTATGCAGCCAACAGACACATGAAAAAATGCTCAT 3866
                            v        i  ii viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_195541040_   3867 CATCACTGTTCAT 3879
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2604 28.36 1.96 0.24  chr2_195575651_195577446      487  1304 (492)    L1M4_orf2#LINE/L1       77   908 (0)  

  chr2_195575651_    487 GATTTA---TAATTCTT--CAAGCTACCATTGACTTTCTTCACAGAATTG 531
                             i ---i   i i --   iv v   vivi i  i  ii     v v
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

  chr2_195575651_    532 GAAAAACCTACTTTAAATTTCATATGGAACCAAAAAAGAGCCCGTATAGC 581
                           v  i iv iii    v           viiv  ii  v  v v     
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr2_195575651_    582 CAAGACAATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCACGCTACCTG 631
                            i      i i iv  i          i      vv    i  v  ii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_195575651_    632 ACTTCAAACTATACTACAAGGCTAAAGTAACAAAAACAGCATGGTACTGG 681
                          i      viv        i    v     iv  i    ii         
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_195575651_    682 TACTAAAAGAGATATATAGACCAATGGAACAGAACAGAGGCCTCAGAAAT 731
                         i iv ii v   i       i        i    iv   ivii       
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_195575651_    732 AACACCACACATCTACAACCGTCTGATCTTTGATAAACCCGACAATAACC 781
                           vv   i    i  iiii ivi    i  i  i  ivvi v   -i   
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACC 375

  chr2_195575651_    782 AG-CAATGGAGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAATCTG 830
                          v-      i     i  vvi  v  i  i              v v   
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_195575651_    831 GCTATCTATATGCAGAAAGCTGAAACTGGACCCCTTCCTTACACCTTATA 880
                          v  ? i i     i  iiv    ii         v   i     v    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_195575651_    881 CAAAAATTAATTTAAGATGGATTAAAGACTTAAACGTAAAACCTAAAACC 930
                                   i i  i      i ?    i    i    i v       i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_195575651_    931 ATAAAAACCCTAGAAGAAACC-TAGGCA-ATATCATTCAGGACATAGACA 978
                               vi i         v -    ?i- v   -   iv   v v ivv
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT 574

  chr2_195575651_    979 TGGGCAAAGACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGTC 1028
                          i     v ii   v iiv  vi            vvi          vv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_195575651_   1029 AAAATTGACAAATGGGATCTAACTAAACTAAAGAGCTTCCACAAAGCAAA 1078
                              v  i    v   ii v ii   v v  i i   iiiiivvv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_195575651_   1079 AGAAACTATCATCAGTGTGAATAGGCAACCTACAGAATGGGAGAAAATTG 1128
                         i  v       vv iv     v  i     i                 vv
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_195575651_   1129 TTGCAATCTCTCCATCTCACAAAGGGCTAATATCTGGAATCTACAAGGAA 1178
                               viiv vi    v i  i  i  vi    ii    v  i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_195575651_   1179 CTT----AAATAAAT--TAACAAGAAAAAAAACC--ATCAAAAAGTGGCT 1220
                           i----  v v   --   v    v   v    --  i?    i   vi
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_195575651_   1221 GAAAGATATGAATAGATACTTCTCAAAAGAAGACATTTATGTGGCCAACA 1270
                         i  i   v        i i     v        i  vi vi       i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_195575651_   1271 AACATATGAAAAAAAGCTCATCATCACTGGTGAT 1304
                          i  i       i v     v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (136 / 92)
Gap_init rate = 0.01 (10 / 832), avg. gap size = 1.80 (18 / 10)  


1501 23.70 5.81 8.01  chr2_195676135_195677774      512  1148 (492)    L1M4_orf2#LINE/L1      286   908 (0)  

  chr2_195676135_    512 AGATATATC-ATCAATGAAACATAATAGAGAACCCAAATATAAAGCCACA 560
                            i    v-       i  i v   v    ii   i v     v   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_195676135_    561 TGCCTGCAACCAATTGATCATTGACAAAGTCAACAAAAATAAACAATGGT 610
                         iiii iiiii        iv i     i viiv   i vi vv      v
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_195676135_    611 GAAAAAACACCATATTTGATAAATGGTGCTGGGAAAATTGACTAGCCATA 660
                             i  i viv v  ii i              v  i  iv  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_195676135_    661 TGTAGAAGAATGAAACTGGACTCCTATCTGTCTCCATATACAAAAATTAA 710
                           i i         ii     i    i  vv v                 
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_195676135_    711 CTCAAGATGGATTAAAGACTTAAACATGAGACCTGAAG-TATAAAAATCC 759
                              i      i ?    i    ii i   v  i  i-       v  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_195676135_    760 TAAAAGAAAACCTAGGAATGACTCTTC-------TGGG------AATTGA 796
                           i        v    ?i i v     -------    ------   v v
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_195676135_    797 --CCTAGACA-------AAGAGCTTATG--ACAAAG------ATAGACAA 829
                         -- i    i -------  i   vi v --     i------     i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_195676135_    830 ATGGGACATAATTAAA-CTAAAAA--TCTGCAAGGCAAAAGAAATAATTA 876
                           v    v v  i   -i      -- i  iivvv    i  v iv  i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_195676135_    877 AGA--GTAAACTCATAGCCTACAGAATGAGATAAAATATTTGCAAACTAT 924
                            --  i  vvv i i  i        i  v              ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_195676135_    925 TCATCTGACAAGGGACTAATATACAGAATACACATGGACGTAAACCACTG 974
                         vi      i        vi   v       i --------    ----- 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATA--------TAAA-----G 772

  chr2_195676135_    975 AACAGTAAAAACAAAAAAAGGAGAAGAGAAAAAAAAAAGAAAAAAACAAG 1024
                            vv v v   vv  v  v-------------------     i    i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAAT-------------------AAAAAGACAAA 803

  chr2_195676135_   1025 CAACAACAACAACAAAAAAAAATTCCATCAAAAAGTGGGCAAAGGATCTG 1074
                         i   -------------------i v  i?    i            i  
  L1M4_orf2#LINE/    804 TAAC-------------------CCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_195676135_   1075 AGTAGACATTTCTCAAAAGAAGACATACAAATGTTCAATAGGTATATAAA 1124
                          i            v        i         vi     i i i  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_195676135_   1125 GAAATGTTCAACATTACTAATCTT 1148
                         i i   i       i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (93 / 54)
Gap_init rate = 0.02 (15 / 623), avg. gap size = 5.87 (88 / 15)  


 234 22.64 0.00 1.89  chr2_195685149_195687778.rev      837   889 (1741)    L1M4_orf2#LINE/L1        3    54 (854)  

  chr2_195685149_    837 GAAAAACATTCCATGCTCATGAATTGAAAAAGTCAATGTTGTTAAATATT 886
                             i i  i     i     i    i  i v i   i       i-  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-ATG 51

  chr2_195685149_    887 GCA 889
                            
  L1M4_orf2#LINE/     52 GCA 54

Transitions / transversions = 5.00 (10 / 2)
Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1)  

2081 26.94 3.59 4.38  chr2_195685149_195687778.rev      890  1780 (850)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr2_195685149_    890 ATAGGAAAA-TGAATATTGGGTCATTTTTTAAAATGGCTATACTACTGAA 938
                           v    i - v       ---------    i     v     v iv  
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTG---------TTAAGATGGCAATACTCCCCAA 65

  chr2_195685149_    939 AACAATTTACAGATTCAATACTATTTCTATCAAATGACCAA-TGTCTTTT 987
                          vii  i           ii v  ii        vvv   i-  i     
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_195685149_    988 TTCACAGAATTAGAAAAAACT-ATTCTAAAACTCATATAAAA--GCAAAA 1034
                           -i     v v  v  i-  -  i      i      ii  --    --
  L1M4_orf2#LINE/    116 TT-GCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAA-- 161

  chr2_195685149_   1035 AAGGGCCTCA--ATAGACAAAAG----CTAAGTAAAAAGTACGAATTCTG 1078
                         --   v i  --    v     v----i i iv  i   v  i  v iv 
  L1M4_orf2#LINE/    162 --GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_195685149_   1079 AGTCATCACACCACTCGACTTCAAACTATACTACAGGGCTACAGTAACCA 1128
                           vvv      iv i i i      viv       ii          i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_195685149_   1129 AAACATCATGGTACTGTTACAAAAACAGACACGTAGACCAATGGGACAAG 1178
                          i   vii        vi i  ii i     ii    i      i i ii
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_195685149_   1179 TTAGAGAACCCAGAAATAAACATCTATTACACATCTATTACCATCTGATC 1228
                         v v    ii            -- i  ---    i   vii  vi    i
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAAC--CCAT---ACATTTATGGTCAATTGATT 354

  chr2_195685149_   1229 TTTGACAAAGTTGACAATAACAAGCAGTGGAAATAGGACTTCCTATTCAG 1278
                           i     i v  v   v v  vv  i   ii v  i ivvi  v    i
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_195685149_   1279 TAAATGGTGCTGGGATAACTAG----CCATTTGCAGAAGATTAAAACTGT 1324
                         i              i    i ----   iv    i    v i  ii  v
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_195685149_   1325 ATCTCTTCCCTTA-ACCATATA-AAAAATAAACTCAAGATGGATTAGAAG 1372
                          i i  -v   i -        -      v       i      i ? ii
  L1M4_orf2#LINE/    455 ACCCCT-ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_195685149_   1373 CTTAAATGTAA-------AATGATAAAAGCCCTAAAAGAGAATCTAGGAA 1415
                          i         -------  iv      vi i  i    i  iv    ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_195685149_   1416 ACAGCATTC-TGAATACAGACCGTGGCAAAGATTTCAT-GATGGAGACTC 1463
                         vv iiv   -   vivii iiii-     v i    v -   iv-   v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATAT-GACAC 601

  chr2_195685149_   1464 CGAAAGCAATTGCAACAAAAACAAAAATTGATAAGTGTGTCCTGATTATA 1513
                          i      vvv         iv      v     i vv v i v  i v 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_195685149_   1514 GTAAAGAGCTTCTACATAGCAAAAGAAACTATCAACAGAGTAAACAGACA 1563
                         i v  i i   i iiiivv    i  v        v i   i  v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_195685149_   1564 ACCTACAAAATGGGAGAAAATATTTGCAAACTATGCATTGGACAAAAGTC 1613
                            i   i                      ii  ii  iv  i  ii v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_195685149_   1614 TAATATCTAGAATCTATAAAGAACTT----AAATCAAAAAGCAAAGAAAA 1659
                          vi    i     v           i----  v    v  vv   ii v 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_195685149_   1660 AACAACCCTATT-AAAGATGGGCAAAGGGCATTGTATTAGTCAGTTACCA 1708
                           i     v   -   i           --   vv v   v  v  ----
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGG--ATTTGAATAGACATTT---- 845

  chr2_195685149_   1709 TGCTGCTAATAAAGACATACCTGAGACTGGGTAATTTGTAAA-GGAAAGA 1757
                         --  - i  vi    i    --- i -   vi   vv i v - i     
  L1M4_orf2#LINE/    846 --CT-CCAAAGAAGATATAC---AAA-TGGCCAATAAGCACATGAAAAGA 888

  chr2_195685149_   1758 GGTTTAATTGACTCACAGTTCAG 1780
                         v i i  i-- -   ????????
  L1M4_orf2#LINE/    889 TGCTCAAC--A-TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.04 (31 / 884), avg. gap size = 2.29 (71 / 31)  

 290 20.55 0.00 0.00  chr2_195685149_195687778.rev     2066  2138 (492)    L1M4_orf2#LINE/L1      836   908 (0)  

  chr2_195685149_   2066 ACAGACACTTCTCAAAAGATGACATACACACAGTCATCAAGCATACAAAA 2115
                          i     i     v     v  i     v ii i  vi     i ii   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_195685149_   2116 AAATGCTCAACATCACTAATTAT 2138
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.00 (0 / 0)  


2163 26.54 5.92 2.51  chr2_195735910_195738108      832  1709 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195735910_    832 TGGACAACTCTACCACATTCAAGGATTGGAAGGCTCAATATTATTATGAT 881
                             v iv v v   ii    v          i  i      i   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195735910_    882 GGAATTTCTCCCCAAATTGGTCTATGTATGCAACTCAAACACTATATAAA 931
                           v v v            i    iiv  v    v   v v    -i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-CAAA 99

  chr2_195735910_    932 ATACTAACAGTGTTTTT-----AGATTGAC----TGATTTC----TTTAC 968
                           v i i v iv     ----- i      ----    iii----  i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_195735910_    969 ATAAAAATTCAAAGGACCTAGAAAAGCCAAAATAACATTATAAAATTTGT 1018
                           ii    v   i     i    v        i  iv  iv    vvv v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_195735910_   1019 -TAAAGTTTGAGAAC----ACTACTTAATTTCAAGACTTACTATAAAGGT 1063
                         -i      v   i  ----   v ii        i        i    v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_195735910_   1064 GCAGCAATCAAGTCATTGTAATATTGGCACAAGGATAGACATATAGAGTA 1113
                         i   i       v  v   ii  i     i                 vi 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_195735910_   1114 AAGGAACCAAACAGAACAT---GAAATAAACCAACCTATATGTGGTCAAC 1160
                          v    ivi  iv  ivi ---          v ivi  v i       i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_195735910_   1161 AGATTTTTTCCAATAAATTTATCAAG-CTATTTCAGTGGGGAGAAAAAAA 1209
                         v      --- i i  ivv ii    - i   -  i      i i  v i
  L1M4_orf2#LINE/    350 TGATTTT---CGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAG 395

  chr2_195735910_   1210 TTTTTTTAACAAATGGTGATGAAACAACTGGGTAT----ATACAGGGG-- 1253
                          i    i           v  ii        i  ?----  i  iii --
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_195735910_   1254 TGAAAT--GAACCTTGAACTTTTCCTCGTCTATGAAAATTAACTCAAAAT 1301
                             i --  v  i --  i iv vi i v  ii                
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCT--ACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_195735910_   1302 TAATC-TATACCTACATGTAAAAGTCAAAGCTATAAAATGTCTCA-AAGT 1349
                         vi   -? v     v      i  ii   i        i-   i -   v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGA 542

  chr2_195735910_   1350 AAATGCAGTAG-AAATTCTCA--GTCATAGGGTAGAAAAACGTTTCTTAA 1396
                            iii  v? -    ii  i--ii v i  v   iv  vv        i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_195735910_   1397 GTGGGATACAAATAAAACAAGTAA---ATGAAAAAA---ATAATTTGTAC 1440
                         i iv  i  v  v iv     i  --- v       ---    v   v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_195735910_   1441 TTTATCAAAGCTAAACATTTATGTTCTTTGAAAGACACTGTTAAGGAAAC 1490
                           i      ii    v i  v   v   ii  i      i i   i  ii
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_195735910_   1491 GAAAAGACTAGTCATAGACTAATATAAAATATTTGTAAAAGATATACCTG 1540
                                 v vi  i   v iiv v          i   vv     i   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_195735910_   1541 CTTTAAAAACTTA-ATCTAGAATATAGATTTTTAAAAGCTCATATAG--- 1586
                         v v- iii    i-   i        v -----  i i   v  i i---
  L1M4_orf2#LINE/    743 ATA-AGGGACTTGTATCCAGAATATATA-----AAGAACTCTTACAACTC 786

  chr2_195735910_   1587 AATATAGATTTTAAAAAGCTCTTACAACCCAAC--AAAAATGAACAAAGA 1634
                             ---  ---      v- vv i       i--       ii     i
  L1M4_orf2#LINE/    787 AATA---AT---AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_195735910_   1635 ACT-AAACAGCCACTT-TATAAA-ATGAAATATAAATG-CCAATTAGGAA 1680
                          i -i  i  v  i  - vi   - v  v   i     -     - i v 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCA 878

  chr2_195735910_   1681 CAT-ATAAGATATTTGCCATGATAGGCCTT 1709
                            - v     ii iiv   v ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (141 / 89)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 2.11 (74 / 35)  

 313  7.84 0.00 0.00  chr2_195735910_195738108     1885  1935 (264)    L1M4_orf2#LINE/L1      858   908 (0)  

  chr2_195735910_   1885 TATACAAATGGCCAACAAGCATATGAAAAAATGCTTAACATCACTAATCA 1934
                                        i     i       i     i       ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_195735910_   1935 T 1935
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.00 (4 / 0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.00 (0 / 0)  


3353 25.99 0.55 0.55  chr2_195758004_195769778      493  1400 (10375)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr2_195758004_   1400 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 1351
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_195758004_   1350 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1301
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_195758004_   1300 TACCAATGACTTTCTTCACACAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1253
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chr2_195758004_   1252 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 1203
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr2_195758004_   1202 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1153
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr2_195758004_   1152 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1103
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr2_195758004_   1102 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 1055
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chr2_195758004_   1054 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1005
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chr2_195758004_   1004 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 955
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chr2_195758004_    954 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 905
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chr2_195758004_    904 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 855
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chr2_195758004_    854 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 805
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chr2_195758004_    804 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 755
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chr2_195758004_    754 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 705
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chr2_195758004_    704 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTCCT-CATCTGACA 656
                           i     i   i             v  i    v-  v -i      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATA 745

C chr2_195758004_    655 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 606
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chr2_195758004_    605 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 556
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chr2_195758004_    555 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 506
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chr2_195758004_    505 CATCACTGGCCAT 493
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

3156 25.56 2.59 0.34  chr2_195758004_195769778    10396 11283 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195758004_  10396 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCTTGAAAAT 10445
                              ii i  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195758004_  10446 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 10495
                            v     v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195758004_  10496 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAACGTTC 10542
                          v   -   v    i  -i     -   -- v  i  - iii   vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_195758004_  10543 CTATGGAACCAAAAAAGAGCCTGCAAAGCCAAGACAATCCTAGCAAA-AA 10591
                         v       viiv  ii  v  v v v      i      i iiv   -  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_195758004_  10592 GAATAAACCTGGAGGCATCACACTACCGGACTTCAAACTATACTACAAGG 10641
                            i   vi      vv       v  vi i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_195758004_  10642 CTACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGAC 10691
                                  i   i    ii       v i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_195758004_  10692 CAACGGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACAACCA 10741
                            i    i     v   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_195758004_  10742 TCTGATCTTCGACAAACCTCACAAAAACAAGCAATGGGGAAAGGATCCCC 10791
                         vi    i        ivv vv   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_195758004_  10792 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTTG 10841
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_195758004_  10842 AAACTGGATCCCTTCCTTACACTGTATACAAAAATTAACTCAAGATAGAT 10891
                           ii    i    v   i    ii                   i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_195758004_  10892 TAAAGATTTAAATGTAAGACCTAACACCATAAAAACCCTAGAAGAAAACC 10941
                         i ?   ii           v    v  i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_195758004_  10942 TAGGA---------CGTAGGCATGGG-----CAAGGACTTCATGACAAAA 10977
                             ?---------   iiv v    -----   v ii   v iivv vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_195758004_  10978 ACACCAAAAGCAATGGCAACAAAAGACAAAATAGACAAATGGGATCTAAT 11027
                                     vvi           v        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_195758004_  11028 TAAACTAAGGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 11077
                         i   v v ii i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_195758004_  11078 GGCAACCTACAGAATGGGAGAAAAT-TTTGCAATCTACCCATCTGACAAA 11126
                          i     i                 -       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_195758004_  11127 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAAAAAAA 11176
                           i  vi          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_195758004_  11177 AAAAAA-AA---AATCAAAAAGTGGGCAAAGGATATGAACAGACCCTTCT 11222
                         i v   -  ---   i?    i            v    i    vi    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_195758004_  11223 CAAAAGAAGACATTTATACAGCCAACAGACATATGAAAAAATGCTCATCA 11272
                          v        i  vi v ii     i ii  i       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_195758004_  11273 TCACTGGTCAT 11283
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (133 / 90)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.36 (26 / 11)  


 340 17.19 0.00 0.00  chr2_195787182_195790010     1271  1334 (1495)    L1M4_orf2#LINE/L1        3    66 (842)  

  chr2_195787182_   1271 GAAAGATATTCCATGCTCATGGATTGCAAGAACTAATATTCTTAAAACGC 1320
                                  i     i          v    vi       v    i i v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_195787182_   1321 CAACACTACCCAAA 1334
                            i   v      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAA 66

Transitions / transversions = 1.20 (6 / 5)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.00 (0 / 0)  

2333 24.00 7.12 3.00  chr2_195787182_195790010     1538  2337 (492)    L1M4_orf2#LINE/L1       76   908 (0)  

  chr2_195787182_   1538 AGATTCAATGCAATCCTTATAATAATACCAATGAAATTTTCCATAGACA- 1586
                                 i       i   v v   v   iivivv    iiii   v -
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr2_195787182_   1587 --AAAAAAAAATCCTAAAATTTATATGGAACCACAAAACATGCAGAATAG 1634
                         -- v  ivvi           i        vii   iiv iv        
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr2_195787182_   1635 CCAAAAAAAAAAAAAAAAAAAAAACTGTGAGCAAAAAGAACAGAGCTGGA 1684
                               v  v--------------  -   iv  i       i  i    
  L1M4_orf2#LINE/    176 CCAAAACAAT--------------CT-TGAAAAAGAAGAACAAAGTTGGA 210

  chr2_195787182_   1685 GGCATTACACTGTCTCACTTCAAAATATACTAGAAAGCTATAACAACCAA 1734
                           vv i     vi iv i       iv     v       i ii  i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_195787182_   1735 ATTAGCATGGTACTGGCATAAAAACAAACACACGGATCAATAGAAAAAAA 1784
                         ivi  ii              ii i i   i ii       i   v i  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_195787182_   1785 TAGGTAACACAGATATAAATCCATGCATTTACAGCCAATTCATTTTCAAC 1834
                          v iv iiv    v     i    i      ii i     v      i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_195787182_   1835 AAAGGGGCCAAGAACATACAATGGGGAAAGAATAATCTT--CAATAAATG 1882
                           i  v       v   v                i    --   i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_195787182_   1883 GTGCTGGGAAAACTAAATAACCATATGCAGAAGAATAAAACTAGACCCCT 1932
                                  v    ii   ?   i     i      i  ii i       
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_195787182_   1933 ATCTCTCACCATATACAAAAATTAACTCAA-------------CCTA--- 1966
                          i   v                        -------------    ---
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_195787182_   1967 --------------TACAA---TCGTAGAAGAAAACCTAGGAAATACTCT 1999
                         --------------  i  ---  v           v    ?ivv v   
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_195787182_   2000 TC-TGGTCATTAGCCCCGGCAGAAAAAAAGTAT----GACTAAGACCTCA 2044
                           -  ii -  i viiv    ----- vi  v ----  -  v   vi  
  L1M4_orf2#LINE/    561 TCGTGACC-TTGGGTTAGGCA-----ATGGTTTCTTAGA-TATGACACCA 603

  chr2_195787182_   2045 AAAGCACATTCAACAAAAATGAAAACTGA-AAATTGTGACCTAATTAAAC 2093
                                 vv        ivi    iv  -      -   i v  i   v
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG-GACTTCATCAAAA 652

  chr2_195787182_   2094 TAAAAGCCTTCTACATAGCAAAATAAACTATGAATAGAGTAAAAAGACAA 2143
                          v   iv   i iiiivv    iv v     v  v i   i         
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_195787182_   2144 CCTATATAATGGGAGAAAAATGTTTGCAAACTGCATAT--GGCAAAGGGC 2191
                           i i v            - i        iiii    -- ii  i  i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_195787182_   2192 TAATATCCAGAATCTAGAAGGA--TCTTA-AA-TCAACAAGCAAAAAACA 2237
                          vi          v  v  i  --     -  -    i  vv    i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_195787182_   2238 AGT-------TGTTAAAGTGCGTAAAGGACAAGAACAGACACTTCTCAAG 2280
                          i ------- v?v   i  v i      ivv   i     i     v i
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_195787182_   2281 AGAAGACATGCAAGTGGCCAACAAACCTATCAAAAAATGCTCAACATCAT 2330
                               i  i   i       i  i vi  v    i             ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_195787182_   2331 TAATCAT 2337
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.59 (116 / 73)
Gap_init rate = 0.02 (20 / 833), avg. gap size = 4.05 (81 / 20)  


3232 17.75 3.61 1.25  chr2_195864814_195866525      501  1221 (491)    L1M4_orf2#LINE/L1      171   908 (0)  

  chr2_195864814_    501 AATAAACAAAACAATCTTGA----GAATAACAAAATTTAGAGG-CTCATG 545
                             iv              ----   v      i  -i    -    ii
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT-GGAGGACTCACA 219

  chr2_195864814_    546 CTTCC--ATTTCAAAATGTATTACAAAGCTACAATCATTAAAAC--TGTG 591
                              --         iv  i            i v  i  i  --    
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_195864814_    592 GTACTAGCATAAGGATAGATATATAGATCACTGCAATAGAATTGAGAGTG 641
                              i             i          v  v               v
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_195864814_    642 CAGAAATAAACCCACACATCTATAGCCAACTGATTT-CAATGAGGCTGTC 690
                                       i    i   i i   i      - i ii   v  i 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_195864814_    691 AAGATTATTTAATAGAGAAAGAACAGTCTCTTCAACAAATGATTCTGGGA 740
                             ii   i   i i       i     i           i v      
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_195864814_    741 CAACAGGATATCCACATGTAAAA-ACTAAAGTTCAACTTCTACCTCACAC 789
                             v     ?       i    - v i     vi  ii           
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_195864814_    790 CACATACAAAAAAAAATTAATCCAAAATAGATAAATGACCTAAATAGAAG 839
                           i         ----    ii      i   v ?v         iv   
  L1M4_orf2#LINE/    470 CATATACAAAAA----TTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_195864814_    840 AGCTAAAACTATTAAACTTTTAGAAGAAAACAAAGGGGTAAATCTTCATG 889
                                     v     i             v   ?          i  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_195864814_    890 AT-----ATTAG--------TTCTTAGATTTGACACCAAAAACACAAACA 926
                          i-----i    --------         v           i     i  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_195864814_    927 AAAGAAGAAAAAA-AGATAAGTGGGACCTTGAGAAAACTGAAAATTTCTG 975
                          v i         -      i v    i iivv    i i    i  i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr2_195864814_    976 TTCAGCAAAGGATGCTATCAAGTACATAAAAAAGACAGCCAACAGAATGG 1025
                          v vv       ii        v vi i    -    i  v         
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GACAACCCACAGAATGG 714

  chr2_195864814_   1026 GAGAAAATGTTTGTAAACAATATATCTGATAATGGTAGTCTAGTATCAAA 1075
                                 i    i   iv             v  - --  v     v i
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGG-A--CTTGTATCCAG 761

  chr2_195864814_   1076 AATATAAAAAGGACACTTACAACGCAATAACACACAGAAAAATAATG-AA 1124
                               v    i  v        v      i v v   v      iv-  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_195864814_   1125 TTTAAAAATGATCAAAATGCTTAAGTTGACATTATTCCAAAGACAATATA 1174
                           ?       iv    ivii  i i v      vi        vi     
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_195864814_   1175 TAAATGCCCAAAAAATACATGAAAAGATGCTCAACATCCTTTAGGTA 1221
                         i     v    v  ii                      v????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (77 / 47)
Gap_init rate = 0.02 (15 / 738), avg. gap size = 2.33 (35 / 15)  


3248 27.20 0.55 0.55  chr2_195879610_195886101      955  1862 (4629)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195879610_    955 TGGAAGAATATTCTATGCTCATGGATAGGAAGAATCAGTGTCGTAAAAAC 1004
                              ii    i i   i        v      v i i i i  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195879610_   1005 GGTCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 1054
                           iv     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195879610_   1055 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1102
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_195879610_   1103 TATGGAACCAAAAAAGAGCCCGCATTCCCAAGTCAATCATAAGCGAAAAG 1152
                                viiv  ii  v  v v  vv    iv     v i ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_195879610_   1153 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1202
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_195879610_   1203 TACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGAGACATAGACC 1252
                                 i   i   iii         i iv ii i   v i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_195879610_   1253 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 1300
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_195879610_   1301 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGGTTCT 1350
                          vi    i  i     ivv  v   i v  vvv           ii vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_195879610_   1351 CTATTCAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1400
                           v                    v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_195879610_   1401 GAAACTGGATCCCTTCTTTATACCTTATACAAAAATTAATTCAAGATGGA 1450
                            ii    i    v i i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_195879610_   1451 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1500
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_195879610_   1501 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1549
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_195879610_   1550 AAACACCAAAAGCAATGGCAACACAAGCCGAAATTGACAAATGGGATCTA 1599
                         vi            vvi      v   vvi    v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_195879610_   1600 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1649
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_195879610_   1650 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 1699
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_195879610_   1700 AAGGGCTAATATCCAGAATCTACAAAGAACTTGAACAAATTTACAAGAAA 1749
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_195879610_   1750 AAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACACTT 1799
                           i     i     v  i? v  i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_195879610_   1800 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGTTCAT 1849
                            v        i  vi viii     i ii          i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_195879610_   1850 CATCACTGGCCAT 1862
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (149 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

1859 27.04 1.45 1.09  chr2_195879610_195886101     4543  5093 (1398)    L1M4_orf2#LINE/L1        1   553 (355)  

  chr2_195879610_   4543 TGGAAGAAACGTACCATGCTCACGGATCAGAAGAATCGATATCATTAAAA 4592
                              - i ii v     i   i    ii     v ii    ii    i 
  L1M4_orf2#LINE/      1 TGGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_195879610_   4593 TGGCCGAACTGCCTAAAA-AATTTACAGATTCAATTCA-CCTCTGTCAAA 4640
                             viv   v  i   v-i  i           iv  -i i  i     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_195879610_   4641 TTACCAA-TGTCATTTTTCACAGAATTAGAAAAAAACATTCTTAATATTT 4689
                         v v   i-  i -     ii     v v  v  ivvv  i  v  -   i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAA-ATTC 147

  chr2_195879610_   4690 ATATGTAACCAAAAAAGAGCCCACAG-AGCCAAAGCAATCCTAAGCAAAA 4738
                              v  viiv  ii  -    v i-       i     i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_195879610_   4739 AGAACAAATCTGGAGGCATCACTCTACCTGACTTCAAATTATATTACAAG 4788
                                 vi      vv    v  v  ii i      viv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_195879610_   4789 GCTATAGTAACCAAAACAACATGATACTGGTACAAAAATAGAAGCACAGA 4838
                             i     i   i   iii  i      i i  ii     vii i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_195879610_   4839 TCAATGTAACAGAATAGAGAACCCAGAAATAAAGCCACATAGCTACAGCC 4888
                               v  i     v    ii           v   i i vi  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_195879610_   4889 AACTTATCTTTGCCAAAGTCAACAAAAATAAACACAGTGGGGAAAGGGTT 4938
                           i v  i  i v   i viiv   i vi --iv  i         ii v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCA--TTCAATGGGGAAAGAATA 394

  chr2_195879610_   4939 CTCTATTAAATAAATGGTGCTGGGAAAATTGGATTGCCACATGAAGAAGA 4988
                         v   v  v  i              v  i     v?       v i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_195879610_   4989 ATGAAACTGGACCCCTATCTCTCACCATACACAAAAATTAACTCAAGATG 5038
                              ii          i   v       i                i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_195879610_   5039 GATTAAACACTT----GTAAGACCTGAAACTAAAAAAATTCCAGAAGAAA 5084
                            i ? v  i ----      v  i      v    v iii        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_195879610_   5085 ACTCAGGAG 5093
                           vi   ? 
  L1M4_orf2#LINE/    545 ACATAGGNG 553

Transitions / transversions = 1.81 (94 / 52)
Gap_init rate = 0.02 (10 / 553), avg. gap size = 1.40 (14 / 10)  

1037 24.52 3.58 1.10  chr2_195879610_195886101     5638  6000 (491)    L1M4_orf2#LINE/L1      537   908 (0)  

  chr2_195879610_   5638 AAAACAAAACCTAAGAAATACTCTTTTGGACATTGGCCTAGGCAA----- 5682
                          i  v     v  i ?ivv v    ivv   v    vi       -----
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_195879610_   5683 -ATAACATAAGACACCAAAATCA--AACTAAACAAAAACAAAAATAGACA 5729
                         -v v v   v          v  -- i --       iv         i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGC--AACAAAAGAAAAAATAGATA 634

  chr2_195879610_   5730 AATGGGACTTAATTAAACTCAAAAGCTTCTGCATAGCAAAAGAAATAAT- 5778
                            v      v  i   v i    i   i  iiivv    i  v iv  -
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_195879610_   5779 -AGTA--TAAATAGACAACTCACAGAATGGTAGCAAATATTTGGAAGCTA 5825
                         -  v -- i  v       i          v  v         v  iii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_195879610_   5826 TGCATCTGGCAAAGGACTAGTATCCAGAATCTACAAGGAACTTAAACAAC 5875
                          ii     ii  i     v           v  i  i     ivv     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_195879610_   5876 TCAACAAGAAGAAG-TAAATGTCCACATTAAAAAATGTGCAAACAACATT 5924
                             i  v  i   -i    iv  vv   ?       v     vi iv v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_195879610_   5925 AACAGACATTTTTCAAAAGAAGACATACAAGCAGCCAACAAATATATGAA 5974
                           i        i  v        i      iii     i  ii i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_195879610_   5975 AAAAGAAGCTCAACATCACTAACCAT 6000
                           --  v           ????????
  L1M4_orf2#LINE/    885 AA--GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (46 / 41)
Gap_init rate = 0.02 (7 / 372), avg. gap size = 2.43 (17 / 7)  


3130 22.66 3.91 2.57  chr2_195898159_195900342.rev      797  1692 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195898159_    797 TGGAGAGATATTCTATGTTAATGGATAGGAAGACATAATATCATTAAGAC 846
                             i      i i     v      v       v      ii      i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195898159_    847 GTCCAT-TTTCCCAACTTATTCTAAAGATTTAATGCAATCCCAATAAAAC 895
                          v v  -i i     v  iv    v     i  i        v  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195898159_    896 TCTCAGCAAATTATTTTTGTAGATATCG-TAAAC-GATTATAAAGTTTAT 943
                           i    vivi -      i   v  i -i  i -   iv    i  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_195898159_    944 ATGGAGAGGCAAAAGACCCATAATAGTCAACAAAATACTC----AAGGAG 989
                              i v    ii      v     i   v v   -  i----   i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAG 198

  chr2_195898159_    990 AACAAAGTTGGAGGACTGACACTACCCAAATTTAATACTTACTATAAAAC 1039
                                          v     v     v  i  v        i   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_195898159_   1040 CATAGTAATTAAGAGAATGCGGTATTGGTGAAAGAATTGACAAATAGAGC 1089
                         i i      i    v i  i    i   iiv   i  v    v     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_195898159_   1090 CATGGAACAGAATTAAGAACCTAGAAAAAAGGCTCACATAAATATAGGCA 1139
                         v      i      i   ii i     v  i- i  i i vv   i v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTCA 347

  chr2_195898159_   1140 ACTGATCTTTGACAGAGGAGCAAAGACAATGGAGGCAGTCTTTGACAATG 1189
                          i    i  i    ii  v  v     --------  ----  --     
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGAC--------CA----TT--CAATG 383

  chr2_195898159_   1190 GAGTAAGGGTAGTGATTTTAACAAGTGATGCTGGAACAACTGGACATCCA 1239
                          i v   ii    vv   i     i  i      i         i ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_195898159_   1240 CATGTCAAAAAGTTAATTTAGACACAGCTCTTACACTTT-CAGAAAAGAT 1288
                             iv   i i v  v  i   v vvvi  i    iv -i v    -  
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA-AT 482

  chr2_195898159_   1289 TAACTTCAAAATGGATGATAGACCTGAATGTAAAATGC-AAAATTATGTA 1337
                              -          v ?      i       i -  -    i   iv 
  L1M4_orf2#LINE/    483 TAACT-CAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAA 530

  chr2_195898159_   1338 ACTCCTATAA-----CATAGGAG-AAATCTT-GTG--TATGG--TGAGCA 1376
                             i  v  -----      ? -       -   --iv   -- ii   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_195898159_   1377 -TGACTTTTTAGATACAACATCAAA-GTATGATTCATGAAAGA-----TA 1419
                         -  ii  i       ii   i    - i ii viv ii     -----  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_195898159_   1420 GATTAGCTAGACTTCATTAAAATTAAAAACCTCTGCCCTGCAAAAGACTC 1469
                            v ii i        i            i i  iv  v    i   v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_195898159_   1470 TGTCA-GAA--TGAGAAGACAAGCCATAGAGCGGGAGAAAATATTTTTAA 1516
                          i   -   --   i       v   i   ii              vi  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_195898159_   1517 AAGACACGCCTGATAAAGGACTGTTATCCAAAATATACAAAGAACTCTTA 1566
                          vv i iii       i     vv      i      i            
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_195898159_   1567 AAACTCAACATTAAGAAAACAAACAATCGA--TTAAAAATGGGACAAATA 1614
                         v       i v   i  i     i  i v -- ?         -    vi
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG-CAAAGG 829

  chr2_195898159_   1615 CCTT-AACAGATACCTCACCAAGAAATATATATACAGATGGCTAATAAGC 1663
                         vi  -  i   i ii  v    ii  v     --  i     i       
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATA--CAAATGGCCAATAAGC 877

  chr2_195898159_   1664 ATATAAAAA--TGCTCCACATCATATGCCAT 1692
                          i  i    --     v      ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (128 / 71)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 1.93 (58 / 30)  


3247 26.76 0.55 0.55  chr2_195913741_195924441     3643  4550 (6151)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195913741_   3643 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3692
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195913741_   3693 GGCCATACTGTCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3742
                            v     vi    iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195913741_   3743 TACCAATGACTTTCTTCACAGCA-TTGGAAAAAACT-ACTTTAAAGTTCA 3790
                          v   iivi i  i  ii   v -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_195913741_   3791 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 3840
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_195913741_   3841 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGGC 3890
                                i      vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_195913741_   3891 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3940
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_195913741_   3941 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGGCGCATATCTACAACT 3988
                                i    i--    i  --        vvv ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_195913741_   3989 ATCTGATCTTTGACAAACCTGACAAAAACAAAAAATGGGGAAAGGATTCC 4038
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_195913741_   4039 CTGTTTAATAAATGCTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4088
                           v  i  i     v        v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_195913741_   4089 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATGCAAGATGGA 4138
                            ii    i    v   i     v              iv   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_195913741_   4139 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4188
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_195913741_   4189 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGGTTTCATGTCTA 4237
                         v    ?i- v i -   iv   v v  vv i     v      v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_195913741_   4238 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4287
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_195913741_   4288 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTAAA 4337
                           i   v v  i i   i  ii vv    i  v  i i  vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_195913741_   4338 CAGGCAACCTACAGAATGGGAGACAATTTTTGCAACCTACTCATCTGACA 4387
                         v  i     i             v   v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_195913741_   4388 AAGGGCTAATATCCAGAATCTATAATGAACTCCAACAAATTTACAAGAAA 4437
                          i  i  vi          v     v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_195913741_   4438 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 4487
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_195913741_   4488 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 4537
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_195913741_   4538 CATCACTGGCCAT 4550
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

3044 26.77 1.33 0.88  chr2_195913741_195924441     9306 10209 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195913741_   9306 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 9355
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195913741_   9356 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 9405
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195913741_   9406 TACCAATGACTTTCTTCACAGCA-TTGGAAAAAACT-ACTTTAAAGTTCA 9453
                          v   iivi i  i  ii   v -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_195913741_   9454 TATGGAACCAAAAAAGAGCCCGCATCTCCAAGTCAATCCTAAGCCAAAAG 9503
                                viiv  ii  v  v v  vv    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_195913741_   9504 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 9553
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_195913741_   9554 TA-----ACCAAAACAGCATGGTACTGGTACCAAAACAAGAGATATAGAT 9598
                           ----- i   i    ii         i iv ii i -  v        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGAT 297

  chr2_195913741_   9599 CAATGAAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 9646
                              i  i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_195913741_   9647 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 9696
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_195913741_   9697 CCTATTTAATAAATGGTGCTGGGAAAAGTGGCTAGCCATATGTAGAAAGC 9746
                         i  v  i  i              v  v   v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_195913741_   9747 TGAAACTGGATCCCTTCCTTACACCTCATACAAAAATCAATTCAAGATGG 9796
                             ii    i    v   i     vi          i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_195913741_   9797 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAATACCCT-AGAAGAAA 9845
                           i ?   ii    i  v   v       i     -  i  -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAA 544

  chr2_195913741_   9846 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 9894
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_195913741_   9895 TAAAACACCAAAAGCAATGGCATCAAAAGCCAAAATTGACAAATGGGATC 9944
                           vi            vvi   v      vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_195913741_   9945 T-ATTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 9993
                          -  iv   i    i -   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_195913741_   9994 GAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTG 10043
                            v  i     i                 v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_195913741_  10044 ACAAAGGGCTAATATCAAGAATCTACAATGAACTCAAACAAATTCACAAG 10093
                          i  i  i  vi    v     v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_195913741_  10094 AAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACA 10143
                              i     i     v  i?    i    ii     iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_195913741_  10144 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 10193
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_195913741_  10194 CACCATCACTGGCCAT 10209
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


2790 25.54 1.85 3.15  chr2_195933295_195935808     1103  2022 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195933295_   1103 TGGAAACACATCCCATGCTCATGGAAGGGTAGAATCAATATTGTGAAAAT 1152
                               v i        i       vv  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195933295_   1153 GACCATAGTGCCAAAAGCAATCTACAAATTCAATGCAATTCCTATCAAAA 1202
                          i v   v v  v   vii       i      i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195933295_   1203 TACCA-CCACTATTCTTCACAGAGA--AAAAAAC-AATCCTAAAATTCAT 1248
                          v   - ii i-  i  ii    i --i v  i -i              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_195933295_   1249 ATGGAACCAAAAAAGAGCCCAGA-TAGCCAAAACAAGACTAAGCAAAAAG 1297
                               viiv  ii  -      -            vvi i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_195933295_   1298 AACAAATCTGGAGACATCACATTACCTGATTTCAAACTATACTATAAGGC 1347
                               vi     ivv     i v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_195933295_   1348 -ATAATCATCAAAACAGCATGGCACTGGTATAAAAAATAGCCACATAGAC 1396
                         - i i v     i    ii   i     i    ii -   v  i     i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGAT 297

  chr2_195933295_   1397 CAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATGCTTACAGCCA 1446
                                 i     v    ii           v   v iii   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_195933295_   1447 ACTGATCTTTGACAAAGCAAACAAAAACAT---------AAAGAG-ACCC 1486
                          i    i  i     i vviv   i v   ---------     i- vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_195933295_   1487 AATTCAACAAATGGTGCTAGGATAATTGACAAGGCACACGTAGAGAAATA 1536
                         vv                i   i  i  ivv ?v    i i i ii   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_195933295_   1537 AAACTATATCCTCATCTCTGACCTTATACAGAAATCTACTCAAGATGGAT 1586
                           ii iv i  ii i   vv   v      i    iv      i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_195933295_   1587 CAAGTACTTACATCTAAGACCTGAAACCATAAAAATTCTAGAAGATTGCA 1636
                           ?iv  i  v  v     v  i    i      v ii       vvi  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_195933295_   1637 TCGGAAAAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACC 1686
                          v  ?iv   ---i    vv   v    v        v i    v iivi
  L1M4_orf2#LINE/    548 TAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_195933295_   1687 AAGAACCCAAAAGCAAATGCAACAAAAACAAAGATAAACAAATGGGACTT 1736
                          v  vv         v v         iv   i   i i    v      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_195933295_   1737 AATTAATCTAAAAAGCTTCTGCACAGCAAAAGAAACAATGAGTAGAGTAA 1786
                         v  i  vv v    i   i  ii vv    i  v  v  v iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_195933295_   1787 ACAGACAACCCACAGAGTGGGAAAAAATCTTCACAATCTATACATCTGAC 1836
                          v              i     i     v  ii   vii   i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_195933295_   1837 AAAGAACTAACAATCTATATATCTGACAAAGATATCCAGAATCTACAAGA 1886
                           i i   ---------------  -------          v  i  ii
  L1M4_orf2#LINE/    745 AAGGGACT---------------TG-------TATCCAGAATATATAAAG 772

  chr2_195933295_   1887 AACTCA-AAAAATTAGCAAGAAAAAAACAAATGATTCCATCAAAAAAGTG 1935
                              v- v  v i ii  v     i      i ii v  i?     -  
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TG 821

  chr2_195933295_   1936 GGCTAAGGACACGAAAAGATAATTCTTAAAAGAAGATATACAAATGGCCA 1985
                            v     ivi   v   i v    iv                      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_195933295_   1986 ACAAACATATGGAAAAATGCTCAACATCACTAACTCT 2022
                          i  i  i   i   i             ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (140 / 91)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.07 (46 / 15)  


3112 23.58 3.00 2.00  chr2_195936240_195939598     1969  2867 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_195936240_   1969 TGAAAAGACATCC-ATGTTCAATGATCAGAAGACTGAATACTGTTAG--T 2015
                           i     i    -       vv   ii       v    i     i-- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195936240_   2016 GTCTGTACTAACCAAAGAAATACACAGGTTCAATGCAATCCCTACCAAAA 2065
                          v vi    vv     vvi  vi    i     i          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195936240_   2066 TCCCAGTGGCATTTT--AGAAAAATAGAAGAAAGAATTCTAAATTCCACG 2113
                               iv  v    --iv i    v  vi ivvi  i     v i  ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_195936240_   2114 TGGAACCAGAAAAAAACCCTGAATAGCCAAAATAACTGTAGGAAAGAAGA 2163
                              vi- v  iii    v            i  iiv iii        
  L1M4_orf2#LINE/    151 TGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_195936240_   2164 GCAAACCTTGAGGCATCATGGTTTCTGACTTCAAAACATATTACAAAAC- 2212
                         i    vi v    vv   iiv  i ii i        v  i      i -
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_195936240_   2213 ACAGTCA-CTACACAGGGTGTTCCTGGCATAAA-AGAGTCATCTAGAACA 2260
                              v - v v    v   v v         i- v  v   v    v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_195936240_   2261 ACAGAACAGAATAGAGAGCCCAGAAATGAACCCACAC--TAATGCAGTCA 2308
                          ii   i     v     i        i      i  -- v   --    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG--GTCA 347

  chr2_195936240_   2309 ACCGATCTTCCACAAAAATGCCATGA--ATACACACAAGGAAAGGATAAC 2356
                          ii   i   v    iii     v  --  v  - iii      i   ii
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAGAATAGT 396

  chr2_195936240_   2357 ----TCAAGGATAATGGTGTTGGGGGAACTGGATATACACATGCAAAAGA 2402
                         ----    vi --      i    iv         ?v             
  L1M4_orf2#LINE/    397 CTTTTCAACAA--ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_195936240_   2403 ATGAAACTGGACCCTTACCTTGCACTATAGAGAAAAATCAAATCAAAATG 2452
                              ii       i     ii   i   v v      i  v        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_195936240_   2453 AATTAAAGACTTAAACATAAGACTTGAAACTGTGACACTCCTGAAAGAAA 2502
                         i  i ?    i    ii     vi i     i i v    i ii      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_195936240_   2503 ATATAGAA-TACAAGCTTTATGACACTGGTCTTGGCAATAATTTCTTGGC 2551
                          i    i?-  -  v   ii    vi   vi v      ii      i v
  L1M4_orf2#LINE/    545 ACATAGGNGTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_195936240_   2552 TATGACACCAAAAGCATAGGCGTTTGTAG------TATGGTCCCAAACTT 2595
                                         i i  iviviv  ------  - i ---   -  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GAT---AAA-TT 638

  chr2_195936240_   2596 GAGACCACCTCAAACTGAAAAGCTTCTGCACAGCAAAGGAAACAAGCAAC 2645
                          -   iv v     v v    i   i  ii vv       v  v v   v
  L1M4_orf2#LINE/    639 G-GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_195936240_   2646 AAAGTGAAAAAGCAACCTATGGGATAGGAAAAAATAGTTGTAAACCCCTT 2695
                                   ii     i ii i  i   i      v   i   i viv 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_195936240_   2696 ATCTGATAAGAGAATAAAACCCA--ATATATAAGAAACTCCTA--ATTTA 2741
                                   i  v viv i   --        ii     i  -- i i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_195936240_   2742 ATAGCAAAAAGCCAAATAACCCAATTAAAAAAATGAGCAAAGGTCTTGAA 2791
                            ii      v              ?     -  i       vi     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chr2_195936240_   2792 TAGACAGACATTTCTCCAAAGAAGACATACAAATGGACAAGAGGCATATG 2841
                               ----               i          v   v i   i   
  L1M4_orf2#LINE/    837 TAGACA----TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_195936240_   2842 AAAAGATGCTCAACATCACTAATCAT 2867
                                           ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (129 / 79)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.88 (45 / 24)  


 789 28.12 0.89 0.89  chr2_195954479_195960569.rev     4967  5190 (901)    L1M4_orf2#LINE/L1        1   224 (684)  

  chr2_195954479_   4967 TGGAAGAACCTTGCATGCTCATAGATAGGAAGAATCAATATCGTGAAAAT 5016
                              ii iv iv    i    i   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_195954479_   5017 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5066
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_195954479_   5067 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5114
                          v   iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_195954479_   5115 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAACCAAAAAG 5164
                                viiv  ii  v  v v  v     i      i i vv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_195954479_   5165 AACAAAGCTGGAGGCATCACGCTACC 5190
                                i      vv    i  v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCC 224

Transitions / transversions = 1.62 (39 / 24)
Gap_init rate = 0.01 (3 / 224), avg. gap size = 1.33 (4 / 3)  

1183 26.23 1.47 1.72  chr2_195954479_195960569.rev     5192  5599 (492)    L1M4_orf2#LINE/L1      502   908 (0)  

  chr2_195954479_   5192 GACTTCAACTATACTACCTAAAGCCATAAAAACCCTAGAAGAAAACCTAG 5241
                            i v  - i  vv v     i i      vi i           v   
  L1M4_orf2#LINE/    502 GACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_195954479_   5242 GCAGTA--CCATTCAGGGTATAGGGATGGGGAAAGGCTTCATGACTAAAA 5289
                          ?-   --i -   iv iiv v   v i  v  v  i   v iiv  vi 
  L1M4_orf2#LINE/    551 GN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_195954479_   5290 CACCAAAAGCAATGGCAACATAAGCCAAAATAGACAAATAGGATCTAATT 5339
                                    vvi      v   vv        i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_195954479_   5340 AAACTAAAGAGCTTCTTCATGGCAAAAGAAACTACCATCAGAGTGAACAG 5389
                            v v  i i   i viiivv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_195954479_   5390 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAATG 5439
                         i     i                 v       vii ivi      i  v 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_195954479_   5440 GGCTAATATCTAGAATCTACAAAGAACTCAAACAAAT---TTACAAGAAA 5486
                          i  vi    i     v  i         vv    v --- v i  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_195954479_   5487 ACAAACAACCCCATCAAAAAGTGGGCAAAGGACACTTCTCAA-AGACACT 5535
                              i     v  i?    i           ---- i v  -     i 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGA----TTTGAATAGACATT 844

  chr2_195954479_   5536 TCTCAAAAGAAGACATCTATGCAGCCAACAGACAGATGAAAAAATGCTCA 5585
                             v        i  vi viii     i ii  v       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_195954479_   5586 CCATCACCGGTCAT 5599
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (57 / 48)
Gap_init rate = 0.02 (7 / 407), avg. gap size = 1.86 (13 / 7)  


3179 26.85 0.88 0.55  chr2_196063698_196069971.rev     4878  5782 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_196063698_   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_196063698_   4928 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCTTCCCCATGAAGC 4977
                            v     v     iv i  i  i        i  vv    i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_196063698_   4978 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTGAAAGTTC 5024
                          v   i-       i  -i     -   -- v  i  - iiiv   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_196063698_   5025 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCATAA 5074
                                 viiv  ii  v  v v  vi    iv     i i ivv v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_196063698_   5075 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5124
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_196063698_   5125 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5174
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_196063698_   5175 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5222
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_196063698_   5223 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5272
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_196063698_   5273 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5322
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_196063698_   5323 TGAAACTGGATCCCTTCCTTACG---TATACAAAAATCAATTCAAGATGG 5369
                             ii    i    v   i  i---           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_196063698_   5370 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5419
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_196063698_   5420 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5469
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_196063698_   5470 AAACACCAAACGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5519
                         vi        v   vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_196063698_   5520 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGGAACTACCATCAGAGTGAA 5569
                           i   v v  i i   i  ii vv    i iv    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_196063698_   5570 CAGGCAACCTACAAAATGGGAGAAAATTTTCACCACCTACTCATCTGACA 5619
                         v  i     i   i             v  ii v vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_196063698_   5620 AAGGGCTAATATCCAGAATCTACAATGAACCCAAACAAATTTACAAGAAA 5669
                          i  i  vi          v  i  v    i vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_196063698_   5670 AAAACAAACAACGCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5719
                           i     i   v v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_196063698_   5720 CTCAAAAGAAGACATTTATGCAGCCAGAAAACACATGAAAAAATGCTCAC 5769
                            v        i  vi viii    iv  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_196063698_   5770 CATCACTGGCCAT 5782
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2849 26.88 5.56 0.35  chr2_196212733_196219073     4987  5849 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_196212733_   4987 TGGAAGAACATTCCCTGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5036
                              ii i  i  v  i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_196212733_   5037 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5086
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_196212733_   5087 TACCAATGACGTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5134
                          v   iivi v  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_196212733_   5135 TATGGAACCAAAAAAGAGCCCGCATCTCCAAGTCAATCCTAAGCCAAAAG 5184
                                viiv  ii  v  v v  vv    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_196212733_   5185 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5234
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_196212733_   5235 TACAGTAACCAAAACAGCATGGGACTGGTA----------CATA------ 5268
                                 i   i    ii   v     i ----------    ------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_196212733_   5269 -ACG----------------------------CCGCATATCTACAACTAT 5289
                         - i ----------------------------  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_196212733_   5290 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGCAAAGGATTCCCT 5339
                         i    i  i     ivv  vv  i v  vv       v    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_196212733_   5340 ATTTAATAAATGGTGCTGGGACAACTGGCTAGCCATATGTAGAAAGCTGT 5389
                         v  i  i                     v  ?   i   i i  iiv  v
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_196212733_   5390 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGACGTATT 5439
                          ii    i    v   i     v              i    i i v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_196212733_   5440 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5489
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_196212733_   5490 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5538
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_196212733_   5539 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5588
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_196212733_   5589 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5638
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_196212733_   5639 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5688
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_196212733_   5689 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5738
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_196212733_   5739 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5788
                         i     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_196212733_   5789 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 5838
                          v        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_196212733_   5839 TCACTGGCCAT 5849
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.38 (132 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 6.38 (51 / 8)  


1867 24.17 14.25 3.94  chr2_196414219_196416195      692  1477 (500)    L1M4_orf2#LINE/L1        1   867 (41)  

  chr2_196414219_    692 TGAAGAGCTATACCAGGTTCAGGGACCAGAAGACT----ATTGTTAAGAT 737
                           i i  v   v   v     v   iii       ----           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_196414219_    738 GTTAATTTTTTCC---------TATAGACACAGTGCATTCTCAGTAAAAA 778
                          vi   vi ii  ---------  i   iv  ii   v  i vi v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_196414219_    779 ATCCAGCAGGCTTTTTTGCAGAGATGAACA-GCTT-TTTTAAAAATTTTA 826
                         vi     v v            i  vi   -   v- ii     --  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA--TTCA 148

  chr2_196414219_    827 TATGGAAAGGGGAAGGAACTTGAATAGCCAGTAGAATTTTGCAAAAGGGC 876
                                 v vi i   v iv         iv v   i   v     iiv
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_196414219_    877 AGCAAAGTTG------------------ATTT-AAGATTTACTATAAAGC 907
                          i        ------------------    -  i i      i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_196414219_    908 CACCGTAATCAAAACAGT-TGGAATTGGTGAAAGAGTAGACACATAAAGC 956
                         i  v        i     -   v i   iiv   ii      i   i v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_196414219_    957 AGTGGAACAAAGCAAAGAGTCC----------TCA--CATATATGG-CAA 993
                          i     i i iivi       ----------i  --   v     -   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_196414219_    994 TTAATCTTCAACAAAAGTACAAAGAAAATTCCATGTTGAAAGGATGGGAT 1043
                           i  i   i    ii  i v    vv    v   vv     i  -----
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT----- 393

  chr2_196414219_   1044 AGTATTTTCAACAAATGGCGCTGTAACAATTGGACATCTACATGCAATTA 1093
                            v              i    vi    i    i ? i        ---
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA--- 440

  chr2_196414219_   1094 AAAAAAAAGGAAGAAAGAAAAATACCTTTGACCCATATCTCAC--TATAG 1141
                         ---  i  v    -------------  v     v  i     --i   v
  L1M4_orf2#LINE/    441 ---AAGAATGAAG-------------TTGGACCCCTACCTCACACCATAT 474

  chr2_196414219_   1142 AAAAAACAATGAACTCAAAGTAGGT----AATCTAAATG---GAGATT-- 1182
                          v    --  v        i i i ----i i       ---   v v--
  L1M4_orf2#LINE/    475 ACAAAA--ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_196414219_   1183 -CT-TAAAAAT---AGAAGAAAATATAGA---ATATCTCTGTGTCTTTGG 1224
                         -  -     v ---         i    i--- v    ii   v i    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr2_196414219_   1225 GTTAGGCAAAGTATTCTTAGATACAGCACTAA--GCATACTCCATTAAGG 1272
                                  v vv          iii   i  --   i vv v iv  i 
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_196414219_   1273 AAAACAGTCATAAAATACACTTCTTACAAATTAAAAACTCTT----CACA 1318
                             v vvv     v iv     v vv            i  ----iv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_196414219_   1319 AAAGACA--GTTAACAAA-----AAGGGAAGCCACAAACTGGGACAAAAT 1361
                           i    --i i  v   -----   iv  v     i v     v     
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_196414219_   1362 ATTTGGACAATACATATCTGACAAAAGACTT------------------- 1392
                              v v vi i        i  ii     -------------------
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_196414219_   1393 -------------CAATCATAGTAAAACAAACAGCCCAACAAAATAAAAT 1429
                         -------------    v   iv  i     i i     iv?  --    
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA--AAAT 820

  chr2_196414219_   1430 AGACAAAAAGACTTGAACAAATGTTTCACTGAAGAAAGTATACAGATG 1477
                         i i    i-  i     i i ii    v ii     ii      i   
  L1M4_orf2#LINE/    821 GGGCAAAG-GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

Transitions / transversions = 1.44 (111 / 77)
Gap_init rate = 0.03 (29 / 867), avg. gap size = 4.93 (143 / 29)  


3069 27.57 1.00 0.44  chr2_196433776_196439973     4804  5706 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_196433776_   4804 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4853
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_196433776_   4854 GGCTGTACTGCCCAAGGTAATTTACAGATTCAATGCTATCCCCATCAAGC 4903
                            vi    v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_196433776_   4904 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4951
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_196433776_   4952 TATGGAACCAAAAAAGAGCCCACATCGCGAAGTCAATCCTAAGCCAAAAG 5001
                                viiv  ii  v  viv  v  v  iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_196433776_   5002 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5051
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_196433776_   5052 TACAGTAACCGAAACAGCATGGTACTGGTACCAAAACAGAGATAGAGACC 5101
                                 i i i    ii         i iv ii i   v   v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_196433776_   5102 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCTTATCTACAACT 5149
                                i    i--    i  --        vv  iivi  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_196433776_   5150 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5199
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_196433776_   5200 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 5249
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_196433776_   5250 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5299
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_196433776_   5300 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5349
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_196433776_   5350 CAAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5399
                         vv   ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_196433776_   5400 AACACCAAAAGCAATGGCAACAAA-GCCAAAATTGACAAATGGGATCTAA 5448
                         i            vvi        - vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_196433776_   5449 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5498
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_196433776_   5499 AAGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5548
                          ii     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_196433776_   5549 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5598
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_196433776_   5599 AAACAA----CCCCATCAAAAAGTGCGTGAAGGACATGAAAAAACACTTC 5644
                          i    ----   v  i?    i  v ii     iv    v i   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_196433776_   5645 TCAAAAGAAGACATTTATGCAGCCAAAAACCACATGAAAAAATGCTCACC 5694
                           v        i  vi viii     v  v          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_196433776_   5695 ATCACTGGCCGT 5706
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3310 25.70 1.78 0.78  chr2_196452095_196456368     2884  3782 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_196452095_   2884 TGGAAAGATATTCCATGTCAATGGATTGGAAGAATCAATATTGTTAAAAT 2933
                                    i      iv             v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_196452095_   2934 GTCCATCCTACCAAAAGCAGTCTATAGATTCAGTGCAACCCCCATCAAAA 2983
                          v v  v  v  v   viii    i       ii    i   i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_196452095_   2984 TACCTATGACATTCTTTATAGAAATAGAAAAAAAAAAACGCTAAAACTTA 3033
                          v  viivi v  i   ii      v  v  ivvi --iv      i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chr2_196452095_   3034 TATGGAACCACATAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAATG 3083
                                vii  vii                 i v   i   iv  i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_196452095_   3084 ATTAAAACTGGAGGAATCACATTACCTGATTTCAAATTATACTACAGAGC 3133
                          vi   ii       v     i v  ii        viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_196452095_   3134 TATAATCAACAAAACAGCATGGTACTGGCATAAAAACAGACACACAGCCC 3183
                           i i v v   i    ii              ii i     i i  vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_196452095_   3184 AATAGAACAGGAGAGAGAACCTATAGATAAATCCATACATCTACAGTGAA 3233
                            i   i  i vv    ii i v i     i        i  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_196452095_   3234 CTCATTTTTGACAAAGTTGCCAAGAACATACTTTAGTTG-------ACAG 3276
                         i v     i     i v        v   --- i i v ------- i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCAT---TCAATGGGGAAAGAATAG 395

  chr2_196452095_   3277 TCTCTTCAATAAATGGTGCTGGGAAATCTGGATATTCATATGCAGAAAAG 3326
                            i     i              v v       ?i  i     i  i i
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_196452095_   3327 TGAAACCAGACCCCCATCTTGC--CATAT-TAAAAA---AGTTAAAATGG 3370
                             iiii      i i  ii --     -i     --- v i       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_196452095_   3371 ATTAAAGGCTTAAATCTAAGACCTCAAACTATGAATCTACTGTGAGGAAA 3420
                           i ?  i i     v     v  v       i  v  vi ivi  i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_196452095_   3421 CATTGAAGAAGCTCTCCAGGACCTTGGATTGGGCAAAGATTCCTTGAGTA 3470
                            v i? v iv   i iv        i  i     v i  i   iii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_196452095_   3471 ATACTCCACAGGCACAGACAAACAAAGCAAAAGTAGACAAATGGGATCAC 3520
                         vv  v   v i     ii   vv    v    i    i    v   iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_196452095_   3521 ACCAA--TTAAAAAGCTT-GTCCATAGCAAAAGAAGCAATCAATAAAATG 3567
                          i   --       vi  -  v v --    i  vi v     v   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTG 693

  chr2_196452095_   3568 AACAGAGAACACAGAGAATGGGAGAAAATATTTGCAAACTACCTATCTGA 3617
                           v   v   v  v                        ii iv       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_196452095_   3618 TGAGAGATTAAGAACCAGAATATATAAGATGGTCAAACAACTCTGTAGGA 3667
                          i  i  i viv v             iiviv  vv       vi  iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_196452095_   3668 AAAACTCTAATAATCCAATTTTAAAATGGGCAAAAGATCTGAATAGACAT 3717
                             vv v     i      ?v            i   i           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_196452095_   3718 TTCTCAAAAGAAGACATACAAATGGCAAAAAGGCATACAGAAAGGTGCTC 3767
                              v        i           v  v i   i iii    i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_196452095_   3768 AATGTCACTGATCAT 3782
                           ii   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.56 (23 / 9)  


2638 26.00 2.43 1.58  chr2_196535186_196536999      501  1323 (491)    L1M4_orf2#LINE/L1       79   908 (0)  

  chr2_196535186_    501 TTCAAGGCTACTCCTATCAAACTACCAATGACATTTTTCACAGAATTTGG 550
                              v  v ii         v v   iivi v     ii     v   -
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG- 127

  chr2_196535186_    551 AAAAAGT--ATTCTAAAATTCATATGGAACCAATAAAGAGCCC-GAATAG 597
                         - v   i--  i                 vii-i  i ii   -      
  L1M4_orf2#LINE/    128 -ACAAGCTGATCCTAAAATTCATATGGAAATG-CAAGGGACCCAGAATAG 175

  chr2_196535186_    598 CCAAAGCTATCCTTAGCAAAAAGAACAAAGCCAGAGGCATCACATTATCT 647
                              i v   i v iv  i          iii    vv     i vi i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_196535186_    648 GACTTTGAACTATACTACAAGGCTCCAATAACCAAAACAGCATGATACTG 697
                         i i  ii  viv        i   v  i   i   i    ii  i     
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_196535186_    698 GTGCAA----AAACATA--GATGAATGGAACAGAATAGAGAGCACAGAAA 741
                          iii  ---- i     --   v       i     v     iv      
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_196535186_    742 TAAAGCTGTACACCTACAAGCATCTGATCTTTGACACAGTTGACAAAAAT 791
                             v ii    ii  iiiv  vi    i  i    vi v  v   i vi
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_196535186_    792 AAGCAATGGAGAAAGGACTCCCTATTCAATAAATGGTGCTAGGGTAACTG 841
                          vv      i     i ivvi  v     i          i  ii     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_196535186_    842 GCTAGCCATATGCAGAAGACTGAAATTGGACCCATTCGTTACGCCATATA 891
                          v  ?   i     i    v    i        v v v i  i       
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_196535186_    892 CAAAAATCAACTCAAGATGAATTAAAGACGTAAATGTAAAACCTAAAACT 941
                                i       i   i  i ?    v         i v        
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_196535186_    942 ATAAAAC-CTTAGAAGAAAACCTAGG---AAATACCATTCTAGACATAGG 987
                                -             v    ---    -- -   vv   v v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGG 572

  chr2_196535186_    988 CCCTGGCCAAGATT----AAATGGCAAGGATGCCAAAA--ACAATTGCAA 1031
                         viiv   v v i  ---- i  ---- v  ii      --    --    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGAT----ATGACACCAAAAGCACAA--GCAA 616

  chr2_196535186_   1032 CAAAAACGAAAATTGACAAGTGGGACCTAATTAAACTAAAGAGCTTATTC 1081
                              ivi     v  i  i v    i v  i   v v  i i   v vi
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_196535186_   1082 ACAGCAAAATAAACTATCAGCAGAGTAAATAGACAACCTACACAATGGGG 1131
                         i vv    iv v       iv i   i  v        i   v      i
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_196535186_   1132 AGAAACATTTGCAAACTATGCATCTGACAAAGGTCAATATATCTAGAATC 1181
                         ii   i         ii  ii      i  i  v v- i    i     v
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACT-TGTATCCAGAATA 765

  chr2_196535186_   1182 CATAAGGAACGTAAACAAATTAACAAGCAAAAAACAACTCACCCCTTTAA 1231
                         i    i    vivv    v i  i  vv    i    v v    vv  ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_196535186_   1232 AAAGTAGGCAAAGAACATGAACAGATACTTCTCAACAGAAGACATACACG 1281
                            i i       i iv    i   i i     v v      i     vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_196535186_   1282 CAGCCA-CAAGGATATGAAAAAATGCTCAACATCGCTAGTCAT 1323
                         ii    -i   v i       i            i????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (128 / 83)
Gap_init rate = 0.02 (16 / 830), avg. gap size = 2.06 (33 / 16)  


2931 27.25 1.17 0.58  chr2_196620935_196623862.rev     1561  2415 (513)    L1M4_orf2#LINE/L1        1   860 (48)  

  chr2_196620935_   1561 TGGAAGAACATTCCATGCTCATGGGTAGGAATAATCAATATCATGAAAAT 1610
                              ii i  i     i      i v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_196620935_   1611 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAAG 1660
                            v     v     iv i  i  i        i  v     i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_196620935_   1661 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1708
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_196620935_   1709 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 1758
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_196620935_   1759 AACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAGGC 1808
                                i      vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_196620935_   1809 TACAGTAACCAAAACAGCATGGCACTGTTACCAAAACAGAGATGTAGACC 1858
                                 i   i    ii   i    vi iv ii i   v  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_196620935_   1859 AATGTAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATTTACAACT 1906
                             v  i    i--    i  --        vv   i i     iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_196620935_   1907 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATTGGGAAAGGATTCC 1956
                          vi    i  i     ivv  v   i v  vvv   v       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_196620935_   1957 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2006
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_196620935_   2007 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2056
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_196620935_   2057 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2106
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_196620935_   2107 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 2155
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_196620935_   2156 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTC 2205
                         vi            vvi          vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_196620935_   2206 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 2255
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_196620935_   2256 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 2305
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_196620935_   2306 AAGGCCTAATATCCAGAATCTACAATGAACTCAAACAAAT---TTACAAG 2352
                          i  v  vi          v  i  v      vv    v --- v i  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_196620935_   2353 AAAACAA-CAACCCCATCAACAAGTGGG-GAAGAATATGAACAGACACTT 2400
                           i    -i     v  i? v  i    -i   i  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_196620935_   2401 CTCAAAAGAAGACAT 2415
                            v        i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATAT 860

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.01 (10 / 860), avg. gap size = 1.50 (15 / 10)  


3056 27.59 0.77 0.55  chr2_196637775_196644465.rev     5294  6199 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_196637775_   5294 TGGAAAAAGATTCCATGCTCATGGATAGGAAGAATCAGTATCGTGAAAAT 5343
                               i v  i     i        v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_196637775_   5344 GGCCATACTGCCCAAAGTAATTAATAGATTCAGTGCTATCTTCATCAAGC 5393
                            v     v      v i  iv i       ii  v   iii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_196637775_   5394 TGCTATTGACTTTCTTCACAGAATTAGAAAAAAACC-ACTTTAAATTTCA 5442
                          v i vivi i  i  ii     v v  v  i-- i- iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_196637775_   5443 TATGGAACCAAAAAAGAGCCCTTATAGCCAAGACAATCCTAAGCAAAAAG 5492
                                viiv  ii  v  vvv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_196637775_   5493 AACAAAGCAAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5542
                                ivi    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_196637775_   5543 TACAGTAACCGAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGACC 5592
                                 i i i    ii    i    i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_196637775_   5593 AATGGAACAGAACAGAGACCTCAGAAATCACACCACACATCTACAACCAT 5642
                                i    iv    vii       v vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_196637775_   5643 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAGGCGTTCCCT 5692
                         i    i  i     ivv  v   i v  vv     i    i vi vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_196637775_   5693 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAGGCAGAAAACTGA 5742
                         v  i  i        i     v      v  ?   i v   i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_196637775_   5743 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 5792
                          ii         v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_196637775_   5793 AAAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5842
                          ?    i    i      v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_196637775_   5843 AGGCA-ATACCATTCAGGATACAGGCATGGGCAAAGCCTTCA-AGACTAA 5890
                            ?i- v i -   iv  iviv  vv i     v vi   v-   -  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TAT 596

  chr2_196637775_   5891 AACACCAAAAGCAATGGCAACACAAGCCAAAATTGACAAATGGGATATAA 5940
                         i            vvi      v   vv     v  i    v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_196637775_   5941 TTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTAAAC 5990
                          i   v v  i i   i  ii vv    iv v       vv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_196637775_   5991 AGGCAGTCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 6040
                           i  ii i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_196637775_   6041 AGGACTAATATCCAGAATCTACAATGAACTT----AAGCCAATTTACAAG 6086
                         i     vi          v  i  v     i----  vi    v- i  i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAA 795

  chr2_196637775_   6087 AAAAAAAACAACCCCATCAGAAAGTGGGCAAGGCATGTGAACAGACACTT 6136
                           i v   i     v  i?i   i       i v  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_196637775_   6137 CTCAAAAGAAGACATTTATGTGGCCAACAAACCTATGAAAAAAAGCTCAT 6186
                            v        i  vi vi       i  i vi       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_196637775_   6187 TATCACTGGTCAT 6199
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (143 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3405 23.01 0.64 4.35  chr2_196653092_196657705.rev     3180  4122 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_196653092_   3180 TAAAAAGGTATATTCCATGTTCATGGATTTGAAGAATCAATATTGTTAAA 3229
                          ii    --    i               v     v i           i
  L1M4_orf2#LINE/      1 TGGAAAG--ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr2_196653092_   3230 ATGTTCATACTACCCAAAGCAATCTTCATATTCAGTGTAATCCCTATCAA 3279
                            viv     v      vii    v  v     ii i            
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_196653092_   3280 AATGCCAATGAGATTCCTCACAGAAATAGAAAAAACACTCCTAAATTTTT 3329
                            v   iivivv  ii ii       v  v  i----------------
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---------------- 132

  chr2_196653092_   3330 TTTGTCTCCTGCCCATCCCCACAGTTCTACAATTTTTATGGAACTACAAA 3379
                         --------   ---    ---------  v    iv       v i   i
  L1M4_orf2#LINE/    133 --------CTG---ATCC---------TAAAATTCATATGGAAATGCAAG 162

  chr2_196653092_   3380 AACCTTAGAATAGCCAAAGCTATCTTGAACAAAAAGAACAAAACTGGTGG 3429
                         iiv ii            i v        v  i         ii   v  
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_196653092_   3430 AATCACATTACCTAGTTTCAAA--TTAGGATTCAGAGCTTTAGTAACCAA 3477
                          v     i v  i i       --   vv --  i    vi     i   
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTA--CAAAGCTACAGTAATCAA 260

  chr2_196653092_   3478 AGCAGCATGGTACTGGCAGAAAAACAGACGCATAGACCAATGGAACAGAA 3527
                         ii   ii           v  ii i    ii     i        i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_196653092_   3528 TGGAGAGCCCAGAAACAAATTCATAAATCTACAGTAAATTCATTTTAGAG 3577
                          v     i       i   ii    v  i  ii  v    v     v  v
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_196653092_   3578 AAAAGTGCCAAGGACATACTTTGGGAAAAAGACAATCTCTTCAACAAATA 3627
                           ii        iv   v vv    i   ii i i   i          i
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_196653092_   3628 GTACTGGGAAAACTGGATATTCATATACAGAAGAATGAAGCTAGACCCCT 3677
                           i      v         ?i  i  i  i          i i       
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_196653092_   3678 ATCTCTCACCATATA-AAAAATCAAATCAAAATGGATTAAAGACTTAAAT 3726
                          i   v         -      i  v           i ?    i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_196653092_   3727 CTAAGACCTCAAACTATGAAACTACTACAAGAAA-CATTGGAGAAACTCT 3775
                         v     v  v       i     vi  v      -   v  ? v  v   
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_196653092_   3776 CCAGGAATTTGGACTGGGCAAAAATTTCTTGAGTAATACCCCACAAGCAC 3825
                         i iv  vi    ii i     vii      iii  vv  v   v      
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_196653092_   3826 AGGCAAACAAAGCAAAAGTGGACAAATGGGATCACATCCAG-TTAAAAAC 3874
                          i    vv    v    i i  i    v   iiv    v i-        
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_196653092_   3875 TTCTGCACAACAAAGGAAACAATAAACAACATGAAGAGACAACCCAGAGC 3924
                           i  ii vv       v  v  v  v  vi    i          v  v
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_196653092_   3925 ATGGGAGAAAATATTTGCGAACTACCCATCTGATGAGGGATTAATAACTG 3974
                                           i  ii ivi       i     i vi  v ii
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_196653092_   3975 GAATACATAAGGAGATCATACAACTCTGTTGGAAAATCTCTAATAACCTG 4024
                              i    i  iv  v        vi viv    vvv v       i-
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC- 809

  chr2_196653092_   4025 AATTTAAAA-TGGGCAAAAGATGTGAAGAGACATGTCACAAAAGAAGACA 4073
                             ?    -        i   v    v      v  v v        i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_196653092_   4074 TACAAATGGCAAATAGACATTTGGAAAGGTGTTCAACATCATTGATTAT 4122
                                   v    ii  iv  i    i  i         ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (124 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 4.27 (47 / 11)  


2970 25.81 3.11 2.22  chr2_196668301_196672970     3280  4178 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_196668301_   3280 GGAAAGATATTCCATGTTCATAAATTAGAAGAATCCAATATTGTTAAAAT 3329
                                   i          ii   i     v i-           i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTT-AATATTGTTAAGAT 50

  chr2_196668301_   3330 GTCCATACTACCCCAAA---------------AA-GCAATGTC------A 3357
                          v v     -       ---------------  -     vi ------ 
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_196668301_   3358 ATGTCAATGACATTCCT--CAGAAATAGAAAAAAAAAACTTAAAATTTAT 3405
                           vi  iivi v  ii --       v  v  ivvi v i       i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_196668301_   3406 ACGAAACCGCAAAAACCCCAGAATAGCCAAAGCTATCCGGAGCAAAAAGA 3455
                          i i  vi    iiiv               i v   iv  iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_196668301_   3456 ACAAAACTGGAGGAATCACATTACCTGATTAGAAATTATACTATAGAGCT 3505
                              ii       v     i v  ii   vv   viv     i i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_196668301_   3506 ACAGTAACCAAAATAGCATGGTGCTTGCAGAAAAACTGACACACAGACTA 3555
                                i   i i  ii    i  v   v  ii iv    i i   ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_196668301_   3556 TTGGAACAGAATGGAGAACACAGAAACCAATTCATAAATCTACAGTGAAC 3605
                         v     i     v    iiv      iv  ii    v  i  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_196668301_   3606 TCATTTTCGAGAAAAATGCCAAGAACATACCTTGGGATAAGGACAGTCTC 3655
                          v        v  iii        v   v vv    iv   i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_196668301_   3656 TTCAATAAATGGTACTGGGCAAACTGGATATTCATATGCAGAAGAATGAT 3705
                              i       i     vv         ?i  i     i        v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_196668301_   3706 ACTAGACCTCTGTCTCTCAACATATACAAAAATCAAATCAAAATGGATTA 3755
                         ii i    i  ii   v  v             i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_196668301_   3756 AAGACTTAAATCTAAGACCTCAAACTATGAAACTGCCACAAGGAAACATT 3805
                         ?    i     v     v  v       i     vii v   i      v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_196668301_   3806 GGAGAAACTTTCCAGGAACTTGGACTGGTCAAATATTTCTTGAGTAACAC 3855
                           ? v  v i i iv  v     ii i v   vvi      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_196668301_   3856 ACCACGAGTACAGGCAAACAAAGCAAAATTGGACAAATGGGATCACATCC 3905
                             vi  i   i    vv    v    v i  i    v   iiv    v
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_196668301_   3906 AG-TTAAAAAGCTGCTACATGGCAAAGGAAACGATCAACAACATGAAGAG 3954
                          i-       -  vi iiiivv       v  v     v  vi    i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_196668301_   3955 ACAACCCAGAGCACGGGAGAAAATATTTGCAAACTACCCATCTGACGAAG 4004
                                 v  v i                   ii ivi      ii i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_196668301_   4005 GATTAATAACCAGAACTATACTATTGCAGCACTATACAAGGAGCTCAAAC 4054
                           i vi  v      -----------------    i  i  i   vv  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAA-----------------TATATAAAGAACTCTTAC 781

  chr2_196668301_   4055 AACTCTATAGAAAAATCTCTAATAATCTGATGAAAAAGTGGGCAAATTAT 4104
                              v   iv    vvv v     i ii  v?    i        vv  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_196668301_   4105 CTGAATAGATATTTTTC---AAAAGACATACAAATGGCAAACAGGCATAT 4151
                         i        i    i  --- i    i           v  i i   i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_196668301_   4152 GGAAAGGTGCTCAACATCACCAATCAT 4178
                          i    i            ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (136 / 92)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 4.80 (48 / 10)  


2180 17.32 8.75 6.25  chr2_196694122_196698924     3078  3637 (1166)    L1M4_orf2#LINE/L1        1   574 (334)  

  chr2_196694122_   3078 TGGAAAGACATCCTGTGTTCATGAATTGAAAGACTTAACATTATTAAGTT 3127
                                 i    ii        i    i         i   i     v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_196694122_   3128 A------------AAATTAATGTACAGATGTAATGCATTCCCTATTAAAA 3165
                         i------------     i  v       vi  i   v       i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_196694122_   3166 TCCCAATGGCATTTTTTA-AAAAATGGACAAGTTGCTACTAAAATGCATA 3214
                              iiv  v      i- i    v      i  v v       v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_196694122_   3215 TA-AAATACAAAGGACTCAGAACAAC---AACAATTTTTCAACTCAGAAA 3260
                          i-    i   i    i     i i ---      i  --------    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--------GAAA 192

  chr2_196694122_   3261 AATAAGAACAAAATTGGAGGACTCACACTTCCTTATCTCAAAACTTACTA 3310
                           v         i                   iv  i             
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_196694122_   3311 CAAA---------------ACGGTTTGGTACTGGCATAA----AGACAAA 3341
                             ---------------  i  v              ----     v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_196694122_   3342 TAGGCCAATGAAACAGAATAGAGAGCCCAGAAATAAACCCTCCCATATAT 3391
                            ii     i  i     v     i              viv   v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_196694122_   3392 GGTCAAATGATTTTCAGCAAAGGTGCCAAGACAACTCACTC-----AGAA 3436
                               v        ii   i           v i   v v-----    
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_196694122_   3437 GAGTCTTGC--ACAAATGGTGCTCAGACTACCAGATATCCATATGCAAAA 3484
                         v      vi--            vi   v  ii    ?   i        
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_196694122_   3485 TAATAAATTTGGGCTCCTACCTCAGACCATGTATAAGTTAAAATGAATTT 3534
                         v   i  v    i i         v     i  i  ----    v  i i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAA----AAATTAACTC 488

  chr2_196694122_   3535 GGTTTGTAAA--GGTCAAAAAGGCCTAAATGTAGGAGCTACAACTATAGA 3582
                         i------   -- i   ? i --          i      v       i 
  L1M4_orf2#LINE/    489 A------AAATGGATCAWAGA--CCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_196694122_   3583 ATGATTAGTTCTGTTTACCACACAGGAAAACA----GGTAAATCTTGGTG 3628
                          ivv    --------------- i       ----?         v   
  L1M4_orf2#LINE/    531 ACTCTTAG---------------AAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_196694122_   3629 GCTTTGGAT 3637
                         i i    i 
  L1M4_orf2#LINE/    566 ACCTTGGGT 574

Transitions / transversions = 1.76 (60 / 34)
Gap_init rate = 0.03 (15 / 574), avg. gap size = 5.60 (84 / 15)  

1085 12.82 9.62 9.62  chr2_196694122_196698924     4000  4311 (492)    L1M4_orf2#LINE/L1      597   908 (0)  

  chr2_196694122_   4000 GATACCAAAAGGCACAAACAACCAAAGAAAAAACA--TAAATGAGACTTC 4047
                           i        -     i    v          i --     vi      
  L1M4_orf2#LINE/    597 GACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_196694122_   4048 GTCAAAATTAAAAATATTTGTGCTTCAAAGGATACTATCAA--------- 4088
                         i             iv                i        ---------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_196694122_   4089 ----------------TAGGAGAAA-TATTTGCAAATAATATAATTGATA 4121
                         ---------------- i       -           v     vi     
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_196694122_   4122 AGGGTCTAGTATCCAGAATATACAAAGAACTCTTAAATCTCAACAACAAA 4171
                             v  v              i            v v     i  i   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_196694122_   4172 ATATCAGATATTTTACATGTCAAAAATAAAAATCAGACAACCCAGT-AGA 4220
                          ----   -------------------------  i i      i -?i 
  L1M4_orf2#LINE/    796 A----AGA-------------------------CAAATAACCCAATTWAA 816

  chr2_196694122_   4221 AAATGAACAAAGGGTTTGAATAGACATTT-TCCAAAGATGACAAATAAAC 4269
                              ii      i               -        v  i v i   i
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_196694122_   4270 AGACAATAAGCCCATAAAAAGATAGTCAACATCATTGGTCAT 4311
                         i v        v   i       iv         ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (25 / 14)
Gap_init rate = 0.03 (8 / 312), avg. gap size = 7.50 (60 / 8)  


3203 22.72 1.78 2.67  chr2_196728204_196732702     3111  4008 (491)    L1M4_orf2#LINE/L1       19   908 (0)  

  chr2_196728204_   3111 TCATGGATTGGAAAAATTATTATTGTTAAAATGTCCATACTGCCCAAAGC 3160
                                      i v   v         i   v v     v      vi
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chr2_196728204_   3161 AATCTATACATTCAATACACTCCCTATCAAAATACAAATGACACTCTTCA 3210
                         i     i v      ii  v             v v iivi vi i  ii
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG 118

  chr2_196728204_   3211 CAGACATAGAAAAAACAATCCTAAAATTTATATGGAACCACAAAAGACCC 3260
                             v  v  v  ivii           i        vii   ii     
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr2_196728204_   3261 CAAATAGCCCTAATCCTTAACAACAACAACAACAAAAAGACCAAAAATGG 3310
                         vi       --  -----     i-- vvv  v  i    v    iv   
  L1M4_orf2#LINE/    169 AGAATAGCC--AA-----AACAAT--CTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_196728204_   3311 AGGAATCACACTACCAGACTTCAAAATACAGTACAAAGCTATAGTAACCA 3360
                             v       v  vi i       ivi v          i     i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_196728204_   3361 AAACAGCATAATGCTGATATAAAAACAGACACTTAGACCTGTGGAAAAGA 3410
                          i    ii ii i   ii    ii i     iv    i vi     v   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_196728204_   3411 ATAGAGAAAGCATAAATAAATCCATGCATTTATATTCAACTCATTTTTGA 3460
                           v    ivv  v       i    i       iv    i v     i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_196728204_   3461 CAAAGGTGCCAAAAACATAAATTGGGGAAAGGACAGCCTCTTCAATAAAT 3510
                            i        i v   vv v         i i  i  i     i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr2_196728204_   3511 GGTGCTGGGGAAACTGGGTATCCATATG---AAGAATAAAACTAGACCC- 3556
                                  iv      i  ?   i   ---      i  ii i     -
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_196728204_   3557 TATCTCTCACCATCTACAAAAATAAAATGAAAATGGATTAAAGACTTAAA 3606
                           i   v      v         v  v v         i ?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_196728204_   3607 TCTAAGACCTGAAACTATGAAAGTACTAGAAGAAAACATTGGAA-AAATG 3655
                          v     v  i       i   v vi             v  ?i-    -
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT- 558

  chr2_196728204_   3656 CTTCAGGAGATTGGTCTGGGCAAAGATTTTTTGGGGTAAGACCTCGAAAG 3705
                             iv  vv    vi i     v i   i  i i-  v   vi i    
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAG 607

  chr2_196728204_   3706 CATAAGCAACAAAAGAAAAACAAGATTA---------TATCAAG-CTAAA 3745
                           i                 vv    v ---------i     i-i    
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_196728204_   3746 AATATTTGCATAGCAAAAGAAACAATCAACAGAATGAAGAGAAAACCCAC 3795
                           iv    iiivv    i  v  v     v i i    i   v       
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_196728204_   3796 AGAATGGGAGAAAATATTTGCAAACTATCCATAGACAAGGGATAAGGGAT 3845
                                                 ii  vi  --- ---v         i
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATAT---C---TGATAAGGGAC 751

  chr2_196728204_   3846 TAATAACCAGAATATATAAGGAACTCAAACAACTCAACAACAAATAATAA 3895
                          vi  v             i      vv         i  i   ----  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA----AA 797

  chr2_196728204_   3896 TAATAATAATAATTTGATT-AAAAATGGGCAAATGATCCAAATAGATATT 3944
                         -i i  --    iiii   -             v   iii      i   
  L1M4_orf2#LINE/    798 -GACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_196728204_   3945 TCTCCAAAGAAGATGTACATATGGCCAACAGATGTGTGAAAACTTGCTCA 3994
                                       i    v        i iiiiii      vv      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_196728204_   3995 ACATCTCTAATCAC 4008
                              v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (120 / 81)
Gap_init rate = 0.02 (16 / 890), avg. gap size = 2.50 (40 / 16)  

 312 16.44 4.11 0.00  chr2_196728204_196732702     4427  4499 (0)    L1M4_orf2#LINE/L1      681   756 (152)  

  chr2_196728204_   4427 TACCAATAGTGTGAAAAGATAAGGCACAAACTGGGAGATAATATTTGCAA 4476
                           i   v iv         i  vv    i v       v           
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_196728204_   4477 A--AGATATCTGA-AATGGACTTGTA 4499
                          -- v        -  v         
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTA 756

Transitions / transversions = 0.50 (4 / 8)
Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.50 (3 / 2)  


3016 27.39 1.56 0.45  chr2_196778929_196785291     4974  5871 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_196778929_   4974 TGCAAGAACATTCCATGCTCATGGATAGGAAGAAACAATATTGTGAAAAT 5023
                           v  ii i  i     i        v      vvi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_196778929_   5024 GGCCATACTGCCCAAGGTAATTTATAGATTCAATACCATCCCCATCAAGC 5073
                            v     v     iv i  i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_196778929_   5074 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-AT--TAAAGTTCA 5119
                          v i iivi i  i  ii     -   -- v  i  -  --    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_196778929_   5120 TATGGAGCCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5169
                               iviiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_196778929_   5170 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5219
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_196778929_   5220 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5269
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_196778929_   5270 AATGGAACAGAGTAGAGGCCCTAGAAATAATACCACATCTCTACAACCAT 5319
                                i   i v   ivi i        vv   i iv i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_196778929_   5320 CTGATATTTGACAAACCTGACAGAAAACAAGAAATAGGGAAAGGATTCCC 5369
                         i    v  i     ivv  v  - i v  vvv   i       i  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_196778929_   5370 TATTTCATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5419
                          v  iv i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_196778929_   5420 AAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGAT 5469
                           ii    i    v   i   i v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_196778929_   5470 TAAAGACTTAAATGTTAGACGTAAAACCATAAAAACCCTAGAAGAAAACC 5519
                         i ?    i       v   vv      i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_196778929_   5520 TAGGCA-ATACCATTCAGGACAAAGGCATGGGCAAGGACTTCATAACTAA 5568
                             ?i- v i -   iv   vvv  vv i     v ii   v  iv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_196778929_   5569 AACACCAAAAGCAATGGCAACAAAACCCAAA-----CAAATGGGATCTAA 5613
                         i            vvi         vvv   -----i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_196778929_   5614 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5663
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_196778929_   5664 AGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCTATCCGACAA 5713
                           i     i                 v   i   vii iv    i  i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_196778929_   5714 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5763
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_196778929_   5764 AATCAA----CCCCATCAAAAAGTGGGCAAAGGGTATGAACAGACACTTT 5809
                          iv   ----   v  i?    i          i v    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_196778929_   5810 TCAAAAGAAGACATTTATGCAGCCAACAGACACATTAAAAAATGCTCATC 5859
                           v        i  vi viii     i ii     v    i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_196778929_   5860 ATCACTGGCCAT 5871
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


3181 26.83 1.11 0.44  chr2_197211964_197218230.rev     4874  5775 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_197211964_   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4923
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_197211964_   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4973
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_197211964_   4974 TACCAATGACGTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5021
                          v   iivi v  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_197211964_   5022 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGTCAAAAG 5071
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_197211964_   5072 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5121
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_197211964_   5122 TACAGTAACCAAAACAGCATG-TACTGGTACCAAAACTGAGATATAGATC 5170
                                 i   i    ii  -      i iv ii iv  v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_197211964_   5171 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5218
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_197211964_   5219 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5268
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_197211964_   5269 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5318
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_197211964_   5319 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5368
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_197211964_   5369 TTAAAGATTTAAACGTTAGACCTAACACCATAAAAACCCTAGAAGAAAAC 5418
                          i ?   ii    i  v   v    v  i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_197211964_   5419 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5468
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_197211964_   5469 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5518
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_197211964_   5519 TTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5568
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_197211964_   5569 AGGCAACCTACAGAATGGGAGAAAGTTTTCGCAACCTACTCATCTGACAA 5618
                           i     i               i v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_197211964_   5619 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5668
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_197211964_   5669 AAACAA----CCCCATCAAAAAGTGGGCAA-GGACATGAACAGACACTTC 5713
                          i    ----   v  i?    i       -   iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_197211964_   5714 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5763
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_197211964_   5764 ATCACTGGCCAT 5775
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3182 21.07 1.45 8.16  chr2_197319386_197322131     1287  2254 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_197319386_   1287 AGATATCCTGTGTTCATCTATTGGAAGAGTTAACATTATTAAAATGTCCA 1336
                                 ii       vv         v    i   i    i   v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_197319386_   1337 TACTGCCCAATGTGATCTCTAGATTCAATGTAATCTCTACTAAAATTACA 1386
                             v     vv      vi        i i    i   ii     iv  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_197319386_   1387 GCGGCATTTTTCACAGAAATAGAAAAAAAAAAACAACAATCCTAAAATTT 1436
                           v  v     ii       v  v  i------ --ii           i
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAG------C--TGATCCTAAAATTC 147

  chr2_197319386_   1437 ATATGAAACCACAAAAGACCCCAAACAGAGAAAACCATCTTGAATAAGAA 1486
                              i  vii   ii     vi  i  vv     v        v     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_197319386_   1487 GAACAAAGCTGAAG-----ACA--TC----TTTCAAACTATGTTGCAAAG 1525
                                 i  i  -----   --  ----       viv ii i     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_197319386_   1526 CTGTAGTAATCAAAACAGTATGGTACTGGCATTAAAAACAAACACATAGA 1575
                           ii         i     i            -  ii i i   i     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGA 296

  chr2_197319386_   1576 CCAGTGGAAGAGAATAGACAGCCAAGAAATAAACCCATACATATTTGGTC 1625
                         i  i     v     v  v  i v                  v v     
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_197319386_   1626 TACTAATTTTCAACAAAGGTGACAAGAATACGCAAAGGGAAAAAAATAGA 1675
                         v i i      i    i    v     vi iv   v   i   i     v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_197319386_   1676 TTCTTCAATAAATGGTTCTGGTA-AACTGGATATCCACATGCAGAAAGAA 1724
                         i i     i       v    v -         ?         -----  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-----AA 441

  chr2_197319386_   1725 AGAAAGAAAAGCAAACAAATAGATAAATAATTAAATTGAACTCTTCTCTT 1774
                             v   i--------------------------   i  i i vi  i
  L1M4_orf2#LINE/    442 AGAATGAAG--------------------------TTGGACCCCTACCTC 465

  chr2_197319386_   1775 ATGCCATACACAAAAATCAATTTAAAAGGGATTAATGACCGAAACATAAG 1824
                          ii     i        i  i i    v    i ?v    v   ii    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_197319386_   1825 ACCTGAAACTATAAAAGTCCTAGAAAAAAACATAAAGGAAAA-CTTCACA 1873
                          v  i           v  i     i        ii? v   -    iii
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_197319386_   1874 ACATTGATCTCAGCAATAGTTTTTCAGATTTGATACCAAAAGGACAGGCA 1923
                           v   ivi vi     i    i i    v   i        v   i   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_197319386_   1924 ACAAAAACAGAAATGAGCAATGTACAGTAATAAAACTAAATGTACCTACT 1973
                               ---    -----  ---------   i --     -------- 
  L1M4_orf2#LINE/    616 ACAAAA---GAAA-----AA---------ATAGA--TAAAT--------T 638

  chr2_197319386_   1974 GTACAGTATCAAACTGAAAAGTTTTTGCATAACAAAGAAAACAACCAACA 2023
                          v  vvi      v v    ii     iiivv     i v  v i   v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_197319386_   2024 AAATTAAAAGGCAGCTTATGAACTGGTGGCAAATATTTGTAAACCACATA 2073
                           i v     i  i ii iii v   vi v         i   i  i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_197319386_   2074 TCCAACAATGAGTTGATATTCAAAATATGTAAGGAACTCATAAAACTCGA 2123
                           ii i  v iii vi   i  i     i   i      v  v     i 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_197319386_   2124 TAGCAAAAAAAAAAAAAAACCCTAAATAACCCAATTTAAAAATGGGCAAA 2173
                           ii     i -----------i             ?             
  L1M4_orf2#LINE/    789 TAATAAAAAGA-----------CAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_197319386_   2174 GGACCTGAATAGACACTTTCCCCTAAGAAGACATACAA-TGTCCAACAAC 2222
                            ii          -    i  v       i      -  v    i  v
  L1M4_orf2#LINE/    828 GGATTTGAATAGACA-TTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_197319386_   2223 TATATGAAAAGATGCTCAACCTCACTAATCAT 2254
                         i i                 v   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (129 / 71)
Gap_init rate = 0.02 (18 / 903), avg. gap size = 5.17 (93 / 18)  


3706 21.06 2.11 1.66  chr2_197338117_197341800.rev     2291  3192 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_197338117_   2291 GAAAGATATCCCAGGTTTATGGATTAGAAGAATTAATACTGTTAAAATGT 2340
                                      v   i       i     v      i      i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_197338117_   2341 CTATACTACCCAAAGCCATCTACAGATTCAGGGCAATCCCTATTAAAATC 2390
                          v     v      viv             iv           i      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_197338117_   2391 CCAA-TGTCATTCTTCATAGAAATAGAAAAAC----CTGAAAATTCATAT 2435
                            i-  i -  i  iii      v  v  i ---- iv           
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_197338117_   2436 GGAACCACAAAAGACCCCCAAAATAGCCAAATCAATCTTGAGCAAAAATA 2485
                             vii   ii     -- i          v         iv  i  v 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCC--AGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_197338117_   2486 ACAAAGGTGGAGGCATTGCATTAGCTAATTTCAAA-TATATTACAAAGCT 2534
                               v      vv ii  i vv i         -iv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_197338117_   2535 ATAGTAATAAAGAGAGCATAGTAGCAGCACAAAAA--GACACATTGTCCA 2582
                          i      v    v  ii i   vii   i  ii --    i  v vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_197338117_   2583 ATGAAATAGAATAGATAGCCCAGAAATAAACCCATGCATTTATGGTCAAT 2632
                            i        v  v  i                i              
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_197338117_   2633 TGATTTTCCACAAAGGTGCCAAGAATACACAATGGGGAAAGGACAGTCTC 2682
                                 v    i          vi iv            i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_197338117_   2683 TTTAACCAA--GTATTAGGAAAACTGACTATCCACATACAGAAGAATGAA 2730
                           i   v  --  ii i   v     iv  ?      i  i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_197338117_   2731 ATTGGGCCCTTATTTCACCCCATATACTAGAATCAACTCAGAATGGATTA 2780
                         i    i   i  ii    v        v i   i      i       i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_197338117_   2781 AAGACAGATGTAAAACATAAGACCTGAAACTA--AAACTACTAGAAGAAA 2828
                         ?    -----iv   ii     v  i      --     vi         
  L1M4_orf2#LINE/    500 WAGAC-----CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_197338117_   2829 ACACGAGGGAAAACCTCTTTGACATTGGTCTCAGCAATGATTTCTTGGAT 2878
                            iii ? v   i  iiv    v    vi vi      i      i   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_197338117_   2879 ATGACTCCCAAAGCACAGGCAACAAAAGCAAAAATAGACAAATAGAAATG 2928
                              v  v        i          v         i    v i v v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_197338117_   2929 CATCAAACTAAAAGTCTTCTGCACAGCAATCAAAACA--ATCAACAGAAT 2976
                                v v   iv   i  ii vv   -- ii   --     v i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAA--AGGACACTATCAAGAAAGT 692

  chr2_197338117_   2977 GAAGAGACAACTCACAGACTGGCAAAAGATATTTGCAAATCATACATCTG 3026
                            i       i      v   v i  i                i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_197338117_   3027 ATAAAGGACTAATATTCAAAATATACAAGAAACTCAAACTACTCAATAAC 3076
                             i     vi   i  i      i  ii     vv  v         i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_197338117_   3077 AAGAAAACAA----CCTTATTTTTTAAACATGGACAAAA-ACCGGAATAG 3121
                           i  i    ----  iv   ?---   v    i    i- iiv      
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTW---AAAAATGGGCAAAGGATTTGAATAG 839

  chr2_197338117_   3122 ACATTCCTCAAATGAAGACATACAAATGGCCAACTTGATACATTAAAAAA 3171
                              i   v  v     i              - viii    -i    i
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACAT-GAAAAG 887

  chr2_197338117_   3172 ATACTCAACATCACAAATCAT 3192
                           i          ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (118 / 68)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 2.12 (34 / 16)  


3921 19.15 2.19 1.85  chr2_197371447_197375792.rev     2988  3854 (492)    L1M4_orf2#LINE/L1       39   908 (0)  

  chr2_197371447_   2988 TATTATTGAGATTGTAATACTCTTCAAATTGATCTACAGATTCAATGTAA 3037
                             i  i    v i       ii                     i i  
  L1M4_orf2#LINE/     39 TATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAA 88

  chr2_197371447_   3038 ACCTTACCAAAATTCCAGCTGTTCTTTTTTACAGAAATGGAGAGTCTGGT 3087
                         v  i  i      i       i-       i       v  v iv   i 
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGAT 137

  chr2_197371447_   3088 CCTAAAATTCATATAGAAATGCAATG-ACCCAGAATGGCTAAAACAATCT 3136
                                       i         v -         i  i          
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_197371447_   3137 TTAAAAAATAACAACAAAAAAAAAAGTTGGAAGATTCACATTTA--GACG 3184
                          v     i--------  i  v         i  i     i  v--i iv
  L1M4_orf2#LINE/    188 TGAAAAAG--------AAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_197371447_   3185 TCAAAACTTCCTACAAAACAATAGTAATCAAGACTGTGTGGTATTAGCAT 3234
                                  v       i v i            v        i i    
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_197371447_   3235 AACGACAGACATATAGATCAATGCAAGATAATTAAGAGTCTAGAAATAAA 3284
                           v  i                 v  v v    i      i         
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_197371447_   3285 CTTACATATCTATGATTAATTGATTTTTGACAGGGGAGTGAAAACTATTC 3334
                          ii i i  i    i i          i    i   v iv  i  i    
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_197371447_   3335 CATAGAAAGAATGAATGATCTTTTCAACGAACAGTACTCGGACAATTGTA 3384
                         v  i i--   v    ii          i  ii  i  v      i  v 
  L1M4_orf2#LINE/    380 AATGGG--GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_197371447_   3385 TATCTGTAGCCAAAATAATGAAGTCAAACCCTTACCTCATAGCACATATA 3434
                           ? iii vv     v        iii    i       i v  i   i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_197371447_   3435 AAA-TAAACTCAAAGTGGATCAAAGACCTAAAT-TAATACATAAAACTAT 3482
                            - v        i       ?          -   v vv         
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_197371447_   3483 TAAAAAAATTTTAAAATATAAAATAGGTATAAATCTATATGATCTTGAGT 3532
                         ---    v i   i  v v  v     ?i       vii   i    i  
  L1M4_orf2#LINE/    528 ---AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_197371447_   3533 TAGGCAAGAGTTTCTCAACTATAATACTCAAA-CACAAACAATCCAAGGA 3581
                                vi      i iv   i i  iv   -     i   ivv   i 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_197371447_   3582 AACACAGATAAACCAAACTT----AAAATTTTTAAAACTTTTATGCATCA 3627
                           v i       iiii    ----      v--         i   v   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTA--AAAACTTTTGTGCTTCA 672

  chr2_197371447_   3628 AAGGACATTATCAAT---GTAAAAATACAACCCACAGAATGGGAGAAAAT 3674
                                i      v---  i    v                        
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_197371447_   3675 ACCTGCAAATCATAT--CTGATAAGGTTGTAGTATCTAAAATATGTAAAA 3722
                          ii            --         vvv v     i i     i    i
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_197371447_   3723 AACTCATACAAGTTGATAATTAAAAGA----TAATCCCTTTTAAAAATAG 3768
                              v     v ii     v      ----   i  vv  ?      i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_197371447_   3769 ACAAAGGATCTGAATAGACATTTCTCCAAAGAAGATATATAAATGGCCAG 3818
                         i        i                             i         i
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_197371447_   3819 TAAGCACACAAGAAGCTGCTTAACGTCATTAGTTAC 3854
                                 ii i   v    i   i   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (106 / 56)
Gap_init rate = 0.02 (14 / 870), avg. gap size = 2.50 (35 / 14)  


3125 27.09 0.47 0.47  chr2_197378259_197380764.rev     1141  2000 (506)    L1M4_orf2#LINE/L1        1   860 (48)  

  chr2_197378259_   1141 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1190
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_197378259_   1191 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1240
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_197378259_   1241 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1288
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_197378259_   1289 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 1338
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_197378259_   1339 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAATTATACTACAAGGC 1388
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_197378259_   1389 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACACAGATATAGATC 1438
                                 i   i    ii         i iv ii i v v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_197378259_   1439 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 1486
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_197378259_   1487 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGAATTCC 1536
                          vi    i  i     ivv  vv  i v  vv               vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_197378259_   1537 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1586
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_197378259_   1587 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 1636
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_197378259_   1637 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1686
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_197378259_   1687 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1736
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_197378259_   1737 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1786
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_197378259_   1787 TTAAACTAAAGAGCTTCTGCACATCAAAAGAAACTACCATCAGAGTGAAC 1836
                          i   v v  i i   i  ii v     i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_197378259_   1837 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 1886
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_197378259_   1887 AGGGCTAATATCCAGAATCTACAGTGAACTCAAACAAATTTACAAGAAAA 1936
                         i  i  vi          v  i iv      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_197378259_   1937 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 1986
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_197378259_   1987 TCAAAGGAAGACAT 2000
                           v  i     i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATAT 860

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.01 (5 / 860), avg. gap size = 1.60 (8 / 5)  

 771 27.49 0.95 0.47  chr2_197378259_197380764.rev     2284  2494 (12)    L1M4_orf2#LINE/L1        1   212 (696)  

  chr2_197378259_   2284 TGGAAAAACATTCCATGCTCATGGATAAGAAGAATC-ATGTCATTAAAAT 2332
                               i i  i     i        vi     v i-  i ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_197378259_   2333 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCCATTAAAC 2382
                            v     v      vii  i           i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_197378259_   2383 TACCATTGACATTCTTCACAGAACTCGAAAATACT-ATTTTAAAATTTAT 2431
                          v   vivi v  i  ii     v i  v  -i  -  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_197378259_   2432 ATGGAACCAAAAAAGAGCCTGAACAGCTAAGAAAATCCTAAGCAAAAAGA 2481
                               viiv  ii  v  v   i   i  i v    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_197378259_   2482 ACAAAGCTGGAGG 2494
                               i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG 212

Transitions / transversions = 2.05 (39 / 19)
Gap_init rate = 0.01 (3 / 212), avg. gap size = 1.00 (3 / 3)  


2891 26.01 2.97 0.83  chr2_197395035_197401363.rev     4996  5837 (492)    L1M4_orf2#LINE/L1       49   908 (0)  

  chr2_197395035_   4996 ATGGCCATACTGCCCAAGGTAATTTATAGATTCAAGGCCATCCCCATCAA 5045
                              v     v     iv i  i  i        v  v     i     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_197395035_   5046 GCTACCAA-TGACTTTCTT-CA------------CT-ACTTTAAAGTTCA 5080
                         iv v   i-  v    i  -  ------------  - iii    i    
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_197395035_   5081 TATGGAACCAAAAAGGAGCCCGCATTGCCAAGGCAGTCTTAAGCCAAAAG 5130
                                viiv  i   v  v v  v     ii  i    i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_197395035_   5131 AACAAAGCTGGAGGCATCATGCTACCTGACTTCCAACTATACTATAAGGC 5180
                                i      vv   ii  v  ii i   v  viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_197395035_   5181 TGCAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGATATATAGACC 5230
                          i      i   i    ii           iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_197395035_   5231 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACC 5278
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_197395035_   5279 ATCTGATCTTTGACAAATCTGACAAAAACAAGAAATGGGGAAAGGATTTC 5328
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_197395035_   5329 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5378
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_197395035_   5379 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5428
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_197395035_   5429 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5478
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_197395035_   5479 CTAAGCA-ATACCATTCAGGACATAGGCCTCGGCAAAGACTTCATGACTA 5527
                         v  i ?i- v i -   iv   v v  vi v     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_197395035_   5528 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5577
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_197395035_   5578 ATTAAACTAAAGAGCTTCTGCATAGCAAAATAAACTAACTACCATGAGAG 5627
                           i   v v  i i   i  iiivv    i--i  --    i  v  i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAG--GAC--ACTATCAAGAAAG 691

  chr2_197395035_   5628 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCT 5677
                             v  i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_197395035_   5678 GACAAAGAGCTAATATCCTGAATCTACAAAGAACTTAAACAA----AT-- 5721
                           i  i ii  vi     v    v  i        ivv    ----  --
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_197395035_   5722 TTACAAGA-AAACAACCCCATCAAAAAGTTGGCGAAGGATATGAACAGAC 5770
                          v v    -   i     v  i?    i v   i      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_197395035_   5771 AGTTTTCAAAAGAAGGCATTTATGCAGCCAACAGACACATGAAAAAATGC 5820
                          v  i  v       ii  vi viii     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_197395035_   5821 TCATCATCACTGGCCAT 5837
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (129 / 86)
Gap_init rate = 0.02 (13 / 860), avg. gap size = 2.46 (32 / 13)  


3031 25.72 1.78 0.78  chr2_197427420_197433547.rev     4739  5636 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_197427420_   4739 GGAAAAACATTCCATGCTCATGGATAGGAAGAATCAACATTGTGAAAATG 4788
                              i i  i     i        v      v i  i     v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_197427420_   4789 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATGCTCATTAAACT 4838
                           v     v      v i  i  i        i  v  v ii  i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_197427420_   4839 ACCATTGATGG--TCTTCACAGAATTAGAAAAAACT-ACTTTAAAATTCA 4885
                         v   -- v  v-- i  ii     v v  v  i-  - iii         
  L1M4_orf2#LINE/    102 CCCA--GCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_197427420_   4886 TATGGGACCAAAAAAGAGCCTGAATAGCCAAGACAATCCTAAGCAACAAC 4935
                              i viiv  ii  v  v          i      i i iv  v  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_197427420_   4936 AACAATGCTGGACCA-TCACACTACCTAACTTCCACCTATACTACAAAGT 4984
                              v i    vv -       v  i  i   v vviv          i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_197427420_   4985 TACAGTAACCAAAACAGCATGGTACTGGTACCAGAACAGACACATAGACC 5034
                                 i   i    ii         i iv  i i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_197427420_   5035 AACAGAATAGAATAGGGAACTCAGAAATAAGACCGCACACCTATAACCAT 5084
                           ii         v i  iii         iv  ii   ii   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_197427420_   5085 TTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGGAAAGGATTCCC 5134
                              i  i     ivv  v   i v  vv        -    i  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTC 397

  chr2_197427420_   5135 TATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGTAAAAAATGG 5184
                          v     i              i      v  ?   i   i    i vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_197427420_   5185 AAACTGGACCCCTTCCTTAAGCCATATACCAAAATTAACTCATAATGGAT 5234
                           ii         v   i vi        v            v       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_197427420_   5235 TAAAGACTAAAATGTAAAGCCCAAAACTATAAAAATGCTAGCAGAAAATC 5284
                         i ?    iv        iiv i            v vi   v      iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_197427420_   5285 TGGGCA-ATATCATTTAGGACACAGGCACGGGCAAAGATTTCATAACAAA 5333
                          i  ?i- v   -  iiv   viv  vvii     v i    v  ivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_197427420_   5334 AACACCAAAAGCAATTGCAACAAAAGCAAAAATTAACAAATGGGATCTAA 5383
                         i            vvv          v      vi i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_197427420_   5384 TTAAACCAAAGAGCTTCTGCACAGAAAAAGAAACTATCATCAGAGTGAAC 5433
                          i   viv  i i   i  ii vvv   i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_197427420_   5434 AGACAACCTACAGAATGGGAGAAAATTTTTGCTG-TCTAATCTTTCTAAC 5482
                                 i                 v     vi-  --  v v   i i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATC--ATATATCTGAT 744

  chr2_197427420_   5483 AAAGGTCTAATATCCATAGTCTACAAGGAACT--TA-AATTTA-CAAGAA 5528
                           i  v  vi      v i v  i  i     --  -  i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_197427420_   5529 AAAAA-----AACCTCATTAAAAAGTGGGCAAAGGACATGAACAGACACT 5573
                            i -----    iv   ?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_197427420_   5574 TCACAAAAGAAGACATACATGTGGCCAACAAATATATGAAAAAAGG-TCA 5622
                           v v        i     vi       i  ii i       i v -   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_197427420_   5623 ACATCACTGATCAT 5636
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (129 / 98)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 1.53 (23 / 15)  


2853 27.05 2.11 1.44  chr2_197443115_197448933.rev     4426  5327 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_197443115_   4426 TAGAAAAACATTCCATGCTCATGGACAGGAAGAGTCAATATCATGAAAAT 4475
                          i    i i  i     i       iv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_197443115_   4476 GGTCATACTTCCCAAAGTAATTTACAGATTCAATGCTATCCCCATCAAGC 4525
                           iv     i      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_197443115_   4526 TACCA-TTGACTTTTC-ACAGAA-TTGGAAACAA-CT-ACTTTAAATTTC 4570
                          v   -i  v     i-i     -   ---    -  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_197443115_   4571 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGATAATCCTAAGCAAAAT 4620
                                 viiv  ii  v  viv  v     i i    i i iv  i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_197443115_   4621 GAACAAAGCTGAAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 4670
                                 i  i   vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_197443115_   4671 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAATATATAGAC 4720
                                  i   i    ii         i iv ii i i i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_197443115_   4721 CAATGGAACAGAACAGAGACCTCAGAAATAACATCACACATCTACAACCA 4770
                                 i    iv    vii         vvi  i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_197443115_   4771 TATGATCTTTGACAAACATGACAAAAACAAGCAATGGGGAGAGGATTCCC 4820
                         vv    i  i     ivi  v   i v  vv         i  i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_197443115_   4821 TATTTAATATAATGGTTTCGGGAAAACTGGCCAGCCATATGCAGAAAGCT 4870
                          v  i  i -      vii    v      vi ?   i     i  iiv 
  L1M4_orf2#LINE/    398 TTTTCAACA-AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_197443115_   4871 GAAACTGGATCCCTTCCTTACATCCTTACATCTTATACAAAAATTAACTG 4920
                            ii    i    v   i   i -----  ---               v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACC-----AT---ATACAAAAATTAACTC 488

  chr2_197443115_   4921 AAGATGGATTAAAGACTTAAACATAAGACATACAACCATAAAAACCCTAG 4970
                           i      i ?    i    ii     vv  v   i      vi i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_197443115_   4971 AAGAAAACCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAACACTT 5019
                                 v    ?i- v i -   iv   viv  vv i     vvii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_197443115_   5020 CAT-GCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAAT 5068
                          v - v  vi            vvi          vv        i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_197443115_   5069 GGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAGAGAAACTATCATC 5118
                         v   ii v  i   v v  i i   i  ii vv   ii  v       vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_197443115_   5119 AGAGTGAACAGGCAACCTACAGAATGG-AGAAAATTTTTGCAATCTACCC 5167
                          i      v  i     i         -       v       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_197443115_   5168 ATCTGACAAAGCACTAATATC-------TACAAAGAACTTAAACAAATTT 5210
                               i  i v   vi    -------  i        ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_197443115_   5211 ACAAGAAAAA----AAGAGCCCTATCAAAACCTGGGTGAAGGATATGAGC 5256
                          i  v     ----  v i   v  i?   vv    ii      v   ii
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_197443115_   5257 AGACACTTCTCAAAAGAAGGCATTTATGCAGCCAACAAACATATGAAAAA 5306
                              i     v       ii  vi viii     i  i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_197443115_   5307 ATGCTCATCATCACCATTATT 5327
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (147 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.13 (32 / 15)  


2834 26.35 2.69 1.05  chr2_197548148_197552281     2781  3634 (500)    L1M4_orf2#LINE/L1        1   868 (40)  

  chr2_197548148_   2781 TAGAAAGCAATTCCATCTATGTTCATGGATTGAATGATTTAGCATTGTTA 2830
                          i     vv  i    ----            i v  i   ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT----GTTCATGGATTGGAAGACTTAATATTGTTA 46

  chr2_197548148_   2831 AACTGTCTATACTACCTCAAGCAATGTCTAGATTCAATGAAATCCCCATC 2880
                          iv  v v     v  iv  vii  v vi        i v      i   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_197548148_   2881 AAAATACCAATGAGAGTCTTCACTGGTATAGGAAAAACAATCATAAAAT- 2929
                              v   iivivvv i  ii v iv  v iv  ivii   v      -
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_197548148_   2930 CATATGGTACCACAAATGACTGCAAATAGCAAAAAAAGTCCTGAGCAAAA 2979
                                v vii   iv   ivvi      v    v i  i   iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_197548148_   2980 AGAACAAAGCTGGAGGCAATCACATTACCTGACTTCAAAATACACTACAA 3029
                                  i      - v     i v  ii i       ivi       
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_197548148_   3030 AGATATGGCAACCAAAACAGTTTAGTACTGGCATAAA-ACAGATACATAA 3078
                           v  ii i  i   i     v i            i- i   i i   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_197548148_   3079 GCCAATAGAACATAATAGAGAACCCAGAAAT----CCACTCATTTACAGC 3124
                         ii    i   i v   v    ii        ----   iv      ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_197548148_   3125 CAGCTAATTTTCACTAAAGGCAACCAAAAC-ATACATTGGAGAAAGGATA 3173
                           ii i      ivi  i  ii-    i  -  v  v   i     i   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_197548148_   3174 GTCTTTTCAATAAATGGTGCTGGGAAAACTGGATATTTATATGCAGAAGA 3223
                                   i              v         ?ii i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_197548148_   3224 AAGAAACTAGATCCCTATCTTTCATCATATGCAAAAATTAAATCAAAAT- 3272
                          v   ii i  i     i  iv  i     i          v       -
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_197548148_   3273 ----AAAGACTTAAATTTAAAACCCGAAACGACGAAACTACCACAAGAAT 3318
                         ---- ?    i     v   i v ii    v ii     vii v     v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_197548148_   3319 ATATTGGAG-AAATGCTTTGGGACACTGGTCTGGGCAAAAATTTTTTGGG 3367
                          i  v  ? -    -   i v   vi   vi i     vii   i  i i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_197548148_   3368 TAAGACCTCAAAAGCACATACAATAAAAGCAAAATGAGATAA-------- 3409
                           v   vi          vi   i     v    vv      --------
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_197548148_   3410 -TATCAGGCTAAAAGGCTACTGCACAGCAAAGGCAACAAACAACAAAGTG 3458
                         -i    iiv v   ii  vi  ii vv      vv  v v   v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_197548148_   3459 AAGAGATAAGCCAAAGACTGGGAAAAAAT-TTTGCAAACTATCCATCTGA 3507
                           i   i  v   v   v     i     -        ii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_197548148_   3508 TAAAGGATTAATAACCAGAATATATAAGGAACTCAAACAACTCAACAGCA 3557
                            i   i vi  v             i      vv         i ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_197548148_   3558 AAACAAACAAATACTCTAATTTTAAAAGTGGCCAAAAGATCTGAACAGAC 3607
                            - i       vi i    ?-    i   v    i   i    i    
  L1M4_orf2#LINE/    794 AAA-AGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_197548148_   3608 ATTTCTCAACAGAAGAAATACCAATGG 3634
                                v v      v    v     
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGG 868

Transitions / transversions = 1.54 (134 / 87)
Gap_init rate = 0.02 (14 / 868), avg. gap size = 2.29 (32 / 14)  


3324 26.76 0.44 0.44  chr2_197595318_197601597     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_197595318_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_197595318_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_197595318_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_197595318_   5029 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_197595318_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_197595318_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_197595318_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_197595318_   5227 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_197595318_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_197595318_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_197595318_   5377 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_197595318_   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_197595318_   5477 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5526
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_197595318_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_197595318_   5577 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_197595318_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_197595318_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_197595318_   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_197595318_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 541 22.29 3.01 4.22  chr2_197744935_197746549.rev        9   174 (1441)    L1M4_orf2#LINE/L1       94   257 (651)  

  chr2_197744935_      9 ATCAAAATCCCAGCAGGGTTTTTTTTTTGTGTGTAAATTGAAAAGCTGAT 58
                                       v ----ii       ii- -       v        
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTG----CCTTTTTTGCA-G-AAATTGACAAGCTGAT 137

  chr2_197744935_     59 TTTAAATTTTATACAGACATGCAAAGGGTAAAGAATATATGAGGCAATCT 108
                         ii    v  i   ii  v      i  iivv      vvii ii      
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_197744935_    109 TGAAAAAGAACAAC----CTGG-GGACTTAGACTTCCAGATATAAAAAAT 153
                                   v   ----i   -     i v      vi  v v    v 
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_197744935_    154 CTGTTACAAAACTATAGTAAT 174
                         - ii      i   i      
  L1M4_orf2#LINE/    238 -TACTACAAAGCTACAGTAAT 257

Transitions / transversions = 1.64 (23 / 14)
Gap_init rate = 0.04 (6 / 164), avg. gap size = 2.00 (12 / 6)  

 249 28.75 0.00 0.00  chr2_197744935_197746549.rev      421   500 (1115)    L1M4_orf2#LINE/L1      244   323 (585)  

  chr2_197744935_    421 AAAGCTATAGTAATGAAAACAGTATGGTATTAGAGCAAAGATAGATGAAC 470
                                i      v  i     i     i i vii  i      iiv i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_197744935_    471 TCATCAAAAGAACAGAATAAAGAGTTGAGA 500
                         vv     vi   i     vi     iv   
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGA 323

Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.00 (0 / 0)  

1507 26.73 6.45 4.25  chr2_197744935_197746549.rev      501  1136 (479)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr2_197744935_    501 AAAACAGTATGGTATTAGGGCAAACATAGATGAACTAATCAAAAGAACAG 550
                           i     i     i i vii  iv     iiv ivi     vi   i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_197744935_    551 AATAGGGAGTTGAAAAATGGATCCACACATATGTGGT--ATCCTGATTAA 598
                            v i    iv i    ii i   i    v i    --  --     vv
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT--TGATTTT 356

  chr2_197744935_    599 TGATAAAGGTGCATAG-TAGTTCAGTAGAGAAA--ATTATCTTTTCACCA 645
                         i  i  i     vv  -ivi    i i i    --  vi        v  
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_197744935_    646 AATAGTGCTAGGTTAA-TAAATATGTATATGGAGGAAAATGAA------- 687
                            i     i  vi  - ii   ?vi i   v ii i      -------
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_197744935_    688 ---TATTCTTTTACCATATACAAAACTGAATTCAAGATGGATTGCAGATC 734
                         ---  i-  ivi             v v  i    i      ii?   i 
  L1M4_orf2#LINE/    457 CCCTAC-CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_197744935_    735 TATACGTGAAAGGTACAACAATAATGTTTTTAGAAGTAAGCGTAAGAGAA 784
                           v i  i i  v  v   v    vii i       v  i i  i ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_197744935_    785 CATCTTCATGAC-TCA---CAGAAAAAGATTTTTTA-ATAAGATGC-AAA 828
                         v      i    - ii---i  iv  v i   i   -   v  ii -   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_197744935_    829 ATTA-ATGAACCAAAAGGAATAACTGGATATATTGGACTCTATTAACGTT 877
                          vi - v v v      i  -  v i    v        ii  i  vi  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_197744935_    878 AAAAGCTTT-GTCCATTAAAAGGCACCATTAAGAGAGAACAAAGGCAAGC 926
                             i    -  v v i   i i   i  i    i  viv    i   v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_197744935_    927 TTCAGAGTGC-----AATA---------CATATATATGAAAAAGGTCTTG 962
                         iv    i  v-----    ---------       v   v  i  v    
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_197744935_    963 TATCCAGAATATATGAAGAACTCCTACAGAACATATAAAGAAACCTTAAA 1012
                                       i        i    i---------------  ----
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAA---------------CT---- 785

  chr2_197744935_   1013 AGCCAATAAGAAAAAAATAGATAACCCAATAGAAAAATGGGCAAAAAACT 1062
                         ---      v     i i i          v?             ii i 
  L1M4_orf2#LINE/    786 ---CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_197744935_   1063 TGAACAGGCACTTCAC--AAGAGGATGTCCAAGTATTTA-TAAACATGTG 1109
                             i  i  i   v --    i   i v   i ivii -   i  ii  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_197744935_   1110 AAAAAAGTATTCAGCTTTAATAGTCAT 1136
                             i - ii   i v i ????????
  L1M4_orf2#LINE/    883 AAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (111 / 55)
Gap_init rate = 0.03 (21 / 650), avg. gap size = 3.24 (68 / 21)  


2725 25.42 9.47 0.60  chr2_197752217_197758352     4811  5644 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_197752217_   4811 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4860
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_197752217_   4861 GGCCATAATGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4910
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_197752217_   4911 TACCAATGACTTTCTTCACAGAA-TTGGTAAAAACT-ACTTTAAAGTTCA 4958
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_197752217_   4959 CATGGAACCAAAAAAGAGCCCGCGTTGCCAAGACAATCCTAAGCCAAAAG 5008
                         i      viiv  ii  v  v vi v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_197752217_   5009 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5058
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_197752217_   5059 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 5108
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_197752217_   5109 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACT 5156
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_197752217_   5157 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5206
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_197752217_   5207 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5256
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_197752217_   5257 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 5306
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_197752217_   5307 TTAAAGACTTAAATGTTAGACCTAACACC-TAAAAACCCTAGAAGAAAAC 5355
                          i ?    i       v   v    v  i-     vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_197752217_   5356 ---------------------------CTAGGCAATGCCATTC--AG--- 5373
                         ---------------------------i         vi-   --  ---
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATA 595

  chr2_197752217_   5374 -GACAT---AGGCCTGGGCAA----------------------GGACTTC 5397
                         -    i--- i  viii    ----------------------       
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_197752217_   5398 AT----GTCTAAAAC------AC--CAAAAG-CACCATCAG---AGTGAA 5431
                           ----i iv     ------i --    i -   i    i---      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_197752217_   5432 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5481
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_197752217_   5482 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5531
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_197752217_   5532 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5581
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_197752217_   5582 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCAT 5631
                            v        i  vi viii     v  i        i i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_197752217_   5632 CATCACTGGCCAT 5644
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (138 / 71)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.94 (84 / 17)  


1872 21.99 21.13 0.52  chr2_197845210_197846791      501  1082 (500)    L1M4_orf2#LINE/L1      193   894 (14)  

  chr2_197845210_    501 AAGAAGAATAAAATTGGAGAACTAACATTACCTGATTTCAGAGCTTATTA 550
                                 i   i      i   v   i v  ii      i i    i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_197845210_    551 TAAAGTTACAGTAATCAAAACAATATGGTATTGGTGCAAAGA-------- 592
                         i    i            i   i i     i   iii  i  --------
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_197845210_    593 ----------------------------------AAACTC---------T 599
                         ----------------------------------    i --------- 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_197845210_    600 GGT----------------------------------------GAAAGAA 609
                            ----------------------------------------       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_197845210_    610 TAGCCTTGTCAACAAATGGTCCTAGAACAATGAGATAT------------ 647
                            i   v            v  i i    ivi    ?------------
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_197845210_    648 ---TAAACTTTGGGCCATACCTTGAACCCTAAACAAAAATTAAATCAAAA 694
                         --- i  v  v iv  v     iiv   v  v           v      
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_197845210_    695 TGGATCACAGAACTAAATGTAAAACTTAAAATTATAAAATATCT--AAAG 742
                                ?   v          i vi     i       i-   --i   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAG 541

  chr2_197845210_    743 GAAACATAGGCA-AGATCTTT-TCACCTTGGGTTAAGCAAAGATTTCTTA 790
                         i         ?i- i     i- v           i    v i       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_197845210_    791 GATATGACATCAGA-GCAAAACCCATAAAAGGATAAATTGGTAAATGGAA 839
                                  i  i -   v  v v i     i v    v i     v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_197845210_    840 TTTTATCAAAATGAATAATGTCCACTCTTTGAAACACACTGGTAAGAGAA 889
                         i  i        v  v  iv iiiiv   ii  iv     ivi    i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_197845210_    890 TGAA--GATAAGCCACAGACTGGGGGAACATATTTGTAAAGCATATATTG 937
                             --  i  v       v    i   v       i   v       iv
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_197845210_    938 GATAAAGGACTTCTATCTAGAACCTACAAAACAACTCT-------CAATA 980
                              i      v    i    iv  i   i-      -------     
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAG-AACTCTTACAACTCAATA 790

  chr2_197845210_    981 ACTATGAAAGCAAACAATCCAATTAAAAAGTAGGCAAAAGATTTGAACAG 1030
                          -  vi  ii    i  i      ?    i i      i        i  
  L1M4_orf2#LINE/    791 A-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_197845210_   1031 ATATTTCACCAAAGA---TATACAGATAGCAAATAAGCATATAAAACAAT 1077
                          i     v       ---      i  i  v        i  i   vi  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_197845210_   1078 GCTCA 1082
                              
  L1M4_orf2#LINE/    890 GCTCA 894

Transitions / transversions = 2.10 (84 / 40)
Gap_init rate = 0.02 (14 / 702), avg. gap size = 9.00 (126 / 14)  


3047 27.08 1.66 0.89  chr2_198252978_198257238.rev     2869  3769 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_198252978_   2869 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATACAGTGAAAAT 2918
                              ii    i     i        v      v i    iv  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_198252978_   2919 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2968
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_198252978_   2969 TACCAATGACTTGCTCCACAGAATCAGAAAAAACT-ACTTTAAATTTCAT 3017
                          v   iivi i vi iii     viv  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_198252978_   3018 ATGGAACCAAAAAAGAGTCTGCATTGCCAAGACAATCCTAAGCAAAAAGA 3067
                               viiv  ii  vi v v  v     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_198252978_   3068 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAA--CTATACTACAAGGC 3115
                               i      vv   ii  v  ii i     --  -        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr2_198252978_   3116 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAAACC 3165
                                 i   i    ii         i iv ii i   i     i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_198252978_   3166 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACCCATCTACAACC 3213
                                i    i--    i  --        vv   iv   i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_198252978_   3214 ATCTGATCTTTGACAAACCTGATGAAAACAAGAAATGGGAAAAAGATTCC 3263
                          vi    i  i     ivv  vii i v  vvv      i   ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_198252978_   3264 CTATTTAATAAGTGGTGCTGGGAAAACTTGCTAGCCATATGTAGAATGCT 3313
                           v  i  i  i           v    v v  ?   i   i i  viv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_198252978_   3314 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTTAAGGTGGA 3363
                            ii    i    v   i     v              i i  ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_198252978_   3364 TTAAAGACTTAAATATTAGGCCTAAAACCATAAAAACCCTAGAAGAAAAC 3413
                          i ?    i     i v  iv       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_198252978_   3414 CTA--CGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 3461
                         v  --? i  - i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_198252978_   3462 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3511
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_198252978_   3512 AATTAAACTAAAGAGCTTCTG-----CACAGAA-ACTACCATCAGAGTGA 3555
                         v  i   v v  i i   i  -----  v  i -    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_198252978_   3556 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGTAATCTACCCATCTGAC 3605
                          v  i     i                 v    i  vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_198252978_   3606 AAAGGGCTAATATCCAGAATCAACAAAGAACT--TACAAATTTACAAGAA 3653
                           i  i  vi          vv i        --     v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_198252978_   3654 AAAAAATCAAACAATCCCATCAGAAAGTGGGCAAAGGATATGAACAGACA 3703
                            i --    i  i  v  i?i   i            v    i     
  L1M4_orf2#LINE/    795 AAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_198252978_   3704 CTTTTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGTT 3753
                         i  i  v        i  vi viii     i ii          i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_198252978_   3754 CATCATCACTGGCCAT 3769
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (151 / 89)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


3268 26.40 0.55 0.66  chr2_198325218_198331491.rev     4874  5782 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_198325218_   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4923
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_198325218_   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 4973
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_198325218_   4974 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5020
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_198325218_   5021 ATATGGAACCAAAAAAGAGCCCGCGTCGCCAAGGCAATCCTAAGCCAAAA 5070
                                 viiv  ii  v  v vi v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_198325218_   5071 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5120
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_198325218_   5121 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAGAGATATAGA 5170
                                  i   i    ii         i iv ii i -  v       
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGA 296

  chr2_198325218_   5171 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAA 5218
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_198325218_   5219 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5268
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_198325218_   5269 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5318
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_198325218_   5319 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5368
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_198325218_   5369 GATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5418
                            i ?    i    ii v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_198325218_   5419 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5468
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_198325218_   5469 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5518
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_198325218_   5519 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5568
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_198325218_   5569 ACAAGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5618
                          v ii     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_198325218_   5619 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5668
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_198325218_   5669 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5718
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_198325218_   5719 TCTCAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTCA 5768
                             v        i  vi viii     v  ii         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_198325218_   5769 TCATCACTGGCCAT 5782
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2960 23.43 6.61 1.39  chr2_198351622_198356518.rev     3544  4405 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_198351622_   3544 GAAAAGACATCTCATGCTCATGGATTGGAAGAATTAATACTGTTAA---- 3589
                          i     i   i    i               v      i      ----
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_198351622_   3590 --AATACTGCCCAAGGCAATCTACAGATTCCATTCAATCCCTATCAAAAT 3637
                         --      v     ivii            v iv                
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_198351622_   3638 ACCAG-TGTCATTTTCACAGAAATAGAAAAAAAAAATACCAAAATTTTTA 3686
                         v    -  i v    ii       v  v  ivvi - v i      iv  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATA 150

  chr2_198351622_   3687 TGGAACCACAAAAGAGTCAGAATAGCCAAAA-AATTTTAGGAAAAAAAGA 3735
                              vii   ii  vi              -   i  - i    i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT-GAAAAAGAAGA 199

  chr2_198351622_   3736 ACAAAGCTGGAAGCATCACACTACCTGACTTTCAAATATATTAGAAGGTT 3785
                               i    i vv       v  ii i  iv   iv  i  v  i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_198351622_   3786 ATAGTAGCCAA-ACAGCATGGTATTGG--------------TATAGACCA 3820
                          i    ii   -    ii     i   --------------      i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_198351622_   3821 ATGGAACAGAATACAGAACCCAGAAATAAATTTGCATATTTACTGTCAAC 3870
                               i     vv   ii           iiiii i     iv     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_198351622_   3871 TGATTTTCAAAAAAAGTGTCAAGAGCATACACTGGGGAAAGGACACCCTC 3920
                                 i v  ii   i     v   v  v         i i vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_198351622_   3921 TTCAATAAATGG---------------ATATCCATATGCAGAAGAATGAA 3955
                              i      ---------------   ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_198351622_   3956 ACCAGACCACTATCTATCTGTCACCAT-TACAAAAATCAACTCAAACTGG 4004
                         iiii    ----i   i  vv      -         i        v   
  L1M4_orf2#LINE/    450 GTTGGACC----CCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_198351622_   4005 ACTAAAGACTTAAACATAAGACCCAAAACTATAAAACTACTAGATAAAAA 4054
                          ii ?    i    ii     v i              vi    vi    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_198351622_   4055 TGTAAGAAAAACACTTCAGGACATTGGCCTAGGAAA-GATTTTATGGCTA 4103
                         ii  i ?iv  vv    iv   v    vi    v  - i   iv i v  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_198351622_   4104 AGACCTCAAAAGCACAGGCACCTAAAATAAAAATAGACAAATAGGATTAT 4153
                         v   vi          i   v v   iv         i    v   i vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_198351622_   4154 ACTAAACTGAAAAGCTTC---ACAGCAAAGGAAGCAATCAACAGA----- 4195
                          ii   v v    i   i---i vv       vi v     v i -----
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_198351622_   4196 AAGAAAACTTACAGAATAAGAGAAAATATTTGCAAATTATTCATCCAACA 4245
                             v   ii       ii                  i  vi   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_198351622_   4246 AGGGACTAACATCCAGAATATACACAAGGAACTCAAACACGTCAACAATT 4295
                                vii            i -- i      vv   vv    i   -
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATA--AAGAACTCTTACAACTCAATAAT- 792

  chr2_198351622_   4296 TTTAAAAA------TCAC---GTTAAAAAGTGGGCAAATTACATGAATAG 4336
                         ---     ------ v  ---i  ?    i        vv iv       
  L1M4_orf2#LINE/    793 ---AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_198351622_   4337 ACAATTCTCAAGAGAAGACATACAAATGGCCAACAGGTATATGAAAGAAT 4386
                            v     v i      i              i i i i      ii  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_198351622_   4387 GCTGAATATCACTAATCAC 4405
                            v  i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (126 / 72)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 4.06 (69 / 17)  


 808 26.81 9.67 6.59  chr2_198371163_198375392      668  1122 (3108)    L1M4_orf2#LINE/L1       15   483 (425)  

  chr2_198371163_    668 ATATTCATAGTCAGTTTTAGGAACCCTTAATATAGTAAATATGTCAAC-C 716
                           i     i ---i  ---    vv        v  v  v   v   i- 
  L1M4_orf2#LINE/     15 ATGTTCATGG---ATT---GGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr2_198371163_    717 TCCCCCAGCCCTTGACACCTAACATTGAGCTATAGATTTAATGCAATGGT 766
                              ---------------  -     v   i     i  i     vvi
  L1M4_orf2#LINE/     59 TCCCC---------------AA-ATTGATCTACAGATTCAACGCAATCCC 92

  chr2_198371163_    767 GACCTAAA-CCCAACAGG-TCTTTGGCAGGGAACTTGTCAAGTTGATTTT 814
                         v i v   -    i v v- i   v    --  v   v    i    ii 
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAG--AAATTGACAAGCTGATCCT 140

  chr2_198371163_    815 AATAGTTACGTGGAAGATAAAAGGG-CAAAAAATGGCTAAGATTCTTCTG 863
                           v v i ii     -  iv     - vv i   i  i  i ivv ii  
  L1M4_orf2#LINE/    141 AAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_198371163_    864 AA---GAAGAATA----CGGAGGACAGGTAAATTCTTCATATATTAAAAT 906
                           ---      i ----i       --vi v i iii  -  v i    i
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGAC--TCACACTTCCCA-ATTTCAAAAC 236

  chr2_198371163_    907 TTAGTATAAAGCTATAGTAATTAAAATAGTGT--TTTTAGCA-AGGCATA 953
                            v  i       i      i  i i     -- vi i   - i v   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_198371163_    954 GATAAATTAGCCAATACAATAGC-TAAAGAGCCTAGAAAGAGACCCGACA 1002
                           i v  viii    iv     v- vi    i i     v i    - i 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC-ATA 335

  chr2_198371163_   1003 CAT-----GAAAATGTAATATATGATGAAGGTGGCATGGTAGGTCAGTGG 1047
                            ----- vv   - i  v vi  ii i    v  v iiviv   i   
  L1M4_orf2#LINE/    336 CATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_198371163_   1048 AGAAA-------------------TGGAACTGAGAAAACTGGTTATCCAT 1078
                         i    -------------------   vi   i  v      v  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_198371163_   1079 ATG---GGGAA--AAATTGGATCCCTACCTCCTGCTATACACAAAACTT 1122
                            ---ii   --  i     i         vii i   i      v  
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

Transitions / transversions = 1.52 (73 / 48)
Gap_init rate = 0.05 (23 / 469), avg. gap size = 3.22 (74 / 23)  

2414 27.86 0.28 0.28  chr2_198371163_198375392     1960  2684 (1546)  C L1M4_orf2#LINE/L1   (0)   908   184  

C chr2_198371163_   2684 ATCCTAAGCAAAAAGAACAAAGTTGGAGGCATCAAGCTACCTGACTTCAA 2635
                            i i iv  i                 vv   vi  v  ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

C chr2_198371163_   2634 GCTATACTACAAGGCTACAGTAACAAACACAGCATGGTACGGGTACCAAA 2585
                         iviv        i          iv  v    ii      v  i iv ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

C chr2_198371163_   2584 ACAGAGATATAGACAAATGGAACAGAACAGAGACCTCAGAAATAACACCA 2535
                          i   v       iv       i    iv    vii         vv   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

C chr2_198371163_   2534 CACATCTACAACCATCTGATCTTCAACAAACCTGACAAAAACAAGCAATG 2485
                         i    i  iiii  vi    i   i    ivv  v   i v  vv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

C chr2_198371163_   2484 GGGAAAGGATTCCCTGTTTAATAAACGGTGCTGGGAAAACTGGCTACCTT 2435
                                i  vvi  v  i  i   i          v      v  ? iv
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

C chr2_198371163_   2434 TATGCAGAAAACAGAAACTGGACCCCTTCCTTACATCTTGCACAAAAATT 2385
                         i     i  i vv   ii         v   i   i v ii         
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

C chr2_198371163_   2384 AACTCAAGATGGATTAAAGACTTAAATGTAAAACTCAAAACCACAAACAC 2335
                                i      i ?    i         i vii     i i   -  
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-AC 532

C chr2_198371163_   2334 CCT-AGCAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAA 2287
                         i  -  v       v    ?i- v i -   iv   v v  vv i     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA 581

C chr2_198371163_   2286 AGACTTCATGACTAAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTG 2237
                         v ii   v iiv  vi            vvv          vv     v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

C chr2_198371163_   2236 ACAAATGGGGTCTAATTAAACTAGAGAGCTTCTGCACAGCAAAAGAAACT 2187
                          i    v  iii v  i   v vi i i   i  ii vv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

C chr2_198371163_   2186 ATCATCAGTGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAAT 2137
                             vv iv     v  i     i                 v       v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

C chr2_198371163_   2136 CTATCCACCTGGCAAAGGTCTAATATCCAAAATCTACAAGGAACTTAAAC 2087
                         ii  vi i   ii  i  v  vi      i   v  i  i     ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

C chr2_198371163_   2086 AAATTTATAAGAAAAAAACAAACATCCCCATCAAAAAGTGGGTGAAGGAT 2037
                           v iv    v     i     i v   v  i?    i    ii      
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

C chr2_198371163_   2036 ATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATAT 1987
                         v    i     i     v        i  vi viii     i  i  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

C chr2_198371163_   1986 GAAGAAAAGCTCATTATCACTGCTCAT 1960
                            i i v     vi    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (115 / 83)
Gap_init rate = 0.01 (4 / 725), avg. gap size = 1.00 (4 / 4)  

 215 28.77 1.37 0.00  chr2_198371163_198375392     2827  2899 (1331)    L1M4_orf2#LINE/L1      688   761 (147)  

  chr2_198371163_   2827 AATGTGAAAGGGCAAGATACAAATTGGTGGGTGATACTTGCAAATTAT-C 2875
                           v      i i   vvi   i v   vi ivi   i        i  -i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_198371163_   2876 AACTAATAAAGGAATAGTATCCAG 2899
                          v  i    i   v v        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAG 761

Transitions / transversions = 1.33 (12 / 9)
Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1)  

 291 21.67 8.89 5.56  chr2_198371163_198375392     3559  3738 (492)    L1M4_orf2#LINE/L1      723   908 (0)  

  chr2_198371163_   3559 ATTTAAAAA--ATAAATCTAAAAAA-----TGCATAGAGAAAAAGTATAT 3601
                             iv   --   v    i v  i-----  i  vv    ----     
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA----TATAT 768

  chr2_198371163_   3602 AAAGAACTCCTGCAAATAAGTAAAGAAAAAGACAAG----CCAATAGAAA 3647
                                  i i   v v i   -v          i----     v?   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAA 817

  chr2_198371163_   3648 AACAGGCACAAAATATCAATAGGTGTGTCACAGGCAAAGTA---ACACAT 3694
                           ii    v ii  v v     iii v  v ---     v --- i   v
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTC---CAAAGAAGATATACAA 864

  chr2_198371163_   3695 ATGGTTCAAGTA--TATATGAGGAGATGCTCAACTTCAATTGTATT 3738
                             i-   -  --i i    ii           v   ????????
  L1M4_orf2#LINE/    865 ATGGC-CAA-TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (21 / 17)
Gap_init rate = 0.05 (10 / 186), avg. gap size = 2.60 (26 / 10)  


 436 34.13 0.00 0.96  chr2_198378016_198384291.rev        1   208 (6068)    L1M4_orf2#LINE/L1       85   290 (618)  

  chr2_198378016_      1 GCAGTTCCCATCAAAATAGCATCATCATTCTTCACAGAACTAGAAAGAAC 50
                            i i  i        vv  v vv v  i  ii     v v  v iivi
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr2_198378016_     51 AATCCTAAAATTCATATGGAACCAAAAAGGAGACCACATAACGAAAGAAA 100
                         i                    viiv  i   vv viv   i v   iv  
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr2_198378016_    101 GACTAAACAAAAATAACAAATCTGGTGATATCACATTACCCCCACTTCAA 150
                         vvi i  v  i  v      vi   v ivv     i -i   v i     
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT-TCCCAATTTCAA 233

  chr2_198378016_    151 ACTATGGTACAAGTTTATAGTTACCAAAATAGCATGGTACTAGTATTAAA 200
                          viv iv     ivi  i   v i   i i  ii       i i  -  i
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAG 282

  chr2_198378016_    201 AATAGGCA 208
                         i    i  
  L1M4_orf2#LINE/    283 GATAGACA 290

Transitions / transversions = 1.22 (39 / 32)
Gap_init rate = 0.01 (2 / 206), avg. gap size = 1.00 (2 / 2)  

3285 26.32 0.55 0.55  chr2_198378016_198384291.rev     4877  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_198378016_   4877 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i i    i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_198378016_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_198378016_   4977 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5023
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_198378016_   5024 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5073
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_198378016_   5074 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACCATACTACAAGG 5123
                                 i      vv       v  ii i      v v        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_198378016_   5124 CTACATTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5173
                              v   i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_198378016_   5174 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAAC 5221
                                 i    i--    i  --        vv  ii i ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_198378016_   5222 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5271
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_198378016_   5272 CCTATTTAATAAATGGTGCTCGGAAAACTGGCTAGCCATATGTAGAAAGC 5321
                         i  v  i  i          v   v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_198378016_   5322 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5371
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_198378016_   5372 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5421
                           i ?   ii    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_198378016_   5422 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5471
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_198378016_   5472 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5521
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_198378016_   5522 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5571
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_198378016_   5572 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5621
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_198378016_   5622 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5671
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_198378016_   5672 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5721
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_198378016_   5722 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5771
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_198378016_   5772 CATCACTGGCCAT 5784
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3306 26.10 0.66 0.66  chr2_198418693_198424954     4863  5770 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_198418693_   4863 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4912
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_198418693_   4913 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4962
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_198418693_   4963 TACCAATGACTTTCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCA 5010
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_198418693_   5011 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5060
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_198418693_   5061 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5110
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_198418693_   5111 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAGAGACC 5160
                                 i   i    ii         i iv ii i   v   v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_198418693_   5161 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5208
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_198418693_   5209 ATCTGATCTTTGACAAGCCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5258
                          vi    i  i      vv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_198418693_   5259 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5308
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_198418693_   5309 GAAACTGGATCCCTTCCTTACACCTTACACAAGAATTAATTCAAGATGGA 5358
                            ii    i    v   i     v  i    i      i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_198418693_   5359 TTAAAGACTTACATGTTAGACGTAAAACCATAAAAACCCTAGAAGAAAAC 5408
                          i ?    i  v    v   vv      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_198418693_   5409 CTAGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCATGTCTA 5457
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_198418693_   5458 AAACACCAAAAGC-CATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5506
                         vi           -  -i          vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_198418693_   5507 AATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5556
                         v  i   v i  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_198418693_   5557 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5606
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_198418693_   5607 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5656
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_198418693_   5657 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 5706
                            i     i     v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_198418693_   5707 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5756
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_198418693_   5757 TCATCACTGGCCAT 5770
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


 481 23.31 8.45 8.78  chr2_198437672_198444277      208   503 (6103)    L1M4_orf2#LINE/L1      124   418 (490)  

  chr2_198437672_    208 ATTGATA-GTAAATCTTAAGATCCAACTGTGGAAATT--ATTGTTTCAGA 254
                              i - ivi   i   i  i  -- i       v-- vv vii    
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCA--TATGGAAATGCAAGGGACCCAGA 171

  chr2_198437672_    255 ACA---AAATTATAATATTAAAAAAGTAATAAAACAATGT------ACTT 295
                          i ---   -- i   v  i      -  --i     v  ------   i
  L1M4_orf2#LINE/    172 ATAGCCAAA--ACAATCTTGAAAAAG-AA--GAACAAAGTTGGAGGACTC 216

  chr2_198437672_    296 AAACTGGGAGGTAAATGCTAATTTCTTAATCTTTCACCACACTGATTTAA 345
                          v   ---------- v i      vv  -   --  i   --i vi  v
  L1M4_orf2#LINE/    217 ACACT----------TCCCAATTTCAAAA-CTT--ACTACA--AAGCTAC 251

  chr2_198437672_    346 AACATACCATGCACA---TGGTACTGGTACAA----AAACACA--GACCA 386
                          ii - i  v -   ---         i i  ---- i   i --  i  
  L1M4_orf2#LINE/    252 AGTA-ATCAAG-ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_198437672_    387 ATGGAACAGGATAGAGAACTCA--AATAAGACCACATATTTACAACCATC 434
                               i  i  v    iii  --     iv   i i     iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_198437672_    435 TGATTTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT--TCCT 482
                                 i    ivv  v   i v  vv            i  --  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_198437672_    483 TGTTTAATAAATGGTGCTGGG 503
                          -- i  i             
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGG 418

Transitions / transversions = 2.00 (46 / 23)
Gap_init rate = 0.07 (20 / 295), avg. gap size = 2.55 (51 / 20)  

3116 26.66 2.36 0.22  chr2_198437672_198444277     5226  6114 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_198437672_   5226 TGGAAAAACATTCCATGCTTATGGATAGGAAGAATCAATATTGTGAAAAT 5275
                               i i  i     i i      v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_198437672_   5276 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 5325
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_198437672_   5326 TACCATTGACTTTCTTCACAGAATTAGAAAAAACTAGTT-TAAATTTCAT 5374
                          v   vivi i  i  ii     v v  v  i-  ii i-    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_198437672_   5375 ATGGAACCAAAAAAGAGGCCATATAACCAAGACAATCCTAAGTGAAAAGA 5424
                               viiv  ii  vv viv   i    i      i i ivi i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_198437672_   5425 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5474
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_198437672_   5475 ACACTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5524
                            v   i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_198437672_   5525 ATGGAACAGAACAGAGACCTCAGAAATAACATCACACATCTACAACCATC 5574
                               i    iv    vii         vvi  i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_198437672_   5575 TGATCTTTGACAAACCTGACTAAAACAAGAAATGGGGAAAGGATTCCCTA 5624
                             i  i     ivv  v v i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_198437672_   5625 TTTAATAAATGGTGTCGAGAAAACTGGCTGGCCATATGCAGAAAACTGAA 5674
                           i  i        ii i  v      v i?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_198437672_   5675 ACTGGACCTCTTCCTTACACCTTATACAAAAATTAACTCACGATGGATTA 5724
                         ii      i  v   i     v                  vi      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_198437672_   5725 ATGACTTAAATGTAAGAACTAAAACCATAAAAATCCTAGAAGAAAACCTA 5774
                         ?v   i           i       i      v  i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_198437672_   5775 GGCA-ATACCATTCAGGACAT------AGGCA-TGACT----AAA----A 5808
                           ?i- v i -   iv   v ------     -  ii ---- i ---- 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_198437672_   5809 CACTAAAAGTAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5858
                            i     i vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_198437672_   5859 AGACTAAAGAGCTTCTGAACAGCAAAAGAAACTATCATCAGAGTGAACAG 5908
                          i v v  i i   i  vi vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_198437672_   5909 GCAACATACAGAATGGGAGAAAATTTTTGCCATCTATCCATCTGACAATA 5958
                         i    vi                 v     v vii  vi      i  vi
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_198437672_   5959 GGCTAATATCTAGAATCTAAACAGAACTTAAACAAATTTACAAGAAAAAA 6008
                          i  vi    i     v  v v      ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_198437672_   6009 ACAA----TCCCATCAAAAAATGGGTGAAGGATATGAACAGACACTTCTC 6054
                             ----i  v  i?         ii      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_198437672_   6055 AAAAGAAGATATTTATGTGGCCACCAAACATATGAAAAAAAGCTCATCAT 6104
                         v           vi vi      vi  i  i       i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_198437672_   6105 CACTGGTCAT 6114
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.56 (23 / 9)  


3019 26.74 2.92 0.90  chr2_198519811_198525290     4099  4988 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_198519811_   4099 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATAGTGAAAAT 4148
                               i i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_198519811_   4149 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATTCCTATCAAGT 4198
                            v     v      v i  i  i       ii  v  i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_198519811_   4199 TACCATTGACTTTCTTCACAGAATTAGAAAAAACTGGTTC-AAATTTCAT 4247
                          v   vivi i  i  ii     v v  v  i-   i i -   v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_198519811_   4248 ATGGAACCAAAAAAGAGCTGGTATAGCCAAGACAATCCCCAGCAAAAAGA 4297
                               viiv  ii  v ii v        i      iiv iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_198519811_   4298 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTGTACTACAAGGCC 4347
                               i      vv   ii  v  ii i      viv        i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_198519811_   4348 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGATCA 4397
                                i   i    ii         i iv ii i   i          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_198519811_   4398 GTGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAGCCATC 4447
                         i     i    iv   ivii         vv   i    i  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_198519811_   4448 TGATCTTTGACAAACCTGACAAAAACAAGCAGTGGGGTAAGATTC-CCTA 4496
                             i  i     ivv  v   i v  vv  i     v    v v-i  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_198519811_   4497 TTTAATAAATGGTGTTGGGAAAACTGGCTCGCCATATGCAGAAAACTGAA 4546
                           i  i        i     v      v v?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_198519811_   4547 ACTGGACCCCTTCCTTAAACCTTATGCAAAATTTAACTCAAGATGGATTA 4596
                         ii         v   i v   v   i     v         i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_198519811_   4597 AAGAGTTAAACATAATACCTAAAACCATAAAA------------AACCTA 4634
                         ?   vi    ii   v v       i      ------------   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_198519811_   4635 GGCA-ATACCATTTAGGACATGGGCATGGGCACAGACTTCATGACTAAAA 4683
                           ?i- v i -  iiv   v v  vv i    vv ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_198519811_   4684 CACCAAAA---CAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4730
                                 ---   --          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_198519811_   4731 TTAAACTAAAGAGCTTCTGCACATCAAAAGAAACTGTCATCAGAGTGAAC 4780
                          i   v v  i i   i  ii v     i  v   i   vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_198519811_   4781 AGGCAACCTACAGAATGGGAGAAAATTTTTGC----CATGTAGCCATCTG 4826
                           i     i                 v     ----   i  ----    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA----TCTG 742

  chr2_198519811_   4827 ACAAAGGGCTAATATCCAGAATCTACAAAGAGCTTAAACAAATTTACAAG 4876
                          i  i  i  vi          v  i     i  ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_198519811_   4877 AAAAAAACAA----CCCCATCAAAAAGTGGGTGACAGATATGAACAGACA 4922
                              i    ----   v  i?    i    ii vi   v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_198519811_   4923 CTTCTCAAAAGAAGACATTTATGTGGCCAACAAACATACGAATAAAAGCC 4972
                         i     v        i  vi vi       i  i  i i   v i v  i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_198519811_   4973 TGTCATCACTGGTCAT 4988
                         iiv     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.09 (34 / 11)  


3707 21.21 1.51 3.77  chr2_198626233_198628276.rev      624  1552 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_198626233_    624 TGGAAAGATTATCCATGCGCATAGATTGGAAAAAATAACATTGTTAAAAT 673
                                  vvi     iv   i        i vv   i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_198626233_    674 GTCCATCCTATGCAAAT-GGTGTACAGATTCAATGCAATCCCCACCAAAA 722
                          v v  v  viv     - i v           i        i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_198626233_    723 TTTCAATGACATTTCTCACAGACACAGAAAAAGCAGTTCTAAAATTCATA 772
                          ii  iivi v   i ii    v iv  v  iviii i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_198626233_    773 AAGGATAT-TACAGGACCCCAAATAGCAAAAACAATCTTGAAAAAGAA-- 819
                         v-   v  -i vi      vi      v                    --
  L1M4_orf2#LINE/    151 T-GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_198626233_    820 -CAAAGCTGGAAGCC---CACTTCTTGATTTCAAAACATCCTA-AAAGCA 864
                         -     i    i v ---      iii          v v   -     v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_198626233_    865 ACAGTAGTTGAGACAGTGTGCTACTGGCATAAAG-TAGCATACATAAATC 913
                               i ii          v           i -   - i i   i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG-ACATATAGATC 298

  chr2_198626233_    914 AACAGAACAGAATAGACATCCCAGAAATAAATTTATGCATTTATGGTCAA 963
                           ii   i     v  v vi           iii  i             
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_198626233_    964 TTGATCTTTGGCAAGTGTGCTAAGAACACACAATGAAGAAAGGACAGTCT 1013
                              i  i i    v    i    v  iv     ii     i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_198626233_   1014 CTTCAATAAATAGTTCTGGGAAAACTGGGTATCCATATGCAGAAGAAAGA 1063
                         i     i    i  v      v      i  ?   i     i     v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_198626233_   1064 AAATGGACCTTTATCTCACACCAAATTCAAAAAGCAACTCAAAGCAGATT 1113
                          iv      ii  i         v  v      vi        iii   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_198626233_   1114 GAAGACTTAAATATAGGACCTGAAACTATAAAACTACTAGCAGAAAACAC 1163
                         i?    i     i  i  v  i             vi   v        i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_198626233_   1164 AGGGGGAAAGCTACGTGACATTGGTCTAGGCAATGATTTTTTTGTATATG 1213
                            ? v   v  v      v    vi         i   i  v -     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-ATATG 597

  chr2_198626233_   1214 ACTTTAAAAGCACAAGCAAAAAACCTTAAGCACCTTAAAAGCACAAGCAA 1263
                           -----------------------------   --              
  L1M4_orf2#LINE/    598 AC-----------------------------ACC--AAAAGCACAAGCAA 616

  chr2_198626233_   1264 CAAAAGCAAAAATAGACAAACGGAATTACAT-AAAACTAAAAAGTTCTGG 1312
                               v         i   iv i i v   -    i      v  i  -
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG- 665

  chr2_198626233_   1313 CACAGCAAAGGAAACAATCAACAGAGTGAAGAGACAACTCACAGAATGGT 1362
                         ii vv       v  v     v i      i       i          v
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_198626233_   1363 AGAAAATATCTGCAGACTGTACATCTGATAAGAAGTTAATATTCAAAATA 1412
                                  i    i iii  i          iiii vi   i  i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_198626233_   1413 TATAAGAAACTTAGGCAACTCAATAGCAAGAAAACAAATAACTCAATTTT 1462
                              ii    ivvi          ii  i  i         i     ?v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_198626233_   1463 AAAACAGGGAAAAGACTTGAACAGACATTTCTC---AAAAGACATACAAA 1509
                             ii  v   i  i     i           --- i    i       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_198626233_   1510 TGGCCAACGGGTATATGAAAACATGTTCAACATCACTAATCAT 1552
                                iii i i       v   i         ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (128 / 65)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.50 (49 / 14)  


3831 21.32 3.06 0.11  chr2_198698685_198703324.rev     3267  4148 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_198698685_   3267 TGGAAAGACATCCCATGCTCATGGGTTGAAAGACTTAATATTGTAAAGTT 3316
                                 i        i      i   i               v   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_198698685_   3317 GTCCATAATACCCAAAGCAACCTACAGATACAATGCAAACTCTATAAAAA 3366
                          v v   v v      vii i        v   i    v i    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_198698685_   3367 TTCCAATGACACTTTTTGCATAAACAGAAAAA-TAATTATAAAATTC-TA 3414
                          i   iivi vi        v   iv  v  i- i  iv        -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_198698685_   3415 CAGGATCTTAAGGGGCCCAAAAGAGCCAAAACAATCTTGAAAAAGAA--- 3461
                         ii i vivi     i    i  v                        ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_198698685_   3462 CAAAGTCAGAGGCATCACACTTCTTGATTTCAAAACCTACTGCAAAGAAA 3511
                               ii    vv         iii          i    i     vv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_198698685_   3512 CAGTAATTAAGACAGTGTGGTA-TGGCCTAAAGTAAGATACATAAACCAA 3560
                                i              -    v   i vv   i i   i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_198698685_   3561 CGGAGTAAAATAGAGAGCCCAGAAATAAACCACTGCATATATGACCAAAT 3610
                         i   i  i   v     i             vv i   v    ii   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_198698685_   3611 GATTTTCAGCAAGAGTGCCAAGACCACACAACAGAGAAAAGACAGCCTCT 3660
                                ii    i            iv   ii i    ii i  i  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_198698685_   3661 TCAACAAGTAGTGTTGGAAAAATAGGATATTCAAATGCAAAAAGAGTGAA 3710
                                i i   i   i v  iv     ?i  v        -  i    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAA 449

  chr2_198698685_   3711 TTTGGGCCCTTGCCTTGTACCATACATAAAAATTAACTCAAAATGAATTA 3760
                         v    i   i i   iii      i i                  i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_198698685_   3761 AAGACCTAAAAATTAGACTTAAAACTGTTAAACTCCTAGAAAGAAACATA 3810
                         ?         vi v   vi       i v      i     ii       
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_198698685_   3811 GGGGTAAAGCCTCAGGACTTTGAATTTAGCAATGATTTCTTAAATATGAC 3860
                           ?     v i  iv   i   ii  vi      i       i       
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_198698685_   3861 ACCAAAAGCACAGACAACGAAATCAAAAATAAACAAAT-GGA----ATGA 3905
                                     ii    i   vv       i i    -   ----  v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_198698685_   3906 CA--CAAAAACTTTTTCATGTCAAAGGAAACAATCAACAGAGTGAAATTG 3953
                         v --i          viiiv        v  v     v i       vvi
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_198698685_   3954 CAACCTATAAAATGGGAGAAAATAATTGCAAATAATATATCTGAAAAGGG 4003
                              i i i              v        v          v     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_198698685_   4004 GTTAATATCCAAAATATATAAGAAACTTTAACAAC-----AACAAAAAAA 4048
                         ii vi      i         ii    i v     -----  i     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_198698685_   4049 T--------TGATTCTAAAATAGGCAAAGAACTTAAACTGACATTTCTCC 4090
                         i--------ii   ?v     i       i i  i  iv           
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_198698685_   4091 AAAGAAGATATACAAATGGCCCATAAGCACTTGAAAAGATGAT-AACATT 4139
                                              v        v          v -     i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_198698685_   4140 ACTAATCAT 4148
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.88 (120 / 64)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.55 (28 / 11)  


3096 27.73 0.77 0.44  chr2_198707667_198714388     5326  6230 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_198707667_   5326 TAGAAAAACTTTCCATGTTCATGGATAGGAAGAATCGATATAGTGAAAAT 5375
                          i    i iv i              v      v ii    v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_198707667_   5376 GATCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTTCTGTCAAGC 5425
                          iiv     v      v i  i  i        i  v  ii  i    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_198707667_   5426 TTCCA-TTGAATGTCTTTACATAATTAGAAAAAACT-ACTTTAAATTTCA 5473
                          i   -i  vv - i   i  v  v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_198707667_   5474 TATGGAACCAAAAAGGAGCCGGTATAGCCAAGACAATTCTAAGCAAAAAG 5523
                                viiv  i   v  i v        i     ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_198707667_   5524 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTGCAAGGC 5573
                                i      vv   ii  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_198707667_   5574 TACAGTAATCAAAATAGCATGGTGCTGGTACCAAAACAGAAATATAGACC 5623
                                     i i  ii    i    i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_198707667_   5624 AATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAT 5673
                                i    iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_198707667_   5674 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5723
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_198707667_   5724 AGTTAATGAGTGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5773
                         vv i  ii i     i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_198707667_   5774 AACTGGACCTCTTCCTTACACCTTATACAAAAATTAACTCAAGAGGGATT 5823
                          ii      i  v   i     v                   i v    i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_198707667_   5824 AAAGATTTAAATGTAAAACCTAGAACCATAAAAACCCTAGAAGAAAACCT 5873
                          ?   ii         i v   i   i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_198707667_   5874 AGGCA-ATACCATTCAGGACATAAGCATGGGCAAAGACTTCA-AGACTAA 5921
                            ?i- v i -   iv   v vi vv i     v ii   v-   -  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TAT 596

  chr2_198707667_   5922 AACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGAGATCTAA 5971
                         i            vvv          vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_198707667_   5972 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGTCATCAGAGTGAAC 6021
                          i   v v  i i   i  ii vv    i  v   i   vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_198707667_   6022 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGTCAA 6071
                           i     i                 v       vii  vi     vi  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_198707667_   6072 AGGGCTAATATCCGGAATCTACAAGGAACTTAAACAAATTTACAAGAGAA 6121
                         i  i  vi     i    v  i  i     ivv    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_198707667_   6122 A---AAACAACCCCATCAAAAAGTGGGCGAAGGATATGGACAGACGCTTT 6168
                          ---   i     v  i?    i     i      v  i i    ii  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_198707667_   6169 TCAAAATAAGACATTTATTCGGCCAATGAACATATTTTAAAAAGCTCATC 6218
                           v   v    i  vi vvi       i i  i  vvv  i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_198707667_   6219 ATCACTGGTCGT 6230
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.22 (11 / 9)  


3162 25.29 0.75 3.43  chr2_198888321_198892401     2657  3589 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_198888321_   2657 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 2706
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_198888321_   2707 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCTCCATCAAGC 2756
                            v     v     iv i  i           i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_198888321_   2757 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2804
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_198888321_   2805 TATGGAACCAAAAAAGAGCCCTCATTGCCAAGACAATCCTAAGCCAAAAG 2854
                                viiv  ii  v  vvv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_198888321_   2855 AACAAAGCTGGAAGCATCACATTACCTGACTTCAAACTATACTACAAGGC 2904
                                i    i vv     i v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_198888321_   2905 TACAGTAACCAAAACAGCATAGTTCTGGTACCAAAACAGAGATATAGACC 2954
                                 i   i    ii i  v    i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_198888321_   2955 AATGGAATAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 3002
                                     i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_198888321_   3003 ATCTGATATTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3052
                          vi    v  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_198888321_   3053 CTATTTAATAAATGGTGCTAGGAAAACTGACTAGCCATATGTAGAAAGCT 3102
                           v  i  i          i   v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_198888321_   3103 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGTA 3152
                            ii    i    v   i     v              i    i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_198888321_   3153 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAACTCT-AGAAGAAAAC 3201
                          i ?    i       v   v       i          -          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_198888321_   3202 CTAGGCA-ATACCATTCAGGACATAGCAT-AGGCAAGGACTTCATGTCTC 3249
                         v    ?i- v i -   iv   v v vi -      v ii   v ivv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_198888321_   3250 AAACACCAAAAGCAACAGCAACAAAAGCCAAAATAGACAAATGGGATCTA 3299
                         vi            vv           vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_198888321_   3300 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACAAAGAGCTTCTGCAC 3349
                           i   v v  i i   i  i-------------------     -----
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGT-------------------GCTTC----- 671

  chr2_198888321_   3350 AGCAAAAGAAACTGCCATCAGAGTGAACAGGTAACCTACAGAATGGGAGA 3399
                         ---   i  v   ii  vv i      v  ii    i             
  L1M4_orf2#LINE/    672 ---AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_198888321_   3400 AAATTTTTGCAATCTATTCATCTGACAAAGGGCTAATATCCAGAATCTAC 3449
                             v       vii  vi      i  i  i  vi          v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_198888321_   3450 AAAGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAG 3499
                                  vv    v iv i  v     i     i     v  i?   i
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_198888321_   3500 GCGGGTGAAGGGTATGAACAGACACTTCTCAAAAGAAGACATTTATGCAG 3549
                         ii   ii    i v    i     i     v        i  vi viii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_198888321_   3550 CCAACAGACACATGAAAAAATGTTCATCACCACTGGCCAT 3589
                             i ii          i   i   v  i  ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (142 / 90)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.55 (39 / 11)  


2943 28.49 1.11 0.44  chr2_199116109_199119675.rev     2174  3075 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_199116109_   2174 TAGAAAAACATTCCATGCTCATGGATACAAAGAATCAATATCGTGAAAAT 2223
                          i    i i  i     i        vvi    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_199116109_   2224 GACCATACTGCCCCAAGTAATTTATACATTCAATGCTATCTCCATAAAGC 2273
                          i v     v   v  v i  i  i v      i  v   i i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_199116109_   2274 TACCATTGACTTCCTTCACAGAATTGGAAAAAACAACTTTAAATTTCATA 2323
                          v   vivi i ii  ii     v v  v  ivii iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_199116109_   2324 TGAAACTAAAAAAGAACGCACATAGCCAAGACAATCCTAAGCAAAAAGAA 2373
                           i  v iv  ii  v vviv        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_199116109_   2374 CAAAACTGGAGGCATCATGCCACCTGATTTCAAACTATACTACAAGGCTA 2423
                             ii      vv   ii iv  ii        viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_199116109_   2424 CAGTAACAAAAAGAGCACAGTACTGGTACCAAAACAGATATATAGACCAA 2473
                               iv  i v  iiii       i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_199116109_   2474 TGAAACAGAACAGAGGCCTCAGAAATAACACCACACACCTACAACCATCT 2523
                           i  i    iv   ivii         vv   i   ii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_199116109_   2524 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT--TCCTT 2571
                            i  i     ivv  v   i v  vvv           i  --  i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_199116109_   2572 ATTTAATAAATGCTGTTGGGAAAATTGGCTAGCCATACGCAGAAAGCTGA 2621
                         -- i  i     v  i     v  i   v  ?   i i   i  iiv   
  L1M4_orf2#LINE/    401 --TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_199116109_   2622 AACTGGATCCCTTCGTTACACCTTATACAAAAATTAACTCAAGATGGATT 2671
                          ii    i    v v i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_199116109_   2672 AAAGACTTAAATGTAAACCCTAAAACCATACAAACCCT-AGAAGAAAACC 2720
                          ?    i         ivv       i   -    i  -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACA 547

  chr2_199116109_   2721 TAGGCA-ATACCATTCAGGACGTAGGCATGGGCAAAGACTTCATGACTAA 2769
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_199116109_   2770 AACACCAAAAACAATGGCAACAAAAGACAAAATTAACAAATGGGATCTAA 2819
                         i         i  vvi           v     vi i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_199116109_   2820 TTAAACTAAAGAGCTTCTGCACAGCAAAAGCAACTATCATCAGAGTGAAC 2869
                          i   v v  i i   i  ii vv    i vv       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_199116109_   2870 AGGCTACCTGCAGAGTGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 2919
                           i v   ii    i           v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_199116109_   2920 AGGGCTAATATCCAGAATCTACAAAGAACTT----AATTTTACAAGGAAA 2965
                         i  i  vi          v  i        i----  i iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_199116109_   2966 AAACAAACAACCCCATCAAAAAGTAGGCAAAGGATATGAACAAAC--TTC 3013
                          i     i     v  i?    i i          v    i i  --   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_199116109_   3014 TCCAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCATC 3063
                                    i  vi viii     i  i  i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_199116109_   3064 ATCACTGGTCAT 3075
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (157 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


 824 29.19 8.23 3.26  chr2_199203097_199205489.rev      503  1146 (1247)    L1M4_orf2#LINE/L1      121   796 (112)  

  chr2_199203097_    503 GATATTGTCAAGCTGAT--TAAAACTTTATATGAAAATTCAAAAGACCAA 550
                           v    v         --     -  i     i    v   ii    v 
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAA-TTCATATGGAAATGCAAGGGACCCA 169

  chr2_199203097_    551 GAATAACCATCACACTCTCCAA---GAAAAACAAAGTGAGAGGATTGAT- 596
                              i   vv   v   iv  ---   i        vi     i v i-
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_199203097_    597 CTACCTGA---CAAAAATTTTTATAAACTCACAGTTA-CAT--CAGTATA 640
                           v  ii ---     v  vi  i   vii     v -  v--    i i
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_199203097_    641 GTATTGCTTT--GGA--GACAAATAAAACAAAAGAATCAAATACAGACCT 686
                            i  viv --   --    v   i v   vi    vi   vv   vii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_199203097_    687 CAAAAACAAATCCAGGCATATATGG-CAGTTGATT--CATTAAATATGTC 733
                           i   i   i   vi   v     -  i      -- ivi  ivi  i 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_199203097_    734 ACTTAGG---TACAA--AGGAAAAAACAAATCTTTTTAATAAATGCTCTT 778
                          ---  i--- v   --i     i  i i-      i  i     v vi 
  L1M4_orf2#LINE/    370 A---AGACCATTCAATGGGGAAAGAATAG-TCTTTTCAACAAATGGTGCT 415

  chr2_199203097_    779 GATAGAGATG-ATG-----AGGGAGGAGAATAGGGGTAGAAAGACTTCTA 822
                          iv v iv  -  i----- v v ii     - ii  v ---   ii   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAAT-GAAGTTG---GACCCCTA 461

  chr2_199203097_    823 TG-CATTACTATACTTCAAAATACATTGCAAAATG--TTGTAAATCTTAA 869
                         iv-  i-  i   iviv     vv i -       -- ii? i i  v  
  L1M4_orf2#LINE/    462 CCTCAC-ACCATATACAAAAATTAACT-CAAAATGGATCAWAGACCTAAA 509

  chr2_199203097_    870 TGTGAAATGTAAAGCAACAGTG-TCTCAAAACAA--TTTAGGAAAGTATT 916
                            i i vv    i v i ivi-   i i  v  --iv    ?iviv  i
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_199203097_    917 TTCATGATCTTGGGTTTATGAAACA-TTTCTGAAAGAATACACAAAAAGC 965
                            i   i        - v v  ii-     v i v vv    v      
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTT-AGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_199203097_    966 ACAAATCATAAAACATAAGGAAGGCTGCCAAGTCTGACTTCATTATAATT 1015
                             iiv i    v v  iiv  ii----  i iv        i v    
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGAT----AAATTGGACTTCATCAAAATT 654

  chr2_199203097_   1016 AATATTTTTT---CATCAAAA-ACATTATTAATAGTGTGAA--GACAGT- 1058
                           v vi    --- v     i-   i   i  v iv     --    ii-
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_199203097_   1059 -A-AGATACATGGGA-AAGTCATTTTTAGTACATATAACCAA--AAGGAC 1103
                         - -   ---      -  ivi    vi ivv      v ii -- i    
  L1M4_orf2#LINE/    705 CACAGA---ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_199203097_   1104 TAATA--CAGAATATAGAAA-AACTTCTGTGA-TCAATAAGGTAAAA 1146
                          vi  --         v   -    ii iii -       --     
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA--TAAAA 796

Transitions / transversions = 1.42 (109 / 77)
Gap_init rate = 0.06 (40 / 676), avg. gap size = 1.85 (74 / 40)  

 212 28.00 4.00 0.80  chr2_199203097_199205489.rev     1777  1901 (492)    L1M4_orf2#LINE/L1      780   908 (0)  

  chr2_199203097_   1777 ATAAATAAATAGGTAAAAAAAATAATAACTGG--TACAAGA-GAGCAAAT 1823
                          i  v v    i-      i vv      ivi-- ?v  i - i     v
  L1M4_orf2#LINE/    780 ACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_199203097_   1824 AAA--AAGCAAACATTTCATTAAAGAATATCTATAAATGGCCAACAAACA 1871
                         i v--i ii i       vii      v  v  i          i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_199203097_   1872 TATGTAACGTTGCTCAGCTTCATTAACAAA 1901
                         i   v  v v      i v   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (19 / 15)
Gap_init rate = 0.03 (4 / 129), avg. gap size = 1.50 (6 / 4)  


2559 26.03 4.13 2.68  chr2_199252700_199255488.rev     1403  2297 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_199252700_   1403 TGGAAAAACATTCCATGCATATGGATATCAAGAATCAATATTGTTAAAAT 1452
                               i i  i     ivi      vvv    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_199252700_   1453 GGCCACACTACCCAAAGCAATTTACAGATTTCAATGCTATTCCTATCAAA 1502
                            v i   v      vii  i        -   i  v  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT-CAACGCAATCCCTATCAAA 99

  chr2_199252700_   1503 CTGTCAATGACATTATGCACAGAATTAGAAGAAACT-ATCCTAAAATTCA 1551
                         v vi  iivi v  v vii     v v  v-  i  -             
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCA 148

  chr2_199252700_   1552 TTTGGAACCAAAAAAGAGCCCAAATTGCCAAAGCAATTCTAAGCGAAAAG 1601
                          v     viiv  ii  v  vi   v      i    ii i ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_199252700_   1602 AACAAAGCTGGAGGCATCACATTGCCCTACTTCAAACTATACCACAAGGC 1651
                                i      vv     i v   v i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_199252700_   1652 TACAATAACCAAAACAGCATGGTGCTGATACAGAAACAGATACCCAGGAC 1701
                             i   i   i    ii    i   ii i iii i   i ivi  iv 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_199252700_   1702 AATGGAACACAATAGGGAGCCCAGAAATAAAGCCACACACCTACAGCTAT 1751
                                i v   v i   i           v   i   ii  ii ii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_199252700_   1752 CTGATCTTTGGCAAATTCAACCAAAACAAG-AAATGGGGAAATCAT-GCC 1799
                         i    i  i i   ivvii-    i  v v-v          vv  - i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_199252700_   1800 TATTCAGTAAATGGTGTCAAGATAACTGGCTAGCCACATGCACAAGATTA 1849
                          v    ii        iiii  i      v  ?         v    v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_199252700_   1850 AAACTCTACCCCTTCCTTTCA----------AAATTAACTCAAGATGGAT 1889
                           ii vv      v   iv  ----------            i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_199252700_   1890 TAAAGACTTAAATGTAAAACCTAAAACTTTATAGTTTTATATAAAACCCT 1939
                         i ?    i         i v        ------------       i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACT------------ATAAAACTCT 535

  chr2_199252700_   1940 -AGAAGAAAACTTAGG---AAATACCATTCTGGACATAGACTTTGGCAAA 1985
                         -          v    ---    -- -   vv   v v iv  v     v
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAAT 582

  chr2_199252700_   1986 GATTTCAT-GATGAAGACACCAAAAGCAATTGCACCAAAAACAAAAACGG 2034
                          i    v -   - v             vvv   v     iv     ii 
  L1M4_orf2#LINE/    583 GGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_199252700_   2035 ACAAATGGGACCTAATTAAACTGAAGAGCTACTACACAGCAAAATAAATG 2084
                          i    v    i v  i   v v  i i  vi iii vv    iv v iv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_199252700_   2085 ATCAAGAGAGT-------TTATTTCTACAGAATAGGATAAA-TATTTGCA 2126
                                i   -------iv i-- i       i   v   -        
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAAC--CCACAGAATGGGAGAAAATATTTGCA 729

  chr2_199252700_   2127 AACTATCCATCCAACAAAGATCTAATATCCAGAATCTATAAGAAACTTAA 2176
                           ii  vi   ii i  i iv  vi          v     ii    ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_199252700_   2177 ATAA---AATATCAAGCAAAAAACAAGCAACCCCATTAGAAAGTGGGCAA 2223
                          i  ---    vi  ---   i    ii     v   ?i   i       
  L1M4_orf2#LINE/    780 ACAACTCAATAATAA---AAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_199252700_   2224 AGGAC----ACAGACAATTTTC---AGAAGACATACATGTAGCCAACAAG 2266
                             i---- i     v  i  ---      i     vi i     i   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_199252700_   2267 CATATAAAAA-ATGCTCAACATTACTCATCAT 2297
                           i  i    -           i ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (140 / 90)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.77 (61 / 22)  


2381 26.79 0.29 0.59  chr2_199265221_199266882      500  1182 (480)    L1M4_orf2#LINE/L1      228   908 (0)  

  chr2_199265221_    500 TTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGT 549
                                viv        i          i   i    ii         i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_199265221_    550 ACCAAAACAGAGATATAGACCAATGGAACAGAACAGAGACCTCAGAAATA 599
                          iv ii i   v       i        i    iv    vii        
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_199265221_    600 ACGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAA 649
                          vv  ii i  i  iiiii vi    i  i     ivv  vv  i v  v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_199265221_    650 GCAATGGGGAAAGGA--GTCCCTATTTAATAAATAGTGCTGGGAAAACTG 697
                         v            i --   -- v  i  i    i         v     
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_199265221_    698 GCTAGCCATATGTAGAAAGCTGAAACTGGATCGCTTCCTTACACCTTATA 747
                          v  ?   i   i i  iiv    ii    i v  v   i     v    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_199265221_    748 CAAAAATCAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACC 797
                                i  i    i      i ?    i    i  v   v       i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_199265221_    798 ATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCAT 847
                               vi i           v    ?i v viv   iv   v v  vv 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_199265221_    848 GGGCAAGGACATCATGTCTAAAACACCAAAAGCAATGGCAACAGAAGCCA 897
                         i     v iiv  v ivv  vi            vvi      i   vv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_199265221_    898 AAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAA 947
                             v  i    v   ii v  i   v v  i i   i  ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_199265221_    948 GAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTT 997
                           v    i  vv i      v  i     i   i             v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_199265221_    998 TGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAAC 1047
                              vii ivi      i  i  i  vi          v  i  v    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_199265221_   1048 TCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCA 1097
                           vv    v iv i  v     i     i     v  i?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_199265221_   1098 AAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAA 1147
                              iv    i     i     v        i  vi viii     v  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_199265221_   1148 ACACATGAAAAAATGAGCAAAGTATTAATCTCTTC 1182
                         i          i   vv   --i  i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAA--CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (104 / 75)
Gap_init rate = 0.00 (3 / 681), avg. gap size = 2.00 (6 / 3)  


 361 22.47 0.00 2.25  chr2_199271707_199276241      181   269 (4266)    L1M4_orf2#LINE/L1      809   895 (13)  

  chr2_199271707_    181 CAGTGTAAGAATGGACTAATACAGTCTGAATGGACATTTCTTCAAAGATG 230
                           i v?  i     i -  - vii i     i         i      v 
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGC-AA-AGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_199271707_    231 ATACAAAAATGGCCCATGCACATATAAAAAGATGCTCAA 269
                            i v        v  ivi  i  i             
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.02 (2 / 87), avg. gap size = 1.00 (2 / 2)  

3287 26.87 0.44 0.44  chr2_199271707_199276241     3136  4043 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_199271707_   3136 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3185
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_199271707_   3186 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 3235
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_199271707_   3236 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3283
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_199271707_   3284 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGGCAATCCTAAGCCAAAAG 3333
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_199271707_   3334 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3383
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_199271707_   3384 TACAGTAACCAAAACAGCATGGTCCTGGTACCAAAACAGAGATATAGATC 3433
                                 i   i    ii    v    i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_199271707_   3434 AACGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3481
                           i    i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_199271707_   3482 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3531
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_199271707_   3532 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3581
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_199271707_   3582 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATAGA 3631
                            ii    i    v   i     v           i  i    i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_199271707_   3632 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3681
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_199271707_   3682 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 3731
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_199271707_   3732 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 3781
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_199271707_   3782 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3831
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_199271707_   3832 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 3881
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_199271707_   3882 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3931
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_199271707_   3932 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 3981
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_199271707_   3982 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 4031
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_199271707_   4032 ATCACTGGCCAT 4043
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 336 20.45 1.14 0.00  chr2_199358508_199360122.rev      416   503 (1112)  C L1M4_orf2#LINE/L1   (0)   908   820 *

C chr2_199358508_    503 TGGGCAAAAGATATGAATAGATATTTTT-AAAAGAAATCATATAAACAGA 455
                                 i   v        i    i -v      ivi   i   ii v
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

C chr2_199358508_    454 AAACAAACATATGAAAAAATGCTCAATATCACTATTCAT 416
                         v  i  i  i       i        i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.01 (1 / 89), avg. gap size = 1.00 (1 / 1)  

2141 26.18 1.79 0.33  chr2_199358508_199360122.rev      501  1115 (500)    L1M4_orf2#LINE/L1      248   871 (37)  

  chr2_199358508_    501 CCACAGTAACCAAAACAGCATGGTACTGGTATAAAAAGAGGCACATAGAT 550
                          i       i   i    ii         i    ii v  i  i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_199358508_    551 CAATGGAATAATATAGAGAAGTCAGAAATAAAGCCACATACCTACAGCCA 600
                                   iv  v    ivi          v   i i ii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_199358508_    601 ACTGATCTTTGACAAAGTTAACAAAAACATACACTGGAGAAAGGACACCC 650
                          i    i  i     i v iv   i v   v  v   i     i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_199358508_    651 TATTTAATAAAGGGTACTGAGAAAACTGGATTGCCATATGCAAAGGAATG 700
                          v  i  i   v   i   i  v        v?   i       i     
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_199358508_    701 AAACTGGACCCCTATCTCTAACCATATACAAAAAGTTAC-CATGGTTGAT 749
                           ii          i   vv              v v  -  vii v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_199358508_    750 TAAAGACTTAAATGTAAAATCTGAAACTATATAAATGCTAGAAGAAAACC 799
                         i ?    i         i v  i        v  v vi           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_199358508_    800 TTGGAAAAATTCTTCTGGATATTGGCCTAGACAAAGAATTCGTGACTAAG 849
                          v  ?iv  v     vv  iv    vi   i   v iv   v iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_199358508_    850 ACCTCAAAATCAAATGCAACAAAACCAAAAATAGACAAATGGGACTTAAT 899
                           vi     v  v v         vv         i    v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_199358508_    900 TAAACTT-----CTCCAGTGT---AAAAGAAATAATTGACAGAGTGAATA 941
                         i   v  -----  iiv   i---   i  v iv  ii v i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_199358508_    942 AAAACCCTGCAGAATGGGAGATGATATTTGCAAAGTATGCATCTGACAAA 991
                         i v v  ii            vi           vi  ii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_199358508_    992 CGACTAATATCCAAACTCTACAAATA-CTCAAACAACTCAAAACAATAAC 1040
                         v    vi      i v v  i   v -   vv         --i     v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA--TAATAAA 795

  chr2_199358508_   1041 AACA-AAATAACTCCATTAAAAAGTGGGCAAAGGACACAAACTGATATTT 1089
                           v -       i v   ?    i           ivii  iv  i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_199358508_   1090 TCCAAAAGAAGACATACAAATGGTCA 1115
                         ii v        i          i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.28 (88 / 69)
Gap_init rate = 0.01 (6 / 624), avg. gap size = 2.17 (13 / 6)  


3070 22.86 5.89 2.31  chr2_199369569_199373412     2487  3352 (492)    L1M4_orf2#LINE/L1       12   908 (0)  

  chr2_199369569_   2487 CTCATGTACACTGATGAAAAGACTTACTATTGTTAA-ATACTTATACTAC 2535
                          i     v  iv   vii        v         -  iviv     v 
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chr2_199369569_   2536 CCAAAGCAATCTACAAATTCAAGGCAATCCCTGTCAAACTCTGAATGACA 2585
                              vii       i      v         i     v  iv iivi v
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_199369569_   2586 TTTGTTTGCAGAAATAGATAAAACAATCCTAAAATCCCTATGGAATCACA 2635
                            -           v  i  ivii          i v       vii  
  L1M4_orf2#LINE/    112 TTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_199369569_   2636 AAGAACCCTAAATTTTCAAAACAATCTTGAGAAAGAA---CAAAGCTAGA 2682
                          i i    vi   vvi              i      ---     i i  
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_199369569_   2683 G---------------ACTTCGAAACATATTACAAAGCAACTGTAAT--- 2714
                          --------------- i   i    v  i        v  v     ---
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_199369569_   2715 ---AGTGTAGTACTGGCATGAACGTAGACATATAGACCAATGGGA----- 2756
                         ---     i          i ivi            i      i -----
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_199369569_   2757 ---------CAGCAATAAAACCCATCCATGTATGGTCAAATGATGTTCGA 2797
                         ---------   v      -     v   v         v    v     
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_199369569_   2798 CAAAAGTGTCAACACTACACACAGTGGGGAAAGGGT--TCAACTCAACCC 2845
                            ii   i   v  --  iv  i         ii --  vvi     vv
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGAC--CATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_199369569_   2846 A--GTG---GGAAAACTGGATGTCTTCATGCAGAAGAATGAAATTGGGCC 2890
                          --   ---   v        i? iv      i         i    i  
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_199369569_   2891 CTTATGTTGTATTATACATAAAAATCAACTCAAAATGGATTA--GACATA 2938
                          i  iv iii ii   i i      i              i --   v  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_199369569_   2939 AATGTAAGACCTTAAACTACAAAATTCCTGGAAGAAAACACAGAAGAAAA 2988
                                  v  v      i    i  i i          i  i? v   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_199369569_   2989 GTTTCATAATATCAGTCTTAGCAATTATTTTTTGGATATGACACCAAAAG 3038
                         vi   i i iv ii vi vi     vi   i  i                
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_199369569_   3039 CACAGGCAATAAAAGAAAAAAAAAGTCAAGTGGGAGTGCATCAAACTTTA 3088
                             i    i           v ii -  i v   v v       v  v 
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGAT-AAATTGGACTTCATCAAAATTAA 656

  chr2_199369569_   3089 GTTTGCTTCTGCCCAGCAAAAG-TAGTAATCAACAGAGTGAAAAAGCAAT 3137
                         iv--i   i  iv vv    i -i v  -    v i        ii   i
  L1M4_orf2#LINE/    657 AA--ACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAAC 703

  chr2_199369569_   3138 CTATAGAGTAGGAGAGTAGGAGAAAATATGTACAAACAATATGTATGATA 3187
                          i i   i i     --------      v i    iv    i v     
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGA--------AAATATTTGCAAATCATATATCTGATA 745

  chr2_199369569_   3188 AGGAGTTAATATCCAAAATATATAAATAACTTCTACAATTCAATGGCAGA 3237
                            iii vi      i          v    ii     i     iii i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_199369569_   3238 AACAAATAAAAAACTTGGTAAAAAAATGTGCAAAGAATGTGAATAGACAT 3287
                           --i i   v   iiii v?       v      i  v           
  L1M4_orf2#LINE/    796 AA--GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_199369569_   3288 TTCTCCAAATAAGACATGAACAA--GATCAATAGGTATATAAAAAGATGC 3335
                                  v    i  --    -- ii     i i i  i         
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_199369569_   3336 TCAACATCACTAGTCAT 3352
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (126 / 69)
Gap_init rate = 0.02 (20 / 897), avg. gap size = 3.55 (71 / 20)  


2857 26.85 2.92 0.90  chr2_199374189_199380892     5323  6212 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_199374189_   5323 TAGAAAAACATTCCATGCTCATGGATAGAAAGAATCAATATCATGAAAAT 5372
                          i    i i  i     i        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_199374189_   5373 GGCCATACTGCACAAAGTAATTTATAGATTCAATGCAATCCCCATCAATC 5422
                            v     v v    v i  i  i        i        i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_199374189_   5423 TACCATTGACTTCCTTCACAGAATTAGAAAAAACAACTTTAAATTTCATA 5472
                          v   vivi i ii  ii     v v  v  ivii iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_199374189_   5473 TGGAACCAAAAAAGCGCCCACA-TAGACAAGACAATCCGAAGCAAAAAGA 5521
                              viiv  ii -i    v -   v   i      ivi iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_199374189_   5522 ACAAAGCTGGAGGTATCACACTACCTGACTTCAAACTATACTACAAGGCT 5571
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_199374189_   5572 ACAGTAACCAAAACAACATGGTACTGGCACCAA-ACAGATAAATAGACCA 5620
                                i   i   iii           iv i- i   i v     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_199374189_   5621 ATGGGACAGAACAGAGGCCTCAGAAATAACACCACACATCT-TCATCCAT 5669
                             i i    iv   ivii         vv   i    i - vi  v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_199374189_   5670 CTGATCTGATCTTTGACAAACCTGACAAAAACAAGCAATG---------- 5709
                         ------    i  i     ivv  v   i v  vv     ----------
  L1M4_orf2#LINE/    350 ------TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_199374189_   5710 ------TTTAGTAAAAGCTGTTGGAAAAACTGGCTAGCCATATGCAGAAA 5753
                         ------  i ii   v v  i   i v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_199374189_   5754 ACTGAAACTGGACCCCTTCCTTACACCTTCTTCAAAAATTAACTCAAGAT 5803
                          v    ii         v   i     v v v               i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_199374189_   5804 GGATTAAAGACCTAAATGTAAGACCTAAAAGTATAAAAACCCTAGAAGAA 5853
                             i ?                v      v       vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_199374189_   5854 AACCTAGACA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 5902
                            v   i?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_199374189_   5903 CTAAAACACCAAAGGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5952
                         v  vi        i   vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_199374189_   5953 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 6002
                         i v  i   v v  i i   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_199374189_   6003 GAACAGGCTACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTG 6052
                            v  i v   i                 v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_199374189_   6053 ACAAAGGGCTAATATCCAGAATCTACAAAGAATTTAAACAAATTTACAAG 6102
                          i  i  i  vi          v  i      i ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_199374189_   6103 AAAAA-----ACAACCCTATCAAAAAGTGAGTGAAGGATATAAACAGACA 6147
                              ----- i     v  i?    i  i ii      v i  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_199374189_   6148 GTTCTCAAAAGAACACATTTATGCAGCCAACAAACATATGAAAAAA-GCT 6196
                         v     v      v i  vi viii     i  i  i       i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_199374189_   6197 CATCATCACTGGTCAT 6212
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.40 (34 / 10)  


2788 28.18 0.77 1.21  chr2_199474304_199477156.rev     1450  2361 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_199474304_   1450 TAGAAAAACACTCAATGCTCATGGGTAGGAAGAATCAATAGCATGAAAAT 1499
                          i    i i ii v   i      i v      v i    vii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_199474304_   1500 GGCCATACTGGCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGG 1549
                            v     vv     v i  i  i        i  v     i     ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_199474304_   1550 TACCA-TTGACTTTCTT-CACACAATTAGAAAAAACTACTTT---ATTTC 1594
                          v   -i  v    i  -  v -    i-- v  i  iv ii--- v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_199474304_   1595 ATATGGAACCAAAAAAGAGCCCATATAGCTAAGATGATTCTAAGCAAAAA 1644
                                 viiv  ii  v  viv     i  i ii  ii i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_199474304_   1645 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATACTATGAGG 1694
                                 i      vv   ii  v  ii i      viv     ii i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_199474304_   1695 TTACAGTAACCAAAATAGCATGGTACTTGTACCAAAACAGATGTATAGAC 1744
                         i        i   i i  ii       v i iv ii i   ii      i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_199474304_   1745 CAATGGAACAGAACAGAGGCCTCAGAAATAATAACGCCACACATGTACAA 1794
                                 i    iv   ivii         --  -   i    v  iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAA--AC-CCATACATTTATGG 344

  chr2_199474304_   1795 CCATGTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 1844
                         i  vv    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_199474304_   1845 CCCTATTTAATAAATGGTGTTGGGAAAACAGGCTAGACATATGCAGAAAA 1894
                         vi  v  i  i        i     v   v  v  ?v  i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_199474304_   1895 CTGAAACTGGACCCCTTCCTTACACATTATACAAAAATTAACTCAAGATG 1944
                         v    ii         v   i    vv                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_199474304_   1945 TATTAAAGACCTAAATGTAAGACCTAAAACCATAAAAACTCT-AGAAAAG 1993
                         v  i ?                v       i      -    -    i i
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chr2_199474304_   1994 AACCTAGACA-ATACCATTCAGGACATAGGCATGAGCAAAGACTTCATGA 2042
                            v   i?i- v i -   iv   v v  vv ii    v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_199474304_   2043 CTAAAACATCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGAT 2092
                         v  vi   i        vvv          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_199474304_   2093 CTAGTTAAACTAAAGAGCTACTGCATAGCAAAAGAAACTATCATCAGAGT 2142
                         i vi i   v v  i i  vi  iiivv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_199474304_   2143 GAACAGGAAACCTATAGAATGGGAGAAAATTTTTGCAATTGATACATATG 2192
                            v  iv    i i               v       v v   i  v  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_199474304_   2193 ACAAACGGCTAATGTCCAGAATTGACAAGGAACTTAAACAAATTTACAAG 2242
                          i  iv i  vi i        vv i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_199474304_   2243 AAAAAAACCAAACAACCCCATCAAAAGGAGGGCAAAGGATATGAACAGAC 2292
                              i  -   i     v  i?   iiv           v    i    
  L1M4_orf2#LINE/    793 AAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_199474304_   2293 AGTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAGAAAAAA 2342
                          v     v        i  vi viii     i  i  i     --  i v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA--AAGAT 889

  chr2_199474304_   2343 GCTTACCATCACTGGCCAT 2361
                            i v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (148 / 105)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.38 (18 / 13)  


 221 18.37 2.04 0.00  chr2_199522088_199525372     1720  1768 (1517)    L1M4_orf2#LINE/L1        1    50 (858)  

  chr2_199522088_   1720 TGGAGATATGTACCATGTTCCTGGATTGGCAGA-TTCGTATTATTAAGAT 1768
                             i v  i v        v        v   -  vi    i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

Transitions / transversions = 0.80 (4 / 5)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1)  

2536 25.20 4.20 2.92  chr2_199522088_199525372     1937  2793 (492)    L1M4_orf2#LINE/L1       41   908 (0)  

  chr2_199522088_   1937 TTTTTAAAATGTCAATTATCTCAAAATTGATTGATAGATTCAATGCAGAC 1986
                           v    i   v    vv  i v        iv i        i   iv 
  L1M4_orf2#LINE/     41 TTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chr2_199522088_   1987 CAT-TTATAATCCCA-TAGACTTTTTT-TAGAAATT---AAACTGGTTCT 2030
                          v - i v       -iv v       -i       ---  i   i i  
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr2_199522088_   2031 AAAATTTACATG-AAATTCGAAGCACTTAAAATATTTAAAGCAATCTTGA 2079
                               i i   -    v i i v  ii i    vii   i         
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_199522088_   2080 CAAA-AGGAACATAGTTGGAGGATTTACACCACCTGATTCCAAGACCTGC 2128
                         v   - i     v          i i    iv  ii   i   i  i i 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_199522088_   2129 TATTAAAGCTACAGTAATCAAGACAGTGTGGCTCTGCCATAAGGATAGAC 2178
                           i-                           iv   v             
  L1M4_orf2#LINE/    241 TAC-AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_199522088_   2179 AAATAGACAAATGGAACAGAAGAGAGAGCCCAGACATAAATCCA--CAGT 2226
                          v     iv       i    vv     i     v     i   --  v 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_199522088_   2227 TATACAGTTATTTGCTTTTTGACAAAGGCACCAAAGCAGTCCAAATGAGA 2276
                            i--  i v   v    i     i  ii    ii vi i   -  i i
  L1M4_orf2#LINE/    340 TATG--GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGG 386

  chr2_199522088_   2277 AAAAAAAAAATGTATTTTTAGCACATGGTGTTGAAATAACTGGCTACTGA 2326
                            i  v ---  v    i i  v      i  ii i      v  ?iv 
  L1M4_orf2#LINE/    387 AAAGAATA---GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_199522088_   2327 TATGGGGAAAAAAAAAAAAACAACTTCAGGCCCAAACTTATACCATACAT 2376
                         i   v---    i  vi  i----  viiv   v v  i i      i i
  L1M4_orf2#LINE/    434 CATGC---AAAAGAATGAAG----TTGGACCCCTACCTCACACCATATAC 476

  chr2_199522088_   2377 ACAAATACATTTGAGATGGAACACAGATCTAAACATAA-ATCTAAAACAG 2425
                          v    vv i ii i     v  ?   i     ii   - v       vi
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_199522088_   2426 TACAGCTTTTAAAGAAAAATATAAGAGTCGATATTCAGGGCTTGGGGGTA 2475
                           v i  i   i ii    i   i ?  vi  v   iv i i v   v  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_199522088_   2476 GGTGAAGATTTCTTAGG-----CAGCAAAAATCAATAACTATAAGATAAA 2520
                           ii v i        i-----  v     i-  vv i v i  i v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAG-CACAAGCAACAAAAGAAA 625

  chr2_199522088_   2521 TAATTGATAATTTAGACTTTGTCAAAGTTAAAAACTCTCCCACTAGTTAT 2570
                         v   v     v  i     ii     i         i ivii  -- i v
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT--TCAA 673

  chr2_199522088_   2571 AAGACACCATCAACTTTCAATAAAAGT-AGCAGTCAATCCACAGAGCATG 2619
                          i     i     --------i     - iv  v   i       iiiv 
  L1M4_orf2#LINE/    674 AGGACACTATCAA--------GAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_199522088_   2620 AGGAAATATTCGCAAAATATATATCTGACAAAGGAATAGTATCTAGGAAA 2669
                           i       i     vi          i  i   v v     i  i v 
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_199522088_   2670 ACTAAAGAACTACTACAAAACAAAAATAAAGAGATAAACTACCCAGT-AA 2718
                         vv         vi     vv   v      i   i   iv     i -? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_199522088_   2719 TAAATAGCCAAA------------ACATTT-----AAACAGATATACAAA 2751
                         v    i v    ------------      -----  iv           
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_199522088_   2752 TGGCCCATA-GCTCTTGAAAAACTGCTACACATCATTAATAAC 2793
                              v   -  v v      iv    vv      ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (127 / 85)
Gap_init rate = 0.03 (23 / 868), avg. gap size = 2.65 (61 / 23)  


2148 26.03 7.95 2.05  chr2_199542703_199544441      518  1247 (492)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr2_199542703_    518 ATTTTGAAATTCATACGGAACAACAACAACAAAAAAGCCCAAATAGCCAA 567
                           ii i         i    ----- ii-   iii v  vi         
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAA-----ATG-CAAGGGACCCAGAATAGCCAA 179

  chr2_199542703_    568 GGCAATACTAAGCAA-AAGAACAAAGCTGCAGCCATTACACTACCTAACT 616
                         ii    vi i iv  -          i  v  vvv i     v  i  i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_199542703_    617 TCAAACTATATTACAGGGCTACAGTAACCGAAATAGCATGGTACTAGCAT 666
                              viv  i    ii          i i i i  ii       i    
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_199542703_    667 AAGAACGGACACATAGACCAATGGAACAAAATAGAGGGTCCAGAAATAAA 716
                            i ii    i     i        i i   v   i             
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_199542703_    717 GCCACACACCCACAACCATCTGATCTTTGACAAAGCTGACAAAAACAACC 766
                         v   i   iii iiii  vi    i  i     i v  v   i v  vi 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_199542703_    767 ACTGGGGAAAGGATTCCCCATTTAATAAGCAGCGCTGGGATAATTGGCTA 816
                          v         i  vvi iv  i  i  iii i       i  i   v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_199542703_    817 GCCATAAGCAGAAGAATGAAACTGGACTCTTTCCTTGTATCATATATAAA 866
                         ?   i v   i         ii     i i v   iii i      i   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_199542703_    867 AATTAACTCAAGATGAATTTAAGAC------------------------- 891
                                    i   i  iv?    -------------------------
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_199542703_    892 -ATTCCTAG--GCAATCCCA----------TTCTTGACATAGGAATTGGC 928
                         - i  i   -- v  v vi ----------   v    v v  iv v   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_199542703_    929 AAAGATTT------TATGACAAAGATGCCAAAAGCAATTGCAACAAAAAC 972
                           v i   ------       ------         vvv         iv
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAACAAAAGA 623

  chr2_199542703_    973 AAAAATTGACAAATATGATCTAATTAAACTAAATAGCCTCTGCACAGCAA 1022
                               v  i    vv  ii v  i   v v  v i i i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_199542703_   1023 AAGAAACCATCAGTAAAGTAGACAGACAACCTACAGAATGGGAGAAAATG 1072
                          i  v  i    iv     ii v        i                 i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_199542703_   1073 TTTGCAACCTATACATCTGACAAAGTCCTAATATCTAGCATCTATATAAA 1122
                                vii   i      i  i vv  vi    i  v  --       
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT--ATATAAA 771

  chr2_199542703_   1123 CAAAT-TTAC----CAG-------AAAACAACCA-CCCACATTAAAACGT 1159
                         v  v -    ----  i-------  i    vi -    -   ?   vi 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA-ATTWAAAAAT 820

  chr2_199542703_   1160 GGGCAAAGGATATGAACAAACGATTTTCAAAAGAAGACATATATGCGGCC 1209
                                    v    i i  iv  i  v        i   i vii    
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_199542703_   1210 AATAAGCAAATGAGGAAAAGCTCAACATCACTGATCAT 1247
                                 v    ii i v           ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (121 / 66)
Gap_init rate = 0.02 (14 / 773), avg. gap size = 5.21 (73 / 14)  


2121 26.57 3.43 0.90  chr2_199544822_199546473      499  1168 (484)    L1M4_orf2#LINE/L1      222   908 (0)  

  chr2_199544822_    499 TTCTGACTTCAAACTATACTATAAGGCTACAGTAACCAA-ACAGCATGGT 547
                          i ii i      viv     i  i          i   -    ii    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_199544822_    548 ACTAGTACAAAAACAGACACATAGACCAATGGAACAGAATAAAGAACTCA 597
                            i i i  ii i     i     i        i     vi   iii  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_199544822_    598 GAAATAAAACCAAGCATTTACAGCCATCTGATCTTTGACAAAGTCAACAA 647
                                 v   vi      ii i  vi    i  i     i viiv   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_199544822_    648 AAGCA----ATGGGGAAAGGACTTCCTATTCAATAAAAGGTGCTGAGATA 693
                         i v  ----          i ivvi  v     i   v       i  i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_199544822_    694 CCTGGCTAGCAATATGTAGAAAAATGAAACTGGACTTCTACCTTGAGTTG 743
                         v    v  ? v i   i i  i      ii     ii      iiviiii
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_199544822_    744 -ATACAAAAATCAACTCAAGATGAATTAAAGATTTAAATGTAAAACCTCA 792
                         -          i       i   i  i ?   ii         i v  - 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-A 520

  chr2_199544822_    793 AAAC-ATAAGAATTATAGAAGAAAACCTAGG---AAATACCATTCTGGAC 838
                             -    i v iv           v    ---    -- -   vv   
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGAC 567

  chr2_199544822_    839 TTTGGCTTTGGTAAAGAATTTATGACTAAGTCCTCAAAAGCAATTGCAAC 888
                         i    v  v  i  v iv  iv iiv  v v vi        vvv     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_199544822_    889 AAAA----AAATTGACAAGTGGGACCTAATTAAACTGAAGAGCTTCTGCA 934
                             ----    v  i  i v    i v  i   v v  i i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_199544822_    935 CAGCAAAAGAGACTATCAACAGAGTAAACAGACAACCTACAGAATGGGAG 984
                          vv    i  v        v i   i  v        i            
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_199544822_    985 AAAATGTTCACAAACTATGCATTTGACAAAGATCTAATATCCAGTATCTA 1034
                              i  ii    ii  ii  i   i  i iv  vi       v  v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_199544822_   1035 TAAGGGACT--TAACCAATTGAACAAACAAATAACAATTAACCCCATT-A 1081
                            i i   --  --   i v  i  vv   vi    v      v   - 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTA--CAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_199544822_   1082 AAAATGAGTAAAAGACATGAA----CACTTAACAAAAGAAGACATACAAG 1127
                               i i   i  iv    ----  i  vv v        i      i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_199544822_   1128 CAGCTAACAA--ACATGAGAAAATGCTGTATAGCACTAATGAT 1168
                         ii  i  i  --      i  i     vv i v  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (114 / 62)
Gap_init rate = 0.02 (14 / 687), avg. gap size = 2.07 (29 / 14)  


3988 19.22 2.33 1.78  chr2_199615674_199617586      524  1423 (490)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_199615674_    524 AAAG-TATCCCATGCTCATTAATCAGAAGAC---ATACGATTTGGATAGC 569
                             -         i    vi  ii      ---   ivi  vi   i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_199615674_    570 AATATCCCCCAAACCGATCTACAGATTTAATGTAATACTCATTAGA--TC 617
                             ii       ii            i  i i   v ii  i i --i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_199615674_    618 TAGCTGATTTCTTTGTAGAAACTGACAAGCTAATTCTAAAATTGATATGG 667
                         i     vi  i    i     i         i  i        v      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_199615674_    668 AAATTGTAAGGGACCAAGAAGAGCCAAAACATTCTTGAAAAA--AGAACA 715
                             - i        v    v          v          --      
  L1M4_orf2#LINE/    154 AAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_199615674_    716 AAATATGAAAAACTCATACTTCTCAATTACAAAACTTAATTGCAAAGCAA 765
                           i -  i ii     i     i     v         -i i      v 
  L1M4_orf2#LINE/    203 AAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAAAGCTA 250

  chr2_199615674_    766 TGGTAATCAAGACAATGTGACATTAGAATAACCATAGATATATAAATCAA 815
                         ii            i    ii i i v    vv     i     i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_199615674_    816 TGGAATAGAATTGAAAGTCCAGAAATAAATCCCATGCCTATATGGTCAAC 865
                                       i              -     i v v         i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTCAAT 349

  chr2_199615674_    866 TCATTTTTGACAAGACTACCAAAACCATTCAATGAGAGAGTAATAGTTTT 915
                          v     i      iv i    i           i ii iv      i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_199615674_    916 TTCAACAAGTAGCATTGGAATAACTGAATA-CCACAAGTGAAATAATAAA 964
                                 i i iii   i i     i   -     v ii   v   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_199615674_    965 GTTTTACTCTTACTTCATACTATTT-CAAAAGCTAACTCAAAATGGATCA 1013
                            vv  i i   i   i  i  v -     ii                 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_199615674_   1014 AATAATTAAATGTTAAGACCTGAAACTACAGAAACCTTAGAAGAAAACAT 1063
                         ? v vi       -    v  i      i i  vi               
  L1M4_orf2#LINE/    500 WAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_199615674_   1064 AGGGATAAATCTTCAT-ACCTCACGTTTGGCCATAGTTTCTTCTGTCTGA 1112
                            ?i         i -    iiv   v   v  i       vvi v   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_199615674_   1113 CAACAAAAGCACAGGTAGCAAAAGAAAATATAGACAAATTGAGCTTCACC 1162
                           v          i i i          v     i      ii     i 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_199615674_   1163 AAAATTAAAAACTTTTGTGCATAAAGGAATGCTATCAAAAAAGTGAAAAA 1212
                                             v v  i i ii       i          -
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA- 697

  chr2_199615674_   1213 GACAATCTACACAATTCAAGAACATATCTGAAAACCATATATCCAATAAG 1262
                              i i   v   vvi    v    i  v   i        ii     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_199615674_   1263 AGTCTATTACCTAGAATATATAAATAACTCTTACAACTCAACAATAAAAA 1312
                         i v  vv  i i            v                i        
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_199615674_   1313 GACAAA---CCCAATTTAAAA-TGGACACAGGACTT----AGAGATTTC- 1353
                               ---       ?    -   i  v    i  ----   v     -
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_199615674_   1354 -AGAAGAAGAAACACAAATGGCCAACACACACACACATACACACACAAAG 1402
                         -vi       v i            i vi    ii--------- -    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATG---------A-AAAG 887

  chr2_199615674_   1403 ATGCTCAACATAATTTATCAT 1423
                                    v ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (117 / 53)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 1.95 (37 / 19)  


2054 24.85 3.22 3.36  chr2_199628123_199630200      501  1184 (894)    L1M4_orf2#LINE/L1       97   779 (129)  

  chr2_199628123_    501 AAAATTCCAGAAGGCTTTTATTTTTGGTTGAAATTGGCAAGCTGATTTTA 550
                              i    ----  vii-     v iv       i         ii  
  L1M4_orf2#LINE/     97 AAAATCCCAG----CTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr2_199628123_    551 AAATTTATAAGGGAATGTGAAA-ACATAGAGC-GCACAAAACAATTTTGC 598
                              i   v  i    ii ii-  vi   ii-  -         i   v
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGC-CAAAACAATCTTGA 190

  chr2_199628123_    599 AAAAGAT---CAAAGTTATAGGACTCATATTACCTGATTTCAAGATCT-- 643
                               v---       iv        i i v  ii       i ii --
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_199628123_    644 TATAAATCTGTA-TAATCAGGACA---TGGT---GGCATAAGGATAGACA 686
                           i   v  ii -      i    ---    ---                
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_199628123_    687 TATAGATTAACATAACAGAAT--AGAATCCAGAAATAAAGCCACACATAT 734
                                i  iiv  i     --   i            v   i    v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_199628123_    735 ATTTGCAATTGATTTTTGACAAAGG-GCTTAGGTAAGTCAGTGGGAAAAT 783
                           vvv           i     i  -  iv  iiv v   i    i   v
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_199628123_    784 AATAGTCTTTTCTAAAATTGTTTCTGGAATAATTGGATATTCATATGGAA 833
                                     v v  v  v v    i i  i      ?i  i   v  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_199628123_    834 AA--ATAATATTTTCAAATCCTTACCTCACATCATATGCAAATGTTATTT 881
                           --  i vi  ---ii i  i         i     i    vi   vi 
  L1M4_orf2#LINE/    441 AAGAATGAAGTT---GGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_199628123_    882 CAAAATATATTATATATATTATATGCATAAAAATAAAAGCTGAAACGTTA 931
                               iv  i ? v --------- v    vi   i    i    vv  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGA---------CCTAAATGTAAGAGCTAAAACTATA 528

  chr2_199628123_    932 AAACTTATAAAAAGAAACATAACAA-AAATCTTTGTAACATCAAAGTAGG 980
                              iv  i  ii       iv?i-       i  i  v iiiiv    
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_199628123_    981 TAAAATTTTCTCAAATAGGACATTAAAAATGTA--CCGTAAAGGAAAAGA 1028
                         i  viv     i i   v    ii    iiii -- vii   i     i 
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_199628123_   1029 AAGATAAATTGGAATTTACCATAATTAAAGATGTGTGCTCTGCAAATGAC 1078
                         v            v  i i  v       i iv v  iv  v    v   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_199628123_   1079 ACAATTATAAAGAAAATTAAAACACATGTCACAGGCTAGCAGAAAAAAAT 1128
                           ---   v      i v    v   vvi     iv i v      v v 
  L1M4_orf2#LINE/    679 AC---TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_199628123_   1129 TATAAAACATATATATATGAAAAAGCACTTGTATCCAGACTAGATAGAGA 1178
                          ii   v       v --  v  i v             v  v   i   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCT--GATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_199628123_   1179 ACTCTT 1184
                               
  L1M4_orf2#LINE/    774 ACTCTT 779

Transitions / transversions = 1.53 (101 / 66)
Gap_init rate = 0.03 (19 / 683), avg. gap size = 2.37 (45 / 19)  

 405 20.29 6.52 1.45  chr2_199628123_199630200     1449  1586 (492)    L1M4_orf2#LINE/L1      764   908 (0)  

  chr2_199628123_   1449 TACATAAAAAATTCTTTTAACATTCATTTATAAGAA---AAATGATCTAA 1495
                           i     i  i    vi   --   v v    i  ---    i i i  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAAC--TCAATAATAAAAAGACAAATAACCCAA 811

  chr2_199628123_   1496 T--AAAAATGGGCAAAAAATT-AAATA--TATTT-TACAAAAAAGATGTA 1539
                          --             ii   -i    --i    - v    i     i  
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_199628123_   1540 TGAATTGCCAGTAAGCACTCAAAAAGACTCTCAACATTAATAGCTGA 1586
                         ii   v    i       vii      iv        i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (21 / 7)
Gap_init rate = 0.04 (6 / 145), avg. gap size = 1.83 (11 / 6)  


2907 20.43 5.47 0.43  chr2_199641598_199643284.rev      501  1195 (492)    L1M4_orf2#LINE/L1      179   908 (0)  

  chr2_199641598_    501 AAACATTATTTAAAAAGAGAAACAAATTTGGAGGTCTCATACTTCCTGAT 550
                              v v  v       ii      v       v    i      ii  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr2_199641598_    551 TTTAAAACTAACTTAGAAAGCTACAGTAGTAAAAACAATGTGGTACTGGC 600
                           i      v   - v            i v  i   i            
  L1M4_orf2#LINE/    229 TTCAAAACTTACT-ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_199641598_    601 ATGAAGACAGGTAGTTAGACCAGTAGAATAGAATAGACAGCCCAGAAGCA 650
                           i i  i  ii vv    i  i i         v  v  i      ii 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_199641598_    651 AACACTCTCATAAAAGGTCAAATAAGTTTTGAGAAGGGTGCCAAGACCAT 700
                            v viv   vv v      v i v   i  v                 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_199641598_    701 TCAGTGAGAGAAGGACAGCCTTTTCAAAACATAATGCTGGGAAACCTCGG 750
                            i  i ii   i i  i        v v  ii        v v  v i
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_199641598_    751 TATCCACATGCAGAA-AATTAAGTTA------TACTTTACATTATACACA 793
                           ?         i  -   v     i------   i i   ii   i   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_199641598_    794 AATATTAACTTAAAATGGATTAAAGACCTAAATGTAAGACCTAAAACTAT 843
                           v       i         i ?                v          
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_199641598_    844 AACACTCCTAGGAGAAACCATAAGAGAAGAGATTTATGACACTGAATTTG 893
                           v    i   i     v    i ? v i vv  ii    vi  ii  v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_199641598_    894 GCAATGATTTCTTAG-----------------CAAGGAA--AGAAAAAAA 924
                               i        -----------------    v  -- i i     
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_199641598_    925 ATAGATAAATTAAACT--A-CAAAATGTAAAACTTCTGTACTTCAAATGA 971
                                    ii   -- -      vv       i   i       v  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_199641598_    972 CACAATCAATGGAGTGAAAAGCCAACCTATGAAATGAGAAAAAATATTTG 1021
                            v     vii         v     i iii    i  i          
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_199641598_   1022 CAACTCATTTGTCTGTT--GGGAGTTA-ATCTACAGAATAT-TAAATAAC 1067
                            v    v i    v --    v  i-   --        -    v   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATC--CAGAATATATAAAGAAC 775

  chr2_199641598_   1068 TTCTACAACTCATCAATAATAAAA-----AACCTGATCAAAAAACATGCA 1112
                          ii         vi     v  i -----    ii  i?     iiv   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_199641598_   1113 AAGAAATTGAATAGGTATTTCTCCAAAGATGATATACAAATGACCAACAA 1162
                            i v        ii             v            i    i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_199641598_   1163 ATATATGAAAAGATGCTCAACATCATTAATTAT 1195
                         ii i                     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (85 / 53)
Gap_init rate = 0.02 (12 / 730), avg. gap size = 3.42 (41 / 12)  


2715 27.55 1.01 0.25  chr2_199716925_199724579      493  1287 (6368)  C L1M4_orf2#LINE/L1   (0)   908   108  

C chr2_199716925_   1287 TGTCTTTATAGCAGCA--TGA---ACT-ACTTTAAAGTTCATATGGAATC 1244
                           i    v v    v --   ---i  - iii    i           vi
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

C chr2_199716925_   1243 AAAAAAGAGCCCGCGTTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGTT 1194
                         iv  ii  v  v vi v     iv     i i ivv i            
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

C chr2_199716925_   1193 GGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAAC 1144
                              vv    i  v  ii i      viv        i          i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

C chr2_199716925_   1143 CAAAACAGCATGGTACTGGTACCAAAACAGAAATACAAATGAATGGAACA 1094
                            i    ii         i iv ii i   v   i i  v       i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

C chr2_199716925_   1093 GAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACTATCTGATCT 1046
                            i--    i  --        vv   i i  i  iiiii vi    i 
  L1M4_orf2#LINE/    308 GAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTT 355

C chr2_199716925_   1045 TTGACAAACCTGAGAAAAATAAGCAATGGGGAAAGGATTCCCTATTTAAT 996
                          i     ivv  vv  i vi vv            i  vvi  v  i  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

C chr2_199716925_    995 AAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGATGAAACTGGA 946
                                       v      v  ?   i   i i  ii     ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

C chr2_199716925_    945 TCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACT 896
                         i    v   i     v              i    i      i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

C chr2_199716925_    895 TAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATA 846
                             ii v   v       i      vi i           v    ?i  
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

C chr2_199716925_    845 ACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCGAA 796
                          viv   iv   v v  vv i     v ii   v ivv  vi     i  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

C chr2_199716925_    795 AGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAA 746
                             vvi          vv     v  i    v   ii v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

C chr2_199716925_    745 AGAGCTTCTGCATAGCAAAAGAAAGTACCATCAGAGTGAACAGGCAACCT 696
                          i i   i  iiivv    i  v v  i  vv i      v  i     i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

C chr2_199716925_    695 ACAAAATGGGAGAAAATTTTCTCAACCTACTCATGTGACAAAGGGCTAAT 646
                            i             v  iv   vii ivi  v   i  i  i  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

C chr2_199716925_    645 ATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACA 596
                                  v  i  v      vv    v iv i  v     i     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

C chr2_199716925_    595 ACCCCATCAAAAAGTGGGCAAAGGACATGAGCAGACACTCCTCAAAAGAA 546
                             v  i?    i           iv   ii     i i   v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

C chr2_199716925_    545 GACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGC 496
                           i  vi viii     v  i          i       v     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

C chr2_199716925_    495 CGT 493
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.42 (126 / 89)
Gap_init rate = 0.01 (5 / 801), avg. gap size = 2.00 (10 / 5)  

3021 26.07 1.53 2.08  chr2_199716925_199724579     6251  7163 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_199716925_   6251 TGGAAGAATATTCCATACTCATGGATAGGAAGAATCAATAGCATGAAAAT 6300
                              ii    i    ii        v      v i    vii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_199716925_   6301 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCCATCCGCCCCCACA 6350
                            v     v      v i  i           i  v    - ivi  - 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC-CTATCA-A 98

  chr2_199716925_   6351 AATCAAGTTACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACATT 6398
                             ------ i iivi i  i  ii     -   -- v  i  - ivi 
  L1M4_orf2#LINE/     99 AATC------CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCT 140

  chr2_199716925_   6399 AAAGTTCATGTGGAACCAAAAAAGAGCCTGTATTGCCAAGACAGTCCTAT 6448
                            i     i     viiv  ii  v  v v  v     i   i  i iv
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_199716925_   6449 GCAAAAAGAACAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTATAC 6498
                         iv  i          i i    vv   ii  v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_199716925_   6499 TACAAGGCTACAGTAACCAAAACAGCATGACACTGGTACCAAAACAGATA 6548
                              i          i   i    ii  ii     i iv ii i   i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_199716925_   6549 TATAGACCAATGGAATAGGTCAGAGGCTCAGAGGCCTCAGAAATAACACC 6598
                               i           i------ii v    v  --        vv  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGA------ATTGAGAGTCC--AGAAATAAACCC 332

  chr2_199716925_   6599 ACACATCTACAACCATCTGATCTTTGACAAACTTGACAAAAACAAGAAAT 6648
                          i    i  iiii  vi    i  i     ivv  v   i v  vvv   
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_199716925_   6649 GGGGAAAGTATTCCCTATTTAACAAATGGTGCTCGGAAAACTGGCTAGCC 6698
                                 v  vvi  v  i             v   v      v  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_199716925_   6699 ATATGTAGAAAGTTGAAACTGGATCCCTTCCTTACACCTTATACAAAAAT 6748
                          i   i i  iiv    ii    i    v   i     v           
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_199716925_   6749 TAATTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAATCATAAAAA 6798
                            i    i      i ?    i       v   v      ii      v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_199716925_   6799 CCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAA 6847
                         i i           v    ?i- v i -   iv   v v  vv i     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA 581

  chr2_199716925_   6848 AGTTTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTG 6897
                         v v    v iiv  vi            vvi          vv     v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_199716925_   6898 ACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACT 6947
                          i    v   ii v  i   v v  i i   i  iiivv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_199716925_   6948 ACCATCAGAGTGAACAGGCAACCTACAGAATGGG-GAAAATTTTTGCAAT 6996
                          i  vv i      v  i     i          -      v       v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_199716925_   6997 CTACCCATCTGACAAAGGTCT---A---AGAATCTACAAAGAACTCAAAC 7040
                         ii ivi      i  i  v  --- ---     v  i         vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_199716925_   7041 AAATTTACAAGAAAAAAACAA----CCCCATCAAAAAGTAGGCATAGGAT 7086
                           v iv i  v     i    ----   v  i?    i i    v     
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_199716925_   7087 TTGAACAGACACTTCTCAAAAGAAGACATCTATGCAGCCAACAGATACAT 7136
                              i     i     v        i  vi viii     i iii    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_199716925_   7137 GAAAAAATGCTCATCATCACTGGTCAT 7163
                              i       v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.36 (33 / 14)  


 955 29.39 6.87 5.60  chr2_199733632_199735409.rev      501  1286 (492)    L1M4_orf2#LINE/L1      113   908 (0)  

  chr2_199733632_    501 TTTTTATGAAACTTGACAAACTAATGCTAAAATTCACATGCAAGAGGAAA 550
                              iiii  v       i  i  v          i   v  iv v  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_199733632_    551 GGACCAGGAATA-CTGGCAC--TTCTGAAGATGAAG--------TGG--- 586
                              vi     - iiiv  -- ii    i v    --------   ---
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_199733632_    587 -TTTCCCCTACCCAATATGAAAAATTACTACAAA---ATGGTAATTTTAA 632
                         -i iv v  v      v v    v          --- ii     ivvi 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_199733632_    633 CAATTTGATATTGGCACAAGAAT---CAAATCAGCCAACAGAATAGTGTA 679
                           i v  i  i     i   i  ---  v  viii   ii      vi v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_199733632_    680 GGGAGTACAGAAACAGAGCCATGTATTGATGGATATCTGAT---AGACTG 726
                          i    v      i i v    ii   v    vi vi    ---v   --
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC-- 360

  chr2_199733632_    727 AAGAGCTTGTATTGAAGG----TCACTGGGGAAAGGATAGTCTGATCAAT 772
                            i --  iv---   i----   v         i       vv    i
  L1M4_orf2#LINE/    361 AAGGG--TGCC---AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_199733632_    773 GCATGGTGTTGAAACAAAAGGTTATTT-TATG-GTTAGAA-AAAG--GGA 817
                         iv      i  ii    vv  v  ?ii-i   -ivv    -i   --   
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_199733632_    818 TCCTTGAATCAAACCATATCAAAATAAATGAATGAGTAAATTTGAGGTGG 867
                         i  i ivv   v       ---- i   ------ i v  i ii ii   
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATAT----ACAAA------AATTAACTCAAAATGG 495

  chr2_199733632_    868 ATCAAGAGTTTACATGTCAAAAGC-AAAACTTTAGAATGCATTCCAGAAA 916
                             ?iiiii  v    -  i   -      v  i  iv -  vv ii  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTC-TTAGAAGAA 543

  chr2_199733632_    917 AATATATGAG-AACTATTTCAATGAGCTGAGGCTATGGAA-GA------A 958
                           i   v ? -  --  i ivi   v  vi  i  v v  - i------ 
  L1M4_orf2#LINE/    544 AACATAGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_199733632_    959 GAGGAGAGA--AGAAG-ACAAAGAAATGGAAGAGAAAGGAGAGGAGGAAG 1005
                           viv  v -- i   -    - v  iii    i   iv   vi --- v
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAA---AT 637

  chr2_199733632_   1006 AGGAAGAAGGGTAAACCTTAA--AAAATGTATATAAAACTTCTCCTTATC 1053
                         v   ------------   v --     ---  -       i viviv  
  L1M4_orf2#LINE/    638 TGGA------------CTTCATCAAAAT---TA-AAAACTTTTGTGCTTC 671

  chr2_199733632_   1054 AA--GACAATATAAAGAAAGGGAAATGACACGCCAAAAATTGGGAAAAGA 1101
                           --    v   v       v    v    vv   v i v     i  i 
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr2_199733632_   1102 TATTTACAATACATGCAACCTACAAATGACTGGTGTTTGGTAATATTATA 1151
                              i   vv   ii v iv i  iv    v  i iii -     -   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG-AATAT-ATA 769

  chr2_199733632_   1152 TGAGACTCCTGTGAATCATTAACATCAAAGCAAACAATGTAAC--AAAAA 1199
                         viii    i iii v   v   i vv  ii    i  ivi  i--     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_199733632_   1200 TGGGCAAA--ATCATGAGCAAGTAATTCACAAAAGAATAAGCCTGAATGG 1247
                                 --  i-   ii iii v   v v      v viivii     
  L1M4_orf2#LINE/    820 TGGGCAAAGGATT-TGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_199733632_   1248 C-AACAAACATGTGGAAAGGAGCTGAACTTCATGGTAAGA 1286
                          -  i  i  ii  i    iv   v   v   ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.05 (39 / 796), avg. gap size = 2.51 (98 / 39)  


3371 24.30 1.78 0.56  chr2_199752178_199754593     1028  1924 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_199752178_   1028 TGGAAAAATATTCCATGTTCATGAATTGTAAGAATAAATATTGTTAAAAT 1077
                               i    i           i    v    v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_199752178_   1078 GTGCA-TACTACCCAAAGCAATCTACAGATTCAATGAAATCCCTTTCAAA 1126
                          -   -    v      vii              i v       v     
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_199752178_   1127 ATACCAAGAACATTCTTCACAGAAGTAGAAAAAACAATCCTAAAATGTAT 1176
                           v   ivvi v  i  ii     i v  v  ivii          vi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_199752178_   1177 ATGGAACCACAAAACACCCAGAATAACCAAAGCTATCCTAAGCAAAAAGA 1226
                               vii   iiv          i     i v   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_199752178_   1227 ACAAAACTGGAGAAATCATATTACCTGACTTCAAATTATACTTCAGAGCT 1276
                              ii     i v   i i v  ii i      viv    v  i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_199752178_   1277 ATAGTAATCAAAACAGCATGGTACTGACATAAAAATAGACACATAGACAA 1326
                          i         i    ii        i     ii       i     iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_199752178_   1327 ATGGAACAGAATAGAGAACCTAGAAACAAATGCAC-CACCCACGGTGAAC 1375
                               i     v    ii i     i   iv  i-  iii i   v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_199752178_   1376 TCATTTTTGACAAAGATGCCAAGACCATACACTGGGGAAAAGACAGTCTC 1425
                          v     i     i i            v  v        ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_199752178_   1426 TTTAATAAATGGTAGTAGGAAAACTGGATATCC-CACGAGGAAGAATGAA 1474
                           i  i       iv i   v         ?  -  i vii         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_199752178_   1475 ACTAGCCCCCCATCTCTCACTATATACAAAAATCAAATCAAAATGGATGA 1524
                         ii i v    i i   v   i            i  v           v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_199752178_   1525 AAGACTTAAATCTAAAACCTAAA-CTATGAAACTACTGCAAGAAATCATT 1573
                         ?    i     v   i v     -    i     vi iv      v   v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_199752178_   1574 GGGGAAAATCTCCAGGACAGTGGTTTGGGCAAAGATTTATTGAGTAATAC 1623
                           ? v      i iv   vv   v  i     v i   v  iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_199752178_   1624 -CCAACAAACACAGGCAATCAAAATAAAAATGGACAAATGGGATCACATC 1672
                         -    -  i    i    iv   iv      i  i    v   iiv    
  L1M4_orf2#LINE/    600 ACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_199752178_   1673 AGG-TTAAAAAGCTTCTGCACAGCAGAGAGTACAATTAATGAAG-AATGA 1720
                          ii-       -   i  ii vv  i  iii  v  i  vi   -i vi 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_199752178_   1721 GACAAACCCACAGCATGAGAAAAGATATTTGCAAACTAT-----TAATA- 1764
                              -       v   i  i  i           ii  ----- i   -
  L1M4_orf2#LINE/    698 GACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_199752178_   1765 GGGATT---AACCAGAATATATAAGGAGCTCAAGCAATTCTATAGGAAAA 1811
                             i --- v             i  i   vvi   i  v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_199752178_   1812 GAATCTAAAAATCCGATCAAAAACTAGGCAAAACATTTGAATAGACATTT 1861
                         ii - v  v  i  i  i?    v i      iv                
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_199752178_   1862 CTGAAAAGAAGACATACAAATGGCAAACAGGCATATGAGACATTGCTCAA 1911
                           vv        i           v  i i   i    i viv       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_199752178_   1912 CATCATTGACCAT 1924
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (137 / 77)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.40 (21 / 15)  


 241 19.51 0.00 0.00  chr2_199767449_199770498        7    47 (3003)  C L1M4_orf2#LINE/L1   (630)   278   238  

C chr2_199767449_     47 TACTACAAGTCTACAGTAACCAAAACGGCATGGTACTGGTA 7
                                 iv         i   i  i ii         i 
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

Transitions / transversions = 7.00 (7 / 1)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  

1860 26.98 10.63 0.41  chr2_199767449_199770498     1560  2293 (757)    L1M4_orf2#LINE/L1        2   810 (98)  

  chr2_199767449_   1560 GGAAAAAT----CATTTTTCTGGATTAGAAGTCTCAACATAATAAAGATT 1605
                              i  ----   v  iv      i    v  i  i  vi v     v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_199767449_   1606 TCAATTCTCCACAAATTGATGTATAGGTTTAATGCAATGCCTATATAAAT 1655
                         v    v    v         v  i  i  i  i     v     vv    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_199767449_   1656 CTCAG-TAAGGTTTTTGCAAACATAGATAAGCTTATTCCAAAATTTATAT 1704
                          i   - ivvv        i v  v  i     v  i i      i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_199767449_   1705 GGTAAGTG-AAAGGCCCTAGAACAGTAAAAATGATTTTGAAAAA-ATGAA 1752
                           -  i  -  i  v  i    i  iv    ii  i        - v   
  L1M4_orf2#LINE/    152 GG-AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_199767449_   1753 CAAAAAAGCAGGAATTCTTCTTTCCAATGTTAAGACATACTATATAGCTT 1802
                             ivv v    v iviv   i     v i  i  v     i v    v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_199767449_   1803 CAGTAATCAAGACAGAGTAG---------AGTGATAAACACATTTATCAA 1843
                                        v  i --------- iv    i   i  vv     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_199767449_   1844 TGAAACAAAATGGGAAGCCTAGAAATAGATCCACACAAATGTGTCCAGCT 1893
                           i  i i   v ii  i i       i i   i   vv i  vi  ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_199767449_   1894 AATTTCTAGCAAAGG----------------------------------- 1908
                         i    iiii   i  -----------------------------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_199767449_   1909 --AACAAA---------AACAACTGT-TAAACATACATAAAAAATATGAA 1946
                         --      ---------i       v-  ?v  i iii    i -     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-ATGAA 449

  chr2_199767449_   1947 CTTCAAACTAAACCTCCCACCTTATTAAAAAATTAACTCAC--TGAATAA 1994
                         v  vi v ivv     v    v   vv             v--  i  v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_199767449_   1995 TGAATGTAA-TTTAAAACTTAAAACTATAAAATGTCTT----TAAAA-AT 2038
                         ?ii iv   - v   i vi             i-    ----v    -  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACAT 548

  chr2_199767449_   2039 AGGAGAAAGTATTCAGGACCTACAACAACAGAAAGAGTTCTTAGACTTGA 2088
                            ? v  i v   iv     vviiiv viv  v iv        iv   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_199767449_   2089 CACCAAAAGCATAACCCAAAAGAGGAGGACTTGATGAATTGGACCTCATC 2138
                                    i  v v v  i  i ii v v   i        i     
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_199767449_   2139 AAAATTAAAAACCTTT-TGCTCTGTGAGATTCTGTAAGGAAGGTGAA--G 2185
                                     i   -    iiivii  iv  i v i   i     -- 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_199767449_   2186 AAAAT--ATAGACTGGAAAAAAA-ATTTGCAAATCACATATCTGACAAAT 2232
                          v  i-- i   v   i i    -            i        i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_199767449_   2233 AATTAGAATCTAGAATATATAAAGAACTCTCAAAATTCAACATTAAAAA- 2281
                         i i v v   i                   i v  i    i v      -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_199767449_   2282 ACAAACAGGCCA 2293
                              i iv   
  L1M4_orf2#LINE/    799 ACAAATAACCCA 810

Transitions / transversions = 1.32 (111 / 84)
Gap_init rate = 0.02 (20 / 809), avg. gap size = 4.05 (81 / 20)  

 326 19.05 9.52 3.17  chr2_199767449_199770498     2433  2558 (492)    L1M4_orf2#LINE/L1      775   908 (0)  

  chr2_199767449_   2433 CTCTTAAAA---AATAATAATTTTAAA-------AATCCAACTAGAAAAT 2472
                               v  ---        ----   -------  i    i ?i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAA----AAAGACAAATAACCCAATTWAAAAAT 820

  chr2_199767449_   2473 AGGTAAAAGAATTACA-AGACATTTCACTAAAGAGAATATACAGACAGCA 2521
                         i  i   i  v  iv -         v i     ii       i ii  v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_199767449_   2522 AATAAGGAAAT-AAAAGATGCCTAACATTATTAGTCAT 2558
                               v v  -         ii     i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.04 (5 / 134), avg. gap size = 3.20 (16 / 5)  


2690 25.63 3.30 3.52  chr2_199923693_199927899.rev     2807  3715 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_199923693_   2807 GGAGAGCTGTTTCCTGTTTATGCACAGGAAGACACAATATTGTTAAGATG 2856
                            i  v i ii v    i   v iv       vi               
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_199923693_   2857 TCAACTCTTCCCAACTAGATTTATAGATTCAGTGTAATCCAAAT-AAAAT 2905
                         v   iv  i     v v   i  i       ii i     vv  -     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_199923693_   2906 TCCA-TTGT-TATTTCGCAGAAACTGAAACACTGATTTTAAAGTTTATGT 2953
                         i   -i  i- v   i       i   v vi     ii    i  i  i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_199923693_   2954 GGAAG-ACAGAAGATCCATTATAGCCAATACAATATTGAAAGAGAAAAAT 3002
                             i-i  iii  i   vv        v     v      i    i  i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_199923693_   3003 AA-TCTGGAAGACTGACACTACTTAACTTCAATACTTATTATAAACCTAC 3051
                           -vi    i    v     v ii  i     v     i  i   v    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_199923693_   3052 AGCAATCAAGATGGTATGATAATGGCAAAAGAATAGACAAATAGATCAAC 3101
                           i        ii  i  i  v     v   i       v         i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_199923693_   3102 GGAACAGGATAGAAAAGCTTATAATTTGACCCGCACAAATATAGTTAACT 3151
                             i  i  v  i - iii v  v vi    ii   vv   i  i  i 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGA-GTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_199923693_   3152 GATATTTCACAAAGGAGCAAAGTCAAGTCAATGG---AAAAATAGTGTTT 3198
                            v  iv    i  v  v   v v v       ---  i      v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_199923693_   3199 TCAATT--TGATACAGGAACAATTGGACATC-ACATGCAAACAAACAAAC 3245
                             iv--  i i v  i    i    i ? -         vi  ii  -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA- 449

  chr2_199923693_   3246 AAAAAACAATCTAGACAGAGGGCTTTTACCTTCCAC--------AAAATC 3287
                         --------i i--------  i iii     iv   --------     i
  L1M4_orf2#LINE/    450 --------GTT--------GGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_199923693_   3288 AACTCAAA-TGTATAATAGGCCTAAGTATAAAACACAAAACTATAAAACC 3336
                                 -  v  v ?  i     i i   i vvi             i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_199923693_   3337 AACATATAACATATAACTGAAGATACCATAGGAAAATATCTAGGTAATCT 3386
                         --------- v  -----     v v      ?iv v    vv  i i  
  L1M4_orf2#LINE/    534 ---------CTTA-----GAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_199923693_   3387 TGGTTTTGATGATGAGTTTTTAGATGTAACACCAAAAGTATGATTCATGG 3436
                            v  v iii   iv  i      i i          i ii viv iii
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_199923693_   3437 AAGAAAAAATTGATAAGTTGGACTTTATTTAAATTAAAAGCTTGTGCTCT 3486
                                   v     i        i  iv         i   v  iv  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_199923693_   3487 GCTAAAGACACTGTTAAGAGAATAAAGCAACAAGTCATAGACTGGGAGAA 3536
                         v v  i      i i    i i i  ivi    vi  i   v        
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_199923693_   3537 AGTATCTTAAAATCAAATATA-AATAAAG-ACTTTTA-CCAAAATATTAA 3583
                          i   i vv      v    v-i    i -    v  -   i     vv 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_199923693_   3584 AATAACTCTTAAAACTCA-CAATAAGAA----AAGAACCCAACTGGAAAC 3628
                           v        v      -i     i  ----  v       i ?i   v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_199923693_   3629 TAGATAAAAGAGCTGAACAGATACATCATCAAAGAAGATACACAGATGGA 3678
                          i ii   i  vi    i   i iv  vi           i   i    v
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_199923693_   3679 AAGTAA-CATATAAGAA-ATGCACCACATCATATGTGAC 3715
                         v i   -  i  i i  -    v v      ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (142 / 87)
Gap_init rate = 0.02 (22 / 907), avg. gap size = 2.82 (62 / 22)  


3129 26.36 1.89 0.89  chr2_199930087_199935775.rev     4299  5197 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_199930087_   4299 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCATGAAAAT 4348
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_199930087_   4349 GGCCATACTGCCCAAGATAATTTATAGATTTAATGCCACCCCCAACAAGC 4398
                            v     v     iv i  i  i     i  i  v i   i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_199930087_   4399 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4446
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_199930087_   4447 TATGGAACCAAAAAAGAGCCCACGTTGCGAAGACAAACCTAAGCCAAAAG 4496
                                viiv  ii  v  vivi v  v  i    v i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_199930087_   4497 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGCC 4546
                                i      vv   ii  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_199930087_   4547 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4596
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_199930087_   4597 AATGGAACAGCACAGAGGCCTCAGAAATAACACCACATATCTACAACCAT 4646
                                i  v iv   ivii         vv   i i  i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_199930087_   4647 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 4696
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_199930087_   4697 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 4746
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_199930087_   4747 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 4796
                          ii    i    v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_199930087_   4797 AAAGACTTAAATGTTAGACCTAAAACCATCAAAACCC--AAAAGAAAACC 4844
                          ?    i       v   v       i  -     i -- i        v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chr2_199930087_   4845 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTC------AC 4887
                             ?i- v i -   iv   v v  vv i     v ii   ------ i
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_199930087_   4888 GAC--TAAAAGCAATGGCAACAAAAGCTAAAATAGACAAATGGGATCTAA 4935
                            --i       vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_199930087_   4936 TCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4985
                              v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_199930087_   4986 AGGCGACCTGCAGAATGGGAGAAAATTTTTGCAATCTGCCCATCTGACAA 5035
                           i i   ii                v       viiiivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_199930087_   5036 AGGGCTAATATCCAGAATCTACAAAGAACT--TA-AACT-AATTTCCAAG 5081
                         i  i  vi          v  i        --  -    -   ----  v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT----AAT 792

  chr2_199930087_   5082 AAAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATTTGAACAGATG 5131
                              iv    i     v  i?    i                 i   ii
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_199930087_   5132 CTTCTCAAAAGAAGACATTCATGCAGCCAATAGACACATGAAAAAATGCT 5181
                         i     v        i  v  viii       ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_199930087_   5182 CATTATCACTGGCCAT 5197
                           vi    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (146 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.92 (25 / 13)  


3001 26.19 1.77 1.44  chr2_200220270_200222449      784  1688 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_200220270_    784 TGGAAACACATCCCGTGATCATGGATGGGTAGAATCAATATTGTGAAAAT 833
                               v i     i  v        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_200220270_    834 GGCCACACTGCCAAAAGCAATCTACAAATTCAATGTAATTCCCATAAAAA 883
                            v i   v  v   vii       i      i i   i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_200220270_    884 TACCACCATCATTCTTCACAGCATTAGAAAAAAACAATTCTAGAATTCAT 933
                          v   v vv v  i  ii   v v v  v  iv-ii  i   i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_200220270_    934 ATGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGG 983
                               viiv  ii  v  viv         i   vvi i iv  i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_200220270_    984 ACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATGCTATAAGGAC 1033
                              vi      vv       v  ii        viv i   i  i vi
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_200220270_   1034 ATAGTCACCGAAACAGCATGGTACTGGTATAAAAATGG-CACATAGACGA 1082
                          i   v i i i    ii         i    ii  i -  i     iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_200220270_   1083 ATGGAATAGAATAGAGAACCCAGAAGTAA-CCCAAATACTTACAGCCAAC 1131
                                     v    ii      i   -    v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_200220270_   1132 CAAACTGACTCTTGGGAAAAGCAAACAAAAACAAAAAGTGGAAAAAGGAC 1181
                         -----   i i i iv  ii iiv-   i v  vvv i   ii    i i
  L1M4_orf2#LINE/    350 -----TGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAAT 393

  chr2_200220270_   1182 ACCCTTTTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAG 1231
                          vi                       i  i   vv ?       i ii  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_200220270_   1232 AATGAAACTGGATTCTCATCTCTCACTTTATACAAAAATCAACCAAAGAT 1281
                               ii    ii ii i   v   iv           i   iv  i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_200220270_   1282 GGATTA-AGACTTAAACCTAAGATCTGAAACTGTAAAAATTCTAGAAGAT 1330
                             i -    i    iv     v  i     i     v ii       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_200220270_   1331 AACATTGGAAAAACCCTTCCAGACATTGGCTTACGCAAGGATTTC----- 1375
                              v  ?iv  vi    vv   v    v   v    v i    -----
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_200220270_   1376 -ATGACCCAGAACTCAAAAGCAAATGCAATGAAACAAAGA-TAAGTAGCT 1423
                         -     -----  -        v v    ii   v   i -  ii  iv 
  L1M4_orf2#LINE/    594 TATGAC-----AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_200220270_   1424 GGGACCTAATTAAACTTAAGAGCTTTTGCACGGCAAAAGGAACAGTCAGC 1473
                         v    i v  i   v    i i      ii vv    i iv  vi   iv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_200220270_   1474 AGAGTAAACAGACAACCCACAAAGTGGGAGAAAATCTTCACAATCTACAC 1523
                          i   i  v            i i           v  ii   vii i i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_200220270_   1524 ATCTGACAAAGGACTAATATCTAAAATCTACAATGAACTCAAACAAATCA 1573
                               i  i     vi    i i   v  i  v      vv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_200220270_   1574 GTAAGAAAAAAACAA-T--CCCA---TAAAAATTGGCTAAGGACATGAAT 1617
                         i   v     i    - --    ---?      v   v     iv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_200220270_   1618 AGATAATTCTTAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAA 1667
                            i v    iv                       i  i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_200220270_   1668 ATGCTCAACATCACTAACGAT 1688
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.23 (29 / 13)  


1926 25.68 3.05 2.57  chr2_200253828_200255450.rev      501  1123 (500)    L1M4_orf2#LINE/L1      270   895 (13)  

  chr2_200253828_    501 GTATTGGCATAATGATAAA----TTGGCCATCATAATACAA-----AGCC 541
                            i        v    i ---- v ii  viiv    v  -----  i 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_200253828_    542 CAGAAATAGATACATACATAGATAATTGATTTTTTTTC-ACACGAGTGCA 590
                                 i iv       vv  ii ii   vv     -   v i    v
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_200253828_    591 AAGGCAATTCAGTGAAGAAAATGGAGGTTTTTCAATAAAGGGTGCTAGAA 640
                            i v     i  ii    iviv  vi       i   v      i i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_200253828_    641 CAGTCAAATACCCATATGCAAAATAGTAAACTTCCATCCACATTTCATAC 690
                           iiiii   ?   i        v i i  v  vv i  vi ii   i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_200253828_    691 TATATTTAAAAAATTAACTCAAAATGGACCTCAGAATTAAAAGTAAAACA 740
                         i    vi     -               i v?   vi    v    i vv
  L1M4_orf2#LINE/    470 CATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_200253828_    741 CAAAACTCTAACACTTCTAGGATAAAGTATGAGAGAAAATTTTTATGACT 790
                         i      v   v   ii   i v   ii  ii ? v    i  ii    i
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chr2_200253828_    791 TTGAATTAGGCAAAATTTTCTTAAGGCAATTTCAACACCCAAAAGCA--A 838
                            ii        viv       i----  v -i     -       -- 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAG----ATAT-GACACC-AAAAGCACAA 612

  chr2_200253828_    839 GCTGTAAAAGAAATAAAAAGACAAATTATGCTTCATCGAA-TGAAAAACT 887
                           vii        -   v   i     ivi       i  - v       
  L1M4_orf2#LINE/    613 GCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_200253828_    888 TCT---CTCTGAATTATGCTGTTAAAGAA-TAAAAAGACAAACCCCAGAC 933
                          i ---  iii  vv ii  i i  ii  - i         v  v    v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_200253828_    934 TGGGAGAAAGTATTTACAAAGTATACATCTGATAAAAGGGTTATATCCAG 983
                                  i     i    vi   i         ii iv  i       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_200253828_    984 TATATATAATGAAGAACTCTCTCAAAACTCAACAATAAGAAAACAAATAA 1033
                         v        ---        iv   --     i     i  i        
  L1M4_orf2#LINE/    762 AATATATAA---AGAACTCTTACAA--CTCAATAATAAAAAGACAAATAA 806

  chr2_200253828_   1034 CCC--TTTCGAAAAAAGGGGTAAAAGTATTAAACAACCACTTCACTGAAG 1081
                            --  ?---     v   i   i vv  i  i iv  i   v ii   
  L1M4_orf2#LINE/    807 CCCAATTW---AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_200253828_   1082 AAAATATATGAATGGCAAATAGGCATATAAAAAGATGCTCAA 1123
                           i     ii      v    i   i  i             
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.89 (102 / 54)
Gap_init rate = 0.03 (16 / 626), avg. gap size = 2.19 (35 / 16)  


 866 28.23 3.74 1.02  chr2_200328820_200333439.rev     2906  3199 (1421)    L1M4_orf2#LINE/L1        2   303 (605)  

  chr2_200328820_   2906 GGAAACACATCCCATACTCATGGATGAGTAAAATCAATATTGTGAAACTG 2955
                              v i       ii        vi v i v i        v  iv  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_200328820_   2956 ACCATACTGCCCAAAGCAATCTACAAATTCAACACAATTCCCATCAAAAT 3005
                         i v     v      vii       i       i    i  i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_200328820_   3006 ACCACCATCATTCTTCACAAAATTAGAAAAAGCAATTCTAAAATTCATAT 3055
                         v   v vv v  i  ii  i  v v  v  ivii  i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_200328820_   3056 GGAACCAAAAAAGAGCCCACATAGCCAAAGCAA----GACAACAAAAAGA 3101
                             viiv  ii  v  viv         i   ----  -  -  i    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AA-AAGAAGA 199

  chr2_200328820_   3102 ACGAATCTGGAGGCATCACATTAACTGATTTCAAA--CTATAAGTAAGGC 3149
                           i  vi      vv     i vv ii        --i  iv -i  i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA-CAAAGC 248

  chr2_200328820_   3150 CATGGTCACCAAAA-----TGGTATTGGTATAAAAATAGGCACATAGGCC 3194
                         i ii  v i   i -----     i   i    ii    i  i    ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_200328820_   3195 AGGGG 3199
                          iv  
  L1M4_orf2#LINE/    299 AATGG 303

Transitions / transversions = 1.68 (52 / 31)
Gap_init rate = 0.02 (6 / 302), avg. gap size = 2.33 (14 / 6)  

2197 24.19 2.44 1.46  chr2_200328820_200333439.rev     3513  4128 (492)    L1M4_orf2#LINE/L1      287   908 (0)  

  chr2_200328820_   3513 GGCACATAGATCAATGGAGCAGAATAGAGAACCCAGAAATAAACCCAAAT 3562
                          i  i             ii     v    ii               v i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_200328820_   3563 ACTTACAGCCAACCGATCTTCAAAGCAAA-----CAAAAACATAAAGTGG 3607
                          i   ii i   ii   i   i --   i-----   i v   vv i   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGA--CAAGGGTGCCAAGACCATTCAATGG 384

  chr2_200328820_   3608 GGAAAGGACACCCTTCTCAACAAATGTTGCTGGGATAATTGGCTAGTCAT 3657
                               i i vi   i          v        i  i   v  ?i  i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_200328820_   3658 ACGTAGGAGAATGAAACTGGATCCTCATCTCTCACCTTATACCAAAATCA 3707
                          i i ii        ii    i  ii i   v    v     v     i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_200328820_   3708 ATTCAAGGCTGATTAAGGACTTAAATCTAAGACCTGAAGCTATAAAAATT 3757
                          i    iiiv   i ?i   i     v     v  i  i        v i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_200328820_   3758 CTAGAAGATAGCATTGGAAAAGCCCTTCTAGACATTGGCCTAGGCAAGGA 3807
                         i       v i   v  ?iv ivi    vv   v    vi       v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_200328820_   3808 TTTCAT-GACCAATAAT-CCAAAAGCAAATGCAATAAAAACAAA----GA 3851
                             v -  i--  i i-         v v    i    iv   ----  
  L1M4_orf2#LINE/    585 TTTCTTAGAT--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_200328820_   3852 TAAATTGCTAAGAGTTAATTAAACTAAAGAGCTTTTGCATGACAATAGGA 3901
                                ----  v  v  i   v v  i i      iiivv   -    
  L1M4_orf2#LINE/    633 TAAATTG----GACTTCATCAAAATTAAAAACTTTTGTGCTTCAA-AGGA 677

  chr2_200328820_   3902 -ACAGTCAGCGGAGTAAACAGACAGCCCACAGAGTAGGAAAAAATCTTCA 3950
                         -  vi   ivii   i  v     i        i i   i     v  ii
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_200328820_   3951 CAATCTATATGTCTGACAAAGGACTAATATCCAGAATCTACAATGAACTC 4000
                            vii    i     i  i     vi          v  i  v      
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_200328820_   4001 AAGCAAATCAACAAGAAAAA-ACCAACAATCCCATCAAAAAGTGGGCTAA 4049
                         vvi   v    i  v     -  v  i  i  v  i?    i     v  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_200328820_   4050 GGACATGAATAGACAATTCTCGAAAGAAGATATACGAATGGCCAACAA-- 4097
                            iv          v     v             i         i  --
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_200328820_   4098 ACATGAAAAAATGCTCAACATCACTAACGAT 4128
                                  i             ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (93 / 52)
Gap_init rate = 0.02 (11 / 622), avg. gap size = 2.18 (24 / 11)  


3054 19.37 5.88 7.07  chr2_200338402_200342992.rev     3181  4099 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_200338402_   3181 TGGAAAGATATCCCATGTTCATGGGTTGGAAGAATTAGTACTGTTAAAAT 3230
                                                 i        v   i  i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_200338402_   3231 GCCCATACCACCCCAAGTTT-TCTATAGATTCAATAGAATCCCTATCAAA 3279
                          v v    i-      i  v-    i        iiv             
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_200338402_   3280 ATTTCAATGGCATTTTTTTTGCAGAAATAGAACAAAC-AATTTTAAAGTT 3328
                           ii  iiv  --i              v  -   i -i  ii    i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGC--CTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATT 146

  chr2_200338402_   3329 CATATGGAA-T-CAAGAAAGACCCTGAATAGCCAAAGAAATCTCGAGAAG 3376
                                  - -    i--     v           iv     i  i  i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_200338402_   3377 GAA---TAAAACTGGAGGCATCATCACACTTCTTGCTTTCAAACTGTATT 3423
                            ---i   ii      - i--         iiiv       viv  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGG-AC--TCACACTTCCCAATTTCAAAACTTACT 241

  chr2_200338402_   3424 ACAAAGCTGTAGTAATAAAAGCAATATCTTACTGGCATAAAATCAGACAC 3473
                                 ii      v  ii  i i vv           iivi     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_200338402_   3474 TCAAAATA-ATCAAAAATAAAGTTATTCCATATTTATCCTGGAATAAATC 3522
                         -----   -     -------------------------       i --
  L1M4_orf2#LINE/    292 -----ATAGATCAA-------------------------TGGAATAGA-- 309

  chr2_200338402_   3523 CTGTTCATATGCCAATGGAATAATAGCCCAGAAATAAACTTATGCATATA 3572
                         --------------  v  i----  i            ii  i   v  
  L1M4_orf2#LINE/    310 --------------ATTGAG----AGTCCAGAAATAAACCCATACATTTA 341

  chr2_200338402_   3573 TGGTCAAATAATATTTGATAAGGGTATCAAGAATAA-CAA-GGGGAAAGG 3620
                                v i  v  i  i      ii     vi v-   -        i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_200338402_   3621 ATGGTCTTTTCAACAAATGGTGTTGTGTTGAGAAAACTGTAATGTCCACA 3670
                           i                   i  -----i  v     -i  i?     
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTG-----GGACAACTG-GATAKCCACA 435

  chr2_200338402_   3671 TGTAAAAAAATGAAATCGGACCCCTATCTAATAACACTCACAAAAATTAA 3720
                           i    i      i i         i  v i v  ivi           
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_200338402_   3721 CTCAAGATAGATAAAAGACTTAAACATAAGACCTGAATCTATAAAACTCA 3770
                              i  i   v ?    i    ii     v  i  v           v
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_200338402_   3771 TAGACAAAAACATAGGAGAAAACCTTCTTGACAATGATCTTGGCAGTGAT 3820
                             vi          ? v   i    v    vv  ivi v    i  i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_200338402_   3821 TTTTTGGATATGATACAAAAAGCATAGGCAACAAAAGTAAAAATAAACAA 3870
                           i  i       i  v       i i          v       i i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_200338402_   3871 GTGGAAATACATCAAA-CTAAAAGTTTCTGCACAGCAAAGGAAAC----- 3914
                         i v i v v       -i     ii  i  ii vv       v  -----
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_200338402_   3915 ---AAGT-AAAAGGCCACCTATAAAATAAAAGAAAATATCTGCAAACCAT 3960
                         ---    -     i v   i i i   iii         i      i   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_200338402_   3961 ATATCCAGTAAGGGGTTAATATCTAAGATACATAAAGAACTCATACAACT 4010
                              iii      ii vi    i ii   i           v       
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_200338402_   4011 CAGTAA---AAAAACAAA--AC-------AAAA-----CAAAACA---AA 4040
                           i   ---   i     --  -------    -----    iv ---i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_200338402_   4041 ATA-ACA-----ACAA--------TACAAATGGCCAATAGGTATATGAAA 4076
                            -   -----v   --------               i i i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_200338402_   4077 AGGTGCTCCATATCACTGATCAA 4099
                           i     v i    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.43 (124 / 51)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 3.84 (119 / 31)  


3107 27.41 1.22 0.44  chr2_200577486_200582727     3850  4750 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_200577486_   3850 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 3899
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_200577486_   3900 GGTCATACTGCCCAAAGTAGTTTATAGATTCAATGCTATCTCCATCAAGC 3949
                           iv     v      v ii i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_200577486_   3950 TACCATTGACTTTCTTCACTGAA-TTGGAAAAAAACT-ACTTTAAATTTC 3997
                          v   vivi i  i  ii v   -   --- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_200577486_   3998 ATGTGGAACCAAAAAAGAGCCCATATAGCCAAGAAAATCCTAAGCAAAAA 4047
                           i     viiv  ii  v  viv        i v    i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_200577486_   4048 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATGTTACAAGG 4097
                                 i      vv   ii  v  ii i      viv ii     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_200577486_   4098 CTACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGATATATAGAC 4147
                                  i   i    ii    i    i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_200577486_   4148 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCATACATCTACAACCA 4197
                                 i    iv   ivii         vv        i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_200577486_   4198 TCTGATCTTTGACAAACCTGACAAAAACAAACAATAGGAAAAGGATTCCC 4247
                         vi    i  i     ivv  v   i v  vv    i  i    i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_200577486_   4248 TATGTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGCAGAAAACTG 4297
                          v vi  i              v      v  ?   v     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_200577486_   4298 AAACTGGAACCCTTCCTTACACCTTATACAAAAATTAACTTAAGATGGCT 4347
                           ii    v    v   i     v                i  i    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_200577486_   4348 TAAAGACTTAAAGGTAAAACCCAAAATCATAAAAATCCTAGAAGAAAACC 4397
                         i ?    i    v    i v i    ii      v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_200577486_   4398 TAGGCA-ACACCATTCAGGGCAAAGGCATGGGCAAAGACTTCATGGCTAA 4446
                             ?i- v i -   iv i vvv  vv i     v ii   v i v  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_200577486_   4447 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTAA 4496
                         i            vvi          vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_200577486_   4497 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 4546
                          i   v v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_200577486_   4547 AGGCAACCTACAGAATGGAAGAAAATTTTTGCAATGTATCTACCTGACAA 4596
                           i     i         i       v       vvi  v  i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_200577486_   4597 AGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 4646
                         i  i  vi          v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_200577486_   4647 A--------ACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAGTTG 4688
                          --------    v  i?    i            v    i     v  v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_200577486_   4689 TCAAAAGAAAATATTTATGTGGCCAAAAAACTTATGAAAGAAAGCTCATC 4738
                           v      i    vi vi       v  i vi      ii v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_200577486_   4739 ATCACTGGTCAT 4750
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.50 (15 / 6)  


3609 17.83 2.88 0.82  chr2_200594698_200598081.rev     1589  2317 (1067)    L1M4_orf2#LINE/L1        1   744 (164)  

  chr2_200594698_   1589 TGGAAAGATCTCCCATATTCATGGATCAGAAGACTTA---TTGTTAAGAT 1635
                                  v      i         ii         ---          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_200594698_   1636 GACAGTTCTTTTCAAATTGATCTACAGATTCAATGCCATTTGTATCACAA 1685
                          i  i v  iii                     i  v  iiv     v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_200594698_   1686 TTCCAGCTGCCTCTTTTGCAAAAATGTTTAAGCTGATCCTAAGATGTGTA 1735
                          i          i       i    vvvi             i  vii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_200594698_   1736 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAAATGAT 1785
                                                                     i v  v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_200594698_   1786 CAAAGTTGGAGGGCTCACATTTCCCCATTTCAGTACTTACTACAGAGCTA 1835
                                     i      i     v      iv          i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_200594698_   1836 CAATAATCAAGACAGTGCA-TATTGGTATGAGGATAGGCATGTAAAACAG 1884
                           i              ii-  i   i  i       i   i  i v  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_200594698_   1885 TAAAATAGGATCGAGAGTCTAGAAATAGACCC-TAAATTTACGGTCAAAT 1933
                          ii     i  i       i       i    -  v     i      v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_200594698_   1934 GTTTTTCAACAAAAGTGCCAAGATAATTCAATGGGGAAAAAA-AGCCTTT 1982
                          v     i    ii         iv              i  -  i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_200594698_   1983 T-AACAAGTGGTACAGGGTCAAATGGATAGACACATGCAAAAAAA-GGAG 2030
                          -     i    i v   v   v      ?v           i  - i  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_200594698_   2031 TTGGATCCCTTCTTTAAGC---ATTCAAAA-----CTCAAAAGGGGGTGT 2072
                              i    v i i vi ---  v     -----       v  ivii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_200594698_   2073 AGAACTAAATATATGAGCTAAAACTATAAAATTTTTAGAAGAAAAAAATA 2122
                            v      i  v                 i i           v -  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-TA 549

  chr2_200594698_   2123 GAAGTAAACCTTCATGACTTTAGCTTAGCCAAAGCCTTCTCATATATCGC 2172
                          i?     i    i    i  i v    v   v vi    i v    vi 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_200594698_   2173 ACCAAAAGCACAAGATTAA--AAAAAAAAAAGAGGCAAATCGCACTTTTA 2220
                                       --i  --   i      v  ii    i v    i- 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAG--CAACAAAAGAAAAAATAGATAAATTGGACTTC-A 646

  chr2_200594698_   2221 TCTAA-TTAGAAAAAGTTTAGTGCTTCAAAGAACACCAATA-GAAAATGA 2268
                           v  -   --    v   v           i    i vi -    i   
  L1M4_orf2#LINE/    647 TCAAAATTA--AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_200594698_   2269 AAAGACAGCCCACAGAATGAGAGAAAATGTTTGGAAATAACATA-CTGGT 2317
                                i           i        i    v    v i   -   i 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

Transitions / transversions = 1.89 (83 / 44)
Gap_init rate = 0.02 (16 / 744), avg. gap size = 1.69 (27 / 16)  

 785 17.99 4.76 1.06  chr2_200594698_200598081.rev     2704  2892 (492)    L1M4_orf2#LINE/L1      713   908 (0)  

  chr2_200594698_   2704 GGGGACAAACATC--CAAACTATACCATTGGTTGAAGGATTTATATCCAA 2751
                            iiv   i  i--    ii   i-  iv v i i   i  i      i
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGGGACTTGTATCCAG 761

  chr2_200594698_   2752 AGTATAAAAACCACTCTTACTACTCAGTAATAAAAAGACAA----CCCAA 2797
                          i    v   vv        v     i              ----     
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_200594698_   2798 TTTTTTAAAGGGGTAAAGGATCTGAATAGACATTTCAC---AGAAGATAT 2844
                           ?vv-   v   i       i              v ---         
  L1M4_orf2#LINE/    812 TTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_200594698_   2845 ACAAATAAACAATAAGCACATGAGAAGATGCTCAACACCATTAGCCAC 2892
                               iiv              i             i  ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (21 / 12)
Gap_init rate = 0.03 (5 / 196), avg. gap size = 2.20 (11 / 5)  


3082 25.79 1.31 2.50  chr2_200746378_200751807     4020  4938 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_200746378_   4020 TGGAAAAATATTCTGTGCTCATGGATAGGAAGATTCAATATTGTTAAAAT 4069
                               i    i ii  i        v      i i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_200746378_   4070 AGCCATACTGCC--AATGCAATTTACAGATTCAATGTTATTCATATCAAA 4117
                         i  v     v  --   -ii  i           i iv  i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_200746378_   4118 CTACCAATGACATTCTTTTCAGAATTAGAAAAATCTATTTTAAAATTCAT 4167
                         v v   iivi v  i   v     v v  v  iiiv  ii          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_200746378_   4168 ATGGCACCAAAAAAGAGCCTGAATAGCCAAGGGTATCCTTAACAAAAAGA 4217
                             v viiv  ii  v  v          iivv   i v  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_200746378_   4218 ATAAAGCTGGAGGCATCATGTTACCTGACTTCGAACTATACTA-AAGGCT 4266
                          i    i      vv   iii v  ii i   i  viv     -  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_200746378_   4267 ACAGTAACCAAAAAAACATGAAACTGGTGCAAAACCAGGCACATAGACCA 4316
                                i   i v iii  iv     iii  iivi  i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_200746378_   4317 ATAGAGCAGACTAGAGGGCCCAGAAATAATGCCACACATCTACAACCATC 4366
                           i  ii   v v   i i          vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_200746378_   4367 TGATCTTTGACAAAGTTGACAAAAACAAGCAATGGGGAAAGGACCTCCTA 4416
                             i  i     i v  v   i v  vv            i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_200746378_   4417 TTCAATAAATGGTGCTGGGGTAACTGGCTACCCATATGCAAAGGACTGA- 4465
                              i             ii      v  ?   i       i  v   -
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_200746378_   4466 ------CCCCTTCCTTACACTATATACGAAAATCTATTCATGATGGATTA 4509
                         ------     v   i    i      i     iv i   vi      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_200746378_   4510 AAGACTTAAATGTAAAACTTAAAACTATAAAGACTCT-GGAAGATAACCT 4558
                         ?    i         i vi            -     -i     v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACAT 548

  chr2_200746378_   4559 AGGAAATACTCTTCTGGACATAGACCCTGGCAAACATTTCAT-GATGAAG 4607
                            ?ivv v     vv   v v iviiv     vvi    v -   - v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr2_200746378_   4608 ATGCCAAAAGCAATTTCAACAAAAATAAAAATTGACAAATGGGACCTAAT 4657
                          ii         vvvv        iv      v  i    v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_200746378_   4658 TAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCAACAAAGTAAACA 4707
                         i   v v  i i   i  iiivv    i  v        v     i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_200746378_   4708 GACAAGGCATAGAATGGGAGAAAATGTTTGCAAACTATGCATCTGATTCT 4757
                              vv  i               i        ii  ii       ---
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT--- 744

  chr2_200746378_   4758 AAGCATCTATATTCTTATAGATTCTAATATCCAGAATTTATAAATAGCTT 4807
                            ---------------i  --  vi          v      v i  i
  L1M4_orf2#LINE/    745 AAG---------------GGA--CTTGTATCCAGAATATATAAAGAACTC 777

  chr2_200746378_   4808 AAACAAAGTAAGAAGCAAAAAACAAATAACCCCATTAAAAAGTAGGCAAA 4857
                         vv    vvi  v  vv    i           v   ?    i i      
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_200746378_   4858 GGACATGAACAGATGCTTTTCAAAAGAAGACATACACATGACCAACAAGC 4907
                            iv    i   iii  i  v        i     v   i    i    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_200746378_   4908 ACATGAAAAAATGTTCAACATCATGGATCAT 4938
                                  i   i         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.18 (35 / 11)  


1856 25.96 6.55 6.43  chr2_200787189_200791545.rev     2640  3448 (909)    L1M4_orf2#LINE/L1        1   810 (98)  

  chr2_200787189_   2640 TGGAGAAATATACCATGTTCATGCATTGGAAAACTCTATACTGTTATGAT 2689
                             i i    v           v       i   iv   i     v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_200787189_   2690 GTC--TGCTTTTTGCCAAGTTAATCTGTAGGTTTAATGCACTTTATCTAA 2737
                          v -- i  ii---    i  i    ii  i  i  i   ----------
  L1M4_orf2#LINE/     51 GGCAATACTCC---CCAAATTGATCTACAGATTCAACGCA---------- 87

  chr2_200787189_   2738 GTTGATCTGTGGATTTAATGCTGTAGCAATCAACATCCCAGCAGGATTTT 2787
                         ----   i------------  ------     v        v vv    
  L1M4_orf2#LINE/     88 ----ATCC------------CT------ATCAAAATCCCAGCTGCCTTTT 115

  chr2_200787189_   2788 T-GTAGAACTTG-TAAATCGATTC--AAATTTATATGGAAATGCAAAGGA 2833
                          - i    v   -i  iii   i --     i              i   
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_200787189_   2834 CCTGGAATAGCCAAAGCCATCTTGAAAAAGCAAAACAAAAGTGGAAGACT 2883
                           ii           i v            v i      iv    i    
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_200787189_   2884 TAAACTATCTAATTTTAAGATTAAACGCAA-GTTCCAGTAATTAAGATAG 2932
                         i v   vi i     i  i i v vii   - i v       i    i  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_200787189_   2933 TTTAGTATTGCTGAAAAGGTAGACAAAGAGATTAGTGGAAACAAATAAAG 2982
                          v i   i  viiv  i i      v v    i i     vvi   vi  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_200787189_   2983 AGACCAGAAGTAAACCTACACTTATATGACTAGTTGATTTT-GACCAAGG 3031
                           v      i      i i  v v    iii i        -   v i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_200787189_   3032 TGACAAAGCACCTAAACATCTC--TAGGAAAGAAATA-TCTTTTCAACAA 3078
                           v   ii -------   -  -- i  i  ii    -            
  L1M4_orf2#LINE/    366 TGCCAAGAC-------CAT-TCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_200787189_   3079 ATGAAAA-AGAATAACTGGATGT----ATGGAAGAAAA-AAAATTGA--- 3119
                            iviv-i i i        i?----   v  i i  -i  i   i---
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_200787189_   3120 CATACTTCACATT-CACAAAAAAATTAATTTGAGATAGATCATATAACCT 3168
                          v   i     ii-i i v         i ii i  i     ? -i    
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA-GACCT 506

  chr2_200787189_   3169 AAACATTATGGCTGAAACTTTAGTGTTTCTGGATAAATACGTAAGAGAAC 3218
                            ii v vi   i     v  ivii ii i  vi  v  i  i ? v v
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_200787189_   3219 ATATGTACAAATTTGAAATAGGCAAAGATTACTTAGACAGAATCCCTAGA 3268
                           v viiii vi   iiv       v i  v      i vi iv  --i 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC--AA 604

  chr2_200787189_   3269 AATTACTGATGCACACAACACTGATAAAATAGAGTAACTGGA-------- 3310
                           vi  -- v   -    v --  v        vv  i    --------
  L1M4_orf2#LINE/    605 AAGCAC--AAGCA-ACAAAA--GAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_200787189_   3311 --AGTA-----TTCCACATTTCAAAAGACATTGTTAA-AAAGTAAATAGG 3352
                         -- v  -----  iiiiii      i    i i i  -     i  v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_200787189_   3353 CAAGCTACATACTGGGATAAAAGATTCCCAA----TATATGTTAT----- 3393
                            v i   v v     v    v   iv   ----     v v  -----
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_200787189_   3394 -CTATATACACACACTACA------ATTCCTGCAACTCAATAATAAAAAG 3436
                         -  - i  iv  v v  i ------ i  i i                  
  L1M4_orf2#LINE/    750 ACT-TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_200787189_   3437 GCAAATAACCTA 3448
                         i         i 
  L1M4_orf2#LINE/    799 ACAAATAACCCA 810

Transitions / transversions = 1.92 (136 / 71)
Gap_init rate = 0.04 (31 / 810), avg. gap size = 3.39 (105 / 31)  

 381 16.10 5.08 1.69  chr2_200787189_200791545.rev     3748  3865 (492)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr2_200787189_   3748 AAAAAAAAAAAGGCAAGCAACCTAATTTTTCAAAGTGGGCAAAACATCT- 3796
                           v  v      i   ii    i    --?v   i        iv  i -
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATT--WAAAAATGGGCAAAGGATTTG 834

  chr2_200787189_   3797 AACAGACATTTC-ACAAGGAAGATATACAAGTGGCCAAGAAGCAAAGGAA 3845
                           i         -v   i            i       v     v v   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_200787189_   3846 AA-ATGC---ACATCATAAATCAT 3865
                           -    ---      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (10 / 8)
Gap_init rate = 0.04 (5 / 122), avg. gap size = 1.60 (8 / 5)  

 267 26.47 8.09 0.74  chr2_200787189_200791545.rev     4136  4271 (86)    L1M4_orf2#LINE/L1      712   857 (51)  

  chr2_200787189_   4136 TGGAAGAAAATATTTCTAATGAATATAACGGATATGGG--TTATTAGGCA 4183
                            i           vi  vvv     v v    v   --  i - vv  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT-ATCCA 760

  chr2_200787189_   4184 GAATACACGAAGAACTCTTATAAATTAATTTTAAAA-GACAA----CTCA 4228
                              i ii           i  v i   vv     -     ---- i  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_200787189_   4229 ATAGAAAAA-AGGTAAAAATTGTGACCAAGCAGTGTTC---AGAAGA 4271
                           v?     -i  i   iiv v   vi ii  v vi  ---      
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

Transitions / transversions = 0.94 (17 / 18)
Gap_init rate = 0.04 (6 / 146), avg. gap size = 2.00 (12 / 6)  


3111 26.95 0.66 0.77  chr2_200803767_200809580.rev     4414  5322 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_200803767_   4414 TGGAAGAACATTCCATGCTCATGGATAGAAAGAATCAATATCGCAAAAAT 4463
                              ii i  i     i        v i    v i     i iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_200803767_   4464 GGCCATACTGCCCAAGGAAATTTATAGATTCAATGCCATCCCCATCAAGC 4513
                            v     v     ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_200803767_   4514 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4561
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_200803767_   4562 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGGCAATCCTAAGCAAAAAG 4611
                                viiv  ii  v  v v  v     ii     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_200803767_   4612 AACAAAGAAAAAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4661
                                vvii   vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_200803767_   4662 TACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4711
                                 iv  i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_200803767_   4712 AATGGAACAGAA--GAGAGGCCTCAGAAATAACACCACACATCTACAACC 4759
                                i    --     v  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_200803767_   4760 ATTGGATGTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4809
                          v v   v  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_200803767_   4810 CTATTCAATAAATGGTGCTGGGAAACCTGGCTAGCCATATGTAGAAAGCT 4859
                           v     i              v v    v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_200803767_   4860 GAAACTGGATCTCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGA 4909
                            ii    i i  v   i    iv              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_200803767_   4910 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAAACCCTAGAAGAAAA 4959
                          i ?    i       v   v       i      v-i i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chr2_200803767_   4960 CCTAGGCA-ATACCATTCAGGACACAGGCGTGGGCAAGGACTTCATGACT 5008
                          v    ?i- v i -   iv   viv  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_200803767_   5009 AAAACACCAAAAGCAATGGAAACAAAAGCCAAAATAGACAAATGGGATCT 5058
                          vi            vvi v        vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_200803767_   5059 AATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5108
                         v  i   v i  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_200803767_   5109 ACAGGCAACCTATAGAATGGGAGAAAATTTTTG-AGATCTACCTGTCTGA 5157
                          v  i     i i               v    - i   - iv i     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGA 743

  chr2_200803767_   5158 CAAAGGGCTAATATCCACAATCTACAAAGAACTTAAACAAATTTACAAGA 5207
                         i  i  i  vi      v   v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_200803767_   5208 AAAAATCAAACAACCCCATCAAAAACTGGGCAAAGGATATGAACAAACAC 5257
                             iv    i     v  i?    v            v    i i   i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_200803767_   5258 TTTTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTT 5307
                           i  v        i  vi viii     i ii          i     i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_200803767_   5308 ATCATCACAGGTCAT 5322
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


1318 17.84 0.00 3.72  chr2_200876974_200879710     1029  1297 (1440)    L1M4_orf2#LINE/L1        1   259 (649)  

  chr2_200876974_   1029 TAGAACTACATCCCATGTTCATGGATCAGAAAGCATAATATTCTTAAAAT 1078
                          i   vv i                 ii   ii v       v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_200876974_   1079 GGCAGTATGCTCCAAACTGATCTTTAGATTCAACACAATCTCTATCAAAA 1128
                             i  iv i     i      vi         i     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_200876974_   1129 TCCAAGTTTAGCTTTTTTTTTTGGCAGAAACTGACAAGTTGATTCTAAAA 1178
                            v  i --  i      ----       i       i    i      
  L1M4_orf2#LINE/    101 TCCCAGCT--GCCTTTTTT----GCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_200876974_   1179 TTAATATGAAAATGAAAAGCACACAGAATCGCCAAAACAACCTTGAAAGA 1228
                           v     i     v  i v  v      v          i       i 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_200876974_   1229 GAAAAACAAAGTTTGAAGGCTTGCACTTCCTTATTTCAAAACTTACTATA 1278
                            i         v  i i  ii       iv                i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_200876974_   1279 GGCCAGGTATAGTGACTCA 1297
                         i---  v  i   i -   
  L1M4_orf2#LINE/    245 A---AGCTACAGTAA-TCA 259

Transitions / transversions = 2.20 (33 / 15)
Gap_init rate = 0.02 (4 / 259), avg. gap size = 2.50 (10 / 4)  

3279 13.81 3.45 4.75  chr2_200876974_200879710     1558  2252 (485)    L1M4_orf2#LINE/L1      223   908 (0)  

  chr2_200876974_   1558 CCCTATCTCAAAAAAATAACTACAATAAAGTTTCAATAAAAAATATAGTG 1607
                            v  i      v-- v       ---  i v  i   vv  v i    
  L1M4_orf2#LINE/    223 CCCAATTTCAAAAC--TTACTACAA---AGCTACAGTAATCAAGACAGTG 267

  chr2_200876974_   1608 TGACATTGGCATAACAGTAAGCACATAGGTCAATGCAATAGAACTGAGAA 1657
                           ii i        vii  ii  i    i      v       i     i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_200876974_   1658 TTCAGAAATAAATTCTTACATTTATAGTCAATTGATTTTCAACAAGCATG 1707
                          i          ii v         i              i     vi  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_200876974_   1708 CCAAGACAATTCAATGGGGAAAAGAATAGTCTTTTCAACAAATGGC-CTG 1756
                                v              -                      i-   
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_200876974_   1757 TGGACAACTTGATATCCACATGCAAA-GAATGAAGTTGAAACCATACCTC 1805
                         -        v    ?           -           i v  v      
  L1M4_orf2#LINE/    417 -GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_200876974_   1806 ACATCATATACAAAAATTAACTCAAAATGAATCATAGACCTAAATGTAAG 1855
                            i                         i    ?               
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_200876974_   1856 AGCTAAAGCTA--AAACTCTTAGGA-AAAAGAGAGGTAGAAATCTTCATA 1902
                                i   --          i -    v v   ?iv        i i
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_200876974_   1903 ACCTTGG-TTAGGCAATGGTTTCTTAGATATGACAACAAAAGCACAGGCA 1951
                                -                           v          i   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_200876974_   1952 GAAAGAGCAACAAAAAAGTATGTGAATTGAACTTCACATAAAACATTTCT 2001
                         iv  i  -----     i  vi i     i      --------------
  L1M4_orf2#LINE/    616 ACAAAAG-----AAAAAATAGATAAATTGGACTTCA-------------- 646

  chr2_200876974_   2002 GTTTTATCACAATTAAAAACATTTTTGCATTAAAGGACTCTATCAAGAAA 2051
                         ------   v          v   v   v i       v           
  L1M4_orf2#LINE/    647 ------TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_200876974_   2052 GTCAAAAGAAAACCCATAGAATGGGTGAAAATATTTGCAAATCATATATC 2101
                           v      v      i        v                        
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_200876974_   2102 CAATAAAAATCTAGTATCCGG-------------TTCTTAACAACTCACC 2138
                         ii    iiiv  v      i -------------i     -       vi
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAAT 789

  chr2_200876974_   2139 AACAAAAAGACAA-----CCAGTTAAAAAATAGGCAAAGGACTTGAATAG 2183
                           i          -----   i  ?      i         i        
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_200876974_   2184 ACATTTCTCCAAAGAAGATATACAAATGGCCAAAAACCACAAGAAAAAAA 2233
                                                          v  v    v     i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_200876974_   2234 GCTCTAAGTCGTTAGTCAT 2252
                             v vi  i????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (54 / 38)
Gap_init rate = 0.02 (14 / 686), avg. gap size = 4.07 (57 / 14)  


 676 26.34 4.84 0.00  chr2_200887736_200889783      500   685 (1363)    L1M4_orf2#LINE/L1      162   356 (552)  

  chr2_200887736_    500 GAGATGCCAAATAGCCAAAATAACCTTGAGCAAAAAGAACGAAGCTGGAG 549
                          i  iv vi           i  i     iv  i      i   i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_200887736_    550 GCATTACATTCCTTGATTTCAAAATATCCTATAAAGGGATTATAATCAAA 599
                          vv i   i i iii         iv v   i    vv ivi       i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_200887736_    600 ACAGCATGAAACTG-TGTAAGAACAGACACATTGATCA---GGATAGAA- 644
                             ii  iv    -ii    i i     i  v     --- i      -
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_200887736_    645 ----AGCCCAGAAATAAACCCAAAAATTTACAGTCGATTTTTTTT 685
                         ----  i               v v     ii   i   vv    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 2.06 (33 / 16)
Gap_init rate = 0.02 (3 / 195), avg. gap size = 3.00 (9 / 3)  

1968 25.31 1.05 3.49  chr2_200887736_200889783      984  1556 (492)    L1M4_orf2#LINE/L1      350   908 (0)  

  chr2_200887736_    984 TGATTTTTGACAAAAGTGCCAAAAAAAAAAACA--CAATGGCGCAAGGAA 1031
                                i     ii       i v------  --      v v   i v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC------CATTCAATGGGGAAAGAAT 393

  chr2_200887736_   1032 AATATCTTCAATAAATGTTGTTGAAA-AACTAGATATCCACATACAGAAG 1080
                          i v i     i     v  i  ii -    i    ?      i  i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_200887736_   1081 AATGATATTAGACCTTTATCTTGATATTAGAACCTTACACCATATACAAA 1130
                              vi  i    ii  --------------   i              
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTA--------------CCTCACACCATATACAAA 479

  chr2_200887736_   1131 AGTCAGCTCAATATGGATTAAAGACTTAAATCTAAGACCTGAAACTTTAA 1180
                          i i i     v      i ?    i     v     v  i     v   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_200887736_   1181 AACTTCCAGAAGAAAACCCAGGGGGAAAGCTCCACTACATTGGTCCGGGC 1230
                             iii          vi   ? v   v  i iiv  v    viii   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_200887736_   1231 AGTGATTTTTTGGATAGGATTCCAAATGTACAGGGAACAAAAGTAAAAGT 1280
                          i  i   i  i    v  iv     v i   i v        v    i 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_200887736_   1281 AGACACATTG-ATGGCGTCAAGCTAACAAGTTCCCGCACAGCAAAGAGAA 1329
                            i v    - ivv i    iv v v  ii iii ii vv     iiv 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_200887736_   1330 CAATTAAAAGAGTGAAGAGACAACCCACAGAATGAGGGAAAATATTTACA 1379
                          v  i  i i      i                 i i          i  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_200887736_   1380 AACCATACATCTAAGAAGAAGTTAATACCCAAAATATATAAGGAAGCCAA 1429
                           i    i    i v   iiii vi  i   i         i   vi vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_200887736_   1430 ACAACTCAACAGCAAGAAAATAAATAAGCCAGCTGAAAATTGGCTAAAGG 1479
                                  i ii  i  i i      v   ii ?    v   vi     
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_200887736_   1480 ACCTGACTGACCAATTTTCAAAAGAAGACATACAAATGGT-AATAGGTAT 1528
                          ii   v iiv  v  i  v        i          i-    i i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_200887736_   1529 ATGAAAA-ATTCTCAGCACCACTAATCAT 1556
                                -  v    i  i  ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (96 / 45)
Gap_init rate = 0.01 (7 / 559), avg. gap size = 3.71 (26 / 7)  


3216 25.64 0.66 1.66  chr2_201023983_201025879.rev      501  1405 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr2_201023983_    501 CTATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATACTGCC 550
                          i   i      i v      v i     i  v  i     v     v  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_201023983_    551 CAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAATGACTT 600
                            iv i  i  i        i  v     i     iv v   iivi i 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_201023983_    601 TCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCACATGAAAACAAA 648
                          i  ii     -   -- v  i  - iii    i    i   i   iiv 
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_201023983_    649 AAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGA 698
                          ii  v  v v  v     iv     i i ivv i          i    
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_201023983_    699 GGCATCACGCTATCTAACTTCAAACTATACTACAAGGCTACAGTAACCAA 748
                           vv    i  vi i  i      viv        i          i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_201023983_    749 AACAGCATGGTACTGGTACCAAAACAGATATATAGATCAATGGAACAGAA 798
                         i    ii         i iv ii i   i                i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_201023983_    799 C--AGAGCCCTCAGAAATAATGCCACATATCTACAACTATCTGATCGTTG 846
                         i--    i  --        vv   i i  i  iiiii vi    iv i 
  L1M4_orf2#LINE/    311 TTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_201023983_    847 ACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAA 896
                             ivv  v   i v  vvv           i  vvi  v  i  i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_201023983_    897 TGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCC 946
                                    v      v  ?   i   i i  iiv    ii    i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_201023983_    947 CTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGACTTAA 996
                           v   i     v           i  i    i      i ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr2_201023983_    997 ATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATAC 1045
                             v   v       i      vi i           v    ?i- v i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_201023983_   1046 CATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAG 1095
                          -   iv   v v  vv i     v ii   v ivv  vi          
  L1M4_orf2#LINE/    559 C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_201023983_   1096 CAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAA-CTAAA 1144
                           vvi          vv     v  i    v   ii v  i   -i    
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_201023983_   1145 GAGCTTCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAAC 1194
                         i ----   i  ii vv    i  v    i  vv i      v  i    
  L1M4_orf2#LINE/    658 AA----CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_201023983_   1195 CTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTA 1244
                          i                 v  i    vii ivi      i  i  i  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_201023983_   1245 ATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAAACAAA 1294
                         i          v  i         vv    v iv i  v     i     
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_201023983_   1295 CAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCTCAAAAG 1344
                         i     v  i?    i    ii      v    i     i     v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_201023983_   1345 AAGACATTTATGTAGCCAAAATGCTCATCATCATGAAAAAATGCTCATCA 1394
                             i  vi vi i     ----- v v  -        i       v  
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAA-----TAAGCA-CATGAAAAGATGCTCAACA 897

  chr2_201023983_   1395 TCACTGGCCAT 1405
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (138 / 90)
Gap_init rate = 0.01 (11 / 896), avg. gap size = 1.91 (21 / 11)  


3222 27.18 0.77 0.44  chr2_201251539_201253955.rev     1021  1925 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_201251539_   1021 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 1070
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_201251539_   1071 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1120
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_201251539_   1121 TACCAATGACTTCCTTCACAGAATTGGAAAAACCTACTTTAAAGTTCATG 1170
                          v   iivi i ii  ii     v v  v  i iv iii    i     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_201251539_   1171 TGGAAACACAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGAA 1220
                               ii   ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_201251539_   1221 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACAATACTACAAGGCTA 1270
                              i      vv    i  v  ii i      vvv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_201251539_   1271 CAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 1320
                            i  i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_201251539_   1321 TGGAACAGAAC--AGAACCCTCAAAAATAATACCACACATCTACAACCAT 1368
                              i    i--   ii  -- i      vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_201251539_   1369 CTGATATTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 1418
                         i    v  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_201251539_   1419 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1468
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_201251539_   1469 AACTGGATCCCCTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 1518
                          ii    i   iv   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_201251539_   1519 AAAGACTTACATGTTAGACCTAAAACCATAAAAAACCTAGAAGAAAACCT 1568
                          ?    i  v    v   v       i      vv i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_201251539_   1569 AGGCA-ATACCATTCA-GGCCACAGGCATGGGCAAGGACTTCATGACTAA 1616
                            ?i- v i -   i- i  vii  i- i     v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT 596

  chr2_201251539_   1617 AACACCAAAAGCAATTGCAGCAAAAGCCAAAATTGACAAGTGGGATCTAA 1666
                         i            vvv   i      vv     v  i  i v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_201251539_   1667 TTAAACTAAAGGGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1716
                          i   v v  iii   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_201251539_   1717 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 1766
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_201251539_   1767 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 1816
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_201251539_   1817 AATCAAACAACCCCATCAAAAAGTGGGTGAAGGAT---AACAGACACTTC 1863
                          iv    i     v  i?    i    ii      ---  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_201251539_   1864 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 1913
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_201251539_   1914 ATCACTGGCCAT 1925
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (151 / 91)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3096 26.46 1.37 0.46  chr2_201295488_201298099.rev     1240  2112 (500)    L1M4_orf2#LINE/L1        1   881 (27)  

  chr2_201295488_   1240 TGGAGAAACATTCCATGCTCATGGATAGGAAGAATCAATACCATGAAAAT 1289
                             i i i  i     i        v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_201295488_   1290 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATCCCCATCAAGC 1339
                            v     v      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_201295488_   1340 TACCATTGACTTTCTTCACAGAATTAGAAAAACT-ACTTTAAATTTCATA 1388
                          v   vivi i  i  ii     v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_201295488_   1389 AGGAACCA-AAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGAA 1437
                         v    vii-  ii  v  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_201295488_   1438 CAAAGCTGGAGGCGTCACACTATCTGACTTCAAACTATACTACAAGACTA 1487
                              i      vv       vi ii i      viv        ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_201295488_   1488 CAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGATATATAGACCAG 1537
                               i   i    ii           iv ii i   i       i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_201295488_   1538 TGGAACAGAACAGAGACCTTAGAAATAAAACCACACATCCACAACCATCT 1587
                              i    iv    viii         v   i    ii iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_201295488_   1588 GATCTTTGACAAACTTGACAAAAACAAGCAATGGGGAAAGAATTCCCTAT 1637
                            i  i     ivv  v   i v  vv               vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_201295488_   1638 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAA-AACGAAA 1686
                          i  i              v      v  ?   i     i  -  i   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_201295488_   1687 TTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTGA 1736
                                   v   i     v                   i      ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_201295488_   1737 AGACTTAAATGTAAAACCCAAAACCATAAATACCCT-AAAAGAAAACCTA 1785
                             i         i v i     i     -  i  - i        v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATA 549

  chr2_201295488_   1786 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 1834
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_201295488_   1835 CACTAAAAGCAATTGCAGCAAAAGCCAAAATTGACAAATGGGATCTAATT 1884
                            i       vvv   i      vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_201295488_   1885 AAA-CTAAAGAGTTT-ATGCCTAGCAAAAGAAATTAGTGTCAGAGTGAAC 1932
                            -i    i v   -i   i --    i  v i  viivv i      v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_201295488_   1933 AGGCAACCTACAGAATGCGAGAAAAGTTTTGCAATCTACCCA-CTGACAA 1981
                           i     i        v       vv       vii ivi -    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_201295488_   1982 AGGTCTAATATCCAGAATCTGCAAGGAACTTAAATAAATTTATAAGGAAA 2031
                         i  v  vi          v ii  i     ivv i  v iv    vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_201295488_   2032 AAGCAA----CCCCATCAAAAAATGGGCAAAGGATATGAACAGACACTCC 2077
                          ii   ----   v  i?                 v    i     i i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_201295488_   2078 TCAAAAGAAGACATTTATGTGGCCAACAAACATAT 2112
                           v        i  vi vi       i  i  i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.01 (12 / 881), avg. gap size = 1.33 (16 / 12)  


2990 25.61 2.45 1.34  chr2_201333539_201337828.rev     2901  3798 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_201333539_   2901 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAACATTGTGAAAAT 2950
                               v i        i        v  v   v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_201333539_   2951 GGCTATACTGCCAAAAGCAATCTACAAATTCAGTGCAATCCCCATCAAAA 3000
                            v     v  v   vii       i     ii        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_201333539_   3001 TACCACCATTG--TTCTTCACAGAATTAGAAAAAACAATTCTAAAGTTCA 3048
                          v   v --  --  i  ii     v v  v  ivii  i     i    
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_201333539_   3049 CATGATACCAAAAAAGAGCCCGCATAGCCAAAGCAAGAGTAAGCAAAGAG 3098
                         i   iv viiv  ii  v  v v         i   vvv i iv  ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_201333539_   3099 AACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGC 3148
                               vi      vv       v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_201333539_   3149 CATAGTCAACAAAATGGTGTAGTAGTG-TATAAAAATAGGCACATAGAAA 3197
                         i i   v v   i ii    i   v  -i    ii    i  i     --
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA-- 296

  chr2_201333539_   3198 CCAGTGGAACAGAAT--AGAG----------AACCCAAATACTTACACCC 3235
                         i  i     i     --    ----------      v i i   iivi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_201333539_   3236 AACTGATCTTTGACAAAGCGAACAAAAACGTAAAGTGGGGAAAGGACATC 3285
                           i    i  i     i vviv   i v i vv i         i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_201333539_   3286 CTTTTCAACAAATGGTGCTAGGA----TGGCTAGCCACATGTAATGAGAA 3331
                                            i   ----   v  ?       i  -i    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA-AAGAA 445

  chr2_201333539_   3332 TGAAACTGGATCCTCATCTCTGACCTTATACAAAAATTAACTCAAGATGG 3381
                             ii    i  ii i   vv   v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_201333539_   3382 ATTAAGGACTTAAACCTAAGACCTGAAACTATTAAAATTCT-AGAAGATA 3430
                           i ?i   i    iv     v  i       -    i   -      v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAA 544

  chr2_201333539_   3431 ACATTGGA--AAATCCCTTCTAGATATTGGCTTAGGCAAGGATTTCATGA 3478
                             v  ?--     --   vv  iv    v        v i    v ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_201333539_   3479 CCAAGAACTCAAAAGCAAATGCGATAAAAACAAAGATAAATAGCTGGGAG 3528
                         vi v  vvi        v v  i i    iv   i   i   iv v   v
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_201333539_   3529 CTAATTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCCAGCA 3578
                         i v  i   v v  i i      iiivv    i iv  vi   ---  - 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA---AG-A 688

  chr2_201333539_   3579 GAGTAAACAGACATCCCACAGAGTGGGAGAAAATCCTCACAATCTATACA 3628
                         i   i  v     v        i           vi ii   vii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_201333539_   3629 TCTGACAAAGGACTAATATCCATAACCTACAAGAAACTCAAACAAATCAG 3678
                              i  i     vi      v  iv  i  ii     vv    v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_201333539_   3679 TAAGAAAAAAACAAACGACCCCATCAAAAAGTGGGCTAAGGACATGAATA 3728
                            v     i     ii    v  i?    i     v     iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_201333539_   3729 GACAATTCACAAAACAAGATATAGAAATGGCCAACAAAAATATGAAAAAA 3778
                             v   v v   v        v          i  iv i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_201333539_   3779 TGTTCAACATCACTAATGAT 3798
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (132 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.43 (34 / 14)  


3104 26.40 0.88 1.42  chr2_201408284_201412492     2805  3717 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_201408284_   2805 TAGAAAAACTTCTCATGCTCATGGATAGGGAGAATCAATATCATTAAAAT 2854
                          i    i iv  i    i        v  i   v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_201408284_   2855 GGCTATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 2904
                            v     v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_201408284_   2905 TACCAATGACATTCTTCACAGAATTAGGAAAAAAACT-ATTTTAAAATTC 2953
                          v   iivi v  i  ii     v v --- v  i  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_201408284_   2954 ATATAGAATCAAAAAAGAGCCTGAATAGCCAAGGCAATCCTAAGCCAAAA 3003
                             i   viiv  ii  v  v          ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_201408284_   3004 GAACAAAGCTGGACACATCACATTACCCAGCTTCAAGCTGTATTACAGGG 3053
                                 i    vivv     i v    ii     iviv  i    ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_201408284_   3054 CTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGGCACATAGAC 3103
                                  i   i    ii         i i  ii i  i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_201408284_   3104 CAATGGAACAGAAAAGAGAGCCCAGAAATAGGCC-ACACGTCTATGATCA 3152
                                 i    vv     i         ii  - i  i i    i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_201408284_   3153 CCTGATCCTCAACAAAAACTGGAAAAAAAAAGAAATGAGGACAAGACT-- 3200
                         vi    ii  i    iii-  vv  i vv vvv    i   -    v --
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGA-AAGAATAG 395

  chr2_201408284_   3201 -CCCTTCAATAAATAGTGCTGGGATAACTGGCTAGTCATATGCAGAAGAT 3249
                         - ii     i    i         i      v  ?i  i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_201408284_   3250 TTAAACTGGACCCCTTCCTCACACCATACACAAAAATCAATTCAAGATGG 3299
                          v  ii         v            i        i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_201408284_   3300 ATTAAAGACTTAAATATAAAACCCAAAACTATAAAAAGGCAGCCTGGAAG 3349
                           i ?    i     i   i v i            --- -v i i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA---C-TCTTAGAAG 541

  chr2_201408284_   3350 ACAACCTAGGCGCTACCATCCCAGACATAGGAACAGGCAAAGATTTCATG 3399
                          v   v    ? iv viv i vv   v v  ivi      v i    v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_201408284_   3400 ACAAAAACACCAAAAGCAATCA--TAACAAAAGCAAAAATTGACAAGTGG 3447
                         ivv vi            --  --i        v      v  i  i v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_201408284_   3448 TATCTAATTAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAG 3497
                         v ii v  i   v    i i   i  ii vv    i  v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_201408284_   3498 AGTAAACAGACAACCTACAAAATGGGAGAAGATATAGGCAAACTATGCAA 3547
                            i  v        i   i          i    vv     ii  ii v
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_201408284_   3548 CTGACAAAGGTCTAATATCCAGCATCTGTAAGGAACTTAAACAAATTTAC 3597
                             i  i  v  vi       v  v i   i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_201408284_   3598 AAGAGAAAAATAAACAACCTCATTTAAAAAAATGGGCAAATGACATACAC 3647
                           v i   i i   i    iv   ?     --        v  iv iv i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAAT 837

  chr2_201408284_   3648 AGATACTTTTCAAAAGAAGACATACATGTGGCCAACAAGCATATGAAAAA 3697
                            i i  i  v        i     vi       i     i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_201408284_   3698 A-GCTCAATATCATTGATGAT 3717
                          -      i    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (150 / 87)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


3202 25.97 1.55 0.78  chr2_201715658_201719947     2898  3798 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_201715658_   2898 TGGAAGAACATTCCATGTTCATGGACAGGAAGAGTCAATATTGTGAAAAT 2947
                              ii i  i             iv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_201715658_   2948 GGCCATACTACCCAAGGTAATTTATAGATTCAATGCCATCCCCAACAAGC 2997
                            v     v     iv i  i  i        i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_201715658_   2998 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 3045
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_201715658_   3046 ATATGGAACCAAAAATGAGCCCATATTGCCAAGACAATCCTAAGCCAAAA 3095
                                 viiv  iv  v  viv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_201715658_   3096 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 3145
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_201715658_   3146 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 3195
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_201715658_   3196 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAAC 3243
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_201715658_   3244 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAACGGGGAAAGGATTC 3293
                           vi    i  i     ivv  v   i v  vvv  i        i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_201715658_   3294 CCTATTTAATAAATGATGCTGGGAAATCTGGATAGCCAAATGTAGAAAGC 3343
                         i  v  i  i     i        v v       ?   v   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_201715658_   3344 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 3393
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_201715658_   3394 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3443
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_201715658_   3444 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTC------ 3486
                          v    ?i- v i -   iv   v v  vv i     v ii   ------
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_201715658_   3487 ATGAC--TAAAA-CACCAGGCAACATAAGCCAAAATAGACAAATGGGATC 3533
                              --i    -   - i      v   vv        i    v   ii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCAC-AAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_201715658_   3534 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTGTCAGAGTG 3583
                          v  i   v v  i i   i  ii vv    i  v    iiivv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_201715658_   3584 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTAA 3633
                           v  i     i                 v       vii ivi    i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_201715658_   3634 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAGATTTACAAGA 3683
                         i  i  i  vi          v  i        ivv   iv iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_201715658_   3684 AAAAATCAAACAACCCCATCAAAAAGCGGGCAAAGCATATGAACAGACAC 3733
                             iv    i     v  i?    ii        v  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_201715658_   3734 TTCTCAAAAGAAAACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 3783
                              v      i i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_201715658_   3784 ATCATCACTGGTTAT 3798
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (141 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.91 (21 / 11)  


2921 26.67 1.56 0.67  chr2_201858014_201860588     1190  2089 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_201858014_   1190 TGAAAAAACATTCCATTCTCGTGGATAGGAAGAATCAATATCATGAAAAT 1239
                           i   i i  i    vi  i     v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_201858014_   1240 GGCCATACTACCCAAAGTAATTTATAGGTTCATTGCTATTCCCATTAAAC 1289
                            v     v      v i  i  i  i    vi  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_201858014_   1290 TACTATTGACATTCTTCACAGAATTAGAAAAAAACT-ACTTTAAAATTCA 1338
                          v i vivi v  i  ii     v v  v  i--  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_201858014_   1339 AATGGAACCAAAAAAGAGCCCGTATAACCAAGACAACAATAAGCAAAAAG 1388
                         v      viiv  ii  v  v v   i    i    ivv i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_201858014_   1389 AACAAAGCTGGAAGCATCACACTACCCAACTTCAAAGTATACTGCAAGGC 1438
                                i    i vv       v     i      iiv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_201858014_   1439 TACAGTAGCCAAAATGGCATGGTACTGGTACAAAAACAGACACATAGACC 1488
                                ii   i ii ii         i i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_201858014_   1489 AATGGAACAGAATAGAGA--CCAGAGAAAGAAGACCACACATCTACAGCC 1536
                                i     v    --     --  v  iv   i    i  ii i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGA--AATAAACCCATACATTTATGGTC 346

  chr2_201858014_   1537 ATCTGATCATCGACAAACCTGACAAAAACAAGCAATGGGGAAAAGATTCC 1586
                          vi    iv       ivv  v   i v  vv           ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_201858014_   1587 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAATT 1636
                           v  i  i              v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_201858014_   1637 GAAACTG-ACCCCTTCCTTACACCTTATACAAAAATTAACTCAA----GA 1681
                            ii  -      v   i     v                   ----  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_201858014_   1682 TTAAAGACTTAA-TGTAAAACCTAAAACTATAAAAACCCTAGAAGAAAAT 1730
                          i ?    i   -     i v              vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_201858014_   1731 CTA--TTTAATACCATTCAAGACATAGGCACAAGCAAAGGTTTCATGACA 1778
                         v  --?v   - i -   iv   v v  vvi i    v      v iivv
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_201858014_   1779 AAAACATCAAAAGCAATTGCAACAAAAGCAAAAAT-TACAAATGGGATCT 1827
                          vi   i        vvv          v      -v i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_201858014_   1828 AATTAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTATCATTAGAGTGA 1877
                         v  i   v v  i i  ii  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_201858014_   1878 ACAGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTATCCATCTGAC 1927
                          v  i     i              v  v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_201858014_   1928 AAAGGTCTAATATCCAGAACCTACAAGGAACT--TAAAACAAATTTACAA 1975
                           i  v  vi         iv  i  i     --  v   vv v v i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_201858014_   1976 GGAAAAAAACAACCCCATCAAAAAGTGGACAAAGGACATGAACAGACACT 2025
                         ii i v   i     v  i?    i   i       iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_201858014_   2026 TCTCAAAAGAAGACATTTATGTGGCCAACAAACATATAAAAAAAAGCTCA 2075
                             v        i  vi vi       i  i  i  i    i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_201858014_   2076 ACCTTACTGATCAT 2089
                           v i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


 615 16.19 0.95 0.00  chr2_201904740_201906838.rev      554   658 (1441)    L1M4_orf2#LINE/L1        1   106 (802)  

  chr2_201904740_    554 TGGAAAGATATCTCGTGTTCATGGGTTAGAAGAA-TAATCTTGTTAAAAT 602
                                     i i         i  i     v-    v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_201904740_    603 GACCATACTACCCAAGGTGACCTACAGATTTAATGCAGTCCCTATCAAAA 652
                          i v     v     iv   i         i  i   i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_201904740_    653 TACCAG 658
                          v    
  L1M4_orf2#LINE/    101 TCCCAG 106

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.01 (1 / 106), avg. gap size = 1.00 (1 / 1)  

2769 25.73 0.89 1.52  chr2_201904740_201906838.rev      811  1599 (500)    L1M4_orf2#LINE/L1      105   888 (20)  

  chr2_201904740_    811 AATTACATTCTTCACATAAATAGGGAAAAAAACCCTAAAATGTATATGGA 860
                          ii i v  i  ii  v    v iv  ivvi i        vi       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_201904740_    861 ACCACAAAAGACCCCAAATAGTGAAAGCAATGCTGAGCAAAAAGAACAAA 910
                          vii   ii     vi     iv   i    vi   iv  i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_201904740_    911 ACTGGAGGCATCCCACCACCTGACTTCAAAATATACTACAAATCTAGAGT 960
                         ii      vv  v   iv  ii i       iv         v   v   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_201904740_    961 TACCAAAACAGCATGGTAGTGGTATAAAAACAGACACATAGATCAATAGA 1010
                         v i   i    ii     v   i    ii i     i          i  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_201904740_   1011 ACAGAATATAGATCCCAGAAATAAATTCACACACCTACAGCCAACTGATT 1060
                          i     vv   vi           ii  i   ii  ii i   i     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_201904740_   1061 TTTGACAAAGGTGCCCAGAACACACAATAGGTAAAAGAGAATCTCTTCAA 1110
                           i     i      v   v  iv    i  v   ii v i   i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_201904740_   1111 AAAACGGTGCTGGGAAAATTGAATATCCATACACAGAAAAATGAGACTAA 1160
                         v   i          v  i  i   ?   i ii  i  i     iii ii
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_201904740_   1161 CCACTTACCTCTCACCATAAACAAAAACCAACTCAAAATGTGT--AAGAC 1208
                         v v i      v       v       ii           vi --?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_201904740_   1209 TTAAATGTAAAACCTGAAACTATGAAGCTGCTGCAAGAAAACA---GGGC 1255
                         i         i v  i       i  i  vi iv         --- ? i
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_201904740_   1256 AAACATATCATGACATTGGGTTGGGCAAGGATTTTTAAAACAAGACTTCA 1305
                            iv -  i    v       i     v i   i v i i v   vi  
  L1M4_orf2#LINE/    555 AAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_201904740_   1306 AAAGCACAGACAACAAAAGCAAAAATAGACAAATGAGTTTACATCAAA-T 1354
                                 ii         v         i    vi vi v       - 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_201904740_   1355 TAAAACCCTTTTGCACGGCAAAAAAAAAAAAAAAAAAAAAAAAACCGAGG 1404
                              v -     ii vv    ii v vv vv  i   ---------- v
  L1M4_orf2#LINE/    654 TAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAA----------GT 692

  chr2_201904740_   1405 GAAGAGACAACCTACAAAATAGGAAAAAA-ATTTGCAAATTATACATCTC 1453
                            i        i   i   i   i    -          i   i    v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_201904740_   1454 ACAAGGAGTTAATATTTAGAATACATAAGGAACTTAAATAACTCAACAGC 1503
                          i    iii vi   ii      i    i     ivv i       i ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_201904740_   1504 AAAAAAACAAATAACCCCATTTAAAAATGGGCAAAAGACTTTAACAGACA 1553
                              i           v   ?             i  i  v  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_201904740_   1554 TTTCTCAAAAGAAGACATACAAATGGTCCACAGGTATAAGAAAAAA 1599
                               v        i          i v i i i i v     i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.97 (132 / 67)
Gap_init rate = 0.01 (7 / 784), avg. gap size = 2.71 (19 / 7)  


3106 26.79 0.99 0.88  chr2_201980274_201986653     4982  5888 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_201980274_   4982 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAACATCGTGAAAAT 5031
                              ii i  i     i        v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_201980274_   5032 GGCCATAATGCTCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5081
                            v   v v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_201980274_   5082 TACCAATGATTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5129
                          v   iiviii  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_201980274_   5130 TCTGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCA-AAG 5178
                          v     viiv  ii  v  v v  v     iv     i i ivv -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_201980274_   5179 AACAAAGCTGGAGGCATCTCGCTACCTGACTTCAAACTATACTACAAGTC 5228
                                i      vv  v i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_201980274_   5229 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5278
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_201980274_   5279 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCATATATCTACACT- 5325
                                i    i--    i  --        vv     i  i  iiv -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_201980274_   5326 ATCTGATCTTTGACAAATCTGACAAAAACAAGAAATGGGGAAAGGAT--T 5373
                          vi    i  i     ivv  v   i v  vvv           i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_201980274_   5374 CCTTATTTAATAAATGGTGCTTGGAAAACTGGCTAGTCATATGTAGAAAG 5423
                          i  -- i  i          v   v      v  ?i  i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_201980274_   5424 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5473
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_201980274_   5474 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5523
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_201980274_   5524 ATCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5572
                          iv    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_201980274_   5573 TAAAACACCAAAAGCAATGGCAACAAAAGCCTAAATTGGCAAATGGGATC 5622
                           vi            vvi          vvv    v ii    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_201980274_   5623 TAATTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTACCATCAGAGTG 5672
                          v  i   v v  i i      ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_201980274_   5673 AACAAGCAACCTACAGAATGAGAGAAAATTTTTGCAACCTACTCATCTGA 5722
                           v ii     i        i        v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_201980274_   5723 CAAAGGGTTAATATTCCAGAATCTACAATGAACTCAAACAAATTTACAAG 5772
                         i  i  ii vi   -       v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTAT-CCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_201980274_   5773 AAAAAAACAAACAACCCCATGAACAAGTGGGCAAAGGATATGAACAGACA 5822
                              i     i     v  v? v  i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_201980274_   5823 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGTT 5872
                         i     v        i  vi viii     v ii          i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_201980274_   5873 CATCATCACTGGCCAT 5888
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


 802 23.78 7.34 4.55  chr2_201989667_201996074      115   400 (6008)    L1M4_orf2#LINE/L1       27   320 (588)  

  chr2_201989667_    115 TGGATAGATTCAATACTCTTAAGA-ATTAAT-CTCGCCACAGATTGATCT 162
                             -   i i    i v      -ivi   -   -  -  i        
  L1M4_orf2#LINE/     27 TGGA-AGACTTAATATTGTTAAGATGGCAATACTC-CC-CAAATTGATCT 73

  chr2_201989667_    163 TTATATTCAATGAAATCCCAGTCAAAATATCAGCAAACTTCCTTGATAAG 212
                         vi v      i v      vi       vi    viv   ii   v--  
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC--AG 121

  chr2_201989667_    213 CTAATTCTAAATTGACAAGCTAGTTCTAACATTTATGTAAAAATACAAAG 262
                         --------             ii i    v   i  i ii    i   i 
  L1M4_orf2#LINE/    122 --------AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_201989667_    263 CATGTGGAA-AGGCAAAATAATCTTGAAAAACAATAGCAAAGCTAGATAA 311
                         v ivii   -  v     i            v  v i     i i  vi 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_201989667_    312 CCTTTGCTACCCGATTTCAAA-CTT------------CAGTAGTCAAGAC 348
                          iivii  v   i        -   ------------     i       
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_201989667_    349 AATGTGTTGTTGACCTAAGTATGGAAAAATAG-TCAA----ACAGAACGG 393
                          i    v ii  i v    v  i  v v    -    ---- i    iv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_201989667_    394 AGAGTCC 400
                                
  L1M4_orf2#LINE/    314 AGAGTCC 320

Transitions / transversions = 1.72 (43 / 25)
Gap_init rate = 0.04 (12 / 294), avg. gap size = 2.83 (34 / 12)  

3118 27.61 0.55 0.66  chr2_201989667_201996074     5008  5916 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_201989667_   5008 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5057
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_201989667_   5058 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATTAAGC 5107
                            v     v     iv i  i           i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_201989667_   5108 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACTACTTTTATGGTTCA 5156
                          v   iivi i  i  iii    -   -- v  i  iv ii  vii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_201989667_   5157 TTTGGAACCATAAAAGAGCCTGTATTGCCAAGACAATCCTAAGCCAAAAG 5206
                          v     viii  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_201989667_   5207 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5256
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_201989667_   5257 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACATAGATATAGACC 5306
                                 i   i    ii         i iv ii i v v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_201989667_   5307 AATGGAACAGAAC--AGAGCCCTCAAAAATAATACCACGCATCTACAA-C 5353
                                i    i--    i  -- i      vv   ii   i  iii- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_201989667_   5354 AATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGTACTC 5403
                            -    i  i     ivv  v   i v  vvv           v ivv
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_201989667_   5404 CCTATTTAATAAATGGTGCTTGGAAAACTGGCTAGCCATATGTAGAAAGC 5453
                         i  v  i  i          v   v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_201989667_   5454 TGAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGG 5503
                             ii    i    v   i   i v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_201989667_   5504 ATTAAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAGGGAAA 5553
                           i ?    i       v   v       i      vi i    i i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_201989667_   5554 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5602
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_201989667_   5603 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5652
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_201989667_   5653 AAATAATCTAAAGAGCTTCTGCACAGCGAAAGAAACTACCATCAGAGTGA 5702
                         v vi  vv v  i i   i  ii vv i  i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_201989667_   5703 ACATGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5752
                          v vi     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_201989667_   5753 AAAGGGCTAATATCCACAATCTACTAAGAACTTAAACAAATTTACAAGAA 5802
                           i  i  vi      v   v  iv       ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_201989667_   5803 AAAATCAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACT 5852
                            iv    i     v  i? v  i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_201989667_   5853 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACACGAAAAAATGTTCA 5902
                             v        i  vi viii     i ii    i     i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_201989667_   5903 TCATCACTGGCCAT 5916
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2947 25.00 0.42 5.04  chr2_202004218_202010457     3575  4526 (1714)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_202004218_   3575 TGGAAACACATCCCATGCTCACTGATGGGTAGAATCAATATTGTGAAAAA 3624
                               v i        i   iv   v  v   v i        v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_202004218_   3625 GATCATACTGCCAAAAGCAATCTACAAATTTAATGCAATTCCCATCAAAA 3674
                          iiv     v  v   vii       i   i  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_202004218_   3675 TACCACCATCGTTTTTCACAGAACTAGAAAAAAAACTCCTTAAATCCATA 3724
                          v   v vv v     ii     v v  v  ivviv    v    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_202004218_   3725 TGGAACCAAAAAAGAACCCACATAGCCAAAGCAAGACTAAGCAAAACAAA 3774
                              viiv  ii  v  viv         i   vvi i ----------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---------- 190

  chr2_202004218_   3775 ACAAAGCAAAACAAGCAAACAAAAAATCAAAAAGCAAAAAACCTAACAAA 3824
                         -------    v   -----------------------------      
  L1M4_orf2#LINE/    191 -------AAAAGAAG-----------------------------AACAAA 204

  chr2_202004218_   3825 TCTGGAGGCATCACATTACCTGATTTCAAACTATATTATATGGCCATAGT 3874
                         vi      vv     i v  ii        viv  i  i vi  i i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_202004218_   3875 CACCAAAACACCATGGTACTGGTATAAATATAGGCACATAGACCAATGGA 3924
                         v i   i   vii         i    iv    i  i     i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_202004218_   3925 ACAGAACAGTGAACTCAGAAATAAACCCAAATACTTACAGCCAACTGATC 3974
                          i    iv v  iii              v i i   ii i   i    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_202004218_   3975 TTTGACTAAGCAAACACAAATATAAAGTGGGGAAAGCACA-TCTTATTCA 4023
                           i   v i vviv  vi vi  vv i         v i -    -    
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-TTCA 403

  chr2_202004218_   4024 ACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAAACTG 4073
                                         i  i   v  ?       i ii        ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_202004218_   4074 GATCCTCATCTCTCATCTTACACAAAAATAAACTCAAGATGGATCAAGGA 4123
                           i  ii i   v  i v  i        v       i        ?i  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_202004218_   4124 CTTAAATCTAAGACCTGAAAATATAAAAATTCTAGAAGATAACATCAGAA 4173
                          i     v     v  i   v       v ii       v     vi ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_202004218_   4174 AAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATTACCAAGAACAC- 4222
                         v  vi    vv   v    v        v i    -   vvv vi    -
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGACACC 602

  chr2_202004218_   4223 AAAAGCAAATGTAATAAAAACAAAGATAAATGGCTGGGACTTAATTAAAC 4272
                                v v i  i    iv   i   i  iiv v      v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_202004218_   4273 TAAAGAGCTTTTGCATGGCAAAAAGAACAGTCATCAGAGCAAACAGACAA 4322
                          v  i i      iiivv    iiiv  vi   vv i  ii  v      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_202004218_   4323 CCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGGACT 4372
                                 i           v  ii   vii   i      i  i     
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_202004218_   4373 AATATCCAGAATCTACAACAAACTAAAACAAATTAGCAAGAAAAA-ACAA 4421
                         vi          v  i  vi    vvv    v i ii  v     -    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_202004218_   4422 ATAACCCA-TCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCAAAA 4470
                                 - i?    i     v     iv          v     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_202004218_   4471 GAAGATATACAAATGGCCAACAAACATATGAAAAAGTGCTCAACATCACT 4520
                                             i  i  i       ii            ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_202004218_   4521 AATGAT 4526
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.27 (131 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 6.50 (52 / 8)  

1952 29.19 1.28 0.16  chr2_202004218_202010457     5114  5740 (500)    L1M4_orf2#LINE/L1      226   859 (49)  

  chr2_202004218_   5114 AATTTAAAAA---AATATAAGGCTACAGTAACCAAAACAGCTTGGTACTG 5160
                              v    --- v  i  i          i   i    iv        
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_202004218_   5161 ATACAAAAACAGACACATAGATCAATGGAACAGAATAGCAAACTCAGAAA 5210
                         ii i  ii i     i              i     v vi iii      
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_202004218_   5211 TAAAGCTGCACACCTACATCCATCTGATCTTCAACAAAGTAGACAAAAAC 5260
                             v iii   ii  iivi  vi    i   i    i vv v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_202004218_   5261 AAGTGGTGGGGAAGGAGTTCCCTATTCAATAAATGATGCTGGGATAGCTG 5310
                          vviii       i  i vvi  v     i     i        i i   
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_202004218_   5311 GCTAGCCATATGCAGAAAAATAAAACTGGGCCCCTACCTTTCACCATATA 5360
                          v  ?   i     i  i   i  ii   i         iv         
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_202004218_   5361 CAAAAATCAACCCAAGATGCCTTAAAGATTTAAACATAAGAACTCAAACT 5410
                                i   i   i   vv i ?   ii    ii     i  v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_202004218_   5411 CTAAGAATCCTAGAAGAAAACCTAGGAA-ACACCATTCTGAACACTGGCC 5459
                         v   i v  i           v    ?i- v i -   vvi  vi   vi
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT 574

  chr2_202004218_   5460 TTGGGAAAGAATTTATGACTAAGTCCTCAAAAGCAACTGCAACAAAAACA 5509
                          v  v  v iv  iv iiv  v v vi        vvv         iv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_202004218_   5510 AAAATTGACAAGTGGGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 5559
                              v  i  i v    i v  i   v v  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr2_202004218_   5560 AAAACCCGTCAACAAAGTAAACAGGCAACCTACAAAAAAAGAGAAAATAT 5609
                         ii vv ii    v     i  v  i     i   i  vii          
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_202004218_   5610 TCACAAACTACGCATCTGACAAATATCTAATATCCAGAATCTATAAGTAA 5659
                          ii    ii iii      i  iviv  vi          v     iv  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_202004218_   5660 CTTAAACAATTGAACAAGCAAAAAACAA----CCCCATTAAAAAGTGGGC 5705
                           ivv    i v  i  vv    i    ----   v   ?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_202004218_   5706 AAAAGACATGAACAGACACTTCTCAAAAGAAGACA 5740
                            i  iv    i     i     v        i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

Transitions / transversions = 1.63 (111 / 68)
Gap_init rate = 0.01 (4 / 634), avg. gap size = 2.25 (9 / 4)  


3305 24.72 1.78 0.67  chr2_202012365_202018300     4547  5444 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_202012365_   4547 TGGAAATGCATTCTATGCTCATGGATTGGAAGAATCAACGTTGTGAAAAT 4596
                               vii  i i   i               v i  ii    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_202012365_   4597 GACCATACTGCCCAAAGTAATCTTGCATTACAGATCCAGTGCAATTCCCA 4646
                          i v     v      v i    ------      i  ii     i  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCT------ACAGATTCAACGCAATCCCTA 94

  chr2_202012365_   4647 TCAAAATATCAACATTATTTTTCACAGAATTAGAAAAAAAG-TTCTAAAA 4695
                                vi  i vviv     ii     v v  v  ivv - i      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_202012365_   4696 TTCATATGGAACCAAAAAAGAGCCAGAATAGCCAAAGCAATACTAAGCAA 4745
                                    viiv  ii  v              i    vi i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_202012365_   4746 AAAGAACAAATCTGGAGGTATCACATTACTAGACTTCAGATTATACTACA 4795
                         i         vi      vv     i v ivi i    i viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_202012365_   4796 AGGCTATAGTTACCAAAACAGCATGGTACTGGTATAAAAGTAGGCACATA 4845
                          i    i   v i   i    ii         i    iii   i  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_202012365_   4846 GGCCAAGGAAACAGAACAGAAAACCCAGAAATGAAGCCAAATATGTATAG 4895
                          ii   v i  i    iv  i ii        i  v   v i  v   i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_202012365_   4896 CCAACTTATCTTTGACAAAGCAAACAAAAACATAAATTGGGGAATGA-TA 4944
                         i   i v  i  i     i vviv   i v   vv v       v  -  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_202012365_   4945 CTTTATTTAATAAGTGGTGCTGGGAGAATGGGCAAGCCACATGTAGAAAA 4994
                         v i v  i  i  i           v  iv  vv ?       i i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_202012365_   4995 ATGAAACTGGATCCATATTTCTCACCTTATACAAAAATCAACTCAAGATG 5044
                              ii    i  v  ii  v    v           i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_202012365_   5045 GATCAAAGACTTAAATATGAGACCCGAAACTATAAAAATTCTAGAAGA-- 5092
                              ?    i     i i   v ii           v ii       --
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_202012365_   5093 -CATTAGAAAAACTCTTCCAGTCATTGGCTTAGGCAAATAATTCATGACT 5141
                         -   vi ?iv  v     vv v v    v        vviv   v iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_202012365_   5142 AAGACCCCAAAAGCAAATGCAACAAAACCAAAAATAAATAAATAGAACCT 5191
                          v   v         v v         vv       i      v i  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_202012365_   5192 AATTAAACTAAAAAGCTTCTGTACAGCAAAAGA-------AATAA--TAA 5232
                         v  i   v v    i   i   i vv    i  -------  v  -- i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_202012365_   5233 ACAGACAACCCACAGAATGGGAGAAAATATTTGCAAACTATGCATCTGAC 5282
                          v                                   ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_202012365_   5283 AAAGGACTAGTAATCAAAATCTACAAGGAATTCAAACAAATCAGCAAGAA 5332
                           i     v   vi  i   v  i  i   i  vv    v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_202012365_   5333 AAAAACAAATAATCCCATTAAAAAGTGGGCAAATGACATGAATAGATATT 5382
                            i        i  v   ?    i        v  iv        i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_202012365_   5383 TCTCAAAAGAAGATATACAAATGGCCAACAA--ACATGAAAAAGTGCTCA 5430
                             v                       i  --         ii      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_202012365_   5431 ATATCACTAATCAT 5444
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (127 / 91)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.14 (22 / 7)  


 683 23.38 11.69 3.46  chr2_202026628_202030479.rev     2203  2433 (1419)    L1M4_orf2#LINE/L1        1   250 (658)  

  chr2_202026628_   2203 TGGAAAGACATTTCACCCATGCTTATGGACTGGAAGAATTAAGATCGCCA 2252
                                 i  ----      i i     i       v    v  i ii 
  L1M4_orf2#LINE/      1 TGGAAAGATAT----CCCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chr2_202026628_   2253 AAATGGCCATGCTGCCCAA------------------TGCAATCCCTA-- 2282
                          i     v  i  v     ------------------i          --
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_202026628_   2283 -AATTACCAA-TGTCACTTTTCACAGAAATAGAAAAAATAATTCTAAAGT 2330
                         -  v v   i-  i -i    ii       v  v  iv i  i     i 
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_202026628_   2331 TCATATGGAA---CAAAAGATGAGCCAGAATAGCCAAAGCAATCCTGTGG 2377
                                   ---   ii  i---              i     i  vii
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_202026628_   2378 G-GAAAAA-AAATCTGGAGTTATCACATTACCTGACTTCAAAATATATTA 2425
                         i-   i  -   vi     vvv     i v  ii i       iv  i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_202026628_   2426 CAAGACCA 2433
                            ii i 
  L1M4_orf2#LINE/    243 CAAAGCTA 250

Transitions / transversions = 2.38 (38 / 16)
Gap_init rate = 0.04 (9 / 250), avg. gap size = 3.89 (35 / 9)  

2148 23.52 5.61 4.55  chr2_202026628_202030479.rev     2702  3360 (492)    L1M4_orf2#LINE/L1      243   908 (0)  

  chr2_202026628_   2702 CAAGGCTATCATAACCAAAATGGCAAGGTATTAGTATAAAAATAGACATA 2751
                            i    ivi   i   i ii iiv    i i i    ii         
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_202026628_   2752 TAAA-CATAAAGCATGGAACAGAATAGAGAATCCAGAAATAAATTCATGT 2800
                           i -  ------      i     v    i            ii   ii
  L1M4_orf2#LINE/    293 TAGATCA------ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_202026628_   2801 AATTACAGCCAACTGATCTTTGACAATGCTGTCAAGAACATACACTGGGA 2850
                          v   ii i   i    i  i     v v  i     v   v  v    i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_202026628_   2851 ACAGGGCACCCTCTTCAATAAATGATGCTGGGAAAACTGAATAACCATAT 2900
                          v  iii vi  i     i     i        v     i   ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_202026628_   2901 GCAGAAGGGTGAAACTAGACCCCTATCTCTCATCATGTACAAAAATGAAC 2950
                            i   ii    ii i        i   v  i   i         v   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_202026628_   2951 TCAAGATGGATTAAAGTCTTAAATGTAAGATCCAAAGCTATAAAAATACT 3000
                             i      i ?  v i           v i   i        v vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_202026628_   3001 AGAAGAAAACCTAGGGAAAAGTCTTCAGGACATCGGTCTAGGCAAAGATT 3050
                                   v    ?iv  i     iv   v i  vi       v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_202026628_   3051 TTATGACCAAGACTTTGAAAGCACAGGCAACAAAAACAAAAAAAGACAAA 3100
                          iv iivi v   viii        i         iv     v   i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_202026628_   3101 TGAGACTATATTAAACTAAAAAGCTTCTACACG-CAAAAGAAACCATCAA 3149
                          vi    vi  i   v v    i   i iii v-    i  v  i     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_202026628_   3150 CAGAGTGAAGAGACATTCTCTTAAATGGGAGAAAATATTTGCAAACTACT 3199
                         v i      i     vi ivivi                      ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_202026628_   3200 CATTTGACAGAGGACT------CAAA------------------CAATTC 3225
                         i  i   i ii     ------  i ------------------   i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_202026628_   3226 AACAGTAAAACAAACACA-AATTCA--TTAAAAATGGGTAAAGGACATCT 3272
                           i i     - i   v -  ii  -- ?         i      ---- 
  L1M4_orf2#LINE/    787 AATAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGA----T 831

  chr2_202026628_   3273 TTCTTAAAAGACATTTCTTAAAAGAAGACATTTCTTAAAAGAAGACATAC 3322
                           -------  -  -----------          iv        i    
  L1M4_orf2#LINE/    832 TT-------GA-AT-----------AGACATTTCTCCAAAGAAGATATAC 862

  chr2_202026628_   3323 GAATAGCCAACAAGTA--TG------TGTTCAACATCACTAATCAT 3360
                         i   i     i   i --  ------  i         ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.51 (108 / 43)
Gap_init rate = 0.02 (14 / 666), avg. gap size = 4.79 (67 / 14)  


2438 25.34 12.18 0.49  chr2_202054499_202065760     4133  4945 (6317)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_202054499_   4133 TGGAAAAATATTTTATGATAATGGATAGGAATACTCAATATCATTACAAT 4182
                               i    iii   v v      v    v   i     ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_202054499_   4183 GGCCATACTGCCCCAAAC-AATGTACAGAGTGAAAACTATTCTTATCAAA 4231
                            v     -       i-i  v      v v  vi v  i i       
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_202054499_   4232 CTACCAATATCATTTTTCACAGAACTAGAAAAAAAGCATTCTAAAATTCA 4281
                         v v   iivv v     ii     v v  v  ivv -  i          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCA 148

  chr2_202054499_   4282 TATGGAATCAAAAAGGAGCCTAAATAGCCAAAGCAATCCTAAGCAAAAAG 4331
                                viiv  i   v  vi          i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_202054499_   4332 AGAAAAGCTGGAGGCATCTCATTACCTGACTTCAAACTACACTACAAAGC 4381
                          iv    i      vv  v  i v  ii i      vivi          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_202054499_   4382 TACAGTAACCAAAATGGCATTGTATTGGTACAA----AAACATA--GATC 4425
                                 i   i ii ii v   i   i i  ---- i     --    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_202054499_   4426 AGTGAAACAGAATACCGAATCCAGAAATAAAGCCACACACCTACAGCCAT 4475
                          i  i  i     vvv  i            v   i   ii  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_202054499_   4476 TTGATCTTTGACAAAGTCAACAAAAATAAGCAGTGGGAAAAGGACTCCCT 4525
                              i  i     i viiv   i vi vv  i    i    i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_202054499_   4526 ATTCAATAAATGGTGTTGGGACAGCTGGCCAGCCATATGCAGAAGAATGA 4575
                         v     i        i       i    vi ?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_202054499_   4576 AACTGGACCCTTACCTTTCACCATATATAAAAATCAA----AGATGGATT 4621
                          ii       i     iv         i      i  ---- i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_202054499_   4622 AATGATTTAAATATAAGACCTCAAACTGTAAGAATCCTAGAAGAAACC-T 4670
                          ?v  ii     i     v  v     i   i v  i         v - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_202054499_   4671 AGG---AAA----CATTATTTTGGACATGGGC--------CTTGG----- 4700
                            ---   ---- i v ii    ii- i   --------   i -----
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chr2_202054499_   4701 ------------------------GAAAGAATTTAT------GACT---- 4716
                         ------------------------    i   vv  ------    ----
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_202054499_   4717 ---------AAGC-------CCTC---------------GATAGTAAACA 4735
                         ---------  i ------- i  ---------------  v   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_202054499_   4736 GACAACCTATATAATGTGAGAAAATTATTTGCAAACTATGCATCTGACAA 4785
                                i i v    v        -         ii  ii      i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAAT-ATTTGCAAATCATATATCTGATAA 746

  chr2_202054499_   4786 AGGTCTAATATCCAGGATCTATAAGGAACTTAAACAACTGAATGGGCAAA 4835
                         i  v  vi       i  v     i     ivv      v   iivv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_202054499_   4836 AACTTAATAAACCCATTTAAAAATGGTCAAAACACATGAACAAACACTTC 4885
                          iviv     v  v   ?        v    iv iv    i i   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_202054499_   4886 TCAAAAGAAAACATACAAGTGGACAACAA--ACATGAAAAAATGCTCAAC 4933
                           v      i i      i   v   i  --         i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_202054499_   4934 ATCACTAATCGT 4945
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (125 / 78)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 5.72 (103 / 18)  

3028 26.96 1.10 0.77  chr2_202054499_202065760     9863 10767 (495)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_202054499_   9863 TGGAAAAACGTTCCATGCTCATGGATAGGAAGAATCAATACCGTGAAAAT 9912
                               i ii i     i        v      v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_202054499_   9913 GGCCATACTGCCCAAAGTAATTTATAGATTTGATGCTATCCCCATCAAGC 9962
                            v     v      v i  i  i     ii i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_202054499_   9963 TACCA-CTGACTTCCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTC 10009
                          v   -   v   ii  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_202054499_  10010 ATACGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAAAA 10059
                            i    viiv  ii  v  v v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_202054499_  10060 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGA 10109
                                 i      vv    i  v  ii i      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_202054499_  10110 CTACAGTAACGAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 10159
                                  iv  i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_202054499_  10160 CAAGGGAACAGAAC--AGAGCCCTCAGAATTAACACCACACATCTACAGC 10207
                            v    i    i--    i  --    v   vv   i    i  ii i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_202054499_  10208 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 10257
                           vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_202054499_  10258 CCTATTTAATAAAATGGTGCTGGGGAAACTGGCTAGCCATATGCAGAAAG 10307
                         i  v  i  i   -          iv      v  ?   i     i  ii
  L1M4_orf2#LINE/    396 TCTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_202054499_  10308 CTGAAACTGTATCCCTTCCTTACACCTCATACAAAAATTAACTCAAGATG 10357
                         v    ii  v i    v   i     vi                  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_202054499_  10358 GATTAAAGACTTAAACATAAGCCCTAAAACCATAAAAACCCTACAAGAAA 10407
                            i ?    i    ii    vv       i      vi i  v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_202054499_  10408 ACCTAGGCA-ATACCATTTAGAACATAGGCATGGGCAAAGACTTCATGAC 10456
                           v    ?i- v i -  iivi  v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_202054499_  10457 TAAAACACCAAAAGCAATGGCAGCAAAAGTCAAAATAGACAAATGGGATC 10506
                           vi            vvi   i      vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_202054499_  10507 TAATTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGAG 10556
                          v  i   v v  i i   i  ii vv v  i  v    i  vv i  v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_202054499_  10557 AACAGGCAACCTAGAGAATGAGAGAAAATTTTTGCAATCTATCCATCTGA 10606
                           v  i     i v      i        v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_202054499_  10607 CAAAGGGCTAATATCCAGACTCTACAAAGAACTTAAAAAAATTTACAACA 10656
                         i  i  i  vi        v v  i        ivv v  v iv i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_202054499_  10657 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 10706
                             i     i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_202054499_  10707 TTCTCAAAAGAAGGCATTTATGCAGCCAGCAAACATATGAAAAAA----A 10752
                              v       ii  vi viii    ii  i  i       i ----v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_202054499_  10753 AACCTCATCACTGGT 10767
                            v   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


3012 24.26 2.09 1.98  chr2_202213218_202220743     4284  5190 (2336)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_202213218_   4284 TGGTAAAATATTCCATGCTCATGGAGAGGAAGAATTAATATTGTTAAAAT 4333
                            v  i    i     i       vv      v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_202213218_   4334 AGCCATACTGCCCCAAGAAATTTATAGATCCAATACTATTCCTACCAAAC 4383
                         i  v     v   v  vvi  i  i    i   ii v  i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_202213218_   4384 CACCAATGACATTCTTTGCAGAATTAGAAAAAAGCT-ATTCTAAAATTCA 4432
                         iv   iivi v  i         v v  v  --   -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr2_202213218_   4433 TATGGA---GCCAAAAAGAGCCAAAATAGTCAAAGCAATCTTAAGCAGAA 4479
                               ---  --  ii  v   i     i    i       i iv ii 
  L1M4_orf2#LINE/    149 TATGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_202213218_   4480 AGAACAAAGCTGGAGGCATCACACTACCCAACTTCAAA--CTACAGTACA 4527
                                  i      vv       v     i      --i   --    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACA 244

  chr2_202213218_   4528 AGGTTACAGTAACCAAAACAGCATGGTATTGGTACAAAAACAGACACATA 4577
                          i i        i   i    ii     i   i i  ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_202213218_   4578 GACCAATGGAACAGAATGGTGAACCCAGAAATAAAGCCACACACCTACAT 4627
                           i        i     v v  ii           v   i   ii  iiv
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_202213218_   4628 CCATCTGATTTTTGACAAAGTCGACAATAACAAGCAGTGGGAAAGGCACT 4677
                         i  vi       i     i vi v   v v  vv  i    i  i v iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_202213218_   4678 CCCCACTCAATAAATGGTGCTAGGATAACTTGCTAGCCACATGCAGAAGA 4727
                         vi ivi    i          i   i    v v  ?         i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_202213218_   4728 TTAAAAC-AGACCCCTTCCTTTCACCATCTACCAAAATCAACTCAAGTTA 4776
                         v i  ii-i       v   iv      v   v     i       iv i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_202213218_   4777 GATTAAAGACTTAAATGGAAAACCTAAAACTATAAAAACCCTAGAAGGAA 4826
                            i ?    i      v  i v              vi i      i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_202213218_   4827 ACCTAGGAA-ACACCATTCTGGACATAGACCCTGGAAAAGATTT---AAT 4872
                           v    ?i- v i -   vv   v v iviiv  v  v i   --- iv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_202213218_   4873 TATGAAGACTCCAAAA--ACAATTGCAACAAAAATAAAAATTGACAAGTA 4920
                              --- v      --    --         iv      v  i  i v
  L1M4_orf2#LINE/    594 TATGA---CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATT 638

  chr2_202213218_   4921 GGACCTAATAAAAACTAAAGAGCTTCTGCACAGCAGAAGAAACTATCAAC 4970
                             i v  v    i    i -   i  ii vv  i i  v        v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_202213218_   4971 AGAGTAAACAGACAACTTAAAGAATGGGAGAAAATATTTGCAAACTACAC 5020
                          i   i  v       ii v                        ii i i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_202213218_   5021 TTCTGAAAAAAGTCTAATATCCAGAATCTATAAGGAACTTGAATCAACAA 5070
                         v     v  ii v  vi          v     i     ivv -    --
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAAC-- 784

  chr2_202213218_   5071 GCAAAAAGCGAAAAAAAAAAAAAAC---ATTAAAAAGTGGGCAAAGGACA 5117
                         v   v  v--     i v   v   ---   ?    i           iv
  L1M4_orf2#LINE/    785 TCAATAAT--AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_202213218_   5118 TGAACAGACACCTATC---AAAAGATATATACACCACCAATAAACGTATG 5164
                             i     ii v  --- i        i v ivi       i ii   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_202213218_   5165 AAAATATGCTCAACATTACTCATCAT 5190
                             v           i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (128 / 88)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.95 (37 / 19)  

3158 24.78 1.75 2.19  chr2_202213218_202220743     6124  7035 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_202213218_   6124 TGGAAAGATAGACCATATTCATGAATTGTAAGAATTAATATTTTTAAAAC 6173
                                   vv    i      i    v    v        v    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_202213218_   6174 ATCCATACTACCCAATGCAGTCTACAGATTCAATCCAATTCCCACTAAAA 6223
                         iv v     v     vviii             iv    i  i ii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_202213218_   6224 CTCCAA-TGTCATTTTTCACAGAAATAGAAAAAATAATCCTAAAACCCAT 6272
                         ii   i-  i -     ii       v  v  iv i         ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_202213218_   6273 ATGGAACCATAAAATACCCCAAACAGCCAAAGCAATCTCGAGCAAAAAGA 6322
                               viii  iiv    vi  i       i      i  iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_202213218_   6323 ACAAAGCTAGATGCATCACAACTCCCTGGTTTCAAATTATGTTATAAAGC 6372
                               i i  v vv     -  i  iii       viv ii  i     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACA-CTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_202213218_   6373 TATTGTAATAAAAACAGCATGGCACTGGCACAA----AGACACATAAACC 6418
                           iv     v  i    ii   i       i  ----     i   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_202213218_   6419 AATGGAACAGG-TAGACAACCCAGTAATAAACCCAAGTATTCAGTATTTA 6467
                                i  i- v  v ii    v          --  i-----     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TAC-----ATTTA 341

  chr2_202213218_   6468 TAATTAGTTGATATTTGACAAAGATGCCAAAAACA--CAAAAGGGAAAGA 6515
                          ii i i     v  i     i i      i v  --   vi        
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_202213218_   6516 ACAGACTCTTTAATAAATGATGTTGGGAAAAATAGATATGGCC-----CA 6560
                          i  v  i  i  i     i  i     v  v i    --?  -----  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA--KCCACATGCA 439

  chr2_202213218_   6561 GAAGA-TAAAATTGGACACTTATCTCACACCATACACAAAAATCATCTCA 6609
                         i    - i  i      v i  i           i        i v    
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_202213218_   6610 AAATGTATAAAAGACTTATATGTAAGATGTGGAAATGTGGAATTGTAAAG 6659
                              v  v ?    i  v        - i------- ii  i i    i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGA-GC-------TAAAACTATAAAA 531

  chr2_202213218_   6660 TTAATAGAGGAAAACATAAGGGAAAATCTCCACAATACTGGTCTATGCAA 6709
                         i vv    i         i ? v      i iii ivi   vi  v    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_202213218_   6710 TGATTTCTTGGATAGGACTCCAAAAATGCAGGCACGAAAAGCAAAAATAA 6759
                           i      i    v   v      iii  i   vv     v       -
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA- 630

  chr2_202213218_   6760 GACAAATGGAGTTGCATCAAA-TCAAAAGCTTCTGTACAGAAAAGGAAAC 6808
                           i    v iii v       - i    i   i   i vvv      v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_202213218_   6809 AATGAACAGAGTGAAGAGACAAAACATGAACTGGAAGAAAATATCTGCAA 6858
                         v  v  v i      i      vv  iii v   i         i     
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_202213218_   6859 ACCATACAGCTGATAAGGGGCTAATATTCAAAATATATAAGGTACACAAA 6908
                          i    i v          i  vi   i  i         i v  v vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_202213218_   6909 CAACCCAAAAGCAAGAAAACAAATAACCTAATTTTAAAATGGGCAAAGGA 6958
                             i   v ii  i  i          i    ?v               
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_202213218_   6959 ACTGAACAGACATGGCTCAAAGGAAGACATATGAAAGGCCAATAGATATA 7008
                         vi    i      vv   v  i     i   ii  v        iii i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_202213218_   7009 CTAAAA-ATACTCAATATCTCTGATCAT 7035
                         iv    -  i     i   v????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (145 / 77)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.25 (36 / 16)  


3842 21.63 2.12 1.00  chr2_202232339_202234537.rev      811  1707 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_202232339_    811 GGAAAAATATCCTGTGTTCATGAGTTTGAAGATTTAATACTCTGAAAAAT 860
                              i      ii        ii  v     i      i v v  i - 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-T 50

  chr2_202232339_    861 GTTCATACTACCCAAAGCAATCTACAGATTCAGTGCAATCTCTATCAAAA 910
                          viv     v      vii             ii      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_202232339_    911 TTCTAATGGTGTTTTTCACAGAAGTAGAAAAAGCAATCCTAAAATTTATG 960
                          i i iiv iv     ii     i v  v  ivii           i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_202232339_    961 TGGAACCACAGAGGACTCTGGATAGTCAAAACAGTCTTGAGAAAGAAGAA 1010
                              vii  ii    i v i    i       i      i         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_202232339_   1011 CG----TGGAGGTATCACACGTTCTGATTTCAAAATGTATTACAAAACTA 1056
                          i----      vv      v i ii         iv  i      i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_202232339_   1057 TAGCAATTAAAATAGCATGG-ACTGGCATAAAGATAAACATATAGATCAA 1105
                         i  i   i  i i  ii   -          i    i             
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_202232339_   1106 TAGAATAGAAGAGAGAGCCTAGAAATAAACCCATGCAAATGTGATGAACT 1155
                          i        vv     i i              i  vv i  i v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_202232339_   1156 GATCTTTGAGAAGTGTGCCAAGAATACACACAATGAGGAAAGAATAGTCT 1205
                            i  i  v   v         v--  iv     i              
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGAC--CATTCAATGGGGAAAGAATAGTCT 398

  chr2_202232339_   1206 TTTCAGCAAATGGTGTTGGGAAAACTGGATATTCACATGCAAAAGAATTG 1255
                              i         i     v         ?i               - 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT-G 447

  chr2_202232339_   1256 AAATTAGACTTTTGCTTAACACCATAAACAAAAATCAATTCTCAATGGAT 1305
                           i  i   iii i i v        v        i  i  vv       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_202232339_   1306 TAATGACTTAAATGTAAGACTGGAAACTGTAAAACTCCTAGAAGAAAACA 1355
                         i ?v   i           vivi     i        i            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_202232339_   1356 TAGGGGAAAATCTCATTGACACTGGTGTT-GGCAATGATTTATTGGATAA 1404
                             ? v      ivv    vi   -   -       i   v  i    v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATAT 596

  chr2_202232339_   1405 GACACCAAAGGCACAGGCAACAAAAACAAAAACAGACAG-TGGGGCTATA 1453
                                  i     i         iv     i   i i- v  i  vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_202232339_   1454 TCAAA-TTAAAAAGCTTCTACACAGTAAAGGAAAC----AACAGAGTGAA 1498
                              -       -   i iii vvi      v  ----  v i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_202232339_   1499 GAGGAAACCTACAGAATGGGGGAATATATTTGTAAACCATATATTTGTTA 1548
                         i  iv    i          i   v       i   i       i  v  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_202232339_   1549 AAGGGCTAATATTCCAAAACATATAAGGAAACTTTT-CAACTCAATAGCA 1597
                          i  i  vi   -   i  i      i   -  i  -          ii 
  L1M4_orf2#LINE/    746 AGGGACTTGTAT-CCAGAATATATAAAGAA-CTCTTACAACTCAATAATA 793

  chr2_202232339_   1598 AAAAAATAAATAA----AT-AAAAAATGGACTGAGCACTTGAATACATAT 1642
                             i i      ----  -?        i vi  v i       v i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_202232339_   1643 TTATCCAAAGAAGACATTACAAGTGTCCAATGGGTATACAAAAAC-TGTT 1691
                           v           i  -    i  v     ii i i ii    v-  i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATAT-ACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_202232339_   1692 TATCATCATTAATCAT 1707
                         i v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.22 (131 / 59)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 1.56 (28 / 18)  


 314 23.53 3.53 0.00  chr2_202280466_202286475.rev      413   497 (5513)  C L1M4_orf2#LINE/L1   (0)   908   821  

C chr2_202280466_    497 GGGCACAGA---CAAACGGATACTTTTCAAAAGAAGACACACATGTGGCC 451
                              v  i---ii  ii  i i  i  v        i i   vi     
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

C chr2_202280466_    450 AACAATCATGTGAAAAAAAGCTCAACATCACTGATCAT 413
                           i  v  ii      i v           ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (15 / 5)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 3.00 (3 / 1)  

3207 26.71 0.88 0.66  chr2_202280466_202286475.rev     4613  5518 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_202280466_   4613 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4662
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_202280466_   4663 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4712
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_202280466_   4713 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 4760
                          v   iivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_202280466_   4761 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4810
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_202280466_   4811 AACAAAGCTGGAGGCATCACACTACCTGACTTCGAACTATACTACAAGAC 4860
                                i      vv       v  ii i   i  viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_202280466_   4861 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAAGAGAGATATAGATC 4910
                                 i   i    ii         i iv ii v   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_202280466_   4911 AATGGAACAGAGC--AGAGCCCTTAGAAATAACGCCACATATCTACAACT 4958
                                i   ii--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_202280466_   4959 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5008
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_202280466_   5009 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5058
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_202280466_   5059 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5108
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_202280466_   5109 TTAAAGACTTAAAACGTTAGACCTAAAATCATAAAAACCCTGGAAGAAAA 5158
                          i ?    i    -i  v   v      ii      vi i i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_202280466_   5159 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5208
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_202280466_   5209 AAACACCAAAAGCAATGGCAACAAAAGCCTAAATTGACAAATGGGATCTA 5258
                         vi            vvi          vvv    v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_202280466_   5259 ATTAAACTAAAGAGCTTCTTGCACAGCAAAAGAAACTACCATCAGAGTGA 5308
                           i   v v  i i   -   ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTT-TTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_202280466_   5309 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5358
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_202280466_   5359 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5408
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_202280466_   5409 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5454
                            i    ----   v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_202280466_   5455 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACTTGAAAAAATGCTCT 5504
                             v        i  vi viii     v  i   v      i      v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_202280466_   5505 CCATCACTGGCCAT 5518
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3250 27.67 0.22 0.11  chr2_202302329_202308699     4973  5879 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_202302329_   4973 TGGAAAAACATTACATGCTCATGGATAGGAAGACTCAATATTGTGAAAAT 5022
                               i i  iv    i        v        i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_202302329_   5023 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5072
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_202302329_   5073 TACCAATGACTTTCTTCACAGAATTGGAAAAAAT-ACTTTAAAGTTCATA 5121
                          v   iivi i  i  ii     v v  v  iv - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_202302329_   5122 TGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAGAA 5171
                              viiv  ii  v  viv  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_202302329_   5172 CAAAGCTGGAGGCATCATGCTTTCTGACTTCGAACTATACTACAAGGCTA 5221
                              i      vv   ii   i ii i   i  viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_202302329_   5222 CAGTAACCAAAACATCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5271
                               i   i   vii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_202302329_   5272 TGGAACAGAATAGAGCCCCCGGAAATAATACCACACATCTACAACCATCC 5321
                              i     v   vvi  i       vv   i    i  iiii  vii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_202302329_   5322 GATCTTTGACAAACCTGACATAAACAAGAAATGGGGAAAGGATTCTCTAT 5371
                            i  i     ivv  v  vi v  vvv           i  vv   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_202302329_   5372 TTAATAAATGGTGTTGGGAAAACTGGCTCGCCATACGTAGAAAGCTGAAA 5421
                          i  i        i     v      v v?   i i i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_202302329_   5422 CTGGATCCCTTCCTTACGCCTTATACAAAAATTAATTCAAGATGGATTAA 5471
                         i    i    v   i  i  v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_202302329_   5472 AGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5521
                             i       v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_202302329_   5522 CCA-ATACCATTCAGGATATAGGCATGGCCAAGGACTTCATGACTAAAAC 5570
                         v?i- v i -   iv  iv v  vv i v   v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_202302329_   5571 ACCAAAAGCAATGGCAACCAAAGCCAAAATCGACAAATGGGATCTAGTTA 5620
                                   vvi     v    vv     v  i    v   ii vi i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_202302329_   5621 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAGAGTGAACAGG 5670
                           v v  i i   i  ii vv    i  v    v  vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_202302329_   5671 CAGCCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGG 5720
                           i  i                 v       vii  vi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_202302329_   5721 GCTAATATCCAGAATCTACAAAGAACTGAAACAAATTTACAAGAAAAAAA 5770
                         i  vi          v  i        vvv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_202302329_   5771 CAAACAACCCCATCAAAAAGTGGGCAAAGTATATGAACAGACACTTCTCA 5820
                             i     v  i?    i         v  v    i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_202302329_   5821 AAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCATC 5870
                                 i  vi viii     i ii          i       v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_202302329_   5871 ACTGGCCAT 5879
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.40 (144 / 103)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.00 (3 / 3)  


2241 14.38 7.10 22.78  chr2_202408421_202412964     2994  4064 (480)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_202408421_   2994 AGGTGTTCTATGTTCATGGGTTG-AAGAGTCAATATT---AAGATGGCAA 3039
                           i i i i          i   -    v i      ---          
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr2_202408421_   3040 TTCTCCCCAAATTAATCTATAGATTCAATGCAATCTCTATCAAAATCTTA 3089
                          v           i     i        i      i           ii 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr2_202408421_   3090 GCAAGGTTTATTGCAGAATCTTGATAAGCCAGTCCTAAAATTTATATGAA 3139
                           vivv   v        -v    i    iii          i     i 
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_202408421_   3140 AAGTCAAAGAATCTAGATTGGCCAGAACAATTTTGAAAAAGAA---CAAA 3186
                           vv   i i i i   v i    i      i           ---    
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_202408421_   3187 TTTGGAGGACTTATA-TTCCTGATTTCACAACTTACTAGGAATCAACAGT 3235
                         v          i i -    ii      v         vi  v v     
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_202408421_   3236 AATCTAGATGGTGTGGTATTAACACAAGGAGAGACATGTTTATCAGTGAA 3285
                             v   ii        i ii  i     v      i vv    i  i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_202408421_   3286 ATGTAACTGAGAGACCAGAAATAAACACAT---TTTCTGGTCAA------ 3326
                           iv  i      v            v   ---   v       ------
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_202408421_   3327 -----CAAAGGTGCCAAGA---TTCAATGGGAAAAG-------------- 3354
                         -----   i          ---         i    --------------
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_202408421_   3355 ------GTGTTGGGAAATTTGGATAGCCATATGCAAAAAGATTAGTTTGG 3398
                         ------   i     v vi      ?   i        ii  v iv    
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_202408421_   3399 ACACATAACTCAGCCCATATACAAAAGTTATCTTAAAATGAATCACAGAC 3448
                           v v  v    vv            i   v  i      i    ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_202408421_   3449 CTAAATATAAAAGGCAAAACTATAAAACTTTCATTTTTTTTTTAGACGGA 3498
                               i   i  vi              i -----------    ----
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCT-----------TAGA---- 539

  chr2_202408421_   3499 GTCTCGCTCTGTCACCCAGGCTGGAGCACAGTGCCACGATTTCGGCTCAC 3548
                         ----------------------i  -------------------------
  L1M4_orf2#LINE/    540 ----------------------AGA------------------------- 542

  chr2_202408421_   3549 TGCAAACTCCGCCTCCCAGGTTCACGCCATTCTCCTGCCTCAGCCTCCTG 3598
                         ---    -------------------------------------------
  L1M4_orf2#LINE/    543 ---AAAC------------------------------------------- 546

  chr2_202408421_   3599 AGTAGCTGGGACTACAGGTGCCCGCCACCACGCCTGGCTAATTTTTTGTA 3648
                         ------------- i   ? ------------------   ---------
  L1M4_orf2#LINE/    547 -------------ATAGGNG------------------TAA--------- 556

  chr2_202408421_   3649 TTTTTAGTAGAGATGGGGTTTCACCATGTTTGCCAGGATGATCTTGATCT 3698
                         ----------------------------------------     -----
  L1M4_orf2#LINE/    557 ----------------------------------------ATCTT----- 561

  chr2_202408421_   3699 CCTGACCTCGTGATCTACCTGCCTTGGCCTCCCAAAGTGCTGGAATTACA 3748
                         --------     --------      -----------------------
  L1M4_orf2#LINE/    562 --------CGTGA--------CCTTGG----------------------- 572

  chr2_202408421_   3749 GGTTTGAGCCAACAGGCAAAGACTTCTTAGACATAACATCAAAAGCATAA 3798
                         -   ---------      v ii        i  i   i        i  
  L1M4_orf2#LINE/    573 -GTT---------AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_202408421_   3799 TTCATAAAAT------TTTTTA---TAGAGTTTATTAAAATGAAAAACTT 3839
                         viv i    v------ vvv  --- i  v  i  i     v        
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_202408421_   3840 TTCTATTTCAAAAGACACTATTAAGAAAAT-AAAAGACAAGTCA--GACT 3886
                           v ii      i        i      i -         vi  --  v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_202408421_   3887 GCAAGAAAATATTTACAAATCATAT--CTGATAAAGGACATGTATCCAGA 3934
                          vi           i          --       i    v          
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_202408421_   3935 ATACAGAAAGAACCCATACAATTCAACAA---GAGTACAAACAA---AAT 3978
                            i v       i v     i    i  ---i iv     i  ---   
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_202408421_   3979 TTTAGAAATAGGCCAAG-ATCTGAATAGACATTTCATCAAAGAAGATATA 4027
                          ?- i    i   v   -  i              vi             
  L1M4_orf2#LINE/    813 TW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_202408421_   4028 TGAATCACTAATAAGCA----------TGTTCTACATCATTAGTCAC 4064
                         ii   vi i        ----------  i  v      ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (95 / 55)
Gap_init rate = 0.03 (29 / 903), avg. gap size = 11.03 (320 / 29)  


 340 24.24 0.00 4.04  chr2_202865025_202867467      501   599 (1844)    L1M4_orf2#LINE/L1       71   165 (743)  

  chr2_202865025_    501 TCTATAAATTCAGTGCAATTTCAATTTTAAAAATCCCCAACAGGGTTTTT 550
                             i i     ii     ii v  i---        - i v vv     
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATC---AAAATCCC-AGCTGCCTTTTT 116

  chr2_202865025_    551 GGCAGAACATGATTAGCTGATATTAAAATTCATATAGAAAAGCCAGAAA 599
                         v      vv   iv       vi            i    v  v  ii 
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

Transitions / transversions = 1.18 (13 / 11)
Gap_init rate = 0.02 (2 / 95), avg. gap size = 2.00 (4 / 2)  

 575 28.91 13.03 2.84  chr2_202865025_202867467      986  1407 (1036)    L1M4_orf2#LINE/L1      173   637 (271)  

  chr2_202865025_    986 TAGCCAGTATAATTTTGAAAAAAAA---TAAAGT-GGAAG-TTTGCCCTG 1030
                               iv i   i        i  ---i     -   i -i ii v  v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr2_202865025_   1031 ACAAATATAAAAACTTATTTTAAAGCTGTAAAAAATAAAACTGTGTGCTA 1080
                         v v   v v        i vi      ii iv  vi  i  v     v  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr2_202865025_   1081 TTGGCTTAGAGACAGACA------------GAAGAGAATAGAGAATCCAG 1118
                         i    v  ii  i     ------------   v     v    i     
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_202865025_   1119 AAATAAATGTGCCCACA----TATGGAAACTTGATATATGGCAATGGCAT 1164
                                ----    i ----     vv v     v vi i   v  ---
  L1M4_orf2#LINE/    323 AAATAAA----CCCATACATTTATGGTCAATTGATTTTCGACAAGGG--- 365

  chr2_202865025_   1165 TATAAAGGGAAAT-AGTGGAGAAAGGATGATCTATTATTCACTATATAAT 1213
                          iiv   ivv v - i   i     i  ii   -  --   vi v  ii 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCT-TT--TCAACAAATGGT 412

  chr2_202865025_   1214 TTTGAGACAACTGGTTATGCA-ATTT-------TAAAATT-----CTCAC 1250
                         vi  i         v  ?v  -  vi------- i  i  ----- ii  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_202865025_   1251 CTCACA--------AAATATCAG------GTGTATTCAGGAGCTTAATGT 1286
                               --------   v  i i------i  v  iv?i  v  v     
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_202865025_   1287 CAAAAAGC-AAAATT-TAA--CTTTTAGAGGAAAATATAGCAGAATATTT 1332
                         --  i   -    i -   --  i     i     i    v? v v  i 
  L1M4_orf2#LINE/    513 --AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr2_202865025_   1333 TTATGAATTTTGGAAAGGAAAAAACTTTTTACCTATTAT-TCATAA-CAC 1380
                          ii   vi  v  vv   v  viii  i   vv   v i-i  v  -   
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr2_202865025_   1381 AAACCATAAAGAAAATTATTGATAAAT 1407
                           i v i   ii   vv  v       
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAAT 637

Transitions / transversions = 1.25 (66 / 53)
Gap_init rate = 0.05 (21 / 465), avg. gap size = 3.19 (67 / 21)  

 363 28.63 5.39 5.81  chr2_202865025_202867467     1703  1943 (500)    L1M4_orf2#LINE/L1      632   871 (37)  

  chr2_202865025_   1703 ATGAATCTGACTATATTAAAGTTTGAAGTTTT-------CAACAAGACAA 1745
                           i   iv    vi  i   i  vi  ii   -------   - i    v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACAC 680

  chr2_202865025_   1746 CAT----GAAGTTAAAAGCCAAATTGCAGATTAGAAGGAGATACCTGCAA 1791
                         i  ----i    v     v   viii    v i i  i i   ii     
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_202865025_   1792 TGCATGTAACCAACAAAGCATTAGTAACCAAAATGCAGCAGCATTTCTTC 1841
                         vv   i  v ii i  i v i v   v   i   ii vv iv vi    v
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_202865025_   1842 C--CTCTACAAATAGGGAAAGAAAAAGACAATCAACCCAAAGGAAAAATG 1889
                          --   ----    ----- v          vi       vv?       
  L1M4_orf2#LINE/    781 CAACTC----AATA-----ATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr2_202865025_   1890 AGCAAATGATGTGAACAGGCAACTAACAGAAGAAGAAACACAAATAAATG 1939
                         i     v   v    i  i  vi vv vi       v i      ---- 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT----G 867

  chr2_202865025_   1940 GCCA 1943
                             
  L1M4_orf2#LINE/    868 GCCA 871

Transitions / transversions = 1.27 (38 / 30)
Gap_init rate = 0.03 (7 / 240), avg. gap size = 3.86 (27 / 7)  


 796 15.12 25.37 0.00  chr2_202906245_202908121      501   705 (1172)    L1M4_orf2#LINE/L1      274   530 (378)  

  chr2_202906245_    501 TGGCATATGGACATATAGATAGATCAATGGCATAAAATTGAGAGCCAAGA 550
                                v   i v i v            v   i         i v   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr2_202906245_    551 AA-AAACCCTTATATCTATAGTCAATT---TTTTGACAAGGATACCAGAA 596
                           -      v  i  i   i       ---   i       i i   ii 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr2_202906245_    597 CAATTCAGTGAGAAAAGGACAGTCTTTTCAACTAATGGT-CTGGGACAA- 644
                          v     i  i i    i i            v      -         -
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr2_202906245_    645 ---------ACAC--------------------------------CCATA 653
                         ---------   i--------------------------------     
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_202906245_    654 ---AAAAATTA-TTCAAAATG-ATGAAAGATTTAAATGTAAGAGCTAAAA 698
                         ---        -i        -  v ?   ii                  
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_202906245_    699 CTATAAA 705
                                
  L1M4_orf2#LINE/    524 CTATAAA 530

Transitions / transversions = 2.33 (21 / 9)
Gap_init rate = 0.03 (8 / 257), avg. gap size = 6.50 (52 / 8)  

1665 16.48 5.49 0.55  chr2_202906245_202908121     1022  1385 (492)    L1M4_orf2#LINE/L1      527   908 (0)  

  chr2_202906245_   1022 TAAAACTCTTA-----AACCACAAGCGTAAACCTTTGTGACCCTGGATTA 1066
                                    -----  v  i i ?     i   i      i   i   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_202906245_   1067 GGTAATGGTTTCTTAGATA---------AATTACAAGCAACAAAAGAAAA 1107
                           i                ---------  vi                  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_202906245_   1108 AACAGATGAACTTAATTT-ACCAAAATTAAAAACTTT-ACGCTGCAAAGA 1155
                           i    i  i vi i  - i                -ii   v     i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_202906245_   1156 ATAAAACCAAGAAAGTGAAAAGACAACTCAAAGA-TAGGAGAAAATCCAT 1204
                          i vv i                    i  v   - i         viv 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_202906245_   1205 GCAAATCATATATATGATAAAGGTCTAATACCCAGAATA---AAAGACAT 1251
                                      v      i  v  vi  i        ---     vv 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_202906245_   1252 ATTACCACTCAACAATAAAAAGACAACTAACCCAATTTAAAAATGGGCAA 1301
                         v    v      i             v          ?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_202906245_   1302 AAGATCTAAAGAACTTCATTTTTCCAAAGAAGATGTACTAATGGCCAATA 1351
                          i   i i  v iv--     i            i   v           
  L1M4_orf2#LINE/    827 AGGATTTGAATAGA--CATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_202906245_   1352 AGTACATAAAAAAATGCTTGGCATCATTAGCCAT 1385
                           i    i    i     iii     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (38 / 20)
Gap_init rate = 0.02 (7 / 382), avg. gap size = 3.14 (22 / 7)  


 905 12.57 15.43 0.00  chr2_203169587_203172481.rev      600   774 (2121)    L1M4_orf2#LINE/L1        1   202 (706)  

  chr2_203169587_    600 TGGAAAGATATC--GTGTTCATGAATTAAGAGACTTTCTATTGTTAATAT 647
                                     --i        i   iii      vv         v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_203169587_    648 AGCAATACTCCCCAAACTG---------------------CCTATCAAAA 676
                         i               i  ---------------------          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_203169587_    677 TCCCAGTTGTCTTTTTT-CAGATATGGA-AAACTGATC--ACAATTCATA 722
                               i  i       -    v  v  -  i      -- v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_203169587_    723 TGGAAATGCAAGGAACCCAAAACAGCCATAATAATCTTGAAAAAGAAAAA 772
                                      i     i  i     v  i               i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_203169587_    773 CA 774
                           
  L1M4_orf2#LINE/    201 CA 202

Transitions / transversions = 2.14 (15 / 7)
Gap_init rate = 0.02 (5 / 202), avg. gap size = 5.40 (27 / 5)  

 932 12.85 0.00 6.15  chr2_203169587_203172481.rev     1098  1276 (1619)    L1M4_orf2#LINE/L1      189   356 (552)  

  chr2_203169587_   1098 GAAAAAGAAGAACAAAGTTGGAGAACTCAGCTTTCTCTATTTTAAAACTA 1147
                                                i     vvi   i v    i      v
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_203169587_   1148 ATTACAAAGCAATAGTTATCAAGACAGTGTGGTCCTGGCATAAGGATCAA 1197
                          i        v i   v                v             ---
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT--- 285

  chr2_203169587_   1198 TGGATCCTTGACATATTGATGAATGGAATAGAATTAAGAGTTCAGAAATA 1247
                         --- -----       v   v              i     i        
  L1M4_orf2#LINE/    286 ---A-----GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_203169587_   1248 CACCTTTGCACTTACGGTCAATTGATTTT 1276
                         v   iv i  i   i              
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 1.09 (12 / 11)
Gap_init rate = 0.01 (2 / 168), avg. gap size = 5.50 (11 / 2)  

1342 14.94 2.07 0.41  chr2_203169587_203172481.rev     1583  1823 (1072)    L1M4_orf2#LINE/L1      344   588 (320)  

  chr2_203169587_   1583 GTCAATTGATTTTTGACAAGGATACCAAGACTTTTCAATTGGGAAA-AAT 1631
                                      i       i i       iv      v      -   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_203169587_   1632 AATATTTTCCACAAAAGATACTGGAA-AACTGGATATCAA---ACAAAAG 1677
                          i v     v     v i i    i -         ? v ---i      
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_203169587_   1678 AATGAAGTTGGACTCCCTACCTCATGCCATATACAAAAATTAACTCAAAA 1727
                                      -          ii                        
  L1M4_orf2#LINE/    444 AATGAAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_203169587_   1728 TGGATCACAGACCTAAATGTAAGAGCTAAAACTATAAAACCCCAAGAAAA 1777
                                ?                                i iv    i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_203169587_   1778 AAACACAACAGCAAACCTTTGTGACTGTGTATTAGAAAATGGTTTC 1823
                              i iv? i   i   i     iv  vi    iv         
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

Transitions / transversions = 2.00 (22 / 11)
Gap_init rate = 0.02 (4 / 245), avg. gap size = 1.50 (6 / 4)  

 861 18.63 14.07 1.14  chr2_203169587_203172481.rev     2141  2403 (492)    L1M4_orf2#LINE/L1      612   908 (0)  

  chr2_203169587_   2141 AGTGACAAAATAAAAAA-AGATAAATTAGACTTCATTAAAAATGTCAAAA 2189
                           ii      v      -         i        i    v i--    
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA--AAAA 659

  chr2_203169587_   2190 CTAT-GTACCTCAAAGAATACCACCAACTAAGTAAAATGACAAGCCAAAG 2238
                           v -  i i      i i  i i   vv    i   v     v   v  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_203169587_   2239 AATGAGA----------------------------------CTTGTATCT 2254
                             i  ----------------------------------        i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_203169587_   2255 ACTATGTAAAAAGAACTTTTACAACTCAACAATAAAAAGACAAATATGCA 2304
                          vv  i  v        i           i                -i v
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA-ACC 808

  chr2_203169587_   2305 CAATTTTTATATGGGCAATGGGTTTGAATTAACATTTTACCAAATAAAAT 2354
                              ?vv v        v  i       vi      iv     v  i  
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_203169587_   2355 ATACAA-TGTTTAAGAAGCACAGGAAAAGATGCTCATCACCATTATTCAT 2403
                               -  vii  v       v             v  i  ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (25 / 23)
Gap_init rate = 0.02 (6 / 297), avg. gap size = 6.67 (40 / 6)  


1930 23.68 15.35 1.90  chr2_203375323_203376904      407  1090 (492)    L1M4_orf2#LINE/L1      133   908 (0)  

  chr2_203375323_    407 CTGATCCTAAAATTTATATGAAACTGCAAAGA--CTAAAATAGCCAAAAC 454
                                       i     i  v     i i-- i i            
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr2_203375323_    455 AATATTGAAAAGGAATAATTAAAATTAAAGAACTTACATTGC---GTTT- 500
                            v       i   v  i-   i  ii  i   i   i v ---i   -
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAAC-AAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_203375323_    501 -------------------------------------------------- 500
                         --------------------------------------------------
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_203375323_    501 GGACAGAGGTACAGATAAATGGAAAATAATAGAACATTGAGAAATAA-TT 549
                            i   vi  i    v       v v   v  ivi iv        -ii
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_203375323_    550 CACAC----------------TTCTCGATAAAGGTTCCTAAGGTAATTCA 583
                           i  ----------------  i    i  i   v  -   iiv     
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC-AAGACCATTCA 380

  chr2_203375323_    584 GTGGGAGAAAGAATAGTATTTTCCACAAACAGTTTTGGAGCAACTGGATA 633
                         i    -           v     v     ii  vi   ii          
  L1M4_orf2#LINE/    381 ATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_203375323_    634 TCCATAT---AGGGGAGGGGGATAATCCCTTTCCTTAAACTGTACACAAA 680
                         ?   i  --- ii i v ii v iiv   i v   i v  ii  i     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_203375323_    681 AGTGAACTCCAAATGGATGAAAGACCTACATATGAAGGGTAAAATGGAAA 730
                          i v     v        v ?       v  i i ii v     iviv  
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_203375323_    731 GACTTCTAGAAGAAAACATAGGAGCAAATCATCTTGACCTTGGAGTAGGC 780
                         i   ii                ? i     v  v         iv     
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_203375323_    781 AAAGGTCTTTTAG----GACACAAAAAGCATGAACTATTAACAGAAGTAG 826
                           v   i i    ----     v       ii i v i-  v    iv i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-AAAAGAAAAAA 628

  chr2_203375323_    827 TCGATAAATTGTAGTCTATTAAAATTAAAAA-----ATGCTATTCGAAAG 871
                          v         v v ii  i           -----i    --  i  i 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGG 676

  chr2_203375323_    872 GCACCATTAA-AAATTGAGAAGACAAGCCAAAAAGAAGACAAGGCAAAAC 920
                         i   i  i  -   v   i       v   v i ---- iii iv    -
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGA----ATGGGAGAAAA- 721

  chr2_203375323_    921 TGTTTGTATG-CATATATTTGACAGAGAACTTGCATCCAGAATACATAAA 969
                          i    i vi-       i   i ii i     i          i     
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr2_203375323_    970 ----TC---CAATTCAATAA---GAAGACAAACCTA--TCAGTTAAAAAA 1007
                         ----  ---   i       ---i        --  --i  i  ?     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAA--TAACCCAATTWAAAAA 819

  chr2_203375323_   1008 TGGACAATGGATTTGATCAGACATATCACTGAAGAAAATGTGTAAGTGGC 1057
                            i   v        vi      v  v ii     i  i ii  i    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_203375323_   1058 CAAAAAGCACTTTAA------CTCAACCTCATTTGGTAC 1090
                            v      v v  ------      v   ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (106 / 52)
Gap_init rate = 0.03 (23 / 776), avg. gap size = 5.13 (118 / 23)  


3017 21.93 7.44 0.52  chr2_203398826_203401131.rev      635  1400 (906)    L1M4_orf2#LINE/L1        6   824 (84)  

  chr2_203398826_    635 AGGCATTTCATGTTCATGGACTGGAAGACTTTTAATACTGTTAAAACACC 684
                           ii  ii            i          --    i      i iiv 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTT--AATATTGTTAAGATGGC 53

  chr2_203398826_    685 CACACTACCCAAAGTCATCTACAAATTCAATGCAATCCCTATCAAAATCC 734
                         v i   v      v v       i      i                   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_203398826_    735 CAG-TGGCATTTTTATGGAAATAGGTAA--TAATTCTAAAACTCGTGTGA 781
                            -  v v     iii     v ii  -- i  i      i  i i  i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_203398826_    782 AACTACAAAAGACCACGAATAGCCAAATAAATTTTGAGAAAGAA---CAA 828
                           v i   ii    vv           vv   i    i      ---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_203398826_    829 AGCTAGAGGCATCATACTTCTCGATTTCAAAACATATTACAAAGTTACAG 878
                           i i    vv   i     i i          v  i       i     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_203398826_    879 TAATAAAAATAATATAGTACTGGCATAAAGATAAGACATACA--TCAATG 926
                             v  i i i i i            i    -      i --      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGATCAATG 302

  chr2_203398826_    927 GGACAGTATAGACAGCCCATAAATAAATCCACACATTAACACTCAACCAA 976
                          i i  v  v  v  i   v       i   i     v iiv    iii 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_203398826_    977 TCTTCAATGAGGGTGCCAA----------TGGGGGAAGGACAGTCTCTTC 1016
                          i   i ii          ----------     i   i i     i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_203398826_   1017 AACAAATGGTGCTGGGGAAACTGAATATCCTCATGCAAAAGAAAGAAGCT 1066
                                         iv     i   ?  v            v    i 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_203398826_   1067 AGACTCTTACCCCA-------TACAAAAATCAACTTAAAATTGATTCAAG 1109
                         i   i i    i  -------         i    i     v   iv?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_203398826_   1110 ATTTAAATATAAGA-CACAAACTATAAAACTCCTAGAAATAAACATAGGG 1158
                          ii     i     - vv              i     iv         ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_203398826_   1159 GACAAGCTTCATGATATTGGTCTTGACAATGATTTCATGGCTATGACATC 1208
                          vv  v    i   iv    vi v i     i    v i v       i 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_203398826_   1209 AAAAGCACAGAC--CAAAAAAAG-------------------CA--AAAA 1235
                                  ii --     i  i-------------------  --    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_203398826_   1236 CTAAAAAGCTTATGCACAACACAGAAAACAATCAACAGAGTAAAAAG-CA 1284
                         i      -   v  ii vv  v  i v  v     v i   i     -  
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_203398826_   1285 ACCTAAGAAATA--AGAAAATATTTGCAAACTATATATTTGATAAGAGGC 1332
                            i vii   i--                ii      i       i i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_203398826_   1333 TAATCTCCAAAATACGTAAGAAACACATACAACTCAATGGCAATAAAACT 1382
                          vi v    i    ii   ii   v v           iii  v  i  v
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_203398826_   1383 AATAA-----TTAAAAAATGGGC 1400
                              -----  ?          
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGC 824

Transitions / transversions = 2.09 (111 / 53)
Gap_init rate = 0.02 (16 / 819), avg. gap size = 3.81 (61 / 16)  

 516 17.02 0.00 0.00  chr2_203398826_203401131.rev     1721  1814 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_203398826_   1721 AAAAGTGGGCTAAGGACTTGAATAGACATTTCTCCAAAGAAGATGCACAA 1770
                             i     v     i                           ii    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_203398826_   1771 ATGACCAAGAGGTATGTAAGAAAATGTTCAACATTAGTCATTGG 1814
                            i    v i i ii i i  i   i       i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 7.00 (14 / 2)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


2449 23.93 6.01 6.78  chr2_203435327_203439391     2721  3635 (430)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_203435327_   2721 TGGAAAGATATCCTATGTTCATAG----GAAGAATTCATGTTGTTAAAAT 2766
                                      i        i ----     v  v  i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_203435327_   2767 GACCATACTATCCAAAGCAATCTATAGATTGATTGCAATTAAAATATTAA 2816
                          i v     vi     vii     i     v vi     i----------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATC---------- 90

  chr2_203435327_   2817 TTGTTTATGTTAAAGTACCAATGACATTCTTCACAGAAATAGAAGAAACA 2866
                         ---ii   --i   i v   iivi v  i  ii       v  vi ivii
  L1M4_orf2#LINE/     91 ---CCTAT--CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chr2_203435327_   2867 ATCCTAAGATTTGAATGGAACCACAAAAGTCCCCAAATAGAGCCATA-CA 2915
                                i   iiv      vii   ii v   vi     --   v -  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG--CCAAAACA 183

  chr2_203435327_   2916 A-----AGCAAAAAGAACAAAGCTAGAGGCATCATACTACCTGACTTCAA 2960
                          ----- iv  i          i i    vv   i   v  ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_203435327_   2961 AATATATTACACAAAGCTATAGTCATCCAAACAGCATGG----------- 2999
                           iv  i    --      i   v   v i    ii   -----------
  L1M4_orf2#LINE/    234 AACTTACTACA--AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_203435327_   3000 --------------ATCCACGGAACAGAATAAAGAACCCAGAAATAAATT 3035
                         --------------   v i    i     vi   ii           ii
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_203435327_   3036 CATGCATTT-CAGCCAGCTGATTTTTCACAGAAGTGCTAAGAACATACAC 3084
                            i     -ii i  ii       iv   iii    i    v   v  v
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_203435327_   3085 TGGAGGAAAGAACA---TCTTCAATAAATAGTGCTGGGAAAACTGATT-- 3129
                            -        i --- i     i    i         v     iv --
  L1M4_orf2#LINE/    382 TGG-GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr2_203435327_   3130 ---TATGCAGAAGGATGAAAGTAGACCATTATCTCTTACCACATATAAAA 3176
                         ---i     i   i     iv i    vi  i   vi    i   i    
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_203435327_   3177 ATCGACCTAAAATGGATTAAAGCCTTAAAGGTAAGACCCAAAACTACAAA 3226
                           ii  ii         i ?  v i    v      v i       i   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_203435327_   3227 ACTCCTGGAAGAAAACATAGGGG-AAATGTTTCAGCACATTGGTCTAGGC 3275
                             i i              ? -    -i   ivv  v    vi     
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGC 579

  chr2_203435327_   3276 AAAGATTTTATGGCTAGGACTACAAAAGCCTAGGTAACAAAA--AAATAT 3323
                           v i   iv i v  v   vv       vi i i       --   v  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_203435327_   3324 ATACAAATGAGACTATATTAAATTTAAAAGCTTCTGTACAGCAAAGGAAA 3373
                          v i    vi    vi  i   v      i   i   i vv       v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_203435327_   3374 C----AACAGAGTGAAGAGAAAACCTGTTGAATGGAGGAAAATATTTGCA 3419
                          ----  v i      i   v    iiiv      ii             
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_203435327_   3420 AACTATTCATCCAACAAGGAACTAACATCGAGAATCTTCAAGGAACTCA- 3468
                           ii  vi   ii i    i   vii   v     v vi  i      v-
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_203435327_   3469 ATAGCAAAA-AACAACAACAACAAAGAATCCCATTAAAAAATGGGCAATC 3517
                          i i vv  -  i  v  -i     v  i  v   ?            --
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAA-- 826

  chr2_203435327_   3518 TGACTAGACATTTCTTAGAAGAGACAGATTAAATGTCTGACTAGACATTT 3567
                         ---------------------  ---    -------   v         
  L1M4_orf2#LINE/    827 ---------------------AG---GATT-------TGAATAGACATTT 845

  chr2_203435327_   3568 CTCAAAAAAAGACATAGATTAAATGGCCAACAAATATATATTTTAAAAA- 3616
                            v   i    i   ---i          i  ii i  i----    i-
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATA---CAAATGGCCAATAAGCACATG----AAAAGA 888

  chr2_203435327_   3617 -GTTCATCTTTACTAGTCAT 3635
                         - i   v v i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (140 / 76)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 4.68 (117 / 25)  


1182 27.43 1.94 0.24  chr2_203538575_203548610     3409  3820 (6216)  C L1M4_orf2#LINE/L1   (0)   908   490  

C chr2_203538575_   3820 AAATAG--TAAAGACTGAAATGTTAGACCTAAAACCATAAAAACCCTAGA 3773
                             i --i ?    iv      v   v       i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

C chr2_203538575_   3772 AGAAAACCTAGGCA-ATACCATTCAGGACATAGGCAGCGGCAAGGACTTC 3724
                                v    ?i- v i -   iv   v v  vvvv     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

C chr2_203538575_   3723 ATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATG 3674
                         v ivv  vi            vvi          vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

C chr2_203538575_   3673 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATGA 3624
                            ii v  i   v v  i i   i  ii vv    i  v    i  v  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

C chr2_203538575_   3623 GAATGAACAGGCAACCTACAGAATGAGAGAAAACTTTTCCAATCTACTCA 3574
                         i i    v  i     i        i       iv   v   vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

C chr2_203538575_   3573 TCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATT-- 3526
                              i  i  i  vi          v  i         vv    v i--
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

C chr2_203538575_   3525 ---TACAAGGAAAAAAAACCCCATCACAAAGTGGGAGAAGGATATGAACA 3479
                         ---  v  i  v   v     v  i?v   i    vi      v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

C chr2_203538575_   3478 GACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGACAAAA 3429
                             i     v        i  vi viii     v ii       v  i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

C chr2_203538575_   3428 TGCTCGTCATCACTGGCCAT 3409
                              iv     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.04 (56 / 54)
Gap_init rate = 0.01 (4 / 419), avg. gap size = 2.25 (9 / 4)  

 843 22.46 4.66 2.54  chr2_203538575_203548610     4496  4731 (5305)    L1M4_orf2#LINE/L1      272   512 (396)  

  chr2_203538575_   4496 ACTGGCCATCAGAGAAATGCATAT-GACCAATGGAACAGAAC--AGAGCC 4542
                               -  v  -  v vi     -  i        i    i--    i 
  L1M4_orf2#LINE/    272 ACTGGC-ATAAG-GATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_203538575_   4543 CTCAGAAATAATACCACACATCTACAACCATCTGATCGTTGACAAACCTG 4592
                          --        vv   i    i  iiii  vi    iv i     ivv  
  L1M4_orf2#LINE/    320 C--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_203538575_   4593 ACAAGA------AATGGGGAAAGGA--GTCCCTATTTAATAAATGGTGCT 4634
                         v     ------           i --   -- v  i  i          
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCT 415

  chr2_203538575_   4635 GGTAAAACTGGCTAGCCATATATAGAAAGCTGAAACCAGAACCCTTCCTT 4684
                           v v      v  ?   i  ii i  iiv    iiii  v    v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_203538575_   4685 ACACCTTATACAAAAATTAATTCAAGATTGATCAAAGACTTAAATGT 4731
                              v              i    i  v     ?    i       
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.03 (8 / 241), avg. gap size = 2.12 (17 / 8)  

1155 26.65 1.71 1.47  chr2_203538575_203548610     5024  5432 (4604)    L1M4_orf2#LINE/L1      499   908 (0)  

  chr2_203538575_   5024 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5073
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_203538575_   5074 AGGC-CATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5122
                            ?-i v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_203538575_   5123 ACAGCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5172
                            v        vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_203538575_   5173 TAAACTAAAGGGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5222
                         i   v v  iii   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_203538575_   5223 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5272
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_203538575_   5273 GGGCTAATATCCAGAATCTGCAAAGAACTCAAACAAATTTACAAGAAAAA 5322
                           i  vi          v ii         vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_203538575_   5323 AA-----AACCCCATCAAAAAGTGGGCAAAGAATATGAACACACACTGCT 5367
                         i -----     v  i?    i         i  v    i v   i v  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_203538575_   5368 CAAAAGAAGACATTTATGCAGCCAACAGACACGTGAAAGAAAAGAATTTT 5417
                          v        i  vi viii     i ii   i     ----  -  vi 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA----AG-ATGCT 892

  chr2_203538575_   5418 CAAC-CCAGAATTTCA 5432
                             -i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (57 / 49)
Gap_init rate = 0.01 (6 / 410), avg. gap size = 2.17 (13 / 6)  

3086 26.03 2.01 0.56  chr2_203538575_203548610     8650  9544 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_203538575_   8650 TGCAAAGACATTCCAAGCTCATGGATAGGAAGAATCAATATCATGAAAAT 8699
                           v     i  i   v i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_203538575_   8700 GGCTATAGTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 8749
                            v   v v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_203538575_   8750 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 8798
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_203538575_   8799 ATGGAACAAAAAAGGAGCCCATA-TAGCCAAGACAATCCTAAGCAAAAAG 8847
                               - viv    ii    v -       i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_203538575_   8848 AACAAAGCTAGAGGTATCATGCTACCTGACTTTGAACTATACTACAAGTC 8897
                                i i    vv   ii  v  ii i  ii  viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_203538575_   8898 TACAGTAACCAAAACAGCATGGTACC------AGAAAAGATACATAGATC 8941
                                 i   i    ii      i------  i v   i i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_203538575_   8942 AATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAC 8991
                                i    iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_203538575_   8992 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGA--GTCC 9039
                         i    i  i     ivv  v   i v  vv            i --   -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chr2_203538575_   9040 CTATTTAATAAATGGTGTGGGGAAAACTGGCTAACCATATGCAGAAAACA 9089
                         - v  i  i        iv    v      v  ?   i     i  i vv
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_203538575_   9090 GAAACTGGACCCCTTCCTCACACCTTATATAAAAATTAACTCAAGATGGA 9139
                            ii         v         v    i              i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_203538575_   9140 TTAAAGACTTAA-TGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 9188
                          i ?    i   -       v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_203538575_   9189 CTAGGCAATAACCTTCAGGACATAGGAATGAGCAAAGACTTCATGACGAA 9238
                         v    ?ivv  i    iv   v v  iv ii    v ii   v iivv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_203538575_   9239 AACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAA 9288
                         i            vvi      i   vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_203538575_   9289 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAAAGTGAAC 9338
                          i   v v  i i   i  ii vv    i  v       vv        v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_203538575_   9339 AGGCAACCTACAGAATGGGGGAAAATTTTTGCAATCTATCCTTCTGACAA 9388
                           i     i          i      v       vii  viv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_203538575_   9389 AGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 9438
                         i  v  vi          v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_203538575_   9439 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATGTGAACAGACACTTC 9484
                          i    ----   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_203538575_   9485 TC---AAAAGACATTTATGTGGCCAAGAAACATACGGAAAAAAAACTCAT 9531
                           --- i    i  vi vi       v  i  i i -    i vi    v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTCAA 895

  chr2_203538575_   9532 CATCACTGGTCAC 9544
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (133 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


3257 23.64 4.09 0.91  chr2_203592897_203595808     1541  2420 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_203592897_   1541 TGGAAAGATATTCCAGGATCATGGATTGGAAGAATTTAATATTGTTAAAA 1590
                                    i   v v               -i             i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA-CTTAATATTGTTAAGA 49

  chr2_203592897_   1591 TGTCCATAGTACCCAAAGCAACCTACAGATTCAATGCAATCCTTATCAAA 1640
                           v v   v v      vii i            i       i       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_203592897_   1641 ATACCAATGACATTCTTCACAGAAA--AAAAAA--AATCCTAAAATTTAC 1686
                           v   iivi v  i  ii      --i v  i--i           i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_203592897_   1687 ATGGAACCACAAAAGAACCAGAATAGCCAAAGCTACCTTAAGCAAAAAGA 1736
                               vii   ii  v              i v i   i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_203592897_   1737 ACAAACTTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCT 1786
                              v        v     i v  ii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_203592897_   1787 ATAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACACATACACCA 1836
                          i     i   i    ii              ii i     i   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_203592897_   1837 ATGGAACAGAATAGAGAAGCCA-AAACAAATCCACACATCTACAGTGAAC 1885
                               i     v    iv   -   i   i   i    i  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_203592897_   1886 T------------------CAAACCTA--CACTGGGGAACAGCCAGTCTC 1915
                          ------------------   iv i --  v       viivi     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_203592897_   1916 TTCAATAA-TGGTGCTGGAAAAACTGGGTATCCATATGCAAAAAAAATGA 1964
                              i  -         i v      i  ?   i        i  -   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGA 448

  chr2_203592897_   1965 AACTAGACCCCTATCTCTTGCCACATACAAAAGTCAAAACAAAAGGGATT 2014
                          ii i        i   vii   i        i i  vv     v    i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_203592897_   2015 AAAGACTTAAATATTTGTAAGACCTCGAACTATGAAACTAATACAAGAAA 2064
                          ?    i     ----      v  vi      i     vv  v      
  L1M4_orf2#LINE/    499 AWAGACCTAAAT----GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_203592897_   2065 ACATTGGGGAAACTCCCCAGGGCAGTGGTCTGGGCAAAAATTTCTTGAGT 2114
                             v  ? v  v  ii iv i vv   vi i     vii      iii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_203592897_   2115 A--ATACCACACAAGCACAGGCAATCAAAGCAGAAATAGACAAATGCGAT 2162
                          -- i    - -       i    iv    v i       i    vv  i
  L1M4_orf2#LINE/    595 ATGACACCA-A-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_203592897_   2163 CCCATCAGG-TTAAAAA-----GCACAGCAAAGGAAACAATTAACAAAGT 2206
                         ii     ii-       ----- ii vv       v  v  i  v     
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_203592897_   2207 GAAGAGACAACCCACAGAATGGGAATAATTATTTGCCAACTACCCATCTG 2256
                            i                    iv  v       v  ii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_203592897_   2257 ACAAGGGATTAATAACCAGAATATATAAGGAGCTCAAAAAGCTCTGTAGG 2306
                          i      i vi  v             i  i   vv v i   vi  iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_203592897_   2307 TAAAAATTTAATAATCTGATTAAAAATTGGGCAAAAGGTTTGAACATACA 2356
                         v    iviv     i ii   ?    v        i i      i v   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_203592897_   2357 TTTCTCAAAAGAAAAT-T-CAAATGGCAAACAGGTAAATGAAAGGGTGCT 2404
                               v      i  - -        v  i i i v      i i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_203592897_   2405 CACCATCACTGATCAT 2420
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (129 / 75)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.75 (44 / 16)  


 455 20.39 1.94 0.00  chr2_203618759_203620765.rev      539   641 (1366)    L1M4_orf2#LINE/L1        1   105 (803)  

  chr2_203618759_    539 TGGAAAGACATCGCAT--TTATGGAGTGGAATAATTAATATTGTGAAAAT 586
                                 i   v   -- i     v     v v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_203618759_    587 GACCATACTACCAAAGGCGATCAACAGATTCACTGCAATCCTTATAAAAA 636
                          i v     v  v  ivi    v         vi       i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_203618759_    637 TACCA 641
                          v   
  L1M4_orf2#LINE/    101 TCCCA 105

Transitions / transversions = 0.62 (8 / 13)
Gap_init rate = 0.01 (1 / 105), avg. gap size = 2.00 (2 / 1)  

2364 24.83 10.15 1.65  chr2_203618759_203620765.rev      784  1512 (495)    L1M4_orf2#LINE/L1       81   871 (37)  

  chr2_203618759_    784 CAACAAAAGCCC---CGAAATCCCAATGATAGTCTTCACACAAATAGAAA 830
                             iv  v   --- i        iiviivv i  ii  v    v  --
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA-- 128

  chr2_203618759_    831 CAACAAA--AACCTTAAAATTTGTATGGAACCACAAAAGACCTTGACTAG 878
                         ---   i--i i i       ii       vii   ii    iv  v   
  L1M4_orf2#LINE/    129 ---CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr2_203618759_    879 CCAAAGCAATCCTAAGCAAAAAGAACAAAGCTAGAAGCATCATACTATCT 928
                              i     i i iv  i          i i  i vv   i   vi i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_203618759_    929 GGCTTCAAAATATATTACAAAGCTATA-TAACCAAAACATCACAGTACTG 977
                         iii       iv  i          i -   i   i   viiii      
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_203618759_    978 GCATAAAAACAGACACAC----CAATGGAAGAGAATAGAAAACAAACAAA 1023
                               ii i     i i----        v     v  i iivv v   
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_203618759_   1024 CAAACAAAATCTACGCACTTACAGCCAATTGATTTTCAACAAAGGTACCA 1073
                         i    ----- i ii  i   ii i            i    i   i   
  L1M4_orf2#LINE/    326 TAAAC-----CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_203618759_   1074 AGAATATTCACTGGGGAAGGGACAGTCCCTTTGATAAAAGGTCCTGGGAA 1123
                            vi     v       i i i    ii  ii i   v   v      v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_203618759_   1124 AACTGGATATCTGTATGCAGTAAAATGAAAGTAGACCCCTAGCTCTCACC 1173
                                  ? iii     iv i      iv i        v   v    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_203618759_   1174 ATATATAAAAACCAACTAAAAATGGATTAAAGACTTAAATGTGAGACCTG 1223
                              i     ii    v         i ?    i       i   v  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_203618759_   1224 GAACTATAAAACTACCAGAAGAAAACACAGGGGTAATGCTTCAGGACATT 1273
                         i            vii           i   ?    vv    iv   v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_203618759_   1274 GGTCTAGGCAAAGATTTTTATGGCTAAGACCTCAAAAGCA---------- 1313
                           vi       v i   i - i v  v   vi        ----------
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCT-TAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_203618759_   1314 -----AAAATAGACAAAT-GGATTTGTATCAAACTAAAAAGCTTTTGTAC 1357
                         -----        i    -   i  -i      v v    i       i 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTT-CATCAAAATTAAAAACTTTTGTGC 668

  chr2_203618759_   1358 AGCAAACTAAACAAGCAACAGAGTGAAGAGACAACCTGCAGAGTGGAAGA 1407
                         vv    vv v  v v   v i      i        ii    i   i   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_203618759_   1408 AAATATTTGCAAACTAT---TCC-ACGAGGGATT---------------- 1437
                                      ii  ---  i- ii     i ----------------
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr2_203618759_   1438 ---------------------AATAAA----TAAATAATTTCATTTAGAA 1462
                         ---------------------      ----i      iiiv   ? i  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_203618759_   1463 ATGGACAAATGAGCTGAACAGACATCTCTCAAAAGAAGATATACA---GG 1509
                             i    v  vi    i      i    v              ---  
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_203618759_   1510 CCA 1512
                            
  L1M4_orf2#LINE/    869 CCA 871

Transitions / transversions = 2.16 (121 / 56)
Gap_init rate = 0.02 (15 / 791), avg. gap size = 5.73 (86 / 15)  


2586 27.91 1.19 0.71  chr2_203635799_203639717.rev      988  1829 (2090)    L1M4_orf2#LINE/L1        2   847 (61)  

  chr2_203635799_    988 GAAAAAAAAATCCATGCTCATGGACAGAAAGAATCAATATCATTAAAATG 1037
                          i   i v vi     i       iv i    v i     ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_203635799_   1038 GCCACACTGCGCAAAGCAATTCACAGATTCAATGCTATTCCTATCAAACT 1087
                           v i   v v    vii  ii          i  v  i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_203635799_   1088 GCCAATGGCATTCTTCACAGAACCAGAAAAAAACT-ATTTTAAAACTCAT 1136
                         v   iiv  v  i  ii     -- vvi v  i  -  ii     i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_203635799_   1137 ATAGAACCAAAAAAAGGCCA-AATAGCCAAGGCAATCCTAAGCAAAAAGT 1185
                           i   viiv  iiiiv   -         ii     i i iv  i   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_203635799_   1186 AGAAAGCTGGAGGCATTATGTTACCTGACTTCAAACTATACTACAAGGCT 1235
                          v    i      vv i iii v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_203635799_   1236 ACAGTAACCAAAACAGCATGGTACTGGTATGAAAACAGACATATAGACCA 1285
                                i   i    ii         i  i ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_203635799_   1286 ATGGAACAGAAGAGAGAGCCCAGAAACAAGGCTGCACACCTGCAACCATT 1335
                               i    vv     i       i  iv iii   ii iiiii  v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_203635799_   1336 TCATCTTCAACAAAGCTGACAAAAACAAGCATTAGGGAGACAACTCCCTG 1385
                          v  i   i    i v  v   i v  vv  v i    i v  ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_203635799_   1386 CTAAGTAAATGGTGCCAGGATTACAGGTTAGCCACATGCAGAAGACAGAA 1435
                         i v ii         ii   iv  v  v  ?         i    vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_203635799_   1436 GCTGGACCCCTTCCTCACACCATATACAAAAATAAACTCAAGATAGACTA 1485
                          i         v                     v       i  i  ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_203635799_   1486 AAGATTTAAATATAAAACCCAAAACTATAAAAACCT-GGAAGACAGCCTA 1534
                         ?   ii     i   i v i            vi  -i     v i v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_203635799_   1535 GGCA-ATACCATCCTGGACAAGGGAATGGGCAAAGATTTCATGACAAAGA 1583
                           ?i- v i v  v  -  vvv  iv i     v i    v iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_203635799_   1584 CACTAAAAGCAATCA--CAACAAAAGCAAAAATTGGAAAATGGAATCTAA 1631
                            i       --  --         v      v iv    v i ii v 
  L1M4_orf2#LINE/    599 CACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_203635799_   1632 ATAAACTTAAGAGCTTCTATACAGCAAAAGAAACTATCAACACAGTAAAC 1681
                         vi   v    i i   i i i vv    i  v        v v   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_203635799_   1682 AAACAACCTGAAGAATGGGAGAAAATATCTGCAAACTATACATCTGACAA 1731
                          i      iiv                 i      ii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_203635799_   1732 AGGTCTATTATCCAGCATCTATATCGAACT--TAAAAC-AAATT-TACAA 1777
                         i  v  vv       v  v    vv     --  v   -v   v-  -  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA-AA 795

  chr2_203635799_   1778 AAGAAAAACAACACCATTGAAAAGTGGGCAAAGGACACAAACAGACATTT 1827
                             v   i   v v   ?    i           ivii  i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_203635799_   1828 CT 1829
                           
  L1M4_orf2#LINE/    846 CT 847

Transitions / transversions = 1.46 (137 / 94)
Gap_init rate = 0.01 (12 / 846), avg. gap size = 1.33 (16 / 12)  

2614 25.36 3.88 0.91  chr2_203635799_203639717.rev     2594  3366 (553)  C L1M4_orf2#LINE/L1   (0)   908   113  

C chr2_203635799_   3366 TTTATGTTGAAACTAGATAAAACT-ACTTTAAATTTCATATGGAACCAAA 3318
                            v  iv    i -  i  i-  - iii    v           viiv 
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATT-GACAAG-CTGATCCTAAAATTCATATGGAAATGCA 160

C chr2_203635799_   3317 AAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGAACAAAGCTAGA 3268
                          ii  v  v v        i      i i iv  i          i i  
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

C chr2_203635799_   3267 GGCATCATGTTACTTGACTTCAAACTATACTACAAGGCTACAGTAACCCA 3218
                           vv   iii v iii i      viv        i          i v 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

C chr2_203635799_   3217 AACAGCATGGTACTGGTATCAAAACAGATATACAGACCAATGGAACAGAA 3168
                         i    ii         i  v ii i   i   i   i        i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

C chr2_203635799_   3167 CAGAGGCCTCAGAAATAACACGACACATCTACAACCATCTGATCTTTGAC 3118
                         iv   ivii         vv v i    i  iiii  vi    i  i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

C chr2_203635799_   3117 AAACCTGACAAAAACAAGAAATGGGGAAAGGATTCTCTATTTAATAAATG 3068
                           ivv  v   i v  vvv           i  vv   v  i  i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

C chr2_203635799_   3067 GTGCTGGGAAAACTGGCTAGCCGTATGCAGAAAACAGAAACTGGACCCCT 3018
                                  v      v  ?  ii     i  i vv   ii         
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

C chr2_203635799_   3017 TCCTTACACCTTATACAAAAAATTAATTCAAGATGGATTAAAGGCTTAAA 2968
                         v   i     v          -    i    i      i ?  i i    
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAA 509

C chr2_203635799_   2967 CGTAAAACCTAAAACTATAAAAACCCTAGAAGAAAACCTAGGC---AATG 2921
                         i    i v              vi i           v    ?---   -
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT- 558

C chr2_203635799_   2920 CCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAACACCAAAA 2871
                         - -   iv   v v  vv i     v ii   v iiv  vi         
  L1M4_orf2#LINE/    559 -C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

C chr2_203635799_   2870 GCAATTGCAACAGAAGCTAAAGTTGACAAATGGGATCT------AATTAA 2827
                            vvv      i   vv   i v  i    v   ii ------      
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

C chr2_203635799_   2826 AGAGCTTCTGCTCAGCAAAAGAAACTATCAG---AGTGAACAGGCAACCT 2780
                          i -   i  iv vv    i  v       i---      v  i     i
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

C chr2_203635799_   2779 ACAGAATGGGAGAAAATTTTTGCAAGCTATCTATCTGACAAAGGTCTAAT 2730
                                          v       iii  v       i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

C chr2_203635799_   2729 ATCCAGAATCTACAAGGAAGTTAAACAAATTTACAAGAAAA--------- 2689
                                  v  i  i   v ivv    v iv i  v    ---------
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

C chr2_203635799_   2688 -TCCA-TCAAAAAGTGGGCAAAGGATATGAAAAGACACTTTTCCAAAGAA 2641
                         -i   - i?    i            v    v     i  i         
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

C chr2_203635799_   2640 GACATTTATGTGGCCAACAA--ACATAAAA----GTTCATCATCATCGGT 2597
                           i  vi vi       i  --    i   ---- i   v     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

C chr2_203635799_   2596 CAT 2594
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.46 (114 / 78)
Gap_init rate = 0.02 (14 / 796), avg. gap size = 2.64 (37 / 14)  

 222 22.22 1.39 0.00  chr2_203635799_203639717.rev     3362  3433 (486)    L1M4_orf2#LINE/L1      836   908 (0) *

  chr2_203635799_   3362 ATAAACTTTTC-AAAAAGAAGACATACATGCAGTCAACAAGCATATGAAA 3410
                            i  v    -vv        i     viii i   i     i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_203635799_   3411 AAAAGCTCAATATAACTAATCAT 3433
                          i v      i  v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1)  


 352 26.53 9.18 0.00  chr2_203790229_203796280.rev     4094  4191 (1861)    L1M4_orf2#LINE/L1        1   107 (801)  

  chr2_203790229_   4094 TGGAAAAATATTCCATGTTTATGAATAGGAAGAATCAATACTGTTAAAAT 4143
                               i    i       i   i  v      v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_203790229_   4144 AACCATACTGCCTGGGCTGGTGTGGGGGCTCA-CGC-----CTGT---AA 4184
                         ii v     v  iiiii  i v ivi ii   -   -----  i ---  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_203790229_   4185 TCCCAGC 4191
                                
  L1M4_orf2#LINE/    101 TCCCAGC 107

Transitions / transversions = 3.33 (20 / 6)
Gap_init rate = 0.03 (3 / 107), avg. gap size = 3.00 (9 / 3)  

2415 26.62 7.95 0.13  chr2_203790229_203796280.rev     4449  5203 (849)    L1M4_orf2#LINE/L1       46   859 (49)  

  chr2_203790229_   4449 AAAATGACCATACTGCCCAAAGCAATTTACAGATTCAGTGCTATTCCTAT 4498
                           i   i v     v      vii  i          ii  v  i     
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_203790229_   4499 CAAACTACCAGTGGCATTCTTCACAGAATTAGAAAAACCTATTTTAAAAT 4548
                             v v    iv  v  i  ii     v v  v  i iv  ii      
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_203790229_   4549 TAATATGGAACCAAAAAAGAGCCTGAATAGCCAAGGCAATCCTAGACAAA 4598
                          v        viiv  ii  v  v          ii     i ii v  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_203790229_   4599 AAGAACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTACACTACGA 4648
                                   i      vv     i v  ii i      vivi     i 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_203790229_   4649 GATTACAGTAACCACAACAACATAGTACTGGTACAAAAACAGACACATAG 4698
                         iii        i  vi   iii i       i i  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_203790229_   4699 ACCAGTAGAACAGAAAAGAAAGCCCAGAAATAATGCTGCACACCTACAGC 4748
                          i  i i   i    vv  i  i          vv iii   ii  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_203790229_   4749 CATCCAATCTTTGACAAACATGACAAAAACAAGCAATGGGAAAGGGCT-- 4796
                           viii  i  i     ivi  v   i v  vv       i  i iv --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_203790229_   4797 CCTTTTCAATAAATAGTACTGGGATAACTAGCTAGCAATATGCAGAAGAC 4846
                         i        i    i  i      i    i v  ? v i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_203790229_   4847 TGAAACTGGACCCCTTCCTTACA--ATACACAAAAATCAACTCAAGATGG 4894
                             ii         v   i   --   i        i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_203790229_   4895 ATTA--GACTTAAATGTAAAA----------------------------- 4913
                           i --   i         i -----------------------------
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_203790229_   4914 --TAGG--------------ACCT-------GGCAAAGATTTCAT-GATG 4939
                         --    --------------    -------     v i    v -   -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr2_203790229_   4940 AAGCCATCAAAAGTAACTGCAACAAAAACAAAAATTGACAAATGGGACCA 4989
                          v v  i      i vvv         iv      v  i    v    iv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_203790229_   4990 AATTAAACTAAAGAGCTTCTGCACAACAAAGGAAACTATCAACAGAGTAA 5039
                         v  i   v v  i i   i  ii vv       v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_203790229_   5040 ACAGACAACCTACAGAATGGGAGAAACTATTTGCAAACCATGCATCCAAC 5089
                          v        i               v          i   ii   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_203790229_   5090 AAAGGTCTAATATCCAGAATCTATAAGGCACTTAGACAAATCAACAAGTA 5139
                           i  v  vi          v     i v   ivv    v    i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_203790229_   5140 AAAG-CAAATAACCCGACTAAAAAGTGCGCAAAGGACAAGAACGGACACT 5188
                             -          i i ?    i  v        ivv   ii    i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_203790229_   5189 TTTCAAAAGAAAACA 5203
                          i  v      i i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATA 859

Transitions / transversions = 1.76 (127 / 72)
Gap_init rate = 0.01 (9 / 814), avg. gap size = 6.78 (61 / 9)  

 206 14.55 7.27 0.00  chr2_203790229_203796280.rev     5506  5560 (492)    L1M4_orf2#LINE/L1      850   908 (0)  

  chr2_203790229_   5506 AAAGAAAACATGCA----GCCAACAAGCATATTAAAAAATGCTAAACATC 5551
                               i i  i  ----     i     i  v    i     v      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_203790229_   5552 ACTAATCAT 5560
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 4.00 (4 / 1)  


1108 22.76 2.85 0.00  chr2_204026729_204029860     1005  1250 (1882)    L1M4_orf2#LINE/L1        1   253 (655)  

  chr2_204026729_   1005 TGGGAAGATATCCCGTGCTCATGAATTGGTAGATTTGATATTGTTAACAT 1054
                            i          i  i     i     v   i  i          v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_204026729_   1055 GTCCATACTACACAAAGCCATCTACAGATTTAATGCAATCTCTATCAATA 1104
                          v v     v v    viv           i  i      i       v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_204026729_   1105 TTCCAATGGTATTTTTCACAAAAATAGAAAAAC----CCTAAAATTCATA 1150
                          i   iiv iv     ii  i    v  v  i ----             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_204026729_   1151 GGAAACCACAAAATACTTTGAATAGCCAAAGCAGTTTTGAA---TAAGAA 1197
                         v i  vii   iiv  iiv           i  i i     ---v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_204026729_   1198 CAAAGTTGGAGGTATCATACTTCCTGATTTCAAACTATATTACAAAGCTA 1247
                                     vv   i      ii        viv  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_204026729_   1248 TAG 1250
                         i  
  L1M4_orf2#LINE/    251 CAG 253

Transitions / transversions = 1.55 (34 / 22)
Gap_init rate = 0.01 (2 / 253), avg. gap size = 3.50 (7 / 2)  

1219 19.27 7.27 0.73  chr2_204026729_204029860     1535  1809 (1323)    L1M4_orf2#LINE/L1      244   536 (372)  

  chr2_204026729_   1535 AAAGCTATAGTAATCAAAACAGTGTGTTACTGGCATAAA---AGACATGT 1581
                                i         i        v           i---      i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_204026729_   1582 AGACTAATGGAACAGAAT--GGAGCCCGGAAATGTAGCCA--CATCTGTG 1627
                            ii       i     --i   i  i     iv v   --   i i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_204026729_   1628 CAGTCAACTAAGCTTTGATAAAGGCACCAGGTACA--CAATGGGGAAAGG 1675
                         --     i i vi  i  i  i  ii   i vv  --            i
  L1M4_orf2#LINE/    344 --GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_204026729_   1676 ATAAT----TCAGTAAATGGTATTGGGAAAACT--ATATCCACATGCAAA 1719
                            i ----   ii       ii     v    --   ?           
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_204026729_   1720 AGAATGAAATTTGATTGTTATATCACAC---ATACAAA--TTAGCTAGAA 1764
                                 i  v  iivi  iv      ---       --   i  vi  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_204026729_   1765 ATGGATTAAAGACTTAAATGTAAGATCTGAAATTATAAAACTCTT 1809
                               i ?    i           v  i   i            
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

Transitions / transversions = 3.25 (39 / 12)
Gap_init rate = 0.03 (9 / 293), avg. gap size = 2.44 (22 / 9)  

 984 16.89 3.95 21.05  chr2_204026729_204029860     2185  2640 (492)    L1M4_orf2#LINE/L1      531   908 (0)  

  chr2_204026729_   2185 ACTCCTAGAAGAAAACATAGGGGAAAAAGCTCCTTGATTCTGGTCTTGAC 2234
                             i                ? v   -v  i v   iii   vi v i 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGC 579

  chr2_204026729_   2235 AATGGTTTTTATAAATATGACACCAAAAGCACAGGCAACAAAAGCAAGAA 2284
                                 i -  i                   i          v  i  
  L1M4_orf2#LINE/    580 AATGGTTTCT-TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_204026729_   2285 AAGATGAGAGTG-ACTACATCAAACTAAAAGGCTTCTGCACAGCAAAGGA 2333
                         v    i - v  -   v       v v   ii   i  ii vv       
  L1M4_orf2#LINE/    629 TAGATAA-ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_204026729_   2334 CAC-------AAAATGAAAAGGCAATTTATGGAATGGGAGAAAATGT--G 2374
                            -------   i       i   iii ii              i -- 
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_204026729_   2375 CAAACCATACATCTATCTGATAAGGGGTTTATATCTGTGTGTGTGTGTGT 2424
                             i    ----             ii  i    i--------------
  L1M4_orf2#LINE/    728 CAAATCATA----TATCTGATAAGGGACTTGTATCC-------------- 759

  chr2_204026729_   2425 GTGTGTATATGTATATATATATATATATATATATATATAAATATATATAT 2474
                         --------------------------------------------------
  L1M4_orf2#LINE/    760 -------------------------------------------------- 759

  chr2_204026729_   2475 ATATATATAAATATATATATATATATATATATATAAAGGATTCATACAAC 2524
                         -------- i -----------------          i i  v      
  L1M4_orf2#LINE/    760 --------AGA-----------------ATATATAAAGAACTCTTACAAC 784

  chr2_204026729_   2525 TTAATAGCAAAAAACCAAATAACCAGATTTTAAAA--------AGACCTA 2566
                          i    ii     iv         vi   ?v    --------i  ii i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_204026729_   2567 AGTAGACATTTTTTCAAAGAAGACACACAGGCGTCCAACAGGTATGTGAA 2616
                          i         i i         i i   iii v    i i i ii    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_204026729_   2617 AATGTGCTCAACATCACTAATCAT 2640
                           vi            ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.95 (56 / 19)
Gap_init rate = 0.03 (10 / 378), avg. gap size = 11.40 (114 / 10)  


 767 21.56 5.05 3.67  chr2_204212093_204214928      563   780 (2056)    L1M4_orf2#LINE/L1        2   222 (686)  

  chr2_204212093_    563 GGACAGATATGCCATCTTAATAGATTAGAAGATGCAATATTATCAA--TG 610
                            v      v    v  v  i    i     ivi      i i  --  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_204212093_    611 CCTATTCTCCCCCAAAATGAACTAGGTATTCAATGTAATTACAACCAATG 660
                         v v  v      -   v   v   viv      i i   iv v i   vi
  L1M4_orf2#LINE/     52 GCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_204212093_    661 TCCCAGTGGGCATTTTTTTACAGAAACTGACAAGAGTATTCTAAAATTTA 710
                               iv v --      i      i       vvv  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_204212093_    711 TATGGAAAAGCAAATGACCTAGACTAGCCAAAAGAACCTTGAAAAGG--- 757
                                 v    iv    i   v         v  i        i ---
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_204212093_    758 ------GTTGGGTGCAGTGGCTCACACCT 780
                         ------     ----  - i       i 
  L1M4_orf2#LINE/    199 AACAAAGTTGG----AG-GACTCACACTT 222

Transitions / transversions = 0.96 (23 / 24)
Gap_init rate = 0.03 (6 / 221), avg. gap size = 3.17 (19 / 6)  

 657 21.76 5.18 2.07  chr2_204212093_204214928     1061  1253 (1583)    L1M4_orf2#LINE/L1      178   376 (532)  

  chr2_204212093_   1061 AAAAGAACCTTGAAAA----GAGTAGGG---GAGGAATGA-ATTTTACCT 1102
                             v  i        ----  ii ii ---     v v - i  --  i
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT--CCC 225

  chr2_204212093_   1103 GATTTCAAGACTCACTATCCAGCTA-AATAATCAAGACAATGTAGTACTG 1151
                         i       i   i    ivv     - i           i   i      
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_204212093_   1152 GCAAAAGGATAGAGA-ATCACATCAATGTAACAGAATGGAAAGTCCAGGA 1200
                            v         v -  - v       v  i     v  i       i 
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATAT-AGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr2_204212093_   1201 ATAGACCCACACATAAAATGTCAAACAATTTTCAGTAAGGATGCCAGAGG 1250
                            i     i    vv vv     vii      iii    i     -  i
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA-AGA 373

  chr2_204212093_   1251 TCA 1253
                         i  
  L1M4_orf2#LINE/    374 CCA 376

Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.04 (8 / 199), avg. gap size = 1.75 (14 / 8)  

 820 26.03 8.22 0.68  chr2_204212093_204214928     1566  1857 (979)    L1M4_orf2#LINE/L1      379   692 (216)  

  chr2_204212093_   1566 CAATGAGGAAAG-----TGTTTTTAACAAATGACACTGGCACAACTAGAT 1610
                              i      ----- v    i        iii    v      i   
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_204212093_   1611 AT--AAATGGGGCAGA--------GGGCTCG-ATATCAC-TCATAAACAA 1648
                          ?-- v   viiv   --------  i i v- iv    -i    v    
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_204212093_   1649 AAATTAATTCAAAATGGATTGTAGACTAAAATGTAAAAGCTAAAATTATA 1698
                                i           ii?    iv        i        i    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_204212093_   1699 AA-CTCCAAGGAGAAAATATGGAAATATACTTTC-TGAACTTTGGTGTAG 1746
                           -   iv  i      i  i i?i  v ii   -   v   v   -   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAG 577

  chr2_204212093_   1747 GCAAAAATTTATTAG----GGCACAAACGACACTAACCATAAAAGGAAAA 1792
                             vii   v    ---- i   v  vii   v i v i     i    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr2_204212093_   1793 ATTGGTAATTTTGA-TGAAGCCCAATATAAAAACTTCTGCTCTTTGAAAA 1841
                           v i   v  v  - vv v vv   -         i  iv   ii  ii
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGG 676

  chr2_204212093_   1842 ACACCATTAAAAAAAT 1857
                             i  i  i   i 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGT 692

Transitions / transversions = 1.61 (45 / 28)
Gap_init rate = 0.04 (11 / 314), avg. gap size = 2.36 (26 / 11)  

 339 21.90 18.57 2.86  chr2_204212093_204214928     2135  2344 (492)    L1M4_orf2#LINE/L1      666   908 (0)  

  chr2_204212093_   2135 TGTCTCAAAAG-------TAAAAAATAAAAAAGACAAGCTAAGTTACAGA 2177
                           ii     i -------i  i   vvi         v i -----    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA-----CAGA 710

  chr2_204212093_   2178 CTAAGAGAAAATATTTGCAAAT---ATATCCAATAAAGAACTTGTATCGA 2224
                         v ii                  ---     ii    i i         v 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_204212093_   2225 G------TAAATAATTGTTA-AACTAAATTTAAAAAATATATACAATCTT 2267
                          ------    v  i v   -    v   vvv     v i v i  i iv
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_204212093_   2268 ATTTTTTAAATGGGCAAAG-ACTTG--CTGTCACTTCCC----------- 2303
                            ?vv-            - i   --iv v  i   i -----------
  L1M4_orf2#LINE/    811 ATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_204212093_   2304 ---AAATGAC---TAAGAACATTACAT--TGCTCAACATCAATAATAAT 2344
                         ---     i ---    v    v v v--            ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.05 (23 / 22)
Gap_init rate = 0.05 (11 / 243), avg. gap size = 4.09 (45 / 11)  


 698 27.92 16.63 4.96  chr2_204460941_204462757.rev      524  1329 (488)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr2_204460941_    524 TATGCTATGTATTTAGATGTGAAAATTTAATGTATAAATATATGTAAGTA 573
                            v i    viv i   vv   i i     i ------- i -    --
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATAT-------TGT-TAAG-- 48

  chr2_204460941_    574 CATA--AATACTTTCTCCCCAAATTGACCTTTAAAGTTAATGAAATTCCA 621
                         -  i--      ----           i  vi i v i  i v   i  v
  L1M4_orf2#LINE/     49 -ATGGCAATACT----CCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr2_204460941_    622 ATCCTAATACCAATAAGATTTTTCACAGAACTTGGTAAGTTAACTCTAAA 671
                            vv   v   iivivv     ii     v   ii   i i ii     
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr2_204460941_    672 ATTTACATAAAA---CAA----------ATAGCCAAGGTACTCCTGAA-- 706
                            i i  ii  ---   ----------        iii v  i    --
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_204460941_    707 -GAGGACCA---TCAGAAAGC-----------------AAGATTTATTAT 735
                         -  i  v  --- ii  iii -----------------  i i   i  i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_204460941_    736 AGAGCCATAGTTATCAGGGGAA-GTCA-ATT----TTAGG-TCAACAAAA 778
                          i   i i   v    i iv i-  vi- i ---- v   - vi   v -
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA- 292

  chr2_204460941_    779 TGGAGTTAACTGAAACAAAATAGAGAGTCCATAAATAGACCCA--CATCC 826
                          i  - i  -  i  i i   v         v     i     --   ii
  L1M4_orf2#LINE/    293 TAGA-TCAA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_204460941_    827 AC---------ATGT-------GGGTGGCATTACACAT-CAGTA------ 853
                          i---------  v -------     v  vv  -   -  i i------
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAA 389

  chr2_204460941_    854 ----------------AAATGGTG---GAACAAATGAAGATCTACAT-TG 883
                         ----------------        --- i    v  i v ? i    -ii
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_204460941_    884 AAAAAATAAAAGTGTATCCCAACTTCATACTATCTTCAAAAAAATCAATT 933
                            i   i  iv  v i   v  i   i  i  v v      -- i  i 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACT 487

  chr2_204460941_    934 TCAAATACATTGTGGACTTATATGTGAAAGACAAACTTA-AAAACCTTTA 982
                         iv    iv  ii?i   i  v    i i  vi   vi  -     ii   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_204460941_    983 GA-GAAAATATG----------TTTATGATCTCAGGTAAGA----GATTT 1017
                           -     i  i----------  ii   i  ii   v  i---- i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_204460941_   1018 -TTAAAAATGGAACCCAAACACACAAACT-TAAAAGGAAAAC-------- 1057
                         -   i v   iv   v   -i     i v-i     i    v--------
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_204460941_   1058 ----ACTTTAGGCAGAAATTATCAA-TTTTAT--CTCAGCCAAGACGACA 1100
                         ----    i v-  -      vv  -    i --i   ---   --    
  L1M4_orf2#LINE/    637 TTGGACTTCAT-CA-AAATTAAAAACTTTTGTGCTTCA---AAG--GACA 679

  chr2_204460941_   1101 TCGTAAAGGTCATGTAAAGATAAAACACAAAATGG----AAATATGCGCT 1146
                         iii v   ivvi  v     i  vv    i     ----      ---- 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT----T 725

  chr2_204460941_   1147 TGTAA--CACATAAATAACAAAGAACCAGAATTCAGAAAATATGAAGAAC 1194
                           i  --  i   vv i i  i i  iv v  i     v    i      
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr2_204460941_   1195 TCCTTA-AAGTAGAGGAAAAATAGGGAGAAAAAAAAAGCACAGAAAAAAA 1243
                           -   -  v v----  v    iii   v   v  vv  - vv?     
  L1M4_orf2#LINE/    776 TC-TTACAACTC----AATAATAAAAAGACAAATAACCCA-ATTWAAAAA 819

  chr2_204460941_   1244 TGGATAGAAGGCTTATACTGGA-ATTTTACATAAGAGAAAACATAAATAG 1292
                            ii i i ii  i- v i  -    iv vv    ii v i i    i 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTG-AATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_204460941_   1293 CCAAAAA--ACATAAAATG-TACTCAACCTGATTTGTAAC 1329
                             v  --    i   v - i      v v ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (142 / 80)
Gap_init rate = 0.06 (51 / 900), avg. gap size = 3.41 (174 / 51)  


 821 25.00 8.33 10.29  chr2_204667577_204671735     2555  2962 (1197)    L1M4_orf2#LINE/L1       80   479 (429)  

  chr2_204667577_   2555 TCAATAAAATGCCAATCAAAATCCTAGCAGGATTTTTGGTATAAATTCAC 2604
                             iiv   v  v          i   v vv     v i v     v  
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chr2_204667577_   2605 AAGATGCTTCTAAAATTTATATGAAAGTGCAAAGGAAATAGAATAAATGA 2654
                            v  v i        i     i  i     i   vvi      ivii 
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_204667577_   2655 AACGA----AAAAAAGAAGGA--AAGTTGGTAGATTTATATGATCTGAGT 2698
                            i ----i         i --       vi  i i i ivvi ii v 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_204667577_   2699 T-AAGACTTCCTAGAAAGCTATAGTAATTCAAGAAATTGTGACATTGGCA 2747
                          -  i    v   v       i      -     v v    ii i     
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAAT-CAAGACAGTGTGGTACTGGCA 278

  chr2_204667577_   2748 TAAGGATAGACATAGAGAT--------------TGACA---CA------- 2773
                                       v    --------------   v ---  -------
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_204667577_   2774 --TCACACATATACAGTCAATTGATTTTTAAGATAGGGACCAGCAAAATT 2821
                         --i  i    v  ii             ii v vi  vi   iv vv   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_204667577_   2822 CAGCAGGGCGCTGAGGGGCAGAGTTTAATTTCTTCTGGGAATTGCACAAT 2871
                           iii   ----------- i  vv  i i i   ------------  -
  L1M4_orf2#LINE/    379 CAATGGGG-----------AAAGAATAGTCTTTTC------------AA- 404

  chr2_204667577_   2872 GTGAGGGAGTTTATATGCAAATAGCTCTGTAATAATTGGACATCTGT-TG 2920
                         -----------------     i iv   vi i  i    i ? iii-  
  L1M4_orf2#LINE/    405 -----------------CAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_204667577_   2921 GGAAAAATTAAACTTTGTCCCTTACCTCATACCATACTCAAA 2962
                         vi   i v i  v  v v   i       i      iv    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

Transitions / transversions = 1.46 (60 / 41)
Gap_init rate = 0.03 (11 / 400), avg. gap size = 6.91 (76 / 11)  

 963 21.16 8.84 6.05  chr2_204667577_204671735     3230  3659 (500)    L1M4_orf2#LINE/L1      445   886 (22)  

  chr2_204667577_   3230 ATAGAGTGTGACTCC-ATCTCCAATAATA-ATAATAAA--AACTCAAAAT 3275
                           ii   vv   i  - i   vv iv   - i  -   --          
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAA-AAATTAACTCAAAAT 493

  chr2_204667577_   3276 GGATCATAAACTTAAATAAAATAATCAAAACTATAAATCTCCTAGAAGGA 3325
                               ? i  i     iv  v iii           v   i      i 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_204667577_   3326 AGCATAAGACAAAATTTT-ATGAC------TTAAATAAAGATTTCTTAGG 3368
                          i    i ?vv    i  -i    ------   iii  v i        i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_204667577_   3369 AAGGAAACCAAAA-TATAAATTATG---GAAAAAAT-TATAACTTAGATT 3413
                         v v  v       -i i  iiv ii---        -v    v  i  i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_204667577_   3414 TCAT--AAATTGGA--CTTTCTGT-TTTTGAAACATACTATTAAGAAAAT 3458
                             --     ii --    -   -i  ii  iv i     i      i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_204667577_   3459 AAAAAGACAAGTCGTAGACTGGTAGAAAATATT-GTTAATACCTATATCT 3507
                         i         vi ii   v   v          - iv   - v       
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT-CATATATCT 741

  chr2_204667577_   3508 TACAAGAGACTTATATCCAGAAGATATAA-------------CTCAATAA 3544
                         v i   i     i         v      -------------        
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_204667577_   3545 TTAGAAGAAAAACATCCCAATT-AAATATGGGCACAAGATTTGAAGATGT 3593
                          v i    v   i v       -   v       v i        -----
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA----- 836

  chr2_204667577_   3594 CAACTGGTATGTATACAATTCACAAAAGAGAGATATATATATATATACAG 3643
                         -----------  v   v   v v     -       i v  i------ 
  L1M4_orf2#LINE/    837 -----------TAGACATTTCTCCAAAGA-AGATATACAAATG------G 868

  chr2_204667577_   3644 CCAACAA--ACATGAAAA 3659
                             i  --         
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAA 886

Transitions / transversions = 1.54 (54 / 35)
Gap_init rate = 0.05 (21 / 442), avg. gap size = 3.05 (64 / 21)  


3236 23.97 0.47 2.94  chr2_204781959_204785928.rev     2205  3055 (915)    L1M4_orf2#LINE/L1        1   830 (78)  

  chr2_204781959_   2205 TGAAAAGGTGTCCTATGTTCATGGATTAGAAGAATCTATATTGTTAAAAT 2254
                           i    i i   i             i     v iv          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_204781959_   2255 GTTTACACATGCCAAAGCAATCCATAGATTCAATGTGATACCTATCAAAA 2304
                          viv i  viv     vii   i i        i ii  v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_204781959_   2305 TTTCAATGGCATTTTTTCACAGAAATAGAAAAAACAGCACTAAAATTTAT 2354
                          ii  iiv  v      -i       v  v  iviiiiv        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_204781959_   2355 ATGAAACAATAAAATACATGAAAAAGTCAAAGCAATCTTTGGAAAGAAGA 2404
                            i  vvii  iiv  viii  v  i    i       vii        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_204781959_   2405 ACAGAGCTGGAAGCAACATGCTTCCTGATTTCAAACTATATTACAAAGCT 2454
                            i  i    i vvv  ii     ii        viv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_204781959_   2455 TTAGTAATCAAAACAGTTTGACACTGGTGTAAAAGCAGACACATAGAACA 2504
                         vi         i     v  ii     ii   iiii     i     v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_204781959_   2505 AAGGAACAGAATTGAGAGCCTAGAACTATATCCATACATGTATGGTCAAC 2554
                          v    i           i i    v  v i        v         i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_204781959_   2555 AAATATTTGACAAGGGCACCAAGAATATGTAATTGAGAAAGAATAGTCTC 2604
                         vi  v  i        ii      vi  vi   v i             i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_204781959_   2605 TTCCATAATTAGTGTTGGGAAAAACAGGATATCCACATAAAAAAGAATGT 2654
                            v i  v i   i     v  - v     ?      iv         v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGA 448

  chr2_204781959_   2655 AATTGGACCCCTGTCTTACACCACTTACAAAAATTAACTTGAACTGGATT 2704
                          i          ii  i      iv              ii  v     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_204781959_   2705 AACGACTTAAATGTAATACCTGAATCCATAAAACTCCTGGAAGAAAACAT 2754
                          ?v   i         v v  i  v i         i i           
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_204781959_   2755 AGGATAAAAGCTTCTTGACATTAATCTTGGCAATTATTTTTTTGGGTAAG 2804
                            ?vv   v    v    v  iivi v      vi   i  ----- ii
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-----AGA 593

  chr2_204781959_   2805 TATGATACCAAAAGCAAAAGCACAGGCAACAAAAGCAAAAGTAAACAAGT 2854
                              i          ------  i          v    i  i i  i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCA------CAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_204781959_   2855 GTGACTACATCAAACTAAAAAGCTACTGCACAGCAAAGGAAAC----AAT 2900
                         vv    v       v v    i  vi  ii vv       v  ----  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_204781959_   2901 AAAATAAAAAGGTAACCTATGGAATGGGATAAAATATTTGCAAACCTTAT 2950
                            i i     ii    i ii        v              -- i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA--TCAT 735

  chr2_204781959_   2951 ATATCTGATAAGAGGTTAATATCCAAAATATATAAGAAACTCATACAACT 3000
                                     i ii vi      i         ii     v       
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_204781959_   3001 CAACAGCAAAAAATAAATAAAAAACTAACAATTCAATTAAAAAATGGGCA 3050
                            i -------     ---  i  v  i  ii     ?           
  L1M4_orf2#LINE/    786 CAATA-------ATAAA---AAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_204781959_   3051 ATGGA 3055
                          v   
  L1M4_orf2#LINE/    826 AAGGA 830

Transitions / transversions = 1.74 (127 / 73)
Gap_init rate = 0.01 (8 / 830), avg. gap size = 3.62 (29 / 8)  

 437 17.69 3.08 0.77  chr2_204781959_204785928.rev     3349  3478 (492)    L1M4_orf2#LINE/L1      776   908 (0)  

  chr2_204781959_   3349 TCTCAAAAAACAAAAACAAAAA--CAAATA-CAAAAACAAAAAACAGGGC 3395
                            i v  vv   v  i     --      - vv  vi?     i-    
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT-GGGC 824

  chr2_204781959_   3396 AATGGACTTGAATAAACATTTTCCCAAAGAAGACATACAA-TGGCTAACA 3444
                           v   i       i      ii          i      -    i  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_204781959_   3445 GACACATGAAAAGCTGCTCAACATCACTAATCCT 3478
                         ii           v            ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.03 (4 / 133), avg. gap size = 1.25 (5 / 4)  


2169 25.75 6.14 2.41  chr2_205038829_205041387.rev     1249  2079 (480)    L1M4_orf2#LINE/L1       47   908 (0)  

  chr2_205038829_   1249 AAATAAGAATTTTCCTCTAAATTGATCTTTACATCTAATGCAACCCCTAT 1298
                          i  iiv   vi   i -          vi v  ii  i    i      
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_205038829_   1299 AAAAACCCCAGCAGGGTTTTATGTAGAA-TTGACAAGCTAATTCTAAAAT 1347
                         v    i      v vv    v  i    -          i  i       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_205038829_   1348 TTATATTGCAAAACAAAG-ATCTAGAATACCCAAGACAATTTTGCAAAAG 1396
                          i    v v  vi   i - i i      v    i     i   v     
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_205038829_   1397 AAGAGCACATTTGGATGACTTATACTCTCTGATTTCAAGGCTTATTATAA 1446
                             i  v v     v    i i   ii ii       ii    i  i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_205038829_   1447 AGCTAAAGTAATCAAGACATGGTAATATTTTTGTAAGAATTAACATATAA 1496
                              v             vv  ii  i vvii    i  vi       i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_205038829_   1497 ATAATTAAAACAGAATGAAGAGTACAGATGTAGACCCACACAT------- 1539
                           v v ii  i     vi     v    vi  i     i    -------
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_205038829_   1540 -----GATTTCCAACAAATATCCCAAG-TAATTCAATGAAAAAAG--TAG 1581
                         -----     i i    ivi v     -iv        iii    --   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_205038829_   1582 TCATTTTAACCAATAATTTAATATTGGAA--ACAGGATGTCGATA---AA 1626
                           v   i   v   ii -----ii   i --  v    i? v i ---  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGT-----GCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_205038829_   1627 GGAAACAAATTTTGACCCCTTCCTTGCTTGTACTTTGACCCTTTA---GA 1673
                         iii  ii  v  v       v   ii ----------   v v  ---i 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCAC----------ACCATATACAAAA 480

  chr2_205038829_   1674 GTTAA-TCTGAATG-ATCACATTTTTAAGAATAAAAGCAAAAA--ATTAT 1719
                         i    -  vi    -    ? vvii   ivi   i   v    --  v v
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_205038829_   1720 ACCATTAGAA-AAAATATAGGCAAAAAAATT-GTGACCTTAGAATCAGCA 1767
                           iv      -    i     ?iv   vv  -        i iv vi   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_205038829_   1768 AAGATTCCTTAGA-----CACAAAAAGCACTAACTATAAAAGAAAAATAT 1812
                          v i  i      -----   v        v i v i          -  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-AT 629

  chr2_205038829_   1813 TAATAAATTGGTCTTAAT----ATTAACATTTTTTCT-CTTTATAAGAAA 1857
                         vi         v   v  ----     v vi    v -   i -   i -
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGA- 677

  chr2_205038829_   1858 TCACTCTCAAAACAG---AAGGGTAAGCCACAGACTGGTTGCTGATATTC 1904
                         -    v    i v  ---  i ii  v       v   vv vvi     i
  L1M4_orf2#LINE/    678 -CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_205038829_   1905 ATAATACATATATCTAACAAAGGATTTGTAACCACAATATATAAAGAACA 1954
                         ii  vv         i i  i   i     v   v              v
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_205038829_   1955 CATACAATTCAATCATTAGAAGACAA----TGCAGT-AAAAACTGGGCAA 1999
                          v     i     v  v i       ----iv  i -?    v       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_205038829_   2000 AAGATTTGAACCTATATTCTATAAAAGAAGACATGTGAATGGAAAATAAG 2049
                          i        ivv i   iiviv        i  iii     vv      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_205038829_   2050 CACATAAAAA-ATA-TCTATTTCATTAATCAT 2079
                              i    -  i-  v iv   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (121 / 89)
Gap_init rate = 0.03 (27 / 862), avg. gap size = 2.63 (71 / 27)  


2370 27.24 5.08 1.57  chr2_205089054_205090862      492  1317 (492)    L1M4_orf2#LINE/L1       54   908 (0)  

  chr2_205089054_    492 AAAACCCCACCAAATTGACCTATAGATTTAATATAATTCCAATCAAAATC 541
                           v  i  -         i   i     i  iii   i  v         
  L1M4_orf2#LINE/     54 AATACTCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_205089054_    542 T-AGCAATATTTACTTATGTAAATTGGAAAGATGATATTAAAATTTATAT 590
                         i-   viiv   -i  iiiv      iv   v    vi       i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_205089054_    591 GGAAATGCAAAGGACTTAGAATGGCCAAGACAATCTTGA-------GGAT 633
                                   i    ii     i     i          ------- i i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_205089054_    634 AAATTTACCGTATGTACACTGTCAGAGTTTGAGACCTTTAATAAAGCTAT 683
                            v  ivv v ivi     vi vi v  ii i  i viv i       i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_205089054_    684 -GTAATTAAGACAGTGTGGTGTTTGGATATGAATA----CATAGATCTAT 728
                         -     i             ii v v   v i   ----i       v  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_205089054_    729 GGAACATAATAAAAAAATCCAGAAATAGACCCACATCCATTTA--ATTAC 776
                             i v   vi i i-          i     i --      --i i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAG-TCCAGAAATAAACCCATA--CATTTATGGTCAA 348

  chr2_205089054_    777 TTGATTT-CAATGAAAGCCCCAGTGCATTTCAGTGAAGAAAGGGAT-GTC 824
                                - i ii ii iv   ivi vv    i  ii     i-  -   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTC 397

  chr2_205089054_    825 TTTTCAATAAACAATGCTGAAACAACAGGATGTCCCTATAGGGACAAAGT 874
                                i   iii     ii     v    i?  vi  - vi v i i 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAAT 446

  chr2_205089054_    875 AAATGTTG-ACCCCTAATTCATACTGTACACATAAATTAATTTGAAATTT 923
                         i  -    -       vi   i  ii  i   v       i ii    vv
  L1M4_orf2#LINE/    447 GAA-GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_205089054_    924 ATCAAAGACCTAAATGGAAGGACATAAGCCATAAAGTTTCTAGAAGAAAA 973
                             ?           v   ii vv  i i     ii ii          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_205089054_    974 CATCAG------------TGACCTTGGGGTGAAGAAAGATTTCTTGGGTG 1011
                            vi ------------          v iiiv  v i      i i i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_205089054_   1012 GAATGCAAAAAGTACTAACCGCGAAAGAAAATGTA-ATAATAATAGGCCT 1060
                         vi ii v     i  v i vi i        vi  -    --  v  v  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA--ATTGGACT 643

  chr2_205089054_   1061 TCATAAAAACTTTAAACTTCT---CATCAAAAGATGTGTTTAAGAAAGTA 1107
                             v    i vv      i --- v     i  iiivv i        i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_205089054_   1108 AGAATGGAAGCCCTAGGCTATGAGATAATATTT-TAAACACATATATTTG 1156
                          i  viv  v  vi  iv iv    v       -i   i-       i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT-CATATATCTG 742

  chr2_205089054_   1157 ACAAAGGATTCATAGGTAGAATATATAATGAACT---GCAAACCAATAAG 1203
                          i  i   i ii  vvi           v     ---i   vi      v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_205089054_   1204 AAAATGACAAGTATTCCA--TAAAACAAATAG-CAAAAGACTT-ACTAGG 1249
                             v     i  vi   -- ?   --   i -    i  i  - v   i
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAA--AATGGGCAAAGGATTTGAATAGA 840

  chr2_205089054_   1250 CACTTCACAAAAGAATATATCCAAGTGGCCAGTAAGCATACAAAAAGACA 1299
                           i   v v      v    v   i      i      i ii      ii
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_205089054_   1300 TTCAACATTATCAATCAT 1317
                         i       i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (146 / 76)
Gap_init rate = 0.03 (26 / 855), avg. gap size = 2.12 (55 / 26)  


2836 27.27 1.77 1.11  chr2_205115591_205117970      987  1888 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_205115591_    987 TGGAAACATATTCCATGCTCATGGATAGGAAGAATGAATGTTGTTAAAGC 1036
                               v    i     i        v      v v   i       iii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_205115591_   1037 GGCCAGACTGCCCAAAGCAATTCACAGGTTCAATGCAATTCCTATCAAAT 1086
                            v v   v      vii  ii    i     i     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_205115591_   1087 TACTAATGACATTCTTCAAAGAATTAGAAAAAACT-ATTTCAAAATTCAT 1135
                          v i iivi v  i  iiv    v v  v  i-  -  iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_205115591_   1136 ATGGAACCAAAAAAAGCCC-TAATTGCCAAGGCAATCTTAAGCAAAAAGA 1184
                               viiv  iiii   -v   v     ii       i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_205115591_   1185 ACAAAGCTGGAGTCATTACATTACCTGACTTCAAACTATTCTTAAAAGAT 1234
                               i     vvv i   i v  ii i      viv v  vv    v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_205115591_   1235 ACAGTAAGCAAAACAGCATGGTACTGGGACAAAAACAGACACATAGACCA 1284
                                v   i    ii         v i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_205115591_   1285 ATGGAACAGAATAGAGAGCCCAGAAATAATGCCACACACCTACAGCCATC 1334
                               i     v     i          vv   i   ii  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_205115591_   1335 TGATCTTCAACAAAG---TCAAAACAAT-CAGTGGGGAAAGGACTCCCTG 1380
                             i   i    i ---i   i  v  -  i         i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_205115591_   1381 TTTAATAAATGGCCCTAAGATAACTGGCTAGCCATAAGCAGAAGA-TGAA 1429
                           i  i      iv  ii  i      v  ?   i v   i    -    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_205115591_   1430 ACTAGACCCCTTTCTTATACTGTACACAAAAATTAACTCAAGATGGATTA 1479
                         ii i       vi  i i  ii  i                i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_205115591_   1480 AAGACCTAAATGTAAAACCTAATACTGATACTATAAAAATTCTGGAAGAT 1529
                         ?              i v    ----- -         v ii i     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAA-----A-ACTATAAAACTCTTAGAAGAA 543

  chr2_205115591_   1530 AACCTAGAAAATAACATTCTGGACACAGGATCTGGCAAAAATTTCATAAC 1579
                            v   i?ivv  iv   vv   viv  i iv     vii    v  iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_205115591_   1580 AAAGACATAAAAAGGAATTGCAGCAAAAACAAAAATTGACAAATGGAAAC 1629
                         v v    iv     v vvv   i     iv      v  i    v i vi
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_205115591_   1630 TAATTGTA-TCAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGT 1678
                          v  iiv - i   i -   i  ii vv    i  v        v i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_205115591_   1679 AAACAGACAACCTAAAGAATGAGAGAAAATATTTACAGACTACACATCTG 1728
                         i  v        i v      i            i  i ii i i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_205115591_   1729 ACAAAGATCTAATATCTAGCATGTATAAGGAACTGAAACAAATTTACAAG 1778
                          i  i iv  vi    i  v  i     i     vvv    v iv i  -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA- 791

  chr2_205115591_   1779 TATAAAAACAAG----CCTATTAAAAAGTGAGTAAAGGACATGAA----C 1820
                           v   i    i----  v   ?    i  i i      iv    ---- 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_205115591_   1821 ACTTTTCAAAAGAAGAAACACATGTGGCCAATAAGCATCTAAAAAACATG 1870
                          i  i  v        v i   vi             iv i    i-   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG-ATG 890

  chr2_205115591_   1871 CTTAACATCACTAATTAT 1888
                           i       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.86 (26 / 14)  


2286 23.55 5.23 1.16  chr2_205289670_205291349.rev      502  1189 (491)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr2_205289670_    502 AAAAAGAACAAAGCTGCAGGCATCACAGTACCAGACTTCAAAATATACTA 551
                           i          i  v   vv     v v  vi i       iv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_205289670_    552 CAAAGCTATAGTAACCAAAACATCGTGGTACTGGCATAAAAGCAGGCACA 601
                                 i     i   i   vi               iiii  i  i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_205289670_    602 CAGACCAATGGAACGGAATAGTGAAACCAGCAATTAACCTATGTATGTAC 651
                         i   i        ii    v v  iv    v   v    i  ii  v  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_205289670_    652 AGCTAATTGATGTTTGACAAAGGTGCAAAGAATATTAAA----GAAAGAA 697
                         i ii       v  i     i     v    vi   v  ----       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_205289670_    698 CAATCTCTTCAATAAATGGTGCTAGGAAAACTAGGTATCAATAAGGAAAA 747
                         i i   i     i          i   v    i i  ? v i v v    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_205289670_    748 AA--GAA--CAGACTCCCATCTCTC----TATACAAAAATCAACTCAAAA 789
                         i --   --ii   i  i i   v ----           i         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_205289670_    790 TGGATTAAATGTCTTACATAATGTAAGACATGAAACTATGAAACTAACAG 839
                              i ? - v i  ---         vv i       i     vvi  
  L1M4_orf2#LINE/    493 TGGATCAWA-GACCTA---AATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_205289670_    840 AAGAAAACACAGTGGAAACACTTTAAGACATTGGTTTGAAAAAGGATTTT 889
                                  i  v? v  vv   iiv   v    v  iiiv  v i   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_205289670_    890 ATGAATA--ACACCTCAAAAGCACAAGCAACAAAAGCA----TAAATAAA 933
                         v ii   --     --                    v ----  i     
  L1M4_orf2#LINE/    589 TTAGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_205289670_    934 TGGGATTATATACAAACTAAAATGATTCTGCACAGCAAAGGAAACAATCA 983
                          v   i vi  vv   i     -iv  i  ii vv       v  v    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_205289670_    984 GAGAAA----AAAGGCAACCTACAGAATGGCAGAAAATACATGCAA---- 1025
                         -     ----    i     i         v        iv     ----
  L1M4_orf2#LINE/    686 -AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_205289670_   1026 ----TCTGACAGGGGATTAATATTCAAAATAAATAG-GAACTCAAAGAGC 1070
                         ----     i i    i vi   i  i    v   i-      vv v i 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_205289670_   1071 TCAATAGCAAAAAAA-----AATCCAATTTAAAAATGAGCAAATGCTCTG 1115
                               ii     i -----  i      ?       i     v v i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_205289670_   1116 AACAGGTATTTTTCAAAAGAACACATATAAATGGCCAAAAAATATGTGAA 1165
                           i  ii    i  v      v i   i          v  ii ii    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_205289670_   1166 AAAATGCTTAACATCCTACTCATG 1189
                           i     i      v????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (97 / 61)
Gap_init rate = 0.02 (15 / 716), avg. gap size = 2.93 (44 / 15)  


3267 23.93 1.98 2.09  chr2_205493561_205497629     2671  3577 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_205493561_   2671 GAAAGCTACTCCATGTTCATGGATTGGAAGAATCAATATTGCTAAAATGT 2720
                              v  ii                     v i       i   i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_205493561_   2721 ACGTTCTGCCCAAAGCAAACCGCAGATGCAATACAACCCCTGTGAAAGTG 2770
                         vvi v  v      vii v ii     v   ii   i    i v   i -
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT- 101

  chr2_205493561_   2771 CTCA--TGACATTCTTCAAAAAAATAGGGAAAAAAAAAATCCTAAAATTC 2818
                          i  --  v -  i  iiv i    v --- v  ivvi            
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_205493561_   2819 ATGTGGAACCACAAACGACCCAGAATAGTCAAAGACA-TCTGGAACAAAA 2867
                           i     vii   iv            i    -   -   v   v  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGA 196

  chr2_205493561_   2868 AGAACAAAACTGGAGGAATCATACTACCTGACTTCAAA--TTATTCTACA 2915
                                 ii       v   i   v  ii i      --   --     
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACA 244

  chr2_205493561_   2916 GAGCTGTGGTAACCAAAAAAGCATGGTACTGGCATAAAAACAGACACATA 2965
                         i    iii    i   i v  ii              ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_205493561_   2966 GACCAATGGAACAGAATAGGGAACCTAGAAAGAAATCCACAAATCTACAG 3015
                           i        i     v i  ii i     v   i   i v  i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_205493561_   3016 TGAACTAACTTTTGACAAAGGTACCAAGAACATACATTGGGGAAAAGATA 3065
                          v  i i i   i     i   i      v   v  v        ii   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_205493561_   3066 GTCTT--CAATAAATAGTGCTGAGAAAACTGGATATTTATATGTAGAAGA 3113
                              --   i    i      i  v         ?ii i   i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_205493561_   3114 ATGAAACTAGACCCCTCTCTCTTGCCATATATTAAAATCAAATCAAAATG 3163
                              ii i       vi   vii       iv     i  v        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_205493561_   3164 GATTAAAGACTTAAATGTAAGACCTGAAGCTATGAAACTATTTGAGACTA 3213
                            i ?    i           v  i  i    i     v  ------- 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT-------A 537

  chr2_205493561_   3214 AAAGAAAACATTGAGGAAGCTCTTCAGAACGTTGTTCTGGGCAAAGATTT 3263
                         i          v i? v iv     ivi  v   vvi i     v i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_205493561_   3264 ATTGAGTAATACTTCACAAGCACAGGCAACCAAAGCAAAAATAGACAAAT 3313
                         v  iii  vv  vi  v       i     v    v         i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_205493561_   3314 -GGATTACATCAAGTTTAAAAGCT---GCACAACAATGGAAATACTCAAC 3359
                         -   i v      iv      i  --- ii vv   v   v ivv    v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_205493561_   3360 AAAGTGAAGAGAGAACCCACAAAATGGTAGAAAATATTTGCAAACTATTT 3409
                                 i   v        i     v                ii  v 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_205493561_   3410 GTCAGACA--GGATTAAGAACCAGAATGTATAAGGAGCTCAAACAATTTT 3457
                         i  v  i --   i viv v       i     i  i   vv    i iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_205493561_   3458 ATGGGAATAAAAT--CTAATAATCTGATTTTTTAAATGGGCAAAAGATTT 3505
                           ---       v-- v     i ii   ?vv-           i     
  L1M4_orf2#LINE/    788 AT---AATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTT 833

  chr2_205493561_   3506 GAATAGTCATTTCT---AAAAAGACATACAAATGGTAAACAGCTATGTAA 3552
                               v       ---  i    i          iv  i ivi ii i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_205493561_   3553 AAATGTGCTCAACATCATTGCATTA 3577
                            vi            ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (133 / 80)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 2.18 (37 / 17)  


2430 22.89 10.91 3.20  chr2_205503009_205506637.rev     2295  3137 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_205503009_   2295 TGGAGAGATATGTTATACCTTCTTCATAAGTTAGAAAACTCAACATTATT 2344
                             i      vii  i-----     iii  i   i   i  i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATG-----TTCATGGATTGGAAGACTTAATATTGTT 45

  chr2_205503009_   2345 AAGATG-CAAGTTCTCCCTAAATTGGACTATATCTTGAACATAATCCCT- 2392
                               -   - v     i      iv   i vv  v   ii       -
  L1M4_orf2#LINE/     46 AAGATGGCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_205503009_   2393 TCAAATTCCCAGCAGGCACTGCTGCAGAAATTGACATGCTGATTCTA--- 2439
                              v       v v vi vi              v      i   ---
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_205503009_   2440 ------TGAAAATGCAAAGAACCTAGAATAGCCAAGACAATTATGAAAAA 2483
                         ------  i        i i   i           i     iv       
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_205503009_   2484 AGA-AACAAAGTTAAAGGGCCAATATGACTTC---ATTTCAAAACTTACA 2529
                         ii -         ii   i iv i ---    ---              -
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACA---CTTCCCAATTTCAAAACTTAC- 240

  chr2_205503009_   2530 ATATTATAAAGAGATAGTAATCAAGATAGT----------CATGAG---- 2565
                         ----  i    vv i           i   ----------   i  ----
  L1M4_orf2#LINE/    241 ----TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_205503009_   2566 ----------CCAA-GAAATA----------TCCAAAAGTA--------- 2585
                         ----------i   - i    ----------    i  i  ---------
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_205503009_   2586 ---TATGGACATCAG--AATTTTCAAGCAAGGTGCAAATGGCAATACAGC 2630
                         ---     ---   i--i      i vv i     v  - i v  v  ii
  L1M4_orf2#LINE/    337 ATTTATGG---TCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAAT 382

  chr2_205503009_   2631 GTAGAAAGAATAGTCTCTTTTGA-AAATGGTTCTCAAGCAGCTGAATATC 2679
                          vi             -   ii -       v  viii  i   i   ? 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCT-TTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_205503009_   2680 CATGTA-AAAAAAATAAACTTGAACTCATGTCTCACTCTTTATAGAAAAA 2728
                           ii i-    i   i  v   i  i v ii     v iv    v     
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_205503009_   2729 TTAATT---AATAGATCATTGACCTAATTTGAAAACTTAAAATGATAAAA 2775
                             i ---   i     ?v       v vv  i vi     iv      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_205503009_   2776 CTTCTAAAAGAAAATTTAGTAGAAAACCTTTGCAAACTGAGATTAGGCAA 2825
                           ii  i       iv   v? v   i   i ii v  vi i        
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_205503009_   2826 AAGTTTCTTAGACATGACACTAAAAGCATGGTCCATGAA-GAA------- 2867
                         vi          i       i       iiiv v ii  -   -------
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_205503009_   2868 -TAAATTGAACATCATGAAAAT-AAAAGCTTCCACTATTTGTGT------ 2909
                         -       i  v    v     -    i   -------     i------
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTT-------TTGTGCTTCAAA 674

  chr2_205503009_   2910 -AACATTTTTAAGAAAATAAGAAGATAATCCACAGCCTGA-AGAAAGTAC 2957
                         -i   i v i      i i i    i  i      vv  i-     i  i
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_205503009_   2958 TATCAAATCATATATCAAATAAAGG-CCTGTACTCAAAGTGTATAAAGAA 3006
                          vv             vi    i  - i    ii  i i i         
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_205503009_   3007 CTATGAAAACTCAGTAATAAAG---CAATTAATCCAATAAAATAAATATG 3053
                           v v v      i       i---   v   i     v?  -    iv 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGG 823

  chr2_205503009_   3054 CAAAAT-TTTAAACAAACTCTTTACCAAAGAAAATATACAAATGGCAAAG 3102
                             iv-   i  i i  vi  iv        i             v  v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_205503009_   3103 AAGTACATAAAAAGAGGCTCAACGTTATTATTAGG 3137
                            i    i      v       i i ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (126 / 63)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 3.84 (119 / 31)  


2145 23.18 4.90 4.11  chr2_205546027_205547771.rev      500  1254 (491)    L1M4_orf2#LINE/L1      148   908 (0)  

  chr2_205546027_    500 ATATGGAACAAGAAAAGACCCATAACAACCAAAGCAATCTTGAGCAAAAC 549
                                 vviv  ii      v  i i     i         --    v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAG 195

  chr2_205546027_    550 AAACAAACAAACAAAAAACCTGGAGGCATTACACACTGATCTAAAAAAGA 599
                           i------      i---i      - i -      --  iv  vvvv 
  L1M4_orf2#LINE/    196 AAG------AACAAAG---TTGGAGG-ACT-CACACT--TCCCAATTTCA 232

  chr2_205546027_    600 AAA--TCCTAAAACTCTTTTATAATCAAAACAGCATGGTACTGGATGGCA 647
                            -- v   v  vv  vivi       i    ii         ----  
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG----CA 278

  chr2_205546027_    648 TAAA-ACAGACACGTCAACCAATG-AACAGGACAGAAAACCCAGAAAGAA 695
                            i- i     ii vi i     -  i  i iv  i ii       v  
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_205546027_    696 ATCTAAGTATTTATAGTAAATTATGAC-----ACACAGGTGCCAAAAT-- 738
                          i i vii      i  v    --  i-----   vi        i i--
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATT--GATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_205546027_    739 -----TGGAAATAAGTACAGTCTCTTTAATAAATGGTGGTGGGAAAATGG 783
                         -----   ii -   v i     i  i  i        v     v  iv 
  L1M4_orf2#LINE/    377 TTCAATGGGGA-AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_205546027_    784 GATATTCACAAGCAGAAAAATGAAATTGAACTTTTATCTCACAACATATT 833
                             ?i    v   i  i      i   i  iii  i      v     v
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_205546027_    834 CAAAAATTTACTCAAAA-GAATAAAGAAATCTAA-CATAAAACTTGAAAC 881
                                 v        - i  v ?- i i    -ii   i vi i    
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAW-AGACCTAAATGTAAGAGCTAAAAC 524

  chr2_205546027_    882 TATAAG-----TAGAAGAAAACA-AGGG--AAATGCTCCATGACACCAGT 923
                              i-----            -   ?--    -  i i    viii v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGG 573

  chr2_205546027_    924 CTGGGAAATGATTTATTGGATAGCATTCCAAAAGCACAGGCAATGAAAGC 973
                         i i  v    i   v  i    vv iv           i    ii    v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_205546027_    974 AAAAACAGAAAAACAGGATTGCATCAAA-CTAAAAATTGTTTCCTCTGCA 1022
                              i   v   iv   i v       -i      i ------ i  ii
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT------TTTGTG 667

  chr2_205546027_   1023 CAACAAAGGAAACAGTTAACAGAGTGAAGATACAACCTA--GATTGGGAG 1070
                          vv       v  vi i  v i      i v      i --  v      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_205546027_   1071 AAAATATTTGCAAACCGTCCATCTGATAAGGGGCTAATATTCAAAATATA 1120
                                       i i vi            i  vi   i  i      
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_205546027_   1121 TAGGGAACTCCCACAATTCAACAG---AAAGA-AAA----CTGTTTTAAA 1162
                           ii      ii    i    i i---     -   ---- iiv  ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_205546027_   1163 AATGGGCAAAGGATCTGAACAGGCATTTCTCAGAAGAAGAAATACAAATG 1212
                                       i    i  i        vi       v         
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_205546027_   1213 ACCAAAATATATATGAAAATAATGCTCAACATCTCTAATCAT 1254
                         i    v vii i       -i            v????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (113 / 58)
Gap_init rate = 0.04 (28 / 761), avg. gap size = 2.43 (68 / 28)  


 674 32.00 2.00 0.40  chr2_205681557_205687835.rev      215   464 (5815)    L1M4_orf2#LINE/L1        2   255 (653)  

  chr2_205681557_    215 GAGAAGATATAGCATGTTCATTCATGTGAAGACTCAGTATTGTAAGAATG 264
                          ii       vv         vv  vv       i i      v ii   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_205681557_    265 CCAATTCTCTCCAAACTAATCTACAAATTCAATTCAATCCCAATCAAAAT 314
                         v    v   i     i i       i      iv       v        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_205681557_    315 CTCATAGGTTTCTGCTTCTGAAATTTAACCGGCCAGTTCTAAAATTAAAG 364
                          i  vvv ii i vi v v      -i  vi  iii i        v vi
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCATA 150

  chr2_205681557_    365 TGGAAGAACAAAGGGCCAAGAACAGCCTGACCATTCTTGGCTGTGAACAA 414
                              ivi   i  i  v    i    vi v  v     ivviv   v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_205681557_    415 CACAG-----GAACCTACCCTGACAGATATCACGGAGTATTATAAAGTTA 459
                           v  ----- i  ii  v  vv vi  v   viivv  i  i    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_205681557_    460 GGGTA 464
                         vi   
  L1M4_orf2#LINE/    251 CAGTA 255

Transitions / transversions = 1.05 (41 / 39)
Gap_init rate = 0.01 (2 / 254), avg. gap size = 3.00 (6 / 2)  

3237 26.98 0.66 0.66  chr2_205681557_205687835.rev     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_205681557_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_205681557_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_205681557_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_205681557_   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_205681557_   5078 AACAAAGCTGGAGGCATCACACTACTTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v iii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_205681557_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_205681557_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACGTACCTACAACT 5225
                                i    i--    i  --        vv   iii ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_205681557_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT--T 5273
                          vi    i  i     ivv  vv  i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_205681557_   5274 CCGTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5323
                          -- v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_205681557_   5324 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5373
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_205681557_   5374 GATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5423
                            i ?   ii    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_205681557_   5424 ACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAAGACTTCATGTCC 5473
                           v    ?i v viv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_205681557_   5474 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5523
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_205681557_   5524 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAA 5573
                         v  i   v v  i i   i  ii vv    i  v    i  vv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_205681557_   5574 ACAGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5623
                          v  i     i   iv            v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_205681557_   5624 AAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAA 5673
                           i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_205681557_   5674 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACG 5723
                            i     i     v  i?    i    ii     iv    i     iv
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_205681557_   5724 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACGCATGAAAAAATGCTCA 5773
                             v        i  vi viii     v  i i        i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_205681557_   5774 TCATCACTGGCCAT 5787
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


3537 23.11 1.31 1.86  chr2_205717042_205719014.rev      569  1481 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_205717042_    569 TGGAGAGAGATCTCACGTTCATGGATTAAAAAA-TTAATATTGTTAAAAT 617
                             i   v   i  i           ii  i -             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_205717042_    618 GTCCATACTACCCAAAGTGATCCACAGATTCAGTTTAATTCCTATATAAA 667
                          v v     v      v     i         iivi   i     vv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_205717042_    668 TTCCAATTCTATTTTTCACAGAAACAGAAAAA--AACCCTAAAATTCATA 715
                          i   ii viv     ii      iv  v  i--i i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_205717042_    716 TGGAACCACAAAAAGCCCCCAAATA-CCAAAAGTAATCTTGAGCAAAAAG 764
                              vii   ii- v   vi    -      -i        iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAG 198

  chr2_205717042_    765 AACAAAGCTGGAGGCATCATAC--CCTGATTTTAAACTGTATTACAAAAG 812
                                i      vv   i  --  ii    i   viv  i      --
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-- 246

  chr2_205717042_    813 TACATAGCCACAGTAAT-AAAACAGTATGGTATTGGCATAAAAACAAGAC 861
                         ------  i        -  i     i     i        ii i -   
  L1M4_orf2#LINE/    247 ------GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GAC 289

  chr2_205717042_    862 ACATTGACCAATGGAACAGAACAGAGAGCACAAAAATAAACCTGTGCATA 911
                          i  v  i        i    iv     iv  i         ii i   v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_205717042_    912 TATGGTCAACTAATCTTTGACAAGAGTGCCAAGA--ATGCAAAATGGGGA 959
                                  i i  i  i      i         --  v   --      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGA 387

  chr2_205717042_    960 AAGGATAGTCTCTTCAATAAATGATGCTGTGTGAACCAAATATACACATG 1009
                            i       i     i     i     v vv   iii   ?v      
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_205717042_   1010 CAATATAATGAAATTAGGCCCTTATCTTACCTCATATACAAAAATTAACT 1059
                            v v      i  i i   i  i  i  vi                  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_205717042_   1060 CAAAAAAGACTAACGACTTAAATGTAACATCTGAAAATGTAAAATTCCTA 1109
                              vi  ii ?v   i         v v  i   v i     i  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_205717042_   1110 GGAAAAAGCACAGTGAAAAAGCTCCTTTACATTGATCTTGGCAATGATAT 1159
                          i i   i  i  v?iv   v  i v v  v   ivi v       i v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_205717042_   1160 -TTGGATATGACACTAAAAGCACAGGCAACAAAAGCAAAGGCAAACAAGC 1208
                         -  i          i         i          v   iii i i  ii
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_205717042_   1209 AGGACTACACCAAACTAAAAAGCTTCTGCACAGCAAAGGAAAAAAAAATC 1258
                         v     v  i    v v    i   i  ii vv       v vv ---  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA---TC 684

  chr2_205717042_   1259 CACAAAATGAAAAGGCAACCTATGAATTGGGAAAAATTATTTGCAAACTG 1308
                         v v   i       i     i iii v     i   v          iii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_205717042_   1309 TATATTTGATGAGGGATTAGTCTCCAAAA-ATATTATAAATTCAAGCAGC 1357
                              i    i     i v  v    i  -    v vi  i  vvi  i 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_205717042_   1358 TCAATA-TCAAAAAACAAATAACCAGATTTAATAATGGGCAAAGGACATG 1406
                               - v    i          vi   ?  v             iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_205717042_   1407 AATAGACATTTTTTTCAAAGAATACATACAAATGGCCAACAGATATATAA 1456
                                    i i-       v i              i iii i  i 
  L1M4_orf2#LINE/    835 AATAGACATTTCTC-CAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_205717042_   1457 AAAGGTGCACAACATCACTAATCAT 1481
                             i   v        ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (135 / 72)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.81 (29 / 16)  


4300 15.62 4.86 1.50  chr2_205790092_205791947      501  1364 (492)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_205790092_    501 TGTTCATGGATTGAGAGACTTTATGATGGTTA-GATTGTGATACTCTCCA 549
                                      ii      v  -  v    -   v ii      i   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAAT-ATTGTTAAGATGGCAATACTCCCCA 64

  chr2_205790092_    550 AATTGATCTATGTATTCAATGCAATCCCTAGCAAAAACCCAACTGTTTTT 599
                                   iiv      i          v     v    i   ii   
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr2_205790092_    600 TTTTTGCAGATATTAACAAACTGATTCCAAAATTAATATGGAAATGCAAG 649
                            --     v   i    i     i i      v               
  L1M4_orf2#LINE/    115 TTT--GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_205790092_    650 AGACCCAGCATAGCCAAAGCAATCTTGAAAAATAAGAACGAATTTGGAAG 699
                         i       v         i             v      i  v     i 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_205790092_    700 AATCACACATCCTGATTTCAAAATTTAGTACAAAGCTACAATAATT--GA 747
                          v      v   ii         i   v            i    i--  
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_205790092_    748 CTGTGTCGTACTGACATAAGAATAGACAGGTATAGATCAATGAATAAAAT 797
                          v    v      i      i       --            i ----  
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACA--TATAGATCAATGGA----AT 306

  chr2_205790092_    798 ACAATTGAGGATCCGGAAATATACCCTTACATTTTTGGAAAATTCATTTT 847
                          v       ii   i      v    v       v   vv    v     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_205790092_    848 CTTTAAGGGTGTCGAGACAATTCAATGAATAAAAAAACAATCTTTTCAAT 897
                          vvi       i i    v        ii-i   i  i i         i
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTTTTCAAC 405

  chr2_205790092_    898 GAATGATACTAGCACAACTAGATATCCACATGCAAA-GAATGAATTTGAA 946
                         i    i i  i v      i    ?           -       v   i 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_205790092_    947 CTCCTTCCTCACACAGTGTGCAGGAATGAACTCAAAATG-ATAATAGGCC 995
                          i   v        vi i i  ii   v           -  v ?  i  
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_205790092_    996 TAAATGTAAGAGCTAACACCGTATAAGATTCTTATAATAAAACAAAGGTG 1045
                                         v  --     i i     v  v      v   ? 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAAC--TATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_205790092_   1046 TACATCTTTGTGACCTTATATTAGGCAATG-TTTCTTAGATACAAAACCA 1094
                           v     i        ivi          -           ii v    
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_205790092_   1095 AAAACACAAGCTACAAAAGAAAAAATAAATACATTGGACTTCGTTAACAT 1144
                            i       v               i   v          i i  v  
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_205790092_   1145 AAAAAACTTTTGTGCTTTAAAGGACAC-ATGAAGAAAGTGAA--GACAAC 1191
                         v                i         -  v           --      
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_205790092_   1192 CCAAAGAACAGGAAAACATATTTGTAAATCATATATTGGATAAGAAATTT 1241
                            v    ii   i  v       i           iv      ii i  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_205790092_   1242 GTATATGGAATATTTAAAGAACTCTCTACAGGTCAATAATAAAAAGACAA 1291
                             vii      v           -    iv                  
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCT-TACAACTCAATAATAAAAAGACAA 802

  chr2_205790092_   1292 ATA---------------------------------GACATTTCTCCAAA 1308
                            ---------------------------------              
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_205790092_   1309 GAAGATACACAAAGGGCCAATAATCACAGGGAAAGAAGCTCAACATCATT 1358
                                i     v         v    v i     v           ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_205790092_   1359 GGTCAT 1364
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.44 (78 / 54)
Gap_init rate = 0.02 (15 / 893), avg. gap size = 3.67 (55 / 15)  


1921 27.22 0.36 1.42  chr2_205915089_205917631.rev      502  1063 (1480)    L1M4_orf2#LINE/L1      112   667 (241)  

  chr2_205915089_    502 TTCTTCACAGAAACAGAAAAAAAGACAATCCTAAAATCTATGTCATATCA 551
                           i  ii      iv  v  --- vii          ii  i viv vii
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAA---GCTGATCCTAAAATTCATATGGAAATG 158

  chr2_205915089_    552 CAAAAGGCCCAGAATAGCCAAAGCCATCCTGAGCAAACTGAACAAAACTA 601
                            ii i               i v   i   iv  ivv       ii i
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_205915089_    602 GAGGAATCACATTACCTGACTTCAAATTATACTACACAGCTAAAGTAATC 651
                              v     i v  ii i      viv       v     v       
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_205915089_    652 AGAACAGCATGATCCTGGCATAAAACTAGAGTCATAGATTAATGGGACAG 701
                          ii    ii  i v         iiv    vvi      i     i i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_205915089_    702 AACAGAGAAACTAGAAAGAAATCCATATATCCACAATGAACTTATTTTTG 751
                           iv    iv i     v   i     i  ii iii v  i v     i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_205915089_    752 ACAAATAAGCCAAGAACATACACTGGGGAAAGAACAGTCTCTTCAATAAA 801
                             iviv       v   v  v           i     i     i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_205915089_    802 CGGTACTGGGAAAACTGGATATTCATATGCAGGAGAATGAAACTAGACTC 851
                         i   i      v         ?i  i     ii        ii i   i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_205915089_    852 TTATCTCTCACCATATAAAAAAAAATCAAATCTACATGGATTAAATACTT 901
                         i  i   v         v     -- i  v  v v      i ? v  i 
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAA--TTAACTCAAAATGGATCAWAGACCT 506

  chr2_205915089_    902 ACATATAAAACCCCAAACCATGAAACTACTACAAGAAAACATCAGGG-AA 950
                          v  i   i v iv    i  i     vi  v          vi ? -  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_205915089_    951 ATGCTCCAGGACATTAGACTCGGCAACGATTTCTTGAGTAATACTCCACA 1000
                           -  i iv   v  i ii v     i i      iii  vv  v   v 
  L1M4_orf2#LINE/    557 AT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_205915089_   1001 AGTACAAGCAACCAACTGCAAACATGGGCAAATGGGATCACATCAAA-TT 1049
                           i         v  v- v   v  i ii    v   iiv       -  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_205915089_   1050 AAAAAGCTTTTTTG 1063
                              -     v  
  L1M4_orf2#LINE/    655 AAAAA-CTTTTGTG 667

Transitions / transversions = 1.63 (93 / 57)
Gap_init rate = 0.01 (7 / 556), avg. gap size = 1.43 (10 / 7)  

 398 19.77 2.33 0.00  chr2_205915089_205917631.rev     1421  1506 (1037)    L1M4_orf2#LINE/L1      671   758 (150)  

  chr2_205915089_   1421 CAAAAGAAACAGTGAACAAAGTGAAGAGACAATCCACAGAATGGGTGAAA 1470
                             i  v  vi v  v        i      i            v    
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_205915089_   1471 ATATTTGCAAACTACCCATCTGATATGG--TTTGTCTC 1506
                                    ii ivi        v  --i    v  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 2.00 (2 / 1)  

 488 23.81 2.98 1.19  chr2_205915089_205917631.rev     1884  2051 (492)    L1M4_orf2#LINE/L1      738   908 (0)  

  chr2_205915089_   1884 ATCTGAAAATGGATTATTAAACAGTATACATAAAGAGCTCAAACAACTCC 1933
                               v  v   i vv  vv   v   i       i   vv       v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_205915089_   1934 AGAGGAAAAAAATCTAAAAATCTGATTTTAAAAATGGACAAAATATCTGC 1983
                          v iv     i - v  v  i ii   ?-        i    iv  i  v
  L1M4_orf2#LINE/    788 ATAATAAAAAGA-CAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGA 835

  chr2_205915089_   1984 ACAGATATTTCTC-----AAGACATAAAAATGGCAAACAGGTATAGTAAA 2028
                          i   i       -----    i   v       v  i i i i vv   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_205915089_   2029 AGGTGCTCAACATCATTGATCAT 2051
                           i            ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.95 (19 / 20)
Gap_init rate = 0.02 (3 / 171), avg. gap size = 2.33 (7 / 3)  


2949 21.70 10.91 0.85  chr2_206265856_206268051.rev      879  1703 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_206265856_    879 TGGAGAGACATTCCATGTTTATGGAT-GGAAGACTCAATACTCTCAAGAT 927
                             i   i  i       i      -        i    i v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_206265856_    928 GTCAGTTCTTCCCAACTTGATCTACAGATTCAATGCAATCCCAATCAAAA 977
                          v  i v  i     v                 i        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_206265856_    978 ACAGAGAAAGTCTTTTTTG--GATATTTACAAACTGATGCTAAAGTTTAT 1025
                         v vv  vv- i        --  v   v    i     v     i  i  
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_206265856_   1026 ATGCAGAGGGAAAAGACCAAGAAGAGT--AAACCAAATATTGAAGGAGAA 1073
                            v i v v  ii    v    v  i--    --   v     ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAAC--AATCTTGAAAAAGAA 197

  chr2_206265856_   1074 GAATAAACTTAGAGAACCGATAATAGCCAACTTTAAGATTTACTATAAAG 1123
                            i   v  i   i  iv i v vv    i  i  i i      i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_206265856_   1124 CTACACTAATCATGACACTGTGGTATTGGTGAAAGAATAGACAAAGAGAT 1173
                              v      v    v       i   iiv   i       v v    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_206265856_   1174 CAATGGAACAGAATAGGAAGTCCGGAAGTAGACCCAT---TTTAGCATAG 1220
                                 i     v ii     i   i  i      ---    --- i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA---TGG 344

  chr2_206265856_   1221 TCAACTGACCTTTGACAAAG-CACCAAAGGCAATACAATGGAGAAGAGAT 1269
                             i   ii  i     i -ii    - i v  v      i   iii  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAAT 393

  chr2_206265856_   1270 CGTCTTTTCAACAAAGGATGCTGGAACAACTGGACATCCACATGCAAAA- 1318
                         v              v i      i         i ?            -
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_206265856_   1319 AATGAATCTAGACACAGACCTTATGCCCTTCACAAAAATTAACTCAAAAT 1368
                               vi i   v vv    i ii  v vi                   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_206265856_   1369 GACTCACAGATCTAAATTTAAAATGTGAAACCATAAAACTCCTAGAAGAT 1418
                          iv   ?   i      v   i vv i    i         i       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_206265856_   1419 AAAATAGGAGAAAACCTAGATGACCTTGGGCATGGTGATGACTTTTTAGA 1468
                           v     ? v   i  vvi          ivv  ii   ii  i     
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_206265856_   1469 TA---CATCAAAGTCACAA------------------------------T 1485
                           ---  i    iv     ------------------------------ 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_206265856_   1486 CCATGAAAA--AAAAA------------AAAG------------------ 1503
                         i   v    --     ------------    ------------------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_206265856_   1504 ----------CCACCAATTGGCAGAAAATATTTGCAAAAGACACATCTGT 1543
                         ----------    vi v   v                vv i i     v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_206265856_   1544 TAAAGGACTGTTATC-AAAATATACATAGAA-TGTGAAAACTCAACAGTA 1591
                            i     vv    - i      i v    - v v v       i i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_206265856_   1592 AGAAAACAAA---CTCAATTACAAAATGGGCCAAAGACCTTAACAGACAC 1638
                          i  i     --- i     ?v         v  i  ii v  i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_206265856_   1639 CTCATCAAAGAAGATATACACATGGCAAATCAGTATATGAAAAGATACTC 1688
                         i  vi               v     v   v  i i          i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_206265856_   1689 TGCATCATACGTCAT 1703
                         vi     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (101 / 74)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 5.39 (97 / 18)  


3176 24.03 3.17 0.23  chr2_206357074_206360959.rev     2561  3413 (473)    L1M4_orf2#LINE/L1       10   887 (21)  

  chr2_206357074_   2561 ATTCCATGTTTATAGATTAGAAGAATTAATATTGTTAAAATGACCA---- 2606
                           i       i  i    i     v             i   i v ----
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_206357074_   2607 CTACAAAGCAATCTACAGATTCGATACAATCCCTTTCAAAATACCAA-TG 2655
                          iv    vii            i ii        v       v   i-  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_206357074_   2656 TTATTTATCACAGAAATAGAAAAAATAATCCTAAAGTTTGTAAGGAACCA 2705
                         iiv   - ii       v  v  iv i        i  ii  v    vii
  L1M4_orf2#LINE/    110 CCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_206357074_   2706 AAATGAAGCCCAAATAGCCAAAGCAATTCTGAACAAAAAGAGCAAAGCTG 2755
                         v  v i v  vi          i    ii    v  i    i     i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_206357074_   2756 GAGGCATCACACTACCTGAT------AC--ATTGCAAGGGTAGAGGAGGC 2797
                             vv       v  ii  ------  -- i i   i v  v  v iv 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_206357074_   2798 AACACAGCGTGGTATTGCTATAAAAATAGTCACATACACCAATGGAACAG 2847
                           v    i      i  vi    ii    v  i   v i        i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_206357074_   2848 AATAGAGAACATAGAGATAAATCTATGCATGTACAGCAAAACGATTTTCA 2897
                            v    iivi   i     i i  i   v  ii iv  vi       i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_206357074_   2898 ACAAAGATGCCAAGAACATAAACTGGGGAAAGGATA-TCTTCTTAAATAA 2946
                             i i        v   vv v         i   -    -  v  i  
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-TTCAACAA 407

  chr2_206357074_   2947 ATGATGCTGGGAAAATTGGATATCCATATGCAGAACAATTAAACTGGACC 2996
                            i        v  i      ?   i     i  v   v  ii      
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_206357074_   2997 CCTGTCTC--------TACAAAAATCAACTCAAGGTGGATTAAAGACTTA 3038
                            ii   --------         i       ii     i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_206357074_   3039 AATGTAAGACCTAAAACTATAAAACTACTAGAAGAAAACATAGGGGAAAC 3088
                                  v                vi                ? v  v
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_206357074_   3089 ACTTCAGGACATTGATCTAGGCAAAGATTTTATGGCTAAGACTTCAAAAG 3138
                         v    iv   v   ivi       v i   iv i v  v   vi      
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_206357074_   3139 CATAGCCAACAAAAACAAACATAGACACCTAGGACCACAATAAACTAAAA 3188
                           i iv        iv   v     i vv v    iv  vi   v v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_206357074_   3189 AGCTTCTGCACAACAAAGGAAACAA--AACAGAGTAAAGAGACAACCTGT 3236
                          i   i  ii vv       v  v --  v i   i  i        iii
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_206357074_   3237 TGAATGGGAGAAAATATTTGCAAACTATTCATCTGACAAGGGACTAATAT 3286
                         v                       ii  vi      i        vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_206357074_   3287 CCAGAATATACAAGGAACTCAAACAACTCAACAGTATAAAAATAAATAAT 3336
                                   i  i      vv         i i  v   i i      i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_206357074_   3337 CCCATTAAAAAGTGGGCAAAGGATGTGAATAGACATTTCTCAAAAAAAAA 3386
                           v   ?    i            v                v   i  i 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_206357074_   3387 AAAAAAAAAAA--AAAAAG-ACATAGAAAG 3413
                         v v v   vii--  v   -    ii    
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAG 887

Transitions / transversions = 1.42 (118 / 83)
Gap_init rate = 0.01 (11 / 878), avg. gap size = 2.64 (29 / 11)  


1587 28.95 8.84 3.49  chr2_206982237_206984402      830  1689 (477)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_206982237_    830 GAAAGAAATTTTCATGTTCATGGATTG-AAGAATCAATATTGTAAACATG 878
                               v  ii-               -    v i        v  v   
  L1M4_orf2#LINE/      3 GAAAGATATCC-CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_206982237_    879 TCAGTTCTGCCTAGATTGTTATATTTATCCAATGTAATTTCAATCAAAAT 928
                         v  i v  v  i i    v v  ivv  i   i i   ii v        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_206982237_    929 CTCAGAGAAGTATTTTTTTT-TAA----TGAAAAGCCAATTCCAAAAATA 973
                          i   v---- iii      -i i----   v    ii  -  v     v
  L1M4_orf2#LINE/    102 CCCAGC----TGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATT 146

  chr2_206982237_    974 AATGTGGGAAAGTAAAAGGCTCAGAAGAACTAGGATAATCTT-------A 1016
                         v  i   i  v i  ii i i     v i i ii i      ------- 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_206982237_   1017 AGAACAAAGTGAATAGATGTCCTCTATCAGATACTAAAACTTAT---GAA 1063
                                   viivi  iviv v  vi vi  vii        i---i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_206982237_   1064 ACTTTAGTCTTTAGTCTTTAAAATAGTGCAGTTTTGCTGCAGAGTTAGA- 1112
                         i  vi   ---- i  ---  i i    ii  vi  viii ii v    -
  L1M4_orf2#LINE/    247 GCTACAGT----AATC---AAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_206982237_   1113 A---AGACCA-TGGAAAAAAACCAGGAATTCCAGAAACAGAC----ACAT 1154
                          ---   i  -     v i  iiii  i -       i i  ----    
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGT-CCAGAAATAAACCCATACAT 338

  chr2_206982237_   1155 TTATGGATGTCTGATTTGTGACAAAGGTGCT--GCACAG-CAGTGAGGAC 1201
                               viivi      vi     i     i-- vv  v-  i  i   v
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_206982237_   1202 AGGAC--TTTCTTCAATAAATGATACTGGGTCAATTGAATATTCATATGG 1249
                           i i-- i i     i     i i     v   i  i   ?i  i   v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_206982237_   1250 AGAGGAAAATGAAACTTTATTGCCGAATCACCCTGCATATAAAAATCAGT 1299
                          i -- i      ii vv iiv iivv    v iii   i      i ii
  L1M4_orf2#LINE/    439 AAA--AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_206982237_   1300 TAGAAGTAGACTAT-GATTTGGCTACATGTTGTAGCCAAAATAGTAAAGC 1348
                          vi  i i  ii ?-  i----   v    viv   i    ivi    i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGAC----CTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_206982237_   1349 TTCTAGAA------ACAGGAGAAAATCTCTATGACTTTGATGGTAAAGAG 1392
                          ii     ------ i   ? v      iii    i   --   v i vi
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG--GGTTAGGCA 580

  chr2_206982237_   1393 A-GATTTCT--G----GCCACAAAAAGCAC---TGACAAA-GAAAAAA-A 1430
                          - i     -- ---- v   v        ---ii     -       - 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_206982237_   1431 GATAAAACCGGACTGCAATAAAGTTAAA-------------CAATGGAAG 1467
                               -ii     v  vi   i     -------------   v   v-
  L1M4_orf2#LINE/    631 GATAAA-TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC- 678

  chr2_206982237_   1468 ATGATTAAGAAAGTGAAAAGA--AGCTGCAGAGAGGAAGATGGTACTTGA 1515
                          iv  i               -- v ii    iv  i   vii  i   v
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_206982237_   1516 AACACATATAATTGAGCAAAGAACTGGTGTCCTGAATA----GGGAATTT 1561
                           vv      vi   -i  i i   v  i   v     ----ii   i i
  L1M4_orf2#LINE/    729 AAATCATATATCTGA-TAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_206982237_   1562 CTACAAGTCCATAAGGAAGAGACAGAACATCCATTTGAAAAACAG---AG 1608
                         i     v  v    vi  i     i vv i   v  ?     ii --- i
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_206982237_   1609 AGACTTGAACAGACCCAATGTA---AAAGAGGATATCCAGATGGCTAGTA 1655
                         i  i     i    ---  v v---     i     v  i     i i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGAC---ATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_206982237_   1656 A--ATATGAAAAGCTATTGCAAAAATTACAGATTAA 1689
                          -- i        v ii -   v - i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCT-CAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.99 (163 / 82)
Gap_init rate = 0.05 (41 / 906), avg. gap size = 2.59 (106 / 41)  


3547 18.04 3.99 2.32  chr2_207029132_207030899.rev      501  1276 (492)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr2_207029132_    501 AGCAATTGTTAAGTCAAT-------TTCATACATGGAATCTCAAGAGGTC 543
                           v     vi   iii  -------      --     viv    i ii 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATA--TGGAAATGCAAGGGACC 167

  chr2_207029132_    544 ACAAATAACCAAAACAAATCTTTAAAAAGAAAAACAAAGTTTGAGATCTC 593
                         vvi    i         -    v        i         v   iv   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr2_207029132_    594 ACACTTTCTGATTTCAGAACTTACTACAAAACTACAGTAAGCAAAGCAGT 643
                               i ii      i             i         v   ii    
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr2_207029132_    644 GTGGTACTAGCATAAAGATAGACATATAGACCAATGGAATAGAAAAGAGA 693
                                 i      i              i             vv    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_207029132_    694 TCCCAGAAATAAACCCTTGCATATATAGTCAAATGATTTTCAACAAGGAT 743
                         vi              v i   v   i     v        i      i 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_207029132_    744 GCCAAGATCATTCAATGGGGAAAAGACAGTCTTTTCAACTAAATGCTGCT 793
                                i               ii i            -     v    
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC-AAATGGTGCT 415

  chr2_207029132_    794 GGGAAAACCAGATATTCACATGCAAAAATTAAAAAAAAAATGAAGTTGGA 843
                             v   ii    ?i           i----------            
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAG----------AATGAAGTTGGA 455

  chr2_207029132_    844 CTCTTACTTTAGACCATATGTAAAAATTATCTCAAACTAGATCAAAGACT 893
                          i i   i i v       ii        v      v i     ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_207029132_    894 TAAATGTAAGAGCTAAAGTTATAAAACTCATAGAAGAAAAT--------- 934
                                          ii          v          i---------
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_207029132_    935 ----TTTGTGTCATTGATTTTGGAAATGATTTCTTGGATATGATGACAAA 980
                         ----  i   v v   iv  v  v    i      i       iiv    
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_207029132_    981 AATTCAGGCAACAACAACAAAACCAGATTAAGTTGGACTGTA-CA----T 1025
                          iiv  i       v iv    vi    -  i       vi -  ---- 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGAT-AAATTGGACTTCATCAAAATT 654

  chr2_207029132_   1026 ATAAAACTTCTGTGCATCAAAGGACATGATTAACAGAGTTAAAAGGCAAA 1075
                          -       i     v          iv  i  v i   v     i   v
  L1M4_orf2#LINE/    655 A-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_207029132_   1076 CCACAGAATAAGAGGAAATATCTGCAACTGACATATCTGATAAGGAGTTG 1125
                                  ii   i      i     v v i             iii v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_207029132_   1126 ATATCCATAATAAATGAAGAACCCCTGCAACTCAACAACAA-----CAAA 1170
                         i      v    v  i      i i i        i  i  -----    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_207029132_   1171 AAACCGTGCTTTTTAAAATGAGTGAAGGGTTTGAATGGATATTTCTCCAA 1220
                         v    vvi--  ?v      i ii    i       i  i          
  L1M4_orf2#LINE/    804 TAACCCAA--TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_207029132_   1221 AGAAGATATACAAATGGCCAACAAGCACA-AAAAGGATGTTCAACATCAC 1269
                                              i       -i   i    i         ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_207029132_   1270 TAATCAT 1276
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.91 (90 / 47)
Gap_init rate = 0.02 (13 / 789), avg. gap size = 3.77 (49 / 13)  


3672 21.95 0.97 2.81  chr2_207062735_207064685.rev      535  1459 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207062735_    535 TGGAAAGATATCTCATGTTCATGCATTGGAAGAATTAATATTCTTAAAAA 584
                                     i          v         v        v    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207062735_    585 GTCCATGCTACCCAGAGCAACCTATAGATTTAATGCAATCCCTATTAAAA 634
                          v v  i  v    i vii i   i     i  i           i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207062735_    635 TTCCAATGACATTTTTTGCAAAAATAGATAAAACAATTCAAAAATTTGTA 684
                          i   iivi v         i    v  i  ivii  i v      ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_207062735_    685 TGGAACCACAAAAAAAACCCTGAATAGCCAAATCAATCTCGAGCAAGAA- 733
                              vii   iii --   v           v      i  iv     -
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_207062735_    734 --CAAAACTCCAGGCATCACACTACGTAATTTTGAAATATACTACATAGC 781
                         --    ii vv   vv       v vi     ii   iv       v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_207062735_    782 TACAGTAATCAAAACAACATTGTACTGGTGCA-AAAAACAGAAATAAAAA 830
                                     i   iii v       --  -  ii i   v   v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGG--CATAAGGATAGACATATAGA 296

  chr2_207062735_    831 CCAACAGAACAGAAGAGAGAGCCCAGAAATAAATCCATACATTTATGGTC 880
                         i   ii   i    vv     i           i                
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_207062735_    881 AACAGATCTTCAACAAGGATGCTAGGAACACACAATGGGGGAAGAACAGG 930
                           iv   i   i      i   i i  v  iv        i     i  v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_207062735_    931 CTCTTGAATAAATGGTGTTGGAA-AATTGTATATCTGCATGCAGAAGAGT 979
                           i  v  i        i   i -  i  v   ? ii      i    i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_207062735_    980 GAAACTGGACCCATATCTCATACCTTATACAAGAATCAAGTCAAAATGGA 1029
                            ii       v  i    i   v       i   i  v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_207062735_   1030 TTAAGGACTTAAACTTAATACCTGAAACTGTAAAACTACTAAAAGAAAAC 1079
                          i ?i   i    iv   v v  i     i       vi  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_207062735_   1080 ATAGGGGGAAAGCTTCTTGAAATTGGTCTGAGCAATGATTTTTTTTTGGA 1129
                              ? v   v    v   vv    vi ii      i   i  ---i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT---AGA 593

  chr2_207062735_   1130 TATGACCCCAAAATGACAGGCAACAAAAGAAGCAACAAAAGAAAAAAATA 1179
                               v      ------   -   -----                -  
  L1M4_orf2#LINE/    594 TATGACACCAAAA------GCA-CAA-----GCAACAAAAGAAAAAA-TA 630

  chr2_207062735_   1180 GACAAATGGGGTTACATTTTCAC--TTAAAGTCTTCTACACAGCAAGGAA 1227
                           i    v  ii v   ---  v--     iv   i iii vv   i i 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCAT---CAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_207062735_   1228 TACAATCA-GTAGATGAAGGGACAACCTACAGAATGAGAGAAAGTATTTG 1276
                         i  v    - v ii    ii       i        i      i      
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_207062735_   1277 CAAGCCATACATTTGATAAGGGGTTAATATCCGAAATATATAAGGAACTC 1326
                            ii    i  i         ii vi     ii         i      
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_207062735_   1327 AAACAACTCAACAGCAAATAAATAAATAAAACCCAATTTTGAAATGGGCA 1376
                         vv         i ii   v i i      --       ?vi         
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAA--CCCAATTWAAAAATGGGCA 825

  chr2_207062735_   1377 AAGGACCTTAATAGACATTTCTCAAAATAAGACATAAAAATTGCCAA-AT 1425
                              ii v              v   v    i   v    v     - v
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_207062735_   1426 GTATTTGAAGAAAATGCTTAACATCATAAGTCAT 1459
                          i iv    -  i     i       ????????
  L1M4_orf2#LINE/    876 GCACATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (129 / 70)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.19 (35 / 16)  


1337 24.56 8.10 1.52  chr2_207074347_207077872     1887  2281 (1245)    L1M4_orf2#LINE/L1        9   429 (479)  

  chr2_207074347_   1887 TATGCCATGTTCATTAATTAAAAGACTAAGTACTGTTAAGATGCCAAGTT 1936
                            v          vi   ii      v i  i          v   vvi
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr2_207074347_   1937 TCCCTAAGTTG----------------TAATCTCAACCAGAATTCCAA-- 1968
                             i  i   ----------------i    i v i  i   i   i--
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_207074347_   1969 GA-TTTTTTAAAAAGTAATTGATAATCTAACTTTCAAATTTATATGGAAA 2017
                          v-      iv i --      i  v  i iii v     i         
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGA--AATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_207074347_   2018 TACAAAGAACCTGAAATAACCAAAA--ACTTTGTAAAATAAGGAGAAAGT 2065
                          i   i i   iii    i      -- ii   v    v   i v     
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_207074347_   2066 TTAGGGGCT----------GATTTCAAGACTTATTATAAAGATACAGTAA 2105
                          vii  i  ----------i       i     i  i    v        
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_207074347_   2106 TCCAGGCAGTGTAGTATCAGCATAAAGTGAAAAAACTAAACCAATGAAAC 2155
                           v  i      i   iii      i vv i v vv  i i     i  i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_207074347_   2156 AATATAGACAGTCTAGAAACAGACCCATACGTATATATGGTCAATTGATT 2205
                          iv  v  v    i     i i        --  v               
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATAC--ATTTATGGTCAATTGATT 354

  chr2_207074347_   2206 TTTGACAAATTTGCCAAGGCAATTCAGTGGGGGAAAGGAGAGTCTTT-CA 2254
                           i     ivv       i v     i     -    i v       -  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCA 403

  chr2_207074347_   2255 ACAAAATGGCACTAGAAAAATTATATA 2281
                              -   ii  i i v  i iv   
  L1M4_orf2#LINE/    404 ACAAA-TGGTGCTGGGACAACTGGATA 429

Transitions / transversions = 2.03 (65 / 32)
Gap_init rate = 0.02 (10 / 421), avg. gap size = 3.80 (38 / 10)  

 817 24.95 8.75 4.60  chr2_207074347_207077872     2586  3042 (484)    L1M4_orf2#LINE/L1      433   908 (0)  

  chr2_207074347_   2586 ACATGGATACCAAAATAAACCTTATCCCTTATGTCATATCATACAGGAAA 2635
                              v v -- i   i  vi viv   i  iv   i i    i vi   
  L1M4_orf2#LINE/    433 ACATGCAAA--AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr2_207074347_   2636 ATAAAGTTGAAATTGATCATATCCCTAAAT---------AAAACAATAAC 2676
                           v  v ii    v     ? vv       ---------     v    v
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr2_207074347_   2677 ACTTTTAGAATAAAACATAAGAGAAAACCTTGGTGATCT-GTTTTTGTTG 2725
                            i      v        i ? v   i   v    i  - vv  v vii
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_207074347_   2726 A-AGTTTTTAAAACAGCATACAAAGA----AAGGAATAAAAAAGGAAAGT 2770
                          -i    i v i i vv i  v  i ----   v  i    i ii   - 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-T 629

  chr2_207074347_   2771 CAATTATTTGGACTTCACCACAAAATGAAAATACTTT-GTGCATCATAG- 2818
                         vi  v v          i  --    v    -     -    v   v  -
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCA--AAATTAAAA-ACTTTTGTGCTTCAAAGG 676

  chr2_207074347_   2819 ACATGGT-AAGAATGTGAAAGGGCAAACCACAGAATGAGAGAATATCTTT 2867
                            ivi -     v      i i   v          i     v  v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_207074347_   2868 TTGAA--AGATATTTGACAAAAGATT-------ACAGTATAAAAAGAACC 2908
                         vii  -- v    i   i  ii  i ------- v i    v       i
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_207074347_   2909 GTTACAACTCCAGGATCCTAAGACCAAAAAAATAAAAAATAAAAAAACTT 2958
                         v         v ------   ---i     i i   ---   vvv  i ?
  L1M4_orf2#LINE/    777 CTTACAACTCAA------TAA---TAAAAAGACAAA---TAACCCAATTW 814

  chr2_207074347_   2959 GTGAAAAATGGGCCAA--ACTTGCATA-----------AAAGTTGATATA 2995
                         ---          v  -- i   v   -----------    vv      
  L1M4_orf2#LINE/    815 ---AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_207074347_   2996 AGAATGGCAGATAGGCCCATGGAAAGATGCTTCATAGCCTTACTCAC 3042
                         vi      vi   i  v    i         iv i v v????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.98 (55 / 56)
Gap_init rate = 0.04 (19 / 476), avg. gap size = 3.21 (61 / 19)  


3102 27.16 1.22 0.55  chr2_207184548_207189637     3697  4598 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207184548_   3697 TGGAAGAACACTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3746
                              ii i ii     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207184548_   3747 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3796
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207184548_   3797 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTTA 3844
                          v   iivi i  i  ii     -   -- v  i  - iii    i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_207184548_   3845 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 3894
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_207184548_   3895 AACAAAGCTGGAGGCATCGAGCTACTTGACTTCAAACTATACTACAAGGC 3944
                                i      vv  ivi  v iii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_207184548_   3945 TACAGTAACCAAAACAGCATGTTACTGGTACCAAAACAGAGATGTAGACC 3994
                                 i   i    ii  v      i iv ii i   v  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_207184548_   3995 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 4042
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_207184548_   4043 ATCTGATCTTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCC 4092
                          vi    i  i     ivv  v   i vv vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_207184548_   4093 CTATTTAATAAATGGTGCTGGGAAAACTGGCTACCCATATGTAGAAAGCT 4142
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_207184548_   4143 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4192
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_207184548_   4193 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTACAAGAAAAC 4242
                          i ?    i  v    v   v       i      vi i  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_207184548_   4243 CTAGGCA-ATACCATTCAGGACAGAGGCATGGGCAAGGACTTCATGTCTA 4291
                         v    ?i- v i -   iv   vvv  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_207184548_   4292 AAATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4341
                         vi i          vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_207184548_   4342 ATTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4391
                           i   v v  i i      ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_207184548_   4392 CAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 4441
                         v  i  i  i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_207184548_   4442 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4491
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_207184548_   4492 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACATTT 4537
                           i    ----   v  i?    i    ii      v    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_207184548_   4538 CTCAAAAGAAGATATTTATGCAGCCAA-AAAAACATGAAAA-ATGCTCAT 4585
                            v           vi viii     -  iv         -       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_207184548_   4586 CATCACTGGCCAT 4598
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3028 26.20 2.13 0.45  chr2_207268722_207273303.rev     3198  4090 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207268722_   3198 TGGAAATACATCCCATGCTCACAGATGGGTAGAATCAATATT-TGAAGAC 3246
                               v i        i   ii   v  v   v i      - v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207268722_   3247 GAGCATACTGCCAAAAGCAATCTACAAATTCAACACAATCCCCATCAGAA 3296
                          ivv     v  v   vii       i       i       i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207268722_   3297 TACCACCATCATTCTTCACAGAA-TTAGCAAAAACAATTCTAAAACTAAT 3345
                          v   v vv v  i  ii     -  ii   iv-ii  i      i v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_207268722_   3346 ATGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAA-AAGA 3394
                               viiv  ii  v  viv         i   vvi i iv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_207268722_   3395 ACAAATCTGGAGGCATTGCATTACCTGATTTCAAACTATACTGTAAGGCC 3444
                              vi      vv ii  i v  ii        viv    ii  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_207268722_   3445 ATAGTCACCAAAACAGCATGGCACTGGTATAAAAATAGGCATATAGACCA 3494
                          i   v i   i    ii   i     i    ii    i        i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_207268722_   3495 ATGGCATA---T--AGAACCCAGAAATAAACCCAAATACTTACAGCCAAC 3539
                             v   --- --   ii               v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_207268722_   3540 TGATCTTTGATAAAGCAAACAAAAC-ATAAAGTGGGGAAAAGGACACCCT 3588
                             i  i  i  i vviv   i  -  vv i        - i i vi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCT 398

  chr2_207268722_   3589 TTTCAATAAATGGTGCTGGGATAAATGGCTAGCCACATGTAGGAGAATGA 3638
                               i              i  v   v  ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_207268722_   3639 AACTGGATCTTCATCTCTCACCTTAAAGAAAAATCAACTCAAGATGGATT 3688
                          ii    i iii i   v    v  v v      i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_207268722_   3689 AAGGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGAAAACAT 3738
                          ?i   i    iv     v  i           v ii             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_207268722_   3739 TGAAA-AACCCTTCTAGACATTGGCTTATAGGCAAAGATTTCATGACCAA 3787
                         v i?i-  vi    vv   v    v   --     v i    v iivi v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATAT 596

  chr2_207268722_   3788 GAACCCAAAAGGAAATGCAATAAAAACAAAGATAAATAGTTGGGACCTAA 3837
                           vv       v v v    i    iv   i   i   iv v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_207268722_   3838 TTAAACTAAAGAACTTTTGCATGGCAAAAGGAAAAGTCAGCAGAGTAAAG 3887
                          i   v v  i        iiivv    i iv vvi   iv i   i  i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_207268722_   3888 AGACAACCCAAAGAATGGGAGAAAATCTTCATAATCTATGCATCTAACAA 3937
                                   v               v  iii  vii  ii    i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_207268722_   3938 AGAAATAATATCCAGAATCTACAATGAACTCAAACAAATCAGTAAGAAAA 3987
                         i i v vi          v  i  v      vv    v   i   v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_207268722_   3988 A---AAACAATCCCATCAAAAAGTGGGCTAAGGAT------AGACAATTC 4028
                          ---   i  i  v  i?    i     v      ------     v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_207268722_   4029 TCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAGATGCTCAAC 4078
                           v                       i  i  i                 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_207268722_   4079 ATCACTAATGAT 4090
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


3346 23.02 4.08 1.13  chr2_207569621_207571944.rev      951  1832 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207569621_    951 TGGAAAGATTTCCTATGCTCATGGATCAGAAGAAATAATATTGTTAAAAT 1000
                                  v   i   i        ii     vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207569621_   1001 GTTCATACTACCCAAAGCAATATTATGTGGATTCAACCTAATCCCTATAA 1050
                          viv     v      vii  -i  ii--        vi         v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT-CTACA--GATTCAACGCAATCCCTATCA 97

  chr2_207569621_   1051 AAATCCCAATGGCATTCTTCACAGAAATAGAGAAAACAATCCTGAAATTT 1100
                                 iiv  v  i  ii       v  v  ivii     i     i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_207569621_   1101 GTATGGAAACATAAAGGACCCTGAATAGTCAAAACAATTCTGAGAAAGGA 1150
                         i        iii  i      v      i         ii   i    i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_207569621_   1151 GAACAAAGTTGGAGGCATCACATTTCCTGATTT--AAAGTGATATTACAA 1198
                                        vv     i    ii    --   v --  i     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT--TACTACAA 245

  chr2_207569621_   1199 AGTGATAGTAATTAAAACAGCATACTAGTGGAATAAAAACAGACACGTAG 1248
                           iv i      i  i    ii iv  v   v    ii i     ii   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_207569621_   1249 AGCAGTGGAACAGAATACAGAGCCCAGAAATAAATCCAAATGTTTATGGT 1298
                          v  i     i     vv    i           i   v ii        
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_207569621_   1299 CAACTAATTTTTGATAAGGGTACCAACAAGGCACAATGGGGAAAGAGTAG 1348
                            i i     i  i      i    v vviiv             i   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_207569621_   1349 GCTCTTTAAGAAATGGTACTAGGAAAAATGGATTTTCACAAGTAAAAAAA 1398
                         v  i  i  v       i  i   v  v     v?i    v i    i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_207569621_   1399 TGAAATTGGGCTC-TA----ATACCATATACAAAAATCACTTCAACATAG 1443
                             i    i i -  ---- i               i vi    v  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_207569621_   1444 ATAAAAGACCTAAATATAAGACTGGAAACCATAAAACTCCTAGAAGAGAA 1493
                           v ?          i     vivi    i         i       i  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_207569621_   1494 CAT-GGAGAAAAGCTCCTGGGCATTGGCTTTGGCAATG-TTTTTTAAAGG 1541
                            -  ? v   v  i vv i v    v  v       -   i   i --
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-- 593

  chr2_207569621_   1542 TACCACATGAAAAGCTCAGTTCACAAAAGCAAAAATAAATAAATGGGAAT 1591
                           iv   iv      v  iviv       v       i      v   v 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_207569621_   1592 CTATCAAAATAAAAATCTTCTG-ATAGCAAAGGAAACAATGATCAAAATG 1640
                         ii        v    v   i  -iivv       v  v  v vv   i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_207569621_   1641 AAGAAATGGCCCATGGATTGAGAAAAAATATTTGCAAATCGTATGTCTGA 1690
                           i i iii    ii  v  i  i                i   i     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_207569621_   1691 TAAGCTGG--TAATATTCA-AATTTATAAAGAACACATATAAC------- 1730
                             --  -- vi   i  -   v          v v  i   -------
  L1M4_orf2#LINE/    744 TAAG--GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_207569621_   1731 -------------AACCTTATTTTTTAAATGGGCAAAAGACCTGAATAGA 1767
                         -------------    iv   ?vv-           i  ii        
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGA 840

  chr2_207569621_   1768 CATTTCTCCAAGGAA-ATAAACA--TTGCCCACAGGTATATGAAAGGGTG 1814
                                    i   -   v   -- v   v i i i i      i i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_207569621_   1815 TTCAACATCATTAATCAT 1832
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (123 / 76)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.71 (46 / 17)  


 665 21.58 0.00 0.00  chr2_207584695_207591080.rev      352   490 (5896)    L1M4_orf2#LINE/L1        2   140 (768)  

  chr2_207584695_    352 GGAAAGATATTCCATGATCATGGGTTGGAAGAATCAATATTGTTAAAATG 401
                                   i     v      i        v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_207584695_    402 GCTATACTACCTAAAGCAATCTACAGAATCAATGCAATTCCTATGAAAAT 451
                           v     v  i   vii         v    i     i     v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_207584695_    452 ACCAATGACATTCTTCACAGAAATAGAAAAGGTAATGCT 490
                         v   iivi v  i  ii       v  v   v i  v  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 1.14 (16 / 14)
Gap_init rate = 0.00 (0 / 139), avg. gap size = 0.00 (0 / 0)  

3255 26.62 0.44 0.55  chr2_207584695_207591080.rev     4986  5894 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207584695_   4986 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAATATCATGAAAAT 5035
                               i i  i    vi        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207584695_   5036 GGCCTTACTGCCCAAAATAATTTATAGATTCAATGCTATCCCCATCAAGC 5085
                            vv    v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207584695_   5086 TACCAATGAATTTCCTCACAGAA-TTGGAAAAAAACT--TCTTTAAACTT 5132
                          v   iivivi  ii ii     -   --- v  i  --  i -   v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCT-AAAATT 146

  chr2_207584695_   5133 CATATGGAACCAAAAAAGACCCCGCATAGCCAAGACAATCCTGGGCAAGA 5182
                                  viiv  ii     v v        i      i  iiv    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_207584695_   5183 AGAACAAAGCTGGAGGCATCATGTTACCTGACTTCAAACTATACTACAAG 5232
                                  i      vv   iii v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_207584695_   5233 GCCACAGTAACCAAAACAGTACGGTACTGGTACCAAAACAGAGATATAGA 5282
                           i       i   i     ii        i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_207584695_   5283 CCAATGGAACAGAAAGGAGGCCTCAGAATTAACACCACACATCTACCACC 5332
                         i        i    vv   ivii     v   vv   i    i  ivii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_207584695_   5333 ATCTGATCTTTGACAAACATGACACACACAAGCAATGGGGAAAATATTCC 5382
                          vi    i  i     ivi  v  vivv  vv           iv  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_207584695_   5383 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5432
                           v  i  i        i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_207584695_   5433 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGATGGA 5482
                            ii         v   i     v           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_207584695_   5483 TCAAAGACTTAAACATAAGACCTAGGACCATAAAAATCCCAGAAGAAAAC 5532
                            ?    i    ii     v   ii  i      v  ii          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_207584695_   5533 CTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTA 5581
                         v i  ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_207584695_   5582 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATTTA 5631
                         vi            vvi          vv     v  i    v   i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_207584695_   5632 ATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5681
                           i   v v  i     i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_207584695_   5682 CAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTATCCATCTGACG 5731
                         v  i     i                vv       vii  vi      ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_207584695_   5732 AAGGGCTAATATCAAGAATCTACAAAGAACTTACACAAATTTACAAGAAA 5781
                          i  i  vi    v     v  i        ivi    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_207584695_   5782 AAAGCAAACAACCCCATCAAAAAATGTGCAAAGGATATGAACAGACACTT 5831
                           ii    i     v  i?       v         v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_207584695_   5832 CTCAAAAGAAGACATTTATGCAGTCAACAGACATATGAAAAAATGCTCTT 5881
                            v        i  vi viii i   i ii  i       i      vv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_207584695_   5882 CATCACTGGTCAT 5894
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3286 26.52 0.77 0.44  chr2_207597766_207604032     4871  5775 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207597766_   4871 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4920
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207597766_   4921 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4970
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207597766_   4971 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5018
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_207597766_   5019 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5068
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_207597766_   5069 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5118
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_207597766_   5119 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5168
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_207597766_   5169 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5216
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_207597766_   5217 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5266
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_207597766_   5267 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5316
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_207597766_   5317 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5366
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_207597766_   5367 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5416
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_207597766_   5417 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5466
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_207597766_   5467 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5516
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_207597766_   5517 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGAAC 5566
                          i   v v  i i   i  ii vv    i  v    i  vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_207597766_   5567 AGGCAGCCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5616
                           i  i  i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_207597766_   5617 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5666
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_207597766_   5667 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5716
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_207597766_   5717 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA-- 5764
                           v        i  vi viii     v  i          i       --
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_207597766_   5765 -TCACTGGCCAT 5775
                         -   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


 489 28.46 0.00 0.00  chr2_207616748_207622847     4375  4497 (1603)    L1M4_orf2#LINE/L1        1   123 (785)  

  chr2_207616748_   4375 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATTAATATCATGAAAAT 4424
                               i i  i     i        v      v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207616748_   4425 GGCCATAGTGCCCAAAGCAATTTATAGATTCAATGCTATTCCCATTAAAC 4474
                            v   v v      vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207616748_   4475 TATCATTGATATTCTTCACAGAA 4497
                          vi  viviiv  i  ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA 123

Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.00 (0 / 0)  

2259 27.33 3.02 0.53  chr2_207616748_207622847     4848  5608 (492)    L1M4_orf2#LINE/L1      129   908 (0)  

  chr2_207616748_   4848 CAAGGCAATCCTAAG---CAAAAAAAAA-ACAAAAA--CAAAAACAA--A 4889
                             vii       i---  v vii   -i   iii-- v i  i i-- 
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr2_207616748_   4890 AAACAACC------AAAAAAAACAAAGCTGGAGGCATCACACTACCCAAC 4933
                               i ------  i  i       i      vv       v     i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr2_207616748_   4934 TTCAAATTATACTACAAGGCCACAGTAACCAAAACAGCATGGTACTGGTA 4983
                               viv        i  i       i   i    ii         i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_207616748_   4984 CAAAAACAGGCACATAGACAAATGGAACAGA-TAGAGAACTCAGAAATAA 5032
                         i  ii i  i  i     iv       i   - v    iii         
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_207616748_   5033 AACTGCACATCTACAACCATCTGATGTTCAACAAACCCAACAAAAACAAG 5082
                          v iii    i  iiii  vi    v   i    ivviiv   i v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_207616748_   5083 CAATGGGAATAGGATTCTCTACCTAATAAATGATGCTGGGAGAACTGGCT 5132
                                i v  i  vv   viii  i     i        v      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_207616748_   5133 AGCTATGTGCAGAAAATTGAAACTGGATCCCTTCCTTACACCTTATACAA 5182
                          ? i ii    i  i v    ii    i    v   i     v       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_207616748_   5183 AAATTAACTCAAGATGGATTAAAGACTTAAACATAAAACCCAAAAGTATA 5232
                                     i      i ?    i    ii   i v i    v    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_207616748_   5233 AAAACCCTAGAAGAAAATCTAGGCA-ATACCATTCAGAACATAGGCATGG 5281
                            vi i          iv    ?i- v i -   ivi  v v  vv i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG 577

  chr2_207616748_   5282 GCAAAGATTTTATGAAGAAAT--TGCCAAAAGCAATTGCAATGAAAGCAA 5329
                             v i   iv --   v  --ii         vvv    ii    v  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTT--AGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_207616748_   5330 AAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAT 5379
                             v  i    v   ii v  i   v v  i i   i  ii vv    -
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA- 674

  chr2_207616748_   5380 GGA-ACTATCATCAGAGTGAACAGACAACCTACAGAGTAGGATAAGTTTT 5428
                            -       vv i      v        i     i i   v  iv v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_207616748_   5429 CTGCAATCTATTCAACTGACAAAGGGCTAGTATCCAGAATCTACAAAGAA 5478
                         i     vii  vi v    i  i  i  v           v  i      
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_207616748_   5479 ATTAAGCAAATTTACAAGAAAAAAACAAACAACCCCATTAAAATGTAGGC 5528
                         v ivvi   v iv i  v     i     i     v   ?   vi i   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_207616748_   5529 AAAGTATACGAACAGACACTTCTCAAAAAAAGACATGCA----GCCAACA 5574
                             v  vi   i     i     v   i    i  i  ----     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_207616748_   5575 AACATATGAAAAATAGCTCAACATCACTGATCGT 5608
                          i  i       ivv           ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (127 / 77)
Gap_init rate = 0.02 (13 / 780), avg. gap size = 2.08 (27 / 13)  


2854 24.44 7.44 0.24  chr2_207635741_207638541     1463  2309 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207635741_   1463 TGGAAAG----TCCATGTTCACAGACAGGAAGACTGAGTATTGTTAAGAT 1508
                                ----i         ii  iv        v i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207635741_   1509 GTCAGTTCCTCCCAACTTGAT----AG---CAA----------------- 1534
                          v  i v ii     v     ----  ---   -----------------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207635741_   1535 -----GTTAC----TTTGTGGTTATTGACAAACTGATTCTAAAGTTTTTA 1575
                         ----- i i ----    ii vv        i     i     i  iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_207635741_   1576 TGGAAAAGTGAAAGACCGAAAATATTCAACTCAATATTGAAAGAGAAGAA 1625
                               v ii ii    v i    vi   vv    v      i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_207635741_   1626 CAAAGTCAAAGGACTGACAGTACCCAACCTCAAGACTTAATATAAAGCTA 1675
                               iii      v   v v     ii    i     v  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_207635741_   1676 CAGTAATCAAGACAG-GTGTTATTGGTAACAAAATTAACAAATAAATCAA 1724
                                        -   v  i   i vv ii  vi   v   i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_207635741_   1725 AGGGAGAAAATAGGGATCCCATAAATAAACCTACATAAATATAGTCAAAA 1774
                         v  i v i   v i  vi   v         i i i vv   i     vv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_207635741_   1775 GATCTTTGACAAAGG----AA-------CAA---------AACAGTCTTT 1804
                            i  i     i  ----  -------   ---------  i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_207635741_   1805 TCAGCAAATAGTGCTGGAACAACTAGACATCCAAATGCAAAATAAGTAAA 1854
                            i     i       i      i  i ?   v        v  - i  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAA 449

  chr2_207635741_   1855 TCTAGACATAGACATCGCACCTT-CACAAATATTAATTCAAAATGTATCA 1903
                         vi i   vivv  v  i    v -i     v     i        v    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_207635741_   1904 TAGACCTGAATAGAAAATGC-AAAACTATAAAACTCT-AGAAGATAGCAT 1951
                         ?      i   iv  i -  -                -      v i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_207635741_   1952 AAGAGAAAACCTAGATGACTATGGGTATGGTGATGAGTTTTTAGATACAA 2001
                          i ? v   i  vvi    iv     vv  ii   iv  i       ii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_207635741_   2002 CACACATGGCACAATCCTCGAAAGTAAGAATTGATAAGCTAGACTTCATT 2051
                            vv vi      v vv i    v  i   v     ii i        i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_207635741_   2052 AAAATTGGAAACTTCTACTTTGCAAAAGACAATGTTAAGAAA-CAAAAAG 2100
                               ii      i iivi v    i    v i i      -ii     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_207635741_   2101 ACAAGCCACAAACTGACAGAGTATATTTTCAAAACACACATCTGATAAAG 2150
                             v     i v  iv   iv      v    v  i i         i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_207635741_   2151 GACTGTTATCCAAAATATATAAATAACTCTTAAAACTCAACAACAAGAAA 2200
                             vv      i          v        v       i  i  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_207635741_   2201 AGGAATAACTTGAATAAAAAATTGGCAAAAGACTTGAACAGACACCTCAT 2250
                          vi      iii v ?      v      i  i     i     ii  vi
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_207635741_   2251 CAAAGAAAATATAGAGACAGCGAGAAAACATA-AAAAAGATATTCCACAT 2299
                                i     v i ii  v iv  i  i -i       ii  v    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_207635741_   2300 CATATGTCAC 2309
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.54 (123 / 80)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.06 (65 / 16)  


2045 25.85 9.17 2.47  chr2_207689499_207696913      662  1512 (5903)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207689499_    662 TGAAGAAATACACCATGTTCATGGATTGGAAAAATCTCTATTGTTAAGAT 711
                           i i i   iv                   i v ivv            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207689499_    712 GTCAATTCTCCCCAAACAAATTTAAAGATTCTACACAATATCAATCAAAA 761
                          v    v         ivi  i  v      v  i    vi v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207689499_    762 TCTCAACTGACTTTTCT-------TT----------TCTTAA---TTATT 791
                           i  i   v     i -------  ----------  i   --- i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_207689499_    792 TGAAAAATGTTTTAAA--ACTTAAAATAGCCAAAATAATTTTGGAAA--- 836
                           i   -  i---  i--  ii i           i   i   i   ---
  L1M4_orf2#LINE/    151 TGGAAA-TGC---AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_207689499_    837 --------GTTGGAATAGGTGTATTGT----TTTCCAAACTCACTATGAA 874
                         --------      iv vviii i vi----    v     i    ii  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_207689499_    875 GGTATAATAATCAA--CGATATGGAATTGGTATCAGGATAGACAAATAGG 922
                          v  i i       -- ii i   v i   i  v          v    i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_207689499_    923 TCACTAGAGCAGAGC--AGAATTTAGAAATAGACACATA----TAAAGTC 966
                            v i  ii   ii--   i ii       i  v    ----  vi   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_207689499_    967 AACTGATTTTCAACAAAGGAACCAAGGCAATTCAATAGGGAAAGAA-AAT 1015
                           i        i    i  vi     i v       i         - i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_207689499_   1016 CTTTTCAACAAATGGTGTCGG-----CT--ATAT--ATAGGGAAGAAAAA 1056
                                          ii  -----  --   ?-- i v v  -  i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA-AAGAA 445

  chr2_207689499_   1057 TAAACTGTGACCCTTACCTCTCACCCTCCACAAAA-TTAAGTTAAAACGG 1105
                          i  v vv     i      v    v vi      -    v i    i  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_207689499_   1106 CCTCTAGACCTAAACAAAAGGGCTTAAATTACATAGTTTTCTAGAAGAAA 1155
                         viiv?         iiv   i   v   i  i v ii i -         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAA 544

  chr2_207689499_   1156 ATAGAAGAGAAACACT----GAATCCAGGTGTTGGCAAAAATTT---AGA 1198
                          i v i ? v  vv  ----  viiii   - v     vii   ---   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGA 593

  chr2_207689499_   1199 CAAGAC-TCAAAAGCACTGATCATAAAAGAAAATAATTGGCAGTATGGTA 1247
                         i v   -i         viiiv i         -   v ii ivv   vv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGAC 642

  chr2_207689499_   1248 GCCATCAAAATTCACA-TTTTTCT-CCTCAAAAAACACAATTAAGTAAGT 1295
                         vi          v v -i    v - i     ii    v  i   v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_207689499_   1296 GAAAAGGCAAGTC------TGGGAAAATACAAT--CATATTAATTGTATC 1337
                               i   vi ------     i  v i v --  v  i -- i    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA--TATATC 740

  chr2_207689499_   1338 TGAAAAA----TTATCGCCCATAATTTACAAACAACAACAACAACAAAAT 1383
                            v  i----  i -ii   v   v  i   v   vviv     vv   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_207689499_   1384 TTCTATAAATCCACAAGTCAAAGATAACCAAATTTTAAAATAGGTGAAAA 1433
                         v---     -----   v    --     v    ?v     i  ii  ii
  L1M4_orf2#LINE/    790 A---ATAAA-----AAGACAAA--TAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_207689499_   1434 ACATGAACAGATAATTCACAAAAGCAGATCTATAAATAGCCAATACACAT 1483
                          iv    i   i v   v v    v    v  i    i       vi  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_207689499_   1484 GTGGAAAAGTGCTCAAAATCATTAGTCAT 1512
                         i  i   ii       v    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (129 / 87)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.00 (99 / 33)  

3315 26.76 0.44 0.44  chr2_207689499_207696913     6016  6923 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207689499_   6016 TGGAAGAACATTCCATGCTCATGGGTAGGAACAATCAATATCGTGAAAAT 6065
                              ii i  i     i      i v    v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207689499_   6066 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGTCATCCCCATCAAGC 6115
                            v     v     iv i  i           i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207689499_   6116 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTTA 6163
                          v   iivi i  i  ii     -   -- v  i  - iii    i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_207689499_   6164 CATGAAGCCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 6213
                         i   i iviiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_207689499_   6214 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6263
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_207689499_   6264 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGATC 6313
                                 i   i    ii         i iv ii i             
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_207689499_   6314 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 6361
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_207689499_   6362 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 6411
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_207689499_   6412 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6461
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_207689499_   6462 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 6511
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_207689499_   6512 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 6561
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_207689499_   6562 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 6611
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_207689499_   6612 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 6661
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_207689499_   6662 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 6711
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_207689499_   6712 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 6761
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_207689499_   6762 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 6811
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_207689499_   6812 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 6861
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_207689499_   6862 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 6911
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_207689499_   6912 ATCACTGGCCAT 6923
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1120 25.08 4.76 0.63  chr2_207714590_207721093     4507  4821 (1683)    L1M4_orf2#LINE/L1       30   357 (551)  

  chr2_207714590_   4507 AGGAATTAATATTGTTAAAATGACCATACTACCAAAAGCAATCTACAGAT 4556
                          i  v             i   i v     v  v   vii          
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGAT 79

  chr2_207714590_   4557 TAAATGCAATCCTTATCAAAATACCAATGGCATTCTTTACCAAAATAGAA 4606
                          v  i       i         v   iiv  v  i   i vi    v  v
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chr2_207714590_   4607 AAAACAATCCCAAAAT----GTG----TACAAAAGATCCCAAGTAG---- 4644
                           ivii    i     ----i  ---- i   ii  i  vi i   ----
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_207714590_   4645 -ATAATTCTAAACAAAAAGAACAAACTTGGAGGTATCATACCACCTGACT 4693
                         - i   ii i  v  i         v       vv   i  iv  ii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_207714590_   4694 TCAAAATATATTACAAACCTACTGTAATTAAAACAAGATGGTACTGGTAT 4743
                               iv  i      v    v     i  i   ivi         i  
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_207714590_   4744 AAAAATAGACACATGGACCAATGGAACAGAAT--AGAACACAAAGAAATA 4791
                           ii       i  i  i        i     --   iiv  --      
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA--GAAATA 327

  chr2_207714590_   4792 AATTCATTTATTTATAGACAACTGATTTTC 4821
                           ii   vi      i v   i        
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTC 357

Transitions / transversions = 2.04 (53 / 26)
Gap_init rate = 0.02 (5 / 328), avg. gap size = 3.40 (17 / 5)  

1607 22.95 2.91 7.29  chr2_207714590_207721093     5126  5674 (830)    L1M4_orf2#LINE/L1      346   870 (38)  

  chr2_207714590_   5126 CAACTGATTTTCAACAAAGGTTCCAGGAATATATATTGGGAAAATGTA-A 5174
                            i        i    i   v   i  vi  vi v    i   - v - 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATA 394

  chr2_207714590_   5175 GCTTTTTCAATAAATGGTGCTGGAAAAACTGGATATCCATATGGAGAAGA 5224
                          ii       i            i v         ?   i   v i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_207714590_   5225 ATGAAACTAGGCTCACGTATCTCACCACATACAAAAATCAACTCAAACTA 5274
                              ii i i i viiiv  v     i          i        v i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_207714590_   5275 GACTTAAAAGATTTAAGTATAAGATCCCAAACTAGAAAACTCCTAGGAAA 5324
                           -- v ?   ii   i i     v iv      v       i   i i 
  L1M4_orf2#LINE/    495 GA--TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_207714590_   5325 AAAAACCGGGG-AAATGCTTTGGGACATTGGTCTGGGAAAATATTTTGTA 5373
                            v iv  ? -    -   i v   v    vi i  v  vvi   iv  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_207714590_   5374 -------CCCCAAAAGCACAGGCAGCAAAAGCAAAAATAGGGGAATCTAT 5416
                         ------- v           i   i      v        ----------
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG---------- 631

  chr2_207714590_   5417 CAAATATCTAAAATAGTATTATATCAAACTAAAAAACTTT-GCACAGCAA 5465
                         ---   -----   v v i vi      v v         - ii vv   
  L1M4_orf2#LINE/    632 ---ATA-----AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_207714590_   5466 AGGAAACAACCAACGTAGTAAAGGGACAATCTGTAGAATGGAAGGAAATA 5515
                             v  v i   viv   i  ii     i iii       i  i     
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_207714590_   5516 TTTGCAAACTATACAT---ACAAGTGATTAATATCTAGAATATACAAGGA 5562
                                 ii   i  --- i   v  i vi    i        i  i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_207714590_   5563 ACTCAAACAACAGGAAAAAAATGACAACAACAACAACAAAACAATGAATA 5612
                             vv     ---------- -----   i  i  v  i    ---   
  L1M4_orf2#LINE/    774 ACTCTTACAAC----------T-----CAATAATAAAAAGACAA---ATA 805

  chr2_207714590_   5613 ATCTAACTTTAAAGTGGACAAAGGATCTGAATAGGCACTTCTTTAAAAAA 5662
                          i i  i ?v   i   i        i       i  i    ii   i  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_207714590_   5663 GACATACA---GGCC 5674
                           i     ---    
  L1M4_orf2#LINE/    856 GATATACAAATGGCC 870

Transitions / transversions = 1.84 (79 / 43)
Gap_init rate = 0.03 (14 / 525), avg. gap size = 4.00 (56 / 14)  

 231 12.50 5.36 1.79  chr2_207714590_207721093     5957  6012 (492)    L1M4_orf2#LINE/L1      851   908 (0)  

  chr2_207714590_   5957 AAAAAGACATACAAATGGCCAA---GTATTATGAAAAAATACTCAACATT 6003
                           i    i              --- i -i       i  i        i
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCA-CATGAAAAGATGCTCAACATC 899

  chr2_207714590_   6004 ACTAATCAT 6012
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.00 (7 / 0)
Gap_init rate = 0.03 (2 / 58), avg. gap size = 2.00 (4 / 2)  


2989 23.28 7.57 1.86  chr2_207899220_207902279     1712  2570 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207899220_   1712 TGGAATAACATTCCATGCTCATGGATTAGAAGAATCAATATCATTAAAAT 1761
                              vi i  i     i         i     v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207899220_   1762 GGCCATACTTCCCAAAGCAATCTACAGATTCAGTGCTATTCCTATCAAGC 1811
                            v     i      vii             ii  v  i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207899220_   1812 TACCAGCATCGTTTTTCACAGAATTATAAAAAAACT-ATTCTAAAATTCA 1860
                          v     vv v     ii     --  vi v  i  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr2_207899220_   1861 TATGGAAACAAAAAAGAGTCCAAATAGCCAAAACAATCCTAAGCAAAAAG 1910
                                 iiv  ii  vi vi                i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_207899220_   1911 AACAAAGCCAGAGACAC-CACATTACCTGACTTCAAACTACC--CTATAA 1957
                                iii   i-  -    i v  ii i      --  i--   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAA--ACTTACTACAA 245

  chr2_207899220_   1958 GGCTACAGTAACCAAAACAGTATAGTATTGGTACAAAAACAGACACATAG 2007
                         i          i   i     i i   i   i i  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_207899220_   2008 ACCAATGGCAGAGAATAGAGAACCCAGAAATAAAGCTGCACACCTATAGC 2057
                          i      v v     v    ii           v iii   ii   i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_207899220_   2058 CATCTGATCTTTGACAAAGTTGACAAAAATAAACAATGAGTAAAAGATCC 2107
                           vi    i  i     i v  v   i vi vv     i v   ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_207899220_   2108 CCTGTTCAATAAATGGTGCTGGGATATCTGACTAGCCATATGCAGAAGAA 2157
                         i  v     i              i v   iv  ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_207899220_   2158 TGAAGTTTTTGTACCCCTACCTTTCACCATATACAAAAATGAACGGAAAA 2207
                                --- v          iv                v   vv    
  L1M4_orf2#LINE/    446 TGAAGTT---GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_207899220_   2208 TGAGCTAAAGATTTAAATCTAAGACCTTAAACTATATGAATCCTAGAAGA 2257
                           iiii ?   ii     v     v  v        vi v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_207899220_   2258 AAACCTAGGAG-ACACCATTCTGGACATTGGCCTTGGGAAATAAT----- 2301
                             v    ? - v i -   vv   v    v-  i  v   ii -----
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTT 590

  chr2_207899220_   2302 --ATATGACAAAGTCCTTAAAAGTAATTGCAATGAAAATAAAAATTGACA 2349
                         --        ----  --     i vvv    ii   iv      v  i 
  L1M4_orf2#LINE/    591 AGATATGACA----CC--AAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_207899220_   2350 AGTGAGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATT 2399
                          i vi   i v  i   v v  i i   i  ii vv    i  v     i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_207899220_   2400 AACAGAGTAAACAGACAACTTACAGAATGGGAGGAAATATATGCAAACTA 2449
                           v i   i  v       ii            i      v      ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_207899220_   2450 TGCAT-TGACAAAG--------TC-----------AAGAAC--------- 2470
                          ii  -   i  i --------  -----------      ---------
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_207899220_   2471 ----------------------CCCATTTAAAAAATGGGCAAAAGACTTG 2498
                         ----------------------    v  ?             i  i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_207899220_   2499 AGCAGATATTTCTCAAAAGAAGACATACAAGTGGCCAAGAA--ACATGAA 2546
                          ii   i       v        i      i       v  --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_207899220_   2547 AAAATGCTCAACATTGCTAATCAT 2570
                           i           ii????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (128 / 68)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.50 (81 / 18)  


4194 18.54 4.10 0.80  chr2_207989842_207994334     3130  4008 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_207989842_   3130 TAGAAAAACATTTCACTTTGATGAATTGAAGGATTTAATATTGTTAAGTT 3179
                          i    i i  ii  iv  v   i    i i  i              v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_207989842_   3180 GGTAATACTCCCCAAACTAAGCTACAGATTCAACAAAATCCCTATCAGAA 3229
                           i             i i v             iv           i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_207989842_   3230 TCCCAACTGGCTTTTTTGTAGAAACTTGCAAGGCAATTCTAAAATTCATA 3279
                              i   v        i     i vi    vii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_207989842_   3280 TGAAATTGGAAGG-AGTCAGAATCACTAAATTCATCCTAAAAA----GAG 3324
                           i  v  v    - vi      vi i   viv   i i    ----  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_207989842_   3325 TAAAGTTGGAGGATACACACTCACCAATTTCAAAACTTACTACAAAACAA 3374
                         i            iv      iv                       i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_207989842_   3375 CAGTAATCAAGACAGTATGATGCTGACATATAGTTACAAATAAACATGTA 3424
                                         i  i i   i    -  -----i   i    i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATA-AG-----GATAGACATATA 294

  chr2_207989842_   3425 CACCAATGGATTAGCACTGACTGTCCAGAAGTAAACCCATGTGTCT---- 3470
                         v i       v   v i   vv        i         iii i ----
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_207989842_   3471 -CAACTGTCTTTCTACAA---TGCCGAGACAATTCAATTGGAAAAAAATA 3516
                         -   i  vi    v    ---    i    v       v  i   i    
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_207989842_   3517 ATACTTTTAACAAATAGTGCTGGAACAAATGCATAGCTACAGGCAAAAGG 3566
                         i vi   i       i       i    v  v   ? i   v       i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_207989842_   3567 ATGAAATAGGACCCTTACCTTA-----------AAAGTTAACTCAAAATG 3605
                              i v      i     i -----------   i             
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_207989842_   3606 GATCA-AAACCTAAGTATAAAAGCTAAATTTCTAAGACTTATAGAAGAAA 3654
                              - i      i i   i       vi v   i   iv         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_207989842_   3655 ATATAGGGGTAAATCTACCTGACCTCAGATTTGACAATGTATTCTTAGAT 3704
                          i     ?        v v      ii i  v i     vv         
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_207989842_   3705 ACCACACCAAAAGCATGATCAACAAAAGAAAAAATAGGTAAGTTGGACTT 3754
                          iv            ii v                  i   i        
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_207989842_   3755 CATCAAAATTTAAAACTTCTTTGCTTTAAAGAACACTGTCAACAAAATGA 3804
                                   v       i v     i    i     i    v   i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_207989842_   3805 AAGGACAACCCACAGTATGGGAGAAAATATTTACAAATCACATAT----- 3849
                           i            v                i       i    -----
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_207989842_   3850 AAGGAACCTGTACACAAAATATATAA-GAAGTCTTCCAACTCCTTAATAA 3898
                             i  i    iv  i         -   v    v      vv      
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_207989842_   3899 AAAGGCAA----CTTGGTTTTAAAATGTGCAAAGGATTTGAATAAATGTT 3944
                             i   ---- iiii  ?v      v                i ii  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_207989842_   3945 -CTCCAAAGAAGATACACAAATGGCCAACAAACACATGAAAAGATGTCCA 3993
                         -              i            i  i              ii  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_207989842_   3994 TCTATTAGTCATCAG 4008
                         v -  i ????????
  L1M4_orf2#LINE/    895 AC-ATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (107 / 53)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.31 (43 / 13)  


3047 26.95 3.17 0.34  chr2_208033899_208040549     5277  6159 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_208033899_   5277 TGGAGAAACATTCCATGCTCATGGATAGGAAGAATCAATAATATGAAAAT 5326
                             i i i  i     i        v      v i    v i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_208033899_   5327 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 5376
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_208033899_   5377 TACTATTAACTTTCTTCACAGAATTAGAAAAGACT-ACCTTAAATTTCAT 5425
                          v i vivi i  i  ii     v v  v   -  - i i    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_208033899_   5426 ATGGAACCGAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 5475
                               vi v  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_208033899_   5476 ATAAAGCTGGAAACATCACACTACCTGGCTTCAAACTATATTACAAGCCT 5525
                          i    i    iivv       v  iiii      viv  i     iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_208033899_   5526 ACAGTAACCAAAACAGCTTGGTCCTAGTATCAAAATAGATATATAGACCA 5575
                                i   i    iv    v  i i  v ii     i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_208033899_   5576 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATGTACAACCATC 5625
                               i    iv   ivii         vv   i    v  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_208033899_   5626 TGATCTTTGACGAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5675
                             i  i   i ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_208033899_   5676 TTTAATAAACGGTGTTAGGAAAACTGGCTAGTCATATGCAGAAAACTGAA 5725
                           i  i   i    i i   v      v  ?i  i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_208033899_   5726 ATTGGACCCCTTCTTTTTACCTTATACAAAAATTAACTCAAGATGGATTA 5775
                         i          v i ivi   v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_208033899_   5776 AAGATTTAAACATAAGACCTAAAACCATAAAAATCCTACAAGAAAACCTA 5825
                         ?   ii    ii     v       i      v  i  v        v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_208033899_   5826 GGCA-ATACCATTCA-GAGCATAGGCATGGGCAAGGACTTCATGTCTAAA 5873
                           ?i- v i -   i-  v v i  i- i     v ii   v ivv  vi
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chr2_208033899_   5874 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATTTAAT 5923
                                     vvi          vv     v  i    v   i  v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_208033899_   5924 CGAACTAAAGAGCTTCTG-----CACAG----CTGTTCAGA--GTGAACA 5962
                          i  v v  i i   i  -----  v  ----  i iv   --     v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_208033899_   5963 GGCAACCTACAGAATGGGAGAAAATTTTTGCAAGCCATCCATCTGACAAA 6012
                          i     i                 v       ii   vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_208033899_   6013 GGGCT--------------ACAAGGAACTTAAACAAATTTACAAGAAAAA 6048
                           i  -------------- i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_208033899_   6049 AACAAACAACTCCATCAAAAAGCAGGCAAAGGATATGAACAGACACTTTC 6098
                         i     i   i v  i?    iii          v    i     i  ii
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_208033899_   6099 CAAAAGAAGACATTTATGCGGCCAACAAACATATGAAGAAAAGCTCATCA 6148
                          v        i  vi vii      i  i  i     i i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_208033899_   6149 TCACTGGTCAT 6159
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.60 (144 / 90)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.10 (31 / 10)  


3834 16.81 4.92 1.32  chr2_208051640_208053409.rev      448  1280 (490)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr2_208051640_    448 AAGAAGGCAACAATTA--AAAGCCATTTATAGATGT--TGCAACCCACTA 493
                             v     i v iv--   viv  i  i    vi--i    i  -   
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC-CTA 94

  chr2_208051640_    494 ACACTAGAAT---AGTTTTCCTTTTTG-AGACAAGAAGGAGTTGA----- 534
                         v  ---i   ---  i vi i      -   v vvi vi  i   -----
  L1M4_orf2#LINE/     95 TCA---AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr2_208051640_    535 AAATTCATATGGAAATGCAAGGGACCCAGAATAACCCAAACAATCTTGAA 584
                                                          i  v             
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_208051640_    585 AAAGAA---CAAAGTTAGAGGACTCACACTTTCCAATTACAAAACTTACT 631
                               ---       i              i      v           
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_208051640_    632 ACAAAGTAACAGTAATCAGGACAGTGTGGTTCTGGGACAAAGATAGGCAT 681
                               iv          i           v    v i  i     i   
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_208051640_    682 ATTGATCAATGGAACAGAAATGAGAATCCAGAAATAAACCTACATGTCTA 731
                           v           i    v     i              i i ii i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_208051640_    732 TGGTAAATTGGTTTTCAACAAAAGTGCCAAGTTCATTAAAAGGAGAAAGA 781
                             v     i     i    ii        vi    v  v  i      
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_208051640_    782 ATGGTCTATTCAACAAATCGTGCTGGTGTAACTGGATAGCCACATGCAAA 831
                           i    v          v       vii         ?           
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_208051640_    832 AGAATGAAGTTGGATTACCACTTTAAACGATATACAAAAATTAACTCAAA 881
                                       iiv i  i i v  v                     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_208051640_    882 ATGAATTGAAGACCTAATGATAAGAGC-AAAACTATAAAACTCGTAGGTG 930
                            i  ii?        vvi       -               v   iv 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_208051640_    931 AAAACATAGGGGTGAATCTTTGTGACCTTAGATTTGGCAATGGATTCTTA 980
                                   ?  i      i        i i  v        v      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_208051640_    981 GATATGACACCAAAAGCACAAACAA--AAGGAAACAAATAGATAAACGGG 1028
                                              i   --  i    -           iv  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGG 640

  chr2_208051640_   1029 ACTTCTCTAACATTTAAAACTTCCCTTCTTGTTCAGAGAATAC----AAG 1074
                              vii  v   v       ---  v vv    i  i i  ----   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTT---TTGTGCTTCAAAGGACACTATCAAG 687

  chr2_208051640_   1075 AAAGTAAAAAAG--ACTGACAGAAAGGGAGAAGAAAATATT--CAAATCA 1120
                              i    ii--  iv      v       ---      --       
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAA---AATATTTGCAAATCA 734

  chr2_208051640_   1121 TATATTTGATAAGGGACTTATATCTAGAGTGT-TAATG----CTTACAGC 1165
                              i             i    i   i i -   v ----      i 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_208051640_   1166 TCAATACTAGATAACCAGACA------TT--AAAATGGGCAAAGGATTTG 1207
                               v  i v iv  i i ------  --                   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_208051640_   1208 AATAGAAATCTCTCTAAAAAAGATATATAAAAGCCCGACAAGCACAAGAA 1257
                               v  i    i   i        i   v v  i i       v   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_208051640_   1258 ATGACACACAACA-CATTATTAGC 1280
                          v  ii v     -  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (83 / 54)
Gap_init rate = 0.02 (21 / 863), avg. gap size = 2.48 (52 / 21)  


 482 24.04 17.79 0.48  chr2_208115887_208117691       49   256 (1549)  C L1M4_orf2#LINE/L1   (42)   866   623  

C chr2_208115887_    256 AAAAAGTGAGATAAATTGAATTACAT------TAAGAACT---------- 223
                              i -          i i v   ------   i    ----------
  L1M4_orf2#LINE/    623 AAAAAAT-AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

C chr2_208115887_    222 ---GGTTACAATTAGAAGAGTGAAAAGGCAAGCCACAGAAT--------- 185
                         ---  vi  v  i ii i         i   v         ---------
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

C chr2_208115887_    184 ---TTGTAATATATGCATTTGTTAAAGGATTTGTATTCAGAATA-ATAAA 139
                         ---   i  vvi  ii  i  v   i   i      i       -     
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

C chr2_208115887_    138 ---TTGTAACAAATCAGTAAGAAAAA--CAGACCACCCAATAGAAAAATG 94
                         ---i v v    v   i   v     --  i iv       v?       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

C chr2_208115887_     93 GGCAAAAGACTTAAGCAGGCAATTGACAAAAGAGGACATATACAT 49
                               i  i  i ii  i  v  vv v     i  i   i v  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

Transitions / transversions = 1.72 (31 / 18)
Gap_init rate = 0.03 (7 / 244), avg. gap size = 5.43 (38 / 7)  

4033 13.50 5.15 5.28  chr2_208115887_208117691      501  1315 (490)    L1M4_orf2#LINE/L1       95   908 (0)  

  chr2_208115887_    501 TCAAAATTCCAATTGGCTTTTTTGCAGAAATTGACAAGTTTATCCTAAAA 550
                                i   ii  v                      i v         
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_208115887_    551 TTCATATGGAAATTCAAGAGATCCAGAA-AACCAAAACAATCTTAAAAAG 599
                                      v    i  i      - i             i    i
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_208115887_    600 AAAAAAGCAAAGTAGGAGGCCTCACACTTTTCAATGTCAAAACTTACTAT 649
                         i  i  -      v     v         ii    v             i
  L1M4_orf2#LINE/    195 GAAGAA-CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_208115887_    650 AAAGCTATAACAAACAGGACAATGCAGTACTGGCATAAGGGCAGG----- 694
                                i ii  v  i    i  ii              ii  i-----
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_208115887_    695 ---TCAATGCAATAGAATTTAGAGTCCAGAAATAAACCTATGTACTT--G 739
                         ---      v         v                  i  ii i  -- 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_208115887_    740 GTCAATTGATTTTCAACAAGGGCACCTAGACCATTCAAT----------- 778
                                       i       ii  v            -----------
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_208115887_    779 AGTATTTTCAACAAATGGTGCTAAGACAACTGGACAAGCACAGGCAAAAG 828
                            v                  ii          i ?v    v       
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_208115887_    829 ATCG---TTGGACTCCCTACCTCACATCATATACGAAAATTAATTCAAAG 875
                          vi ---      -            i       i        i     i
  L1M4_orf2#LINE/    444 AATGAAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_208115887_    876 GGGATTCAAGGCCTAAACGTAAGTTCTAAAACTATAAAACTTTTGGAAGA 925
                         v    iv?  i      i     vv                i  i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_208115887_    926 AAATGTAAACATAAACCTTCATGATCTTGGATTAGGCCATAGTTTGTCAG 975
                            ii  ii?i    i    i   i     i      v  i    v i  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_208115887_    976 ATACAACACAAAAAGCAAAAGCACCAAAATAAAAAAAACAGATAAATTGG 1025
                            ii    v       v     v     --i      i           
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAA--GAAAAAATAGATAAATTGG 640

  chr2_208115887_   1026 ACTTCATCAAGATG--------TTATACTGCAAAGAACACTACCAAGAAA 1067
                                   i  v--------  i i  v     i      i       
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_208115887_   1068 GTGAAAAGACAGCCCACAGAATGGGAGAAAATGTTAGCAAATCATGTACC 1117
                                    i                    i  v         i  i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_208115887_   1118 TGATAAGGGACTTATATCTAGAATGTATAAAGAATTCATACAACTCAATA 1167
                                      i    i     i         i  v            
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_208115887_   1168 ATAAAAAGATCCAGGTAAGATGTGGAAAATAATTAATAATAATAAAGATA 1217
                                  i----------------      ------------------
  L1M4_orf2#LINE/    791 ATAAAAAGAC----------------AAATAA------------------ 806

  chr2_208115887_   1218 TATAGCCCAATTTAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 1267
                         -----       ?                                     
  L1M4_orf2#LINE/    807 -----CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_208115887_   1268 AGAAGATATACAA--------TAAATACATGAAAAGGTATGCAACA-CAA 1308
                                      --------   ii          i iiv     -  ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_208115887_   1309 TCAGGGA 1315
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.79 (78 / 28)
Gap_init rate = 0.02 (13 / 814), avg. gap size = 6.54 (85 / 13)  


2535 23.48 6.63 0.55  chr2_208275827_208277542      501  1224 (492)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr2_208275827_    501 AAAATTCTTATGGAACCAAAAACAGCCCA-AATAGCCAAAGCATTCCTGA 549
                                v       viiv  ivii    -          i  v  i   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_208275827_    550 ACTAAAAGAACAACATGGAAGGCATCACACTACCTGACTTCAAAATATAC 599
                          vv i        vi v i   vv       v  ii i       iv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_208275827_    600 TACAAAGCTATAGTAACCAAAACA---TAGTATTGATATAA----AAACA 642
                                   i     i   i   --- i   i  ii    ---- i   
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_208275827_    643 CATAGACCAGTGGAACAGAATAAAGAACACAGAA-TAAATCTACTTATTT 691
                         i     i  i     i     vi   iiv     -    i i ivi    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_208275827_    692 ACAG---------------CAAATGTGCCAAGAACATACATTGGGGAAAG 726
                          ii ---------------   iv         v   v  v         
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_208275827_    727 GACACTCTCTTCAATCAATGGTATTGGGAAACCTGGATATCTGTGTGCAG 776
                         i i v   i     iv      ii     v v       ? iiii    i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_208275827_    777 A-GAATGAAACTAGATACCTATC----ACCATACCCAAAAATCCACTCCA 821
                          -       ii i  iv    i ----      iv       iv    v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_208275827_    822 AGTGGATTAAATACTTAAACATAAGACCCCAAACTCTTAGACTACTAGAA 871
                          i     i ? v  i    ii     v iv     v v i   vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_208275827_    872 GAAAACATGGGGG-AAATGCTTCCTGACATTAGACTTGGCAAAAACTTCA 920
                                 i  ? -    -    v    v  i ii v     viii   v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_208275827_    921 TGGCTAAGACTCCAAAAGCACAAGCAACAAAAAGAAAAATAGTTAAGTGG 970
                          i v  v   v                     ii        v   i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_208275827_    971 AAAT--ATTAAACTAAAAAGCTTCTGAACAGCAAAGGAAAC-------AG 1011
                         i v --  i   v v    i   i  vi vv       v  ------- i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_208275827_   1012 AGTGAAGAGACAACCTGCAGAATGGGAGGAA-TATTTACAAACTGTTCAT 1060
                               i        ii           i  -     i    iii vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_208275827_   1061 CTGACAAGGGACTGATAACCAGGATATATAAGGAACTC----AACCGAAC 1106
                             i        vi  v    i        i      ----   iv  i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_208275827_   1107 AGGAAAACAAACAAA-AATCCTATTAAAAAGTGGACAAAAGGTCTGAATA 1155
                          iv    - i     -  i  v   ?    i   i    i i i      
  L1M4_orf2#LINE/    790 AATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_208275827_   1156 GACATTTCTCAAAAGAAGACATACAAATGGCCAAGAAATATATTTGAAAA 1205
                                   v        i              v  ii i  --     
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT--GAAAA 886

  chr2_208275827_   1206 G---CTCAACATTACTAATTGT 1224
                          ---        i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (107 / 59)
Gap_init rate = 0.02 (17 / 768), avg. gap size = 3.06 (52 / 17)  


1996 16.67 2.50 0.28  chr2_208335853_208339720     2098  2457 (1411)    L1M4_orf2#LINE/L1        1   368 (540)  

  chr2_208335853_   2098 TGGAAAGCTATTCCATGTTTGTGGATCACAATAC--ACTATTATTAAGAT 2145
                                v   i       ii     iiv  v  -- v    i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_208335853_   2146 GATAATAC-CCTCAAATTGATCTACAGATTCAGTGCAATACCTATCAAAA 2194
                          ii     -  i                    ii     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_208335853_   2195 ATTCCAGCTAGACTTTTTGGAGAAATTGGCAAGTTAATTCTAAAATTCAG 2244
                         - i      ivvi      v        i    i i  i          v
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_208335853_   2245 AAGAAAATGCAAGAGACCTAGAATAGCCAAACCAATCTTGAAAAAGAA-- 2292
                          v i         i    i            v                --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_208335853_   2293 ----AGTTGGAGGATTCACACTTCTCAATATCAAAACTTACTACAAAGCT 2338
                         ----          i         i    v                    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_208335853_   2339 CTAGTAACCGAGGCTGTGTGGAACTGACATAAAGAGAGACATGTAGACCA 2388
                         vi     i i  i v      v    i     i  v      i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_208335853_   2389 ACAGAATAGAATTGGAAGTCCAGAAATAAACCTTTACATTTATGGTAAAC 2438
                          ii           ii                iv            v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_208335853_   2439 TGAGCATCAGCAAGGGTGC 2457
                            viv  ii         
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGC 368

Transitions / transversions = 2.00 (40 / 20)
Gap_init rate = 0.01 (4 / 368), avg. gap size = 2.50 (10 / 4)  

2664 15.13 5.75 0.38  chr2_208335853_208339720     2859  3380 (488)    L1M4_orf2#LINE/L1      359   908 (0)  

  chr2_208335853_   2859 ACACAGGTGCCAAGAGAATTCAATGGGGAAATAACAGTCTTTTTAGAAAA 2908
                            vi          vv              v  i        i iv   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_208335853_   2909 TAGGGATGAGACAACTGG-TATCCACATGCAAAAGAATGAAGTCAGACCC 2957
                          i v v  i         -  ?                     ii     
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_208335853_   2958 TTACCTCTCACACCATACAAAAAGATTGACTCAAAATGGATCAAAGACCA 3007
                         i      --        i v   i   i               ?     v
  L1M4_orf2#LINE/    459 CTACCTC--ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_208335853_   3008 AAACATAAGAGCTAAAATTATAAAATTCTTTGAAGGAAACACAAGAGTAA 3057
                            ii            i       i    v    i     i i ?    
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_208335853_   3058 ATCTTCATGGCCTTGGACTAGGCAATGCCTTTTAAGATGTAACACCCAAA 3107
                               i  i      ii         vi  i v    i i     v   
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_208335853_   3108 GCACAAGTGACAAAAGAAAACATGGA-AAATTGGACTTCATCAAAATTAA 3156
                                ii           v  i  -                       
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_208335853_   3157 AA-TATTTGTGCTTCAAAGGAAAGCATCAAGCAAGTTAAAAGACAATC-- 3203
                           -iv                v vi      v    v         i --
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_208335853_   3204 -AGAA--GGAGGAAATATTTACAAGTCATTTGTCTGATAAGGGAATTGCA 3250
                         -    --    i        i   i    v i            v   i 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_208335853_   3251 CCCAGAATACATAAAGAACACTTACAGCTCAA----------------AA 3284
                         i        i         v      i     ----------------  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_208335853_   3285 C---ACTTAAAAATGGGACAAGGATTTAAATAGACATTTCTCCAAAGA-- 3329
                          --- i ?         vv        i                    --
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_208335853_   3330 -TATACAAAAAGCCAATAAGCATATGAAACAATGCTCAACTGTAGTTTTT 3378
                         -        vi           i      vi         vvi ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_208335853_   3379 TT 3380
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.68 (47 / 28)
Gap_init rate = 0.02 (9 / 550), avg. gap size = 3.56 (32 / 9)  


2270 23.13 2.87 1.59  chr2_208630981_208632606      508  1134 (492)    L1M4_orf2#LINE/L1      274   908 (0)  

  chr2_208630981_    508 TGGCATCAAAACAGACATACACACATAGACCAATGGAACAGAAC-AAGAA 556
                               v ii i       ------    i        i    i-i   i
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATA------TAGATCAATGGAATAGAATTGAGAG 317

  chr2_208630981_    557 CCCAGAAATAAATCCATGCATTTACAACCAACTCATTTTCAACAAAGCTG 606
                         i           i    i      iiii   i v      i    i v  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_208630981_    607 CCAAGGACC-TACACTGGGGAAAGGACAGTCTCTTCAGTAAATGGTGCTG 655
                              -   - v  v         i i     i    ii           
  L1M4_orf2#LINE/    368 CCAAG-ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_208630981_    656 GGAAAACTGGATATTCATATGCAGAAGAATGAAACTAGACCCC---CTCA 702
                            v         ?i  i     i         ii i      ---    
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_208630981_    703 GG--ATATACAAAAATCAAATAAAAATGTATTACAGACTGAAATGTAAGA 750
                         vi--            i  v v      v  i ?    iv          
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr2_208630981_    751 CCTGACAA--ATAAAATGACCAGAAGGAAGCATTGAAA-AAATGCTTCAG 797
                         v  i -  --      ivvii     i  i   v i?i-    -    iv
  L1M4_orf2#LINE/    517 GCTAA-AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGT 564

  chr2_208630981_    798 AACATTGGCCTGGGCAAAGATTATTTGGGTAAGACCTCAAAAGCACAGGC 847
                         i  v    vi i     v i  vi  i i  v   vi          i  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_208630981_    848 AACAAGAGCAAAAATAGATAGGTAGGATTACATCAAGCTAGAAAGCTTCT 897
                              i  v           ii v   i v      iv vi   i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_208630981_    898 GCATAGCAAAAGAAACAACCAATAAAGTGAAGAGACAATGTACAAAATGG 947
                          iiivv    i  v  v i   v        i      ivi   i     
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_208630981_    948 AAGAAAATATGTGCAAGCCATTAATCTGACAAGGGATTAATAACCAGAAT 997
                         i         v     ii   vv      i      i vi  v       
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_208630981_    998 ACATAAGCAACTC----AACCCAGTAGCAACAAAAATAAAT---CTTATT 1040
                          i    iv     ----   i  i  ii  -   i i    --- iv   
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAA-AAAGACAAATAACCCAATT 813

  chr2_208630981_   1041 TTAAAACGAGCAAAAGATCTGAATAGACAATTCTC-AATAAACACATACA 1089
                         ?v    i i     i   i          v     -  vi  v i     
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_208630981_   1090 AATAGCCAACAGGTATGTTAAAAAATGCTCAACATCACTAATCAT 1134
                            i     i i i ii v    i             ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (96 / 45)
Gap_init rate = 0.02 (14 / 635), avg. gap size = 2.00 (28 / 14)  


2755 25.09 4.95 0.46  chr2_208770651_208775271     3261  4129 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_208770651_   3261 TGGAAA--CATTCCA-GTCTTATGGATGGGTAGAATCAATGTTGTGAAAA 3307
                               --i  i   -  - i      v  v   v i   i    v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGT-TCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_208770651_   3308 TGACCATACTGCCAAAAGCTATCTACAAATTCAATGCACTTCCCATTAAA 3357
                           i v     v  v   viv       i      i   v i  i  i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_208770651_   3358 ATACCATCATCATTCTTCATAGAACTAGAAAAAACAATCCTAAA-TTCAT 3406
                           v   v vv v  i  iii    v v  v  ivii        -     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_208770651_   3407 ATGGAACCAAAAAAAGTGCCCACA-TAGCCAAAGCAAGACTGAGCAAAAA 3455
                               -- viv  i vi    v -        i   vvi   iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_208770651_   3456 GAACAAATCTGGAGGCATCACATTACTCAACTT-A-----TACC-CAAGG 3498
                                vi      vv     i v i   i  - -----   i-   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_208770651_   3499 TTATAGTCACCAAAACAGCATGATACTGGCATAGAAATAGGTACAAACAC 3548
                         i  i   v i   i    ii  i          iii    ii i v v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_208770651_   3549 CAATGGAGCAGA---GAA---CCAGAAATAAAGCCAAA----TACAGCCA 3588
                                ii   ---  i---           v   v ----  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_208770651_   3589 ACTGAACTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGAAACCC 3638
                          i   vi  i     i vviv   i v   vv i         i v vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_208770651_   3639 TACTCAACAAATGGTGCTGG--CAA-------GCCACATGTAGAAGAATG 3679
                          vi                 --   -------?       i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_208770651_   3680 AAACTAGATCCTCATCCCTCACCTTATACAAAAATCAACTCAAGATGGA- 3728
                           ii i  i  ii i i v    v           i       i     -
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_208770651_   3729 AAAAGACTTAAATCTAAGACCTGAAACCATAGAAATTCTAGAAGGTAACA 3778
                         v ?    i     v     v  i    i   i  v ii      iv    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_208770651_   3779 TCAGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCGTGACCAAG 3828
                          vi ?iv  vi    vv   v    v        v ii   v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_208770651_   3829 AACCCAAAAGCAAATGCAACAAAA--ACAAACAGATG----GGACTT--- 3869
                          vv         v v         -- v   i    i----      ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_208770651_   3870 --AAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAACAGAGTAAAC 3917
                         --   i      -   i  ii vv    i  v iv     v i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_208770651_   3918 AGATAACCCACAGAGTGGGAGAAAATCTTTGCAAGCTATGCATCTGACAA 3967
                            i          i           v       iii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_208770651_   3968 AGGACTAATATCCAGAATCTATAAGGAACTCAAACAAATCAGAAAGAAAA 4017
                         i     vi          v     i      vv    v   iv  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_208770651_   4018 AAACAAACAATCCCATCAAAAAGTGAGCTAAGGACGTGAATAGACAATTC 4067
                          i     i  i  v  i?    i  i  v     iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_208770651_   4068 TGAAAAGAAGATATACAAATGGCCAACAAACATATGGAAAAATGCTCATC 4117
                          vv                       i  i  i   i   i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_208770651_   4118 GTCACTAATTAT 4129
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (125 / 89)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.47 (47 / 19)  


3063 24.09 0.86 3.64  chr2_208841130_208844011     1496  2429 (453)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_208841130_   1496 TGGAAAAATATTCTATGATCATGGATTAGAAGAAACAATATTGTTAAAAT 1545
                               i    i i   v         i     vvi           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_208841130_   1546 GGCCATACTGCCCAAAACAATTTACAGATTCAATGCTATTCCTATCAAGC 1595
                            v     v      vii  i           i  v  i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_208841130_   1596 TACCAA-TGTCATTCTTTACAGAATTAGAAAAAAAGTATTCTAAAATTCA 1644
                          v   i-  i -  i   i     v v  v  ivv -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCA 148

  chr2_208841130_   1645 TATGGAACCAAAAAAAAAAAAAAAGCCCA-AATAGCCAAAGCAATCCTAA 1693
                                viiv  iii --------    -          i     i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA--------CCCAGAATAGCCAAAACAATCTTGA 190

  chr2_208841130_   1694 GCAAAAAGAACAAAGCCAGAAGCATCACACTACTCAATTTCAAACCATAT 1743
                         iv  i          iii  i vv       v i          ---- i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----AC 236

  chr2_208841130_   1744 ATACTATTAGGCTACAGTAACCAAAATATCATGGTACAGGTAGGAAAACA 1793
                         v     iv i          i   i i vii      v  i vi ii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_208841130_   1794 GACACATAGACCAGTGGAACAGTACAAAAAACTCAGAAATAAAGTTGCAC 1843
                             i     i  i     i  v ivi i iii          viiii  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_208841130_   1844 ACCTACAATCATCTGATCTCCAACAAGACTGACAAAAACAAGCAATGGGA 1893
                          ii  iii   vi    i i i     iv  v   i v  vv       i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_208841130_   1894 AAAGCACTCCCTAGTCAACAAATGGTTCTAGGATAACTGGCTAGCCATAT 1943
                             v ivvi  vv            v  i   i      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_208841130_   1944 GCAGAAGATTGAAACTGGACCCTTACCTTTTACCATATA-AAAAAGTAAC 1992
                            i    v    ii       i     ivi        -     v    
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_208841130_   1993 TCAAGAAGGATTAAAGATTTAAATGTAAGACCCCAAAATATAAAATTCT- 2041
                             i v    i ?   ii           v iv   v       i   -
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_208841130_   2042 AGAAGAAAATCTAGG---AAATACCTTTTTCAACATTGGCTTTGGCAAAG 2088
                                  iv    ---    --   iv -i  v    v  v     v 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT--CTTCGT-GACCTTGGGTTAGGCAATG 583

  chr2_208841130_   2089 AATT-TTGGCTAAGTCCCCAAAAGCAATTGCAACAAAAACAAATATTGAC 2137
                         iv  -  i v  v v v         vvv         iv   v  v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_208841130_   2138 AAGTGGGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGCAACTAT 2187
                           i v    i v  i   v v  i i   i  ii vv    i vv     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_208841130_   2188 TAACAAAGTAAACAGAAAACCTACAGAATGGGAGAAATTATTTGCAAATT 2237
                         i  v     i  v   v    i               v           i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_208841130_   2238 ATGCATCTGACAAATGTCTAATATCCACAATCTATAAGGAACTTAAACAG 2287
                           ii      i  iv v  vi      v   v     i     ivv   i
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_208841130_   2288 TTCAACAAGCAGAAAAAAAAATAATCCCATTAAAAAATGGGCAAAGGACA 2337
                         i    i  -i i   i v      i  v   ?                iv
  L1M4_orf2#LINE/    784 CTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_208841130_   2338 TGAACAGACATTTCTCAAAAGAAGACATACAAGTGTCCAACAAATGCTCA 2387
                             i           v        i      i  v    i  --  v  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA--GCACA 880

  chr2_208841130_   2388 TTACTACTCTTCAGAAAAATGCAAATCAAAACCACAGTGAGA 2429
                          v -----------   i    ---    v i  ????????
  L1M4_orf2#LINE/    881 TGA-----------AAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (130 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.62 (42 / 16)  


3016 23.37 3.31 6.40  chr2_208950639_208953724     1660  2596 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_208950639_   1660 TAAAAAGACATCTCATGTTTATGGGTTGAAAGAATTAATATTGTTAAAAT 1709
                          ii     i   i      i    i   i    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_208950639_   1710 G---------TCCAAAGTGATCCACAGATTCAATGCAATCCCTATAAAAA 1750
                          ---------i     v     i          i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_208950639_   1751 TTCCAA-TGACTTTTTCGCACAGCTAGAAAAAA-AAGTCTAAAATTCCTA 1798
                          i   i-  v      i   v iv v  v  iv-i vi         v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_208950639_   1799 TGGAATGACAAAAGAGGCTGAATAGCTAAAGAATTCTTGAGCAAAAAGAA 1848
                              vvi   ii  vv v       i   iv v      iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_208950639_   1849 CAAAGCTAGAAGCATCATACTGCTTGATCTCAAAATACACTACAAAGCTA 1898
                              i i  i vv   i   v iii  i      ivi            
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_208950639_   1899 CAGTAATCAGAACAGCATGGTACTGGCAGAGAAACAGACAAACCAACTGA 1948
                                  ii    ii           v iii i     ----------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA---------- 290

  chr2_208950639_   1949 ACAGAATAAAGAGTCTATCAGTTAATAGGATGCTCATTTTTAAAAAAAAA 1998
                         ------  v   --------- i   i i  -------------------
  L1M4_orf2#LINE/    291 ------TATAGA---------TCAATGGAAT------------------- 306

  chr2_208950639_   1999 TAAAAAGTGAAAAAAAGAATAAAGAGTCCAGAAGTAAATTTACCCATTTA 2048
                         ---------------     vi           i    iii iv      
  L1M4_orf2#LINE/    307 ---------------AGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_208950639_   2049 CAGTCAATTG---TTCAATAAGGG-GACAAGAATACACTATAGGGAAAGG 2094
                         ii        ---   i i     - v     vi iv v  i       i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_208950639_   2095 ATATTCTCTTCAATAAGTAGTAATGGGTAAATGGGATATCCATATGCAGG 2144
                            v   i     i  i i  iv    vv  iv     ?   i     ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_208950639_   2145 AGAATGAAATTAGAGGCTTATCTCATACCATATATAATAATCAACTCAAA 2194
                                 i  i  vv i  i    i        i  v   i        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_208950639_   2195 -TAAATTGAAGACGTTATGTGTACCCCCTGAAACTGTAAAA--------- 2234
                         - ii  ii?    -i  vi    vvvv  i     i     ---------
  L1M4_orf2#LINE/    492 ATGGATCAWAGAC-CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_208950639_   2235 ---AACGAGAGGGAAAAGCTCCATGACATTGGTCTGAGTAGTGATTTTTT 2281
                         ---   ivii ? v   v  i i    v    vi ii i i  i   i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_208950639_   2282 AGATATGACCCCAAAAGCACAGGCTACAAAAGCCAAA-TAGACAAATGGG 2330
                                  v           i  v       vv   -    i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_208950639_   2331 ATTACATAAAACTGAGAAGTTTCTACAGAGCAAGGGTTACAATAGACAGA 2380
                          i v   v   v v i  ii  i iiivvv   i  vi  v  vi v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_208950639_   2381 CTGAAGAGACAAC--AGAGAACAGGAGCAAATATTTGCCAGCCATACATC 2428
                         v    i       -- v    ii    v          v ii    i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_208950639_   2429 TGATAAAGGGATAATATCCAAAATATATAAGGAACTCAAACAACTCAATA 2478
                               i  iv vi      i         i      vv           
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_208950639_   2479 GTAAGAAAGCAAATAATCTGATTATAAAATGGGCAAAGGATGTGAATAGA 2528
                         i   i  ii       i ii   ?v                v        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_208950639_   2529 CATTTCTCAAAAGAGGACATACAAATGGCCAACAGGTATATGAAAAAAAG 2578
                                 v     i  i              i i i i       i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_208950639_   2579 TTCAACGTAATTAATCAT 2596
                         i     i v ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (137 / 78)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 7.00 (91 / 13)  


2681 27.06 0.78 0.26  chr2_209006353_209008121      513  1277 (492)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr2_209006353_    513 TAAAGTTCGTATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTA 562
                             i   i       viiv  ii  v  v v  v     iv     i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_209006353_    563 AGCCAAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATA 612
                          ivv i          i      vv    i  v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_209006353_    613 CTACAAGGCTACAGTAACCAAAACAGCGTGGTACTGGTACCAAAATAGAG 662
                               i          i   i    i          i iv ii     v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_209006353_    663 ATATAGATCAATGGAACAGAAC--AGAACCCTCAGAAATAACACTGCATA 710
                                         i    i--   ii  --        vv iii i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACA 337

  chr2_209006353_    711 TCTACAACTATCCGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGA 760
                          i  iiiii vii   i  i     ivv  vv  i v  vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_209006353_    761 AAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGCCTAACCATATG 810
                            i  vvi  v  i  i              v     vv  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_209006353_    811 TAGAAAGCTGAAACTGGATTCCTTCCTTACATCTTATACAAAAATTAATT 860
                         i i  iiv    ii    ii   v   i   i v              i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_209006353_    861 CAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTA 910
                            i      i ?    i    i  v   v       i      vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_209006353_    911 GAAGAAAACGTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTT 960
                                  i    ?i v viv   iv   v v  vv i     v ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_209006353_    961 CATGTCTAAAACACCAAAAGCAACGGCAACAAAAGCCAAAATTGACAAAT 1010
                          v ivv  vi            vvi          vv     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_209006353_   1011 GGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATC 1060
                         v   ii v  i   v v  i i   i  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_209006353_   1061 AGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTC 1110
                          i      v  i     i   i             v  i    vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_209006353_   1111 ATCTGACAAAGGGCTAATATCCACAATCTACAATGAACTCAAACAAATTT 1160
                               i  i  i  vi      v   v  i  v      vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_209006353_   1161 ACAAGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAAC 1206
                          i  v     i    ----   v  i?    i            v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_209006353_   1207 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAA 1256
                              i     v        i  vi viii     v ii          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_209006353_   1257 ATGCTCATCATCACTGGCCAT 1277
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (118 / 85)
Gap_init rate = 0.00 (3 / 769), avg. gap size = 2.67 (8 / 3)  


2934 21.51 9.39 1.83  chr2_209052666_209057088.rev     2046  2812 (1611)    L1M4_orf2#LINE/L1        4   828 (80)  

  chr2_209052666_   2046 AGAAACATCTCACATTCATGGATT---AGACTTAATATTATTAAGATGTT 2092
                          i i i   i  ii          ---            i        vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_209052666_   2093 AATATCACTCAAAACAGTCTACAGATTCAATTCAATCCTTATCAAAATTC 2142
                             iiv i    viii             iv      i         i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_209052666_   2143 CAATAGCATTTGTTGCAGAAATAGAAGAATTCATCCTAAAATTGATATGG 2192
                           iiv  v   v          v  vi ii v           v      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_209052666_   2193 AATCTCAAAGGGCCC-TAAGAGTCAAA-CAATTTTGAAAAAGAAGAATAA 2240
                           viv   i  i   -v  v  i    -    i              i  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_209052666_   2241 A------------------------------------------------- 2241
                          -------------------------------------------------
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_209052666_   2242 --------ACAGTGTGGTACTGGAATAAAGACAGATATACAAATCAATAG 2283
                         --------               v    i  i   i   i i      i 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_209052666_   2284 AACAGAATAAAGAGCCCAGAAATAAACTTGTGTACACATGGCCAACTGAC 2333
                           i     vi    i            iii ii ivi    i   i   i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_209052666_   2334 CTCCAAGAAGAGCTCCAACAGCACTAAATGGGAAAAGGACAGTCTGGTCA 2383
                         i i i v   i iv    v v  i v      i    i i     vv   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_209052666_   2384 ACAAATGATGCTGGGAAAACTGGATATTTACATGCAAAACAATGCAGTTG 2433
                                i        v         ?ii          v    v     
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_209052666_   2434 GACCTGTTTCTTACACCACATACAAAAATTAACTCAAAATGGACTAAAGA 2483
                             iv vi  i      i                        ii ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_209052666_   2484 CTTAAACCAAAGACCCAAAGCAATAAAACTTCTGGAAGAAAACATAGAAA 2533
                          i    ivv    v i   i v        ii i             i?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_209052666_   2534 AAAATCGTCAGGACATTGAATGTGGATATGACACATTCCACATTCTTGGA 2583
                         v     v  iv   v   ii vv  vv   ii----------     i  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGT----------TTCTTAGA 593

  chr2_209052666_   2584 TATGACACCAAAATCACAGGCAACCAAA--AAAAATGGACAAATGGGACT 2631
                                      v    i     v   --      i  i    v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_209052666_   2632 GCATCAAACATAAAAACTTTTGTTCATTGAAGGACACAAT------AGTG 2675
                         v       vv             v v ii        v  ------    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_209052666_   2676 AAAAGGCAACCTACAGAATGAGGGAAAATGTTTTGCAAATCATAT--TTG 2723
                              i     i        i i      i   -           --i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTG 742

  chr2_209052666_   2724 ATAAGATGTTAGCATCCATAATATATAAAGAATTCCTACAATTCAACAAC 2773
                              ivii v i     v             i  i     i    i  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_209052666_   2774 AAAATAATCAAATTACTCTATTTTTTAAAATGGACAAAG 2812
                             vi -     v  i v   ?v--       i     
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWA--AAAATGGGCAAAG 828

Transitions / transversions = 1.78 (103 / 58)
Gap_init rate = 0.01 (11 / 825), avg. gap size = 7.82 (86 / 11)  

 887 26.32 3.51 0.00  chr2_209052666_209057088.rev     2813  3097 (1326)    L1M4_orf2#LINE/L1      614   908 (0)  

  chr2_209052666_   2813 CAACAAAAACAAAAATTGACAAGTAGTACCTAACTAAACTAAAGAGCTTC 2862
                                 iv      v  i  i v v  i v ii   v v  i i   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_209052666_   2863 TGCATAGCAAAAGAAACTATCAACAGAGTAAA----CAACCTATGGAATG 2908
                           iiivv    i  v        v i   i  ----     i ii     
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_209052666_   2909 GGAGAAAATATTCACAAACTATGCATTTGACAAAGGTCTAATATCCAGAA 2958
                                     ii    ii  ii  i   i  i  v  vi         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_209052666_   2959 TCTACATGAAACT----TAAATTAACAAGCAAAAAACAAACAAGCCCATT 3004
                          v  i vii    ----i  v i  i  vv    i     i  v  v   
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_209052666_   3005 AAAAAGTGGGCAAATGACAGGAGCAGACACTTCTCAAAAGAAGACA--CA 3052
                         ?    i        v  ivv  ii     i     v        i --  
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_209052666_   3053 TGCGGCCAACAAGCATTTGAAAAAATGCTCTACATCACTAATCAT 3097
                         vii      i     iv      i      v      ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (47 / 27)
Gap_init rate = 0.01 (3 / 295), avg. gap size = 3.33 (10 / 3)  

 518 13.68 0.00 1.05  chr2_209052666_209057088.rev     3837  3931 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_209052666_   3837 AAAAATAGACAAAAGACTTGAATAGACATTTTTTCCAAAGATGATATATA 3886
                               i i    i  i              i -       v      i 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCT-CCAAAGAAGATATACA 863

  chr2_209052666_   3887 AATGACCAACAAGCATATGGAAGGATGCTCAACACCAGCAATTAT 3931
                             i    i     i   i  i           i  ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 12.00 (12 / 1)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


1195 28.17 1.29 1.55  chr2_209192265_209197146.rev      582   968 (3914)    L1M4_orf2#LINE/L1      379   764 (144)  

  chr2_209192265_    582 CAATGGGGAAAATATTCCCTGTTTAATAAATGGTGCTGGGAGAACTGGCT 631
                                    iv  vvi  v  i  i              v      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_209192265_    632 AGCCATATGCAGAAAATTGAAACTGGACCCCTTCCTTACACCTTATACAA 681
                          ?   i     i  i v    ii         v   i     v       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_209192265_    682 AAATTAATTTGAGGTGGATTAAAGACTTAAATGCAAAACCCAAAGCTATA 731
                                i ii ii     i ?    i      i  i v i   i     
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_209192265_    732 AAAAC--TAAAAGAAAATCTAAGCA-ATATCATTGAGGACACAGTCAAGG 778
                            vi--  i       iv  i ?i- v   v i v iv vii viv   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_209192265_    779 ACAAAGATATTATTTAAAAAAAAAAACATCAAAAGCAAGTGCAACAAAAG 828
                         -   v i -  v  ---- i v vi   i        viv          
  L1M4_orf2#LINE/    579 -CAATGGT-TTCTT----AGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_209192265_    829 CAAAAATTGACAAATGGAATCTAATTAAACTAAAGAGCTTCTGCACAGCA 878
                         v      v  i    v i ii v  i   v v  i i   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_209192265_    879 AAGAA-ACTATCATCAGAGCAAACAGGCAACCTATAGAATTGGAGAAAAT 927
                            i -       vv i  ii  v  i     i i     v         
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_209192265_    928 TTTTGCAATCTATCCATCTGGTGGTGG-CTCATGCCTATAAT 968
                         v       vii  vi     i iiv  -  ii ii i v   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

Transitions / transversions = 1.52 (64 / 42)
Gap_init rate = 0.02 (7 / 386), avg. gap size = 1.57 (11 / 7)  

 508 22.42 2.42 3.03  chr2_209192265_209197146.rev     1244  1408 (3474)    L1M4_orf2#LINE/L1      745   908 (0)  

  chr2_209192265_   1244 AAAAGTCTAATATCCAAAATATACAAGGAACTTAAACAAATTTACAAGAA 1293
                           ii v  vi      i      i  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_209192265_   1294 AAAAACAA----CCCCATTAAAAAATGGGCAAAGGACATGAATAGGCACT 1339
                            i    ----   v   ?                iv       i  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_209192265_   1340 TCTCAAAAGAAGACATTTATGTGGCTAACAAACATGAAAAAAAAAAAAAA 1389
                             v        i  vi vi    i  i  i  i----- vi    i v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCAC-----ATGAAAAGAT 889

  chr2_209192265_   1390 GCTCAACATCACTGGTCAT 1408
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (22 / 14)
Gap_init rate = 0.01 (2 / 164), avg. gap size = 4.50 (9 / 2)  

3255 26.00 1.33 0.88  chr2_209192265_209197146.rev     3487  4390 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209192265_   3487 TAGAGAGATACTCCTTTGT-CA-GGATAGGAAAGCTCAATATTGTCAACA 3534
                          i  i     -   iv   -  -    v    ii  i        i  v 
  L1M4_orf2#LINE/      1 TGGAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_209192265_   3535 TGTCAGTTCTTCCAAAATTGATCTATAGATTCAATGAATTCCCTATTAAA 3584
                           v  i v  i  v           i        i v v       i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_209192265_   3585 ATTCAAGC-AAGTTTTTTATAGATATTGACAAATTCATTCCAAAGGGTAT 3633
                           i v   -ivv      ii   v        ii v  i i   ivvi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_209192265_   3634 AAAAAGAAGCAAAAGACCCATAATAGTCAACATGACATTGAGGGAGAAGA 3683
                          vii i v    ii      v     i   v ii iv    iii      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_209192265_   3684 ACAAAGCTGGAA-ACCCGCAGTATCCTACTTCAAGACTTACTATAAAACT 3732
                               i    i-  i i  v vi  v i     i        i   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_209192265_   3733 ATAGTAATCAGGACAGTGTGGTATTTGTGAAAAAATAAA----TAGATCA 3778
                          i        i            i v iiv  ii   i ----       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_209192265_   3779 ATAGAACAGGAAGCAGAACCCAGAAATAGACTGACATAAATAAAGTCAAC 3828
                           i   i  i vvv   ii         i  iv i i vv  vi     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_209192265_   3829 TGATTTTTGACAAATAAGCAAAGGCAATACAGTGGAGAAAATAGAGCCTT 3878
                                i     iviv  v   i v  v  i   i    iv v  i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_209192265_   3879 TTCAACAAATGGTGCTGGAAAAACTGGACATTCACATGCAAGAAAAAACA 3928
                                           i v       i ?i         --  i  ii
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA--AAGAATG 447

  chr2_209192265_   3929 AAAAGAATCAGACATAGATGTTA-ACCCTTCATATAAATTGACTCAAAAT 3977
                           i---- ii   vivv iv i -   v vi i v     i         
  L1M4_orf2#LINE/    448 AAG----TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_209192265_   3978 AAATCACAGGCCTAAATGTAAAATGC-AGAACTGTAAAGCTCCCAGAACA 4026
                         ii    ?  i           i -  - i    i    i   ii    v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_209192265_   4027 TAACATAAAAGAAAACCTTGACAACCTTGGGTATGGTGATGACTTTTTAG 4076
                         v      ii? v   i   viii         vv  ii   ii  i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_209192265_   4077 ATATGGAACCAAACACATGGTCAATAAAATAAATAACTGATAAGCTGGAC 4126
                              iv      vi  iiiv   i    v   v  iv     ii     
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_209192265_   4127 TTCATTAAAATTGAAAATTTTTACTCTATGAAAGACATTATCCACAGAAT 4176
                              i      i    i    iiv  vii  i    i    v v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_209192265_   4177 GAAAAGCTAAATCATAGACTGAGAGAAAATATTTGCAAAAGACGCATCTG 4226
                               vi  vi  i   v  i                 vv iii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_209192265_   4227 ATAAAGGGCTTTTATCCAACATATACCAAGAACTCTTAAAACACAACAAT 4276
                             i  i   v      iv     iv           v   v   i   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_209192265_   4277 AAGAAAGTAAACACCCCAATTAAATAATGGGCCAAAGACCTTAACAGAAA 4326
                           i  iii   i v       ?  v       v  i  ii v  i   v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_209192265_   4327 CCTCACCAAA-AAG-TATACAAATGGCAAATAAGCATGTGAAAAGATGCT 4374
                         ii  v     -   -            v        ii            
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_209192265_   4375 CCACATCATATGTTGC 4390
                          v      ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (150 / 81)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


2388 22.19 5.74 7.47  chr2_209207021_209209976.rev     1548  2471 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209207021_   1548 TGGAGAGATATAATACACTGGTGGAGCAGAAGACTTAATATTGTTAAGAC 1597
                             i      vvi iii vi    vii                     i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209207021_   1598 ACCAGTTTTACCCAAATTAATCTATAGATTTAATACTATTCCAATCAAAA 1647
                         iv  i vi v        i     i     i  ii v  i  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209207021_   1648 TCTTAGCAGTCTTTCTTGCAGAGGTTGA-AAGTTGATCCTAAAACTTATA 1696
                           ii   v i    i       ii    -   i           i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_209207021_   1697 GAGAAATGCAAAGGACTAAGAATAGCCAAAGTAATTTTGAAAAA--AGA- 1743
                         vi         i    iv            ii   i        --   -
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_209207021_   1744 CAAAACTGGAGGAAAAAAACTCTTGCCTGGTTTTTAAAATGTATTATAAA 1793
                             ii       vvv v   i---  iii   i-    iv  i  i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTT---CCCAATTTC-AAAACTTACTACAAA 246

  chr2_209207021_   1794 GCT----TAA--AATAAAACTTATTTTTGGCATAAAGGTAGATATATAGA 1837
                            ----   --  v v iiv iv vi        i i    i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_209207021_   1838 TTCATGGAACAGAATAGAGAGTACATAAATAAACCCACAACAAC-ATAGT 1886
                          iv      i     v      v  v           i -  vi-  i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGT 345

  chr2_209207021_   1887 CAATTAATTTTAGACAATGCCGCCCAGGTAATTTCAATGGACAAAAGAAT 1936
                              i     v     v vi   v  iiv   -      i-i       
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGG-GAAAGAAT 393

  chr2_209207021_   1937 AGTCTTTTTCAGTAAATAGTGCTGTAACAACTGAATATCTACATAGGAAA 1986
                                 -  ii    i      vi       i   ? i    ivi   
  L1M4_orf2#LINE/    394 AGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_209207021_   1987 AAATAAGCACTGAACAATTCCTCATATATATGTATATATATATATACAAA 2036
                         i   i i-ii  i  ---i   ----------------------------
  L1M4_orf2#LINE/    443 GAATGAA-GTTGGAC---CCCT---------------------------- 460

  chr2_209207021_   2037 TTTATACATATACACATATGTGTATATATACAAATATAAACTCAAAATGA 2086
                         -----  v ---    i-------i         v  v           i
  L1M4_orf2#LINE/    461 -----ACCT---CACAC-------CATATACAAAAATTAACTCAAAATGG 495

  chr2_209207021_   2087 ATCATAATTCTTAACATAA--------ACCCTAACATTCTTAGAAGAAAG 2128
                             ? ivi  v  ii   --------  iv   v i            i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_209207021_   2129 CATAAGAGAAAATCCT--TGACCTTGAGATGGAAAAAGAT--CTTAGG-- 2172
                             i ? v     i --        i v i iv  v i --     i--
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_209207021_   2173 -----CCATAAAAACAATTAATCAAA--AAAAATTGACAAATTGTACTTC 2215
                         -----   v  iv    vi  iv   --      v  i      v     
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_209207021_   2216 ATCAAAATTTTGAAGTTCAGCTCTTAAAAAGGCATCATTTAGAAAATAAG 2265
                                  vvi  v  iv iv   v   i i  ii  iv     i i i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_209207021_   2266 AAGACTAGT-ACAGA------GAAAATACAAAACCACAAAACGTATTTCT 2308
                              v vi-     ------       i----iii    v i   v   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATAT----TTGCAAATCATATATCT 741

  chr2_209207021_   2309 AA-AAATGAATTGTATCCAGAA-ATATTAAGAATTTATACAACTCAACAA 2356
                         i -  iv  v            -    v     i iv          i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_209207021_   2357 TTAAAGGACAAATAACCTAAT---AAGATG--CAAAAA---TAAATATAT 2398
                          v   i           i   ---  i   --    ii--- i    v i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_209207021_   2399 CTTTTGTATATCTTCATAGAAGAAGATATATGAATGGCCAATAAGCACAA 2448
                         v   -------  i  ---           ii                 v
  L1M4_orf2#LINE/    842 ATTT-------CTCCA---AAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_209207021_   2449 AAAAGGAT----AAAATCATTAGTCAT 2471
                         i   i   ----  v    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (131 / 71)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.70 (122 / 33)  


3004 26.91 1.22 0.66  chr2_209210038_209216710.rev     5279  6181 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209210038_   5279 TGGAAAAACATCCCATGTTCATAGATAGGGAGAACCAATATCATGAAAAT 5328
                               i i             i   v  i   vii     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209210038_   5329 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 5378
                            v     v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209210038_   5379 TACCA-CTGACTTTCTTCACAGAGTTAGAAAAAAACT-ACTTTAAATCTC 5426
                          v   -   v    i  -i    iv v  v  i--  - iii    vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr2_209210038_   5427 ATATGGAACCAAAAAAGAGCACGTATAGACAAGACAATCCTAAGTGAAAA 5476
                                 viiv  ii  v vv v    v   i      i i ivi i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_209210038_   5477 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAAATATACTACAAAG 5526
                                 i      vv       v  ii i       iv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_209210038_   5527 CTACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5576
                               i  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_209210038_   5577 CAATGGAACAGAACAGAG-GTATCAGAAGTGGTGCCACATATCTACAATC 5625
                                 i    iv   -  -i     i iivv   i i  i  iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGT-CCAGAAATAAACCCATACATTTATGGTC 346

  chr2_209210038_   5626 ATCTGATCTTTGATAAACTTGACAAAAACAAACAATGGGGAAAGGATTCC 5675
                          vi    i  i  i  ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_209210038_   5676 CTATTTAATGAAAGTTTTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5725
                           v  i  ii  v v vi     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_209210038_   5726 GAAACTGGACCTCTTCCTTCCACCTTATACAAAAATTAACTCAAGATGGA 5775
                            ii      i  v   iv    v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_209210038_   5776 AGAATGACTTAAACAGCCAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5825
                         vv ?v   i    iivvvi v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_209210038_   5826 CTAGGCA-ATACCATTCAGGACATAGGCATGGGTAAAGACTTCATGACTA 5874
                         v    ?i- v i -   iv   v v  vv i  i  v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_209210038_   5875 AAACATCAAAAGCAAAGGCAACAAAAGCCAAACTTGACAAACGGGATCTG 5924
                         vi   i        v i          vv   v v  i   iv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_209210038_   5925 ATTAAA-TAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5973
                           i   - v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_209210038_   5974 CAGGCAACCTACAGAATGGGAGAAAACTTTTGCAATCTATCCATCTGACA 6023
                         v  i     i                iv       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_209210038_   6024 AAGGGCTAATATCCAGAATCTGCAAAGAACTTAAACAAATTTACAAGAAA 6073
                          i  i  vi          v ii        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_209210038_   6074 AA---AAA-AACC--ATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 6117
                           ---   -    --  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_209210038_   6118 CTCAAAAGAAGACATTTATGTGGCCAAGAAACATATGAAAAAAAAGTTCA 6167
                            v        i  vi vi       v  i  i       i v- i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCA 894

  chr2_209210038_   6168 TCATCACTGGTTAT 6181
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.31 (17 / 13)  


 787 29.32 16.42 2.63  chr2_209275474_209277259      497  1294 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209275474_    497 TGAAAGAGATAATGTACTATATTCACGAATAGGAAAACTCAATATTGTAA 546
                           i  -     --- v i  i    i i  v    i   i        v 
  L1M4_orf2#LINE/      1 TGGAA-AGATA---TCCCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chr2_209275474_    547 GGATGCTAAT-TTCCCCTAA---ATCTGTGGGTTTTATACAATCA--AGC 590
                         i    vi   -i     v  ---    iii i  iv ii     v-- v 
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_209275474_    591 AAATTCTCTA-TG-----TGTGTGAAAATTAAAAAGCTGATTCTAAAATG 634
                            v  i vi-  ----- v  iii     i v        i       v
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_209275474_    635 TATTTAAAAGAGCGTAGGGCC---AATAAT----ATA--CTCGAGAATTA 675
                         i  v ii  iv  ivi  i  ---    ii---- i --  i  i  -- 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA--A 194

  chr2_209275474_    676 AAAGAGTAAGATGGAGAAGACTTGCCTTATCAAATATCAAGCCCCATTTT 725
                         i    ii  ii v -  i    ii vi vi v   v    iv ii i vi
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTG-GAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_209275474_    726 AAAGTCATAATGATTAAGATAGTG--------GCACAGAAATAGACAAAT 767
                             ii i i i  i    i    --------   i iii       v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_209275474_    768 AGACCAAGTGAAAAAGA-CAAAGAACTTAGAAAGAGACTCAGACTTATAT 816
                            i   -  i  v   -ivi   iiii     v i  i  v  v v   
  L1M4_orf2#LINE/    294 AGATCAA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_209275474_    817 G--CAACTTGGATAGGTAACAGAGCTGCCATTGTAGTCCAGTGGAGAAAG 864
                          --   i --   vvvii   ii v     vviivi i  i   i     
  L1M4_orf2#LINE/    343 GGTCAATT--GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_209275474_    865 GAGGAAATATTCAATAAAAGTTGCTAGCATAATTG-AT---TATATAGAA 910
                         i viivv v     i   v v    i v i  i  -  ---i i  iv  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_209275474_    911 ATTAATAACATTGAATT------TCACACCATGTACAAAAATCAATTCCA 954
                          vv   i vi   i ii------         i         i  i  v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_209275474_    955 GAT--ATAATA-AC--ACATGTGATAAC-AAAA-TATTAATATTTTAGAA 997
                         i  --  v ? -  -- v    i v i -    -   v  vv i      
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_209275474_    998 TGAAATA-AGAGATAA-TCTTTAT----------TA---------TTCTA 1026
                         vi   i -  i?i   -    ii ----------  ---------    v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_209275474_   1027 AGACA-------------------------GGAAAGAATTTTTAAA---- 1047
                            i -------------------------i    i   vvv    ----
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_209275474_   1048 ACT------AAACCAAATACCTTT--------AAG----TTA--AAAAAA 1077
                            ------   ii   v  i   --------   ----i  --  i   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_209275474_   1078 GTGAAAAATAAGATGAGCCACAAACTTTAAAAAGAAACTTGCAAA--ATA 1125
                                ----  ii v     i v vvi i  i v i       --   
  L1M4_orf2#LINE/    691 GTGAAAA----GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_209275474_   1126 TAT--AATA-GTGTCTTATA--AAGAATATGTAAACGTAGAATTCCAAAA 1170
                            --i   - v v   i  --v       i    ----   i  iv v 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAA----GAACTCTTACA 782

  chr2_209275474_   1171 ATTTCTTAAGAAAAAAATAAGTAATCTAATAGAAAAATATAGAAAG-ACA 1219
                          i ivv   v     i i  i   i i   v?      iviv    - iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_209275474_   1220 TGAATAAGCATTTCAC---AGAAGATTTTAACAAATGGTTAATAAATATA 1266
                               ii      v ---       v --        ii     ii i 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATAT--ACAAATGGCCAATAAGCACA 880

  chr2_209275474_   1267 AGAAAAGCTGC-CAATTATCATTAATAAT 1294
                         v      v   -   i-    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (149 / 82)
Gap_init rate = 0.05 (46 / 908), avg. gap size = 3.30 (152 / 46)  


2147 27.54 3.23 1.24  chr2_209323594_209325385.rev      497  1302 (490)    L1M4_orf2#LINE/L1       87   908 (0)  

  chr2_209323594_    497 AACTCCTATCAACCAATC--AACATCATTTTCAACAGACATAGAAAGAAC 544
                           ii        --    -- i vv v    ivi    v  v  v - i 
  L1M4_orf2#LINE/     87 AATCCCTATCAA--AATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGC 133

  chr2_209323594_    545 TC-TTCTAAAATTCATATGGAAC--CAAAAAAACAGCCCA-AATAGCCAA 590
                          v- i                 v--   iii ----    -         
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGA----CCCAGAATAGCCAA 179

  chr2_209323594_    591 TGCAATCCTAAGCAAAAAGAACAAAGCCAGAGGTATAACA-TTGCCAACT 639
                         vi     i i iv  i          iii    vv v   -  v    i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_209323594_    640 TCAAATTATACTGTGAGGCTACAGGAATTAAGACAGCATGGTACTGGTAC 689
                              viv    iii i       v   i       ii         i i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_209323594_    690 AAAAACAGATATGTAGGTCAGTGCAATAGAATAAAGAACCCAAAAATAAA 739
                           ii i   i  i   i   i  v        vi   ii   i       
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_209323594_    740 GCCACAGACCTACAGT-AATCTAATCTTAAACTTAGTCAACAAAAATAAA 788
                         v   i v ii  ii  -   - i  i  vi  vvi viiv   i vi vv
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_209323594_    789 CGATGG--AAACATGACTCTATTTAATAAACGGTGCTAGAATAACTGGCC 836
                          i    --   v vv v   v  i  i   i      i i i      vi
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_209323594_    837 AGCCATATGTAGAAGAATAAAACTGGACCCTTACATTTCAACATATACAA 886
                          ?   i   i i      i  ii       i   v iv  v         
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_209323594_    887 AAATTAACTGCAGCTGGATTAAAGATTTAAATGTAAGAACTCAAACTGTA 936
                                  vv iv     i ?   ii           i  v     i  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_209323594_    937 AAAATACTAGAAGAAAATCTAGGAAATACTCTTCTCAACAACAGTCTTGG 986
                            v vi          iv    ?ivv v     vii  vvii vi v  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_209323594_    987 CAAAGAATTAT-GGCTAAGTCCTCAAA--CGCCAGCAACAAAAACAAAAA 1033
                            v iv  v -i v  v v vi    -- i v          iv     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_209323594_   1034 TTGAAAAGTGGGACCTAATTAAACAAAACAGCTTTTGCACAGCAAAAGAA 1083
                          v  v  i v    i v  i   vvv  v i      ii vv    i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_209323594_   1084 ACTATCAATAGAGTAAAGAGGCAACCTAAGGAATTGGAGAAAATATTCAC 1133
                                 v i   i  i  i     i vi    v            ii 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_209323594_   1134 AAACTATGCACTCAACAAAGGTCTAATATCCAGAATCTATAA-GAA---- 1178
                            ii  ii iiii i  i  v  vi          v     -   ----
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_209323594_   1179 -ACAAATGAACAAGCAAAAATCAAACAACCTCACTTTTAAAATGTGCAAA 1227
                         -    v v  i  vv    iv    i    -  v  ?v      v     
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACC-CAATTWAAAAATGGGCAAA 827

  chr2_209323594_   1228 AGA-----ACAGACACTTTCCAAAAGAAGATATACAAGTGGCCAAGAA-- 1270
                         i  ----- i     i  ii v               i       v  --
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_209323594_   1271 ACATGAAAAAAATGCTAATCATTGCTAATCAT 1302
                                  i -    v v   ii????????
  L1M4_orf2#LINE/    878 ACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (126 / 92)
Gap_init rate = 0.02 (19 / 822), avg. gap size = 1.89 (36 / 19)  


3128 26.74 1.44 1.10  chr2_209366733_209377242.rev     5015  5919 (4591)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209366733_   5015 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTTAAAAT 5064
                              ii i  i     i        v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209366733_   5065 GGCCATATTGCCTTAGGTAATTTATAGATTTG-TGCCATCCCCATCAAGC 5113
                            v   i v  iv iv i  i  i     ii-i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209366733_   5114 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ATTTTAAAGTTC 5161
                          v   iivi i  i  ii     -   --- v  i  -  ii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_209366733_   5162 ATATAGAACCAAAAAAGAGCCCGCATCACCAAGTTAATCCTAAGCCAAAA 5211
                             i   viiv  ii  v  v v  vi    ivi    i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_209366733_   5212 GAACAAAGCTGGTGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5261
                                 i   v  vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_209366733_   5262 CTACAGTAACCAAAACAGCATGGTACTGG--TACCGATGCAGAGATATAG 5309
                                  i   i    ii         --  vv   --   v      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT--AGACATATAG 295

  chr2_209366733_   5310 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACA 5357
                          i        i    i--    i  --        vv   i    i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr2_209366733_   5358 ACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT 5407
                         iii vi    i  i     ivv  v   i v  vvv           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_209366733_   5408 --TCCCAATTTAATAAATGGTGCTGGGAAAACTGCCTAGCCATATGTAGA 5455
                         --  ii--  i  i              v     vv  ?   i   i i 
  L1M4_orf2#LINE/    394 AGTCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_209366733_   5456 AAGCTGAAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAG 5505
                          iiv    ii    i    v   i     v i            i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_209366733_   5506 GTGGATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAG 5555
                         i     i ?    i  v    v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_209366733_   5556 AAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 5604
                              v    ?i- v i -   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_209366733_   5605 GTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 5654
                         ivv  vi            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_209366733_   5655 ATCTAATTAAACTAAAGAGCTTCTGCAC---AGAAGACACTACCATCAGA 5701
                          ii v  i   v v  i i   i  ii --- i i       i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_209366733_   5702 GTGAACAGGCAGCCTACAAAATGGGACAAAATTTTTGCAATCTACTCATC 5751
                              v  i  i  i   i       v     v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_209366733_   5752 TGACAAAGGGCTAATATCCAGAATCTACAACGAACTCAAACAAATTTACA 5801
                            i  i  i  vi          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_209366733_   5802 ACAAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGA 5851
                          i     i     i     v  i?    i    ii      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_209366733_   5852 CACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATG 5901
                           i     v        i  vi viii     i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_209366733_   5902 CTCATCATTACTGGCCAT 5919
                             v   i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (148 / 90)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  

2600 27.61 4.47 0.46  chr2_209366733_209377242.rev     9146 10018 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209366733_   9146 TGGAAAAACATTTCAGACTCAGGAATAGAAAAAAATAATATGGTTAAAAT 9195
                               i i  ii  vii   v i  v i  i vv      v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209366733_   9196 TGCCATACTTCCCAAAGCAATTTACAGATTCAATACTATTTCTATGAAAC 9245
                         v  v     i      vii  i           ii v  ii    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209366733_   9246 TACCAATGACATTCATCACAGAATTAGAAAAAAAAAGTTCTAAAATTCAT 9295
                          v   iivi v  iv ii     v v  v  ivvi - i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr2_209366733_   9296 ATGGAAACAAAAAAGAGCCCGAACGGCTAAAACAGTCCTAAGCAAAAAGA 9345
                                iiv  ii  v  v   ii  i      i  i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_209366733_   9346 ACGAAGTCAGAGGCATCACGTTATCCAACTTCGAACTATACAACAAGGCT 9395
                           i    ii    vv    ii vi    i   i  viv   v    i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_209366733_   9396 ACAATAACCCGAGCAGCACGATGGTGATACAATAACAAACACATAGACCA 9445
                            i   i viii   iii i iv  ii i  vi i i   i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_209366733_   9446 ATGGAACATAATAGAGAGCCCAGAAATAAAGCCACACATTCAAAACCATC 9495
                               i v   v     i           v   i     i viii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_209366733_   9496 TGATCTTTGACAAAGTCAACAAAAGCTAGCAATGAGGAAAGGACCCCCTA 9545
                             i  i     i viiv   i v vvv     i      i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_209366733_   9546 TTCGATAAATGGTGCCGGGATAACTGGCTACCCATATGCAGAAAATTGGA 9595
                            i i         i    i      v  ?   i     i  i v  i 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_209366733_   9596 ATCAGACCTCTACCTTTCACAATATGCAAAAATCAACTCAAGATGGATTA 9645
                         i ii    i      iv   v    i       i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_209366733_   9646 ACAACTTAAATGGAAAATTTAAAACTATAAAAA-CTTAG--GAAA----- 9687
                         ?vi  i      v  i vi             v-     --    -----
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_209366733_   9688 --TGC---TATTCTAGACATAGGCCCTGGCAAAGATTTCAT-GATGAAGA 9731
                         --? i--- v   vv   v v  viiv     v i    v -   - v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGA 598

  chr2_209366733_   9732 TGACAAAAGCAATTGCAACAAAAAAAAAACT-GACAAATGGGACCTAATT 9780
                         iiv        vvv         i     v -  i    v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_209366733_   9781 AAA-TTAAAGAGCTTCTGCACAGCAAAAGAGACAACCAACAGAGTAAACA 9829
                            -     i -   i  ii vv    i  v  v i   v i   i  v 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_209366733_   9830 GATAACCCACAGAATGGGAGAAAATAT-----------ACATCTGACAAA 9868
                           i                        ----------- i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_209366733_   9869 GGTCTAATATCCCAGAATCTATCAGAAACT--TA-AATTTACAAGCAAAA 9915
                           v  vi     -     v   v ii    --  -  i i vv ii    
  L1M4_orf2#LINE/    748 GGACTTGTATCC-AGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_209366733_   9916 AACCA-----CCCCTTTTAAAAGTGGGCAAAGGACTC----AGACACTTC 9956
                          iv  -----   vv  ?    i           i i----     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_209366733_   9957 TCCAAAAAAGACATACATACAGCCAACAAGCATATGAAAAAAAGCTCAAC 10006
                               i    i     v ii     i     i       i v       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_209366733_  10007 ATCACTGTTCAT 10018
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.69 (43 / 16)  


2474 27.05 3.65 1.60  chr2_209416937_209420978.rev     2675  3550 (492)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_209416937_   2675 ATGCTCATGGACAGGGAGAATCAATATTATTAAAATGCCCATACTGCCCA 2724
                            i       iv  i   v i      i    i   v v     v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_209416937_   2725 AAGCAACGGACAGATTCAATGCTATTCCTGTCAAACTACTAATCATCATT 2774
                           vii ivv          i  v  i   i     v v i iiiii -- 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC--T 112

  chr2_209416937_   2775 TTTTCACAGAATTAGAGAAAACT-ATTCTAAATTTCATATAGACCTAAAA 2823
                             ii     v v  v  i-  -  i     v       i  vv iv  
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_209416937_   2824 AAAGGCCA-AATAGCTGAAGCAATCCTAAGCAGAAAGAACAAAACCAGAA 2872
                         iiiiv   -      ii  i     i i iv ii         iiii  i
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_209416937_   2873 GCATCATACTACCTAACTTTAAACTATACTATGAGGCAAAAGTAACAAAA 2922
                          vv   i   v  i  i  i   viv     ii i  v v     iv  i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_209416937_   2923 ACAGAAT--TACTGGTACATAGACAGACCCATATACATTGGTTAGAAGCA 2970
                             vi --      i i vi  i    --     v  iii -- i ii 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGAC--ATATAGATCAAT--GGAATA 307

  chr2_209416937_   2971 GGTTAGAGAACCCGGAAATAAAGCTGCACACCTATA--------ACTTT- 3011
                          iv v    ii  i        v iii   ii   i-------- i   -
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_209416937_   3012 AACAAAGTCTACAAAAATAAGCAATGGGGAAAGGACTCCCCATTCAATAA 3061
                         i    i vivv   i vi vv            i ivvi iv     i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_209416937_   3062 ATGGTGCTAGGATAAATGGGTAGCTACATGCAAAAAGATTAAGACTAGAC 3111
                                 i   i  v   i  ? i          ii  v   -i i   
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG-TTGGAC 456

  chr2_209416937_   3112 TCCTGCCTTTCGCCATATCCAAAAATCAACTCAGAATAGATTAAAGACAT 3161
                         i   i   iv i      v       i      i   i   i ?    v 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_209416937_   3162 AAATATAAAACCTAAAGCTTTAGAAATCTTAGAAGAAAACCTAAG---AA 3208
                             i   i v     i  v  i  v              v  i ---  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_209416937_   3209 ATACCATTTTG-GACATAGGCCCTGGCAAAGATTTCACGACAAAGACAAC 3257
                           ----i  i -   v v  viiv     v i    viiivv v    v 
  L1M4_orf2#LINE/    557 AT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_209416937_   3258 AAAAGCAATCGCAACAAAAACAAAAACTGAAAAATGGGACTT------AA 3301
                                vvv         iv     iv  v    v      ------  
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_209416937_   3302 TTAAAGAGCTTCTGCACAGCAAA--ACA--ATCAACAAAGTAAAGAGACA 3347
                              i -   i  ii vv    --   --     v     i  i     
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_209416937_   3348 ACCAACAGAATGAGAGAAAATATTTGCAAACTATGCGTCCTATGAAAGTC 3397
                            v        i                 ii  iii  iv  i ii v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_209416937_   3398 TAATACCCAGAATCTAGAAACAACT--TA-AACATATTAAGGAGTAGA-A 3443
                          vi  i       v  v   v    --  -   vi v   vi iv   - 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_209416937_   3444 AACAACCCCATTTAAACACAGGCAAAGGACATGAACAGGCACTTCTCAAA 3493
                           i     v   ?   v ii         iv    i  i  i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_209416937_   3494 AGAAGACATACATGTGGCCAA-AAGCATATGAAAAAAATGCTCAACATCA 3542
                               i     vi       -     i       i -            
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCA 900

  chr2_209416937_   3543 CTAATCAT 3550
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.66 (146 / 88)
Gap_init rate = 0.02 (22 / 894), avg. gap size = 2.09 (46 / 22)  


2600 27.91 2.54 0.58  chr2_209423817_209428030.rev     2856  3722 (492)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr2_209423817_   2856 ATTAGAAGAATTAATATCATTAAAATGGCCATATTGCACAAAGCAATCTA 2905
                            i     v       ii    i     v   i v v    vii     
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr2_209423817_   2906 CAGATTCAATGCTATTTCTATCAAACTATC-GATATCACCTTTTACAGAA 2954
                                  i  v  ii        v vi - v ii -ii    i     
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAA 123

  chr2_209423817_   2955 TTAGAAAATACT-ATTCTAAAATTCATATGGAACCAAAAAAGAGCCCAAA 3003
                         v v  v  -i  -  i                 viiv  ii  v  vi  
  L1M4_orf2#LINE/    124 ATTGACAA-GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr2_209423817_   3004 TACCTAACACAATACTGAGCAAGAAGAAAAAAGCTGGAGGTTATCACATT 3053
                           v i  v     vi   iv        v    i      vi-     i 
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC-TCACACT 221

  chr2_209423817_   3054 ACTCAACTTCAAAATATACAATGAAGCTGCAGTAAATACAACAACATGGT 3103
                         v i   i       iv   v ii     i      vi vi   iii    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_209423817_   3104 ACTGGTACAAAACCATACACATAGACCAATGAAACAGAATAGAGAACCCA 3153
                              i i  iivi v   i     i     i  i     v    ii   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_209423817_   3154 GAAATAAAGTTGCATACCTACAGCCATCTGATCTTTGACAAAATCTACAA 3203
                                 viiii i ii  ii i  vi    i  i     iivivv   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_209423817_   3204 AAATAAGCAAAGGGGAAAAGACTCCCTATTCAATAAATGGTGCTGGGACA 3253
                         i vi vv   v       ii ivvi  v     i                
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr2_209423817_   3254 GCTGGCTAGCCATTTACAGAAGAAAGAAATTGGATCCAGACATTTCACCA 3303
                         i    v  ?   iv i  i     v   i     i  vv  v iv     
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_209423817_   3304 TATACAAAAATTCACTCGAGATCAATTG-AGATCTTAAATGTAAAACCTC 3352
                                     v    i i  vi  ii-   i  -        i v  v
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCT-AAATGTAAGAGCTA 520

  chr2_209423817_   3353 AAACTATAAGAATCTTAGAAGAAAATCTAGAAA-ACACCATTCTGGACAT 3401
                                  i v             iv   i?i- v i -   vv   v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT 569

  chr2_209423817_   3402 TGGCCTTGGGAA---------AGA-ATTATGCT-----CAAAAGCAACAA 3436
                            vi v  v  ---------   -  v ii i-----  v         
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_209423817_   3437 TAACAAAAATTGGCCAGTGGGACCTAGTTAAACTAAAGAGCTTCTGCACA 3486
                         v iv      v iiv i v    i vi i   v v  i i   i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_209423817_   3487 GCAAAAGAAACTATCAACAGAGTAAACAGACATCCTAAAGAATGAGAGTA 3536
                         v    i  v        v i   i  v     v  i v      i   v 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_209423817_   3537 AATATTTGCAAACAATGCATCCAACAAAGGTCTAATATCCAGAATCTATC 3586
                                     iv  ii   ii i  i  v  vi          v   v
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_209423817_   3587 AGGAAATTAAACAATTCAATGAGCACAA-ACAGGTAACCCT-TTAAAAAA 3634
                          i   v ivv    i     i vv v  -   ii      v-  ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_209423817_   3635 TGGGCAAAGAACGTGAATGCACACTTCTAAAAAGAAGACATACAAGCAGC 3684
                                  i iv     iv   i    vv        i      iii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_209423817_   3685 CAACAAAAATATGAAAAAATGTT-ATCATCACTAATTAT 3722
                            i  iv i       i   i - v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.02 (15 / 884), avg. gap size = 1.80 (27 / 15)  


3251 25.71 1.10 1.32  chr2_209436970_209443375.rev     5005  5914 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209436970_   5005 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATCGTGAAAAT 5054
                              ii i  i     i      i v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209436970_   5055 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5104
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209436970_   5105 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5152
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_209436970_   5153 TATGGAACCAAAAAAGAGCCCACAAC-GCCAAGTCAATCCTAAGCCAAAA 5201
                                viiv  ii  -    v  i-     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_209436970_   5202 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5251
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_209436970_   5252 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATATAG 5301
                                  i   i    ii         i iv ii i   i     -- 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA--G 295

  chr2_209436970_   5302 ATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACA 5349
                                   i    i--    i  --        vv   i i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr2_209436970_   5350 ACTATTTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT 5399
                         iii v     i  i     ivv  vv  i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_209436970_   5400 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5449
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_209436970_   5450 GCTGAAACTGGATCCCTTCCTTACACCTTATACAACAATTAATTCAAGAT 5499
                         iv    ii    i    v   i     v       v      i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_209436970_   5500 GGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5549
                             i ?    i    i  v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_209436970_   5550 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5599
                            v    ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_209436970_   5600 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5649
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_209436970_   5650 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5699
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_209436970_   5700 AACAGGCAACCTACAAAATGGGAGAAAATATTCGCAACCTACTCATCTGA 5749
                           v  i     i   i                i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_209436970_   5750 CAAAGGGCTAATATCCAGAGTCTACAATGAACTCAATGAAATTTA-CAAG 5798
                         i  i  i  vi        i v  i  v      v- iv  i i -i  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAACTCAATAAT 792

  chr2_209436970_   5799 AAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGAATATGAACAGACA 5848
                              i     i     v  i?    i         i  v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_209436970_   5849 CTTCTCAAAGGAAGACCTTTATGCA----GCCAAAAGACACATGAAAAAA 5894
                         i     v  i     ----   i  ----     v ii          i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_209436970_   5895 TGCTCATCATCACTGGCCAT 5914
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (143 / 87)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


3335 23.17 3.44 2.77  chr2_209443471_209445792.rev      929  1830 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209443471_    929 TGGAAAGAGATCTTGTGTTCATGGAGTGGAAGAATTAACGTTTCTAAAAT 978
                                 v   iii          v       v    ii  vi   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209443471_    979 GCCCATACTACATGAAGTGATCTACAGATTCGATGAAATCCCTATCAAAA 1028
                          v v     v vii  v              i i v              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209443471_   1029 TTCCAAAGGCATTTCCT-CACAAATAGAAAATACAATTCTACAATTCATA 1077
                          i   ivv  v   ii -  v    v  v  vvii  i   v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_209443471_   1078 TGGAAACACAAAAGACTCCAAATCACCAGAGCAATCTTGAGAAAGAAGAA 1127
                               ii   ii   i vi   vi   i i         i         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_209443471_   1128 CAAAGCTAGAGGGATCATATTCCCTGGTTTCAAAATATATTACAAAGCCA 1177
                              i i    iv   i i i  iii        iv  i        i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_209443471_   1178 CAGTAATCAAAACAATATGGTACTGGCATAAAAACAGACACATAGACCAA 1227
                                   i   i i              ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_209443471_   1228 TCTAACAAAGTAGAGAGCCCAGAAATAAAACCGTGCATATTCAGTCAACT 1277
                          vv  i i i v     i           v  i i   v vii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_209443471_   1278 GATCTTTAGCAAGGATGTTAAGAACACACAGTGGGAAAAGA-CAGCCTCT 1326
                            i  iii     i  ii    v  iv  i    i     -i  i  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_209443471_   1327 TCAATAAATGGTGTTAGAAAAACTGAATATCCTCATGAAAAAGAATGGAA 1376
                             i        i i i v     i   ?  v    v         i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_209443471_   1377 TTAGACTCCTAATTTACACCATATACAAAAGTTG-CTCGAAATGGATTAA 1425
                           i   i    vi i               i  i-   i        i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_209443471_   1426 AGACTTAAACATAAGACCTGAAACTGTAAA-CTCC-AAAAGAAA-CACAG 1472
                             i    ii     v  i     i    -   i- i      -  i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_209443471_   1473 GGGAAAATCTTTTGGGCAATGGTCTTGTCAATTATTTCATGAATTTGACG 1522
                          ? v       ivv i vv   vi v v    vi    v ii  v    i
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_209443471_   1523 C---------AAGCAGCAAAATAAAAAA---ATAGATGGAACTACGTCAA 1560
                          ---------     i     v      ---   i  v i   v i    
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_209443471_   1561 A-TTAAAATGCTCTGCACAGCAATGAAAAAAATCAA---AGTAAAGAGGC 1606
                          -      vvi i  ii vv   v i v vv     ---   i  i  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_209443471_   1607 AACCTATGGAACAAGAGAAAATATTTGCAAACCATCTATCTCATAAGGGA 1656
                             i ii   iii                 i   v     v        
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_209443471_   1657 TTAATACCCAAAATGTATTA-GAATTTGTCCTACAACTGAATAGCAAAAA 1705
                         i vi  i   i   i   v -   i --- i       v    ii     
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACT---CTTACAACTCAATAATAAAAA 797

  chr2_209443471_   1706 AACAAA----CTGAT-GAAAAATGGGCAAAGGATTTCAACAGCACTTGTA 1750
                         i     ---- ii  -?                   -------------i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTT-------------G 834

  chr2_209443471_   1751 AATAAAAAGGTCTTTCATTTTTCCAAAGA---CATACAAATAGCCAACAG 1797
                             i ---------     i        ---i        i     i i
  L1M4_orf2#LINE/    835 AATAGA---------CATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_209443471_   1798 GTATATGAAAAGCTGCTCAGCATCACCAGTCAT 1830
                          i i        v      i     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.20 (141 / 64)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.29 (56 / 17)  


3060 26.65 1.10 1.10  chr2_209450710_209456273     4165  5072 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209450710_   4165 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4214
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209450710_   4215 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4264
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209450710_   4265 TACCAATGACTTTCTTCACAGAA-TTGGAAACAA-CT-ACTTTAAAGTTC 4311
                          v   iivi i  i  ii     -   ---    -  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_209450710_   4312 ATATGAAACCAAAAAAGAGCCCACATCGCCAAGTCAATGCTAAGCCAAAA 4361
                              i  viiv  ii  v  viv  v     iv    vi i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_209450710_   4362 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 4411
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_209450710_   4412 CTACAGTAAACAAAACAGCATGGTACTGGTGCCACAACACAGATATAGAC 4461
                                  v   i    ii         iiiv vi i v v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_209450710_   4462 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 4509
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_209450710_   4510 TATCTAATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGCATTC 4559
                         i vi i  i  i     ivv  v   i v  vvv           v  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_209450710_   4560 TCTATTTAATAAATAAATGGTGCTGGGAAAACTGGCTAGCCATAAGTAGA 4609
                            v  i  i    ----          v      v  ?   i v i i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAAT----GGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_209450710_   4610 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAG 4659
                          iiv    ii    i    v   i     v              i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_209450710_   4660 ATGAATTAAAGACGTACATGTTAGACCTAAAACCATAAAAATCCTAGAAG 4709
                            i  i ?    v  v    v   v       i      v  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_209450710_   4710 AAAACCTAGGCA-ACACCGTTCAGGACATAGGCATGGGCAAGGACTTCAT 4758
                              v    ?i- v i -   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_209450710_   4759 GTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGT 4808
                         ivv  vi            vvi          vv    iv  i    v v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_209450710_   4809 ATCTAATTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTACCATCAGA 4858
                          ii v  i   v v  i i   i  ii vvi   i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_209450710_   4859 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATC 4908
                              v  i     i                 v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_209450710_   4909 TGACAAAGGGCTAATATCCAGAATCTAAAAAGAACTCAAACAAATTTACA 4958
                            i  i  i  vi          v  v         vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_209450710_   4959 AGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGTATATGAACAGA 5004
                          v     i    ----   v  i?    i         v  v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_209450710_   5005 CACTTCTCAAAAGAGGACATTTGTGCAGCCAACAGACACATGAAAAAATG 5054
                           i     v     i  i  viiviii     i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_209450710_   5055 CTCATCATCACTGGCTAT 5072
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (137 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


3013 27.43 1.11 0.66  chr2_209473987_209480409     5028  5931 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209473987_   5028 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5077
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209473987_   5078 GGCCACACTGCCCAAGGTAATTTACAGATTGAATGCCATCCCCATCAAGC 5127
                            v i   v     iv i  i        v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209473987_   5128 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGCTCA 5175
                          vi  iivi i  i  ii     -   -- v  i  - iii    ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_209473987_   5176 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5225
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_209473987_   5226 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5275
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_209473987_   5276 TACAGTCACCAAAACAACATGGTACTGGTACCAAAACAGAGATATAGATC 5325
                               v i   i   iii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_209473987_   5326 TGTGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5373
                         vi     i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_209473987_   5374 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5423
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_209473987_   5424 CTATTTAATAAATGGTGCTGGGAAAACTGGCTATCCATATGTAGAAAGCT 5473
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_209473987_   5474 GAAACTGGATCCCTTCCTTACACCTTATACAAAAAGTAATTCAAGATGGA 5523
                            ii    i    v   i     v          v   i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_209473987_   5524 TTAAAGACTTACATGTTAGACCTAAAACTATAAAAACCGTAGAAGAAAAC 5573
                          i ?    i  v    v   v              vi v           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_209473987_   5574 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5622
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_209473987_   5623 AAACACCAAAAGCAATGGCAACAAAAGCCAAAAGTGACAAATGGGATCTA 5672
                         vi            vvi          vv    vv  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_209473987_   5673 ATTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5721
                           i   -     i -   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_209473987_   5722 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5771
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_209473987_   5772 AAAGGGCTAATATCCAGAATCTGCAATGAACTC--A-AACACATTTACAA 5818
                           i  i  vi          v ii  v      -- -   v  v v i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_209473987_   5819 GAAAA-AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACG 5867
                         i  i -   i     v  i?    i     i     iv    i     iv
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_209473987_   5868 TCACAAAAGAAGACGTTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5917
                           v v        ii vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_209473987_   5918 CCATCAATGGCCAT 5931
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


3182 27.54 0.88 0.44  chr2_209490371_209496774     5009  5912 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209490371_   5009 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5058
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209490371_   5059 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCGCCATCGAGC 5108
                            v     v     iv i  i  i        i  v   v i   i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209490371_   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_209490371_   5157 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5206
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_209490371_   5207 AACAAAGCTGGAGGCATCATGCTACCTGACTTCCAATTATGCTACAAGGC 5256
                                i      vv   ii  v  ii i   v  viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_209490371_   5257 TACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5306
                               v i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_209490371_   5307 AATGGAACAGAAC--AGAGCCCTCAGAAATAACTCTACATATCTACAGCT 5354
                                i    i--    i  --        vi i i i  i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_209490371_   5355 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5404
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_209490371_   5405 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5454
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_209490371_   5455 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5504
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_209490371_   5505 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5554
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_209490371_   5555 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5604
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_209490371_   5605 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5654
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_209490371_   5655 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5704
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_209490371_   5705 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5754
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_209490371_   5755 AGGGCTAATATCCAGAATCTGCAATGAACTC--A-AACACATTTACAAGG 5801
                         i  i  vi          v ii  v      -- -   v  v v i  ii
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_209490371_   5802 AAA-AAGCAGCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5850
                          i -  ii i   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_209490371_   5851 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAGAAAATGCTCATC 5900
                           v        i  vi viii     v ii       i  i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_209490371_   5901 ATCACTGGCCAT 5912
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3216 28.30 0.00 0.00  chr2_209501352_209507626     4876  5783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209501352_   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209501352_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209501352_   4976 TACCAATGACTTTCTTCACAGAACTGGAAAAAACTACTTTAAAGTTCATA 5025
                          v   iivi i  i  ii     v v  v  iviv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_209501352_   5026 TGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAGAA 5075
                              viiv  ii  v  v v  v     ii     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_209501352_   5076 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5125
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_209501352_   5126 CAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGATCAA 5175
                             v i   i    ii         i iv ii i   v i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_209501352_   5176 TGGAACAGAACAGAGGCCTCAGAAATAACGCCACATATCTACAACTATCT 5225
                              i    iv   ivii         vv   i i  i  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_209501352_   5226 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 5275
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_209501352_   5276 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5325
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_209501352_   5326 CTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAA 5375
                         i    i    v   i     v           i  i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_209501352_   5376 AGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5425
                             i    i  v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_209501352_   5426 GCATTACCATTCAGGACATAGGCATAGGGAAGGACTTCATGTCCAAAACA 5475
                          ?i v viv   iv   v v  vv    v  v ii   v ivvi vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_209501352_   5476 CCAAAAGCAATGGCAACAAAAGCCAAAAGTGACAAATGGGATCTAATTAA 5525
                                  vvi          vv    vv  i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_209501352_   5526 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 5575
                          v v  i i   i  ii vv    i  v    i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_209501352_   5576 AACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAGTG 5625
                             i   i             v  ii   vii ivi      i  i vi
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_209501352_   5626 CTAATATGCAGAATCTACAATGAACTCAAACAAATTTACAGGAAAAAAAC 5675
                           vi   v      v  i  v      vv    v iv i iv     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_209501352_   5676 AAACAACCCCATCAAAAAGTGAGCGAAGGATATGAACAGACACTTCTCAA 5725
                            i     v  i?    i  i  i      v    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_209501352_   5726 AAGAAGACATTTATGCAGCCAATAAACACATGAAAAAATGCTCATCATCA 5775
                                i  vi viii        i          i       v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_209501352_   5776 CTGGCCAT 5783
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.43 (149 / 104)
Gap_init rate = 0.00 (0 / 908), avg. gap size = 0.00 (0 / 0)  


3126 26.92 1.56 0.56  chr2_209524686_209527703     1628  2526 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209524686_   1628 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1677
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209524686_   1678 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1727
                            v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209524686_   1728 TACCAATGACTTCCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 1775
                          v   iivi i ii  ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_209524686_   1776 TATGGAACCAAAAAAGAGCCCGTATTGCCAAGTCAATCCTAAGCCAAAAG 1825
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_209524686_   1826 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1875
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_209524686_   1876 TACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1925
                               v i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_209524686_   1926 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 1973
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_209524686_   1974 ATCTGATGTTTGACAAACCTGACAAAAACAAGCAAATGGGGAAAGGATTC 2023
                          vi    v  i     ivv  v   i v  vv   -         i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAG 395

  chr2_209524686_   2024 CCTTTTTAATAAATGGTGCTGGGAAAATTGGCTATCCATATGTAGAAAGC 2073
                         i     i  i              v  i   v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_209524686_   2074 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGG 2123
                             ii    i    v   i     v              i    ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_209524686_   2124 ATTAAAGACTTACATGTTAGATCTAAAAC---------CCTAGAAGAAAA 2164
                           i ?    i  v    v   v       --------- i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_209524686_   2165 CCTAGGCATTACCATTGAGGAGATAGGCATGGGCAAGGACTTCATGTCTA 2214
                          v    ?i v viv  viv  vv v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_209524686_   2215 AAACACCAAAAGCAATGGCAACAACAGCCAAAATTGACAAATGGGATCTA 2264
                         vi            vvi       v  vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_209524686_   2265 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 2314
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_209524686_   2315 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 2364
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_209524686_   2365 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACACATTTACAAGAAA 2414
                          i  i  vi          v  i  v      vv   vv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_209524686_   2415 AAG-CAAACAACCCCAACAAAAAGTGGGCAAAGGATATGAACAGACACTT 2463
                            -    i     v vi?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_209524686_   2464 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 2513
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_209524686_   2514 CATCACTGGCCAT 2526
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.38 (19 / 8)  


2603 28.65 1.77 1.66  chr2_209540104_209546522.rev     5024  5927 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_209540104_   5024 AAAAACATTCCATGCTCATGGACAGGAAGAATCAATACTGTTAAAGTTGC 5073
                            i i  i     i       iv      v i    i      ii v  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_209540104_   5074 CATACTGCCTAAAGCAATTTAGAGATTCAATGTTATTCCTATCAAACTAC 5123
                         v     v  i   vii  i  v        i iv  i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_209540104_   5124 CAATGACATTCTTCACAGAACTAGAAAAAAAATCT-ATTTAAAAATATAT 5172
                           iivi v  i  ii     v v  v  i----  -  iiv     vi  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATTCAT 149

  chr2_209540104_   5173 ATGGAATCATAAAGGAGCTCAAATAGCTAAGGCAATCCTAACTAAGCAAA 5222
                               viii  i   v ivi      i  ii     i i --  --  i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AA--AAG 195

  chr2_209540104_   5223 AAGAATAAAGCTGGAGGCATCATGTTACCCAACTTCTAACTACACTACAG 5272
                              i    i      vv   iii v     i   v  vivi      i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_209540104_   5273 -GCTACAGTAACCAAAACAGCATGATATGGGTACAAAAACAGACCCACAG 5321
                         -          i   i    ii  i  iv  i i  ii i    vi i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_209540104_   5322 ACCAATGTAACAAAATACAGCACCCAAAAATAATGCCACACACCTACAAC 5371
                          i     v  i i   vv  vii   i      vv   i   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_209540104_   5372 TGTCTGATCTTTGACAAAGTCAACAAAAACAAGCAATAGAGAAATAATTC 5421
                         iivi    i  i     i viiv   i v  vv    i i    v   vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_209540104_   5422 CCTATTCAATAAATGGTGTTGGAATAATTGGCTAGCCATATGCAGAAGAT 5471
                         i  v     i        i   i i  i   v  ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_209540104_   5472 TGAAACTGGATCTCTTCTTTACATCATCTACAAAAATCAACTCAAGATGG 5521
                             ii    i i  v i i   i   v         i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_209540104_   5522 ATTAAATACTTAAATATACAATCTAAAACTATAAAAAGTCTGGAAGATAA 5571
                           i ? v  i     i  vi v              vvii i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_209540104_   5572 CCTAAG---AAATACCATTATGGAGATAGGAATGGGCAAAGATACCCATG 5618
                          v  i ---    -- v ii  - vv v  iv i     v i vi i- i
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--CTTCGTG-ACCTTGGGTTAGGCAATGGTTTCT-TA 591

  chr2_209540104_   5619 AAGATG---CCAAAAGC-CATTTCAACATA-GCAAAAATTGACAAGTGGT 5663
                         i v   ---        -  vv-     v - v      v  i  i v v
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_209540104_   5664 ACCTAAT-----TTAATGGAGCTTCTGCAAAGCAAAAGAAACTATCAATA 5708
                           i v  -----    --i i   i  iivvv    i  v        v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAA--AAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_209540104_   5709 GAGTAAACAGGCAACCTACAGAAGGGGAGAATGTATTTCCAGGT-ATGCA 5757
                         i   i  v  i     i      v       vi     v  ii -  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_209540104_   5758 TCTGACAAAGTTCTAATATCCAGAATCTATACAGAACTTAAACAAATTTA 5807
                              i  i vv  vi          v    v      ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_209540104_   5808 CAAGAAAAAAACAAATAACCTCATTAAAAATTGGACAAAGGACATGAACA 5857
                         i  v     i          iv   ?    v   i       iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_209540104_   5858 TACCCTTTTCAAAGGAAGACATACACATAGCCAACAAACATATGAAAAAA 5907
                         v  vi  i  v  i     i     v  i     i  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_209540104_   5908 TGTTTAACGTCACTTATCAT 5927
                           i i   i   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (159 / 97)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 1.94 (31 / 16)  


3102 25.40 1.07 4.48  chr2_209566794_209569130.rev      918  1854 (483)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_209566794_    918 AAAGCTATCCCACGTTCATGGATGGGAATAATTAATATTGTTAAAATGTC 967
                             v       i          v    v v             i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_209566794_    968 CATACTACTGAAAGCAATCTACAGATTTAATGTAATCCCTATCAAAATAC 1017
                         v     v iv   vii           i  i i               v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_209566794_   1018 CAATGACATTCTATATGGAAACTGAAAAAAC-ATCCTGAAATTTATATGG 1066
                           iivi v  i v iii    i   v  ivi-     i     i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_209566794_   1067 AACCACAGAATACCTCAAATAGCTAAGGCAATCTTGAGCAAAATGAACAA 1116
                           vii  iiiv   ivi      i  ii         iv  i v      
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_209566794_   1117 AACTGGATGCATCATATTGCCTAACCTCAAAATCTACTACAAAGCTATAA 1166
                          ii    v vv   i i v  i  ii      ii             i i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_209566794_   1167 TAACCAAAACAGCATGGTACTGTCATAAAAACAGACACGTAGGCCAATGG 1216
                            i   i    ii        v     ii i     ii   ii      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_209566794_   1217 AAGAGAATGGAGAGCCCAGAATTAAATGCATGTATCCA----CAGCTGAT 1262
                           v     v     i      v    iv   ii  ii ----  ii    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_209566794_   1263 TTTTGACAAAAGTGCCCAGAACAAACACTGGGGAAAGGACAGTCTCTCCA 1312
                            i     ii     v   v  vv  v         i i     i i  
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_209566794_   1313 ATAAATGGTGCTGAAAAAATTGGATATCCATGAGCAGAAAAATAAAACTA 1362
                          i           ii v  i      ?   iiv   i  i   i  ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_209566794_   1363 CATCCATATCTCTAACCAAATTCAGAAATCAACTCAAAATGGATTAAAGC 1412
                         v i  v  i   vv    v  v  i    i              i ?  v
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_209566794_   1413 CTTAAATGTAAGAACCAAGGCTATGAAACTACTAGAAGAAAACATAGGTA 1462
                          i           i i  ii    i     vi                ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_209566794_   1463 -AAATGCCTCATCACATTGGTCTAGTCAATGATTATTTTAGATAAGATTT 1511
                         -    - i  i v  v    vi   v     i  - i       v  ivi
  L1M4_orf2#LINE/    554 TAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAGATATGACAC 601

  chr2_209566794_   1512 CAAAAACACAGGCAACAAAAGCAAAAATAGACAAAGGAGATTACATCAAA 1561
                              i    i          v         i   vvi  i v       
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_209566794_   1562 CTAAAAAGCTTCTTTACAGCAGAAGAAACAATTGAG----TGAAGAGACA 1607
                         v v    i   i v i vv  i i  v  v  ii  ----    i     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_209566794_   1608 ACCTACAGAAAAAGAGAAAATGTTTACAAACAATAAATGTGACAATAAGT 1657
                            i      vii        i   i    iv   v  v   i  viiii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_209566794_   1658 TAATATTCAGAATGTCCAAGAAACTCAAACATCTAAATGGCAAAGAAGCA 1707
                          vi   i      i vi  ii     vv   v  v   iii   i ii  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_209566794_   1708 AACAGTCCAAATTAAAAATGGGCAAAAAACATTAAGAGACAGTCCAAATT 1757
                           i ii    v ?             ii ------------- iii   -
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGA-------------TTTGAAT- 837

  chr2_209566794_   1758 AAAAATGGGCAAAAAACATTCAGAGACATTTCTCAAAAGAAGACATATGA 1807
                         -----------------------           v        i   ii 
  L1M4_orf2#LINE/    838 -----------------------AGACATTTCTCCAAAGAAGATATACAA 864

  chr2_209566794_   1808 GTACCAAACAGGTACATTGAAAAATGTTCAGAAGCATCAATCACCAA 1854
                         i iv v  i i i    vi   i   i   i---     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAA---CATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (157 / 77)
Gap_init rate = 0.01 (9 / 905), avg. gap size = 5.78 (52 / 9)  


3133 27.28 0.66 0.77  chr2_209584405_209590059     4255  5163 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209584405_   4255 TGGAAGAACATTCCATGCTCATGGCTAGGAAGAATCAATATCATGAAAAT 4304
                              ii i  i     i      v v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209584405_   4305 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4354
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209584405_   4355 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4402
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_209584405_   4403 TAGGGAACCAAAGAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 4452
                           v    viiv iii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_209584405_   4453 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4502
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_209584405_   4503 TACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4552
                               v i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_209584405_   4553 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 4600
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_209584405_   4601 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGTTTCT 4650
                          vi    i  i     ivv  vv  i v  vv            iv vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_209584405_   4651 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4700
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_209584405_   4701 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4750
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_209584405_   4751 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4800
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_209584405_   4801 GTAGGCAGTA--CCATTGAGGAGATAGGCATGGGCAAGGACTTCATGTCT 4848
                         i    ?-   --i v i v ivvv i  i- i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr2_209584405_   4849 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCT 4898
                          vi            vvi          vv     v  i    v i ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_209584405_   4899 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 4948
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_209584405_   4949 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 4998
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_209584405_   4999 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAAGAAATTTACAAGAA 5048
                           i  i  vi          v  i  v      vv v  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_209584405_   5049 TAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5098
                         v  i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_209584405_   5099 TCTCAAAAGAAGACATTTATGCAGCTAAAAAAACACATGAAAAAATGCTC 5148
                             v        i  vi viii  i  v  i-          i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTC 893

  chr2_209584405_   5149 ATCATCACTGGCCAT 5163
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


3063 26.95 1.78 0.67  chr2_209598208_209603482     3886  4783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209598208_   3886 TGGAAATACATCCCATGCTCATGGATGAGTAGAATCAATATTGTGAAAAT 3935
                               v i        i        vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209598208_   3936 GGCTGTACTGCCCAAGGCAATCTACAAATTTAATGCAATTCCCATCAAAG 3985
                            vi    v     ivii       i   i  i     i  i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209598208_   3986 T----ACTGCCATCATCTTTCACAGAGCTAGAAAAAACAATTGAAAAATT 4031
                          ----i     ---- i   ii    iv v  v  ivii  ivv      
  L1M4_orf2#LINE/    101 TCCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_209598208_   4032 TATATGGAATCAAAAAAGAGCCTGCACAGCCAAAGTGAGACTAAGCAGAA 4081
                         i        viiv  ii  v  v v i       iii vvi i iv ii 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_209598208_   4082 AGAACAAATCGGGGAGGCATCACATTACCTGATGTCAAACTATACCATAA 4131
                                 viv  ii i -     i v  ii  v     viv   i i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_209598208_   4132 GGCTATAGTCACCAAAACAGCATTGTATTGGTATAAAAATAGACACATAG 4181
                         i    i   v i   i    ii v   i   i    ii       i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_209598208_   4182 ACCAATGAAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTATAGC 4231
                          i     i  i     v    ii           v   v i i    i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_209598208_   4232 CAACTGATCTTTGACAAAGCAAAGAAAAGCATAAAGTGGGGAAAGGACAT 4281
                            i    i  i     i vvivv  i v   vv i         i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_209598208_   4282 CCTACTCAACAAATGGTGCTGGGATAATTGTCAAGCCACATGCAGAGGAA 4331
                         i  vi                   i  i  vvv ?         i i   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_209598208_   4332 TGAAATTGGATCCTCATCTCTCACTTTATACAAAAATCAATTCAAGATCG 4381
                             i     i  ii i   v   iv           i  i    i  v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_209598208_   4382 ATCAATGACTTAAATCTAAGACCTGAAACCATAAAAATTATAGAAGATAA 4431
                             ?v   i     v     v  i    i      v iv       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_209598208_   4432 CATTGGAA-AAACCCTCTTAAACATTGGAATAGGCAAAGACTTCATGACC 4480
                            v  ?i-   i i  v i v -    iv       v ii   v iivi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_209598208_   4481 AAGAACCTAAAAGCAAATGCAATAAAAACAAAGAGAAATAGATGGGACTT 4530
                          v  vv i       v v    i    iv   i v i   i  v      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_209598208_   4531 AATTAAACTAAAAAGCTTCTGCATAGCAAAAGAAATAATCCGCAGAGTAA 4580
                         v  i   v v    i   i  iiivv    i  v iv   viv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_209598208_   4581 ACAGACAACCTACAGAGTGGGAGAAAATCTTTGCAAACTGTGCATCCAAA 4630
                          v        i     i           v        iii ii   ii v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_209598208_   4631 AAAGGACTAATGTTCAGAATGTA--AATAAGTTTTA-------GCAAGAA 4671
                           i     vi i i      i  --  v  v i   -------ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_209598208_   4672 AAAAACAAATAATCCCATC-AAAATTGGGCTAAGGATATGAATAGACAGT 4720
                            i        i  v  i-    v     v      v          v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_209598208_   4721 TCTCAAAAGAAGATACACAAATGGCCCATAAACATATGAAAA-ATGCTCA 4769
                             v          i          v    i  i       -       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_209598208_   4770 TCATCACTAACTAA 4783
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.44 (22 / 9)  


2909 26.19 2.00 1.22  chr2_209611710_209616590.rev     3489  4389 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209611710_   3489 TGAAAAAATATTCCATACTCATGGATTGAAAGAATCAATATTGTTAAAAT 3538
                           i   i    i    ii          i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209611710_   3539 GACCATACTGTCAAAAACAAACTATAGATTCAAAACTATTCCTATCAAAC 3588
                          i v     vi v   vii v   i        vi v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209611710_   3589 TGCCAA-TGTCATTTTTTCACAGAACTAGAAAAAACTG-TTGTGAAATTA 3636
                          v   i-  i --     ii     v v  v  i-   - iv i     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr2_209611710_   3637 ATATGAAGGTAAAACGAGAGCCTGAGTTGCCAAAAGAATCCTAAACAAAA 3686
                              i ii iv  - i  v  v  i v       v    i i  v  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_209611710_   3687 AGGACAAAGCCAGTGATATCACATTACCTGACTTCAAGCTATACTACAAT 3736
                           i      iii v ivv     i v  ii i     iviv        v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_209611710_   3737 GTTACAGTAACCAAAACAGCATGGTACTGGTATAAA-ACAGAAACATAGA 3785
                          i        i   i    ii         i    i- i   v i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_209611710_   3786 CCAATGGAACAGAATAGAGAACCCAAAAATAAAACTACACACCTACAGCC 3835
                         i        i     v    ii   i       v i i   ii  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_209611710_   3836 ATCTGATCTTTGACAAGGTTGACAAAAATAAGTAATGCAGAAAGGACTCC 3885
                          vi    i  i       v  v   i vi vvi    vi     i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_209611710_   3886 CTATTCAATAA-TGGTGCTGGGATAGCTGGCTAGCCATATTTGGAAGAAT 3934
                           v     i  -           i i    v  ?   i  viii      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_209611710_   3935 GAAAGTATACCCATACCTTTCACCATATACAAAAATTAACTCAAGATGAA 3984
                            iv iv    v     iv                        i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_209611710_   3985 TTAAAGATTTAAATGTAGGACTTCAAATGGTAAGAATCCTAGAAGAAAGC 4034
                          i ?   ii        i  vi v   ivi   i v  i         i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_209611710_   4035 A-GGAAATACCATTCTGGACATCAGCCTTGGG--AAATAACTGGTGACT- 4080
                          -i i?i  -- v   v-- i v -       -- iii  -    vv  -
  L1M4_orf2#LINE/    547 ATAGGNGTA--AATCTT--CGTGA-CCTTGGGTTAGGCAA-TGGTTTCTT 590

  chr2_209611710_   4081 AAAT----CCTCGAAAGCACTTGCAACAAAAACGAAAACTGACCAGTGGG 4126
                          i  ---- vi i       vv         ivi    iv  iv i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_209611710_   4127 AACTAAATGAGCTAAAGAACTTCTGTACAGCAAGAGAAACTATCAACAAA 4176
                          vi v vii iv v  i     i   i vv   ii  v        v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_209611710_   4177 GTTAAACAGACAACCTACAGAATGGGAGAAAATATTTACAAACTATGCAT 4226
                           v   -        i                     i    ii  ii  
  L1M4_orf2#LINE/    691 GTGAAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_209611710_   4227 CTAACAAGGT-CTAATATCCAGAATCTACAAGGAACTT---CAA-TCAAC 4271
                           i i    v-  vi          v  i  i     i---   -    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_209611710_   4272 AAGCAAAAAACAATTAACCACATT-AAAAATGGGCAAAAGATATGAACAG 4320
                           vv    i    v     vv   -             i   v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_209611710_   4321 ACTCTTCTGAAAAGAAGACATACCAGCAGCCAACAATCAAACGAAAAACT 4370
                           vi    vv        i    v iii     i  v  v i     iv 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_209611710_   4371 ACTCAACATCACTGATTAT 4389
                         i          ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (144 / 89)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.45 (29 / 20)  


2813 26.23 3.28 1.29  chr2_209649453_209655067     3912  4765 (850)    L1M4_orf2#LINE/L1        1   871 (37)  

  chr2_209649453_   3912 TGGAAAAACATTCCTTGCTCATGAGTAGGAAGAATCAATATAGTTAAAAT 3961
                               i i  i  v  i     ii v      v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209649453_   3962 GGCCATACTGCCCAAAGCAATTTATAGACTCAGTGCTATTCCTGTTAAAT 4011
                            v     v      vii  i  i   i   ii  v  i   i i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209649453_   4012 TACTAATGAGATTCTTCACAGAAATAGATAACACT-ATTTTAAAATTCAT 4060
                          v i iivivv  i  ii       v  i  -i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr2_209649453_   4061 ATGGAAACAAAAAAAACGCCTGAACAGCCAAGGCAATTCTAAGCAAAAAG 4110
                                iiv  iii  -  v   i      ii    ii i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_209649453_   4111 AACAAATCTGGAGGCATCAAGCTACTCAGCTTCAAA-CTAATATGGCAGG 4159
                               vi      vv   vi  v i  ii      -  --  ivi  ii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT--TACTACAAA 246

  chr2_209649453_   4160 GCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACTGACACATAGA 4209
                                   i   i    ii         i i  ii iv    i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_209649453_   4210 CCAATGGGACAGAATAGAGAGCCCAGAAATAAGACTGGATACCTACAACT 4259
                         i      i i     v     i          iv iiv i ii  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_209649453_   4260 ATCTGATCTTCAACAAAGTTGACAAAAACAAGCAATGGGGAAAGGACTTC 4309
                          vi    i   i    i v  v   i v  vv            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_209649453_   4310 CTATTCAATAAATGATGCTGGGATAACTGTCTAGCCATACGCAGAAGATT 4359
                           v     i     i        i     vv  ?   i i   i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_209649453_   4360 TAAACTGGTCCTTTTCCTTATACCACATATACAAATCAACTCGAGACGGA 4409
                         v  ii   v  ii v   i i    i   i v    i     i i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_209649453_   4410 TTAAAGA---AAATGTAAAACCCAAAACTGTAAAATCCCTAGAAGACAAC 4456
                          i ?   ---        i v i      i     ii i       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_209649453_   4457 GTAGG--TAATACCATTCAGGACATGGGAATGGACAAAGATTTC------ 4498
                         i    --   - i -   iv   v v  iv i i   v i    ------
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_209649453_   4499 ATGATA--AAAATGCAGCAATTGCAACAGAAGCAAAAATAGACAAATGGG 4546
                             i --    -   -   --      i   v         i    v  
  L1M4_orf2#LINE/    595 ATGACACCAAAA-GCA-CAA--GCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_209649453_   4547 ACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACA-- 4594
                           i v  i   v v  i i   i  ii vv    i  v        v --
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_209649453_   4595 --GAATAAACAACCTACAGGATGGGAGAAAATTTTTGCACACTATGCATC 4642
                         --   v i      i    i            v      v ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_209649453_   4643 GGATAAAGGTCAAATATTCAGCATCTATAAGGAACT--TA-AAC-CAATT 4688
                         v     i  v vvi   i   v  v     i     --  -   -    v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_209649453_   4689 -TAAAACAGAAAAACAACTCCATGAAAAAGTGAGCAAAGGATATGAACAG 4737
                         -     -   v   i   i v  v?    i  i         v    i  
  L1M4_orf2#LINE/    791 ATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_209649453_   4738 ACACTTCTCAAAAGAGAACATA----TGGCCA 4765
                            i     v     ii i   ----      
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.99 (147 / 74)
Gap_init rate = 0.02 (21 / 871), avg. gap size = 1.86 (39 / 21)  

 263 16.07 1.79 0.00  chr2_209649453_209655067     5069  5124 (491)    L1M4_orf2#LINE/L1      852   908 (0)  

  chr2_209649453_   5069 AGAAGACATATATGTGGCCAACAAGCATATGAACAAA-GCTCAACATCGC 5117
                               i   i vi       i     i     v i -          i?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_209649453_   5118 TGATCAT 5124
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1)  


3300 26.84 0.22 0.33  chr2_209685049_209687164      716  1624 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209685049_    716 TGGAAAAACATTCCATGTTCATGGGTAGAAAGAATCAATATTGTGAAAAT 765
                               i i  i            i v i    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209685049_    766 GGCAATACTGCCCAAAGTAATTTATAGATTCCATGCTATCCCCATCAAGC 815
                                  v      v i  i  i      v i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209685049_    816 TACCATTGACTTTCTTCACAGAAGTAGAAAAAAACT-ACTTTAAATTTCA 864
                          v   vivi i  i  ii     i v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_209685049_    865 TACGGAACCAAAAAAGAGCCCGTATAGTCAACAAACTCCTAAGCAAAAAG 914
                           i    viiv  ii  v  v v    i   v v v  i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_209685049_    915 AGCAAAGCTGGAGGCATCACACTACCTGACTTCAAGCTATGCTACAAGGC 964
                          i     i      vv       v  ii i     iviv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_209685049_    965 TACAATGACCAAAACAGGATGGTACTGGTACCAAAACAGATATATAGACC 1014
                             i i i   i    vi         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_209685049_   1015 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAGTCAT 1064
                                i    iv   ivii         vv   i    i  ii    v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_209685049_   1065 CTGATCTTTGACACACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 1114
                         i    i  i    vivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_209685049_   1115 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAGACTGA 1164
                         v  i  i              v      v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_209685049_   1165 AACTGGACCCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGATT 1214
                          ii         v   i    iv                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_209685049_   1215 AAAGACTTAAACATAAGACTTAAAACCATAAAAACCCTAGAAGAAAACAT 1264
                          ?    i    ii     vi      i      vi i             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_209685049_   1265 GGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 1313
                         i  ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_209685049_   1314 ACACCGAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTAAT 1363
                              i      vvi     i    vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_209685049_   1364 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGCGTGAACA 1413
                         i   v v  i i   i  ii vv    i  v       vv iv     v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_209685049_   1414 GGCTATGTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 1463
                          i v ivi                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_209685049_   1464 GGGCTAATATCCAGAATCTATAAAGAACTTAAACAAATGTAAAAGAAAAA 1513
                           i  vi          v           ivv    v vv v  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_209685049_   1514 AAGAAACAACCCCATCAAAAAGTGGGCAAAGGATATGACCAGACACTTCT 1563
                         i v   i     v  i?    i            v   vi     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_209685049_   1564 CAAAAGAACACATTTATGTGGCCAACAAACATATGAAAAACAGCTCATCA 1613
                          v      v i  vi vi       i  i  i       ivv     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_209685049_   1614 TCACTGGTCAT 1624
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.31 (136 / 104)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.25 (5 / 4)  


2878 27.46 2.01 0.67  chr2_209710915_209716290     3990  4885 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209710915_   3990 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4039
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209710915_   4040 GACGATACTGCTCAAAGTAACTTATAGATTCAATGCTATCCCAATCAAGC 4089
                          i i     v i    v i ii  i        i  v     v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209710915_   4090 TACCA-CTGACTTTCTTCACAGAATTAGAAAAACT-ACTTTAAACTTCAT 4137
                          v   -   v    i  -i     v v  v  i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_209710915_   4138 ATGGAACCAAAAAAGAGCCTGCACAGCCAAGACAATCT-GGTCTAGAAGA 4186
                               viiv  ii  v  v v i      i       - ivvv      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_209710915_   4187 ACAAAGCTGGAGGCATCACGCTACCTGACTTTAAACTATACTACAAGGCT 4236
                               i      vv    i  v  ii i  i   viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_209710915_   4237 ACAGAAACTGAAACAGCATGTCACTGGTACCGAGACAGATATATGGACTA 4286
                             v  iii i    ii  vi     i ivii  i   i    i  ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_209710915_   4287 ATGGAACAGAACGGAGGCCTCAGAAATAACACCACACAGTGGCTACAA-C 4335
                               i    iv   ivii         vv   i   v ---  iii- 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT---TATGGTC 346

  chr2_209710915_   4336 AATCTGATCTTTGACAAACCTGACACACACAAGCAATAGGGAAAAGATTC 4385
                            -    i  i     ivv  v  vivv  vv    i      ii  vv
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_209710915_   4386 CCTATTTAATAAATTGTATTGGGAAAACTGGCTAGACAAATGCAGCAAAC 4435
                         i  v  i  i    v  ii     v      v  ?v  v     iv i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_209710915_   4436 TGAAATTGGACCCCTTCCTTACACCCTTTACAAAAATCAACTCAAGATGG 4485
                             i          v   i     v v         i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_209710915_   4486 ATCAAACACTTAAATGTAAGACCTAGGACCATAAAAATCCTAGAATAAAA 4535
                             ? v  i           v   ii  i      v  i     v    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_209710915_   4536 CCTGGGCA-ATACCATTCAGGACATAGCCATGGGCAAAGACTTCATGACT 4584
                          v i  ?i- v i -   iv   v v vvv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_209710915_   4585 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGACCT 4634
                          vi            vvi          vv     v  i    v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_209710915_   4635 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGTCATCAGAGTGA 4684
                         v  i   v v  i i   i  ii vv    i  v   i   vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_209710915_   4685 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 4734
                          v  i     i                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_209710915_   4735 AAAGGGCTAATATCCAGAATCTACAAAAAAAATTTACAAG--------AA 4776
                           i  i  vi          v  i   i  vvi      v--------  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_209710915_   4777 AAAAA-----AACTGCATCAAAAAATTGGCAAAGGATATGAACAGACTCT 4821
                            i -----   ivv  i?      v          v    i    vi 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_209710915_   4822 TCTCAAAAACAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTCA 4871
                             v   iv   i  vi viii     i ii  i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_209710915_   4872 TCATCCCTGGTCAT 4885
                         v    v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (136 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.18 (24 / 11)  


2649 26.26 2.91 1.45  chr2_209742676_209746667     2617  3511 (481)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209742676_   2617 TGGAAATACATCCCATACTCATGGATTGGAAAATTCAATATTATGAAAAT 2666
                               v i       ii             i i i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209742676_   2667 AGTCATACTGCCCAAAGTAATTTACAGATTCAATGCAGTTCCTATCAAAA 2716
                         i iv     v      v i  i           i   i i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209742676_   2717 TACCAATATCATTTTTCACAGAATTAGAAAAA--AATCCTAAAATTCATA 2764
                          v   iivv v     ii     v v  v  i--i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_209742676_   2765 AGGATCCAAAAAAGAGCCTGACTAGCTAAAGCAATTCTAACCAAAAAAGA 2814
                         v   vviiv  ii  v  v  v    i   i    ii i v-   i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chr2_209742676_   2815 ACAGACCTGGAGACATCACATTACATAACTTCAAATTATATTATAATTAA 2864
                            i vi     ivv     i v vi  i      viv  i  i  -- i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA--AG 247

  chr2_209742676_   2865 ATA-AGTAACCAAAACAGCATGGTCCTGGGAGAAAAATAGATACATAGAC 2913
                         v  -     i   i    ii    v    v v  ii     i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_209742676_   2914 CACTGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATATTTACAACCA 2963
                           v     i     v    ii           v   v i     iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_209742676_   2964 ACTGATCTTTGACAAAGCATACAAAAAATATTT--TGG--AAAGGAC-GC 3008
                          i    i  i     i -i i v  i vi   i--   --    i i- i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_209742676_   3009 CTTATTCAATAAATGGTGCTGGGTAAAC--AATAGCCACATGTAGGAGAG 3056
                            -     i             vv   --i   ?       i ii   i
  L1M4_orf2#LINE/    397 CTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_209742676_   3057 TGAAACTG-ATCTCT--CTCTTATCATATACACAAAAATCAACTCCAGAT 3103
                             ii  - i i  --   vi i        --     i     v i  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACA--AAAATTAACTCAAAAT 493

  chr2_209742676_   3104 AGATTAAAGACTTAAATTTGA-AGCCATAA--ATAA---TCT-AGATAAA 3146
                         i   i ?    i     v i -   i v  --    ---   -   vi  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_209742676_   3147 AACTCAGGAAAAACTCTTATGGACATTGGCCTAGGCAAAGAATTTATGAC 3196
                            vi   ?iv  v    vvv   v    vi       v iv  iv iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_209742676_   3197 TAAGACTCCAAAAGCAAATGCAAAGAAAACAAAAATAAATAAATGGGACC 3246
                           v   v         v v    vi   iv       i      v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_209742676_   3247 CAATTAAACTAAAATGCTTCTGCATAGCAAAAAAAAA-ATCATTAGAGTA 3295
                         iv  i   v v   vi   i  iiivv    ii v v-    vv i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_209742676_   3296 AACAAACAACCCACAGAATGAAAGAAAATATTTGTAAACTATGCATCTGA 3345
                           v i               ii            i   ii  ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_209742676_   3346 AGAAGGACTAATATCCAGAGTCTACAAGAAACTCAAACAAATCAGCAAGA 3395
                         vi i     vi        i v  i  ii     vv    v   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_209742676_   3396 AAAAAA-AAATCATCCCATC-AAAAGTGAGCAAA---TTCCAGAAATAGA 3440
                             i -    v i  v  i-    i  i     ---  i---i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT---GAATAGA 840

  chr2_209742676_   3441 GACTTCTCAAAAGAAGATATAAAAATGTCCAGTAAACATATGAACAAATG 3490
                         v i     v            v     v   i   i  i     v i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_209742676_   3491 CTAATCAATATTGCTCATTAC 3511
                           ---   i  ii????????
  L1M4_orf2#LINE/    891 CT---CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (144 / 88)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.70 (39 / 23)  


2553 27.93 1.69 0.24  chr2_209793526_209795349      506  1332 (492)    L1M4_orf2#LINE/L1       70   908 (0)  

  chr2_209793526_    506 ATCTAAAAGTTCAATGCAATTCCCATCCAAATACCACCATCACTCTTCAC 555
                              v ii     i     i  i   v    v   v vv vi i  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chr2_209793526_    556 AGAACTAGGAAAAGC-AATCCTAAAATTCGGATGGAACCAAAAAAGAGCC 604
                             v -v  v    -i            iv      viiv  ii  v  
  L1M4_orf2#LINE/    120 AGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chr2_209793526_    605 TGCATATTCAAAGCAAGACTAAGCAAAAAAGAACAAATCTGGAGACATCA 654
                         v v   vi    i   vvi i i-   i         vi     ivv   
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAA-AAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_209793526_    655 CATTACCTGACTTCAAACTATACTATAAGGCAATAGTCACCAAAAAAGCA 704
                           i v  ii i      viv     i  i  v i   v i   i v  ii
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_209793526_    705 TGGTACTGGTATCAAAATAGGCATATAGACCAATGGAACAGAATAGAGAA 754
                                  i  v ii    i        i        i     v    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_209793526_    755 CCCGGAAATGAAGTCAAATACTTACAGCCAGCCGATCTTTGACAAGGCAA 804
                         i  i     i  vi  v i i   ii i  iii   i  i       vvi
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_209793526_    805 ACAAAAACATAAAGTCGGGAAAGGACACCCTATTTAACAAATGGAGCTGG 854
                         v   i v   vv i v       i i vi  v  i         v     
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_209793526_    855 GATGACTGGCAAGCCATATGTAGAAGAATGAAACTGGATCCTCATCTCTC 904
                           ii     vv ?   i   i i         ii    i  ii i   v 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_209793526_    905 ACCTTACA------TCAACTCAACATGGATCAAGGACTGAAATCTAAAAC 948
                            v  i ------ i       v        ?i   iv    v   i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_209793526_    949 CTGCAACCATAAAAATTCTAGAAGATAACATTGGAAAAACCCTTCTAGAC 998
                           iv   i      v ii       v     v  ?iv  vi    vv   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_209793526_    999 ATTCGCTTAGGCAAAGACTTCATGACCAAGAACCCAAACGCAAATACAAC 1048
                         v  v v        v ii   v iivi v  vv     v   v vi    
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_209793526_   1049 AAAAACAAAGATAAATAAATGGGACTTAATTAAACTATAAAGCTACTGCA 1098
                             iv   i   i      v      v  i   v vv   i  vi  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_209793526_   1099 CAGCAAAAGAAACAATCAGCAGAGTAAACAGACAACCCACAAAGTGGGAA 1148
                          vv    i  v  v    iv i   i  v            i i     i
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_209793526_   1149 AAAATCTTCACAATCTATACATTTGACAATAAACTAATATCCAGAATCTA 1198
                              v  ii   vii   i  i   i  vii   vi          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_209793526_   1199 CAAAAAACTCAAACAAATCAGCAAGAAAAAAA-----AATCCCATCAAAA 1243
                         i   i     vv    v   ii  v     i -----  i  v  i?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_209793526_   1244 AGTGGGCTAAGGACATGAATAAACAATTATCAAAAGAAGATATACAAATG 1293
                          i     v     iv      i   v  v  v                  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_209793526_   1294 GCCAACAA--ACATGAAAAAATGCTCAACGTCACTAATGAT 1332
                              i  --         i         i   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (129 / 98)
Gap_init rate = 0.01 (6 / 839), avg. gap size = 2.67 (16 / 6)  


3191 24.10 3.14 1.35  chr2_209797444_209799579      753  1644 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209797444_    753 TGCAAAGGTATTCTGTGTTCATAGATTGGAAGAATCAATATAGTTAAAAT 802
                           v    i   i ii       i          v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209797444_    803 GTTTATACTATCCAAAGCAATCTACAGATTCAGTGTAATTCCTATAAAAA 852
                          viv     vi     vii             ii i   i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209797444_    853 TGCCAATGACAATCTTCACAGAAATAGATT-TTTAATTATAAAATTTACA 901
                          v   iivi vv i  ii       v  iv-vi i  iv       i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_209797444_    902 TGGAA----------CCCAGAATAGCCAAAGATATCCCAAGCAAAAAGAA 941
                              ----------               ivv   iii iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_209797444_    942 CAAAACTGGAGGAATCACATT----AACTTTCATCAAATTATACTACAGA 987
                             ii       v     i ----  -     --   i -       i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAA-TTTCA--AAACT-TACTACAAA 246

  chr2_209797444_    988 GCTATATTAACCAAAACAGCATAGTACCAGCAGAAAAACAGACACATAGA 1037
                             i v   i   i    ii i    ii   v  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_209797444_   1038 CCAGTGGAACAGAACAGATAACATATAACCCAGAAATAAATCCATACATC 1087
                         i  i     i    iv  v ii-------           i        i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGT-------CCAGAAATAAACCCATACATT 339

  chr2_209797444_   1088 TACAGTGAATTCATTTTCAACAAAGGTGCCAAGAATATACATTGGAGAAA 1137
                           ii  v    v      i    i          vi  v  v   i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_209797444_   1138 GGACAACTTATTCAATAAATGGTGCTGGGA-AACTGAATATCCATATGCA 1186
                          i i iii v     i              -     i   ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_209797444_   1187 GAAGAATGAAACTAGAACCCTATCTCTAACCATATAGAAAAGTCAAATCA 1236
                         i         ii i  v     i   vv        v    i i  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_209797444_   1237 AAATGGGT-ATCGAC--AAATCTCATTCTTCAAACTG-AAATCTCC-AAA 1281
                               i - ?v   --    v v vvvi v     i-   v   i- i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_209797444_   1282 AGAAAACATTAGGGAAACTCTCCAGGACATTGGACTGGACAAAGATTTCT 1331
                                  vi ? v  v   i iv   v    ii i i   v i     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_209797444_   1332 T-----TG-C-CCACAAGCATAGGCAACCAAAGCCAAAATGGACAAATGG 1374
                          -----  - -   v     i i     v    vv     i  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_209797444_   1375 GATCACATCAAGTTTAAAAGCTTCTGCACAGAAAAGGAAACAATCCATAA 1424
                           iiv      iv      i   i  ii vvv      v  v   v v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_209797444_   1425 AGTGAAGAGACAACTCATAGAATAGGAAAAAATATTTGCAAACTATCCAT 1474
                               i       i  i     i   i              ii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_209797444_   1475 TTGACAAGGGATTAATAAGCAGAATATATAAGGGAATGAAACAATTCTAT 1524
                         i   i      i vi  vv            i i v vvv    i  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_209797444_   1525 AAGAAAAATATCTAATAATCCAATTTAAAAATTGACAAAAAACCTGAAGA 1574
                           v     v - v     i      ?      v i    ii ii    v 
  L1M4_orf2#LINE/    790 AATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_209797444_   1575 GACATTTATCAAAAGAAGACATACAAGTGGCAAACAGGTATATGAAAAGG 1624
                                v  v        i      i    v  i i i i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_209797444_   1625 TGCTCAACATCATTGATCAT 1644
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (131 / 80)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.50 (40 / 16)  


3060 25.61 2.78 1.78  chr2_209816412_209824536      493  1390 (6735)  C L1M4_orf2#LINE/L1   (0)   908     2  

C chr2_209816412_   1390 GAAAAGATATCT-ATGTTCATGGGTTGGAACAATTAATATTGTCAAAATA 1342
                          i         i-          i      v v          i  i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

C chr2_209816412_   1341 TCCATACTACCTAAAGCAATCAGCAGATTCAATGCAATGCCTATCAAAAT 1292
                         v v     v  i   vii   vi         i     v           
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

C chr2_209816412_   1291 TCCAATGACATTTC--ACAGAAACAGAAAAAAAAATCC-AAAATTTGTAT 1245
                         i   iivi v   i--i      iv  v  ivvi    -      ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

C chr2_209816412_   1244 GGAGCCACAAAAGACGCAGAATAGC-AATACAAATCTTGAGCAGAAACAA 1196
                            ivii   ii   v         -  v    -      iv ii  v  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAA 200

C chr2_209816412_   1195 CAAAGCTAAAGGCATCACACTACTTATTTTGAAAATCAACTAGAAAGCTA 1146
                              i ii   vv       v ii v   v    iiv    v       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chr2_209816412_   1145 TAGTAACCAAAACAGCATGATACAGACATAGAAACAGACACATAGACAAA 1096
                         i     i   i    ii  i   v i    iii i     i     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

C chr2_209816412_   1095 TAGGACACTATAGAGAGGCCAGAAATAAATCCACACATTTATAGCCCATT 1046
                          i i i vv  v     v           i   i        i i v   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

C chr2_209816412_   1045 GATTTTTGACAAAGATGCCAAGAATACAAAATGGAAAAAGGATAGTCTCT 996
                               i     i i        vi ivv     ii    i       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

C chr2_209816412_    995 TTAATAAATGGTTTGGGGGAAAATGGAATATTCAC-TGTAGAGGAAAGAT 947
                          i  i       viv   iv  v    -  ?i   -  i i i   v  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGA-TAKCCACATGCAAAAGAATGAA 449

C chr2_209816412_    946 ATTAGACCCTCATCTTATACCACATATAAAAATAAACTAAAAAAGTATTA 897
                         i  i     ii i  i i    i   i      v    v    v v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chr2_209816412_    896 AAGACCTGAA-------------AC-ATGAAACTATTAGAAGAGAAAAAG 861
                         ?      i  -------------  -  i     v        i  v --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-- 547

C chr2_209816412_    860 TAGTAGAGAAAAAGCTCTATGACGTTGGTCTGAGCAATGATTTTTTGAAT 811
                         ---   i?iv   v  iii    v    vi ii      i   i  ii  
  L1M4_orf2#LINE/    548 ---TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

C chr2_209816412_    810 ATAACCCCAGAAGCACAGGCAACAAAAGCAAAAACAAGTAAGTAGGATTA 761
                           i  v   i       i          v     i ii   i v   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

C chr2_209816412_    760 TATCAAA-CTAAAAATTTTCTGCACAGCAAAAAAATAATAATAATAACAG 712
                         i      -i      i   -  ii vv    ii ----i v  vi  v i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTT-TGTGCTTCAAAGGA----CACTATCAAGAA 689

C chr2_209816412_    711 AATGAAGAGACAACTTACAGAATAAGAAAAGAAATATTTTTTGAAGCACA 662
                          i    i       ii       ii  i  --       vi-i  v  i 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAA--AATATTTGC-AAATCATA 736

C chr2_209816412_    661 CATCTGGTAAGGGTTTAATATTCAAAATATACCAGGAACTCATATAATTT 612
                         i     i      vi vi   i  i      iv i      v  i  i i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

C chr2_209816412_    611 AACAGCAAAGAAACAA----TCTGATTTTAAAAATGGGTAAAGGACCTGA 566
                           i ii   i i    ----i ii   ?-         i      ii   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGA 835

C chr2_209816412_    565 ACAGACATTTTTCAGAAGAAAATATACAAATGACCAACAGGCATATGAAA 516
                          i        i  vi     i           i    i i   i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

C chr2_209816412_    515 AAATGCTCAACATCACTCATCAT 493
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.32 (158 / 68)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 2.41 (41 / 17)  

3256 26.65 0.55 0.55  chr2_209816412_209824536     6726  7633 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209816412_   6726 TGGAAGAACATTCCATGCTCATGGCTAGGAAGAATCAATATCGTGAAAAT 6775
                              ii i  i     i      v v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209816412_   6776 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 6825
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209816412_   6826 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 6872
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_209816412_   6873 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAACCCTAAGCCAAAA 6922
                                 viiv  ii  v  v v  v     ii   i i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_209816412_   6923 GAACAAAGCTGGAGGCATCACACTACGTGACTTCAAACTATACTACAAGG 6972
                                 i      vv       v vii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_209816412_   6973 CTACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 7022
                                v i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_209816412_   7023 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCACATCTACAAC 7070
                                 i    i--    i  --        vv iii    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_209816412_   7071 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAGTGGGGAAAGGATTC 7120
                         i vi    i  i     ivv  vv  i v  vv  i         i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_209816412_   7121 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 7170
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_209816412_   7171 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 7220
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_209816412_   7221 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 7270
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_209816412_   7271 CCTAGGCATCACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 7320
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_209816412_   7321 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 7370
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_209816412_   7371 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 7420
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_209816412_   7421 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 7470
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_209816412_   7471 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACACATTTACAAGAAA 7520
                          i  i  vi          v  i  v      vv   vv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_209816412_   7521 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 7570
                           i     i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_209816412_   7571 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGTTCAT 7620
                            v        i  vi viii     v  i          i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_209816412_   7621 CATCACTGGCCAT 7633
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3251 25.30 0.76 1.74  chr2_209853367_209859031     4257  5173 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209853367_   4257 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4306
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209853367_   4307 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4356
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209853367_   4357 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTC 4403
                          v   i-       i  -i     -   -- v     - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_209853367_   4404 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 4453
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_209853367_   4454 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 4503
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_209853367_   4504 CTACAGTAACCAAAACAGCATGGTACTGGTAGCAAAACAGAGATATAGAT 4553
                                  i   i    ii         i vv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_209853367_   4554 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAAC 4601
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_209853367_   4602 TATCCACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGG 4651
                         i ---------  -    i  i     ivv  vv  i v  vv       
  L1M4_orf2#LINE/    346 CA---------AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_209853367_   4652 GAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATA 4701
                              i  vvi  v  i  i              v      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_209853367_   4702 TATAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAA 4751
                          ii i  iiv    ii    i    v   i     v           i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_209853367_   4752 TTCAAGATGGATTAAAGACTTAAACGTTAGATCTAAAACCATAAAAACCC 4801
                         i    i      i ?    i    i  v   v       i      vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_209853367_   4802 TAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGA 4850
                                    v    ?i- v i -   iv   v v  vv i     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_209853367_   4851 CTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACA 4900
                         i   v ivv  vi            vvi           v     v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_209853367_   4901 AATGGGATCTAATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACC 4950
                            v   ii v  i   v v  i i   i   i vv    i  v    i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_209853367_   4951 ATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTA 5000
                          vv i      v  i     i   i             v  ii   vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_209853367_   5001 CTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACACA 5050
                         ivi      i  i  i  vi          v  i  v      vv   vv
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_209853367_   5051 TTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAA-GGACATG 5099
                          iv i  v     i     i     v  i?    i       -   iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_209853367_   5100 AACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAA 5149
                           i     i     v        i  vi viii     v ii        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_209853367_   5150 AAAATGCTCATCATCACTGGCCAT 5173
                           i       v     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (136 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


3627 20.19 7.51 0.94  chr2_209885717_209889954     2895  3746 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209885717_   2895 TAAAAGGACACCTCATGTTCATGGGATGGAGGACTTAATCTTGTTAAAAT 2944
                          ii  i  i i i           iv    i        v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209885717_   2945 ATCAATACTAGCCCCCCAAA--AACCTACAAATTCAATGCAATTCCTATG 2992
                         iv       ----       --i i     i      i     i     v
  L1M4_orf2#LINE/     51 GGCAATACT----CCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_209885717_   2993 AAAATCCCAATGATGTTTTTCACAGAAAT-AAAAAATCCATCCTTAAATT 3041
                                  iiviiv     ii       -i v  iiiv     v     
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_209885717_   3042 TATATGTAA-TCTGAAAGATCTATGAATAGCCAAAACAACCATGAAAAAA 3090
                         i     v  - vii ii  i i -               i v       i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_209885717_   3091 GAAAGAGCAAATTTGGAGAACCCACACTTCCTGATTTCAAAACTTACTAC 3140
                         --    i    v      i  i         ii                 
  L1M4_orf2#LINE/    196 --AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_209885717_   3141 AAGGCTCCAGTAATCAAAACAATGTAGTACTGGCATCAAGACAGATATAC 3190
                           i   v          i   i   i          v i  i   i   i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_209885717_   3191 AGAACACTGGAATATAATAATGAGCCCAGAAATAAACCCTTGTATATATT 3240
                            v  v       v   viv   i              v ii  v   v
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_209885717_   3241 GCCAA--GA---------AGAGTGTCAAGACCTTTCAATGAGAAAAGGAC 3279
                          i   --  ---------  i   i       v       i i    i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_209885717_   3280 AGTCT--------GATGGTGCTGGGAAAACTGGATATCTACATGCAAAAA 3321
                              --------i            v         ? i          i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_209885717_   3322 AATGAAGGTGGATGTTTACCTAACACCATATACAAAATTTAACTTAAAAT 3371
                                v    ivii     v               v      i     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_209885717_   3372 GAATTATAGACTTAAATCTAAGAATGAAAACTATAAAACACTCAGAAAGA 3421
                          i  i ?    i     v     iiv             v  i    ii 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_209885717_   3422 AACACAGGGCAAAAGTTATATGACATTGGATTCAGCAATGATTTCTTCAA 3471
                             i   ?vv   vi vii    v    i  vi      i      vi 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_209885717_   3472 TATGACACTAAAGGCACAGGCAACAGAAGAAAAAATAAGACAAATTGGAC 3521
                                 i   i     i      i           -  i         
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGAC 642

  chr2_209885717_   3522 TTTGTGAAAATTAAAGACTTTTATGCATCAAAGGGCATTATCAATAGAGT 3571
                           ii v         i      i   v       i  i      v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_209885717_   3572 GAAAAGGCAACTGAAAGAATGGGATCAACTATTTGCAAATCATATATATG 3621
                               i    iv v         vv  v                  v  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_209885717_   3622 ACAAGGAATTAATAGCC-GTATATATAAAGAACTTCTAAAACTCAGTGAC 3670
                          i    i i vi  v  - v              ii  v      i i i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_209885717_   3671 AACAA---AAGCCACCTGAT----------GCAAA--------------- 3692
                           v  ---  iiv   ii  ----------     ---------------
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_209885717_   3693 ------------AGATATACACATGCCCAATAAGTACATGTAAAGGTGAT 3730
                         ------------         v   v        i     v    i  v 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_209885717_   3731 TAACATCACTAATCAT 3746
                         i       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (111 / 58)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 5.14 (72 / 14)  


2235 27.32 5.39 1.63  chr2_209905643_209910357     3426  4223 (492)    L1M4_orf2#LINE/L1       81   908 (0)  

  chr2_209905643_   3426 CATTGCAATTCCGATAAAAA-CACAACCATCATTCTTCACTGAACTAGAA 3474
                           vi     i  v  v    - v  i iii -  i  ii v   v v  v
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGAC 129

  chr2_209905643_   3475 AAAACAATGTAAAAACAACCTAAAATCCATATGAAACCAAAAAGAGCCCA 3524
                           ivii  ----------        i      i  viiv  i ii    
  L1M4_orf2#LINE/    130 AAGCTGAT----------CCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_209905643_   3525 CA-TAGGCAAAGCAAGACTAAGCAAAAAGAACAAATCTGGAGGCATTATG 3573
                         v -   v    i   vvi i iv  i         vi      vv i ii
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_209905643_   3574 TTACCCATCTTCAAACTATACTATAAGGCCATAGTCACCAAAATAACATG 3623
                         i v    vi      viv     i  i  i i   v i   i i iii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_209905643_   3624 GGACTGGTATAAAAACAGGCACATAGACCAATGGATCAGAATAGAGAATC 3673
                          v     i    ii i  i  i     i       vi     v    i  
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_209905643_   3674 CAGAAATATAGCCAAATACTTACAGCCAACTGATCTTCAGCAAAGCAAAC 3723
                                 v v   v i i   ii i   i    i   ii   i vviv 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_209905643_   3724 AAAAACATAAAGTGGGGAAAGGACACCCTATTCAACAAATGGAGCTGGGA 3773
                           i v   vv i         i i vi  v            v       
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_209905643_   3774 TAATTGGCAAGCTACATGTAGAAGAATGAAACTGGATTCTCATCTCTCAC 3823
                         i  i   vv ? i     i i         ii    ii ii i   v   
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_209905643_   3824 CTTAAACAAAAATCAACCTAAGATGGATCAGAGACATAAAT--------- 3864
                          v  v        i   ii  i        ?    v     ---------
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_209905643_   3865 --------------------------CATTGGAGAAACCCTTCTAGACAC 3888
                         --------------------------   v  ? v  vi    vv   vi
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_209905643_   3889 TGTCTTAGGCAATA-CTTCAT-GACAAGA-ACCCAAAGAAAACACAACAA 3935
                           vv         i-i   v -  i v  -   v    v v vi      
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_209905643_   3936 AAACAAAGATAAATAGATGGGACCTAATTAAACAAT--AAAGCTTCTGCA 3983
                           iv   i   i   i  v    i v  i   --  --   i   i  ii
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAA--ATTAAAAACTTTTGTG 667

  chr2_209905643_   3984 CAGCAAAAGAAATAATCAGCAGAGTAAACAGACAACCCACAGAGTGGGAG 4033
                          vv    i  v iv    iv i   i  v              i      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_209905643_   4034 AAAATCTTTGCAAGCTATACATCTGACAAAGGATTAATATCCAGAATCTA 4083
                              v       iii   i      i  i   i vi          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_209905643_   4084 CAACAAACTCAAACAAATCACCAAGAAAAAC-CAATTAATCCCATCAAAA 4132
                         i  vi     vv    v   vi  v     v-   v   i  v  i?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_209905643_   4133 AGTGGGCTAAGGACATGAACAGGCAATTCTCAGAAGAACATATACAAATG 4182
                          i     v     iv    i  i  v     vi     v           
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_209905643_   4183 GCCAACAAACATATAAAAATATGCTCAGTATCACTAATTAT 4223
                              i  i  i  i    v       ii    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (128 / 86)
Gap_init rate = 0.01 (11 / 828), avg. gap size = 5.09 (56 / 11)  


3161 27.01 0.66 0.55  chr2_209933776_209937473     2300  3206 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209933776_   2300 TGGAGAAAGATTCCATGCTCATGGATAGGAAGAATCAATATCCTGAAAAT 2349
                             i i v  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209933776_   2350 GACCATACAGCCCAAAGTAATTCATAGATTAAATGCTATCCCCATCAAGC 2399
                          i v    vv      v i  ii i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209933776_   2400 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAACTTCAT 2448
                          v   iivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_209933776_   2449 ATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAAGA 2498
                               viiv  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_209933776_   2499 ACAAAGCTGGAGGCATCAGGCTACTTGACTTCAAACTATATACTACAAAG 2548
                               i      vv   vi  v iii i      -- iv          
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAG 247

  chr2_209933776_   2549 CTACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 2598
                                  iv  i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_209933776_   2599 CAAAGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACCACCA 2648
                            v    i    iv   ivii         vv   i    i  ivii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_209933776_   2649 CCTGATCTTTGACAAACCTGTCAAAAACAAGAAATGGGGAAAGGATTCCC 2698
                         vi    i  i     ivv  i   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_209933776_   2699 TATTTAATAAATGTTGTTGAGAAAACTGGCTAGCCATATGCAGAAAACTG 2748
                          v  i  i     v  i  i  v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_209933776_   2749 AAACTGGACCCTTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 2798
                           ii       i v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_209933776_   2799 TAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAATC 2848
                         i ?    i           v       i      vi i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_209933776_   2849 TAGGCA-ATACCATTCA-GAACATAAGTATGGGCAAAGACTTTATGACTA 2896
                             ?i- v i -   i-  v v ii  - i     v ii  iv iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr2_209933776_   2897 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2946
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_209933776_   2947 ATTAAACTAAAGGGCTTCTGCACAGCAAAAGAACCTATCATCAGAGTGAA 2996
                           i   v v  iii   i  ii vv    i  vv      vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_209933776_   2997 TGGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACA 3046
                         vi i     i                 v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_209933776_   3047 AAGGGCTAATATCCAGAGTCTACAAGGAACTTAAACAAATTTACAAGAAA 3096
                          i  i  vi        i v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_209933776_   3097 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 3146
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_209933776_   3147 CCCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA- 3195
                          i v        i  vi viii     v ii          i       -
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_209933776_   3196 --TCACTGGTCAT 3206
                         --   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2955 26.42 2.13 0.59  chr2_209938200_209942765     3223  4066 (500)    L1M4_orf2#LINE/L1        1   857 (51)  

  chr2_209938200_   3223 TGAAAGAATATCT-ATGTTCATGGATTGTAAAATTTCATATTGTTATAAT 3271
                           i  ii     i-              v  i i  v         vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209938200_   3272 GTTCATACTACCAAAAGCAATCGACATATTCAGTACAATCCCTAATAAAA 3321
                          viv     v  v   vii   v   v     iii         vi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209938200_   3322 TTCCAATGGATTTTTTTAAAGAAATAGATAATTCTATCCAAAAATTCATA 3371
                          i   iiv vi      iv      v  i  viiv    v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_209938200_   3372 TGGAACCAGGAAAAACTCCAAATAACCAAAGCAATCTTGAGAAGGTAGAA 3421
                              viivi iii  i vi    i     i         i  i v    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_209938200_   3422 CAAAGCTGGAGATTTCACATTTCCTGATTTCAAAATAT-TTGTAGAGCTA 3470
                              i     ivi     i    ii         iv -i ii i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_209938200_   3471 CA--AATTAAG-CAGTATGATA-TGGCATAAAAATGGACAAACACACAAA 3516
                           --   i   -    i  i  -        ii  i    v i v iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_209938200_   3517 TGGAATAAAAAAGAGAGTCGAGAAATAAATCAACAAACATACAGCCAACT 3566
                                i  vv       v         i v i v iv  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_209938200_   3567 GATTTTCACCAAGAATTTCAAAA--ATGCAATGGGGAAAGGATAATCTCT 3614
                                iv    ii vi   i --  v            i   i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_209938200_   3615 TTAACACATGGTGTTGGATCA-CAGGACATCCATGTGCACAAGAATAAAA 3663
                          i    v      i   iv  - v   i ?   ii    v      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_209938200_   3664 TTGGATTCATATTTTACAAAATACACAAAAATCAACTCCAAATAGATGAA 3713
                              ii v  ii i   vv   i        i     v    i   v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_209938200_   3714 ACATTTAA---TAATACCCGAAACTATAAAACTCCTAGGATAAGA---AA 3757
                          v ii   ---   v v ii              i   i v  i --- i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_209938200_   3758 GGAAAAAGTTTCATGACATTGGTCTTGGCAATGATTTTTTTTTTAATATG 3807
                          ?iv   vi   i    v    vi v       i   i  v---i     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA---GATATG 597

  chr2_209938200_   3808 ACACAGAAAGCACAAGCAACACAAGCAAAATTAGACAAATGGTACTAGAT 3857
                             vi               v   v    v    i    v v   vv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_209938200_   3858 -AAAACCAGAAAGCTTCTGCACAGCAAAAGAAA--ATTAACAGTATGAAA 3904
                         -    ii i   -   i  ii vv    i  v --  i  v ivi     
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_209938200_   3905 AGGCAACCTAAATACTGGGGGAAAATATTTGCAAACCACATATCTGAGAA 3954
                           i     i v v v    i               i  i        v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_209938200_   3955 AATGTTAATGTTTAAAATGTATAGGGAACTTCTACAACTCAGTAACAAAA 4004
                         iivii vi i ii i   i    ii     ii         i   i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_209938200_   4005 ACACAAATAACTTGATTACAACATGGGCACAAAACTTGAATAAAACATTT 4054
                          v         iii   ?v  v       v ii i       i -     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA-CATTT 845

  chr2_209938200_   4055 CTCTAAAGAAGA 4066
                            i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGA 857

Transitions / transversions = 1.81 (141 / 78)
Gap_init rate = 0.02 (14 / 857), avg. gap size = 1.64 (23 / 14)  


3197 26.90 0.66 0.55  chr2_209951165_209957512     4950  5856 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_209951165_   4950 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4999
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_209951165_   5000 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5049
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_209951165_   5050 TACCAACGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTTCA 5097
                          v   i vi i  i  ii  -      -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_209951165_   5098 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACGATCCTAAGCCAAAAG 5147
                                viiv  ii  v  viv  v     i  i   i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_209951165_   5148 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATACTACAAGGC 5197
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_209951165_   5198 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5247
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_209951165_   5248 AATGGAACAGA-T--AGAGCCCCGGGAAATAATACCACACATCTACAACC 5294
                                i   - --    i  --i       vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_209951165_   5295 ACCTGATCTTTGACAAACCTGACAAAAACAACAAATGGGGACAGGATTCC 5344
                          vi    i  i     ivv  v   i v  viv        v  i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_209951165_   5345 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACAGGTAGAAAGCT 5394
                           v  i  i              v      v  ?     v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_209951165_   5395 GAAACTGGATCCCTTCCTTACACCTTATACAGAAATTAACTCAAGATTGA 5444
                            ii    i    v   i     v      i            i  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_209951165_   5445 TTAAAGACTTAAATGTTAAACCTGAAACCATAAAAACTGTAGAAGAAAAC 5494
                          i ?    i       v i v  i    i      viiv           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_209951165_   5495 CTAGGCA-ATACCATTCAGGACATGGGCATGGGCAAGGACTTCATGACTA 5543
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_209951165_   5544 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAAGTGATCTA 5593
                         vi            vvi          vv     v  i   vvv  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_209951165_   5594 ATTAAACTACAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5643
                           i   v vv i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_209951165_   5644 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5693
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_209951165_   5694 AAGGGCTAACATCCAGAATCTACAAAGAATTTAAACAAATTTACAAGAAA 5743
                          i  i  vii         v  i      i ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_209951165_   5744 AAATCAAACAACCCCATCAAAAATTGGGCAAAGAATATGAACAGACACTT 5793
                           iv    i     v  i?    v         i  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_209951165_   5794 CTCAAAAGAAGACATTTATGCAGCCAATAGACACATGAAAAAATGCTCAT 5843
                            v        i  vi viii       ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_209951165_   5844 CATCACTGGCCAT 5856
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


4172 17.38 4.06 1.58  chr2_210099582_210102197     1239  2124 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_210099582_   1239 TGGAAAGACACCATGTGTTTATGGATTAGAAGATTTAAT--TGTTAAAAT 1286
                                 i i vii    i       i     i     --      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_210099582_   1287 AGCAATGC-CCCCAAACCGATCTATAGATTCAATGCAATCTTTATCAAAG 1335
                         i     i -       ii      i        i      ii       i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_210099582_   1336 TTGCAACTTCCTTTTTGTGTTATTGTCACAGAAATTGACTAGCTGATCCT 1385
                          iv  i  v       -------  ---           v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-------TG---CAGAAATTGACAAGCTGATCCT 140

  chr2_210099582_   1386 AGAATTCATATGGAAATGCAAGGAACTTAAAGTGGCCAGAATAGCCTAGA 1435
                          i                     i  ii i i i    i  i ii  v  
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_210099582_   1436 AAAAGAA---CAAAGTTGGAGGACTCACACTTCCTAATTCTAAAAGTTGC 1482
                                ---                        i    ii    v  i 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_210099582_   1483 TCCAAAATTACAGTAATTAAAACAGTGTGCTGCTCCTATAAAAATAGACA 1532
                          v    ii         i  i        v i  vvi    ii       
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_210099582_   1533 CATAGCTCAATGGAATAGAAATGAGAGTCCAGAAATAAACCCTCACAGTT 1582
                         i    v              v                     vi   v  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_210099582_   1583 TTGGTCAACTGATTTTAAA-GAGTATGCCATGACAAATCAATAGGGGAAA 1631
                         v       i       vi -i  vi     v   v v     -       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAA 389

  chr2_210099582_   1632 GAGTCGTCTT--CAACAAATGTTGGTGGGACAACTGGTTATCCACATGCA 1679
                           i v     --         v  v            v  ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_210099582_   1680 AAAGA-TGAAGTTGGACTCGTATCTCATATCTTATA--AAAAGTAACTCA 1726
                              -           i v  i    i i v    --    v       
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_210099582_   1727 AAACGGACCAAGCACCTAAATGTA----C--AAACTATAAAACTCCTAGA 1770
                            i   i  ?iv           ---- --              i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_210099582_   1771 AGAAAA-A-AGGTATACATCTTCATGACCTTAAATTAAGCAATATTATTT 1818
                               - -   ?i  v      i       iii   i     iv v i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_210099582_   1819 TAGAAATAACATCAAAAGTACAAGCAATCAAAGAAAAAAATGAATTAATT 1868
                             v  i   i      i        -    ii       ii  v    
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAA-CAAAAGAAAAAATAGATAAATT 638

  chr2_210099582_   1869 GGACTTTATAAAAATTGAAAACTTTTGT--TATAACGGAGAGAATCAAGA 1916
                               i  v      i           -- vi  v   v vv       
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_210099582_   1917 AAGTGAAAAAGGGAATTCATAGAATCAGAGAAAATATTTGCAAATCATAT 1966
                                  - iv  ii  i     vi                       
  L1M4_orf2#LINE/    689 AAGTGAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_210099582_   1967 GTCTGATAAAGGATTAGTATCCAAAATGTGTAAAGAAC-------ACT-A 2008
                         i        i   i v       i   i i        -------   - 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_210099582_   2009 ACGATAAAACTATAGATAATCTAATTTTTTAAATAGGCAAAGGAT----- 2053
                          ii      vv i i    i i    ?vv-    i          -----
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAA 836

  chr2_210099582_   2054 -AGACAATTTTTCACATAAAATATATAAGTGGCCAATAAGCACATGAAGA 2102
                         -     v  i i  v v  i     i  i                   i 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_210099582_   2103 CATGCTCAACATTATTAGTCAT 2124
                         v           i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (100 / 50)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.38 (50 / 21)  


2965 25.94 1.71 1.48  chr2_210105073_210109258     1122  2000 (2186)    L1M4_orf2#LINE/L1       28   908 (0)  

  chr2_210105073_   1122 GGAAGGCTCAATATTGTCAATATCTCAGTTCTTCTCAACTTGATATGTAA 1171
                              i  i        i  v  vv  i v  i i   v     v ii i
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chr2_210105073_   1172 ATTAAATGCAATCTCAATCAAAATCTCAGCAAGTTACTTTGTGGATATCT 1221
                            v  i      i v         i    vivi vi    ii  v  iv
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chr2_210105073_   1222 ACAAACTTATCCTACAGTG-ATATGGAAA----AGAGAACCAGAATGTCC 1266
                             i  v      v i v-         ----  i  v       iv  
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_210105073_   1267 AACACAATGTGTAAGTAGAAGAACAA-GTTAGAGGACTGACACTATCCAA 1315
                           v     v vv  iv          -   i       v     vi    
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_210105073_   1316 TATTAATATTTACTATAAAACTATAGTAATGAAGACAGTGCAGTACTGGC 1365
                          v i  v i      i   i   i      v         ii        
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr2_210105073_   1366 AAAAACAAACAAACCAAAACAGACAAATAGACCAATAGAACAGAATAGAA 1415
                          v  i------------i i     v     i    i   i     v  i
  L1M4_orf2#LINE/    278 ATAAG------------GATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_210105073_   1416 AATGCAGAAATAGACCTGCACAAATATAGTAAATTGATCTTTGACAAAGA 1465
                          i v        i   iii   vv   i  v       i  i     i i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_210105073_   1466 AAGAAAGGCAATACAATGGAGAGAAGATAATTTTTTCAACAAATGATGCT 1515
                         vivv   i v  v      i  i ii   i i             i    
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_210105073_   1516 TAAACAATTGGACATGTGAAAGCAAAAAAATGAATCTAGATGCTAATCTT 1565
                         vii    i    i ?viiv v      i      vi i  iv iv i  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chr2_210105073_   1566 ACCTCTTCCACAAAAATTAACTCAAAATTAATTATAGGCCTAAATGTAAA 1615
                           vi v vi                   vi  i ?  i           i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_210105073_   1616 ACACAAAGCAATTAAACT-TTAATAGATAACATAAGAGAAAATCCTTGTG 1664
                          vvi   i v  v     -   iv   v      i ? v     i i   
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_210105073_   1665 ACCTTGTACTTGGTAATGAGTTTTTAGATACAAAACTAAAAG-ACAATCT 1713
                               vii v  i    iv  i       ii v  i     -    v v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_210105073_   1714 ATGAAAAACAAATTA-ATAAATTGGACTTCATTAAGATTAAAAAGCTCTT 1762
                          ii   i v   v  -                i  i        -  i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTT 664

  chr2_210105073_   1763 CT-CTGTGAATATCACTATTAAGAAGATGAAAAGGTAAGCCACAGATTTG 1811
                         v -  vii  viv      i     ii       ii  v       v v 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_210105073_   1812 GAGAAAACATTTGTGAAACACATATTCGATAAAGGACTTGAATACAAAAT 1861
                                i     ii  v  i    ii     i       v  v  i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_210105073_   1862 ATA-AAGAAACTCTTGAAACTCAACAATAAGAAAATATGTAAT----TTA 1906
                            -  ii       iv       i     i  i i vi   i----  ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_210105073_   1907 AAAAATGGGTAAAATATTTGAATAACTACTATACCAAGGAACATATACAG 1956
                                  i   iv         ivi i viv    i   v       i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_210105073_   1957 GCAGCAAATAAGCATATAAGGTGATGCTCAAAATTATATGTTAC 2000
                         iii  v        i  i iiv         v  i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.01 (11 / 881), avg. gap size = 2.55 (28 / 11)  

1982 26.67 10.91 1.82  chr2_210105073_210109258     2889  3713 (473)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr2_210105073_   2889 TATACCATGTTCATTGATTGGAAGACTCAATATTTTTAAGACAGCAATTC 2938
                            v          v            i      v      ii     v 
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr2_210105073_   2939 TGCCAAAATTGATCTACAGACCTGAGAAAATTCCAAAGAAAA-CATAA-- 2985
                          v  v               iiii viv   i  v vv    - vi i--
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_210105073_   2986 ----TTTTTACTTAAATTGACAAGTTGACATCAATATTTGTATGGAAATG 3031
                         ----     i vv           i   ivii  v   ii          
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr2_210105073_   3032 CAAAAGACT-ACAAGAGCCAAAAGAAATTTGTAAAAGAAGAATAAGATTG 3080
                            ii   i- v  v        v  vi   v          i  ii   
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr2_210105073_   3081 TATTACTTGCCATGTCTGATTATAAGATTTACCATAAAGCTAGAGTAATC 3130
                         v vv   ii vv vi ii   vi  i i    i i       v       
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr2_210105073_   3131 AAAATAATGTGAAATTGTCATAAGAAT------------CAATGACATGG 3168
                           i i i    iv i  v      i  ------------     iv  i 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_210105073_   3169 CA----GAGTTCAGGAACAGACCTATATATATATGACCAATTGATTTCTG 3214
                         v ----    i   i  i i   i   i  v    ii          ii 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_210105073_   3215 ACAAAGATGTTATGGTCATTCAATGAAGAAAGGATGGTCTTTTCACAAAA 3264
                             i i  ii v ii         ii     i  i         vv   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_210105073_   3265 TAATTCTGGAACAACTG-ATATCTATACGGAAAAAAATAATCAGT--AA- 3310
                          ii v    i       -   ? i i i v    i   i --   --i -
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA--AGTTGGAC 456

  chr2_210105073_   3311 ---TACCTTATATCATATCTA----CTAATTTGAAATAGATCATAGA--- 3350
                         ---     i i i     vi ----i   i ii    i     ?   ---
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_210105073_   3351 -AAT--------TAAAACTATCAAATTTCTAGAAGAGAACAGAAAA--AA 3389
                         -   --------         v   i ii       i    v ii?--  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_210105073_   3390 A-----GTAGCTCTGGAGTAAATGAAAGATTTCTTAGATATGACCAAAAA 3434
                          -----  ii ii   iv  iii-  v i               - vv  
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTAGATATGAC-ACCAA 604

  chr2_210105073_   3435 AAACACAAAGCATAAAAAGAAAATTTGATTGAGGAAATAGGGCTTTATCA 3484
                           i     ivv i    ii    v v   -----    v  i   i    
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGAT-----AAATTGGACTTCATCA 649

  chr2_210105073_   3485 AAATTAAAGGAGTTCGCACTTCCAAAAGATGACATTTAGAAAATGAAATG 3534
                                 iivv  i ii    -   i  iivi  iv     i     v 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTC-AAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_210105073_   3535 -CAAACAAAAAATTGGAGGAAAATATTATCAAA--ATATATTC------- 3574
                         -   v v v i v   ii         vv    --      ii-------
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_210105073_   3575 --CTT---------ATATAT------TCCTTGTA------TATTGGAA-G 3600
                         --   ---------      ------ii   ii ------  v ii  - 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_210105073_   3601 ATACACAACCCAATT-AAAAATTAGCAAAATATTAGAACAGACACTTCAC 3649
                          i v i         -      vi     iv   v   i     i   v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_210105073_   3650 AACACAAAATCTGATGCAAGAATAACCAACAAGAACACAGAGACATATT- 3698
                         v v v  i  ---  i   --  ii    i   v   iii i v  ii -
  L1M4_orf2#LINE/    849 CAAAGAAGAT---ATACAA--ATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_210105073_   3699 GGCATCATTGGTCAT 3713
                         ii     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (144 / 73)
Gap_init rate = 0.03 (29 / 900), avg. gap size = 3.62 (105 / 29)  


2952 26.97 2.11 1.33  chr2_210177728_210184424     5305  6205 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_210177728_   5305 TGGAAAAACATTCCATGCTGATGGATAGGAAGAAACAATATCATGAAAAT 5354
                               i i  i     i v      v      vvi     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_210177728_   5355 GGCCATACTGCCCAATGTAATTTATAGATTCAATGCTACTCTCATCAAGC 5404
                            v     v     vv i  i  i        i  v ii ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_210177728_   5405 TACCA-CTGACTTTCTTCACAGAATTAGGAAAAAGCT-ACTTTAAATTTC 5452
                          v   -   v    i  -i     v v -- v     - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_210177728_   5453 ATACAGAACCAAAAAAGATCCTGTATAGCCTAAGCAA----------AAA 5492
                            ii   viiv  ii  i  v v      v  i   ----------i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_210177728_   5493 GAGCAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATACTACAAGG 5542
                           i     i      vv   ii  v  ii        viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_210177728_   5543 CTACATTAACCAAAATGTTATGGTACTGGTACCAAAACAGATACATAGAC 5592
                              v   i   i iiv i         i iv ii i   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_210177728_   5593 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCA 5642
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_210177728_   5643 CCTGATCTTTGACAAATGTGACAAAAACAAGCAATGGGGAAAGGATTTCC 5692
                         vi    i  i     iv   v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_210177728_   5693 TATTTAATAAATGGTGTTGGGAAAACTCGCTAGCCATATGCAGAAAACTG 5742
                          v  i  i        i     v    v v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_210177728_   5743 AAACTGGACCCCTTCGTTACACTGTATACAAAAATTAATGCAAGATGGAT 5792
                           ii         v v i    ii              iv   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_210177728_   5793 TAAAGATTTAAACATAATACCTAAAACCATAAAAACCCTAGAAGAAAACC 5842
                         i ?   ii    ii   v v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_210177728_   5843 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5891
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_210177728_   5892 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGACAAATGT 5941
                         i            vvi          vv     v  i    ------  -
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT------TG- 639

  chr2_210177728_   5942 GATCTAATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGTCATCAG 5991
                           ii v  v   v v  i i   i  ii vv    i  v   i   vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_210177728_   5992 AGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCTATCTATCCAT 6041
                               v  i     i                 v     v vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_210177728_   6042 CTGACAAAGGGCTAATATCCAGAGTCTACAAGGAACTTAAACAAATTCAC 6091
                             i  i  i  vi        i v  i  i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_210177728_   6092 AAGAAAAA-----ACAATCCCACCAAAAAGTGGGCAAAGGATATGAACAG 6136
                           v     ----- i  i  v ii?    i            v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_210177728_   6137 ACACTTCTC-AAAGTAAGACATTTATGTGGCCAACAAACATATGAAGAAA 6185
                            i     -    -    i  vi vi       i  i  i     i i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_210177728_   6186 AGCTCCTCATCACTGGTCAT 6205
                         v    vv     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


3137 27.32 0.88 0.44  chr2_210436663_210442938.rev     4881  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_210436663_   4881 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4930
                              ii i  i   i i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_210436663_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_210436663_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_210436663_   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_210436663_   5079 AACAAAGCTGGAGGCATCACACTACGTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v vii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_210436663_   5129 TACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                            i    i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_210436663_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_210436663_   5227 ATCTGATCTTTGAAATACCTGAGAAAAACAAGCAATTGGGAAAGGATTCC 5276
                          vi    i  i  v vivv  vv  i v  vv    v       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_210436663_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_210436663_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_210436663_   5377 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_210436663_   5427 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_210436663_   5477 AACACCAAAAGCAATGGCAACAAAAGACAAAATTCACAAATGGGATCTAA 5526
                         i            vvi           v     vv i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_210436663_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_210436663_   5577 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_210436663_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_210436663_   5677 AAACAAACAACCCCATCAAAAAGTGGGCAA-GGACATGAACAGACACTTC 5725
                          i     i     v  i?    i       -   iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_210436663_   5726 TCAAAAGAAGACATTTATGCAGCCAA---ACACATGAAAAAATGCTCATC 5772
                           v        i  vi viii     ---i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_210436663_   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2857 25.90 2.09 1.51  chr2_210445751_210451095     3994  4854 (491)    L1M4_orf2#LINE/L1        1   866 (42)  

  chr2_210445751_   3994 TGGAAACACATTCCATGCTCATGGATAGGAAGTATCAATATTGTTAAAAT 4043
                               v i  i     i        v     vv i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_210445751_   4044 GACCATACTGCCCAAAGTAATTTACAGATTCAACGCTATTCCTATCAAAC 4093
                          i v     v      v i  i              v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_210445751_   4094 TATCACTAATATTTTTCACAGAATTAGAAAA--------TAAAATTCATA 4135
                          vi  viviiv     ii     v v  v  --------           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_210445751_   4136 TGGAA---CAAAAAAAGCCC-GAATAGCCAGAGCAACCCTAAGCAAAAAC 4181
                              ---   iii --   -         i i   i i i iv  i  v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_210445751_   4182 AATAAAGCCATAGGCATCACACCATCCAACTTCAAACTATACTACAAGGC 4231
                           i    iiiv   vv      ivi    i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_210445751_   4232 CACAGTAACCAAAACAGCATGGTACTGTTACAAAAACGGACACATAGACC 4281
                         i       i   i    ii        vi i  ii ii    i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_210445751_   4282 AATGGAACAGGCTAGAGAACCCAGAGATGAAACCACACACCTATAGCCAT 4331
                                i  iv v    ii     i  i  v   i   ii   i i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_210445751_   4332 CTGACTTTCAACAAAGTGGACAAAAATGAACAATGGGGAAAGGACTTGT- 4380
                         i   i    i    i vv v   i viivv            i - v  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTC 397

  chr2_210445751_   4381 TATTCAATAAATGGTGCTGGGATGACTGGCAAGCCATATGCAGAAGATTG 4430
                          v     i              ii     vv ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_210445751_   4431 AAATTGGACCACTTCCTTTCACCATATACAAAAATCAACTCAAGATGGAT 4480
                           i       v  v   iv                i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_210445751_   4481 TAAAGACTTCAATGTAAAACCTAAAACTATTAAAAGAAAGTTC--AGAAG 4528
                         i ?    i v       i v          ------   ii  --     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT------AAAACTCTTAGAAG 541

  chr2_210445751_   4529 AAAACCTAG---TCAATACCATTCTGGACACAGGAACAGGCAAATATTTC 4575
                              v   --- v   -- -   vv   viv  ivi      vvi    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_210445751_   4576 ATGAAGAAAACTCCAAAAGCAATTTCAGCAAAAACAAAAACTGACAAGTG 4625
                         v ii v vi  v         vvvv  i     iv     iv  i  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_210445751_   4626 GGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAGATTATCAACA 4675
                             i v  i   v v  i i   i  ii vv    i  v i      v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_210445751_   4676 GAATATATAGACGAATGACAAAATGGGAAAAAAAGATGTGCAAACTATGC 4725
                         i i iv v    i viv   i       i    -v  v      ii  ii
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATAT 737

  chr2_210445751_   4726 ATCTGACAAATGTCTAAGATCCAGAATCTATAAGGAACTTAAACAAATTA 4775
                               i  iv v  viv         v     i     ivv    v i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_210445751_   4776 ACAAGTAAAAAACAAACAATCCCATTGAATAATGGGCAAAGGACATAAAC 4825
                          i  vv    i     i  i  v   ?  v             iv i  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_210445751_   4826 AGACATTTCTTTAAAGAAGATGTACATAT 4854
                                   ii         i    v  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAAT 866

Transitions / transversions = 1.39 (128 / 92)
Gap_init rate = 0.01 (12 / 866), avg. gap size = 2.58 (31 / 12)  


2606 14.40 4.17 12.92  chr2_210612625_210614335.rev      477  1219 (492)    L1M4_orf2#LINE/L1      231   908 (0)  

  chr2_210612625_    477 CAACAATTA-TACAAATATCTGCA-TA-TCAAGATTTCATGGTACTGAGA 523
                            v v   -      v--  i  -  -      ivvii        iv 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAG--CTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_210612625_    524 GAAGGATTGACATACAGATCAGTAGAACAGAACTGAAAAACCATAAATAT 573
                         v      v      i      i i   i    i   i iv   v     v
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_210612625_    574 ACTACTACATTTATGTTCAATTGCTTTTTGACAAAGGTGCCAAGAAAATT 623
                           ivv          v       v    i     i          vv   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_210612625_    624 CAATGGAGAAA--ATGGTCTTTTCTATGAATAGTGCTGGGACAACTAGTT 671
                               i    --  i        v ii   i              i v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_210612625_    672 ATCTAAATGCAAAA--------TT------CTAACTCATAACATA-ACAC 706
                          ? i v        --------  ------   v    i v    -   v
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_210612625_    707 ATATTAACTCAAAGTTGATTACACACCTAAATATAAATGCTAAAACT--- 753
                          v           i v   i ? v        i   iv         ---
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr2_210612625_    754 -----CTTAGAAGAAAACATAGGAGTAAATCTTTGTGACCTTGGATTAGA 798
                         -----                  ?         i          i    i
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr2_210612625_    799 CAAATTGTGACCTTGGATTAGACAAATTGCGACCTTGGATTAGACAATTG 848
                            --------------------------------   ------------
  L1M4_orf2#LINE/    579 CAA--------------------------------TGG------------ 584

  chr2_210612625_    849 TTTCTTAGATATGACACTAAAAGCACAAATGACAAAAGAAAAA-CACACA 897
                                          i          iii            -i v i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_210612625_    898 CATTGGACCTAATTAAAAT-AAAAAATTTTGTGCCTCAAAGTTACCTTTA 946
                         v       i v  i     -     v        i      ---------
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG--------- 675

  chr2_210612625_    947 AGAAAATAAAAAAGACACTCGCTTCTCAGCCTTTTGGCTAAGATCAAGTG 996
                         -------------      -----------------------      --
  L1M4_orf2#LINE/    676 -------------GACACT-----------------------ATCAAG-- 687

  chr2_210612625_    997 AAGAAAGTAAAAAGACAAACTACGAAATGGGAGAAAATATTTGCAAATCA 1046
                         ---     i         v i  ii                         
  L1M4_orf2#LINE/    688 ---AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_210612625_   1047 TATATCTGATAAGTGACTTATATCCAGAATGTATAAATAGTTCTTATAAT 1096
                                      v     i          i      v ii     i  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_210612625_   1097 TTAACAGTTAAAAGACAAATTGCCCAATTTAAAG-TGGGCAAAAGATTTG 1145
                          i  i i v           vi       ?   i-        i      
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_210612625_   1146 AATGAATACTTTTACAAAGAAGATATACATATGGTCAATAAGCATATGAA 1195
                            ii i i  i v               v    i         i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_210612625_   1196 AAGATGCTCCATACCATTTGTCAT 1219
                                  v i i  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (64 / 39)
Gap_init rate = 0.03 (17 / 678), avg. gap size = 7.47 (127 / 17)  


 672 24.15 3.86 1.93  chr2_210813726_210818755     2833  3039 (1991)    L1M4_orf2#LINE/L1        1   211 (697)  

  chr2_210813726_   2833 TGGAAACAAATCCCATATTCATGGATTGGAAGACTTAATGTTGTTAAGCT 2882
                               v v       i                      i        v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_210813726_   2883 ATCAAAACTACTCAAAGAAATCTAGAGTTTCAGTGCA-TCCCTATCTAAA 2931
                         iv   v   v i    vvi     v  v    ii   -        v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_210813726_   2932 TCTCCACAACTCTTTTTATAGACAGAAA---AAAAACTTATCCTAAAGGT 2978
                           i vi vi ii     i----      --- v  i  v        iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG----CAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_210813726_   2979 CATACAAAATCTCATGAGACCTCAAA--GCCAACACAATCTCTAAAAAAA 3026
                             iii  viv  v i    ivi  --     v       iv     i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_210813726_   3027 C--ACAAATCTAGAG 3039
                         v--     vi i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAG 211

Transitions / transversions = 1.08 (26 / 24)
Gap_init rate = 0.02 (5 / 211), avg. gap size = 2.40 (12 / 5)  

 407 21.28 3.19 0.00  chr2_210813726_210818755     3335  3428 (1602)    L1M4_orf2#LINE/L1      191   287 (621)  

  chr2_210813726_   3335 AAATAAATAACAAATCTGGAAGACTCACG--TCCTGATTTCAAAAATTAT 3382
                            vi  v      vi    i       i--   ii         v   i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_210813726_   3383 TACAAAACTACAGAAATCAAAATAATGTGATACTGGC-CAGGCATAG 3428
                               i      v      i i i    i       -i i v    
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.02 (2 / 97), avg. gap size = 1.50 (3 / 2)  

1876 19.16 3.50 0.70  chr2_210813726_210818755     3585  4012 (1018)    L1M4_orf2#LINE/L1      263   702 (206)  

  chr2_210813726_   3585 CAATGTGGTACTGGCATAAAGACAGACCTATATTCCAATGGGATAGAATA 3634
                           i                i  i    v    vvi      i       v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_210813726_   3635 GAGAACCCAGAAATAAACCCTAACATATATGGTCAAATGTTTTTTGACAA 3684
                             ii              vv    v         v  v    i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_210813726_   3685 ACTTTTCAAGGCCATTCAATGG---AAAAACAGTCTTTTCAACCA--GGT 3729
                         ivv vi    i           ---  i  i            v --   
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_210813726_   3730 ------AAAACTGAATATCTGAATGAAAACAAATGAAACTGGACCCTTAC 3773
                         ------ v     i   ? iiv   v   vi      ii       i   
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_210813726_   3774 CTAACACCACACACAAAAATTAACACAAAACGGATCAAAGCTCTCAATGT 3823
                           v      i i            v     i      ?  vi  v     
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_210813726_   3824 AAAACCTAAAACTATAAAACTCTAAGAAGAAA-TATAGG-GTAAGTGCTT 3871
                           i v                  v        -i     -    i -   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTT 561

  chr2_210813726_   3872 CATGACATTAGATTTAGCAATGATTTCTTAGCTATGACACCAAAGGCACA 3921
                          i    v  i i  vi      i        v            i     
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_210813726_   3922 GGTAATAAAAGAAAAAGTAGACAAATGGGACTTCAGAAAAATTTTGAAAA 3971
                         i i  i          i    i    v        vv      --i    
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT--AAAAA 659

  chr2_210813726_   3972 --TTTGGGCAGGAAAAGATAATATCAACAGAGTAAAAATGCAA 4012
                         --    v  vvv   i  i v      v i   i    vi   
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

Transitions / transversions = 1.22 (44 / 36)
Gap_init rate = 0.02 (8 / 440), avg. gap size = 2.25 (18 / 8)  

 847 17.84 4.15 3.32  chr2_210813726_210818755     4298  4538 (492)    L1M4_orf2#LINE/L1      666   908 (0)  

  chr2_210813726_   4298 TGCCTCAAAAAAAA--A--AAAAAAAAAAAAAAGCAACACATAGAATAGG 4343
                            i     ii v -- --  i   ivi    ii    v  i     i  
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr2_210813726_   4344 AAAAAATATTTATAAATCATATATCTGATAAGAAATTAATATCTACTATA 4393
                          i         ii                   ii i vi    i vv   
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_210813726_   4394 TATT--GAA---TTAAAACGCAACAAGAAAAAAACAAGCAAGCAACCCAA 4438
                            v--   ---   v   v   i  v     i    ii  ----     
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA----CCCAA 811

  chr2_210813726_   4439 TTCAAAAATGGGCAAAGGACTTGAATAAGTACTTCTCCAAAGAAGATATC 4488
                           ?                i       iii i                 v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_210813726_   4489 CAAAAGCCAAGCCAGTA-GCACATGAAATGATGTTCAACATCATTAATCA 4537
                             v ----    i  -          v    i         ???????
  L1M4_orf2#LINE/    862 CAAATG----GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_210813726_   4538 T 4538
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.23 (29 / 13)
Gap_init rate = 0.03 (7 / 243), avg. gap size = 2.57 (18 / 7)  


2623 24.90 6.48 1.27  chr2_210829382_210831840.rev      816  1602 (857)    L1M4_orf2#LINE/L1        1   828 (80)  

  chr2_210829382_    816 TGGAAAAACATCCTGTGTTCACGGATTGGAAGA------GTTGTTAAAAT 859
                               i i    ii      i           ------i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_210829382_    860 GTCCATACAACCCAAAGCAATCTACAAATTCCATATCATTGTTATCAAAA 909
                          v v    vv      vii       i    v iiiv  ivi        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_210829382_    910 TTCCACTGGCATTTTCCATAGAAATGGGAAAA--AATTCAAAAATTTATG 957
                          i   viv  v    iiii      v iv  i--i  i v      i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_210829382_    958 TAAAACCAAGCAAG--ACCCC--ATGAGCCAAAGCAATCTTGAGCAAAAA 1003
                          ii  -- v     --    v--  -       i         iv  i  
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAAT-AGCCAAAACAATCTTGAAAAAGAA 197

  chr2_210829382_   1004 GAACAAAGCTGGAGGCAC-CACATTACCTGACTTCAAAATACATTGAGAA 1052
                                 i      -  -    i v  ii i       ivi i - v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACT-ACAA 245

  chr2_210829382_   1053 AACTATAATAGTCAAAACAGCATGCCACTGGAATTAAAAACACACATATG 1102
                          i   i i  i    i    ii  vi     v  -  ii i v      i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATA 294

  chr2_210829382_   1103 --CCTATGAAACAGAATAGAGAGCCTAGAAATAAATCCATGCATTTATGG 1150
                         --i v   i  i     v     i i         i    i         
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_210829382_   1151 CCAATTATTCTTTAATAAAGATGCCACGGGCACACAATGAGGAAGGGATA 1200
                         i     iv i  ii i  i i     v iv  iv     i    i i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_210829382_   1201 GTCTTTTCAACA----GTGTTGGGAAAATGGGTTATCTACATATCAAAGG 1246
                                     ----   i     v  iv  v  ? i    iiv    i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_210829382_   1247 ATGAAATTGGACCCTTATCTTACTCCTTATTCCCACATCAACTTAAGGTG 1296
                              i        i  i  i  v  v   v vv v  i    i  ii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_210829382_   1297 -ATTAAAGACTTCAACATAAGACCTGAA----TAAAAC-------AGAAA 1334
                         -  i ?    i v  ii     v  i  ----      -------     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_210829382_   1335 A---AG--------CTTCTCGACATTGATGTT-GGCAAATATTTTTTGGA 1372
                          ---  --------    vi   v   i-   -     vvi   i  i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGA 593

  chr2_210829382_   1373 TATG-CACTCCAAAGCACAGGTAACAAAAGCAAAAATAGACAAATGAAAT 1421
                             -   - v        i i        v         i    vii i
  L1M4_orf2#LINE/    594 TATGACAC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_210829382_   1422 TGCATCAAACTAAAAAGGTTTGACACAGCAAAAGAAAC----AGCAGAGT 1467
                          v       v v    iv   viii vv    i  v  ---- iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_210829382_   1468 GAAGAGACAACCTATGAAATGGGAGAAAATATTTGCAAACTATACGTCTG 1517
                            i        i iii                      ii   ii    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_210829382_   1518 AAAAGGGA---GGATTTCCAAAGTACATATGGAAGTTAAATTACTCAATA 1564
                          v      --- v  --   i i  i   vi   v ivv iv        
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTAT--CCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_210829382_   1565 GTAAGAAAACAAATAACCTGATTAAAAAATGGGCAAAG 1602
                         i   i  i          ii   ?              
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 2.02 (129 / 64)
Gap_init rate = 0.03 (24 / 828), avg. gap size = 2.54 (61 / 24)  

 512 11.34 0.00 5.15  chr2_210829382_210831840.rev     1871  1967 (492)    L1M4_orf2#LINE/L1      817   908 (0)  

  chr2_210829382_   1871 AAATGGGCAAAGGACCTGAATAGACAATTTCTTTTTCCAAAGAAGATATA 1920
                                       ii          -----   i               
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACA-----TTTCTCCAAAGAAGATATA 861

  chr2_210829382_   1921 CAAATGGCCAACACATAGATGAGAAAGTGCTCAACATCACTAATCAT 1967
                                    i vii v    i  ii            ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.01 (1 / 92), avg. gap size = 5.00 (5 / 1)  


2997 27.52 1.22 0.44  chr2_210870813_210877467     5263  6163 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_210870813_   5263 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5312
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_210870813_   5313 GGCCATAATGCCCAAAGTAATTTATAGATTCAGTGCTATCCCCATTAAGC 5362
                            v   v v      v i  i  i       ii  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_210870813_   5363 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5411
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_210870813_   5412 ATGGAACCACAAAAGAGACAATATAGCCAATTAAATCTTAAGCTAAAAGA 5461
                               vii   ii  vv  iv        vvv      i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_210870813_   5462 GCAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5511
                         i     i i    vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_210870813_   5512 ACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATATAGACCA 5561
                                i   i    ii  i      i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_210870813_   5562 ATGGAACAGAACAGAGGCCTCAGAAATTACCCCACACATCTACTACCATA 5611
                               i    iv   ivii       v v    i    i  ivii  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_210870813_   5612 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAATGATTCCCTA 5661
                             i  i     ivv  v   i v  vv           vi  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_210870813_   5662 TTTAATA----GTGTTGGGAAAACTGGCTAGCCATATGCAGAAAATTGAA 5707
                           i  i ----   i     v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_210870813_   5708 ACTGCACCCCTTCCTTATGACTTATACAAAAATTAACTCAAGATGGATTA 5757
                         ii  v      v   i iiv v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_210870813_   5758 AAGATGTAAATGTAAGATCTAAAAACCATAAAAACCCTAGAAGAAAACCT 5807
                         ?   iv           v      - i      vi i           v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACAT 548

  chr2_210870813_   5808 AGGCA-ATACCATTCAGGACATAGGCATGGGCCAAGACTTCATGACTAAA 5856
                            ?i- v i -   iv   v v  vv i   v v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_210870813_   5857 ACACCAAAAGCAACTGCAACAAA-GCCAAAATTGACAAATGGGATCTAAT 5905
                                     vvv        - vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_210870813_   5906 TAAGCTAAAGAGCTTCTGCACATCAAAAGAAACTATCATCAGCGTGAACA 5955
                         i  iv v  i i   i  ii v     i  v       vv iv     v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_210870813_   5956 GGCAACCAACAGAATGGGAGAATATTTTTGCAATCTATCCATCTGATGAA 6005
                          i     v              v  v       vii  vi       i i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_210870813_   6006 GGGCTAATATCCAGAGTATACAAGGAATTTAAACAAATTTAGAAGATAAA 6055
                           i  vi        i    i  i   i ivv    v iv v  v -   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA-AAA 796

  chr2_210870813_   6056 AAACAACT---CCAAC-AAAAAGTGGGTGAGGGAGATGAACAGACACTTC 6101
                          i    v ---    i-?    i    ii i   vv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_210870813_   6102 TCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTCATC 6151
                           v        i  vi vi       i  i  i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_210870813_   6152 ATCACTGGTCAT 6163
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (138 / 106)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2876 24.13 7.11 1.28  chr2_210933129_210935557.rev     1081  1938 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_210933129_   1081 TGGAGAGATATTCCATGTTCATTGATAGGAAGACTGTGACATTGTCAAAA 1130
                             i      i          v   v        - i i     i  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACT-TAATATTGTTAAGA 49

  chr2_210933129_   1131 TGTCAGGTTTTCCCAATTTGATCAATAGATTCAGTGCAATCCCAATCAAA 1180
                           v  ivvi i     v      v i       ii        v      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_210933129_   1181 TTCTCAGTAAGTTATTTTGCAGATATCAACTAACTGGACTCTAAAATCTA 1230
                         v  i   ivivi v         v  ii  v i   - ii       ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCA 148

  chr2_210933129_   1231 CATGGAAAAGCAAAAGACCCAGAATAGCCAACACCGTATTGAAGGAGAAG 1280
                         i       v    ii                v  vi v     ii     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_210933129_   1281 AACAAAGTCAGAAGTCTGATACTACCTGACTTTAAGACTTGCTATTAAAC 1330
                                 ii  i v  v i   v  ii i  i  i    i   iv  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_210933129_   1331 TACAGTAATCAAGACAGTG----A-------AAGAATAGACAAACAGATC 1369
                                            ---- -------   i       v i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_210933129_   1370 AATGAAATAGAACAGAGAATTCAGA------CCCACAAAAACAGAGTCAA 1413
                             i       iv    i i    ------    i v vvi vi     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_210933129_   1414 CTAATATTTGACAAAGGAGCAAAGGCAATGCGATGAAGCAAAGA------ 1457
                         i i  v  i     i  v  v   i v  v i   ii -     ------
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTC 397

  chr2_210933129_   1458 TTCTCAACCAGTGGCATTACAACAACTACACATCCACATTTTAAAAAATG 1507
                           i     v i   iii ivi      iv i ?      viv   i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_210933129_   1508 AATCTAGAAACAGACTTTACACCTTTTACAAAAATT----CAAAATAGAT 1553
                           vi i  vv vv  i i     v v          ----      i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_210933129_   1554 CATAGACAGAAACAGAAAA--TGGAAATGAACAAAACTGTTAGAAGATGA 1601
                           ?    vv   iiv  i -- ii  v -- i      v        vi 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACT--ATAAAACTCTTAGAAGAAAA 545

  chr2_210933129_   1602 CATAGGAGAAAACCCAGATAACCTTGG-TTATCACAATGACTTTTTAGAC 1650
                               ? v   i ivvi i       -   v-i     ii  i     i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAG-GCAATGGTTTCTTAGAT 594

  chr2_210933129_   1651 ATAACGCCAAAGGCACAATCCATGAAAGAAACAACTGATAAGCTGGACTT 1700
                           i  i     i      v v ii       v  iv     ii       
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_210933129_   1701 CATTAAAATTTAAAACTTCTGCTCTGCAAAAGGCAC-------------- 1736
                            i      v       i  iv  v    i i   --------------
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_210933129_   1737 --AGAC-----------TGAGA-AAAATACTTGCAAAAAGTGTATCTGAT 1772
                         --    -----------  i  -      i       vvi i        
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_210933129_   1773 AAGGAACTGTTATCTAAAATATACAAACAATTCTTAAAACTCAGTAAGGA 1822
                             i   vv    i i      i   v  i     v      i   vi 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_210933129_   1823 GAAAGCAGGTTTAAAACCTGATTTAAAAATGGGCCAAAGGCTTT-AACAG 1871
                         i  ii  ii ----    ii   ?          -     v   -  i  
  L1M4_orf2#LINE/    795 AAAGACAAAT----AACCCAATTWAAAAATGGGC-AAAGGATTTGAATAG 839

  chr2_210933129_   1872 ACCCCTCATAAAAGAAGATATGCAGATGGA-AATAAGCATATGAAAAGAT 1920
                           vii  viv           i  i    v-        i          
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_210933129_   1921 GCTCCACAT-ATGTTATCA 1938
                             v    - ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (128 / 75)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.60 (72 / 20)  


2522 25.92 5.41 1.15  chr2_210964720_210967067.rev      989  1856 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_210964720_    989 AAAAAAATTCCATGCTCATAGATAGGAAGAATCAATATCATGAAAATGGC 1038
                            i v  i     i    i   v      v i     ii v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_210964720_   1039 CATACTGCCCAAAGT---------ATTC--------CCC---CAAGCTAC 1068
                         v     v      v ---------    --------   ---   iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_210964720_   1069 CA-TTGACTTTCTAGGCAGAATTAGAAAAAACT-ATTTTAAATCTCATAC 1116
                           -i  v    i -v      v v  v  i-  -  ii    vi     i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTT-TGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chr2_210964720_   1117 GGGACCAAAAAAGAGCCCATAG-GGCCAAGACAATCCTAAGCAAAAAGAA 1165
                           i viiv  ii  -    v i-i     i      i i iv  i     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_210964720_   1166 CAAAGCTGGAGGCATCAGGCTATCTGACTTCAAACTATACTACAAGCCTA 1215
                              i      vv   vi  vi ii i      viv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_210964720_   1216 CAGTAACCAAAACAGCATGATGCTTGTACCAAAACAGATATATAGACCAA 1265
                               i   i    ii  i i  v i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_210964720_   1266 TGGAACAGAATAGAGGCCTTAGAAATAACACCACACATCTACAACCATCT 1315
                              i     v   iviii        vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_210964720_   1316 GATCTTCCACAAATCTGACAAAAACAAGCAATGGGGAAAGGAT--TCTCT 1363
                            i   v    ivv  v   i v  vv            i  --   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_210964720_   1364 --AATAAACGGGGCTGGGAAAACTGGCTAGCCATATGCAGAAAACAGAAA 1411
                         --  i   i  v       v      v  ?   i     i  i vv   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_210964720_   1412 CTGGACCCCTCCTTTACACCTTATAAAAAAATTGACTCAAGATAGATTAA 1461
                         i         v i i     v    v       i      i  i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_210964720_   1462 AGACTTAAATGTAAAACCCAAAACCATAAAAACCT-AGAAGAAAATGTAG 1510
                             i         i v i     i      vi  -         ii   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_210964720_   1511 GC-TATACCATTCAGGACATAGGCATGGGCAAAGACTTCAT-GAC-TAAA 1557
                          ?-  v i -   iv   v v  vv i     v ii   v -  i- i v
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_210964720_   1558 ACTGAAA--ACAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1605
                           ii   --    --          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_210964720_   1606 TAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGGACA 1655
                         i   v v  i i   i  ii vv    iv v       vv i    i v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_210964720_   1656 GGCAGCCTACAGAATGGGAGAACATTTTTGCAATCTACCCATCTGACAAA 1705
                          i  i  i              v  v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_210964720_   1706 GGTCTAATATCCAGAATCTACAAGGAACT--------TCCATGTACAAGA 1747
                           v  vi          v  i  i     --------  v  i- i  i 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAAA 796

  chr2_210964720_   1748 AAA-AAACAACCCCATCAAAAAGTGGGCAAAGGATACGAACAGACACTTC 1796
                          i -   i     v  i?    i            vi   i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_210964720_   1797 TCAAAAGAAGATA--CTGATGCAGCCAACAAACATAAGAAAAACAAGCTC 1844
                           v          -- vi   --     i  i  i v     i- v    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAG-ATGCTC 893

  chr2_210964720_   1845 A---TCACTGGTCAT 1856
                          ---   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (134 / 87)
Gap_init rate = 0.03 (25 / 905), avg. gap size = 2.28 (57 / 25)  


 554 30.05 2.82 0.94  chr2_210969240_210974494.rev     3414  3626 (1629)    L1M4_orf2#LINE/L1       28   244 (664)  

  chr2_210969240_   3414 GGAAGG---AATATTGTGGAAATGACCATACAACCAAAAGTGATCTATAG 3460
                              i---        vi i   i v    vv  v   v       i  
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chr2_210969240_   3461 ATTCAATGCAATGCTTATCAAAATATCAATGACATTCTTCACAGAAACGG 3510
                               i     v i         vi  iivi v  i  ii      iv 
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chr2_210969240_   3511 AAAAAAAAATTCTAAA-TTTACATGGA--TTCACAAAGACATCAAACAGC 3557
                          v  ivvi  i     -  i i     -- v  - ii   vivi  i   
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCA-AGGGACCCAGAATAGC 176

  chr2_210969240_   3558 CAAGGCAATCCTAAACAAAACTAACAAAACTGGAGGCATCACAATATTAG 3607
                            ii     i i  v  i vv      ii      vv     v viivi
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr2_210969240_   3608 ACTTCAAAGTTATATTACA 3626
                          i      ii -  i    
  L1M4_orf2#LINE/    227 ATTTCAAAACT-TACTACA 244

Transitions / transversions = 1.56 (39 / 25)
Gap_init rate = 0.02 (5 / 217), avg. gap size = 1.60 (8 / 5)  

1326 22.19 8.73 2.00  chr2_210969240_210974494.rev     3823  4223 (1032)    L1M4_orf2#LINE/L1      238   665 (243)  

  chr2_210969240_   3823 TAC-ACAAAGCTATATTAGCCAAAATAGCATGCTATTGGAATAAAAACAG 3871
                            -         i v  ii   i i  ii  v  i   v    ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_210969240_   3872 AC--------CAATGGAACAAAATAGGAAACCCAGAAATAAATCCACATA 3913
                           --------        i i   v ii ii           i   i i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_210969240_   3914 TTTACAACCAATCGATTTTTCACACAAAGGCACCAAGAAGATTCATTGAG 3963
                             iiii    i      - i-    i  ii      vv     v  i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTT-CG-ACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_210969240_   3964 GAA-GAACAGTCTGTTCAATAAATGGTGCTGGGAAAACTGAATATCCGTA 4012
                            -   i     v     i              v     i   ?  ii 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_210969240_   4013 TGCAGAAGAATGAAACTG-ACCCC-ATCTCTCACCATACATAAAGATCAA 4060
                             i         ii  -     - i   v       i i   i  i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_210969240_   4061 CTCAAAATGAATTAAAGAAAACTTAAATATA-----------TATGAAAA 4099
                                  i  i ?   --- i     i  -----------   --   
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGA---CCTAAATGTAAGAGCTAAAACTAT--AAA 530

  chr2_210969240_   4100 A---TTAGAAGAAA-CATAGGGA-AAATGCTTTAGGACACTG-------C 4137
                          ---          -      ?i-    -   iiv   vi  ------- 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGC 579

  chr2_210969240_   4138 AAAGATTTAATGGAGAAGACCTCAAAAGCACAAGCAACCAAAACAAAAAT 4187
                           v i   vv i  v v   vi                v   iv      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_210969240_   4188 AGACAAATGGGATAATATCAAACTAAAAAGTTTCTG 4223
                            i    v   ivvi      v v    ii  i  
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 2.44 (61 / 25)
Gap_init rate = 0.04 (15 / 428), avg. gap size = 2.87 (43 / 15)  

 811 19.09 4.55 1.36  chr2_210969240_210974494.rev     4544  4763 (492)    L1M4_orf2#LINE/L1      682   908 (0)  

  chr2_210969240_   4544 ATCAACAAAG-----AGACAAGCTGCAGAATGGGAGAAAATATTTGCAAA 4588
                              v    -----      v ii                         
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_210969240_   4589 GTATTCATCTGACAAGAGATTAATATCCAAAATATACAAAGAACTCA-AC 4637
                         vi  vi      i   i  i vi      i      i         v-  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_210969240_   4638 AGC--AATATTAAT--TATAATTATAATCCAATTTTAAATTGGGCAAATG 4683
                          i --    v   v--v i  --    i      ?v   v        v 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAA--ATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_210969240_   4684 AGCTGAATCGACATCTCTCAAAAAAAGACATAAAAATGGTCAAAAGGTAT 4733
                          vi     v     i    v   i    i   v      i   v i i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_210969240_   4734 ATGAAAAAAATGTTCGACATCACTAATTAA 4763
                                i -  i  i      ????????
  L1M4_orf2#LINE/    880 ATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (24 / 17)
Gap_init rate = 0.03 (6 / 227), avg. gap size = 2.17 (13 / 6)  


1156 25.55 2.52 0.95  chr2_211016525_211020381.rev     2136  2452 (1405)    L1M4_orf2#LINE/L1        1   322 (586)  

  chr2_211016525_   2136 TGGAAATACATTTCATGCTCATGGATCAGAAGAATTAATATTGTTAAAAT 2185
                               v i  ii    i        ii     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_211016525_   2186 GGCCATGCTGCCCAAAGCAATCAACAGTTTCAATGGAATCCCTATCAAAA 2235
                            v  i  v      vii   v    v     i v              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_211016525_   2236 TACCAA-TGTCATTTTTCACAGAATTAGAAAAAACAATCCTAAAATTTTC 2284
                          v   i-  i -     ii     v v  v  ivii           -- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT--C 147

  chr2_211016525_   2285 ATGGGGCCAAGTAAGAG-CCCAAAA--ACCAAAGCAA-CATGAACAAAAA 2330
                           iv  vv v i   i -    i  --i     i   - v    v  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_211016525_   2331 GAACAAAGCTAGGGGCATCACCTTACCTGATTTTAATATATATTACAAGA 2380
                                 i i i  vv    vi v  ii    i  v iv  i     ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_211016525_   2381 CT---TTAACTAAAACAGCATAGTATTAGTATAAAAACAGTTACATAGAC 2427
                           ---v   ii  i    ii i   i i i    ii i  vi i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_211016525_   2428 TAATGGAATAGAATGGAGAATCCAG 2452
                         i             v    i     
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAG 322

Transitions / transversions = 1.89 (53 / 28)
Gap_init rate = 0.02 (7 / 322), avg. gap size = 1.57 (11 / 7)  

2025 23.35 1.77 4.35  chr2_211016525_211020381.rev     2745  3365 (492)    L1M4_orf2#LINE/L1      304   908 (0)  

  chr2_211016525_   2745 AAAAAAATAGAGAATCCAGAAATAAATCCATGTATTTACAGCCTACTGAT 2794
                           v i   v    i            i    ii     ii i v i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_211016525_   2795 TTTTGACAAATGTGCCAAGAACATCCATTGGGGAAATGACAGTATCTTCA 2844
                            i     iv         v   i  v        vi i   v i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_211016525_   2845 ATTAATGGTGATGGGAAATTTGGATATCTACATGCAGAAGAATATAGGTA 2894
                          iv       v     v vi      ? i       i      i- i  -
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG-AAGT- 451

  chr2_211016525_   2895 TCTTCTATCTAAGCCCCTATCTT-CACTACAT-CACATATTAATTCAAGG 2942
                         --------- iii      i  i-   i i  -  v v     i    ii
  L1M4_orf2#LINE/    452 ---------TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_211016525_   2943 TACATTATAGACTTAAAC-----ACTTAAAACTATAAAACTACTAGAAGA 2987
                          iv  i ?    i    i----- vi               vi       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_211016525_   2988 AAACAGAGGGAAAACTCTTCAGTACATTGGTCCGGGCAAAGAT--CTTAC 3035
                              v   ?iv  v     ivv  v    viii     v i --    v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_211016525_   3036 ACCTAAGACCTCAAAATCACAGGCAACAAAAACTAAAATAGACAAATGGT 3085
                          --  v   vi     v    i         ivv        i    v v
  L1M4_orf2#LINE/    593 A--TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_211016525_   3086 AGCATATTAAACCAAAAAGCTTCTGCATATCAAAAGAAACAACCAAGAGA 3135
                          vivi  i   viv    i   i  iiiv     i  v  v i     i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_211016525_   3136 GTGAAAAGACAACCTGTAAAATGGGAGAAAATATTTGTAAGCTATTCATC 3185
                                       iii i                  i  iii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_211016525_   3186 CAACAAGGCATTAATATCCAGAATAT-CAAGGAACTCAAACAATTCAACA 3234
                         ii i    v i vi            -i  i      vv    i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_211016525_   3235 ACCAAAAAAAACCCCACAAATAATCATATTAAAAAGTGGGCAAAGGATAT 3284
                          i--     i  -----      i vv   ?    i            v 
  L1M4_orf2#LINE/    791 AT--AAAAAGAC-----AAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_211016525_   3285 GAACAGATATTTCTG-AAAGTAAGGCACACAAATGGCCATATACAAATGG 3333
                            i   i      v-    -   ii i           --- i  --- 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAG-AAGATATACAAATGGCCA---ATAA---G 876

  chr2_211016525_   3334 TATATGAAAAAATACCCAACATCACTATGCAT 3365
                         i i       i  i i        ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (92 / 49)
Gap_init rate = 0.02 (14 / 605), avg. gap size = 2.71 (38 / 14)  


1831 25.05 1.14 0.57  chr2_211035767_211046745      493  1019 (9960)  C L1M4_orf2#LINE/L1   (0)   908   379  

C chr2_211035767_   1019 CAATAGGGAAAGGATTCCCTATTTAATAAATGAGGCTGGGAAATCTGGCT 970
                             i       i  vvi  v  i  i     iv       v v    v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

C chr2_211035767_    969 AGTCATATGCAGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACAA 920
                          ?i  i     i  i v    ii         v   i     v       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

C chr2_211035767_    919 AAATTAACTCAAGATGGATTAACTACTTAAATGTAAAATCCAAAACCATA 870
                                     i      i ?vv  i         i v i     i   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

C chr2_211035767_    869 AAAAAATCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCAT 821
                            v--  i           v    ?i- v i -   iv   v v  vv 
  L1M4_orf2#LINE/    529 AAAC--TCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTT 575

C chr2_211035767_    820 GGGCAAAGACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCTA 771
                         i     v ii   v iiv  vi            vvi          vv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

C chr2_211035767_    770 AAATTGACAAATGGCACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAG 721
                             v  i    v v  i v  i   v v  i i   i  ii vv     
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

C chr2_211035767_    720 GAAACT--CAA---ACTGAACAGGCAACCTACAGAATGGGAGAAAATGTT 676
                           v   --   --- v    v  i     i                 i  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

C chr2_211035767_    675 TGCAATCTGTCTATCTGACAAAGGCCTAATCTCCAGAATCTACAAGGAAC 626
                              viii v       i  i  v  vi v        v  i  i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

C chr2_211035767_    625 ATAAACAAATTTACAAGGAAAATACAAACAAACCCATCAAAAAATGGGCA 576
                         vivv    v iv i  vi    v     i  v  v  i?           
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

C chr2_211035767_    575 AAGGTTATGAACAGACACTTCTCAAAAGAAGACGTTTATGTGGCCAAGAA 526
                             v v    i     i     v        ii vi vi       v  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

C chr2_211035767_    525 ACATAAGAAAAAAAGCTCATCATCACTGGTCAT 493
                         i  i v     i v     v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (64 / 64)
Gap_init rate = 0.01 (5 / 530), avg. gap size = 1.80 (9 / 5)  

1105 30.05 0.78 1.04  chr2_211035767_211046745     1313  1698 (9281)  C L1M4_orf2#LINE/L1   (522)   386     2  

C chr2_211035767_   1698 GGAAAAAAGTTCCATGCTCATGGATAGGAAGAATCAGTATCATAAAATTG 1649
                              i vi i     i        v      v i i   ii v  iv  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

C chr2_211035767_   1648 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCTACTCCCATCAAGGT 1599
                           v     v      v i  i  i        i  v ii  i     ii 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

C chr2_211035767_   1598 ACCA-TTGACTTTCTT-CACAAAGTTAGAAAAAACT-ACATTAAATTTCA 1552
                         v   -i  v    i  -  v   -  i-- v  i  - ivi    v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAA-TTG--ACAAGCTGATCCTAAAATTCA 148

C chr2_211035767_   1551 TATGGAACCAAAAAAGAGCCCACGTAGCCAAGACAATCCTAAGCAAAACC 1502
                                viiv  ii  v  vivi       i      i i iv  i vv
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr2_211035767_   1501 ATCAAAGCTGGAGACATCATGCTACCTAACTTCAAACTATTCTACAAGGC 1452
                          v     i     ivv   ii  v  i  i      viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr2_211035767_   1451 TACAGTAACCAAAACAGCATGGTACTCGTACCAAAACATATATATAGACC 1402
                                 i   i    ii       v i iv ii i v i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr2_211035767_   1401 AATGGAACAGAACAGAGGCCTCAGAAATAACACTACACATCTACAACCAT 1352
                                i    iv   ivii         vv i i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

C chr2_211035767_   1351 CTGATCTTCCACAAACCTGACAAAAAACAAGCAATAGGG 1313
                         i    i   v    ivv  v   i v-  vv    i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGG 386

Transitions / transversions = 1.58 (71 / 45)
Gap_init rate = 0.02 (6 / 385), avg. gap size = 1.17 (7 / 6)  

3194 26.41 1.10 0.77  chr2_211035767_211046745     9583 10487 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_211035767_   9583 TGGAAGAACATTCCATGCTCATGGGTAGGAACAATTAATATCATGAAAAT 9632
                              ii i  i     i      i v    v v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_211035767_   9633 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 9682
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_211035767_   9683 TACCAATGACTTTCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCA 9730
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_211035767_   9731 TATGGAACCAAAAAAGAGCCTGCATTGTCCAGTCAATCCTAAGCCAAAAG 9780
                                viiv  ii  v  v v  v i v iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_211035767_   9781 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 9830
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_211035767_   9831 TACAGTAACCAAAACAGCATGGTACCAGTACCAAAACGGAGATATAGACC 9880
                                 i   i    ii      ii i iv ii ii  v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_211035767_   9881 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATATACAACC 9928
                                i    i--    i  --        vv   i i  v  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_211035767_   9929 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 9978
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_211035767_   9979 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAAGCT 10028
                           v  i  i              v      v  ?   i i i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_211035767_  10029 GAAACTGGATCCCTTCCTTACACCTTATGCAAAAATTAATTCAAGATGGA 10078
                            ii    i    v   i     v   i          i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_211035767_  10079 TTAAAGACTTAAATGTTAGAACTGAAACCATAAAAACCCTAGAAGAAAAC 10128
                          i ?    i       v   i  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_211035767_  10129 CTAGGCAGTACAAT--TCAGGACATAGGCATGGGCAAACACTTCATGACT 10176
                         v    ?-   -   --  iv   v v  vv i     vvii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGN-GTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_211035767_  10177 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 10226
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_211035767_  10227 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCA-CAATCAGAGTG 10275
                         v  i   v v  i i   i  ii vv    i  v  i -   v- i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTG 693

  chr2_211035767_  10276 AACAGGCAACCTATAAGATGGGAGAAAATTTTTGCAATCTACTTATCTGA 10325
                           v  i     i i ii            v       vii iv       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_211035767_  10326 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 10375
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_211035767_  10376 AAAAAACAAACAACCCCATCAACAAATGGGCAAAGGATATGAACAGACAC 10425
                             i     i     v  i? v               v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_211035767_  10426 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 10475
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_211035767_  10476 A---TCACTTGCCAT 10487
                          ---   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (144 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


2808 26.14 2.44 1.88  chr2_211102626_211106492.rev     2473  3375 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_211102626_   2473 TGGAAAAACATTCCATGCTCGTGGATCGGAAGAATCAATATCACTCAAAT 2522
                               i i  i     i  i     i      v i     iii v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_211102626_   2523 GGCCATACTGCCCAAAGCAATGTATAGATTCAATGCTATTCCTCTCAAAT 2572
                            v     v      vii  v  i        i  v  i   v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_211102626_   2573 TGCCAATGGCATTTTTCCACAGAATTAGAAAAAAACAACTATAAAATTCA 2622
                          v   iiv  v     i-i     v v  v  iv-ii iiv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chr2_211102626_   2623 TATGAAATCAAAAGAGAGCCCAAATAACCAAAGCAATCCTAGGCACAAAG 2672
                             i  viiv   i  v  vi    i     i     i iiiv vi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_211102626_   2673 AACAAAGCTGAAAGCATAACACTAC----TTTCAGACTGTGCTACAAGGC 2718
                                i  i i vv v     v ----     i viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_211102626_   2719 CAAAGTA-TCAGTTTTGTATCAGTTTAGTACTGATACAAAAACAGTCACA 2767
                         i v    -   i------iv    v i      ii i  ii i  v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAA------GACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_211102626_   2768 TAGACCAATTGAAAAGAATAGAGAACCCAGAAATAAAGCTGCACACCTAC 2817
                             i    v   v     v    ii           v iii   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_211102626_   2818 AACTATCTGATCTTTAACAAAATTGACAACTACAAGCAATGGAGAAAGGA 2867
                         iiii vi    i  ii    iiv  v   vvv  vv      i     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_211102626_   2868 CTCTCTATTCAATAAATGCTACTGAGATAACTAGCCAGCCATATGCAGAA 2917
                         ivv   v     i     v i   i  i    i vi ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_211102626_   2918 GACGATTGAAACTGGACTCCTTCCTTTCACCACATACAAAAATCAACTCA 2967
                           --  -   ii     i   v   iv     i          i      
  L1M4_orf2#LINE/    443 GA--AT-GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_211102626_   2968 AAATGGATTAAAGACTTGAATGTAAAACCTAAAACTATAAAAATCCCAGG 3017
                                 i ?    i i       i v              v  ii  i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_211102626_   3018 AGAAAACCTA----CAATACCATTCTTGACATTGGCCCTGGCAAAGATTT 3063
                                v  ----i  - i -   v    v    viiv     v i   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_211102626_   3064 CATGGCAAAGACTCCAAAAGCAATTGCAA--AAAGAAAAAAT-GACAAGT 3110
                          v i vv v   v         vvv    --           -  i  i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_211102626_   3111 GAGGACCT------AATTAAAAGTTTCTGGACAGCAAAATAAACTATCAA 3154
                         v-    i ------        ii  i  vi vv    iv v        
  L1M4_orf2#LINE/    638 T-GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_211102626_   3155 CAGAGTAAGACAGACAACCTGCAGCGTAGAAGAAAGTATTTGCAAACCAT 3204
                         v i   i i -        ii   vi i i     i          i   
  L1M4_orf2#LINE/    687 GAAAGTGAAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_211102626_   3205 GCATCTGACAAAGGTCTAATATTCAGAATCTATAAGGAACGGAAACAAAT 3254
                         ii      i  i  v  vi   i      v     i    vvvv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_211102626_   3255 TAACCAGTAAAAA-ACAAC---CCCATTTTAAAAATGGGCAAAGGACATG 3300
                         i  i- i      -    v---    v  ?                iv  
  L1M4_orf2#LINE/    786 CAAT-AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_211102626_   3301 AAGAGACATTTCTCAAAAGAATATGTACATGCAGCCAACAAGCATATGAA 3350
                           v           v      v  i    viii     i     i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_211102626_   3351 TAAAATGCTTGACATCACTAATTAT 3375
                         -  i     ii      ????????
  L1M4_orf2#LINE/    885 -AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.05 (39 / 19)  


3096 26.65 2.13 0.45  chr2_211135761_211141471     4327  5219 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_211135761_   4327 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGGGAA-AT 4375
                               i i  i     i        v      v i       vv  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_211135761_   4376 GACCACACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATTAAGC 4425
                          i v i   v      v i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_211135761_   4426 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAACTAGTT-TAAATTTCA 4473
                          v   -   v    i  -i     v v  v  i-  ii i-    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_211135761_   4474 TATGGAACCAAAAAAGAGCCTGCATAGCCAAAAGAATCTTAAGCAAAAAG 4523
                                viiv  ii  v  v v          v      i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_211135761_   4524 AACAAGGCTGGATGCATCATGCTACCTGACTTCAAACTATACTACAAGGG 4573
                              i i    v vv   ii  v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_211135761_   4574 TCCATTAACCAAAACAGCATGGTACTGGTACCAAAAACAGATATATAGAC 4623
                          v  v   i   i    ii         i i-  ii i   i       i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGAT 297

  chr2_211135761_   4624 CAATAGAACAGAACAGAGGCCTCAGAAATAACACCACACACGTACAGCCA 4673
                             i   i    iv   ivii         vv   i   iv  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_211135761_   4674 TCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAGGATTCCC 4723
                         vi    i  i     ivv  v   i vi vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_211135761_   4724 TACTTAATAAATGGTGCTGGGATAACTGGCCAGCCATATACAGAAAACTG 4773
                          vi i  i              i      vi ?   i  i  i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_211135761_   4774 AAACTGGACCTCTTCCTTATACTTTATACAAAAATTAACTCAAGATGGAT 4823
                           ii      i  v   i i  iv                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_211135761_   4824 TAAAGACTTAAATGTAAGGCCTAAAACCATAAAATCACTAGAAGACAACC 4873
                         i ?    i          iv       i      iivi       v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_211135761_   4874 TAGGCA-ATACCATTCAGGACATAGGCATGTGTAAAGACTTCATGACTAA 4922
                             ?i- v i -   iv   v v  vv iv i  v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_211135761_   4923 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4972
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_211135761_   4973 TTAAACTAAAGAGCTTCTGAATATCAGAAGAAACTATCATCAGAGTGAAC 5022
                          i   v v  i i   i  viiv   i i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_211135761_   5023 ATGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 5072
                          vi     i i               v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_211135761_   5073 AGGGCTAATATCCAGAATCTACAAA-----TTTACAAG--------AAAA 5109
                         i  i  vi          v  i   -----i      v--------    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_211135761_   5110 AAACA--TAACTCCATCAAAAAGTGGGCAAAAGATATGAACAGATACTTC 5157
                          i   --    i v  i?    i        i   v    i   i i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_211135761_   5158 TCAAAAGAAGACATTTATGTGGCCAACAAAGATATGAAAAAAAGCTCATC 5207
                           v        i  vi vi       i  iv i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_211135761_   5208 ATCACTGGTCAT 5219
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


3125 26.67 0.88 1.21  chr2_211195151_211201522     4970  5880 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_211195151_   4970 TGGAAGAACATTCCATGCTCATGGGTAGGAACAATCAATATCGTGAAAAT 5019
                              ii i  i     i      i v    v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_211195151_   5020 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5069
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_211195151_   5070 TACCAATGACTTTCTTCACAGAATTGGAGAAAACT-ACTTTAAAGTTCAT 5118
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_211195151_   5119 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGA 5168
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_211195151_   5169 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCA 5218
                               i      vv       v  ii i      viv        i  v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_211195151_   5219 ACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGAGATCTAGACCA 5268
                                i v i    ii         i iv ii i   v  v    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_211195151_   5269 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACGTTATCTACAACT 5316
                               i    i--    i  --        vv   iii-  i  iiiii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATAC-ATTTATGGTC 346

  chr2_211195151_   5317 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5366
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_211195151_   5367 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5416
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_211195151_   5417 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5466
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_211195151_   5467 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5516
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_211195151_   5517 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGGCAAGGACTTCA 5565
                         v    ?i- v i -   iv   v -----    iv   -   v ii   v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCT-----TGGGTTAGG-CAATGGTTTCT 589

  chr2_211195151_   5566 TGTCTAAAACACCCAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGG 5615
                          ivv  vi     v      vvi          vv    iv  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_211195151_   5616 GAACTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAG 5665
                           vi v  i   v v  i i   i  ii vv    i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_211195151_   5666 AGTGAATAGGCAACCTACAGAATGGGACAAAATTTTTGCAATCTGCTCAT 5715
                               v  i     i           v     v       viiiivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_211195151_   5716 CTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTAC 5765
                             i  i  i  vi          v  i         vv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_211195151_   5766 AAGAAAAAAACAA----CCCCATCAACAAGTGGGCGAAGGATATGAACAG 5811
                           v     i    ----   v  i? v  i     i      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_211195151_   5812 ACGCTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAAT 5861
                           ii     v        i  vi viii     v ii          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_211195151_   5862 GCTCATCATCACTGGCCAT 5880
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


2830 26.78 1.31 2.08  chr2_211203158_211207021.rev     2460  3374 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_211203158_   2460 TGGAAAAACATTTTATGTTCATGGATAGGAAGAATCAATATTATTAAAAT 2509
                               i i  iii            v      v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_211203158_   2510 GGCCACACTTCCCAAAGCAAGCTACAGATTCAACACTATTCCTATCAAAC 2559
                            v i   i      vii v             i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_211203158_   2560 AACCAA-TGTCATTTTTTACAGAACTAGAAGAAACT-ATTCTACAATTCA 2607
                         vv   i-  i -      i     v v  v-  i  -  i   v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCA 148

  chr2_211203158_   2608 TATGGAACCAAAAAAGAGCTTGAGAAGCCAAAGGAATACTAAGCAAAAAG 2657
                                viiv  ii  v iv  iv       iv   vi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_211203158_   2658 AACAAAGCTGGAAACATAACATCACCCAACTT-AAAACTATACTATAAAG 2706
                                i    iivv v   iiv     i  -      -     i    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_211203158_   2707 CTACAGTAACAAAAACAGCATGCTACTGCTACAAAAACAGGCATATAGAC 2756
                                  iv  i    ii  v     vi i  ii i  i        i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_211203158_   2757 CAATGAAACAGAATAGAGAGCCCAGAAACAGTGCCACG----TACAGCCA 2802
                              i  i     v     i       i ivv   ii----  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_211203158_   2803 TCTGATCTTTGACAAACTCAACAAAAACAAGCAATGGGGAAAGAACTTCC 2852
                         vi    i  i     ivviiv   i v  vv              ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_211203158_   2853 TATTCAATAAATTGTCCTGGGATATCTGACTAGCCATATGCAGAAAAATG 2902
                          v     i    v  v      i v   iv  ?   i     i  i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_211203158_   2903 ACACTGGACTCCTACCTTTCACCATACACAAAAAGCCACTGAAGATGGAT 2952
                          vii     i       iv       i       viv   v  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_211203158_   2953 TAAAGATTTAA-TGTAAGACCTCAAACTATAAGAATCCTAGAAGAAAGCC 3001
                         i ?   ii   -       v  v         i v  i         i v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_211203158_   3002 TAAGAA-ACACCATTCTGGACATTGGCCTTGGGAAAGAATTTATGACTAA 3050
                           i ?i- v i -   vv   v    vi v  v  v iv  iv iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_211203158_   3051 GTCCTCAAAAGCACTTGCAACAGAAACAAAAATTCACAAGTGGGACCTAA 3100
                          v vi         vv      i  iv      vv i  i v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_211203158_   3101 TTAAACTAAAGAGCT---GCACAGCAGAAGAAACTATCAACAGAGTACAC 3147
                          i   v v  i i  --- ii vv  i i  v        v i   iv v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_211203158_   3148 AGACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCCAACAA 3197
                                 i                          ii  ii   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_211203158_   3198 AGGTCTACTATCTGGAATCTATAAGCAACTTCAACAATTCAACAGGCAAA 3247
                         i  v  vv    ii    v     iv    iiv    i    i ivv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_211203158_   3248 AACCAACTTAACCCCATTAAAAAACAGGCAACAGACATGGACAGACATTT 3297
                          iv   v -     v   ?     ii     vi  iv  i i        
  L1M4_orf2#LINE/    797 AGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_211203158_   3298 CTCACAAGAAGACATACAACGTATGTCTTCTCATATGTCAGCAAACATAT 3347
                            vv       i      ---   ----------- i  ii  i  i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAA---ATG-----------GCCAATAAGCACAT 881

  chr2_211203158_   3348 GAAATAATGCTCCACATAACTGTCAGA 3374
                             vi      v    v ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (140 / 101)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.21 (31 / 14)  


2662 29.80 0.88 0.77  chr2_211460409_211462862     1057  1962 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_211460409_   1057 GGAAAAAAAATCCATGCTCATAGATAGGAAGAATCAATATCATAAAAATG 1106
                              i v vi     i    i   v      v i     ii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_211460409_   1107 GTCATACTGCCTAAAGTAATTTATAGATTTAATGCTATTCCCATCAAGCT 1156
                          iv     v  i   v i  i  i     i  i  v  i  i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_211460409_   1157 ACCATTGACTTTCTTCGCAGAATTAGAAAAAAACTG----TAAATTTCAT 1202
                         v   vivi i  i  i      v v  v  i--   ----    v     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCAT 149

  chr2_211460409_   1203 TTTGGAACCAAAAAGAAGCTCATATAGCCAAGACAATTCTAAGCAAAAAG 1252
                         v -    viiv  i i v iviv        i     ii i iv  i   
  L1M4_orf2#LINE/    150 AT-GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_211460409_   1253 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1302
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_211460409_   1303 TACAGTAACCAAAACAGCATGGTACAGGTACTAAAACAGATATATAGACC 1352
                                 i   i    ii      v  i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_211460409_   1353 AATGGAACAGAACAGAGACCTCAGAATTAACACCACACTTCTACAACCAT 1402
                                i    iv    vii     v   vv   i  v i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_211460409_   1403 CTGATCTTAGACAAACATGACAAAAAAAAGCAATGGGGAAAGGATTTCCT 1452
                         i    i  v     ivi  v   i vv vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_211460409_   1453 GTTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATGTGCAGGAAACAAA 1502
                         v  i  i   i          v      v  ?   ii    ii i vvi 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_211460409_   1503 AACTGGACCCCTTCCTTATACCTTATACCAAAATTAACTCTTAGTGAGTT 1552
                          ii         v   i i   v     v           vv i  ii i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_211460409_   1553 AAAGACTTAAATGTAAAACCTAAAGCCATAAAAACCCTAGAAAAAAATCT 1602
                          ?    i         i v     i i      vi i     i    iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_211460409_   1603 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 1651
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_211460409_   1652 ACACCGAAAGCAATGGGAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1701
                              i      vvi v        vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_211460409_   1702 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAATGAACA 1751
                         i   v v  i i   i  ii vv    i  v       vv i i    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_211460409_   1752 GGCAGACTACAGAATGGGAGAACATTTTTGCAATCTATCCGTCTGACACA 1801
                          i  iv i              v  v       vii  vii     i vi
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_211460409_   1802 AGTCTAATATCTGGATTCTACAA-GAACT--TAAAACAAATTTACAAGAA 1848
                         i v  vi    ii  v v  i  -     --  v   --- iv i  v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAAC---TCAATAATAA 794

  chr2_211460409_   1849 AAAAACAACAAACCCCATCAAAAAGTGAGAGAAGGATCTCAACAGGTACT 1898
                            i    vv     v  i?    i  i vi      i v  i  ii i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_211460409_   1899 TCTCAAAGGAAGACATTGATAGGGCCAACAAACATATGAAAAACAGCGAA 1948
                             v  i     i  vv v v      i  i  i       ivv  vv 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_211460409_   1949 TCATCACTAATCGT 1962
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (152 / 114)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 1.88 (15 / 8)  


2540 21.48 0.67 13.39  chr2_211517356_211521641.rev     2757  3794 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_211517356_   2757 GAAAAACATCCCATGCTCATGTATTGGAAGAATCAATATTGTGAAAATGA 2806
                             i i        i     v         v i        v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_211517356_   2807 CCATAG-ACCCAAAGCAATCTACATATTCAGTAAAATTCTTACTAAAATA 2855
                          v   v-v      vii       v     iiiv   i i  ii     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_211517356_   2856 CC-GTGGTCATTTTTCACAGAATTTGAAAAACCAATCCTGAAATTCATAT 2904
                           - iv i -     ii     v    v  i ii     i          
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_211517356_   2905 GGAACCCAAAAAGAGCCTGATTAGCCAAAGAAATCCTAAGTGAAAAGAAC 2954
                             vivv  ii  v  v  v        iv    i i ivi i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_211517356_   2955 AAATCTGGAGGCATCACATTTACCTGACTTGAAATTATACTACAAGGCTA 3004
                            vi      vv     i  -  ii i  v   viv        i    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_211517356_   3005 TAGTAACCAAAACAGTATGATACTGATATAAAAATAAACACA--GACCAA 3052
                         i     i   i     i  i     ii    ii   i   i --  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_211517356_   3053 TGGAACAGAACACAGAGTGCAGAAATAAAGCCAACTACTTACAACAAACT 3102
                              i    ivv     v          v   vvi i   iiiiv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_211517356_   3103 GATTTTTGACAAAAAAGT-AAAAGCATACACTGGGTAAAGGACATCCTAT 3151
                               i     iiiv i-  i v   v  v    v    i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_211517356_   3152 TCAATAAATGATGCTGAGAAAATTGGATAGCCACATGCAGAAGAATGAAA 3201
                             i     i     i  v  i      ?         i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_211517356_   3202 TTGGATTCCTATCTTTTACTGTATATAAAAATTAACTCAAGCTGGATTA- 3250
                              ii    i  ivi  ii    i              iv     i -
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_211517356_   3251 AGTCTTAAATTTAAGATCTGAAACCGTAAAAATTCTACAAGAAAACCTAG 3300
                           v i     v     v  i    ii     v ii  v        v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_211517356_   3301 GAAAAACTCTTCAGGACTTTGGCCTAGGTAAAGAATTTATGACAAA-GAC 3349
                          ?iv  v     iv   i    vi    i  v i-   v v v v -   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGAC 599

  chr2_211517356_   3350 CCCAAAAGCAAATGCAATGAAAACAAAATAAATCAACCCACCTTAACAAA 3399
                         v         v v    i-    v    --   --------------- i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAAC-AAAAGAAAA--AAT---------------AG 631

  chr2_211517356_   3400 ATAAATCAGACCTACCTAATTAAACTGGAAATTTTCTGCACAGCAAAAGA 3449
                               ii   i -- --  i   v vi   vi  i  ii vv    i  
  L1M4_orf2#LINE/    632 ATAAATTGGACTT--C--ATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr2_211517356_   3450 AATAATCCACAGAATAAATAGACAACCTATACAATGGGAGAAAATATTTG 3499
                         v iv   v v i i i  v        i i v                  
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_211517356_   3500 CAAACTTTATAACTTTGATAAAGGACTAAAAGCCAGAATCTCAAACAAAA 3549
                             iiv    -- i      i     viv v       v vv  - i  
  L1M4_orf2#LINE/    728 CAAATCATATA--TCTGATAAGGGACTTGTATCCAGAATATATAA-AGAA 774

  chr2_211517356_   3550 CTGCAAGAAGATGCTTGACCCGGGAGGTGGAGGTTGCAGTGAGCCAAGAT 3599
                           -----------   ----------------------------------
  L1M4_orf2#LINE/    775 CT-----------CTT---------------------------------- 779

  chr2_211517356_   3600 CATACCACTGCACTCCAGCCTGGCAGACAGGGTGAGACTCCATCTCAAAA 3649
                         --------------------------   i-------------     v 
  L1M4_orf2#LINE/    780 --------------------------ACAA-------------CTCAATA 790

  chr2_211517356_   3650 ACAAAACAAAACAAAACAAAAACTGCAGGAAGAAAACAAATAATCCCATT 3699
                          i    --------------------------- i        i  v   
  L1M4_orf2#LINE/    791 ATAAAA---------------------------AGACAAATAACCCAATT 813

  chr2_211517356_   3700 AAAAAGTGGGCAAATGACATGAACAGACATTTCTCAAAAGCAGATATACA 3749
                         ?    i        v  iv    i           v    v         
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_211517356_   3750 AATGGCCAATAAACATATGAAAAAATGCTCATCACCAGTCAACAG 3794
                                     i  i       i       v  i  ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (132 / 88)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 7.30 (146 / 20)  


2655 28.59 1.32 1.21  chr2_211556168_211562059     4495  5400 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_211556168_   4495 GGAAAAATATTCTATGCTCATGGATAGGAAGAATCAATATCATGAAAAAG 4544
                              i    i i   i        v      v i     ii v  i v 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_211556168_   4545 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATTTAACT 4594
                           v     v      v i  i  i        i  v  i  i  iv  v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_211556168_   4595 ACCATTGACATTCTTCACA-AAATTAGGATAAACTG-TTTTAAAATTCAT 4642
                         v   vivi v  i  ii  -     --  i  i   - ii          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCAT 149

  chr2_211556168_   4643 TTGGAACCAAAAAATGCTCATA-TAGCCAAGACAATCCTAAGCAA-AAGA 4690
                         v     viiv  iivi i  v -       i      i i iv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_211556168_   4691 ATAAAGCTGGAGGCATCATGCTACCAGACTTCGAACCATACTACAAGGCT 4740
                          i    i      vv   ii  v  vi i   i  v v        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_211556168_   4741 ACAGAAACCAAAACAGCATGGTACTGGTCCAAAAACAGACACATAGACCA 4790
                             v  i   i    ii         ivi  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_211556168_   4791 ACAGACCAGAAGAGAGAACTCAGAAGTAAGACTGCACATCTACAACCATC 4840
                          ii  vi    vv    iii     i   iv iii    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_211556168_   4841 CGATCTTAGACAAACCTG--AAGAAAATAAGCAATGAGGAAAGGGTTCCC 4888
                         i   i  v     ivv  --    vv  --v     i      ii vvi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAATAGTC 397

  chr2_211556168_   4889 TATTTAATAAACAGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAATTG 4938
                          v  i  i   ii         v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_211556168_   4939 AAACTGGACCCCTTCCTTACACCTTATGCAAAAATTAACTCAAGATACAT 4988
                           ii         v   i     v   i               i  iv  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_211556168_   4989 TAAAGGCTCAAATGTAAAACCCCAAATTATAAAAACCCTGGAAGAAAATC 5038
                         i ?  i ii        i v iv   i       vi i i        iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_211556168_   5039 TAAGCA-ATACCATTCAGGACATAGGCATGAGCAAACATTTTAT-GACAA 5086
                           i ?i- v i -   iv   v v  vv ii    vvi   iv -  i v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_211556168_   5087 AATCACAAAAAGCAATTGCAACAAAAGCAAAAATCGACAAGTGGGATCTA 5136
                         i -   v       vvv          v      v  i  i v   ii v
  L1M4_orf2#LINE/    597 GA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_211556168_   5137 ATTAAACTAAAGAGCTTCTACCCAGCAAAAGAAACTATCATCAGAGTGAG 5186
                           i   v v  i i   i iiv vv    i  v       vv i     i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_211556168_   5187 CAGGCCATCTACAGATTTGGGGAAAACTTTTGCAATCTATCCATCTGACA 5236
                         v  i v i i     v v  i     iv       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_211556168_   5237 GAGGTCTCATATCCATAAGCCACAAGGAACTCAAACAAATTTACCAGAAA 5286
                         ii  v  ii      v  vvi i  i      vv    v ----  - v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT----CA-ATA 790

  chr2_211556168_   5287 ATAAAAA-ACAAAAAACCCCATTAAAAAATGGGCAAAGGAGGTGAACAGA 5335
                                -     v     v   ?                vv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_211556168_   5336 CCCTTCTC-AAAAAAGACATTCATTCAGTCAACAAACATGTAAAAAA--G 5382
                          vi     -   i    i  v  vvii i   i  i  ii i    i-- 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_211556168_   5383 CTCAACGTCATTGAATAT 5400
                               i   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (154 / 101)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 1.44 (23 / 16)  


2652 27.63 1.54 1.97  chr2_211579138_211584410     3870  4781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_211579138_   3870 TGGAAAC-CATTTCATGCTCATGGGTAAGAAGAGACAATATTGTTAACAT 3918
                               v-i  ii    i      i vi     vvi           v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_211579138_   3919 GTCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTTTCAAAC 3968
                          v v     v      vii  i           i  v  i   v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_211579138_   3969 TACCAAGGACGGTTTTTTACAGAATCAGAAATAAC-AATTATAAACTTCA 4017
                          v   ivvi v-      i     viv  v - i -i  iv    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chr2_211579138_   4018 TATAGAACCAAAAAAGAGCTCAAATAATCAAAACAATTCTAAGCAAAAAG 4067
                            i   viiv  ii  v ivi    ii         ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_211579138_   4068 AACCAAGCTAGAGGAATCTTACTACCTGACTTCAAACTATAATACAAGGC 4117
                            v   i i     v  vi   v  ii i      viv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_211579138_   4118 AAGCAA-AACCAAAACAGCATGGCGCTGGTACAAGAACAGACACAGAGAT 4166
                         v -  i-  i   i    ii   ii    i i   i i     i v    
  L1M4_orf2#LINE/    249 TA-CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_211579138_   4167 CAATGGAACAGGTTAGGGAATATGGAAATAAAGCTGCACACGTACAATTA 4216
                                 i  iv v i  i vii        v iii   iv  iii i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_211579138_   4217 TCTGATTTTTGACAGAGTTGACAATAACAAGCAATGGAGAAAGAACTTTC 4266
                         vi       i    ii v  v   v v  vv      i       ivv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_211579138_   4267 TATTCAATAAACAGTGCTGGCATATCTGGCTAGCCATATGCAGAAGTTTG 4316
                          v     i   ii       v i v    v  ?   i     i   vv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_211579138_   4317 AAACTGGATCCCTTCCTTTCACCATATGTAAGAATTTTCACCAATTCAAG 4366
                           ii    i    v   iv        ii  i    ------  i    i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATT------AACTCAAA 491

  chr2_211579138_   4367 ATTGATCAAAGACTTAAATGTAAAATCTAAAACTATGAAAACTCT-AGAA 4415
                           v     ?    i         i v          -        -    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAA 540

  chr2_211579138_   4416 GTAAACCTAGG---AAA----CACCACTCTGGAAATAAGCCCTGGCAAAA 4458
                          v    v    ---   ---- iiv  ii   i-- v  -----    vi
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAG-----GCAATG 583

  chr2_211579138_   4459 ATTTCATAATGAAGACTCCAAAAGCAATTGCAACAAAAACAAAAATTGAC 4508
                         i    v  ivv v   v         vvv         iv      v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_211579138_   4509 AAGTGAGA-TCCAGTTAGTCTAAAGAACTCTACACAGCAGAAGAAACTAT 4557
                           i vi  - i  viv ivi    i vi i iii vv  i i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_211579138_   4558 CAACAGAGCAAACAGACAATCTACAGAATGGGAGAAAAATTTTGCCAACT 4607
                            v i  ii  v      i i                vv     v  ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_211579138_   4608 ATACATCTAACAATGGTCTAATATCCAGTGTCTATAAGAAACTTAAAGAA 4657
                            i    i i  v  v  vi       vi v     ii    ivv v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_211579138_   4658 ATAAACAAGCAAATAGCAAACGACCCAATTAAAAAAATGGGCAAAAGACG 4707
                         v v  i  vv   vii    ii        ?     -        i  iv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATT 832

  chr2_211579138_   4708 TGAACAGACACTTCTCAAAAGAAGTCATACATGGAGCCAATAA--ACGTG 4755
                             i     i     v       vi     vivi        --  i  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_211579138_   4756 AAAAAATACTCAACATCACTAATCAT 4781
                             i  i          ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (144 / 105)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.00 (32 / 16)  


1986 25.27 3.87 7.62  chr2_211630731_211633178      660  1486 (962)    L1M4_orf2#LINE/L1        2   797 (111)  

  chr2_211630731_    660 GGAGAGGTATACTGTGTTCATGTATCTGAAAACTCAGTGTTGTTAGGATG 709
                            i  i   v ii        v  iv   i   i i i      i    
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_211630731_    710 GCATTTCTTCTTGAACTGCT-TATAGATTCAATTTAATTTCTATCCAAAC 758
                            v v  i iii  i  v -  i        ivi   ii     v   i
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_211630731_    759 ACTAGCATGCTTTTTAAATGAACATTGGCAAATTAATTATAATATTAATA 808
                         v i   -   i    vviiii v    i   ii i  iv   v   v   
  L1M4_orf2#LINE/    102 CCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_211630731_    809 TACAAATGCAAAAAACTTAAAATAGCAAAATGAACTTTGAGAAAGAA--- 855
                          iv        iii  ii i      v   vv  ii    i      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_211630731_    856 ---AGTGAGAAGGCTTACAGTATCAGGATTTAAATA-TTACTATAAATCT 901
                         ---   vi  i i  i   v -  vvi    v  v -      i   v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACT-TCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_211630731_    902 ACAGTAATCA-----------TATTGGCATAAAGATAGACATATGGAACA 940
                                   -----------  i        i           i  v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_211630731_    941 ACAGATAAGAATAAACATTCCATATACAGAAACACACGGACACACATACA 990
                          ii  vv     vi v v    ------    i v  -------------
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCA------GAAATAAAC------------- 330

  chr2_211630731_    991 CACACACACACACACACACTCATTAGCCACTAGATTTTCAACAAATGTGC 1040
                         ---------- -  i   i i  -i i  v v       i    iv    
  L1M4_orf2#LINE/    331 ----------C-CATACATTTAT-GGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_211630731_   1041 CATGATACTTCAATGGAGAAATAATATTCTTTTCAACAAATGGTATTTGA 1090
                           v  ivv        i    v    v                 ii v i
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_211630731_   1091 ACAACTGGGCATTGCTATACAAATAATATATTTTTTAAAAAACTCAATTT 1140
                                 ii ?ivvi  i    vi -  i---------  ii vi iii
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGA-ATG---------AAGTTGGACCC 458

  chr2_211630731_   1141 TTAATGTACTCGATTGTACATTATATACAAAAGTTAACTCAACCTGGATC 1190
                         i  v----   ------   ii          i         vv      
  L1M4_orf2#LINE/    459 CTAC----CTC------ACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_211630731_   1191 CTATAACTAAATCTAAGAACTAAAATTATAAAATGTATCAAGGAGAAAAT 1240
                         v? v v      v     i      i       iviv --  i      i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT--AGAAGAAAAC 546

  chr2_211630731_   1241 ACAGGAGAAAATTGATAGGACCTTGGATTAGGCATAGATTTTATATATAG 1290
                          i   ? v    ivviiv        i       vv i   iv  v   v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_211630731_   1291 GTCATGTCAA---TGCAAATTATTTTCAAAAGT-----TTGATAAATCCT 1332
                          v  i--   ---ii   iiv ----      v----- v       ivv
  L1M4_orf2#LINE/    597 GACAC--CAAAAGCACAAGCAA----CAAAAGAAAAAATAGATAAATTGG 640

  chr2_211630731_   1333 ATTTTATTAGAGTTAAAAACCTCTATTCTTCAAAA-ACTTTGTTAAGAG- 1380
                          i  i  i i i        i i i v       i-  vi i i    i-
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_211630731_   1381 TTGAAAAGGCAGGCCATA-ACTGGGG--AAATATTTGTAAAACATACACC 1427
                         v       i  iv   i - v    i--         i   v    i i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_211630731_   1428 TGATAAAAATACTTATATCCATAATATATCATAGAACTCTTGCAACTCAA 1477
                               iii-    i      v       v -         i        
  L1M4_orf2#LINE/    741 TGATAAGGG-ACTTGTATCCAGAATATATAA-AGAACTCTTACAACTCAA 788

  chr2_211630731_   1478 TAATAAAAA 1486
                                  
  L1M4_orf2#LINE/    789 TAATAAAAA 797

Transitions / transversions = 1.64 (128 / 78)
Gap_init rate = 0.03 (25 / 796), avg. gap size = 3.80 (95 / 25)  


3203 26.87 0.66 0.66  chr2_211669262_211678170.rev     3081  3988 (4921)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_211669262_   3081 TGGAAGAACATTCCATGCTCATGGACAGTAAGAATCAATATTGTGAAAAT 3130
                              ii i  i     i       iv v    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_211669262_   3131 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3180
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_211669262_   3181 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3228
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_211669262_   3229 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 3278
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_211669262_   3279 AACAAACCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3328
                               vi      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_211669262_   3329 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3378
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_211669262_   3379 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 3426
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_211669262_   3427 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3476
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_211669262_   3477 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAAGCT 3526
                           v  i  i              v      v  ?   i i i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_211669262_   3527 GAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTCAAGATGGA 3576
                            ii    i    v   i    iv              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_211669262_   3577 TTAAAGACTTAAACGTTAGACCTAAAACCATCAAAACCCT-AGAAGAAAA 3625
                          i ?    i    i  v   v       i  -     i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chr2_211669262_   3626 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 3674
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_211669262_   3675 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3724
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_211669262_   3725 AATTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACCACCATCAGAGTGA 3774
                         v  i   v v  i i   i vii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_211669262_   3775 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 3824
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_211669262_   3825 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 3874
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_211669262_   3875 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGAATATGAACAGACACT 3924
                            i     i     v  i?    i    ii   i  v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_211669262_   3925 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 3974
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_211669262_   3975 TCATCACTGGCCAT 3988
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  

3048 28.59 0.55 0.44  chr2_211669262_211678170.rev     7512  8417 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_211669262_   7512 GGAAAATCGTTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAATG 7561
                              ivii i     i        v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_211669262_   7562 GCCATACTTCCCAAAGTAATTTATTAATTCAGTGCTATCCCCATTAAGCT 7611
                           v     i      v i  i  ivi     ii  v     i  i  iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_211669262_   7612 ACCATTGACTTTCTTCACAGACTTGGAAAAACT-ACTTTAAATTTTATAT 7660
                         v   vivi i  i  ii    vv v  v  i  - iii    v  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_211669262_   7661 GAAACCAAAAAAGCGCCCACA-TAGTCAGGACAATTCTAAGCAAAAAGAA 7709
                          i  viiv  ii -i    v -   i  ii     ii i iv  i     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_211669262_   7710 CAAAGCTGGAGGCATCACGTTACCTGACTTCGAGCAA--TATTACAAGGC 7757
                              i      vv    ii v  ii i   i --  --  i     i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAA--AACTTACTACAAAGC 248

  chr2_211669262_   7758 CACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 7807
                         i       iv  i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_211669262_   7808 AGTGGGACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACTAT 7857
                          i   i i    iv   ivii         vv   i    i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_211669262_   7858 CTGATCTTTGACAAACCTGACAAAAACAAGCAACGGGGAAAGGATTTCCT 7907
                         i    i  i     ivv  v   i v  vv   i        i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_211669262_   7908 ATTTAATAAATGGTGTTGGGAAAAGTAGCTAGCGATATGCAGAAAAGAGA 7957
                         v  i  i        i     v  v i v  ? v i     i  i iv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_211669262_   7958 AACTGGACCCCTTCTTTATACCTTATACAAAAATTAACTCAAGATGGATT 8007
                          ii         v i i i   v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_211669262_   8008 AAAGACATAAATGTAAGACCCAAAACCATAAAAACCCTAGAAGAAAACCT 8057
                          ?    v           v i     i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_211669262_   8058 AGGT-TATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 8106
                            ?-  v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_211669262_   8107 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 8156
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_211669262_   8157 TAAACTAAAGGGCCTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 8206
                         i   v v  iii i i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_211669262_   8207 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTGTCCATCTGACAAA 8256
                          i     i                 v       viii vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_211669262_   8257 GGGCTAATATCCCGAATCTAAAAAGAACTTAAACAAATTTACAAGAAAAA 8306
                           i  vi     v    v  v        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_211669262_   8307 AACAAACAACCCCATAAAAATGTGGGTGAAGGGTACGAACAGACACTTCT 8356
                         i     i     v  v?   vi    ii    i vi   i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_211669262_   8357 CAAAAGAAGACATTTATGTAGCCAACAAACTTATTAAAAAATGCTCATCA 8406
                          v        i  vi vi i     i  i vi  v    i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_211669262_   8407 TCACTGGTCAT 8417
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.60 (157 / 98)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 1.29 (9 / 7)  


2848 25.68 3.73 1.02  chr2_211709612_211714130.rev     3144  4027 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_211709612_   3144 TGGAAATACATTCCATGCTCATGGAGGGGTAGAATCAGTATTGTGACAAT 3193
                               v i  i     i       vv  v   v i i      v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_211709612_   3194 GACGATACTGCCAAAAGCAATCTACAAATTCCATGCAATATCCATCAAAA 3243
                          i i     v  v   vii       i    v i     vi i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_211709612_   3244 TACCACCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAAGTCATA 3293
                          v   v vv v  i  ii     v v  v  ivii         v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_211709612_   3294 TGGAACCAAAAAAGGGCCTGAATAGCCAAAGTAA----GACAAAGCGAAA 3339
                              viiv  ii iv  v           ii  ----  v    ---- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG----A 196

  chr2_211709612_   3340 AGAACAAATCTAGAGGCAC-CACATTACCTGACTTGAAACCGTACTATAA 3388
                                 vi i    -  -    i v  ii i  v   v v     i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_211709612_   3389 GGCCATAGTCACCAAAACGGCATGGTACTGGTATAAAACTAGGCACATAT 3438
                         i  i i   v i   i  i ii         i    iiv   i  i   v
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_211709612_   3439 ACCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAGC 3488
                          i        i     v    ii           v   v i i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_211709612_   3489 CAACTGATCTTTGACAAAGCAAACAAAAACA--AAATGAGGAAAGGACAC 3536
                            i    i  i     i vviv   i v  --v    i      i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_211709612_   3537 CCTGTTCAACAAATAGTGCTGAGATAACTGGCAAGCCACATGTAGAAGAA 3586
                         i  v          i      i  i      vv ?       i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_211709612_   3587 TGAAACCAGATTCTCACCTCTCACCTCATACAAAAATCAACTCATGATTG 3636
                             iiii  ii ii     v    vi          i      vi  v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_211709612_   3637 ATCAAGGACTTAAATCTAAGACCTGAAACAATAGACATTCT-AGAAGATA 3685
                             ?i   i     v     v  i    v   i - i   -      v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAA 544

  chr2_211709612_   3686 ACATCAGAG-AAATCCTTTTAGTCATTGGCTTAGGCCAAGACTTCTT-GA 3733
                             vi ? -     i iv iii -    v      v v ii     -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_211709612_   3734 TCAAGAACCCAAAAGCAAATGTAACAAAAACAAAAATAAATACATGGGAC 3783
                          - v  vv         v v i       iv       i   v  v    
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_211709612_   3784 TT-----AAGCTAAAAAGCTTCTACATAGAAAAAGAAACAATCAGCAGAG 3828
                           -----  ii      -   i iiiivvv   i  v  v    iv i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_211709612_   3829 TAAACAAACAATCTACAGAGTGGGAGAAAATCCTTACAATCTATACATCT 3878
                          i  v i    i i     i           vi  i   vii   i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_211709612_   3879 GACAAATGACTAATATCCAGAGTCTACAAGGAACTC----AAATAAATAA 3924
                           i  iv    vi        i v  i  i      ----  v v     
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_211709612_   3925 GAAAAAAA-----AATCTCATCAAAAAGTGGGCGAA--------ATAGAC 3961
                         v     i -----  i iv  i?    i     i  --------      
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_211709612_   3962 TGTTCTCAAAAGAAGATATGCAAATGGCAAACAAACATATGAAAA-ATGC 4010
                         vv     v           i        v  i  i  i       -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_211709612_   4011 TCAATATCACTAGGAAA 4027
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.47 (42 / 17)  


2404 26.88 1.50 0.82  chr2_211788609_211790323.rev      497  1229 (486)    L1M4_orf2#LINE/L1      171   908 (0)  

  chr2_211788609_    497 AACAGTCAAGGCAATCCTAAGCAAAAAGAACAAAGCTAGATGCATCACAT 546
                           i  i   ii     i i iv  i          i i  v vv     i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_211788609_    547 TACCCAAATTCAAATTACACTCTAAGGCTGCAGTAACCAAAAAAGCATGG 596
                          v     v      vivi   vi  i   i      i   i v  ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_211788609_    597 TACTGGTACAAAAACAGCCTCATACACCAATGACACAGAATAGAGAGACC 646
                               i i  ii i  v vi   v i     iv i     v     v  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_211788609_    647 AGAAATAGTGCTGTACATCTACAA-CAATCTGATCTTCAACAAACCTGAT 695
                                ivv ii     i  iii-    -    i   i    ivv  vi
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAAT-TGATTTTCGACAAGGGTGCC 369

  chr2_211788609_    696 AAAAATAAGCAAATGGGAGAGGAACAATTT----AATAAATTGTCCTGGG 741
                           i vi vv   -    ii i   i i i ----  i    v  v     
  L1M4_orf2#LINE/    370 AAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_211788609_    742 ATAACTGGCTAGCAATATGCAGAAGACTGAAACTGGACTCCTACCTTACA 791
                          i      v  ? v i     i    v    ii     i       i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_211788609_    792 TCATATACAGAAATTAACTCAAGATGGATTAAAGAGTTACATGTAAAACC 841
                         i        i            i      i ?   vi  v      i v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_211788609_    842 TGAAACTACAAAAACCCTGGAAGAAAACCCAGG---AAATACCATTCCG- 887
                          i      i    vi i i         vi   ---    ----i i  -
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT----CTTCGT 564

  chr2_211788609_    888 GACGTAGGCCCTGGCAAAGATTTCATGACAAAGATGCCAAAAGCAATTAC 937
                            v v  viiv     v i    v iivv v  ii         vvvi 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_211788609_    938 AACAAAAACATAAATGGACAAATGGGACCTAATTACACTAAAGAGTTTCT 987
                                iv v    i  i    v    i v  i v v v  i ii  i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_211788609_    988 GCACAGCAAAAGAAACTATCAACAGAGTAAATAGACAACCTAGAGAATGG 1037
                          ii vv    i  v        v i   i  v        i v       
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_211788609_   1038 GAGAAAATATTTGCAAAGTATGGATCTGACAAAGGTCTAATATCAAGACT 1087
                                          vi  iv      i  i  v  vi    v   v 
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_211788609_   1088 CTATAAGAAACAA--ACAAATCAACAAACATGAAACAAACAACCCCATCA 1135
                         v     ii   vv--    v    i  vv vi i     i     v  i?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_211788609_   1136 AAAAGTGGGCAAAGGGCTCGAAAAGACACTTTTCCAAAGAAGACATGCAT 1185
                             i          ii i   v     i  i           i  i  v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_211788609_   1186 GTGGCCAATAATCATATGAAAAAATGCTCAAGGTCACTAATCAT 1229
                         i          v  i       i        vi   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (117 / 77)
Gap_init rate = 0.01 (8 / 738), avg. gap size = 2.12 (17 / 8)  


 800 27.74 14.49 3.18  chr2_211790475_211792038      509  1074 (490)    L1M4_orf2#LINE/L1      279   908 (0)  

  chr2_211790475_    509 TAAGGGGAAA-AGATATATGAAAGGAACAGAA--GAGAGTGCAGAAATGG 555
                              iv i - v   v  v  v    i    --      v       ii
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_211790475_    556 ACCT-CACATACACAACCTCTTGATTTACACCAGAAGCACCAATGCACTT 604
                            i-i    vi iiii vv       v iv  iii ii    vi vv  
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr2_211790475_    605 CAAAGGGAAAATAAATA-TCTTCAAAATAAATGGTATTGGAGCCATGGGA 653
                            v   i   -i    -    ivv  i       ii   ii v iv   
  L1M4_orf2#LINE/    379 CAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_211790475_    654 TATTCATAAAAAATTATAAATAAATAAA--TAAACCCTATATGCTCCTTT 701
                           ?i  i ------ ii   vi   i  -- ii    ------  v i i
  L1M4_orf2#LINE/    428 TAKCCACA------TGCAAAAGAATGAAGTTGGACCC------CTACCTC 465

  chr2_211790475_    702 ACATTACACAGGGAAATTAAGTT-------------GACTTAACTGTAGT 738
                            ii i i vii       v i-------------   i   v    iv
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_211790475_    739 AGTTAAAAGTATAA---TTTTCCCATAAAACATAAAAGAATATCTTCATG 785
                           i     v     --- i  vvv v        ii? v v      i  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr2_211790475_    786 GAATTAGATT-GACAAAGATTTCTTATACAAAGCAACAAAATCCCTAGCT 834
                         ivv  i i  - i   v i       v i vii  v     v v v   v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr2_211790475_    835 ACGAAAAGAAAAAATAACCTGGTAAATTGTAATTTACCCAACTTGTACA- 883
                           -             ---- i       v v  i i v  v  iv v -
  L1M4_orf2#LINE/    616 AC-AAAAGAAAAAATA----GATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr2_211790475_    884 TTTTAT-CATCAAAAGATACCATTAAGAAAGTAAAAATGTAAGCATCAGA 932
                             i - v     i  i  i  i        i    vii  v vv    
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_211790475_    933 CTGGG-GAAAATAC------ATAATA-----GACAAAGAACT-GCACATG 969
                         v    -       i------  v   -----  i  i i   - i ivii
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_211790475_    970 TAATATATATTAAACT--TACAA-----TACGAAAAAGG------ACC-- 1004
                         v        vvi    --     -----  vv      i------   --
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_211790475_   1005 ----AAAAATGGCCAAAAGA---GAATA------TCCC------------ 1029
                         ----        v    i  ---     ------  i ------------
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_211790475_   1030 ---AATGGACAATAAACATATGAAAATGCGCTTAATATAATTAATCAG 1074
                         ---     v      i  i       vii   i  i  v ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (90 / 65)
Gap_init rate = 0.04 (26 / 630), avg. gap size = 3.85 (100 / 26)  


3225 26.80 0.89 0.33  chr2_211909052_211915325     4880  5782 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_211909052_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_211909052_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCACTGCCATCCCCATCAAGC 4979
                            v     v     iv i  i          vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_211909052_   4980 TACCAA-TGCCTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCAT 5023
                          v   i-       i  -i     v v  v  i--- --     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_211909052_   5024 ATGGAACCAAAAAAAAGTCCGCATCACCAGGTCAATCCTAAGCCAAAAGA 5073
                               viiv  iii vi v v  vi   iiv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_211909052_   5074 ACAAAGCTGGAGGCATCACACTACCTGACTTCAGACTATACTACAAGGCT 5123
                               i      vv       v  ii i    i viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_211909052_   5124 ACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5173
                           i    i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_211909052_   5174 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTA 5221
                               i    i--    i  --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_211909052_   5222 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5271
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_211909052_   5272 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5321
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_211909052_   5322 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5371
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_211909052_   5372 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5421
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_211909052_   5422 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAA 5471
                             ?i v viv   iv   v v  vv i     v ii   v ivvi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_211909052_   5472 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5521
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_211909052_   5522 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5571
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_211909052_   5572 GGCAACCTACAAAATGGGAGAAAATTTTCGTAACCTACTCATCTGACAAA 5621
                          i     i   i             v  i i  vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_211909052_   5622 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5671
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_211909052_   5672 AACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAAGAGACACTTCT 5721
                         i     i     v  i?    i     i     iv    v     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_211909052_   5722 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5771
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_211909052_   5772 TCACTGGCCAT 5782
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


2620 27.91 2.09 2.31  chr2_212052610_212054711      701  1610 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_212052610_    701 TGGAAAAACATTCCATGCTCATGGATAGGATGAATCAATATTGTAAAAAT 750
                               i i  i     i        v   v  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_212052610_    751 GACCACACTGCCTAAAGCAATTTATAGATTCACTGCTATTCCCGTTAAAC 800
                          i v i   v  i   vii  i  i       vi  v  i  ii i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_212052610_    801 TACCATTGACGTTCTTCACAGAATAAGAAAAAAGCT-ATTTTAAAAGTAA 849
                          v   vivi v  i  ii     -- vvi v     -  ii     v v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr2_212052610_    850 TATGGCATCAAAAAAGAGCCCAAATAGCCAAGGCAATCCTAAGCAAAAAG 899
                              v viiv  ii  v  vi         ii     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_212052610_    900 AACAAAGTTGGAGGCATCATGCTACCTAACTTCAAACTATACTACAGGGC 949
                                       vv   ii  v  i  i      viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_212052610_    950 TACAGTAACCAAAACAGCATGGTACTGGTACACGCACAGACACGTAGACC 999
                                 i   i    ii         i i v v i     ii    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_212052610_   1000 AATGGAACAGAATAGAGAACCCAGAAATAAGACTGCACCACTACAACCAT 1049
                                i     v    ii          iv iii  vvi  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_212052610_   1050 TTGATCATCAACAGAACTGACAAAAAAAACAAAAAAGCAATGGGGAAACA 1099
                              iv  i   iiiv  v   i vv vi-------           v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATT-------CAATGGGGAAAGA 391

  chr2_212052610_   1100 TT--TCCTCATTTAGTAAATGGTGCTGGGAGAACTGGCCAGCCATATGTA 1147
                         v --  i --  i ii              v      vi ?   i   i 
  L1M4_orf2#LINE/    392 ATAGTCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_212052610_   1148 GAAAATTGAAACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCA 1197
                         i  i v    ii         v   i                 i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_212052610_   1198 AGGTAGATTAAAGATTGAAATGTAAAACCCAAA-CTATAAAGACCCTAGA 1246
                          ii i   i ?   iiv        i v i   -       ivi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_212052610_   1247 AGAAAACCTAGGCAATACTTACAAT--TCAGGGCATAGGCATGGGCAAAG 1294
                                v    ?i-----  -   --  iv i v v  vv i     v 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNG-----TA-AATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_212052610_   1295 ATCTCATGGACAAAGATGCCAAAAGCAATTGCAACAAAAGTGTCAGTTGA 1344
                         i i  v i  i v-  ii         vvv          vivv i v  
  L1M4_orf2#LINE/    584 GTTTCTTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_212052610_   1345 CAAGTGGGATCTAATGAAACTAAAGAGAATCTGCACAGCAAAAGCAACTA 1394
                         i  i v   ii v  v   v v  i ivv i  ii vv    i vv    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr2_212052610_   1395 TCAA-----T----AGACAACATACAAAATGGGAGAAAATTTTTGCAA-- 1433
                             ----- ----       vi   i             v       --
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_212052610_   1434 CCTATTCCATATGACAAAGGTCTAATATCCGGCATCTACGAGGAACTTAA 1483
                          v   ---  v   i  i  v  vi     i v  v  ii i     ivv
  L1M4_orf2#LINE/    733 CATAT---ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_212052610_   1484 ACAAATTTACAAGAGAAAAACAAACAATCCA-TTATAAGGTGGGCAAAGG 1532
                             v iv i  v i   i     i  i   -  ?v  ii          
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_212052610_   1533 ATATGAACAAACACTTCTTAAAAGACAACATACATGCAGGCAGCAAACAT 1582
                           v    i i   i    iv     vi i     viii v  ii  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_212052610_   1583 ATGAAAAAA-ACTCAACATCACTGATCAT 1610
                                i -i          ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (152 / 98)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.50 (40 / 16)  


 777 29.60 0.00 0.00  chr2_212194647_212199118     3040  3262 (1210)    L1M4_orf2#LINE/L1      196   418 (490)  

  chr2_212194647_   3040 AAGAACAAAGCAGGAGGCATCACATTGCCCAACTTCAAGCTATGCTATAA 3089
                                   iv     vv     i v     i     iviv i   i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_212194647_   3090 GGCTACAGTAACAAAAACAGCATGGTACAGGAAGAAAAACAGATACATAG 3139
                         i          iv  i    ii      v  v v  ii i   i i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_212194647_   3140 ACCAGTTAAACAGAATAGAGAACCCAGAAATAATCCCACATACCTACAGC 3189
                          i  i vi  i     v    ii          v    i i ii  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_212194647_   3190 CATCTGATCTCTGACAAAGTTGACAAAAATAAGCAATGAGGACAGGACTT 3239
                           vi    i ii     i v  v   i vi vv     i   v  i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_212194647_   3240 CCTATTCAATAAATGATGCTGGG 3262
                         i  v     i     i       
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGG 418

Transitions / transversions = 1.87 (43 / 23)
Gap_init rate = 0.00 (0 / 223), avg. gap size = 0.00 (0 / 0)  

2432 25.63 1.81 0.56  chr2_212194647_212199118     3263  3980 (492)    L1M4_orf2#LINE/L1      182   908 (0)  

  chr2_212194647_   3263 CAATCCTAAGCAAAAAGAGCAAAGCTGGAGGCATCACACTACCTGACTTC 3312
                              i i iv  i    i     i      vv       v  ii i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_212194647_   3313 AAACTATACTATAAGGCTACAGTAACCAAAACAGCATGGTAGTGGTAACA 3362
                            viv     i  i          i   i    ii     v   i vv 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_212194647_   3363 AAACAGATATATAGACCAATGGAACAGAATAGAGACCTCATAAATAACAC 3412
                         ii i   i       i        i     v    vii  v      vv 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_212194647_   3413 AACACATCTACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAA 3462
                         v i    i  iiii  vi    i  i     ivv  v   i v  vv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_212194647_   3463 TGGAGAAAGGATTCCCTATTTAATAAAAGGTTCTGGGAAAACTGGCTAGC 3512
                            i     i  vvi  v  i  i   v   v      v      v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_212194647_   3513 CATATGCAGAAAACTGAAACTGGACCCTTTCCTTACACCTTATACACAAA 3562
                           i     i  i v    ii       i v   i     v      v   
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_212194647_   3563 TTAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCTAAATCATAAAA 3612
                                  i      i ?    i         i v iv   ii      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_212194647_   3613 ACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCA 3661
                         vi i           v    ?i- v i -   iv   v v  vv i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chr2_212194647_   3662 AAGACTTCATGACTAAAACACAAAAAGCAATTGCAACAAAACCCAAAATT 3711
                          v ii   v iiv  vi    v       vvv         vvv     v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_212194647_   3712 GACAAATGGGATCTAATCAAACTAAAGAGCTTCTGCACAGCAAAAGAAAC 3761
                           i    v   ii v      v v  i i   i  ii vv    i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_212194647_   3762 TATCATCAGAGTGAACAGACAACCTACAGAATGGGAGAAAATCTTTGCAA 3811
                              vv i      v        i                 v       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_212194647_   3812 TCCACCCATCAGACAAAGGTCTAATATCCAGAATCTACAAGGAACT--TA 3859
                         vi  ivi   v  i  i  v  vi          v  i  i     --  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_212194647_   3860 -AATTTA-CGAGAAAAAAACAA----CCCCATCAAAAAGTGGGCGAAGGA 3903
                         -  i i -ii v     i    ----   v  i?    i     i     
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_212194647_   3904 TATGAACAGACATTTCTCAAAAAAAGACATTTTGCA----GCCAACAAAC 3949
                          v    i           v   i    i  ---i  ----     i  i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATAT---ACAAATGGCCAATAAGC 877

  chr2_212194647_   3950 ATATGAAAAAAAGATCATCATCACTGGTCAT 3980
                          i       i v v   v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (101 / 79)
Gap_init rate = 0.01 (8 / 727), avg. gap size = 2.12 (17 / 8)  


 869 25.50 1.20 2.79  chr2_212217748_212222301     2842  3092 (1461)    L1M4_orf2#LINE/L1        1   247 (661)  

  chr2_212217748_   2842 TGAAAAGATACTCCATGTTCATGAACCAGA-TATTCAATATTGTTAAAAT 2890
                           i       ii           i iii  -v i i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_212217748_   2891 GTCTAGACTACAATACCTAAAGCAACCTACAGATTCAATGCAATCCTTAT 2940
                          v v v   - ----  i   vii i            i       i   
  L1M4_orf2#LINE/     51 GGCAATACT-C----CCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_212217748_   2941 CAAAATACCAACGATATTTTTCACAGAAATGGAAGAAACAATCTTAAAAT 2990
                               v   i viiv     ii       v  vi ivii   i      
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_212217748_   2991 TTATATGGAACCATAAAAGACCCAGAATAGCCATAGCTAACCTAAGCAAA 3040
                          i        viii  ii               v i v v i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_212217748_   3041 AACAACAAAACTGAAGGAATCACATTACCTGACTTCAA--CTTACACTAC 3088
                           v      ii  i    v     i v  ii i     --     --   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TAC 243

  chr2_212217748_   3089 CAAG 3092
                         v   
  L1M4_orf2#LINE/    244 AAAG 247

Transitions / transversions = 2.20 (44 / 20)
Gap_init rate = 0.02 (5 / 247), avg. gap size = 2.00 (10 / 5)  

2455 25.78 1.34 0.60  chr2_212217748_212222301     3392  4062 (491)    L1M4_orf2#LINE/L1      233   908 (0)  

  chr2_212217748_   3392 AAATTATATTACAGAGCTCTAGTAACCAAAACAGCATGGTACTCACATAA 3441
                            i -  i    i    vi     i   i    ii       vi     
  L1M4_orf2#LINE/    233 AAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_212217748_   3442 AAACAAACATGTAGACCAGTGGAACAAATTAGAGAACCCAGAAATAAATC 3491
                         ii i i    i    i  i     i i v v    ii           i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_212217748_   3492 CACACATCTATAGTAAACTCATTTTTGACAAAGGTACCAAGAACATACTT 3541
                           i    i   i  v  i v     i     i   i      v   v vv
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_212217748_   3542 TGGGAAAACGACAGTCCCTTTTATAAATGGTTCTGGGATAGCTAGATATC 3591
                             i   vi i    ii  iv i       v      i i  i    ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_212217748_   3592 CATATCTACAAGAATTAAACTAGACCC-TATCTCTTACCATATTAAAAAA 3640
                           i  vi v      v  ii i     -  i   vi       vv     
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_212217748_   3641 TCAAATTTTACAGTGGATTAAATACTTAAATCGAAGACATCAAAGTATGA 3690
                          i  --i i v i     i ? v  i     vv    vv v   v   i 
  L1M4_orf2#LINE/    482 TTAA--CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_212217748_   3691 AACTATTAAAATAAAACATTGGGGACACGTTTTGAGACACTGGAGTGGGC 3740
                             v   i  v       v  ? vv vvi  i v   vi   iv i   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_212217748_   3741 AGAGATTTATTGAGTAATACTCTGCAAGCACAGGTAACCAGAGCAAAAAA 3790
                          iv i   v  iii  vv  v iiv       i i   v i  v     v
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_212217748_   3791 GGACACATGGGATCACAT-GAAGTTAAAAAGCTTTTGCACAGCAAAGGGA 3839
                         i  i v  v   iiv   -i  i       -      ii vv      iv
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chr2_212217748_   3840 ACAATCAATAAAGTGAAGAGACAACCCACAGAATGGGAGAAAATATTTGC 3889
                           v     v        i                                
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_212217748_   3890 AAACTATCCATCTGACAAGGGATTAATAACCAGAA-------GGAACTCA 3932
                            ii  vi      i      i vi  v      -------i      v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_212217748_   3933 AACAACTCTATAGGAAAAAATCTAATAATCTGTTCAAAAAATGGGCAATA 3982
                         v       v   iv     iv v     i iiv i?            vi
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_212217748_   3983 GATCTGAACAGACATTTCTCAAAAGAAGACATGCAAATGGTAAACAGTTA 4032
                            i    i           v        i  i       iv  i ivi 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_212217748_   4033 CATGAAAAGGTGCTCAACATCATTGATCAA 4062
                                  i            ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (101 / 68)
Gap_init rate = 0.01 (6 / 676), avg. gap size = 2.17 (13 / 6)  


2392 27.91 1.13 1.38  chr2_212246461_212248256      506  1304 (492)    L1M4_orf2#LINE/L1      112   908 (0)  

  chr2_212246461_    506 TTCTTCACAGAACTAAAGAAAACT-ATTTTAAAATTCATATGGAACCAAA 554
                           i  ii     v vi v  i-  -  ii                viiv 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_212246461_    555 AAAGAGCCTGAATAGCCAAAGCAATTCTAAGCAAAAAGAACAAGGCTGGA 604
                          ii  v  v           i    ii i iv  i        i i    
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_212246461_    605 GGCAC-CATGTTACTCAACTTCAAGCTATACTACAGGGCTATGGTATCCA 653
                           -  -  iii v i   i     iviv       ii    ii   vi  
  L1M4_orf2#LINE/    211 GG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_212246461_    654 ACACAGCATGGTACTGGTACAAAAACAGACACATAAACCAATGGAATAGA 703
                          v    ii         i i  ii i     i   i i            
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_212246461_    704 AGAAAGAACCCAGAAATAAGGCTGCATACCTTCA--ACTATCTGATCTTT 751
                          vvi   ii          iv --     v  i --iii vi    i  i
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCAATTGATTTTC 357

  chr2_212246461_    752 GACAAACCTGACAAAAAACAAGCAATGGGGAAAAGATTTCCTATTTAATA 801
                              ivv  v   i v-  vv           ii  vvi  v  i  i 
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_212246461_    802 AATGGGGCTGTAATAACAACTGCCTAGCCATATGGAGAAGATTGAAACTG 851
                              v    vi ---      vv  ?   i   v i    v    ii  
  L1M4_orf2#LINE/    407 AATGGTGCTGGGA---CAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_212246461_    852 GACCCCTTCCTTACACCATATACAAAAATCAACTCCAGATAACTTAAAGA 901
                                v   i                 i     v i  iiv i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_212246461_    902 TTGCATTGTAAAACCCAAAACTATAAAAACCATGGAAGACAACGTAGACA 951
                         iivv v     i v i            vi v i     v   i   i?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_212246461_    952 -ATACCATTCAGGACATAGGCATGGACAAAGATTTCAT-GATGAAGATAC 999
                         - v i -   iv   v v  vv i i   v i    v -   - v  i  
  L1M4_orf2#LINE/    554 TAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACAC 601

  chr2_212246461_   1000 CAAAAGGAATTGCAAGAAAAACAAAAATTGACAAGTGGGGTCTAATTAAA 1049
                               v vvv    v    iv      v  i  i v  iii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_212246461_   1050 -TCAAAGAGCTTCTTCACTGCAAAAGAAACTATCCACAGAGTGAAAAGAT 1098
                         - i   i -   i vii  v    i  v      v v i          i
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_212246461_   1099 AACTTACAGAAAGGGAGAAAATTTTTGCAAACTATGCATTCAACAAAGAT 1148
                            ii      v          v        ii  ii  iii i  i iv
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_212246461_   1149 CTAATATCTAGCATCTATATGGAACTTAAACAAATAGACAAGAAAAAAAC 1198
                           vi    i  v  v    vi     ivv    v vi i  v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_212246461_   1199 AGA--ACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAA 1246
                          i --    v   ?    i           iv    i     i  i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_212246461_   1247 AAGAAGTCGTACACGCAACCAGCAAGCATATGAAAAAAAGCTCAACATCA 1296
                               vii    viiii   ii     i       i v           
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_212246461_   1297 CTGATCAT 1304
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.61 (135 / 84)
Gap_init rate = 0.02 (15 / 797), avg. gap size = 1.33 (20 / 15)  


1665 30.30 2.99 1.63  chr2_212373675_212377595.rev     1608  2343 (1578)    L1M4_orf2#LINE/L1       13   758 (150)  

  chr2_212373675_   1608 CTGTGTTCCTGTATTGAATAGCTCAAAATCATAAAGATGTCAATTCTCCC 1657
                          ii     v  v    i vii  i  v  ii v      v    v     
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr2_212373675_   1658 TAAACTGATATACAGCTTTAGTACAATTCTTATCAAAATATCAAAAAGGT 1707
                         i   i    v     v  i iii    i i         vi  ivvivv 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_212373675_   1708 TTGTTG-AGATAGAGACAAGATTATTATACAATTTGTATGGAAAGGCAAA 1756
                           v   -   v vv      v v  iv  v    ii        v    i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_212373675_   1757 CAAGTTAGTCCAACTAAAACAATTTTGGAAAAGAAACAAATGAAATGGGA 1806
                         vi vii  vvi i i        i   i       i--  ii  i v   
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG--AACAAAGTTGGA 210

  chr2_212373675_   1807 ATATTCAGTCCACATATTTTCAAGAATTATTACATAGCTGCCATAATTAA 1856
                         iv i   vv iv vi v      i v   i    v    i vi    i  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_212373675_   1857 GGCTGTGTGTTATTGGTA-GAGGATA-ATACACAGATCAATAAAACAAAC 1904
                          i v     v  i   i -i      - i i i        ii  i i v
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_212373675_   1905 T--------CAGAAATAA-CTGACACAAATATACCCAATATATTTTTTAC 1945
                          --------         - iv i   vv   ivi    vv     iv  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_212373675_   1946 AAAGGTGCAAAAGCAATTAATTAGAGGAAGGGTAGCCTTTAAAGCAAATA 1995
                           i     v  ii v   v v i i i   ii   i    vv i     i
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_212373675_   1996 GTGCCAGAGCAAATGAACATCTATAGAGCAAATAAACGAACCCTAAGCTA 2045
                             ii ii   v  i i ? i i v-     vi  i   viivi v iv
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAATGAAGTTGGACCCC 459

  chr2_212373675_   2046 CATCTCACATCTTATAAAAACATTAACTTTCAAAACAGGTCATGAGAT-T 2094
                         i i      i v    v   v       --     ii i   ?-   i- 
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACT--CAAAATGGATCAW-AGACCT 506

  chr2_212373675_   2095 AAATGTAAAATATAAAGCTATAAAATTTTGAGGTAAAAA-AT-GGAG-AA 2141
                                 i vv    i        i i v  ivi    -  -  ? -  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_212373675_   2142 ATCATTAGGGATTTAGAGTTAGGTGAAAAGAATT--TAGAGTTTG-CATG 2188
                            -  v v  ii v i      i--  v iv  --    - v  -  iv
  L1M4_orf2#LINE/    557 ATC-TTCGTGACCTTGGGTTAGGC--AATGGTTTCTTAGA-TATGACACC 602

  chr2_212373675_   2189 CAAAGAACAATCCATAAAAAACAAAAT-GATAAATTCAACTTCATCAAAA 2237
                         v    v    v v i    i v     -        vi            
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_212373675_   2238 TTAAAAACATTTGCTCTGTAAAATATCCTAAGATAAGAATGAAAGTATAA 2287
                                 v    iv  vi   iv iv   vv vi i i     iv i  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_212373675_   2288 GCTACAGATTAGGAGAGGAGATATT--CAAATCAGATAGTTGTTACAGAA 2335
                         v i     v i     -- i     --       v   vi  v  vi i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGA--AAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_212373675_   2336 CCGATATC 2343
                          ivi    
  L1M4_orf2#LINE/    751 CTTGTATC 758

Transitions / transversions = 1.29 (124 / 96)
Gap_init rate = 0.03 (21 / 746), avg. gap size = 1.62 (34 / 21)  

 280 23.18 3.97 5.96  chr2_212373675_212377595.rev     3279  3429 (492)    L1M4_orf2#LINE/L1      761   908 (0)  

  chr2_212373675_   3279 GAATATATAAAGAACAAAAAGTAGCACTAAATAGCAAATAAATAAATAAA 3328
                                        vv---v  vv   v    ii   v i i      -
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTC---TTACAACTCAATAATAAAAAGACAAATAA- 806

  chr2_212373675_   3329 CGAAATCTAATT--ACAGTGGTCAAAA-ATACGAAGAAACATTTCTCTGG 3375
                         -----i i    -- v i   v    i-  vi   v i         iii
  L1M4_orf2#LINE/    807 -----CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_212373675_   3376 AGAG--TATATAAATGAAAAATAAGCATATTAAAA-ATGTTTGACATTAT 3422
                            i--    i     ivv        i  v    -   i ii    i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_212373675_   3423 TAGCCAT 3429
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.50 (21 / 14)
Gap_init rate = 0.04 (6 / 148), avg. gap size = 2.50 (15 / 6)  


1261 28.43 10.14 2.71  chr2_212544832_212546521.rev      501  1200 (490)    L1M4_orf2#LINE/L1      157   908 (0)  

  chr2_212544832_    501 TGCAAAGGCCCAAGGACAAACAGAATATTCTTGAAGAAAAAGATCAAATT 550
                              i  v  v  i i iv  i  i v       i  i    v    v 
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_212544832_    551 TGGGGGACTAAAACTACTGGATATTAAGACTCATCATAAAGCTACAGTA- 599
                            i     v v   v ivi  v i  i   i ii i            -
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_212544832_    600 -CA---CAGTATGCCTATTATTGGTAAAAGGGCAGAGAAATAGA-CAAAG 644
                         -  ---    i  v----  i   i v    ii   v v     -   v 
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGG----TACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_212544832_    645 TAATATAATTC----TCACATAGAGGGAGTC-----TTTATGAAAGAATT 685
                         v    v    v----  -  v i vii vi -----      ivv-    
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTC-AATT 350

  chr2_212544832_    686 GGTATTGGAGGAGAA----AAG---------TGGATGAAGGCCAGTGTTT 722
                          i v  v  vi  ii----   ---------   ivi   ivi   v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_212544832_    723 TTAATAAATGTTGTTGGAATAATGAGATATCTA--TGTA-------GAAA 763
                          i  i     v  i   i i  ivi    ? i --  i -------   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_212544832_    764 TTGTCTTGATTCAAATCTCACACCATAGACAAAAATCAATTACTGGTAGA 813
                            ----  ii vv i           v        i  i vvvii i  
  L1M4_orf2#LINE/    451 TTG----GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_212544832_    814 TTGTGGATGTAAATGTTAAAGGTAAAA------AACTTTTAGAGGAAAAC 857
                          ii?i  iv       v i  v     ------    i     i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_212544832_    858 ----GAGAATATTTTTATTACCTTGAG---GACA-----CACATACACAT 895
                         ---- ? v v  i  ii v      i --- i  -----iv v  v i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_212544832_    896 GTATACATACCAATC-CACTAATTATGAAGCAAAAGATTGATAAAT---- 940
                          ----- i     vv-   v iiv ii  iv    i  v       ----
  L1M4_orf2#LINE/    597 G-----ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_212544832_    941 CTTATACTAAAATTAGAA--CTTCATTCATCAAAGGGCATAATTTTAAGA 988
                            -i ii       i  --i  ii v v       i  iv  ivvi i 
  L1M4_orf2#LINE/    642 CTT-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_212544832_    989 GTGACAAGAAAAGTCATTTAGTGGGAGAC----TTTTCAAATGTTTATAA 1034
                             v    v  vi  ivv i       v----   v     -iv    v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT-CATATAT 739

  chr2_212544832_   1035 CTGGCAAAG-ACTTATATCCAAAATATAAAAAGGAATTCTACAATTCCTT 1083
                            ii  i -    i      i      v    i v ii     i  vv 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_212544832_   1084 AAGGCAAAGACAGGTAACTCAAT-AAAAAATGTGCAAA--ATCTTGAAGG 1130
                           viv       ii    i    -?       v     --  -     vi
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATA 838

  chr2_212544832_   1131 AGCACT-CTCCAACAGAAGATATCCAAAGACCCACTGTATACATGAAAAG 1179
                         ii  i -      -         v    viv   v ivii          
  L1M4_orf2#LINE/    839 GACATTTCTCCAA-AGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_212544832_   1180 CTTCCCAACATAATTACTAAT 1200
                         v v i      v ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (112 / 83)
Gap_init rate = 0.04 (30 / 752), avg. gap size = 3.00 (90 / 30)  


3188 27.34 0.55 0.44  chr2_212578268_212584553     4888  5794 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_212578268_   4888 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4937
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_212578268_   4938 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 4987
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_212578268_   4988 TACCAAG-ACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5034
                          v   iv-i i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_212578268_   5035 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5084
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_212578268_   5085 AACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAAGGC 5134
                                i      vv     i v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_212578268_   5135 TACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGAGATATAGATC 5184
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_212578268_   5185 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 5232
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_212578268_   5233 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAAGGGGGAAAGGATTCC 5282
                          vi    i  i     ivv  vv  i v  vv   v        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_212578268_   5283 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5332
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_212578268_   5333 GAAACTGGATCCCTTCCTTACACTTTATACAAAAATCAATTCAAGATGGA 5382
                            ii    i    v   i    iv           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_212578268_   5383 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5432
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_212578268_   5433 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5482
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_212578268_   5483 AACACCAAAAGCAATGGCAACAAAAGCCTAAATTGACAAATGGGATCTAA 5532
                         i            vvi          vvv    v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_212578268_   5533 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAGCTACCATCAGAGTGAAC 5582
                          i   v v  i i   i  ii vv    i  vi   i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_212578268_   5583 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5632
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_212578268_   5633 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5682
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_212578268_   5683 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5732
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_212578268_   5733 TCAAAAGAAGACATTTATGCAGCCAAGAAACACATGAAAAAATGCTCATC 5782
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_212578268_   5783 ATCACTGGCCAT 5794
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2918 27.03 0.65 2.49  chr2_212744551_212750950     4986  5910 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_212744551_   4986 TGGAAGAACATTCCATTCTCATGGATAGGAAGAATCAATATTATGAAAAT 5035
                              ii i  i    vi        v      v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_212744551_   5036 GGCCATATTGCCCAAGGTAATTTAATAGATCCAATGCCATCCCCATCAAG 5085
                            v   i v     iv i  i  -i    i   i  v     i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTA-CAGATTCAACGCAATCCCTATCAAA 99

  chr2_212744551_   5086 CTACCAATGACTTTCTTCACACAA-TTGGAAAAAACTGCTT-TAAAGTTC 5133
                         v v   iivi i  i  ii  v  -   -- v  i   v i-    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_212744551_   5134 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATTCTAAGCCAAAA 5183
                                 viiv  ii  v  viv  v     i     ii i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_212744551_   5184 GAACAAAGCTGGAGGCATCATGCTACCTGATGTCAAACTATACTACAAGG 5233
                                 i      vv   ii  v  ii  v     viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_212744551_   5234 CTATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5283
                            i     i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_212744551_   5284 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5331
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_212744551_   5332 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGAGAAAGATTC- 5380
                           vi    i  i     ivv  v   i v  vvv     i      v v-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_212744551_   5381 CCTATTTAATAAATGGTCCTGGGAAAACTGGCTAGCCAAGTGTAGAAAGC 5430
                         i  v  i  i       v      v      v  ?   vi  i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_212744551_   5431 TGAAACTGGATCCCTCCCTTACACCTTATACAAAAATTAATTCGAGATGG 5480
                             ii    i    v   i     v              i  i i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_212744551_   5481 ATTAAAGACTTAAACATTAGATCTAAAACCATAAAAACCCTAGAAGAAAA 5530
                           i ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_212744551_   5531 CCTAGACA-ATACCACTCAGGACACAGGCATGGGCAAGCACTTCATGTCT 5579
                          v   i?i- v i -i  iv   viv  vv i     vvii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_212744551_   5580 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5629
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_212744551_   5630 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAATACCATCAGAGTGA 5679
                         v  i   v v  i i   i  ii vv    i  v v  i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_212744551_   5680 ACAGGCAAACTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5729
                          v  i   v i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_212744551_   5730 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAATT 5779
                           i  i  vi          v  i        i--------      v -
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTC--------TTACAACT- 785

  chr2_212744551_   5780 ACAATTGTTGTTACAAAAAAACGAACAATTCCATCAAAAAGTGGGCAAAG 5829
                         -    vi ------     i  i  i  ii v  i?    i         
  L1M4_orf2#LINE/    786 -CAATAAT------AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_212744551_   5830 GATATGAACAGACACTTCTCAAAATAAGACATTTATGCAGCCAACAGACA 5879
                            v    i     i     v   v    i  vi viii     i ii  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_212744551_   5880 CATGAAAAAAATGCTCATCATGACTGGCCAT 5910
                                 i -      v   v ????????
  L1M4_orf2#LINE/    879 CATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.23 (29 / 13)  


2687 27.48 1.99 1.77  chr2_212902000_212904055      659  1564 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_212902000_    659 TGGAAAAACATTCCATCCTCATAGACAGGAAGAATCAAAATCATGAAAAT 708
                               i i  i    vi    i  iv      v i  v  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_212902000_    709 GGCCATACTGTCCGAAGTAATTTATAGATTCCATGCTATTTTCATAAAAC 758
                            v     vi  i  v i  i  i      v i  v  iiii  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_212902000_    759 TATCATTGACATTCTTCACAGAA-TTAAAAAAAAAAAAGGACTTTAAATT 807
                          vi  vivi v  i  ii     -  i v  iv-----v  iii    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-----TGATCCTAAAAT 145

  chr2_212902000_    808 TCATATGGAA-T-CAAAGAAAGACCCCTA-TAGCCAAGACAATCCTATGC 854
                                   - -   i ---     vv -       i      i iviv
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGG---GACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_212902000_    855 AAAAAGAACAAAGCTGGAGGCGTCAGGCTACCTGACTTCAAACTATACTA 904
                           i          i      vv   vi  v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_212902000_    905 CAAGGCTACAGTAACCAAAACAGAATGGTACTAGTAACAAAACAGACATG 954
                            i          i   i    vi       i i vv ii i      i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_212902000_    955 TAGACCAATGGAGCAGAACAGAGACCTCAGACATAACACCACACATCTAC 1004
                             i       ii    iv    vii    v    vv   i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_212902000_   1005 AACCATCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGAAAAAGCA 1054
                         iii  vi    i   i    ivv  v   i v  vv      ii    v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_212902000_   1055 TCTCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATTTACAGAA 1104
                          vvi  v  i  i              v      v  ?   iv i  i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_212902000_   1105 AACCGAAACTGGACCCCTTCCTTATGCCTTATACAAAAATTAACTCAAGA 1154
                         i vi   ii         v   i ii  v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_212902000_   1155 TGGTTTAAATACTTAAATGTAAAAGCCAAAATCTATAAAAATCCTAGAA- 1203
                            v i ? v  i         i   i    -        v  i     -
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAG 541

  chr2_212902000_   1204 AAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTC-- 1250
                              v    ?i- v i -   iv   v v  vv i     v ii   --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_212902000_   1251 ----ATGACAAAAATGCCAAAAGCAATTGCAACGAAAGCCAAAATTGACA 1296
                         ----      ------         vvv     i    vv     v  i 
  L1M4_orf2#LINE/    591 AGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_212902000_   1297 AATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGAAAAGAA-ACTATC 1345
                            v   ii v  i   v v  i i   i  ii vvv    i -      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_212902000_   1346 ACTCAAGTGAACAGGCAACCTAC-GAATAGGAGAAAATTTTTGCAATCTA 1394
                          vvv       v  i     i  -    i         v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_212902000_   1395 CCCATTTGACAAAGGTGTAATATCCAGAATTTACAAGGAACTTAAACAAA 1444
                         ivi  i   i  i  vv vi          v  i  i     ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_212902000_   1445 TTTACAAGAAAAAAACAA----CCCCATCAGAAAGTGGGAAAGGGATATG 1490
                          iv i  v     i    ----   v  i?i   i    v  i    v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_212902000_   1491 AACAGACACTTCAAAAAAGAAGACATTTACACAGCCAACAAACGTATGAA 1540
                           i     i   vvv        i  vi v ii     i  i ii     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_212902000_   1541 AGAAAGCTCAACATCACTGATCAT 1564
                          ii v           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.27 (34 / 15)  


2576 25.81 3.58 2.12  chr2_213331579_213334587.rev     1623  2517 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_213331579_   1623 TGGAAACTCAACCCATGTT---------GAA---TCAATATTGTGAAAAT 1660
                               vvi v        ---------   --- i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_213331579_   1661 GACCATACTCCCAAAAGCAATCTATAAATTCATTGCAATTCCCATCAAAA 1710
                          i v        v   vii     i i     vi     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_213331579_   1711 TATCACCATCATTCTTTACAGAACTGGAAAAAA-AATTCTAAAATTCATA 1759
                          vi  v vv v  i   i     v v  v  iv-i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_213331579_   1760 TGGAATCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAGAAAGAT 1809
                              viiv  ii  v  viv         i   vvi i iv ii    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_213331579_   1810 CAAATCTGGAGACATCACGTTACCTGACTTCAAACTACACTATAAGGACA 1859
                             vi     ivv    ii v  ii i      vivi    i  i vi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_213331579_   1860 TATTCACCCAAAAC--CATGGTACTGGTATAAAAATAG-CATATAGACAA 1906
                         i v v i -  i  --ii         i    ii    -        iv 
  L1M4_orf2#LINE/    251 CAGTAATC-AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_213331579_   1907 ATG-AACAGAATAGATAACCCAGAAATAAAGCCAAATACTTATAGCCAAC 1955
                            -  i     v  v ii           v   v i i    i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_213331579_   1956 TAATCTTTGACAAAGCATACAAAAAC--TTAAAGTGGGGAAAGGACACCC 2003
                          i  i  i     i -i i v  i  --  v  -         i i vi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAA-TGGGGAAAGAATAGTC 397

  chr2_213331579_   2004 TATTCAACAAATGGTGCTGGGATACTTGACAAGCCA-ATGTTGAAGAATG 2052
                          v                    i vi  ivv ?   -   ivi       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_213331579_   2053 AAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGAT 2102
                           ii    i  ii i   v    v           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_213331579_   2103 CAAAGACTTTAATCTAAGAAGTGAAACCATAAAAATTCTAGAAGGTGACA 2152
                           ?    i v   v     iv i    i      v ii      ivi   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_213331579_   2153 TTGGAAAAACTCTTCTAGAGATTGGCTTAGGCAAAGACTTCATGACCAGG 2202
                          v  ?iv  v     vv  vv    v        v ii   v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_213331579_   2203 AACCCAAAAGCAAATGTAACAAAACCAAAGATAAATAGTTGGAACTTAAT 2252
                          vv         v v i       vv   i   i   iv v i    v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_213331579_   2253 TAAA-CTAAAAA-------GCTTCACACAACAACAACAAAACAAATAATC 2294
                         i   -i      -------      v vi   vi v   i -  i i --
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA-AAGTGA-- 694

  chr2_213331579_   2295 AGCAAATAGACAACCCACAGAGGGGGAGAAAATCTTAGCAA--TATATAC 2342
                         ---   --             iv          v  v    --i     -
  L1M4_orf2#LINE/    695 ---AAA--GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA- 738

  chr2_213331579_   2343 TTCTGACAAAGGACTAATATCTAGAATCTACAAGGAACTCAAACCAATCA 2392
                         -     i  i     vi    i     v  i  i      vv  v v   
  L1M4_orf2#LINE/    739 -TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_213331579_   2393 GCAAGATAAAAACA--CAATCCCATCAAAAAGGGGACTAAAGACATGAAT 2440
                         ii  v v   i   --i  i  v  i?    iv  i v  i  iv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_213331579_   2441 AGACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACCAACAAACAT 2490
                              v     v                       i  i ------    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC------ACAT 881

  chr2_213331579_   2491 GAAAAACTGCTCAGTATCACTAATGAT 2517
                              iv      ii    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (129 / 98)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.55 (51 / 20)  


2765 25.66 2.54 2.10  chr2_213363959_213368279.rev     2926  3829 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_213363959_   2926 TGGAAAAACTTTCCATGCTCATGGATTGGAAGAATCAATATTATTAAAAT 2975
                               i iv i     i               v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_213363959_   2976 GGCCAGACTGCCCAAAGTATTATAATTTACAATTTCAATGCTATTCCTGT 3025
                            v v   v      ---  i--  i    iv     i  v  i   i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA---TTG--ATCTACAGATTCAACGCAATCCCTAT 95

  chr2_213363959_   3026 CAAACTGCCAAATTTATTATTCACAGAATTAGAAAAGATGATTCTAAAAT 3075
                             v v   iv viv  v  ii     v v  v   v    i       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_213363959_   3076 TCATATGGAAC--CAAAAAACAGCCTGAATAGCCAAAGGATTCCTAAGCA 3123
                                   v--   iii  --  v           iv v  i i iv 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_213363959_   3124 AATAGGAGATAGCCAGAGGCATCACATTACCCAACTTCAAACTAGACTAT 3173
                          iv  i v v  iii    vv     i v     i      vivv    i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_213363959_   3174 AATATTACAGCAACCAAAGCAGCATGGTACTTGTATAAAAAACAGACAGA 3223
                           vii     i  i   ii   ii       v i    ii -i     v 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATA 292

  chr2_213363959_   3224 TAGAGCAAAGGAACAGAATAGAAAATTCAGAAATAAAGCCACACACCTAG 3273
                             v   v    i     v  i i i          v   i   ii  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_213363959_   3274 AACCATTTGATCTTTGAAAAAGCCAACAAAAACAAGCAATGCAAAGTGAC 3323
                         iii  v     i  i  v  i viiv   i v  vv     vii iv  v
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_213363959_   3324 TC-CCTATTCAATAAATGGTGCTGGGATAATTGGTTACCCATATGCAGAA 3372
                          v-i  v     i              i  i   v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_213363959_   3373 GAATGAAACTAGACCCTTACCTTTCAC-------AAAAATTTACTCAAGA 3415
                                ii i     i     iv   -------       v      i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_213363959_   3416 TGGATTAAAGATTTAAATGTAACATCTCAAACTATAAAAATTCTAGAAGG 3465
                              i ?   ii         v v  v           v ii      i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_213363959_   3466 AAACCTAAG---AAATTCCATTCTGGGCATTGACCTTGGCAAATAATTT- 3511
                             v  i ---    i---   vv i v   ivi v     - ii   -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC---TTCGTGACCTTGGGTTAGGCAA-TGGTTTC 588

  chr2_213363959_   3512 TTGGCTAAGTTCCCCAAAGAAATTGCAA-CAACAACAACAAAAAATTGAC 3560
                           i v  v viv  v    v ----   -      -  v       v  i
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCA----CAAGCAACAA-AAGAAAAAATAGAT 633

  chr2_213363959_   3561 AAGGGGGACCCAATTAAACCGAACAGCTTCTGCACAGCAAAATAAACTAT 3610
                           ivv    iiv  i   viv  v i   i  ii vv    iv v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_213363959_   3611 CAGCAGAGTAAACAGAGAACCT-CAGAATGGGAGAAAATATTTGCAAACT 3659
                           iv i   i  v   v    i-                         ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_213363959_   3660 TTGCATCTGACAAAAGTCTATTATCCAGAATCTATAAAGAACTTAAACAA 3709
                         v ii      i  ii v  vv          v           ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_213363959_   3710 ATCAACAA-ACAAAAACAAGTAACCCCATTAGAAAATGGGCAATAGGAGA 3758
                         v    i  - v   i    i      v   ?i           -    vv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA-AGGATT 832

  chr2_213363959_   3759 TGAACAGATATTTCT-----GAAAATA-ATAAAGCAGACAACAAACATAT 3802
                             i   i      -----   i   - i   -ii v   i  i  i  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACAT 881

  chr2_213363959_   3803 GAAAAAATGCTCATGATCACTAATCAT 3829
                              i       vv    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (129 / 100)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.10 (42 / 20)  


3015 27.50 0.66 0.77  chr2_213446380_213452766     4987  5895 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_213446380_   4987 TGAAAAAACATTCTACCTTCATGGATAGCAAGAATCAGTATCATGAAAAT 5036
                           i   i i  i i iv         v v    v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_213446380_   5037 GGTCATACTGCCCAAAGCAATTTATAGATTCAATGCTATCCCCATCAATC 5086
                           iv     v      vii  i  i        i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_213446380_   5087 TACCA-TTGACTTTCTT-CACAGATTTAGAAAAAACT-ACTTTAAATTTC 5133
                          v   -i  v    i  -  v i   ---i v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chr2_213446380_   5134 ATATGGAACCAAAAAAGAGCCTGTATAGCCAAGAGAATCCTAAGCAAAAA 5183
                                 viiv  ii  v  v v        i v    i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_213446380_   5184 GAACAAAGTTGGAGACATCACGCTACCTCACTTCAAACTATACTACAAGG 5233
                                       ivv    i  v  iv i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_213446380_   5234 CTACAGTAACCAATACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5283
                                  i   v    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_213446380_   5284 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCA 5333
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_213446380_   5334 TTTGATCTTTGACAAACCTGACAAAAACAAGGTACGGGAAAAGGATTCCC 5383
                         v     i  i     ivv  v   i v  vvvv i   i    i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_213446380_   5384 TATTTAATAAATGGAGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5433
                          v  i  i      v i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_213446380_   5434 AAACTGGACCCCTTCCTAACAGCTTACACAAAAATTAACTCAAGATGGAT 5483
                           ii         v   v   v v  i                i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_213446380_   5484 TAAATACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5533
                         i ? v  i           v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_213446380_   5534 TAGGCAGTA--TCATTCAGGACATAGGCATGAGCAAAGACCTCATGACTA 5581
                             ?-   --  -   iv   v v  vv ii    v iii  v iiv  
  L1M4_orf2#LINE/    548 TAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_213446380_   5582 AAATACCAAAAGCAATGGCAACAAAAGCCAAAAACTGACAAATGGTATCT 5631
                         vi i          vvi          v-     iv  i    v v ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTT 644

  chr2_213446380_   5632 AATTAAACTAAGGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTAA 5681
                         v  i   v v ii i   i  ii vv    i  v       vv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_213446380_   5682 AGAGGCAACCTACAGAATGGGAGAAGTTTTTTCGCAATCTATCCATCTAA 5731
                          i  i     i              iv v   -    vii  vi    i 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGA 743

  chr2_213446380_   5732 CAAAGGGCTAATATTCAGAATCTACGAAGAACTTAAACAAATTTATAAGA 5781
                         i  i  i  vi   i      v  ii       ivv    v iv    v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_213446380_   5782 AAAAAA-AATCAACCCCATCAAAAAGTAGGCGAAGGATATGAACAGACAC 5830
                             i -  vi     v  i?    i i   i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_213446380_   5831 TCCTTGAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTC 5880
                          i  iv        i  vi vi       i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_213446380_   5881 ATCGTCACTGGTCAT 5895
                          v i   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (145 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3141 26.68 1.10 0.99  chr2_213474859_213481250     4994  5900 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_213474859_   4994 TGGAAGACTATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5043
                              iiv   i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_213474859_   5044 GGCCATACTGCCTAAGGTAGTTTATAGATTCAATGCCATCCCCATCAAGC 5093
                            v     v  i  iv ii i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_213474859_   5094 TACCAACGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5141
                          v   i vi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_213474859_   5142 TACGTAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5191
                           i v  viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_213474859_   5192 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5241
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_213474859_   5242 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5291
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_213474859_   5292 AAGGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5339
                           v    i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_213474859_   5340 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5389
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_213474859_   5390 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5439
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_213474859_   5440 GAAACTAGAGCCCTTCTTTACACCTTATACAAAAATTAATTCAAGATGGA 5489
                            ii i  v    v i i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_213474859_   5490 TTAAAGACTTACATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5539
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_213474859_   5540 CTAGGCA-ATACCATTCAGGACATAGGCATGGG-AAGGACTTCATGTCTA 5587
                         v    ?i- v i -   iv   v v  vv i  -  v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_213474859_   5588 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5637
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_213474859_   5638 ATTGAACTAAAGAGCTTCTGCACAGCAAAAGAAACCAACATCAGAGTGAT 5687
                           ii  v v  i i   i  ii vv    i  v  i v  vv i     v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_213474859_   5688 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5737
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_213474859_   5738 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAT 5787
                          i  i  vi          v  i  v      iv    v iv i  v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_213474859_   5788 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATAGACACTT 5837
                           i     i     v  i?    i            v          i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_213474859_   5838 CTCAAAAGAAGACCTTTATGCA----GCCAAAAGACACATGAAAAAATGC 5883
                            v        ----   i  ----     v ii          i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_213474859_   5884 TCATCATCACTGGGCAT 5900
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


3125 26.61 0.78 0.89  chr2_213565444_213571842     5007  5908 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr2_213565444_   5007 ACATTCCATGCTTATGGATAGGAAGAATCAATATCGTGAAAATGGCCATA 5056
                          i  i     i i      v      v i     i  v  i     v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_213565444_   5057 CTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAAT 5106
                           v     iv i  i  i        i  v     i     iv v   ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr2_213565444_   5107 GACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCACATGGAA 5154
                         vi i  i  ii     -   -- v  i  - iii    i    i      
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAA 155

  chr2_213565444_   5155 CCAAGAAAGAG-CCCACATT-GCCAAGACAATCCTAAGCCAAAAGAATAA 5202
                         -- v v   i -    v v -     i      i i ivv i     i  
  L1M4_orf2#LINE/    156 --ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_213565444_   5203 AGCTAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTACAG 5252
                           i i    vv   ii  v  ii i      viv        i       
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_213565444_   5253 TAACCAAAACAGCATGGTACTGGTACCAAAACAAAGATATAGACCAATGG 5302
                            i   i    ii         i iv ii i i v       i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_213565444_   5303 AACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACTATCTG 5350
                           i    i--    i  --        vv   i    i  iiiii vi  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_213565444_   5351 ATCTTTGACAAACTTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATT 5400
                           i  i     ivv  v   i v  vvv           i  vvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_213565444_   5401 TAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGACAGCTGAAAC 5450
                         i  i              v      v  ?   i   i i viiv    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_213565444_   5451 TGGATCCCTTCCTTACACCTTATACAAAAAGTAATTCAAGATGGATTAAA 5500
                             i    v   i     v          v   i    i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_213565444_   5501 GACTTAAATGTTAGACCTAAAACCATAAAAAGCCTAGAAGAAAACCTCGG 5550
                            i       v   v       i      vv i           v v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_213565444_   5551 CA-ATACCATTCAGGATGTAGGCATGGGCAAAGACTTCATGACTAAAACA 5599
                         ?i- v i -   iv  iv v  vv i     v ii   v iiv  vi   
  L1M4_orf2#LINE/    552 NGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_213565444_   5600 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAA 5649
                                  vvi          vv     v  i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_213565444_   5650 ACTAAAGAGCTTCTTCACAGCAAAAGAAACTACCATCAGAGTGAACAAGC 5699
                          v v  i i   i vii vv    i  v    i  vv i      v ii 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_213565444_   5700 AACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACAAAGGG 5749
                             i                 v   i   vii ivi      i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_213565444_   5750 CTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAATC 5799
                           vi          v  i        ivv    v iv i  v     iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_213565444_   5800 AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATAGACACTTCTCAA 5849
                            i     v  i?    i            v          i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_213565444_   5850 AAGAAGACATTTATGCAGCCAACAGACACATGAAAAAAATGCTCATGATC 5899
                                i  vi viii     i ii          i -      vv   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATC 899

  chr2_213565444_   5900 TCTTGCCAT 5908
                         v????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (11 / 901), avg. gap size = 1.36 (15 / 11)  


2979 28.15 0.44 0.22  chr2_213573912_213578593     3285  4190 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_213573912_   3285 TAGAAAAACATTTCATGCTCATGGATAGGAAGAAGCAATATCGTGAAAAT 3334
                          i    i i  ii    i        v      vvi     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_213573912_   3335 GGCCATACTGCACAAAGTAATTTATACATTCAATGCTATCCCCATCAAGC 3384
                            v     v v    v i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_213573912_   3385 TACCA-CTGACTTTCTTCACAGAATTAGTAAAACCTACTTTAAATTTCAT 3433
                          v   -   v    i  -i     v v vv  i iv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_213573912_   3434 ATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAGA 3483
                               viiv  ii  v  v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_213573912_   3484 ACAAA-CTGGAGGCATCACACTACCTGACTTCAAACAATACTGCAAGGCA 3532
                              -i      vv       v  ii i      vvv    i   i  v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_213573912_   3533 ACAGTAACTGAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 3582
                                iii i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_213573912_   3583 GTGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCATC 3632
                         i     i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_213573912_   3633 TGATCTTTGACAAACCTGACAAAAACAAACAATGGGGAAAGGATTCCCTA 3682
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_213573912_   3683 TTTAATAAATGGTGCTGGGAAAAGTGACTAGTCATATGCAGCAAACTGAA 3732
                           i  i              v  v  iv  ?i  i     iv i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_213573912_   3733 ACTGTACCCCTTCCTTACAGCTTATACAAAAATTAACTCAACTTGGATTT 3782
                         ii  v      v   i   v v                   vv     iv
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_213573912_   3783 AAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAAGAAACCTA 3832
                         ?    i           v       i      vi i     ii    v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_213573912_   3833 GACA-ATACCATTCAGGACGTAGGCATGGGCAAAGACTTCATGACTAAAA 3881
                          i?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_213573912_   3882 CATCAAAAGCAAAGACAACAAAAGCCAAAATTGACAAATGGTAGCTAATT 3931
                           i        v ii         vv     v  i    v v vi v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_213573912_   3932 AAACTAAAGAGCTTCTGCACAGCAATAGAAACTATCATCAGAGTGAACAG 3981
                            v v  i i   i  ii vv   vi  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_213573912_   3982 GCAACCTACAGAATGGGAGAAAATTTCTGCAATCTATGCATCTGACAAAG 4031
                         i     i                 v i     vii  ii      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_213573912_   4032 GGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAGTAAC 4081
                          i  vi          v  i  i     ivv    v iv i  v iv  v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_213573912_   4082 -CAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCCC 4130
                         -    i     v  i?    i            v    i     i   i 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_213573912_   4131 AAAAGAAGACATTTATTTAGCCAACACATATATGAAAAAAACCTCATCAC 4180
                         v        i  vi vv i     i vii i       i vv    v  i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_213573912_   4181 CACTAGTCAT 4190
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.28 (141 / 110)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.00 (6 / 6)  


2147 22.15 11.54 1.23  chr2_213666289_213667916.rev      487  1136 (492)    L1M4_orf2#LINE/L1      192   908 (0)  

  chr2_213666289_    487 AAAGGAAAGGAAAGTTGGAGGGCTACCACAGCTTAATTTCAAGACTTATT 536
                             i i iv           i  vv   vv ii        i     i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_213666289_    537 GGAAAGCTACAGTCATGAAGACAGCATGATATCGGTGTAA---------T 577
                         iv           v  v       ii  i  ii  ii   --------- 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_213666289_    578 AT----CA-------------------CCTATATTACACCTATAT----- 599
                           ----  -------------------  viv v  v   i   i-----
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_213666289_    600 TG--CAACTGATTTTTGACAGAGTTGCAAGGGCAATTCAATGGAGAAAGG 647
                           --   i       i    ii v   v i i v         i     i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_213666289_    648 ACAGTCTTTTCAACAAAGGATGCTGGAATAATTGGATATACATATGTCAT 697
                          i               v i      i i  i      ?v  i   iv v
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_213666289_    698 AAAATGAATGCTG-ATTCATATCTCATACCATGTATAAAAATTAACTATT 746
                          i      - i  - ii v  i    i     i  i           vvv
  L1M4_orf2#LINE/    442 AGAATGAA-GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_213666289_    747 AATGGTTCACAGACCTAACTACAAAACCTAAAACTA--AAATTTCTAAAA 794
                              v   ?        v ii  i v         --   i ii  i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_213666289_    795 GGAAACATA-------ATTTTT-TACTCTTGAATTAGGTAGAAATTTCTT 836
                          i       -------  i  i- ivi    ii     i ivii      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_213666289_    837 AGATATAACACCAAGAACATGATCAA-AGAAGAAAA--TAAGTAA----G 879
                               i       i i  ii v   - i       --  ii   ---- 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_213666289_    880 ATTTCATCAAAATTAAAAACATTT---TTCTGAAAGATATTGTTAAGAAG 926
                          i                  v   ---i iii  i  i i i i     i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_213666289_    927 ----AAAGTCAA-----AAACTGGAAGAAAAATATTTGAAAATCATATTT 967
                         ----    v   ----- i v   i      -      v         v 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATAT 739

  chr2_213666289_    968 CTGATAAAGGGACTTGCCTCCAGAATAAATAAAGTACTTTCA-AACTCAG 1016
                                -        iv         v      v   i i -      i
  L1M4_orf2#LINE/    740 CTGATAA-GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_213666289_   1017 TG-TAAGAAAACAAATAATCCAATTAAAAAAAAACTGGCAAAAACTTTGA 1065
                          i-   i  i        i      ?     vi---      iiv     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATG---GGCAAAGGATTTGA 835

  chr2_213666289_   1066 A--GACACTTTGCCAGGGAAGTAATATACA--TGACAAATTAACACATGA 1111
                          --    i  iv   ii    --       --  i v   v i       
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAG--ATATACAAATGGCCAATAAGCACATGA 883

  chr2_213666289_   1112 AAAGATGGTCAACATCACGAGTTAT 1136
                                v         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.28 (98 / 43)
Gap_init rate = 0.03 (24 / 717), avg. gap size = 3.46 (83 / 24)  


2934 25.06 6.15 0.81  chr2_214021334_214024949     2263  3124 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_214021334_   2263 TGGAAAGACATTACATGTTTATGGGTTCTAAGAATCAATATTGTTAAAAT 2312
                                 i  iv      i    i  vv    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214021334_   2313 GTCCATACTACCCTAAGCAACCTACAAATTCAGTGTGACCCCTATCAAAA 2362
                          v v     v   v  vii i     i     ii ii i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214021334_   2363 TACCCA--TGAGATTCTTCACAGAAATAGAAAATACAATCCTAAAATTTA 2410
                          -    --  -vv  i  ii       v  v  vvii           i 
  L1M4_orf2#LINE/    101 T-CCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_214021334_   2411 TGTAGAATCACAAAAGATCCAGAATAGGCAAAGCTATCCTAAGCAAAGAG 2460
                          i i   vii   ii  i         v    i v   i i iv  ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_214021334_   2461 AACAAAACCGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAAA 2510
                               iii      v     i v  ii i      viv       i iv
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_214021334_   2511 TATAGTAACCAAAACAACATGGTACTGACATAAAACCAAACACATAGACC 2560
                           i     i   i   iii        i     iivi i   i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_214021334_   2561 AATGGAACAGAATAGAGAA-CCAGAAACAAAACCACATACCTACAGTGAA 2609
                                i     v    i-       i   v   i i ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_214021334_   2610 CACATTTTTGACATAAGTGCCAAGAACATACACTGTGGAAAAGGCAGTCT 2659
                         ivv     i    vii         v   v  v  v     iiii     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_214021334_   2660 CTTCAATAAATGGTGCTGGGAAAACTGGATATCTATATGAAGAAGAATCA 2709
                         i     i              v         ? i i   v i      v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_214021334_   2710 AACTGGAATACTATGTCTCATCATGTGCAAAAATCAAATCAAAATG---- 2755
                          ii    viv   iv  v  i   i i       i  v        ----
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_214021334_   2756 ------------------------------AAATTCCTAAGAGAAAAC-T 2774
                         ------------------------------   i  i  ii       - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_214021334_   2775 AAAAGAAACTCTCAATGACATTGGTCTAGGCAGAAATTTCTTGAGTAATA 2824
                          ii? v  v   ivi    v    vi      ivii      iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_214021334_   2825 CCCTACAAGCACAGGCATCCAAAGAAAATAATGGACAAATGGCATCACAT 2874
                          v i v       i   v v        -   i  i    v v iiv   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCAT 647

  chr2_214021334_   2875 CAA-GTTAAAAAGCTTCTGCATAGAAAAGGGAATAATCAACAAAGTGAAG 2923
                            -i       -   i  iiivvv     iv iv     v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_214021334_   2924 AGACAAACCCATAGAATGGGAGAAAATATTTGCAAACGACTCATCTGATA 2973
                               -    i                        iv ivi        
  L1M4_orf2#LINE/    697 AGACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_214021334_   2974 AG--ATTAATAACCAGAATATATAAGAAACTCT---------ATAGGAAA 3012
                           -- i vi  v             ii      ---------   iv-  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AA 794

  chr2_214021334_   3013 AAAGTCTAATACTCCAATTAAAAAAATGGACAAAAAATTTGAACAGACTT 3062
                             v v    vi      ?     -   i    ii       i    v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACAT 843

  chr2_214021334_   3063 TTCTCTAAAGA---CATACAAATGGCAAACAGGTATATGAGAAGGTGTTC 3109
                              i     ---i           v  i i i i    i   i  i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_214021334_   3110 AACATCATTGATCAT 3124
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (139 / 74)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.00 (60 / 15)  


3297 26.02 0.77 0.66  chr2_214034864_214039636.rev     3377  4283 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_214034864_   3377 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3426
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214034864_   3427 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCTATCAGGC 3476
                            v     v     iv i  i  i        i  v          iiv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214034864_   3477 TACCCA--TGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTC 3523
                          -    --  v    i  -i     v v  v  i-  - iii    i   
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr2_214034864_   3524 ATATGGATCCAAAAAAGAGCCTGCATTGCTAAGTCAATCCTAAGCAAAAA 3573
                                vviiv  ii  v  v v  v  i  iv     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_214034864_   3574 GAACAAAGCTGGAAGCATCACGCTACCTGACTTCAAACTACACTACAAGG 3623
                                 i    i vv    i  v  ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_214034864_   3624 CTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGAC 3673
                                  i   i    iii        i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_214034864_   3674 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAAC 3721
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_214034864_   3722 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 3771
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_214034864_   3772 CCTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3821
                         i  v  i  i  i           v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_214034864_   3822 TGAAACTGGATCCCTTCCTCACACCTTATACAAAAATTAATTCAAGATGG 3871
                             ii    i    v         v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_214034864_   3872 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3921
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_214034864_   3922 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 3970
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_214034864_   3971 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4020
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_214034864_   4021 AATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGA 4070
                         v  i   v v  i i   i  ii vv    i  v    i ivv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_214034864_   4071 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 4120
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_214034864_   4121 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACCAATTTACAAGAA 4170
                           i  i  vi          v  i         vv  v v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_214034864_   4171 AAAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACT 4220
                            i     i     v  i? v  i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_214034864_   4221 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 4270
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_214034864_   4271 TCA-CACTGGCCAT 4283
                         v  -  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3556 18.39 4.28 0.38  chr2_214078372_214080380      724  1517 (492)    L1M4_orf2#LINE/L1       84   908 (0)  

  chr2_214078372_    724 CACAATTTCTATCAAAATCCCAAAGACCTTTTTTTTGCAAAAACATAAAA 773
                          i    ii              ivvi        --   i   ivv v  
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT--GCAGAAATTGACAA 131

  chr2_214078372_    774 ACCCATCCTAAGTTTCGTATAGT--CTCAAGGGACACTGATTAGCCCAAA 821
                         i iv       iv   i   i v--iv        v v  v     v   
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr2_214078372_    822 CAATCTTGCAAAAGAAGAACAAACTTGGAAGACTCATACTTTCTTATTTC 871
                                 v              v     i      i    i iv     
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr2_214078372_    872 TAAACT-ACTGCAAAGCTACAGTAATCAAAACAGTATGGTACTGGCATAA 920
                         v     -   i                  i     i              
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_214078372_    921 AGACAGACATATAGACCAATGGAATAGACTAAACAGCCCAGAAATAAACC 970
                         i  i           i            v vi v  i             
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_214078372_    971 CTCACATATATGATCAAATGATTTT-GACAATAGTACCAAGACCAATCAA 1019
                          vi    v    i    v       -     vi  i         v    
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_214078372_   1020 TGGGGAAAGA-CAGTCTTTTTACCAAATTGTGCTGGGAATACTGGGTATC 1068
                                   -i        i v     v         vv     i  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_214078372_   1069 TACATGCAAAATAATAAAGTTGGACCCTTAC-TAATACCATATACAAAAA 1117
                         i          v   i           i   - v i              
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_214078372_   1118 TTAACTCAAAATA-ATCAAAGACCTAAATATAAGACACAAAACTATAAAA 1166
                                     i-    ?          i     vvi            
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_214078372_   1167 CTCTCAGAAGAAAATATAGGACAAAAGTATCATGGCATTGATTTTAACAA 1216
                             i         i     ?vv   viv  i  i v   iv  vii   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chr2_214078372_   1217 TGATTTCTTAGATATGACACAAAAGGCACAGGCAACAATAGAAAAA---- 1262
                           i                 v   i     i       v       ----
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr2_214078372_   1263 -----CTGGACTTTATAAACATTTTAAAATTTGGGGCATCGAAAGAC--T 1305
                         -----i       i  v  v   vv   v   v v  v  i  i   -- 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_214078372_   1306 GTCATCAGAGTAAAAAGGCAACCAATAGAATGGGAGAAAATATCTGTAA- 1354
                         i   vv i   i     i     v i                 i  i  -
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_214078372_   1355 TCATATATCTGGCAAGGAATTAATATACAGAATATATAGAGAATTCCTAA 1404
                                    ii    i i vi   v           i    i  i  v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_214078372_   1405 AACTCAACAACAA-----CAAAAAGTCCAATCCAAAAA-------AGGAC 1442
                                i  i  -----    v ii     i?     -------    i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_214078372_   1443 TTTAATAACACATTTCTAGATTGAAGATATATAAATGGT-AA--AGTACA 1489
                           v    i-        vv vv         i      i-  --  i   
  L1M4_orf2#LINE/    832 TTGAATAG-ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_214078372_   1490 TGAAAAGATGCTTAACATCATTAATCAT 1517
                                     i       ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (80 / 62)
Gap_init rate = 0.02 (15 / 825), avg. gap size = 2.47 (37 / 15)  


 854 27.86 2.29 1.15  chr2_214120029_214125444     3815  4076 (1340)    L1M4_orf2#LINE/L1        1   265 (643)  

  chr2_214120029_   3815 TGGAAAAACATCCCATGCTCATGGAGTGGAAAAATTAATGGTATTAAAAT 3864
                               i i        i       v     i v     iv i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214120029_   3865 GACCATA-TACCCAAAGCAATCTACAGGTTTAATACAATTCCTATCAAAA 3913
                          i v   - v      vii        i  i  ii    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214120029_   3914 TACCAA-TGTCATT---ATAAAGAATTATAAAGTATAATCTTAAAATTTA 3959
                          v   i-  i v  ---ii i -    ivv   i- i   i       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGC-TGATCCTAAAATTCA 148

  chr2_214120029_   3960 TATGGAATCATAAAAGAGCCCAAATAGCTAAATAAATTCTAAGCAAAAAG 4009
                                viii  ii  v  vi      i   vv   ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_214120029_   4010 AATAAAACTGGAGGTACT-GCATTACCTAACCTCACATTTTACCACAAGG 4058
                           i   ii      -   -i  i v  i  ii   v vi    i    i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_214120029_   4059 CTATGGCAACCCAAACAG 4076
                            ii i  i v i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAG 265

Transitions / transversions = 2.65 (53 / 20)
Gap_init rate = 0.03 (7 / 265), avg. gap size = 1.29 (9 / 7)  

1939 22.66 3.58 0.20  chr2_214120029_214125444     4422  4924 (492)    L1M4_orf2#LINE/L1      389   908 (0)  

  chr2_214120029_   4422 AGGACACTGTTTTCAATAAATGGTGCTGGGAAAATTGGATAGCCGGATGC 4471
                           i i v v       i              v  i      ?  iv    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_214120029_   4472 AGAAGGATAAAACTAGACTCCTATCTCTCAGCATATAGAAAAATCAACTC 4521
                          i   i  i  ii i   i    i   v  v      v      i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_214120029_   4522 AAGTTGGATTAAAGTCTTAAATATAAGACCTGATACTATTAAAATACTAG 4571
                           iv     i ?  v i     i     v  i v     v   v vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_214120029_   4572 AAAAAGACCTAGGAA-AAATACTTCTGGACATTGATTTACGCAAGGAATT 4620
                           i  i  v    ?i-    -    vv   v   iv   v    v iv  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_214120029_   4621 TATGACTAAGACCTCAATAGCACAAGTAATAAAAACAAAAATAGATAAGT 4670
                         iv iiv  v   vi   v        i  i    iv            i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_214120029_   4671 GGGACTTAATTAAACTAAATAGCTTCTGCCCAGCAAAGGAAATAATTAAC 4720
                         v      v  i   v v  v i   i  iv vv       v iv  i  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_214120029_   4721 AGAGTTAACAGACAACTTGCAGAATAGGAGAAAGTATTTGCAAACTATGC 4770
                          i   v  v       iii      i       i          ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_214120029_   4771 ATCTGATAGGGGACTGATATCCAGAATTTATAGGGAACTCAAACAAC--- 4817
                                 i      vi          v    ii      vv     ---
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_214120029_   4818 --AATCAAAAGA-AAA----CCA-TTAAAAAGTAGGCAAA-----TAAAT 4854
                         --   v      -   ----   -  ?    i i      ----- i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_214120029_   4855 AGATATTTTTCAAAAGAAGATATATAAATGGCTAACAAGCATA-GAAAAG 4903
                            i    i  v            i       i  i     i -      
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_214120029_   4904 ATGCTCAACATTACTAATCAT 4924
                                    i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (63 / 47)
Gap_init rate = 0.02 (8 / 520), avg. gap size = 2.38 (19 / 8)  


 470 14.44 12.22 0.00  chr2_214134445_214136439      333   422 (1573)  C L1M4_orf2#LINE/L1   (807)   101     1  

C chr2_214134445_    422 TGGAAAGATATCTCATGTCCATGGATTAGATGAATCAACATTGTTAAAAT 373
                                     i     i        i  v  v i  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_214134445_    372 GCCCATACTACCCAAA-----------ATTTAATGCAATCCCTATCAAAA 334
                          v v     v      -----------   i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_214134445_    333 T 333
                          
  L1M4_orf2#LINE/    101 T 101

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.01 (1 / 101), avg. gap size = 11.00 (11 / 1)  

1694 26.43 16.67 1.20  chr2_214134445_214136439      501  1166 (829)    L1M4_orf2#LINE/L1      112   880 (28)  

  chr2_214134445_    501 TTTTTCATAGGAAAAGAAAAAA-AATTCTAAAATTTATATGAAACCACAA 549
                              iii  i  vv  v  iv-i  i        i     i  vii   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_214134445_    550 AATACCCAGAATAGACAGAATAATGCTGATCAAAAAGAACAAAGCTGTAG 599
                         iiv           v  i  i   vi   vv  i          i  v  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_214134445_    600 TCATCATACTACCTGGCTTCAAAATATACTACAACACTATAGTAACCCAA 649
                         vvv   i   v  iiii       iv        vi   i     i v i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_214134445_    650 ACAGTATGGTACTGGCATAAAAATAGACATATAGACTAATATTAGAAACA 699
                              i              ii             ii   ---- i  i 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT----GGAATA 307

  chr2_214134445_    700 AAAGACAAAATTCAGAAATAAATCCACTCATTTACAGTCAACTCCTTTTT 749
                         i  vvv i i i          i   iv      ii     i vv    i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_214134445_    750 GATAAAGGCACCAAGAACATATATTGGAGAAGGGAAATCCTTGTCAATAA 799
                           i  i  ii      v   vi v   i   i i v vi   v    i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_214134445_    800 ATGATGCTGGGAAAACTGAATATCCATATGCAGAAGAATGAAACCGGACC 849
                            i        v     i   ?   i     i         iii     
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_214134445_    850 CCTGTCTCTCACCATATATAAAAATCAA----------ATTAAGGAC--- 886
                            ii   v         i      i  ----------  i ?i   ---
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_214134445_    887 -------------------------------------------------- 886
                         --------------------------------------------------
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_214134445_    887 ------------------AGGCA-CAGT------AATAT--CACTAAAA- 908
                         ------------------     -ii  ------i    --   i    -
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_214134445_    909 CACAGGTGACCAAAGCAAAAATGGACAAATGGAATCACACCAAACTAAAA 958
                             i ii  v    v      i  i    v i iiv  i    v v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_214134445_    959 ATCTTCTGCGCAACAATGAGAACA--ACCAAACAAAATGAAGAGACAACC 1006
                          v   i  i  vv   --  i   -- i   i-   i    i        
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAA--AGGACACTATCAAG-AAAGTGAAAAGACAACC 704

  chr2_214134445_   1007 TACAGAACGGAAGAAAATACTTGCAAACGATTCAACTGACAAGAGATTAA 1056
                         i      i  i        i       iv  vi v    i   i  i vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_214134445_   1057 TAACCAGAGTATATAAGGAATTCAAAAAGTTCAATAGAAAAAACCTCAAG 1106
                           v     i       i   i  vv v ii      iv     vv-   i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAA 803

  chr2_214134445_   1107 TAATCTGATTAGAAAATGGACAAAGA-----------------TCAAAAG 1139
                            i ii   ?i       i     i-----------------  v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_214134445_   1140 AAGACATATCAATGACCAACAGATATA 1166
                             i   iv    i    i iii i 
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACA 880

Transitions / transversions = 2.20 (119 / 54)
Gap_init rate = 0.02 (13 / 769), avg. gap size = 9.15 (119 / 13)  

 222 17.39 0.00 0.00  chr2_214134445_214136439     1458  1503 (492)    L1M4_orf2#LINE/L1      863   908 (0)  

  chr2_214134445_   1458 AAATGACCAACAGATATGTGAAAAAATGCTCAACATCACTAATCAT 1503
                              i    i iii ii      i             ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (8 / 0)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.00 (0 / 0)  


3207 24.89 2.91 1.35  chr2_214206681_214208937      875  1766 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_214206681_    875 GAAAATCATTCCATGTTCATGGCTTGGAAGAATCAGCATTGTTAAAATGA 924
                             ivi  i            v        v i ii        i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_214206681_    925 CCATACTGCCCAAAGCAATTTACAGATTCAGCACTACTCTTATCAAACTA 974
                          v     v      vii  i          i i v ii i       v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_214206681_    975 CCAA-TGTCATTTTTCACAGAAGTAGAAAAAGCT-ATCCTAAAATTCATA 1022
                            i-  i -     ii     i v  v  -   -               
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATA 150

  chr2_214206681_   1023 TGGAACCAAAGAAGAGCCTGAATATTCAAAGCAATCCTGAGCAAAAGGAG 1072
                              viiv iii  v  v     vi    i     i   iv  i i  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_214206681_   1073 CAAAGCTGAACACTTCATACTACCCAATTTCAAACTATATTATAAGGCTA 1122
                              i  i vivi   i   v            viv  i  i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_214206681_   1123 CAGGAACCAAAACATCATTGCACTTGTATAAAAACAGACACATAGACCAG 1172
                            v  i   i   vii v i   v i    ii i     i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_214206681_   1173 TGGAACAGAATAGAATAGAAAACTCAGAAATAAAGCCACACA-------- 1214
                              -----      v  i iii          v   i   --------
  L1M4_orf2#LINE/    301 TGGAA-----TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_214206681_   1215 CATCTGATCTTTGGCAAGGATGACAAAAACA---AATGGAGAAAGGGCTC 1261
                           vi    i  i i     i  v   i v  ---     i     iiivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_214206681_   1262 CCTGTTCAATAAATAGTGCTGGGACAATCGGCCCGTTATATGGAGAATAA 1311
                         i  v     i    i            ii  viv?ii i   v i  v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_214206681_   1312 TGAAACTGGACCCTTACCTTTTACCATATACAAAAATTAACTCAAGATGG 1361
                             ii       i     ivi                       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_214206681_   1362 ATTAAAGATTTAAATGTAAGACCTAAAACTATGAAAATTCTAGAAGAAAA 1411
                           i ?   ii           v          i   v ii          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_214206681_   1412 CCCTAGG---AAGTTCCCTTCTTGAGATGGGCCTTGGCAAAGATTT-TTG 1457
                          v-    ---  i ---    v   vv v  vi v     v i   -  i
  L1M4_orf2#LINE/    546 CA-TAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_214206681_   1458 GACTAAGGCACCAAAAGGAACTTCAACAAAAACAAAAATTGACAAGTAGG 1507
                           -  v i         v vvvv        iv      v  i  i v  
  L1M4_orf2#LINE/    592 GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_214206681_   1508 ACCTAATTAAATAGAAGAGTTTCTGTACAACAAAAGAAATTATCAATAAA 1557
                           i v  i   vvv  i ii  i   i vv    i  v i      v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_214206681_   1558 CTAGATAGACACCCTACAGAATGGGAGCAAATATTCACAAACTATGCATC 1607
                         v ii v     v  i            v       ii    ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_214206681_   1608 TGGCAAAGGCCTAGTATCTAGAATCTGTAA-GAA--------ACTTAACA 1648
                           ii  i  v  v     i     v i   -   --------   i  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_214206681_   1649 AGCAAAAAACAAATAACCCCACTGATAAATGGGCAAAGGACCTGAATAGA 1698
                          vv    i           v i ? v              ii        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_214206681_   1699 CACTTTTCAAAACAACACATACAAGTGGCCAACAGACATATGAAAACATG 1748
                           i  i  v   v  v i      i       i ii  i       v   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_214206681_   1749 CTCATCATCTGCCATCAT 1766
                             v    v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (136 / 83)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 2.71 (38 / 14)  


3303 26.87 0.44 0.44  chr2_214257714_214263992.rev     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_214257714_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214257714_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214257714_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_214257714_   5028 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_214257714_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_214257714_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_214257714_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_214257714_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_214257714_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_214257714_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_214257714_   5376 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_214257714_   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_214257714_   5476 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5525
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_214257714_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_214257714_   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_214257714_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_214257714_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_214257714_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_214257714_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2783 27.05 0.91 0.68  chr2_214325464_214330006.rev     3174  4049 (494)    L1M4_orf2#LINE/L1        1   878 (30)  

  chr2_214325464_   3174 TGGATACACATCCCATGCTCATGGACAGGTAGAATCAATATTGTAAATAT 3223
                             v v i        i       iv  v   v i        v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214325464_   3224 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 3273
                          i v     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214325464_   3274 TACCAACATCATTCTTTACAGAACTAGAAAAAATAATCCTAAAATTCACA 3323
                          v   i vv v  i   i     v v  v  iv i             i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_214325464_   3324 TGGAACCAAAAATGAGTGCACACACATGATCAAAACAAGACTAATCAAAA 3373
                              viiv  iv  --- v  v -  iii        vvi i vv  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGA-ATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_214325464_   3374 AGCACAAATCTGGGGGCATAATATTACCCAACTTCAAACTATACTACAAG 3423
                           v     vi   i  vv v i i v     i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_214325464_   3424 GCTATAGTCATGAAAACAGCAAGGTACTGGCATAAAAATAGGCACACAGA 3473
                             i   v  v  i    iiv             ii    i  i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_214325464_   3474 CCAATGGAACAGAATAAAGAACCCCCAAATAAACCCAAATACTTACAGCC 3523
                         i        i     vi   ii  vv           v i i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_214325464_   3524 AACTGATCTTTGACAAAGCAAACAAAAATATAAAGCGGGGAAAATACACC 3573
                           i    i  i     i vviv   i vi  vv ii       iv i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_214325464_   3574 CTATTCAACAAATGGTACTGGGAAAATTGGCAAGCCACATGTAGAAGAAT 3623
                           v             i      v  i   vv ?       i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_214325464_   3624 AAAACTAGATCCTCATCTCTCACCTTATACAAAAAATCAACTCAAGATGA 3673
                         i  ii i  i  ii i   v    v          - i       i   i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGG 495

  chr2_214325464_   3674 ATCAAAGACTTAAATATAAGACCAGAAACCATAAAAATTTCAGAAGACAA 3723
                             ?    i     i     v vi    i      v i i      v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_214325464_   3724 CATTGGAAAAACTCTTTTAGACATTGGCTTAGGCTAAGAGTTCATGACCA 3773
                            v  ?iv  v    ivv   v    v      v v iv   v iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_214325464_   3774 AGTAC-CCAAAAGCAAATGCAACAAAAGGAAAGACAAATAGACGGTACTT 3822
                         v -  -         v v          i   i i i   i iv v    
  L1M4_orf2#LINE/    596 TG-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_214325464_   3823 AATTAAACTAAAATGCTTCTGCACAGCAAGAAATA--ATCAGCAGAGCCA 3870
                         v  i   v v   vi   i  ii vv   iii i --    iv i  iv 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_214325464_   3871 GCAGACAACCCACAGAGTGGAAGAAAATTTTTGCAAACTATACATCTGAC 3920
                         iv              i   i       v        ii   i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_214325464_   3921 AAAGGAATAATATTCAGAATCTACAAGGAACTCAAACAAATCAGCA-TGA 3969
                           i   v vi   i      v  i  i      vv    v   ii - i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_214325464_   3970 AAA-AC---TAATCCCATCAAAAAGTAGGGAAAGGACATGAATATAAAAT 4015
                            -  ---   i  v  i?    i i  v      iv      v v v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_214325464_   4016 TCTCAAAAGAAGATATACAAATGGTCAAGAAACA 4049
                             v                   i   v  i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

Transitions / transversions = 1.28 (131 / 102)
Gap_init rate = 0.01 (9 / 878), avg. gap size = 1.56 (14 / 9)  


2408 23.97 2.29 0.76  chr2_214452143_214453774      486  1140 (492)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr2_214452143_    486 AAAACAACAAAAAACAA-ACAGTATGGTACTAGAATAAAGACAGCTATAT 534
                            i v   iv  v   -     i       i v    i  i  vi    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_214452143_    535 AAACCAATGAAACAGAAAACAGAACCTAGAAATAAACCCACACATATGCA 584
                          i i     i  i    vvv   ii i             i    v iii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_214452143_    585 ATCAAATTATCTTCAACAAGGGGGCTAAGAACACACAATGGAGAAATAAT 634
                         i    v v  i   i       v  i    v  iv      i    v   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_214452143_    635 AGTTGTTTCAACAAATGAATTTGGAAAAACTGGTTACCCTCATGTAAAAG 684
                            iv            ivvi   i v      v  ?  v    i     
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_214452143_    685 AATGAAATTGAACCCTTACCTTGCACCATACACAAAAATAAAC----AGT 730
                               i   i    i     ii       i        v   ---- i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_214452143_    731 --ACTAAAAATTTTAACA-AAGACCTGAAACTATAAA--TCCTATTTAAG 775
                         -- ii ? i ii v  ii-    v  i          --  i  v--   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG--AAG 541

  chr2_214452143_    776 AAAACTTAGGGGAAAATTTT-ATAACATTTGTCTTGGCAATGATTGCTTG 824
                              v    ? v    i  -i i  v  v vi v       i  v   i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_214452143_    825 GATAAGGCACCAAAAGCGTAGGCAACAAAGGCAGAGATA-ATAAGTCGAA 873
                             v i          ii i        i v i i   -    i i i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_214452143_    874 CTACACCAAACTAAAAAGCTTCTGTACAACAAAGGAAGCAATCCAACAGA 923
                           v  i    v v    i   i   i vv       vi v   -  v i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC-AAGAAA 690

  chr2_214452143_    924 GTGAAAATGCAGTCCACGGAATGGGGGAAAGTATTTGCAAGTTGCAAATC 973
                                vi  ii    i       i    i         i iii v   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_214452143_    974 TTATAAGGGGTCAATCTTTAAAATATGGAAAGAACTCCTACAACTCAATA 1023
                          v       iiivi v ii i     iv         i            
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_214452143_   1024 GTTAAAAAAACCAAATAACCTTATTTAAAAATGGGCAAAGAACTTGACTA 1073
                         i -     i  -        iv   ?              i i    v  
  L1M4_orf2#LINE/    791 AT-AAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_214452143_   1074 GACATTTCTCCAAAGA---CATAAAAATGTTCAACAGGTGTATGTAAAGG 1120
                                         ---i   v     vi   i i iii   v    i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_214452143_   1121 TGCTCACCATCACTAATCAC 1140
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (99 / 54)
Gap_init rate = 0.02 (12 / 665), avg. gap size = 1.67 (20 / 12)  


2792 22.19 3.95 0.46  chr2_214487796_214490170.rev      721  1378 (997)    L1M4_orf2#LINE/L1        1   681 (227)  

  chr2_214487796_    721 TGGAATAGCATCCTATGTTCATGTATCAGAAGACTTAATATTGTTAAGAT 770
                              viii    i         v  ii                      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214487796_    771 GGCAATACTCTACAAATTGGTCTATAGATTCAATGGAATCTCTATCAAAA 820
                                   iv       i    i        i v    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214487796_    821 TCTCTGCTTTTTTGGTTTTGCAAAAACTTACAAGCTGATCCTAAAATGTC 870
                           i v   vii  --       i   i v                  viv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_214487796_    871 TACATAAATACAAAGATGCCA-AATTGCCAAAGAAACCTTAAAAAATAA- 918
                           iiv    i   i ivv   -   v      iv  i   i     v  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_214487796_    919 --CAAATTTGGAGGAATTACATTTCCCCATTTCAAAACTTATTACAAACC 966
                         --    v        v i   i     v             i      v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_214487796_    967 TACAGTAA--GGAATAG---GGTACTGGCATGATGACAGACATGTAAATA 1011
                                 --iii i  ---           i v  i      i  i  v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_214487796_   1012 AATGGAATATAATTAAGAACCCAGTAATAAACTCTTACATTTATGATCTA 1061
                                  v    i   ii    v       i v          i  v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_214487796_   1062 TTGATTTTTTAACAAATATGCTAGGAAATTTTAATAGGAAAGGAATAGTC 1111
                                 i-i    ivi   i i  vvv  i   i  i  i        
  L1M4_orf2#LINE/    349 TTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_214487796_   1112 TTTTTAAGAAATGGTGCTGAGACAATTGGGCATCCAT-TGTAAAAATATA 1160
                             i  v           i     i   ii ?   i-  i    iv  i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_214487796_   1161 AATTTCTACCCTTATTTCACAGCATACAGGAAAATTAAATAAAAATGGAT 1210
                           v  vv    i  ii     v    i vi        v v         
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_214487796_   1211 CACGGACCTAAACATAAGAGGTAAGGTTATAAAAC-------AGAAAACA 1253
                           ?i        ii      v   iii        -------        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_214487796_   1254 TTGGAGTAAATTTTCATAATCTTGGGTCACTCCCTGACTCATTAGAT-TG 1302
                          v  ?      i   i i i       i vv vv  ii iv      -  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_214487796_   1303 -TATTAAAAGTACAAGTGATAAATAAACAA-----TACACTAGGCTTCAT 1346
                         -i ii     i     ii i   vi  v  -----  v i i i      
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_214487796_   1347 CAGAATTTAAAAGTTTTATGCTTCAAA--ACATT 1378
                           i    v    v    i         --   i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

Transitions / transversions = 1.86 (93 / 50)
Gap_init rate = 0.02 (12 / 681), avg. gap size = 2.42 (29 / 12)  

 947 19.72 3.67 0.46  chr2_214487796_214490170.rev     1672  1889 (486)    L1M4_orf2#LINE/L1      684   908 (0)  

  chr2_214487796_   1672 CAAACAAACAAACAAAAAATGCCATAGAATGGGAGAAAATATTTGCAAGT 1721
                            iv  iii  v i v  i-   i                       i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAAC-CCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_214487796_   1722 CATAAGTCTGATAAGGGATTTATATCTAAAATATATAAAGAACGCTTACA 1771
                             vi            i  i    i i              v      
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_214487796_   1772 AGTCAATAACAAAAGAGTAAATAATTCAAC----AAATGGTTAAGGGAAT 1817
                          v       i    iiii      ii   i----      vi  i   v 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_214487796_   1818 TGAA----CATTTTTCCAAAGAAGATATATGACTGGGCAATAAGCACATG 1863
                             ----     i               ii v   v             
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_214487796_   1864 AGAAGGTACTCAGGAGTAGTCATTAG 1889
                          i   i i    iv vi ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.58 (31 / 12)
Gap_init rate = 0.01 (3 / 225), avg. gap size = 3.00 (9 / 3)  


2836 25.53 2.68 1.78  chr2_214568140_214572132.rev      786  1682 (2311)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_214568140_    786 AAAGTAACATTCCATGCTCATGGATTGGGAGAGTCAATATCATTAAAATG 835
                             -- i  i     i           i   v i     ii    i   
  L1M4_orf2#LINE/      4 AAAG--ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_214568140_    836 ACCATACTGCCCAAAGCAATTTACAGATTCAATGCCATTCCTATCAAACT 885
                         i v     v      vii  i           i  v  i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_214568140_    886 ACAAACATCATTCTTCACAGAATTAGGAAAAAACT-ATTCAAAAATTCAT 934
                         v v i vv v  i  ii     v v -- v  i  -  i v         
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_214568140_    935 GCGGAAC--CAA-------AAAAGAGCCTTAACAGGTCATTCAAACAAAG 975
                         ii    v--   ------- i  v    vv    i-  -  v   --   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TC-TTGAAA--AAG 195

  chr2_214568140_    976 AAGAGCAAAGCCTGAGGCATCACATTATCTGACTTCAAACTATACTGAAC 1025
                             i     iiv    vv     i vi ii i      viv    iv v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_214568140_   1026 AGCTACAGTAACCAA-ATGGCATGGCACTGCTACAAAAAGAGACATA--G 1072
                                    i   - ii ii   i    vi i  ii v       -- 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_214568140_   1073 ACTAATGCATCAAAATAGAGAACCCAGAAATAAAGTCACACACCTACTGC 1122
                          ii    v vi i   v    ii           vi  i   ii  iv i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_214568140_   1123 CATCTGATTTTCAACAAAGCTGACAAAAATATGCGATGGGGAAAGGACTC 1172
                           vi        i    i v  v   i vi  v i          i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_214568140_   1173 TCTATGTAATAAATGGTGCTGCAATAGCTGGCTAGTTATATGCACAAGAA 1222
                            v vi  i           vi i i    v  ?ii i     v     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_214568140_   1223 TGAAACTGGACCCTTACCTTTCATCATATATAAAAATTAACTCAAAATGT 1272
                             ii       i     iv  i      i                  v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_214568140_   1273 GTTAAAGAATTAAATGTTAAGACCTCAAACTATAAAAATCCTAGAAGAAA 1322
                         i i ?   vi       -    v  v           v  i         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_214568140_   1323 ACCTAGG---AAATACCATTCTTGACATCAGCTTTGGCAAATAATTT-TT 1368
                           v    ---    -- -   v    v ii v  v     - ii   -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAA-TGGTTTCTT 590

  chr2_214568140_   1369 GGCTAAGTTGCCAAAA--ACAATTGCAATAAACACAGAAATTGACAAGTG 1416
                         i v  v vii      --    --    i   viv i    v  i  i v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATT 638

  chr2_214568140_   1417 AGACCTAATTAAA-CTAAAGA--TCTGCACAGCAAAAGAAAGTATCAACA 1463
                         i   i v  i   -i    i -- i  ii vv    i  v v      v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_214568140_   1464 GAGTAAACAGGCAATCTGCAGAAATGGGAGAAAATATTCTCAAACAATGC 1513
                         i   i  v  i   i ii     -              iv    iv  ii
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATAT 737

  chr2_214568140_   1514 ATCTGGCAAAAGTTTAATATACAGAATCTACAAGGAACTTAAACAAATCA 1563
                              ii  ii vi vi   v      v  i  i     ivv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_214568140_   1564 ACAAGCAAATAACAGGTAACCTCATTAAAAAGTGGGCAAAGGCCATGAAC 1613
                          i  vv   vi   ii     iv   ?    i          viv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_214568140_   1614 AGACACTTCTCAAAAGAGGACATACAAGGAGCCAATA--CACATGAAAAA 1661
                              i     v     i  i      ivi       --          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_214568140_   1662 ATGCTCATCATCACTAATCAT 1682
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.02 (22 / 905), avg. gap size = 1.82 (40 / 22)  

3037 25.41 1.77 1.44  chr2_214568140_214572132.rev     2609  3513 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_214568140_   2609 TGGAAAACCATCTCATGCGCATGAATTGGAAGAATGAATATCA-----AT 2653
                               ivi   i    iv    i         v v     ii-----  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214568140_   2654 GACTATACTATCCAAAGCAATCTACAGTTTAAGTGCAATCTCTATCAAAA 2703
                          i v     vi     vii        v  v ii      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214568140_   2704 TACCAA-TGTCATTTTTCACAGAATTAGAAAAAAAAATCCTAAAATTCAT 2752
                          v   i-  i -     ii     v v  v  ivvi              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_214568140_   2753 ATGGAATCAAAAAAAGAGCTCA-AATAGACAAAGCAATCCTAAGCAAAAA 2801
                               -- viv  i ii i  -     v    i     i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_214568140_   2802 GAACAAATTTGGAGGCATCACATTACCTGACCTCAAATTATACTACAAAG 2851
                                v       vv     i v  ii ii     viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_214568140_   2852 CTACAGCAACCAAAACAGCATTGTACTGGTATCAAAATAGACA-ACAGAT 2900
                               i  i   i    ii v       i  v ii       - i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_214568140_   2901 TGACAGAACAGAATAGAGAACCCAGAAATTAAATCACACATCCACATCCA 2950
                         ii ii   i     v    ii        v  vi  i    ii iivi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_214568140_   2951 CCTGATCTTTGACAAAGTTGTTGTCAAAAACATGCACTGGGGAAAGGGCA 3000
                         vi    i  i     i --  - i   i v   v  v         iii 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG--GT-GCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_214568140_   3001 CCCTTTTCAA-AAATGGTGCTGGGAAAACTGGATTGCTATATGCAGAAGA 3049
                         vi        -              v        v? i i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_214568140_   3050 ATAAAGCTGGACCCCTATCTCCCACCATATACAAAAATCAACTTAAGATG 3099
                           i   i          i   v                i    i  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_214568140_   3100 GATTAAGAATTTAAATGTAACACTCGAAACTATTAAAAT----GATGAAA 3145
                            i ?ii ii         v viii       v   v ----  v    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_214568140_   3146 ACAGAGAA--AACTCTTCTGGATGGTGGTTTAGGCAAAGAATTTATGACT 3193
                            v  i?--  v     vv  ivv   v        v iv  iv iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_214568140_   3194 AAGACCTCAGAAGCACAAGCAACAAAAACCAAACTAGACAAAT-AGACTT 3242
                          v   vi  i                 ivv   v    i    -i     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_214568140_   3243 AATTAAACTGAAAAGCTTCTGCACAGAAACATAAATAATCAACAGAGTAT 3292
                         v  i   v v    i   i  ii vvv  viv v iv     v i   iv
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_214568140_   3293 ACAGGCAACCTGCAGGATGGGAGAAAATATTTGCAAACTATGTATCTGAC 3342
                          v  i     ii   i                     ii  i       i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_214568140_   3343 AGGGTAATGATATCCAGAATTTACAAGGAACTCAAAAAACTCCGCAATAA 3392
                          i  v v vi          v  i  i      vv v     ---     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC---AATAA 791

  chr2_214568140_   3393 CAAAAATTCCCAATAGCCCCAATAAAAAGTGGGCAAAGAAAATGAATAGA 3442
                         i     v-v v    i   v v ?    i         i vv        
  L1M4_orf2#LINE/    792 TAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_214568140_   3443 TATTTTCCAAAAGAAGACAGACAAGTGGCCAAAAAGCATATTGACAAATA 3492
                         i    ii v        i v    i       v     i  vi v i  i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_214568140_   3493 CAAGTTAAAAACACAAGGAGA 3513
                          --- i  v v  ????????
  L1M4_orf2#LINE/    891 C---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (132 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.93 (29 / 15)  


3108 21.63 3.43 6.21  chr2_214583899_214586935     1615  2548 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_214583899_   1615 TGAAAAGATATTTCATGCTCACGGATTGGAAGAATTAATACTTTTAAAAT 1664
                           i        ii    i   i           v      i v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214583899_   1665 GACAATACTACCCAAAGTGATCTACAGATTCAATGCAATCCCTATCAAAA 1714
                          i       v      v                i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214583899_   1715 TACCAA-TGCCATTTTCACAGAAATAGAAAAAGCAATCATAAAATTCCTA 1763
                          v   i-    v    ii       v  v  ivii   v        v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_214583899_   1764 TGGAACTAAAAAAGGCCCTGAATAGCCAAAGCAATCCTGAGCAAAAAGAA 1813
                              v iv  ii i   v           i     i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_214583899_   1814 CAGAGCTGGAG---TCACACTACCTGACTTCAAAATTTATTACAAAGACA 1860
                           i  i     ---       v  ii i       i   i       vi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_214583899_   1861 TAGTAACCAAATTATTGTGGTA--------AAAATAGACTCATAAACCAA 1902
                         i     i   ivi v       -------- ii      vi   i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_214583899_   1903 TGGAACAGAATAGAAGACCCAGATATAAATCCGTGCATTTGCATCCAACT 1952
                              i     v  iiii     v     i  i i     iiivi   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_214583899_   1953 CATCTTTGGCTAAGGTGCTAAGAACAT--AATGGGGAAAGGATATTCTAC 2000
                         v  i  i i v i     i    v   --           i   v   --
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT-- 398

  chr2_214583899_   2001 ATATGTTCTCACTCATGTGGAAGCTATATTTAATAAATGGTACTGGGAAA 2050
                         -----  ---------------------- i  i       i      v 
  L1M4_orf2#LINE/    399 -----TT----------------------TCAACAAATGGTGCTGGGACA 421

  chr2_214583899_   2051 ACTATATAATTA--TGTAGAAGAATAAAACTGGATCCCCATCTTTTACCA 2098
                            iv   ?ii --  i i      i  ii    i   i i  ivi    
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_214583899_   2099 CACACAAAAAT-AA----AAATGGACTAAAGACTTAAATCTCAGACCTGA 2143
                         i i        -  ----       ii ?    i     v v   v  i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_214583899_   2144 AACTATGAAACTGCTAGAAGAAAGCATTGG-GTAAGCACCCCAGGACATT 2192
                               i     vi         i   v  -    ii- ii iv   v  
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTT 570

  chr2_214583899_   2193 GGTCTGGACAAAGATTTTGTG--TTTCATACTGTAAAAGCACAGGCAACT 2240
                           vi i i   v i   iv i-- v v i  i--         i     v
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACC--AAAAGCACAAGCAACA 618

  chr2_214583899_   2241 AAAGCAAAAAATAAAAAATAAAAAAAAATGAAAAGAAAAACCAGGATTAT 2290
                             -        i ---    -------------------iv   i vi
  L1M4_orf2#LINE/    619 AAAG-AAAAAATAGA---TAAA-------------------TTGGACTTC 645

  chr2_214583899_   2291 ATCAAGGT-AAAATCTTCTGCACAATAAATGGA-ATTATCAACAAAGTGA 2338
                              ii -    v   i  ii vvi   -   - i      v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGA 694

  chr2_214583899_   2339 AGAGACAACCCATAGAATGGAAGAAAATATTTGCAAATTATCCATCTGAT 2388
                          i          i       i                 i  vi       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_214583899_   2389 --GGAATTAATAACCAGAATATATAAGGAGCTCAAACAACTCAATAGCAA 2436
                         --  i i vi  v             i  i   vv           ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_214583899_   2437 ATGAATAAATTGTCCAGT---AAAATGG-CAAACAGACCTGAATAGACGT 2482
                          vii i    vii   i ---       -    -i  ii         i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAA-GGATTTGAATAGACAT 843

  chr2_214583899_   2483 TTATCAAAAGAAGACATACATATGGCCAAAAGGTATATGAAAAAAATACT 2532
                           v  v        i     v        v i i i       i - i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr2_214583899_   2533 CATCACTAATCATCAG 2548
                           v  ii ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.28 (139 / 61)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.75 (90 / 24)  


2401 21.74 5.08 5.99  chr2_214644672_214646401.rev      500  1267 (462)    L1M4_orf2#LINE/L1      148   908 (0)  

  chr2_214644672_    500 ATACAGAAATCCAAGAGATCCAGA----TTAAAGTGATCTTAAAAAAGAA 545
                            ii     v    i  i     ----ii   iii     i        
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_214644672_    546 ---CAAAGTTGGAAAA--------TCCTGACTTCAAAACTTACTATAAAG 584
                         ---          ii --------   ii i              i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_214644672_    585 CTACAGTAATTAAGACAGTGTGGTACTATTATAAGGATAGACATGTAGAT 634
                                   i                ivi              i     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_214644672_    635 CAATCTGACAGAATTAAGAGTCTAATAATAAACTACTATATTTATAGTTA 684
                             vvi i      i      i iv       ivv  i      i  i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_214644672_    685 AATGATTTTCAACAAGCGTACCCCAACAAGTCAAGGATGAAATAGCGTTT 734
                          v        i     v  i  vvi  v v    v iv    --------
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-------- 389

  chr2_214644672_    735 TCATCAAAT-GTCTTTTCAACTAAA----GTTTGAACAAGTGAACATCCA 779
                         -----i   -           -   ---- i v i    v  i i ?   
  L1M4_orf2#LINE/    390 -----GAATAGTCTTTTCAAC-AAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_214644672_    780 CATGTAAAAGAATACAGTTGAACTTT--CTTTATAACATAGACCAAAATT 827
                             i        iv     i  iii-- i i i v    v  v      
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_214644672_    828 AACTCAAAATGGATCATAGACCTAAATTTAAAGGTCAAAATCATAAAACT 877
                                         ?          v   ii ii    ii        
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_214644672_    878 CCTGGAAGAAAACATAAGAAAAATAAGAGTAAATGCTTATTATCTTGTGT 927
                          i i            i ?---------      vi ii v i    v  
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGN---------GTAAATCTTCGTGACCTTGGGT 574

  chr2_214644672_    928 TTGGTAATGACTTCTTAGATGCAACACCCAAAGTACAAGCAATGAAGAAA 977
                          v  i    ii         iii     v    i        ii  ii  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_214644672_    978 TTATAAATTTATTCTTTGAAGAATTGATAAATC--ATTTAACCAAAATTA 1025
                         ------------------- i   v       i-- i  v i        
  L1M4_orf2#LINE/    625 -------------------AAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_214644672_   1026 AAGGCATTTGTGCTGCAAAATATACCAT--AAAAAGTGAACAGACGAGCC 1073
                           ii v        v    iv i  i  -- i        v    i v  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_214644672_   1074 AGAAAATAGGAAAAAAT--TTGAAAATTATTTGCCTAATAAAAAAAGAAA 1121
                          v i   i   i     --   v    i  v ii  i    ii---  vv
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG---GACT 752

  chr2_214644672_   1122 TAAA---AGAAATATGTAAAGAAATCTTACAACTGAATAA----AACTTA 1164
                          iv ---    -   i       v          v     ----  vvi 
  L1M4_orf2#LINE/    753 TGTATCCAGAA-TATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_214644672_   1165 CATAAATGAATTTAAAA-TGGGCAATGAATATGAATAGACATTTATTCAA 1213
                         v    viv    ?    -       v i  v             v i   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_214644672_   1214 AGAAGACATGCACATGAATAAAATGTGAATGGAAAA---CACAACGTTAC 1260
                               i  i  v   ivi  v v iiv   i   i--- v    i i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_214644672_   1261 TATCAGG 1267
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.91 (107 / 56)
Gap_init rate = 0.02 (19 / 761), avg. gap size = 4.47 (85 / 19)  


1114 26.75 1.82 1.52  chr2_214762759_214765526     1039  1367 (1401)    L1M4_orf2#LINE/L1        8   337 (571)  

  chr2_214762759_   1039 ATATTTCATGTCTGTGCATTGGAAGAACTCAATAGCATAAAGATGTCAAT 1088
                             ii     iii  v        -   i    vii v      v    
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGATGGCAAT 56

  chr2_214762759_   1089 TCTTCTCAAATTGATCTATAAATTTAGTGAAATACCAAATAAAACATTCC 1138
                         v  i i            i i   i ii v   v  v vi    -- i  
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA--TCCC 104

  chr2_214762759_   1139 AGCAGTTTCTTTTATAGAAA--GACAAG-TGATTCTAAAATTCTTATGGC 1185
                            v ii i    ii     --      -    i         v     v
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_214762759_   1186 AATACAAAGGGTCAGGGATAGTACAGACAAGCTTTAAAAAGAA---CAGA 1232
                            i   i  ii vi i    ivv i    v   v        ---  i 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_214762759_   1233 GTTGGAAAACTTACACTACCAGATATCAAGACCTACTATAAGTCTTACTT 1282
                               ii   i     v  vi  v    i  i     i  iv -   vv
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC-TACAG 253

  chr2_214762759_   1283 TAATAATGACATGGTGATATTGGCTCAAAAATAGACAAGTAGAGTAATGG 1332
                             v v    vv   i  i    vi  ii       vi    vi     
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_214762759_   1333 AACAAAATAGAAGGCCTAAAACTGAGACCCATATA 1367
                           i i   v  ii i i i  v i -       i 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAA-ACCCATACA 337

Transitions / transversions = 1.75 (56 / 32)
Gap_init rate = 0.02 (7 / 330), avg. gap size = 1.57 (11 / 7)  

 826 27.61 8.49 4.05  chr2_214762759_214765526     1759  2276 (492)    L1M4_orf2#LINE/L1      368   908 (0)  

  chr2_214762759_   1759 CTAAGACATAAATACAATGG---AAGAGAGGTTGTTTTTATGAATGATAT 1805
                          i     v---  v      ---    ivi  iv   iv ii    i ii
  L1M4_orf2#LINE/    368 CCAAGACC---ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr2_214762759_   1806 AGGATCAATTTCATATTCATATG-ACAAGTAATAAACTATTG--CTCCAA 1852
                         v  iv   i vv   ?i  i   - v   -   i  --i   -- i  v 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAG-AATGAA--GTTGGACCCCTA 461

  chr2_214762759_   1853 ACTTATACAATACACAGGAATTAATCCTAGATAAACTATATACCTTAAAG 1902
                         v  i i  v   i   ii      ii v i  ii ii ? v    v  v 
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_214762759_   1903 TGAAGTGC-AAAGCAATAA--TTTTTAAAGAAGATAATGGAAGGGAATAG 1949
                          -   v  -   i v    --i i   --     v  iiv i ? -----
  L1M4_orf2#LINE/    512 T-AAGAGCTAAAACTATAAAACTCTTA--GAAGAAAACATAGGNG----- 553

  chr2_214762759_   1950 TCTAATCATCTT--TGACTTTTGGGTATGTGAGGATTTATTAAATGGGCC 1997
                         --   --     --    i  v  v  v ii v i   v   i  iv v 
  L1M4_orf2#LINE/    554 --TAA--ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_214762759_   1998 ACAACATGTATTATTACTGAAAGAGAAGATAGAAACACTTTCAATT--AT 2045
                           v v v i iv vi vii     i  i     v v --  vi i --  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA--TTGGACTTCAT 647

  chr2_214762759_   2046 CAAAATCAAGAAATTCCATTCATTAA----CGCCATTATGAAC-TGAAAA 2090
                               i  i  v  iii v v i  ---- i i  i v   v-      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_214762759_   2091 GACAACC---AGAGTGGGAGAAAATACCTGAAAA----AAAGCT----AG 2129
                                ---   i            ii  v   ---- v v  ----  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_214762759_   2130 GG-----TA--CAGAA-ATATGAAGCACTCCTGTAAGTCA-TAATAAAAA 2170
                           -----  --     -    i   v    i ii  v   -         
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_214762759_   2171 GACAGTT--TTCAATTAAAAAACAGGCAAGAGATTTGAACAGTACATAT- 2217
                             iv --ii     ?     ii     ii        i  -    v -
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG-ACATTTC 846

  chr2_214762759_   2218 ---ACAAAAAATATTCAAAGGACTAATAAATATATTAAAAGGCATTAAAC 2264
                         --- v i  i    v    v i i     ii i  v     iiii v   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_214762759_   2265 ATCATTAGTCAT 2276
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (85 / 54)
Gap_init rate = 0.05 (27 / 541), avg. gap size = 2.41 (65 / 27)  

 248 28.72 13.30 2.13  chr2_214762759_214765526     2581  2768 (0)  C L1M4_orf2#LINE/L1   (128)   780   572  

C chr2_214762759_   2768 GGGTATGTGAGGATTTATTAAATGGGCCACAAAATGTATTATTACTGAAA 2719
                           v  v ii v i   v   i  iv v   v   v i iv vi vii   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

C chr2_214762759_   2718 GAGAAGATAGAAACACTTTCAATT--ATCAAAATCAAGAAATTCCAT--- 2674
                           i  i     v v --  vi i --        i  i  v  iii ---
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAA--TTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

C chr2_214762759_   2673 TCACTAACGCCATTAT----GAACTGGAAAGACAACC---AGAGTGGGAG 2631
                            --  v v  i   ----i  v  i          ---   i      
  L1M4_orf2#LINE/    670 TCA--AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

C chr2_214762759_   2630 AAAATACCTGAAAA----------AAAAAAG--CTAGGGTACAGAA-ATA 2594
                               ii  v   ----------i v  i --  v vi v     -   
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

C chr2_214762759_   2593 TGAAGCACTCCTA 2581
                          i   v    i  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTA 780

Transitions / transversions = 1.25 (30 / 24)
Gap_init rate = 0.04 (9 / 209), avg. gap size = 3.22 (29 / 9)  


3150 25.36 1.11 0.55  chr2_214888586_214890314.rev      336  1238 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_214888586_    336 TAGAAACACATTCCATGTTCATGGATGGGAAGATACAATATTGTGAAAAT 385
                          i    v i  i              v      ivi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214888586_    386 GACCATACTGCCTAAAGCAATCTACAGATTCAATGTAATTCTCATTAAAA 435
                          i v     v  i   vii              i i   i ii  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214888586_    436 CACCATCATCATTCTTCACAGAACTAGAATAAAC-AATCCTAAAATTCAT 484
                         iv   v vv v  i  ii     v v  -i  i -i              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chr2_214888586_    485 ATGGAGCCAAAAGTAGCCCACA-TAGCCAAAACAATACTAAGCAAAAAGA 533
                              iviiv   vii    v -             vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_214888586_    534 ACAAATCTAGAGGCATCACATTACCCGACTTCAAATTATACTACAAGGCA 583
                              vi i    vv     i v   i i      viv        i  v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_214888586_    584 ATAATTATCAA-ATAGCATGATACTGGTATAAAAATAGGCATGTAGACCC 632
                          i i v     - i  ii  i      i    ii    i   i    i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_214888586_    633 AGGGAACAGAATAGAGAACCCAGAAATAAGCCAA-ATACTTATAGCCAAC 681
                          v    i     v    ii          i  v - i i    i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_214888586_    682 TGATCTTCGACAAAGCAAACAAAAACA--CAAATTGGGGAAAGGACACCC 729
                             i        i vviv   i v  --   --         i i vi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTC 397

  chr2_214888586_    730 TGTTCAATAAATGGTGCTGGGAAAACTG-ACAAACACATGTGGAAGAATG 778
                          v     i              v     - i ?v      iii       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_214888586_    779 AAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGAAGGAT 828
                           ii    i  ii i   v    v           i       i v    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_214888586_    829 CAAAGACTTAAATCTAAAACCTGAAACCATAAAACTTCTAGAAGTTAACA 878
                           ?    i     v   i v  i    i        ii      vv    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_214888586_    879 TCGGAAAAACTCTTCTAGACATTGGCTTAGGCAAATAATTCATGACTTCA 928
                          v  ?iv  v     vv   v    v        - ii  iv v vv vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATAT 596

  chr2_214888586_    929 GACCACAAAAGCAAATGCAACAAAAACAAAAATAAATAAATGGAACCTAA 978
                            vv        v v         iv       i      v i  i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_214888586_    979 TTAAA-TGAAAAAGCCTCCGCACAGCAAAAGAAACAATCATCAGAATAAA 1027
                          i   - v     - i ii ii vv    i  v  v    vv i i i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_214888586_   1028 CAGGCAGCTGAGAGAGTGGAAGAAAATATTCACAAACTACACATCTGACA 1077
                         v  i  i iv v   i   i          ii    ii i i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_214888586_   1078 AAGGGCCACTATCCAGAATCTACAAGGAACTCA-ACAAATCAGCAAGACA 1126
                          i  i ivv          v  i  i      v-    v   ii  v v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_214888586_   1127 AAAACAAGTAATCCCATCAAAAAGTGGACAAAG-ACATGAATAGAGAGTT 1175
                           i    i   i  v  i?    i   i     - iv        v v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_214888586_   1176 CTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAA 1225
                            v                       i  i  i       i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_214888586_   1226 TATCCCTAATTAT 1238
                         i   v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.15 (15 / 13)  


1547 26.09 12.16 6.49  chr2_214945930_214948814.rev     1547  2393 (492)    L1M4_orf2#LINE/L1       14   908 (0)  

  chr2_214945930_   1547 CATTTCCACGGATTGCAAGA-----TAC----AAAATA-TAATTATGCCC 1586
                            v i  i      v    -----  i----  i  i-i   vv v   
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr2_214945930_   1587 AAATTAATCTATACATTCCACAC---------CAAAAGAGTTCCCA--TA 1625
                              i     i v    v  i ---------     ----     -- i
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAA----TCCCAGCTG 109

  chr2_214945930_   1626 A-TTTTTTAAACAAATTGACAAGATG---TTAAAATTTATATGGAAATGC 1671
                         v-      iv v           v  ---i       i            
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_214945930_   1672 AAAAAATAAAAACTTTGAATAGGTAAAAGAATCTTGAAAA-GAAAAACAG 1720
                           iii ------ iiv      vi    v           -   i    i
  L1M4_orf2#LINE/    160 AAGGGA------CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_214945930_   1721 CTTTGGAGGACTTCTAACCGTTTGACTTTAAGACTTATTATAATGCTACA 1770
                         vv          ivi - iviiii i  i  i     i  i  v      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACA-CTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_214945930_   1771 TTAA---GGAAAGTGTGGTACTGGCATAAAAATTGACA-ATAGATCAATG 1816
                         v   ---i  v                  ii  v    -           
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_214945930_   1817 TAACAAACTGAAGAGGCAATAGAAAGTAGACTCATATAT--ACAACCATT 1864
                         v  i i v vi    v --i     -  i  i    i  -- iiii  v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTC--CAGAAA-TAAACCCATACATTTATGGTCAAT 349

  chr2_214945930_   1865 TCACATTTAATAAAGGCACCAAAGGAACCCAGTGTGGACAGTTAAGGGTT 1914
                          v iv  ii i  i  ii    iivv ii  i  v   v  --  vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG--AATAGTC 397

  chr2_214945930_   1915 TGTTGTTGTTCTTGTTGTTGTTGTTGTTTGTTTGTTTGTTTTAAACACAT 1964
                          --------------------------------------   v    v  
  L1M4_orf2#LINE/    398 T--------------------------------------TTTCAACAAAT 409

  chr2_214945930_   1965 GGTGCTGAAATCATCAGGTAACAATCAGCAACAACAAAAACTCTCGCCCA 2014
                                ii iv iii i  ? v ivv    v iv vi  v ivvi   v
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr2_214945930_   2015 GATTT-ATAACATACAGAAAAGTTAATTTCAGATGGATCATAGATC--AA 2061
                         v ii - i v    i v    i    i iv i        ?   i --  
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_214945930_   2062 TATA----TTAAAACTATAAAGCTTTTAGAAAACAGCAAAGGAGAATACC 2107
                          i  ----i            i  i      i v i  v   ? v v i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_214945930_   2108 TTTTCAAATAAGAAGTAGACAGAGGTTTCTAGGACAGGTC-CTAAGAGGC 2156
                           ivii vivv iiv   i  iv       vi  i v v - i  i  - 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG-C 608

  chr2_214945930_   2157 ACTAACCGTAAAAGAAAAGA--AATAAATGAG-------CAA-------- 2189
                           v i vii         i --i      vi -------   --------
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr2_214945930_   2190 --------GCCACAAA-----CTA----------GAAAAAACAA------ 2210
                         --------  iv    -----   ----------     i    ------
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr2_214945930_   2211 ---------------TTTGCAAAACATATATCTGGCAAAGGACTGATGTC 2245
                         ---------------        v          ii  i     vi i  
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr2_214945930_   2246 TACAATAAATAACTAAGTTCTACTGCTCAGCAATAAAAAGACAAACAAGC 2295
                         i v    v    vv  v ii   vi    ii              i  v 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr2_214945930_   2296 CAATT-AAAAATGGGCAAAATATT-GAGTAGGTTCATCATTAAAAAAGGT 2343
                              -             iv   -  i   iiviv  vii   i   i 
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_214945930_   2344 GTATGAATGGCCAATACGTGCATGAAAAGGTGCTCAACATCATTAGACAT 2393
                         i  ii           v ii         i            ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (136 / 82)
Gap_init rate = 0.03 (31 / 895), avg. gap size = 5.10 (158 / 31)  


2664 17.05 0.17 20.80  chr2_214956171_214958814     1010  2153 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_214956171_   1010 TGGAAAGATACCCCATGTTTGTGAATTGAAAGAATTAATATTGTTAAAAT 1059
                                   i        ii  i    i    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214956171_   1060 GTCCATACTACCCAAAGCATTCTATAGATTCAATGTAATAACTATCAAAA 1109
                          v v     v      viiv    i        i i   vv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214956171_   1110 TTCCAA-TGTCATTCTTCACAGAAATAGAAAAAAAAATCCTAAAATTTGT 1158
                          i   i-  i -  i  ii       v  v  ivvi           ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_214956171_   1159 ATGGAACTACAAAAAATCCTGAATAACTAAAGTAACTTTTACCAAAAAGA 1208
                               v i   iii i  v     i i   ii  ---------------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA--------------- 184

  chr2_214956171_   1209 TAAAAAGCTAAAAAGATTTTTAAAAAAAGATTAAAAAGATTAAAAAATAG 1258
                         ----------------- i  i     i--------------  i  i -
  L1M4_orf2#LINE/    185 -----------------TCTTGAAAAAG--------------AAGAACA- 202

  chr2_214956171_   1259 ATAAAAAGATAAAAGCTGGAGGCACT-ATACTACTGGATTTCAAAATATG 1307
                         ------------   i      -   - i   v ivi         iv i
  L1M4_orf2#LINE/    203 ------------AAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_214956171_   1308 TTACAAACCTATAATAATCCAAACAGTATGATACTGGCATAAAAACAGAC 1357
                         i      v   i i     v i     i  i           ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_214956171_   1358 ATATTGACCAGTGGAATAGGATAGAGAGCCCAGAAATAAACCCATACATT 1407
                             v  i  i        i  v     i                     
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_214956171_   1408 TATGGTGAATTGATTTTTGACAAAGGTGCAAAGATCATACAATTGGGAAA 1457
                               v          i     i     v    i   v    v      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_214956171_   1458 GGACAGTCCCTTCAAAAAATGATATTAGGAATACTGGATATTCATATACA 1507
                          i i    ii     v     i ii i   vv        ?i  i  i  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_214956171_   1508 GAAGAATAAAAATAGGCTCTTATTTCAAACCTTGTATAAGAATCAACTCA 1557
                         i      i  iv i i i i  ii   v   v i  i  i   i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_214956171_   1558 AAGCAGGTTAAAGCCTTAAATGTAAGACCTGAAACTATAAAACTATTAAA 1607
                           iii i i ?  v i           v  i             v   i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_214956171_   1608 AGAGAACATAATGGGAAAATATCCATAACATTGACTGGTCTGGGCAATGA 1657
                            i      i- ? v    v i i i  v   ---   - i       i
  L1M4_orf2#LINE/    540 AGAAAACATAG-GNGTAAATCTTCGTGACCTTG---GGT-TAGGCAATGG 584

  chr2_214956171_   1658 TTTATTGGATATAACCTCAAAAGCACAAGCACCAAGAGAAAATAAAGATA 1707
                            v  i     i  vi              v   i      --------
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA-------- 626

  chr2_214956171_   1708 TCACAAATAAATGGAAAGATATCCCACAAATAAATTCTTTTGTGGATTGA 1757
                         -----    i  -------------------     -------   i --
  L1M4_orf2#LINE/    627 -----AATAGAT-------------------AAATT-------GGACT-- 643

  chr2_214956171_   1758 AAGAATTAATAGTTAAAATGTCCATACTACCGAAAGCATTCTATAGATTC 1807
                         ------------------------------------------------  
  L1M4_orf2#LINE/    644 ------------------------------------------------TC 645

  chr2_214956171_   1808 AATGCAATATCTATCAAAATTCCAATGTTATTCTTCACAGAAATAGAAAA 1857
                          ------------        ---------------------------- 
  L1M4_orf2#LINE/    646 A------------TCAAAATT----------------------------A 655

  chr2_214956171_   1858 AAAATCCTAGAATTTGTATGGAACTACATGGGCTTATATCAGATTGAAAG 1907
                             --  ----     --------------    ----  -----  i 
  L1M4_orf2#LINE/    656 AAAA--CT----TTTGT--------------GCTT----CA-----AAGG 676

  chr2_214956171_   1908 CTTCTGCACAGTAGGGTAAACAACAGAGTGAAGAGAAAACCCATAGATCA 1957
                         -------   v  --- ---   v i      i   v      i   vii
  L1M4_orf2#LINE/    677 -------ACACTA---T---CAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_214956171_   1958 GGAGAAAATGTTTGCAACTCATATATCAAACAAGAGGGTAATAGCCAAAA 2007
                                  i       v         vi i   i iv vi  v   i  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_214956171_   2008 TATACAAGGAAATCAAACTACTTAATAAGTAGAAAAACAAATAACCCCAT 2057
                             i  i   v  vv  v   i     -  i   i           v  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAAT 812

  chr2_214956171_   2058 TAAAAAGTGAGTAAAGGACTCAAATGGACATTTCTCAAAAGAAGAGATAC 2107
                          ?    i  i i      i ii   i          v        v    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_214956171_   2108 AAATTGCCAACAGATACATGAGAAAATGCTCAACATCTCTAATTAT 2153
                             v     i iii      i  i            v????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (133 / 58)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 9.60 (240 / 25)  


3112 27.22 0.55 0.88  chr2_214962773_214969178.rev     5004  5914 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_214962773_   5004 TGGAAGAACATTCCATGCACATGGATAGGAAGAATCAATATCGTGAAAAT 5053
                              ii i  i     iv       v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214962773_   5054 GGCCATACTGCACAGGGTAACTTACAGATTCAGTGCAATCCCCATCAAGC 5103
                            v     v v  iiv i ii          ii        i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214962773_   5104 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAATTTCA 5151
                          v   iivi i  i  ii     -   -- v  i   v i-    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_214962773_   5152 TATGGAAACAAAAAAGTGTCTGCATTGCCAAGGCAATCCTAAGCAAAAAG 5201
                                 iiv  ii vvi v v  v     ii     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_214962773_   5202 AACAAAGCTGGAAGTATCACACTACCTGACTTCAAACTATGTTACAAGGG 5251
                                i    i vv       v  ii i      viv ii     i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_214962773_   5252 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGATACATAGACC 5301
                                 i   i    ii         i  v ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_214962773_   5302 AATGGAACAGAACAGAGGCCTCAGGAATAACACCACACATCTACAAT-AA 5350
                                i    iv   ivii   i     vv   i    i  iii -  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_214962773_   5351 TCTGATCTTTGACAAACCTGACAAAAAAAAGAAATAAATGGGGAAAGGAT 5400
                          -    i  i     ivv  v   i vv v---- v           i  
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCAT----TCAATGGGGAAAGAAT 393

  chr2_214962773_   5401 TCACTATTTAATAAATGGTGTTGGGAAAACTGGCTAGTCATATGTATAAA 5450
                         vvv  v  i  i        i     v      v  ?i  i   i v  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_214962773_   5451 GCTGAAACTAGATCCCCTCCTTACACCTTACACAAAAATTAATTCAAGAT 5500
                         iv    ii i  i   iv   i     v  i           i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_214962773_   5501 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5550
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_214962773_   5551 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGGCTTCATGT 5599
                            v    ?i- v i -   iv   v v  vv i     v  i   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_214962773_   5600 CTAAAATACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGAT 5649
                         v  vi i          vvi          vv        i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_214962773_   5650 CTGATTAAA-CTAAGATCTTCTGCACAGCAAAAGAAACTACCATTAGAGT 5698
                         i v  i   -i   i v   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_214962773_   5699 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCGATCTACCCATCGG 5748
                            v  i     i                 v     i vii ivi   v 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_214962773_   5749 ACAAAGGGCTAATATCCAGAATCAACAAAGAACTTAAACAAATTTACAAG 5798
                          i  i  i  vi          vv i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_214962773_   5799 AAAAAAACATACAACCCCATCAAAAAGTGTGCAAAGGATATGAACAAACA 5848
                              i   v i     v  i?    i  v         v    i i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_214962773_   5849 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCT 5898
                         i     v        i  vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_214962773_   5899 CATCATCACTGGCCAT 5914
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2145 27.66 4.51 1.75  chr2_214978414_214980595.rev      501  1299 (883)    L1M4_orf2#LINE/L1        9   829 (79)  

  chr2_214978414_    501 TATCCCAGGCTTATGGATTGGGAAACTCAATTTTGTTAAATTTTCA-TAC 549
                                v i i         i i   i   v       iv vv  -   
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr2_214978414_    550 TGCTTAAAGC-ATCTATAGATCCTATGCATTTCCTATCAAAGTAAGAA-T 597
                          v ii   vi-     i    i v i   v i         i vvv i- 
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_214978414_    598 GTCACTTTCCACAGAA-TTAAAAAA--AATTATAGAATTCATATCAAACC 644
                          i -i   iii     -  i v  i--i  iv  i         vi  vi
  L1M4_orf2#LINE/    109 GCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_214978414_    645 AAAAAAGAGCAAGAAAAGCCAAAACAATCCTCAGCCAAAGGAACAAAGCT 694
                         iv  ii  v v    v             i v ivv i i        i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr2_214978414_    695 GAAGACTTCACACTACCCAACTTCAAAATATGTTAGACGGCTATAATAAC 744
                          i  ivi       v     i       iv ii  v vi    i i   i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr2_214978414_    745 CCAAACAAACAGCATGGTTTTGTTATAAGAGCAGACACATAGACCAATGG 794
                          -  i---    ii    vi  vi     iii     i     i      
  L1M4_orf2#LINE/    258 C-AAG---ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_214978414_    795 ATCAG---TGAG--TCCAGAAGTAAATCCATATATTTATTGCCAACTTAT 839
                          vi  ---    --       i    i     i      v i   i v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_214978414_    840 TTTTGATAAAGGCATTAAGAACATGC--TGGT-AAAGGACATCCTCTTCA 886
                            i  i  i  iiii    v   v --   v-    i i vi  i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_214978414_    887 ATAAACGGTTCTGGGAAAATTAGATGTACATATGTAAAATAATGAATCTG 936
                          i   i   v      v  i i   i?v  i   i    v      vi  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_214978414_    937 GACTGCT--CTC-TAT-ATATAGAAAAATTAACTCAAGATCCATGAAAAA 982
                            iv  --   -i i-     v              i  vv  v ? i 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_214978414_    983 CTTAAACATTAGACCTGGAACTGTAAAAATACTAGAAAAGAACACAGA-- 1030
                          i    ii v   v  ii    i     v vi     i i    i  i--
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_214978414_   1031 -AAATACACTTCAAGACATCAATCTTA--CAAACATTTCATGGCTAAGAC 1077
                         -    ---    iv   v iiiv-   --   vvi    v i v  v   
  L1M4_orf2#LINE/    554 TAAAT---CTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_214978414_   1078 CCCAAAAGCGCAGAGAACTATAACAAAAATAGACAAATGTGACT--ATTA 1125
                         v        i  iiv   v v iv         i    vv    --  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_214978414_   1126 AA-CTAAAAA-------GCTACATAGCAAGGAAACAATCCGTTGAGTGAA 1167
                           -i      -------   v  ----     v  v   vivvi      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCA----AAGGACACTATCAAGAAAGTGAA 695

  chr2_214978414_   1168 GAGACAACCTGTTGAATGGGAGAAAATATTTGCCAGCTATTCATGCAACA 1217
                         i        iiiv                    v iii  vi  vii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_214978414_   1218 AGAGGCTAATATCTGAAATATACAAGAAACTCAAAACAACTCATCAACAA 1267
                           i i  vi    iii      i  ii     vv -       vi  i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATAA 794

  chr2_214978414_   1268 CAA--CAAA-AATCCTATTAAAAAGTGGGCAAAGG 1299
                         v  --    -  i  v   ?    i          
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.66 (136 / 82)
Gap_init rate = 0.03 (26 / 821), avg. gap size = 1.92 (50 / 26)  

 275 22.41 9.48 1.72  chr2_214978414_214980595.rev     1577  1692 (490)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr2_214978414_   1577 CTCAAATAAATAAATAAATAAATAAATAAATAAATAAGTGGGCAAAGGAC 1626
                              -   -    v i i      viv   v? v  i           i
  L1M4_orf2#LINE/    784 CTCAA-TAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_214978414_   1627 ---AATAGACATTTCTC--AAAAAGA------AATGATCAAGTGGTATAT 1665
                         ---              --  i    ------    ii   vvi i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_214978414_   1666 GATAAAATACTCAGTATTGCTAACCAG 1692
                           v  i  i    ii  ii????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (17 / 8)
Gap_init rate = 0.04 (5 / 125), avg. gap size = 2.60 (13 / 5)  


2022 27.07 2.25 5.32  chr2_214986371_214989114.rev      898  1743 (1001)    L1M4_orf2#LINE/L1        1   820 (88)  

  chr2_214986371_    898 TAGAAAAACATTCCATGCTTTTGGAACTGAAAAC-----ATTATTAAAAT 942
                          i    i i  i     i iv    viv   i  -----   i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214986371_    943 GATCATACTTCC-AAAGCAATCTACAGTATCAATGCAATTTCTATCAAAT 991
                          iiv     i  -   vii        vv    i     ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214986371_    992 TACTAA-TGTCATTTTTCACAGAATTTGAAAAAACAATCTTAAAATTCAT 1040
                          v i i-  i -     ii     v    v  ivii   i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_214986371_   1041 ACAAAACCAAAAAAAAAAAAAGAGCCA-AATAGCCCAAGCAATCTTAAGC 1089
                          iii  ------- viv  ii  v   -       v  i       i iv
  L1M4_orf2#LINE/    150 ATGGAA-------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_214986371_   1090 AAAAAGAACAAAGCTGGAGGCATCACAATACCTGACTGCAAATTATACTG 1139
                           i          i      vv     v v  ii i v    viv    i
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_214986371_   1140 TAAGTCTATAGTAACTAAAACTGCATGGTTCTGATACAAAAATAAAATAC 1189
                         i  iv   i     ii  i  v ii    v   ii i  ii   i -i i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA-CAT 291

  chr2_214986371_   1190 ACAGATCTATTAAACAGAATAGAGAACCCAGAAATAAAGCCACATATGTA 1239
                          i     v  vi  i     v    ii           v   i i  v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_214986371_   1240 CGACCAACTTATATTTTC--CAATGTCAGCAAAAATAAACAATGGGGAAA 1287
                         i ii   -  i-      --   v viiv   i vi vv           
  L1M4_orf2#LINE/    342 TGGTCAA-TTG-ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_214986371_   1288 GAAAGAAACAATGATAATAAACAATATCATCCAATAAATGGCACTGGAA- 1336
                            -----------  i --------iiv i   i      ii    i -
  L1M4_orf2#LINE/    390 GAA-----------TAGT--------CTTTTCAACAAATGGTGCTGGGAC 420

  chr2_214986371_   1337 AACAGGCTAGTCATATGCAGAAGAATGAAACTGGACCCATACCTCTCACC 1386
                            v  v  ?i  i     i         ii       v      v    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_214986371_   1387 ACATGCAAGAATTAACTCGAGGTAGATTAAAGACTTAAATGTAAGACCTG 1436
                          i  i   i         i ii i   i ?    i           v  -
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT- 519

  chr2_214986371_   1437 AAAATATAAAAATAAATATAAAAATCCTAAAAGAAAACTTAAGAAAGACT 1486
                         --------    i---       v  i  i        v  i ?ivi v 
  L1M4_orf2#LINE/    520 --------AAAAC---TATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_214986371_   1487 GCTC-TGAACATTTGGCCTAAGCAAAGAATTTATGACTAAGACCTCAAAA 1535
                         vi  -   v --    vi  i    v iv  iv iiv  v   vi     
  L1M4_orf2#LINE/    559 CTTCGTGACC--TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_214986371_   1536 ACAAGTGCAACAAAAACAAAAATATACAAATGAGACTT-----AAACCAA 1580
                         i  viv         iv       v i    vi     -----   ii  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_214986371_   1581 AAAGCTTCTGCATAACAACAAAAA--ATTAACAGAGTAAACTGACAACCT 1628
                            -   i  iiivv   vii v --  i  v i   i  vv       i
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_214986371_   1629 ACAGAATTGAAGAAAATAATTGCAAATTATGACTCCGACAAAAGATTAAT 1678
                                v i        v        i  ivv  i  i  ii  i vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_214986371_   1679 CTCCAGAATCTACAAAGGACTCAAAAAACTCAACAACAATAACAAAAACA 1728
                         v        v  i    i    vv v       i  i  v  v v   i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_214986371_   1729 ACCCCATTAAAAAGT 1743
                             v   ?    i 
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAAT 820

Transitions / transversions = 1.71 (142 / 83)
Gap_init rate = 0.02 (20 / 820), avg. gap size = 3.20 (64 / 20)  

 388 18.89 1.11 0.00  chr2_214986371_214989114.rev     2163  2252 (492)    L1M4_orf2#LINE/L1      818   908 (0)  

  chr2_214986371_   2163 AGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGTCATACAAGTG 2212
                          i            v    i     i     v       vi      i  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_214986371_   2213 GCTAATAAACATGTAATAAAA-GGTAAACATCACTAATCAT 2252
                           i     i  ii i v  i - v v       ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.01 (1 / 91), avg. gap size = 1.00 (1 / 1)  


2595 29.11 1.10 0.99  chr2_214994857_215000298.rev     4044  4950 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_214994857_   4044 TGGAAAAACATTCCATGATCATGGATAGAAAGAATCAATATCATTAAAAT 4093
                               i i  i     v        v i    v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_214994857_   4094 GGTCATACTGCCCAAAGCAATTTATAAATTAAATGCTATTCCTATCATAC 4143
                           iv     v      vii  i  i i   v  i  v  i       v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_214994857_   4144 TACCAATGACATTCTTCAAAGAACTAGAAAAAAAAAACT-ATTTTAAAAT 4192
                          v   iivi v  i  iiv    v v  v  i-----  -  ii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAAT 145

  chr2_214994857_   4193 TCAGATAGAACCAAAAAAGAGCCCAAATTGACAAGGAAATCCAAAGCAAA 4242
                            v  i   viiv  ii  v  vi   v v   iiv    ivi iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_214994857_   4243 AAGAACAAAGCTGGAGGCATCATGCTACCAGATTTCAAACTATACTTCAG 4292
                                   i      vv   ii  v  vi        viv    v  i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_214994857_   4293 GGCTATGGTAACCAAAACAGCATGGTTCTGGTAAAAGAATAGACACATAG 4342
                         i    ii    i   i    ii    v    i v   i       i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_214994857_   4343 AGCAGTGGAACAGAATCAAGAACCAAGAAATAAGACTGAACAGCTACAAC 4392
                          v  i     i     ii   ii v        iv iiv   vi  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_214994857_   4393 TATCTGATCTTTGA-AAACATGACAAAAACAAGCAATAAGGAAAAGGTTT 4441
                         i vi    i  i  -  ivi  v   i v  vv    ii     iii vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_214994857_   4442 CCTATTCAATAAATGGTGCTAGGATAACTGGTGAGGCATATACAGAAGAT 4491
                         i  v     i          i   i      vv ?v  i  i  i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_214994857_   4492 TGAAACTGAATCCCTTCCTTATAGTATATACAAAAATTAATTCAAGATAC 4541
                             ii  i i    v   i i vi               i    i  iv
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_214994857_   4542 ATTAAAGACTTAAATGTAAAACCCAAAACTATAAAATCCAAGGAAGAGAG 4591
                           i ?    i         i v i            ii vvi     i i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_214994857_   4592 CCTAGGCA-ATACCATTAAGGACATAGGCACAGGCAAAGATTTCAT-GAT 4639
                          v    ?i- v i -  viv   v v  vvi      v i    v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_214994857_   4640 GAAGACACCAAAAGCAATTGCAACAAAATGAAAAAGTTGACAAATGGGAT 4689
                         - v             vvv         -      i v  i    v   i
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGAC 642

  chr2_214994857_   4690 CTAATTAAACTAAAGAGATTCTGCACAGCAAAAGAAAATTATCAACAAAG 4739
                         i v  i   v v  i iv  i  ii vv    i  v -i      v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGAAAG 691

  chr2_214994857_   4740 ATAACAGAAAACCTACAGAATGGGAGAAAATTTTTGCAAAC--TGCATCT 4787
                         vv  v   v    i                 v        i-- ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_214994857_   4788 GACAAAGGTCTAATAACAAGAGTCTACAAGAAACT--TA-AATTTA-CAG 4833
                           i  i  v  vi  v v   i v  i  ii    --  -  i i -i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_214994857_   4834 GCAAGAAACAAAGAACTCCATTAAAAAATGAGCAACGGATATGAACAGGC 4883
                         vv  i i     v   i v   ?       i    v    v    i  i 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_214994857_   4884 ACTTTTCAAAAGAAAACATACATGCAGCTAACGAACATATGAAAAAAAGT 4933
                          i  i  v      i i     viii  i  ii i  i       i v i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_214994857_   4934 TCAACATCACTGATCAT 4950
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (157 / 103)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


2656 25.87 2.39 4.67  chr2_215146021_215150135.rev     2704  3623 (492)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_215146021_   2704 ATTCCATGTTCATGGATCAGAAGA----ACATTGCTAAAAGGATGCTTCT 2749
                           i              ii     ---- i    i   i v iiiv v  
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_215146021_   2750 ACCCAAAGCATTCTAGAGACTCAACGCAATTTCTTTCAAAATACAAATAA 2799
                         v      viiv    v   i          ii  v       v v iivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_215146021_   2800 CATTTTTCACAGAAATTTTTTAA--AATTCTAAAATTTGTATGGAATAAA 2847
                          v     ii        vviv i--i  i        ii       vviv
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_215146021_   2848 AAAGGAGTCTGAATACTCAAAGCAATCTTGAGCAAAAAGAACAAAGCTGA 2897
                           i   vi v     vi    i         iv  i          i  i
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_215146021_   2898 AAGCATCACACT-----ACTTCAAAATAAATTAAAAAGTTATAATAACCA 2942
                          i vv       ----- i       ivv i  v    i  i i   i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_215146021_   2943 AAACATCATGCTGTTGATATAAAAACAAACACACAGACCAACAGAACATA 2992
                          i   vii  v ii  ii    ii i i   i i   i   ii   i v 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_215146021_   2993 ATAAAGAACCCAAAAATAAATCCATATATTTACAGCCAATTGATATTTGA 3042
                           vi   ii   i       i     i     ii i        v  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_215146021_   3043 CAAAGATGCCAAGAACACATAGTGGGGGGAGAAAACACTTTCTTCAATAA 3092
                            i i        v  ivi i     -- i i  i v i i     i  
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGG--AAAGAATAGTCTTTTCAACAA 407

  chr2_215146021_   3093 ATGGTACTGGGAAAAGTAGATGTTCATAAGCAAA-GAATAAAACTAG--- 3138
                              i      v  v i   i?i  i v     -    i  ii i ---
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_215146021_   3139 --TGTCTTTCACCATATG-AAAAATCAACTCAAAATGGATTAAAGACTTA 3185
                         -- ii  iv        i-      i              i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_215146021_   3186 GAAGTAAGACCCCAAACTATAAAACTAGTAGAAGAAATCATAGGGGAAAA 3235
                         i v      v iv             vv         v      ? v   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_215146021_   3236 GCTCCAGGATGTTGGTCTAGGAAAATATTTTATGGCTA--ACGCCTCAAA 3283
                         v  i iv  iv    vi    v  vvi   iv i v  --  i  --   
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC--AAA 605

  chr2_215146021_   3284 AGTACAGGCAACAAAAATAAAAATAGACACATGGGACTATATTACTATAT 3333
                           i   i         iv         i v  v     vi  i ------
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA------ 649

  chr2_215146021_   3334 TAAACTAAAAATCTTTTGCACAGCAAAGAATACAATCAACAGAGTAAAGA 3383
                         -   i      -      ii vv     i i  v     v i   i  i 
  L1M4_orf2#LINE/    650 -AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_215146021_   3384 GACAGTAAGTTGAATGGGAGAAAGTATTTGTGAACTTTTCATCTGACAAA 3433
                             iivviiv            i      ii  iiv vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_215146021_   3434 GGCGTAATGTCCGGAATATACAAGGGACTCAACAGCAAAAAACAAAACAA 3483
                           vv vi i   i       i  i i    -----------------iv 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTC-----------------TTA 780

  chr2_215146021_   3484 AAACCCCCAAACAAAAAAACCCAAACAAA-AACCAAACAATCACATTAAA 3532
                         v   i ---  i  v    --- i     -    ---    ----- ?  
  L1M4_orf2#LINE/    781 CAACTC---AATAATAAAA---AGACAAATAACC---CAAT-----TWAA 816

  chr2_215146021_   3533 AAGTAGACTAAGGATCTGAACAGACATTTCTCAAAAGAAGACATGCCAAT 3582
                           i i i v      i    i           v        i  i v   
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_215146021_   3583 AGCCAACAGGTATATAAAAA-ATGATCAGCATCACTAATCAT 3623
                         i     i i i i  i    -   v   i     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (156 / 78)
Gap_init rate = 0.02 (18 / 899), avg. gap size = 3.61 (65 / 18)  


2607 27.56 1.07 4.06  chr2_215347098_215351479.rev     2955  3890 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_215347098_   2955 TGGAAAAACATTCGATGCTCATGGGTGGGAAGAATCAATATCATTAAAAT 3004
                               i i  i v   i      i v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_215347098_   3005 GGCCATACTGCCCAGAGCAATTTATAGATTCAATGCTATTCCTATCAGAC 3054
                            v     v    i vii  i  i        i  v  i       i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215347098_   3055 TACCAATGAAATTCTTCAAAGGACTAGGAAAAACT-ATTTTATAATTCAT 3103
                          v   iivivv  i  iiv  i v -v  v  i  -  ii  v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr2_215347098_   3104 ATGGAACAAAAAAAGAGCCCA-AATAGCTAAGGCAATCCTAAGCAAAAAG 3152
                               - viv  i ii    -      i  ii     i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_215347098_   3153 AACAAAACTGGAGGCATCACCATCACGTTCCGTGTCTTTAAACTATACTA 3202
                               ii      vv    ----  -    vvi i iv     -     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCAC----AC-TTCCCAATTTCAAAACT-TACTA 242

  chr2_215347098_   3203 CAGAGCTACAATAACCAAAACAACATTGTACTGGTACAAGAACAGACAAG 3252
                           i       i   i   i   iii v       i i   i i     vi
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_215347098_   3253 TAGACCAGTGGCACAGAATGGAGA-CCCAAAAATAAGGCCGCAGACCTAA 3301
                             i  i   v i     v    -i   i      iv  ii v ii  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_215347098_   3302 AACTATCTTATCTTCAACAAAGCTGACAAAAACAAGCAATGAGGAAAAGA 3351
                         iiii vi v  i   i    i v  v   i v  vv     i     ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_215347098_   3352 CTACCTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAA 3401
                         ivii  v     i              i      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_215347098_   3402 GATTGAAACTGGACCCCTTCCTTACACTGTATACAAAAATAAACTCAAGA 3451
                           v    ii         v   i    ii           v       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_215347098_   3452 TAGATGAAAGACTTAAACATAAAATCCAAAACTATAAAAACCCTGGAAGA 3501
                          i   v ?    i    ii   i v i            vi i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_215347098_   3502 CAATCTAGGCAATACTATTCTGAAAATAGGAACAGGAAAGGACCTCATGA 3551
                         v  iv    ?ivv v v   vvi vv v  ivi   v  v iii  v ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_215347098_   3552 CCAGCATGCCAAAAGCAATTGCAATAAAAGCAAAAATTGATAGATGGG-- 3599
                         vi vv ii         vvv    i     v      v    i  v  --
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_215347098_   3600 TTCAAATAAAACTAAAGAGCTTCTACACAGCAAAAAAAAAAAAAAAAAAA 3649
                             v-i    i    i -   i iii vv    ii v -----------
  L1M4_orf2#LINE/    643 TTCAT-CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA----------- 679

  chr2_215347098_   3650 AAAAAAAAAAAAAAAAGCTATCAACAGAGTGAACAGACCACCTACAAAAT 3699
                         -----------------       v i      v    v   i   i   
  L1M4_orf2#LINE/    680 -----------------CTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_215347098_   3700 GGGAGAAAATATTTTCAAACTATGCATCTGACAAAGGTCTAATATCTAGT 3749
                                       v    ii  ii      i  i  v  vi    i  v
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_215347098_   3750 ATCTATAAGGAACTTAAACAAAGCTACAATAAAAAAA-----AACCCCAT 3794
                           v     i     ivv    vv v i        i -----     v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_215347098_   3795 TAAGAAGTGGGCAACAGACATGAACAGACACTTTTCAATAGAATACATAC 3844
                          ? i  i       vi  iv    i     i  i  v v    v i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_215347098_   3845 CTGCAGCCAACAATCATAAGAGAAAAAGCCCAACATCACTGATCAT 3890
                         vviii     i  v  i v  i  i v  i        ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (154 / 100)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.69 (48 / 13)  


 411 29.63 8.64 4.94  chr2_215355048_215358388.rev      710  1033 (2308)    L1M4_orf2#LINE/L1        4   339 (569)  

  chr2_215355048_    710 AGAGATATGGTATATCCAAGGATGAGATTACATAACATGGGAAAGACC-T 758
                          i      vvi  i i  v    vi  vv  v   i  v vv    iv-i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_215355048_    759 AATTTTCTCCTCCAAATTAATCT-TAAATGTAATGCCATTCTAGTTAGAA 807
                            v--    -       i    -i i  vi  i  v  i ivi i i  
  L1M4_orf2#LINE/     54 AATA--CTCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215355048_    808 TTCCTGGAGGATTCTTT-CATGAAATTTGAGAAACTGGCTTTCTAAAATT 856
                          i  v vv vv  i   -  -      -  v  i   i-- i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATT-GACAAGCTGA--TCCTAAAATT 146

  chr2_215355048_    857 AATATGGAAAAATAAAAG-CCCATAAATAAATGTAAACTTTTTTAAATAA 905
                         v         vii  ii -    -i    ivii-    vv i  i  v  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCA-GAATAGCCA-AAACAATCTTGAAAAA 194

  chr2_215355048_    906 AAAAAA-------GGGGGA---ATGTGTC---ATATCAACACTTGGGATC 942
                         i  i  -------  i   --- iiiv  ---  v    v    ------
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT------ 238

  chr2_215355048_    943 TAGTACAAAG----AGTAA---AAACAGCATGACACTGGTGTAGGAAAAG 985
                         - v       ----     --- i    ii  ii     ii  i i v  
  L1M4_orf2#LINE/    239 -ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_215355048_    986 ATA-ACTGACTAAAGGAACAGTATCAAAGGTCCAGAAGTA---TCATGTA 1031
                          i - iv  ii  v    i  v  ii ii        i  ---i   ii 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_215355048_   1032 TT 1033
                           
  L1M4_orf2#LINE/    338 TT 339

Transitions / transversions = 1.74 (61 / 35)
Gap_init rate = 0.06 (19 / 336), avg. gap size = 2.32 (44 / 19)  

 333 30.96 8.91 4.45  chr2_215355048_215358388.rev     2406  2854 (487)    L1M4_orf2#LINE/L1      440   908 (0)  

  chr2_215355048_   2406 AAAAAATAAAAT-AGACTTGCTAATTAACACCATATG--------GCCTT 2446
                            i   i  i -i   ii-   vi v         i--------iv  i
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACTC 488

  chr2_215355048_   2447 CAGATGGGTTAAAAACTTAAATAATAAAGATGACGTTACAAAA---TTAA 2493
                         v i    i i ? i  i     ivv i  v i vii  i    ---   i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_215355048_   2494 ATAACATAAAACATGAGAATA--TCTTTATTATCTTGAACTGTGGAAGGA 2541
                          ---- v       ii ?i  --    ii v i    iii iv v  v i
  L1M4_orf2#LINE/    539 A----AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_215355048_   2542 TTTAAAAAATTAGATTCTCTAAAGTAAAAACCATTAG-GTAAAGCTTCAT 2590
                            vvv i  vv  iv - v    i v  i v iv i- v   iv vv  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACAC-CAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_215355048_   2591 GCTTTTTACTTTAACCACAATT------TTTTTTGTTTAAAAAAGTTACC 2634
                         ivv  vv    i -i  v    ------    v  i  v   i- vi  i
  L1M4_orf2#LINE/    634 AAATTGGACTTCA-TCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACT 681

  chr2_215355048_   2635 ATCACCAAGTT---AAGATATGCTGCTAGACTGGGAGAAGATATTTGCAA 2681
                             vv  iv ---    i vv ii -   v        i          
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCAC-AGAATGGGAGAAAATATTTGCAA 730

  chr2_215355048_   2682 --TATGTAAAATATAAAAGGGGATTAAATATCTAGAACATAGAGTAAATG 2729
                         --i  i  --- v i v i    i vi-    i    i   v ivi  i-
  L1M4_orf2#LINE/    731 ATCATATA---TCTGATAAGGGACTTG-TATCCAGAATATATAAAGAAC- 775

  chr2_215355048_   2730 TC---CAAATTAGCAAGAAAAAGGACAG-----CCAATAGATATTTGGGC 2771
                           ---   v i ii  v      -   i-----     v? v vv     
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAG-ACAAATAACCCAATTWAAAAATGGGC 824

  chr2_215355048_   2772 AAAGA---TGATGAGGTAATTC---AGAGAAGAGAAAACCAAATGGCTAA 2815
                             i---   vv  ii v   --- i      v v --        i  
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA--CAAATGGCCAA 872

  chr2_215355048_   2816 TAAGTATATAACAAAAAGATGTTCAAGAGAAATGCAAGT 2854
                             i i  i ---       i    v vv ????????
  L1M4_orf2#LINE/    873 TAAGCACATGA---AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (76 / 60)
Gap_init rate = 0.05 (24 / 469), avg. gap size = 2.50 (60 / 24)  


3274 26.98 0.44 0.44  chr2_215373527_215383134     4858  5765 (3843)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_215373527_   4858 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4907
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_215373527_   4908 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4957
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215373527_   4958 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5005
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_215373527_   5006 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5055
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_215373527_   5056 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5105
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_215373527_   5106 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5155
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_215373527_   5156 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5203
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_215373527_   5204 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5253
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_215373527_   5254 CTATTTAATAAATGGTGCTGGGAAAACCGGCTAGCCATATGTAGAAAGCT 5303
                           v  i  i              v   i  v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_215373527_   5304 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5353
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_215373527_   5354 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5403
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_215373527_   5404 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5453
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_215373527_   5454 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTAA 5503
                         i            vvi          vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_215373527_   5504 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5553
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_215373527_   5554 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5603
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_215373527_   5604 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5653
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_215373527_   5654 AAGCAAAGAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5703
                          ii    v     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_215373527_   5704 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5753
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_215373527_   5754 ATCACTGGCCAT 5765
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

4673 17.62 0.77 1.76  chr2_215373527_215383134     8209  9116 (492)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_215373527_   8209 ATCCTATGTTCATAAATTGGAAGACTTAATATTGTTAAGATAGCAATACT 8258
                             i        ii                          i        
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_215373527_   8259 CCCCAAATTGATTTACAGATTCAATGTGATTCCCAAAAAAACTCCATCTG 8308
                                     i           i ii  i  i vv    ii   v   
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_215373527_   8309 CCTTATTTTTTTGGCAAAAATGGACAAGCTGGTTCTAAAATTCATGTAGA 8358
                             ----     -  i    v         i i           i i  
  L1M4_orf2#LINE/    110 CCTT----TTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_215373527_   8359 AATTCAAAAGAC--AGAATTGCTAAAACAATATAATAAAAGAAGAACAAA 8406
                            v   ii   --     v  i        v viv              
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_215373527_   8407 GTTGGGAAATTAACATCTCTCAATTTCAGAACTTACTACAGA-CTTCAGT 8455
                              iii i v   ii  i        i           i -  v    
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_215373527_   8456 AATCAAGGTAGTGTGATACTGGCATAAAACTAGTCATATAAATTAA-GGA 8504
                                ii      i           iiv   v      i  i  -   
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_215373527_   8505 ATAGAATTTGAGAGTCCAAGAATAAACCTTTACATTGATGGTCAATTGAT 8554
                                 -         ii        iv      v             
  L1M4_orf2#LINE/    305 ATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_215373527_   8555 TTTTGACAAGGATGCTAAGGTCGTCCAGTGGGGAAGGAATCATCTTTTCA 8604
                            i       i   i   ii i i  i       i    vi        
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_215373527_   8605 ACAAATAGTGCTGGGACAACCAGATATCCACATGCAAAAGAATTCAGCAG 8654
                               i             ii    ?                vv  iv 
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_215373527_   8655 AATTCCTATCTGAAACCGTATGCAAAAACTAACTCAGAGTAGATTATAGA 8704
                         i ii    i  v v   i   i      i       i i i   i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_215373527_   8705 TCTAACCATAAGGGTTAAAACCATTAAACTTTTAGAAGGTATTATAGGAG 8754
                         i    vii    i i      i  v     i       iv vi     ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_215373527_   8755 TAAATCTTCATGTCCTCAGATTAGGCAACAGTTTCTCAGATATGACACCA 8804
                                  i  v   ii i        ii      i             
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_215373527_   8805 AAAGCACAAGTGGCAAAAGCAACAACAAAAAAAAGATAAATAAGACATCA 8854
                                   iii      -------      v        vi   v   
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAG-------AAAAAATAGATAAATTGGACTTCA 646

  chr2_215373527_   8855 TCAAAATTTAACAGGTATTGT--TTCAAAGAATACCATCAAGAAAGTAGA 8902
                                 -  v iv v    --       i i  i           ii 
  L1M4_orf2#LINE/    647 TCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_215373527_   8903 AATACAACTCACAGCATGGGAGAAAATATTTGCAAATTGTATATCTGACA 8952
                           v     i     v                      ii         i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_215373527_   8953 AGGCACTTGTATCTAGCATATACAAAGAACACTTACAACTCAATAATAAA 9002
                            v         i  v     i       v                   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_215373527_   9003 AAGGCAAACTACTCAATCAAATCATGGGCGAAG-AGGTGAATAGGCCTAC 9051
                            i    iv  i    i?  vv      i   - vv       i -- i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC--AT 843

  chr2_215373527_   9052 CTCTCCAATGAAGATAAACAAATGGTCAATAGGCACATGAAAAGATATTT 9101
                         i       v       v        i     i              ii i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_215373527_   9102 GACATTATTAGTTAT 9116
                         i    i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.55 (112 / 44)
Gap_init rate = 0.01 (11 / 899), avg. gap size = 2.09 (23 / 11)  


2973 26.53 4.61 0.00  chr2_215390573_215395741     3811  4677 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_215390573_   3811 GGAATGATACCCTATGCTCCTGGATTACAATAATTAATATTG---AAATG 3857
                             v    i  i   i  v      iv  v v         --- i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_215390573_   3858 ACAGTACTACCCAAAGCAATCTACAGATTCAATGCAAACCCTATCAAAAT 3907
                         i  i    v      vii              i    v            
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_215390573_   3908 ACCAATGGCATTCTTCA-AAAAACTAGAAAAAAAATCCTAAAATTTTTAT 3956
                         v   iiv  v  i  ii- i   i iiv  ivvi           iv   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_215390573_   3957 GCAACCACAAAGAACCATAACTGGCCAAAGAAATACTGAGCAAAAATTAA 4006
                          v  vii   i i   vvi v i      iv   vi   iv  i  vv v
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_215390573_   4007 AAAGCTGGAGGCATCACACTACCTGACTTAAAAATATACCACAAAACTAT 4056
                             i      vv       v  ii i  v    iv   i     i   i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_215390573_   4057 AGTAATCAAAGTAGCATGGTATTGGTATAAAAACAGACATATAGACCAAT 4106
                                  iii  ii     i   i    ii i           i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_215390573_   4107 GGAATGGAATAGAGAACCTAGAAATAAATCAACATATTTACAGCCAACTG 4156
                              i    v    ii i         i v i i     ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_215390573_   4157 ATTTTCAACAAAGGCACCAAGAACATACAATGTGGAAAAGACCTCCTCTT 4206
                               i    i  ii      v   v     v     ii ivvi  i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_215390573_   4207 CAGAAAACAGTGATGAGAAAACTGGGTATCAATTTGCAGAACAATAAAAC 4256
                           iv   ii   v  i  v      i  ? v iv    i  v   i  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr2_215390573_   4257 TAGACCCTTATCTCCCACCATAT-CAAAAA------------GGATTAAA 4293
                          i     i  i   v        -      ------------    i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr2_215390573_   4294 GCCTTAAGAGTAAGATCTGAAACTGCAAAATTAGTAGAAGAAAACA---- 4339
                          v i   iv      v  i     ii    i vv            ----
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr2_215390573_   4340 -------CTCCAGGACATTTGTCTCATCAAAGATTTTATGGCTAGGACTT 4382
                         -------  i iv   v  v vi viv   v i   iv i v  v   vi
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_215390573_   4383 CAAAAGCACAGGCAACAATAACAGAAATAGACAAATGAGACTATATTAAA 4432
                                   i       v iv i       i    vi    vi  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_215390573_   4433 CTAAAAAGCTTCTGCACAGCAAAG--CA--ATCAAGAAAGTGAA------ 4472
                         v v    i   i  ii vv     --  --              ------
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_215390573_   4473 -CCTGTAGAACGTGAGAAAAAATTTGCAAACTATTCATCTGACAAGGAGC 4521
                         -  iii    i v       v         ii  vi      i    ii 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_215390573_   4522 TAGTATCCAGAATATACCAGAAACTCAAACAACTCAACAGCAAAAACTCA 4571
                          v              iv ii     vv         i ii     vv  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_215390573_   4572 GCTAATCTCATTAAAAACTAGGCAAAGGATCTAAATAGACATTT-TCCAA 4620
                         iv   i iv   ?    v i          i i           -     
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_215390573_   4621 AAGAGGCATAGTAATGACCAATAGATAGGTGGAAAAATGCTCAACATCAC 4670
                          ii  ii   vv    i      iii vi  i   i             ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_215390573_   4671 TTACCAG 4677
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.70 (143 / 84)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 4.44 (40 / 9)  


3963 18.37 5.54 1.06  chr2_215607887_215610819     1585  2433 (500)    L1M4_orf2#LINE/L1        1   887 (21)  

  chr2_215607887_   1585 TGGAAGCACATCTCATGTTCATAGACTGGAAAACTTACTATTGTTAAGAT 1634
                              iv i   i         i  i     i     v            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_215607887_   1635 GTCAACACTACCCAAATCTATCTATAGATTCAACGCAATTCCTATCAAAA 1684
                          v   i   v       iv     i              i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215607887_   1685 TCCCAATGACATTTTTTTGCAGAAATAAAAAACGCCAA-CCTAAAATTCA 1733
                              iivi -i              vi v  -  ii -           
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chr2_215607887_   1734 TACAGACTCTCAAGGGGTCCCAAATAGCCAAAACAGCCTTGAAAAAGACA 1783
                           ii  vviv      ii  vi             ii           vi
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_215607887_   1784 AACCAAACTGGAGGATTCACACTTCCTGGTTTCAAAACTTACTACAAAGC 1833
                            v  ii       i          iii                     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_215607887_   1834 GACAGTAATCAA-ACAATGTGGAACTGGCATAAAGACAGGTATACAGACC 1882
                         v           -   i     v          i  i  ii   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_215607887_   1883 CATGGAACAGAATAGGGAACCTAGAAGTAAACCCTCACATATATGATCAA 1932
                         v      i     v i  ii i    i       vi    v    i    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_215607887_   1933 ATGATTTTTGACTAGGGTGCCAAGTCCATTCAGTGGGGAAAGAATAGTCT 1982
                         v       i   v           v       i                 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_215607887_   1983 TTTCAACAAATGGTGTTGGAAAAACTAGATATCCATATGCAAATGAAAGA 2032
                                        i   i v    i    ?   i       v   v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_215607887_   2033 AGTTGGA-----------------ATACAAAA-TTAGTTCAAAATGAATC 2064
                                -----------------        -   ii        i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_215607887_   2065 AGGAACCTAAATGTCAGTCCTAAAACTATAAAGTCCTTAGGAAAAAAAAC 2114
                          ?ii          v  vv             iii     --  i     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG--AAGAAAAC 546

  chr2_215607887_   2115 AT-TGAGTAAAAGCTTCATAGCATTGAATTTGGCAATG------------ 2151
                           -v ?     -v    i ii v   ii  v       ------------
  L1M4_orf2#LINE/    547 ATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_215607887_   2152 --ACATTAAAGGCATAGAAAACAAAAGGAAAAACAGACAAATTTGAACTT 2199
                         --   ii   i   i iiv        i     i   i     - i    
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT-GGACTT 644

  chr2_215607887_   2200 CATGGACATTTTTAAAAA---TCATGCATCAAAAGGCACTATCAACAGAG 2246
                            vi v   ---     --- ii   v     i i         v i  
  L1M4_orf2#LINE/    645 CATCAAAATT---AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_215607887_   2247 TAAAAAGGCAACTGACACAATAGT-GAAAATATTTGTAAATAATATATTT 2295
                          i     i    iv   v   i v-           i    v      i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_215607887_   2296 TATAAGGGATTAGTATCCAGACTGTATAGAGATCTTCTACAGCTCAAT-- 2343
                         v        i v         v i    i   v  ii    i      --
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_215607887_   2344 ------GACAAACAACCCAATTCAAAAATGAGCAAAAGACTTGAATAAAC 2387
                         ------      i         ?       i     i  i       i  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_215607887_   2388 ATTTCTCCAAAGAAGATATAAAAATAGCTAATAAAAACATGAACAG 2433
                                             v    i  i     iv       v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

Transitions / transversions = 2.10 (103 / 49)
Gap_init rate = 0.02 (15 / 887), avg. gap size = 3.73 (56 / 15)  


2965 26.49 1.55 1.32  chr2_215628446_215632799.rev     2957  3862 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_215628446_   2957 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 3006
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_215628446_   3007 GGCCATACTGTCCAAAGTAATTTATAGATTCAGTGCTGTCCCCATCAAGC 3056
                            v     vi     v i  i  i       ii  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215628446_   3057 TACCA-TTGTCTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 3104
                          v   -i  i    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_215628446_   3105 TCTGGAACCAAAAAAAGAGCCCCT--ATAGCCAAGACAATTCTGAGCAAA 3152
                          v     --- viv   i v   v--        i     ii   iv  i
  L1M4_orf2#LINE/    149 TATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_215628446_   3153 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACCACAA 3202
                                   i      vv   ii  v  ii i      viv   i    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_215628446_   3203 GGCTACAGTAACCAAAACAGCATGATACTGGTACCAAAACACATATATAG 3252
                         i          i   i    ii  i      i iv ii i v i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_215628446_   3253 ACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAAC 3302
                          i        i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_215628446_   3303 CATCTGATCTTTGACAAAGCTGACAAAAACAAGCCATGGGGAAAAGATTC 3352
                           vi    i  i     i v  v   i v  vv v         ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_215628446_   3353 CCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCTATATGCAGAAAAC 3402
                         i  v  i  i        i     v      v  ? i i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_215628446_   3403 CGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAATTCGACATGG 3452
                         i   ii         v   i     v              i  i v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_215628446_   3453 ATTAAAGACTTAAACATAAACATAAACACTTAAACATAAAAACCCTAGAA 3502
                           i ?    i    ii   iviiv  v   -----      vi i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACT-----ATAAAACTCTTAGAA 540

  chr2_215628446_   3503 GAAAATCTAGGCA-ATACCATTCAAGACACAGGCGTGGGCAAAGACTTCA 3551
                              iv    ?i- v i -   iv   viv  vv i     v ii   v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_215628446_   3552 TGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGG 3601
                          iiv  vi            vvi          vv        i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_215628446_   3602 GATCTAATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCAG 3651
                           ii v  i   v v  i     i  ii vv    i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_215628446_   3652 AGTGAACAGGCAACCTACAGAACGGGAGAAAATTTTTGCAATCTATCCAT 3701
                               v  i     i      i          v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_215628446_   3702 CTGACAAAGGGCCAACATCCAGAATCTACAAAGAACTTAAACAAATTTAC 3751
                             i  i  i ivii         v  i        ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_215628446_   3752 AAGAAACAAA-AAA-AACCCA-TCAAAAAGTGGTCAAAGGATATGAACAG 3798
                           v   v i -   -      - i?    i   v        v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_215628446_   3799 ACACTTCTCAAAAGAAGACATTTATGCTGCCAACAA--ACATGAAGAAAA 3846
                            i     v        i  vi viiv     i  --       -  i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGA 888

  chr2_215628446_   3847 T-CTCA---TTACTGGTCAT 3862
                          -    --- i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.62 (26 / 16)  


1378 28.77 0.46 1.14  chr2_215808492_215810428.rev      502   939 (998)    L1M4_orf2#LINE/L1      258   692 (216)  

  chr2_215808492_    502 CAAAACAGCATGGCACTGGTCCAAAAACAGGTGCATATAACAATGGAACA 551
                            i    ii   i     ivi  ii i  iiii   v v        i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr2_215808492_    552 GAATTGGAAACAGAGAAATAAAGCGACATACTCACAACCAACTGATCTTT 601
                               ii iivv         v v i i i i iiii   i    i  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_215808492_    602 GACAAGGCTCACAAAACCAAGCAATGGGGGATAGGACTCCCTATTCAATA 651
                                v vv   i    vv        i -  i ivvi  v     i 
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAATAGTCTTTTCAACA 406

  chr2_215808492_    652 AGAGGTGCTGGGATAACTGACCAGCCATATGCAGAAGAATAAAACTGGAC 701
                          iv          i     ivi ?   i     i      i  ii     
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr2_215808492_    702 CCGTACCTTTCCCCATATATAAAAATTAACTCAAGATGGATTAGAGACTT 751
                           v     iv v       i              i      i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr2_215808492_    752 AACTGTAAGACCTCAAACTCTAAAAATCCTAAAAGAAAATCTAGGAAGTA 801
                           v       v  v     v     v  i  i       iv    ?ivv 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_215808492_    802 CCCTTCTCAACATTGGCCTTGGCAAATCATTT-TTGGCTAAGTCCCCAAA 850
                         vi    vii  v    vi v     - vi   -  i v  v v v     
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAA 605

  chr2_215808492_    851 AGCAATTGTAACAAAACTAAAAATTAATAAATGGGACCTAATTAA-GTTA 899
                             vvv i       vv      vi      v    i v  i  -i   
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_215808492_    900 AAGAGCTTCTACCCAGCAAAAGAAATCATCAGCAGGGAGT 939
                           i -   i iiv vv    i  v ii    --  ii   
  L1M4_orf2#LINE/    656 AAAA-CTTTTGTGCTTCAAAGGACACTATCA--AGAAAGT 692

Transitions / transversions = 1.46 (73 / 50)
Gap_init rate = 0.01 (6 / 435), avg. gap size = 1.17 (7 / 6)  

 781 22.77 3.12 0.45  chr2_215808492_215810428.rev     1222  1445 (492)    L1M4_orf2#LINE/L1      679   908 (0)  

  chr2_215808492_   1222 ATTATCAATAGAGGAAACAGATAACCTAAAGAATGGGAGAAAATATTCTC 1271
                          i      v i  vi  v   i    i v                  iv 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_215808492_   1272 AAACTATGCATGTAACAGAGGTCTAATATCCAGAATCTATAAGAAACT-- 1319
                            ii  ii  v i i ii  v  vi          v     ii    --
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_215808492_   1320 --TAAATCAACAGCAAAAA-ACAAATAATCCCATTTAAAAAACGGGCAAA 1366
                         --i  v    i ii     -        -    v  ?     i       
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAA-CCCAATTWAAAAATGGGCAAA 827

  chr2_215808492_   1367 AGACATGAACAGACACTTCTCAAAAGATGACATACAAGAGGCCAACAAAC 1416
                         i  iv    i     i     v     v  i      iv      i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_215808492_   1417 ATATAAGAA--TGCTCATCCTCACTAATCAT 1445
                          i  i i  --      v v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (33 / 17)
Gap_init rate = 0.02 (4 / 230), avg. gap size = 2.00 (8 / 4)  


3385 25.53 0.89 0.11  chr2_215814284_215818554.rev     2879  3779 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_215814284_   2879 TGGAAACACATCCCATGCTCATGGATGGGTAGAATAAATATTATGAAAAT 2928
                               v i        i        v  v   v v      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_215814284_   2929 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATACCCATCAAAA 2978
                          i v     v  v   vii       i      i     v  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215814284_   2979 TACCA-CCATCATTCTT-CAGAGTTAGAAAAAGTAATTCTAAAATTCATA 3026
                          v   - iii v  i  -    iv v  v  iv i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_215814284_   3027 TGGAAC--CAAAAAGCCCACA-TAGCCAAAGCAAGACTAAACAAAAAGAA 3073
                              v--   iiii    v -        i   vvi i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_215814284_   3074 CAAATCTGGAGGCATCACACTACCTGATTTCAAGCTCTACTATAAGGCCA 3123
                             vi      vv       v  ii       ivii     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_215814284_   3124 TAGTCACCAAAACAGCATGGTAGTGGTATAAAAATAGGCACATAGACCAA 3173
                         i   v i   i    ii     v   i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_215814284_   3174 TGGAACAGAATAGAGAACCCAGAAATAAGCCCAAATACTTACAGCCAACT 3223
                              i     v    ii          i    v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_215814284_   3224 GATCTTCCACAAAGCAAACAAAATCATAAAGTGGGGAAAGGACACCCTTT 3273
                            i   v    i vviv   i i   vv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_215814284_   3274 TCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGGATGAAA 3323
                                            i  i   v  ?       i ii  i     i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_215814284_   3324 CTGGAGCCTCATCTCAC--CTTATACAAAAATCAACTCAAGGTGGATTAA 3371
                         i    v  ii i     -- v           i       ii     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_215814284_   3372 GGACTTAAACCGAAGACCTGAAACTATAAAAATTCTAGAAGATAACATTG 3421
                         i   i    ivv    v  i           v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_215814284_   3422 GAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAAC 3471
                          ?iv  vi    vv   v    v        v i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_215814284_   3472 CCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTAATTAA 3521
                                  v v    i    iv   i   i   iv v    i v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_215814284_   3522 A-TGAAACAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAATAAACAGA 3570
                          - v   - i      ii vv    i iv  vi   iv i i i  v   
  L1M4_orf2#LINE/    651 AATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_215814284_   3571 CAACCCACAGAGTGGGAGAAAATCTTCACAATCTGTACATCTGACAAAGT 3620
                                    i           v  ii   viii  i      i  i v
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_215814284_   3621 ACTAATATCCAGAATCTACAATGAACTCAAATTGATCAGCAAGAAAAAAA 3670
                            vi          v  i  v      vv iviv   ii  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_215814284_   3671 CAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAACAGAGAATTCTCA 3720
                             i  i  v  i?    i     v     iv    i   v v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_215814284_   3721 AAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAGCATT 3770
                                                i  i  i       i       i   i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_215814284_   3771 ACTAATGAT 3779
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.54 (137 / 89)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3155 26.70 1.33 0.33  chr2_215819210_215823489.rev     2890  3788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_215819210_   2890 TGGAAAAACATTCCATGCTCATGAGTTGGAAGAGTCAATATTGTTAAAAT 2939
                               i i  i     i     ii        v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_215819210_   2940 GACCATATTCCC-AAAGCAATCTATAGACTTAATGTAATTCCTAACAAAT 2988
                          i v   i    -   vii     i   i i  i i   i    v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215819210_   2989 TAGTAACATCATTTTTCACATAATTAAAAAAAAAAATCCTAAAGTTTACA 3038
                          vvi i vv v     ii  v  v vi v  ivvi        i  i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_215819210_   3039 TAGAAC--CAAGAGAAAGCCC-GAATAGCCAAAGTACTCCTAAGGAA-AA 3084
                          i   v--    i  ---   -           ii v  i i ii  -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_215819210_   3085 GGACAAATCTGGAGACATCACATCGCCTGACTTCAAATTATACTACAAGG 3134
                          i     vi     ivv     iiv  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_215819210_   3135 CTATGGTAACTAAAACAGCATGATACTGATACAAAAATAGACACA--GAT 3182
                            ii    ii  i    ii  i     ii i  ii       i --   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_215819210_   3183 CAATGGAACAGAATAGAGAACCCCAAAATAAAGCCACATACCTACATCTG 3232
                                 i     v    ii  vi       v   i i ii  iiviii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_215819210_   3233 ACTGATCTTCAATAAGGCTAACAAAAATAA-CAATGCAGAAAGGACATCC 3281
                          i    i   i i    v iv   i vi v-     vi     i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_215819210_   3282 TATTCAATAAATGGTGCTGGG-TAACTAGCTAGCCATATGCAGAAGAATG 3330
                          v     i             -i    i v  ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_215819210_   3331 AAACTGGATCCCTATTTCTCATCACATACAAAAATTAACTCAAGATGGAT 3380
                           ii    i     ii  v  i  i                  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_215819210_   3381 TAAAGACCTAAACATAAGA-CTTAAACTATAAAAATCCTAAAAGAAAGCC 3429
                         i ?         ii     -  v           v  i  i      i v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_215819210_   3430 T-GGAAAAACTTTTCTGGACATTAGCCTAGGCAAAGGATTTATAATGAAG 3478
                          -  ?iv  v i   vv   v  i vi       v  v  iv  ivv v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_215819210_   3479 ACCCCAAAAGCAAATGCAACAAA-GCAAAAATAGACAAATGGGACTTAAT 3527
                           v         v v        - v         i    v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_215819210_   3528 CAAACCAAAATGTTTCTGCACAGCAAAAGAAATAATCAACAGGATAAGCA 3577
                             viv   vii  i  ii vv    i  v iv     v iii i iv 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_215819210_   3578 GACAATCTACAGAATGGGAGAAATTATTTACCAATTATGCTTCTGAAAAT 3627
                              i i               v     i v   i  iiv     v  v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_215819210_   3628 GAATTAATATCTAGAATCTATAACGAACTCAAACAAATCAACAGAAAGAA 3677
                          i i vi    i     v     v      vv    v    i iv  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_215819210_   3678 AACGAACAACCCCATTAGAAACTGGGCAAAGGATATGAGCAGATGTTTCT 3727
                         i  i  i     v   ?i   v            v   ii   ii     
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_215819210_   3728 CAAAAGAAGAAATACAAGTGGTCAACCAACACATGAAAAAATTCTCAATA 3777
                          v        v      i   i   iv i          i  v     i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_215819210_   3778 TCATGAATCAT 3788
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.74 (150 / 86)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


3409 24.75 1.10 1.21  chr2_215854094_215857775     2282  3190 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_215854094_   2282 TGGAAACACATTCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2331
                               v i  i     i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_215854094_   2332 GACCATACTGCCAAAAGCAATCTACAAATTCAACACAATCCCCATCAAAA 2381
                          i v     v  v   vii       i       i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215854094_   2382 TACCACCATCATTCCTCAAAGAGATAGAAAAACCAATTCTAAAATTCATA 2431
                          v   v vv v  ii iiv   i  v  v  i ii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_215854094_   2432 TGGAACCAAAAAAGAGTCCGCATAGCCAAAGCAAAACTAAACAAAAAGAA 2481
                              viiv  ii  vi v v         i   vvi i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_215854094_   2482 CAAATCTGGAGGCATCACACTACCTGATTTCAAACTCTACTATAAGGCCA 2531
                             vi      vv       v  ii        vii     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_215854094_   2532 TGGTCACCAAAACAGCATGGTACTGGCATAAAAATAGGTGCATAGACCAA 2581
                         ii  v i   i    ii              ii    iiii     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_215854094_   2582 TGGAACAGAATAGAGAACCCAGAAATAAACTCAAATACTTAGAGCCAACT 2631
                              i     v    ii            i  v i i   vi i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_215854094_   2632 GATCTTCGACAAAGCAAACCAA-ACCAT--AAAGTTGGGGACAGGACACC 2678
                            i        i -ivi    -     --  ---      v  i i vi
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAA---TGGGGAAAGAATAGT 396

  chr2_215854094_   2679 CTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAAT 2728
                                                i  i   v  ?       i ii     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_215854094_   2729 GAAACTGGATCCTCATCTCTCACCTTATATAAAAGTCAACTTGAGACGGA 2778
                            ii    i  ii i   v    v    i    i i    ii i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_215854094_   2779 TTAAGGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGATAAC 2828
                          i ?i   i    iv     v  i           v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_215854094_   2829 ATTGGAAAAACCCTTCTGGACATTGGCTTAGGCAAAGATCTC------AT 2872
                           v  ?iv  vi    vv   v    v        v i i  ------  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_215854094_   2873 GACCAAAAACCGAAAAGCAAATACAATAAAAACAAAGATAAATAGCTGGC 2922
                            -----   -       v vi   i    iv   i   i   iv v v
  L1M4_orf2#LINE/    597 GAC-----ACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_215854094_   2923 ACCTAATTAAACTAAAGAGCTTTTGCACAGCACAAGGA-ACAGTCAGCAG 2971
                           i v  i   v v  i i      ii vv  -     -  vi   iv i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGAA 689

  chr2_215854094_   2972 AGTAAACAGACAACTCACAGAGTAGGAGAAAATCTTCACAATCTATACAT 3021
                            i  v       i      i i         v  ii   vii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_215854094_   3022 CTGACAAAAGACTAATATCCAGAATCTACAACGAACTGAAATAAATCATT 3071
                             i  ii    vi          v  i  v     vvv i  v   v 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_215854094_   3072 AAGAAAAAAACAAACAATCCCATCAAAAAGTGGGCTAAGGACGTGAACAG 3121
                           v     i     i  i  v  i?    i     v     iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_215854094_   3122 ACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAAT 3171
                            v     v                       i  i  i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_215854094_   3172 GCTCGGCGTCACTAATGAT 3190
                             ii i   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (139 / 82)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.33 (21 / 9)  


3189 27.04 0.66 0.44  chr2_215909973_215916310     4941  5846 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_215909973_   4941 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4990
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_215909973_   4991 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCGTCAAGC 5040
                            v     v     iv i  i  i       ii  v     ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215909973_   5041 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5089
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_215909973_   5090 TGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGAA 5139
                              viiv  ii  v  viv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_215909973_   5140 CAAAGCTGGAGGCATCACACTACCTGACTTCAGACTATACTACATGGCTA 5189
                              i      vv       v  ii i    i viv       vi    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_215909973_   5190 CAGTAACCAAAACGGCCTGGTACTGGTACTAAAACAGAGATATAGACCAA 5239
                               i   i  i iv         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_215909973_   5240 TGGAAAAGAAC--AGAGCCCTCAGAAATAATGCCGCACATCTACAACTAT 5287
                              v    i--    i  --        vv  ii    i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_215909973_   5288 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGG-AAAGGATTCCCT 5336
                         i    i  i     ivv  vv  i v  vv       -    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_215909973_   5337 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5386
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_215909973_   5387 AACTGGATGCCTTCCTTACACT-TATACAAAAATTAATTCAAGATGGATT 5435
                          ii    iv   v   i    i-              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_215909973_   5436 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5485
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_215909973_   5486 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5534
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_215909973_   5535 ACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5584
                                     vvii         vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_215909973_   5585 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5634
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_215909973_   5635 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5684
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_215909973_   5685 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAA 5734
                           i  vi          v  i         vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_215909973_   5735 AAACAAATAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACGTC 5784
                         i -          v  i?    i     i     iv    i     iv  
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_215909973_   5785 TCAAAAGAAGACATTTATACAGCCAAAAAACACATGAAAAAATGCTTATC 5834
                           v        i  vi v ii     v  i          i     i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_215909973_   5835 ATCACTGGCCAT 5846
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


1117 29.34 6.56 1.93  chr2_215921836_215924803     1212  1729 (1239)    L1M4_orf2#LINE/L1        1   542 (366)  

  chr2_215921836_   1212 TGGAAAGGTAGACCAT-TTCCTGGATAAGAAAACTTTCTATACTAAAGAA 1260
                                i  vv    -   v     vi   i    vv   vv v    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_215921836_   1261 ATCACTTCTTCCTAAATTGACCGAGAGATTCAATATAATTCAGATTAGAA 1310
                         iv  v v  i  i       i v v        iii   i vv  i i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215921836_   1311 TCTCCAAGGGTTATTTTGGAGAAATTGTCAAACTCATTCTCAAAATTTAC 1360
                           i vivv vi v     v        v   i  v  i  -      i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAATTCAT 149

  chr2_215921836_   1361 ATAGAAGAGCTTAGGACC----ATGATGAAAATATTACTGAA---GAAAA 1403
                           i   iv  vvi     ----  iiiv    i v vi    ---   i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_215921836_   1404 GTAAA--TGGAAGAAACTTGCCCTACTGGATATCAAGCCTTATTATAAAG 1451
                         ii   --    i  --  ii v  v ivi  v    iv    i  i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGA--CTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_215921836_   1452 CTA-AATAATTAAGACA-TGCCATGATATTGGCACAGGGATAGACAAATA 1499
                            - i    i      -  ---  i  i     i i         v   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTG---TGGTACTGGCATAAGGATAGACATATA 294

  chr2_215921836_   1500 GACAAATAGAACAGAACAGAAAGCCCAGAGACAGCCCTATGCA------G 1543
                           iv   i   i    iv  i  i     i i iv  i  i  ------ 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_215921836_   1544 AAAAT--AT----AATAAAATTGGCACTACAGATGTA--GAGAAAAGGA- 1584
                         vv   --  ----i i  iiv  v  vv  v-  vi -- i i    i -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACC-ATTCAATGGGGAAAGAAT 393

  chr2_215921836_   1585 AGGCACTGCAGGAAATAGTTCTGAAACAATTGAGTATATCCATATGGACA 1634
                           v vi v  iv    i  v   ii    i  i--   ?   i   v v 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGG--ATAKCCACATGCAAA 441

  chr2_215921836_   1635 AAAATGAAAGTGGGTTACTACTTCACACTATATGAAAAAAATCAATTTCA 1684
                          i      iv   iiiv    i      i    - v      i  i iv 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAA 490

  chr2_215921836_   1685 GATTGATTAAAGATTT----GTAAG-GC-AAAA-TATACAACTGTTAAGA 1727
                         i  v   i ?   ii ----     -  -    -    v    v   ii 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_215921836_   1728 GA 1729
                           
  L1M4_orf2#LINE/    541 GA 542

Transitions / transversions = 1.42 (88 / 62)
Gap_init rate = 0.04 (21 / 542), avg. gap size = 2.10 (44 / 21)  

 456 26.69 17.04 0.64  chr2_215921836_215924803     2170  2480 (488)    L1M4_orf2#LINE/L1      547   908 (0)  

  chr2_215921836_   2170 ATATGAGAACATCTTCATGAACTCAGGGTAGAAAGAGATTTCCT-GA--- 2215
                            v ? v v      i   v  ii  v   iv iv i    i -  ---
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_215921836_   2216 GACCTAAAAATCAC---CAACCTTAAAGAAGATTGA-AAATT-------- 2253
                            viv    v   ---    vvv i i  i  v  -     --------
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_215921836_   2254 --AAAATTCAGGACTTTTATTCAATAAATGACACCACTATAAAAGTAAGA 2301
                         --      v ii      i v vvi   v     i ii vi     i i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_215921836_   2302 AAATAAGCCACAAACTGA-ACAAGATAT-----------------GA-AA 2332
                          i i  v     i v  i- v  i    -----------------  -  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_215921836_   2333 G---CTTGGCATCCAGGATATGTAAAGTATAGCTATGAATCAACAAGAAA 2379
                          ---    -i      i    i     v ivvi  ii v    i  v   
  L1M4_orf2#LINE/    747 GGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_215921836_   2380 ATGACAGA----CCAATTGAAAAATAGTCAAAGGAAT-GAA-AGAT---- 2419
                          v    i ----      ?      i v       v -   -   i----
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_215921836_   2420 ---CACAGAAACAAGCACAAAGGGCCCAGGAACATATGAAAAGATGCTCA 2466
                         ---  v    i- vii     v    v vi i  i               
  L1M4_orf2#LINE/    846 CTCCAAAGAAG-ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_215921836_   2467 ACCTTATAGAATGA 2480
                           v i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (44 / 37)
Gap_init rate = 0.04 (15 / 362), avg. gap size = 3.67 (55 / 15)  


3212 26.96 0.66 0.33  chr2_215942701_215949096     5000  5904 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_215942701_   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5049
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_215942701_   5050 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5099
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_215942701_   5100 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ATGTTAAAGTTCA 5147
                          v   iivi i  ii ii     -   -- v  i  -  vi    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_215942701_   5148 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5197
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_215942701_   5198 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACAATACTATAAGGC 5247
                                i      vv    i  v  ii i      vvv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_215942701_   5248 TACAGTAACCAAAACAGCATGGAACTGGTACCGAAACAGAGATATAGACC 5297
                                 i   i    ii   v     i iviii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_215942701_   5298 AATGGAACAGAAC--AGCCCTCAGAAATAATGCTGCATATCTGCAATTAT 5345
                                i    i--  vvii         vv iii i  i iiii i v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_215942701_   5346 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGG-AAAGGATTCCCT 5394
                         i    i  i     ivv  vv  i v  vv       -    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_215942701_   5395 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5444
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_215942701_   5445 AACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAAAATGGATT 5494
                          ii    iv   v   i     v              i           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_215942701_   5495 AAAGACTTACATGTTTGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5544
                          ?    i  v    vv  v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_215942701_   5545 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5593
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_215942701_   5594 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCAT 5643
                                     vvi          vv     v  i    v   ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_215942701_   5644 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5693
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_215942701_   5694 GGCAACCTACAGAATGGGAGAAAATTGTTGCAATCTACTCATCTGACAAA 5743
                          i     i                 vv      vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_215942701_   5744 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATCTACAAGAAAAA 5793
                           i  vi          v  i  v      vv    v  v i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_215942701_   5794 AACAAACAGCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5843
                         i     i i   v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_215942701_   5844 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGTTCACCA 5893
                          v        i  vi viii     v  i          i   i   v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_215942701_   5894 TCACTGGCCAT 5904
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.38 (139 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


1233 16.27 0.00 0.48  chr2_216011450_216015156.rev     1477  1685 (2022)    L1M4_orf2#LINE/L1        4   211 (697)  

  chr2_216011450_   1477 AAAGACACCCCATGTTCACAGACTGGAAGATTTAATATTCTTAGGATGGT 1526
                              i i          ii  i       i        v   i     i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_216011450_   1527 AACATTTCCCAAATTGATCTACAGATTCAACACAATACCTATGAAAATTC 1576
                           i i i                        i    v     v     i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_216011450_   1577 CAACTGCGTTGTTTTGCAGAAATGGACAAGCTGATTCTAAAAATCATGTG 1626
                           i    v  -            v           i      v    i  
  L1M4_orf2#LINE/    104 CAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_216011450_   1627 GAAATGCAAGGGACTCTGAAGAGTCAAAGTCATCTTGAATAAAAAAAACG 1676
                                       i v   v  i    iiv        v  i  i   i
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_216011450_   1677 AAGTTGGGG 1685
                                i 
  L1M4_orf2#LINE/    203 AAGTTGGAG 211

Transitions / transversions = 2.40 (24 / 10)
Gap_init rate = 0.00 (1 / 208), avg. gap size = 1.00 (1 / 1)  

1086 20.78 23.38 0.97  chr2_216011450_216015156.rev     1981  2288 (1419)    L1M4_orf2#LINE/L1      168   544 (364)  

  chr2_216011450_   1981 CAAAACAAAC-AAACAAACAAAAAACAGAAAAATGAAGTTGGAGGACTCA 2029
                           i  i iv -      v vvi   v    i  ii               
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_216011450_   2030 CACTTGCTGATTTCAAAATTTGTTACCAGCCTATAGTAAT------AGTG 2073
                              v ii         i  ii   v iv   i      ------    
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_216011450_   2074 TAGTACTGGCATAACAGCAGGCACATGGACCAA----------------- 2106
                          i            viii  i  i  i  i   -----------------
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_216011450_   2107 ---------------------------------------------GGGTG 2111
                         ---------------------------------------------     
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_216011450_   2112 CCAAGACCATTCGATTGGGCAAAGAACAGTCTTTTCAACAAATGATGCTG 2161
                                     i -    v      i                 i     
  L1M4_orf2#LINE/    368 CCAAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_216011450_   2162 AGACAACTAGACAGCCACATACAAAA---TAAAATAAGACTTCTATTTCA 2208
                         i       i  i ?      i     --- i  i vi   ii   ii   
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_216011450_   2209 TGTCTGTATATGAAAATTAACTTAAAATGAACCAAAGACTTAAGTATAAG 2258
                         iii -i    ii          i      i i  ?    i   i i    
  L1M4_orf2#LINE/    467 CACC-ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr2_216011450_   2259 AGCTAACACTAAAATAACTCTTAAAAGAAA 2288
                               v    v  -        i      
  L1M4_orf2#LINE/    516 AGCTAAAACTATAA-AACTCTTAGAAGAAA 544

Transitions / transversions = 3.77 (49 / 13)
Gap_init rate = 0.02 (7 / 377), avg. gap size = 10.71 (75 / 7)  

 632 15.20 3.20 0.00  chr2_216011450_216015156.rev     2601  2725 (982)    L1M4_orf2#LINE/L1      539   667 (241)  

  chr2_216011450_   2601 AAGAAAATATACACAAAAATCTTCATCACTGAGGATTAGGCAATGGTTTC 2650
                                i   vi?iv        i v  ivv  i               
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_216011450_   2651 TTAGACATGACACCATTAACACAAGCAACAAAAGAAAAAATA----AATT 2696
                              i         vv i                       ----    
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_216011450_   2697 CAACATCATCAAAATTAAAAACTTTTGTG 2725
                         vi  v                        
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTG 667

Transitions / transversions = 1.00 (9 / 9)
Gap_init rate = 0.01 (1 / 129), avg. gap size = 4.00 (4 / 1)  

 576 18.02 24.77 3.60  chr2_216011450_216015156.rev     2994  3215 (492)    L1M4_orf2#LINE/L1      640   908 (0)  

  chr2_216011450_   2994 GACTCCGTCTCAAAAAAAAGAAAAAACTT--GTGATGATCAAAGGAAACC 3041
                             i i  ------    vv        --   v --        v  i
  L1M4_orf2#LINE/    640 GACTTCATC------AAAATTAAAAACTTTTGTGCT--TCAAAGGACACT 681

  chr2_216011450_   3042 ATCAAGAAAG-GCTAACACAATCCATAGAATGAGAGGAAATA-------- 3082
                                   - vv  v    i   i      i   i     --------
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_216011450_   3083 -----------------------------------------AACT--TAC 3089
                         -----------------------------------------    --   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_216011450_   3090 AACTCAATAATAAACAGATAAATACCTCAACT-AAAAATGGACAAGAGGT 3138
                                       v   i     v i   i -        i   ii i 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_216011450_   3139 CTCAACAGACATTTCTCCAAAGGAGGTAAACAACTGGCTAGGAAGCACAT 3188
                         i v  i                i  i  v    v    i iv        
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_216011450_   3189 CCAACGGTGTTCCACATTATTTGGAAA 3215
                         vv  v i  i  v    i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (23 / 17)
Gap_init rate = 0.03 (7 / 269), avg. gap size = 9.00 (63 / 7)  


 629 29.01 10.62 5.40  chr2_216271149_216272729      501  1093 (488)    L1M4_orf2#LINE/L1      285   908 (0)  

  chr2_216271149_    501 TAGTCAGATATACCATTGGAACAGAATAGAAAATCTAGAAATATACCTGA 550
                            v  v   v i  v     i     v  i i  i       v   ii-
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA- 333

  chr2_216271149_    551 TTACAT--ATGGAAATTTAGTATTTGATAGTATTTCATATATAAGACTA- 597
                         -     --    vv v  ii v  i  i iviv v -----i     i -
  L1M4_orf2#LINE/    334 -TACATTTATGGTCAATTGATTTTCGACAAGGGTGC-----CAAGACCAT 377

  chr2_216271149_    598 --AATGACGAAAG--TAG-CTTTTCAAATAAATGGGAAAAAGAACAAAAT 642
                         --    iv     --   -        -i      ---------------
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAA-CAAATGG--------------- 411

  chr2_216271149_    643 TTTTAAGGATTACTGAATAACTGAATCTAAAAGA-TAAAATTGGGCTCAT 691
                          vi i-   iv    i   ? iiv  vi      - i  i    i i v 
  L1M4_orf2#LINE/    412 TGCTG-GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_216271149_    692 TCTTCACATCATACATAAGGATAAATTCCAAATAAATTAGCAATCTAAAA 741
                         v i     i    i i  ii  v  i  v    ii  i ?vi i     v
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr2_216271149_    742 GTAAAAAATGAATTCCTACAAA--TCTCAGAAGA---CTTGGATG--AAT 784
                             i iv i  --v   i   --   i      --- v i i? --   
  L1M4_orf2#LINE/    511 GTAAGAGCTAAA--ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_216271149_    785 CCTTTAGTAACTTT---TTA--TAATG-----------ATGAC-TTAAAA 817
                          --  v  i  i  ---   --i    -----------     -ii    
  L1M4_orf2#LINE/    559 C--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_216271149_    818 ACACA--TTATAAATTA-----TTGGTAAATTTGACTGCAT------TAA 854
                         i    --iv i   vv ----- v i      v    v   ------   
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_216271149_    855 AAAATTTTG-GCT---AAAAATACC-TCTGGTAAAGTAAGAAAACAAATG 899
                            v     -   ---  ii i  i-  vi -     i i  i    viv
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAAAGACAACCC 705

  chr2_216271149_    900 ACAAATTGTAAAAATAATGTTTGCAACT--TCTATCAGACCAAGGTTTAA 947
                            i v  vi i  -   i       v -- v    v  iv i  vi vi
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAA-AATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_216271149_    948 TACCCTTGACATATTAATAACACTTAAGTTTCAA--------AGTTTCAA 989
                           i  vvi i    v  v   v    vivi    --------  v--   
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CAA 802

  chr2_216271149_    990 ACTACTTGATT-GAAAGTGAGTAAAATATATGAGCAGGCCCTTCACAGAT 1038
                          iv  iii   -i   i  i i   iv  v   ii  i vi   v vi v
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_216271149_   1039 AAAGAAATGAAAATGACCCCAAAACATAT-AAAGGGTGGTCAACTTTGTT 1087
                         i    v  iv     i  vvv  i  i  -   i i  v     v ii??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr2_216271149_   1088 CATGGT 1093
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.49 (101 / 68)
Gap_init rate = 0.05 (32 / 624), avg. gap size = 2.97 (95 / 32)  


3218 25.28 1.33 0.67  chr2_216320077_216325186.rev     3727  4628 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_216320077_   3727 TGGAAAAACATTCCATGTCCATGGATAGGAAGAATCAATAATGTTAAAAT 3776
                               i i  i      i       v      v i    v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_216320077_   3777 GGCCATGCTGCCCAAAGCAATTTACAGATTCAATGATATTCCTATCAAAC 3826
                            v  i  v      vii  i           i vv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_216320077_   3827 TATCAGTGACATTCTTCACAGAATTAGAAAAAAACT-ATTTTAAAATTCA 3875
                          vi   ivi v  i  ii     v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr2_216320077_   3876 TATAGAGAACCAAAAAGAGCTTGAATAGTCAAGACAATTCTAAGCAAAAA 3925
                            i  i vv   ii-  v iv      i   i     ii i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_216320077_   3926 GAACAAAGCTGGAGGCATCA-GTTACGCAACTTTAAACTATACTACAGAG 3974
                                 i      vv   -ii v v   i  i   viv       i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_216320077_   3975 CTATAGTAATCAAAACAGCATAGTACTGGTAGAAAAACAGACACATAGAC 4024
                            i         i    ii i       i v  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_216320077_   4025 CAATGAAACAGAATAGAAAACCCAGAAATAAAGCCACACACCTACAACCA 4074
                              i  i     v  i ii           v   i   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_216320077_   4075 ACTGATATTTGACAAAGTTGACGCAAACAAGCAATGGGGAAAGGAATC-C 4123
                          i    v  i     i v  v ivi v  vv            -   v-i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGT 396

  chr2_216320077_   4124 CTATTCAATCAATGGTGTTGTGATAACTGGCTAGCCATATGCAGAAGATG 4173
                           v     iv       i  v  i      v  ?   i     i    vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_216320077_   4174 GAAACTGGATCCCTCCCTTACACCATATACAATAATCAATTCGAAGTGGA 4223
                            ii    i    v   i             v   i  i  i  i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_216320077_   4224 TTAAAGACTTAAATGTAAAACCTAAAACTATAAAACCCT-GGAAGATAAC 4272
                          i ?    i         i v               i  -i     v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_216320077_   4273 CTAGGA-TATACCATTCAGGACATAGGCCCTGACAAAGATTTCATGACAA 4321
                         v    ?-  v i -   iv   v v  viiv i   v i    v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_216320077_   4322 AGACACCAAAAGCAATTGCAACAAAAACAAAAAGTGATAAGTGGGATGTA 4371
                         v             vvv         iv     vv     i v   iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_216320077_   4372 AGTAAA-CTAAGAGCTCCTGCACAGCAAAATAAACCATCAGCAGAGTAAA 4420
                          vi   -i   i i  ii  ii vv    iv v  i    iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_216320077_   4421 CAGACAACGTATAGAATGGGAGAAAATATTTGCAAAC--TGCATCTGACA 4468
                         v       vi i                        i-- ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_216320077_   4469 AAGGTCTAATATCCAGTATCTATAAGGAACT--TA-AATTAACTAGCAAA 4515
                          i  v  vi       v  v     i     --  -  i v v  ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_216320077_   4516 AA-ACAAAAAACCCCATTAAAAAGTGGGCAAAGGATATGAACAAACACTT 4564
                           -     v     v   ?    i            v    i i   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_216320077_   4565 TTCAAAAGAAAACATACAGGTGGACAAAAAGCATATGAAAAAATGCCTTA 4614
                         i  v      i i     ii   v   v     i       i    - i 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC-TCA 894

  chr2_216320077_   4615 ATATCAATGATCTT 4628
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (136 / 88)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.20 (18 / 15)  


4564 16.70 2.35 0.78  chr2_216491605_216493866      879  1770 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_216491605_    879 GAAAGATATCCCATGTTCATGGACTGGAAGATACAATATTGTTAAGATGA 928
                                                i       ivi               i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_216491605_    929 CAATACTTCTCAAATTGATGTATAGATTTATCACAATCCCTATCAATGTC 978
                                i i         v  i     i v i             vi  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_216491605_    979 ACAGCTAGCTTCTTCACAGAAATTGACAAGCTGATCCCAAAATTCCAATG 1028
                         v     iv   i  ii                     i       vv   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_216491605_   1029 AAAATTTAATTAATCCAGAATATCTAAAACAATGTTGAAAAAGA----CA 1074
                         i    vi  vvi i        v i        v          ----  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_216491605_   1075 AAGTAGGAGGGCTCACACTTCCTGATTTCAAAATTTACTACAAAGCTACA 1124
                             v     i           ii         i                
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_216491605_   1125 GTAATCAAGAAAATACGGTACTGGCATA-GGAAAGATATGTAGATTAATA 1173
                                   v i ii            -   v   i  i     i   i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_216491605_   1174 AAACAGAATTGAAAGTCCAAAAATAAACC-----ATTGGGTATTAGATCA 1218
                         i  i        i      i         -----   ---   -- i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATT---TAT--GGTCA 347

  chr2_216491605_   1219 ACTGATTTTCAGCAAGAGTGCCAAGATATTTCAATGGAGAAAGAGTAATT 1268
                          i        ii    i         ivv        i      i  i i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_216491605_   1269 TTTTTAATAAATGGTGTTGGGACAACTGGATATCCATGTGCAAAAG---G 1315
                             i  i        i               ?   ii        --- 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_216491605_   1316 AAGTTGGACCACTAACTCACACCATATACAAAAATTAGCTTAAAATGAAT 1365
                                   v   v                      i  i      i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_216491605_   1366 CTAAAAGCTAAACGTAAGAGCTAA--CTGTAAAACTTTT-GAAGGAAACA 1412
                          v? i v     i           --  i       i  -    i     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_216491605_   1413 TAACTACAAATCTTTGTGACTTTGAATTTAGCAATGATTGCTTAGATATG 1462
                           iv?ii       i     i   ii  vi      i  v          
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_216491605_   1463 AAACCAAAAGCACAATTAAAAAAAGAAAAAAAAATGAAAAATTGAAAATT 1512
                          v             vi  v           v --  v      i vv i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTC 645

  chr2_216491605_   1513 GTCAAAATTAAAAACTTTTGTACTGAAAAGGATATCATGTAGAAAGTTTA 1562
                         i                    i  vv      i ii  vv       vv 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_216491605_   1563 AAAACAGCCCACAGAATGGGAGAAAATATTTGCAAATTGCATATCTGATG 1612
                           i   i                              iii         i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_216491605_   1613 AGGCATGTATATCTAGAATAGTTAGAGAACTATTTCAACTCAGTAATGAA 1662
                            v iv i    i      vv  i      v  v       i    i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_216491605_   1663 AAGACAA----CCCAATT-AAAAATGAGCAAAATATCGGAACAGACAGTT 1707
                                ----       -       i     iv  iv   i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_216491605_   1708 CTCCAAACTAGATACACAAATGAACAATAAGCACATTAAATTATGCTCAA 1757
                                vv     i       iv            v   vv        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_216491605_   1758 CATCATTAGTCAT 1770
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (93 / 53)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 2.55 (28 / 11)  


3133 27.05 1.11 0.44  chr2_216508759_216515451     5300  6201 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_216508759_   5300 TGGAAAAACATTTCATGCTCATGGATAGGAAGAATCAATATGGTGAAAAT 5349
                               i i  ii    i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_216508759_   5350 GGTGATACTGCCCAAAGTTATTTATAGATTCAATGTTATCCCCATCAAGC 5399
                           ii     v      v v  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_216508759_   5400 TAC-AATTGCCTTTATTCACAGAATTAGA-AAACATACTTTAAATTTCAT 5447
                          v - ii       -  ii     v v  -  i vv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_216508759_   5448 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCTTAAGCAAAAAGA 5497
                               viiv  ii  v  viv        i        i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_216508759_   5498 ACAAGGCTGGAGGCATCACGATGCCTGACTTCAAACTATACTATAAGGCT 5547
                             i i      vv    iv v  ii i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_216508759_   5548 GCAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGATATATAGACCA 5597
                         i      i   i    ii           iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_216508759_   5598 ATGGAACAGAACAGAGGCCTCAGAAATAATGCCACAAATCTACAACTGTC 5647
                               i    iv   ivii         vv   i v  i  iiiiiivi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_216508759_   5648 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGACTCCCCA 5697
                             i  i     ivv  v   i v  vv            i ivvi iv
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_216508759_   5698 TTTAATAAATGGTTCTGGGAGAACTGGCTAAACATATGCAGAAAGCTGAA 5747
                           i  i       v      v      v  ?v  i     i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_216508759_   5748 ACTGGACCCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGATTA 5797
                         ii         v   i    iv                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_216508759_   5798 AAGACTTAAAGGTAAGACCTAAAACCATTAAAACCCT-AGAAGAAAACCT 5846
                         ?    i    v      v       i  -     i  -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chr2_216508759_   5847 AGGCAACGCTATTCAGGACAT-AGGCAAGGCAAAGACTTCATGACTAAAA 5895
                            ?ivviv v   iv   v -i  iv      v ii   v iiv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_216508759_   5896 CACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAGTT 5945
                                    vvi      i   vv     v  i    v   ii vi i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_216508759_   5946 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGCAAACAG 5995
                            v v  i i   i  ii vv    i  v       vv i  ii  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_216508759_   5996 GCAACCTACAGAATGGGAGAAAATTTTTGCAA-TCTTCCATCTGACAAAG 6044
                         i     i                 v       -  v vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_216508759_   6045 GGCTAATATCCAGGATTTACAAGAAA----TGTAAATAAATTTACGAGAA 6090
                          i  vi       i  v  i  ii  ---- ii  v v   -- vv i  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT--AATAAAA 796

  chr2_216508759_   6091 AGA-AAACAACCCCATCAAAAAGTGGGTGATGGATATGAACAGATATTTC 6139
                            -   i     v  i?    i    ii v    v    i   i     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_216508759_   6140 TCAAAAGAAGATATTTATATGGCCAACAAACATTTTAAAAAAAGCTCATT 6189
                           v           vi v        i  i  iv v    i v     vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_216508759_   6190 ATCACTGGTCAT 6201
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


3089 25.91 1.66 1.33  chr2_216677831_216684553     5329  6231 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_216677831_   5329 GAAAAACATTCCATGCTCATGGATAGGAAAAATCAATATCATGAAAATGG 5378
                             i i  i     i        v    i v i     ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_216677831_   5379 CCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGCTA 5428
                          v     v      v i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_216677831_   5429 CCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCATA 5476
                            -   v    i  -i     v v  v  i-  - iii    v      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chr2_216677831_   5477 TGGAACCAAATAAGAG-CCC-GTATAGCCAAGACAATCCTAGGCAAAAAG 5524
                              -- vii   i -   - v        i      i iiiv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_216677831_   5525 AACAAAGCTGGAGACATCATGCTATGCTACCTGACTTCAAACTATATTAC 5574
                                i     ivv   ii  ---- -  ii i      viv  i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACT----T-CCCAATTTCAAAACTTACTAC 243

  chr2_216677831_   5575 AAGGCTACAGTAACCAAAACAACACAGTACTAGTACCAAAGCAGATAATG 5624
                           i          i   i   iiiii     i i iv iiii   i - i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA-TA 292

  chr2_216677831_   5625 CAGACCAATAGAACAGAACAGAGGCCTCAGAAGTAACGCCACACATCTAA 5674
                         i   i    i   i    iv   ivii     i   vv   i    i  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_216677831_   5675 AACCATCTGATCTTTGACAAACTTGACAAAAACAAGCAATGGGGAAAGGA 5724
                         iii  vi    i  i     ivv  v   i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_216677831_   5725 TCTGCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAA 5774
                          vvv  v  i  i        i     v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_216677831_   5775 AACTGAAACTGGACCCCTTCCTTATACCTTACACAAAAATTAACTCAAGA 5824
                         i v    ii         v   i i   v  i                i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_216677831_   5825 TGGATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGGAGA 5874
                              i ?    i    ii     v       i      vi i   i   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_216677831_   5875 AAACTTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATG 5923
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_216677831_   5924 AATAAAACACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5973
                         i   vi         i  vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_216677831_   5974 TT------AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCACCAGA 6017
                         i ------   i    i -   i  ii vv    i  v       vv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_216677831_   6018 GTGAACAGGCAACCTACAGAATGAGAGAAAATTTTTGCAATCTATCTATC 6067
                              v  i     i        i        v       vii  v    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_216677831_   6068 TGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAATAAATTTATG 6117
                            i  i  i  vi          v  i  i     ivv i  v iv  i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_216677831_   6118 A--GAAAGA-AAACAACTCCATCAAAAAGTGAGCAAAGGATATGAACAGA 6164
                          --i     -   i   i v  i?    i  i         v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_216677831_   6165 CACTTCTCAAAAGAAGACATTTGTGCGGCCAACAAACATATGAAAAAA-G 6213
                           i     v        i  viivii      i  i  i       i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_216677831_   6214 CTCATCATCACTGGTCAT 6231
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (148 / 82)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 1.59 (27 / 17)  


2193 25.52 0.19 0.19  chr2_216937783_216940734     1186  1718 (1234)    L1M4_orf2#LINE/L1        1   533 (375)  

  chr2_216937783_   1186 TGGAAAGATATTCCATGTTCATGAATAGGAAAAGTCAATATTATTAAAAT 1235
                                    i           i  v    i v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_216937783_   1236 GTCCATACTACTCAAAGCAACCTACAGATTCAGTGCAATCCCTATCAAAA 1285
                          v v     v i    vii i           ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_216937783_   1286 TACCAGTGATATTTTTCACAGAAATAGAAAAAAAAATCATAAAATGTATA 1335
                          v    iviiv     ii       v  v  ivvi   v      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_216937783_   1336 TGAAACCACAAAAGGCCCAGAATAGCCAAAGCTATTCTGACCAAAAAGAA 1385
                           i  vii   ii i               i v  ii   vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_216937783_   1386 CTAAACTGGAAGAATAACATTATCTAACTTCAAATTATACTACAGAGCTA 1435
                          v  ii    i  v v   i vi i  i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_216937783_   1436 TAATAA-AAAAACAACATGGTATAGGCATAAAAACTGACACATAGACTAA 1484
                         i i   -v  i   iii     iv       ii iv    i     ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_216937783_   1485 TGAAACAGAACAGAGAACACAGAAATAAGTCTGTCCATCTACAGTGAACT 1534
                           i  i    iv    iiv         ii ii v   i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_216937783_   1535 CATTTTTGACAAAGGTGCCAAGAACATACATTGGGGAAAGGACAGTATCT 1584
                         v     i     i          v   v  v         i i   v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_216937783_   1585 TCAATAAATGGCACTGGGAAAAACTGGATATCCATATACAGAAGAATGAA 1634
                             i      ii      v  -       ?   i  i  i         
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_216937783_   1635 ACTAGACCCCAATTTCTCACCATATACAAAAATCCAATCAAAATGGGTTA 1684
                         ii i      v ii  v                iv v         i i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_216937783_   1685 AAGACTTAAATCTAAGAACCCAGACTTTGAAACT 1718
                         ?    i     v     i iv i   v i     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

Transitions / transversions = 1.98 (89 / 45)
Gap_init rate = 0.00 (2 / 533), avg. gap size = 1.00 (2 / 2)  

1418 23.21 1.53 0.77  chr2_216937783_216940734     2069  2460 (492)    L1M4_orf2#LINE/L1      514   908 (0)  

  chr2_216937783_   2069 AGAGCCAAACCCTATCACACT---ACAAGAAAGCATTGGAGAAACGCTCC 2115
                              i   v -   v v   --- v      i   v  ? v  vv  i 
  L1M4_orf2#LINE/    514 AGAGCTAAAAC-TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_216937783_   2116 AGGACATTGGTCTGGGCAAAGATTTCTTGACTAATACCCCCACATGCACA 2165
                         iv   v    vi i     v i      iiv  - iv v   v v     
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGACACCAAAAGCACA 611

  chr2_216937783_   2166 GGCAACCAAAGCAAAAATGGACAAATGGGATTACATCAAG-TTAAAAAGC 2214
                         i     v    v      i  i    v   i v      i-       - 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-C 660

  chr2_216937783_   2215 TTCTGCACAGCAAAGGAAACAATAAACAAAGTAAAGAGACAGCCCACAGA 2264
                           i  ii vv       v  v  v  v     i  i     i        
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_216937783_   2265 GTGGGAGAAAATATTTGCAAACTATCCATCTGACAGGGAACTAATAACCA 2314
                         i                    ii  vi      i i  i   vi  v   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_216937783_   2315 GAATATATAAGGAGCTCAAACAATTCAATAGGAAAATATCTAATAATTTC 2364
                                   i  i   vv    i      iv    viv v     iiiv
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_216937783_   2365 ATC--AAAATGGGCAAAAGATCTGAATAGAGATTTTTCAAAAGAAGACAT 2412
                           i--            i   i        v    i  v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_216937783_   2413 ACAAATGCCAAACATATATATGAAAAGGTGCTCAACACCATTGATTAT 2460
                                v v  i vii i        i         i  ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.14 (48 / 42)
Gap_init rate = 0.02 (6 / 395), avg. gap size = 1.50 (9 / 6)  


2093 25.29 1.97 0.33  chr2_217002369_217003969.rev      501  1109 (492)    L1M4_orf2#LINE/L1      290   908 (0)  

  chr2_217002369_    501 ACATAGATCAATGGAACAGAATAGAGAACCCAGAAAAAAAGCCACATACC 550
                          i              i     v    ii       v   v   i i ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_217002369_    551 TACAACAAATTGACCTTTCACAAACTTGACAAAAATAAACAATGGGGAAA 600
                           iiiiv      ii  iv    ivv  v   i vi vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_217002369_    601 GGACACCCTATTCAGTTAATGGTGCTGGGATAATTGGCTAACAAGGTGCA 650
                          i i vi  v    iiv             i  i   v  ? v vi    
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_217002369_    651 GAAGAATGAAACTGGACCCCTCTCTCTCACCATACACAAAAATTAACTCA 700
                         i         ii         vi   v       i               
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_217002369_    701 AGGTGGATTAAAGAC-TAAATGTAAGACTTGAAACTATAAAAATCCTAGA 749
                          ii     i ?    -           vi i           v  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_217002369_    750 AGAAAGCCAAGAAAAAACTCCCTG-GACATTGGTCTAGGCAGAGAATTTA 798
                              i vv  i?iv  v  iii -   v    vi      iv iv  iv
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_217002369_    799 CAATGAAGATCCCAAAAGCA-AAGCAACAAAACCAAAAACAGACAAATGG 847
                         i ivv v  iv         -           vv     i   i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_217002369_    848 GACTTAGTTAAACCAAAAAAGCTTCTGCACAGCAAAATAAAATAATCAAC 897
                              vi i   viv     -   i  ii vv    iv v v -     v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT-ATCAAG 687

  chr2_217002369_    898 AGAGCAAACAGACAACCTATAGAATGGGAGAAAATAATTGCAAATTATGC 947
                          i  ii  v        i i                v        i  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_217002369_    948 CTCTGACAAATGACTAATGTCCAGAACCTACAGGGAACTCAAATAACTCA 997
                         v     i  iv    vi i       iv  i ii      vv i      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr2_217002369_    998 ACAAGAAAAA---------CTCCATTAAAAACTGGGCAAAGGGCATGAAT 1038
                          i  v     --------- i v   ?    v          iiv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_217002369_   1039 AGACATTTCTCGAAAGAAGACATCCAAGCAGCTAACAAACACACCAAAAA 1088
                                    v        i  v   iii  i  i  i    iv    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_217002369_   1089 ATGCTCAACATCATTAACCAT 1109
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (89 / 61)
Gap_init rate = 0.01 (6 / 619), avg. gap size = 2.33 (14 / 6)  


1492 28.38 6.91 2.50  chr2_217022475_217024125      486  1165 (486)    L1M4_orf2#LINE/L1      199   908 (0)  

  chr2_217022475_    486 AACAAAGCTGT----CTGA-ACTACCAGATATTAAGACTAATGATATAGC 530
                                i  v----  v -   v  vi  v i  i   v iv i v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_217022475_    531 CATAGTAATTAATTCAGTGTGGTATTGAATTAAATTGA-AGG-----AGA 574
                         i i      i  vv          i  ivv   i--  -  i-----   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAG--GATAGACATATAGA 296

  chr2_217022475_    575 TTAGTGGAATAGAG--AAGGGTACAGACATAGATCCACATACACGGATAC 622
                          i i         i--i  i  v    v   i i   --    ---- vi
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACA----TTT 340

  chr2_217022475_    623 ACAATTACTTGATTTATGACAAGTGTG---AAATGGTAGGGTGGTGAGGG 669
                          iii i v       vi      v   --- i ivi vvii   v  ii 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_217022475_    670 AAAGTTAGTCTTCTTAATAAATAGTTGCTGTGTAAATTGCATATCCATAC 719
                           ---       i i  i    i  -    v vv  i  v   ?   i i
  L1M4_orf2#LINE/    391 AA---TAGTCTTTTCAACAAATGGT-GCTGGGACAACTGGATAKCCACAT 436

  chr2_217022475_    720 -CAAAAAAAGTGCATCTTGAACCC--ACCCAATCCCATACACAAAAACCA 766
                         -     i  -  v v-   i    --   iv iv     i       ii 
  L1M4_orf2#LINE/    437 GCAAAAGAA-TGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_217022475_    767 GTTCTAGATGGAT--------TAAATGTGAAAGGAAAATCCATAACTCTT 808
                         ii  v i      --------       i i  vv   v i    vv  i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_217022475_    809 CTAGAAGAAAACAAAGAAGAATGTTTTCATGATCTTTGGGACAGGCAAAA 858
                         i            v  i? v vi i   i   i   -   vi      vi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT-GGGTTAGGCAATG 583

  chr2_217022475_    859 TTTTCTTACATAC-ACACAAATACCATTAATTATATAAAGGGAAAAATTG 907
                         v       v   i-    v  v v  i-  vi - i   i i      v 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCAC-AAGCA-ACAAAAGAAAAAATAG 631

  chr2_217022475_    908 ATAAA---------------ATTAAGAACATTAGCTCAGCCAAAGATTTA 942
                              ---------------     i   v  v iv vv v  i  iviv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_217022475_    943 ATTTAGAGAGTAAAGGGGCAAGCCCCAGAATAGAAGAAGATATTTGCAAA 992
                           iv   i   i  ii i   v  v      i i    i           
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_217022475_    993 ACGCATATATGCCAAAGAACTGAAATTCAAAACATATAAAGAACTCTTAA 1042
                         v ii    v  vi  i i   viv  i  i  i                v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_217022475_   1043 AAACCAA----AAAGAGACAGCTAACCCTGTAGAAAAATGAGTAAAAGGC 1088
                           vi   ----   i     iv      vi v?       i i   i ii
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_217022475_   1089 TTGAACAGGTACTTCACAAAAGAAGATGGCCAAAGGGCGAATAAATTTAT 1138
                              i  ii i   v v         ivv    v   v     iivi  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_217022475_   1139 GAAAAAGTGTTCAGTTTCAGTGCTCGT 1165
                              ii  i   iiv   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (113 / 77)
Gap_init rate = 0.03 (22 / 710), avg. gap size = 2.91 (64 / 22)  


3151 27.86 0.33 0.33  chr2_217144445_217150826     4983  5890 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_217144445_   4983 TGGAAGAACATTCCATACTCCTGAATAGGAGGAATCGATATCATGAAAAT 5032
                              ii i  i    ii  v  i  v   i  v ii    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_217144445_   5033 GGCCATACTGCCCAGGGTAATTTATAGATTCAATGCCGTCCCCATCAAGC 5082
                            v     v    iiv i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_217144445_   5083 TACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 5132
                          v   iivi i  i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_217144445_   5133 TGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGAA 5182
                              viiv  ii  v  viv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_217144445_   5183 CAAAGCTGGAGTCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5232
                              i     vvv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_217144445_   5233 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATCTAGACCAA 5282
                               i   i    ii         i iv ii i   v  v    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_217144445_   5283 TGGAACAGAAC--AGAGCCCTCAGAAACAATACCACACATCTACAACTAT 5330
                              i    i--    i  --     i  vv   i    i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_217144445_   5331 CTGATCCTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5380
                         i    ii i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_217144445_   5381 ATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5430
                         v  i                 v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_217144445_   5431 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5480
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_217144445_   5481 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5530
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_217144445_   5531 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5579
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_217144445_   5580 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5629
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_217144445_   5630 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5679
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_217144445_   5680 GGAAACCTACAGAATGGGAGAAAAGTTTTGCAATCTACTCATCTGACAAA 5729
                          iv    i                vv       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_217144445_   5730 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTGCAAGAAAAA 5779
                           i  vi          v  i         vv    v ivii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_217144445_   5780 AACGAACAACCCCATCAACAAGCGGGCAAAGGATATGAACAGACACTTCT 5829
                         i  i  i     v  i? v  ii           v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_217144445_   5830 CAAAAGAAGACATTTATTCAGCCAACAGACACATGAAAAAATGCTCATCA 5879
                          v        i  vi vvii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_217144445_   5880 TCACTGGCCAT 5890
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


2238 22.77 9.76 1.70  chr2_217317802_217319494.rev      495  1201 (492)    L1M4_orf2#LINE/L1      145   908 (0)  

  chr2_217317802_    495 TTCGTATGGAAC--CAAAAAAC--AGTGCAAATAGACAAAGCAATCCTAA 540
                            i       v--   iii  --  ----     v    i     i i 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAG----AATAGCCAAAACAATCTTGA 190

  chr2_217317802_    541 GCAAAAAGAACAGAGTCAGAGGCATCACATTACCTGACTTCAAACTATAC 590
                         iv  i       i   ii    vv     i v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_217317802_    591 TATAAGGCTACAGGAACAAAAACAGCATGACATTGGTACAAAAACAGACA 640
                           i  i       v  iv  i    ii  ii i   i i  ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_217317802_    641 CATAGACCAATGGAACAGAATAGAGAACCCAGA--------CATA----- 677
                         i     i        i     v    ii     --------    -----
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_217317802_    678 ATG-----TT--------ACAAAGTTGAGAAAATAAG-CAATGGGGAAAG 713
                            -----  --------    i v  vv  i iv v-            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_217317802_    714 --TA-CCTAGTCAATAAATAGTGCTGGGATAGCTTGCTAGCCATATGCAG 760
                         --  -i  vv    i    i         i i  v v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_217317802_    761 AAGAAAGAAACTGGACCCCTACCTCTCACCATATACAAAACTGAACTCAA 810
                              v   ii              v              v v       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_217317802_    811 GATGGATTAAAGATTTAAGTGTAAGACCTCAAACTATAAGAATTATAGAA 860
                         i      i ?   ii   i       v  v         i v iv     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_217317802_    861 GAAAACCTAGGAA-ACACCATTCTGGACATCATCCTTGGG------AAAG 903
                               v    ?i- v i -   vv   ------      ------  v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGAC------CTTGGGTTAGGCAATG 583

  chr2_217317802_    904 AATTTGTGACTAAGGCCTCAAAAGCAATAGCAACAAAAACAAAAATTGAC 953
                         iv  iv iiv  v i vi        vv          iv      v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_217317802_    954 AAGTGGGACCTAATTAAACTAAAAAGCTTGTGCACAGCAAAATAATCTAT 1003
                           i v    i v  i   v v    i   v  ii vv    iv vv    
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_217317802_   1004 CAGCAGAGT-AACAGACAACCTACAGAATGGGAGAAAATATTTGCAAACT 1052
                           iv i   -  v        i                          ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_217317802_   1053 ATGCATCTGATAAAAGTTTAATATCCAGAA----------------ACAA 1086
                           ii         ii vi vi         ----------------    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_217317802_   1087 TTCAACAAGGAAAAAAGCAAATAACCCCATTAAAAAGTGGGCAAAGC--- 1133
                         i    i  vi    i -          v   ?    i         v---
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_217317802_   1134 --------CACTTCTCAAAAGAAGACAGACAAGTGGCCAATAAACATATG 1175
                         --------  i     v        i v    i          i  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_217317802_   1176 AAAAAATGCTTAACAACACTAATCAT 1201
                             i     i    v  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (95 / 62)
Gap_init rate = 0.02 (18 / 764), avg. gap size = 4.50 (81 / 18)  


3211 27.56 0.33 0.22  chr2_217436907_217442008     3704  4610 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_217436907_   3704 TGGAAACACACCTCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3753
                               v i i i    i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_217436907_   3754 GACCATACTACCAAAAGCAATCTACAAGTTCAACATAATCCCCATAAAAA 3803
                          i v     v  v   vii       ii      ii      i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_217436907_   3804 TACCA-CCATCATTCTT-CAAGACTTAGAAAAAACAATTCTAAAGTTCAT 3851
                          v   - iii v  i  -  ii v  -  v  ivii  i     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chr2_217436907_   3852 ATGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGG 3901
                               viiv  ii  v  v v         i   vvi i iv  i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_217436907_   3902 ACAAATCTGGAGGCATTACACTACCTGATTTCAAACCCTACTATGAGGCC 3951
                              vi      vv i     v  ii        v i     ii i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_217436907_   3952 GTAGTCACCAAAACAGCGTGGTACTTGTATAAAAATAAACACATAGACCA 4001
                         ii   v i   i    i        v i    ii   i   i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_217436907_   4002 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACT-ACAGCCAAC 4050
                               i     v    ii               v i i - ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_217436907_   4051 TGATCTTCAATAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTT 4100
                             i   i i  i vviv   i v   vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_217436907_   4101 TTCAGCAAATGGTGCTGGGATAATTGGCTAGACATGTGTAGGAGAATGAA 4150
                             i               i  i   v  ?v  ii  i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_217436907_   4151 ACTGGATCCTCCTCTCTCACCTTATACAAAAGTCAACTCAAGATTGATTA 4200
                         ii    i  iivi   v    v         i i       i  v   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_217436907_   4201 AGGACTTAAACCTAAGACCTGAAACTATAAAACTTCTAGAAGATAACATT 4250
                         ?i   i    iv     v  i             ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_217436907_   4251 GGAAAAACCCTTCTAGACATTGGCTTAGACAAGAATTTCATGACCAAGAA 4300
                           ?iv  vi    vv   v    v    i   vii    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_217436907_   4301 CCCAAAAGCAAATGCAATAAAAACAAAGGTAAATAGCTGGGACCTAATTA 4350
                         v         v v    i    iv   ii  i   iv v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_217436907_   4351 AACTAAAGAGCTTTTACATGGCAAAAGGAACAGTCAGCAGAGTAAACAGA 4400
                           v v  i i     iiiivv    i iv  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_217436907_   4401 CAACCCACAGAGTGAGAGAAAACCTTCACAATCTATACATCTCACAGAGG 4450
                                    i  i       iv  ii   vii   i    v i ii  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_217436907_   4451 ACTAATATTTAGAATCTACAATGAACTCAAACAAATCAGTAAGAAAAAAA 4500
                            vi   ii     v  i  v      vv    v   i   v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_217436907_   4501 ACAAACAATCCCATCAAAAAGTGGGCTGAGGACATGAATAGACAATTCTC 4550
                         -    i  i  v  i?    i     vi    iv          v     
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_217436907_   4551 AAAAGAGGATACACAAATGGCCAACAAACATATGAAAAAATGCTCAACAA 4600
                         v     i    i            i  i  i       i          v
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_217436907_   4601 CACTAATGAT 4610
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.70 (155 / 91)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


2156 27.70 0.66 0.82  chr2_217666893_217673390.rev     4793  5402 (1096)    L1M4_orf2#LINE/L1        1   609 (299)  

  chr2_217666893_   4793 TGGAAAAACATTCCATGCTTATAGATAGGAAGAATCAATATCGTGAAAAT 4842
                               i i  i     i i  i   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_217666893_   4843 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 4892
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_217666893_   4893 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAAACAACTTTAAATTTCA 4941
                          v   -   v    i  -i     v v  v  iv-ii iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chr2_217666893_   4942 TACAGAACAAAAAAAGAGCTCATA-TAGCCAAGAGAATTTTAAGCAAAAA 4990
                           ii   - viv  i ii i  v -       i v   i  i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_217666893_   4991 GAACAAAGTTGGAGGCATCATGCTACCTGACTTCAAACTATATTACAAGG 5040
                                        vv   ii  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_217666893_   5041 CTATAGTAACCAAAACAGCATGGTGCTGGTACAAAAACAGATGTATAGAC 5090
                            i     i   i    ii    i    i i  ii i   ii      i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_217666893_   5091 CAATGGAACAGAACAGAGGCCTCAGAAATAACACTACACATCTACAACCA 5140
                                 i    iv   ivii         vv i i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_217666893_   5141 TCTGATCTTTGATAAAGCTGACAAAAACAAGCAATGGAGAAAGGATTCCC 5190
                         vi    i  i  i  i v  v   i v  vv      i     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_217666893_   5191 TACTTAATAAGTGGTGTTGAGAAAACTGGCTAGCCATACGCAGAAAACTG 5240
                          vi i  i  i     i  i  v      v  ?   i i   i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_217666893_   5241 AAACTGGACCCCTTCCTTACACCTTATACAAAAATCAACTCGAGATGGAT 5290
                           ii         v   i     v           i     i i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_217666893_   5291 TAAAGATTTAAACTG-AAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5339
                         i ?   ii    -  -    v       i      vi i           
  L1M4_orf2#LINE/    498 CAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_217666893_   5340 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5388
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_217666893_   5389 AAACACCAAAAGCA 5402
                         vi            
  L1M4_orf2#LINE/    596 TGACACCAAAAGCA 609

Transitions / transversions = 1.96 (110 / 56)
Gap_init rate = 0.01 (9 / 609), avg. gap size = 1.00 (9 / 9)  

 985 26.14 0.33 0.33  chr2_217666893_217673390.rev     5701  6006 (492)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr2_217666893_   5701 AAAAGCAATTGCAACAAAAGCTAAAATTGACAAATGGGATGTAATTAAAC 5750
                                vvv          vv     v  i    v   iv v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_217666893_   5751 TAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAA 5800
                          v  i i   i  ii vv    i  v    i  vv i      v  i   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_217666893_   5801 CCTACAGAATGGGAGAAA-TATTTTGCAATCTATTCATCTGACAAAGGGC 5849
                           i               -     -    vii  vi      i  i  i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGATAAGGGAC 751

  chr2_217666893_   5850 TAATATCCAGAATCTACAAGGAACTTAAATAAATTTACAAGAAAAAAACA 5899
                          vi          v  i  i     ivv i  v iv i  v     i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr2_217666893_   5900 AACAACCCCATCAAATAGTGGGCGATGGATATGAACACACACTTTTCAAA 5949
                           i     v  i?  v i     i v    v    i v   i  i  v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_217666893_   5950 AGAAGACATTTATGAGACCAACAAACATATGAAAAAAAGCTCATCATCAC 5999
                               i  vi viv i    i  i  i       i v     v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_217666893_   6000 TTGTCAT 6006
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.14 (42 / 37)
Gap_init rate = 0.01 (2 / 306), avg. gap size = 1.00 (2 / 2)  


2027 27.98 1.91 1.91  chr2_217821117_217831031.rev     1166  1794 (8121)    L1M4_orf2#LINE/L1        1   629 (279)  

  chr2_217821117_   1166 TGGAAAAACATTCCATGCTCATGGATCGGAAGAATCAATATTGTTAAAAT 1215
                               i i  i     i        i      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_217821117_   1216 GGCCACACTGCCCAAAGCAATCTATAGATTCAATGCTATTCTCGTCAAAC 1265
                            v i   v      vii     i        i  v  i iii     -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr2_217821117_   1266 AGCCAATGTTG--TTTTTCACAGAATTAGAACAAACT-ATTCTAAAATGT 1312
                          v  v - i  --     ii     v v  -   i  -  i       vi
  L1M4_orf2#LINE/    100 ATCCCA-GCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTC 147

  chr2_217821117_   1313 ATATGGAGCCAAAGAAGAGCCAGAATAGTCAAAGCATTCCTATGCAGAAA 1362
                                iviiv iii  v         i    i  v  i iviv ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_217821117_   1363 GAGCAAAGCTAGAGGCATCATATTGCCTAACTTCAAACTATACTATAACA 1412
                           i     i i    vv   i i v  i  i      viv     i  vi
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_217821117_   1413 CTACAGTATCCAAAACAGCATGGTATTGGTCCAGAAACAGACACATAGAC 1462
                                 vi   i    ii     i   ivi iii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_217821117_   1463 CAATGGAGCATGATAGAAAACCCAAAAATAAAGCCACACACCTACAACCA 1512
                                ii vi  v  i ii   i       v   i   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_217821117_   1513 TCTGATCTTCAACAAAGCTGACAAAAATAAGCAATGAAGAAAAGAGGCCC 1562
                         vi    i   i    i v  v   i vi vv     ii    ii vivi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_217821117_   1563 TATTTAATAAATGGTGCTGGTATAGCTAGCTAGCCATATACAGAAGAATG 1612
                          v  i  i            v i i  i v  ?   i  i  i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_217821117_   1613 AAACTGAACTTCTACCTGTCACCATATACAAAAATTAATTTAAGATAGAT 1662
                           ii  i  ii      vv                   i i  i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_217821117_   1663 TAAAGATTTAAATATAAGACCTCAAACAATAAGAATCCTAAAAGAAAACA 1712
                         i ?   ii     i     v  v    v    i v  i  i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_217821117_   1713 TAAGAA-ACACCATGCTAGACATCAACCTTGGA--AAAGAAT------TT 1753
                           i ?i- v i v ------ i -i       i-- iiv   ------  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTT------CGT-GACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_217821117_   1754 ATGATGAAGTCCTCAGAAGCAATTGCAACAAAAACAAAAAT 1794
                          -   - v v vi  i     vvv         iv      
  L1M4_orf2#LINE/    591 A-GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

Transitions / transversions = 2.20 (119 / 54)
Gap_init rate = 0.02 (12 / 629), avg. gap size = 2.00 (24 / 12)  

 839 27.40 1.03 0.00  chr2_217821117_217831031.rev     2076  2367 (7548)    L1M4_orf2#LINE/L1      614   908 (0)  

  chr2_217821117_   2076 CAAAAAAAAAAAAAATTGACAAGTAAGACCTAATTACACTAAAGAGCTTG 2125
                            v    i       v  i  i vi   i v  i v v v  i i   v
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_217821117_   2126 TGCACAGCAAACGAAACTATAAACAAAGTAAGCAGGCAACCTACAGAAT- 2174
                           ii vv    v  v     v  v     i iv  i     i       -
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr2_217821117_   2175 CGAGAAAATATTCACAAACTATGCATCTAACAAAGGTCTAATATACAGAA 2224
                         v           ii    ii  ii    i i  i  v  vi   v     
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_217821117_   2225 TATATAAGGAACT-TCAGAATTCCACAAACAAAAAACAGATAACCCTATT 2273
                                i     - i v  i  v i  vv    i   i       v   
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_217821117_   2274 TAAAAGTGGGCAAAATACGTGAACAGACGCTTTACAAAAGAAGACATATG 2323
                         ?    i        iv iv    i    ii  iv v        i   ii
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_217821117_   2324 AGCAGCCAACAAAAATGTAAAAA-ATGCTCATCACCAATTATGAG 2367
                          iii     i  iv ii i    -       v  i  ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (49 / 30)
Gap_init rate = 0.01 (3 / 295), avg. gap size = 1.00 (3 / 3)  

2671 27.85 0.53 3.63  chr2_217821117_217831031.rev     6745  7681 (2234)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_217821117_   6745 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAATATCGTGAAAAT 6794
                               i i  i    vi        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_217821117_   6795 GGCCATACGGCCCAAGGTAATTTACAGTTTCTATGCTATTCCCATCAAAC 6844
                            v    vv     iv i  i     v   v i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_217821117_   6845 TACCA-TTAACATTCTT-CAAATAATTAGGAAAAACC-ACTTTAAATTTC 6891
                          v   -i iv v  i  -  i -    --  v  i i- iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATT--GACAAGCTGATCCTAAAATTC 147

  chr2_217821117_   6892 ATATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATACTAAGCAAAAA 6941
                                 viiv  ii  v  v v        i     vi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_217821117_   6942 GAACAAAGCTGGAGGCATCATGCTACCTGACTT-GAAACTATACTACAAC 6990
                                 i      vv   ii  v  ii i  -i     -        v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chr2_217821117_   6991 GCTATGGTAACCAAAACAGCATTGTACGGGTACCAAAGCAGACATACAGA 7040
                             ii    i   i    ii v    v  i iv iiii       i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_217821117_   7041 CCAATGGAACAAAATAGTGACCTCAAAAATTACACCACATATCTACAACT 7090
                         i        i i   v v  vii  i    v vv   i i  i  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_217821117_   7091 ATCTGATCTTCAACAAAACTGACAAAAACAAGCAATGGGGAAAGGATTCC 7140
                          vi    i   i    iiv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_217821117_   7141 CTATTTAACGAACAGCACTGCGAAAACTGGCTAGCCATATGCAGGAAACT 7190
                           v  i   i  ii ii   v  v      v  ?   i     ii i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_217821117_   7191 GGAACTGGATCTCTTCCTTACACCTTATACAAAAATTAACTTAGGATGGA 7240
                          i ii    i i  v   i     v                i ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_217821117_   7241 TTAAAGACTTATATGTAAAACCCCAAACCATAAAAACCCTAGAAGAAAAC 7290
                          i ?    i  v      i v iv    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_217821117_   7291 CTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAAGATTTCATGACAA 7339
                         v    ?i- v i -   iv   viv  vv i     v i    v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_217821117_   7340 AAACACCACAAGCAATTGTAACAAAAGCTAAAATTGACAAATGGGATCTA 7389
                         vi      v     vvv i        vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_217821117_   7390 ATTAAACTAAAGAGCTTCTGCACGGCAAAAAACAAACAAACAAACAAAAA 7439
                           i   v v  i i   i  ii vv    ii   ----------------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA---------------- 679

  chr2_217821117_   7440 TAAACCGAAAAAACTATCATCAGAGAGAACAGGTAACCTACAGAATGGGA 7489
                         -------------      vv i  v   v  ii    i           
  L1M4_orf2#LINE/    680 -------------CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_217821117_   7490 GAAAAATTTTGCAATCTACCCATCTGACAACAGTCTAATATCCAGAATCT 7539
                              vv       vii ivi      i  vi v  vi          v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_217821117_   7540 ACAAGGAACTTAAACAAATGTACAAGAAAAAAGAAAACAACCTTATCAAA 7589
                          i  i     ivv    v vv i  v     iiv   i    iv  i?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_217821117_   7590 AAGCGGGCAAAGGATATGAACAGACACTTCTCAAAGGAAGACATTTACAT 7639
                           ii           v    i     i     v  i     i  vi v  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_217821117_   7640 GGCCAACAAACATATGAAAAAAAGCTCAACATCACTGATGAT 7681
                               i  i  i       i v           ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (151 / 106)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.90 (39 / 10)  

4003 16.99 3.82 1.69  chr2_217821117_217831031.rev     8535  9423 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_217821117_   8535 TGCAAAGACATCT-ATGCTCATGAAATGGAAGATGTAATATTGTTAGGAT 8583
                           v     i   i-   i     i v       iv           i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_217821117_   8584 GGCAATATTCCCCAAATTGATCTAAAGATTTGATGTAATCCCTATCAAAA 8633
                                i                v     ii i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_217821117_   8634 TCTCAACTGTCTTTTT-GCTGAAAATGATAAGTTGATACTAAA-TTCATA 8681
                           i  i   i      -  v    v   i   i    v     -      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_217821117_   8682 TGGAAATA-AAAGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA--- 8727
                                i-  i                                   ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_217821117_   8728 TAAAGTTGAAGGACTGA---TT---AATTTCAAAAATTAGTACGAAGCTA 8771
                         i       i      v ---  ---          v   v   i      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_217821117_   8772 CACTAATCAAGACTGTGTGGTATTGGCATA-GGATAGACATATTATATTG 8820
                           v          v        i       -            --- -- 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT---A--G 295

  chr2_217821117_   8821 ATCA-TGAAATAAAATTGAGAGTCCAGAAATAAAGTTATTCATT-ATCGT 8868
                             -  i    i                     vii  v    -  v  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_217821117_   8869 CAAGTGATTTTTGATAATGGTACCAAGGCAATTTAATGCAGGAA--ATAA 8916
                            v       i  i  v   i     i v   i    vi i  --   i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_217821117_   8917 TGTTTTCAACAAAGAATGCTGGAGTAACTAGATATCCAGATGCAAAAGAA 8966
                          v           vii      iii    i    ?   v           
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_217821117_   8967 TAAAGTTGTTGAACCACTTCCTCATAACATACATAAAAATGTACTCAACA 9016
                          i      ---i   v  v     i v    i i      vv      v 
  L1M4_orf2#LINE/    446 TGAAGTTG---GACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_217821117_   9017 TGAACTA-AAACTTAAGTGTAAGA-CTAAAAATGAAAAAAATTATTAAAT 9064
                           i ii - i  i   i       -      v -- v    i v   i v
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACT--ATAAAACTCTTAGAA 540

  chr2_217821117_   9065 GAAAACACACAAGTAAATATTCATGACCTTAAACTAGGCAATGATTTCAT 9114
                                i vi?      v   i       iiii         i    v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_217821117_   9115 ATATATGACACCAAAAGCACAAGCAACAAAATTTAAAATAGATACATTGG 9164
                          v                             vvv          v     
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_217821117_   9165 ACTTAAATCAAAATTTAAAACTTTTGTGCTTCAAATATTATTATTTAAAA 9214
                             v -        v                   vivi i   iv i  
  L1M4_orf2#LINE/    641 ACTTCA-TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_217821117_   9215 ACTGTAAATGCAATCTAGATATTGGGAGAAAATTGTTGCAAATCATATAT 9264
                          v  v   vi   i i v v v           vv               
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_217821117_   9265 TTGATAAGGGTCCATCATCCAGAATATATAAAGAACACTTAGAGTAACTC 9314
                         i         v ivvi                    v    ---i     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA---CAACTC 786

  chr2_217821117_   9315 AAACGTTATGTAGTTAAATAACCCAATT-GAAAATGGGCAAAGTATTTGA 9363
                           -iiv  viv  vi             -i             v      
  L1M4_orf2#LINE/    787 AA-TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_217821117_   9364 ACAGATATTTATCCAAA-------------TGGCCAGTAAGCACATGAAA 9400
                          i   i    v      -------------      i             
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_217821117_   9401 GGATGTTTATCATTAATCATTAG 9423
                         i    i i v   i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (85 / 64)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.23 (49 / 22)  


2855 27.04 3.05 0.34  chr2_218036018_218041394.rev     4002  4885 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_218036018_   4002 TGGCAAAACATTCTATGCTCAAGGATAGAAAGAATCAATATTGTTAAAAT 4051
                            v  i i  i i   i   v    v i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_218036018_   4052 GGCCATACCACCAAAAGCAATTTATAGATTCAATGCTATTACTATCAAAC 4101
                            v    iv  v   vii  i  i        i  v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_218036018_   4102 AACCAATGACATTCTTCACAGAACTAGAAACAGCTG-TTTTAAAATTAAT 4150
                         vv   iivi v  i  ii     v v  v -     - ii       v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr2_218036018_   4151 ATGGA--TCCAAT---TTTAGGA--GCAAAGGCAATCCTAACCAAAAATA 4193
                              -- v   v---iii  i --  v  ii     i i vv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_218036018_   4194 ACAAAGCTGGAGGCATCATGCTATCCAACTTCAAACTATACTACAGAGCT 4243
                               i      vv   ii  vi    i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_218036018_   4244 ACAGTAGCCAGAACAGCATGGTACTGGTACAAAGATAGACACAGAGACCA 4293
                               ii  ii    ii         i i  i        i v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_218036018_   4294 ATGGAACAGAA--GAGAGCCAAGAAATAAGGCCACACACCTACAACCATC 4341
                               i    --     i v        iv   i   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_218036018_   4342 TGATCTTTAATAAAGCTGATAAAAACAACCAATAAGGAAAGGACTGTTTA 4391
                             i  ii i  i v  vi  i v  vi    ii      i iv  i v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_218036018_   4392 TTCAATAAATTGTGCTGAGATAACTGGCTAGCCATATTCAGAAGATTGAA 4441
                              i    v      i  i      v  ?   i  v  i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_218036018_   4442 ACTGCACCCCTTGTTTACACCATAAACAAAAATTAACTCAGGATGAATTA 4491
                         ii  v      vvi i        v               ii   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_218036018_   4492 AAGACTTAAATGTAAAACCCAAAACTGTAAAATCCCTAGAAGATAGCCTA 4541
                         ?    i         i v i      i     ii i       v i v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_218036018_   4542 GGC-TATACCATCCTGGACATAGGAACAGGAAATGATTTCAT-GATCAAG 4589
                           ?-  v i v  v  -  v v  ivi   v    i    v -   - v 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chr2_218036018_   4590 ATGCCAAAAACAACTGCAA-AAAAGCAAAAACTGGCAA-TAAGACCTAAT 4637
                          ii      i  vvv    -     v     iv ii  - vi   i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_218036018_   4638 TAAACTAAAGAGTTTCTGCACAGTAAAAGAAACTATCAACCAAGTAAA-- 4685
                         i   v v  i ii  i  ii vvi   i  v        vv    i  --
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_218036018_   4686 --CGACCTACAGAATGGGAGAAA-TATTTGTAAACTATGCATCTGACAAA 4732
                         -- i   i               -      i   ii  ii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_218036018_   4733 GGTCTAATATCCAGCATCTATAAGGAACT--TA-AATTTACAAGTGAAAA 4779
                           v  vi       v  v     i     --  -  i i vv i i    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_218036018_   4780 -ACAAACAACTCCATTAAAAAGTGGTCAAAGGACAGGAACAGACACTTTT 4828
                         -     i   i v   ?    i   v       ivv   i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_218036018_   4829 CAAAAGAAGACATACATGTGGCTAACAAGCATACAAAAACAGGT----CA 4874
                          v        i     vi    i  i     i ii    v v i----  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_218036018_   4875 TCACTGATCAT 4885
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.67 (147 / 88)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.67 (30 / 18)  


2502 21.93 2.19 11.67  chr2_218103567_218107544     2484  3486 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_218103567_   2484 TGGAGAGATTACATCATGTTCACGGGTCAGAACA-TTCATGTTGTTAAGA 2532
                             i    - ivi        i  i ii   v -  v  i         
  L1M4_orf2#LINE/      1 TGGAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_218103567_   2533 TGTCAGTTCTCTCAAGATTGAGCTATAGATTCAGTGCAATCCTAATCAAA 2582
                           v  i v   i v i     v   i       ii       iv      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_218103567_   2583 ATTCCAGCAGA-TTTTTGGTATAT-TTAACAAACTGTTTCTAAAGTTCAT 2630
                           i     v v-     v i v v-  i    i   v i     i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_218103567_   2631 GTGACAATTTAAAAGATCTAAAACAAATTTCAAGCAAAATTGAAAAAGAA 2680
                         i  iv   vi  ii  i i i  i i--iiv  i   vv           
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAG--CCAAAACAATCTTGAAAAAGAA 197

  chr2_218103567_   2681 AAACAAAGTTGGATGACTAACACTATCTGAGCTCAAGATTTATTGTAAAA 2730
                         i            v    v     vi ii vi    i i   i ii   -
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA- 246

  chr2_218103567_   2731 GCTGAAGAAATCAGGACAGGGTGCTATTGGCATCAAGACCAACAAACAAA 2780
                            iv  v     i     v   v  i      v i  ivi   v i i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_218103567_   2781 CCAATGGAGCAGAA--GACATGGTCCAAAAATAGATCCACGCAGAGATGG 2828
                         i       ii    --  v --     i     i i   ii  vvv    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGA--GTCCAGAAATAAACCCATACATTTATGG 344

  chr2_218103567_   2829 ACAACTTGGTTTTTTACCAAGGTACAAAGATGATTTAGAGTAGGAAAGG- 2877
                         v   -   i    iv  v i   i v    iv   i iv -i      i-
  L1M4_orf2#LINE/    345 TCAA-TTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAA 392

  chr2_218103567_   2878 TAGGCTG--CAAAAAATTGTGCTGTAACATTTGGATATCCGCATGCCAAA 2925
                            v  v--   v    v      vi   vi      ?  i     v   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_218103567_   2926 GAATGACCTTCAATCCATATTTCACCTCATAATA-AAAAATTAACCCAAA 2974
                               vv  vi i  v  ii    vi    -  -          i    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATA-TACAAAAATTAACTCAAA 491

  chr2_218103567_   2975 ATACATCCCA---CTA--TGTAAAATCTAAA-CTATAAAACCTTCACAAG 3018
                           iv   v? ---   --     i v     -         ii i v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_218103567_   3019 ACAGCACAGGATAAAAACATGGCACATGTATGCATATGTAACTAACCTGC 3068
                          -------------      i ----------------------------
  L1M4_orf2#LINE/    542 A-------------AAACATAG---------------------------- 550

  chr2_218103567_   3069 ACATTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAGAAA 3118
                         ----- ? -----------    v   -----------------------
  L1M4_orf2#LINE/    551 -----GNG-----------TAAATCTT----------------------- 561

  chr2_218103567_   3119 AAAAAAACATTTGTGAACTTGAATTAGGCAAAGATTTCTTAGGTCTTACA 3168
                         -----------i    v    ii        v i        i v v   
  L1M4_orf2#LINE/    562 -----------CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_218103567_   3169 CCTAAAGCATAATCCATAAAAGGAAAA-TAAATCATATATTGG-CTT--T 3214
                           v      i  v v i     i    -  i  v ---     -   -- 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA---ATTGGACTTCAT 647

  chr2_218103567_   3215 CAAAGTTAAAAACTTCTCCTCTTCAAAAGACAGAATTTTGTAAATTCTGT 3264
                             i          i viv       i    --------------  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACA--------------CTAT 683

  chr2_218103567_   3265 AAAGAGAATTAAAAGATAAAAGGCAGCATAGGAGAACATATTTGTAAATA 3314
                         v    i i v      i  vvvi   v  i      v       i    v
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_218103567_   3315 ATATATCTGACAAAGAAGCTGTATTTAGAATTCATAAAGAACTCTCAAAA 3364
                                   i  i i vi     ii     vi            i v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_218103567_   3365 TTCAATAATAAGAAAGCAAGTAATCAAAT--ACAAATGGTCAAAAGATTT 3412
                         i          i  ii   i   i v   -- v      v    i     
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_218103567_   3413 GAACAGACAGT-CACTAAAGAAAAAGTATGGTTGGCAAATAAATAGACGG 3461
                            i     v - v i      i vi  iiiv    v     ii v i i
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_218103567_   3462 AAAGATGCTCAACATCAGCAGTTGT 3486
                                          ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (130 / 87)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 4.96 (139 / 28)  


2883 21.44 5.63 2.40  chr2_218238761_218240586      500  1334 (492)    L1M4_orf2#LINE/L1       47   908 (0)  

  chr2_218238761_    500 AGATTTCAATTCTCCCCAAAATTAGCTTATAGATTCAATGCACTCCCAAT 549
                             vv    v         -  iiii  i        i   v    v  
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTAT 95

  chr2_218238761_    550 CAAAAATCCCAGCAGGCTTTTTTGTAGAAATTGGCAAGATTATTCTAAAC 599
                              -       v v        i        i    v v  i     v
  L1M4_orf2#LINE/     96 CAAAA-TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_218238761_    600 TTCAAATGGAAATGCAAAAAA-----AAT-GTTTTGGCTATTTTAGAAAA 643
                             v            iii -----   - iivvii v  i  ii    
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_218238761_    644 ATATAAAAACAAAAAGTTGGAGGTCTAACACTACCTGACTTCAAAACTCA 693
                         i---  i      --        v  v     v  ii i         i 
  L1M4_orf2#LINE/    195 G---AAGAACAAA--GTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_218238761_    694 T---GAAGTTACAATAATCAACACGCTATGGTGTTGGCATAAAGATAAGA 740
                         i---i   i    i       v  iv i    ii        i    -  
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GA 288

  chr2_218238761_    741 CACATAGATCAATGAAACA---TTAAGAGAGATTCTAGAAATAGACCCAC 787
                           i           i  i ---  i    ----  i       i     i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAG----TCCAGAAATAAACCCAT 334

  chr2_218238761_    788 ACCTATACGTACAAGTGATTTTTGCCAAGG-TACAAAGGCAATTTGGAAG 836
                           v v  i vv   v       i v     - i v   i v   iiivi 
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_218238761_    837 GGAAAATACAATCTTT-CAATAAATGCTGCTGAAACAAATGGATATCCAC 885
                              iv i i     -   i     v     ii    v      ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_218238761_    886 ATGCAAAAAAAAGGAGCTTTCATTTATACCTCATGCCATGTACAAAAATT 935
                                 i  v i  -  vv iiiv       ii    i          
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_218238761_    936 AACTGAAAGTGGTTCACGGAC------GTAA-AG-TAAAATGATAAGACT 977
                             v   i   v   ?i   ------    -  -     iv    i   
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_218238761_    978 TTCAGAAGAAAATAAATGGTAAAATCTTTGTGA------GTTACACAAAG 1021
                         i i         i v v ?vv       i    ------    vi   v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_218238761_   1022 GTTTCTTAGGTACAACACCAAAA---CAATCATCCATAAAAGAAAACAAT 1068
                                  i  ii         ---   v  --- i         -   
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCA---ACAAAAGAAAA-AAT 629

  chr2_218238761_   1069 AGA---------CTTCAGCAAAATTAAAAACTGCCACACTTTAAAAGACA 1109
                            ---------     v              viiiii   i   i    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_218238761_   1110 CTGTTAAGGTAATGACAAAGGCAAGCCATAGTCTGGGAGGAAATATTTTC 1159
                           i i   iv i   -    i   v   i  vv      i        v 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGA-AAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_218238761_   1160 AAATCACATATCTGATAAAATAACTT-TATATAGTCTATATTTAGAACTC 1208
                               i           ii-i    -   vi  vv     vv       
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGG-GACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_218238761_   1209 TCGAAACCCA-TAATAAAAAAGGCAAATAAA--AATTTAAAA-TGA-CAA 1253
                          iiv   i  -         - i       v--    ?    -  i-   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_218238761_   1254 AAGATACGAG-ACACACTTCATCAAAGAAGCTATACTGATGGCAAATAGG 1302
                          i   vi  i- v   i   vi        v     vi     v    i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_218238761_   1303 TACATGATAAGATGTTCAACATCAATAGTCAT 1334
                         i      v      i         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (109 / 66)
Gap_init rate = 0.03 (30 / 862), avg. gap size = 2.23 (67 / 30)  


3173 27.48 0.66 0.44  chr2_218364602_218368627.rev     2629  3534 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_218364602_   2629 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2678
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_218364602_   2679 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCTATCCCCATCAAGC 2728
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_218364602_   2729 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2776
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_218364602_   2777 TATGGAACCAAAAGAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 2826
                                viiv   i  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_218364602_   2827 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTGCAAGTC 2876
                                i      vv       v  ii i      viv    i   iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_218364602_   2877 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2926
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_218364602_   2927 AATGGAACAGAAC--AGAGCCCTCAGAAATAACATCGCATATCTACAACT 2974
                                i    i--    i  --        vvi ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_218364602_   2975 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3024
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_218364602_   3025 CTATTTAATAAATGGTGCCGGGAAAACTGGCTAGCCACATGTAGAAAGCT 3074
                           v  i  i         i    v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_218364602_   3075 GAAACTGGATCCCTTCCTTACACCTTATATAAAAATTAATTCGAGATGGA 3124
                            ii    i    v   i     v    i         i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_218364602_   3125 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3174
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_218364602_   3175 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTGA 3224
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_218364602_   3225 AACACCAAAAGCAATGGCAACAAAAGCCAAAATGGACAAATGGGATCTAA 3274
                         i            vvi          vv     i  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_218364602_   3275 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3324
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_218364602_   3325 AGGCAACCTACACAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 3374
                           i     i   v             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_218364602_   3375 AGTGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3424
                         i vi  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_218364602_   3425 AAACA--CAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 3472
                          i   --i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_218364602_   3473 TCAAAAGAAGACATGTATGCAGCCAAAAAACACATGAAAAAATGCTCCCC 3522
                           v        i  ii viii     v  i          i      vv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_218364602_   3523 ATCACTGGCCAT 3534
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3211 27.59 0.44 0.22  chr2_218793063_218799409.rev     4950  5855 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_218793063_   4950 TGGAAGAACATTCCATGTTTATGGATAGGAAGAATCAATATTGTGAAAAT 4999
                              ii i  i       i      v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_218793063_   5000 GGCCATGCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5049
                            v  i  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_218793063_   5050 TACCAATGACTTTCTTCACAGAACTGGAAAAAACTACTTTAAAGTTCATA 5099
                          v   iivi i  i  ii     v v  v  iviv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_218793063_   5100 TGGAACCAAAAAAGAGCCCGCATTGCCAAGATAATCCTAAGCCAAAAGAA 5149
                              viiv  ii  v  v v  v     i i    i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_218793063_   5150 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCTATACTACAAGGCTA 5199
                              i      vv    i  v  ii i     iviv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_218793063_   5200 TAGTAACCAAATCAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5249
                         i     i   iv   ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_218793063_   5250 TGGAACAGAATAGAGCCCCCGGAAATAATACCACACATCTACAACTATCT 5299
                              i     v   vvi  i       vv   i    i  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_218793063_   5300 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 5349
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_218793063_   5350 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGGAA 5399
                          i  i              v      v  ?   i   i i  iiv  i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_218793063_   5400 CTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGATTAA 5449
                         i    i    v   i   i v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_218793063_   5450 AGACTTAAATATTACACCTAAAATCATAAAAACCCTAGAAGAAAACCTAG 5499
                             i     i v v v      ii      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_218793063_   5500 G--TAATACCGTTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5547
                          --   - i -   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    551 GNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_218793063_   5548 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5597
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_218793063_   5598 AAACCAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5647
                            viv  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_218793063_   5648 GCAACCTACAGAGTGGGAGAAAATTTTTGCTTTCTACCCATCTGACAAAG 5697
                         i     i     i           v     vvvii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_218793063_   5698 GGCTAATATCCAGAATCTACAAAGAACTTAAACAAATGTAGAAGAAAAAT 5747
                          i  vi          v  i        ivv    v vv v  v     v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_218793063_   5748 -CAAATAACCCCATC-AAAAGTGGGCAAAGGATATGAACAGACACTTCTC 5795
                         -          v  i-    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_218793063_   5796 AAAAGAAGACATTTATGCAGCCAACAGACCCATGAAAAAATGCTCATTAT 5845
                         v        i  vi viii     i ii v        i       vi  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_218793063_   5846 CACTGGCCAT 5855
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.38 (144 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


2474 27.19 1.85 1.36  chr2_219204877_219206677      501  1309 (492)    L1M4_orf2#LINE/L1       96   908 (0)  

  chr2_219204877_    501 CAAGCTACCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAA 548
                            iv v   -   v    i  -i     v v  v  i-  - iii    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAA 143

  chr2_219204877_    549 TTTCATAGGGAACTTTTTTTTTTTAAGAG-CCC-GTATAGCCAAGACAAT 596
                         v      v    v vi--------   i -   - v        i     
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGC--------AAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_219204877_    597 CCTAAGCAAAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAAC 646
                          i i iv  i          i      vv    i  v  ii i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_219204877_    647 TATACTACAAGGCTACAGTAACCAAAACAGCATCGCACTGGTACCAAAAC 696
                         iv        i          i   i    ii v i     i iv ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_219204877_    697 AGATATATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACA 746
                            i       i        i    iv   ivii         vv   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_219204877_    747 CATCTACAGCCATCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGG 796
                            i  ii i  vi    i  i     ivv  v   i vi vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_219204877_    797 GAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATA 846
                              i  vvi  v  i  i              v      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_219204877_    847 TGCAGAGAACAGAAACTGGACCCCTTCCTTACATCTTACGAAAAAATTAA 896
                             i ii vv   ii         v   i   i v  iiv         
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_219204877_    897 CTCAAGATGGATTAAACACTTAAACGTAAAACCTAAATCCATAAAAACCA 946
                              i      i ? v  i    i    i v     v i      vi v
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_219204877_    947 CAGAAGAAAACCTAGACA-ATACCATTCAGGACATAGGCATGAGCAAAGA 995
                         i          v   i?i- v i -   iv   v v  vv ii    v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_219204877_    996 CTTCATGACTAAAACACCAAAAGCATTTGCAACAAAAGCCAAAACAGACA 1045
                         i   v iiv  vi            ivv          vv    i   i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_219204877_   1046 AATGGGATCTAATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTATC 1095
                            v   ii v  i   v v  i ii  i  ii vv    i  v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_219204877_   1096 ATCAGAGTGAACAGGTAACTTACAGAACGGGAGAAAATTTTTGCAATCTA 1145
                          vv i      v  ii   ii      i          v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_219204877_   1146 TCCATCTGACAA---AC----ATCCAGAGTCAACAAGGAACTTAAACAAA 1188
                          vi      i  ---  ----       i vv i  i     ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_219204877_   1189 TTTACAAGAAAAAC-CAAACAATCCCATCCAAAAGTGGGTGAAGGATATG 1237
                          iv i  v     v-    i  i  v  i?    i    ii      v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_219204877_   1238 AACAGACACTTCTCAAAAGAAGACATTTATGCGGCTAACAA--ACGTGAA 1285
                           i     i     v        i  vi vii   i  i  --  i    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_219204877_   1286 AAAAAGCTCGTCATCACTGGTCAT 1309
                           i v    iv     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (128 / 88)
Gap_init rate = 0.02 (13 / 813), avg. gap size = 2.00 (26 / 13)  


3075 26.76 1.78 0.56  chr2_219457150_219464111.rev     5574  6470 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_219457150_   5574 TGGAAGAACATTCCATGATCATGGATAGGAAGA----ATATCATGAAAAT 5619
                              ii i  i     v        v      ----    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_219457150_   5620 GGCCATACTGCCCAAGGTAATTTATAGACTTAATGCCATTCCCATCAAGC 5669
                            v     v     iv i  i  i   i i  i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_219457150_   5670 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5717
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_219457150_   5718 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGGCAATCCTAAGCAAAAAG 5767
                                viiv  ii  v  v v  v     ii     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_219457150_   5768 AACAAAGCTGGAGGCATCATGCTACTTGACTTCAAACTATACTACAAGGC 5817
                                i      vv   ii  v iii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_219457150_   5818 TACAGTAACCAAAACATCATGGTACTGGTTCCAAAACAGATATATAGACC 5867
                                 i   i   vii         iviv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_219457150_   5868 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5917
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_219457150_   5918 CTGATTTTTGACAAACCTGATAAAAACAAGAAATGGGGAAAGGATTCCCT 5967
                         i       i     ivv  vi  i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_219457150_   5968 ATTTAATAAATGGTGCTGGGAAAACAGGCTTAGCCACATGTAGAAAGCTG 6017
                         v  i  i              v   v  v - ?       i i  iiv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCAAAAGAATG 447

  chr2_219457150_   6018 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 6067
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_219457150_   6068 TAAAGACTTAAATGTTAGACCTAAAACCATTAAAACCCT-AGAAGAAAAC 6116
                         i ?    i       v   v       i  -     i  -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAAC 546

  chr2_219457150_   6117 CTAGGCA-ATACCATTCAGGACATAGGCATGCGCAAGGACTTCATGACTA 6165
                         v    ?i- v i -   iv   v v  vv iv    v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_219457150_   6166 AAACACCAAAAGCAATGGCAACAAAAGGCAAAATAGACAAATGGGATATA 6215
                         vi            vvi          iv        i    v   iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_219457150_   6216 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 6265
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_219457150_   6266 CAGGCAACCTACAAAATGGGAGAAAATTTTTGTAATCTACCCATCTGACA 6315
                         v  i     i   i             v    i  vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_219457150_   6316 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAGCAAATTTACAAGAAA 6365
                          i  i  vi          v  i        ivvi   v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_219457150_   6366 AA---AAA-AACCCCATCAAAAAGTGGGCAAAGGATATGAAAAGACACTT 6411
                           ---   -     v  i?    i            v    v     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_219457150_   6412 CTCAAAAGAAGACATTTCTGCAGCCGA----CACATGAATAAATGCTCAT 6457
                            v        i  vivviii   i ----        v i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_219457150_   6458 CATCACAGTCATC 6470
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


3455 16.29 2.28 1.07  chr2_219492585_219495933.rev     1018  1674 (1675)    L1M4_orf2#LINE/L1        1   665 (243)  

  chr2_219492585_   1018 TGGAAAGTCATCC-ATGTTCATGGATTAGGAGACTTAATATTGTTAAAAC 1066
                                vi    -             i i                 i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_219492585_   1067 AGCAGTACTCCCCAAGGCAAACTACAAATTCAATGCATTCCCTTTCAAAA 1116
                         i   i          ivii v     i      i   v     v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_219492585_   1117 TTCCA--TAGCCTTTTTGCAGAAATGGAAAACCTGATCCTAAAATTAATA 1164
                          i   -- iv i             v  v  v              v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_219492585_   1165 TGGAACTGCAAGGGGCCCTAAATAGCCAAAACAATATTAAAAAAGAA-AA 1213
                              v        i   vi               v  i        -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_219492585_   1214 CAATGTTGGAACATTCCCATTTTCTGATTTCAAAACTTACTGCAAAGCTA 1263
                            v      iv i  v  i  i ii               i        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_219492585_   1264 CAGTAATCAAAACAGTAAGTTACTAGTGTAAGTGTAGACATATAGACCAA 1313
                                   i     iv v    i ii    vi            i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_219492585_   1314 TGGAATACAACTGAGAATTCAGAAATACACTAGAACATCTACAGTCAACT 1363
                                v  i     i i        v  iviv    i  ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_219492585_   1364 GATTTTTGACAAGGGTGCACAGACCATTCAATGGGGAAAGAA-AGTCTCT 1412
                               i           vv                      -     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_219492585_   1413 TCAACAAATGGTACTGGGACCACTGGATAACTAAATGCAAAAGAATGAAG 1462
                                     i       v        ? i v                
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_219492585_   1463 CTGGACCCCTACCTCACTCCATATACAAAAATTAATTCAAAATGGATCAA 1512
                         i                v                 i             ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_219492585_   1513 CAATCTAAAAAGAAGAGCTAAAACTATAAAACTCT--GAATAAAATATAA 1560
                         vi i     viv                       --   v    i   i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_219492585_   1561 GGGTAAGTCTTCATGACCCTGGATATGTCAATGAATTCTTAGATTTGATA 1610
                          ?    i     i     i   i vv v     iv         v   i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_219492585_   1611 ACAAATGCATGAG--------GAATTTTTTTTAAATAGATAAATAGTTCT 1652
                         v    v   ii  --------   v-------            v vv  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAA-------AAATAGATAAATTGGACT 643

  chr2_219492585_   1653 TCATAAAAATTAAAAACTTTTG 1674
                             v                 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.36 (60 / 44)
Gap_init rate = 0.01 (7 / 665), avg. gap size = 3.14 (22 / 7)  

 997 15.64 1.68 0.00  chr2_219492585_219495933.rev     2269  2447 (902)    L1M4_orf2#LINE/L1      650   831 (77)  

  chr2_219492585_   2269 AAATTTAAAACTTTTGTGCCTCGAAGGACATTATCAAGAATGTGAAAAGA 2318
                              v             i  i       i         v         
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_219492585_   2319 CAGCTTATAGAACGAGAGAAAATATTTGTAAATCATATATCTGATAAGGG 2368
                           i ii i    i i             i                     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_219492585_   2369 TTTAATATCCAGAGTATACAAAGAACTGTTACAACCCAACAACAAAAAGA 2418
                         vi vi        i    i        v       i   i  i       
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_219492585_   2419 CAAAT---TCAGTTTAAAAATAAGCAAAGAAT 2447
                              ---i  i  ?      ii      i  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 4.40 (22 / 5)
Gap_init rate = 0.01 (1 / 182), avg. gap size = 3.00 (3 / 1)  

 555 14.91 0.00 0.88  chr2_219492585_219495933.rev     2744  2857 (492)    L1M4_orf2#LINE/L1      796   908 (0)  

  chr2_219492585_   2744 AAAATAAATAAATTAATTAATTAAATAAGCAAAGAACTTGAATAGACATT 2793
                           i i      vii    ? -v    ii      i i             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_219492585_   2794 TCTCCAATGAAGATATGCAAATGGCCTATAATCACAAGAAAAGATGTTCA 2843
                                v        i         v    v    v         i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_219492585_   2844 ACATCATTTGTCAT 2857
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.01 (1 / 113), avg. gap size = 1.00 (1 / 1)  


 419 26.06 8.45 1.41  chr2_219623238_219626860.rev      952  1093 (2530)    L1M4_orf2#LINE/L1        2   153 (755)  

  chr2_219623238_    952 GAAAAGAAA--CCATGTTAGTGAATTATAAAACTCAAGAGTGTTAA---- 995
                          i     v --       vi  i   iv  i   i  v v      ----
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_219623238_    996 ----TTTTTCCCTAATTTATTACTACA--TTAAATGTAATCCTAACCAAA 1039
                         ---- vi i   v    v  --     --  v  i i     iv i    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGAT--CTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_219623238_   1040 ATCTTAGTAGATGTTTCAATGGAAATTGACAGGCTGATTCTAAAATTTAT 1089
                            ii  iv viv   iviii          i      i        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_219623238_   1090 ATGG 1093
                             
  L1M4_orf2#LINE/    150 ATGG 153

Transitions / transversions = 1.64 (23 / 14)
Gap_init rate = 0.03 (4 / 152), avg. gap size = 3.50 (14 / 4)  

 712 24.34 8.24 4.49  chr2_219623238_219626860.rev     1430  1696 (1927)    L1M4_orf2#LINE/L1      141   417 (491)  

  chr2_219623238_   1430 AAAATT-ATGTGGAAAT-CAAAG-AGTCACAATAACAAAGACAATCTTGA 1476
                               -  i       -   i - vi  v    i v  i          
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_219623238_   1477 A---GAAAAATCA-GCTGGAAGCCTTAT--TTACTAGATATCAAGGCTTA 1520
                          ---   i  iv - i    i v  i i--  v i -  v    ii    
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTA 239

  chr2_219623238_   1521 TTATACATCTGCTATAATTAAAACAATATGGTATTGGTCCAAGGATAGAC 1570
                         i  i v v  i vi    i  i   i i     i   ivi          
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_219623238_   1571 AAGTAGAGCA---GAA--GA---GAGAGTCTACGAATAGATCTCCAAACT 1612
                          vi    v  ---   --  ---       i vi    i i ivi v i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_219623238_   1613 TATGGGCACTTGATTTATGATAAAGGTATGTTCCAATGCC-CCCA----G 1657
                              v  v       vi  i  i   i----    vi  -ii  ---- 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTG----CCAAGACCATTCAATGGG 385

  chr2_219623238_   1658 GAAAGGATGATTTTCTTCCTTTTCAATAAATAGTGCTGG 1696
                              i  ii -------        i    i       
  L1M4_orf2#LINE/    386 GAAAGAATAGT-------CTTTTCAACAAATGGTGCTGG 417

Transitions / transversions = 2.25 (45 / 20)
Gap_init rate = 0.05 (14 / 277), avg. gap size = 2.43 (34 / 14)  

 425 28.98 11.93 0.57  chr2_219623238_219626860.rev     2019  2194 (1429)    L1M4_orf2#LINE/L1      448   643 (265)  

  chr2_219623238_   2019 AAATTGTCATCTCTAGCTCATTCCATACACAAAAATCCATTCTATATGGA 2068
                           i   v- i i   v    iv     i        iv i  v v     
  L1M4_orf2#LINE/    448 AAGTTGG-ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_219623238_   2069 TCATAGACCTAA------------------TAAAGCTTCTCGAGGATACC 2100
                            ?        ------------------    i  ii v  i  v v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_219623238_   2101 ATAGGAGAGTATTTTCATGAC-TTGGCGTAGGCAAAAATTTCTTAAACAG 2149
                              ? viv  i   i    -    vv       vii       i i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_219623238_   2150 ATCAT--AAATCACCAGCCATCTCAAAAACAATTGATAAACTAGGCT 2194
                         iv  i--   v   v   v ivvv i   v   v      i i i  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

Transitions / transversions = 1.04 (25 / 24)
Gap_init rate = 0.02 (4 / 196), avg. gap size = 5.50 (22 / 4)  

 240 20.69 7.76 0.86  chr2_219623238_219626860.rev     2488  2603 (1020)    L1M4_orf2#LINE/L1      603   726 (182)  

  chr2_219623238_   2488 AAAAGAA-AAGAAAAACAAAAAACAATTGATAAACTGGACTACATTAAAA 2536
                              v -   v  v v  i   v   v      i      v   i    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_219623238_   2537 T---GAACTGTT-TAC--CAAAAGCCACAATTTAGGA-GTAAAAACGA-A 2578
                          ---i    v  - i --    i v   v  iv  i -  i    -  - 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GACA 701

  chr2_219623238_   2579 ACCCAAAGAGTGGGAGAAGAAATTT 2603
                              v   i        i v    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTT 726

Transitions / transversions = 0.85 (11 / 13)
Gap_init rate = 0.06 (7 / 124), avg. gap size = 1.43 (10 / 7)  

 384 26.64 4.37 6.11  chr2_219623238_219626860.rev     2903  3131 (492)    L1M4_orf2#LINE/L1      684   908 (0)  

  chr2_219623238_   2903 CAAAAAAAAAAAAAAAAAA-----AGAGAGAGAGAAAGAA----AAAGAA 2943
                            i   ivi    i v  -----   iv i      iv ----v  ivv
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_219623238_   2944 ATATATACACTAAAGGACTGGC-TCCAGAATATGAAAAGAATTCCAGAAT 2992
                               viiv   i     v i-          iv      i  i---- 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT----T 779

  chr2_219623238_   2993 AGAAAAAGAATAGATCCATTAGAAAAAGACAGATAACTCAATTTTTAATA 3042
                          v  v---------  v  v v         i     i     ?vv  - 
  L1M4_orf2#LINE/    780 ACAAC---------TCAATAATAAAAAGACAAATAACCCAATTWAAAA-A 819

  chr2_219623238_   3043 TGGGTAAAGGGCTTTAACAAATGTTTTTTAAGTGGAGATGTATAAATGGC 3092
                             i     ii  v  i i ii   i iv iv i    i  i       
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_219623238_   3093 CATTGAGCTTTTGAAAAGGTACTAAACCTCATTAAACCT 3131
                           v i   viv       i i  v   v   ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (34 / 26)
Gap_init rate = 0.03 (6 / 225), avg. gap size = 4.00 (24 / 6)  


2882 22.93 5.88 1.27  chr2_219631174_219633418.rev      886  1753 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_219631174_    886 TGGAAAAATATTCCATGCTCATGGACTGGAAGAATCAATAGTGTTAAAAT 935
                               i    i     i       i       v i    v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_219631174_    936 GCTCATACTGCCCAAAGCAATTTGCAGATTCAATGCTATTCCTATCAAAC 985
                          viv     v      vii  i i         i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_219631174_    986 TACCAA--GCACATTTTCACAGAATTAGAAAAAAAAATATTCTAAAATTC 1033
                          v   i--  - v    ii     v v  v  ivvi  --i         
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGAT--CCTAAAATTC 147

  chr2_219631174_   1034 ATATGGAACCAAAAAGAGACCA-AATAGCCAACACAATCCTAAGCAAAAA 1082
                                 viiv  i iiv   -         v      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_219631174_   1083 GAACAAAGCTGAAGGCATCATACTACCTGGCTTCTAACTATACCATAAGG 1132
                                 i  i   vv   i   v  iiii   v  viv   i i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_219631174_   1133 TTACAGTAACCAAAATAGCATGGTA-----ACAAAAACAGACACACAGAC 1177
                         i        i   i i  ii     ----- i  ii i     i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_219631174_   1178 CAATGGAACAGGCTTAAGAACCCAGAAATAAAGCCACACACCTAT----A 1223
                                 i  iv  i   ii           v   i   ii   ---- 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_219631174_   1224 ATTGTCTATCTTCAACAAAGTCAACAAAAGCA----ATGGGGAAAG--TA 1267
                             ---  i   i    i viiv   i v  ----          --  
  L1M4_orf2#LINE/    348 ATTG---ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_219631174_   1268 CTCCCT------AGT--TGCTGGGATAACTGGCTAGCCAT--------GA 1301
                         v  ii ------ i --        i      v  ?   i--------  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_219631174_   1302 TTGAAACTGGATCCCTTCCTTTCACTATATACAAACATCAACTCAAGATG 1351
                         v    ii    i    v   iv   i         v  i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_219631174_   1352 GATTAAAGACTTAAATGTAAAACCTAAAACTATAAAAACTCT-AGAAGAA 1400
                            i ?    i         i v              -    -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chr2_219631174_   1401 AACATAGG---AAATACATTCTGGACATAGGCCCCGGAAAAGATTTTAT- 1446
                                 ---    - -   vv   v v  viiv  v  v i   iv -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_219631174_   1447 GAGAAGACACCAAAA--ACAATTGTAACAACATCAAAAATTGATAAATGG 1494
                           v v          --    -- i     v vv      v       v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_219631174_   1495 GAACTAATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTATCAACAG 1544
                           vi v  i   v v  i i   i   i vv    i  v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_219631174_   1545 AGTAAACAGATAACCTAGAGAATGGGAGAAA-TATTTGCCAACTATACAT 1593
                            i  v   i    i v             -       v  ii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_219631174_   1594 CC-ACAAAAGTATAATATCCAGAATCTATAAGGAGCTT----AAATCAAT 1638
                          i- i  ii vv vi          v     i  i  i----  v     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_219631174_   1639 AAGCAAAA-ACAAACAACCCAATT-AAAAATGGGCAAAGGACATGAACAG 1686
                           vv    -     i         -                iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_219631174_   1687 ACGCTTCTTAAAAGAAGACATATATGTGG--AAAAACCATATGAAAAAAT 1734
                           ii    iv        i   i vi   --  v  v  i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_219631174_   1735 GTTCAACATCATTAATCAC 1753
                          i         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (120 / 77)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.38 (62 / 26)  


 340 30.08 14.78 3.43  chr2_219635000_219637185      483   861 (1325)    L1M4_orf2#LINE/L1      260   681 (227)  

  chr2_219635000_    483 AAACAGTTCTGTACTGAT-------TAGATAAATAGACAAGTCTAAGAGA 525
                          i     viv      ii-------    i v     iv i vv  v   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_219635000_    526 A--AAGAGCTCAGAAATAGACC-ACACAAATGTGGAAAATGTATTCATGA 572
                          --i    ii        i   - i   vv i   vv   vv   ivi  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr2_219635000_    573 GAGAGGTGGCACTGAAAAT-CAGTGGGAAAAAG---GGCTAATCCATAAA 618
                         v ii    v  v-  vv  -  i    i   ii--- v  vv  v i   
  L1M4_orf2#LINE/    360 CAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_219635000_    619 TGGTGCTGGGAAAAGAGGCTTTCCAT-TGTTTAAGAA-GAAAAAAAATCC 666
                                    v  vv  v v?   i-  ivv     -   ivvii i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr2_219635000_    667 CTAATTCACACC-CAAATAAAAAC--AC-----ATAGCTTCAATAAAC-- 706
                            vi       -i v i     i--  -----  i v i-- ? i  --
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATC--AWAGACCT 506

  chr2_219635000_    707 AAATGTAAGCCTTAAAACTTTTAAAAACCTTTTAAAGTTCTAGGTTTAGG 756
                                  vvi       v --     ii  vi   v--- iiiv    
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTAT--AAAACTCTTAGAAGA---AAACATAGG 551

  chr2_219635000_    757 AG--AATATT---GATTTCAAATGAGGGAAGGACTTCTAAAATTAGATAT 801
                         ? --   v  ---  ii iiii v   v  v ii    -----       
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT-----TAGATAT 596

  chr2_219635000_    802 G------------CAAACCTTAAAGGAAAAGATACATAA---------CA 830
                          ------------   i vvi   i     i   v    ---------  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_219635000_    831 C----ATAAAAAACTTCCACTCATCAAAAGACACT 861
                         i----  v        iiiiv v     i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

Transitions / transversions = 1.18 (60 / 51)
Gap_init rate = 0.05 (21 / 422), avg. gap size = 3.29 (69 / 21)  


 283 32.62 12.30 1.07  chr2_220005062_220007630.rev      452   638 (1931)    L1M4_orf2#LINE/L1       98   305 (603)  

  chr2_220005062_    452 AAATCATATCTACCTGCCTTA-AGAAAACAAAATAACAGAACCT----TT 496
                              vi v  i   vii  i-     vii v - i v  v   ----  
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATT 146

  chr2_220005062_    497 CAAAATAAAAATGTGAAAGAT---GAATAA--AAGATGTTTTTGAAAA-G 540
                           v - ii     ii ii  i---     i--  i iiv i       - 
  L1M4_orf2#LINE/    147 CATA-TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_220005062_    541 A----------TGGATGGTTTGCTTTACCTGATATCAAGACTTAGTATGA 580
                          ----------    v ii ii vi v  ii  v    i     v  ii 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_220005062_    581 AGCCATAGTATTTAAGAAAGTGTGCTATTGATGTAAAGACAGTCAGGTGG 630
                            i i    v i    v      v  i  iii   i  i  v  vi i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_220005062_    631 ATC--TAGAA 638
                            -- i   
  L1M4_orf2#LINE/    296 ATCAATGGAA 305

Transitions / transversions = 2.21 (42 / 19)
Gap_init rate = 0.04 (9 / 208), avg. gap size = 2.78 (25 / 9)  

 299 31.20 6.80 4.00  chr2_220005062_220007630.rev     1283  1532 (1037)    L1M4_orf2#LINE/L1      403   659 (249)  

  chr2_220005062_   1283 AAAAAAGAGTACAGAAACAATTAGGTATCTT--TGTAGAAGAAAAACTCA 1330
                           v   vi  i v ii    i i i  ? iv--  i i     vi --- 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA---A 449

  chr2_220005062_   1331 CCTTTACCCGTAGCTTACAGCATACACAAAAATGGAATCTAA-TGGATTA 1379
                         vi vv    v  v  i   v    i        vi v  v  -     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_220005062_   1380 TAGACC-------AAGTATTCAA-CAATGAAGAATTTAGAAGATAGTGTA 1421
                         ?     -------   vii v  - v  i  ivvi        v iii  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_220005062_   1422 AGAATAA--CCTCATGACCTCAAAATTAAAGGTCGTGAAGTTTTCTTAAA 1469
                         i ?i   -- i  i      iiii-   --  ivi  i---       i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGG-TTA--GGCAATGG---TTTCTTAGA 593

  chr2_220005062_   1470 GAGGGAAC-AAAGGTGCTAGAAAATTAAGGAAAAGATAG-TACATTTGAC 1517
                         v v iv  -   i ii v  v  -iv  i     i    -  v   v   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAA-CAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_220005062_   1518 C-CATTAAA-TTAAGAA 1532
                         i-   i   -    i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA 659

Transitions / transversions = 1.59 (46 / 29)
Gap_init rate = 0.05 (14 / 257), avg. gap size = 1.93 (27 / 14)  

 658 23.08 5.98 3.85  chr2_220005062_220007630.rev     1845  2078 (491)    L1M4_orf2#LINE/L1      670   908 (0)  

  chr2_220005062_   1845 TCAAAAGATACCATTAGGAGAGTGAAAAAGGAAACCACAGA-TTGGAGAA 1893
                              i  i  i  i i  i        iiv  v       - v      
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_220005062_   1894 TATATTTCCTACTTATATGCCT-ACAAAAAGCTGGTATCCAGAATATATA 1942
                         v      v v v i    ii  - i  iiii  v                
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_220005062_   1943 AACAA-TCCTGCAAATCAGTAA------GACAAATATTTTTTAAACCCAA 1985
                           v  -  i i   v   i   ------        --------      
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATA--------ACCCAA 811

  chr2_220005062_   1986 T-AAAAAATTGGCAAGACACTTGAACAGGTA---CTTTAAAACATGATCT 2031
                          -?      v     iiv i     i  ii ---  ii   iv -   v 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-GATAT 860

  chr2_220005062_   2032 TCAAATAATCTATAAACTCAT-AAAAGGTATTCAACATCGGCGGGGCA 2078
                         v     iii v    i v   -     i ii        i????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (36 / 17)
Gap_init rate = 0.04 (9 / 239), avg. gap size = 2.56 (23 / 9)  


3934 13.01 1.01 17.25  chr2_220102541_220104738      623  1706 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_220102541_    623 TGGAAAGACATCTCATGTTCATGAACTGGAACACTTAATATTGTTAAGAA 672
                                 i   i          i i     v                 -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr2_220102541_    673 TACCATTACTACTCAAAGTGATCTATAGATTCAGTATAATGCCTATCAAA 722
                          iv  v    v i    v       i       iiii   v         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_220102541_    723 ATCTCA-CCAACATTTTTGCAGAAATAGAAAAATCCATCCTAAAATTCAT 771
                            i  - iiv v             v  v  iiiv              
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_220102541_    772 AAGGAATTTCAAGAGACCTCAAATAGCCACAA-ATTTTTGAAAAAGAA-- 818
                          v    v v    i    ivi        v  - v i           --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_220102541_    819 -CAAAGATGGAGAACTCACATTTTCTGAGCTCAAAATTTACTACAAAGGT 867
                         -     v     i       i  i ii vi      i           v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_220102541_    868 ACAGTTATCAAAACAGTGTGTGGTACCAGCATAAAGACAGACATACAGAC 917
                              v     i        --    ii      i  i       i   i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTG--GTACTGGCATAAGGATAGACATATAGAT 297

  chr2_220102541_    918 CAACAGAATATAATAGAGAGCCCAGAAATAAACCCTCACAC--GTGGTTA 965
                            ii     v   v     i              vi   i--i    i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_220102541_    966 AATTATTTTCATCCCAGGTGCCCAGACCATTCAGTGGGGGAAAGGGTAGT 1015
                          v v      iv vvi      v          i     -    ii    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGT 396

  chr2_220102541_   1016 CTTTTCAACAAATGGTGCTGAGA-AACTGGATATCCACATGCAAAAAAAC 1064
                                             i  -         ?            i  i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_220102541_   1065 AAAGCTGGACTCTTACCTTATACCATACATAGAAATTAACTCAAAATGGA 1114
                         i   i     i i     i i      i i i                  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_220102541_   1115 TAAAACAGCCAGGCCCACATTGGCTCATGCCTGTAATTTTGGCACTTTGG 1164
                          -------------------------------------------------
  L1M4_orf2#LINE/    497 T------------------------------------------------- 497

  chr2_220102541_   1165 GAGACCGAGGTGGAAGGATCGCTTGATCCCAGGAGTTTGAGGTTGCAGTG 1214
                         --------------------------------------------------
  L1M4_orf2#LINE/    498 -------------------------------------------------- 497

  chr2_220102541_   1215 AGCTATGATGGCACCACTGTAATCCAGCCTGGGTAACAGAGCAAGACCCT 1264
                         ------------------------------------  ?  ---------
  L1M4_orf2#LINE/    498 ------------------------------------CAWAG--------- 502

  chr2_220102541_   1265 GTTTCAACAACAACAACAACAACAAACAGACATGATACCTAAACATAAGA 1314
                         ------------------------------------       ii     
  L1M4_orf2#LINE/    503 ------------------------------------ACCTAAATGTAAGA 516

  chr2_220102541_   1315 GCTAAAA-TATAAAATTCTTAGAAGAAAACAAAGAGGAAAATCTTCATGA 1363
                                -       i               v  i? v        i   
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr2_220102541_   1364 CATTGGATTTGGCGATGATTTATTGAATATGACACCAAAAGCATAGGCAA 1413
                          v    i  v   i   i   v  ii                 i i    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_220102541_   1414 TAAAATAAAAAATAGATAAATAGGACTTGATCACAATTACAAACTTTTGT 1463
                         i    v               v      v    v     v          
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_220102541_   1464 TCATCAAAGGACATTATCAACAGAGTGAAAAGGCAAACCACAGAATGGGA 1513
                         v v          i      v i         i   v             
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_220102541_   1514 GAAAATATTTGCAAATCATATATCTGATAAGGGATTAATATCCAGAGTAT 1563
                                                           i vi        i   
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_220102541_   1564 ATAAAGAACTCCTGCAACTCAACAACAAAAAATCCCCAAACAACCCAATT 1613
                                    i i        i  i     i---v    i         
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAG---ACAAATAACCCAATT 813

  chr2_220102541_   1614 CAAAAATGGGCAAAGGATTTGAA--GACATTTTGCCAAAGAAGATATACA 1661
                         ?                      --       iv                
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_220102541_   1662 GATTACCAGTAAGCGCATGAAAAGATGCTCAACATCACTGATCAT 1706
                         i  vi   i     i                      ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (89 / 48)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 15.23 (198 / 13)  


2816 26.30 0.64 1.65  chr2_220342866_220347204     2604  3390 (949)    L1M4_orf2#LINE/L1        1   779 (129)  

  chr2_220342866_   2604 TGGAGAGACATACTACGTTCCTGGATTGGAAGATTCAGCATTGTAAAGTT 2653
                             i   i  v i i    v            i i ii     v   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_220342866_   2654 GTCAATTTGTCCTAAACTAATATATATAGGTTTAATGCAATTTTTATTGA 2703
                          v    vivi  i   i i  v  i -- i  i  i     iii   ii 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA--GATTCAACGCAATCCCTATCAA 98

  chr2_220342866_   2704 AATCTAAGCAAAGCTTTTTTGTAGATATAGACAAAATTATTTTAGAATTT 2753
                             iv   viv-        i   v  v     iv v  ii  i    i
  L1M4_orf2#LINE/     99 AATCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_220342866_   2754 ATATGGAAAGGCATAGAAACCAGAATAGCTAAAATAATTTTGTAAAAGGA 2803
                                  v   vi i v          i    i   i   v     i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_220342866_   2804 GAATAAAGTGGGATGAATCAGTTTACCTGATTTTAAGACTTATTATATAG 2853
                            i     v   v  v   vvi v  ii    i  i     i  i v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_220342866_   2854 TTACAGTAATCAAGACTGTGTGGTATTGGTGGAGGGATAGTTGCAAAGAC 2903
                         i               v        i   iiv i      viii v   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_220342866_   2904 TGATAGAACAGAATTTAAAAACCTAGAAATAGACCAACATAAATATACCC 2953
                         ii  i   i      -i i ii i       i   v i i vv   ivi 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_220342866_   2954 AACCAATTTTTGACAAAAGGTGCAAAAGTAATTCATTGAAGAAAAAATAC 3003
                           iii     i     i-     v  iiiv     v  ii    i    v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAG-GGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_220342866_   3004 CCTTTTCAACAAATGGTGATGGAGCAAAAGGACATCCATTGGCAAACACA 3053
                         i                 v   ii   vv   i ?   i------ ii  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC------ATGCA 439

  chr2_220342866_   3054 AACAAACAAAACTCTGATATAAATCTCATACCTTATGCAATAATTAACTC 3103
                           vi  ii  ii v-  ivivv i    i   v   i   v         
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTG-GACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_220342866_   3104 AAAATAGATCATAGAATTAAATGTAAAACTTGAAACTATAAACATTTTTA 3153
                              i     ?   vi         i vi i          - i i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTA 537

  chr2_220342866_   3154 GAAGAAAACA--GGAGAACATCTTTG-GGTTTAGGGTTAGGCAAAGAGTT 3200
                                   --  ? v v     i - iii v           v iv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_220342866_   3201 CTTTGACTTGACAACAAAAGCATAA--AAGGAAAGAAAAAATTGATTAAA 3248
                            v  iv     v        i  --  vi           v   v  v
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_220342866_   3249 TAGACTTCACTAAAATTTTAAAATTTTATGCTGCAAAAGACCTTGTTAAG 3298
                          i       ii      vv   v    i    v    i   vi i i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_220342866_   3299 AGGATGAAAAAACAAAGTACAGAGTGGGAGAAAATATTTGCAAACCACAT 3348
                          iii      i    vvi     i                    i  i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr2_220342866_   3349 ATCTAATAAAGGACTAGTGTCTTGACTATATAAAGAATTCCT 3390
                             i    i     v  i  iv  v           i  i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

Transitions / transversions = 1.83 (132 / 72)
Gap_init rate = 0.01 (10 / 779), avg. gap size = 1.80 (18 / 10)  

 497 24.29 0.71 0.71  chr2_220342866_220347204     3713  3852 (487)    L1M4_orf2#LINE/L1      769   908 (0)  

  chr2_220342866_   3713 AAAAAATTCCT-CAATCTCAACATCAAAAAACCAAACCATCCACTTAAAA 3761
                            i  i  i -   -     i vi     iv    iv i   v  ?   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAA-CTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr2_220342866_   3762 AATGGGCAAAAGACATGAAGAAAAATTTTACTGAAGAGAATATGCAGATG 3811
                                   i  iv    v i v    iv ii    ii    i  i   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr2_220342866_   3812 GCAAATAAGCACATGAGAAGGTGTTCAATCTTATTAGCTAT 3852
                           v             i   i  i    iv i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.30 (23 / 10)
Gap_init rate = 0.01 (2 / 140), avg. gap size = 1.00 (2 / 2)  


2910 23.58 9.36 1.78  chr2_220496225_220501111.rev     3552  4395 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_220496225_   3552 TGGAAAGGTATTCTATGTTTGTAGATTGGAAGAATCAATATTGTCAAAAA 3601
                                i   i i     ii i          v i        i  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_220496225_   3602 GTCCATACTACCCAAAGCAATCTACAGAT----------------CAAAA 3635
                          v v     v      vii          ----------------     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_220496225_   3636 TTTCTGCGGTGTTTTGCACAGAAACAGA-AAACCAATCATGAAGTTCATT 3684
                          ii v  v iv    vii      iv  -  i ii   v i  i     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_220496225_   3685 TGGAACTAACAAAAGACACTTAATAGCTAAAGCAATTT------------ 3722
                              v i-   ii   v vv      i   i    i ------------
  L1M4_orf2#LINE/    151 TGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_220496225_   3723 ---------GAGGCATCATACTTCCTTATTTTAAATTATATTACAAATCT 3763
                         ---------    vv   i      iv    i   viv  i      v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_220496225_   3764 ATAGTAATCAAAACAATATGATACTAACATAA--------------ACCA 3799
                          i         i   i i  i    ii     -------------- i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_220496225_   3800 ATGGGA--------------CAGAAATAAACCCATTCACACCCAGTGTTC 3835
                             i --------------               --   iii -  v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT--ACATTTA-TGGTC 346

  chr2_220496225_   3836 ---TAATCTTTGACAAAGGTACCATGAATACACAACAGGGAAAGGATAGT 3882
                         --- i  i  i     i   i   v  vi iv   ii       i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_220496225_   3883 CTCTTCAATAAATAGTGTTGGGA-AACTGAATATTCACATGCCAAAAAAA 3931
                           i     i    i   i     -     i   ?i       --    i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC--AAAAGA 444

  chr2_220496225_   3932 GGGAAATTGGGTCCTTAT-----ACTATACACAAAAATCAACTTGAAATG 3976
                         iv   i    ii  i  i-----  i   i        i    ii     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_220496225_   3977 AATTAAAGATTTAAACATAATACCTAAAACTACAAAACTTCTAGAAGAAA 4026
                         i  i ?   ii    ii   v v         i      ii         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_220496225_   4027 ACAAAAGTGAAAAAAGCTTCATGATATTGGTCTTGGCAATGATATTTTTG 4076
                            v i ? v   --v    i   iv    vi v       i -  i  i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTA 591

  chr2_220496225_   4077 GATATGACACCAAAAGTACAAACAACAAAAGCAAAAATAAACACAGGAGA 4126
                                         i    i         v       i i v vvi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_220496225_   4127 CTACATCAAACTACAATATTTCTGCACAGCAAAGGAAACCATCAACCAAA 4176
                           v       v vv  v i  i  ii vv       v  i     vv  i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_220496225_   4177 TGAGAAG-CACCTCATGAAATGGGAGAAAATACTTGCAGACTGTATATCC 4225
                            i   -  v i  iii              i     i iii      i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_220496225_   4226 AATAAGGGCTTAATATCCAAAATACATAAGGAACTC--ACAACTCAAGAG 4273
                         i       vi vi      i    i    i      --         v i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_220496225_   4274 CAAAAATAAGTAAATAAACAAACCAATTTTTAAAAGGGCAAAGGATCCAA 4323
                         i     ------i i   i  v      ?vv   v           iii 
  L1M4_orf2#LINE/    792 TAAAAA------GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr2_220496225_   4324 ATGGACATTTTTC-AAAGAGGATATACAAACAGCCAACAAATATATGAAA 4372
                           i       i  -     i          ii     i  ii i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_220496225_   4373 AAATGTTCGACATCACCACTCAT 4395
                          i   i  i      ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.36 (137 / 58)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 5.22 (94 / 18)  


3230 27.09 0.44 0.44  chr2_220503985_220510385.rev     5002  5909 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_220503985_   5002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5051
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_220503985_   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_220503985_   5102 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_220503985_   5150 TATGGAACCAAAAAAGAGCCCGCCTTGCCAAGTCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  v vv v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_220503985_   5200 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5249
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_220503985_   5250 TACAGTAACCAAAACAGCATGGTACCGGTACCAAAACAGAGATATAGACC 5299
                                 i   i    ii      i  i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_220503985_   5300 AATGGAACAGAAC--AGAGCCCTCAGAATTAATGCCACATATCTACAACT 5347
                                i    i--    i  --    v   vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_220503985_   5348 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5397
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_220503985_   5398 CTATTTAAGAACTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5447
                           v  i  v  v           v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_220503985_   5448 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5497
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_220503985_   5498 TTAAAGACTTAAATGTGAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5547
                          i ?    i       i   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_220503985_   5548 CTAGGCATTACCATTCAGGACATAGGCATCGGCAAGGACTTCATGTCTAA 5597
                         v    ?i v viv   iv   v v  vv v     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_220503985_   5598 AACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTAA 5647
                         i            vvi   i      vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_220503985_   5648 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5697
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_220503985_   5698 AGGCAACCTACAAAATGGGAGAAAAGTTTTGCAATCTACTCATCTGACAA 5747
                           i     i   i            vv       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_220503985_   5748 AGGGCTAATATCCAGAATCTACAATGAACACAAACAAATTTACAAGAAAA 5797
                         i  i  vi          v  i  v    v vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_220503985_   5798 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGTTATGAACAGACACTTC 5847
                          i     i     v  i?    i     i    v v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_220503985_   5848 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5897
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_220503985_   5898 ATCACTGGCCAT 5909
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (140 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1806 18.52 1.11 22.27  chr2_220524855_220526828.rev      495  1482 (492)    L1M4_orf2#LINE/L1      130   908 (0)  

  chr2_220524855_    495 AAAATGATCCCAAAATTTGTGTGGGACCACAAACATTCGTGTGAATCTCA 544
                           iv      i      ii i   i vii   i--------- i i ivi
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAG---------GGACCCAG 170

  chr2_220524855_    545 AATAGCCAAAGCAATATTGAGCCAAAAGAACAAAGCTGAAGACATCATAC 594
                                   i    v    ivv i          i  i  ivv   i  
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_220524855_    595 AACCTGATTTCAATATATACTGTAAAGCTACAGTAATCAAAACAGGATGG 644
                         vv  ii       v iv    ii                 i    vi   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr2_220524855_    645 TACTAGCATGAAAGTGGAAATATAGATCAATGGAGCAGAATAGTGAGCCC 694
                             i    i iii i  v               ii     v v   i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr2_220524855_    695 AGAAATAAATCCACACTTTTACAGTCAACTGATCTTCTACAAAGTTTCCA 744
                                  i   i  v    ii     i    i   v    i v v   
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_220524855_    745 GGAACACACAATGGGAAAA-AACAGACTCTTCAATAAATAATATTGAAAA 793
                         i  v  iv       i   -  i  v  i     i    ii ii  ii v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_220524855_    794 AAATT--TATCCACATGCAGAAAAATAAAACCGAACCCTCACTTTTTTTT 841
                           v v--  ?         i  i   i  iii i    ii  --------
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC-------- 462

  chr2_220524855_    842 TTGAAACAGAGTTTCACTCTGTCACTCAGGCCAAAGTACAGTGTCACAAT 891
                         ------------------------    vi   v -    ----- v   
  L1M4_orf2#LINE/    463 ------------------------CTCACACCATA-TACA-----AAAAT 482

  chr2_220524855_    892 CATAGCTCACTGTAACCTCTAACTCCTGGGCTTAAGCAATTCTTCTGCCT 941
                         --  i    ----  v--- iiv  v?i i i   i---------  -- 
  L1M4_orf2#LINE/    483 --TAACTCA----AAA---TGGATCAWAGACCTAAA---------TG--T 512

  chr2_220524855_    942 CAGCTTCCCACGTAGCTGGAACTACAGGCATGCACCATCACACCTGGCTA 991
                         v  ----------    ii     --------------------------
  L1M4_orf2#LINE/    513 AAG----------AGCTAAAACTA-------------------------- 526

  chr2_220524855_    992 TTTTTTAAAACATTTTTGAAGAGGCAGGGTATTGCTATGTTGCCCAGGCT 1041
                         -----      - i  v     ----------------------------
  L1M4_orf2#LINE/    527 -----TAAAAC-TCTTAGAAGA---------------------------- 542

  chr2_220524855_   1042 GATCTCAAACTCCTGGCGTCAGGCAATCCTCCTGCCTTGGCCTCCCAAAG 1091
                         ------    ----------------------------------------
  L1M4_orf2#LINE/    543 ------AAAC---------------------------------------- 546

  chr2_220524855_   1092 TGTTGGAATTATAGGCCTGAGCCACCATTCCTGGCCAAGAAAAAGCCACT 1141
                         ----------     ?v i ii ----   v  i  --------------
  L1M4_orf2#LINE/    547 ----------ATAGGNGTAAATC----TTCGTGACC-------------- 568

  chr2_220524855_   1142 TGACATTGATCTAGGAAATGATTTTTTTGGATATGAC-TCAAAAGCTCGG 1190
                         -----   ivi    v    i   i  -i        -i       v ii
  L1M4_orf2#LINE/    569 -----TTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAA 612

  chr2_220524855_   1191 GCAGTAAAAGCAAAAACAAACA--TGGGGTTGCGTCAAACT--AAAATGT 1236
                            ii     v     i i i -- v  ii v i     v --    iv 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_220524855_   1237 TTCTGC---ACAGCAAACAATCAACACAGTGAAGAGACAATCTGCAGAAT 1283
                           v   --- v  v v  v     v v      i      i ii      
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_220524855_   1284 GGGAGAAGATATTTGCAAATCATACATCTGATAAAGGGTTAATATCCAAA 1333
                                i                i         i  ii vi      i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_220524855_   1334 ATATATTTTAAAAACTCAGACAATTCAATAGGAAGAAAACAAATAACCCA 1383
                               v--  i     vv    i      iv  i  i            
  L1M4_orf2#LINE/    763 ATATATA--AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr2_220524855_   1384 ATTTAAAAATGGGCAAAAGGACCTGCATAGACATTTCTCAAAAGATGACA 1433
                            ?             -   ii  v             v     v  i 
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAA-GGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_220524855_   1434 TACAAATGGCCAATGGGCATATGAAAATATGCTCAACATTATCAATCAT 1482
                                       ii   i       v           i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (119 / 60)
Gap_init rate = 0.03 (25 / 779), avg. gap size = 9.24 (231 / 25)  


3168 27.31 0.55 0.55  chr2_220621545_220627817     4874  5781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_220621545_   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4923
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_220621545_   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4973
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_220621545_   4974 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5021
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_220621545_   5022 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5071
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_220621545_   5072 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5121
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_220621545_   5122 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5171
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_220621545_   5172 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5219
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_220621545_   5220 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5269
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_220621545_   5270 CTACTTAAGAACTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5319
                           vi i  v  v           v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_220621545_   5320 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5369
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_220621545_   5370 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 5418
                          i ?   ii    i  v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr2_220621545_   5419 CCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCA 5468
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_220621545_   5469 AAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGAATCTA 5518
                         vi            vvi     v    vv     v  i    v i ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_220621545_   5519 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5568
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_220621545_   5569 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5618
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_220621545_   5619 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5668
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_220621545_   5669 AAAACAAACAACCCCATCAAAAAGTGGGTGAGGGACATGAACAGACACTT 5718
                           i     i     v  i?    i    ii i   iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_220621545_   5719 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5768
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_220621545_   5769 CATCACTGGCCAT 5781
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2951 25.27 2.56 1.34  chr2_220830019_220833889.rev     2177  2995 (876)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr2_220830019_   2177 TGGAAAGGTATCT-GTGTTCATGAACTGGAAGAACTAGTATTATTAAAAT 2225
                                i    i-i        i i       vi  i    i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_220830019_   2226 GTTCATACGACCCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 2275
                          viv    vv      vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_220830019_   2276 TTTCAA-TGTCATTCTTCAAAGAAATAGAAAAAGCAATTCTGAAATTCAT 2324
                          ii  i-  i -  i  iiv      v  v  ivii  i  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_220830019_   2325 ATGGACCCACAAAACACCCCTAATAGCTGAAGCAACCTGGACTAA----A 2370
                              vvii   iiv    vv      ii  i   i  v  vv  ---- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_220830019_   2371 ACAAAGCTAGAGGTATTACACTACCAGATTTCAAAATACATTACAAAGAT 2420
                               i i    vv i     v  vi         ivi i       v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_220830019_   2421 ATGGTAATCAAAACAACATG-CAATGGTACAAAAACAGACACACTGACCA 2469
                          ii        i   iii  -i v   i i  ii i     i iv  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_220830019_   2470 GTGGAACAGGATATAGAGCCCAGAAAAAAAAAATAAA---ACACATCCCT 2516
                         i     i  i  vv    i       -------    --- i    iiv 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAA-------TAAACCCATACATTTAT 342

  chr2_220830019_   2517 AGACAATTGATTT--GACAAGGGTGCCAAGATCACACAATGGGGAAAGGA 2564
                         i v          --                i  iv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_220830019_   2565 CTGCGTCTTTT-AATAAATGGTACTGAGGAAACTGGATATTGACATATAG 2613
                         - i-       -  i       i   i iv         ?iv    ii i
  L1M4_orf2#LINE/    393 -TA-GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_220830019_   2614 AGTAACAAAAATGAACTCTTATCTCGCCTTTTTTACATGAATCAACTCAA 2663
                          iv  ii  iv  i  i i  i   i viiv v    vi   i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_220830019_   2664 AATAAATTAAACACTTAAATATTAAGACCTGAAACTATAAAACTACTAGA 2713
                            ii  i ? v  i     i -    v  i             vi    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_220830019_   2714 AGAAAACATAAGGGAAAAGTTTTATGACATTGGTCTGGACAATGATTTCT 2763
                                   i ? v   vi  ii    v    vi i i     i     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_220830019_   2764 GGAGTACAACCCCAAAAGCACAGGCAATAAAAGCAAAAATAGACAAATGG 2813
                         viii  ii  v           i    i     v         i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_220830019_   2814 GATTGCATCAAACTAAAAATCTTCTGCACTGCAAAGGAAACAATAAATAG 2863
                           i v       v v    v   i  ii  v       v  v  v  v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_220830019_   2864 AATGAAGAGACAACCCACTGACTG--AGAAAATATTTGCAAATTATACAT 2911
                          i    i           v  v  --                 i   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_220830019_   2912 T------GGTTCTAATATCCACAATAAACAAGGAACCCAAACTATTTAGT 2955
                         i------  vv  vi      v    v i  i    i vv  v i i i 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_220830019_   2956 AACAAGAAAACAAATTACTCAGTTAAAAAATGGGCAAAGG 2995
                           i  i  i      v  i  i  ?               
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.90 (133 / 70)
Gap_init rate = 0.02 (14 / 829), avg. gap size = 2.29 (32 / 14)  

 397 20.21 0.00 0.00  chr2_220830019_220833889.rev     3288  3381 (490)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr2_220830019_   3288 AAAATTGGGCAAAGGACTTGAACAGACATTTGTCAAAAGAAGACATATAA 3337
                             v           i     i        v  v        i   i  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_220830019_   3338 ATGGCCAACAGATAAATTTTTAAATGCTCAACATTTCTAATCAT 3381
                                 i iii v  vvvv i           iv????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


2597 14.73 6.09 0.39  chr2_220874643_220876638      501  1009 (987)    L1M4_orf2#LINE/L1      189   726 (182)  

  chr2_220874643_    501 GAAAATAGAAGAATAGAGTTGGAAGACTCAC----------TTCAGAACT 540
                              -       i i       i       ----------    i    
  L1M4_orf2#LINE/    189 GAAAA-AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_220874643_    541 TACTACAAAGCTACAGTAGTCAAGAC--TGTGTTACTGGCATAAAGATAG 588
                                           i       --    v           i     
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_220874643_    589 ACATACAGATCAATG-AATATAATTTATGGTCCAGGAATAAACTCTTTCA 637
                              i         -    v    v vi      i       i v v  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_220874643_    638 TTTATCATCAACTGATTTTCAACAATGGTGGCAAAGCAAATCAATGGGGA 687
                              vi    i        i    v    v   ii v v          
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_220874643_    688 AGGAATAGTCATCTCAACAAATGG-------ATAACTGGAAGTCTACATA 730
                          i        v i           ------- i       vi? i    i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_220874643_    731 TAAGAGAATGAAATTGGACCCCTTCCTAATATCACA-ACAAACATTAATT 779
                         i  i        i          v   v i i  i -     v     i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_220874643_    780 AAAAATGGATCACTGACCTAAATAGAAGAGCTAAGACTATAAAACTCTTA 829
                         v           ?v         iv         i               
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_220874643_    830 GTGTAAAGAATAGGAGTAAGTCTTAATAATCTTGGGTTAGGCAATTATTT 879
                          viv   iv     ?    i    vi i i               vi   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_220874643_    880 CTTAGATATGACACAAAAAGAGCAAGTTAAAAAAAGAAAAAATA-ATA-- 926
                                       v     vi    i-  v             -   --
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAA 636

  chr2_220874643_    927 -----CT--ATCAAAATTAAAAACTTTTATACTTCAAATGTCACTATCAA 969
                         -----  --                   i i       v v         
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_220874643_    970 GAAAGTGAAAAGACAACCTGCAGAATGGGAGAAAATATTT 1009
                                           ii                    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

Transitions / transversions = 1.48 (43 / 29)
Gap_init rate = 0.02 (10 / 538), avg. gap size = 3.30 (33 / 10)  

 887 15.22 5.43 0.00  chr2_220874643_220876638     1321  1504 (492)    L1M4_orf2#LINE/L1      715   908 (0)  

  chr2_220874643_   1321 GAGAACATATTTTCAAATTATACATCTGATAGGAAATGAGCATCTAGAAT 1370
                              v      v     i   i        i ii ivv i   i     
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_220874643_   1371 ATAGAAA-AACTCTTACAACTCAA------AAATATGAACAACCCAATTA 1413
                            v   -                ------   v ii  i         ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_220874643_   1414 TAAAATGGGCAAGGGATTTGAACAGATATTTCTCCAAAGAAGCTATGCAA 1463
                         v           i         i   i               v   i   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_220874643_   1464 ATGACCAATAAGAACA---AAAGATGTTCCACATCATTAAAATT 1504
                            i        v   ---       i  v      ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.02 (3 / 194), avg. gap size = 3.33 (10 / 3)  


3051 27.39 0.55 0.66  chr2_221072693_221079076.rev     4984  5892 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_221072693_   4984 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCCTGAAAAT 5033
                              ii i  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_221072693_   5034 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5083
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_221072693_   5084 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5131
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_221072693_   5132 TATGGAACCAAAAAAGAGCCCGCCTTGCCAAGTCAATCCTAAGCCAAAAG 5181
                                viiv  ii  v  v vv v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_221072693_   5182 AACAAAGCTGGAGGCATCACGCTACCTGACCTCAAACTATACTACAAGTC 5231
                                i      vv    i  v  ii ii     viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_221072693_   5232 TACGGTAACCAAAACAGCATGGTACTGGTACCAAAACACAGATATAGACC 5281
                            i    i   i    ii         i iv ii i v v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_221072693_   5282 AATGGAACAGAAC--AGAGCCCTCGGAAATAATACCACACATCTACAACT 5329
                                i    i--    i  --i       vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_221072693_   5330 ATCTGATCTTTGACAAACCTGAAAAAAACAAGAAATGGGGAAAGGATTCC 5379
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_221072693_   5380 CTATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGCT 5429
                           v  i  i          i   v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_221072693_   5430 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGA 5479
                            ii    i    v   i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_221072693_   5480 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5529
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_221072693_   5530 CTAGGCA-ATACCATTCGGCACATAGGCATCGGCAAGGACTTCATGTCTA 5578
                         v    ?i- v i -    vv  v v  vv v     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_221072693_   5579 AAACACCAAAAGCAACAATAACAAAAGCCAAAATTGACAAATGGGATCTA 5628
                         vi            vv ii        vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_221072693_   5629 ATTAAACTAAAGAGATTCTGCACAACAGAAGAAACTACCATCAGAGCTAA 5678
                           i   v v  i iv  i  ii vv  i i  v    i  vv i  iv  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_221072693_   5679 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATGTACCCATCTGACA 5728
                         v  i     i                 v       vvi ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_221072693_   5729 AAGGGCTAATATCCAGAATCTACAAAGAACACAAACAAATTTACAAGAAA 5778
                          i  i  vi          v  i       v vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_221072693_   5779 AAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5828
                           i -    i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_221072693_   5829 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5878
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_221072693_   5879 TCATCACTGGCCAT 5892
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2789 28.89 1.44 0.78  chr2_221097023_221102387.rev     3974  4873 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_221097023_   3974 GAAAAA-ATTCCACACTCCTTGATAAGAAGAATAAATATGATTAAAATGG 4022
                             i -  i   iii  v v   vi     v v     vi    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_221097023_   4023 CCATACTGCCCAAAGTAGTTAACAGATTCAATGCTATTCCTATCAAACTA 4072
                          v     v      v ii iv          i  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_221097023_   4073 CCAAATACATTTTTCACA-AAATTAGAATGAATCTATTTTAAACATTATG 4121
                            iv i v     ii  -     i-- ii iiiv  ii    vv i  i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chr2_221097023_   4122 GGGGACCA-AAAAAAGCTAGACTAGTCAAGGCAATCCTAAAGGAAAAGAA 4170
                         v  i vii-  iii v i   v   i   ii     i i  ii i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_221097023_   4171 CAAAGCTGGAGGATTCACATTACCCAACTTCTAATTATACTGCAGGTCTA 4220
                              i       i     i v     i   v  viv    i  iiv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_221097023_   4221 CAGTAACCAAAACAGTGTGGTACTTGTACAAAAACAGACACATAGACCAA 4270
                               i   i             v i i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_221097023_   4271 TCAAACAGAATAGGGAGCCCAGAAGTAATGCCACACCCCTACAGCCATCT 4320
                          vi  i     v i   i      i   vv   i  vii  ii i  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_221097023_   4321 GATCTTCAGCAAAACTGACAAAAATAAGCAATGGGGAAAGGATTCCCCAT 4370
                            i   ii   iiv  v   i vi vv            i  vvi iv 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_221097023_   4371 TTAATAAATTGTGCTAGGATAAGGAGCTAGTCATATGCAGAAGATTGGAA 4420
                          i  i    v     i   i  vvi v  ?i  i     i    v  i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_221097023_   4421 CTAGACTACTACCTTACACCACATAAAAAAATCAACTCAAGATTGGTTAG 4470
                         i i   iv      i      i   v      i       i  v i i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_221097023_   4471 AGGCTTAAATATAAAACCTAAAACTATAAATAC-CTTGGAAAGTAACCTA 4519
                           i i     i   i v             -  -   i   iiv   v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATA 549

  chr2_221097023_   4520 GG---AAATACTATTTTG-GACACAGGACTGGGCAAATATTTTATGACCA 4565
                           ---    ----i  i -   viv  ii i     vvi   iv iivi 
  L1M4_orf2#LINE/    550 GGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_221097023_   4566 AGAAGCCAAAAGCAATTGCAACAAAAACAAAAATTGACAAATGAGACCTA 4615
                         v  vi         vvv         iv      v  i    vi   i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_221097023_   4616 ATTAAACTAAAGAGCTTCTGCAGAGCAAAATAAACTATCAACAGAGTAAA 4665
                           i   v v  i i   i  iivvv    iv v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_221097023_   4666 CAGACAACCTACAGAATAGGAGAAAATATTTGCAAACTCTGCATGTGGCA 4715
                         v        i       i                  iiv ii  v  ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_221097023_   4716 AAGATCTAATATACATAATCTATAAGGAAC----GGAAATTTACAAGCAA 4761
                          i iv  vi   v  v   v     i    ----iv  v iv i  vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_221097023_   4762 AAAACAAACAACTCCATTATAAAGTGGGCAAAGGACCTTAACAGACACTT 4811
                           i     i   i v   ?v   i           ii v  i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_221097023_   4812 TTCAAAAGAAGATATACATGCAGCCAACAAGCATATAAAAAG-TGCTCAA 4860
                         i  v              viii     i     i  i     -       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_221097023_   4861 CACCACTAATGAT 4873
                           i  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (163 / 94)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.82 (20 / 11)  


 352 28.38 15.54 3.83  chr2_221264762_221266645.rev      356   799 (1085)    L1M4_orf2#LINE/L1      119   614 (294)  

  chr2_221264762_    356 CAAAACTTGGCAGGCTGTTCCAAAAACTAAGAGTGAAAAAGACAGGG-CT 404
                           i  v   i  i    v   v    i v v -  i   v vv    - i
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATA-TGGAAATGCAAGGGACC 167

  chr2_221264762_    405 AAGACTAGCCAAACCAATTTCAAAGAACAATA-CAAAG--GGAAAA-TCA 450
                         v   v        v    i ii  i  v  v -     --   ii -   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_221264762_    451 GTGTAGTATAACATATCAAAA---ATCACAAGATT---GTAAACAA---- 490
                         ---i v vivvv  v      --- ii    iii ---    v   ----
  L1M4_orf2#LINE/    218 ---CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_221264762_    491 ---------TGGGATAAAGA----------GACCAACAGCAAAGAA--GA 519
                         ---------   v    i  ----------  i   ii v v    --  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_221264762_    520 GAGATCAGACCCAGACCCACACACATATGGTGACTCCATAAATGACACAG 569
                            vi    vvi i     i   iv      v v iv  vvvi    vi 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr2_221264762_    570 TTGC-------ATTCTGCATAATGAGAAGAGTAGCTAGTCA---CAACTA 609
                         v   -------    -----    i i i  v --     v---    --
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTC-----AATGGGGAAAGAA--TAGTCTTTTCAAC-- 405

  chr2_221264762_    610 AAATAGC-------CAAGTTAGTGATCTATATG----AAAAT--AGT-AG 645
                             i i-------   -i i vv ? i i   ---- i   --   -i 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_221264762_    646 ATACCTATATTACATCATACACAAAAATAAAATCCAAATTGACTG-AGAT 694
                          iv    iv i   i    i        v  v  v    v  iii-   -
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA- 503

  chr2_221264762_    695 CCTTACTATAAATAGC-AAAGCTTTAAAACTTTTTAGAA-AAAATATGAG 742
                            v v i   i-   -   i  v       i  -    -    i  ii 
  L1M4_orf2#LINE/    504 CCTAAATGTAAG-AGCTAAAACTATAAAACTCTT-AGAAGAAAACATAGG 551

  chr2_221264762_    743 ATCA--TCTTTCTGACATTGAGATATGAAAAAAAATCTTAA----GATAC 786
                         ?vi --    iv    v   i v  v v  viivv     i----  i  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_221264762_    787 TAAAAGTACAGGC 799
                         i     i   i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGC 614

Transitions / transversions = 1.18 (67 / 57)
Gap_init rate = 0.06 (29 / 496), avg. gap size = 2.97 (86 / 29)  

 402 29.19 7.38 2.68  chr2_221264762_221266645.rev     1095  1392 (492)    L1M4_orf2#LINE/L1      597   908 (0)  

  chr2_221264762_   1095 GATACTAAAAGTACAAACTCTGAAGAAGGAAAT-TATAAATCTAACTACA 1143
                           i  i     i    i vvii  ii ii    -v      ivi   v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_221264762_   1144 TCAAAATTGAAAGCATCTATGAACAAAATGA-A-----AAGACAAAGAAA 1187
                                 i   i v i i  vviv   v  - -----    v iv    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_221264762_   1188 AGACAA---AC----TGG---AAAGTCATTTGCAACCCACATAAAAAACA 1227
                               ---  ----   ---   i -        vi  i   vvvi i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAAT-ATTTGCAAATCATATATCTGATA 745

  chr2_221264762_   1228 AAGAATTTATAATCGAAACATATAAAGAATTCCCATAAATCAATACAAAA 1277
                          i i i  i  vi ii  i          i  ii i  v      vv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_221264762_   1278 TAAATCAGTAGCCCAAGAAAGAAATTTGGCCAGTGAATAAGGTTAAATGA 1327
                         v i iv i  i     vv? i    --  v  iv i  ----  i   - 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAAT--GGGCAAAGGAT----TTGAAT-A 838

  chr2_221264762_   1328 GCCA-----CAGAAGAGGATACTTGGATGGCCACTAAATAGAAGAAAATA 1372
                          v  ----- vi    i    iviii       v   ii v v     v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_221264762_   1373 TGCTCAATTTCATTAAGGAA 1392
                                iv   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (52 / 34)
Gap_init rate = 0.04 (11 / 312), avg. gap size = 2.73 (30 / 11)  


2847 24.55 5.18 2.93  chr2_221284948_221287823     1497  2384 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_221284948_   1497 TAAAGAGAAATACCATATTTATGGATTAAAAGACTCAGTATTTCCAAAAT 1546
                          ii i   v  v    i  i       ii      i i    vii  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_221284948_   1547 CTTAATTCCCCCCAACTTGACCCATAGATTTAG-GCATTGCCATTGAAAA 1595
                         vvi   v i      v    i i i     i i-   v v  vv v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_221284948_   1596 TCCAAGGAAGCATATTTTATAGATGTTTATAAAC--ATTTTAAAATTTAT 1643
                            v  vv-  v v    ii   vi  v i  i --  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_221284948_   1644 GTGGAAAGAAAAAGGAAGTAGAATAGCCAAAATTATCCTGGAAAAAAAAA 1693
                         i      viv  i   vvi             iv   i  i    i  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_221284948_   1694 ACAAAAACAAAGAGGACTCACATTACCTAATTTCAAGATATACTATGAA- 1742
                              ivii--           i v  i        i iv     ii  -
  L1M4_orf2#LINE/    200 ACAAAGTTG--GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_221284948_   1743 CTACAGTAATGAAGACAATGTGGTATTGACAAATGGGTAGA--------T 1784
                                   v      i       i  i  v v  i    -------- 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_221284948_   1785 CAATGGAAGAGAATAGCTAGCCCATATATAGACCCATAAACATATA-CCA 1833
                                 v     v vv  i   v v   i       v iv   i-i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_221284948_   1834 ACTGATTTTTAACAATGGCGTGAAAGCAATTAGATGGAGAAAGGATAGTC 1883
                          i       ii    v  i iv  ii v   vi    i     i      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_221284948_   1884 TTTTCAATAATTGTTGCTGGAACACTTAAATACTCACATGACAAAAGG-- 1931
                                i  v  v      i   vi ii   ?i      -      i--
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAAT 446

  chr2_221284948_   1932 GAATCTCAATACCTACCTTAT-TTATTCCTGATACAAAAATTAACTCAGA 1980
                            vi vi iv       i i-ii  -----                 i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCAT-----ATACAAAAATTAACTCAAA 491

  chr2_221284948_   1981 GGAGATCATGGACCTAAACGTAAAATATTAAAAA-ATAAAACTTT---AA 2026
                         ivi     ?i        i    i -ii     v-        i ---  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAA 540

  chr2_221284948_   2027 GAAAACATAGGAAAAAATCTATATGATGTTTGTATTGTCATATTGGGTTT 2076
                                    ?iv      -------------- i  v iv       v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCT--------------TCGTGACCTTGGGTTA 576

  chr2_221284948_   2077 GTCAGAGGTTTTTTAGATGTGACACCAAAAGTATGATCCATAAAA----- 2121
                          v  iv     i      i            i ii v v i    -----
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_221284948_   2122 --CCTATAAGTTGGGCTCTATCAATATTAAAAACTT--AGGCTCAATGAA 2167
                         --ivv    i    i  ii     v           --iv   iv --  
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AA 674

  chr2_221284948_   2168 AAACCCTGTTAGGAGAATGTAAAGATAAGCCCCAGCA-GGGAGAAAATAT 2216
                         ii  v  i i i  i i  v     i  v  v   v -            
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr2_221284948_   2217 TTGCAAGCCATATATCTGATAAAGGACCTACACCCAGATGATATCAAGAA 2266
                               ii              i    i ii i     vv    v     
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr2_221284948_   2267 CACTTAAAATTCAACAATATG--------TAA--------AGAAATGAAC 2300
                          v    v  i    i    vi--------   -------- i     ii 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_221284948_   2301 AAAAGATTTGAACAGACACTTCACTGAAGAAGATATATAGATGACAAATG 2350
                            i        i     i   v ii           i i   i v   i
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_221284948_   2351 AACACATGAAAATACGCTCAATGTCATTTGTCAT 2384
                          i          v i      ii   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (138 / 77)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.43 (72 / 21)  


 581 23.12 3.75 1.25  chr2_221428469_221430586.rev      937  1096 (1022)    L1M4_orf2#LINE/L1       47   210 (698)  

  chr2_221428469_    937 AGGTGTCAGTTCTCACTAA-TTGATGTACAGGTTCAGTGCAGTTTTAATC 985
                           i  v  i v   v i  -     v     i    ii   i iiiv   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_221428469_    986 AAAATTCC-GCAGGCTTTTTGGGTCATAC-TTGGCAAACTGATTCTAA-- 1031
                              i  -  v v      v --  v v-   i   i     i    --
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTG--CAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_221428469_   1032 TTTATATTAAAATGCAAACGACT-AGACTAGTAAAAATAATTTTGAAAAA 1080
                           i    vi        iv   i-   v   iv    i   i        
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_221428469_   1081 GAAAAACAAATTTGGA 1096
                            i      v     
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGA 210

Transitions / transversions = 1.47 (22 / 15)
Gap_init rate = 0.04 (6 / 164), avg. gap size = 1.33 (8 / 6)  

1592 22.61 3.50 1.40  chr2_221428469_221430586.rev     1198  1626 (492)    L1M4_orf2#LINE/L1      471   908 (0)  

  chr2_221428469_   1198 ATATATAAAGGCTGGTAAAAAATAG--CATG---CTAA---TAAATGC-A 1238
                              i   iii iiivv     i --  ?i---    ---   iv  - 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_221428469_   1239 AAGCCACACAATCCCTAGAAGATAGCACGGGAGGAAATCTAGGTGACTTT 1288
                           i i i v  ii i       v i  ii  ? v      vv     i  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr2_221428469_   1289 GGGTTTGGTGATGACTTTTTAGATGCAACACCAAAAGTACAATCCATGAA 1338
                              v  ii   ii  i      iii          i    v v ii  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_221428469_   1339 AGAAAAAAATCAATAAGTTGCACTTCGTTAAAATTAAAAACTTCTGCTCT 1388
                                 - vi    i   v     i i              i  iv  
  L1M4_orf2#LINE/    621 AGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_221428469_   1389 ACAAAAGACATTAC---GACAATTAAAAGACAAGCCACAGATTTGGAGAA 1435
                         v    i    i  i---  v i v         v       v v      
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_221428469_   1436 AATTTTTGCAGAGCACAT-TTT-ATAAAGGACTAGTATTCAACATATACA 1483
                            v      i v  i  - i -    i     v    i  iv     i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_221428469_   1484 AAGAACTCTTAAAACTCTACAATAAGAAAACAACCAACCTACTTTAAAAA 1533
                                    v     v i     i  i    vi    i v  ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_221428469_   1534 AAAAATGGGCAAAAGATTTAAACAGAAATTTCACCAAAGAAGATGTATGG 1583
                         -----        i     i  i   v     v           i  iii
  L1M4_orf2#LINE/    820 -----TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr2_221428469_   1584 ATG-CAGATAAGCACATGAAAAGATGTTCAGCATCATATGTCAT 1626
                            - vi                   i   i     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (63 / 31)
Gap_init rate = 0.02 (10 / 438), avg. gap size = 2.10 (21 / 10)  


2065 25.23 7.41 4.05  chr2_221507665_221509510.rev      501  1364 (482)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_221507665_    501 TGTTCGTGGATTGGAAGACTCAATGTTATTAACAGTTAAGATAACAATTC 550
                              i              i   i  -------        ii    v 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATT-------GTTAAGATGGCAATAC 58

  chr2_221507665_    551 TCACCAAATTGATGTACAGATTTAATGAAATCCTAGTTGCAACCAAAGCA 600
                           v          v        i  i v     ivi iiv  i vv   v
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr2_221507665_    601 ACTGTTTTTACCAAAATGGGCGAATCAATTTTAAAACTTAATATGGAAAT 650
                         i iv     i vi    v i i iiii  ii     -  v          
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCATATGGAAAT 157

  chr2_221507665_    651 AAAAAAGACCTATAAAAAGCCGAAACAGTCTTGAAAAATAAGGGGAGAAA 700
                         iv  ii    i -i  v    i     i          v   iiv i iv
  L1M4_orf2#LINE/    158 GCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_221507665_    701 TGGAGG-CTGTATACATTT---GATTTCACAGCTTACCTTAA-GTTGCA- 744
                               -  ---i   i  ---i      v i     ivi  - i i  -
  L1M4_orf2#LINE/    207 TGGAGGACT---CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_221507665_    745 --------ACAGTG--GTATTGGCACATGGATGGACAAATAGATCAATGA 784
                         --------      --   i     i v    i    v           i
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_221507665_    785 AAGAAAAT--AGAATCCAGAAATAAATTCTCAAATATCAA--GTCAATTG 830
                           v i   --   i            -- i  v i  iv --        
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAA--CCCATACATTTATGGTCAATTG 351

  chr2_221507665_    831 ATTTTAAGTAAAGAT-TCAAGGCAATTTAATGGAGAAAG--TTGTTTTTT 877
                              viii  i i -i    i v   i     i     -- v  i    
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_221507665_    878 TTTTTTTTTCACCTACAAATGGCACTGCATCAACTAGATAAATGAC-TGG 926
                         ---------  ---        ii   viv     i    ?vi-  -  v
  L1M4_orf2#LINE/    402 ---------CA---ACAAATGGTGCTGGGACAACTGGATAKCC-ACATGC 438

  chr2_221507665_    927 AAAAGTATGTACATTGATCCCTACCTCACATCACACA---AAATGTATTT 973
                              v   v vv v  i            i  i i ---    vv i i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_221507665_    974 GAAGTGTATCATAGACCTACATATAAAAGCTAATATTATAAAGCTTTTTG 1023
                         i  i  v    ?       v  i   i      v i      i  i  v 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_221507665_   1024 AAAA---------TGTA----TTTATTATCTTATAGTAAGAAACAAATTT 1060
                           i ---------?   ----  ii v i   iviv  i v  iii-   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTT 587

  chr2_221507665_   1061 ATTGGAAA--ATACAAAAATCCCTAACTATAAAAAATAGAAGTTATAAAG 1108
                         v  i  v -- i  v    v v v i v i    i v i  vvv     v
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_221507665_   1109 TG-ACTTCACCAAATTTAAATGACTTTCCT-CATCAAAAACATAGTATTA 1156
                           -      i    v     -i     iv - v     ii- i v   i 
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGG-ACACTATCA 685

  chr2_221507665_   1157 AGAAAATATAAAAGACAAGCCCCAAACTGAGAGAAA-TATTTG-AAATAC 1204
                              i i-         v  v  i v  i      -      -    - 
  L1M4_orf2#LINE/    686 AGAAAGTG-AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT-C 733

  chr2_221507665_   1205 ATATACCTAACAGATTATTTATATTCAGAATGTATTTTTAGAAACTCTTA 1254
                              i  i i iivv i  i   i      i   v--- ii        
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATA---AAGAACTCTTA 780

  chr2_221507665_   1255 AAACTTAGTGATAACACGAC------TCAAGTTTAAAAATTGT---ACGA 1295
                         v    i i i    v v   ------i v i  ?      v v--- v  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_221507665_   1296 CTTGAACAGAAGCTTTACAAAAGAAGA------AATGTCTAACAAGCACA 1339
                         i     i   vii  iv v        ------    v i  i       
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_221507665_   1340 TGAAAAGGGA---AACTTCACTGACCAC 1364
                                ivi---   v   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (132 / 82)
Gap_init rate = 0.04 (36 / 893), avg. gap size = 2.75 (99 / 36)  


1625 27.14 8.93 4.17  chr2_221552964_221554877      575  1414 (500)    L1M4_orf2#LINE/L1       15   894 (14)  

  chr2_221552964_    575 ATGTTCATGGATTAGAAAACTCATCATTGTAAATATTTTTATTCTCCACA 624
                                      i   i   i vi     v  v  vviv  v    v  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_221552964_    625 AATTTAACCTATGGATTT----CA-----TATCA---TACTAATAG---- 658
                             -i i   ii    i----  -----     --- v i iiv ----
  L1M4_orf2#LINE/     65 AATT-GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_221552964_    659 -------AAAATGGAAAAGTCT--TCCTAAAATGCATATGGTGATGAAAA 699
                         -------i    v  v   -  --         v       vi   v  i
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_221552964_    700 GTGCTGAAAATAACCAAGACTATTTT--AAATGT----CAAAGTTGGGAG 743
                          vi iv i    i    i  v  i  --   v v----         ii 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_221552964_    744 ACTAACAGTAAGAGATAGTAAGACTGA--ATCAGGCT---GTAATTATAG 788
                            v   v vvvvi  vvi  i   v -- iv i   ---     i vii
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_221552964_    789 CAGTTTTATACTGGTACAAGGAAAGACA----AACTAATAGTACTGAAT- 833
                             v vi      i i     v     ----i ii   i v iv    -
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_221552964_    834 -AGAGTCCACAAATCAAT--ACACATGTGCAAACACATGATTTACACCAA 880
                         -        v    v  i-- i    v iiiiv  vv      v iv   
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_221552964_    881 AA----CAACACTAG--AGTGGAATAGAAAAGATGGCCTTTTCAATGAGC 924
                         ii----   v  i v-- i   i---    ii  i i        ii ii
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGG---GAAAGAATAGTCTTTTCAACAAAT 409

  chr2_221552964_    925 AATGCTGGGTCAACTTGTTATCCACATGGATTAG--TAACGTGTGTCTTG 972
                         ii       v     v v  ?       v vv  -- i v  -  ---- 
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT-TG----G 454

  chr2_221552964_    973 GCTTCTATTTTGTATCATATACAAAATGCAACTCCAGATGGATTGCAGAT 1022
                         i ii   ii iii i           vvi     v i      ii?   i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_221552964_   1023 CTAAATGTGGAAGGAGAAACAATAAAGCTTTTAGAGGAAAATACAGGAGG 1072
                                 iii  vvi    v     i  i     i     i i   ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr2_221552964_   1073 ACATTCTTGTGACCTTGGTGTT-GGCAATGATTTCATAAACAGGACAC-A 1120
                          v  ii i          -   -       i    v  i i v     - 
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_221552964_   1121 AAAGGACCTAACTATAAACAAACAAAAAAGACAGATCAA--AGACAAATT 1168
                             v  v- i ----      - i    i i    v  --i   ---  
  L1M4_orf2#LINE/    604 AAAGCACA-AGC----AACAAA-AGAAAAAATAGATAAATTGGAC---TT 644

  chr2_221552964_   1169 TATTTTAACATCAAGAACTTGCGTTCATCAAAAGACATCACTGAG----T 1214
                         i  i--  v  i  i     vi  v v     i    ii iii  ---- 
  L1M4_orf2#LINE/    645 CATC--AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_221552964_   1215 AAAAATACAGCCC-CAAAAGTAGTTGAAGTTATTCTCAATATGTGTATCT 1263
                         i    v   i   -  i  - i vv   iv    iv   vvii i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_221552964_   1264 GGCAATAAG----TCACATCCAGAATACATAAACAATCCCAACAAATTAA 1309
                          ---     ---- iii          i     v  ii iv    v i  
  L1M4_orf2#LINE/    742 G---ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_221552964_   1310 TAATAATAAAAAAGACAGACCATAGAAT--AAAAAAAGTCAAAAGACACT 1357
                               ----       i iv ivv   --     vi v    i  i-- 
  L1M4_orf2#LINE/    789 TAATAA----AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT--T 832

  chr2_221552964_   1358 TGAATAGAC---CCTTAAAAACAGAAGATAT-TAAATGAC----AAGTAT 1399
                                  ---i  iv   ---        -i     i ----   i i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAA---GAAGATATACAAATGGCCAATAAGCAC 879

  chr2_221552964_   1400 ATGATAAGGTGCTCA 1414
                             v   i      
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCA 894

Transitions / transversions = 1.59 (138 / 87)
Gap_init rate = 0.05 (41 / 880), avg. gap size = 2.68 (110 / 41)  


 912 26.00 1.20 2.00  chr2_221946630_221949065       35   284 (2152)  C L1M4_orf2#LINE/L1   (660)   248     1  

C chr2_221946630_    284 TGAAAAGGTTTTCTGTGTTCATGGATTGAAAGAATTAA-ATCATTAAAAT 236
                           i    i v i ii             i    v    -  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_221946630_    235 GTCCATACTACCCAAAAACAATCTACAGATTTAATACCATCCCTATCAAA 186
                          v v     v      v-ii           i  ii v            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

C chr2_221946630_    185 ATACCAATGACATTCTTCATGGAAAT--ATATGTTCAAAAATCCTAAAAT 138
                           v   iivi v  i  iiii     -- i v i ----i          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT----GATCCTAAAAT 145

C chr2_221946630_    137 TTGTATGGTACCACAAAAGACCTGGAATAGCCAAAGCTATATTGAGCAAA 88
                          ii     v vii   ii    ii           i v  v    iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

C chr2_221946630_     87 AAGAACAAAGCTGGAGGCATCACACTAGTTGACTTCAAAATACAATACAA 38
                                   i      vv       vviii i       ivi v     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

C chr2_221946630_     37 AGC 35
                            
  L1M4_orf2#LINE/    246 AGC 248

Transitions / transversions = 1.95 (43 / 22)
Gap_init rate = 0.02 (4 / 248), avg. gap size = 2.00 (8 / 4)  

1025 25.31 1.24 0.00  chr2_221946630_221949065      501   741 (1695)    L1M4_orf2#LINE/L1      184   427 (481)  

  chr2_221946630_    501 ATCTTGATCAA-AAGAATAAAGCTGAAGGCATCACACTTCCTGACTTCAA 549
                                vv  -     i    i  i   vv          ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr2_221946630_    550 AATATACTACAAAGCTATAGTAACCAAAACAGTATGATGCTGGCATAAAA 599
                           iv             i     i   i     i  i i         ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr2_221946630_    600 ACAGACACGTAGACTAAAGGATCA--ATAGAAAGCCCATAAATAAACTCA 647
                          i     ii    ii  v   vi --  v  i  i   v        i  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr2_221946630_    648 TGCATCTACATCCAAATCATTTTTGACAAAGGTGCCAAGAATACACAATG 697
                          i   i  iivi   v v     i     i          vi iv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr2_221946630_    698 AAGAAAGGACAGTCTCTTTAATAAATGGTTGTGAGCCAGTTAGA 741
                         ii     i i     i  i  i       vv  i v  ii i  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

Transitions / transversions = 2.59 (44 / 17)
Gap_init rate = 0.01 (2 / 244), avg. gap size = 1.50 (3 / 2)  

1513 21.43 4.63 6.95  chr2_221946630_221949065     1429  1946 (490)    L1M4_orf2#LINE/L1      403   908 (0)  

  chr2_221946630_   1429 AATAAATGGTTGTGAGAAAACTGGACATC-ATATGCAGAAGAATGAAATT 1477
                           i       vv  i  v       i ? - i     i         i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_221946630_   1478 AGACCCTTGTCTCACACCATATACAAAAGTTAACTTAGAATGGATTAAAG 1527
                         i     i ii                  i      i i       i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_221946630_   1528 ACTTAAATTTAAGAGCCAAAACTATAAA-CTTCTAGAATAAAACCT---- 1572
                           i     v       i           -  ii     v     v ----
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_221946630_   1573 GTGAAT----ATG-----------GGCAACAACTTTGTGGATAAGACCTT 1607
                           i   ----i  -----------     iiii  iv i    v   vii
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_221946630_   1608 AAAATCATAGGCAACAAAAGTGAAAATAAACAAAGAGAATTACATCAAAC 1657
                             v  i i          vi      i i   vv i i v       v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_221946630_   1658 TGAAAAAAAAAAAGTATGCACAGCAAAAAAAAAAAAAAAATCAGTAGAGT 1707
                          v     v-----v v  ii vv    ii v vv -----   iv i   
  L1M4_orf2#LINE/    653 TTAAAAAC-----TTTTGTGCTTCAAAGGACACTA-----TCAAGAAAGT 692

  chr2_221946630_   1708 GAAGAGACAACCTACAGAATGAGAGAAAATACATACATACATACATACCT 1757
                            i        i        i         i------------------
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATAT------------------ 724

  chr2_221946630_   1758 CATAAAATACAAATTGCATACATCAGATAAGGGGCTATTATCCAAAATAT 1807
                         -- ---- i     --    i   v        i  vv      i     
  L1M4_orf2#LINE/    725 --T----TGCAAAT--CATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_221946630_   1808 ACAAAGAACCAAAACTACTCTATAACAAGGAAACAAATAACTCTATTAAA 1857
                          i       ivvv  v    v    i  ii i         i v   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_221946630_   1858 AAATAGGCAGAGAACTTGAAGAGACAGTTCTC---AAAAGACATACAAAT 1904
                             i    i  i i     v     v     --- i    i        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_221946630_   1905 GGCCAACAGATATATGAAAAAGTGATCAACATTTCTAAGCAT 1946
                               i iii i       ii  v       iv????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (70 / 38)
Gap_init rate = 0.02 (11 / 506), avg. gap size = 5.45 (60 / 11)  


 498 26.61 0.00 0.00  chr2_222095195_222097009.rev      306   429 (1386)  C L1M4_orf2#LINE/L1   (784)   124     1  

C chr2_222095195_    429 TGAAGAGCTATCCTACCCTCATGAATTGCAAAGCTTAATATTGTTAAAAT 380
                           i i  v     i ivi     i    v  ii              i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr2_222095195_    379 GTCTATCCTACCCAAGGTGACCTACAAATTCAAGGCAAACCCTATCAAAA 330
                          v v  v  v     iv   i     i      v    v           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr2_222095195_    329 TACCAATGACATTCTTCACTGGAA 306
                          v   iivi v  i  ii v i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA 124

Transitions / transversions = 1.36 (19 / 14)
Gap_init rate = 0.00 (0 / 124), avg. gap size = 0.00 (0 / 0)  

2559 25.61 0.97 4.49  chr2_222095195_222097009.rev      500  1323 (492)    L1M4_orf2#LINE/L1      114   908 (0)  

  chr2_222095195_    500 TTTCACAAAAATAGGAAAAAAAAATCCTAAAGTTTGTATGGAACCACAAA 549
                            ii  i    -v  v  ivvi        i  ii       vii   i
  L1M4_orf2#LINE/    114 TTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr2_222095195_    550 ACACCCAAAATAGCTAAAGAAATCCTGAACAAAAACAGCAAAAGCAGAGG 599
                         iv     i      i   iv    i    v  i  v i    ivii    
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_222095195_    600 CAC-CACATTACCTTATTTTGAATTATATTATAAAGTTATAGTAATCAAA 648
                         -  -    i v  iv    ii  viv  i  i    i  i         i
  L1M4_orf2#LINE/    213 -ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_222095195_    649 ACAGCATGGTACTGGTATAAA-ACAGACATAGTGACATAGAACAATGGCA 697
                             ii         i    i- i       ------    v      v 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATA------TAGATCAATGGAA 305

  chr2_222095195_    698 CAGAATAGAGAACCGAGAAATAAATTCATTCACTTACAACGAACTCATTG 747
                         i     v    ii v         ii   v  i   iiiiv  i v   v
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_222095195_    748 TTGACCAAGGTGCCAAGAACATACATTGAAGAAAGGACAGTCTCTTTAAT 797
                          i   v i          v   v  v  ii     i i     i  i  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_222095195_    798 AAATGGTGCTGGGAAAACTGGATATCTATATGTAGAAAAATGAAACTAGA 847
                                       v         ? i i   i i  i      ii i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_222095195_    848 TTTCTTCTTT-CACCATATGCAAAA-TGAACACAAAATGGAGTGAAGATG 895
                         iii  v i i-        i     - v   v         vii?   iv
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_222095195_    896 TACATGTAAGACCTGAAGCTAGAAAACTACTAAAAGAAAACACTGGAG-A 944
                           v        v  i  i   v      vi  i         iv  ? - 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_222095195_    945 AATGTTACAGAACATTGATCTGGGCAAAGATTAGTTGGGTAAGATCTCAA 994
                            v  - ivi  v   ivi i     v i  vv  i i  v  ivi   
  L1M4_orf2#LINE/    556 AATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_222095195_    995 AAGCTCTGGCAACAAAAGTAAAAATAGATAAATGTGATTATGTCAAGCTA 1044
                             v vi          v              vv  i vii    iv v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr2_222095195_   1045 AAAAGTGCCTGCACAGCAAAAAAAAAAAAAAAAAACAAAAACAAAAACAA 1094
                             iivii  ii vv    ii ------------------------  -
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGA------------------------CA- 679

  chr2_222095195_   1095 AAATCATCAACAGAGTGAAAAGACAACTTACAGAATGGGAGAAAATATGT 1144
                         ---ii     v i              ii                   v 
  L1M4_orf2#LINE/    680 ---CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_222095195_   1145 GCAAAT-GTCCCTCTGACAAGACCTTAATAATCAGAATATGTAAGAAACT 1193
                               -i viv     i   ivvi vi  vi        i   ii    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_222095195_   1194 CAAACAACTCAATAGCAAAAAGAAAGAT--CCCAATTAAAAAATAAACAA 1241
                          vv           ii       v i  --       ?      iii   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_222095195_   1242 AAGTCCTAAATTGACATTTCTCAAAAGAAGACATGCAAATGGCCAACAGG 1291
                          i vii i   v          v        i  i           i i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_222095195_   1292 TATATGAATACATGCTCTACATTACTAATCAT 1323
                         i i     v v      v    i ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (133 / 74)
Gap_init rate = 0.02 (13 / 795), avg. gap size = 3.46 (45 / 13)  


3019 23.32 2.82 4.34  chr2_222411548_222414020.rev     1060  1981 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_222411548_   1060 TGAAAAGACATCTCATGCTCTTGAATTGGAAAAAAATAATATTTTCAATA 1109
                           i     i   i    i  v  i       i vv-       v i  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACT-TAATATTGTTAAGA 49

  chr2_222411548_   1110 TGATCATACTACCCAAAGCAATCTACAGAGTCAATGCAGTCCCTGTCAAA 1159
                           iiv     v      vii         v    i   i     i     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_222411548_   1160 ACACCAATGACATTCTTCACAGAAATAGAAAATTTCTAAATCTTCTATTA 1209
                          iv   iivi v  i  ii       v  v  ------------------
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAA------------------ 131

  chr2_222411548_   1210 TTGTTCATGTGAATTTCCTAAAATTCGTATGAAACCATAAAG-ACCTA-- 1256
                         -- i -----  ---           i    i  viii  i -   i --
  L1M4_orf2#LINE/    132 --GCT-----GA---TCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_222411548_   1257 ------AAAGCAATCCTGAGTAAAAACAACAAACCTGCAGGCATTACATT 1300
                         ------   i     i   iv  i  v      vi  v   vv i   i 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_222411548_   1301 ACCAGATTTCAAAATATACTACAAAGCTATAGTAATCAAAACAACATGCT 1350
                         v  vi         iv             i         i   iii  v 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_222411548_   1351 ACTGGCATAAAAACAGACACATAGACCAATAAAACCAAATAGAAAATCAA 1400
                                   ii i     i     i    ii  ivi   v  i i  v 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_222411548_   1401 GAAATAAAACCACATATTTATGGCTGTCA---GATTTTTGACAAAAGC-C 1446
                                 v   i i        ---   ---      i     ii i- 
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGG---TCAATTGATTTTCGACAAGGGTGC 368

  chr2_222411548_   1447 C----CTTTTCATTGGGAGAAGGATAGTCCCTTCAACAAGTGGTTCTAGG 1492
                          ---- iv    v    ii   i      ii        i    v  i  
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr2_222411548_   1493 AAGACTAGATATCTATTTGCAGAAGAATGGAACTATGTCTCTAACTCTCA 1542
                          vi   i    ? i iv    i       i ii ivii i   v   v  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr2_222411548_   1543 CCATTTACAGAAACCAACTTAATATGGATTAAATACTTAAATGTAAGAAC 1592
                             v    i   ii    i  v      i ? v  i           i 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr2_222411548_   1593 TAAAACTACAAAACTACTAAAAGAAAACA--GGGG-AAATGCTTTATGAC 1639
                                 i      vi  i         --  ? -    -   ii    
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGAC 567

  chr2_222411548_   1640 ATTGGTCTAGGAAAAGATTTTACGGCTAGGACTTCAAAAGCACAGGTAAC 1689
                         v    vi    v  v i   ivii v  v   vi          i i   
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_222411548_   1690 ATAAACAAAAACAGGCAAATAGGGCTATATCAAACTAAAAAGCTTCTGGA 1739
                          v  iv     i  ii    v  i  vi      v v    i   i  vi
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_222411548_   1740 CAGCAAAGGAAACAATCAACAGAGTGAAAA-ACAACCTGTAGAATGAG-G 1787
                          vv       v  v     v i        -      iii      i - 
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_222411548_   1788 AAAATAATTGCAAA--ATATTAATCTGACAAAGGATGAATATTCTGTCTA 1835
                               v       --    --      i  i   ivvi   i v vv  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATAT--ATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_222411548_   1836 TACAAA-AACTCAAACATCTCAACAGCAAAATAATAATAATAATAATCCA 1884
                           i   -     vv   v     i ii    vi i  -----    i   
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAA-----ATAACCCA 810

  chr2_222411548_   1885 ATT-ATAATTGGTCAAAGGATCTGAATAGACATTTCTCAAAGGAAAGCAT 1933
                            - v  v   v        i                v  i   iii  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_222411548_   1934 ACAAATGGCCAATAGGTATATGAAAAAATAGTCAACATCACTAATCAT 1981
                                       i i i       i  iv         ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (136 / 76)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.30 (66 / 20)  


4158 18.74 2.92 1.01  chr2_222548698_222553911.rev     3832  4722 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_222548698_   3832 TAAAAAGATATGCCATGTCCATGGATTGGGAAATTT-----TGTTAAGAT 3876
                          ii        v      i          i i i  -----         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_222548698_   3877 GGCAATATTTCCAAAGTT-ATGTACAAATTTGATGCAATCTCTGCCAAAA 3925
                                i i  v  i  -  v    i   ii i      i  ii     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_222548698_   3926 CCCCAATTTCCTTTTCTGAATAAATGGAAAAGCTGATTCTAAAATTAATA 3975
                         i    ii v      i  v v    v  v        i        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_222548698_   3976 TTACATTTTACGGAACTCTGAGTAGCCAAA-CAATCTTGAAAAAGAAGAA 4024
                          viv v vi v  i  i v  i        -                   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_222548698_   4025 TAAATTTGGAAGACTTATACTTATTGAATTCAAAACTTATTACAAATGTA 4074
                         i   v     i    i i    viii v           i      vv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_222548698_   4075 CAGTAATCAAAACAATGTGGAACTGATATAAGGGTAGACATATAGATCAA 4124
                                   i   i     v    ii      i                
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_222548698_   4125 TGAAATGAAATTTAGAGTTCAGGGATAAACCTGTACATTTATGGTAAAAT 4174
                           i   ii    v     i   ii       ii            v  v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_222548698_   4175 CATTTTTGACAAGGGTGTACCAAGACCATTCAGTGTGGAAAGAATAATCT 4224
                         v     i          --             i  v          i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG--CCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_222548698_   4225 CTTCAACAAAATTTGCTGGGATGACTGAATAACCACAGGCAAAAGAATGA 4274
                         i         vvv        ii    i   ?     v            
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_222548698_   4275 CACTAGACCCTTACCTCATACCACATACAAAATTTTTTTCAAAATGAATC 4324
                         vii i     i       i    i        v  vvi        i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_222548698_   4325 AAAGATCTAAATGTAAAAG-------TATAAAACTCTTAGAAAAAAGCAT 4367
                          ?   i          i  -------                i   i   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_222548698_   4368 AGATGTAAATGTTTATGACTTTGAGTTTGGCAATGGTTTGTTACATAT-- 4415
                           i?      v  ii    i   i   v           v   v    --
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_222548698_   4416 ------ATG-ACAAGCAACAAAATAAAAAATAGATAAATTGGACTTCATT 4458
                         ------ v -             v                         i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_222548698_   4459 CAAATTTAAACCTTTTATGCATCAAAGGACATTGTCAAGAAAGTAAAAAA 4508
                         v     v   v     i   v          i i          i    i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_222548698_   4509 AAAGCCAGACCACAGGGCGGGGAGAAAATATTTGCAAACTATAAATCTAT 4558
                          v i  ----     iii   -                ii   v    iv
  L1M4_orf2#LINE/    699 ACAACC----CACAGAATGGG-AGAAAATATTTGCAAATCATATATCTGA 743

  chr2_222548698_   4559 T--GAGTCTTGTATATAGAACATATAAAGCACTTGAATAACTAAACAACA 4606
                          -- i v       vi    i        v   ivv i    v  i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_222548698_   4607 AAAATACCAAAAAATCTCAATT-AAAAATAGGTAAGGGACTTTAATAGAT 4655
                             v  -   v  i -     -      i  i  i   i  v      i
  L1M4_orf2#LINE/    794 AAAAGAC-AAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_222548698_   4656 ATGTCTTCCAAGAGGATATACAAATGGCCAATAATCACATAACATTATGC 4705
                           v   i v    i                    v     i v vv    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_222548698_   4706 TAAACACCACTAGTCAC 4722
                          v    i  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (101 / 63)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.69 (35 / 13)  


2698 26.89 3.00 2.11  chr2_222566179_222570021.rev     2452  3351 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_222566179_   2452 TGGGAAAACATTCCATGCTCATGGATTGGAAGAATCATTACAGTAAAAAT 2501
                            i  i i  i     i               v i v  iv  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_222566179_   2502 GATCATACTGCCCAAAGCAATTTACAGATTCAATGTTATTCCTATCAAA- 2550
                          iiv     v      vii  i           i iv  i         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_222566179_   2551 --CTAGCAAGGTCATTCTTCATATAACTAGAAA--AAAAAACT-ATTCTA 2595
                         -- i   --v i v  i  ------i -     --i v  i  -  i   
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTT------GC-AGAAATTGACAAGCTGATCCTA 141

  chr2_222566179_   2596 AAATTAATATAGAAACACGAAAGAGCCCAAATAGCCAAAGCAATTCCAAG 2645
                              v    i    ii i ii  v  vi          i    iiii i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr2_222566179_   2646 CAAAAAGAACAAAGTCAGAGGCATCACACTACCTGTCTTCAAACTATGCT 2695
                         v  i           ii    vv       v  iivi      viv i  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_222566179_   2696 AGGAAGCCACAGTAACAAAAGCAGGTTGGTATTCGTACAAAAATTGACAC 2745
                          vi    i       iv  ii   vv     i v i i  ii  v    i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_222566179_   2746 ACAGACCAATGGAACAGAATAAAAAACTCAGAAATAAAGCTGCACCTCTA 2795
                          i   i        i     vi i iii          v iii  v i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_222566179_   2796 AAACCATCTGATCTTCAACAGGGCCAACAAAAACAAGACATAGGGAAAGG 2845
                         viii  vi    i   i   i  viiv   i v  vvvv  i       i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_222566179_   2846 ACTGTCTATTCAATAAATGCTGCTGTGATAACTGGTTAGCCATATGAAGA 2895
                          iv    v     i     v     v  i      v  ?   i   v i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_222566179_   2896 AAATTGAAGCTGGAACCCTACCTTTCACCATATA-AAAAATTAACTTAAA 2944
                          i v     i    v        iv         -           i   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_222566179_   2945 ATGGGTCA--------AATGTAAAACCTCAAGCTATAAAAATCCTGAAAG 2986
                             i   --------       i v  v  i        v  i ii   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_222566179_   2987 ATAACCTTGG---AAATACTCTCTCAACACCAGTCTTGACAAATAATTTT 3033
                          v   v v  ---    -  -  vii  viii vi v i   - ii   i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CT-TCGTGACCTTGGGTTAGGCAA-TGGTTTC 588

  chr2_222566179_   3034 T---GTCTGAGTTTTCAAAAGCAATTGCAA-CAACAACAAAAAAAAATTG 3079
                          ---i v   --ivi        ----   -      -  i       v 
  L1M4_orf2#LINE/    589 TTAGATATGA--CACCAAAAGCA----CAAGCAACAA-AAGAAAAAATAG 631

  chr2_222566179_   3080 ACAAGTGGGATCTAACTAAACTAAAGAGCTTCTGCATAGCAAAAGAAATG 3129
                          i  i v   ii v ii   v v  i i   i  iiivv    i  v iv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_222566179_   3130 ATCAACAAAGCAAACCGGTGACCTACAGAATGTGAGAAAATATTTGCAAA 3179
                              v    ii  vv iii   i        v                 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_222566179_   3180 CTATGCATCAGACAAAGACCTAGTATCTAGGGTCTACAGAGAACTT---- 3225
                         ii  ii   v  i  i iv  v     i  ii v  i i      i----
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_222566179_   3226 AAATCAACAAGCAAAAAACCAATAATCCCATT-AAAAATGGGCAAAGGAT 3274
                           v    i  vv    i  v     i  v   -                 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_222566179_   3275 ATGAACAAGCACTTCTCAAAAGAAGACATACAAGCAGCCAACAAACACAT 3324
                         v    i ii  i     v        i      iii     i  i     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_222566179_   3325 GAACACATGCTCAGCATCACTAATCAA 3351
                            v v       i     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (155 / 86)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.42 (46 / 19)  


1489 30.13 8.23 3.24  chr2_222592273_222596232     2606  3468 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_222592273_   2606 GAAGGGTCATCTATACCCATGAATTGGAGAACTCAATGGTAACATGGTAA 2655
                            i i vvi i  iii    i      ii   i   ---- i-  v   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT----AT-TGTTAA 47

  chr2_222592273_   2656 GATGTCAGT-TTTTCCACATTGATGTATGGATTCAAT-CGATCTCGTTAA 2703
                             v  i -i ii   v      v  ii       i- i   i vv v 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_222592273_   2704 AAATTCCAACAGTATGTTT-GTCTAACTTGATAGTCTGATTATAAAATAT 2752
                             i   i v iv v   - ivv  v    i iv     iv      vi
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_222592273_   2753 GTATGAAAATAC--------TAGAATAGCCAAGACAATCATGGGTTAAAA 2794
                         i    i    i --------i           i      v  i---    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAA 194

  chr2_222592273_   2795 GGAAAA-AAAATAGAAAAATTAATCACT---AGATAGCTAAAATTATCAT 2840
                          i i  -   i v i ii i v -    ---vi  vv v   v   ii i
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTAC 243

  chr2_222592273_   2841 AAAGCTA-AGTAATTAAAAGAGCACCATATTAAGGCAAGGATATACAAAT 2889
                                -      i  i v  iiivi  i iivii       v   v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_222592273_   2890 AGATTAATGGAACAAAGCAGAAAGTAAAGGAAAAGACC---ACAT----- 2931
                             i       i i iiv  i   vv  i  v i   ---    -----
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_222592273_   2932 -------GATTTATGACAAAGTTGACAGTGCAGTGCAGTGTAGAAAGGAT 2974
                         -------     vi     i v  v  ivi vi v  i  vi     i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_222592273_   2975 GGTCTTCTTAATAAATAATGCTAAATTTAATGGATGTCTACATATTTTTT 3024
                         i     i i  i    ii    iiiviv v     i? i    ii-----
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC----- 438

  chr2_222592273_   3025 AAATAAATCA---TAATCCCTCAGAT-ACATTAGAAACAAAAACCAACTG 3070
                            vi   v --- iiv   ii vv -   ii v v       ii    v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_222592273_   3071 CAGGTAGATTGTAAACCTAAAATGTGAAAACTAAAACAATAAAATTTTCT 3120
                         v ii i   ii? i       -   i i i       v      i i - 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCT-T 536

  chr2_222592273_   3121 GGAAGAAAATATTGACAACAATTTTTATGGCCTTTGGGAAAAAACAAAGA 3170
                         i        i  v i?ivv   i  ii  i    --  ivv ii   v i
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTT--GGGTTAGGCAATGG 584

  chr2_222592273_   3171 TTTAATAAACAT----TCAAAAG----AGCTCTAAAAAAGGAGATAATAA 3212
                            vv  i i  ----i      ----   ---  v   i  i v    -
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGC---AACAAAAGAAAAAATA- 630

  chr2_222592273_   3213 TTGATAAATCATCCTATATTAAAATTAAGAACATCTATATATCAAAAT-C 3261
                         --       iivv  vi  i        i   v i i iiv     iv- 
  L1M4_orf2#LINE/    631 --GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_222592273_   3262 ATTATTAAGAGGGTATTAAAGCATCATACAGAGTAGGGAAAGATACT--- 3308
                          i   i    ii  ivv  ii  v vi     i i  ii  i   i ---
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_222592273_   3309 -----------CTG------GATTCATAGCCAGAATACATAAAGAACTCC 3341
                         -----------   ------  i ii  v        i           i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_222592273_   3342 CGCAAATCAAGAAGCAAAATATAGACAGATAA----ATAGAAAAATAGTC 3387
                         ii   v    v  -i    ---     i    ----  v?      i v 
  L1M4_orf2#LINE/    779 TACAACTCAATAA-TAAAA---AGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_222592273_   3388 ACA---TATAAATAGACATTTCACATAAAAGAATAGACAAATGACCAATA 3434
                          v --- v i            v vv  i ii   v       i      
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr2_222592273_   3435 AACATATTAAAACATGTTCAATATTATTAGACCT 3468
                          i  i  v    v   i    i  i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (168 / 88)
Gap_init rate = 0.03 (30 / 906), avg. gap size = 3.30 (99 / 30)  


3162 27.88 0.66 0.22  chr2_222674287_222680562     4881  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_222674287_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_222674287_   4931 GGCCATACTGTCCAAGGTAATTTACAGATTCAGTGCCATCCCCATCAAGC 4980
                            v     vi    iv i  i          ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_222674287_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_222674287_   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_222674287_   5079 AACAAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGTC 5128
                                i      vv   i   v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_222674287_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_222674287_   5179 AATAGAACAGAACAGAGACCTCAGAAATAATGCCGCATATCTACAACTAT 5228
                            i   i    iv    vii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_222674287_   5229 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGAGAAAGGATTCCCT 5278
                         i    i  i     ivv  vv  i v  vv      i     i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_222674287_   5279 ATTTAATAAATGGTGCTGGGAAAACTGTCTAGCCTTATGTAGAAAGCTGA 5328
                         v  i  i              v     vv  ?  vi   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_222674287_   5329 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5378
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_222674287_   5379 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5428
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_222674287_   5429 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAA 5478
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_222674287_   5479 CACCAAAAGCAATGGCAATAAAAGACAAAATTGACAAATGGGATCTAATT 5528
                                    vvi    i      v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_222674287_   5529 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGATTCAACAG 5578
                            v v  i i   i  ii vv    i  v    i  vv i v v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_222674287_   5579 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 5628
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_222674287_   5629 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5678
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_222674287_   5679 ACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 5724
                             ----   v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_222674287_   5725 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 5774
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_222674287_   5775 CACTGGCCAT 5784
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.00 (8 / 4)  


2893 26.81 2.34 1.33  chr2_222711537_222713528      602  1500 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_222711537_    602 TGGAAAAACACTCCATGCTCATAGATCAGAAGAATTAATATTGTTAAAAT 651
                               i i ii     i    i   ii     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_222711537_    652 GACCATACTACCCAAAGTAATCTACAGACTCAATCTTATACCTACCAAAG 701
                          i v     v      v i         i    iviv  v    i    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_222711537_    702 TACCAACATCATTCTTCACAGAATTACAGA-AAACT-ATTCTAAAATTTA 749
                          v   i vv v  i  ii     -- iv  -  i  -  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr2_222711537_    750 TATGGAAGCACAAAAGAGCCTGAAGATCCAAAGCAACC---AAGCCAAGA 796
                                iii   ii  v  v   v v     i   i ---  i--    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA--AAGA 196

  chr2_222711537_    797 -GAATAGAGCCTGAGGCATCACATTACCCAACTTCAAACTATACTATAAG 845
                         -   i i  iiv    vv     i v     i      viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_222711537_    846 GCTACAGTAGCCAAAACATCATGGTACTGGTACAAGAACAGACACATAGA 895
                                  ii   i   vii         i i   i i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_222711537_    896 TCAATGGTGTAGAATGGAGAACTCAAAAACAAAACCACACACCTACAACC 945
                                vi      v    iii  i   i   v   i   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_222711537_    946 ATCTGATCTGCAACAAAGTTGACAAAAATAAACAATGGGAAAAGGAC--T 993
                          vi    i v i    i v  v   i vi vv       i    i i-- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_222711537_    994 CCTTATTAGAATAGTTGTGCTGGAATAACTGGGCTAGCCATATGTGGAAG 1043
                          i  - i iv - i v       i i      i-  ?   i   iii   
  L1M4_orf2#LINE/    397 CTTT-TCAACA-AATGGTGCTGGGACAACTGGA-TAKCCACATGCAAAAG 443

  chr2_222711537_   1044 AGGGAACCTGGATCTCTACTTTTCATCATATATAAA--TTAAGTCAAGAT 1091
                          iv   vi    i i    i iv  i      i   --    v    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_222711537_   1092 GAATGAAAGATTTAAGTATAAGACCTCAAGCTATAAAAATCCTAGAAGAA 1141
                          i  v ?   ii   i i     v  v  i        v  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_222711537_   1142 AATCTAGG---AAATACCCTTCTCAACACTGGCCTTGGCAAATAATTTAT 1188
                           iv    ---    ---    vii  vi   vi v     - ii   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chr2_222711537_   1189 -GGCTAAGTCCTCAAAAGCAATGGCAACAAAAACAAAAAATTGACAAACG 1237
                         -i v  v v vi        vvi         i-       v  i   iv
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATT 638

  chr2_222711537_   1238 GGGCCTAATTAAACTAAAGAGTTTCTGCACAACAAAAGATAATATCAGCA 1287
                           i i v  i   v v  i ii  i  ii vv    i  i v     iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_222711537_   1288 GAGTAAACAAGCAACCTACAGAATAGAAGAAAATATTCACAAACTATGCA 1337
                         i   i  v ii     i       i i          ii    ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_222711537_   1338 TCCAACAAAGACCTAATATTCAGAACCTATAGGGAACTTAAACAAATCAA 1387
                           ii i  i iv  vi   i     iv    ii     ivv    v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_222711537_   1388 CAAGCAAAAG-CAAATAACCCCATTAAAACATGGGCAAAGGAT------A 1430
                         i  vv     -          v   ?   v             ------ 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_222711537_   1431 GACACTTCTCAAAAGAAGACATGCAAGTGTCCAAGAAACTTACGAAAAAA 1480
                             i     v        i  i   i  v    v  i vi i     i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_222711537_   1481 TGCTCATCATCACTAATCAT 1500
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (158 / 80)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.83 (33 / 18)  


3195 27.53 0.44 0.44  chr2_222840078_222844865.rev     3389  4296 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_222840078_   3389 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATGTCATGAAAAT 3438
                              ii i  i     i      i v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_222840078_   3439 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3488
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_222840078_   3489 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3536
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_222840078_   3537 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3586
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_222840078_   3587 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGTC 3636
                                i      vv       v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_222840078_   3637 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3686
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_222840078_   3687 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATACCTACAACT 3734
                                i    i--    i  --        vv   i i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_222840078_   3735 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3784
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_222840078_   3785 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3834
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_222840078_   3835 GAAACTGGATCCCTTCCTTACACCTTATAGAAAAATCAATTCAAGATGGA 3884
                            ii    i    v   i     v    v      i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_222840078_   3885 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3934
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_222840078_   3935 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 3984
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_222840078_   3985 AACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAA 4034
                         i            vvi     v    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_222840078_   4035 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4084
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_222840078_   4085 AGGCAACCTACAAAATGGGAGAACATTTTCGCAACCTACTCATCTGACAA 4134
                           i     i   i          v  v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_222840078_   4135 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4184
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_222840078_   4185 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 4234
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_222840078_   4235 TCAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTCATC 4284
                           v        i  vi viii     v  ii         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_222840078_   4285 ATCACTGGCCAT 4296
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2637 21.18 5.65 3.34  chr2_222952330_222954102      503  1281 (492)    L1M4_orf2#LINE/L1      112   908 (0)  

  chr2_222952330_    503 TTTTTTGTAGATACAGACAAACTAATTAACAAATTTATGTGGACAAACAG 552
                                i   v iv     i  i  ivvv     i  i    v vi  i
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_222952330_    553 AGGACT-AGAATAGCTAAAAACAATTTT-AAAAAGAAGAATAAAGTTAGA 600
                         i    i-        i    -    i  -           i      i  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_222952330_    601 GGAATCACATTTTTTGATTTTAAGAATTATTCTGAAGTCACAGTAATCAA 650
                            v     i  iiii    i  i v   i vii   ii           
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_222952330_    651 GACATTGTGGTA------TAAGGAAAGACACAGATATATAT--ATGGAAC 692
                             v       ------      v     ----    v  --      i
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACA----TATAGATCAATGGAAT 306

  chr2_222952330_    693 AGAACAGACAATTCAGAAACAA--CCACAAAAATATGGACAGTCAATTTT 740
                             iv  v i i      i  --   i v vv     v  i ii     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_222952330_    741 TGACAAAGGTGCAAATGCAACTGAATGGAGAAAGGAACGACTTTTCAACC 790
                         i     i     v  vi v i v     i     i vv v         v
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_222952330_    791 AACAGTGTTGAAACAGTTAGACATACAGATGCAAAAAATACATTAA--TA 838
                           ii   i  ii   ii i  i ?v  v        i ---  v  -- i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA---ATGAAGTTG 453

  chr2_222952330_    839 AACCTTGCCCTAAACCTAACACCACCACATACAAAAATTAACTGAAAATG 888
                         i   ----    --   --   -    i               v      
  L1M4_orf2#LINE/    454 GACC----CCTA--CCT--CAC-ACCATATACAAAAATTAACTCAAAATG 494

  chr2_222952330_    889 GGTCATAGAACTAAATGTAA-AGT-----CTATA---TTTTCAGAA---- 925
                          i   ?   v          -  i-----     ---i i i    ----
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_222952330_    926 ---TA--------TTTTCAGGACCA-AGGCTAGTCAAATAGTTT-TTAGA 962
                         ---  -------- i   iv    v-i  i   v   - i    -     
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA 593

  chr2_222952330_    963 TGTGATGCTTAAAAGCACAACTGATAAAATAAAAAATTGACAAATTGGAC 1012
                          i   ii i-          vii i    v       v  i         
  L1M4_orf2#LINE/    594 TATGACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_222952330_   1013 TTCATCAAAAT--AAAACTTTCATTCTGCAAAAGCCATGGTTAAAAGAAT 1060
                                    --        ii v  v    i v  ivi i  i i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_222952330_   1061 GAAAAGGCAATGTAGAGATTGAGAGAAAATATTTGCAAATCACATATCTG 1110
                               i   ivi v   v  i                    i       
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_222952330_   1111 ACAAAAGACCTGCATTGAGAATATAAGAAGAACTTTCAAAACTCAACAAT 1160
                          i  ii   i  i  iv        vi       i i v       i   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_222952330_   1161 ATGAAAACAAAATATTTAAC--AATTTTTAAAAATGAGCAAAAGAGTTGA 1208
                          vi  i     -----    --    ?--       i     i  v    
  L1M4_orf2#LINE/    793 AAAAAGACAAA-----TAACCCAATTW--AAAAATGGGCAAAGGATTTGA 835

  chr2_222952330_   1209 ATAGACATTTCACCAAAGAGGATATATGGTTGGCAAATAAGGACATGAAA 1258
                                    v       i      iiiv    v      v        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_222952330_   1259 AGTTGTCCAACATCATTAGCCAT 1281
                           v  ii        ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (107 / 55)
Gap_init rate = 0.03 (26 / 797), avg. gap size = 2.69 (70 / 26)  


1235 20.00 0.42 0.00  chr2_223018773_223020908.rev      501   740 (1396)    L1M4_orf2#LINE/L1       80   320 (588)  

  chr2_223018773_    501 TCAATGCAACCCCTATCAGAATTCCAA-TACTTTTTTTGCAAATGTAGAA 549
                             i    i        i   i   i- i i         i vi v  v
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chr2_223018773_    550 AAATTCATTCTAAGATTCATGTGGAATCTCAAGGGGCCCTGAATAGCCAA 599
                           ii v  i    i      i     viv      i   v          
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_223018773_    600 AACAAATTTGGAAAAGAAGAACAAAGTTGGAGCATTCACACTTCCTGATT 649
                              vi   i                     v i          ii   
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_223018773_    650 TCAAAACATATTACAGAGCTACAGAAATCAAAACAATGTGGCACTGTCAC 699
                                v  i    i        v      i   i     i    v  i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_223018773_    700 AAGCACAGACAAATAGACCAACGAAATAAAATAGAGAGCCC 740
                            v i     v     i   i i    i   v     i  
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

Transitions / transversions = 2.20 (33 / 15)
Gap_init rate = 0.00 (1 / 241), avg. gap size = 1.00 (1 / 1)  

2736 21.06 1.00 0.66  chr2_223018773_223020908.rev     1042  1644 (492)    L1M4_orf2#LINE/L1      304   908 (0)  

  chr2_223018773_   1042 AAAAAAATAGAGAGCCCGGAAATAAACCCATG--TGTATAATCAAATGAT 1089
                           v i   v     i  i             i-- v   ii    v    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_223018773_   1090 CTTTGACAGGGGTGCCAAGGTCACTCAAGGGGGAAAGGACAGAGAAGTGG 1139
                         i  i    i          ii  i    v        i i  vvvvv vi
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_223018773_   1140 AGAAATGGTACTGAGAAAACTGGATATACATGTGCAAAAGGATGAAGCTG 1189
                          v       i   i  v         ?v  ii        i      i  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_223018773_   1190 -ACTTTTATTTTATACCATATACAAAAATTAAATCAAAATGAATTAAAGA 1238
                         -  iii  ii i i                  v        i  i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_223018773_   1239 CCTAAAAGTAAGACCTAAAATTATACAACTCATAGAAGAAAATATATAAG 1288
                               v      v      i    v     v          i   vi? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_223018773_   1289 TGAAGCTTCATGACACTAGACTTGGCAATGATTTCTTGGATACAATACCA 1338
                          i  v    i    vi i ii v       i      i    ii i    
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_223018773_   1339 AAAGCACTGGCAACAAAAGCAAAA-TAGACAAATGGGACTGCATCAAACC 1387
                                vi          v    -    i    v     v       vi
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_223018773_   1388 TAAAAACTTCTCCACGTTGAAGGACACAATCAACATAATGAAAAGGCAAC 1437
                                  i vii v ii        v     v v i       i    
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_223018773_   1438 CTATGGGATGGGAGAAAGTATTTGCAAATCATATATTT-ATGGGGG-TTA 1485
                          i ii i          i                  i -  ii   -i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_223018773_   1486 ATATCCAGAATATGTCAGGAATTTCTACAATGACTCAATGACAAAAAAAT 1535
                         i            i v i   i ii     ---      i i     i i
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAA---CTCAATAATAAAAAGAC 800

  chr2_223018773_   1536 TTAATAACCTAATTAGAAAATGGGCCAAGGCATTGAACAGACATTTCTCC 1585
                         v-       i    ?i         v    vv     i            
  L1M4_orf2#LINE/    801 A-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_223018773_   1586 AAAGATGATATACAAATGGCTAACGGGCATATGAAAAGTTGCTCAATATC 1635
                              v              i  iii   i        v       i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_223018773_   1636 ACTAATCAT 1644
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.00 (82 / 41)
Gap_init rate = 0.01 (7 / 605), avg. gap size = 1.43 (10 / 7)  


3200 26.56 0.55 0.88  chr2_223274103_223280500     4996  5906 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_223274103_   4996 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5045
                              ii    i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_223274103_   5046 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_223274103_   5096 TACCAATGACTTTCTTCACGGAT-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   iivi i  i  ii i  v-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_223274103_   5144 TATGGCACCAAAAAAGAGCCTGCCTTGCCAAGACAATCCTAAGCAAAAAG 5193
                              v viiv  ii  v  v vv v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_223274103_   5194 AACAAAGCTAGAGGCATCATGCTACCTCAAACTTCAAACTATACTACAAG 5243
                                i i    vv   ii  v  i--  i      viv        i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCC--AATTTCAAAACTTACTACAAA 246

  chr2_223274103_   5244 GCTACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGA 5293
                                   i   i    ii        vi iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_223274103_   5294 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAA 5341
                         i        i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_223274103_   5342 CCATCTGATCTTTGACAAACCTGACAAAAACAAAAAATGGGGAAAGGATT 5391
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_223274103_   5392 CCCTATTTAACAAATGGCGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5441
                         vi  v  i         i       v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_223274103_   5442 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5491
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_223274103_   5492 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAATAAA 5541
                            i ?    i       v   v       i      v  i     v   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_223274103_   5542 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGAC 5590
                           v    ?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_223274103_   5591 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGTATC 5640
                           vi            vvi          vv        i    v v ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_223274103_   5641 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5690
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_223274103_   5691 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 5740
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_223274103_   5741 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 5790
                         i  i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_223274103_   5791 AAAAATCAAACAACCCCATCAAAAAGTAGGCGAAGGATATCAACATGTAC 5840
                             iv    i     v  i?    i i   i      v v  i vii i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_223274103_   5841 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAAATGCT 5890
                              v        i  vi viii     i ii          i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr2_223274103_   5891 CATCATCACTGGCCAT 5906
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


1875 23.45 1.45 4.73  chr2_223368069_223370219.rev      497  1046 (1105)    L1M4_orf2#LINE/L1       59   590 (318)  

  chr2_223368069_    497 TCTACAAATTAAACTATAAGCTAATTCCAATCAAACAGCAATCCCAATCA 546
                           iv      i v   i i----    ------   -        v    
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAG----ATTC------AAC-GCAATCCCTATCA 97

  chr2_223368069_    547 AAATCCCAGGAGGGTTTTTTGGTGTGGAAATTGTTAACCTGATCCTAAAA 596
                                  vv vv       ---ii       vi  v            
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTG---CAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_223368069_    597 TGCATATGGAACTGATAAGGACGTGGAATAATCAAAACACCTGTGAAAAA 646
                          v         v  vv i    vii     ii       viiv       
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_223368069_    647 CAATACCACCAACAAAGTTTGAAGACTAACAGTATCTGATTTCAAGAATT 696
                         v  v ------        v  i    v   v vi ii       i v  
  L1M4_orf2#LINE/    195 GAAGA------ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_223368069_    697 ATTATAAAGCTATAATAATCAAAACAACAGGGTACTGGCATCAAGATAGA 746
                          i  i       i i       i   iiiv           v i      
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_223368069_    747 TGAACAGATCAATGGCACAGACTAGAGAGTCTAGAAATAAACCCATGCAT 796
                         iiv i          v i   v v       i              i   
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_223368069_    797 ATATGGGCAATTGATATTTGATAAAGGCACAAGGGCAATGCAGTAGAGAG 846
                         v     v        v  i  i  i  ii v i i v  v  i i i  i
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_223368069_    847 CAGATAGTGATCTACCAAAAAA--GAGCTGGAACCATTGGATTATATATA 894
                         vii     vv i --   v   -- v     i  v i     - ?vi i 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTT--CAACAAATGGTGCTGGGACAACTGGAT-AKCCACA 435

  chr2_223368069_    895 TGCAGAAAAATGGATTTAGAC----ACT--GTACCACACACAAAAATTAA 938
                             i  i    i v  i   ----  i--ii    i i           
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_223368069_    939 CCCTAAATAGATCATAGATCTATATGGAAAACCTAAAACTATTAACACTG 988
                          i v    i     ?   i   v   v  i v          -  v   v
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTC 534

  chr2_223368069_    989 GTAGGAGAAAATATAGAAGAAAATTTTTGTGACCTTGGATTAAGCAAAGA 1038
                         v   i      i    i? v    i  i          i   i    v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_223368069_   1039 ACTTTTTT 1046
                         --   i  
  L1M4_orf2#LINE/    585 --TTTCTT 590

Transitions / transversions = 1.42 (74 / 52)
Gap_init rate = 0.02 (12 / 532), avg. gap size = 2.83 (34 / 12)  

1104 22.63 3.98 0.92  chr2_223368069_223370219.rev     1339  1665 (486)    L1M4_orf2#LINE/L1      572   908 (0)  

  chr2_223368069_   1339 GATTAAGCAAAGATTTTAAAGATACGACACCCAA--CACAATCTATTAAA 1386
                          i   i    v i   ivv     i      v  --     v v iv   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr2_223368069_   1387 ---AAAATGGATACAATTA-ACTTCATCAAAATTAAAA-CTTCTGCTCTT 1431
                         ---     i    -    i-                  -   i  iv   
  L1M4_orf2#LINE/    622 GAAAAAATAGATA-AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_223368069_   1432 CAAAAGACATTGTTAAGAGATTGAAAGGATAATCCATAGACTGAAAGAAA 1481
                             i    i i i    i v     i  i  i   i   v  ii     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_223368069_   1482 AATCTATACAAAGCTCATCGCTGATAAATGACTTTATATCTAGAATACAC 1531
                          - v v i    v vi  vv       iv     -i    i      i i
  L1M4_orf2#LINE/    721 A-TATTTGCAAATCATATATCTGATAAGGGACTT-GTATCCAGAATATAT 768

  chr2_223368069_   1532 AA-GAACTCTCAAAACTCAGCAATAGGAAAACAAGCAATCCAAT-AAAAA 1579
                           -       i v      ii    ii  i    ii  i     -?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_223368069_   1580 CCAGGCAAAAGATTTAAACAGATACTTCAACAAGGAA----TAGAGATGG 1625
                         vii      i     i  i   i i   vv   i   ----  v i    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_223368069_   1626 CAACTAAGCACATGAAAAGATGCTCACGGTCATTAGTCAC 1665
                          v v                      vvi   ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (47 / 26)
Gap_init rate = 0.03 (10 / 337), avg. gap size = 1.60 (16 / 10)  


2850 22.58 3.55 5.44  chr2_223438976_223440811.rev      501  1346 (490)    L1M4_orf2#LINE/L1       79   908 (0)  

  chr2_223438976_    501 TTCAGTGCAATTTTTATCACAATTCCAATGACATTTTTCACATAAGTAGA 550
                             ii     iii     v   i   iivi v     ii  v  i v  
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chr2_223438976_    551 AAAAACAATTCTAAAATTAACATGGAAACAAAAAAGACCCTGAATAGCCA 600
                         v  ivii  i        v i       iiv  ii     v         
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr2_223438976_    601 AAACAATTTTGAGAAAGAA---CAAAGCTGGAG-----ACAGTTGCTGAT 642
                                i    i      ---     i     -----   v  v ii  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr2_223438976_    643 TTCAAACTATGTTACAAAGCTATAGTAGTGAAAACAGGATAGTACGTGCA 692
                               viv ii          i    i v  i    vi i    vv   
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_223438976_    693 TAAAACTGAACACATAGACCAATGGAACAGAAT-AATATGCCCATAAATA 741
                            iiv ii   i     i        i     -i v - i   v     
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGA-GTCCAGAAATA 327

  chr2_223438976_    742 AACCCATGCAAATAAATAGTCAACTAATTTTTGACAAAAGCACCAAGAAC 791
                                i  vv  -- i     i i     i     ii ii      v 
  L1M4_orf2#LINE/    328 AACCCATACATTTA--TGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_223438976_    792 ATGCAATGGGGAAAGGAAACTCTCTTTAACAAATGATGTTGGGAAAATTG 841
                           v            i v v   i  i        i  i     v  i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_223438976_    842 AATATCTACATGCAAAATAATAAAAGTGGATCCTTGTTTTATAACATATT 891
                         i   ? i          v   i  iv    i  i iii i i v     v
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr2_223438976_    892 CAAAAATTAACTTGAAATAAATTTAAGAATTACATATAAGATCTAAGACC 941
                                     ii    ii  iv?   vi  v  i     v    i  i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr2_223438976_    942 ATAAAATTCCTAACAGAAAACATGGCCAAAAAGCTCTTTGTA---TTGG- 987
                               i  i  iv         i v?iv   --    i  i---    -
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGG 573

  chr2_223438976_    988 --AAGCAATGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGC 1035
                         -- i      i   i  ------------------------------i v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTT------------------------------AGA 593

  chr2_223438976_   1036 CATGACACCAAGAGCACAAGCAACAAAAGCAAAAATAAACAAGTGGGACT 1085
                         i          i                 v       i i  i v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_223438976_   1086 ACATCAAACTAAAAAGCTTCTGCAC-------AACA--ATCAAAAAAAGG 1126
                         v       v v    i   i  ii -------i   --     i   iv 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_223438976_   1127 AAGAGGCAGCTAACAATAGAATGGGAGAAAATATTTGAAAACCATATATC 1176
                           i  i  i iv   ---                   v   i        
  L1M4_orf2#LINE/    694 AAAAGACAACCCACA---GAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_223438976_   1177 CAATAAGGAGTCAATATCCAAAAAATATAAAGAACTCACACAACTCAATA 1226
                         ii      iiiivi      i  v             vi           
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_223438976_   1227 GCAAATAAATGAATAAATAAATAATCTGATTAAAAAATGTGCAAAGGTCC 1276
                         --------  i  v i i      i ii   ?       v       vii
  L1M4_orf2#LINE/    791 --------ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_223438976_   1277 TGAATGGACATTT-TCCAAAGAAGACTTACA----GTCAATGGATATATG 1321
                              i       -           iv    ---- i    iiii i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_223438976_   1322 AAAA-ATGCTCAACATGACTAATCGT 1346
                             -           v ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.34 (131 / 56)
Gap_init rate = 0.02 (16 / 830), avg. gap size = 4.75 (76 / 16)  


2996 26.72 1.88 1.22  chr2_223540882_223542801      527  1428 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_223540882_    527 TGGAAAAACATTCTGTGCTCATGGGTTGGAAGAATCAATATTGTTAAAAT 576
                               i i  i ii  i      i        v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_223540882_    577 GGCCATACTGCCCAAAGCAATCTACAGATTCAGTGCTATTACTATCAAAC 626
                            v     v      vii             ii  v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_223540882_    627 TACCAA-TGTCATTTTTCACAGAACTATAAAAAACTAGTC-TAAAATTCA 674
                          v   i-  i -     ii     v - i v  i  ii  -         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chr2_223540882_    675 TGTGGAACCAAAAAAGAGCCCAAATAACTAAAAGAATCCCAAACAAAACC 724
                          i     viiv  ii  v  vi    i i    v    iii  v  i vv
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_223540882_    725 AACAAGGCTGAAAGCATCACTTTACCCAACTTCAAACTACACTACAAGGC 774
                              i i  i i vv    vi v     i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_223540882_    775 TACAGTAATGAAACCAACATGATGCTGGTACAAAAAAAGACACACAGACC 824
                                  v  iv  iii  i i    i i  ii v     i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_223540882_    825 TATGGAACAGAATAGAGAACCCAAACATAAAGCCACACATCTATAATCAT 874
                         v      i     v    ii   i v     v   i    i   ii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_223540882_    875 CTGATCTTTGACAAAGTTGGCAAAAATAAGCAATGGGGAAAGGACTCCCT 924
                         i    i  i     i v  v   i vi vv            i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_223540882_    925 AGTCACTAAATGGTGCTGGGATAACGGGCCATCTATATGCAGAAAAATGA 974
                         vv   vi              i   v  vi ? i i     i  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_223540882_    975 AGCTGGACCCCTACTTATCACCATAGGCAAAAATTAA-TCAAGATAAATT 1023
                           i           i vv       vi          -    i  ii  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_223540882_   1024 AACAACTTAAATGTAAGACCTCAAACTATAAAAATCCTAGAAGAAAATCT 1073
                          ?vi  i           v  v           v  i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_223540882_   1074 AGG---AAATACCATTTTG-GACATCAGTCTTGACAAACGATTTATGGCT 1119
                            ---    ----i  i -   v ii vi v i   vv v  iv i v 
  L1M4_orf2#LINE/    549 AGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_223540882_   1120 AAGTCCTCTAAT---CAATTGCAACAAAAACAAAAATTAACAAGTGGGAT 1166
                          v v vi v  v---   --         iv      vi i  i v   i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_223540882_   1167 CTAATTAAACCAAAAAGCATCTGCACAGTAAAAGAAACTATCAACAGAGT 1216
                         i v  i   viv    i v i  ii vvi   i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_223540882_   1217 AAACAGACAACCTACAGAATGGGAG----TACTTGCAAACTATGCATCCA 1262
                         i  v        i            ----  i       ii  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr2_223540882_   1263 ACAAAGGTCTAATATTCAGAGTCTGTAAGGAACTTAAAAAA---AATTAC 1309
                          i  i  v  vi   i    i v i   i     ivv v  ---   v i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_223540882_   1310 AAGCAAAAGACAAATAATCCCATTAAAAAGTGGGCAAAGTCTGTGAACAG 1359
                           ---            i  v   ?    i         vv v    i  
  L1M4_orf2#LINE/    793 AA---AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_223540882_   1360 ACACTTCTCAAGAAAAGGCACACAAGCGGCCAACAAGCATATGAAAAAAT 1409
                            i     v i i   ii i    ii      i     i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_223540882_   1410 GTTCATCATCACCAATCAT 1428
                          i   v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (148 / 90)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.15 (28 / 13)  


3070 27.10 1.22 0.77  chr2_223702311_223707988     4283  5186 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_223702311_   4283 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCTTGAAAAT 4332
                              ii i  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_223702311_   4333 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4382
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_223702311_   4383 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4430
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_223702311_   4431 TATGGAA-TGAAAAAAGAGCCCACATT-GCCAAGTCAATCCTAAGCCAAA 4478
                                -  v  i-- ii    v v -     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_223702311_   4479 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 4528
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_223702311_   4529 GCTACAGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGAGATATAGA 4578
                                   i   i    ii     v   i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_223702311_   4579 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAA 4626
                         i        i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_223702311_   4627 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCCATGGGGAAAGGATT 4676
                         ii vi    i  i     ivv  vv  i v  vv v          i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_223702311_   4677 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 4726
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_223702311_   4727 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 4776
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_223702311_   4777 GATTAAAGACTTAAATTTTAGACATAAAACCATAAAAACCCTAGAAGAAC 4826
                            i ?    i     v v   vv      i      vi i        v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_223702311_   4827 ACCTAGGCA-ATACCATTCAGGATATAGGCATGGGCAAGGACTTCATGTC 4875
                           v    ?i- v i -   iv  iv v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_223702311_   4876 TAAAACACCAAAAGCAATGGCAACAAAAGCTAAAATTGACCAATGGGATC 4925
                           vi            vvi          vv     v  iv   v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_223702311_   4926 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTG 4975
                          v  i   v v  i i   i  ii vv    i  v    ii vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_223702311_   4976 AACAGGCAATGTACAGAATGGGAAAAAATTTTTGCAATCTACTCATCTGA 5025
                           v  i   ivi           i     v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_223702311_   5026 CAAAGGGCTAACATCCAGAATCTACAAAGAACCCGAAAAAATTTACAAGA 5075
                         i  i  i  vii         v  i       i vv v  v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_223702311_   5076 AAAAAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAAGAGACAC 5121
                             i    ----   v  i?    i     i      v    v     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_223702311_   5122 TTCTCAAAAGAAGACATTTATGCAGCCAACAGATACATGAAAAAATGCTC 5171
                              v        i  vi viii     i iii         i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_223702311_   5172 ATCATCACTGGCCAT 5186
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


4047 15.47 8.95 3.37  chr2_223729645_223732270     1304  2163 (463)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_223729645_   1304 TGCAAAGTCATTCTGTGTTCATGGATTGGGAGACTCGATATTGTTAAGAT 1353
                           v    vi  i ii              i     ii             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_223729645_   1354 GGCAACACTCCTAGATTTGATCTACAGACTCAATGCAATTGGTATCAAAC 1403
                              i     ivi v            i    i     ivv       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_223729645_   1404 TTCCAACTGCCCTTTTT--AAAAA-------------------------- 1425
                          i   i     i     -- i   --------------------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_223729645_   1426 --------------------AATAGCCAAGACAATCTTGAAAAGGAGAAA 1455
                         --------------------         i             i  ii  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_223729645_   1456 TAAAGTTGGATGACTTATGCTTTCTGATTTCAAAGCTTAGTGCAAGG-TG 1504
                         i         v    i ii   i ii        i    v i   i - i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_223729645_   1505 CAGTATTCAAAACAGTGTGGTACTGAAATAAGGCTAGACATATAGATCAA 1554
                              v    i              iv      v                
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_223729645_   1555 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATATATCTATGGTCAATT 1604
                                                            i  i           
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_223729645_   1605 GATTTTCCACAAGAATACCAAGGCCATTCAATAGGGAAAGAATAATCTTT 1654
                                v     ii i     i         i           i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_223729645_   1655 TCAACAAATGGTGTGGGGACAATTGGATACCCACATGTAGAA-AATAAAT 1703
                                      iv       i      ?       i i  -   i  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_223729645_   1704 TTGGACCTCTACCTCACATCACACATGAAACTTTAGCTCAAAATGGATCA 1753
                                i          i  i i ii   v  - i              
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATT-AACTCAAAATGGATCA 499

  chr2_223729645_   1754 AGAAACTAAATGGAAGAGCTACAACT---------TTAGAAGGAAACATA 1794
                         ?ii v       v        v    ---------       i       
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_223729645_   1795 GGTATAAATT---ATG-----------GGCAACAATTTCTTAGTTATGAC 1830
                           ?i     i---i  -----------     iii        v      
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_223729645_   1831 ACCAAAAGCACA-GCAACAAAAGAAAAAAGAGATAAACTGGCCTTCATCA 1879
                                     -                v       i   v        
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_223729645_   1880 AAATTAGAAACTTTTATGCATCAAAGGACACTATCAAGAACATGAAAAGA 1929
                               i        i   v                    vi        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_223729645_   1930 CAACTCA--GAACGGGAAAAAATGTT-GCCAATCATCCAGAATGATTTAG 1976
                             i  --   i    i     i  -  v      -------------i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-------------A 736

  chr2_223729645_   1977 TATCCAGCATATATAGAGAATTTAGTATCCAGAATAAATAGGGAATTCTT 2026
                             ii------   ii i i  -            v   ii   i    
  L1M4_orf2#LINE/    737 TATCTG------ATAAGGGACTT-GTATCCAGAATATATAAAGAACTCTT 779

  chr2_223729645_   2027 ATAACACAACAATAAAATGACAAACAAACCAACTGAAAAATAGGCAAAGG 2076
                          i   v   i       v      i  v    i ?      i        
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_223729645_   2077 ACTTGAATAGATGTTTCTTCAAAGAAGAAATACAAATGGCCAGAGATAAG 2126
                          i         ii     i         v             ---     
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA---ATAAG 876

  chr2_223729645_   2127 AGCAAAGGTATAGAGTATGCACAGTTTCAAATGAGCC 2163
                         vi  ---- iv i  -    v  iiv   ????????
  L1M4_orf2#LINE/    877 CACA----TGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.79 (95 / 34)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 6.24 (106 / 17)  


2897 26.61 3.40 0.57  chr2_223932006_223935768.rev     2389  3271 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_223932006_   2389 TGGAAAAACATTCCATGCTCATGGATAGGAAGGATCCATATCATAAAAAT 2438
                               i i  i     i        v     iv iv    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_223932006_   2439 GGCCATACTGCCCAAAGCAATTTACAGATTCAATTCTATTCCTATTGAAC 2488
                            v     v      vii  i           iv v  i     ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_223932006_   2489 TACCATTGATATTCTTCATAGAATTAGAAAAGAATATTTTAAAATTCATA 2538
                          v   viviiv  i  iii    v v  v   vvv  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_223932006_   2539 TGGAACCAAAAAAAGAGCCCA-AATAGCCAAGACAATCCTAAGCAAAAAG 2587
                              -- viv  i ii    -         i      i i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_223932006_   2588 AACAAAGCTGGAGAAATCACGCTACCTGATTTTAAATGATACTACAAAGC 2637
                                i     i v    i  v  ii    i   vvv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_223932006_   2638 TACAGTAACCAACACAGCATGGTACTGGCATAAGAACAAACACATAGACC 2687
                                 i   v    ii               i i i   i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_223932006_   2688 AATGGAACAGAATAGAAAACCCAGAAATAAAACCACACACCTACAACCAA 2737
                                i     v  i ii           v   i   ii  iiii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_223932006_   2738 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTACCT 2787
                         i    i  i     ivv  v   i v  vv            i  vii  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_223932006_   2788 CTTTAATAAGTCGCTCTGGGAGAACTGGCTAGCCATATGCAGAAAATTGA 2837
                         i  i  i  i v iv      v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_223932006_   2838 AACTGGACCCCTTCATAATACTGTATATAAAAATCAACTCAAGATGGATT 2887
                          ii         v v v i  ii    i      i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_223932006_   2888 AGAGAGTTAAATATAAAACCCAAAACTATGAAAACCCTAGAAGAAAATCT 2937
                          ?   vi     i   i v i        i   vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_223932006_   2938 AAGCAATACTATTCAGGAC-------------ATAGATTTCAT-GATGAA 2973
                          i ?ivv v v   iv   -------------  i -    v -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGAT-AT 596

  chr2_223932006_   2974 GATGCCAAAAGCAATTGCAATAA--GCAAAAATTGACAAACAGGATCTAA 3021
                           ii         vvv    i  -- v      v  i   iv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_223932006_   3022 TTAAACTAAAGAGATTCTGCACAGCAAAAGAAATGATCATCAGCATGAAC 3071
                          i   v v  i iv  i  ii vv    i  v iv    vv ivi    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_223932006_   3072 AGACAA--------ATGGGAGAATATTTTTGCAATCTATTCATCTGACAA 3113
                               --------         v  v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_223932006_   3114 AGGTCTAATATCCAGTATCTACAAGGAACTTAAACAAATTTACAAGAAAA 3163
                         i  v  vi       v  v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_223932006_   3164 A-----ATAACCCCATTAAAAAGTGGGCAAGTGATATGAACAGATACTTT 3208
                          -----       v   ?    i       iv   v    i   i i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_223932006_   3209 TCAAAAAAAAGACATACATGTGGCCAAAAAGCATATGAAAAAATGCCCAA 3258
                           v   i  -  i     vi       v     i       i    i   
  L1M4_orf2#LINE/    847 TCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_223932006_   3259 TATCACTGATCAT 3271
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (137 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.50 (35 / 10)  


2288 25.98 9.58 0.92  chr2_223968160_223969862.rev      491  1252 (451)    L1M4_orf2#LINE/L1       81   908 (0)  

  chr2_223968160_    491 CAATGTAAT---TATCAAAATACCAA-TGTAATTTTTCACAAAAGTAGG- 535
                            i i   ---         v   i-  iv-     ii  i  i v i-
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGAC 129

  chr2_223968160_    536 AAATAAATCCTAAAATTTGCATAGAACCACAAAAGACCTTGAATAATCAA 585
                           iivi           iii  i   vii   ii    iv     ii   
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_223968160_    586 AGCAATCCTAAGCAAATAGAACAAATCTGGAGGCATCACACTACATGACT 635
                          i     i i iv  iv        vi      vv       v vii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_223968160_    636 TCAAAATATATTACAAGGCTATAGTAACCAAAACAGCATAGTATTGATAT 685
                               iv  i     i    i     i   i    ii i   i  ii  
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_223968160_    686 TAA-ATAGATGCATAGACCAATGGAACAAAACAGAGAA--CTGAAAT--- 729
                         v i-     iii     i        i i  iv    i-- v     ---
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_223968160_    730 -CTAAATATTCATAGCCAATTAATCTTTGATAAAGCTACCAAGAGCATAC 778
                         - i v i   i  i i     i  i  i  i  i v i      v   v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_223968160_    779 ATTGGGGAAAGGACATTCTATTCAATAAATGGTGCTGGTAAAACTGGATA 828
                          v         i i v   v     i            v v         
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_223968160_    829 CCCCTATGCAGAAGAATGAAACTGGACTCCTATCTCTCACCATGTACGAA 878
                         ?  vi     i         ii     i    i   v      i   i  
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_223968160_    879 AGTCAACTTAAGATGAATTAAACACTTAAACATAAGA------------- 915
                          i i    i  i   i  i ? v  i    ii     -------------
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_223968160_    916 ----------------CAT---------------------TAGTCTAGGC 928
                         ----------------   --------------------- i vi     
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_223968160_    929 AAAGATTTTATGGCTAAGATCTCAAAAGCA-AGGCAACAAAAACATAAAA 977
                           v i   iv i v  v  ivi        - i         iv -    
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA-AAAA 628

  chr2_223968160_    978 TAGACAAATGGGACTCTATTAAAGTAAAAAGCTTCTGCACAGCAAAGGAA 1027
                             i    v     ii  i   i v    i   i  ii vv       v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr2_223968160_   1028 ACAAT-AAGA--GTGAAGAGACAGCCTCTTGAATGGGAGAAAATATTTGT 1074
                           v  -    --     i     i  iviv                   i
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_223968160_   1075 A--CCCTATTAATCTAACAGGAGACCAATGACCAGAAAATACAAGGAACC 1122
                          --i v   --    i i i i   ivi iv      v   i  i    i
  L1M4_orf2#LINE/    729 AAATCATAT--ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_223968160_   1123 CAAACAACTCAATGGCAAAAA-ATGTATAACCTCATT-AAAAATGGGGAA 1170
                          vv          iii     - iiv      iv   -         v  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_223968160_   1171 AAGATATGAATAGACATTTTTA-AGAGAAGACATAAAAATGGTTGACAGA 1219
                          i   v             i v- i      i   v      iii i ii
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_223968160_   1220 TATATTTTTAAAA--TGTTCAATACCACAAATCAT 1252
                         i i  v---    --  i    i i  ????????
  L1M4_orf2#LINE/    877 CACATG---AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.44 (139 / 57)
Gap_init rate = 0.02 (20 / 828), avg. gap size = 4.00 (80 / 20)  


2569 28.19 1.50 4.18  chr2_223978057_223981230.rev     1750  2682 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_223978057_   1750 TAGAAAAACATTCCACGCTCACAGATAGGAAGAATCAATATATTAAAAAT 1799
                          i    i i  i   i i   ii   v      v i     vv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_223978057_   1800 GGCCATACTGCCCAAAGTAATTTATAGATTTGATGCTAACCTCATTGAGC 1849
                            v     v      v i  i  i     ii i  v v  ii  ii iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_223978057_   1850 TACCATTGATTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATCTCAT 1898
                          v   viviii  i  ii     v v  v  i-  - iii    vi    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_223978057_   1899 ATGAAACCAAAAAAGAGCCCATATAACCAAGATGGTCCTAAGCAAAAAAA 1948
                            i  viiv  ii  v  viv   i    i iii  i i ---------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--------- 190

  chr2_223978057_   1949 AAAAAAAAGAAAAAAAGAAAGAAAGAAAAGAAAAGTAAAAAAGCTGGATG 1998
                         -    i     v   --------------------------- i    v 
  L1M4_orf2#LINE/    191 -AAAAGAAGAACAAA---------------------------GTTGGAGG 212

  chr2_223978057_   1999 CATCATGCTACCTGACTTCAAACTATACTACAAGGCCACAGTAAACAAAA 2048
                         vv   ii  v  ii i      viv        i  i       v   i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr2_223978057_   2049 CAGCGTGATACTAGTACCAAAACAGATATATGGACCAATGAAACAGAACA 2098
                            i   i    i i iv ii i   i    i  i     i  i    iv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_223978057_   2099 GAGGCCTCAGAAATAATGCCACACATTTACAACCATCTGATCTTTGACAA 2148
                            ivii         vv   i       iiii  vi    i  i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_223978057_   2149 ACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGT 2198
                         ivv  v   i v  vv            i  vvi  v  i  i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_223978057_   2199 GTTGGGAAAACTGGCTAGCCATATGCATAAAACGGAAACTGGACCACTTC 2248
                          i     v      v  ?   i     v  i vv   ii      v  v 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_223978057_   2249 CTTACACCTTATACAAAAATTAA-----GATGGATTAAAGACTTAAACAT 2293
                           i     v              -----i      i ?    i    ii 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_223978057_   2294 AAGACCTAAAACCATAAAAACCCTGGAAGAAAACCTAGGCA-ATACCATT 2342
                             v       i      vi i i         v    ?i- v i -  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TT 561

  chr2_223978057_   2343 CAGGACATAGGCATGGGCAAAGACTTCATGACTAAAACACCGAAAGCAAT 2392
                          iv   v v  vv i     v ii   v iiv  vi     i      vv
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_223978057_   2393 GGCAACAAAAGCCAAAATTGAAAAATGGGATCTAATTAAACTAAAGAGCT 2442
                         i          vv     v  v    v   ii v  i   v v  i i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_223978057_   2443 TCTGCACAGAAAAAGAAACTATCATCAGAGTGAACAGGCAACCTACAGAA 2492
                          i  ii vvv   i  v       vv i      v  i     i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_223978057_   2493 TGGGGGAAAATGTTTGCAATCTATCCATCTGACAAAG-------ATCCAG 2535
                             i      i       vii  vi      i  i -------      
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_223978057_   2536 AATCTACAAGGAACTTAAACCAATTTACAAGAAAAAAACAAGCAACCTCA 2585
                            v  i  i     ivv  v v iv i  v     i    ii    iv 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_223978057_   2586 CCAAAAATTAGGAGAGGGATATGAACAGACACTTCTCAAAAGAAGACATT 2635
                         ii?    v i  vi i    v    i     i     v        i  v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_223978057_   2636 TATGTGACCAACAAACATATGAAAAAAAGCTCATCATCACTGGTCAT 2682
                         i vi  i    i  i  i       i v     v     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (157 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 6.62 (53 / 8)  


3253 27.01 0.55 0.44  chr2_224020240_224026640     5003  5909 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_224020240_   5003 TGGAAGAACATTCCATGCTCATGGATAGAAAGAATCAATATCGTGAAAAT 5052
                              ii i  i     i        v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_224020240_   5053 GGCCATACTGCCCAAGGTAGTTTATAGATTCAATGCCATCCCCATCAAGC 5102
                            v     v     iv ii i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_224020240_   5103 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5150
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_224020240_   5151 TATGGAACCAAAAAAGAGCCCGCATTTTCAAGTCAATCCTAAGAAA-AAG 5199
                                viiv  ii  v  v v  vvi   iv     i i i   -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_224020240_   5200 AAGAAAGCTGGAGGCATCACACTACCTGACTTCAAACTAGACAACAAGGC 5249
                           v    i      vv       v  ii i      vivv  v    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_224020240_   5250 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATATAGACC 5299
                                 i   i    ii  i      i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_224020240_   5300 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5349
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_224020240_   5350 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5399
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_224020240_   5400 CTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAAGCTG 5449
                         i  i  i              v      v  ?   i   i i  i i-  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TG 447

  chr2_224020240_   5450 AAACTGGATCCCTTCCTTACATCTTATACAAAAACTAATTCAAGATGGAT 5499
                           ii    i    v   i   i v          i   i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_224020240_   5500 TAAAGACTTAAATGTAAGACCTAAAACCCTAAAAACCTTAGAAGAAAACC 5549
                         i ?    i           v       iv     vi             v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_224020240_   5550 TGGGCA-ATATCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5598
                          i  ?i- v   -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_224020240_   5599 AACACCAAAAGCAATAGCAACAAAAGTCAAAATAGACAAATGGGATCTAA 5648
                         i            vv           vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_224020240_   5649 TTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAGTGAAC 5698
                          i   v v  i i   i  iiivv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_224020240_   5699 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACGCATCTGACAA 5748
                           i     i                 v       vii iii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_224020240_   5749 AGGGCTAATATCCAGAATCTA-AAAGGGCTTAAACAAATTTACAGGAAAA 5797
                         i  i  vi          v  -    ii  ivv    v iv i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_224020240_   5798 AAGCAAACAACCGCATGAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5847
                          ii    i    vv  v?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_224020240_   5848 TCAAAAGAAGACATTTATGCAGGCAACAGACACGTGAAAAAATGCTCACC 5897
                           v        i  vi viii v   i ii   i      i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_224020240_   5898 ATCACTGGCCAT 5909
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


3073 25.22 1.44 1.00  chr2_224037330_224042250     3526  4429 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_224037330_   3526 TGAAAACACATTCCAGGCTCATGAATTGGAAGAATTAATATCGTGAAAAT 3575
                           i   v i  i   v i     i         v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_224037330_   3576 GACAATGCTGCCAAAAGCAATCTACAGAATCAATGCAATTCCTATCAAAA 3625
                          i    i  v  v   vii         v    i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_224037330_   3626 TACCAACATCATTTTCCACAGAATTAGAAAAAGCAATCTTAAAATTCATA 3675
                          v   i vv v    iii     v v  v  ivii   i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_224037330_   3676 TGGAACCAAAAGAGAGCCTGAATAGCCAAAACAGTCCTAAGCAAAAAGAA 3725
                              viiv   i  v  v              i  i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_224037330_   3726 CAA-TCTGGAGGCATCACATTACCTCACTTCAAATTATACTACAAGACTA 3774
                            -vi      vv     i v  iv i      viv        ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_224037330_   3775 TAGTTACCAAAATAGCATGGTGCTGGTATAAAAGTAGACTCATAGACCAA 3824
                         i   v i   i i  ii    i    i    iii     vi     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_224037330_   3825 TGGGACAGAATAGAAAACCCAGAAATAAAGCCAAAATAGAT--ACAGCCA 3872
                            i i     v  i ii           v   ---  v  -- ii i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCA---TACATTTATGGTCA 347

  chr2_224037330_   3873 ACTGACCTTCAACAAAGCATATAAATAC-AT--AAGTTGGGGAAAGGATA 3919
                          i   ii   i    i -i iiv  v  -  --  --         i   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAA--TGGGGAAAGAATA 394

  chr2_224037330_   3920 TCCTACTTAATAAACGCAGCTGGGAAAACTGGATAGCCACATGTAGAAGA 3969
                         vi  vi i  i   i vv       v         ?       i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_224037330_   3970 ATAACACTGGATCCCTATCTCTCACCTTACACAAAAATCAACTCAAGATG 4019
                           i vii    i     i   v    v  i        i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_224037330_   4020 GA-AAAAGACTTAAATCTAAGACATGCAACCTCAAAAATTCTAAAAGATA 4068
                           -v ?    i     v     vv iv   ivi    v ii  i    v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_224037330_   4069 ACCTAGAAAAAACTCTTCTAGACATTGGCCTAGGCAAAGAATTTATGGCT 4118
                           v   i?iv  v     vv   v    vi       v iv  iv i v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_224037330_   4119 AAGATCCTAAAAACAAATGCAACAAAAATAAAATAAATGAATAAATGTGA 4168
                          v  iv i    i  v v         i-    --   ii      vv  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAG-AAAA--AATAGATAAATTGGA 641

  chr2_224037330_   4169 CCTAATTAAACTAAAAAGCATTTATACAGCAAAAGAAATAATCATCAGAG 4218
                          i v  i   v v    i v   i i vv    i  v iv    vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_224037330_   4219 TAAACAGACAACCCACAGAATGGGAGAATATATTTGCAAACTATGCATCT 4268
                          i  v                       v           ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_224037330_   4269 GACAAAGGACTAATATCCAGAATCTACAAGGAGCTCAAACAAATCAGCAA 4318
                           i  i     vi          v  i  i  i   vv    v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_224037330_   4319 GAAAAA--CAAAT--TCCA--TAAAAAGTGGACAAATGACATCAACAGAC 4362
                         v     --     --i   -- ?    i   i    v  iv v  i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_224037330_   4363 ATTTCTCAAAAGAAGATATACAAATGTCCAACAGGCATATGAAAAACTCC 4412
                                v                  v    i i   i       iv v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_224037330_   4413 TCAACATTACTAATCAT 4429
                                i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (131 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


2550 27.75 4.70 1.15  chr2_224084055_224088196.rev     2785  3656 (486)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr2_224084055_   2785 AGATATTTTATGTGCACATGAGTTGAAAGGCT--ATA-------GCTGTC 2825
                               iii    v  --  ii   i   i  --   ------- v  v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCA--TGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_224084055_   2826 AATTTTTTTTCTCATTCGACCTATACATTTAATGTCATCCCAATCAAAAT 2875
                            vi ii-- iv v i  i   i v   i  i iv     v        
  L1M4_orf2#LINE/     54 AATACTCC--CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_224084055_   2876 CTCAGCACGCAATTTTGTAGGTATCATCAAGCTCATTCTAAAGTTTATAT 2925
                          i    vvv vv     i  iv  iiv      v  i     i  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_224084055_   2926 GAAAAGGCAAAGGACCCAGAATAGTCAACACAATACTGAAGAA------- 2968
                          i   v    i             i   v     vi    i  -------
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_224084055_   2969 -----TAGAGAACTCATAGTACCTGATTTCAAGAGTTAATACAAAGAT-T 3012
                         ----- i   i     i v v  ii       i v   v       v -i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_224084055_   3013 AATAAAAAAGATGATGTGGTGTTGGCAAAAGAATGCGTACATAGATCAAA 3062
                          i   vv    iii      ii     v   i  ivii i         v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_224084055_   3063 GGAACAGAATTGAGAGGCTAGAAATTAGATCACACCAATACAGTAAACTG 3112
                             i           v i      v ivi  i  vvv  ii  v  i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_224084055_   3113 ATTTTTGAAAAAAGGTGGAAAGGCAATTCAAAGGAGAAAGGACAGTATTT 3162
                              i  v  i-    vv   i v      v  i     i i   v   
  L1M4_orf2#LINE/    352 ATTTTCGACAAG-GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_224084055_   3163 TTAATAAATAGTACTGAAACAATTAAACTTTCATACCCTAGAAAACTAAT 3212
                          i  i    i  i   ii    i ii iv?i  i iv v i i  iv  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_224084055_   3213 CTAGACACAGACATTACATCCTCCGCAAATATTAACTCAAGATCCATCAT 3262
                         i i   v vv  v i   i v vii    v          i  vv    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_224084055_   3263 AGACCTAAATACCAAATGC-AAAACTATAAAAGTTCTAGAAGAAAACATG 3311
                                   iiv i -  -            v ii             i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_224084055_   3312 AGAAAAAATATTTATTTGATCTTGGGTTTGGTAATGCATT-TTAGATACA 3360
                         i ?iv    v  ii --  i        v  i    vv  -       ii
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT--GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_224084055_   3361 TCACCAAATTCATAATTTATAAAATAAAAAATTGATATTTTGGACTTTAC 3410
                         v       vv  i  viv i    v       v    vv        i i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_224084055_   3411 TAAAATTAAAA-TGTCTGCTCTGTGAAAAACACTGTTAAGCGAATAAAAA 3459
                         i          -iv i  iv  vii  ii     i i   vi i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_224084055_   3460 GACAAGCCACAGAATGGAAGATAACATTACTAAAGT---TATCTGATAAA 3506
                              v           i   v  i   vvi   vi---          -
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA- 746

  chr2_224084055_   3507 GGGATTGGTATCTGAAATTATTCAAAGTAATC------------AGTGAA 3544
                             i v     iii   -  vi    v v  ------------ i i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAAT-ATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_224084055_   3545 AAAATAAACAACCCAATTAAAAAATTGGCAAAATATCTGACCAGACATCT 3594
                           i i   i         ?      v      iv  i   vi      i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_224084055_   3595 CATCAAAGAAGATATACAGATGACAAGTAA-CATATAAAAACATATTCAT 3643
                          vi               i   i v i   -  i  i    v  ii   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_224084055_   3644 GTTCAATTCATTT 3656
                         vv   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.02 (17 / 903), avg. gap size = 3.00 (51 / 17)  


3081 26.35 0.77 0.66  chr2_224116100_224120027.rev     2530  3436 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_224116100_   2530 TGGAAACACATCCTATGCTCATGGCTGGGTAGACTCAATATTGTGAAAAT 2579
                               v i    i   i      v v  v     i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_224116100_   2580 GACCATACTGACAAAAGCAATCTACAAATTCAATGCAATTTCCATCAAAA 2629
                          i v     vv v   vii       i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_224116100_   2630 TAACACCATCATTCTTCACAGAACTAGAAAAAACAACCCTAAAATGCATG 2679
                          vv  v vv v  i  ii     v v  v  ivii i        v   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_224116100_   2680 TGGACCCAAAAAAAGGGCCCTC--ATAGCCAAAGAAAGACTCAGCAAAAA 2727
                             ---  viv     v  iv--         iv  vvi v iv  i  
  L1M4_orf2#LINE/    151 TGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_224116100_   2728 GAACAAATCTGGAGGCATCACATTACCTGATTTCTAAATATACTATAAGG 2777
                                vi      vv     i v  ii     v   iv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_224116100_   2778 CCATAGTCACCAAAACAGCATGGTACTGGTTTAAAAATAGGAATATAGAT 2827
                          i i   v i   i    ii         iv   ii    iv        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_224116100_   2828 CAATGAGAACA-AATAGATAATCCAGAAATAAATCCAAATACTTATAGTC 2876
                              -   i -   v  v i            i   v i i    i   
  L1M4_orf2#LINE/    298 CAATG-GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_224116100_   2877 AACTGATCTTTGACAAAGTGAACAAAAACATAAAGTGGGAAAAGGATATC 2926
                           i    i  i     i vviv   i v   vv i    i    i   vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_224116100_   2927 CTATTCAACAAGTGGTGCTGGGATAATTGACAAGCCACATGTAGAAGAAT 2976
                           v        i           i  i  ivv ?       i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_224116100_   2977 AAAACTGGGTCCTCATCTCTCACCTTATACAAAAATCAACTCAAGAGAAA 3026
                         i  ii   ii  ii i   v    v           i       i vii 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_224116100_   3027 TCAAAGACTTAAATCTAAGACCTGTAACCATAAAAATTCTAGAAGATAAC 3076
                            ?    i     v     v  iv   i      v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_224116100_   3077 ATTGGAAAAACCCTTCTAGACATTGCCTTAGGCAAAGACTTCATGACCAA 3126
                           v  ?iv  vi    vv   v   vv        v ii   v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_224116100_   3127 GAACCCAAAAGCAAATGCAACAAAAACAAAAATAAATAGAT--GATATCC 3174
                           vv         v v         iv       i   i  --  iv  -
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC- 645

  chr2_224116100_   3175 AATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTTA 3224
                         -  i   v v    i   i  ii vv    i  v iv    iv i   v 
  L1M4_orf2#LINE/    646 -ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_224116100_   3225 ACAGACAACCCATAGAGTGGGA-AAAATCTTTGCAATCTATATTTCTGAC 3273
                          v          i   i     -     v       vii    v     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_224116100_   3274 AAAGGATTAATATTGAGAATCTACAAGAAATTCAAACAAATCAACAAGAA 3323
                           i   i vi   iv     v  i  ii  i  vv    v    i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_224116100_   3324 AAAAGCAAACAATCTCATCAAAAAGTATGTTAAGGATATGAACAGACAGT 3373
                            ii    i  i iv  i?    i iv iv      v    i     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_224116100_   3374 TCTCCAAAGAATATATACAAATGGCCAACGAACATATAAAAA-ATGCTCA 3422
                                    v                ii i  i  i    -       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_224116100_   3423 ACATCACTAATTAT 3436
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (132 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2797 24.92 4.17 1.80  chr2_224129867_224132096.rev      852  1738 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_224129867_    852 TGGAAAGACATACCGTGCTCATGAACTGGAAGACTCAACATAGTAAAGAT 901
                                 i  v  i  i     i i         i  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_224129867_    902 GTCAATTCTCCTCAAATTGATCTATAGGCTTAATGCAGTTCCTATCAATA 951
                          v    v    i            i  ii i  i   i i        v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_224129867_    952 TTCAGGAT----TCTTTGTAGGTATAGATAAAATGATTGCAAAATTTATA 997
                          i vi v ---- i    i  iv  v  i  iv    ivi      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_224129867_    998 TGTGTAATGCAAAGGAACAAGAATAGACAAAACAAATTTGAAAAAGAAGA 1047
                           - v       i   v v       v        vi             
  L1M4_orf2#LINE/    151 TG-GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_224129867_   1048 ATATGGTTGGAGAAATCACACTTCCCAAATTTAAGGCTT-CTACA--GTT 1094
                          i vi       i v             v  i  ii   -     -- i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_224129867_   1095 ATAGTAGTCAAGACGGTGTGGTATTGACAGATGAACA--CACATAAATCA 1142
                          i    i       i        i  i  v v i i --  i   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_224129867_   1143 ATAGAAGAGAAGAGAAGAGAAGAGAAGAAAATCCTGGATAGACCCACTCA 1192
                           i   v    vv  -   vvv    -----------   i     iv  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGA-GAGTCCAGAA-----------ATAAACCCATACA 337

  chr2_224129867_   1193 AGTACAGCCAACTGGTACTTGACAAAGATGCAAAAGCAACTCAATGGAGA 1242
                         vv  ii i   i  i vi i     i i   v  ii v i       i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_224129867_   1243 AAAGATCATCTTTTCAACAATTGGTATTGAAACAATTGGACATTGAAAGG 1292
                           ii  vi            v    ii  ii    i    i ?iv v v 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_224129867_   1293 CAAAATAATGAACTCTGACATAAACCTCACATGTTATGCAAAAATTAACT 1342
                              v      v iv   vivv        ivv   i            
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_224129867_   1343 CAAAGTGGATTATAGATGTAAATGCACACATGC---AACTTTAAAACTTT 1389
                             i     i ?   iv      i - v -  ---    v       i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTA-AGA-GCTAAAACTATAAAACTCT 535

  chr2_224129867_   1390 --GAAGAA----------CAAATTTTTATTACTAAGCATTAGGGA--GAC 1425
                         --      ----------i    i  ii v  ivv vi     v -- ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_224129867_   1426 TTCTTAGA-ATTAAACCAAAGTCAAAATTTACCTAAGAAAATTT-GATAA 1473
                                 -  v v      iv  v  viv  vv       vv -     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_224129867_   1474 ATAAGACGTTATCAAAATTAA---CTATTGATTTTCAAAAGACATTGTTA 1520
                           vi   v i           ---  v   vvi      i    i i i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_224129867_   1521 AGAGAATGAAAAGAAAAACCAGAGAGTGGGAGAAAACATTTGCATGTTAT 1570
                            i i        v  v   v   i          i       vi i  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_224129867_   1571 ATATCTAA--ATG--CTTATATCTGTAATATATATGAAACTCTCTA-AAC 1615
                               i -- v --   i    iiv        vii      -  -   
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAAC 784

  chr2_224129867_   1616 ACAAAAATACGAAAACAAA-AATTTAATTAACTAATGAGCTAAAGACTTG 1664
                         v   v    vi  i     -  iii    ? vv    i  v  i  i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_224129867_   1665 ACCAAACACTTCACAAAGGAAGATATGCAGATGGAAAATAGCCACATAAA 1714
                          vi i   i   v v  i        i  i    vv    iv     i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_224129867_   1715 AATGTAGTTAGCATCATTAGCCAT 1738
                           vi iv i i     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (127 / 91)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.52 (53 / 21)  


2320 20.35 0.96 3.45  chr2_224209412_224212260.rev      808  1328 (1521)    L1M4_orf2#LINE/L1        7   514 (394)  

  chr2_224209412_    808 GACACCTCATTTTCATGAATCAAAAGATTTAATGTTATTAAGATGACAAT 857
                           i i i   v      i  iii    i     i  i        i    
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_224209412_    858 ATGACCCAAATTGATCCACAGATTTAACAAAATCCCTATTAAAATGATAT 907
                          ivv            i       i   iv         i     vvi v
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_224209412_    908 CTAGCTCTTT-GCAGAACTTGTCGATCTAATCCTGAAATTTATTTGAAAA 956
                           iv  i   -      v   v i v  i     i     i  v  i   
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr2_224209412_    957 TGCTAGGAACCCAGGATAGTCAAAACAGTCTTGAAAAAGAA---CAAAGT 1003
                            v   i      i    i       i             ---      
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr2_224209412_   1004 TGGAAGACGCACAGTTCCTGATATAAAAACGTACTACAAACCTGCAGTAA 1053
                             i   v    v    ii  v v     v         v  i      
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr2_224209412_   1054 TCAAGACAGTGTGTTATTGGCATAAGAACAGACTAATAGGTTAATGTAAT 1103
                                      v  i         i i    vv    i i    v   
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr2_224209412_   1104 AAAATTGGAAGTCCAGAAATAAATCTTTACATTTATGGCCAATCAATTTT 1153
                          i     ii              i iv           i    ii     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr2_224209412_   1154 CAACAAGAGTGCCAACAGAATTCAACAGAGGAAAAGAACAGTCTTTTTAA 1203
                          i     i       v vv      ii i --      i        i  
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGG--AAAGAATAGTCTTTTCAA 404

  chr2_224209412_   1204 TGAGCAGTGGTGGTGCCAA-TGTATATTCACATACAAGAGAATAAAACTG 1252
                         ii iii   v   - v   -  v   ?i     i   i     i  ii  
  L1M4_orf2#LINE/    405 CAAATGGTGCTGG-GACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_224209412_   1253 GACCACTGTCTCACAGCACATACAAAAATTACAAAAAAAAAAAACCCTCA 1302
                             v  ii      v  i            ------------  i ---
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTA------------ACTC--- 488

  chr2_224209412_   1303 AAAAAGGGTCCTACACCTAAAAGTAA 1328
                             v  i  v? v       v    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAA 514

Transitions / transversions = 1.89 (68 / 36)
Gap_init rate = 0.01 (7 / 508), avg. gap size = 3.29 (23 / 7)  

1454 19.56 7.58 1.96  chr2_224209412_224212260.rev     1955  2363 (486)    L1M4_orf2#LINE/L1      477   908 (0)  

  chr2_224209412_   1955 AAAAAATAATAATAACAATAAAATAAAAAT-TAAA---AAAATTTAAAAT 2000
                              v   i-- v v   ii vi ? i i-    ---  i vi     i
  L1M4_orf2#LINE/    477 AAAAATTAAC--TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_224209412_   2001 TATAAAGGTCTAAGGAGAAA-CATTGGATTAAATCTTTATGATCTTAGGT 2049
                               iv   v  i     -   v  ?v        ii   i   i   
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_224209412_   2050 TGGGTGATGGTTACTTAGATATGACACCAAAAGCATGTGTGAAAAAAGTG 2099
                          i  ii      v                      iiv ii v     vi
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_224209412_   2100 AAAATAGATACACTGGACTTCA----AATTTAACACTTTTTTTTTTTGCT 2145
                                   v i         ----    v  v      v -----   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT-----GCT 669

  chr2_224209412_   2146 GTAAATGATAGTATCAAGAAAATGAAAGGTCAAGT-ATAGAAGGAAAGGA 2194
                         vi   v  i v          i     i v   vi- i    v ii  i 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_224209412_   2195 AATAT--------------------AAGAGACTTATATTCACAGTATGTA 2224
                              --------------------   i     i   i  v i   i  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_224209412_   2225 AAGAACTCTTAGAACTCAAAAATGAAAACACAAATAACCAAATTTCAAAA 2274
                                    v       v   i    v          v    ?-    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAA 818

  chr2_224209412_   2275 ATGGGAAAAGCATTTGAATAGCCATTCCTCCACAGAAGATATACAAATGG 2324
                              v    v          v    i     v                 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_224209412_   2325 CCAATAAGCACATGAAAAG-TGCCCACTAGCCTTTAGGGA 2363
                                            -   i  vi v v????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (42 / 35)
Gap_init rate = 0.02 (10 / 432), avg. gap size = 3.90 (39 / 10)  


 651 28.20 11.95 4.68  chr2_224312592_224315072.rev     1194  2005 (476)    L1M4_orf2#LINE/L1       38   908 (0)  

  chr2_224312592_   1194 ATATTGTAAAGGTATCAATTCTCATGAAATTAATTT-TACATTCAATGGA 1242
                                v   i iv    v   viv     i  i -i v      i v 
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chr2_224312592_   1243 ATAGCATTTATCAA--TCCCATTGAACTTT-----AAAAA-----GAACT 1280
                           -- -ii      --     viviv    ----- i   -----i i  
  L1M4_orf2#LINE/     88 AT--C-CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr2_224312592_   1281 --TGCTAAACTT-ATTTGGAGA-G-AAGGAAGATCCAAGGCATCCAAGTT 1325
                         -- v     v  -  v    i - -    --  i   iiii v    ivi
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAAC 182

  chr2_224312592_   1326 AACCTTAAAAA-------TA---TTG-AGTAT--GTACTGACC--TTTAC 1360
                           i   i    -------i ---   -  v i--ii   vv  --   - 
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT-C 231

  chr2_224312592_   1361 AGAAATTAACCTACAAAGTCATTATAAT-AAAA-AGTACAGCATATGTTC 1408
                          i  v   --        ii ivi    -  i -   iii i i-  v- 
  L1M4_orf2#LINE/    232 AAAACTTA--CTACAAAGCTACAGTAATCAAGACAGTGTGGTAC-TGG-C 277

  chr2_224312592_   1409 ATTAG--CAGATATAGAGACCAATGGGATACAATGGAGAG--CAGAGAGA 1454
                           v  --i   i   v   i      i   v   v     --    i v 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_224312592_   1455 GAGAGCCCATGAATATACAG--AACT--TTGTGTACAATAAATTTAACAC 1500
                         i ---     iv  v  ii --  i --  v vv    viivvii  v  
  L1M4_orf2#LINE/    328 AA---CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr2_224312592_   1501 CACAGATCAATAGGGAATTCACAGA-TAA-CTT---ACTAGTTGAGATTG 1545
                           i---     i     -----   -  i-   --- vi iv  ivii  
  L1M4_orf2#LINE/    375 CAT---TCAATGGGGAA-----AGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_224312592_   1546 GGAAAAGTGGCTTACTCTAAGGAGAAAAATAAAACTGGATTTCTAA-TAA 1594
                            v  v   v v? ivi v v i  i   i  ii    iii   v- v 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_224312592_   1595 TACCACA-ACCAAAGGTAGACCTTTAAAGGGATTGAAGACCTAAATA-AA 1642
                         i    i -  v   iv  i--  iv   v    ii?          i-  
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAA--CTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_224312592_   1643 GATAGTAAAACTATAAACCTCATATGTAGTAAAAGAATATAGAA-TAT-T 1690
                           -iv            v   --- -   -  i i  i    i?-  v- 
  L1M4_orf2#LINE/    515 GA-GCTAAAACTATAAAACTC---T-TAG-AAGAAAACATAGGNGTAAAT 558

  chr2_224312592_   1691 TTTTGTGACACAGTGGTAGAGGA-AATCTTTTAAA----ATAC-AAAACC 1734
                         i  i     viv v v   ivi -ii i i   i ---- i  -    v 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr2_224312592_   1735 TCAAATGAATATTTTAGAATAAAAAAT-GATTATTTTGATAATATCCAAA 1783
                         v   iii ------i i  v       -   v v  v  ivvi   v   
  L1M4_orf2#LINE/    609 ACAAGCAA------CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_224312592_   1784 TTATAAATTTCTGTTCAACAAAAGACGCCAT-AAGCAAAGTTAATAGATG 1832
                            v   i  i   v vv    i   i i  -   -     v  v   ii
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAAAGACA 701

  chr2_224312592_   1833 GC----ATAATGGGATAAAATGGTTGAAATATT-TAAAACTGACAAGGGA 1877
                         i ---- v       v     iv   v  -  i-  v v    i      
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATAAGGGA 750

  chr2_224312592_   1878 TTTAAATCTAGA------------CTCT-ACAA---GATATCA----GCC 1907
                         i  iv   i   ------------    -    ---i   vi ---- v 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_224312592_   1908 ACAAAAC-------AAAAATAGTCAAAGGATACAAATAGAC---TAACCA 1947
                          v v   -------      i v        vii       --- vv   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_224312592_   1948 GAAGAGGAAGTCCAAA-GACCTTCAAGCACATGGAGTCTTGTTCAAACTC 1996
                         -    i  vi v    - i  vvi         i ivvv  i    vv  
  L1M4_orf2#LINE/    851 -AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_224312592_   1997 ATTAGTAAT 2005
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.31 (128 / 98)
Gap_init rate = 0.07 (60 / 871), avg. gap size = 2.25 (135 / 60)  


3011 27.85 0.77 0.44  chr2_224348492_224353785     3898  4802 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_224348492_   3898 TGAAAACACCTCTCGTGCTCATGGGTGGGTGGAATCAATATTGTGAAAAT 3947
                           i   v iv  i i  i      i v  vi  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_224348492_   3948 GATCATACTGCTAAAAGCAATCTACAAATTCAACGCAGTTCCCATCAAAA 3997
                          iiv     v iv   vii       i          i i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_224348492_   3998 TACCACCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTTATA 4047
                          v   v vv v  i  ii     v v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_224348492_   4048 TGGAAC--CAAAAAACAGCTTGCATGGCCAAAGCAAGACTAAGCAAAAAG 4095
                              v--   iii  -- iv v  i      i   vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_224348492_   4096 AACAAATCTGTAGGCATCAAATTACCAGATTTCAAACTATACCATAAAGC 4145
                               vi  v   vv   v i v  vi        viv   i i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_224348492_   4146 TGTAGTCTCTAAAACAGCATGGTACTGGTATAAAAATAGGTACATTGACC 4195
                          ii   vvii  i    ii         i    ii    ii i  v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_224348492_   4196 AATGGAATTGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAA 4245
                                 v    v    ii               v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_224348492_   4246 CTGATCTTTGACAAAGCAAACAAAAACAT--AATGTGGGGAAAGGACACC 4293
                         i    i  i     i vviv   i v   --    --       i i vi
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATG--GGGAAAGAATAGT 396

  chr2_224348492_   4294 CTATTCAGCAAATGGTGCTGGTATAATTGGCAAGCCACATGTAGGAGAAT 4343
                           v    i             v i  i   vv ?       i ii     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_224348492_   4344 GAAACTGGATCCTCATCTCTCACTTTATACAAAAATCAACTCAAGGTGGA 4393
                            ii    i  ii i   v   iv           i       ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_224348492_   4394 TCAAAGACTTAAATCTAACACCTGAAACCATAAAAATTCTGTAAGATAAC 4443
                            ?    i     v   v v  i    i      v ii iv    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_224348492_   4444 ATTGAAAAACCCCTTCTAGACACTGGCTTAGGCA--GACTTCATGACCAA 4491
                           v i?iv vvi    vv   vi   v       -- ii   v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_224348492_   4492 GAACCCAAAAGCAAATGCAACAGAAACAAAGATAAGTAGATGGGACCTAA 4541
                           vv         v v      i  iv   i   ii  i  v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_224348492_   4542 TTAAAGTAAAAAGCTTCTGCAGACCAAAATAAATAATCAGCAGAGTTAAC 4591
                          i   i v    i   i  iivvi    iv v iv    iv i   v  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_224348492_   4592 AGACAACT-ACAGAGTAGGAGAAAATCTTCGCAATCTATAGATATGGCAA 4640
                                i-     i i         v  i    vii   v  v  ii  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_224348492_   4641 AGGACTAATATACGGAATCTACAAAGAACTCAAACAAACCAGCAAGAAAA 4690
                         i     vi   v i    v  i         vv    vi  ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_224348492_   4691 AAGCAAACAATCCCATCAAAAAGTGGGCTAGCGACATGAATAGACAATTC 4740
                          ii    i  i  v  i?    i     v iv  iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_224348492_   4741 TCAAAAGAAGATATACTAATGGCCAACAAGCACATGGAAAAATGCTCAAC 4790
                           v             v         i         i   i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_224348492_   4791 ATCACTAATGAT 4802
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


2259 24.18 2.35 9.69  chr2_224480521_224483706     1715  2694 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_224480521_   1715 TGGAAAAACATTCCATTCTCATGGACAGAAAGAATCAATATC-TGAAAAT 1763
                               i i  i    vi       iv i    v i     i- v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_224480521_   1764 GACCATATTGCACAAAGCAATGTACAGATTCAATGCCATTCCCATTAAAC 1813
                          i v   i v v    vii  v           i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_224480521_   1814 TACCATTGACATTATTCACAGAATTAGAAAAAACT-ATTTTAAAATTCAT 1862
                          v   vivi v  v  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_224480521_   1863 ATGGAACCAGAAAAGAGCCTGAATAGCCAAGACAATCCTAAGCAAAAAGA 1912
                               viiv  ii  v  v          i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_224480521_   1913 ACAATGCTGGAGGCATTATGCTACCCAAACTATACTACAAGGCTACTACT 1962
                             v i      vv i ii  v     --------------------- 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAA---------------------T 228

  chr2_224480521_   1963 TTGAGGCTACTATACTGCTTCAAACTATGCTACAAGGCTATAATAACCAA 2012
                           v -----------------     - i      i    i i   i   
  L1M4_orf2#LINE/    229 TTCA-----------------AAACT-TACTACAAAGCTACAGTAATCAA 260

  chr2_224480521_   2013 AACAGCATGGTACTGGTACAAGAACAGACACGTTGACCA-TGGAACAGAA 2061
                         i    ii         i i   i i     ii v  i  -     i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_224480521_   2062 TAGAAAACTCAGAAATAAGACCTCACACCTACAACCATCTGATCTTCAAC 2111
                          v  i iii         iv  vi   ii  iiii  vi    i   i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_224480521_   2112 AAACCTGACAAAAATAAGCAATTTTTTGCTTATTTTATTAAATAAATAAA 2161
                           ivv  v   i ---------------------ii   v   iiiv   
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGA---------------------CCATTCAATGGGGAAA 389

  chr2_224480521_   2162 -AATAATCATTTATTAAAAGGATTCCCTATTTAATAAATGGTGCTGGGAG 2210
                         -    i  -   ------------------ i  i              v
  L1M4_orf2#LINE/    390 GAATAGTC-TTT------------------TCAACAAATGGTGCTGGGAC 420

  chr2_224480521_   2211 AACTGACTAGCCACACGCAGAAGATTGAAACTGGGCTCCTTCCTTATACC 2260
                              iv  ?     i   i    v    ii   i i   v   i i   
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_224480521_   2261 ATATA-AAAAATCAACTCAAGATGGATTAAATACTTAAATGTAAAA-CCA 2308
                              -      i       i      i ? v  i         i - i 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_224480521_   2309 AAACTATAGAAACCATAGAAGAAAAGCTAGGCA-ATACCATTCAGGACAT 2357
                                 i  vi v          vv    ?i- v i -   iv   v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT 569

  chr2_224480521_   2358 --AGTCACGAGCA--GATTTC------ATGACAAAAATGCCAAAAGCAAT 2397
                         --i  i --i   -- i    ------      ------         vv
  L1M4_orf2#LINE/    570 TGGGTTA--GGCAATGGTTTCTTAGATATGACA------CCAAAAGCACA 611

  chr2_224480521_   2398 TGCAATAAAAGCAAAAATTGACAAATGGGATCTACTTAAACT--AAAGTT 2445
                         v    i     v      v  i    v   ii vv i   v --   ii 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr2_224480521_   2446 TCTGCAGAGCAAACGAAACTGTCATCAGAGTAGACAGACATCCTACAGAA 2495
                          i  iivvv    v  v   i   vv i   ii v     v  i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_224480521_   2496 TGAGAGAAAATTTCTGCAATCTAGTCATCTGACAAAGGTCTAATATCCAG 2545
                           i        v i     vii vvi      i  i  v  vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_224480521_   2546 CATCTACAAGGAACTTAAACAAATTTACAAGAAAACAAACAAACAAACAA 2595
                         v  v  i  i     ivv    v iv i  v    ----- i     i  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAA-----AGACAAATAA 806

  chr2_224480521_   2596 ACCCATT--AAAGTAGGCAAAGGACAAGAACAGATACTTGTCAAAAGAAG 2643
                         v  v   --   i i         ivv   i   i i  v  v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_224480521_   2644 ACATACATGTAGCCAACAA--ACATGAAAAAAAAGCTCAGCATCACTAAT 2691
                          i     vi i     i  --         i v-     i     ?????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACATCAZZZZZ 905

  chr2_224480521_   2692 CAT 2694
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.60 (144 / 90)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 4.72 (118 / 25)  


2807 26.26 2.68 1.23  chr2_224805790_224810072     2897  3791 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_224805790_   2897 TGAAAATACACTCCATACTCATGGATTGGAAGAATCAGCATTGTGAAAAT 2946
                           i   v i ii    ii               v i ii     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_224805790_   2947 GACCATACCACTCAAAGCAATGTACAGATTCAATGCAATTTCTATCAAAA 2996
                          i v    iv i    vii  v           i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_224805790_   2997 TACCAACATCATTTTTCACAGAATTAGAAATAAC-AATTCTAAAATGCAT 3045
                          v   i vv v     ii     v v  v - i -i  i       v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr2_224805790_   3046 ATGGAA-T-CAAAAAA---GGAAT-----------TCTATGCAAAA--AT 3077
                               - -   iii ---i    -----------   -  v    -- v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT-TGAAAAAGAAG 198

  chr2_224805790_   3078 AACAAATCTGGAGACATCACGATAACCCAACTTCAAACTATACTACAATA 3127
                               vi     ivv    - ivv     i      viv        --
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTTACTACAA-- 245

  chr2_224805790_   3128 TACTAACTGTAGTTACCAAAACAACATGGTACTGGTATAAAAATAGATAT 3177
                         ---- i  ii   v i   i   iii         i    ii     i  
  L1M4_orf2#LINE/    246 ----AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_224805790_   3178 ACAGACAAATGGAACAGAACAGAAAATCCAGAAATAAAGCCAAATATTTA 3227
                          i   iv       i    iv  i i            v   v i     
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_224805790_   3228 -GAACAAATTATCTTTGACAAGGTATATGAAAAC-ATAAATTGGGAAAAG 3275
                         - iv   v v  i  i       -i iiv  i  -  vv v    i    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_224805790_   3276 GATACCTTGTTCAATAAATGGTTCTAGGAAAACTGGGTAGCCACATGGAG 3325
                         i   vii v     i       v  i   v      i  ?       v i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_224805790_   3326 AAGAATCAAACTGGATCCCTGTCTCTCACCATATACACAAATCAACTCAA 3375
                               v  ii    i    ii   v           v    i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_224805790_   3376 GATAGATTAAAGACTTAAATCTAAGACTTGAAATCATAAAAATTATAGAA 3425
                         i  i   i ?    i     v     vi i   ii      v iv     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_224805790_   3426 GAAAATCTAGGAATATCTCTTCTGAACATTGGCCTAGGTAAAGAATTCAT 3475
                              iv    ?i  vv     vvi  v    vi    i  v iv   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_224805790_   3476 GACTAAGAACCCAAAAGCAAATGCAACTAAAGCAAAAATAAATCCATGGG 3525
                         iiv  v  vv         v v     v    v       i  vv  v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_224805790_   3526 ACTTAATCAAA-CAGAAAACTTCTGGATAGCAAAAGAAATAACCATCAGC 3574
                             v      -ivi       i  viivv    i  v iv i  vv iv
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_224805790_   3575 ATGAACATACAGTGCACAGAGTGGGAGAAAACATTTGCAAACTCTGCATC 3624
                         i    v v   iiv      i          i         iiv ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_224805790_   3625 CAAGAAAGGACTAGTATCTAGAATCTGCAAGGAACTGAAGCAAATCAGCA 3674
                         ii v  i     v     i     v ii  i     vvvi   v   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_224805790_   3675 AGGGAAAATCAAGTAATTCCATCAAAAAGTGGGCAAATGACATTGAATGA 3724
                          vii   iv   i   ii v  i?    i        v  i-      ii
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAG 839

  chr2_224805790_   3725 ACACTTTTCAAAAGCAGATATACAAATGGCCAACAA--ACATGAAAAAAT 3772
                            i  i  v    v                  i  --         i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_224805790_   3773 GCTCAACAGCACTAATCAG 3791
                                 v  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (134 / 97)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.19 (35 / 16)  


2968 24.58 4.64 1.81  chr2_224842687_224844865.rev      805  1687 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_224842687_    805 TGGAAA-ACATTCCATGCTCTTGAATGGAAAGAATCAATACTGTTAAAAT 853
                               - i  i     i  v  i  v i    v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_224842687_    854 GGCCATACTGCCCAA--TGAACTTTACAGATTCAATGCTATCCATATCAA 901
                            v     v     --   -- i           i  v    v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGA--TCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_224842687_    902 ACTACTAA-TGCCATT---------ATTCACAGAGC--ATTCTAAAATTC 939
                          v v i i-    v  ---------   v   -   --  i         
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTC 147

  chr2_224842687_    940 TTATGGAACCAAAAAGGAGTCTGAAAAGCCAAGGCAATTGTAAGCAAAAA 989
                         v       viiv  i   vi v   v      ii    iv i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_224842687_    990 GAACAAAGTTGGAGACATCACATTATCCAGTTTCAAACTGTACTACAATG 1039
                                       ivv     i vi   i       viv        v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_224842687_   1040 TTACAGTAACTAAAACAGCATGATATTGGTACAAAAACAGACACATAGAC 1089
                         i        ii  i    ii  i  i   i i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_224842687_   1090 CAGTGGAATAGAATAGAGAGCCCAGAAGTAATTCTGCACACCTACAACCA 1139
                           i           v     i      i   vi iii   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_224842687_   1140 TTTGATCTTCAACAAAGTTGACAAAAACAAGCAATGGGGAAGAGACTCCC 1189
                         v     i   i    i v  v   i v  vv          iii ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_224842687_   1190 TATTCAATAAATGGTGCTGAGATAACTGGCTAGCCATATGCAGAAGATTG 1239
                          v     i           i  i      v  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_224842687_   1240 AAACTGGACCCCATCCTTACAGTATATACAAAAGTCAACTCGAGATAGAT 1289
                           ii        vv   i   vi          i i     i i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_224842687_   1290 CAAAAACTTAAATGTAAAACCTAAAACTATAAAAACCCTGGAAGATAATC 1339
                           ? i  i         i v              vi i i     v  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_224842687_   1340 TCTG---AAATACCATTCTAGACTTAGGACCTGGCGAAGATTTC------ 1380
                          vv ---    -- -   vv   i v  iiiv   i v i    ------
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_224842687_   1381 ATGACAAAGTTGCCAAAAGTAATCGCAACAAAAACAAAAATTGACAAATG 1430
                               ------       i vvv         iv      v  i    v
  L1M4_orf2#LINE/    595 ATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_224842687_   1431 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAGACTA-----A 1475
                            ii v  i   v v  i i   i  ii vv    i  v    ----- 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_224842687_   1476 GAGTAAACAGACAACCTATAGAACGGGAGAAAATATTTGCAAACTATGTA 1525
                         i   i  v        i i    i                   ii  i  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_224842687_   1526 TCCAACAAAGGTCTAATATCTAGAATCTATAAGAAACT-TAAAGACATTA 1574
                           ii i  i  v  vi    i     v     ii    - v vi  - i 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCA 787

  chr2_224842687_   1575 ACAAACAAAAAACAAACAACCCCCCCAAAAAAGTGGGCAAAA-ACATGAA 1623
                          i  vv    i     i     vvii?     -        i- iv    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chr2_224842687_   1624 CAGACACTTTTT------AAATCCATGCA----GCCAACAAGCATATGAA 1663
                         i     i  i i------ i  --  i  ----     i     i     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGAT--ATACAAATGGCCAATAAGCACATGAA 884

  chr2_224842687_   1664 AAAATACTCAACATCAGTAATCAT 1687
                           i  i          ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (139 / 75)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.85 (57 / 20)  


2672 25.54 4.09 1.02  chr2_224921742_224926032.rev     2920  3800 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_224921742_   2920 TGGAAAAATATTCCATGTTCATTCATCGAAAAAATCAATGTTGTTAAAAT 2969
                               i    i          vv  i i  i v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_224921742_   2970 GGCCATACTACTCAAAGCAATTTAAAGATTCAATGCTATTCCCATCAAAC 3019
                            v     v i    vii  i  v        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_224921742_   3020 TACCAA-TGACATATTCATAGAATTAGATAAAACT-ATTCTAAAATTTTA 3067
                          v   i-  v v v  iii    v v  i  i-  -  i        ivv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_224921742_   3068 ATGGAAC--CAAAAAAGCCCAAATATCCAAGGCAATCCTAAGCAAAAATA 3115
                               v--   iii v  vi    v    ii     i i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_224921742_   3116 AAAAATTTGGAGCCAC-CACACTACCTGATTTCAAACTATACTACAAGGC 3164
                          v   v      v-  -      v  ii        viv        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_224921742_   3165 TACAATAACCAAAACATCATGGTACTAGTACAAAAACAGAC--------C 3206
                             i   i   i   vii       i i i  ii i    -------- 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_224921742_   3207 AATAGAACAAGACAGAGAAAACAGAAAG----TCACACACCTCTAACTGG 3252
                            i   i ii iv    ivv      v----i  i   ii v iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_224921742_   3253 CTGATCTTTGACAAAGTCAACAATAACAAGCATTGGGGAAAGGAT----- 3297
                         i    i  i     i viiv   v v  vv  v         i  -----
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_224921742_   3298 --TCAATAAATGGTGCTAGGATAACTGGCTAGTCGTATACAGAAGATTGA 3345
                         --    i          i   i      v  ?i ii  i  i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_224921742_   3346 AACTGGACCCCTTCCCTACACCGTATAAAAAAATTAACTCAAGATGGATT 3395
                          ii         v  ii     i    v              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_224921742_   3396 AAAGACTTAAATGTAAGATGTAAAACAATAAAAACCCTAGAAGAAAACCT 3445
                          ?    i           vv      v      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_224921742_   3446 AGG---AAATACCATTCTGGACATTGGCCTTGGTAAATAATTTAT--GAC 3490
                            ---    -- -   vv   v    vi v  i  - ii   v --  -
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA- 593

  chr2_224921742_   3491 TAAGTCCCCAAAAGCAACTGCAACAAAAACAAAAATTGACAAGTGGGACA 3540
                           v v v         vvv         iv      v  i  i v    v
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_224921742_   3541 TAATTAAACTAGAGAACTTCTGCATAGAAAAATAAACTATCAAGAGAGCA 3590
                          v  i   v vi i     i  iiivvv   iv v          i  ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_224921742_   3591 GACAGACAACCTACAGAATGGGAGTAAATATTTGCAAACTATACAT-TCA 3639
                         i v        i            v             ii   i  - v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_224921742_   3640 TCAAAGATGTAATATCCACAATCTA-AAAGAAC-CTTA-AA-TCAGCAAG 3685
                          v ii  iv i-      v   v  -       -    -  -   ii  v
  L1M4_orf2#LINE/    744 TAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_224921742_   3686 CAAAAACCAAATAACTCCATTTAAAAAATGGGCAAAGAGCATAAACAGAC 3735
                         v    iv        -   v  ?              iiiv i  i    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAAC-CCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_224921742_   3736 ATTTCTC-AAAGAAGAGATACATGCTGCCAAAAAATATATGAAAA-ATGC 3783
                                -        v     viiv     v  ii i       -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_224921742_   3784 TCATCATCCCTACTTAT 3800
                            v    v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (129 / 93)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.88 (45 / 24)  


 863 23.43 8.74 4.55  chr2_225150148_225152079      501   786 (1146)    L1M4_orf2#LINE/L1      204   501 (407)  

  chr2_225150148_    501 AGTTAGAGGCCTGACACTACCTGACTTCAATAATTATTATAGAGCTATAA 550
                             i    v  v     v  ii i     v v   i  i i     i i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_225150148_    551 TAATTAAGACAGCATGGCATGGGCCAATAA--ATAGACCAATAGATCAAT 598
                             i       ii   i iv   --    --      vv          
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGC--ATAAGGATAGACATATAGATCAAT 301

  chr2_225150148_    599 GGAACAAAATAGAGAACACAGAAATA----CATAC--------TCAACTG 636
                             i i   v    iiv        ----     --------    i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr2_225150148_    637 ATTTTTGACAAAGGAACAAGGGTAATTCAATGGAAAAAGAG-AATTCCTG 685
                              i     i  vi v i iiv         ii     i- i iii v
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_225150148_    686 CAATAAATGGT---------ACTGGACATCCACATGCAAAAAAAAAAAAA 726
                            i       ---------      i ?            i  ------
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA------ 445

  chr2_225150148_    727 AAAAAAGAACCTAGACACAGACCTTGCACATTTCACAAAAATTAACTCAG 776
                         -----v   vi i   v vv    ii   vv vi               i
  L1M4_orf2#LINE/    446 -----TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_225150148_    777 A-TGAATTATA 786
                          -  i  i ? 
  L1M4_orf2#LINE/    491 AATGGATCAWA 501

Transitions / transversions = 1.95 (43 / 22)
Gap_init rate = 0.03 (8 / 298), avg. gap size = 4.75 (38 / 8)  

1397 23.59 3.33 0.51  chr2_225150148_225152079     1051  1440 (492)    L1M4_orf2#LINE/L1      508   908 (0)  

  chr2_225150148_   1051 AATATGAAATGC-AAAACTCTAAAACTTTCAGAAAATTACTTGGAAGAAA 1099
                            i i i -  -      v       i i    i vv  v i i? v  
  L1M4_orf2#LINE/    508 AATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_225150148_   1100 ATTTATGTGACCTGGGGTTTGACAATGAGTTTTTAGATTCAACATCAAAA 1149
                           i vi       v     v i     iv  i      vii   i     
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr2_225150148_   1150 GCATGATCTATAAGAGAAACAAAT-GA-AAGCTGGACTTTACTAAAATGT 1197
                            ii v v i  i     -    -  -  ii       i ii     vv
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_225150148_   1198 CAGACTTCCCTGT---AAAACACACTGTTAAAAGAATGGAA-GACAAGCC 1243
                         v i    iiv  i---   iv     i i  i i i  i  -     v  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr2_225150148_   1244 ACAAATTGGGAGGAAATATTTGCAAAACATGTATCTTATAAAGGACTTAC 1293
                            i v      i             v   i     v    i      ii
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr2_225150148_   1294 ATACAAAATGTACAAAGAACTCTTAAAACTCTACAGTAAGAAAACAA--- 1340
                           v  i   i  i            v     v i i   i  i    ---
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr2_225150148_   1341 -CCCAATTTTAAAGTGGGCAAAATATCTGAACAGATAATTCATCAA-GAA 1388
                         -       ?v   i        iv  i    i   i v   vi   -   
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr2_225150148_   1389 GATCTACTGATGGCAAA-AAATATATGAAAAGATGCTCAACATCATATGT 1437
                            v   vi     v  -  ii i                     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr2_225150148_   1438 CAT 1440
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.90 (59 / 31)
Gap_init rate = 0.02 (10 / 401), avg. gap size = 1.50 (15 / 10)  


2027 25.68 6.42 0.32  chr2_225184238_225185845      494  1116 (492)    L1M4_orf2#LINE/L1      248   908 (0)  

  chr2_225184238_    494 CTGCACTA-TCAAGACAGCATAAAACTGGCATAAAGACAGACATAGAGAT 542
                           i  v  -         ii iiv          i  i       v    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_225184238_    543 CAATGAAACAGATCAGACAGCATAAAAATAGACCCACCCATATATGATCA 592
                              i  i   viv  v  ivi i     i     iv   v    i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_225184238_    593 ATTGATTTTTAAATAATGACGACAAGGTAATTCGGTGGGAAAAAAATAGT 642
                                  ii -i  v ii v    iiv    ii    i   i      
  L1M4_orf2#LINE/    348 ATTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_225184238_    643 GCCTTCAACAAATGATGCTGGAACAAACAACTGACAGCGTGAGGGGAAAT 692
                         vii           i      i    viiiv i? vi i  viiiii   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_225184238_    693 GTATCTTAATCCTTACCTTATACTATATAAAAAAATTAACCTAAAATTCA 742
                          v vi vi i  i     i i  i     v          ii     vv 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_225184238_    743 TCGTAGACATACATGTAAAAGCTAAAATTACGAA-CTATT----GAAAAA 787
                           i?    v  v      i        i  ii  -  v  ----     v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_225184238_    788 ATAAAAGTAAATCGTTACAAATTCAGGGTAGGCAATAATTTCTTAGG--- 834
                            ii?       v iiii vi ii  v        ii        i---
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_225184238_    835 ---ACTTAAAGCACAAACTACAAAAAGCAAAGT-GATTAACTGGACTTTT 880
                         ---  iv         i v      iiv   i -   v  i       iv
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_225184238_    881 TCAGTATTTTAAAACTCT-GCTCTTCAAAAGACACCATTAAGAAAATGAA 929
                            iv   v-      i - iv       i     i  i      i    
  L1M4_orf2#LINE/    647 TCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_225184238_    930 AAGGCAAGCAACAGACTGAAA-AAAATACTCAGAGCACATATATCTGACG 978
                            i   v v     v  ii -      i iiv ivv           ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_225184238_    979 AAGGACTTGTATCCAGAATTTATAAAGAACTTTTACAAT---GTAGTAAG 1025
                          i                 v           i      i---i  i   i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_225184238_   1026 AAAACAA----CTCAA-------------AAAAGAT----ACAAACACTT 1054
                           i    ---- i   -------------   i   ---- i i   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_225184238_   1055 CACCAAACAAGATATATCAGTGGCATATTAACACAT-AAAAGATGCTCAA 1103
                          v     v        iv i    vv  v i     -             
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_225184238_   1104 CATCATCATCAAA 1116
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (106 / 51)
Gap_init rate = 0.02 (14 / 661), avg. gap size = 3.00 (42 / 14)  


3054 26.16 4.30 1.47  chr2_225415046_225418608.rev     2213  3095 (468)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_225415046_   2213 TGGACAGATATTCCATGCCCACTGGTTGGAAGAATCAATATTGTTAAAAT 2262
                             v      i     ii  iv i        v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_225415046_   2263 GTCCATACTACCCAAAGCAATCTACAGATTCAGTGCAATCCCTATCAAAA 2312
                          v v     v      vii             ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_225415046_   2313 TACCAATGACATTCCCCACCGAAATAAGAAAAAC-AATTGCAAAATTTGT 2361
                          v   iivi v  iiiii v     v-  v  i -i  ivi      ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chr2_225415046_   2362 ATAAAATTACAGAAGACCTCGAATAGCTTAAAGCAATCTCAATCTTGAGC 2411
                           ii  v i  iii    iv       iv   -------         iv
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAA-------CAATCTTGAAA 192

  chr2_225415046_   2412 AAAAAGAACAAAACTGGAGGCATCACACTACCTGATCTCATATTATACTA 2461
                           i         ii      vv       v  ii  i   v viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_225415046_   2462 CAAGGCTATAGTAGACAAAACAGCATGATATTGGCATCAAAACAGACACA 2511
                            i    i    iv   i    ii  i  i      v ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_225415046_   2512 TAGACCAATGGAACAGCACAGAAAACCGAGAAATAAATTCACACACTTAG 2561
                             i        i  v iv  i ii v         ii  i   i   v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_225415046_   2562 AGACAACCCATTTTCAACAAAGATGCCAGGAACATGCATTGGGGAAAAGA 2611
                         i v   iiv      i    i i     i  v   v  v        ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_225415046_   2612 CAGCCTCTATAATAAATGGCATTGGGGAAACTGGATAACCATACGCAGAA 2661
                         i  i  i vi  i      iii    iv         ?   i i   i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_225415046_   2662 GAGTAACACTACATCCCCATCTTTCACCATATACAAAAATCAAATTAAAA 2711
                           i i vii iv i   i i  iv                i  v i    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_225415046_   2712 TGGATTAAAGACTTAAATGTAAGGCCTGAAACCATGAAATGACTAGAAGA 2761
                              i ?    i          iv  i    i  i   ivvi       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_225415046_   2762 AAACACTGGG--AAACACTTCAGAACAGTGGTTTGGGCAA-AGTTTTCTG 2808
                              iv  ?--   i-    ivi  vv   v  i     -i    ii i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_225415046_   2809 GGCAAGACCTCAAAAGCACAGGCAACAAAAGCCAAAATAGGTAAATAGGA 2858
                          ii v   vi          i          vv       i     v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_225415046_   2859 TTACATCAA----------------GCT-----------------AAAAA 2875
                         i v      ----------------   -----------------i   i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_225415046_   2876 TGAAGAGACAACCTACAGAATGGGA-AAAATATTTGCAAATTATCCATCC 2924
                             i        i           -               i  vi   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_225415046_   2925 AAAAAGAGATTAATAACCAGCATATACAGGGAAAGCAAACACCTCAGTAG 2974
                         i v   i  i vi  v    v     i ii   vv vv   v    i  i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_225415046_   2975 CAAATAAATAAATAATCTAATTTAAAAATGGGCAAAAGACCTGAATAGAC 3024
                         i   v i i      i i    ?             i  ii         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_225415046_   3025 ATTTCCCAGAAGATGACATACAAATGGCCAGCAGGTATACAAGGGAAATG 3074
                              i vi    v  i             ii i i i ii ii- i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATG 890

  chr2_225415046_   3075 TGAATTAACCACAATGAGATA 3095
                         i--- i   vv  ????????
  L1M4_orf2#LINE/    891 C---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (157 / 70)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 4.64 (51 / 11)  


 322 23.08 8.65 0.96  chr2_225787668_225790494.rev     1235  1338 (1489)    L1M4_orf2#LINE/L1       31   142 (766)  

  chr2_225787668_   1235 AGACTCAATACCATT-----GTCAGTTTTCCCCAAATTAAT-TATAGATT 1278
                              i    iii  ----- v  i vi          i  -  i     
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chr2_225787668_   1279 CAATGTAAACCCAATCAAAATTGTAAAT-CTTTTTTTGTA--AATTCAGA 1325
                            i i  v   v        ivi iv - i       i --    v v 
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA 130

  chr2_225787668_   1326 AGCCTGATTCTAA 1338
                            -    i    
  L1M4_orf2#LINE/    131 AGC-TGATCCTAA 142

Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.04 (5 / 112), avg. gap size = 2.00 (10 / 5)  

1396 25.93 8.43 3.24  chr2_225787668_225790494.rev     1719  2335 (492)    L1M4_orf2#LINE/L1      260   908 (0)  

  chr2_225787668_   1719 AGACAGTGTGAT---GATAAAAGGCTAGGCGCAGAGATCCTTGGAGCAGA 1765
                                   i --- ii v    v   i ii v     vv    ii   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_225787668_   1766 AGAAGGAATCCAGAAATAGAGTCTACGCATATAGAGCCAATTTATTTT-G 1814
                          vvii  i          i -i i ii   v  vi i     v     - 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_225787668_   1815 ACAAAGAGGAAATTTAATGG-AAGA--ATTTAATGAAAGAAGCATAGTCT 1861
                             i i----------  v-    --   i    iiii   v       
  L1M4_orf2#LINE/    359 ACAAGGG----------TGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_225787668_   1862 TTCCAACAAGTAGTGTGGGTACAATTGGATATCCATATGCAGAA-AATGA 1910
                           i      i i   iv  v    i      ?   i     i  -     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_225787668_   1911 ACAGGGACTTACATCTCATGCATTATAGAAAAGT-AACTCAAAACGGATC 1959
                          vvv    iivi i    ii vv    v    i -         i     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_225787668_   1960 ATAGATCAAAATGTAAAACTTAAAAC-ATACAAATGT----GGAAAATAT 2004
                          ?   i v        i vi      -   v  v v ----i     i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_225787668_   2005 ---------TTTT---AATCATGGATTAGGCAAAGATTGCTTCAATATGA 2042
                         --------- i  ---i i v   i        v i  v   vi      
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_225787668_   2043 TACCAAAAAC-CATGACTCATAAAGAAAACATTGATAAATTGGACTTTAG 2091
                         i       i -  v vvv  -        v  v              i v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_225787668_   2092 CATACTTAA---CCTCTGCTCTGAGAAAGACAGTTT--AGAGAATAAAAA 2136
                           v v    --- i i  iv  vvi  i    v v --   i i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_225787668_   2137 GACAAGCCATAAAACAAGAAAAGA------CAAAT-ATGTAGTCTATATA 2179
                              v   i i  iii  i  i ------     -  i  -   i-   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA-TCTG-ATA 745

  chr2_225787668_   2180 TATGTCTTATATATAAGACTACATGAAGTAGTCCCAAAATGTAATAA--- 2226
                         viv v   i   vi -  v  i  i   v v  ii v  ivi     ---
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCA-GAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_225787668_   2227 ------AAACAACCCAATTTTTAAAATGGACAAAA-ATTCAAAT---TAC 2266
                         ------   i         ?v-       i    i-   ii   ---i i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_225787668_   2267 TTCACTAAAGAAAACACACAGATGGTAAATAAATGTGACCATGAAAACAG 2316
                            v i      i i i   i    iv     iii----        v v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCA----CATGAAAAGAT 889

  chr2_225787668_   2317 AGTCAACATCATTGATCAT 2335
                         iv         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (97 / 60)
Gap_init rate = 0.04 (26 / 649), avg. gap size = 2.77 (72 / 26)  


2509 26.80 4.01 1.72  chr2_225844930_225847340.rev     1047  1919 (492)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_225844930_   1047 TGTTCGTGTATTGGATGACTCAATATTAGTAAGATGTCAAATCTTCTGAA 1096
                              i  v      v    i      iv       v   vv  i iv  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_225844930_   1097 ATTGATGCATAGATTTAATGCAATTTTAATCAAAATCCCAGTAGACAATT 1146
                               vi i     i  i     iiiv             iv v --  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC--TT 113

  chr2_225844930_   1147 TCATGTATACA--AACAAAATGAGCCTAAAGTTTATATAAAAATGGGAAG 1194
                          iv  i v v --i    iv   v      i  i    ii     vi i 
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_225844930_   1195 G-TCTAGAATAGCCAAAACAGTACTGAAAAAAAAAAAAAACCTTAGATGA 1243
                          -i i               i vi       i  i  v  vv  i  v  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr2_225844930_   1244 AGGACACTATCT--TTT------TTACTATAAAGCTACAAAAATCATGAA 1285
                         vvv     vi i--   ------      i         iv     v  v
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr2_225844930_   1286 AGCCTGGTATTAGTGAGAGAATGAATACATATATCAATGGAACAAAATAC 1335
                           iv     i i iivi  i  ii i i   v          i i   vv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_225844930_   1336 ACAGTCCAGGAACAAACTCACAAAT--ATAGTCAGCTAATCTTTCAGGAG 1383
                          v       i  i    i  i v  --  i    ii i  i  iv vi  
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_225844930_   1384 G----CAAAATAAATTCAATGGAGAAAACATAGTGTTTTCAATAAATAGT 1429
                          ----   i iv -        i    iv     v       i    i  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_225844930_   1430 GCTGAAATAATTCAATGTCCATA--CAAAA-AATAAA------TCCATAA 1470
                             ii i  i vi  i?   i --     -   i  ------i  v  -
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA- 461

  chr2_225844930_   1471 CAGATCTTCCATCTTTCACCAAAATTAACTCAAAATGGATCATAAACCTA 1520
                         ----i  iv  i v vi  v                      ? i     
  L1M4_orf2#LINE/    462 ----CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_225844930_   1521 AATATAAAGTGC-AATATTATGAAACTTATAGAAAAAAAAACAAAAGGGA 1569
                            i   - v  -  v i   i     iv     i    --  v i ? v
  L1M4_orf2#LINE/    508 AATGTAA-GAGCTAAAACTATAAAACTCTTAGAAGAAAA--CATAGGNGT 554

  chr2_225844930_   1570 AAATCTCTGTGACCTTAAGTTTGGTCATGAGTTTTTAAATACAATATCAA 1619
                               ii        ii   v  iv   iv  i   i   ii i i   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr2_225844930_   1620 AAATATAATTCAATGAAGAGAAAAATTGATAAATTAGACTTTATTCAAAT 1669
                           ii i  v-   ii  iii      v        i     i  iv    
  L1M4_orf2#LINE/    605 AAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_225844930_   1670 AAAAAACTTCTGCTCTGTGAAAGGCCTTGTTAACAGAATGAAGTGTCCAA 1719
                         v        i  iv  vii  i i vi i i  v i i    iv -v   
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG-ACAA 702

  chr2_225844930_   1720 GTCACAGACTGGCA-AAAATATTTGCAAAATCCAT-TAAATGATAAACAA 1767
                         vi      v   v -              --i   -  vv      ivi 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAA--TCATATATCTGATAAGGGA 750

  chr2_225844930_   1768 CTTGCATCCAAAATACATAAAGTAGA--TA-AACTCAATAATAAGGAAAC 1814
                             i     i    i      v vv--  -             ii i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_225844930_   1815 GAACAACACAATTAGATAGTGGACAGACATACGGAACAGACA---CCTCA 1861
                         i  i   v     ?i v i   i  i vivviv   i     --- ii  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_225844930_   1862 CAGAAAATATGCAGATAGAAAATAACCACATGAAAACATGCTCAAAATCA 1911
                         v    i    i  i  i vv     v          v        v    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_225844930_   1912 GATGTCAT 1919
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.67 (144 / 86)
Gap_init rate = 0.03 (23 / 893), avg. gap size = 2.17 (50 / 23)  


3299 25.30 0.99 0.88  chr2_225950527_225954804     2882  3786 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_225950527_   2882 GAAAAATATTCCGTGTTTATGGATTGGAAGAATCAATATTGTTAAAATGT 2931
                             i    i  i    i             v i           i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_225950527_   2932 TTATACTACCTAAAGCAATCTACAGATTCAATGCAGTCCCTACCAAAATA 2981
                         iv     v  i   vii              i   i      i      v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_225950527_   2982 CCAATGACATTCATCAAAGAAGTAGGACAA-----TCTTAAAATTTATAT 3026
                            iivi v  iv iiv    i -v     -----  i       i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATAT 151

  chr2_225950527_   3027 GGAACCTCCAAATACCCAAGGTAGGCAAAACTATCCTAAGCAAAAAGAAC 3076
                             viv v iiv     iii   v      v   i i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_225950527_   3077 AAAACTAGAGGAATCACATTACCTGACTTCAAACTATACTACCGTGATAT 3126
                            ii i     v     i v  ii i      viv      viv v  i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_225950527_   3127 AG-AACCAAAATAGCATGGTACTGGCATAAAAAACAGACATATAGACCAA 3175
                           -  i   i i  ii              ii -i           i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAA 300

  chr2_225950527_   3176 TAGAACAGAAAAAGAGAACCCAGAAACACATCCACACACCAACAATGAAC 3225
                          i   i    -vv    ii       i v i   i   iiv iii v  i
  L1M4_orf2#LINE/    301 TGGAATAGAA-TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_225950527_   3226 TCATTTTTGACCAAGCTGTGAAGAATATACACTGGGGAAAAGATATTTTC 3275
                          v     i   v i v  iv    vi  v  v        ii   v i i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_225950527_   3276 TTCAATAAATGATGCTGGGAAAACTGAACATCCATATGCAGAAGAATGAG 3325
                              i     i        v     i i ?   i     i        -
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA- 448

  chr2_225950527_   3326 TGAAGCTAGACCCCTACCTCTCACCATATACAAAAATCAAACCAAAATAG 3375
                         ---  i i            v                i  vi      i 
  L1M4_orf2#LINE/    449 ---AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_225950527_   3376 ATTAAAGACTTAAATCTAAGACCTCACGCTATGAAACTACTACAAGAAAA 3425
                           i ?    i     v     v  v vi    i     vi  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_225950527_   3426 CATTGGAGAAACTCTCCAGGATATTGATCTGGACAAAAGTTTCTTGAGTG 3475
                            v  ? v  v   i iv  iv   ivi i i   vi       iii i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_225950527_   3476 ATACCCCAGAAACACAGGCAACCAAAGCAAAAATAGACAAATGGGATCAT 3525
                         vv  v   i  i    i     v    v         i    v   iivi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_225950527_   3526 ATCAA-GTTAAAAAGCTTCTGCACAGCAAAGGATACAATCAACAAAGTGA 3574
                              -i       -   i  ii vv       i  v     v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_225950527_   3575 AGACACAACCCATAGAATGGGAGGGAATATTTGCAAACTACCCATCTCAC 3624
                          i v        i          ii            ii ivi    v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_225950527_   3625 AAGGGATTAATAACCAGAATATATAAGGAGCTCAAACAAATCTATAGGAA 3674
                               i vi  v             i  i   vv    v  v   iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_225950527_   3675 AAAATGTAATAATTCCACC-AAAAATGG-CAAAATAAATAAATAGACATT 3722
                            ivvv     ii v ii-        -    iv vv i          
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_225950527_   3723 TCTCAAAAGAAGATATACAAATGGCAAACAGGCATATGAAAACGTAGTCA 3772
                             v                    v  i i   i       vi iv   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_225950527_   3773 GCTTCATCAATCAT 3786
                         i v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (139 / 87)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.70 (17 / 10)  


3365 26.39 0.55 0.11  chr2_226230763_226235029.rev     2874  3775 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_226230763_   2874 GAAAAATATTCCATGTTCATGGATTGGAAGGATCAATAATGTTAAGATTT 2923
                             i    i                    iv i    v         vv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_226230763_   2924 CCATATTCCCCAAAGCAATATCCAGATTCAATGCAACCTTTATCAAAATA 2973
                          v   i        vii  v v         i    i ii         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_226230763_   2974 CCAATGACATTCTTCACAGGAATAGAAAAAC-AATTCTAAAATTTATATG 3022
                            iivi v  i  ii   i   v  v  i -i  i        i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_226230763_   3023 GAACCACAAAGT-CCTAGAATAGCTAAAGCTATCTCAAGCAA-AAGAACA 3070
                            vii   i v-  i        i   i v    ii iv  -       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_226230763_   3071 AAACTGGAGGAATCATATTACTTGACCTCAAATGATATTGCAGAGGTATA 3120
                           ii       v   i i v iii ii     vvv  i i  i  v  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_226230763_   3121 GTAACACAAACAGCATAGCACTGGCATAAAAACAGACACATAGACCAATG 3170
                             ivv i    ii i i          ii i     i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_226230763_   3171 GAACAGAACAGAGAACCTAGAAACAAATTCATATATCTAAAGTAAAATCC 3220
                            i    iv    ii i     i   ii    i  i  vi  v  v vv
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_226230763_   3221 TCTTCAACAAAAGTTCCAAGAACATACATTTGGGAAAAGACAGTCTCTTC 3270
                          i   i    ii  v      v   v  v v      ii i     i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_226230763_   3271 AATAAAAGGTGCTTGGAAAATGGGATATCCATATGCAGAAGAATGAAATT 3320
                           i   v      v   v  iv     ?   i     i         i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_226230763_   3321 AGATCCCTATCTCTTGGCATATACAAAAATCAAATCAAAATGGATTAATG 3370
                         i  i     i   viiv             i  v           i ?v 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_226230763_   3371 ACTTAAATCTAAGACCTCAAATCATGAAACCGCTAAAATTAAACATTGGG 3420
                           i     v     v  v   ii  i    ivi  i  vv      v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_226230763_   3421 GAAACTCTCCAGGACATCGGACTGGGCAAAGATTTATTGAGTAATACCCC 3470
                          v  v   i iv   v i  ii i     v i   v  iii  vv  v  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_226230763_   3471 AGAAGCACAGGCAACTAAAGCAAAAATGGACACATGGGATTATATCAAGT 3520
                          i       i     v    v      i  i v  v   i vi     iv
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_226230763_   3521 TTAAAAGTTCCTAAACAGCAAAGGAAACAATAAACAAAGTGAAGAGACAA 3570
                               ii ii ivi vv       v  v  v  v        i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr2_226230763_   3571 CCTACAAAATGGAATAAAATATTTGCAAACTATCCACCTAACAAGGGATT 3620
                           i   i     i v              ii  vi i  i i      i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr2_226230763_   3621 TAAAACCTGAATATATAAGGAGCTCAAACAACTCTATAGTAAAAA-ATAT 3669
                          iv v  v          i  i   vv       v   i      - i -
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA- 801

  chr2_226230763_   3670 AATAACCTGACTTAAAAATGGGCAA-CTATCTGAACAGATATTTATCATA 3718
                                ii i ?            -vv  i    i   i    v  vv 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_226230763_   3719 AGAAGACATACAAATTGCAAACAGGTATATGAAAAGGTGTCCAACATCAT 3768
                               i        v  v  i i i i        i  ii        ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr2_226230763_   3769 TGATCAT 3775
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.66 (146 / 88)
Gap_init rate = 0.01 (6 / 906), avg. gap size = 1.00 (6 / 6)  


2719 26.77 4.46 0.57  chr2_226513997_226520681     5320  6193 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_226513997_   5320 TGGAAAAACATTCCATTCTTACAGATAGGAAGAATCAGTATCATGAAAAT 5369
                               i i  i    vi i ii   v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_226513997_   5370 GGTAAT---------------TTATAGATTCAATGCTATTCC-ATTGACA 5403
                           i   ---------------i  i        i  v  i  -  ii v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_226513997_   5404 TTC-----------TTCACAGAGTTAGAAAAAACT-ACTTTAAATTTCAT 5441
                          i -----------  ii    iv v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_226513997_   5442 ATGGAACCA-AAGAGAGCCCATATAGCCAAGACAATCCTAAGCAGAAAGA 5490
                               vii-   i  v  viv        i      i i iv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_226513997_   5491 ACAAAGCTAGATGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5540
                               i i  v vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_226513997_   5541 ACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGA--TACAGACCA 5588
                                i   i    ii         i  v ii i   --  i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_226513997_   5589 ATGGAACAGAACAGAGACCTCAGAAATAACACAACACATCTACAACCATC 5638
                               i    iv    vii         vv v i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_226513997_   5639 TGATTTTTGACAAACCTGACAAAAACTAGCAATGGGGAAAGGAT--TCCT 5686
                                i     ivv  v   i v vvv            i  --  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_226513997_   5687 TACTTAATAAATGGTGGTGGGAAAACTGGCTAGCTA--TGCAGAAAACTG 5734
                          -- i  i        v     v      v  ? i --    i  i v  
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_226513997_   5735 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 5784
                           ii         v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_226513997_   5785 TAAAGACTTAAATGTAAAATCCAAAACCATAAAAACCCTAGAAGAAAATC 5834
                         i ?    i         i v i     i      vi i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_226513997_   5835 TAGGCA-ATACCATTCAGGACATAAGCATGGGCAAAGACTTCAT-GATGA 5882
                             ?i- v i -   iv   v vi vv i     v ii   v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr2_226513997_   5883 AAACTTCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5932
                         vi  vi        vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_226513997_   5933 AATAAACTAAAGAGCTTCTGCACAGCAAAATAAACTAGCATCAGAGTGAG 5982
                          vi   v v  i i   i  ii vv    iv v    v  vv i     i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_226513997_   5983 CAAACAACCTACAGAATGGAGGAAAATTTTTGCAATCTACCCATCTGACA 6032
                         v i      i         ii      v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_226513997_   6033 AAGGTCTAATATCCATAATCTACAAGGAACTTAAACAAATTTACAAGACT 6082
                          i  v  vi      v   v  i  i     ivv    v iv i  v vv
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_226513997_   6083 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATGTGAACAGACACTT 6132
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_226513997_   6133 CTAAAAATAAGACATTTATGTGGCCAATAA--ACATGAAAAAAAGCTCAT 6180
                           vv   v    i  vi vi          --         i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_226513997_   6181 CATCACTGATCTT 6193
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.93 (44 / 15)  


1036 26.76 7.68 7.47  chr2_226541883_226546662.rev     3067  3548 (1232)    L1M4_orf2#LINE/L1        3   485 (423)  

  chr2_226541883_   3067 GAGAGACATTCCATTTCCATGGGT---A----TTAATA-----AAGATGT 3104
                           i   i  i    v i     i --- ----      -----      -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG- 51

  chr2_226541883_   3105 G----ACTTCTCAAATTGATATACAGGTTTAATGTAATTCCTATCAAG-T 3149
                          ----   i i         v     i  i  i i   i        i- 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_226541883_   3150 CTCAGAAGATTTTTTTTTTTGCAAA---TGAGA--CT-ATTCTAAAATGT 3193
                          i   ----i vii         i ---   v --  -  i       vi
  L1M4_orf2#LINE/    102 CCCAG----CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_226541883_   3194 ATATGAAAAGGTAAAATAACTAGAAAGGCTAAAATAATTCTGAAAAAAAA 3243
                              i   v i  iiv v i    vi  i    i   ii       i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_226541883_   3244 --ATGAAGGGAGAGGAATCATCCTAACTGAATTTAAGACTTATTATACAG 3291
                         -- ii   vvi     v   iv  vv ii v  i  i     i  i v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_226541883_   3292 CTACAGTTATCATATGGCTACAGTTATATGACTCCTTATTACATGGTTGT 3341
                                v    ---------  -----------------   -----  
  L1M4_orf2#LINE/    248 CTACAGTAATCA---------AG-----------------ACA-----GT 266

  chr2_226541883_   3342 GGGGTATTTGTGGAAGGATGTCCATATAGATCAATAGAACAGAGTACTGA 3391
                          v    i v iiv      ivv             i   i   i vvv  
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr2_226541883_   3392 ATCCAGAAATAGATTTATATAAATATGCCCAATTAATATTTGACAAAGGA 3441
                         i          i iii   i vv    vi     i  v  i     i  v
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_226541883_   3442 GCAAAG-CAATTCAGCAGCAGCTGGATTGCTTCCCCAATAAATGATACTG 3490
                           v   - v     iii viivv i  v ii iii   i     i i   
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr2_226541883_   3491 AAGAAATTCAGCATCTACAGACAGAAAAA-GTAG----------ACCTCA 3529
                         iiiv  i viii ? i   vi  i  i  - v  ----------      
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_226541883_   3530 CACTTTATACAAAACCTAA 3548
                            iv         vi   
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAA 485

Transitions / transversions = 1.98 (85 / 43)
Gap_init rate = 0.04 (17 / 483), avg. gap size = 4.29 (73 / 17)  

1024 27.27 10.86 1.77  chr2_226541883_226546662.rev     3893  4288 (492)    L1M4_orf2#LINE/L1      477   908 (0)  

  chr2_226541883_   3893 AAAAATTAACTCAAAATGTATTATGGAGTTAAATGTAAAGCCTCAAACTA 3942
                                           v  i ?i  vi         iiv  v      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_226541883_   3943 TAAAACATTAAGAAGATAAAC-TAGGAGAAAATTTTCAC-ACTGTAGGTT 3990
                               vi v      -    -    ? v    i   ii-  iv i    
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGA-AAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_226541883_   3991 CTGCACTGTGAAGACTTTTGAGATGTGAGACTGAAGGCACATTCTGTAAA 4040
                         vv   v  -----ii  i v    i   v  ii  i     vv vii   
  L1M4_orf2#LINE/    576 AGGCAATG-----GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr2_226541883_   4041 A----AAAT---CTAACTGAAATTTGTCATAACTAAACATTTTTACTCTG 4083
                          ----    ---iv  i  i v  ii   v  i    v i    iiv  v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr2_226541883_   4084 TGAAAGACATTGTTAGAAGAATTAAAGGATAAGCTACAAGA-GGTAAAAA 4132
                         ii  i    i i i ii i i v   i  i  v i   ii -  v i   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_226541883_   4133 ATAAATTGCCAATCACATAGCTGGCAAAAGACTCACATCTAAAATGTATA 4182
                            v-    v     i   v   ii  ii    iii   i i   i    
  L1M4_orf2#LINE/    721 ATAT-TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_226541883_   4183 A---------------------------------CAACCCCATCAAAAAG 4199
                          ---------------------------------i     v  i?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_226541883_   4200 TGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGC 4249
                              i     iv    i     i     v        i  vi viii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_226541883_   4250 CAAAAAACACATGAAAAAATGCTCATCATCACTGGCCAT 4288
                            v  i          i       v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (70 / 35)
Gap_init rate = 0.02 (9 / 432), avg. gap size = 5.56 (50 / 9)  


2305 22.46 7.45 5.98  chr2_226548151_226552495     2970  3855 (490)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr2_226548151_   2970 ATTCCTTGTACATAAACTGGAAGACTCAATATT---AAGATGTTGATTCT 3016
                           i  v   v   ii i         i      ---      vii  v  
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr2_226548151_   3017 TCCCAGATTGACCTATAGAATGTATGTAATCCTAATCAAACTTCCTGAAA 3066
                         i    i     i   i   v vv i i     iv      v i  v vvi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr2_226548151_   3067 GATATTTTGTAGATATCAACAAATTGATTCTTAAATTAATATGGAAAGGC 3116
                         vv v     i   v  ii    ii    i  v     v         v  
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_226548151_   3117 AAATGAACTGGAATAACAACCACAATTTTGAAAAAGAAGAACAAAGTTGG 3166
                           iv  v ii     i v vv     i                       
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_226548151_   3167 CA-ACTTACAC--CTCAACTTCAAGGCATACTATTAAGCTATGATAATCA 3213
                         vi-   i    -- i   i     ii v     iv      iii      
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_226548151_   3214 AGACACAGTGGTAATAGTGAAACAATAGACCTTTAAATCAAAGGAAC--- 3260
                              vv      v i iiv  vi      v v  i     v    i---
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_226548151_   3261 ---------CCAACAAATTGACCCAAAGAG--AT--TCAAATAACT---G 3294
                         ---------   i-    vi     v v v--  --    v i i --- 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAG-AAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_226548151_   3295 GCAAAGATGCAAAGGCAATTCAATGGAGAAAAGATGGTCTCTTAATCAAA 3344
                         i   i i   v   i v         i    ii  i    i  v v    
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr2_226548151_   3345 TGGTGCTGGAACTATTGGA-ATCCACATGCATAAATAAAAATTTAAAAAG 3393
                                  i  v i    - ?         ---------------    
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCA---------------AAAG 443

  chr2_226548151_   3394 TAAACGAACTTAGACATAGCCCT--TGCATATCGCA--CAAACATTAACT 3439
                         --  i   v  i   ----    --iv  i i ii --    v       
  L1M4_orf2#LINE/    444 --AATGAAGTTGGAC----CCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_226548151_   3440 GGAAATAGATCACAGATGTAAATGT------TAAAACTATA---CTTTTT 3480
                         vi    i     ?   iv       ------          ---  i  -
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT- 536

  chr2_226548151_   3481 TTTAGAAGAAAACATAA---CAAAGTGTAGTTGACTTTCAGTTTGGTGAT 3527
                         ---             i---i   viv v  -   i  vi   v  ii  
  L1M4_orf2#LINE/    537 ---AGAAGAAAACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAAT 582

  chr2_226548151_   3528 GGATTTTTAGATACAACACAAAATTGTATAACACAAAATTTTGTAACCAT 3577
                           v  i       ii    v   ------ i     ------ i   v -
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAA------AGCACAA------GCAACAA- 619

  chr2_226548151_   3578 TTATAAAATAAAAATGGATAGTTTGGACTTTATTAAATTTTAAAATTCAC 3627
                         ----  i -      i    iv        i  i   v  v    i ---
  L1M4_orf2#LINE/    620 ----AAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT--- 661

  chr2_226548151_   3628 ATTTGTG----AAAGAA-ACTGTTGTGAGA---AGAAGATAAGCCACAGT 3669
                         -      ----    i -   i iiv  i --- i    i  v      v
  L1M4_orf2#LINE/    662 -TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr2_226548151_   3670 CTATGAGAAAATGGTGACAAAATATATTTCTGAAAAAAGACTTGTA--CA 3717
                         v iv        iv vi    vi    v     v  ii        --  
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr2_226548151_   3718 TGAATATGTAAATAA-TCTT-TAATGTCAACAATAAGAAGCCACATAACC 3765
                         -      i    v  -    -i  i-    i     i   v  v      
  L1M4_orf2#LINE/    761 -GAATATATAAAGAACTCTTACAAC-TCAATAATAAAAAGACAAATAACC 808

  chr2_226548151_   3766 CAACC---AAAT---------ATCTGGATAGACGCTTTACCAAAGAAGAT 3803
                            ii---    ---------  i  i      ii  iv           
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr2_226548151_   3804 ATACAGAGGACAAACAAGGACACACAAAAAAATGCTCAATATAATTTGTC 3853
                              i v i v  i   --    ii    i        i  v ??????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAG--CACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_226548151_   3854 AT 3855
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.53 (119 / 78)
Gap_init rate = 0.04 (35 / 899), avg. gap size = 3.40 (119 / 35)  


3613 24.07 0.77 0.99  chr2_226589151_226593399     2848  3757 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_226589151_   2848 TGGAAAGATACTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 2897
                                   ii                     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_226589151_   2898 GTTTCTACTAGCCAGAGCAATCTAAAGATTCAATGCAGTCCTTGCTAAAA 2947
                          vivv    vv   i vii     v        i   i   i iii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_226589151_   2948 TACCAATGACATTCTTCACAGAAATAGCTACAAA--AATCCTAAATTTTA 2995
                          v   iivi v  i  ii       v --    i--i        v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_226589151_   2996 CATGGAACCACAAAAGACCCAGAATAGCCAAAGCTAACCTGAGCAAAAAG 3045
                         i      vii   ii                 i v v i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_226589151_   3046 AACAAAACTGGAAGAATTACATTACCTGACTTCAAATTATATTGCAGAGC 3095
                               ii    i  v i   i v  ii i      viv  i i  i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_226589151_   3096 TATAGTAACCAAAAGAGCATGGTGTTGACATAAAAACAGA--TACAGATC 3143
                           i     i   i v  ii    ii  i     ii i   --  i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_226589151_   3144 AATGGAACACAATAGAGAATGCAGAAACAAATCCACCC-CCTAGAGTAAA 3192
                                i v   v    i v      i   i   iv -ii  vi  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_226589151_   3193 CTCATTTT-GACAAATGTGTCAAGAACGTACATTGAGGAAAAGACAGTCT 3241
                         i v     -     iv   i     v i v  v  i     ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_226589151_   3242 TTTCAATAAATAATGCTGGGAAAACTGAATATCCATATGCAAAAGAATAA 3291
                               i    ii        v     i   ?   i            i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_226589151_   3292 AACTAGACCCCTATTTCTCACCATATGCAAAAATCAAATGAAAATGGATT 3341
                          ii i        ii  v        i       i  v v         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_226589151_   3342 AAAGACTTAAATCTAAGACCTCATACTATGAAACTACTACAAGAAAACAT 3391
                          ?    i     v     v  v v     i     vi  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_226589151_   3392 TGGGGAAAGTCTCCAGGACATTAGTCTGGGCAAAACTTTTTTGAGCAATA 3441
                         v  ? v  i   i iv   v  i vi i     viv   i  iiii vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_226589151_   3442 CCCCACAAGCACAGGCAACCAAAGCAAAAATGGACAAATGGGATCACATC 3491
                          v   v       i     v    v      i  i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_226589151_   3492 AAG-TTAAAAGGCTTCTGCACAGCAAAGGATACAATAAAAATAAAGTGAC 3540
                           i-      i-   i  ii vv       i  v  v  i --      v
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA--AAGTGAA 695

  chr2_226589151_   3541 AAGACTATCCACAGAATGGGATAAAAAATTTGCAAACTACCTATCTGACA 3590
                              v i             v    v         ii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_226589151_   3591 AGGGATTAATAACCAGAATATATAAGGAGCTCAAACAACTCCACAGGAAA 3640
                              i vi  v             i  i   vv       v i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_226589151_   3641 AAATCAAATAACCTGATTTTAAAATGGGCAAAATATTTAAATAGACGTTT 3690
                           iv         ii   ?v            iv    i       i   
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_226589151_   3691 CTGAAAAGAAGACATACAAATGGCAAATAGACATATGAAAAGGTAGGTGT 3740
                           vv        i           v    ii  i        i ---- i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT----GC 891

  chr2_226589151_   3741 TCAACATCATTGTTCAT 3757
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (136 / 79)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


3242 22.09 7.76 1.06  chr2_226604293_226606176.rev      543  1393 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_226604293_    543 TAAAAAGATATTTCATGCTCATGGATTGGAAAAATTA-TATTGTTAAAAT 591
                          ii        ii    i             i v   -         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_226604293_    592 GACAGTTCTACTCAAAGCAATTTACAGATTCAATGCAATCTCTATCAAAA 641
                          i  i v  v i    vii  i           i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_226604293_    642 TACCTA--TGTCATTTTTCATAGAAATAGGAAAAGTAATCCTAAAATTTA 689
                          -  i --  i -     iii      v iv  iv i           i 
  L1M4_orf2#LINE/    101 T-CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_226604293_    690 TATGAAATCACAAAAGACCCAGAATAACCAAAGCAATCCTGAGCAAAAAG 739
                             i  vii   ii           i     i     i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_226604293_    740 AACAAAGCTGGAGGTGTCACACTACCTAATTTCAAAATTTACTACAAAGC 789
                                i      vv       v  i          i            
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_226604293_    790 TCTAATAACCAAATGGGTCATCTTGGTACTGGCATAAAAACAGACAAATA 839
                          vi i   i   ---- v  viv              ii i     v   
  L1M4_orf2#LINE/    249 TACAGTAATCAA----GACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_226604293_    840 GATCAGTGAAACTGAATAAAGAAACCCAGATATAAATCCATGCATTTATA 889
                              i  i  iv    vi   i-i     v     i    i       i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAG-TCCAGAAATAAACCCATACATTTATG 343

  chr2_226604293_    890 GACAAC--ATTTTCAACAAAAGTGTCAAGAACATATAACAGGGATAGGAC 937
                          v   i--      i    ii   i     v   vi  ii    v  i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_226604293_    938 AGTCCCTTCAGTAAATGATTCTGGGAAAACTGGATATCCATATGCAGAAG 987
                             ii    ii     i v      v         ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_226604293_    988 AATGAAACTAGACCCCTATCTCTCATTGTATACACAAATCAAATAAAAAT 1037
                               ii i        i   v  iii      v    i  v v     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_226604293_   1038 AGATTA----------------------AACTATGAAACTATTAGAAGAA 1065
                         i   i ----------------------      i     v         
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_226604293_   1066 AACAC-TGTGTGAAATGCTCCAGAACATTGGTCTGGGCAAAGATTTTTTG 1114
                             i-v ?  -    -  i ivi  v    vi i     v i   i  i
  L1M4_orf2#LINE/    544 AACATAGGNGT-AAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_226604293_   1115 TGTAGGATCTCAGAAGCACAGGCAACCAAAGCACAAATAGAGAAGTGGGA 1164
                         vi  v  ivi  i       i     v    v v       v  i v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_226604293_   1165 TTACATCAAG-CTAAACA-------GC---AAAGGAAACAATCAACAAAG 1203
                         i v      i-i    v -------  ---      v  v     v    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_226604293_   1204 TGAAGAGATAATGCACAGAATAAAAGAAAATATTTGCAAGCTATGCATCT 1253
                             i   i  iv        iii               iii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_226604293_   1254 GACAAGGAATTAATAAACAGAATATATAAGGAGCTC-------------- 1289
                           i    i i vi  vv            i  i   --------------
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_226604293_   1290 -----AAACAAACAG----ATTTAAAAATCGGCAAAAGACATGAATTGAC 1330
                         ----- i     i i----   ?      v      i  iv     v   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_226604293_   1331 ATTTCTCAAAAGAAGACTTACAAATAGCCAA---ATACATGAAAA-ATGT 1376
                                v        iv       i     ---ii         -   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_226604293_   1377 TCAACATCCTTAATCAT 1393
                                 v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (126 / 59)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.17 (75 / 18)  


 476 25.81 9.68 1.61  chr2_226671578_226677209     3540  3725 (1907)    L1M4_orf2#LINE/L1        4   204 (704)  

  chr2_226671578_   3540 AAAGATATCA-GTGTTTATGGATTAGAAGACATAACATTATTAGGAGGGC 3588
                                  v-i    i       i      v   i   i   i  v   
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_226671578_   3589 AATGCTCCTTAAATTGATCTACAAATTCAACAAAATCCCTGTTAACATTC 3638
                            i    ii             i       iv       i i  v  i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_226671578_   3639 TGACTTTAACTAACCTGCACAATGTGCACATGT--ACCCTAAAACTTA-- 3684
                         iii  vi--  vvii    v  vv  -   v i-- i       i i --
  L1M4_orf2#LINE/    104 CAGCTGC--CTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCATA 150

  chr2_226671578_   3685 ---AAGTATAATAAA---AAAA-----AAAATAAT--TAAAAAAACAAAA 3721
                         ---  i ii  vii --- i  -----    i   -- i     iv i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_226671578_   3722 CAAA 3725
                             
  L1M4_orf2#LINE/    201 CAAA 204

Transitions / transversions = 2.43 (34 / 14)
Gap_init rate = 0.04 (8 / 201), avg. gap size = 2.62 (21 / 8)  

1107 21.76 0.84 0.00  chr2_226671578_226677209     3847  4085 (1547)    L1M4_orf2#LINE/L1      130   370 (538)  

  chr2_226671578_   3847 AAGCTTATCCTAAAATCCCAAAGAAAATGCAAGCAACAAAGAATAGCCAA 3896
                              v          i vv v i         vi  vv           
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_226671578_   3897 AACAATTTTGAAAAAGATCAACAAATTTGGAGGACTCAGGTTTTTTGATT 3946
                               i          vv      v            vii  iiii   
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_226671578_   3947 TCAAAACCTACTAGAAAGCTACCATAATCAAAACACTGTACTACTAACAT 3996
                                i     v        vi       i   v   iv    ii   
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_226671578_   3997 GAAGGT-GACATACGGATCAATATAATAGAACTGAAACTTCAGAAATAAA 4045
                         i i i -      ii       iv       i   i v i          
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_226671578_   4046 CCCATACACCTAGGGTTAACTGATTTTTG-CGAGGCTACTA 4085
                                 ii  v   i  i       i - i   v i i 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

Transitions / transversions = 1.74 (33 / 19)
Gap_init rate = 0.01 (2 / 241), avg. gap size = 1.00 (2 / 2)  

2225 20.26 2.21 1.29  chr2_226671578_226677209     4598  5140 (492)    L1M4_orf2#LINE/L1      361   908 (0)  

  chr2_226671578_   4598 AAAGGTACTGAAACAATGTAATGCAGAAATAATCATATTTTCAACTCATG 4647
                           i   i ii i  v  vi    vi    v   vi v        vv   
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_226671578_   4648 GTGCTAGGACAACTAGATATCTATATGCTAAAGAATAAATTTGGATCTGC 4697
                              i        i    ? i i    v       i  v     i i- 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC-C 459

  chr2_226671578_   4698 TACTTTACACCACACATAACG-TCAACTCAAAATGGATCAAATACCTAA- 4745
                            i i      i i i  vi- i                ? v      -
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr2_226671578_   4746 -----GATTTAAAGCTCTAAATCTCTTGGAAGAAAAC-CAGATGTAAATC 4789
                         -----  vi    i  v    v     i         -i  i?       
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr2_226671578_   4790 TTCATGACCTTAA-TTAGGCAACTTTTTTTTTTTATGTATGACACCAAAA 4838
                            i       ii-        --- vv   i   vi             
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAA---TGGTTTCTTAGATATGACACCAAAA 606

  chr2_226671578_   4839 GCACAAGCAACCAAGGAATAA-TAGATAAATTGGACCTCAGCAAAATTAG 4887
                                    v  i   v  -              i   v        i
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_226671578_   4888 AGCCATTTGTGCATCAGAGGACAGTATCATGTAATTGAAAAGACAAATCA 4937
                          iv v       v   i      v     v v  v           vi  
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_226671578_   4938 AAGAATGGAAGAAAATATGTGTAAATCGTATATCTGATAATGTG-TAGTA 4986
                         v       i         v  i     i            v vi- v   
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_226671578_   4987 TCAAGGATATATTTATAGAACTCTCAAACCTCAACAATAAAAAGACACAT 5036
                           v  i      -- v        i v v     i            v  
  L1M4_orf2#LINE/    757 TCCAGAATATAT--AAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_226671578_   5037 AAGCAAAAT-AAAAACGAGCAAAACAAATGTAATAGACATCTCTGTGAAG 5085
                           v v  v -     i i     iv vv  -         i   vii   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTG-AATAGACATTTCTCCAAAG 853

  chr2_226671578_   5086 AAGGTAGACAAATGGCAAATAAACATCTGAGAAGATGTTCATCATTATCA 5135
                            i  v         v     i  iv   i      i   v   i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_226671578_   5136 TCCTC 5140
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.14 (57 / 50)
Gap_init rate = 0.02 (11 / 548), avg. gap size = 1.73 (19 / 11)  


1231 27.34 2.03 2.53  chr2_226786464_226788992        2   396 (2133)    L1M4_orf2#LINE/L1      103   495 (413)  

  chr2_226786464_      2 CCAA-TGTCATTCTTTACAGAA-TTAAAAAAAAAAACT-ATTCTACAATT 48
                            i-  i -  i   i     -  i v  i-----  -  i   v    
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAATT 146

  chr2_226786464_     49 CACTTCTAACCA-AAGAGACCTCAAATAGCCAAAGCAATCCTAAGTAAAA 97
                           iv vv  vii-   i    ivi          i     i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_226786464_     98 AGAATGAAGCTGGAGGCATCACACTACCTGACTTTAAACTATACTATAAG 147
                             ii   i      vv       v  ii i  i   viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_226786464_    148 GTTACAGTAACCAAAACAGCATGGTGCTGGGGGAAAAAAAAAAAGACATA 197
                          i        i   i    ii    i    v---- v  ii v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGC----ATAAGGATAGACATA 292

  chr2_226786464_    198 TAGACCAATGGAA-AAAATAGAAAACTCAGAAATAAAGCCACGCATCTAC 246
                             i        - i   v  i iii          v   ii   i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_226786464_    247 TACCATCAGATCTTTGACAAGGTCAATTAAACCAAGCAATGGAGAAAGAA 296
                         vii  viv   i  i       viiviv i    vv      i       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_226786464_    297 TATGCTATGCAACAAATGGTCCTGGGATAACTGGCTAACCATATGCAGAG 346
                           vv  v v           v      i      v  ?   i     i i
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_226786464_    347 GAATGAAAC---ACCCTTACCTTTCACTGTAAATAAAAACAAACCTGAGA 393
                                ii---    i     iv   ii  v i     iv   iii i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_226786464_    394 TGG 396
                            
  L1M4_orf2#LINE/    493 TGG 495

Transitions / transversions = 2.06 (72 / 35)
Gap_init rate = 0.02 (9 / 393), avg. gap size = 2.00 (18 / 9)  

 266 22.08 7.79 0.00  chr2_226786464_226788992     1156  1232 (1297)    L1M4_orf2#LINE/L1        8    90 (818)  

  chr2_226786464_   1156 ATATACTTTGTTCATGGACTGGT-GACTTAATCTT---AAGA--ACAATT 1199
                             v iv          i   v-        v  ---    --i    v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr2_226786464_   1200 CTACTGAAATAGATTTATAGCTTCAGTGCAATC 1232
                           v iv    v   i  i  v    ii      
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATC 90

Transitions / transversions = 0.89 (8 / 9)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 2.00 (6 / 3)  

1383 26.70 11.62 2.00  chr2_226786464_226788992     1291  2039 (490)    L1M4_orf2#LINE/L1       88   908 (0)  

  chr2_226786464_   1291 ATTCATAACTAAATTCTAACACAATTCATTAAAGAAATTGATAAACTGTT 1340
                           i v  v v    i i i vvvv  iv  iv         i  i   v 
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chr2_226786464_   1341 TTTAAAAAT-ATATTTAAATTTTAAGAAGCAGGAATATATAAAATAAT-T 1388
                         ii     v -    vv    viv i i v vi     vvi    i   - 
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr2_226786464_   1389 TGAAA--------CAAACT--GAAAAC-----CTGCCTGATTG-AAAGCT 1422
                              --------    v --  ii  -----  v  ii   v-   i  
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_226786464_   1423 TATTGTAACTCTACAGTATTAAAGGCAGTTTGGAATTGGTGTGTAGATAC 1472
                           i ii  vv        v v   i    v   v i   ii ivi    v
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_226786464_   1473 ACATAGAAATTAGTAAAACATGATAAAGAGTCCAAAAAGAAACCAATGC- 1521
                              v i  i i ii  i vi  vi        i   v     v  i -
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_226786464_   1522 -TCATGGTCAAATGATGTTTTTA-AAAATTGCCAAGGCAATTAAATGGGG 1569
                         - i        v    -   iv -  iiv       i v   v       
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_226786464_   1570 ACAAAGTGAGTCTTTT--------GGTGCTAGAACAACTGTATATCTTCA 1611
                          v i i -        --------      i i       v   ? iv  
  L1M4_orf2#LINE/    387 AAAGAAT-AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_226786464_   1612 TA-AAAAAAATTATTTCCAGCCCTTGCCTTACATCATACA-AAAAATCAA 1659
                          i-    i   v vv ivii   i i   i   i    i -      i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_226786464_   1660 CTC-----------------TAAATG----AGCTAAAGTTTCAA--CTTC 1686
                            -----------------      ----       ii vi  --  ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_226786464_   1687 TAGATGAAAAAAGGAGAA-AAATATTTGTGAC----AATTAGGCAAACAA 1731
                             v     v vii ?i-    v  i     ----ii        vviv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_226786464_   1732 TTTTCA-ATCTGGACAC---AAGTACAAACTCTTAGTGGAA-AAAAAATA 1776
                           i i -  v  -    ---   i    i ---- iiii  -        
  L1M4_orf2#LINE/    586 TTCTTAGATATG-ACACCAAAAGCACAAGC----AACAAAAGAAAAAATA 630

  chr2_226786464_   1777 ---AAATTGGACCCAAATTTCTCCTCATTACACA-TTTTGCTCTTCAAAA 1822
                         ---         -----  iv  vvv    v v -     iv       i
  L1M4_orf2#LINE/    631 GATAAATTGGAC-----TTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_226786464_   1823 AATATAGTTTAAAAAGC-ATAAGACAAGCCACAGTCTGGCAAAAATATTT 1871
                         i i ivi iv i    i- v       v      vv   v i   -  v 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA-ATAT 724

  chr2_226786464_   1872 TTGCAAGACATACA---GGAAAGGGCTTTTCCTCACAGAAAATACATAGA 1918
                               iv    i --- iv     vi  viv  -     v   i v   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATC-CAGAATATATAAAGA 773

  chr2_226786464_   1919 ATTCTT-----TAAATAATAAGAAAACAAAC--CACAG---AAAAAAGGG 1958
                          i    ----- v        i  i     i-- v  i---     v   
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_226786464_   1959 CAAATGATTTGAATACACATTTATCAAATGAAG-TGT-C---TGTGTCAA 2003
                             v          v      v  v  v    - i - ---  - i   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG-GCCAA 872

  chr2_226786464_   2004 TAAGCACAAGGAAAGGTGTTAAACATTGCAAGTTAT 2039
                                 v i    i  i v     ii????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (110 / 88)
Gap_init rate = 0.05 (37 / 821), avg. gap size = 2.76 (102 / 37)  


2881 25.25 3.45 2.45  chr2_226791542_226793749.rev      821  1719 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_226791542_    821 TGGAAAGACATTT-GTGTTCATTGATTGGAAGAATTAATATTGCTTTAAT 869
                                 i  ii-i       v          v         i vvi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_226791542_    870 GTCTATACTACCCAAA--GAGTTAAATATTTAATATAATCGCTACCATAA 917
                          v v     v      --  vi  v v   i  iii    v   i  v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_226791542_    918 TCCCAA-TGGCATTTTTACAGAAA--AAAAAA---ATCCTAAAATTTATA 961
                              i-  v v     i      --i v  i---           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_226791542_    962 TGAAGCCAGAAAAGACCACAAACAGCCCAATAAAGGAGCTAGAAAAAGAA 1011
                           i iviiv  ii    vvi  i    -  --  vi v  v         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCC-AA--AACAATCTTGAAAAAGAA 197

  chr2_226791542_   1012 ------AGCTGGTGGCATCACCATTCCTAATTTCAAAATATATTACAAAA 1055
                         ------  i   v  vv    vv    i          iv  i      i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_226791542_   1056 CTACAGTAATCAAAACAGTATTGTACTGGCATAAAATCAAACATCTAGAT 1105
                                      i     i v            iivi i    v     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_226791542_   1106 CAATGGAACAACATAGGCAGCCCTACAATAA-CCCAAGCATAGACTGTTC 1154
                                 i iv  v iv  i  viv     -    vi   vv iv  iv
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_226791542_   1155 ACTGAGTTTTAAAAAGGATATCAAGACTACTCAATGGGAAAAGGATAGTC 1204
                          i   v   ii v    i ii      i i        i    i      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_226791542_   1205 TCCTTAATGAATGCTGCTGAAAAATCTGGATATTCACATGCCAAAAAAAA 1254
                          ii i  ii    v     ii v v       ?i       ---------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC--------- 438

  chr2_226791542_   1255 AAAAAAAAAGAAAGAAATTGGGCCCTTATCTTACACCATACACAAAAACC 1304
                         -----       v   i    i   i  i  i        i       ii
  L1M4_orf2#LINE/    439 -----AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_226791542_   1305 AATTCAAAATAGGTGAAAGACCTAATCATAAAATCTGAAGAGATAAAACT 1354
                           i       i i v ?        vii   i v  i  ivv        
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_226791542_   1355 TCTAGGAAAAAACAAAGCAAAAGAGCTTATTGACATTGGCTTTTGCAATA 1404
                         ii   i i      v  v?iv i v   vv    v    v  vv     i
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_226791542_   1405 ATTTTT----------ACCAAAAGCAAAAGCAAGAAAAGCAGAAACCAAC 1444
                         i   i ----------          v      v     v i   ivi i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_226791542_   1445 AAATGGGATTCTATAAAAATCAAAAGCTCT-GAACAACAAAAGAAAT--- 1490
                             v   i ii  v     i    i  i - vi vv    i  v i---
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_226791542_   1491 -AACAAAATGAAAAGGCAATCTATAAAATATGAGATAATATTTGCAAACC 1539
                         -  v   i       i   i i i i   iv    v            i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_226791542_   1540 ATGTATTCGATAAAGAGTTAATATCCAAAGAGTATAAGGAACTCCTATAA 1589
                           i   ii     i iii vi      i ivi     i      i  i  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_226791542_   1590 CTCAATAGCAATAAAACTAAATAACCCAATTTTTAAAAAATGGGCAAAGG 1639
                                ii  v  i  -             ?---               
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGAC-AAATAACCCAATTW---AAAAATGGGCAAAGG 829

  chr2_226791542_   1640 GACTGAAAAGACATTTTACCGAGCACAACATACAAATGGCCAACAGATAT 1689
                         ivi    v        iv  i iv vi i              i iii i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_226791542_   1690 ATGAAAAAGATGCTCAACAATACTAGTCAT 1719
                                -           vi ????????
  L1M4_orf2#LINE/    880 ATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (139 / 84)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.31 (53 / 16)  


3138 27.09 0.77 0.77  chr2_226797411_226803385     4576  5483 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_226797411_   4576 TGGAAGAACTTTCCATGCTCATGGGTAGGAAGAATCAATGTCATGAAAAT 4625
                              ii iv i     i      i v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_226797411_   4626 GGCCATACTGCCCAAGATATTTTACAGATTCAATGCCATCCCCATCAAGC 4675
                            v     v     iv iv i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_226797411_   4676 TACCAATGACTTCCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4723
                          v   iivi i ii  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_226797411_   4724 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATTCTAAGCCAAAAG 4773
                                viiv  ii  v  viv  v     iv    ii i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_226797411_   4774 AACAAAGCTGGAGGCATCACCCTACCCGACTTCAAACTATACTACAAGGC 4823
                                i      vv    v  v   i i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_226797411_   4824 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4873
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_226797411_   4874 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 4921
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_226797411_   4922 ATCTGATCAATGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 4971
                          vi    ivvi     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_226797411_   4972 CTGTTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATGTGTAGGAAGCT 5021
                           v  i  i   i          v      v  ?   ii  i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_226797411_   5022 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5071
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_226797411_   5072 TTAAAGACTTAAATGTTAGATCTGAAACCATAAAAACCCTAGAAGAAAAC 5121
                          i ?    i       v   v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_226797411_   5122 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5170
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_226797411_   5171 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5220
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_226797411_   5221 ATTAAAGTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5270
                           i   i v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_226797411_   5271 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAA--TATACTCACCTGA 5318
                         v  i     i                 v       --i   i-- i    
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chr2_226797411_   5319 CAAAGGGCTAATATCCAGAATCTACAATGAACCCAAAGAAATTTACAAGA 5368
                         i  i  i  vi          v  i  v    i vv v  v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_226797411_   5369 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5418
                             i     i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_226797411_   5419 TTCTCAAGAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5468
                              v i      i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_226797411_   5469 ATCATCACTGGCCAT 5483
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


1487 26.91 5.29 3.24  chr2_226836751_226838414      493  1172 (492)    L1M4_orf2#LINE/L1      215   908 (0)  

  chr2_226836751_    493 TTATACAGCCCTATTTCAAGACTTACTATAAGGCCACCATAATAAAAACA 542
                          i i  vv   v       i        i  i  i  vi    v  i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr2_226836751_    543 GTGTAGCGCTGGCA-AAGAATCAACAAATACATCAATGAAATAAAATAGA 591
                             i ii      -   i  vi   v   v       i    i   v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr2_226836751_    592 GAGCCCAGAAATATATTCA--CATTATATGATCATTTGATATTCACCACA 639
                            i         v ii  --    -    i   v     v   iv  vi
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATT-TATGGTCAATTGATTTTCGACAAG 363

  chr2_226836751_    640 GG-GACACAACAATCCTACGAGAAAAGGAAAAGCTTTTAAACAAATGATC 688
                           - v  vi  v  i v i i i    i v iv     v        i v
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_226836751_    689 CTGGAACAATACGCTATGCAAATTAAAAAG--TAAACTTTGACCCCTATC 736
                             i    ivv v  ?v  v  vv     -- i  v  v        i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_226836751_    737 TCACACCATGTACAAACATTAATTTGAGATGGATTCTCGAATCCATCTCA 786
                                  i      v     i ii i      iv?v  -----i  v 
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA-----CCTAA 508

  chr2_226836751_    787 ACATAATAGCTAAAACTATAAG-TTTTTAAAA------ATAG---TATAT 826
                          ii   v              i-i i   i  ------    ---  v  
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr2_226836751_    827 TTTTGTGGATTCCAAATAGAGAAAAGTTTCTTTAAAAAT--CATAGAAAA 874
                         i  i   ivi iviiv   iv  vi       - i v  --  ivi   i
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAG 607

  chr2_226836751_    875 CAATATCAATGAAATAAAAATACATATAAATTGTATTTTTAAAAAATTAA 924
                           vv v   ii   v     - i v        v i  ivvv        
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_226836751_    925 CAACTTTGGTTCATCTAAAGACA---TCAAGTAAATGAACAGGCAAGCTG 971
                         v      v  v v  v  i    ---     v  i    v  i   v ii
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_226836751_    972 TAGACTGAGACA---TACTTGAAGTTTACACACCTGACTTAGGACTGGTA 1018
                         i   v  i  v ---  i   v iv i i i i    ivvi     v   
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_226836751_   1019 ACTAGCATACATTTTCAGAAAC----AAAA---AATAATAAAGTTTATAA 1061
                         v i  v   i  ---v ii   ---- v  ---         ------  
  L1M4_orf2#LINE/    757 TCCAGAATATAT---AAAGAACTCTTACAACTCAATAATAAA------AA 797

  chr2_226836751_   1062 GGCAATCATAAA--AAGAAAAAAATGGAAAAAAGATTTGAACATA---TG 1106
                          i   --    v--  vv?        iv   i        i v --- v
  L1M4_orf2#LINE/    798 GACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_226836751_   1107 CACAAAAGAGGCTAATTTATAAACAACCAATAAGCACATGAAAAAGCACT 1156
                          v v     i v  ---  i   iii                  iiii  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATA---TACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_226836751_   1157 GAATATTATTAGATAT 1172
                         v  i  i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (98 / 82)
Gap_init rate = 0.03 (22 / 694), avg. gap size = 2.64 (58 / 22)  


4000 19.31 4.11 0.34  chr2_226986804_226988847      678  1552 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_226986804_    678 TGGAAAGATGTCCAATGTTCGTGGATTGGAAGACTTAATATTGCTAAGAT 727
                                  i   v      i                      i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_226986804_    728 GTGAATACTACCCAAAGCCATCTACAGATTTAAT-TAATACCAATTAAAA 776
                          vv      v      viv           i  i-i   v  v  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_226986804_    777 TCCTAATGACATTTTTTGCAAAAATGGAAAACTTCATCACAAAGTTCATA 826
                            i iivi v         i    v  v  vi v   vi   i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_226986804_    827 TGGAATCTCAAGGAACCTCAAATTTCCAAAACAATCTTGAAAAAGAA--- 873
                              viv     i   ivi   vv                      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_226986804_    874 CAAAGTTGATG---------------ATTTTACAACTTACTACAAAGTTG 908
                                 iv ---------------    i v              i i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_226986804_    909 TAATTATCAAAACAGTGTGGTACTGGCATAAAGGTGGACATATAGACCAA 958
                         i i v     i                    i i i          i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_226986804_    959 TGCAATAGAATAGAGAGCCTAGAAATAAACTC-T-CATGTACAGTCAAAT 1006
                           v        v     i i          i - -   v  ii     v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_226986804_   1007 AATTTTTGACAAGGGTGCCAAGACAAGTCAATAGGAAGAGAACATTCTTT 1056
                         i     i                 v v     i  i i    i v     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_226986804_   1057 TCAAAAATAATAGTGTTGGGAAAACTGTATATCCACATGGGAATAAATGA 1106
                             v  --  i   i     v     v   ?       vi  vi     
  L1M4_orf2#LINE/    401 TCAACAA--ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_226986804_   1107 AATTGGACCCTTAACTTACAATATATACAAAAATTAATCCTAAAGGCATC 1156
                          i        i  v  i   vi               ii v   v v   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_226986804_   1157 AAAGAGTTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAAAAAACA- 1205
                          ?   vi                                   i      -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_226986804_   1206 -GAAGGAGATCTTCACAACACTGGATTTGAAAATAATTTCTTGTATTTGA 1254
                         - i? v i      iii  vi   i  v iv   ii      iv  v   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_226986804_   1255 CACCAAA-GCATAGGCAACAAAAGTAAAGATCAATAAATTGGACAACACT 1303
                                -   i i          v   i  vi           vv  ii
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_226986804_   1304 AAAATGTGAAAACTATTGTATATCAAAATACACAATCAACAGAGTGAAAA 1353
                              - i      v    iiv     iv    v     v i        
  L1M4_orf2#LINE/    649 AAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_226986804_   1354 GGCAACCTACGGAGTGGTA---AATATTTGTAAATCCTATACCTGATATG 1400
                          i     i  i  i   v ---        i     v    i      v 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_226986804_   1401 TGATTAATACCCAAAATTTACAAAGAACTCCTACAACTCAACAACAAAAA 1450
                         v  i vi  i   i   v  i         i          i  i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_226986804_   1451 ---------TCTGATTTAAAAATGGGTAAATGTCTTGAATAGACATTTCT 1491
                         ---------i ii   ?         i   v vi                
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_226986804_   1492 CCAAAGAAGATAAACGAATGTCCAATAAGTATATGAAAAGATGCTCATCA 1541
                                     v  i    v        i i               v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_226986804_   1542 TCACAAACCAT 1552
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (98 / 67)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.55 (39 / 11)  


3070 25.91 1.87 1.76  chr2_227276554_227282299.rev     4348  5254 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_227276554_   4348 TGGAAAAACATTCCACACTCATGGATAGGAAGAATTGATACCGTGAAAAT 4397
                               i i  i   iii        v      v  i   ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_227276554_   4398 GGCCATACTGCCCAAAGTACTTTATAGATTCAATGCTATTTCCATTAAAC 4447
                            v     v      v iv i  i        i  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_227276554_   4448 TAACATTAACATTCTTCACAGAATTAGAAAAAGTTATTTTAAAATTCATA 4497
                          vv  vivi v  i  ii     v v  v  iv v  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_227276554_   4498 TGGAACCAAAAAAGAGCCAAAATAGCCAAGACAATCCTAAGCAAAAAGAA 4547
                              viiv  ii  v   i         i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_227276554_   4548 TAAAGCTGGAGGCATCATGCTAACTGACTTCAAACTATACTACAAGGCTA 4597
                         i    i      vv   ii  vv ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_227276554_   4598 TAGTAATCAAAACAGCATGGTACTGGTACAAGAACAGACACATAGACCAA 4647
                         i         i    ii         i i   i i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_227276554_   4648 TGGAACAGAATAGAGCAGTC-AGAAATAAGACCACACACCTACAGTCAAC 4696
                              i     v   -    -        iv   i   ii  ii     i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_227276554_   4697 TGATTTTTTATAACGTTGACAAAAACAAGCAATGGGGAAAGGATCCTCTA 4746
                                iv i  v v  v   i v  vv            i  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_227276554_   4747 TTTAATAAATGTTGCTGTGTGAACTGGCTAGCCATATACAGAAAATTGAA 4796
                           i  i     v     v vv      v  ?   i  i  i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_227276554_   4797 ACTGAACCCCTTCCTTATACCATATACAAAAATTAACTCTAGATGGATTA 4846
                         ii  i      v   i i                     v i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_227276554_   4847 AAGACTTAAATCTAAAACCCAAAA-----------TTAGAAGAAAATCTA 4885
                         ?    i     v   i v i    -----------           iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_227276554_   4886 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTGATGAGGAAAA 4934
                           ?i- v i -   iv   v v  vv i     v i   vv iiiv vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_227276554_   4935 TGCCAAAAGTAATTGCAACAAAAGCAAAAATTGACAAATTGGATCTAATT 4984
                         ii       i vvv          v      v  i        ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_227276554_   4985 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGACTGAACAG 5034
                            v v  i i   i  ii vv    i  v       vv i v    v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_227276554_   5035 ACAACTTACATAATGGGAGAAAATTTCTGCAATCTATCCATCTGACAAAG 5084
                              ii   v             v i     vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_227276554_   5085 GTCTAATATCCAGAGTCTACAAGGAACTTAAATAAATTTATAAAAAACAA 5134
                          v  vi        i v  i  i     ivv i  v iv    v   ---
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA--- 795

  chr2_227276554_   5135 AGCAAAACAAAACCACACACAACCCCATTAAAAAGTGGGCAAAGGGCATG 5184
                         ---  i     --------i     v   ?    i          iiv  
  L1M4_orf2#LINE/    796 ---AAGACAAA--------TAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_227276554_   5185 GACAGACACTGCTCAAAAGAAGACATTCACA---CCAACAAACATATGAA 5231
                         i i     i v   v        i  v  v ---    i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_227276554_   5232 AAAA-GCTCAACATCACTGATAAT 5254
                           i -           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (135 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.67 (33 / 9)  


3318 21.45 6.64 1.52  chr2_227518383_227521989.rev     2258  3115 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_227518383_   2258 GACATTTCACATTCATAGAATGGAAGCCTCAATATTGTTCAAATGACACT 2307
                           i  ii  ii     i  v      v  i         v i   i  v 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_227518383_   2308 CCTTCTTAAATTAACCTATACATTCAATACACAATCCCT--CAAAATTTC 2355
                         v  i ii     i i   i v      -- i        --      ii 
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAA--CGCAATCCCTATCAAAATCCC 104

  chr2_227518383_   2356 AGCAGGCTTTTTTGGGGTACACACTTCACAAGCTGGTCCCTATAATCTA- 2404
                            v v        ---i v v -  v        i   -  v   ii -
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTG---CAGAAA-TTGACAAGCTGATCC-TAAAATTCAT 149

  chr2_227518383_   2405 ---GAA---TAAAAGAACTAGAATGGCCAAAACAGTTTTGAAAAAGAAGA 2448
                         ---   ---i  ii  v i     i         i i             
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_227518383_   2449 ATAAAGTTGGAGGAATTATACTACTTAATTTCAAAATGTGTTATAAAGTT 2498
                          i            v i i   v ii          iv ii  i    i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_227518383_   2499 ATAGTAATCGTGACAGTGTGCTATTGGTGTAAGAATAGGCATAAAGATCA 2548
                          i       iv         v  i   ii    i    i    v      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_227518383_   2549 ACAGAATAGAACTGA---------AATAACCCCCTA----TGTGGTCAGT 2585
                          ii        i   ---------     v   v  ---- i      i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_227518383_   2586 TGATTTTCAACAAAATTGCTAAGGCAATTTAATGGGGAAAGGATAGTCTT 2635
                                 i    iiv   i   i v   i           i        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_227518383_   2636 T-CAACAAAGAATGCTGGCAGAGTTGGATGTC----TGAAAAAAACTATG 2680
                          -       vii      v v ii     i? ----  v    i --   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA--ATG 447

  chr2_227518383_   2681 AACTTGGGCCC-------ACACAATGCACAACAATTAACTCCAAAGGGAT 2723
                           v    i   -------    v  ii    v         v   v    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_227518383_   2724 CATAGGCTTAAATGTAACAGCTAAAACTATAAAATTTCTAGAAAAAATCA 2773
                           ?  i i         v                i ii     i   v  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_227518383_   2774 CAAAAGAAAATCTTTGTCATCTTAGATTAGGCAAAGACTTCT-ACATATG 2822
                         i ii? v       i  v i   i i        v ii    - v     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_227518383_   2823 ACAGGAAAAGTACAATCCACAAAAGAAAAAATTGATAAATTGGACCTCA- 2871
                            vv     i    v v              v            i   -
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_227518383_   2872 -AAATTTAAAAAAT---ATACTT-AAAAGACATCATTAAGAAAATGAAAA 2916
                         -   v       v ---i i   -   i    ii  i      i      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_227518383_   2917 TCATGATAG-----AGATTGGAAGAAAATATTTGCAAATATTGTATCTAA 2961
                         ----  i i-----   v   i                 vv i     i 
  L1M4_orf2#LINE/    698 ----GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_227518383_   2962 TAGAGGATTTTCCTCTGGAATATTTAGATTACTCTTACCAGTCAA--GTA 3009
                           ii   i  viv  ii      v  i vv        v v    --i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_227518383_   3010 GAAA-----ACAATTCAGTTAAAAAGTGGGCAAAAGATTTGAATATATTC 3054
                         i   ----- i  ii  i  ?    i        i          v ivi
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_227518383_   3055 TTCATCAAAGAAGATATATGAGT----AATAAACATATGAAAATATTCTC 3100
                            vi             ii i ----     i  i       v  v   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_227518383_   3101 AGCATCATTAGTCAT 3115
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (120 / 60)
Gap_init rate = 0.02 (22 / 902), avg. gap size = 3.18 (70 / 22)  


3485 24.07 0.66 1.31  chr2_227608788_227613346.rev     3154  4067 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_227608788_   3154 TGGAAACATATTCCGTGTTCATGGATTGGAAGACTCAATATTGTTAAAAT 3203
                               v    i  i                    i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_227608788_   3204 GTCCATACTACCCAAAGCAAACTACAGATTCAATGCAACCCCTATCAAAA 3253
                          v v     v      vii v            i    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_227608788_   3254 TACCAATGACATTCTTCACAGAAATAGAAAAAGTAATTGTAATATTTACA 3303
                          v   iivi v  i  ii       v  v  iv i  iv   v   i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_227608788_   3304 TGGGACCACAGAAGACCAAGAATAGCCAAAGCTATCCCGAGCAGAAAGAA 3353
                            i vii  iii    v            i v   ii  iv ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_227608788_   3354 GCAAACTGGAAGGA-TCACATAACCCCACTTTGAATTATACTACAAAGCT 3402
                         -    v v i    -     ivv   v i  ii  viv            
  L1M4_orf2#LINE/    201 -CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_227608788_   3403 ATAATAACCAAAAGACCATGGTACTGGCATAAAACCAGACACATAGATCA 3452
                          i i   i   i v vii              iivi     i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_227608788_   3453 GTGGAAGAGAACAGAGAACCCAGAAACAAATCCATACATTTATGTTGATC 3502
                         i     v    iv    ii       i   i             v v vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_227608788_   3503 TCATTTTCAAAAAAGGTGCCAAGAGAATACACTGGGGGAAAGGACAGTCT 3552
                          v      i v  i          vv  v  v     -    i i     
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCT 398

  chr2_227608788_   3553 CTTCAATAAATACTCCTGAGGGAACTGGATATCCATATGCAGAAGAATGA 3602
                         i     i    iv v   i iv         ?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_227608788_   3603 AACTAGACCCCTATCTCTCACCATATACAAAAATCAATTTGAAATGGATT 3652
                          ii i        i   v                i  i ii        i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_227608788_   3653 AAAGACTTACATCTAAGACCTCAAACTATGAGTCTACTAAAAGAAAATGT 3702
                          ?    i  v  v     v  v       i iv  vi  i       ii 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_227608788_   3703 TGGGGAATCTCTCCAGGACATTGGATT-GGCAAAGATTTATTGAGTAATA 3751
                         v  ? v vv   i iv   v    i  -     v i   v  iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_227608788_   3752 CTCCACAAGCACAGGTCA-AAAAGCAAAAATCAGCAAATGGGATCACACC 3800
                          v   v       i iv -     v      viii    v   iiv  i 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_227608788_   3801 ATG-TTAAAAGCCTTCTTTACAGGAAAGGAAACAATCAACAAAGTGAAGA 3849
                          vi-      i i  - v i vvv      v  v     v        i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_227608788_   3850 GACAACTCACAGAATGGGAGAAAATATGTGCAAACTATCCATCTGACAAG 3899
                               i                    v      ii  vi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_227608788_   3900 AGGCTAATAACAAGAATATATAAGGAGTTCAAATAGCTGCTTACATATTG 3949
                         i i  vi  v v           i  ii  vv i i  ---i -   ---
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CA-ATA--- 790

  chr2_227608788_   3950 GATAAAAC--CTAATAATCTAATTTTTAAACTGTGCAAAAGATCTGAATA 3997
                         -      v-- v     i i    ?v-   v  v     i   i      
  L1M4_orf2#LINE/    791 -ATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATA 838

  chr2_227608788_   3998 GACATTTCCCAAAAGAAGGCATACAAATGGCAAAAAGGCATATGAAAAGG 4047
                                 i v       ii           v  v i   i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_227608788_   4048 TTCTCAATATCACTGATCCT 4067
                          v     i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (126 / 90)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


 967 26.20 7.35 2.24  chr2_227617447_227622804.rev      609   921 (4437)    L1M4_orf2#LINE/L1        1   329 (579)  

  chr2_227617447_    609 TGGAGAAATATACCATATTCATGGATTGAAAAACTCATTGTTGTTAAGAT 658
                             i i    v    i           i  i   i v i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_227617447_    659 GTTAATTTTTCCCAAACTGATCTATAAAGTCAA---AATC----TTGGGA 701
                          vi   vi i      i       i i v    ---    ---- iiii 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_227617447_    702 TTTT-------TTTTTTCAGTAGATATCAACAAGCTTCTTCTGAAATTCA 744
                          iii-------      -- i   v  ii       vv i  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_227617447_    745 TGCAGAAAGGCAAAAGATCTAGAATACCCAAAGTAATTTTAAAAAAGAA- 793
                          iii    v    ii  i i      v     ii   i  i        -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_227617447_    794 --CTAAG----AGGATCCATGCTATCTGATTCCAGGATTGATTATACAGC 837
                         -- v   ----    ii  ii  vi ii   i  ii i v i  i v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_227617447_    838 AAAAGAAATCAAATCATT-TAGTATTGGTG-AAGGACAGATTTCCACATA 885
                         v v  v      iv  v - i   i   ii-     i   ----  i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA----CATATA 294

  chr2_227617447_    886 GATCAATGAAAAAAATACAGAAAGTCCAGAAATAGA 921
                                 i  v i - iv  i            i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGA-ATTGAGAGTCCAGAAATAAA 329

Transitions / transversions = 2.90 (61 / 21)
Gap_init rate = 0.03 (10 / 329), avg. gap size = 3.00 (30 / 10)  

2815 25.09 3.53 0.80  chr2_227617447_227622804.rev     1678  2554 (2804)  C L1M4_orf2#LINE/L1   (0)   908     8  

C chr2_227617447_   2554 ATGTCCCATGTTCAGGTATTGGAAGAATCAATATCATGAAAATGACCATA 2505
                           i           v v         v i     ii v  i   i v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

C chr2_227617447_   2504 ATGCCTAAAGCAATCTGCATATTCAATGCAATTCCTATCAAGATACTAAC 2455
                         v v  i   vii    i  v      i     i        i  v i i 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

C chr2_227617447_   2454 ACTG--TTTTTCACAGAAATGTAAAAAATAACCCAAAAATTCATATGGAA 2407
                         --  --     ii       vv v  iv i i  v               
  L1M4_orf2#LINE/    108 --TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

C chr2_227617447_   2406 CCAAAAAAGAGCCTGAAT-GCCAAAGCAGTCCGAAGCAAAAAGAACAA-T 2359
                         viiv  ii  v  v    -      i  i  ivi iv  i        -v
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

C chr2_227617447_   2358 CCAGAGGCATCACATTACCTGACTTCAAATTACACTACAAGGATGTAGTA 2309
                         iii    vv     i v  ii i      vivi       i v ii    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

C chr2_227617447_   2308 ACTAAAACAGCATGGTACTGCTGTAAAAGTCGATACAAAGACCAATGGAA 2259
                          ii  i    ii        vii   iii v  i i v   i        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

C chr2_227617447_   2258 CAGAATAGAGAACCCAGAAATAAAGCCAAATACTTAAAACCAGCTGATCT 2209
                         i     v    ii           v   v i i   viii  ii    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

C chr2_227617447_   2208 TCAACAAAA---CTTAAAC-ATTAATTGAGGAATGGACACCCTATTCAAT 2163
                           i    ii--- iv i  -   v v  i    v i i vi  v     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

C chr2_227617447_   2162 AAATGGTGCTGGGAAAAC-----AGCCACATGCAGAATA-TGAAACT--A 2121
                                       v   ----- ?         i  v -    ii -- 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

C chr2_227617447_   2120 TCCCTATCTCTCACCATATA-AAAAATTAA-----AATCAATTAGAGACT 2077
                         i     i   v         -         -----   vi  i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

C chr2_227617447_   2076 TAAATCTTAAGACCTGAAACCATAAGAATTCTAGAAGAAAACCTAGGAA- 2028
                              v -    v  i    i    i v ii           v    ?i-
  L1M4_orf2#LINE/    506 TAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

C chr2_227617447_   2027 AAACTTCCCTGGACATTGGCCTAGGCAAAGAATTTATGACTAAGACCCCA 1978
                            ii i v  -  v    vi       v iv  iv iiv  v   v   
  L1M4_orf2#LINE/    555 AAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

C chr2_227617447_   1977 AAAGCAAATGCAACAAAAACAAAAATAAATAAATGGGAGC-CAGTTAAAT 1929
                               v v         iv       i      v   vi-  viv    
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

C chr2_227617447_   1928 TAAG----TTTCTGCATGGCAAAAGAAATAATTATCAGAGT-AAAATACA 1884
                            i----   v   v --    i  v iv  i vv i   -    v   
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACA 701

C chr2_227617447_   1883 ACCCACAGAATGGGAGGAAATATTTGCAAATTATGTATCTGACAAAGGAC 1834
                                         i              i  i       i  i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

C chr2_227617447_   1833 TAATATCCAGAATCTACAATGAATTCGAACAAATCAACAAGAAAAAAA-- 1786
                          vi          v  i  v   i  vv    v    i  v     i --
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

C chr2_227617447_   1785 AATAAACCTGTCAAAAACTGGGCAAATGACATGAATAGACATTCCTCAAA 1736
                              v  vi i?    v        v  iv            i   v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

C chr2_227617447_   1735 ATAATACATACAAATGACCAAGAAACGTATGAAAAAAATGCTTAACATCA 1686
                          v  v i         i    v  i ii       i -    i       
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCA 900

C chr2_227617447_   1685 CTAATCAT 1678
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.45 (128 / 88)
Gap_init rate = 0.02 (20 / 901), avg. gap size = 1.90 (38 / 20)  

1862 26.02 4.96 0.35  chr2_227617447_227622804.rev     4314  4878 (480)    L1M4_orf2#LINE/L1      318   908 (0)  

  chr2_227617447_   4314 TTCAGAAATAGACTGATGTAAACATATTCAATTGTTATTTGAAAAAAGTA 4363
                          i        i  iv  ii vvi  iv       v v  i  v  ii  i
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_227617447_   4364 CAAAGGCAATTCATTGGAGAACTGATAGTCATTTTTACAAATGGTGCTGA 4413
                          v   i v     v   i   vvi      v   iv             i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_227617447_   4414 AATATTTGGAAGTCCACAAGCAAAA-AACAAACTTTGGTTCATACCTCAC 4462
                         i i vi    vi?     v      -  ii  v  v iii v        
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_227617447_   4463 ATCTTATATAAAAACTAACTCAAAATGGGCTATATATCTAAATGTAAATT 4512
                          i v    i     i             iii ? v i          ivv
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_227617447_   4513 TTAAGACCATGGAACTCCTAAAAGAAAATGTAGCAGAAAATC---ATGGT 4559
                         i   i  i  ii     i  i       ii   v? v     ---i  ii
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_227617447_   4560 CTTGGGTTACATCAAAAGATTCTTAGATACAACACTAAATGCTTGA-CA- 4607
                                  vi-   vi v          ii    i   v  vii -  -
  L1M4_orf2#LINE/    568 CTTGGGTTAGG-CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_227617447_   4608 CA----------TTGATAAATTGTGCTTCATCAAAATTATAAACTTTTGT 4647
                           ---------- v         vi              v          
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_227617447_   4648 GCCACAAAAGATACTTTTAAGAGAATGGGGGAAAAAGCCACAGACTCAGG 4697
                           iv    i  i   v i    i i  iiiii v  v       v vi i
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_227617447_   4698 GAAAATATTTGCAAATCACCTATCTTATGAAGCGCTTTTATTCAGAATAT 4747
                                           iv     v  i i vi   v   i        
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr2_227617447_   4748 ATAAAGAATTCCCTA-AACTCAAAGATAAGAAAACAAACAATCCAATT-A 4795
                                 i  i-  -       vi    i  i     i  i      - 
  L1M4_orf2#LINE/    767 ATAAAGAACTCT-TACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_227617447_   4796 AAAGTAGACAAAATAATGGAACAGAAACTTCAGCAAAGAAGATATATAGG 4845
                            i i i    iv v v   i   v i   vv             i ii
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_227617447_   4846 TAGTCGATAAACA---GAAA-------CATCATTAGTCATTAG 4878
                          i i i    i  ---    -------  v   i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (92 / 52)
Gap_init rate = 0.02 (11 / 591), avg. gap size = 2.73 (30 / 11)  


3176 27.31 0.55 0.55  chr2_227754607_227765032     4846  5753 (4673)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_227754607_   4846 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4895
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_227754607_   4896 GGCCATACTGCCCAAGGCAATTTACAGATTCAATGCCATCCCCATCAAGC 4945
                            v     v     ivii  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_227754607_   4946 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 4993
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_227754607_   4994 ATATGGAACCAAAAAAGAGCCGGCATCGCCAAGTCAATCCTAAGCCAAAA 5043
                                 viiv  ii  v  i v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_227754607_   5044 GAACAAAGCCGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5093
                                 ii     vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_227754607_   5094 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5143
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_227754607_   5144 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5191
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_227754607_   5192 TATCTGGTCTTTGACAAACCTGAGAAAAACAAGCAATAGGGAAAGGATTC 5241
                         i vi  i i  i     ivv  vv  i v  vv    i       i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_227754607_   5242 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAAGC 5291
                         i  v  i  i              v      v  ?   i i i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_227754607_   5292 TGAAACCAGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGACGG 5341
                             iiii  i    v   i     v           i  i    i i  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_227754607_   5342 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5391
                           i ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_227754607_   5392 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5441
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_227754607_   5442 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5491
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_227754607_   5492 ATTAAACTAAAGAGCTTCTGCACAGAAAAAGAAACTACCATCAGAGTGAA 5541
                           i   v v  i i   i  ii vvv   i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_227754607_   5542 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5591
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_227754607_   5592 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5641
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_227754607_   5642 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5691
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_227754607_   5692 CTCAAAAGAAGACATTTATGCAGCCAAAAAACA-ATGAAAAAATGCTCAC 5740
                            v        i  vi viii     v  i  -       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_227754607_   5741 CATCACTGGCCAT 5753
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (150 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  

2791 27.77 0.55 0.88  chr2_227754607_227765032     9024  9934 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_227754607_   9024 TGGAAATGCATCCAGTGTTTATGGATTGGGATAATTGATAATGTGAAAAT 9073
                               vii    vi    i         i v v  i   v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_227754607_   9074 GACCACACTTCA-AAAGTAATCTACAGATTCAGTGGAATTCCCATCAAAA 9122
                          i v i   i v-   v i             ii v   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_227754607_   9123 TATGCACATCATTTTTCATAGAATTAGAAAAAACAATCCTGAATTTTGTA 9172
                          vivvi vv v     iii    v v  v  ivii     i  v  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_227754607_   9173 TTGAACCAAAAAAGAGCCTGAATAGACAAAGCAATCCTAAGCAAAAAAGA 9222
                          v   viiv  ii  v  v      v    i     i i i-   i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chr2_227754607_   9223 ACAAATCTGGAGACATCACATTACTGAACTTCAAATTATACTACAAGGCT 9272
                              vi     ivv     i v iv  i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_227754607_   9273 TTAGTTACCAAAACAGCATGGTACTGTTGTAAAAGTAGGCACATACACCA 9322
                         vi   v i   i    ii        vii   iii   i  i   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_227754607_   9323 ATGGAACAGCACAGAGAATCCAGAAACAAAGCCAAATATCTACAGCTAAC 9372
                               i  v iv    i        i   v   v i  i  ii ii  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_227754607_   9373 TGATCTTTAACAAAGCATACAAAAACAAAAAATTGGGGGGTGGACACCCT 9422
                             i  ii    i -i i v  i  v vvv v     iiv i i vi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_227754607_   9423 ATTTAATAAATGATGCTGGGAAAACTGCCAAGCTACATGTATTAGAAGAA 9472
                         v  i  i     i        v     vvv ? i     i ---i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA---AAAGAA 445

  chr2_227754607_   9473 TAAAACCGGATTCCTATCTCTCACCTTATACAAAAATCAACTGAAGATGG 9522
                          i  iii   ii    i   v    v           i    v  i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_227754607_   9523 TTCAAAGACTTAAATATAAGACCTGAAACTATCAAAATTCT-ATAAGACA 9571
                         v   ?    i     i     v  i       -    i   - v    v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAA 544

  chr2_227754607_   9572 ACATTGGAAAAACTCATATAGATATTGGCCTCAGCAAAGAATTCATGAAT 9621
                             v  ?iv  v  v vvv  iv    vi vi    v iv   v ii  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_227754607_   9622 AAGACCCCAAAAGCAAATGCAACAAAA-ACTAAATACATAAATGGGACCC 9670
                          v   v         v v         - vv     v      v    ii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_227754607_   9671 AGTTAAACTAAAAGGCCTCTGCACAACAAAAAAAATAAATAAGTAGAGTA 9720
                         vi i   v v   ii i i  ii vv    ii v iv vi   - i   i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTG 693

  chr2_227754607_   9721 AACAGA-AACCCACAGAATGGGAGAAGCTATTTGCAAACTATGCATCCGA 9769
                           v   -                   iv          ii  ii   i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_227754607_   9770 CAAAGGGCCAGTATGCGGAATCTACAAAGAACTCAAACAAAACACCAAGA 9819
                         i  i  i iv    v i    v  i         vv    vv  vi  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_227754607_   9820 AAAAAACAAATAATCCCATTAAAAAGTGGGAAAAGGACATGAATAGACAT 9869
                             i        i  v   ?    i    v      iv           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_227754607_   9870 TTCTC-AAAGTAAGATAAACAAATGGACAACAAGCATGTGAAAAAATACT 9918
                              -    -      v        v   i     ii      i  i  
  L1M4_orf2#LINE/    844 TTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_227754607_   9919 CAACATCACTAATCAT 9934
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (142 / 107)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.18 (13 / 11)  


2313 21.82 8.43 2.21  chr2_227847731_227849454      510  1233 (491)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr2_227847731_    510 TAAAATCCATATATATGTAAATGCAAATGACCTAGAATAGCCTAAGCAAT 559
                               i     ---- v        iv    i         v  i    
  L1M4_orf2#LINE/    140 TAAAATTCATAT----GGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_227847731_    560 TTTTATAAAAAGCAACAAAGTTGAAGGACTTACACT----AGT------- 598
                         i  v v   i iv          i      i     ---- i -------
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_227847731_    599 CTTGCTAAAAAACTA--GTCAT-AAGA----ATGAT---GGTAAATGAAT 638
                            i   v   i   --  v  -    ----i  i ---  i v v i  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr2_227847731_    639 AGACATGTAGATAAATGGAA-------------CCAAAAG---ACTCAAA 672
                               i     v       -------------   i  i---  i  v 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_227847731_    673 CATG-ATGATCAATTGATTTTTCACAAAGGTGCCATGGCAATCATGGCAA 721
                            v-   i            iv    i       v --- i   -----
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG---ACCAT----- 377

  chr2_227847731_    722 TTTAGTGGGGGAAAAA--GTCTTTTCAACAACTGGTGCCACAACAAGTGG 769
                         - i i     i  i  --             v      iivi    v   
  L1M4_orf2#LINE/    378 -TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_227847731_    770 ATATTCACATGGAAAAAAAATTTAA--TGAATCCTTATCTCATACCATAC 817
                            ?i      v    i  -- v  --  i i  i  i    i      i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAA--TGAAGTTGGACCCCTACCTCACACCATAT 474

  chr2_227847731_    818 CCAGAAATTAACTTAAAAGAGATCATTGAGGTAAAAGTAA----CAATAC 863
                         v  i         i    vi     ?v  vv    v    ----i  v  
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr2_227847731_    864 TACACAA------GAAGAAAACATAGGAGAAAATTTCTGCAATTTTGGCA 907
                           i v  ------              ? v    i ii ii ii    vv
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr2_227847731_    908 TAGGTATAGAGTTCTCAGGTA--ACAAGAAAAGCACAAATCACAAAAGAA 955
                             i vv iv    i  i  --   vv          iiv         
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr2_227847731_    956 AAAAATTATAAATTATATTCCATCAAAAT-AAAAACTTTTGCTTCTTAAA 1004
                             vvv       iv i i         -           - v   v  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAA 673

  chr2_227847731_   1005 AA-----TAATAAGAAAATGAAAAGACAATTCTCAGAATGGGAGAAAATA 1049
                          i-----  vi      i           ii v                 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_227847731_   1050 CTCACAATACTTGTATCTAACATTGATCTTGTATCCACAATATATAAATA 1099
                         i ii   vv v i     i i vv iv          v          v 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_227847731_   1100 ACTCTTACTATTCAACAATAAGAAGATAAAAAGCCAAATTTTAAG-CGGA 1148
                                 v i    i     i    i   v i  v    ?v  i-i  i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_227847731_   1149 AAAAAGATTTGAATAGGCACTTCACAAAAGAAGCTACATGAATGTTCAAT 1198
                         v   i           i  i   v v       v  i ii    vi    
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_227847731_   1199 AAGTACATTAAAAGATATTCAACATCGTTAGTTAT 1233
                            i    v       ii        i????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (91 / 63)
Gap_init rate = 0.03 (22 / 769), avg. gap size = 3.50 (77 / 22)  


1182 28.98 12.50 3.12  chr2_227901795_227903403.rev      414  1117 (492)    L1M4_orf2#LINE/L1      139   908 (0)  

  chr2_227901795_    414 CCAAGAGTCATA-AAAAATGTAAAGCACCC----T-TCTAAAATGTATTT 457
                          i  i v     -ii     i  i v    ---- -v i    ii-  i 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA-ATCT 187

  chr2_227901795_    458 GGAAGTGCAATGGGAGGGACCCAG--GAGGGAGCTTGCCCTTCTAGATTC 505
                         v   i---  ---  i i  vv  -- ii   -  ii v    ivi   i
  L1M4_orf2#LINE/    188 TGAAA---AA---GAAGAACAAAGTTGGAGGA-CTCACACTTCCCAATTT 230

  chr2_227901795_    506 CAACACTTATAGTATAAAATTATAGTAATTAAGATACTGTGGTGTTGGTG 555
                            v     i--  i   ii  i      i    i v      ii   ii
  L1M4_orf2#LINE/    231 CAAAACTTAC--TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_227901795_    556 TACAGATGGACAAATGTACCAATGGAACAGCATAGAGAACCCAGAAGTGG 605
                           vi   i    v  iv i        i  v  v    ii      i ii
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_227901795_    606 GTCC-TCCATATGTAGAAACCTCATATATGGCAGACCTGGCACTACAGA- 653
                         ii  - v   v i i vv vi v  v vi i  ii---  ii i -   -
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAG---GGTGCCA-AGAC 374

  chr2_227901795_    654 --TTCC-TGGGGAAAGGACAG--------ATAAAGAG-GCTGAGTGCATT 691
                         --   v-         i i  -------- i   vi -    i vvv i 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_227901795_    692 GGTCATTCATATAGAAAACAATGCAAAGTT---TCTCTAACTCATA---- 734
                           vi ?i  i  iv    v    --     ---i i   v    i ----
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATG--AAGTTGGACCCCTACCTCACACCAT 472

  chr2_227901795_    735 ----AAAGTTCAATGCCAAATGAACTAAGGACTCAAATGGAAAAGCCAAA 780
                         ----   iv i  iv v     i ii ?i   ii     v  i   i   
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr2_227901795_    781 ATTTTAAAACCTTTAGGGGGAAGTTTCAGAGG-GTA--TCTTTATGACCT 827
                          i v      ii    ii i  i---  v   -   --    ii      
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAA---CATAGGNGTAAATCTTCGTGACCT 569

  chr2_227901795_    828 TGGGGTAGGGAAAGATATCATTAAAAA-GATGC-AAAAACATAAACTATA 875
                             v    v  v i v  -   i v -  ii -    i  i  i v i 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTC-TTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_227901795_    876 AAGGAAAAGATGGATAAATTCTACTATATTAAAATTTAAGAA--TTTGTT 923
                           i     i  i        vv   vi  i      -  i  --     v
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATT-AAAAACTTTTGTG 667

  chr2_227901795_    924 TCTCAGAAGATGTCAT-----AGGT------------CACAAACTGTGAT 956
                         ii   i i  iiii  ----- i  ------------    i v  v  v
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_227901795_    957 G---TATTTGCAA----TATCTATAACAAAGAATTAGTGCCCA------- 992
                         i---         ----   v v i i  i i i v  ii   -------
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr2_227901795_    993 ---AGAA----------TCAATAAGAAAAAGACAAAAAAAAACAA--AAA 1027
                         ---    ----------       v           v  vv-   --?  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC-CAATTWAA 816

  chr2_227901795_   1028 AAACAG--AAAAGATACGTGCAGTCATTTTTCAGAAGAGGATACACAAAT 1075
                            ii --   i   vi vii  v     i  vi    i    i      
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_227901795_   1076 AATCCATAAACATATAAACACATGCTCAATGTCATGAGTATT 1117
                         iii v    i  i  i  v v        ii   ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (136 / 65)
Gap_init rate = 0.05 (36 / 770), avg. gap size = 3.06 (110 / 36)  


3224 26.13 0.99 0.88  chr2_228230668_228237343.rev     5278  6184 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_228230668_   5278 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5327
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_228230668_   5328 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5377
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_228230668_   5378 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTGAAAGTTCA 5425
                          v   iivi i  i  ii     -   -- v  i  - iiiv   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_228230668_   5426 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAG 5475
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_228230668_   5476 AACAAAGTTGGAGACATCACGCTACCTGACTTTAAAACTATACTACAAGG 5525
                                      ivv    i  v  ii i  i      -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr2_228230668_   5526 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAATATATAGAC 5575
                                  i   i    ii         i iv ii i i i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_228230668_   5576 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5623
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr2_228230668_   5624 CATCTGATATTTGACAAACCTGACAAAAACAAGAAATGGGAAAAGGATTC 5673
                           vi    v  i     ivv  v   i v  vvv      i    i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_228230668_   5674 ACTATTTAAGAAACGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGC 5723
                         v  v  i  v   i          v      v  ?       i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_228230668_   5724 TGAAATTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGG 5773
                             i     i    v   i     v i            i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_228230668_   5774 ATTAAAGACTTAAGTGTTAGACCTAAAACCATAAAAACCCTAGAAGAATA 5823
                           i ?    i   i   v   v       i      vi i        v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_228230668_   5824 CCTAGGCA-ATACCATTCAGGACACAGGAATGGGCAAGGACTTCGTGACT 5872
                          v    ?i- v i -   iv   viv  iv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_228230668_   5873 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGAGATCT 5922
                          vi            vvi          vv        i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_228230668_   5923 AATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGA 5972
                         v  i   viv  i i   i  ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_228230668_   5973 ACAGGCAACCTACAGAATGGGAGAAAATTTCTGCAATCTACCCATCTGAC 6022
                          v  i     i                 v i     vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_228230668_   6023 AAAGGGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTACAAGAA- 6068
                           i  i  vi          v  i        --  -  i --   v  -
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--CAATAAT 792

  chr2_228230668_   6069 AAAAAATCAAACAACCCTATCAAAAAGTGGGCGAAGGATATGAACAGACA 6118
                              iv    i     v  i?    i     i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_228230668_   6119 CTTCTCAAAAGACAACATTTATGCAGCCAACAGACACATGAAGAAATGCT 6168
                         i     v     vi i  vi viii     i ii        i i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_228230668_   6169 CTTCATCACTGGCCAT 6184
                          vv     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (146 / 87)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


3180 23.57 2.80 5.06  chr2_228379877_228384702     3406  4334 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_228379877_   3406 TGGAATGATATTCCATATTCATGGACTGGAGGAATCAATATTGTTAAAAT 3455
                              v     i    i        i    i  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_228379877_   3456 GCCCATACTATCCAAAGCAATTTACAGATTCAATGCAATCCCTATTAAAA 3505
                          v v     vi     vii  i           i           i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_228379877_   3506 TGCCAAGGATATTCTTCACAGAAATAGAAAAAGCAATTCTAAAATTTATA 3555
                          v   ivviiv  i  ii       v  v  ivii  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_228379877_   3556 TGAAACCACAGAAGACCCAGAATAGTCAAAGCTATCCTAAGCAAAACAAA 3605
                           i  vii  iii            i    i v   i i iv  i - i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA-AGA 199

  chr2_228379877_   3606 ACAAAATGAAACAACAACAACAACAACAACAAAAAACTGGAGGAATCACA 3655
                              i ------------------------------       v     
  L1M4_orf2#LINE/    200 ACAAAGT------------------------------TGGAGGACTCACA 219

  chr2_228379877_   3656 TTGCCTGACTTTGAATTACACTATAGAGCTATAGTAACCAAAACAGCATA 3705
                         i v  ii i  ii  vivi    i i     i     i   i    ii i
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_228379877_   3706 GTTCTGGCATAAAAGCAGACATGTAGACCAATGGAACAGAAGAGTGAACC 3755
                           v         iiii      i    i        i    vv v  ii 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_228379877_   3756 CAGAAACCCAATAGTGAACCCACACACCTACAGTAAACTCATTTTCACCA 3805
                               -------- i      i   ii  ii  v  i v      iv  
  L1M4_orf2#LINE/    320 CAGAAA--------TAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_228379877_   3806 AAGATGCCAGGAACATACATTGGGGAAAAGACAGTCTCTTCAACAAATGG 3855
                          i i     i  v   v  v        ii i     i            
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_228379877_   3856 TGCTGGGAAAACTGAATATCCGTATGCAGAAGAATGAATGAAAGTAGACC 3905
                                 v     i   ?  ii     i         ----iv i    
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA----GTTGGACC 457

  chr2_228379877_   3906 CCTATCTCTCACTATATACAAAA-TCAAGTCAAAATGGATTAATGACTTA 3954
                             i   v   i          - i  v           i ?v   i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_228379877_   3955 AATCTAAGACCTCAAATTATGAAACAACTACAAGAAAACATTGGGGAAAC 4004
                            v     v  v   i   i    vvi  v          v  ? v  v
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_228379877_   4005 TCTCTGGGACGTTGGAGTGGGCAAAGATTTCTTGAGTA---CCCCACAAA 4051
                            ii v   v    iv i     v i      iii  --- v   v  i
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_228379877_   4052 CACAGGCAACCAAAGCAAAAATGGACAAACGGGATCACATCAAG-TTAAA 4100
                             i     v    v      i  i   iv   iiv      i-     
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_228379877_   4101 AAGCTCCTG------------CACAGCCAAGGAA----AGAGGCCACCCA 4134
                           -  ii  ------------   vii    i  ---- i  i v     
  L1M4_orf2#LINE/    658 AA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_228379877_   4135 CAGAATGGAAAAACAAATTTGCAAACTACCCATGTGACAAGGGATTAAAA 4184
                                 i i  v v         ii ivi  v   i      i viv 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_228379877_   4185 ACCAGAATATATAAGGAGTTCAAACAACTCTACAGGGAAAAAAAGTCTAA 4234
                         v             i  ii  vv       v i --- v      v v  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATA---ATAAAAAGACAAA 803

  chr2_228379877_   4235 TAATCAGATT-AAAAATGGGCAAAA-ATCTGAACAGATGTTTCTTTAAAG 4282
                            i vi   -             i-  i    i   ii     ii    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_228379877_   4283 G---CATGCGAATGGCAAACAGGTATATGAAAAGGTGCTCAACATCATTG 4329
                         i---i  i i      v  i i i i        i            ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_228379877_   4330 ATAAG 4334
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.04 (145 / 71)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 5.21 (73 / 14)  


4095 17.84 1.82 0.97  chr2_228498794_228500607.rev      501  1324 (490)    L1M4_orf2#LINE/L1       78   908 (0)  

  chr2_228498794_    501 ATTTAACACAATTTCTATTAAAATCCTGGCTGGCTTCTTTGTAGAAATGG 550
                            i   i    ii    i       ii    v   i    i      v 
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chr2_228498794_    551 AAAAGCCAATACTCAAATTCATGTGAAATTGCAAGGGACCTTGAATTGAT 600
                          v    ii  v  v        i  i  v           iv    v vi
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr2_228498794_    601 AAAACAATCCCAAAAAGGAAGAATAAAGTTGGAAGACTCACACTTTCTGA 650
                                  iii    i      i         i           i ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr2_228498794_    651 TTTCAAAATTTACTAAAAAATCACACTAAATCAAGACA-TGTGAAAATTG 699
                                 i      v   iii   v   -        -    iv v v 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAA-TCAAGACAGTGTGGTACTGG 276

  chr2_228498794_    700 CATGAGTGTTCACAT------CAATGGCATACAATTGAGA-------AAT 736
                            i  vi vv    ------      v   v        -------   
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_228498794_    737 AAGCCCCCATGTCTATGGTCAACTGATTTTGTGTTAGGGTGGCAAGACCA 786
                           i   vi ii i         i       vviiv      v        
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_228498794_    787 TTCAATGGGGGAAGAACAGTCTTTTCAACAAATAGTGCTGGAACTACTGG 836
                                   i     i                i       i  v     
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr2_228498794_    837 ATATTCACA-GCAAAAGAATAAAGTTAGACCATTACTTCACACTATATAT 885
                            ?i    -          i     i    vi   i      i     i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_228498794_    886 AAAAATTAATTCAAAATGGATCATAGATCTCAATGTAAGAGTTAAAAACA 935
                                  i             ?   i  v          i     vi 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_228498794_    936 TGAAATTCTTAGAAGAAAACATAGGAGAAAATCTTCATGACCTTGGGTTG 985
                          i   i                   ? v        i            i
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_228498794_    986 GGCAATGACTTGTTAGATACAACACCAAAAGCTCAAACAATAAAATTAAA 1035
                                ii  v       ii           v   i   i    vv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_228498794_   1036 AATTAACGAACTGGACCAAATCAAAACTAAACATTTTTATGCTTCAAAGG 1085
                            vi ii  i     ivv       i    v i    i           
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_228498794_   1086 ACACTATAAAGAATGTGAAAAGAAAACGCATAGAAAGGAAAGGAAAAATT 1135
                                v     v         v   v  i    v  i - i   v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA-GAAAATATT 725

  chr2_228498794_   1136 TGCAAGTCATATATATGATAAGGGACATTTACTTGTATAGAGAATATATA 1185
                              i        v           ------      vv          
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGAC------TTGTATCCAGAATATATA 769

  chr2_228498794_   1186 AAGAACTCTTACAACTCAATAAGAAGAAGATGAGTGACCCAATTAAAAAA 1235
                                               v  i    ii i i        ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_228498794_   1236 TGAGGAAAACAGCTGAATAGACATTTCTCCTAAGAAGATAAATAAATGTC 1285
                           i v   iv vi                 v         v i     v 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_228498794_   1286 CAACAAGCACATAAAAAGATGCTCAAAATTTTTAGTAAG 1324
                            i        i             v  iv????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (88 / 55)
Gap_init rate = 0.01 (7 / 831), avg. gap size = 3.29 (23 / 7)  


3182 26.38 0.99 0.77  chr2_228655205_228659653.rev     3052  3957 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_228655205_   3052 TGGAAGAACATTCCATGCTCATGGATAAGACGACTCAATATCGTGAAAAT 3101
                              ii i  i     i        vi  v    i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_228655205_   3102 GGCCATACTGCCCAAGGTAATTTATAGATTCAATACCATCCCAATCCAGC 3151
                            v     v     iv i  i  i        ii v     v   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_228655205_   3152 TACCAATGACTTTCTTCACAGAACTGGAAAAATCTACTTTAAAGTTCATA 3201
                          v   iivi i  i  ii     v v  v  iiiv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_228655205_   3202 TGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCACAAAGAA 3251
                              viiv  ii  v  v v  v     i      i i iv vi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_228655205_   3252 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGCTA 3301
                              i      vv       v  ii i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_228655205_   3302 CAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATACACCAA 3351
                               i   i    ii    i    i iv ii i   v     v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_228655205_   3352 TGGAATAGGAC--AGAGTCCTCAGAAATAACACCACACATCTACAACCAT 3399
                                 i i--       --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr2_228655205_   3400 CTGATCTTTGACAAACCTGACCAAAACAAG-AAATGGGGAAAGGACC-CC 3447
                         i    i  i     ivv  -    i  v v-v           i iv-i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_228655205_   3448 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTA 3497
                          v  i  i              v      v  ?   i   i i  iiv i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_228655205_   3498 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 3547
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_228655205_   3548 TAAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 3597
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_228655205_   3598 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 3646
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_228655205_   3647 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGA-TCCA 3695
                         i            vvi          vv    iv  i    v   - i  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_228655205_   3696 GTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCATCAG---AGTG 3742
                         viv   i    i -   i  ii vv    i  v   --    i---    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT--ATCAAGAAAGTG 693

  chr2_228655205_   3743 AACAGGCAACCTACAGAATGGGAGAAAATTTTGGCAATCTACCCATCTGA 3792
                           v  i     i                 v  v    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_228655205_   3793 CAAAGGGCTAATATCCAGAATCTACAAAGAACATAAACAAATTTACAAGA 3842
                         i  i  i  vi          v  i       vivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_228655205_   3843 AAAAAACAAATAACCCCATCAAAAAGTGGGCAAAAGATATGAACAGACAC 3892
                             i           v  i?    i        i   v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_228655205_   3893 TTTTCAAAAGAAGACATTTATGCAGGCAACAGACACATGAAAAAATGCTC 3942
                           i  v        i  vi viii v   i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_228655205_   3943 ATCATCACTGGTCAT 3957
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3093 27.88 1.00 0.55  chr2_228692042_228697787.rev     4351  5254 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_228692042_   4351 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAATGTCGTGAAAAT 4400
                              ii i  i     i    i i v      v i   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_228692042_   4401 AGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4450
                         i  v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_228692042_   4451 TACCAATGACTTTCTTCACAGA--TTGGAAAAAACT-ACTTTAAAGTTCA 4497
                          v   iivi i  i  ii    --   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_228692042_   4498 CATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4547
                         i      viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_228692042_   4548 AACAAAGCTGGAGGCATCACGCTGCCTGACTTCAAACTATACTACAAGGC 4597
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_228692042_   4598 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGGTATAGACG 4647
                                 i   i    ii         i iv ii i   vi      iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_228692042_   4648 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 4695
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_228692042_   4696 ATCTGATCTTTAACAAACCTGATGAAAACAAGAAATGGGGAAAGGATTCC 4745
                          vi    i  ii    ivv  vii i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_228692042_   4746 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4795
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_228692042_   4796 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4845
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_228692042_   4846 TTAAAGACTTACATGTTAGACCTAAAACCATAGAAACCCTAGAAGAAAAC 4895
                          i ?    i  v    v   v       i   i  vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_228692042_   4896 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4944
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_228692042_   4945 AAACACCAAAAGCAATGGCAACAGAAGCCAACATAGACAAATGGGATCTA 4994
                         vi            vvi      i   vv  v     i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_228692042_   4995 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5044
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_228692042_   5045 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5094
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_228692042_   5095 AAGGGCTAATATCCAGAATCTACAAAGAACACAAACAAATTTACAGGAAA 5144
                          i  i  vi          v  i       v vv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_228692042_   5145 AA---AAACAACCTCATCAAAAAGTGGGTGAAGGAGATGAGCAGACACTT 5191
                           ---   i    iv  i?    i    ii     vv   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_228692042_   5192 CTCAAAAGAAGACATTTATGCAGCCAACAGACACGTGAAAAAATGCTTAT 5241
                            v        i  vi viii     i ii   i      i     i v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_228692042_   5242 CATCACTGGCCAT 5254
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (153 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3359 26.21 0.55 0.55  chr2_228720616_228727015     5001  5908 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_228720616_   5001 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5050
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_228720616_   5051 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5100
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_228720616_   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5148
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_228720616_   5149 TATGGAACAAAAAAAGAGCCTGTATCGCCAAGTCAATCCTAAGCCAAAGG 5198
                                vviv  ii  v  v v  v     iv     i i ivv i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_228720616_   5199 AACAAAGCTGGAGGCATCACACTGCCTGACTTCAAACTTTACTACAAGGC 5248
                                i      vv       v  ii i      vi         i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_228720616_   5249 TACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGATATAGATC 5298
                                 i   i    ii   i     i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_228720616_   5299 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 5346
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_228720616_   5347 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5396
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_228720616_   5397 CTATTTAATAAATGGTGCTGGGAAAACTGGCTGGCCATATGTAGATAGCT 5446
                           v  i  i              v      v i?   i   i i viiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_228720616_   5447 GAAACTGGATCCCTTCCTTATGCCCTATACAAAAATTAATTCAAGATGGA 5496
                            ii    i    v   i ii  v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_228720616_   5497 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5546
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_228720616_   5547 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5595
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_228720616_   5596 AAACACCAAAGGCAATGGCAACAAAAGCCAAAATTGACAAAGGGGATCTA 5645
                         vi        i   vvi          vv     v  i   vv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_228720616_   5646 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5695
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_228720616_   5696 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5745
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_228720616_   5746 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5795
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_228720616_   5796 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5845
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_228720616_   5846 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCCT 5895
                            v        i  vi viii     v  i          i      vv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_228720616_   5896 CATCACTGGCCAT 5908
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 210 20.00 4.35 16.52  chr2_228884020_228885764.rev       17   131 (1614)    L1M4_orf2#LINE/L1       59   159 (749)  

  chr2_228884020_     17 TTCCCAAATTAATATATAAATTCAGTGCAAACCT-----AAATCATACCA 61
                          i        i  v  i i     ii    v  i-----     ---   
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC---CCA 105

  chr2_228884020_     62 GCAGGCTTTCCCATAGAGATCTGTTAAGAACTGAATATTTGTGTTTCTTC 111
                           v v    iiiii   i  -  vi   --    -----------  i -
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAAT-TGACAAG--CTGA-----------TCCT- 140

  chr2_228884020_    112 AAAATTCATGTGTTAAATAC 131
                                  i  v-    i 
  L1M4_orf2#LINE/    141 AAAATTCATATGG-AAATGC 159

Transitions / transversions = 2.83 (17 / 6)
Gap_init rate = 0.07 (7 / 101), avg. gap size = 3.43 (24 / 7)  

1815 25.68 6.65 4.30  chr2_228884020_228885764.rev      487  1253 (492)    L1M4_orf2#LINE/L1      124   908 (0)  

  chr2_228884020_    487 ATCAATCAGCT-ATCTCTAAAATTTTTTTGTTGAAA-------GAACTAG 528
                           ii iv    -   -        iv v  --    -------  v i  
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATC-CTAAAATTCATATG--GAAATGCAAGGGACCCAG 170

  chr2_228884020_    529 AATAGCCGAAAGAACTTTGATAATGAAGAACAAAATTGGAGGGCTCACAC 578
                                i   v  ii    v  v          i       i       
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_228884020_    579 TAACTGATTTTAAGGCTCACTATAAAGTTACAGTAATGAAGACTGTCATA 628
                          vv ii    i  ii  i    i    i         v     v  -i i
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT-GTG 269

  chr2_228884020_    629 GTAGTGACAAATGGATAAACACACAGAAGAGTATAGCAGAATAGAAAGTC 678
                            v  i  v v     i   i i   vv i iv ii     v  i    
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_228884020_    679 CAGAAATAGACATACACAAATATGGTCAAGTGATTGTTGACAAAGTTGCA 728
                                 i  vi i   vv         v     v i     i v   v
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_228884020_    729 AAGACAATTTAATGGAGAAAGGATATTCTTTCTAACAAACTGTTTTGGAA 778
                              v   i     i     i   v     ii      iv  vi   i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_228884020_    779 CAATGAAACATTTACATGAAGAAGA-TAACATCA-ACCAATATCTTATTC 826
                            ivii i ?ii     v i    - i vi ii-   vv  i  i iv 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_228884020_    827 TTTATACAAAAATTAATACAAAATGGATTATAAACTTAAATGTAA----- 871
                         iv              iv          i ? i  i         -----
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_228884020_    872 --AATTATAAAACCTTTAGAAAAA----TAAGA--AAAT----------- 902
                         --  i        ii      i  ----  i ?--    -----------
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_228884020_    903 TAGGCTAAGAAAAGAGTTCTTGAAAATGACACCAAAATCAT--GCTTCAT 950
                          i  i  i v  v iv     ii v            v  i--  --- v
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC---AA 616

  chr2_228884020_    951 CAAAGAAAAAAATTGACAAATTAGACTTCAACAAAATGAAAAACTTTGTT 1000
                             ii       v  i     i       v      v         vv 
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_228884020_   1001 ACCATGAAAGGC-CTGTTAAGAGAATAGAAACATAACTTACAAACTGTAA 1049
                         i ivii  i i -  i i    i i ii   v i   ii   i v  vi 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr2_228884020_   1050 ATAAAATATCTATTGATTATATATCTGAAAAATTTGGTATTATATTTAGA 1099
                         i-       i iivi  i          v  i---  vv  i   ii   
  L1M4_orf2#LINE/    717 G-AAAATATTTGCAAATCATATATCTGATAAG---GGACTTGTATCCAGA 762

  chr2_228884020_   1100 ATGTGTGTGTGAATGAGTGTAAAAC-CTCAAAACTCAACAATGTTTCAAT 1148
                           i --------  i ---- i   -  i v       i   -----  -
  L1M4_orf2#LINE/    763 ATAT--------ATAA----AGAACTCTTACAACTCAATAAT-----AA- 794

  chr2_228884020_   1149 TTCTAAAAAAAGG-----------AAAAATGGATAAAAC-TTTGAACAGA 1186
                         ----   i v ii-----------        ii   iv-      i   
  L1M4_orf2#LINE/    795 ----AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_228884020_   1187 TAAATCATTACGGAAGATGTGTAGATGGAAAAGAAGCACA-GAAAAGACA 1235
                         i vv  vii vi      i ii i    vv  v       -       ii
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_228884020_   1236 TTAAACATCAGTAATCAT 1253
                         i v       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (127 / 67)
Gap_init rate = 0.03 (24 / 785), avg. gap size = 3.50 (84 / 24)  


3176 27.48 0.66 0.44  chr2_228889609_228896020.rev     5015  5920 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_228889609_   5015 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5064
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_228889609_   5065 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5114
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_228889609_   5115 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5162
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_228889609_   5163 TATGGAACAAAAAAGAGCCC-GCATCACCAAGTCAATTCTAAGCCAAAAG 5211
                                vviv  i ii   - v  vi    iv    ii i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_228889609_   5212 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGC 5261
                                i      vv       v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_228889609_   5262 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATC 5311
                                 i   i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_228889609_   5312 AATGGAACGGAAC--AGAGCCCTCGGAAATAATGCCACATATCTAAAACT 5359
                                ii   i--    i  --i       vv   i i  i  viiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_228889609_   5360 ATCTGATCTTTGTCAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5409
                          vi    i  i v   ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_228889609_   5410 CTATTTAATAAATGGTGCTGGGAAAACTGGCTGGCCATATGTAGAAAGCT 5459
                           v  i  i              v      v i?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_228889609_   5460 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGA 5509
                            ii    i    v   i     v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_228889609_   5510 TTAAAGACTTACATGTTAGACCTAAAACCATAAAATCCCTAGAAGAAAAC 5559
                          i ?    i  v    v   v       i      ii i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_228889609_   5560 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5609
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_228889609_   5610 AACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCTAA 5659
                         i            vvi          vv i   v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_228889609_   5660 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5709
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_228889609_   5710 AGGCAACCTATAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5759
                           i     i i i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_228889609_   5760 AGGGCTAATATCCAAAATCTATAATGAACTCAAACTAATTTACAAGAAAA 5809
                         i  i  vi      i   v     v      vv  v v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_228889609_   5810 AAACAAACAACCCCATCAAAAAGTGG-CAAAGGACATGAACAGACACTTC 5858
                          i     i     v  i?    i   -       iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_228889609_   5859 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5908
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_228889609_   5909 ATCACTGGCCAT 5920
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3334 26.65 0.33 0.33  chr2_228919498_228925236.rev     4340  5247 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_228919498_   4340 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4389
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_228919498_   4390 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4439
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_228919498_   4440 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 4488
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_228919498_   4489 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTGAGCCAAAAGA 4538
                               viiv  ii  v  v v  v     iv     i   ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_228919498_   4539 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 4588
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_228919498_   4589 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 4638
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_228919498_   4639 ATGGAACAGAACAGAGCCTTCAGAAATAACGCCGCATATCTACAACCATC 4688
                               i    iv   vv i         vv  ii i  i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_228919498_   4689 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 4738
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_228919498_   4739 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 4788
                           i  i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_228919498_   4789 ACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTA 4838
                         ii    i    v   i     v           i  i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_228919498_   4839 AAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 4888
                         ?    i    i  v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_228919498_   4889 GGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 4936
                           ?-   --i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    550 GGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_228919498_   4937 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 4986
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_228919498_   4987 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAACA 5036
                         i   v v  i i   i  ii vv    i  v  i i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_228919498_   5037 GGCAACCTACAAAATGGGAGAAGATTTTAGCAACCTACTCATCTGACAAA 5086
                          i     i   i          i  v  v    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_228919498_   5087 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5136
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_228919498_   5137 AACAAACAACCCCATCAGAAAGTGGGCAAAGGACATGAACAGACACTTCT 5186
                         i     i     v  i?i   i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_228919498_   5187 CAAAAGAAGACATTTATGCAGCCAGAAAATACATGAAAAAATGCTCACCA 5236
                          v        i  vi viii    iv  ii         i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_228919498_   5237 TCACTGGCCAT 5247
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


3109 20.37 3.23 0.28  chr2_228970493_228972196      501  1212 (492)    L1M4_orf2#LINE/L1      176   908 (0)  

  chr2_228970493_    501 CCAGAACAATCTC--AAAAGA-GAACAAAGT-AGAGGACTTCAATTTCAT 546
                            i        i--      -         -i       ivv i   vi
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr2_228970493_    547 GATTCCAAAATTTACTATGAGGCTATAATAATGAAAACAGTGTGGTATTG 596
                         i   i     i      ii i    i i    v  i           i  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr2_228970493_    597 GAATAAAAACAGACATGTAGACCGGTGGAATAGA-------GTCCAGAGA 639
                          v    ii i      i    i ii         -------       i 
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_228970493_    640 TAAATTCTCATGTACGTGGTCAAATTATTTTTGACTAGGGTGCCAGAACC 689
                             ii vi ii vii       v v     i   v         ii   
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_228970493_    690 ATTCATTGTCGAAAGGATAAGTCTTTTCAACAAATAGTGC-AGGAAAACA 738
                              v  vv     i   -               i    -i   v   v
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATA-GTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr2_228970493_    739 GGGTATCCATGTGCAAAAATAATAAA-TTGAACCCTTACCTAATACCATA 787
                           i  ?   ii       i-   i  -   i    i     v i      
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAG-AATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_228970493_    788 TGCAAAAATTAACTCAAAGTGGGTCAGAGACCTGAATGTAAGAACCAATA 837
                          i                i   i   ?      i         i i  v 
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_228970493_    838 CTATAAAACTCCTAGAAGGAAACAAAGGGAGAAAGCTTCATGACATTGGA 887
                                    i      i     v   ?iv   v    i    v    i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr2_228970493_    888 TTTGGAACTGATTTATTGAATGTTAAACCTAAAGTACAAGCAATAAAATA 937
                           v  v v  i   v  ii  i v v   v    i        i    v 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_228970493_    938 AAAAATAGACAAATTGAACTTCAATGA---TAAGAAATTTTGTGCATTAA 984
                                  i      i      vii ---   i  v        v i  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_228970493_    985 AGAACACTATCAACACAGTAAAAAGGCAACCCACAGAATGTGA-AAAATT 1033
                           i          v v   i     i              v  -     v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_228970493_   1034 TTTGCAAATTACATGTCTGAGATGATATTAATATC-AGAACATAGAGAAA 1082
                                  i i  i     v v iv i vi    -    i   v i i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_228970493_   1083 ACTCCTAAAACTCAGTAACAAAA---CAAAAGACCCTATTAAAAAACCAG 1129
                             i  v      i   i    ---    vi    v   ?     ivi 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_228970493_   1130 CAAATGACTTAAATAGACATTTTGCCAA-GATGATATACAAATGACCAAT 1178
                             v  i  i           iv    -  v            i     
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_228970493_   1179 AAATACAC-AAAAGATGCTCAACATCACTAATCAT 1212
                           ii   i-                  ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (93 / 48)
Gap_init rate = 0.02 (14 / 733), avg. gap size = 1.79 (25 / 14)  


2716 27.99 2.09 2.41  chr2_228975111_228978374.rev     1867  2777 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_228975111_   1867 TGGAAAAATATCCCATGCTGATGGATTGGAGGAATCGATATTGTTAATAT 1916
                               i          i v          i  v ii          v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_228975111_   1917 GACTATACTGCCCAAATCAGTTTATAGACTTAAGGCTATTCCAATCAAAC 1966
                          i v     v       iii i  i   i i  v  v  i  v      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_228975111_   1967 TACCAA-TGTCACAGAACTATTTTTGTGACATTTTTCACAGAATTAGAAA 2015
                          v   i-  i --------------------     ii     v v  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--------------------TTTTTTGCAGAAATTGACA 130

  chr2_228975111_   2016 ACACT-ATTCTAAAGTTCACACAGAACCAAAATAGAACCCGAATAGCCAA 2064
                          -i  -  i     i    i ii   viiv  vi  v  v          
  L1M4_orf2#LINE/    131 A-GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr2_228975111_   2065 AGTAATCATAAGCAAAAAGGACAAAGCCACAGGCATTACATTGCCCAACT 2114
                          ii    v i iv  i   i      iiiv   vv i   i v     i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr2_228975111_   2115 TCAAA-TATGCTACAAAGCTACGGTAACCAGAACACCATGTTATTGGTAC 2163
                              -iv i            i    i  ii   vii  v  i   i i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_228975111_   2164 AAAAACAGACACGTAGACCAAAGGAACAGCATAGAGAAATCAGAAATAAA 2213
                           ii i     ii    i   v    i  v  v    ivi          
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_228975111_   2214 GTAATGTGCCCACAATTATCTGATCTTCAACAAAAAT---AAG------C 2254
                         viv  iiiiii iii i vi    i   i    iii ---   ------ 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_228975111_   2255 AATAGGGAAAATACACCCTATTCAAAAAATGATGCTGGAATAATTGTCTA 2304
                            i      iv i vi  v     v     i      i i  i  vv  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr2_228975111_   2305 AACATATACAGAAGAATGAAACTGGACCCCCAACTATCATCATATACAAA 2354
                         ?v  i  i  i         ii        i v  vv  i          
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr2_228975111_   2355 AATTAACTCAAGGTAGATTACAGACTCTAATGTGAGATCTAAAACTATAA 2404
                                    ii i   i ?    iiv     i   v            
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr2_228975111_   2405 AAACCCTAGAAGAAAACCTGGAAATAC-CCTTCTCAATATTGGCCTTGAC 2453
                           vi i           v i i?i  v-i    vii iv    vi v i 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_228975111_   2454 AAAAAATGTATGGCTAAGTCCTCAAAAGCAATGGCAATGAACACAGAAAT 2503
                           viiv viv i v  v v vi        vvi    ii  viv i    
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_228975111_   2504 TGATAAGTGGGACCTAAT-AAAATTAAAGGGCTTATGCACAGCAAAAGAA 2552
                         v     i v    i v  -         ii-   v  ii vv    i  v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chr2_228975111_   2553 ACTACCAACAGAGTAAAAAGACAACCTACAGA-TGGGAGAAACTATTTAC 2601
                             i   v i   i           i     -         v     i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_228975111_   2602 ACATTATGCATCCAACAAAGGTCTAATATCCAGAATCTATAAGGAACTTA 2651
                          v  i  ii   ii i  i  v  vi          v     i     iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_228975111_   2652 AACAGTTCAATAACTGAAAAACAATTAACTTCATTAAAAAGTACTCAACA 2701
                         v   ii       ivi   i    v    iiv   ?    i ivv   vi
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chr2_228975111_   2702 GACATGAACAGACACTTCTCCAAAGAAGGCATACAAGCAGCCAACA--CA 2749
                           iv    i     i             ii      iii     i --  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr2_228975111_   2750 CGTAAAAAAATGCTCAGC--CAGGTGCAAT 2777
                          i i    i       i --  ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (164 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.15 (41 / 13)  


2438 18.83 7.14 2.44  chr2_229038724_229040331.rev      501  1116 (492)    L1M4_orf2#LINE/L1      264   908 (0)  

  chr2_229038724_    501 AATGTGGTACTA-CACA-GGACAGACATATAGATAAA-AGAATAGAATTG 547
                          i         i-  i -   i            v  -i           
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_229038724_    548 ATAGTCCAGAAATAAACTGATACATCTGTGGTTGAGTGATTTTTTACAAG 597
                          v               iv      i i    ii v       iv     
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_229038724_    598 GATATCAAGTCT-TTCAAATAGAGAAAGAGTAGTCTTTTCAATAAACAGT 646
                          i ii    v i-     - i i      i            i   ii  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr2_229038724_    647 GTAAGGACAACGGAATATTCATATGCAAAAAAACAAAGTTGAACCTCT-- 694
                          ivi       v i   ?i  i        i  ii      i   i  --
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr2_229038724_    695 CTCGCATCAGAGGAAAAAAATACCTCAAAATAGATCAACAACC------- 737
                            i  i  v viv     v  v        i     ?vi   -------
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_229038724_    738 -------AAAA---------TC-------AAAACAGAGGCACAAATCTTT 764
                         -------    ---------  -------      v   ?ii       i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr2_229038724_    765 GTGATCTTACATTAGAAAATGATTTATTAAA-ATGACACTAACTAAAAGC 813
                             i   ivi    iv    i   v   i -       i  ----    
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA----AAGC 608

  chr2_229038724_    814 ACAATCAACCAAGGGAAAAACAAACAGATAAAATACACTTCGTCAAAATT 863
                             v    -  ii      --- i       v iv     i        
  L1M4_orf2#LINE/    609 ACAAGCAAC-AAAAGAAAAA---ATAGATAAATTGGACTTCATCAAAATT 654

  chr2_229038724_    864 GAAAG-TTTTATGCTTCAGAGGATACTATAAAGAAAATAAAA------CC 906
                         i   i-    i       i    i     v      i i   ------  
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_229038724_    907 AACAAAATGAATGACATTTGTAACATTTGCAAATCATATATCTCATAAAG 956
                         v   i    iiv  - -----  i                   v    i 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGA-A-----AATATTTGCAAATCATATATCTGATAAGG 748

  chr2_229038724_    957 TACTTGAATCTAAAATATATAAACAATACTTGCAATTCCGTAATAAAAAG 1006
                         v     v   i i          v  iv   i   i  vi          
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_229038724_   1007 ACAAATGACCCAATTAAAAAGTGGGCAAAGGAGTCTTATAGATATTTTTC 1056
                               i        ?    i           v ivv     i    i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_229038724_   1057 AAAAGAAGATATAGAAATGGCCTATGAGCACATGAAAAGATGCTCAATAT 1106
                         v            v        v  i                     i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_229038724_   1107 CATTAGTCAC 1116
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.11 (76 / 36)
Gap_init rate = 0.03 (17 / 645), avg. gap size = 3.47 (59 / 17)  


3213 26.90 0.44 0.44  chr2_229110462_229116590.rev     4731  5637 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_229110462_   4731 GGAAGAACATTCCATGCTCACGGGTAGGAAGAATCAATATCGTGAAAATG 4780
                             ii i  i     i   i  i v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_229110462_   4781 GCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCT 4830
                           v     v     iv i  i           i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_229110462_   4831 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 4878
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr2_229110462_   4879 ATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAGA 4928
                               viiv  ii  v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_229110462_   4929 ACAAAGCTGGGGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 4978
                               i   i  vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_229110462_   4979 ACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGATATAGATCA 5028
                                i   i    ii       v i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_229110462_   5029 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACTA 5076
                               i    i--    i  --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_229110462_   5077 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5126
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_229110462_   5127 TATTTAATAAATGGGGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTG 5176
                          v  i  i      v       v      v  ?   i   v i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_229110462_   5177 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5226
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_229110462_   5227 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5276
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_229110462_   5277 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5326
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_229110462_   5327 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5376
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_229110462_   5377 GAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5426
                         v   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_229110462_   5427 GGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5476
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_229110462_   5477 GGGCTAATATCCAGAATCCACAATGAACTCAAACAAATTTACAAGAAAAA 5526
                           i  vi          vi i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_229110462_   5527 AACAAACAACCCCAACAAAACGTGGGCGAAGGACATGAACAGACACTTCT 5576
                         i     i     v vi?   vi     i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_229110462_   5577 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5626
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_229110462_   5627 TCACTGGCCAT 5637
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (5 / 907), avg. gap size = 1.60 (8 / 5)  


3209 27.20 0.44 0.44  chr2_229257979_229264257     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_229257979_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4929
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_229257979_   4930 GGTCATACTACCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                           iv     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_229257979_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_229257979_   5028 TGTGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                          i     viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_229257979_   5078 AACAAAGCTGGAAGCATCACACTACCTGACTTCAAGCTATACTACAAGCC 5127
                                i    i vv       v  ii i     iviv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_229257979_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_229257979_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_229257979_   5226 ATCTGATCTTTGACAAACCTTAGAAAAACAAGAAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv vvv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_229257979_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTGGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v i?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_229257979_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_229257979_   5376 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCGAGAAGAAAAC 5425
                          i ?    i       v   v       i      vi iv          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_229257979_   5426 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_229257979_   5476 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5525
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_229257979_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_229257979_   5576 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_229257979_   5626 AGGGCTAATATCCAGAATCTATAATGAACACAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v     v    v vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_229257979_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_229257979_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACAAGAAAAAATGCTCATC 5775
                           v        i  vi viii     v  i    v     i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_229257979_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3058 16.51 3.89 0.62  chr2_229362084_229363708.rev      498  1139 (486)    L1M4_orf2#LINE/L1      246   908 (0)  

  chr2_229362084_    498 AGC-ACAGTTATCATAACAGGGTAAGTACTGGCATAAGAAGAGATGCATA 546
                            -     v    vi    v  -i             i v   --    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGT-GGTACTGGCATAAGGATAGA--CATA 292

  chr2_229362084_    547 TACATCAATGGAATGGAGTTGAGAATCCAGAAATAAATCTTTACATTTAT 596
                           v           i  i      i            i iv         
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_229362084_    597 GACCAAT-GATTTT-GACAAGAGCACCAAGACAATTCAATGGGCAAAGA- 643
                          ii    -      -      i ii       v          v     -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_229362084_    644 TAGGTCTTTGCCAAAAAGGATGCTGGAACAACTGGATATCCACATGTTAA 693
                            -     v v v   v i      i           ?       iv  
  L1M4_orf2#LINE/    393 TAG-TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr2_229362084_    694 AGAATTTAGTTGGGCCCCTTCCTCACACCATACACAAAAATTACCTCATT 743
                              vv      i     v            i          v    vv
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_229362084_    744 ATGGATCATAAACCTAACTGTAAAA---AAAAATACAAAACTCTTATAAG 790
                                 ? i      v     i ---    v  i          v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr2_229362084_    791 AAAACATAGGAATAAAT---TGTGACCTTAGATTTGGCAGTGGTTTTGTA 837
                                   ?i     ---i        i i  v    i      iv  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_229362084_    838 GATA-GGCCCCAGAACCACAAACAACAAAAGACAATATAGATAAATTGGA 886
                             - i v   i  v     i          v  v              
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr2_229362084_    887 CTTCAATAAAATTA----CTTGTGTGCTGCAAATGATACTATCAAGAACA 932
                              vi       ----   v      v    v  i           vi
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_229362084_    933 TGAAAAGATAACCCATATAA-----GAAAATATTTGCAAATCATGTATCT 977
                                 i      i v  -----                   i     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_229362084_    978 TATAAGGGACTTATATCCACAATATATAAACCACTGTTACAAATCAATAA 1027
                         v           i      v          vv   v      v       
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr2_229362084_   1028 CAGAAAAATAAAT--TTTAATT-AAAAATGAGCCAAGGATCTGAATATAC 1074
                         i i   i i    --iii    -       i  v      i      v  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_229362084_   1075 GTTTCTCCAAAGAAGACCTAAAAATAATCA--GAGTACATTAAAAGATGC 1122
                         i               iv  v    iii  --i  i    v         
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_229362084_   1123 ACACTGTCTGTGATATT 1139
                         v  vii  v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (55 / 48)
Gap_init rate = 0.02 (15 / 663), avg. gap size = 1.93 (29 / 15)  


2076 26.92 4.81 3.55  chr2_229399818_229402751.rev     1569  2441 (492)    L1M4_orf2#LINE/L1       25   908 (0)  

  chr2_229399818_   1569 ATTAGAAGACTTGATATTGTTAAGATGTCACTTCTTTCCAAACTGATTTA 1618
                            i        i              v  v v  ii     i    i  
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr2_229399818_   1619 CAAGGTAAACACAATCACAATCATT-TTTCAGCAGGTTTTTTTTTTTTTT 1667
                           iiv v   i     v v    vv- ii    v vi      -------
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT------- 117

  chr2_229399818_   1668 TTTTTTTTTGGTAGAAGCAGACGTGGAAATTCTAAAACTTACATAGAAAG 1717
                         ---------- i    iiv   iv vvi  i      i i i  i    v
  L1M4_orf2#LINE/    118 ----------GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr2_229399818_   1718 GCAGAGAACATCGA-TATTCAAAACAATACCTTGAAAAAGAACAAACA-- 1764
                            ii i  viv  -  vi         --            -i    --
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAAT--CTTGAAAAAGAA-GAACAAA 204

  chr2_229399818_   1765 -TT--AACATTTACACTGCCTGATTGTAATACTT--TAC---GTTATAAT 1806
                         -  -- iv i i     v  ii   vi  v    --   --- i  i i 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_229399818_   1807 AATCAAGGGAGTGAGATACAGACAGAAGTATTGACAAATTTATCAATGAA 1856
                                iv    v i   v i  v   v  v    v  vv       i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_229399818_   1857 ACAGA---GAGA--CCAGAAAAAGACACACACTTACATAGTTATCTGATT 1901
                          i   ---    --       v i  v  i  v vi  i  i vi     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_229399818_   1902 TTTCAATAAAGTTGCCAGTGGA--ATCCAAAGACGAAAGGAAAGTATTTT 1949
                           - i i  i v     i--  --  i   v iv     i v   v    
  L1M4_orf2#LINE/    355 TT-CGACAAGGGTGCCAA--GACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_229399818_   1950 TAGCAAGTGATGCTGAAATAATTGGATATCTGCGTGGGGAAAAAAATGAA 1999
                         i i   i  i     ii i  i      ? ii i  v--    i      
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGC--AAAAGAATGAA 449

  chr2_229399818_   2000 CATTAACCTATTACTTT-CACTGCATGTAAAAGT-AAGTAGAGATAGAAC 2047
                         -i  iiv ivi   i i-   iii  ii    i -  v vi i  i  v 
  L1M4_orf2#LINE/    450 -GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_229399818_   2048 ATTGACCTGAATGTAAAATCTAAAACTATAACGATTTTAGAAGTAAACAG 2097
                          ?v     i       i v            viv i       v     v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_229399818_   2098 AGAAGGATATCTTTATGACTTGAGGGTAGACAAACATTTCTCAGATC--A 2145
                           i? v v     ii    i vi  v   i   vvi     i    v-- 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_229399818_   2146 CAATTAGAA--ATAATCA-TAAAAGAAACATCAAA-AAACTAGATTTTAT 2191
                           -ii i  -- i  v  -i        v vi i -   i i  i  i  
  L1M4_orf2#LINE/    599 CA-CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_229399818_   2192 CCAA-TGAAAAATAATCTTAT----CAAAA-ACACCATTAAGAAAATTAA 2235
                          v  - v     i-- i  i ----    i-    i  i      i v  
  L1M4_orf2#LINE/    648 CAAAATTAAAAAC--TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_229399818_   2236 TAGGCAAGGCATAAACATGG-AGAAAATAGTCACAGG--ATATATCTGAC 2282
                         v  i   vv  i i -    -        v ii  ii--          i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGA-ATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_229399818_   2283 GATGTATTGGTGTCCAGGATATATAAAGAACACCTAAAACTCAGTCATAA 2332
                         i v v i v  i     i             v i  v      i v    
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_229399818_   2333 ACTTGCAAGTAACCCCAT-AAAATATGGGACAAAGATTTCA-CAGGCATT 2380
                          vvvi   i      v  -?   v     vv  i     v -i  i    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_229399818_   2381 ----CACAAAATGACGTACAAATGGCTAAGAAACTCATTAAAAAGTTCTT 2426
                         ----  v i  -  ii          i  v  i v   v    ii v  i
  L1M4_orf2#LINE/    845 TCTCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_229399818_   2427 ACCATCATAGTCATC 2441
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (140 / 91)
Gap_init rate = 0.04 (34 / 884), avg. gap size = 2.15 (73 / 34)  


3261 24.63 2.28 1.25  chr2_229428716_229430940.rev      849  1725 (500)    L1M4_orf2#LINE/L1        1   886 (22)  

  chr2_229428716_    849 TGGAAAGATATTTTATACTCATGGATTAAAAGAAGTAATATTGTCAAAAT 898
                                    iii  ii         ii    vv         i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_229428716_    899 GACAATAGTGCCCAAAATAATTTACAGATTCAATGCAATCCTTATAAAAA 948
                          i     v v      v i  i           i       i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_229428716_    949 ATACCAATGACATTTTTCACAGAAATAGAATTTTAAA---ATCCTAAAAT 995
                         - v   iivi v     ii       v  ----i  i---          
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTTTTTTGCAGAAATTGA----CAAGCTGATCCTAAAAT 145

  chr2_229428716_    996 TTATGTGGAACCACAGAAGACACTGAATAGCCAAAGTAATCCTGAGCAAA 1045
                          i  i     vii  iii   v v           ii    i   iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_229428716_   1046 ATTAACAAAGCTGAAGGCAC-CACACTACCTGACTTCAACATTTACTACA 1094
                          vv       i  i   -  -      v  ii i     v i        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_229428716_   1095 AAGCTACAGTAACCAGATCAGCCTGGTATTGGCATAAAAACAGACACATA 1144
                                     i  iiv   iv     i        ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_229428716_   1145 AACCAATGGAACAGAATAGAGAGCCCAGATATAAGTCCACACATTTAGGG 1194
                         i i        i     v     i     v    ii   i       v  
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_229428716_   1195 CCAACTTATCTTCAAGAAAGATGCCATGAGCATGCAAAGAGGAAGGGACA 1244
                         i   i v  i   i v  i i     v  v   v   v i    i i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_229428716_   1245 GCCTT--CAATAAATAGTGCCGGGAAAACTAAATCACTATATACCGAAGA 1292
                          i   --   i    i    i    v    ii  v? i i  i vi    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_229428716_   1293 ATGAAATTAGGCCTCTCTCTCTTGCCATACACAAAAATCAA--------- 1333
                              i  i i  i  vi   vii     i        i  ---------
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_229428716_   1334 -ATCATAGACTTAAGTTTATGACCTAAACCTATGAAAACTACTGGAAGAA 1382
                         -    ?    i   i v  v  v     v    -      vi i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAA 543

  chr2_229428716_   1383 AACATTGGGG-AAATGCTCCAGGACTTTGCTTTGGGCAAAGATTTTTTTG 1431
                              v  ? -    -  i iv   i   vv  i     v i   i  v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr2_229428716_   1432 TGTAAGATTTCAAAGGCACAGCCAACCAAAGCAAACAACAGACAAGTGGG 1481
                         -i  v  ivi    i     iv    v    v   -  i   i  i v  
  L1M4_orf2#LINE/    593 -ATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGG 640

  chr2_229428716_   1482 ATTACATCAAG-TGGAAAGCTTCTGCACAGTAAAGAAAATAATCAACAAA 1530
                          i v      i- vi   i   i  ii vvi    i v iv     v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_229428716_   1531 GTGAAGAGA-AATCCACGGAATGGGAGAAAATTTTTGGGAACTATCCATC 1579
                              i   -  i    i              v    vi  ii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_229428716_   1580 TGACAAGAGATGAATAACCAGAATATATAAGGAGCTCAAACAACTCAACA 1629
                            i   i  ivvi  v             i  i   vv         i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_229428716_   1630 GCAAAAATCTCAAGGAATCCAATT-AAAAATTGGCAAAATATCTGAATAG 1678
                         ii     vv-   iv  i      -      v      iv  i       
  L1M4_orf2#LINE/    791 ATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_229428716_   1679 ATATTTCTCAAAAGAAGAAATACAGATAACCAACAAGTATATAAAAA 1725
                          i       v        v     i  ii    i   i i  i    
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.92 (140 / 73)
Gap_init rate = 0.02 (16 / 886), avg. gap size = 1.94 (31 / 16)  


3288 26.87 0.44 0.44  chr2_229445415_229451693     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_229445415_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_229445415_   4930 GACCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                          i v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_229445415_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_229445415_   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_229445415_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_229445415_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_229445415_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_229445415_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_229445415_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_229445415_   5326 GAAACTGGATTCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    ii   v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_229445415_   5376 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_229445415_   5426 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGGCTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v  i   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_229445415_   5476 AACACCAAAAGCAATGGAAACAAAAGACAAAATTGACAAATGAGATCTAA 5525
                         i            vvi v         v     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_229445415_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_229445415_   5576 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_229445415_   5626 AAGGCTAATATCCAGAATCTACAATGAATTCAAACAAATTTACAAGAAAA 5675
                         ii i  vi          v  i  v   i  vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_229445415_   5676 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_229445415_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCCTC 5775
                           v        i  vi viii     v  i          i      vv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_229445415_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2067 23.22 2.21 4.42  chr2_229493398_229495022.rev      501  1133 (492)    L1M4_orf2#LINE/L1      290   908 (0)  

  chr2_229493398_    501 ACATAGACTAGTGGAACCTAAT----AGCCCAGAA-CAAACCCGTTCATA 545
                          i     ii i     ivv   ----  i      -i      i v   v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_229493398_    546 TATGCTCAACTAATTTTTGACAAAGGTTCCAATAATATACAATGGAGGAA 595
                             v    i i     i     i   v    v vi  v      -    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAA 388

  chr2_229493398_    596 AGTATAGACTCTTTAATAAATGGTGTTGGAAAAACTTGATATTGACAAGC 645
                           v    v  i  i  i        i   i v    v    ?iv   v  
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_229493398_    646 AAACCT-TAAAATCAGATCTTTCTCTTATATCATACACAGAAATGAATTC 694
                            vvv- i  i ii  i ii vi  i i i    i   i    v  i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_229493398_    695 AAAATGGTTTAAAGACTTACATGTAAGACCTGAAACCATGACACTCCCAG 744
                                v i ?    i  v        v  i    i  i v    ii  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_229493398_    745 AAGAAAACATGAAGGAAAAGCTCTTTGACATTGGTCTTGGCAATGATTTT 794
                                   iii? v   v  iiv    v    vi v       i   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_229493398_    795 TTAGATTTGATCTCAAAAGTACAGAAAATAAAAGCAAAAATAAACA---- 840
                               v   ivi      i   iiv  i     v       i i ----
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_229493398_    841 GGACTACATCAAA-CTAAAAACTTCTGTACAGCAAATGAAACAATGAAGA 889
                              v       -i         i   i vv    v  v  v  v    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_229493398_    890 AA-CAAAAAGGCAACCTACAGAA-AAAAGAAAATATTTGTAAACCATATA 937
                           -ii     i     i      -iii            i   i      
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_229493398_    938 TCCAGTAAGGTGTTAATATCCCAAATATATAAGCAACTCATAAAACTTAA 987
                           iii     vii vi     vi         iv     v  v    i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_229493398_    988 TTGCAAAAACAAGTAACAAAAATAAACAAAAAACACCCCAAATAACTCAA 1037
                          -------------------      ---  i   -----      i   
  L1M4_orf2#LINE/    789 T-------------------AATAAA---AAGACA-----AATAACCCAA 811

  chr2_229493398_   1038 GTTAAAAATGGGCAAAGGACATGAATAGACATTTTCACAAAGAAGAC-CA 1086
                         v ?                iv             iiv         i-i 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_229493398_   1087 AAAATAGCCAACAGATACATGAAAAGATGATGAATATCATCAATCAT 1133
                         v    i     i iii             v v  i    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (90 / 53)
Gap_init rate = 0.02 (12 / 619), avg. gap size = 3.50 (42 / 12)  


3255 25.64 2.35 0.67  chr2_229500562_229504755.rev     2810  3702 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_229500562_   2810 TGGAAAGATTGTCCATGTTCATGAATTGGAAGAATCAATATTGTTAAGAT 2859
                                  vvi           i         v i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_229500562_   2860 GTTT-TACTACCCAAAGCAATCTTCAGATTCAATTCAATCCCTATCAAAA 2908
                          viv-    v      vii    v         iv               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_229500562_   2909 TACCAATTACCTTCTACACATAAATAGAAAAAA-AACCCTAAAATTTATA 2957
                          v   ii i    i vii  v    v  v  iv-i i         i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_229500562_   2958 TAGAACCACAAAAGACCCAGAGTAACTACAGCTATCCT----AAGGAAAA 3003
                          i   vii   ii        i  i i v i v   i ----   i i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_229500562_   3004 CTAAGCTGAAGGAGTCACATTACCTGTCTTCAAATTATACTACAGAGCTA 3053
                          v   i  i    v     i v  iivi      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_229500562_   3054 TAGTAGCCAAAACAACATGACACTGGTTTTAAAAGAGACATA--GACTAA 3101
                         i    ii   i   iii  ii     iv v ii v       --  ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_229500562_   3102 TGCAACAGATTAGGGAACCTCAAAACAAATTCACACACCTACAATGAACT 3151
                           v  i   v v i  ii ivi   i   ii  i   ii  iii v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_229500562_   3152 CATGTTTCAACAAACGTGCCAAGAATATACCCTGGAGAAAAGATAGTCTC 3201
                         v  -    i    iv         vi  v vv   i    ii       i
  L1M4_orf2#LINE/    351 GAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_229500562_   3202 TTCAATAAATGGTGCTGGGAAAATTGGGTATCCATATGCAGAAGAATGAA 3251
                              i              v  i   i  ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_229500562_   3252 ACTAGACCCCTATCTCTTGCCATATTAAAAAATCAAATCAAAATGGATTA 3301
                         ii i        i   vii      vv      i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_229500562_   3302 AAGACTT-----TAAGTTCTTCAGCTATGAAACTACTATAGAAAAACATT 3346
                         ?    i -----    vv  vv i    i     vi  v ii       v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_229500562_   3347 GGAGAAAATCTCTAGGGCTTTGATTTGGGCAAAAATTTCTTGAGCA--AT 3394
                           ? v      iiiv i i   iv  i     vii      iiii -- i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_229500562_   3395 ACCC----CACAAGCAGCCAAAGTAAAAATGGACAGATGGGATTACATCA 3440
                            v----        i v    v      i  i i  v   i v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_229500562_   3441 GG-TTACAAAGCTTCTACACAGCAAAAGAAACAATTAACAAAATGAAGAA 3489
                         ii-   -   i   i iii vv    i  v  v  i  v   i    i i
  L1M4_orf2#LINE/    650 AAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_229500562_   3490 ACAATACACAGAATGGGAGAAAATATTTGCATACTAACCATCTGACAAAA 3539
                             iv                         v ii vvi      i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_229500562_   3540 GATTAATAACCAGAATATATAAGGAGCTCAAACAACTCTATAGGACAAAA 3589
                           i vi  v             i  i   vv       v   -- i    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA--ATAAAA 796

  chr2_229500562_   3590 AATCTAATAATCTGATTTTTAAAAATGGGTAAAG-ATTTGAAAAGACATT 3638
                          iv v     i ii   ?--         i    -       v       
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_229500562_   3639 TCTCAAAAGAGGATATACAAATGGAAAACAGGCACTTGAAAAGGTGCTCA 3688
                             v     i             vv  i i    v       i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_229500562_   3689 ACATCATTGATCAT 3702
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (145 / 80)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.08 (27 / 13)  


2805 25.80 2.44 1.88  chr2_229678070_229680988     1525  2427 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_229678070_   1525 TGAAAGAACACCCCATGCTCATACATAGGAAGAATCAGTGAAATTAAAAT 1574
                           i  ii i i      i    iv  v      v i i ivvi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_229678070_   1575 GACCATACTGCCCAAAGCAATTTACACATTCAATGATATTCTTATCAAAC 1624
                          i v     v      vii  i    v      i vv  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_229678070_   1625 TACCAGTGACATTCTTCACAGAACTAGAAAAAACT-ATTCTAAAATTCAT 1673
                          v    ivi v  i  ii     v v  v  i-  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_229678070_   1674 ATGGAACCATAGAAGAGCCAGAATAGCCAAAGCAATCCTAAGCAAAAAGA 1723
                               viii iii  v              i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_229678070_   1724 ACAAAGCTGGAGGAATCACATTGCCTGACTTCAAACTGTAGTACAAGGCT 1773
                               i       v     i v  ii i      viv  v     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_229678070_   1774 ACAACAAACAACACATCATGGTACTGGTACAGAAACAGACACATAGACCA 1823
                            ii  v   v   vii         i i iii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_229678070_   1824 ATGGAACAGAATAGGGAACCCAGAAATAAGGCCATAAGTCTACAATCATC 1873
                               i     v i  ii          iv     vi i  iii   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_229678070_   1874 TGATATTTGAGAAAACTGACAAAAAACAAGAAGTAGGGAAA--AGAGTCC 1921
                             v  i  v  iiv  v   i v-  vvv i i      -- v    -
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTC- 397

  chr2_229678070_   1922 CTGTTTAATAAATGGTGCTGGGATAACTGGCTAGCTATATGGAGAAGATT 1971
                         - v  i  i              i      v  ? i i   v i    v 
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_229678070_   1972 GAAACTGGACCCCTTCCTTATACCACATATAAAAATCAACTCAAGATGGA 2021
                            ii         v   i i    i   i      i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_229678070_   2022 GTAAAGACTTAAATATAA-AGCTCAACACTACAAAAACCCTGGAAGACAA 2070
                         vi ?    i     i   -    v  -    i    vi i i     v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAA-ACTATAAAACTCTTAGAAGAAAA 545

  chr2_229678070_   2071 CCTAGGCA-ACACCATTCTGGACATAGGAAAAGGCAAAAATTTTATGATG 2119
                          v    ?i- v i -   vv   v v  ivv      vii   iv ----
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT---- 590

  chr2_229678070_   2120 AAGATGAGATGCCAAAA--ACAATTGCAACAAAAGCAAAAATTGACAAAT 2167
                         -    iv  ii      --    --          v      v  i    
  L1M4_orf2#LINE/    591 -AGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAAT 637

  chr2_229678070_   2168 GGAACCT-----AAACTAAAGAGCTTCTGCGCAGGAAAAGAAACAGTTAA 2212
                         v i  i -----   i    i -   i  i  vvv   i  v  vi i  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chr2_229678070_   2213 CAGAGTGAAAAGGCAACCTACAGACTGAGAGAAAGTATTTGAAACTC-TG 2261
                         v i         i     i     v  i      i      v  v  - i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr2_229678070_   2262 CATCTGCTGACAAAGGTCTAATATTCAGAATCTACAAGGAACTTAAACAA 2311
                         i     --- i  i  v  vi   i      v  i  i     ivv    
  L1M4_orf2#LINE/    737 TATCTG---ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_229678070_   2312 ATGTACAAACAAAAAACAAC--ACC--ATTCAAAAGTGGGCACAGGACAT 2357
                         v vv i  vv    i    v--   --   ?    i      v    iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_229678070_   2358 GAA----CACTTTTCAAAAGAAGACATACATGTGTCCAACAAGCATATAA 2403
                            ----  i  i  v        i     vi  v    i     i  i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_229678070_   2404 AAA-ATGCTCAATATCACTAATCAC 2427
                            -        i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (139 / 90)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.95 (39 / 20)  


3501 25.66 1.11 0.66  chr2_229750586_229753951.rev     1973  2876 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_229750586_   1973 TGCAAAGTTCTCTTTTGCTTATGGATTGGAACTATTAATATTATTAAAAT 2022
                           v    v v  iiv  i i           vvv        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_229750586_   2023 CTCCATACTATCCAAAGTGATCTACAGGGTCAATACAATTTCTGTCAGAA 2072
                         vv v     vi     v          iv    ii    ii  i   i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_229750586_   2073 TTCTAA-TGTCATTTTTTTCAAGGAAATAGAAAATATAATCCTAAAATTC 2121
                          i i i-  i -      v  --     v  v  vv i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCA--GAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_229750586_   2122 ATATGGAACCATAAAACACCCCAAATAGTGAAAGCAATCTTGAGCAAAAA 2171
                                 viii  iiv    vi     iv   i         iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_229750586_   2172 GAACAAAACTGGATGCATCACACTATCTGACTTCAAAATCTATTACAAAG 2221
                                ii    v vv       vi ii i       ii  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_229750586_   2222 TTGTAGTAATCAAAACAGCATGGTACCAGCATAAAAAGAGATACATTGGC 2271
                         i ii         i    ii      ii      ii v   i i  v ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_229750586_   2272 TAATGGAACAAAATAAACATCCTAGAAATTTACCCACCAATTTATAGTCA 2321
                         i       i i   vi v vi i      vv     ivv      i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_229750586_   2322 ATTGTTTTTTTTGATGAAGATGCCAAGAGCACGCAATGGAGAAAG-GCAA 2370
                             v    --i  ii i i        v  iv      i     -ii i
  L1M4_orf2#LINE/    348 ATTGATTTT--CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_229750586_   2371 TCTTTTCAATAAATGCTGTTGGGAAAACTGGTTCTCCACATGCAGAAGAA 2420
                                  i     v  i     v      v v?         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_229750586_   2421 TGAAATTGGACCCTTATCTCACATCATATACAAAAATCAATTCAATTTGG 2470
                             i        i  i      i             i  i    vv   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_229750586_   2471 ATTAAAGACTAAAGAGAAAGGCCTGAAACTATAAAATTACTAGAAGAAAA 2520
                           i ?    iv  iv v   iv  i           i vi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_229750586_   2521 CATAAAGGCAAAGTTCTACGACATTTGTCTGGGCAAAGATTTCTTGGATA 2570
                             ii? i   vi iiii   v  v vi i     v i      i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_229750586_   2571 TGACCCTAAAAGCACAGGTAATAAAAGCAAAAAATAAATAA----GATTG 2616
                             v i         i i  i     -        i    ----  i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTT 644

  chr2_229750586_   2617 CATCAATAT----GGCCTCTGCACAGCAAGGTAAACAATCAGTAGAATGA 2662
                               v  ----ii i i  ii vv   i v v  v    iv i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_229750586_   2663 AGTGGCAATGCACAGACTGGGAGAAAATATTTGCAAACCATTTGTGGGAT 2712
                          iv i   iv      v                    i   v i vv   
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_229750586_   2713 AAGAGGCTATAATCCAAAATTTATAAAGAATTCAAACAACCCAATAACAA 2762
                            i i  vvv     i   v         i  vv     i      i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_229750586_   2763 GAAAACAAATTATCTAATCAAAAAATGGACAAGTGACTTAAATAGATATT 2812
                         i  i      v i i   i?        i   iv  i  i      i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_229750586_   2813 TCTCAAAAGAAAACATACAAATGGCCAACAGATATATGAAGAATCGCTCA 2862
                             v      i i              i iii i     i ivi     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_229750586_   2863 TCACTAATCATCAG 2876
                         v  ii ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (147 / 81)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


2493 25.86 5.86 1.49  chr2_230016919_230019727     1448  2317 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_230016919_   1448 TGGACACATACATCATATTTGTGGATTTGAGGATTCAATATTGGTCATAT 1497
                             v v   ivi   i  ii      v  i  i i       v v v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_230016919_   1498 GTTATTTCAACCCAAACTGACCCATAGATTTAAGGCAACCCC----AGAA 1543
                          vi v v vv      i   i i i     i  v    i   ---- i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_230016919_   1544 -----G--GTTTTGTTTTTAGAAATTGGCAGGCTGATTCTAAAATGTATA 1586
                         ----- -- ii  v   vi        i  i      i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_230016919_   1587 TAAAAA-ACAAAAGTACCTAGAATTGCCAAAATAATATTGAAAGGAATGG 1635
                          ii   -i   ii -   i     v       i   v      iii v i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_230016919_   1636 GCAGAGTTATATAACTAACACCAGCTGATTTCAAAAC--AGTATA--GTT 1681
                         i  i    iv vi   v    ivv ii          -- v  i -- i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_230016919_   1682 ACGGTAATAAAGACAGTG--GCACTGGTGTGAGGATGGTCATTTAGATCA 1729
                           i     v         -- i     ii i     i v   v       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_230016919_   1730 ACGTGGCCAAAAC--AGAGTCAAGAAAGAGAACCAAT-CAG--ATCATCA 1774
                          i - ivi i  i--      v     v -    v  -  v--  vi   
  L1M4_orf2#LINE/    300 ATG-GAATAGAATTGAGAGTCCAGAAATA-AACCCATACATTTATGGTCA 347

  chr2_230016919_   1775 GCTGGTTTTTGGCAAAGATATCAAAGCTATTCAA------AAGGATTTTC 1818
                         ii  i    i i   i i ii   ii i      ------   i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_230016919_   1819 TTTCCAACAAATGGT---------ACTATATATTCATTTGGAAGAAAATG 1859
                            i           ---------   iv   ?i  iv  v  i i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_230016919_   1860 AACATTGTCTCTTACTTTACACCATTTGCAAATATTAACTCAATCACAGT 1909
                           vv v v i i   i i       v i    v          -v ii -
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA-AATGG- 495

  chr2_230016919_   1910 ATTGTAGACTTAAATGTAAAGGCTAAT-CTATTAAAGTCATCTATAAGAA 1958
                           ii?    i         ii     v-    v   v  v -----    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT-----AGAA 540

  chr2_230016919_   1959 ACAAATGCAAGAAAAAATCTTCATGATTTGGAGGAAGGCA--GATTTCTT 2006
                         iv   iii i ?iv        i   ii v i vv     -- i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_230016919_   2007 GGAGAGAAGAC--AGAGCATATAAATCATAAAAGAAAAAA-ATATAATTT 2053
                         i  v vi v  -- i    i -- iiv i           - v    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACA--AGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_230016919_   2054 GGACTGTATAAAAAATAAAGACATATGC-CTTCCAAAGACTGCAACAAGA 2102
                              vi  v    v    i  v v  i-    v  i   vvi v     
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_230016919_   2103 AAATGAAAAGGTGAGCCACAGACTGGAAAAAAATAGATACAAAACAGATA 2152
                           i       iii v       v   i i      vv i    v  v   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_230016919_   2153 AATGACAAAGGCCAGGTGTTCAGAGTATATAAAGAAATGCTATAAATTAA 2202
                         vv   i  i  v vv  i i    i           v vi  i  v i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr2_230016919_   2203 TAATAAAAAGACAA----CCCAATTTTTTAAATGGGCAAAG-ATTTGATC 2247
                                       ----       ?vv-            -      vi
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAAT 837

  chr2_230016919_   2248 AGACATTTC-ATGAAGAATATATATAAATGGCCAAGAAACACTGGAAAAG 2296
                                  -vii     v     i          v  i   vv      
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_230016919_   2297 ATGCTCAACATCATTAGTCAA 2317
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (129 / 92)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.29 (64 / 28)  


3065 27.50 0.22 0.66  chr2_230070691_230077458     5368  6276 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_230070691_   5368 AAAAACATTTCATGCTCATGGATAGGAAGAATCAATATCATGAAAATGGC 5417
                            i i  ii    i        v      v i     ii v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_230070691_   5418 CATACTGCCCAAAGTAATTTACACGTTCAATGCTATCCCCACCGAGCTAC 5467
                         v     v      v i  i    vi     i  v     i i i iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_230070691_   5468 CA-CTGACTTTCTTCACAGAATTGGAAAAATCTACTTTAAAGTTCATATA 5516
                           -   v    i  -i     v v  v  iiiv iii    i       i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_230070691_   5517 GAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAACAGAACA 5566
                            viiv  ii  v  v v        i      i i iv  iv      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_230070691_   5567 AAGCTGGAGGCATCATGTTACCTGATTTCAAACTATACTACAAAGCTACA 5616
                            i      vv   iii v  ii        viv               
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_230070691_   5617 GTAACCAAAACAGCATGGTACTGGCACCAAAACAGATGTACAGAGTAATG 5666
                             i   i    ii           iv ii i   ii  i   vi    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_230070691_   5667 GAAAAGAACAGAGGCCTCAGAAATGATGCCACATATCTACAACCATCTGA 5716
                            v    iv   ivii       i vv   i i  i  iiii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr2_230070691_   5717 TCTTTGATAAACCTGATAAAAACAAGCATTGGTGAAAGGATTCCCTATTT 5766
                          i  i  i  ivv  vi  i v  vv  v   v     i  vvi  v  i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_230070691_   5767 AATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACGGAAACT 5816
                           i        i     v      v  ?   i     i  i vv   ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr2_230070691_   5817 GGACCCCTTCCTTACACCTTATACAAAAACTAACTCAAGATGGATAAAAG 5866
                                 v   i     v          i        i      v ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr2_230070691_   5867 ACTTACACGTAAGACCTAAAACTGTAAAAACCCTAGAAGAAAACCTAGGC 5916
                           i  v i      v        i     vi i           v    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr2_230070691_   5917 A-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAACAC 5965
                         i- v i -   iv   v v  vv i     v ii   v iiv  vi    
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr2_230070691_   5966 CAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAATTAAA 6015
                                 vvi          vv     v  i    vi  ii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr2_230070691_   6016 CTAAGGAGCTTCTGGACAGCAAAAGAAACTATCATCATAGTGAACAGACA 6065
                         v v ii i   i  vi vv    i  v       vv v      v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr2_230070691_   6066 ACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGGAAAAGGGC 6115
                            i                 v       vii  vi     iv  i  i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr2_230070691_   6116 TAATATCCAGAATCTACAAAGAACTTAAAAAAATTTACAAGAAAAAAAAA 6165
                          vi          v  i        ivv v  v ---   v  v     i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAAAAAG 798

  chr2_230070691_   6166 ACAAACAACCACATCAAAAAGTGGGCAAAAGGTATGAACAGATACCTCTC 6215
                              i    vv  i?    i        i i v    i   i ii    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_230070691_   6216 AAAAGAAGACATTCATGCAGCCAACAAAAATATGAAAAAAAAGCTCATCA 6265
                         v        i  v  viii     i  iv i       i v-     v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACA 897

  chr2_230070691_   6266 TCACTGGTCAT 6276
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.34 (141 / 105)
Gap_init rate = 0.01 (6 / 905), avg. gap size = 1.33 (8 / 6)  


1645 17.76 1.82 28.42  chr2_230186158_230191020     2839  3992 (871)    L1M4_orf2#LINE/L1        1   847 (61)  

  chr2_230186158_   2839 TGGAAAGATTTCCTGTGTTCATGGATGGGAAGAGTTAATATTGTTAAAAT 2888
                                  v   ii           v      v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_230186158_   2889 GTCCATTTTATCTAAAGCAATCTACAGATTCAATGAAATTCCTACAAAAA 2938
                          v v  vi vi i   vii              i v   i    iv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_230186158_   2939 TTCCAATGACATTTTCCACAGAAATTT-TAAAAAAATTCTAAAATTTGTA 2987
                          i   iivi v    iii        v-i  ivvi  i        ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_230186158_   2988 TGGAACCACAAAAGACTCCAAATAGCTAAAATCAATCTTGAGTAAAAAGA 3037
                              vii   ii   i vi      i    -         iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGA 199

  chr2_230186158_   3038 GCAAAGCAGGAGGGATCACACTACCTGATTTCAAAATATACTACAAAACT 3087
                         i     iv     iv       v  ii         iv         i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_230186158_   3088 ATAGCAATCAAAACAGCATGGTGCTGGCATGAAAACAGATGCATA--CTA 3135
                          i  i      i    ii    i       i ii i   iii   --ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_230186158_   3136 ATGGAACACAACAGAGAGCTTAAAAACAAATCTATGCTTTTGCAGTCACT 3185
                               i v  iv     iii i   i   i i  i v   iii    v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_230186158_   3186 TGATTTTCAACAATGATGCCAAGAACATAAAATGGGGAACAGGGCCAGGT 3235
                                 i    v i        v   vv         -----------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA----------- 388

  chr2_230186158_   3236 GCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCA 3285
                         --------------------------------------------------
  L1M4_orf2#LINE/    389 -------------------------------------------------- 388

  chr2_230186158_   3286 GATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAATATGGTGAAAT 3335
                         --------------------------------------------------
  L1M4_orf2#LINE/    389 -------------------------------------------------- 388

  chr2_230186158_   3336 CCTGTCTCTAATAAAATTGAAAAATTAGCTGGGCATGGTGGTGGGTGCCT 3385
                         --------------------------------------------------
  L1M4_orf2#LINE/    389 -------------------------------------------------- 388

  chr2_230186158_   3386 GTAGTCCCAGCTACTCAGGAGTTTGAGGCAGGAGAATCGCTTGAACCCAG 3435
                         --------------------------------     -------------
  L1M4_orf2#LINE/    389 --------------------------------AGAAT------------- 393

  chr2_230186158_   3436 GAAGCAGAGGTCACAGTGAGCCAAGATCATGCCACTGCACTCCAGCCTGA 3485
                         --------------------------------------------------
  L1M4_orf2#LINE/    394 -------------------------------------------------- 393

  chr2_230186158_   3486 GCAACACAGCAAGACTCCAACTCAAAAAAAAAAAAAAAAAGGAAATTTAA 3535
                         --------------------------------------------------
  L1M4_orf2#LINE/    394 -------------------------------------------------- 393

  chr2_230186158_   3536 AAATTGGGAATAGACAGTCTCTAAAATAAATGGTGGTGGGAAAACTGGAC 3585
                         ---------------     i vv  i        v     v       i
  L1M4_orf2#LINE/    394 ---------------AGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_230186158_   3586 ATCCACATGCAGAAGAATGAAATTGGACTCTGATCTCACATCATATGCAA 3635
                          ?         i         i      i iv i      i     i   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr2_230186158_   3636 AACATCAATTTAAA----------GACTTAAATATCAGACCTGAAACTGT 3675
                           -  i  i i   ----------   i     i v   v  i     i 
  L1M4_orf2#LINE/    479 AA-ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_230186158_   3676 TAAAC----AGAAAAAAAAAAATAGAAG---AGCTCTGTGGCAATTGTCT 3718
                         v    ----    i    v --   i? --- v  ii   i vv v vi 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACA--TAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr2_230186158_   3719 GTGCAATGATTTTTTTTGCATATAACCCCAAAAGCCCAGGCAACAAAAGC 3768
                         iv      i   i  --iv    i  v        v  i          v
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTT--AGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr2_230186158_   3769 AAAAATAGACAAACGGGATTACATCAAACTAAAAAGCTTCTGCATGGCAA 3818
                                  i   iv   i v       v v    i   i  iiivv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr2_230186158_   3819 AAGAAGCGATCAATGGAGTGAAAATACAACCTGCAGAATAAGAGAAAATA 3868
                          i  vi v     vii        v      ii      ii         
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr2_230186158_   3869 CTTGCAAACCACACGTCTGATAAAGAATTGCTATTTCAAATATATAAGGT 3918
                         i       i  i ii        i i i vv   iivi         i v
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr2_230186158_   3919 ATTCAAACAACTCAATAGCAAGAAAACAAATGAGCCAATTTTAAAAATGG 3968
                          i  vv           ii  i  i      i v      ?-        
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGG 822

  chr2_230186158_   3969 GCAAAAAATCTGAATAGAC-TTTCT 3992
                              ii  i         -     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCT 847

Transitions / transversions = 2.06 (136 / 66)
Gap_init rate = 0.02 (13 / 847), avg. gap size = 26.85 (349 / 13)  

 308 14.86 4.05 1.35  chr2_230186158_230191020     4298  4371 (492)    L1M4_orf2#LINE/L1      833   908 (0)  

  chr2_230186158_   4298 TGAATAAGC-TTTCT--AAAGAAAGACATACAAATGGCCAACAAGTATAT 4344
                               ii -     --      -  i              i   i i  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAA-GATATACAAATGGCCAATAAGCACAT 881

  chr2_230186158_   4345 GAAAGAAGACTCAAAATCACTGATCAT 4371
                             ii vi     v    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.04 (3 / 76), avg. gap size = 1.33 (4 / 3)  


1633 24.02 5.44 4.88  chr2_230392784_230394833      501  1033 (1017)    L1M4_orf2#LINE/L1      160   695 (213)  

  chr2_230392784_    501 AAAGGCTCTAGAGTAACCAAAATAATTTTGCAGGTGGTGGGGAGAAGGGG 550
                           i  vi i   i  i      i   i   ------------ i  i i-
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTG------------AAAAAGA- 196

  chr2_230392784_    551 GGAGAACATATTTACAGGACTCA-AC---CTGATTTTAGGACTTACTATA 596
                         --      v v  iv        -  --- ii    i ii        i 
  L1M4_orf2#LINE/    197 --AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_230392784_    597 A--CTACAGTAGTCTCAAGATAGTGTAGAATTGGCAAAAAGA--GACATA 642
                          --        i  --    i     i v i     v  i  --      
  L1M4_orf2#LINE/    245 AAGCTACAGTAATC--AAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_230392784_    643 ------AATGTAATAAAATAAAGAGTCCAGAAATAGACCCACACATGCTT 686
                         ------    v    i   vi              i     i    viv 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_230392784_    687 GGTCAAATGATTTTAAACAAAGGTACCAAAATAATTCAGTGGAGATAGA- 735
                               v       vi    i   i    i iv     i   i  v   -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_230392784_    736 CAGTCTTTTCAACAAATGTTTCTGAAACTATTAGACATTTGTAAGCAAAA 785
                         i                 v v   ii  v i i  i ?iiii v      
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_230392784_    786 AAAAAGAACGAAAACT--ACCCATACATTGCACCACATAGAAAGAGACGA 833
                         -----   i   i-i --    v   v ii     i   v   i --iv 
  L1M4_orf2#LINE/    443 -----GAATGAAG-TTGGACCCCTACCTCACACCATATACAAAAA--TTA 484

  chr2_230392784_    834 TCTTAAAATGGGTCAAAGACCTTCATGTCAAACCTTAAATGATA------ 877
                         v  i       i   ?      vv    v i v  v   iv   ------
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_230392784_    878 -CATGAGAAAACAAGAGGGG---ATTTTTGTGGCCTTGGGTTAGGCAAAG 923
                         -i vi        -v   ? ---  i  i   i               v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACA-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_230392784_    924 ATCTCTCAGATAGGACACAAAAAGTACAAACCATAAAAGAAAAAATGGAC 973
                         i i   i     v     v     i    i v i            i  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_230392784_    974 CAATCAGACTTCATTGGTCTCTAAAACCT--GTCCTTTGAAAGACCTTGT 1021
                         v   ii        iiivv iv     i --  v   ii  i   vi i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_230392784_   1022 TAAGAAAAGGAA 1033
                         i      iv   
  L1M4_orf2#LINE/    684 CAAGAAAGTGAA 695

Transitions / transversions = 1.98 (83 / 42)
Gap_init rate = 0.03 (17 / 536), avg. gap size = 3.24 (55 / 17)  

 566 18.18 19.79 0.00  chr2_230392784_230394833     1372  1558 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_230392784_   1372 AAGAAAGGGAAAGGAGAAGCCACAGATTGGGAGAAAATATTTGCAAATCG 1421
                                v    i  v  v       v                      i
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_230392784_   1422 CATATCAAGTAAGGGATTTGAATTT-GAATC-----AGAA---------- 1455
                         i     vii       i   v  ii-    v-----    ----------
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_230392784_   1456 ---ATA-TGGAAAAACAA----CC----TCAGAACT---CA-----TTTG 1485
                         ---   - ii   i    ----  ---- ? i  v ---  -----    
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_230392784_   1486 AATAGACATTTCATCAAAGAAGAGGCATGGATAGCAAATA-GCATATGAA 1534
                                     vi         vii iii  i  v    -   i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_230392784_   1535 AAGATGTTCAACACCATTAATCAT 1558
                               i      i  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (22 / 11)
Gap_init rate = 0.04 (9 / 224), avg. gap size = 4.11 (37 / 9)  


1830 18.93 1.49 21.70  chr2_230434427_230436836.rev      501  1509 (901)    L1M4_orf2#LINE/L1       50   854 (54)  

  chr2_230434427_    501 TGTCATTACTCAGTAGATGCAATTACAGATTTAACACAATTACAAATAAA 550
                           v  v     vvi i  vv vi        i   i    iv ---  --
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC---TA-- 94

  chr2_230434427_    551 ATTAAAATATCAGCATGA-TTATTTGTAAATCTAGGCAAGCTAATTCCTA 599
                         - i     vi    -  v-  v    i i vv v i      i  i iv 
  L1M4_orf2#LINE/     95 -TCAAAATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr2_230434427_    600 AATGTATATGGAAAGGCAAATAAACTAGAATAGCCAAAACGACTTTGAAA 649
                            vi         v    ivi v i              i ii      
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_230434427_    650 AAGAAAATTAAAGCTGGAGGAATCCCACTCTCTGACTTTAGGACTTGCTA 699
                              i vi    i       v  v    ii ii i  i ii    i   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr2_230434427_    700 TAAAGTTAGAGTAATCAAGACAGTGTGATATTAGCAAAGGGATTTATATT 749
                         i    i  v                  i  i i   v i    ---- --
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT----A-- 286

  chr2_230434427_    750 GGCATATAGATGAATGAAACAGG-TAGAGAGTCCAGAAATAGACTCACAC 798
                          i         v    i  i  i- v               i  i  i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_230434427_    799 ATATGTGTTCGACTAATTTTTTGACAAAGATGCAAAGAATGGAGGAAATT 848
                           v i  v  i i i     i-     i i   v    vi-------   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTC-GACAAGGGTGCCAAGACC-------ATT 378

  chr2_230434427_    849 CAGTGGAGGAAAGACAGCCTTCTCAACAAATGGCAAAGGAACAATTAGAC 898
                           i   i i  ii i  i   i           iivv  i    i i  i
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr2_230434427_    899 ATCCATAGGCCAAAAAAATGAACTTTGAACTAAACCTC-CACCTTATATA 947
                          ?   i v  -    i      v  v  v ivv     -    v    i 
  L1M4_orf2#LINE/    429 AKCCACATGC-AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_230434427_    948 AAAATTAACTCAAAACGGAGCATAGAACTGCATGTAAAACAAAAAACTAT 997
                                        i   v  ?   v  iv      i vvv        
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_230434427_    998 AAAACAAGGCTGGGACTAGGGTGAAAAAAGGAATGTACCTAGGATGCAAA 1047
                              ---------------------------------------------
  L1M4_orf2#LINE/    528 AAAAC--------------------------------------------- 532

  chr2_230434427_   1048 ATTTAAGGAGGCACTCACTTTAGTTATGCAAGTATGATCCTGAAAGTGAG 1097
                         --------------------------------------------------
  L1M4_orf2#LINE/    533 -------------------------------------------------- 532

  chr2_230434427_   1098 AGGCTTTTTAAATTTTGTGCCCTAGGCACCTCCCTTATGTCACCCTAGTC 1147
                         ----- i   ----------------------------------------
  L1M4_orf2#LINE/    533 -----TCTTA---------------------------------------- 537

  chr2_230434427_   1148 CAGGTTTTGCTATACAGCTTTAAGAAGAAAACATAAGAGAACATCTTCAC 1197
                         -----------------------            i ? v v      ii
  L1M4_orf2#LINE/    538 -----------------------GAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_230434427_   1198 AGCCTGAGTTTAAACAAAGGGCTCTTAGCCATAACAT-AAAACCACAATT 1246
                         ii   vi v   ii   v  vi      vi  i   i-    v     vi
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_230434427_   1247 TATGAAAGAAAAAAATCAATAAATTGGACTTC-TCAAGATTAAGAACTTT 1295
                         v ii          - vi              -    i     i      
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr2_230434427_   1296 TGT----CAAAG-ACACTGGTAAGAGAATTGAAAGACAAATTAACAAACT 1340
                            ----     -     ivi    i i vi        vii -  i v 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA-CAGAAT 712

  chr2_230434427_   1341 GGGAGAAAATATTTGCAAATCACATATTTGACCAAGGATTTGTATATGTA 1390
                                               i    i   i-    -------------
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGAT-AAGG------------- 748

  chr2_230434427_   1391 ATAGACATATATTCTGGTACATTGTATACAGAATATGTAAAGAGCTCTCA 1440
                         ---   ---------------      v        i      i    i 
  L1M4_orf2#LINE/    749 ---GAC---------------TTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_230434427_   1441 AAACAGAACAATACAAAAAGAAACAATCTAATGAAAAAGTGGACAAAGGA 1490
                         v   vv  i    v   i v   i  i i   v?    i   i       
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_230434427_   1491 CTTGGTTA-----TTTGCCAAAGA 1509
                         i   iv  -----  iv       
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGA 854

Transitions / transversions = 1.71 (118 / 69)
Gap_init rate = 0.03 (23 / 805), avg. gap size = 10.17 (234 / 23)  


 420 27.12 0.00 0.85  chr2_230706899_230708635      146   263 (1474)    L1M4_orf2#LINE/L1       15   131 (777)  

  chr2_230706899_    146 ATATTCATGGATGGGAAAATTTAATATTGTTCAAATGTCTGTATTACCTA 195
                           i         v    i i           v i   v vi  i v  i 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_230706899_    196 AAGAAATATGCAGATTTAATACAGTGCCTATCAAAATTCCCAAGGACATT 245
                           vvi  v i      i  ii  i v           -    ivvi v  
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAAT-CCCAGCTGCCTT 113

  chr2_230706899_    246 CTTCACAGAAATAGAAAA 263
                         i  ii       v  v  
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAA 131

Transitions / transversions = 1.29 (18 / 14)
Gap_init rate = 0.01 (1 / 117), avg. gap size = 1.00 (1 / 1)  

3142 21.57 1.49 1.22  chr2_230706899_230708635      500  1236 (501)    L1M4_orf2#LINE/L1      136   874 (34)  

  chr2_230706899_    500 ATCCTGAAATTAATATAGAACCACAAAATACTTAGAATAGCCAAAGCAAT 549
                              i     v    i   vii   iiv  ii            i    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr2_230706899_    550 ACTGAGA--GAA----AATGTTTGAGGCCTCACACTTCCTGATTT-AAAA 592
                         vi   i --   ----  v   v    v           ii    -    
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr2_230706899_    593 TTATATTATAGAGCTATACTAATCAAAACACTATAGTACTGGCAGAAAAA 642
                         i -  i  i i     i v       i   v i i         v  ii 
  L1M4_orf2#LINE/    236 CT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr2_230706899_    643 CGGAAACATAGACCAATGGAACAAAATTGAAAGCCCAGAAATAAGTCCAA 692
                         ii  v i     i        i i      i  i          ii   v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_230706899_    693 ACACATAGGATCAATTAATTCTCAACAAGGGCACCAAGAGGACAAAATGG 742
                            iv  v i      i   i  i       ii      vv ivv     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_230706899_    743 GGATAGGATAATGTCTTCAATAAATGGTGCTGGGAAAACTAGATTGCCAC 792
                            v  i   i v i     i              v    i   v?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_230706899_    793 -TGCAAAAGAATGAAATTTGACCCTTACCTTACACCATACATAAAACTCA 841
                         -              i  v     i     i        i i    v i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_230706899_    842 ACTCAAAATGGATAAAAGACCTAAATGTAAGACCTGAAACCATAAAACTT 891
                                      v ?                v  i    i        i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_230706899_    892 CTAGGCGAAAACTCCTCCTCCTGGGC-TCAGTCCT--TGACATAGGCCTT 938
                         i   iv      --------v i  ?- v i  i --    v v  vi v
  L1M4_orf2#LINE/    535 TTAGAAGAAAAC--------ATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_230706899_    939 GGCAATGATTTTTTGGATATCATACCAAAAAACCAGGCTACGAAAGCAAA 988
                                i   i  i     v i       ivv  i  v  i    v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_230706899_    989 AATAAATAAATGGGATGATACCAAACTAAAAAACCTTTGCAGAGCAAAGG 1038
                             i      v   ivvi i    v v      i    iivvv      
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_230706899_   1039 AAACAATCAACAAAATGAAAAGGCAGCTTACAGACTAGAAAACAATATTT 1088
                          v  v     v   i       i  i ii     v i i i v       
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_230706899_   1089 GCAAACCACATATCTGATAAGGAGTTAATATCCAAAATGTATAAAGAACT 1138
                              i  i             iii vi      i   i           
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_230706899_   1139 CTTACAACTCAATAACAAAAAAACAAATAACCCTATTAATAAATGGGCAA 1188
                                        i     i           v   ? v          
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_230706899_   1189 AAGATCTAAACAGACATTTCTCCAAAGAAGACATAAAAATGCCCAACA 1236
                          i   i i  i                    i   v     v    i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.77 (99 / 56)
Gap_init rate = 0.01 (8 / 739), avg. gap size = 2.50 (20 / 8)  

 223 17.39 0.00 0.00  chr2_230706899_230708635     1375  1420 (317)    L1M4_orf2#LINE/L1      863   908 (0)  

  chr2_230706899_   1375 AAATGGCCAGCAGGTATATAAAAAGGTGATCAACATCACTAATCAG 1420
                                  ii i i i  i     i  v         ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 7.00 (7 / 1)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.00 (0 / 0)  


2888 25.90 1.53 2.30  chr2_230785642_230788247.rev     1200  2114 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_230785642_   1200 TGGAAA-ATATTCCGTGCTCATGGATTGCAAGAATCAGTATCATTAAAAT 1248
                               -    i  i  i          v    v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_230785642_   1249 GGCCTTATTATTGCCCAAAGCAATCTACAGATTCAATGCTATTTCTATCA 1298
                            --- v  i v      vii              i  v  ii      
  L1M4_orf2#LINE/     51 GGC---AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr2_230785642_   1299 AACTACCAAGGTTA--TTTTTCACAGAATTAGAAAAAACT-ATTCTAAAA 1345
                           v v   -- i i--     ii     v v  v  i-  -  i      
  L1M4_orf2#LINE/     98 AAATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAA 144

  chr2_230785642_   1346 TTCATATGGAACCAAAAAAATAGCCTATATAACCAAAGCAATTCTAAGCA 1395
                                    viiv  iii- v  viv   i     i    ii i iv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_230785642_   1396 AAATGTACAAAGCCAGAAGCATCACATTAATCC--ACTTCAAACTATACT 1443
                          i v v      iii  i vv     i --   -- i      viv    
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACT--TCCCAATTTCAAAACTTACT 241

  chr2_230785642_   1444 ATAAGGCTACAGTAACCAAAACAACATGGTACTGGTACAAAAATAAACAG 1493
                          i  i          i   i   iii         i i  ii   i   v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_230785642_   1494 ATAGGCCAATGGAACAGAAAAGAGAACTCAGAAATAAAGCCACACACCTA 1543
                             ii        i    vv    iii          v   i   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_230785642_   1544 CAGCCATCTAATCTTTGACAAAATCAACAAAAATAAGCAATGGGAAAAGA 1593
                         ii i  vi i  i  i     iiviiv   i vi vv       i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_230785642_   1594 A--GTCCCTATTCAATAAATGGTGGTGGGATA-CAGGCTAGCCATATGCA 1640
                          --   -- v     i        v     i - v  v  ?   i     
  L1M4_orf2#LINE/    392 ATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_230785642_   1641 GAAGAATGAAGTTGGACCCCTACCTTTCACCATTTATAATAACTAACTCA 1690
                         i                        iv      v  i  v  i       
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_230785642_   1691 AGATGGATTAAAGATTTAAATGTAAGACTTCAAACTATCAGAATCCTAGA 1740
                          i      i ?   ii           vi v       v i v  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_230785642_   1741 AGAATATTTACGAAGCA--CCATTCTGGACATGGGCCTTAGGAAAGAATT 1788
                             v iv  - i? i --i v iv  iv v    --     v  vii  
  L1M4_orf2#LINE/    540 AGAAAACATA-GGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTT 586

  chr2_230785642_   1789 TATTAC-TAAGATCTCAAAAGCAATTGCAAAAAAAAAAACACCAAAAATT 1837
                          v   v-  v  ivi        ----   iv  v    v --      v
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCA----CAAGCAACAAAAGA--AAAAATA 630

  chr2_230785642_   1838 GACAAGTGGTATCTAATTAAACTAAAAAGCTTCTGCACACCAAAAGAAAT 1887
                           i  i v v ii v  i   v v    i   i  ii vi    i  v i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_230785642_   1888 AGTCAACTGAGTAAACAGACAACCTACAGACTGGGAGAAAATATTTGCAA 1937
                         vi    vvi   i  v        i     v                   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_230785642_   1938 ACTATGCATCCAACAAAGGTCTCATATCCCGAATCTATAG-GAACTTAAA 1986
                          ii  ii   ii i  i  v  ii     v    v    i-     ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_230785642_   1987 CAATTGAACTAGCAAAAA-ACAAATAATTCCATTAAAAAATGGGCACAAG 2035
                            i v  -  ii     -        ii v   ?           v i 
  L1M4_orf2#LINE/    781 CAACTCAA-TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_230785642_   2036 ACATGAACAGACACTTCTCAAAAAATGGCATACAAGTGGACAACAAACAC 2085
                          iv    i     i     v   i v ii      i   v   i  i   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_230785642_   2086 ATAGAAAAATGCCGATCATCACTAATCAT 2114
                           ii   i    iv v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (147 / 86)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.67 (35 / 21)  


2634 23.42 1.93 2.89  chr2_230792521_230794235.rev      498  1223 (492)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr2_230792521_    498 AAAAAAAAGAACAAAATTAGAGGAATCACATTACCTGACTTCAAATTATG 547
                              i         i  i     v     i v  ii i      viv i
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_230792521_    548 CTACAGAGCTATAGTAACCAGAACAGCATGATACTGTCATAAAAATAGAC 597
                              i     i     i  ii    ii  i     v     ii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_230792521_    598 ACATAGACAAATGGAACAGAATAGAGAACCCAGAAACAAATCCACATGCC 647
                          i     iv       i     v    ii       i   i   i iiii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_230792521_    648 TATAGTGAACTCATTTTTGACAAAGGCACCAAGAACATACACTGGAGAAA 697
                            i  v  i v     i     i  ii      v   v  v   i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_230792521_    698 AAACAGTCTCTTCAATAAATGGTGCTGGGAAAAATGGATATCCATATGCA 747
                         i  i     i     i              v  v      ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_230792521_    748 GAAGAATAAAACTAGACCCCTACCTCTCACCATATACAAAAACCAAATCA 797
                         i      i  ii i            v               ii  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_230792521_    798 AAATGGATTAAGAACTTAAATCTAAGACCTCAAACTACAAAATTACTGCA 847
                                 i ?ii  i     v     v  v      i    i vi iv 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr2_230792521_    848 AGAAAACTTTGGGAAAAATCTCTAGGATATTGGCCTTGGAAA-AATTTTT 896
                                v v  ?iv      iiiv  iv    vi v  v  -ii   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_230792521_    897 TGAACAATACCTCACAAGCACAGGCAACCAAAGCAAAAACAGACAGATGG 946
                          ii i vv  vi  v       i     v    v     i   i i  v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_230792521_    947 GTTCACATCAAGTTTAAAAACTTCTGCAAAGCAAATAAAACAATCAACAA 996
                          viiv      iv          i  iivvv    vi v  v     v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_230792521_    997 AGTGAAAAGACAGCCCACAAAACGAGGGAAAATATTTGCAAAGTGAAAAG 1046
                                     i      i  i i i               vi------
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC------ 733

  chr2_230792521_   1047 ACAAACCTACAAAATGGGAGAAAATATCTGGATAAATAACCAGAATATAT 1096
                          i v i  ---------  v  iiv ii  v  ------           
  L1M4_orf2#LINE/    734 ATATATCT---------GATAAGGGACTTGTAT------CCAGAATATAT 768

  chr2_230792521_   1097 AAAGAACTCAAACAACTCTATTGGAAAAAATCTAATAACCTGATTCGAAA 1146
                                  vv       v  viv     iv v       ii   ?i   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_230792521_   1147 ATGGGTGAAATATTTGAATAGACATTTCTCAAAAGAAGACATACACATGA 1196
                              ii  iv                   v        i     v   i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_230792521_   1197 C-AATCAG------------TGCTCAACATCACTGATCAT 1223
                          -   v  ------------            ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (104 / 62)
Gap_init rate = 0.01 (6 / 719), avg. gap size = 5.83 (35 / 6)  

1386 25.67 5.13 1.56  chr2_230792521_230794235.rev     1268  1715 (0)    L1M4_orf2#LINE/L1      255   718 (190)  

  chr2_230792521_   1268 AATTAAAATGGCTTATATCCTGGTATCAAAACAGACACATAGACCAATGA 1317
                            i  i ii iv i-i v    i  v ii i     i     i     i
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTG-GTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_230792521_   1318 AACAAAATAGAGATCTCAGAAATAA--CCAT--------------CTGAT 1351
                           i i   v    vii         --    --------------i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_230792521_   1352 CTTCAACAAACCTGACAAAAACAAGCAATGGCAAAAG----GTCCTCCAT 1397
                         i   i    ivv  v   i v  vv      vi    ----   i --- 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT---T 400

  chr2_230792521_   1398 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAAAAAACTGAAA 1447
                          i  i              v      v  ?   i        i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_230792521_   1448 CTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGACTAA 1497
                         i         v   i     v                   i     ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_230792521_   1498 AGACTTAAATGTAAAACCCAAAACCATAAAAACCCAAGAAAAAAATCTAG 1547
                             i         i v i     i      vi iv    i    iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_230792521_   1548 GCATTACTACTCAGTGAA--TAGGCATGGGCAAAGATTTTAT-GATGAAA 1594
                          ?i v v vi  -    v-- i  i- i     v i   iv -   ivi 
  L1M4_orf2#LINE/    551 GNGTAAATCTTC-GTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGA 598

  chr2_230792521_   1595 TCACCAAAAGCAATTGCAACAAAAGCTAAAATTGACAAATAGGATCTAAT 1644
                         -           vvv          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    599 -CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_230792521_   1645 TAAACTAAAGAGCTTCTACACAGCGAAAGAAACTATCATCAGAGCAAACA 1694
                         i   v v  i i   i iii vv i  i  v       vv i  ii  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_230792521_   1695 GACAACCTACAGAATGGGAGA 1715
                                i             
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGA 718

Transitions / transversions = 1.55 (68 / 44)
Gap_init rate = 0.02 (10 / 464), avg. gap size = 3.00 (30 / 10)  


3258 27.00 0.33 0.66  chr2_230802532_230808971.rev     5038  5948 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_230802532_   5038 TGGAAGAACATTCCCTGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5087
                              ii i  i  v  i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_230802532_   5088 GGCCATACTGCCCAAGGTGATTTATAGATTCAATACTATCCCCATCAAGC 5137
                            v     v     iv    i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_230802532_   5138 TACCA-CTGACTTTCTTCACAGAATTGGAAAAATCTACTTTAAAGTTCAT 5186
                          v   -   v    i  -i     v v  v  iiiv iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_230802532_   5187 ATAGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAACAGA 5236
                           i   viiv  ii  v  v v        i      i i iv  iv   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_230802532_   5237 ACAAAGCTGGAGGCATCATGTTACCTGACTTCAAACTATACTACAAGGCT 5286
                               i      vv   iii v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_230802532_   5287 ACAGTAACCGAAACAGCATGGTACTGGTACCAAAACAAGATATATAGACC 5336
                                i i i    ii         i iv ii i -  i       i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGATC 298

  chr2_230802532_   5337 AATGGAACAGAACAGAGGCCTCAGAAATAGCACCACACATCTACCCTAAC 5386
                                i    iv   ivii        ivv   i    i  --- iii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA---TGGT 345

  chr2_230802532_   5387 CATCTGATCTTTGACAAACGTGACAAAAACAAGAAATGGGGAAAGGATTT 5436
                           vi    i  i     iv   v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_230802532_   5437 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGC 5486
                         i  v  i  i              v      v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_230802532_   5487 TGAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGG 5536
                             ii    i    v   i    iv                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_230802532_   5537 ATTAAAGACTTAAATATAAGACCTAACACCATAAAAACCCTAGAAGAAAA 5586
                           i ?    i     i     v    v  i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_230802532_   5587 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAATGACTTCATGACT 5635
                          v    ?i- v i -   iv   v v  vv i       ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_230802532_   5636 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAAACAAATGGGATCT 5685
                          vi            vvi          vv      i i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_230802532_   5686 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5735
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_230802532_   5736 ACAGGCAACCTACAGAATCTGAGAAAATTTTTATAATCTATCCATCTGAC 5785
                          v  i     i       vv        v   ii  vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_230802532_   5786 AAAGGGCTAATTTCCAGAATCTACAAAGAACTTAAACAAATTTACAGGAA 5835
                           i  i  vi v        v  i        ivv    v iv i iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_230802532_   5836 AAAAACAAACAACCCC-TTCAAAAGCGGGCAAAAGATATGAACAGACACT 5884
                            i     i     v-  ?    ii       i   v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_230802532_   5885 TCTCAAAAGAAGACATTTATGCAGCCAACAGACATGTGAAAAAAAGCTCA 5934
                             v        i  vi viii     i ii  ii      i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_230802532_   5935 TCATCACTGGTCAT 5948
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3278 25.64 0.66 0.33  chr2_230949912_230954213.rev     2906  3810 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_230949912_   2906 TGAAAATACATCCCATGCTTCATGGATGGGTAGAATCAATATTGTGAAAA 2955
                           i   v i        -         v  v   v i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATG-TTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_230949912_   2956 TGATCATACCGCCAAAAGCAATC-ACAAATTCAATGCAATCCCCATCAAA 3004
                           iiv    iv  v   vii   -   i      i        i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_230949912_   3005 ATACCA-CCATCTTCTTCACAGAATTAGAAAAAACACCTCTAAAATTCAT 3053
                           v   - iii   i  ii     v v  v  iviivii           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_230949912_   3054 ATGGAACCAAAAAGGAGCCCACAA-AGCCAAAGCAAGACTAAGCAAAAAG 3102
                               viiv  i   -    v  -       i   vvi i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_230949912_   3103 AACAAATCTGGAGGCATCACACGACATGATTTCAAACTATACTATAAGGC 3152
                               vi      vv      vv vii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_230949912_   3153 CATAGTCACCAAAACAGAGTGGTACTGGTACAAAAATAGACGTA--GACC 3200
                         i i   v i   i    v          i i  ii      i  --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_230949912_   3201 AATGAAACAGAACAGAGAACCCAGAAGTAAACCCAAATACTTACAGCCAA 3250
                             i  i    iv    ii      i        v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_230949912_   3251 CTGATCTTTGACAAAGCAAACAA-ACCATAAAGTGGGGAAAGGACACCCT 3299
                         i    i  i     i vviv   -     vv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_230949912_   3300 ATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAGAATGA 3349
                         v                    i  i   vv ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_230949912_   3350 AACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATC 3399
                          ii    i  ii i   v    v           i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_230949912_   3400 AAGGACTTAAATCTAAGGCCTGAAACTATAAAAATTCTGGAAGATAACAT 3449
                          ?i   i     v    iv  i           v ii i     v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_230949912_   3450 CAGAAAAACCCTTCTAAACATTGGCTTAGGCAAGGCCTTCATGACCAAGA 3499
                         vi ?iv  vi    vvi  v    v        v vi   v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_230949912_   3500 ACCCAAAAGCAAATGAAAGAAAAACAAAGATAAATAGCTGGGACTTAATT 3549
                         vv         v v v  v    iv   i   i   iv v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_230949912_   3550 AAACCTAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAG 3599
                            vi   i i      ii vv    i iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_230949912_   3600 ACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAA 3649
                                     i           v  ii   vii   i      i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_230949912_   3650 GACTAATATCCATAATCTACAATGAACTTAAACAAATCAGTAAGAAAAAA 3699
                             vi      v   v  i  v     ivv    v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_230949912_   3700 ACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAGTTCGT 3749
                              i  i  v  i?    i     v     iv          v   vi
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_230949912_   3750 AAAAGAAGATATACAAATGGCCAATGAACATATGAAAAAATTGCTCAACA 3799
                         v                        i i  i       i  -        
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACA 897

  chr2_230949912_   3800 TCACCAATGAT 3810
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


2832 26.46 1.87 1.76  chr2_230991480_230995885     3008  3914 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_230991480_   3008 TGGAAACATGTCCTATGCTCGTGGATGGGTAGAATCAATATTGTGAAAAT 3057
                               v  i   i   i  i     v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_230991480_   3058 GATCATATGGCCAATAGCAATCTGGAAAGTCAATGCAATTCCCATCAAAA 3107
                          iiv   ivv  v v vii    iv i v    i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_230991480_   3108 TACCA--TGATCATTTTTCACAGAACTAGAAAAAACAATTCTAAAATTCA 3155
                          v   --  -- v     ii     v v  v  ivii  i          
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr2_230991480_   3156 TACAGAACCAAAAAAGAGCTCATGTAGCCAAAGCAAGACTAAGCACAAAG 3205
                           ii   viiv  ii  v ivivi        i   vvi i iv vi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_230991480_   3206 AAAAAACTTGGAGGCATCACATTACCTGACTTCAAACTATACTACAAGGC 3255
                           v   v       vv     i v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_230991480_   3256 TATAGTCACCCAAACAACATAGTCCAGGTATGAGAATATACCAGTACACA 3305
                           i   v i v i   iii i  v v  i  i  i   ----- -   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-----G-ACATA 292

  chr2_230991480_   3306 TAGACCAATGGAACAGAAGAAAGGACCCAGAAATAAAGCCAAATATTTGC 3355
                             i        i    vvi  iii           v   v i    ii
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_230991480_   3356 AGCCAGCTAACCTTTGACAAAGCAAACAAAAGCAT-AAAGGGGGAAAGGA 3404
                         i i  ii i ii  i     i vviv   i v   -v  v        i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr2_230991480_   3405 CACCCCATTCAACCAATAGCACTGGCATAATTGGCAAGCCACATTTAGAA 3454
                         i vi iv      v   i ii    v i  i   vv ?      vi i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr2_230991480_   3455 GAATGAAATTGAATCCTCATCTCTCACCTTATACAAAAATCAACTAAAGA 3504
                                i   i i  ii i   v    v           i    v  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_230991480_   3505 TGGATCAAAGACTTAAATCTAAGACCTGAAACCATATAAATTCT-AGAAA 3553
                                ?    i     v     v  i    i   -   i   -    i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAG 541

  chr2_230991480_   3554 ATAACATTGGAAAAACTCTTCTAGGCATTGGCTTAGGCAAAGAGTTC--A 3601
                          v     v  ?iv  v     vv i v    v        v iv   -- 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr2_230991480_   3602 G----GACCAAAAACGCAAAAGCAAATGCAAGAAAAACAAAGATAAATAG 3647
                          ----   -----  -        v v    v    iv   i   i   i
  L1M4_orf2#LINE/    592 GATATGAC-----AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_230991480_   3648 ATGGGATTTAATTAAACTAAAAGGCTTCTATACAGCAAAAGAAAT----A 3693
                           v   i  v  i   v v   ii   i i i vv    i  v i---- 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_230991480_   3694 ACAGAATAAACAGACAACCCACAGAGTAGGAGAAAATATTTGCAAACTAT 3743
                          v i i i  v              i i                  ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_230991480_   3744 GCATCCGACGGAGGACTAATATCCAGAATCTACAAGGAACTCAAAGCAA- 3792
                         ii   i  iiii     vi          v  i  i      vv -   -
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAAC 784

  chr2_230991480_   3793 TCAGCAAGAAAAAATCAAATAATCCCATCAAAAAGTGGGCTAAGGACATG 3842
                            ii  v     iv       i  v  i?    i     v     iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_230991480_   3843 AATAGACAATTCTCAAAAGAAGATATACAAATGGCCAACGA--ACATGAA 3890
                                 v     v                       ii --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_230991480_   3891 AAAATGCTCAGCATCACTAATTAT 3914
                           i       i     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


3309 27.53 0.33 0.33  chr2_231026965_231033233.rev     4870  5777 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_231026965_   4870 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4919
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_231026965_   4920 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4969
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_231026965_   4970 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5018
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_231026965_   5019 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5068
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_231026965_   5069 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAGGGCT 5118
                               i      vv   ii  v  ii i      viv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_231026965_   5119 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGATCA 5168
                                i   i    ii         i iv ii ii  v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_231026965_   5169 ACGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCGTATCTACAACTA 5216
                          i    i    i--    i  --        vv iiiii  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_231026965_   5217 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5266
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_231026965_   5267 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5316
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_231026965_   5317 AAACTGGATCCCTTCTTTACACCTTATACAAAAATTAATTCAAGGTGGAT 5366
                           ii    i    v i i     v              i    ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_231026965_   5367 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACA 5416
                         i ?    i  v    v   v       i      vi i            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_231026965_   5417 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5466
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_231026965_   5467 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5516
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_231026965_   5517 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5566
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_231026965_   5567 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5616
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_231026965_   5617 GGGTTAATATCCAGAATCTACAATGAACTTAAACAAATTTACAAGAAAGA 5666
                           ii vi          v  i  v     ivv    v iv i  v   i 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_231026965_   5667 AACAAACAACCCGATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCT 5716
                         i     i     i  i?    i     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_231026965_   5717 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 5766
                          v        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_231026965_   5767 TCACTGGCCAT 5777
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.59 (151 / 95)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3612 23.48 1.66 1.11  chr2_231053135_231057367.rev     2839  3741 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_231053135_   2839 TGGAAAGATACCCCATGTTCATGGATTGGATTAATTAATATTCTTAACAT 2888
                                   i                   vv v        v    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_231053135_   2889 GTTCATACTATCCACAGTGCTCTAAAGATTCAGCGCAAATCATATAAAAG 2938
                          viv     vi   v v  v    v       i     vi v   v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_231053135_   2939 TTCCAAAGACATTTTTTTCTGAAATAGAAAAAC-AATTA-AAAATTTGTA 2986
                          i   ivvi v      v v     v  v  i -i  iv-      ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_231053135_   2987 TAAAAGCACAAGAGACCCCAACTAGCCAAAGCAATTTTAAGCAAAAAGAA 3036
                          ii  iii    i     vi v        i    i  i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_231053135_   3037 CAAAGCTGAAAGCATCACACTACCTGACTTCAATATATACTACAAAGCTA 3086
                              i  i i vv       v  ii i     v iv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_231053135_   3087 TAATAATCAAAAGAACATGGTACTTGCATAAA-ATAGACACATAGACAAA 3135
                         i i       i v iii       v      i-       i     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_231053135_   3136 TGGAACAAAATAGAGAGCT------TGAATCCATGCATTTTTGGTCAACT 3179
                              i i   v     ii------ i  i    i     v       i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_231053135_   3180 GATTTTCAACAAAGGTGCCAAGAACACGCAATGGGGAAAGGACAGTCTCT 3229
                                i    i          v  iv            i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_231053135_   3230 TTAATAAATGATGTTGGGACAACTGGATCTTCACGTGCAGAAGAATGAAA 3279
                          i  i     i  i              v?i   i    i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_231053135_   3280 TTAGACCC-TATTTCATGCCATATTAAAAAATCAACCCAACATGGATTAA 3328
                           i     -  ii   ii      vv      i   i   v      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_231053135_   3329 ATATTTAAATTTAATACCTGAAGCTGCAAAATTACTGGAAGAAAACA--G 3376
                          v ii     v   v v  i  i  ii    i vi i          -- 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_231053135_   3377 GGGAAAAGCTCCATGACATTGGTCTGAGCAATTATGTTTTTGGTATGACA 3426
                          ? v   v  i i    v    vi ii     vi v i  v i       
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_231053135_   3427 CCAAAAACACAATCA-CAAAAGCAAAAATAAAGAAGTGAGACTACATCAA 3475
                               i     v  -      v       i v  i vi    v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_231053135_   3476 ACTAAAAAGTTTCTGCATGGGCAAGGAAACAATCAGCAGAGTGAAGAGAC 3525
                          v v    ii  i  iiivvvv     v  v    iv i      i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_231053135_   3526 AACCTACAGAA-GGGAGAAAATATTTGCAAACCATATGTCTGATAAGGG- 3573
                             i      -                   i     i           -
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_231053135_   3574 CTAATATCTAAAATATGTAAGGAACTCAACCAACTCCATACTAAAAAAAA 3623
                           vi    i i     i   i      vvv      v   v      i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA- 799

  chr2_231053135_   3624 AAACAAAAACAAATAAACAGATTATAAAGTGGGCAAAGGATTCAAACAGA 3673
                         ---------       v vi   ?v   i             ii  i   
  L1M4_orf2#LINE/    800 ---------CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_231053135_   3674 TATTTCTCAAAGGAACACATACAAATGACCATCAGGTATGTGAAAAAATG 3723
                         i       v  i   v i         i   vi i i ii      i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_231053135_   3724 CCCAGCATCACAAATCAT 3741
                          i  i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (128 / 80)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.50 (25 / 10)  


3109 15.38 3.38 16.63  chr2_231122331_231124456.rev      607  1640 (486)    L1M4_orf2#LINE/L1       12   908 (0)  

  chr2_231122331_    607 CCAATGTTCATGGATTGAAAGACTCAATATGTTTAACATGGTAATTCTCT 656
                           v              i      i     vv    v    i   v   i
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chr2_231122331_    657 CCAAATTGATCTAGAGACTCAGTATGATTCCTATCAAAATCTCCAATGGC 706
                                      v   i   iiiii  i            -   iiv  
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC-CCAGCTGC 110

  chr2_231122331_    707 CTTTT--GCAGAAATTGAGAAGCTGATCCTAAAATTTACATGGAATTGCA 754
                              --           v                 i i      v    
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_231122331_    755 AAGAACCCAGAATATCCAAAACAGTCTTGAAAAAGAAGAAAAAAGTTGGA 804
                          i i          v        i                v         
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr2_231122331_    805 AGACTTATACTTTGTGATTTCAACACTTACTATAAAGCTGCATGAATCAA 854
                         i    i i    ivii       v        i      i  vv      
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr2_231122331_    855 GACAGT-----ACTGGCATAA--ATATATATAAAAATCAATACAACAGAA 897
                               -----          --   v i   v i      iv  i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr2_231122331_    898 CTGAGAGTGCAGAAATAAATCCTTAGGTTTTTGGTCAATTGATTTTCAAC 947
                         i       v          i  v  vi   v                i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr2_231122331_    948 AAAAGTGCCAAGGCAATTAAATGAGGAAAAGATAGTCTTTTCAACAAATA 997
                           ii        i v   v    i     ii                  i
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_231122331_    998 GTACTAGTATAACTGGATAGGCACATGCAAAAATATGAAATTAGACCCTT 1047
                           i  i v i         ?v           iv     i  i     i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr2_231122331_   1048 ACCTCACACCATATGCATAAATCAACTCAAAATGGATCATGCATCTCTAA 1097
                                       i  v    i                ?iv i  --  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT--AA 508

  chr2_231122331_   1098 ATGTAAAAGCAGGGATGGCTTTATGGGCATGCATCCTGTGCAGTCACAAA 1147
                               i   ----------------------------------------
  L1M4_orf2#LINE/    509 ATGTAAGAGC---------------------------------------- 518

  chr2_231122331_   1148 AGACTCTGTGCTTAGTTTAGTGTTCTGCTTTCACTGTTTTGAAATCCTTA 1197
                         --------------------------------------------------
  L1M4_orf2#LINE/    519 -------------------------------------------------- 518

  chr2_231122331_   1198 ATAATTTTTGAACAAGGATCCCCCCATTTTCATTTTTCACTGCGTTTCCC 1247
                         --------------------------------------------------
  L1M4_orf2#LINE/    519 -------------------------------------------------- 518

  chr2_231122331_   1248 AAATTATGCAGTAGTCTTGTAAAACAGCAAAAATGATAAGACTTTTGGAA 1297
                         -------------------      -------- -    i   i  i   
  L1M4_orf2#LINE/    519 -------------------TAAAAC--------T-ATAAAACTCTTAGAA 540

  chr2_231122331_   1298 GAAAACACAGGAA-AAATCTTTGTGACTTTAGGTAAGACAAAGA---ATT 1343
                                i   ?i-       i     i  i   v  i   v i---v  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_231122331_   1344 AGCTAC--CAC-AAAAGTATAATCA-TAAGAGAATAAAT-GATG--TTAA 1386
                           v  i--   -     i i  v  -i  i    v    -   i--  ii
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_231122331_   1387 AATTTAACAAAATTTAAATCTTTTGTGCCTCAAAT-ATACCATAAAGAGA 1435
                          v  i v       v   v         i     v- i  i  v    i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_231122331_   1436 AAGAAAAGATTAGTCACAGTCTGGGAGAAAATATTAGCCAATCATATTTT 1485
                         iv       iv vi     vv              v  v        v i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_231122331_   1486 TAATAAACTACTTGTATTCAGA-TATGTAAAGAATTCTGACAACTCAATA 1534
                          i    ivv        i    -   i       i   v           
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_231122331_   1535 A---GAAGACAAG----CCAATT-AAAAATGGACAAATGATTTGAACAGA 1576
                          ---i       i----      -        i    v        i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_231122331_   1577 TATTTCTCCAAAAGACATATGAAAAATAA-----AAACATGTGAAAAGAT 1621
                         i           ii v    - v    ii-----  i  ii         
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATAT-ACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_231122331_   1622 GTTCAGTAGCATTCATTAT 1640
                          i   ii v  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (100 / 56)
Gap_init rate = 0.02 (22 / 897), avg. gap size = 9.41 (207 / 22)  


 525 21.82 0.00 0.00  chr2_231141117_231146364.rev     3560  3669 (1579)    L1M4_orf2#LINE/L1        1   110 (798)  

  chr2_231141117_   3560 TGAAAAGATACCCCATGTTCATGGATTGGAGGAATTAATATTGTTAAAAT 3609
                           i       i                   i  v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_231141117_   3610 GTCCAGACAACTCGAAGTCCTCTAAAGATTCAGTGCAATACCTATAAAAA 3659
                          v v v  vv i i  v vv    v       ii     v     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_231141117_   3660 TTCCAATGGC 3669
                          i   iiv  
  L1M4_orf2#LINE/    101 TCCCAGCTGC 110

Transitions / transversions = 0.85 (11 / 13)
Gap_init rate = 0.00 (0 / 110), avg. gap size = 0.00 (0 / 0)  

3077 23.79 2.24 1.12  chr2_231141117_231146364.rev     3961  4763 (485)    L1M4_orf2#LINE/L1       97   908 (0)  

  chr2_231141117_   3961 AAAATTCAAA-TGGCATTTTTG-AGAAATAGAAAAAC-AATTTAAAAATT 4007
                              i v i-  v v      -      v  v  i -i  iiv      
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_231141117_   4008 TGTGTGGAGGCACAAAAGACTCCAACTAGCCAAAGGAATTTTAAACAAAA 4057
                         ii i    iiii   ii   i vi v        iv   i  i  v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_231141117_   4058 AGAACAAAGCTGAAAGCATCACACTACCTGATT-CAATATATACAGCAAA 4106
                                  i  i i vv       v  ii   -   v iv   vi    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_231141117_   4107 GCTATGTTAATCAAAAGAGCATGGTGCTTGCATAAA-ATAGACATGTAGA 4155
                             iiv       i v  ii    i  v      i-        i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_231141117_   4156 AAAATGGAACAAAATAGAGAGCTTGGA------TCCATGCATTTATGGTC 4199
                         vv       i i   v     iiii  ------i    i           
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_231141117_   4200 AATTGATTTTCAACAAAGGTGCCAAGAATATGCAATGGGTAAAGGATATC 4249
                                    i    i          vi  v       v    i   --
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-- 394

  chr2_231141117_   4250 TATCTCTTTAATAAATGGTGTTGGGACAACTGGATATCCACATGCAGAAG 4299
                         -i   i  i  i        i               ?         i   
  L1M4_orf2#LINE/    395 -GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_231141117_   4300 AATGAAATTTGACCCC-ATCTCATGCCATATTAAAAAATTAACTCAAAAT 4348
                               i  v      - i    ii      vv                 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_231141117_   4349 GGACTAAATACTGAAATTTAATACCCAAGGTTGTAAAACTACTAGAAGAA 4398
                            ii ? v  iv    v   v v i  iii i       vi        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_231141117_   4399 AATATAGAGGAAAAGCTTCACGACATTGGTCTGAGCAAATATTTTTTGGG 4448
                           i    i? v   v    ii   v    vi ii    vvi   i  i i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_231141117_   4449 TATAACACCAGAAGCACAATCA-CAAAAGCAAAAA--GA--ACTGGGATT 4493
                            i      i        v  -      v     --  -- v v   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_231141117_   4494 ACATCAAACTAAAAAGCTTCTGCATAGGCAAGGAAACAATCAACAGAGTG 4543
                         v       v v    i   i  iiivvvv     v  v     v i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_231141117_   4544 AAGAGACAACCTACAGAATGGGAAAAAATATTTGCAAACCATGTGTCTGA 4593
                           i        i           i              i   i i     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_231141117_   4594 TAAGG-ATTATTATCCAAAATACATAAGGAGCTCAAACAACTCAATATTA 4642
                              - i vv      i    i    i  i   vv           ---
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA--- 790

  chr2_231141117_   4643 AATACAAACAAACAAACAAACAGATTTTTAAATGGGCAAAGGACCTGAAT 4692
                         --- i   v i     i  v vi   ?vv              ii     
  L1M4_orf2#LINE/    791 ---ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr2_231141117_   4693 AAACATTTCTTAAGGGAACACATGCAAATGGCTAACAGGTATGTGAAAAA 4742
                          i        iv ii   v i  i        i  i i i ii      i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_231141117_   4743 ATGCCCTGCCTCGGATATCAT 4763
                             i vi v  i????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (120 / 67)
Gap_init rate = 0.02 (13 / 812), avg. gap size = 2.08 (27 / 13)  


2943 25.71 1.97 2.63  chr2_231176649_231181887.rev     3834  4747 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_231176649_   3834 TGAAAAAACATTCCAACCTTATGGATAGGAAGAATCAATATCATGAAAAT 3883
                           i   i i  i   vvi i      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_231176649_   3884 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATTCCCATCAAAC 3933
                            v     v      v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_231176649_   3934 TACCATTGACATTCTTCACAGAATTAGACAGAATTAGAAAAAACT-ACTT 3982
                          v   vivi v  i  ii     v v    ----------- i  - iii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-----------AGCTGATCC 139

  chr2_231176649_   3983 TAAATTTCATTTGGAA-T-CAAAGAAGACCCCATACAGTCAAGACAATCC 4030
                             v     v     - -   i --     viv i  i   i      i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCT 187

  chr2_231176649_   4031 TAAGCAAAAAGAACAAAGCTGGAGGCATCAGCCTACTTGATGTCAAATTA 4080
                          i iv  i          i      vv   vv  v iii  v     viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_231176649_   4081 TACTACAAGGCTACAGTAACCAAAACACCCCCATGGTACTGGTACCAAAA 4130
                                 i          i   i   vi---i         i iv ii 
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGT---GTGGTACTGGCATAAGGA 284

  chr2_231176649_   4131 CAGACATATAGACCAATGGAACAGAACAGAGACCTCAGAAATAACACCGC 4180
                         i           i        i    iv    vii         vv  ii
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr2_231176649_   4181 ATATCTGCAACCATCTGATCTTTGACAAACCTGACAAAGACAAGT-AATG 4229
                          i  i iiiii  vi    i  i     ivv  v   -   v v -    
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATG 383

  chr2_231176649_   4230 GGGAAGGGATCTCCTATTTGATAAATGGTGTTGGGAAAACTGGCTAGCCA 4279
                              i i  vvi  v  ii i        i     v      v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_231176649_   4280 TATGCAGAAAACTGAAACTGGACCCCTTGCTTATGCCTTACACAAAAATT 4329
                         i     i  i v    ii         vv  i ii  v  i         
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_231176649_   4330 AACTCAGGATGGATTAAAGACTTAAAATGTATAACCCAAAGCCATAAAAT 4379
                               ii      i ?    i    -    vi v i   i i      i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAAC 532

  chr2_231176649_   4380 CCCTGGAAGAAAACATAGGCA-AAACACTGAGGACACAGGCATGGGCAAA 4428
                         i i i              ?i-   ivi viv   viv  vv i     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_231176649_   4429 GACTTC------ATGACAAAAATGCCAAAAGCAATTGCAACAAAAGCAAC 4472
                          ii   ------      ------         vvv          v  v
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_231176649_   4473 AATTGACAAATGGGATCTAATTAAACTAGAGAGCTTCTGCACAGCAAAAG 4522
                            v  i    v   ii v  i   v vi i i   i  ii vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_231176649_   4523 AAACTATCATCAGAATGAACAGGCAACCTACAGAATGTGAGAAAATTTTT 4572
                          v       vv i i    v  i     i        v        v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_231176649_   4573 GCAATCTATCCATCTGACAAAGGTCTAATATCCAGAATTTATGAGGAACT 4622
                             vii  vi      i  i  v  vi          v   i i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_231176649_   4623 TTAACAAATTTACAAGAAAAA-ACAAA--ACC--ATCAAAAAGTGGACAA 4667
                         i v    v iv i  v     -     --   --  i?    i   i   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_231176649_   4668 AGGATATGAACAGACACTTCTCAAAAGAAGACATTTACGTGGCCAATGA- 4716
                              v    i     i     v        i  vi vi        i -
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_231176649_   4717 -ACATGAAAACAAGCTCAACATCACTGAACAT 4747
                         -         v v           ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.62 (42 / 16)  


3100 26.45 1.79 0.45  chr2_231215165_231221549     4999  5894 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_231215165_   4999 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5048
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_231215165_   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5098
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_231215165_   5099 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5145
                          v   -   v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr2_231215165_   5146 ATATGGAACCAAAAATGAGCCCACATAGCCAGAACAATCCTAAGCAAAAA 5195
                                 viiv  iv  v  viv       i       i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_231215165_   5196 GAACAAAGCTAGAGGTATCATGCTACCTGACTTCAAACTATAATACAAGA 5245
                                 i i    vv   ii  v  ii i      viv  v     ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_231215165_   5246 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5295
                                  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_231215165_   5296 CAATGGAACAGAACAGAGGCCTCAGAAATAACATCACACATCTACAACCA 5345
                                 i    iv   ivii         vvi  i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_231215165_   5346 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTTCC 5395
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_231215165_   5396 TATTTAATAAATCGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5445
                          v  i  i    v         v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_231215165_   5446 AAACTGGACACCTTCCTTACACCTTACACAAAAATTAACTCAACACAGAT 5495
                           ii     v   v   i     v  i                v ii   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_231215165_   5496 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5545
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_231215165_   5546 TAGGCA-ATACCATTCAGGATATAGGCATGGGCAAAGACTTCATGACTAA 5594
                             ?i- v i -   iv  iv v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_231215165_   5595 AACACCAAAAGCAATTGCAACAAAAGCCAAAATAGACAAATGGGTTCTAA 5644
                         i            vvv          vv        i    v  vii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_231215165_   5645 TTAAA-TAAAGAGCTTCTGCACAGCAAAAGAACCTATCATCAGAGTGAAC 5693
                          i   - v  i i   i  ii vv    i  vv      vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_231215165_   5694 AGGCAACCTACAGAATGGGAGAATATCTTTGCAATCTACCCATCTGAGAA 5743
                           i     i              v  v       vii ivi      v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_231215165_   5744 AGGGCTAATATCAAGAATCTACTAAGAACTT----AACTTTACAAGAAAA 5789
                         i  i  vi    v     v  iv       i----    iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_231215165_   5790 A-----ACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTT 5834
                          ----- i     v  i?    i            v    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_231215165_   5835 TCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAATGCTCATC 5882
                           v        i  vi viii     i  --         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_231215165_   5883 ATCTCTGGTCAT 5894
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


1019 27.98 10.11 3.61  chr2_231251974_231254620      997  1550 (1097)    L1M4_orf2#LINE/L1        1   590 (318)  

  chr2_231251974_    997 TGGAAGGATATATTATGTTCAGGGATTGGAAGA-TGAATATTGT------ 1039
                              i     vii       v           - v        ------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_231251974_   1040 --CCATTCTCCTCAAAATGATCTACAGAAACAACCCATGTTGTTTCCATT 1087
                         -- v  v    i    v           vv    v  ----i ii i  i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA----ATCCCTATC 96

  chr2_231251974_   1088 TTAAACATCAACAGCATTTTT-GTGGAAATTGACCAGTTGATTCTAACAT 1136
                         v-   ivi  i v  v     - ii         v  i    i    v  
  L1M4_orf2#LINE/     97 A-AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr2_231251974_   1137 GTAATATTGGAACACAAAGAACTGGAAATAACCCAGACAAT-TTGAAAAA 1185
                         - v    v i  ii   i i  ivii    i  v i     -        
  L1M4_orf2#LINE/    146 -TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_231251974_   1186 GGTGAACACAACTAAAGGACTT-CACTACAAGATATCAAGATTTAA-ATA 1233
                          iv     v ii ii      i-    v vvi  v    i i   v- i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_231251974_   1234 AAGCTACTCTAATTAAA------TGGTATTGTCTCAAAGATAGAAAAATA 1277
                                vv    i  i------     i  v vi  i      v v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_231251974_   1278 AGCCAGTTGAA---------------AGAAA-AGACTCATGCCTATTTGG 1311
                         iii  i v   ---------------     - i  i   i v v v   
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_231251974_   1312 GCGGTTGATTTACTACAAAGGTGACATGGCAAAACTGTGTGGCAAAGACA 1361
                         v ii       v v    i    v  v i v vv vi  v  v  ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_231251974_   1362 ATACT--CA------GTTACTTGGATACCT--ACATCTAATAAATCTTGA 1401
                         i vi --  ------ v i  v   i v  -- i ? i ------ v  v
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA------CATGC 438

  chr2_231251974_   1402 AGAAAAA-GAAATCCAGGCCCTCTAATCCACACCA-----AGCAATTA-C 1444
                          i  i  -   i i--  v  i   vii       ----- iv     - 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTT--GGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_231251974_   1445 T---GGTGGATTTTAGATAAAAATGTAAAAAGATAAAACAATAGCATTTT 1491
                          ---ii     iv?   ivv        i - v      v   iv i i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCT 535

  chr2_231251974_   1492 GAGAAGATAACCTAAAA-TAATATCTTCATAAACTCTGGGTGGGTAGGGA 1540
                         v      v   v  ii?-   -      i i v  -     ---    v 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCT-TGGGT---TAGGCA 580

  chr2_231251974_   1541 AAGATTTTTT 1550
                          v i   i  
  L1M4_orf2#LINE/    581 ATGGTTTCTT 590

Transitions / transversions = 1.24 (84 / 68)
Gap_init rate = 0.04 (26 / 590), avg. gap size = 2.92 (76 / 26)  

 664 28.30 5.03 2.52  chr2_231251974_231254620     1843  2160 (487)    L1M4_orf2#LINE/L1      583   908 (0)  

  chr2_231251974_   1843 GATTTCTTAAACAGAATGCAAAAAGCACTTAACCCTAAAGGAAATAATTT 1892
                          i       i i vi ii v        v- i vvi   i    v   vv
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAG 631

  chr2_231251974_   1893 ATATACTGGACTACACTAAAATTAAAAAATTTC---CTTCACTCAAAGAT 1939
                            v i      v  ii           v   i---     ---  i  i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA---AAGGAC 678

  chr2_231251974_   1940 ACCATTAAGATCATGAAAATGCAAACCGAAGAGTAGACAAAGATTTTTGA 1989
                           i  i    vvi      vi   v  iv   i i ivi  i  v    v
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_231251974_   1990 AACCTATTTATCCAAACAAGGGCTCATATTCAGAGTATCTAAAGGACCCT 2039
                           vii  v    ii vv i  i  ii   i    i   v     i  i  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_231251974_   2040 TATACTTCAATA-TAAGAAATGCAGTGAATCC----CAGAA----GTAAA 2080
                           i vi      -   -   vi  ivv  i  ----? i  ---- i   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_231251974_   2081 GATACTTGAATAGGAACTTCACAAAAGTAGATATTCCAAAGGTCAGTCTA 2130
                          i- i        iv i   v v    v      v v  v  i  i -- 
  L1M4_orf2#LINE/    828 GG-ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT--A 874

  chr2_231251974_   2131 AACACATGAAAG--TGCTC--TCTCATTAGCAGT 2160
                          i         i--     --iv   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (53 / 36)
Gap_init rate = 0.03 (11 / 326), avg. gap size = 2.18 (24 / 11)  


2193 24.55 11.61 1.81  chr2_231278097_231279712      303  1129 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_231278097_    303 TGGAAAGGTAT-----ATTTGTGGATTG-AAGACTAAATATT---AATAT 343
                                i   -----i  ii       -      v      ---  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_231278097_    344 GTAAGTTATCCCCAA-CTGATTCATAGATTCAATATAATTTTAAT-AAAA 391
                          vv i vv       -i    ii i        iii   iiiv  -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_231278097_    392 TTCAAGTGGAATTGTTTGTGGAAATTGACAAATTGATTTTAAAATATAAA 441
                          i v  iv vv  v    ii           ii    ii      vi v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_231278097_    442 TGAAAATGCAAAAGACCAAAGTTAGCCAAAAGAGTCTTGAAAAAGAATCA 491
                           i        ii    v iiv         v i             vv 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_231278097_    492 CAATGTT-------------TT---AACTTCA--------TATAAAGTTA 517
                            v   -------------  ---  i    --------  i    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_231278097_    518 CAATAACTAAGACAACATGATATGGGCATAAAGATAAACATATAAATCAA 567
                           i   ii      iii  i  iv       i    i       i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_231278097_    568 CAGAGACTACAA--GAAAG---AGAAACA----CACACAT--AAGGTCAC 606
                         ii  i--  v  --  i  ---     i ----  i    -- v     v
  L1M4_orf2#LINE/    301 TGGAA--TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_231278097_    607 CAAATTTACAACAAAGACACCGCCACATTTCAGTGGGGAAAACGATGGTC 656
                         ivi    v i    i iii  ivv  vv    i        i-i  i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTC 397

  chr2_231278097_    657 ACTTCATGAAATGGTATTG------TTGGA---------GCAA------- 684
                         vi    vv       ii  ------i    ---------    -------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_231278097_    685 ---TTGAACACCCTACCTCATACCATACACAAAAATTTATTTCAAATGAA 731
                         ---   i  -          i      i         v i iv     i 
  L1M4_orf2#LINE/    448 AAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_231278097_    732 TCATAGACCTAAATATGAAAGATAAAATAGTAAAGCTTCTAGA-GCAGGT 780
                            ?          i i i  v     ivi    i  ii    - v iii
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_231278097_    781 A---GTATAATATCTTCTTGGCTTAAGGT-AGGCAAAGATTTCTTGCAAA 826
                          --- ?i   -      v  i i vi   -      v i      iv v 
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_231278097_    827 AGATCCCAAAA-CACTAACTATGAAAGAAACCACTGACAAATTAGACTTA 875
                         v  iv      -   v i v ii       vv iv  i     i     v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_231278097_    876 CTTAAAACTAAGAACTTTTGTTCATCAAAAGACACTATTAAGAGAGTGAA 925
                         v i    i   i         v v     i        i    i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_231278097_    926 AAAA--AGCCACAGAATATGTGAAGATATTCACAA--CACATATCCAACA 971
                           i -- v         iv v   i     ii   --  i     ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_231278097_    972 GAAGACTTCTATGTAGAACATGTAGGAAGAATGTCT--------AGTAAT 1013
                         iii     v   vi    i  i  --     i-   -------- i    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATA--AAGAAC-TCTTACAACTCAATAAT 792

  chr2_231278097_   1014 TAGAACACAAAAATCCCAATTTTTTTTAAAAAAATAGGCAAA--AT---A 1058
                         v i  v     v v       ?-------      i      --  --- 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTW-------AAAAATGGGCAAAGGATTTGA 835

  chr2_231278097_   1059 ACAGGCATTTCAT--AACAAAATACTCAAATGACCAATAAACATATCAAA 1106
                          i  i      vi--  v  i   iv      i       i  i  v   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr2_231278097_   1107 AAGTGCTCAAAAGCATTGTTTTT 1129
                          ii       v v  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (131 / 69)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 3.47 (111 / 32)  


3065 27.84 1.34 0.22  chr2_231297411_231300093     1294  2191 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_231297411_   1294 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1343
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_231297411_   1344 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCCAGC 1393
                            v     v      v i  i  i        i  v     i   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_231297411_   1394 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATCTCAT 1442
                          v   vivi i  i  ii     v v  v  i-  - iii    vi    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_231297411_   1443 GTGGAACCATAAAAGAGCCCGTATAGCCAAGATAATCCTAAGCAAAAAGA 1492
                         i     viii  ii  v  v v        i i    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_231297411_   1493 ACAAAGCTGAAGGCATCACACTACCTGACTTTAAACAATACTACAAGCCT 1542
                               i  i   vv       v  ii i  i   vvv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_231297411_   1543 ATGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGATCA 1592
                          ii    i   i    ii         i iv ii i   i          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_231297411_   1593 GTGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACAACCATC 1642
                         i     i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_231297411_   1643 TGATCTTTGAAAAACCTGACAAAAGCAAGCAATGGGGAAAGGATTCTCTA 1692
                             i  i  v  ivv  v   i v  vv            i  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_231297411_   1693 TTTAATAAATGGTGTTGGGAAAACTAGCTAGCCATATGCAGAAAACTGAA 1742
                           i  i        i     v    i v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_231297411_   1743 ACTGGACCCATTCCTTACACCTTA-AAAAAAATTAACTCAACACGGATTA 1791
                         ii       v v   i     v  - v              v i    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_231297411_   1792 AAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTGGAAGAAAACATA 1841
                         ?    i           v       i      vi i i            
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_231297411_   1842 GCAATA--CCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 1889
                          v?i  --i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_231297411_   1890 CACCGAAAGCAATGGAAACAAAAACCAGATTTGACAAATGGGATCTAATT 1939
                             i      vvi v       ivv i v v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_231297411_   1940 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGTACAG 1989
                            v v  i i   i  ii vv    i  v       vv i    v v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_231297411_   1990 GCAACCTAGAGAATGGGAGAAAAATTTTGCAATCTATCCACCTGACAAAG 2039
                         i     i v              vv       vii  vi i    i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_231297411_   2040 GGCTCATATCCAGAATCTACAAAGAAC----ATAAATTAACAAGAAAAAA 2085
                          i  ii          v  i       ---- i  v i  i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_231297411_   2086 ACAA----CCCCATCAAAAAGTGGGCAAAGAGTATGAACAGACACTTCTC 2131
                             ----   v  i?    i         ii v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_231297411_   2132 AAAAGAAGACATTTATGCAGCCAACAAACATACGAAAAAATGCTCATCAC 2181
                         v        i  vi viii     i  i  i i     i       v  i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_231297411_   2182 CACTGGTCAT 2191
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.56 (150 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  


3002 26.64 1.66 0.89  chr2_231308985_231315721     5345  6245 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_231308985_   5345 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 5394
                              ii i  i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_231308985_   5395 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5444
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_231308985_   5445 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAAACTA--CTTAAAGTT 5490
                          v   -   v    i  -i     -   --- v  i  i-- i    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr2_231308985_   5491 CATATGGAACCAAAAAAGAGCCTACATAGCCAAGACAATCCTAAGCAAAA 5540
                                  viiv  ii  v  viv        i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_231308985_   5541 AGAACAAA-CTGGAGGCATCACGCTGCCTGACTTCAAACTATAGTACAAG 5589
                                 -i      vv    i  v  ii i      viv  v     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_231308985_   5590 TCTACCATAACCAAAACAGCATGGTACTGCTACCAAAACAGATATATAGA 5639
                         v    vi   i   i    ii        vi iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_231308985_   5640 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACC 5689
                         i        i    iv   ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr2_231308985_   5690 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGGAAAGGATTC 5739
                          vi    i  i     ivv  v   i v  vvv       -    i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAG 395

  chr2_231308985_   5740 CCTATTTGATAAATGGTGCTGGGAAAACTGGCTAGCTATATATAGAAAGC 5789
                         i  v  ii i              v      v  ? i i  ii i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_231308985_   5790 TGATACTGGATCCCTTCCTTACACCTTATCCAAAAATTAACTCAAGATGG 5839
                            vii    i    v   i     v   v               i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_231308985_   5840 ATTAAAGACTTAAATGTAAGACCTAACACCATAAAAATCCTAGAAGAAAA 5889
                           i ?    i           v    v  i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_231308985_   5890 CCTAGGCA-ATACCATTCAGGACGTAGGCATGGGCAAAGACTTCATGACT 5938
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_231308985_   5939 GAAACACTAAAAATAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5988
                         ivi    i    ii vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_231308985_   5989 ------AATTAAAGAGCTTCTGCAGAGCAAAAGAAACTATCACCAGAGTG 6032
                         ------       i -   i  iivvv    i  v       vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_231308985_   6033 AACAGGCAACCTACAGAATGGGAGAAAA-ATTTTTCAATCTATCCATTTG 6081
                           v  i     i                -    viv    -  vi  i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTG 742

  chr2_231308985_   6082 ACAAAGGGCTAATATCCAGAATCTACAAAGAACATAAACAAATGTACAAG 6131
                          i  i  i  vi          v  i       vivv    v vv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_231308985_   6132 AAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGCTATGAACA--CA 6179
                              i     i     v  i?    i          v v    i --  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_231308985_   6180 CTTCTCAGAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAAAGCT 6229
                         i     vi       i  vi viii     i ii  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_231308985_   6230 CATCATCACTGGTCAT 6245
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


 315 27.44 21.61 4.26  chr2_231323714_231325322      505  1138 (471)    L1M4_orf2#LINE/L1      165   908 (0)  

  chr2_231323714_    505 ATTTAAATTATTCAGAAAATTTTTGAAAAGGAAGAA--AAATGAGAGGAT 552
                          iii i v  vi  i  v v i       i      --  i vi     i
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr2_231323714_    553 T-AGACTTGCTATATATAAAAGCACATTATAAAGC-ACAAGTAATTAAAA 600
                          - v    v i -  v v   i vi i  i     -   -     i  i 
  L1M4_orf2#LINE/    215 TCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACA-GTAATCAAGA 262

  chr2_231323714_    601 --GTTTGTCATCAGAGCAAAAATAGACC----AATCTATGAAATAAAACA 644
                         --  v  vi iii vii  ii      v----i   v   i    i  iv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr2_231323714_    645 GAAAGCCCAGAAATAGCCACCAAGTGCATATGGGATAAA--GA------A 686
                           i  i         iv -   -- i   v iv i v  --  ------ 
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAAC-CCA--TACATTTATGGTCAATTGATTTTCGA 359

  chr2_231323714_    687 TAAGAG-G--AAGGTATCATTTTAAATTAGTAGGGTAGGATACATGACT- 732
                         i   i - --   -- i    i------ i i   v i  - i - v  -
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAG--ACCATTC------AATGGGGAAAGA-ATA-GTCTT 399

  chr2_231323714_    733 --CAATAAATGGT-CTCAG------GGATATT------------------ 755
                         --   i       -  vi ------     ?i------------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_231323714_    756 GTT-----CTTACCTC-CAGGATA----------AATTTAAGATAGATTT 789
                            ----- i      -  vv   ----------  i i  i  i   iv
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_231323714_    790 ----TTTTAATGTAATGCAAAACTTAAGTCATAAAA------GAGGAAAA 829
                         ----ii v       ----i i  v  iii      ------  i     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAA----GAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_231323714_    830 CATA----TGAATTTAGTTATACTCTTGGCATAGAGAAGGCCTTTGTAG- 874
                             ---- i   i -- ii ivi     vv   iv  v vi  iv   -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_231323714_    875 CACGATAT---ATTCAGACACCATAAAAGGAAAATTTTGT---TTCATTT 918
                         i i  i i--- vv  v vi v i     i    v vvi ---  vivi 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_231323714_    919 TTGTCTAAAT-AAAAACTTTAG-ACTTC---------T-TCAAGAAA--- 953
                          ii  v    -         v -i    --------- -        ---
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_231323714_    954 --AGGACAAACCA-------GGAGAAAGTATTTACAGAT-GTATGGCTAC 993
                         -- i     v   -------       i     i  i  -i   iv  iv
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_231323714_    994 T---TTACTTAAATCCA------ATAAAG---TCTTAATAATCAACATAT 1031
                          ---vv    iv     ------      ---     vv v    i -  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-AT 792

  chr2_231323714_   1032 AAGAG-----ATAACCCAAGTGGAAAAAAAATGGGTAAAGGAAT-GAATA 1075
                           i i-----         v ----?         i      v -     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATT----WAAAAATGGGCAAAGGATTTGAATA 838

  chr2_231323714_   1076 -------CTTGATAGGAAACAATAAAAACAGCCATTAAGCATG-AAAAAA 1117
                         -------  iv v  i i i -  v   ii    v      ii-i    i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATA-TACAAATGGCCAATAAGCACATGAAAAG 887

  chr2_231323714_   1118 ATACATAACTTTAGTAATTAA 1138
                           i vi   v i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (108 / 64)
Gap_init rate = 0.07 (49 / 744), avg. gap size = 3.35 (164 / 49)  


2875 23.88 8.73 0.48  chr2_231458604_231463043     3124  3948 (492)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_231458604_   3124 TGTTCATGGGTTGGGAAACTCAATATTGTTAAAATGTCACTTCTCTCCAG 3173
                                  i    i i   i           i   v  v v   i   i
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_231458604_   3174 ATGTATCTAGAGATTCTGTGCAATTCC------------AGCAGGATTTT 3211
                           vv     v      vii     i  ------------   v vv    
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_231458604_   3212 T-----AAATCAAAGAGTTTGTTCTAAAATTTGAATGGAAGTGCAAAAGA 3256
                          -----    ii vi  i vi i        iiv      i     ii  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_231458604_   3257 CCTGGAGTAATCAAAATAA-CT-----AATTAAAACAAAGTTGGAGGGCT 3300
                           ii  i  ii     i  -  -----  vv i              i  
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_231458604_   3301 CACACTGTCTGATTTCTAGACTTA--A-AAAGCTACGGTTGTTAAAACAG 3347
                               vi ii     v i     -- -        i  vi i  i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_231458604_   3348 TGTGGTGTCAGTGCAAAGATAGATATAT----TAATGGAACAGA-TTGGG 3392
                               iiii iii  i      i    ----i       i   -   i 
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_231458604_   3393 -GTGCAGAAATAGACCTACACATGTATGGAACATTGATTTTTGACAAAGG 3441
                         -  v        i   i i    v     vvv         i     i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_231458604_   3442 CATAAATGCAGTT--GTGCAGAAAGAAGGTAGTTGTTTCAACAATTGGTG 3489
                         iiiv  vi vi  --i  vi       --    iv         v     
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAA--TAGTCTTTTCAACAAATGGTG 413

  chr2_231458604_   3490 CTGAAACTATTTAGTAG------GCAGAAAGATA-----GGACTCAGACC 3528
                            ii  v i vii  ?------   i  ii  i-----    i vv   
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_231458604_   3529 TCATACCATATTTAAAAATTAACTCAAAATGGATCACATAGCCAAATGTA 3578
                            i       vi                       ? v v i       
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_231458604_   3579 AGACCTAAAATTATAAAGTTGCCAGAAGAAAA------------TCTTTG 3616
                            v      i      ii vii         ------------    i 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr2_231458604_   3617 TGACCTTGGGTTAGGCAAATAATTT-TTGGATGTTATGCAAAAAGCACAA 3665
                                           - ii   -  i   i v ii v          
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_231458604_   3666 TTCATTTTAAAAAAAAT-GATAAAT-GGAATTCATAAAAATTAAAACCT- 3712
                         viv ivvv i       -       -   v     v          v  -
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_231458604_   3713 --GCTCTTCAGAAGACACTGTTAGAAGAATGAAAAAGACAAACCACAAAC 3760
                         -- iv     i i      i i ii i i      -     v     i v
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GACAACCCACAGAA 711

  chr2_231458604_   3761 TGGAAGAAAGT--CTGCAAAGCATATATCTGATAAAAGACT-GCATCTAG 3807
                            i     i --i      v              ii    - i   i  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_231458604_   3808 AATATATAAAGAATTCTCAGAATTTAACAGTTAGAA-----ACAATCCAG 3852
                                      i   i v  i i  i i v i  ----- i  i   i
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_231458604_   3853 TT-AAGAGTGGGCAAGATACTCATATATGCATTTCACCAAAGGAGATAGG 3901
                           -  i i       iiv i iiv   vi      v      i     vi
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_231458604_   3902 CAGATGTCAAATAAGCCCTTGAAAAGATGTTAATCATTAGGAAATTG 3948
                           i   v v       v v          i v v   i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (130 / 65)
Gap_init rate = 0.03 (24 / 893), avg. gap size = 3.17 (76 / 24)  


2851 23.73 4.97 2.37  chr2_231547585_231550241     1281  2165 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_231547585_   1281 TGGAGAAATATACCATGTTCATGGATTTGAAA--TCAAAATTGTTGAGAT 1328
                             i i    v               v   i-- i  v      i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_231547585_   1329 ATCATT-TTCCCCAAAATTGGTTTATAGATTTAACATAAGCCCAATTAA- 1376
                         iv  v -i        -   i i  i     i   ii  v   v  i  -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_231547585_   1377 -TACCAACAGATTTTCTTTTGTAGAATTTGATAAACCAATTC--AAATGG 1423
                         - v   i v vi   --    i    v    i  i ii  i --    --
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTT--TTTGCAGAAATTGACAAGCTGATCCTAAAAT-- 145

  chr2_231547585_   1424 TTATTTGGGTATTCAAAGGATCTAGAAAAGCTCAA-CAGTCTCGAAAAAG 1472
                          i  v   iv  v   i   i i    v   iv  -  i   i       
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr2_231547585_   1473 ----------TCAGAGTACTCATACTGTCTGATGTTAATACTTATTAGAA 1512
                         ---------- ii   v     i   vi ii  v i  v     i  v  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr2_231547585_   1513 ATCTAAAGTGATCAAGATAGTGTGAAATTGGCATAAGGATAGAAAAAAAT 1562
                          v   v   i       i      iv i               v v -- 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA--T 293

  chr2_231547585_   1563 AAACTAATGTAACAGAACAAAGAGTCTAGAAATAAATCCATTAAACGTT- 1611
                          i ii    v  i    ivi      i         i    ---  i  -
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT---ACATTT 340

  chr2_231547585_   1612 ---GTCAATTGGTCTTTGACAAAGATGCCAAAACAATTAAATGAGAAAAA 1658
                         ---        i i  i     i i      i  v   v    i i   i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_231547585_   1659 CAAAATTTCTTAAACAAATACTGCTGGGACACCTGTATAACCATATGGAA 1708
                         v v i i i  v       iv          v   v   ?   i   v  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_231547585_   1709 AAGAAATAAACCTCAATCCCTACCTCATACCTTACATTAAAAAATCAATT 1758
                              - i  vi vi i          i   v  i i--      i  i 
  L1M4_orf2#LINE/    441 AAGAA-TGAAGTTGGACCCCTACCTCACACCATATAC--AAAAATTAACT 487

  chr2_231547585_   1759 AAAAGTGGATCACAGACCTATATGTGAAACCTAAAACTATAAAGCTTCTG 1808
                         v   i       ?       v    i i v             i  ii i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_231547585_   1809 AAAGAAAGAATATGAGAATATCTTCAAAATTTGAACATGGGTGTTTAAAG 1858
                         i      iv   v ? v v      i-----   v v     ---  iiv
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCG-----TGACCTTGGGT---TAGGC 579

  chr2_231547585_   1859 AAT----TTTTAGACAGGACATTAAAAGCACTAACAATAAAATTAAAATT 1904
                            ---- i     i v    ii        v i   i    vv    v 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_231547585_   1905 -TATACATTGAGCTTGATCAAAATTATAAATTTCTACTCATGAAAAGACA 1953
                         -v   v    ii   v          v   i  i iiv v v   i    
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_231547585_   1954 AAATTTTAAAAGTGAAA---TA--CCACAGTCTGAAAGGAAATATTCACA 1998
                         vv  ivvi         ---i --      vv  ii  i       ii  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_231547585_   1999 ATGAATATACATGACAAAAGACTTGTATCCACAATATAAAACGAATTCCT 2048
                          vvv     iv   i  ii            v      v  v   i  i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr2_231547585_   2049 ACAAATCAATAATTAAAAGACAG----TCTAA-------ATGACCAAAAG 2087
                             v        v        i----i i  -------   iv    i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_231547585_   2088 ACTTAAGCAGACACTTCACAAAAGAAGATATACAAATGGCCAATAC-CAC 2136
                          i  i ii     i   v v                         v-   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_231547585_   2137 ATAAAAAGATGTTCAGCATCATTAGTCAT 2165
                           i        i   i     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (126 / 81)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.83 (65 / 23)  


 315 26.26 6.06 1.01  chr2_231572846_231575897.rev     1395  1493 (1559)    L1M4_orf2#LINE/L1        4   107 (801)  

  chr2_231572846_   1395 AAAAATA--CCATGTTCATGGGTGAGAGCACTCAATATCCT---GATTTC 1439
                            i   --            i vi  iv   i     iv ---   vv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_231572846_   1440 AATTCTCCCCAAGTGGATCTATAGATTTCATATAAGTCC-ATTAAGAACC 1488
                            v        i v      i     iv iii  vi  -  i  -  i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-AATC 102

  chr2_231572846_   1489 TCAAC 1493
                         i  i 
  L1M4_orf2#LINE/    103 CCAGC 107

Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.04 (4 / 104), avg. gap size = 1.75 (7 / 4)  

 606 28.46 13.04 9.09  chr2_231572846_231575897.rev     1794  2552 (500)    L1M4_orf2#LINE/L1       97   885 (23)  

  chr2_231572846_   1794 AGAACCTCAACAGAATTTTCCATGAAACTTGGCA-GTTGTTTCTAAAATG 1842
                          i  i i  i v vv    iiiiii  v   i  - i  v i       v
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_231572846_   1843 CATATG--AACAAAAAGGGCCAAGAATAGGCATGGCACTGCTGGA---GA 1887
                               --  iiv  i  i  v       v  vii  v vi  i ---  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_231572846_   1888 GAATCAAGGTAGGAA-ACTTTTAGTACCAGGTAGCAAGACTTACT----- 1931
                         ii v   i  v   i-   ivi v v  vii vv   i       -----
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_231572846_   1932 ----------TTAAG----TGTGGTTATGGTCCAACGGATAGACCT---G 1964
                         ---------- i   ----      vv   ivi  -        v --- 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAA-GGATAGACATATAG 295

  chr2_231572846_   1965 ATGAACAAAACAGAA-----AGCCCAGAAGTAGACCT-TACATATAGAGA 2008
                           v  iii  i    -----  i      i  i   i-     v  vi v
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_231572846_   2009 AACTTGATCCTTGCAGACATATACTGTAAC---TCAGTGGGGAAGGAA-A 2054
                         v v     ii i - v vivi i iivi  ---   i       i   - 
  L1M4_orf2#LINE/    346 CAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_231572846_   2055 --------AACAAA------------AAC------------------AGA 2066
                         --------      ------------   ------------------   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_231572846_   2067 ACAAATCGTT--ATTCCTACCTCACATCAGAC-CAGGGATTAAATTCCTG 2113
                          ii  --   -- ii           i  v i-  iii     v ivvvi
  L1M4_orf2#LINE/    445 ATGAA--GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr2_231572846_   2114 GGGATTCAA-----AAATGTAAAATACAAAACTCTAAAATGAATAGAAGA 2158
                         v    iv? -----        i vvi      v     ivvv       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr2_231572846_   2159 AATTGTAGAA-TAATGCCTCTTCA--ACCTTAGGATGGGAAA-GATTTCT 2204
                           vii   i?-   ---v     i--     i  v i  v  - i     
  L1M4_orf2#LINE/    543 AAACATAGGNGTAA---ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_231572846_   2205 --GAAATGATATAAAAGGCCCTAACCACAAGGAAAAAGATGAATAAATTT 2252
                         --  v    i iv   i  v v i v    iii    i  ii       v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_231572846_   2253 GACTGCATTAAAATCAATAATTTCTGTTCATCAAAGTGACCACAAAGAAA 2302
                             v   i     i  v  i  i   v v      -   ----------
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GAC---------- 678

  chr2_231572846_   2303 GTGAGAAAGCTATGTACACGTGATGCTGTTTGTAAAAAAAAAAAAAAGGT 2352
                         --------i    -------------------i  i   ---------  
  L1M4_orf2#LINE/    679 --------ACTAT-------------------CAAGAAA---------GT 692

  chr2_231572846_   2353 GAGAAGGCAAGCCATGAACTAACTTGGGTAAGATACTTACCACCCATCAA 2402
                           i   i   v   iii v i----  iv  i   i  i v vi   ---
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATG----GGAGAAAATATTTGCAAATCAT--- 735

  chr2_231572846_   2403 TGAAAATATGTAAAATATAAAA--TGTAT---AAATATATAAATAACTCC 2447
                         -----    v i --  viii --     ---i          v     i
  L1M4_orf2#LINE/    736 -----ATATCTGA--TAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_231572846_   2448 TACAAAT---TAGTAAGAAAACAAAGCAACCAATAGAAAAATAGGCCAAA 2494
                              v ---  i   i  i     vv v     v?      i   -   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC-AAA 827

  chr2_231572846_   2495 GAAAGCAAGTCGGCATTTTACAGGAAAGGAAATTTGAGGGTTCAATAAAC 2544
                          i vvii i v i     iv vii i i  v  vii iv vi      i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_231572846_   2545 ATGTGAAA 2552
                          ii     
  L1M4_orf2#LINE/    878 ACATGAAA 885

Transitions / transversions = 1.57 (130 / 83)
Gap_init rate = 0.05 (36 / 789), avg. gap size = 4.67 (168 / 36)  


 519 26.47 2.21 0.00  chr2_232131314_232138345.rev     4169  4304 (2728)    L1M4_orf2#LINE/L1        1   139 (769)  

  chr2_232131314_   4169 TGGAGAGATACACCATGTTTGTAAATTAAAAGACTTAATATTGTTAACGT 4218
                             i     iv       ii ii   ii                  vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_232131314_   4219 GTCAGTTCTCTCCAAGCTTATTTACAGATTCAACCCAATC---AACATAA 4265
                          v  i v   i    ii v  i            v     --- v  v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_232131314_   4266 TCTCAGAAAAGCTTTGAATAGAAATTGACAAGATGGGCC 4304
                           i   vvivvi   vvii             v  iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

Transitions / transversions = 1.25 (20 / 16)
Gap_init rate = 0.01 (1 / 139), avg. gap size = 3.00 (3 / 1)  

 336 17.65 1.47 0.00  chr2_232131314_232138345.rev     4604  4671 (2361)    L1M4_orf2#LINE/L1      120   188 (720)  

  chr2_232131314_   4604 AGAACTTGACAAGATGATTTGAAAACTTATATAGAAATGCAAAACAC-TA 4652
                             v        v    iiv    i i    i         iiv  -i 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_232131314_   4653 GAATAGCCAAAACAATCTT 4671
                                            
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTT 188

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1)  

 954 22.18 5.28 3.87  chr2_232131314_232138345.rev     4971  5254 (1778)    L1M4_orf2#LINE/L1      177   464 (444)  

  chr2_232131314_   4971 CAAAACAATCTTAAAAAGTAAAAGAAACAAAGTTGGAGGACTTATACTAA 5020
                                     i    -- i     -               i i   vv
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAA--AGAAGAA-CAAAGTTGGAGGACTCACACTTC 223

  chr2_232131314_   5021 ATGATTTTAAGGTTTAATATAAAGCTACAGTAATAAAAAATAGCGTGGTA 5070
                         vii    i  iii   v  i              v  i -i  i      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTA 272

  chr2_232131314_   5071 TTGTTATAGGGA-AAATATATACATCAGTGACACAGACTAGAAAGTC--- 5116
                         i  vi   i   - i i     v    i  iv i   v v  i    ---
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_232131314_   5117 -AATAAACCATTCCTCATATAT--ATAGTTAATTTATTTTTAATAAAGGT 5163
                         -        ------    i  --  i  i    v     ii i  i   
  L1M4_orf2#LINE/    323 AAATAAACC------CATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr2_232131314_   5164 ACGCAGG--TATTCAATGGGAAAAGA---GTCTTTTCATCAAATAGTGTT 5208
                         i -  i --i          i     ---         v     i   i 
  L1M4_orf2#LINE/    367 GC-CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_232131314_   5209 TTGAAAACTGGATATTCATATG-GGCTGAGTGCAGT--GGCTCCAACCT 5254
                         vv  v         ?i  i   -iivv  i  v   -- i i  v    
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

Transitions / transversions = 2.26 (43 / 19)
Gap_init rate = 0.04 (12 / 288), avg. gap size = 2.17 (26 / 12)  

 870 27.87 3.14 1.39  chr2_232131314_232138345.rev     5809  6095 (937)    L1M4_orf2#LINE/L1      439   730 (178)  

  chr2_232131314_   5809 AAAAAAAAGAGCTTTGTCTTTCACTTCATATTATATACAAGAATTAATTT 5858
                             i  v  iv  v v iiii  i   i ii        i      i i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_232131314_   5859 GAGACAGGTTATAGATATAAATACAAAGCCTAAAATCATAAAGCTTTTAG 5908
                         i i ii i i ?   iv     ii  iiv      ii     i  i    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_232131314_   5909 AAGCAAA----GAAGAATATCTTTATGATTAAGGGT-AGGGAAAGATGTC 5953
                            v   ---- i? v v     ii   iivv    -   v  v i v  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_232131314_   5954 TTAGAGAGGATACAAAAGGCATTAACCATAAATGAGACAAAAAAGATAAA 6003
                              v v  i  v   i   iv i v i   --   v    v       
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAA--AGAAAAAATAGATAAA 636

  chr2_232131314_   6004 CTGGACT-CATCAGAACTAAAA---TGTCTGCTCATTAGAAGACACTGTT 6049
                         i      -     i  i     --- v v    -- i i i      i i
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTATC 684

  chr2_232131314_   6050 GAGAAAATGAAGAGACAAGCCACAGGTTGGGAGAAAATCTTTACAA 6095
                         i     i    i      v      iv           v   i   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

Transitions / transversions = 2.00 (52 / 26)
Gap_init rate = 0.02 (6 / 292), avg. gap size = 2.17 (13 / 6)  

 355 21.13 9.15 3.52  chr2_232131314_232138345.rev     6416  6557 (475)    L1M4_orf2#LINE/L1      735   884 (24)  

  chr2_232131314_   6416 TATTTTTGACAAAGCATTTGTATC-ATAATATATAAAGAA---TTACTAA 6461
                            v i   i  i v i       - v             ---    v v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_232131314_   6462 TCCATAATAAAAAGACAATTGATAAC--------AAAATGGACTAAAGGC 6503
                           v               ---     --------       i v  i ii
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAA---ATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr2_232131314_   6504 TTGAACAGATACTTTATAAAAGAAGATATCTGGACAGCAAAAAAAAGCAC 6553
                              i   i i  iviv           viii ii  v  v  --    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA--GCAC 879

  chr2_232131314_   6554 A-GAA 6557
                          -   
  L1M4_orf2#LINE/    880 ATGAA 884

Transitions / transversions = 1.50 (18 / 12)
Gap_init rate = 0.04 (6 / 150), avg. gap size = 3.00 (18 / 6)  


 585 28.24 9.84 3.63  chr2_232467315_232469221      501   886 (1021)    L1M4_orf2#LINE/L1      232   641 (267)  

  chr2_232467315_    501 AAATCATATTATAAAGCTATAATAATTCAATCAAATGTG-TATAGGTACA 549
                            v v  i  i       i i    -   vvv i    -  iv  i i 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAAT-CAAGACAGTGTGGTACTGGCATA 280

  chr2_232467315_    550 AGAAGAGACAAATAGATCAATGAAACAGAA---ATAATCCAAAAAAAAAC 596
                           i v     v           i  i    --- v i    i   v    
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr2_232467315_    597 CTATGT-CTTATGAAAATTTAGTATATGACAAGGATGGCATTTCAAAAC- 644
                          i  ii-i     ivv v  ii v vi       i  -----i   i  -
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTG-----CCAAGACC 375

  chr2_232467315_    645 ----AGTGAGGAAAAGATGGACTAACTACTTAGTAAATAGTACTGGAACT 690
                         ---- i  i     ii  i v  --i -- i ii    i  i    i  v
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCT--TT--TCAACAAATGGTGCTGGGACA 421

  chr2_232467315_    691 ATTGGCTATCCAAA--CAGCAGAA-GTACTTAGATGTCTACCACATACCA 737
                          i   v  ?   v --  iv    - v v  i  ivi     v  i    
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr2_232467315_    738 AATGTGTAAATACGTTCCAGGTGGATTA-------------AAGAGCTAA 774
                         v  iiiv    vvii  v ii     i -------------         
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr2_232467315_    775 ACATTGAAAAG-----AGAAGAAAAGATAGGA-TA---TTTAGTTAATCT 815
                          - i iv   i-----         v     ?-  ---i  v  -i i  
  L1M4_orf2#LINE/    522 A-ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACCT 569

  chr2_232467315_    816 TGGGATAAGAAA-GATCTTTTTAAACAAGATACAAAATGCAAAAGC--CA 862
                             v  i v  - i -  i   i i v  i  v   v   v    --  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr2_232467315_    863 GATGGCAAATATTAATAAATTTGA 886
                         i v iv   -  vi       v  
  L1M4_orf2#LINE/    619 AAAGAAAAA-ATAGATAAATTGGA 641

Transitions / transversions = 1.55 (65 / 42)
Gap_init rate = 0.05 (20 / 410), avg. gap size = 2.60 (52 / 20)  

 240 22.49 19.68 1.61  chr2_232467315_232469221     1168  1416 (491)    L1M4_orf2#LINE/L1      615   908 (0)  

  chr2_232467315_   1168 AACAAATGAAATAA--AATAAATTTGAA---ATGACAATTTAAAAATTCT 1212
                               v    v  --i       v  v---  v v    v    v  i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr2_232467315_   1213 GT---TCAA----------CAAAAAAG----GAGACAATACAT----TGA 1241
                           ---    ----------   i    ----i      iv  i----  i
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr2_232467315_   1242 AAGAAAATATTTGCAAAATACATAATAGGCAAAGGATTGATATT-ACAAT 1290
                         i                vi i   viv ii  i   i vi   i- v   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr2_232467315_   1291 ATGTAAAGAACATCTACAA----ATAAGAAAAA--TAAACAAT--AGT-- 1330
                           i        vii     ----    v     --i   i  i-- i --
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr2_232467315_   1331 -AAAATGGGCAAAAACAAAATT--AACAAACAATTTAC---AGAAGAAAA 1374
                         -            ii----   --  i i   v  iv ---      v v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGG----ATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr2_232467315_   1375 AGAAATGGCCAA-----ATA-GAAGAGATGTGCAACTTCTCTAATAAT 1416
                          v          ----- i -   i     iv    v  v????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (32 / 24)
Gap_init rate = 0.05 (16 / 294), avg. gap size = 3.31 (53 / 16)  


3592 14.44 2.08 4.44  chr2_232640287_232641998      501  1220 (492)    L1M4_orf2#LINE/L1      206   908 (0)  

  chr2_232640287_    501 TTGGAAGACTCGCACTTCTCAATTTCAAAACTTAGTATAAAGTTATAGTG 550
                              i     i      i               v  i    i  i   i
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr2_232640287_    551 ATCACAACAGTGTGGTATTGTCATAAGTATAGATACATAGATCACTGTAA 600
                             vi           i  v      v     i i        v  v  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr2_232640287_    601 TAGAATGGGGA-TACAGAAATAAATCCGTATATCTGTGGTCAACTGATTT 649
                               v i  - v          i  i  i  i i       i      
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr2_232640287_    650 -CAAAAAGGATCTCAAGACCATTCAATGGGAAAGGAAGAGTCTTTTCAAT 698
                         - i v    i vi                 i  i   v           i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr2_232640287_    699 AATTGGTACTGGGACAACTGGATATCCACATGCAAAAGAGTGAAGTTGAA 748
                           v    i                ?              i        i 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr2_232640287_    749 CTCTGACCTCACACCATGCGTAAAAATGAACTCAAAATGGATCAAAGATC 798
                          i iv            iiii      v                ?   i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr2_232640287_    799 TAAATGTATGAGCTAAAATGATAAAACGCTTAGAAAGAAACA--ATTGTA 846
                                 v         iv       v       ii     --iv?   
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_232640287_    847 AATCTTCACGACCTTCAATTAGGCAACAGTTTCTTAGATATAATACTTAA 896
                                ii      vii        ii             i i  iv  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_232640287_    897 AGCAAAAGCAACCAAA--AAAGATGAATAATTTGGACTTCATCAAAAGTA 944
                             v       v   --   i  ii    v                v  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_232640287_    945 AAA-CGTTTGTTTGTTTCATCAAAGGACAGTATCAAGATAGATAATGAAA 993
                            - v     -- i    ---       v        v  ----     
  L1M4_orf2#LINE/    656 AAAACTTTTGT--GCTTCA---AAGGACACTATCAAGAAAG----TGAAA 696

  chr2_232640287_    994 ATGGAATGTAATTCCTGTACATAACCCACAGAATGGGGGAAAA-ATTTAC 1042
                          --  ----------------i               i     -    i 
  L1M4_orf2#LINE/    697 A--GA----------------CAACCCACAGAATGGGAGAAAATATTTGC 728

  chr2_232640287_   1043 AAATC-------TGATAAAGGTCTAGTATCCAGAATATATAAAGAACTCT 1085
                              -------      i  v  v                         
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chr2_232640287_   1086 TACAACTCAACAATAAAAAAGACATATAACTCAATTGAAATATGGGCGAG 1135
                                   i        -    v     i     ?   v      i i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_232640287_   1136 AGACTTGAAGAGACATTTCTCCAAAAAAGATATACAAATGGTCAATAAGT 1185
                         i  i     v               i               i       i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_232640287_   1186 ACACGAAACAACAGATGCTCCCTATCACTAGCCAT 1220
                            i    ----        vvi    ????????
  L1M4_orf2#LINE/    878 ACATGAAA----AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (66 / 34)
Gap_init rate = 0.02 (14 / 703), avg. gap size = 3.36 (47 / 14)  


 567 28.71 9.09 0.48  chr2_232653049_232654946.rev      498   706 (1192)    L1M4_orf2#LINE/L1      288   514 (394)  

  chr2_232653049_    498 ACCTATAGAACAATGGAACAGAACAGAAAACTCAGAAATAAAGCCACACA 547
                           v      v        i    iv  i iii          v   i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_232653049_    548 CCTACAACCATATGATCTTCAACAAACTGACAAAAAACA---AATGGAGA 594
                         ii  iiii  vv    i   i    ivvvi v  i v  ---     i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_232653049_    595 AGGGACTCCCTATTCAATAAATGGTGCTGGGATAACTAACTAGCCACATG 644
                          i i ivvi  v     i              i    iiv  ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_232653049_    645 CAGAAGATATAAAACTGTATA--TATTTCATG--ATATACA-----TAA- 684
                           i    -  i  ii  v iv--  ii   ii--       -----   -
  L1M4_orf2#LINE/    438 CAAAAGA-ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_232653049_    685 ------TGGGTTAAAGATTTAAATGCAA 706
                         ------   i i ?   ii      i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAA 514

Transitions / transversions = 2.41 (41 / 17)
Gap_init rate = 0.03 (6 / 227), avg. gap size = 3.33 (20 / 6)  

 912 24.51 3.88 6.31  chr2_232653049_232654946.rev     1000  1411 (487)    L1M4_orf2#LINE/L1      507   908 (0)  

  chr2_232653049_   1000 AAATAAAAGACCTCAAGCTATAAAAATCCTAGAAGAAAACCCAGG---AA 1046
                             iv    v  v  i        v  i           vi   ---  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr2_232653049_   1047 ATACACTTCTTGACACTGACCTTGGCAA--ATTT-TTGGCTAAGTCCCCA 1093
                           ---    v    vi  ivi v     --i   -  i v  v v v   
  L1M4_orf2#LINE/    557 AT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_232653049_   1094 TAAGCAACTGCAGCAAAAACAAAAATTGACAAGTTGGAACTAATTAAACT 1143
                         v     vvv   i     iv      v  i  i     vi v  i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_232653049_   1144 --AGAGCTTCTGCACAGCAAAAGAAATTATCAACAGATTAAACAGACAAC 1191
                         -- i i   i  ii vv    i  v i      v i v i  v       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_232653049_   1192 CTACAAAATGGGCGAGAATATTCACAAACTATGCATCTGACAAAGGTCCA 1241
                          i   i      v  i      ii    ii  ii      i  i  v iv
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_232653049_   1242 ATATCCAGAATCCCTATGGAACTT----AAATCAACAAGCAAAAAACAAA 1287
                         i          viv  vi     i----  v    i  vv    i     
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_232653049_   1288 TAAGCCCATTTTTAAAAATGGCCAAAGGACATGAA----CACTTCTCAGA 1333
                            -    v  ?-        v       iv    ----  i     vi 
  L1M4_orf2#LINE/    804 TAA-CCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_232653049_   1334 AGAAATACAAAAAGAAAAAACCACGACATACAAGCAGCCAACAAATATAT 1383
                             --------------------  i      iii     i  ii i  
  L1M4_orf2#LINE/    852 AGAA--------------------GATATACAAATGGCCAATAAGCACAT 881

  chr2_232653049_   1384 GGAAAACATGATCATGACTAATTATCAG 1411
                          -    v   v   vv ii ????????
  L1M4_orf2#LINE/    882 G-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (55 / 45)
Gap_init rate = 0.03 (11 / 402), avg. gap size = 3.82 (42 / 11)  


1905 24.59 3.48 0.61  chr2_232691021_232693259.rev      536  1023 (1216)    L1M4_orf2#LINE/L1        1   502 (406)  

  chr2_232691021_    536 TGGAAAGATATCCCATGTTCATGATTGTGGAATACTGTAACAGTGT---- 581
                                                iv -     v   -   i v   ----
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-TGGAAGACT-TAATATTGTTAAG 48

  chr2_232691021_    582 ----CCTTACTACCCAAAGCAATCTACAGATTCAATATAATCTCTACCAA 627
                         ---- vv    v      vii              iii    i   i   
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_232691021_    628 AATTCCA--TGACATTTTTCACAAAAATAGAAAAAGCAATCCTAAAATTC 675
                            i   --  v -     ii  i    v  v  ivii            
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_232691021_    676 ATATAGAATCACAAAAGACCCCAAATAGGCAAAGCAATCTTGAGCAAAAA 725
                             i   vii   ii     vi     v    i         iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_232691021_    726 GAATAAAGCCTGAGGCATCACACTACCTGATCTCAAAATATA--GC---- 769
                            i    iiv    vv       v  ii  i      iv  --i ----
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_232691021_    770 CTACAGTAATCAAAACAGCACAGTACTGGCATCAAAGCAGACACACAGAG 819
                                      i    iiii          v iiii     i i   v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_232691021_    820 CAATGGAACAGAATAGAAAACCCAGAAATAAAAAAGCACATTTACTATCA 869
                                 i     v  i ii           vvvii       ivi   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_232691021_    870 ATTGGCCCTCAA-AAAGATGCCAAGAATACGTAGTGGGGAAAGGACAATC 918
                             iiii  i -  i i        vi ivi i         i i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_232691021_    919 TCTTCAATAAATGGTACCGAGAGAACCGGATTTCTATTTGCAGAAGAATG 968
                          i     i       i i i  v   i    v? i iv    i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_232691021_    969 AAATTAGACACTCATCTCACAACATATACAAAAACCAAGTCAAAATGGAT 1018
                           i  i   v ii i      v            ii  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_232691021_   1019 TAAAG 1023
                         i ?  
  L1M4_orf2#LINE/    498 CAWAG 502

Transitions / transversions = 2.37 (83 / 35)
Gap_init rate = 0.02 (8 / 502), avg. gap size = 2.50 (20 / 8)  

 888 23.75 8.06 6.10  chr2_232691021_232693259.rev     1289  1747 (492)    L1M4_orf2#LINE/L1      441   908 (0)  

  chr2_232691021_   1289 AAGAATAAA-----ACTCC-ATCTCAAAAAAAAAAAAAAAA--AA---AA 1327
                               i  -----  i  - i    v vv v v v     --  ---  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_232691021_   1328 AA-GAATTAAAGATTTAAATGTAAGGCCTGACACTG-AAAACCACTGGGA 1375
                           - i  i ?   ii          iv  i v   i-     ivi i i 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_232691021_   1376 AAAAACATGGAGTTAAATAAAGTTCCATGACATTGA-TCAGGGCAAAGAT 1424
                         i       i i?v     ----i i i    v   i- i   -   v i 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT----CTTCGTGACCTTGGGTTAGG-CAATGGT 585

  chr2_232691021_   1425 TTTTTTTCTTTAAAAATA----CAAAAGCACAGGCAACAAAAGCAAAAAA 1470
                           i  ------ i v  i----          i          -------
  L1M4_orf2#LINE/    586 TTCTT------AGATATGACACCAAAAGCACAAGCAACAAAAG------- 622

  chr2_232691021_   1471 AAAAAAAAAAAAAAAAAGACAAATGGCATTCCACTAAGCTAAGAAGACTC 1520
                         ---------      v   i    v v i i  ii  iv v i  -   i
  L1M4_orf2#LINE/    623 ---------AAAAAATAGATAAATTGGACTTCATCAAAATTAAAA-ACTT 662

  chr2_232691021_   1521 T---GTT---AAGCAAAAAATCAACAGAGCAAAGAGACAAT-----GAAT 1559
                          --- i ---   v v vv     v i  ii  i      i-----    
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_232691021_   1560 GAGAGAATATATTTGCAAACCATACATATAATAG----TTAATATCCAAA 1605
                          i     v           i    i  v i   i----i vi      i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_232691021_   1606 ATGCACAAGGAACTCAAACAA-TCAATTGCAAGAAAACAAATAATCCAAT 1654
                           ii i  i      vv    -     vii  i  i        i     
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr2_232691021_   1655 TTAAAAATGGGAAAAGGACCTAGGTAGACATTTCTC---AAAAGACCCAT 1701
                          ?         v      ii iii            --- i    ivi i
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr2_232691021_   1702 AAATTACCAACAGGTATATGAAAAAATGCTCAATATCACTAATCAT 1747
                             vi    i i i i       i        i    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (74 / 32)
Gap_init rate = 0.04 (19 / 468), avg. gap size = 3.42 (65 / 19)  


2841 27.75 2.94 0.11  chr2_232721976_232728707.rev     5358  6240 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_232721976_   5358 TGGAAAAATATTCCATGCTCATAGATAGGAAGAATCAATATTGTGAAAAT 5407
                               i    i     i    i   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_232721976_   5408 GGCCATAGTGCCCAAAGTAATTTA--GATTCAATGCTATTCCAAGCAAGC 5455
                            v   v v      v i  i  --       i  v  i  v v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_232721976_   5456 TACCATTGACTTTCTTCACAGAATTAGAAAAA---ACTTTAAATTTCATA 5502
                          v   vivi i  i  ii     v v  v  i--- iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_232721976_   5503 TGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAACAA 5552
                              viiv  ii  v  viv        i      i i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_232721976_   5553 TAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5602
                         i    i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_232721976_   5603 CAGTAATAAAAACAGCATGCTACTGGTACCAAAACAGATATATAGACCAA 5652
                                v  i    ii  v      i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_232721976_   5653 TAGGACAGAATATAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5702
                          i i i     vv  ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_232721976_   5703 GATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAC 5752
                            i  i     ivv  v   i v  vv            i  vvi  vi
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_232721976_   5753 TTAATAAATGGTGCTGGGAAAACTAGCTAGCCATATGTAGAAAACTAAAA 5802
                          i  i              v    i v  ?   i   i i  i v i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_232721976_   5803 CTGGACCCCT-----------TATACAAAAATTAACTCAAGATGGATTAA 5841
                         i         -----------                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_232721976_   5842 ATGTTTATATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5891
                          viii  v        v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_232721976_   5892 GCA-ATACCATTCAGGACATAAGCATGGGCAAAGACTGTATGACTAAAAC 5940
                          ?i- v i -   iv   v vi vv i     v ii viv iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr2_232721976_   5941 ACAAAAAGCAATTGCAACAAAAACCAAAATGGACAAATGGGATCTAATTA 5990
                           v       vvv         ivv     i  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr2_232721976_   5991 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAGG 6040
                           v v  i i   i  ii vv    i  v       vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_232721976_   6041 CAACCTACAGAATGGGAAAAAATTTTTGCAATCTATCCATCTGACAAAGG 6090
                              i           i     v       vii  vi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr2_232721976_   6091 GATAATATCCAGAATCTACAAGGAACTTAAACAAAT---TTACAAGAAAA 6137
                         iv vi          v  i  i     ivv    v --- v i  i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr2_232721976_   6138 CAAA----CCA-TCAAAAAGTGGGCAAAGGATATGAACAGACACTTTTCA 6182
                             ----   - i?    i            v    i     i  i  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_232721976_   6183 AAAGAAGACATTTATGTGGCCAACAGACATATAAAAAAAGG-TCATCAAC 6231
                                 i  vi vi       i ii  i  i    i v -   v  v 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr2_232721976_   6232 ACTGGTCAT 6240
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.00 (27 / 9)  


1790 26.15 4.07 3.06  chr2_232744362_232747399     1354  1942 (1096)    L1M4_orf2#LINE/L1       15   609 (299)  

  chr2_232744362_   1354 ATGGTCATGGACTGTAAAATTCATTATGGTAAAAATATTAATTCTTCCCA 1403
                            v       i  v  i i i v   v  v  i  ivi   v  i    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr2_232744362_   1404 AATTGATTGCTGCA--TTTAACAGAATCCAAGCCAACATTCCAGCAATCG 1451
                                --  i  --  i   iv     vvii   v  i     vii v
  L1M4_orf2#LINE/     65 AATTGAT--CTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr2_232744362_   1452 TTGTTGTGTGTGTGTGGAAAGTAACAAGCTGATTTTAAAAAT-AGATGGC 1500
                           -  -------  ii    v i          ii     v - v    v
  L1M4_orf2#LINE/    113 TT-TT-------TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_232744362_   1501 AATGTGAAGGACC-AAAATAACCAAGACAATTTTGAA------GTACAAA 1543
                             ii i     - i    i    i     i     ------ v     
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_232744362_   1544 GCTGGAGTTCTTAAACTGCCCAACATCAAGACTTACCATAAGTGAGC-AC 1592
                          i     vv  i v   v     iv    i      i i  ---   -  
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA---AGCTAC 251

  chr2_232744362_   1593 AGTTA-CAA--TAGTTTGGTATTTAGTATAAGGAGAGACACATAAGCTAG 1639
                            v -   --i   v     i -i i       v     i   iiii i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACT-GGCATAAGGATAGACATATAGATCAA 300

  chr2_232744362_   1640 TG-AATGGGATAGAAAGTCCAGAAATAGACTCATA----TATGGTCACTT 1684
                           -   i i  v  i            i  i    ----        v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_232744362_   1685 GATTAT-GATAAAGGGAACAGTGCACTGCAGTGGAGGAAAGAATGCTCTT 1733
                             v -  i  i  viv  ivi vv v  i   -         iv    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTT 399

  chr2_232744362_   1734 TTCAACAAGTGGTGCAAGGCTGATTGGCTACCCACTTGGAGAAAAAGGAT 1783
                                 i      vi  vii i   v  ?    v  v i  i  v  v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_232744362_   1784 GTTG-ACCTTTATTTCATACCATGCACAAAAATCAATTCTAGGTAGATAA 1832
                             -   ii  ii   i     ii        i  i  v ii i   v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_232744362_   1833 AATAACTAAATGTGAAAGGTAGAACAGTAAAGCTTTTCAAGGAAAACATA 1882
                         ? v v        i i  v  i   vi    i  i  vi i         
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_232744362_   1883 ATACCATATTTTCATGACTTTAGG---GGCACCAAAAATTTCTTAAACAG 1929
                         iv?vi v  i   i    i  i  ---    --- vii       i i v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCA---ATGGTTTCTTAGATAT 596

  chr2_232744362_   1930 GACACAAAAAATA 1942
                              v    ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCA 609

Transitions / transversions = 1.70 (95 / 56)
Gap_init rate = 0.03 (19 / 595), avg. gap size = 2.21 (42 / 19)  

 546 26.17 7.05 3.36  chr2_232744362_232747399     2253  2550 (488)    L1M4_orf2#LINE/L1      600   908 (0)  

  chr2_232744362_   2253 ACAAAAAACAGTAACCATGAAGGAGAAAAATTAATAGATTGGAGTACATT 2302
                           v    i  vv i v ii  i  -      vi   i      v v   i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATC 648

  chr2_232744362_   2303 AAAG-----AACT------CTTCAAAA-ATACCACAAGGAAAGTAAATAT 2340
                            i-----    ------       i- i  i iv i      i  v v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_232744362_   2341 -TAATCTGCACAGTGGGAGAAGATGTATGCAACCAGAT-ATATATTCAAC 2388
                         -i  i ii  v i        i  i v     ----  -      iii i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAA----ATCATATATCTGAT 744

  chr2_232744362_   2389 AAACGACTCCTAACTAGAATTTATAAAGAATTCCC-TGACATAATTGAGA 2437
                           iv    iv  v i     v         i  ii-ii  vi   -- iv
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT--AAT 792

  chr2_232744362_   2438 AAAAAAACAGACAACA-AATAGAAAAATGGGAGAATGACTGATACAGGC- 2485
                              i   i i   v-   v?         vi  v  i viv i  i -
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_232744362_   2486 --TCTTCACAAAAAGCTATCCAAATGGCCAAT--GCACTTAGGAAAAGAT 2531
                         --   i  -  i   v   v            --    -- v        
  L1M4_orf2#LINE/    843 TTTCTCCA-AAGAAGATATACAAATGGCCAATAAGCAC--ATGAAAAGAT 889

  chr2_232744362_   2532 TCTCAGCTTTATCAGTTAT 2550
                         v    i v i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (48 / 29)
Gap_init rate = 0.05 (14 / 309), avg. gap size = 2.21 (31 / 14)  


 917 27.27 0.41 0.00  chr2_232797417_232800827     1721  1962 (1449)    L1M4_orf2#LINE/L1        2   244 (664)  

  chr2_232797417_   1721 GGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATATTGTGAAAATG 1770
                              i i  i     i               v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_232797417_   1771 ACCATACTGCCCAAAACAATTTTTAGATTAAATGCTATTCCCATTAAACT 1820
                         i v     v      vii  i vi     v  i  v  i  i  i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_232797417_   1821 ACCATTGACATTCTTCACAGAATTAGAAAAACT-ATTTTAAAATTCATAT 1869
                         v   vivi v  i  ii     v v  v  i  -  ii            
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_232797417_   1870 GGAACCACAAAAGTGCCTGAATAGCCAAGGCGATCCCAAGCAAAAAGAAC 1919
                             vii   ii vv  v          ii i   iii iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_232797417_   1920 AAAGCTGGAGGCATCACCCTACCCAACTTTAAACTATACTACA 1962
                             i      vv    v  v     i  i   viv       
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

Transitions / transversions = 1.44 (39 / 27)
Gap_init rate = 0.00 (1 / 243), avg. gap size = 1.00 (1 / 1)  

2086 25.08 6.07 0.78  chr2_232797417_232800827     2278  2919 (492)    L1M4_orf2#LINE/L1      233   908 (0)  

  chr2_232797417_   2278 AAACTGTACTACAGTGATTCAGTAACCAAAACAGCATGGTATTGGTACAA 2327
                              -       iv v v      i   i    ii     i   i i  
  L1M4_orf2#LINE/    233 AAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_232797417_   2328 G-------ACACAGACCAATGGACCAGAGTAGAGAACCCAGAAATAAGAT 2370
                          ------- i i   i       vi   i v    ii          ivi
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_232797417_   2371 TGTACATCTACAGCCATCTGATCTTTGACAAACCTGACAAAATAAG-CAA 2419
                         ii     i  ii i  vi    i  i     ivv  v   i iv v-   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_232797417_   2420 GGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAGAACTGG----- 2464
                         v        i  vvi  v  i  i              v      -----
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_232797417_   2465 ------CAGAAAATTGAAATTGGGCCCCTTCCTTACACTATATACACAAA 2508
                         ------  i  i v    i    i     v   i    i       v   
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr2_232797417_   2509 TCAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCTAAACTATAAAA 2558
                          i       i      i ?    i         i v iv           
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr2_232797417_   2559 GACCTAGAAGAAATCCTAGACA-ATACCATTCAGGATATAGG--TACCAG 2605
                         vv i         v v   i?i- v i -   iv  iv v  --  --i 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTA--GG 578

  chr2_232797417_   2606 CAATGATTTCATGAA---GACACCAAAAGCAATTGCAACAAAAGCAAAAA 2652
                              i    v ii ---             vvv          v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr2_232797417_   2653 TTGACAAATGGTATCT------AATTAAAGAGCTTCTGCATAGCAAAAGA 2696
                          v  i    v v ii ------       i -   i  iiivv    i  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

  chr2_232797417_   2697 AACTACCAACAGAGTAAACAGACAACCTACAGAATGGGAGAAA-TGTTTG 2745
                         v    i   v i   i  v        i               - i    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr2_232797417_   2746 CAAACTATCCATCTGACAAAAGTCTAATATTTAGCATCTATAAGGAATTT 2795
                             ii  vi      i  ii v  vi   ii  v  v     i   i i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_232797417_   2796 AAACAAAT---TTACAAGAAAACACAT--CCCCATTAAAAAGTAGGCAAA 2840
                         vv    v --- v i  i  i   v  --   v   ?    i i      
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_232797417_   2841 GGACGTGAACAGACCCTTCTCAAAAGAAGACATGCATGTGGCCAACA--T 2888
                            iv    i    vi     v        i  i  vi       i --i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_232797417_   2889 TTGTAAAAAAAAGCTCAACATCATTAATCAT 2919
                         vii i    i v           ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (98 / 60)
Gap_init rate = 0.02 (15 / 676), avg. gap size = 2.93 (44 / 15)  


3233 27.09 0.44 0.44  chr2_232839663_232844864.rev     3803  4710 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_232839663_   3803 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3852
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_232839663_   3853 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3902
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_232839663_   3903 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3950
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_232839663_   3951 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4000
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_232839663_   4001 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4050
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_232839663_   4051 TACAGTAACCAAAACAGCACGCTACTGGTACCAAAACAGAGATATAGATC 4100
                                 i   i    iii v      i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_232839663_   4101 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCTTACCTACAACT 4148
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_232839663_   4149 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4198
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_232839663_   4199 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 4248
                           v  i  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_232839663_   4249 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4298
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_232839663_   4299 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4348
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_232839663_   4349 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 4398
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_232839663_   4399 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4448
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_232839663_   4449 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4498
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_232839663_   4499 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 4548
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_232839663_   4549 AGGGCTAATATCCAGAATCTACAATTAACTCAAACAAATTTACAAGAAAA 4598
                         i  i  vi          v  i  vv     vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_232839663_   4599 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 4648
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_232839663_   4649 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 4698
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_232839663_   4699 ATCACTGGCCAT 4710
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3233 27.09 0.44 0.44  chr2_232862592_232872327.rev     3655  4562 (5174)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_232862592_   3655 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3704
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_232862592_   3705 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3754
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_232862592_   3755 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3802
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_232862592_   3803 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3852
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_232862592_   3853 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3902
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_232862592_   3903 TACAGTAACCAAAACAGCACGCTACTGGTACCAAAACAGAGATATAGATC 3952
                                 i   i    iii v      i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_232862592_   3953 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCTTACCTACAACT 4000
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_232862592_   4001 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4050
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_232862592_   4051 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 4100
                           v  i  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_232862592_   4101 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4150
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_232862592_   4151 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4200
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_232862592_   4201 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 4250
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_232862592_   4251 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4300
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_232862592_   4301 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4350
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_232862592_   4351 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 4400
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_232862592_   4401 AGGGCTAATATCCAGAATCTACAATTAACTCAAACAAATTTACAAGAAAA 4450
                         i  i  vi          v  i  vv     vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_232862592_   4451 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 4500
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_232862592_   4501 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 4550
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_232862592_   4551 ATCACTGGCCAT 4562
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

3021 11.47 1.47 27.11  chr2_232862592_232872327.rev     8030  9250 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_232862592_   8030 TGGACAGACATCCCATGTTCATAGGTTGGAAGACTTAACAGTGTTAAGAT 8079
                             v   i             i i             i v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_232862592_   8080 GGAAATGCTCCCCAAACTGATCTACAGACTCAGAGCAATTCTTATGAAAA 8129
                           v   i         i           i   iv     i i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_232862592_   8130 TCCTGAGTGCCTCCT-----GAAATTGACAAGCTGATCCTAAAATATATA 8174
                            iiiv     ii -----                         vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_232862592_   8175 TGGCAATGCAAAGAACCCAGAATAGTAGAAA-AATCTGAAAGAAAAAAAA 8223
                            v       i i           ivi   -     vi  i  i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_232862592_   8224 GCAAAGTTGGAAGAATCACACTTCTCAATTTCAAAACTTACTACAAAGTT 8273
                         -          i  v         i                       i 
  L1M4_orf2#LINE/    201 -CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_232862592_   8274 ACAATAATTTAGACAGTGTGGTACTGGCATAAAGACAAATATACAGATCA 8323
                            i    iv                      i  i i i   i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_232862592_   8324 ATGGAACAGAATTGAGAGTCCAGAAATAAACCAATACATTTATGGTCAAA 8373
                               i                         v                v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_232862592_   8374 TAATTTTTGACAAGAAATGCCAAGACAATTTCATGAAGAAAGAATCATCT 8423
                          i     i      ii-         v   iv   ii        vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_232862592_   8424 TGTCAACAAGTTTTTCTTATGGTGCTGAAACAACTGGTTATCCACAAGCA 8473
                          v       ---------         ii        v  ?     v   
  L1M4_orf2#LINE/    399 TTTCAACAA---------ATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_232862592_   8474 AAAAAATGAAGTTTGACCCATACCTCACACCATTTACAAAGATTAACTAA 8523
                            i         v     v             v      i       v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_232862592_   8524 AAATGGATCATAAATATAACAACTAACAGTATAAAGTTCATAGAAGAAAA 8573
                                   ? i i-------    ------------------------
  L1M4_orf2#LINE/    490 AAATGGATCAWAGAC-------CTAA------------------------ 508

  chr2_232862592_   8574 CTTATGTTGGCCAGGCACGGTGGCTCATGCCTATGATCCCAGCACTTTGG 8623
                         ---    -------------------------------------------
  L1M4_orf2#LINE/    509 ---ATGT------------------------------------------- 512

  chr2_232862592_   8624 GAGGCTGAGGCTGGTGGATCACTTGAGGTCAGGAGTTGGAGACCAGCCTG 8673
                         ------------------------------ i   i -------------
  L1M4_orf2#LINE/    513 ------------------------------AAGAGCT------------- 519

  chr2_232862592_   8674 CCCAGCATAGCAAAACCCCATCTCTATAAAAACACAAAAAAATTGGCAGG 8723
                         -----------     --------       -------------------
  L1M4_orf2#LINE/    520 -----------AAAAC--------TATAAAA------------------- 531

  chr2_232862592_   8724 GTGTGGTGATGGGTGCCTGCACTCCCAGCTACTTGGGAGGCTGAGGCAGG 8773
                         ---------------------   ii  ----------------------
  L1M4_orf2#LINE/    532 ---------------------CTCTTAG---------------------- 538

  chr2_232862592_   8774 AGAATCGCTTGAACCAGGGAGGCAGAGGTTGCAGCTGAGCTCGCACTACT 8823
                         --------------------------------------------------
  L1M4_orf2#LINE/    539 -------------------------------------------------- 538

  chr2_232862592_   8824 GCACTCCAGCCTGGATAACAGAGACGCCATCTCAAAACAAACAAACAAAA 8873
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    539 -------------------------------------------------A 539

  chr2_232862592_   8874 AGAAAACATATGTCTAACTCTTTGTGATCTTCGC-----CAATGGTTTTT 8918
                                   v ?v   v    i    i   v v-----         i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr2_232862592_   8919 ATAGATATGACACCAAAAACACAAGCAACCAAAGAAAAAACAGACTAAAC 8968
                         -                 i          v          i   -    i
  L1M4_orf2#LINE/    590 -TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA-TAAAT 637

  chr2_232862592_   8969 GGGTCTTCATCAAATTTTGAAACTTT-GTGCTTCTAAGAACACCATCAAG 9017
                         v  v          v  vi       -       v   i    i      
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_232862592_   9018 AAAGTGCAAGATAGCCAGCCCACA-AGTAGGAGAAAATATCTGCAAATCA 9066
                               v  ---  v  i      - i i           i         
  L1M4_orf2#LINE/    688 AAAGTGAAA---AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_232862592_   9067 TATATCTGATAAATGACCAGTGTTTGGAATACAGAAACTACACTTATAGC 9116
                                     iv   iv  i iii     i v   vv  v    i i 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_232862592_   9117 TCAACAATAGAAAGGCAA----TCCATTTTAAAAATGG-CAAAGGATCTG 9161
                             i    i    i   ----i   v  ?        -        i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_232862592_   9162 AATAGATACTATCTGAGTAGATTTTTCTTCAAAGAAAATATACAAATGAC 9211
                               i ---------------     i       i           i 
  L1M4_orf2#LINE/    835 AATAGACA---------------TTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_232862592_   9212 CAATAAGCACATCAAAATACATTCAGTCTCATTAGTCAT 9250
                                     v    v iii   iiv   ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (89 / 47)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 16.62 (349 / 21)  


1694 26.30 5.70 3.52  chr2_232878104_232879692      501  1097 (492)    L1M4_orf2#LINE/L1      299   908 (0)  

  chr2_232878104_    501 AACAGAACAGAATAGAGAATCCAGAATTAGATCCACACAAATATGCCTGA 550
                           ii   i     v    i       v  i i   i   vv    viii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_232878104_    551 CTGATTTTTAACAGAGGAGCAAACGCAGTTCAATGTAGGAAGGATAGCCT 600
                         i       ii   ii  v  v  vi vi       vi i   i    i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_232878104_    601 TT-CATAAAATGGCATTAGAGGAATTTGCCATACATAGGCAAATAAATGA 649
                           -  vv      iii i iiv  i v vi ?v  i v     vi     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_232878104_    650 ACTTCGATCTAAACCTCATGCCTTATGCAAAAGTTAACTCAAAATGGGTC 699
                          v  v  i ivv      ii  v   i     i              i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_232878104_    700 ATGGGCTTAAGTATAAAATGTAAAAGTATAAAACTTAATAGAAATGAGCA 749
                          ?i i i   i i   i vv     v         iv-     ivi i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAACA 547

  chr2_232878104_    750 TAGAAGAGTA---CTTACAGGATGTAGGACTAGAGAAAGAGTTCTTAGAC 796
                            -- ?   ---   - iv  iv v  ii   iv  v iv        -
  L1M4_orf2#LINE/    548 TAG--GNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGA- 593

  chr2_232878104_    797 TTTGACAT----AGTACAGTCCACAGAAGAAGAGGTTGGTAAATTGGATC 842
                          v     i----  i   iv v   i     i ii v i         ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_232878104_    843 TCATCAGAATTAAAAACTTTCTGT-CTATGAAAGATGCTGTTAAGAAAAG 891
                               i             -   -  vii  i  ii  i i      iv
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_232878104_    892 AAAAAGATGAGCTGCAGAAAATTCTTTCTGCAGCTGGGAGAAAATATTTG 941
                         i      ii v ii     ---------------                
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAA---------------TGGGAGAAAATATTTG 727

  chr2_232878104_    942 TAAACCACATATCCAACAAGAGACTAGTATCTAGAGTACGTAAAGAACCT 991
                         i   i  i     ii i   i    v     i   i  ii        ii
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr2_232878104_    992 TTAAAACC---------AAAG-----CAATCCAATTAGAAAATGGACAGA 1027
                            v   i---------    -----i  i      ?i       i  i 
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr2_232878104_   1028 AGAC----ATA--CA-----CTGAAGAGGATATACAAATGGAAAACAAGC 1066
                         i  i----   --  ----- ii    i             vv  i    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr2_232878104_   1067 AAATTAAAAAATGTTTAACATCACGACCCAT 1097
                          v  v    i   i i       ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.26 (106 / 47)
Gap_init rate = 0.02 (15 / 610), avg. gap size = 3.67 (55 / 15)  


1664 26.56 17.32 2.34  chr2_233001694_233003903.rev      943  1710 (500)    L1M4_orf2#LINE/L1        1   883 (25)  

  chr2_233001694_    943 TAGAGGGAGGTACCATGTTTGTG------AAGACTCATTATCATAAAAGT 986
                          i  ii  vi v       ii  ------      i v   ii v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_233001694_    987 GTTGATTTTTCCCAAATTGACATATGGATTCAAAGCAATCTCAATATAAA 1036
                          vii  vi i          iv  ii       v      i v  vv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_233001694_   1037 TCCTAGCAAGTTTGTGTGCATGTATGTGGCAACTGACAATCTGATTCTAA 1086
                            i   vivi  v v    -------- v  i      v     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA--------GAAATTGACAAGCTGATCCTAA 142

  chr2_233001694_   1087 AATCTATATGGAAATGGAATGGGCCAAGAATAGCATAGGTGCTCTTTATA 1136
                            ii           v  v  i  v        vv iiiiv    v v 
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr2_233001694_   1137 GAAAAAGTCCAAGTTGGAAAGTGTAGCTC-TACTGGCTA---TCAAGATT 1182
                         i i  iiv v        iii-----   -i   vv i ---    i i 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGA-----CTCACACTTCCCAATTTCAAAACT 237

  chr2_233001694_   1183 T-TTA------TACAAACATGAAGGTAGTGTGGTACTGGTACAAGAATAG 1225
                          -i  ------    ivv  v   ii             i i   i    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr2_233001694_   1226 ATATATAAACCAGTGACACAGAATGGAGAG--CAGAAACAGATCTGTGCA 1273
                          i     i i  i  iv i     v     --      i i i ii i  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr2_233001694_   1274 T--ATGGGTACTTCATTTTTGACAAAGGTGGCAGTGCTAAGCTATGGGAA 1321
                          --    vi v  v     i     i    v  ivi i vv v     i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr2_233001694_   1322 A------GTATTTTCAAAAAATGATGCTGGGTCAAC-AGATACCCATATG 1364
                          ------  v       v     i       v    -i    ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr2_233001694_   1365 --AAAAAATAAACTTG-----CTGT-----ACCATTTTCAAAAATCAATT 1402
                         --   i   i  v   -----  ii-----     v v       i  i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_233001694_   1403 CTAAGTAGATT---------------------------------CTTTTA 1419
                          v  i i   i---------------------------------  i   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_233001694_   1420 GAA-------TA-------------------------TAGACAAAGATTT 1437
                            -------  -------------------------   i   v i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_233001694_   1438 CTTAAATGGTATACAAAAAGCATTTAACCATAATAAAAAAGATCGACATA 1487
                             i  ivv i  v       iv- i v i  v i    i  v  i v 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAA 636

  chr2_233001694_   1488 CTGAACTCCATTAAAATTAAGTACTTCTGTACGTTAAAATAACACCA--G 1535
                         i  i   i   i        iv    i   i v i   i-i    i --i
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCA 685

  chr2_233001694_   1536 AGGCAGTAAAAAAGCAAACTACACAGTGGAAGA---TATTTGCAA--CAT 1580
                           iv   i    ii   v i   v i   i   ---         --   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_233001694_   1581 GTATAAGCAACAAAGAACTGATATCCAGAATATA--GAGGACT---ATAA 1625
                         i   vv -- i  i i   vi             --i  i   --- i  
  L1M4_orf2#LINE/    736 ATATCTG--ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_233001694_   1626 ATCAAGAAGAAAAA--CAGAAAACCCAGTAGAAAAACAGGCAAGAAATTT 1673
                         v    v  v     --  i v      i v?     ii     iii    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_233001694_   1674 GAAAAGGCA---CTC-----------TACTGAATGGCCAATAAACAGATG 1709
                            v  i  ---   -----------   -i            i  v   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATAC-AAATGGCCAATAAGCACATG 882

  chr2_233001694_   1710 A 1710
                          
  L1M4_orf2#LINE/    883 A 883

Transitions / transversions = 1.77 (129 / 73)
Gap_init rate = 0.03 (29 / 883), avg. gap size = 5.21 (151 / 29)  


3037 26.53 2.01 0.78  chr2_233044954_233051212     4871  5767 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_233044954_   4871 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4920
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_233044954_   4921 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCAATCAAGC 4970
                            v     v     iv i  i           i  v     v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_233044954_   4971 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5018
                          v i iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_233044954_   5019 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5068
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_233044954_   5069 AACAAAGCTACAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5118
                                i iv   vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_233044954_   5119 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5168
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_233044954_   5169 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCTTAC--CTACAA 5214
                                i    i--    i  --        -   - v   --i  iii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAA-ACC-CATACATTTATGG 344

  chr2_233044954_   5215 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5264
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_233044954_   5265 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5314
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_233044954_   5315 CTGAAACTTGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5364
                         v    ii v  i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_233044954_   5365 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5414
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_233044954_   5415 ACCTAGGCATTACCATTCAGGGCATAGGCATGGGCAAGGACTTCATGTCT 5464
                           v    ?i v viv   iv i v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_233044954_   5465 AAAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCT 5514
                          vi            vvi     v    vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_233044954_   5515 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG--- 5561
                         v  i   v v  i i   i  ii vv    i  v    i  vv i  ---
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_233044954_   5562 -----CAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5606
                         -----     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_233044954_   5607 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5656
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_233044954_   5657 AAAAAACAAACAACCCCATCAAAAAGTGGGC----GACATGAACAGACAC 5702
                            i -    i     v  i?    i     ----  iv    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_233044954_   5703 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5752
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_233044954_   5753 ACCATCACTGGCCAT 5767
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.27 (25 / 11)  


3298 18.09 2.10 1.40  chr2_233489593_233491293.rev      499  1211 (490)    L1M4_orf2#LINE/L1      191   908 (0)  

  chr2_233489593_    499 AAAAGAAAAACAAAGCTGGAGGACTCACATTTCCTGATTTCAAAATTTAT 548
                                i       i             i    ii         i   i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_233489593_    549 TGCAAAGATAGAGTAATCAAAACAGTGTAATGCCAATATAAAGACAGACA 598
                          i     v  v         i       ii i iiii    i  i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_233489593_    599 TATAGAACAATAAAATAGAACAGAGGGCCCCAAAATGAACCAGAGTACAT 648
                               v    ii       iv   i i  vi    i    vi--     
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACAT 338

  chr2_233489593_    649 ----GGTCAAAT-ATTTT-GAAAAGGATGCCAAGACTATTCGATGGAAAA 692
                         ----      v -     -  v    i         i    i    ii  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_233489593_    693 AGGACAGTCATTTTAACAAACGGTATTTGGAAAATTGGATATCCACATGC 742
                           i i    v   i      i   ii v   v  i      ?        
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_233489593_    743 AAAAGAATGAAATTGGATTCTTGCCTAACACCATACTCAAAAA----CTC 788
                                    i     ii i i   v        iv      ----   
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_233489593_    789 AAAATGGATCAAAGATCTAAGTGCATGACCTAAATCTGTAAAACTCTCAG 838
                                    ?   i    i  i v  v     v  i         i  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_233489593_    839 AAGAAAACACAGG-GCAAATGCTTTATATAACATTGGATACAATAATGAT 887
                                  i   - i    -   ii i--  v    i vviii    i 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT-CTTCGTG--ACCTTGGGTTAGGCAATGGT 585

  chr2_233489593_    888 TTCTAGGATATGACACCAAAGGCATAGGCAACAAA-GCAAAAATAGACAA 936
                             vi              i   i i        - v         i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_233489593_    937 ATTGGACTTCTTGAAAATTAAAAAAAAAAAAGTGCATGACAAGACATTAT 986
                                   v v           vvvvv--    v v v i    i   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTT--GTGCTTCAAAGGACACTAT 683

  chr2_233489593_    987 CAGCAGAGTAAAAAGGCAACCCAAAGAATGGGAGAAAATATTTACAAATC 1036
                           iv i   i     i       v                   i      
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_233489593_   1037 ATATATCTTATAAGGGATTAGCATCCAGAATATATAGAGAACT---AAAA 1083
                                 v        i v i              i      --- v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_233489593_   1084 CTCAGCAACAAAAAAATTAACAACCCAATTAAAAAAAAAAAGGCAAAGGA 1133
                             ii  i     i iv  i         ?     vi---         
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG---GGCAAAGGA 830

  chr2_233489593_   1134 CTTGAATAGACATTTCACCAAAGAAGGTATACAAATGGCTAATAAGCACA 1183
                         i               v         i            i          
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_233489593_   1184 TGAAAAGATGCTTAACATTCCTTATGAT 1211
                                     i     iv????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (86 / 40)
Gap_init rate = 0.02 (12 / 718), avg. gap size = 2.08 (25 / 12)  


3222 22.72 1.54 3.51  chr2_233600485_233604281.rev     2427  3337 (460)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr2_233600485_   2427 TGTTTATGGATTGAAAGATTCAATATAGTAAAGATGTTAATTCTCTTCCC 2476
                             i        i    i i     v  v      vi   v   --   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC--CCC 63

  chr2_233600485_   2477 ATATTTATCTATACATTCCATGCGACTCCAGTCAAAATCCCAGC---ATT 2523
                          v   v     i v    v i  i ii  vi             ---v  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr2_233600485_   2524 TTCTGTGGTCATAGACAAAATTATCCTAAAATTTATCAGAAAAGGCAAGA 2573
                           i  ii vv  v     iv v           i  vv i   v     i
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chr2_233600485_   2574 TAACTAGAATAGCCCTGAACAGTTTTCAAAAATAA---TAAAGCTGGAGG 2620
                         v v i         v-i    i i  v     v  ---i    i      
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCA-AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr2_233600485_   2621 AGTCATACTATCTGATTTTAAGACA-ACTAAAAAGTTTACAGTAATCAAG 2669
                          v   i   vi ii    i  i  v-    v    i -            
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT-ACAGTAATCAAG 261

  chr2_233600485_   2670 GCAGTGGGGGTATT--CATGAAATTACAGACACATAGATCAGTGGAACAG 2717
                         i     v  -  i --   i ii-- i     i        i     i  
  L1M4_orf2#LINE/    262 ACAGTGTGG-TACTGGCATAAGG--ATAGACATATAGATCAATGGAATAG 308

  chr2_233600485_   2718 AAAAGAAAATTCAGAAATAAACCCACAACAAGTATGGTTGATTGATATTT 2767
                           vv  i i i              i -  vv      ii      v  i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGTCAATTGATTTTC 357

  chr2_233600485_   2768 GGCAAAACAACAAAAGCAAATTAATGGAAAAAGGACAGTCTTTTCAACAA 2817
                          i   iivvi v  ii v v i     ii    i i              
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_233600485_   2818 ATATTGAACATTGATGCTGGAACCATTGGATATATATATGCAAAAACATT 2867
                           ---------- i      i  v i      ?vi i        iv  v
  L1M4_orf2#LINE/    408 AT----------GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_233600485_   2868 AACCTCAACCTAAACCTCATGCCTCATAACAAAAATTAACTCAAAATGGA 2917
                           vi vi   ivv      ii  vi   -                     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATA-CAAAAATTAACTCAAAATGGA 496

  chr2_233600485_   2918 TCATGGATCTAAATGTAAAATGAAAAACTTTAAAACTTTTAGAGGAAAAC 2967
                            ?i  i          i vvv      v       i     i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_233600485_   2968 ATAGGAGAAAACCTTCATTACCTGAGGTTAG-CAAAGAGTTCTCAGATAC 3016
                              ? v   i    i v    vi      -   v iv    i     i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_233600485_   3017 AACACCAAAACCAATCATGCA-TAAACAAAAAAATGGATCAGTTGGTCTT 3065
                         i         v  --  v   -i   vi       i   v i    v   
  L1M4_orf2#LINE/    597 GACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_233600485_   3066 GATCAGAGTTTAAAACTTCTGCTCTGCAAAAGACACAGTTAAGAGAATGA 3115
                         v    i i  v       i  iv  v    i     vi i    i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_233600485_   3116 AAAGAGAAGCTACAGATGGGGAGGAAATATTTGCAAATTACTTAACTGAT 3165
                              v  v i     vv     i              i iv  v     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_233600485_   3166 AAAGGACTTGCATCCGGAATACACAATAGAACTC--AAAACTCAACAGTA 3213
                           i       i    i     i i  -       -- v       i i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAA-AGAACTCTTACAACTCAATAATA 793

  chr2_233600485_   3214 AAAAAACAA-CAGTCCAATTTAAAAATGGTCAAAAGACTTAAATAGATAC 3262
                             i    -i ii      ?        v    i  i  i      i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_233600485_   3263 TTCACCAAAGCAGATATACAGAAGGCAAGAAAGTAATACACACTTGCTTA 3312
                            v      v         i v   -------i    vi   v  --- 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGC-------CAATAAGCACATG---A 883

  chr2_233600485_   3313 AAAAAGCTTTAAAATCATGGCAGTC 3337
                            i vvi i  v    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (121 / 82)
Gap_init rate = 0.02 (20 / 893), avg. gap size = 2.30 (46 / 20)  


1564 26.92 13.11 1.75  chr2_233651956_233654717     1212  1783 (979)    L1M4_orf2#LINE/L1       43   679 (229)  

  chr2_233651956_   1212 GTTAACGTATGCATTAAACCTGAAATTTATCTGTAGAGACAATGCAATTT 1261
                              vi i-   v  vv  iv     v    ii   vv   i     ii
  L1M4_orf2#LINE/     43 GTTAAGATG-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chr2_233651956_   1262 CAACTGAAATTCTAGCTGAATTTTTTTTGGTAGAAATTGACAAACCGATT 1311
                          v iii    i i     --ii       -i            i i   i
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTG--CCTTTTTTG-CAGAAATTGACAAGCTGATC 138

  chr2_233651956_   1312 CCAAAATTTGTACAGAAATGCAAAAGATTTAAAATAGTCAAGACTATATT 1361
                          i      ii  ii         ii  iii i     i   i  v  v  
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chr2_233651956_   1362 TAA---TAAGAACAAAGTAGGAGGGTTTACACTACCAGATTTTAAGATTA 1408
                         v  ---v           v     ii i     v  vi    i  i i v
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr2_233651956_   1409 AGCATAAAGCAACAGTATTTAAGACACTATGGTAGTGGCATAAAGATAGA 1458
                          vi i     v      v i      v i     v        i      
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_233651956_   1459 AAATTAGATCAATGAAACAGAAT-AAAAGTTCAGAAATAGACCCACATGT 1507
                         v vv          i  i     -i i   i        i     i ii 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_233651956_   1508 CTACGGTCATTGGACTTTTGAAAAAAGTACCAATGCAGCTCTTTGATGGA 1557
                         i  i     v v  i   i  v  ii  i    ---ii iv  ii    i
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAA---GACCATTCAATGGG 385

  chr2_233651956_   1558 -ACAGAA-AACTTTCTCAATAAACAGTGCAAGAGCAACTAGA-------- 1597
                         - v    - iii  i    i   ii    vi ii     i  --------
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_233651956_   1598 ------------------GATC--------------TATA---------- 1605
                         ------------------  i --------------    ----------
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_233651956_   1606 -------TGGACCATAGACCCAAATGTGAAAATGAAGAGTCTAAAACTTC 1648
                         -------    i  ?     i      i i iiv  i v v       ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_233651956_   1649 TATAAGAAAACGTAGCAGAGTA--TCTTCATGACTTCAAAGTGGTCTACT 1696
                           v        i   -- ?   --     i    i iiiiv i v v iv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAG--GNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_233651956_   1697 ATTTCTTAGGATAT------AAAAGGACAAACAATAAAA----AAATTTC 1736
                         i        -    ------     v    i   i    ----    vvv
  L1M4_orf2#LINE/    584 GTTTCTTAG-ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_233651956_   1737 TAACTTAGTCTTCATCAAAATTAAAAATTTCTGCTCATTAAAAGACA 1783
                            v  i v                  i  i  iv v i   i    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

Transitions / transversions = 2.23 (105 / 47)
Gap_init rate = 0.03 (16 / 637), avg. gap size = 5.31 (85 / 16)  

 507 24.29 12.86 1.90  chr2_233651956_233654717     2062  2271 (491)    L1M4_orf2#LINE/L1      676   908 (0)  

  chr2_233651956_   2062 GACTCCATCTCAAAAAAAAAGACAAG-TAAGTCACAGGCCAGTAGAAAAT 2110
                            v i   ---  i   iv  v   -i  vi     ivii v       
  L1M4_orf2#LINE/    676 GACACTATC---AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_233651956_   2111 ATTTACAGTACACATATGTGAGCAAAGACTTGTGTTCAAGATATATAGAG 2160
                             i  ivv  i    v   vv ii       i i  ii       i  
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_233651956_   2161 AACTCCTACAAATTAAAAATATAATAAAAAATAA---------AAAATGG 2201
                              i     v i  v    v  vi v      ---------       
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_233651956_   2202 TTAG-GCATCTTAAACAGGCA-----CCA-----------TGAATGGCCA 2234
                         vi i- v  -  i  i  i  -----   -----------ii        
  L1M4_orf2#LINE/    823 GCAAAGGAT-TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_233651956_   2235 ATAAACATATGAAAAGGTGTTCAACATCCTTAGTTAT 2271
                             i  i        i  i        v????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.03 (7 / 233), avg. gap size = 4.43 (31 / 7)  


 666 31.60 13.15 3.62  chr2_233786375_233788102.rev      408  1236 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_233786375_    408 TGGAGAGAGAAACCATGATCTCAAATTGAAGGACTTGATGTTAT-AAGAA 456
                             i   v vv     v  viii    i i     i  i  i -    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_233786375_    457 CATAAGTTATTTAT-AAATTAACCTATTAATTACATGTAATTGC-A-CAA 503
                         vii  --  i ivi-     i i   ivi   vv i i   iv - -   
  L1M4_orf2#LINE/     51 GGCAA--TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_233786375_    504 AATTCTAACTGGGATTTTTTCAGAGAACTTGACAAGCTGATTTTAAAAAT 553
                            i i i   v--i     iiv    v             ii     v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_233786375_    554 CACCTGGAAA----AGAAAAT--GCATGGC--AAGCAAGGACT--AATGA 593
                           iv      ----  ii vi-- v  i  --  i   v--  --  vi 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT--CTTGAAAAA 194

  chr2_233786375_    594 GAATAATAAA--TGG-GAACTTAGTCTGCCAGATAAGGAAACACACAAGA 640
                            v  i   --   - i   i vv  v  vi  vvvi    vi  v v 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_233786375_    641 AAGCCACCTCGATTAAACCTATGCAG--CTGGGTCAAGAGTAGATTAATC 688
                             i  vvii  i  iv vi  ii --    vvi   ii    ivv  v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_233786375_    689 TATCAATGGAACAGGAGGAGGCGTTTCAAATCAGATTAGGAC---TATGG 735
                         v          i  i vvii v  iivi  vi i iiviv  ---     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_233786375_    736 GGGAAATTAGCACATGAT-----ATAATGGCATTGTGA--AT-CAATGGG 777
                         ------ i ii---    ----- i  v  iiiiiv  --  -       
  L1M4_orf2#LINE/    345 ------TCAAT---TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_233786375_    778 AAAAGGATGGGCTATTTAATA--CGGTGTTGG-----CT----ATCCATT 816
                         i    i  i v  v  i  i --i    i   -----  ---- ?   iv
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_233786375_    817 TG---GACGGTGAAGTTATAGTCCCTATTTTATACCAAACATAAAAAT-- 861
                           ---i vii       iv -i     ii i i    v i i      --
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGA-CCCCTACCTCACACCATATACAAAAATTA 484

  chr2_233786375_    862 -----AAAT-----AAAGAGCTAAACATAAAAAC--ACATTA-AAAATTG 898
                         -----    ----- ?   v     ii   i i -- v i  -    i v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_233786375_    899 TTAGAAGAAAATA---GC----ATTTTC----CCTAAA--TAAATAATA- 934
                                    i --- ?----  i   ----   vii--  iii   i-
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_233786375_    935 ---TTGGGATGGGTGATTCACAAAACTCAGAATCCGTAAATGAAAACAT- 980
                         ---i vi   i--   --   v   vv  v  v vii   v     v  -
  L1M4_orf2#LINE/    585 TTTCTTAGATA--TGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_233786375_    981 ------TTG-ACTACCTAATGGTTTTAAACTTCCACATGACAAAACGCAC 1023
                         ------   -   v v v vii  vv      iiiiiivv    ivi   
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_233786375_   1024 CATAAACAATGTTTAAAAACA--TTGCAGGCTGG-AGAAAATATTT---- 1066
                         i  v  v  v  vv   i   --iii   iv   -           ----
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_233786375_   1067 -TCATATAACTTACCCCCAAA--ATTAATATACAAAACATATAAAGGGTT 1113
                         -       v  v i----  i-- i vi   v  i  i        iii 
  L1M4_orf2#LINE/    731 ATCATATATCTGAT----AAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_233786375_   1114 TTTAAAA-TCGGAAATATTTTTAAAAAGG--------------AAAAAAT 1148
                         i   v  -  ---    v ---      i--------------?      
  L1M4_orf2#LINE/    777 CTTACAACTC---AATAAT---AAAAAGACAAATAACCCAATTWAAAAAT 820

  chr2_233786375_   1149 GGAAAAAGAATATAAATAGGCAATTGACAGGAAAAGAAACACAAATGGTG 1198
                           iv    i  v i     i  v  vv vii i    v i        iv
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr2_233786375_   1199 AATGCATATATGAAAATAGGCTCAGTGTCATTTCTTTT 1236
                            ivii i       v v     iii   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (156 / 102)
Gap_init rate = 0.05 (47 / 908), avg. gap size = 2.96 (139 / 47)  


2172 23.64 12.52 1.39  chr2_234101590_234104193.rev     1322  2112 (492)    L1M4_orf2#LINE/L1       30   908 (0)  

  chr2_234101590_   1322 AAGATTCAATGTTATTAAGATAGCAATTCTCCCCAAATTGATCTACAGAT 1371
                             i i   i  i       i     v                      
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGAT 79

  chr2_234101590_   1372 TTAACACAATCTCAAACAAAATTCTAGCAGGCCTCACTTATAGAAATTGA 1421
                          i   i     i v v      i i   -v    ivi  ii         
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGC-TGCCTTTTTTGCAGAAATTGA 128

  chr2_234101590_   1422 CAAACTAATATTAAAATTTATATGAAAATGCTAAGTACTTAGAATA---- 1467
                            i  i  vi       i     i      v i v  ii      ----
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr2_234101590_   1468 AAGCTATGTTAGAAAAGAA---CAAAG----ATGACTC--------TAAT 1502
                           i v  v  ii       ---     ---- v     --------i   
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr2_234101590_   1503 TTCAACACTTCCTATAAAACTACAGTAATCAACAAAGTGTAGAATTATTT 1552
                              v    v   i   i             v v     i v i iv--
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG-- 276

  chr2_234101590_   1553 CAGTAAAGGCAGACATAATATAGTTCAATAAAACAAAATAGAAAATCTGG 1602
                           -   i ii       ---   v     ii  i i   v  i i  ii 
  L1M4_orf2#LINE/    277 CA-TAAGGATAGACATA---TAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr2_234101590_   1603 AAAGAGACTCAAAAATAAAAGGTTAATTGACTTTTGAAAAAAGGCAGCAA 1652
                            v i  i  v v  vv v   i      i   i  v  ii v--  v 
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT--GCCA 370

  chr2_234101590_   1653 AGGTAATTAAATGAGGAATGGAAT-GTATCTTCAATAAACGCTGCCTCAA 1701
                           iiv   v    i    -i    -  v i     i   i v   ivvi 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAA-AGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_234101590_   1702 AAACTGAATATCCATATG----GGGGTCGGG--GGA----------AGAA 1735
                         v     i   ?   i   ----i ii vii --   ---------- v v
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr2_234101590_   1736 CAT---CAATAAT--------AAT----------CCCAACTGTAAAACCT 1764
                            ---   v   --------   ----------  i  v     i v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr2_234101590_   1765 AAAACTACAAAACTTATAGAAGAAAA------------TCTTTGCAAGCC 1802
                                i      iv          ------------    i ii v i
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr2_234101590_   1803 GAGGT-AGACAAGGGTTTTCTGGATAGAATACTAGAAGAATGAGCCATT- 1850
                         vi   -  i   v     ii i    vi i  i i   v ii   v iv-
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_234101590_   1851 --TAAAAAACTGATAAGTTGAATTTCACCAAAAAGAAAGACTTCTGTTCT 1898
                         --v      iv     i   i i    i     vv   i    i   v  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_234101590_   1899 --AAAAG----TGTCATTAAAG--AAAACACAAGCCACAGACTGAGA-AA 1939
                         --   i ---- i   vv    --    v    v       v  i  -  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_234101590_   1940 AACATTCACAACACATGTATCAGACAAAGGACTTACATCCAAAATACATA 1989
                           i   ii   vv   i    v  i  i      ii     i    i   
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_234101590_   1990 AAGAAGTCTTACAACTCAATAA------GA------ACCCAATTAAAAAA 2027
                              v                ------  ------        ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_234101590_   2028 ATGGATAAATG-TCCTAGCACACATTTCAC---AAAAGACATACAAATGA 2073
                         -   ii   v - iiv ii v       v --- i    i         i
  L1M4_orf2#LINE/    820 -TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr2_234101590_   2074 CCAACAAACACATGAAAAGATGTT-GACATCATTAGTCAT 2112
                             i  i              i -i      ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (118 / 67)
Gap_init rate = 0.03 (30 / 879), avg. gap size = 3.67 (110 / 30)  


 238 18.18 3.03 1.52  chr2_234121477_234124000       70   135 (2389)  C L1M4_orf2#LINE/L1   (0)   908   842  

C chr2_234121477_    135 ACTTCCTCACAGAAGAAATACAAAATGGATAATAAGCAAGTAAAAAGCTG 86
                          i   ii  v      v       -   vi        vi i     v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACATGAAAAGATG 890

C chr2_234121477_     85 CTTAA--TCACTCTAGTC 70
                           i  --   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (7 / 5)
Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.50 (3 / 2)  

2634 22.21 2.73 7.79  chr2_234121477_234124000      509  1278 (1246)    L1M4_orf2#LINE/L1        1   731 (177)  

  chr2_234121477_    509 TGGAAAGATACTCCACGTTCATGGACTGGAAGAATCAACATTGTGAAAAT 558
                                   ii   i         i       v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_234121477_    559 GTTCGTATTACCCAAAGCAGTCTACAGATTCAATGCAATTCCTATTAAAA 608
                          vivi  i v      viii             i     i     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_234121477_    609 TACCAATGACATTCTTCACAGAAATGGAAAAAATAATTCTAAAATTTATA 658
                          v   iivi v  i  ii       v  v  iv i  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_234121477_    659 TGGATCCAGAATAGCCAAAAGACCCAGAATAGCCAAAATTCTCCTGATGA 708
                             -----   i--   ii                  ivv  i   vi 
  L1M4_orf2#LINE/    151 TGGA-----AATG--CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_234121477_    709 AAAA--------TTGGAGGAATCACATTTTCTGACTTCACATTATACTAC 750
                          i  --------        v     i  i ii i    v viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_234121477_    751 AGAGCTATACTAACCCAAACGGCGTGGTACTGGCATAAAAACAGACACA- 799
                          i     i v   i v i  i i               ii i     i -
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_234121477_    800 -GAACAATGGAACAGAATAGAGAGCCCAGAAATAAATTCATACATCCACA 848
                         -  v        i     v     i           ii       ii ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_234121477_    849 GTGAACACATTTTTGACAAACGTACCAAGAACATATACTGAGGAAAGGAC 898
                           v  ivv     i     iv  i      v   vi v  i      i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_234121477_    899 AGTCTCTTCAATAAATGGTGCTGGGAAAACTGGTTATCCATATGCAGAAG 948
                              i     i              v      v  ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_234121477_    949 AATGAAACTAGACTCCCATTTATTGCCATATGCAAATATCAAATCAAAAT 998
                               ii i   i  i ii vvii      i    v  i  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_234121477_    999 GGATTAAAGACTT-----TAAGACCTCAAACTATGAAACTGT-----GAA 1038
                             i ?    i -----     v  v       i     v -----   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_234121477_   1039 AACACTGGGGAAACTTTCTAGGACGTTGGACTGGGCAAAGGTTTCTTGAG 1088
                             iv  ? v  v i iiiv   v    ii i     v        iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_234121477_   1089 TA-ATTCCCACAAGCACAGGCAACCAAAGCAAAAAGTGGACAAATGGTTA 1137
                           -iviv   v       i     v    -     i i  i    --- i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAAT---TG 639

  chr2_234121477_   1138 AAGCTCCTGCATTAGCAATGCAGGAAAAAAGCAGTGAAAAAAAGCTCCTG 1187
                         i ----  v   i ------------------------------------
  L1M4_orf2#LINE/    640 GA----CTTCATCA------------------------------------ 649

  chr2_234121477_   1188 TTTTTAACAAGTTAAAAAGTTCCTGCACAGCAAAGGAAACAGTCAACAAA 1237
                         --------  i       v  i-  ii vv       v  vi    v   
  L1M4_orf2#LINE/    650 --------AAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_234121477_   1238 GTGAGGAGACAGCCTACAGAATGGGAGAAAATATTTGCAAA 1278
                             ii     i  i                          
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

Transitions / transversions = 2.00 (112 / 56)
Gap_init rate = 0.02 (12 / 731), avg. gap size = 6.75 (81 / 12)  

 541 24.14 6.40 0.49  chr2_234121477_234124000     1830  2032 (492)    L1M4_orf2#LINE/L1      694   908 (0)  

  chr2_234121477_   1830 AAAAAACAAA--ACAAAACAAAACAAAA-ATT-GAAAACTATTCCTCTGA 1875
                             i    v--   i  iiii v    -   - v   ii  viv     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_234121477_   1876 CAAGGGA-TTATAACCAGAATAAATCGAGAGCTCAAATAATTCAAAAGGG 1924
                         i      -  i  v        v  vi   i   vv i  i    v ivi
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_234121477_   1925 GAAAAATCTAATCATCCAGTTAAAAAATAGGAAAAG--------TAGACA 1966
                         i   i - v   v i   i  ?      i  v    --------      
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_234121477_   1967 TTTCTCAAAAGAAGACATACATATGGCAAGTAGGTATATGAAAAAGTGCT 2016
                               v        i     v     v i  i i i       ii    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_234121477_   2017 CAATATCATTGATCAT 2032
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (30 / 18)
Gap_init rate = 0.03 (6 / 215), avg. gap size = 2.33 (14 / 6)  


2207 24.22 1.47 1.80  chr2_234196147_234198229      501  1111 (972)    L1M4_orf2#LINE/L1      141   749 (159)  

  chr2_234196147_    501 AAAATTCATAAGGAACCACAAAAAAACCCAAATAGTCAAAGCAATTGTGA 550
                                   v    vii   iii v  vi     i    i    iv   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_234196147_    551 GCAAAAAGAACAGAGCTGGAGGCAC-CATACTGCCTTACTTCAAAATATA 599
                         iv  i       i  i      -  -  i   v  iv i       iv  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_234196147_    600 CTACAAAGCAAAAGTAACCAAAACAGCAGGGTACTGGCAAAAAGTCTGAC 649
                                  v v     i   i    iiv          v  i viv   
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_234196147_    650 ACATAGGCCAAAGCACCAGAATAAAGAGCCCAGAAATAAATTCACAAACT 699
                          i    ii   v v vi     vi    i           ii  i v i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_234196147_    700 TAACAGCCAACTAATTTTTGATAGATGTGCCAAGAACACACATTGGGAAA 749
                           -ii i   i i     i  i iiv         v  iv  v    i  
  L1M4_orf2#LINE/    340 TA-TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_234196147_    750 ATGATAGTCTCTTCAACAAATGGTTCTGGGAAAATTGGATCTCCACATGC 799
                          vi       i             v      v  i     v?        
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_234196147_    800 AGAATAATGAGACTAGATTCCCTAACTCTCACTAAATACAAAAATCAACT 849
                          i  v     iii i  i-     v   v   i v          i    
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_234196147_    850 CAAAATGGTTTAAATGCTTAAATGTAAAACCCAAAACAATGAAACTACTA 899
                                 v i ? vi i         i v i     v  i     vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_234196147_    900 AAGGAAAACATAGGGGGAACACT--ATGACACTGGATTAGGCAAGAATTT 947
                         i i           ? v  vv  --i    vi   i        vii   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_234196147_    948 TTAAAATAAGCTTTGGTTGCCTCAAAAGCACAGGCAACAAAAGAACA--T 995
                         i v i   -----  i--- vi          i            v -- 
  L1M4_orf2#LINE/    588 CTTAGATA-----TGA---CACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_234196147_    996 AGACAAATGGGATTATAGCAAACTAAAAAGCTTTTGTACAGCAAAAGAAA 1045
                            i    v   i vi v    v v    i       i vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_234196147_   1046 C----AACAGAGTAAAGAGACAACCTACAGAATGGGAGAAAATGTTTGCA 1091
                          ----  v i   i  i        i                 i      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_234196147_   1092 AAGTATAAATCTAACAAAGG 1111
                           vi   v    i i  i  
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGG 749

Transitions / transversions = 1.59 (89 / 56)
Gap_init rate = 0.01 (9 / 609), avg. gap size = 2.22 (20 / 9)  

 539 19.54 3.45 5.17  chr2_234196147_234198229     1418  1591 (492)    L1M4_orf2#LINE/L1      738   908 (0)  

  chr2_234196147_   1418 ATCTAACAAAGAGTTAATATCCGGAATATATTATATAAGGAACTTAAACA 1467
                             i i  i iii vi     i        -----  i     ivv   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATAT-----AAAGAACTCTTACA 782

  chr2_234196147_   1468 ATTCAACAGCAAAAAAA-AAGTA-CCTGATATAAAAATTGGCAAAAGACT 1515
                          i    i ii     i -  i  -  ii  v?      v      i  i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_234196147_   1516 TTAGTAAACATTTCTC---AAAAGACATACAAATGGCCAACAGGTACGCA 1562
                          v i  i         --- i    i              ----  v   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA----TAAGCA 878

  chr2_234196147_   1563 CACAAAAA-ATGCTCAACATCACAAATCAT 1591
                           ii    -             ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.71 (26 / 7)
Gap_init rate = 0.04 (6 / 171), avg. gap size = 2.50 (15 / 6)  


3263 26.40 0.44 0.55  chr2_234268733_234275016.rev     4884  5792 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_234268733_   4884 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4933
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_234268733_   4934 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4983
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_234268733_   4984 TACCAA-TGCCTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCA 5031
                          v   i-       i  -i     v v  v  i-  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr2_234268733_   5032 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5081
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_234268733_   5082 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5131
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_234268733_   5132 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5181
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_234268733_   5182 AATGCAACAGAAC--AGAGCCCTCACAAATAATGCCACATATCTACAACT 5229
                             v  i    i--    i  -- v      vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_234268733_   5230 ATCTGATCTTTGACATACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5279
                          vi    i  i    vivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_234268733_   5280 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5329
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_234268733_   5330 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5379
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_234268733_   5380 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5429
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_234268733_   5430 CTAGGCATTACCATTCAGGACATAGGCATGGGTAAGGACTTCATGTCTAA 5479
                         v    ?i v viv   iv   v v  vv i  i  v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_234268733_   5480 AACACCAAAAGCAATGGCAACCAAAGACAAAATTGACAAATGGGATCTAA 5529
                         i            vvi     v     v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_234268733_   5530 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5579
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_234268733_   5580 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5629
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_234268733_   5630 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5679
                         i-  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    747 G-GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_234268733_   5680 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5729
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_234268733_   5730 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5779
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_234268733_   5780 CATCACTGGCCAT 5792
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


2979 27.45 0.77 0.66  chr2_234302950_234305296.rev      949  1855 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_234302950_    949 TGGAAAAACATTCCACGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 998
                               i i  i   i i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_234302950_    999 GGTCATACTGTCCAAGGTAATTTATACATTCAATGCTATCCCCATCAAGC 1048
                           iv     vi    iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_234302950_   1049 TACCATTGAATTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 1096
                          v   vivivi  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr2_234302950_   1097 ATATGGAACTAAAAAAGAGCCAGTATAGCCAAGACAATCCTAAGCAAAAA 1146
                                 v iv  ii  v    v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_234302950_   1147 GAACAAAGCTGGAGGCATCACGCTACTTGACTTCAAACTATACTACAAGA 1196
                                 i      vv    i  v iii i      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_234302950_   1197 CTACAGTAACCAAAACAGCATGGTACTTGTACCCAAACAGATATATAGAC 1246
                                  i   i    ii       v i ivvii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr2_234302950_   1247 CAATGGAACAGAACAGAGGCCTCAGAAATTATGCCACACATCTACAACCA 1296
                                 i    iv   ivii       v vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_234302950_   1297 TCTGACCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACGATTCCC 1346
                         vi   ii  i     ivv  v   i v  vvv          vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_234302950_   1347 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATTTGTAGAAAACTG 1396
                          v  i  i        i     v      v  ?   iv  i i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_234302950_   1397 AATCTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 1446
                           vi         v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_234302950_   1447 TAAAGCCTTAAACATAAGACCTAAAACCATGAAAACCCTAGAAGAAAACC 1496
                         i ?  v i    ii     v       i  i   vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_234302950_   1497 TAGGCAATAACCATTCAGGACATAGGCATGGGCAAAGACTTCATAACTAA 1546
                             ?i-   viv   iv   v v  vv i     v ii   v  iv  v
  L1M4_orf2#LINE/    548 TAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_234302950_   1547 AACACCAAAAGCAATGGCAACCAAAAGCCAAAATTGACAAATGGGATCTA 1596
                         i            vvi     -     vv     v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_234302950_   1597 ATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGATGGAA 1646
                           i   viv  i i   i  ii vv    i  v       vv i vv   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_234302950_   1647 CAGGCAACTTAAAGAATTGGAGAAAAGTTTTGCAACCTATCCATCTGACA 1696
                         v  i    ii v     v        vv       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_234302950_   1697 AAGGGCTAATATCCAGAATCTAAAAGGAACT--TA-AAC-CAATTTACAA 1742
                          i  i  vi          v  v  i     --  -   -    v- i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAA 794

  chr2_234302950_   1743 GAAAA-AAACAACCCCATCAAAAAGTGCGCAAAGGATATGAACAGACACT 1791
                         i  i -   i     v  i?    i  v         v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_234302950_   1792 TCACAAAAGAAGACATTTATATGACCAGCAAACATATCAAAAACAGCTCA 1841
                           v v        i  vi v   i   ii  i  i  v    ivv     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_234302950_   1842 TCATCACTGGTCAT 1855
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2808 28.32 0.88 0.44  chr2_234321735_234326544.rev     3415  4318 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_234321735_   3415 TGGAAAATCATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 3464
                               ivi  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_234321735_   3465 GGCCGTACTGCTGAAGGTAATTTATAGATTGAATGCTATCCACATCAAGC 3514
                            vi    v iv  iv i  i  i     v  i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_234321735_   3515 TACCATTGACTTTCTTCACAGAATAGGAAAAAACT-ACTTTAAAGTTCAT 3563
                          v   vivi i  i  ii     - vvi v  i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_234321735_   3564 ACGGAGCTAAAAAATAGCCTGTATATCCAAGACAATCCTAAGCAAAAAGA 3613
                          i   iv iv  iiv v  v v   v    i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_234321735_   3614 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATACTACAAGGCT 3663
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_234321735_   3664 ACAGTAACAAAAACAGCATGGTACTTGTACCCAAACAGATATATAGACCA 3713
                                iv  i    ii       v i ivvii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_234321735_   3714 ATGGAACTGAACAGAGGCCTCAGAAATTATGCCACACATCTACAACCATC 3763
                               iv   iv   ivii       v vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_234321735_   3764 TGACCTTTGACAAACCTGACAAAAACAAGAAATGGGGCAAGGATTTCCTA 3813
                            ii  i     ivv  v   i v  vvv       v   i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_234321735_   3814 TGTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAACTGAA 3863
                          vi  i        i     v      v  ?   i   i i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_234321735_   3864 TCTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 3913
                         vi         v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_234321735_   3914 AAGACTTAAACATAAGACCTAAAACCATGAAAACTCT-AGAAAAAAACCT 3962
                         ?    i    ii     v       i  -        -    i     v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chr2_234321735_   3963 AGGCA-ATACCATTCAGGAAATAGGCATGGGCAAAGACTTCATAACTAAA 4011
                            ?i- v i -   iv  vv v  vv i     v ii   v  iv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_234321735_   4012 ACACCAAAAGCAATGACAACCAAAAGCCAAAATTGAGAAATGGGATCTAA 4061
                                     vvii    -     vv     v  v    v   ii v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_234321735_   4062 TTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTATCATCAGACTGAAC 4111
                          i   v v  v i   i  ii vv    i  v       vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_234321735_   4112 AGGCAACTTACAGAATGGGAGAAAAATTTTGCAATCTATCCATCTGACAA 4161
                           i    ii                vv       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_234321735_   4162 AGGGCTAATATCCTGAATCTACAAGGAACT--TA-AAC-CAATT-TACAA 4206
                         i  i  vi     v    v  i  i     --  -   -    v-  v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_234321735_   4207 GAAAAAAAAACCCCATCAAAAAGCGGTCGAAGGATATGAACAGACACTTC 4256
                         ii v   v     v  i?    ii  v i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_234321735_   4257 ACAAAAGAAGACATTTATACAACCAACAAGCATATCAAAAAAAGCCGATC 4306
                         v v        i  vi v iii    i     i  v    i v  iv v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_234321735_   4307 ATCACTGGTCAT 4318
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (139 / 113)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.09 (12 / 11)  


3528 23.12 2.92 1.01  chr2_234730998_234735252     2873  3763 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_234730998_   2873 TAAAAAGGCAACTTATGTTTTATGAATTGCAAGAAATACTATTGTTAAAA 2922
                          ii    ii v ii     i-   i    v    vv  v         i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTC-ATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr2_234730998_   2923 TGTTCATGCTACCCAAAGAAATCTAAAGATTCAATGCAATTTCTACCAAA 2972
                           viv  i  v      vvi     v        i     ii   i    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_234730998_   2973 ATTCTAATGGCATTTTAATTGAAATAGAAA---AGAAAGAAATTCTATAA 3019
                           i i iiv  v    --   ---i     --- v  ivvi  i   v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTT--TTG---CAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_234730998_   3020 TTTATATGGAACCACAGAAGACC-A-------CAAATCAATCTTCAGAAA 3061
                           i        vii  iii    - -------    v       v i   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_234730998_   3062 GAA---CAAAACTGGAGGTGTTACACTATTTGATTTCAAAA-----TATA 3103
                            ---    ii      vv i     viiii         -----  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_234730998_   3104 --GCTATAGTAATGAAAACACTGTGGTTCTTGCCTAACGATAGACATATA 3151
                         --    i      v  i   v      v  v  v   v            
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_234730998_   3152 GACAAATAGAACAGAATAGAGAGCCCAGAAATTAATCTATACAAAAAGTG 3201
                           iv   i   i     v     i        v  i i     vvv -  
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TG 343

  chr2_234730998_   3202 ATCAATTGCTCTTTGCCAAGGGAGCCCAGAGTAAACAGTGGGGAAACATT 3251
                         i       v i  i v      v   v   vi vv  i        v v 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr2_234730998_   3252 AGTGTCTTCAATGAATGGTATTGGAAAAACTGGATATCCATGTGTAAAAG 3301
                            v i     ii      ii   i v         ?   ii  i     
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_234730998_   3302 A--GA--TTGGATCCTAATCTTGCGCCATACACAAAAATCAACTCAAAAT 3347
                          --  --     i  iv i  ii i     i        i          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr2_234730998_   3348 GGATTAAAAAGTTAAACATAAGACTTAAAACTGTAAAACTCCTAGAAGAA 3397
                             i ? i vi    ii     vi       i        i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr2_234730998_   3398 AACATATGGGAAAATCTTCATGACATTGGTCTTGGCAGTGATTTCTTGGA 3447
                               v ? v        i    v    vi v    i  i      i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_234730998_   3448 CATGACACCAAAAGCACAGGCAACTAAAACAAGAATAGACAAGTAGGA-T 3496
                         i                 i     v   iv  i      i  i v   - 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_234730998_   3497 TAATTAAACTGAAAGACTTCTGCACAGTGGAGTAAACAACCAATAGTGTG 3546
                          v  i   v v   i    i  ii vviii  v v  v i   v iv   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_234730998_   3547 AAAAGGAAACCTACAAAATGGCAGAAAATATTTGCAAATTGTGCATCTGA 3596
                              iv    i   i     v                 ii ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_234730998_   3597 TAAGGGATTAATGTCTGAAATATATAAGGAACTTCTATAACATAATGGCC 3646
                                i vi i  iii         i     ii  i   vi   iiiv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_234730998_   3647 AAAAGCCACAAATAACCCAATGAAAAAATTGGCAAAAGATTTGAATAGAC 3696
                              --              v?      v      i             
  L1M4_orf2#LINE/    794 AAAAG--ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_234730998_   3697 ATTTCCCCAAAGAAGACATATAAATGGCTAACCAGTATATGAAAAGATGC 3746
                              i          i   i       i  iv  i i            
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_234730998_   3747 TCAACATCACTAGTCAT 3763
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (127 / 75)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.50 (35 / 14)  


2678 27.56 0.27 0.27  chr2_234883233_234884988      501  1251 (505)    L1M4_orf2#LINE/L1      110   860 (48)  

  chr2_234883233_    501 CTTTCTTCACAGAATTGGAAAAAACCACTTTAAAGTTCATATGGAACCAA 550
                          i  i  ii     v v  v  iviv iii    i           viiv
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr2_234883233_    551 AAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAGCAAAGCTGG 600
                           ii  v  v v  v     iv     i i ivv i    i     i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr2_234883233_    601 AGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCA 650
                            vv    i  v  ii i      viv        i          i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr2_234883233_    651 AAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGA 700
                          i    ii         i iv ii i   v                i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr2_234883233_    701 AC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTATCTGATCTTT 748
                          i--    i  --        vv  ii i  i  iiiii vi    i  i
  L1M4_orf2#LINE/    310 ATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr2_234883233_    749 GACAAACCTGAGAAAAACAAGCAATGGGGAGAGGATTCCCTATTTAATAA 798
                              ivv  vv  i v  vv         i  i  vvi  v  i  i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr2_234883233_    799 ATGGTGCTGGGAAAACTGGCTGGCCATATGTAGAAAGCTGAAACTGGATC 848
                                     v      v i?   i   i i  iiv    ii    i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_234883233_    849 CCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTA 898
                            v   i     v              i    i      i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_234883233_    899 AACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTAT 948
                           i  v   v       i      vi i           v    ?i v v
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_234883233_    949 GATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAG 998
                         vv   iv   v v  vv i     v ii   v ivv  vi          
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_234883233_    999 CAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTAAAG 1048
                           vvi           v     v  i    v   ii v  i   v v  i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_234883233_   1049 AGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTAC 1098
                          i   i  ii vv    i  v    i  vv i      v  i     i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr2_234883233_   1099 AAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATAT 1148
                          i             v  i    vii ivi      i  i  i  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr2_234883233_   1149 CCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAAT 1198
                                v  i  v      vv    v iv i  v     i     i  i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr2_234883233_   1199 CCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGA 1248
                           v  i?    i            v    i     i     v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_234883233_   1249 TAT 1251
                            
  L1M4_orf2#LINE/    858 TAT 860

Transitions / transversions = 1.39 (118 / 85)
Gap_init rate = 0.00 (2 / 751), avg. gap size = 2.00 (4 / 2)  

 376 30.32 5.16 4.84  chr2_234883233_234884988     1415  1724 (32)    L1M4_orf2#LINE/L1      598   908 (0)  

  chr2_234883233_   1415 ACTTCAAAAGCA-AAGC--CAGAAGGTGAAATGTGATTAATTTGATTACA 1461
                           vi        -    --  i   ivi    i-   v    v  i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTCA 646

  chr2_234883233_   1462 TTAGCATTGATAATTTCCATTCATCAAAGAACAATGTAAACGAAATCATT 1511
                          i iv   i v  i  iii v v      i   v i v  vi  i v vv
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_234883233_   1512 -GAGAAATCACAGAATAGGAGATGATTCTTGC----TGTACCTATGATAA 1556
                         -  v  vi        i     vi  vi    ----ii  iv v      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_234883233_   1557 ACAGGAGATTGCTATCTAGAGCACACA--GAACTCCTGCAAAACGATAAG 1604
                         ---- i  i vv    i   ii i i --      i i   vv i    v
  L1M4_orf2#LINE/    747 ----GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr2_234883233_   1605 GAAATGATAG-CATCCCAGTAGAAAAAAAAATGGGCAAAGGACAATAATG 1653
                         i   v  i i-i v    i v----?                i-- --  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATT----WAAAAATGGGCAAAGGAT--T--TG 834

  chr2_234883233_   1654 AATAAGCA---CGTTAGAGAAAAAGCCCAAGAAACTTCAAAGAGTGCA-- 1698
                             ii  --- vii i    i viiv   ivii --   vi  ii  --
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGC--CAATAAGCACATG 882

  chr2_234883233_   1699 AAGACAGGCTCAGAATCATTAGTAAT 1724
                           i v v     iv    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (56 / 37)
Gap_init rate = 0.05 (14 / 311), avg. gap size = 2.21 (31 / 14)  


1117 31.29 5.57 3.57  chr2_234960825_234962509      501  1200 (485)    L1M4_orf2#LINE/L1      195   908 (0)  

  chr2_234960825_    501 GAAGAACCAAACCAGGAGACTTGAACT--ACAGCTCTCAAAACCTGCTAC 548
                                v  iiii ii    iiv   --v  ii -       i i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATT-TCAAAACTTACTAC 243

  chr2_234960825_    549 A---CTGCAAGCATGAAGGGGATGCAATATTGACATATGAACCGATAGAC 595
                          ---  i  ivv  v   ivii  iii  i  i    v ----       
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG----GATAGAC 289

  chr2_234960825_    596 A-GTGGACTGCCAGCATAGGAT-AAGA-TCCAGAAACAGACC-ACACATA 641
                          -i i  iiivii v    i  -i   -        i i   - i    v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_234960825_    642 TGAAGCCATTTGATTTATGATAAAAGTGACGTGACAAGCATGGAAGTTAG 691
                          ivi i  v       vi  i  ii   v iv   ---   vv  -- i 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC---CATTCAA--TGG 384

  chr2_234960825_    692 GAGGTGAATAAACTTTTCAAGAAGCGTTGCTTGATGGATTGGCTTTCCAT 741
                          iiiv     iv        v  ii v    v ivvi i   v v?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_234960825_    742 ATAGAAAAAAATGTGTCTTGACAGCTA--TCATGCCATATACAAAAAAAA 789
                           iv    i    vivi v   vv   --   ii             ---
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA--- 481

  chr2_234960825_    790 ATCAATTCCACACACATTTCAAATCTACACAAGAAGGGC-AATATAATCA 838
                         - i  i  v v iiv  iv? i i   v ii-v   i  -  v iv  v 
  L1M4_orf2#LINE/    482 -TTAACTCAAAATGGATCAWAGACCTAAATG-TAAGAGCTAAAACTATAA 529

  chr2_234960825_    839 CACTTTTAGAAAAAAA---AGAC-TAGATCTTTATGAG--TAGAACAGTC 882
                         v   i      i    ---  i?-  i     ii   v-- i ivi  v 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr2_234960825_    883 AAAGATTTCTTAAATAGGATAGAGAAAGCATTAAC--CTACAGCAAAAAT 930
                           v i       i   v  i vvi      iv i -- v v  v      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr2_234960825_    931 A-ATA--TTAAACTATATTAAAATTAAGAATCTCTTTTCATCAAAC-ACC 976
                          -   --  ii   vi  i        i  ii i v v v     v-  v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr2_234960825_    977 TCATTAGAAGAGTGAAAAGGTGGCATGGAGACTTGAAGA---TATTGGCA 1023
                         ii  i ii i         iiii viiv   v v i   ---    v   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr2_234960825_   1024 --TTACATTATACCCAACAAAGGACTTGTATC-AGCA---ATAAATAGCA 1067
                         -- i ---    i ii i  i           -  v ---     v i v
  L1M4_orf2#LINE/    730 AATCA---TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_234960825_   1068 CCTACAAATCAGTAAGTTAAAGGGACAA----TTCAATGGAAAAATCACC 1113
                          i     v   i   --    ii     ----ii    v?      viv 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAA--TAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr2_234960825_   1114 GAAAGACTTGAATAGGTACTTCATAAATGAGGGTATTCAGTTGGCACCCA 1163
                         i  i  i        ii i   viv  v  i i   v  iv    -- v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC--CAA 872

  chr2_234960825_   1164 TA--TATATAAAAAGCTGTGCAGCTACATTATCAAGAAA 1200
                           --i i  i     v  iv  ---    i ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCA---ACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (135 / 80)
Gap_init rate = 0.04 (31 / 714), avg. gap size = 2.06 (64 / 31)  


1091 27.53 0.35 0.00  chr2_235079020_235080911      501   787 (1105)    L1M4_orf2#LINE/L1      264   551 (357)  

  chr2_235079020_    501 AGCATGGTGCTGGTGCCAAAACAGATATATAGACCAACGGAACAGAACAG 550
                           ii    i    iiiv ii i   i       i   i    i    iv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr2_235079020_    551 AGACCTCAGAAATATCACTACGCTTCTACAACCATCTGATATTTGACAAA 600
                            vii        vvv i ii v i  iiii  vi    v  i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr2_235079020_    601 CCTGACAAAACAA-GCAACGGGGAAAGGATTCCCTATTTAATAAATGGTG 649
                         vv  v   i  v -v   i        i  vvi  v  i  i        
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr2_235079020_    650 CTGGGAAAACTGGCTAGCCATCTGCAGAAAACAGAAACCGGACCCCTTCC 699
                               v      v  ?   iv    i  i vv   iii        v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr2_235079020_    700 TTACACCTTCTACAAAAATTAACTCAAGTTGGATTAAAGGCTTAAATGTA 749
                          i     v v                 iv     i ?  i i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_235079020_    750 AAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGG 787
                          i v       i      vi i           v    
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

Transitions / transversions = 1.66 (48 / 29)
Gap_init rate = 0.00 (1 / 288), avg. gap size = 1.00 (1 / 1)  

 922 24.93 6.16 1.68  chr2_235079020_235080911     1044  1400 (492)    L1M4_orf2#LINE/L1      536   908 (0)  

  chr2_235079020_   1044 TAGAAGAAAACTTAGGCAGTA--CCATTAAGGACATAGACATGGGCAAAG 1091
                                    v    ?-   --i -  viv   v v ivv i     v 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chr2_235079020_   1092 ACTTCACGACTAAAACACCAAAA--ACAATTGCAACAGAAGCCGAGATTG 1139
                         ii   viiiv  vi         --    --      i   vvi i  v 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAG 631

  chr2_235079020_   1140 ACAAATGGGATCT------AATTAAA-----CTGCACAGCAAAAGAAACT 1178
                          i    v   ii ------       -----i  ii vv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_235079020_   1179 ATCATCAGAGTGAACAGGCAACCTACAGAGTGGGAGAAAAT-TTTGCAAT 1227
                             vv i      v  i     i     i           -       v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_235079020_   1228 CTGTCCATCTGACAAATGTCTAATATCCAGAATCTA-GAAGTA-TCTTAA 1275
                         iii vi      i  iv v  vi          v  -i   v -     -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA- 780

  chr2_235079020_   1276 ACAAATTTACAAGAAAAAAACAA----CCCAATCCAAAAGTGGCTGAAGG 1321
                         -   v iv i  v     i    ----      i?    i   vii    
  L1M4_orf2#LINE/    781 -CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_235079020_   1322 ATATGTATAGACACTTCTCAAAAGAAGACATTGATGCGGCCAACAAACAT 1371
                           v  v       i     v        i  vv vii      i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_235079020_   1372 ATGAAAAAAAGCTCATCATCACTGCTCAT 1400
                                i v     v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (47 / 40)
Gap_init rate = 0.03 (12 / 373), avg. gap size = 2.33 (28 / 12)  


1531 29.09 8.29 2.22  chr2_235417442_235419416      630  1485 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_235417442_    630 TGAAAGAATATACGATGTTCATACATTGCAAGACTCAAAATTGA-AAGAT 678
                           i  ii    v v        iv    v      i  v    v-     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_235417442_    679 GTTCATTCTTTCCAAATT----TAC----TCAGTACAATTCTGATTAAAA 720
                          viv  v  ii       ----   ----   iii    i iv  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_235417442_    721 ACTTCGGAAAGTTTTCTATGAAAACTGAAAAAAATGATTCTATAATTTTT 770
                         v iiv vvivv    i iiii   i   v  iv-    i   v    iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr2_235417442_    771 GTG-AAATGCAGTGGTACAAGTGCAGCAAAGACAATCTCAAAAAA----- 814
                         i  -       iv  vv v  vii   v  i       ii     -----
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_235417442_    815 -CAAAGTTGGAAGTCTCAAATGACTATATATCAAGACTTATTATGAAGTC 863
                         -          i v    v ivv ivv  v    i     i  ii   ii
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_235417442_    864 ATAGAAACTAAGACA-TA----ACTAG---------AGACAAACAGATGA 899
                          i  v  ii      - i----   i ---------     v i    v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_235417442_    900 ATAAAACAAAAC-AAGATTACAACAGT----CCACAAA---ATG-TCACT 940
                           ii  i i  i-i   v v  iv i ----   i v ---   -   v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_235417442_    941 TTATTTATGGAAAAGGTTAC--ATATTATAGCAGTGAGGAAAAGTTGATC 988
                          v    - v  v    v i -- v ii  -v  i  i     iiv ii  
  L1M4_orf2#LINE/    350 TGATTT-TCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGTC 397

  chr2_235417442_    989 TTTGCACTAAA--GT-------CAACTGGGTATCTTTATTTTTAAAAATG 1029
                            v  vi   --  -------       i  ? ivi  vivv  i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_235417442_   1030 AATTTTGACTCCTTTCTTATATTTTAAACAAAAATCAATACCATTTGGAT 1079
                           v  v   i   vi  i i iiv  v        i  iv v vv     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_235417442_   1080 TATAGGCATAAATGTGAAAGGTAAAAA-ATAATAAGTTTCTAGAAGAGAA 1128
                         i ?  i v       i i  v     v-    -- ii ii       i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAA--AACTCTTAGAAGAAAA 545

  chr2_235417442_   1129 TTTAAGAGAATGTCTTCATGGTCTTGTGT--AGCAAAAGTTCCTTTTTTA 1176
                         iv  i ? v vi     i  ii    v  --i    vi   i   vvv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_235417442_   1177 GGGAACAATAAGTCCTAAACA-TAACAGGAAAATGATAAA--AATTAGAC 1223
                         v iv  v v   iv -  i  -i  v  i    --   i --    i   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCAC-AAGCAACAAAAGAAAAA--ATAGATAAATTGGAC 642

  chr2_235417442_   1224 TATATTAAAATTAAGAACTT--GTG-TTCAACAAAGACAAAATTAAAGGA 1270
                          vi  i        i     --   -     -- i    vv  i  iii 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAA--AGGACACTATCAAGAAA 690

  chr2_235417442_   1271 GTGAAAAAGCAGACCATAGAATGG-AGAAAACATATGTAATAAATGTGTC 1319
                                ii  iv   i       -      i  v  i  vvv  i i  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_235417442_   1320 TGACAGATAACTCGAATCTGCTATACACAGGGAAGTCTT-CAAATCAATT 1368
                            i iivi   i v   iivv   i i ii   v    -   v     -
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT- 789

  chr2_235417442_   1369 TAA-AAAAAGAAAAAGCAGACAACT-AATAGAAAACTGGACAAAAGACT- 1415
                         -  -       -----  i i   i-   v?    v   i    i  i -
  L1M4_orf2#LINE/    790 -AATAAAAAGA-----CAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_235417442_   1416 GAAT------TTAACTTCACAGAAGATATA-AAGTGTTCAGTAAACACAT 1458
                             ------  --  i  v          -  i  vi  i   i     
  L1M4_orf2#LINE/    834 GAATAGACATTT--CTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_235417442_   1459 AAAAAGATGCTTAACATTCTCAACTGT 1485
                         i          i     iv????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.04 (38 / 908), avg. gap size = 2.37 (90 / 38)  


3263 26.98 0.44 0.44  chr2_235445598_235448669.rev     1673  2580 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_235445598_   1673 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1722
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_235445598_   1723 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCATCAAGC 1772
                           iv     v     iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_235445598_   1773 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 1821
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr2_235445598_   1822 ATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAGA 1871
                               viiv  ii  v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_235445598_   1872 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 1921
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_235445598_   1922 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 1971
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_235445598_   1972 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCACATCTACAACTA 2019
                               i    i--    i  --        vv  ii    i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr2_235445598_   2020 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 2069
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_235445598_   2070 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 2119
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_235445598_   2120 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 2169
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_235445598_   2170 TACAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 2219
                         i ?    i     i v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_235445598_   2220 TAGGCA-ATACCATTCAGGATATAGGCATGGGCAAGGACTTCATGTCTAA 2268
                             ?i- v i -   iv  iv v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_235445598_   2269 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 2318
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_235445598_   2319 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2368
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_235445598_   2369 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 2418
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_235445598_   2419 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2468
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_235445598_   2469 AAACAATCAACCCCATCAAAAACTGGGCAAAGGATATGCACAGACACTTC 2518
                          i    vi     v  i?    v            v  v i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_235445598_   2519 TCAAAAGAAGACATTTATGTAGCCAAAAGACACATGAAAAAATGCTCATC 2568
                           v        i  vi vi i     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_235445598_   2569 ATCACTGGCCAT 2580
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


3169 27.34 0.66 0.55  chr2_235465631_235472039     5011  5917 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_235465631_   5011 TGGAAGAACATTCCATGCTCATGGAT-AGAAGAATCAATATCATGAAAAT 5059
                              ii i  i     i        -i     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_235465631_   5060 GGCCATACTGCGCAAGGTAATTTATAGATTCAGTGCCATCCCCTTCAAGC 5109
                            v     v v   iv i  i  i       ii  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_235465631_   5110 TACCAATGATTTTCTTCACATAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5157
                          v   iiviii  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_235465631_   5158 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5207
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_235465631_   5208 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5257
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_235465631_   5258 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATTGACC 5307
                          i      i   i    ii         i iv ii i   v    v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_235465631_   5308 AATGGAACAGAAT--AGAGCCCTCAGAAACAATATCACACATCTACAACC 5355
                                i     --    i  --     i  vvi  i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_235465631_   5356 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5405
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_235465631_   5406 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5455
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_235465631_   5456 AAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCATGATGGA 5505
                         i  ii    i    v   i     v              i   vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_235465631_   5506 TTACAGACTTAAATGTTAGACCTAACACCATAAAAACCCTAGAAGAAAAC 5555
                          i ?    i       v   v    v  i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_235465631_   5556 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5604
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_235465631_   5605 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5654
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_235465631_   5655 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5704
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_235465631_   5705 CAGTCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5754
                         v  v     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_235465631_   5755 AAGGGCTAATGTACAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5804
                          i  i  vi i v      v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_235465631_   5805 AAATCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGGCACTT 5854
                           iv    i     v  i?    i    ii      v    i  i  i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_235465631_   5855 CTCAAAAGAAGATATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5904
                            v           vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_235465631_   5905 CATCACTGGCGAT 5917
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3313 26.18 0.55 0.66  chr2_235578534_235584809     4876  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_235578534_   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_235578534_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_235578534_   4976 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 5022
                          v   i-       i  -i     -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chr2_235578534_   5023 CATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAA 5072
                                  viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_235578534_   5073 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5122
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_235578534_   5123 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5172
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_235578534_   5173 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAA 5220
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_235578534_   5221 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5270
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_235578534_   5271 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAGAG 5320
                         vi  v  i  i              v      v  ?   i   i i iii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_235578534_   5321 CTGAAACTGGATCCCTTCCTTACACTTTATACAAAAATCAATTCAAGATG 5370
                         v    ii    i    v   i    iv           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_235578534_   5371 GATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5420
                            i ?    i    ii v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_235578534_   5421 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5470
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_235578534_   5471 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5520
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_235578534_   5521 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5570
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_235578534_   5571 ACAGTCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5620
                          v  v     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_235578534_   5621 AAAAGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5670
                           ii i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_235578534_   5671 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5720
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_235578534_   5721 TCTCAAAAGAAGACATATATGCAGCCAAAAAACACATGAAAAAATGCTCA 5770
                             v        i   i viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_235578534_   5771 TCATCACTGGCCAT 5784
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


1047 22.57 1.04 6.60  chr2_235813115_235816336.rev     1535  1822 (1400)    L1M4_orf2#LINE/L1       17   288 (620)  

  chr2_235813115_   1535 GTTCATTGTCTAAAAGACTCAATATTGTTAGCATGTCAGTTCTTCCCAAC 1584
                               v vi ii      i          iv   v  i v  i     v
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chr2_235813115_   1585 TTTGATTTATACATTCAGTGCAATCCCCGACAAATAAAAATTCCAGATTT 1634
                           -   i  i v     ii        i-----  v     i    v vi
  L1M4_orf2#LINE/     67 TT-GATCTACAGATTCAACGCAATCCCT-----ATCAAAATCCCAGCTGC 110

  chr2_235813115_   1635 TTTTTCTTGGAGTTGGGGGTGGGGGGATTGACAAACTGGTTCTAAAATTT 1684
                         i    -   v  ------------ii        i   i i        i
  L1M4_orf2#LINE/    111 CTTTT-TTGCAG------------AAATTGACAAGCTGATCCTAAAATTC 147

  chr2_235813115_   1685 TTATGGAAATATAAAGAAACTAGAATAGTCACAACAATTTTGAAAAAGAA 1734
                         v         ii  i i v i       i  v      i           
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_235813115_   1735 AAACAACATTAGAAAACTTAAACTACTTGATTTCAAGAC--ACTATGAA- 1781
                         i     vi  i  ii   i v   v iii       i  --    ii  -
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr2_235813115_   1782 CTACAGTAATCAAAGCAGTGTGGTATTAGAATAAAAATGGA 1822
                                      ii          i i v    ii  i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

Transitions / transversions = 2.61 (47 / 18)
Gap_init rate = 0.02 (6 / 272), avg. gap size = 3.67 (22 / 6)  

1896 22.33 4.94 4.31  chr2_235813115_235816336.rev     2111  2737 (485)    L1M4_orf2#LINE/L1      278   908 (0)  

  chr2_235813115_   2111 ATAGAGGTAGACATATAAATCAATGGAAGAAAAT--AGAGTCTAGATATA 2158
                            ii i          i          v i   --      i   v   
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr2_235813115_   2159 GACCCATAT-TACATGGTCAGTTGATTTTTGACAAAGGTGCAGAGATAAT 2207
                         i       i- vi       i        i     i     vi   iv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr2_235813115_   2208 TTAGAGGGGCAATAACAATGTTTTCAACAAAAGGTGCTAGAACAATTGGA 2257
                          i iv    v  v  i i v           v      i i    i    
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr2_235813115_   2258 CAGCCACATACATAAGAAT----T---ATCTTTTCCTCACATAATACACA 2300
                         i ?      i  v      ---- --- i ii v       iv   i   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr2_235813115_   2301 AAAGTTAACTCAAAATAGATTATAGACCTTAATCTAAGAGTCAAAAC-AT 2349
                            i            i   i ?      v   v      ii     -  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr2_235813115_   2350 AAAGACTTTCAGAAGAAAGCATAAGAGAAAATCTTAGCAATGTTGGGTTT 2399
                            -   i i        i    i ? v       v ii iv       v
  L1M4_orf2#LINE/    528 AAA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr2_235813115_   2400 CCCAAGGATTTAAAAAGTAGGAT-TTAAAAATAAAAACTACTAATTCCAA 2448
                         vv   v i   vvv ii  v  i-ii    ii v  i ----  ---   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC----AA---CAA 619

  chr2_235813115_   2449 AAGAAAAGAATCAGCCAACTGGACCTCATCAAAATGAAAAACTTT-GCTC 2497
                                -   viiiv  i     i          v         - iv 
  L1M4_orf2#LINE/    620 AAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr2_235813115_   2498 TTCAAAAGACAGTGTTACAAAAATGAAAAGACAAGCCACAGACTGGAAGA 2547
                               i    v i i vi   i           v       v   i   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr2_235813115_   2548 AAACATCTGTAAATCATGGACGTAATCGAAGTCATACACAAAGGACTTGT 2597
                            i  i  i       iv iv i  -------------  i        
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGAT-------------AAGGGACTTGT 755

  chr2_235813115_   2598 GTATGGAGAGTACAGAAAGA---CTCAAAAAT--ACAATTGAAAAAGAAA 2642
                         --  vv   i  i v     ---  i v  v -- i   --       v 
  L1M4_orf2#LINE/    756 --ATCCAGAATATATAAAGAACTCTTACAACTCAATAAT--AAAAAGACA 801

  chr2_235813115_   2643 AACAACATGAT----------ACAAAA---TTGACCAGACACTTCACCAA 2679
                           i   vii  ----------i    i---    vi     i   v    
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr2_235813115_   2680 AGAGCATATACAGATGGCAAATAAGCATACACAAAGTTACTCATGAATCA 2729
                            iv       i     v        i iiv    v i    -iv    
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA-ACATCA 900

  chr2_235813115_   2730 TTAAGGAA 2737
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.69 (86 / 51)
Gap_init rate = 0.03 (19 / 631), avg. gap size = 3.05 (58 / 19)  


1042 33.25 5.24 2.38  chr2_235978996_235980822      501  1339 (488)    L1M4_orf2#LINE/L1       46   908 (0)  

  chr2_235978996_    501 AAGATCTCAGTTCTCCCACAAGTTAAATTGGTAAATTTAACAAACTTCCA 550
                              vv  i v     -   i  i - ivii i   i   iv v i  v
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCC-CAAATTGA-TCTACAGATTCAACGCAATCCCT 93

  chr2_235978996_    551 ATTAAAATATCAATAGGTGGTTTTA-AGAAGCT-ACGGAAGTTGATACCG 598
                           i     vi  iiv vivv    i-    ii -  --   i    v ii
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTA 141

  chr2_235978996_    599 AAGTTCATGTAGCAAAT-TAAACATGCAAGAATAGCTAGGGAAACCGAGG 647
                           i     i i -    -i  ivivv v        i iiiv  i vv i
  L1M4_orf2#LINE/    142 AAATTCATATGG-AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_235978996_    648 ATAAAGAAAAATACCATGATG-AGATCTTGGCCTTCCAGGTGTGAATACA 696
                          -      i  i -- v v  -  iv  iivv     vii v v  v  v
  L1M4_orf2#LINE/    191 A-AAAGAAGAACA--AAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr2_235978996_    697 TGCTAGCAGTCCTCC-GTAAGTGAAACGATGGAGGACTGGGGCATGAATA 745
                          i   -  ivv  v -    vii i  ii  vi v     vii v i   
  L1M4_orf2#LINE/    238 TACTA-CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_235978996_    746 AACAGCCAGACAGGTGAAATCAAACTAAAAGTCCAGAAATAGACCCAAGT 795
                         i   vvi   ivii  i   vi  i i i            i     -- 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--T 334

  chr2_235978996_    796 GCATGTGAAAATTTAGCGTATGTTAGATA---GTATTTTGA--AT-CACC 839
                         i   v - vii iv vi -  v  v  i ---  iiivv  --  -  vi
  L1M4_orf2#LINE/    335 ACATTT-ATGGTCAATTG-ATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr2_235978996_    840 AGAGTAAAAATGAACTTTTAAATAAACGGCACTAGGGCAATGAGGGAGAC 889
                         i i v  i   iiv     v  i   i  ii  i  i   ivi iv ?v 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_235978996_    890 ACTTGGGAAAAGTTCAAATTAGATCCACACCTCACACCATATGCAAGAAG 939
                           v  vi   iiv v  i  i  i  vi              i   i  v
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_235978996_    940 AAACTCTAAATGGATCAGAGATCTCAATGCAAATCTTGAAGCTACACACA 989
                         v     v          ?   i  v    i  ivvi i  i   i v vv
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr2_235978996_    990 TATTACATATAAAAGTGGGG--AATTCTTCA--ACTTTAGTATAGGGAAA 1035
                          v   v viv   vi i  ?--  v     i--  i  i vv    v  v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_235978996_   1036 AGCTTTCTAACTATGATACAAATTGTAAAAGCAATCATAGTAAAGATTGT 1085
                         i i  ii  iv     i  v  vv i v      iv v  v   i  v v
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_235978996_   1086 TACGTTTGACTCCATAAATATAAAAAAATCTTTTGCATAGCAAAAT-CAT 1134
                           vi  v    i   v  v  v     --      iiivv    iv-  i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACAC 680

  chr2_235978996_   1135 TGTAAATAAAGTCAAAAGATAAATGACA-ATTAGGAGGAAATATTCATAA 1183
                          i v  v     v      i  viv   - v i    i       iii  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_235978996_   1184 --TGTATATCAGGACAAAG----TGTAATAGTCCTAA---TATAAATAAT 1224
                         --ii      -v  i  i ----    ----   vi ---      v  i
  L1M4_orf2#LINE/    731 ATCATATATC-TGATAAGGGACTTGTA----TCCAGAATATATAAAGAAC 775

  chr2_235978996_   1225 TCTTTAAAATTAAGAGAAAAGTGACCAAAAGCCTGATAGATAAATGGGCA 1274
                             vv  v i  v iv   iv   v  v i  ii  v? v         
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr2_235978996_   1275 AAAGCC--------ACAATT-TACAAA-AAGATACAAAAATGACCCACAA 1314
                           i vi--------   v  - v    -      i v     i  v i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr2_235978996_   1315 --AAATGAGAA--TGCTT----TCATTCTCATA 1339
                         -- v    i  --    i----   ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (151 / 124)
Gap_init rate = 0.04 (34 / 863), avg. gap size = 1.88 (64 / 34)  


3269 18.52 0.81 0.16  chr2_235999262_236001999     1042  1662 (1076)    L1M4_orf2#LINE/L1       13   637 (271)  

  chr2_235999262_   1042 CCGTGTTTATGGACTGGAAAACTTATTATTGCTTAAG-TGGAAATACTCT 1090
                           i    i     i     i     v     -     -   v       i
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTG-TTAAGATGGCAATACTCC 61

  chr2_235999262_   1091 CCAAAACAGTCTATAAATTCGATGCAAATCTTATCAAGATCTCAGCTTCC 1140
                              viii    i i    i i    vi i      i   i     v  
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr2_235999262_   1141 TTTTTTACAGAAATAGAAAAACTCATCCTAAAATGCATGTGGAAATGCAA 1190
                               i       v  v  i  v          v   i           
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr2_235999262_   1191 GG-ATCTAGAGTAGCCAAAATTATCTTTAACAATAAGAACAAAGTTGGAA 1239
                           - i i   i         iv     v  v  v               i
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr2_235999262_   1240 CACTCATACTTCCCATTTTCAAAACTTATCACAAAGGGATAGCTACGAAA 1289
                         v     i        v            ii      vv i  iv iv  i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr2_235999262_   1290 ATAGTGTGTTATTAGTGTGAAGACAGACATATTGGTCAATGAAATAGAAT 1339
                          i      v  i i ii i i  i        v i      i        
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chr2_235999262_   1340 TGAGTGTCTGGAGATAACCCCGTACATCTATGGTCCATTGATTTTTGACA 1389
                             v   ii  i    v   i     i       v         i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr2_235999262_   1390 AGGATGCCAAGA-TATTCAATGGGGAAAGACTTGTCTTTTCAACAAATGG 1438
                            i        -i                v v                 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr2_235999262_   1439 TGCAGGGATAGCTGGATATCTACACGAAAAAGAAAGAAGTTGGACCTGTA 1488
                            v    i i       ? i   i v       v           iv  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr2_235999262_   1489 TCTTACATCATATACAAAAATTAACTCAACATGAATCACAGACTCATATG 1538
                         i  i   i                     v   i    ?    ii v   
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_235999262_   1539 TAAGAGCTAAAATTATAAAACTCTTAGAAAATAA-ATAGGAGTAAATCTT 1587
                                     i                i v  -     ?         
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr2_235999262_   1588 TATGACCTTCAGTTGGGCAAACG-TTCTTAGATCAGACCCCAAAAGCACA 1636
                         ii       vi   i     vv -         vv   v           
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr2_235999262_   1637 AAAAACCAAAGCAAAGCTAGATATAT 1662
                          iv   v    v   iv      v  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAAT 637

Transitions / transversions = 1.55 (68 / 44)
Gap_init rate = 0.01 (6 / 625), avg. gap size = 1.00 (6 / 6)  

1331 18.15 1.78 0.00  chr2_235999262_236001999     1967  2247 (491)    L1M4_orf2#LINE/L1      623   908 (0)  

  chr2_235999262_   1967 AAAAGCTAGATAAATTGAACTTCATAAGCATGAAAAACTTGTGTCTTTTA 2016
                             iv           i       v iv  v        v   vi  i 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_235999262_   2017 AAAGACACTATCAAGAAAGAGAGAAGACAA----TGGAATGGGAGAAACT 2062
                           i                v  i       ----ii            v 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_235999262_   2063 ATTTGCAAATCAAGTATCTGATTAGAGTCTTGTATTCAGAATATATAAAG 2112
                                     vi        v  i v       i              
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_235999262_   2113 AACTTTTACAACTCCACAATATAAAGAAAAATAACCCAATCTTAAAATAG 2162
                             i         v i    v     v            i?v     i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_235999262_   2163 GCCAAAGATTTGAATAGACTATTCTCTTAAAAAGAGGTATAAATGACCA- 2211
                           v  i             vv     iv  i    vi  i     i   -
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr2_235999262_   2212 TGAGTACATGCAAAAGTGTTCAATATCTTAGTCATT 2247
                          i  i     v   ii  i    i   v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (28 / 22)
Gap_init rate = 0.01 (2 / 286), avg. gap size = 2.50 (5 / 2)  


2114 13.71 2.72 29.30  chr2_236749321_236752312      667  1731 (1261)    L1M4_orf2#LINE/L1        1   782 (126)  

  chr2_236749321_    667 TGAAAAGACATC--ATGTTCACGGATTGGAA-------TAT--------- 698
                           i     i   --       i         -------   ---------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_236749321_    699 GGCAGTACTCTTCAAATCGATGTACAGAGTCGGCAAAATCACTTTCAGAA 748
                             i     ii     i   v      v  ii iv    v  v   i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_236749321_    749 TCTCAGCTGCCTGTTTTTTTCCCAGAAATTTGACA-GCTAATCCTAAAAT 797
                           i         ----    iv        -    -   i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT----TTTTTGCAGAAATT-GACAAGCTGATCCTAAAAT 145

  chr2_236749321_    798 TCATATGGCACAGTAAGAGACCGTCA-AATA-TCAAAACGGTCTTGAAAA 845
                                 v vv i   i    --  -    -i      ii         
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACC--CAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_236749321_    846 AAGAATGAA-GAAGTTGGAGATCTCACACTTTCTGATTTCAGAATTTACT 894
                          -   -   -i         iv         i ii      i  i     
  L1M4_orf2#LINE/    194 A-GAA-GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_236749321_    895 GCAAAAGCATGGTGATCCAAGCCTGTGTGATATTGGTGTAAAAATAGACA 944
                         i    ivi ii  i   -   v v     i  i   ii   ii       
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATC-AAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_236749321_    945 CACACGTCAATGAAGCGGAATCGAGAGTCCAGAAATGAGCCCCTTCATCG 994
                         i i vi      i iii    i              i i   v v   iv
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_236749321_    995 GTGGGCAGTTGATTTCCAAAAAAGATGCCAAGACATCTTCCCCAT-CAAT 1043
                         i   v  i       i i v  i i         --------   -    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC--------CATTCAAT 382

  chr2_236749321_   1044 GGGGAAGGAATAGTCTTTTTAGGAAGTGGTGCTGGGACAACTGGATATCC 1093
                               i            i iv  i                     ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_236749321_   1094 ACTTGTGAAAGAATGAAGTTAGACTCTTATCTAATGCTATATATAAAAAT 1143
                           v  ii             i   i i  i  v ii i     i      
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_236749321_   1144 TAACTCCAACACCTGTAATCCTAGCACTTTGGGAGGCTGAGGCGGGTGGA 1193
                               --------------------------------------------
  L1M4_orf2#LINE/    483 TAACTC-------------------------------------------- 488

  chr2_236749321_   1194 CACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCC 1243
                         --------------------------------------------------
  L1M4_orf2#LINE/    489 -------------------------------------------------- 488

  chr2_236749321_   1244 GTCTCTCCTAAAAATAGAAAAATTAGCTGGGCATGGTGGCATGCACCTGT 1293
                         ----------     i  --------------------------------
  L1M4_orf2#LINE/    489 ----------AAAATGGA-------------------------------- 496

  chr2_236749321_   1294 AACGCCAGCTACTTGGGAGGCTGAGGTAGAATAATCACTTGAACCCAAGA 1343
                         --------------------------------------------------
  L1M4_orf2#LINE/    497 -------------------------------------------------- 496

  chr2_236749321_   1344 GTTGGAGGTTGCAGTGAGCCGAGATCGCACCACTGCACTCCAGCCTGGGT 1393
                         --------------------------------------------------
  L1M4_orf2#LINE/    497 -------------------------------------------------- 496

  chr2_236749321_   1394 GACAGAGCAAGACTTCGTCTCAAAACACACACACACACACAAATTAATTC 1443
                         --------------------------------------------------
  L1M4_orf2#LINE/    497 -------------------------------------------------- 496

  chr2_236749321_   1444 CAGATTGATCAAAGCCTTGAGTGCAAAAACTGAAACTATAAAACTTTTAG 1493
                         --------   ?  v i i i  i  i i  i             i    
  L1M4_orf2#LINE/    497 --------TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_236749321_   1494 AAGAAAATAC-GGGGTAAATCTTTGTGACTTTAGATTAGGCAGTGGTTTC 1542
                                i i-  ?         i     i  i i       i       
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_236749321_   1543 TTAGATATGATACCTAAAGTGCAAGCAATAAAAGAAAAAATAGATAAATT 1592
                                   i   v    ii       i                     
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_236749321_   1593 GAATATTAGCCAAATTAAAAATTTTAGTGCTTCAAAGGGCAGTGTCAGAA 1642
                          i iv i v v          i   v            i  v i   ii 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr2_236749321_   1643 AAGTAAAAA-----TGCACAGAATGGGTGAAAACATTTGAAAATTAAATA 1687
                             i    -----iv           v     i     v    i v   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr2_236749321_   1688 TCCAGTAGGGATCTGGTATCCAGAATATATAAAGAACGGTTACA 1731
                           iii  i  iv  v                      vv     
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

Transitions / transversions = 2.86 (106 / 37)
Gap_init rate = 0.02 (19 / 782), avg. gap size = 17.95 (341 / 19)  

 238 22.03 1.69 0.00  chr2_236749321_236752312     2045  2103 (889)    L1M4_orf2#LINE/L1      769   828 (80)  

  chr2_236749321_   2045 AAAGAATACTTAAAACTCAACAATAGAAGG-TAGATTGTCCAATTTAAAC 2093
                               iv    v       i    i  i -i i  vii      ?   v
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr2_236749321_   2094 ATGGGCAAAG 2103
                                   
  L1M4_orf2#LINE/    819 ATGGGCAAAG 828

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1)  

 453 18.11 9.45 0.00  chr2_236749321_236752312     2374  2500 (492)    L1M4_orf2#LINE/L1      770   908 (0)  

  chr2_236749321_   2374 AAGACCTCGT----CTGAAAAATAAAA---TAAGTAA---AAAATAAAAA 2413
                             v   v ----  v  v       ---i  i   ---  vv?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr2_236749321_   2414 TGGGCTAAGACTCTAAATAGACATTTCTCCA--GAAAATATAAAAATGGC 2461
                              v   iv i i                --   i     v       
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr2_236749321_   2462 CAGTAAATACATGAAAAGATGCCTAATGTCATTACTTTT 2500
                           i   ii              ii  ii   ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.03 (4 / 139), avg. gap size = 3.00 (12 / 4)  


1089 26.56 4.92 1.31  chr2_236921916_236926661     2499  2803 (1943)    L1M4_orf2#LINE/L1        1   316 (592)  

  chr2_236921916_   2499 TGGAGGAGTATATTGTGTGCATGATTTGAAAGCCTCAATATTTTTAT--T 2546
                             iiii   viii   v    iv   i   v  i      v   v-- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_236921916_   2547 TTTATTTTTCTCCAAATTGATTTATAGATTTGGACAACATAACCC----- 2591
                         vvi v vi  i          i  i     ----    ii  i  -----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT----CAACGCAATCCCTATC 96

  chr2_236921916_   2592 AGGA----AGCTA----TGTTGTAGAAATGGATGAACTGAATCTAAAATT 2633
                          ii ----    i---- v   i      v  ii i    vi        
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr2_236921916_   2634 CATCTGGAAATGCAAAGGAGCTAGAATAGCCAAAACAACTTCAAGAAGGA 2683
                            v           i   v i                ii ii i  i  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_236921916_   2684 AGAACTATGCTTGAAAACTTATACTACCTGACTTCAAAATTTATTATAAA 2733
                              v v i v  ii   i i   v  ii i       i   i  i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_236921916_   2734 GTTACAATATTCAAGACAGTATGGTATTGGTGTTAAAACAGGCAAATAGA 2783
                          i    i  v          i     i   ii v ii i  i  v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_236921916_   2784 GCAATGAAACAGAATAGAGA 2803
                         v     i  i     v    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGA 316

Transitions / transversions = 2.38 (57 / 24)
Gap_init rate = 0.02 (5 / 316), avg. gap size = 3.80 (19 / 5)  

2117 20.88 1.93 5.61  chr2_236921916_236926661     3320  3889 (857)    L1M4_orf2#LINE/L1      313   861 (47)  

  chr2_236921916_   3320 GAGAGCTCAGAAATAAACTCACGCATATATAGTCCATTCATTTTTGACAA 3369
                              ii           i  ii   v   i   v   v     i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr2_236921916_   3370 AGGTGCAAAGACCGTTTGGTGGAGAAAGGAAGGGTTTAGATTCACAAATA 3419
                         i     v      i  iii   i     i ------   --  -------
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAA------TAG--TC------- 397

  chr2_236921916_   3420 CTTATTTTCTACTAACAGTGCTGGAACTGTCAGATATCCACATGCAAAAA 3469
                         ----     v  v  ii       i  viiii    ?            i
  L1M4_orf2#LINE/    398 ----TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr2_236921916_   3470 TAAATAAAAAAGCTTCAATCCCTACCTCACATCATATTCAGAAATGAACT 3519
                         --   i  i----  vi i            i     v  i    v    
  L1M4_orf2#LINE/    444 --AATGAAG----TTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_236921916_   3520 CAAAATGGATCACAGACTTAAATGTAAAATGTAAAGTTATGAAATTTCTA 3569
                                     ?    i         i vv    ii   i   i ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_236921916_   3570 GAAGAAAATATAAGAGAAAATCTGTATGACCTTGGGTTAGGCAGATTTTT 3619
                                 i   i ? v      vii                 -  vv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTT 586

  chr2_236921916_   3620 TTTTAGATATCATAACCCAA---CCTAATCCTTAA-AAGAGAAAAAATGG 3665
                          i        v i --    --- vi  v ---  -  i         i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACA--CCAAAAGCACAAGC---AACAAAAGAAAAAATAG 631

  chr2_236921916_   3666 ATAAACTGGACTCCATAAAAATTAAGAACTTCTGTTCTTCAAAAGACATT 3715
                              i      i   v        i     i   v       i    i 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr2_236921916_   3716 GCTAAGAGAAT-AAAATCTAAGCCAGAGACTGGCAGGTAATACTTATCAA 3764
                         iii    i i -    vvi  v   v   v   v  iv    i  iiv  
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_236921916_   3765 TCACATATCTCACAAGAGATTCATATCTAGAATATCCCAAGAAACCTCA- 3813
                            i      v i   i  i ii    i       viv     vi  i -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr2_236921916_   3814 AACTTAA--ATAAGAAAAC---CAACCCAATTTTAAAAATGGGCAAAAGA 3858
                             i  --    i  i  ---i         ?-             i  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGA 830

  chr2_236921916_   3859 TTTGAACTGACACTTTACCAAAGAAGATACA 3889
                               iv    i  iv            i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATA 861

Transitions / transversions = 2.29 (80 / 35)
Gap_init rate = 0.03 (15 / 549), avg. gap size = 2.87 (43 / 15)  

 223 21.57 0.00 0.00  chr2_236921916_236926661     4205  4255 (491)    L1M4_orf2#LINE/L1      858   908 (0)  

  chr2_236921916_   4205 TATGTGGATGGCAAGTAAGTTCATGAAACAATGCTCAACATCGCTAGTTA 4254
                            iiii     v i    iv       vi            i???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_236921916_   4255 C 4255
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.00 (0 / 0)  


1151 26.06 5.63 8.63  chr2_237004344_237007822     1116  1683 (1796)    L1M4_orf2#LINE/L1        1   551 (357)  

  chr2_237004344_   1116 TGGGAA-ATATC--ACTTTCATGGACTGGAAAACTCAATAATGTAAAGAT 1162
                            i  -     -- iv        i     i   i    v   v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_237004344_   1163 GTCTGTTCTTCTCAAATTGATCTATAGATTCAATATAATTTACATTAAAA 1212
                          v vi v  i i            i        iii   iivi  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_237004344_   1213 TATTAGTT----TTTTGGTGGAAATGCATAAGCTGATTATAAA-TTCCTT 1257
                          vii  i ----    v ii     vv i        iv    -   v v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_237004344_   1258 TAGAAGTGCAAAATGTCAAGCATATCTAAGACACTTTGGA----GAAAAA 1303
                          i   i     iivii v  v   v i  i   v i v  ----   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_237004344_   1304 CAAGGTGGGATGACTTACTCT-----ATGGATGCAAACCATTATTGTAAA 1348
                            i  v   v    i  v  -----  --- v    v -   i ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAAT---TTCAAAAC-TTACTACAAA 246

  chr2_237004344_   1349 GCTACAGTGCTCAAGTCAATGTGATATTGGCAGAATGATAGACAGATG-- 1396
                                 iv     v  i    i  i     v  v        v  i--
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_237004344_   1397 -CAGTAGATCAGAATAGAGGATTTGTAAGCAAATCACTGTCTACATAAAC 1445
                         -  i i  vi     v   ii iiiv  ii   i --------    -- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--------CATA--C 336

  chr2_237004344_   1446 ACTTGTTTTCATTGTTGTTGTTGTTTTTAAATACTTGTTTTCAATGATAG 1495
                          i  i vv   --------i   -------------i     ---  i -
  L1M4_orf2#LINE/    337 ATTTATGGTCA--------ATTG-------------ATTTTC---GACA- 361

  chr2_237004344_   1496 AGGGCACTGAAAAGCACT----GGGAAAAGAACAGTCTTTTCAAGAAATG 1541
                             ii i-  i v  i ----   i      i           v     
  L1M4_orf2#LINE/    362 AGGGTGCC-AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr2_237004344_   1542 GTGCTGGAGCT-TTGGGTCAATCACATATTCATATGGCTCTGAAATAAGA 1590
                                ii v-i   i - ?i     i--  v v iv --   i vi  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGAT-AKCCACATG--CAAAAGAAT--GAAGTTGGA 455

  chr2_237004344_   1591 C-------TTGAACCATGAACAAAAATCAATTCCAGGTAAACTCGCAGAT 1633
                          ------- iiv     iv        i  i  v ii ii -  i?   i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA-TCAWAGAC 504

  chr2_237004344_   1634 ATAAATGTGATAAGTGAAACAATAAAGCTTCTGAAAAGGGGAGAAATAGG 1683
                         v       i v iv i    v     i  ii ii  --- i i v     
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA---GAAAACATAGG 551

Transitions / transversions = 1.92 (96 / 50)
Gap_init rate = 0.04 (24 / 551), avg. gap size = 3.38 (81 / 24)  

 252 28.57 1.79 2.68  chr2_237004344_237007822     2336  2447 (1032)    L1M4_orf2#LINE/L1      561   671 (237)  

  chr2_237004344_   2336 TCATAATCTTGAGGTAGGCAAAGAACTCTTAACATAGGACACAAAAAA-A 2384
                           i i i    i v       v ivi     i-   v     v    i- 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-ATATGACACCAAAAGCA 609

  chr2_237004344_   2385 CT-GTAACCACAAAGACAAAGTTGATAAGCCAAGTTTCCTTAACATTAAG 2433
                          v- i   - -     v   i v     iiiiiii   v i  v     i
  L1M4_orf2#LINE/    610 CAAGCAAC-A-AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr2_237004344_   2434 AACTTATTTTCTTC 2447
                              v v v    
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTC 671

Transitions / transversions = 1.46 (19 / 13)
Gap_init rate = 0.05 (5 / 111), avg. gap size = 1.00 (5 / 5)  

 402 30.80 8.86 1.69  chr2_237004344_237007822     2755  2991 (488)    L1M4_orf2#LINE/L1      655   908 (0)  

  chr2_237004344_   2755 AAGAACTTT----CATTAAAAGACACCATTATGACAGTGAGATGG-AAGC 2799
                           i      ---- v i   i     i  i v  v     i v i-  v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr2_237004344_   2800 TAAAGAGTGGGAGACAATATTCACAA-CCATGCACCTG-CAAACAGCTTC 2847
                         i v   i       v      ii   -i   ii i   -i  ivii   v
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr2_237004344_   2848 TCACTAAAA-GTATAAAA------------TTAATAAGAAAGAAATAGAC 2884
                          vv i i  -i      i------------ i     v   i i i i i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr2_237004344_   2885 AACCCAATGGAAAAATAGACAACCAACTC-AGCGGGTTTTATTAAAAAGT 2933
                                 v?      i i   vvi i i- iii iiv  vi vv    v
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr2_237004344_   2934 ACGGTAATATTCAAGTGATCACTATGCATATGAAAAGATGTGCAACCCCA 2983
                          ----i    v   i  ii  v  v   i           iv    vi  
  L1M4_orf2#LINE/    855 A----GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_237004344_   2984 GTAGTCAT 2991
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.88 (47 / 25)
Gap_init rate = 0.03 (8 / 254), avg. gap size = 3.12 (25 / 8)  


4418 16.39 3.37 1.46  chr2_237029305_237031260.rev      574  1464 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_237029305_    574 TGGAAAGACATTT-GTATTCATTGGTTGAAAGACTTAATCTTGTTAAGAT 622
                                 i  ii-i i     v i   i          v          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_237029305_    623 GGTAATAATTCCCAAATTGGCCTACATATTCAATGCAATTCCCAT-GAAA 671
                           i    v i         ii     v      i     i  i  -i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_237029305_    672 TCTCAGCCAGCTTATTTGCAGAAATTGGTAA-CTGATCCTAAAATTCATC 720
                           i    iiv   v             ii  -                 v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_237029305_    721 CAGAAATTCAGGAGATCCAG-----CCAAAACATTCTTCAAAA-GAAAAA 764
                         ii     v  i i  i    -----        v    v    -   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_237029305_    765 TAAAGTTGGGGGACTCACATGTCCCAATTTCATTTTCCAACTTACCACAA 814
                         i        i         iv           -----v       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCA-----AAACTTACTACAA 245

  chr2_237029305_    815 AGCTACAACAATCAAGACAGTGTGG-ACTTGCCTAAGAAGAGACATA--G 861
                                ii                -   v  v    i v       -- 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr2_237029305_    862 ATCAATGGATCAGAATCAGGAATCCAGTAATAAAGCCTTACATT-ACAGT 910
                                  vi     iii  i     v      v  v      - ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr2_237029305_    911 ---TCG--TTTTGACAAAGGTGCAAAGACAATTCAATTCAGAAAGAATAA 955
                         --- i --   i     i     v     v       vvi         i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr2_237029305_    956 TCTTTTCAACAAGTAATGCTGGGACTGTTGAATTGCTGCCTGCAAAAGAA 1005
                                     i ii         vii  i  v? ii v          
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr2_237029305_   1006 AGA-GTTGGACCCTTACCTCACGCCATATACAAAAATCAACTGATAATGT 1054
                         v  -         i        i              i    v v    v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_237029305_   1055 ATCAAAGACCTAAAAATAAGGGCTAAAACTAGAACACTCTTACAAGAAAA 1104
                             ?         vi    i          v  v       v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr2_237029305_   1105 TATAGGCATAAATTTT-GTGACCTTAGATTAGGCAGTTGTTCCTTAGATA 1153
                         i     ?i     i  -        i i       i v   i        
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_237029305_   1154 TGACACCAAAAGTACAGGCCACAAAA--------AGA-AAATTGCAACTC 1194
                                     i   i  v      --------   -      v vi  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_237029305_   1195 ATCAAAATTAAAAACTTTTTTGCTGCAAAGGACATCCTCAAGAAAGTGAA 1244
                                            v    v         iiv             
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_237029305_   1245 AAGACAACCCACAGAACAGAAGAAAATGTTTGCAAACCATGTA-ATATTG 1293
                                         ii i       i        i   i  -v iv i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_237029305_   1294 AGGGACTTCTATCTATTAATAGAACCTACAAAGAACCCTTACAACTCAAT 1343
                                 v    i ------   iv  i       i             
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCA------GAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_237029305_   1344 AATAAAAAGACAAATAACCCAACTTTTAAAGTGGGCCAACAATCTAAATA 1393
                                               -  ?v   i     v  vi  i i    
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAATA 838

  chr2_237029305_   1394 CACATTTTTCCAAATAAGATACACAAATGACCAATAAGCACATGAAAAGA 1443
                         v      i      v      i       i                    
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr2_237029305_   1444 CGCAGGAACATCATTAGCCGT 1464
                         i  -vv       ????????
  L1M4_orf2#LINE/    889 TGC-TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (90 / 52)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.26 (43 / 19)  


2544 25.23 5.54 5.43  chr2_237071854_237074027.rev      791  1674 (500)    L1M4_orf2#LINE/L1        1   885 (23)  

  chr2_237071854_    791 TAGACAGACATACCATATTCATGAATTGGAAGACTCAACATAGTAAAAAT 840
                          i  v   i  v    i      i           i  i  v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_237071854_    841 GTCCATTAGGATATTTTT---ATAGG---ATAGGATTAATGCAATTC-TA 883
                          v ------i   i iii---  v i--- i  iv i  i     i -  
  L1M4_orf2#LINE/     51 GGC------AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_237071854_    884 TCAAAATCCCAGAAATATAATTTGTAGACATAGACAAATTTATTCTAAAA 933
                                     vviiv vv    i   v  v     ii v  i      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_237071854_    934 TTTTTATGGAAAGGTAATGGAACTAGAATAACTAAAGCAATTTTGAAAAA 983
                           iv        v i  v   v i      i i   i    i        
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_237071854_    984 GAAGAATAAAGTGAGAAGGAC-CA-ATTTACTCAATTTTAAGGCTTATCA 1031
                               i     vi  -    -  - i  - i      i  ii    ii 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGA-GGACTCACACTT-CCCAATTTCAAAACTTACTA 242

  chr2_237071854_   1032 TATTGCTACAGTAATCAAGACTGTATGCTATTGGTAAAGAGCTAAACACA 1081
                         i vv                 v  i  v  i   i v ii v  i   i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr2_237071854_   1082 TAGATCAGTGGAACAGGACAGAGATCCTAGAAATAGGCCCACACAAACAT 1131
                                i     i  i iv    vi i       ii    i   vvi  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr2_237071854_   1132 GCCTACCTGACTTTTGATGAAGGTGCAAAAGCAATTCAAAGGAGGAAAGA 1181
                          vii vi   i   i  ii i     v  ii v      v  -       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGA 391

  chr2_237071854_   1182 GACA--CTTTTGAATAAGTAGTGCCAGAGTAACTGGAGATCCATAAGCAA 1229
                         - i --     v  i  i i    ii iii       v ?   i v    
  L1M4_orf2#LINE/    392 -ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_237071854_   1230 AAA---GAAAT-GGACCTCAACCTAAGTCTCACACATTATATAAAAATTA 1275
                           i---   i -     ----    --i       vv    i        
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACC----CCTA--CCTCACACCATATACAAAAATTA 484

  chr2_237071854_   1276 ATTCAAAATGGGTCACAGACTTAA-----------------------CTT 1302
                          i         i   ?    i   -----------------------  i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr2_237071854_   1303 TTAGAA--AAACAAAAAGAGAAGACTTTGGGGGCT-AGGCTAGATAAAGA 1349
                               --     v ii?iv  iv   i v iv  -i  i   ii  v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr2_237071854_   1350 GTTCTTAGAATTAGCATCCAAAACACAATTTTTAAAAGGAAA--TA---- 1393
                         v        vv ii  i v   i     vivvi     i   --  ----
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr2_237071854_   1394 --TTGGACTTCATCAAAACTAAAGATGATTGCTCTGTGAAAGACCCTGTT 1441
                         --                i    i ivv   iv  vii  i   v  i i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_237071854_   1442 AAGAGGATAAAAAGACAAGCTACAGACTGGGAGGAAATATTTGCAAACCA 1491
                             iii i         v i     v      i             i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_237071854_   1492 CATATCTGACAAAGATCTAGTATTCATATACTAGACATATATAGAACTCT 1541
                         i        i  i iv  v    i  ------------------------
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCA------------------------ 760

  chr2_237071854_   1542 GAAACAATAAACATATAAAGAACTCTCAAAACTCAGAAGTTAAGAAACAA 1591
                         --------i  i              i v      iv i v  i i    
  L1M4_orf2#LINE/    761 --------GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr2_237071854_   1592 GCAACCCAATTAGAAAACAAGTGAAAGACATAAAGAGACATCACACTGAA 1641
                         ii         ?i    iii ii  i  iv i  v      iv v ii  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr2_237071854_   1642 GAGGATGTACAGATGGCAAATAAGCACATGAAA 1674
                           i   i    i     v               
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAA 885

Transitions / transversions = 2.13 (149 / 70)
Gap_init rate = 0.02 (21 / 885), avg. gap size = 4.62 (97 / 21)  


3224 27.02 1.00 0.44  chr2_237074559_237078021.rev     2069  2971 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_237074559_   2069 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2118
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_237074559_   2119 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 2168
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_237074559_   2169 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2216
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_237074559_   2217 TATGGAACCAAAAAAGAGCCCGCGTCGCCAAGTCAATCCTAAGCCAAAAG 2266
                                viiv  ii  v  v vi v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_237074559_   2267 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2316
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_237074559_   2317 TACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGATC 2366
                                 i   i    ii        ii iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_237074559_   2367 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCAAATATCTACAACT 2414
                                i    i--    i  --        vv   v i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_237074559_   2415 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2464
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_237074559_   2465 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2514
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_237074559_   2515 GAAACTGGATCCCTTCCTTACACCTTATGCAAAAATCAATTCAAGATGGA 2564
                            ii    i    v   i     v   i       i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_237074559_   2565 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2614
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_237074559_   2615 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2664
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_237074559_   2665 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 2714
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_237074559_   2715 TTAAACTAAAGAGCTTCTGCACAGCAAAAGACACTACCATCAGAGTGAAC 2764
                          i   v v  i i   i  ii vv    i       i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_237074559_   2765 AGGCAACCTACGAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 2814
                           i     i  ii             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_237074559_   2815 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2864
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_237074559_   2865 AAA-----GACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 2909
                          i -----i    v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_237074559_   2910 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAGC 2959
                           v        i  vi viii     v  i          i       i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_237074559_   2960 ATCACTGGCCAT 2971
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.17 (13 / 6)  


3708 23.13 1.79 0.34  chr2_237115543_237119908.rev     2983  3877 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_237115543_   2983 TAGAAAGATATCCTGTACTCATGAATTGGAAGAATTAATGTTGTAAAAAT 3032
                          i           ii ii     i         v     i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_237115543_   3033 GAACATATTACCCAAAGTGATCTATAGATTCAGTGTAATGACTATCAAAA 3082
                          ivv   i v      v       i       ii i   vv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_237115543_   3083 TTTCAGTGACACTTTTTCACAGAAATAGAAAAAGCAATTCTAAAATTTAT 3132
                          ii   ivi -      ii       v  v  ivii  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_237115543_   3133 ATGGAACCACAAAACACCTCAAATATCCAATGAAATCTTGAGCTAAAAGA 3182
                               vii   iiv   ivi    v    viv        ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_237115543_   3183 ACAAAGCTAAAGACATCACACTTCCTGATTTCCAAATATATTACAAAGCT 3232
                               i ii  ivv          ii     v   iv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_237115543_   3233 ACAGAAAGCAAAACAGCGTGATACTGGCATAAAAACAGACATAAAGATCA 3282
                             v  v   i    i   i           ii i       v      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_237115543_   3283 GTGGAACAGAAGAGAGAGCCCAGAAATAAATCCACACACT-ACAGCAAAT 3331
                         i     i    vv     i           i   i   i - ii iv   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_237115543_   3332 TGATTTTCAACAAAGGTGTCAAGAACACACAATGGAAGAAGGATAAGTCT 3381
                                 i    i    i     v  iv      iii   i   -    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-GTCT 398

  chr2_237115543_   3382 CTTTGATAAATGGT-TTGAGAAAACTATATATCCACATGCAGAACAAGGA 3430
                         i  ii i       -i  i  v    iv   ?         i  v  v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_237115543_   3431 AATTGAACCCTTATCTCACACCATATACACAAATCAACTCAAAATGAGTG 3480
                          i   i    i  i               v    i           ii v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_237115543_   3481 AAAGCCATGAACAAAAGACCAGAAGCTATAAAACTACTGTAAGAAAACAT 3530
                          ?  v v i  iiv    v vi  i          vi iv          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_237115543_   3531 AGGGG-AAATCTCCATGACATTGATCTGGGCAGTGATTTTCTGGATATGA 3579
                            ? -      i i    v   ivi i    i  i   ii i       
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_237115543_   3580 CCCCAAAAGCACAGGCAACAAAAGTAAAAACAGGTAAATGGGATTGCACC 3629
                          v           i          v     i  i     v   i v  i 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_237115543_   3630 AAACTAAAAAACTTCTGCACAGCAA-GGAAAC------AAAAGAGAAGAG 3672
                            v v        i  ii vv   -   v  ------i    v   i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_237115543_   3673 TCAACCTATGAATTGGGAGAAAATATTTGCAAACCATACATCTGATAAGG 3722
                         v     i iii v                    i    i           
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_237115543_   3723 CGTTAATTTCCAAAATATATAAAGAATT-TAAAGACTGCTATAGCAAGAA 3771
                         vii vi v    i             i - v vi   - v   ii  i  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACT-CAATAATAAAAA 797

  chr2_237115543_   3772 AACAA----CCTAATTTAAAATTGGGCAAAGGACATGAATAGACATTTCT 3817
                         i    ----  i    ?    v           iv               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_237115543_   3818 CAAAAGAAGACATACAAATGGTCAACATGTATATGGAAAAATGCTGAACG 3867
                          v        i          i   i v i i   i   i     v   i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_237115543_   3868 -CAACAGACAT 3877
                         -  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.90 (133 / 70)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


 754 31.49 6.30 5.97  chr2_237122654_237125412.rev     1364  2268 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_237122654_   1364 TGGAAAAGCATATCATGCTCGTAGGTAGGAATGCTCA-CACCAT--ACAT 1410
                               iii  vi    i  i i i v    vi  i -i iii -- v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_237122654_   1411 ACCTTGACTCCTAAACATCATCTATAGACATAATATGATCCAAATGAAAA 1460
                         iv vvv     iv  vv v     i   ivi  iiii    vv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_237122654_   1461 TACCAATAGCATTATATTG-GGGCATTGGCGGGGAGGAGGCAGGGAGGAT 1509
                          v   iiv  v  v -   -i iv    i ------- i  -------- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTGAC-------AAGC--------T 134

  chr2_237122654_   1510 GACCAAACTAAACTTTAAGTAGAAA-GCAAATAACCAAGAATAACCAGTG 1558
                           i ---     v  i vi i    -    ivi   v      i   ivi
  L1M4_orf2#LINE/    135 GATC---CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr2_237122654_   1559 GAATTCTGAAAATGAAG--CATAGTGAGGAGGAACTAGCTTTGCCAGGTA 1606
                         v   ii      v    --  v   v-      vii vvi  v   iv -
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTT-GGAGGACTCACACTTCCCAATT- 229

  chr2_237122654_   1607 TGAAAACATATT------CT-TAGGAGCC----CACTG--GCACAGACAA 1643
                          v     v  i ------  -i  v ii ----  v  -- i  v i  v
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr2_237122654_   1644 AAGACTAAAAAGGCACATCAATGGAAAAGAACAGAAAATCAAGAAATAGA 1693
                            iv  i v vii v          v    iv  i i  v       i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr2_237122654_   1694 CCCAAATACATACGG--AA---ATTTATAATAAAGA---CAGCATC-TCA 1734
                             v i iv  i  --  ---    vii i  i i---  iv i - iv
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr2_237122654_   1735 AATGTGAAAGGAAAAAAGGA-------AATAAATGGTATAAGAAGAGCCA 1777
                             ----i     i  vii-------  i       iivi i v i ii
  L1M4_orf2#LINE/    380 AATG----GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr2_237122654_   1778 GGTTGTCATCTAAGAAAAAAGAAAATTAAATTCCCAAGTCTTTATACTTT 1827
                          i v?i  iv ivi   i  vi  i  ii ii  i --- i i i  iv 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA---CCTCACACCAT 472

  chr2_237122654_   1828 ACTTTGGAATGATTCCAAAA-GGATCAAACACTTACGTATAAAACAAAAC 1876
                          ivivii   v vii     -      ? v  i  vi i   i ---ivi
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA---GCT 519

  chr2_237122654_   1877 AAAAC-ACAAAAGGACTAGAAGAAGCTA-AGAAAGAAATATGTCATAACC 1924
                              - i    vvvi        ivi -  i?iv    v -  i i   
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT-TCGTGACC 568

  chr2_237122654_   1925 TCAGAATGGGAAA-GATCTTTCTAATTATGATAC-AAACCCAGAAATCAT 1972
                          ii iv i  v  - i i i -  iv     i  -   vv  v  ii---
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCT-TAGATATGACACCAAAAGCACAAGC--- 614

  chr2_237122654_   1973 AGCAGAAAAAAAAATTGATAAATTCAACCACACACACAAAATTG----TT 2018
                          i  i  i       v        vi  iv  i---       i----i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCAT---CAAAATTAAAAACT 661

  chr2_237122654_   2019 TTAATCCTACAT-GGAAACAATGACCCCTGAGTAAGGGAAATGACAGATG 2067
                           vi v  v  v-   v  v  v ------  v   v    v    iviv
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCA------AGAAAGTGAAAAGACAACCC 705

  chr2_237122654_   2068 ACACCCTGAGAGAAT-TATTTGTGATGGGTATCACA-----GACAAGAGT 2111
                            vvv  i     v-      ii -----    i -----  i   i v
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAA-----ATCATATATCTGATAAGGGA 750

  chr2_237122654_   2112 CCTTTCTTC-TAATATGTAAGGAACTCCTACAGCTCTACAAGAAAAAGAA 2160
                          i v v i -v     i   i      i    i   v i  v       v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_237122654_   2161 TAATAACCCAATACAAAAAACAGCAAAAGGATATGAATAGACAGTGCTCA 2210
                         v           -i?     ii vv       v          v v   v
  L1M4_orf2#LINE/    801 AAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr2_237122654_   2211 GAAAAGAAAACTCAAATG---AATTCGAAACATAATAAAAGATGTTCAAC 2257
                         i  i ii v iv      ---   ---  i  i vv        i     
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAAT---AAGCACATGAAAAGATGCTCAAC 896

  chr2_237122654_   2258 AT-ATGAAAAGA 2268
                           - ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (164 / 117)
Gap_init rate = 0.05 (43 / 908), avg. gap size = 2.58 (111 / 43)  

1176 23.08 2.24 0.32  chr2_237122654_237125412.rev     2291  2602 (157)    L1M4_orf2#LINE/L1      591   908 (0)  

  chr2_237122654_   2291 AGAAATGCAAATTAAAACTACAC-TGACAAAC---AAAATTGATCAACTG 2336
                            v   - v ii    vi   v-ii     v---     v   v  i  
  L1M4_orf2#LINE/    591 AGATATG-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr2_237122654_   2337 AACCTCAACAAAATGCAAAACTTTTGCACTTCAAAAGATACCATTAAGAA 2386
                         i  i   v      vv          ii       i  i  i  i     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr2_237122654_   2387 AATGAAGATACAAGTAACAGACTGGGAGAAAATATTTACAGAATACCTAC 2436
                          i    i v    viv     v               i  i vi iv  i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr2_237122654_   2437 CTGTTAAAGGACTTACAGCCAGAAAATACAGAGTACTCTTACACCTCAAT 2486
                            v   i      ii v      v   i i  v         v      
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr2_237122654_   2487 AA---GAAGACAAACAATTCAGTCAAAAAACAGGCAAAAGATTTGAACAG 2533
                           ---i        i  ii  i i?     ii      i        i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr2_237122654_   2534 ACAATTCACAAAGGAAGATGTATGGATGGCTAGTAAGAACATGAAAAGAT 2583
                            v   v v  i      i  iii     i i    v            
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr2_237122654_   2584 GTTCAACATTATTCATCAT 2602
                          i       i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (46 / 25)
Gap_init rate = 0.01 (4 / 318), avg. gap size = 2.00 (8 / 4)  


1753 25.51 8.24 2.18  chr2_237230429_237232058.rev      503  1145 (485)    L1M4_orf2#LINE/L1      227   908 (0)  

  chr2_237230429_    503 ATTTAAATACTTACTATAAAGTTACAATAATCACGACTGTGTGCTATTG- 551
                             v  v        i    i    i      v   v     v  i  -
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_237230429_    552 TGTAAAGACAGATGTGCAAATTCATGGAGCAGGAT--AGACCCTAGAAAC 599
                         ii   i  i   ii ii i  iv     ii  i  --   vi i     i
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr2_237230429_    600 AGGCACACACATACATGATTGATCAATTTCCCACAAAGACACCAATGCGA 649
                          ii v  i    vi   i ii  ii    i v    i iii    vi v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr2_237230429_    650 T-CAATGAGGAAAGGGTGGTCTCTTCAGTAAATGGAG---GAAAAATGTG 695
                          -     i      ii i    i    ii      v --- i v  i-  
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC-TG 425

  chr2_237230429_    696 GATAACCACGTGAGGAAAAAAATGAACCTCAACCCTTATTTTGCACCACA 745
                             ?    i  v--    i      vi vi    i  ii ii     i 
  L1M4_orf2#LINE/    426 GATAKCCACATGC--AAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr2_237230429_    746 CATTAAA-TTCATTCCAAATGGATCCTAGATGTAAATGTAAAAGATTAAA 794
                         i iv   -  v i  v         v?   iv         i  v v   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr2_237230429_    795 TTATATAACTTATATAAGGAAA--------TAAATGTTCTGTGACCTTGA 836
                         i    v    iv  v   i   --------     v   -         i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGG 572

  chr2_237230429_    837 GGCAGG-AA-GATTTCTTAGA----ACATGAAAAACACTAAACATTAATG 880
                          vi   -  - i         ----   iv    i   -  i  vi  vi
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC-AAGCAACAAAA 621

  chr2_237230429_    881 TAAAAAAT-GACAAATTTGAGTTAATCAAAGT-AAAACCTGCTGCTTTTC 928
                         v       -  i     v  v  v      i -    v  vi  ivi   
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr2_237230429_    929 AAAAGACACCTAT---AAAAATGAAGAGGCAAGTCAGAGACTGGAGAAAG 975
                            i     -   ---i   i    i  i   vi  v   v   iii  i
  L1M4_orf2#LINE/    672 AAAGGACAC-TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr2_237230429_    976 ATATCTGCAAA----------------GGGCTGGTGTCCAGAATATAGAA 1009
                             i      ----------------  i  v  i           v  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr2_237230429_   1010 AGAACCCGTATAACTCAATAA---GAAGACACATAACCTAACAAAAAAAA 1056
                              i v  i          ---i      v      i  iv?     -
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA- 819

  chr2_237230429_   1057 AAACAGACAAAAGAC--GAACACAAAATTTATTTACA-----TACATGAA 1099
                         ---ii i    i  i--   i -i v    v ii v -----  i ii  
  L1M4_orf2#LINE/    820 ---TGGGCAAAGGATTTGAATA-GACATTTCTCCAAAGAAGATATACAAA 865

  chr2_237230429_   1100 TGGTCATTAAGCAAATGAAAAGATTTTCAACTGAATTATCATCAGA 1145
                            i  v      v          vi     ---  i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAAC---ATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (108 / 53)
Gap_init rate = 0.04 (24 / 682), avg. gap size = 2.79 (67 / 24)  


3318 21.40 5.10 2.27  chr2_237339228_237343710.rev     3109  3991 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_237339228_   3109 TAGAGACACATTCTGTGATCATGGATTGGAAGACTCAATGTTGTTAAAGG 3158
                          i  i v i  i ii  v                 i   i       -- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA--G 48

  chr2_237339228_   3159 AT--TAATTCTTCCCATTTTGATGTATAGATTCAATGTAATCCCAATTAA 3206
                           --i   v  i    vv     v  i        i i      v  i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_237339228_   3207 AATCCCAGCAAGGCTTTTTTTTTGTAGACATTGACAAGCTGATTTTAAAA 3256
                                  --v  i      -- i   v              ii     
  L1M4_orf2#LINE/     99 AATCCCAGC--TGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_237339228_   3257 TTTATATGAAAAGGCAAAGGAACTAGAATAGCCAGGATAATTTTGAAAAA 3306
                           i     i   v    i   v i          ii i   i        
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_237339228_   3307 GAA---CAAAGTTGGAGAACTCAGATTACTTGATG-CAAGAATTGTTATA 3352
                            ---           i     v i v iii  v-   i v  ii  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_237339228_   3353 AAACTATGGTAATCAAGTTGGTGCAGTATTGGTGAAATAACAGATACACA 3402
                           i   ii         vii   ii   i   iiv  vi i   i i i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_237339228_   3403 GACCAATGAAACAGAACAGAGAGTTCAAAAATAGACCCCCCAGGATAC-- 3450
                           i     i  i    iv      i  i     i    ------    --
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC------ATACAT 338

  chr2_237339228_   3451 ----GGTCAATTAATTTTCAACAAACACACCAAGGCAATTCAATGAAGAA 3496
                         ----        i      i    iviii     i v        ii   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_237339228_   3497 AGGATATTCTTTTCAACGAATGGATTTTAA---AATTGGACATCCATATG 3543
                           i   v          i     - vi ii---  i    i ?   i   
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGG-TGCTGGGACAACTGGATAKCCACATG 437

  chr2_237339228_   3544 CAAAAACAAAAATCTTGATCTATATCTCATACCTTATATAAAACTTAACT 3593
                              iv vi  vi v  i iv  i    i   v    i    v      
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_237339228_   3594 CAAAGTGGATTATAGACCTAAATGTAA-------AATTATAAAGC-CTTA 3635
                             i     i ?              -------  i      i -    
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_237339228_   3636 -AAGAAAACGTAAGAAACAAATCT--GTGACATTGTGATGGGCAAAGATT 3682
                         -        i  i ?i-i      --     v   v v i     v i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_237339228_   3683 TCTCAGATAAGACAAAGAAAGCACAATCCGTAAAGGAAAACAAAT-GATA 3731
                            i     v    vvi         v vii   i     --   -    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA--AATAGATA 634

  chr2_237339228_   3732 AATTAGACATCATCAAAATTTAAAAATCTTTGTTCT-------ATAATA- 3773
                             i   v           -     ii     v  ------- i v  -
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr2_237339228_   3774 -AATAA--TGGGAAGACAAGCCACCTACTGAGAGAAAATATTTGCAAATC 3820
                         -  v  --  ii       v    vv v  i                   
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_237339228_   3821 ACGTAACTGACAATAAACTTGTACCAAGAATATATAAACAACTCTTGAAA 3870
                          ii  v    i  vii       i v            v       iv  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_237339228_   3871 TTCAACAG---AAAACCAAA--GCCCAATTTTTAAAAAATGGACCAA--A 3913
                         i    i i---   iv    --i       ?---        i v  -- 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTW---AAAAATGGGCAAAGGA 830

  chr2_237339228_   3914 TTTTAAAAAATACTTTACCAAAGAAAACATACAGATGGCAAATAAGCCTA 3963
                            v  v i i i  iv        i i     i     v       vi 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_237339228_   3964 TGAAAAGATGCTCAAAATCATTACTAAT 3991
                                        v    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (125 / 60)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.60 (65 / 25)  


 306 12.96 5.56 0.00  chr2_237767682_237771415.rev     2413  2466 (1268)    L1M4_orf2#LINE/L1        3    59 (849)  

  chr2_237767682_   2413 GGAAGACATCCCTTGTTCATGGATTGGGAGACTTTATATTAT---GATTG 2459
                          i    i     v              i      v     i ---   v 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_237767682_   2460 CAATACT 2466
                                
  L1M4_orf2#LINE/     53 CAATACT 59

Transitions / transversions = 1.33 (4 / 3)
Gap_init rate = 0.02 (1 / 57), avg. gap size = 3.00 (3 / 1)  

3429 18.06 3.48 1.94  chr2_237767682_237771415.rev     2468  3242 (492)    L1M4_orf2#LINE/L1      122   908 (0)  

  chr2_237767682_   2468 AAATTCACAAGCTGATCCTAAAATTCATATACAAACTTAAGGAATGCAGA 2517
                              v                        iv   ivi    i iv    
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr2_237767682_   2518 ATACCCCAAAACAGTCTTGAAAACAAAGAACTA---TG-AGGATTCATAC 2563
                            v  -      i         vi      v ---  -    i   i  
  L1M4_orf2#LINE/    172 ATAGCC-AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr2_237767682_   2564 TTTCTGATATCAAAACCTACTGTTAAGCTACAATAATAAACATTAGATAG 2613
                           i ii  v       i    iiv        i    ---  ------  
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT---CA------AG 261

  chr2_237767682_   2614 ACATTTCGGTAAATGGATAATAAGAGTAGACATAAAGATCAATTAAATAG 2663
                            v vi    v-   v--     ii        v        vi     
  L1M4_orf2#LINE/    262 ACAGTGTGGTAC-TGGC--ATAAGGATAGACATATAGATCAATGGAATAG 308

  chr2_237767682_   2664 AATTGAGGATGCAGAAATGAGCCCTTGCATTGATAGTCAATTGATTTTCA 2713
                                ii v       i i   v i    v  i              i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr2_237767682_   2714 ACCAGGGTATCAAGACCATTCAGTGGGGGAAAGAACAGTCTTCTCAACAA 2763
                           v     ii            i     -      i      i       
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAA 407

  chr2_237767682_   2764 ATGATGGTTGAACAACTGTATAGCTACATGCAGAAAAATGAAGTTGGACC 2813
                            i  v v i       v   ? i       i  i              
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr2_237767682_   2814 TCTATCTCAGACCACCTACAAAAATTAACTCAAAATAGATCTAAGACGTA 2863
                         i   i    v    iv                    i    v?    v  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr2_237767682_   2864 AGTGTGAGAGCTAAAACTATA---------GAAAAAAA--TAGGA-TAAA 2901
                          i   i               ---------   i    --    ?-    
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_237767682_   2902 TCTTTATGTCCAGGCATTGGGCACTGATTTCTTAGATATGACACCAAAAG 2951
                             ii  v  vv vi  i    v  i                       
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_237767682_   2952 CACAAGGAACAAAAGAAAAAAATCGATAAATTGGACATTATCATAATTAA 3001
                               v              - v            v i    v      
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAA 656

  chr2_237767682_   3002 A--CTTTTGTTCTTCGAAAGACACCATCAA-AAAGTGAAAAGA--ACC-A 3045
                          --       v    i  i     i     -            --   - 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr2_237767682_   3046 -AGAATTGAAGAATATTTTTACAAGTCACATGCCAGATAAAAGACTTGAA 3094
                         -     v i    v  v   i   i   i  ii v     ii      v 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr2_237767682_   3095 TTTAAAATATATTGATAATTCTTAAAACTCAAAAATAAAAAGGCAAATAA 3144
                          ii i       vi v  i     v       v         i       
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr2_237767682_   3145 CCTGATGTTAAGATGGAGTAAGGATTTGCTCAGATGTCTCTCCAAAGAAG 3194
                           ii  v?v  i    ivv         vvi   ii i            
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr2_237767682_   3195 A----CAGATGTTCAAAACACACGTGAAAAGATGTTCTACGTCATTAGTC 3240
                          ----  i   vi   v vi   i          i  v  i   ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr2_237767682_   3241 AT 3242
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.47 (81 / 55)
Gap_init rate = 0.02 (18 / 787), avg. gap size = 2.33 (42 / 18)  


3074 24.35 7.06 0.47  chr2_237797031_237799822     1451  2300 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_237797031_   1451 GAAAGATACACTGTGTTTAATGAATTGGAATAACTAATATTGTTGAATTG 1500
                                 iv ii    i -  i       v vi          i iv  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCA-TGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_237797031_   1501 TTCATACTACCCAAAGTGACCTACAGACTCAGTGCAATCCCTGTCAAAAT 1550
                         viv     v      v   i       i   ii         i       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_237797031_   1551 ACCAATGACATTCTTCACAGAAATAGAAAAATGAATCCAAAAATTGATAT 1600
                         v   iivi v  i  ii       v  v  iivi    v      v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_237797031_   1601 GGAACCACAATAGACCTTAAATAGCCAAAGCAATCTTGACAGAAAAAAAA 1650
                             vii   vi    ivi          i         - i  i  i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAGAA 200

  chr2_237797031_   1651 AAAAGCTGGAGGCATCACACTCTCTGACTTCAAAGTATATTACAAAGCTG 1700
                         v    i      vv       ii ii i      iiv  i         i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_237797031_   1701 TAATAGCCAAAAACTCATAGTACTGGCATAAAAACAGACACACAGAACA- 1749
                         i i  ii   i vvvii i            ii i     i i   v  -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_237797031_   1750 ------------GAGAGCCCAG----------------------CCAACT 1765
                         ------------     i    ----------------------i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_237797031_   1766 GATTTTTGGCAAAGATTCTAAGAACACACCTTGGAGAATGGACATTCTCT 1815
                               i i   i i v i    v  iv vv   i   v i i v   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_237797031_   1816 TCAATAAATGGTGTTGGGAAAACTGGATATTCACATGTGGAAGA-TGAAA 1864
                             i        i     v         ?i      iii    -    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_237797031_   1865 TGAGACCCTTATCTC-CACCGTATA-AAAAAT-AA---AAAATGGATTAA 1908
                          vi     i  i   -    i    -      -  ---         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_237797031_   1909 AGACTTACATGTCAGATCTAAAATTATGAAACTATTAGAAGAAAACACGG 1958
                             i  v    v   v      i   i     v             ii 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_237797031_   1959 GA--AATTCCTTATGACATTGGTCTGTGCAAGGATGTTTTGGATAAGACC 2006
                          ?--  v  i ii    v    vi iv    v i v i  i    v   v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_237797031_   2007 TTAAAAGCACAGCCAATGAAAGCAAAAATAGACAAAT-GGGCTTACATCA 2055
                         ii         iv   ii    v         i    -  i   -     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATCA 649

  chr2_237797031_   2056 AACTAAAAAGCTTCTGTATAGCAAAGGATACAATCAACAGAGTTCAGAGA 2105
                           v v    i   i   iivv       i  v     v i   vv i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr2_237797031_   2106 CAACCTGTAGAAATGGGAGAAAATACATATAAACTATACATATGACAAGT 2155
                              iii    -            iv ii   ii   i  v   i   v
  L1M4_orf2#LINE/    700 CAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_237797031_   2156 GGCTAATATTCAAAATACGCAAAGA--TCTTA--AC---------AAAAA 2192
                          i  vi   i  i    iii     --     --  ---------    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_237797031_   2193 ACAAATAGCCCATTTAAAAAATGGGCAAAGGACGTGAATAAACATTTCTC 2242
                                i    v  ?                iv      i         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr2_237797031_   2243 -AAAGAAGACATACAAG-GTCCAATAGATGTATGAAAAAATACTCAGCAT 2290
                         -        i      i- v      iiiii       i  i    i   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_237797031_   2291 CACTAATTAT 2300
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.12 (138 / 65)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 3.56 (64 / 18)  


3961 16.90 5.90 2.43  chr2_237863644_237865576.rev      578  1441 (492)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr2_237863644_    578 ATATTCATGGATTAAAAGACTTAATGTTCTTAAGATGTCAATAATGTTGT 627
                           i          ii          i  --------------------  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATT--------------------GT 44

  chr2_237863644_    628 TAAGATGTCCATACTACCCGAAGTGATCTACACAGTCAATGTATTCCCTA 677
                                v v     v   i  v         v v    i i v      
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr2_237863644_    678 TCAAAATCTCAA-TGACGTTTCTGAGGAAGTAGAAAAAACCATCCTAAAA 726
                                 i  i-  v v   i  vi   i v  v  iviv         
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_237863644_    727 GTTGTATG-AAATCTCAGGGACCTTTAATAGCCAAAGCAATCTTGAAAAA 775
                         v ii    -    viv       ivv          i             
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_237863644_    776 GCAGAAGAAAGCTGGAAGACTCACAGTTCCTGGTTTCAAAACTTGCTACA 825
                          v    v    i    i        v    iii           i     
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_237863644_    826 AAGCTATAATACTCAAAACAGTGTGGTACTGGCATAA------------A 863
                               i i  v    i                    ------------ 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_237863644_    864 AACCAATGGAATTGAATAGACAGCCCTGAAATAAACCC-TGTATGTATGG 912
                         i i         v    v  v  i  v           - ii  v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr2_237863644_    913 TCAAATGATTTTTGACAAGGGTACCAAGATGATTCAATGGGGAAAGGACA 962
                             v       i         i      iv               i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_237863644_    963 GTCTTTTCAACAAATGTTGCTGTGA-AACTGGGTATCCACATGAAAAAGA 1011
                                         v     v  -      i  ?       v      
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_237863644_   1012 ATAAAGTTAGACCCTCACCTAACACCATATACAAAAATTAGCTCAGAATG 1061
                           i     i     ii    v                   i    i    
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_237863644_   1062 GATCAAAGACCTAAATGTAAGA-CCAAAACTACAAAAATCTTAGAATAAA 1110
                              ?                - i       i    v        v   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_237863644_   1111 ACATCAGG---AAATCTTTATAATATTGAATTCTGTAATGATTTCTTGGA 1157
                             -   ---       ii i iv   ii  vv i    i      i  
  L1M4_orf2#LINE/    545 ACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr2_237863644_   1158 TATGACACCAAAGGCACAGGCAGCAAAAGTAAAAG-AAACAAATTGAACT 1206
                                     i     i   i      v    i- i i      i   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_237863644_   1207 TCATGAAAGTTAGAAG--TTTGTGCATCAAAAGACAATATCAACAGAGTA 1254
                             v   i   i  i--       v     i    v      v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_237863644_   1255 AAAACGCAACCAACAGAGTGGAAGAAAATAATTGCAAAT---ATATCTGA 1301
                             vi     v     i   i        v        ---        
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_237863644_   1302 TAAGGGATTATTACCCAGAATATATAGAGAACTCGTAAAACTCACCAATA 1351
                                i vv  i            i       v  v      vi    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_237863644_   1352 AAGAAACAAATAG----ATTTTAAAATGAGCAAAGGGCTTAAGTAGACAT 1397
                           i i       i----   ?v      i       ii  i i       
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_237863644_   1398 ATC-----AG----------------CAGTAAGCACATAGAAAGATGTTC 1426
                         v  -----  ----------------  i         ii       i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_237863644_   1427 AATATCACAAATTAT 1441
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (89 / 54)
Gap_init rate = 0.02 (15 / 894), avg. gap size = 4.80 (72 / 15)  


2893 27.06 1.78 0.67  chr2_237962424_237967679     3867  4764 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_237962424_   3867 TGGAAA-ACATCCCATGCTCATGGATAGAAATAATCAATATCATTAAAAT 3915
                               - i        i        v i  v v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_237962424_   3916 AGCCATACTGCCAAAAGCTATTTACAGATTCAATGCTATTGCTATGAAAC 3965
                         i  v     v  v   viv  i           i  v  iv    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_237962424_   3966 TACCAATGACATACTTCACAGAACTAGGAAAAAACT-ACTTTAAAAT-CA 4013
                          v   iivi v vi  ii     v v -- v  i  - iii      -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_237962424_   4014 TATGGAACCAAAAAAGAGCGTGGATAGTCAAGGCAATCCTAAATAAAAAG 4063
                                viiv  ii  v vv i    i   ii     i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_237962424_   4064 AACAAAGCTGGAGGCATCACACTAGCCAACTTCAGACTATACTACAGGGC 4113
                                i      vv       vv    i    i viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_237962424_   4114 TAACATAACCAAGACAGCATGGCACGGGCACAATAACAGACATACAGACC 4163
                           vvi   i        ii   i  v    i  vi i       i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_237962424_   4164 AATGGAACAGAATAGAAAGCCCAGAAATAAGGCCACAGACCTACAACCAT 4213
                                i     v  i  i          iv   i v ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_237962424_   4214 CTGACCTTTGACAAAACTGACAAAAACAAGTGATGGGGAAAGGACTCCCT 4263
                         i   ii  i     iiv  v   i v  vvii          i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_237962424_   4264 ATTTAATAAATGGTGATTGGATAACAGGCTAGCCAAATGCAGAAAATTAA 4313
                         v  i  i        v v   i   v  v  ?   v     i  i v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_237962424_   4314 AACTGGATCCCT----TACATTATATACAGAGATCAACTCAAGATGAATT 4359
                          ii    i    ----i   ii       i i  i       i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_237962424_   4360 AAAGGCTTAAATGTAAAACCCAAAGCTATAAAAGCCCTGGAAGACAACCT 4409
                          ?  i i         i v i   i        vi i i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_237962424_   4410 AGGCA-ATACCTTCCTGGACATAGGAGCAGGTAAAGATTTCAT-GATCAA 4457
                            ?i- v i    v  -  v v  ivi   i  v i    v -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr2_237962424_   4458 GACACCAAAAGCAATCA--CAACAAAAGCAAAAGTTGGCAAATGGGATCT 4505
                                      --  --         v    i v ii    v   ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_237962424_   4506 AATTAAACTTAAGAGCTTCTGCACGGTGAAAGAAACTATCAAGAGAGTAA 4555
                         v  i   v    i i   i  ii vvii  i  v          i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_237962424_   4556 ACAGACAACCTACAGAATGGGAGAAAATATTTGCAAATGATGCAACTGAC 4605
                          v        i                           v  ii v    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_237962424_   4606 AAAGGTCTAATATCCAGCATCTATAAGGTACTTAAACAGATTTACAAGAA 4655
                           i  v  vi       v  v     i v   ivv   iv iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_237962424_   4656 AAA---AAAAAACC--ATTAAAAAGTGAGCAAAGGACATGAACAGCCACT 4700
                            ---   v    --   ?    i  i        iv    i  v  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_237962424_   4701 TTTCAAAAGAAAAAATACATTCAGCCAACAAGCATATGAAAAAAATCTCA 4750
                          i  v      i v     vvii     i     i       i vv    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_237962424_   4751 ATATCACAGATTGT 4764
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


2054 12.31 2.90 30.14  chr2_238120582_238122671      494  1598 (492)    L1M4_orf2#LINE/L1      105   908 (0)  

  chr2_238120582_    494 AGCTAACTTCTTGGTAGAACTTGACAAACTGATTCTAAAATTCA------ 537
                             iv   i  v i    v       i     i          ------
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_238120582_    538 ----CAAGGTACCCAGAATA----------TCATGTAAAAGTAGAGCAGA 573
                         ----     v          ----------  v  v     v   i  i 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_238120582_    574 GCTGAAGGACTCACTCTTCCTGATTCCAAAACTTACTACAAACCAACAGG 623
                          i  i         v     ii   i                v v    v
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_238120582_    624 AATCAAGACCACATGGGACTTACATAAGGATAGACATATAGATTAATG-A 672
                                  viii   v   vi                     i    - 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_238120582_    673 ATCCAA--AAAGGCCCAGCAATAGACTCTTACATTTATGTTTAATTGATA 720
                           vv  --i ii i    v    i  i v          v i       -
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT- 353

  chr2_238120582_    721 ACTAAACCTTTACATTTATGTTCAACAAGAGCACTAAAACAACTCCA-AG 769
                         --------------   ----- i     i ii i  i  v i  v -i 
  L1M4_orf2#LINE/    354 --------------TTT-----CGACAAGGGTGCCAAGACCATTCAATGG 384

  chr2_238120582_    770 GGAAACAGTTGTCTTTTCCATCA-T--TCTTGGGAAAACAAGATATCCAC 816
                              v i v        v iv - -- vi     v   vi    ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr2_238120582_    817 ATCCAAAAGAATGAACTTTGATCCCTACCTCACCTCATATACAAAAATTA 866
                           v            v  v  i           vi               
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr2_238120582_    867 ACTCAAAATGAATCAAAGACCTAAATGTGGCTTGATGCAGTGACTCATTT 916
                                   i    ?            ----------------------
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGT---------------------- 512

  chr2_238120582_    917 CTACAATCCTAATGCTTTTGGAGGCCAAGGTGGGAGGATCACTTGAGCCC 966
                         --------------------------------------------------
  L1M4_orf2#LINE/    513 -------------------------------------------------- 512

  chr2_238120582_    967 AAAAGTTTGAGACCAGCCTGGGCAACATAGTGAGACCACGTCTCTACAAA 1016
                         --------------------------------------------------
  L1M4_orf2#LINE/    513 -------------------------------------------------- 512

  chr2_238120582_   1017 AGAGTTAAAAAATTAGCCATGCATGGTAGCACACAACTGTAGTTTCAGCT 1066
                         --------------------------------------------------
  L1M4_orf2#LINE/    513 -------------------------------------------------- 512

  chr2_238120582_   1067 ACTCAGGAGGCTGAGGTGGGAGGAGCTGGAGCCCAGGAGGTTGAAGCTGC 1116
                         --------------------------------------------------
  L1M4_orf2#LINE/    513 -------------------------------------------------- 512

  chr2_238120582_   1117 ACTGTGATCACACCACTGCACTCCAGCCTGGACCATGGAGCAAGATCCTG 1166
                         --------------------------------------------------
  L1M4_orf2#LINE/    513 -------------------------------------------------- 512

  chr2_238120582_   1167 TCTCAAAAAAAAAAACAAAAAAACAACTAGCCATAAGAGCTAAAACTATA 1216
                         ----------------------------------                
  L1M4_orf2#LINE/    513 ----------------------------------AAGAGCTAAAACTATA 528

  chr2_238120582_   1217 AAAACTCCTAGAAATAGATATAGGGGTATATCTTCACAACCTTAGATTAG 1266
                            -   i     iv i i     ?   v      iii     i i    
  L1M4_orf2#LINE/    529 AAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr2_238120582_   1267 CCAATGGTTTTTTTTTTAGATATGACACATAAAAA---AAGCAACAAATA 1313
                         v         i  ----           -i    i---          vi
  L1M4_orf2#LINE/    578 GCAATGGTTTCTT----AGATATGACAC-CAAAAGCACAAGCAACAAAAG 622

  chr2_238120582_   1314 GAAAAATAGAAAAATTGGACTTCATCAAATTTTAAAACTATTGTGTTTCA 1363
                         i         v                  v  v      v     i    
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_238120582_   1364 AAAGACACTTTTAAGAAAGTGAAAAGACACCCCACAGAATGGGAAAAAAT 1413
                           i      v i                 v              i     
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_238120582_   1414 ACTTGCAAATCACATATCTCATGAGAGATTTGTATCTAGAATAAATTATG 1463
                          i          i      v  i  i  i       i      v  v v 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_238120582_   1464 AGTTCTCACAACTCAATAA--AAGATAAAAAAAACCCAATCTGTAAAATG 1511
                          ii   i            --  i v v   v        i?i-      
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATG 821

  chr2_238120582_   1512 GGCAAAGCGCCTAAATAGACATTTCTCCAAAGGAGATGTACAAATGACCA 1561
                                viii i                   i    i        i   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr2_238120582_   1562 ATAAGTGTATGAAAAGATGCCCAATGTCACCAGTCAT 1598
                              iii            i   ii   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (82 / 50)
Gap_init rate = 0.02 (16 / 804), avg. gap size = 22.81 (365 / 16)  


1597 28.24 3.78 2.52  chr2_238158606_238160496.rev      501  1056 (835)    L1M4_orf2#LINE/L1      237   799 (109)  

  chr2_238158606_    501 TTACTATATAGCTACAGTAATCAAAACTGCGAGGTACTGGTAGAGGGGTA 550
                               i v               i  v i v        i v i  i  
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr2_238158606_    551 AACATGTAGTTTCATGGAATAACATAGAAAACCCAGAAACAGACCTACAC 600
                         i    i   v iv        iv  v  i ii       i i   i i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_238158606_    601 AAATATGCCCAACTAATACTTAACAAGGGTACAAGGGCAATCTGATGGAG 650
                          vv    vi   i i  vi ii        i v i i v  iii    i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_238158606_    651 GAAGCGCTGCCTTTTAAACAAATGGTGTTGGAGA-----GGG-------- 687
                         i   viiv i     v           i   -  -----  i--------
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGG-GACAACTGGATAKCCACA 435

  chr2_238158606_    688 -GCAAAAATATAAACCTCAACTTCAGCCTCACACATTATATAAAA-TTAA 735
                         -      iv  i  vi vi  ii vi        vv    i    -    
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_238158606_    736 CCCCAAGTGGATTACAGACTTGCATTTAAGCTGTGAAAGCACTAAACTTT 785
                          i v  i     i ?    i iv  v    vvv i   vi iv     i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_238158606_    786 TAGGGAAAAAAATAGGAGAAAATATTTTGGACCAAGGGCTAGGTGAAGAG 835
                            iii    v     ? v    v  ivv    vv   i    ii ----
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA---- 581

  chr2_238158606_    836 GTAGTTGCCT-GACTTGATACCACAGGCACAATTAA--AAAGGCACAATC 882
                         - i   v i -  iv   i    v i      vi  --    i---  --
  L1M4_orf2#LINE/    582 -TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA---AA-- 625

  chr2_238158606_    883 CATAAATGGATGAATTGGAC---ATCAAAACTCACAGGTCTTGCTCTGTG 929
                         ---    i   i        ---       i v v iv i   iv  vii
  L1M4_orf2#LINE/    626 ---AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_238158606_    930 AAAGACTCTGTTATAAGGCTGAAAAGCAAAGCCACACCTTGGGAGAACAT 979
                           i   v  i i vi iiv       vv  v     vvv        v  
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_238158606_    980 ATTTGCAACCCACATATCCAACAAAAGATTAGTATCTGGAATATATAAAG 1029
                                 vi  i     ii i  ii  i v     ii            
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_238158606_   1030 AACTCTTAAAATTCAACAGTAAAAAAA 1056
                                 v  i    i i      i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGA 799

Transitions / transversions = 1.58 (95 / 60)
Gap_init rate = 0.02 (10 / 563), avg. gap size = 3.50 (35 / 10)  

 398 23.39 0.00 1.61  chr2_238158606_238160496.rev     1276  1399 (492)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr2_238158606_   1276 AAAAAAAAAAAAATCCAAACAATTCCATTAGAAAACGGGCTAAGGACATG 1325
                           v  v     i --    i  ii v   ?i    i    v     iv  
  L1M4_orf2#LINE/    787 AATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_238158606_   1326 AACAGGTATTTCATCAAAGATAATACACAGTTAGCAAATAAGCTCATGAA 1375
                           i  ii     vi      vi   i   iv i  v       v      
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_238158606_   1376 AAAATGGTCAACACCATTAGCTAT 1399
                           i   v      i  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (17 / 11)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 2.00 (2 / 1)  


3568 24.78 1.11 1.11  chr2_238343396_238345415      625  1528 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr2_238343396_    625 AAGATATCCCATGTTCATGGACTGGAAGAATTAATATTGTTAAAATGCCC 674
                                              i       v             i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr2_238343396_    675 ATGCTACCCAAAGCAATCTACAGATTCAATGCAGTCCCTATCAAAACTCC 724
                           i  v      vii              i   i            ii  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr2_238343396_    725 AATGACATTGCTCACAAAAATAGAAAAAATAA-AATAAAATTTGTACCAA 773
                          iivi v  vi ii  i    v  v  iv i -vv       ii  ivi 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_238343396_    774 ATCAGAAAAGACTCCTAATAGTCAAAGCAATCTTGAGCAATAAGAACAAA 823
                          viiv  ii   i vv     i    i         iv  v         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_238343396_    824 GCTGGAGACATCACACTACCTGATTCCAAAATCTAATGCAAAGCTGTAAC 873
                          i     ivv       v  ii   i     ii  v i       ii ii
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_238343396_    874 CATCAAAACAGCATGGTACTGGCATAAACAGAAACAGGTGGACCAGTGGA 923
                         v     i    ii              iv v i   vi i  i  i    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_238343396_    924 A--GAATAGCGAGCCCAGAAATAAATCCACGCATTTCCAGTCGATTGTTT 971
                          --    v v   i           i   ii     vii   i    v  
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_238343396_    972 TTTGACACAGTTGCCAAGATCACACTATGGGGAAAGGATAATCTCCTCAA 1021
                           i    vi v        i  iv v          i   i   ii    
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_238343396_   1022 TAAGTGATGTTGGGGAAAACTG----TCCACCTGCAGAAGAATGAAATTA 1067
                         i  i  i  i    - v     ----?    v    i         i  i
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGG-ACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_238343396_   1068 GACCCTCATCTCATTCCATATAAAAAAATCAACTCAAAATGTATTAAAGA 1117
                              ii i    iv       v      i           v  i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_238343396_   1118 CTTAAATGTAAGACCTGAAACTATAAAACTAGTAGGAGAAAACATAAGGC 1167
                          i           v  i             vv   i          i ?v
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_238343396_   1168 GAAAGCTCCATGATATTG--TTCCAAAAACAATGATTTTTTTGGATATGA 1215
                         v   v  i i   iv   --  ---- ii     i   i  -i       
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTT----AGGCAATGGTTTCTT-AGATATGA 598

  chr2_238343396_   1216 C-TCAAGAGCACAGGCAACAAAAGAAAAAACAGACAAACGGGATTGCACT 1264
                          -i   i      i                i   i   iv   i v  ii
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_238343396_   1265 AAACTAAAAAGCCTCTGCACAGCAATGGAAACAACAGAGTAAAATGACAA 1314
                            v v    i i i  ii vv   v   v  v ivi  -   i   v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAAA 697

  chr2_238343396_   1315 ACTAACCTACGGAATGGGAGAAAATATTTGTAAACTGTGCATCTGTTAAG 1364
                         ivi    i  i                   i   iii ii     v    
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr2_238343396_   1365 GGGTTAATATCCAAAATAAACAGTAAATATAAACAAATTAATAGCAAGAA 1414
                           ii vi      i    v i ivi  ivivv    v i    ii  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_238343396_   1415 AACAAATAACCTGGTTTTAAAATGGACAAAGGACCCAAATAGGCATTTTT 1464
                         i          iii  ?v       i       iiii     i     i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_238343396_   1465 CAAAAGAAGACATACAAATGGCCAATAGATACGTGAAAAAAAAATGCTTG 1514
                          v        i                iii  i      i ---    ii
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA---TGCTCA 894

  chr2_238343396_   1515 ACATCATTAATCAT 1528
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (150 / 70)
Gap_init rate = 0.01 (10 / 904), avg. gap size = 2.00 (20 / 10)  


 914 17.11 4.81 0.00  chr2_238530367_238531974        1   187 (1421)    L1M4_orf2#LINE/L1      570   765 (143)  

  chr2_238530367_      1 TGGATTTAGCACTGATTT---GGATATGACAACAAAAGCATGGACAACAA 47
                            i  vi   v  i   ---i         v        iiii      
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_238530367_     48 AAGAAGA--TACATATATTAGACTTCATCAAAATCAAGAACTT--GAACA 93
                              i --  v   v   i              i  i     -- vi v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_238530367_     94 TCAAAGGACACTATCAAAAGAGTGAAAAGGCAGCCCATAGAATG--AGAA 141
                                          i i         i  i    i      --    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_238530367_    142 AATATTTATAAATCATATATCTGATAAGGGGTTAATACCCAGAATA 187
                                ii                     ii vi  i        
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

Transitions / transversions = 3.00 (24 / 8)
Gap_init rate = 0.02 (4 / 196), avg. gap size = 2.25 (9 / 4)  

2114 23.19 2.74 2.58  chr2_238530367_238531974      496  1116 (492)    L1M4_orf2#LINE/L1      287   908 (0)  

  chr2_238530367_    496 GGCACATAGACCAATGGAACAGAATAGAAACCTCAGAAAATAATGCACAC 545
                          i  i     i        i     v  i vii      vv  iv  i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_238530367_    546 --TTGTAA-CAATCTGATCTTCAACGAAGTCAACAAAAACAAGCAATGGA 592
                         --  i ii-    -    i   i  i i viiv   i v  vv      i
  L1M4_orf2#LINE/    337 ATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr2_238530367_    593 GAAAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGGTTAGCCATA 642
                              i ivvi  v     i              i      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr2_238530367_    643 TGCAGAAGACTGAAACTAGACCCCTTCCTTATACCATATACAAAAGTCAA 692
                             i    v    ii i       v   i i             i i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_238530367_    693 CTCAACATGGATTAAAGACTTAAGTGTACAGCCTAAAACTTATAAAAACC 742
                              v      i ?    i   i    viiv        -      - i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT-ATAAAA-CT 533

  chr2_238530367_    743 CTT-GAAGAAAACCTAAGAATTACCATTCTGGACAGTAGGACAATTACAT 791
                            -         v  i ?i v viv   vv   vv i  ----   ---
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG----TTA--- 576

  chr2_238530367_    792 TCTGGCCAAGATTTCAT-GATGAAGATGCCAAAAGCAATTACAACAAAA- 839
                         ---   v v i    v -   - v  ii         vvvi        -
  L1M4_orf2#LINE/    577 ---GGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAG 622

  chr2_238530367_    840 ---AAATTGACAAATGGGACCTAATTAAACTAAAGAGCTTGTGCACAGCA 886
                         ---    v  i    v    i v  i   v v  i i   v  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr2_238530367_    887 AAAGAAACTATCAACAGAGTAAACAGATAACCCACAGAATATGAGAAAAT 936
                           i  v        v i   i  v   i            iv        
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr2_238530367_    937 ATTTGCAAACTATGTATCTGACAAAGGTCTAATATGCAGAATCTGTAAGG 986
                                  ii  i       i  i  v  vi   v      v i   i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr2_238530367_    987 AACTT----AAATTAACAAGAAAAA----AATAACCCCATTAAAAAATGG 1028
                             i----  v i  i  v     ----        v   ?        
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr2_238530367_   1029 GTGAAGGACATGAACAGACATTTGTCTCAAAAGAATACATTCACGTGGCC 1078
                          ii     iv    i        --   v      v i  v  vi     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTT--CTCCAAAGAAGATATACAAATGGCC 870

  chr2_238530367_   1079 AACAAGCATATGAAAAAATGCTCAGTATCACTAATCAT 1116
                           i     i       i       ii    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (82 / 58)
Gap_init rate = 0.02 (14 / 622), avg. gap size = 2.36 (33 / 14)  


3092 27.28 0.66 0.77  chr2_238534359_238540712.rev     4954  5862 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_238534359_   4954 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATAAATATTGTGAAAAT 5003
                              ii i  i     i        v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_238534359_   5004 GGCCATGCTGCCCAAGATAATTTATAGATTCAATGCCATGCCCATCAAGC 5053
                            v  i  v     iv i  i  i        i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_238534359_   5054 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5101
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr2_238534359_   5102 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5151
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_238534359_   5152 AACAAAGCTAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5201
                                i i    vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_238534359_   5202 CACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGACC 5251
                         i       i   i    ii         i iv ii i   v  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_238534359_   5252 AATGGAACAGAAT--AGAGCCCTCGGAAACACTACCACACATCTACAACC 5299
                                i     --    i  --i    i vvv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr2_238534359_   5300 ATCTAATCTTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCC 5349
                          vi i  i  i     ivv  v   i vv vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr2_238534359_   5350 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCT 5399
                           v  i  i              v      v  ?i  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr2_238534359_   5400 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5449
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr2_238534359_   5450 TTAAACACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5499
                          i ? v  i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr2_238534359_   5500 CTAGGCA-ATACCATTCAGGACATAGGCACGGGCAAGGACTTCATGACTA 5548
                         v    ?i- v i -   iv   v v  vvii     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_238534359_   5549 AAACACCAAAAACAATGGCAACAAAAGCCAAATTTGACAAATGGGATCTA 5598
                         vi         i  vvi          vv   v v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr2_238534359_   5599 A-CGTAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGA 5647
                          - iv  i    i -   i  ii vv    i  v    i  vv i i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_238534359_   5648 ACAGGCAACCTACAGAGTGGGAGAAAATTTTTACAATCTACCCATCTGAC 5697
                          v  i     i     i           v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr2_238534359_   5698 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5747
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_238534359_   5748 AAAATCGAACAACCCCCATCACAAAGTGGGCGAAGGATATGAACAGACAC 5797
                            iv i  i     v-  i?v   i     i      v    i     i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr2_238534359_   5798 TTCTCAAAAGAAGACATTTATGCAGCCAACAGGCACATGAAAAAATGCTC 5847
                              v        i  vi viii     i i           i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr2_238534359_   5848 ATCATCACTGGCCAT 5862
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2637 24.16 3.81 0.44  chr2_238676082_238678382.rev      603  1285 (1016)    L1M4_orf2#LINE/L1        1   706 (202)  

  chr2_238676082_    603 TGGAAATATATACTCTGTTCAAATATTTGAAGAATTAATATTGTTAAAAT 652
                               v    v iv      viv   v     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_238676082_    653 GTCCATACTACCCAAAGCAATCTACAGATTCAGTGCAATCCCTATCAAAA 702
                          v v     v      vii             ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_238676082_    703 TTCCAATGGCATTTTTCACAGAAATTAAAAAAACAATTCTAAAATTTGTC 752
                          i   iiv  v     ii        i v  ivii  i        ii v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_238676082_    753 TGGAATCACAAAACACCCCGAAAAACCAAAGCAG-CTTGAAAAAGAA--- 798
                              vii   iiv    v   v i     i  i-            ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_238676082_    799 CAAAGTTGTAAGCATCACACTTTCTGATTTCAA-------------GCTA 835
                                 v i vv        i ii       -------------    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_238676082_    836 TAGAAATCAAAATAGCACAGTACTGGCTTAAAAACAGACACACAGAACA- 884
                         i  v      i i  iiii        v   ii i     i i   v  -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_238676082_    885 --GAA---AAT--AGAATCCAGAAGTAAACCTAAGCATATAAAAGTCAAC 927
                         --   ---   --   i       i      i vi   v  vi-     i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG-GTCAAT 349

  chr2_238676082_    928 TAATTTATGACACAGGTACCAAGAAAACACCATGGGGAAAGGATAGTTCC 977
                          i    vi    vi   i      vv iv v          i     iii
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_238676082_    978 TTCAATAAATGGTGTTGGGAAAACTGGATATTCACATGCAAGGGAATAAA 1027
                              i        i     v         ?i         ii    i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_238676082_   1028 ATTGGCTTCTTATCTTATACCATACATGAAAAATCAACTCAAAATGAATT 1077
                         i    vii i  i  i i      i i-      i           i  i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAAATGGATC 498

  chr2_238676082_   1078 AAAGACTTAAATGTAAGACCTGAAAGTATAAAACTCCTAGAAGAAAAGAT 1127
                          ?    i           v  i   v          i          v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_238676082_   1128 AGGGAATAAGT-TCCTTAACAAGGGCCTTGGCAATGATTTTTTTGATATC 1176
                            ?i-   i - i v i  vvv  vi v       i   i  v     v
  L1M4_orf2#LINE/    549 AGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_238676082_   1177 ACACCAAAAGCTCAGAGAACAAAAGCAAAAATAAGCAAGTGGGATTACAT 1226
                                    v  iiv        v       iii  i v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_238676082_   1227 CAAACTAAAAAGCTTCTGTACAATAAAGGAAACAATCAGCAAAATAAAAA 1276
                             v v    i   i   i vvi      v  v    iv   i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr2_238676082_   1277 GGCAGCCTA 1285
                          i  i  i 
  L1M4_orf2#LINE/    698 GACAACCCA 706

Transitions / transversions = 1.70 (102 / 60)
Gap_init rate = 0.01 (10 / 706), avg. gap size = 2.90 (29 / 10)  

 822 19.72 5.63 0.47  chr2_238676082_238678382.rev     1597  1809 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_238676082_   1597 AAGAAAA-GAAAAGGTAGTCTATGAATTGGGAGAAAATATTTACAAATCA 1645
                               i-      ii ii i iii v               i       
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_238676082_   1646 TATATTCGACAAACAGATTAATATCTAAAATATATAAGGAAATCACACAA 1695
                              ii  i  i-i  i vi    i i         i   v  vi    
  L1M4_orf2#LINE/    735 TATATCTGATAAG-GGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_238676082_   1696 CTCAATAGCAAAAAAA----------AATT-AAAAATGGGCAAAAAACAT 1734
                                ii     i ----------    -             ii iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr2_238676082_   1735 GAATAGACATATCTCCAAAGAAGAAATAAAAATGGCCAACAGATATATGC 1784
                                   v             v   v          i iii i   v
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr2_238676082_   1785 AAAGGTGCTCAACATCACTGAACAT 1809
                             i            ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.67 (33 / 9)
Gap_init rate = 0.02 (4 / 224), avg. gap size = 3.25 (13 / 4)  


 241 18.52 3.70 0.00  chr2_238694473_238699879.rev     2774  2827 (2580)    L1M4_orf2#LINE/L1        1    56 (852)  

  chr2_238694473_   2774 TGGAGATATAAACCATGTTCATGGATTAGAAGATGTGATA--ATTAAGAT 2821
                             i v   vv               i     iv i   --i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_238694473_   2822 GACAAT 2827
                          i    
  L1M4_orf2#LINE/     51 GGCAAT 56

Transitions / transversions = 1.50 (6 / 4)
Gap_init rate = 0.02 (1 / 56), avg. gap size = 2.00 (2 / 1)  

1606 22.22 4.02 7.09  chr2_238694473_238699879.rev     3223  3744 (1663)    L1M4_orf2#LINE/L1       46   551 (357)  

  chr2_238694473_   3223 AACACAGCAATTCTCCCCAAATTGATTTACATTAGAGTCAATGCAGTCCT 3272
                           v ii     v              i    ---  v    i   i   i
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACA---GATTCAACGCAATCCC 92

  chr2_238694473_   3273 AATCAAAATCTCAGC-AAGTTTTTTGCCGAATTTCACAGGCTGATTCTAA 3321
                         v         i    -ivv        v   v  v   i      i    
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr2_238694473_   3322 AGTGTATGTGGAAAAGTAAAGGAACAAAAATCACCAAAATAATTTTCTAC 3371
                          i vi  i      v i  i   v v i   vi      i   i  v---
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG--- 189

  chr2_238694473_   3372 CAAAAAGTAGAAAAATGTTGAAGGAGTCAGAGGTCACATGATGGGATTTC 3421
                         -      v    v  v    i    v   v vv  v  -------     
  L1M4_orf2#LINE/    190 -AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-------ATTTC 231

  chr2_238694473_   3422 AAGACTTACTATAAAGCCATAATAATCAAG-CAGTA--GTATTTGTACAA 3468
                           i        i     i i i        -    i--   i v i i  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr2_238694473_   3469 GTGTAGACGTGCAGAACAATGGAATGGAAC--AGAGTCCAGAAGCACACC 3516
                          vi     i ii   v         i   i--           ii v   
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr2_238694473_   3517 CACACACATATAGTCATGTAATGT-CAACAAAGGTGCCAAGGTAAGTCAA 3565
                           i   iv   i    vv i  v - i    i         iiv v    
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr2_238694473_   3566 TGGGAAAAC-----CCTGTTCAACAAATGGTGCTAG---AAATGGACA-- 3605
                             i   v-----i  v                i ---  v    i --
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr2_238694473_   3606 ---ATGCAAAAAAGAGATAGAAAAAAAAAACCAGAAAACTACACTCTTCT 3652
                         ---        i ---  i----------------  ii iv  i i vi
  L1M4_orf2#LINE/    432 CACATGCAAAAGA---ATG----------------AAGTTGGACCCCTAC 462

  chr2_238694473_   3653 CTTGTATAATATGTGAAAATTAACTCAAACTGGATCACAGACCTAACCAT 3702
                           iii iv    iii              v       ?        vii 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr2_238694473_   3703 AAAACCTAGAGCTATAAAACTTCTGCTTTTAAAAAAATA-AGG 3744
                           i v   i i          ----   vv  i    i -   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACT----CTTAGAAGAAAACATAGG 551

Transitions / transversions = 1.61 (71 / 44)
Gap_init rate = 0.03 (15 / 506), avg. gap size = 3.87 (58 / 15)  

 471 25.55 9.85 2.92  chr2_238694473_238699879.rev     4651  4924 (483)    L1M4_orf2#LINE/L1      616   908 (0)  

  chr2_238694473_   4651 ACAAAGAAAACAATC-ATAAGTTGGATATCCCCAAATGAATTTAAAATAC 4699
                              ii   v   v-    i     iv  vi    ---   v    ivi
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA---ATTAAAAACTT 662

  chr2_238694473_   4700 ATGGTCTTTAAAAGGT-CT-TTAAGGAAAT--AAAGACGAGCCATAGACT 4745
                         v  vv   i   i ii-  - i   i  i --      i v   i   v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr2_238694473_   4746 AGGAAAAAACATTTATAAA--ACACATCTGATAAAAGAC--GTATC---- 4787
                         i   i    i    ii   -- i i         ii   --     ----
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr2_238694473_   4788 -TATGGTAAAGAACTCTTAAAATCCCACAATAAGAAAA-AAA-AACCTTA 4834
                         -   i-             v  ii v i     i  i -   -    iv 
  L1M4_orf2#LINE/    763 ATATA-TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_238694473_   4835 TTTTTTTTTAAATGAGCACAACAGTTGAGCAGACGCATCTCCAAAAAAGA 4884
                           ?vv----     i   v iv v    ii    iiv        i    
  L1M4_orf2#LINE/    812 TTWAA----AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr2_238694473_   4885 GACA------GTCATTAAGAAAATGCAAA-----TTAATACCACAATTAA 4923
                         v i ------ i  v    v v   v   ----- i  i i  ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr2_238694473_   4924 A 4924
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.76 (44 / 25)
Gap_init rate = 0.05 (14 / 293), avg. gap size = 2.50 (35 / 14)  


4518 14.32 4.24 0.57  chr2_238762778_238769483.rev     5345  6217 (489)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_238762778_   5345 AAAGACATCACATGTTCATGGATTGGAAAAC--AATATTGTTATGGTAGC 5392
                              i   v                  i  --          v i i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_238762778_   5393 AATACTGACCAAATTCATCTACAGATTCAATTCAATCCCTATCAAACTCC 5442
                               vv       v              iv              v   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_238762778_   5443 TAGCTAGATTTTT-GCAGAATTTAACAAGCTGATCCTAAAATTC-TTTTG 5490
                         i    ivv     -      v  i                    - v v 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_238762778_   5491 AGATGTCAACAGATGCAGAATAGCCAAAACAATATTAAAAAATAA---CA 5537
                          i   -   vi  iv                  v  i     v  ---  
  L1M4_orf2#LINE/    154 AAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr2_238762778_   5538 AATTTGGAGAACTCCTACTTTCCTGTTTCAAAACTTACTACAAA-CTACA 5586
                           v      i    vi    i  vi                   -     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr2_238762778_   5587 GTAATCATAACAGTTTGGTACCAATCTAAGAACAGAAATACAGGTAAATG 5636
                                vi     v      iiiiv    i i   v   i  i v    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr2_238762778_   5637 GAATAGAGTTGACAGTCAAGAAATAAACCCTCACATATTACGGTCAACTG 5686
                                i    v    v            vi    -   i      i  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-TTATGGTCAATTG 351

  chr2_238762778_   5687 ATTTTCAATAAGGGTGCCAAGACCATCCA-TGG---AAGAAGAGTCTTTT 5732
                               i i                 i  -   ---     v        
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr2_238762778_   5733 CAACAAATG-TGCTGGAACAACTGGATGTCCACATGCAAAAAAAGTAAAT 5781
                                  -      i          i?            i  - i  v
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAG 450

  chr2_238762778_   5782 TTGGACTCCTCCCTCACACCACACACAAAA-TTAACTCAAAATGTACCAC 5830
                               i   v          i i      -             v i  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_238762778_   5831 AGATTTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAATAT-- 5878
                            ii                                        i  --
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_238762778_   5879 GAGTACATTTTCATGACCTTGGGTAGGACAAAATCTTCTTAGACATGACA 5928
                          ?   v  i   i           vi i   vivi        i      
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr2_238762778_   5929 C--AAGGAACAA-CAACAACAACAAAAATAGA---------CTTCATCAA 5966
                          --  i v    -      v iv         ---------         
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr2_238762778_   5967 AATGAAAAGCTTCTGTTCTTCAAAGGATACCAT---GAGAGC-AAGAGCA 6012
                            v    i   i   v          i  i  ---  i  i-  i  vv
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr2_238762778_   6013 AACCCACAGAATGAGAGAAAATATTTACAAATCATCTATCTGACAAGGGA 6062
                                      i            i        v       i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr2_238762778_   6063 CTTGTATCAAGCATATATAAAGAACTCTTACAACTCAATAA---AAAGAC 6109
                                 v  v                             ---      
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr2_238762778_   6110 AAGTCATCCAATTAAAATAGGAGCAA-GGACTTTAATAGACATTTTTCCA 6158
                           i v i      ?   v v i    -   i  v           i    
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_238762778_   6159 AAGAAGATATATACAAATGGCCAAGGAGTACATGAAA-GATGCTCAACAC 6207
                                    --           vi  i        -           i
  L1M4_orf2#LINE/    851 AAGAAGATATA--CAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr2_238762778_   6208 TACTGGCCAT 6217
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (71 / 50)
Gap_init rate = 0.02 (22 / 905), avg. gap size = 1.91 (42 / 22)  


 294 27.37 10.53 0.00  chr2_238777400_238781321     2502  2596 (1326)    L1M4_orf2#LINE/L1        3   107 (801)  

  chr2_238777400_   2502 GAGACACATGCCGTGTTCATAGATTGGAAGATTCTACATACCAAAGATGT 2551
                           i v i  v  i       i          i iv i  vviv      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_238777400_   2552 CAA--------AGGTGGATATACAAGCCTAAC--AATTTCTATCAAAATC 2591
                            -------- ii v   v    iiiii   --   ii           
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_238777400_   2592 CCAGC 2596
                              
  L1M4_orf2#LINE/    103 CCAGC 107

Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.02 (2 / 105), avg. gap size = 5.00 (10 / 2)  

 353 25.70 5.59 5.59  chr2_238777400_238781321     2600  2778 (1144)    L1M4_orf2#LINE/L1      293   471 (437)  

  chr2_238777400_   2600 TAGATCAATGGAGGAGAAT--AGACCCAAACAGAAATAGGCCCATATGAG 2647
                                     iv     --   vi ---        ii      i- v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTC---CAGAAATAAACCCATAC-AT 338

  chr2_238777400_   2648 TTACGGGTGCA---GATA--CAACCGCAGGAGACGCAAATCAGTTCAGCA 2692
                            i  - -  ---   v-- i  v--   ivi vv i i  -    iii
  L1M4_orf2#LINE/    339 TTATGG-T-CAATTGATTTTCGACA--AGGGTGCCAAGACCA-TTCAATG 383

  chr2_238777400_   2693 GATGAAAGT-TAGCCTTT-CAACAGATCGTGCCAAGGCAGTTAGACATCC 2740
                          i-     v-   i    -     i  v    iii i  ii i  i ?  
  L1M4_orf2#LINE/    384 GG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr2_238777400_   2741 ATAGGCAAAAGA-TGAACCTTGACCCAAGTCTTACACCA 2778
                          i v        -    vi v     vvii  i      
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

Transitions / transversions = 2.00 (30 / 15)
Gap_init rate = 0.07 (13 / 179), avg. gap size = 1.54 (20 / 13)  

1461 24.09 4.09 0.91  chr2_238777400_238781321     2991  3430 (492)    L1M4_orf2#LINE/L1      455   908 (0)  

  chr2_238777400_   2991 ACCCCTGTCTTACACCTCATA-AAATAGTGTCTCAAAATAGATCTTGAAA 3039
                               ii  i     vi   -   v v iv        i    v?ii v
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_238777400_   3040 TTAAATGTAAAACATAAAGCAATAAAACCGTTTAAAA------ATAGA-- 3081
                         i         i vv    i v       i-i   i  ------    i--
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNG 553

  chr2_238777400_   3082 -AAATCTTCAAGTTCTAGGACTAGGCAAAGAGTTCTTAGACTTGACACCA 3130
                         -        iv vi  v  ii       v iv        iv        
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_238777400_   3131 AAAGCAT---CCATAAAAGGAAAAATTGATAAATTAGACTTCATCAGAAT 3177
                               i--- v i     i      v        i          i   
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_238777400_   3178 TTAAAGCTTTTGCTCTGGGAAGGACCATATTAAGAGGATGGGAAGATAAG 3227
                          v   i      iv  vvi      vv   i    iii  ii    i  v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_238777400_   3228 CTA-AATCTAGGAAAAAATATTTTCAAATGACATATCTGACAAAGAAATG 3276
                          i - ivv i   i         v     v i        i  i i v v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_238777400_   3277 GTATCTAGAATATATAAAGAACTCACAAAACTCAACAGCAAAAATAATAT 3326
                              i                  vi v       i ii     v ---i
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA---C 800

  chr2_238777400_   3327 AAAAAATTCAATCTGAAAATAGGGAAAAAATATAAACAGACATTTCACCA 3376
                            v  ii    i?i     i  v   ii  v i  i         v   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr2_238777400_   3377 AAGAGGAGACCCA---GGT-AATAAGCACAGGAAAAGATGTTCAACAGCA 3422
                             i  v iv  ---  i-          v         i      v  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr2_238777400_   3423 TTAGTTAT 3430
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.54 (63 / 41)
Gap_init rate = 0.02 (9 / 454), avg. gap size = 2.44 (22 / 9)  


 636 30.90 2.58 0.43  chr2_239083431_239085820.rev      746   978 (1412)    L1M4_orf2#LINE/L1        1   238 (670)  

  chr2_239083431_    746 TGAGAAGACACACTGTGTCCATGGAATGGAAGACAGGACACAGTAAAGAC 795
                           ii    i iv ii   i      v        vvi i iv  v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_239083431_    796 ATGAATTTTCCCCAAACCGATACGCATGTTTAATGCAAATCCTACCAAAC 845
                         ivv   vi        ii   vii  vi  i  i    vi    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_239083431_    846 TTGCAGCCAATGTTTTTGTATA----GACAAGATTATCCTAAAATGTATA 891
                          iv    iiviv      i v ----      v v          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_239083431_    892 CAGAAAGGCAAAGGAACTACAATAGCTAAAACA-TTTTCAGAAA-AAGAA 939
                         ii    v    i   v i v      i      - i  v i   -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_239083431_    940 TAAAGACAGAAATAACCAGTCTACCCAATTTCAAGGCTT 978
                         i    vii  ii- vi  vv  v           ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTT 238

Transitions / transversions = 1.48 (43 / 29)
Gap_init rate = 0.02 (4 / 238), avg. gap size = 1.75 (7 / 4)  

1831 25.43 9.73 2.98  chr2_239083431_239085820.rev     1262  1898 (492)    L1M4_orf2#LINE/L1      229   908 (0)  

  chr2_239083431_   1262 TTCAAGTCTTTTTATACAATTACAGTAATCAAGACAGTGCAGTATTGACA 1311
                              iv   vi  i v ii                   ii   i  i  
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr2_239083431_   1312 GAGGGACA------TAGATCAAATGAACAGAACACAGAATCCAAAAGTAG 1355
                         v i   i ------        vv   i    ivv   i    i  i  i
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr2_239083431_   1356 ATCCATACGAATATGTCCATATGCCCAAGCAATCTTTGACAAAGGTACAA 1405
                          i      ----  - ---    vi   vii  i  i     i   i v 
  L1M4_orf2#LINE/    329 ACCCATAC----AT-T---TATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr2_239083431_   1406 AAGCAATTTAGTGGCAGAGAGAG----CTTTGCACCATTTGGCACTGGGT 1451
                          ii v   i i   -i  i   i----    v  v  vv   ii     v
  L1M4_orf2#LINE/    371 AGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr2_239083431_   1452 TAAGTGGACATCCATAAGCCAAAAAACAAACAAAACGTTGA--CCTAATC 1499
                         i  v    i ?   i v  v   i  ii  ------    i--  iv i 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAA------GTTGGACCCCTACC 463

  chr2_239083431_   1500 TCATATCTTAAACAAAAATTAACTCGAAATGGACTATGGATTTAAATATA 1549
                            i i v  v              i       ii ?i  ii     i  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr2_239083431_   1550 A----T----CTATAAAACTTTAAGATAAAAAACACAGGAGGAAAAAGTC 1591
                          ---- ----          i v   - i      i   ? v   ---  
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGA-AGAAAACATAGGNGTAAA---TC 559

  chr2_239083431_   1592 TTTGGGATCTAGGACTAGGCAAAGAGTTCGAAGACTTGACACCAAAAGCA 1641
                           i v  i  v  ii       v iv   vv   iv              
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr2_239083431_   1642 TGA----CAAAA-------------------ATTTCA-----------AA 1657
                         ii ----     ------------------- i    -----------  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr2_239083431_   1658 TGTTTGCTCTGCGAAAGACCCTGGGAAGAAGCCGCAAAGGTAAGTCACAG 1707
                         iv    iv  v i  i   v  ivv     ivi v    ii  vi     
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr2_239083431_   1708 AATGAGCAAAAACAACTGCAAATCACACATCCAATAAAGGACTTATAGCT 1757
                             i vi    i vi         i i   ii    i      i  v i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr2_239083431_   1758 AGAATATGCAAAGAACTCTTAAAACACAACAGCAAGAAAGCAAATAATTC 1807
                                ii            v   v   i ii  i  ii       ii 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chr2_239083431_   1808 AATTAGAAAATGGGCAAAAGAC--------ACATTTCACTGAAGAAGATA 1849
                             ?i            i  i--------       v ii         
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr2_239083431_   1850 TAAGGATGGCCAACACACACATGAAAATATGTTTGAAATCATTAGGCAT 1898
                           vii        i vi          v   i ii v    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (107 / 51)
Gap_init rate = 0.02 (16 / 680), avg. gap size = 5.06 (81 / 16)  


 356 31.54 8.80 4.40  chr2_239132204_239135216.rev     1531  1939 (1074)    L1M4_orf2#LINE/L1      131   557 (351)  

  chr2_239132204_   1531 AGTTGATATATAAAGTTCATCTGTAAGATG-AAAGAATATGAAA-----A 1574
                           i    vi-    i     v  v  -   -  i i iviii  ----- 
  L1M4_orf2#LINE/    131 AGCTGATCC-TAAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCA 178

  chr2_239132204_   1575 AGACAAGC------AAGAAGGGGGTGGTGGGAGGTAGCCACAC--CATAA 1616
                          i    v ------      iivivi  v     - vi     -- vi  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAA 227

  chr2_239132204_   1617 GT--GAAGTTTATTATAAAGGCTAAA--AAT-AAAAC--TGTGGCACTGG 1659
                         v --i  ii   i  i    -   v --   -  i  --     i     
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAG-CTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr2_239132204_   1660 TATGTGAACAAA-ATTGACAGAATGATGGAACTTTACA---GAAAATCTT 1705
                         i  iv i i i -  -- i   vii      ---  v ---  i i  iv
  L1M4_orf2#LINE/    277 CATAAGGATAGACAT--ATAGATCAATGGAA---TAGAATTGAGAGTCCA 321

  chr2_239132204_   1706 GAAATGGGCCAAATTGCAC--ATAGAAATTTCATATATGATAAAGG---C 1750
                              iii  v -- i  i--  i vv v  v  v vi  i  i  --- 
  L1M4_orf2#LINE/    322 GAAATAAACCCA--TACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr2_239132204_   1751 AGTATC--TCAAACAAGGGAGGGTGTAGATGTTTTACTAAGTGTTTTTTG 1798
                          iv i --    v--i    ii vi   viv   i vi  i  v vi - 
  L1M4_orf2#LINE/    370 AAGACCATTCAAT--GGGGAAAGAATAGTCTTTTCAACAAATGGTGCT-G 416

  chr2_239132204_   1799 GGGTAACTGGACATCCATATGGAAAAAGGTAAAAGTATATCCATTCACCA 1848
                           ii       i ?   i   v    iii i  iv iv i  v v vi  
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr2_239132204_   1849 TAGCATATACTGGAATAAATTCCAAACTGACCATA-ACTTAAAACGTAAA 1897
                         i v       vii   v  i  v   iv  i  ? -  i    -i    i
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA-TGTAAG 515

  chr2_239132204_   1898 ATATGAAACCATGCAAAAACT---AGAAAAAAACCTCTAAGTAAA 1939
                          vv i    i  ---      ---    i     v vvi?     
  L1M4_orf2#LINE/    516 AGCTAAAACTAT---AAAACTCTTAGAAGAAAACATAGGNGTAAA 557

Transitions / transversions = 1.68 (79 / 47)
Gap_init rate = 0.06 (26 / 427), avg. gap size = 2.08 (54 / 26)  


2882 11.84 1.23 26.73  chr2_239153206_239155546.rev      647  1862 (479)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_239153206_    647 GGAAGATATCTTGGGATAATGAATTATTAGACTTAATATTGTTAAGATGG 696
                          i        iiiv v v   i   ivv                      
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_239153206_    697 AAATATTCCCCCTAATACTCAATGGATTCAACACAATTACTATAAAAACC 746
                         v    i     vv v iv  v ii        i    iv    v    i 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_239153206_    747 CCAGCTGCCTTTTTTTGAAGAAATTGACAAGCTGATCCTAAAATTCATAT 796
                                        - v                                
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_239153206_    797 GGAAATGTAAGAAACCCAGAATAGCCAAAATGATCTTGAAAAACAA---C 843
                                i   ii                 ii           v  --- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_239153206_    844 AAACTTGCAGTACTCATACTTCATGATTTCAAAACTTATTACAAAACAAC 893
                            v   v  v     i     vii             i      i v  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_239153206_    894 AGTAATCAAGACAGTATTGTATTGCCATAAGGTTAGAAATACA--TCAAT 941
                                        i v   i  v       v    v   i --     
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_239153206_    942 AGAATTGAGAGTCCAAAATAAAACCTTATATTAATGGTCAATTGATTTTC 991
                         i    --   ------------------------------     -----
  L1M4_orf2#LINE/    302 GGAAT--AGA------------------------------ATTGA----- 314

  chr2_239153206_    992 CTTTTTTTTTTTTTTTTTTTTTGAAATGGAGTGTCCCTCTGTCCCCCAGG 1041
                         ----------------------------    -------------    -
  L1M4_orf2#LINE/    315 ----------------------------GAGT-------------CCAG- 322

  chr2_239153206_   1042 CTGGAGTGCAGTAGTGCACTCTTGGCTCACTACAACCTCCACCTCCTGGG 1091
                         --------------------------------------------------
  L1M4_orf2#LINE/    323 -------------------------------------------------- 322

  chr2_239153206_   1092 TTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTATAGGCA 1141
                         ---  ii  ---------------------------------------- 
  L1M4_orf2#LINE/    323 ---AAATAA----------------------------------------A 329

  chr2_239153206_   1142 CCCATCACCACCCCCAGCTAATTTGTATTTTTAGTAGAGATGGGGTTTCA 1191
                              ----  ---------------    --------------------
  L1M4_orf2#LINE/    330 CCCAT----AC---------------ATTT-------------------- 340

  chr2_239153206_   1192 CCATGTTAGCCAGGCTGATCTCAAACTCCTGACCTCAGGTGATCCACCTG 1241
                         --------------------------------------------------
  L1M4_orf2#LINE/    341 -------------------------------------------------- 340

  chr2_239153206_   1242 GCTTGGCCTCCCAAAGTGCTGGAATTACAGGTGTGAGCCACCACACCCAG 1291
                         --------------------------------------------------
  L1M4_orf2#LINE/    341 -------------------------------------------------- 340

  chr2_239153206_   1292 CCATGGTCAACTGATTTTTGACAAGGGCACCAAGACAACTCAATAGAGGA 1341
                         --        i       i        ii       v i     i -   
  L1M4_orf2#LINE/    341 --ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGA 387

  chr2_239153206_   1342 AAGAATAGACTATTCAACAAAAATAATTGCTGGGAAAACTGGATATCTAC 1391
                                 v  v         -- ii -       v         ? i  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAA--TGGT-GCTGGGACAACTGGATAKCCAC 434

  chr2_239153206_   1392 ATACAAAAGAATGAAGTTAGGCCCCCTACCTTACACCATATGTACACATT 1441
                           i               -  v         i         ii v v   
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTT-GGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_239153206_   1442 AATTCAGAGTGGATCAAAGACATAAAATGTAACAACTAAGAGACTATAAG 1491
                           i   i i       ?    v    -     v i    i --      i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAA-TGTAAGAGCTAAAA--CTATAAA 530

  chr2_239153206_   1492 ACT--TGGAAGAAAGCATGGGAGTAAACCTTCATGATCTTGGATCGAGCA 1539
                            -- i       i   i  ?     i    i   i     i iii   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr2_239153206_   1540 ATGGATTCTTAGATCTGACATCAAAAGCACAAGTAA--AAATGAAAAATA 1587
                             v         v     i            i  --   vi       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr2_239153206_   1588 GATAAGTTGGACTTCTTCAAAATTAAATGCCTTTGTGCTTCAAAGAACAT 1637
                              i         v           vi i              i   i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_239153206_   1638 CATGAAGAAAGTTAAAAGAAAACCTACAGAATGGGAGAAAATATTTGCAA 1687
                         i  v        v      v    i                         
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_239153206_   1688 ATCAAATATCTGATAAGAGAATCATATCCAAAATATATAAAGACCTCTTC 1737
                             v            i  v ii      i            v     v
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_239153206_   1738 TAAGT-AACAATAAAAAGACAA----CTCAATTTTAAAACGTGCAAAGGA 1782
                         i  v -  i             ---- i     ?v    i v        
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_239153206_   1783 TCTAAACATACATTTCTC-AAAGGACATATGTAAACAGCCAAAGAGCACA 1831
                          i i  i v         -    i v    ii   ii     vi      
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_239153206_   1832 TGAAAAGATGTGTGGTAGTATCACTCACTAG 1862
                                   i- --i ii    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGC-T--CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (89 / 51)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 13.60 (340 / 25)  


3154 26.25 1.56 0.56  chr2_239297844_239302148     2915  3813 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_239297844_   2915 TGGAAACACATCAAATGCTTATGGATGGGTAGAATCAATATTGTGAAAAT 2964
                               v i   vv   i i      v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_239297844_   2965 GACCATACTGCCAAAAGCAATCTAT-GATTTAATGCAATTTCCATCAAAA 3013
                          i v     v  v   vii     i-    i  i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_239297844_   3014 TACCACCATCATTCTTCACAGAACTAGAAATAAAACAATTATAAAGTTCA 3063
                          v   v vv v  i  ii     v v  --i  ivii  iv    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCA 148

  chr2_239297844_   3064 TATGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAA 3113
                                viiv  ii  v  v v         i   vvi i iv  i  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_239297844_   3114 AACAAATCTGGAGGCATCACATTACCTGATTTCAAACTATACTCTAAGGC 3163
                               vi      vv     i v  ii        viv    vi  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_239297844_   3164 TATGGTCACCAAAACAGTATGGTACTAGTATTAAAAATAGACACATAGAC 3213
                           ii  v i   i     i       i i  -  ii       i     i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGAT 297

  chr2_239297844_   3214 CAATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATGCTTACAGCCA 3263
                                 i     v    ii               v iii   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr2_239297844_   3264 ACTGATCTTCAAAAAAG----CAAA--CATAAAGTGGGGAAAGGACACTC 3307
                          i    i   i v  i ----   i--   vv i         i i v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_239297844_   3308 TATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACACGTAGAAGAATG 3357
                          v                    i  i   vv ?     i i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_239297844_   3358 AAACTGGATCCTCATCTTTCACTTTATACAAAAATTAACTCAAA-TGGAT 3406
                           ii    i  ii i  iv   iv                    -     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_239297844_   3407 TAAGAACTTAAATTTAAGACCTGAAACTATAAAAATTCTAGAAGATAACG 3456
                         i ?ii  i     v     v  i           v ii       v   i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_239297844_   3457 TCAGA--AAACCTTTCTAGACATAGGCTTAGGCAAAGATTTCATGAGCAA 3504
                          vi ?--   i   iv -   v v  v        v i    v iiii v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr2_239297844_   3505 GAATCCAAAAGCAAACACAACAAAAAGATAAATAGGTG----GGACTTAA 3550
                           vv         v vi        ii v      i i----      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_239297844_   3551 TTAAACTAAAAACCTTTTTCACTGCAAAAGGAACCAGACGGCAGAGTAAA 3600
                          i   v v    v     vii  v    i iv  i v- iiv i   i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT-CAAGAAAGTGAA 695

  chr2_239297844_   3601 CAAACAACCCACAGAGTGGGAGAAAATCTTTCCAATCTATACATCCAACA 3650
                         v i            i           v   v   vii   i   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr2_239297844_   3651 AAGGACTAATAGCCAGAATCTACAAGGAATGCAAACAAATTGGCAAGAAA 3700
                          i     vi  v       v  i  i   iv vv    v iiii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr2_239297844_   3701 AAAACAAACAATCCCATCAAAAATTGGGCTAAGGACATGGACAGACAATT 3750
                           i     i  i  v  i?    v     v     iv  i i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr2_239297844_   3751 CTCCAGAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAG 3800
                              i                     i  i  i       i       i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr2_239297844_   3801 CATCACTAATGAC 3813
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (142 / 90)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


3328 25.67 1.79 0.67  chr2_239365795_239370237.rev     3059  3954 (489)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr2_239365795_   3059 GAAAGACATCCCATGCTCATGGATTGGAAAAATTAATACTGTGAA-ATGA 3107
                               i        i             i v      i   v  -   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_239365795_   3108 CCATACTACCAAGAGTGATCCATAGATTCAATGTAATAACTATCAGAACA 3157
                          v     v  v i v     i i        i i   vv      i  iv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr2_239365795_   3158 CCAAG-ACATTCCTCACAGAAATAGAAAAAGCG-TTTTAAAATCCACATG 3205
                            iv-i v  ii ii       v  v  ivi - ii      i  i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr2_239365795_   3206 TGGAATCACAGAAGGCTTCCTAAAT-GCCAAAGCAATCCTGAGCAAAAAG 3254
                         - i   -i  iii i --  vi   -      i     i   iv  i   
  L1M4_orf2#LINE/    153 -GAAAT-GCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_239365795_   3255 AACAAAACTGGAGGTATCAC-CTACCTGACTTCAAAATATACTATAAAAC 3303
                               ii      vv    -  v  ii i       iv     i   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_239365795_   3304 TATAATAACAAAAACCGCATGGTACTAGCATAAAAACAGATACATAGACC 3353
                           i i   iv  i  v ii       i      ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_239365795_   3354 AGTGGAACAGAATAGAGAACCCAGATATAAATCCATGTATGTACAGCCAA 3403
                          i     i     v    ii     v     i    ii  v  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr2_239365795_   3404 TTGATTATTGACAAAGGCACCAAGAACATTCAGTGGAAAA---------C 3444
                               v i     i  ii      v      i   ii  ---------i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr2_239365795_   3445 TTTCAATAAATGGTGCTGACAAAACTGGATATCCATATGCAGAAAAATAA 3494
                               i           iv v         ?   i     i  i   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr2_239365795_   3495 ACCTAGACTGCTATCTCTCACCACATACAAAAATCAACTCAAAATGAATT 3544
                          vi i   iv   i   v     i          i           i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_239365795_   3545 AAAAACTTAAATGTAAGACCTGAAACTATGAGAATACTAGAAGAAAACAT 3594
                          ? i  i           v  i       i i v vi             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_239365795_   3595 TGGAGAAACATTTCAAAACACTGGACTGGCCAAAAACTTTTTGTGTAAAA 3644
                         v  ? v  vvi   ivi  vi   ii i v   viii  i  ivi  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_239365795_   3645 CCTCAAAAGCACAGAGAACAAAAGAAAAA-TAGACAAATGAGATTCCATC 3693
                          vi          iiv             -    i    vi  i i    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_239365795_   3694 AAGCTAAAAAGCTTCTGCACAGCAAAAGAGACAATTAACAGAATAAAGAG 3743
                           iv v    i   i  ii vv    i  v  v  i  v i i i  i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_239365795_   3744 ACAATCTACAGAATGGGGGAAAATATTTGCAAGCTACCCATCTGACAAAT 3793
                             i i          i              iii ivi      i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_239365795_   3794 AATTATTAATCAGAATATGTAAAGGACTTGAACAACTCAATGGCAAAAA- 3842
                         i i vv  vi        i     i   ivv          iii     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr2_239365795_   3843 ATAATAATAATCTGATTTTTAAATGGGCAAATGATTTGAATAGACATTTC 3892
                          i  --    i ii   ?vv           v                  
  L1M4_orf2#LINE/    799 ACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_239365795_   3893 TCAAAAGAAGATACACAAGTGGTTAATAGGTATATGAAAAAATGCTCATC 3942
                           v          i    i   ii    i i i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr2_239365795_   3943 ACTAATTACCAA 3954
                          ii ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.37 (159 / 67)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 1.83 (22 / 12)  


3179 23.88 4.94 0.69  chr2_239422855_239427740.rev     3529  4399 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_239422855_   3529 TGGAGATATATTTCATATTTATGGATTGAAAGGCTTAATATTGTTAAGAT 3578
                             i v    ii   i  i        i   i                 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_239422855_   3579 CTCAATTCTTATCAACTTGACCTATGTATTCAGTGCAATCCTGATCAAAT 3628
                         vv    v  ivi   v    i   iiv     ii       iv      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_239422855_   3629 TCCCAGTGAGTTATTTTGTGGACATGAATAAATTGATC--AAAGCTTACA 3676
                               ivivi v     ii  v  vi i  ii     --   ii i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_239422855_   3677 TGAAAATTCAAAACCCTCAGAAGAGTCAACATAATACTGAA---GAAGAA 3723
                           i    v   iivv i     v  i   v i   vi    ---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_239422855_   3724 CAAAGTCAGAAGACTGACACTACCCAACTTCCAGACTGACTATAAAGCTA 3773
                               ii  i    v     v     i   v i   v    i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_239422855_   3774 TAGTAATCAAGACAAT-TGGTATTGGTGAAAGAATAGACAAATAGATCAA 3822
                         i             i -     i   iiv   i       v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_239422855_   3823 TGGAATAGAAT---------------AGACCCACACAAATATAGTCAACT 3857
                                    --------------- i     i   vv   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_239422855_   3858 TATCTTTGACAAAAGTGCAAAGGCAATTCAATAGAGAAAGCATATTCTAT 3907
                         v  i  i     ii    v   i v       i i     v   v   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_239422855_   3908 TCAA-AAATGATACTGGAACAATTTGGCATCCATATGCAAAAAAA----A 3952
                             -     i i    i    i v ii ?   i        i  ----i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_239422855_   3953 TCGAGATACAAACTTCATGTCTTTCACAAAAATTAACTCAAAATGG-TCA 4001
                          i -  iv vv  i   iii v vi                     -   
  L1M4_orf2#LINE/    451 TTG-GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_239422855_   4002 TAGAGCTAAATATAAAATGTAAAACTATAAAATTTCTAGACTATCACATA 4051
                         ?   v      i   i vv             i ii    vv vv     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_239422855_   4052 GGAGAAAAATCTAGGTGACTCTGGGTTTGGCAATGAGTTTTTAGATACAA 4101
                           ? v   -   vv     ii      v       iv  i       ii 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_239422855_   4102 CACCAAAAGCACAACCTATGATAGAAAAATTA-ATAGTTTAGGCTTCCCT 4150
                                       v v ii v       v  -   iv  i i    vii
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_239422855_   4151 AAAATTTAAAAATTCTGCTATGC--CAAAG-ACACTATTAAGAGAG--AA 4195
                               -     i i -- i   --     -       i    i  --  
  L1M4_orf2#LINE/    649 AAAATT-AAAAACTTT--TGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr2_239422855_   4196 GAAACAAGCCACAAACTGAAAGAAAAATATTTGCAAAATACGTAACTTAT 4245
                         i i    v     i v  ii      -          vi ii  v  v  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGAT 744

  chr2_239422855_   4246 AAAGAAC--------AAAATATACAAAGAACTCTTAAAATTCAAATCTAA 4287
                           i i  -------- i      i            v  i    vvv   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr2_239422855_   4288 GAAAAGAAACAACTCA-TTTAGAAATGGACAAAAGACTTGAACAGATATC 4336
                         i  i v   i   i  -  ? i      i    i  i     i   i  i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr2_239422855_   4337 TCATGAAAAAAGATGTACAGATGGTGAATTAGTATATAAAAAGATGTTCA 4386
                           viv   i     i    i    iv   v  i i  i        i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr2_239422855_   4387 -TATCCATTTGTCA 4399
                         -i   v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (131 / 73)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.58 (49 / 19)  


2863 25.77 2.65 2.21  chr2_239588800_239593274     3080  3983 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_239588800_   3080 TGGAGGGACATACCATGTTCATGGATTGGAAGACTCAACATAGTAAAGAT 3129
                             ii  i  v                       i  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_239588800_   3130 GTCTATTCTCCTGAAACTGATGTGCAGGTTTAACAAAACTTTGGTCAAAA 3179
                          v v  v    iv   i    v i   i  i   iv  iiiivi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_239588800_   3180 CCTCAGCAAGATTTTTTGTAGAAACTGACAATATTATTCTTGTCTATTCA 3229
                         i i    vivv       i     i      vv v  i  viv--     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA--ATTCA 148

  chr2_239588800_   3230 TCTGAAAAGGCAAAGCAATTA--ATAGCTAAAACAA-CTTGCAAAAGAA- 3275
                          v  i   v    i v vii --     i       -    v       -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr2_239588800_   3276 --TAAAGTGGAAGGAATCAGTCCATCCAATTTCAAGACTTATTGTGTAGC 3323
                         --i     v i    v   vv ivi          i     i iiiv   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr2_239588800_   3324 CAAAGTAATCAAGAGTGTATGACATTAGCAGAGGGAGAGACACATAGATC 3373
                         i v           vv  i  ii i i   v i   v     i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr2_239588800_   3374 AATGGAACAGAACAGAGAACCCAGAAGTAGACGCACACCAATA-GATCCA 3422
                                i    iv    ii      i  i  v  i  vvv  - i  - 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC-A 347

  chr2_239588800_   3423 ACTGATTTTTTAAAGAGGTACAAAGACAATTCAAGGAAGGAAAGATAGCC 3472
                          i       iv v ii   i v     v      v ii i  ii    i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr2_239588800_   3473 TTG-CACTATATGGTGCTGGAGCAATTGGACATCAAAAGGCAAAACA--- 3518
                           v-  vi v          ii   i    i ? v v v      v ---
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr2_239588800_   3519 ----TGAACCACAGCCTAAGTCTCACTCCTTATA-AAATATTAACTCAAA 3563
                         ----  i   ----    --i     v  v    -   v           
  L1M4_orf2#LINE/    448 AAGTTGGACC----CCTA--CCTCACACCATATACAAAAATTAACTCAAA 491

  chr2_239588800_   3564 ATGGATCACGGACTTAAATGTAAAACCCAAAACTATAAA-CGTTTAGTGG 3612
                                 ?i   i         i v i           - vi    -ii
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG-AA 540

  chr2_239588800_   3613 GAAGTGGGGGGAACAGAAGAGAAAATCTTTGAG-TCTAGGGCTAGGCAAA 3661
                            --------    v i ? v       i v -i  v   i       v
  L1M4_orf2#LINE/    541 GAA--------AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr2_239588800_   3662 GCCTTCTTAGACTTGACACCAAAAATCCAAGCTATCAAAGGAAAAATTAA 3711
                          vi        iv           iiv     v iv    i      vi 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr2_239588800_   3712 TAAACTGGACCTCATCAAAACCTTAATACTTTTTCT-CTGTGAAAGATCC 3760
                             i     i         --    v vi    v -  vii  i  iv 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAA--TTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr2_239588800_   3761 TGTTAAGAGGATGAATAAACAAATTATATACCTGGAGAAAATATGTGCAA 3810
                          i i    iii    v i    vii i v viv           v     
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr2_239588800_   3811 ACCACATATTTGACAGAAGAGAAGTATCAAGACTATATAAAGACCTC--A 3858
                          i  i    i   i iii  vvv     v   v          v   -- 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr2_239588800_   3859 CCACTCAATAGTAAAAAAATCAAT---TCAAATAGAAAATGGGCAAAGAA 3905
                          v        i      i iv   ---i   v ?i             i 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr2_239588800_   3906 GGAGCACAGACATTTTACAGAAAACAATCTACAGATTGCAAATAAGTATG 3955
                         vvv v i        iv vi  i vi  v    i  v  v      i ii
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_239588800_   3956 TGAAAATATAGTCAACATTATCAGCCAC 3983
                               v  iv       i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (130 / 99)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.32 (44 / 19)  


2827 24.49 4.74 2.26  chr2_239610313_239613300.rev     1611  2496 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_239610313_   1611 TAGAACATTATATCATGTTCATGAATCAAAAGTCT--ATACCATTAAGAT 1658
                          i   viv   vi          i  iii   v  --   iii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_239610313_   1659 GTCAGTTCTCCTCAAATTGATCTAT-GATT-AATGCAATCCTAAGAAAAA 1706
                          v  i v    i            i-    -  i       iv vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_239610313_   1707 TTCTAGCAGCTTTCTGTTTTGTAGAATTCAGCAAGCTGATT-TGGTATTT 1755
                          i i   v  i  ---     i    v iii         i- iiv   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT---TTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_239610313_   1756 ATAGAGAAATGCAAAGGATGGGCAATAGTCAAAACATTTATTTCTTTAAG 1805
                            vi         i   ivviv     i       ---  --   v  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA---AT--CTTGAAA 192

  chr2_239610313_   1806 TAAAAAGAGCAAAGTTGGAAGACATATGCTACCTGATTTCAAGGCTTTGT 1855
                         -  i    i          i   vi ii  v  ii       ii   vv 
  L1M4_orf2#LINE/    193 -AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr2_239610313_   1856 ATAAAACTACAGATATCAAGGCTGTGCAGCACTGGCATAAGGACAGCTGT 1905
                          i   i      vv      i v   ii i             i  vii 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_239610313_   1906 GTAGATATATGGAACAGAAC--AGAGCCCAGAAAAACACTCGAGCATATG 1953
                         i     vv      i    i--    i       v v  i ivi   v i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_239610313_   1954 TGGTCACTAGATTTTCAACAGAGGTGCCAAGATAATTCACTGGAAGGAAG 2003
                               v v       i   ii          iv     v   i- i   
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAG 390

  chr2_239610313_   2004 GACAGCCTTC-CAGCAA-TGGTGCTGGAACCA-TGGGTATATCTGTGTAA 2050
                         i i  i   i-  i   -         i  v -   i  ?vivii  i  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_239610313_   2051 AATAAAAGAACCTCTACCCTTACCTCACACCACATACAAAAATTAACTTG 2100
                           -i  v   vi vv    i            i               ii
  L1M4_orf2#LINE/    441 AA-GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr2_239610313_   2101 AAGTGAACTGTAAACCTAAATATAAAAGCTAAAACCCTAACATTTCCTGT 2150
                           i  i iii? i        i   i         iv   v i - i iv
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAG 538

  chr2_239610313_   2151 AAGAAAACATAGGAG-AAA----CA-GAT----GATTAGAAAA-AATTTC 2189
                                      ? -   ---- i-  i---- i    iv  -ii    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr2_239610313_   2190 TTATTTAGGACAT--AAAGTA--GGC--CAAAA----AAATTGATAGATT 2229
                            vv  v    i--    i --i  --     ----    v    i   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr2_239610313_   2230 AGACTTTATGAAAACTAAAAAGATTTGTTCCTTTCAAGG-CACTATTTAT 2278
                         i     i  v    i      vv     v -  iv    -      iv v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAG 687

  chr2_239610313_   2279 AACTTTAAGATGGATGATGCATTC----TTGAAGAAAATATTTTCACATC 2324
                           vv v  i --  ii iv  -- ---- v i           v  v   
  L1M4_orf2#LINE/    688 AAAGTGAAAA--GACAACCCA--CAGAATGGGAGAAAATATTTGCAAATC 733

  chr2_239610313_   2325 ---TATCTGATTAAGGACTCACATCCAAACTATATG--GGACTCTTACAA 2369
                         ---        v i     iii     i v     i-- i          
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr2_239610313_   2370 GTCAATATAATAAGAAGACAAACATTCTGATTAAATAAATGGGGAAAAGA 2419
                         v      --    i        i vi ii   ?  -       v   i  
  L1M4_orf2#LINE/    784 CTCAATA--ATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGA 830

  chr2_239610313_   2420 TTT-AATGCACATTTTACTTAAGAAGGTATATGAATAGTTAATAAGCACA 2468
                            -   iv      iv iv      i    ii   i ii          
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr2_239610313_   2469 TGAAAAGGCTCCCAACTTCATCAGTCAT 2496
                                iiv i    v   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (139 / 74)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 1.82 (62 / 34)  


2953 25.55 1.10 1.10  chr2_239614634_239620306     4274  5181 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_239614634_   4274 TGGAAACACATCCCATGCTCACGGATGGGTAGAACCAATATTGTGAAAAT 4323
                               v i        i   i    v  v   vii        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_239614634_   4324 TACCACACTGCCAAAAATAATCTACAAATTCAATGCAATTCCCATCAAAA 4373
                         vi v i   v  v   v i       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_239614634_   4374 TACCACCATCATTCTTCAC-GAACTAGAAAAAA-AATCCTAAATTTTATA 4421
                          v   v vv v  i  ii -   v v  v  iv-i        v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_239614634_   4422 T-CAAATGAAAAAAAAGAGTCCAC-ATAGTCAAAGCAAGACTAACCAAAA 4469
                          -v     v  iii ----i   v-    i    i   vvi i vv  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_239614634_   4470 AGAACAAATGTGAAGGCATCACATTACCTGACTTCAAACTATAGTATAGG 4519
                                 vv  i   vv     i v  ii i      viv  v  i ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_239614634_   4520 GTCATAGTCACCAAAACAGCATGGTACTAGTATAAAAATAGGCACATA-- 4567
                          ii i   v i   i    ii       i i    ii    i  i   --
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_239614634_   4568 CCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAACTGATCTTTGA 4617
                         i        i     v    ii           v   v  --  i v  i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC--ATTTATGG 344

  chr2_239614634_   4618 -CAACTAATCTTCGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACA 4666
                         -   i i  i        i vviv   i v   vv i         i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_239614634_   4667 CCCTATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACGTGTAGAAGA 4716
                         vi  v                    i  i   vv ?    i  i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_239614634_   4717 ATGAAACTGGATCCTCATCTGTTACCCTATACAAAAATCAACTCAAGATT 4766
                              ii    i  ii i  vvi   v           i       i  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_239614634_   4767 GATCAAAGACTTAAATCTGAGACCTGAAACAATAAAAATTCTGGAAGGTA 4816
                              ?    i     v i   v  i    v      v ii i    iv 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_239614634_   4817 ATATCAGAAAAACTCTTCTAGACATTGGTTTAAGCAAAGACGTCATGACC 4866
                          i  vi ?iv  v     vv   v    v   i    v iiv  v iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_239614634_   4867 AAGAACACC-AAAGCAAATGCAGCAAAAACAAAGATAAATAGATGGGACT 4915
                          v -     -      v v   i     iv   i   i   i  v     
  L1M4_orf2#LINE/    595 ATG-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr2_239614634_   4916 TCATTAAA-TGAAAAAGCTTCTGCACAGGAAAATAAATAATCAGCAGAGG 4964
                             i   - v     -   i  ii vvv   iv v iv    iv i  v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr2_239614634_   4965 TAACAGACAACCCACAGAGTGGGAAAAAA-ATCTTCACAATCTATACATC 5013
                         v  v              i     i    -  i v  -    -   i   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATC 740

  chr2_239614634_   5014 TGAAAAAGGACTAATATCCAGAATCTATAAATAACTCAAACAAATTAGCA 5063
                            v  i     vi          v      v     vv    v i ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_239614634_   5064 AGAAAAAAACAAACAATCCCATCAAAAAGTGGGCAAAGGAAATGAATAGA 5113
                          v     i     i  i  v  i?    i           vv        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_239614634_   5114 CAATTCTCAAAAGAAGATATACAAATGGCCAACAAGCATATGGAAAAATG 5163
                           v     v                       i     i   i   i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_239614634_   5164 CTCAGCATCACTAATGAC 5181
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (128 / 100)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.33 (20 / 15)  


3251 22.25 7.81 1.07  chr2_239688667_239691536.rev     1534  2378 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr2_239688667_   1534 GACATTCTGTGTTTATGGATTGAAAGACTCAATGTTGTCAAGATTGTAAT 1583
                           i  i ii    i        i      i   i    i     v i   
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr2_239688667_   1584 TCTTCCAAAATTGATGTATAGAGTCAATGAAATCT-TGCTAAAA-CCCAG 1631
                         v  i  v        v  i   v    i v    i- iii    -     
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr2_239688667_   1632 CAGGATTTTTGTGGTAGAAGTAGGCAAACTGACCATAAAATTTGCTTAGA 1681
                          v vv     -  -i    i v i   i    i v       iiiv i  
  L1M4_orf2#LINE/    107 CTGCCTTTTT-TG-CAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr2_239688667_   1682 AATGCAAAGAAATCCGAATAGCCAAAACAATTTTGAAAAAGAA---CAAA 1728
                                i i vi v                i           ---    
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr2_239688667_   1729 ATGAGAGCACTTCCACCACCAGATTTTAAAACTTTCTGTAAAGCTATGGT 1778
                         i vi   v   iv   iv  vi    i       v  ii       ii  
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr2_239688667_   1779 AATCA--------------TCGCACA------------CAGATCAATGGG 1802
                              -------------- v   i ------------i          i
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr2_239688667_   1803 AGACGATCGAGAGTTCAGAAATAAGC----ACGTCTATGGTCACCTGATT 1848
                          v vi  i      i         i ----  i i        vi     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr2_239688667_   1849 TTCAACAAAGCTGCCAAGACGGT-CAATAAAGAAAAGATGGTCCTTTCAA 1897
                            i    i v         vi -    iii    ii  i   i      
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr2_239688667_   1898 CAAATGGTGCTGGAGCAGTTAGATACCCAG--GCAAAAAGACGAA-TTAG 1944
                                      ii  ii i    ?   v--      ii i   -  i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr2_239688667_   1945 ACCTTTACTGCATGTAATACACAAAAATTCACTCAAAGTGACTCATAGAC 1994
                            ii   iv  iiiv   i         v       i  iv   ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr2_239688667_   1995 CTAACT--------TAAAACTATAAAACTCTGAGAAAAAAAAACATAGGG 2036
                             v --------                 v    i    --      ?
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA--CATAGGN 552

  chr2_239688667_   2037 GACAATCTTTGGGACCTTGGGTTAGGAAACAAGTTCTTAGATTTGATACT 2086
                          vv      i v              v  iiiv         v   i  i
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr2_239688667_   2087 AAAAACATAATCCATAAAA------AT-GATAAATTGGACTTCATCGAGA 2129
                             i  i  v v i    ------  -                  i i 
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr2_239688667_   2130 TTGAAAGCTTTTATATATACATCATAAGACATGATTAAGATAATGAAA-G 2178
                           i   i     i i---- v   v i    iv  i    v i     - 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTG----CTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_239688667_   2179 ACAAGCTTCAGA-CAGGAGAAAATGTTTTACAAATTATATATCTGGTGAA 2227
                             v iv    -ii         i   -i     i         i i i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGATAAG 747

  chr2_239688667_   2228 ATATTTGAATCCAGGACATATAAAGAACTTTCATCATTCAATAACAA--- 2274
                         iv i   v      i i            i i iv i       i  ---
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr2_239688667_   2275 GATCAACAGCCTAATT-AAAAATGGATAAAAGATATAAACAGCTATTTCA 2323
                           iv  i i  i    -        ii   i   v i  i  vi     v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr2_239688667_   2324 CCAAAGC---TGTACAAATGGCTAATAAGC-CA--AAAAGATGCCCAATA 2367
                               v--- i          i       -  --         i   i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr2_239688667_   2368 TCATTAGTCTT 2378
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.36 (130 / 55)
Gap_init rate = 0.03 (24 / 902), avg. gap size = 3.12 (75 / 24)  


 312 23.46 2.47 8.64  chr2_239990833_239994182     1696  1857 (1493)    L1M4_orf2#LINE/L1        3   154 (754)  

  chr2_239990833_   1696 GAAAGAAATTACAGATGCTCGAAAAAAATAGAGAGACGTAGCATATTCGT 1745
                               v  iv  --  i  --- vii  v ii    v  --     -  
  L1M4_orf2#LINE/      3 GAAAGATATCCCA--TGTTC---ATGGATTGGAAGACTTA--ATATT-GT 44

  chr2_239990833_   1746 --AGATTAGAAGACTCCTAATAAACTGATTT-CATATGCAAATCAGTGGA 1792
                         --    viv  v     i--i   i    i -  v  v   vv  ---- 
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCC--CAAATTGATCTACAGATTCAACGCA----A 88

  chr2_239990833_   1793 TCCCAATTGAGACCACAGCAGG-TATTCTGTTGAAATTGAAAAGCTGATT 1841
                             v  ii i i v    v v- v  i  iv        v        i
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chr2_239990833_   1842 TTAAAATTCATATGGA 1857
                         i               
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGA 154

Transitions / transversions = 1.00 (19 / 19)
Gap_init rate = 0.06 (9 / 152), avg. gap size = 2.00 (18 / 9)  

1170 26.88 13.23 3.98  chr2_239990833_239994182     2158  2860 (490)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr2_239990833_   2158 AAAATCCATATGGAAATGCAAAGGGCTAAAAAGAACCAAAACAAGCTTTG 2207
                              i               i  i iv i  v i         v   vi
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr2_239990833_   2208 AAAAGTTTTAAAAAGTTGGAAGACCTACATTATTAGATACTATGGTTAAC 2257
                              vvvv v         i   ii   i viivi  vii viii v  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr2_239990833_   2258 TGCAAATCTAT--TAGTTAAGACAGTGTTGCACTGGTACACAGATATGCA 2305
                          i    v   i--  i i          v i     i i vi    vi  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_239990833_   2306 AACAGACCAATGAACTAGAAT--AAAGTGCAAAAACAGATCCATTTATAT 2353
                         v i   i     i v      -- i   v  i   i i i    vi  v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_239990833_   2354 A-ATTTATTTCACTTATGACAAAGTTGC-------ATTGGATAGCAGAGA 2395
                          -iv i v  v i  vi     i v   -------   vi  i ------
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG------ 384

  chr2_239990833_   2396 AGAAAGGATGACTCTTTTAAATAAATACTGTTAGGCCAACTGAATTTCCA 2445
                         i     i  - v      v  i    iv  i i  v      i  v?   
  L1M4_orf2#LINE/    385 GGAAAGAAT-AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_239990833_   2446 AACGGAAAAG--TAACTCTCAATCCCTACCTCACAC-ATAAAAAAAAAAA 2492
                         v i v     -- i vvi vi i             -   v v     vv
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr2_239990833_   2493 AATTCCCAGTGGATCACAGATCTAAATG--AGTGATAGAACAATGAAGTT 2540
                           i  vv i       ?   i       --  v v  i   v  i  ii 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr2_239990833_   2541 TATCAAAAATAATATAGA---ATATCTTCA-AA--------TAGGCA--- 2575
                         iv vi  i v  i    i--- v      i-i --------      ---
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr2_239990833_   2576 ------TAGATA--------AAACTAT----------------------T 2589
                         ------      --------   vi i---------------------- 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr2_239990833_   2590 AAATTGGACT--ATTAAAATTAAGAGCATCTGTTCAGCAAAAAAAAAAAA 2637
                                   --  i        i i v i   v vv    ii ------
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA------ 677

  chr2_239990833_   2638 AAAAAAAAAACACCATTAAGAAAGGGAAAACGCAGCACACACA-T---AG 2683
                         ----------   i  i       v     vi  i v    v - ---  
  L1M4_orf2#LINE/    678 ----------CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr2_239990833_   2684 AAAATA---GCAA--CAAACAAC--AAAAAGCTCATTCATAGCCAGTGTA 2726
                               ---    --  v i v -- v  i v-- i ii  v    vi  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGG--ACTTGTATCCAGAATA 765

  chr2_239990833_   2727 CAGAAATAGCTCCTACAACTCAGTAAGAAAAATAAAGACAAACCAATTTC 2776
                         i v   v i   i         i   v     v v i i  v      ?v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_239990833_   2777 ----T---TAAA-----TGAATAGAAACTTCTCCACCAAAGATGACATCT 2814
                         ---- ---i   -----        v i       ---    v  i  vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCA---AAGAAGATATAC 862

  chr2_239990833_   2815 AGTTGGTCAATAAACGTATGAAAAGGTATTCAACATTTTTAGTAAT 2860
                          iv   i      i ii        i ii       iv????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (107 / 79)
Gap_init rate = 0.04 (27 / 768), avg. gap size = 4.48 (121 / 27)  


1346 30.57 11.95 1.38  chr2_240020172_240022410      945  1739 (500)    L1M4_orf2#LINE/L1        2   880 (28)  

  chr2_240020172_    945 GGAGGAATATACCATGTGCATGGACCGGAAACCCCAATGAGATTCCGATG 994
                            iii    v      v      ii    iv ii   ivvi  vv    
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_240020172_    995 TCAATGTTTTGCAAAGTAATCGGCAG--TCAATGCAATCGCAATCAAAAT 1042
                         v    ii iiv    v i   vi   --    i      v v        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_240020172_   1043 CCCAGCAGAATTTTTT-TGAAAACTGACAA-----TTTTACATTTTAAAT 1086
                               v vv      -iii   i      ----- ii  v v  i v  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_240020172_   1087 GGAAGCACAAAGAACCTGAAATAGC------AATCTGGAA---GAGAAAC 1127
                             iii   i i   iii      ------     v   ---  ii   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_240020172_   1128 AAGCTTGGGGGACTCACACTACCAAATATCAAGACTT-CTTCTAAACT-- 1174
                           iv    i           v  v   v    i    -  v v  i  --
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_240020172_   1175 --T----------GTGTAAT-------TAAAG---------TAAACCAA- 1195
                         -- ----------    ii -------   i ---------  i i   -
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr2_240020172_   1196 GGA---GAATATG-----CTAGAATGAGACCAACACAG----AGTCATCT 1233
                            ---    -  ----- i    vv i   v i   v----i    vi 
  L1M4_orf2#LINE/    302 GGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_240020172_   1234 GATTATTG-TGAGGATTCCACCCCAAATCCATAGGGAAAACAGGGTCTTT 1282
                             v i -ii   i v   vvv v v  v  i      iv vi      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_240020172_   1283 TCAATATGCAGTGCTTGCGTCAGCTGC-TCTTTG-ATGCTAAA---TGAA 1327
                             i viii     v - v  i   v- v?iii-    v   ---    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGG-GACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_240020172_   1328 CCACAGCCCATACAGCCCGCCATG-ATGGAAATTAGTATGAGCTGGATCA 1376
                         vivvii   v   vv v i    i- iii      iivii iv       
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_240020172_   1377 CAGACCTAAATGTTAAAGGTAAG-CAATGAGGCCTGGTCT-AAAAGACAA 1424
                         ?            v i  v   i- v  i ii ----   - i    v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAAC----TCTTAGAAGAAAA 545

  chr2_240020172_   1425 CA-ACAAA-AAAT-------ATCTTCAGGTGGGCAAAGAT-----AGACA 1460
                           - vi?i-    ------- i   vi v i     v i -----   i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr2_240020172_   1461 -GATGTTAAAAAGGTACTGACCATGAAGGAAAGAAAATGATAAATTGTGC 1509
                         -  iiii    -- i  vii v ii  i    i  v -         vi 
  L1M4_orf2#LINE/    596 TGACACCAAAA--GCACAAGCAACAAAAGAAAAAATA-GATAAATTGGAC 642

  chr2_240020172_   1510 TGCACTCAA--TTAAGAACACTCATTTATCAAAAGATGC-----AGAAGA 1552
                          v  -    --    i   vi ii viv     i  ii -----    - 
  L1M4_orf2#LINE/    643 TTCA-TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA-A 690

  chr2_240020172_   1553 GGGAAAAGGCAAGCCACAAAATAGAAGAGACC--CTGCCACACATACACC 1600
                          v      i   v     i   i i   i vi--i   v vv    i i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_240020172_   1601 CAGCAAGGGACGGATATTCAAAATGTATAAATAATTCTTACAAATCACTA 1650
                         iiii       vvi   i  i   i      v  i        v   v  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_240020172_   1651 AGAAAAAGGCAGACAACCTGAATGAAAAATAAGCAAAACACATCAACAGG 1700
                          v      i  i i    ii v ?      ii     iv iv v  i  i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_240020172_   1701 TACTTTACAAGACAGGAT-TCCAAGTGGTCAATCAACACA 1739
                         i i  iv v i v i   - v   i   i    v i    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.04 (37 / 879), avg. gap size = 2.86 (106 / 37)  


2332 27.18 8.00 1.18  chr2_240581904_240585817     2573  3422 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_240581904_   2573 TGGAGAGAAATACCACATTCATGAATTGGAAAACT--------------- 2607
                             i   v  v   ii      i       i   ---------------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_240581904_   2608 --CAATTCTCCCTAAATTCATCTATAGTCTTAGTGTAGTTCTTATTAAAA 2655
                         --    v     i     v     i  vi i ii i i i i   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_240581904_   2656 TCCTAGCAGAAATCTGTGCAGATGTGAATAAGCATATCTTATATTTTATA 2705
                            i   v vvv i v      vi vi i    vv   i  v v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_240581904_   2706 TGGAAAGGAAAATAAACTAGACTAGCTTAAACAAATTTTGAAAAAGAAGA 2755
                               v v  ivi v i   v    iv      - i             
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGA 199

  chr2_240581904_   2756 AAAATGTGGGAGGAATCACTCTACCTGATTTTAATTTTTACTCCATCATT 2805
                          v  v  v      v    v  v  ii    i  vvi     v  vvii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_240581904_   2806 ACGGTAATCAAGAC-------------TATA--GAGAAACAGAGAGA-AA 2839
                           i           -------------i   --  v i   v v   -v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_240581904_   2840 AGAGAACAGAATAAAGAACCTAGAAACAGATCCATACAAGTACTTCCAAT 2889
                          vi   i     vi   ii i     i i i       vv  ivvi    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_240581904_   2890 TGATGTTTGACAAAGGTGCAAAAGCAATTCAATGGGGAAGGGATAGTCTT 2939
                             v  i     i     v  ii v             i i        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_240581904_   2940 TCTACAAATAAATGGTGCTGAAGTGAGTGAACATCCATTGGCAAAAGAAA 2989
                          ii --- i           iiiii v  i i ?   ivv         -
  L1M4_orf2#LINE/    400 TTCA---ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA- 445

  chr2_240581904_   2990 TGAACTGCGACCTAAGTCTCCCTTTATGTACAAAAATTAACTCACAATGG 3039
                             v vv    ivvii   v vii  i                v     
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr2_240581904_   3040 ACCACAGACTTAAATGTAA-AGTGTAAAACTACTAAACTTGCAGAAAACA 3088
                          i  ?    i         -  i-        iv     ivi    i v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_240581904_   3089 ACAGAGAAGGTCATCTTTGAGATCTAGGGTTAGGTGAAGAATTCTTAAGA 3138
                            v  i? vvv     i v  i  v        ii v iv      -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GA 593

  chr2_240581904_   3139 CTTGACTCGTAAAGTATTATCAATTAAA--AAATATACATAAAATTGGAC 3186
                         iv    v vv    i iv v   iv   --   v   v     -      
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA-TTGGAC 642

  chr2_240581904_   3187 CTCACGCAAATTTAAG--TTTTTGCTCTGTGAAAAGCCCTAGTGACAGAA 3234
                         i   i-    v    i--i     iv  vii  iii v   vii v i i
  L1M4_orf2#LINE/    643 TTCAT-CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr2_240581904_   3235 TGAAAAGACAAGCTACAAGGTGGGAGA-------------TCAC----CT 3267
                                    v i   iii       -------------   i----  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr2_240581904_   3268 GGCAGAGGACAAA-ATCTGAAATACATAAAGAAGGTCTCAAATCTCAACA 3316
                          ii ii    vvi-   iii    i        v-   i v v     i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAAC-TCTTACAACTCAATA 790

  chr2_240581904_   3317 ATGATCAGCTCAGT---CCAGTTAGAAAATGTGCAAAAGACATGAACAGA 3363
                           i vv  viv i ---   i  ?i      v     i  iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_240581904_   3364 TATTTC-ACAAAGAGGATATACAGAT------TA-GCACATGAAAACATG 3405
                         i     -v      i        i  ------  -           v   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_240581904_   3406 TT-AACATCACCAGTCAC 3422
                         i -       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (130 / 97)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.39 (78 / 23)  


3623 23.44 0.99 1.53  chr2_240693741_240697959.rev     2815  3727 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_240693741_   2815 TGGAAAGATACTTCATGCTTATTAGTTGGAAGGATTAATATTGTTAAAAT 2864
                                   iii    i i  vii       iv             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_240693741_   2865 GACAATACTTCCCAAAGGAATTTGCAGATTAAATGTAATCTCTATCAAAA 2914
                          i       i      vvi  i i      v  i i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_240693741_   2915 TACCAGTGATATTCTTCAAAGAAATAGAAAAAA-AATCCTAAAATTTATA 2963
                          v    iviiv  i  iiv      v  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_240693741_   2964 TGGAATCACAAAAGACCCCTAATAACCAAAGCAATCCTGAACAAAAAGAA 3013
                              vii   ii     vv    i     i     i    v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_240693741_   3014 CAAAGGTGGAGGCCTCACACGACGTGACTTCAAGATATACTATAAAGCTA 3063
                              v      v       vv vii i     i iv     i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_240693741_   3064 CCGTAACCAAACCAGCATGTTACTAGCATAGAAACAGACACATAGACCAA 3113
                          v    i   iv   ii  v    i     iii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_240693741_   3114 TGGAACAGGATAGAGAACCCAGATATAAATCCACACATTTACAGTGAACT 3163
                              i  i  v    ii     v     i   i       ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_240693741_   3164 CCTTTTCAACAAAGGTGCCAAAGACATATGATGAGGAAAGGATAGTCTCG 3213
                         vv     i    i        iiv   vii   i      i       iv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_240693741_   3214 TCAATAAATCGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAAA 3263
                             i    v         v         ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_240693741_   3264 CTAGACCCCCATCTCTCACCACATACAAAAATTCAATCCAAATGGATTAA 3313
                         i i      i i   v     i           v v  v        i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_240693741_   3314 AGACTTAAATCTAAGACTCAAAACTATAAAACCACTAGAAGAAAACATTG 3363
                             i     v     vii             ivi             v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_240693741_   3364 CGGAAACACTCCAGGACATTGGTCTGGGCAAAGAATGATCTTGTGTAAGA 3413
                         v? v  vv  i iv   v    vi i     v iv --    ivi  v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT--TCTTAGATATGA 598

  chr2_240693741_   3414 CCTGGAAAGAACAGGCAACCAAAGCAAAAACAGAGAAATAAGATTACATC 3463
                          vivi    v   i     v    v     i   v    vi  i v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_240693741_   3464 AAACTAAAAAGTTTCTACACAACAAAGGAAACAATCAACAGAGTGAAGAG 3513
                            v v    ii  i iii vv       v  v     v i      i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr2_240693741_   3514 ACGACCCACAGAA--------AATGTTTACAAACTATCTATCTGACAAGG 3555
                           i          --------   i   i    ii  v       i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr2_240693741_   3556 GATTAATAACCAGAATATATAAGGAGCTCAAACAACTCAGTGGCAAAAAA 3605
                           i vi  v             i  i   vv        i ---  v   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT---AATAAA 795

  chr2_240693741_   3606 AAAGCAAAAAACCCAAATGATCTCATTTAAAAATGGGCAAAAGATCTGAA 3655
                           ii    v       ---------  ?             i   i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAA---------TTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_240693741_   3656 TATATATTTCTCAAAAGAATACATACAAATGGCAAACAGGTTTGTAAAAA 3705
                           v i       v      v i           v  i i ivii i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_240693741_   3706 AATGCTCAACATCACTAATAAT 3727
                         i             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (129 / 81)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 4.60 (23 / 5)  


 747 32.02 7.25 0.91  chr2_240740092_240745018     3259  3589 (1338)    L1M4_orf2#LINE/L1        3   354 (554)  

  chr2_240740092_   3259 GAGATGTATCTTGTATTCAATAAGCAAAAGACTCAATAGTATTAAAATGT 3308
                           i vi    iii i    vvi viii      i    v i    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr2_240740092_   3309 CAAATTTCCTCCCAAATT-ACCAATAGATTAATTGCACTTATAGTCAAAA 3357
                            -- v ii        - i v i     v vi   v ivivi      
  L1M4_orf2#LINE/     53 CAA--TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_240740092_   3358 TAACACCTGACATTTTAATAGAAGTTAACAAG-TGAATTTGTAATTTTTG 3406
                          vv  v   v v    vii    i  i     -   vii iv    iv i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_240740092_   3407 TGGAAATGCAGAGAACATGGAGTGGCCAAAATAGTTTTGAAGAGAAATTA 3456
                                   ii i  vii  i i       i i i     i ii  vv 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_240740092_   3457 -AAAATTGGAGGACTTAAACCACTTGATTTAAGTCCTTACTGTAAAAACT 3505
                         -   i          i v  iv iii    v ivv      ii   i-  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG-CT 249

  chr2_240740092_   3506 AACATAATCACAACAATGTTGTTTGGGTAC---------C---------- 3536
                          vvi      vi   i   v  viv  i i--------- ----------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_240740092_   3537 -TGGAACAGAATCAAGGTTACAGAA-TAGACCTACACAGGTATGGTCAAT 3584
                         -     i     ii  iv v     -  i   i i   vv          
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_240740092_   3585 TGATT 3589
                              
  L1M4_orf2#LINE/    350 TGATT 354

Transitions / transversions = 1.65 (66 / 40)
Gap_init rate = 0.02 (8 / 352), avg. gap size = 3.38 (27 / 8)  

1840 22.04 5.93 0.93  chr2_240740092_240745018     3896  4435 (492)    L1M4_orf2#LINE/L1      342   908 (0)  

  chr2_240740092_   3896 TGGTCAATTGATTTTTGACAAAACTGGCAGAGTAAATCAATGAGGGAAAG 3945
                                        i     iiv  v  iiiiv v      -       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAG 390

  chr2_240740092_   3946 GATAGTTTTTTCAAAAATTTGTGCTGAAACACTTGGATATCAACACACAA 3995
                         i     i       v  v v      ii   vi      ? v   ii   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr2_240740092_   3996 AACAATAA----GAACATCAACCTTA--------ACAATAATTAACTCAA 4033
                           v   i ---- i  vi v    i --------    v           
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr2_240740092_   4034 A-TGGATAAAATCCCTAAGTATAAGAGCTAAA-CTTTAAAACATCTAGAA 4081
                          -     v ? vv     i i           -  v      vii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr2_240740092_   4082 -AAAGTAAAAGAGAAAATCTTTGAGATGTTAGGTTAGGCAAAGATGTCTT 4130
                         -   ii v i ? v       i v  iv  i          v i v    
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_240740092_   4131 -GATAGGAC--CACAGAGTAGAAGCTACAGAGAGGGAGAATTTGATTATT 4177
                         -    v   --  - i  i v    v   i -  ii i   v-   v v 
  L1M4_orf2#LINE/    591 AGATATGACACCA-AAAGCACAAGCAACAAA-AGAAAAAATA-GATAAAT 637

  chr2_240740092_   4178 TGGACTT--TTAAAATTAAAAATATTTGCTTTACAAAATATATTTT---- 4221
                                -- i           iv    ivi v    iv i i v ----
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_240740092_   4222 AAAATCAAAGTCCAGC------AATGAAGAGAAAATACTTGCAGAAGACA 4265
                            i v   ivv  i ------    i-         i     i vv i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGG-GAGAAAATATTTGCAAATCATA 736

  chr2_240740092_   4266 TATTTAATAAAGGACTTATATCTAGTATATATAAAGAACTCTT-CAACTC 4314
                            i i    i      i    i  v                 -      
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr2_240740092_   4315 AATAGCAAGAAGACAAACAACCTAGTT-AAAAATGGGCAAAAGCTTTGAA 4363
                             ii  i        i    i i  -             i v      
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr2_240740092_   4364 CAGATATTTCACAATAGAAAACATAAGAATGGCAAATAAGCATATGAAAA 4413
                         i   i     v v v    i i   vi      v        i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr2_240740092_   4414 GATTCTCAGCATCATTAGTCAT 4435
                            v    i     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (68 / 48)
Gap_init rate = 0.03 (17 / 567), avg. gap size = 2.18 (37 / 17)  

 290 32.06 3.05 3.05  chr2_240740092_240745018     4796  4926 (1)    L1M4_orf2#LINE/L1        1   131 (777)  

  chr2_240740092_   4796 TGAAAAGACAGGCATTCCATGTTCATGGGTAGGAAGAGTTAACATGACAA 4845
                           i     i ---- i            i v      v    i  viiv 
  L1M4_orf2#LINE/      1 TGGAAAGATA----TCCCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chr2_240740092_   4846 TGAAATCAAT-TATCTCAAA---ACCTATAGATTTAGTACAAATCTAATC 4891
                         v  viv    -ivi i    --- i   i     i iii   vi iv   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr2_240740092_   4892 AACATTTTAGTAGGCTTTTGAATGGAAATTGTCAA 4926
                           v  iii  iv v     vviii       v   
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

Transitions / transversions = 1.62 (26 / 16)
Gap_init rate = 0.02 (3 / 131), avg. gap size = 2.67 (8 / 3)  


3060 24.81 0.98 2.71  chr2_240756149_240761552     3990  4912 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr2_240756149_   3990 GGAAACGCATCCCATGCTCCTGGATTGGAAGAATGAGTATTGTGAAAATG 4039
                              vii        i  v            v v i      v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr2_240756149_   4040 ACCAAACTGCCCAAAGCAATCCACAGATTCAATGCAATTCTCATCAAAAT 4089
                         i v v   v      vii   i          i     i ii        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr2_240756149_   4090 ATCATCATCATTCTTCACAGAATTAGAAAAAA-AATCCAAAAATTCATAT 4138
                         vi  v vv v  i  ii     v v  v  iv-i    v           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr2_240756149_   4139 GGAACCATAAGAGAGCCCAAATAGCCAAAGCAATCCTAAGCAAAAAGAAC 4188
                             viii   i  v  vi          i     i i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr2_240756149_   4189 AAATCTGGAGGCATCACATTACCAGACTTCAAATTACACTACAAGACTAT 4238
                            vi      vv     i v  vi i      vivi       ii   i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr2_240756149_   4239 AGTTACTAAAACAGCATGGTACTGGTATAAAAGTAGGTAAGTAGGTACAT 4288
                            v ii  i    ii         i    iii   ----------    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG----------ACAT 291

  chr2_240756149_   4289 ATA--CCAATTTAACAGAATAGAGAAGCCAGAAATAAAGCCAAATACATA 4336
                            --i    vv  i     v    iv           v   v i iv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr2_240756149_   4337 CAGACAACTGATCCTCAACAAAGCACCCAAAAC-ATAAATTGGGGAATGG 4385
                         ii v   i    ii  i    i vvv    i  -  vv v       v i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr2_240756149_   4386 ACACCCTATTTAATAAATGGAGCTGGGAAAACTGTCAT-GCCACACTTAG 4434
                          i vi  v  i  i      v       v     v-  -?     ivi i
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG-ATAKCCACATGCAA 440

  chr2_240756149_   4435 AAGAATGAAACTGGATCCCTATCTATCTCTCACCATACACAAAAATCAAC 4484
                                  ii    i     i  ---- v       i        i   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCT----CACACCATATACAAAAATTAAC 486

  chr2_240756149_   4485 TCAATATGGAACAAAGACTTAAATATAAGGCCTGAAACCATAAAAATTCT 4534
                             v     v  ?    i     i    iv  i    i      v ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_240756149_   4535 AGAAGACAATGTTGGAAAAACTCTTCCAGACATTGTCCTAGGCAAAGAAT 4584
                               v  ii v  ?iv  v     vv   v   vvi       v iv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_240756149_   4585 TCATGACTAAGACCCCAAAAGCAAATGTGATAAAAACAAAAATAAATAAA 4634
                           v iiv  v   v         v v ii i    iv       i     
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr2_240756149_   4635 TGGGACCTGATTAAACTAAAAAGCTTCTGCACAGCAAATAATAATAATAA 4684
                          v    i v  i   v v    i   i  ii vv    vi ---------
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA--------- 677

  chr2_240756149_   4685 TCATCATCATCAGAGGAAACGGACAACCCACAGAATGGGAGAAAATATTT 4734
                         -  ii    vv i  vi  vi                             
  L1M4_orf2#LINE/    678 -CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_240756149_   4735 GCAAACTACACATCCAATAAAGAACT---ATCCAGAATCTATAACGAACT 4781
                              ii i i   ii    i i   ---         v     v     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_240756149_   4782 CAAACAAATCAGCAAGAAAGA-ACAAATAATTCCATTAAAAAGTGGGCAA 4830
                          vv    v   ii  v   i -        ii v   ?    i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_240756149_   4831 AGGATACGGATAGACATTTCTCAAAAGAAGATATACAAATGGCCAAGAAA 4880
                              vi i             v                       v  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_240756149_   4881 CATATAGACAAATACTCAACATTACTAATCAT 4912
                           i  ii v i  i        i ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (128 / 97)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 3.40 (34 / 10)  


 633 28.18 7.57 5.64  chr2_240773654_240775261.rev      501  1121 (487)    L1M4_orf2#LINE/L1      276   908 (0)  

  chr2_240773654_    501 GTAGAAGAATGGACAAATAGCTCAATAGGACAGAATATAGACTCTAGAAA 550
                          i v   i  i    v    v     i i i     vv   v  i     
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr2_240773654_    551 TCAATC--TACATATAGAGACACTTGGTTTATGACAAGA-TGACA---CT 594
                          v  i --     v  vi v  v   i   vi      i-  v  --- i
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr2_240773654_    595 GTATAACACTGGAATAAAAATG-----TTTAAAATGTGGT-------CAG 632
                         i vi  ---   iiv  i   i-----  i  v vi    -------  i
  L1M4_orf2#LINE/    376 ATTCAA---TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr2_240773654_    633 CAGGATAACCATATGGAAAACA-TGAAGCTGTTAATCCCCTCTATCACAG 681
                          v     ?   i   v    v -     i  --i -     viv     v
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTG--GA-CCCCTACCTCACAC 469

  chr2_240773654_    682 AA-ACA-AAAAATAATAATTTTATGTGACTTATAAATACTAATATGAAAG 729
                         v - i -      --   i iv vi  iv i ? i i-    -   v   
  L1M4_orf2#LINE/    470 CATATACAAAAAT--TAACTCAAAATGGATCAWAGAC-CTAA-ATGTAAG 515

  chr2_240773654_    730 ACTTAGTGAAAAGACCTCACCAAACTAT---AAGATAA-AGAAGAATATA 775
                          ---- iv    ---  - iv     v ---    v  - v i ?i  v 
  L1M4_orf2#LINE/    516 A----GCTAAAA---CT-ATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr2_240773654_    776 TTTTTG-GATCTAACGC-AGGCAAATATTCTTTAAACATGACA--AAAAA 821
                          i  i -  i  viv i-      vvi  ii   i i      --    i
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr2_240773654_    822 TG-AAGTACCTATGAAGGAAATGACTCATAAGCTTATCTT-ATTGAGCAA 869
                         ii-   i --- ii  i    vi ivv    ii viv   -  ----   
  L1M4_orf2#LINE/    608 CACAAGCA---ACAAAAGAAAAAATAGATAAATTGGACTTCAT----CAA 650

  chr2_240773654_    870 GTTTAAGAAATTATGTTAATCAAA-----CTTAAAATCGACATGAGTGTA 914
                         iv    i  v  v   vvv     -----  ----   i v -i    v 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACT----ATCAAGA-AAGTGAA 695

  chr2_240773654_    915 AATACAGAAGCTTCAAAGTGGGAGAAA-TATTTGCAAGCCATATAACCAA 963
                           v   -- v iv  i i         -         ii      v ii 
  L1M4_orf2#LINE/    696 AAGACA--ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_240773654_    964 AAACAGGCTCATATTCAGAATATGTGAATAATT-TTATGA-TCAATA-TG 1010
                         v  vi i  ii   i        i i  v  i -   ii -      - i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_240773654_   1011 GAAAAGCAAAGCAACACGGTAGAAATAAAGGGCAAAACAC----ATATAC 1056
                         i   ii    -i   v ii v?   -  v       iv i----   v  
  L1M4_orf2#LINE/    794 AAAAGACAAA-TAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGAC 841

  chr2_240773654_   1057 GTC---CTAAAAAAGAATATCCAAATGACTGCTAACTATATGAAAAGCTG 1103
                         i i--- i   i    -   v      i iiv   vi i        v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGA-TATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_240773654_   1104 ATTAAGCTCTATAGCCAC 1121
                         v i  vv  v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (100 / 71)
Gap_init rate = 0.06 (39 / 633), avg. gap size = 2.10 (82 / 39)  


 770 30.93 11.02 3.11  chr2_240897043_240898712.rev      476  1183 (487)    L1M4_orf2#LINE/L1      145   908 (0)  

  chr2_240897043_    476 TTCACAGGGAAGAATTAGAAAGCAGGAATAGCCAGGA-AATCCCTGGAAA 524
                             i v    iviiv  ii v vi         ii -    i-  i   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT-TGAAAA 193

  chr2_240897043_    525 AGGAGGGCAGGGTGAAGTTGGTGGGGT-AGACTATGCCA--TATAATACA 571
                           i  ii  -----       v  iv - v   - v   -- vi  v  v
  L1M4_orf2#LINE/    194 AGAAGAACA-----AAGTTGGAGGACTCACACT-TCCCAATTTCAAAACT 237

  chr2_240897043_    572 TGTTATAAAGCTTCTGTGAGCACAACAGCATGGCATT--CATTCGTTTAC 619
                          ii  i      v v  i v  vi    ii   i i --   vv v-- i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG--AT 285

  chr2_240897043_    620 AGATGAATGGACCAGTGGAATAGA-----GAATCCAGAGATAGACCCACA 664
                            iiv  i  i  i         -----  i      i   i     i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr2_240897043_    665 AGCA---GTGGGCTGTTG----TCAAGGTGGGTGGCATCCCAAG-----T 702
                         --  ---i   v vi   ----  i viv     -----     ----- 
  L1M4_orf2#LINE/    336 --CATTTATGGTCAATTGATTTTCGACAAGGGTG-----CCAAGACCATT 378

  chr2_240897043_    703 GAGTGGGAGAAGA-TGGACTCTGTAACCAAGGG-GTTCGGGATG-CTGCA 749
                         v i    ii    - i v  i vi   v  v  - i -    ii-   v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT-GGGACAACTGGA 427

  chr2_240897043_    750 GAGCCACATGCAAAGAGAA---AATTGGATCC--ACTTCTCACAGTGGAC 794
                         v ?           -    --- i     i  --  i  v   vi iv  
  L1M4_orf2#LINE/    428 TAKCCACATGCAAA-AGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr2_240897043_    795 A----------CCAAGTGAATCAGAGA------TG---GAGTTA------ 819
                          ---------- v  i  i    ?   ------  ---   i  ------
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr2_240897043_    820 CACAAGTATTAGAAAATAA-ATCAGGTTACTTCCTTTACAACCTAAGATG 868
                         i v  v v      i v  -  vi ?v  vv  -  iiii    vi i v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTT 575

  chr2_240897043_    869 GAGAAAAGCTTTTATAACCATGACTCAAAATCCAGAAGCAATCA--GGCA 916
                         ii v  v v   iv  ivi     v v   vv  v      iv -- iv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr2_240897043_    917 AGTTGAACAAATTTGTCTCCA-CAAAATTAAGA-CCTTTATATGGGAAAA 964
                          iv ii i     v v  i  -         i - i   i iivvv   i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr2_240897043_    965 TACACCATCTTCAAAGTCAAAGGACAG----------GTAAGACAATATT 1004
                         v    i   vvv     v   i    i---------- vi   v      
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr2_240897043_   1005 TGCAACTAATATTACAGATGCAAGGCTAATATCACTGA-TATACAAAAAG 1053
                              v v    vv v   ivii i  vi    - v  -    i   i i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATC-CAGAATATATAAAGAA 774

  chr2_240897043_   1054 TTCC--CAA---AATGAAGAAAATGTCCAAAGATCTG-TAGGAAAATAGG 1097
                         i  i--   ---   -  v    v v v  vi i ii- v?i     i  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAAT-AATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr2_240897043_   1098 TACAAGATAGGAACAAATAGTTTGTAAAAGAAAAAATGCAAATGCCTCTT 1147
                         i v i   vv   i i i v  iviv      i v  i      v ivv 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr2_240897043_   1148 AAACATAGGAAAAGGTGACTCAATCTTGCTCATATA 1183
                           i  i v      i  -     iv ii????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATG-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (119 / 96)
Gap_init rate = 0.05 (38 / 764), avg. gap size = 2.63 (100 / 38)  


2340 28.54 4.04 2.36  chr2_240924938_240927037.rev      719  1608 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr2_240924938_    719 AAAAAAATTCCATGCTTATGTGTAGGAAGAATCAATATTGTTAAAATGGC 768
                            i v  i     i i   vi v      v i           i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr2_240924938_    769 CATACTGCCCAAAGCAAT-TACAGATTCAATGCTATTTCAATGACACTAC 817
                         v     v      vii  -           i  v  ii v  v v v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr2_240924938_    818 CAACATAAGTTTCCACAGAATTAGAAAAAACAGTTTTACAATTTGTATGG 867
                           i vvvvv   iii     v v  v  iviii ii  v    ii     
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr2_240924938_    868 GACCCAAACAGATCCCGATTCCCCAAAGCAATCCTAAGAAAAAAGAACAA 917
                         i vivv  vi  i  v  v vv     i     i i i   i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr2_240924938_    918 CGCTGGAGGCATCACACTACCCAACTTTAAACTATACTACTAGGCTCCAG 967
                         v i      vv       v     i  i   viv      v i   v   
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_240924938_    968 TAACCAAAAGCTCATGGTACTGGTACAAAAA-AGATACATAGACCAATGG 1016
                            i   i vvvii         i i  ii -   i i     i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_240924938_   1017 AACGGATTAGAGAACACAGAAATGAAGTCACACACCTACAACCATCTG-T 1065
                           ii  v v    iiv       i  vi  i   ii  iiii  vi  - 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_240924938_   1066 T--------GGTTGT---------------AGGAAAAAACTCCCTATTTA 1092
                          --------  v  i---------------i     i  ivvi  v  i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr2_240924938_   1093 ATAAAGGGTGCTGGGATAAGTGGCTAGCCATACACAGAAGGTTGAAGCTG 1142
                          i   v          i  v   v  ?   i ii  i   iv     i  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr2_240924938_   1143 GACTC-TACCTTTCACCATAAACAAAAATTAACTCAAGATGGATTAAATA 1191
                            i -     iv       v                i      i ? v 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr2_240924938_   1192 CTTAAATATAAGACCTAAAACAGTAAAAAACCTGGAAGAAAACCTAGGAA 1241
                          i     i     v       vi     vv i i         v    ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr2_240924938_   1242 ATAGCATTCTGAACATCAACCTTGGA------AATGAATTTATAC-TAAG 1284
                         -  i-  ii --- i -i       i------    iv  iv  v-  v 
  L1M4_orf2#LINE/    554 -TAA-ATCTT---CGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_240924938_   1285 TTCCCAAAAGCAATTGCAACAAAAACAAAAATTTATAAGTGGGACC-AAT 1333
                         viv         vvv         iv      vv    i v    i-v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr2_240924938_   1334 TAAACTAAAGAATTTCTGCACAGCAAAACAAAAACAAAAACAAAAAACCA 1383
                         i   v v  i  i  i  ii vv    i----------i   ----- i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAG----------GACA-----CTA 682

  chr2_240924938_   1384 TCAACAGAGTAAACAGATAACTTCCAGAATGGGAGAAAGTATTTGCAAAC 1433
                             v i   i  v   i   iiv              i          i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr2_240924938_   1434 TATGTATCCAACAAAGGTCTAAT-TGCAGAATCTATAAAAAATATAAACA 1482
                         i  i    ii i  i  v  vi - v      v      i  ivivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_240924938_   1483 ATTCAACAAAGAAAAACCAAATATGCTGATTAAAAAACAGGCAAAAGACA 1532
                          i    i  vi    iv      vv ii   ?     ii      i  iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr2_240924938_   1533 TGAACAGACACTTCTCAGAAGAAGACATATATGCAGCCAACAAATATGGG 1582
                             i     i     vi       i   i viii     i  ii iiv 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr2_240924938_   1583 AAAAAATGTTCATCATCAGTAATCAT 1608
                             i   i   v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (150 / 100)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 3.56 (57 / 16)  


3447 23.38 2.24 0.67  chr2_240939198_240943343     2761  3654 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_240939198_   2761 TGGAGAGATATTCCATGTTAATGGATTGGAAGAATCAACATT---AAAAT 2807
                             i      i       v             v i  i   ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_240939198_   2808 GTCCATACTACCCAAAGCAATCTGCAGATTCAGTTCAGTCTCTCTCAAAA 2857
                          v v     v      vii    i        iiv  i  i  v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_240939198_   2858 TACCAATGATGTTCTTCACATATATAGAAACAATAATCCTAAAATTTATA 2907
                          v   iiviiv  i  ii  v v  v  v viv i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_240939198_   2908 TGGAACCACAAAAGACCCAAAATAGCTAAAGCTATCCTGAGCAAAAAGAA 2957
                              vii   ii      i      i   i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_240939198_   2958 TAAAAGTGGAGGAATCCCATTACCTGGATTCAAATTTTATGACAGACCTA 3007
                         i   iv       v  v  i v  iiiv      vi   iv   i v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_240939198_   3008 TAGTAATCCAAAGAGTGTGATACTGGCATAAAAACAGACACATAGAACT- 3056
                         i       v i v      i           ii i     i     v v-
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_240939198_   3057 TGGAACAGAATAGAG-GACCAGAAATAAATCCATACATCTACAGTGAACT 3105
                              i     v   - v           i        i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_240939198_   3106 CATTTTTGACAAAGGTGCCAAGTACATACATTGGGGAAAGGACAGTCTCT 3155
                         v     i     i         vv   v  v         i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_240939198_   3156 TCAACAAATGATGCTGGGAAAACTGGATATCCAGATCCAGAAGAAAAAAA 3205
                                   i        v         ?   v  v  i     vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_240939198_   3206 AATACAGACCTCTATCTCTCACTACATA-AAAAATCAAAACAAAATGGAT 3254
                         -- -ii    i   i   v   i i   -      i  vv          
  L1M4_orf2#LINE/    451 --T-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_240939198_   3255 TAAAGACTTAA-TCTAAGACCTAAAACTATACAACTACTAAAAGAAAACA 3303
                         i ?    i   - v     v           v    vi  i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_240939198_   3304 TTAGGGAAACTCTCCAGGACCTTGGACTGGGCAAAGATTTCTTGAGAAAT 3353
                          vi ? v  v   i iv        ii i     v i      -   v  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATAT 596

  chr2_240939198_   3354 GCC-CCACAAGCACAGGCAACAAT-GCAAAAATGGACAAATAGGATCACA 3401
                          v -   v       i       v- v      i  i    v   iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr2_240939198_   3402 TCAAGCTAAAAGGCTTATGCACAACAAGGGAAACAATCAACACAGTGAAG 3451
                             iv v   ii   v  ii vv   i   v  v     v v      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_240939198_   3452 AGACAACCCACAGAGTGGGAGAAAATACTTGCAAACTACTCATCCAACAA 3501
                                       i            i       ii ivi   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_240939198_   3502 GGGATTAATAACCAGAATATATAAGGAGCTCAAACAACTCAACAG-AAAA 3550
                             i vi  v             i  i   vv         i i-    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_240939198_   3551 AAA-----AATCTAAT-----AATGGGGAAAATATCTGAATATACATTTC 3590
                          i -----  i i   -----      v   iv  i      v       
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr2_240939198_   3591 TCGAAAGGAGACAAACAAATGGCAAGCAGGTATCTATGCAAAGGTGCTCA 3640
                           v    i   i v         v ii i i i--   v    i      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCAC--ATGAAAAGATGCTCA 894

  chr2_240939198_   3641 ATATCATTGATCAT 3654
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (122 / 84)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.86 (26 / 14)  


4657 15.59 1.31 2.29  chr2_240974491_240976618      720  1636 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_240974491_    720 TGGAAAGACTTCCCATGTTCATGGATTGGAACATTTA-TATTGTTAAAAT 768
                                 iv                     v i   -         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_240974491_    769 GGCAGTACTCCTCAAATTGATGTACAGATTCAACTCAATCTCTATCAAAA 818
                             i      i         v            v     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_240974491_    819 TCCTAGCTAGATTTTTTTTTGCAAAAATTAACAAGCTGATTCTACAATTC 868
                            i    i---ii         i     i          i   v     
  L1M4_orf2#LINE/    101 TCCCAGCTG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_240974491_    869 ATATGGACATGCAAGGGACCAATAATAGCTAAAACAATTTTGAAAAAGAA 918
                                v            v v      i        i           
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr2_240974491_    919 ---CAAATTTGGAGGACTCACACTTCTCAATTTCAATATATAGCTGAAGT 965
                         ---    v                  i         ----- i  v --i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA-----AACTTA--C 240

  chr2_240974491_    966 TATATAGCTGCAATATTTCAAAGC--TATACTAATGAAGGCATAATGATA 1013
                           i v    i  i  v -   ii -- i iv  v  ---      v    
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAAT-CAAGACAGTGTGGTACTG---GCATAAGGATA 286

  chr2_240974491_   1014 GACATACAGATCAATGGGATATAACTGAAAGTTCAGAAATAAACCCTTAA 1063
                               i          i   v  i   i   i             v  v
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr2_240974491_   1064 ATTTATGGTCAGTTGATTTTCGACAAAGATACCAAGACAATGTAATTGGG 1113
                                    i              i i i       v  vi   v   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr2_240974491_   1114 AAATAATTGTCTTCTCAACAAATTTGTGC-AGGACAACTGGACATCCATA 1162
                            v   v     i         v-    -i           i ?   i 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATG-GTGCTGGGACAACTGGATAKCCACA 435

  chr2_240974491_   1163 TGCAAAAGAATGAAGTTGGACCCCTACCTCACATTATATACAAAAGTTAA 1212
                                                          ii          i    
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr2_240974491_   1213 CTCAAAGTGGAACATAGACCTAAATGTAAGAGCCAAAACTACAACAATCC 1262
                               i    v  ?                  i       i  v v  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr2_240974491_   1263 TAAAAGAAAGCATAGGGATAAATTTTTATGACATTAGGTTAGGAAATGGA 1312
                           i      i      ?i     i  ii    v  i       v     v
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr2_240974491_   1313 TTCTTAGATATGACATGAAAAGTACAGACCACAAAGGAAAAAAATAGGTA 1362
                                        iv     i   ii v     i       -   i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATA 634

  chr2_240974491_   1363 CACTGGACTTCATCAAAAT-GGAAACCTGTGTGAGGCACAGGATATCATC 1411
                         v i                -ii    i v    vvv  v    i ii   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr2_240974491_   1412 AAAAAACTGAAGAGAC---CAACAGAGTGGGAGAAAATACTTCCAAATTA 1458
                           i   v    i    --- v     i            i  v     i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr2_240974491_   1459 TATATACCTGATGAAGGACTTGTATCCAGAATATGTAAAGAACTCTTACG 1508
                              --     i i                   i              i
  L1M4_orf2#LINE/    735 TATAT--CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr2_240974491_   1509 ATTAAATAATCCAAAGACAAAATATCCAACTACAAAAATGAGTAAAA-AT 1557
                          i v      vv         vv i    i ?-       i i   i-  
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGAT 831

  chr2_240974491_   1558 TTGAATAGACATCAATCTAAAGAAGATTTACACATGGCCAATAACCATAT 1607
                                     ivv  i         v    v           v  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr2_240974491_   1608 ATGAAAATATATTCAAAATCATTATTCAT 1636
                         --     v  ii    v    ????????
  L1M4_orf2#LINE/    882 --GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (86 / 53)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.94 (33 / 17)  


2933 17.82 7.60 2.76  chr2_241087410_241089125.rev      501  1224 (492)    L1M4_orf2#LINE/L1      150   908 (0)  

  chr2_241087410_    501 ATGGGCATGAAACAAGGATATTCCCTGAATAGCCACA-TAGTCTTAAAAA 549
                             iv   ---     i- --   v         v -i i    i    
  L1M4_orf2#LINE/    150 ATGGAAATG---CAAGGG-A--CCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr2_241087410_    550 ACAAAAACAGAGTTGGAGGACTCA-GTTTCCCAGTTTCAAAACTTACTAC 598
                          v  i    i              -ii      i                
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr2_241087410_    599 AGTACAAAGCTACAGTAATCAAAACAGTTTGATATTGGCATGAAGGCGGA 648
                          -----                i     v  i  i      i i iii  
  L1M4_orf2#LINE/    244 A-----AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr2_241087410_    649 CATGTGGACAAATGGAATAGAA----GAGTTCAGACACAAACCCACACAC 694
                            i i  iv            ----    i    v i       i   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr2_241087410_    695 CTGTGGTCAATT--TTTTGGGACAAGGATGCCAAGATTATTCAATGAGAC 742
                         i i         --    v -      i        ii        i i-
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGG- 386

  chr2_241087410_    743 AAAGAGTAGTCTCTTCAACAAGTGGTACAGGGACAA-------------- 778
                              i      i        i    i v       --------------
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr2_241087410_    779 --------ATGAAGCTAGACCC-TACCTCACACCATACACAACAGGGAAC 819
                         --------      i i     -              i    v ivv   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr2_241087410_    820 CCAAAATGGACCAAAACCCCCAGTG----AGC-AAAA-------ACTCTT 857
                         i         i  ? iv  iv i  ----   -    -------      
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr2_241087410_    858 AGAAGAAAATATTGGGG-AAATCT-CATGACATTGGATTTGGCAAGAGAT 905
                                  i  v  ? -      - i    v    i  v     vi v 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr2_241087410_    906 TCTTGGATATGAAACAAAAAACACAGGCAATAAAAGAAAAAAACAGAAGA 955
                             i       v  v    i    i    i           -i   vi 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAA 635

  chr2_241087410_    956 ATTGGACTTTATGAAAATTTGATAGTACCCTTTGTGTTTCAAAGGGTACT 1005
                                  i  v      vi ---- v i      i        ii   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAA----AACTTTTGTGCTTCAAAGGACACT 681

  chr2_241087410_   1006 ATCAAAACAGTGAAAAGACAAACCACAGAATGGTAGGATTTTTTTGCACA 1055
                              i v             v           v  i vv v      v 
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr2_241087410_   1056 TCATATATCTCATGAATGTCTAGTTTCCAGAAGAAAAAAAAAAAACTCTT 1105
                                   v  i iv v  v  v       v v v   i  --     
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA--CTCTT 779

  chr2_241087410_   1106 -CAACACAACAGCAAAAAGTCAG-T-------TTTAAAAATAG-CAAAGA 1145
                         -    v   i ii      v  i- -------  ?      i -     i
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_241087410_   1146 ATTTGAATAGACACCTTCCCAAAGATGATATGCAAATGACTAATAATCTC 1195
                                      ii ii       v     i      i i     v v 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_241087410_   1196 ATGAAAAGATGCTCAGTATCACTAGTCAT 1224
                                        ii    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (81 / 45)
Gap_init rate = 0.03 (24 / 759), avg. gap size = 3.12 (75 / 24)  


2640 24.83 1.23 0.68  chr2_241143135_241144867      509  1241 (492)    L1M4_orf2#LINE/L1      172   908 (0)  

  chr2_241143135_    509 ATAGCGAAGACAATCCTAACCAAAAAGAACAAAGCTGGAGGCATTACGCT 558
                              v  i      i i vv  i          i      vv i  i  
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr2_241143135_    559 ACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGT 608
                         v  ii i      viv        i          i   i    ii    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr2_241143135_    609 ACTGGTACCAAAACAGAGATATAGACCAATGGAACAGAACAGAGGCCTCA 658
                              i iv ii i   v       i        i    iv   ivii  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr2_241143135_    659 GAAATAATGCCATACATCTACAACCATCTGATCTTTGACAAACCTGACAA 708
                                vv        i  iiii  vi    i  i     ivv  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr2_241143135_    709 AAACAAGCAATGGGGGAAATGATTCCCTATTTAATAAATGGTGTTGGGAA 758
                         i v  vv        -   vi  vvi  v  i  i        i     v
  L1M4_orf2#LINE/    372 GACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr2_241143135_    759 AACTGGCTAGCCATATGCAGAAAACTGAAACTGGACCCCTTCTTTACACC 808
                               v  ?   i     i  i v    ii         v i i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr2_241143135_    809 TTATACAAAAATTAACTCAAGATGGATTAAAGACTTAAATGTAAGACCTA 858
                         v                   i      i ?    i           v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr2_241143135_    859 AAGCCATAAAAACGCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACAT 907
                           i i      vivi           v    ?i- v i -   iv   v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT 569

  chr2_241143135_    908 AGGCATAGGCAAAGACTTCATGACTAAAACACCAAAAGCAATGGCAACAA 957
                         v  vv       v ii   v iiv  vi            vvi       
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr2_241143135_    958 AAGCCAAAACTGACAAATGGGATCTAATTAAAAT--AGGGCTTCTGCACA 1005
                            vv    iv  i    v   ii v  i     -- iii   i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr2_241143135_   1006 GCAAAGGAAACTATCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAA 1055
                         v       v       vv i      v  i     i              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr2_241143135_   1056 AATTTTTGCAGTCTATCCATCTGACAAAGGGCTAATATCAAGAATCTACA 1105
                            v      ivii  vi      i  i  i  vi    v     v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr2_241143135_   1106 AAGAAGT---A-AACACATTTACAAGAAAAAAACAAACAACCCCCTCAAA 1151
                              v --- -   v  --- i  v     i     i     vv i?  
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCA---ATAATAAAAAGACAAATAACCCAATTWAA 816

  chr2_241143135_   1152 AAGTGGGCAAAGTATATGAACAGACACTTCTCAAAAGACGACATTTATGC 1201
                           i         v  v    i     i     v     v  i  vi vii
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr2_241143135_   1202 AGCCAACAA--ACATGAAAAAAAGCTCATCATCACTGGTCAT 1241
                         i     i  --         i v     v     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (102 / 76)
Gap_init rate = 0.01 (8 / 737), avg. gap size = 1.75 (14 / 8)  


3235 24.12 2.84 1.14  chr2_241146647_241151272.rev     3248  4126 (500)    L1M4_orf2#LINE/L1        1   894 (14)  

  chr2_241146647_   3248 TGGAAAGACATCCCATGTTCATGGGTTGGAAGAATTAATATTGTGAAAAT 3297
                                 i               i        v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_241146647_   3298 GGCCATACCACCAAAAGCAATATACAGAGTCAATACAATCCCTATCAAAA 3347
                            v    iv  v   vii  v      v    ii               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_241146647_   3348 TACCAA-TGCCATTCTTCACGAAAACAGAAAAAACAATCCTAAAATTCAT 3396
                          v   i-    -  i  ii ii   iv  v  ivii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_241146647_   3397 ATAGAACCA-AAAAAATCCCAAATAGCCAAAGCAGTCTGGAACAAAAAGA 3445
                           i   vii-  iii i  vi          i  i   v   v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_241146647_   3446 ACAAAGCTAGAGACATCACATTACCTGGATTCAAAATATACTACAAAGCT 3495
                               i i   ivv     i v  iiiv       iv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr2_241146647_   3496 ATAGTAACCAAAACAGCATG-TACTGATGTACAAATAGACACATAGACCA 3544
                          i     i   i    ii  -     iii  vii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr2_241146647_   3545 ATGAAACAGAATAAAGAACCCAGAAATAACACCAAATATTTACAGCCAAC 3594
                            i  i     vi   ii          vv   v i     ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr2_241146647_   3595 TGATCTCTGTCAAAGCTGATAAGAACATACACTGGGGAAAGGACACTTTC 3644
                             i ii v   i v  vi    v   v  v         i i v i i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr2_241146647_   3645 TTCAGTAAATGGTGCTGGGAAAATTGGATAGCCACATGCAGAAGAATGAA 3694
                             ii              v  i      ?         i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr2_241146647_   3695 AGTGGACCTTTATCTCTCACCATATATAAAAATAGACTCTACATGGACTA 3744
                         iv      ii  i   v         i      vi    v v     ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr2_241146647_   3745 AAGACTTAAACACAAGACTTGAGACTATAAAAATATTC----AAAATTTA 3790
                         ?    i    iii    vi i i         v v  v----    iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr2_241146647_   3791 GG-GCAAATTCTCCTGGACATTGATCTAGGCAAAGA------AGGTATGA 3833
                           - i    ii  v  -  v   ivi       v i------  i     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_241146647_   3834 CTAAGACTTCAAATACACAGGCAACAAAACCAAAAATAGACAAATGGGAT 3883
                          ----  --    vi    i         vv         i    v   i
  L1M4_orf2#LINE/    599 C----AC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr2_241146647_   3884 TTAAT-AAAACTAAAGAGTTTC-TGCATAATGAAAGAAATAATCAACATA 3931
                           v  -    i    i v   i-   v v --  i  v iv     v v 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAAA 690

  chr2_241146647_   3932 GTGAAGAGA--ACCTGGTGAATGG-AGAAAACATTTGCAAACTATTTACC 3978
                              i   --   iivv      -      i         ii  v  i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_241146647_   3979 TGACAGGAGACTAATATTCAGAATATACAGGGTACTCATACAATTCAACA 4028
                            i i i    vi   i         i ii v    v     i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_241146647_   4029 GGAAAAA-----ATAATCCTATT-AAACTTGGGTAAATGACATGAATTGA 4072
                         iv     -----    i  v   -   vv    i   v  iv     v  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr2_241146647_   4073 CATTTCTCAAAAGAAGACGTACAAACAGCCAGTGGGTGTATGAAAAAATG 4122
                                 v        ii      ii    i ii iii       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr2_241146647_   4123 CTCA 4126
                             
  L1M4_orf2#LINE/    891 CTCA 894

Transitions / transversions = 1.84 (136 / 74)
Gap_init rate = 0.02 (17 / 894), avg. gap size = 2.06 (35 / 17)  


3178 26.43 0.88 0.88  chr2_241203402_241209684     4884  5791 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_241203402_   4884 TGGAAGAACATTCCATGCTCATTGGGA--GGAAGAATCAATATCGTGAAA 4931
                              ii i  i     i    --   --      v i     i  v  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCAT--GGATTGGAAGACTTAATATTGTTAAG 48

  chr2_241203402_   4932 ATGGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAA 4981
                              v     v     iv i  i           i  v     i     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr2_241203402_   4982 GCTACCAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTT 5029
                         iv v   iivi i  i  ii  -      -- v  i  - iii    i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chr2_241203402_   5030 CATATGGAATCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAA 5079
                                  viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_241203402_   5080 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5129
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr2_241203402_   5130 GCTACAGTAACCAAAACAGCATGGGACTGGTACCAAAACAGAGATATAGA 5179
                                   i   i    ii   v     i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr2_241203402_   5180 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAA 5227
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr2_241203402_   5228 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5277
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr2_241203402_   5278 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5327
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr2_241203402_   5328 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5377
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr2_241203402_   5378 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5427
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr2_241203402_   5428 CC-TAGGCATTACCATTCAGGACATAGGCATGGGCAACGACTTCATGTCT 5476
                         v -    ?i v viv   iv   v v  vv i     i ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr2_241203402_   5477 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5526
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr2_241203402_   5527 AATTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTA 5575
                         v  i   -     i -   i  ii vv    i  v    i  vv i   i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr2_241203402_   5576 AACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGA 5625
                           v  i     i   i             v  ii   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr2_241203402_   5626 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAAACAAATTTACAAG 5675
                         i  i  i  vi          v  i  v      vv -   v iv i  v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAAT 792

  chr2_241203402_   5676 AAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACA 5725
                              i     i     v  i?    i    ii     iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr2_241203402_   5726 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGTT 5775
                         i     v        i  vi viii     v  i          i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr2_241203402_   5776 CACCATCACTGGCTAT 5791
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


 635 28.66 1.22 0.00  chr2_241318220_241320943.rev     1018  1181 (1543)    L1M4_orf2#LINE/L1        1   166 (742)  

  chr2_241318220_   1018 TGGAGAGATACTTCACGCTCATGGACAGGAAGCCTCAATATTATTAAGAT 1067
                             i     iii  i i       iv     v  i      i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_241318220_   1068 GTCACTTCTTCTCAACTTGATGTATAGATTCAGTACAACCCCAATCAAAA 1117
                          v  v v  i i   v     v  i       iii   i   v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_241318220_   1118 TCCCAGCAAGTAATTTTGTGGATATCAACAAATAAATTCTAAAGTTTCTG 1167
                                vivivv     ii  v  ii    iivi  i     i  iv i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_241318220_   1168 TGGAG--GCCAGGCAC 1181
                             i--  v   v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC 166

Transitions / transversions = 1.76 (30 / 17)
Gap_init rate = 0.01 (1 / 166), avg. gap size = 2.00 (2 / 1)  

2664 26.64 1.57 0.66  chr2_241318220_241320943.rev     1471  2232 (492)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr2_241318220_   1471 TAAAGTTTATGTGGAGAGGCAAAGGACTCAGAGTA-TTAATACAATACTG 1519
                             i  i  i    i v    i    i    i  -ii  v     vi  
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr2_241318220_   1520 AAGGAGAAGAACAAAGCCGGAGAACTTAC--TT---GACTTCAAGACTCA 1564
                           ii            ii    i   i  --  ---i i     i   i 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr2_241318220_   1565 CTATGAAGCTACAGTAATCAAGGCAGCGTGGTACTGGTGAACAAATAGAC 1614
                            ii                 i   i          iiv vii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr2_241318220_   1615 AAA-AGATGAATGGAACAGAAT--AGAGGCCCGTAATAGAAGCACATAAA 1661
                          v -    v       i     --    v  v v    i vv  i i vv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr2_241318220_   1662 TATAGTCAATGGATCTTTGACAAAGGAGCAAAGGAAATACAGTAACAAAA 1711
                            i      v   i  i     i  v  v   ivv  v  i iivi   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr2_241318220_   1712 AGATAATCCCTTCAACAAATGATACCGGAACAACTGGACATCCATGTGTA 1761
                         ii   i  ii           i i i  i         i ?   ii  i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr2_241318220_   1762 AAAAAAAAAGAATCTAGACAG--ACTTTACACTTTTCACAAAAATAAACT 1809
                            i  v--   vi i   vv--  i i    iv vi        v    
  L1M4_orf2#LINE/    440 AAAGAAT--GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr2_241318220_   1810 GAAAATGGATAACATCCTTAAATGTAAAACACAAAACTGTAGA-CCCTTA 1858
                         v         v ? vv i         i vvi      i  i - i    
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr2_241318220_   1859 GAAACTAACATAGGAGAAATTCTAGAGGATCTTGGGTTTGGTGATGACTT 1908
                            ivv        ? v  v   vviv  i        v  ii   ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_241318220_   1909 TTTAGACACAACACCAAAGACAATAGCCATGAAAGAAAGAAAAGGTAAGT 1958
                         i     i ii        ii  vv   v ii       i  v  i   i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_241318220_   1959 TAGACTTTGCTGAAATTAAATATTTCTGCTCTATAAGAGACATTGTCAAG 2008
                          i     iiiii        v i  i  iv  vi  ii    i i     
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr2_241318220_   2009 AGAATGGAAATGCAAGCCACAGACAAGGAATGACATGTCTTTGCAAATGA 2058
                          i i  i   vi   v       - v  i vi v  i --        v 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGA-ATGGGAGAAAATAT--TTGCAAATCA 734

  chr2_241318220_   2059 TGTATCTGATAAAGGACTCTCATCCAAAATATACAAAGAACTCCTAAAAC 2108
                          i          i     ivi     i      i         i  v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr2_241318220_   2109 TCGAAAATAAGAAAACAAACGACCCAATTAAAAGATGGGTCAAAGACCTT 2158
                           i v     i  i     ii        ?   i     iv  i  ii v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_241318220_   2159 AACAGATACCTCAGCAAAGAAGATAAGCAGACAGTAAATAAGCATACGAA 2208
                           i   i ii  vv           vi  i ii iv        i i   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr2_241318220_   2209 AAGATGCTCCACATCACATGTCAT 2232
                                  v      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (134 / 65)
Gap_init rate = 0.01 (10 / 769), avg. gap size = 1.70 (17 / 10)  


 745 27.14 3.81 0.95  chr2_241363843_241367241.rev     1058  1267 (2132)    L1M4_orf2#LINE/L1        1   216 (692)  

  chr2_241363843_   1058 TGGAGAGACATTCTGTGCTTACGGATTGGAAGATTCAGTGTTGTTAAGAT 1107
                             i   i  i ii  i i i           i i i i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_241363843_   1108 GTCAGTTTTTCCTAG-TTGGTGCTATAGATTCAATGCATTCCCAGTCAAA 1156
                          v  i vi i  i i-   i -   i        i   v    vi     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT-CTACAGATTCAACGCAATCCCTATCAAA 99

  chr2_241363843_   1157 ATCCCAGCAAGCTAAT---CAGATACTGACACACTGATTCTGAAGTTTAT 1203
                                 viv  vv ---    v i     vi     i  i  i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr2_241363843_   1204 ACGCAGAGGGGAAAGACATAGAATAGCCAACACA----TGAGAAACAAAA 1249
                          i v i v vi ii   vi           v   ----   i   v  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr2_241363843_   1250 ATCATGTTGTAAGGCCTC 1267
                          iv v    -i   v   
  L1M4_orf2#LINE/    200 ACAAAGTTG-GAGGACTC 216

Transitions / transversions = 2.00 (38 / 19)
Gap_init rate = 0.02 (5 / 216), avg. gap size = 2.00 (10 / 5)  

1535 26.97 4.92 4.63  chr2_241363843_241367241.rev     2225  2936 (463)    L1M4_orf2#LINE/L1      195   908 (0)  

  chr2_241363843_   2225 GAGGAACAAAGTTGGAGGACTCACATGACCTGACTTCCTGACTTACTGTA 2274
                           i                      ivv  ii i   vvi       ii 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr2_241363843_   2275 AGGCTTACA-TAGTCAGGATCATGCAGGATT--CACAAGACTGGTCCTAT 2321
                          i   -   -  i   i  ivi  ii v i --  i   iv i v v   
  L1M4_orf2#LINE/    245 AAGCT-ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr2_241363843_   2322 CGGTGCACCAAACAGAGTAATAGGGAGCCCAGAGG-AGACCCACAC--CA 2368
                         v i vv ivi  i   ---  v i   i     ii- i     i  --iv
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGA---ATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_241363843_   2369 ATGGCGCCAACTGGTC-----CAAAGGAGCAAAGGCAAGTGAGTGGAGAC 2413
                             i--   i  i i-----   i  v  v   i v v v i   i  v
  L1M4_orf2#LINE/    341 ATGGT--CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr2_241363843_   2414 GGGG-AGTCTTTCCAGCAGAAGGTGCTCCGACAAACGGATGCCCACATGC 2462
                         i ii-       i  i  i v      vv     vi    i?        
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_241363843_   2463 AGAAGGAGGCACACACAAAGCACCAGAAGGATGTGGTCACAGACCTCCCA 2512
                          i   i v --------   i------------   v v vv     v  
  L1M4_orf2#LINE/    439 AAAAGAATG--------AAGT------------TGGACCCCTACCTCACA 468

  chr2_241363843_   2513 CCTTCTACAGAGGTTCAGCCAAAAGGAATCCCAGACCTAAACGTAAAACG 2562
                           v v    i ii  v vi     v i   v?         i    i - 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-G 517

  chr2_241363843_   2563 C-AAAACTACAAAACCGTTAGAAGAAAACATTGGAAAAAATCTGGGTGAT 2611
                          -       i     iv              v  ?iv      vv    i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_241363843_   2612 CTTCGGTTAGGCTCTGAATTATTTAGATAAAACACCAAAAGCATGATCCA 2661
                            v        vv  iv  -i       vi            ii v v 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTT-CTTAGATATGACACCAAAAGCACAAGCAA 616

  chr2_241363843_   2662 TAAAAGAGAAAATCAGTAAGATGGACTGTATAAAATTTAAAATGGTTTGC 2711
                         i      i     vii   iv      vi  v   v      vvv    i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr2_241363843_   2712 TCTGCAAAGG----------GAATGT--AAGGA-AAGCCACAGACGTGGA 2748
                         v  v      ----------   v  --  i  -  v       -i   i
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA-ATGGG 715

  chr2_241363843_   2749 GGAAAATCTTTGCAAAATACACACCGGACAAAGGACTGGCATCCA-AATA 2797
                         i      v        vi i i i v  i  i     v i     -    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr2_241363843_   2798 TAGGAAGAATGCTTAAAATTCAGCAACAAGAAAACAAAGAGCTCAATTAA 2847
                           vi     iv    v  i   ii  i  i  i     v i i     ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr2_241363843_   2848 AAAGGAGGTAAAAAATCCAAACAAAC--CTCATCAAAGAAAACACACAGA 2895
                            ivi  i   ii  iii  i i  --i  vi       i i i   i 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr2_241363843_   2896 GAGC----AAGGAGGTAAAAA-AT-CCAAACAAACCTCATCAAAGAA 2936
                         vi  ----   v vi i    -  - iv    ----   ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACA----TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (113 / 75)
Gap_init rate = 0.03 (24 / 714), avg. gap size = 2.83 (68 / 24)  


2062 29.24 4.55 0.45  chr2_241539265_241543528.rev     2584  3243 (1021)    L1M4_orf2#LINE/L1       16   702 (206)  

  chr2_241539265_   2584 TGTTTGTGAAATGGAA---TTTATACT-TTA---TTTCCATTTTCCTTAA 2626
                             ii  i v     ---  v   i -   --- vv v  vi   ii  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr2_241539265_   2627 CTTGATATATAGATTTGGTGCAGTTCCTACCAAAATTTCAGCAAGCTATT 2676
                         v     v  i     iiii   i i    i      ii    viv  v  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr2_241539265_   2677 CTGAAGAAATAGACAACATGAATCTAAAACGTACACAGAAATTCAAAGGA 2726
                         i  v      v     vv   vi      ivi i ii     v   i   
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chr2_241539265_   2727 TGTAGAATA--CAAAA-AACCTTTAAAAGGGAGAAAAACATTGGAGGACT 2773
                         ivi      --     -  i   v    i i    v  vi          
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr2_241539265_   2774 TG---TTCTTAATTTCAAGAGTTATTGTAAAGCTACAATATTTGCAACAG 2820
                         ii---   ii        i v   i ii         i  v iivi    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr2_241539265_   2821 CATGGGATTGACACGAGGATG-----------CAATGAAACAGAA--GAG 2857
                         ii   v i  i  ii     i-----------     i  i    --   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr2_241539265_   2858 AGGCTGTAAATAGACCTATGAATGTGTAGTCAACTGATTTTTAACAAAGT 2907
                           v iiv     i   i  iv  v i i     i       ii    i v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr2_241539265_   2908 TGTCAAGTCAGTTCAATGGGGAAAGGAAAGTCTGTTTAACAAACGTTACT 2957
                           i    v vi              i v     v  i      i v i  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr2_241539265_   2958 GG---AACTGGGATATCAGTATGGATAAAAATGAACCTTGACCCCCTTTC 3004
                           ---      -   ? vii   v v  i      vi v      iviii
  L1M4_orf2#LINE/    416 GGGACAACTGG-ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr2_241539265_   3005 TACACTGTGCACAAAA-TTAATATGAGGTGTATCATAGACCTAAATACAA 3053
                         i    ii ii      -    ivii ii  v    ?          ii  
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr2_241539265_   3054 AAGCTGACACTGTAAAGTTTCTAGAAGAAAACACAGGAAGATACCGTCCA 3103
                         i    i v   i    ii ii            i   ?iv v i v  vv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr2_241539265_   3104 GACCTCAAAGTAGGCAAAGGTTTCTTAGACAAGATACAAACAGCCCAGAC 3153
                              iiiiv       v           i v  i  v  v   v  ii 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr2_241539265_   3154 CATAGAAAAAAACTCATTCATAAATACGACTTCACCAAAATTGAAAATAC 3203
                         v i i  i    v--  vv      vv       i       i    ivi
  L1M4_orf2#LINE/    615 AACAAAAGAAAAA--ATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr2_241539265_   3204 CTGCTCTTTGAAAGACACAATTAAGAAAATGAATAGGTAA 3243
                         i  iv   ii  i     v  i      i    v  ii  
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

Transitions / transversions = 1.88 (124 / 66)
Gap_init rate = 0.02 (12 / 687), avg. gap size = 2.75 (33 / 12)  

 674 18.84 10.63 2.42  chr2_241539265_241543528.rev     3566  3772 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr2_241539265_   3566 AAGAAAATGAACAGGTAAGCCACAGAGAGGGAGGAAATATTCATGCCA-- 3613
                               i    v  ii  v       iv     i       --   v --
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT--TGCAAAT 732

  chr2_241539265_   3614 CACGTATCTGATA--------GTATCTAGAATATATTTTAAAATGATCAC 3655
                           ii         --------     i         ---   iviv  vi
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATAT---AAAGAACTCTT 779

  chr2_241539265_   3656 ACA--TTGACAATAAGAAGATAAA-AATCCAAAT-----ATGAACAAAAT 3697
                            -- ii i     i    i   -  i    v -----   ii    iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr2_241539265_   3698 ATTTGAACTGACACTTTTC---AGAAGATCTACAAACGGCCGATA-GCTC 3743
                                iv    i  i  ---       v      i    i   -  v 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr2_241539265_   3744 ATGAGAAGTTGCTCAACATCAATAGGCAT 3772
                             i   v            ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (26 / 13)
Gap_init rate = 0.04 (9 / 224), avg. gap size = 3.00 (27 / 9)  


3565 17.74 4.05 0.56  chr2_241686962_241688669.rev      501  1216 (492)    L1M4_orf2#LINE/L1      168   908 (0)  

  chr2_241686962_    501 CAGAGTAGTCAAAACAATCTTGGAAAGGAAGTACAATATTGGAGGACTTA 550
                             i   i             i   i    v    vi          i 
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr2_241686962_    551 CACTTCCAGATTTCAAAACTTACTACAAATCTCCAGTAATCA-----GTG 595
                                vi                    v  v         -----   
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr2_241686962_    596 TGGTACTGGCATAAAGACAGATATACAGACTGATGGAATGAAAC--AGAA 643
                                       i  i   i   i   iii       ii  i--   i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr2_241686962_    644 CCCAGAAATAAGCCT-TCGATATATAATCAAACGATTTTC-ACAAGGGTG 691
                         i          i  i- vv  v   ii    vi       -         
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_241686962_    692 TCAAGAGCATTCAGTGAGGAAAGGACAGTCTTTTTAACAAATGGTGCCAG 741
                         i     v      i  i      i i        i            ii 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_241686962_    742 CAAAACTGGACATCCACATACAAAAGGATGAAGTTGGGCCCTTACCTAAC 791
                         v v       i ?      i      i          i   i     v  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr2_241686962_    792 ACCATATACAAAAATTAACTCAATATAGAGCCAAAACCTAAACATAAGAG 841
                                                v  i  v v? i       ii      
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr2_241686962_    842 CTAAGACTGTAAAACTCTTAGAAGAAACAATAGGGCAAAAGCTTCATGAC 891
                             i   i                  vv     ?vv   v    i    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr2_241686962_    892 GCTGGATTTGGAAATGATTTCTTGGATATTACACTAAAGGCACAGGCAAC 941
                         vi   i  v  v    i      i     v    i   i     i     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr2_241686962_    942 AAAAGAAAAAACAGACAAATCGGACTTCATGAAAATTAAAAATTTTCCTG 991
                                    i   i    i         v           i   iv  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr2_241686962_    992 CATCAAAATACACTATTAACAGAGTAAAAAGGCAGCCTGAAAACAAAATA 1041
                          v     iv       i  v i   i     i  i  i----   i   i
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC----ACAGAATG 713

  chr2_241686962_   1042 ACAGAAAATATTTGCAAATCATATATCTGATAAAGGATTAATATCCTGAA 1091
                         iv                               i   i vi     v   
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr2_241686962_   1092 TATAGAGAGAGCTCCTAAAACTCAACAACAAAAAACC------CTTGTTT 1135
                             v i   i   i  v       i  i     iv ------ iiiv  
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr2_241686962_   1136 CAAAAATGAG-AAAGGACTTGAACAGACATTTCTCCAAAGAA-------- 1176
                         ?       i -      i     i                  --------
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr2_241686962_   1177 -----CCAATGAGCACCTGGAAACATGTTCAACATCACTGCTATT 1216
                         -----     i     v  i   v   i         ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (84 / 39)
Gap_init rate = 0.01 (8 / 741), avg. gap size = 4.12 (33 / 8)  


3280 25.65 1.09 2.39  chr2_241703951_241705971      625  1544 (477)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_241703951_    625 TGGACAGACATACCATGTTCATGGATTAGAAGACTCAACGTAGTAAATAT 674
                             v   i  v               i       i  ii v  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_241703951_    675 GGCAGTGCTCTCTAAATTGATTTATAGATTTAACATGATTCCAACAGAGG 724
                             i i   i i        i  i     i   iii  i  v ivi ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_241703951_    725 TCTCAGCAGAATCTTTTGTAAATGTAGACAAACTGCTTCTAAAATTTATA 774
                           i    v vv i     i i vi v     i   v i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr2_241703951_    775 TGGCAAGAAAAAGAATTTAGAA-AACCAAAACAATTTTGAT---GAAGAA 820
                            v  viv  i i iii    - i          i    v---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr2_241703951_    821 TAAATTTTGAGGAATCACACTACTGAGTATTAAGATTTACTGTAAAGCCA 870
                         i   v  v     v       v iv i v i  i i     ii     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr2_241703951_    871 CAGTGATCAATTCAGTGTGATATTGGCAAAGGGACTGACACATGGATCAA 920
                             i     vv       i  i     v i   iv    i  i      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr2_241703951_    921 TGAAACAGGAGAGGAAATTCAGAATTAAGCCCAAACAAATATAGCCAATT 970
                           i  i  i vv ii i i     v   i    v   vv   i i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr2_241703951_    971 AATTTTTGAAAAAGAT-TTAA----ATCCAATGGAGAAATGATAATCTTT 1015
                         i     i  v  i i -ii  ----  i      i    vi   i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr2_241703951_   1016 TCAACAAATGGGGTTGAAACAATTAAATATCCTTATATGTATAAAAAAAA 1065
                                    v i  ii    i ii   ?  -- i   i -   i  vi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCC--ACATGCA-AAAGAATG 447

  chr2_241703951_   1066 AACCTCAACTTCAACCTCACACCTTATACAAAGATTAACTCAAAATGGAT 1115
                           vi vi  ii v          v        i                 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_241703951_   1116 CATAGACCTAAATGGAAAAACATAAACTATAAGATTTTTAGAAGAAAACA 1165
                           ?           v  i i vv         i i i             
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_241703951_   1166 TAGGCAAAAAAAAAAAAAATTTATGACCTGGTCTTAAGCAAAGTGTTCTT 1215
                             ?iv   vv-------  ii      v vv   i    v vv     
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-------TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr2_241703951_   1216 AGATAAGACAGCAAAAGCATGATTCATTAAAAAGAAAA-AGATAAATTAG 1264
                              v    v        ii viv iv   i i    -         i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr2_241703951_   1265 ACTTCATCAAAATTTAAAACTTTTGCTTTGTGAAAGACATGGTTAAAAGA 1314
                                       v          ivi vii  i    ivi i  i i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr2_241703951_   1315 ATAAAAAGACAAGCTACAGACCAGGAGAAAACGTTTGCAAAACTCATACC 1364
                         i i         v i     vii        ii        v vi   i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr2_241703951_   1365 CAACAAAGGACTTGTGATCAGAATACACCAAGAATTCTCAAATCTCAACT 1414
                         ii i  i        ivi       i iv     i   i v v     iv
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr2_241703951_   1415 GTGAGAAAACAAACAACCCAATTTTAAAAATGGACAAAAGACTTGAACGG 1464
                         i i i  i     i         ?-        i    i  i     ii 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAG 839

  chr2_241703951_   1465 ATACTTGGCCACAAAAGATACATATATGGAGGTGAATAAACGGATGGAAA 1514
                          i i  vv   v i      i i v    ---iv     i iv   i   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGG---CCAATAAGCACATGAAAA 886

  chr2_241703951_   1515 AATACTCTTGTCATTAATATCAGCCATTAG 1544
                         i  i   --------  i    ????????
  L1M4_orf2#LINE/    887 GATGCTC--------AACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (155 / 77)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.91 (32 / 11)  


 311 13.79 0.00 0.00  chr2_241734368_241736468.rev      309   366 (1735)  C L1M4_orf2#LINE/L1   (586)   322   265  

C chr2_241734368_    366 GTGTGGTAATGGGTTAAGGATAGGCATTTAGATCAGTGGAAAAGAACTGA 317
                                 v   vv         i   v       i     v    i   
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

C chr2_241734368_    316 GAGTCCAG 309
                                 
  L1M4_orf2#LINE/    315 GAGTCCAG 322

Transitions / transversions = 0.60 (3 / 5)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.00 (0 / 0)  

1203 31.09 11.40 2.40  chr2_241734368_241736468.rev      777  1609 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_241734368_    777 TGGAGAGACATCCCATGTCCATGGAT--ATAGACTTACTATCCTAAAGAT 824
                             i   i         i       --iv       v   iv v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_241734368_    825 GTCAATTTTCACAAAAATGGTCAATGGATTGAATGCACACCCAGTCATCA 874
                          v    vi  v v   v  i  v ii    v  i   vv   ---i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC---TATCA 97

  chr2_241734368_    875 TTATCTCAAAGGCCTTTTCCATAGAGTGTGACTAG---ATTTGAAGGTGT 921
                         vv   i  ivv       iiii   ivv    v  ---  iiv  ii vi
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr2_241734368_    922 ATATGTGGAAGAAAAAAGGCCAAGGGTAGCAATGATACTTCTGAAGATGA 971
                              - i  viv  ii i  v  ii    v vi i v ii    i v  
  L1M4_orf2#LINE/    148 ATATG-GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr2_241734368_    972 AGAGTAAAGG-AAAGGA-----ACTTTGCCAATCAGTTCCAGGACTTAC- 1014
                            ii    v-ii    -----    i-     ---- i  ii      -
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTC-CCAAT----TTCAAAACTTACT 241

  chr2_241734368_   1015 --AAAGTTAGAGTGAACA---CAGGGCAGTATTGGCA----------CAG 1049
                         --    i  v   i v  ---   v ii   i     ----------  v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr2_241734368_   1050 ATGTATCAA---------ATTGACGCCGCCAGAATTCTACTTTTATAT-- 1088
                           iv     ---------     - vvv      v vv  iiv  i  --
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACATTT 340

  chr2_241734368_   1089 GTGG------AATTTT-------GATACTGA-------CAGTGGGGGAAA 1118
                         i   ------i     ------- i i ii -------  i     i  i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chr2_241734368_   1119 AAGGGACTTTTTAGCATGAAGAGATGAAAAATCCAGTTTACCCATATGCA 1168
                           vi v     i i  vivi v v  ii v v ii v - ?   i     
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCA 439

  chr2_241734368_   1169 TAAAAAATGAAATTGTAGCCCAACTTCTCAC-ACACACACAGTCTAAC-- 1215
                         -   i      i   v v   v  i  v   - i i   v ivi    --
  L1M4_orf2#LINE/    440 -AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_241734368_   1216 -----AGATTAATGACCTACAGGTCAAAAGC-AAAACTTTACATCTTTGT 1259
                         -----i   i ?v      v v  -  i   -      v  v v  i vv
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTA 537

  chr2_241734368_   1260 GAAAAAAATATACATGAATAACTTTCTAACTTTGGTGTGGGGAAGGATAT 1309
                            i    i   vi? v v v   iv i  i    vv i  v  v i --
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-- 585

  chr2_241734368_   1310 TTTTTAAAGAAGGCTCCCAACTTGTTAACCACTAATGC-----TTGATAA 1354
                           i   i v v i v  v  vviiiv i v  v  v v----- v     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr2_241734368_   1355 ATTTGA-----------TTATGAACTTTTCTCTATTAGGAAGTACCACCA 1393
                            v  -----------   vi       v viv i iiiiii  i i  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr2_241734368_   1394 AGAACAGGGAAGGACAAGCCAGAGGCTGGAGGAAGATACCTGCAGAACAC 1443
                             viv i  i     v   v  iv   ii   i   ii    i v  i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr2_241734368_   1444 AGACCTGACAAAGGATCAGTATC-AAAACATATAA-GAATTTTGACAAAT 1491
                          v i    i  i   iiv     - i  i      -   i i v    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr2_241734368_   1492 GAATAA-AAAGAGTACAAATAACCCAACATAAA----GTCAAAAGGCGTG 1536
                         v     -   i  -             iv?   ---- v    i iiv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr2_241734368_   1537 ATCAGGCATTTCAC---AGAAGCAAACACCTTTGGTGGAT--GCCCATGA 1581
                          vi  i      v ---     - v i  vvv   ivi  --  v     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAGCACATGA 883

  chr2_241734368_   1582 GGAGAGGCGCAGTCACATCAGTGCCCAG 1609
                         ii   v  v  ---      ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCA---ACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (140 / 115)
Gap_init rate = 0.04 (35 / 908), avg. gap size = 3.29 (115 / 35)  


1733 25.14 11.61 3.83  chr2_241990131_241992336      984  1715 (491)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr2_241990131_    984 AAAAATTAACAAGCTGATTCGGAAGTTTAAATGTAAATGTAGAGGGCCTA 1033
                          i     i          i vi  i  i v   v     i ii  i  i 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_241990131_   1034 GAACAGACAAAAACAGTTTAGAAAAAGAG---CAGAGTTGGAGGATT-AC 1079
                            i  v     -  i i v        i---  i          i -  
  L1M4_orf2#LINE/    170 GAATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chr2_241990131_   1080 AGTCCCTGATTTCAAGACTTA--ACAG-----CAGTAATCAAGACAGTGT 1122
                          v i  ii       i     --   i-----                  
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr2_241990131_   1123 GGTA--------AGGGTAGATACACAGATCTACTAAACAGAGC-AACAGC 1163
                             --------   i    i i i     v ivi  i   ii-i v  i
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr2_241990131_   1164 CAAGAAGTAGACCCATCAATATAATAAGTTCAATTGTTTTTTTGGTTTCG 1213
                          v    i  i      -- i  v-  v v       v    i--------
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCAT--ACATT-TATGGTCAATTGATTTTC-------- 357

  chr2_241990131_   1214 TTTTTTGAGAAAAAAGCCAAGTTGATTCAGTGGGGGCAAGTTTAGTCTTT 1263
                         ------  v  iiiv      viv     i     i-   vv        
  L1M4_orf2#LINE/    358 ------GACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATAGTCTTT 400

  chr2_241990131_   1264 TTA-CA----GT-CTGTAACAACTAGATGATTATGTGTGAAAAAATGAAC 1307
                          i -  ----  -   vi      i   i?ii ii  ii   i      v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr2_241990131_   1308 TTCAACTCCTGCTTCACACTGTATATCA----CAACCTGAAATT-ATAGT 1352
                           vi  i   i i      ii    iv ----i   iii    v-  vi?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr2_241990131_   1353 AGATTTAAATGTAA-AGCTA----TA-AAAACT---ACAAGAAAA--TGG 1391
                            ii         -     ----  -      --- v       -- i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr2_241990131_   1392 GCAAAAAAATTTTTATGACTTTGTAGTAAGCA--GATTTCTTAA----GA 1435
                          ?iv   -- i  ii    i   viv  i   -- i       i----  
  L1M4_orf2#LINE/    551 GNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_241990131_   1436 CATGAAGAATAGAAATTATAAAAACAA-----------TTG---TGCATT 1471
                           iv  i ii v  iiv i    iv  -----------   --- v   i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_241990131_   1472 A---TTAAAAGTTTGCCTTCTTGAAAAGACATCAATAGGAAAATAAAACG 1518
                          ---      ii  viv v   v   i    ii vi i    i i   --
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA-- 696

  chr2_241990131_   1519 TGAGG-AACTCA----------GAAAGTATTCATAGTACCATAT--CTGA 1555
                         --  i-   i  ----------    i    iii i- i     --    
  L1M4_orf2#LINE/    697 --AGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGA 743

  chr2_241990131_   1556 CAAAGGATATGTGTCCAGAATATATAAAAATATTGCACAGATCAGTAA-- 1603
                         i  i   iv   i               i vv ivi   iv   i   --
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_241990131_   1604 ----GACGAATGACCCACTTACAAAGAGGGGGCAAAAGATCTGAATAGAC 1649
                         ----   i   i     v  ?--  i iv       i   i         
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGAC 841

  chr2_241990131_   1650 ATTTCACTAAGGAAGATAAACAAATAGCCAATAAACCCACATAAAGGTG- 1698
                              v i  i       v      i        i v  iiv    i  -
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr2_241990131_   1699 TCCACATCTTTGGTGGT 1715
                           v     v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (127 / 53)
Gap_init rate = 0.04 (35 / 789), avg. gap size = 3.23 (113 / 35)  


2451 18.57 5.72 13.55  chr2_242183301_242185148      501  1356 (492)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr2_242183301_    501 AGACATAGACAAGCTGATTCTAAAATGCATATGGAAAAGCAAAGACACTA 550
                            v  v           i       v          v    i ivv i 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr2_242183301_    551 TAATACTCTAAACAATTTTCAAACAGAAAAATAAAGTTAAA----TCGTA 596
                         v    vi v       i  v   v    i  i      ii ----  ii 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr2_242183301_    597 CTCCCCACTTTTAAGCCTTCCTATAAG----------------CAGTGTA 630
                           i    v   i  iv   v   i  i----------------      i
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr2_242183301_    631 GTTTGGGTAAAGGGATATATACACAGGTCATTTGAACA--AT--AGGATC 676
                           viv  i v i     v i i i  i   v v   i --  --  ii  
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr2_242183301_    677 CAGCAGTAGGCCACACACAT--ACAGCTAACTGATTTCTGACAAGG-TGC 723
                            v i  ii  -  i    -- ii ii  i      ii       -   
  L1M4_orf2#LINE/    320 CAGAAATAAACC-CATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr2_242183301_    724 AAAAACAAGTCAACAGAGAGAAGAATAGTCTTTTCAATGAAGGGCGCTGG 773
                         v  i  v v    ii i  -                 ii  v  i     
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGA-AAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr2_242183301_    774 AACAATTGGACATTCATATACCAAAAAAAGAGGT--AATCTCAACTTAAA 821
                         i    i    i ?i  i  i v   i  v  i  --i i i v  i ---
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT--- 464

  chr2_242183301_    822 CCACAAGCTTTATACAAAAATTGATATAAA-TGGGTCATAGGTCTAAATG 870
                         -    -- iv            i ivi   -   i   ?  ii       
  L1M4_orf2#LINE/    465 -CACA--CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr2_242183301_    871 TAAAAAATATAACATTATAAAATTTTTAGGTGAAAATATCTAAAATCCTT 920
                            i ---------------------------------------------
  L1M4_orf2#LINE/    512 TAAGA--------------------------------------------- 516

  chr2_242183301_    921 GTGACCTGGGAAAAGAGTTCTTAGATATAATACCAAAGCACAATCCATAG 970
                         --------------------------------------------------
  L1M4_orf2#LINE/    517 -------------------------------------------------- 516

  chr2_242183301_    971 AACCAAAACCATGCTAAAGCTATAAAACTCCCAGAAGAAAACATCAGAAA 1020
                         ------------      i           ii            -  i?i
  L1M4_orf2#LINE/    517 ------------GCTAAAACTATAAAACTCTTAGAAGAAAACAT-AGGNG 553

  chr2_242183301_   1021 AAAATCTTTGTGATCTTGGATTTGGTGATGGTTTCTGAAATGTGACACCA 1070
                         v       i    i     i  v  ii         v i  i        
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr2_242183301_   1071 AAAGGACAAGCAGCAAAAGAAAAA-T---TAAATTGAACTGCATCAAAAT 1116
                             v       i           - ---       i   v         
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr2_242183301_   1117 TAAAA-CTTGTGTACATCAAAGGACACTCTCAAGAGAGTGAAAAGAGAAT 1165
                              -   v   i v            v      i          v  i
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr2_242183301_   1166 CCG-----TGGAAGAAAATGCTTGCAAATTATATATCTGATAAGAGTTTA 1210
                           i-----   i       ii        i              i vi v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr2_242183301_   1211 ATATCCAGAATATATAAGGAACTCCTACAACTCAGCAACAT-----CAAA 1255
                         i                i      i         ii  i v-----    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr2_242183301_   1256 CAACTCAATTGAAGAATAGACAA----CTTTAATAGACATTTTCCCAAAG 1301
                         i   i     ?  i   i i   ----i  v           ii      
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr2_242183301_   1302 AAAACATACAAATGGCCAAGAAGCACACAAAAAGATGCCCGCCATCACTA 1351
                           i i              v       ii         i iv     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr2_242183301_   1352 ATCAT 1356
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.44 (110 / 45)
Gap_init rate = 0.03 (20 / 789), avg. gap size = 8.25 (165 / 20)  


1705 25.69 9.11 2.28  chr2_242246971_242249403      752  1366 (1067)    L1M4_orf2#LINE/L1       13   669 (239)  

  chr2_242246971_    752 CCATGG-CACTGGATTGGAGGACTCAGT-TTGCCTAAGATGGCACTTCTT 799
                              v-  -         i    i i -   i-          v v  i
  L1M4_orf2#LINE/     13 CCATGTTCA-TGGATTGGAAGACTTAATATTGT-TAAGATGGCAATACTC 60

  chr2_242246971_    800 CCCAAATTAATTTAGAAATTCAA-GTAGTTCCAATGAAAAT----G---- 840
                                 i  i  v i      - i i i  v  v     ---- ----
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr2_242246971_    841 ----TTTCTAGAAACTGACAAGCTGATTCTGAAATTCATAAGGAAATGCA 886
                         ----   vi     i            i  i         v         
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr2_242246971_    887 AAGGGTCCTAGGATAGCCAAAACAATTTTGGAAAAAAGAAAAAGAAGAAA 936
                          -   v  i  i              i   --        i  v  ----
  L1M4_orf2#LINE/    161 A-GGGACCCAGAATAGCCAAAACAATCTTG--AAAAAGAAGAACAA---- 203

  chr2_242246971_    937 AGTTGGGTAACTTCTATCACCTGATT-CAA-------TATAAAGCTACAA 978
                               ivi   ivi iiv  ii   -   -------  i         i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr2_242246971_    979 TGATCAAGACAGCATGGTAACAGTATAAAGACCGAAACAGAGAAGAGTGG 1028
                          i          ii     vii i    i  iv  v i v   vv i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr2_242246971_   1029 GACAGAAGAGAGAGTCCTGGGGAAGAACCACACACACAAAGTGAGTTGAT 1078
                         i i    vv        v iiiv i v   i   ivi vi  v i     
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr2_242246971_   1079 TTTCGACAAAAGCACTGCATAC--TTTAATAAATTAAGGGTTCTCTTTTC 1126
                                  ii ii ii- v  --  i   iiivv   ii vv       
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr2_242246971_   1127 AACAAATGGTGCTGGAA--ACGAGGTATCTGTATGAGGAAAAATGGAAAA 1174
                                        i --  vi i  ? iii   vii  i    ---  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG---AA 449

  chr2_242246971_   1175 AACGTGACTACTACCTCATACCATCTAGAAATAGCAATTCCAAATAG--C 1222
                         ivi -   iv        i     v  v   v vi  i  v    i -- 
  L1M4_orf2#LINE/    450 GTTG-GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr2_242246971_   1223 ATATATCT------------TAAAACTATAAAACTTCTTGAAGAAAATGC 1260
                          ? v i  ------------               ii v        iii
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr2_242246971_   1261 AGGTGAAAATCTTTGCTGCCT-GGGCTAGGTGAAAAATTTTAAGACAGGA 1309
                            ? v       i ivi   -   i    ii viiv  i v   i v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr2_242246971_   1310 CACAAAAAGCAC---TGACTAGAGAAAAAA------AAT-GG----TAAC 1345
                            v        ---ii  v i        ------   -  ----i v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr2_242246971_   1346 AGAATTAAAACATTTGGTTCT 1366
                          i        vv   v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCT 669

Transitions / transversions = 1.77 (99 / 56)
Gap_init rate = 0.04 (24 / 657), avg. gap size = 2.92 (70 / 24)  

 674 26.35 3.97 5.95  chr2_242246971_242249403     1590  1942 (491)    L1M4_orf2#LINE/L1      563   908 (0)  

  chr2_242246971_   1590 GTGAGCTGAGATCAGGCCATTGCATTCCAGCCTGGGCAACGAGAGCA--A 1637
                             v  vi i i    v  v iv iii  vivv i  v i i    -- 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr2_242246971_   1638 ACAATGTCTCAAAAAAAAAAA-AGAAAAAGAAAAGAAACCCCCCACCCCC 1686
                         i   -----     i      -   v   vvii ------------ ii 
  L1M4_orf2#LINE/    613 GCAA-----CAAAAGAAAAAATAGATAAATTGGA------------CTTC 645

  chr2_242246971_   1687 ACCAAAAAAAACAACATTTGGTTCTTCAAATGGTACTGTCTAGGAAACAG 1736
                          i     vv  v   -   v  v       v ii   i  v  i  iiii
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr2_242246971_   1737 AAAGGCAAGGCACAGGATAGGAATATCGTGTTGGCAAGT---ACACCTGA 1783
                             i   vv     i  i   iv -vi i  v    i --- i i    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCATATATCTGA 743

  chr2_242246971_   1784 TAAAGGACTTATACCCAGAACAAACAACAGGCTCTTACAACTCAGGAATA 1833
                            i      i  i      i v i  viii             iv    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr2_242246971_   1834 ACA---CAAA-----CACTTAAACAAATGGGCAAAAAATCTGAATGTTCA 1875
                          v ---    -----  v  ?  -           ii  i     ivv  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACA 842

  chr2_242246971_   1876 TTTCACAAAACAAGAAATACAAGTGGCAAATAAGTACAACAAAAAGATGA 1925
                             v v   v    v      i    v      i   -ii        v
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA-TGAAAAGATGC 891

  chr2_242246971_   1926 GCAGCATCGTTACTCAG 1942
                         v  i    i????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (54 / 38)
Gap_init rate = 0.03 (11 / 346), avg. gap size = 3.18 (35 / 11)  


 867 30.41 8.60 2.87  chr2_242250393_242252007      501  1128 (487)    L1M4_orf2#LINE/L1      245   908 (0)  

  chr2_242250393_    501 AAGCCATGATAATGAAGACAGTGTGGTATTGGCACAGGGACTGACAAACA 550
                             i iii    v              i     i i   iv    v i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr2_242250393_    551 GACCACCTGGAACCAGAGAGAGGGTG-AGAAGCAGACCC---C-----TG 591
                           i  v-     ivii vv   i  v-    ii i    --- -----  
  L1M4_orf2#LINE/    295 GATCAA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr2_242250393_    592 ATGAAG-GAT-----ACTGAGGGGCTCAGGGGGCAGTTGCATGGGTGAAC 635
                         i v  v-   -----  vii  v  iv  i--- vi  vv     -   -
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGA---CCATTCAATGGG-GAA- 388

  chr2_242250393_    636 AGGGGGGCCGGGCTCTTCATGCAG--GGTGCAGGG-TAGCTGG---CCCT 679
                           iivi i ---- i    -i  i--     v   -i i    ---?  v
  L1M4_orf2#LINE/    389 AGAATAGTC----TTTTCA-ACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr2_242250393_    680 CATCTGAGAACAAGGAGAGGGGACAGC-ACTTCACACTATACACACAACT 728
                            vii -  v  v  iivv    vv -  i      i   i   v  v 
  L1M4_orf2#LINE/    434 CATGCAA-AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr2_242250393_    729 CAGCCCCAGGTGGATTAATGACCTAAAGGAAAGATTTTAGGTTGAACTGT 778
                         i i i v ii     i ?v        v v    vi v -----    i 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA-----AACTAT 527

  chr2_242250393_    779 GAAGCTTCCAGAAAAATTCA---GAATACATATTT-TGACCTGTTAGTGA 824
                         i  i  iii    i  vv  --- ?i  v  v  i-      - vi  v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT-TGGGTTA 576

  chr2_242250393_    825 GGAAA-GACTGCTTAACTAAGACATTAAAAACAGAATCCATAAAGGAAGA 873
                           v  - ii v    iv  v    ii    i  v  v v i   i   i 
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr2_242250393_    874 GATTGGCAAACTGAACCACAT-AAAATCCAGAACCTCTGTTCTTCAAAA- 921
                         i  v ii   i  i  iv   -     iv i   i i   v       i-
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr2_242250393_    922 ACAAT-TTGTAAAACTCAAAAGATAATC-ACAGACCGAAA-AAGCTATTT 968
                            v - iivi   v v      i  i -     vi ii -  iv     
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr2_242250393_    969 GCAACACATTTAGCTAACAGAG--CTT-TATTCAAATCATATAAAGAACT 1015
                             vv   v  v  i i ii --   -   i  i vi            
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr2_242250393_   1016 CTGACATGTCAGCCA-GAAAAGGCA-------CAGT--GGAAATGGTCAC 1055
                           v   vv   iiv -i     i  -------  i --ii      v  v
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr2_242250393_   1056 CAGACCTGAACAGGCACCTCGCTGGAG--GATG-AC------CCAGCAAC 1096
                         vi  ii    i  i  ii  v iii  --   i-  ------   ii  v
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr2_242250393_   1097 GACGTGAAAAGATGCTCAAGCTCGCAGGTCAC 1128
                         v  i               vv  i????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (114 / 74)
Gap_init rate = 0.05 (34 / 664), avg. gap size = 2.12 (72 / 34)  


3844 18.19 3.16 4.25  chr2_242705113_242709564     3043  3960 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr2_242705113_   3043 TAGAATGATATTTTATGCTTATGGATTGGAAAACTTAACACTGTTAAGGT 3092
                          i   v     iii   i i           i      i i       i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr2_242705113_   3093 ------------CAAATTGATCTGCAGATTCAACAAAATCCCTTTCAAAA 3130
                         ------------           i          iv       v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr2_242705113_   3131 ATTTCAACTCAGCTGCTTTACTTCTAGAAATTGACTAGTTAATCCTAAAA 3180
                         -- i ----       i  vi  vi          v  i i         
  L1M4_orf2#LINE/    101 --TCC----CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr2_242705113_   3181 TTCATATGGAAATATAAGGAGCTACAAACACCAAAAACAATCTTAAAGAA 3230
                                      ii    ii ivvi  i v v           i  i  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr2_242705113_   3231 AATTTTAAACAAAGTTGTTGGATTCGTGCTTCATGATTTCAAAGTGGCAC 3280
                         i v---i          vv   i  iii    vii        iiv-i  
  L1M4_orf2#LINE/    195 GAA---GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TAC 240

  chr2_242705113_   3281 AGCCAAGCTACAGTAGTAAAAACAGTATGACAGAGGCATAAAGATAGATA 3330
                         vi v           i v  i     i  ii vv       i      i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr2_242705113_   3331 CATACATCAATGAAATTGAACTGAAAGTCTAGAAATAAGCCCTTATATTT 3380
                         i   v       i   v   i   i    i        i   v  i    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr2_242705113_   3381 ATGGCCAATTGATTTTTGACAAGTGTGCCAATGGA--ATTCAAGGAGGAA 3428
                             i           i      v       --  --      v i    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAA--GACCATTCAATGGGGAA 388

  chr2_242705113_   3429 AGAATGGTCTTTACAACAAATGGTACTAGGACAACTGGATATCCACCTGC 3478
                              i      v           i  i             ?    v   
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr2_242705113_   3479 AAAAGAATGTAATTTGATTTCTACTTCACACCATATACAATT-TTAATTC 3527
                                  v i  v  iii    i               vv-    i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr2_242705113_   3528 AAAATGAATCATAGGTCTAAAAGTAAG-GTTAAAACTATAAAACTTTTAG 3576
                               i    ?  ii     v     - i               i    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr2_242705113_   3577 CAGAAAACATAGGAGTACATTCTGTGTGACCTTGGATTTGGCGATGATTT 3626
                         v            ?   v  -  vi          i  v   i   i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr2_242705113_   3627 ATTAGAACTGACACCAAAAGCACAAGCAACAAAAGACACATCAGATAATT 3676
                         v     vv                            v v vi      v 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr2_242705113_   3677 TGGACTTTATCACAATTTTGTAAATATTCAAAATAAATTTAAAGATTATC 3726
                                i    v    ------------    --- i  -----  i -
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATT------------AAAA---ACTT-----TTGT- 666

  chr2_242705113_   3727 TTGCAGTTTCAAAAGACACCCTCAAGTATGTGTAAAGACAACACACAGAA 3776
                         ----- i      i     iv     v v   v         v       
  L1M4_orf2#LINE/    667 -----GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr2_242705113_   3777 TGGGAGAAAATATTTGCAAATCACAAATCTGATAAAGCACTGTTATACA- 3825
                                                i v         i v   vv   v  -
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr2_242705113_   3826 AATATATAAAGAATGCTAATAAC-CAGTGATAAAAAGAAATACAAGCAAA 3874
                                      iv  v i   -  i i         v v i  v v  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr2_242705113_   3875 TT---AAATGAACAAAA------ACTAGATAGTTCTCCTAAAAAGATATA 3915
                           ---     ii    i------ v    i v      v  i        
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr2_242705113_   3916 CAGATGACCCATAAGCCTTTGAAAA--TGCTCAAAATTATTAATTAG 3960
                           i   i  v      viv      --       v  i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (97 / 67)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.58 (68 / 19)  


 299 23.35 18.56 0.60  chr2_242760005_242761617        5   171 (1442)    L1M4_orf2#LINE/L1      507   703 (205)  

  chr2_242760005_      5 AACTGTAAAAGGCTAAAACTGTAAAGTTTTAAGAAGAAAATA-------A 47
                           v     i  -        i    ii i v         i ------- 
  L1M4_orf2#LINE/    507 AAATGTAAGAG-CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr2_242760005_     48 TATTTTCACAATGTAAAGT-AGGCA--GATTGCTTA----CCACACAAAA 90
                         v  i   iii iv vii  -     -- i  v    ----iv    v   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr2_242760005_     91 ACCACAAGCTGTGAAAGAAAAAA-AGATAAA-----CTTTAT----ATTA 130
                          v       viii          -       -----   i  ----    
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr2_242760005_    131 AAAACTT--ATACCT--AAAGTCATCATTA-GAAAG-GCAGAG-CAAC 171
                                --i i i --  i v  ii  i -     - v i  -    
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

Transitions / transversions = 2.25 (27 / 12)
Gap_init rate = 0.07 (13 / 197), avg. gap size = 2.46 (32 / 13)  

1646 22.91 9.64 6.00  chr2_242760005_242761617      481  1113 (500)    L1M4_orf2#LINE/L1      231   886 (22)  

  chr2_242760005_    481 CAAGATTTACTATAAAATGTAAAATCACCACAATCAAGAGAGTGGTATGT 530
                            i i      i   ii-  v i ------        v    ----- 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGC-TACAGT------AATCAAGACAGTG-----T 268

  chr2_242760005_    531 GGTATTGGTGAAAAGATAGATACACAGGTCAGTGGAACAGAACAGAGGAC 580
                             i   iiv  i      i i i  i   i     i    iv   - v
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG-AG 317

  chr2_242760005_    581 CCCAGA--TAAGTCCATACAGATATGGTTGGTTTATTTTTGACAGTGGTG 628
                         i     --   ii       vv      iii  v     i    iv    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chr2_242760005_    629 TAAAGGCACCTCTTAATATATTCCATGGAGAAAGTGTAATCTTGTCAACA 678
                         iv   --   ---------    v    i     vi  i    v      
  L1M4_orf2#LINE/    368 CCAAG--ACC---------ATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr2_242760005_    679 AATGG-ACTAGAA-AACTAGATGTGTATATGCAAAAATAAATAAATAAAT 726
                              -i  i i -    i   i?vi i        i--   i  --iv 
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG--AATGAA--GTT 452

  chr2_242760005_    727 AAATAACCTGTACAGCTCACATTTTATACAAAAATGAACTCAAAATGGAT 776
                         ii ---  iv   --      iiv           v              
  L1M4_orf2#LINE/    453 GGA---CCCCTAC--CTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr2_242760005_    777 CATATACCTAAATGTAGAATGTAAAACTGTAGAACTTATGGAAGAAACC- 825
                           ? v           ii vv       i  i    iv i       v -
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr2_242760005_    826 CAAAGGAAAGTCTGCATGATCTTGGG-----CA--GAGTTTTTAGATATG 868
                         i ii? v  i   v i   i      -----  -- iv  i         
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr2_242760005_    869 ATACCAAAAGCACAATCCATAAAAGAAAAAAATCTATAATTTGCATTTTA 918
                          i             v v i           - vv    v   v i  i 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCA 646

  chr2_242760005_    919 TCAAAATTTTAAAATTCT--------------ACTCTCA----------- 943
                                 vv   v  i --------------   v   -----------
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr2_242760005_    944 ------------------GAGAACACATTTGTAAGTCACATATCTGACAA 975
                         ------------------     v i     i  i   i        i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr2_242760005_    976 AGGGTTAGTATCCAGAATA-ATAAAGAACACTTAAAACTCAACAATAAGA 1024
                         i  ii v            -         v    v       i     i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr2_242760005_   1025 AAACAG----CCCAGTAAAAAATTGGGGAATAGTTTTGG-TGAACCTGTA 1069
                          i   i----    i v?    v    v  vi v    i- ii  ---- 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC----A 842

  chr2_242760005_   1070 CTTCACCAAACAACTTGCATGGATTGCAGAGAAGCCCATGCAAA 1113
                         i   v     v  vv ii iii  v  vi v    v    v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.61 (87 / 54)
Gap_init rate = 0.04 (23 / 656), avg. gap size = 4.30 (99 / 23)  


3309 25.93 0.55 0.77  chrX_1866740_1873006.rev     4867  5776 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_1866740_18   4867 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4916
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_1866740_18   4917 GGCCATACTGCCCAAAGGTAATTTACAGATTCAGTGCCATCCCCATCAAG 4966
                            v     v      v- i  i          ii  v     i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_1866740_18   4967 CTACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 5013
                         v v   i-       i  -i     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_1866740_18   5014 CATATGGAACCAAAAAAGAGCCCGCATAGCCAAGTCAATCCTAAGCCAAA 5063
                                  viiv  ii  v  v v        iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_1866740_18   5064 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5113
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_1866740_18   5114 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5163
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_1866740_18   5164 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAA 5211
                                  i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_1866740_18   5212 CTATCTGATCTTTGACAAACCTAAGAAAAACAAGCAATGGGGAAAGGATT 5261
                         ii vi    i  i     ivv ivv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_1866740_18   5262 CCCTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAG 5311
                         vi  v  i  i              v  i   v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_1866740_18   5312 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5361
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_1866740_18   5362 GATTAAAGACTTAAACGTTAGACCTGAAACCATAAAAATCCTAGAAGAAA 5411
                            i ?    i    i  v   v  i    i      v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_1866740_18   5412 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5461
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_1866740_18   5462 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5511
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_1866740_18   5512 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5561
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_1866740_18   5562 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAG 5611
                          v  i     i   i             v  i    vii ivi      v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_1866740_18   5612 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5661
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_1866740_18   5662 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5711
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_1866740_18   5712 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATAAAAAAAATGCTC 5761
                             v        i  vi viii     v ii     i    i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chrX_1866740_18   5762 ATCATCACTGGCCAT 5776
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3189 26.49 0.88 0.66  chrX_2970229_2976616     4990  5895 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_2970229_29   4990 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5039
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_2970229_29   5040 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCTCCATCAAGC 5089
                            v     v     iv i  i  i        i iv   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_2970229_29   5090 TACCAATGACTTTCTTCACAGAATTGGGAAAAACGACTTTAAAGTTCATA 5139
                          v   iivi i  i  ii     v v iv  ivi  iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_2970229_29   5140 TGGAACCAAAAAAGAGCCCAGATT-GCCAGGTCAATCCTAAGCAAAAAGA 5188
                              viiv  ii  -      v -    iiv     i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_2970229_29   5189 ACAAAGCCGGAGGCAC-CATGCTACCTGACTTCAAACTATACTACAAGGC 5237
                               ii     -  -  ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_2970229_29   5238 TACAGTAACCAAAACAGCATGGTACT--CATACCAAAACAGAGATATAGA 5285
                                 i   i    ii       --    -- ii i   v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATATAGA 296

  chrX_2970229_29   5286 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCATACATCTACCACC 5335
                         i        i    iv   ivii         vv        i  ivii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_2970229_29   5336 ATCTGATCTTTGACAAACCTGACAAAAACCAG-AAATGGGGAAAAGATTC 5384
                          vi    i  i     ivv  v   i -   v-v          ii  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAG 395

  chrX_2970229_29   5385 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGT 5434
                         i  v  i  i              v      v  ?i  i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_2970229_29   5435 TGAAACTGGATCCCTTCCTTACACTTTATACAAAA-TTAATTCAAGATGG 5483
                             ii    i    v   i    iv         -    i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_2970229_29   5484 ATTAAAGACTTACATGTTAGACCTAAA-CCATAAAAACCCTAGAAGAAAA 5532
                           i ?    i  v    v   v     - i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_2970229_29   5533 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 5581
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_2970229_29   5582 AAAACAACAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 5631
                          vi   v        vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_2970229_29   5632 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5681
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_2970229_29   5682 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTGTACCCATCTGAC 5731
                          v  i     i                 v      ivvi ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_2970229_29   5732 AAAGGGCTAATATCCAAAATCTACAAAGAACATAAACAAATTTACAAGAA 5781
                           i  i  vi      i   v  i       vivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_2970229_29   5782 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5831
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_2970229_29   5832 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5881
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_2970229_29   5882 CCATCACTGGCCAT 5895
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (145 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.17 (14 / 12)  


1659 28.24 7.35 3.44  chrX_4082498_4084673.rev      815  1685 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_4082498_40    815 AAAGAAATTTACCCTGCTCATGGGTTGGAAAACTTAATATTGTGAAATTG 864
                              v  i--  v  i      i      i            v  iv  
  L1M4_orf2#LINE/      4 AAAGATATC--CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_4082498_40    865 CTAGTTATCCCTAAATTGATCTATAAATTCCAAACAAATCAAATGAAACA 914
                         vi i vv    i           i i    v vi   vi vv  v   vv
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_4082498_40    915 CCCAGA-G----TTTTGCAGATATTGGCAAGCTGAGACTACAATTTA-AT 958
                              v- ----         v    i        vv   v    i -  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_4082498_40    959 GTAAGTGTAAAGGATCTAGAGTTGCCAAAAAGAAACCTTGAAAATAAAGG 1008
                          v  i  i  i   i i   i v       v--  i        vi   i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAAC--AATCTTGAAAAAGAAGA 199

  chrX_4082498_40   1009 AAAAAATT-----------ATTTGACCTGATTTTAAA-TGTGTTATGAAA 1046
                          v   i  ----------- i  --  ii    i   -iv ii  ii  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTT--CCCAATTTCAAAACTTACTACAAAG 247

  chrX_4082498_40   1047 CTACGGTAATGAAGACAATGTGTTACTGGTATAAGGATAGACAGA--GAC 1094
                             i     v      i    v      i             v --  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_4082498_40   1095 TGATAGAATAGAGTCGGTAGTTCAGAAATAGACCCACTCATACTCA---- 1140
                         ii  i       i i iv   i        i     iv   -- i ----
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT--TTATGGT 345

  chrX_4082498_40   1141 CAAACAATTTT-GACAATTGCATCAC-ACAAATCAATGGGGAAAGATAAG 1188
                            vii     -     vv iii  v-  v v              -- v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA--AT 393

  chrX_4082498_40   1189 AGGTTTT------AATGA--CTGGGAC---TGGAT--TCACTAGTAAAGG 1225
                           vi   ------    i--       ---     --i   vv i   i 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_4082498_40   1226 AAATGTACGTCTTCATCTATATTTCACACTGTCCCCTAAAATAAACTGAG 1275
                           -  - v  - vv i iv  ii      ii viv v     v    v i
  L1M4_orf2#LINE/    444 AA-TG-AAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_4082498_40   1276 AATGATTTGTAGACTGAAATATAAAAGACTAAAATGATAATAAAAAGTAA 1325
                             iv ii?    iv    i   i  -      i------------  -
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAG-CTAAAAC------------TA- 526

  chrX_4082498_40   1326 ATAAAACT---AGAAGATGACATGGGAGAATGTCTTTGCAACTTGGGAAC 1372
                         -       ---      vi    i  ? v vi    i ii  i v  ivi
  L1M4_orf2#LINE/    527 -TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_4082498_40   1373 AGACAAAGATTTTCTGAGCAGAATACTAATCTTATAA-TAATAA------ 1415
                           i   v i   ii iiii vi i  i  vvvi i  -i  i  ------
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_4082498_40   1416 ---TA--TAAACTGGAGA-CATCAAAGTTTAAAACTTTT---CATCCAAA 1456
                         ---  --    i    vv-       i  v         --- v  v  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_4082498_40   1457 GAAAC-ATTAAATAAATAAAAAGGGAAGGCATAAAGTGAGCAAATGTATT 1505
                           v  -  i  iv  i i     iv  vv  i i i  i vi  vi    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_4082498_40   1506 TGTAATATAA-ATGCCTGGCAATGAACTCATAGTCATATTTTACACAAAC 1554
                           i  -  v -  ii   ii  v i   ii  vi  v v v  i v i v
  L1M4_orf2#LINE/    726 TGCAA-ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_4082498_40   1555 TTAATATATATCAATAATAAAGGCATAAACAATTCAA---AAAAA-GAAC 1600
                         i vv  i vv           iiv i   i  ii   ---     - ii 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_4082498_40   1601 AAAAGTTTTAAATAGACACATATAGGAACAAAGATAAAGGACTGTACAAC 1650
                            i v   i        iv v vvi  -i      v vi v  vv   i
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAA-GAAGATATACAAATGGCCAAT 873

  chrX_4082498_40   1651 ACACTCATAAAATGATTCTCATTATCATTACTTAT 1685
                          vi v   i   v   v    vi    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.04 (36 / 905), avg. gap size = 2.61 (94 / 36)  


3095 24.50 1.56 2.78  chrX_4617629_4619518.rev      502  1399 (491)    L1M4_orf2#LINE/L1       22   908 (0)  

  chrX_4617629_46    502 TGGATTGGAAGAATTAATATTGTTAAGCTGCCCATACTTCCTAAAGAGAT 551
                                     v              v  v v     i  i   vv   
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGAT 71

  chrX_4617629_46    552 AGACAGATTCAATACAATCCCTATCAAAATTCCAATGGTATTTTTCACTG 601
                         vv          ii                i   iiv iv     ii v 
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAG 121

  chrX_4617629_46    602 AAATAGGAAAACAAGTTCTAAAATTTGTATGGAATCACAAAAGGTCCCGA 651
                             v iv  i vii i        ii       vii   ii ii  v  
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chrX_4617629_46    652 ATAGCCATAGCAACCTTAAGCAAGAAAAAGAAAGCTGGAAGCATCAAACT 701
                                v i   i   i iv     i  v    i    i vv   v   
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_4617629_46    702 TTATGATTTCAAATTATAACTACAAAGCTACAGTAAAATCAAAACAGTAT 751
                          ivii        viv  -                 --    i     i 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTA-CTACAAAGCTACAGTAA--TCAAGACAGTGT 268

  chrX_4617629_46    752 GATGCTGGTGTAACAACAGACACACGGAG----GGAATAGAATAAAGAAC 797
                          i i    ii   vi i     i ii  v----          vi   ii
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_4617629_46    798 GCAGAAATAAAGGCAAACATATACAATCAACTCATTCTTGACAAGGCCAC 847
                         v          vv  v    v  iii    i v   i i       vii 
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_4617629_46    848 CAAGAACACACAATGGAGAAAAAAAAGAATAGCCTCTTTGGTAAATGGTG 897
                              v  iv      i    -----      i  i  iiii        
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAA-----GAATAGTCTTTTCAACAAATGGTG 413

  chrX_4617629_46    898 TTTGGATATCTGGCTGTCAACATGCAAAAGAGTGAAATTGGACCCTTATC 947
                         i v   i v    v i? v            i    i        i  i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_4617629_46    948 TTCCACCATACACAGAAGTCAATTCAACATGGATTAAAAACCCAAACTTA 997
                          iv       i   i  i i  i    v      i ? i   i   iv  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_4617629_46    998 CAACCTGAAATCCTTTAACTAAACTTCTAGAACAAAACAGAGGAA-AAGT 1046
                         vi v  i   --  v   ---    ii     v      v   ?i-  i 
  L1M4_orf2#LINE/    514 AGAGCTAAAA--CTATAA---AACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_4617629_46   1047 GTTT-TG---CTGGCCTCGACAATGACTT-TTGCAAATCACACCGAAAGC 1091
                         v  i-  ---i   vi v i     ii  -  iv v  v     i     
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_4617629_46   1092 TCAGGTAACAAAAGAAGAAATAGAGAAGTGAGACTACATCCAA-CAAAAA 1140
                         v  i i          i       v  i vi    v    v  -iv    
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_4617629_46   1141 ACTCTGCAGAACTAAAAAAAATAAAATAAAATAAAAAAG-AAAAAGAAAA 1189
                            i v-- vi  vv   ii i vv  ----i  i    -i      ---
  L1M4_orf2#LINE/    659 ACTTTT--GTGCTTCAAAGGACACTAT----CAAGAAAGTGAAAAGA--- 699

  chrX_4617629_46   1190 AGTCACTCTACAGAACAGGAGAAAA-ATGTGTAAACCATATATCTGACAA 1238
                         ---  vi i      ii        -  v  i   i           i  
  L1M4_orf2#LINE/    700 ---CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_4617629_46   1239 GGGGTTAATATTCAAAGTATATAAGGAACTCACACAACTCAATAACAAAA 1288
                            ii vi   i  i i       i      vi            i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_4617629_46   1289 -GACAATTAACCCAATTAAAATACAGACAAAGGACTTGAATAGGCATTTC 1337
                         -     v          ?   v ii i       i        i      
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_4617629_46   1338 TCCATAGAAAACTTAAAAATAGCAAACAGATATATGAAAAGGTGCTCAAC 1387
                             v    i iv  v    i  v  i iii i        i        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_4617629_46   1388 ATCACTAATCAA 1399
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (139 / 77)
Gap_init rate = 0.02 (17 / 887), avg. gap size = 2.29 (39 / 17)  


3219 27.42 0.44 0.44  chrX_5257734_5263996     4863  5770 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_5257734_52   4863 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATAGTGAAAAT 4912
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_5257734_52   4913 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4962
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_5257734_52   4963 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5010
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_5257734_52   5011 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5060
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_5257734_52   5061 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5110
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_5257734_52   5111 TACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5160
                               v i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_5257734_52   5161 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCGTATCTACAACT 5208
                                i    i--    i  --        vv  iiii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_5257734_52   5209 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5258
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_5257734_52   5259 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAAAAAGCT 5308
                           v  i  i              v      v  ?   i   i    iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_5257734_52   5309 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATGAATTCAAGATGGA 5358
                            ii    i    v   i     v           v  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_5257734_52   5359 TTAAAGACTTAAACGTTAGACCTAAAACCACAAAAACCCTAGAAGAAAAC 5408
                          i ?    i    i  v   v       i i    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_5257734_52   5409 CTCGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5458
                         v v  ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_5257734_52   5459 AACATCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5508
                         i   i        vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_5257734_52   5509 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5558
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_5257734_52   5559 GGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5608
                         i i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_5257734_52   5609 AGGGCTAATATCCAGAATCTACAATAAACTCAAACAAATTTACAAGAAAA 5658
                         i  i  vi          v  i  vi     vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_5257734_52   5659 AAACAAACAACTCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5708
                          i     i   i v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_5257734_52   5709 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTTATC 5758
                           v        i  vi viii     v  i          i     i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_5257734_52   5759 ATCACTGGCCAT 5770
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2292 25.37 2.51 7.72  chrX_5323951_5326021.rev      636  1593 (478)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_5323951_53    636 TGGAAAAACATTCCATGCTTATGAACTGGAAGAAACAATA--GTTAAAAT 683
                               i i  i     i i   i i       vvi    --     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_5323951_53    684 CGCCGTACTGTCCAAAGCAACTTA-AGATTCAATGCTATTCCTTTCAAAC 732
                         v  vi    vi     vii ii  -        i  v  i   v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_5323951_53    733 TACTAA-TGTCGTTTTACACAGAGTTGGAGAAAACT-ATTTTAACATACA 780
                          v i i-  i v    -ii    iv v  v  i-  -  ii   v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_5323951_53    781 TATGGAGCCAAAGAAGAGCCTGAATAGCCCAAGCAATCCTAAGCAAAAAG 830
                               iviiv iii  v  v        v  i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_5323951_53    831 AATAAAGCTGGAGGTATCACATTACCTGACTTCAAACTATCCTACAAGGC 880
                           i    i      vv     i v  ii i      viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_5323951_53    881 TATAATAACCAAAACAGCATGGTATT--CATTCAAAACGGGACACATAGC 928
                           i i   i   i    ii     i --   --  iivvi    i    v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGA 296

  chrX_5323951_53    929 CCAATGAAACAGAATAGAGAGCCCAGAAATAAAGCTGTACACCTAATAGA 978
                         i     i  i     v     i           -----------------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAA----------------- 329

  chrX_5323951_53    979 GAGCCCAGAAATAAAGCTGTACACCTAATAGAGAGCCCAGAAATAAAATA 1028
                         ---    ------------    ---------------------------
  L1M4_orf2#LINE/    330 ---CCCA------------TACA--------------------------- 337

  chrX_5323951_53   1029 AAGCTGTACAGCCATCTAATCTTCAACAAAGTTAACAAAACTAAGCAATG 1078
                         ---- v  ii i  vi i  i   i    i v iv   i  i vv     
  L1M4_orf2#LINE/    338 ----TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_5323951_53   1079 GGGAAAGGATTCCCTATTCAAAAAATGGTGCTAGGATAAGTGATTAGCCA 1128
                                i  vvi  v     v          i   i  v  iv  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_5323951_53   1129 AATATAAAAGAATGAAGTTTAACCCCTATCATATACCATATGCAAATATT 1178
                         v  ii              vi       i vi i       i    v   
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_5323951_53   1179 AACACAAAATGGATGAAAGATTTACATATAAGACCTCAAACTATAAGAAT 1228
                            v          v ?   ii  v  i     v  v         i v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_5323951_53   1229 CCTAGAAGAAAACCTAGGAA-ACACCATTCTGGACATCATCCTTTAGA-A 1276
                          i           v    ?i- v i -   vv   v -- vvv    i- 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT--TGGGTTAGGCA 580

  chrX_5323951_53   1277 ATAATTTAT--GACTAAGTCTTCAAAAGCAATTTCAACAAAAATTAAAAT 1324
                           ii   v --  -  v v vi        vvvv        ivv     
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_5323951_53   1325 TGACACATGGGACCTAATTAAACTACAGAACGTGTGCACAGTGAAAGAAA 1374
                         v  i v  v    i v  i   v vv i   v v  ii vvii  i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_5323951_53   1375 CTGTCAACAGAGTAAACAGGTAATCTACAGGATGGG-GAAAATATTATCA 1423
                           i    v i   i  v  ii  i i    i     -         vv  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_5323951_53   1424 AACTATGCATTTAACAAAGGACTAATATCCAGAATCTGTAAGAAACTTTA 1473
                           ii  ii  i i i  i     vi          v i   ii    i v
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_5323951_53   1474 ACAATTTGACAA-GCAAATACCAAT--CCCACTTTAAAAAAATGGGCAAA 1520
                             i ii i  -iv   v  v   --    v  ?     --        
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA--TGGGCAAA 827

  chrX_5323951_53   1521 AGAT-------GACAGTTCTCAAAAGAAGACACACAAACAACCAACGA-- 1561
                         i   -------    v     v        i i     iii    ii --
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_5323951_53   1562 ACATGAAAAAAAAGGTCCACATCAGTAATCAT 1593
                                  i v- v  v      ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 4.08 (98 / 24)  


2351 23.18 4.48 5.63  chrX_5358162_5359948      514  1294 (493)    L1M4_orf2#LINE/L1      137   908 (0)  

  chrX_5358162_53    514 TCTTAAAAAGTATATGAACCCACAAAAGACTTCAAATAGCCAAAGCAATT 563
                           i     vvi     i vvii   ii   iivi          i    i
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_5358162_53    564 TTGAGAAAGACAAA-AAAGCTGGAGAA-TCACACTTCCTGATTTCAAA-T 610
                             i     vi  -    i     i -          ii        -i
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_5358162_53    611 ATATTATAGAGCTACAGTAATCAAAGCTGTATGATACTGGCATA------ 654
                         v  i  i i               ii v  i  i          ------
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_5358162_53    655 ------TGGATCAATGCAACAGAATAAACAGCCCAGAAATTAACCTATGC 698
                         ------ i        v  i     vi v  i        v    i  i 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_5358162_53    699 ATGTACCATCAAAAGATCTT--GCAAGGATAC----AC-----AACAGAG 737
                           v  ivi    vv   i  --i     i i ----  -----  ii i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_5358162_53    738 AGAGGAGAGTCTCTTGGACAAATGGTGTTGGGAAAACTGGATATCCATAT 787
                          i  i v     i  vi          i     v         ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_5358162_53    788 GCAAAAAGAATGAAATTGGACCATTAC---ACAACAGA-AAAAAAACGAA 833
                               -       i       vi   ---   v  v - v     iv  
  L1M4_orf2#LINE/    437 GCAAAA-GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_5358162_53    834 CTAAAAATAGATTCAAGACTTCACATAAGACATGTAAGGACTTCACATAA 883
                           v     i   iv?    i -----  ---       ii  ------  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCT-----AA---ATGTAAGAGCT------AA 521

  chrX_5358162_53    884 GACCCTGTAAAACTCCAAAAAGAAAATATAAGGAATAA--CTTGTTGACA 931
                         i  -- i        iv i       i   -  ?i   --   vv    v
  L1M4_orf2#LINE/    522 AAC--TATAAAACTCTTAGAAGAAAACATA-GGNGTAAATCTTCGTGACC 568

  chrX_5358162_53    932 TTGGCCTTGGCAATGATTTCTTGGACATGACACTGAAACCACAGGCAGTG 981
                             vi v       i      i  i       ii   v    i   iii
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_5358162_53    982 AAAGCAAAAGAGGACAAGTGGAATGACATTTAA-CTAAAAAGTTCTGCAC 1030
                             v    ivi  i  i v i ivv   iv  -i      v  i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_5358162_53   1031 AGTAAAGAAAGCAATCTACAGATTGAGAAAGTATCCTATGGAATGGGAGA 1080
                         vvi    i vi v   v v i v   i  iii v  i ii          
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_5358162_53   1081 AAACATTGGCAAACCATGCAGCTAATAAAGAATTAGTATACAAACTAAAT 1130
                            i   v     i   ii v  i    i i i v    v  i v  v  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_5358162_53   1131 AAGGAACTCCTTCAACTCAACACAAAAACATGTACAACAACAACAACAAA 1180
                           i      i v        i ----------------------- i   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATA-----------------------ATAAA 795

  chrX_5358162_53   1181 AAAACACCAAATAATTCAATT-AAAAATCGCCAAAAGACT-AAATAGACA 1228
                           i   ---     ii     -      v v    i  i -i        
  L1M4_orf2#LINE/    796 AAGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_5358162_53   1229 TTTCTCCAAAGAAAACATACAAATGGCCAACAGGTACCTGAAAAGGTGCT 1278
                                      i i              i i i  v       i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_5358162_53   1279 CGACATTATTACCCCA 1294
                          i    i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (120 / 58)
Gap_init rate = 0.03 (21 / 772), avg. gap size = 3.76 (79 / 21)  


1996 27.86 1.25 0.94  chrX_5376231_5379675.rev     1672  2310 (1135)    L1M4_orf2#LINE/L1        1   641 (267)  

  chrX_5376231_53   1672 TGGGAAAACGTTCCATGCTCATGGACAGAAAGAATCAGTGTTGCTAAAAT 1721
                            i  i ii i     i       iv i    v i i i   i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_5376231_53   1722 TGCCGTAGTGCCCCAAGCAATTTACAGATTCAATACTATTCCTATGAAAC 1771
                         v  vi  v v   v  vii  i           ii v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_5376231_53   1772 TACCATTGACATTATTCACAGAAAT-AAAAAATAGTATTTAAAAATTCAT 1820
                          v   vivi v  v  ii       -i v  iiv -  iiv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chrX_5376231_53   1821 ATGGAACCAAAAAAGAACCTGAATAGCTAAGGCACTCT-AAGAAAAAAGA 1869
                               viiv  ii  v  v       i  ii  v   -i i   i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_5376231_53   1870 ACAAAGCTGGAGGCATCATGCTACCCACCGTCAAACTATACTACAAGCCT 1919
                               i      vv   ii  v    viv     viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_5376231_53   1920 ATAGTAACCAAAATGGCATGGTACTGGTACAAAAATAGACACATAGACCA 1969
                          i     i   i ii ii         i i  ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_5376231_53   1970 GTGGAACAGAATAGAGAACCCAGAAATAAGACCA--CATTCCTACAACTA 2017
                         i     i     v    ii          iv   --    --  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCA 347

  chrX_5376231_53   2018 TCTGATCTTTGA-AAATCTCACAAAAACAAGCAATGTGGAAAGAATTCCC 2066
                         vi    i  i  -  ivv vv   i v  vv     v         vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_5376231_53   2067 TGTTCTATAAATTGTGCTGGGAGAACTGGCTAGACATATGCACAAGATTA 2116
                          v   v i    v         v      v  ?v  i     v    v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_5376231_53   2117 AAACTGGACCACTTCCTTATACCATATACCAAAAATTAACTCAAGATGTT 2166
                           ii      v  v   i i         -              i   vv
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAAATGGA 496

  chrX_5376231_53   2167 TTAAAGACTTAAATGTAA-ACCCAAAACTATAAAAACCCTGGAAGACAAC 2215
                          i ?    i         - v i            vi i i     v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_5376231_53   2216 CTAGGCA-ATACCACTCAGGACATAGGCACGGGCAAAGATTTCAT-GATG 2263
                         v    ?i- v i -i  iv   v v  vvii     v i    v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chrX_5376231_53   2264 AAGATGTCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGA 2310
                          v  iii        vvv          v      v  i    v   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

Transitions / transversions = 1.30 (99 / 76)
Gap_init rate = 0.02 (12 / 641), avg. gap size = 1.17 (14 / 12)  

 794 25.19 2.63 1.13  chrX_5376231_5379675.rev     2689  2954 (491)    L1M4_orf2#LINE/L1      639   908 (0)  

  chrX_5376231_53   2689 GGATCTAATTAAAATAAACAGCCTCTGCACAGCAAAAGAAACTATCAACA 2738
                            ii v  i     v  v i i i  ii vv    i  v        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_5376231_53   2739 GAATAAAAAGACAACCTACAGAATGAGAGAACATTTTTGCAAACTGTGCA 2788
                         i i i           i        i     v  v        iii ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_5376231_53   2789 TCTGACAAAGGTCTTATATTCAGCACCTG-AAACAAAT-TTATAA---GA 2833
                              i  i  v   i   i   v iv i-   v  v -   i  ---i 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_5376231_53   2834 -AAGAAAAAAACCAAACAACCCCATTAAAGAGTAGGCAAAGAACATGAAC 2882
                         -  v     i  -   i     v   ?  i i i       i iv    i
  L1M4_orf2#LINE/    789 TAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_5376231_53   2883 AGATACTTTTA-AAAGAAGGCATACATATGGCCAACAATCATATTTAAAA 2931
                            i i  i v-       ii     v        i  v  i  --i   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT--GAAA 885

  chrX_5376231_53   2932 AAAAGCTTAACATCACTGACCAT 2954
                          i v   i       ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (45 / 21)
Gap_init rate = 0.03 (7 / 270), avg. gap size = 1.43 (10 / 7)  


1774 23.83 5.32 9.04  chrX_5487962_5490073      687  1626 (486)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_5487962_54    687 AGAAATATACAATATTAAAAG-TCAGAACATTCGAAATTGTTAATATGTC 735
                          i i    v v  i  v vi - ii   v i ii v        v   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_5487962_54    736 AATTATCCCCAAATGTG-CCCGGGCATTTCATAAAATCACAGTCAAATTC 784
                            vv         -  -i iiviv   iv iiv    v vi     v  
  L1M4_orf2#LINE/     54 AATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_5487962_54    785 ACAGCAAGCTCTCTGGGGGAAAGATGACAAGCTGAATTGGAAATGCATAT 834
                         v    viv  i i v vi    v-           viivi    v     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATAT 151

  chrX_5487962_54    835 GGAAATGCCAAGGACCTTGACTGGTCAAAATAACTTTGAAAAAGAAGAAT 884
                                 v i     iv  v i i     i  ii              i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_5487962_54    885 AAAGTTGGAGAAC--ATACTTTACCTGATTTCAAGATTTTATTGTAAAGG 932
                                   i  -- i    --  ii       i i  - i ii    v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTT--CCCAATTTCAAAACTT-ACTACAAAGC 248

  chrX_5487962_54    933 TAATATAATCAAGACAGTATGCTATTGTCAACCAACACAGACAAGTAAGT 982
                           vvi             i  v  i  v  -iv iv i     vi  ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGAT 297

  chrX_5487962_54    983 CAAGGGAATAGAATACCATATCCTGAAGTAGACACACACACACACACACA 1032
                            v          ---------   i--  v -----------------
  L1M4_orf2#LINE/    298 CAATGGAATAGAAT---------TGAG--AGTC----------------- 319

  chrX_5487962_54   1033 CACACACACACACACACACACATATATATATAGAAAATCGATTTCTGAAA 1082
                         --------  v v i v  v    i  v   i vv   i     ii  v 
  L1M4_orf2#LINE/    320 --------CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_5487962_54   1083 AATGTTTCAAAGGCAATTCCGTGGAAAATGTTTA---TTTTAAACACGTG 1129
                          iv  vi   - i v    vi   ii  v vv  ---    v    vi  
  L1M4_orf2#LINE/    362 AGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_5487962_54   1130 GTGCTGGAATAATCAGATATCCATATGCAAACAAAAAAGAA--TAGCAAT 1177
                                i i  iii    ?   i       -- i  v   -- i -- i
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAA--AGAATGAAGTTGG--AC 456

  chrX_5487962_54   1178 ATATACCTTGCACCATATA-AAAAATTAACTCAAAATGAACCATTGGCCT 1226
                         viv     ii         -                  i i  ?v i   
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_5487962_54   1227 AAATTTAAATTTAGATTTAAAACCTAAATCTTTAATACTTCTAGAATAAA 1276
                             v   -----  vi      -  ------   v   ii     v   
  L1M4_orf2#LINE/    507 AAATGTAA-----GAGCTAAAAC-TA------TAAAACTCTTAGAAGAAA 544

  chrX_5487962_54   1277 -CATAGGAAAAATAAAT----GTGACCTAGGCCTAACAAAAGATTTCTTG 1321
                         -      ?i---     ----       v  vi  ivv  v i      i
  L1M4_orf2#LINE/    545 ACATAGGNG---TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_5487962_54   1322 GATCTAACACCAAACTCATACTCCATAAAACAAA-------TAAATAGAA 1364
                            v i        vv  i vv v i    v   -------     v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_5487962_54   1365 C---ATAAAAATTAAAA---TATCTGCTTTACAAAAGATATTTGAAAGAT 1408
                          ---  v          --- v v     --    i  i ----------
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACA---------- 679

  chrX_5487962_54   1409 ATTCTGTTAACAGAATGAAAAGATAAGCCA--GATTGAGAGAA----CTT 1452
                         ---  i i  v i i        i  v   --  v  i     ----i  
  L1M4_orf2#LINE/    680 ---CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_5487962_54   1453 GCA-------TTTCTGATCAAGAAATTGTAATCAGAAGACA--GAGAACT 1493
                            ------- v      v i i v     vi     v i --i      
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_5487962_54   1494 CTCA-AA---AATGATTAATAG-CAAATAATGCAATTTTTTAGAATAG-C 1537
                           i -  ---   i  v  v  -       iv     ?v-- i   i - 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA--AAAATGGGC 824

  chrX_5487962_54   1538 GAAG-ATTTGAACAGACACTGTACCAAGGACTTAAGATATATGAACAGCA 1586
                         i   -       i     i viv    i  ----       ii  ii  v
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGA----AGATATACAAATGGCC 870

  chrX_5487962_54   1587 AATAAGAAGATGAAAATATACTCAATTTATTAGTCATTAG 1626
                               v v       v  i     i--  i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAAC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (122 / 98)
Gap_init rate = 0.04 (40 / 905), avg. gap size = 3.38 (135 / 40)  


 824 28.52 0.78 2.73  chrX_5812328_5814583.rev      472   727 (1529)    L1M4_orf2#LINE/L1       64   314 (594)  

  chrX_5812328_58    472 AGATTAATTTAAAATTGGGATTTGGCAAGTAATTTCTATCGAAATCTCAG 521
                          i   i  i  v -----    iii -- i   ii     i     i   
  L1M4_orf2#LINE/     64 AAATTGATCTACA-----GATTCAAC--GCAATCCCTATCAAAATCCCAG 106

  chrX_5812328_58    522 CAGGAGTTTTTATTGCAACTAACAAGCTGATTTGGAAAGTTTCATGGAAA 571
                          v vvv     iiv v  i i          iivi   v ivi       
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_5812328_58    572 GGCAAAGGATCTAGAGCAATCAAAAAGACCTTGGAAAAGGGGAAGAAAGT 621
                         v    i   i i   ii ii     vi i    i     ii   v     
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_5812328_58    622 TGGAGGGCTTCCATTTCTCTATTTTAAAAGGTACTATAAAGATATAGTAA 671
                               i  iv  i   i v    i    vv     i    v  i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_5812328_58    672 TCAAGATAGCAGGCAACTCACAT--GGGTATAAATTTAGACCAATGAAAT 719
                               i  iiv vv   vi   --  i  v v  v    i     i   
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_5812328_58    720 ATAATTAA 727
                          v    i 
  L1M4_orf2#LINE/    307 AGAATTGA 314

Transitions / transversions = 1.81 (47 / 26)
Gap_init rate = 0.01 (3 / 251), avg. gap size = 3.00 (9 / 3)  

1851 22.59 5.48 6.31  chrX_5812328_5814583.rev     1164  1765 (491)    L1M4_orf2#LINE/L1      312   908 (0)  

  chrX_5812328_58   1164 TAAGGGTTTAGAAATAAATCCTTCAATTTGTAGTCAATAGATTTTTAACA 1213
                          i  i  ii         i  v vv    i i      v      ii   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_5812328_58   1214 ATGGTGCCAAAACAATTAAAGGAGGCAAGGATAGTCTTTTCAATAAATGG 1263
                          v        i  v   v  v i  v   i             i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_5812328_58   1264 TGCTGAGACAATTGGATATTCATATGTAAAAAGATCAATTTCAACTCTTA 1313
                              i     i      ?i  i   i    ii  v  v  vi  i i  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_5812328_58   1314 CCTCTTATTGTACCCAAAAATTAACTCGAACGACAGGT----GGC---AA 1356
                             vi iii  iv             i  -- ii i ---- i ---  
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAA--ATGGATCAWAGACCTAAA 509

  chrX_5812328_58   1357 TATAAGAATTAAAGCTCTTAAACTTTTAGGAAACTTCAGCAACACAGGAG 1406
                          i     ii    i  v v     i    i i ---- --    i   ? 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGA----A--AACATAGGNG 553

  chrX_5812328_58   1407 AAGGTCTTCAGGGCCATGGATTGGGAAA-GATTTCATAAATATGACCTCA 1455
                         v ii     iv i  v   i  i  v  - i    v  i       vi  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_5812328_58   1456 AAAGTACAATCCTTAAAAGAA----TTGATCAAGTGAAACTCATCAAAAT 1501
                             i    v vvi       ---- v   v  v  i vi          
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_5812328_58   1502 TAAAAACTTTTACACTTCAAAAGGCACTATTGAGAACATAAAGTGCTATT 1551
                                    iii       i i      ii    -----    -----
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA-----AGTG----- 693

  chrX_5812328_58   1552 TGTTGAGAAAACCAAAAGACAAGCCATAAACTGGGAGAGGAGATTTGCCA 1601
                         -------------         v   i i v       ii v      v 
  L1M4_orf2#LINE/    694 -------------AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_5812328_58   1602 ACCATATTCCCAATAAAAGACTTTTATTTAGAAAATATGTAAACAAACCA 1651
                          i     vi ii    ii     v   ii    --   i    -i   i-
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAA--TATATAAA-GAACT- 776

  chrX_5812328_58   1652 CTTACTATTCAATAATAAGAAGGAAAGAAATT--ATTTTTTAATGGGCAA 1699
                              v i          i   iv  iv  ii--   ?vvv         
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_5812328_58   1700 AAATAAATT--AATAGACATTTCTGCAAAGA---------------CAGT 1732
                          ii---   --             v      ---------------  i 
  L1M4_orf2#LINE/    827 AGG---ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_5812328_58   1733 --GTACATGAGAAGATATTTAATATCATTAGTTAC 1765
                         -- i      i     ii i  i    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (91 / 42)
Gap_init rate = 0.03 (17 / 597), avg. gap size = 4.18 (71 / 17)  


3299 26.87 0.44 0.44  chrX_6362044_6367160.rev     3719  4626 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_6362044_63   3719 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3768
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_6362044_63   3769 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3818
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_6362044_63   3819 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3866
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_6362044_63   3867 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 3916
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_6362044_63   3917 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3966
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_6362044_63   3967 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4016
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_6362044_63   4017 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 4064
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_6362044_63   4065 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4114
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_6362044_63   4115 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4164
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_6362044_63   4165 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4214
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_6362044_63   4215 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4264
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_6362044_63   4265 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 4314
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_6362044_63   4315 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4364
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_6362044_63   4365 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4414
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_6362044_63   4415 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4464
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_6362044_63   4465 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4514
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_6362044_63   4515 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 4564
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_6362044_63   4565 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 4614
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_6362044_63   4615 GTCACTGGCCAT 4626
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3348 26.43 0.44 0.44  chrX_6709759_6716171     5013  5920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_6709759_67   5013 TGGAAGAACATTCCATGCTCATGAGTAGGAAGAATCAATATCGTGAAAAT 5062
                              ii i  i     i     ii v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_6709759_67   5063 GGCCATACTGCCCAAGGTAATCTACAGATTCAATGCCATCCCCATCAAGC 5112
                            v     v     iv i              i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_6709759_67   5113 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5160
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_6709759_67   5161 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5210
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_6709759_67   5211 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5260
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_6709759_67   5261 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5310
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_6709759_67   5311 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5358
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_6709759_67   5359 ATCTGATCTTTGACAAAACTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5408
                          vi    i  i     iiv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_6709759_67   5409 CTATTTAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5458
                           v  i ii              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_6709759_67   5459 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5508
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_6709759_67   5509 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5558
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_6709759_67   5559 CTAGGCATTACCATCCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5608
                         v    ?i v viv i iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_6709759_67   5609 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5658
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_6709759_67   5659 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5708
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_6709759_67   5709 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5758
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_6709759_67   5759 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5808
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_6709759_67   5809 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5858
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_6709759_67   5859 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5908
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_6709759_67   5909 ATCACTGGCCAT 5920
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 879 31.00 6.00 6.88  chrX_6776727_6780488     2354  3269 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_6776727_67   2354 TGACAAGTTATAGCATAATCTTGAATAGGAAGACACAACATTTTCAAGAA 2403
                           iv   v   vv   iv  v  i  v       vi  i   v i    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_6776727_67   2404 GTCACTACTCCTCTATTCAATCTGTAGAT-AGATTTAATTTCAGTCAAAT 2452
                          v  v      i v v ii    ii    -vi ivi   ii vi     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_6776727_67   2453 GCCAAGAAGA-TTTTTAGGGAAAATT-------TGATTCTAAAATATATA 2494
                         v  v  vv v-     v vii     -------    i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_6776727_67   2495 TGAAAGAACAAAGAGCCATAAATAACCAAGATACTTCTGAGAAA-AAGAA 2543
                           i  ivi   i ii  vvi    i    i i v ii   i   -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_6776727_67   2544 GAAGATGGAAAAACTTA----TTCTA--TTCAGAA-TTAATATAAAATTT 2586
                         v  ii v i ii   i ---- i i --    i  -   v  i   ii v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_6776727_67   2587 TGGTGGTTAAACCCATGTAGAATTAGGACTGGAACAGACATACTAGACAA 2636
                         ii  ii i  iv vi   i v i i v ivi i i       -    ---
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGA--- 296

  chrX_6776727_67   2637 TTCAAAAGATAAAGAGCCATTTGGGTCATGAACAGACGCATTGACCAGTG 2686
                         -    ----------------   ------  i   ---     ------
  L1M4_orf2#LINE/    297 -TCAA----------------TGG------AATAGA---ATTGA------ 314

  chrX_6776727_67   2687 AAAAGAATCGAGATCAGAGAAAC----AGACTTA-AGTCCCTTGAATTTT 2731
                         ----  i  v   ---i v    ---- v i   -i   vv    -    
  L1M4_orf2#LINE/    315 ----GAGTCCAGA---AATAAACCCATACATTTATGGTCAATTGA-TTTT 356

  chrX_6776727_67   2732 CATGTATAACGG-AAAGAGATTTTCTGATGTGTGGGAAAATACAA----- 2775
                          i--- i  v  -ivvi   iiv iii   ---      iv i i-----
  L1M4_orf2#LINE/    357 CG---ACAAGGGTGCCAAGACCATTCAATG---GGGAAAGAATAGTCTTT 400

  chrX_6776727_67   2776 --AATAAATGGTACTAGGACAAGGGGTTATTTATACATACGGAAAAAAGG 2823
                         --  i       i  i      vv  v  ?ii --   i ii  i  v i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCA--CATGCAAAAGAATGA 448

  chrX_6776727_67   2824 AGAGCTCAAACTAC-ATCTCACACTCTACACAAAAATAAAATCCAGATGA 2872
                           --- iii  iv - i       iv  i        v  v  v i   i
  L1M4_orf2#LINE/    449 AG---TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_6776727_67   2873 TTGAAAAATTTAAATGCCAAAGTCAAATGCT-TAACACT-TCACAAGACA 2920
                         v v ? i ii      iv i  ii   -i  -   v   - i v    v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAA-ACTATAAAACTCTTAGAAGAAA 544

  chrX_6776727_67   2921 ATTTAGGGGACAATCT-CATGTCCTATGGATAGGAAAGCACTTCTTAAAT 2969
                          iv    ? vv     - i  v   vv  v    v  vvii      i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_6776727_67   2970 CAAATAAAATAATAATCAATAGCCATAAATAAAAAGAGACACAAACTTGA 3019
                         ---  i v iv v  v  vv   v i   vi    i v v i   i v  
  L1M4_orf2#LINE/    595 ---ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_6776727_67   3020 CTATAT-----TCAACAAACTTCAGTTTGTCAAAAAATGCCATAAAGA-- 3062
                           vi  ----- i  -      iv  viv     ii ii i  v    --
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_6776727_67   3063 --GAAAAAATTAAGCCATA-AATAAAAGATGATATTTGCAACACGTAAGT 3109
                         --     i i-  v   i -   iii   vi          vv i  vi 
  L1M4_orf2#LINE/    691 GTGAAAAGAC-AACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_6776727_67   3110 C--ACCATGGCTCAGTCTCTAGACTACATTTAAAACGTCTAGAAATCAAT 3157
                          -- iv v  viiv  v  i   v  i  vv i   vii  v  v     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_6776727_67   3158 ATAAAAAAGATAAACCACCCAACAGAAAAAAATAAAGAAAATACCTGAAT 3207
                          vv       i   iv      iv--?      iiiv   iv ii     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATT--WAAAAATGGGCAAAGGATTTGAAT 837

  chrX_6776727_67   3208 GAAGACTTTGTAAAAGAGGAAACACAAA------AT---CATATGGAAAG 3248
                         ii v i  iviv     i  v i     ------  ---  i   i    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_6776727_67   3249 ATGTTCAATCTCATTAATAAT 3269
                            i    iv   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (163 / 117)
Gap_init rate = 0.04 (38 / 908), avg. gap size = 3.11 (118 / 38)  


3366 20.75 5.36 2.05  chrX_6879028_6882084     1689  2565 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_6879028_68   1689 GAAAGACATCTTATGCCCATGGATGGGAAGACTTAATATT---AAGACAT 1735
                               i   ii   ii       v               ---    iiv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_6879028_68   1736 TCATAGCATGCAAAGCAATCCTACAGATTCAATGCAATCCCTATCAAAAT 1785
                         iv   viviv    vii   -           i                 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATC-TACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_6879028_68   1786 CCCAATGGCATTTTGAGCAGAAACAGAGAAATACATCCTAAAATTCATA- 1834
                             iiv  v    vv       iv  v  iivv               -
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_6879028_68   1835 AAAAATCTCAAGGGATCCCAAATAGCCATAACAATCTTGAAAAAGAA--- 1881
                         ii    v-       i  vi        v                  ---
  L1M4_orf2#LINE/    152 GGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_6879028_68   1882 CAAAATCGGAGGTCTCACATGTCCTGATTTCCAAACATATTACAAAGCTA 1931
                             i i     v      iv   ii     v    v  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_6879028_68   1932 CATTCATCAAAACAGTGCAGTACTGGCCTA--------CATAC----TAA 1969
                           v v     i      ii        v  --------    i----i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_6879028_68   1970 TAGAATAGAATAGATAGCCCAGAAATACACTCTCACGTATTT---GTCAA 2016
                          i         v  v  i         v  i vi  --    ---     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC--ATTTATGGTCAA 348

  chrX_6879028_68   2017 ACGATCTTCAACGAGCCAGCCAAGACTACTCAATGGGGAAAAGATAAGTC 2066
                         vi   i   i  i  vvv        i i            ii   -   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-GTC 397

  chrX_6879028_68   2067 TCTTCAACAAACAGTGTTGGGAAAACTGGACATCCACGTACAAAAGAATG 2116
                          i         ii   i     v       i ?    i i          
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_6879028_68   2117 AAGCTAGATTC-TAATTAACACCATACACAAGAATTAACTCAATATGGAT 2165
                            i i  ii -  vi v        i    i           v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_6879028_68   2166 TAAAGTCCTGAATGTAAGACCTAAAACTA--AAACTCCAGGAAGAAAACA 2213
                         i ?  v   i         v         --      ivi          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_6879028_68   2214 TAAAT-TAAAGTTTCATGAAATTGGAATTGGCAATCATTTCTTGGCTATG 2262
                           ii?-    vi   i   vv    iv v      vi      i v    
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_6879028_68   2263 ACACCAAAAGCACAGGTAACAAGAGCAAAATTAGACAAATGAGATGACAT 2312
                                       i i     i  v    v    i    vi  i-----
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC----- 642

  chrX_6879028_68   2313 ATGTCAAATTCATCTAA-TCAAAAACTT--ATGC--------ACACCAAC 2351
                         --------      v  - i        --i   --------    i v 
  L1M4_orf2#LINE/    643 --------TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_6879028_68   2352 AACTAAGCGAAAAGGGAGCC---AGAATGGGAGAAAATGGTCATAAGTCA 2398
                           vv   i      iv i  ---               iv iii  i   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_6879028_68   2399 TATGTCTGATAACAGTTTAACATTCAAAATACATAAGGAACTCCTACAAC 2448
                            i        vi vi vii  i  i    i    i      i      
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_6879028_68   2449 ATAAAAACAAAAACACAAA-AATC------AAAAATAAGCAAAGGATGTG 2491
                         vi  v  i     v     -  i ------      ii         v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_6879028_68   2492 CACAGACATTTCTTCAAAGATAATACAGAAATGGCCAACAAGCAAATGAA 2541
                         v i          i      vi   i v          i     v     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_6879028_68   2542 AAGATTCTTGCCATCCCCAATCAT 2565
                              v  iiv    v????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (109 / 70)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 3.25 (65 / 20)  


2478 26.22 0.43 0.43  chrX_7112636_7114321.rev      502  1195 (491)    L1M4_orf2#LINE/L1      215   908 (0)  

  chrX_7112636_71    502 TCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACA 551
                             i  v  ii i      viv        i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_7112636_71    552 GCATGGTACTGGTACCAAAACAGAGACATAGACCAATGGAACAGAAC--A 599
                          ii         i iv ii i   v i     i        i    i-- 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_7112636_71    600 GAGTCCTCAGAAATAAGACCACACAACTATAACTATCTCATCTTTGACAA 649
                               --        iv   i   vi   iiii vi v  i  i     
  L1M4_orf2#LINE/    315 GAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_7112636_71    650 ATCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAACAAATGGT 699
                         ivv  v   i v  vvv           i  vvi  v  i          
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_7112636_71    700 GCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTGAAACTGGATCCCTTC 749
                                v      v  ?   i   v i  iiv    ii    i    v 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_7112636_71    750 CTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGACTTAAATGG 799
                           i     v           i  i    i      i ?    i      v
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_7112636_71    800 TAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATT 848
                         v   v       i      vi i           v    ?i- v i -  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TT 561

  chrX_7112636_71    849 CAGGACACAGGCATGGGCAGGGACTTCACGTCTAAAACACCAAAAGCAAT 898
                          iv   viv  vv i    iv ii   viivv  vi            vv
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_7112636_71    899 GGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCT 948
                         i           v     v  i    v   ii v  i   v v  i i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_7112636_71    949 TCTGCACAACAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAA 998
                          i  ii vv    i  v    i  vv i      v  i     i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_7112636_71    999 TGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAGGGCTAATATCCAG 1048
                                    v       vii ivi      i  i  i  vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_7112636_71   1049 AATCTACAAAGAACTCAAACACATTTACAAGAAAAAAACAAACAACCCCA 1098
                            v  i         vv   vv iv i  v     i     i     v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_7112636_71   1099 TCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATT 1148
                          i?    i           iv    i     i     v        i  v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_7112636_71   1149 TATGCAGCCAACAGACACATAAAAAAATGTTCATTATCACTGGCCAT 1195
                         i viii     i ii     i    i   i   vi    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (106 / 72)
Gap_init rate = 0.01 (4 / 694), avg. gap size = 1.50 (6 / 4)  


3348 26.04 0.55 0.77  chrX_7301616_7306814     3797  4706 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_7301616_73   3797 TGGAAGAATATTCCATGCTCATGCATAGGAAGAATCAATATCTTGAAAAT 3846
                              ii    i     i     v  v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_7301616_73   3847 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCTATCAAGC 3896
                            v     v      v i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_7301616_73   3897 TTCCAATTACTTTCTTCACAGAA-TTGGAAAAAAACT-ATTTTAAAGTTC 3944
                          i   ii i i  i  ii     -   --- v  i  -  ii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_7301616_73   3945 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAA 3994
                                 viiv  ii  v  viv  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_7301616_73   3995 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 4044
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_7301616_73   4045 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 4094
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_7301616_73   4095 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACTACATATCTACAAC 4142
                                 i    i--    i  --        vv i i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_7301616_73   4143 CATCTGATCTTTGAAAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 4192
                           vi    i  i  v  ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_7301616_73   4193 CCTATTTAATAAATGATGCTGGGAAAGCTGGCTAGCCATATGTAGAAAGC 4242
                         i  v  i  i     i        v i    v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_7301616_73   4243 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 4292
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_7301616_73   4293 ATTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACACTAGAAGAAAG 4342
                           i ?   ii       v   v       i      vivi         i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_7301616_73   4343 CCTAGGCA-ATACCATTCAGGACATAGGGATGGGCAAGGACATCATGACT 4391
                          v    ?i- v i -   iv   v v   v i     v iiv  v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_7301616_73   4392 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 4441
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_7301616_73   4442 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 4491
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_7301616_73   4492 ACAGGCAACCTACACAGTGGGAGAAAATTTTTGCAATCTACCCATCTGAC 4541
                          v  i     i   v i           v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_7301616_73   4542 AAAGGACTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 4591
                           i     vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_7301616_73   4592 AAAAACAAACAACCCCATCAAAAAGTGGGCAGAGGGTATGAACAGACACT 4641
                            i     i     v  i?    i      i   i v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_7301616_73   4642 TCTCAAAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAAATGCTC 4691
                             v        i  vi viii     i ii          i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chrX_7301616_73   4692 ATCATCACTGGTTAT 4706
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3300 26.87 0.33 0.33  chrX_7365621_7372029.rev     5011  5918 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_7365621_73   5011 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5060
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_7365621_73   5061 GGCCATACTGCCCAAGGTAATTGATAGATTCAATGCCATCCCCATCAAGC 5110
                            v     v     iv i  iv i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_7365621_73   5111 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5159
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_7365621_73   5160 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCAAAAAGA 5209
                               viiv  ii  v  v v  v     iv     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_7365621_73   5210 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5259
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_7365621_73   5260 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5309
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_7365621_73   5310 ATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGTATATCTACAACTA 5357
                               i    i--    i  --        vv  i  i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_7365621_73   5358 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5407
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_7365621_73   5408 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGAAAGCTG 5457
                          v  i  i              v      v  ?  ii   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_7365621_73   5458 AAACTGGATCCCTTCCTTTCACCTTATACAAAAATCAATTCAAGATGGTT 5507
                           ii    i    v   iv    v           i  i    i    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_7365621_73   5508 TAAAGACTTAAATGGTAAACCTAAAACCATAAAAACCCTAGAAGAAAACC 5557
                         i ?    i      vv i v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_7365621_73   5558 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5607
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_7365621_73   5608 ACACCAAAAGCGATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5657
                                    ivvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_7365621_73   5658 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 5707
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_7365621_73   5708 GGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5757
                          i         i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_7365621_73   5758 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5807
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_7365621_73   5808 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 5857
                         i     i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_7365621_73   5858 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCA 5907
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_7365621_73   5908 TCACTGGCCAT 5918
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


1429 19.42 1.23 26.50  chrX_7951179_7953391.rev      514  1728 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_7951179_79    514 TGGAAAGATAGTCCAGGCTCATAGATTGACAGGATTAATATTGTATAAAT 563
                                   vi   v i    i     iv  iv          vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_7951179_79    564 CACAATACTCACCAAAGCGATTAACAGATTAAATGCAAGTCCTATCAAAA 613
                         vi        v     vi   iv       v  i    vi          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_7951179_79    614 TACCAATGACATTCTTCACAGAAATAGGAAAAAACTTAT---AATATTCA 660
                          v   iivi v  i  ii       v -- v  i  v  ---  v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_7951179_79    661 TAGGAAACCATAAAATACCTCAAATAGCCAAAGCAATCCTGAGCAAAAAG 710
                           v i  viii  iiv   ivi          i     i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_7951179_79    711 TGAAAAGCTGGAAGCATCACACTACCTGACTTCAAAATTTACTACAAAGC 760
                         viv    i    i vv       v  ii i       i            
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_7951179_79    761 TATAGTAAACCAAGCAGCATGGTACTGGCTTAAAAACAGACACAGAGACA 810
                           i     v v ii   ii          v   ii i     i v   iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_7951179_79    811 AATGGAGCAGAATAGAGAACCCATATATAAAGCCACATGCTTACAACCAA 860
                               ii     v    ii   v v     v   i iii   iiii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_7951179_79    861 CTCAACTGAAACAAAGACAAAAAGAACATATGATGCTGAAAAGACCGACA 910
                         i v vi vvi    i iiivv    v   vii   vv    ii iv v v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_7951179_79    911 TGTCAATAAATAGTACTAGAA-AGCTGGATAAGTATATGCAGAAGAATGA 959
                          v    i    i  i  i i - i       ?vi i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_7951179_79    960 AACTAGATTCCTATCTTTCACCACACACAAAAAGCAAATCAAAAATGGGT 1009
                          ii i  ii    i  iv     i i       vi  v      -   i 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGAT 497

  chrX_7951179_79   1010 TAAAGACTTGAATCTGGCTGGGAGTGGTGGCTCACGCCTGTAATCCTAGC 1059
                         i ?    i i   --------------------------    -------
  L1M4_orf2#LINE/    498 CAWAGACCTAAAT--------------------------GTAA------- 514

  chrX_7951179_79   1060 ACTTTGGGAGGTCGAGGTGAGTGGGTCACTTGAGGTCAGGGGTTTGAGAC 1109
                         ---------------------------------------------   --
  L1M4_orf2#LINE/    515 ---------------------------------------------GAG-- 517

  chrX_7951179_79   1110 CAGCCTGGCCAGTATGGTGAAACCCCGTCTCTACAAAAACTACAAAACTT 1159
                         ------------------------------   ---      i      -
  L1M4_orf2#LINE/    518 ------------------------------CTA---AAACTATAAAACT- 533

  chrX_7951179_79   1160 AGCCAGGTGTGGTGGTGCACACCTGTAATCCCAGCTACTCTGGAGGCTGG 1209
                         --------------------------------------------------
  L1M4_orf2#LINE/    534 -------------------------------------------------- 533

  chrX_7951179_79   1210 GGCACGAGAATCACTTGAACCGAGGAGGTGGATGTTATAGTGAACTGAGA 1259
                         -------------   ----------------------------------
  L1M4_orf2#LINE/    534 -------------CTT---------------------------------- 536

  chrX_7951179_79   1260 TGGTGACACTGCACTCCAGCCTAGGCCTGAACAACAGAGTGAGATGAGAC 1309
                         --------------------------------------------------
  L1M4_orf2#LINE/    537 -------------------------------------------------- 536

  chrX_7951179_79   1310 TCTGTTGAAAAAAAAAAAGAAAAAAAGACTTGAATTTATGACCTGTAACT 1359
                         -----------------    i    ------------------------
  L1M4_orf2#LINE/    537 -----------------AGAAGAAAA------------------------ 545

  chrX_7951179_79   1360 GAAACCACCAAGAAACATTGGGG-AAATGCTCCAGGACATTGGTCTGGGC 1408
                         ---------------   v  ? -    -  i iv   v    vi i   
  L1M4_orf2#LINE/    546 ---------------CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGC 579

  chrX_7951179_79   1409 AAAGACTTCTTGAGTACGACCTCAAAAGCACAAG-AACCAAAGCAAAAAT 1457
                           v ii     iii  i   vi            -   v    v      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_7951179_79   1458 AAACTACTGGGATTACATCAAG-TTAAAAAGCTTCTGCATAGCAAAGGAA 1506
                          i iv v v   i v      i-       -   i  iiivv       v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chrX_7951179_79   1507 ATTATCAACCAAGTGAAGAGACAACCCACAGAATGGCAGAAAATATTTGC 1556
                          i      vv       i                  v             
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_7951179_79   1557 AAAGTATCCATCTGATAAGGGATTCATAATCAGAATACATAAGGAGCTCA 1606
                            vi  vi             i ii  vi       i    i  i   v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_7951179_79   1607 AAAAATTTAATAA--------CAAACAATCTGACTTAAAAATGGACAAAT 1648
                         v v  i i     --------    i  i ii i ?        i    v
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_7951179_79   1649 AATCTGAATAGATATTTCTCAAAAGAAGACACAAAAATGACCAGCAGGCA 1698
                         i  i        i       v        i i v     i   ii i   
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_7951179_79   1699 TATGAAAATATGCTTATTATGAATCATCAG 1728
                         i       v     i vi  v ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (146 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 19.82 (337 / 17)  


1558 27.74 5.48 4.57  chrX_8046504_8048679      811  1686 (490)    L1M4_orf2#LINE/L1       25   908 (0)  

  chrX_8046504_80    811 ATTAGAATACTCATCATT-TTATAATG-CAATTTCTCTTTCAGTTGATAC 858
                            i   v   i vi   -   vi   -    v-   iiiv i     vi
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATA-CTCCCCAAATTGATCT 73

  chrX_8046504_80    859 AAAAATTCAATCCAATTCCAATACAAATTCCAAAAA----TTTTACTAAA 904
                          v i      iv    i  v  vv    i   ivvi----    i vi  
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAA 123

  chrX_8046504_80    905 ATTAACAAGTTGTTGCTCAAATGTATATAGAAATGCAAAGGAATTATTTC 954
                            i     i  v v  v    vi    i         i   vii vvvi
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chrX_8046504_80    955 AACCAAGACAAGGATGGAAGATAAGGAATAAAATCGGAATATTTATATTA 1004
                          i    i    vvv  i  i v   -  i   i i   iv i i i i v
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAG-AACAAAGTTGGAGGACTCACACTT 222

  chrX_8046504_80   1005 TCTAATTTCAGGACTTACTGTGAAGCTACAGTAATAGACATAGTGTGGCG 1054
                         i i       ii       iii             vi v i       ii
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_8046504_80   1055 TTAACCTAAGGACCAAAAAATAAATCAAAGCAACAGAGT--AGAGTCCAG 1102
                         i ii v      ivi v v   i     v v  i   i --         
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_8046504_80   1103 AAATACAACTATTCATAAATGATAACTAGTTTTTTTTCAAAGGCACTACC 1152
                              v v i  v   vv   i v v v v    ivv   i  --- i  
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG---TGCC 369

  chrX_8046504_80   1153 AAAA---TTCAGTGGGGATTGCAAGGTCTTTTCACCAA-TTATACTATAA 1198
                           i ---    i      vv v vi         v   - vi i  ivi 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_8046504_80   1199 AAACTGGATACCTATATG-GAAAGAGTATACTCTGACC--------AAA- 1238
                         v         ? i i   -i     i iv v iv    -------- v -
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_8046504_80   1239 -ATTCACAATAATTGATTTGAGATGTAACCGAGAGCAAAATGCAAGAGCT 1287
                         -  vi    v    i i ii i   v v v?   v v     i       
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_8046504_80   1288 AACACTATAAAGCTTCTGGAAGGA--TATAGGAATGTATGTAGTTAATCT 1335
                           v        i  ii i    i --i     ?i iv  v vvv i i  
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_8046504_80   1336 CAGCATTAG-TGATAATTTCTTGGTCAGGATG--AAAATTGCACTATTTA 1382
                         ii -i    -ii  ii      i vi v  ii--    --    v vi- 
  L1M4_orf2#LINE/    570 TGG-GTTAGGCAATGGTTTCTTAGATATGACACCAAAA--GCACAAGC-A 615

  chrX_8046504_80   1383 ATAAGTAATAAAAAGAG-TAAATTGGACTACATGGAAATGAAAAAC---- 1427
                          i  ivi -     v  -           v   vi    v      ----
  L1M4_orf2#LINE/    616 ACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_8046504_80   1428 ATGCCCTCAAAAAATACACAATTAAGAAAGTTT---TATAATTCTCATA- 1473
                         i   i-     ii --   v  i        vv---v i  ii v  v -
  L1M4_orf2#LINE/    665 GTGCT-TCAAAGGA--CACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_8046504_80   1474 TGGTGAGAAAATATGTGCAATTCATATATCAAACAAAAGAACTT-TAATC 1522
                            -          v     v         vi i  ii  -   -  vi 
  L1M4_orf2#LINE/    712 TGG-GAGAAAATATTTGCAAATCATATATCTGATAAGGGA-CTTGTATCC 759

  chrX_8046504_80   1523 GACATTTATAATAAACT--TACAAATCAAGAA---AAAGACAAACAACCC 1567
                         iiv  v     vi    --     v    v  ---         i     
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_8046504_80   1568 TGTTTTTAGATGGGCTAATTTCTTAAAAAAATGGATAAAAGTTTTCATTA 1617
                         ----------------    ?-----        ii   i v   v v  
  L1M4_orf2#LINE/    810 ----------------AATTW-----AAAAATGGGCAAAGGATTTGAATA 838

  chrX_8046504_80   1618 GGCAATT----AATATGAGAAGATAACCAAATTTCCAGTAA-CATAGGAA 1662
                          i  v  ----  ----        vv     vv   i   -  i v   
  L1M4_orf2#LINE/    839 GACATTTCTCCAA----AGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_8046504_80   1663 AAGATATTCAACAGAAATATAAAT 1686
                              ii      vv ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (132 / 107)
Gap_init rate = 0.04 (35 / 884), avg. gap size = 2.51 (88 / 35)  


1675 28.55 9.36 1.90  chrX_8200104_8202003.rev      566  1409 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_8200104_82    566 GGAAATATATC--ATGTTTATAGTCTGGAGGACCCAATATTTTTAAGATA 613
                              v     --     i  i vi    i   ii      v       i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_8200104_82    614 CCCATTTTTCCAAGCTTG--------------TGCAATCCCTATCAATAT 649
                         v v  vi i  v iv   --------------i              v  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_8200104_82    650 TTTA-CCAAAGATTTTGTGGAAATTGTGAAACTGACTTGTAAAATTTATA 698
                         iii - iivvvv     ii       vv  i    - iv       i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATA 150

  chrX_8200104_82    699 TCCAAAGCCGAAGTACCTAAAAAGCAGCTAAGGTAGCCTTGAA---GAAA 745
                          vv   vv i i v   i i  --i   i  iii ii      ---   i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAA--TAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_8200104_82    746 AACAAAGGCCAAATACTTA-ATTTACCAGATATCAAGAATTACAACGAAG 794
                                vivi iv   i - i  v   -  v    i v    v  i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAG 247

  chrX_8200104_82    795 CTATGGTAATCAAGATAGTA--------GCACAAGAATACACTAAAAGAT 836
                            ii          i   i--------   i   i   v  vv v    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_8200104_82    837 ACATAGAAAACAGAGTCTAGAATCTAGAG-TACATCCCATATATGCA--G 883
                         vv  i   --i   i iv   i  i   i-  v -      i  vi -- 
  L1M4_orf2#LINE/    298 CAATGGAA--TAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGG 344

  chrX_8200104_82    884 TCGACATATTTATGA-AAAAGTGTTACAGCAATTCATTGGCGGGAAAGAA 932
                           i ivv    vi  -  ii   ii vii v     v   --        
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG--GGAAAGAA 392

  chrX_8200104_82    933 TGGTTGCTTAAATAGGTGTTGTTGGTTCCATTGGATTTCAATATTTTAAA 982
                          i  ivi  v  i ii  v  i   vv v i     v? v i  viv   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_8200104_82    983 -AATAAAGTTTTACCTCTACTTCAAAT---------AAATTAATATGAAA 1022
                         -   i     vv   i    i   v i---------       ivii   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_8200104_82   1023 TAGGTCACAGA--TGATCTGTAAAA--TACGAATTATAAAACTTATAGAA 1068
                          i i   ?   -- i -v     i --  -i  i         iv     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAA-ATGTAAGAGCTA-AAACTATAAAACTCTTAGAA 540

  chrX_8200104_82   1069 AAAAACA-AGAAGAATATGTTTATGAGCTTGGGATATACAACAATTT-TT 1116
                         i      -  i? v v  v  ii   v      v  vi   iii   -  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_8200104_82   1117 AAAGAGAACACAAAAATTACTAGGCA------TAAAAAACTGATAAATTG 1160
                          i v vi    v    vi  - i   ------v      iv         
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCAC-AAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_8200104_82   1161 GTTATCATTAAAATTAAAAAACTTTGCTCATCACTAGACATCACTAAGAG 1210
                          viv    i           vi    iv v   vvi    ii ii    i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_8200104_82   1211 AGTTAAAGGATA--TGATAACGAATGAGA-----------CA--TTATA- 1244
                            v   i  i --iv i --     i  -----------  -- i   -
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACA--GAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_8200104_82   1245 GTCTC-CAGAGGACTGATATTTAGAATATATTAAGAAATCCTATAAATTA 1293
                         i   v-i ii     vi   ii         v     v  i  i  v i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_8200104_82   1294 GTACAAAAAAGACAA----CTCGATT-AAACATTTTCAGAAGATTTAGAC 1338
                         i  vv          ---- i i   -   v  vvv  i i     ii i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_8200104_82   1339 AGACCATTTC--CAAATAAAGATTTCTGACTGGCCCATAAGCATATGGAA 1386
                             -     --    -i     v vii v     v       i   i  
  L1M4_orf2#LINE/    838 AGAC-ATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_8200104_82   1387 AGTTACTCAACAGCATTCCTTAT 1409
                           v i       v  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.04 (36 / 907), avg. gap size = 2.64 (95 / 36)  


1812 28.74 0.20 0.20  chrX_8238104_8240329      514  1021 (1205)    L1M4_orf2#LINE/L1        1   508 (400)  

  chrX_8238104_82    514 TGGAAAGATAGTCCATGCTCATAGATTGACAGGATTAATATCGTTAAATT 563
                                   vi     i    i     iv  iv       i     iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_8238104_82    564 GACAATACTCCCCAAAGCAATTTGCAGATTCAATGCAATCCCTATCAAAG 613
                          i              vii  i i         i               i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_8238104_82    614 TACCAATGACATACTTCACAGAAATAGGAAAA-TACTTATAATATTCATA 662
                          v   iivi v vi  ii       v iv  i- iv iv   v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_8238104_82    663 TGAAACCATAAAAGACCTCAAATAGCCAAAGCAATCCTGAACAAAAAGCA 712
                           i  viii  ii    ivi          i     i    v  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_8238104_82    713 GAAAGCTGGAGGCATCACACTACCTGACTTCAATATTTACTACAAAGCTA 762
                         v    i      vv       v  ii i     v i              
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_8238104_82    763 TAGTAAACCAAGCAGCATGGTACTGGCATAAAAACAGAAACAGAGACAAA 812
                         i     v v ii   ii              ii i   v i v   iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_8238104_82    813 TGGAACAGAATACAGAACCCAGATATAAAGCCACATGCTTAAAACCAACT 862
                              i     vv   ii     v     v   i iii   viii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_8238104_82    863 CAACTTCAACAAAGACACGAAGAACATATGATGCTGAAAAGACAGATATT 912
                         v vi   i    i iii v    v   vii   vv    ii i  viv  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_8238104_82    913 TCAATAAACAGTGGTAGGAAAGCTGTATAAGTATATGCAGAAGAATGAAA 962
                             i   ii   v i   v i   v   ?vi i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_8238104_82    963 TTAGATTTCTATCTCTCACCACACATAAAAAGCAAATAAAAAATGGATTA 1012
                           i  iii   i   v     i i i     vi  v v    -     i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGATCA 499

  chrX_8238104_82   1013 AAGACTTGA 1021
                         ?    i i 
  L1M4_orf2#LINE/    500 WAGACCTAA 508

Transitions / transversions = 1.88 (94 / 50)
Gap_init rate = 0.00 (2 / 508), avg. gap size = 1.00 (2 / 2)  

1345 23.99 6.28 0.45  chrX_8238104_8240329     1291  1736 (490)    L1M4_orf2#LINE/L1      437   908 (0)  

  chrX_8238104_82   1291 GCGACAGAATGA-----GACTC-TGCCTCA-ACAAAAAACAAAAA----- 1328
                           i v       -----   i - i     -  v v v       -----
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_8238104_82   1329 -CAAAAAAAA--AAAGACTCAAAACTATGACTTGAAAC-A-GAAACGACC 1373
                         -     vii -- ?    ii   vv  v  vi i    - -i    vvii
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_8238104_82   1374 AGAAGAAAACATTGGGG-AAATGCTCCAGGACATCAGTCTGGGCAAGGAT 1422
                                     v  ? -    -  i iv   v ii vi i     v i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_8238104_82   1423 TTCTTGAGTAAGACTTCAAAAGCACAAG-AACCAAAGCAAAAGTAAACCA 1471
                              iii  v   vi            -   v    v    i  i iv 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_8238104_82   1472 CTGGGATTACATCAAG-TTAAAAAGCTTCTGCATAGCAAAGGAAATTATC 1520
                         v v   i v      i-       -   i  iiivv       v i    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chrX_8238104_82   1521 AACCAAGTGAAGAGACAACCCACAGAATGGCAGAAAATATTTGCAAACTA 1570
                           vv       i                  v                ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_8238104_82   1571 TACATCTGATAAGTGATTCATAACCAGAATACATAAGGAGCTCGAAAAAC 1620
                           i          v  i ii  v        i    i  i   vv v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_8238104_82   1621 TTAATAA--------CAAACAATCTGACTTAAAAATGGACAAATAATCTG 1662
                          i     --------    i  i ii i ?        i    vi  i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_8238104_82   1663 AATAGGCGTTTCTCAAAAGAAGACACAAAAATGGCCATCGGGCATATGAA 1712
                              i i      v        i i v         viii   i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_8238104_82   1713 AATATACTCATCACGAATCATCAA 1736
                           v  i    v  iv ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (62 / 42)
Gap_init rate = 0.03 (13 / 472), avg. gap size = 2.31 (30 / 13)  


3093 27.10 1.00 0.55  chrX_8331890_8335863     2578  3481 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_8331890_83   2578 TGGAAAAACATTCCATGCACATGGATAGGAAGAATCAATATCGTGAAAAT 2627
                               i i  i     iv       v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_8331890_83   2628 GGACATACTACCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 2677
                           vv     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_8331890_83   2678 TACCATTGACTTTCTTTACAGAATTAGAAAAAACT-ACTTTAAATTTTAT 2726
                          v   vivi i  i   i     v v  v  i-  - iii    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_8331890_83   2727 ATGGAACCAAAAAAGAGTCCATATAGCCAAGACAATCCTAAGCAAAAAGA 2776
                               viiv  ii  vi viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_8331890_83   2777 ACAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTACACTACAAGGCT 2826
                               i      vv   ii  v  ii        vivi       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_8331890_83   2827 ACAGTAACCAACACAGCATGGTACTGGTAACAAAACAGATATATAGACCA 2876
                                i   v    ii         i vv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_8331890_83   2877 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 2926
                               i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_8331890_83   2927 TGATCTTTGACAAACCTGACAAAAGCA----ATAAGGAAAGGATTCCCTA 2972
                             i  i     ivv  v   i v  ----  ii      i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_8331890_83   2973 TTTAATAAACGGTGCTGGGAAAACTGACTAGCCATATGCAGAAAACTGAA 3022
                           i  i   i          v     iv  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_8331890_83   3023 ACTGGGTCCCTTCCTTTCACCTTATACAAAACTTAACTCAAGATGGATTA 3072
                         ii   ii    v   iv    v         v         i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_8331890_83   3073 AAGATTTAAATGTTAGACCTAAAACCATAAAAACACTAGAAGAAAACCTA 3122
                         ?   ii       v   v       i      vivi           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_8331890_83   3123 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 3171
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_8331890_83   3172 CACCAAAAGCAATTGCAACAAAAGCCAAAGTTGACAAATGGGATCTAATT 3221
                                    vvv          vv   i v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_8331890_83   3222 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAGAGTGAACAG 3271
                            v v  i i   i  ii vv    i  v    v  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_8331890_83   3272 GCAACT-ACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGTCAAAG 3320
                         i    i-                 v       vii  vi     vi  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_8331890_83   3321 GGCTAATAATATCCAGAATCTACAGGAAACAAATA-AATTTA-CAAGAAA 3368
                          i  -- i-          v  i iii   vvv  -  i i -i  v   
  L1M4_orf2#LINE/    749 GACT--TG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_8331890_83   3369 AAAACAAACAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 3418
                           i     i   i v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_8331890_83   3419 CTCAAAAGAAGACATTTATGCGGCCAATAAACGTATGAAAAAAAGCTCAC 3468
                            v        i  vi vii         i ii       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_8331890_83   3469 CATCACTGGTCAT 3481
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2391 27.51 0.68 0.68  chrX_8550112_8556539     5124  5861 (567)    L1M4_orf2#LINE/L1        1   738 (170)  

  chrX_8550112_85   5124 TGGAAAAATATTCCATGCTCATGGATAGGAAAAATCAATATTGTGAAAAT 5173
                               i    i     i        v    i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_8550112_85   5174 GGCCATACTGCCCAAAGTAACTTATAGATTCAATGCTCTCCCAATCAAGC 5223
                            v     v      v i ii  i        i  vv    v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_8550112_85   5224 TACCA-CTGACTTTCTTCAAAGAAATGGAAAAAACTACTTTAAATTTCAT 5272
                          v   -   v    i  -iv      v  v  iviv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_8550112_85   5273 ATGGAACCAAAAAAGAGCCCGCATAGCCAAGACAATCCTAAGCAAAAAGA 5322
                               viiv  ii  v  v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_8550112_85   5323 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5372
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_8550112_85   5373 ACAGTAACCAAAACAGTGTAGAACTGGTATCAAAACAGATATATAGATCA 5422
                                i   i       i v     i  v ii i   i          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_8550112_85   5423 ACGGAACAGAACAGAGGCCTCAGAAATAACACAACACATCTATAACCATC 5472
                          i    i    iv   ivii         vv v i    i   iii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_8550112_85   5473 TCGTGTCTGACAAACCTGACAAAAACAAGAAATGTGGAAAGGATTCCCTG 5522
                          vi v ii     ivv  v   i v  vvv    v      i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_8550112_85   5523 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAGCCAGAAAACTGAA 5572
                           i  i        i     v      v  ?   i vv  i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_8550112_85   5573 ACTGGACCCTTTCCTTAAGCATTATACAAAACTTGGCTCATGATGGATTA 5622
                         ii       i v   i vi vv         v  ii    vi      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_8550112_85   5623 AAGACTGAAACGTAAAACCTAAAACTATAAAAACC-CAGAAGAAAACCTA 5671
                         ?    iv   i    i v              vi -i          v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_8550112_85   5672 GG--TAATACCATTCAGGACATAAACATGGGCAAAGACTTCATGACTAAA 5719
                           --   - i -   iv   v viivv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    550 GGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_8550112_85   5720 ACACCAAAAACAATGGCAACAAAAGCCAAAACTGACAAATGGGA-TCTAC 5768
                                  i  vvi          vv    iv  i    v   - ii i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_8550112_85   5769 CTAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATCATCAGAGTGAAC 5818
                          v   i    i -   i  iv vv    i  v       vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_8550112_85   5819 AGGCAACCTACAGAATGGGAGAAAAAAGTGGGCAAAGTATATA 5861
                           i     i                v v -v     vi     
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATT-TGCAAATCATATA 738

Transitions / transversions = 1.18 (109 / 92)
Gap_init rate = 0.01 (9 / 738), avg. gap size = 1.11 (10 / 9)  

 263 22.97 0.00 0.00  chrX_8550112_8556539     5862  5935 (493)    L1M4_orf2#LINE/L1      835   908 (0)  

  chrX_8550112_85   5862 AACAGACACTTCTCAAATGAAGACATCTATGCTGCCAATAAACATATGAA 5911
                           i     i     v  v     i  vi viiv        i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_8550112_85   5912 AAAAAGCTCATAATCACTGGTCAT 5935
                           i v     vv    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.00 (0 / 0)  


3096 27.20 0.66 0.66  chrX_8710191_8716123.rev     4535  5442 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_8710191_87   4535 TGGAAAAACATTCCGTGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4584
                               i i  i  i  i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_8710191_87   4585 GGCCATATTGCCCAAAGTAATTGATAGATTCAACACTATCCTCATCAAGC 4634
                            v   i v      v i  iv i         i v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_8710191_87   4635 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 4683
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_8710191_87   4684 ATGGAACCAAAAAAGAGCCTGTATAGCTAAGACAATCCTAAGCAAAAAGA 4733
                               viiv  ii  v  v v     i  i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_8710191_87   4734 GCAAAGCTGGAGGTATCAAGCTACCTGACTTCAAACTATACTACAAGGCT 4783
                         i     i      vv   vi  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_8710191_87   4784 ACGGCAATCAAAACAGCGTGATACTGGTACCAAAACAGATATATAGACCA 4833
                           i i      i    i   i      i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_8710191_87   4834 ATGGAACAAAACAGAGGCCTCAGAAATAATGCCAAACATCTACAGCCATC 4883
                               i i  iv   ivii         vv   v    i  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_8710191_87   4884 AGATCTTTGACAAACGTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 4933
                         v   i  i     iv   v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_8710191_87   4934 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCACATGCAGAAAACTGAA 4983
                           i  i        i     v      v  ?         i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_8710191_87   4984 ACTGGACCCCTTCTTCGCACCTTACACAAAAATTAACTCAAGATGTTTTA 5033
                         ii         v i  i    v  i                i   vv i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_8710191_87   5034 ATGGCTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5083
                         ?v i i    ii     v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_8710191_87   5084 GGCATTACCATTCAGGACATAGGCATGGGCAAAGACTTC---AATACTAA 5130
                           ?i v viv   iv   v v  vv i     v ii   ---i   i---
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT--- 596

  chrX_8710191_87   5131 AACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGATAAAATGCGATCTA 5180
                         i            vvi   i      vv     v      v  -  ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG-GACTTC 645

  chrX_8710191_87   5181 ATTACACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATGAGAGTGAA 5230
                           i v v v  i i   i  ii vv    i  v       v  i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_8710191_87   5231 CAGGCAACCTAGAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5280
                         v  i     i v               v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_8710191_87   5281 AAGGGGTAATATCCAGAATCTACAAGAAACTTAAACAAATTTACAAGAAA 5330
                          i  iv vi          v  i  ii    ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_8710191_87   5331 AA-ACAAACAACCCCATC-AAAAATGGGCAAAGGATATGAACAGACACTA 5378
                           -     i     v  i-                 v    i     i v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_8710191_87   5379 TTCAAAAAAAGACATTTATGTGGCAAACAAACATATGAAAAAAAAGCTCG 5428
                         i  v   i    i  vi vi    v  i  i  i       i v-    i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCA 894

  chrX_8710191_87   5429 TCATCACCAGTCAT 5442
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3080 25.22 1.43 1.86  chrX_8739894_8742582     1285  2196 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_8739894_87   1285 TGGAAAAGCATTCCATGTGCGTGGATAGGAGAAATCAATATTGTTAAAAT 1334
                               iii  i      v i     v   ii v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_8739894_87   1335 GGCCATACTGTCCAAAGCAATTTACAGATTCAATACTATTCCTATGAAAC 1384
                            v     vi     vii  i           ii v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_8739894_87   1385 TACCAGTAACATTCTTCACAGGAATAGAAAAAAATATTTTAAAATTCATA 1434
                          v    ivi v  i  ii   i   v  v  ivvv  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_8739894_87   1435 TGGAACCAAAAGAGAGCCTGAATAGCCAAGGCAATTCTAATCAAAAAGAA 1484
                              viiv   i  v  v          ii    ii i vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_8739894_87   1485 CAAAACTGGAGGCAACATGCTACCTGACTTCAAACTACC--CTATAAGGC 1532
                             ii      vvv  ii  v  ii i      --  i--   i  i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAGC 248

  chrX_8739894_87   1533 TGCAGTAACCAAAACAGCATGGTACTAGTTCAAAAATAGACATATAGACC 1582
                          i      i   i    ii       i ivi  ii             i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_8739894_87   1583 AGTGAAACAGAATAGAGAGCCCAGAAATAATGCCACACACCTACAAACA- 1631
                          i  i  i     v     i          vv   i   ii  iiiv  -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_8739894_87   1632 TTGGTCTTTGACAAAGCTTGACATAAACAAGCAATGGAGAAAAGATTCCC 1681
                            i i  i     i v - v  vi v  vv      i    ii  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_8739894_87   1682 TATTCAATAAATGGTGCTGGAATAACTGGCTAGTCATATGAAGAAGATTT 1731
                          v     i            i i      v  ?i  i   v i    v v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_8739894_87   1732 AAACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGAT 1781
                           ii         v   i                 i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_8739894_87   1782 TAAAGACTTAATTGTAAAACCTAAAACTCTAAAAAACCTGGAAGATAACC 1831
                         i ?    i   v     i v        v     vv i i     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_8739894_87   1832 TAGG---AAATACCATTTGAGACACAGACCCTGGCAAAGATTTC---AAT 1875
                             ---    -- -  i v   viv iviiv     v i    ---i  
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_8739894_87   1876 GCAAAGATGCCAAAAGCAACTGCAACGAAAACAAAAAAT-GATGAATAGG 1924
                         --- v  ii         vvv     -    v       -   i   v  
  L1M4_orf2#LINE/    595 ---ATGACACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGG 640

  chrX_8739894_87   1925 ATCTAATTAAA-TGAAAGAGCTTGTGCACAGCAAAAGAAACTATCAACAG 1973
                          ii v  i   - v   i -   v  ii vv    i  v        v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_8739894_87   1974 AGTAAAGGGACAACCTACAGAATGGGAGAAAATTTTTGCAAACTATGTAT 2023
                            i  ii       i                 v        ii  i   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_8739894_87   2024 GCAACAAAGGTCTGTTACCAAGAATCTATAAGGAATTTGAACAAATTAAC 2073
                         vii i  i  v  vv  i v     v     i   i ivv    v i  i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_8739894_87   2074 AAGCAAAAAAAAAAAAAAAAAACC--ATTAAAAAGTGGGCAAAGGACATG 2121
                           v-----     i v   v    --   ?    i           iv  
  L1M4_orf2#LINE/    790 AAT-----AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_8739894_87   2122 AACAGACACTTTTCAAAAGAAGACATATATGTGGCCAACAAGCATATTTA 2171
                           i     i  i  v        i   i vi       i     i  v- 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-A 883

  chrX_8739894_87   2172 AAAAATGCCCAACATCACTAATTGT 2196
                            i    i        ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (138 / 89)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


2662 25.79 5.74 0.94  chrX_8770568_8772408      500  1352 (489)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_8770568_87    500 ATGGTGATTAATTAGAA-----AATATTGTTAAAATGTTCATAATGCTCA 544
                            v v  vi   i   -----           i   viv   v v i  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_8770568_87    545 AAGCAATCTACAAATTCAATGCAATTTCTTTCAAAGTTGCAATGGCATTT 594
                           vii       i      i     ii  v     i iv  iiv  v   
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_8770568_87    595 TTCATAGAAATAGGGAAAA-AATCTTAAAATTCATAAAGAACCACAAAAG 643
                           iii      v iv  iv-i   i           vi   vii   ii 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_8770568_87    644 ATCCC-AATAGCCCATTTATTCTTGGACAAAAAAAA-AAAGCTGGAGGCA 691
                          i  v-       v vvi v     i v  i  i  -    i      vv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_8770568_87    692 TCATACTGCTTGAATTTTAAATTATACTGCAAAGCAATACTAATAAAAAC 741
                            i   v ii-     i   viv    i      v i v    v  i  
  L1M4_orf2#LINE/    215 TCACACTTCCC-AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_8770568_87    742 AGTATTCTCCAATG--ATAAAAACAGATACATAGACCAATGGAAGAGAGT 789
                            i vv v --  --    ii i   i i     i        v   i 
  L1M4_orf2#LINE/    264 AGTGTGGTAC--TGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_8770568_87    790 AGAGGG-CCAGACATAAGCC-ACACATATA-AGTGTATTGAT-------- 828
                         v   i -     v    i  - i    v  -i  vv      --------
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_8770568_87    829 ---------AAAT-ATACGATGGAAAAAGGACAGTCCCCTTAACAAATTG 868
                         --------- i i-  v i    ii    i i    iii i       v 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_8770568_87    869 TGTTGGGAAAACTTGATAACCACATACAGAATGATAAAATTGGACA--TA 916
                           i     v    v    ?      i  i  vi  i  i      v--  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_8770568_87    917 TGTTACACCATATACGAACATTTACTTGAAATGGATTAAAGACTTAAATG 966
                         iv i           i  v   v   ii        i ?    i      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_8770568_87    967 TAAAACCTGAAGTCATAAAATTCCTAGAAGAAAACACAGGGAAAAAGTTC 1016
                            i v  i  iii      i  i            i   ?iv   vi i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_8770568_87   1017 CATGACATTTTTCTGGGCAATGATTT-TTGGATATAACCTCAAAAGCACA 1065
                          i    v  vvvi i       i   -  i     i  vi          
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_8770568_87   1066 GGCAGCAAAAGCAAAAAATACATAAATGGGATTACAACAAGCTAAAAAGC 1115
                         i   i      -        v      v   i v  v   iv v    i 
  L1M4_orf2#LINE/    612 AGCAACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_8770568_87   1116 TTCTAAACAGCGTAAAAGA----ATTAATAGAGTGAAGAGACAATCTATG 1161
                           i ivi vv --   i  ----  i  v i      i      i i ii
  L1M4_orf2#LINE/    661 TTTTGTGCTTC--AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_8770568_87   1162 CCATGGTAGAAAATATTTGCAAATCATATATCTGATAATTAGTTAATATC 1211
                         vv    v                               vviii vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_8770568_87   1212 CAAAATACGTAAAGAACACATGCGACTCAATAGCAAGAAAACAAATAACC 1261
                           i    ii        v v i i        ii  i  i          
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_8770568_87   1262 CAATTTTTTAAAATGGGCCAAGGATCTGAATAACCATTTTTGCATAGAAG 1311
                              ?v--         v      i      iv     i v  v     
  L1M4_orf2#LINE/    809 CAATTWA--AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_8770568_87   1312 ACATACA--TG---------TATGTGAAAAATTGCTAAACCTTATTAATC 1350
                          i     --  ---------i ii      iv    v   v i ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_8770568_87   1351 AT 1352
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.60 (133 / 83)
Gap_init rate = 0.02 (20 / 894), avg. gap size = 2.85 (57 / 20)  


3080 27.46 1.00 0.44  chrX_9281169_9286625     4062  4964 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_9281169_92   4062 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAG 4111
                               i i  i     i        v      v i i   ii v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_9281169_92   4112 GGCCATATTGCCCAAAGTACTTTATACATTCAATGTTGTTCCTGTCAAAC 4161
                            v   i v      v iv i  i v      i ivi i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_9281169_92   4162 TACCATTGACATTCTTCACAGAATTAGGAAAACCTATTTTAAATTTCATA 4211
                          v   vivi v  i  ii     v v iv  i iv  ii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_9281169_92   4212 TGGAA-T-CAAAGAAGATCCCACGTAGCCAAGACAATCCTAAGCAAAAAG 4259
                              - -   i --  i  vivi       i      i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_9281169_92   4260 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGT 4309
                                i      vv   ii  v  ii i      viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_9281169_92   4310 TACATTAACAAAAACAGCATGGTATGGGTACCAAAACAGACATATAGACC 4359
                             v   iv  i    ii     iv  i iv ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_9281169_92   4360 AGTGGACCAGAACAGAGACCTCAGAAATAACACCATACATCTGTAACCAT 4409
                          i    vi    iv    vii         vv        i i iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_9281169_92   4410 CTGATCTTCGACAAATCTGCCGAAAACAAGCAATGGGGAAAGGATCTCCT 4459
                         i    i        ivv    i i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_9281169_92   4460 TATTCAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGCTGAAAACTG 4509
                          -    ii              v      v  ?   i    vi  i v  
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_9281169_92   4510 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATAGAT 4559
                           ii         v   i     v              i    i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_9281169_92   4560 TAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGATAACC 4609
                         i ?    i         i v i     i      vi i       v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_9281169_92   4610 TAAGCA-ATACCATTCATGACATAGGCATGGGCTAAGAGTTCATGACTAA 4658
                           i ?i- v i -   i    v v  vv i   v v iv   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_9281169_92   4659 AACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4708
                         i            vvv          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_9281169_92   4709 TTCAACTAAAGAGCTTCTGCTCAGTAAAAGAAACTATGATCAGAGTGAAC 4758
                          iv  v v  i i   i  iv vvi   i  v     v vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_9281169_92   4759 AGGCAACCTACAGAGTGGGAGAAAACTTCTGCAATCTACCCATCTGACAA 4808
                           i     i     i          iv i     vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_9281169_92   4809 AGGTCTAATATCCAGAATTTGCAAGGAACT--TA-AACATATTTACAAGA 4855
                         i  v  vi          v ii  i     --  -   vi v v i  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_9281169_92   4856 AAA-AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 4904
                          i -   i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_9281169_92   4905 TCAAAAGAAGACATTTACACAGCCAACAAGCA--TGGTAAAAAGCTCAAC 4952
                           v        i  vi v ii     i     --  iv  i v       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_9281169_92   4953 ATCACTGATCAT 4964
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3961 17.08 1.19 3.11  chrX_10179053_10182344.rev     1458  2294 (998)    L1M4_orf2#LINE/L1        3   823 (85)  

  chrX_10179053_1   1458 GAAAAACATCCCATGTTTCTGGATTGGAAGAC--AATATTGTTAAGATGC 1505
                             i i          iv             --               v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_10179053_1   1506 T----CTCCCCAAAAAGACC-ACATATTCAATGCAAATACTATTGAGATC 1550
                         i----         vv  i -   v      i    viv    ii i   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_10179053_1   1551 CTAAC-AAATTTTTTGTAGAAATAGAAAAATTCACTGTAAAATTAATATG 1599
                          i i -ivv       i      v  v  ii v iiv       v     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_10179053_1   1600 GAATCTCAAGGAATTCTGGATAGTCAAAACAACTTTGTTCAAGAACAAAG 1649
                            viv     i ii v i    i        ii   ------  -    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG------AA-AAAG 195

  chrX_10179053_1   1650 TTCTTTTTCAAGAACAAAGTTGGAGGTCTCACACTTCCTGATTTCAAAAC 1699
                         ---------                 v           ii          
  L1M4_orf2#LINE/    196 ---------AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_10179053_1   1700 TTACTGCAAAACTGCAGTAATCAAAACAGGGTGGTACTCACATAAAGACA 1749
                              i    i  i          i    v        vi     i  i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_10179053_1   1750 GACATATAGGCTAATGGAATAGAATAGAGATCCCAGATATATAAACCCTT 1799
                                  iii             v    vi     - -        v 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGA-A-ATAAACCCAT 334

  chrX_10179053_1   1800 ACATATATGGTCAAGTGATTTCCAACAAGGGTGCCAAGACCATTTAATGG 1849
                             v         v      i i                    i     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_10179053_1   1850 AGAAAGAAGAGTCTTTTCAACGAACGGTTTTGGGAAAACTGGATATTCGC 1899
                         i       v            i  i   vi     v         ?i i 
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_10179053_1   1900 ATCCAAAAAGATTAAATTGGATCCTTATCTTACACCATATACAAAGATTA 1949
                           v     ii  v  i     i  i  i  i              i    
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_10179053_1   1950 ACTAAAAATAGATAAAATATCTGTAAACATAAGAGCTAAAACTATAAAAC 1999
                            v     i   v ? v i  --   ii                     
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCT--AAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_10179053_1   2000 TCTTAGAAGAAAACACAGGGGAAAAGCTCCTTGACATTAAGTTTGGCAAT 2049
                                        i   ? v   v  i v    v  ii   v      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_10179053_1   2050 GATTTCTCGAATATGACACCAAAAACACAGGCAACAGAAGAAGAAAACCC 2099
                          i     iii              i    i      i     -    ivv
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA-AAAATAG 631

  chrX_10179053_1   2100 ATAATTTGGACCACAGAAAAATTTGAAAACTTTTGCCCATCAAAGGGCAC 2149
                             v      iv  vv      -i          iv v       i   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_10179053_1   2150 TATCAACAGAGTGAAAAGGCAACCCATAGAATGGGAGAAAATATTTGCAT 2199
                               v i         i       i                      v
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_10179053_1   2200 ATCATATATCTGATAAGGGGTTGATATCCAGAATATATTCAGAACTCCTA 2249
                                            ii vi              vv       i  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_10179053_1   2250 CAAGT-AA-AACAACTAAAAACAAACACAACCCAGTTTAAAAATGGG 2294
                            v -  -  i  --   i     i --     i  ?         
  L1M4_orf2#LINE/    781 CAACTCAATAATAA--AAAGACAAATA--ACCCAATTWAAAAATGGG 823

Transitions / transversions = 1.67 (87 / 52)
Gap_init rate = 0.02 (16 / 821), avg. gap size = 2.25 (36 / 16)  

 538 14.42 2.88 0.00  chrX_10179053_10182344.rev     2698  2801 (491)    L1M4_orf2#LINE/L1      802   908 (0)  

  chrX_10179053_1   2698 AATGGCCTAAT---ACAACGGGCAAAGGACTTGAATAGACAGTTCTCAAA 2744
                            ii  i   --- v  i          i           v     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_10179053_1   2745 AGAAGATATATAAATGGCCAATAAACACACGAAAAGGGATTCAACATCAT 2794
                                   i             i    i      ivii         ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_10179053_1   2795 TAATAAT 2801
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.01 (1 / 107), avg. gap size = 3.00 (3 / 1)  


 647 28.19 3.52 1.76  chrX_10265831_10268666.rev      710   936 (1900)    L1M4_orf2#LINE/L1        8   238 (670)  

  chrX_10265831_1    710 ATGTATCATGTT-ATGGGGTA-AAGACTCAGAAAAGTTATGATTTCTGTT 757
                           i vi      -    iv i-      i iv vv    v   vv vi v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_10265831_1    758 CTTTCCACATCAACCTGTAGATTCAACATAATCTCAATGAAAATTCCAGC 807
                           ii   v  ii i  ii         ii    i v  v     i     
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_10265831_1    808 AGGTTATTTTGCAGAAATTGACAAGCCGATTCTAAAGTTCATATTAGAAT 857
                         v vi v                    i   i     i       vii   
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_10265831_1    858 GCAAAGGATATAGCATAATCATTTAAA--ACTTTGAAAAATAG--ACCGG 903
                             i   ivi  v   ii  ---   -- ii        v i--  vii
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCA---AAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_10265831_1    904 GTGCGGTGG-CTCACACCTAT-AATCCCAGCACTT 936
                           -i  v  -       i vi-   ii  iv    
  L1M4_orf2#LINE/    205 GT-TGGAGGACTCACACTTCCCAATTTCAAAACTT 238

Transitions / transversions = 1.67 (40 / 24)
Gap_init rate = 0.03 (8 / 231), avg. gap size = 1.50 (12 / 8)  

2544 23.56 2.80 0.88  chrX_10265831_10268666.rev     1176  1854 (982)    L1M4_orf2#LINE/L1      166   857 (51)  

  chrX_10265831_1   1176 CTCAAAAAAAAAAAAAAAAACTTTGAAAATAATAACAAAGTTGGAGAACT 1225
                          i  i  v ivv    v  v   vi    v  v             i   
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_10265831_1   1226 AACATCAGCTGATTTCAAGATTTATTATAAGGCTTCAGAAATCAATATAA 1275
                         v   iivv ii       i i   i  i  i   v   v      v i i
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_10265831_1   1276 GGTGGTATTTGTATAAAGATAGACAAATAGATCAAAGGATCAGCAAAAAG 1325
                         v      i v i    i        v         v   vi  v vvi  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_10265831_1   1326 ACTTGAGAAGTAGATTCATACATATATGGACAAGTGATTTTCAACAAAGA 1375
                          v iv    i  i ii       v     v   v        i    i i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_10265831_1   1376 TGCAAAGGCAATTTCAGTGGAGAAAGGATTGTCTTTTTAGTAACTGGTGC 1425
                            v   i v   -  i   i     i  v       i ii  v      
  L1M4_orf2#LINE/    366 TGCCAAGACCATT-CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_10265831_1   1426 TGGAGCAATTGGATATCTGTATGTAAGAATATGAAGTTTGATCCATACTT 1475
                            ii   i      ? iii   i  i iv        v  i  v   i 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_10265831_1   1476 CACATTATATACAAGACTTTACTCAAAATTGATTATATATCTAAATGTAA 1525
                             ii        i v  v         v   i ? v i          
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_10265831_1   1526 AAGGTAAAAGCTGTAAAACTCCTAGAAGAAAACGT-GGAGGAGATCTT-- 1572
                         i  v     -  i        i           i -  ? v i     --
  L1M4_orf2#LINE/    515 GAGCTAAAA-CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_10265831_1   1573 -GACCTTGGGTTAGGCAAAGATTCTTTACATACAGATGACAAAAGCATTA 1621
                         -                 v i  ii   v   i-  iiv        iv 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCACAA 612

  chrX_10265831_1   1622 TCCATAAAAGAAAATATTTATATGTTGGGTTTCATCAAAATTAAAAACCT 1671
                         v v i         v  vv   vi    ii                  i 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_10265831_1   1672 -----CTTCAGAATGCACTGTTAAGAGACTGAAAAGACCAACCACAAACT 1716
                         -----     i ivi    i i    i v         v v     i v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_10265831_1   1717 AGGCGAAAATATTTACAAATTATTTATTTTAATAAAGGA-TTGTATCCAG 1765
                         i  v          i     i  v   i -i    i   -          
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCT-GATAAGGGACTTGTATCCAG 761

  chrX_10265831_1   1766 AATATATAACAAATTCTCAAAACTCATTAATAAGAAAACAAG---CCT-- 1810
                                  vi  i   i v      v      i  i    i---  i--
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_10265831_1   1811 TTCACCAAAATGCATAAAAGATTTGAA--AAC--TTTACCAAAGAAGA 1854
                           ? --      vii   i        --i  --  iv          
  L1M4_orf2#LINE/    812 TTWA--AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

Transitions / transversions = 1.52 (94 / 62)
Gap_init rate = 0.02 (13 / 692), avg. gap size = 1.92 (25 / 13)  

 235 14.29 0.00 2.04  chrX_10265831_10268666.rev     2297  2345 (491)    L1M4_orf2#LINE/L1      861   908 (0)  

  chrX_10265831_1   2297 ACAGATGGTAAATAAGCACGTGAAAAGATGGTTCAGTATCATTAGTCAT 2345
                            i    iv         i          -i   ii    ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATG-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 6.00 (6 / 1)
Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1)  


3060 27.23 0.66 0.55  chrX_10337554_10339909      957  1863 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_10337554_1    957 TGGAAAAAAAATCCATGCTCATGGAT-AGAAGAATCAGTATCGTGAAAAT 1005
                               i v vi     i        -i     v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_10337554_1   1006 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 1055
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_10337554_1   1056 TACCATTGACTTTCTTCACAGAATTAGAAAAGCT-ACTTTAAATTTAACG 1104
                          v   vivi i  i  ii     v v  v     - iii    v  v ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_10337554_1   1105 TGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAATCGAA 1154
                              viiv  ii  v  viv        i      i i iv  ivv   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_10337554_1   1155 CAAAGCTGGAGGCATCACACTACCTGACTTCAAA--CTA-TACGAGGCTA 1201
                              i      vv       v  ii i      --i  -   i i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_10337554_1   1202 CAGTAACCAAAAACAGCAGGGTACTGGTACCAAAACAGATATATAGACCA 1251
                               i   i -   iiv        i iv ii i   i       i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_10337554_1   1252 ATGGAACAGAACAGAGACCTTGGAAATAACACCACACATCTACAACCATC 1301
                               i    iv    viiii       vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_10337554_1   1302 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATTCCCTA 1351
                             i  i     ivv  v   i v  vv      i     i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_10337554_1   1352 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACAGAA 1401
                           i  i        i     v      v  ?   i     i  i vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_10337554_1   1402 ACTGAACCCCTTCATTACATCTTATACAAAAATTAACTCACGATGGATTA 1451
                         ii  i      v v i   i v                  vi      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_10337554_1   1452 AAGACTTAAATGTAAAACCCCAAACCATAAAAACCCTAGAAGAAAACCTA 1501
                         ?    i         i v iv    i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_10337554_1   1502 GGCA-ATACCATTCAGGACATAGGCATGGGCAAGGATCTCATGACTAAAA 1550
                           ?i- v i -   iv   v v  vv i     v i i  v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_10337554_1   1551 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 1600
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_10337554_1   1601 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 1650
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_10337554_1   1651 ACAACCTACAGAATGGGAGAAAAATTTTACAATCTACCCATCTGACAAAG 1700
                               i                vv   i   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_10337554_1   1701 GGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAA 1750
                          i  vi          v  i        ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_10337554_1   1751 TCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 1800
                         v    i     v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_10337554_1   1801 AAAAGAAGACATTTATGCAGCCAACAAACATATGAAGAAAAAAAGCTCAT 1850
                         v        i  vi viii     i  i  i     ---  i v     v
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAA---AAGATGCTCAA 895

  chrX_10337554_1   1851 CATCACTGGTCAT 1863
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3211 26.98 0.66 0.66  chrX_10415362_10421702     4941  5848 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_10415362_1   4941 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4990
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_10415362_1   4991 GGCCGTACTACCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5040
                            vi    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_10415362_1   5041 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5088
                          vi  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_10415362_1   5089 TATGGAACCAAAAATGAGCCCACATTGCTAAGACAATCCTAAGCCAAAAG 5138
                                viiv  iv  v  viv  v  i  i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_10415362_1   5139 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGTT 5188
                                i      vv    i  v  ii i      viv        ivi
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_10415362_1   5189 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGACC 5238
                                 i   i    ii  i      i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_10415362_1   5239 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5286
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_10415362_1   5287 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAAGATTCC 5336
                          vi    i  i     ivv  v   i v  vvv          ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_10415362_1   5337 CCATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5386
                          iv  i  i        i     v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_10415362_1   5387 GAAACTGGATACCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 5436
                            ii    iv   v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_10415362_1   5437 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5486
                          i ?    i           v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_10415362_1   5487 CTAGGCA-ATACCATTCAGAACGTAGGCATGGGCAGGGACTTCATGTCTA 5535
                         v    ?i- v i -   ivi  v v  vv i    iv ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_10415362_1   5536 AAACACCAAAAGCAATGGCAACAAAAGCCAAAAAT-GACAAATGGGATCT 5584
                         vi            vvi          v-      -  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTT 644

  chrX_10415362_1   5585 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5634
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_10415362_1   5635 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGAC 5684
                          v  i     i                 v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_10415362_1   5685 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5734
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_10415362_1   5735 AAAATCAAACAGCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5784
                            iv    i i   v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_10415362_1   5785 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACGTGAAAAAATGCTCA 5834
                             v        i  vi viii     i ii   i      i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_10415362_1   5835 TCATCACTGGCCAT 5848
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (150 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3146 28.22 0.44 0.33  chrX_10492336_10498735     5001  5907 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_10492336_1   5001 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5050
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_10492336_1   5051 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5100
                           iv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_10492336_1   5101 TACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 5150
                          v   iivi i  i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_10492336_1   5151 TGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGAA 5200
                              viiv  ii  v  v v  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_10492336_1   5201 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5250
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_10492336_1   5251 CAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATACAGACCAA 5300
                               i   i    ii  i      i iv ii i   v   i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_10492336_1   5301 TGGAACAGAAC--AGGGCCCTCAGAAATAATGCTGCATATCTACAACTAT 5348
                              i    i--  i i  --        vv iii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_10492336_1   5349 CTCATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5398
                         i v  i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_10492336_1   5399 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCTGA 5448
                         v  i  i              v      v  ?i  i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_10492336_1   5449 AACTGCATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGATT 5498
                          ii  v i    v   i     v     v        i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_10492336_1   5499 AAAGATTTAAATGTTAGACCTAACACCATAAAAACCCTAGAAGAAAACCT 5548
                          ?   ii       v   v    v  i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_10492336_1   5549 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTACA 5597
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  ii
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_10492336_1   5598 ACACCAAAAGCAATGGCAACAAAAGCGAAAATTGACAAATGGGATCCAAT 5647
                                     vvi          vi     v  i    v   iiiv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_10492336_1   5648 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTACCATCAGAGTGAACA 5697
                         i   v v  i i   i  ii vv    i  v i  i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_10492336_1   5698 GGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5747
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_10492336_1   5748 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5797
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_10492336_1   5798 AACAAAGAACCCCATCAAAAAGTGGGCAAAGAATATGAACAGACACTTCT 5847
                         i     v     v  i?    i         i  v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_10492336_1   5848 C-AAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 5896
                          -        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_10492336_1   5897 TCACTGGCCAT 5907
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (153 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


1163 29.63 1.71 0.00  chrX_10509271_10511997     1003  1353 (1374)    L1M4_orf2#LINE/L1        1   357 (551)  

  chrX_10509271_1   1003 TGGAGGCATATACCATGATTAGGGATTATAAAATTCAACATTGCTAAAAT 1052
                             iiv    v     v i v     iv  i i i  i    i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_10509271_1   1053 GTCAATTCTCCCCTAATTGATCTATAGAGTCAATACAACTTCAATTAAAA 1102
                          v    v      v          i   v    ii   iii v  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_10509271_1   1103 GCTTTACAAGTTGTTTTGTAGAAACTGACAAGTTGATTCCAACATTTATG 1152
                         v iivi vivi v     i     i       i    i i  v   i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_10509271_1   1153 TGAAAATGCAAAAGAATTAGAACAGCCAAA-CAATCCTTAA-CAGAATAA 1200
                           i        ii  vii    i       -     i v  -v    v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_10509271_1   1201 CAAAGTTAAAGAACCCATCCTACTCTATTTAAAAACTAACTATAACATGA 1250
                                ii  i  i  iv  v i v    v      v    i  viiv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_10509271_1   1251 CAGTAGCTGACATCATTTATTTTTGGCTTAAGGACAGA--TTGAGACCAA 1298
                              iiii v ivi v iv vi    v      i   -- vv   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_10509271_1   1299 GGAAACAAAAT--AGAGTCCAGAAATACATTTTCACATACATGGTAAGTT 1346
                         v i  i i   --              v iiivi    vi     v i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_10509271_1   1347 GATTTTC 1353
                                
  L1M4_orf2#LINE/    351 GATTTTC 357

Transitions / transversions = 1.60 (64 / 40)
Gap_init rate = 0.01 (4 / 357), avg. gap size = 1.50 (6 / 4)  

1442 24.01 3.43 6.35  chrX_10509271_10511997     1667  2249 (478)    L1M4_orf2#LINE/L1      343   908 (0)  

  chrX_10509271_1   1667 GGTAAGTTGATTTTCAATAAAGAGGCCAAGGTAACTAAATGGGGAAAAGA 1716
                            v i         i i  i iv      iiv i v          -  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GA 391

  chrX_10509271_1   1717 ATCATCATTTCAATAAATGGTGCTAGAATAACTAGATAATCATTTGAGTA 1766
                           vi  v      i          i i i    i    ?i  iv  vi- 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-A 440

  chrX_10509271_1   1767 AAAAATGAACCCTCACCTCTACCTCACACTACACACAGTCATTAATTTGA 1816
                           i      viivv   i           i i i   ivv     i ii 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_10509271_1   1817 GATAGATCATAAACCTAAACTTAAAAGCAAAAGCTAGAAAACTTCTAGAA 1866
                         i  i     ? i       iv   i   v   i   v      ii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_10509271_1   1867 AAAATCAGAGGCAAACATCT-CACAACCATAGGGCAGGAAAATTTTTTTT 1915
                         i   v  v   ?iv v    - iii   v i  vi   v  vvv   i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_10509271_1   1916 AGAGAGGGTGCAAAATGTAATAAACA-TAAAAGAAAAAATAAA--AATTG 1962
                            v v iii v   v i -i  i  -i             i --     
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_10509271_1   1963 TATTT-ATTATAAATTCAAAAGTT--GTGCTTATCAAAATACACT-TGAA 2008
                         v i  -  i -     v    v  --      --    iv     - v  
  L1M4_orf2#LINE/    640 GACTTCATCA-AAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAA 686

  chrX_10509271_1   2009 AAA--TGAAAAGGCAAGCTATACATTGAAAAGAATATTGGGAAGACTATC 2056
                         i  --       i   v i i ---------    ----  i   -----
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACA---------GAAT----GGGAGA----- 718

  chrX_10509271_1   2057 ATACACACACAGACATATACACA-CATATATCTGACACAGGGCTTGGATA 2105
                         ---------- i i  v i  v -           i vi  i    v  v
  L1M4_orf2#LINE/    719 ----------AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_10509271_1   2106 TAGAATATATAAAGTACCCTTAAAATTCAATAATTAAAAGACAA----CT 2151
                         i             v  i    v  i        v         ---- i
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_10509271_1   2152 CAAT--AAAAACGAGCAAAC-ATGTGAACAGAAACTTCTTAATGGAAGGC 2198
                             --     i i     v-  v    i   v i    iv vi    ii
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_10509271_1   2199 ATATGAATTACCAATAAGCACAGGGAAA--TGTAAATTAAAACCACAGAA 2246
                            ii   vi            v i   --  i--- i  v i  ?????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGC---TCAACATCAZZZZZ 905

  chrX_10509271_1   2247 AGT 2249
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.63 (85 / 52)
Gap_init rate = 0.04 (21 / 566), avg. gap size = 2.71 (57 / 21)  


3012 26.57 0.88 0.77  chrX_10731097_10736607     4112  5018 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_10731097_1   4112 TGGAAAAACATTCCACGTTCATGGACAGGAAGAATCAATATTGTGAAAAT 4161
                               i i  i   i         iv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_10731097_1   4162 GTACATACTGCCCAACGCAATTTATAGATTCAATGCTATTCCCATAAAAC 4211
                          vvv     v     vvii  i  i        i  v  i  i  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_10731097_1   4212 TGACA-CTGACATTCTTCACA-AAATTAGAAAAAACT-ATTTTAAAATTT 4258
                          vv  -   v -  i  ii  -     i-- v  i  -  ii       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_10731097_1   4259 ATATGGAACAAAAAAGAGAGCCCAAATATTCAAG-CAATCCTAAGCAAAA 4307
                                 - viv   i  v  vi    vi   i-     i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_10731097_1   4308 AGAGCAAAGCTAGAGACATCATGCTACCTGACTTCAAACTATATTACAGG 4357
                            i     i i   ivv   ii  v  ii i      viv  i    ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_10731097_1   4358 GCTACAGTAACCAAAACAGTGTGGCACTGGTATAAGAACAGACACATAGA 4407
                                   i   i         i     i     i i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_10731097_1   4408 CCAATGGAACAGAATAGAGAACCCAGAAATAAGACTGCATATCTACAACC 4457
                         i        i     v    ii          iv iii i  i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_10731097_1   4458 ATCTGATCTTTGACAAACCTGACTAAAACAAGT-AATGGGGAAAGGATCC 4506
                          vi    i  i     ivv  - i  i  v v -           i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_10731097_1   4507 CCTATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCACATGCATAAAAT 4556
                         i  v  i  i              v      v  ?         v  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_10731097_1   4557 TAAAACTGGACCCCTTCCTTACACCATATACAAAAATCAACTGAAGATAG 4606
                          i  ii         v   i                 i    v  i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_10731097_1   4607 ATTAAAGTCTTAAATGTAAAACCCACAACTATAAAACATCTAGAGGAAAA 4656
                           i ?  v i         i v i v           vii    i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_10731097_1   4657 CCTAGGCA-ATACCATTCAGGACATAGGCACAGGCAA-GATTTCATGACA 4704
                          v    ?i- v i -   iv   v v  vvi      - i    v iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_10731097_1   4705 AAGACAACAAAAGCAATTGAAACAAAAGCAAAAATTGACAGATGAGATAT 4754
                          v    v        vvv v        v      v  i i  vi  iv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_10731097_1   4755 AATTTAACTAAAGAGCTTCTGCACAGAAAAAGAAACTATCAACAGAGTAA 4804
                         v  iv  v v  i i   i  ii vvv   i  v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_10731097_1   4805 ACAGACAACCTACACAATAGGAGAAAATTTTTGCAAACTATCCATCTGAC 4854
                          v        i   v   i         v        ii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_10731097_1   4855 AAAGGTCCAATGTCCAGCATCCATACGGAACTGAAACAAATTAACAAGAG 4904
                           i  v ivi i     v  vi   vi     vvv    v i  i  v i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_10731097_1   4905 GAAAACCAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGGCAC 4954
                         i  i  -   i     v   ?    i           iv    i  i  i
  L1M4_orf2#LINE/    795 AAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_10731097_1   4955 TTCTCAAAAGAAGACCTATATGCAGCCAACAATCATATGAAAAAA-GCTC 5003
                              v        iv  i viii     i  v  i       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_10731097_1   5004 AACATCACAGATCAT 5018
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.07 (15 / 14)  


3212 27.33 0.33 0.66  chrX_10796006_10803527.rev     6121  7031 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_10796006_1   6121 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAACATTGTGAAAAT 6170
                              ii i  i     i        v      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_10796006_1   6171 GACCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCTTGGATGCA 6220
                          i v     v     iv i  i  i       ii  v    i --  -  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT--AT-CA 97

  chrX_10796006_1   6221 AGCTACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTC 6270
                          iv v   iivi i  i  ii     v v  v  iv v iii    i   
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_10796006_1   6271 ATATGGAACCAAAAAAGAGCTCACATTCCCAAGACAATCCTAAGCCAAAA 6320
                                 viiv  ii  v iviv  vv    i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_10796006_1   6321 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCTATACTACAAGG 6370
                                 i      vv    i  v  ii i     iviv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_10796006_1   6371 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGCTATAGAC 6420
                                  i   i    ii         i iv ii i   vv      i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_10796006_1   6421 CAATAGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 6468
                             i   i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_10796006_1   6469 CATCTGATCTTTGACAAACCTGACAAAAACATGAAATGGGGAAAGGATTC 6518
                           vi    i  i     ivv  v   i v   vv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_10796006_1   6519 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 6568
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_10796006_1   6569 TGAAGCTGCATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGG 6618
                              i  v i    v   i     v     v        i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_10796006_1   6619 ATTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 6668
                           i ?   ii       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_10796006_1   6669 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 6717
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_10796006_1   6718 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGCATCT 6767
                          vi            vvi          vv     v  i    v v ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_10796006_1   6768 AATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 6817
                         v  i   v v  i     i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_10796006_1   6818 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCGATCTACTCATCTGAC 6867
                          v  i     i                 v     i vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_10796006_1   6868 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 6917
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_10796006_1   6918 AAAAACAAACAGCCCCATCAGAAAGTGGGCGATGGATATGAACAGACATT 6967
                            i     i i   v  i?i   i     i v    v    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_10796006_1   6968 TCTCAAAGGAAGACATTTATGCAGCCAACAGACACATGAAAAAATACTCA 7017
                             v  i     i  vi viii     i ii          i  i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_10796006_1   7018 TCATCACCGGCCAT 7031
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3234 21.89 3.40 7.12  chrX_10821818_10826011.rev     2763  3703 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_10821818_1   2763 GAAAGATACTCCATGTTCATGGATTAGAAGAATCAATATTGTTAGAATGT 2812
                                 ii               i     v i          ii   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_10821818_1   2813 CCATATTATCCAAAGCAATCTACAGATTCAATGCAATCTCTATCAAAATA 2862
                          v   i vi     vii              i      i          v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_10821818_1   2863 CCAATGACATTCTTCACAGAAATAGGAGAAAC-AATCCTAAAATTTATGT 2911
                            iivi v  i  ii       -v  v  i -i           i  i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATAT 151

  chrX_10821818_1   2912 GGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAAAGAAC 2961
                             vii   ii                 i v   i   iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_10821818_1   2962 AAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCTAT 3011
                            ii       v     i v  ii i      viv       i     i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_10821818_1   3012 AGTAACCAAAACAGTATGGTACTGGCATAAAAACAGACACATAGGCCAAT 3061
                              i   i     i              ii i     i    ii    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_10821818_1   3062 TGAACAGATTAGAGAACACAGAACCAAATACATACACCTACAGTGCACTC 3111
                         v   i   v v    iiv     vi   iv      ii  ii  vv i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_10821818_1   3112 ATTTTTGAAAAAGGTGCTAAGAATATGCCTTGGAGAAAGGGCAGTCTCTT 3161
                              i  v  i     i    vi  v vv   i     iii     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_10821818_1   3162 CAATAAATGGTGTTGGGAAAACTGGATATCCATATGCAAGAGAATGAAAC 3211
                            i        i     v         ?   i      i        ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_10821818_1   3212 TTGATTCCTATCTTTCATCATATACAAAAATCAAATCAAATTGGATTAAA 3261
                          v  ii    i  iv  i             i  v     v     i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_10821818_1   3262 GACTTAAATCTAAGATTTCAAACTATGAAACTACTACAAGAAAATGTTGG 3311
                            i     v     vi v       i     ------------------
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACT------------------ 533

  chrX_10821818_1   3312 GGGCCATCCTGCATGTAGAATTCTTAAAAGAAAAAAGCAAATAAGAATAA 3361
                         ----------------------    i       ---  --  i ?i   
  L1M4_orf2#LINE/    534 ----------------------CTTAGAAGAAAA---CA--TAGGNGTAA 556

  chrX_10821818_1   3362 AAAAGAAAACACTGGGGAAACTCTCCAGGACATTGGTCTGGCTAAAAATT 3411
                          --------------------   i iv   v    vi i vi  vii  
  L1M4_orf2#LINE/    557 A--------------------TCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_10821818_1   3412 TCTTGATTAATACACCACAAGCACAAGCAACCAAAGCAAAAATGGACAA- 3460
                             iiv  vv      v             v    v      i  i  -
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_10821818_1   3461 TGAGATCACATCAAG-TCAAAAACCTTCTGCACAGCAAAGGAAACAACTG 3509
                          vi  iiv      i- i      i  -  ii vv       v  v iii
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCA 685

  chrX_10821818_1   3510 GTAAATTGGAGCGACAACCCACAGAATGGGAGAAAATATTTGCAAATGAT 3559
                         iv   v  i iv                                   v  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_10821818_1   3560 CCATCTAACAAGGGATTAATAACCAGAATATATAAGGAGCTCACACAACT 3609
                         vi    i i      i vi  v             i  i   vi      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_10821818_1   3610 CTATA-----------------------------TGGTCAAAATATTTAA 3630
                          v   -----------------------------   v    iv    i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_10821818_1   3631 AGAACCATTTCTCAAAATATGACACACAAATGGCAAACAGGTATATGAAA 3680
                          v iv        v   v v  i i         v  i i i i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_10821818_1   3681 AGGTGCCCAACATCATTGATCAT 3703
                           i   i        ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (130 / 73)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 9.90 (99 / 10)  


3327 26.76 0.44 0.44  chrX_11484526_11490804     4879  5786 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_11484526_1   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_11484526_1   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_11484526_1   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_11484526_1   5027 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_11484526_1   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_11484526_1   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_11484526_1   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_11484526_1   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_11484526_1   5275 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_11484526_1   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_11484526_1   5375 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_11484526_1   5425 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_11484526_1   5475 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5524
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_11484526_1   5525 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5574
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_11484526_1   5575 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5624
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_11484526_1   5625 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_11484526_1   5675 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_11484526_1   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5774
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_11484526_1   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3061 19.52 9.02 5.48  chrX_11616630_11618952.rev      962  1837 (486)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_11616630_1    962 GGGAAG-CATTCCATATTCATAAATTGACACACTCAGTACTGTTAAAATG 1010
                           i   -i  i    i     ii    iv v   i i  i      i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_11616630_1   1011 GCATTTCTCCCCAAACTGATCTACAGATTCAATATAATCCCTATTAAAAT 1060
                            v v         i                iii         i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_11616630_1   1061 CTCATCACACTGTTTTATAGAAATTGACAAACTGATTCTAAAATTTATAT 1110
                          i  v vvv  v    ii            i     i        i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_11616630_1   1111 GGAAATGCAG----C--------GTTAAAATATTTTTGAAAAAGGAGAAA 1148
                                  i---- -------- ii    i v i         i    -
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA- 200

  chrX_11616630_1   1149 CAAAGTTAGAGGACTTACATATCC-AATTTCAAAACTTACTGTAAAACCA 1197
                                i       i   iv   -                ii   i i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_11616630_1   1198 CTGTAATCTAAAGAATATGAGATTGGCATA-TGATAGGTATATAGACCAA 1246
                          v      v i v i i  iv i       -v     ii       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_11616630_1   1247 TAGAACAGAATTGAGAGACCAGAAATAAACCCTTTCAATTATGTTCAAGT 1296
                          i   i           v              v v  v     v    v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_11616630_1   1297 TACATTCAACAAAGGCACTGAGACAATTCAATGAGAAAAACAAACAAACA 1346
                         v iv   i    i  ii ii    v        i ---------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGG--------------- 385

  chrX_11616630_1   1347 AACAGAAAAAACAGCCTTTACAACATACGGTGCCAGGAAAATTGAGAATC 1396
                         ----    i  i  i    v     v i     ii   v  i  iiv ? 
  L1M4_orf2#LINE/    386 ----GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_11616630_1   1397 AATTTGCAAAACAAGAAAAAAGAAAGAAAGAAAGAAAAGGAACTTAGCGG 1446
                         v iv       ------------------   v   ivv i  i------
  L1M4_orf2#LINE/    432 CACATGCAAAA------------------GAATGAAGTTGGACC------ 457

  chrX_11616630_1   1447 CTTACCACATACCACACATGAAAATTAACTCAGAGTATATCCTAGACCTA 1496
                          i    v  i    i i ii            i i iv   v?       
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_11616630_1   1497 AATGTAAGAACTAAACCTATAAAACAATTTTTAGAAGAAAACAGAAAA-- 1544
                                  i     v         --- i             v ii?--
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAAC---TCTTAGAAGAAAACATAGGNGT 554

  chrX_11616630_1   1545 AACTCTTCATGACCTT--------CAA------CTTA------------- 1567
                           v     i       --------   ------    -------------
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_11616630_1   1568 ----------------------------TAAATTGGACTTTATTGAAATT 1589
                         ----------------------------            i  ii     
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_11616630_1   1590 AAAATATTTTTCACTTCAAAG-ACACAATTAAAAAATT-AAAACACAAAC 1637
                             vv    vii        -    v  i  i   v -    v    v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_11616630_1   1638 CACAGAAAAGAATAAAATATT-ACAAATCATATATCTAATAAAGGGCTTT 1686
                                vi i v        -i              i    i  i   v
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_11616630_1   1687 TATATAGAATATGTAAAGAACTCTTGCAACTCAGTAATAAAAAGGCAAAC 1736
                            vi       i            i       i          i    i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_11616630_1   1737 AACACAATTTTAAAAATGGGTAAAAGACTTAAATAGGCACTTCACCAAAA 1786
                            v     ?-         i   i  i  i     i  i   v     i
  L1M4_orf2#LINE/    805 AACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_11616630_1   1787 AAGACATACAAATAACTAATAAGTATATGAAAGGATGC----CATTAGTC 1832
                             i        ii i      i i      i     ----   i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_11616630_1   1833 ATTAA 1837
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.15 (114 / 53)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 6.68 (127 / 19)  


4325 18.60 1.13 1.69  chrX_11626112_11628464      974  1860 (493)    L1M4_orf2#LINE/L1       27   908 (0)  

  chrX_11626112_1    974 TGGGAGATTTAATATCATTAAGATGTCAATACTACCCAAAGCTATATCCA 1023
                            i   i       ii        v       v      viv  v v  
  L1M4_orf2#LINE/     27 TGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACA 76

  chrX_11626112_1   1024 GATTTAATCCAAGCCCTATCAAAATCCCAATAGCATTTTTTGAAAAAATA 1073
                             i  iv   v                iiv  v       v i    v
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

  chrX_11626112_1   1074 GAAAAGTTCATCGTAAAATTCATGTAGAACCTCAAGGGAGCCCAAATAAC 1123
                           v   i v   v          i i   viv       v  vi    i 
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chrX_11626112_1   1124 CAAAACAGTCTTGAAAAAGAAAAA---AGTTGGGGGCCTCATACTTTTAG 1170
                                i             i  ---      i  v    i    iivi
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_11626112_1   1171 GTTTCAAAACTTATCACAAAGCTACAGTAATCAAAACAGTGTGGTACTGT 1220
                         i            ii                   i              v
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_11626112_1   1221 CATAAAGACAGACATGTGGACCTGTGGAATAGAATAGAGAGCCCAAAAAT 1270
                              i  i      i i  i vi           v     i   i    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_11626112_1   1271 AAACACTCACATAACATGGTCAAATGATTTTTAATGAGAGTGCCAAGACA 1320
                             v vi    v-i        v       ii ii  i          v
  L1M4_orf2#LINE/    327 AAACCCATACATT-TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_11626112_1   1321 ATTCAATGTGGGAAAGGACAGGTTTTTTTTTTTTTTTCCAACAAGTGGTA 1370
                                 -       i i  ----------- i   i      i    i
  L1M4_orf2#LINE/    376 ATTCAATG-GGGAAAGAATAG-----------TCTTTTCAACAAATGGTG 413

  chrX_11626112_1   1371 T---AAAAAAGAGATATCCACATGCAGAACAATGAACTTGGACCTTTATC 1417
                         i---i v  vvi    ?         i  v      v       ii  i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_11626112_1   1418 TTATATCACATATAAAAATTAACTCAAAGTAGATCAAAAGCCTAAACATA 1467
                          i i i  i   i               i i     ? ii      ii  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_11626112_1   1468 TGTGCTAAAACTATAAAACTCTTTGAAGCAAACATAGGAGAAAAACTTCA 1517
                         v v                    v    v         ? v   v    i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_11626112_1   1518 TGACTTTGGATTTGGCAATGATTTCTTGAATATGACACCAAAAGCATAGG 1567
                             i    i  v       i      ii                 i i 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_11626112_1   1568 CAACAAAATAAAAA-TAGATAAACCGGATTATGTCAAAATTTAAAACATC 1616
                                 v     -        ii   i vii        v     v i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_11626112_1   1617 TGTGCATCAAAGGACACAATCAACAGAATGGAAAGCCAACCTATGGAATG 1666
                              v           v     v i i  i    v     i ii     
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_11626112_1   1667 GGAGAAAATATTTTCAAATCATATATCTGATAAGGGGCTAATATATTCAG 1716
                                      v                      i  -- i   i   
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT--TGTATCCAG 761

  chrX_11626112_1   1717 ACTATATGAAGAACCTCTACAGCTCAACAACAAAC---CAAATAACCTGA 1763
                          v     i      iii    i     i  i   v---         ii 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_11626112_1   1764 CTAAAAAATGGGCAAGGGATTTGAATAGACAATTCTCCAAAGAAGACATA 1813
                         i ?            i               v              i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_11626112_1   1814 CAAATGACCAACCAGCATATGAAAAGTTGTTCATCATCACTAATTAT 1860
                               i    iv    i        v  i   v     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (105 / 56)
Gap_init rate = 0.01 (8 / 882), avg. gap size = 3.12 (25 / 8)  


3103 25.41 1.43 1.54  chrX_11701691_11706437     3346  4254 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_11701691_1   3346 TGGAAAAACATTCTATGCTCACGTATAGGAAGAATCAATATTGTTAAAAT 3395
                               i i  i i   i   i v  v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_11701691_1   3396 GGTCATACTGCCCAAAGCAATTTATACATTCAATGCTATTCCTATTAAAG 3445
                           iv     v      vii  i  i v      i  v  i     i   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_11701691_1   3446 TACCATTGAGAATCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 3494
                          v   vivivvv i  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_11701691_1   3495 GTGGAACCAAAAAGGAGCCTGAATAGCCAAGGCAATCCTAAGCAAAAAGA 3544
                         i     viiv  i   v  v          ii     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_11701691_1   3545 ACAAAGCTGGAGGCATCACACTACCCAACATCAAAACTGTACTACAGGGC 3594
                               i      vv       v     iv        -       ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_11701691_1   3595 TACAGTAACCAAAACAGCATGGTACTAGTACAAAAACAGACCCATAGACC 3644
                                 i   i    ii       i i i  ii i    vi     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_11701691_1   3645 AATGGAACATAATAGAGAACCCAGAAATAAGACCACACACCTAAGGCTAT 3694
                                i v   v    ii          iv   i   ii  v  ii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_11701691_1   3695 CTGATCTTCGACAAACCTGACAAAAACAAGCAATGAGGAAAGGAT--TCC 3742
                         i    i        ivv  v   i v  vv     i      i  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_11701691_1   3743 TAATTCAATTA-TGATGCTAGGATAACTGGCTAGCCATATGCAGAAGATT 3791
                          --     iv -  i    i   i      v  ?   i     i    v 
  L1M4_orf2#LINE/    399 T--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_11701691_1   3792 GAAACTTGACCCATTCCATATACCATATACAAAAATTAGCTCAAGATGGA 3841
                            ii v     v v  vi i                 i     i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_11701691_1   3842 TTAAACACCTAACTGTAAATCCCAAAAGTATAAAAACCCTGAAAGACAAC 3891
                          i ? v      v     ivv i    v       vi i ii    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_11701691_1   3892 CTAGGCA-ATACCATTGAGGACATAGGCACAGGTACAGGTAAAGATTTCA 3940
                         v    ?i- v i v i -v   v v  -----  -i   i  v i    v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCG-TGACCTTGG-----GT-TAGGCAATGGTTTCT 589

  chrX_11701691_1   3941 T-GATGAAGACACCAGAA--ACAATTGCAACAAAAGCAAAAATTGACAAA 3987
                          -   - v       i  --    --          v      v  i   
  L1M4_orf2#LINE/    590 TAGAT-ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAA 636

  chrX_11701691_1   3988 TGGGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAA 4037
                          v    i v  i   v v  i i   i  ii vv    i  v        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_11701691_1   4038 AAGAGTAAACAGACAACCTACAGAATGGGAGAAGATTTTTGCAAACTATG 4087
                         i i   i  v        i              i  v        ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_11701691_1   4088 TATCCAACAAAAGTCTAATATCCAGCATCCATAAGTAACTTAAACAATCT 4137
                             ii i  ii v  vi       v  vi    iv    ivv    iii
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_11701691_1   4138 TACAAGAACAAAACAA----TCCCATTAAAAAGTGGGCAAAGGGCATGAA 4183
                         v i  v  v  i    ----i  v   ?    i          iiv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_11701691_1   4184 CAGACACTTTTCAAAAGAAGACATATGTGTGGCAAACAATCATATGAAGA 4233
                         i     i  i  v        i   iivi    v  i  v  i     i 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_11701691_1   4234 AA-GCTCAACATCACTGATGAT 4254
                         i -           ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.69 (27 / 16)  


3331 26.65 0.44 0.44  chrX_11713312_11719590.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_11713312_1   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_11713312_1   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_11713312_1   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_11713312_1   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_11713312_1   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_11713312_1   5129 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGATC 5178
                                 i   i    ii         i i  ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_11713312_1   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_11713312_1   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_11713312_1   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_11713312_1   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_11713312_1   5377 TTAAAGATTTAAATGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii       v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_11713312_1   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGCACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     vvii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_11713312_1   5477 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5526
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_11713312_1   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_11713312_1   5577 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_11713312_1   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_11713312_1   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_11713312_1   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_11713312_1   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3283 26.25 1.00 0.44  chrX_11883703_11890104     5007  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_11883703_1   5007 TGGAAGAACATTCCATGCTCATGGATAGGAAAAATCAATAT-ATGAAAAT 5055
                              ii i  i     i        v    i v i     -i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_11883703_1   5056 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5105
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_11883703_1   5106 TACCAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTTCA 5153
                          v   iivi i  i  ii  -      -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_11883703_1   5154 TATGGAACCAAAAAAGGGCCCGCATTCCCAAGACAATCCTAAGCCAAAAG 5203
                                viiv  ii iv  v v  vv    i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_11883703_1   5204 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5253
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_11883703_1   5254 TACAGTAACCAAAACAGCATGGTACTGGTGTCAAAACAGAGTTATAGACC 5303
                                 i   i    ii         ii v ii i   vv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_11883703_1   5304 AATGGAAGAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5351
                                v    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_11883703_1   5352 ATCTGATCTTTGACAAACCTGACAAAAACAGGAAATGGGGAAAGGATTCC 5401
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_11883703_1   5402 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 5451
                           v  i  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_11883703_1   5452 GAAACTGGATCCCTTCCTTACACGTTATACAAAAATTAATTCAAGATGGA 5501
                            ii    i    v   i    vv              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_11883703_1   5502 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5551
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_11883703_1   5552 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5601
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_11883703_1   5602 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAA 5651
                         i            vvi          vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_11883703_1   5652 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5701
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_11883703_1   5702 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAAACTACTCATCTGACAA 5751
                           i     i                 v        ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_11883703_1   5752 AGGGCTGCTATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5801
                         i  i  vv          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_11883703_1   5802 AAACAA----CCCCATCAACAAGTGGGCGAAGGATATGAACAGACATTTC 5847
                          i    ----   v  i? v  i     i      v    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_11883703_1   5848 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5897
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_11883703_1   5898 ATCACTGGCCAT 5909
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3126 22.35 1.69 5.51  chrX_11966184_11969425     1814  2757 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_11966184_1   1814 TGAAGAGATATCCCATGTTCTTGGATAGGAAGACTTAATATTGTCAAGAT 1863
                           i i               v     v                 i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_11966184_1   1864 ATCAGTTCTTTCAGATTTAATCTATGGGTTCAATACAATCCCAGTCAAAA 1913
                         iv  i v  ii vi v  i     ii i     ii       vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_11966184_1   1914 TCCCAGGAAGTTATTTTGTGGATGTTGACATTTTGATTCTAATGTTTATA 1963
                               vvivi v     ii  vi      vvi    i    vi  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_11966184_1   1964 TGGAGAGGCAGAAGACCCACACAAAGAACAAAGCCAGAGGACTGACACTA 2013
                             i v   iii      ------   i --    i ------   v -
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCA------GAATA--GCCAAA------ACAAT- 185

  chrX_11966184_1   2014 CCTAACTTCAAGAATTACTATAGAGACCAAAGCCAGATGACTGACACTAC 2063
                         -----   v  i  -------ii   v     iii  v    v     v 
  L1M4_orf2#LINE/    186 -----CTTGAAAAA-------GAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_11966184_1   2064 CCAACCTTAAGACTTACTATAAAACTACAGTAATCAAGACATTGTGGTGT 2113
                             ii i  i        i   i                 v      ii
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_11966184_1   2114 TGGCAAAAGAATAGACAAATCAGAGATCAGGGGATCAAAAT--AGAATCC 2161
                              v   i       v  ---      iv   vi i   --   i   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATAT---AGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_11966184_1   2162 AGAAGTAGACTCACATTAATATTATTAGTCACCTGATCTTTGACAAAGGA 2211
                             i  i  i  i i--  -    -i    vi    i  i     i  v
  L1M4_orf2#LINE/    321 AGAAATAAACCCATAC--AT-TTAT-GGTCAATTGATTTTCGACAAGGGT 366

  chrX_11966184_1   2212 GCAAAGACAATACAGTGGAACAAAAATAGTCTTTTCAACAAATGTTGATT 2261
                           v     v  v  i   iiv  i                    v  v v
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_11966184_1   2262 GAACAACTAACGGGACATCCACATTAAAAAAAAAAAAAAAGAATCTACAC 2311
                          i      ----   i ?      ------iv    i  v   vi iv  
  L1M4_orf2#LINE/    417 GGACAACT----GGATAKCCACAT------GCAAAAGAATGAAGTTGGAC 456

  chrX_11966184_1   2312 ACAAACTTGATGCC-TGTCACAAAAAT-AACTCAAAATGGATCACAGACC 2359
                         v vv  i v ii  - i -        -                ?     
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_11966184_1   2360 TAGAAGTAAAATGCAAAAAAGTTATAAAACTCTTAGAAAATAACTTTGGA 2409
                           i v    i -  v    --i                i v   v v  ?
  L1M4_orf2#LINE/    506 TAAATGTAAGA-GCTAAAA--CTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_11966184_1   2410 GAATACCTACATGACCTCAGGTGTAGTGAA-GACTTTTTAGATTCAACAC 2458
                          v v i  v i      ii   -   vv  - ii  i      vii    
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_11966184_1   2459 CAAGGGCACAATCCATGAAGGAAAAAAATTGATAAGCTGGATTTCATTGA 2508
                            ii      v v ii  i       - v     ii    i     ii 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAA 650

  chrX_11966184_1   2509 AATTAAAAACTTCTCTTCTGCAAAAGACACTGTTCAGAGAATGAGAAGAC 2558
                                     i v v  v    i      i iv   i i   i     
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_11966184_1   2559 AAGCCACAGACTAAAAGAAAATATTTGCAATTGACATATTTGATAAAGAA 2608
                           v       v iii               v v i    i      i i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_11966184_1   2609 CTGTTATCCAAAATATACAAAGAACTCTTAGAATTCAACAAGAACACAAC 2658
                           vv      i      i            v  i    i  v  v vi  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_11966184_1   2659 A------CAAATTTTAAAATGAGCCAAAGACATTAACAGACACGTCATCA 2702
                          ------ v    ?v      i  v  i  iv v  i     iv  vi  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_11966184_1   2703 AAGAAGAGA----GATGGCAAATAAGCTTATGGAAAGATGCTCTTAGCAT 2748
                                v ----i     v       vi   i          -- i   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC--AACAT 898

  chrX_11966184_1   2749 -ATATCATCA 2757
                         - ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (125 / 82)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.83 (68 / 24)  


3283 26.98 0.55 0.55  chrX_12249811_12255002     3792  4699 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_12249811_1   3792 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 3841
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_12249811_1   3842 GGCCATAATGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3891
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_12249811_1   3892 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCG 3939
                          v   iivi i  i  ii     -   -- v     - iii    i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_12249811_1   3940 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 3989
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_12249811_1   3990 AACAAAGCTGGAGGCATCACACTACCTGACTTCAGACTATACTACAAGGC 4039
                                i      vv       v  ii i    i viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_12249811_1   4040 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4089
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_12249811_1   4090 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 4137
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_12249811_1   4138 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGACTGC 4187
                          vi    i  i     ivv  v   i v  vv            i iv i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_12249811_1   4188 CTATTTAATAAATGGTGCTGGGAAAACTGGCTGGCCATATGTAGAAAGCT 4237
                           v  i  i              v      v i?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_12249811_1   4238 GAGACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4287
                           iii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_12249811_1   4288 TTAAAGACTGAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4337
                          i ?    iv      v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_12249811_1   4338 CTAGGCA-ATACCATTTGGGACATAGGCATGGGCAAGGACTTCATGTCTA 4386
                         v    ?i- v i -  i v   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_12249811_1   4387 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4436
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_12249811_1   4437 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4486
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_12249811_1   4487 CAGGCAACCTACAGTATGGGAGAACATTTTTGCAATCTACTCATCTGACA 4536
                         v  i     i    v         v  v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_12249811_1   4537 AAAGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4586
                          ii i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_12249811_1   4587 AAAACAAACAACCCCATCAAGAAGTGGACGATAGATATGAACAGACACTT 4636
                           i     i     v  i? i  i   i i vi   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_12249811_1   4637 CTCAAAAGAAGACATTTATGCAGCCAACAGACACGTGAAAAAATGCTCAT 4686
                            v        i  vi viii     i ii   i      i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_12249811_1   4687 CATCACTGGCCAT 4699
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3005 27.57 1.33 0.78  chrX_12290248_12293592.rev     1952  2854 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_12290248_1   1952 TGGAGAAACATTCCATGCTCATGGATAGGAAGAATCAATACCTTGAAAAT 2001
                             i i i  i     i        v      v i    iiv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_12290248_1   2002 GGCCATACTGCCCGAAGTAATTTATATATTCAGTGCTATTCCCATTGAAC 2051
                            v     v   i  v i  i  i v     ii  v  i  i  ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_12290248_1   2052 TACCATTGACATTCTTCACAGAA-TTAGCAAAAACT-ACTTTAAAATTCA 2099
                          v   vivi v  i  ii     -  ii   i--  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_12290248_1   2100 TATGGAACCAAAAAGGAGCTCATATAGCCAAGACAATCCTAAGCAAAAAG 2149
                                viiv  i   v iviv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_12290248_1   2150 AACAAAGCTTGAGGCATCACTCTACCAGACTTCAAACTATATTGTAAGGC 2199
                                i v    vv    v  v  vi i      viv  i ii  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_12290248_1   2200 TACGGTAACCAAAACAGCATGGTACTGGTAGAAAAACGGACACATAGACC 2249
                            i    i   i    ii         i v  ii ii    i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_12290248_1   2250 AATGGAACAGAATAGATATCTCAGAAATATGACTGCACATTTACAATGAT 2299
                                i     v  v vii        viv iii       iii v v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_12290248_1   2300 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGAATTCCCT 2349
                         i    i  i     ivv  v   i v  vv               vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_12290248_1   2350 ATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGTAGAAAATTGA 2399
                         v  i  i              v      v  ?   i   i i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_12290248_1   2400 AACTGGACCCCTTCCTTAGATCTTATACAAAAATTGACTCCAGAGCGATT 2449
                          ii         v   i v i v            i    v i vv   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_12290248_1   2450 AGAGACTTAAATGTAAAACACAAAACTATAAAATCCCTAGAAGAAAATCT 2499
                          ?    i         i vvi            ii i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_12290248_1   2500 AGGCAGTA--CCATTCAGGACGTAGGCACAGGCAAAGATTTCAT-GATGG 2546
                            ?-   --i -   iv   v v  vvi      v i    v -   iv
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_12290248_1   2547 AAACATCAAAATCAATTGCAACAGAAACAAAAACTGACAAATAGGATCTA 2596
                         i -  i     v  vvv      i  iv     iv  i    v   ii v
  L1M4_orf2#LINE/    597 GA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_12290248_1   2597 ATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGAA 2646
                           i   v v  i i   i  ii vv    iv v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_12290248_1   2647 CATACAATATATAGAATGGGAGAAAATTTTTGCAA--TATATCCATCTGA 2694
                         v v    ivi i               v       --i    --      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chrX_12290248_1   2695 CAAAGGTCTCATATCCAGAATCTACAAGGAATTTAAACAAATTTACAAGA 2744
                         i  i  v  ii          v  i  i   i ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_12290248_1   2745 AAAA-----ACAACCCTATTAAAAAGTGGGCAAAGGATACGAACAGACGC 2789
                             ----- i     v   ?    i            vi   i    ii
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_12290248_1   2790 TTCTCAACAGAAGACATTTATGTGGCCAAGAAATATATGAAGAAAAGCTC 2839
                              v v      i  vi vi       v  ii i     i i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_12290248_1   2840 AACATCACTGATCAT 2854
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


3222 26.32 0.77 0.77  chrX_12315161_12321777     5217  6124 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_12315161_1   5217 TGGAAGAACATTCCATGCTCATGGAT-AGAAGAATCAATATCATGAAAAT 5265
                              ii i  i     i        -i     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_12315161_1   5266 GGCCATACTGCCCAAGGTAATTCATAGACTCAATGCCATCCCCATCAAGC 5315
                            v     v     iv i  ii i   i    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_12315161_1   5316 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5363
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_12315161_1   5364 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAA 5413
                                 viiv  ii  v  viv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_12315161_1   5414 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5463
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_12315161_1   5464 CTACAGTAACCAAAACAGCATGGTACTGGTATCTAAACAGAGATACAGAC 5513
                                  i   i    ii         i  vvii i   v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_12315161_1   5514 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5561
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_12315161_1   5562 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAAGATTC 5611
                           vi    i  i     ivv  v   i v  vvv          ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_12315161_1   5612 CCTTTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGC 5661
                         i     i  i              v      v  ?   i   v i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_12315161_1   5662 TGAAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGG 5711
                             ii    i    v   i     v i            i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_12315161_1   5712 ATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5761
                           i ?    i  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_12315161_1   5762 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATTTCT 5810
                          v    ?i- v i -   iv   v v  vv i     v ii   v vvv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_12315161_1   5811 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5860
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_12315161_1   5861 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5910
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_12315161_1   5911 ACGGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACTCATCTGAC 5960
                          vi i     i                 v      ivii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_12315161_1   5961 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAACTCA-CAAGA 6009
                           i  i  vi          v  i         vv    -    -i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chrX_12315161_1   6010 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 6059
                             i     i     v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_12315161_1   6060 TTCTCACAAGAAGACATTTATGCATCCAAAAGACACATGAAAAAATGCTC 6109
                              vv       i  vi viiiv    v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_12315161_1   6110 ATCATCACTGGCCAT 6124
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2586 25.63 9.22 0.48  chrX_12541543_12544170     1301  2135 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_12541543_1   1301 TGGAAACACATTCCATGCTCATGGGTGGGAAGAATCAATATCTTGAAAAT 1350
                               v i  i     i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_12541543_1   1351 GGCCATATTGTCCAAAGTAATTTATATATTCGATGCTATCCCCAACAA-- 1398
                            v   i vi     v i  i  i v    i i  v     i v   --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_12541543_1   1399 -CCTA-CT---------------ATTGAC---TT--TCTT---------- 1416
                         -  i -  ---------------      ---i --  i ----------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_12541543_1   1417 ---------------CTCAGAAT--------------TGGAAAA----AA 1433
                         --------------- i      --------------  i    ----  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_12541543_1   1434 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 1483
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_12541543_1   1484 CAGTAACAAAAACAGCATGGTACTGTTACCAAAACAGATACATAGACCAA 1533
                               iv  i    ii        vi iv ii i   i i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_12541543_1   1534 TGGAACAGAA--GAGAGGCCTCAGAAATAACGCCACACATCTAAAAACAT 1581
                              i    --     v  --        vv   i    i  viiv  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_12541543_1   1582 CTGATCTTTGACAAACCTGATGAAAACAATCAGTAGGGAAAGGATTCCCT 1631
                         i    i  i     ivv  vii i v  v   i i       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_12541543_1   1632 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTCA 1681
                         v  i  i              v      v  ?   i   i i  iiv v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_12541543_1   1682 AACTGGATCCCT---TC-CACCTTATACAAAAATGAACTCAAGATGGATT 1727
                          ii    i    ---  -    v           v       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_12541543_1   1728 AAAGACTTAAACGTAAGATCTAAAACCATAAAAACCCTAGAAGAAAAC-T 1776
                          ?    i    i      v       i      vi i           - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_12541543_1   1777 AGGCA-ATACCATTTAGGACACAGGCATGGGCAAAGACTTCATGACTTAA 1825
                            ?i- v i -  iiv   viv  vv i     v ii   v iiv vvi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_12541543_1   1826 ACACCAAAAGCAATGGCAACAAAAGCCAAATTTGACAAGTGGGATCTGAT 1875
                                     vvi          vv   v v  i  i v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_12541543_1   1876 TAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1924
                         i   -     i -   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_12541543_1   1925 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATGTGACAA 1974
                           i     i                 v  i    vii ivi  v   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_12541543_1   1975 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 2024
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_12541543_1   2025 AAACAAACACCCCA-TCAAAAAGTGGGCAAAGGATATAAACAGACACTTC 2073
                          i     i v    - i?    i            v i  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_12541543_1   2074 TCAAAAGAAGACATTTATGCGGCCAATAAACATATGAAAAAAAGCTCATC 2123
                           v        i  vi vii         i  i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_12541543_1   2124 ATCACTGGTCAT 2135
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (126 / 84)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.50 (81 / 18)  


2892 27.54 1.55 1.11  chrX_12611059_12612777.rev      325  1228 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_12611059_1    325 TGGAAGAACATTCCATGCTCATGGATAGGAAAAAACAATATCCTGAAAAT 374
                              ii i  i     i        v    i vvi     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_12611059_1    375 GGCCGTATTTCCCAAAGTAATTTATGGATTCAATGCA-TACCCATCAAGC 423
                            vi  i i      v i  i  ii       i   - v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_12611059_1    424 TACCATTGACTTTCTTCTCAGAATTAGAAAAAAAAACT-ACTTTAAATTT 472
                          v   vivi i  i  iv     v v  v  i----  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chrX_12611059_1    473 CATATAGAA---CCAAAAATACATACCATATAGCCAAGTCAATCCTAAGC 519
                              i   --- v iii iv  v ----        iv     i i iv
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGA----ATAGCCAAAACAATCTTGAAA 192

  chrX_12611059_1    520 AAAAAGAACAAAGCTGGAGGCATCACGCTAACTGACTTCAAACTATATTA 569
                           i          i      vv    i  vv ii i      viv  i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_12611059_1    570 CAAGGCTACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGATATA 619
                            i          i   i     i         i iv ii i   i   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_12611059_1    620 AAGACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTAC 669
                         v   i        i    iv   ivii         vv   i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_12611059_1    670 AACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGA 719
                         iii  vi    i  i     ivv  v   i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_12611059_1    720 TTCTGTATATAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAA 769
                          vv v v vi  i        i     v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_12611059_1    770 AACTGAAACTGGACCCCTTCCCTACAACTTATACAAAAATGAACTCAGGA 819
                         i v    ii         v  ii   v v           v      ii 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_12611059_1    820 TGGATTAAAGACTTAACTGTAAGACCTAAAACCACAAAAATCCTAGAAGA 869
                              i ?    i   v       v       i i    v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_12611059_1    870 AAACCTAGGCA-ATACCATTCA-GGCCACAGGCACGGGCAAAGACTTCAT 917
                             v    ?i- v i -   i- i  vii  i-ii     v ii   v 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTT 590

  chrX_12611059_1    918 GACTAAAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAAT--G 965
                         iiv  vi            vvi      i   vv     v  i    -- 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_12611059_1    966 ATCTAATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTACCATCAGA 1015
                          ii v  i   v v  i i   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_12611059_1   1016 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTGTCCATC 1065
                              v  i     i                 v       viii vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_12611059_1   1066 TGACAAAGGGCTATTTTCCAGAATCTACAAGGAACTTAAAGAAATTTACA 1115
                            i  i  i  vv v        v  i  i     ivv v  v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_12611059_1   1116 AGAAAAAAACAAACAACGCCATCAAAAAGTGAGTGAAGGATATGAACAGA 1165
                          v     i     i   v v  i?    i  i ii      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_12611059_1   1166 GACTTCTCAAAAGAAGACATTTATGTGGCCAAGAAACATA-GAAA----G 1210
                         v i     v        i  vi vi       v  i  i -    ---- 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_12611059_1   1211 CTCATCATCACTGGTCAT 1228
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.00 (24 / 12)  


3034 26.29 0.88 0.99  chrX_12626838_12633479.rev     5243  6151 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_12626838_1   5243 TGGAAGAACATTCCATGCTCATGGATAGGAACAACCAATGTCGTGAAAAT 5292
                              ii i  i     i        v    v vii   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_12626838_1   5293 GGACATACTGCCAAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGA 5342
                           vv     v  v   v i  i  i        i  v     i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_12626838_1   5343 TACCATTGACTTTCTTCTCAGAATTAGAAAAAGCT-ACTTTAAATTTCAT 5391
                          v   vivi i  i  iv     v v  v  -   - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_12626838_1   5392 ATGGAATAAAAAATGAGCCCATA-TAGCCAAGACAATCCTAAGCAAAAAG 5440
                               - viv  v ii    v -       i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_12626838_1   5441 AGCAAAGCTGGAGGCATTACACACTACCTGACTTCAAACGATACTACAAG 5490
                          i     i      - i -      v  ii i      vvv        i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACT-CACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_12626838_1   5491 GCTGCAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGA 5540
                            i      i   i    ii  i      i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_12626838_1   5541 CCAATGGAACAGAAC--AGAGCCCTCAGAGATAACACGACACATCTACAA 5588
                         i        i    i--    i  --   i    vv v i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_12626838_1   5589 CCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5638
                         i  vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_12626838_1   5639 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTGTATGCAGAAAA 5688
                         vi  v  i  i              v      v  ? iii     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_12626838_1   5689 TGGAAACTGGACCCTTTCCTTACACCTTATTCAAAAATTAACTAAAGATG 5738
                         vv   ii       i v   i     v   v            v  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_12626838_1   5739 GATTAAAGACTTAAATATAAAACCTAAAACCATAAAAACCCTAGAAGAAA 5788
                            i ?    i     i   i v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_12626838_1   5789 ACTTAGGCA-ATACCATTCTGGACATAGGCGTGGGCAAAGACTTCATGAC 5837
                           v    ?i- v i -   vv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_12626838_1   5838 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5887
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_12626838_1   5888 TAATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCATCAGAGTG 5937
                          v  i   v v  i i   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_12626838_1   5938 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5987
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_12626838_1   5988 CAAACGGCTAATATCCAGAATCTACAAAGAACTCAAAGAAACTTA-TAAG 6036
                         i  iv i  vi          v  i         vv v  -  i -   v
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAAT 792

  chrX_12626838_1   6037 AAAAAAACAAACAACCCCATCAGAAAGTGAGTGAAAGATATGAACAGACA 6086
                              i     i     v  i?i   i  i ii  i   v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_12626838_1   6087 CTTCTCAAAAGAAGACATTTATGCAACAAAGAA--ACATGAAAAAAAAGC 6134
                         i     v        i  vi viiii v  v  --         i v-  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GC 891

  chrX_12626838_1   6135 TCATCATCACTGGTCAT 6151
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.21 (17 / 14)  


3174 26.37 0.66 0.88  chrX_12636326_12642717.rev     4992  5901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_12636326_1   4992 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATCAATATCGTGAAAAT 5041
                              ii i  i     i       iv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_12636326_1   5042 GGCCATAGTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5091
                            v   v v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_12636326_1   5092 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAGCT-ACTTTAAAGTTC 5139
                          v   iivi i  i  ii     -   --- v     - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_12636326_1   5140 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 5189
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_12636326_1   5190 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5239
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_12636326_1   5240 CTACACTAACCAAAACAGCATGGTACTGGTATCAACACAGAGATATAAAC 5289
                              v   i   i    ii         i  v iv i   v     i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_12636326_1   5290 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5337
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_12636326_1   5338 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGCATTC 5387
                           vi    i  i     ivv  v   i v  vvv           v  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_12636326_1   5388 CCTATTTAATAAATGGTGCTGGGAAAGCTGGCTAGACATATGTAGAAAGC 5437
                         i  v  i  i              v i    v  ?v  i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_12636326_1   5438 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5487
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_12636326_1   5488 ATTAAAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5537
                           i ?    i    i      v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_12636326_1   5538 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5586
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_12636326_1   5587 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5636
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_12636326_1   5637 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5686
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_12636326_1   5687 ACAGGCAACCTAAAGAATGGGAGAACATTTTTGCAATCTACTCATCTGAC 5736
                          v  i     i v            v  v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_12636326_1   5737 AAATGGCTAATATCCAGAATCTACAAAGAACTCAAAGAAACTTA-CAAGA 5785
                           iv i  vi          v  i         vv v  -  i -i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chrX_12636326_1   5786 AAAAAACAAACAACCCCATCAGAAAGTGGGCAAAGGATATGAACAGACAC 5835
                             i     i     v  i?i   i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_12636326_1   5836 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAAATGCT 5885
                              v        i  vi viii     i ii          i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chrX_12636326_1   5886 CATCATCACTGGCCAT 5901
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


3253 27.09 0.44 0.44  chrX_12910346_12916742.rev     4999  5906 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_12910346_1   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5048
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_12910346_1   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCCTCAAGC 5098
                            v     v     iv i  i  i        i  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_12910346_1   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_12910346_1   5147 TATGGCACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGTCAAAAG 5196
                              v viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_12910346_1   5197 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5246
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_12910346_1   5247 TACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5296
                               v i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_12910346_1   5297 AATGGAACAGA--TCAGAGCCCTCAGAAATAATGCCACATATCTACAACT 5344
                                i   -- v    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_12910346_1   5345 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5394
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_12910346_1   5395 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5444
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_12910346_1   5445 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCGAGATGGA 5494
                            ii    i    v   i     v              i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_12910346_1   5495 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5544
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_12910346_1   5545 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5594
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_12910346_1   5595 AACACCAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGGGATCTAA 5644
                         i            vvi          iv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_12910346_1   5645 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5694
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_12910346_1   5695 AGGCAACCTACACAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5744
                           i     i   v             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_12910346_1   5745 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5794
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_12910346_1   5795 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5844
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_12910346_1   5845 TGAAAAGAAGACATTTATGCAGCCAAAAAACACACAAAAAAATGCTCACC 5894
                          vv        i  vi viii     v  i    ii    i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_12910346_1   5895 ATCACTGGCTAT 5906
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1221 29.36 13.51 1.97  chrX_13132601_13134510.rev      648  1461 (449)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_13132601_1    648 TGCAGAAATATAGCAGGTTCATGAAAGGAAAGAC--AAGATCGGGAAGAT 695
                           v i i    vv  v       i vv i     --  v  i vv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_13132601_1    696 G---ATGCTTCTCAAACTAATCTATAAATGCAATGTAATTCAAATCAAAA 742
                          ---  i  i i    i i     i i  v   i i   i vv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_13132601_1    743 TCTAGAAAGGATTTTCTGTGGAAACTGATGAGCTGACCTTAACATTCATA 792
                           iviivv vv    i  ii    i   ii      i i   v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_13132601_1    793 TAGATGAGAAAGAGACC-ATAATAGTTAAGACA--CATGAAA-------- 831
                          i  viv v   i    - v     ii  i   -- v     --------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_13132601_1    832 -------------CTTGCCCTACCAAATATCAAGACTTACTTTTTAAAA- 867
                         -------------  ii v  v  v   v    i       vi--   i-
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC--AAAGC 248

  chrX_13132601_1    868 TATAGTAATTTAGATAGCATGCTACTTGTGCAGAGTTGGACA-------- 909
                           i      iv   i  ii  v    v iii ii v i    --------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_13132601_1    910 ----AAACAGA--------TCCAGGCATA--CACAGAGATTT-------- 937
                         ----i  i   --------     iv   -- v  v v    --------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_13132601_1    938 --GATGCGTGACAGAG-----AAGATCTTACAAATTAGTGGGGCAAGTAT 980
                         --   vivi    ii -----    i v v   -----     v   v  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAA-----TGGGGAAAGAAT 393

  chrX_13132601_1    981 AAACTATTCAACAAACGAGTCTGGGA-AATTAGTTATCCTTCTG-AAAAG 1028
                          iv  v         i ivv      -  i i v  ?  viv  -     
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_13132601_1   1029 AA---AATTAAGTCACTAGCTTATATCACA--CAAAGATAAATTCCAGA- 1072
                           --- i  iiii v   v  i i i  i --    i  v  i  v i -
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_13132601_1   1073 ----CAAAGATTTAAATGTCAAAAG---AAACCATGTAAACTTCTGGAAG 1115
                         ----  ?   ii       -  i  ---    i  i-     ii i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGT-AAGAGCTAAAACTATA-AAACTCTTAGAAG 541

  chrX_13132601_1   1116 AAAATAAAGGAGAAAATCTTTATAATCTTAAATC---------TTCCATA 1156
                             i v   ? v       ii i i   iii i---------  i v  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_13132601_1   1157 GACAAG-CACAAGAAAACAAAACCCTTAATTAAGGAAAAAATAGACAAAT 1205
                           i v -   v -   i  v  v ---  iv  i           i    
  L1M4_orf2#LINE/    592 GATATGACACCA-AAAGCACAAGC---AACAAAAGAAAAAATAGATAAAT 637

  chrX_13132601_1   1206 ATAACTACACTAAAATTACAAACTTAAATACAAGAAAAAAGCACCTT--- 1252
                         vvi   v  ii       v      vvi i vvv   ii -   iv ---
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-CACTATCAA 686

  chrX_13132601_1   1253 -AAAATTAAAAGA-AATT-ATAGACAGGAAGAAGATATTTGCAATGCATA 1299
                         -   i v      -  ii- i   vv  i    i          vv    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_13132601_1   1300 TAATCAACAAATG-TTGGTATTTAAAATATGTAAAAAAATGTTTACAATT 1348
                           viii i  iv -i v    ii i     i    i  v -i      i 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT-CTTACAACT 785

  chrX_13132601_1   1349 CAGCAAGAAAAAGACAAATACTCCAA-------ATGGGCAAAATATATGA 1391
                           ii  v             vi    -------         iv  v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_13132601_1   1392 AAAAGCAAATTCACAGAAGAGGAAACTTGAATACCAAATGA----ATGGA 1437
                          v ii  v-   v vi    i  v ivii   iv v   i ----   i 
  L1M4_orf2#LINE/    836 ATAGACAT-TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_13132601_1   1438 ATGTTGCTCTATTTCTCTAGTTTT 1461
                          v v     v iv  v????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 3.71 (126 / 34)  


2006 27.31 0.38 0.58  chrX_13501909_13508604     4978  5497 (1199)    L1M4_orf2#LINE/L1        1   519 (389)  

  chrX_13501909_1   4978 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5027
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_13501909_1   5028 GGCCATACTGCCCAAGGGTAATTTATAGATTCACTGCCATCCCCATCAAG 5077
                            v     v     -iv i  i  i       vi  v     i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA-ATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_13501909_1   5078 CTACCAATGACTTTCTTCACAGAA-TTGAAAAAAACT-ACTTTAAAGTTC 5125
                         v v   iivi i  i  ii     -    v  --i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTC 147

  chrX_13501909_1   5126 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTCAGCCAAAA 5175
                                 viiv  ii  v  viv  v     i      i v ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_13501909_1   5176 GAAGAAAGGTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5225
                            v    v      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_13501909_1   5226 CTACAGTAACCAAAACAGCATGGTACTGGTACCGAAACAGATATATAGAC 5275
                                  i   i    ii         i iviii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_13501909_1   5276 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5325
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_13501909_1   5326 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5375
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_13501909_1   5376 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAACCTG 5425
                          v  i  i              v      v  ?   i   i i  ivv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_13501909_1   5426 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5475
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_13501909_1   5476 TAAAGACTTAAATGTTAGGGCT 5497
                         i ?    i       v  i   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCT 519

Transitions / transversions = 1.75 (89 / 51)
Gap_init rate = 0.01 (4 / 519), avg. gap size = 1.25 (5 / 4)  

1211 25.22 5.31 0.88  chrX_13501909_13508604     5752  6203 (493)    L1M4_orf2#LINE/L1      437   908 (0)  

  chrX_13501909_1   5752 GCAACAAGAGTGAA-----ACTTC-GTCTCAAA----AAACAAAAAACAA 5791
                             -    i    -----  ii -ii    v ---- v       vi  
  L1M4_orf2#LINE/    437 GCAA-AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_13501909_1   5792 ACAAAAA------AAAGACTTAAATGTTAGACCTAAAACCATAAAAACTC 5835
                         viv    ------ ?    i       v   v       i      -   
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTC 534

  chrX_13501909_1   5836 T-AGAGGAAAACCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGG 5883
                          -   i      v    ?i- v i -   iv   viv  vv i     v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chrX_13501909_1   5884 ACTTCATGACTAAAACACCAAAAGCAATGACAACAAAAGCCAAAATAGAC 5933
                         ii   v iiv  vi            vvii         vv        i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_13501909_1   5934 AGATGGGATCTAATTAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTAC 5983
                          i  v   ii v  i   v v  i i   i  ii vv    i  v    i
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_13501909_1   5984 CATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCT 6033
                           vv i      v  i     i                 i       vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_13501909_1   6034 ACCCATCTGACGAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAA 6083
                          ivi      ii i  i  vi          v  i         vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_13501909_1   6084 ATTTATAAGAAAAA---AAAAAACCCCATCAAAAAGTGGGCAAAAGATAT 6130
                         v iv    v     ---   v     v  i?    i        i   v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_13501909_1   6131 GAACAGAGACTTCTCAAAAGAAGACATCTATGCAGCCAACAGACACATGA 6180
                            i   v i     v        i  vi viii     i ii       
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_13501909_1   6181 AAAAAATGCTCA---TCACTGGTCAT 6203
                            i -      ---   ????????
  L1M4_orf2#LINE/    884 AAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (63 / 48)
Gap_init rate = 0.03 (12 / 472), avg. gap size = 2.33 (28 / 12)  


3339 12.26 7.90 0.48  chrX_13620964_13622571.rev      498  1117 (491)    L1M4_orf2#LINE/L1      243   908 (0)  

  chrX_13620964_1    498 CAAAACTACA------AAGCTACCGTGTGGTACTGGCCTAAGAATGGACA 541
                             i     ------   --  v             v    i  i    
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAG--ACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_13620964_1    542 TATAGATCAATAGGATATCATTGAGAGTCCAGAAATAA-CCCTTATGTTT 590
                                    i i   vv                   -   v  ii   
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_13620964_1    591 ATAGTCAATTGATTTTCATCAAGGATACTAAGACAATTCAGTGGGGAAAG 640
                           i              iv     i i i     v     i         
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_13620964_1    641 AATACTCTTTTCAATAAATGGTGCTGGGACAATTGGATATCCACATGTAA 690
                             v         i                 i      ?       i  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_13620964_1    691 AAGAATGAAGTTGCACCCCTACCTCATA---TACACAAAAATTAACTCAC 737
                                      v            i ---  i               v
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_13620964_1    738 GATGGATCATAGACCTAGATGTAAAAACTAAAATTATAAAACTGTTAGAA 787
                         i        ?       i      i i      i         v      
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_13620964_1    788 GAAAACACAGGAGTAAATCTTCATGACCTTGGTTTAGACAGTGGTTTCTT 837
                                i   ?          i         v    i  i         
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_13620964_1    838 AGATGCAACA--------ATA-GCAACAAAGGAAAAGAATAGATACATTG 878
                             iii   -------- i -        i     -        v    
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTG 639

  chrX_13620964_1    879 GACTTTATCAGAATTAAAAACTATTGAGCTGCAAAGGACACCATCAAGAA 928
                              i    i           v   v   v          i        
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_13620964_1    929 AGTAAAAAGAGAACTCACAGAATGGGAGAAAATATTTA-AAATCATATAT 977
                            i      v   i                      i-           
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_13620964_1    978 CT---AAGAGACTTGCATCCAGAATATATTAAAA-----------TTAAT 1013
                           ---   i      i             v  i ----------- i   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_13620964_1   1014 AATAA---GACAA----CCCAAAATAAAAAT----AAAGGATGTGA-TAG 1051
                              ---     ----     vv?      ----       v   -   
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_13620964_1   1052 GCATTTCTCTAAAAAA--TTTACAAATATCCAATAAGCTTATGAAA-GAT 1098
                         i        i   i  -- v       iv         vi      -   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_13620964_1   1099 GTTCAACATCATTAGTTGG 1117
                          i         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (48 / 24)
Gap_init rate = 0.02 (16 / 666), avg. gap size = 3.25 (52 / 16)  


3297 25.88 0.66 0.66  chrX_13881972_13885502.rev     2133  3040 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_13881972_1   2133 TGGAAGAACATTCCATGCTCATGGGTAGGAAGCATCAATATCGTGAAAAT 2182
                              ii i  i     i      i v     vv i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_13881972_1   2183 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCTCCATCAAGC 2232
                            v     v     iv i  i           i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_13881972_1   2233 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2279
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_13881972_1   2280 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 2329
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_13881972_1   2330 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 2379
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_13881972_1   2380 CTACACTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 2429
                              v   i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_13881972_1   2430 CAACGGAACTGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 2477
                            i    iv   i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_13881972_1   2478 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 2527
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_13881972_1   2528 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2577
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_13881972_1   2578 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 2627
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_13881972_1   2628 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2677
                           i ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_13881972_1   2678 CCTAGGCA-ATACCATTCAGGACATAGGCATAGGCAAGGACTTCATGTCT 2726
                          v    ?i- v i -   iv   v v  vv       v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_13881972_1   2727 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 2776
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_13881972_1   2777 AATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGA 2826
                         v  i   v v  i i   i   i vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_13881972_1   2827 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 2876
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_13881972_1   2877 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 2926
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_13881972_1   2927 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 2976
                            i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_13881972_1   2977 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 3026
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_13881972_1   3027 TCATCACTGGCCAT 3040
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (137 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


 239 18.64 6.78 0.00  chrX_13933514_13935231.rev      456   514 (1204)  C L1M4_orf2#LINE/L1   (0)   908   846 *

C chrX_13933514_1    514 CTTTAAAGTAGTTATGCA----GCCAAAAGACACGTGAAAAAATGCTCAT 469
                           ii    v  v   i  ----     v ii   i      i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chrX_13933514_1    468 CATCACTGGCCAT 456
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.02 (1 / 63), avg. gap size = 4.00 (4 / 1)  

2484 25.77 1.69 0.70  chrX_13933514_13935231.rev      510  1219 (499)    L1M4_orf2#LINE/L1      140   856 (52)  

  chrX_13933514_1    510 TAAAGTTCATATGGAAC--CAAAAAAGCCCGCATTGCCAACGCAATCCTA 557
                             i           v--   iii v  v v  v     vi     i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_13933514_1    558 AGCCAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTT-GAAACTAT 606
                          ivv i          i      vv   ii  v  ii i  -i     - 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-T 238

  chrX_13933514_1    607 ACTAAAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGA 656
                             v  i          i   i    ii         i iv ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_13933514_1    657 GATATAGACAAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACAC 704
                         v       iv       i    i--    i  --        vv   i  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATAC 336

  chrX_13933514_1    705 ATCTACAACCATCTGATCTTTGACAAGCCTGATAAAAACAAGCAATGGAG 754
                           i  iiii  vi    i  i      vv  vi  i v  vv      i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_13933514_1    755 AAAGGATTCCCTACTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAT 804
                             i  vvi  vi i  i        i     v      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_13933514_1    805 GCAGAAAACTTAAACTGGGCCCCTTCCTTACACTTCATACAAAAATTAAT 854
                            i  i v v  ii   i     v   i    ivi             i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_13933514_1    855 TCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCT 904
                             i      i ?    i       v   v       i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_13933514_1    905 AGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGAC 953
                                   v    ?i- v i -   iv   v v  vv i     v ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_13933514_1    954 TTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAA 1003
                            v ivv  vi            vvi          vv     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_13933514_1   1004 ATGGGATCT------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTACC 1047
                           v   ii ------       i -   i  ii vv    i  v    i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chrX_13933514_1   1048 AGCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTA 1097
                          iv i      v  i     i                 v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_13933514_1   1098 CTCATCTGACAAAGGGCTAATGTCCAGAATCTACAATGAACTCAAACAAA 1147
                         ivi      i  i  i  vi i        v  i  v      vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_13933514_1   1148 TCTACAAGAAAAAAACAAACAGGCCTATCAAAAAGTGGGCGAAGGATATG 1197
                           v i  v     i     i iv  v  i?    i     i      v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_13933514_1   1198 AACAGACACTTCTCAAAAGAAG 1219
                           i     i     v       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAG 856

Transitions / transversions = 1.42 (105 / 74)
Gap_init rate = 0.01 (9 / 717), avg. gap size = 1.89 (17 / 9)  

1443 23.53 8.47 2.12  chrX_13933514_13935231.rev     1218  1642 (76)  C L1M4_orf2#LINE/L1   (383)   525    74  

C chrX_13933514_1   1642 ACAAAGTTCAATTCAATCCCAATAAAAATCCTAGCAGATTTCTATGTAAG 1593
                            i -     iv       v  v       i   v vi  i v  i ii
  L1M4_orf2#LINE/     74 ACAGA-TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

C chrX_13933514_1   1592 AATTGTGAAACCTTTTCTAAAATATGTATACAAATGCAAAAGACCTAGAT 1543
                              vv  i ivv i       vii   iv        ii    i   v
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

C chrX_13933514_1   1542 TAGCTAAAATAATCTTTACAAAGAAGAATAAATTTAGAGGATTTACACTT 1493
                             i    i      v v         i   v  i     i i      
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

C chrX_13933514_1   1492 CTCAATTTTAAAAATTACTACAAAGCTACAGAAATCAAGA--GTGTGATA 1445
                          i      i    v                 v        --     i  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

C chrX_13933514_1   1444 TTGGCATAAAAATAGACA----AATCAATGGATCAGAAT--AGAGTTCAC 1401
                         i        ii       ----i         vi     --     i  v
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

C chrX_13933514_1   1400 AAACAGACTTACATGCATG-ATGGCCAACT-ATTTTTGACAAAAGTGCTA 1353
                            i i  i--   i   v-    i   i -     i     ii    i 
  L1M4_orf2#LINE/    323 AAATAAACC--CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

C chrX_13933514_1   1352 GG--------------------TA----TTTCAACAAATGATGATGA-AC 1328
                         i --------------------  ----            i  v  i-  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

C chrX_13933514_1   1327 AACTGCTTATCCATGTGGAAAGAAATGAAATTTGAGTACTACATTGTGTT 1278
                              vv  ?   ii  v   ii      i  v  viv    v iiiii-
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC- 469

C chrX_13933514_1   1277 ACACATGCAAAG-TTAATTTCAGATCGATCATAGATAGACCCAAACATAA 1229
                         -  i  i    i-    i iv i  v     ?   ----  i   ii   
  L1M4_orf2#LINE/    470 -CATATACAAAAATTAACTCAAAATGGATCAWAGA----CCTAAATGTAA 514

C chrX_13933514_1   1228 GAGTTAAAGCT 1218
                            i    i  
  L1M4_orf2#LINE/    515 GAGCTAAAACT 525

Transitions / transversions = 2.16 (67 / 31)
Gap_init rate = 0.03 (13 / 452), avg. gap size = 3.46 (45 / 13)  


3435 24.24 2.82 0.45  chrX_13945505_13949792.rev     2911  3797 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_13945505_1   2911 TGGAAAGATATTTTATGTTCATGGATTAGAAGAATCAATATTGTTAAAAT 2960
                                    iii             i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_13945505_1   2961 GTCCATAATACCCAAAGCAATCTACAGATTCAATGCAATCCTTATCAAAG 3010
                          v v   v v      vii              i       i       i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_13945505_1   3011 TACCAATGACATTCTTCACAGAAATAGAAAAAACAATTCTAAAACGTTTA 3060
                          v   iivi v  i  ii       v  v  ivii  i      iviv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_13945505_1   3061 TGGAGCCAGAAAATACCCAGAATAGCCAAA---------------GAGAA 3095
                             iviiv  iiv                ---------------i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_13945505_1   3096 TGAAACTGGGACAACCATATTACCAGACTTCAAATTATACTACAAAGCTA 3145
                         ii  ii   iiv vi  i i v  vi i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_13945505_1   3146 TAGTCATCAAAACAGCATGGTACTGGCATAAAAACAGACACATGGATCAG 3195
                         i   v     i    ii              ii i     i  i     i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_13945505_1   3196 TGGAACAGAATAAAGAACACAGAGATAAAGCCATACATCTACAGTGAACT 3245
                              i     vi   iiv    i     v        i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_13945505_1   3246 CATTTTTGACAAAGTTGCCAAGAACATACTCTGGGGAAAGGACAGTCTCT 3295
                         v     i     i v        v   v vv         i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_13945505_1   3296 TCAATAAATGGTACTGGGGAAACTGGATCATTCATATGCAAAAGGATGAA 3345
                             i       i     iv        - ?i  i         i     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCAAAAGAATGAA 449

  chrX_13945505_1   3346 ATGAGACCCCCTATCTC-TGCCATATACAAAAATCAAATCAAAATAGATT 3394
                         i vi      -  i   -ii              i  v       i   i
  L1M4_orf2#LINE/    450 GTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_13945505_1   3395 AAAGGCTTACATCTCACATTT-GAACTATGAAACTACTACAAGAAGACAT 3443
                          ?  i i  v  v v v vi -i      i     vi  v     i    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_13945505_1   3444 TGGGGAAAATTTCCAGAACATTGGTCTGGGCAAAGATTTCTTGAACAATG 3493
                         v  ? v    i i ivi  v    vi i     v i      ii i -  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TG 597

  chrX_13945505_1   3494 CC-CCACAAGCACAGGTAACCAAAGCAAAAATGGGCAAATGGGATCACAT 3542
                         v -   v       i i   v    v      i ii    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_13945505_1   3543 CAA-GTTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAG----- 3586
                            -i       -   i  ii vv       v  v     v    -----
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_13945505_1   3587 AGACAACCCACAGAATAGGAGAAAATATTTGTAAATAACCCATCTAACTA 3636
                                         i              i    v ivi    i iv 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_13945505_1   3637 GGGATTAATAACCAGAATACATAAGAAGCTCAAACAACTCTATAGGTAAA 3686
                             i vi  v        i    ii i   vv       v   ivv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_13945505_1   3687 AGTCTGATAATCCCATC-AAACATGGGCAAAATATGTAAATAGACATTTC 3735
                           v vi    i  v  i-   v         iv  v i            
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_13945505_1   3736 TCAAAAGAAGACATACAAATGGCAAGCAGGCATATGAAAGGGAGCTCAAC 3785
                           v        i           v ii i   i      i iv       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_13945505_1   3786 ATCATTGATCAT 3797
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (132 / 80)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.64 (29 / 11)  


3203 25.84 2.25 0.22  chrX_13965662_13971622.rev     4581  5470 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_13965662_1   4581 TGGATAAACATTCCATGCTCATGAATAGGAAGAATCAATATCGTGAAAAT 4630
                             v i i  i     i     i  v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_13965662_1   4631 GGCCATACTGCCCCAAGTAATTTATAGATTCAATGCTATTCCCATTAAAC 4680
                            v     v   v  v i  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_13965662_1   4681 TACTATTGACATTCTTCACAGAATTAGAAAAA---AAACTAAAGTTCATA 4727
                          v i vivi v  i  ii     v v  v  i--- vv     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_13965662_1   4728 TGGAACCAAAAAAGAGCCCAAGTAGCCAAAGTAATCCTAAGCAAAAAGGA 4777
                              viiv  ii  v  vi i        ii    i i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_13965662_1   4778 CAAAGCTGGAGGCATCATGCTACTTGACTTCAAACTATACTACAAGGCCA 4827
                              i      vv   ii  v iii i      viv        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_13965662_1   4828 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACCAA 4877
                               i   i    ii         i iv ii i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_13965662_1   4878 TGGAACAGAATAGAGAACCCAGAAATAAGACCACACATCTACA--CATTT 4925
                              i     v    ii          iv   i    i  ii--  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_13965662_1   4926 GATCTTCAACAAACCTGACAAAAGCA----ATGGGGAAAGGATTCCCTAT 4971
                            i   i    ivv  v   i v  ----          i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_13965662_1   4972 TTAATAAATAGTGCTGGGAGAACTGGCTAGCTATATGCAGAAAATTGAAG 5021
                          i  i    i         v      v  ? i i     i  i v     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_13965662_1   5022 CTGCACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 5071
                         i  v      v   i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_13965662_1   5072 AGACTTAAATGTAAAACCTAAAACTATAAAAACCCTAGAAGAAAATCTAG 5121
                             i         i v              vi i          iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_13965662_1   5122 GCA-ATACCATTCAGGACATAGGCACAGGCAAAGATTTCAT-GATGAAAA 5169
                          ?i- v i -   iv   v v  vvi      v i    v -   - vi 
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGA 598

  chrX_13965662_1   5170 TGTCAAAAGCAATTGCAACAAAAGCAAAAGTTGACAAACGGGATCTAATT 5219
                         iii        vvv          v    i v  i   iv   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_13965662_1   5220 AAACTACAGAGCTTCTCCACAGCAAAAGAAGCTATCATCAGAGTGAACAG 5269
                            v vv i i   i vii vv    i  vi      vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_13965662_1   5270 ACAACCTACAGAATGGGAGAAATTTTTTGCAATCTATCCATCTGACAAAG 5319
                               i               v v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_13965662_1   5320 GGCTAATATCCAGAATCTATAAGGAACT--TA-AATTTA-CAAGAAAAAA 5365
                          i  vi          v     i     --  -  i i -i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_13965662_1   5366 ACAA----CTCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 5411
                             ---- i v   ?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_13965662_1   5412 AAAAGAAGACATTTATGCAGTCAACAAACATATGAAAAAA-GATCAACAT 5460
                         v        i  vi viii i   i  i  i       i - v       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_13965662_1   5461 CACTGATCAT 5470
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.57 (138 / 88)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


3146 26.46 0.88 0.77  chrX_13978722_13985271.rev     5155  6061 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_13978722_1   5155 TGGAAGAACATTCCATGTTCACGGATAGGAAGAATCAATATTGTGAAAAT 5204
                              ii i  i         i    v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_13978722_1   5205 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5254
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_13978722_1   5255 TACCAA-TGCATTTCTTCACAGAA-TTGGAAACAA-CT-ACTTTAAATTT 5300
                          v   i-   v   i  -i     -   ---    -  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chrX_13978722_1   5301 CCTATGGAACCAAAAGAGAGCCCACATTGCCAAGACAATCCTAAGCCAAA 5350
                          v       viiv   i  v  viv  v     i      i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_13978722_1   5351 AGAACAAAGCTGGAGTCATCACGCTACCTGACTTCAAACTATACTACAAG 5400
                                  i     vvv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_13978722_1   5401 GCTACAATAACCAAAACAGCATGATACTGGTACCAAAACAGAGATAGAGA 5450
                               i   i   i    ii  i      i iv ii i   v   v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_13978722_1   5451 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAA 5498
                         i        i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_13978722_1   5499 CCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5548
                         i  vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_13978722_1   5549 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5598
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_13978722_1   5599 CTGAAACTGGATACCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5648
                         v    ii    iv   v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_13978722_1   5649 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5698
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_13978722_1   5699 ACCTAGGCA-ATACCATTCAGGGCACAGGCATGGGCAAGGACTTCATGAC 5747
                           v    ?i- v i -   iv i viv  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_13978722_1   5748 TAAAACACCAAAAGCAATGGCAACAAA-GCCAAAATTGACAAATGGGATC 5796
                           vi            vvi        - vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_13978722_1   5797 TAATTAAACTAAAGAGCTTCTGCCCAGCAAAAGAAACTACCATCAGAGTG 5846
                          v  i   v v  i i   i  iv vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_13978722_1   5847 AACAGGCAACCTATAAAATGGGAGAAAATTTTTACAATCTACCCATCTGA 5896
                           v  i     i i i             v   i   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_13978722_1   5897 CAAAGGGCTAATATCCAGAATCTACAGAGAACTTAAACAAATTTACAAGA 5946
                         i  i  i  vi          v  i i      ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_13978722_1   5947 AAAAATCAAACAACCCCATTAAAAAGTGGGTGAAGGACATGAACAGACAG 5996
                             iv    i     v   ?    i    ii     iv    i     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_13978722_1   5997 TTCTCAAAAGAAGACATTTATGCAGCCACCAAACACATGAAAAAATGCTC 6046
                              v        i  vi viii    vi  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_13978722_1   6047 ATCATAACTGGCCAT 6061
                          v   v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


3275 24.89 2.58 0.78  chrX_14054669_14057177     1125  2016 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14054669_1   1125 TGGAAAAACATCCCATGCT----GATCAGAAGAATTAACACTGTTAAAAT 1170
                               i i        i ----   ii     v    i i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14054669_1   1171 GACCATATTGCCCAAAGCAATCTACAGATTCAATGCAATCTCTATCAAAC 1220
                          i v   i v      vii              i      i        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14054669_1   1221 TACAAACGTTATTCCTCACAGAATTAGA-AAGC-AATCCTAAAATTCATA 1268
                          v v i vviv  ii ii     v v  -    -i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_14054669_1   1269 TGGAACAAAAAAAAGAGCCAGAATACCCAAAGCAACACTGAACAAAGAGA 1318
                              - viv  ii  v        v     i   ivi    v  ii   
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_14054669_1   1319 ACGAAGCTGGAGGCATCACGTTACTTGACTTCAAAATATATTACAAGGCT 1368
                           i   i      vv    ii v iii i       iv  i     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_14054669_1   1369 ATAGTAAGCAAAACAGTATGGTATTGATGTAAAAGTAGACACACAGACCA 1418
                          i     v   i     i     i  iii   iii      i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_14054669_1   1419 ATGGAACATAATAGAGAACCCATAAATAAAACCACATATTTACAGCTAAC 1468
                               i v   v    ii   v       v   i i     ii ii  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_14054669_1   1469 TAATTTTTGATGAAG---CCAACGTGAACTTACATTGGGGAAAGGACATT 1515
                          i     i  ii i ---    ---  v v v  v         i i v 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAA---GACCATTCAATGGGGAAAGAATAGT 396

  chrX_14054669_1   1516 CTCTTTAATAAATAGTGTTGGGAAAACAGGATATCCACATACAGAAGAAT 1565
                           i  i  i    i   i     v   v     ?      i  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_14054669_1   1566 GAAACTGGACTCCTATCTCTCACCATATATAAAAATCAACTCAAAATGGG 1615
                            ii     i    i   v         i      i            i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_14054669_1   1616 TTAAAAACTTAAACACAAGACCTGAAACTATAAAAACACTAGAAGAAAAT 1665
                          i ? i  i    iii    v  i           vivi          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_14054669_1   1666 CAGGGAG--AACGTTCCTGGATATTCGTCCAAGCAAAGAATTTATGACTA 1713
                         vvi  ? --  iv   v  - iv  v vii i    v iv  iv iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_14054669_1   1714 AGACCTCAAAAGAACTGGCAACAAAAGCAAAAACAGAAAAATGGGACTAC 1763
                         v   vi      v  vi          v     i   v    v     v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_14054669_1   1764 ATTAAA--------CTATAGTATAGCAAAGAAGAAAATCAACAAAGTGAA 1805
                           i   --------  v v  iivv     i v vv     v        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_14054669_1   1806 GAAACAACCTATTGAATGGGAGAAAATATTTGTAAACTATTCATCTGACA 1855
                         i i      i iv                   i   ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_14054669_1   1856 GGTGACTAATATCCAGAATGTACAAGGAAATC----AAACCAACAGGAAC 1901
                         i v    vi          i  i  i   v  ----  vi   i iv  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_14054669_1   1902 AAAACCAAAAAAGTCCTATTTAAAAGTGGGCAAAGGATGTGAATAGAAAT 1951
                           i  --   v ii  v   ?    i            v        v  
  L1M4_orf2#LINE/    796 AAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_14054669_1   1952 TTCTCAAAAGAAGATGTACAGATGGCCAACAGGTATATGAAAAAATGCTC 2001
                              v         i    i        i i i i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_14054669_1   2002 AACGTCACTAGTCAT 2016
                            i   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (140 / 78)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.73 (30 / 11)  


3242 27.53 0.33 0.33  chrX_14064638_14067322.rev     1287  2194 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14064638_1   1287 TGGAAGAACATTCCATGCTCGTGGGTAGGAAGAATGAATATCATGAAAAT 1336
                              ii i  i     i  i   i v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14064638_1   1337 GGCCATACTGCCCAAGGTAATTGATACATTCAATGCCATCCCCATCAAGC 1386
                            v     v     iv i  iv i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14064638_1   1387 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1434
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_14064638_1   1435 TACGGCACCAAAAAAGAGTCTGCATTGCCAAGACAATCCTAAGCCAAAAG 1484
                           i  v viiv  ii  vi v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_14064638_1   1485 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1534
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_14064638_1   1535 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1584
                           i     i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_14064638_1   1585 AATGGAACTGAACGGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT 1634
                                iv   iv   vvii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_14064638_1   1635 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 1684
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_14064638_1   1685 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1734
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_14064638_1   1735 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 1784
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_14064638_1   1785 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAACC 1833
                          ?    i    i  v   v       i      -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chrX_14064638_1   1834 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 1883
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_14064638_1   1884 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 1933
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_14064638_1   1934 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1983
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_14064638_1   1984 GGCAACCTATAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAA 2033
                          i     i i i             v  ii   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_14064638_1   2034 GGGCTAATATCCAAAATCTACAAAGAACTCAAACAAATTTACAAGAAAAA 2083
                           i  vi      i   v  i         vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_14064638_1   2084 AACAAACAACCCCATTAAAAAGTGGGCGAAGGACATGAACAGACACTTCT 2133
                         i     i     v   ?    i     i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_14064638_1   2134 CAAAAAAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 2183
                          v   i    i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_14064638_1   2184 TCACTGGCCAT 2194
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


3170 26.46 0.66 0.55  chrX_14124822_14128583      492  1398 (2364)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_14124822_1   1398 TAGAAAAACATTTTGTGCTCATGGAAAGGAAGAAATAATGTTATTAAAAT 1349
                          i    i i  iiii  i       vv      vv    i  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_14124822_1   1348 GACCATACTGCCCAAAGCAATCTACAAATTCAACGCAATCTCCATTAAAA 1299
                          i v     v      vii       i             i i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_14124822_1   1298 TATCAACATCATTTTTCACAGAAATAGAAAAA--AATTCCAAAAATGCAT 1251
                          vi  i vv v     ii       v  v  i--i  -  v     v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

C chrX_14124822_1   1250 ATGGAA-TGAAAAAAAAGCCCA-AATAAGCAAAACAATCCTGAGCAAAAA 1203
                               -  v  iii --    -    iv          i   iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chrX_14124822_1   1202 AGACAAAGCTGGAGGCATCACACTACTCGACTTCAAAATATATTAAAAGG 1153
                         ii      i      vv       v i i i       iv  i  v  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chrX_14124822_1   1152 CTATCATGGCCACGACAGCATAGTATTGGTATAAAAGCAGATATATAGAT 1103
                            ivi iii  v     ii i   i   i    iiii   i        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chrX_14124822_1   1102 CAATGGAAGAAAATAAAGAACCCCAAAATAAATGTACATACTTACAGCCA 1053
                                 v i   vi   ii  vi       ivi i i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

C chrX_14124822_1   1052 ACTGATTTTTGACAATGGTGCCAAGAACATACGCTGGAGAAAGGATAGCC 1003
                          i       i     v          v   v iv   i     i    i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chrX_14124822_1   1002 TCTTCAATGAATGGCGCTGGGAAAACTGGATAGCCACATGCATAAGAATG 953
                          i     ii     i       v         ?         v       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chrX_14124822_1    952 AAACGGGCCCCCTATCACTCACCCTATAAAAAAACCAACTCAAGATGGAT 903
                           iiv  v      i v v    v    v     ii       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

C chrX_14124822_1    902 TAAATACTTAAATGTGAAGTCCAAACCTATAAAATTAATAGAAAAAATTA 853
                         i ? v  i       i iiv i   v        i vv     i   vi 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

C chrX_14124822_1    852 CAGGAA-AAATACTTCAGGACACTGGTCTAAGCAAATATTTTATGGCTAA 804
                         i   ?i-    -    iv   vi   vi  i    vvi   iv i v  v
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_14124822_1    803 GACCTCAAAAGCACTGGCAAGAAAAACTAAAATACACAAATGAGACTATA 754
                            vi         vi    v    ivv      v i    vi    vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_14124822_1    753 TTAAACTAAAATGATTTTACACAGCAAAGGAAACAATCAGCAAAGTGAGG 704
                          i   v v   viv    iii vv       v  v    iv       ii
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_14124822_1    703 AGACAACCTGTTGAATGACAGAACATTTTTACAAACTATTCAACTGACAA 654
                                 iiiv     iv    v  v   i    ii  vi v    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chrX_14124822_1    653 ACAACTAATATCTAAACCATA-AAAGTAACTCAAACAACTCAACAGGAAC 605
                         ivi   vi    i i vi   -    -     vv         i iv  v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAG-AACTCTTACAACTCAATAATAAA 795

C chrX_14124822_1    604 AAAACAAATTATTCTATTTAAAAGTGGGCAAAGGACAAGAATAGACATTT 555
                           i      v ii v   ?    i           ivv            
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chrX_14124822_1    554 CTCAAAAGAAGACACACAAATGGCCAACAGTTATATGAAAAAATGCTCAA 505
                            v        i i            i ivi i       i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chrX_14124822_1    504 CATCACTAATAAT 492
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (145 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.22 (11 / 9)  

3573 23.81 0.66 0.55  chrX_14124822_14128583     2363  3269 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14124822_1   2363 TGGAAAGATATACCATGGTCACGTATTAGAATAATCAATATTGTTAAGAC 2412
                                    v     v   i v   i   v v i             i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14124822_1   2413 AGCCGTACTATCTAAATCAATCTACAGATTAAATGCAATCCCTATGAAAA 2462
                         i  vi    vi i    ii           v  i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14124822_1   2463 TACCAA-TGTCATTATTCACAGAAATAGAAAAAAACAATCCTAAAATGTA 2511
                          v   i-  i v  -  ii       v  v  iv-ii          vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chrX_14124822_1   2512 TATGGAGCCAGAAAATACCCACAATGCCCAAAGCTACCCTAAGCAAAAAG 2561
                               iviiv  iiv     v   iv     i v i i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_14124822_1   2562 AACAAAACTGGAGTAATCACATTACCAGACTTCAAATTATACTACAATGC 2611
                               ii     v v     i v  vi i      viv        v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_14124822_1   2612 TATAATAATCAAAACAGCATGGTACTGACATAAAAACAGACACATGGATC 2661
                           i i       i    ii        i     ii i     i  i    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_14124822_1   2662 AGTGGAACAGAAAAAAGAATGCAGAGATAAAGCCATATATCTACAGTGAA 2711
                          i     i    vvi   i v    i     v     i  i  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_14124822_1   2712 CTCATTTT-GACAAAGTTCACAAGAACATATGTTGGGTAAAGGACAGTAT 2760
                         i v     -     i v vv     v   viiv    v    i i   v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_14124822_1   2761 CTTCAATAAATGGTGCTGGGAAAACTGGATATTTATATGCAAAGGGATGA 2810
                         i     i              v         ?ii i       i i    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_14124822_1   2811 AACTAGACCCCCTATCTC-TGCCATATACAAAAACCAAACCAAAATTGAT 2859
                          ii i      -  i   -ii             ii  vi      v   
  L1M4_orf2#LINE/    449 AGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_14124822_1   2860 TAAAAGCTTAAATCTCAGGCCTCAATCTATGAAACTACTACTAGAAAACA 2909
                         i ? ii i     v v  iv  v  v    i     vi  vv        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_14124822_1   2910 TTGGGGGAAATCTCTAGGACATTGGTTTGGGCAAATATTTCTTGAGTAAT 2959
                          v  ? v      iiiv   v    v  i     vvi      iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_14124822_1   2960 ACCCCACAAGCACAGGCAACCAAAGAAAAAATGGACAAATGGGATCACAT 3009
                           v   v       i     v           i  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_14124822_1   3010 CACA-TTAAAAAGCTTCTGCACAGCAGAGGAAACAATCAACAAAGTAAAA 3058
                           v -       -   i  ii vv  i    v  v     v     i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_14124822_1   3059 AGACAGCTCACAGAATGGGAGAAAATATTTGCAAAGTACCCATCTGACAA 3108
                              i i                           vi ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_14124822_1   3109 GGGATTAATAACCAGAATATATAAGAAACTCAAACAACTCTATAGGAAAA 3158
                             i vi  v             ii     vv       v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_14124822_1   3159 AGTCTGATAACCCCATC--AAAATGGGCAAAAGATCTTGACTAGACATTT 3206
                           v vi       v  i--            i   -    v         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGACATTT 845

  chrX_14124822_1   3207 CTCAAAAGAAGACATGCAAATGGCAAGCAGGCATATGAAAAGGTGCTCAA 3256
                            v        i  i        v ii i   i        i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_14124822_1   3257 CATCATTGAACAT 3269
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (125 / 88)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.10 (11 / 10)  


1854 24.74 3.09 0.21  chrX_14235902_14242281.rev        2   486 (5894)    L1M4_orf2#LINE/L1      329   827 (81)  

  chrX_14235902_1      2 ATCCATCTATCTACAGCCAACTCACTTTCAACAAAGGCACCAAGAATATT 51
                          i    vi  i  ii i   i v i    i    i  ii      vi   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_14235902_1     52 CATTGGGGAAAGGATAATCTCTTCAATAAATGGTGCTGGGAAAACTGGAT 101
                           v         i   i   i     i              v        
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_14235902_1    102 ATCCATATGCAGAAGAATAAAACTAGACCCCCACCTCTCACCTTATATAA 151
                          ?   i     i      i  ii i      i     v    v    i  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_14235902_1    152 AAATCAACTCCAAATGCAGTGAAGACTTAAATGTAAGACCCAAAACTATA 201
                             i     v     v vii?    i           v i         
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_14235902_1    202 AAACTCCT-GTGAAAAACATAGAAG-AGATGCTCCAGGATATTGGTCTGG 249
                               i - vii         i? - i  -  i iv  iv    vi i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAG 577

  chrX_14235902_1    250 GAAAACATATTGTGAATAAGACCTCAAAAGCACAGGCAACAAAATCAAAA 299
                          v  vvi v iv ii   v   vi          i         vv    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_14235902_1    300 ATAAATAAATTG-----TATCAAACTAAAAAGCTGCTGCACATCAAAGAA 344
                            i        -----i      v v    i  vi  ii v      i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_14235902_1    345 AACAATCATCAGAGTGAAAGGAAAACCTACAGAATTGGAGAAAATATTTG 394
                         v  v    vv i       i  v    i       v              
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_14235902_1    395 CAAACTATCCATTTGCTGGGGAATTAATATCTATAATATACAAAGAACTC 444
                             ii  vi  i  v ii  i i vi    i v      i         
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_14235902_1    445 AAACATCTCAACAGCAAAA-------CAATCTGATT-AAAAGTGGGAAAA 486
                         vv   v     i ii    -------i  i ii   -    i    v   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

Transitions / transversions = 1.79 (75 / 42)
Gap_init rate = 0.01 (6 / 499), avg. gap size = 2.67 (16 / 6)  

3157 27.75 0.55 0.55  chrX_14235902_14242281.rev     4982  5889 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14235902_1   4982 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5031
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14235902_1   5032 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5081
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14235902_1   5082 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5129
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_14235902_1   5130 TATGGAACCAAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCCAAAAG 5179
                                viiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_14235902_1   5180 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAAGTATACCACAAGGC 5229
                                i      vv    i  v  ii i      iiv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_14235902_1   5230 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGTTATAGACC 5279
                                 i   i    ii         i iv ii i   vv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_14235902_1   5280 AATGGAACAGAAC--AGAGCCCTCAGAAATAGCGCTGCATATCTACAACT 5327
                                i    i--    i  --       ivv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_14235902_1   5328 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTTC 5377
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_14235902_1   5378 CTATTTAATAAATGGTGCTAGGAAAACTGGCTAGCTATATGCAGAAAGCT 5427
                           v  i  i          i   v      v  ? i i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_14235902_1   5428 GAAACTGGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAGATGGA 5477
                            ii    i    v   i     v    i         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_14235902_1   5478 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5527
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_14235902_1   5528 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAGGGACTTCATGTCTA 5576
                         v    ?i- v i -   iv   v v  vv i    iv ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_14235902_1   5577 AAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCGA 5626
                         vi            vvii         vv     v  i    v   iivv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_14235902_1   5627 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5676
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_14235902_1   5677 CAGGCAACCTGCAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5726
                         v  i     ii                v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_14235902_1   5727 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5776
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_14235902_1   5777 AAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTT 5826
                           i     i     v  i? v  i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_14235902_1   5827 CTCAAAAGAAGACATTTATGCAGCCCACAGACAGATGAAAAACTGCTCAT 5876
                            v        i  vi viii   v i ii  v       iv      v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_14235902_1   5877 CATCACTGGCCAT 5889
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2149 17.34 1.19 1.43  chrX_14344449_14347802     1318  1738 (1616)    L1M4_orf2#LINE/L1        1   420 (488)  

  chrX_14344449_1   1318 TGGAAAAACATCCCTTATTAAGTCATGAGTAGGAAGAC--AATATATTTA 1365
                               i i     v i  ----    ii v       --     vv   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTT----CATGGATTGGAAGACTTAATATTGTTA 46

  chrX_14344449_1   1366 AGGTGTCAATACTACCCAAAGTTATCTACAGATTCAATGCAATCCCTATC 1415
                           i  v       v      v v              i            
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_14344449_1   1416 AAAATTCCAACAGCCTTTTTTGGCAGAAGTGGA-AAACTCAATCCTCAAC 1464
                              i   i v          -     i v  -  i  -i     v  v
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCT-GATCCTAAAA 144

  chrX_14344449_1   1465 TTCATATTAAATTGCAAGGGGCCCTGAATAGTCAAAATAACCTTGAAAAT 1514
                                vi  v        i   v      i     i  i        v
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_14344449_1   1515 GAAGAACAAAGCGGAAGGACTCACAATTCCTAACTTCAAAACTTAATACA 1564
                                    iv i          v    i  i           v    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_14344449_1   1565 AAACCACATTA-TCAAAACAGTGTCATACTGGCATAAGGATAAATATGTT 1613
                           i i   v  -    i       vi                i i  i v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_14344449_1   1614 GACCAATAGAATAAAATTGATAGTTCAGAAATAAACCCACACACCTATGG 1663
                           i    i     i      v   i              i   ii     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_14344449_1   1664 CCAGTTGATTTT-GACAGGGTTGGCAAGTCCATTTAATGAGGAAAAACCA 1712
                         i  i        -    i  v  v    v     i    i     i vi 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_14344449_1   1713 GTCTCCTCAAGAAATAGTGCTGGGAC 1738
                             ii    v    i          
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGAC 420

Transitions / transversions = 1.61 (45 / 28)
Gap_init rate = 0.02 (7 / 420), avg. gap size = 1.57 (11 / 7)  

1241 16.73 1.99 0.40  chrX_14344449_14347802     2052  2302 (1052)    L1M4_orf2#LINE/L1      403   657 (251)  

  chrX_14344449_1   2052 AAGAAATAGTGCTGGCACAACTGAATTTCCACATGCAAAACAATGAAGTT 2101
                           v    i       v       i  v?            v         
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_14344449_1   2102 GGACCTCT--CTCATACCATATACAAAAATTATCTCAAAATGAATCAATT 2149
                              i  --    i                 v         i    ?vv
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_14344449_1   2150 ACCTAAATGTAAGCGTTAAAACCAAAAAGCTGCTTTT--TAAAATATAGG 2197
                                      v i      i v   i  -   vv--v    i     
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGG 551

  chrX_14344449_1   2198 GGTAAACGTTCATTACCTTGGATTTGGCAATTGATCCTTGGATATGAAAC 2247
                         ?     iv   i v       i  v      v v i   i       v  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_14344449_1   2248 CAAA-GCATAAGAAACAAAAGAAAAAATAGGTAAATTAAACTTTATCAAA 2296
                             -   i   v                 i      ii    i      
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_14344449_1   2297 ACTAAA 2302
                          i    
  L1M4_orf2#LINE/    652 ATTAAA 657

Transitions / transversions = 1.05 (20 / 19)
Gap_init rate = 0.02 (4 / 255), avg. gap size = 1.50 (6 / 4)  

1092 17.63 7.55 0.00  chrX_14344449_14347802     2584  2861 (493)    L1M4_orf2#LINE/L1      610   908 (0)  

  chrX_14344449_1   2584 CAAAAAAGAAAAAAACAAACAAACAAA--AAAAGCCA-CAACCCTAAAAA 2630
                            iv  v    i  v   i i i   --ii vvi  -   vvi      
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_14344449_1   2631 CTTTTATGCATCAAAGGACATTATGAAGAAAGTGAAAAAACAAT------ 2674
                              i   v          i   v             i    i------
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_14344449_1   2675 AA----AGAAAATATTTGTAAATCATGT--CTGAGGAGGGTTTAATATCC 2718
                           ----            i       i --    vi    vi vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_14344449_1   2719 AGAACATGTAAAGAACT---ACAATTCAATAA---AATGACAAAATACCC 2762
                             i  i         ---    i       ---  v      vv    
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_14344449_1   2763 AATTCAAAAATGGGTAAAGGGCTTGAAGAGATATTTATCCAAAGAAAATA 2812
                             ?         i     ii     v   i    v         i   
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_14344449_1   2813 TACAAATAGCCAGTAAGTACATGAAAAGATGCTCAATGTCATTACTCAT 2861
                                i    i    i                  ii   ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (31 / 17)
Gap_init rate = 0.02 (7 / 299), avg. gap size = 3.00 (21 / 7)  


1905 23.33 5.16 2.10  chrX_14364819_14367623.rev     1117  1639 (1166)    L1M4_orf2#LINE/L1        1   539 (369)  

  chrX_14364819_1   1117 TGGAAAAACAACCCATGCTCATACATTTGAAGA----ATATCATTAAAAT 1162
                               i i v      i    iv   v     ----    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14364819_1   1163 AGTCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 1212
                         i iv     v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14364819_1   1213 TAACAA-TGTCATTTTTCACACAATTAGAAA--AAAAAACT-ATTCTAAA 1258
                          vv  i-  i -     ii  ------    --i v  i  -  i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCA------GAAATTGACAAGCTGATCCTAAA 143

  chrX_14364819_1   1259 ATTCATACAGAAC--CAAAAAACAGCCCAGA-TAACCAAAGCAATCCTAA 1305
                                ii   v--   iii  ---     -  i     i     i i 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGA 190

  chrX_14364819_1   1306 GCAAAAAGAAGAAAGCTGGAGGCATCACACTACCCAAGTTCAAACTGTAC 1355
                         iv  i     v    i      vv       v     v      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_14364819_1   1356 TATAAGGCTACAGTAATAAAAACAACATGGTACTGGTACAAAAACAGACA 1405
                           i  i           v  i   iii         i i  ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_14364819_1   1406 CATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCACACAC-- 1453
                         i     i        i     v    ii           v   i   i--
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_14364819_1   1454 --AACCAGCTGATCTTTGACAAAA----CAAG-C-------TGGGGAAAG 1489
                         --iii  ii    i  i     ii----    - -------         
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_14364819_1   1490 GACTCCTTTTCCCAAAAAATGGTGCTGGAATGACTAGCTAGCCATATGCA 1539
                         i - vv i  ii   v            i ii   i v  ?   i     
  L1M4_orf2#LINE/    391 AA-TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_14364819_1   1540 GAAGAATGAAACTGGACTACCACCTTTTACTATATACAAAAATTAAATCT 1589
                         i         ii     iv i    ivi  i               v  v
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_14364819_1   1590 AGATGGATTAAAGATTTAAGTGTATGGCCTCAAACTATAAAAATCCTAGA 1639
                          i      i ?   ii   i    v iv  v           v  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

Transitions / transversions = 2.43 (85 / 35)
Gap_init rate = 0.03 (14 / 539), avg. gap size = 2.71 (38 / 14)  

1129 26.67 3.64 3.43  chrX_14364819_14367623.rev     1820  2314 (491)    L1M4_orf2#LINE/L1      413   908 (0)  

  chrX_14364819_1   1820 GCTGAGGCAA---GAAAATCACTTG-AACCCAGGAATGGAGTTGTCAGTG 1865
                             i i   ---  v ?i   v  -  --- i     i     ----- 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAA---AAGAATGAAGTTG-----G 454

  chrX_14364819_1   1866 AGCCA-AGATCACACCAC-TGCA--------CTCCAGCCTGGGTGACAGA 1905
                          v  v- vv        i- i  --------   v iv-   i v ?   
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGATCAWAGA 503

  chrX_14364819_1   1906 GTGAGATGTTGTCTCAAAAGAAAAAAAAAAAAAAATCCTAGACAGAAGC- 1954
                         viv i    ------  i  vv    vv v    v  i    vii  i -
  L1M4_orf2#LINE/    504 CCTAAATGT------AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_14364819_1   1955 TAGGAA-ACACCATTCTTGACACTGGCCTTGGAAAATTATTT-TTAGACA 2002
                             ?i- v i -   v    vi   v-  i iv   vi   -     i 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATA 595

  chrX_14364819_1   2003 AGTCCCCAAAAGCAATTATAACAAAAACAAAAGTTGCCAAATGGGACTTA 2052
                         v v v         vvvii       iv    i v vi    v      v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_14364819_1   2053 ATTAAACCAAAGAGCTTCTTCACAGCAAAAGAAATTATCAATAGAGTAAA 2102
                           i   viv  i i   i vii vv    i  v i      v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_14364819_1   2103 CAGACAAGTTACAGAATAGAAGAAAATGTTCACAAACTATGCATCTGATA 2152
                         v      vii       i i       i  ii    ii  ii        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_14364819_1   2153 AAAGCCTAATATCCAGAATCTATAGGGAACTTAAGCCAATCAATAAGCAA 2202
                          ii v  vi          v    ii     ivvi v v       vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_14364819_1   2203 AAAACAAATAGCCCCATT-AAAAATGGGCAAAGGACATGAACAGACACTT 2251
                           i       i   v   -                iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_14364819_1   2252 CTCAAAAGAAGACATACACATGGTCAACAAACATAGGAGAAAATGTTCAT 2301
                            v        i     v    i   i  i  i v  i  i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_14364819_1   2302 CATCACTGGTCAT 2314
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (70 / 59)
Gap_init rate = 0.03 (15 / 496), avg. gap size = 2.33 (35 / 15)  


3085 26.37 2.35 0.89  chrX_14399391_14403976.rev     3201  4095 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14399391_1   3201 TAGAAGAACATTCCATGCTCATGGATAGGAAGAATCGATATTGTGAAAAT 3250
                          i   ii i  i     i        v      v ii       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14399391_1   3251 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCTTCAAGC 3300
                            v     v     iv i  i  i        i  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14399391_1   3301 TACCAATGACTTTCTTCACAGAA-TTGGAAACAA-------CTAAAGTTC 3342
                          v   iivi i  i  ii     -   ---    -------     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_14399391_1   3343 ATATGGAACCAAAAAAGAGCCTGCATTGCTAAGACAATCCTAAGCAAAAA 3392
                                 viiv  ii  v  v v  v  i  i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_14399391_1   3393 GAGTAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 3442
                           ii    i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_14399391_1   3443 CTACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGATATATAGAC 3492
                                  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_14399391_1   3493 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTATAAC 3540
                                 i    i--    i  --        vv   i    i   iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_14399391_1   3541 CATCTGATCTTTGACAAACCTAACGAGAACAAGAAATGGGGAAAGGATTC 3590
                           vi    i  i     ivv iv i   v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_14399391_1   3591 CCTATTTAATAAATGGTGCTGAGAAAACTTGCTAGCCATATGTAGAAAGC 3640
                         i  v  i  i           i  v    v v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_14399391_1   3641 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 3690
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_14399391_1   3691 ATTAAAGACTTAAATGTTAGACCTAAAAC---------CCCAGAAGAAAA 3731
                           i ?    i       v   v       --------- ii         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_14399391_1   3732 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAA-GGTCTTCATGAC 3779
                          v    ?i- v i -   iv   v v  vv i     -   -   v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGA 593

  chrX_14399391_1   3780 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 3829
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_14399391_1   3830 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 3879
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_14399391_1   3880 AACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACCCATCTGA 3929
                           v  iv    i                 v      ivii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_14399391_1   3930 CTAAGTTCTAATATACAGAATCTACAAAAAACTTAAACAAATTTACAAGA 3979
                         iv i vv  vi   v      v  i   i    ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_14399391_1   3980 AAAAAATCAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACA 4029
                             i -    i     v  i? v  i     i      v    i     
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_14399391_1   4030 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCT 4079
                         i     v        i  vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_14399391_1   4080 CATCATCACTGGCCAT 4095
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.64 (29 / 11)  


1935 19.61 0.68 23.27  chrX_14460581_14467218.rev     4975  6147 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14460581_1   4975 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCCTGAAAAT 5024
                              ii i  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14460581_1   5025 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCAATCAAG 5074
                            v     v     iv i  i  i        i  v     i -    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAAA 99

  chrX_14460581_1   5075 CTACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 5121
                         v v   i-       i  -i     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_14460581_1   5122 CCTATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAA 5171
                          v       viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_14460581_1   5172 AGAACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAG 5221
                                  i      vv    v  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_14460581_1   5222 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATCTAGA 5271
                                   i   i    ii         i iv ii i   v  v    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_14460581_1   5272 CCAATGGAACAGAACGGAGCCCTCAGAAATAATACCACACATCTACAACC 5321
                         i        i    iv   vvii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_14460581_1   5322 ATCTGATCTTTGACAAACCTGGCAAAAACAAGAAAAGGGGAAAGGATTCC 5371
                          vi    i  i     ---------------------   ----------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAA---------------------GGG---------- 365

  chrX_14460581_1   5372 CCATTTATTTATTTATTTTTTAGTTTTTTATTTTTGAAACCCAAGTTTTA 5421
                         ----------------------------------  ----     ---- 
  L1M4_orf2#LINE/    366 ----------------------------------TG----CCAAG----A 373

  chrX_14460581_1   5422 CTATTCTGTACATTCACGTAGCAAAATCCCATCAAATTAATGTCATAGAC 5471
                          i    --------------------------------    --------
  L1M4_orf2#LINE/    374 CCATTC--------------------------------AATG-------- 383

  chrX_14460581_1   5472 ATTATAGGCCCATAATAAAATTCTTAGCTAAGAATTCTCCATGGCCCTAC 5521
                         -----i  ---------   -----------    ---------------
  L1M4_orf2#LINE/    384 -----GGG---------AAA-----------GAAT--------------- 393

  chrX_14460581_1   5522 TGATTCTGCTTTTTTTTTTATTATTATACTTTAAGTTTTAGGGTACATGT 5571
                         ---------------------------------   i  -----------
  L1M4_orf2#LINE/    394 ---------------------------------AGTCTT----------- 399

  chrX_14460581_1   5572 GCACAATGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCA 5621
                         --------------------------------------------------
  L1M4_orf2#LINE/    400 -------------------------------------------------- 399

  chrX_14460581_1   5622 CTGCATTAAATAGGATTCCCTATTTAATAAATGGTGCTGGGAAAATTGGC 5671
                         ----------------------  i  i              v  i   v
  L1M4_orf2#LINE/    400 ----------------------TTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_14460581_1   5672 TAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACA 5721
                           ?   i   i i  iiv    ii    i    v   i     v      
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_14460581_1   5722 AAAATCAATTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCAT 5771
                              i  i    i      i ?    i       v   v       i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_14460581_1   5772 AAAGACCCTAGAAGGAAACCTAGGCA-ATACCATTAGGACATAGGCATGG 5820
                            ivi i      i    v    ?i- v i v iiv   v v  vv i 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_14460581_1   5821 GCAAGGACTTCATGTCTACAACACCAAAAGCAATGGCAACAAAAGCCAAA 5870
                             v ii   v ivv  ii            vvi          vv   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_14460581_1   5871 ATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGA 5920
                           v  i    v   ii v  i   v v  i i   i  ii vv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_14460581_1   5921 AACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTG 5970
                         v    i  vv i      v  i     i                 v    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_14460581_1   5971 CAATCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTC 6020
                            vii ivi      i  i  i  vi          v  i  v      
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_14460581_1   6021 AAACAAATTTACAAGAAAAAAACAA----CCCCATCAACAAATGGGCAAA 6066
                         vv    v iv i  v     i    ----   v  i? v           
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_14460581_1   6067 GGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGAC 6116
                            iv    i     i     v        i  vi viii     i ii 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_14460581_1   6117 ACATGAAAAACTGCTCATCATCACTGGCCAT 6147
                                  iv      v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 15.61 (281 / 18)  


3092 23.86 5.02 1.37  chrX_14544727_14550418.rev     4332  5207 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14544727_1   4332 TGGAGAAACATTCCATGCTCATGGATAGGAAAAATCAATATAATGAAAAT 4381
                             i i i  i     i        v    i v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14544727_1   4382 GGCTATACTGCCCAAAGTAATTTATAGATTCAATGCAATTCCCATTAAAC 4431
                            v     v      v i  i  i        i     i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14544727_1   4432 TACCA-CTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAAATTAA 4479
                          v   -   v -  i  ii     v v  v  i-  - iii       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_14544727_1   4480 TATGGAACCAAAAAAGAGCCCAAATAGCCAA------------------G 4511
                                viiv  ii  v  vi         ------------------ 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_14544727_1   4512 AACAAATCTGGAGGCATCACACTACCCAACTTCAAA--CTA-TACAAGCC 4558
                               vi      vv       v     i      --i  -     iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_14544727_1   4559 TACAGTAACCAAAACAGCATGGTACTGGTATAAGAACAGACATATAGACC 4608
                                 i   i    ii         i     i i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_14544727_1   4609 AATGGAACAGAATAGAGAACTCAGAAATAAGACTGAACACCTACAACCAT 4658
                                i     v    iii         iv iiv   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_14544727_1   4659 CTGATCTTCAACAAAACTGACAAAAACAAGCAATAGGGAAAGGACTGTCT 4708
                         i    i   i    iiv  v   i v  vv    i       i iv    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_14544727_1   4709 ----AATAAATGGTGCTGGGAGTGCTGGCTAGCCATATGCAGAAAACTGA 4754
                         ----  i              vvi    v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_14544727_1   4755 AACTGGACTCCTTCCTTGCACCATATACAAAAATTAACTCAAGATGGATT 4804
                          ii     i   v   ii                        i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_14544727_1   4805 AAAGATTTAAATGTAAAATCCAAAACTATAAAATTCCTGGAAGAAAATCT 4854
                          ?   ii         i v i            i  i i        iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_14544727_1   4855 AGGCA-ATACCATTCAGGACATAGGCACAGGCAAAGATTTC------ATG 4897
                            ?i- v i -   iv   v v  vvi      v i    ------   
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_14544727_1   4898 ACGAAATTGCCCAAAGCAATAGCAACAAAAGCAAAAATTGACAAATGGGA 4947
                           i------  v      vv           v      v  i    v   
  L1M4_orf2#LINE/    598 ACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_14544727_1   4948 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAAGAGAG 4997
                         ii v  i   v v  i i   i  ii vv    i  v          i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_14544727_1   4998 TAAACAGACAACCTACAGAGTGGGAGAAAATTTTTGCAATCTCTCCATCT 5047
                          i  v        i     i           v       viiv vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_14544727_1   5048 GACAAAGGTCTAATATCCAGAGTCTACAAAGAACTTAAACAAATTTGCAA 5097
                           i  i  v  vi        i v  i        ivv    v ---   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAA 788

  chrX_14544727_1   5098 GAAAAAAAAAACAA----------TGAAAAGTGGACAAAGGATATGAATA 5137
                         v  v     i    ---------- ?    i   i        v      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_14544727_1   5138 GATACTGCTCATAAGAAGATGTACATGGGGCCAACAAACATATTAATAAA 5187
                           i i v   vv        i    viv      i  i  i  v  v i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_14544727_1   5188 AGCTCAATGTCACCGATCAT 5207
                         v      ii   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (124 / 81)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.00 (56 / 14)  


 578 21.71 1.55 0.00  chrX_14586474_14592861      354   482 (5906)    L1M4_orf2#LINE/L1        1   131 (777)  

  chrX_14586474_1    354 TGGAAAAATATTCCATGTTCATGGGTTGGAAGAATTAATATTGTTAAAGT 403
                               i    i            i        v             ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14586474_1    404 ATCCATACTACCCATAGCAATCTATAGATTCAATGCAAGCCCTATCAA-- 451
                         iv v     v    v vii     i        i    v         --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14586474_1    452 TACCAACAACATTCTTCAAAGAAATAGAAAA 482
                          v   i vi v  i  iiv      v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

Transitions / transversions = 1.15 (15 / 13)
Gap_init rate = 0.01 (1 / 131), avg. gap size = 2.00 (2 / 1)  

3257 25.83 1.22 0.55  chrX_14586474_14592861     4994  5895 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14586474_1   4994 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCCTGAAAAT 5043
                              ii i  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14586474_1   5044 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5093
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14586474_1   5094 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5140
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_14586474_1   5141 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAA 5190
                                 viiv  ii  v  v v  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_14586474_1   5191 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACCACAAGG 5240
                                 i      vv   ii  v  ii i      viv   i    i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_14586474_1   5241 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5290
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_14586474_1   5291 CAATGGAACAGAACAGA-AGCCTCAGAAATAACATCACACATCTACAACC 5339
                                 i    iv  -  i -         vvi  i    i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTC 346

  chrX_14586474_1   5340 ATCTGATTTT-GACAAATCTGACAAAAACAAGAAATGGGGAAAAGATTCC 5388
                          vi       -     ivv  v   i v  vvv          ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_14586474_1   5389 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5438
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_14586474_1   5439 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5488
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_14586474_1   5489 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5538
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_14586474_1   5539 CTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGACTA 5587
                         v    ?i- v i -   iv   viv  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_14586474_1   5588 AAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTA 5637
                         vi            vvii         vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_14586474_1   5638 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5687
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_14586474_1   5688 CAGGCAACCTACAGAATGGGAGAAAATTTCTGCAATCTACTCATCTAACA 5737
                         v  i     i                 v i     vii ivi    i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_14586474_1   5738 AAGGGCTAATATCCAGAATCTACAAAGAA-----ACAAATTTACAAGAAA 5782
                          i  i  vi          v  i      -----    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_14586474_1   5783 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5832
                           iv    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_14586474_1   5833 TTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5882
                         i  v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_14586474_1   5883 CATCACTGGTCAT 5895
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


 220 10.53 5.26 0.00  chrX_14682513_14685410      575   612 (2286)    L1M4_orf2#LINE/L1        1    40 (868)  

  chrX_14682513_1    575 TGAAAAGACATGT--TGTTCATGGATTGGAAGACTTAATA 612
                           i     i  vi--                         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA 40

Transitions / transversions = 3.00 (3 / 1)
Gap_init rate = 0.03 (1 / 40), avg. gap size = 2.00 (2 / 1)  

4166 14.73 2.97 1.81  chrX_14682513_14685410     1235  2008 (890)    L1M4_orf2#LINE/L1       22   804 (104)  

  chrX_14682513_1   1235 TGGATATGGAGGGCCGACTGTATTGTTAAGAGGTCAACACTTCCCAAATT 1284
                              -    i i iv --i           v v   i   i        
  L1M4_orf2#LINE/     22 TGGAT-TGGAAGACTTA--ATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chrX_14682513_1   1285 GATCTACTGATTCAGTGCAGTCCCTATCAAAAGCCCAGCTGCCTTTTTTG 1334
                                v      ii   i            v                 
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG 118

  chrX_14682513_1   1335 CAGAAATGGATATGTTTGTCCCAAAATTCATATGAAAATGCAAGAAACCA 1384
                                v  i v i vi   i            i         ii   v
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chrX_14682513_1   1385 AGAGTAGTCAAA----TCTTGAAATAGAAACACAGAGTTGGAGGACTTAA 1430
                            i   i    ----        v    iv   i            i -
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA- 217

  chrX_14682513_1   1431 CACTTCCTGATTTCAAAATTTACTACAAAGCTACAGCAATCAAGACATTG 1480
                                ii         i                 i          v  
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_14682513_1   1481 GGCATGTATGGGCATAAGGATAAACGTATAGATCAGTGAAATCGAATTGA 1530
                         v ---   iv            i  i         i  i   v       
  L1M4_orf2#LINE/    268 TG---GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_14682513_1   1531 GGGTCCAGATATAAACCCTAATGTTTATTATGGTCAGTTGATTTTTTTTT 1580
                          i       v        --  iiv -         i        iv---
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCC--ATACAT-TTATGGTCAATTGATTTTCG--- 358

  chrX_14682513_1   1581 ACAATGGTGCCAAGACTATTCAGTAGAGAAATAA-GGCTTTTTAAATAAA 1629
                             v           i     i i i    v  -i ii    v  i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_14682513_1   1630 AGGTGCTAGGACAACTGGGTATCCACATTCAAAGGAATGAAGTTGGACCC 1679
                         v      i          i  ?      v    i                
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_14682513_1   1680 C-ACCTTACATCATATATAAAAATTAATTCAAAATGAATCAGAAACCTAA 1728
                          -    i   i      i         i        i    ? i      
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_14682513_1   1729 ATGTAAGAGCTAAA--T------CTCTTAGAAGAAA-CACAGGATTAAAT 1769
                                       -- ------             -  i   ?v     
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_14682513_1   1770 CCTTGTG--CTTGGATTGGGCAATGGTTTCTTAGATATGACAACAAAAGC 1817
                          i i   --     i  i                        v       
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_14682513_1   1818 ACAAGCAACAAAATAAA---CAGATAACATTGGACTGCATTAAAATTGAA 1864
                                      v   ---i      -        v   i      i  
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAA-ATTGGACTTCATCAAAATTAAA 657

  chrX_14682513_1   1865 AACTT--GTGCCTTCAAGGACACTACCAAGTAGGTGAAAAGACAATTCTC 1912
                              --    i iv          i    v i            ii v 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_14682513_1   1913 AGAATGGAAGAAATCATTTACAAACCATACATTTTATAAGGGACTTAT-T 1961
                                i     vi    i    i    i  i v           i - 
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_14682513_1   1962 CTAGAATATATAAAGAACTCTTACAATGCAATGTTAAAAAGACAAGT 2008
                          i                        iv    iv           i 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

Transitions / transversions = 2.26 (77 / 34)
Gap_init rate = 0.02 (18 / 783), avg. gap size = 2.06 (37 / 18)  

 566 15.25 5.93 0.00  chrX_14682513_14685410     2288  2405 (493)    L1M4_orf2#LINE/L1      784   908 (0)  

  chrX_14682513_1   2288 CTCAA----AAAAAAACAAGTAACCCAATT---AAACGAGTGAAATATTT 2330
                              ----     i    i          ---   i i ii  iv    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_14682513_1   2331 GAATAGATGTTTTTCTAAAGAAGATAAACAAATGGGCAATAAGCACATAA 2380
                                ii   i  i          v        v            i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_14682513_1   2381 AGAGATGCTGAGCATCAGTAGTCAT 2405
                          i       v i     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.50 (14 / 4)
Gap_init rate = 0.02 (2 / 125), avg. gap size = 3.50 (7 / 2)  


3192 27.42 0.55 0.55  chrX_14747025_14749142.rev      721  1628 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14747025_1    721 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCCTGAAAAT 770
                              ii i  i     i        v      v i i   iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14747025_1    771 GGCCATACTGCCCAAGGTAATTGATAGATTCAATGCCATCCCCATCAAGC 820
                            v     v     iv i  iv i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14747025_1    821 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 868
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_14747025_1    869 TATGGAACCAAAAGAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 918
                                viiv   i  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_14747025_1    919 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACAATACTACAAGGC 968
                                i      vv   ii  v  ii i      vvv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_14747025_1    969 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAGAGACC 1018
                                 i   i    ii         i iv ii i   v   v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_14747025_1   1019 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 1066
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_14747025_1   1067 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1116
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_14747025_1   1117 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAGCT 1166
                           v  i  i              v      v  ?   ii  i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_14747025_1   1167 GAAACTGGATTCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1216
                            ii    ii   v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_14747025_1   1217 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1266
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_14747025_1   1267 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1315
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_14747025_1   1316 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1365
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_14747025_1   1366 ATTAAACTACAGAGCTTTTGTACAGCAAAAGAAACTACCATCAGAGTGAA 1415
                           i   v vv i i       i vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_14747025_1   1416 GAGGCAACCTGCAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 1465
                         i  i     ii                v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_14747025_1   1466 AAGGGCTAATATCCAGAATCTACAGAGAACTTAAACAAATGTACAGGAAA 1515
                          i  i  vi          v  i i      ivv    v vv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_14747025_1   1516 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1565
                           iv    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_14747025_1   1566 CTCAAAGGAACACATTTATGCAGCCCACAGACACATGAAAAAATGCTCAT 1615
                            v  i   v i  vi viii   v i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_14747025_1   1616 CATCTCTGGCCAT 1628
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2590 26.35 0.28 0.83  chrX_14776614_14778313      487  1207 (493)    L1M4_orf2#LINE/L1      192   908 (0)  

  chrX_14776614_1    487 AAAGGACATGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTAT 536
                             i ---        i      vv    i  v  ii i      viv 
  L1M4_orf2#LINE/    192 AAAGAA---GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_14776614_1    537 ACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGA 586
                                i          i   i    ii         i iv ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_14776614_1    587 GATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCGT 634
                         v                i    i--    i  --        vv iiiii
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATAC 336

  chrX_14776614_1    635 ATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGG 684
                           i  iiiii vi    i  i     ivv  vv  i v  vv        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_14776614_1    685 AAAGGATTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAC 734
                             i  vvi  v  i  i        i     v      v  ?   i i
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_14776614_1    735 GTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATATAAAAATTAAT 784
                          i i  iiv    ii    i    v   i     v    i         i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_14776614_1    785 TCAAGATGGATTAAAGACTTAAATGTGAGACCTAAAACCATAAAAACCCT 834
                             i      i ?    i       i   v       i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_14776614_1    835 AGAAGAAAACCTAGGCACTACCATTCAGGACATAGGCATGGGCAAGGACT 884
                                   v    ?iiv viv   iv   v v  vv i     v ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_14776614_1    885 TCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAA 934
                           v ivv  vi            vvi          vv        i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_14776614_1    935 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAT 984
                          v   ii v  i   v v  i i   i  ii vv    i  v    i  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_14776614_1    985 CGGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACT 1034
                         vii      v  i     i   i             v  i    vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_14776614_1   1035 CATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATT 1084
                         i      i  i  i  vi          v  i  v      vv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_14776614_1   1085 TACAAGAAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGA 1134
                         v i  v     i -    i     v  i?    i     i     iv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_14776614_1   1135 ACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAA 1184
                          i     i     v        i  vi viii     v  i         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_14776614_1   1185 AAATGCTCACCATCACTGGCCAT 1207
                          i       v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (113 / 73)
Gap_init rate = 0.01 (4 / 717), avg. gap size = 2.00 (8 / 4)  


3049 25.67 2.12 0.78  chrX_14844103_14846030      540  1435 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14844103_1    540 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 589
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14844103_1    590 GGCCATAGTGCCCAAAGTAATTTATAGATTCAATGCTATTTCCATTAAAC 639
                            v   v v      v i  i  i        i  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14844103_1    640 TACCATTGACATTCTTCACAGAATTAGAAAAA--AATTTTAAAATTCATC 687
                          v   vivi v  i  ii     v v  v  i--i  ii          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_14844103_1    688 TGGAACCAAAAAAGAGCCCATATAGCCAAGACAATACTAAGCAAAAAGAA 737
                              viiv  ii  v  viv        i     vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_14844103_1    738 TAAAGCCGGAGGCATCAAACTACCAGACTTCAAACTATATTACAAGGCCA 787
                         i    ii     vv   v   v  vi i      viv  i     i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_14844103_1    788 CAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCAA 837
                               i   i    ii         i i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_14844103_1    838 TAGAACAGAATAGAGATCTCAGAAATAAGACCACATATCTACAATGATCT 887
                          i   i     v    vii         iv   i i  i  iii v vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_14844103_1    888 GACCTTCAACAAACCTGACAAAAACAAGCATTGAGGAAAGGATTACCTAT 937
                           ii   i    ivv  v   i v  vv  v  i      i  vii  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_14844103_1    938 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAATTGAAA 987
                          i  i              v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_14844103_1    988 CTGGACCACTTCCTTACACCTTATACAAAAATTAATGCAAGATGGATTAA 1037
                         i      v  v   i     v              iv   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_14844103_1   1038 AGACTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGAAAATCTAG 1087
                             i         i v i            vi i          iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_14844103_1   1088 GTAATACAT-TTAGT-ACATAGGCATGGGCAAAGATTTCAT-GATGAAAA 1134
                          ?i-  v  -  v  -  v v  vv i     v i    v -   - vi 
  L1M4_orf2#LINE/    551 GNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGA 598

  chrX_14844103_1   1135 CACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTGATT 1184
                                    vvv          v      v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_14844103_1   1185 AAACTAAAGAGCTTCTGTGCAGCAAAATAAACTGTCATCAGGGTGAAGAG 1234
                            v v  i i   i     vv    iv v   i   vv ii     i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_14844103_1   1235 ACAACCTACCTAAAGAGTGGGAGAAAA-ATTTTGAAATCTATCCATCTGA 1283
                               i  ----   i          -    vv     -  vi      
  L1M4_orf2#LINE/    699 ACAACCCAC----AGAATGGGAGAAAATATTTGCAAATC-ATATATCTGA 743

  chrX_14844103_1   1284 TGGAAGTCTAATATCCAGAATCTACAAGGAACT--TA-AATTTA-TAAGA 1329
                          iiii v  vi          v  i  i     --  -  i i -   v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_14844103_1   1330 AAAAAA------ACC--ATTAAAAAGTAGGCAAAGGACATGAACAGACAC 1371
                             i ------   --   ?    i i         iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_14844103_1   1372 TTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAA-GCTC 1420
                              v        i  vi viii     i  i  i       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_14844103_1   1421 AACATCAGAGAAATG 1435
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  


3251 26.80 1.00 0.44  chrX_14865701_14872088     4993  5895 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14865701_1   4993 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5042
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14865701_1   5043 GGCCATGCTGCCCAAGGTAATTGATAGATTCAATGCCATCCCCATCAAGC 5092
                            v  i  v     iv i  iv i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14865701_1   5093 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5140
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_14865701_1   5141 TATGGAACTAAAAAACAGTCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5190
                                v iv  iiv vi v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_14865701_1   5191 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5240
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_14865701_1   5241 TACAGTAACCAAAACAACACGGTACTGGTACCAAAACAGAGATGTAGACC 5290
                                 i   i   iiii        i iv ii i   v  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_14865701_1   5291 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5338
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_14865701_1   5339 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTGC 5388
                          vi    i  i     ivv  vv  i v  vv            i  v i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_14865701_1   5389 CTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGTAGAAAGCT 5438
                           v  i  i           i  v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_14865701_1   5439 GAAACTGGATCCCTTCCTGAAACCTTATACAAAAATTAATTCAAGGTGGA 5488
                            ii    i    v   v v   v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_14865701_1   5489 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5538
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_14865701_1   5539 CTAGGC-CA----TTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5583
                         v    ?-i ----   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_14865701_1   5584 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5633
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_14865701_1   5634 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAA 5683
                          i   v v  i i   i  ii vv    i  v    i  vv i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_14865701_1   5684 AGGCAACCTACAGAATGGGAGAAAACTTTTGCAACCTACTCATCTGACAA 5733
                           i     i                iv       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_14865701_1   5734 AGGGCTAATATCCAGAATCTACAGTGAACTCCAACAAATTTACAAGAAAA 5783
                         i  i  vi          v  i iv      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_14865701_1   5784 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5833
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_14865701_1   5834 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5883
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_14865701_1   5884 ATCACTGGCCAT 5895
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2108 23.57 4.65 8.67  chrX_14960790_14963114.rev      891  1836 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_14960790_1    891 TGGAAACACATCCCATGCTCCTTGGTTGGAAGAATCAATATTGAGAAAAT 940
                               v i        i  v v i        v i       vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_14960790_1    941 GACCATACTGCCCAAAGCAATCTACAGATTCAATGCAATTCTCATCAAAA 990
                          i v     v      vii              i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_14960790_1    991 TATCAACA-------TAACAATAGCTG-CAAA--AATATTAAAATACTTA 1030
                          vi  i v------- vi  iv ii  -   i--i  vi      v v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_14960790_1   1031 GGAATATACCTAA------CAAAGGAGTTGAAA-GACCTCTACAAGGAAA 1073
                         v i v  i --  ------  i iv  iii   -i i  iv v  i   i
  L1M4_orf2#LINE/    151 TGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_14960790_1   1074 ACACAAA------------ACACTACTGAAAGAAATCATAA---ACGACA 1108
                          -     ------------     v iv  vv---   v  ---  v   
  L1M4_orf2#LINE/    199 A-ACAAAGTTGGAGGACTCACACTTCCCAATT---TCAAAACTTACTACA 244

  chrX_14960790_1   1109 CAAACAAACGTAAACACATCCAGTGCTCATGG-ATGGGTA---GAATCAA 1154
                         -  i v vv    v  - vv     ----   - iv  i --- i  vi 
  L1M4_orf2#LINE/    245 -AAGCTACAGTAATCA-AGACAGTG----TGGTACTGGCATAAGGATAGA 288

  chrX_14960790_1   1155 TACTGTGAA--AATGGAAAGGAATAGAGAACCCAGAAATAAAGTCAAATA 1202
                         i - i ii --       vi    v    ii           vi  v i 
  L1M4_orf2#LINE/    289 CA-TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_14960790_1   1203 TGTACAGCCAACTGATCTTTGACAAAGCATACAAAAAC-ATACACTGGGG 1251
                          v  ii i   i    i  i     i -i i v  i  -  v  v     
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGG 386

  chrX_14960790_1   1252 AATGTACATCCTATTTAATAAATGGTGCTGGGAAAACTGACAAGCCACAT 1301
                           v v i vi  v  i  i              v     ivv ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_14960790_1   1302 ATAGAAGAATGAAACTGGATTCATATCTCTCACTATGTATTACTTTCAAA 1351
                         ii i         ii    ii v  i   v   i  --------------
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT-------------- 472

  chrX_14960790_1   1352 TGGCAAAAACCACAATTACTTTTGCACCAACCTAATAAAAAAATCAACTC 1401
                         ----------------------------------   v      i     
  L1M4_orf2#LINE/    473 ----------------------------------ATACAAAAATTAACTC 488

  chrX_14960790_1   1402 AGGGTGGATCAAAGACTTAAATATAAGACCTGAAACCATAAAATGTCTAG 1451
                          iii       ?    i     i     v  i    i      ivii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_14960790_1   1452 AAGACAATGTTGGAAAAACTCTTCTAGACATCGACCTAGGCAAAGGCTTT 1501
                             v  ii v  ?iv  v     vv   v i ivi       v  i  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_14960790_1   1502 ATGACTAAGACCCCAAAAGCAAATGCAACAGAAACAAAAAATAAATGAAT 1551
                         v iiv  v   v         v v      -   v        i  i   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAAT 637

  chrX_14960790_1   1552 GGAACCTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGA----ATAATA 1597
                         v i  i v  i   v v    i   i  ii vv    i  ----  v vi
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_14960790_1   1598 AAAGTAAACAGATAACCCACAGAATGGGAGAAAATATTTGCAAACTATGC 1647
                              i  v   i                               ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_14960790_1   1648 ATCTAGCAAAGGACTGTACTGTAGTTTCCAGAATCTACAAGGAACTTAAA 1697
                             iii  i     ----    ---        v  i  i     ivv 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACT----TGTA---TCCAGAATATATAAAGAACTCTTA 780

  chrX_14960790_1   1698 CAAATCAGCAAGGAAAAAACAAAAACAAAAACAAATAATCTCATCAAAAA 1747
                            v   -------- v  i     ----i        i iv  i?    
  L1M4_orf2#LINE/    781 CAACTCA--------ATAATAAAAA----GACAAATAACCCAATTWAAAA 818

  chrX_14960790_1   1748 GGGGGCAAAGAACATGAATAAACATTTCTCAAAAGAAGATATACAAATGG 1797
                         iv        i iv      i         v                   
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_14960790_1   1798 TTAACAAACACATGAAAAGATGCTCAACA-CAATGAACGT 1836
                         ii  i  i                     -  ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (130 / 89)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 4.67 (126 / 27)  


2034 20.14 15.51 0.36  chrX_15412687_15414239      500  1060 (493)    L1M4_orf2#LINE/L1      263   908 (0)  

  chrX_15412687_1    500 CAGCATGGTAGTGGCATCAAAACAGACACATAGACAAATGGAACAGAATA 549
                            ii     v      v ii i     i     iv       i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_15412687_1    550 GCAAGGACAGAAATAAATCCATGCACTTATGGTCAACAGATCTTCAACAA 599
                          vi  vv          i    i  i          iv   i   i    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_15412687_1    600 AGATGGCAAGAACACACAATGAGGAAAGAACAATCTCTTCAATAAAAGGT 649
                         i i  v     v  iv     i        i i   i     i   v   
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_15412687_1    650 GTTAGGAAAACTGGATATCTCGATGCAAAAGAATGAAACTGGATTGTTGT 699
                          i i   v         ? ivv               ii    iivi ii
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_15412687_1    700 CTCACACCAAATACAAAAATCAACTCAAAATAGATTAAAGACTTAAACCT 749
                                  v          i          i   i ?    i    iv 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_15412687_1    750 AAGACCTGAAACTATAAAACTACTAGAAGAAAACATAGGAGAAAAGCTCC 799
                             v  i             vi                ? v   v  i 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_15412687_1    800 ATGACATTGGTCTGGGCAATG--------------ACCCCAAAAGCACAA 835
                         i    v    vi i       --------------  v            
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_15412687_1    836 A-AACAAATTCAAAAATAGACAAATGGGATTTACATCAAAAT--GAAACG 882
                         i-      vvv         i    v   i  -         --i    v
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTT-CATCAAAATTAAAAACT 661

  chrX_15412687_1    883 TTTCTGC-------------------------------------ACAG-- 893
                            v   -------------------------------------    --
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_15412687_1    894 ----------------CAAA---------------GGAGTTAATATCCAA 912
                         ----------------    ---------------  iii vi      i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_15412687_1    913 AAATATATAAGAAACTCAAACAACTCAATAACAAGAAAACAAATAACCCA 962
                           -       ii     vv            i  i  i            
  L1M4_orf2#LINE/    762 AA-TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_15412687_1    963 ATTTTAAAATGGGGAAAGGATGTCAATAGAAAATTTTCAAAAGAAGACAT 1012
                            ?v        v       v v      v v  i  v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_15412687_1   1013 ACAAATGCCCAACGGGTACATGAAAGAATGCTCAACTTCACTAATCAT 1060
                                v    iii i        ii         v   ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (66 / 43)
Gap_init rate = 0.01 (8 / 646), avg. gap size = 11.12 (89 / 8)  


2715 25.82 1.36 2.60  chrX_15505382_15507252.rev      498  1380 (491)    L1M4_orf2#LINE/L1       37   908 (0)  

  chrX_15505382_1    498 AATATCATTAAAATGGCCATACTGCCCAAAGCTATTTACAGATTCAATGC 547
                              ii    i     v     v      viv  i           i  
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chrX_15505382_1    548 TATTCCTATCAAACTATCAATGACACTCTTCACAGAACTAGAAAAAACT- 596
                         v  i         v vi  iivi vi i  ii     v v  v  i-  -
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTG 135

  chrX_15505382_1    597 ATTTTAAAATTCACATGGAAC--CAAAAAACGGGCTA-AATAGCCAAGGC 643
                           ii         i      v--   iii  --- i -         ii 
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGAC---CCAGAATAGCCAAAAC 182

  chrX_15505382_1    644 AATTCTAAGCAAAAAGAACATCGCTGGAGGTATCATATAATCTGATTTCA 693
                            ii i iv  i       vv i      vv   i ivvi ii      
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_15505382_1    694 AACTATACTACAGGGCTACAGTAACCAAAACAGCATGGTATTGGTACAAA 743
                           viv       ii          i   i    ii     i   i i  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_15505382_1    744 AACAGACACATAGACCAATGGAACAGAATAGAGAGCCCAGAAATAAGGC- 792
                         i i     i     i        i     v     i          iv -
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_15505382_1    793 --ACACTTAAAACCATCTGATCTTCAACAAAATCGACAAAAAAAAAAAAA 840
                         --   i   viii  vi    i   i    iivi v   i vv vvv  v
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_15505382_1    841 AAAAAAAAAAGAAGAGCAAAAGTATTCCCTATTCAATAAAAGGTGATGGG 890
                         iiii   i  v ---------  v  -----     i   v    v    
  L1M4_orf2#LINE/    383 GGGGAAAGAATA---------GTCTT-----TTCAACAAATGGTGCTGGG 418

  chrX_15505382_1    891 ATAACTGGCTAGCCATATGCAGAAGACTGAAACTGGACCCCTTCCTTACA 940
                          i      v  ?   i     i    v    ii         v   i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_15505382_1    941 CCACATACAAAAATCAACTCAAGATGGATTAAAGGCCCAAATGTAA-AGC 989
                            i          i       i      i ?  i  i        -   
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_15505382_1    990 TAAAACTATAAAAATCT-GGAAGATAACCTAGGAA-ATATCATTCTGGAC 1037
                                      v   -i     v   v    ?i- v   -   vv   
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGAC 567

  chrX_15505382_1   1038 ATAGGACCTCACAGAGATTTCAT-GATGAAGTCTCCAAAAGAAACTGCAA 1086
                         v v  iiivvi  iv i    v -   - v v v       v vvv    
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAA 616

  chrX_15505382_1   1087 CAAAACCAAACATTGACAAATGGGACCTAATTAAACTAAACAGCTTCTGT 1136
                              vv   v  v  i    v    i v  i   v v  v i   i   
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_15505382_1   1137 ACA-CAAAAGAAACTATCAACGGAGTAAACAGACAACCTACAGAATGGGA 1185
                         i v-    i  v        vii   i  v        i           
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_15505382_1   1186 AAAGATATTTGCAAACTATGTATCTGACAAAGGTCTAATATCCAGAACCT 1235
                         i  i           ii  i       i  i  v  vi         iv 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_15505382_1   1236 GTGAGGAACTTAAACAAATTTACAAGCAAAAACTAAACAATCCCCCATTA 1285
                         i i i     ivv    v iv i  vv    ivi   i  --   v   ?
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA--CCCAATTW 814

  chrX_15505382_1   1286 AAAAGTGGGCAAAGGACATGAGCTAACACTTTTCAAAAGAAGACATACAC 1335
                             i           iv   iivi   i  i  v        i     v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_15505382_1   1336 ATGGTCAAACAGGCATATGAAAAAAACCTCGACATCACTAATCAT 1380
                             i   -i i   i       i vv   i      ????????
  L1M4_orf2#LINE/    865 ATGGCCAA-TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (134 / 90)
Gap_init rate = 0.02 (17 / 872), avg. gap size = 2.06 (35 / 17)  


2859 20.40 3.07 2.15  chrX_15701329_15702933.rev      463  1114 (491)    L1M4_orf2#LINE/L1      251   908 (0)  

  chrX_15701329_1    463 CAGTAATCAAAAGCAAAGAAAAGCCCAGTGTGGTACGGGCATA------- 505
                                   i -------------           v      -------
  L1M4_orf2#LINE/    251 CAGTAATCAAGA-------------CAGTGTGGTACTGGCATAAGGATAG 287

  chrX_15701329_1    506 -------GACCAGTGGAAAAGAATAGAAAGCCCAGAAATAAACTCACGGA 548
                         -------  i  i     v     v  i  i            i  iiv 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_15701329_1    549 TATATGGTCAACTAATCTTGGACAAAAGTGCCGAGAATACACAATGGGGG 598
                          v         i i  i  v     ii     i   vi iv        i
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_15701329_1    599 AA-AATAGTCTCTTCAATCAGTGGTGCTGGGAAAACTGGATACCCACATG 647
                           -        i     iv i           v         ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_15701329_1    648 CAAAAGAATAAGATTGGACCCTCATCTTATACCATACACAAAAATCAACT 697
                                  i ii        ii i  i i      i        i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_15701329_1    698 CAAAATG-ATTAAAGACTTAAATGCAAGACCTAAAACCATAAAGCTTCTA 746
                                -  i ?    i      i    v       i     i  ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_15701329_1    747 GAAGAAAACATGGATAAAAAGCTCCTTGACACTGATCTTGGCAGCAATTT 796
                                    i i?iv   v  i v    vi  ivi v    iiii   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_15701329_1    797 TTTGGATATGACACAAAAAGCACAGGAAACAAAAGCAAAAATAAACAAGT 846
                         i  i          v         i v        v       i i  i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_15701329_1    847 TGGGACTATATCAAACTAAAAAGGTTCTTCACAGCAAAGAA-ATAATCAT 895
                            -   vi      v v    iv  i vii vv     i - iv    v
  L1M4_orf2#LINE/    638 TGG-ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_15701329_1    896 GAAAATGAAAAGGCAACCTATGGAATAGGAGAAAATATTAGCAAGCCACA 945
                             i       i     i ii    i            v    ii  i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_15701329_1    946 TATTTGATAAGGGGTTAATATCTAAAATATATAAGGAACTCTTAAAATTC 995
                            i         ii vi    i i         i         v  i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_15701329_1    996 AATAGCAAAAA-ATAGA--ACCCAATTTAAAAATGGGTAGAGGATCTAAA 1042
                             ii     - i i --        ?         i i     i i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_15701329_1   1043 TAGATATTTTTCCAAAGAAGACACGCAAATGGCCAACAGGTATATGAAAA 1092
                             i    i           i ii           i i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_15701329_1   1093 AGTGCTCAACATCACTAATCAG 1114
                         ii            ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.03 (97 / 32)
Gap_init rate = 0.01 (8 / 658), avg. gap size = 4.25 (34 / 8)  


3298 26.22 0.44 1.63  chrX_16008708_16015136.rev     5020  5938 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_16008708_1   5020 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5069
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_16008708_1   5070 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5119
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_16008708_1   5120 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5167
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_16008708_1   5168 TATGGAAACAAAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCCAAAAG 5217
                                 iiv  ii  v  v v  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_16008708_1   5218 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5267
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_16008708_1   5268 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5317
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_16008708_1   5318 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5365
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_16008708_1   5366 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5415
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_16008708_1   5416 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5465
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_16008708_1   5466 GAAACTGGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5515
                            ii    i  i v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_16008708_1   5516 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5565
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_16008708_1   5566 CTAGGCATTAGCATTCAGGACATAGGCATGCCTATGTCATGGGCAAGGAC 5615
                         v    ?i v iiv   iv   v v  ---------  i --     v ii
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGG---------GTTA--GGCAATGGT 585

  chrX_16008708_1   5616 TTCATGTCTAAAACACCAAAAGCAATGGCAAGAAAAGCCAAAATTGACAA 5665
                            v ivv  vi            vvi    v     vv     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_16008708_1   5666 ATGAGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCA 5715
                           vi  ii v  i   v v  i i   i  ii vv    i  v    i  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_16008708_1   5716 TCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTAC 5765
                         vv i      v  i     i   i             v  ii   vii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_16008708_1   5766 TCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAAT 5815
                         vi      i  i  i  vi          v  i  v      iv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_16008708_1   5816 TTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGA 5865
                         iv i  v     i     i     v  i?    i     i     iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_16008708_1   5866 ACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAA 5915
                          i     i     v        i  vi viii     v  i         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_16008708_1   5916 AAATGCTCACCATCACTGGCCAT 5938
                          i       v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.71 (19 / 7)  


2821 25.14 2.71 4.33  chrX_16051310_16055917.rev     3195  4117 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_16051310_1   3195 TGGAAACCCATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAG 3244
                               vvi        i        -----------------  i  --
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-----------------TGGAA-- 31

  chrX_16051310_1   3245 GGTGGAATCAATATTGTGAAAATGACTATAATGCCAAAAGCAATCTACAA 3294
                         ----  v i        v  i   i v   v v  v   vii       i
  L1M4_orf2#LINE/     32 ----GACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chrX_16051310_1   3295 ATTCAATGTAATTCCCATAAAAATACCACCATACCATCATCATTCTTCAA 3344
                               i i   i  i  v     v   v - i  -------  i  ---
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGC-TGCC-------TTTTT--- 116

  chrX_16051310_1   3345 AGAATTACAAAAAAAAAGAAAAAAATCCTGAAATTCATATGGAACCAAAA 3394
                         ----- i  i   vvi v  ivvi     i              viiv  
  L1M4_orf2#LINE/    117 -----TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_16051310_1   3395 AGAGCCCACA-TAATCAAAGAAAGACTAAGCAAATAGAACAAATCTGGAG 3443
                         i ii    v -  ii    iv  vvi i iv  iv        vi     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_16051310_1   3444 GCATCACATTACCTGACTTCAAACTATACTGTAAGGCCATAGTCACCAAA 3493
                          vv     i v  ii i      viv    ii  i  i i   v i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_16051310_1   3494 ACAGCATGGTACTAGTATTAAAATTGGCATATAGACCAATGAAACAGAAT 3543
                             ii       i i  v ii  v i        i     i  i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_16051310_1   3544 AGAGACCCCAGAAATAAAGCCAAATACTTACAGTCAACTGATCTTCAACA 3593
                         v    vi           v   v i i   ii     i    i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_16051310_1   3594 AAGCAAACAAAAATATAAAGTGGGGAAAGGACACCCTATTCAACAAACGT 3643
                          i vviv   i vi  vv i         i i vi  v         i v
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_16051310_1   3644 TGCTGGGATAATTGGCAAGTCACATGTAGAAGAATGAAACTGGGTCCTCA 3693
                                 i  i   vv ?i      i i         ii   ii  ii 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_16051310_1   3694 TCTCTCACCTTATACAAAAATCAACTCAACATGGATCAAAGACTTAAATC 3743
                         i   v    v           i       v        ?    i     v
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_16051310_1   3744 TAAGACCTGAAACTGTAAAAATTCTAGAAGATAACATTGGAA-AAACCCT 3792
                              v  i     i     v ii       v     v  ?i-   i i 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_16051310_1   3793 TATAGACATGGGTTTAGGCAAAGAATTCATGTCCAAGAACCCAAAATCAA 3842
                         ii -   v v  v        v iv   v ivvi v  vv      v  v
  L1M4_orf2#LINE/    562 CGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_16051310_1   3843 ATGCAACAAAAACAAAGAAAAATAGATGGGACTTAATTAAACTAAAAAGC 3892
                          v         iv   i v i   i  v      v  i   v v    i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_16051310_1   3893 TTCTGTACAGCAAAAGAAATAATCAGCAGACTAAACAAACAACCCACAGA 3942
                           i   i vv    i  v iv    iv i v i  v i            
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_16051310_1   3943 GTGGGAGAAAATCTTCACAATCCATACATCTGACAAAGGACTAATATTCA 3992
                         i           v  ii   vi    i      i  i     vi   i  
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_16051310_1   3993 GAATCTATAAGGAATTC-----------------------AAACAGTCCC 4019
                             v     i   i  -----------------------   i ii  v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_16051310_1   4020 ATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCAAACGAAGATAT 4069
                           i?    i     v     iv          v     v  v        
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_16051310_1   4070 ACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCACTAATGAT 4117
                                     i  i  i       i             ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (134 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 7.22 (65 / 9)  


3222 27.12 0.55 0.44  chrX_16098926_16105331     5007  5913 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_16098926_1   5007 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCCTGAAAAT 5056
                              ii i  i     i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_16098926_1   5057 GGCCATACTGCCCAAGGTAACTGATAGATTCAATGCCATCCCCATCAAGC 5106
                            v     v     iv i iiv i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_16098926_1   5107 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5154
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_16098926_1   5155 TATGGAAGCAAAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCCAAAAG 5204
                                iiiv  ii  v  v v  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_16098926_1   5205 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5254
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_16098926_1   5255 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5304
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_16098926_1   5305 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5352
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_16098926_1   5353 ATCTGATCTTTGACAAACCTGAGAAAACCAAGCAATGGGGAAAGGATTCC 5402
                          vi    i  i     ivv  vv  i    vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_16098926_1   5403 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5452
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_16098926_1   5453 GAAACTGGATCCCTTCCTTACACCTTATACCAAAATCAATTCAAGATGGA 5502
                            ii    i    v   i     v     v     i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_16098926_1   5503 TTAAAGACTTACACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5552
                          i ?    i  v i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_16098926_1   5553 CTAGGCATTAGCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5602
                         v    ?i v iiv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_16098926_1   5603 AACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTAA 5652
                         i            vvii         vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_16098926_1   5653 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5702
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_16098926_1   5703 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5752
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_16098926_1   5753 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5802
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_16098926_1   5803 A-ACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5851
                          -     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_16098926_1   5852 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5901
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_16098926_1   5902 ATCACTGGCCAT 5913
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


1319 27.53 0.28 0.28  chrX_16117408_16120555.rev      920  1275 (1873)    L1M4_orf2#LINE/L1        1   356 (552)  

  chrX_16117408_1    920 TGGGAAAACATTACATGTTCATAGATTGGAAGAATCAATATCATTAAAAT 969
                            i  i i  iv         i          v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_16117408_1    970 GGCCATACTGCCCAAAGCAATCTACAGATTCAATCGCTATTTGTATCAAG 1019
                            v     v      vii              -   v  iiv      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAA 99

  chrX_16117408_1   1020 GTATCAACATCATTTTTCACAGAATTAGAAAAAACTATTCTAAAATTTGT 1069
                         i vi  i vv v     ii     v v  v  iviv  i        ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_16117408_1   1070 GTGGAACAAAAAAGAGCCCA-AATAGCCAAAGAATTCCTAAGCAAAAAGA 1118
                         i     vviv  i ii    -          iv v  i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_16117408_1   1119 ACAAAGCCAGAGGCATCACACTACCTGACTTCAAACTATACTATAAGGCT 1168
                               iii    vv       v  ii i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_16117408_1   1169 GCAGTAACCAAAACAGCATGGGACTGGTACAAAAATAGACACAAAGACCA 1218
                         i      i   i    ii   v     i i  ii       i v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_16117408_1   1219 ATGAAATAGAATAGAGAACCCAGAAATAAAGCAGCACATCTACAACCATC 1268
                            i        v    ii           v vii    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_16117408_1   1269 TGATTTT 1275
                                
  L1M4_orf2#LINE/    350 TGATTTT 356

Transitions / transversions = 1.97 (65 / 33)
Gap_init rate = 0.01 (2 / 356), avg. gap size = 1.00 (2 / 2)  

1349 22.71 5.78 4.98  chrX_16117408_16120555.rev     2156  2657 (491)    L1M4_orf2#LINE/L1      403   908 (0)  

  chrX_16117408_1   2156 AATAAATGGTGCTGGGATAACTGGCTATCCATATGCAGAAGAATGAAACT 2205
                           i              i      v  ?   i     i         ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_16117408_1   2206 AGACTCCTACCTTTCAGCACATACAAAAA-------AAGATGGATTAAAG 2248
                         i   i       iv  v  i         -------  i      i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_16117408_1   2249 ATTTGAATGTAAGACCTCAAACAATAAAAATCCTAGAAAAAAA-ATCCAG 2297
                          ii i         v  v    v      v  i     i    -  --  
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT--AG 550

  chrX_16117408_1   2298 GAA-AGATCCTTCTCAACATTGGCCTTACCTGATGATAAAGTGAAAAATT 2346
                          ?i- i   -   vii  v    v-   vvii   i -----------  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGT-----------TT 587

  chrX_16117408_1   2347 CTTA-------CAAAAAAAAAACAAGAATTGTAACAAAAATAAAATTTGA 2389
                             -------  vv    iv     -----i       iv    v v  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAG-----CAACAAAAGAAAAAATAGA 632

  chrX_16117408_1   2390 CAATTGGGACCTAATTAAA-TGAAACAGCTTCCGCATAGCAAAAGAAATG 2438
                         i  v v    i v  i   - v   - i   ii iiivv    i  v iv
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACT 681

  chrX_16117408_1   2439 ATCAAAAAACAGAA----CA-CCTATAGAATGGGAGAAAGTATTCACAAA 2483
                              i   vv   ----  -  i i             i    ii    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_16117408_1   2484 CTATGCATCTGAGAAAGGTCTAATATCCAGAATCTGTAAAGAACTTAAAC 2533
                         ii  ii      v  i  v  vi          v i         ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_16117408_1   2534 AAATCAACAAGCTGAAAA------CAACCCCATT-AAAAATGAGCAAAGG 2576
                           v    i  -- i    ------i     v   -       i       
  L1M4_orf2#LINE/    782 AACTCAATAA--TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_16117408_1   2577 ACATGAGTAGAGACACTTCTCAAAAGAAGACATATAAGCGGCCAAAAAAA 2626
                          iv   i    --  i     v        i   i  ii      v  iv
  L1M4_orf2#LINE/    830 ATTTGAATAGA--CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_16117408_1   2627 GTATGAAATAATGTTCATCTTCACGAATCAT 2657
                         ii      vi   i   v v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (68 / 43)
Gap_init rate = 0.03 (17 / 506), avg. gap size = 3.18 (54 / 17)  


3209 27.23 0.55 0.44  chrX_16137357_16143748     4993  5899 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_16137357_1   4993 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5042
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_16137357_1   5043 GGCCATACTGCCCAAGGTAACTGATAGATTCAATGCCATCCCCATCAAGC 5092
                            v     v     iv i iiv i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_16137357_1   5093 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5140
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_16137357_1   5141 TATGGAAGCAAAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCCAAAAG 5190
                                iiiv  ii  v  v v  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_16137357_1   5191 AACAAAGCTGGAGGCATCACGCTAACTGACTTCAAACTATACTACAAGGC 5240
                                i      vv    i  vv ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_16137357_1   5241 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5290
                          i      i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_16137357_1   5291 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5338
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_16137357_1   5339 ATCTGATCTTTGACAAACCTGAGAAAACCAAGCAATGGGGAAAGGATTCC 5388
                          vi    i  i     ivv  vv  i    vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_16137357_1   5389 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5438
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_16137357_1   5439 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5488
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_16137357_1   5489 TTAAAGACTTAAACGTTAGACCTAAAGCCATAAAAACCCTAGAAGAAAAC 5538
                          i ?    i    i  v   v     i i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_16137357_1   5539 CTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5588
                         v    ?v v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_16137357_1   5589 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5638
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_16137357_1   5639 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5688
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_16137357_1   5689 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5738
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_16137357_1   5739 AGGGCTAATATCCAGAATCTACGATGAGCTCAAACAAATTTACAAGAAAA 5788
                         i  i  vi          v  ii v  i   vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_16137357_1   5789 AAA-AAACAACCCCATAAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5837
                          i -   i     v  v?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_16137357_1   5838 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5887
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_16137357_1   5888 ATCACTGGCCAT 5899
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3197 27.04 0.66 0.44  chrX_16274637_16281025     4991  5896 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_16274637_1   4991 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5040
                              ii i  i   i i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_16274637_1   5041 GGCCATACTGCCCAAGGTAATTTATAGAGTCAATGCCATCCCCATCAAGC 5090
                            v     v     iv i  i  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_16274637_1   5091 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_16274637_1   5139 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5188
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_16274637_1   5189 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5238
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_16274637_1   5239 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5288
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_16274637_1   5289 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5336
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_16274637_1   5337 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5386
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_16274637_1   5387 CTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGGAGAAAGCT 5436
                           v  i  i              v     iv  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_16274637_1   5437 GAAACTGGATCCCTTCCTTACACCTTATACCAAAATCAATTCAAGATGGA 5486
                            ii    i    v   i     v     v     i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_16274637_1   5487 TTAAAGACTTAAATGTTAGACCTAAAACCACAAAAACCCTAGAAGAAAAC 5536
                          i ?    i       v   v       i i    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_16274637_1   5537 CTAGGCATTACCATTCAGGACATAGGCATTGGCAAGGACTTCATGTCTAA 5586
                         v    ?i v viv   iv   v v  vv v     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_16274637_1   5587 AACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAACGGGATCTAA 5636
                         i            vvii         vv     v  i   iv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_16274637_1   5637 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5686
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_16274637_1   5687 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5736
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_16274637_1   5737 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5786
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_16274637_1   5787 A--CAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5834
                          --    i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_16274637_1   5835 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTTACC 5884
                           v        i  vi viii     v  i          i     i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_16274637_1   5885 ATCACTGGCCAT 5896
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3438 22.39 0.84 4.96  chrX_16736963_16740182     1781  2727 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_16736963_1   1781 TGGAAAGATATGCCATGTTTATGCATTGGAAAAATTAATAGTGTTAAATT 1830
                                    v       i   v       i v      v      iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_16736963_1   1831 GTCCACACTACCCAAAACAATATACAGGTTCAATGCAATCCCTATCAAAA 1880
                          v v i   v      vii  v     i     i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_16736963_1   1881 TACCAATGGCATTTTTCACAGAAATAGAAAAAACAATTCTAAAATTCATA 1930
                          v   iiv  v     ii       v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_16736963_1   1931 TGGTGTGACAAAAGACCTAGAATAGCCGAAACAGTCTTGAGAAACAAAAA 1980
                            vivvi   ii    i         i     i      i   v  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_16736963_1   1981 CAAGGTTGGAGGCATCACACTTCCTTAGATTATAATAC--AGTATAAAGC 2028
                            i        vv          i--i   vi  v  -- v  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCC--AATTTCAAAACTTACTACAAAGC 248

  chrX_16736963_1   2029 AGTAGAAATTATGATAGTATA-TCCTGGCATAAAAACAGACATATAGATC 2077
                         vii  v   i v  i   i i- v         ii i             
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_16736963_1   2078 AATAGAATAGAACAGAGA-TCCGAGAAATATACAGTATATATACAGAAAT 2126
                            i        iv    -   -       -----------------  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC-AGAAATA-----------------AAC 330

  chrX_16736963_1   2127 CCAAGTATATACAGTCAACTAATTTTTGACAAGGCCACCAAGGAGACACA 2176
                            vii  v  ii     i i     i       vii     ivv iv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_16736963_1   2177 GTGGGGAAAGGATAGTCTCTTCAATAAATGATATTGGGAAAACTGGATAT 2226
                         i         i       i     i     i ii     v         ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_16736963_1   2227 TCACAGGCAAAAGAATGAAGCTGGATGCTTATATACAAAAATCAACTCAA 2276
                         i    v              i    iv i  i-------------    v
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTAC-------------CTCAC 467

  chrX_16736963_1   2277 AATGTGTCTTTAAAATATACAACAA--AACCTGAAAATGGAAAAGAAGAC 2324
                          ------ i-----        v  --   - v        vv -?    
  L1M4_orf2#LINE/    468 A------CC-----ATATACAAAAATTAAC-TCAAAATGGATCA-WAGAC 504

  chrX_16736963_1   2325 CTAAATGTTAATAACTCAAACCATTGAACTCCTAGAAGAAAACATAGGGG 2374
                                 -  v i  v    i  vi     i                ? 
  L1M4_orf2#LINE/    505 CTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_16736963_1   2375 AAAAGCTCCTTGATATCGGCCTTGGCAATGATTTTTTAGACATCACACCA 2424
                         v   v  i v   iv i  vi v       i   i     i  v      
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_16736963_1   2425 AAAGCACAGGCAACAAAAGCAAAAAGAAACAGGTGGTACTACATCAGACT 2474
                                 i          v     v i i ii v v   v     i v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_16736963_1   2475 AAAAAGCTTCTGCATGACAAAGGGAACAATCC-GCAAATAAAAGGGCAGC 2523
                         v    i   i  iiivv      iv  v   v- v  i i   i i  i 
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_16736963_1   2524 CTATGAATTGGAAGAAAATATTTGCGACCCATATATATGATAAGGAGTTA 2573
                          i iii v   i             i vi       v        iii v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_16736963_1   2574 ATATCAAAAATATATAAGGAACTCCCAGAACTCAATGGTAAGAAAATGAA 2623
                         i    v i         i      ii v        ii   i  i ii  
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_16736963_1   2624 TAACCCGATTAAAAAATAGGCAAAGGACTTGATTATTCATTTTCCCAAAG 2673
                               i   ?      i         i    v  vv     ii      
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_16736963_1   2674 AAGCCATACAAATGGCCAGCAGGT-TGTGAAAAGGTACTCAGTATCACTA 2722
                            vi             ii i i-ii       i i    ii    ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_16736963_1   2723 ATCAT 2727
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.70 (131 / 77)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.67 (55 / 15)  


2880 25.63 4.90 1.59  chrX_16765902_16767972      703  1580 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_16765902_1    703 GGGAACATA--CCATGTTCCAGGATTGGAAGACTCAACATAGTAAAGATA 750
                           i  v   --        vv             i  i  v  v     i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_16765902_1    751 TCATTTCTCCCCCAAATTGATATACAGGTTTAATGTAATTCCTGTCAAAA 800
                         v  v v      -        v     i  i  i i   i   i      
  L1M4_orf2#LINE/     52 GCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_16765902_1    801 TCTTAGTAAGATTTTTTTGTAGATAT---------AATTATAAAATTTAT 841
                           ii  iv- vi       i   v  ---------i  iv       i  
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_16765902_1    842 ATGGAAAGGGAAAAGAACTAGACTAGCTGAAACAATTTTGAAAAAGAATA 891
                                v v  ii  v i   v    ii       i           v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_16765902_1    892 ATAAAGCAGGAGGAATCAGTCTGTAAGATTTTAAGACATAT-----AACT 936
                          i    iv      v   vv  vivvi    i  i  v  i----- i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_16765902_1    937 ACAGTAATCAAGACTGTGTGATATTGGTGGAGGGATACATGTATAGATCA 986
                                       v     i  i   iiv i     v ii         
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_16765902_1    987 ACGGAACAGAACAAAGAACCTAGAAATAGACCAACAGAAATGTGCCCAAT 1036
                          i    i    ivi   ii i       i   v i v vv i  vi    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_16765902_1   1037 TGATCTTTGACAAAATTGCAACAGCAATTGAACGGAGAAGGAAAGATAGC 1086
                             i  i     iiv   v vii v   v  i  i   i   ---   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA---TAGT 396

  chrX_16765902_1   1087 CTTTTTGACAAATGGTGCTAGGTCAATTAAACATCAATATGTCAAAAAAA 1136
                              ii            i  v   i ii i ? v i   -     i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAA 445

  chrX_16765902_1   1137 AAAAA--AAACTCTTGCTGTAAATAGTACACGTTATATGAAAAATAACTC 1184
                         vi  i--ii  i i i i----- --i    vv    ii    v      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACC-----T--CACACCATATACAAAAATTAACTC 488

  chrX_16765902_1   1185 CAAATGTATCACAAACTTCAATGTAAAACATAAAACTATAAAAATAATTA 1234
                         v     v    ? i  i v       i vv             v v-   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC-TTA 537

  chrX_16765902_1   1235 GA-GAAAA------------TCTTCAGGATCTAAGGCTAGGCA--GAGTT 1269
                           -     ------------     iv  i  vi  i      -- iv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_16765902_1   1270 CTTAGACCTGACACCAAAGGTATGATCCATAAAAGAA----TTGATAAAT 1315
                               iv          i i ii v v i       ---- v       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_16765902_1   1316 TGGATTTCATCAAAATAAAAAATACTTACTCTGAGAAAGACCTCAT-AAG 1364
                             i           v     ivi  iiv  vvi  i   vii  -   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_16765902_1   1365 AGGATGAAAAGACAGACTACAGAGTGGGGGGAAATATTTGCAAACTACGT 1414
                          iii          iv i     i    i i             ii ii 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_16765902_1   1415 ATCCGACAAAGGACTGGCATCTAGAATATATAAATAACTTTCAAAACTTA 1464
                            i  i  i     v i   i            v    i i v    i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_16765902_1   1465 ACAGTAGAAA-----ACAACCCAGTTAGAAAGTGGAAAAAATACAAGAAG 1509
                          i i  i   ----- i      i  ?i   i   iv   iv ivv   v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_16765902_1   1510 GGACATTTCACTGAAGAGCATATACAGATGACAGATAAGCATGTGAAAAG 1559
                         i        v ii    iv       i   i vi       ii       
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_16765902_1   1560 ATGTTCAACATAATTAGCCAC 1580
                            i       v ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (143 / 79)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 3.35 (57 / 17)  


4867 14.74 2.81 0.67  chrX_16861927_16863905.rev      600  1488 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_16861927_1    600 TGGAAAAACATCCTGTGTTCATGCATTGGACAACTTAATGTTATTAAAAC 649
                               i i    ii        v      vi       i  i    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_16861927_1    650 CGCAATACTAACCAAACTGATATACAAATTCAATGCAAGCCATACCAAAA 699
                         v        vv     i    v    i      i    v  v  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_16861927_1    700 TCCCAGCTGGCTTTTTTGTTTTTACAGAAATTGACAAGCTGATCATAAAT 749
                                  v        ------                    v    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG------CAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_16861927_1    750 TTCATGTGGAAATGCAAGGGACTCAGAATAACCAAAACAATCCTGAAAAA 799
                              i                i       i           i       
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_16861927_1    800 GAA---TAAAGCAGGAGGACTCACGCTTCGCAATTTCAAAACTTACTATA 846
                            ---i    iv           i    v                  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_16861927_1    847 AATCTACAATTATCAAGACACTGTGGTACTGGCATAAGGATAGACCTATA 896
                           v     i v         v                        v    
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_16861927_1    897 GACCAACAGAACAGAACTGAGAGTCCAGAAATAAATCCTTATGTTTATGG 946
                           i   ii   i    i                  i  v  ii       
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_16861927_1    947 TTAATTGATTTTCAACAAAGGTGCCAAGAAAATTAAATGGATAATTAATA 996
                          i           i    i          vv   v     iv  vv    
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_16861927_1    997 GTCTTTTCAACAAATGGTACTGGGACAACTGTATATCCACATGCAGAAAA 1046
                                           i            v   ?         i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_16861927_1   1047 ATGAATTTGGACTCCTAACTCATGCCATATAAAAAAATTAACTCAAAACA 1096
                              v      i    v    ii       v                ii
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_16861927_1   1097 GAACGAAGACGTAAATGTAAGACCTAAAACTATAAGACTTTTAGAAGAAA 1146
                           v i?    v           v            i   i          
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_16861927_1   1147 AGA--GGAGTG----TTTGTGACCTTGAGTTAAGCAATGGTTTTTTAGAT 1190
                          v --  ?  i----  i         i    i          i      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_16861927_1   1191 ATGACAGCAAAAGCACAAGCAACAAAA-------TACATAAATTAGACCT 1233
                               v                    -------  v       i   i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_16861927_1   1234 CATCAAAATTAAAATCTTTTATGATTCAAAGGACACCATCAAAAAGATGA 1283
                                       v     i  v            i     i  ii   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_16861927_1   1284 AAGGACAACCCACAGAACGAAGGAAAATATTTGTAAATCAAATATCTGTA 1333
                           i              i iii           i      v       vv
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_16861927_1   1334 AAGGAACTTTTATGCAAAATATATAAAGAACATTTACAAATCAACAATAA 1383
                             i    v   v  i              vi      v    i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_16861927_1   1384 AAAGACAA----CCCAATTTTTAAATGAGCAAAGATTCTGAACA-----T 1424
                                 ----       ?vv     i      iv i    i ----- 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_16861927_1   1425 TCTCCAAAGACAACATAAATATGACCAATAAGTACATGAAAAGATGTATA 1474
                                   vi i   v v   i        i             ivi 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_16861927_1   1475 ACATCATTAGCCAT 1488
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (77 / 50)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 4.43 (31 / 7)  


2483 19.54 4.23 1.58  chrX_16867409_16869391.rev      502  1069 (914)    L1M4_orf2#LINE/L1      263   845 (63)  

  chrX_16867409_1    502 CAGTATAGTGCTAGCATAAAAATAAACATATAAATCAACAGAACAGAATG 551
                             i i  i  i      ii   i       i     ii   i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_16867409_1    552 CAGTGTCCAAAAATAAGCCCTTATATTTAACAGACAAGTGATTCTCAACA 601
                         v  v     i      i   v  i     -ii v   v     i  i   
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAATTGATTTTCGACA 361

  chrX_16867409_1    602 AAGGTGCCAAGGC-----AACAGGAAAAGGAGAGTATTTTTTGACAAATA 646
                          i         i -----  ii  i    i v   -i    ii      i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT-CTTTTCAACAAATG 410

  chrX_16867409_1    647 GTGCTGGGATAACTGGATATTCATATACGAAGAGATTAACTTAGATCCTT 696
                                  i         ?i  i  i i  iii  v  v  i  i  i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_16867409_1    697 ACCTCACACCTTATACAAAAATTAAATCAAAATGGATTCAAGATCTTAAC 746
                                   v              v           iv?   i  v  i
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_16867409_1    747 GTAAGAGCTAAAACTATAAAAATTTTACAACAAGAAA-------AAATCT 789
                                              v i   v  v  i v -------      
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_16867409_1    790 TCAAGACCTTGGGTTAGGCA--GACTTCTCAGATATGACATCAAAAGCAC 837
                           iv                -- ii    i          i         
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_16867409_1    838 AATC--CAAAAGGAAAAA-ATTTAACATTACACTTTGTCAAAACTCAAAA 884
                           v --      i     - vv   -   iv    ii      i v    
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAA-ATTGGACTTCATCAAAATTAAAAA 659

  chrX_16867409_1    885 CTTCTGTACTTCAAAACATATCATTAAGAAAACAAAAAGACAAGTCACAG 934
                            i   i       iv i ii  i      iii         vi     
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_16867409_1    935 ACTGTG-GAAAATATTTGCAAATCATCTATCCGATAAAGGATTTGTATCC 983
                          v  v -                   v    i     i   i        
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_16867409_1    984 AGAATATATAAAGAATTACAGAATATACAACTCAACAATAA---GACAAA 1030
                                        i ------iv          i     ---      
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACT------CTTACAACTCAATAATAAAAAGACAAA 803

  chrX_16867409_1   1031 CA-CCCAATTTTTTAATGAGCA--TGATTTGAGTAGACATCT 1069
                         i -       ?vvv    i   --v       i       i 
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

Transitions / transversions = 2.27 (75 / 33)
Gap_init rate = 0.02 (13 / 583), avg. gap size = 2.54 (33 / 13)  

 313 17.39 0.00 0.00  chrX_16867409_16869391.rev     1424  1492 (491)    L1M4_orf2#LINE/L1      840   908 (0)  

  chrX_16867409_1   1424 ATATCTCATCAAATAAAATACAGGAATAACTAATAAGCACATGAAAAGAT 1473
                          i  i  vi    v  i   i vi   ii i                   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_16867409_1   1474 GCTCAACATCATTAATCAT 1492
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.00 (0 / 0)  


2878 22.20 8.17 1.83  chrX_16919086_16920897      500  1319 (493)    L1M4_orf2#LINE/L1       37   908 (0)  

  chrX_16919086_1    500 AATATCTTTTCAAATGTTATTTTTCTCCAAAGTAGTCTATAGATTTATTA 549
                              - v  v i   vi v vi  i     v ii    i     i vii
  L1M4_orf2#LINE/     37 AATAT-TGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACG 85

  chrX_16919086_1    550 CAAAACCAATAAAAATCCCAGCAGGATTTTTTGTGAGTATAGACAAGCTA 599
                            vv  v  v           v vv       iiiiv  v        i
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chrX_16919086_1    600 ATCCCAAAACTTATATGTAAAGGCCAAGGAGCTGGAATTGCTTAAACAAA 649
                             i    i i     v   v  v i   v ii    v  iv      v
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_16919086_1    650 TTTGAAAAGGAAGAACAAAGTTGGAGGAATCAC----------------- 682
                         i       i                   v    -----------------
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_16919086_1    683 TTTACTGTCAAGCTCCAGTAATCAAGA--------TGCTG---------- 714
                         i     iiv     v            -------- i   ----------
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_16919086_1    715 --ATGCACAGGTCAGTGGAATAGGATACAGAGTCCTGAAATAGACCACAT 762
                         -- iii i  i   i        i  vv       v      i   -   
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC-CAT 334

  chrX_16919086_1    763 GAAA--ACAGCCATTTGATCTTTGACAAAGGTGCAAAATCGATTCAATGA 810
                         iv v-- ii i  v     i  i     i     v  iv v        i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_16919086_1    811 G-AAATAATAGT--TTTCAACAAATTGTTTTATAACAATTTGTCATTTGC 857
                          -   v      --           v  vi ivi    i v vi ?iii 
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_16919086_1    858 ATTTAAAAAAATAACCTTGA---TCTAAGCCTCACATC-TATACAGAGAT 903
                           vi    i   i vv   i---i   --       i -      i i  
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTA--CCTCACACCATATACAAAAAT 482

  chrX_16919086_1    904 TAACTTGAAATGAGTCATAGATGTAAATGTAAAACATAGAGCTATAAAAT 953
                              ii     ii   ?   iv         i vv  i i        i
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_16919086_1    954 TTTTAGAAGAAAACAGAA----AAATCTTCATGATCTGGAGTTAG----- 994
                          i             v i----        i   i  v i     -----
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_16919086_1    995 --------AAATA--ACACCAAAAGCACAATCTATAACAGAGAAAAACTA 1034
                         -------- i   --               v v i  v   i    --  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA--TA 630

  chrX_16919086_1   1035 AAAAAATTGGACTTCATCAAAATTAAAACCTTTTATTTTGCCAAGCACA- 1083
                         i v                         v     i vi v v   v   -
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_16919086_1   1084 -GTTAAGAAAATTAAGAGACAAGCTGCTGAGTGGGAGAAAGTATTTGCAA 1132
                         -i i      i v  i      v ii v  i         i         
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_16919086_1   1133 AACACGTATTTGATAAAAGACTTATATCTCAATTATATAAAGAACTCTTA 1182
                          v  ii   i      ii     i    ivi v                 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_16919086_1   1183 AAACTCAATAATAAGAACTCTCAAAACCAAAGCATCTCAATTTAAAAATG 1232
                         v             --------   iv    -i v i     ?       
  L1M4_orf2#LINE/    781 CAACTCAATAATAA--------AAAGACAAA-TAACCCAATTWAAAAATG 821

  chrX_16919086_1   1233 GGCAAAGGATTTGAACAGACACTTCACTAAAGAATATATAAAGATGGCAA 1282
                                        i     i   v i      v     v i     v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_16919086_1   1283 ATAAGTACATGAGAAGATATTCAACATCATTAGCCAT 1319
                              i      i     ii         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (108 / 71)
Gap_init rate = 0.02 (18 / 872), avg. gap size = 4.56 (82 / 18)  


3253 22.68 5.50 1.49  chrX_16967443_16969629      822  1694 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_16967443_1    822 TGGGAACACATACCATGTTCATCCCTCAGAAAATTCAATATTGTTTAGAT 871
                            i  v i  v          vvv ii   i i i         v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_16967443_1    872 GTCAGTTCTCCACAAATTGATTTATAAATTCAATGCAATCCTAATCAAAA 921
                          v  i v    v         i  i i      i       iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_16967443_1    922 TTCCAGCAGGATTTTTTTGGGGGGTAGATATGTATAAACTGATTCTAAAA 971
                          i     v vv      ------ i   v  vv i  i     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT------GCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_16967443_1    972 TTTACATGGAAAAGGAAATGGACT-AAAATAGCCAAAATAACTTTGAAAA 1020
                           i i       v v  i-    i- i           i  ii       
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_16967443_1   1021 AGAG---CA------GAGAAGTAACACTATTTAATTTCAATACTTACTAT 1061
                            i---  ------   i v v     viii        v        i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_16967443_1   1062 AAAGCCACATTAATCAACATAGTGTGGTATTGGTG-AAAGACAGAAACAT 1110
                              i   v       v i         i   ii-  i  i   v i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_16967443_1   1111 AGATCAATGAGAAAGAACAGAAAGTCCAGAAGTTAACCTACTCAAATACA 1160
                                  ii v    iv  i         i v    i iv  vv  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_16967443_1   1161 GTCCATTGATTTTCATTAAAGTTGCAAAGGCTTTGCAGTGGAGAAAGAAT 1210
                            v          ivi  i v   v   i iv v  i   i        
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_16967443_1   1211 AATATTTTAAATAAATGGTGCTGGAACAATTGGACATCCATATGCGAAAA 1260
                          i v    v  i            i    i    i ?   i    i   i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_16967443_1   1261 GATGAACCTTGACCCA-ACTTCACAACTTATACAAAAATTAATCTCAAA- 1308
                         i     vi v     v-  i     v v              -      -
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA-CTCAAAA 492

  chrX_16967443_1   1309 TGGATCATAGACATAAATATAAAAACCAGTAAGCTACAAAGCTTTTAG-- 1356
                                ?    v     i   i i i --  i   i   i  i    --
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTA--AAACTATAAAACTCTTAGAA 540

  chrX_16967443_1   1357 GAAAACAGAGGAGGAAGTCTTTGTGACC----------CAAGGAGTCCTT 1396
                                v   ? v  i    i      ----------   v iv i   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_16967443_1   1397 AGACACGACACAAAAAACATGATCCATAAAATAAAAAATTGATAATAAAT 1446
                            i i     v    i  ii v v i    v       v     ---  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA---AT 637

  chrX_16967443_1   1447 TAGATTTTATCAAAATTAAAAATGTCTGCTCTTCAAAAGACATTGTTAAG 1496
                          i  i  i              iv i  iv       i    i i i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_16967443_1   1497 AGAATGTAAAGACAA---GCAGATTGAAAGAAAATACTTACAAATCACAA 1543
                          i i  v        ---i    v  ii        i  i       i v
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_16967443_1   1544 TTCTGACAAGA-ACTGATATCCCAAATATACAAAGAACTCTCCAAATTCA 1592
                         v     i   i-   vi     vi      i          ivv  i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_16967443_1   1593 GCAATAAGAA-------------------AAATGGGCAAATGATTTGAAC 1623
                         ii     i  -------------------           v        i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_16967443_1   1624 AAACATATCATCAAAGAAGATATATGAATGATAAACAGGTATATTAAAAG 1673
                          i    v  vi             ii    iiv  i i i i  v     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_16967443_1   1674 AAGCTCACCATCATTAGTCAT 1694
                          v     v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (124 / 71)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.81 (61 / 16)  


3289 26.30 0.88 0.55  chrX_17008052_17012929.rev     3483  4387 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_17008052_1   3483 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3532
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17008052_1   3533 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3582
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_17008052_1   3583 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3630
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_17008052_1   3631 TATGGAACCAAAAAAGAGCCTGCATGGCCAAGTCAATCCTAAGCCAAAAG 3680
                                viiv  ii  v  v v  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_17008052_1   3681 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3730
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_17008052_1   3731 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3780
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_17008052_1   3781 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 3828
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_17008052_1   3829 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGAAAAGGATTCC 3878
                          vi    i  i     ivv  vv  i v  vv       i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_17008052_1   3879 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3928
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_17008052_1   3929 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3978
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_17008052_1   3979 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4028
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_17008052_1   4029 CTAGGCA-ATACCATTCAGAACATAGGCATGGGCAAGGACTTCATGTCTA 4077
                         v    ?i- v i -   ivi  v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_17008052_1   4078 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACACATGGGATCTA 4127
                         vi            vvi          vv     v  i v  v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_17008052_1   4128 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4177
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_17008052_1   4178 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCCAACA 4227
                         v  i     i                 v       vii ivi   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_17008052_1   4228 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4277
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_17008052_1   4278 AA---AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATAGACACTT 4324
                           ---   i     v  i?    i            v          i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_17008052_1   4325 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 4374
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_17008052_1   4375 CATCACTGGCCAT 4387
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3781 22.27 0.87 1.75  chrX_17034496_17039065     3162  4077 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_17034496_1   3162 TGGAAAGATATCTCATGATCATGGATTGTAAGAGTTAATATTGTTAAGAT 3211
                                     i    v          v    v                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17034496_1   3212 GTCCATACTACCCAAAGTGATCTACAGATTCAATTCAATCCCTGTCAAAA 3261
                          v v     v      v                iv        i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_17034496_1   3262 TTCCAATAACATTTTTGACAGAAATAGAAAAAACAATCCTAAAATTCAGA 3311
                          i   iivi v     vi       v  v  ivii             v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_17034496_1   3312 TGGCAACCACAAAAGACCCTGAACAGCCAAAGCAATCCTGAGTAAACAGA 3361
                            v  i-i   ii     v   i       i     i   iv  iv   
  L1M4_orf2#LINE/    151 TGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_17034496_1   3362 ACATAGCTGATAGCATCCCCCTATCTGACTGCAAGATATACTACAAAGCT 3411
                            v  i  ivi vv  v v  vi ii i v   i iv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_17034496_1   3412 ATAGTAACCAAAACAACATGGTACTTGCATAAAAACAGATACATAGACCA 3461
                          i     i   i   iii       v      ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_17034496_1   3462 ATGGACCAGAGGAGAAAACCCAGAAATGAATCTATATCTTTATAGCCAAC 3511
                              vi   ivv  i ii        i  i i   iv     i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_17034496_1   3512 TGACTTTTGACAAACGTGCCAAGAACATACATTGGAGAAAGAACACCCTC 3561
                            i   i     iv         v   v  v   i       i vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_17034496_1   3562 TTCAATAAATAGTGCTGGGAAAATTGGATATCCATATGCAGAAGAATGAA 3611
                              i    i         v  i      ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_17034496_1   3612 ACTAGACCCCTATCTCTCACCATATACAAAAATTAATTCAAGATAGATAA 3661
                         ii i        i   v                   i    i  i   v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_17034496_1   3662 AAGAT-TAAATGTAAGACCAAAGCCTATAAAACTACTGGAAGAAAACACA 3710
                         ?   i-           v v  iv          vi i          i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_17034496_1   3711 GGGG-ATATGCTTCAGGACATTGGTCTGAGCAAAGATTTTTTGGATGAGA 3759
                           ? - v  -    iv   v    vi ii    v i   i  i   iv  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_17034496_1   3760 CCTCAAAAAGCACAGGCCATAAAATAAAAAATAGACAAATGGGATGATAT 3809
                          vi     -     i  v i    v          i    v   ivvi  
  L1M4_orf2#LINE/    599 CACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_17034496_1   3810 CCAACCTAAAAGCTTCTGCACAACAAAGGAAAC-ACCAAAA---T--AAA 3853
                          v  vi     i   i  ii vv       v  - i   i --- --   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_17034496_1   3854 GAGAACCTAGAGAATGGGAGAAAATATTTGCAAACAGTTCAACTGACAAA 3903
                           v    i v                        ivi vi v    i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_17034496_1   3904 GAACTAATATCCAAAATATATAAGGAACTCAAACAACTCAATAGGAAAAC 3953
                          i   vi      i         i      vv           -------
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA------- 790

  chrX_17034496_1   3954 AAACAAACAAAAAACCAAATAATCTGATTTAAAAATCGACAAACGTTCTG 4003
                         ------ i     iv       i ii   ?      v i    v v i  
  L1M4_orf2#LINE/    791 ------ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_17034496_1   4004 AATAGACATTTCTCAAAAGAGGACATACAAATGGCTAACAGGTATATGAA 4053
                                       v     i  i           i  i i i i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_17034496_1   4054 AAATTGCTCAATATCACTAGTCAT 4077
                           iv       i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (124 / 76)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  


3501 24.67 1.22 0.33  chrX_17079843_17084420.rev     3188  4087 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_17079843_1   3188 TGGAAACACATCTCATGTTCATGGATGGGTAGAATCAATATTGTGAAAAT 3237
                               v i   i             v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17079843_1   3238 GACCATACTGCCAAAAGCAATCTAGAAATTCAATGCAAATCCCCATCAAA 3287
                          i v     v  v   vii     v i      i    -    i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAA-TCCCTATCAAA 99

  chrX_17079843_1   3288 ATACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCAC 3337
                           v   v vv v  i  ii     v v  v  ivii  i          i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_17079843_1   3338 ATGGAACCAAAAAAGAGCCCGTATAGCCAAAGCAAGGCTAAGGAAAAAGA 3387
                               viiv  ii  v  v v         i   vvi i ii  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_17079843_1   3388 ACAAACCTAGAAGCATTACACTACCTGATTTCAAA-----CTATAAGGCC 3432
                              vi i  i vv i     v  ii        -----   i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_17079843_1   3433 ATAGTCACCAAAACAGCATGGCACTGGTATAAAAATAGGCACATAGACCA 3482
                          i   v i   i    ii   i     i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_17079843_1   3483 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAAC 3532
                               i     v    ii               v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_17079843_1   3533 TGATCTTCAACAAAACAAACAAAAACATAAAGTGGGGAAAGGACACCCTT 3582
                             i   i    iivviv   i v   vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_17079843_1   3583 TTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAA 3632
                                             i  i   v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_17079843_1   3633 ACTGGATCTTTATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTA 3682
                         ii    i ii  i   v    v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_17079843_1   3683 AGGACTTAAATCTAAGACCTGAAACTATAAAAATTCTAAAAGATAACATT 3732
                         ?i   i     v     v  i           v ii  i    v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_17079843_1   3733 GGAGAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCAT-GACCAACA 3781
                           ? v  vi    vv   v    v        v i    v -  i-- ii
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATG 597

  chrX_17079843_1   3782 ACCCCAAAA-CAAACACAATAAAAACAAAGATAAATAGTTGGGACTTAAT 3830
                           v      -  v vi   i    iv   i   i   iv v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_17079843_1   3831 TAAACTAAAGAGCTTTTGCACGGCAAAAGGAATAGTCAGCAGAGTAAACA 3880
                         i   v v  i i      ii vv    i iv ivi   iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_17079843_1   3881 GAAAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAA 3930
                           v          i           v  ii   vii   i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_17079843_1   3931 GGACTAATATCTAGAATTTACAACAAACTC----AAATCAGTGAGAAAAA 3976
                              vi    i     v  i  vi     ----  v   i i v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_17079843_1   3977 AACAAACAATCCCATCAAAAAGTGGGCTAAGGATATGAATAGACAATTCT 4026
                         i     i  i  v  i?    i     v      v          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_17079843_1   4027 CAAAAGAAGATATACAAATGGTCAATAAACATATGAAAAAATGCTCAACA 4076
                          v                   i      i  i       i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_17079843_1   4077 TCACTAATGAT 4087
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.60 (134 / 84)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.33 (14 / 6)  


3352 26.65 0.44 0.44  chrX_17120512_17126792.rev     4883  5790 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_17120512_1   4883 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4932
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17120512_1   4933 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4982
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_17120512_1   4983 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5030
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_17120512_1   5031 TATGGAACCAAAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCCAAAAG 5080
                                viiv  ii  v  v v  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_17120512_1   5081 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5130
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_17120512_1   5131 TACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGATC 5180
                                 i   i     i         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_17120512_1   5181 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5228
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_17120512_1   5229 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5278
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_17120512_1   5279 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5328
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_17120512_1   5329 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAGATGGA 5378
                            ii    i    v   i     v  i        i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_17120512_1   5379 TTAAAGACTTAAATGTTAGACCTAACACCATAAAAACCCTAGAAGAAAAC 5428
                          i ?    i       v   v    v  i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_17120512_1   5429 CTAGGCATTAGCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5478
                         v    ?i v iiv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_17120512_1   5479 AACACCAAAAGCAATGGCAGCAAAAGACAAAATTGACAAATGGGATCTAA 5528
                         i            vvi   i       v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_17120512_1   5529 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5578
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_17120512_1   5579 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5628
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_17120512_1   5629 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5678
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_17120512_1   5679 AAACAAACAACCCCATCAAAAAGTAGGCAAAGGACATGAACAGACACTTC 5728
                          i     i     v  i?    i i         iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_17120512_1   5729 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5778
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_17120512_1   5779 ATCACTGGCCAT 5790
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (146 / 92)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3991 17.62 1.74 0.67  chrX_17177101_17180374     1429  2177 (1097)    L1M4_orf2#LINE/L1        1   757 (151)  

  chrX_17177101_1   1429 TAGAAAGACATCTTGCGTTCGCGGATCAGAAGATTCAACGTTTGCGAGAT 1478
                          i      i   iiii    ii    ii     i i  ii  vvii    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17177101_1   1479 GGCTATACTCCCTAAATCAATATACAGATTCAATGCAATCCATATCAAAA 1528
                            v        i    ii  v           i       v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_17177101_1   1529 TCCCAGCTGACTTTTTTGCAGTAATTGACAAAGTGATCCTAAAATTAATG 1578
                                  v           v         iv             v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_17177101_1   1579 TGGAAAGGGAAGGAACCCAAAATAGCCAAAAAACAGTCTTGAAAAAGAAG 1628
                               v v    i     i           --  i              
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAA--CAATCTTGAAAAAGAAG 198

  chrX_17177101_1   1629 GACAAAGTGGGAGAACTCACACTTCCCAGTTTTGAAACTTATTACAAAAC 1678
                         i       v    i              i   ii       i      i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_17177101_1   1679 TACAGTAATCAAGACAGTGTGGAGCTGGTGTAAGGATGCAGATATAGATC 1728
                                               vi    ii       iv v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_17177101_1   1729 AATGGAACAGAGTCAAAACTCCAGAAATAAGTTTTTACATTTATGATCAG 1778
                                i   i ii i v           iiiiv          i   i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_17177101_1   1779 TTGATTATCGATAAGGGTGCCAAGACAATTCAATGGGGGGAAACAATAGT 1828
                               v    i              v           --   v      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAAGAATAGT 396

  chrX_17177101_1   1829 CTTTTCAACAAATGGTGCTGGGACAGCTGAATATCCACATGCAAAAGAAT 1878
                                                  i   i   ?                
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_17177101_1   1879 GAGGTTGGGCCCCCTCCTTATATCAT-CACAACATTTAACTCAAAAGCAG 1927
                           i     i    iv   i i i   -i    v v           vvii
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_17177101_1   1928 TCATAGCTTTAAACTTAAGAGTTAAAACTATAAAGCTCTTATAAGCAAA- 1976
                            ?  vii    iv      i            i      v   v   -
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_17177101_1   1977 ------GTAAGTCTTTATGACCTTGGATAGGGCAATTAATTCTTAGATAT 2020
                         ------    i    ii         i vi      viv           
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_17177101_1   2021 GAATCTTACAGTACAAGTGACAAAAGAAAAAATAAATA----GGACTTCA 2066
                           vv iv v  i     ii               i   ----        
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_17177101_1   2067 TAGAAATAAAGAACTTT-GTCCTTCAAAGGATGCCATAAACAAAGTGAAA 2115
                          vi    v  i      -  v          ii i  v  v         
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_17177101_1   2116 AGTCAACCCACAAAATGGGAGAAAGTATTTGCAGGTCATTTACCTGAAAA 2165
                           v         i           i        ii    v  i    v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_17177101_1   2166 GGCACTTTGTAT 2177
                           v    -    
  L1M4_orf2#LINE/    747 GGGACTT-GTAT 757

Transitions / transversions = 1.89 (85 / 45)
Gap_init rate = 0.01 (7 / 757), avg. gap size = 2.57 (18 / 7)  

 834 12.35 3.09 0.62  chrX_17177101_17180374     2620  2781 (493)    L1M4_orf2#LINE/L1      743   908 (0)  

  chrX_17177101_1   2620 ATAACAGGCTTGTATCCAGAATACATAAAGAAAGTATATAACTCAACAAT 2669
                             vi i               i        vviv  i       i   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_17177101_1   2670 AAAAAGACAA----CCTAATTTTTTAAGTGGGCAAAAGATTTGAATAGAT 2715
                                   ----  i    -?vv  i        i            i
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_17177101_1   2716 ATTACTCCAAAGAAGACATAAAAATGGCCA-TAAGCACATGAAAAGATGC 2764
                            v            i   v         -                   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_17177101_1   2765 TCAACATCACTAGTCAC 2781
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (11 / 8)
Gap_init rate = 0.02 (3 / 166), avg. gap size = 2.00 (6 / 3)  


3250 26.62 0.44 0.55  chrX_17346697_17353109.rev     5014  5922 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_17346697_1   5014 TGGAAAAACATTTCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAC 5063
                               i i  ii    i        v      v i        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17346697_1   5064 GGCCTTACTGCTCAAAGTAATTTATAGATTCAATTTTATCCCCATCAAGC 5113
                            vv    v i    v i  i  i        iviv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_17346697_1   5114 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 5160
                          v   -   v    i  -i     -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chrX_17346697_1   5161 CATATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTGGGCAAGA 5210
                                  viiv  ii  v  viv        i      i  iiv    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_17346697_1   5211 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAAGTATGCTACAAG 5260
                                  i      vv   ii  v  ii i      iiv i      i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_17346697_1   5261 GCCACAGTAACCAAAACAGCATGCTACTGGTACCAAAACAGATATATAGA 5310
                           i       i   i    ii  v      i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_17346697_1   5311 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCATACATGTACCACC 5360
                         i        i    iv   ivii         vv        v  ivii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_17346697_1   5361 ATCTGATCTTTGACAAACCTGACACACACAAGCAATGGGGAAATGATTCC 5410
                          vi    i  i     ivv  v  vivv  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_17346697_1   5411 CTATTTAATAAAAGGTGTTGGGAAAACTGGCTAGTCATATGCAGAAAACT 5460
                           v  i  i   v    i     v      v  ?i  i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_17346697_1   5461 GAAACTAGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGATGGA 5510
                            ii i       v   i     v           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_17346697_1   5511 TCAAAGACTTAAATGTAAGACCTAGTACCATTTTAATCCTAGAAGAAAAC 5560
                            ?    i           v   iv  i  vvv v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_17346697_1   5561 CTGGGCA-ATACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTA 5609
                         v i  ?i- v i -   iv   v v  vvii     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_17346697_1   5610 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5659
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_17346697_1   5660 ATTAAACTAAAGAGCTTCTGCCCAGCAAAAGAAACTATCATCAGAGTGAA 5709
                           i   v v  i i   i  iv vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_17346697_1   5710 CAGGCAACCTAGAGAGTGGGAGAACATTTTTGCAATGTATTCATCTGACA 5759
                         v  i     i v   i        v  v       vvi  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_17346697_1   5760 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5809
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_17346697_1   5810 AAAGCAAACAACCCCATCAAAAAATGGGCAAAGGATATGAACAGACACTT 5859
                           ii    i     v  i?                 v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_17346697_1   5860 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5909
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_17346697_1   5910 CATCACTGGCCAT 5922
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (135 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3034 23.57 3.08 3.41  chrX_17441227_17443921.rev     1297  2204 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_17441227_1   1297 AAAGCTATAGCATATCCAGGGCCTG-AAGATACAACATTGTTAAAAATGT 1345
                             v   vv   i i  v  vi  -    ivi  i        i -  v
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-TGG 52

  chrX_17441227_1   1346 CCATGCTCTCCAAATCCATCCATATATTCAAATGAATGCCAATCAAAATC 1395
                          v  i   i      iv   i i v      vvv   v  v         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_17441227_1   1396 ATACCATGC-TTTTTTGAAGAAATTGACAAGCTGATTCTAAAATGTATAT 1444
                         vi v -   -       v                  i       vi    
  L1M4_orf2#LINE/    103 CCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_17441227_1   1445 GAAAATGCACAGGTTCTAGAATAGCTAAAACAATCTTGACAGAGAA---C 1491
                          i       vi  vi i        i             v i    --- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_17441227_1   1492 AAATTTGGAGGATTTTTACTATCTGATTTCAAGACTTACTATAAATCTAC 1541
                            v        i ivi   vi ii       i        i   v    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_17441227_1   1542 AGAGGTCAAGACAGTGTGGTTTTGGCAAGAAAGTAGACATTATAGATCAA 1591
                           vii               vi     vi iii       -         
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT-ATAGATCAA 300

  chrX_17441227_1   1592 TGAAGCAGCACAGAGAATTCAGAAATAGACCCACACATACACAGTTGAAC 1641
                           i ii  v iv    i i        i     i    vi ii  i-  i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC-AAT 349

  chrX_17441227_1   1642 TGATTGTTTGAAAAAGGCGTTAAGTCAATTCCATGGGAGAAAGGAAGGAG 1691
                              -  i  v  i  i ii   v v    v     -     i -----
  L1M4_orf2#LINE/    350 TGATT-TTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAA----- 392

  chrX_17441227_1   1692 TTTTCTGGTTTTCTTTTTACAAATGGTTCTGGAACAACTAAATATACATA 1741
                         ----- i  i  --  iv         v    i      ii   ?v  i 
  L1M4_orf2#LINE/    393 -----TAGTCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_17441227_1   1742 TGGGGAAAAATGAATTTTGACCC-TACCTTACTCCATACACAACCGGTAA 1790
                           vii  i      v  v     -     i  v     i    vviv   
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_17441227_1   1791 TTAGGGAAGGACCATAGACCTAAACATAAAAGCTAGAACCATAAAACTCC 1840
                         i viii v   i  ?         ii   i     i   i         i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_17441227_1   1841 TAGAAGAAAATGTATGAAATAATATTCATGAACTTGAGGGAAGCAGATTG 1890
                                   ii  v ?ivv   v   i   v    i vv i   -  v 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGG 584

  chrX_17441227_1   1891 TT-CT--GACCGTG-C-CCAAAAGAGGCTAGTCATAAAAGAAAACATTGA 1935
                           -  --  i-i  - -       vi- v  iv i         v  v  
  L1M4_orf2#LINE/    585 TTTCTTAGAT-ATGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGA 632

  chrX_17441227_1   1936 TAA-TTGGACTTTGTCAAAATTAAAAATTTCTGCTTATCAAGAGAACACT 1984
                            -        ii             i  i  iviv    -  i     
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACT 681

  chrX_17441227_1   1985 ATTAAAAAACAGGGCAGGTAA-----GGACTGGGAGTAAATATTTGCAAT 2029
                           i  i   vv iiv  ii  -----i  v      v            v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_17441227_1   2030 ACAAATATCTAACAAAGAACTTTTACTCAGTGTATATGAAGAGCTACTAC 2079
                         v  v      i i  i i    v  ii   vi     i    i  vi   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_17441227_1   2080 AAATAAAAAATATCAATAATAAAAAGACAAAGAA------TTAAAAATGA 2123
                           v ---------                  v  ------ ?       i
  L1M4_orf2#LINE/    782 AACT---------CAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_17441227_1   2124 GAAAAAGGCTTAATTAGACACCTCAC-----AAGATATATGAATGTCTAC 2168
                          v   i ii  i v      ii  v -----        ii    v i v
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_17441227_1   2169 TAAGCACGTGAAAAGGTGTTCAGCATTATTTGTCAT 2204
                                i       i  i   i   i ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (129 / 81)
Gap_init rate = 0.03 (25 / 905), avg. gap size = 2.36 (59 / 25)  


 625 33.89 9.48 1.18  chrX_17476241_17478383      630  1051 (1092)    L1M4_orf2#LINE/L1        1   457 (451)  

  chrX_17476241_1    630 TAGAAAGACATCCCCTGTTCTTGGATAGAATGATTCAACACTACAAACAA 679
                          i      i     v     v     v i v  i i  i i iiv  v v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17476241_1    680 ATCAGTTCTCTCTAAGTTACTTAATAAGTTTAACACAATTTCAATAAAAA 729
                         iv  i v   i i  i  iv iv i ii  i   i    ii v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_17476241_1    730 TACCAATAAGCTTTATTTTATGGAGTTA-------GATACT--------T 764
                          v   iiviv    v  vi - i i  i-------   v  -------- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_17476241_1    765 ATGGGAAAACAAACATATAAGACTAGCCAGGAAAACACTGAAAAAGGA-A 813
                             i  vi   ivivviv   v      ii v  ivi        i - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_17476241_1    814 AC------------CTAGCCCTACCAGACATTAAGATATAGT-TAAAGCC 850
                           ------------  vi v  v  vi iv i  i iv  v -i     i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_17476241_1    851 TCTATAATTACAATATTGTGGTATTGGCACATGAATAGACAGATATATCA 900
                         v vi    i vi i v       i     i v i       v   v    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_17476241_1    901 GTAGAATAAAACACAAAGTCCAGAAAGAGACCAGAGTATATATAA--AA- 947
                         i i     i  ivv i          v i   vivii  v   ii--  -
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_17476241_1    948 --ACATTCAATAAAGGCAACATCACAAATAACTGAGGCAAGAGATGGAGT 995
                         -- iv   i i  i  iiv  vv  v v v v  i  v    -  --   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-AT--AGT 396

  chrX_17476241_1    996 TTTTT-----AATGATGCTGGAACAACTGCATAGCCATTTGGTGAAAGGA 1040
                         i    -----    i      i       v   ?   iv  -ii    i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAA 445

  chrX_17476241_1   1041 -AAAATTTGATC 1051
                         -i  i  v  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACC 457

Transitions / transversions = 1.41 (83 / 59)
Gap_init rate = 0.03 (13 / 457), avg. gap size = 3.46 (45 / 13)  

 627 27.78 6.02 3.94  chrX_17476241_17478383     1258  1689 (454)    L1M4_orf2#LINE/L1      468   908 (0)  

  chrX_17476241_1   1258 ACCATACACAACAGTAAACTCCAAATGGATCAGGGACCTAAACCTAAAAA 1307
                               i    v i v     v          ?i        iv   i i
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_17476241_1   1308 ATGAAACCACACAAGTACTAGAAGAAAATAT--GCATGAACTATTCTT-- 1353
                         v i    i i v  v vi          i  -- ?i i  ----    --
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA----TCTTCG 563

  chrX_17476241_1   1354 TGACCTCAGTCCAGGGAAACACTTTCTAACTTTGGC--TAAAAATACAGA 1401
                               ii vii   v  vvii  ii  iv v  i --i    ii   i-
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA- 612

  chrX_17476241_1   1402 GGAAAGAAAAGAAAAAAGAAA-AGATTGA--TGCATTTAAACAGTAAACA 1448
                         - v  v           v i - i    i-- v   iv   i--    v 
  L1M4_orf2#LINE/    613 -GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT--TAAAAA 659

  chrX_17476241_1   1449 TTTTTGCATGCC-CAAA---CACCGTAAAGGAAATCAAAAGACAACTGAA 1494
                         i     --   i-    ---   ii v   i  i v          iv v
  L1M4_orf2#LINE/    660 CTTTTG--TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_17476241_1   1495 AAACTGGGAGAAGATATGTGCAA--CA-------GAAAAAGGGCTAATAC 1535
                          i v        i    v     --  -------  v  i  i  vi  i
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_17476241_1   1536 CTCTAATTGATAAATACCTCTTAAAAACTGAGGGATAAAGAAAAGAGCAA 1585
                          ivv   vv     v v      v  -  v ---    vi      -   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAA-CTCA---ATAATAAAAAGA-CAA 802

  chrX_17476241_1   1586 A--ACCTTGGAAGAAAAATTGAGGAAAAGATGTGAACAGACAATTC--AG 1631
                          --   i--i vv?    v  i v   i   v    i     v   --vi
  L1M4_orf2#LINE/    803 ATAACCC--AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_17476241_1   1632 AAAAAAATATAGGCATGTTTCTTCAACTGAAGAAAAATTGTTCAAGCTCA 1681
                           i  i     viv   viivv v i vv v     iv  i    vv   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_17476241_1   1682 CTCTCAAT 1689
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.09 (61 / 56)
Gap_init rate = 0.04 (19 / 441), avg. gap size = 2.26 (43 / 19)  


3227 27.17 0.44 0.55  chrX_17559405_17565666.rev     4863  5771 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_17559405_1   4863 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4912
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17559405_1   4913 GGCCATACGGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4962
                            v    vv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_17559405_1   4963 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5010
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_17559405_1   5011 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5060
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_17559405_1   5061 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5110
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_17559405_1   5111 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5160
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_17559405_1   5161 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5208
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_17559405_1   5209 TATCTGGTCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5258
                         i vi  i i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_17559405_1   5259 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGC 5308
                         i  v  i  i              v      v  ?   i v i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_17559405_1   5309 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAATATGG 5358
                             ii    i    v   i     v           i  i    v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_17559405_1   5359 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5408
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_17559405_1   5409 CCTAGGCATTACCATTCAGGACATAGGCAAGGGGAAGGACTTCATGTCTA 5458
                          v    ?i v viv   iv   v v  vvvi  v  v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_17559405_1   5459 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5508
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_17559405_1   5509 ATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGAA 5558
                           i   v v  i i   i  iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_17559405_1   5559 CAGGCCACCTACAAAATGGGAGAAAATGTTTGCAACCTACTCATCTGACA 5608
                         v  i v   i   i             i       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_17559405_1   5609 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5658
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_17559405_1   5659 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5708
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_17559405_1   5709 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5758
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_17559405_1   5759 CATCACTGGCCAT 5771
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.80 (9 / 5)  


2662 24.37 4.19 4.08  chrX_17667538_17670634     1698  2604 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_17667538_1   1698 TGGAGAGACATATCATGTCCATGGGTTGAAAGATTCAACATAGAAAAGAT 1747
                             i   i  vi     i     i   i    i i  i  v vv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17667538_1   1748 TGCAATTCTCACCAAATTTATATACTTGCTTAACACAATTTCTATCAAAA 1797
                         v     v   v       v  v   vvii i   i    ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_17667538_1   1798 TCCCAGCAAGATTTATTTTTTAGTTATAGGCAAGATTATCTCACAGTTTA 1847
                                v- vi  -    vi  vv  v i    v v   ii v i  i 
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_17667538_1   1848 TATGGAAAGGCAAAGGAACTACAGTAGCTAAAGCAGTTTGGGGCAAGGAG 1897
                                 v    i   v i v i    i   i  i i v iiv   i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_17667538_1   1898 AATAAAGTGGGAGGA-TAACTTTACCTAATATTAA---T---------GT 1934
                           i     v      - v  vi v  i   v i  --- --------- i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_17667538_1   1935 TACCGTAATCAGAACAGTGTGGT-TTGTT----GGA--GATACATAGATC 1977
                            v       ii          -i  vi----   --  i i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_17667538_1   1978 AATGAAACAGAATAGAGATCCTAGAAATATACCCATATAAATATGCCAAA 2027
                             i  i     v    vi i       v       i vv    viv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_17667538_1   2028 CTGATTTCTGATAAAGGTGCAAAAACAACTCAAAAGAAGAAGGATAACCT 2077
                         i      ii  i  i     v  i  v i    vi iii   i   ii  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_17667538_1   2078 TTTCAACAAATGGTGCTGTAGCAACTGGACCATCCATAAGCAAACAAACA 2127
                                           vii        i- ?   i v     vi  ii
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCAAAAGAATG 447

  chrX_17667538_1   2128 AAACAAACAAAAAGGATCTCGACCTAAACCTCGCACATTACCACATTATA 2177
                           iiv--------   i i v    --------    ---   ---    
  L1M4_orf2#LINE/    448 AAGTT--------GGACCCCTACCT--------CACA---CCA---TATA 475

  chrX_17667538_1   2178 CAAAAA---ACTCAAAATGGATCATAAACTTATATACAAAATGTCAAACT 2224
                               ---               ? i  i  v  ii  i vv v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_17667538_1   2225 ACAATACATTTGTTTTAAAA------ATAGCAG--AATGTCTGAGCTCTA 2266
                          i  v  ----- i   i  ------    v? --   v ii v vi  v
  L1M4_orf2#LINE/    526 ATAAAAC-----TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_17667538_1   2267 GAGCTAGACAA-GAAGTCTTAGACTTGATACCAAAAGTGTGATATGATCC 2315
                          i i   i   - ivv       iv   i        i----- ii v v
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC-----ACAAGCA 615

  chrX_17667538_1   2316 ATAAAAGGAAAAATGGATAAATTGGACTTAATCTGCAT-AAAAGGTTTTG 2364
                          i     i      i              v   viv  -    iv     
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_17667538_1   2365 TTCTGTGTAA-ACCCTATAGAAGAAGGT--AAAGACAAGCTATAGACTGA 2411
                          v  viiv i-  v    v-     i  --        v i i   v  i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATC-AAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_17667538_1   2412 GATAAAATATTTGCAAACCACATATCCAACAAAGAACTAGTACCTAGAAT 2461
                           v              i  i     ii i  i i   v   i i     
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_17667538_1   2462 ATAGAAAGAACTC--AAAAGTTAACATTAAAAACCTCAAACAACCCAATT 2509
                            v         -- v  v i  i v      vv-    i         
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATT 813

  chrX_17667538_1   2510 ATAAAATAGACAAAAGACACGAACAGACATTTCAACAAAGAGGATATACA 2559
                         ?v     i i    i  ivi   i         vv      i        
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_17667538_1   2560 GATGGCAAATACTCACAAGAAAAGATGTTCACCATCATGAACCAT 2604
                         i     v    vv    v         i   v     ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (127 / 90)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.00 (75 / 25)  


3856 22.46 1.79 0.34  chrX_17869565_17871477.rev      528  1422 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_17869565_1    528 TGGAAATACACTCCATGTTCATGGATTGGAAGAATGAATATCGTCAAAAC 577
                               v i ii                     v v     i  i  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17869565_1    578 AATCATACTGCCCAAAATGATCTACAGATTCAATGTAATCTCTATCAAAA 627
                         iiiv     v      v                i i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_17869565_1    628 TACTGAGGT-CGTTTTTCACAGAAATAGAAAAAAC-ATCTTAAAATTTGT 675
                          v i-  v - v     ii       v  v  ivi-   i       ii 
  L1M4_orf2#LINE/    101 TCCC-AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_17869565_1    676 ATAGAACCACAAAAGACCCTGATTACCCAAAGCAACCCTGAGCAAAAAGA 725
                           i   vii   ii     v  v  v     i   i i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_17869565_1    726 AGAAAGCTGGAGGCATCACACTGCCTGACTTCAAAATATACTACAAAGCT 775
                          v    i      vv       v  ii i       iv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_17869565_1    776 ATAGTAACCAAAACATCATGGTA------TAAAAACAGA--TATAGACCC 817
                          i     i   i   vii     ------   ii i   --      i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_17869565_1    818 ATGGAACAGTATAGAGAGTCCAGAAATAAATCCCC-CATATACAGCCAAC 866
                               i  v  v                 i  vi-   v  ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_17869565_1    867 TGATTTTCAATAAAGGCACCAAGAACATATGTTGGGGAAAGGACAGTCTC 916
                                 i i  i  ii      v   viiv         i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_17869565_1    917 TTCAATAAGTAGTGCTGGGAAAACTGGATATTCATATACAGAAGAATGAA 966
                              i  i i         v         ?i  i  i  i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_17869565_1    967 ACTAGGACCCTATCTCTAACCATATACAAAAATCAATTCAAAATAGACTA 1016
                         ii i iv     i   vv               i  i       i  ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_17869565_1   1017 AAGACTTAAATGTAAGTCCCAAAACTATAAAACTACTAGAAGAAAACATA 1066
                         ?    i          vv i              vi              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_17869565_1   1067 GGGG-AAATGCTTCAGGACATTGGTCTGGGCAAAGATTTTTATGGCTAAG 1115
                           ? -    -    iv   v    vi i     v i   i - i v  v 
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCT-TAGATATG 597

  chrX_17869565_1   1116 ACTTTAAAAGCACAGGCAGCAAAAGCAAAAATAGGCAAATAGGATTATAT 1165
                           vii         i   i      v        ii    v   i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_17869565_1   1166 CAAACTAAAAAGTTTCTGTACAGCAAAGAAAAC----AACAGAGTGAAGA 1211
                             v v    ii  i   i vv     i v  ----  v i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_17869565_1   1212 GACAACTCCTTGAATGGGAGAAAATATTTGCAAGATATTCATCTGACAAG 1261
                               i viv                      ivi  vi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_17869565_1   1262 GAATTAATATCCAGAATATGCAAGGAGCTAAAACAATTCAACAGTGGAAA 1311
                          i i vi            ii  i  i  vvv    i    i i ii   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_17869565_1   1312 AACAAATAATGCAATTAAAAAATGGGCAAATGATCTGAATAGATATTTCT 1361
                         i        iv     ?             v   i        i      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_17869565_1   1362 CAAAAGAAGACATACAAATGGCCAAGAAGTATATGAAAAAATGCTCAGTA 1411
                          v        i              v   i i       i       ii 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_17869565_1   1412 TCACTAATTTT 1422
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.98 (131 / 66)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


3417 26.10 0.44 0.44  chrX_17883503_17888442     3540  4447 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_17883503_1   3540 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3589
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_17883503_1   3590 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3639
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_17883503_1   3640 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3687
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_17883503_1   3688 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3737
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_17883503_1   3738 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3787
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_17883503_1   3788 TACAGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3837
                                 i   i v  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_17883503_1   3838 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 3885
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_17883503_1   3886 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTTC 3935
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_17883503_1   3936 CTATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCATGTGTAGAAAGCT 3985
                           v  i  i              v      v  ?   ii  i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_17883503_1   3986 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4035
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_17883503_1   4036 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4085
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_17883503_1   4086 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4135
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_17883503_1   4136 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 4185
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_17883503_1   4186 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4235
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_17883503_1   4236 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAAGCTACTCATCTGACAA 4285
                           i     i                 v       iii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_17883503_1   4286 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4335
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_17883503_1   4336 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 4385
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_17883503_1   4386 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 4435
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_17883503_1   4436 ATCACTGGCCAT 4447
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2736 24.57 5.86 1.61  chrX_18057110_18062938     4466  5336 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_18057110_1   4466 TGGAAAAATATCCCATACTCATGGATTGGAAGACTCAATATCATTAAAAC 4515
                               i         ii                 i     ii    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_18057110_1   4516 AGCCATACTGTGTAAGGCAATTTACAGATTCAACACTATTGCTAACAAAC 4565
                         i  v     vivi  ivii  i            i v  iv   v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_18057110_1   4566 TATTAG-TGTCATTCTTCACA-AAATTAGAAAAAAACT-ATTCTAAAATT 4612
                          vii  -  i -  i  ii  -     i--- v  i  -  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chrX_18057110_1   4613 CATACCGAAC--CAAAGGAGAGCCCA-AATAACCAAAGCAATCCTACACA 4659
                             iv   v--   i   ---    -    i     i     i iv - 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAA-A 192

  chrX_18057110_1   4660 AAAAAGAACAAAGCCAGAGGTATCACACTACCCAACTTTAAA-----CTA 4704
                           i          iii    vv       v     i  i   -----   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_18057110_1   4705 TA---CTATA-----------AGCATGGTACTGGTACAAAAACAGACA-- 4738
                         i ---   i -----------  ii         i i  ii i     --
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_18057110_1   4739 --GACCAATGGAACAGAACAGAAAACCCAGAAATAAAGCCATATACCTAC 4786
                         --  i        i    iv  i ii           v     i ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_18057110_1   4787 AACCATCTGATCTTGTGCAAGACCAACAAAAACAAACAATGGAGAAAGGA 4836
                         iii  vi    i  vvi    iviiv   i v  vv      i     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_18057110_1   4837 CTCCCTAATTCAATAAATGGTGCTGCGATAAGTGGCTAGCCATATGCAGA 4886
                         ivvi  v-     i           v  i  v   v  ?   i     i 
  L1M4_orf2#LINE/    393 TAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_18057110_1   4887 AGAATGGAACTAAACCCTTACCTTTCACCATATACAAAAATTAACTCAAG 4936
                               i ii ii    i     iv                        i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_18057110_1   4937 ATGGATTAAAGATTCAAATGTAAGACCTCAAACTATAAAAATCCTAGAAG 4986
                               i ?   iii          v  v           v  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_18057110_1   4987 AAAACCTAG---CAAATACCCTCTCAACATTGGCCTTAGCAAAGAATTTT 5033
                              v   ---i    -- i  vii  v    vi vi    v iv  i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_18057110_1   5034 TAGCTAAGTCCTCAAGAGC-CAGTGCAACGAAA-------TTGACAAGTG 5075
                            v  v v vi   i   -  i-     i   ------- v  i  i v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATT 638

  chrX_18057110_1   5076 GGAGCTAATTAAA--CAAAGGAGCTTCTGCACAGCCAAAGAAACCATCAG 5123
                            vi v  i   --i   -- i   i  ii vv v  i  v  i    i
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAA--AACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_18057110_1   5124 CAGAATAAACAGACAACCTACAGAATGGGAGAAAATATTCACAAAATACA 5173
                         v i i i  v        i                    ii    vi i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_18057110_1   5174 CATCCAACAAAAGTCTAATATCCAGAATCTATAAGAAACTT----AAATC 5219
                         i   ii i  ii v  vi          v     ii    i----  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_18057110_1   5220 AACAAGCAAAAAATAAATAACCCCATTTAAAAATGGACACAGAACATGAA 5269
                           i  vv    i i         v   ?        i  v  i iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_18057110_1   5270 CAGACACTTCTC---AAAAGACATACATATGGCCAACAA--ACATGAAAA 5314
                         i     i     --- i    i     v        i  --         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_18057110_1   5315 AATGCTCATCATCACTAATTAT 5336
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (142 / 69)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.71 (65 / 24)  


1523 18.00 2.00 26.64  chrX_18073831_18077889     2078  3177 (882)    L1M4_orf2#LINE/L1        1   829 (79)  

  chrX_18073831_1   2078 TGGAAAGACATCCCATGCTTATGGATCAGAAGAATTAATATTGTTAAAAT 2127
                                 i        i i      ii     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_18073831_1   2128 GAACACACTACCCAAAACAAGCTACAGATTCAATGCAATCTTTATCAAAA 2177
                          ivv i   v      vii v            i      ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_18073831_1   2178 TACCAA-TGTCACTCTTCACAGAAATAGAAAAAACAATCCTAAATTTTAT 2226
                          v   i-  i -i i  ii       v  v  ivii        v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_18073831_1   2227 ATGAAACCAAAAAGAGCCCATA-TAGCCAAAGTAATCCTGAGCAAAAAAA 2275
                            i  viiv  i ii    v -        ii    i   iv  i  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_18073831_1   2276 AGAGAGC---AGTA-TCACACCACCTGACTTCAAAATACATTGCAAGGCT 2321
                          v i  i---  v -      iv  ii i       ivi i i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_18073831_1   2322 ATAGTAACCAAAACAGCATGGTATTAATATAAAAACAAATACATTGACCT 2371
                          i     i   i    ii     i iii    ii i i i i  v  i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_18073831_1   2372 ATAAAACAGAA-----AACCCAGAAATAAGCCCATCTATTTACAGCTAAC 2416
                           ii  i    ----- ii          i     vi     ii ii  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_18073831_1   2417 TGATTTTTGACAAAGGCGCCAAGAACGTACATTGGGACACGGACACCGTT 2466
                                i     i  i       v i v  v    iv v i i viv  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_18073831_1   2467 TTCAATAAACAGTGCTAGGAAAACTGGATATCCATATGTAAAAGAATGAA 2516
                              i   ii     i   v         ?   i   i           
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_18073831_1   2517 ACTAGGCCAGGCGTGGTGGCTCATGCCTGTAACCCCAGCACTTTGGGAGG 2566
                         --------------------------------------------------
  L1M4_orf2#LINE/    450 -------------------------------------------------- 449

  chrX_18073831_1   2567 CCAAGGCAGGCAGATCACCTGAGGTCAGGAGTTCGAGACCAGACTGGCCA 2616
                         --------------------------------------------------
  L1M4_orf2#LINE/    450 -------------------------------------------------- 449

  chrX_18073831_1   2617 ACATGGGGAAACCCCGTCTCTAACTGATGGGTAACCCAGCTGCTCGGGAG 2666
                         --------------------------------------------------
  L1M4_orf2#LINE/    450 -------------------------------------------------- 449

  chrX_18073831_1   2667 GCTGAGGTAGAAGAACTGCTTGAACCCAGGAGGCAGAGGTTGCAGTGCAC 2716
                         --------------------------------------    --------
  L1M4_orf2#LINE/    450 --------------------------------------GTTG-------- 453

  chrX_18073831_1   2717 CAAGATTGCACTGCACTCCAGCCTAGGTGACAGAGTGAGACTGTGTCTCA 2766
                         --------------------------------------------------
  L1M4_orf2#LINE/    454 -------------------------------------------------- 453

  chrX_18073831_1   2767 CAAAAAAGAAAAAAAAAAAGAAACTAGTCCCCTAGACCCCTCTCTCTCAC 2816
                         ----------------------------------       vi   v   
  L1M4_orf2#LINE/    454 ----------------------------------GACCCCTACCTCACAC 469

  chrX_18073831_1   2817 CATATACAAAAAACAACTCAAAATGCATTAAAGACTTAAACATAAGGCCC 2866
                                     vi           v  i ?    i    ii    ----
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG---- 515

  chrX_18073831_1   2867 GAAACTATAAAACTATGAAACTACTAGAAGGAAACATAGGAGAAACAGTT 2916
                         -- i   --       i     vi      i         ? v  vvv  
  L1M4_orf2#LINE/    516 --AGCTA--AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_18073831_1   2917 CAGCACATTGGTCTAAGCAAAGATTTTATGGCTAAGACCTCAAAAGCACA 2966
                          ivv  v    vi  i    v i   iv i v  v   vi          
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_18073831_1   2967 GGCCACAAAAACAAAAACAGACAAGTGGGACTACAT-AAAACTAAAAAGC 3015
                         i  v      iv     i   i  i v     v   -    i      - 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-C 660

  chrX_18073831_1   3016 TTATGCACTGCAAAGGAAACAATCAACAGAGTGGA--GACAACCCTT-GA 3062
                           v  ii  v       v  v     v i    i --        vi-  
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_18073831_1   3063 ATAGGAGAAAATATTTGTAAACTATTTATCCCACAAGGGACTAATAACCA 3112
                           i              i   ii  v    iv i        vi  v   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_18073831_1   3113 GAATATACAAGGAACTC----AAC--AGCAAGAAAAA-ACTAATAATCCC 3155
                                i  i      ----   -- ii  v     -  v     i  -
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC- 809

  chrX_18073831_1   3156 TTAATTAAAAAGTGGACAAAGG 3177
                         --    ?    i   i      
  L1M4_orf2#LINE/    810 --AATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 2.03 (130 / 64)
Gap_init rate = 0.02 (18 / 829), avg. gap size = 17.50 (315 / 18)  

 521 12.77 0.00 0.00  chrX_18073831_18077889     3473  3566 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_18073831_1   3473 AAAAGTGGACAAAGGATCTGAATAGACACTTCTCAAAACAATACATACAA 3522
                             i   i        i          i     v   v  v i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_18073831_1   3523 ATGGCCAACAAGTATATGAAAAAATGCTCAACATCACTAATCAT 3566
                                 i   i i       i             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


4142 11.17 9.69 0.54  chrX_18415954_18417698      510  1252 (493)    L1M4_orf2#LINE/L1       98   908 (0)  

  chrX_18415954_1    510 AAATCCCAGCTGGCTTCTTTGCAATGATGGACAAGTTAGT--TATAATTC 557
                                     v   i      ivi  v      i ii --  v     
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_18415954_1    558 ATATGGAAATTCAAGGAACCCAGAATAGCCAAAACAATCCCGAA------ 601
                                   v     i                      ii   ------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_18415954_1    602 GAGCAAAGTTGGAGGACTCACATGCCCCAATTTCAAAACTTACTACAAAG 651
                           i                   ivi                         
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_18415954_1    652 CTACAATAATGAAGAAAGTGAGGTA------------------------- 676
                              i    v    v    v    -------------------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_18415954_1    677 -------ATAGAATTTGGAGTCCAGAAATAAACCCTCTCACATTTATGGT 719
                         -------        vi                  vi--           
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT--ACATTTATGGT 345

  chrX_18415954_1    720 CAATTGTTTTTTGACAAGGGTGCCAAGATCATTCAATGGGGGAAAGAATA 769
                               v    i                i            -        
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chrX_18415954_1    770 GTCTTTTCAGCAAATAGTGGTGGGACAACTGGATATCCACATGCAAAAGA 819
                                  i     i   v               ?              
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_18415954_1    820 ATGACGTTGGACTCCTATTTCACACCATATACAAAAATTAACTCAAAATG 869
                             v       i    ii                               
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_18415954_1    870 GAACAAAGATCTAACTGTAAGAGGTAGAACTATAAAACTCATAGAAGAAA 919
                           v  ?   i    v        v  i             v         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_18415954_1    920 ACATAGGGGTAAATCTTCATGACCTTGGATTTGGCAGTGGTTTCTCAGAT 969
                                ?          i         i  v    i        i    
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_18415954_1    970 ATGACACCAAAGGCACAAGCAA--AGAGAAAAA-----TAAATTGGACTT 1012
                                    i          -- i       -----            
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_18415954_1   1013 CATCAAATATTTAAAA-TTTTGTGCTTAAGAGGACTCTATCGAGAGGGTT 1061
                                -   v    -          v i     v     i   ii  v
  L1M4_orf2#LINE/    645 CATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_18415954_1   1062 AAAAAG--ATCCACAGAATGGGAGAAAATATTTGCAAATCATAT--CCAA 1107
                             ii-- i                                  -- ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_18415954_1   1108 TAAGGGAATT------AGAATATACAAAGAATTCTTA-AACTCAGTAA-- 1148
                                v  ------        i      i     -      i   --
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_18415954_1   1149 ----GTTG--TAAGCCGATTTAAAA-TGGGCAGAGGATCTGAA-AAACCT 1190
                         ---- vii--   v  i   ?    -      i     i    - i  v 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_18415954_1   1191 TTATCCAAAGA---TGTACAAATGGCCAGTAAACACATGAAAAGATGCTC 1237
                           v        --- i            i   i                 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_18415954_1   1238 AACATCATTAGTCAC 1252
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (51 / 28)
Gap_init rate = 0.02 (18 / 811), avg. gap size = 4.22 (76 / 18)  


3229 27.01 0.66 0.55  chrX_18512154_18518534.rev     4984  5890 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_18512154_1   4984 TGGAAGGACATTCTGTGTTCATGAATAGGAAGAATCAATATCGTGAAAGT 5033
                              i  i  i ii        i  v      v i     i  v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_18512154_1   5034 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5083
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_18512154_1   5084 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCC 5131
                          v   iivi i  i  ii     -   -- v  i  - iii    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_18512154_1   5132 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAAACCTAAGCCAAAAG 5181
                                viiv  ii  v  viv  v     i    v i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_18512154_1   5182 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5231
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_18512154_1   5232 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGACC 5281
                                 i   i    ii         i iv ii i   v i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_18512154_1   5282 AATGGAACAGAAC--AGAGTCCTCAGAAATAATACCACACATCTACAACC 5329
                                i    i--       --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_18512154_1   5330 ATCTGGTATTTGACAAACCTGACAAACACAAGAAATGGGGAAAGGGTTCC 5379
                          vi  i v  i     ivv  v   ivv  vvv           ii vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_18512154_1   5380 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5429
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_18512154_1   5430 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5479
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_18512154_1   5480 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5529
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_18512154_1   5530 CTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGACTA 5578
                         v    ?i- v i -   iv   viv  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_18512154_1   5579 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5628
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_18512154_1   5629 ATTAAACTAAAGAGCTTCCGCACAGCAAAAAA-ACTATCATGAGAGTGAA 5677
                           i   v v  i i   ii ii vv    ii -       v  i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_18512154_1   5678 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACA 5727
                         v  i     i                 v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_18512154_1   5728 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5777
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_18512154_1   5778 AAATCAAACAACCTCATCAAAAAGTGGGCAAAGGATATGAACAGATACTT 5827
                           iv    i    iv  i?    i            v    i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_18512154_1   5828 CTCAAAAGAAGACATTTATGCAGCCAACGGACACATGAAAAAATGCTCAT 5877
                            v        i  vi viii     iiii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_18512154_1   5878 CGTCACTGGCCAT 5890
                          i   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2963  9.54 3.95 29.28  chrX_18528215_18532272.rev     2352  3567 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_18528215_1   2352 TGGAAAGACACC--------ATGGGTTGAAAGACTTG-TATTGTGAGGAT 2392
                                 i i --------    i   i       i-      v i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_18528215_1   2393 GGCAATTATTACCCAAAGTGATATAGCAATTCAACGCAATCCCTATCAAA 2442
                               - i v      v    v  vvi                      
  L1M4_orf2#LINE/     51 GGCAAT-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_18528215_1   2443 ATCCCAATAGGCTTTTTTGCAGAAATGGAAAATTTGATCTTCAAATTCAT 2492
                               iiv v               v  v  vi     i v        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_18528215_1   2493 -------TGCAAGGGACCCCAAATAGCCAAAACAATAATGAAGAACAATT 2535
                         -------            vi               vv    i  -----
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA----- 194

  chrX_18528215_1   2536 TCAACACTGCAAAAGAACAAAGTTGAAGGACTCACACTTCCCTATTTCAA 2585
                         -----------i             i                v       
  L1M4_orf2#LINE/    195 -----------GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_18528215_1   2586 AACTTACTACAAAGCTACAGCAATCAAGACAGTGTGGTACTGGCACA--- 2632
                                             i                        i ---
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_18528215_1   2633 ---GACACATAGACCAATAGAATAGAACTGAGAGTCCAATAACAAACCCA 2679
                         ---    i     i    i        i          iv  i       
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_18528215_1   2680 GATATCTATGGCCTATAGATTTTTATTTGTTTGTTTTTTTGAGATGGAGT 2729
                         v i  i     ---------------------------------------
  L1M4_orf2#LINE/    334 TACATTTATGG--------------------------------------- 344

  chrX_18528215_1   2730 CTCGCTTTCTCGCCCAGGCTAGGGTGCAGTGGCACGATCTCGGCTCACTG 2779
                         --------------------------------------------------
  L1M4_orf2#LINE/    345 -------------------------------------------------- 344

  chrX_18528215_1   2780 CAACCTCCACCTTTTGGGTTCAAGCAATTCTTCAGCCTCAGCCACCTGAG 2829
                         -------------------    ---------------------------
  L1M4_orf2#LINE/    345 -------------------TCAA--------------------------- 348

  chrX_18528215_1   2830 TAGCTGGGATTACAGGCATGAGCCACCATGCCTGGCTAATTTTTGTATTT 2879
                         --------------------------------------------------
  L1M4_orf2#LINE/    349 -------------------------------------------------- 348

  chrX_18528215_1   2880 TTAGTAGAGACAGGGTTTCATCATGTTGGCCAGGCTACTCTTGAACTCCT 2929
                         --------------------------------------------------
  L1M4_orf2#LINE/    349 -------------------------------------------------- 348

  chrX_18528215_1   2930 GACCTCAGGTGATGCACCCGCCTCGGCCTCCCAAAATGTTGGGATTACAA 2979
                         --------------------------------------------------
  L1M4_orf2#LINE/    349 -------------------------------------------------- 348

  chrX_18528215_1   2980 GCATGAGCCACTGTGCCCGGCCTGGCCTATTGATTTTTGACAAGGGTGCA 3029
                         -----------------------------        i           v
  L1M4_orf2#LINE/    349 -----------------------------TTGATTTTCGACAAGGGTGCC 369

  chrX_18528215_1   3030 AAGACCACTCAATGGGGAAAGAACAGTCTCTTCAACAGATGGTGCTGGGA 3079
                                i               i     i       i            
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_18528215_1   3080 CAA-TGCATATCCATATGCAAAA-AATTAATTTTGACT------TCATAC 3121
                            -  v   ?   i        -   v  v  v   i------   i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_18528215_1   3122 CATATATAGAAACTAACTCAAAATCATTCACAGACATAAGTGTAAAGGCT 3171
                               i i   i           viv   ?    v   i     ii   
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_18528215_1   3172 AAAACTATAAAACTCTTAGAAGAAAACACAAAGGCAAGTCTTCATGACCT 3221
                                                     i ii? i  i     i      
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_18528215_1   3222 TAGATTTGACAATGGATTCTTAGATATGACACCAAAAGCACAAGCAACCA 3271
                          i i  v i      v                                --
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-- 617

  chrX_18528215_1   3272 AGACACCAAAAGCACAAGCAACCAAGAAAAAACATGGATGAACTGGACTT 3321
                         -------     --------------      i --   i  i       
  L1M4_orf2#LINE/    618 -------AAAAG--------------AAAAAATA--GATAAATTGGACTT 644

  chrX_18528215_1   3322 TATCAAAATGTAACGCTTTTATGCATCAAAGTACATTATCAAGAAAATGA 3371
                         i        vv  vi     i   v      v   i          i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_18528215_1   3372 AAAAACAACCTACAGAACGGGAGAAAATATTTGCAAATCATATATCTGAT 3421
                            i      i      i                                
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_18528215_1   3422 ACGGAATTTATATCCAGAA-------AGAACTCTTATAACTCAATAATAA 3464
                          v  i i  i         -------          i             
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_18528215_1   3465 AAAG--------CCTGATTTTAAG-TGGGCAAAGAATCTGCACAGA--TT 3503
                             --------  ii   ?v  i-         i  i  v i   --  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_18528215_1   3504 TCTGCAAAGAAGGTATACAAATGGCCAATAAATACATAAAAAGATGCTCA 3553
                            v        i                  ii    i            
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_18528215_1   3554 ACATCATTAGTCAT 3567
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (75 / 37)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 22.44 (404 / 18)  


3213 11.70 1.11 25.28  chrX_18567472_18571901.rev     2768  3938 (491)    L1M4_orf2#LINE/L1       21   908 (0)  

  chrX_18567472_1   2768 ATAAATGGAAAGAC-----ATC-TCAAGACAGCCATAGTACCCAAATTGA 2811
                           ii  v i     -----  i- i    ii  v   v v          
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chrX_18567472_1   2812 CCTACAGATTCAAGGCAA-CCCTACCAATATCCCAGCTGC-TTTTTGGTA 2859
                         i            v    -     i   v           -     v i 
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chrX_18567472_1   2860 GATATTGACAAATCAATCCTAAAATTCATATGGAAATTCAAGGGGCCCAG 2909
                           v        iiii                      v      i     
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chrX_18567472_1   2910 AATAGCCAAAACGATCTGGAAAAAGAAGAAGAAAGTTGGAGAACTCACAC 2959
                                     i    v            v          i        
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_18567472_1   2960 TTCCCAATGTTAAAACTTCCCACAAAGCTACAGTAATCAAAATTGTACAG 3009
                                 v i       v i                   i iv  iii 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_18567472_1   3010 TACTGACATAAGGATAAACATAGAGATTG-TGAAATATAATTAAGAGTCT 3058
                              i          i     v    ii-  i    v    i      i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_18567472_1   3059 AGAAATAAACCCTTTTATT-ATGGTTAACTGATTTTTTGATAAGGGTGTC 3107
                                     v vi   -     i  i       i-  i       i 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTC-GACAAGGGTGCC 369

  chrX_18567472_1   3108 AAGAAAATTTAACAAGGAAAGTATAGTCTTTTTAAGAAATGGTGCTGGTG 3157
                             vv   i  iii      v          i  ---------------
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA--------------- 404

  chrX_18567472_1   3158 GCCGGGCACAGTGGCTCACACCTGTAATCCCAGCAGTTTGGGAGGCCGAG 3207
                         --------------------------------------------------
  L1M4_orf2#LINE/    405 -------------------------------------------------- 404

  chrX_18567472_1   3208 GCGGGCAGATCACCTAAGGTCAGGAGTTTGAGACCAGCCTGGTCAACATG 3257
                         --------------------------------------------------
  L1M4_orf2#LINE/    405 -------------------------------------------------- 404

  chrX_18567472_1   3258 GTGAAATCTCATCTCTACTAAAAATACAAAAATTAGCCAGGCGTGGTAAT 3307
                         --------------------------------------------------
  L1M4_orf2#LINE/    405 -------------------------------------------------- 404

  chrX_18567472_1   3308 GCATGCCTGTAATCCAAGCTACTACTCAGGAGGCAAAGGTTGCAGTGAGC 3357
                         --------------------------------------------------
  L1M4_orf2#LINE/    405 -------------------------------------------------- 404

  chrX_18567472_1   3358 CGAGATCGTGTCACTGCACTCCAGCCTGGGTAACAGAGCGAGACTCTGTC 3407
                         --------------------------------------------------
  L1M4_orf2#LINE/    405 -------------------------------------------------- 404

  chrX_18567472_1   3408 TCAAAAAAAAGAAAAAAAAAATTGGTGCTGGGATAACTAAATATCCACAT 3457
                         -    -----------------           i    ii   ?      
  L1M4_orf2#LINE/    405 -CAAA-----------------TGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_18567472_1   3458 AAAACAGAAAGAATTTGGAATCTCACCTCCCACCACACACAAAAATTAAC 3507
                         iv  v    v   v     vi ii     v     i i            
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_18567472_1   3508 TCAAAATGGATCAGACACCTAAATTTAAGAGCTAAATGTATAAAACTCTT 3557
                                      ? v        v           vv            
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_18567472_1   3558 AGAAGAAAACAAAGTAATAGATCTTTATGACTTTGGATTAGGCAATAG-- 3605
                                    v  v?i  i     ii    i    i         i --
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_18567472_1   3606 -CTTAGATACAACACCAAAAACACGAGCAACCAAAGAGAAAAAATATATC 3654
                         -        ii         i   i      --  i          v  v
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAAC--AAAAGAAAAAATAGATA 634

  chrX_18567472_1   3655 ATTTTGACTGGGCATCACCAAAATTAAAAACTGCTGTACTGCAAAGGACA 3704
                          v  v    -----   i              vi   i  v         
  L1M4_orf2#LINE/    635 AATTGGACT-----TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_18567472_1   3705 CCATCAAGAAAGGGGAAAAGACAACCCACAGAATGGGAGAGGGTATTTGC 3754
                          i          v -                         iii       
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTG-AAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_18567472_1   3755 AAATAATATACCTGATAAAGGATTTGTATTTAGAATATATTCAAAAAACC 3804
                             v     i       i   i      ii         --   i   -
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT--AAAGAAC- 775

  chrX_18567472_1   3805 TCCTACAATGCAATAATAAAAAGATAAATAACTCAGTTTTTAAGATGGGC 3854
                           i     iv              i       i  i  ?v-  i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGC 824

  chrX_18567472_1   3855 AAAGGATCTGAATAGACAATTCTCCAAAGAAGATCTACAAATATCCAATA 3904
                                i          v               v       iv      
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_18567472_1   3905 AACACATGAAAAGATGCTTGACATCATTAGTCAT 3938
                          i                ii      ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (87 / 46)
Gap_init rate = 0.02 (16 / 888), avg. gap size = 19.31 (309 / 16)  


1774 25.19 1.13 1.50  chrX_18588713_18594165.rev     1275  1806 (3647)    L1M4_orf2#LINE/L1      379   908 (0)  

  chrX_18588713_1   1275 CAATGGGGAAAGGACTCCCTATTCAATAAATGACACGGGGATAACTGGCT 1324
                                     i ivvi  v     i     iii v    i      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_18588713_1   1325 ATTCATACGCAGAAGAATGAAACTGGACCTCTACCTATCACCATATGCAA 1374
                          ?i  i i   i         ii      i      vv        i   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_18588713_1   1375 AAATTAACTCAAGATGGATTA--GACTTATTAATAAATGTAAGACCTCAA 1422
                                     i      i --   i  ------         v  v  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTA------AATGTAAGAGCTAAA 522

  chrX_18588713_1   1423 ACTGTAAAAATCCTAGAAGAAAACCTAGGACATACCCTTCTGGACATCAG 1472
                            i     v  i           v    ?vvv vi    vv   v ii 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_18588713_1   1473 CCTTAGCAAATAATTTAT--GACTAAGTCCTCAAAAGCAATTGTAACAAA 1520
                         v-    vv   ii   v --  -  v v vi        vvv i      
  L1M4_orf2#LINE/    573 G-TTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAA 620

  chrX_18588713_1   1521 AACAAACATTGACAAATGAGAACTAATTAAACTAAAGAACTTCTGCACAG 1570
                          iv   v  v  i    vi  vi v  i   v v  i     i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_18588713_1   1571 CAAAAGAAAATATCAACAGAGTAAGCAGGCAACCTAAAGATTGGGAGGAA 1620
                             i  v v      v i   i iv  i     i v   v      i  
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_18588713_1   1621 ATCTTCACAAACTATGTATGCAACAAAGGTCTAATATCCAGAATTTATAA 1670
                           v  ii    ii  i   vii i  i  v  vi          v     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_18588713_1   1671 GGAACTTAAACTATTCAACAAGCAAAAAACAAATAGCCCCATTAAAAAGC 1720
                         i     ivv  v i    i  vv    i       i   v   ?    ii
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_18588713_1   1721 GGGCAAAGGATATGAACAAACACTTCTCAAAACAAGACCTATAAGCGGCC 1770
                                    v    i i   i     v   v    iv  i  ii    
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_18588713_1   1771 AACCA--ACATGAAAAAATGCTCAACATCACTGAACCT 1806
                           iv --         i             ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (71 / 60)
Gap_init rate = 0.01 (6 / 530), avg. gap size = 2.33 (14 / 6)  

3647 16.13 5.29 1.95  chrX_18588713_18594165.rev     3761  4479 (974)    L1M4_orf2#LINE/L1        1   743 (165)  

  chrX_18588713_1   3761 TAGAACAAAATTTCATGTTCATGGATTGGACAACTTAATATTGTTAAGAT 3810
                          i   vi v  ii                 vi                  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_18588713_1   3811 GGTAACAGCCTTCAAATTGATCTACAGACTCAACATAATCCCTATCAAAT 3860
                           i  i vi ii                i     ii             v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_18588713_1   3861 TCTCAGCTGGTATTTTTGCA--AATTGACAAGCTGATTCTGAAATTTACA 3908
                           i      viv        --               i  i     i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_18588713_1   3909 TGAAAATGCAAGGGACCCAAAATAGCCAAAACAATCTTTAAAAAGAAGTG 3958
                           i                i                  v         vi
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_18588713_1   3959 CAACGTTCAA---CTCACATTTACCAGTTTTAAAACTGTAGTAAGTTTGT 4005
                            v   vi ---      i  v   i   i      -  v  ------i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTA------C 243

  chrX_18588713_1   4006 AAAGTTACAATAATTAGGACAGTGTGGTCCTAGCATTAGGATAGACATAG 4055
                             i    i    i i           v  i    v            -
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA- 292

  chrX_18588713_1   4056 ACATAGACAAATAGAATACAATTTAAAGGCCAGAAACAAACCCTTATATT 4105
                         ---    iv   i     v    v i  v       i      v  i   
  L1M4_orf2#LINE/    293 ---TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_18588713_1   4106 -ATGGTCAACTGATTTTTGACAAGAGTGCCAAGA----------AGGAAA 4144
                         -        i       i      i         ----------i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_18588713_1   4145 GAACAGTCTTTGAGTCA-----TGGTTCTGGGACAACTGGATATCCACAT 4189
                            i       ---   -----    v                ?      
  L1M4_orf2#LINE/    390 GAATAGTCTTT---TCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_18588713_1   4190 GTAAAAGAATAAAGCTGAACCCTTCCTTCACACCATACACAAAAATTAAC 4239
                          i        i   i  i    i v i          i            
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_18588713_1   4240 TCAAAATGGATCAGAAACCTAAGTGTAGGAGCTAAACCTATAAAACTCTT 4289
                                      ? i      i    i        v             
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_18588713_1   4290 AGAAGAGAACATAGGAATGAATCCTTATGACTCTGAGTTAGGCAATGCCT 4339
                               i        ?i i    i ii    ii  i           vi 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_18588713_1   4340 TCTTAGATACAACACCA----C--------CAAAA----AAGCACATAAA 4373
                                  ii      ---- --------     ----  ii v     
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_18588713_1   4374 TTGGATTTCATCAAAATGAAAAATGTTTGCACTACAAATAATACCACAGA 4423
                              i           v     iv    ii  v    vi i  i ivi 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_18588713_1   4424 GAAAGGGATAAGAGATCCCACAGAATGAGAGAGAATGTTTGCAAATCAAA 4473
                              v  v    v v           i    i   i           v 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_18588713_1   4474 TA-CTGA 4479
                           -    
  L1M4_orf2#LINE/    737 TATCTGA 743

Transitions / transversions = 2.23 (78 / 35)
Gap_init rate = 0.02 (13 / 743), avg. gap size = 4.00 (52 / 13)  

 582 15.25 8.47 2.26  chrX_18588713_18594165.rev     4786  4962 (491)    L1M4_orf2#LINE/L1      721   908 (0)  

  chrX_18588713_1   4786 ATATATATATAT-ATATATACTGAATAAGTGATGTGTATATAGAATA--- 4831
                             v ii v  -      -    -    v  iv     vi      ---
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATAT-CTGA-TAAGGGACTTGTATCCAGAATATAT 768

  chrX_18588713_1   4832 -AAGAACTCTTGCAATGCAAAAATAAAGAG-----TGAC--AATT-AAAA 4872
                         -          i   iv   v      i  ----- i  --    -    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_18588713_1   4873 ATGGAAAATGTACCTGAAATATAATATTTCT--AAAGAAGATGTACAAAT 4920
                             iv  v v ii    -  -i i      --         i       
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAA-TA-GACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_18588713_1   4921 GTCCAATAAGCACATGGAAAGACGCTCAACATCATTAATCAT 4962
                          v              i     i           ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (16 / 11)
Gap_init rate = 0.05 (10 / 188), avg. gap size = 1.90 (19 / 10)  


3129 13.07 1.98 0.20  chrX_18919944_18926223        1   505 (5775)    L1M4_orf2#LINE/L1      111   624 (284)  

  chrX_18919944_1      1 CTTTTTAATAGAAATTGACAAGCTAATCTGAAGATTCATATGGGAATGCA 50
                               vii               i   iv  i          i      
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_18919944_1     51 AGGGATCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAATTTAGA 100
                              i                                      v  i  
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_18919944_1    101 ---CTCAAACTTACCAATTTCAAAACTTACTGCAAAGCTATGTTAATCAA 147
                         ---    v    v                  i        iiv       
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_18919944_1    148 GACAGTGTAGTATTAGCATAAGGACAGACATATAGATCAATGCAATAGAA 197
                                 i   i i         i                 v       
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_18919944_1    198 ----GAGTCCA-AAATAAACTCTTATATTTATGGCCAATTGATTTTCAAC 242
                         ----       -        i v  i        i            i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_18919944_1    243 AAGAGTGCCAAAACAATTCAATAGGGCAAGAATCGTCTATTTCAACAAAT 292
                            i       i  v       i   v      v    -           
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT-TTTCAACAAAT 409

  chrX_18919944_1    293 GGTGCTGGGACAACTGGATATCCACATGCAA--GAACTAAATTGGATCCC 340
                                             ?          --   iv  i     i   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_18919944_1    341 TACTTTATACCATATACAAAAATTAACTCAAAGTGGATCAAAGACCTAAA 390
                            i i i                        i       ?         
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_18919944_1    391 TATTAGAGCTAAAATGATGAAACTCTTGGAAGAAAACATAGGCCTAAACC 440
                          i v          iv  i        i              ?v    i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_18919944_1    441 TTCCTGGACTTGGATTGGGCAATGATTTCTTGGATATGATATCAAAAGCA 490
                            v  iv     i  i       i      i       i i        
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_18919944_1    491 CAAACAACGGGAGGA 505
                            i    iii  i 
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAA 624

Transitions / transversions = 2.71 (46 / 17)
Gap_init rate = 0.01 (5 / 514), avg. gap size = 2.20 (11 / 5)  

3268 27.09 0.44 0.44  chrX_18919944_18926223     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_18919944_1   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_18919944_1   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_18919944_1   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_18919944_1   5028 TATGGAACCAAAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_18919944_1   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_18919944_1   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_18919944_1   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5225
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_18919944_1   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAACAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_18919944_1   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_18919944_1   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_18919944_1   5376 TTAAAGATTTAAACGTTAGACCTAAAACCCTAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       iv     vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_18919944_1   5426 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_18919944_1   5476 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5525
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_18919944_1   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_18919944_1   5576 AGGCAACCTACAACATGGGAGAAAATTTTCACAACTTACTCATCTGACAA 5625
                           i     i   iv            v  ii   v i ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_18919944_1   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_18919944_1   5676 AAACAAACAACCCCATCAAAAAGTGGGCAAGGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i       i   iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_18919944_1   5726 TCAGAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           vi       i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_18919944_1   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3039 25.36 2.91 2.57  chrX_18998151_19000035.rev      502  1396 (489)    L1M4_orf2#LINE/L1       11   908 (0)  

  chrX_18998151_1    502 TCCCATGCTTATGGATGGGTAGAATCAATATTGTGAAAATGACCATACTG 551
                                i i      v  v   v i        v  i   i v     v
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chrX_18998151_1    552 CCAAAAGCAATCTACAAATTCAACACAATTTCCATCAGAATACCACCATC 601
                           v   vii       i       i    ii i    i   v   v vv 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_18998151_1    602 ATTCTTCACAGAATTACAAAAAGC-AATTCTATAATTCATATGGAACCTA 650
                         v  i  ii     v -ii v    -i  i   v             vivv
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_18998151_1    651 AAAAGAGCCCGCATAGC----------------AAAAAGAACAAATCTGG 684
                           ii  v  v v     ----------------  i         vi   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_18998151_1    685 AGGCATCACACTACCCGATTTCAAACTATACTATAAGGCCATTGTCACCA 734
                            vv       v   i        viv     i  i  i iv  v i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_18998151_1    735 AAACAGCATGGTGCTGGTATAGAAATAGGTACATAGACCAATGGAACAGA 784
                          i    ii    i    i   iii    ii i     i        i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_18998151_1    785 ATAGAGAACCCAGAAATAAACCCAAGTACTTACAGCCAACTGATCTTTGA 834
                           v    ii               vii i   ii i   i    i  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_18998151_1    835 CAAAGCAAACAAAACATAAAGTGGGGAAAACACAAACAAAACGTGGGGAA 884
                            i vviv   i  -----------------  vv   ----       
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGAC-----------------CATTCAA----TGGGGAA 388

  chrX_18998151_1    885 AGGACACCCTTTT--------GGTGCTGGGGCTATTGGCTAGCCACATGT 926
                           i i vi     --------         i v i   v  ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_18998151_1    927 AGGAGAATGAAACTGGATCCTCATCTCTCACCTTGTACAAAAATCAACTC 976
                          ii        ii    i  ii i   v    v i         i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_18998151_1    977 AAGATGGATTAAGGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAG 1026
                           i      i ?i   i    iv     v  i           v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_18998151_1   1027 AAGATAACATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTC 1076
                             v     v  ?iv  vi    vv   v    v        v i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_18998151_1   1077 ATGACCAAGAATCCAAAAGC-CAATGCAATAAAAACAAAGATAAATATCT 1125
                         v iivi v  vv        -   -    i    iv   i   i   vv 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAAT 637

  chrX_18998151_1   1126 GGGGCCTAATTAAACTAAAGAGCCTTTGCATGGCAAAAGGAACAGTCAGC 1175
                         v  i i v  i   v v  i i i    iiivv    i iv  vi   iv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_18998151_1   1176 AGAGTAAACAGAAAACCCACAGAGTGGGAGAAAATCTTTACAATCTATAC 1225
                          i   i  v   v          i           v   i   vii   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_18998151_1   1226 ATCTGACAAAGGACAAATATCCAGAATCTACAATGAACTCAAACAAATCA 1275
                               i  i    vvi          v  i  v      vv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_18998151_1   1276 GTAAGAAAAAAACAAACGACCCCATCAGAAAGTGGACTAAGGACATGAAT 1325
                         i   v     i     ii    v  i?i   i   i v     iv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_18998151_1   1326 AGACAATTTTCAAAAGAAGATATACAAATGGGCCACAAACATATGAAAAA 1375
                              v  i  v                   v v i  i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_18998151_1   1376 ATGCTCAACATTGCTAATGAT 1396
                                    ii????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (133 / 90)
Gap_init rate = 0.01 (8 / 898), avg. gap size = 6.12 (49 / 8)  


1989 21.30 6.87 3.17  chrX_19044737_19050139     3599  4166 (1237)    L1M4_orf2#LINE/L1        2   590 (318)  

  chrX_19044737_1   3599 GGAGATATATACCGTGTTCGTGGATTAGAAGGCTCAATATCGTTAAGATG 3648
                            i v    v  i     i      i    i  i     i         
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_19044737_1   3649 TCACCTGTTCCCAAATTCATTTAGAGATTCAGGACAATCTCAATCAAAAT 3698
                         v  vivv i        v  i  v       ivi     i v        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_19044737_1   3699 CTCAGCAGGCTTTTTTGAAGAAGTTGACAAGCTGATTCTAAAGTGCATAT 3748
                          i    v v        v    i             i     i v     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_19044737_1   3749 GGAAACACAAATGACCTAGAATACCCAAAACAATTTTGAAAAA--AGAAC 3796
                              ii   iv    i      v          i        --     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_19044737_1   3797 AAAGCTGGAAGACCTACATTACCTGATTTCAAGACTTACTATAAAGCTAA 3846
                             i    i   ii   i v  ii       i        i       v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_19044737_1   3847 AGTAAGGAAGACAATGTGGTAA-GG--TAAATATATACTTTTAGATCAAT 3893
                              vv      i       v-  --   iv   v  v v         
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_19044737_1   3894 GAAACCAGAAT--AGAGTCCAGAA-TAAAGTCACATATAAAACATCAATT 3940
                          i  i-     --           -    vi  i i  vv vvi      
  L1M4_orf2#LINE/    302 GGAAT-AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_19044737_1   3941 GATTTTTTTTTAAAAAAAGGTGCCAAG-TCAGCTAAT-----AAGAACA- 3983
                               i-----i v  i         -i  vii   -----     i -
  L1M4_orf2#LINE/    351 GATTTTC-----GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_19044737_1   3984 --TTTCCAACAAATAGTGCTGA-ATAGTGCTGAAACAATTAGCCATATGC 4030
                         --   i        i      i- i i--   i -----  ?   i    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAA--CTGGA-----TAKCCACATGC 438

  chrX_19044737_1   4031 AACAAAA-AAACTTGCAACTTTTACCTCATACCAGATGTAGAATTTAAGT 4079
                           v i  -i  v   -i  iii       i    v  ii i  v    v 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTG-GACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_19044737_1   4080 -AAAA---------------AATATAAGAGCTAAAATTGTAACGCTTCTA 4113
                         -    ---------------   i            i i   vi  ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_19044737_1   4114 GAAGAAAA--TAGGGA-AAATTTTAGGCAAAGACTTTTTGTTAAAAAA-G 4159
                                 --    ?i-    i  v v----   i  vv    iiv  - 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGT----GACCTTGGGTTAGGCAATG 583

  chrX_19044737_1   4160 ATTTTTT 4166
                         i   i  
  L1M4_orf2#LINE/    584 GTTTCTT 590

Transitions / transversions = 1.77 (76 / 43)
Gap_init rate = 0.04 (21 / 589), avg. gap size = 2.71 (57 / 21)  

 759 24.35 3.48 0.43  chrX_19044737_19050139     4681  4910 (493)    L1M4_orf2#LINE/L1      672   908 (0)  

  chrX_19044737_1   4681 AAAAGTCAGCTACAAAGA---TAAAAAGGCAAGCCACAGTCTGGGAGAAG 4727
                            i v  -   iv    --- i     i   v      vv        i
  L1M4_orf2#LINE/    672 AAAGGACA-CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_19044737_1   4728 ATATTTGCAAGACATAGATCTGACAAAGGACTTGAATATAAAACGTG-AA 4776
                                   iv    v      i  i       v  vi i  ii i-  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_19044737_1   4777 GAAACTCTCCTAACTCAATAA---GAAGACAAGCAATATAATTTAAAAGC 4823
                         ii      ivi          ---i       ii  ivi    ?    ii
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_19044737_1   4824 TGGCAAAAAATTTGAACAGGTACTTTATCAGAGAAAACATAAAGATAGCA 4873
                         v      ii       i  ii i  ivi  i    i i   v i  i  v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_19044737_1   4874 AATAAGCA-ATGAAAATATCCTCAATATCAATTATTAT 4910
                                 -       v  v     i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (38 / 17)
Gap_init rate = 0.02 (5 / 237), avg. gap size = 1.80 (9 / 5)  


3108 27.11 1.67 0.78  chrX_19051394_19057782.rev     4999  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_19051394_1   4999 TGGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5048
                              ii i  ii    i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_19051394_1   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_19051394_1   5099 TACCAATGACTTTCTTCACGGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5146
                          v   iivi i  i  ii i   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_19051394_1   5147 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5196
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_19051394_1   5197 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5246
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_19051394_1   5247 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5296
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_19051394_1   5297 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5344
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_19051394_1   5345 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGA--GT 5392
                          vi    i  i     ivv  v   i v  vv            i --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_19051394_1   5393 CCCTCTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5442
                          -- i  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_19051394_1   5443 CTGAAACTGGATCCCTTCCTTAAACCTTATACAAAAATTAATTCAAGATG 5492
                         v    ii    i    v   i v   v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_19051394_1   5493 GATTAAAGACTTACATA--------AAAACCATAAAAACCCTAGAAGAAA 5534
                            i ?    i  v  i--------     i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_19051394_1   5535 ACCTAGGCA-ATACCATTCAGGACATAAGCATGGGCAAGGACTTCATGTC 5583
                           v    ?i- v i -   iv   v vi vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_19051394_1   5584 TAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATC 5633
                           vi            vvi           v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_19051394_1   5634 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5683
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_19051394_1   5684 AACAGGCAACCTACAAAATGGGAGAAAATGTTTGCAATCTACTCATCTGA 5733
                           v  i     i   i             i       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_19051394_1   5734 CAAAGGGCTAATATCCAGAATCTACAATAAACTCAAACAAATTTACAAGA 5783
                         i  i  i  vi          v  i  vi     vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_19051394_1   5784 AAAAAACAAACAACCCCATCAACAAGTGGGCAAAAGATATGAACAGACCC 5833
                             i     i     v  i? v  i        i   v    i    vi
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_19051394_1   5834 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACATGTGAAAAAATGCTC 5883
                              v        i  vi viii     v ii  ii      i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_19051394_1   5884 ATCATCACTGGCTAT 5898
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (151 / 89)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.20 (22 / 10)  


4402 16.04 5.50 1.49  chrX_19074139_19076220.rev      719  1591 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_19074139_1    719 TGGAAAGACATCTCATGTTCATAGGCCAGAAGAATTAATATCATTAAGAT 768
                                 i   i         i iiii     v       ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_19074139_1    769 GGCAATAGTTCTCAAACTGATCTACAGATTTCATGTAATCCCTATCCAAA 818
                                v i i    i             iv i i          v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_19074139_1    819 CCCCAGCTAGCTTCTTTGCAGAAATAGACAAACTGACCCTAAAATTGACA 868
                         i       iv   i           v     i    i         v i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_19074139_1    869 TGGAAATTCAAGAGACCCAGAGTAGCTCAAACAACCTTGAAAAAGAAGAA 918
                                v    i        i    iv      i               
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_19074139_1    919 CAAAGTTGGAGGACTTAAATATCCCAATTTCAAAACTTACTACAAAGCTA 968
                                        i v iv                             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_19074139_1    969 CAACAATCAAGACAGTGTGGTACTTGTATAAGGTTGGACATATAGCTCAA 1018
                           ii                    v i      v i         v    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_19074139_1   1019 TGGAATAAAATTGTGAGTCCAGAAATAAATC---ACATTTACAGTTAATT 1065
                                i     v               i ---       ii  i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_19074139_1   1066 GATTTTTGACAAAGGTAACAAAATAATTCAATTGGGGGAAGA---GTTTT 1112
                               i     i   iv   i iv       -    i    ---  i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTT 399

  chrX_19074139_1   1113 TTCAGTAAATAGTACTGG-ACAACTGGATACTCACATG-AAAAGAATGAA 1160
                             ii    i  i    -           ?i      -           
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_19074139_1   1161 GTTAGAACTCTTCTTCACATTACATACAAAAATTCACTCAAA-TAGATCA 1209
                            i  v i  v i     ii i           v       - i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_19074139_1   1210 --------------------AAAA-TA-AAAACTCACAGAAGAAAA-ATA 1236
                         --------------------    -  -       vi         -   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_19074139_1   1237 GGCCTAAGTCTTTATGACTTCAGATTAGGCA-TGATTTCATAGATATGAC 1285
                           ?v   i    ii    i ii i       -  i    v          
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_19074139_1   1286 ACCAGATATGACACCGAAGGTATAGGCAACAAAAGAGAAAGTAGATAAAT 1335
                             ------------  i i i i           i   i         
  L1M4_orf2#LINE/    600 ACCA------------AAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_19074139_1   1336 TTGATTCCATCAAAATCAAAGAGTTTTGTGCCCGAAAGGACAGTATCAAA 1385
                          v  i i         i   i v        iiv        v      i
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_19074139_1   1386 ACAGTGAAAAGACAACCCACAGAGGGACAGAAAAGTTTTGTAAATCAGAT 1435
                          v                     iv iv      vv    i      v  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_19074139_1   1436 GTCTGATAAGGAATTCATATCTAGGATGTATAAAGAACTC---------A 1476
                         i          i i ii    i  i  i            --------- 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_19074139_1   1477 ACAATGAAAA--CAACTAA----ATTAAAAAATAGGAAAGGGCTCTGAAT 1520
                          i   i    --   v   ----   ?      i  v  i  v i     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_19074139_1   1521 AGACTGCTCTGCAAAGAAGGTGTACAAATGACCAATAAGCACATGAAAAG 1570
                             vvi   v        i i        i                   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_19074139_1   1571 ATACTCAACATCATTCATTAC 1591
                           i          ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.51 (98 / 39)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.07 (61 / 15)  


3086 26.55 1.22 0.88  chrX_19194341_19200714     4978  5881 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_19194341_1   4978 GGAAGAACTTTCCATGCTCCTGGGTAGGAAGAATCAATATCGTGAAAATG 5027
                             ii iv i     i  v   i v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_19194341_1   5028 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 5077
                           v     v     iv i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_19194341_1   5078 ACCAA-TGACTTTCTT-CATGGAATTGGAAAAAACT-ACTTTAAAGTTCA 5124
                         v   i-  v    i  -  - i     -- v  i  - iii    i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_19194341_1   5125 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5174
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_19194341_1   5175 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5224
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_19194341_1   5225 TACGGTAACCAAAACAGCATGCTACTGGTACCAAAACAGAGATATAGACC 5274
                            i    i   i    ii  v      i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_19194341_1   5275 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATAGCTACAACT 5322
                                i    i--    i  --        vv  ii i vi  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_19194341_1   5323 ATCTGATCTGTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGA--GT 5370
                          vi    i vi     ivv  v   i v  vv            i --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_19194341_1   5371 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAG 5420
                          -- v  i  i              v      v  ?   i   v i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_19194341_1   5421 CTGAAACTGGATCCCTTCCTTACACCTTATGCAAAAATTAATTCAAGATG 5470
                         v    ii    i    v   i     v   i          i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_19194341_1   5471 GATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5520
                            i ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_19194341_1   5521 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5569
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_19194341_1   5570 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5619
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_19194341_1   5620 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5669
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_19194341_1   5670 AACATGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5719
                           v vi     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_19194341_1   5720 CAAATGGCTAATATCCAGAATCTACAATAAACTCCAACAAATTTACAAGA 5769
                         i  iv i  vi          v  i  vi     iv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_19194341_1   5770 AAAAAACAAACAATCCCATCAAAAAGTGGGCAAAGAATATGAACAGACAC 5819
                             i     i  i  v  i?    i         i  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_19194341_1   5820 TTCTCAAAAAAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGATC 5869
                              v   i    i  vi viii     v ii          i   v  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_19194341_1   5870 A---TCACTGGCCAT 5881
                          ---   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 1.58 (19 / 12)  


2185 24.43 2.10 3.07  chrX_19593539_19598997.rev     3798  4415 (1044)    L1M4_orf2#LINE/L1        1   612 (296)  

  chrX_19593539_1   3798 TGGAGAGACATACCATATTCATGGACTGGAG---TCAGTGTGGTTAAGAT 3844
                             i   i  v    i        i    i--- i i i v        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_19593539_1   3845 GTTGATTC-CCCCAAATTAACCTGTAGATCTAATGCAATTTCTATCAAAA 3893
                          vii  v -         i i  ii    ii  i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_19593539_1   3894 TTCCAGCAAGATTTTTTTTTGTAGCTATAGACTAGTTTATTTTAAGATTT 3943
                          i     vi---ii       i  vv  v   v  i v  ii   i   i
  L1M4_orf2#LINE/    101 TCCCAGCTG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_19593539_1   3944 ATAAAAGAAAT-CAGGAGAACTACAATAGTCAAAACATTTTGAAAACAAT 3992
                            vi-     -  i i  v i v     i       -----------  
  L1M4_orf2#LINE/    148 ATATG-GAAATGCAAGGGACCCAGAATAGCCAAAACA-----------AT 185

  chrX_19593539_1   3993 TTTGAAAAAGAAGAGCAAAAT---AGGAATC----TACCCAATTTTATGA 4035
                         i             i    i ---    v  ---- v        i vi 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_19593539_1   4036 GTTAACTTTAATAGTTATAGTAATCAAGACAGTCTAGTATTGACACAGGA 4085
                         v   -  vi  -  i  i               v i   i  i  i i i
  L1M4_orf2#LINE/    236 CTTA-CTACAA-AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_19593539_1   4086 ATACACATATAGATAAA-GGAACGGACTAGAGAACCCAGAAATAAACCTA 4134
                            v          v  -    ii  v v    ii             i 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_19593539_1   4135 CACAAATATGCCCAAGTGACTTTTTGACAAAAGGGCAAAAGCAATTCAAT 4184
                         i   vv    vi   v   -    i     ii v  v  ii v       
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGA-TTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_19593539_1   4185 GGAGGAAGGATAGCCTTTTCAACAAATGATACTGGAGTATTTGGACATCC 4234
                           i i   i    i              i i    iii vi    i ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_19593539_1   4235 ATAGACAAAAAAAGTGAAACTCGGCCTAAATCTAACATCTTATTAAAAAA 4284
                          i vi     i  -    ii v i  ivv i  v   i v   vv     
  L1M4_orf2#LINE/    433 ACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_19593539_1   4285 TTAACTCAAAACGGATCATGGATTTAAATGTAAAACATAAAACTATAAAA 4334
                                    i      ?i  ii         i vv             
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_19593539_1   4335 GTGTTAGAATTAAACATAGGCAAACATTTTGGGGACCTAGGCCTAGGTGA 4384
                         v v      vv         ?iv v  i  v v     v  vi    ii 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_19593539_1   4385 AGAGTTCTTAGATATCATACCAAAAACAAAA 4415
                         v iv           v i       i  v  
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAA 612

Transitions / transversions = 1.69 (93 / 55)
Gap_init rate = 0.02 (13 / 612), avg. gap size = 2.46 (32 / 13)  

 891 22.59 12.59 0.37  chrX_19593539_19598997.rev     4699  4968 (491)    L1M4_orf2#LINE/L1      606   908 (0)  

  chrX_19593539_1   4699 AACACAATCTATTAAATAAAAAA-AGATCAATTAGACTTCATCAAAAT-- 4745
                          i     v v iv   v      -    v    i              --
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_19593539_1   4746 ---------GTG-----------------AAGAGGATGAAAAGATAGGTT 4769
                         ---------   -----------------    iii        i ivii
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_19593539_1   4770 ACAGACTGGGAGGAAATATTTGCAAACCACATGTCTGACAAAGGACTTGT 4819
                              v      i             i  i  i     i  i        
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_19593539_1   4820 ATCTAGAATGTGTAGAG--CTCTCAAAATGCAACAGTAAGAAACCAAAAC 4867
                            i     i i  i  --    i v  iv   i i   i  iv    -i
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA-T 804

  chrX_19593539_1   4868 AATCTAAT--GAAAATGGGTGAAATACACGAACAGACATT-CACTGAAGA 4914
                           i i   --i        ii  iv ivi   i       - v ii    
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_19593539_1   4915 GAGTATGCAGATGTAAAATAAGCACATGAAAAGATGTCCAACATCATTAG 4964
                         iii   i  i   vvv                    ii        ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_19593539_1   4965 TCAT 4968
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.81 (45 / 16)
Gap_init rate = 0.02 (7 / 303), avg. gap size = 5.00 (35 / 7)  


3257 27.09 0.44 0.44  chrX_19718297_19724571.rev     4877  5784 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_19718297_1   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_19718297_1   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_19718297_1   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_19718297_1   5025 TATGGAACCAAAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCTAAAAG 5074
                                viiv  ii  v  v v  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_19718297_1   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_19718297_1   5125 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGATC 5174
                                 i   i    ii         i iv ii i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_19718297_1   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5222
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_19718297_1   5223 ATCTGATCTTTGACAAACCCGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivvi vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_19718297_1   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5322
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_19718297_1   5323 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i i   v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_19718297_1   5373 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGATAAC 5422
                          i ?   ii    i  v   v       i      vi i       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_19718297_1   5423 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTTATGTCCAA 5472
                         v    ?i v viv   iv   v v  vv i     v ii  iv ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_19718297_1   5473 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5522
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_19718297_1   5523 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_19718297_1   5573 AGGCAACCTACAACATGGGAGAAAGTTTTCGCAACCTACTCATCTGACAA 5622
                           i     i   iv          i v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_19718297_1   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5672
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_19718297_1   5673 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAATAGACACTTC 5722
                          i     i     v  i?    i           iv          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_19718297_1   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5772
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_19718297_1   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1832 24.96 9.68 1.82  chrX_20026830_20028451.rev      472  1132 (489)    L1M4_orf2#LINE/L1      196   908 (0)  

  chrX_20026830_2    472 AAAAACAAAATGGGAGGA---ACCCTTCCAAATGATTTTAAGACTTACTA 518
                           i      i v      ---  v     v   ---  i  i        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAAT---TTCAAAACTTACTA 242

  chrX_20026830_2    519 TA----TCCAGTACTCAAAATACTGTAGTATTGGCAAGGGGATACACACA 564
                         i ---- v     v    i i v   i   i     vii     v   i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_20026830_2    565 TAGATCAGTGGAATAAGATGGAGAA-CAAGAAATAGACCCACGTAAGTAC 613
                                i       ii  v    i- v       i     iii vv  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_20026830_2    614 AGCCAACTGATTTTTGTCAAAGTTACAAAAGCAGTTTGATAGAGGAAGGA 663
                         i i   i       i v   i v i v  ii vi  ii  i i i   --
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-- 390

  chrX_20026830_2    664 TAAATAGCCTTTTCAACAA-TGGTGTCTGGAGCTATTGCACACCTATAGG 712
                         --     i           -     -    ii v i  v i ? i i v 
  L1M4_orf2#LINE/    391 --AATAGTCTTTTCAACAAATGGTG-CTGGGACAACTGGATAKCCACATG 437

  chrX_20026830_2    713 TAAAACAAT-AAGTCTCAACCCAAATCTCGTACTGTGTA--AAAGTTAAT 759
                         i    v   -    - vi    vv i   ii  ii i  --   i    i
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_20026830_2    760 TTAAAATGGATCATGGATTTGAATGTAA-------AACTAGAAAACTTTT 802
                          i           ?i  ii i       -------     v      i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_20026830_2    803 AGAATTTAGACATAGGAGAAGATCTTCAGGACTGTGGGCTAAATGAAGCA 852
                             vv- i       ? v i      iv   iv    i  iiii v vv
  L1M4_orf2#LINE/    537 AGAAGA-AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_20026830_2    853 TT--TAAACCTGAGACCAAAAGCAAATTCTATAAAAGAAGAAAACAATAA 900
                           --  i iv   v          v vv v i       i   vvi    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_20026830_2    901 ATTGAACTTCTGAAAAATTCAAGACCTTTTAT-------------CTAT- 936
                             i     vvv      v  i  -    i -------------    -
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATC 684

  chrX_20026830_2    937 --GAAA-----AAGAC--TCTGC-GAA-GGG------TAT----GAACC- 964
                         --    -----     --i ii -   -   ------   ----i  i -
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_20026830_2    965 TGTAACTGAGACCGGACTTGTATTTACAATATTCAAAGAACTCTCAAAAC 1014
                          i  v    v vv          ii v     vi          i v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_20026830_2   1015 TCAGCAATAACAAAGACAAGCAATCCAGGCAAAAAATAGACAAAAGAAGT 1064
                            ii     -        ii  i   ivi?      i i    i  vv 
  L1M4_orf2#LINE/    785 TCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_20026830_2   1065 GAACAGACACTTCACCAAAGATGA-------ATAGCAGATAAGCATATGA 1107
                            i     i   v       v  -------  i  vi       i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_20026830_2   1108 AAAGATGTTCAGCATGGTTAACTAT 1132
                                i   i   vi????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (103 / 58)
Gap_init rate = 0.04 (25 / 713), avg. gap size = 3.04 (76 / 25)  


3056 27.07 0.55 0.55  chrX_20052880_20057229     2953  3857 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_20052880_2   2953 AAAAATCATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAATAG 3002
                            i  -  i     i        v      v i     ii v  i  i 
  L1M4_orf2#LINE/      4 AAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_20052880_2   3003 CCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTGCCATCAAGCTA 3052
                          v     v      v i  i  i        i  v  iv i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_20052880_2   3053 CCATTGACTTTCTTCACAGAACTAGAAAAAACT-ACTTTAAATTTCATAT 3101
                            vivi i  i  ii     v v  v  i-  - iii    v       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chrX_20052880_2   3102 GGAACCAAAAAAGAGTCCATATAACCAAGACAATCCTAAGCAAAAAGAAC 3151
                             viiv  ii  vi viv   i    i      i i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_20052880_2   3152 AAACATGGAGGCATCACACTACTTGACTTCAGACTATACTACAAGGCTAC 3201
                            vv      vv       v iii i    i viv        i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_20052880_2   3202 AGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAAT 3251
                              i   i    ii         i iv ii i   i       i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_20052880_2   3252 GGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACAGCCATCTC 3301
                             i     v   ivii         vv   i    i  ii i  vi v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_20052880_2   3302 ATCTTTGACAAACCTGACACAAACAAGCAATGGGGAAAGGATTCCCTATT 3351
                           i  i     ivv  v  vi v  vv            i  vvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_20052880_2   3352 TAATAAATGGTACTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAAC 3401
                         i  i       i      v      v  ?   i     i  i v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_20052880_2   3402 TGGACCCCTTACTTACACCTTATACAAAAATTAACTCAAGATGTTTTAAA 3451
                                  vv  i     v                   i   vv i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_20052880_2   3452 GATTTAAATGTAAGACCTAAATCCATGAAAAACCCTAGAAGAAAACCTAG 3501
                           ii           v     v i  -    vi i           v   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAG 550

  chrX_20052880_2   3502 GCA-ATACCATTCAGAACATAGGCATGGACAAAGACTTCATGGCTAAAAC 3550
                          ?i- v i -   ivi  v v  vv i i   v ii   v i v  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_20052880_2   3551 ACCAAAAGC-CATGGCAACAAAAGCCAAAATTGAACAATGTGATCTAATT 3599
                                  -  -i          vv     v  vv   vv  ii v  i
  L1M4_orf2#LINE/    600 ACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_20052880_2   3600 AAACTAAAGAACTTATGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 3649
                            v v  i     v  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_20052880_2   3650 GCAATCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATGTGAGAAAG 3699
                         i   i i                 v       vii  vi  v   v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_20052880_2   3700 GGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAA 3749
                          i  vi          v  i  i     ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_20052880_2   3750 ACAAACAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTTTC 3799
                              i   i v  i?    i            v    i     i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_20052880_2   3800 AAAAGAAGACATTTATGCGACCAACAA--ACGTGAAAAAAAGCTTATCAT 3847
                         v        i  vi vii i    i  --  i      i v   i v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_20052880_2   3848 CACTGGTCAT 3857
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.32 (137 / 104)
Gap_init rate = 0.01 (9 / 905), avg. gap size = 1.11 (10 / 9)  


3473 20.99 4.29 1.81  chrX_20147947_20150449.rev     1127  2012 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_20147947_2   1127 TGGGAAAATATACCGTACTCGTGGATTGGAAGACTCAATCTTGTTAAGAC 1176
                            i  i    v  i ii  i              i   v         i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_20147947_2   1177 G-CAATTCTCTCCACATTAATCTATACATTCAATGCAATCACAATCAAAA 1225
                          -    v   i   v   i     i v      i      v v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_20147947_2   1226 TCCCAGAAAGCTTTTTTTTTAGAAACTGACAAACCAATTCTAAAATTTAT 1275
                               vv-  i      vi     i      i ii  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_20147947_2   1276 ATGGAAATACAAAGGACTTATGATGAACAAAATTAGACTTAAAAATGAA- 1324
                                 i   i    ii vi  iiv     i- iv   i    v   -
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AATCTTGAAAAAGAAG 198

  chrX_20147947_2   1325 --CAAAATTAGAAGACTTATACTACCTGATT-CAAGACTTACTATAAAGC 1371
                         --    i  i  i    i i   v  ii   -   i        i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_20147947_2   1372 TACAGTAATCAAGAACAGTACTACGGAACGGTATTGGTG-AAGTGATAGA 1420
                                       -    ii--------    i   ii-   -      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGA-CAGTGT--------GGTACTGGCATAAG-GATAGA 288

  chrX_20147947_2   1421 CATATAGATCAATGGAACAGAGTAGAGTGTCCAGGAATAGATCTACACAT 1470
                                          i   i v   v      i    i i i i    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_20147947_2   1471 ATATGACCAATTGATTTTCCATAAAAGTACCAAGGTAAT-CACATGGAGA 1519
                         v    ii            v i  ii  i     iiv  -  -    i  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGA 387

  chrX_20147947_2   1520 AA---TAATCTTTTCAGCAA-CAGTGCTGGAACAA---GATATCCACTTG 1562
                           ---  i        i   -ii       i    ---    ?    v  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_20147947_2   1563 GAAAATGATTAACCTCAGCTCTTACCTCACATCACTCAAAAAACTTAACT 1612
                         v    vi  v  vi vii i i         i  ivi v    v      
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_20147947_2   1613 CAACATGGATCATAGACCTAAATGCAAAAGGTAAAATTATAAAATTTCTA 1662
                            v        ?           i  i  v     i       i ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_20147947_2   1663 AAAGAAAACATAGAAGAATATCTTCATGACCTTGA-T--GGCAAAGATTC 1709
                         i            i? v v      i        i- --     v i  i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_20147947_2   1710 CTTAG----GGCAC-AAAAACGTGAACCATAAAAGAAAAAAATTGATAAG 1754
                              ---- i   -    i iii i v i           - v     i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAA 636

  chrX_20147947_2   1755 TTGAACTTCATCAAAATTTAAAACTTCTACTG-TTCAAAAGAGCCTATGA 1803
                            i              v       i i-  -      i  vv    v 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCA 685

  chrX_20147947_2   1804 AGAAAAAGAAAAGATAAGCCATAGC-TAGTAGAAAAT-TTTATA-----C 1846
                              iv       i  v   i  v- i v       -   ii -----i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_20147947_2   1847 ATATC----AAAAGACTTGTATACAGGTTGTATAGAGAACTCTTAGAATT 1892
                              ----  ii         v   iv i    i          v  i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_20147947_2   1893 CAATAAAAATAAGACGAACAATCTAAATTTAAAATGCACCAAAAGAGTTG 1942
                               v  v     i  i  i i  v ?v      vi -   i  v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC-AAAGGATTTG 834

  chrX_20147947_2   1943 AA----CACTTTATAAAAGAATATATGCAAATGGTCAATAAGCACACAAA 1988
                           ----  i  iviv      v    i       i           ii  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_20147947_2   1989 AAGATGCTTCACATCATTAGTCAC 2012
                                 iv      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.19 (125 / 57)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.00 (54 / 27)  


3547 24.36 1.33 0.44  chrX_20320946_20323905.rev     1571  2469 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_20320946_2   1571 GAAAAGAAATACCATGTTCATGAATTGGAAGAATCAATATTGCAAAAATG 1620
                          i     v  v           i         v i       iv  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_20320946_2   1621 TCCATACTACACAAAGCAATCTACAGATTCAATGCAATCTCTATCAAAAT 1670
                         v v     v v    vii              i      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_20320946_2   1671 ATCAATGACATTCTTCACAGAAATAGAAAAAATAATCCTAAAATTCATAT 1720
                         vi  iivi v  i  ii       v  v  iv i                
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_20320946_2   1721 TCATGAACCACAAAAGACCTGGAGTAGCCAAAGCCATTCTGAACAAAGAG 1770
                         ---v   vii   ii    ii  i        i v  ii    v  ii  
  L1M4_orf2#LINE/    152 ---GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_20320946_2   1771 ATCAAAACTGGAGGAATCACATTACCTGATTTTAAATTATAATACAGAAC 1820
                          v    ii       v     i v  ii    i   viv  v    i i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_20320946_2   1821 TATAGTTAGCAAAACAGCATGGTACTGACATATAAGCAGACATATAGACC 1870
                           i   v v   i    ii        i    viiii           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_20320946_2   1871 AATGGAAAATAATAGAGAACCCAGAAACAAATGTATACATCCACAGCAAA 1920
                                v v   v    ii       i   ivi      ii ii iv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_20320946_2   1921 CTCATTTTTGACAAAGATGTCAAGAATATAAACTGAGGAAAAA---GTCT 1967
                         i v     i     i i  i     vi  vv v  i     i ---    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_20320946_2   1968 CTTCAATAAATGATGCTGGGAAAACTGGATATCCATTTGTAGGAGAATGA 2017
                         i     i     i        v         ?   iv  i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_20320946_2   2018 AACTAGGCTTCTATCTCTCACCATATACAAAAGT-----CAAAATGGATT 2062
                          ii i i ii   i   v              i -----          i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_20320946_2   2063 AAAGACTTAAATCTAAAATCTCAGCCCATGAAACTACTACAGTAAAAAAT 2112
                          ?    i     v   i v  v iv i  i     vi  v iv    v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_20320946_2   2113 TGGGGAAAATCTCCAGGACATTGTTCTGGGCAAAGATTTCTTGAGTAATA 2162
                         v  ? v      i iv   v   vvi i     v i      iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_20320946_2   2163 CCCCACAAGCATGGGCAACCAAAGCAAAAATGGACAAATGGGATCACATC 2212
                          v   v     iii     v    v      i  i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_20320946_2   2213 AA-CTTAAAAAGCTTCTTCACAGCAAAGGAAACAATCAACAAAGTGAAGA 2261
                           -v       -   i vii vv       v  v     v        i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_20320946_2   2262 GACAACCCACAGAATGGGAGAAAATATTTGCAAACTACCCATCTCATAAG 2311
                                                           ii ivi    v     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_20320946_2   2312 GGATTAATAACCAGAATGTATAA-GAGCTCAAACAACTCAATAGGAAAAA 2360
                            i vi  v       i     -  i   vv           iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_20320946_2   2361 ATCTAATAATCCA--TTAAAAATGGGCCAAAGATCTGAATAGATATTTCT 2408
                         iv v     i   -- ?          v  i   i        i      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_20320946_2   2409 CAAATGAAGACATACAAATGGCAAATAGGCATGTAAAAAGGTGTTCACCA 2458
                          v  v     i           v    i   ii i     i  i   v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_20320946_2   2459 TCACTGATCAT 2469
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (130 / 85)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 2.29 (16 / 7)  


3008 26.56 1.33 0.44  chrX_20474413_20476828     1024  1923 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_20474413_2   1024 TGAAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 1073
                           i   v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_20474413_2   1074 GATCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCTCAGCAAAA 1123
                          iiv     v  v   vii       i      i     i ii v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_20474413_2   1124 TATCACCATCATTCTTCAGAGAACTAGATTAAAC-AATTCTAAAATTCAG 1172
                          vi  v vv v  i  iiv    v v  i-  i -i  i          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_20474413_2   1173 ATGGAACCAAAAAAGAGCGTGCATAGCCAAAGCAAGACTAAGCAAAAAGA 1222
                               viiv  ii  v vv v         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_20474413_2   1223 AAAAATCTGGAGGCATCACATTACTCAACTTCAAACCATCCTATAAGGCC 1272
                          v   vi      vv     i v i   i      v v v   i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_20474413_2   1273 ATAGTCACCAAAACAGCATGGTACTGCTATAAAAATTGGCACATAGACCA 1322
                          i   v i   i    ii        vi    ii  v i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_20474413_2   1323 ATGGAAAAGAATAGAGAATCCAGAAATAAACCCAC----TTACAGCCAAC 1368
                               v     v    i                i----   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_20474413_2   1369 TGATCTTCAACAAAGCAAACAAAAACAT-AAATTGGGGGAAAGGACACCC 1417
                             i   i    i vviv   i v   -v   --        i i vi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAAT--GGGGAAAGAATAGTC 397

  chrX_20474413_2   1418 TATTCATCAAATGGTGCAGGGATAATTGGCAAGACACATGTAGAAGAATA 1467
                          v    v          v    i  i   vv ?v      i i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_20474413_2   1468 GAACTGGAACCTCATCTCTCACCTTATA-AAAAATCAACTCAAGATGGAT 1516
                         i ii    v  ii i   v    v    -      i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_20474413_2   1517 CAGAGACTTAAATCTAAGGCCTGAAACCATAAGGATTCTAGAAGATGATA 1566
                           ?    i     v    iv  i    i    iiv ii       vi i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_20474413_2   1567 TCAGAA-AAACCTGTCTAGACATTGGCTTAGGCAAAGAATTCATGACCAA 1615
                          vi ?i-   i  -  vv   v    v        v iv   v iivi v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_20474413_2   1616 GAGCCCAAAAGCAAATGTAACAAAAAGATAAATAGATG---TG-ACTTAA 1661
                           vv         v v i       ii v        i---  -    v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_20474413_2   1662 TTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTAAAC 1711
                          i   v v    i   i  ii vv    i  v iv    iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_20474413_2   1712 AGAAAACCCATAGAGTGGGAGAAAATCTTCGCAATCTATACATCTGACAA 1761
                            v      i   i           v  i    vii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_20474413_2   1762 AGGACTAATATCCAGAATCTACAAGGTACTCAAACAAATTAACAAGAAAA 1811
                         i     vi          v  i  i v    vv    v i  i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_20474413_2   1812 AAACGGACGATCCCATCAAAAAGTGGGCTAAGGACATGAACAGACAATTC 1861
                          i  ii ii i  v  i?    i     v     iv    i     v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_20474413_2   1862 TCAAAAGAAGATATACAAGTGGCCATCAAACATATGAAAAAATGCTCAAC 1911
                           v               i      vi  i  i       i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_20474413_2   1912 ATCATTAATGAT 1923
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (135 / 100)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3763 23.89 1.00 0.11  chrX_20527903_20532109.rev     2817  3716 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_20527903_2   2817 TGGATAGATATTCCATGTTCATGGTTTAGAGGAATCAATATTGTTAA-AT 2865
                             v      i            v  i  i  v i           -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_20527903_2   2866 GTCCATACTACCCAAAGCAATTCACAGATTTAATGTAATCCCTATGAAAA 2915
                          v v     v      vii  ii       i  i i         v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_20527903_2   2916 TATCAATGACATTCTTCACAGAAATAGAAAAGACTATCCTAAAATTTATA 2965
                          vi  iivi v  i  ii       v  v   viv           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_20527903_2   2966 TGGAACCACAGAAGACCCAGAATGGCCAAAGCTATCCTAAGCAAAAAGAA 3015
                              vii  iii          i      i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_20527903_2   3016 CAAAACTGTAGGAATCACATTACCTAACTTCAAATTATACCCCAGAGCTG 3065
                             ii  v    v     i v  i  i      viv   iv  i    i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_20527903_2   3066 TTGTAACCAAAACAGCATGTTACTAGCATAAAAATAGAGACATAGGCCAG 3115
                         iv    i   i    ii  v    i      ii     v i    ii  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_20527903_2   3116 TGAAACAGAATAGAGAACCCAGAAACAAATCCATACATCTATAGTAAACT 3165
                           i  i     v    ii       i   i        i   i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_20527903_2   3166 CATTTTCAACACAGGTTTCAAGAACACACCTTAGGAAAAGGACAGTCTTT 3215
                         v      i   vi   vi     v  iv vv i  i    i i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_20527903_2   3216 TCAATAAATCGTGCTGGGAAAACTTAACATCTGCATGCAGAAGAATGAAA 3265
                             i    v         v    vi i ? ii      i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_20527903_2   3266 CGAGATCTCTATCTCTTGCCACATACAAAAATCCAATCAAAATGGATTAA 3315
                         ivi  i i   i   vii   i          iv v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_20527903_2   3316 AGACTTAA------GACCTCAAACTATAAAACTGCTGAAAGAAAACACTG 3359
                             i   ------  v  v             vi ii         iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_20527903_2   3360 GGGAAACTTTCCAGGACATTTGTCTGGGCAAAGACTTCTTGAATAATACC 3409
                          ? v  v i i iv   v  v vi i     v ii     ii   vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_20527903_2   3410 TCACAGGCACAAGCAACCAAAGCGAAAATGGACAAATGGGATCACATCAA 3459
                         i  v i           v    vi     i  i    v   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_20527903_2   3460 -GTTAAAAAGCTTCTGCACAGCAAACGAAACAATCAACAAAGTGAAAAGA 3508
                         -i       -   i  ii vv    v  v  v     v            
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_20527903_2   3509 CAACCCACAGAATGGGAGAAAATATTTGCAAGCTACCCATCTGACAAGGG 3558
                                                        iii ivi      i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_20527903_2   3559 ATTAATAACCAGAATATATAAGGAATTCAAACAACTCTATAGGAAAAAGT 3608
                          i vi  v             i   i  vv       v   iv      v
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_20527903_2   3609 CTAATCATCCGATTTAAAA-TGGGAAAAAGATCTGAATAGACATTTCTCA 3657
                          v   v i  i   ?    -    v   i   i                v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_20527903_2   3658 AAAGAAGACATACAAATGGCAAATAGGCATATGAAAAGATGCTCAACACC 3707
                                 i           v    i   i                  i 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_20527903_2   3708 ATTGATCAT 3716
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.60 (130 / 81)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.00 (10 / 5)  


 382 16.53 5.79 4.13  chrX_20548650_20554849        2   122 (6078)    L1M4_orf2#LINE/L1      682   804 (104)  

  chrX_20548650_2      2 ATCAACAAAGTGAAGAGACAACCTACAGAATGTGAGAAAACATTTGCAAA 51
                              v        i        i        v       i         
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_20548650_2     52 AAGCTGAATAAA-CTGACAAGGGATTAATAACCAGACTATATAG-GAACT 99
                         --v ---   v -    i      i vi  v     v      i-     
  L1M4_orf2#LINE/    732 --TC---ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_20548650_2    100 C----AAG-CAATAGCAAAAAAGCCAAT 122
                          ----  v-     ii     ii v   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAAT 804

Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.05 (6 / 123), avg. gap size = 2.00 (12 / 6)  

3250 26.33 1.00 0.55  chrX_20548650_20554849     4804  5707 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_20548650_2   4804 TGGAAGAACTTTCCATGCTCATGGATAGGAAGAATCAATACTGTGAAAAT 4853
                              ii iv i     i        v      v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_20548650_2   4854 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4903
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_20548650_2   4904 TGCCAATGACTTTCTTCACAGAATTGGAGAAAACT-ACTTTAAAGTTCAT 4952
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_20548650_2   4953 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAACCCTAAGCCAAAAGA 5002
                               viiv  ii  v  v v  v     i    i i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_20548650_2   5003 ACAAAGCCGGAGGCATCACGCTACCTGACTTCAAACCATACTATAAGGCT 5052
                               ii     vv    i  v  ii i      v v     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_20548650_2   5053 CCAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGATACAGACCA 5102
                         v      i   i    ii           iv ii i   v   i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_20548650_2   5103 ATGGAACAGAGC--AGAGCCCTCAGAAATAATACCACACATCTACAACCA 5150
                               i   ii--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_20548650_2   5151 ACTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5200
                          i    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_20548650_2   5201 TATTTAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5250
                          v  i ii              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_20548650_2   5251 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5300
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_20548650_2   5301 TAAAGACTTAAATGTTAGACCTAAACCCATAAAAGCCCTAGAAGAAAACC 5350
                         i ?    i       v   v     v i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_20548650_2   5351 TAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATATCTAA 5399
                             ?i- v   -   iv   v v  vv i     v ii   v  vv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_20548650_2   5400 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5449
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_20548650_2   5450 TTAAGCTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGAAC 5499
                          i  iv v  i i   i  ii vv v  i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_20548650_2   5500 AGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTACTCATCTGACAA 5549
                           i     i                 i       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_20548650_2   5550 AGGGCTAATATCCAGAATCTACAAAGAACTCAAAGAAACTTA-CAAGAAA 5598
                         i  i  vi          v  i         vv v  -  i -i  v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAA 795

  chrX_20548650_2   5599 AAAACAA----CCCCATCAAAAAGTAGGTGAAGGATATGAACAGACACTT 5644
                           i    ----   v  i?    i i  ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_20548650_2   5645 CTCAAAAGAAAACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5694
                            v      i i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_20548650_2   5695 CACCACTGGCCAT 5707
                           i  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


1924 28.10 5.42 1.28  chrX_20556614_20559820     1500  2200 (1007)    L1M4_orf2#LINE/L1        1   730 (178)  

  chrX_20556614_2   1500 TGGAACAATATACCGTGTTAAATGGATTGTAAAACTTGAAATTGTTAAGA 1549
                              vi    v  i    v -       v  i    i v          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCA-TGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_20556614_2   1550 TGTCATTTTTGTCCAATTTGATCTATAAATCTGATACTACTCCAATCTGA 1599
                           v  v vi vi    v        i i  iii ii v ii  v   vi 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_20556614_2   1600 ATACTAGCAGGCTTTTAAAAATAGAATTTGAAAAGCTGATTCTAAAATTT 1649
                           v i   v v     vvi--i    v    v        i        i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTG--CAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_20556614_2   1650 ATATGGAAATGCAGAGAACTATGAATAGTCAAA-CAATCCTGAAAAAGAC 1698
                                      ii i  ivv      i    -     i         v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_20556614_2   1699 --ACAAAGGCTGG-GCCCTTGCACCTCCTAACTTCAAGGCTTACTATAAA 1745
                         --      -i   - vv  ii   i   i  i     ii       i   
  L1M4_orf2#LINE/    198 GAACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_20556614_2   1746 GCAATATTAGTCAAAGTGGTGTCATATTGGCAAAAAGGTAGACA-----A 1790
                           v i v  i    iiii    vi  i     v  i i      ----- 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_20556614_2   1791 CGAATGGAAGAAAATAAAGAATGCAGAAATAGAAC--TACACTTATAAGT 1838
                         iv       v i   vi   i v        i v --    i    i-  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG-GT 345

  chrX_20556614_2   1839 CCATTGATTTTTAATATATACACTAAAGCAACTCAATGGGAAAAC--TAA 1886
                          v         ii i viviii i  ii v i        i   v--  i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_20556614_2   1887 CCT---CAGTGTATGATTCTTGACAAACTGGATATCCGTACAGAAAATAA 1933
                         i  ---  iiiv   i v  v ivv         ?  ii iiv    v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_20556614_2   1934 TGAACATTGG-CCCC-----------ATACACAAACACCAACTCAAGTTG 1971
                             -i    -    -----------   i     v ii       iv  
  L1M4_orf2#LINE/    446 TGAA-GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_20556614_2   1972 CACTATAGACATGAATGCAAAAGGTAAAATTATAAAGCTTCCAGAAGAAA 2021
                         v ii ?    v i    i  i  v     i      i  iii        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_20556614_2   2022 GTTACTAGAGAATATTTTTGCTATCTGGGGGAATGAAAAGATTTCTTAG- 2070
                         ii- ivi ? v v  i  i iv i  v   vv v v  v i        -
  L1M4_orf2#LINE/    545 AC-ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_20556614_2   2071 ---GGCATAGAAATCAATAAATG-TAAAAGAAAACAATTGATAATTTAGA 2116
                         --- i  ivi   v  -i  iii-i         -   v     v  i  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCA-CAAGCAACAAAAGAAAA-AATAGATAAATTGGA 641

  chrX_20556614_2   2117 TTTCATCAAAATTTAAAA--TTTCTGCTT-ATTAGACA--GTTAAGAAAA 2161
                         i            v    --   v     - vvi    --i i      i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_20556614_2   2162 TGTGAAGGCAAGCCATAGTCTGGTAGAAAATTTTCACAA 2200
                           vi   i   v   i  vv   v       v  ii   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

Transitions / transversions = 1.59 (119 / 75)
Gap_init rate = 0.03 (22 / 730), avg. gap size = 2.14 (47 / 22)  

 340 23.74 7.76 5.48  chrX_20556614_20559820     2501  2719 (488)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_20556614_2   2501 AAGAAAG--AAAAGA-AA-----AGAA---AAGAAAAGTTTCACAATACA 2539
                                --      -  -----    ---i      vv  ii   vv  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_20556614_2   2540 GAGATCTGACAAAAGACTTGTAGTAAAGATATTTAAAGAATGCTTTTAAT 2589
                         v v      i  ii        viv ii    v       iv   vi  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_20556614_2   2590 GCATATATAAAGCATATATAAAGGCAGTCAGTCCAAT--ATAAATGGTGA 2637
                         v  ---    ------  v    i  ivi ii     -- v      vv 
  L1M4_orf2#LINE/    785 TCA---ATAA------TAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_20556614_2   2638 AAATACCAGAACAGACA---CTTAAAAATGGAAGATACACAAATGCCCAA 2684
                           iv iiv   i     ---  iv   ---       i       v    
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAA---GAAGATATACAAATGGCCAA 872

  chrX_20556614_2   2685 TAA-CACATAGAAAAGTGTTCAAATTTATTAGTTAT 2719
                            -     ii   ii  i    vv i ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (29 / 23)
Gap_init rate = 0.04 (10 / 224), avg. gap size = 2.90 (29 / 10)  


2392 25.60 1.05 0.45  chrX_20597327_20598972.rev      499  1166 (480)    L1M4_orf2#LINE/L1      237   908 (0)  

  chrX_20597327_2    499 TTCCTACGGGGATACAGTAACCACAACAGCACGGTACTGGTACAAGAACA 548
                           v    iii v        i  vi    iii        i i   i i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_20597327_2    549 GACACATAGACCAATGGAACAGAATAAAGAACCCAGAAATAAGACCACAC 598
                             i     i        i     vi   ii          iv   i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_20597327_2    599 ACCTACAACTATCTAATCTTCGACAAAGCTGACAAAAACAAGCAATGAGG 648
                          ii  iiiii vi i  i        i v  v   i v  vv     i  
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_20597327_2    649 AAAGGATTCCCTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATAT 698
                             i  vvi  v     i              i      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_20597327_2    699 ACAGAAAATTGCAACTGGACCCCTTCCTTACACTATATACAAAAATTAAC 748
                         i  i  i v  v ii         v   i    i                
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_20597327_2    749 TCAAGACGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCT 798
                             i i    i ?    i         i v i            vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_20597327_2    799 GGAAGACAACCTAAGCA-ATACCATTCAGAACATAGGCATGGGCAAAGAT 847
                         i     v   v  i ?i- v i -   ivi  v v  vv i     v i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_20597327_2    848 TTCAT-GATGAAGATGCCAAAAGCAATTGCAACAAAAGAAAAAATTGACA 896
                            v -   - v  ii         vvv                 v  i 
  L1M4_orf2#LINE/    586 TTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_20597327_2    897 AATGGGATATAATTAAACTGAAGACCTTCTACACAGAAAAAAAAACTATC 946
                            v   iv v  i   v v  i v   i iii vvv   ii v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_20597327_2    947 AACAGAGTAAATAGACAACCTACAGAATGGGAGAAAATTTTTGCAAACTA 996
                           v i   i  v        i                 v        ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_20597327_2    997 TGCATCTGACAAAGGTCTAATATCCAGAATCTATAAGGAACTTAAACAAG 1046
                          ii      i  i  v  vi          v     i     ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_20597327_2   1047 TTTACAAGGAAAAAACAA----CCCCATTAAAAAGTGGTCAAAAGGGCAT 1092
                          iv i  vi    i    ----   v   ?    i   v    -  iiv 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA-GGATTT 833

  chrX_20597327_2   1093 GAACATACACTTCTCAGAAGAAGGCATACATGTGGCCAACAAGCATATGG 1142
                            i v   i     vi      ii     vi       i     i   i
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_20597327_2   1143 AAAAAAAA-CAACATCACTTATCAT 1166
                            i viv-        ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (103 / 64)
Gap_init rate = 0.01 (7 / 672), avg. gap size = 1.43 (10 / 7)  


2848 24.84 2.31 2.53  chrX_20611178_20612777.rev      200  1109 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_20611178_2    200 TGGAGGGATGTACCATATTCATGACTCGGCAAACTCAAAATAGAAAAACA 249
                             ii   i v    i      iv i  v i   i  v  v vv  i--
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-- 48

  chrX_20611178_2    250 AAGTCAATTCTTCATAGTTTGATATACAGGTTTAATACAATAAATATCAA 299
                          v v    v  i vi iv     v     i  i  ii    vvv      
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_20611178_2    300 AATCTCAGCATGACTTGTTTGTAGATATAGAAAAGACT-ATCCTAAAATT 348
                             i    -  v   v    i   v  v  v   -  -           
  L1M4_orf2#LINE/     99 AATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chrX_20611178_2    349 CATATGGAAAGACCAAAGAACATAGAATAGCTAAAAAAAAAAAAAAATCT 398
                                   vi -  i i  vi        i    v  --------   
  L1M4_orf2#LINE/    147 CATATGGAAATGC-AAGGGACCCAGAATAGCCAAAACAA--------TCT 187

  chrX_20611178_2    399 TTTTAAAGAAGAGTAAAGTAGAAGGAATCAATCTACCCTATTTCAAGAAT 448
                          vvv        ii     v i    v   vv  v   v       i v 
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_20611178_2    449 TACTATATCGCTACAGATATCAAAACTGTGTTGATATTGATGAAGAGGTA 498
                              i vv       vv     i  v    - i  i  iiiv ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGT-GGTACTGGCATAAGGATA 286

  chrX_20611178_2    499 GACATATAGGTCATTGGAACAGAATGGAAAACCCAGAAATAATCCCACAT 548
                                  i   v     i     v  i ii          v    i i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_20611178_2    549 AGCCTTATATAGCCAACTTATTTTTGGCA---GT---AAAACAATTTAAA 592
                          ---  -   i i   i v     i i  ---  ---  i  v   i  v
  L1M4_orf2#LINE/    337 A---TT-TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_20611178_2    593 GGAGGAAGGATATTCTTGTCAACAAATGATGCTG----AATTGAATATCC 638
                           i i   i   v    v          i     ----  i  i   ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_20611178_2    639 ATAGGCAAAAAAGTGAACTTCAACCTAAACCTCATA--ATTTACGTTAAA 686
                          i v      i i    v  vi   ivv      i --  v   i--   
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA--AAA 480

  chrX_20611178_2    687 AGTAACTCCAAATGAGTCACAAATGTAAATATAAAGCCTAAAACTATAAA 736
                          v      v     ii   ? i iv     i   iiv             
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_20611178_2    737 ACTTTTAGAATGTAATATGGAAGAAAATGTTTGAGACCTAAGAC--AGCA 784
                            i      viv  i  i i? v    v  i v     vi ii--i   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_20611178_2    785 AAGAGTTCTTAGACAAGACACCAAAAGTGTAATTGATAAAAGAAAGA-TA 833
                          v iv        i v           iii  vii i        i -  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_20611178_2    834 TTAAAATTGGACTTCATCAAAATTTAAAACTTTTTTGT---GAAAGAC-C 879
                         vvv                     v         v  i---i  i   - 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_20611178_2    880 TTGCTAGAAGGATGACAAGATGAGCTTCAGACTGGAAGAAAATATTTGCA 929
                          vv v    i -   v    ii v iv    v   i              
  L1M4_orf2#LINE/    681 TATCAAGAAAG-TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_20611178_2    930 AACTACATACCTGACAAAGGACTCATTTGTATGATATAAAAAGAACTCTC 979
                           ii i   i    i  i     ii v vi vi     v          i
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_20611178_2    980 AAAACTGAACAGTAAAAAAAAAAAAGCAGTGTAATTAGAAAATGGGCAAA 1029
                          v    v  i i      i v   --i iivi    ?i            
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAA--TAACCCAATTWAAAAATGGGCAAA 827

  chrX_20611178_2   1030 AGACATGAAGAGACATTTCCCCAAAGAGGATGAAAGGATGGCAAATAATC 1079
                         i  iv    v         i       i   iv vii     v     v 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_20611178_2   1080 ATACGGAAA-ATGTTCAACATCAGTAGCTAT 1109
                          i i i   -   i         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (128 / 94)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.10 (44 / 21)  


2673 26.20 4.92 1.03  chrX_20613064_20616353.rev     1926  2799 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_20613064_2   1926 TGGAACAACATTCCATGTTCATGGATAGTAAGAATCAATATTGTTAAAAT 1975
                              vi i  i              v v    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_20613064_2   1976 GGCCATATTGCCCAAAGTAATGTACAGATTAAATGCTATTCCTATCAATT 2025
                            v   i v      v i  v        v  i  v  i        --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-- 98

  chrX_20613064_2   2026 AAACTATCAATGTTAC--TTTTCACAGAA-TTAAGAAAAACT-ATTCTAA 2071
                           v i--  -- i i --    ii     -  --  v  i  -  i    
  L1M4_orf2#LINE/     99 AATCC--CA--GCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAA 142

  chrX_20613064_2   2072 AATTAATTTGGAACCAAAAGAGAGCCCAAATAGCCATAGCAATCCCAAGC 2121
                             v  v     viiv   i  v  vi        v i     iii iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_20613064_2   2122 AAAATGAAAAAAGCTGGAGGCATCACATTACCCAACT--A-----TACTA 2164
                           i v   v    i      vv     i v     i -- -----     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_20613064_2   2165 TAAGGTTACAGTAAGCAAAATAACATGGTGCTCATGCAAAAACAGACATA 2214
                         i  i i        v   i i iii    i  viiii  ii i       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_20613064_2   2215 CAGACCAGTGGAACAGAATAGAGAATGCAGAAATAAAGCCATACAACTAC 2264
                         i   i  i     i     v    i v          v       vi  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_20613064_2   2265 AATCATCTGATCATCAACAAAGTTGACAAAAACAAGCAATGAAGAAAGGA 2314
                         ii   vi    iv  i    i v  v   i v  vv     ii     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_20613064_2   2315 CTCCCTACTCAGTAAATGGTGTTCGGATAACTGGCTAGCCATATGCAGAA 2364
                         ivvi  vi   ii        i v   i      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_20613064_2   2365 GAATGAAACTAGGCCCCTACTTT-CACAATATATAAA--TTAACTCAAAA 2411
                                ii i i       i i-   v     i   --           
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_20613064_2   2412 TAGATTAAATACTTAAAGGTAAGACCTAGAAATATAAAAACCT----AGG 2457
                          i   i ? v  i    v      v   i  v       vi  ----  i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_20613064_2   2458 AAATAC---------CCTTCTGGACATTAGCCTTGGCAGAGAATTTATGG 2498
                            i i---------i    vv   v  i vi v    iv iv  iv i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_20613064_2   2499 CTAAGTCCTCAAAAGCAATTGCAACAAAC-ACAAAATTGGCAAGCGGGGC 2547
                         v  v v vi        vvv        v- v     v ii  iiv  i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_20613064_2   2548 CTAATTAAACTAAAGAACTTCTGTACAGCAAAAGAAATTATCAACAGAAT 2597
                         i v  i   v v  i     i   i vv    i  v i      v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_20613064_2   2598 AAACAGCCAGCTCACAGAATGGGAGAAAATATTTTC----TATGCATCTA 2643
                         i  v  v  i i                      v ----i  ii    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_20613064_2   2644 ACAAAGGCCTAATATCCAAAATATGTAAGAAACTTAAGCAA-------AT 2686
                          i  i  v  vi      i     i   ii    ivvi   -------  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_20613064_2   2687 AAACAAGAAAAAAAACTGCGTTAAAAAGTGGGCAACT-ATGTGAACAGAC 2735
                            -    v   v   ivvi  ?    i       vv-  v    i    
  L1M4_orf2#LINE/    793 AAA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_20613064_2   2736 ACTTCTCAAAAGAAGACATACAAGTAGCCAACAAACAC--GAAAA-ATGC 2782
                          i     v        i      i i     i  i   --     -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_20613064_2   2783 TTAGCATCACTAATCAT 2799
                          i i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.60 (52 / 20)  


3139 27.23 0.66 0.55  chrX_20622719_20629151     5034  5940 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_20622719_2   5034 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5083
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_20622719_2   5084 GGCCATACTGCCCAAGGTAGTTTATAGATTCAATGCCATCCCCATCAAGC 5133
                            v     v     iv ii i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_20622719_2   5134 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 5181
                          v   iivi i  i  ii     -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_20622719_2   5182 TATGGAACCAAAAAGGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5231
                                viiv  i   v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_20622719_2   5232 AACAAAGCCGGAGGCATCTCGCTACCTGACTTCAAACTATACTACAAGGC 5281
                                ii     vv  v i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_20622719_2   5282 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5331
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_20622719_2   5332 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCACATCTACAACC 5379
                                i    i--    i  --        vv  ii    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_20622719_2   5380 ATCTGATCTTTGACAAACCTGACAAAAGCAAGCAATAGGGAAAGGATTCC 5429
                          vi    i  i     ivv  v   i v  vv    i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_20622719_2   5430 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGGAGAAAGCT 5479
                           v  i  i              v      v  ?i  i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_20622719_2   5480 GAAACTGGATCCCTTCCTTACACCCTATACAAAAATTAATTCAAGATGGA 5529
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_20622719_2   5530 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5579
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_20622719_2   5580 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5628
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_20622719_2   5629 AAGAATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5678
                         viiv i        vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_20622719_2   5679 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGGGTGAG 5728
                           i   v v  i i   i  ii vv    i  v    i  vv ii    i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_20622719_2   5729 CAGGCAACCTACAAAATGC-AGAAAATTTTCGCAACCTACTCATCTGACA 5777
                         v  i     i   i    v-       v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_20622719_2   5778 AAGGGCTAATACCCAGAATCTACAATGAACTCAAAAATATTTACAAGAAA 5827
                          i  i  vi  i       v  i  v      vv v vv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_20622719_2   5828 AAAACAAACAACCCCATTAAAACGTGGGCAAAGGATATGAACAGACACTT 5877
                           i     i     v   ?   vi            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_20622719_2   5878 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5927
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_20622719_2   5928 CATCACTGGCCAT 5940
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2781 26.21 3.60 1.57  chrX_20652496_20658254     4381  5269 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_20652496_2   4381 GGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATACTGTGAAAATG 4430
                              i i  i     i        v      v i    i   v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_20652496_2   4431 GCCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCACATTAACCT 4480
                           v     v      vii  i  i        i  v  i vi  i  vv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_20652496_2   4481 ACCATTGATATTCTTCACAGAATTAGAAAAAATCT-ATTTTAAAATTCAT 4529
                         v   viviiv  i  ii     v v  v  i--  -  ii          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCAT 149

  chrX_20652496_2   4530 ATGAAA---CAAAAAAA--AGAGCTTTATAGCTAGGACAATCCTAAGCAA 4574
                            i  ---   iii v--   -----     i ii      i i iv  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGA-----ATAGCCAAAACAATCTTGAAAAA 194

  chrX_20652496_2   4575 AAAGAACAAAGCTGGAACCATCACACTACCCGACTTCAAAATATACTACA 4624
                         i          i    ivvv       v   i i       iv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_20652496_2   4625 AGGCTACAGTAACCAAAAAAGCATGGTACTGATACAAAAACAGGCACATA 4674
                          i          i   i v  ii        ii i  ii i  i  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_20652496_2   4675 GACCAACAGAACAAAATAGAGAAGTCAGAAATAAAACTGCACATCTACAA 4724
                           i   ii   i i   v    ivi          v iii    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_20652496_2   4725 CC----------TGACAAAAA---CAAG------CAATGAGGAAAGGATT 4755
                         i ----------i     iii---    ------     i      i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_20652496_2   4756 ACCTATTTAACAAATTGGTTCTGGGAGAACTGGGTAGCCATATGCAGAAA 4805
                         ii  v  i       -   v      v      i  ?   i     i  i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAAT-GGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_20652496_2   4806 AGTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGAT 4855
                          i    ii         v   i     v                   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_20652496_2   4856 GGATTAAAGACTTAAAAGTAAAACCCCAAACTATAAACGCCCTAGAAGAA 4905
                             i ?    i    v    i v iv          vvi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_20652496_2   4906 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTGTAT-G 4953
                            v    ?i- v i -   iv   v v  vv i     v ii viv - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_20652496_2   4954 ATGAAATCGTCAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGGA 5003
                           ivi - ii        vvi          v      v  i    v   
  L1M4_orf2#LINE/    593 ATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_20652496_2   5004 TCTAATTAAACTAAAGAGCTGCTACACAGTAAAAGAGGCTATCATCAGAG 5053
                         ii v  i   v v  i i  vi iii vvi   i  vi      vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_20652496_2   5054 CAAACAAACAACCTACAGAATGGGAGAAAAACTTTGCAA--TATATCCAT 5101
                         ii  v i      i                vv       --i    --  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--AT 739

  chrX_20652496_2   5102 CTGAGAAAGGTCTAATATTCAGAATCTACAAGGAACTTAAGCAAATTTCC 5151
                             v  i  v  vi   i      v  i  i     ivvi   v ivvi
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_20652496_2   5152 AAGAAAAGAACAAATGAATCCA-TTAAAAAGTGGGCAAAAGACATGAACA 5200
                           v    ii      -  i   -  ?    i        i  iv    i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_20652496_2   5201 GACACTTCTC--AAAAAGACATATATGTGGTCAACAAACATATGAAAAAA 5248
                             i     --  i    i   i vi   i   i  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_20652496_2   5249 AGCTCAACATTCACTGATCAT 5269
                         v         -  ????????
  L1M4_orf2#LINE/    889 TGCTCAACAT-CAZZZZZZZZ 908

Transitions / transversions = 1.86 (149 / 80)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 2.42 (46 / 19)  


2847 27.65 1.31 2.08  chrX_20677788_20683215.rev     4023  4937 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_20677788_2   4023 TGGAAAAGCATTCCATGCTCATGGATAGGAAAAAGTCAATATTGTTTAAA 4072
                               iii  i     i        v    i v- i         -  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTT-AAG 48

  chrX_20677788_2   4073 ATAGCCATACTTCCCAAAGCAATTTATAGATTCAATGCTATTTCTATCAA 4122
                           i  v     i      vii  i  i        i  v  ii       
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_20677788_2   4123 ACCACCAATGACATTTTTCACATAA-TTAA--AGC--ATTCTAAAGTTAA 4167
                          viv   iivi v     ii  v  -  i --   --  i     i  v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_20677788_2   4168 TTTGGAACCTAAAAAGAGCCTTAGTAGTCAATGCAATTCTATGCAAAAAG 4217
                          v     vivv  ii  v  vv i   i   vi    ii iviv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_20677788_2   4218 AGCAAAGCTGGAGGCATCACATTACCTGACTTCAAATTATACTACAAGGC 4267
                          i     i      vv     i v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_20677788_2   4268 TACAGTAACTAAAACAACATAGTACTGGTACAAAAGCAGATACATAAACT 4317
                                 ii  i   iii i       i i  iiii   i i   i ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_20677788_2   4318 AATGGAACTGA--TGAGAGAACTCAGAAATAAAGCCTCACACCTACAACT 4365
                                iv  --      --ii          v  vi   ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAG--TCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_20677788_2   4366 ATGTGATCTTTAACAAAGCTGACAATAATAAGCAATGGGGAAAGGACCCC 4415
                          vv    i  ii    i v  v   v vi vv            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_20677788_2   4416 CTATTCAATAATTGGTGATGGGAAAACTGGCTAGCTGTATGCAGAAGATT 4465
                           v     i  v     v     v      v  ? iii     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_20677788_2   4466 GAAACTGGACCGCTTCGTTACACCACATACAAAAATTAACTCATGATGGA 4515
                            ii      v  v v i      i                 vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_20677788_2   4516 TTAAATACTAAATGGATTAAATGTAAAACCCAGAACTATAAAAACCCTGG 4565
                          i ? v  i--------         i v i i          vi i i 
  L1M4_orf2#LINE/    497 TCAWAGACC--------TAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_20677788_2   4566 AAAACAACCTAGGCAATACAATTCTG-GACATAGGAACAGGCAAAGATTT 4614
                           i v   v    ?i-  v vi ii -   v v  ivi      v i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_20677788_2   4615 CATTACAAA-GATGCCAAAAGCAATTGCAACAAAAGCAAAGATTGACAAA 4663
                          -   v v -  ii         vvv          v   i  v  i   
  L1M4_orf2#LINE/    588 C-TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_20677788_2   4664 TGAGATCTAATTACA-TTAAAGAGTTTCTGCACAGCCGAAGAAACTACCA 4712
                          vi  ii v  i v -     i v   -  ii vv vi i  v    i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCA 685

  chrX_20677788_2   4713 ACAGAGTAAACAGACAACCTGTAGAATGGGAGAAAAGTTTTGCAAACTAT 4762
                          v i   i  v        iii              vv        ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_20677788_2   4763 GCATCTGACAAAAGTCTAATGTCCAGAGTCTATAAAG--TTCTTAAACAA 4810
                         ii      i  ii v  vi i      i v       --i     --   
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAA 783

  chrX_20677788_2   4811 ATTTACAAGAAAAAAAACCCAACAACCCCATTAAAAAGTGGGCAAAGAAT 4860
                         v iv i  v     i -- v  i     v   ?    i         i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_20677788_2   4861 ATGAACAGACACTTTTCAAAAGAAGACATGCATGCAGTCTACAAGCATAT 4910
                         v    i     i  i  v        i  i  viii i v i     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_20677788_2   4911 GAAGAAAAGCTCAACATCACTGATCAT 4937
                            i i v           ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (157 / 92)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.82 (31 / 17)  


2585 25.59 0.42 0.28  chrX_20700021_20701740.rev      515  1229 (491)    L1M4_orf2#LINE/L1      193   908 (0)  

  chrX_20700021_2    515 AAAAAGAACAAATATGGAGGCACCACATTATCTGACTTCAAACTATACTA 564
                           i         vv      vvi    i vi ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_20700021_2    565 CAAGGATGTAGTTACCAAAACAACATGGTACTGGTATAAAAATAGGCACA 614
                            i v ii   v i   i   iii         i    ii    i  i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_20700021_2    615 TAGACCAATGGAACAGAATAGAGAACTCAAAAATAAAGGCAAATACTTAG 664
                             i        i     v    iii  i       vv  v i i   v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_20700021_2    665 AGCCAACTGATCTTCAACAAAGCCAACAAAAGCATAAAGTTGGGAAAGGA 714
                         i i   i    i   i    i viiv   i v   vv i v       i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_20700021_2    715 CACCCTATTCTACAAATGATGCTGGGATAATTGGCAAGCCACATGTAGAA 764
                         i vi  v   v       i        i  i   vv ?       i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_20700021_2    765 GAATGAAATTGGATCCTCATCTCTCACCTTATACAAAAATCAACTGAAGA 814
                                i     i  ii i   v    v           i    v  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_20700021_2    815 TGGAACAAAGACTTAAATCTAAGATCTAAAACCATGAAAATTCTAGACGA 864
                             v  ?    i     v     v       i  i   v ii    v  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_20700021_2    865 TAACATTGGAAAAACTCTTCTAGACATTGGTTTAGGCAAAGAGTTCAT-G 913
                         v     v  ?iv  v     vv   v    v        v iv   v - 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_20700021_2    914 ATCAAGAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGACTGGA 963
                           - v  vv         v v         iv   i   i   i i    
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_20700021_2    964 CATAATTAAACTAAAAAGCTTCTGCACAGTAAAAGAAATAATCAGCAGAG 1013
                          v v  i   v v    i   i  ii vvi   i  v iv    iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_20700021_2   1014 TAAACAGATAACCCACAGAGTGGGAGAAAATATTCACAAACTATGCAACC 1063
                          i  v   i          i              ii    ii  ii v i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_20700021_2   1064 AACAAAGGACTAATATCCAGAATCTACAAAGAATTCCAGCAAATCAGCAA 1113
                         i i  i     vi          v  i      i  ivi   v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_20700021_2   1114 GAAAAAAAACAAATAATCCTATCAAAAAGTGGGCAAAGGACATGAATAGA 1163
                         v     i -       i  v  i?    i           iv        
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_20700021_2   1164 CAATTCTCAAAAGAAGATATGCAAACAGCCAACAA--ACGTGAAAAAATA 1211
                           v     v           i    ii     i  --  i      i  i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_20700021_2   1212 CTGAACATCACTCATTAT 1229
                           v       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (108 / 71)
Gap_init rate = 0.01 (4 / 716), avg. gap size = 1.25 (5 / 4)  


3551 22.95 1.88 1.22  chrX_20712264_20716153.rev     2500  3401 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_20712264_2   2500 TGGAAAGATATTTCATATTCATGGATTAAAAAAATCACTAATGTTAAAAT 2549
                                    ii   i          ii  i v i v  v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_20712264_2   2550 GTCCATAGTACACAAAGCAATCTACAGATT-AATCCAATTCCTATCAACA 2598
                          v v   v v v    vii           -  iv    i        v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_20712264_2   2599 TACCAGTTACATTCTTCACAGAAATAGAAAAAAAAAAACT-ATCCTAAAG 2647
                          v    i i v  i  ii       v  v  i------  -        i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG------CTGATCCTAAAA 144

  chrX_20712264_2   2648 TGTATATGGTACCACAAAAGGCCCAGAATAGTCAAAGCTATCCTAAGTAA 2697
                          vi      v vii   ii i          i    i v   i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_20712264_2   2698 AAAGAACAAAACTGGAGGAATCACATTACTTGACTGCAAA--TTATCCTA 2745
                         i         ii       v     i v iii i v    --   --   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTA 242

  chrX_20712264_2   2746 CAGAGCTATAGTAACCAAAACAGTATGGTACTGGCATAAAATCAGACACT 2795
                           i     i     i   i     i              iivi     iv
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_20712264_2   2796 TAGACCAATGGAACAGAAAAGAGAACCCAGAAACAAATGCACACACCTAT 2845
                             i        i    vv    ii       i   iv  i   ii   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_20712264_2   2846 AGTGAACTCATTTTTGACAAAGGTGCCAAGAACATACACTGGGGAAAATA 2895
                         i  v  i v     i     i          v   v  v        iv 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_20712264_2   2896 CAGTCTTTTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAA 2945
                         i           i              v         ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_20712264_2   2946 GAATGAACCTAGCCTTCCATCTCTCGCCATATACAAAAATCAAAT--AAG 2993
                                vi i v ii i i   v i              i  v --  i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_20712264_2   2994 TGGATTAAAGACTTAAACCTAAGACCTCAAACTAAGAAGCTACTACAAGA 3043
                              i ?    i    iv     v  v      vi  i  vi  v    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_20712264_2   3044 AAACATTGGGG-AAA-CTCCAGGATATTAGTCTGGGAAAACATTTCTTGA 3091
                               v  ? -   -  i iv  iv  i vi i  v  vvi      ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_20712264_2   3092 GTA--ACACCACGCAAGCACAGGCAACCAAAGCAAAAATAGAGTAATGGG 3139
                         i  --      v--       i     v    v         vv   v  
  L1M4_orf2#LINE/    593 ATATGACACCAA--AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_20712264_2   3140 ATCACATCAAG-TTAACAAGCTTCTGCACAGCAAAGGGTATAGTCAACAA 3188
                          iiv      i-    -  i   i  ii vv      ii ivi    v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_20712264_2   3189 AGTGAAGATACAACCCACAGAATGAGAGTAAATATTTGCAAACTACCCAT 3238
                               i v               i   v             ii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_20712264_2   3239 ATGACTTGGGATTAATAACCATAATATATAAGGAACTCAAACAACTCTAT 3288
                         v   ivv    i vi  v   v         i      vv       v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_20712264_2   3289 AG-AAAAA----AATAATCTAATC-AAAAATGGGCAAAAGATTTGAGTAG 3332
                          i-     ----     i i   i-             i       i   
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_20712264_2   3333 ATGTTTCTCAGAAGAAGACATACAAATGGCCAACAGGCATATGAAAAGGT 3382
                          ii      vi       i              i i   i        i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_20712264_2   3383 GCTCAACATTTTCATGCTC 3401
                                  iv????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (127 / 77)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.87 (28 / 15)  


2928 25.20 2.56 1.45  chrX_20759701_20765145     4056  4952 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_20759701_2   4056 GAAAAAACATTTCATGCTCGTGGATAGGAAGAATCAATATTGTTAAAATG 4105
                          i   i i  ii    i  i     v      v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_20759701_2   4106 GCCATACTGCCCAAAGCAGTTTACAGATTTATTGTTAATCATATCAAACT 4155
                           v     v      viii i        i vi iv vi v       v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_20759701_2   4156 ATCAA-TGTCGTTTTTCACAGAATTAGAAAAAGCT-ATTGTAAATTTCAT 4203
                         vi  i-  i -     ii     v v  v  -   -  iv    v     
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_20759701_2   4204 ATGGA---GTAAAAAATGAGCCCTAATGTCCAAAGCAATCCTAAGCAGAA 4250
                              --- i  ii---  v  vv   iv     i     i i iv ii 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG---GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_20759701_2   4251 ACAACAAAGCTGGAGGCATTACACTACCCAACTTCAAACTATACTACAAG 4300
                          v       i      vv i     v     i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_20759701_2   4301 GCCTTGGTAACCAGAACAGCATGGTACTGGTACAAAAACAGACACATAGA 4350
                           ivii    i  ii    ii         i i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_20759701_2   4351 CCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCGCACACCTACAAC- 4399
                         i        i     v    ii           v  ii   ii  iiii-
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_20759701_2   4400 -ATTCCAATATTCAGCAAAGTCGACAATAACAAGTAATGGAGAAA--ATA 4446
                         -   --i  v   ii   i vi v   v v  vvi     i    --   
  L1M4_orf2#LINE/    347 AATT--GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_20759701_2   4447 CTCCCTATTCAATAAATAGCACTAGGATAGCTGGCTAGCCATATGCAGAA 4496
                         v  -- v     i    i ii  i   i i    v  ?   i     i  
  L1M4_orf2#LINE/    395 GTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_20759701_2   4497 GACTGAAACTGGACCCTT--TTCATA---TATATAAAAATCAACTCATGA 4541
                           v    ii       i --i   i ---    i      i      vi 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_20759701_2   4542 TGAATTA-AAACTTAAATGTACAACCTAAAACCATAAAAATCACAGAAGA 4590
                           i  i - i  i        vi v       i      v  vi      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_20759701_2   4591 AAATCTAGG---AAATGCTATTTTTGACATAGGCCCCGGCAAAGATTTCA 4637
                            iv    ---    -  -- iv    v v  viiv     v i    v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT-CT--TCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_20759701_2   4638 T-GATGAAGGCTCCAAAAGCAATTGCAACAAAAACAAAAATCCACAAGTG 4686
                          -   - v i v         vvv         iv      vv i  i v
  L1M4_orf2#LINE/    590 TAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_20759701_2   4687 GGACTTAATTAAACTAAAGAGCTTCTGCACAGCAAAGCA-ACTATCAGCA 4735
                               v  i   v v  i i   i  ii vv     v -       iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_20759701_2   4736 GAATAAACAGACAACATACAGAATGGGAGAAAATACTTGCAAACTATGCA 4785
                         i i i  v       vi                  i       ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_20759701_2   4786 TCTGAAAAAGGTCTAATATCCAGAATCTATAAGGAACTGAAACAAATCAA 4835
                              v  i  v  vi          v     i     vvv    v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_20759701_2   4836 CAAGCCCAAAACAAACAACC--ATTAAAAAATGGGCAAAGGACATGAACA 4883
                         i  vvvv  i     i    --   ?                iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_20759701_2   4884 GATGCTTTTCAAAAGAAGACATACACACAGCCAATAAGCATATGAAAA-A 4932
                           iii  i  v        i     v ii           i       - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_20759701_2   4933 TGCTTAACATCACTAATCAT 4952
                             i       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (137 / 87)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 1.71 (36 / 21)  


3426 22.96 2.72 0.36  chrX_20809302_20811107      485  1329 (477)    L1M4_orf2#LINE/L1       44   908 (0)  

  chrX_20809302_2    485 TTAAGACAACAGCATTACCCAAAGCAATCTCTTGATTCAATGCTATCCCT 534
                               iii  ii i v      vii    viv       i  v      
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chrX_20809302_2    535 ATCAAA--TCCAAAGGGCATTTTTGCAGAAATAAATATAACC-ATCCTAA 581
                               --i   ivv v v             vi i - i i-       
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAA 142

  chrX_20809302_2    582 AATTCATATGAAACCACAATGGACCCTGAATACCTAAAACAATCTTGAGC 631
                                   i  vii   v      v     v i             iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_20809302_2    632 AAGATGAACAAAGCTGGAGCCCTCACACTTGCTGAGTTCAAAACACATTA 681
                             v        i     vv         v ii v        vi i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_20809302_2    682 CAAAGCTGCACTAGTCAAAACAAAACAATACTTAGATAAAGAAAAGCATA 731
                                i  v  i    i   iviiii    viv    i  v ii    
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_20809302_2    732 TAAAACAATGGAACAGAATAGAATACCCAGAAATAAACCCATGCATACAC 781
                           i v        i     v  ivii                i   vi i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_20809302_2    782 AGCCAACTAATTTTTAGCAAGGGTGCCAA-ACTACATAATGGGGAAAGGA 830
                         i i   i i     iii            -  i ivi           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_20809302_2    831 TAGTCTTTTCAATAAATGGTGCTAGGAAAACTGAATATCTACATACAGAA 880
                                     i          i   v     i   ? i    i  i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_20809302_2    881 GAATGAAACTGGACCCTTATCT--------ATACAAAAATCAACTCCAAA 922
                                ii       i  i  --------          i     v   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_20809302_2    923 TGGAT-AAAGAGCTAAACATAACACCTGAAGCTGTAAAACTATTAGAAGA 971
                              - ?   v     ii   v v  i  i  i       v        
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_20809302_2    972 AAACATAAGGTTAAATCTTCATAACATTGGTCTTGGCAATAATTTATTGG 1021
                                i ?v         i i  v    vi v      ii   v  i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_20809302_2   1022 ATATGACAACAAAAGCACAGGCATCAACAGCAAAAATAGGCAGGTGGGAC 1071
                                 v          i   v   v  v        ii ii v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_20809302_2   1072 TACATTAAA-CTAAAGACCAT-GCACAGCAAAGGAAAAAATCAGCAGAGT 1119
                          v   i   -i    i  iv - ii vv       v vv    iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_20809302_2   1120 AAAAATACAACCTACAGAATGGGAGAGAATATTTGAAAACCATCTTTTTG 1169
                         i    v      i             i        v   i   v v i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_20809302_2   1170 ATAAGGGGTTAATATCCAAAATACACAAG----TCCTATGACTCAATAAT 1215
                                ii vi      i    i i  i----  i  ii          
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_20809302_2   1216 AACAAAATAA-TAATCCAATTAAACAATAGGCAAAGGACTTGATTAGACA 1264
                           v  i i  -   i      ?  v   i         i    v      
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_20809302_2   1265 TTTCTCCACAGAATACATACAAATAGCTGATAGGTATAT---AACCTGTT 1311
                                 v    v i        i  ii   i i i  ---  vv  i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_20809302_2   1312 CTATAACTCAATAGCAAT 1329
                          v i --   ????????
  L1M4_orf2#LINE/    893 CAACA--TCAZZZZZZZZ 908

Transitions / transversions = 1.79 (122 / 68)
Gap_init rate = 0.01 (12 / 865), avg. gap size = 2.17 (26 / 12)  

 395 21.78 0.00 1.98  chrX_20809302_20811107     1336  1436 (370)    L1M4_orf2#LINE/L1      810   908 (0)  

  chrX_20809302_2   1336 AATTAAGCAACAGGCAAATGACTTGATTAGGCGTTTCTCCAAAGAAGACA 1385
                             ? iv  ii      v  i    v   i i               i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_20809302_2   1386 CACAAATGGCCAGCACGAAAATATGAAATTATTTTCAGCATCACTAATTA 1435
                         i           -- ii iv i      vv  vi   i     ???????
  L1M4_orf2#LINE/    860 TACAAATGGCCA--ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_20809302_2   1436 T 1436
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.01 (1 / 99), avg. gap size = 2.00 (2 / 1)  


1910 24.80 3.40 1.46  chrX_20834375_20835965.rev      484  1100 (491)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_20834375_2    484 AAGAGTACACATTATCATCCAGTAGAAACAGAATAGACAGCCCAGAAATA 533
                            ii  v    -  vivi  i i   -i     v  v  i         
  L1M4_orf2#LINE/    280 AAGGATAGACAT-ATAGATCAATGGAA-TAGAATTGAGAGTCCAGAAATA 327

  chrX_20834375_2    534 AAACTAAATGTATACAGTCACCTAATTTTCAATAAGGTAAACCAGAAGAC 583
                           v i v ii v  ii    vi i      i i    -ivi   --    
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCA--AGAC 374

  chrX_20834375_2    584 -A--CAACGGGGAAAGGATGGTCTCTTCAATGAACAGTGCTACAAAAACC 630
                         - --   i        i  i    i     ii  ii     ivi v   i
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_20834375_2    631 AGATTTCCACATGCAAAAGACTGAA-TCAGACTCTTATCTTACACCATAC 679
                         i   v?              v    - ii   i i  i  i        i
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_20834375_2    680 ACAATAATCAACTCTAAATGGCTAAAAGACCTAAATGTAACA--TAAAAC 727
                             v   i     v      v v ?              v --      
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_20834375_2    728 TGTAAAACTACTAGAAGAGAACATACAGGAAAAACTCCTTGACATTGGGC 777
                          i       vi       i      vi? v   v  i v    v     i
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_20834375_2    778 CTGACAATGATTTTTTGGATATCACCCCAAAAGT-TAAGTCCGCATAAGC 826
                         iv i     i   i  i     v  v       i-i   - vi  v   v
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG-CAACAAAAGA 623

  chrX_20834375_2    827 AAAAATAAATAAATGAGACTACAT-AAAACTAAAAAGCTTCTGCAGAGCA 875
                                i      vi    v   -    i      -   i  iivvv  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCA 672

  chrX_20834375_2    876 AATGAAACAATCAACAAAATGAAGCAGA-AGCCTATATACCAGAAAAAA- 923
                           v  v  v     v   i    i-   - i  i i v vii i i   -
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAA-AGACAACCCACAGAATGGGAGAAAA 721

  chrX_20834375_2    924 ----TGCAAATTATATATCTGATAAGGGTTTGATGTCCAAAATTTATGAA 969
                         ----       i                vi vi i    i   v   i  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_20834375_2    970 TATCTCATACAATTCAATTGTAGGAAAACAAA----CCAATTAAAAGATG 1015
                         v v   v     i     vi  ii  i     ----      ?   i   
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_20834375_2   1016 GAAAAAAAGAATTAAATTGACATTTCTCCAAAGA---CATAAAAAACACC 1062
                          iv   i-  v  i   v                ---i   v   vvi  
  L1M4_orf2#LINE/    822 GGCAAAG-GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_20834375_2   1063 AACAGGTATATGAGAAGGTGCCCAATACCATTAATAAC 1100
                           i i i i    i   i   i   i i  ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (94 / 55)
Gap_init rate = 0.03 (18 / 629), avg. gap size = 1.67 (30 / 18)  


2190 25.16 3.45 0.00  chrX_20844310_20845900.rev      493  1100 (491)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_20844310_2    493 AAAGAAAAACAT-T-GAACAATGGAACAGAAT--A-----CAGAAATAAA 533
                           i  v i    - -  v        i     -- -----          
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_20844310_2    534 TCCACGCATACACAGTCAACTACTTT--AACAAGGGAGCCA-TACTATGT 580
                         i   ii   vi ii     i iv   --i       v    -v  i  vi
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_20844310_2    581 GATAGGGAAAGGACAGTAGGTTCAATAAGTGGTGTTGGGAAAACTGACTA 630
                         i  i       i i   vvv     i  i     i     v     iv  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_20844310_2    631 TCCTCATGCATAAGAATAAAATTTTACTC-TATCTTACACTGTACAGAAA 679
                         ?  v      v      i  i  vv  i -  i  i    ii  i v   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_20844310_2    680 AATCAATTCCAAATGTATTAAAGAC--AAACACAAGAATGGAAACTGTAA 727
                            i  i  v     v  i ?    --   iii    iivi     i   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_20844310_2    728 AACTGCTAGAGGAAA-CATAGGGAAAAATCTTCATAACATTGGTCTTAGC 776
                             vi    i    -      ?iv        i i  v    vi vi  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_20844310_2    777 AATGATTTAGTAGATATAACACTAAAAGCACAGGCAACAAAAGCAAAAAT 826
                             i   vv       i    i         i          v      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_20844310_2    827 AGACAAGTGGGACTATATCAAACTGAAGAGTGTCTGCACAACAAATGAAA 876
                            i  i v     vi      v v  i iiv i  ii vv    v  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_20844310_2    877 CAATCAATAAATTGAAAATGCAACCTATCGAATGGGAGAGAATATTTATA 926
                          v     v   v      vi     i iv          i       ii 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_20844310_2    927 AACCATGTATCTGATAAGGGGTTAACAACCAAAATACATAAG----CCCT 972
                           i   i             ii vii v   i    i    i----i i 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_20844310_2    973 ATAACTCAGTAGCAATAAAACAA-TAACCCAATTAAACAATAGGCAAATG 1021
                          i      i  ii  v  i    -          ?  v   i      v 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_20844310_2   1022 GCTTGATTAGACACTTCTCCAAAAAAGACATATGATGAGCCAACAAGTAT 1071
                         ii    v      i         i    i   ii vvi     i   i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_20844310_2   1072 ATGGAAAGACTTTCAGCATCACTAATCAT 1100
                            i     ivi   i     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (98 / 51)
Gap_init rate = 0.02 (11 / 629), avg. gap size = 1.91 (21 / 11)  


3362 23.56 1.41 2.93  chrX_20877257_20879876     1207  2127 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_20877257_2   1207 GGAAAGCTCTTCCATGTTCATAGATTGGAAGAATCAATATTGTTAAAATG 1256
                               v v i          i          v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_20877257_2   1257 TCTATAATACCCAAGGCATTTTACAGATTCAACGCAATCCCTATCAAATT 1306
                         v v   v v     iviiv i                           v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_20877257_2   1307 ACCCACATGCCTTTCTTCACAGAAATGGAAAAAATAATTCTGAAATTTAT 1356
                         -    vv       i  -i       v  v  iv i  i  i     i  
  L1M4_orf2#LINE/    102 -CCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_20877257_2   1357 ATGGCACCATAAAAGACCCAGAATAGCTAAAGCTATCCAGCAAAA--AGA 1404
                             v viii  ii             i   i v   iv v    --   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_20877257_2   1405 GCAAAACTGGAAGAATCACATTACTTGACTTCAAATTATACTGCAGAGCT 1454
                         i    ii    i  v     i v iii i      viv    i  i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_20877257_2   1455 ATAATAACCAAAACAGCATGGCACTTGCATAAAAACAGAGACATAGACCA 1504
                          i i   i   i    ii   i   v      ii i   v i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_20877257_2   1505 GTGGAACAGAATAAGAAACCCAGAAACAAATCCATACAACTACAGTGAAC 1554
                         i     i     viii ii       i   i       vi  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_20877257_2   1555 TCATTTTTTTTACAAAGGTGCCAAGAACATACAATGGGGAAAATATAGTG 1604
                          v     iv--    i          v   v           iv     v
  L1M4_orf2#LINE/    350 TGATTTTCG--ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_20877257_2   1605 TTTTCAATAAATGGTGCTGGGAAAACTGGATATACCTATGTAGAAGAATG 1654
                                i              v         ?v vi   i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_20877257_2   1655 AAACTAGCTTCCTATCTGTTGCCATA--CTAAAATGCAAAATCAAAATGG 1702
                           ii i vii    i  vvii     -- v     v--  v         
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATT--AACTCAAAATGG 495

  chrX_20877257_2   1703 ATTAAAGGCTTAAATGTGAGAACTGAGACCTCAAACTATGAAACTACTAC 1752
                           i ?  i i       i   i  i -------      i     vi  v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAA-------AACTATAAAACTCTTAG 538

  chrX_20877257_2   1753 AAGAAAATATTAGAGAAACTCTCTAGGACATTGGTCTGGGCAA-AATTTC 1801
                                i  vi ? v  v   iiiv   v    vi i     -ii    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_20877257_2   1802 TTGTGTAGTACCCCACAAGCAGAGGCAGCCAAAGCAAAAATGAACAAATG 1851
                           ivi  vv  v   v     v i   i v    v      ii i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_20877257_2   1852 GTATCACATCAAA-TTAAAGAGCTTCTGCACAGAAACAAGAACCACAACA 1900
                          v iiv       -     i -   i  ii vvv  --  i  -------
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA--AGGAC------- 678

  chrX_20877257_2   1901 ACAACAAAACAATAAAGTGAAGAGGCAGCTCACAGAATGGGAGAAAATAT 1950
                           v i----   v        i  i  i i                    
  L1M4_orf2#LINE/    679 ACTAT----CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_20877257_2   1951 TTGCAAACTACCCATCTGACAAGGGATTAATAACCAGAATATACAGAGAG 2000
                                ii ivi      i      i vi  v          i i   i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_20877257_2   2001 CTCAAACAACTCTATAAGAAAAA---AAAT---CTGGTT-AAAAATGGGC 2043
                            vv       v    v     ---    --- iii  -          
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_20877257_2   2044 AAAAGATCTGAATAGACATTTTTCAAAAGAAGACATACAAATAACAAACA 2093
                            i   i             i  v        i        ii v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_20877257_2   2094 GGAATATGAAAAGGTGCTCAATACCATTGATCAT 2127
                         i v i        i       i i  ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (136 / 78)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 2.50 (40 / 16)  


3191 27.32 1.00 0.55  chrX_20996646_21002735.rev     4696  5599 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_20996646_2   4696 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4745
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_20996646_2   4746 GGCCATACTGCCTAAGGTAATTTATAGATTTAATGCCATCCCCATGAAGC 4795
                            v     v  i  iv i  i  i     i  i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_20996646_2   4796 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4843
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_20996646_2   4844 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 4893
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_20996646_2   4894 AACAAAGCTGGAGGCATCACACTACGTGACTTCAAACTATATTACAAGGC 4943
                                i      vv       v vii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_20996646_2   4944 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 4993
                           i     i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_20996646_2   4994 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5041
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_20996646_2   5042 ATCTGGTCTTTGAGAAACCTGGCAAAAACAAGAAATGGGGAAAGGATTCC 5091
                          vi  i i  i  v  ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_20996646_2   5092 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTT 5141
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_20996646_2   5142 GAAACTGGATCCCTTCCTTGTACCTTATACAAAAATTAATTCAAGATGGA 5191
                            ii    i    v   iii   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_20996646_2   5192 ATAAAGACTTAAATGTTAGACCTAAAATCATAAAAACCCTAGAATAAAAC 5241
                         vi ?    i       v   v      ii      vi i     v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_20996646_2   5242 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5290
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_20996646_2   5291 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 5340
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_20996646_2   5341 ATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5390
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_20996646_2   5391 CAGGTAACCTACAGAATGGGGGAAAATTTTTGCAATCTACCCATCTGACA 5440
                         v  ii    i          i      v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_20996646_2   5441 AACGGCTAATATCCAGAATCTACAATGAACTC----AAATTTACAAGAAA 5486
                          iv i  vi          v  i  v      ----  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_20996646_2   5487 AAAGCAAACATTCCCATCAACAAGTGGGCGAAGGATATGAACAGACATTT 5536
                           ii    i vi  v  i? v  i     i      v    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_20996646_2   5537 CTCCAAAGAAGACATTTATGCAGCCAACGGACACATGAAAAAATGCTCAT 5586
                                     i  vi viii     iiii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_20996646_2   5587 CATCACTGGACAT 5599
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


 222 19.67 3.28 0.00  chrX_21065119_21067322.rev       42   102 (2102)    L1M4_orf2#LINE/L1      846   908 (0)  

  chrX_21065119_2     42 CTCAAAAGAACACATACAAGTGGCCAGCA--TACATGAAAGAGTTCTCAA 89
                            v      v i      i      ii --i        iii v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_21065119_2     90 CACCACTAATCAC 102
                           i  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.02 (1 / 63), avg. gap size = 2.00 (2 / 1)  

2935 27.03 2.22 1.22  chrX_21065119_21067322.rev      815  1713 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_21065119_2    815 TAGAAAGACATTCCATGCTCATGGATAGGAAGAATCATTATTGTAAAAGT 864
                          i      i  i     i        v      v i v      v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_21065119_2    865 GGCTGTACTTCCCAAAGCAATTTACAGATTCAATGCTATTCCCATCAAAC 914
                            vi    i      vii  i           i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_21065119_2    915 TCCCAATGACATTCTTCACAGAAGTAGAAAAAACTG-TTTTAAAATTCAT 963
                              iivi v  i  ii     i v  v  i-   - ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_21065119_2    964 ATGGAACCAAAGAAGATGGCAGA-TAGCCAAGGCAATACTAAGCAAAAAG 1012
                               viiv iii  iv-    -       ii    vi i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_21065119_2   1013 AACAAAGCTGGAGGCATCATATTACCTGACTTCAAACTATACTATGAGGC 1062
                                i      vv   i i v  ii i      viv     ii i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_21065119_2   1063 TATAGTAACCAA-ACAGCCTTATACTGGTATAAAAACAGACACGTAGACG 1111
                           i     i   -    iv vi      i    ii i     ii    iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_21065119_2   1112 AATAGAACAGGATAGAGAGCCTAGAAATAATGCCACTTGCCTACAACCAT 1161
                            i   i  i  v     i i        vv   iviiii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_21065119_2   1162 CTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGAAAAGGAC--TCC 1209
                         i    i  i     i v  v   i v  vv       i    i i--  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_21065119_2   1210 TTATTCAATAAATGGTGATGAGATAACTTACTAGCCATATACAGAAGACT 1259
                           --    i        v  i  i    viv  ?   i  i  i    v 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_21065119_2   1260 GAAACTGGAACCCTTTTTT-CATCACATACAAAAATAAATTCGAAGTGGG 1308
                            ii    v    vii i-  i  i          v  i  i  i   i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_21065119_2   1309 TTAAAGACTTAAATATAA-ATTTAAAACTATTAAAGCCCTAAAAGATAAC 1357
                          i ?    i     i   - vi         v   vi i  i    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_21065119_2   1358 CTAGGAAATACCATTCTGGACATAGACCCTGGA--AAATA----TTTCAT 1401
                         v    ?i-  -- v   v-- i -    i   i-- iii ----    v 
  L1M4_orf2#LINE/    547 ATAGGNG-TA--AATCTT--CGT-GACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_21065119_2   1402 -GATAAAGGCACCAAAAACAAATGCAGGAAAAACAAAAATTGACAAATAG 1450
                         -    v- i        i  v v   iv    iv      v  i    v 
  L1M4_orf2#LINE/    591 AGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_21065119_2   1451 GACCTTATTAAACTCAAGGGCTTCTGCACAGCAAAAGAAGCTATCAATGG 1500
                            i i  i   v i  iii   i  ii vv    i  vi       vii
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_21065119_2   1501 AGTAAATAGACAACCTACAGAACGGGAGAATATATTTGCAAACGATGCAT 1550
                            i  v        i      i       v           iv  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_21065119_2   1551 CCGACAAAGGTCTAATATCCAGAATCTATAAGGAACTTAAATGAATCAAC 1600
                          i  i  i  v  vi          v     i     ivv ii v    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_21065119_2   1601 AAGCAAAAACCAA----CCCAATTAAAAAGTGGACCAAAGACATGAACAG 1646
                           vv    iv   ----       ?    i   i v  i  iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_21065119_2   1647 ACATTTCTCAAAAGAACACATACAAGTGGCCAACA--CACATGAAAAAGT 1694
                                  v      v i      i       i --          ii 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_21065119_2   1695 TTTCAACACCACTAATCAC 1713
                         vi      i  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (160 / 79)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.63 (31 / 19)  


2529 26.48 4.30 0.40  chrX_21099986_21102489.rev      492  1235 (1269)    L1M4_orf2#LINE/L1        5   777 (131)  

  chrX_21099986_2    492 AACATATTATATGTTTGAGGATAGGAAAACTCAATGTTGTTAAGAGGTCA 541
                           v    ivi     iiv    v    i   i   i         v v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_21099986_2    542 GTTCTTCCCAAACTGATCTATAGATTCAACACAATCCCAATCAAAATTCC 591
                         i v  i      i       i         i       v        i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_21099986_2    592 AGCAAAATATGTTGTACATACAGACAAACTGACTCTAAAGTTTA-ATAGG 640
                            vivv v v   i v v iv     i    ii     i  i -  i i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_21099986_2    641 AGGGCAAAATGCCCAGAATAGTCAACACAATGCTGAA---GAAGAATGTA 687
                          iv    iivi          i   v     vi    ---      iiv 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_21099986_2    688 GTCAAAGGACTGACACTACTCAAGTTCAGGACTTACTATAAAGCCACAGT 737
                           iii      v     v i   v    ii        i     i     
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_21099986_2    738 AATCAAGGCATTATAGTATTGGCAAAAGAATGCATGGCTAGATCAATGGA 787
                                i  v i i   i     v   i  iv iivv            
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_21099986_2    788 ACAAAGTAGAGAGCTCAGAAATAGACCTACAAAAATATACTCAACTGATC 837
                          i i i v     ii        i   i i v vv   iv    i    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_21099986_2    838 TTTGACAAAGGATCAAAGGCAATTCAAAGGAGAAAGGATAGGCTTTTTGA 887
                           i     i  vv v   i v      v  i     i    v     ii 
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_21099986_2    888 CAAGTGATGTTAGAACAACTGGATATCCATATGCAAAAAAA-AAAGTTAG 936
                            i  i  i i i           ?   i        i  -i     i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_21099986_2    937 ACACAGAACTTA----GTTTTCACAAAATTATCTCAAAATGGATTATAGA 982
                           v vv v  i ----i v v  -       v            i ?   
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACA-AAAATTAACTCAAAATGGATCAWAGA 503

  chrX_21099986_2    983 TCTAAATGTAAAGTGC-AAAAGTGTAAAGTATCTAGAAAAGTAACAGAAA 1031
                         i          - v  -    v i    iivii     i i-    v ii
  L1M4_orf2#LINE/    504 CCTAAATGTAA-GAGCTAAAACTATAAAACTCTTAGAAGAA-AACATAGG 551

  chrX_21099986_2   1032 AA-ATATCTGGATAACCATGGGTTTGCTGATGACTTTTTAGATACAACAT 1080
                         ?i- v    vvi i   v      v vii   ii  i       ii   i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_21099986_2   1081 CAAATGCATGATTCTTGAATGAAAAAATTGATAAGTTGGATTTCATTATA 1130
                             v   ii vivvii  v        v     i     i     i v 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_21099986_2   1131 ATTAAAAACTTCTGTTCTATGAAATACACAATGAAGA----GAAAAGAAA 1176
                                    i   v  vii  iv    v  v    ----       v 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_21099986_2   1177 ATAAACAGATTTGGAGAAAATATC----------------GATTAAAGAC 1210
                          ivv     v v           i----------------   v ii   
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_21099986_2   1211 TTGTATTGAAAATACACAAA-AACTC 1235
                               iv i    i i   -     
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTC 777

Transitions / transversions = 1.55 (118 / 76)
Gap_init rate = 0.02 (12 / 773), avg. gap size = 2.92 (35 / 12)  


2857 26.89 3.89 0.34  chrX_21113818_21123245     1746  2619 (6809)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_21113818_2   1746 AAAAAAATTCCATGTTCCTGTATTCAAAGAATC--TATTGTTAAAATGTC 1793
                            i v  i        v  v   vi    v i--         i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_21113818_2   1794 TATACTACCCAAAGCAATCTGTAGAGTCAATGCAATCCCTATCAAAGTAA 1843
                         v     v      vii    ii   v    i               i vv
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_21113818_2   1844 CAATGACATTCTTCACAGAAATAGAAAAA---ATCCTAAAATTTATAAGT 1890
                           iivi v  i  ii       v  v  i---           i   v v
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_21113818_2   1891 AACCAGAAAAGATACTGAATAGCCAAAGCTACCCAGAGCAAAAAGAACTG 1940
                           viiv  ii  iv v           i v i iv  iv  i      vi
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_21113818_2   1941 AACTGGAGGAATCACATTACCTAACTTCAAATTATACTACAGAGCTATAG 1990
                          ii       v     i v  i  i      viv       i     i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_21113818_2   1991 TAAGCAAAACAGCACGGTACTGGCATAAAAACAGACACATGGACCAGTGG 2040
                            v   i    iii             ii i     i  i  i  i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_21113818_2   2041 AACAAAATAGACAACCCAGAATTAAATTCAGACATCTTCAGTGAACTCGT 2090
                           i i   v  v ii      v    ii  v    i vii  v  i vi 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_21113818_2   2091 TTTTGACAAAAGTGCCAAAGACATACACTGGGGAAAAGACAGTCTCTTTA 2140
                            i     ii       iiv   v  v        ii i     i  i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_21113818_2   2141 ATAAATAG---------------ATATCCATATGCAGAAGAATGAAACTA 2175
                          i    i ---------------   ?   i     i         ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_21113818_2   2176 GACCCCTATCTCTTGCCATGTACAAAATTCAAATCAAAATGGATTGAAGA 2225
                                 i   vii    i       v i  v           ii?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_21113818_2   2226 CTTAATTCTAAGACTCCAAATTATGAAACAACTCAAAGAAAACTTTGG-G 2274
                          i   v v     viiv   i   i    vvi vi        v v  - 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_21113818_2   2275 TAAACTCTCTACGACGTTTGGATAGGCAAACATTTTTTGAGTAATACCCT 2324
                             -   iiii   v  v  v       vvi   i  iii  vv  v i
  L1M4_orf2#LINE/    554 TAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_21113818_2   2325 ACAAGCCCAAGTAGTCAAAGCAAAAATGGACAAATTGGATCACAGCATG- 2373
                          v    v    i iiv    v      i  i        iiv  v  vi-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_21113818_2   2374 TTAAAAAGCTTCTGCACAGCAAACGAAATAATAAACAAAATGAAGAGACA 2423
                                -   i  ii vv    v  v iv  v  v   i    i     
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_21113818_2   2424 ACCCAGAGAATGGGAGAAAATGTTTGGAAAGTATCCATCTGACAAGGGAT 2473
                              v               i    v   vi  vi      i      i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_21113818_2   2474 TAATAACCAGAATACATTAGGAGATCA-AAAACTCAACTAATAATATGAT 2522
                          vi  v        i  v i  iv  v- v       -      v v  i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAA-TAATAAAAAGAC 800

  chrX_21113818_2   2523 -----------TCTAAAAATGAGCAAAAGATCTGAATATACACTTCTCAA 2561
                         ----------- i?       i     i   i      v   i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_21113818_2   2562 AAGAAGACACACAAATGGAAAAAAGGGATATGAAAAGGTGTGCAAAATTA 2611
                                i i        vv  v i v i        i  iv   v  i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_21113818_2   2612 TTGATCAT 2619
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (10 / 905), avg. gap size = 3.70 (37 / 10)  

3259 26.91 0.78 0.22  chrX_21113818_21123245     8033  8935 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_21113818_2   8033 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 8082
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_21113818_2   8083 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 8132
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_21113818_2   8133 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 8177
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_21113818_2   8178 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 8227
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_21113818_2   8228 CAAAGCTGGAGGTATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 8277
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_21113818_2   8278 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 8327
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_21113818_2   8328 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACTAT 8375
                              i    i--    i  --        vv iii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_21113818_2   8376 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 8425
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_21113818_2   8426 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTGA 8475
                         v  i  i              v      v  ?   i   v i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_21113818_2   8476 AACTGGATCCCTTCCTTACACCTTATACAAAAATTGATTCAAGATGGATT 8525
                          ii    i    v   i     v            i i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_21113818_2   8526 AAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 8575
                          ?    i    ii v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_21113818_2   8576 AGGCATTACCATTCAGGACATAGGCATGGGAAAGGACTTCATGTCTAAAA 8625
                            ?i v viv   iv   v v  vv i  v  v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_21113818_2   8626 CACCAAAAGCAATAGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 8675
                                    vv           vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_21113818_2   8676 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 8725
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_21113818_2   8726 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 8775
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_21113818_2   8776 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 8825
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_21113818_2   8826 ACAAATAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 8875
                                    v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_21113818_2   8876 AAAAGAAGACATTTATGCAACCAAAAGACACATGAAAAAATGCTCACCAT 8925
                         v        i  vi viiii    v ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_21113818_2   8926 CACTGGCCAT 8935
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.25 (9 / 4)  


2642 27.45 2.92 0.79  chrX_21126536_21132312     4396  5284 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_21126536_2   4396 TGGAAGAACATTCCATGCTCATAGATAGGAACAATCAATATCATGAAAAT 4445
                              ii i  i     i    i   v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_21126536_2   4446 AGCCACATTGCCCAATGTAATTTATATATTCAATGCTATTCCCATTAAAC 4495
                         i  v i i v     vv i  i  i v      i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_21126536_2   4496 TACCATTGACATTCTTCACATAATTAGAAAAAACT-ATTTTAAAATTCAT 4544
                          v   vivi v  i  ii  v  v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_21126536_2   4545 ATGTGAACGAAAAAAGAGCCTGAATAGCCAAGACAATCCTAAGCAAAAAG 4594
                            vi  i v  ii-  v  v          i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_21126536_2   4595 TACAAAGCTGGAGGCATCAAGCTACCCAACTTCAAGCTATACTACAAGGC 4644
                         v      i      vv   vi  v     i     iviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_21126536_2   4645 TACAGTAACCAAAACAGCACAGTACTGGTACAAGAACAGAAACGTAGACT 4694
                                 i   i    iiii       i i   i i   v ii    ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_21126536_2   4695 AGCGGAACAGAATAGAGAACTCAGAAATAAGATGGCACACCTACAACCAT 4744
                          ii    i     v    iii         ivivii   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_21126536_2   4745 CTAATCTTCAACAAGCCTGACAAAAGCA----ATGGGGAAAGGATTCCCC 4790
                         i i  i   i     vv  v   i v  ----          i  vvi i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_21126536_2   4791 ATTTAAAAAATGGTACTGGGAGAACTGGCTAGCCCATATACAGAAAATTT 4840
                         v  i  v       i      v      v  ?  - i  i  i  i v v
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCC-ACATGCAAAAGAATG 447

  chrX_21126536_2   4841 AAGCTGGACCCATTCCTTACACCATATACAAAAATTAACTCAAGATGGAT 4890
                            i       v v   i                         i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_21126536_2   4891 TAAAGACTTAAATGAAAAACCCAAAACTATAAAAACCGTAGAAGAAAATC 4940
                         i ?    i      v  i v i            vi v          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_21126536_2   4941 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAATATTTCATGACAAA 4989
                             ?i- v i -   iv   v v  vv i     vvi    v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_21126536_2   4990 AACACCAAAAGCAATTGCAAGAACAGCAAAAACTGACAAATAGGATCTAA 5039
                         i            vvv    v  v  v     iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_21126536_2   5040 T-ACACCTAAAGAGCTCCTGCACATCAAAAGAAACTAT------AATCA- 5081
                          - v vi    i -  ii  ii v     i  v     ------ i v -
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_21126536_2   5082 --GACAACTCATAGAATGGGGTAAAATTTTTGTAATCTATCCATCTGACA 5129
                         --      i  i        iv     v    i  vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_21126536_2   5130 AGAT-CTAATATCCAGAATCTATGAGGAACTTAAACAAATTTACAAGAAA 5178
                           iv-  vi          v   i i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_21126536_2   5179 ----TAAACAACCCCATTAAAAAGTAGACAAAGGACATGAACAGACACTT 5224
                         ----i   i     v   ?    i i i       iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_21126536_2   5225 CTCAAAAGAAGACATT--AGTGCAGCCAACAA--ACATGAAAAAA-GCTC 5269
                            v        i  v-- i  --     i  --         i -    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTC 893

  chrX_21126536_2   5270 AACATCACTGACCAT 5284
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.94 (33 / 17)  


3173 24.52 3.49 1.35  chrX_21191597_21196217.rev     3242  4130 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_21191597_2   3242 TGGAAAGATATTTCATGTTCATGGATTGGAAGAATGAATATTTTTTAAAA 3291
                                    ii                    v v      v  -  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAGA 49

  chrX_21191597_2   3292 TGTCCATATTACTCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAA 3341
                           v v   i v i    vii              i               
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_21191597_2   3342 ATACCAATGACATTCTTCACAGAAATAGAAAAAAGACCATCCTAAAATGT 3391
                           v   iivi v  i  ii       v  v  -- viv          vi
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTC 147

  chrX_21191597_2   3392 ATATGGAATCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAGCAAAAA 3441
                                 vii   ii                 i v   i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_21191597_2   3442 GAACACAACTGGAGGAATCACAGAACT----GACTTCAAATTATACTACT 3487
                              v ii       v     ---  ----i i      viv      v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACA---CTTCCCAATTTCAAAACTTACTACA 244

  chrX_21191597_2   3488 GAGGTATAGTAAACAAGACAGCATGGTGCTGGCATAAAAAGAGACACAGA 3537
                         i  v  i     v        ii    i         ii v     i v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_21191597_2   3538 GACCAGTGGAACAGAACAGAGTACACAGAAAAAAATCCACACACCCACAG 3587
                           i  i     i    iv   viiv      v   i   i   iii ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_21191597_2   3588 TGCACTCATTTTCGACAAAAGTGCCAAGGACATACACTGGAGAAGGC-CA 3636
                          vv i v           ii        iv   v  v   i   i v-i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_21191597_2   3637 GTCTCTTTAATAAATGGTTATGGGAAAACTGGATATCCATGGGCAGAAGA 3686
                             i  i  i       vv     v         ?   iiv   i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_21191597_2   3687 AAGAAACTAGATCTGTATCTCCTGCTATATACAAAA-----TTCAAAATT 3731
                          v   ii i  i iv  i   vii i          -----i       v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_21191597_2   3732 GATTAAAGACTTAAA-----GACCTCAAACTATGAAACTACTACCAGAAA 3776
                            i ?    i    -----  v  v       i     vi  vv     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_21191597_2   3777 ACATTGCAGAAGCTCTCCAGGACACTGGTCTTGGCAAAGATTTCTTGAGT 3826
                             v v? v iv   i iv   vi   vi v     v i      iii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_21191597_2   3827 AATACCCCACAATCACAGGCAACCAAAGCAAAAATGAACAAATGGGG--T 3874
                          vv  v   v  v    i     v    v      ii i    v  i-- 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_21191597_2   3875 CCT-----TTG----CTTCTGCACAGCAAAGGAAACAGTCAACAAAGTGA 3915
                          v -----  i----   i  ii vv       v  vi    v       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_21191597_2   3916 AGAGACAACCCACAAAATGGGAGAACATATTTGCAAGCTACCCACCTGAC 3965
                          i            i          v          iii ivi i    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_21191597_2   3966 AAGGGATTAACAACCAGAATATGTAAGGAGCTCAAACAACTCCATAGGAA 4015
                               i vii v         i   i  i   vv       v   iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_21191597_2   4016 AAAAAAAAATCTAATAATCTGGTT-AAAAATGGGCAAAAGATTTGAATAG 4064
                            i v    -----  i iii  -             i           
  L1M4_orf2#LINE/    795 AAAGACAAAT-----AACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_21191597_2   4065 GCAGTTCTC---AAAAGACATACAAACGGCCA-TAAGGTATATGAAAAGG 4110
                         i  v     --- i    i       i     -    -i i        i
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGA 888

  chrX_21191597_2   4111 TATGCAGCGTCACTGACCAT 4130
                          iiv  i i   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (130 / 85)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.87 (43 / 15)  

 358 22.94 0.92 2.75  chrX_21191597_21196217.rev     4429  4537 (84)  C L1M4_orf2#LINE/L1   (730)   178    72  

C chrX_21191597_2   4537 CTGCAGAACTGCAACA-AATCCCTATCAAAATACCAATGACATTCTTCAC 4489
                           i    -- v    i-               v   iivi v  i  ii 
  L1M4_orf2#LINE/     72 CTACAGA--TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

C chrX_21191597_2   4488 AGAAATAGAAAAAAAAAATCCTAAAATGCATATGGAACCACGAAAGACCC 4439
                               v  v  ivvi -         v         vii i ii     
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGA-TCCTAAAATTCATATGGAAATGCAAGGGACCC 168

C chrX_21191597_2   4438 AGAATAGCCA 4429
                                   
  L1M4_orf2#LINE/    169 AGAATAGCCA 178

Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.03 (3 / 107), avg. gap size = 1.33 (4 / 3)  


2841 25.09 8.05 0.59  chrX_21311964_21317481.rev     4184  5028 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_21311964_2   4184 TGGAAAGACATCACATTTTCATGGATTAGAAGAATTAACATTGTCAAAAT 4233
                                 i   v   v          i     v    i     i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_21311964_2   4234 GACTATACTACCCAAAGCAATCTACAGATTCAATGGAATCCCTGTCAAAA 4283
                          i v     v      vii              i v       i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_21311964_2   4284 TACCAATGACATGCTTTACAGAAATAGAAAAAA-AATCC-AAAATTTGTA 4331
                          v   iivi v vi   i       v  v  iv-i    -      ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_21311964_2   4332 TGGAACCATAAAATACCCCAAATAGCCAAAGCATTTGTGAACAAAAAGAA 4381
                              viii  iiv    vi          i  v iv    v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_21311964_2   4382 CAAAGCTGAAGGCATCACACTGACTGACTTCAAATTACACTACAAAGCTG 4431
                              i  i   vv       vv ii i      vivi           i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_21311964_2   4432 TAATAACCAAATCAGCATTGCACTGGTATAAAAACAGACACACAGCCCAA 4481
                         i i   i   iv   ii v i     i    ii i     i i  vi   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_21311964_2   4482 TCAAACAGAATGGAGTATTCAGAAATAAGTCCGTA--TTTACAGCCGGGT 4529
                          vi  i     v   vi i         ii  i  --    ii i iiv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_21311964_2   4530 GATTTTTGACAAAGGCAACAAGAACATACATTGGGCAAAGGATAGCCTCT 4579
                               i     i  iiv     v   v  v    v    i    i  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_21311964_2   4580 TCAATAAATAGGGCTGGGAAAACTGGATATCCATATTCAGAAAAATGAAA 4629
                             i    i v       v         ?   i  v  i  i      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_21311964_2   4630 CTAGAACCCTATCTCTCACCATGTACACAA-TCAACTCAAAATGGATTAA 4678
                         i i  v     i   v      i    v  - i              i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_21311964_2   4679 ACGCTTAAATATAAGACCCCAAATTATAAAACTACTAGAAGAATACACAG 4728
                          vi i     i     v iv   i         vi        v   i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_21311964_2   4729 GGG-AAATACTTCAGGACATTGGTCTAGGCAA--ATATTTT---TATGGC 4772
                          ? -    -    iv   v    vi       --i v i  ---    i 
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_21311964_2   4773 T---AAGGTTTACATGCAACAAAAGAAAAAAAACAGACAAACGGGATTAT 4819
                         v---  i i--   v                --i   i   iv   i vi
  L1M4_orf2#LINE/    600 ACCAAAAGC--ACAAGCAACAAAAGAAAAAA--TAGATAAATTGGACTTC 645

  chrX_21311964_2   4820 ATCAAACT--AAAAGTCTTATGT-----AGAGCA-----AAGGAA----- 4852
                               v --    v i  i  i-----  ii  -----   i  -----
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_21311964_2   4853 ---ACAATTCA--------------------------------TCTGACA 4867
                         ---    ii  --------------------------------     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_21311964_2   4868 GGGAACTAATATCCAGAATATGCAAGGAACTCAAACAACTCAACAGCAAT 4917
                         i  i   vi            ii  i      vv         i ii  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_21311964_2   4918 AAAAGAAATATTTTTATTTAAAAATGGGCAAATGATCTGAATAGACATTG 4967
                           i v     viiiv   ?             v   i            v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_21311964_2   4968 CGTGAAAGCAGACACACAAATGACCAACTGCTATATAAAAA--TGCTTAA 5015
                          viv    v   i i       i    ivivi i  i    --    i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_21311964_2   5016 CGTCGTTTATCAT 5028
                          i  i????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (135 / 73)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.29 (73 / 17)  


3197 25.63 1.10 1.21  chrX_21322763_21328603     4440  5348 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_21322763_2   4440 TGGAAAGACATTCCATGCTCATGGATAAGAAGAATCAATATCATGAAAAT 4489
                                 i  i     i        vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_21322763_2   4490 GGCCATACTGCCCAAAGTAATTTATAGATTAAATGCTATCCCCATCAAGC 4539
                            v     v      v i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_21322763_2   4540 TACCATTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAGATGTCA 4588
                          v   vivi i  i  ii     v v  v  i--  - iii  i vv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_21322763_2   4589 TACGGAACCAAAAAAGAGCCCATATACCCAGGACAATCCTAAGCAAAAAG 4638
                           i    viiv  ii  v  viv   v   ii      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_21322763_2   4639 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGT 4688
                                i      vv       v  ii i      viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_21322763_2   4689 TACAGTAACCAAAACAGCATT-TACTGGTATCAAAACAGATATATAGACC 4737
                                 i   i    ii v-      i  v ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_21322763_2   4738 AGTGGAACAGAATAGAGGGAGGCCTCAGAAATAAGGCCACACATCTACAA 4787
                          i     i     v   i ----ii         iv   i    i  iii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAG----TCCAGAAATAAACCCATACATTTATGG 344

  chrX_21322763_2   4788 CCATGTGATCTTTGACAAGCCTGACAAAAACAAGCAATGGGGAAAGGATT 4837
                         i  vv    i  i      vv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_21322763_2   4838 TCCTATTTAATAAATGGTGCTGTGAAAACTGGCTAGCCATATGCAGAAAA 4887
                         vi  v  i  i           v  v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_21322763_2   4888 CTGAAACTGGACCCCTTCCTTACACCTTATAGAAAAATTAACTCAAGATG 4937
                         v    ii         v   i     v    v              i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_21322763_2   4938 GATTAAACACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAA 4987
                            i ? v  i    i      v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_21322763_2   4988 ACCTAGGCAGTA--CCATTCAGGACATAGGCATGGGTAAAGGCTTCATGA 5035
                           v    ?-   --i -   iv   v v  vv i  i  v  i   v ii
  L1M4_orf2#LINE/    545 ACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_21322763_2   5036 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGAT 5085
                         v  vi            vvi          vv        i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_21322763_2   5086 CTAATTGAACTAAAGAGCTTCTG-ACAGGAAAAGAAACTATCATCAGAGT 5134
                         i v  ii  v v  i i   i  -i vvv   i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_21322763_2   5135 GAACAGTCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTG 5184
                            v  v     i                 v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_21322763_2   5185 ACAAAGGGCTAATATCCAGAATCTACAAGAAACTT----AATTAAACAAA 5230
                          i  i  i  vi          v  i  ii    i----  i v  i  -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA- 791

  chrX_21322763_2   5231 TGTACAAGA-AAACAGCCCCATCAAAAAGTGGGCAAAGGATATGAACAGA 5279
                          i- v    -   i i   v  i?    i            v    i   
  L1M4_orf2#LINE/    792 TA-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_21322763_2   5280 CACTTCTCAAAAGAAGACATTTATGTGGCCGACAAACATATGAAAAAAAA 5329
                           i     v        i  vi vi     i i  i  i       i v-
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT- 889

  chrX_21322763_2   5330 GCTCATCATCACTGGTCAT 5348
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


3130 17.31 0.67 0.84  chrX_21542564_21544700.rev      505  1099 (1038)    L1M4_orf2#LINE/L1      113   706 (202)  

  chrX_21542564_2    505 TTTTTGCTGAAATACATAAACTGATCCTAAAATTCATATGGAAATGCAAG 554
                                v     vv i  i                              
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_21542564_2    555 AGACCTAGAATAGCCAAA-CAAGCTTGAACAAGAAAAAAATTTTTGGAGG 603
                         i    i            -   v      v     i  v vvv       
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_21542564_2    604 ACTCACACTTCCTGATTTCACAACTTATGACAAAGCTACAGTCATCAAAA 653
                                     ii      v      iv             v     i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_21542564_2    654 TGGTATGGTACTGGCATAAAGATAAATATCTGGATTGACAGAATAGGCTT 703
                         ii  i              i    i i  v i   ii ii      iv  
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_21542564_2    704 GAGAGTTTAAAAATAAATATTTACATTTATGGTCAATTGATTTTCCA-AA 752
                               ii i       iviv                        v -  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_21542564_2    753 GAGTGCTAATATAATTCAATGACAAAAGAATAGTATTTTCAACAAGTGGT 802
                          i    i  v iv        ivi          v          i    
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_21542564_2    803 GCTGGGACAACTGGATATCCACATTTAGAAGAACAAAGCTGTGCCTTTAC 852
                                          ?      vi i     ii   i  vi  ii   
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_21542564_2    853 CTTAGACCACATAGAGAAATTAACTAAAAATAGATCAAAAATCTAAATGT 902
                           i v    i   v i         v     i     ? i i        
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_21542564_2    903 AGGAGCTAGAATTATAAAACTCTTAGAA-AACACATTGGTGCAATTCTTT 951
                          i      i  i                -  v    v  ? i  v    i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_21542564_2    952 GTGACCTTGGATTAGGCAATGGTTTCTTAGCTGTGACACCAAAAGAACAA 1001
                                   i                   v i            v    
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_21542564_2   1002 GCAACCCAAGAAAAAATAAATTTTATTTAGTTATTATTTAAACTTTAAAA 1051
                              vv           i  v-- v  i viv i  iv   --      
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATA--AATTGGACTTCATCAAAA--TTAAAA 658

  chrX_21542564_2   1052 AGCTTTTGCACTTCAAAGGTCACCATCAAGAAAGTGAAA-GACAACCCA 1099
                          -      ii         v   i               -         
  L1M4_orf2#LINE/    659 A-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

Transitions / transversions = 1.56 (61 / 39)
Gap_init rate = 0.01 (7 / 594), avg. gap size = 1.29 (9 / 7)  

 930 14.81 2.31 2.31  chrX_21542564_21544700.rev     1431  1646 (491)    L1M4_orf2#LINE/L1      693   908 (0)  

  chrX_21542564_2   1431 GAACAGACTAATACACCAGGAAACTGGAGAAAATATTTGCAAATCATATA 1480
                            v    -  iv   -  --  iv                         
  L1M4_orf2#LINE/    693 GAAAAGAC-AACCCAC-AG--AATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_21542564_2   1481 TCTGATAAGG-ACTTGTATCCAGACTAAATGAAGAATGCTTACAACTCAA 1529
                                   -             v  v  i     iv            
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_21542564_2   1530 TAATCAAAATGACAAATAGCCAAAT----ATTTCAGAAAATGACCTGAAT 1575
                             v    -        i  v   ---- vv vi v   v  ii     
  L1M4_orf2#LINE/    789 TAATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_21542564_2   1576 AGACACTTCTCCAAAGAAGATATCCCATCAGACAATAAGCACATGAAAAT 1625
                              i                 v v vii v                 v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_21542564_2   1626 ATGCTTGATATCATTAGTTAT 1646
                              ii i    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.78 (14 / 18)
Gap_init rate = 0.03 (6 / 216), avg. gap size = 1.67 (10 / 6)  


3365 26.10 0.22 0.22  chrX_21549521_21553848     2928  3835 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_21549521_2   2928 TGGAAACACATCCCTTGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2977
                               v i     v  i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_21549521_2   2978 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCACCATCAAAA 3027
                          i v     v  v   vii       i      i      v i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_21549521_2   3028 TACCACCATCATTCTTCACAGAATTTGAAAAAACAATTCTAAAATTCACA 3077
                          v   v vv v  i  ii     v    v  ivii  i          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_21549521_2   3078 TGGAACCAAAAAAGAGCCCGCATAGCCAAAGCAAGGCTAACAAAAAAGAA 3127
                              viiv  ii  v  v v         i   vvi i v   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_21549521_2   3128 TAAATCTGGAGGCATCACACTACCTGATTTCAAATTATACTATAAGGCCA 3177
                         i   vi      vv       v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_21549521_2   3178 TAGTCACCAAAACAGCATGGTACTGGTACAAAAATAGGC-CATAGGCCAG 3226
                         i   v i   i    ii         i i  ii    i -i    ii  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_21549521_2   3227 TGGAACAGAATAGAGAACCCAGAAATAAACCCAGATACTTACAGCCAACT 3276
                              i     v    ii               v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_21549521_2   3277 GATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTTT 3326
                            i   i    i vviv   i v   vv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_21549521_2   3327 TTAAGAAATGGTGCTAGGATAATTGGCTAGCCACATGTAGGAGAATGAAA 3376
                          i  v          i   i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_21549521_2   3377 CTGTATCCTCATCTCTCACCTTATACAAAAATCAACTCAACATGAACTAA 3426
                         i  v i  ii i   v    v           i       v   i ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_21549521_2   3427 GGACTTAAACCTGAGACCTGAAACTATAAAAATTCTAGAAGATAACATTG 3476
                         i   i    iv i   v  i           v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_21549521_2   3477 GAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGATC 3526
                          ?iv  vi    vv   v    v        v i    v iivi v  iv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_21549521_2   3527 CCAAAAGCAAATGCAATAAAAACAAAGAAAAAATGGCTGGGACCTAAT-A 3575
                                  v v    i    i-   i  v i  iiv v    i v  - 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCATCA 649

  chrX_21549521_2   3576 AAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAACAG 3625
                            i    i -      iiivv    i iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_21549521_2   3626 ACAAACCACAGAGTGGGAGAAAATCTTCACAATCTATGCACCTGACAAAG 3675
                             v       i           v  ii   vii  ii i    i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_21549521_2   3676 GACAAATATCCAGAATCTGCAATGAACTCAAACAAATCAGTAAGAAAAAA 3725
                            vvi          v ii  v      vv    v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_21549521_2   3726 ACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTC 3775
                              i  i  v  i?    i     v     iv          v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_21549521_2   3776 ACAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACAT 3825
                         vv                      i  i  i       i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_21549521_2   3826 CACTAATGAT 3835
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.00 (4 / 4)  


3130 26.99 1.00 0.55  chrX_21777470_21783860.rev     4997  5900 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_21777470_2   4997 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCGTGAAAAT 5046
                              ii i  i     i      i v      v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_21777470_2   5047 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_21777470_2   5097 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGCTCATA 5141
                          v   iivi i  i  ii     v v  v  i--- --     ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_21777470_2   5142 AGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCAAAAAGAA 5191
                         v    viiv  ii  v  v v  v     iv     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_21777470_2   5192 CAAAGCTGGAGGCAC-CACGCTACCTGACTTCAAATTATACTACAAGGCT 5240
                              i      -  -   i  v  ii i      viv        i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_21777470_2   5241 ATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATACACCA 5290
                          i     i   i    ii         i iv ii i   i     v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_21777470_2   5291 ATGGAACAGAA--AAGAGGCCTCAGAAATAATAACACACATCTATAACCA 5338
                               i    --i    v  --        vvv  i    i   iii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_21777470_2   5339 TTTGATCTTTGACAAACCTGCCAAAAACAAGCAATGGGGAAAAGATTCCC 5388
                         v     i  i     ivv      i v  vv           ii  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_21777470_2   5389 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATACGTAGAAAGTTG 5438
                          v  i  i        i     v      v  ?   i i i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_21777470_2   5439 AAACTGGATCCCTTCCTTACAGCTCATACAAAAATTATTTCAAGATGGAT 5488
                           ii    i    v   i   v vi            vi    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_21777470_2   5489 TAAAGACTTAAATGGTAGACCTAAAACCATAAAAACGCTAGAAGAAAACC 5538
                         i ?    i      vv   v       i      vivi           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_21777470_2   5539 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5587
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_21777470_2   5588 AACACCAAAAGCAATGGCAACAAAAGCCAAAAAAGACAAATGAGATCTAA 5637
                         i            vvi          vv    v   i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_21777470_2   5638 TTAAACTAAAGGGCTTCTGCACGGCAAAAGAAACTACCATCAGAGTGAAC 5687
                          i   v v  iii   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_21777470_2   5688 AGCCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCAACTGACAA 5737
                           v     i                 v       vii ivi v    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_21777470_2   5738 AGGGCTAATATCCAGAATCCACAAAGAATTCAAACAAATTTACAAGGAAA 5787
                         i  i  vi          vi i      i  vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_21777470_2   5788 AAACCAAACAAGCCCATCAAAAGGTGGGCAAAGGATTTGAACAGACATTT 5837
                          i  -   i  v  v  i?   ii                 i        
  L1M4_orf2#LINE/    797 AGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_21777470_2   5838 CTCAAAAGAAGACATGTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5887
                            v        i  ii viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_21777470_2   5888 CATCACTGGCCAT 5900
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


1060 26.54 0.62 3.40  chrX_21786698_21788817      465   788 (1332)    L1M4_orf2#LINE/L1        9   323 (585)  

  chrX_21786698_2    465 TGTCTGATTTCCAAGGGTTGGAAATTTTCTCATGTATATGATTAAAAAGC 514
                          i  iv  v i  v  i      ivi  --- ---    vi    i v v
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTT---A---ATATTGTTAAGATGG 52

  chrX_21786698_2    515 CAATTTGATACCACCCAAAGCAATGTATAGATTCAATCCAATCACTACCA 564
                             -----  iv      vii  v  i        iv     v   i  
  L1M4_orf2#LINE/     53 CAAT-----ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_21786698_2    565 AAATACCAATGACATTCTCAACAGAAATAGGAAAAACGATCCTAAAATGT 614
                             v   iivi v  i ivi       v iv  ivi           vi
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_21786698_2    615 ATATGGAACCACAAAGGACCCCAAATAGTCAAAGCAATCCTGAGCAAAAA 664
                                 vii   i      vi     i    i     i   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_21786698_2    665 GAACAAAGCTGGAGGCATCATACTACTGGACTTCAAAATATACTACAAAG 714
                                 i      vv   i   v ivi i       iv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_21786698_2    715 CTGTAGTAGCCAAAACAGCATGGTACTGACATAAAAACAGACATC--AAC 762
                           ii    ii   i    ii        i     ii i      v--i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_21786698_2    763 CAGTGGAACAGAATAGAGAACCCAGA 788
                           i     i     v    ii     
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGA 323

Transitions / transversions = 1.87 (56 / 30)
Gap_init rate = 0.01 (4 / 315), avg. gap size = 3.25 (13 / 4)  

1925 21.98 9.34 0.18  chrX_21786698_21788817     1088  1633 (487)    L1M4_orf2#LINE/L1      313   908 (0)  

  chrX_21786698_2   1088 GAGAACCCAGATATACATCCACACACC----GCGAACTCATTTTCAACCA 1133
                             ii     v   v i   i   ii---- iv  i v      i  v 
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_21786698_2   1134 AGGTCCCAAGAACATGCAATAGGGAAAGGACAGTCTCTTCAATACATGGT 1183
                         i   v      v   v    i       i i     i     i v     
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_21786698_2   1184 GCTGGGAAAACTGGATAAACATACGCAAAAGAATGAAAGTAGACCCC-AT 1232
                                v         ?v  i i             iv i      - i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_21786698_2   1233 CTC----------CAAA--TCAAATCAAAATGGGTTACAGACTTAAGTAT 1270
                            ----------    -- i  v         i i ?    i   i i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_21786698_2   1271 AAGATCTGAAACTATGGAACATCTAGAAGAAAACGTTGGGG-AAATGGTC 1319
                             v  i       ii   vii           i v  ? -    vv  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_21786698_2   1320 AGGATGTTGGTCTGGGCAAAGATTTTTTGTGTAAGACCTCAAAAGCACAG 1369
                         iv  iv    vi i     v i   i  ivi  v   vi          i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_21786698_2   1370 GCAACTGAAGCAAAAATAGAGAAAAGGGATTACATCAAACTAAAAAGCTT 1419
                              vi   v         v   vv   i v       v v    i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_21786698_2   1420 C---ACAGCAAAGGAAAC-----AGAAA----AGAGACAACCCACAGAAT 1457
                         i---i vv       v  -----     ---- i                
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_21786698_2   1458 GGGAGAATATATTTGCAAACTA-ATGATCTGACAAGGGGTGGATAACTAG 1506
                                v           ii -  -      i     iivvi  v i  
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGGGACTTGTATCCAG 761

  chrX_21786698_2   1507 ACTATATAAGGGGCTCGAACAACTCAGCAA-AAAAA---------TCCA- 1545
                          v       i ii   vv        ii  -     ---------i   -
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_21786698_2   1546 TTCAAAAGTGGGCAAAGGAC----ATA-----TCCTCAAAAGAAGACATA 1586
                           ?    i           i----   ----- i   v        i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_21786698_2   1587 CAGATGGCCAATAGGCATATGAAAAAATGCTCACTAGCACTAATCAT 1633
                           i          i   i       i       vi v  ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (70 / 46)
Gap_init rate = 0.03 (15 / 596), avg. gap size = 3.47 (52 / 15)  


1131 22.81 2.83 17.25  chrX_21859734_21864279.rev     2995  4055 (491)    L1M4_orf2#LINE/L1        1   908 (0) *

  chrX_21859734_2   2995 TGGAAGGATACTCCATGCTTATGAATTAGTAGA----ATATTGTTAAAAT 3040
                              i    ii     i i   i   i v   ----          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_21859734_2   3041 GACAATACCACTGAAAGCAATTTACAGATTCAACACAACCTCTATCAAAA 3090
                          i      iv iv   vii  i            i   i i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_21859734_2   3091 TACCATTGACATTCCTCACA-AAATAGAAAAAACAAATCCTAAATTTTAT 3139
                          v   vivi v  ii ii  -    v  v  i- vi        v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_21859734_2   3140 ATGGAACCACGAAAGACCCCAAATAGCCAAAGCGATCCTGGGCAAAAATA 3189
                               vii i ii     vi          i i   i  iiv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_21859734_2   3190 ACAAAGCTGGAGAA-TCACATTACCTGACTTCAAAATATAGTACAGGGCC 3238
                               i     i -     i v  ii i       iv  v    ii  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_21859734_2   3239 TATGTCTGGAATGGTATTTCCTAGGTTTTCTTCAAGGGTTTTCACAGTTT 3288
                         ---------- ii   ------ --------     -------     v 
  L1M4_orf2#LINE/    250 ----------ACAGTA------A--------TCAAG-------ACAGTGT 268

  chrX_21859734_2   3289 TAGGTTTTACATTTACATCTTTAATCCATCTTGAGTTGATTTTTGTAT-- 3336
                         --   ----- i vi   ----  -------- ii v  iv v iv  --
  L1M4_orf2#LINE/    269 --GGT-----ACTGGCAT----AA--------GGATAGACATATAGATCA 299

  chrX_21859734_2   3337 ATG--ATAAAAGGGATGGGTCCAGTTTCAATCTTCTGCAT--ATGGCTAG 3382
                            --   i  vv  - i      vvvi  v iiv i   --    ii i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_21859734_2   3383 CCAGTTATC--CCAG--CACCACAGTCCTTTACCCATTGCTTGTTTTTG- 3427
                         iiii  v  -- v  --ii   -  v  v  ---  v  --------- -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCA-AGACCATT---CAATG---------GG 385

  chrX_21859734_2   3428 -------TAGACTTTATCAAAGATCAGATGGTTGTTGGTGTGCAGCTTTA 3470
                         -------   v    -    ----  i     - i   - -i  i  vv 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTT-TCAA----CAAATGGT-GCTGG-G-ACAACTGGA 427

  chrX_21859734_2   3471 TTTCTGGGCTGCTTCCATTGATCTATGTATCCGTAGTTGTACCGGCCACA 3520
                          -----i? ii v v  --- --- v v  -- v     v   v- i  -
  L1M4_orf2#LINE/    428 T-----AKCCACATGCA---A---AAGAAT--GAAGTTGGACCC-CTAC- 462

  chrX_21859734_2   3521 CTGTTTTTGTTACTACAGCCTTATACTATAGTTTGAAATCGGGTAATGTG 3570
                           -----------i   -  v     v v i  --  v  ii--    - 
  L1M4_orf2#LINE/    463 CT-----------CACA-CCATATACAAAAATT--AACTCAA--AATG-G 495

  chrX_21859734_2   3571 ATGCCTCCAGCTTTGTTCTTTTTGCTTAGGATTGCTTTGGCTATTCGGGC 3620
                           -----  ---?v vi  vvv  --  i  --------    -------
  L1M4_orf2#LINE/    496 AT-----CA---WAGACCTAAATG--TAAGA--------GCTA------- 520

  chrX_21859734_2   3621 TCTGTTTTGATTCCATATGAATTTTAGAATAGCCTTTTTCTAATTCTGTG 3670
                         --------- vv i   vi v i      -------------------- 
  L1M4_orf2#LINE/    521 ---------AAACTATAAAACTCTTAGAA--------------------G 541

  chrX_21859734_2   3671 AACAATGTCATTGGTAGTTTGATAGAAATAGCATTG-AATCTGTAAATTA 3719
                           -  ---   v  ?-  -------    -- v i -i i  - iii   
  L1M4_orf2#LINE/    542 AA-AA---CATAGGN-GT-------AAAT--CTTCGTGACCT-TGGGTTA 576

  chrX_21859734_2   3720 CTTTGGGCAA-GATTCCAT-GATGAAGATGCCCAAA--ACAATTGCAACA 3765
                         -----     - i  i v -   - v  ii  v   --    --      
  L1M4_orf2#LINE/    577 -----GGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAA--GCAACA 618

  chrX_21859734_2   3766 AAAACAAAAAAT-GACAAACGGGACTTAATTAAACCAAAGAGCTTCTGCA 3814
                            i-       -  i   iv      v  i   viv  i i   i  ii
  L1M4_orf2#LINE/    619 AAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_21859734_2   3815 CAGCAAAAGAAGCTATCAACAGAATAAACAGACAACCCACAGAACGGCAG 3864
                          vv    i  vi       v i i i  v               i  v  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_21859734_2   3865 AAAGTATTTGGAAACTGTGCATCCGACAAAGGTCTAATATCCAGAATTTA 3914
                            i      v   iii ii   i  i  i  v  vi          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_21859734_2   3915 CAAGGAACATAAACAAATTTATAAGCAAAAACCAAACAACCCCATTAAAA 3964
                         i  i    vivv    v iv    vv    iv    i     v   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_21859734_2   3965 AGTAGACAAAGGACATAAACAGACACTTTTCAAAAGAAGACATACGTGTG 4014
                          i i i       iv i  i     i  i  v        i    ivi  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_21859734_2   4015 ACCAACAAGCATATGAAAAAAAGCTCACCATCACTAATCGG 4055
                         i    i     i       i v     v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.06 (59 / 908), avg. gap size = 3.61 (213 / 59)  

1751 25.00 5.42 0.62  chrX_21859734_21864279.rev     3258  3737 (809)  C L1M4_orf2#LINE/L1   (357)   551    49  

C chrX_21859734_2   3737 ATGG-AATCTTGCCCAAAGTAATTTACAGATTCAATGCTATTTCTATCAA 3689
                             -   vi v      v i  i           i  v  ii       
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

C chrX_21859734_2   3688 ACTACCAATGACATTGTTCACAGAATTAGAAAAAGGCT-ATTCTAAAATT 3640
                          v v   iivi v  v  ii     v v  v  --   -  i        
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATT 146

C chrX_21859734_2   3639 CATATGGAATCAAAACAGAGCCCGAATAGCCAAAGCAATCCTAAGCAAAA 3590
                                  viiv  vi  v  v           i     i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

C chrX_21859734_2   3589 AGAACAAAGCTGGAGGCATCACATTACCCGATTTCAAACTATAGTATAAG 3540
                                  i      vv     i v   i        viv  v  i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

C chrX_21859734_2   3539 GCTGTAGTAACAAAAACAGTGTGG--CCGGTACAACTACGGATACATAGA 3492
                            ii     iv  i         -- i  i i  vv ii  i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chrX_21859734_2   3491 TCAATGGAA--------GCAGCCCAGAAATAAAGCTGCACACCAACAACC 3450
                                  --------iv  i           v iii   iiv iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

C chrX_21859734_2   3449 ATCTGATCTTTGATAAAGTCTACAAAAACAAGCAATGGGTAAAGGA---- 3404
                          vi    i  i  i  i vivv   i v  vv       v    i ----
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_21859734_2   3403 CT---------GTGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGATT 3363
                           ---------i           i      v  ?   i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_21859734_2   3362 GAAACTGGACCCATCCCTTTTATCATATACAAAAATCAACTCAAGATGGA 3313
                            ii       v v   ivi i             i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_21859734_2   3312 TTAAAGATGTAAATGTAAAACCTAAAACTGTGAAAACCCTT-GAAGAAAA 3264
                          i ?   iv         i v        i -     i   -        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

C chrX_21859734_2   3263 CCTAGG 3258
                          v    
  L1M4_orf2#LINE/    546 CATAGG 551

Transitions / transversions = 1.57 (72 / 46)
Gap_init rate = 0.02 (9 / 503), avg. gap size = 3.22 (29 / 9)  


2976 24.60 1.49 4.79  chrX_22006770_22013006.rev     4808  5746 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_22006770_2   4808 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4857
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22006770_2   4858 GGCCATACTGCCCAAAGTAATTTAGAGAGAGATTCATTGCTATCCCCATC 4907
                            v     v      v i  i  v   ----    vi  v     i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGA----TTCAACGCAATCCCTATC 96

  chrX_22006770_2   4908 AAGCTACCATTGACTTTCTTTCTTCACAGAA--TGGAAAAAACT-ACTTT 4954
                           iv v   ---i  vi    i  -i     --  -- v  i  - iii 
  L1M4_orf2#LINE/     97 AAAATCCCA---GCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCT 140

  chrX_22006770_2   4955 AAACTTCATATGGAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5004
                            v           ---------------------------- viv  i
  L1M4_orf2#LINE/    141 AAAATTCATATGGAA----------------------------ATGCAAG 162

  chrX_22006770_2   5005 GAGCCCATA-TAGCCAAAACAATCCTAAGCAAAAAGAACAAAGCTGGAGG 5053
                          ii    v -              i i iv  i          i      
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_22006770_2   5054 CATCACACTACCTGACTTTAAACTTTACTACAAGACTGCAGTATCCAAAA 5103
                         vv       v  ii i  i   vi         ii  i     vi   i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_22006770_2   5104 CAGCATGGTGCTGGTACCAAAACAGATATATAGACCAATGGAACAGAAC- 5152
                            ii    i    i iv ii i   i       i        i    i-
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_22006770_2   5153 -AGAGCCCTCAGAAATAACACCACACATCTACAACCATCTGATCTTTGAC 5201
                         -    i  --        vv   i    i  iiii  vi    i  i   
  L1M4_orf2#LINE/    313 GAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_22006770_2   5202 AAACCTGCCAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATG 5251
                           ivv      i v  vv            i  vvi  v  i  i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_22006770_2   5252 ATGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC--AAACTGGATCCCT 5299
                         i  i     v      v  ?   i     i  i v--  ii    i    
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_22006770_2   5300 TCCTTACACCTTATACAAAAATTAACTCAAGATAGATTAAAGACTTAAAC 5349
                         v   i     v                   i  i   i ?    i    i
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_22006770_2   5350 AAACTTAAGACCTAAAGCCATAAAAATCCTAGAAGAAAACCTGGGCA-AT 5398
                         i----     v     i i      v  i           v i  ?i- v
  L1M4_orf2#LINE/    511 G----TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_22006770_2   5399 ACCATTCAGAACATAGGCATGGGCAAAGACTTCATGTCCAAAACACCAAA 5448
                          i -   ivi  v v  vv i     v ii   v ivvi vi        
  L1M4_orf2#LINE/    557 ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_22006770_2   5449 AGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTAATTAAACTAA 5498
                             vvi          vv     v  i    v i ii v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_22006770_2   5499 AGAGCTTCTGCACAGCCAAAGAAACTACCACCAGAGTGAAGAGGCATCCT 5548
                          i i   i  ii vv v  i  v    i  vv i      i  i  v  i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_22006770_2   5549 AAAGAATGGGAGAAAATTTTTGCAATCTATCCATTTGACAAAGGGCTAGT 5598
                          v               v       vii  vi  i   i  i  i  v  
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_22006770_2   5599 ATCGAGAATCTACAAAGAACTTATACAAATTTACAAGAAAAAAACAA--- 5645
                            v     v  i        iv     v iv i  v     i    ---
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_22006770_2   5646 -CCTCATCAAAAAGTGGGCAAAGGCTACGAACAGACATTTCTCAAAAGAA 5694
                         -  iv  i?    i          v vi   i           v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_22006770_2   5695 GACATTTATGCAGCCAACAAACATATGAAAA-ATGCTCATTATCATCACT 5743
                           i  vi viii     i  i  i       -       vi    ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_22006770_2   5744 GGT 5746
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.69 (59 / 16)  


3117 27.62 0.99 0.66  chrX_22019868_22021963      699  1603 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_22019868_2    699 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 748
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22019868_2    749 GGCCATACTGCTCAAGGTAATCTATAGATTCAATGCCAACCCCATCAAGC 798
                            v     v i   iv i     i        i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_22019868_2    799 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTTACTTTAAACTTCA 847
                          v   iivi i  i  ii     -   -- v  i  v iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_22019868_2    848 TATGGAACCAAAAAGGAGCCCATATAACCAAGACAGTCCTGGGCAAGAAG 897
                                viiv  i   v  viv   i    i   i  i  iiv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_22019868_2    898 AACAAAGCTGGAGGCATCACACTACCTGACTTTAAACTTTACTGCAAGGC 947
                                i      vv       v  ii i  i   vi     i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_22019868_2    948 TGCGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATGTAGACC 997
                          i i    i   i    ii         i iv ii i   i  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_22019868_2    998 AGTGGAATAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACCACC 1045
                          i          i--    i  --        vv   i    i  ivii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_22019868_2   1046 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAAGATTCT 1095
                          vi    i  i     ivv  v   i v  vvv          ii  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_22019868_2   1096 GTATTTAATAAATGGTGTTGGGAAAACTGGCTCGCCATATGCAGAAAACT 1145
                         v v  i  i        i     v      v v?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_22019868_2   1146 GAACCTGGACCCCTTCCTTACACCTTAAACAAAAAATCAACTCAAGATGG 1195
                            vi         v   i     v  v       - i       i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGG 495

  chrX_22019868_2   1196 ACCAAAGACTTAAATGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAA 1245
                          i  ?    i           v   ii  i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_22019868_2   1246 CCTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTTATGTCT 1294
                          v i  ?i- v i -   iv   v v  vv i     v ii  iv ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_22019868_2   1295 AAAACACCAAAATCGATGGCAACAAAAGCCAAAATTGACAAATGGAATCT 1344
                          vi         v ivvi          vv     v  i    v i ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_22019868_2   1345 AATTAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 1394
                         v  i  iv v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_22019868_2   1395 ACAGGCAACCTAGAGGATGGGAGAAACTTTTTGCAATCTACCCATCTGAC 1444
                          v  i     i v  i          v v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_22019868_2   1445 AAAGGGCTAATATCCAGAATCTACAAAGGACTTACACAAATTTACAAGAA 1494
                           i  i  vi          v  i    i   ivi    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_22019868_2   1495 AAAAACAA----CCCCATGAAAAAGTGAGTGAAGGGTATGAACAGACACT 1540
                            i    ----   v  v?    i  i ii    i v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_22019868_2   1541 TCTTAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAA-ATGCTCA 1589
                            iv        i  vi viii     i  i  i       -       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_22019868_2   1590 TTTTCACTGGTCAT 1603
                         viv   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3073 22.44 9.17 0.36  chrX_22086308_22088810.rev     1184  2012 (491)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_22086308_2   1184 GATAGTCCATGTCCATGAGTAGGAAGACCCAATTTTGTCAATATG----- 1228
                             vi      i    ii v       ii   v    i  v   -----
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_22086308_2   1229 ------------------------TAATGCAATTCCAATGGAAATTCCAG 1254
                         ------------------------i  i     i  v  vi    i    
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_22086308_2   1255 CAAGTTATTTTGTGAATATCAACAATCTGACTCTAAAGTTTATATGGAGA 1304
                          vivi v     iii v  ii    v    ii     i  i       i 
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_22086308_2   1305 GGCAAAGGGCTCA------------CAGTATTGAA---GAAGAACAAAGT 1339
                         v    i  i i  ------------  i v     ---            
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_22086308_2   1340 -GGAGGATTGATACTACCTAACTTCAAAACTTACTACAGAGCTATAGTAA 1388
                         -      i v i   v  i  i                i     i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_22086308_2   1389 TTAAGACAGTGTAGTATTGGTGAAAGAATAGGCAAATAGATCAATGGAAC 1438
                          i          i   i   iiv   i    i  v              i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_22086308_2   1439 AGAAT--AGAG-CCA----------CGTAAATGTA--GTCAACTCATCTT 1473
                              --    -   ---------- i  v  v  --     i v  i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_22086308_2   1474 TGACAAAGAAGCAAAGTCAATACAATGGAGCAAAGATCATCTTTTTCAAC 1523
                         i     i iv  v   v v  v      i v  ii  vi      -    
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT-CAAC 405

  chrX_22086308_2   1524 AAACGGTGCTGGAACAACTGGATATCCACATGCAAAAAACTGAATCTAGG 1573
                            i        i           ?            i v    vi i i
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_22086308_2   1574 TATAGACCATACGGCTTTCACGAAAATTAAATCAAAATGAGTCATAGACC 1623
                         ivivv   vi  iv v vi  i        v        ii   ?     
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_22086308_2   1624 TGAATGTAACATGC-AAAACTATACAAATCCTAGAAGATAATATAGGACA 1672
                          i       v -  -         v  v  i       v  i     ?vv
  L1M4_orf2#LINE/    506 TAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_22086308_2   1673 AAATCTAGATGACCTTGGGTATGATAGTGACTTTTTAGATACAACACCAA 1722
                               vvi           vv ii i  ii  i       ii       
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_22086308_2   1723 AGGCACAATCCATGAAAGAA----TCGATACACTGCACTTCATTAAAATT 1768
                          i      v v ii      ---- v    v i  v       i      
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_22086308_2   1769 AAAAACTTACGTCCTGTAAAAGACAACATCAAGAGAATTAGAAGAAAAAC 1818
                                 vi  v  vi   i    vi       i i v i    v  v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_22086308_2   1819 CACAGATTAGGA-AAAATATTTGCAAAAGACATACTTGATAAAGGACTGT 1867
                               v i   -              vv i   ii      i     vv
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_22086308_2   1868 TATCCAAAATATACAAAGAACCTCTTAAAACTCAACAATAAGAAAACAA- 1916
                               i      i       -     v       i     i  i    -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAAC-TCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_22086308_2   1917 ---CCTGA---AAAAAGGGGCCAAAGATCTCAGCAGACACCTCACCAAAG 1960
                         ---  ii ---     v    v  i   i v ii     ii  v      
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_22086308_2   1961 A---TATACAAGTGGCAAGTAAGCATATGAAAAGATGTTCCACATCACAT 2007
                          ---       i    v i      i           i  v      ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_22086308_2   2008 ATCAT 2012
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.58 (112 / 71)
Gap_init rate = 0.02 (17 / 902), avg. gap size = 4.65 (79 / 17)  


1434 26.38 0.24 1.44  chrX_22170899_22172822      500   916 (1008)    L1M4_orf2#LINE/L1      274   685 (223)  

  chrX_22170899_2    500 TGGCATATGAGAAAAATAGGCACATAGACCAATGGGACAGAATAGACAAC 549
                                ----- ii    i  i     i      i i     v  v ii
  L1M4_orf2#LINE/    274 TGGCATA-----AGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_22170899_2    550 CCAGAAATAAACCCAAATACCTACAGACAACTGTTCTTCCACAAAGCAAA 599
                                        v i ii  ii v   i  v i   v    i vviv
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_22170899_2    600 CAAAAACATAAAGTGGGTAAAGGACGCTCTATTCAACACATGGTGCTGGG 649
                            i v   vv i    v    i iiv   v       v           
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chrX_22170899_2    650 ATAATTGGCAAGACACATGTAGAAGAATGAAACTGGATCCTCATCTCTCA 699
                          i  i   vv ?v      i i         ii    i  ii i   v  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_22170899_2    700 CCTTATATAAAAATCAACTCAAGATGGGTCAAAGACTTAAATCTGAGACC 749
                           v    i      i       i    i   ?    i     v i   v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_22170899_2    750 TGAAACCATTAAGATTCT-AGAAGATAACATTGGGAAAACCCTTCTAGAC 798
                          i    i  -  i i   -      v     v  ?iv  vi    vv   
  L1M4_orf2#LINE/    519 TAAAACTAT-AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_22170899_2    799 ATTGGCTTAGGCAAAGACTTCGTGACCAAGAACCCAAAAGCAAATGCAAC 848
                         v    v        v ii   v iivi v  vv         v v     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_22170899_2    849 AAAAACAAAGATAAATAGATGAGACTTAATTAAACTCAAAAGCTTCTGTG 898
                             iv   i   i   i  vi     v  i   v i    i   i    
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_22170899_2    899 CAGCAAAAGAAACAATCA 916
                          vv    i  v  v    
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCA 685

Transitions / transversions = 1.28 (60 / 47)
Gap_init rate = 0.01 (3 / 412), avg. gap size = 2.33 (7 / 3)  

 698 21.46 4.11 0.46  chrX_22170899_22172822     1215  1433 (491)    L1M4_orf2#LINE/L1      682   908 (0)  

  chrX_22170899_2   1215 ATCAACAGAGTAAA----CAACCCACAGAGTCGGAGAAAATCTTCTCAAT 1260
                              v i   i  ----           i v         v  iv   v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_22170899_2   1261 CTATATCTCCAACAAAGGACTAATATCTAGACTCTACAAGGAACTCAAAC 1310
                         ii    v  ii i  i     vi    i   v v  i  i      vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_22170899_2   1311 AAATCAGCAAGAAAAA-ACCAAT--CCCA-TCAAAAGGTGGGCTAAGGAC 1356
                           v   ii  v     -  v   --    - i?   ii     v     i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_22170899_2   1357 ATGAACAGACAAATCTCAAAACAAGATATACAAATGGCCAACAAACATAT 1406
                         v    i     vv    v   v                   i  i  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_22170899_2   1407 GAAAAAAATGTTCAACA-CAACTAATGA 1433
                              i -  i      -  ????????
  L1M4_orf2#LINE/    882 GAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (26 / 20)
Gap_init rate = 0.03 (6 / 227), avg. gap size = 1.67 (10 / 6)  


4385 15.70 3.30 1.93  chrX_22235948_22237818      500  1378 (493)    L1M4_orf2#LINE/L1       18   908 (0)  

  chrX_22235948_2    500 TTCATGGACTGGAAGAGTTAACACTGTTAAAATGGCAATACTCCTCAAAT 549
                                 i       v    i i      i             i     
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_22235948_2    550 TGACCTATAGATTAAACG---TCC--ATCAAAATTCAAACTGCCTATTTG 594
                            i   i     v    ---   --        i v i      v   v
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_22235948_2    595 GGGGAGAAATTGACAAGCTAATCCTGAAATTCATATGAGAATGCAAGAGA 644
                          v--               i     i           ii        i  
  L1M4_orf2#LINE/    118 GC--AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_22235948_2    645 CCCAATAGAGCCAAAAACAATCTTGAAAGAGAACAACAAGATTGGAGGAG 694
                             iv v        -           i    v     ii        v
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_22235948_2    695 TCACACTTCCAAATTTCAAATCTTACTACAAACCTACAGTAA---AGACA 741
                                   v         v           v         ---     
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_22235948_2    742 GTATAATACTGGCATAAGGACAGACACA--GATCAATGGAACAGAACTAA 789
                           i ii              i     i --           i    i i 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_22235948_2    790 GAACATAGAAATAAACCTATACATCTACACTCAATTGATTTTTGACAAGA 839
                           iivi           i      i  iiv            i      i
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_22235948_2    840 ATCCCAAGACCACTCAATAGGGAAAGAAAAGTTGTCTTAACAAACAGTGT 889
                         i v         i     i         v   iv i i      ii   i
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_22235948_2    890 TGGAAAAACTGGATATCCATGGGCATTAAAAAAAAAAAAAGTTAGACCAC 939
                            i v         ?   iiv   -----   i  vi     i    v 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCA-----AAAGAATGAAGTTGGACCCC 459

  chrX_22235948_2    940 TACTTAATACCATACA-AAAAATTAACTCAAAATGTAACAAAAACATAAA 988
                            i v i      i -                  v v  ? i  v    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_22235948_2    989 TGTAAGCGCTACAACTATGAAACTCTCAGAAGAAAACATAGGAGTAAATC 1038
                               v    v      i       i               ?       
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_22235948_2   1039 TTTCTGACTTTTTTATTAGGCA-TTGTTTCTTAGATACGACACCAAAACC 1087
                           iv    i  vv-i       - v            i          v 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_22235948_2   1088 -CAAGCAACCAAAGGAAAAGTAGACAAATTGAACTTCATCAAAACTAAGC 1136
                         -        v    i    i    i      i            i   --
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA-- 656

  chrX_22235948_2   1137 TTTTGTAAACTTTTGTGCTTCAAAGGACACCATGAGTGAAGTGAAACGAC 1186
                         ------                        i  v ivi        v   
  L1M4_orf2#LINE/    657 ------AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_22235948_2   1187 AACCTATAAAATGGGGGGAAATATTTGGAAATCATTTATCTGATAAGGGT 1236
                             i i i      i i         v       v             v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_22235948_2   1237 CTATTAAGCAGAATA----AAGAGCCCTTACGACTCATCAACAAAAGGAC 1282
                           vv  vv       ----    i i     i     vi  i    i   
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_22235948_2   1283 AAATAACC-AGCTTGAAAATGGGCAAAGGACTTGAATGGACATTTCTCCA 1331
                                 - ii ?i               i      i            
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_22235948_2   1332 AAGA---TATACAGATGGAAAATAGGTACATG--------CTCAACATCA 1370
                             ---      i    vv    i i     --------          
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_22235948_2   1371 TTAGTCAT 1378
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.85 (87 / 47)
Gap_init rate = 0.02 (16 / 891), avg. gap size = 2.88 (46 / 16)  


 821 23.91 6.92 16.14  chrX_22280746_22282561.rev      502  1325 (491)    L1M4_orf2#LINE/L1      161   908 (0)  

  chrX_22280746_2    502 AAAGACCCAATAAAAGTCAAGACAATCTTGTATGAGAGAAACAAAGCTAG 551
                          ii      i-  v  i   i         v vi   ii       i i 
  L1M4_orf2#LINE/    161 AGGGACCCAG-AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_22280746_2    552 AAGCTTGTCACCACTAGTAATC---AGACTTACTGTAAGACTACA----T 594
                          i vi vv   iv i--i   i--- i       ii  ii     ---- 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCC--CAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_22280746_2    595 TAAGACAGTGTGGTATCTCTG---CAAGGATAGACAAATAGACCAATAGA 641
                         i              ---   ---i           v     i    i  
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTA---CTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_22280746_2    642 AAATAAT--AGAGTT-AGAAATCGACTGACAAATATATGGACATTTGATT 688
                          v v   --     i-      vi  iv i v  v     v  v      
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_22280746_2    689 TACAATAAAGGTTGTAATATAA--CAGTATGAGAAAAAGTCTGGTCCTTT 736
                          v i i  i   vvi  v iv --  i i- i    i i --i   i   
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAAT--AGTCTTTT 401

  chrX_22280746_2    737 TAATAAATGG---------AA-----------------AAAAAATCATCT 760
                         i  i      ---------  -----------------   i   v vv 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_22280746_2    761 TA-ATC---ACCTTATACCACACACCAATATCAATTCCAGGAGGATTGTA 806
                          i- i ---    i i    i i  v  v  i  i  v iiv    ii? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_22280746_2    807 GATCTAATGATG-AAAAGCTAAA----TAAATCATCCAGAAAAAGA-ATA 850
                           i    --   -  i       ----    v viii    i  i -   
  L1M4_orf2#LINE/    502 GACCTAA--ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_22280746_2    851 GAA-TAG--CTTCATGATATTGTAATAGACATGATACTGTAATGATTTCT 897
                          i?-  i--    i   iv   viv   i  ----------   i     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCA----------ATGGTTTCT 589

  chrX_22280746_2    898 TAAACAAGACAC-AAAAACACCAGAAAGAAAAAAGTGATAGTCATTTTTT 946
                           i i v     -    i   v  v  v    i ----------------
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGA---------------- 623

  chrX_22280746_2    947 TAGAGATGGGGTCTCGCTATGTTGTCCAGGCTGGACTGGAACTCCTGGGT 996
                         - i i  i i--------------------- ii i    ----------
  L1M4_orf2#LINE/    624 -AAAAATAGA---------------------TAAATTGGA---------- 641

  chrX_22280746_2    997 TTAAGTGATTCCCCCACTTCAGCTTCCCGAGTACCTGGGACTACAGGTGT 1046
                         ----------------     ---  vvi v  ---iii   ----- v 
  L1M4_orf2#LINE/    642 ----------------CTTCA---TCAAAATTA---AAAACT-----TTT 664

  chrX_22280746_2   1047 GTGCCACCACACCAGGCTATATTTTTTAAGGTAGTAATTTCATCACAAGA 1096
                             -------------------  iv    -------------   ---
  L1M4_orf2#LINE/    665 GTGC-------------------TTCAAAGG-------------ACA--- 679

  chrX_22280746_2   1097 ACCATTAAGAGAGTAAAAAGGCAAGCCACCGATTGTTAGAAGATATTTGG 1146
                         - i  i    i   i     i   v    v  v  vv    i       v
  L1M4_orf2#LINE/    680 -CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_22280746_2   1147 AATACATATAAGTGTCAAAGGGCTTGT-TCATAAAATTCAGAAAGATCTC 1195
                           vv      vv  vi  i  i     -  -i i   vi v     v   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATC-CAGAATATATAAAGAACTC 777

  chrX_22280746_2   1196 CTGCAAATCAATGAGAACAAGGGAGACAACTCAGGAAAAAAA-ACGCGAA 1244
                         i i   v     i v  v   iv i i   i  ivv?     -iv  i  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_22280746_2   1245 AGTCTTGAACAGGCACTTAACTAACAAGAATAGCCAAATAGCCTATAAGC 1294
                         i vi     i  i  i  vv i  vi ii   vv     i   v      
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_22280746_2   1295 ATATATAAAGATGCTTAATTTCATTAGACCT 1325
                          i  iv         i  iv   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (122 / 72)
Gap_init rate = 0.05 (35 / 748), avg. gap size = 5.43 (190 / 35)  


2809 26.78 2.44 1.56  chrX_22305216_22308604     1998  2897 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_22305216_2   1998 TGGAAAAACATTCCGTGCTCATGGATAGGAAGAATCACTATCATTAAAAC 2047
                               i i  i  i  i        v      v i v   ii    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22305216_2   2048 AGCCACATTGCC-AAAGCAATTTACAGGTTCAACGCTGTTCCTATCAAAC 2096
                         i  v i i v  -   vii  i     i        vi i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_22305216_2   2097 TACCAATGACATTCTTCACAGAACTAGAAAAACT-ATTTTAAAATTCACA 2145
                          v   iivi v  i  ii     v v  v  i  -  ii         i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_22305216_2   2146 TGGACCCAAAAAAGAGCCCAAATAGCAAAGGCAATCTTAAGCAAAAACAA 2195
                             vviiv  ii  v  vi      v  ii       i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_22305216_2   2196 AAAAGGAGGGGGCATAATATGACTCTACTTCAAACTATATTACAGGGCTA 2245
                         v    vv  i  vv v i ivv i v i      viv  i    ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_22305216_2   2246 CAGTAACCGAAACAGCAGGGTACTGGCACTGAAACAGACACACAGACAAA 2295
                               i i i    iiv          iviii i     i i   iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_22305216_2   2296 GGGGACAGAATAGAGAGAGCCCAGAAATAAGGCTGCACACTTACAGCTAC 2345
                         v  i i     v     --i          iv iii   i   ii ii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAG--TCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_22305216_2   2346 CTGGTCTTCCACAAAACTGACAAAAACAAGCAATGGGGAAAGAATCA-CT 2394
                         i  i i   v    iiv  v   i v  vv               vi-  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_22305216_2   2395 ATTAAACAAATGGTGCTGGCATAACTGGCTAGCGATACGCAGAAGACTGA 2444
                         v  v               v i      v  ? v i i   i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_22305216_2   2445 AACTGGAACCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGATT 2494
                          ii    v    v   i                 i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_22305216_2   2495 TAAGACTTAAATGTAAAACTCAAAACTATAAAAACCCTGGACGATAACCT 2544
                         v?    i         i vii            vi i i  v  v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_22305216_2   2545 AGGAA-ATATCATTCTGGATATAGGAACTGGCAAAGATTTCATGACAAAG 2593
                            ?i- v   -   vv  iv v  iviv     v i    v --- i v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT---AGAT 594

  chrX_22305216_2   2594 ATGACA---AAAGCAATCGCAACAAAAGCAAAACTTGGCAAATGGGA-TT 2639
                               ---      vvv          v    v v ii    v   -  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_22305216_2   2640 CA-----ATTAAACTAACTTCTGCACAGCAAAAGAAACTATCAACAGAGT 2684
                           -----      --     i  ii vv    i  v        v i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAA--AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_22305216_2   2685 AAATAGACAACATATACAGAATGGGAGAAAATTTTTGCAAACTATGCCTC 2734
                         i  v       vi --                v        ii  iiv  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCA--CAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_22305216_2   2735 TGGCCAAGGTCTAATATCCAGCATCTATAAGGAACTTAAATTTACAAGCC 2784
                           iiv i  v  vi       v  v     i     i----      vi 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTC----TTACAACTC 786

  chrX_22305216_2   2785 AA---------AACAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAA 2825
                           ---------i     i     v   ?    i           iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_22305216_2   2826 CAGATACTCTTCAAAAGAAGACATACATGTGGCCAACAAACACATGAAAA 2875
                         i   i i ii  v        i     vi       i  i          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_22305216_2   2876 AAAGCGCAACACCCTTGTAGCA 2897
                         i v  v     i v????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.57 (36 / 14)  

 930 28.34 0.00 0.00  chrX_22305216_22308604     2888  3134 (255)  C L1M4_orf2#LINE/L1   (661)   247     1 *

C chrX_22305216_2   3134 TGGAAAAATATTCCATGCTCATGGATAGGAACAATCAATATCGTGAAAAT 3085
                               i    i     i        v    v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_22305216_2   3084 GGCCATACTGCCCGAATTAATTTATAGATTCAATGCTATCACCATCAAGC 3035
                            v     v   i    i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_22305216_2   3034 TACCATTGACTTTCTTTACAGAATTAGAAAAAACTACTTTAAATTTCATG 2985
                          v   vivi i  i   i     v v  v  iviv iii    v     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chrX_22305216_2   2984 TGGAACCAAAAAAGAGCCTGTGTAGCCAAGACAATCCTAAGCAAAAAGAA 2935
                              viiv  ii  v  v vi       i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chrX_22305216_2   2934 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATGCTACAAGG 2888
                              i      vv       v  ii i      viv i      i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

Transitions / transversions = 1.41 (41 / 29)
Gap_init rate = 0.00 (0 / 247), avg. gap size = 0.00 (0 / 0)  

 510 24.48 0.70 0.00  chrX_22305216_22308604     3245  3387 (2)    L1M4_orf2#LINE/L1      745   888 (20)  

  chrX_22305216_2   3245 AAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAA 3294
                           i  i  vi          v  i  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_22305216_2   3295 AAAAA-AAACAACCCCATCAAAAAGTTGGCAAAGGATGTGAACAGACACT 3343
                            i -   i     v  i?    i v          v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_22305216_2   3344 TCTCAAAAGAAGACATTTTTGTGGCCAATAAACATATGAAAAAA 3387
                             v        i  vivvi          i  i       i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.43 (20 / 14)
Gap_init rate = 0.01 (1 / 144), avg. gap size = 1.00 (1 / 1)  


1565 24.91 5.12 1.59  chrX_22376143_22378106.rev      502  1067 (897)    L1M4_orf2#LINE/L1      217   802 (106)  

  chrX_22376143_2    502 ACACTACCCTACTTCAAGCATTACTCTAAAGCCCCAGTAATCAAGACAGT 551
                              v   v i     ivv     vi     iv                
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_22376143_2    552 TTGATATTGGCA-AAACAGAAAAAAATGCATCAGTGAAACA--ATACAGA 598
                         v  i  i     -  iv v i v v  iv    i  i  i --  vv   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_22376143_2    599 GCCCCAAAATAAAACCACACAAATATAGTCAACTGATCTTTTACAAAA-T 647
                          i  vi       v   i   vv   i     i    i  iv    ii- 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_22376143_2    648 AACACAGGCAATTCAATGGAGAAAAGATAGTATTTTCAACACGTGGT-C- 695
                         iv  -  i v         i    ii     v         vi    - -
  L1M4_orf2#LINE/    367 GCCA-AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_22376143_2    696 -------CTGGACATCCACATGCAAGAAAAATTAATCTGGACACACACAT 738
                         -------     i ?          -  i   v  vi     v vi  v 
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAA-AAGAATGAAGTTGGACCCCTACCT 464

  chrX_22376143_2    739 TATACCCTTCACCAAAATTAACTCAAAATGGGTCACAGACCTAAATTTAA 788
                         i i   v vi  v                  i   ?          v   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_22376143_2    789 CATGTAAAACTATAAAATTCCTATAAGATAACATGAGAGAAAATCTAGAT 838
                         v vv             i  i  v    v     ii ? v      vvi 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_22376143_2    839 GGCCT-GTGTTCGGCCTTGACTTCTTCTGATACAATACCAAGGTAAGATG 887
                          i   - v   v   vv  ii     v-    ii i     iivv v v 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTA-GATATGACACCAAAAGCACAAG 613

  chrX_22376143_2    888 CA-TGAAAGAAATAA--GTT---TTTAATTTCAGTGAATTCCAA--CTTA 929
                           -ii       v  -- v ---  vi i    vii  v iv  --   -
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT- 662

  chrX_22376143_2    930 TCAGTTAT-CCGCAAACAAAAACT--TAAGAGAATAAAAAGACAAGTTAC 976
                         ----  i - iv    -ii v   --i    i i i         vii  
  L1M4_orf2#LINE/    663 ----TTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_22376143_2    977 AGA-TGGAATAAAATATTTGCAAAAGATATATCTGATAAAGGAGTT--AC 1023
                            -   i v              vv             i   v  -- i
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_22376143_2   1024 CCA-AATACACAAAGAACTCTTAAAAATCAACAATAAGAAAATAA 1067
                            -    i i            v  v    i     i  i i  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

Transitions / transversions = 1.16 (74 / 64)
Gap_init rate = 0.03 (20 / 586), avg. gap size = 1.90 (38 / 20)  

 418 22.73 1.82 0.00  chrX_22376143_22378106.rev     1364  1473 (491)    L1M4_orf2#LINE/L1      797   908 (0)  

  chrX_22376143_2   1364 AGACAAACAATATGATTAAAAGATGAGTAAAAGAGCTGAACAGACACCTC 1413
                                i  ivii   ?   i   i i   i  vi    i     ii  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_22376143_2   1414 ACCAGAGAAGATA--CAGATGGCAAATAAGCCTATGAGATGATGATCAAA 1461
                         v   i        --  i     v       vi    i v    v    v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_22376143_2   1462 ATCATATGTCGT 1473
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.01 (1 / 112), avg. gap size = 2.00 (2 / 1)  


3163 26.22 0.65 1.85  chrX_22386463_22392854     4981  5899 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_22386463_2   4981 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5030
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22386463_2   5031 GGCTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5080
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_22386463_2   5081 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5128
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_22386463_2   5129 TATGGAACCAAAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCCAAAAG 5178
                                viiv  ii  v  v v  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_22386463_2   5179 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5228
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_22386463_2   5229 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5278
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_22386463_2   5279 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5326
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_22386463_2   5327 ATGTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5376
                          vv    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_22386463_2   5377 CTATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGCT 5426
                           v  i  i          i   v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_22386463_2   5427 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5476
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_22386463_2   5477 TTAAAGACTTAAATGTTAGACCTGAAACCATAAAAACCCTAGAAGATACC 5526
                          i ?    i       v   v  i    i      vi i       ----
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA---- 542

  chrX_22386463_2   5527 ATGTTATTAACCTAGGCA-ATACCATTCAGGACAAAGGCATGGGCAAGGA 5575
                         ----- --   v    ?i- v i -   iv   vvv  vv i     v i
  L1M4_orf2#LINE/    543 -----A--AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_22386463_2   5576 CTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACG 5625
                         i   v ivv  vi            vvi          vv     v  ii
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_22386463_2   5626 AATCGGATCTAATTAAA-CTAAAGACTTTCTGCACAGCAAAAGAAACTAC 5674
                            i   ii v  i   -i    i     -  ii vv    i  v    i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTAT 683

  chrX_22386463_2   5675 TATCAGATTGAAAAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCT 5724
                         i vv i v       i     i   i             v       vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_22386463_2   5725 ACTCATCTGACAAATGGCTAATATCCAGAATCTACAATGAACTCAAACAA 5774
                          ivi      i  iv i  vi          v  i  v      vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_22386463_2   5775 ATTTATAAGAAAAAAACAAACCACCCCATCAAAAAGTGGGCAAAGGATAT 5824
                         v iv    v     i     iv    v  i?    i            v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_22386463_2   5825 GAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGA 5874
                            i     i     v        i  vi viii     v ii       
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_22386463_2   5875 AAAAATGCTCATCATCACTGGCCAT 5899
                            i       v     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


3051 27.97 0.55 0.55  chrX_22454126_22460499     4974  5881 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_22454126_2   4974 TGGAAGAACATTCCATACTCATGGATAGGAAGAATCAATATCATGAAAAC 5023
                              ii i  i    ii        v      v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22454126_2   5024 GGCCATACTGCCCAAGGTAATTTTTAGATTCAATGCCATCCCCATCAAGC 5073
                            v     v     iv i  i vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_22454126_2   5074 TATCAATGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCT 5121
                          vi  iivi i  i   i     -   -- v  i  - iii    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_22454126_2   5122 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5171
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_22454126_2   5172 AACAAAGCTGGAGGCATCACGCTACCTGACTTCCAACTATACTACAAGGC 5221
                                i      vv    i  v  ii i   v  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_22454126_2   5222 TACAGTAACCAAAACAGCATGATACGGGTACCAAAACAGAGATATAGACC 5271
                                 i   i    ii  i   v  i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_22454126_2   5272 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCAGACATCTACAACC 5319
                                i    i--    i  --        vv   v    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_22454126_2   5320 ATCTGATCTCTGACAAACCAGACAAAAACAAGAAATGGGGAAAGGATTCC 5369
                          vi    i ii     ivvv v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_22454126_2   5370 CTATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGGAAGCT 5419
                           v  i  i          i   v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_22454126_2   5420 GAAACTGGATCCCTTCCTTACACCTTATACAGAAGTTAATTCAAGACGGA 5469
                            ii    i    v   i     v      i  i    i    i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_22454126_2   5470 TTAAAGACGTAAATCTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5519
                          i ?    v     v v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_22454126_2   5520 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5568
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_22454126_2   5569 AGACACCAAAAGCAATGGCAACAAAACCCAAAATTGACAAATGGGATCTA 5618
                         v             vvi         vvv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_22454126_2   5619 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 5668
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_22454126_2   5669 CAGGCGACCTACAGAATGGGAGAAAATTTTTACAATCTACCCACCTGACA 5718
                         v  i i   i                 v   i   vii ivi i    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_22454126_2   5719 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5768
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_22454126_2   5769 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5818
                           iv    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_22454126_2   5819 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5868
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_22454126_2   5869 CACCACTGGCCAT 5881
                           i  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (150 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 263 29.23 0.00 0.00  chrX_22478287_22480020.rev      480   544 (1190)    L1M4_orf2#LINE/L1      208   272 (636)  

  chrX_22478287_2    480 GGAGAGCTTTCCCTTCCAAAAATCAAGACTTATTATAAAGCTGTTACAAC 529
                             ii  iv v     v  vv    i     i  i      iivii  i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_22478287_2    530 TAAGACAATGTGGTA 544
                         i      i       
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTA 272

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.00 (0 / 0)  

 588 29.75 8.74 4.54  chrX_22478287_22480020.rev      653  1247 (487)    L1M4_orf2#LINE/L1      289   908 (0)  

  chrX_22478287_2    653 CAAATTGGCCAACAAATTAGGATAAAGACCCAAGAAATGTGAATGCATA- 701
                           v  v ii   iii v   i  vi   vi v      i--  iv    -
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA--AACCCATAC 336

  chrX_22478287_2    702 ---TATAG--AACTTTGTTATATGACAGAGGTGTCCTTGCTTATAACTAG 746
                         ---   i --  --   v v vi    ii    i ------- vi  i v
  L1M4_orf2#LINE/    337 ATTTATGGTCAA--TTGATTTTCGACAAGGGTGCC-------AAGACCAT 377

  chrX_22478287_2    747 GCAATAG--AAGGA-----CTCTTTAGCAAATGGTACTGGGAGAAAATGG 789
                         v    i --  i  -----  i  i i        i      v  v-   
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC-TGG 426

  chrX_22478287_2    790 TTGTCCATGTGGAAAATGTAAAGCAATTGGATAGTTACTTAAATTGCAAC 839
                         v i?   ii  v    - -  v v i     ivvi   i v ----  v 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAA-G-AATGAAGTTGGACCCCTACCTCA----CACC 470

  chrX_22478287_2    840 ATTCATAAAAACTAATTGCAGAA-GCATTGAAGACTCTAATGTGAAATGC 888
                           vi i     i   i -  i  - v  ii?    iiv     i i -  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACT-CAAAATGGATCAWAGACCTAAATGTAAGA-GC 518

  chrX_22478287_2    889 -AAAACGTTAAACATTTTC----GAAAATATAGGA-TAA-CCTTTATGAC 931
                         -     vv    - i i i----     i     ?-   -i   ii    
  L1M4_orf2#LINE/    519 TAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_22478287_2    932 CTTCGTGCAGG-GACAGTTTTTTAA----GACAGAAAAAAGATCTG---- 972
                            v vvi   -i ii    i   i----    vv    iv ivv ----
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_22478287_2    973 ---AGTATAA---GATC--TTGGACTGCTCTGTAGTTAAGTATCGCTATT 1014
                         ---  v v  ---   v--       v viiiv i    iv iivi i v
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_22478287_2   1015 CATCAAAAAACAAACTAGAAAAAGAGGGAAAATG-AAGCCACTAACTGGG 1063
                          v     ii   --   vv  i i  v     vi-  v    vi v    
  L1M4_orf2#LINE/    668 CTTCAAAGGACA--CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_22478287_2   1064 AGAAGCTATTTGTAAAGCAAATA----ACAAAGGATTAGTGACCAGAACA 1109
                             iv      i   v  v   ---- i  i   i v  iv      i 
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_22478287_2   1110 AGTCAGAAA----TATAACTGAATAAGATAAACATGAACAACCCAATAGG 1155
                         vi v ii  ----  i    v     v v   v ii  i        v?i
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_22478287_2   1156 AAAGTGGGGTAAATACATAAAACAGGCACTTCACAGACAATGAA-ATATC 1204
                            i    -i   vivv vi  i  i  i   v ---   v   -    v
  L1M4_orf2#LINE/    816 AAAATGGG-CAAAGGATTTGAATAGACATTTCTC---CAAAGAAGATATA 861

  chrX_22478287_2   1205 TA--TAGGCGATAAACA-ATGAAAAGATTCACAA-ATCTTTTACTAA 1247
                         i -- i v i    i  -          v v   -   v????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (97 / 76)
Gap_init rate = 0.05 (34 / 620), avg. gap size = 2.32 (79 / 34)  


1495 19.88 10.43 16.02  chrX_22491566_22493364      502  1306 (493)    L1M4_orf2#LINE/L1      149   908 (0)  

  chrX_22491566_2    502 TATGGAAAAAACAAAGAATC-AGAAAAGTACAAACAACTTTGTAGAAGAG 550
                                 vi-   i i i -    v  ivv      ii   v i    i
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_22491566_2    551 GAACAAAGTTGAAGGATTTATACTACCTAATTTCACAGTTTACAATAAAG 600
                                    i    i i i   v  i       v ii    v i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_22491566_2    601 TGACAG----CAAGGCC-TGTGGCACTGGTGCAAGCCTAGACATATAGAT 645
                         iv    ----    i v-     i     iii   vv             
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_22491566_2    646 CAATAGA----------GAGTTCAGAAATACATCTGTATATATATGTGTG 685
                             i  ----------    i        v i ii  i  v    ----
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG---- 343

  chrX_22491566_2    686 GATATTGGCAAATTGATTTTGAACAAAGGCGCAAAGGTAATTCAATGGAA 735
                         ------- iv          vi    i  i  v   iiv         ii
  L1M4_orf2#LINE/    344 -------GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_22491566_2    736 AGAGAGTACTCTCAACAAGTGGACAAATGGTATTGGGACAATAGGAAGGA 785
                          i   i  v   ivv   -----        ii        iv   ----
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAA-----CAAATGGTGCTGGGACAACTGGA---- 427

  chrX_22491566_2    786 AGGAAGGAAGGAAAGAAGGAAAGAAGGGAGGGAGGGACAGAATAAAGAGA 835
                         -------------------------------v ?vv   --- -------
  L1M4_orf2#LINE/    428 -------------------------------TAKCCACA---T------- 436

  chrX_22491566_2    836 AAGAGAAAAAAGAGAAAAGAGAGAAGAAAGAAAGAAAGAGAGAGAGAGGA 885
                         ---- v    ----------------------------------------
  L1M4_orf2#LINE/    437 ----GCAAAA---------------------------------------- 442

  chrX_22491566_2    886 AGGAAGGAAGGAAGGAAGGACGGGGAACATCGATTCTTTCTTTACACAAT 935
                         ----------   v    v---------- v  ii i v i i    v  
  L1M4_orf2#LINE/    443 ----------GAATGAAGT----------TGGACCCCTACCTCACACCAT 472

  chrX_22491566_2    936 ATGCAAAAATTAACTCTAAATGAATCATAGACCTAAATGTGACA-CT--- 981
                           i             v     i    ?            i v -  ---
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_22491566_2    982 -TTATGAAACTTCTAGATGAAAATATAGAAG-ACATTTTTGTGTTCTTGG 1029
                         -i   i     ii    v     i    i? - v  i  i   vi     
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_22491566_2   1030 GTTAAGCAAAGATTTGCTATATAGGATATAAAAATTGCAAATCATAAAAT 1079
                             i    v i   vi  v   v  i iv    vii   iiv i    v
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_22491566_2   1080 AAAAA---------TTGGACTTCATAAAAATTTAAAATGTCTGCTCTTTG 1120
                              ---------           v      v    iv i  iv   ii
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_22491566_2   1121 AAAGACAC----AAGAGAATGAACAGAGAAGGCACAGACTGAGAGAGAAT 1166
                           i     ----    i i    v   v  vv      v  i    i   
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_22491566_2   1167 ATTTTCAAA-CACTTGTCTGATAAAGGACTT------------------- 1196
                             v    -  iv i        i      -------------------
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_22491566_2   1197 ---------------------------CAAATAACTTGATTTTTTAAAAA 1219
                         ---------------------------        iii   ?---     
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW---AAAAA 819

  chrX_22491566_2   1220 TGGCCAAAA-ATTTGAATAAACATTTTATCAAAGAAGATATGTAAATAAC 1268
                            v    i-         i      ivi            ii    ii 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_22491566_2   1269 AAATAAGCATATGCAT-GCTGCTCAACATCATAAGTCAT 1306
                         v        i   v v- v            ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (95 / 61)
Gap_init rate = 0.03 (22 / 760), avg. gap size = 9.68 (213 / 22)  


1775 17.02 5.32 1.60  chrX_22555490_22557431.rev      502   877 (1065)    L1M4_orf2#LINE/L1      242   631 (277)  

  chrX_22555490_2    502 ACAGAGCCATAATAATAAAAAT--TGCGGTACTGGCTACTAAGGTCTACT 549
                            i   i i i    v  i i--  i         - -     --- - 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC-A-TAAGG---A-T 285

  chrX_22555490_2    550 AGACATTTAGACCAGTAGAATAAAATAGAAGGCCCCCAAATAAGTCTTTG 599
                               v    i  i i     i   v  ii i  vv      ii iv i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_22555490_2    600 CATATATAATCAAATGATTTTTGACAAGGGTACCAAGAAAATTCAGTGGG 649
                            v   ii    v       i         i      vv     i    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_22555490_2    650 GAAAAGAGAGTCTTTTCAACATATGGTGTTGGGAAAACTGGATACCCACA 699
                             ii v             v      i     v         ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_22555490_2    700 TGCAAAAGAATAAAATTGGATATTTACCT---------TACAAAAATTAA 740
                                    i  i     ivii     ---------            
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_22555490_2    741 CTCAAAATGGATGAAAGACCTAAATGTAAGAGCTAAAACGATAAAGCTCT 790
                                     v ?                        v     i    
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_22555490_2    791 TAGAAAAAAACATAGAGGGAAA-----GT----TTTGGTTTGGCAATTAT 831
                              i         i? v   -----  ----  v    v      vi 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_22555490_2    832 TTCTTGGATATGACACCAAAAGTACAGGCAACAGATGAGAAAATAG 877
                              i                i   i      i v  i       
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

Transitions / transversions = 1.90 (40 / 21)
Gap_init rate = 0.02 (8 / 390), avg. gap size = 3.25 (26 / 8)  

1351 16.67 2.08 0.00  chrX_22555490_22557431.rev     1164  1451 (491)    L1M4_orf2#LINE/L1      615   908 (0)  

  chrX_22555490_2   1164 AAAAAAAAAAAAAATAGATAAATTGGACCACATAAAAGTGAAAAACTTTT 1213
                           v    i                    iv   v   i v          
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_22555490_2   1214 ATGTATCAAAGGACACAATCAACAGAGTGAAAAGGCAACCCATGAAATGA 1263
                         i  iv           v     v i         i       iii    i
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_22555490_2   1264 GA-AAAATATTTGCAAATCATATATCTGATAAGGGCCTAATATCTAGGAT 1312
                           -                                v  vi    i  i  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_22555490_2   1313 ATG-AAAGGTCTCCAACAACTTGACAAGAAAGA-ACACATAACCCAATTT 1360
                           i-    iv   iv      ii i  v   i -   v           ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_22555490_2   1361 AAAAATGGGCAAAGAACTTCAGTAGACATTTTTCCAAA--AGACATGAAA 1408
                                       i i  v i         i      --   i  iv  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_22555490_2   1409 ATGTTCAACCA-CACGTGAAAAGATGCTCAACATCACTTTCATT 1451
                            vi   iv -   i                    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (30 / 17)
Gap_init rate = 0.02 (5 / 294), avg. gap size = 1.20 (6 / 5)  


3168 26.30 1.22 0.88  chrX_22568007_22572759     3356  4260 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_22568007_2   3356 TGGAAGGACATTCCACGCTCATGGGTAGGAAGAATCAATAGCCTGAAAAT 3405
                              i  i  i   i i      i v      v i    viv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22568007_2   3406 GGCCATACTGCCCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 3455
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_22568007_2   3456 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3503
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_22568007_2   3504 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 3553
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_22568007_2   3554 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAA--CTACAGTACAAG 3601
                                i      vv    i  v  ii i      --i   --     i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAA 246

  chrX_22568007_2   3602 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 3651
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_22568007_2   3652 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAA 3699
                         i        i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_22568007_2   3700 CCATCTGATCGTTGATAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 3749
                         i  vi    iv i  i  ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_22568007_2   3750 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 3799
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_22568007_2   3800 CTGAAACTGGATCCCTTCCTTACACCATATATAAAAATTAATTCAAGATG 3849
                         v    ii    i    v   i          i         i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_22568007_2   3850 GATTGAAGACTTAAATGTTAGACCTAAAACCATACAAACCCT-AGAAGAA 3898
                            ii?    i       v   v       i   -    i  -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAA 543

  chrX_22568007_2   3899 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 3947
                            v    ?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_22568007_2   3948 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGTGAT 3997
                         v  vi            vvi          vv     v  i    vv  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_22568007_2   3998 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATTATCAGAGT 4047
                         i v  i   v v  i i   i  ii vv    iv v     i vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_22568007_2   4048 GCACAGGCAACCTACAGAATGGGAAAAAATTTTTGCAATCTATCCATCTG 4097
                          v v  i     i           i     v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_22568007_2   4098 ACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAG 4147
                          i  i  i  vi          v  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_22568007_2   4148 AAAAA---AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 4194
                              ---   i     v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_22568007_2   4195 CTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCT 4244
                         i     v        i  vi viii     i  i  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_22568007_2   4245 CATCATCACTGGTCAT 4260
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


1964 25.09 6.68 5.86  chrX_22597603_22600727.rev     1784  2636 (489)    L1M4_orf2#LINE/L1       49   908 (0)  

  chrX_22597603_2   1784 ATGTCAATTCTCTCCAAATTAATACATAGATTGAATGCAATGTCTATGAA 1833
                            v    v   i       i  vi i     v  i     vi    v  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_22597603_2   1834 AATAC-AGGAAGCTTTATTGTAAAAATAGGCAACATTATTCTAAAATGTA 1882
                            v -  vviv    v   i i    v i   vv v  i       vi 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_22597603_2   1883 TCTGGGAAGGCAAAGTACT-ATAATAGCTAAAACCATTTTGAAAAAGAAT 1931
                          v   i  v    i v  i- v      i     v  i           v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_22597603_2   1932 AATATTGTAAGAGGAATCAGTCTATGCTATTTAAAGACTATATT-----G 1976
                           i vv  vi     v   vv  viv v    v  i   -  i ----- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_22597603_2   1977 CTACAATAATCAAGATTATGTGGTA------------TAGATCACATAGA 2014
                              i         ivi       ------------    -  i     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA-CATATAGA 296

  chrX_22597603_2   2015 TCAATGGAACA----TAAGAATTCAGAAATAGACCAACACATATATGCCA 2060
                                  i ---- i   i i        i   v i    v    ---
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG--- 343

  chrX_22597603_2   2061 AGCTGTTTTTAAAAAATTTATTTTATTTTGTTTTATTAGATATTGAAAAG 2110
                         ----  i-------    v     v-------------  i ---- ii 
  L1M4_orf2#LINE/    344 ----GTC-------AATTGATTTTC-------------GACA----AGGG 365

  chrX_22597603_2   2111 TTATAGTTATATT-TTCAGTGGAGGAAAGATAGCCTTTTAAACAAATGGT 2159
                          vvi --- v ii-    i   i i  ii    i     v          
  L1M4_orf2#LINE/    366 TGCCA---AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_22597603_2   2160 ACTGGAGCAATTGGTTGTCCATA-------------AGTT---------- 2186
                         i    ii   i   v i?   i -------------    ----------
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_22597603_2   2187 -TCATACCTTATAGAAAAATTAACTCAAAATTGAGCACAGACTTAATTAT 2235
                         -   i   v    v                 v  v  ?    i   v i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_22597603_2   2236 AACACAAAAACAAAACAAAACTATCAAACCTCTGGAAAATAATCATAGGT 2285
                           -----i i ----i        v    iii i   i v  -      ?
  L1M4_orf2#LINE/    513 AA-----GAGC----TAAAACTATAAAACTCTTAGAAGAAAA-CATAGGN 552

  chrX_22597603_2   2286 AATAATAATCAGGATCTAAGGCTAAGAAAAGTATTATTTGACTGGGTACC 2335
                         ivv   vv  iv  i  vi  i  i v  v vv  v  v  ivv ii   
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_22597603_2   2336 AAAAGGATAATTCATAAAAGGAAAAACTGACAAATCATAATTTATACAAA 2385
                              v i  viv i     i     iv  i    iiv v  i  vv   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_22597603_2   2386 TTAAAGTTTTAGCTTTGTGC-----AATACTCTGTTAATATGATGAAAAG 2430
                              ivi  ----      ----- iv  v  i i  v vii       
  L1M4_orf2#LINE/    653 TTAAAAACTT----TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_22597603_2   2431 GTAAGTTACAAAGTGGGAGAAAACATTTGAAAATCACATATCTGACAAAG 2480
                         ii  vii   i i          i     v      i        i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_22597603_2   2481 GACT-GTATGTAGAATATATAAAGAACTCACAAAACTCAACAGTAAAGAA 2529
                             -    vi                  vi v       i i    i i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_22597603_2   2530 GCAAACAATCCAATGAGAACATGAGGAAAACACACGAC---ACTTTTCAC 2576
                         i    i  i     v?i  v   i v   iv ivi  v---  v    v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_22597603_2   2577 CAAAGAAGGTATACACATGGCAAATAACCATATAAAAAGATGTTGAACAT 2626
                                 i      v     v     v  i  i        i v     
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_22597603_2   2627 TTGCATCCAT 2636
                         iv????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.23 (116 / 94)
Gap_init rate = 0.03 (22 / 860), avg. gap size = 4.86 (107 / 22)  


1800 27.72 3.62 1.10  chrX_22608469_22610095.rev      502  1136 (491)    L1M4_orf2#LINE/L1      258   908 (0)  

  chrX_22608469_2    502 CAAGACAACATCTTA-TAGAAAAATGAGTGAACACATAGGTCAGTGGAAC 550
                                iii vv  - i v v  v  - ii   i    i   i     i
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAATGGAAT 306

  chrX_22608469_2    551 AGAATGAAGAGTCTAGAAAGTGACCCACCATAAGTACACCCAGCTTATTT 600
                              vi      i     vvi     i- i vv  iivi  ii v    
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGGTCAATTGATTT 355

  chrX_22608469_2    601 TTGTCATAGGTGAAAAAGCAATTCAATGGAGGAAGAATGATATTTTCAGT 650
                          i v  vi    vv  ii v         i i      ii v      ii
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_22608469_2    651 AAATCATGTTGGAA-AATTGGTTATCCGTGGACCAAA-AATAATCCTAAA 698
                             vi  i   i -  i   v  ?  iiivi v   -   i vvi ii 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_22608469_2    699 TCTAAATCTCATACCTTATACAAAGATTAACT-GAAATGG--CAGAGATC 745
                         i ivv i    i   v        i       -i      --  ?   i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_22608469_2    746 TAAATGTAAACAGTAAATATATAAAACTTTTATAAGAAAACACAGGAGAA 795
                                  iviv    vv         i   v         i   ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_22608469_2    796 AACCTTCATGAT-TTGAGTTAAGCA--GAGTTTTTAGTCACAATACCAAA 842
                           i    i   i-   i    i   -- iv  i    vi ii i      
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_22608469_2    843 -GCGTAAGCCATAAAAGAAAATAT-GATAAATTTGTCTTTATTAAAAAAT 890
                         -  ii    v i         v  -        v v   i  i    ---
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA--- 652

  chrX_22608469_2    891 TTAAA--CTTTTACTCTGT----GAGACTATTAAGAGGATGAGAAGACAA 934
                              --     iiv  vi----  v     i    iii   i       
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_22608469_2    935 GCCACTGGCTGTAAGAAAAATTTCTACAGATCACATATCCAACATGAAGC 984
                         v    v iv  vi      - v i i  i    i     ii i v iii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_22608469_2    985 TTGTAACCAGAATATCTGAATAACTCTCTA-AACTCAAAGGTAA---GAT 1030
                              v         v i  v      -  -       vii   ---  i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCT-TACAACTCAATAATAAAAAGAC 800

  chrX_22608469_2   1031 AG-CAATCCCATTAGAAAATGG-CAAAAAACTTGATCAGACACTTAAACA 1078
                          i-i  i  v   ?i       -    ii i    vi     i  vvv  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_22608469_2   1079 AAGAGGATATGCGGAGGACAAATAAATACATAAAAATATGTTCAACATTA 1128
                             i     i ii v i v     ii    i    v   i       i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_22608469_2   1129 TTAGCCAT 1136
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.87 (112 / 60)
Gap_init rate = 0.03 (20 / 651), avg. gap size = 1.50 (30 / 20)  


2946 24.84 2.52 3.17  chrX_22643651_22650378     5322  6235 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_22643651_2   5322 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCATTATCATGAAAAT 5371
                               i i  i     i        v      v i v   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22643651_2   5372 GGC---------CACAT--------AGATTCAATGCTATCCCCACCAAGC 5404
                            ---------  v  --------        i  v     i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_22643651_2   5405 TACCATTGACTTTCTTCACA-AAATTAGAAAAAACT-ACTTTAAAGTTCA 5452
                          v   vivi i  i  ii  -     i-- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_22643651_2   5453 TATGGAACCAAAAAAGGG-CCCACA-TAGCAAAGACAATCTTAAGCAAGA 5500
                                -- viv     -    v -    v  i        i iv    
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_22643651_2   5501 AGAACAA-GCTGGAGGCATCATGCTGCCTGACTTCAAACTATACTACAAG 5549
                                - i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_22643651_2   5550 GCTACAGTAAACAAAACAGCATGGTACTGGTACTAAAACAGATACATTGA 5599
                                   v   i    ii         i iv ii i   i i  v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_22643651_2   5600 CCAATGGAAAAGAACAGAGGCCTCAGAAGTAATGCCACACATCTACAACC 5649
                         i        v    iv   ivii     i   vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_22643651_2   5650 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5699
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_22643651_2   5700 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCACATGCAGAAAACT 5749
                           v  i  i        i     v      v  ?         i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_22643651_2   5750 GAAACTAGATGCCTTCCTTACACCTTATACAAAAATTAACTCAAGACGGA 5799
                            ii i  iv   v   i     v                   i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_22643651_2   5800 TTAAAGACTTAAACCTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5849
                          i ?    i    iv     v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_22643651_2   5850 CTAGGTAATACCATTGGACATAAAATCCCTAGTAAAACCTAGGACACAGG 5899
                         v    ?i-------------    --i i v  i --   v  ii-----
  L1M4_orf2#LINE/    547 ATAGGNG-------------TAAA--TCTTCGTGA--CCTTGGGT----- 574

  chrX_22643651_2   5900 CATGGGCAAAGACTTCATGACTAAAACACTAAAAGCAATGGCAACAAAAG 5949
                         -- i     v ii   v iiv  vi    i       vvi          
  L1M4_orf2#LINE/    575 --TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_22643651_2   5950 CCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCAGTGCAGCA 5999
                         vv     v  i    v   ii v  i   v v  i i   iv    vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_22643651_2   6000 AAAGAAACTATCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAAT 6049
                           i  v       vv i      v  i     i                 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_22643651_2   6050 -TTTTCAAATCTATCCATCTGACAAAGAACTAATATCCAGAATCAACAAG 6098
                         -   v      -  vi      i  i i   vi          vv i  i
  L1M4_orf2#LINE/    723 ATTTGCAAATC-ATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_22643651_2   6099 GAACTTAAACAAATTTACTAGAAAAAAACAAACGACCCCATCAAAAAGTG 6148
                              ivv    v iv iv v     i     ii    v  i?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_22643651_2   6149 GGCGAAGGATACGAACAGACACTTCTCAAAAGAAGACATTTATGTGGCCA 6198
                            i      vi   i     i     v        i  vi vi      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_22643651_2   6199 ACAAACATATGAAAAAAAGCTCATCATCACTGGTCAT 6235
                          i  i  i       i v     v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (134 / 89)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.47 (52 / 15)  


2995 23.21 3.21 1.55  chrX_22650901_22653532     1292  2131 (501)    L1M4_orf2#LINE/L1        1   854 (54)  

  chrX_22650901_2   1292 TAGAAAGACATCCCATTTTCATAAATCAAAAGATTTAAGATTGTTAAGAT 1341
                          i      i       v     ii  iii    i    v           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22650901_2   1342 GGTAATAAACCCCATATGTATCTAAAGATTTAATATAGTCCATATCAAAA 1391
                           i    vv     v  vv     v     i  iii i   v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_22650901_2   1392 TTCCAACAGGCTTTCCTACAGTAACTGA-AAGTGTAATTTGAAAATTTAT 1440
                          i   i v v    ii i   v  i   -   i- i  iiv      i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_22650901_2   1441 ATGGAAATGCAAATGATTTAGAACA-CCACAAAAGCATTGAAAAATAA-- 1487
                                     iv  iii    i -   v  v iiv        v  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_22650901_2   1488 -TAAAGTTAGAGAATACGTACTACCCAATTTCAAACACTCAT---GAAGC 1533
                         -i      i   i iv ii   v            -   i i---i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-ACTTACTACAAAGC 248

  chrX_22650901_2   1534 CACAATAATCCAGACAGTACGGCACTGGCCCAAGGATAGACATGTAGATC 1583
                         i   i     v       ii  i      vi            i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_22650901_2   1584 AGTGGAAAAGAATTTAAAAACCAGAAATAAATCCCTGCATTTATGATCAA 1633
                          i     v      v i iv           i  v i        i    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_22650901_2   1634 CCGATTTTTGACAAAACAGCTAAGAT-ATATCAACAGGAAAAGGATAGTC 1682
                         ii      i     iivv  i    i-  -    ii  i    i      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGTC 397

  chrX_22650901_2   1683 TCTTCAACAAACTTAATAATAATAATAATAAAAGA---AGAGG-AGGAGG 1728
                          i         -- ii iv ii-i i  ivii v --- v v - ii  i
  L1M4_orf2#LINE/    398 TTTTCAACAAA--TGGTGCTGG-GACAACTGGATAKCCACATGCAAAAGA 444

  chrX_22650901_2   1729 AGGAACTTTGGCTCTTAAC-CA-ACCACATACATTTAAAAAGTAAT--GA 1774
                          v   v  v i i i  v -  -    i     ----    v   i--i 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACA----AAAATTAACTCAA 490

  chrX_22650901_2   1775 AATAGATAACAGACCTAAATGTAAAAGCTGAAACTATAAAACTTCTGGAA 1824
                            i   v ?              i    i             ii i   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_22650901_2   1825 GAAAACATAGGAGAAAATATTCATGACCTTGGTTTAGGCAGCG-TTTGT- 1872
                                    ? v    v   i         v       ii -   v -
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_22650901_2   1873 -GATATGACTTCAAA-GCACTATTCATAAAAGAACAAATTGACAAATTAG 1920
                         -        vi    -    v viv i       v    v  i     i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_22650901_2   1921 ACTTCATCAAAATAAAAACCTTTTGTACTTTAAAAGATATCTCTATTTAG 1970
                                      v    v       i   i   i  i ---    iv  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA---CTATCAAG 687

  chrX_22650901_2   1971 AGAATGGCAAGCCTCATCATAGATTGGGAGAAAATATTTTCAAATCATAT 2020
                          i i  iv   v vvvi  i   v               v          
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_22650901_2   2021 ATATGATATAGGACCTTTATCCAGAATAAA-GAAGAACACTTCAAATTCA 2069
                           v     vi    i v           v -i      v   vv  i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_22650901_2   2070 ATAA---AAATATAAACAGCCCACTT--GAAATGATCAAAATATTTGAAT 2114
                             ---   v i   i i    v  --i     iv    iv        
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_22650901_2   2115 TGACATTTCACGAAAAA 2131
                         v        v v   i 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGA 854

Transitions / transversions = 1.64 (120 / 73)
Gap_init rate = 0.03 (23 / 854), avg. gap size = 1.74 (40 / 23)  


 434 16.46 3.80 0.00  chrX_22678239_22680366.rev        2    80 (2048)    L1M4_orf2#LINE/L1      214   295 (613)  

  chrX_22678239_2      2 CTCACACTTCCTGATTTTAAATTGTACTACAAAGCTATAGTAATCAAAAC 51
                                    ii    i   viv             i         i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_22678239_2     52 A---TGGTACTGCCATAAAAACAGACACATAG 80
                          ---        v     ii i     i    
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.01 (1 / 82), avg. gap size = 3.00 (3 / 1)  

1340 22.39 5.07 0.30  chrX_22678239_22680366.rev      103   437 (1691)    L1M4_orf2#LINE/L1      558   908 (0)  

  chrX_22678239_2    103 TCTTAGTAATCTTGG------TAATGATTTTTTGGATATGATCCCCCAAA 146
                             v  i i     ------i    i   i  i       iv  vv  i
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_22678239_2    147 CACAGGCAAAAATAGCAAAAATAGATAAGCAGGACTGTATCTAAA----A 192
                             i    v  v  v            iiv     vi   v   ---- 
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_22678239_2    193 AGCTTCTGCACAGCAAAGGAAACAATCAATAAAATGGAAAGGCAGTCTAC 242
                          i   i  ii vv       v  v     v   i  i    i  ii i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_22678239_2    243 AGAATGGGAGAAAATATTTGCAAACCATATATCTGTTAAGGGATCTATAT 292
                                                 i          v       ii i   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_22678239_2    293 CCAAAATATATAACGGAATTCATACAACTAAATAGCAAAAAAATAAAAAA 342
                            i         -i   i  v       v    ii     i i   v  
  L1M4_orf2#LINE/    758 CCAGAATATATAA-AGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_22678239_2    343 T-------AAAAGTGGGCAAAAGACTCGAGTAGACATTTTCTCAAAGGCG 385
                         i-------    i        i  i i  i         iii     iv 
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_22678239_2    386 ACATACGGATAGCCAATAGGAATATGAAGAGGTACTCAAAATAACCAATC 435
                          i    ii  i       i v i     i  i i     v  v ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_22678239_2    436 AT 437
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.26 (52 / 23)
Gap_init rate = 0.01 (4 / 351), avg. gap size = 4.50 (18 / 4)  

2584 19.16 2.06 17.20  chrX_22678239_22680366.rev      568  1637 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_22678239_2    568 TGGGAAGATATTATATGTTCACGGATTAGAAGAGTTAATTTTGTTAGAAT 617
                            i       ivi       i     i     v     v      ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22678239_2    618 GTCCAGACTCCCCAAAGTGGTCTATAGATTCAGTGCAATTCCTATCAAAA 667
                          v v v          v  i    i       ii     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_22678239_2    668 TTCCAA-TGTCATTTTTCACAGAAATAGAAAAA--AATCC-AAAATTCCT 713
                          i   i-  i -     ii       v  v  i--i    -       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_22678239_2    714 GTGGAGCCACGTACATGATGCACATGTGCACGTGCACACACACACACATA 763
                         i    i-----------     viv ------------------------
  L1M4_orf2#LINE/    150 ATGGAA-----------ATGCAAGGG------------------------ 164

  chrX_22678239_2    764 CACACACCCCCCACCAAATAGCCAAGGCAATCTTGGGCAAAAAGAAAACT 813
                         -----    --- --i         ii        iiv  i     v vv
  L1M4_orf2#LINE/    165 -----ACCC---A--GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_22678239_2    814 GCTGAAGCCATGACACTACCTGACTTCAAACTATATTACAAAGATGTAGT 863
                          i  i  vvv v     v  ii i      viv  i       v ii   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_22678239_2    864 AATTAACCCATTTAGGCCTGAGGTTGTAACTTTTGGAATTTTTGCAGTCA 913
                            i  --------------------------------------------
  L1M4_orf2#LINE/    255 AATCAA-------------------------------------------- 260

  chrX_22678239_2    914 GATCTTGGCGATGAACTTAACAGTAGGATATAAATAACTCCCACATGCTT 963
                         ------------------i     i-------------------------
  L1M4_orf2#LINE/    261 ------------------GACAGTG------------------------- 267

  chrX_22678239_2    964 AGCGTTCCATTAATGGAACACCAGGGATTGATGGGCTAAAAGAGCATGGT 1013
                         ----------------------------------------------    
  L1M4_orf2#LINE/    268 ----------------------------------------------TGGT 271

  chrX_22678239_2   1014 ACAGGCATAAAAACAGACACATCAACCAATGGAACTGAATAGGGAGCCTA 1063
                           v       ii i     i  vi i        iv    v i   i i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_22678239_2   1064 AAAAGAAACCCATGCATTTACAGTGAATTGATTTTTGACAAAGATGCCAA 1113
                         i   v        i      ii  v          i     i i      
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_22678239_2   1114 GAACAAACAATGGA-AAAGGACAGTCTCTTCAGTAAAGGGTTTTGGGAAA 1162
                           v  vv      i-    i i     i    ii   v   vi     v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_22678239_2   1163 ACTGGATATCCACATTCAGAAGAATGAAATTAGACCC-TATCTCACAGCA 1211
                                 ?      v  i         i  i     -  i      v  
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_22678239_2   1212 TATACAAAAATCCACTCAAAATGGACTAAAGACTTTAGCATAA-ACCTGA 1260
                                    iv            ii ?    i v iii   - v  i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_22678239_2   1261 AACTATAAAAGTACTAGGAAAAAACGTAGGAG-AAATGCTGTATGACACT 1309
                                   v vi   i i     i    ? -    -  vii    vi 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTT 570

  chrX_22678239_2   1310 GGTCTGGGCAATGATTTCTTGGATATGACTCCAGAAGTACAGGCATCAAA 1359
                           vi i       i      i        v   i   i   i   v    
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_22678239_2   1360 AGCTAAAATAGACAAATGGGATTGCGTCAGACTGAAAAACTTCT-CACAG 1408
                           vv        i    v   i v i   i v v        i -ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_22678239_2   1409 CAAAGG----TAACAACAGAGTAAAGAAACAAACTATGAAATGATAGAAT 1454
                               ----  v   v i   i  i i    v i iii    iv    v
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_22678239_2   1455 ATATTTTCAAGCCGTACATCTGATAAGAGATTAATATCCAAAATATTTAA 1504
                               v   ii i  i          i  i vi      i     v   
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_22678239_2   1505 GTAACTCAGAGAAATCAATATCAAGAA----AATAATCAGATTAAAAAAT 1550
                         iv     vv v  v      vi  i  ----     i vi   ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_22678239_2   1551 GGTCAAAGTACCTGAACAGTCATTTCTCAAAAGAATACATACAAATGGC- 1599
                           v     v ii    i  v        v      v i           -
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_22678239_2   1600 ----AGCACATAAATTAAAAAATGCTCAACATCACTAATGAT 1637
                         ----       i  ----  i             ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAA----AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (125 / 76)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 10.30 (206 / 20)  


2074 24.05 14.11 2.94  chrX_22767059_22770195.rev     1832  2646 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_22767059_2   1832 GAAAAACATACCATACTCAAGGAGTGGAAGACTCAATATAGTAAAAATAT 1881
                             i i  v    ii   v   v         i     v  v  i  iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_22767059_2   1882 AATTTCTCCCC-----------CA-ATTTAATGCAGTTCCTGTCAAAATT 1919
                         v v v      -----------  -   i  i   i i   i       i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_22767059_2   1920 TCAGCAACATTATTTGTGAATATATG-CAAGCTTATTCTAAAGTTTATAT 1968
                         i    vi v  v    iii v  -  -      v  i     i  i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATAT 151

  chrX_22767059_2   1969 GAAAAGGCAAATGAACTACAATAGCTAAAACAAATTCGAAAGGGAAGAAT 2018
                          i   v    iv  v i v      i       vi i    ii      i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_22767059_2   2019 AAAG--AGAAAAC--AGTCTACCTGATTTCAAGACTTATTATAAATCTTT 2064
                             --i  ii  -- vv  v  ii       i     i  i   v  vi
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_22767059_2   2065 ATTAACCAAGAC----TGGTATTAGTGAAGGGATGAATATTATAGATCAA 2110
                          v   i      ----     i i iiv i    ii i  -         
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT-ATAGATCAA 300

  chrX_22767059_2   2111 TGGAACAGAATGTAGAACCTAGAAATAGACCGAAACAACCATG-TC---- 2155
                              i     vv   ii i       i   v v   vii   -  ----
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_22767059_2   2156 --CCTTTGACAAAGATGCAAAAGC-----AAT------------------ 2180
                         --ii  i     i i   v  ii -----   ------------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_22767059_2   2181 TCAACAAACATTGCTGGAGCAATTGGACACCCATAGACAAACACGGGAAC 2230
                                 iiv      ii   i    i ?   i vi    viviv   v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_22767059_2   2231 TTG-ACCTAAACCTCTCAACTTA---AAAAATTTAACTCAAAACGGATCA 2276
                            -   ivv     v  v v  ---       -         i      
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATT-AACTCAAAATGGATCA 499

  chrX_22767059_2   2277 GTGGATCAAAATGTAA-------AGCTATAAATCTTTTAGAAGAAA-CA- 2317
                         -?i  i v        ------- i       v  i          -  -
  L1M4_orf2#LINE/    500 -WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_22767059_2   2318 A-----AAATACTTGGGATCT------AGG-AAT----TC---------- 2341
                          -----    vi i v  i  ------   -   ----  ----------
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_22767059_2   2342 -----------------ACAAAAGAAAACAGTTGATACATTGGACTTCAT 2374
                         -----------------           - i v    v            
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCAT 647

  chrX_22767059_2   2375 TGAAATTAAAAA--TTTGCTCTGCAAAAGACTCTGCTATGAAGATGGAAA 2422
                         ii          --    iv  v    i   v  iii v   ii  i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_22767059_2   2423 GACAACCTACAACCTGGGAGAAAATATCTGTAAATCTCTTATCTGACAAA 2472
                                i   ivv             i  i     viv       i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_22767059_2   2473 GGACTTGTATGTAAAATATGCAAAAATATTTCAAAACCCAACAGTAAAAA 2522
                                   vi i     ii   i vv i i v   i   i i      
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_22767059_2   2523 AACCAGAAGAAACAGATAAAAAACACAATCCAATTAGAAAATCAGCAAGA 2572
                         i  --------------   v   -----      ?i     vi    ii
  L1M4_orf2#LINE/    798 GAC--------------AAATAAC-----CCAATTWAAAAATGGGCAAAG 828

  chrX_22767059_2   2573 GA----AATGAACATTTTAC--AAGAGGATATATGGATGGCGAATAAGCA 2616
                           ----   ii      iv --    i      iii     v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_22767059_2   2617 CGTGAAAAGGTATTGAATATTATTAGCTAT 2646
                          i       i ii v  i  i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (127 / 66)
Gap_init rate = 0.03 (30 / 906), avg. gap size = 4.63 (139 / 30)  


 981 27.22 0.63 1.27  chrX_22805976_22808119.rev      151   466 (1678)    L1M4_orf2#LINE/L1      489   802 (106)  

  chrX_22805976_2    151 AAAACGAAAACCATAGACTTAAATGTAAAATGGAAAATTACAAAACTTTT 200
                             i i --i  ?    i         i vvv    i  i      i  
  L1M4_orf2#LINE/    489 AAAATGGA--TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_22805976_2    201 AGAAGAAAGTATAGGAGAAACATTTTCATAATGTGGGATTAGGCAAAGAG 250
                                 ii     ? v  -  i   i i iv v  i        v iv
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_22805976_2    251 TTCATAGACCAAACACCAAAAGTATGAACAATTGAAGAAAAAAATTAACA 300
                            v    ivvi          i ii i   ivi         - vi i 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATA 634

  chrX_22805976_2    301 GAGTGGACTTCATCAAAATTAAAGACTGTTCCTCTGTGAAAGACATTGTT 350
                         i v                    i   v  viv  vii  i    i i i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_22805976_2    351 AAGAGAATGAAAAGGCAAGCTAAAGTCTGGAA--AAATATTTACAAATCA 398
                             i i       i   v i v  vv   i --        i       
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_22805976_2    399 CATACCTAACAAATTATTTCTATTCAGAATAATTAAATAATTATAATAAC 448
                         i   i  i i  ivv i  v   i       vv    v  i v v i   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_22805976_2    449 TCAACATTAAGAAAACAA 466
                             i v   i  i    
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAA 802

Transitions / transversions = 1.71 (53 / 31)
Gap_init rate = 0.01 (4 / 314), avg. gap size = 1.50 (6 / 4)  

2512 26.58 6.21 1.64  chrX_22805976_22808119.rev      800  1653 (491)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_22805976_2    800 TGTTCATGGATTCAGAAGACCCAAGATAATAAATATATCAATTCTTTCCA 849
                                     -i      ii  v  vi v  v  iv    v  ii   
  L1M4_orf2#LINE/     16 TGTTCATGGATT-GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_22805976_2    850 AAT----CTA--GATTGAACACAATTACTAGCAAACTCCCAGAAAAAGTT 893
                            ----   --    v   i    iv   v    v      vviv--i 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC--CT 112

  chrX_22805976_2    894 TTTTTGTAGATA--GATAATCTTATTTTAAAATTAATATCGAAAGGCGAA 941
                               i   v --  i  v  v  ii       v    v    v  i i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_22805976_2    942 GGAGCCAGACTAGCTAAATTAGTTTTGAAAAAGAAGAA------------ 979
                            v     v    i   vi i i              ------------
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_22805976_2    980 --------------ATT--AAATCTTATTATATAGCTACAGTAAGCAAGA 1013
                         --------------   --   v    i  i v           v     
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_22805976_2   1014 CAGTATGGTATTAGTGGAAGGATGTACACATAGATCAGTGGAATTGAATA 1063
                             i     i i iiv      iv   i        i      v    v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_22805976_2   1064 TAGAATCTATAAATAGATCCACAGTTGTACAGCCAACTGTACTTTTGTAC 1113
                         v   i  i v     i i   i vv v  ii i   i  - i   i -  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG-ATTTTCG-AC 360

  chrX_22805976_2   1114 AAAAGTGCAAAAATCCTTTTCAATGGAGGAGAGACAGTCTTTTTAACAAA 1163
                           ii    v  i i v  --      i i iii i        i      
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATT--CAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_22805976_2   1164 TGGTGCTGAAGCAATTGGATAGCTATAGGTTAAGAAAATATAAGCCTTGA 1213
                                 iii   i      ? i i v i-  i i   i-   i- v  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGC-AAAAGAATG-AAGT-TGGA 455

  chrX_22805976_2   1214 TGTAAACTTCACAACTTATACAAAAATAAATTTAAAATGTTTCAGGGGTT 1263
                         ivivv  i     v v           v  i i      vv   ?i iii
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_22805976_2   1264 TAAATGCGA-------AACTATAAAACTCTTAAAAGAAAACATAGGAGAA 1306
                               ii -------                i             ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_22805976_2   1307 CATCTTCAGGACTTAGGGCTAAGTGAAGAGATTTGAGA---GACAACAAC 1353
                         v      iv   i v   i  i ii v ivv i v   ---    v   v
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_22805976_2   1354 TGTATAATTCATAAAAGAAAAAGTTGATAAATTGGACTTAATCAAATTTA 1403
                         v i i  viv i          i v              v      v   
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_22805976_2   1404 AAAACATTTGTATTGTTAGGGATCCTGTTAAGAGGACGAGAAGACAAGCC 1453
                              v     ii viv i   iv  i i    iiii  i       v  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_22805976_2   1454 ACAGACTGGGAGGTTGCATTTGAAAGTCATATGCACAATAAAGAACTGGC 1503
                              v      ivvii     v  i      iivii    i i   v i
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_22805976_2   1504 AGCTAAAACATATTAAGAATACTCAAAATTCAACTCTAAAAA-----ATA 1548
                          v i i  i    v     iv  i v  i    ivv      -----   
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_22805976_2   1549 GTTCAATTGGAATATATGCAAAATACATGAACAGGTATTTC--AGAAGAA 1596
                         iii     ?i  v  iv     iv iv    i  ii     --vi     
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_22805976_2   1597 AAGGGGATACAGATGGCCAAAAAAGTATGTGAAAAGATATTCAACATCAT 1646
                         i v---     i        v  - i ii         ii         ?
  L1M4_orf2#LINE/    856 GAT---ATACAAATGGCCAATAA-GCACATGAAAAGATGCTCAACATCAZ 901

  chrX_22805976_2   1647 TCACCAT 1653
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.59 (137 / 86)
Gap_init rate = 0.02 (19 / 893), avg. gap size = 3.53 (67 / 19)  


3037 24.60 3.95 1.47  chrX_22846393_22852110     4340  5225 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_22846393_2   4340 TGGAAACACATTCCATGCTCAAGGATTGGAAAAATCGATTTTGTTACAAT 4389
                               v i  i     i   v         i v ii  v      vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22846393_2   4390 GGACATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCTTTTCAAAC 4439
                           vv     v      vii  i           i  v  i i v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_22846393_2   4440 TACCAACATCATTTTTCACAGAATTAGAAATAACTT-TTCTAAAATTCAT 4488
                          v   i vv v     ii     v v  v - i  v- i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_22846393_2   4489 ATGGAACCATAAAAGAGCCTGAATAGCCAAATCAATCCTATGCAAAAAGA 4538
                               viii  ii  v  v           v     i iviv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_22846393_2   4539 ACAAAGCTGGAGGCTTCACATTACCTGACTTCAAA-----CTGTAAGGCT 4583
                               i      vi     i v  ii i      -----  ii  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_22846393_2   4584 ACAATAACCAAAACGGCATGATAATTGTACAACAATAGACACATAGACCA 4633
                            i   i   i  i ii  i  v v i i  vi       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_22846393_2   4634 ATGGAACAGGTTAGAGAACCCAGAAATAAAGCTTCACACCTACAACTATC 4683
                               i  iv v    ii           v ivi   ii  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_22846393_2   4684 TGACCTTTGACAAAGTCAACAAAA--A--CAATGGGGAAAGGACTTCCTA 4729
                            ii  i     i viiv   i -- --            i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_22846393_2   4730 TTCAATAAAAGGTGCTGGGATAACTGGCTACCTGTATGCAAAAGATTGAA 4779
                              i   v          i      v  ? iii          v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_22846393_2   4780 ACTGGGCCTTT------CACCACATACAAAAATCAACTCAAGATGGATTA 4823
                         ii   i  ii ------     i          i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_22846393_2   4824 AAGAGTTAAATGTAAGACCTCAGACTAAAAATCTCT-AGAAGAAAATCTA 4872
                         ?   vi           v  v i    v   v    -         iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_22846393_2   4873 GG---AAATACCATTCTGGACATACACCCTGGCAAAGATTTC------AT 4913
                           ---    -- -   vv   v vviviiv     v i    ------  
  L1M4_orf2#LINE/    550 GGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_22846393_2   4914 GACAAAGTCTCCAAAA--ACAATTGCAACAAAAACAAAAATTGACGAGTG 4961
                             ------      --    --         iv      v  ii i v
  L1M4_orf2#LINE/    597 GACA------CCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATT 638

  chrX_22846393_2   4962 GGACCT------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAAT 5005
                             i ------       i -   i  ii vv    i  v        v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_22846393_2   5006 GGAGTAAACAGACAATCTACAGAATGAGAGAAAATATTTGCAAACTATGC 5055
                         ii   i  v      i i        i                 ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_22846393_2   5056 ATCTGACAAAGGTCTAATATCCAGCATCTATAAA-AACTCAAACCAATTA 5104
                               i  i  v  vi       v  v      -     vv  v v i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_22846393_2   5105 ACAACCAAAAAACCAACAACCCCATTAAAAAATGGGCAAGGGACATGAAC 5154
                          i  iv    i  v  i     v   ?            i   iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_22846393_2   5155 GGATACTTCTCAAATGAAGACATATACATGTCTAACAAGCATATGAAAAA 5204
                         i  i i     v  v     i   i v   v i  i     i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_22846393_2   5205 ATGCTCAACATCACTAATCAT 5225
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (133 / 82)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.82 (48 / 17)  


3012 24.67 2.09 2.09  chrX_22873307_22877728     3022  3929 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_22873307_2   3022 TGGAAACACATTCCATGTTCATGAGTAGGATGAATAAATATAATTAAAAT 3071
                               v i  i           ii v   v  v v     vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_22873307_2   3072 GGCCATACTGCCCAAAGCAATCTA--GATGCAATGCTATTCCTATCAAAC 3119
                            v     v      vii     --   v   i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_22873307_2   3120 TACCAACATCACTTTTCACAGAATTAGATAAAACTT-TTCTAAAATTCAT 3168
                          v   i vv vi    ii     v v  i  i-  v- i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_22873307_2   3169 GTGGAACTAAAAGAG--CCTGAATAGCCCAAGCAATCCTAAGCAAAAAGA 3216
                         i     v iv   i --  v        v  i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_22873307_2   3217 ACAAAGGTGGAGGCATCACATTATCCAACCTCAAACTACACTACAAGGCT 3266
                               v      vv     i vi    ii     vivi       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_22873307_2   3267 ACAGTAACCAAAACAGCATGGTACTGGTACAAAAGCAGACAAACAGACCA 3316
                                i   i    ii         i i  iiii     v i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_22873307_2   3317 ATGGGTCAGAATAAAGTGCTCAGAAATAAAGCCTACGACCATTTAATCTT 3366
                             ivi     vi  v ii          -  i ii--      - vv 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATA--CATTTA-TGGT 345

  chrX_22873307_2   3367 CACCTACAACCATCTGATCTTCAAAAAAGTTGACAATAACAAGCAATGGG 3416
                           ---------  -    i   i v  i v  v   v v  vv       
  L1M4_orf2#LINE/    346 CA---------AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_22873307_2   3417 GAAAGAACTTCCTATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATA 3466
                                ivvi  v  i  i              i      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_22873307_2   3467 TGCAGAAGAGTGAAACTGGACCCCTTCCTTTCACCATATACAAAAATAAA 3516
                             i    i    ii         v   iv                v  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_22873307_2   3517 CTCAAGATGGATTAAAAACTTAAATGGAAGACCTAAAACTATAAAAACCC 3566
                              i      i ? i  i      v    v              vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_22873307_2   3567 TAGAAGAAAACA-AGAAATA--CCATTCTGGACATAGGCCTTGGCAAAGA 3613
                                     -  i?i  --i -   vv   v v  vi v     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_22873307_2   3614 TTTCAT-GATGAAGTCTCCAAAAGCAATTGTGACAAAAATGAAAACTGAC 3662
                             v -   - v v v         vvv ii      ivi    iv  i
  L1M4_orf2#LINE/    585 TTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_22873307_2   3663 AAGTGAGACCT-ATTTATACTAAAGAGCTTCTGCATAGCAAAGAAAACTA 3711
                           i vi   i -  iv v i    i -   i  iiivv     i v    
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA 682

  chrX_22873307_2   3712 TTAACCAAGGGACTAGACAACCTACAGAATGGGAGAAAATATTTGCAAAC 3761
                          i  vv   v  vv        i                          i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_22873307_2   3762 TATGCAACCAACGGAGGTCTAATATGCAGAATCTATAAGGAACTTAAACA 3811
                         i  ii v ii iiii  v  vi   v      v     i     ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_22873307_2   3812 AATCAACAAGCAAAACACAA----CTCCGTTAAAAAATGGATAAAGGACA 3857
                          v    i  vv    v    ---- i vi  ?        ii      iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_22873307_2   3858 TGGACAGACACTTTTC-----AAGACATACACACAGCCAACAAGCATATG 3902
                           i i     i  i  -----    i     v ii     i     i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_22873307_2   3903 AAAAAAATGCTCAACCTCACTAATCGT 3929
                             i -        v   ????????
  L1M4_orf2#LINE/    883 AAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (125 / 95)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.00 (38 / 19)  


3307 26.87 0.44 0.44  chrX_23019868_23022068      801  1708 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_23019868_2    801 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 850
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_23019868_2    851 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 900
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_23019868_2    901 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 948
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_23019868_2    949 TATGGAACCAGAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 998
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_23019868_2    999 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1048
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_23019868_2   1049 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1098
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_23019868_2   1099 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCGTATCTACAACT 1146
                                i    i--    i  --        vv  iiii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_23019868_2   1147 ATCTGATCTTTGACAAACTTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1196
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_23019868_2   1197 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1246
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_23019868_2   1247 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1296
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_23019868_2   1297 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1346
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_23019868_2   1347 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 1396
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_23019868_2   1397 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1446
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_23019868_2   1447 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1496
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_23019868_2   1497 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 1546
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_23019868_2   1547 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1596
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_23019868_2   1597 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 1646
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_23019868_2   1647 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 1696
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_23019868_2   1697 ATCACTGGCCAT 1708
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3535 23.58 2.12 0.67  chrX_23030241_23032158      532  1426 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_23030241_2    532 TGGAAAGATGTC---TGTTCATGGATTGAAAGAACTAATATTGTTAAAAT 578
                                  i  ---             i    vi            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_23030241_2    579 GTCTGTATTATACAAAGCACTGTATAGATTCAATGCAATTCCTACCAAAA 628
                          v vi  i viv    viiv v  i        i     i    i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_23030241_2    629 TTTCAA-TGTCATTCTTCACAGAAATAGAAAAA--AATTC-AAAATTCAC 674
                          ii  i-  i -  i  ii       v  v  i--i  i -        i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_23030241_2    675 ATGAAACCACAAAAGACCCCAAATAGCCAAACCA-TCTTGAGCAAAAAGA 723
                            i  vii   ii     vi          v  -      iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_23030241_2    724 ACAAAGTTTGAGGCATCACACTACTGGATGGCAAAATATATTACAAAGAC 773
                                 v    vv       v ivi  vv     iv  i       vi
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_23030241_2    774 ATAATAATCAGAAGAGCATAATACTGGCATAAAAATAGACATATTGACCA 823
                          i i      ii v  ii ii           ii          v  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_23030241_2    824 GTGGAATAAGATAAAAAAGCCCAGACATAAACCTACGCATTTATGGTCAA 873
                         i       ii  vi i - i     v       i ii             
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGA-GTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_23030241_2    874 CTGATTTTCAACAAAGCTTCCAAGAACACACAATGGGGAAAGGAGAGTCT 923
                         i        i    i v v      v  iv            i v     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_23030241_2    924 CTTCAATAAATGGTGTTAGGGAAACTA------CATATGAGGAAGAACGA 967
                         i     i        i i  iv    i------  i   vii     i  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_23030241_2    968 AACTGGAGTTTTATCTCACCCCTTCAATGAGAATCAACTCTAAATGAATT 1017
                          ii    viii  i     v  v vv ii i   i     v     i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_23030241_2   1018 AAAGACTTAAATATAAGACCTGAAACTATAAAACTACTAGAAGAAAACAT 1067
                          ?    i     i     v  i             vi             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_23030241_2   1068 AGAGGAAAAGCTCCATAACAATAGTCTGGGCAATGATTTCCTGGATATGA 1117
                           i? v   v  i i i  vv i vi i       i    i i       
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_23030241_2   1118 CCCCAAAGGCACAGGCAACTAAAGCAAAAATAGATAAATGGGATTATATC 1167
                          v     i     i     v    v              v   i vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_23030241_2   1168 AAACTGAAAAGCTTCTGCACAT-AAATGAAACAATTGA---AGCAAAGGG 1213
                            v v    i   i  ii v -   v  v  v  ii ---  ii  ii 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_23030241_2   1214 ACAACGTACAGATTCGGAGAAAATATTTGCAAATCATACCTCAAATAAAG 1263
                              vi     v v                       iv  vi    - 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA-G 747

  chrX_23030241_2   1264 GGGTTTAATATCCAAAATATACAAGAAACTCAAACTACTCAATAACAAGA 1313
                           ii  i-      i      i  ii     vv  v         i  i 
  L1M4_orf2#LINE/    748 GGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_23030241_2   1314 AAACAAAATAGCTCTATTAAAAAAATGGGCAAAGGATCTGAATAGACATT 1363
                          i     -  i i v   ?     -            i            
  L1M4_orf2#LINE/    797 AGACAAA-TAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATT 844

  chrX_23030241_2   1364 TCTCAAAGGAAGGCATACAAACAACCAAGAGATATATGAAAAAATGCTCA 1413
                             v  i    ii       iii    v iii i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_23030241_2   1414 ACAT-ATTTAATCA 1426
                             - ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (139 / 69)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


2833 26.69 2.93 0.68  chrX_23033506_23039570     4685  5572 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_23033506_2   4685 TGGAGAACCATTCCATGCTCATGGAGAGGAAGAATCAATATCATGAAAAT 4734
                             i ivi  i     i       vv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_23033506_2   4735 TGCCATACTGCCCAAAGTAATTTATAGATTCAATACTATTCCCGTTAAAC 4784
                         v  v     v      v i  i  i        ii v  i  ii i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_23033506_2   4785 TACCATTAACATTCTTCACATAATTAGAAAAAAGAATTC-AAAATTCATA 4833
                          v   vivi v  i  ii  v  v v  v  ivvi  i -          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_23033506_2   4834 TGGA---GCCAAAAAGAGCCTGAATAGCCAAGACAATCCTAAGCAAAAAG 4880
                             ---  --  ii  v  v          i      i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_23033506_2   4881 AACAAAGCTGCAGGCAC-CATGCTACCCAACTTCAAACTATATTACAAGG 4929
                                i  v   -  -  ii  v     i      viv  i     i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_23033506_2   4930 CTACAGTAACCAAAACAGCATGGTACTGGTATGAGAACAGACACATAGAC 4979
                                  i   i    ii         i  i  i i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_23033506_2   4980 CAATGGTACAGAATAGAAAACTCGGAAATAAGACCGCACACCTACAACCA 5029
                               v i     v  i iii i       iv  ii   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_23033506_2   5030 TCTGATCTTTGACAAACCGGACGAAAACAAGCAGTGAGGAAAGGACTCCC 5079
                         vi    i  i     ivvv v i i v  vv  i  i      i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_23033506_2   5080 TATTTAATAAATGGTGCTGTGAGAACTGGCTAGCCATATGCAGAAAATTG 5129
                          v  i  i           v  v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_23033506_2   5130 AAACTGGACCCCTTCCTTACACAATATAGAAAAAATAACTCAAGATGAAT 5179
                           ii         v   i    v     v     v        i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_23033506_2   5180 TAAAGACTGAAATGTAAAACCCAAAACTGTAAAAACCCTAGAAGAAAATC 5229
                         i ?    iv        i v i      i     vi i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_23033506_2   5230 TAGACACTA-TCATTCCGGACACAGACACGGGCAAAGATTTCAT-GATGA 5277
                            i?iiv -  -   vv   viv ivvii     v i    v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_23033506_2   5278 AAACACCAAAAGCAACTGCAACAAAAGCAAAAGTTGACAGATAGGATCTA 5327
                         vi            vvv          v    i v  i i  v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_23033506_2   5328 ATTAAACTAAACAGCTTCTGC----------ACAGCATCAG---AGTGAA 5364
                           i   v v  v i   i  i----------   vi    i---      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_23033506_2   5365 GAGACAACCTACAGAATCAGAGAAAATCTTTGCAATCTATCCATCTGACA 5414
                         i        i       vi        v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_23033506_2   5415 AAGGTCTAATATCCAGAGTCTACAAGAAACT--TA-AATTTA-CAAGGAA 5460
                          i  v  vi        i v  i  ii    --  -  i i -i  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_23033506_2   5461 AAAACAAACAACCCCATTAAAAAGTGGGCAAAGGACAGGAACAGACACTT 5510
                           i     i     v   ?    i           ivv   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_23033506_2   5511 CTCAAAAGAAAACATACATGCAGCCAACAA--ACATGAAAAAAAAGCTCA 5558
                            v      i i     viii     i  --         i v-     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCA 894

  chrX_23033506_2   5559 ACATCACTAATCAT 5572
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (144 / 89)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.00 (32 / 16)  


 423 32.10 17.04 2.96  chrX_23042557_23044472.rev      322   726 (1190)    L1M4_orf2#LINE/L1       38   499 (409)  

  chrX_23042557_2    322 ACATTATTCAGCTGG-AACACTTTTTCCAAATGAATCTATGAATTTATTG 370
                          i   i  v  v   -  i   ii--      vi     iii   i vi 
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCC--CCAAATTGATCTACAGATTCAACG 85

  chrX_23042557_2    371 TAAT----ACCAAAACTCCCACTGAGATTTTTAATGGAACTGGCCAG--- 413
                         i   ---- i     ii  vi   vvv     ivv i  i  i v  ---
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chrX_23042557_2    414 ATTCTACAATCCTTATAGAATAGTAAATGGG---CAGAA-----AAGACG 455
                           i   v   i v   i   vv i  --   ---     -----  i  i
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAA--GGGACCCAGAATAGCCAAAACA 183

  chrX_23042557_2    456 TGTTTGTAAAAG---------------GAACTTAC-----CAAACGTTAA 485
                         vvi   v     --------------- i   i  ----- v  iv i  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_23042557_2    486 GACACATTGTTAAGTGGCTATAGTAATGAGCATAGCATGCTGTTGGTGCA 535
                         i  vi i iiv   ---   i      v iv i  ii  v ii   iii 
  L1M4_orf2#LINE/    234 AACTTACTACAAAG---CTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_23042557_2    536 GGAAGAGACAGGTAGATCA---GAATCAGAATGGAGAACATGGAAACAAA 582
                         i i v     vi       ---    -     v    iivii    i   
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAAT-AGAATTGAGAGTCCAGAAATAAA 329

  chrX_23042557_2    583 ------------TGGAAAATTG--TTCCAGGAAGAAAATGACATTAAA-- 616
                         ------------   vv     --  i iiv   ii--  v  -- i --
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGG--TGCCA--AGACC 375

  chrX_23042557_2    617 AATCAATGAAGAAATGATGAGCCATTCAATAAATCATGTTAGGAAAAT-- 664
                          v      ii    vi  iiv iv     i    vi  i i   v  i--
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_23042557_2    665 GACTTTGACAT-TAAAAA--------TAGACTGCTTTCTCACACCGTTCA 705
                           iv?iv    -i    i-------- i   iv  vi        i vi 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_23042557_2    706 CAAAAATT---TCCAGATAAATTA 726
                                 ---  v i  ii  i 
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCA 499

Transitions / transversions = 1.87 (84 / 45)
Gap_init rate = 0.05 (21 / 462), avg. gap size = 3.86 (81 / 21)  

 542 27.03 6.10 3.78  chrX_23042557_23044472.rev     1088  1431 (485)    L1M4_orf2#LINE/L1      557   908 (0)  

  chrX_23042557_2   1088 ATCTTTATGACCATGATGAATGGG-A--GACTTTAAAAATACAAATCACA 1134
                              ii     v  -- iv i  - -- ii  ivv i   ii --   v
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTG--GGTTAGGCAATGGTTTCTTAGATATGA--CACC 602

  chrX_23042557_2   1135 AAAAGCACAATATGTAA--AAAGAAAACA---ATATATTTGACTACGTCA 1179
                                   --- i  --        v ---   v   v    v i   
  L1M4_orf2#LINE/    603 AAAAGCACAA---GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_23042557_2   1180 ATGT-AGAGACTTTTGCAAGTCAAAGGACACTACTGTATACAAAATTTAA 1228
                          vi - i i       iivv             iii--- v   i vv  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA---AGAAAGTGAAA 696

  chrX_23042557_2   1229 GGAAAAACAACAGATGGGGAGAAACACTTTTAC----CATATGT--GACA 1272
                         i  v  v v     vv        - iv   i ----     i --  i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAA-ATATTTGCAAATCATATATCTGATA 745

  chrX_23042557_2   1273 AATAATTAGTATCCAAAAATGCATAAAGAACCCCTATACCTCAATAAGAA 1322
                          ivi i v       i  - ii         i i  i v        v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAA-TATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_23042557_2   1323 GAGAAAAAATA-TGGAACAGAAAAATGGGCAAAGG--TTGCCCAGGCAAT 1369
                         i ii v     -ivv  iv?               --   vvi  i  v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_23042557_2   1370 TC---AGAAAAGAAATCCAAATATTTAATACATTCTGTGAAAAGAAGTTC 1416
                           --- i i    v  v     ivii    viiv -i        v i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCAC-ATGAAAAGATGCTC 893

  chrX_23042557_2   1417 ATCCTGACTATTAAC 1431
                          v v v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (51 / 41)
Gap_init rate = 0.05 (17 / 352), avg. gap size = 2.00 (34 / 17)  


3109 26.90 1.90 0.56  chrX_23135684_23142059.rev     4990  5885 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_23135684_2   4990 TGGAAGAACATTTCATCCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5039
                              ii i  ii   vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_23135684_2   5040 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5089
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_23135684_2   5090 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5137
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_23135684_2   5138 TATGGAACCAAAAAGGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5187
                                viiv  i   v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_23135684_2   5188 AACAAAGCTGGAGGCATCACGCTAACTGACTTCAAACTATATTACAAGGC 5237
                                i      vv    i  vv ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_23135684_2   5238 TACAGTAGCCAAAACAGCATGGTACTGGTACCAAAACAGAGATATGGACC 5287
                                ii   i    ii         i iv ii i   v    i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_23135684_2   5288 AATGGAACAGAACAGATGCCTCAGAAATAACACCACGCATCTACAACCAT 5337
                                i    iv  vivii         vv   ii   i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_23135684_2   5338 CTGATCTTTGACAAGCCGGACAAGAACAAGAAATGTGGGAAGGATTCCCT 5387
                         i    i  i      vvv v     v  vvv    v  i   i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_23135684_2   5388 ATTTTATAAATGGTGCGGGGAAAACTGGCTAGTCATATGTAGAAAGCTGA 5437
                         v  iv i         v    v      v  ?i  i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_23135684_2   5438 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGTTGGATT 5487
                          ii    i    v   i     v              i    iv     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_23135684_2   5488 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTT-GAAGAAAACT 5536
                          ?    i       v   v       i      - i   -         v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chrX_23135684_2   5537 TAGG--TAATACCATGCAGGACATAGGCATGGGCAAGGACTTCATGACTT 5584
                             --   - i - v iv   v v  vv i     v ii   v iiv v
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_23135684_2   5585 AAACACCAAAAGCAATGGCAACAAAAGCCAACATAGACAAATGGGGTCTA 5634
                         vi            vvi          vv  v     i    v  iii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_23135684_2   5635 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAA 5684
                           i   v v  i i   i  ii vv    i  v    i  vv i i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_23135684_2   5685 CAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATTTACCCATCTGACA 5734
                         v  i     i i               v       v i ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_23135684_2   5735 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5784
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_23135684_2   5785 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGTATTTGAACAGACACCT 5834
                           i     i     v  i?    i         v       i     ii 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_23135684_2   5835 CTCAAAAGAAG------------CCAACAGACACATGGAAAAATGCTCAT 5872
                            v       ------------    i ii      i   i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_23135684_2   5873 CATCACTGGTCAT 5885
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.44 (22 / 9)  


3145 27.02 1.11 0.55  chrX_23201324_23203687.rev      971  1873 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_23201324_2    971 TGGAAGAACATTCTATGCTCATGGGTGGGAAGAATCAATATTGTGAAAAT 1020
                              ii i  i i   i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_23201324_2   1021 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1070
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_23201324_2   1071 TACCAATGACTTTCTTCACAGAATTGGATAAAAACT-ACTTTAAAGTTCA 1119
                          v   iivi i  i  ii     v v  i  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_23201324_2   1120 TATGGAACCAAAAAAGAGCCCGCCTTGCCAAGTCAATCCTAAGCCAAAAG 1169
                                viiv  ii  v  v vv v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_23201324_2   1170 AGCAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACCACAAGGC 1219
                          i     i      vv    i  v  ii i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_23201324_2   1220 TACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATACACC 1269
                            i    i   i    ii         i iv ii i   v     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_23201324_2   1270 AATGGAACAGAAGAGAAACCTCAGAAATAATACAGCATATCTACAACTAT 1319
                                i    vv  i vii         vv vii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_23201324_2   1320 CTGATCTTTGACAACC-TGACAAAAACAAGCAATGGGGAAAGGATTGCCT 1368
                         i    i  i     vv-  v   i v  vv            i  v i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_23201324_2   1369 ATTTAATAAATGGTGCTGGGAAAACTGGATGGTCATATGTAGAAAGCTGA 1418
                         v  i  i              v        i?i  i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_23201324_2   1419 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 1468
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_23201324_2   1469 AAAGACTTACATGTTAGACCTAAACCCATAAAAACCCTAGAAGAAAACCT 1518
                          ?    i  v    v   v     v i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_23201324_2   1519 AGGCATTACCATTCAGGATATAGGCATGGGCAA-GGTCTTCTTGTCTAAA 1567
                            ?i v viv   iv  iv v  vv i     -   -     ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATATG 597

  chrX_23201324_2   1568 ACACCAAAAGCATTGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1617
                                     ivi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_23201324_2   1618 TAAACTAAAGAGCTTCTGCACAGGAAAAGAAACCACCATCAGAGTGAACA 1667
                         i   v v  i i   i  ii vvv   i  v  i i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_23201324_2   1668 GGCAACCTACAGAACGGGAGAAAATTTCTGCAACCTCCT-CATCTGACAA 1716
                          i     i      i          v i     v-  v -i      i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATAA 746

  chrX_23201324_2   1717 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGACAA 1766
                         i  i  vi          v  i         vv    v iv i  v v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_23201324_2   1767 AAACAAC---CCCAAC-AAAAAGTGGGCGAAGGACATGAACAGACACTTC 1812
                          i    v---     i-?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_23201324_2   1813 TCAAAAGAAGACATTTA--TGCGCCAAAAAACACATGAAAAAATGCTCAT 1860
                           v        i  vi --  -     v  i          i       v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATG-GCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_23201324_2   1861 CATCACTGGCCAT 1873
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2680 24.07 4.58 5.66  chrX_23264289_23266579      881  1798 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_23264289_2    881 TGAAAAGATAAGCTATATTCATGGATTGGAAGAAATAATATTGTTAAAGT 930
                           i       vv i  i                vv            ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_23264289_2    931 GTCCATACTACCCAAGTGATTCAAGTGATCTACAATTTCAATGCAATCCC 980
                          v v     v     i --------         iv     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT--------TGATCTACAGATTCAACGCAATCCC 92

  chrX_23264289_2    981 TAACAATTATCCAATGGCATTTTCGACAAAAATACAAAAAAAAAAAAACA 1030
                           v   vvvi   iiv  v    ivi  i    v------------i   
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT------------GACA 130

  chrX_23264289_2   1031 AAAAAAAAAAACCTTTTCTAAAGTGTGTATGGAACCACAAAAGACCCCTC 1080
                          ivvi --------- i     i vii       vii   ii     vvv
  L1M4_orf2#LINE/    131 AGCTGA---------TCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chrX_23264289_2   1081 CTAACCAAAATAATATTAAGACAAAAAAGCAAA--TGAAGGCATCATACT 1128
                         v  i      i   v  i i v i  i i    --  i   vv   i   
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_23264289_2   1129 TCCTGATTTCAT--CTTATATTACAAAGCTATAATAATCAAAACAGTGTG 1176
                            ii      v--    i--          i i       i        
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTAC--TACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_23264289_2   1177 GTATTGGCATAAACACAGACA-A-AGACCAAGGGGACAGAATAGGAACCC 1224
                            i        iv i     - -   i   v  i i     v ii vi 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_23264289_2   1225 CAGAAATAAACTCAAGCCTATATGGTCAACTAATTTTCCACAAGGGCACC 1274
                                    i  vi v v         i i      v       ii  
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_23264289_2   1275 AAGAGTACACAATGGGAAAAGGACAGTCTCTTTAATAAATGGTAATGGGA 1324
                             vi iv       i    i i     i  i  i       iv     
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_23264289_2   1325 AAAGCGGATATCCACAAGCAAAAAAAAAAAAAGACAAGAGAAGAAACTGG 1374
                         v  vi     ?     v      i  v---------------   ii   
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAAT---------------GAAGTTGG 454

  chrX_23264289_2   1375 AACTTT-CTTTA-ACCCCATACA----TCAACTTGAAATGTATTAAAAGA 1418
                          v ii - i i -   vi     ---- i    ii     v  i ? -  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA-GA 503

  chrX_23264289_2   1419 CCTGAACATAAGACCCAAAACTGTAAAACACCAAACAAAAAAT-TGAGTG 1467
                            i  ii     v i      i      v iv iv i    i- ii ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_23264289_2   1468 GAAATTCTTCATGACATTAGCCTGGGTAATGATTTTTTAGATATCACGCC 1517
                         v    -    i    v  i vi i  i    i   i        v  i  
  L1M4_orf2#LINE/    554 TAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_23264289_2   1518 AAAAGTTCAGGTGAGAAAATCAAAAATGAACCAGTTAAACTATATCAAAC 1567
                              iv  i ii v    vv      ii iv i  ii   vi      v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_23264289_2   1568 TAAAAAGCTTTTCCACAGCAAAGGAGACAATCAACAGAATGAAAAAGTAA 1617
                          v    i     vii vv       v  v     v i i      iii  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_23264289_2   1618 CCTACAAAATAGGAGAACATATTTGCTAGCCATATA------------CA 1655
                           i   i   i      v        v ii      ------------ v
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_23264289_2   1656 TATA-----AACATATAAGAAATTCAGACAACTCAATAATAAAAA----- 1695
                          i  -----  i      ii  i  vv                  -----
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_23264289_2   1696 -------AATTAAAAATCAGACAACAGACCTAAATAGACCTAAATTTTTA 1738
                         -------    ?    vii i   vi  ii i       ----    i v
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC----ATTTCTC 848

  chrX_23264289_2   1739 CAAAGCAGATATACAAATGGACAATGGGTATATGAAAAGGTGCTCAACAT 1788
                              v              v    ii i i        i          
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_23264289_2   1789 CACTAATCAT 1798
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.75 (138 / 79)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 4.95 (94 / 19)  


3458 22.84 1.20 1.97  chrX_23304880_23309101     2815  3729 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_23304880_2   2815 TAGAAAAATATTCCATGTTCATGAATTGGAAGAATCAATATTGTTAAAAA 2864
                          i    i    i           i         v i           i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_23304880_2   2865 TGTTCATACTACCCAAAGCGATGTACAGATTTAATGCAATTTCTATAAAA 2914
                           viv     v      vi   v        i  i     ii    v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_23304880_2   2915 ATACCAATGACATTCTTCACAGAAATAGAAAAAGATAATCCTAAAATTTA 2964
                           v   iivi v  i  ii       v  v  - v i           i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_23304880_2   2965 TATGGATCAA--CAAAAGACCAAAAATAGCCAAAGTTATTCT---AAGCA 3009
                               --  --   ii    v i          iiv  ii ---  iv 
  L1M4_orf2#LINE/    149 TATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_23304880_2   3010 AAAATAAATCTGGAGGAATCCCAATACCTGAGTTCAAATTATACTACAGA 3059
                          i  i   vi       v  v  v v  ii v      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_23304880_2   3060 GCTATAGTAACCAAAACAGCATGATAATGGCATAAAAACAGACATATAGA 3109
                             i     i   i    ii  i  v        ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_23304880_2   3110 -CAATATGAACAGAATAGAGAACACAGAAATAAATCCACACACCTACAGC 3158
                         -    i-   i     v    iiv          i   i   ii  ii i
  L1M4_orf2#LINE/    297 TCAATG-GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_23304880_2   3159 GAACTTATTTTCAACAAAGGTGCCAAGAACATATACTGCAGAAAAGACAG 3208
                         v  i v      i    i          v   vi v  vi    ii i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_23304880_2   3209 TCTCTTCAATAAATGGTGCTGGGAGAACTGGATATGCACATGCAGAAGAA 3258
                            i     i              v         ?v        i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_23304880_2   3259 TGAAACTAAACTCCTCTCTCTCTCACAATATACAAAAATCAAATAAAAAT 3308
                             ii ii  i   vi   v --  v            i  v v     
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCAC--ACCATATACAAAAATTAACTCAAAAT 493

  chrX_23304880_2   3309 GGATTAAAGGCTTAAAT-CAAGACCTCAAACTATGAAGCTCCAACAAGAA 3357
                             i ?  i i     -i    v  v       i  i   iv v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_23304880_2   3358 AACATTGGGGAAAATCTCCAGGACATTGGTCTGGGCAAAAATTTCTTGAG 3407
                              v  ? v      i iv   v    vi i     vii      -  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AG 592

  chrX_23304880_2   3408 TAATACCGCACAAGTCACAAAAGC-TAAGTCAACCAAAGCTAAAATGGAC 3456
                         --   ivi   ------       -i   -    v    vv     i  i
  L1M4_orf2#LINE/    593 --ATATGACAC------CAAAAGCACAAG-CAACAAAAGAAAAAATAGAT 633

  chrX_23304880_2   3457 AAATGAGATCGCATCAAGTTCAAAAGCT---GCATGGCAAAGGATACAAT 3503
                             vi  iiv      iv i    i  --- iiivv       i  v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_23304880_2   3504 CCACAAAGTGAACAGACAACTCACAGAATGGGACAAAATATTTGCAAACT 3553
                          v v        v       i            v              ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_23304880_2   3554 ACCCATGTGACAAGGGATTAACAGCCAGAATACATAAGCAGCTCAAACAA 3603
                          ivi  v   i      i vii v        i    iv i   vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_23304880_2   3604 CTCTGTAGAAAAAAAATCTAACAATCCAATCAAAACATGGGTAAAAGATT 3653
                            vi  iv     i - v  i  i     i?   v     i   i    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_23304880_2   3654 TGAATAGACATTTCTCAAAAGAAGACATACAAATGGCAAACAGGCATATG 3703
                                         v        i           v  i i   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_23304880_2   3704 AAAAGGTGTTGAACATCATTGATCAT 3729
                              i  i v       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (127 / 78)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.81 (29 / 16)  


3426 24.06 1.10 0.88  chrX_23320123_23324647     3127  4032 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_23320123_2   3127 TAAAAAGATATTCCATCATCATGGATTAGAAGAATCAGTATTGCTAAAAA 3176
                          ii        i    vv         i     v i i     i   i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_23320123_2   3177 TGACCCAAAGCATACTACACAAAGCAATCTACAGATTCAGTGCAATCCCT 3226
                           i ---  ---    v v    vii             ii         
  L1M4_orf2#LINE/     50 TGGC---AA---TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chrX_23320123_2   3227 ATCAAAATACCAATGACATTCTTCACAGAAATAGAAAAAC-AATCCTAAA 3275
                                 v   iivi v  i  ii       v  v  i -i        
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_23320123_2   3276 ATTTATATGGAACTACAAAACAATCAGAATAGCCAAAACTATCCTGAGCA 3325
                            i        v i   iiv vi               v   i   iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_23320123_2   3326 AATATAACAAAACTGGAGGAATCATATTACCTGGCTTTAAATTATACTAC 3375
                          iv v      ii       v   i i v  iiii  i   viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_23320123_2   3376 AAAGCTGTAGTAACCAAAAGAGCATGGTACTGGCATAAAAACAGGCACAT 3425
                               ii     i   i v  ii              ii i  i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_23320123_2   3426 AGATCAATGGAACAGTATAGAGAACCCAGAAATAAATCCATACATCTACA 3475
                                     i  v  v    ii           i        i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_23320123_2   3476 TTGAACTCATTTTTGAGAAACGTGCCAAGAACATGCATTGGGGAAAGGAC 3525
                         v v  i v     i  v  iv         v   v  v         i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_23320123_2   3526 AGTATCTTCAATACATGGTACTGGGAAAACTGCATCTCTATATGCAAATG 3575
                            v i     i v     i      v     v  v? i i       v 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_23320123_2   3576 AATGAAACTAGACTCCTCTCTCCCACCATATACAAAAATCAAATCAAAGT 3625
                               ii i   i   vi   v                i  v     i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_23320123_2   3626 GGATTAAAGACTTAAATCTAAGACCTAAAACTGTGAAACCACTACAAAAC 3675
                             i ?    i     v     v        i i    ivi  v  i v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_23320123_2   3676 AA-ATTGGAGAAACTCTCCAGGACATTGCATTGGTCAAAGATTTCTTGAG 3724
                           -  v  ? v  v   i iv   v   vi  i v   v i      iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_23320123_2   3725 CAATACCTCACAAGCACAGGCAACCAAAGCAAAAAGGGATAAATGGGATC 3774
                         i vv  vi  v       i     v    v     vi       v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_23320123_2   3775 ACATCAAG-TTAAAACGCTTATACACAGCAAAGGAAACAGCCAACAAAGT 3823
                         v      i-      -i   v iii vv       v  vii   v     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_23320123_2   3824 GAAAAGACA--CTA---AATGGGAGAAAATATTTGCAAATTACCCATCTG 3868
                                  -- i ---                       i ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_23320123_2   3869 ACAAGATATTAATAACCAGAATATATAAAAAGCTCAAACAATTCTAGAGG 3918
                          i   iv i vi  v              i i   vv    i  v v iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_23320123_2   3919 AGAAAATCTAATAATCTGATT-ACAAATGGGCAAAAGATATGAATAGAGA 3967
                          i   iv v     i ii   - v           i   v        v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_23320123_2   3968 TTTCGCAAAAGAAAATACACAAATG-CAAACAGGAATATGAAAAAGTGCT 4016
                             v v      i   i       - v  i i v i       ii    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_23320123_2   4017 CAACATCATTGCTCAC 4032
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (127 / 88)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


3164 27.10 1.11 0.66  chrX_23338680_23345067.rev     4994  5897 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_23338680_2   4994 TGGAAGAACATTCTGTGCTGATGGATAGGAAGAATCAATATCATGAAAAT 5043
                              ii i  i ii  i v      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_23338680_2   5044 GGCCATTCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5093
                            v  v  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_23338680_2   5094 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5141
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_23338680_2   5142 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGTCAAAAG 5191
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_23338680_2   5192 AAGAAAGCTGGAGGCATCACACTACCTGGCTTCCAACTATACTACAATGC 5241
                           v    i      vv       v  iiii   v  viv        v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_23338680_2   5242 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5291
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_23338680_2   5292 AATGGAACAGAAC--AGAGCCATCAGATATAATACAACATATCTACAACT 5339
                                i    i--    i --    v    vv v i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTC 346

  chrX_23338680_2   5340 GTCTGATCTTTGACAAACCTGACAAAAACATGAAATAGGGAAAGGATTCC 5389
                         ivi    i  i     ivv  v   i v   vv   i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_23338680_2   5390 CTATTTAACAAATGGTCCTGGGAAAACTGGGTAGCCATATGTAGAAAGCT 5439
                           v  i          v      v      i  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_23338680_2   5440 GAAACTGGATCCCTTCCTTACACCTTATACACAAATTAATTCAAGATGGA 5489
                            ii    i    v   i     v      v       i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_23338680_2   5490 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5539
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_23338680_2   5540 CTAGGCA-ATACCATTCA-GGTCATAGGCATGGGCAAGGACTTCATGTCT 5587
                         v    ?i- v i -   i- ii v i  i- i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_23338680_2   5588 AAAACACCACAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5637
                          vi      v     vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_23338680_2   5638 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5687
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_23338680_2   5688 ACAGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTACTCATCTGAC 5737
                          v  i     i                 i       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_23338680_2   5738 AAAGGGCTAATATCCAGAATGTACAAAGAACTCAAACAAATTTACAAGAT 5787
                           i  i  vi          i  i         vv    v iv i  v v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_23338680_2   5788 AAAAACAA----CCCCATCAACAAGTGGGCGAAGGATATGAACAGACACT 5833
                            i    ----   v  i? v  i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_23338680_2   5834 TCTCAAAAGAAGACATTTATGCAGCCAATAGACACATGAAAAAATGCTCA 5883
                             v        i  vi viii       ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_23338680_2   5884 TCATCACTGGCCAT 5897
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


1757 15.31 2.65 27.61  chrX_23735804_23737936.rev      514  1643 (490)    L1M4_orf2#LINE/L1       61   908 (0)  

  chrX_23735804_2    514 CCCAAATTGATTAATAGATTCAATGCAACCCTAACCAAAATCCCAGAGAG 563
                                    iv i        i    i  iv i           vv- 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT-G 109

  chrX_23735804_2    564 ATTTTTTTGTAGAAATTGTCAAGGTGGCTTTAAAATTTACATGATAAAGC 613
                         vi       i        v    v  iiii       i i   iv  v  
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_23735804_2    614 AAAGGAACTAGAATAGTCAAAACAATTTTGAAAAAGAAGAGCAAAGTTAG 663
                           i   v i       i         i             i       i 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_23735804_2    664 AGAACTCACAGTACGTGATTTCAAGATGTACTATAAAACTAGAGTAATTA 713
                           i       v v vii       i iv     i   i   v      i 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_23735804_2    714 AGACAGTGTGGTACTGGCAAAAGGACAGACCCATAGATC--TGGAACAGA 761
                                            v     i    vi       --     i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_23735804_2    762 -------GTCCAGACATAGACCCACACATACATGGTCAATTGATTTTTTG 804
                         -------       v   i     i    vi                i- 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC-G 358

  chrX_23735804_2    805 GCAAGAATGCAAAGGCAATTTTTTTTTTTTTTTGAGACGGAGTTTCTTGC 854
                         i    ii   ----------------------------------------
  L1M4_orf2#LINE/    359 ACAAGGGTGC---------------------------------------- 368

  chrX_23735804_2    855 TGCCCAGGCTGGAGTGCAGTGGCGCAATCTTGGCTCACCGCAACCTCTGC 904
                         --------------------------------------------------
  L1M4_orf2#LINE/    369 -------------------------------------------------- 368

  chrX_23735804_2    905 CTCCTGGGTTCAAGTGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGAT 954
                         ----------    ------------------------------------
  L1M4_orf2#LINE/    369 ----------CAAG------------------------------------ 372

  chrX_23735804_2    955 TACAGGCATGTGCTACCATGCTCGGCTAATTTTGTATTTTTAGTAGAGAT 1004
                         --------------     -------------------- i ------  
  L1M4_orf2#LINE/    373 --------------ACCAT--------------------TCA------AT 382

  chrX_23735804_2   1005 GGGGTTTCTCTATGTTGGTCAGGCTGGTCTCGAACCCCCAACCTCAGGTG 1054
                             ----------------------------------------------
  L1M4_orf2#LINE/    383 GGGG---------------------------------------------- 386

  chrX_23735804_2   1055 ATCCGCCTGCCTCTGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCAC 1104
                         --------------------------------------------------
  L1M4_orf2#LINE/    387 -------------------------------------------------- 386

  chrX_23735804_2   1105 CGTGCCAGGCCCAAGAAGGCAATTTTTAAAAAGATAATCTCTTCAACAAA 1154
                         ----------------------------   ii   i   i         
  L1M4_orf2#LINE/    387 ----------------------------AAAGAATAGTCTTTTCAACAAA 408

  chrX_23735804_2   1155 TGTTGCTGGAGCCACTGAACATC-ACAGGCAAGCCAA---AG---GACCT 1197
                           v      ii v    i i ? -   v    ivv  ---  ---    -
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC- 457

  chrX_23735804_2   1198 TCTTGCATACCTCACATTATGTACAAAACAGAACTAAAAATGGATTATGA 1247
                         ----- v         ii  i       vvv    v         i ?ii
  L1M4_orf2#LINE/    458 -----CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_23735804_2   1248 ACCTAAATATAAAATTTAAAACAATAAAACTTTTAGAAGAAGACACAGAG 1297
                                 i   i vi      v        i         i   i  i?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_23735804_2   1298 GAAAATCTTTTTGATCT--GGTTAGACAAAGACTTCTTATTTCTGACACT 1345
                          v       iv   i  --      i   v ii      vv v      i
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_23735804_2   1346 GAAAGGACAATTTGTAAAA-----AACTGATAAGTTGGACTTCACCAAAA 1390
                         i    v    vivii    -----  iv     i          i     
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_23735804_2   1391 CTAAGAACTGCTGCTTTTTGAAAAAACATTATTGAGAAAAGGAAGAAAAA 1440
                         i   i    vi  - vi  v   ii   i   ii     iv   -  i v
  L1M4_orf2#LINE/    653 TTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAA-AAGAC 700

  chrX_23735804_2   1441 AAAACACAT--TGGGAGAAAAATATTTGCAAAACGTATCTCTGATAAAGG 1488
                           vv    v--          -          v i   v        i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGG 749

  chrX_23735804_2   1489 AATTGTAAGCAGAATACATATAGAATTCTCAAAAGTCATTAATAACACAA 1538
                          v     vv       i   v    i   i v  v   v      v - i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA-AG 798

  chrX_23735804_2   1539 ACAACTCAGCCAA---AAAAACGTGCAAAATATTTAAA--GACACTTCAC 1583
                             v v v    ---     i v     iv    i  --    i   v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_23735804_2   1584 CAAATAAAATATACAAATGGGAAATAAGCGTATGAAAAGATGCTTATCAT 1633
                             v  i            vv       ii             i v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_23735804_2   1634 CCTTAGTCAT 1643
                          v????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.43 (100 / 70)
Gap_init rate = 0.03 (22 / 848), avg. gap size = 15.55 (342 / 22)  


2693 24.37 9.56 1.08  chrX_23872475_23875676.rev     1875  2711 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_23872475_2   1875 TGGAGAGATATTTC-----CATGGATTGGAAAACTCAACATAGAAAATAT 1919
                             i      ii -----            i   i  i  v vv  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_23872475_2   1920 GTCAATTTTCTTCAAATTGATATACAGGTATAATACAATTCCTATCAAAA 1969
                          v    vi  ii         v     i vi  ii    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_23872475_2   1970 TCCCAGCAAGATTTTTCTATTGATACCGACAAGCATATTCTAAAATTTAC 2019
                                v- vi    i iiv  v ii       vv  i        i i
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_23872475_2   2020 ATGGAAAGAAAAAGGAACTAGATTAGCTAAATCAATTTTGAAAAAAATGA 2069
                                viv  i   v i   v    i   v    i        i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_23872475_2   2070 ATAAAGGGGAAAGAATAAGTCAACCTGATTTCATGCTTTATTA------T 2113
                          i    vv i i  v v vv vv  ii      vivi   i  ------ 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_23872475_2   2114 ACAGTAATCCAGATTGTGTGATACTGGCAAAGGGACAGACACA--GATCA 2161
                                  v   iv     i        v i   i     i --     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_23872475_2   2162 ATGGAACAGATTAGAGAACCCAGAAACAGGCCCACATGAATATACTCAAC 2211
                               i   v v    ii       i ii    i iivv   iv    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_23872475_2   2212 TGATTTTTAACAA--------AAACC---------------------CTT 2232
                                ii    -------- i   ---------------------   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_23872475_2   2233 TTCAATAACTGGTGCTACAGA-AATTATACATTCATAGGCAAAA--ATGA 2279
                              i  v       i-i  -  i iv i ?i  i v      --    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_23872475_2   2280 GACT---CCACCTAACTGCACACCTTATACAAAAACTAACTCAAAATGGG 2326
                         iii ---  -    v  -      v          i             i
  L1M4_orf2#LINE/    449 AGTTGGACC-CCTACCT-CACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_23872475_2   2327 TCATGGTCTTAAATGTAAAACATAAAACTATAAAACT-TCAGGGAAAAGA 2375
                            ?i v i         i vv               - i  ----    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG----AAGA 542

  chrX_23872475_2   2376 AAAC-TAGA---AAATCTTCAGGATCTAGAGCCAGGCTAAGTGTTCTTAA 2421
                             -   i---        iv  i  v i ii    v v vv      i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_23872475_2   2422 ATTTAACACCCATAGTAT---CA-TACAAGGAAAAGTGGGTAAGTTGAAC 2467
                           v i     v v  i i---  -i v   i    i i i   i   i  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_23872475_2   2468 TTCATTGAAATGTAAAATTTT---GCTGTAATAGAAC-CTGTTTAGAGAA 2513
                              ii    vv    i   ---   vi  -  i  -  i iv   i i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACTATCAAGAAAG 691

  chrX_23872475_2   2514 TAAAAAGTCAGTCTACAGACTGGAAGGAAATATTTGCAAACCACATATTT 2563
                          i     v  ii i     v   i  i             i  i    i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_23872475_2   2564 GACAAAGAATT-------AGGAT------------CTCAAAACTCAACAG 2594
                           i  i i i -------  i  ------------  i v       i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_23872475_2   2595 TAAAAAAGTAAATAATCCAATTACAAAATGAGGAAAGGACATGAACAGTC 2644
                               iii      i      ?v      i v      iv    i  v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_23872475_2   2645 ATTTCATCAAAAAGGATATACAGATGGCAAATAAGCCCATGAAAAGACAT 2694
                              vi    i i        i     v       v          iii
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_23872475_2   2695 TCAATATCATAGCCATT 2711
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (131 / 70)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.87 (89 / 23)  


4444 14.62 3.88 0.12  chrX_23884074_23886652.rev      905  1704 (875)    L1M4_orf2#LINE/L1        1   830 (78)  

  chrX_23884074_2    905 TGGAAAAATATA-TATGTTCATGGATTGGAAAAC-AAACATTGTCAAGAT 952
                               i    v-i                 i  -v  i     i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_23884074_2    953 GATAATACTCCCCCAATTCACCTACAGATTCAATGGAATCCCTATCAAAA 1002
                          ii          v    v i            i v              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_23884074_2   1003 TCCCAGGCTGC----TTTGCAGAAATAGATAATTTAACCATAAAATGCAT 1048
                               -    ----           v  i  vi i i v      v   
  L1M4_orf2#LINE/    101 TCCCAG-CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_23884074_2   1049 ATGAAAACGCACGGGACTCAGAATAGCCAAAAAAATATTGAAAAAGA--- 1095
                            i   i   v     i              v   v          ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_23884074_2   1096 TCAAAGTTGGAGGAGTCACATGTCCCGATTTCAAAACTTACTACAAAACT 1145
                         v             v     iv    i                    i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_23884074_2   1146 ACAGTAATCAAGACAGTGCACTACCGTCATAAGGATAGGCTTATACATCA 1195
                                           iiv   i v           i v    v    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_23884074_2   1196 ATGGAACAGAATTAAGAGCTCAGAAATAAACCCTTACATTTGTGGTCAAC 1245
                               i      i    ii             v       i       i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_23884074_2   1246 TGATTTT-GAGAAGGGTGCCAAGACAATTCCATGGGGAAAGAATAGTCTC 1294
                                -  v              v    v                  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_23884074_2   1295 TTCAACAAATGGTGCTGAGACAACTGGATATCCCCATGCAAAAGAATGAA 1344
                                          i            ?  v                
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_23884074_2   1345 GATGGACCTCTTCCTCACTCAACACACAAAAATGAACTCAAA-CGGATCA 1393
                          v      i  v      v v i i        v        -i      
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_23884074_2   1394 TGG-CCTGAGTGTAAGGGCTAAAACTGGAAAACTCTTAGAAGAAAATTTA 1442
                         ?i -   i i      i         iv                  iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_23884074_2   1443 GGAGTATGTCTTCATTACCTTGGATTTGGCAGTGGTTTCTTAGACACAAT 1492
                           ?   vi     i v       i  v    i            i ii i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_23884074_2   1493 AACAAAAGTACAAACGACGAAAGAAAAAATA----AACTGAGCTTCCTCA 1538
                          v      i    i i  i            ----  i  ii    v   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_23884074_2   1539 AAGTTAAAAACTTTTGTGCTGCAAATGA-----TCAAGAAAGTAAAAAGA 1583
                           i                 v    v  -----          i      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_23884074_2   1584 CAATCCACAAAATGGAAGAAAATATTTGCATATTACATATCT-ATAAGGA 1632
                            i     i     i              v  i i      -      i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_23884074_2   1633 ACCTGTATCTAGAGTACCTAAAGGGTTC---------AATAATAAAAAGT 1673
                           i      i   i  iv     iii  ---------            v
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_23884074_2   1674 CAAATAACCAAATTTAAAAATGGGCAAAGGA 1704
                                  v    ?                
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.69 (71 / 42)
Gap_init rate = 0.01 (12 / 830), avg. gap size = 2.67 (32 / 12)  

 554 11.83 1.08 0.00  chrX_23884074_23886652.rev     1997  2089 (490)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_23884074_2   1997 AAAAATGGGCAAAGGATTT-AATAAACATTTCTTCAAAGAAGATATGCAA 2045
                                            -    i        i            i   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_23884074_2   2046 ATAGCCAACAAATACATGGAAAGATGCTCAGTATCCTTACTTGT 2089
                           i     i  ii     i           ii   v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 10.00 (10 / 1)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


 381 31.61 8.74 4.26  chrX_24000578_24002696.rev      491   936 (1183)    L1M4_orf2#LINE/L1      266   731 (177)  

  chrX_24000578_2    491 TGGGGCACAGTTACAGAGAAAGACAAAT-GACAAATGGAACAAAACAGAG 539
                           v  i  v vi i ii  v     v  -  iv       i i  iv   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_24000578_2    540 ATCCTAGAAGCAGATCCACTTACAC--A-GG--AAT--ATTTTATATATC 582
                          vi i    ii i i   --    i-- -  --   --     vv i --
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCA--TACATTTATGGTCAATTGATTTTCGACA-- 361

  chrX_24000578_2    583 ATGGAGCT--GGCTCTGCAAATTAGTGGGCAAGTATTGATTTTTTCAATA 630
                          v  v  i-- i iv v   -----    v  iv v ii i       i 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAA-----TGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_24000578_2    631 AAGAGT--TG----AACTGTATGAAGTTGAAGTTGAAAAACGTTAAAGT- 673
                           vi  --  ----     v  -- ?iiiv --  v    viv i    -
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGAT--AKCCACA--TGCAAAAGAATGAAGTT 452

  chrX_24000578_2    674 GAATGCTTAACTCACACTATAATCCACATCGAATCCGTTTCA---GGAT- 719
                          i iv i  v       i   - v  v ---   ivii iv ---    -
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATA-TACAAA---AATTAACTCAAAATGGATC 498

  chrX_24000578_2    720 AAAGACATAAGTATGAAAAGTCAAACTACAGAGCTTTAAAAAACTAATAT 769
                          ?    v   i i i i iv v      i i i  i v i  ivv  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_24000578_2    770 CAGAGAATAACCTCATTACT----ATCAGG-AAGGATTTCTTAA----GA 810
                         vi ? v v v i  i v  i----i i   -  v i       i----  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_24000578_2    811 CACATAAAGCATTAAT--CATAAGGAAAA---GATACCAATTTTACCAGG 855
                            vv      iv ii--  v   i    ---    --    vv  ivvi
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA--AATTGGACTTCA 646

  chrX_24000578_2    856 TTATAATGATGAACTTAAGTTAATCAAAAGACAC----AATAGAGTAAAA 901
                          i v   v vi     vv  vvv     i     ----  v i   i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_24000578_2    902 TGGCAAGCCACAGACCAAGAGAAGATATTTACAGA 936
                         v i   v       viii     i      i  i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

Transitions / transversions = 1.26 (77 / 61)
Gap_init rate = 0.05 (25 / 466), avg. gap size = 2.32 (58 / 25)  

 235 24.14 0.00 14.48  chrX_24000578_24002696.rev     1484  1628 (491)    L1M4_orf2#LINE/L1      785   908 (0)  

  chrX_24000578_2   1484 TCAACAAGAAAAATGTAAGTGATCCAATAGAAATGGGCCATTCATAGAAA 1533
                             i  v     vii  i i i     ---------------- ?i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAAT----------------TWAAAA 818

  chrX_24000578_2   1534 ATAGGCCAAAAAAAAAACCAATATAGGCTTGTCACAAAAGAGGAAATGTG 1583
                           i   ----   ii viii -    i v v  v v     i  v  iii
  L1M4_orf2#LINE/    819 ATGGGC----AAAGGATTTGA-ATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_24000578_2   1584 AATAACCAATAAATATGTGAAAAGATGCTCAATATTATTCATAAT 1628
                            ii       ii ii               i  i ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.25 (26 / 8)
Gap_init rate = 0.02 (3 / 124), avg. gap size = 7.00 (21 / 3)  


3047 19.77 4.68 1.69  chrX_24134969_24136729      500  1268 (493)    L1M4_orf2#LINE/L1      117   908 (0)  

  chrX_24134969_2    500 TATAGAAATTGACAAGATGATTCTAAAATGTACAGCTTATGGAAAAGCAA 549
                          ii             v    i       vi -----        v    
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCA-----TATGGAAATGCAA 161

  chrX_24134969_2    550 AATGACT-AGGATAGCCAAAACTACTTTGCAAAAGAAGAACAAAGTTGGA 598
                         ii-   i-  i           v ii   v                    
  L1M4_orf2#LINE/    162 GG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_24134969_2    599 A-AGTATCACTACTTGATTTCAAAATTTATTGTAAAGCTACAGCAATAAA 647
                         i- v vv    v iii         i   i ii          i   v  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_24134969_2    648 GACACAATGATATTGGCACAAAAATAGACAAATAGATCAGTGGAATAGAA 697
                             vvi  i  i     i  ii       v        i          
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_24134969_2    698 ---------CAGAACT----TCATATAT--ATGGTCAATCTTTTTTTTTT 732
                         ---------     v ----i    i  --         ----- vv   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT-----TGATTT 355

  chrX_24134969_2    733 TTAACAAAGGTATAAAGGCAATTCAGTGGAGAAAGAATAGCCTTTTCAAC 782
                          ii    i   iiv   i v     i   i          i         
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_24134969_2    783 AAAGGATGTTGGAATGTTTGGATATCCATATGCAAAA-AATAAAACATGA 831
                            v i  i   i iivi      ?   i        -   i  iivv  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_24134969_2    832 CTTACACTTCACACCTTATACAAAAATGAACTGAAAATGGACCATAAGCC 881
                          iivi  i       v           v    v        i  ? ii  
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_24134969_2    882 TAAATGTAA-AGCTTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGA 930
                                  -    -              ii                ? v
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_24134969_2    931 ATATCTTTGTGACCTTGGGTTAGGTAAATTTTTCTTAGATCTGATACCAA 980
                          v     i                i  vvv          v   i     
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_24134969_2    981 AAGCACACTCCTGAAAAGAAAAG-T-GATAAATTGAATTTCATTAAAATT 1028
                                vv vvv         i- -         i i     i      
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_24134969_2   1029 AAGAGATGCTGCTG-TTCAAAAGACACTGTCAAGAAAATGAAAATATAGC 1077
                           i iv vi  -  -      i      i        i      v i i 
  L1M4_orf2#LINE/    655 AAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_24134969_2   1078 T-ACAGATTGGGAGAAAGTATTTGCAAAACACGTATCTCCTAAAAGACTT 1126
                         i-     v         i          v  ii     vv   ii     
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_24134969_2   1127 GTGTCCAGATCATATAA-GAATTCTCAAACCTCAATGATTAAAA---AAA 1172
                           i      vi      -   i   i v v      i  v    ---   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_24134969_2   1173 T---CCAA---AAAAATAGGCAAAATATTTTAATGGACATGTCACCAAAC 1216
                          ---    ---      i      iv    v   i     v  v     v
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_24134969_2   1217 A---TATATGGATAGAAAATAAGCTCATGAAAATATACTCAGCAGCACTA 1263
                          ---    iii  i vv       v        v  i    i  v  ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_24134969_2   1264 ATTAT 1268
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.57 (91 / 58)
Gap_init rate = 0.03 (21 / 792), avg. gap size = 2.33 (49 / 21)  


2696 25.56 0.93 0.79  chrX_24160858_24162604.rev      502  1256 (491)    L1M4_orf2#LINE/L1      153   908 (0)  

  chrX_24160858_2    502 GAACCACAAAAGACACAGAATAGCCAAAGCTATCCTAAGCAAAAAGAACA 551
                            vii   ii   v             i v   i i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_24160858_2    552 AAACCAGAGGAAACACATTACCTGACTTCAAA--TTATTCTACAGAGCTA 599
                           iiii     vv    i v  ii i      --   --     i     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGCTA 250

  chrX_24160858_2    600 TAGTAACAAAAACATCAGGGTACTGGCACAAAAACAGACACATAGACCAA 649
                         i     iv  i   viiv          i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_24160858_2    650 TGGAACAGAATAGATAACCCAGAAACAAATTTATACATCTACACTGAACT 699
                              i     v  v ii       i   iii      i  iiv v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_24160858_2    700 CACTTTTTACGAAGGTGCCAAGAACATACATCAGTGAGAGGACACTCTCT 749
                         v i   iv  i i          v   v  vii v  i  i i v   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_24160858_2    750 TCAATAAATGGTGCCAGGAAAACTGGATATCCACATGCAGAAGAATGAAA 799
                             i         ii   v         ?         i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_24160858_2    800 CTAGATCACTATCTCTTTCCATACACAAAAATAAAAATAAAAATGGATTA 849
                         i i  i v   i   viv     i        v  v- v         i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAAC-TCAAAATGGATCA 499

  chrX_24160858_2    850 AAGACTGAAATCTAAGACCCCAAACTATGAAACTACTACAAGAAAACTTT 899
                         ?    iv    v     v iv       i     vi  v        v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_24160858_2    900 GGTGAGACTCTCTAGGACATTTGACTGGGCAAACATTTG--AGTTAT-AC 946
                           ? vi v   iiiv   v  v ii i     vvi   v--  v   -  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_24160858_2    947 CCCATAAGCACAGGCAACCAAAGCAAAAATGGACAAACGGGATCACAT-G 995
                         v   v       i     v    v      i  i   iv   iiv   -i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_24160858_2    996 AAGTTAAAAAGCTTCTGCACAGCAAAAGAAACAATCGACAAAGTGAAGAG 1045
                           i       -   i  ii vv    i  v  v   i v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_24160858_2   1046 ATAATCCATGAAATGGGAGAAAATACTTGCAAACTACCCATCTGACAAGG 1095
                          i  i   iii              i       ii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_24160858_2   1096 GATTAATAACCAGAATATATAAGGAGCTGAAATAACTCTATAGGAAAAAA 1145
                           i vi  v             i  i  vvv i     v   iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_24160858_2   1146 AATCTAATAATCTGATTTAAAA-TGGGCAAAAGATCTGAATAGGCATTTC 1194
                          -- v     i ii   ?    -        i   i       i      
  L1M4_orf2#LINE/    799 A--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_24160858_2   1195 TCAAAAGAAGACATACAAATGGCTAACAAATGTATATAAAAAAGCTCAAC 1244
                           v        i           i  i  iiii  iv   i v       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_24160858_2   1245 ATCACTAATTAT 1256
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (121 / 68)
Gap_init rate = 0.01 (9 / 756), avg. gap size = 1.44 (13 / 9)  


4280 17.78 2.44 1.56  chrX_24181656_24183807.rev      762  1661 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_24181656_2    762 TGGAAAGACATCCCATGTTCATGTATTGGAAAACTTAATATTGTTAAGAT 811
                                 i              v       i                  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_24181656_2    812 GCCAATACTACCCACGGTGATCTACAGATTCAATGCAATCCCTATCAAAA 861
                          v       v    viv                i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_24181656_2    862 TCAAAATCCCAATGGTAATTTTTTTTGCAGAAATAGAAAAAAAAACCCTA 911
                           ------   iiv i---i              v  v  ivvi i    
  L1M4_orf2#LINE/    101 TC------CCAGCTGC---CTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_24181656_2    912 AAATTCATATGGAAGCTCAAGGAACTCTGAATAGCCAAAACAATTTTGAA 961
                                       iiv     i  i v                i     
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_24181656_2    962 AAAGAA---CAAATATGGATGACTCACGCTTCCTAATTTCAGAAC--ATT 1006
                               ---    vv    v       i     i       i   -- i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_24181656_2   1007 ACAAAGCTACAGTAATCAAAACAGTGTGGTACTAACATAAAGACAGACCT 1056
                                            i             ii     i  i    v 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_24181656_2   1057 ATAGACCAATAGAATAGAATAGAGAGCCCAGCAATAAATGCATGCATATA 1106
                              i    i         v     i    v      iv   i   v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_24181656_2   1107 TGGTCAAATGATCTTTGGCAAGAGTGCCAA-ACCCCTCAATTAGGAGAGG 1155
                                v    i  i i    i       -   vi     vi   i  i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_24181656_2   1156 GCAGTCTCTT-AACAAATAGGGTTGGAAAAACTGAATATCCACATACAGA 1204
                         ii     i  -       i v i   i v     i   ?      i  i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_24181656_2   1205 AGAATGAAGTTGGACATTTATGTTACACCATA--CAAAAATTAACTAAAA 1252
                                        vii  iv i        --            v   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_24181656_2   1253 ATGGATTAAAGACCCAAATTTAACACCAAAAACGA--AAATTCCTACAAG 1300
                               i ?     i    v   v v v     v --   i  i  v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_24181656_2   1301 AAAACA--GGGGGAAATCTCCATGACACTGAATTTGGCAAGGATTTCTTG 1348
                               --  ? v      i i    vi  ii  v     v i      i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_24181656_2   1349 GATATGACACTAAAAGCACAGGCAACAAAAGAAAAA-TAGGCAAATGGGA 1397
                                   i         i               -   ii    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_24181656_2   1398 CTACATCAAACAT----AACTTCTGCACATCAAGGGAAATAATAAAAGGA 1443
                           v       -  ----     i  ii v    i   v iv  v  iii 
  L1M4_orf2#LINE/    642 CTTCATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_24181656_2   1444 ATGAAAAATCAATCCATGAAATGAGAGAAAGTACTTTCAAATCATATATC 1493
                         i      iv   i   iii    i      i  i  v             
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_24181656_2   1494 TAATAAGGG-TTAATATCCAGAACACATACAGAACT---ACAACTCAACA 1539
                          i       -i vi         i i   v      ---         i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_24181656_2   1540 ACAAGAAAAAATCAAATAACCTGACTAAAAAGTGCACAAAAGACTCGAAT 1589
                          i  i  i ---         ii i ?    i  vi    i  i i    
  L1M4_orf2#LINE/    791 ATAAAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_24181656_2   1590 AGACATTTCTCCAAAGATCATATACAAACGGCCAACAAGCTATATGAAAA 1639
                                          vv         i      i    - i       
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC-ACATGAAAA 886

  chrX_24181656_2   1640 GATGCTCAATGTCATGAATCAT 1661
                                  ii   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (105 / 51)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.25 (36 / 16)  


1692 25.66 4.96 2.83  chrX_24377922_24379983      500  1064 (998)    L1M4_orf2#LINE/L1      141   717 (191)  

  chrX_24377922_2    500 AAAGTTTATATGGAAAGGAAAAAGATCCAGAAAAACCAAATTGATATTGA 549
                            i  i         v v  ii  i      v i     vii  v    
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_24377922_2    550 AGGAGAAGAA-AGTGTCAGAAAACTGACACTATCTGACTTCAAAACCTAC 598
                          ii       - iv  ii  ii   v     vi ii i        i   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_24377922_2    599 TATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCAAAAAGAACAGAC 648
                           i                             i     v  i  -i    
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGAC 289

  chrX_24377922_2    649 AAATACATCAATGGAACAGA-CAGAAAGCCCAGAAATAGACCCAGACAAA 697
                          v   v          i   -iv  i  i         i     v   --
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA-- 337

  chrX_24377922_2    698 TATACAGAGAGCCAGTCTTTGACAAAGGAGCAAAGGC-----AA----GC 738
                          v  ii vv iiiii i  i     i  v  v   i -----  ---- v
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_24377922_2    739 AAACATAGACCTTTCAACAAATGG------AACAAATGGACATTCACATG 782
                           iv    v i             ------i    v    i ?i      
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_24377922_2    783 CAAAAAAAAAAAAAAATTAATCTAGACATA-ACCTTACATCCTTCACAAA 831
                              i  -------- v  vi i   viv-    i   i v vi     
  L1M4_orf2#LINE/    438 CAAAAGAA--------TGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_24377922_2    832 AATCAAATGTAAATG--CCAAACTATATGTAAATGTAAAATGCCAAA-CT 878
                            i  v vv     --i  ? v--- iv         i -  i   -  
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAG---ACCTAAATGTAAGA-GCTAAAACT 525

  chrX_24377922_2    879 ATAAAACTCTACAGAAGAAAACCCAGATGGGTTTCTTC-------TGGGT 921
                                   -i          vi  i? vivv     -------     
  L1M4_orf2#LINE/    526 ATAAAACTCT-TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_24377922_2    922 ATGGTGGTGACTTTTTAGATACAACACCAAAGGCATGAACCGTGACAGAA 971
                         vv  iii  ii  i       ii        i   ii i viii v    
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_24377922_2    972 ACAATTGATAAGGTGGACTTTATTAAAATTAAAAACTTCTGTTCTGCAAG 1021
                          v   v     iv       i  i              i   v  v   i
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_24377922_2   1022 AGACAATGTTAGGAGAATGAGGAAACAAGGCATAGACTGGGGG 1064
                         i    v i i i  i i   ii i    vv  i   v    i 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

Transitions / transversions = 1.84 (92 / 50)
Gap_init rate = 0.03 (15 / 577), avg. gap size = 2.93 (44 / 15)  

 772 22.91 0.88 1.32  chrX_24377922_24379983     1343  1569 (493)    L1M4_orf2#LINE/L1      683   908 (0)  

  chrX_24377922_2   1343 TCGAAAAAAAAAAAAAAAAAGACATGGACTGGGCGAAAAATATTTGAAAA 1392
                           i i   ivi    i v  vv  ii  v    v     -      v   
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAA 731

  chrX_24377922_2   1393 TGATACAACTGATAAAGGACCGCTACCCAAAATATACAAAGAACTCT-AA 1441
                          v   i v       i    ivv  i   i      i          - v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_24377922_2   1442 AACTCAACAATAAGAAAAAAAACAGCTGGATTTTAAAAAATGGGCTACAG 1491
                                i     i  i v   i i ivi   --?          v vi 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATT--WAAAAATGGGCAAAGG 829

  chrX_24377922_2   1492 ACCTTAACAGGTACCTCTCCAAAGAAGATCTACAGATGGCCAGGAAGCAC 1541
                          ii v  i  ii ii              v    i       iv      
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_24377922_2   1542 ATGAAAA-ATGTTCAATATCATATGTCAC 1569
                                -   i    i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.02 (4 / 226), avg. gap size = 1.25 (5 / 4)  


3330 21.69 2.57 0.90  chrX_24563681_24566107.rev      502  1280 (1147)    L1M4_orf2#LINE/L1       31   822 (86)  

  chrX_24563681_2    502 AGAATTAATATTGTTAAAGTATCCATAATCCCCAAAGCAATCTATGGATT 551
                            v             ii iv v   v        vii     ii    
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chrX_24563681_2    552 CAATGTCATTCCTATCAAAATTCCAATGGCATTTTTCACAGAAATAGAAA 601
                            i iv  i           i   iiv  v     ii       v  v 
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA 130

  chrX_24563681_2    602 AAACAATCCTAAAACTTGTATGGAACCACAACAAAAGACCCCAAATAGCC 651
                          ivii         i ii       -- ii-   ii     vi       
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAA--ATG-CAAGGGACCCAGAATAGCC 177

  chrX_24563681_2    652 AAAGTAATCTTAAGAAAGAA---CAAAGCTGGAGGCATCACACTCCCTGA 698
                            ii      i i      ---     i      vv       i  ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_24563681_2    699 TTTCAAACTGTATTACAAAACTATGGTAATCAAAACAATATGGTACTGGC 748
                                viv  i      i   ii        i   i i          
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_24563681_2    749 ATAAAAACAGATACAAAGACCAATGGAACAGAATAGAGAACCCAGAAATA 798
                             ii i   i i v   i        i     v    ii         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_24563681_2    799 AACCCTTGCATACATGGTCAACCGATCTTTGACAAGAGGGTCAAGAACTC 848
                              v i   vi        ii   i  i      i v i     v vi
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_24563681_2    849 ACAACAGGGAAAGAAAAGTCTCCTCAATAAATGGTACTGGGAAAACTAGA 898
                         v   ii         v     ii    i       i      v    i  
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_24563681_2    899 TATCCACATACGAAAGAATAAAATTAAATCCTTGTCTCATACTATATACA 948
                           ?      i i       i  i  ii i  i ii    i  i       
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_24563681_2    949 AAAATTAACTCAAAATGGATCTAAAACTTAAATGTAAGACTGGAAACCAT 998
                                              v? i  i           vivi    i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_24563681_2    999 AAA-CTCCTAGAAGAAAATATAGGGAAAAAAAGCTCCCTGACATTGGTCT 1047
                            -   i          i     ?iv   --v  i v    v    vi 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTT 575

  chrX_24563681_2   1048 TGGCAATAATTTTTTTAGATATGACACCAAAAGCACAGGCAACAACAGCA 1097
                         v      ii   i  -                     i       v  v 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_24563681_2   1098 AAAATAAATAAGTAAGACTGCAACAAA-CTAAAAA-----G------AAA 1135
                               i    i vi    v  v    -i      ----- ------   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_24563681_2   1136 G--CA--ATTAACAAAACAAAAAGACAACCTACAAAATGAGAGAAAATAT 1181
                          --  --  i  v   iii           i   i    i          
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_24563681_2   1182 TTGCAAACCATATTATCTGATAAGGGGTTAATATCTGAAACATATAAGAA 1231
                                i     -            ii vi    iii  i      ii 
  L1M4_orf2#LINE/    725 TTGCAAATCATAT-ATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_24563681_2   1232 ACTCACACAACTCAATAGCACAAAAACAAACAACCAGATTAAAAAATGG 1280
                             vi           ii v   i     i    vi   ?        
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

Transitions / transversions = 2.67 (120 / 45)
Gap_init rate = 0.02 (12 / 792), avg. gap size = 2.25 (27 / 12)  

 499 14.04 5.26 0.88  chrX_24563681_24566107.rev     1823  1936 (491)    L1M4_orf2#LINE/L1      790   908 (0)  

  chrX_24563681_2   1823 AATAAAAATAAAAAATAAA--AAT----AAATGGGCAAAGGACCTGAATA 1866
                                 -i v      v--   ----              ii      
  L1M4_orf2#LINE/    790 AATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_24563681_2   1867 GATATTTTTCCAAAGAAGACACAGAAACGGCCAATAGGTATATGAAAAGG 1916
                           i    i           i i v   i        i i i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_24563681_2   1917 TACTCAACATCACTAATCAT 1936
                          i          ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.33 (13 / 3)
Gap_init rate = 0.03 (3 / 119), avg. gap size = 2.33 (7 / 3)  


2774 20.99 13.40 0.51  chrX_24634021_24635908.rev      607  1397 (491)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_24634021_2    607 TGTTCATATATTGGAAGACTTGACATAATAAAGATGTCAATTGTTCCCCA 656
                                iv            i i  vi v      v    vv i   v 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_24634021_2    657 ATTGAT--ACGGATTTAACACAATTCCAATAAAAAT----------TTTG 694
                               --  i    i   i    i  v  v     ----------   v
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_24634021_2    695 TTA-ATAAG--GACAAGCTGACTCTAAAATTTATATGGAAAGGCAAACAA 741
                           i- v  i--          ii        i         v    ivi 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_24634021_2    742 ACTAGAAT---TAAGACATTTTTGAAAAA----AATAAAAT-GGAAGAAT 783
                         v i     ---i  i   v i        ----  i   i -   i  v 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_24634021_2    784 TGCACT-----ATA-CAAGACTTACTATAAAGCTACAGTAATCAAGGT-G 826
                         ii    -----  v-   i        i                  ii- 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_24634021_2    827 TGTGGTATTGGCAAAAGAATAAACAGAGAGATCAATGGAAGAGATCAAAG 876
                                i     v   i   i   v v            v   vivi  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_24634021_2    877 AGTCCAGAAATAGACCCACACAAATATGCTCAAATGGTTTTTAACACGGG 926
                                     i     i   vv    v    v  i    ii   v   
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_24634021_2    927 TGCAAAAGCAATTCAGTGGAAGAAGGACAGACTTTTCAGCAAATGGTGTT 976
                            v  ii v     i   iii   i i  v       i         i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_24634021_2    977 GGAACAACTGGACACACACAGACCAAAGAAAAAAATTGAACTCTGCCCTA 1026
                           i         i ?v    vi v      vi  i   i  i ivv   v
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_24634021_2   1027 AC----TTTATAAAAATTAATTCAAAATGGATCATAGACATAGAT----- 1067
                           ---- v  i         i             ?    v  i  -----
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_24634021_2   1068 ----------------------------AATAT----------------- 1072
                         ----------------------------  i  -----------------
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_24634021_2   1073 ---TTGAGTT------------CTTAGTCATGAGATCAAAAGCACAATCA 1107
                         ---   i   ------------     vi    v i           v  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_24634021_2   1108 ATAAAAGAAAAATATTGATATACTGGACTTGATAAAAATTAGAACTTTTT 1157
                          i          -  v    v i       v  v       i  vi    
  L1M4_orf2#LINE/    616 ACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_24634021_2   1158 CT-CTGTGAAAGACACTATCAAGAGAATGAAAAGACAAGCTACAGACTGG 1206
                         v -  vii  i             i i           v i     v   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_24634021_2   1207 GACAACATATTTGCAAATCACATATCCAACAAAGGATCTGTATCTAGGAT 1256
                           v  v              i     ii i  i   ii      i  i  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_24634021_2   1257 ATATAAAGAACTTTCAAAACTTAGCAATAAAAAAA-AAA-AATCCAATTT 1304
                                     i i v    i ii        i -   -  i      ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_24634021_2   1305 TTTTTAAATGGGGGAAA-ACTTGG---GACACTTCACCAAAGTGGATATA 1350
                         vv---       vi  i- i   i---    i   v      vi      
  L1M4_orf2#LINE/    815 AA---AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_24634021_2   1351 AGGATGACAAATAAGCAGATGAAAAGATGTTCAACATCATTAGTCAT 1397
                         vii   i v        v           i         ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (100 / 63)
Gap_init rate = 0.02 (21 / 893), avg. gap size = 5.24 (110 / 21)  


2624 21.67 6.00 0.88  chrX_24689217_24690891      500  1182 (493)    L1M4_orf2#LINE/L1      191   908 (0)  

  chrX_24689217_2    500 AAAAGA-GAATAACATTGGAGGAATCAATACAT---AGCTTTAATACTTA 545
                               -   i  vi        v   -i  v --- ii  i  v     
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTA 239

  chrX_24689217_2    546 CTACAAAGCTACAGTAATCAAGACAGTGTGGAACTGGCAAAATAATAGAC 595
                                                        v       v  vi      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_24689217_2    596 ACGTAGACCAATGGAA-------GAGA--------ATAGACTCA--CAAG 628
                          ii    i        -------    --------   i  i  --  vv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_24689217_2    629 TGTGGCCATTTTATTTTTAGCAAACATGCAAAAGCAATTTAATGGAGAAG 678
                          i   i  v  v     iii   ivi   v  ii v   i     i   i
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_24689217_2    679 GGGTAGTCCTTTCAACAAGTGATGATGGAAAAAGTGGATATCCATATGCA 728
                          ii     i         i  i  v   i v  v      ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_24689217_2    729 GAGAAAAATGAACCTTGACCTAAAGCTCATACCTTATACAAAAATTAACT 778
                         i -- i      vi v    ivv v    i   v                
  L1M4_orf2#LINE/    440 AA--AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_24689217_2    779 CCAAATATATCGTAGGTGTAAATGTAA-------AACTATAAAACTTTAA 821
                          v    iv   i?  iiv         -------            i v 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_24689217_2    822 AGAAGTAATGCATAAGAGAAAATCTTCATGACCTAGGGTTAGGCAAAGTG 871
                         -    v  -i    i ? v        i      v           v vv
  L1M4_orf2#LINE/    538 -GAAGAAA-ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_24689217_2    872 TTCTTAGACATGAAACTAAAATTGTGATCCATAAAAGAAAAATGTTGATC 921
                                 i    v  i    viiii v v i          -i v   v
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATA 634

  chrX_24689217_2    922 ACCTGGACTTCATCAAAATTAAAAACCTTTGATCTGCAAAAGACACTGTT 971
                          vi                       i    vv  v    i      i i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_24689217_2    972 AAG-----GCAATGACTGCC-ACAGACTGGGAGAAAATGTTTTCAAATTA 1015
                            ----- v  v   vi  -     v           i   v     i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_24689217_2   1016 CATATCTAACAAAGGTCCTGTATCCAGTATATATAAAGAACTCTCAAAAC 1065
                         i      i i  i  v i         v                i v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_24689217_2   1066 TCAACAGTAAAA---CAAGCAATCCAATTTAAAAAAAAACAAAAGACTTG 1112
                             i i     ---   ii  i      ?     viii    i  i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_24689217_2   1113 AATAGATTCTTCACCATAGGAAATATAAGGATGAC----AAACATGTGAA 1158
                               ivi   v   v  i i     vii   i ----  i  ii    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_24689217_2   1159 AAGATGTTTAACATCACTAGCATC 1182
                               i i       ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (88 / 56)
Gap_init rate = 0.02 (15 / 718), avg. gap size = 3.13 (47 / 15)  


2621 24.52 2.88 6.08  chrX_24865587_24874620.rev     4578  5515 (3519)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_24865587_2   4578 TGGAAAAACATTTTATGTTGGTGGATAGAAAGGATCAATATTGTTTAAAT 4627
                               i i  iii     vi     v i   iv i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_24865587_2   4628 GGCCATACTGCCCAAAGCAATTTACAAATTCAATGCTATTCCCATCAAGC 4677
                            v     v      vii  i    i      i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_24865587_2   4678 TACCAATGACATTCTTCACAGAACTAGAAAAAAACT-ATTTTAAAATTCA 4726
                          v   iivi v  i  ii     v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_24865587_2   4727 TATGGAACCAAAAAAAGCTCA-AATAGCCAAGACAATCCTAAGCAAAAAG 4775
                                viiv  iiii i  -         i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_24865587_2   4776 AACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTATAGGGG 4825
                                i      vv     i v  ii i      viv     i ii v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_24865587_2   4826 TACAGTCACCAAAACAGCATGATACTGGTACAAAAACAGGCACATGGACC 4875
                               v i   i    ii  i      i i  ii i  i  i  i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_24865587_2   4876 AATGGACCAGAATAGAGAGCTCAGAAGTAAGGCCAGACACTTACAACCAT 4925
                               vi     v     ii     i   iv   v   i   iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_24865587_2   4926 CTGATCTTTAGCAAAGCTGACAAAAACAAGCAATGTGGAAAGGACTCCCT 4975
                         i    i  iii   i v  v   i v  vv     v      i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_24865587_2   4976 ACTCAATAAATGGTGCTGTG-----T---TAGCCATATGCAGAAGATTGA 5017
                         vi    i           v ----- ---  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_24865587_2   5018 AGCTGGACCCCTTCCTTAAGCCATATACAAAAATCAACTCAAGATGAATT 5067
                           i         v   i vi              i       i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_24865587_2   5068 AAAGACTTAAATGTAAAACCCAAAACTATAAAAATCCTGGAAGACCACCT 5117
                          ?    i         i v i            v  i i     vv  v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_24865587_2   5118 A--TTCAATACCATACTGGACATAGGAACTGGCAAAGATTTCAT-GATGA 5164
                          --?vi  - i v - vv   v v  iviv     v i    v -   - 
  L1M4_orf2#LINE/    549 AGGNGTAA-ATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_24865587_2   5165 AGACACCAAATGAATTTGCAACAAAAGCAAAACTTGACAAATGGGATTT- 5213
                         v         v v ivv          v    v v  i    v   i  -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_24865587_2   5214 ATTTAAACTAAAGAACTTCTGCACAGCAAAAGAAGCTATCAATACAGTAC 5263
                           iv   i    -     i  i------------   -    ---  v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAA-AACTTTTGT------------GCT-TCAA---AGGAC 678

  chrX_24865587_2   5264 TATCAATACTATCAGTATAGTAAACTATCAATACAGTAAATTATCAATAC 5313
                         -----------------------        v v   i  -----  ---
  L1M4_orf2#LINE/    679 -----------------------ACTATCAAGAAAGTGAA-----AA--- 697

  chrX_24865587_2   5314 AGTAAACAACCTACAGAATGGGAGAAAATAT--GCA---------TCTGA 5352
                         ----i      i                   --   ---------     
  L1M4_orf2#LINE/    698 ----GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_24865587_2   5353 CAAAGGTCA-ATGTCCAGCTTCTATAAGGAACTTGAGCAAATTTACAAGA 5401
                         i  i  v v-i i     vv v     i     ivvi   v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_24865587_2   5402 GAAA-ACAAACAACCCCATTAAAACATAGGCAAAGGACATGAACAGACAC 5450
                         i   -     i     v   ?   v  i         iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_24865587_2   5451 TTCTCAAAAGAAGACATACAAGCGACCAACAAGCATATTTTAAAAAGCTC 5500
                              v        i      ii i    i     i  vvv  i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_24865587_2   5501 AATATGACTGAGCAT 5515
                           i  v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.82 (84 / 22)  

3554 22.20 0.84 0.72  chrX_24865587_24874620.rev     7706  8543 (491)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_24865587_2   7706 ATATACAGATTCAATGCAATCT-TATCAAAATTCCAATGGCATTTTTAAC 7754
                           v           i      i-         i   iiv  v     vi 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_24865587_2   7755 AGAAATAGAAAAAATAATTTTAAAATTATTATGG---TACCAAAAAAATT 7801
                               v  v  iv i  ii       vv     --- i --  iii ii
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC--AAGGGACC 167

  chrX_24865587_2   7802 CCAAATAGCCAAAACAATTTTGAGAAAGAAAAAATAAAGTTGGAGGTATC 7851
                          vi               i    i      i  -i           vv  
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAA-CAAAGTTGGAGGACTC 216

  chrX_24865587_2   7852 ACACTTCCTGATTTCAAATTATATTACAAAGCTACAGTAATCAAGACAGC 7901
                                 ii        viv  i                         i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_24865587_2   7902 ATGGTACTGGCATTAAAACAGGAACATACACCAATGGATTAAAACAGAGA 7951
                         i            v ii i  iv i   v i       v  i  iv    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_24865587_2   7952 GCCCAGAAATAAACTCAAGCATATATGGTCAGCTAATTTTCAAGAAGTCC 8001
                          i            i  vi   v        ii i      i v   vvi
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_24865587_2   8002 ACCAAGAAGAAAAAATGGGGGAAAGGATTGTCTCTTCAATAAATGGTGCT 8051
                         i      vv vvv       -    i  v    i     i          
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_24865587_2   8052 GGGAAAACTAGAAGTCCATATGCAAAAGAATGAAATTAGACCTTTATCTT 8101
                             v    i  vi?   i               i  i    ii  i  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_24865587_2   8102 ATACAATACACAAAAATCAACTCAAAATGGATTAAAGACCTAAACATAAG 8151
                          i  v   i        i              i ?         ii    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_24865587_2   8152 ACTTGAAACCAAAAAACTCCTGGAAGAAAACATAGGGGGATCACTTCTTG 8201
                          vi i    i v       i i              ? v vvv    v  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_24865587_2   8202 ATATTGACCTTGACAATTAATTTTTTTTATATGGCATCAAAAGCACAGGC 8251
                          iv   ivi v i    -ii   i  vv     i  i          i  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAAT-GGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_24865587_2   8252 AACAGAAGCAAAAATAAACAAGTGGGACTGTATCAAACTAAAAAGCTTCT 8301
                             i   v       i i  i v     vi      v v    i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_24865587_2   8302 GCACAGCAAAGGAAACAATCAAGAAAATGAAAAAATAACCTACAGGCTAT 8351
                          ii vv       v  v         i      i i    i    iv iv
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_24865587_2   8352 AAGAAAATATTTGCAAACCATACAGCTGATAAGGAGTTAATATCCAAAAT 8401
                         i                i    i v         iii vi      i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_24865587_2   8402 ATATAAGGAACTCTTACAACCTAACAGCTAAAAAAA-AGATAATTGGATT 8450
                               i             ii  i i-      i - i    iivi   
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATT 813

  chrX_24865587_2   8451 -AAAAATAGGCAAAGGACTGGAATAGATATTTTTCCAAAGACGACATAAA 8499
                         -      i         i v       i    i        v  i   v 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_24865587_2   8500 AATG-CCAACAGGTATATGAAAAGGTACTCAACATCACTAACCAT 8543
                             -    i i i i        i i          ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (121 / 62)
Gap_init rate = 0.01 (10 / 839), avg. gap size = 1.30 (13 / 10)  


2575 31.50 1.21 1.21  chrX_24895169_24901435.rev     4870  5777 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_24895169_2   4870 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATCAATATCATGAAAAT 4919
                              ii i  i     i       iv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_24895169_2   4920 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4969
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_24895169_2   4970 TACCAACGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5017
                          v   i vi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_24895169_2   5018 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAG 5067
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_24895169_2   5068 AACAAAGCTGGAGGTATCACGCTATCTGACTTCAAACTATACCACAAGGC 5117
                                i      vv    i  vi ii i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_24895169_2   5118 TACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATGTGGACC 5167
                                 i   i    ii     i   i iv ii i   v  i i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_24895169_2   5168 AATAGAACAGAACGGAGCCCTCAGAAATGATACCACACATCTGCAACCAT 5217
                            i   i    iv   vvii       i vv   i    i iiiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_24895169_2   5218 CTGGTCTTTGACAAACCTGACCCAAA--CAAGAAATAGGGAAAGGATTCC 5265
                         i  i i  i     ivv  --    i--  vvv   i       i  vvi
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTG--CCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_24895169_2   5266 CTGTTTAATGAATGTTGCTGGGAAGACAGGCTGACCATGTGTAGAGAGCT 5315
                           v  i  ii    v        vi  v  v i?   ii  i i iiiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_24895169_2   5316 GAAGCTGGATCCCTTACTTACACCTCATACAAGAATTGATTCAGGATGGA 5365
                             i    i    vv  i     vi      i    i i   ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_24895169_2   5366 TTAAAGACTTAAATGCTGGACCTGGAACCATGGAAACCCTGGAGGAAGGC 5415
                          i ?    i      ivi  v  ii   i  ii  vi i i  i   ii 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_24895169_2   5416 CTAGGCAGTGCCATC--CGGGACACGGGCATGGGCAAGGACTTCATGACT 5463
                         v    ?-  iv-   --  v   viv  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_24895169_2   5464 GGAGCACCAGAAGTGATGGCAATGGG-GCCAAAATTGACAAATGGGATAT 5512
                         ivii     i   iivvi    iiii- vv     v  i    v   iv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_24895169_2   5513 AATTAAACTAAGGAGCTTCTGCACAGCAGAGGAGGCTACCATCGGAGCAG 5562
                         v  i   v v ii i   i  ii vv  i    vi   i  ----  v i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA----AGAAA 690

  chrX_24895169_2   5563 GCG----GGCAACCTACCAAATGGGAGAAAATTTTTGCAATCTACCCATC 5608
                          i ---- i     i  vi             v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_24895169_2   5609 TGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTGCA 5658
                            i  i  i  vi          v  i        ivv    v ivii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_24895169_2   5659 AGAAAAAAATCAAACAACCCCACTGGAAAGTGGGCAAGGGATATGACCAG 5708
                          v     i -    i     v i ?i   i       i    v   vi  
  L1M4_orf2#LINE/    791 ATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_24895169_2   5709 ACCCTTCTTGGGAGAAGACATCTGTGCAGCCAACAGACACATGAAAGAAT 5758
                           vi    ivii      i  viiviii     i ii         ii  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_24895169_2   5759 GCTCATCATCGCCGGCCAT 5777
                              v    i????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (188 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


2313 16.93 0.33 25.35  chrX_24926261_24928938.rev      977  2187 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_24926261_2    977 TAGAAAAATACTCCAGGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 1026
                          i    i   ii   v                 v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_24926261_2   1027 GTCCATACTACCCAAAACAATATACAGATTCAATACAATCCCGATCAAAA 1076
                          v v     v      vii  v           ii       v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_24926261_2   1077 TACCAATGGCATTCTTCATAGAAATAGAAAAAAAAAATCATAAAATGTAT 1126
                          v   iiv  v  i  iii      v  v  ivvi -  v      vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_24926261_2   1127 ATGGAACTGCAAAAGACCCAGAATAGCCAAAGCTATCCTAAGCAAAAAAG 1176
                               v     ii                 i v   i i i-   i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAG 198

  chrX_24926261_2   1177 AACAAAACTGGAGGAATCACATTGCCCAACTTTGAATTATACTACAA-GC 1225
                               ii       v     i v     i  ii  viv        -  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_24926261_2   1226 TATAGTAACCAAAACAGCATGGTACTGGCATAAA-ACAGACTCATAGACC 1274
                           i     i   i    ii              i- i    vi     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_24926261_2   1275 AATGGAACAGAATAGAGAACCCAGAAACAAATGCACACACCTACAGTGAA 1324
                                i     v    ii       i   iv  i   ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_24926261_2   1325 CTCACTTTTGACAAAAGTGCCAAGAACAGGCCGGGCGCGGTGGCTCACGT 1374
                         i v i   i     ii         -------------------------
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGA------------------------- 373

  chrX_24926261_2   1375 CTGTAATCCCAGCACTTTGGGAGGTCAAGGTGGGTAGATCACGAGGTCAG 1424
                         --------------------------------------------------
  L1M4_orf2#LINE/    374 -------------------------------------------------- 373

  chrX_24926261_2   1425 GAGTTCGAAACCAGCCTGATCAACATGGTGAAACCCCATCTCTACTAAAA 1474
                         --------------------------------------------------
  L1M4_orf2#LINE/    374 -------------------------------------------------- 373

  chrX_24926261_2   1475 ATATGAAAATTAGCCAGGCATGGTGGCGCCCGCCTGTAATCCCAGCTACT 1524
                         --------------------------------------------------
  L1M4_orf2#LINE/    374 -------------------------------------------------- 373

  chrX_24926261_2   1525 CAGGAGGCTGAGGCAGGAGAATCACTCAAACCTGGGAAGCAGAGGTTGCA 1574
                         --------------------------------------------------
  L1M4_orf2#LINE/    374 -------------------------------------------------- 373

  chrX_24926261_2   1575 GTGAGCCAAGATCATGCCATTGCACTGCAGCCTGGGTGACGGAGCAAGAC 1624
                         ----------------     -----------------------------
  L1M4_orf2#LINE/    374 ----------------CCATT----------------------------- 378

  chrX_24926261_2   1625 TGCATCAAAAAAAAAAAAAGTGCCAAGAACATACATTGGGGAAAGGACAG 1674
                         -----------------------   ----------         i i  
  L1M4_orf2#LINE/    379 -----------------------CAA----------TGGGGAAAGAATAG 395

  chrX_24926261_2   1675 TCTCCTCAATAAATGGCGCTGGGTAAACTGGATATCCATATGCAAAAGAA 1724
                            ii    i      i      vv         ?   i           
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_24926261_2   1725 TTAAACTAGATCACTCTCTCTTGTCATATACAAAAATCAAATCAAAATGG 1774
                          v  ii i  i v  vi   viii             i  v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_24926261_2   1775 ACTGAAGACTTAAATCTAAGACCTCAAACTATGAAGCTCCTACAAGAAAA 1824
                          iii?    i     v     v  v       i  i   i  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_24926261_2   1825 CATGAGGGAAAATCTCCAGGACATTGGTCTGGGCAAAAAAATTTTAGCAA 1874
                            ii ? v      i iv   v    vi i     viivv i    vv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_24926261_2   1875 TAAC-CCACAAGCACAGGCAACCAAAGCAAAAATAGACAAATGGGATCAC 1923
                          i  -   v       i     v    v         i    v   iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_24926261_2   1924 ATCAAA-TTAAAAAGCTTCTACACAGCAAAGGATACAATCAACAAAGTGA 1972
                               -       -   i iii vv       i  v     v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_24926261_2   1973 AGAGACAACCCATGGAATGAGAGAAGATATTTGCAAACTACCCACGTGAC 2022
                          i          ii     i     i           ii ivi iv   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_24926261_2   2023 AAGGGATTAATAACCGGAATATATAAGGAGCTCAAACAACCCTGTAGGAA 2072
                               i vi  v  i          i  i   vv     i vi  iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_24926261_2   2073 AAAAACATAATAATTCAATCAAAATATAGGCAAAAGATTTGAATTGACAT 2122
                            i   -     ii    i?   v  i      i         v     
  L1M4_orf2#LINE/    795 AAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_24926261_2   2123 TTCTTAAAAGAAGACATACAAATGGCAAACAGGCATATGAAAAGGTTCTC 2172
                             iv        i           v  i i   i        i v   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_24926261_2   2173 CACATCATTGATCAT 2187
                         v      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (130 / 71)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 28.27 (311 / 11)  


3222 27.53 0.44 0.44  chrX_25105943_25111725     4383  5290 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25105943_2   4383 TGGAAGAACATTCCATGCTCATGGCTAGGAAGAATCAATATCGTGAAAAT 4432
                              ii i  i     i      v v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25105943_2   4433 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4482
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25105943_2   4483 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTAA 4530
                          v   iivi i  i  ii     -   -- v  i  - iii    i  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_25105943_2   4531 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4580
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_25105943_2   4581 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4630
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_25105943_2   4631 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAAATC 4680
                                 i   i    ii         i iv ii i   v     i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_25105943_2   4681 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACGTATCTACAACT 4728
                                i    i--    i  --        vv   iii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_25105943_2   4729 TTCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 4778
                         vvi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_25105943_2   4779 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4828
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_25105943_2   4829 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4878
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_25105943_2   4879 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4928
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_25105943_2   4929 CTAGACATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4978
                         v   i?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_25105943_2   4979 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5028
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_25105943_2   5029 TTAAACTAATGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAA 5078
                          i   v v vi i   i  ii vv    i  v    i  vv i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_25105943_2   5079 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5128
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_25105943_2   5129 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 5178
                         i  i  vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_25105943_2   5179 AAACAAACAACCCCAACAAAAAGTGGGCGAAGGATATGAACAGAGGCTTC 5228
                          i     i     v vi?    i     i      v    i   vii   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_25105943_2   5229 TTGAAAAAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATT 5278
                          iv   i    i  vi viii     v ii          i       vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_25105943_2   5279 ATCACTGGTCAT 5290
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1281 27.49 0.79 0.52  chrX_25138264_25142905.rev     2949  3330 (1312)    L1M4_orf2#LINE/L1       20   402 (506)  

  chrX_25138264_2   2949 CATGGATGGGTAGAATCAATATTGTGAAAATGACCATACTGCCAAAAGCT 2998
                                v  v   v i        v  i   i v     v  v   viv
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chrX_25138264_2   2999 ATCTACATATTCAATGCAATTCCCATCAAACTACCATCATCATTCTTCTC 3048
                                v      i     i  i      v v   v vv v  i  iv 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_25138264_2   3049 AGAA-TTAAAAAA--AAATCTAAAATTCATATGGAATCAAAAAAGAGCCC 3095
                             -  i v  i--i vi                 viiv  ii  v  v
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_25138264_2   3096 ACATAGCCAAAGCAAGACTAAGCAAAAAAGACCAAATCTGGAGGCATCAC 3145
                         iv         i   vvi i i-   i    v    vi      vv    
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAA-AAAGAAGAACAAAGTTGGAGGACTCAC 218

  chrX_25138264_2   3146 ATTACCTGATTTCAAACTATACTATAAGGCCATAGTCACCAAAACAGCAT 3195
                          i v  ii        viv     i  i  i i   v i   i    ii 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chrX_25138264_2   3196 GGGACTGGTACAAAAAATAGGCACATAGACCAATGGAAAAGAATAGAGAA 3245
                           v     i i  ii -   i  i     i        v     v    i
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_25138264_2   3246 CCCAGAAATAAACCCAAATACTGATAGCCAACTGATCTTTGACAAAGCAA 3295
                         i               v i i v  i i   i    i  i     i vvi
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_25138264_2   3296 GCAAAAACATCAAGTGGGGAAAGGACAACCTTTTC 3330
                         v   i v   iv i         i i ii      
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

Transitions / transversions = 1.39 (61 / 44)
Gap_init rate = 0.01 (4 / 383), avg. gap size = 1.25 (5 / 4)  

1911 26.50 0.58 0.00  chrX_25138264_25142905.rev     3635  4151 (491)    L1M4_orf2#LINE/L1      389   908 (0)  

  chrX_25138264_2   3635 AGGACATCCTTTTCAACAAATGGTGCTGGGATACTTGGCTAGCCACATGT 3684
                           i i vi                       i vi   v  ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_25138264_2   3685 AGGAGAATGAAACTGGATCTTCATTTCTCACCTTACACAAAAATCGACTC 3734
                          ii        ii    i iii ii  v    v  i        ii    
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_25138264_2   3735 AAGATAGATCAAGGACTTAAATA-AAGACCTGAAACTATAGAAATTCTAG 3783
                           i  i     ?i   i     i-    v  i        i  v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_25138264_2   3784 AAGATAACATTGGAATAACCCTTCTAGATATTGGCTTAGGCAAGGATTTA 3833
                             v     v  ?i   vi    vv  iv    v        v i   v
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_25138264_2   3834 TTGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATTGCTG 3883
                           iivi v  vv         v v    i    iv   i   i  viv v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_25138264_2   3884 GGACTTAACTAAACTAAAGAACTTATGCACAGCAAAAGGAACAGTCAGCA 3933
                               v ii   v v  i     v  ii vv    i iv  vi   iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_25138264_2   3934 GAGTAAACAGACAACCCACAGAGTGGGAAAAACTCTTCACAATCTATACA 3983
                         i   i  v              i     i   v v  ii   vii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_25138264_2   3984 TCTGACAAAGGACTAATGCCCAGAATCTACAACAAACTCAAACAAATTAG 4033
                              i  i     vi ii       v  i  vi     vv    v i i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_25138264_2   4034 TGAGAAAAAAACAAACAATCCCATCAAGAAGTGGGCTAAGGACCTGAACA 4083
                          i v     i     i  i  v  i? i  i     v     ii    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_25138264_2   4084 GACAATTCTCAAAAGAAGATATACCAATGGCTGACAA--ACATGAAAAAA 4131
                             v     v             v      ii i  --         i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_25138264_2   4132 TGCTCAAAATCACTAATGAT 4151
                                v    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (81 / 52)
Gap_init rate = 0.00 (2 / 520), avg. gap size = 1.50 (3 / 2)  


2926 26.54 0.80 1.48  chrX_25186043_25192457.rev     5039  5916 (499)    L1M4_orf2#LINE/L1        1   872 (36)  

  chrX_25186043_2   5039 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5088
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25186043_2   5089 GGCCATACTGCCCAAGGTAATTGACAGATTCAATGCCATCCCCATCAAGC 5138
                            v     v     iv i  iv          i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25186043_2   5139 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5186
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_25186043_2   5187 CATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAG 5236
                         i      viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_25186043_2   5237 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATTCTACAAGAC 5286
                                i      vv   ii  v  ii i      viv v      ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_25186043_2   5287 TACAGTATCCAAAACAGCATGGTACTGGTACTAAAG-CAGATATATAGAC 5335
                                vi   i    ii         i -   i -i   i       i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGAT 297

  chrX_25186043_2   5336 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACCACATAGCTACAA 5385
                                 i    iv   ivii         -   --  i i vi  iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAA-ACC--CATACATTTATGG 344

  chrX_25186043_2   5386 CCATCTGATCTTTGACAAACCTGACAAAAAAACAAGAAATGGGGAAAGGA 5435
                         i  vi    i  i     ivv  v   i v--  vvv           i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGAC--CATTCAATGGGGAAAGAA 392

  chrX_25186043_2   5436 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 5485
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_25186043_2   5486 AGCTCAAACTGGATGCCTTCCTTACACCTTACACAAAAATTAATTCAAGA 5535
                         iiv v  ii    iv   v   i     v  i           i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_25186043_2   5536 TGGATTAAAGACTTAAATGTTAGACCTAAAACCATTAAAACCCT-AGAAG 5584
                              i ?    i       v   v       i  -     i  -     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAG 541

  chrX_25186043_2   5585 AAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAA--GTACCTC 5631
                              v    ?i- v i -   iv   v v  vv i     --  vi  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_25186043_2   5632 ATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAGAATAGACAAATG 5681
                          -  -  vi            vvi          vv i      i    v
  L1M4_orf2#LINE/    591 A-GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_25186043_2   5682 GGATCTAATTAAACTAACAAGCTTCTACACGACAAAAGAAACTACCATCA 5731
                            ii v  i   v v v  i   i iii vv    i  v    i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_25186043_2   5732 GAGTGAAGAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACCCA 5781
                         i      i  i  i  i                 v       vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_25186043_2   5782 TCTGACAAAGGGCTAATTTCCAGAATCTACAAAGAACTTAAACAAATTTA 5831
                              i  i  i  vi v        v  i        ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_25186043_2   5832 CAAGAAAAAAATCAAACAACCACATCAAAAAGTGGGCAAAGGATATGAAC 5881
                         i  v     i -    i    vv  i?    i            v    i
  L1M4_orf2#LINE/    789 TAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_25186043_2   5882 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAA 5916
                              i     v        i  vi viii     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.02 (16 / 872), avg. gap size = 1.25 (20 / 16)  


3331 25.86 0.55 0.22  chrX_25194427_25202661.rev     2884  3788 (4447)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25194427_2   2884 TGGAAACACATCCCATGCTCATGGATAGGTAGAATCAATATTGTGACAAT 2933
                               v i        i        v  v   v i        v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25194427_2   2934 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 2983
                          i v     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25194427_2   2984 TATCACCATCATTCTTCACAGAATTAGAAAAA--AATTCTAAAATTCATA 3031
                          vi  v vv v  i  ii     v v  v  i--i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_25194427_2   3032 TGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAAACCAAACAAAAAGAA 3081
                              viiv  ii  v  v v         i   vviii  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_25194427_2   3082 CAAATAAGGAGGCATCACATTACCTGATTTCAAACTGTACTATAAGGCCA 3131
                             vvv     vv     i v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_25194427_2   3132 TAGTCACCAAAACAGCATGGTACTGGTATAAAATTAGGCATGTAGACCAA 3181
                         i   v i   i    ii         i    iiv   i   i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_25194427_2   3182 TGGAACACAATAGAGAACCCTGAAATAAACTCAAATACTTACAGCCAACT 3231
                              i v   v    ii  v         i  v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_25194427_2   3232 GATCTTCCACAAAGCAAACAAAAACATAAAGTCAGGAAAGGACATGCTTT 3281
                            i   v    i vviv   i v   vv i vi      i i vv    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_25194427_2   3282 TCAACAAATGGTGCTGGGATTATTGGCTAGCCACATGTACGAGAATGAAA 3331
                                            iv i   v  ?       i vi        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_25194427_2   3332 CTGGATCCTCATCTCTCACCTTATACAAAAATTAACTCAAGATGGATTAA 3381
                         i    i  ii i   v    v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_25194427_2   3382 GGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATTG 3431
                         i   i    iv     v  i           v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_25194427_2   3432 GAATAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAAC 3481
                          ?i   vi    vv   v    v        v i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_25194427_2   3482 CCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTAATTAA 3531
                                  v v    i    iv   i   i   iv v    i v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_25194427_2   3532 ACTAAAGAGCTTTTGCACGGCAAAACGAATA--GTCAGCAGAGTAAACAG 3579
                          v v  i i      ii vv    -- i i --i   iv i   i  v  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAA--GGACACTATCAAGAAAGTGAAAAG 698

  chrX_25194427_2   3580 ACAACCCACAGAGTGGGAGAAAATCATCACAATCTATACATGTGGCAAAG 3629
                                     i           vv ii   vii   i  v  ii  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_25194427_2   3630 GACTAATATCCAGAATCTACAACAAACTCAAACAAATCAGTAAGAAAAA- 3678
                             vi          v  i  vi     vv    v   i   v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_25194427_2   3679 ACAAACAATCCCATAAAAAAGTGGGCTAAGGGCATGAATAGACAATTCTC 3728
                              i  i  v  v?    i     v    iiv          v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_25194427_2   3729 AAAAGAAGATATACAAATGGCCAACAAACTTACGAAAAAATGCTCAACAT 3778
                         v                       i  i vi i     i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_25194427_2   3779 TGCTAATGAT 3788
                         ii????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.28 (129 / 101)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.75 (7 / 4)  

3487 25.08 0.77 0.44  chrX_25194427_25202661.rev     6840  7744 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25194427_2   6840 TGGAAGGATATTCCATATTTATAGATTGGAAAAATTAATAATTTTAAAAT 6889
                              i     i    i  i  i        i v      v v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25194427_2   6890 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCACTGTCAAAA 6939
                          v v     v      vii              i      v  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25194427_2   6940 TACCAATGATATTCTTGACAGAAATAGAAAAAC-AATCCTAAAATTTATA 6988
                          v   iiviiv  i  vi       v  v  i -i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_25194427_2   6989 TAAAACCAGAAAAGACCCAAAATAGCCAAAGCTATCCT-AAGAAGAAGAA 7037
                          ii  viiv  ii      i          i v   i -  i        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_25194427_2   7038 CAAAACTGGAGGAATTACAATATCTGACTCCAAATTATACTACAGAGCTA 7087
                             ii       v i   v vi ii i i    viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_25194427_2   7088 TAGTAACCAAAACAGAATGGTACTTCCATAATAACAGACACACAGACCAA 7137
                         i     i   i    vi       vv     vi i     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_25194427_2   7138 CAGAACAGAATAGAGAACTCTGAAATAAATTCACAGACCTATAGTGAACT 7187
                         ii   i     v    iii v        ii  i v ii   i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_25194427_2   7188 CATTTTTGACAAAGGTGCCAAGAACATACACTGGGGAAAAGACAGTCTCT 7237
                         v     i     i          v   v  v        ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_25194427_2   7238 TCAATAAATGTTGCTGGAGAAACTGGATATTCATATGCAGAAGAATGAAA 7287
                             i     v      iiv         ?i  i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_25194427_2   7288 CTAGACCCCTATCTCTCGCCATATACAAAAGGCAAATCAAAATGGATTAA 7337
                         i i        i   v i            ivi  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_25194427_2   7338 AAACTTAAATCTAAGAATGCAAACTATGAAACTACTACAAGAAAACATTT 7387
                          i  i     v     iivv       i     vi  v          vv
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_25194427_2   7388 GGGGAAATTCTCCAGGACATTGGTCTGGGAAAAGATTTCTTGAGTAATAC 7437
                          ? v    -  i iv   v    vi i  v  v i      iii  vv  
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_25194427_2   7438 CCTACAA--ACAGGAAACCAAAGCAAAAATGGACACATGGGACCACGTCA 7485
                         v i v  --   i v   v    v      i  i v  v    iv i   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_25194427_2   7486 AG-TTAAAAAGCTTCTGCACAGCAAAGGATACAATCAGCAAAGTGAAGAG 7534
                          i-       -   i  ii vv       i  v    iv        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_25194427_2   7535 ACAATCCACAGAATGGGGAGGAAATATTTTTAATCTCCCCATCTGTCAAG 7584
                             i            -  i        vi  viivivi     vi   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGG-AGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_25194427_2   7585 AGATTAATAGCCAGAATATATAAGGAGCTCAAACAATTCTATAGGAAAAA 7634
                         i  i vi  v             i  i   vv    i  v   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_25194427_2   7635 TCCTAATAACTGGATCAAAACATAGGCAAAAGATTTGACTAGACATTTCT 7684
                         vv v      ivi  i?   v  i      i       v           
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_25194427_2   7685 CAAAAAGAAGACATA--GATGGCAAACAGGCATATGAAAAGGTGCTTGAT 7732
                          v   -     i   --i     v  i i   i        i    ii i
  L1M4_orf2#LINE/    848 CCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_25194427_2   7733 ATCACTGATCAT 7744
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (138 / 85)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.22 (11 / 9)  


2789 23.08 4.29 4.51  chrX_25343839_25348090.rev     2852  3761 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25343839_2   2852 TGGAAACACACCTCATGCTCACGGATAGGAAGAAACAATACTGTGAAAAT 2901
                               v i i i    i   i    v      vvi    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25343839_2   2902 GACCACACTTCCCAAAGCAATCTACAGATTCAATACAATTCCCATCAAAA 2951
                          i v i   i      vii              ii    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25343839_2   2952 TACCATCATCATTTTTCACAGAACTAGAAAAAACAATCCTCAAATTCATA 3001
                          v   v vv v     ii     v v  v  ivii     v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_25343839_2   3002 TGGAACCAAAAAAAGAGTCTGAATAGCCAAAGCGATACTAAGCAAAAAGA 3051
                              viiv  ii-  vi v           i i  vi i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_25343839_2   3052 ACAAATCTGCAGGTATCACATCACCAGACTTCAAATTACACTATTAATAC 3101
                              vi  v   vv     iiv  vi i      ----   --  v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACT--TACTAC 243

  chrX_25343839_2   3102 AAGGCTATAGTTACCAAAACAGCACGGTACTGGTATAAAAATAGGCATTT 3151
                           i    i   v i   i    iii        i    ii    i   v 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_25343839_2   3152 AGACCAATGGAACAGAATAGAAAACCCAAAAATAAAGCCAAATACTTACA 3201
                            i        i     v  i ii   i       v   v i i   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_25343839_2   3202 GCCAACTGATCTTCGGCAAAG----------CATACAA-------ATTAC 3234
                          i   i    i    i   i ----------   v   ------- vv i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_25343839_2   3235 A-------CAATAAATGGTGCTGGGAAAATTGGCAAGCCACATGTAGAAG 3277
                          -------   i              v  i   vv ?       i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_25343839_2   3278 AATGAAACTGGATCCCCGTCTTTCACCTTATATAAAAATCAACTCAAGAT 3327
                               ii    i   iii  iv    v    i      i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_25343839_2   3328 GGATCAAACACTTAAATCTAAGACCTGAAATTATAAAAATTCTACAAGAT 3377
                               ? v  i     v     v  i   i       v ii  v    v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_25343839_2   3378 AACATTGGAAAAACTCTTCTGGACATTTGTCTATGCAAATAATTC----- 3422
                              v  ?iv  v     vv   v  v vi  v    - ii  i-----
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAG 592

  chrX_25343839_2   3423 --ATGACTCCAAAAGCAAATGCAACAAAAACAAAAATA----AATGGGGC 3466
                         --     v         v v         iv       ----   v  i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_25343839_2   3467 ATAATTAAACTAGAAAGCTTCTGTAC--AGAAAAAAAATAAAAAAAATAG 3514
                         v v  i   v vi   i   i   i --vi  ii v v  vv  i  ---
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA--- 689

  chrX_25343839_2   3515 TCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATATTTGCAAACTAT 3564
                         ----   i  v              i                    ii  
  L1M4_orf2#LINE/    690 ----AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_25343839_2   3565 GCATCTGACAAAGGACTAGTATCCAGAATCTACAAGGAACTCAAACAAAT 3614
                         ii      i  i     v           v  i  i      vv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_25343839_2   3615 CAGCAAGAACAAAACAAATAATCCCATCAAAAAGTGGGCAATGGACATGA 3664
                           ii  v  v  i        i  v  i?    i       v   iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_25343839_2   3665 ATAGACATTTCTCAAAAGAAGATTGATTAGATATTTCCCAAGAAAAGATA 3714
                                      v         ------------------------   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGAT------------------------ATA 861

  chrX_25343839_2   3715 CACAATCATCCAACAA--ACATGAAAAAATACTCAACATCACTAATCAT 3761
                           -   vi-    i  --         i  i          ????????
  L1M4_orf2#LINE/    862 CA-AATGG-CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (121 / 85)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 5.33 (80 / 15)  


1700 26.08 5.64 5.24  chrX_25405041_25407041.rev      334  1096 (905)    L1M4_orf2#LINE/L1       64   829 (79)  

  chrX_25405041_2    334 AAACCAATTTACAGGCTGGGCTCCATTC-TAGTAAAACCACACATTAC-- 380
                            iii  i     ii vii v v  i -  vi    i v  -ii i --
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA-GCTGCCT 112

  chrX_25405041_2    381 -TTTTACAGAAA---ACTACCGGGCTCTGAAATTCTACATGCACACACAA 426
                         -    i      ---  v v v iii  i      - i   v v ii   
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC-ATATGGAAATGCAA 161

  chrX_25405041_2    427 CAAGA---AGAAGAAC-AAAGCCATCCTTTCAGTCCTTAGGTTCACATCA 472
                         -ii  ---    v i -   i v   --  v i----------- v vv 
  L1M4_orf2#LINE/    162 -GGGACCCAGAATAGCCAAAACAATC--TTGAA-----------AAAGAA 197

  chrX_25405041_2    473 GTTAACAAGGTTAAAGAACTCTGGATGTT-----ACTTCGAAATATAATA 517
                          --     i   ii  i    --- iii ----- i   i   iv  v  
  L1M4_orf2#LINE/    198 G--AACAAAGTTGGAGGACTC---ACACTTCCCAATTTCAAAACTTACTA 242

  chrX_25405041_2    518 CAAGGCTATAGTAACCAAAACAGCAAGGTAC--ATATAAAAATAGAAACA 565
                            i    i     i   i    iiv     --ii    ii     v i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_25405041_2    566 TAGATGAATGGAAAAGAAGAGAAAACCCAGAGATAAAGCCACATACCTAC 615
                              v       v    vv  i ii     i     v   i i ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_25405041_2    616 AGCCAACTGATCTTCAA----------AAAAACATAC--TGGGGAAAAGA 653
                         i i   i    i   i ----------  i v   v --        ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_25405041_2    654 TACCCTCTTGAATAAATGGGGCAGGTGA-AATTGGGCAGCCATTTACAGA 702
                           vi  i  v  i      v  v  -  -  i   ii ?   iv i  i 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGG-GACAACTGGATAKCCACATGCAAA 441

  chrX_25405041_2    703 AGAATGAAACTGGGCCCCTATCTCTCACAATACACAAAAATTAACCCAAT 752
                                 ii   i      i   v   v   i            i   v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_25405041_2    753 GTGGATTAAAGATTTATATGTAAGACCTTAAACTATAAAAATTCAAGAAG 802
                         i     i ?   ii  v        v  v           v iiv     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_25405041_2    803 AAAACCTAAGA--AAACTTCTTCTGGACATTGGCCTAGACAAAGTATTCA 850
                              v  i ?--   --     vv   v    vi   i   v vv   v
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_25405041_2    851 TGAATAAAGCCTCAAAAGTAAATACAACCAAAACAAAAACAGACAAATGG 900
                          ii   vii vi      i v vi    v   iv     i   i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_25405041_2    901 AACT-AACTTAAACTAAAAGCTTCTGTATAGAAAAAGATATGATCAACAG 949
                         i   -v iiv   i     i   i   iivvv   i  i iv     v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_25405041_2    950 AGTGAACAGACCACCAGACAACCTACAAAATGGGAGAAAATATTTGCAAA 999
                               ------ --        i   i                      
  L1M4_orf2#LINE/    690 AGTGAA------A--AGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_25405041_2   1000 CTACGCATCCAACAAAGGACT-----CCAGAATCTACCAGGAATTC--A- 1041
                         ii iii   ii i  i     -----       v  iv i   i  -- -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_25405041_2   1042 AACTCAACAACAACAACAAAAGCCCACAAATAGCCCCAT-AAAAAGTGGG 1090
                                i  i  -----    ---       i   v  -?    i    
  L1M4_orf2#LINE/    782 AACTCAATAATAA-----AAAG---ACAAATAACCCAATTWAAAAATGGG 823

  chrX_25405041_2   1091 CAAAGG 1096
                               
  L1M4_orf2#LINE/    824 CAAAGG 829

Transitions / transversions = 1.95 (129 / 66)
Gap_init rate = 0.04 (29 / 766), avg. gap size = 2.86 (83 / 29)  

 384 25.32 4.43 2.53  chrX_25405041_25407041.rev     1353  1510 (491)    L1M4_orf2#LINE/L1      748   908 (0)  

  chrX_25405041_2   1353 GGACATGTACCCCCTGAATCTAAAATAAA-------AGTTAAAAAATAAA 1395
                             v    i  v--    v  v  vi  ------- ii v  v      
  L1M4_orf2#LINE/    748 GGACTTGTATCCA--GAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_25405041_2   1396 ATAACAATTATGGTTATTTTTTAAAGTGGGAAAAAGACATGAGCAGATAT 1445
                          vi    --  iiiivvv  ?v   i    v   i  iv   ii   i  
  L1M4_orf2#LINE/    796 AAGACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_25405041_2   1446 TTTTCAAAAGAAAACATACAAATGGCCAAAAGATATATGAAAAAATGCTC 1495
                           i  v      i i              v iii i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_25405041_2   1496 AACATCACTAATCAC 1510
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (23 / 16)
Gap_init rate = 0.02 (3 / 161), avg. gap size = 3.67 (11 / 3)  


2971 26.94 2.36 0.45  chrX_25412887_25417475     3206  4096 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25412887_2   3206 TGAAAAGATATTCCATAATAATG-ACTGGACGAATTAATATACTTAACAT 3254
                           i        i    iv v   - i    v  v       vv    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25412887_2   3255 GGCCATCCTGCTCAGAGCAACCTACAGACTCAATGCAATCCCTATAAAAG 3304
                            v  v  v i  i vii i       i    i           v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25412887_2   3305 TACTAATATCATTTTTCACAGAAAT--ACAAAAAAAATTCCTAACATTTG 3352
                          v i iivv v     ii       --    ivvi --      v   ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chrX_25412887_2   3353 TATGGAACCATAAAAGACCCTCAACAGCCAAAGCAATTCTGAGCAGAAAC 3402
                                viii  ii     vv  i       i    ii   iv ii  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_25412887_2   3403 AATGAAGCTGGAGCTATTACACTACCTGACTTCAAAACATATTACAAGGT 3452
                           ii   i     vvv i     v  ii i        v  i     i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_25412887_2   3453 AATATTAACCAAAAGAGCATGATATTGGTATAAAAACAGACAAATAAACC 3502
                         v i v   i   i v  ii  i  i   i    ii i     v   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_25412887_2   3503 AATGGAACAGAATAGAGAATTCCAAAGTAAATTCATGTATTTACAACCAA 3552
                                i     v    i i vi  i    ii   ii     iiii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_25412887_2   3553 CTGATCTTCCACAAAGGCATGAAGAACATACATTGGGGAAATAATAGTCT 3602
                         i    i   v    i  iiiv    v   v  v        v        
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_25412887_2   3603 CTTCAATAAATGATGCTGGGAAAATTGAATATCCATATGCAAAAGAATGA 3652
                         i     i     i        v  i  i   ?   i              
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_25412887_2   3653 AACTGGACGCTTTATCTCTCACCATTTACAAAAATCAACTCAAGATGGAT 3702
                          ii     - ii  i   v      v         i       i      
  L1M4_orf2#LINE/    449 AGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_25412887_2   3703 TAAAT-CTTAAATATATGACCTGAAGCTATAAAACTACTAGAA-AAAACT 3750
                         i ? v- i     i  v  v  i  i          vi     -     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_25412887_2   3751 TTTGGACAATACTTTAGGA-----AATTGGTCAA-AATTTTATGGCTAAG 3794
                          vv ?ii  vv   iiv  -----ii  i v   -ii   iv i v  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_25412887_2   3795 ACTTCAAAAGCACAGACAATAAAA----AATTAGACAAATGGGACTATAT 3840
                           vi          ii   i    ----  v    i    v     vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_25412887_2   3841 TAAA-TGAAAAATCTCTGCACAG-AGAGGGTAGAAATCAACCAAGTGAAG 3888
                         i   - v     ii i  ii vv- i   ii vv -    vv       i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAAA 696

  chrX_25412887_2   3889 ACACAACCTGTTGGATGGGAGACAATATTTG-AAACCACTCATCTGACAA 3937
                          v      iiiv i        v        -   i  ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_25412887_2   3938 GGGAATAAAATCTAGAATATACAATGAATTGAAACAACTCAATAGTAAGA 3987
                             v viv   i        i  v   i vvv           i   i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_25412887_2   3988 AAACAAATACTACCATTACAAAGTGAGAAGAGGATATGAATACATAATTC 4037
                          i       viv v   ?v   i  i v i     v      v i v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_25412887_2   4038 TC---AGAAGAGATACAAATGGCCAACAGATACATGAAAAAATGCCCAAC 4084
                           ---      v              i iii         i    i    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_25412887_2   4085 ATCACTGATTAT 4096
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (147 / 89)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.79 (25 / 14)  


3319 24.10 2.82 0.68  chrX_25577043_25581381.rev     2961  3848 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_25577043_2   2961 GGAAAGATATTCCATGTTCATGGATTAGAATAATCAATATTGTTAAAATG 3010
                                   i               i   v v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_25577043_2   3011 TCCATATGAGCCAAAGCAATCTACAGATGTAATGCAATCTCTATCAAAAT 3060
                         v v   ivvv     vii          vi  i      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_25577043_2   3061 ACCAA-TATATTCTGCACAGAAATAGAAAAA--------AAAAATCA--- 3098
                         v   i- iiv  i vii       v  v  i--------    v   ---
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_25577043_2   3099 -------CAAAAGACCCAGAATAGCCAAAGATATTCTAAGCAAAAAGAAT 3141
                         -------   ii                 ivv  ii i iv  i     i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_25577043_2   3142 AAAACTGGTAGACTCACATTATCTGACTTCAAATAATACTAAAGAGCTAT 3191
                            ii   vi        i vi ii i      vvv     v i     i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_25577043_2   3192 TGTAAACAAAACAGTATGTTACTAGCATAAAAGCAGACACATAGATCAAT 3241
                         v    v   i     i  v    i      iiii     i          
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_25577043_2   3242 GGAACAGAATAAAGAGCCCAGAAACAAATCCACACATCTACAGTGAACTC 3291
                             i     vi    i       i   i   i    i  ii  v  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_25577043_2   3292 ATTTTTGACAAAGGTGCCAAGAACATACACTGGAGAAAAGACGGTCTCTT 3341
                              i     i          v   v  v   i    ii ii    i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_25577043_2   3342 CAATAAACGGTTCTGGGAAAACTGGATATCCATATGCAGAAGGATGAAAC 3391
                            i   i   v      v         ?   i     i   i     ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_25577043_2   3392 TAGACCTTTATCTCTTACCATATACAAAAATCAAATGAAAATGGATTACA 3441
                          i    ii  i   vi               i  v v         i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_25577043_2   3442 GACTTAAATCTATAGTCTCAAACTATGAAACCACTACAGGAAAAC-TGTG 3490
                            i     v  viiv  v       i    ivi  v i      - iv 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_25577043_2   3491 AG-AAATCTCTTG-GACATTGGACTGGGCAAAGAGTTATTAAGTAATACC 3538
                         ? -      - i -   v    ii i     v iv  v   ii  vv  v
  L1M4_orf2#LINE/    552 NGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_25577043_2   3539 CTACAAACACAGGCAACCAAAGCAAAAATGGACAAATGGG--TTAACATC 3586
                          i v  i    i     v    v      i  i    v  --  --    
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT--CATC 648

  chrX_25577043_2   3587 AAG-TTAAAAAAGCTTCTTTACAGCAAAAGAAACAGTCAACAAAGTGAAG 3635
                           i-       --   i v i vv    i  v  vi    v        i
  L1M4_orf2#LINE/    649 AAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_25577043_2   3636 AGACAACCCACAGAATGGGAGAAAATATTTGCAAGCTAGCCCTCTGACAA 3685
                                                           iii vviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_25577043_2   3686 AGGATTAATAACCAGAAGATACAAGGAGCTCACACAACTCTATAGGAAAA 3735
                         i   i vi  v      v   i  i  i   vi       v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_25577043_2   3736 AAATCTAATAATCTGATTTTTTAATGGGCAAAATATTTCAATAGACATTT 3785
                          i - v     i ii   ?vvv          iv    v           
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_25577043_2   3786 ATCAAAGGAAGACATAAAAATGCCAAACACACATATGAAAAGGTACTCAA 3835
                         v  v  i     i   v     v v  i vi  i        i i     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_25577043_2   3836 CATCATTGATCAT 3848
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (127 / 83)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 2.58 (31 / 12)  


2497 24.06 4.26 0.33  chrX_25598491_25600984      746  1356 (1138)    L1M4_orf2#LINE/L1        3   637 (271)  

  chrX_25598491_2    746 GACAGACATCCTGTATTCATGCATTGGAAGACTTAA----GTTAAAATGT 791
                           v   i    ii i      v              ----     i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_25598491_2    792 CTGTACTACCCAAAGTAACCTGCAGATTCAGTGCTATCTCCAACAGAATT 841
                          vi    v      v i i  i        ii  v   i i v  i   i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_25598491_2    842 AGAATAGCATGTTTTATGCAGAAAGAGA-AAATCAATCCTGCAATTCATA 890
                         vv iiv  v -    -        vv  -  iiii     iv        
  L1M4_orf2#LINE/    103 CCAGCTGCCT-TTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_25598491_2    891 TGGAACCACAAATGACCCAGAATAGACAAAGTGATCTTGAGAAAGAA--- 937
                              vii   iv            v    iii       i      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_25598491_2    938 CAAAGTTGGAGGCATCACAGTTCCTGATTTCAAAATGTATTACAA-GCTA 986
                                     vv     v    ii         iv  i     -    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_25598491_2    987 CAATAATTAAAACAATATGGTACTGGCATGAAGATGGAGATATGGACCAA 1036
                           i    i  i   i i            i i   i  v    i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_25598491_2   1037 GGGA---------------CGGAAATAAATCCGTACATATATTGCCAACT 1071
                         v   --------------- i        i  i     v   v i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_25598491_2   1072 GATCTTTGAGAAGAGTTCCAAGAACACACAGTGAGAAAAGGGAA--CTGC 1119
                            i  i  v   i  v      v  iv  i  i i    iiv --  vi
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_25598491_2   1120 TCAACAAATGGTGTTGGGAAAACTGGATATTCACATACATAAGAATACAA 1169
                                      i     v         ?i     i  v      iv i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_25598491_2   1170 TCAGACCCCTATATTACACCACACATAAAAACCAACTCAAAATGGACTAA 1219
                          ii        iv i      i i i     ii             ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_25598491_2   1220 CGACTTAAATGTAGGACCTGAAACCATAAAACCTCAAGAAGAAAACATAG 1269
                         v   i        i  v  i    i       iiiv              
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_25598491_2   1270 GGGAATATCTTCTGGATACTGGTCTTTGCAATGATTTCTTGGATATGATG 1319
                          ? v v      vv  ivi   vi vv      i      i       ii
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_25598491_2   1320 ACAAAAGCTTAGACGACAAAAGAAAAAACAGAGAAGT 1356
                         v       vi ii i             i   v  i 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

Transitions / transversions = 1.88 (94 / 50)
Gap_init rate = 0.01 (8 / 635), avg. gap size = 3.50 (28 / 8)  

1139 17.23 2.62 1.12  chrX_25598491_25600984     1735  2001 (493)    L1M4_orf2#LINE/L1      638   908 (0)  

  chrX_25598491_2   1735 TGGTACTACATC-AAACTAAAATATTTTACACCCCAAATGATATAATCAA 1783
                            -   v    -   i     vv    iii ii    v  i iv     
  L1M4_orf2#LINE/    638 TGG-ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_25598491_2   1784 CAGAATGAAAAGGCAGCCTACAGAATGGGAGAAAATATGTGCAAACTATA 1833
                         v i i       i  i  i                   v      ii   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_25598491_2   1834 CATCTGATAAGGGGCTAATTTCAAAAATATATAAAGAACTCCTACAA--- 1880
                         i            i  vi v  v i                i     ---
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_25598491_2   1881 -ATAGGAAATAAACATATAAACCCAATT-AAAAATGGGCAAAGGACTTGA 1928
                         -   iv   v i   v    -       -                i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_25598491_2   1929 ACAGAAATTTCTCCAA-GAAGACATACAAATGACCAACAAGGTATATGAA 1977
                          i   v          -     i         i    i   -i i     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAA 884

  chrX_25598491_2   1978 AATGTGCTCAAAATCATTAATTGA 2001
                           vi       v    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (30 / 16)
Gap_init rate = 0.03 (7 / 271), avg. gap size = 1.43 (10 / 7)  


3151 26.37 1.90 0.45  chrX_25608703_25611432.rev     1345  2239 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25608703_2   1345 TAGGAAAACATCCCATGTTCATGGATTAAAAGGATCAATATCACTAAAAT 1394
                          i i  i i                  ii   iv i     iii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25608703_2   1395 GACCAGACTTCCCGAAGCAATCTGCA-ATTCACTTCCATTCCTATCAAAA 1443
                          i v v   i   i  vii    i  -     viv v  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25608703_2   1444 TACCAA-TGTCATTTTCACAGAA-TT-AGAAGTAACAATCCTAAAATTCA 1490
                          v   i-  i v    ii     -  - v   i--ii             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chrX_25608703_2   1491 TAGGGAACCATAAAGGAGCCCAAATAGCCAAAGCAATTCTAAGCAAAAAG 1540
                           v    viii  i   v  vi          i    ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_25608703_2   1541 AGCAAAGCCAGAGTCATCACACGACTTGATTTCAAATTATACTG-AAAGT 1589
                          i     iii   vvv      vv iii        viv    i-    -
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG- 247

  chrX_25608703_2   1590 CTGTAATAGCCAAAACAGCATGGTACTAGTATAAAAACAGACACAAAAAT 1639
                           ii i  ii   i    ii       i i    ii i     i v i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_25608703_2   1640 CAATGGAACAGAATGAAGAAATCAGAAATAAAGACAAATACCTACAGCCA 1689
                                 i     vi   ivi          vv  v i ii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_25608703_2   1690 GTTTGATCTTTGACAAAGTCAACAGAAACATACACTGGGAATAGGACACC 1739
                         i  -   i  i     i viiv  ii v   v  v    i v  i i vi
  L1M4_orf2#LINE/    348 ATT-GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_25608703_2   1740 CTTTTCAATAAATTGTGCTGGGAAAATTGGATTCCCATATACAGAAGAAT 1789
                                 i    v         v  i     v?   i  i  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_25608703_2   1790 GAAACTGGACCCCTATCTTTCACCATATGCAAAAATTAACTCAAGATGAA 1839
                            ii          i  iv        i               i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_25608703_2   1840 CAAAATACTTAAATGTAAGACCTGAAGCTATATA--TACTAGAAGTAAAC 1887
                         iv ? v  i           v  i  i     v -- vi      v    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_25608703_2   1888 CTAGAAAAAACTCTTCTGGACATTGCCGTAGGCCAAGAATTCATAACTAA 1937
                         v   i?iv  v     vv   v   vvv     v v iv   v  iv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_25608703_2   1938 GACCTCAAAATTGAATGCAACAAAAACAAAAATAGACAAATGGGACT--- 1984
                            vi     viiv v         iv         i    v     ---
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_25608703_2   1985 --GAAACTAAAG-TTTCTGCACAGCAAAAGAAATAATCAATAGAATGAAC 2031
                         --i   i    i-i  i  ii vv    i  v iv     v i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_25608703_2   2032 AGACAACCTGCAGAATGGGATAAAATGTTCAAAAACTATGCATCTGACAA 2081
                                 ii          v     i  iiv   ii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_25608703_2   2082 GGGACTAATATCCAGAATCTACAAGGAACTC----AACTCCACAGCAAAA 2127
                               vi          v  i  i      ----     v i ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_25608703_2   2128 ATCCAAATAATCCAATCTAAAAATGGACAAATGATCTGAATAGTTATTTC 2177
                          vv       i     i?        i    v   i       vi     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_25608703_2   2178 TTTAAAGAAGACATACAAATGGCCAAAAGGCATATGAAAAAATGCCCATC 2227
                          ii        i              v i   i       i    i  v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_25608703_2   2228 ATCACTAATCAT 2239
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (149 / 83)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


2745 26.27 5.30 0.92  chrX_25618995_25620860.rev      508  1375 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_25618995_2    508 GAACGATATCCCATGTTTATGGATTTGAAGA----ATATTGTTCAAATGA 553
                            v             i       v     ----        v i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_25618995_2    554 CTGTAC-AATCAACTGTGATAAACAGATTCAATGCAATTCCTATTGAAAT 602
                          vi   -vvi   v -    vv          i     i     ii    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_25618995_2    603 ATCAATGACATTTCTCATGGAAATAGAAAAAACAATCCTAAAATTTGTTT 652
                         vi  iivi v   i iiii     v  v  ivii           ii v 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_25618995_2    653 GGAACTACAAAGGACCCAGAATAACTAATGCAATCCAGTACAGAAAGAAT 702
                             v i   i            i i  vi     iv v v ii     i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_25618995_2    703 GAAGCTGGCTGCATCACACTATCTCACTTCAAAACACACCACAAA-CT-- 749
                         i   i   vv vv       vi iv i        vi  i     -  --
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_25618995_2    750 -GTAGTTAAGTAAGCATGGTACTGGCATAAAAACAGATGCATATACCAAT 798
                         -   i i   vv  ii              ii i   iii   v i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_25618995_2    799 AGAACACAATAGAGAATAGAGAAATAAATCCACATGTTTCTAGCCAACTC 848
                         i   i v   v    i vv         i   i ii   v i i   i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_25618995_2    849 ATTTTTGGAAAAGGTGCCAAGAACATAGATTGTGGGAAAAGCAGTCTCTT 898
                              i iv  i          v   vv v  v  i  i ii     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_25618995_2    899 CCATAAATGGGACTGGAAAACCTGCATATCCATTTGCAGAAGAATAAAAC 948
                          v i      vi    i v v   v   ?   iv    i      i  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_25618995_2    949 TAGATCCCTATCTATCACCATATATAAAAATCAAATTGAAATGGATTAAC 998
                          i  i     i  vv         i      i  v ii        i ?v
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_25618995_2    999 GACTTAAATGTAAGACCTGAAACTATGAAATTACTAGAAGAAGACATTGA 1048
                            i           v  i       i   i vi        i    v i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_25618995_2   1049 GG-AAATGCCTTGGGACACTGGTCTGGGCAAAGGCTT--TAGGAGTAAAA 1095
                         ? -    - i i v   vi   vi i     v  i  --   i--  vi 
  L1M4_orf2#LINE/    552 NGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA--TATGA 598

  chrX_25618995_2   1096 TCTCAAAAGCATAGGCAATAAAT---AAAATACCAACAAATGGGATTATA 1142
                         ivi        i i    i   v---      --i i    v   i vi 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTCA 646

  chrX_25618995_2   1143 TCAAGCTAAAAAAATTTCCACCCAGCAAAGGAAACAAT--AGAAGG--AA 1188
                             iv v     v   i-iiv vv       v  v  --    i --  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_25618995_2   1189 GAGACAAGCTACAAAATGGGAGATAATATTTGCAAACTATCCATTTGACG 1238
                         i      v i   i         v            ii  vi  i   ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_25618995_2   1239 AGGAATT---------AATAACTAAA---------CAACTCAATAGCCAA 1270
                            i i ---------    vv    ---------          iiv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_25618995_2   1271 AAAA------ACCCATTTTAAAAATAGATAAATGATTTGAATAGACATTT 1314
                           i ------     v  ?      i ii   v                 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_25618995_2   1315 CT---GAAAAGACATAGAAATGACCAACAGCTATATGAAAAAAAGGCTCA 1361
                           ---i i    i   v     i    i ivi i       i -v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCA 894

  chrX_25618995_2   1362 CCATCATTAATCAC 1375
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 2.84 (54 / 19)  


3357 21.71 4.97 0.58  chrX_25689075_25691122.rev      694  1559 (489)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_25689075_2    694 AAAATATCTCCTGTTCATG-ATAGGAAGAATTATTATTGT---------- 732
                           i     i v        -  v      v   v      ----------
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_25689075_2    733 -------CCAAAACAATCTACAGCCTCAATGCAATCCCTATCAACATCCC 775
                         -------     vii        vi    i              v     
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_25689075_2    776 AATGACATTTTTTCCAGAAATATAAAAAACT-AT--TAAAATTCATGTGG 822
                          iivi v      v       - i v  i  -  --          i   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_25689075_2    823 TACCACAAAAGACCCCCAAACAGCCACA-CAATCTTGATAAAGAAGAACA 871
                         v vii   ii     v-i  i     v -         v           
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_25689075_2    872 AAGCTGGAGACATCACACTTCTTGATTTCAATATATATTACAAAGTTACA 921
                            i     ivv         iii       v iv  i       i    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_25689075_2    922 ACAGTGAAAACAGTAAAGTACTGGCATAAAGACAGACATACAGACTAATG 971
                         ii i v  i     ivi            i  i       i   ii    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_25689075_2    972 GAATGGAATAGAGAATCCATAAATAAAC--ACACATATATGGTCAACTGA 1019
                             i    v    i    v        -- i    v         i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_25689075_2   1020 TCTTTAATGAAGCTTCCAAGAATACCCAATGGAGAAATAATAGGCTCTTC 1069
                          i  ii ii i v v      vi ii      i    v     v  i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_25689075_2   1070 AACAAAGGGTGCAGGGAAAATTGAAAATCCAGCTGGAAAAGAATTAATTT 1119
                               v     v    v  i  i v ?   vv  v        v  v  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_25689075_2   1120 GGATACTTGTCTTACACCATACATTTTATTCAAGTCAAAATGGATTAACG 1169
                            iv i ii  i        i ivvv v i  v           i ?v 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_25689075_2   1170 ACTTAA------GACCTGCAACTGTAACACTTGTTGAAGAAAACACAGGA 1213
                           i   ------  v  iv    i   v   iv v          i   ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_25689075_2   1214 A-AATTCTTCATGACATTGGTCTTGGCAATGATTTCATAGATATGACACT 1262
                         i-  v     i    v    vi v       i    v            i
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_25689075_2   1263 AAAAGCACAGGCAACAAAAGCAAAAATAGATAG-TGGAACTAAGTCAAG- 1310
                                  i          v           i- v i   vvi    i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_25689075_2   1311 TTAAAAAGCTTCTGCACAGCAAAG--CA--AACAACAGAATTAAAAGGCA 1356
                                -   i  ii vv     --  -- v   v i i v     i  
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_25689075_2   1357 ACCTGCGGAATGGGAGAAAATATTTGCAAACCATATAGCAGATAAGGGGT 1406
                            ii i                       i      v v        ii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_25689075_2   1407 TAACTGCCAAAATATATAAAGGACTCA-ATAAC--AACAAAAACAAAACC 1453
                          viivv   i           i    v- i   --  i  v  v  i  v
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_25689075_2   1454 CTAATAACCCAGTT---AAATGGGCTGAGGACTTAAATAGACATTTCTCC 1500
                         --         i  ---        vi    i  i               
  L1M4_orf2#LINE/    802 --AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_25689075_2   1501 AAAGAAGATAGACAAATGTTCAGTAAGTATATCAAAAGATGCTCATCATG 1550
                                   v       vi  i    i i  v            v   v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_25689075_2   1551 ACTAATCAT 1559
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.31 (105 / 80)
Gap_init rate = 0.02 (19 / 904), avg. gap size = 2.53 (48 / 19)  


3224 27.01 0.55 0.44  chrX_25712421_25717357     3538  4444 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25712421_2   3538 TGGAAGAACATTCCATGCACATGGATAGGAAGAATCAATATCATGAAAAT 3587
                              ii i  i     iv       v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25712421_2   3588 GGCCATACTGCCTAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 3637
                            v     v  i  iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25712421_2   3638 TACCAATGACTTTCTTCACAGAATTGGAAAACACT-ACTTTAAAGTTCAT 3686
                          v   iivi i  i  ii     v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_25712421_2   3687 ATGGAACCAAAAAGGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGA 3736
                               viiv  i   v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_25712421_2   3737 ACAAAGCTGGAGCCATCACGCTCCCTGACTTCAAACTATACTACAAGGCT 3786
                               i     vvv    i  i  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_25712421_2   3787 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 3836
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_25712421_2   3837 ATGGGACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACTA 3884
                             i i    i--    i  --        vv   i    i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_25712421_2   3885 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 3934
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_25712421_2   3935 TGTTTAACAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 3984
                          v  i          i      v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_25712421_2   3985 AAACTGGATCCCTTCCTTACAATTTATACAAAAGTTAATTCAAGATGGAT 4034
                           ii    i    v   i   viv         i    i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_25712421_2   4035 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4084
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_25712421_2   4085 TAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAA 4133
                             ?i- v i -   iv   viv  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_25712421_2   4134 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4183
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_25712421_2   4184 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4233
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_25712421_2   4234 AGGCAACCTACAGGATGGGAGAAAATGTTTGCAATCTACTCATCTTACAA 4283
                           i     i    i            i       vii ivi    v i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_25712421_2   4284 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 4333
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_25712421_2   4334 A-ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 4382
                          -     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_25712421_2   4383 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 4432
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_25712421_2   4433 ATCACTGGCCAT 4444
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3435 25.03 1.90 0.56  chrX_25720874_25725389     3129  4023 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_25720874_2   3129 GAAAATACATTCTGTGCTCATGGATTGGACCA-TTAATAGTGCTAAAATG 3177
                          i   v i  i ii  i            vv -      v  i   i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_25720874_2   3178 TCCATACCACCCAAAGAAATCTACAGATTCAATTCAATCCCCATTAAAAT 3227
                         v v    iv      vvi              iv       i  i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_25720874_2   3228 ACCAGTAACATTTTCCACAGAAAGAGAAAAAAATATCCTAAAATGTGTAT 3277
                         v    ivi v    iii      vv  v  ivvv          vii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_25720874_2   3278 GGAACCACAAAAGACCCTGAATAGCCAAAACAATCTTAAACAAAAAGAAC 3327
                             vii   ii     v                   i  v  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_25720874_2   3328 AAAGCTAAAAGCATCACACTATCTGACTTCAAAATATACTACAAAGCTAC 3377
                             i ii i vv       vi ii i       iv              
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_25720874_2   3378 ATCAACCCAAACAGCATGGTACTGCCACATGAACAGACACATAGATGAAT 3427
                          vi  i v i    ii        v  i v i i     i      v   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_25720874_2   3428 GGAACAGAATAGAGAGCCCATAAATAAATCCACGTATTTATAGTCAATTG 3477
                             i     v     i   v       i   iii      i        
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_25720874_2   3478 ATTTTCAATAAGGGTACCAAGAGCACACAATGGGGAAG--ACAGTCTCCT 3525
                               i i      i      v  iv          i-- i     ii 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_25720874_2   3526 CAATAAATGGTGTTAAGAATATTTGATACACACATTCAGAAGAATGAAAT 3575
                            i        i ii  vv i v    ?v     v  i         i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_25720874_2   3576 TAGACCCTTGTCTCATACCATATCCAAAAGTCAATTTAAAATGAACTAAA 3625
                          i     i ii    i       v     i i  i i      i ii ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_25720874_2   3626 GACTGAAATGTAAGATGTGAAACGATACACTTAGTAGAAGAAAACACAGG 3675
                            iv          vv i    v   v vi vv            i   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_25720874_2   3676 AGAACAGCTCCACGATACTGATCTGGGCAATGATTTTTTTGATATGAGTC 3725
                         ? v v v  i ii  ivi  ivi i       i   i  v       vv 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_25720874_2   3726 GAAAAGCCTGA-TAACAAAAACAAAACTAGACAAATGGAATTATGTCAAA 3774
                         v      vii -i       iv    v    i    v i i vii     
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_25720874_2   3775 TTTAA----TTTTCTGCACAGCCAAGGAAACAAACCGTAGAGTGAAGAGA 3820
                         v    ----    v   vi-- v     v  v v viv i      i   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_25720874_2   3821 CAACCTATGGGATGAGAGAATATACTTGCAAACTATACATCTGACAAGGA 3870
                              i ii i   i     v   i       ii   i      i    i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_25720874_2   3871 GTTAATATCCAAAATATATAAGGAACTC----AGCTCAATAGTAAGAAAA 3916
                         ii vi      i         i      ---- i       i   i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_25720874_2   3917 CAG----CCCATTTAAAATATTGGCAAGAGATCTGAATAGAAATTTCTC- 3961
                           i----    v  ?   v  v     ii   i        v       -
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_25720874_2   3962 AAAGGAGACATACGAATAGCCATTAGGTATATGAAAAAAAAATGCTCAAA 4011
                             i   i    i   i    v  i i i       i ---       v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA---TGCTCAAC 896

  chrX_25720874_2   4012 ATTACTAATCAT 4023
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (139 / 81)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 2.44 (22 / 9)  


2855 24.63 4.45 0.91  chrX_25747145_25752323     3810  4686 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25747145_2   3810 TGGAAAAACATTCCATGGATCATGGATTCAAAGAACGAATATTGTTAAAG 3859
                               i i  i     v-         vi    viv           ii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGT-TCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_25747145_2   3860 TGTCTGTACTGCCCAAAGCAATCTACAGATTCAGTAGTATTCCTATCAAA 3909
                           v vi    v      vii             iiivv  i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_25747145_2   3910 TTACT-GATATCATTTTTCACAGAATTAGA-AAAC-GATTCTAAAATTCA 3956
                         v v i- v ii -     ii     v v  -  i -   i          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_25747145_2   3957 CATGGAACCTAAAAAGAGCCTGAATAGCAAAGGAAATCCTAAGCAAAAAG 4006
                         i      vivv  ii  v  v       v  iiv    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_25747145_2   4007 AATGAAACTGGGGGCATCACATTACCTGACTT-AAAACTATACTAAAAGG 4055
                           ii  ii   i  vv     i v  ii i  -      -     v  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_25747145_2   4056 CTACAGTAACCAAAACAGCATGGTACTGGTGCAAAAATATAGGCATAGAC 4105
                                  i   i    ii         iii  ii   v vii     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_25747145_2   4106 CAGTGGAACAGAATAGAGCCTCCTGCAATAAAGC--TGCAT--------- 4144
                           i     i     v   vv   v v      v -- i   ---------
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_25747145_2   4145 ACTGATCTTAAACAAAGTTGACAAAAATAAACAATGGAGAAAGAACTCCC 4194
                          i    i  vi    i v  v   i vi vv      i       ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_25747145_2   4195 TATTCAACAAATGGTGCTGGGATAACTGGCTAACCATATGCAGAAGAATG 4244
                          v                    i      v  ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_25747145_2   4245 AAACTGTACCATTACCTTTCACCATATACAAAAATTAACTCAAGATGGAT 4294
                           ii  v   vi     iv                        i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_25747145_2   4295 TAAATCCTTAAATATAAGACCTCAAACTATAAAAATCCTAGAAGAAAACC 4344
                         i ? vv i     i     v  v           v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_25747145_2   4345 TTGGAAATACTCTT-GTAGATGTTGGCTTCTGCAA-AGTAT----GATGA 4388
                          v  ?ivv v    -  -  iv    v  vv    -i  v ----   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_25747145_2   4389 AGACCCTGAAAACAAAGGTGACAAAATCAAAAACAGACAAATGGGACTT- 4437
                         v   v ii   i  v i ii      vv     i   i    v      -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_25747145_2   4438 -----AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAAGAGATTAT 4482
                         -----       i -   i  ii vv    i  v          i v iv
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_25747145_2   4483 ATAGACAACCCACAGAATGGGAGAAAATATTTGCAAACTATGAT-TCCAG 4531
                          v                                   ii  -  -  iii
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-ATATCTGA 743

  chrX_25747145_2   4532 CAAATGACTAATATCCAGAACCTTTAAGGAACTTAAAAAAATCAATGAGA 4581
                         i  iv    vi         iv v   i     ivv v  v     i v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_25747145_2   4582 AAAAAA------ACCCA-TTAAAAAGTGGGCAAAGGACATAAACAGACA- 4623
                             i ------     -  ?    i           iv i  i     -
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_25747145_2   4624 --CTTCACAAAAGACATACAAGTGACCAACAGACATA-AAAAAAATCACT 4670
                         --  i  v i    i      i  i    i ii  i -i    i  -i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCT 892

  chrX_25747145_2   4671 AAGCATCAGAGAGATG 4686
                         v i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (125 / 87)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.04 (47 / 23)  


3277 24.07 1.32 1.54  chrX_25754687_25760424     4336  5245 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25754687_2   4336 TAGAAAAACATCCCATCCTCATGGATAGAAATAATCAATATTGTGAAAAT 4385
                          i    i i       vi        v i  v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25754687_2   4386 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 4435
                            v     v      v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25754687_2   4436 TACCA-TTGCTATTCTTTACAGAATTAGAAAAAACT-ACTTTAAATTTCA 4483
                          v   -i   i-  i   i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_25754687_2   4484 TATGGAA-T-CAAAGAAGACCCCATATAGCCAAGACAATCCTAAGCAAAA 4531
                                - -   i --     viv        i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_25754687_2   4532 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAAGTATACTACAAG 4581
                                  i      vv       v  ii i      iiv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_25754687_2   4582 GCTACAGTAACAAAAACAGCATGGTACTGGTACCCAAACAGACATATAGA 4631
                                   iv  i    ii         i ivvii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_25754687_2   4632 CCAATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACC 4681
                         i        i    iv    vii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_25754687_2   4682 ATCTGATCTTTGAGAAACCTGACAAAAACAAGCAATGGGGAAAGGATCTG 4731
                          vi    i  i  v  ivv  v   i v  vv            i  vvv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_25754687_2   4732 CTATTCAATAACTGATGCTGGGAAAACTGGCTAGCCATATGCAGAAAACT 4781
                           v     i  v  i        v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_25754687_2   4782 GAAACTGGATGCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 4831
                            ii    iv   v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_25754687_2   4832 TTAAAGACTTAAATGTAAAACCCAAAACCATAAAAAGCCTAGAAGAAAAC 4881
                          i ?    i         i v i     i      vv i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_25754687_2   4882 CTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAAGACTTC------A 4924
                         v    ?i- v   -   iv   v v  vv i     v ii   ------ 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_25754687_2   4925 TGACAAAAATGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAACGG 4974
                              ------         vvv          vv     v  i   iv 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_25754687_2   4975 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCATCATCAG 5024
                           ii v  i   v v  i i   i  ii vv    i  v  i    vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_25754687_2   5025 AGTGAACAGGCAACCTACAGAATGGGAGAAAACTTTTGCAATCTATCTAC 5074
                               v  i     i                iv       vii  v  i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_25754687_2   5075 CTGACAAAGGTCTAATATCCATAATTTACAAGGAACTTAAACAAATTTAC 5124
                             i  i  v  vi      v   v  i  i     ivv    v --- 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---C 786

  chrX_25754687_2   5125 AAGAA-AAAAAAACAAACAACTCCATCAAAAAGTGGGCAAAGGATAGGAA 5173
                           v  -     i     i   i v  i?    i            vv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_25754687_2   5174 CAGACACTTCTCAAAAGAAGACATTCACATGGCCAACCAATATGTGAAAA 5223
                         i     i     v        i  v  v        iv ii ii      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_25754687_2   5224 GAAGTTCAACATCACTGATCAA 5245
                           v i         ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (121 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.00 (26 / 13)  


3349 27.09 0.22 0.22  chrX_25765989_25767913      525  1432 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25765989_2    525 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 574
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25765989_2    575 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 624
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25765989_2    625 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTCA 672
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_25765989_2    673 TATGGAACCAAAACAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 722
                                viiv  vi  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_25765989_2    723 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 772
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_25765989_2    773 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 822
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_25765989_2    823 AATGGAACAGAACAGAGGCCTCAGAAATAACGCCGCATATCTACAACTAT 872
                                i    iv   ivii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_25765989_2    873 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 922
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_25765989_2    923 ATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 972
                         v  i  i       i      v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_25765989_2    973 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 1022
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_25765989_2   1023 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1072
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_25765989_2   1073 AGACATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 1122
                           i?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_25765989_2   1123 CACCAAAAGCAATGGCAACCAAAGACAAAATTGACAAATGGGATCTAATT 1172
                                    vvi     v     v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_25765989_2   1173 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGGGAACAG 1222
                            v v  i i   i  ii vv    i  v    i  vv i  v   v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_25765989_2   1223 GCAACCTACAAAATGGGAGAAAATGTTTGCAACCTACTCATCTGACAAAG 1272
                         i     i   i             i       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_25765989_2   1273 GACTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 1322
                             vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_25765989_2   1323 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 1372
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_25765989_2   1373 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 1422
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_25765989_2   1423 CACTGGCCGT 1432
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


2377 24.60 0.63 0.79  chrX_25781509_25783118      488  1117 (493)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_25781509_2    488 AAGGTCAATGGA-ACATAGACCAATGGAACAGAATAGAAAACCCAGAAAC 536
                             ---  i  - i     i        i     v  i ii       i
  L1M4_orf2#LINE/    280 AAGG---ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_25781509_2    537 AAATCTACATGCCTACAGTGAATTCATTTTTGACAAAAGGTGCCAAGAAC 586
                            i i i iiii  ii  v    v     i     i-          v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAG-GGTGCCAAGACC 375

  chrX_25781509_2    587 ATACACTGGGGAAAAGACAGTCTCTTTAATAAATGGTGCCGGGAAAACTG 636
                           v  v        ii i     i  i  i         i    v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_25781509_2    637 GATATACATATTCGGAAGAATGAAACTAGACCCCTATCTCTTGCCATATG 686
                             ?v  i  v ii         ii i        i   vii      i
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_25781509_2    687 CAAAAATCAAATCTAAATGAATTAAAGACTTAAATCTAAGACCTCAAACA 736
                                i  v  v     i  i ?    i     v     v  v    v
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_25781509_2    737 ATGAAACTACCATAAGAAAACATTGGGGAAAATCTCCGAAACATTGGTCT 786
                           i     vii v          v  ? v      i  vi  v    vi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_25781509_2    787 CAGCAAAGATTTCTTGAGCAATATTCCACAAACACAGGTAACCAAAGCAA 836
                         vi    v i      iiii vv iv   v  i    i i   v    v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_25781509_2    837 AAATGAACAAATGGGATCACACCAAG-TTAAAAAGCTTCTGCAAAGCAAA 885
                             ii i    v   iiv  i   i-       -   i  iivvv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAA 674

  chrX_25781509_2    886 AGATACAATCAACAAAATGAAGAGACAACCCACATAGTGGGAGAAGTTAT 935
                         i  i  v     v   i    i            v i        iv   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_25781509_2    936 TTTCAAGCTACTTATCTGAAAATGGATTAATAACCAGAATATATAAGGGG 985
                           v   iii iv       v  v   i vi  v             i ii
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_25781509_2    986 CTCAAACAACTCTATAGGAAAACATCTAATAATCCAATC-AAAAATGGGC 1034
                            vv       v   iv    viv v     i     i-          
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_25781509_2   1035 AAAACATTTGAATAGACATT-CTCAAAAGAAGACATGTAAATGGCAAACA 1083
                            iv               -   v        i  ii       v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_25781509_2   1084 GGCATATGGAAAGGTTTTCAACATCACTGATCAT 1117
                         i   i   i    i vi         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (95 / 57)
Gap_init rate = 0.01 (7 / 629), avg. gap size = 1.29 (9 / 7)  


2573 20.05 7.28 4.40  chrX_25817726_25819445      500  1227 (493)    L1M4_orf2#LINE/L1      160   908 (0)  

  chrX_25817726_2    500 AAAGGACCCTGAAAAGCCAAAACAATCTTGAGAAAGAAGAACAAAGCTGG 549
                           i      v   v                 i              i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_25817726_2    550 ATGCATCATACTTACTGATTTCAATATATATTACAAAGATAGAGTAATTA 599
                          v vv   i    v ii       v iv  i       v  v      i 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_25817726_2    600 AAACAGTATGGCTCTGGCATAAAGACAGACATATAGACTAGTGGAAGAGA 649
                          i     i   iv         i  i           ii i     v   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_25817726_2    650 GTAGAGA-TCCAGAAATAAGCCCATATATATATATGTTCAATTAATCTTC 698
                         i v    -           i      i  - -    v      i  i   
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACAT-T-TATGGTCAATTGATTTTC 357

  chrX_25817726_2    699 AACAGGGGTGC------------------AAACAGTAGTTTCTTCAA-AA 729
                         i   i      ------------------   v i    i i     -  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_25817726_2    730 ACAGTACTGGGAAAACTGGATATCCATAAGCAAAATAATGGTATTAGACC 779
                          ii  i      v         ?   i v      v    ivi  i    
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_25817726_2    780 CTTAT---ATATCATA--CAAAAGTCAACTCAAAATAAATTAAAGACTTA 824
                          i  i--- i i    --     i i          ii  i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_25817726_2    825 AACATAAAACCTGAAACTGTAAAACTCCTTGAGTAAAACATTGGGG-AAA 873
                           ii   i v  i     i        i v  iv       v  ? -   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_25817726_2    874 TGCCTTGGTTTTTATTTTGTTTTGGAAAAATATTGGCCTGGTAATGAATT 923
                          --   v  v--- ii   ---------------  iiv  i    iv  
  L1M4_orf2#LINE/    558 T--CTTCGTG---ACCTTG---------------GGTTAGGCAATGGTTT 587

  chrX_25817726_2    924 TTTGGATATGACACCAAAAGCATAGGCAACAAAATAAAAAAAAATTAGAC 973
                         i  i                  i i         v      ----    i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA----TAGAT 633

  chrX_25817726_2    974 AG-CAGGACTACAT-AAAATCATAAAGTTTCTGCACAGCAAAGGA----- 1016
                          i-iv     v   -     i -   ii  i  ii vv       -----
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_25817726_2   1017 ---------------AACAAC----AGAGTGGAAGAAAACAGTTTCAAAT 1047
                         ---------------i     ----   i   i      i v  v     
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_25817726_2   1048 CATAGAGCTGATAAGGGATTAATATACGGAATACATAAATAACTCCTACA 1097
                             v v           i vi   v i     i     v     i    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_25817726_2   1098 GCTAAAAACAGCAATAAAACAATAA-TAAAGCAATTTAAAAATGAGAAAA 1146
                         i  -----  ii       vi i  -   vv     ?       i v   
  L1M4_orf2#LINE/    783 ACT-----CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_25817726_2   1147 GGACTTAAACAGATATTTATCCAAAGAAGACATACAAATGGCCAACAGAA 1196
                            i  i  i   i    v           i              i iiv
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_25817726_2   1197 ATATGAAGAGATGCTCAACGTTACTAATTAT 1227
                          i     i           i i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (97 / 45)
Gap_init rate = 0.03 (19 / 749), avg. gap size = 4.47 (85 / 19)  


3260 26.99 0.88 0.44  chrX_25954569_25963879      492  1395 (7916)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_25954569_2   1395 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1346
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_25954569_2   1345 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1296
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_25954569_2   1295 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 1248
                          v   iivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_25954569_2   1247 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATTCTAAGCCAAAAG 1198
                                viiv  ii  v  v v  v     iv    ii i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_25954569_2   1197 AACAAAGCCGGAGGATTCATGCTACCTGACTTCAAACTATACTACAAGGC 1148
                                ii      i   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_25954569_2   1147 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1098
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_25954569_2   1097 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 1050
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chrX_25954569_2   1049 ATCTGATCTTTGACAAACCTGAGAAAAGCA----ATGGAGAAAGGATTCC 1004
                          vi    i  i     ivv  vv  i v  ----    i     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_25954569_2   1003 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCGATATGTAGAAAGCT 954
                           v  i  i        i     v      v  ? v i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_25954569_2    953 GAAACTGGCTCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 904
                            ii   vi    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_25954569_2    903 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 854
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_25954569_2    853 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 804
                         v    ?i v viv   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_25954569_2    803 AACACCAAAAGCAATGGCAACAACAGCCAAAATTGACAAATGGGATCTAA 754
                         i            vvi       v  vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_25954569_2    753 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGGGAAC 704
                          i   v v  i i   i  ii vv    i  v    i  vv i  v   v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_25954569_2    703 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 654
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chrX_25954569_2    653 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 604
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chrX_25954569_2    603 AAACAAACAACCCCACCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 554
                          i     i     v ii?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chrX_25954569_2    553 TCAAAAGAAGACATTTATGCAGCCAAAAAACACAGGAAAAAATGCTCACC 504
                           v        i  vi viii     v  i    v     i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chrX_25954569_2    503 ATCACTGGCCAT 492
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  

2976 28.43 1.00 0.55  chrX_25954569_25963879     7915  8818 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_25954569_2   7915 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCGTGAAAAT 7964
                              ii i  i     i      i v      v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25954569_2   7965 GGCCATAGTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 8014
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25954569_2   8015 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 8062
                          v   iivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_25954569_2   8063 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATTCTAAGCCAAAAG 8112
                                viiv  ii  v  v v  v     iv    ii i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_25954569_2   8113 AACAAAGCCGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 8162
                                ii     vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_25954569_2   8163 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 8212
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_25954569_2   8213 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 8260
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_25954569_2   8261 ATCTGATCTTTGACAAACCTGAGAAAAGCA----ATGGAGAAAGGATTCC 8306
                          vi    i  i     ivv  vv  i v  ----    i     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_25954569_2   8307 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCGATATGTAGAAAGCT 8356
                           v  i  i        i     v      v  ? v i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_25954569_2   8357 GAAACTGGCTCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGA 8406
                            ii   vi    v   i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_25954569_2   8407 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 8456
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_25954569_2   8457 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTGCATGACTA 8505
                         v    ?i- v i -   iv   v v  vv i     v ii v v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_25954569_2   8506 AAACACCAAAAGCAATGGCAACAAAAACCAAAATAGACAAATGTTATCTA 8555
                         vi            vvi         ivv        i    vvv ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_25954569_2   8556 ATTAAACTAAAGAGCCTCTGCAGAGCAAAAGAAATTACCATCAGAGGGAA 8605
                           i   v v  i i i i  iivvv    i  v i  i  vv i  v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_25954569_2   8606 CAGGCACCATACAGAATGCGAGAAAAGTTTTGCAATCTACCCATCTGACA 8655
                         v  i  v vi        v       vv       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_25954569_2   8656 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTATAAGAAA 8705
                          i  i  vi          v  i        ivv    v iv    v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_25954569_2   8706 AAATCAAACAACTCCATCAAAAAGTGGGCGAAGGATATGAACAGACAATT 8755
                           iv    i   i v  i?    i     i      v    i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_25954569_2   8756 CTCAAAAGAAGACATTTATGCCGCCAACAGACATATGAAAAAATGCTCAT 8805
                            v        i  vi viiv     i ii  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_25954569_2   8806 CATCACTGGTCAT 8818
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (151 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2145 22.59 2.06 14.34  chrX_25978959_25981649     1173  2190 (501)    L1M4_orf2#LINE/L1        1   893 (15)  

  chrX_25978959_2   1173 TGGAAAAACATTCCATATTCATAGACAGGAGGAATTAATATTGTTAAGAT 1222
                               i i  i    i     i  iv   i  v                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_25978959_2   1223 GGCCATACTGCCCAAACCAATTCACCAATTCAATG--ATA--TACCAA-- 1266
                            v     v      iii  ii  vi      i --  v--  i   --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_25978959_2   1267 ---CAACGG---TTTTCACAGAAGTAGAAAAAACT-ATCC-AACATTCAT 1308
                         ---  i v ---    ii     i v  v  i-  -    -  v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_25978959_2   1309 ATGAAACCAGAAAAGGGCCC-GAATAGCCAAAGCAATTCTAAGCAAAAGG 1357
                            i  vi- v  i  i   -           i    ii i iv  i i 
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_25978959_2   1358 AGCAAAGCCAGAGCTCTCCCACTACATGACGTCAAATTATACTACAAGTC 1407
                          i     iii   vv   v    v vii iv     viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_25978959_2   1408 TACAGTAACTAAAACAGCAAGTTGCTGGCAGCAAAATAGACACATAGACC 1457
                                 ii  i    iiv v i      vv ii       i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_25978959_2   1458 AATGGAACAGG-TTAAGGAGCCCAGAAATCAAGTCGCACACCTACAACCA 1506
                                i  i-  i  -  i        v  vi ii   ii  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_25978959_2   1507 TCTGATCTTCTGCAAA--TTCTACAATAACAAGCAATGGGGAAAGGAC-- 1552
                         vi    i   vi   i-- v --   v v  vv            i i--
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGC--CAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_25978959_2   1553 TCTTTATTCAATAAATGGTACTGGGATTACTGGCTGGCCACATGCAGAAG 1602
                              --    i       i      iv     v i?         i   
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_25978959_2   1603 AGTGAAACTGAACTCCTTCCTTACACCATATACAAAACTCAATTCAAGAT 1652
                          i    ii  i  i   v   i               v i  i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_25978959_2   1653 GGATTAAAGGCTTAAATGTAAAACCTAAAACTATAAAACCCTT-GAAGAA 1701
                             i ?  i i         i v               i   -      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_25978959_2   1702 AATCTAGGAAATACCATTCTGGACAGAGTTCCCGGCAAACATTTCATGAT 1751
                           iv    ?------------------------- i   i-i   i   -
  L1M4_orf2#LINE/    544 AACATAGGN-------------------------GTAAAT-CTTCGTGA- 566

  chrX_25978959_2   1752 GAAGACACCGTAAGCAATTGTAACAAAAATAACAACAACAAAAAATAGAC 1801
                         -------  --------   ------------------------------
  L1M4_orf2#LINE/    567 -------CC--------TTG------------------------------ 571

  chrX_25978959_2   1802 CAAAAAAAAAACAAAAACAGAAAAATAGACAAAAACAAAAAATAGGCAAA 1851
                         --------------------------------------------  ----
  L1M4_orf2#LINE/    572 --------------------------------------------GG---- 573

  chrX_25978959_2   1852 AATTAGGCAAAAATAAATAAAAAATAGACAAAATACCAAAAATAGACCAA 1901
                         --        vii vvv ------    i vi i       ii ---   
  L1M4_orf2#LINE/    574 --TTAGGCAATGGTTTCT------TAGATATGACACCAAAAGCA---CAA 612

  chrX_25978959_2   1902 AAAAAAAAAAACAAAAACAAAAATAAACAAGTGGGGCCTAATTAAACTAA 1951
                         iv  -------     iv       i i  i v  i i v  i   v v 
  L1M4_orf2#LINE/    613 GCAA-------CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_25978959_2   1952 AGACCTTCTGCACAGCCAAGGAAGCTATCAACAGAACAAACACACAACCT 2001
                          i v   i  ii vv v     vi       v i iii  v v      i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_25978959_2   2002 AAAGAATGAGGGAAAATGTTTTCAAACTATGCATCTGACAAATGTCTAAT 2051
                          v      i i      i   v    ii  ii      i  iv v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_25978959_2   2052 ATCCAGAATCTAAAAGGAATGTAAAGAAATCAATAAGCACAAAACAAACA 2101
                                  v  v  i   ivivv v  v       vv v  i     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_25978959_2   2102 ACCCTAATAAAAAATGGGTGAAGGACCTAAACAGACACTTCTTAAAAGAA 2151
                             v v ?         ii     ii i  i     i    iv      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_25978959_2   2152 GACATACAAGTGGCCAATAAATATATGGGAAAAATGCTC 2190
                           i      i          ii i   i-   i      
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGA-AAAGATGCTC 893

Transitions / transversions = 1.90 (148 / 78)
Gap_init rate = 0.03 (26 / 893), avg. gap size = 6.42 (167 / 26)  


3311 26.19 1.11 0.33  chrX_26059333_26065685.rev     4962  5862 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_26059333_2   4962 TGGAAGAACATTCCATGCTCATAGATAGGAAGAATCAATATTGTGAAAAT 5011
                              ii i  i     i    i   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_26059333_2   5012 GGCCACACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAAC 5061
                            v i   v     iv i  i  i       ii  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_26059333_2   5062 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTCA 5109
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_26059333_2   5110 TACGGAAC--CAAAAGAGCCTGCATTGCTAAGATAATCCTAAGCCAAAAG 5157
                           i    v--   ii  v  v v  v  i  i i    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_26059333_2   5158 AACAAAGCTGGAGGCATCACGCTCCCTGACTTCAAACTATACTACAAGGC 5207
                                i      vv    i  i  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_26059333_2   5208 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5257
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_26059333_2   5258 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACATATCTACAACCAT 5307
                                i    iv   ivii         vv   i i  i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_26059333_2   5308 CTGATTTTTGACAACCCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5357
                         i       i     vvv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_26059333_2   5358 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCTGA 5407
                         v  i  i              v      v  ?i  i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_26059333_2   5408 AACTGGATCCCTTCCTTATACCTTATACAAAATTTAATTCAAGATGGATT 5457
                          ii    i    v   i i   v         v    i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_26059333_2   5458 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5507
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_26059333_2   5508 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 5556
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_26059333_2   5557 ACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACTAGTGCGATCTAAT 5606
                                     vvi          vv        iv i vv  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_26059333_2   5607 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5656
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_26059333_2   5657 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5706
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_26059333_2   5707 GGGCTAATTTCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAATA 5756
                           i  vi v        v  i        ivv    v iv i  v   v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_26059333_2   5757 AACAAACAACCCAATCAAAAAGTGGGCAAAGGATATGAACAGACATTTGT 5806
                         i     i        i?    i            v    i        v 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_26059333_2   5807 CAAAAGAAGACATTTA--TG--CAG-AAACACATGAAAAAATGCTCATCA 5851
                          v        i  vi --  --  i-  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_26059333_2   5852 TCACTGGTCAT 5862
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


3222 27.42 0.44 0.44  chrX_26092443_26098720.rev     4880  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_26092443_2   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_26092443_2   4930 GGCCATACTGCCCAAGGTAATTTACAGGTTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i     i     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_26092443_2   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_26092443_2   5028 TATAGAACCAAAAAAGAACCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                            i   viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_26092443_2   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTGCAAGGC 5127
                                i      vv       v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_26092443_2   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_26092443_2   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_26092443_2   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_26092443_2   5276 CTACTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           vi i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_26092443_2   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_26092443_2   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_26092443_2   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_26092443_2   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_26092443_2   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_26092443_2   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_26092443_2   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_26092443_2   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_26092443_2   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_26092443_2   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3062 26.58 3.05 0.34  chrX_26111286_26117638     4977  5860 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_26111286_2   4977 TGGAAGAACATTCCACGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5026
                              ii i  i   i i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_26111286_2   5027 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5076
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_26111286_2   5077 TACCAATGACTTCCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5124
                          v   iivi i ii  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_26111286_2   5125 TATGGAACCAAAAAAGAACCAGCATTGCAAAGACAATCCTAAGCAAAAAG 5174
                                viiv  ii  v    v  v  v  i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_26111286_2   5175 AACAAAGCTGGAGGCATCACGCTCCCTGACTTCAAACTATACTTACAAGG 5224
                                i      vv    i  i  ii i      viv    -    i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT-ACAAAG 247

  chrX_26111286_2   5225 CTACAGTAATCAAGACAGCATGCTACTGGTACCAAAACAGAGATATAGAC 5274
                                           ii  v      i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_26111286_2   5275 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5324
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_26111286_2   5325 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5374
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_26111286_2   5375 TATTTAATTAATGGTGCTGGGAAAACTGGCTAGCCATACGTACAAAGCTG 5424
                          v  i  iv             v      v  ?   i i i v  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_26111286_2   5425 AAACTGGATTTCTTCCTTACACCTTTTACAAAAATTAATTCAAGATGGAA 5474
                           ii    iii  v   i     v v            i    i     v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_26111286_2   5475 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5524
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_26111286_2   5525 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5574
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_26111286_2   5575 ACACTAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGA--TCAG 5622
                             i       vvi          vv        i    v   --   v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_26111286_2   5623 CAAAA---GAAACT-----------------GCTATCAG---AGTGAACA 5649
                              ---i     -----------------i      i---      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_26111286_2   5650 GTCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACCCCTCTGACAAA 5699
                          v     i                vv       vii iviv     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_26111286_2   5700 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 5749
                           i  vi          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_26111286_2   5750 ATCAAACAACCCCATCAAAAAGTGGGCAAAGCATATGAACACACACTTTT 5799
                         iv    i     v  i?    i         v  v    i v   i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_26111286_2   5800 CGAAAGAAGACATTTATGCAGCCAACAGACACGTGAAAAAATGCTCATCA 5849
                          v        i  vi viii     i ii   i      i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_26111286_2   5850 TCACTGGTCAT 5860
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.75 (30 / 8)  


1972 27.54 10.39 1.21  chrX_26120390_26122801.rev     1093  1920 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_26120390_2   1093 AAAACATTCCTTACTCATGAAT----AGAATCAATATTCTTAACATTGTC 1138
                           i i  i  v ii     i  ----   v i      v    v  v iv
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_26120390_2   1139 ATATTGTCCAAAGCAATTTACAGATTCAATGCTATACCTAGCAAACTACT 1188
                            i vi     vii  i           i  v  v    v    v v i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_26120390_2   1189 -GATGACATTTTCACAGAACTAGAAAAAACT-ATTCTAAATTTCATATGG 1236
                         - v  v v    ii     v v  v  i-  -  i     v         
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGG 153

  chrX_26120390_2   1237 AACCATAAACAGTCCACA-TAGCCAAAGCAATCATGAGAAAAAAGAACAA 1285
                           viii  iviii   v -        i     v   i   i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_26120390_2   1286 AGCCAGAGACATCATGCTACCTAACTTCAAACTATACTACAAGGCTACAT 1335
                           iii   ivv   ii  v  i  i      viv        i      v
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_26120390_2   1336 TAACCAAAACAGCATGGTACTGGCACAATGACAGATACACAGACCAAAGG 1385
                            i   i    ii           i  v  i   i i i   i   v  
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_26120390_2   1386 AGCAGATTAGAGAACCCAGAAATAAAGCTGCACA---------------- 1419
                          ii   v v    ii           v iii   ----------------
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_26120390_2   1420 -------------------ACTATCTGAT--------------------- 1429
                         -------------------  i  iii  ---------------------
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_26120390_2   1430 ----------CTGTGGTAACTGTCAAGCTACATGCAGAAGATTGAAACTA 1469
                         ----------   v ii     vvv ? i       i    v    ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_26120390_2   1470 GACCTTTTTATTTCACCATAT-CAAAAATCAAATCAATATGAATTAAAGA 1518
                             ii viv iv        -       i  v    v   i  i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_26120390_2   1519 CTTAAATGGGAAACCTAAAACTATCAAAACCCCTTTAAAAAAAACTAAGA 1568
                          i      vi i v          -     i -  vi  i     vv  i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTAT-AAAACTC-TTAGAAGAAAACATAGG 551

  chrX_26120390_2   1569 AATACTGTTTTAGAGA---TAGGTCCTGGCAAAGATTTCATGGCAAAGAT 1615
                         ?i  v-i i  v v  --- i   iv-     v i    v i vv v  i
  L1M4_orf2#LINE/    552 NGTAA-ATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATATGAC 599

  chrX_26120390_2   1616 GCCAAAA--ACAATTGGAACAAAAACAAAAGTTGATAAGTGTGACCTAAT 1663
                         i      --    -- v       iv    i v     i vv   i v  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_26120390_2   1664 TAAA-CTAAAAAGTGTCATCC--CAGCCAAGTAAACTATCAACAGAGTCA 1710
                         i   -i      v v ii v --  ---   v v        v i   v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCA---AAGGACACTATCAAGAAAGTGA 694

  chrX_26120390_2   1711 ATTGGCAACCTACAGAATGGGAGAATATATTTGCAAAC--TGAATCCAAC 1758
                          vv i     i              v           i-- iv   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_26120390_2   1759 AAAGGTCTAATATAGATAATCTGTAAGGAACTTAAGCAAAGTAACAAGCA 1808
                           i  v  vi   vv v   v i   i     ivvi   vvi  i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_26120390_2   1809 AAAACCAAACAACCCCATTAAAATGTGGGCAAAGGACATGAACAGACACT 1858
                            iv    i     v   ?   vi           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_26120390_2   1859 TCATAAAGGAAGACATACATGTGGCCAACAAGCATATAAAAA--TGTTCA 1906
                           viv  i     i     vi       i     i  i    --  i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_26120390_2   1907 AGATCAATAATTAT 1920
                          v    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (128 / 96)
Gap_init rate = 0.02 (20 / 904), avg. gap size = 4.80 (96 / 20)  


2937 23.77 1.51 2.26  chrX_26144820_26146606.rev      502  1296 (491)    L1M4_orf2#LINE/L1      120   908 (0)  

  chrX_26144820_2    502 AGAAACAGAAAATACAATACTAAAATTCATATGGCACTGCAGAAGACCTC 551
                              iv  v  vvii  v               v v    iii    iv
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_26144820_2    552 CAACAGCCAAAGCAATATTGAGCAAGAATAACATAACTGGATGCACCACA 601
                         v  i       i    v    iv     v    v ii    v vvi    
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_26144820_2    602 CTTTCTGATTTCAAATTATATTAATTACAAAGCTATGATAATGAAAACAG 651
                            i ii        ---- i v i          iii    v  i    
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAA----ACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_26144820_2    652 CATGATACTGACATAAAAACAGACA-------CAATGTAACAGATTAGAG 694
                         ii  i     i     ii i     -------     v  i   v v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_26144820_2    695 AGCCCAGAAATAAACCCATACTTACACAATCAATTAATTTTTGACAAAAG 744
                           i                  v vi iii      i     i     -i 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA-GG 364

  chrX_26144820_2    745 GCACCAAGAATACACAATGGG-AAAGGATAGTCTCTTCAATAAATGGTAT 793
                          ii      vi iv       -    i       i     i       ii
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_26144820_2    794 TGGCAAAACTGGATATACACATGCAAAAGAATGAAATTGGACACTTGCCT 843
                            v v         ?v                  i      v i i   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_26144820_2    844 TATACTATAACCCCCAAATCGACTCAAAATGGATTATAAAGATTTAAACA 893
                         i i  i   -iv vv    ii             i ? --  ii    ii
  L1M4_orf2#LINE/    465 CACACCATA-TACAAAAATTAACTCAAAATGGATCAWA--GACCTAAATG 511

  chrX_26144820_2    894 TAAGACCTATAACCATAAAAGTCCTGGAAAAAAACACAGGGAAAAAACTC 943
                              v   v   i      v  i i   i      i   ?iv   v  i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_26144820_2    944 CTTCACATTGGCAACTCCTAGTCTTGGCAATGACACTTTGCATATGACCC 993
                          v v  v    ---------  - v       iivii  iv       v 
  L1M4_orf2#LINE/    562 CGTGACCTTGG---------GT-TAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_26144820_2    994 CCAAAACACAGGCAACAAAAGCAAGAATAAACAAGTGAGATTACATCAAA 1043
                          v   i    i          v  i    i i  i vi  i v       
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_26144820_2   1044 CTAAACAGATTCTGCACAGCAAAGGAAAC----AACAAAATAAAAAGGCA 1089
                         v v  v iv  i  ii vv       v  ----  v   i i     i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_26144820_2   1090 ACCTATGGAATGGGAGACTATATTTTCAAATCATATATCTAAAAAGAGAT 1139
                            i ii          vv      v              i v   i  i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_26144820_2   1140 TAGCCTTTAAAATATACAAGGAACTCATACAACTAAACAGTAAAAAAACA 1189
                          v iv ii i      i  i      v       v  i i      i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_26144820_2   1190 AGTGATCCAATTAAAAAATGACCTAAGGACCTGAGTAGACATTTCTCCAA 1239
                          i i i      ?       iv v     ii   i               
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_26144820_2   1240 AGAAGGCATACAAATGACCAACAAGTATATGAAAAGGTGCTCAGCGTCAC 1289
                              ii         i    i   i i        i      i i   ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_26144820_2   1290 TAATCAA 1296
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.80 (119 / 66)
Gap_init rate = 0.01 (9 / 789), avg. gap size = 3.33 (30 / 9)  


4106 17.97 4.72 0.35  chrX_26255399_26257497      750  1617 (482)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_26255399_2    750 GAAAAA-ATTTCATGCACATGGATCATAAGAGGTAAATTTTTTAAATATG 798
                             i -  ii    iv       iiv    vv   vv  v    i-   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-ATG 51

  chrX_26255399_2    799 AAAATGTTTCCCAAATTGATCTATGGTTTCAACACAATCTCCATCAAAAT 848
                         iv   ii i              ii v      i     i i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_26255399_2    849 CTCAGCAGGCTTTTTTGTAAACACTGAAGACTTGATTATAAAATTCATGT 898
                          i    v v        i i v i   vi vi    iv          i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_26255399_2    899 GGAAATGCCAAGGTCCCTAAATACCCAAAACAATCAGGCAAAAGAAG--- 945
                                 v i  v   vi    v           vv v        ---
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_26255399_2    946 ----TTGGAGGACTCACACTCCTCAATTTCAAAACCTACTGCAGAGATAC 991
                         ----                i i            i    i  i  v   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_26255399_2    992 AGTAATCAAAGCAATGTAGTATTGGCATAAGGACAGACAAACAGATAAGT 1041
                                  ii  i   i   i           i     v i    v i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_26255399_2   1042 GGAATAGAATTGAG-GTC-AGAAATAAACTCATACATATATGGCCAACTC 1089
                                       -   -          i       v     i   i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_26255399_2   1090 ATTTTCTACAAGAGTGTCAAGACCATTCACTAGAGAAAGAATAATCTGTT 1139
                               v     i   i            v i i         i   v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_26255399_2   1140 CAACAAATGGTGCAAAGACAACTAGATATCAAC--------GAATGAAGT 1181
                                      vii       i    ? v  --------         
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_26255399_2   1182 TGGGTTCTTACTTCAGACCATACACAAAAATTAACTCAAAATGGATTATA 1231
                            iii i   i   v      i                       i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_26255399_2   1232 GGTATAAATGTAA------------TAAAATCCTTAGAA---AATATGTG 1266
                          iiv         ------------     ii       ---  i  iv 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_26255399_2   1267 AGAAAA-CTTTGTAACCTTGGTTTAAGCAATTGTTTCTTAGTTATGACAC 1315
                         ? v   -   i  i       v   i     v         v        
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_26255399_2   1316 CAAAAGCACCAGCAATGAAA-AAGGAATAGATAAATTGGAGTTCATCAAA 1364
                                  v     ii   -  ii               v         
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_26255399_2   1365 ATTTTAAAACTTTTGTGCTTCAAAGGATAATGCCAAGAAAGTAAAAAGAT 1414
                            v-                      i v ii         i      i
  L1M4_orf2#LINE/    652 ATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_26255399_2   1415 AACCCAAAGTATGAGAGAAAATATTTGCAAAAGTTATCTGTGATAAGA-A 1463
                               v  v   i                 vvv   v v       i- 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_26255399_2   1464 TCTGTATCCAGAATATATAAAGAATGCTCACAACTCAATAATAAATGGAC 1513
                         ii                      iv  i                vi   
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_26255399_2   1514 AAAAAAT---ATTAAAAA--GGGCAAAATATTTGAATAGATGTTTTTGCA 1558
                            v  i---   ?    --       iv           ii   i v  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_26255399_2   1559 AACAATATATGCAGAATGGCCAATAAGAACATGAAAAGATAGTAAATGCC 1608
                           v  v    i  -             v            iv v  iii 
  L1M4_orf2#LINE/    851 AAGAAGATATACA-AATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_26255399_2   1609 ATTGGTCAT 1617
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.53 (92 / 60)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 2.93 (44 / 15)  


2844 24.13 5.22 1.24  chrX_26371556_26373351      500  1303 (492)    L1M4_orf2#LINE/L1       73   908 (0)  

  chrX_26371556_2    500 TACAGATTGAAGGCAATCCCTACCAAAATACCAATGACATTCTTCACAAA 549
                                 v  v          i      v   iivi v  i  ii  i 
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chrX_26371556_2    550 AATAGAAAAAAAAATCCTAAAATTCTTATGGAACCACAAAACACCCAGCA 599
                            v  v  ivvi            v       vii   iiv      v 
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chrX_26371556_2    600 TAGCCAAA-----------------GAACGAAGT-AGAGGCATCATGCTA 631
                                 -----------------    i    -i    vv   ii  v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_26371556_2    632 CCTGACTTCAAAATATACTACAAAGCTATAGTAACCAAAACAGAATGGCA 681
                           ii i       iv             i     i   i    vi   i 
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_26371556_2    682 CAGGCATACAAACAGACACATAGTCCAACAGAACAGAGTAGAGAACGCAG 731
                          v      vii i     i    vi   ii   i   i v    iiv   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_26371556_2    732 AAATAAATGCACACATTTACAGCTAATTCATTTTTTGCCAGAGGTGCCAA 781
                                iv  i       ii ii    v     i- v  ii        
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTC-GACAAGGGTGCCAA 371

  chrX_26371556_2    782 GAGCATACACTGGGGAAAGGATGATCTCTTCAATAAATGGTGCTGAGAGG 831
                           v   v  v         i  ii   i     i           i  vi
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_26371556_2    832 AATGGATATCCATGTGCAGAAGAATGAAACTAGACCTCTCTCTCTCACCA 881
                          v      ?   ii    i         ii i    i  vi   v     
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_26371556_2    882 TATGCAAATATCAAATCAAAGTAGATTAAAGACCTAAATGTAAGACATGA 931
                            i    v  i  v     i i   i ?                vv i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_26371556_2    932 AACTATGAAGCTACTACAAGAAAACTTTGG------TCTGTGCAA----- 970
                               i  i  vi  v        v v  ------   vi ii -----
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chrX_26371556_2    971 ----AGAC-----TTTTTCAGAAA-GACATCAAAATCACAAGCAACCAAA 1010
                         ----  i -----   i i   v -    i     v          v   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_26371556_2   1011 GCAAAAATTGATAAATGGGATCACATCAAGCTAAACAGCTTCTGAGCAGC 1060
                          v      v       v   iiv      iv v  v i   i  v  vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_26371556_2   1061 AAAGGAAACAATCAACAAAATGAAGACACAACCTACAGAATGGGAGAAAG 1110
                               v  v     v   i    i v      i               i
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_26371556_2   1111 TATTCACAAACTATCCATCTGCAGAAGGGTTTAATAACCAGAATATATAA 1160
                             ii    ii  vi     - v     vi vi  v             
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTG-ATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_26371556_2   1161 GGAACTAAAATAATGCAATAGCAAAAAAATAATAATCATTATCATCCAAT 1210
                         i     vvv i  iv     ii     i i  --------  v i     
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAA--------ATAACCCAAT 812

  chrX_26371556_2   1211 TAAAGAATAAACAAGAGATCTGAATAGACAT--CTTAAAAGAAGACATAT 1258
                          ?  i   iii   ii   i           --  iv        i   i
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_26371556_2   1259 AAGTGGTTAACAGGTATACAAAAA-ATGCTCAACATCAGTAATCAT 1303
                           i   ii  i i i i ii    -             ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (121 / 70)
Gap_init rate = 0.01 (11 / 836), avg. gap size = 4.73 (52 / 11)  


2837 25.72 2.78 1.67  chrX_26436357_26438673      927  1824 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_26436357_2    927 TGGAGAAGTATTTTATGTTCATGTATAGGAAGACTCAATATTGTGAAGAT 976
                             i ii   iii         v  v        i        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_26436357_2    977 TTCAGTTCTTTCCAAATTGCTCTATAGATTCAACTCAATCCCAATAAAAA 1026
                         vv  i v  ii        v    i         v       v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_26436357_2   1027 TCT--GGTAAATTATTTTGTGGATATCAAGAAACTGATTCTGACATTTAT 1074
                           i-- v ivv  -     ii  v  ii v  i     i  i v   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_26436357_2   1075 AAGGATAGACAAAGGACAGAGAATAGCCACTACAATATTGGA---GAAGA 1121
                          v   v vi   i    vv          vv     v   i ---     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_26436357_2   1122 ACAAAGTTGGAGATTCCACACTACCCAACTTAAAAATTTACAACAAAGCT 1171
                                     ivii      v     i  v    i    v        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_26436357_2   1172 ATAATAATGAAGATATAATAGCATAGTGTTGGTGAAATAATAGACAACTC 1221
                          i i    v    i ----- ii i  ii   iiv  vi       vv v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACA-----GTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_26436357_2   1222 TATCAGTGGAGTAGAATATAGAACCTATAAATAAACACATGCAAATATAG 1271
                         v    i    i      vv   ii i v        v   i  vv   i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_26436357_2   1272 TCAACTGATCTTTGATAAAG-----AAGGGCAATTAGTAAAGGAAAATGA 1316
                             i    i  i  i  i -----   iv  v i i i--  i   vi 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG--GGGAAAGAA 392

  chrX_26436357_2   1317 TAGTCTTTTAAACAAATGGTGCTAGAAAATCTGAATATTCATGTGCAAAA 1366
                                  v             i i v v   i   ?i  ii       
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_26436357_2   1367 TGGCAATGCAACTAGGCATAAATCTTACAGCTTTCACAAAAGTTAACTTA 1416
                         -- -    v ii i i vivv i  i   v v vi      i      i 
  L1M4_orf2#LINE/    443 --G-AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_26436357_2   1417 TACCTACTATCA---ACCTAAATGTAAAACACAAAACTGTAAAATTCCTG 1463
                         v vivi--    ---            i vvi      i     i  i i
  L1M4_orf2#LINE/    490 AAATGG--ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_26436357_2   1464 GAATGTAACA--GGAGAAAATATAGGTGACCTTCAGTTTGGTAATGACCC 1511
                            viv    --  ? v    v vv        vi   v  i    iiii
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_26436357_2   1512 CTTAAATACAACAGCAAAAGCACAGCCTATGCAAACAAACAAGT-GATAA 1560
                             i   ii   v          iv v --    vi  v  i -     
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAA--CAAAAGAAAAAATAGATAA 635

  chrX_26436357_2   1561 ATTGGTATTCCTTAAAATTGAAAACTTCTGCCCTGAAAAAGACATGGTTA 1610
                              vv   v i      i       i  iv  vv   i    ivi i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_26436357_2   1611 AGAGACTGAAAAGACAAAGTACAGACTGGAAGAAAAAATTT-TAAAACAC 1659
                            i v           vvi     v   i      v    -i   v  i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_26436357_2   1660 AAATATATTAAAGGACTGATATCCAAAATATGCTAAGAACTCTTAAATTT 1709
                          v  v iv   i     vi      i     iiv           v vi 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_26436357_2   1710 TAACAATAAGAA---AAA-----CAATTAAAAAATGGGGAAACGATCTGA 1751
                         i  i     i  ---   -----     ?         v   v   i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_26436357_2   1752 AGAGATACAGCACCAAGAATGATATACAAATAGCAAATAAGCATATGAAA 1801
                          v   i ivv v    ii v           i  v        i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_26436357_2   1802 AGATGTTCAAGGTCACATGTCAT 1824
                              i    vi   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (127 / 101)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.50 (40 / 16)  


1525 26.56 3.93 0.23  chrX_26507413_26511912.rev      525   957 (3543)    L1M4_orf2#LINE/L1        1   449 (459)  

  chrX_26507413_2    525 TAGACAGTTTTTCCATGCTCATGGAGAGTAAGAC--AATATTTTCAAGAA 572
                          i  v  v v i     i       vv v     --      v i    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_26507413_2    573 GTGAGTTTTTTCTAAATTGATCTATAGATTCAATGTAATATCAATAAAAA 622
                          vv i vi ii i           i        i i   vi v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_26507413_2    623 TTCCAACAGGTTATTTTGTGTATCTTGACAAACTTATT-TAAAGTTTATA 671
                          i   i v vi v     iiv vv       i  v  i-    i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_26507413_2    672 TAGACA-GCAAAAGACCCAGAATAGTTAACCCAATATTGAA------GGA 714
                          i  v -    ii            ii  vv    v     ------ i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_26507413_2    715 CAAAGTCAGAGGAGTGACAATAGCTGACTTCAAAATTTACTATAAATCTG 764
                               ii     v v   v vv ii i       i      i   v  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_26507413_2    765 TAATAATCAGGACAGTGTGGAATTGGTGAAATAATAGACAAATAGATCAA 814
                         i i      i          v i   iiv  vi       v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_26507413_2    815 TGGAACCAAAAAGAGAGCCCAGAAATAGACTCACATA------GTCAGCT 858
                              ivi  vv     i         i  i  i i ------    ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_26507413_2    859 TATGTTTGA-ATGGGGAACAAAGTCAGCACAATAGAGAAAAGATATTCTT 907
                         v  v  i  - v   viv   iii  vi-    i i    ii   v    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAGTCTT 399

  chrX_26507413_2    908 TTCAACAAATGGTTCTGGAACAACTGGACATCCACACGTAAAATAATAAA 957
                                      v    i         i ?     i i    v   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

Transitions / transversions = 1.43 (67 / 47)
Gap_init rate = 0.02 (7 / 449), avg. gap size = 2.57 (18 / 7)  

2944 27.26 1.10 0.88  chrX_26507413_26511912.rev     1876  2781 (1719)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_26507413_2   1876 TAGGAAAACATTCCACGCTCATGGATAAGATGAATCAATATCATGAAAAT 1925
                          i i  i i  i   i i        vi  v  v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_26507413_2   1926 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGC--TCCCTCCATCAA 1973
                            v     v      v i  i  i        i  --     --     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT--ATCAA 98

  chrX_26507413_2   1974 GCTACCA-CTGATTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACT 2020
                         iv v   -   vi   i  -i     -   -- v  i  - iii    v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAAT 145

  chrX_26507413_2   2021 TCATATGGAACCAAAAAATAGCCCACATAGCCAAGACAATCCTAAGCAAA 2070
                                   viiv  iiv v  viv        i      i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_26507413_2   2071 AAGAACAAAGCTGGAGACATCACACTACCTGACTTCAAACTATACTCCAA 2120
                                   i     ivv       v  ii i      viv    v   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_26507413_2   2121 GACTACAGTAACCACAACAGCTTGGTACTGGTACCAAAACAGATATATAG 2170
                         ii         i  vi    iv         i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_26507413_2   2171 ACCAATGGAACAGAACATAGGCCTCAGATATAACACCGCACAGCTACAAC 2220
                          i        i    ivv  ivii    v    vv  ii   vi  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_26507413_2   2221 CATCTGATCTTTGACAAACCTGATACAAACAAGCAATGGGGAAAAGATTA 2270
                           vi    i  i     ivv  vi vi v  vv           ii  vi
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_26507413_2   2271 TCTATTTAATAAATGGTGTTGGGAAAACTAGCTAGCCATATGCAGAAAAC 2320
                            v  i  i        i     v    i v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_26507413_2   2321 TGAAACCTCACCCTTTCCTTACACCTTATACAAAAATCAACTCAAGATGG 2370
                             iiivv    i v   i     v           i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_26507413_2   2371 ATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2420
                           i ?    i    ii     v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_26507413_2   2421 CCTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTT--TATGT 2467
                          v i  ?i- v i -   iv   v v  vv i     v ii  --  vi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_26507413_2   2468 CTAAATCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGGAT 2517
                         v i --           vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    595 ATGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_26507413_2   2518 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 2567
                         i v  i   v v  i i   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_26507413_2   2568 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTG 2617
                            v  i     i                 v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_26507413_2   2618 ACAAAGGGCTAATATTCAGAATCAACAAAGAACTTAAACAAATTTACAAG 2667
                          i  i  i  vi   i      vv i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_26507413_2   2668 AAAAAAACAGACAACCCCATCAAAAACTGGGCAAAGAATATTAACAGACA 2717
                              i   i i     v  i?    v         i  v v  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_26507413_2   2718 CTTCTCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAATGCT 2765
                         i     v        i  vi viii     i  --         i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_26507413_2   2766 TATAATCACTGGTCAT 2781
                         i vv    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  

1432 20.58 2.49 9.36  chrX_26507413_26511912.rev     3529  4009 (491)    L1M4_orf2#LINE/L1      461   908 (0)  

  chrX_26507413_2   3529 ATCTTACACCCTTCATAAAAATTAACTCAAAGTGGATCATATACCTAAAT 3578
                          i  i     v vi i               i       ? v        
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_26507413_2   3579 GTAAAATGAC--AAACTATAAAACT---AGAGGATAACATAGGAGAAAAC 3623
                             i --i --             ---   i  v        ? v   i
  L1M4_orf2#LINE/    511 GTAAGA--GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_26507413_2   3624 CTAGATGACCTTGGGAATGGCAAAAAAAAAAAAAAAAAATCTAGATGACC 3673
                           vvi          -------------------------i   ------
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGG-------------------------TTAG------ 577

  chrX_26507413_2   3674 TTGTGTATTGCAATGGCATTATAGGTAAAACACCAAAGACATGATCCATG 3723
                         ---------       iv iv   i  vi        ii  ii v v ii
  L1M4_orf2#LINE/    578 ---------GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_26507413_2   3724 AAATAAATAATTGATAAGCTAGACTTTATTAAAACTAAAAAATTCTGCTC 3773
                            v   v   v     ii i     i  i    i      v  i  iv 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_26507413_2   3774 TGTGAATGACACTGTCAAGAGAATGAGAAGACAAGCCATAAACTGGGAGA 3823
                          vii  v      i      i i   i       v   i i v       
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_26507413_2   3824 AAATATTTTCGAAAATCATAT--CTGATAGAGGACTCTT-CCCATAATTT 3870
                                 v --         --      ii     iv -i   v   v 
  L1M4_orf2#LINE/    719 AAATATTTGC--AAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_26507413_2   3871 ACAAAGAACTCTTAAAAATTCAACAATAAGAAACCAAACTACCTGGTT-A 3919
                          i            v  -i    i     i  iv    iv   iii  - 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAA-CTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_26507413_2   3920 AAAATGGGCAAAAGACTAGAGGAGACACCTCACC---TGAGATTTATAGA 3966
                                     i  i v  iv     ii  v  ---vi    v  i i 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_26507413_2   3967 TGACAAATAAACATATGAAAAGATGCTCCATATCATGTTAGAG 4009
                           i v     i  i              v i    ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (62 / 35)
Gap_init rate = 0.02 (11 / 448), avg. gap size = 5.18 (57 / 11)  


3517 20.65 3.25 1.35  chrX_26614040_26616151.rev      730  1620 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_26614040_2    730 TGGAAGGACATTCTGTGTTTGGGAGTTGGAAGACTTAATATT---AAGAT 776
                              i  i  i ii    iiv ii                 ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_26614040_2    777 ATCAATTCTACCCAACATGATTTATAGATTCAATGCAA-CTCTATTAAA- 824
                         iv    v  v     vv    i  i        i    - i    i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_26614040_2    825 TCTCAACAGCAATTTTTTTA-GGAAAT---CAAA--AATTCTAAAATTCA 868
                           i  i v  --i      i-i     ---   i--i  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_26614040_2    869 TATGGAATTTCAAAATACTCTGAATAGCTAAAACAATTTTCAAAAAGAAG 918
                                v v   iiv  i v       i        i  v         
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_26614040_2    919 AACACAGCTGGAGGCCTCATGCTTTCAGATTTTAAAACATATTACAAAGC 968
                             v  i      v    ii   i vi    i     v  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_26614040_2    969 TACACTAATCAAATCATTGTGGTACTGGTATCATGACAGATATATAAGAC 1018
                             v       iv  v           i  v v  i   i     iiv 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_26614040_2   1019 AATAGAATAGAATAGGCAGTCGAGAAATAAACCCTCATGTGTATGGTCAA 1068
                            i         v iv    v            vi ii v         
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_26614040_2   1069 ATTATCTTTCACAGTAGCTCCAAGACTACTCAATGGGGAAAGCATGATAT 1118
                         v v  i  iv   ivi iv       i i             v  ii v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_26614040_2   1119 CTTCAACAAATGGTGCTTCTAAAACTAGATATCCATATGCAAAAGAAAGA 1168
                         i                vvv v    i    ?   i           v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_26614040_2   1169 CATTGGACCT-------ACATCATTTATGAAAAACAAATCAAAATGGATT 1211
                         vi       i-------   i   v  ii    vi  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_26614040_2   1212 AAAGACCTAAATGTAAGTCC--AAACTATAAAG-TCCTAGAAAAAACCAT 1258
                          ?               vv --          i-  i     i   v   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_26614040_2   1259 AGGAGAAAAGGCTCCATGACACTGCATTTGGCAATGATTTATTGCATTTG 1308
                            ? v   v-  i i    vi  vi  v       i   v  iv  v  
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_26614040_2   1309 AAACCAAAAGTACAGAAAAACAAAAGCAAG--CAGACAAAACGGACTACC 1356
                          v        i   - iv        v  i--i   i   vi     v v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_26614040_2   1357 TCAAACTTAAAAAAACTTTTG--CTAATAAAAGGACACAATTAACAGAGT 1404
                              v       --      --  -- v         v  i  v i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA--CTTTTGTGCT--TCAAAGGACACTATCAAGAAAGT 692

  chrX_26614040_2   1405 AAAAAGGCAACCAATAGAATGGGA-AAAATATTTGCAAATTATATATCTG 1453
                         i     i     v i         -               i         
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_26614040_2   1454 ATAAGGAATTAATTTCTATAATATATGAACAACTACTAAAATTCAATAAC 1503
                               i i vi v  i v       i  v    vi  v  i       i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_26614040_2   1504 AAAAATATCAAATAACCTGTTTAAAAAATGAGCAAAGGACATGAATAGAC 1553
                              v -         iiv  ?       i        iv         
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_26614040_2   1554 ATTTCT---AAGTACATAATATACAAATAGCCAAAAATCATATGAAAAGA 1600
                               ---   v ---i          i     v  v  i         
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAA---GATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_26614040_2   1601 TGCAAAACATCACTAATCAT 1620
                            vv       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (101 / 79)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.05 (41 / 20)  


2023 19.14 9.83 2.76  chrX_26624881_26626452.rev      502  1081 (491)    L1M4_orf2#LINE/L1      288   908 (0)  

  chrX_26624881_2    502 ACATATAGATTATTGGAATAAAATGTAGAGTCCACCAACGCACCCTTATA 551
                                   i v       i   vv        vv  iiv    v  i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_26624881_2    552 TT-ATAGTCAATTGATATTTGATAAGGGTGCCATGATAAATTAACAACAG 600
                           -  i          v  i  i          v  iv -  --   ii 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TT--CAATGG 384

  chrX_26624881_2    601 TGGAAAGAATACCTTTTTTCAACTAATGGTCCTGAGAGAATTAGACATCC 650
                         -          v- i        v      v   i  v  i i  i ?  
  L1M4_orf2#LINE/    385 -GGAAAGAATAG-TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_26624881_2    651 ATACTCAAA------------------------------TATA------- 663
                          i iv    ------------------------------    -------
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_26624881_2    664 -------AAATGGATGATAGACCTAAATATAAAATGTGAAACTATAGAAC 706
                         -------        v ?          i   i vv i        i   
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_26624881_2    707 TCTTAGAAGAAAACATAGAATTGAACATTGGTGACCTTGAATTAGGAAAT 756
                                           i?v i  iv  v         ii     v   
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_26624881_2    757 GGTTTCTTATATATGACACCAAAAGCATAAATGACAAAAGATAACAAACA 806
                                  v                 i  iii        -  -   i 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-AA-AAATA 630

  chrX_26624881_2    807 CATAAAGTGGATGTCATCAAAATTAAAA-TGTTTGTGCCTGAAAGTGCAT 855
                         v     v    iv               -iv       i v    vi  i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_26624881_2    856 CATAGAGAAAGTGAAGTGACAACC-ACAATATGGGACAAAAT----GCTA 900
                         i  vi          iv       -   iv      v     ----  v 
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_26624881_2    901 ATCATATACTTGATAGGGAACTGGC-TTCAACATACAT---GAACTCTTA 946
                                 ii     i  i   v i- i  iv   i  ---         
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_26624881_2    947 TAATCCAATAATTATAAACAAAACAGAACAAATGAACTAGTTTAAAA-TG 995
                         i  ii       -------    -   -     i v i i  ?    -  
  L1M4_orf2#LINE/    781 CAACTCAATAAT-------AAAA-AGA-CAAATAACCCAATTWAAAAATG 821

  chrX_26624881_2    996 ATCAAAATATTTAAATAGACATTTTTT-AAAGAAGATAAATAAATGGCCA 1044
                         iv    iv    i           i i-          v i         
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_26624881_2   1045 ATAAGAACATAATAAAATACTCAAAATCATTGACCAT 1081
                              v    i v  i  i     v    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (64 / 43)
Gap_init rate = 0.03 (19 / 621), avg. gap size = 3.84 (73 / 19)  


2441 25.10 1.00 9.84  chrX_26723891_26727565.rev     2189  3184 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_26723891_2   2189 TGGAAAAACATTCCATGCTCATGGATAGGAATAATCAATGTTGTTAAAAT 2238
                               i i  i     i        v    v v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_26723891_2   2239 GGCCATACTACCCAAAGCAATTTACAAAATCAATGCTATGCCTATCAAAC 2288
                            v     v      vii  i    i v    i  v  v         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_26723891_2   2289 CACCAATGGCATTTTTCACAGAATTAGAAAAAGACT-ATCCTAAAATTCA 2337
                         iv   iiv  v     ii     v v  v  i--  -             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_26723891_2   2338 TATGGAACAGAAAATGAGCCTGAATAGCCAAAGGAATCCTAAGCAAAAAC 2387
                                vv v  iv  v  v           iv    i i --------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-------- 190

  chrX_26723891_2   2388 TGCACTCCAGCCTGGTGACAGAGTGAGACTCTGTCAAAAAAAAAAAAAAA 2437
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    191 -------------------------------------------------A 191

  chrX_26723891_2   2438 AAAGAAGAAGAAGAAAGAAAGAAGAAAGAAAGAAAGAAAGCTGGAGGCAT 2487
                                  v  --------------------------  i      vv 
  L1M4_orf2#LINE/    192 AAAGAAGAACAA--------------------------AGTTGGAGGACT 215

  chrX_26723891_2   2488 CACATTATGCAACTTCAAACTATACTGCAAGACTAGAGTAACCAAAATAG 2537
                             i viv   i      viv    i   ii   v     i   i i  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_26723891_2   2538 TATGGTACTGGTACAAAAACAGACTCATTGACAAATGGAACAGAATACAG 2587
                          i         i i  ii i    vi  v  iv       i     vv  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_26723891_2   2588 AGTCCAGAAATAAAGCTGCACACCTACAACCATCTATTCTTTCATAAACT 2637
                                       v iii   ii  iiii  vi iv i  iv i  ivv
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_26723891_2   2638 TGACAAAAATAAGCAATGGGGAAAGGACTCCCTGTTCAATAAAATGGTGC 2687
                           v   i vi vv            i ivvi  v     i   -      
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA-TGGTGC 414

  chrX_26723891_2   2688 TCAGACGACTGGCTAGCCATATGCAGAAGATTGAAACTGGACTCCTTCTA 2737
                          vi   i     v  ?   i     i    v    ii     i   v iv
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_26723891_2   2738 CTCACCACGTACAAAAATCAACTCAAGATAGCTTAAAGATTTAAATGTAA 2787
                          v     ii         i       i  i v i ?   ii         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_26723891_2   2788 AACCTAACACTATAAAAACCCTAGAAGAAAATCTAGGAAATACTATTC-T 2836
                         i v    v         vi i          iv    ?ivv v v   - 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_26723891_2   2837 GAACACATGCCCTGG-------AATGATTTCAT-GATGAAGATGCCAAAA 2878
                           -------  i   -------    i    v -   - v  ii      
  L1M4_orf2#LINE/    565 GA-------CCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAA 606

  chrX_26723891_2   2879 GCAATTGCAACAAAAACAAAAATTGGCAAGTGGGACCTAATTAAAATACA 2928
                            vvv         iv      v ii  i v    i v  i     ---
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT--- 653

  chrX_26723891_2   2929 TTATAGTATTCTGTACAGTAAAATAAACTATCAACAGAGTAAACAGACCA 2978
                         -  v ivv  i   i vvi   iv v        v i   i  v    v 
  L1M4_orf2#LINE/    654 -TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_26723891_2   2979 CGTATGGCGTTGGAGAAAACATTTGCAAATTCTGCATCCAACAAAGGTCT 3028
                          vi ii vi v        i          iv ii   ii i  i  v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_26723891_2   3029 AACATCCAGAATCTATAAGGAATGTAAACAAATTAACAAGCAGAAAACCG 3078
                         vii         v     i   ivivv    v i  i  vv i  i  vi
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_26723891_2   3079 ACAACCTCATTAAAATGAGGACAAAGAACATGAACACACGCTTTTCAAAT 3128
                          i    iv   ?   viv  i     i iv    i v  ii  i  v  v
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_26723891_2   3129 GAAGACATGCACTTGGCCAACAAGCATATGAAAAAATACTCAACCTCACC 3178
                              i  i  vv       i     i       i  i      v   ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_26723891_2   3179 ATTTAT 3184
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.30 (139 / 107)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 9.82 (108 / 11)  


1979 26.86 8.07 0.31  chrX_26800304_26801942.rev      505  1148 (491)    L1M4_orf2#LINE/L1      215   908 (0)  

  chrX_26800304_2    505 TCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACA 554
                             i  v  ii i      viv        i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_26800304_2    555 GCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC--A 602
                          ii         i iv ii i   v                i    i-- 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_26800304_2    603 GAGCCCTCAGAAATAATGCCACATATCTACAATTATCTGATCTTTGACAA 652
                            i  --        vv   i i  i  iii i vi    i  i     
  L1M4_orf2#LINE/    315 GAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_26800304_2    653 ACCTGAGAAAAACAAGCAATAGGGAAAGGATTCCCTATTTAATAAATGGT 702
                         ivv  vv  i v  vv    i       i  vvi  v  i  i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_26800304_2    703 GCTGGGAAAACTGGA----------------------------------- 717
                                v       -----------------------------------
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_26800304_2    718 ---------------AAAATTAATTCAAGATGGATTAAAGACTTAAACAT 752
                         ---------------        i    i      i ?    i    ii 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_26800304_2    753 TAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTC 802
                         v   v       i      vi i           v    ?i v viv   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_26800304_2    803 AGGGCATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATG 852
                         iv i v v  vv i     v ii   v ivv  vi            vvi
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_26800304_2    853 GCAACAAAAGCCAAAATTGACAAATGGGATCTAATTGAACTAAAGAGCTT 902
                                   vv     v  i    v   ii v  ii  v v  i i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_26800304_2    903 CTGCACAGCAAAAGAAACTACCATCAGAGCGAACAGGCAACCTACAAAAT 952
                         i  ii vv    i  v    i  vv i  i   v  i     i   i   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_26800304_2    953 GGGAGAAAATTTTCCCAACCTACTCATCTGACAAAGGGCTAATATCCAGA 1002
                                   v  iv   vii ivi      i  i  i  vi        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_26800304_2   1003 ATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCAT 1052
                           v  i  v      vv    v iv i  v     i     i     v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_26800304_2   1053 CAAAAGGTGGGCAAAGGACATGAGCAGACACTTCTCAAAAGAAGACATTT 1102
                         i?   ii           iv   ii     i     v        i  vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_26800304_2   1103 ATGCAGCCAAAAAACACATGAAAAAATGCTCGCCATCACTGGCCAT 1148
                          viii     v  i          i      iv     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (100 / 70)
Gap_init rate = 0.00 (3 / 694), avg. gap size = 18.00 (54 / 3)  


1012 23.28 18.25 1.86  chrX_26961358_26962884      500  1036 (491)    L1M4_orf2#LINE/L1      284   908 (0)  

  chrX_26961358_2    500 ATAAACAT-----TTAATTAAACACAATAAAAAGTCCAGAAATA------ 538
                            i    ----- i   vi  i v   vi i            ------
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_26961358_2    539 --------TGGCCAATGAATTTTGGACATGCGTGCCAAGCTAATCTAAGG 580
                         --------   i    vi     v    v v        viv  ii  v 
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_26961358_2    581 GAATAAAGAAGAGTTGTTTTAA-AAA--GCACTGTAACAATTGAATAACC 627
                          ii-      v   iv   i  -   -- ii   vi    i  i   ?  
  L1M4_orf2#LINE/    384 GGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_26961358_2    628 AAATGGAAAA--ATGTACCTGGACACCAATCTTACAC----TACACAAAT 671
                          v   v    --   v vi     v  v i  i    ----    v    
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_26961358_2    672 TTATTCAAAATGGATCTTAGGCTTCAATATAAAAGCAAAATGTATAAAAC 721
                          v i            v?  i i v   i   i   v   vv        
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_26961358_2    722 TTACAGGATAAAATAT-----------TTCA-GTCCTTGCTGTAGGGAAA 759
                          ivi  i v    i  -----------   i- v     vvv    v  v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_26961358_2    760 GATTTCTTAGA-AT------------ACAA------AAAGAAAA----GA 786
                          i         -  ------------    ------        ----  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_26961358_2    787 TAAATTGTATTTTATCAAATATAAAAAAGAACTTTTAC----CAAA---- 828
                                v i  i      -  v     ---     ii----    ----
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAA-ATTAAAAA---CTTTTGTGCTTCAAAGGAC 678

  chrX_26961358_2    829 ATT--CAAGAAA-TGAAA-GACAAGTCATAAACCTAGAGAAAATACTAAC 874
                          i --       -     -     vi  i i vivi         i vi 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_26961358_2    875 AATACATTTACCTGAACAAAGAGCTTGTATCTAGAATACATAAAGAATAA 924
                           vv   v  i    -i  i ii        i      i        ivv
  L1M4_orf2#LINE/    729 AAATCATATATCTGA-TAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_26961358_2    925 TTCCA-CTTGATACTAAAATGACAACTAA---AAT-----ACTGGACAA- 964
                           v  -  ii   v     v     v   ---   ----- v   i   -
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_26961358_2    965 ---TTTTCATGGTTAAATATTTCAGTAAA--AGATAT--------TCAAT 1001
                         ---   ---- iv  i i     vvi   --      --------i    
  L1M4_orf2#LINE/    828 GGATTT----GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_26961358_2   1002 AAGCTCATGAATAAGTTCCCAACATTTTTACTCCT 1036
                             v      v ii v i      iv????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (66 / 57)
Gap_init rate = 0.04 (28 / 625), avg. gap size = 3.86 (108 / 28)  


3039 27.11 1.44 0.56  chrX_27076503_27083196     5302  6201 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_27076503_2   5302 TGGAAAAATATTCCAGGCTCATGGATAGCAAGACTCAATATTGTGAAAAT 5351
                               i    i   v i        v v      i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_27076503_2   5352 GGCCATAATGCCCAAAGTAATTTAGAGATTCAGTGCTATCATCATCAAGC 5401
                            v   v v      v i  i  v       ii  v   vii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_27076503_2   5402 TACCA-TTGACTCTCTT-CAAAGAATTAGAAAAAAACT-ACTTTAAATTT 5448
                          v   -i  v  i i  -  i -    i--- v  i  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAGCTGATCCTAAAATT 146

  chrX_27076503_2   5449 CATATGGAACCAAAAAAGAGCCCGTACAGCCAAGACAATCCTAAGGAAAA 5498
                                  viiv  ii  v  v v i      i      i i ii  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_27076503_2   5499 AGAGCAAAGCTGGAGGCATCACACTACCTGACTTCGAACTATATTACAAG 5548
                            i     i      vv       v  ii i   i  viv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_27076503_2   5549 GCTACAGTAATCA-GCC--T-TGGTACCGGTACTAAAACACATATATAGA 5594
                                      - v -- -      i  i iv ii i v i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_27076503_2   5595 CCAATAGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACC 5644
                         i    i   i    iv   ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_27076503_2   5645 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGTG-AAAGGATTCC 5693
                          vi    i  i     ivv  v   i v  vv     v -    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_27076503_2   5694 CTCTTTAATAAATGGGGTTGGGAGATCTGGCTAGCCATATACAGAAAACT 5743
                           i  i  i      v i     v v    v  ?   i  i  i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_27076503_2   5744 GAAACTGTACCCCTTCCTTACACCTTATACAAAAATTGCCTCAAGATGGA 5793
                            ii  v      v   i     v            iv     i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_27076503_2   5794 ATAAAGACTTAAACATAAGGCCTAAAATCGTAAAAGCCCTAGAAGAAAAC 5843
                         vi ?    i    ii    iv      iii     vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_27076503_2   5844 CTAGGCA-ATACCACTCAGGACATAGGCATGGGCAAAGACTTCATGAATA 5892
                         v    ?i- v i -i  iv   v v  vv i     v ii   v ii   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_27076503_2   5893 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATTGGATCTA 5942
                         vi            vvi          vv     v  i        ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_27076503_2   5943 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5992
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_27076503_2   5993 CAGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTATCCATCTGACA 6042
                         v  i     i                 i       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_27076503_2   6043 AAGGGCTAATATCCAGAATCTACAAGAAACTTAGACGAATTTACAAGAAC 6092
                          i  i  vi          v  i  ii    ivv  i v iv i  v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_27076503_2   6093 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAAGAGACACTT 6138
                           i    ----   v  i?    i    ii      v    v     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_27076503_2   6139 CTCAAAAGAAGATATTTATGCGGCCAACAAACATATGAAAAAAAGCTCAT 6188
                            v           vi vii      i  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_27076503_2   6189 CATCACTGGTCAT 6201
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


2182 27.64 1.51 0.15  chrX_27108887_27110543      503  1164 (493)    L1M4_orf2#LINE/L1      238   908 (0)  

  chrX_27108887_2    503 TACTATAAAGCTAAGGAAACCAAAACAGCTTGGTACTGGTACAAAAACAG 552
                              i       vi v  i   i    iv         i i  ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_27108887_2    553 ACAC-CAGACCAATGGAATAGAACAGAAAACTCAGAAATGTAAGCCATAC 601
                            i-i   i             iv  i iii       i-  v      
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA-AACCCATAC 336

  chrX_27108887_2    602 ACCTACAACCATCTGATCTTTGACAAGTCCAACAAAAACAAGCAATG--- 648
                          ii  iiii  vi    i  i      vviiv   i v  vv     ---
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_27108887_2    649 AAGCAATGGGCATT-CAATAAATGGTGCTGGAATAAGTGGCTGGCCATAT 697
                           iv   i v v  -   i            i i  v   v i?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_27108887_2    698 GCAGAAGATGGAAGCTGGACCCCTACCTTTCATTACATACAAAAATTAAC 747
                            i    vv    i             iv  ii i              
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_27108887_2    748 TCAAAATGGATTAAAGATTTAAATGTAAGACCTCAAACTATAAAAATCCT 797
                                    i ?   ii           v  v           v  i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_27108887_2    798 GGAAGACAACCAAGGAAATACTCTTCTCGACATCAGCCTTGGCAAAGAAT 847
                         i     v   vv   ?ivv v     vi   v ii vi v     v iv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_27108887_2    848 TTTTGGCTAAGTCCCCAAAAGCAATTGCGGTAAAAGCGAAAATAGACAAG 897
                          i  i v  v v v         vvv  iii     vi        i  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_27108887_2    898 TGAAACCTAATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTATCAA 947
                          vii  i v  i   viv  i i   i  ii vv    i  v        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_27108887_2    948 CAAAGC----AGGTAACCTACAGAATGAGAGAAGATATTCATAAACTATG 993
                         v    i----  ii    i        i     i     iii   ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_27108887_2    994 CATGCAACAAATGTCTAATATCCAGAATCTAGAGGGGATTTAAACAAATC 1043
                         i  vii i  iv v  vi          v  v ii i i ivv    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_27108887_2   1044 AACAAGCAAAACACAAATAACCACATTAAAAAATGGGCAAAAGACATGAA 1093
                           i  vv    v          vv   ?             i  iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_27108887_2   1094 GAGATACTTCTCAAAAGAAGACATATGA-CAGCCAACAAACACATGAAAA 1142
                         v   i i     v        i   ii -ii     i  i          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_27108887_2   1143 ATTGCTCAACATCACTAATTAT 1164
                         iv            ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (110 / 69)
Gap_init rate = 0.01 (6 / 671), avg. gap size = 1.83 (11 / 6)  


2079 23.40 0.56 6.55  chrX_27146176_27147902      517  1234 (493)    L1M4_orf2#LINE/L1      234   908 (0)  

  chrX_27146176_2    517 AATTTAC-ACAAAGCCTACAGTTACCAAAACAGCATGGTACTGGTATAAA 565
                           i    -       -      v i   i    ii         i    i
  L1M4_orf2#LINE/    234 AACTTACTACAAAGC-TACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_27146176_2    566 AGTAGACACAGAGACCGATAGAACAAAATAGAAAACCCAGAGACCAATAG 615
                         ii      i v   i i  i   i i   v  i ii     ---------
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA--------- 323

  chrX_27146176_2    616 AACAAAATAGAAAACCCAGAAATGCCAAATACTTACTAACAAATTATCTT 665
                         -----    ---      v v  ---------   iviv   v v  i  
  L1M4_orf2#LINE/    324 -----AATA---AACCCATACAT---------TTATGGTCAATTGATTTT 356

  chrX_27146176_2    666 TGACGAAGCATACAAAAAACATAAATTGGGGAAAGGATACCCTATTCCAT 715
                         i   -   vi i v  i v   vv v         i   vi  v   v i
  L1M4_orf2#LINE/    357 CGAC-AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_27146176_2    716 AAATAGTGCTGGGAAAATTGGCAAGCCACATGCAGAAGAATTAAAATGGA 765
                             i         v  i   vv ?         i      v  iv    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_27146176_2    766 TCCTTATCTCTCACTGTATACAAAAATTAACTCAAGATGAATTAAAGACT 815
                         i  i  i   v   ii                   i   i  i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_27146176_2    816 AAAATCTAAGACTTGAAATCATAAAAATTCTAGAAGATAGCCTTGGAAAA 865
                         v    v     vi i   ii      v ii       v i v v  ?iv 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_27146176_2    866 ACTCTT-GTGTACACTGGCCTATGCGAAGAATTCATGACTAAAACCCCAA 914
                          v    -   -  vi   vi  v  i v iv   v iiv  vi  v    
  L1M4_orf2#LINE/    556 AATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_27146176_2    915 CAGCAAATGCAACTAAAACAAAACTAAACAAATGAGACTTGATTAAACTA 964
                         v    v v     v   iv    v  i i    vi     v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_27146176_2    965 AAAGGCTTCTGTACAGCAATAATAATGATAATCATCATCATCATCATGAT 1014
                            ii   i   i vv   ----- v  ----------  ii    v  -
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAA-----AGGA----------CACTATCAAGA- 688

  chrX_27146176_2   1015 CTGGGTAAACAGACAACCCACAGAATGGGAGAAAATATTTACAAACTATA 1064
                         --ii  i  v                              i    ii   
  L1M4_orf2#LINE/    689 --AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_27146176_2   1065 CATCCAACAAAGGACTAGTATCCAGAGTCTACAATGAACTCAAAGAAATC 1114
                         i   ii i  i     v         i v  i  v      vv v  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_27146176_2   1115 ACCAAGAAATA-ATAA-TAATCCCATAAAAAAGTGGGCAAAGAACATGAA 1162
                          vi  v   v - i  -   i  v  v?    i         i iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_27146176_2   1163 TACACATTTCTCTAAAGAAGATATACAAATGGCCAACAAACATATGAAAA 1212
                           v         i                       i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_27146176_2   1213 AATGCTCAGTATCACTAATCAT 1234
                         i       ii    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (93 / 71)
Gap_init rate = 0.02 (13 / 675), avg. gap size = 3.92 (51 / 13)  


 373 33.15 2.25 0.56  chrX_27151927_27155158     1290  1467 (1765)    L1M4_orf2#LINE/L1        1   181 (727)  

  chrX_27151927_2   1290 TGAAGGGACATACTGCGTTAATGGATGGGAAGACTAAACACAG-TGGGAT 1338
                           i ii  i  v iii   v      v        v  i iv - ii   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_27151927_2   1339 TTCAATTCCCCCCAAATTGATATACAGGTTTAAAACAGTC-TTAACAAAA 1387
                         vv    v i            v     i  i  vi  i  -i  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_27151927_2   1388 TTATAACAATATTTTGTTTTAGAAACAGGCAGGATGGTTCTGA--TAGAT 1435
                          ivi i viiv    -  vi     iv i  i v  i i  i -- vv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_27151927_2   1436 ATGGAAAGAAAAAGAAAACAGGATTGTAAAAA 1467
                                viv  i i vv   i  v iv    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

Transitions / transversions = 1.36 (34 / 25)
Gap_init rate = 0.02 (4 / 181), avg. gap size = 1.25 (5 / 4)  

1701 26.68 6.42 2.28  chrX_27151927_27155158     2039  2739 (493)    L1M4_orf2#LINE/L1      179   908 (0)  

  chrX_27151927_2   2039 AAACAATTTTGAAAATTACAAATAAAGTTGAAGGAAATCACAGTACCCCA 2088
                                i       vv vi  i       i    v-     v v   v 
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAA 227

  chrX_27151927_2   2089 TTTCAAAACATCTTGTATAGCTACACTAATCAAGAAAATGTGATACTGGT 2138
                                  v vi ii v       v         v i    i      i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_27151927_2   2139 GGATGGACAGACACATAGATCAATGGAACAGAAA-GAAAACTCATAA-TA 2186
                         iv v   i     i              i    v-  i iii  v  -  
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_27151927_2   2187 GTACC---ACAGTAA-GGACAACTAATTTTTGATAAAGCTGCAAAGGCAA 2232
                         i-   ---   v v -  v   i i     i  i  i v   v   i v 
  L1M4_orf2#LINE/    328 A-ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_27151927_2   2233 GTTTATGGAGAAAAAA-AAT-TTCTCAA--AATAGTACTAGAGAAATTGT 2278
                         v iv    i    i  - i -  i    --   i  i  i iiv  i  v
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_27151927_2   2279 ATATCCAGAAACAAAAATATAAA------------CCTCATAACTTATGC 2316
                            ?   v vi     iv  i  ------------     i v v   i 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_27151927_2   2317 AGAAATTAACTCATAGTGCATCTAATATTTAAATGTAA-------AACAT 2359
                          i           v i  v   v? v ii         -------   - 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC-T 525

  chrX_27151927_2   2360 AT----TTTTTTAAATAAGA----GGAAGAAATCTTTTGTAATCCAGCAC 2401
                           ----i i  vi  v  i ----  ?iv       i-  i i iv vii
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGGGT 574

  chrX_27151927_2   2402 GTAGTAAAGCGTCCTTAGACTTGACACTAAAAGCATGACCCATGAAGGGG 2451
                         vvi i  v vv i      iv      i       ii v v ii  i ii
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_27151927_2   2452 AAGACTGAGAAATTGGCC--CCTTAAAAATAAAAAATAGAAAAAATGTTA 2499
                           i iv  v       v -- v i    v      v vv------   vv
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT------TGTGC 668

  chrX_27151927_2   2500 TTCAACTTTTTATG-CTGTGTTAAGAGAATGAAAAGACAAACTAAAGACT 2548
                              ------ v - vv i i    i i           v i v   v 
  L1M4_orf2#LINE/    669 TTCAA------AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_27151927_2   2549 GGGAGAAAATATTTTTAAGCCATATATCCAA-AAAAGACTAGTACCTAGA 2597
                                       vi  ii        ii -  ii    v   i i   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_27151927_2   2598 ATATATAAAGA-TTCTCAAAATTTGACAGTATAAA-ATAAACAATCCAAT 2645
                                    -i   i v  i ii i i  v   - i   i  i     
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_27151927_2   2646 TTGAAAATGAGAAAAAGACATAAACAGAAACCTCACTAAAGAGGATATAC 2695
                          ?i      i v   i  iv i  i   v ii  v i     i       
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_27151927_2   2696 AGATGGCAAATGAAAAC--GAAAAGATGTTCAACATCATAGCCATC 2739
                          i     v   i iv  --         i         ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (109 / 74)
Gap_init rate = 0.03 (23 / 730), avg. gap size = 2.65 (61 / 23)  


2098 25.38 6.78 2.11  chrX_27271969_27273815.rev      502  1356 (491)    L1M4_orf2#LINE/L1       14   908 (0)  

  chrX_27271969_2    502 CATGTTAATGGATTAGAAAATTCAATATCGTGACGATGCCAA-------C 544
                               v       i   i i i     i  v v    v   ------- 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chrX_27271969_2    545 AGATTTAGGTATACCTACAGATTCAAAAACATTGCTATTAAAATCTCAGC 594
                          i   -- i ----            vivv  iv    i      i    
  L1M4_orf2#LINE/     64 AAATT--GAT----CTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_27271969_2    595 CTCACTTTTTCAGAGAAATGGAAGAGCTGATATTAAAATTCATATGTAAA 644
                         iv -      iiv      v  vi       vi             v   
  L1M4_orf2#LINE/    108 TGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_27271969_2    645 TGCAAAGGTCCTAGGAGAGCCAAAACAATCTTGATTTAAAA----AATAA 690
                              i  v  i  i v                 ---    ----  i  
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAAGAACAA 203

  chrX_27271969_2    691 -GTGAGAGGATGAAAAATTCACAATTTCAAAACTTAGTACAAAGGGACAG 739
                         -  vi     ivv v v   v               v       vv    
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_27271969_2    740 TAATCTATAGGGCACAGTATTGACATTAGGATGGAAATATCAACCAATGC 789
                              v v vi iiii   i  i   v     i  v    vi i     v
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_27271969_2    790 AACAGAATACAGAGTGCATAAATACATCTATTCATTTTTGATCAACTGAG 839
                           i     vv     v  v     v i i  v     v  i    i   v
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_27271969_2    840 TTTTGACAAAGATTCCAAGACAATTCAATATAGAATGT-TAATCTCTTCC 888
                            i     i i v       v       ivi   v v-  i   i   v
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_27271969_2    889 ACAAATGATACTGGGACATTTGGATATCCATATGCAAA-GAATGAATATA 937
                                i i        vi      ?   i       -       vv i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_27271969_2    938 GAACTTTAGTTTA-ACCATGACACAACCATAGATAAAAAACAAAAAATAC 986
                           v ii  vi i -     - i    vv  vi ivv    iii vv ? v
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCAT-ATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_27271969_2    987 ATATAAAGGTATACGTCAAAACTCCAAAACCATAAGAATAAAATAGAGCA 1036
                          iv    v   viv ii      vi     iv v    v    i v  v?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_27271969_2   1037 GTACGTCTTTGAGCCCCTGAAACATGCAATGATTTCTTACAAA--ACACT 1084
                            vi    i v v  i  iivi v      i       v v --    i
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_27271969_2   1085 AAAA-------CAACTCATGCAAAAAAAAGATCA----GAATTC--CAAA 1121
                             -------    vv v -      v    v ----  v   --    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_27271969_2   1122 ATTAAAACATTTTGACCTTCTAATGGCCAC-ATTGATAAAGAGCAATAAA 1170
                                vv     vv    v  -  v   -  ii v    v -  -  i
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTG-AA-AAG 698

  chrX_27271969_2   1171 ATTAATTTA---AATA--AAACTATATTTGCAAATTATATGTGAGGTAAA 1215
                          i-  iii ---   i-- i vv            i    i vv i   i
  L1M4_orf2#LINE/    699 AC-AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_27271969_2   1216 CAATTTAT-----GAATATA--AAGAAC-----CATTTCAATG-CAAAGA 1252
                         vi i  i -----       --      -----  vi     i-i   i 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_27271969_2   1253 GA-ACAGAACT------AAAACTGTATGTAAAGGATTTGAGTAGACATTT 1295
                           - v v   i------    v  v-- i           i         
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGG--GCAAAGGATTTGAATAGACATTT 845

  chrX_27271969_2   1296 CACTTAAGAA--TATACCAGTTGTGAGCAAGCCCAAGAAAAAATGACCAA 1343
                          v iv     --     v i v iv ii    v  v     i   vi   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_27271969_2   1344 TAGCATATATTTT 1356
                         i v  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 0.96 (105 / 109)
Gap_init rate = 0.03 (31 / 895), avg. gap size = 2.45 (76 / 31)  


1965 24.96 5.58 1.47  chrX_27280369_27282052.rev      514  1194 (490)    L1M4_orf2#LINE/L1      160   868 (40)  

  chrX_27280369_2    514 AAGATAACTAGAATAGCTAAAACAAGTCTGAGAAAAGAAGTAGC----TT 559
                            iv v i        i       vii   -        - i ----  
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAG-AACAAAGTT 207

  chrX_27280369_2    560 AGAGGACTCATACTACCTGATTTTAAGACTTGCTATA----TA----AAT 601
                         i         i   v  ii    i  i    i   i ----  ----   
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_27280369_2    602 ----ATAGTATGATATTG--AGAGAGATAGACACATAGAT-AATGGAACA 644
                         ---- i   i  i  i  -- v ii        i      -       i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_27280369_2    645 AAACAGAGAACAAAAAAGTAGACCCACACCAATATGTCCAATTGATTTTT 694
                         i  iv    iivv i  i  i     i  vvv    vi           i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_27280369_2    695 TTTTTGCAAAAGTGAAAATGCAATTCAATGGAGGAAGGATAATCTTTTCA 744
                         v----i   ii   vv  vi v         i i   i   i        
  L1M4_orf2#LINE/    358 G----ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_27280369_2    745 ACAAATGGTG-TATGACA--------TCCCGAGGCAAAAAAAT-AACCTC 784
                                   - iv    --------?  vv v      i   -  vi v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_27280369_2    785 AACCTAAACCTCAGACCTTATACAAAAATTAATTCAAAATGCATCACAGA 834
                         i   ivv      v   v              i        v    ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_27280369_2    835 TGTAAATACACAAGGTAAAACTATAAAACATTTAAAACAGAACATCAGAA 884
                         iv     ii vi  v              vi   i  v i     -  i?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AGGN 552

  chrX_27280369_2    885 AAAAATTT--ATGACCTAGAGTTAGGCAAAGAGTTCTTAGACATGACACC 932
                         iv    i --i      v i         v iv        i        
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_27280369_2    933 AAAAGCACAATCAATAAAAGCAAAAAAATGGATAAATTGGGCATCACCAA 982
                                   v   i     --       i          i v   i   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAG--AAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_27280369_2    983 A-TTAAATTTTTTGGCCCTGCATATATC-CTGTCAGTAAGATTAAAAGAG 1030
                          -     vvi   v iv  v  v viv -  i   iv  ii v      v
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_27280369_2   1031 AAGCCTCAGACAGGGAAAAAATGG--GAAAATCATATTTCTGACTAGG-A 1077
                           v  v    vv    i     iv-- v         v     iv   - 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_27280369_2   1078 CT-ATTTAAAAAATATATAGGGAACTCTCTGAACTCAACAGTAAGAAAAT 1126
                           -i v vv i        ii       ivv       i i   i  i i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_27280369_2   1127 GAAAAATCTAACAAGAAAATAAGCAAAGG-CTTGAACAGACACTCCACCA 1175
                         i  v  i i  iv?i     ii       -i     i     i i v   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_27280369_2   1176 AAGGAAATGTTAGACATGG 1194
                            i i  i - v v    
  L1M4_orf2#LINE/    851 AAGAAGATAT-ACAAATGG 868

Transitions / transversions = 1.44 (98 / 68)
Gap_init rate = 0.03 (22 / 709), avg. gap size = 2.18 (48 / 22)  


 549 20.00 0.00 0.00  chrX_27289560_27292074      519   623 (1892)    L1M4_orf2#LINE/L1        1   105 (803)  

  chrX_27289560_2    519 TAAAAAGATATCCCGTGTTCATGGATTGGAAGAATTAATATTATTAACAT 568
                          ii           i                  v        i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_27289560_2    569 GCTCACATTACCCAAAGCAATCTACAGATTCAATGTAATCGTTATCAAGA 618
                          viv i i v      vii              i i    vi      i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_27289560_2    619 TACCA 623
                          v   
  L1M4_orf2#LINE/    101 TCCCA 105

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.00 (0 / 0)  

2647 23.05 2.47 3.98  chrX_27289560_27292074      913  1641 (874)    L1M4_orf2#LINE/L1      112   829 (79)  

  chrX_27289560_2    913 TTCTTCACAGCAACAGAAAAAAAAATCTTAAAATTCATGTGTAAATGCAA 962
                           i  ii   v  iv  v  ivvi   i          i  v        
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_27289560_2    963 AAGACCTCAGA-CAGCCAAAACAATCTTGAGCAAAAAAAAAAAAAAAAAA 1011
                         ii    -    -i                 --------------------
  L1M4_orf2#LINE/    162 GGGACC-CAGAATAGCCAAAACAATCTTGA-------------------- 190

  chrX_27289560_2   1012 AAAAAAAAAAAAACAAAGCTGGAGACATCACACTACCTGACTTAAAAATA 1061
                         ---    i  i       i     ivv       v  ii i  v    iv
  L1M4_orf2#LINE/    191 ---AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_27289560_2   1062 TACTA---AGCTACAGTAAACAAAACAGATCAGTACTGGCATAAAAACAG 1108
                              ---           v   i    vvii            ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_27289560_2   1109 ACACGCAGACCAATAAAACAGAGTGCACAACCTGGAAATAAATTCATGCA 1158
                            iii   i    ii  i   i vv v ii ii        ii   i  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_27289560_2   1159 TTTACAGCCAACTTGTTTTTGACAAAAATGCCAATAACAGACATGGAGGA 1208
                             ii i   i vi    i     iii      v v  vv  vv i   
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_27289560_2   1209 AAAGACAGTCTCTTCAATAAATGGTGCTGGGACAACTGTATATCCACATG 1258
                           ii i     i     i                    v   ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_27289560_2   1259 CAGAAGAATGAAACTAGACCCCTATCTCTCACCATACACAAAA-TCAACT 1307
                           i         ii i        i   v       i      - i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_27289560_2   1308 CAAAGTGGATTAAATACTTAAATGTAAAA-CAAAAACTATGAAACTACTA 1356
                             i     i ? v  i         i - v        i     vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_27289560_2   1357 AAAGAAAACATAGAGGAAACTCTTCATGAAATTGGGCTGGGCAAGGATAT 1406
                         i            i? v  v     i   vv     i i     v i v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_27289560_2   1407 TTTGTGTAAGACCTCAAAAGCACAGGCACCTAATGCAAAAATAGACAAAT 1456
                         i  ivi  v   vi          i   v v  v v         i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_27289560_2   1457 GGGATTACATCAAACTAAAAAGCAT-----CTTCAGAGCAATGGAAACTA 1501
                         v   i v       v v    i v -----     i  -----  v    
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-----GACACTA 682

  chrX_27289560_2   1502 TCAACAGAGTGAAGAGGCAACCTACAGAATGGGAGAAAGTATTTGTAAAC 1551
                             v i      i  i     i               i      i   i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_27289560_2   1552 TATGTATTTGGTTAA-------TATCTGGAATATATAAGGAATGCAAACA 1594
                         i  i   i  i v i-------    ii          i   iv vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_27289560_2   1595 ACTCAATAGTATAAAACTAAATAATCTTATTAAAAAATGAGTCAGGG 1641
                                 i  v   ivi      i iv   ?       i iv i  
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.88 (107 / 57)
Gap_init rate = 0.01 (9 / 718), avg. gap size = 5.22 (47 / 9)  

 245 26.32 0.00 1.05  chrX_27289560_27292074     1928  2022 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_27289560_2   1928 AAAAAAGGGAACAAAGTCCTGCATAGACATTTTTCAAAATAATACATTGA 1977
                              v   v -  i vii  v          i  v   v  v i  vv 
  L1M4_orf2#LINE/    815 AAAAATGGGCA-AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_27289560_2   1978 AATTTCCAACAGATGCATGAAAAAATTTTCAGCATCACTAAACAT 2022
                            vv    i iiii        i  vi   i     ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.08 (13 / 12)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


2865 20.22 3.12 11.77  chrX_27406243_27408536.rev      810  1803 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_27406243_2    810 TGGGAATATATCCTATTTTAATAGATTGGAATAATTGAT---GTTAAAAT 856
                            i  v      i  v  v  i        v v  i  ---     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_27406243_2    857 GTCCATACTACCCAG--TGGCCTACAGAGTCATTGCTATTCCTGTCAAAA 904
                          v v     v    i--  ii       v   vi  v  i   i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_27406243_2    905 TTCCAATGGCATTTTTTTACAGACATAGGAAAAC-AATCCTAAAATTCAT 953
                          i   iiv  -i      i    v  v iv  i -i              
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_27406243_2    954 ATGGAGTGATAAAAGACACAGAATAGCTAAAATAATCTTGAGAAAGAA-- 1001
                              ivvii  ii   v         i    i        i      --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_27406243_2   1002 -CAAAGCAGGAAGCATAATACGTCCTGATTTCAAAATATATTATAAAGCT 1050
                         -     iv   i vv v i  v   ii         iv  i  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_27406243_2   1051 AGAGTAATCAAAACAGTTTTGTACTGTCATAAAAACAGACATACAGACCA 1100
                          v         i     v v      v     ii i       i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_27406243_2   1101 ATGGAACAGAATAAAAAGCCCAGAAATAATCCAATGCAT--ATAGTCAAA 1148
                               i     vi i  i          v  v  i   --  i     v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_27406243_2   1149 TGATCTTTGACAAGGGTGCCAATAATGCACAATGGGGAAAGGATAGTCTT 1198
                             i  i              v viiiv            i        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_27406243_2   1199 TTCAACAAATGGTGTTGTGGA-AACTGGATATTGATGTGAAAAAGAAAAG 1247
                                       i  -   -         ?iv ii  v       v--
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCAAAAGAAT-- 446

  chrX_27406243_2   1248 AAAAGAAAGAGAGAGAGAGAGAAAAGGAAGGAAGGGAGAAAGAAAGAAAG 1297
                         --------------------------------------------------
  L1M4_orf2#LINE/    447 -------------------------------------------------- 446

  chrX_27406243_2   1298 AAAAAAGAGAGAGAAAGAAAGAAAGGGAAAGAGAGAGAGAAAGAAAAAGA 1347
                         --------------------------------------------------
  L1M4_orf2#LINE/    447 -------------------------------------------------- 446

  chrX_27406243_2   1348 GAGAGAGAAAGAAATTTAACCTCTACTTTAAACCATACACTAAAATCAGC 1397
                         ----------   i  vi   i    i i v      i  v     i i 
  L1M4_orf2#LINE/    447 ----------GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_27406243_2   1398 TTAAAAAGAA----ATACTGAAATGTAAGGGCTGAAAATGCAGAACTCCT 1443
                          i    v i ---- v  iv         i   i   v ii i     i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_27406243_2   1444 AGAAGAAAACA--GGAGAAGAGTTGCTACACATTTG-TCATGGCAGTAAG 1490
                                    --  ? v i vi v vvv  v  v - i -    i iiv
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA-GGCAATGGT 585

  chrX_27406243_2   1491 TTATTGGCTATGACACCAAAAGCACAGGCAACAAAAGGAAAAATAGACAA 1540
                           v  i v                  i          i         i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_27406243_2   1541 GTGGGCCCACATCAATCTAAAAAGCTTCTG-----CACAGAA-ACAATCA 1584
                         i v  v iv      vv v    i   i  -----  v  i -  v    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_27406243_2   1585 ACAGAATGAAAAG----TCTACAGAATGGGAAAAAAT--TTGTCAACTGT 1628
                          v i i       ----i i           i     --   iv  iii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_27406243_2   1629 ATATCTGACAAGGGATTAATATCCAAAATATATAAGAAACTCATACAATT 1678
                                 i      i vi      i         ii     v     i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_27406243_2   1679 CAACTGCAACAACAACAAACAACCCAGTTTAAAAAATGGGCTAAAGTCTT 1728
                            ivii  v  -i     i      i  ?     -     v  i vi  
  L1M4_orf2#LINE/    786 CAATAATAAAAA-GACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTT 833

  chrX_27406243_2   1729 GAAAATATATTTCTCCAAAAAAGACATACAGATGGCCAACAGGCATATGA 1778
                            v v i           i    i     i        i i   i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_27406243_2   1779 GAAGGTAATCAACATCATTAATCAT 1803
                         i   i iv         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (123 / 75)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 7.79 (148 / 19)  


2836 25.84 3.80 2.24  chrX_27426835_27429600.rev     1382  2275 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_27426835_2   1382 TGGAAAAACATTCCATGCTCATGAATTAGAAGAATCAATATCATTTAAAT 1431
                               i i  i     i     i   i     v i     ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_27426835_2   1432 GGCCATAAGGCTCAAAGCAATTTACAGATTCAACATTGTTCCTATTAAAC 1481
                            v   vvv i    vii  i            iivi i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_27426835_2   1482 TGCCAACATCATTTTTCACAGAACTAGAATAAAAACT-ATTCTAAAATTC 1530
                          v   i vv v     ii     v v  v---  i  -  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC---AAGCTGATCCTAAAATTC 147

  chrX_27426835_2   1531 ATATGGAACCCTAAAAGAGCCCTAATAGCCAAAACAATCCTAAGGAAAAT 1580
                                 vivi  ii  v  vv                i i ii  i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_27426835_2   1581 GAACAGAGCTGGAGGCATCACATTATCTGACTTCAAACTATACTACAGAA 1630
                              i  i      vv     i vi ii i      viv       i i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_27426835_2   1631 CAACAGTAATCAAAACAGCGTTGTCCTGGTACAAAAACAGACACATAGAC 1680
                          v           i    i  v  v    i i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_27426835_2   1681 CAATGGAACAGAATGGAGAACCCAGAAATAAAGCTGCACCCCTACAGCCA 1730
                                 i     v    ii           v iii  vii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_27426835_2   1731 TTCGATCTTCAACAAAGTGAGTAACAAGCCTAT-----GAGGGAAGTGCT 1775
                         v i   i   i    i ---  iv    v i  ----- i  i   viiv
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG---GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_27426835_2   1776 CTCTATTCCATAAATGGTGCTGAGATAGCTGG-----CATATGCAGAAGA 1820
                         v   v   v i           i  i i    -----  i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_27426835_2   1821 ATGAAACTGGACCCCTACCTTTTGCCATATGAAACAATTAACTCAAGATG 1870
                              ii             ivii      iv  v           i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_27426835_2   1871 GATTAAAGATTTAAATATAAGACCTCAAACTATAAGAATCCTGGAAGAAA 1920
                            i ?   ii     i     v  v         i v  i i       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_27426835_2   1921 A-ATTGAGAAGCACCATTCTATGCATCAGCCTTGGG--AAAGAAT----- 1962
                          -  --  i? i -- v   - - i v -       -- iiv   -----
  L1M4_orf2#LINE/    545 ACAT--AGGNGTA--AATCT-T-CGTGA-CCTTGGGTTAGGCAATGGTTT 587

  chrX_27426835_2   1963 -----ATATGACTAAGTCCTCAAAAGCAATTGCAAACAAAAACAAAAATT 2007
                         -----       -- ----i        vvv    -     iv      v
  L1M4_orf2#LINE/    588 CTTAGATATGAC--A----CCAAAAGCACAAGCAA-CAAAAGAAAAAATA 630

  chrX_27426835_2   2008 GACAAATAGGACCTAATTTAACTAAGGAGCTTCTGCACAGCAAAATAAAT 2057
                           i    v    i v  iv  v v ii i   i  ii vv    iv v i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_27426835_2   2058 TATCAACAGAGTAAACAGAAAACCTACGCAATGAGAGAAGATATTTACAT 2107
                               v i   i  v   v    i  iv    i     i      i  v
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_27426835_2   2108 ACTGTGCATCTGACAAATGTCTAATATTAAGAATCCATTAGGAACTT--- 2154
                          iii ii      i  iv v  vi   iv     vi  v i     i---
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_27426835_2   2155 -AATATAACAAACAAAAACCAAACAACCCCATTAAAACATGGGCAAAGGA 2203
                         -  ivi  i  vv    iv    i     v   ?   v            
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_27426835_2   2204 C------AGACGCTTCTCAAAAGAAAACATACATGTGGCCAACAAGCATA 2247
                         i------    ii     v      i i     vi       i     i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_27426835_2   2248 TGAAAAAATGCTCAACACCACTAATCAC 2275
                               i          i  ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (145 / 83)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.00 (54 / 18)  


 323 26.83 0.00 0.00  chrX_27496683_27499515.rev      946  1027 (1806)    L1M4_orf2#LINE/L1       18    99 (809)  

  chrX_27496683_2    946 TTCATAAATTAGAAGACTAAATTTTTTTGAAATGTCAGTTCTTCTCAAAT 995
                              ii   i       v   v  v  i i   v  i v  i i     
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_27496683_2    996 TGATCTATAGATTTAATGGAGTCTTAGTCAAA 1027
                                i     i  i v i  iivi     
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAA 99

Transitions / transversions = 2.14 (15 / 7)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.00 (0 / 0)  

1549 27.50 6.55 1.96  chrX_27496683_27499515.rev     1382  1992 (841)    L1M4_orf2#LINE/L1      165   803 (105)  

  chrX_27496683_2   1382 ATCTACAATAGCTGAAATAGCTTTGAAAAAGAATAAC---TTTGGGGAAC 1428
                          i i v      ii   i iii           v   ---v    i i  
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_27496683_2   1429 TTTTACTGTCTGATT-CAAGACTCACTATAACGATAAAATAATTAATGCA 1477
                          ivi   vi ii   -   i   i    i  v v  v i    i  vi  
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_27496683_2   1478 GTGTAGTATAGGTGTAA---TAGACAT-TATCTAAACGAAACAAAGTCAA 1523
                             i   iv  ii   ---       -  vv v  i i  i i i ii 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_27496683_2   1524 GATTCCAGAAATAGACCCACATATATATGGTGAAGTGGTTTTTGACATAG 1573
                           v          i     i i  v      v  v  i    i    vi 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_27496683_2   1574 GTATTAAGGT-ATTCCAATAGGGGAAATATACATTTTTAAATAAATATTA 1622
                           iii   ii-    -   i   i  iv   vvi    v  i    iv i
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTC-AATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_27496683_2   1623 TTGGAACAATTGGATATCTGTATGGTTAAAAAAA--------AACCCTTG 1664
                         i   i    i      ? iii   --i    i  --------i    i i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATG--CAAAAGAATGAAGTTGGACCCCTA 461

  chrX_27496683_2   1665 ACTCAAAATCATATATAAAATTTAGCTTAAA-TGAATTATAGACCTATAT 1713
                         v    v -i      i    v   i  i   -  i  i ?       v  
  L1M4_orf2#LINE/    462 CCTCACA-CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_27496683_2   1714 GTAAGA--TAAAGATACAAAACCACTT-GAAGAAAACACAGGAAAAAAAT 1760
                               --    iv  i     i-   -          i   ?iv   - 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNGTAAA-T 558

  chrX_27496683_2   1761 CTTTGTCATATTGACTTTGACAA-AGTTTCTTAAGCAGGATATAAAAAAA 1809
                            i  v iv   iv  v i   -i        iii v  i iv    --
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA-- 606

  chrX_27496683_2   1810 GCATAATCCATAAAAGAAAAAA-----AAAC---AC-------AAAT--- 1841
                            i  v v i           -----   i---  -------    ---
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_27496683_2   1842 AGACTTTTGTTCTTTTACAGACATGGTTTAGGAAACAAAATTGATTGCCA 1891
                          i        v   iv vi    ivi iv  i  iii   v-  ivi  -
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-GACAACC- 704

  chrX_27496683_2   1892 TACACCGAATGGAAGAAAATATTTGTAAATCATAAATTTAACAAAGGCCA 1941
                         --   v      i            i        v  i i i  i  v v
  L1M4_orf2#LINE/    705 --CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_27496683_2   1942 TGTATCCAAAAAATATAAAGAACAAATTTAATTCACTATCAAGAAAATAA 1991
                                 i  v           vvv vi  i   v  vi  i  i i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_27496683_2   1992 A 1992
                          
  L1M4_orf2#LINE/    803 A 803

Transitions / transversions = 2.00 (110 / 55)
Gap_init rate = 0.03 (22 / 639), avg. gap size = 2.36 (52 / 22)  


2137 24.72 1.95 1.30  chrX_27510557_27512163.rev      502  1116 (491)    L1M4_orf2#LINE/L1      290   908 (0)  

  chrX_27510557_2    502 ACATAGACAAATGGAACAGAATAGAAAGCTTAGAAGTAAATCCAACCACA 551
                          i     iv       i     v  i  iii    i    i   vv  iv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_27510557_2    552 CATGATCAACTAATTTTTGATAAGGGCACCAAGACCGCACAATGGGGAAA 601
                         i   i    i i     i  i     ii        iiv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_27510557_2    602 GGATATTTTCTTCAATTCATGGTGTTGGGAAAGCTGGATATCCACATGCA 651
                          i   v i i     ivv      i     v i       ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_27510557_2    652 AAATAATGAAATTGAACCCTTATCTTATACTATACACAAAAATCAAATGG 701
                            v      i   i    i  i  i i  i   i        i  v vi
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_27510557_2    702 AAATGGATTAAAGGCCTAAATATAAGAAATGAAATTG--AAATTTCTAGA 749
                                 i ?  i       i     iv i   i i--   i ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_27510557_2    750 AAAAAATACATGGGGGAAAACTCCTTGACATTGGCCTTGGCAATGATTTT 799
                          i    i i -  ? v   v  i v    v    vi v       i   i
  L1M4_orf2#LINE/    540 AGAAAACATA-GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_27510557_2    800 TTGTGGCATATCATACTACAAGCTCAAGCAACAAAAGCAAACATAAA-AA 848
                           i-- -    v i  i v    v             v   v   i -  
  L1M4_orf2#LINE/    589 TTA--G-ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_27510557_2    849 GTGGGATAT-ATCAAACTAAAAAGCATCTGTATAGTAAAGGAAAC----A 893
                         i v   iv -      v v    i v i   iivvi      v  ---- 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_27510557_2    894 ACAAAATGGAAACACATCTTATGGATTAAGAGAAAATATTTGCAAACCAT 943
                          v   i  i   v   v ii ii  v ii                 i   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_27510557_2    944 ATATTTGATAAAAG-CTAATATCCAAAATATATAAGGAACTCACTCTAAT 992
                             i      ii -  vi      i         i      viv v v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_27510557_2    993 CAATGGCGATAATAAAAATAATACCGAATTAAAATATGGCCAAAGGACAT 1042
                             iiii v  v v      --  v    ?   v    v       iv 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAA--CCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_27510557_2   1043 GAATATACATTTTTTCCA-GACG-TAACTAAATATGGTCAACAAATATAT 1090
                              v      i i v -  v -  --  v v    i   i  ii i  
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATA--TACAAATGGCCAATAAGCACAT 881

  chrX_27510557_2   1091 CAAAAG-TGCTCAATATCATTAATCAC 1116
                         v     -       i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (93 / 55)
Gap_init rate = 0.02 (13 / 619), avg. gap size = 1.54 (20 / 13)  


3273 25.74 0.66 0.77  chrX_27535860_27542241     4981  5889 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_27535860_2   4981 TGGAAGAACATTCTATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5030
                              ii i  i i   i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_27535860_2   5031 GGCCATACTGCCCAAGGTAATGTATAGATTCAATGCCATCCCC-TCAAGC 5079
                            v     v     iv i  v  i        i  v     i-    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_27535860_2   5080 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5127
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_27535860_2   5128 TATGGAACTGAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5177
                                v  v  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_27535860_2   5178 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATAGTACAAGGC 5227
                                i      vv    i  v  ii i      viv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_27535860_2   5228 TACAGTAACCAAAACAGCATGGTACTGGTAACAAAACAGAAATATAGACC 5277
                                 i   i    ii         i vv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_27535860_2   5278 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5325
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_27535860_2   5326 ATCTGATCTCTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5375
                          vi    i ii     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_27535860_2   5376 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCT 5425
                           v  i  i              v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_27535860_2   5426 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5475
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_27535860_2   5476 TTAACGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5525
                          i ?v   i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_27535860_2   5526 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5574
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_27535860_2   5575 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5624
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_27535860_2   5625 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5674
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_27535860_2   5675 CAGGCAACCTACAGAATTGGAGAAATTTTTTGCAATCTACTCATCTGAAA 5724
                         v  i     i       v       v v       vii ivi      v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_27535860_2   5725 AATGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5774
                          iv i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_27535860_2   5775 AAAACAAACAACCCCATCACAAAGTGGGCAAAGAATATGAACAGACACTT 5824
                           i     i     v  i?v   i         i  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_27535860_2   5825 CTCAAAAGAAGACATTTATATGCAGCCAACAGACACATGAAAAAATGCTC 5874
                            v        i  vi v   --     i ii          i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTC 893

  chrX_27535860_2   5875 ATCATCACTGGCCGT 5889
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (130 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2681 24.15 4.42 3.97  chrX_27580353_27582226.rev      502  1383 (491)    L1M4_orf2#LINE/L1       23   908 (0)  

  chrX_27580353_2    502 GGATTGGAAAA--TAAGATGATTTAGATGTCAGT---TCTCAAATT-ATC 545
                                  i --   v  vi  v     v  i ---i i      -   
  L1M4_orf2#LINE/     23 GGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATC 72

  chrX_27580353_2    546 T------TTAA-----------TCAAAATCCCAGAAGGATTTTT-GTAGA 577
                          ------ i  -----------            vv vv     - i   
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chrX_27580353_2    578 AGTGAATACACTGACTGTAAAATTAATATGGACATGTGATCGACCAAGAA 627
                          i vi i vi    iiv       v       v   ii vv    v    
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chrX_27580353_2    628 TAGCCAAAACGACTTTGCAAAACAAGAACAAAATAAGAGGACTAATACTA 677
                                   i ii   v    v         i vi       v i   v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_27580353_2    678 CCCAATCTCAAGACTTATTATAAAATTCAAGTAATCATGACAGTGTGGCA 727
                               i    i     i  i   ii vv        v          i 
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_27580353_2    728 TTTTTGTAAAGACAGGCAAATAGATCAGCGAAACAGAATAGAAATACCAA 777
                         i vvii   i  i  i  v        ii i  i     v  i vv   i
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_27580353_2    778 CAATAGACTTCAGCATATAGAAGCAGCTGATTGTCAGCCATGGTGCAAAG 827
                         v    i  iivvi   v  viiv  ii     v  ii v v     v   
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_27580353_2    828 GCAATTCAGTGAAGAAGGGATAATCCTTTCAACATAGGATGATGGAACAG 877
                         i v     i  ii   i i   i  i        v v i  v   i   i
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_27580353_2    878 TTGGAAATACACACACACACAACACAACACAAAACAAAGCAAACAAAACA 927
                         i    v ?v    ii  ------------------    -------  ii
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCA------------------AAAG-------AATG 447

  chrX_27580353_2    928 AAAACTTTCAGTCCACT-CCTTTCACCATATA-GAAAATTAGCTAAAAAT 975
                           i---- ii v  v  -   iv         -i       i  v     
  L1M4_orf2#LINE/    448 AAG----TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_27580353_2    976 GGACCACCAACTTAAATGTAAAATCCAGAGCTATAAAACTACTAGGAAGG 1025
                            i  ?vi  i         i v i i i          vi   -   i
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG-AAGA 542

  chrX_27580353_2   1026 AAACATAAGATAAAACCTTTGTGATCTTTGGCTGGGCAAACATTTCTTAG 1075
                                i ?vv   i   i    i   v  i i     vvi        
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_27580353_2   1076 GCACAACTCCAAAAATACAATCCATAAAATAACAAATTGATTAATTTGCC 1125
                         ii ii  v      ii    v v i    v  v    v   v    v v 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_27580353_2   1126 TTTACCAAAATTGAAAACATATTTTCTTCAAAAGGCACTGCTAAGAGAAT 1175
                           i i       i     v v v v       i i    iii    i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_27580353_2   1176 GAAAAGACAATCTATAGAATGGGATAAAATTTTTGTAAAGCATATATGTG 1225
                                   i i i         v     v    i   v       v  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_27580353_2   1226 AGAAAGGAGTTGTAATCCAGCACTTA-AAATAATTCTCAAAACTCAATAA 1274
                          v  i   v     -     v iv  -   v  i   i v          
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTA-TCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_27580353_2   1275 GAAAA---TAAACAACCCGAT--ATAAATGGGCAAAAGGCTTGAACAGAC 1319
                         v    ---i   i     i  -- v           i ii     i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_27580353_2   1320 AGTTC----AAGAAAGGACAGTTATAAATGTCAAAGAAGCACATAAAA-- 1363
                          v   ----     --  i --  i     v v  v        i   --
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAA--GATA--TACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_27580353_2   1364 -TGCTCAACATCATTAGGCAT 1383
                         -            ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (123 / 87)
Gap_init rate = 0.02 (20 / 886), avg. gap size = 3.70 (74 / 20)  


 655 22.90 1.40 3.27  chrX_27800000_27804802.rev     1750  1963 (2840)  C L1M4_orf2#LINE/L1   (0)   908   699  

C chrX_27800000_2   1963 ACAGACTAATAGA--GGGAGAACAAT-TTTGAAAACTGTGCATCTGATAA 1917
                            -  iv i   --       -   -    v   iii ii         
  L1M4_orf2#LINE/    699 ACA-ACCCACAGAATGGGAGAA-AATATTTGCAAATCATATATCTGATAA 746

C chrX_27800000_2   1916 AAGTCTAATATCCAGCATCTATAATATAAGGTATGTAAACAAATTTACAA 1867
                         ii v  vi       v  -----      i v ivivv    v iv i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAAT-----ATATAAAGAACTCTTACAACTCAATAA 791

C chrX_27800000_2   1866 GAAAAAACTAAACAACCCAATTAAATATTGGGCAAAGGACATGAACAGAC 1817
                         v     ivi   i         ?  v v           iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chrX_27800000_2   1816 ACTTCTCAAAAAAAGACATTTATGTGGCCAACAAGCACATGAAAAAAAGC 1767
                          i     v   i    i  vi vi       i             i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

C chrX_27800000_2   1766 TTAACATCATTGATCAT 1750
                          i       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (28 / 20)
Gap_init rate = 0.02 (5 / 210), avg. gap size = 2.00 (10 / 5)  

3782 20.00 4.18 1.58  chrX_27800000_27804802.rev     3428  4312 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_27800000_2   3428 TGGAAAGACATCCGG-ATTCATGAATAGAGAGACTGAATATTGTTGAGAT 3476
                                 i    vi-i      i  v ii     v         i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_27800000_2   3477 GTCAGTACTACTCAGAGCGATCTACAGATTCCATACAGTCTCTATAAAAG 3526
                          v  i    v i  i vi             v ii  i  i    v   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chrX_27800000_2   3527 ATCCCTATAAAAACAGCTTTGGTTCTGCAGAAGTCAAAATGCCAATCCTC 3576
                              ------ i v  i  --  i       i ii v v  ii     v
  L1M4_orf2#LINE/    100 ATCCC------AGCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_27800000_2   3577 GACTTCATATAAAATTTCAAGAGATACACA-TAGTCAAAAAATTTTTGAA 3625
                         i v       ii  v v    i  iv  v -   i     v v i     
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_27800000_2   3626 AAA------CAGTGTTGGAGGACTCATTGTTTCTAATTTCAAAACTTACT 3669
                            ------  iv             ivv  i i                
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_27800000_2   3670 GCAAATCTACAATGATCAAAACAGGGTGGTACTGCCATAAGGGTAGACAT 3719
                         i    v     i i     i    v         v       i       
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_27800000_2   3720 ATAGGACAATGTGGCAGAATTCATATTTCAAAAACTGACCTATGCATCTA 3769
                             iv     viii      v v v i  i   ivi   i  i   i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_27800000_2   3770 TA-CCAGTTGCTTTT-GACAGGAGTGACACACTCATTCAACAAGGGAAGA 3817
                          i-i  i   v    -    i i   v  vivi       iii  i    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_27800000_2   3818 ATCGTCTTTTCAACAGATGATGCTAGGACAACTGGATTTCCACATTCTAA 3867
                           v            i   i    i            v?      v v  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_27800000_2   3868 AGAATGAAGCTGGACCCCTCTACATCACACCATATACAAATGTTAACTCA 3917
                                  i         --  v                vi        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCT--ACCTCACACCATATACAAAAATTAACTCA 489

  chrX_27800000_2   3918 AAATAAAGCAACAACTTGAATATAAGTGCTAATACCATAAAGCTCTTAAA 3967
                             ii v  ?vi  i i   i    v     v  i     i      i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_27800000_2   3968 AGAGAATATAGAAATAAATTTT-ATGACCTTGGATTTGGCAATGGATCCT 4016
                            i  i    i?i     i  -i         i  v        v i  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_27800000_2   4017 TAGATATGACACCAAAACCATGAGTAACAAAAGAGAAAAACAGATAA--T 4064
                                          v  ii  i         -     i      -- 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATT 638

  chrX_27800000_2   4065 GAACTCCATCAAA-TTAAAAACTTTGGTGCACCAAAGTACACTATCAAGA 4113
                          i   i       -           v    vi     v            
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_27800000_2   4114 GTGTGAAAA-ACAACCTACATAATGGGAGAACATATTTGGAAACTATAGA 4162
                         iv       -      i   v          v       v   ii   v 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_27800000_2   4163 TCTGATAAGG--TTTAATATCCACAATATATAAAGAACATCTACAACTC- 4209
                                   --i  i-      v              vii        -
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_27800000_2   4210 ----TAAAACAAACAAACAACACA------------GTAAAAAATTTGCA 4243
                         ----     - i     i   v  ------------ i   ii     v 
  L1M4_orf2#LINE/    788 ATAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_27800000_2   4244 TAGACATTTATTCAAAAAAAA---ACAAATGGCTAATAGGCTCATGAAAA 4290
                                  v i    i  i ---         i    i  v        
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_27800000_2   4291 TATGTGCAACATTAGTCATTAG 4312
                         v   iv      i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (110 / 64)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.55 (51 / 20)  


 314 27.59 0.00 0.00  chrX_27839031_27841198.rev      502   588 (1580)    L1M4_orf2#LINE/L1       45   131 (777)  

  chrX_27839031_2    502 TGAAATGTCCATACTATCCAAAGGAACATACAGATTCAATGCAATCTCTA 551
                          i i   v v     vi     vvi iv           i      i   
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chrX_27839031_2    552 CCAAAATACCAATGACATTTTTCACAGAAATAGAGAA 588
                         i      v   iivi v     ii       v  v  
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

Transitions / transversions = 1.18 (13 / 11)
Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.00 (0 / 0)  

2916 23.82 1.96 0.79  chrX_27839031_27841198.rev      914  1677 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_27839031_2    914 ATCTTAAAATTAGTATGGAATCACAAAAAACCTTGGATAGCCAAAGGAAT 963
                            i       vi       vii   iii   iv i         iv   
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_27839031_2    964 CCTGGGGAAAAAGAACAAAGCTAGAGGCATCATACTACAGGATTTCAAAT 1013
                          i  iii  i          i i    vv   i   v vvi        v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_27839031_2   1014 TATACTATAAAGCTATAGTAAACAAAACAGTATGGCAGTGGCATAAAAAC 1063
                         iv     i       i     v   i     i   i v        ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_27839031_2   1064 AGACACACATACCAGTGGCACAGAATAGAGAGCCAAGAAATAATTCCATG 1113
                              i i v i  i   v i     v     i v        vi    i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_27839031_2   1114 CATTTA----CACGTGGATTTTCAAAAAAAGGTGCCAAGAAAACGCAATA 1159
                               ----  -i v       i v  -i          vv iv    i
  L1M4_orf2#LINE/    336 CATTTATGGTCA-ATTGATTTTCGACAA-GGGTGCCAAGACCATTCAATG 383

  chrX_27839031_2   1160 GG-AAAGGATAATCTCTGTAATAAATGATGCTGGGACA-CTGGATATCCA 1207
                           -    i   i   i vi  i     i          -       ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_27839031_2   1208 CATGGAGAAGAATGAAATTAGACCCTTATCTCTCTCCATATACAAAAATC 1257
                             v i         i  i     i  i   v v              i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_27839031_2   1258 AAGTCAAAAGTTATTAAAGATTTAAATTTAAGACCAAAATCTATGAAACC 1307
                           v      vvv  i ?   ii     v     v v   v    i    i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_27839031_2   1308 AATAGAAGAAAACAAGAAAACAAA-CTCCATGACATTGTTCTGGGCAATG 1356
                         vv            viii?ii   -  i i    v   vvi i       
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_27839031_2   1357 ATTTTTTTTTTAATGTAACCCCAGAAGCATGGGCAAAAAAAATGGAAATA 1406
                         i   i  ---vi  i i  v   i     iii    v    ivii     
  L1M4_orf2#LINE/    584 GTTTCTT---AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_27839031_2   1407 GACAAATGGAATTACATCAAA-TTAAAAAGTTTCTGCACAGCAAAGGAAG 1455
                           i    v i i v       -       v   -  ii vv       vi
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACA 679

  chrX_27839031_2   1456 CTATCAACAGAGTGAAGGGACAACCTACAGAACAGGAGAAAATATTTTCA 1505
                                v i      ii       i      ii             v  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_27839031_2   1506 AACTGTATATATGATAAGGGTTTAATATCCAAAATATATAAAAAA----- 1550
                           iii     v         vi vi      i          i  -----
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_27839031_2   1551 -TAACTCAATAGAAAGAAAACAGATGACCCAAGTAAAAAATGGTCAAAAG 1599
                         -i         iv  i  i   i  i      v ?        v    i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_27839031_2   1600 ACCTGAATAGACCTTTCTCAAAAAAAGACATACAAATGGCCAACAGGTAT 1649
                          ii         v      v   i    i              i i i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_27839031_2   1650 ACAGAAA-ATGCTGAACATCACTCGTCAT 1677
                          iii   -     v       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (116 / 62)
Gap_init rate = 0.01 (11 / 773), avg. gap size = 1.91 (21 / 11)  


1897 29.82 4.31 2.16  chrX_27856977_27859220      500  1334 (910)    L1M4_orf2#LINE/L1        8   860 (48)  

  chrX_27856977_2    500 ACATACGATGTTAATGGATTATTTATGACATGCTATTGCTAATATATTAC 549
                          i  v v     v       iv-- v   v iv     i   v  i--i 
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGG--AAGACTTAATATTGTTAAGATG--GC 53

  chrX_27856977_2    550 GGTTCTCTCCCAAATTGACCTATAAATTCAATGCAATCCC------AATT 593
                         ii v   -          i   i i      i        ------   i
  L1M4_orf2#LINE/     54 AATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_27856977_2    594 GCAGCTAGATTTTGTTTGTGGAAATTGACAAGCTGGTTTTTAAATGTACA 643
                         v     - vi   -    ii               i ii v    vi i 
  L1M4_orf2#LINE/    103 CCAGCT-GCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_27856977_2    644 TTAAAATATATGGAGCCAAAAAGAGTCAAGGCAAGCTTGAA---GAAGAA 690
                          vi    ii v  ii  v i  v  i   ii   v      ---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_27856977_2    691 CAAGGTTG-AGGATTTTACACTACTAGATATTAAAA---A--AAAAAAAT 734
                            i    -    i i-     v ivi  v i    --- -- v   iv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTC-ACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_27856977_2    735 -CAGTAGTGAAAA--GTATAATGTTAGCTCAGGGATA-ACAAACAGATCA 780
                         -     i v  i --  i ii ii i  vi i     -   v i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_27856977_2    781 ATTGAACGGAATAAAGGATTCAGGAACAGGCCCACACTTACATGATTACC 830
                           v   ii    vi  ii i   i  i ii    i  v vi   i i vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_27856977_2    831 TTATTTAAGATGAAGGTGACACTGCAGTGCAGTGGAGAAAAGATGTTCTT 880
                          v    vv  ii i    v  vvi vi v  i   i    ii  iv    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_27856977_2    881 TTCAATA----GTATTGGATTAATTCTGTGTG---AGATGGGGTAAAAAT 923
                              i ----  ii   ivi  --   vi i--- v   vii-  i   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAA--CTGGATAKCCACATGCAA-AAGAAT 446

  chrX_27856977_2    924 GAAATCTCACTCCTAACTCTCTTCATACACAAAA--TAAATTACAGGTGT 971
                            i ivv  i    v   v vi    i      --   v i - ii  v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA-AAATGG 495

  chrX_27856977_2    972 GTCGTAATCCTAAAAGTCAAAGTTAAAACAATAGTGCTCCTAGAAGATAT 1021
                         i  i? iv      v  v i  i      v   ivi   i       v v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_27856977_2   1022 TATAAAAGAATATTATCATAGTTTTGAGT-AGGCAATGGTTTCATTAAAA 1070
                         i   ii? v v  iv  i iiii   i  -             -   i v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGAT 594

  chrX_27856977_2   1071 A--ACTTTATAAAAGC-TAATCAAAAAGAAAAGAATGATTGATGAATTC- 1116
                          --  vii --     -i  v   v  i i  i  --  v   i    v-
  L1M4_orf2#LINE/    595 ATGACACCA--AAAGCACAAGCAACAAAAGAAAAA--ATAGATAAATTGG 640

  chrX_27856977_2   1117 -TTTCATTAAAATTAAGAATTTCTATTTATAAAAAGACACTTTTA-GAAA 1164
                         -i     i        i  i  i i viv v   i      v i -    
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_27856977_2   1165 GTGAAAAGGCAAGACACAAAATGGGAGAAGATATTTGCAGCACGTCAATC 1214
                                 i   vv    i          i         ivv i vv   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_27856977_2   1215 CAATATAGGACTCATATCCAGA-CATATAAAGAATTTCTACAAATCAACA 1263
                         ii   vi     ii        -i          i ii     v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_27856977_2   1264 AGGAAAGGATTGACAACCAGAATTGAAAATTAGATTAAATATGTCAGCAG 1313
                          vi   i  ivi i    v-    ?    v i iiv  iv  v v ii  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_27856977_2   1314 GGACTTCACAAAAGAGGATGT 1334
                         iv i   v v     i   i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.73 (156 / 90)
Gap_init rate = 0.04 (30 / 853), avg. gap size = 1.80 (54 / 30)  

 257 21.05 0.00 0.00  chrX_27856977_27859220     1695  1751 (493)    L1M4_orf2#LINE/L1      852   908 (0)  

  chrX_27856977_2   1695 AGAGAATATCCAAATGGCCAATAAGCATGTAGCAAGGTGCTAGATATCAT 1744
                            ii    v                 ii iiv   i    vi i    ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_27856977_2   1745 TAGTCAT 1751
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.00 (0 / 0)  


 589 30.00 1.11 0.00  chrX_27913273_27917591.rev     2333  2512 (1807)    L1M4_orf2#LINE/L1        1   182 (726)  

  chrX_27913273_2   2333 TAGAGAAATATTACAT--TCACAAATTGGAAGAGTCAACATAATAAAGAT 2380
                          i  i i    iv   --   iii         v i  i  vi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_27913273_2   2381 GTCAATTCTCCCCAAATTGATATACAGGATTAATGCATTTCCTATCACGA 2430
                          v    v              v     iv i  i   v i       vi 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_27913273_2   2431 TTCCAGCAAGATTTTTTGTAGCTGTAGGTAAGTGCATTCTAAAATGTATA 2480
                          i     vivv       i  vvi v ii   ivv  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_27913273_2   2481 TCAAATGGCAAGAGGACTAGAATAAGTAAAAC 2512
                          vi  vv     i iv i      ivi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

Transitions / transversions = 1.25 (30 / 24)
Gap_init rate = 0.01 (1 / 182), avg. gap size = 2.00 (2 / 1)  

 773 26.27 1.41 9.04  chrX_27913273_27917591.rev     2768  3121 (1198)    L1M4_orf2#LINE/L1      178   504 (404)  

  chrX_27913273_2   2768 AAAACTTTTTTTAAAAAAAAGATGAAAATAGGAGGAATTAGTCTACCCAG 2817
                              vv i  v     i    vv   i v      v i vv  v    i
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_27913273_2   2818 TTTAAAGACTTATTATATACCTACAGTAATGAAACCTGTTTTATGTTGGT 2867
                            v  i     i  i v v          v  iv v  v vi ii   i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_27913273_2   2868 GGAAGGACAGAAACATAAGTCAATGGAACTACTGGCTAGAGAACCCAGAA 2917
                         iv     i   v i   ii         -  -- iv v    ii      
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAA-TA--GAATTGAGAGTCCAGAA 324

  chrX_27913273_2   2918 ATAG--CCATACATGAATATACTCAACTGACTTTTAA--AAAATAACAGA 2963
                            i--        v--   iv    i   i   ii -- iii iv  - 
  L1M4_orf2#LINE/    325 ATAAACCCATACATT--TATGGTCAATTGATTTTCGACAAGGGTGCCA-A 371

  chrX_27913273_2   2964 AACAATTCAATGGAGGAAAGATAGT-TTTTCATTGAATAGTGTTGGAACA 3012
                         i  v         i i  ii     -      vii   i   i   i   
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_27913273_2   3013 ATCAGACATCCCTAGGCAAAAAATAATAATAATAAAAATGAAAATAGAAA 3062
                          iii  i ?  vi v      i --------------     i- -----
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGA--------------ATGAAG-T----- 451

  chrX_27913273_2   3063 TGAATCTTAATCTTAGTTTCACACTTTATATAAAAATTAATTCAAAACTA 3112
                           i i ----- i  -ii      iv    i         i      ivi
  L1M4_orf2#LINE/    452 TGGACC-----CCTA-CCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_27913273_2   3113 AACATAGGC 3121
                          v  ?  i 
  L1M4_orf2#LINE/    496 ATCAWAGAC 504

Transitions / transversions = 1.84 (59 / 32)
Gap_init rate = 0.04 (12 / 327), avg. gap size = 3.08 (37 / 12)  

1188 26.76 2.92 1.46  chrX_27913273_27917591.rev     3418  3828 (491)    L1M4_orf2#LINE/L1      492   908 (0)  

  chrX_27913273_2   3418 ATAAATAATAAA--TAAATGTAAAACATGAACCTATAAAGCTATTAGAAA 3465
                           ii  v ? i --         i vv i  v       i  v      i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_27913273_2   3466 ATAACATAGGTGAATATCTTTAGGACCTAAAGCTTGATAAAGGCTTCTTA 3515
                          v        ? v v     iiv     vii i v ii  v  i      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_27913273_2   3516 GACTTGACATCAAAAGCATGATCATTTAAA--AAAAAT---TTAATTTGA 3560
                           iv     i        ii v  viv   --      --- v    v  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_27913273_2   3561 CTTTATCAAAATTAAG---TTTTATTCTCTATAAAAGATTCCATAAAGAA 3607
                            i           i---    i v  ii --  i  iv i  v     
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAA 689

  chrX_27913273_2   3608 GATGAAAAGACAATGTACTGACCAGAAGAAAATACTTGGAAATCACACAT 3657
                         ii           ivi  v  vii i        i   v      i i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_27913273_2   3658 --GAGAAAGGATTCATATCTAGAATATATAAAGAATGCTCAAAACTCACT 3705
                         --  v  i   i ii    i               iv  i v      --
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-- 787

  chrX_27913273_2   3706 CAACAACAAAAAATCAAAACATTCCATTTGCAAATCGGAAGAAGATATGA 3755
                         -- i  i     iv    vv ii v   ?iv    v  v i i   v   
  L1M4_orf2#LINE/    788 --ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_27913273_2   3756 AGAGATATCTCACCAAAGAGTATATATGGGTGACAAATAAACCCTTGAAA 3805
                          v   i  i  v       iv     iiii  i v     i v v     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_27913273_2   3806 AGATGTTTGACATCACTAACCAT 3828
                              i ii      ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (65 / 42)
Gap_init rate = 0.02 (7 / 417), avg. gap size = 2.57 (18 / 7)  


3166 26.65 0.66 0.66  chrX_27924409_27930956.rev     5150  6057 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_27924409_2   5150 TGGAAGAACATCCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5199
                              ii i        i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_27924409_2   5200 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5249
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_27924409_2   5250 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTAA 5297
                          v   iivi i  i  ii     -   -- v  i  - iii    i  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_27924409_2   5298 TATGGAACCAAAAAAGAGCCTGCATCACCAAGACAATCCTAAGCCAAAAG 5347
                                viiv  ii  v  v v  vi    i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_27924409_2   5348 AGCAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5397
                          i     i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_27924409_2   5398 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5447
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_27924409_2   5448 AATGGAAAAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5495
                                v    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_27924409_2   5496 ATCTGATCTTTGACAAACCTGACAAAAATAAGAAATGGGGAAAGGATTCC 5545
                          vi    i  i     ivv  v   i vi vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_27924409_2   5546 CTATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5595
                           v  i  i       i      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_27924409_2   5596 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5645
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_27924409_2   5646 TTAAAAACTTAAATGTTACACATAAA-CCATAAAAACCCTGGAAGAAAAC 5694
                          i ? i  i       v v vv    - i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_27924409_2   5695 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGATCTCATGACTA 5743
                         v    ?i- v i -   iv   v v  vv i     v i i  v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_27924409_2   5744 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5793
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_27924409_2   5794 ATTAAACTAAAGAGGTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5843
                           i   v v  i iv  i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_27924409_2   5844 CAGACAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACA 5893
                         v        i                 v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_27924409_2   5894 AAGGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAGAAA 5943
                          i  i  vi          v  i   v    ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_27924409_2   5944 AAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5993
                           i -    i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_27924409_2   5994 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAACGCTTA 6043
                             v        i  vi viii     i ii          i i   i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_27924409_2   6044 TCATCACTGGCCAT 6057
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2493 19.11 1.11 15.37  chrX_27970154_27971750.rev      120  1108 (489)    L1M4_orf2#LINE/L1       61   908 (0)  

  chrX_27970154_2    120 CCCAAAGAAATCTACAGATTCAGTGCAATTGCTATCAAAATACCAATGAC 169
                               vvi             ii     iv          v   iivi 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_27970154_2    170 ATTCTTTGCAGAAATAGAAAAA--AATTCTTAAAATTTATATGGAACCAC 217
                         v  i           v  v  i--i  i  -      i        vii 
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAATTCATATGGAAATGC 159

  chrX_27970154_2    218 AAAAGACCCAGAATATCCAAAGCTATCCTAGGCAAAAATAACAAAACTGG 267
                           ii           v     i v   i iiiv  i  v      ii   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_27970154_2    268 AGGAATCACACTACCTGACTT-AAAATTATACTACAGAGATATAGTAACC 316
                             v       v  ii i  -    i -       i  v  i     i 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATC 258

  chrX_27970154_2    317 AACACGGCATGGTACTGGCATGGGTACCATGCCACCATTGGAGTGAGAGT 366
                           v  i ii            i----------------------------
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATA---------------------------- 280

  chrX_27970154_2    367 CTTTGGCAGAATTCCCTTCTAACAAAAAGCAACCCAATAAGTCATTTCTC 416
                         -------  i  ---------------------------  v   v ---
  L1M4_orf2#LINE/    281 -------AGGAT---------------------------AGACATAT--- 293

  chrX_27970154_2    417 TTTCAGCAAAGAGCGGCCTGAAAGATCAGGCTGCAAACACAGATAAGGAA 466
                         ----------------------      --------------  --    
  L1M4_orf2#LINE/    294 ----------------------AGATCA--------------AT--GGAA 305

  chrX_27970154_2    467 GGCAAGTTCTAACACAGAAAGGGACCTCCTGTGTAGACGAACGGAGAAGA 516
                         ---------  iv iv  i  -----   ---------------------
  L1M4_orf2#LINE/    306 ---------TAGAATTGAGAG-----TCC--------------------- 320

  chrX_27970154_2    517 ATGGAGAACCAACGTATCCACACACCTACAGTGAGCTCCTTTTCAACAAA 566
                         ----    vi  --- i   i   ii  ii  v ii vv     i    i
  L1M4_orf2#LINE/    321 ----AGAAATAA---ACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_27970154_2    567 GGTGACAAGAACATACACTGGGGAAG--ACAGTCTTTTCAATAAATGGTG 614
                             v     v   v  v       i-- i           i        
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_27970154_2    615 CTAGGAAAACTGGATATCCATATGTGGAAGAATGAAACTAGACTTCTGCC 664
                           i   v         ?   i   iii         ii i   ii  i  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_27970154_2    665 TTTCACCATATACAAAAATCAAATCAAAATGGATTAAAGACTTAAATCTA 714
                          iv                i  v           i ?    i     v  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_27970154_2    715 AGA-CTTCAACTATGAAACTCCTACAAGAAAACTTTGGGAAAAATCTCTG 763
                            -  vv      i      i  v        v v  ?iv      ii 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_27970154_2    764 GGACATTGGTTTGGGCAAAAATTTCT-AGACCAAT-ACCCCACAGGCACA 811
                         v   v    v  i     vii     -   i--  -  v   v i     
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGACACCAAAAGCACA 611

  chrX_27970154_2    812 GGCAACCAAAGCAAAAATGGACAAATGGGATCACATCAAG-TTAAAAAGC 860
                         i     v    v      i  i    v   iiv      i-       - 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-C 660

  chrX_27970154_2    861 TGCTGCACAGCAAAGGAAACAATCAACAAAGTGAAGATACAATACACAGA 910
                          vi  ii vv       v  v     v        i v    iv      
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_27970154_2    911 ATGGGA-AAAATATCTGCAAACCACCCATCTGACAAAGGATTAATTACCA 959
                               -       i      i  ivi      i  i   i vi vv   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_27970154_2    960 GAAGACATAAGGAGCTCAAACAACTCTATAGGGAAAAAATTCTAATAATC 1009
                            v i    i  i   vv       v   ivi    i -- v     i 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CAAATAACC 808

  chrX_27970154_2   1010 TGAT-AAAAAATGGGCAAAAGATTTGAATAGACACTTCTCAAAAGAAGAC 1058
                         ii  -?             i              i     v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_27970154_2   1059 ATACAAATGGCAAACAGCCATATGAAAAGGTGATCAACATAATTGATCAT 1108
                                    v  i iv  i        i  v       v ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (113 / 72)
Gap_init rate = 0.03 (23 / 848), avg. gap size = 7.09 (163 / 23)  


3243 26.65 0.66 0.66  chrX_27984066_27990313     4848  5755 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_27984066_2   4848 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4897
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_27984066_2   4898 GGCCATGCTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4947
                            v  i  v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_27984066_2   4948 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4995
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_27984066_2   4996 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5045
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_27984066_2   5046 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5095
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_27984066_2   5096 TACAGTAACCAAAACAGCATGGTACTGGTACCTAA--ACAGAGATATAGA 5143
                                 i   i    ii         i --   -- i   v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATAGA 296

  chrX_27984066_2   5144 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATACCTACAA 5191
                                  i    i--    i  --        vv   i i ii  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_27984066_2   5192 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5241
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_27984066_2   5242 CCCTATTTAATAAATGGTGCTGGGAACACTGGCTAGCCATATGTAGAAAG 5291
                         vi  v  i  i              vv     v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_27984066_2   5292 CTGAAACTGCATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5341
                         v    ii  v i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_27984066_2   5342 GATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5391
                            i ?   ii    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_27984066_2   5392 ACCTAGGCATTACCATTCAGGACATAGGTGTGGGCAAAGACTTCATGTCT 5441
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_27984066_2   5442 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCGGATCT 5491
                          vi            vvi          vv     v  i    i   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_27984066_2   5492 AATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGA 5541
                         v  i   v v  i i   i  iiivv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_27984066_2   5542 ACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5591
                          v  i     i   iv            v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_27984066_2   5592 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5641
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_27984066_2   5642 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5691
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_27984066_2   5692 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5741
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_27984066_2   5742 TCATCACTGGCCAT 5755
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


3524 20.60 5.64 1.38  chrX_28108989_28110930.rev      583  1451 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_28108989_2    583 GAGAGACAGTC-ATGTTTAGGGATGGGAATATTCATTATTGTAAAGATGG 631
                           i   i vi -     i v    v    v i i v      v       
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_28108989_2    632 AAATTCCCCATAAATTGATCTATAAATTCAATGCAATCCTTATCAATAAT 681
                         v   v i  vi           i i      i       i      v vi
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_28108989_2    682 CCAGCAGGAATTCTTGTATAAATTGGCAAGCTGATCCTAAGATTTATAAG 731
                              v vvv  i   i v      i              i   i   v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_28108989_2    732 CAAATGCAGAGAACTCTGAATAGCCAAAGCAATATTGAAAAGGAAGAA-- 779
                         v       ii i  i v           i    v       i      --
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_28108989_2    780 -AGTTGGAGGACTCACACTTCCTGATTTCAAAAC-------------ACA 815
                         -                     ii          -------------   
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_28108989_2    816 ATAATCAAGACTATGCTGTACTGGTATAAGGATAAACATATAGACCATGG 865
                         i          vi  iv       i         i         i  vv 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_28108989_2    866 GAATAGAGTTGAGAGTCCAGAAGCAAAAACCCTTAAATATATGACCAACT 915
                                i              -- v      v  v  v    ii   i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAA--ATAAACCCATACATTTATGGTCAATT 350

  chrX_28108989_2    916 GATTTTTGACAA----------ACAATTCATGGAAGAAAGGA-AATCTTT 954
                               i     ----------  v     vv ii     i - i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_28108989_2    955 TCAACAAATGATGTTGATACAATTGAACATTCATGTGCAAAAAAAATGAA 1004
                                   i  i  iv    i  i i ?i  ii       i  -    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAA 449

  chrX_28108989_2   1005 CTTAGACCCTTACCTCATACCCTGCCTAAAATTTAATTCATGAAACATGA 1054
                         v  i     i       i   v iivi    v    i   --   --  i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA--AAA--TGG 495

  chrX_28108989_2   1055 AACATAGACTT-----TAAGAGCTAAAACTATTAAACTTCTACAAGAAAA 1099
                          v  ?    i -----                v     ii  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_28108989_2   1100 CATAGAAGAAAACAATCATCACCCTGAATTCGGCA--GAGTTCTTTGATA 1147
                              i? v   ivv  i v   i  ii  v    -- iv     v    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_28108989_2   1148 CAACAC-AAAAACATGAGCCATAAGAGAAAAATTTGATAAATTGGGCTTT 1196
                         ii    -    i  ii   v i  i       v v          i   i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_28108989_2   1197 AT-AAAACTAAAAACTTTTGTGCTGCAAAAGACATCAATGAGAAAATGAA 1245
                           -    i                v    i    ii vii     i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_28108989_2   1246 AAGACAAGTTATAGGCTGGGGACAACATATTTGCAAATCATACACCTAAT 1295
                                vii i  iv    - v  v                i i  i  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGG-AGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_28108989_2   1296 AAAGGCATTGTATTCAGA-TATCTA-----TTCTTACAATTTAATAATAA 1339
                           i  vv      i    -   v  -----i        i i        
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_28108989_2   1340 GAA---AAACAACTCAATT-AAAAATGGGCAAAAAATTCATATAGACATT 1385
                         i  ---   i   i     -             ii   iiv         
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_28108989_2   1386 TCACCAAAGAAGATACATGAATAGTTAATA-GTG-GTGAAGATAAATATG 1433
                           v            i ii   i ii    - ii-i    ----  v   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA----AAGATG 890

  chrX_28108989_2   1434 CTTATCATCACCACTTAT 1451
                           i v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (114 / 62)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 2.90 (61 / 21)  


3090 27.39 1.89 0.78  chrX_28140117_28146495.rev     4991  5888 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_28140117_2   4991 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5040
                               i i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_28140117_2   5041 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5090
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_28140117_2   5091 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_28140117_2   5139 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTGAGCCAAAAG 5188
                                viiv  ii  v  viv  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_28140117_2   5189 AACAAGGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGT 5238
                              i i      vv   ii  v  ii i      viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_28140117_2   5239 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5288
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_28140117_2   5289 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5336
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_28140117_2   5337 ATCTGATCTTTGACAAATCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5386
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_28140117_2   5387 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5436
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_28140117_2   5437 CAAACTGGATCCCTTCCTTACACCTTAT------------TCGAGATGGA 5474
                         v  ii    i    v   i     v   ------------  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_28140117_2   5475 TTAAAGACTTAAATGTTAGACCGAAAACCATAAAATCCCTAGAAGAAAAC 5524
                          i ?    i       v   v v     i      ii i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_28140117_2   5525 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5573
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_28140117_2   5574 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5623
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_28140117_2   5624 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAATTACCATCAGAGTGAA 5673
                           i   v i  i i   i  ii vv    i  v i  i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_28140117_2   5674 CAGGTAACCTACAGAATGGGAGAAAAATTTTTGCAATCTACTCATCTGAC 5723
                         v  ii    i                - v       vii ivi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGAT 744

  chrX_28140117_2   5724 AAATGGCTAACATCCAGAATCTACAAAGAACTCAAACAAATTTACGAGAA 5773
                           iv i  vii         v  i         vv    -i i vv iv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chrX_28140117_2   5774 AAAAAACAAACAATCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 5823
                             i     i  i  v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_28140117_2   5824 TTCTCAAAAGAAGACATGTATGCAGCCAACAGACACATGAAAAAATGCTC 5873
                              v        i  ii viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_28140117_2   5874 ATCATCACTGGCCAT 5888
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (151 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.40 (24 / 10)  


3092 23.92 1.94 4.31  chrX_28456464_28459552.rev     1672  2599 (490)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_28456464_2   1672 GAAATGATGTCCTGTGTTCATTGATTAGAAAAATTAGTATTGTTAAAATA 1721
                             -   i   ii       v    i   i v   i         i  i
  L1M4_orf2#LINE/      3 GAAA-GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_28456464_2   1722 TTCACACTACCCAAAATGATCTATGATCTATACACTGAATGCAATCCCTA 1771
                         viv i   v      ------ -       i v i v  i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAA------T-TGATCTACAGATTCAACGCAATCCCTA 94

  chrX_28456464_2   1772 TCTAAATCCTAATGGCATTCTTTACAGAAATGTAAAAATT---CTTAAAA 1818
                           v      i iiv  v  i   i       vv v  ii --- i     
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_28456464_2   1819 TTCATATAGAACCACAAAGACTCCA-AATAGCTGAAGCAATCTTGAGCAA 1867
                                i   vii   i ivi   -      ii  i         iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_28456464_2   1868 GAAGATTAAAACTGAAGGCATCATACTTCCTGGTTTCAAAATAATGTATT 1917
                              vi   ii  i   vv   i      iii        i-- -  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC--T-TACT 241

  chrX_28456464_2   1918 ACAAAGCTACAGCAATGAAAACAGTATGGCGATGGCATAAAAACAGGCAT 1967
                                     i   v  i     i   iiv        ii i  i   
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_28456464_2   1968 AGAAACCAATAGAACAAAAT----AGCCCAGAAATAAATCCACACATTTA 2013
                          v i i    i   i i   ----  i           i   i       
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_28456464_2   2014 TGGTCAACTGATGCTTAACAAAGATGCCCAGAAAATAAAATGGGGAAAAG 2063
                                i    vi ii    i i    v   vv  vv          ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_28456464_2   2064 ATAGTCTCTTTAATAAATGGAGTTAAGAAAACTGGATATCTATGTGCAGA 2113
                                i  i  i      v i ii  v         ? i ii    i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_28456464_2   2114 ATAATAAAACTGTGCTTTTATTTCACACCACATTCAAAAATCAGTTCAAA 2163
                          v   i  ii  vi iii  ii        i  v       i ii     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_28456464_2   2164 GTGG-TTAAATATTTAAATGTAAGACCTGAAACCTTATAACTATTAAAAG 2212
                         i   - i ? v ii           v  i    iv  v    v   i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_28456464_2   2213 AAAACAGAGGAG--AAGTTTCTTGATATTGCTCCTGCCAATGACTTTTTT 2260
                               v   ? --  vi   v   iv   vviiv v     ii  i  v
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_28456464_2   2261 GTAATGACACCAAGAGCTCAAGCAACAAAATCAAG----GACAAGTGAGA 2306
                          vv          i   v            vv  i----  i  i vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_28456464_2   2307 TTACATCAAGCTAAAAAGCTTCTACACAGCAAACAATTAACAAAGTAAAA 2356
                         i v      iv v    i   i iii vv    vi i--  v -- v  i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC--ACTA--TCAAG 687

  chrX_28456464_2   2357 AAAATAAAAACAAAAACAAAACTTACGAAGTGGGAGAAAATATGTGCAAA 2406
                            i i    ----i    -- ii  ii i             v      
  L1M4_orf2#LINE/    688 AAAGTGAAAA----GACAA--CCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_28456464_2   2407 CTATATAACTAATAAGTGGTTAATATCCAAAATATATGAGGAACTCATAC 2456
                         ii     v  i     v ii vi      i       i i      v   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_28456464_2   2457 AAT--AATGAAAACGAAATAATGGAAAAAAAACCCGAAT-AAAAATGGGC 2503
                           i--   i v  --   -----  v   v     i v -          
  L1M4_orf2#LINE/    782 AACTCAATAATAA--AAA-----GACAAATAACCCAATTWAAAAATGGGC 824

  chrX_28456464_2   2504 AAAGGATCTGAATAGATATTTCTCTAAAGAAGACATACAAATAAGACATA 2553
                                i        i       i        i        --------
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT-------- 866

  chrX_28456464_2   2554 TCTGGCCAACAGATAATATGAAAAGTTGCTCAACATCGCTAATTAT 2599
                         ---      i iii -i        v           i????????
  L1M4_orf2#LINE/    867 ---GGCCAATAAGCA-CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (148 / 71)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 2.76 (58 / 21)  


3355 26.43 0.44 0.44  chrX_28498619_28503056.rev     3040  3947 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_28498619_2   3040 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATTAATATCATGAAAAT 3089
                              ii i  i     i        v      v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_28498619_2   3090 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3139
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_28498619_2   3140 TACCAATGACTTTCTTCGCAGAATTAGAAAAAGCT-ACTTTAAAGTTCAT 3188
                          v   iivi i  i  i      v v  v  -   - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_28498619_2   3189 ATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGA 3238
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_28498619_2   3239 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 3288
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_28498619_2   3289 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACCA 3338
                                i   i    ii         i iv ii i   v   i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_28498619_2   3339 GTGGAACAGAAC--AGAGCCCTCAGAAATAATTCCACACATCTACAACCA 3386
                         i     i    i--    i  --        vi   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_28498619_2   3387 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 3436
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_28498619_2   3437 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 3486
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_28498619_2   3487 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 3536
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_28498619_2   3537 TAAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 3586
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_28498619_2   3587 TAGGCA-ATACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAA 3635
                             ?i- v i -   iv   v v  vvii     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_28498619_2   3636 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3685
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_28498619_2   3686 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGCAC 3735
                          i   v v  i i   i  ii vv    i  v    i  vv i    v v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_28498619_2   3736 AGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 3785
                           i     i i               v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_28498619_2   3786 AGGGCTAATATCCAGAATCCACAAAGAACTCAAACAAATTTACAAGAAAA 3835
                         i  i  vi          vi i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_28498619_2   3836 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 3885
                          i     i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_28498619_2   3886 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATACTCATC 3935
                           v        i  vi viii     i ii          i  i    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_28498619_2   3936 GTCACTGGCCAT 3947
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


3379 25.99 0.55 0.55  chrX_28726964_28728930.rev      569  1476 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_28726964_2    569 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 618
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_28726964_2    619 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 668
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_28726964_2    669 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 715
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_28726964_2    716 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 765
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_28726964_2    766 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 815
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_28726964_2    816 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 865
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_28726964_2    866 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATACCTACAAC 913
                                 i    i--    i  --        vv   i i ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_28726964_2    914 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 963
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_28726964_2    964 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCCTATGTAGAAAGC 1013
                         i  v  i  i              v      v  ?  vi   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_28726964_2   1014 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 1063
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_28726964_2   1064 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1113
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_28726964_2   1114 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGATTTCATGTCTA 1163
                          v    ?i v viv   iv   v v  vv i     v i    v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_28726964_2   1164 TAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 1213
                          i            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_28726964_2   1214 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1263
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_28726964_2   1264 CGGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 1313
                         vi i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_28726964_2   1314 AAGGGCTAATATCCAGAATGTACAATGAACTCAAACAAATTTACAAGAAA 1363
                          i  i  vi          i  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_28726964_2   1364 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 1413
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_28726964_2   1414 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1463
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_28726964_2   1464 CATCACTGGCCAT 1476
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (140 / 92)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2170 25.61 12.13 0.86  chrX_29066187_29068171.rev      679  1494 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_29066187_2    679 TGGAGGCACATACTGTACTCACAGATAGTGAGACTCAATATGGTAAAGAT 728
                             iiv i  v ii ii   ii   v vi     i     v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_29066187_2    729 ATCAATTCTCCTCAAATTGATCCATAGGCTTAATGAAACTGCTATCAAAA 778
                         iv    v    i          i i  ii i  i v  iiv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_29066187_2    779 TTCTAGTAAGGATTTTTGTAGACATAGACAAACTTATGCTATAATTTACA 828
                          i i  ivivvv      i   v  v     i  v  v   v    i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_29066187_2    829 TGAAAA-ATAATAGGCCCTATAATAGCTAAACACAATCTTTAAAAAGACA 877
                           i   -ii  -i  v  i v      i   -        v       vi
  L1M4_orf2#LINE/    151 TGGAAATGCAA-GGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAG 198

  chrX_29066187_2    878 TATAAAGTAGGAGGAATCACTCTAGTTGATATTTTCA----CCACCATAT 923
                         v i     v      v    v  --- vvi v     ----ii  i i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACT---TCCCAATTTCAAAACTTACTACAA 245

  chrX_29066187_2    924 AGCTATACTAATCAATACAGTTTGGTATTGGCAGAGGGATAGACA-A-AG 971
                              i v       v     v     i     v i         - -  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_29066187_2    972 GT--ATGGAATAAAA-----AACACAGAAATTAACCTACAAAAATATGCT 1014
                         i --        i  ----- iiv       v    i i v vv    v 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_29066187_2   1015 CAATGGATTCTGAATAAAGATGCAAAAGCAATTCAATGGAGGAAGCATAG 1064
                             v    i vi i  i i   v  ii v         i i   v    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_29066187_2   1065 CCTTTTCAACAAATGGTGCTGGGACAACTGGACATCCA------------ 1102
                         i                               i ?   ------------
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_29066187_2   1103 ---------ACCCC-----------ATA-----AAACTAA--------GA 1119
                         ---------     -----------   -----   i   -------- i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_29066187_2   1120 CTTA---ACCTAAAC----------AAAC-ATCAG--TCCT-GAAATAAA 1152
                         v i ---       i----------    -  v i--  i -   iv   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_29066187_2   1153 TAT-----TAA---TTCA-------AAATTAAG-----ATTTCAT-GATG 1181
                         i  -----   ---   i-------iii   i -----i    v -   -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chrX_29066187_2   1182 AAAATGCCAAAAGTAATTGCGACAAAAGCAAAAATTGACAAATGGGATCT 1231
                          vi ii       i vvv  i       v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_29066187_2   1232 AATTAAA-CTAAAGAGTTTTGCACAGCAAAAGAAACTATCATCAGAGTGA 1280
                         v  i   -i    i v     ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_29066187_2   1281 ACAGACAACCTAAGGAATAGGAGAAAATTTTTGCAATCTGTCCACTTGAC 1330
                          v        i vi    i         v       viii vi ii   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_29066187_2   1331 AAAGGTCTAATATCCAGAGTCTACAAGGAACTTAAAAAAACTTA-TGAGA 1379
                           i  v  vi        i v  i  i     ivv v  -  i - i v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chrX_29066187_2   1380 AAAAAACAAACAACTCCATTAAAAAGTGGGCAAAGGATATGAACAGATAC 1429
                             i     i   i v   ?    i            v    i   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_29066187_2   1430 TTCTCAAAAGAAGACATTTAAGCGGCCAACAAACATATGAAAAAACGTTC 1479
                              v        i  vi  ii      i  i  i       i i i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_29066187_2   1480 AACATTACTTATCAT 1494
                              i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (127 / 80)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.93 (106 / 27)  


2955 26.08 2.55 2.22  chrX_29149451_29152557.rev     1716  2616 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_29149451_2   1716 AAAACATTCCATGCTAATGGATTGGAAGAATCAATATTGTTAAAGTAGCC 1765
                           i i  i     i v             v i           ii i  v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_29149451_2   1766 ATACTGCCCAAAGCAATTTACATACTCAATGCTATTTCTATCAAACTACA 1815
                              v      vii  i    v i    i  v  ii        v v v
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_29149451_2   1816 AG-TGTCATTTTTCACAGAATTAGAAAAAC-GATTCTAAAATCCATGTGG 1863
                           -  i -     ii     v v  v  i -   i       i   i   
  L1M4_orf2#LINE/    105 AGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_29149451_2   1864 AGCCAAAACAGAGCCTGAATAGCTAAAGCAATCCTAAGCAAAAAGAACAA 1913
                          iviiv  vi  v  v       i   i     i i iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_29149451_2   1914 AGCCAGAGTCATCACACTACCTGACTTTGAACTATACCATAAGGCTACAG 1963
                           iii   vvv       v  ii i  ii  viv   i i  i       
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_29149451_2   1964 TAACCAAAGCAGCATG-TATTGGTACAAAAAAAAAAAAAAAAAAAAAAAG 2012
                            i   ii   ii  -  i   i i  ii ----------------v  
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGA----------------TAG 287

  chrX_29149451_2   2013 ACACATAGACCAATGGAATAGAACAGAAAACTCAGAAATAAAGCTGCACA 2062
                            i     i             iv  i iii          v iii   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_29149451_2   2063 CCTACAA-CAATCTGATCTTTGATGGGGCTAACAAAAGCA----ATGGGG 2107
                         ii  iii-    -    i  i  iii  v iv   i v  ----      
  L1M4_orf2#LINE/    338 TTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_29149451_2   2108 AACGGACTTCCTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATAT 2157
                           v i ivvi  v     i              i      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_29149451_2   2158 GCAGAATAATGAAACTGGACCCCTACCTTTCACCATATGCAAAAATTAAC 2207
                            i  v      ii             iv        i           
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_29149451_2   2208 CCCAGATGGATTAAAGACTTAAATGTAAGGCCTCAAACTATGAAAATTCT 2257
                         i v i      i ?    i          iv  v       i   v ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_29149451_2   2258 AGAAGAAAACCTAGGAAACAGCCTTCTCAACATGGGCACTGACAAATAAT 2307
                                   v    ?ivv ii    vii  v v  vviv i -   ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC-AATGGT 585

  chrX_29149451_2   2308 TTCT-GGCAAAGTCTTGAAAAGCAATTGCAACGAAACCAAAAATTGACAA 2356
                             -i vv v v viv       vvv     i   vv      v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_29149451_2   2357 GTGGGACCT------AATTAAAGAGCTTCTGCACAGCAACATAAACTATC 2400
                         i v    i ------       i -   i  ii vv   viv v      
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chrX_29149451_2   2401 AACAGAGTGAACAGGCAACCTACAGAATG--AGAAAATATTCACAACT-A 2447
                           v i      v  i     i        --          ii   v - 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_29149451_2   2448 TGCATTTGGCGAAAGTCTAATATTCAGAATCTATAAGAAACT----TAAA 2493
                          ii  i  iii ii v  vi   i      v     ii    ----i  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_29149451_2   2494 TCAACAGGCAAAAAACAAATAACTCAATT-AAACATGGGCAAAGGATATG 2542
                             i ivv    i         i     -   v             v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_29149451_2   2543 AACAGACACTTCTCAAAGGAAGACATACAAGCAACCAACAAACATATGAA 2592
                           i     i     v  i     i      iiii    i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_29149451_2   2593 CAAATGCTCATCATCACTAATTAT 2616
                         v i       v     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (149 / 83)
Gap_init rate = 0.02 (16 / 904), avg. gap size = 2.69 (43 / 16)  


 889 30.87 8.48 1.99  chrX_29303667_29306183      882  1435 (1082)    L1M4_orf2#LINE/L1        1   590 (318)  

  chrX_29303667_2    882 TAGAAAGACATTCCTTGTTCTTCAATAGGACATCACAACATCATTAAGAT 931
                          i      i  i  v     v vi  v   viv vi  i  ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_29303667_2    932 GCCACTTCTCTCTGAATTAATTTA--AATTTAATGTGATGCCAATAAAAA 979
                          v  v v   i ii    i  i  --i   i  i ii  v  v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_29303667_2    980 TACCAACATGCTTTGCTATATGGAGCTAGGCAAGTTGAAACTAAGGTTAA 1029
                          v   i -   i  vi - iii  iv v i    i   vv    ii  v 
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_29303667_2   1030 AATGAAAAAATAATGAACA-AAAATATCTGGGAAAAACA--CT--AAAAA 1074
                         v   i   vii  v i  v- i    v i----      --  --     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCC----AAAACAATCTTGAAAAA 194

  chrX_29303667_2   1075 GGA----AAAGCT--ATGACTAGCCCTACCAGATATTAGCATGTACTACA 1118
                          i ----    i -- v    vi v  v  vi  v i iv iv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_29303667_2   1119 AAGCCTCAACAAATAA--CAGTGT--CAATAGCACATGAATGGACA---- 1160
                             iv  ii  vi  --      --i v i   i v i  i    ----
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_29303667_2   1161 GACCAATGGAATAAAATCAAAAGTCCTGAAATAGAACCAAATACATATAG 1210
                           i          i   ii i     v      i v   v i iv   i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_29303667_2   1211 --AATTGTAATATATAATAGAGGTGACATCTCAAATAACTGGGGCAAAGT 1258
                         --     --  v vii i ii    v  vvv v v v v     v  iiv
  L1M4_orf2#LINE/    345 TCAATTG--ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_29303667_2   1259 TGAACTTAATAATAAATGGT-----------------TTCGTAT--AAAA 1289
                          iiv   vvi  i       -----------------?i ii  --    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_29303667_2   1290 GAG-GAAATTAGATGTCTTCCTCAAGCCATACACGAGAATAAACTTCAAA 1338
                           i-   i  i  ivi  v     vi     i  i i   v    iv   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_29303667_2   1339 TGAATCAGAAAACTAAATGTACCAAGGAAAACTATACAGGTACTAGAAGA 1388
                           i    ? i v         vv ivv         v iv vi       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_29303667_2   1389 AAATATTGGTG-AATTATTTTAG-GAC-TTGCATGTAGGGAA-GGACTCT 1434
                            i  v  ? -  --  i  v -   -   vi -    v  -  vi   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAA--ATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCT 589

  chrX_29303667_2   1435 T 1435
                          
  L1M4_orf2#LINE/    590 T 590

Transitions / transversions = 1.27 (94 / 74)
Gap_init rate = 0.04 (23 / 590), avg. gap size = 2.52 (58 / 23)  

 505 27.36 11.85 1.82  chrX_29303667_29306183     1706  2034 (483)    L1M4_orf2#LINE/L1      547   908 (0)  

  chrX_29303667_2   1706 ACAGGCGTGAGCCGCTGTG-CCT--GGCTGGG-AAGGACTTTCTAAGTAT 1751
                          i   ?  i ii vii   -   --  i i  -  v ii  ii  ii   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_29303667_2   1752 GAC--TAAAAATTCAAATGCCACAAATAAAAAGATTAATACATTTTACT- 1798
                            --i    iiv   --  v     vi    i  vi   v   vv   -
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_29303667_2   1799 -AT----ATTAAAAACTTC---GC-----ATGACAAAATCAA--AAGCCA 1833
                         -  ----           i---  ----- v    vv     --   iv 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_29303667_2   1834 AAAGAAAAC--------TGGAAAAAATGCATATATTGTAATGTATATCAC 1875
                              v   --------   i i   ---    -   i  vvi    vv 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAA---ATAT-TTGCAAATCATATATC 740

  chrX_29303667_2   1876 AGATAAAGAGTTAATGTCCTTAATATATAAAGAACTTTTAAAAATTAA-- 1923
                         v     i iii vi i   vv               i   v  v i  --
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_29303667_2   1924 GTGGGAACACAGAT---CCTGTAGAAAGATGGACAAAA-ATATAAATAGA 1969
                         i iii  v   i  ---  vi v?   i    i    i-  v i      
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_29303667_2   1970 CAATT-TACAAAAAA--TATATAAATGATCCTTAAGCATATGAGAAGATG 2016
                           v  - v    i  --    i     ii vv      i    i      
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_29303667_2   2017 ATTGCTTTCACTAACAAT 2034
                         v iiviv   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (53 / 35)
Gap_init rate = 0.05 (18 / 362), avg. gap size = 2.50 (45 / 18)  


3131 27.37 0.77 0.55  chrX_29316217_29319459     1851  2756 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_29316217_2   1851 TGGTGAAACATCCCATGCTCATGGGTTGGAATAGTCAATATCATTAAAAT 1900
                            vi i i        i      i      v v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_29316217_2   1901 GGTCATATTGTCCAAAGCAATCTACAGATTCCACACTATTCCTATCAAAC 1950
                           iv   i vi     vii            v  i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_29316217_2   1951 TACCAACATCGTTTTTCACAGAACTAGAAAAAAACT-ATTCTAAAATGTA 1999
                          v   i vv v     ii     v v  v  i--  -  i       vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_29316217_2   2000 TTTGGAAACCAAAAACAGCCTGAATAGTTAAAGCAATACTAAGCAAAAAG 2049
                          v      ivv  iiv v  v      ii   i    vi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_29316217_2   2050 AACAAAGCCAGAGGCATCACACTACCCAACTTCAAA-TTAACTATAAGGC 2098
                                iii    vv       v     i      -i v    i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_29316217_2   2099 TGCAGTAGCTTAAACTGCATGGTACTGGTACAAGATCAGACACATAGACC 2148
                          i     iiiv i  v ii         i i   ivi     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_29316217_2   2149 AATGGAACAGAATAGAGGACCCTGAAATAAAGCCGCATACCTACAGTCAT 2198
                                i     v   iii  v        v  ii i ii  ii    v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_29316217_2   2199 CTGATCTTTGACAAAGTTGACAAAAATAAGCAATGGGGAAAGGACTCCCT 2248
                         i    i  i     i v  v   i vi vv            i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_29316217_2   2249 ATTCAATAAATGGTGCTGGGGTAATTGGCTAGCCATATGCAGAATAATAA 2298
                         v     i             ii  i   v  ?   i     i  v   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_29316217_2   2299 TACTGGACCCCTGCCTTTCACCATGTACAAAAATTAACTCAAAATGGGCA 2348
                         vii         i   iv      i                      iiv
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_29316217_2   2349 AAATATTTAAATATAAGAGCTCATACTCTAATAATCCAAAAAGAAAAACT 2398
                          ? v ii     i        v v   v   v v  iv i       vv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_29316217_2   2399 AGGAA-ACACCATTCTGGACATTGGCCTTGGCAAAGAATCTATGACTAAG 2447
                            ?i- v i -   vv   v    vi v     v iv iiv iiv  v 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_29316217_2   2448 TTCTGAAAAGCAATTGCAACAAAAACAAAAATTGACAAGTGGGACCTAAT 2497
                         viviv       vvv         iv      v  i  i v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_29316217_2   2498 TAAACTCAAGAGCTTCTGCACAGCAGAAGAAACTGTCAGCAGAGTAAACA 2547
                         i   v i  i i   i  ii vv  i i  v   i   iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_29316217_2   2548 GACAACCTACAGAATGGGAGAAAATATTTGCAAAT-ATGCCTCTGACAAA 2596
                                i                           -  iiv     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_29316217_2   2597 GGTCTAATATTTAGAATCCATAAGGAATGTAAAAAGTTGGACAAACTAAA 2646
                           v  vi   ii     vi    i   ivivv v ii vi i  --    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA--TAAA 795

  chrX_29316217_2   2647 AA--CAAATAACCCCATT-AAAACTAGGCAAAAGACGTGAACAGACACTT 2693
                           --          v   -    v i      i  iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_29316217_2   2694 CTCAAAAGAAGACATATAAGTGACCAATAAACACATGAAAAAATGCTCAA 2743
                            v        i   i  i  i       i          i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_29316217_2   2744 AATCGCTCTTAGT 2756
                         v   i????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3078 25.31 2.01 0.78  chrX_29372765_29377343.rev     3192  4088 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_29372765_2   3192 TAGAAACACATACTATGCTCATGGATGAGTAGAATCAATATTGTGAAAAT 3241
                          i    v i  v i   i        vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_29372765_2   3242 GACCATACTGCCAAAAGCAAACTACAAATTCAATGCAATTTCCATCAAAA 3291
                          i v     v  v   vii v     i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_29372765_2   3292 TTCCAACACCATTCTTCACAGAACTAGAAAAGCCG-TCCTAAAATTCATA 3340
                          i   i vv v  i  ii     v v  v    i -              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_29372765_2   3341 TGGAACCAAAAAAAGAACCT-GCATAGCCAAAGCAAGACTAAGCAAAAAG 3389
                              -- viv  i i   i- v         i   vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_29372765_2   3390 AACAAATCTGGAGGCATCACACTACCCGATTTCAAACTATACTATAAGGC 3439
                               vi      vv       v   i        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_29372765_2   3440 CATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACC 3489
                         i i   v i   i    ii         i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_29372765_2   3490 AATGGAACAGAATAGAGAACCCAGAAACACACCCAAATACTTA------- 3532
                                i     v    ii       i v     v i i   -------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_29372765_2   3533 --GATTTTTGACAAAACAAACAAAAACTTTTATAAACTGGGGAAAGGACA 3580
                         --      i     ii-ivi v  i  iv  -i  --         i i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATT-CAA--TGGGGAAAGAATA 394

  chrX_29372765_2   3581 CCCTATTTAACAAATGGTGCTGGGATAATTGGCAAGCTACACACAGAAGA 3630
                         vi  v  i                 i  i   vv ? i   ii  i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_29372765_2   3631 ATGAAACTGGATCCTCATCTTTCAGCTTATACAAAAATCAACTCATGATG 3680
                              ii    i  ii i  iv  v v           i      vi   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_29372765_2   3681 GATCAAAGACTTAAATCTAAGACCTAAAACCA-AAGATTCT-AGAAGATA 3728
                              ?    i     v     v       i -  i i   -      v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_29372765_2   3729 ACGTTGAAAAAAACCCTTCTAGATGTTGGCTTAGGCAAAGACTTCATGAC 3778
                           i v i?iv   i -   vv  iv    v        v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_29372765_2   3779 CAAGAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGACT 3828
                         i v  vv         v v         iv   i   i   i  v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_29372765_2   3829 TAATTTAAGTAAAAAGCTTCTGCACAGCAAAAGAAATAATCA-GAA--TT 3875
                          v  iv  i v    i   i  ii vv    i  v iv    -   -- v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_29372765_2   3876 AACAGAAAATCCACAGAGTGGGAGAAAATCTTCACAA-CCTTACATGAAA 3924
                           v   v  i       i           v  ii   -i v  i  vvi 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_29372765_2   3925 CAAAGGACTAATATCTAGAATCTACAAAGAACTCAAACAAATTAGCAAGA 3974
                         i  i     vi    i     v  i         vv    v i ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_29372765_2   3975 AAAA-ACAAACAATCCCATCAAAAAGTGGGCTAAGGACACAAACAGACAA 4023
                             -     i  i  v  i?    i     v     ivii  i     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_29372765_2   4024 CTCTCCAAAGAAGATATATAAATGGCCAACAAGCATACGGAAAAATGCTC 4073
                         i                 i          i     i i i   i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_29372765_2   4074 AACATCACTAATTAT 4088
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (136 / 87)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.79 (25 / 14)  


3433 23.20 2.11 1.55  chrX_29425056_29429309     2861  3761 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_29425056_2   2861 GAAGAATATTT-GTATTCACAAACTGGAAGAATAAATACTGTTACAATGT 2909
                            ii    ii-i i    iii i       v v    i     vi   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_29425056_2   2910 CCATACTACTCAAAGTGATCTACAGAGTCAATGCAATCTCTATCAAAATA 2959
                          v     v i    v           v    i      i          -
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT- 101

  chrX_29425056_2   2960 CCCA--TGACACTTTCCACAGAAATAGAACAAAG-AATCCAATAGGTTTT 3006
                             --  v -i   iii       v  -   iv-i    --  iiv  i
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGA-CAAGCTGATCC--TAAAATTC 147

  chrX_29425056_2   3007 ATA---AACTGCAAAAGACACAAAAGAGCCAATGCAATCTTGAGCAAAAA 3053
                            ---  v     ii   v  i  v      vi         iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_29425056_2   3054 GAACAATGCTGGAGGCATCACACTACCTGACTTCAAAATGTACTGTGATG 3103
                               v i      vv       v  ii i       iv    iii v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_29425056_2   3104 CAATAGTAACCAAAATAGCATGATACTGGCATAA----AAACATA--GAC 3147
                          v i     i   i i  ii  i           ---- i     --  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_29425056_2   3148 CAATGAAGCAGAATGAAGAGCCCAGAAATAAATCTACACATTTACAGCTA 3197
                              i ii     vi    i           i i i       ii ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_29425056_2   3198 ACTCATTTTTTTTTTTTCAAAAACTGCCAAGAATACACAATGGGGAAAAA 3247
                          i v     ivv-----   iii-        vi iv           i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGA-----CAAGGG-TGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_29425056_2   3248 GCAGTCTCTTCAATAAATGGTTTTGGGAAAACTGGATAGCCACATGCAGA 3297
                         ii     i     i       vi     v         ?         i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_29425056_2   3298 AAAATGAAATTAGACTATTATATCTCACTCTATACAAAAATCAATTCAAA 3347
                          i      i  i   ivi  iv  v   iv           i  i     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_29425056_2   3348 ATGGATTAAAGAC--AAAGGTAAGACCCACAAGTGTAAAACTATTAGAAG 3395
                               i ?    --   v      v i v  v i       v       
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_29425056_2   3396 AGAACATAGGGGGAAAACTCCATGACACTGTTTTGGGCAATGATTTTTTG 3445
                          i        ? v   v  i i    vi  vv  i       i   i  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_29425056_2   3446 GATGTGACTTCAAAAACAGAGGCAACAAGAGCAAAAAAAATAGACAAATG 3495
                            i    vi     i  v i       i  ---          i    v
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAG---AAAAAATAGATAAATT 638

  chrX_29425056_2   3496 GAATTTTATCAAACTAAGAAGCTTCTGCACAGCAAAAGAAAAAATCAATA 3545
                          i i  i      v v i  i   i  ii vv    i  v vv     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_29425056_2   3546 GAAT-AAAAG-CAGCCTATAGAATGAAAGAAAATATTTGCAAACTATACA 3593
                         i i -     -  i  i i      ii                ii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_29425056_2   3594 TCTGATAAGGGATTAATATACAAAATATATAAGGAATTCAAACAACTCAA 3643
                                     i vi   v  i         i   i  vv         
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_29425056_2   3644 TAGAAAAAAGTCAAATAACCCA--TTAAAAATGGGCAATAGACAGGTATA 3691
                           iv      v           -- ?            vi  ivv v   
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_29425056_2   3692 GACATTTCTCAAAAGAAAACATACAAATAGCCAACAGGTACGTCAAAAAA 3741
                                   v      i i        i     i i i  i v    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_29425056_2   3742 TGTTCACCATCACTAATCAT 3761
                           i   v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (135 / 70)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 1.94 (33 / 17)  


 346 31.77 6.16 5.17  chrX_29486244_29488824.rev        8   413 (2168)    L1M4_orf2#LINE/L1       13   422 (486)  

  chrX_29486244_2      8 CCATGCTCATGGATAAAAAGACTCAGAATTATAAAGATAAAGGTGATGAT 57
                              i        vii      i iv   i v     ---  ii  - i
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT---GGCAAT-AC 58

  chrX_29486244_2     58 TCTCTAAACTTATCTATAAATTGGAATCAATTTTTAAAAAATAAATTTCA 107
                           i i   i v     i i   vi vv    iii  vv   ---  ii  
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA---ATCCCA 105

  chrX_29486244_2    108 GTAGGAATTTTCACAGATTTTGATAAACAGATCCGAAGATTCACACTTAA 157
                          iv vvv    ii    vv    i  i v     v  i     i ivv  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_29486244_2    158 TAGCAAAG--TCAAGAATAG--AACATAAATTTAAGATAACAAACAAGAG 203
                         vv    i --i v       --  v i  vi  i i -  v  iv vi i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGAAGAACAAA 204

  chrX_29486244_2    204 GTTATCTAGCAGA-TAACAAGATTTCCATAAATTTC----TTT--TATAA 246
                            i---- vi  - v   v--  i   ---     ----i  --  i  
  L1M4_orf2#LINE/    205 GTTG----GAGGACTCACAC--TTCCCA---ATTTCAAAACTTACTACAA 245

  chrX_29486244_2    247 AACTGTTTGTTAGTAAATATAGTAAGGTAT--ACATACAGGA---ACAAA 291
                          i  ii--iv  i v  v i   iv    i--i    -    ---   v 
  L1M4_orf2#LINE/    246 AGCTAC--AGTAATCAAGACAGTGTGGTACTGGCATA-AGGATAGACATA 292

  chrX_29486244_2    292 TAGACCAATAAAATA-AATTTAGTAATCTAAGATCAGATCCACACAT--- 337
                             i    ii    -    v  - i  i ii vi i i   i    ---
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTA 341

  chrX_29486244_2    338 -GGAAACTTAAGTGTTAA-AAATGTCACAAAAATA---AGGGAAGAAAAG 382
                         -  vv v  i v v ii -  iv  vv   i vi --- iv ii    ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_29486244_2    383 ATAAACTATTCAATAAAAGTTTCTAGAACAA 413
                            iv  v     i   v v v  i i    
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

Transitions / transversions = 1.48 (77 / 52)
Gap_init rate = 0.05 (21 / 410), avg. gap size = 2.19 (46 / 21)  

2903 22.01 9.84 3.51  chrX_29486244_29488824.rev     1238  2091 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_29486244_2   1238 TGGAAAGATATCACATGTTCATAGATTGGAAGATTTAATATTGTTAAAAT 1287
                                     v         i          i             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_29486244_2   1288 GTCCATACTACCCAAAGTGATCTACAGATTCCTTGGTGTACTTATCGAAA 1337
                          v v     v      v              vvi vvi v i    i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_29486244_2   1338 TTCCAA-TGTTATTTTTCACAGAAATAGAAAAAGCAATCCTAAAATTCAT 1386
                          i   i-  ii-     ii       v  v  ivii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_29486244_2   1387 ATGGAACCAGCAAAGACTCCAAAA-AGCAAAAGCAAACATGAGCAAAAAG 1435
                               vi-    i ivi   i  -   v   i   v v   iv  i   
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_29486244_2   1436 ACCAACACTGGAGGCATCACACTCCCTGATTTCAAAATATCTTACAGAGC 1485
                          v   vii      vv       i  ii         iv vi    i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_29486244_2   1486 TATTGTAATCAAAACAGTATGGTCCCGACAAAACAAAACAAAACAAAACA 1535
                           iv        i     i    v i i  v  -----------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAA----------------- 281

  chrX_29486244_2   1536 AAAAAAGAGACACATCGACCAATGGAACAGGATAGAAAGCCCAGAAACAA 1585
                         ---ii v     i  v  i        i  i  v  i  i       i  
  L1M4_orf2#LINE/    282 ---GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_29486244_2   1586 ACCCATATATTTATGAACAATTGATTTTCAA-AAAGGTGCTAAGAAAACA 1634
                                i       iv            i -  i     i    vv iv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_29486244_2   1635 CAATGGGGAAATGGCGATTTCTCCAAAAAAAATAGTGTTGGAAAAACTGG 1684
                                    viiiii i i i   v   -- i   i   i v      
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAA--TGGTGCTGGGACAACTGG 426

  chrX_29486244_2   1685 ATATCCACATGTAGAAGAATGAAACTGAACACCGTATATGTCACACCATA 1734
                            ?       i i         ii  i  v  ---  iv          
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCC---TACCTCACACCATA 473

  chrX_29486244_2   1735 TACATAACTCAACTCAAAATGAACAAAAGGCTTAAATGTAAGACCTGAAA 1784
                             v  v i           i iv ?  i i           v  i   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_29486244_2   1785 CTCTAAAGCTACTT-GCAGAAAACATAGGGGAAAAACACCACAACATCAG 1833
                           v    i  -   - v            ? v   v vi iii  v ii 
  L1M4_orf2#LINE/    524 CTATAAAACT-CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_29486244_2   1834 TCTGGGCAATGATTTCTTGGATAGGACTACAAAAGCACAGGTAACGAAAG 1883
                         vi i       i      i    v   vv          i i   i    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_29486244_2   1884 CAAAAACAAGACAGATAGGATTGCATCAAA-------------------- 1913
                         v     i -  i i  v   i v       --------------------
  L1M4_orf2#LINE/    623 AAAAAATA-GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_29486244_2   1914 -------------------------------------------------- 1913
                         --------------------------------------------------
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_29486244_2   1914 ----------CCATACATCTAATAACAGGCTAATATCCCAAATATATAAG 1953
                         ----------i    i    i    vi i  vi     vi         i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_29486244_2   1954 GAACTCAAACAACTCAACAGCAGGAAAACAAATAACCCAATTAAAATATG 2003
                               vv         i ii ii  i               ?   v   
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_29486244_2   2004 GACAAAGGATCTGAACAAATATTTATCAAAAGAAGAGATACAAATGGCCA 2053
                          i        i    i i i    v  v        v             
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_29486244_2   2054 ACAGATACATGAAATAAATGCTCAACATCTCTAATCAC 2091
                          i iii        - i            v????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAA-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (117 / 67)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 8.77 (114 / 13)  


1793 27.27 0.19 1.93  chrX_29759758_29766159.rev        1   517 (5885)    L1M4_orf2#LINE/L1       16   523 (385)  

  chrX_29759758_2      1 TGTTCTTGGATTGGAAAAATCAATATGGTTAAAATGTCTGTATTGCCCAA 50
                              v          i v i     v     i   v vi  i v     
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_29759758_2     51 AGCAATCTTCAGATTCATTGCAATCCCTATAAAAATACCAAAAACATTCT 100
                          vii    v        vi           v     v   ivvi v  i 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_29759758_2    101 TCATAGAAATAGAAAAAACAATTCTAAAATTTATACCGAACCACAAAAGA 150
                          iii      v  v  ivii  i        i   iv   vii   ii  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_29759758_2    151 ACCAGAATAGCCATAGCTATAGTGAGCAACAATGACAAAACTGGAGGAAT 200
                         v            v i v  vv   iv  v  vi     ii       v 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_29759758_2    201 CATATTACATGCATTCAAATGATACTACAGAGGTGTAGCAACCAAAACAG 250
                           i i v viivv      vvv       i  v ii  i  i   i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_29759758_2    251 CATGGTGCTAGCATAGAAACAGATACGTAGACCAATGGAACTCAATAGAG 300
                         ii    i  i     iii i   i ii    i        ivv   v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_29759758_2    301 AACCCAGAAACATATCCATACATTTACAGTGAACTCATTTTTGACAAAGG 350
                          ii       i v i           ii  v  i v     i     i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_29759758_2    351 CACCAAGAACATGCACTAGGTAAAGA-CAGTGTCTTCAATAAAGAAATGG 399
                         ii      v   v  v i  v     -i   v i     i   ----   
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA----TGG 411

  chrX_29759758_2    400 TGCTCAGAAAACTGGATATCCATATGCAGAAGAATGAAACTAGACTTCTA 449
                             vi  v         ?   i     i         ii i   ii   
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_29759758_2    450 TCTGTCAGCATATACAAAAATCGAGTCAAAATTGATTTTAAAAACTTAAA 499
                         i  vv  v             ii v       v   --i ? i  i    
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGAT--CAWAGACCTAAA 509

  chrX_29759758_2    500 TAGGGGGAGGAGCCAAGA 517
                          ---- v i    i  i 
  L1M4_orf2#LINE/    510 T----GTAAGAGCTAAAA 523

Transitions / transversions = 1.53 (84 / 55)
Gap_init rate = 0.01 (4 / 508), avg. gap size = 2.75 (11 / 4)  

3278 27.09 0.44 0.44  chrX_29759758_29766159.rev     5004  5911 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_29759758_2   5004 TGGAAGAACATTCCATGCTCATGTGTAGGAAGAATCAATATCGTGAAAAT 5053
                              ii i  i     i     vi v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_29759758_2   5054 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5103
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_29759758_2   5104 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5151
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_29759758_2   5152 TATGGAACCAAAAAAGAGCCCGTGTCACCAAGTCAATCCTAAGCCAAAAG 5201
                                viiv  ii  v  v vi vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_29759758_2   5202 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5251
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_29759758_2   5252 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5301
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_29759758_2   5302 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATACCTACAACT 5349
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_29759758_2   5350 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5399
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_29759758_2   5400 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5449
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_29759758_2   5450 GAAACTGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5499
                            ii  i i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_29759758_2   5500 TTAAAGACTTAAACGTTAGACCTACAACCATAAAAACCCTAGAAGGAAAC 5549
                          i ?    i    i  v   v   v   i      vi i      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_29759758_2   5550 CTAGGTATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5599
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_29759758_2   5600 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5649
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_29759758_2   5650 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAT 5699
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_29759758_2   5700 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5749
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_29759758_2   5750 AGGGCTAGTATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5799
                         i  i  v           v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_29759758_2   5800 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5849
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_29759758_2   5850 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5899
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_29759758_2   5900 ATCACTGGCCAT 5911
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 855 23.62 2.01 0.50  chrX_29812590_29814498.rev      502   700 (1209)    L1M4_orf2#LINE/L1      292   493 (415)  

  chrX_29812590_2    502 ATAGACCAAGGGAAC-CAATAGAGAACTAAGAAAATAAACCCATGCATCT 550
                              i   v    i-v   v    iiiv  -            i   i 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAG-AAATAAACCCATACATTT 340

  chrX_29812590_2    551 ACAATGAATTCATTTTTGACAACAGTGCCAAGAACATACACTGGGGAAAA 600
                          iii v    v     i     vi         v   v  v        i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_29812590_2    601 GATGGTCTCCTCAATAAATGGTGCTGGGAAAACTGG---TCCATATGCAG 647
                         i  i    ii    i              v      ---?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_29812590_2    648 AAGAATGAAAATAGTCTTTTGTCTCTCACTGTGTACAAAAATCAAGTCAA 697
                                  iv i v iii ii   v   ii i         i  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_29812590_2    698 AAT 700
                            
  L1M4_orf2#LINE/    491 AAT 493

Transitions / transversions = 2.07 (31 / 15)
Gap_init rate = 0.01 (3 / 202), avg. gap size = 1.67 (5 / 3)  

1162 25.17 7.19 1.12  chrX_29812590_29814498.rev      982  1426 (483)    L1M4_orf2#LINE/L1      437   908 (0)  

  chrX_29812590_2    982 GCAACAAGAGTGAA-----ACTCC-ATCTCAAA--A-AGACAAACA--AA 1020
                             -    i    -----  i  - i    v -- - v     v --  
  L1M4_orf2#LINE/    437 GCAA-AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_29812590_2   1021 CAAAAAACAAACAAAACACTTAAATCTAAAGCCTCAACCTGGGAATCTAC 1070
                          vv    iii iv ? v  i     v   iiv  v  v  ivi  v  vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_29812590_2   1071 TAAAATAAAACATTGGAA-AAACCTCCCCAGGACATTGGACTTGAGCAAT 1119
                           i  v       v  ?i-   i  i --iv   v    i-  ii     
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTC--GTGACCTTGGG-TTAGGCAAT 582

  chrX_29812590_2   1120 AGC---------------CCACAAGCACAGGCAACTAAAGCAAAAGTGGA 1154
                         i i---------------   v       i     v    v    i i  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_29812590_2   1155 CAAACGGGGTCACGTCAAG-TTAAAAAGCTTCTGCACAGCAAGGGAAACA 1203
                         i   iv  iiiv i    i-       -   i  ii vv   i   v  v
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT 681

  chrX_29812590_2   1204 GTCAACAAAGTGAAGAGACAACTCATGGAATGGGAGAAAATATTTGCAAA 1253
                         i    v        i       i  ii                       
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_29812590_2   1254 CTACCTCTCTGAGAAGGGATTAATAACCAGAAGATATAAGGAAGTCAAAC 1303
                         ii iv v     v      i vi  v      v      i   v  vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_29812590_2   1304 AACTCTATAGAAAAAAATCTAATAATCCAATTTAAAA-TGGGCAAAAGAT 1352
                              v   iv     iv v     i      ?    -        i   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_29812590_2   1353 CTGAATAGACATTTTTC---AAAAGATATACAAATGGAAAACAGGTATAG 1399
                         i             i  --- i               vv  i i i i v
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_29812590_2   1400 GAAAAGGTACTATATATTATTAATTAT 1426
                               i i  vv i  i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (63 / 46)
Gap_init rate = 0.03 (14 / 472), avg. gap size = 2.64 (37 / 14)  


3340 24.73 0.32 3.10  chrX_29832063_29836343.rev     2857  3790 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_29832063_2   2857 TGGAAAGATATTCTATGTTTTTGGATTGGAAGAATCAATATTGTTAAAAT 2906
                                    i i     iv            v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_29832063_2   2907 GTCAATACAATCCAAAGCAATCTATGGATTCCATGCAATCCCTATCAAAA 2956
                          v      vvi     vii     ii     v i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_29832063_2   2957 TGCCAATGACATTCTTCACAGAAACAGAAAAAACAATCCTAAATTTTTTT 3006
                          v   iivi v  i  ii      iv  v  ivii        v  iv v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_29832063_2   3007 TGGAATTGCAAAACACCCAGAATAGTCAAAGCTATCCTAAGCAAAAACAA 3056
                              v     iiv           i    i v   i i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_29832063_2   3057 CAAAACTGGAGAAATCACATTATGGGCTTTCAAATTATACTGCAGAGCTA 3106
                             ii     i v     i vivviv       viv    i  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_29832063_2   3107 TAGTAACCAAAATAGCATGATATGGGCATAAAAACTGACACATAGACCTA 3156
                         i     i   i i  ii  i  iv       ii iv    i     i v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_29832063_2   3157 TGGAACATTAAAATAGAGAACCCAGAAATGAAACCGTACATCTACAGTGA 3206
                              ---  i   v    ii        i  v  i     i  ii  v 
  L1M4_orf2#LINE/    301 TGGAA---TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_29832063_2   3207 ATTCATTTTTGACAAAGGTGCCAGGAACATACACTGGGGAAAGGACAGTC 3256
                            v     i     i       i  v   v  v         i i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_29832063_2   3257 TCTTGAAAAAAACGGTGCTGGGAAAACTGAATATCCATATGTAGAAGAAT 3306
                          i  v  v   -i          v     i   ?   i   i i      
  L1M4_orf2#LINE/    398 TTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_29832063_2   3307 GAAACTAGACTTTTGTCTCTCACCATATACAAAATTCAAATCAAAATTGA 3356
                            ii i   iii ii   v              v i  v       v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_29832063_2   3357 TTAAAGTGTTAAATCTAAGACCTCAAACAATGAAACTACCTCA--ATAAA 3404
                          i ?  vvi     v     v  v    v  i     --  i -- v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT--CTTAGAAGAAA 544

  chrX_29832063_2   3405 GTATTGGGAAAACTCTCCAGGACATTGGACTAGGCAAAGATTTCTTAAGA 3454
                         ii  v  ?iv  v   i iv   v    ii       v i       i--
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-- 592

  chrX_29832063_2   3455 AATACCTCACCCTCACAAGCACAGGCAACCAAAGCAAAAATGGACAAATG 3504
                         -   ivv    --- v       i     v    v      i  i    v
  L1M4_orf2#LINE/    593 -ATATGACACC---AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_29832063_2   3505 GGATCACATCGAACATAAAAGCTAATCGAATATAAAAGCTACTGCACAGC 3554
                            iiv    i  ----------------  -     i  vi  ii vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAA----------------AT-TAAAAACTTTTGTGCTTC 671

  chrX_29832063_2   3555 AAAGGAAACAATCCACAAAGTGAAGACACAACGTGCAGAATGGGAATGAA 3604
                               v  v   v v        i v     vii          ivi  
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_29832063_2   3605 CATTTGTAAACTACACATCTGACAAGGAATTAATAACCAGAATATGTAAG 3654
                         i     i   ii i i      i    i i vi  v         i   i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_29832063_2   3655 GAGCTCAAACAACTCTCTAGGAAAAAGTCTAATAATTGGATT-AAAAATA 3703
                           i   vv       vv  iv      v v     iivi   -      i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_29832063_2   3704 AGCAAAAGATCTGAATAGACATTTCTGAAAAGAAGATATACAAATGGCAA 3753
                         i     i   i               vv                    v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_29832063_2   3754 ACTGGTATATGAAAATTTGCTTGACATTAATCATCAG 3790
                          ivi i i       vv    ii    i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (137 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.56 (32 / 9)  


 628 26.97 2.25 0.00  chrX_29857131_29859409.rev      317   494 (1785)    L1M4_orf2#LINE/L1      428   609 (299)  

  chrX_29857131_2    317 TATCCACATGCAAAAACATGAATCTATGCACAGACCTTACACCCTTCATA 366
                           ?            iv     vi ivi v vv    i     v vi i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_29857131_2    367 AAAATGAACTCAAA-TGGGTCATAGAACTAAATTTAAAATGAAAAACTAT 415
                              v        -   i   ?   v      v   i vvv        
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_29857131_2    416 AAAACTCCTGGAAGATGATATAAGAGAAAATCTCAATGACCTTGGGTATG 465
                                i i     vi i   i ? v      ivi           vv 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_29857131_2    466 GTGATAACTTTATAGATAT---ACCAGGGGCA 494
                          ii  iii  iv       ---    iii   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCA 609

Transitions / transversions = 1.25 (25 / 20)
Gap_init rate = 0.01 (2 / 182), avg. gap size = 2.00 (4 / 2)  

3066 24.61 2.02 1.69  chrX_29857131_29859409.rev      891  1780 (499)    L1M4_orf2#LINE/L1        3   895 (13)  

  chrX_29857131_2    891 GAGAGCTACTCTATGTTTATTGTTAAAAAGACCCAATATTTTCAAAATGT 940
                           i  v  ii i     i  v v vii     ii      v i  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_29857131_2    941 CAGTTCTTCCCAATATGATCTACAGATTCAAAAGAATCCCTATCAAAATA 990
                           i v  i     vv                viv               v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_29857131_2    991 CAACAA--GCTATTTTTGTGGATATTGACAAAC-GACACAAAAATGTATA 1037
                          --  i--  iv      ii  v        i -  iv v     vi   
  L1M4_orf2#LINE/    103 C--CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_29857131_2   1038 -GGAAATGGCAAAAGACCCAGAATAGCAAAGACAATATTGAAGGAGAAGA 1086
                         -       -   ii             v  i     v     ii      
  L1M4_orf2#LINE/    151 TGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_29857131_2   1087 ACA--GCTGGAGGACTGACCATAGCTGACTTCAAGACTTGTAATAAAGAT 1134
                            -- i         v  vv vv ii i     i    iiv i    v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_29857131_2   1135 ACAGTAATCAGTACAGCATGGCACTGGTAAAAGAATAGACAAATAGATCA 1184
                                   iv    ii   i     i v   i       v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_29857131_2   1185 GTGGGACAGAATAGAGAGTCCAGAAATAGCCACACATAAATATAT--TTT 1232
                         i   i i     v               i--  v    v  v   -- iv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAA--ACCCATACATTTATGGTCA 347

  chrX_29857131_2   1233 ACTGATATTTGACAAAAGAGCCAAAGAAATGTGATGGAGAAAAGATAGCA 1282
                          i    v  i     ii v     iivv  vii    i    ii    iv
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_29857131_2   1283 TTTTCAA---ACGTTGCAGGAATAACTAAATATTCATATGCAAAAAAATA 1329
                                --- i v   v  i i    ii   ?i  i        i   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_29857131_2   1330 AAAAAACGAATCTATACA-CAGACCATACATTCTTCCTACAAATGAATCC 1378
                           iv--i i i iv   v-  v      i i------- v    v  ii 
  L1M4_orf2#LINE/    448 AAGT--TGGACCCCTACCTCACACCATATAC-------AAAAATTAACTC 488

  chrX_29857131_2   1379 AAAATAGATCATAGACCTAAATATAAAATGAAAAACAATAAAACTCCTAA 1428
                              i     ?          i   i vvv     v         i  i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_29857131_2   1429 AAGTTGACATAGGGGAAAATCTCAATGACCTTGGGTATAGTGATGACTTT 1478
                            vvi       ? v      ivi           vvi ii   ii  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_29857131_2   1479 TTAGAGACAACACTAAAGGCCTGACCCATAAAAGAAATAATTGATAAATT 1528
                              v ii    i   i  vii v v i        v   v        
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_29857131_2   1529 GGACTACATTAAAATTAAAAGCAT--ATGCTCGTGAAAAATACTGTCAAG 1576
                              v   i          i v --i    i-ii  ii i   i     
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTT-CAAAGGACACTATCAAG 687

  chrX_29857131_2   1577 AGAATGAGAAAA-AAGCCACAGACTGGG-GAAAATATTTGTAAAG-ATAC 1623
                          i i   i  i -  v       v    -           i   v-   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_29857131_2   1624 ATTTGATAAAGGACTATTATCCAAATTACATAAAGAACTCCTAAAGCTCA 1673
                           i      i     vv      i v  i           i  v i    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_29857131_2   1674 AAAATAAGAAAAGGAACAATCCAATT-AAAAATGGGCAAAAGATCTGAGT 1722
                          v     i  i vi  i  i      -             i   i   i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_29857131_2   1723 ATATATCTCATCAAAGAAAATATACAAATATTAAGTAGGCATATTAAAAT 1772
                          v i  i  vi       i          iviv i  i   i  v    v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_29857131_2   1773 ATGCTCAA 1780
                                 
  L1M4_orf2#LINE/    888 ATGCTCAA 895

Transitions / transversions = 1.67 (135 / 81)
Gap_init rate = 0.02 (18 / 893), avg. gap size = 1.83 (33 / 18)  


 236 16.67 3.33 0.00  chrX_29860191_29863413.rev        6    65 (3158)  C L1M4_orf2#LINE/L1   (45)   863   802  

C chrX_29860191_2     65 AATAAC--AAACAACAAATAGGCAAAGGATATGAACAGACACTTCTCAAA 18
                               --  vi? v    i          v    i     i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

C chrX_29860191_2     17 AGAAGACATACA 6
                               i     
  L1M4_orf2#LINE/    852 AGAAGATATACA 863

Transitions / transversions = 1.25 (5 / 4)
Gap_init rate = 0.02 (1 / 62), avg. gap size = 2.00 (2 / 1)  

 745 24.59 1.09 0.00  chrX_29860191_29863413.rev     1040  1222 (2001)    L1M4_orf2#LINE/L1        1   185 (723)  

  chrX_29860191_2   1040 TGGAAAGATATTTCATGTTCATGGATTAGAAGCATCAATATTATTAAAAT 1089
                                    ii              i    vv i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_29860191_2   1090 GTCCATACTACCCAAAGCGCTTGAAGGATTCAATGCAATCCCTATCAAAA 1139
                          v v     v      vi v iv vi       i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_29860191_2   1140 TATTAAATACATTCTTCACAAAAAT--ATAAAATAATCCTAAATTGTATA 1187
                          vii iv i v  i  ii  i    -- i  iv i        v vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_29860191_2   1188 AGGAACAACAAAAGACCCAGAATAGCCAAAGCTAT 1222
                         v    vvi   ii                 i v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

Transitions / transversions = 1.37 (26 / 19)
Gap_init rate = 0.01 (1 / 185), avg. gap size = 2.00 (2 / 1)  

1515 26.18 3.07 1.42  chrX_29860191_29863413.rev     1565  1988 (1235)    L1M4_orf2#LINE/L1      111   541 (367)  

  chrX_29860191_2   1565 CTTTTCTTCATAAATTACCCAG----TCTCAGATATTTCTTTATGGCAGT 1610
                              i v  v     iv v  ----  ii i -   iv --    v i 
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAA-ATTCAT--ATGGAAAT 157

  chrX_29860191_2   1611 GTAAGAATGGACT-AATATAGCTA------TCCTGAGCAAAAAGAACAAA 1653
                          i   ---    i- iv     i ------  i   iv  i         
  L1M4_orf2#LINE/    158 GCAAG---GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_29860191_2   1654 ACTGGAAGAATTGCATTACCCGATTTCAAATTATACTACAGATCTATAAT 1703
                         ii    i  v ii  i v   i        viv       i v   i i 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_29860191_2   1704 AACCCAGATAGCATGGTACTGGCATAAAAACAGACACATAGATCAATGGA 1753
                           i v   i  ii              ii i     i             
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_29860191_2   1754 ACTGAAGAGAGAACCCAGAAACAAATCCACACACCTACAGCTAACTCATT 1803
                          iv   vv    ii       i   i   i   ii  ii ii  i v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_29860191_2   1804 TTTGACAAAGGTGCAAAGAACATAAACTGAGGAACAGACAGTTTCTTCAG 1853
                           i     i     v    v   vv v  i    vii i   i i    i
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_29860191_2   1854 TAAATGGTGTTGGGAAAACTAGATATCCACAAGTAGAAGAATGAAAT--G 1901
                         i        i     v    i    ?     v i i         i -- 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_29860191_2   1902 ACCCTTATCTCTCATGATCTACAAGAGTAAAATGAAAATGGATTAAAGAT 1951
                             i  i   v  iv  v     i i v  v v         i ?   i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_29860191_2   1952 TTAAATCTAAGACCTCAATGTATGAAACTATTATAAG 1988
                         i     v     v  v  vv   i     v   v   
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

Transitions / transversions = 1.79 (70 / 39)
Gap_init rate = 0.02 (7 / 431), avg. gap size = 2.71 (19 / 7)  

1073 23.12 1.56 0.94  chrX_29860191_29863413.rev     2413  2732 (491)    L1M4_orf2#LINE/L1      587   908 (0)  

  chrX_29860191_2   2413 TCTTGAGTAATACTCCACAAGCACAGGCAACCAAATCAAGAAATGGACAA 2462
                             iii  vv  v   v       i     v   v-  i    i  i  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAA 635

  chrX_29860191_2   2463 ATAGAATCACACCAAG-TTAAAAAAACTTCTGCACAGCAAAGAAAACAAC 2511
                           v i iiv  i   i-       --   i  ii vv     i v  v i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTAT 683

  chrX_29860191_2   2512 CAACAAAATGAAGAGGCAACCCAGAGAATGGGAGAAAATATTCACAAACT 2561
                            v   i    i  i       v                  ii    ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_29860191_2   2562 ATCCATTTGATAAGGGATCAATCACCAGAATATATAAA-ATCTCAAACAA 2610
                           vi  i          iivi vv              - v   vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_29860191_2   2611 CTCCATAG-AAAACATCTAATAATCCAATT-AAAAATGAACAAACGTTTT 2658
                            v   i-    viv v     i      -       ii    v v   
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_29860191_2   2659 GACTAGAC-TTTTTTTAAAAAAGACATACAAATGGAAAGCAGGCATATGA 2707
                           v     -   i ii   i    i          vv ii i   i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_29860191_2   2708 AAAGGTGCTCAACATCACTGATCAT 2732
                             i            ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (44 / 30)
Gap_init rate = 0.02 (7 / 322), avg. gap size = 1.14 (8 / 7)  


 273 22.67 2.67 0.00  chrX_30100269_30104209.rev      442   516 (3425)  C L1M4_orf2#LINE/L1   (0)   908   832  

C chrX_30100269_3    516 TTGAATTGA--TCCCTTAAAAGAAGACATTTATGCAGCCAAAAGACACAT 469
                               v  -- ii  iv        i  vi viii     v ii     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

C chrX_30100269_3    468 GAAAAAATGCTCATCATCACTGGCCAT 442
                              i       v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.01 (1 / 77), avg. gap size = 2.00 (2 / 1)  

2982 26.79 0.89 1.90  chrX_30100269_30104209.rev     2590  3485 (456)    L1M4_orf2#LINE/L1        1   887 (21)  

  chrX_30100269_3   2590 TGGAAGAACATTCCATGTTCATGGGTAGGAAGAATCAATATCATGAAAAT 2639
                              ii i  i            i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_30100269_3   2640 GTCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2689
                          v v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_30100269_3   2690 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2737
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_30100269_3   2738 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 2787
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_30100269_3   2788 AAGAAAGCTGGAGGCGTCACGCTACCTGACTTCAAACTATACTACAAGGC 2837
                           v    i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_30100269_3   2838 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2887
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_30100269_3   2888 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 2935
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_30100269_3   2936 ATCTGATCTTTGACAAACCTGAGAAAAGCAAGCAATGGGGAAAGGATTCC 2985
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_30100269_3   2986 CTATTTAATAAATGATGCTGGGAAAACTGGCTAGCCGTATGTAGAAAGCT 3035
                           v  i  i     i        v      v  ?  ii   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_30100269_3   3036 GAAACTGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3085
                            ii  i i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_30100269_3   3086 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3135
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_30100269_3   3136 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 3185
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_30100269_3   3186 AACACCAAAAGCAATGGCAACAAAAGCTGAAATTGACAAATGGGATCTAA 3235
                         i            vvi          vvi    v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_30100269_3   3236 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 3285
                          i   v i  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_30100269_3   3286 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3335
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_30100269_3   3336 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATGTACAAGAAAA 3385
                         i  i  vi          v  i  v      vv    v vv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_30100269_3   3386 AAA-AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 3434
                          i -   i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_30100269_3   3435 TCAAAAAATCTGTTAAAAGA-ATAGATTTAATGTTCAATAATGCACA--A 3481
                           v   i ---------   -   v ---    vi      -     -- 
  L1M4_orf2#LINE/    847 TCCAAAGA---------AGATATACA---AATGGCCAATAA-GCACATGA 883

  chrX_30100269_3   3482 AAAG 3485
                             
  L1M4_orf2#LINE/    884 AAAG 887

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (11 / 887), avg. gap size = 2.27 (25 / 11)  


2734 26.47 4.07 1.36  chrX_30126440_30128399      584  1467 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_30126440_3    584 TGGAGATGCATTCTGTGTTTATGGACTTGAAGAATCAACAT-ATTAAGGG 632
                             i vii  i ii    i     i v     v i  i  -i     i-
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_30126440_3    633 TGTTCATTCTCCCCACATTGTTCAATAGTTTTAAAACAGTACCAGTTGAA 682
                           viv  v       v    v  v i  v  i  vi  i v  vi ii  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_30126440_3    683 ATTCCAGCAATATTTTTGGTATATATAGACAACCTAATTATAAAACTTAT 732
                           i     viiv     v i v v  v     v  i  iv     i i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_30126440_3    733 ATGATAAGGAAAACAAAGTAGAATAGCTAAAACAATTTTGAAAAGGAAGA 782
                            iv  v v  ivi vvi        i        i       i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_30126440_3    783 ATAAAATGGGAAGAATCACTTTAATCAATATTAAGACTTACTGTATAGTT 832
                          i   i v   i  v    vi vvi    v i  i       ii v  i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_30126440_3    833 TCAGTAATCAACAAAGTGTGGTACTGG-AGGAGATATAAACACATAGATC 881
                         v          v v             - vi  i-   i   i       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAGACATATAGATC 298

  chrX_30126440_3    882 AATAGA-CAGAATAGAGCTCCCCCATACAAACCAAT-------TGGGCAT 923
                            i  -i     v   vvi  vv v i     v  -------   v  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_30126440_3    924 TTAATTTTTGGCAAAACTGC-AAAAGAAATCCATGGAGAAGGA-TAGACT 971
                           i     i i   iiv   -  i vv v  v    i   i  -   v  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_30126440_3    972 TTTCAACAAAAGATCAATGGT-TTGGAACAATTGATCATCCATATGCAAA 1020
                                   -------    -i   i    i  ivi ?   i       
  L1M4_orf2#LINE/    399 TTTCAACAAA-------TGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_30126440_3   1021 AAACTTAATTCCAACC--TACTTCTCACTTTATACAAGGCTTATCTCAAA 1068
                          i v v  v ivi   --   i  v   iv       iiv   v      
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_30126440_3   1069 GTGGATCATAGATTTAAATATAAACA-TAAAATTATAAAACTTTTAGAAA 1117
                         i       ?   ii     i   ivi-     i         i      i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_30126440_3   1118 AAAACATAAG---AAATCGTCTTTGTAACTTGAATTTAGATGAAGAATTC 1164
                                 i ---     ---  i  i  i viiv    iii v iv   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_30126440_3   1165 TTAG----GACATGAAACACACAATTCATAGAAGGAAATATA-------- 1202
                             ----    iv   vi     viv i i   i   v   --------
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_30126440_3   1203 --AGTTTACAAAAATTAATAACTTTTGTTCTGTTAAAGACATTATTAA-- 1248
                         -- v  i iv        v         v  viv  i    i   i  --
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_30126440_3   1249 AAGAAAAAAGACAATTAGCAGACTGGGAGAAAATATTCACAAATCTCATG 1298
                            vi         iivi    v              ii      vi  i
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_30126440_3   1299 TTTGACAAATGACATTTA-CCAGAAGATATAAAGAACCCTCAAAATTCAA 1347
                          i   i  iv   v v  -      v           i  i v  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_30126440_3   1348 CAATAGGAAAATAAATAACCCAACTTAAAAATGGGCAAAGGACTTCAGCA 1397
                         i    ii  i i           i ?                i  v ii 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_30126440_3   1398 GACACTTCACCAAAGAGGATGTAAGAATGGCAAATATGCACATGAAACAG 1447
                             i   v       i   i  vi      v    v          vii
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_30126440_3   1448 TGTTAAATGTCATAGTCCTT 1467
                           i v  ii   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (137 / 94)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.67 (48 / 18)  


1684 30.99 5.76 1.84  chrX_30238550_30240722.rev      820  1687 (486)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_30238550_3    820 GATATATTATCTTTGTGGACCAATTGGTTTGTTATTGTATACATAACAAT 869
                              vii  v  ii    iiiivv ii  iv      vv v  ii    
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_30238550_3    870 TATTCC--AAATTAATCCACTGGATTCAATAAAATGCCAACCAAAAACCC 917
                         - i   --     i   i  -i       iiv   v  v i     v   
  L1M4_orf2#LINE/     57 -ACTCCCCAAATTGATCTAC-AGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_30238550_3    918 ATCAAATTTTTTAGTGAAACTTGACAAACTTATCCTGAAATTTAGATGGG 967
                          v vivi     v iii  v       i  v     i     i v    i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_30238550_3    968 AATACAAAAGGCT--AAACAGACCAAATTATCTTTGAAGGATATTAACAA 1015
                            i   ii i i--i  i  v v   iv     -   ii v vv     
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTT-GAAAAAGAAGAACAA 203

  chrX_30238550_3   1016 GGTAGGGAGTCTTGCACTACTGGATATCAAAACCTATTATAAAAG-ATAG 1064
                         i  v  ii v  ii    v ivi  v       i  i  i   iv- i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_30238550_3   1065 CAGTTA--------TTGTACTGGTATGCAGATAAATAAATAGAACAATGG 1106
                         i i i -------- v       i  ivi    i i v     v      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_30238550_3   1107 AACTGATTAGGAAAGCCAGATGTAAGTCCAAACATGAATGGACACTCGAT 1156
                           iv  v v ii iv     vi   ii   v    vv    v  v i   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_30238550_3   1157 TTGTGACAGACTGGG---CATGGC-----AGTGGAGCAAGGACAGTTTTT 1198
                           vi    i---   ---  v i ----- i   i v   i i   i   
  L1M4_orf2#LINE/    354 TTTCGACAA---GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_30238550_3   1199 TCAATAAGTGAGGCTGGGACAATTGGATAATGATATGACAAAAAAAAAGA 1248
                             i  i  iv          i      ?iv i   -     i  v-  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAAT-GA 448

  chrX_30238550_3   1249 AACAGCAATCTGTTCCTCAAACCATACATAACA--TAATTTCTAGATGTA 1296
                          iiv -i i iv v     v      i i  v --   i - v i   v 
  L1M4_orf2#LINE/    449 AGTTG-GACCCCTACCTCACACCATATACAAAAATTAACT-CAAAATGGA 496

  chrX_30238550_3   1297 TCATAAACCTTAATGTGAAAAGC-AAAATGATAAAATTTCTATAAGTAAA 1345
                            ? i    v     -  i   -    iv      i ii  v   v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_30238550_3   1346 TATAAATGAATATTTTCATAACCTCAAGGTAGGGAAAGACTTCTTACACA 1395
                         i   ii? v v  i   i i    iii v    v  v ii      v i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_30238550_3   1396 GAATAGTAAAATCACTAACCATTAAGGATTAAGATCAATAATTTTAAATT 1445
                         vi i vi    v   v i v iv  i  v-  i  vi    v  vi v  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAA-AAAATAGATAAATTGGACTT 644

  chrX_30238550_3   1446 AGGAGCAAATATCAAAAA---TCATG-----------ACTAACATGTAAA 1481
                         v-- v    -  i     --- ii  -----------    v  v -   
  L1M4_orf2#LINE/    645 C--ATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAA 690

  chrX_30238550_3   1482 ACGAAAGG------CACAGAGTGGAAGATGAGATTTGCAA--TATGCGGC 1523
                         ii    i ------      i   i   vi v        --i  iiiv 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_30238550_3   1524 CAAAAAAGGACTACCACTGGGGATATATAAAGAACTCCTACAAGTAAATG 1573
                         ii v  i     vvi iivi i               i     v v   i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_30238550_3   1574 AGAAAAATACAAACAATCCTGTAGGAAAATGGTCCAAAATCATGAACAGA 1623
                          v     v     i  i  vi v?i       v v  iiviv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_30238550_3   1624 TACTGCGT-AAAGATGACAT-CAAGTGAT-AA-AAGCACAGAAAAAGTTG 1669
                         i i v vi-     v  i  -   i  ii-  -       vi     v  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_30238550_3   1670 CTCAATTCCATTTATAAT 1687
                              ivi  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (159 / 106)
Gap_init rate = 0.03 (29 / 902), avg. gap size = 2.28 (66 / 29)  


 719 28.33 9.23 3.44  chrX_30255522_30257749     1105  1743 (485)    L1M4_orf2#LINE/L1      233   908 (0)  

  chrX_30255522_3   1105 AAACATACTATAAAG-------AAATAAAATGATGTGACATTGGCAGAGG 1147
                             v     i    -------  vi  i iii    ii i     v i 
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_30255522_3   1148 AATAAACACATAGATCC-TGAAAAAGAAT--AGAGTACAGA------CCC 1188
                         i   i   i       v-  i  v     --     v    ------   
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_30255522_3   1189 ATCCCATAAGAG--AATTTCTTAATATGAAAAAATGGAATTTCAAA---- 1232
                           v vv v vi --    vv  -- vi  v  ---- ii vi   i----
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATT--TTCGACAA----GGGTGCCAAGACCA 376

  chrX_30255522_3   1233 -TCAATGGGGGAAAATGAATTATTTTA-CAAATGGTGTTGGTACAAGTGT 1280
                         -         i  i vv i iv   i -         i   v    v  v
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_30255522_3   1281 CT-GTCACTCTGGAAAAAAA-AAAACTAATATGCTATCCTTCACACCATA 1328
                         v -?i   -v  v    i  -i  ii iivviv   i --          
  L1M4_orf2#LINE/    427 ATAKCCAC-ATGCAAAAGAATGAAGTTGGACCCCTACC--TCACACCATA 473

  chrX_30255522_3   1329 CACAAAAATAAATTGCGAATGGGTGAAATATCTTAAGATTTAA-AG-TAA 1376
                         i        v  i vvi     i v ? v i  -- i  v   -  -   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCT--AAATGTAAGAGCTAA 521

  chrX_30255522_3   1377 AACTACAAAAGTACCT-GAAGAAAACAGAGTAGAGCATTTTCATATTCCT 1425
                              i    v - i -          v  v? viv  i   i ivi i 
  L1M4_orf2#LINE/    522 AACTATAAAACT-CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_30255522_3   1426 GATATGGG-AGGGCCCTCTTAACCAAGACAATGAACTCAGAAACCACCAA 1474
                          ivv i  - iv vii     ivi v    vii  vv  v  i v  v  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_30255522_3   1475 A-AAATGTTTGATGAAATTTG-CTAAATGAAAGTAGAAAACTTCTACATT 1522
                          -   viv v   -     v -  vv  v   i vi       i iiii 
  L1M4_orf2#LINE/    621 AGAAAAAATAGAT-AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_30255522_3   1523 ACAAAAGAGAGTAT-AGGCAGAGTTAAAAGATTAGCAAAAACACTAAA-- 1569
                         v    i  v v   - i - i   v      iv v -----   vi  --
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAG-AAAGTGAAAAGACAACC-----CACAGAATG 713

  chrX_30255522_3   1570 GCAAAATATATTTG-AGA-CATAGATCAGGCAAAGAA-TTGTCATCCATA 1616
                          v i  v       - i -    v   v ii  i i -    -     v 
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT-ATCCAGA 762

  chrX_30255522_3   1617 TTTTTTAAA----TCTTAAAA---ACTAAGAAAATGACAAACATAAC--- 1656
                         v v v    ----     v  --- v   v    v      --    ---
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA--TAACCCA 810

  chrX_30255522_3   1657 ----AAAAATAGGCAAAGAACATGAACAGATAGTTTACAAAATAA---AT 1699
                         ----      i       i iv    i   i v  iv v   v  ---  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_30255522_3   1700 TCAGATGGTCCATAAGTATGTGATAAAA-GC---ACCTCACTAGTAAT 1743
                         v  i    i v     i ii   v  i -  ---  v   ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.02 (90 / 88)
Gap_init rate = 0.05 (37 / 676), avg. gap size = 2.19 (81 / 37)  


2386 26.69 1.44 8.21  chrX_30312854_30316646     2327  3300 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_30312854_3   2327 TGAAAAAACATTCTATGCTCATGGATAGGAAGAATCAATATCTTTACAAT 2376
                           i   i i  i i   i        v      v i     iv   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_30312854_3   2377 GGCCACACTGCCCAAGGCAATTTACAGATTAAATGCTATTCCTGTCAAAC 2426
                            v i   v     ivii  i        v  i  v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_30312854_3   2427 CACCAATGACATTCTTCACAGAATTAGAAAAATCTATTTTGACATTTATA 2476
                         iv   iivi v  i  ii     v v  v  iiiv  ii i v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_30312854_3   2477 TGGAACCAAAATAGAGCCTGAATAGCCAAGGCAATTATAAGCAAATATAA 2526
                              viiv  vi  v  v          ii    iv i iv  iv v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_30312854_3   2527 CAAAGCTGGTGTCATCACGTTAGCTAACTTCAAACTATACTACAGGGCTA 2576
                              i   v vvv    ii vv i  i      viv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_30312854_3   2577 CAGTAACCAAAACAGCACGGT--TGGTACAAAAACAAACACACTGGCCAA 2624
                               i   i    iii   --   i i  ii i i   i iv ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_30312854_3   2625 TAGAACAGAATAGAGAGATCAGAAATAGTTCTATATACCTACAACCATTT 2674
                          i   i     v     vi        ivi i   i ii  iiii  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_30312854_3   2675 GATCTTCAACAAAGTCAACAAAAACAAGCAATGGGGAATGGACTCCCTAT 2724
                            i   i    i viiv   i v  vv          v i ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_30312854_3   2725 TCAAAAAATAGTGCAGGGATAGCTGGTTAGCCATATGCATAAGACTGAAA 2774
                             v    i    v    i i    v  ?   i     v    v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_30312854_3   2775 CTGGACCCCTTCCTTATACAATAATACAGAAATCAACTCAAGATGGATTA 2824
                         i         v   i i  -------------------------------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACAC------------------------------- 469

  chrX_30312854_3   2825 AAGGCTTAAATTGCAGAAGATTGGAACTGGACCCTTTCCCTATACCATAT 2874
                         ---------------------------------------------     
  L1M4_orf2#LINE/    470 ---------------------------------------------CATAT 474

  chrX_30312854_3   2875 ACAGAAATCAACTCAAGATGGATTAAAGACTTAAATGTAAAACCTAAAAT 2924
                            i    i       i      i ?    i         i v      i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_30312854_3   2925 TTTTAAAAC-CGTAGGAGAAAATCTAGGAACTACCATTCTGGACATAGTA 2973
                          v -     - v   i      iv    ?iiv viv   vv   v v vi
  L1M4_orf2#LINE/    525 TAT-AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_30312854_3   2974 ACGGGAAAAGATTTCATGGCAAAGATGCCAAAAGCAATTACAA-AAAAAA 3022
                         vii  v  v i    v i vv v  ii         vvvi   -    i 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_30312854_3   3023 AAAAATTGACAAATGGGACCTAATTAAACTAATGAGCTTCTCTGCACAGC 3072
                               v  i    v    i v  i   v v vi i   i v   vi-- 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--C 671

  chrX_30312854_3   3073 AAAAGAAACTATTAACAAGGTAAACAGACAGCCTACAGAATGGGAGAAAA 3122
                            i  v     i  v  i  i  v     i  i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_30312854_3   3123 TATTTGCAAACTATGCCTCTGACAAAGGTTTAATATCCAGAATCTATAAG 3172
                                   ii  iiv     i  i  vi vi          v     i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_30312854_3   3173 GAACTTAAGCAAATTTACAAGTAAAAA---AAA-AACC--ATTACAAAGT 3216
                              ivvi   v iv i  -      ---   -    --   ?v   i 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_30312854_3   3217 AGACAAAGGAC----ATTAATACTTTTCAAAAGAAGATGTATATATGGCC 3262
                         i i       i----  vi i i  i  v         i  i v      
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_30312854_3   3263 AAGAAACATATGAAAAAAAGCTCAATATCACTGATCAC 3300
                           v  i  i       i v      i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (154 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 8.55 (94 / 11)  


2122 24.64 5.67 0.97  chrX_30393240_30394848      500  1116 (493)    L1M4_orf2#LINE/L1      263   908 (0)  

  chrX_30393240_3    500 CAGT-TGGTATTGGTGTAAAGTTTGATAAATAGGTCAGTTGATCAGAATA 548
                             -     i   ii   i v v  i v    i   i v  vi     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_30393240_3    549 GGGAATCCAAAAATAGACCCATATCAGTATAGTCAATTGGCTTTTTACAA 598
                          i  i    i     i       ivvv   i        ii   iv    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_30393240_3    599 AGGTACAATGGCAATTCAGCAGAGAAAAGCTAGTCTATTCAACAAATTGT 648
                         i   i v v i v     iii i    iiv      v          v  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_30393240_3    649 GCTGGAACAGTTGGATATTCAACCATATTCAAAA-AAGAAACTTAAATTC 697
                              i   ii      ?----   i  v     -  vi  v  ii ii 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAK----CCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_30393240_3    698 ACGCTTTGCAGTATATACAAAA-TTAACTGAAAATATATCAGAGACCCAA 746
                         vii i ii  vi          -      v     iv    ?     i  
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_30393240_3    747 AGGTAAAGTCTATAACTATACAACTTCTAGAAAAAAA--TAAGAGAAAAT 794
                          v    iiv   v       v    ii     i    --  i ? v    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_30393240_3    795 CTTTGTTACATTGGGTTTGGCAGTGATTTCTTAGATATAACATCAAAACC 844
                            i  v  v       v    i  i            i   i     v 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_30393240_3    845 GTGATACATAAAATAAAAGAAATGGTAAATTGGACTTCGACCATATTAAG 894
                         iii vvv i    v    i v - i             iv v v     i
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTCATCAAAATTAAA 657

  chrX_30393240_3    895 AGCTTTCACTCCCCAAAAAA-A-TACTAAGAGAATTAAAAGATAAACCAC 942
                          i    iiiv ii    ii - -  ii    i i v      i  v    
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_30393240_3    943 AGATTGGGATAATATGTATGCAAATTGCATATCTGTTAAAGAACTAGTAT 992
                            v     v  v  i v       iii       v   i i   v    
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_30393240_3    993 CCAGAATATATAAAGAA---------------------------AACAAC 1015
                                          ---------------------------  i   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_30393240_3   1016 TCAATT-AAAAGTGGGTGAAAATTTTGAATAGACATCTCACCTAAGAAGA 1064
                         i     -    i    ii  iiv             i  v  v       
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_30393240_3   1065 TATATAGATGTCAAATAAGCACATTAACAGATGATTCAACACCATTAGTT 1114
                             i i   v v           v  v     -i      i  ??????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATG-CTCAACATCAZZZZZZ 906

  chrX_30393240_3   1115 AA 1116
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.66 (93 / 56)
Gap_init rate = 0.02 (11 / 646), avg. gap size = 3.73 (41 / 11)  


2628 21.46 4.61 7.98  chrX_30527981_30531005.rev     1643  2532 (493)    L1M4_orf2#LINE/L1       18   877 (31)  

  chrX_30527981_3   1643 TTCA--GATTGGAAAA----ATA--GTTAAGATGTCTGTACTACCCAAAA 1684
                             --        i ----   --         v vi    v      v
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_30527981_3   1685 CAATCTATAGATTCAATGCAATTTGCGTTGAATTAGATAGAAGGAGTTGA 1734
                         ii     i        i     i---------------------------
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATC--------------------------- 90

  chrX_30527981_3   1735 GCTTTTAATTTGTATTCCTATCAAAATTCCAA-TGTCTTTTTCACAAAAA 1783
                         ----------------           i   i-  i      ii  i   
  L1M4_orf2#LINE/     91 ----------------CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chrX_30527981_3   1784 TAGA------AATTATAAAATTCATAGGGAACCATG-AAG--ACCCCAAA 1824
                          v  ------i  iv           v    --   -   --    vi  
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAA--ATGCAAGGGACCCAGAA 172

  chrX_30527981_3   1825 CAGCCAAAGCAACCCTGAGCAAAAAGAACAATGCTGGAGGTATCACACTA 1874
                         i       i   i i   iv  i        v i      vv       v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_30527981_3   1875 CCTGATTTCAAAATCTACTACACAAAGCTATTGTAACCAAAACATTATAG 1924
                           ii         ii       --      iv    i   i   v i i 
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACA--AAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_30527981_3   1925 CACTGGCATAA--ACAGACACATAGATCAATGGAACAGAATAGAAACACC 1972
                         i          -- i     i              i     v  i -ii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA-GTC 319

  chrX_30527981_3   1973 CAGCAGTAAACCCAGA-ATATATGGTCAACTAACTTTTGATAAGGGCACA 2021
                            v i        v -  v         i i i   i  i     ii v
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_30527981_3   2022 AAGATGACACCATGGGGAAACAATAGTCTTTTCATTAAGTAACACAAGGA 2071
                             iv iv v         v             vi  i iiii vi   
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_30527981_3   2072 AAACTGGATATCCACGTGTAAAAGAATGAAACTGGACCCTTATGCCATAC 2121
                         v         ?    i  i           ii       i  ivi  i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_30527981_3   2122 ACGCATGAAAAAACCCACCCAACCCAAAATGTATTAAAAACCCAAACATA 2171
                         - ii  iv     ii-----   i       v  i ? i   i   ii  
  L1M4_orf2#LINE/    470 -CATATACAAAAATT-----AACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_30527981_3   2172 AAACCTGAAACCATAAAACTC-------AACACACAGGAAAAGAGTTT-- 2212
                          i v  i    i         -------  v   i   ?iv i vi  --
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_30527981_3   2213 -GACAT-GGGTCATAGCAATGATTTTTTTGGTTATGACATCAAAAGCACA 2260
                         -   v -    i -i      i   i  v i -      i          
  L1M4_orf2#LINE/    564 TGACCTTGGGTTA-GGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACA 611

  chrX_30527981_3   2261 GGCAACAAAA---AAACTAAAGAAGTGGGATCACATCAAA--CAAAAAAG 2305
                         i         ---   v  i v  i v   iiv       --i     --
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-- 659

  chrX_30527981_3   2306 GCTTCTGAACAGCAAAGGAAACAGTTAACAAAATGAGAAGGCAATTTATA 2355
                         -   i  vi vv       v  vi i  v   i   i   i   iii i 
  L1M4_orf2#LINE/    660 -CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_30527981_3   2356 GGTTGGGAGAAAATATTTGCAAGCTACATAT--AATAAGGGG-TTATCAA 2402
                          iv                   iii i    --i       i-  i - v
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT-AT 757

  chrX_30527981_3   2403 CCAAAATATATAAAGAGCTCACCTAACTCAATAGCAAAAAAAAAAAAAAA 2452
                            i            i   vivi         ii     i v   ----
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA---- 803

  chrX_30527981_3   2453 AAAAAGATAAACTGGTTTAAAAATGGGCAAAGGACCTCAGTAAACATTTG 2502
                         -------   v iii  ?                ii v i  i      v
  L1M4_orf2#LINE/    804 -------TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_30527981_3   2503 TCCAA-GAGGACATAAAAATAGCCAGTATGC 2532
                              -  i  i   v    i    i  v  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGC 877

Transitions / transversions = 2.34 (131 / 56)
Gap_init rate = 0.03 (28 / 860), avg. gap size = 4.00 (112 / 28)  


3082 26.66 1.22 0.77  chrX_30545791_30550906.rev     3722  4625 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_30545791_3   3722 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 3771
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_30545791_3   3772 GGCCATACTGCCCAAGGAAATTTATAGATTCAATGCCATCCCCATAAAGC 3821
                            v     v     ivvi  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_30545791_3   3822 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAGCC-ACTTTAAAGTTC 3869
                          v   iivi i  i  ii     -   --- v    i- iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_30545791_3   3870 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAA 3919
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_30545791_3   3920 GAACAAAGCTGGCGGCATCACACTACCTGACTTCAAACTATACTACAAGG 3969
                                 i   v  vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_30545791_3   3970 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 4019
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_30545791_3   4020 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 4067
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_30545791_3   4068 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 4117
                         i vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_30545791_3   4118 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 4167
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_30545791_3   4168 TGAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGG 4217
                             ii    i    v   i i   v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_30545791_3   4218 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4267
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_30545791_3   4268 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGAACTTCAT-GAT 4315
                          v    ?i- v i -   iv   v v  vv i     viii   v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_30545791_3   4316 GAAAACAACAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATC 4365
                         - vi   v        vvi          vv     v  i i  v   ii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_30545791_3   4366 TAATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 4415
                          v  v   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_30545791_3   4416 AACAGGCAACCTACAGAATGGGAGAAGATTTTTGCAATCTACTCATCTGA 4465
                           v  i     i              i  v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_30545791_3   4466 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 4515
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_30545791_3   4516 AAAAAACAAACAACCCCATCAATGAGTGGGCGAAGGA----GAT-GTCAA 4560
                             i     i     v  i? vi i     i     ----i  - v  v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_30545791_3   4561 ATGTCAAAAGAAGACATTTATGCAGCCAAAAGGCACATGAAAAAATGCTC 4610
                         v v  v        i  vi viii     v i           i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_30545791_3   4611 ATCATCACTGGCCAT 4625
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


2753 18.71 12.26 0.16  chrX_30552941_30556435.rev     1565  2184 (1311)    L1M4_orf2#LINE/L1        1   695 (213)  

  chrX_30552941_3   1565 TAGAAAGTCATCC-ATGGGGATAGATCAGAAGATTTAACATTGTTAAAAT 1613
                          i     vi    -   vvv  i   ii     i    i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_30552941_3   1614 GATAATATTCCCCAAACTGATGTACAGATTTGATGCAGTACTTATCAGAA 1663
                          ii    i        i    v        ii i   i v i     i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_30552941_3   1664 TGCTAGTTGATTTCTTTGAATAAATTGACAAGCTGATTCTCCATTTCATA 1713
                          v i  i  vi  i    v v                i  vv v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_30552941_3   1714 AGGAAACACAAGG-AGCCAGA-T-GCCAACACAGTCTTCAAAAA------ 1754
                         v     ii     - v     - -     v   i    v     ------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_30552941_3   1755 TAAAGTTAGAGGAGTCACACTTTCCAATTTCAAAACTTACTTCAAAGCTA 1804
                         i      i     v        i                  v        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_30552941_3   1805 CAGTAGTCAAAACAGCATGATACTGGCATGAGGATGGACATGTATATCAA 1854
                              i    i    ii  i         i     i     i  v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_30552941_3   1855 TGGAAAAGAATTGAGACTCCAGAAATTAATTCTTATGTTTATGGTTAATT 1904
                              v          v         v  ii v  ii        i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_30552941_3   1905 GATTTTCAACAAGGTTGTCAAGATAATTCAATGGGGGGACGAATGGTGTT 1954
                                i      v  i     iv           ii -    i  v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTT 399

  chrX_30552941_3   1955 T-CAATAAATGGTGGTGGGACCACTGAATATTCACATGAAAAAGAA---- 1999
                          -   i        v      v    i   ?i      v       ----
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_30552941_3   2000 GTAGGACC---------------------AAATT---------------- 2012
                           v     ---------------------     ----------------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_30552941_3   2013 -----------GTAGGAGTTCCAACTATAAAATTCTTAGAAGAAAACA-- 2049
                         -----------   i   i vv          i               --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_30552941_3   2050 --CGTAAGTCTTCATGACTTTAGATTAGACCACAGTTTCT-AGACATGGC 2096
                         --?    i     i    i  i i    i v ii      -   i   i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_30552941_3   2097 ATTAAAAACATAAGTAATAAAATA-----TAGGTAAATTGGATTACATAA 2141
                          ii    i  i   i  i    v -----   i         i v   v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_30552941_3   2142 AAATTTAAAACTTTTGT---TCAAATGATACCATTAAGAAAGTGAA 2184
                              v           ---     v  i  i  i           
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

Transitions / transversions = 1.92 (75 / 39)
Gap_init rate = 0.02 (14 / 695), avg. gap size = 5.50 (77 / 14)  

1127 12.72 1.32 3.07  chrX_30552941_30556435.rev     2777  3004 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_30552941_3   2777 AAGAAAGTGAAAAGACAGCCCACAGAATGGGAGAAAATATTTACAAGGCA 2826
                                          i                        i   ----
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA---- 730

  chrX_30552941_3   2827 TATATCAGATATCAGATAAGCTACTGGTATCCAGAATATAAAAAGTACCT 2876
                         ---    v     v      vv   v              v    v  ii
  L1M4_orf2#LINE/    731 ---ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_30552941_3   2877 TCACAACTCAATAA---AAAGGCAAATAATCCAATTTAAAAATAGGGAAA 2923
                          i            ---    i       i      ?      i  v   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_30552941_3   2924 GGAGATGAATAGACATTTCTATAAAGAAGATACACACATGGCTAACAAAC 2973
                            vv               vi          i   v     i  i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_30552941_3   2974 ACATTAAAAGAGGCTCAACATTATTACACAT 3004
                             v      v         i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (14 / 14)
Gap_init rate = 0.01 (2 / 224), avg. gap size = 5.00 (10 / 2)  


 626 23.50 3.00 5.00  chrX_30614739_30617822.rev     1377  1576 (1508)    L1M4_orf2#LINE/L1        1   196 (712)  

  chrX_30614739_3   1377 TGGAGTGATATACCATGTTCATTAACTGACTGAATCAATATTTTTGAGAT 1426
                             iv     v          vi i  ivv  v i      v  i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_30614739_3   1427 ACCTGTTCTTACAAGGTTGATATATAGATACAGTGTAATACCAATTATAA 1476
                         iv vi v  iv v ii     v  i    v  ii i   v  v  i v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_30614739_3   1477 CCCCATTAGGTGGTAGTGCATTTTT------AATTAACAAACTGATTATA 1520
                         i    ------- i--   v     ------    i    i     iv  
  L1M4_orf2#LINE/    101 TCCCA-------GC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_30614739_3   1521 AAATTCATATGGAAATACAGAAAGTCCTAGAACATCCAAAACAATCTTGA 1570
                                         i  - ii v  i    i v               
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_30614739_3   1571 AAAAGA 1576
                               
  L1M4_orf2#LINE/    191 AAAAGA 196

Transitions / transversions = 1.24 (26 / 21)
Gap_init rate = 0.02 (4 / 196), avg. gap size = 4.00 (16 / 4)  

2111 23.97 8.09 1.62  chrX_30614739_30617822.rev     1923  2602 (482)    L1M4_orf2#LINE/L1      185   908 (0)  

  chrX_30614739_3   1923 TCTCCAAAAAGGAAAAAAAAGT-------CTTAGACTAACCAACTTCAGG 1965
                            iv      i i  v     -------  i v   vv    i    ii
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_30614739_3   1966 ACTTACTATAAAGCTACAATAACCA---CAGTGTGATATTGGTATAGGAA 2012
                                 i         i   i  ---       i  i   i   i i 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_30614739_3   2013 TAAACAAATAGATCACTGGAACAGAATAGGGAGCCCAGGTTTATACCCCC 2062
                           i   v        v     i     v i   i    ivv  v    vi
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_30614739_3   2063 -CAGTCACACTGTCATTTGATATTTGACAAAAGCACCAA-AGCAACCAAT 2110
                         -  v i ii--    v     v  i     ii ii    - v  vi    
  L1M4_orf2#LINE/    335 ACATTTATG--GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_30614739_3   2111 AGACAAAGGAACATTTTTTTCAACAGGCAGAGCTGGAAGAACTGGATATC 2160
                         i iv    -  i v i         iiii v     i v         ? 
  L1M4_orf2#LINE/    383 GGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_30614739_3   2161 CATGTGGAAGAAACACACAGTCTGATCTCTACCTACCTCACATCATACAC 2210
                           ii  v  i i - iiv   iv  i ----           i    i  
  L1M4_orf2#LINE/    432 CACATGCAAAAGA-ATGAAGTTGGACC----CCTACCTCACACCATATAC 476

  chrX_30614739_3   2211 AAAAATT----TGAGATAGCTCATACACCTAAGTATAAAAGTTAAA-CTA 2255
                                ----ii i  i v   ? v      i i   i  i    -   
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_30614739_3   2256 TAAAGCTTCCAGAACAGAATAT----------CTTTGCAAT-TTAGGT-- 2292
                             i  iii    v i  i  ----------   i ii i-  i   --
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_30614739_3   2293 -ATAAAAGTTT-TTGGACAGGTCAC---AGG---AAGCAATAAAAAGAAA 2334
                         -ii  vi    -  i  i v v   --- i ---      i    ii   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_30614739_3   2335 AACAATTGATAAATTAGTCTTCATTAAAGTTTTACACTTCTGCTCATCAA 2384
                           i ---        i v      i   i  vv v    i  iv v    
  L1M4_orf2#LINE/    627 AATA---GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_30614739_3   2385 GTGACACTATTAAGAAAATGAAAAGGCAAACCACAGACCAGGAGAAAATA 2434
                         iv        i      i       i   v       vii          
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_30614739_3   2435 TTTGTAAAATATGTATCTGATGAAGGA-TGGTATCCAGAGTATATAAAGA 2483
                             i   vi  i        i i   - v         i          
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_30614739_3   2484 ATTTCTACAACACAGTAATAAAAAGACAA----CTCAAT--AAAAAAGGG 2527
                          i ii      v  i              ---- i    --     v   
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_30614739_3   2528 TAAAACACTTGAACAGACACTTG-ACAAAGGA-ATATATATATGA----- 2570
                         i   iv i     i     i  v-v     i -     i v   i-----
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_30614739_3   2571 AAGACCATGAAAAAAGA---AATATCAAGGAATTT 2602
                            vv        i vi---  i    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.22 (111 / 50)
Gap_init rate = 0.03 (24 / 724), avg. gap size = 2.75 (66 / 24)  


4721 13.79 3.45 2.78  chrX_30850520_30852425.rev      517  1415 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_30850520_3    517 AAAGACATCCCATGTTTATGGACTAGAAGAGTTAATATT---AAGATACC 563
                              i          i     i i     v        ---     iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_30850520_3    564 AATATTCCCACAAAT-GACTTACAGGTTTAATGCAATCCCTAACAAAATC 612
                             i    -     -  ii     i  i  i          v       
  L1M4_orf2#LINE/     54 AATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_30850520_3    613 CCAGTAGGCTGGTTTTTAAAAAAAAAAAAAAAAAAAAAAACGAAATTGAC 662
                             iv v  --     iv ---------------------         
  L1M4_orf2#LINE/    103 CCAGCTGCCT--TTTTTGCA---------------------GAAATTGAC 129

  chrX_30850520_3    663 AAGCATATCCTAAAATTCATA-GGAAATTCAAGGGACCCAGAATAGCCAA 711
                             vv               -      v                     
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_30850520_3    712 AGCAATCTCTGCA---GAAGAGCAGAGTTGGATGACT-ATACTTCCCAAT 757
                          i      -  v ---     i  i       v    - i          
  L1M4_orf2#LINE/    180 AACAATCT-TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_30850520_3    758 TTCAAAACTTACTACAAAGCTATAGTAATCAAGCCAGTGTTGTGCCAGCA 807
                                               i          v      v  i ii   
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_30850520_3    808 TCAGTTTAGACACATAGATTGACAGAACAGAATTGGGAGTCCCGAAATAA 857
                          v  vv      i      ii ii   i       i      v       
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_30850520_3    858 ACCCATACATCTATGGTCAATTGATTTTTGACAAGTGTGCCAAGACCATC 907
                                   i                 i      v             i
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_30850520_3    908 TAGTGGAGAAAGAATGGTCTTCTCAACAAATGGTGCTAGGACAACTGGAT 957
                         i i   i        i     i               i            
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_30850520_3    958 ATCCACACACAAAGGAATGAAATTGGACAATGACCTCATATCATATACAA 1007
                          ?     ii    i       i      vviv      i i         
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_30850520_3   1008 AAATTAACTCAAAATGAGTTAGAAACTTAAATGTAAAAGCTAAAACTGTA 1057
                                         ii i ? i  i         i          i  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_30850520_3   1058 AAATTATTCAAAGAAAACCTGGACATAAATGTTTATGACCTTGAATTAGG 1107
                            i v  vi        v i i?i     v  ii        ii     
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_30850520_3   1108 CAATGGTTTCTTAGATAGGACACTAAAAGCACAAGTGACAAGAGAAAAA- 1156
                                          v     i           ii    i       -
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_30850520_3   1157 CAGAAAAATTGAAC---AT---AATTAAGAACTTT-GTGCTTCAAAGGAC 1199
                         i   v      i  ---  ---      i      -              
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_30850520_3   1200 ACCATTAAGAAAGTGAAAAAAAAA---ACAGAATGAGAGAAAATATTTGC 1246
                           i  i             i v  ---        i              
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_30850520_3   1247 AAATCATATATCTGAAAAAGGACTGGCACACATAATATATATAGAACTCT 1296
                                        v  i     v i iv  v        v        
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_30850520_3   1297 TAAAACTCAGCAATAAAAGTACAAATAACCCAATTTTAAAATGGACAAAA 1346
                           v      ii       iv               ?v       i    i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_30850520_3   1347 GACTTGAATAGAGTTTTCTCCAAAGAAGATA--CAAATGACTA------- 1387
                           i         vv                 --      i i -------
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_30850520_3   1388 --TGAAAAGATGCTCAACATCAATAGCCAT 1415
                         --                    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (82 / 38)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 3.50 (56 / 16)  


3232 26.76 0.55 0.55  chrX_30855341_30861737.rev     4999  5906 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_30855341_3   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5048
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_30855341_3   5049 GGCCATACTGCCCAAGGAAATTTACAGATTCAATGCCATCCCCATCAAGC 5098
                            v     v     ivvi  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_30855341_3   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_30855341_3   5147 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5196
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_30855341_3   5197 AACAAAGCTGGAGGTATCACACTACCTGACTTCAAACTATACTACAAGGC 5246
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_30855341_3   5247 TACAGTAACCAAAACAGCATGGTAATGGTACCAAAACAGAGATATAGACC 5296
                                 i   i    ii     v   i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_30855341_3   5297 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5344
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_30855341_3   5345 ATCTGATCCTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5394
                          vi    ii i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_30855341_3   5395 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAATCT 5444
                           v  i  i              v      v  ?   i   i i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_30855341_3   5445 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5494
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_30855341_3   5495 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5544
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_30855341_3   5545 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5593
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_30855341_3   5594 AAACACCGAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5643
                         vi     i      vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_30855341_3   5644 ATGAAACTAAAGAGCTTCTGCACAGCAAAATAAACTACCATCAGAGCGAA 5693
                           v   v v  i i   i  ii vv    iv v    i  vv i  i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_30855341_3   5694 CAGGCAACCTATAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5743
                         v  i     i i               v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_30855341_3   5744 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5793
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_30855341_3   5794 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGGTATGAACAGACACTT 5843
                           i     i     v  i?    i          i v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_30855341_3   5844 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGTTCAT 5893
                            v        i  vi viii     v ii          i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_30855341_3   5894 CATCACTGGCCAT 5906
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3017 26.90 3.29 0.23  chrX_31243212_31249010.rev     4428  5308 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_31243212_3   4428 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4477
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_31243212_3   4478 GGCCATACTGTCCAAAGTAATTTATAGATTCAATGCAGTCTCCATCAAGC 4527
                            v     vi     v i  i  i        i   i  i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_31243212_3   4528 TACCATTGACTTTCTTCACATAATTAGAAAAACT-ACTTTAAATTTCATA 4576
                          v   vivi i  i  ii  v  v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_31243212_3   4577 TGGAACCAAAAAAGAGCCCACATAGCCAAGTCAATCCTAAGCAAAAAGAA 4626
                              viiv  ii  v  viv        iv     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_31243212_3   4627 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTT 4676
                              i      vv   ii  v  ii i      viv        i   v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_31243212_3   4677 CAGTAACCAAAACAGTATGGTATTGGTACCAAAACAGATATATAGACCAA 4726
                               i   i     i     i   i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_31243212_3   4727 TGGAACAGA-----GGCCTCAGAAATAATGCCACACATCTACAACCATCT 4771
                              i   ----- ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_31243212_3   4772 GATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATTCCCTAT 4821
                            i  i     ivv  v   i v  vv      i     i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_31243212_3   4822 TCAGTAAATGGTGCTGGGTAAACCGGCTAGCCATCTACAGAAAACTGAAA 4871
                            ii             vv   i  v  ?   iv i  i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_31243212_3   4872 CTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAA---------- 4911
                         i         v   i     v                   ----------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_31243212_3   4912 -GACTTAAACATAAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 4960
                         -   i    ii   i v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_31243212_3   4961 GCA-ATACCATTCAGGATATAGGCATGGGCAAAGACTTCACGACTAAAAC 5009
                          ?i- v i -   iv  iv v  vv i     v ii   viiiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_31243212_3   5010 ACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTAATTA 5059
                                   vvi          vv     v  i    v i ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_31243212_3   5060 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAAG 5109
                           v v  i i   i  ii vv    i  v       vv i      v ii
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_31243212_3   5110 CAACCTACAGAATGGGAGAAAATGTTTGCCATCTATTCATCTGACAAAGG 5159
                              i                 i     v vii  vi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_31243212_3   5160 GCTGATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA-- 5207
                         i  vi          v  i  i     ivv    v iv i  v     --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_31243212_3   5208 ------ACCTAATCAAAAATTGGGCAAAGGATATGAACAGACACTTCTC- 5250
                         ------   i   i?    v            v    i     i     -
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_31243212_3   5251 AAAGTAAGACATTTATGCGGCCAACAA--ACATGAAAAAAAGCTCATCAT 5298
                             -    i  vi vii      i  --         i v     v   
  L1M4_orf2#LINE/    850 AAAG-AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_31243212_3   5299 CACTGGTGAT 5308
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.44 (31 / 9)  


2469 27.04 3.73 1.81  chrX_31343143_31345917.rev     1406  2289 (486)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_31343143_3   1406 ATATGGCATGTTTATAGACTGGAAGAGTCAGCATAGCAAATATGTCAGTT 1455
                             vv      i  i  i       v i ii  v iv  v   v  i v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_31343143_3   1456 CTTCTCAAATCAATCTAAAGGTTTAATTTAGTTTCTATCAAAATCTTATC 1505
                           i i     ii     v  i  i  ivi i ii           ii v 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_31343143_3   1506 AAGGATTTCTGTACACATAGACAAGCATACTCTAAAATCTATAAGAAAAG 1555
                         vivvv   i  i v v  v       vv ii       ii   v i   v
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_31343143_3   1556 TCACAGGCCACAGAATAACTAAAACAGTCTTTTAAAAAGGTAAATAAAGT 1605
                         v  vi  v v       i i      i    v-      ivi  i     
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTG-AAAAAGAAGAACAAAGT 206

  chrX_31343143_3   1606 GGGAGTAACCTCTCTACCCAATATTATGGCTAACAATATAG-TAAGGCTA 1654
                         v    v vi v v  v      v i vii  v  v i v  -  vi iv 
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_31343143_3   1655 TCAATACAGTATGATGTTGCTGGAGGGATAGACTCATAGACCAAATGAAA 1704
                             v     i  i ii  viiv i        vi     i   -  i  
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA-TGGAA 305

  chrX_31343143_3   1705 CAGAATAGAGAACCCAAAAACAGACCCATGCAAATGTGCCCAACAGATTT 1754
                         i     v    ii   i   i i      i  vv i  vi   iv     
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_31343143_3   1755 TTGATAAAGTTGCAAAAGCAATTCAATAGAGAAAGC-TCACCTTTTCAAC 1803
                          i  i  i v   v  ii v       i i     v- vii         
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_31343143_3   1804 AAATGGTCCTGCAGA-AATTGGACATCCCTAGAGTGGGAAAAAAAAAGAA 1852
                                v   -i  -  i    i ?  vi ---  v--    i  v   
  L1M4_orf2#LINE/    406 AAATGGTGCTG-GGACAACTGGATAKCCACA---TGC--AAAAGAATGAA 449

  chrX_31343143_3   1853 CTTCAACCTAAATCTCACACCTTGTA-AAAACTTAATTCAAAATAGATCA 1901
                         v  vi   ivv i        v i  -    v    i       i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_31343143_3   1902 TGGACTTAAATGTAAAACATAAAACTATCAAAAT-TTAGGGAAAAAT--- 1947
                         ?i   i         i vv         v   v -    iii    i---
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_31343143_3   1948 -GAGAAAATCTTCAGGCTCTAGGGCTAG--AAT-------------TGGC 1981
                         - ? v        iv vi  v   i   --   -------------  i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_31343143_3   1982 ATTGAAAGCATGATCCACACACAGAAAAAA---ATCAGTTGGACTGCATC 2028
                          iii      ii v v   v -        ---  v i       v    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAA-AGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_31343143_3   2029 AAGATTTAAAACCTTTGCACTGCAAAAGAC-CTGTGAGGGAGGATGAAAA 2077
                           i   v     i    ii  v    i   -  i v i i i -      
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG-TGAAAA 697

  chrX_31343143_3   2078 GACAAGCTACAGACTGATAGAAAATATTTTCAAGCCATATAGCCAA-AAG 2126
                              v i     v  iv           v   ii      v ii -   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_31343143_3   2127 ATGGA----TGTCTAGAATATATAAAGAACTCTCAAAACTGCAAGGTAAA 2172
                         --   ---- i  i                   i v    -   --   v
  L1M4_orf2#LINE/    748 --GGACTTGTATCCAGAATATATAAAGAACTCTTACAACT-CAA--TAAT 792

  chrX_31343143_3   2173 ACAAGAAACAAACAATGCAATTAGGAAATGGGCAAGACACATCAAGAAAC 2222
                          -  i i     i  iv     ?ii          iiv iv v  v i  
  L1M4_orf2#LINE/    793 A-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_31343143_3   2223 GTTTCACCAAAAAGGATATACAGATAGCAAATAGGTGCATGAAAAGATTA 2272
                         i    v     i i        i  i  v    i ii           vv
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_31343143_3   2273 TCAAAAACATTAGCCAT 2289
                             v v  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.03 (23 / 901), avg. gap size = 2.13 (49 / 23)  


3009 23.12 5.45 0.97  chrX_31468680_31472889     2884  3709 (501)    L1M4_orf2#LINE/L1        1   863 (45)  

  chrX_31468680_3   2884 TGGAAAGAT-TTCTGTGTTCATAAATTGGAAAAATTAATATTGTTAAA-- 2930
                                  - i ii       ii       i v             i--
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_31468680_3   2931 --CA--------TAAAGCAATCTAAAGATTCGACACAATAC-TAACAAAA 2969
                         --  --------i   vii     v      i  i    v -  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_31468680_3   2970 TCTGCATATTG--TTCTTTATAGAATTTTTTTTAAAAA----ATCCTAAA 3013
                           i-  -ii  --  i   ii    v  -----i v  ----        
  L1M4_orf2#LINE/    101 TCC-CA-GCTGCCTTTTTTGCAGAAATT-----GACAAGCTGATCCTAAA 143

  chrX_31468680_3   3014 ATTTGCATGGAACCACAAAAGACCCTGGATAGCCAAAGCTGTCTTTACTA 3063
                            iii      vii   ii     v i         i vi    v vv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_31468680_3   3064 AAAAGAATAAAATTGGAAGTATGTCACTACTGGATTTCAAAATGTATTAC 3113
                          i     i   i     i vv vv    v ivi         iv  i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_31468680_3   3114 AAAGCTATAATAATCAAAACAGCATGGCAAGTACATAAAAACAGAC---- 3159
                                i i       i    ii   i vvvi     ii i    ----
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_31468680_3   3160 ----CAATGGAATAAGACAAAGAGGACTAAAATAAACCTACACACCTTTG 3205
                         ----          ii ivi    vv vi         i i   ii v  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_31468680_3   3206 ATCAATTGATTTTTGACAAAGGTAGCAAGAACACACAATAGGGAGAGGAC 3255
                         i            i     i   iv     v  iv    i    i  i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_31468680_3   3256 AGTCTCTTCAATAAATGGTATTGGGAAAACTGAATGTTCACATACA---G 3302
                              i     i       ii     v     i  i?i     i  --- 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_31468680_3   3303 AATAAAACTGGACCCTTATCTCACCCCTTATACAAGAATCAACTCAAAAT 3352
                            i  ii       i  i     v  v       i   i          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_31468680_3   3353 GGATTAAAGCCTTAAATGTAATACCTGAAACTA-AAAACT-----ACAAA 3396
                             i ?  v i         v v  i      -      ----- vi  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_31468680_3   3397 AACATAAGAGAAGAGCTCCATGACATTGGTCTGGGCAGTGGTTTCTTGCA 3446
                               i ? v i v  i i    v    vi i    i         iv 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_31468680_3   3447 TATGACCCCCAAA-CACAATCAACACAA----AAATAGGTAAGTAAGATT 3491
                               v  v   -     v     v  ----      i   i vi  i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_31468680_3   3492 GCATCAAA-CTAAAAAGCTTTGCACAGCAAAGGAAACAATTAATGGAATA 3540
                         v       -i      vi    ii vv       v  v  i  vii i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_31468680_3   3541 AAGAGACAACCCACAGATTGGGAGAAGATATTTGCAAATCATACATTAGA 3590
                           i              v        i                i  iv  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_31468680_3   3591 TAAGGTGCTAATATCCAAAATATACAAGGAACTCAAGCTACTCAATAACA 3640
                              vi  vi      i      i  i      vvi v         i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_31468680_3   3641 AGAAAACAAATAACCCTAATAAAAAAATGGGCAAAT-ATATGAATAGACA 3689
                          i  i           -   v?             v-  v          
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_31468680_3   3690 TT-CTCAAAAGATGACAAACA 3709
                           -   v     v  i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.75 (119 / 68)
Gap_init rate = 0.02 (19 / 863), avg. gap size = 2.79 (53 / 19)  


1563 27.98 2.78 1.79  chrX_31620741_31623099.rev      652  1155 (1204)    L1M4_orf2#LINE/L1        1   509 (399)  

  chrX_31620741_3    652 TGGAGAAACATTCCATGTTAATGGAAAGGAAGAATCAATATCATTAAAAT 701
                             i i i  i       v     vv      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_31620741_3    702 GGACATACTGCTTAAAGCAATCTACAGATTCAATGCTATTCCTATCAAA- 750
                           vv     v ii   vii              i  v  i         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_31620741_3    751 --CTAGCAATGTCATTTTTCACAGAATTATAAAAAACT-ATCCTAAAATT 797
                         -- i   --  i -     ii     v - i v  i  -           
  L1M4_orf2#LINE/    101 TCCCAGC--TGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATT 146

  chrX_31620741_3    798 CATATG--AATCTAAAAAACAGTCTGAAGAGTAAAAACAATGCTAAGTGA 845
                               --   vi  iii  --i v   v  iv        vi i ivi 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_31620741_3    846 AAAGAATAAAGCATG--------ATATTAACCAACTTCAAACTATACTAT 887
                         i     i    i-  -------- i i vv    i      viv     i
  L1M4_orf2#LINE/    195 GAAGAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_31620741_3    888 AAGGCTACAGTTACCCAAAGAGAATGGGACTTCTACAAAAACAGAAACTT 937
                           i        v i v i v  vi   v   vvi i  ii i   v iv 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_31620741_3    938 GGACCAGTAGAACAGAATAGAGAACTCAGAAATAAAGCCGCATACCTACA 987
                         i  i  i i   i     v    iii          v  ii i ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_31620741_3    988 GCCATCTGATCTTTAACAAAGTAAACAAAAAAAAAAAAAATGGGGAAAGG 1037
                          i  vi    i  ii    i vviv   i vv vvv  --         i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGA 391

  chrX_31620741_3   1038 ACTCCCTACTCAATAAACGGTGCTGGGATAGCTGGCTAACCGTATCCAGA 1087
                          ivvi  vi    i   i          i i    v  ?  ii  v  i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_31620741_3   1088 GGAATGAAACTGGACTCCTACCTTTCACTATATACAAAAATTAACTCAAG 1137
                         i       ii     i       iv   i                    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_31620741_3   1138 ATGGATTAAAGATTTAAA 1155
                               i ?   ii    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAA 509

Transitions / transversions = 1.96 (92 / 47)
Gap_init rate = 0.02 (10 / 509), avg. gap size = 2.30 (23 / 10)  

 894 28.90 3.07 1.53  chrX_31620741_31623099.rev     1478  1868 (491)    L1M4_orf2#LINE/L1      512   908 (0)  

  chrX_31620741_3   1478 TAAAATCTCAAACTAGAAGAATCGCAGAAGAAAACCTAGGAAATACTATT 1527
                            i v  v      v  i v  vi          v    ?ivv v v  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_31620741_3   1528 CTGGACATCAGCCTTCAGAAA-GAATTCATGACTAAGTCCTTAAAAGCAA 1576
                          vv   v ii v-  vi v  - iv   v iiv  v v vii       v
  L1M4_orf2#LINE/    562 CGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_31620741_3   1577 ATGTAACAAAACCAAAAATTAACAAGTGGGATCTAATTAAACTAAAGAGC 1626
                          v i       vv      vi i  i v   ii v  i   v v  i i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_31620741_3   1627 TTCTACACAGCAAAAGAAACTATCAACAGAGTAAACAGACAACCCACAAG 1676
                           i iii vv    i  v        v i   i  v            ii
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_31620741_3   1677 ATGAGAGAAAATATACACAAACTATCCATCAGACAAAGATCTAATATCCA 1726
                            i          vii    ii  vi   v  i  i iv  vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_31620741_3   1727 TAATCTATAGGGAACTT---------AACAAGCAAAACGCAGATAACCCC 1767
                         v   v    ii     i---------  i  vv    vi  i       v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_31620741_3   1768 ATGTAAAAAGTGGGCAAAAGACATGAATATATAGATACTTCTCAAAAGAA 1817
                           - ?    i        i  iv      ----  i i     v      
  L1M4_orf2#LINE/    811 AT-TWAAAAATGGGCAAAGGATTTGAATA----GACATTTCTCCAAAGAA 855

  chrX_31620741_3   1818 GACAAACGGGTGGCTAACAG--ATATGAAAAAATGCTCCACATCACTCAT 1865
                           i v  iii    i  i i-- i       i      v      ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_31620741_3   1866 CAT 1868
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.18 (60 / 51)
Gap_init rate = 0.02 (6 / 397), avg. gap size = 3.00 (18 / 6)  


3148 22.88 2.74 1.79  chrX_31833485_31836770     1955  2793 (493)    L1M4_orf2#LINE/L1       62   908 (0)  

  chrX_31833485_3   1955 CCAAACC-ATCTACAGATACAGTGTAATTCCTATCATAATCCCAATCGCA 2003
                              ii-          v  ii i   i       v       iii  v
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chrX_31833485_3   2004 TTTTTTACAGAAAT----AAGGTAAATTTCCTAAAATTCATATGAAACCA 2049
                               i       ----   v i ---                i  vii
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGA---TCCTAAAATTCATATGGAAATG 158

  chrX_31833485_3   2050 CAAACGACTCCAAATAGCCAAAACAGTCTTGAGGAAGAAGAATAAA-CTG 2098
                            iv   i vi             i      ii        i   -i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_31833485_3   2099 GAGGCATCACACTTGCTAGTTTCAAAATGAATTACCAAAGCTACCTCAGT 2148
                             vv        v i i        ivv i   -        vvi i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTAC-AAAGCTACAGTAAT 257

  chrX_31833485_3   2149 CAAGAGCGCACGATAGTGTCATAAAGGCAGACATATAGACCAATGGAACA 2198
                              vv iii i  v  v     i ii           i        i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_31833485_3   2199 GAATAGAGATCCCAGAAATAAACCTA-GCATC------------ACCTTC 2235
                             v    vi             i -i   i------------ ii   
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_31833485_3   2236 AATAGGGGTGCCAAGAATACACAACTGGGAAAGGATATCCTCTTCAACCA 2285
                         i i i           vi iv   iv       i   vi  i      v 
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_31833485_3   2286 ATGGTGCTGGGAAAACTGGATATACACATTGCAAA-GAATGGAATTGGAC 2334
                                     v         ?v     -     -     i i      
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAATGAAGTTGGAC 456

  chrX_31833485_3   2335 CTTTAACTTAAACTATACATAAAAATCAACTCAAAATGAAATGGAGTAAA 2384
                          ii  v  i v  i   i i      i           -----  vi ? 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATG-----GATCAWA 501

  chrX_31833485_3   2385 GACTTAAAAATAAGATCTGAAACTATGAAACTCATAGAAGAAAACATAAG 2434
                            i    vi     v  i       i      v              i 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_31833485_3   2435 GGAAAAATTTCCTGACATTGGTCTTCACAATAATTTTTTTTGGATATGAC 2484
                         ? v   vi   v    v    vi vvi    ii   i  --i        
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--AGATATGAC 599

  chrX_31833485_3   2485 GCTAAAAGGACAGCCAACAAAAACAAAACTAGATAAGCAGAAATATATCA 2534
                         i i     v   iv        iv    v       iiv i v vi    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_31833485_3   2535 AACTAAAAAGCTTCTACAAAGCAAGGGAAACAATCAACAGAATTAAAAG- 2583
                           v v    i   i iiivvv   i   v  v     v i i v     -
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_31833485_3   2584 CAACCTATAGAATGAGAGAAAAGGTTTGCAAACCATATATCTGATAAGGT 2633
                              i i      i       vi        i                v
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_31833485_3   2634 GTCAATATCTAAAATACATGAGGAACGTAATAACAAC--AACAACAAAAA 2681
                         iiivi    i i    i  i i    vi-- v     --  i  i     
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCAATAATAAAAA 797

  chrX_31833485_3   2682 TTCGAACAACCCAATTTTTAAAGTGAACAAAGGAATTGAATAGATATTTC 2731
                         vv i  i         ?v-   i  ii       v         i     
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_31833485_3   2732 TCCAAAGAAGACATTAAAATGACCAACAGTTATATGAAAAGATGTTCAAC 2781
                                    i  vv     i    i ivi i           i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_31833485_3   2782 ATCACTAACTAC 2793
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (120 / 68)
Gap_init rate = 0.02 (15 / 847), avg. gap size = 2.53 (38 / 15)  


2598 26.75 1.04 0.65  chrX_32151330_32153095.rev      506  1275 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_32151330_3    506 ATTCTAAAATTCATATGGAACCAAGAAAGGG--CCTGAACAGCTAAAGCA 553
                           i                 -- v v     --  v   i   i   i  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_32151330_3    554 ATCCTAAGCCAAAAGAACAAAGTTGAGGGCATTACATTGCCCCACTT-AA 602
                            i i ivv i             ii  vv i   i v   v i  -  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_32151330_3    603 AATATACTACAAAGCTGTAGTAACGCAAACAGCATAATACTATTACAGAT 652
                           iv            ii     ivv i    ii ii    ivi i iiv
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_32151330_3    653 ATAGACACCTAGATCAATGGAACAGAATAGAGAACTCAGAAATAAAGCTG 702
                                iv             i     v    iii          v ii
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_32151330_3    703 CACACCTACAACCAACTGATTTTTGACAAAGTTGGCAAAAATAAGCAACA 752
                         i   ii  iiii   i       i     i v  v   i vi vv   ii
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_32151330_3    753 GAGAAGGGACACCTTATTCATTAAATATTGCTAGGATAGCTGGCTAGCCA 802
                          i   i i i vii v    vi    iv    i   i i    v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_32151330_3    803 TATATAGAGGAATGAACCTGGACCCCTACCTTTCACCATATACAAAAATT 852
                         i  ii i i       vi             iv                 
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_32151330_3    853 AACTCAAGATGGATTAAAGTCTTAAATGTAAGCCCTGAAACTACTAAAAA 902
                                i      i ?  v i          vv  i      -     v
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA-TAAAAC 532

  chrX_32151330_3    903 TCCTAGAATAAAACCTAGGAAAAGTTCTTCTGGACACTGGCTTAGGCAAA 952
                           i     v     v    ?iv iv     vv   vi   v        v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_32151330_3    953 GAATTTATGACCAAGACCTCAATGACAAATGCAACAAAAACAAAAATTGA 1002
                          iv  iv iivi v   vi   vii  v v         iv      v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_32151330_3   1003 CAAATGAGAGTTAATTAAA-TTAAAG-CTTCTGTACAGAAAAAGAAACAA 1050
                         i    vi  v  v  i   -     i-   i   i vvv   i  v  v 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_32151330_3   1051 TCAACACAGTAAACAGATAACCTCCTGAATGGGAGAAAATATTTGCAAAC 1100
                             v v   i  v   i    iv v                       i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_32151330_3   1101 TTTGCATCTGACAAAAGAATAATATCCAGAATCTATAAGGAACT--TA-A 1147
                         iv ii      i  ii  v vi          v     i     --  - 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_32151330_3   1148 ACTTGTCAACAAGAAATTAAAAAAAAACAGATTAAAAACAGGACAAAGAA 1197
                            iivi  i  i  i-- v   v  v vi   ?    vv  i     i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAG--ACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_32151330_3   1198 CGTGAATAGACACTCCTCGAAAGAAGACATACAAGCGGCCAATGAGCATA 1247
                         iv          i i   v        i      ii       i    i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_32151330_3   1248 TTAAAAAATCTTCAATATCACTAATCAT 1275
                          v    i  vi    i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (122 / 80)
Gap_init rate = 0.01 (9 / 773), avg. gap size = 1.44 (13 / 9)  


2791 25.45 1.91 0.51  chrX_32175967_32177766      522  1307 (493)    L1M4_orf2#LINE/L1      112   908 (0)  

  chrX_32175967_3    522 TTCTTCACAGAAATAGAAAAAACAATCTTAAAATTTATATGGAACTGCAG 571
                           i  ii       v  v  ivii   i       i        v    i
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_32175967_3    572 CAGACCCAGAATAGCCAAATATATCCTAAGCAAAAAAGAATGAAACTGGA 621
                         vi                 vvv   i i i-   i     ii  ii    
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAACAAAGTTGGA 210

  chrX_32175967_3    622 GGAATCACTTTACCTAACTTTAAATTATACTACACAGCTATAGTAACCGA 671
                            v    vi v  i  i  i   viv       v     i     i i 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_32175967_3    672 AACAGCATGGTACTGGCTTAAGCGCAAACACACAGCCCAATAGAACAGAA 721
                         i    ii          v    vii i   i i  vi    i   i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_32175967_3    722 TAGAGAACACAGAGATAAATCCATACATCTACAGGGACCTAATTTTTGAC 771
                          v    iiv    i     i        i  ii vv vi i     i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_32175967_3    772 AAAG-TGCCAAGAACACACTTTGGGGAAAGGA--GTCCTT-CAATAAATG 817
                           i -        v  iv vv         i --   i  -   i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_32175967_3    818 GTGCTGGGAAAATTGGATATCCAAATGCA---GAATAAAACCAGACCTCT 864
                                  v  i      ?   v     ---    i  iiii    i  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_32175967_3    865 ATCTTGAACCGTATACAGAAATCAAATCAAAATGGATTAAATACTTAAAT 914
                          i  iiv   i      i    i  v           i ? v  i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_32175967_3    915 CTAAGACCTCAAATTATGAAACTACCACAAGAAAACTTTGGGAGAAACCT 964
                         v     v  v   i   i     vii v        v v  ?iv   i  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_32175967_3    965 CCAGAACATTGGTCTAGGCAAGAAATTCTTGAACCATACCA-CACAAGCA 1013
                         i ivi  v    vi       viiv     ii -i  iv  -  v     
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCA 609

  chrX_32175967_3   1014 CAGGCAACCAAAGCAAAAATGGACAAATGGTAACACACC-AAGTTAAAAA 1062
                           i     v    v      i  i    v v viv  i -  i       
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_32175967_3   1063 TCTTCTTCACAACAAAGCATACAACCCACAAAGTGAAGAGACAACCCATG 1112
                         -   i vii vv     v i  v i v v        i          ii
  L1M4_orf2#LINE/    660 -CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_32175967_3   1113 GAATGGGAGAAAATATTTCCAAACTACCCATCTGACAAGGGATCAATAAC 1162
                                           v    ii ivi      i      iivi  v 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_32175967_3   1163 TAGAATATATAAAGAGCTCAAACAACTCTATAGGAAAAA-ACTAATAATC 1211
                         i              i   vv       v   iv     -  v     i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_32175967_3   1212 TGATT-AAAAATGGGCAAAATATCTGAATAGACTTTTTTTTGAAAGAAGA 1260
                         ii   -             iv  i         v   i ii-        
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC-AAAGAAGA 857

  chrX_32175967_3   1261 TA----AATGACAAACGGGTATATGAAAAGGGTCTCAATATCACTGATCA 1306
                           ----    i v  iii i i        ivv     i    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_32175967_3   1307 T 1307
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.70 (124 / 73)
Gap_init rate = 0.02 (13 / 797), avg. gap size = 1.46 (19 / 13)  


1921 26.35 3.97 2.41  chrX_32202966_32204664      501  1206 (493)    L1M4_orf2#LINE/L1      192   908 (0)  

  chrX_32202966_3    501 AAAGAAATACAGCTAGT-GGAGGCATCATGTTAGCTGACTTCAAACTATA 549
                               iv   i--   -     vv   iii vv ii i      viv  
  L1M4_orf2#LINE/    192 AAAGAAGAACAA--AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_32202966_3    550 CTACAGTGCTACAGTAACCAAAACAACACAGTACTGGTACAAAAACAGTC 599
                              iv          i   i   iiiii       i i  ii i  v 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_32202966_3    600 ACATAGACCAATGAAACAGAATGGAAAGCCCAGAAATAATGCCACACACC 649
                          i     i     i  i     v  i  i          vv   i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_32202966_3    650 TATACCCTTCTGATCTTCGACAAAGCCGACAAAAGCAAGCAATGAGGAAA 699
                            ivi vvi    i        i vi v   i v  vv     i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_32202966_3    700 GGACTCCCTATTCCATAAATGGTGCTGGGATAACTGGCTAACCGTATACA 749
                          i ivvi  v   v i              i      v  ?  ii  i  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_32202966_3    750 GAAGAATAAA-----------ACCTTACACCATATACAAAAATCAACTCA 788
                         i      i  -----------    i                 i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_32202966_3    789 AGATGAATGAAAGACTTAAAATGTCAAAGC-AAAACTTTAAAAACCCTGG 837
                          i   i  v ?    i    -   v i   -      v     vi i i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_32202966_3    838 AGGATAACCTAGGCA-ATACCATCCTGGACATAGGAATGGGAAAAGATGT 886
                          i  v   v    ?i- v i v  v  -  v v  iv i  v  v i v 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTT 587

  chrX_32202966_3    887 ----AATGATGATGTCAAAAGCAATTGCAACAAAAGCAAACACTGACAAA 932
                         ----i  -    iii        vvv          v   v iv  i   
  L1M4_orf2#LINE/    588 CTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_32202966_3    933 TGAGACCTAATTAAA-TTACACAACTTCCTCACAGAGTTCCTCTGTTGAA 981
                          vi   i v  i   -   v -     ii-------  v i  viv- i 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAA-AACTTTT-------GTGCTTCAAA-GGA 677

  chrX_32202966_3    982 CTCTGTCAACAGAGTAAACAGACAAACTACAGAACGGGAGAAA-TATTTT 1030
                          v  i    v i   i  v      v i      i        -     -
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT- 726

  chrX_32202966_3   1031 GCAAACTGTGAATCTGATAAAGGTTTAACATCCAGAATCTCTAAGTAACT 1080
                              iii iv         i  vi vii         v v   iv    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_32202966_3   1081 TAAACAAATTTATTTTAAAAACTC---TACTCCA--TTAAAAATGGGCAA 1125
                         ivv    v iv  vv      vv ---  vi   -- ?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_32202966_3   1126 AGGACATGAACACACATTTTTCACAAGACGACACACATGTGGCCAACAA- 1174
                             iv    i v      i  vv    v  i i   vi       i  -
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_32202966_3   1175 --TATGAAAAAAAATGCTCAATATCACCAACCAT 1206
                         --i       i --       i    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (105 / 77)
Gap_init rate = 0.03 (19 / 717), avg. gap size = 2.37 (45 / 19)  


1879 28.23 8.90 1.19  chrX_32327545_32331100     2221  3063 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_32327545_3   2221 TGGAAAAATATTCTATGCTCATGGA-----AGAATCAATATTGACAGAAT 2265
                               i    i i   i       -----   v i       vi ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_32327545_3   2266 GGCCATAATGCCTAAAGCACTTTTTA-ATTCAATGCTATTCCCAAAAAAC 2314
                            v   v v  i   viiv i vi -      i  v  i  i vv   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_32327545_3   2315 TACCAATAACATTCTTCACTGAATAAGAAAAAGACT-ATTTAAAAATTCA 2363
                          v   iivi v  i  ii v   - vvi v   -  -  iiv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_32327545_3   2364 GTTGGAGCCACTAAAAGAGCCAGAATAGCCAAGGTAATCCTAAGCAAAAA 2413
                         vv    ivii -  ii  v             iii    i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_32327545_3   2414 GAAAAAAGCTGGAACCATCCCATTGCCTGACTGCAAACTATACTACAAGG 2463
                            v    i    ivvv  v  i v  ii i v    viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_32327545_3   2464 ATATAGTAACCAAAACAGCATGGTAC----A-AAAAACAGACACATAAAC 2508
                         v  i     i   i    ii      ---- -  ii i     i   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_32327545_3   2509 CAATGGAAAAGAATAGAGAGTCGAGAAATAAGGCTGCACACCTACAACCA 2558
                                 v     v       v        iv iii   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_32327545_3   2559 TCTGTTCTTCAATGAAATCAACAAAAACAAGCAATGGGAAAAGGACTGCC 2608
                         vi  v i   i ii iiviiv   i v  vv       i    i iv i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_32327545_3   2609 TATTCA-------------------------------------------- 2614
                          v    --------------------------------------------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_32327545_3   2615 ---TTGGACCCCTTCCTTACACCATATACAAAAATTAACCCGAGGTGGAT 2661
                         ---          v   i                     i i ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_32327545_3   2662 TAAAGACTTAAATCTAAAACCAACAACTATAAAAACCTAAGAAGATAACC 2711
                         i ?    i     v   i v v v          vi  v      v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_32327545_3   2712 CAGGT---AATGCCACTCTG-GACATTGAAACT--GCAAAGACTTCATAA 2755
                         i   ?---   ----  ii -   v   ii-i --    v ii   v  i
  L1M4_orf2#LINE/    548 TAGGNGTAAAT----CTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAG 592

  chrX_32327545_3   2756 CAAAGACACCAAAA--ACAATTGAAACAAAAACAAAAATTGAAAACTGGG 2803
                         vv v          --    -- v       iv      v  v  v v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_32327545_3   2804 ACCTAATTAAACTAAAGAACTTCTACACAACAAAAGAAACTATCAACAGA 2853
                           i v  i   v v  i     i iii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_32327545_3   2854 GTAAACAGACAACCTGCAGAATGGGAGAAAAATTTTGCAAACTTTCCATC 2903
                           i  v        ii               vv        iiv vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_32327545_3   2904 TGACAAGGGTCTAATATCTGGAATCTACAAGGAACT--TA-AATTTA-CA 2949
                            i     v  vi    ii    v  i  i     --  -  i i -i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_32327545_3   2950 AGCAAAAACCAAACATCACCATTAAAAAGTGGGCAAAGGACATGAAC--- 2996
                          vv    iv    i v v v   ?    i           iv    i---
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_32327545_3   2997 CCTTTC-CAGAAAAAGACATACATACAGAAAACATTCATATGAAAAAATG 3045
                          v    - vi  i    i     v ii vv  i vv  i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_32327545_3   3046 CTGAACATCAATAATCAT 3063
                           v       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.05 (85 / 21)  


2039 28.68 2.40 0.00  chrX_32332841_32334499      501  1166 (493)    L1M4_orf2#LINE/L1      227   908 (0)  

  chrX_32332841_3    501 ACTTCAAACTATACTACAAGGTTACAGTCACCAGAAAAGCAGGGTACTGG 550
                          i      viv        i i      v i  ii v  iiv        
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_32332841_3    551 TACAAGAACAGACACATAGACCAATGAAACAGAATAGAGAACTCAGAAAT 600
                         i i   i i     i     i     i  i     v    iii       
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_32332841_3    601 AAGACCACGCACCTACAACCATCTGATCTTCGACAAACCTGAAAAAACAA 650
                           iv   ii  ii  iiii  vi    i        ivv  vv  i  v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_32332841_3    651 -GCAATGGGGAAAGGACTGCCTATTTAATACATAGTGCTGGGA------- 692
                         -v            i iv i  v  i  i v  i         -------
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_32332841_3    693 -TAGTCCTATGCAGAAAATTGAAAGTGGACTTCTTCCTTACAATCTATAC 741
                         -  ?i vi     i  i v    iv     ii  v   i   viv     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_32332841_3    742 AAAAATTAACTCAAGATGGATTAAAGACTTAAATGCAAAACCCCAAACAA 791
                                       i      i ?    i      i  i v iv    v 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_32332841_3    792 TAAAAACCTTAGAAGAAAACCTAGGTAATAAGATTCAGGACATAGGCATG 841
                              vi             v    ?ivv  vv   iv   v v  vv i
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_32332841_3    842 GGCAAAGGTTTCATGAGGAAAATGGCAAAAGCAACTGCAACAAAAGCAAA 891
                              v      v iiiv vi iiv        vvv          v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_32332841_3    892 AACTGACAAAGGGGATCTAATTAAACTAAAGAACTTCTGCACAGCAAAAT 941
                           iv  i   vv   ii v  i   v v  i     i  ii vv    iv
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_32332841_3    942 AAACTACCGTCAGAGTAAATAAACAGCCTACAGAATGGGAGAAAAGTTTT 991
                          v    i ivv i   i  v i   i  i                vv   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_32332841_3    992 GCCATCTATCCATCTGACAATGG-------TCCAGAGTCTACAAGGAACT 1034
                           v vii  vi      i  v  -------      i v  i  i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_32332841_3   1035 TAAACAAATTTACAAGAAAAAAACAAATAACCTCATTAAAAAGTGGGCAA 1084
                         ivv    v iv i  v     i          iv   ?    i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_32332841_3   1085 AGCACATAAACAAACACTTCTCAAAAGAAGACATACATGTGACCTAAAAC 1134
                           v iv i  i i   i     v        i     vi  i  v v  v
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_32332841_3   1135 GATATGAAAGAAAACTCAACATCATTGATCAT 1166
                         v i      ii vi          ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (106 / 81)
Gap_init rate = 0.00 (3 / 682), avg. gap size = 5.33 (16 / 3)  


2652 25.28 4.23 3.12  chrX_32380294_32384079     2396  3293 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_32380294_3   2396 TGGAAAAACTTTCCCTGCTCATGGATTGGGAGCATCAATATTGTTAAAAT 2445
                               i iv i  v  i           i  vv i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_32380294_3   2446 AACCACACTGCTCAAAGCAATTTACAGATTGAACACAGTCCTTAT-AAAT 2494
                         ii v i   v i    vii  i        v   i  i   i   -   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_32380294_3   2495 TACCAACATCATTTTTCACAGAATTAGAAAAA--GATAGTAAAATACATA 2542
                          v   i vv v     ii     v v  v  i--   vv      v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_32380294_3   2543 GAGAATCAAAAAAGAGCCCAAATAGTCAAAGCAATGCTAAGCAAGAAGAA 2592
                         vi   viiv  ii  v  vi     i    i    vi i iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_32380294_3   2593 TAAAGTTGAAGGCATCACATTACCTGACTTCAAATTATACTAAAAGGCTA 2642
                         i       i   vv     i v  ii i      viv     v  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_32380294_3   2643 CAGTAACCAAAACAGTATGGTACTGGTATAAAAACAGATACATATAGATT 2692
                               i   i     i         i    ii i   --         i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA--CATATAGATC 298

  chrX_32380294_3   2693 GATTTAACCAAATTAAGAACCCAGATATAAAACCACATATCTATGACCAA 2742
                         i  vv  ivi    i   ii     v     v   i i  i    ii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_32380294_3   2743 CACATCTTTAACAAAG-TAAAAAAATGTATATATACACTGGGGAAAGGAC 2791
                         ivv  i  ii    i - ivv  i i-----i  v  v         i i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGAC-----CATTCAATGGGGAAAGAAT 393

  chrX_32380294_3   2792 ATCCTATTCAGTAAATTGTGCTGTAAATATTGGATAGTCATAAGCAGAAG 2841
                          vi  v    ii    v      vi vv i      ?i  i v   i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_32380294_3   2842 AATGAAACTGGGTCA-TAAATCAC--CATATACAAAAATTAACTCAAAAT 2888
                               ii   ii v-  vv    --                        
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_32380294_3   2889 GTATTAAAGACTTAAATGTAAGACCTGAAAATATAAAAATCCTAAAAGAA 2938
                          v  i ?    i           v  i   v       v  i  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_32380294_3   2939 AACCTAGGAAAAACTCTTCTCGACACTGGCTTGGGCAAAGAATT------ 2982
                            v    ?iv  v     vi   vi   v  i     v iv  ------
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_32380294_3   2983 TATGACT----AAGTACT-----CAAAAACAAAAGTAGACAAATGGAACT 3023
                               v----   i  v-----     iv    i    i    v i   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_32380294_3   3024 TAATT----TTAAAATCTTCTGAACAGCAAAAACAAACAAACAAAAAAAC 3069
                          v  i----      v   i  vi vv    ii---------------  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGG---------------AC 678

  chrX_32380294_3   3070 AAAAAACAATCAACAGAATGAACAGACAACTTATAGAATGG---AAAACA 3116
                          ----- v     v i i    v       ii i       ---    i 
  L1M4_orf2#LINE/    679 A-----CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_32380294_3   3117 ATTCCGAACTATACATCTAACAAAAAACTAATATCTAGAATCTA-AAAG- 3164
                         v  v i  ii   i    i i  iii   vi    i     v  -    -
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_32380294_3   3165 -------TAACTCAACAAGAAGAAAAATAGATAACCCCATTAAAAAGTAG 3207
                         -------i       i  v  -   i i i       v   ?    i i 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_32380294_3   3208 GCAAAGGACATTAGCAGACATTTTTTAAAAGAAGATATACAAGTGGCCAA 3257
                                 iv v ii        i iv               i       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_32380294_3   3258 CAAACATATGAGAAAATGCTCAACATCACTAATCAT 3293
                         i  i  i    i  i             ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (137 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.88 (66 / 17)  


2035 25.95 3.03 2.58  chrX_32394604_32396254      500  1158 (493)    L1M4_orf2#LINE/L1      247   908 (0)  

  chrX_32394604_3    500 GCCATAGTAACCAAGACAGCATTGTATTAGCATAA----AAAC-T---GA 541
                           i i     i        ii v   i i      ---- i  - ---  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_32394604_3    542 TCAGTGGAACATAATAGAGAACCCAGGAATAAATTAATGCATTTGCATTC 591
                            i     i v   v    ii    i      iiv  i     iiiv  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_32394604_3    592 AACTGATTTTGGACATGGGTGTCAAGAACACACCGTGAGGACAGGACACC 641
                           i       v    v     i     v  iv vi  i   v  i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_32394604_3    642 CTCTTCAGCAAATGCTACCAGGAAAAGTAAGAATCTACATGCAGAAGAAT 691
                           i    i      v i ii   v  v iiiv ? i       i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_32394604_3    692 GAAATTAGACCCTTATCCCTTGCCACATACAAAAACCAATTTGAAATGGA 741
                            i  i     i  i i vii   i         ii  i ii       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_32394604_3    742 TTAAAAACTTAAATTTAAGACTCAAAACTCTCAATCTATTAGTAGAAAAC 791
                          i ? i  i     v     vii      v v  v  v    v       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_32394604_3    792 ATAGAGGACAAGCTTCATCACAATTATTTGGGCAATAACTT-TTGAATAT 840
                             i? vv  v    i v  vv viv  i      iii  -  ii    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_32394604_3    841 GACTGTAAAAGCACAAGCAACAAAAGCAAAAATAGACTGA--GGACTT-A 887
                            vvi                    v         ivi --      - 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_32394604_3    888 TACCAAACTAAAAATTTCTGCACAGCAAAAAA-ATTAAAATTAAAATTAA 936
                          - v   i      i  i  ii vv    ii - i  --------- i  
  L1M4_orf2#LINE/    647 T-CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA---------TCAA 686

  chrX_32394604_3    937 AAATTAACAGAGTAAAGAGATATCCAATAGAATGAGA-AAAATATTTGCA 985
                         i  -------   i  i   i v  v i      i  -            
  L1M4_orf2#LINE/    687 GAA-------AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_32394604_3    986 AACTATATATCTGATGGGGG-TTCATATA-AAAATATGGAAGAAATTCAA 1033
                           ii           ii   -i ii   v- i     iv  ii  i  vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_32394604_3   1034 CCAACTCCATAGCAAGAAAACAAATAACCTGATT-AAAAATAGGCAAAAG 1082
                         v      v   ii  i  i          ii   -      i      i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_32394604_3   1083 ACCAAAATAGACATTTATCATAAAAGGG---ACAAATGGATAACACAGAT 1129
                          iivi           v  vv  i i i---        vi  i viv i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_32394604_3   1130 ATGAAAAAATGCTCAACAGCACTAATCAT 1158
                                i          v  ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (113 / 55)
Gap_init rate = 0.02 (15 / 662), avg. gap size = 2.47 (37 / 15)  


 375 20.78 0.00 0.00  chrX_32498728_32500494.rev      117   193 (1574)    L1M4_orf2#LINE/L1        1    77 (831)  

  chrX_32498728_3    117 TGGGAAAATATCCCATGTTTGTAGACTGGAAGAAGTAATATTGTTAAAAT 166
                            i  i            ii i  i       vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_32498728_3    167 TTCCATACTACCCAAATGGATATATAG 193
                         vv v     v       v   v  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAG 77

Transitions / transversions = 1.00 (8 / 8)
Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.00 (0 / 0)  

2307 25.70 8.82 1.15  chrX_32498728_32500494.rev      495  1276 (491)    L1M4_orf2#LINE/L1       67   908 (0)  

  chrX_32498728_3    495 TTGACTGTACAAATTTAATGTAATCCCTGTGAAAATCTAAATGGCATTTT 544
                             - v    i   i  i i       i v      iv iiv  v    
  L1M4_orf2#LINE/     67 TTGA-TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_32498728_3    545 TTTTCACAGAAATAAAAGAGC--ATTATAAAACTTACATG-AAAT----- 586
                           ---i       vi vi   --  iv     i i i   -    -----
  L1M4_orf2#LINE/    116 TT---GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_32498728_3    587 ---CCCA-AATAGCCAGAACAATCTTGAGGAAAAA----AAAGTTGGAA- 627
                         ---    -        i           ii  i  ----         i-
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_32498728_3    628 ----ATACTGCTCTTTGGATTTGAAATTATATCATAAATCTACAGTATTA 673
                         ---- i   v i ----i    v   viv  ii i   v        v v
  L1M4_orf2#LINE/    213 ACTCACACTTCCC----AATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_32498728_3    674 AAAAGAGTATTGTAATGCCATAAAAACAGACACATAAACTGATGGAACAG 723
                           i v   i v   v  v     ii i     i   i iii      i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_32498728_3    724 AATAGAGATCTCACAAATAAACCTAAGCCTATATAATCAACTAATTTTGG 773
                            v    vii  v         i vi v v   ii    i i     v 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_32498728_3    774 ACAGGACCACCAAGAAGATATG-TGGGGAAAGGACAGTCTCTTCAATAAA 822
                            i ivii      vv  vii-         i i     i     i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_32498728_3    823 TGGTGTTG---------------------TAAA---------TTGTACCC 842
                              i  ---------------------i   ---------   v    
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_32498728_3    843 TTGTCTTATACTGTACACAAAAATTAAGTGAAAATGGACTAAAGACTTAA 892
                         i ii  i i  ii  i           v v        ii ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_32498728_3    893 ATATAAGACCTAAAATCATAAGACTCCTAGAAGAAAACAGAGAGGAAAAA 942
                           i     v      ii    i    i            v  i? v   -
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA- 557

  chrX_32498728_3    943 GCTCTCTGACAGTCGCCTTTGCAAGGATTTTTTGAATATCACATCAAAAT 992
                         v  iiv    vv v vi vv    v i   i  ii    v   i     v
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_32498728_3    993 TTCAGGCAAGAAAACAAAAA-TAAACTAGTGGAACTACATTAATCTAAAA 1041
                         iv  i    v    v     -  i iv i v i   v   i  vv v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_32498728_3   1042 AGCTTCTG-G----AAAG--------CAAAAGA---AAAACACAGCCTAC 1075
                          i   i  - ----    --------   i i ---    v   i  i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_32498728_3   1076 AGATTATGAGTAGATATTTGCAAAACATATATCTGATAAGGGTTTAATAT 1125
                            v iv   v i           v                 vi vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_32498728_3   1126 CCAAAATATATAAGGAACTTGCACAATTCCATAGTGACAAACTAAATAAC 1175
                            i         i     ivi    i  v   i i v  ivi       
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_32498728_3   1176 CCAATTAAAAAATTGGGAAAGAACTTGAACATTTTTTTTTTCAAAGAAGA 1225
                               ?      v  v    i i     i vviv   i i         
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_32498728_3   1226 TGTGCAAACGGCCAACAGGGAAATTAAAACGTGCTCAATATCACTATTAG 1275
                          i i    i      i i v v  v    vi       i    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_32498728_3   1276 G 1276
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.61 (122 / 76)
Gap_init rate = 0.02 (18 / 842), avg. gap size = 4.33 (78 / 18)  


3193 26.79 0.66 0.55  chrX_32508173_32514451     4880  5786 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_32508173_3   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_32508173_3   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGTCATCCCCATCAAGC 4979
                            v     v     iv i  i           i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_32508173_3   4980 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTG 5026
                          v   i-       i  -i     -   -- v  i  - iii    i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_32508173_3   5027 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCACTCCTAAGCCAAAA 5076
                                 viiv  ii  v  v v  vi    iv  v  i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_32508173_3   5077 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5126
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_32508173_3   5127 CTGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5176
                           i      i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_32508173_3   5177 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACCAC 5224
                                 i    i--    i  --        vv  ii i  i  ivii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_32508173_3   5225 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5274
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_32508173_3   5275 CCTATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGC 5324
                         i  v  i  i          i   v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_32508173_3   5325 TGAAACTGGATCCCTTCCTCACACCTTATACAAAAATCAATTCAACATGG 5374
                             ii    i    v         v           i  i    v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_32508173_3   5375 ATTAAAAACTTAAACGTTAGACCTAAAACCATAAAAACCCTGGAAGAAAA 5424
                           i ? i  i    i  v   v       i      vi i i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_32508173_3   5425 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5474
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_32508173_3   5475 AAACACCAAAAGCAATGGCAACAAAAGCCAGAACTGACAAATGGGATCTC 5524
                         vi            vvi          vv i  iv  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_32508173_3   5525 GTTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTACCATCAGAGTGAA 5574
                         i i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_32508173_3   5575 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5624
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_32508173_3   5625 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5674
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_32508173_3   5675 AA-ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAATT 5723
                           -     i     v  i?    i     i     iv    i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_32508173_3   5724 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5773
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_32508173_3   5774 CATCACTGGGCAT 5786
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2602 23.41 4.94 3.25  chrX_32542331_32544911.rev      794  1562 (1019)    L1M4_orf2#LINE/L1        1   782 (126)  

  chrX_32542331_3    794 TGAAAAGGAACCCCAGGTTTATGAAATGGAACACTCAATATTGTTGTTGA 843
                           i    iv i    v   i   i v     v   i         i--- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA---A 47

  chrX_32542331_3    844 GGTATCCGAGTTACTCAAAACAAACTACACATTCAGTGCCATCTCTAAGA 893
                          i iv vivii v i    vii v     v     ii  v   i   vv 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_32542331_3    894 AAATCCCAATTAGTTTTTCTGCAGAAATAGACAACTCTATCA-AAAATTC 942
                                 ii ivi    i         v     viiv   v-       
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_32542331_3    943 CCATGTAA-TCTCATGGATCCAGGAATAGTTGAAACGATCTTGAAAAA-- 989
                         vi   v  - viv v   i    -     iii    i           --
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAG-AATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_32542331_3    990 AGAATGAAGTTGAAGGG-TCATACGTCCTGATTTCAAAACTTACTACAAA 1038
                             ii      i   i-   i  v   ii                    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_32542331_3   1039 GCTACCATAATCAAAACACTGTGGTATTGGCTTAAAAAAAGGGAATGTAG 1088
                              vi       i   v       i    v   ii v  iv - i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA-TATAG 295

  chrX_32542331_3   1089 AACAATAGAATATAAT----AGCCCTGAAGTAAACTC-TACTATATATTG 1133
                          v    i     v   ----  i  v   i     i -   -  v   v 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC-ATTTATGG 344

  chrX_32542331_3   1134 TCAAACAATTTTCCATAAGGTTGCCAAGGTTTTTTAATGA---------- 1173
                             vii      v i    v       iiiv  i    i----------
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_32542331_3   1174 -TTTTTTAATGAAGCCACAAATGTTGCTAAGA-AACTGAATATATACATT 1221
                         - i    ------- v       v    ii  -     i   ?vi    v
  L1M4_orf2#LINE/    395 GTCTTTT-------CAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_32542331_3   1222 TAAAATAAATGAAGTTGGACTCTTAT---AAA--ATACACAAAAATTAAG 1266
                         i    -i             i i  i--- v --   i           v
  L1M4_orf2#LINE/    438 CAAAA-GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_32542331_3   1267 TCAAAATGGATCA-GGAAGTAAACGTG---GCCAAAAGTACAGAACTTTT 1312
                                      -i  vv    i  i---  i    v  i i    i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_32542331_3   1313 AGAAGAAAGCGTAGACATTTGGAAGAAAA----CATAAACATTAGATTGG 1358
                                 i i   i?i --------   ---- i i v -  i i  i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGT--------AAATCTTCGTGACC-TTGGGTTAG 577

  chrX_32542331_3   1359 GCAATTAAATATCTTGGATATGACACTAAAAGCTCAGGCTACAACAGAAA 1408
                              --ii v    i          i      v  i  v    v     
  L1M4_orf2#LINE/    578 GCAAT--GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_32542331_3   1409 AATTAGGTAAATTGAAATGCATCAACATTAAAAACTTCTGTGCATGAATG 1458
                           v   i       i v v      v           i     v v  v 
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_32542331_3   1459 AACACCATCAG---AGTGAAAAGGCAACTTACGGAATGGGAGAAGATGTT 1505
                         i    i    i---         i    ii  i           i  i  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_32542331_3   1506 TGCGAATCATATATTCAATAGGGAATTAATATCCAGACTGTGCCAAGAAC 1555
                            i          iii   i  i i vi        v i iiv      
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_32542331_3   1556 TCCTATA 1562
                           i  i 
  L1M4_orf2#LINE/    776 TCTTACA 782

Transitions / transversions = 1.83 (115 / 63)
Gap_init rate = 0.03 (23 / 782), avg. gap size = 2.74 (63 / 23)  

 286 26.09 16.30 2.72  chrX_32542331_32544911.rev     1908  2091 (490)    L1M4_orf2#LINE/L1      700   908 (0)  

  chrX_32542331_3   1908 CAACTC-CAACATTGGGGA------TTACAATTCAACATGAGATTTGAGT 1950
                             i -  iv  v  i  ------  i   v   -i  ---  i   vv
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TAT---ATCTGATA 745

  chrX_32542331_3   1951 GGGGAC--ACAGTTAAATTATATCA-----TCGTAGAATTCAACAACAGA 1993
                         i     --ii vii i v     v -----  v  v  i    i  i i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_32542331_3   1994 AAAACAG------CAATTAAAAAAATGAATAAATGAGTTGATCAGAAATT 2037
                           i   i------     ?     -  iii   v  v    vi   v   
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATT 844

  chrX_32542331_3   2038 TCTCTAAAG----T-T-----TGGCCAGTAAGACCATGAGTAGATAATCG 2077
                             i    ---- - -----      i    vv     iv    iv  i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_32542331_3   2078 ATATCGCTGATCAT 2091
                          i   i????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (29 / 18)
Gap_init rate = 0.05 (11 / 209), avg. gap size = 3.18 (35 / 11)  


2538 23.09 8.56 2.11  chrX_32568979_32574138     3815  4667 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_32568979_3   3815 TGGAAAGTCATCCCATGTTTATCGGTCAGAAGAATTAATGTTATTAACAT 3864
                                vi          i  v i ii     v     i  i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_32568979_3   3865 GATCTTTCTACTCAAAGCATTCTACATTGAAT-AATGCAGTCCCTATCAG 3913
                          iivv v  v i    viiv      --  v -  i   i         i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA--GATTCAACGCAATCCCTATCAA 98

  chrX_32568979_3   3914 AAT----------------ACAGAAATGGAATAAAAAG-TGATCATAAAA 3946
                            ----------------i       ---- i v   -     v     
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAAT----TGACAAGCTGATCCTAAAA 144

  chrX_32568979_3   3947 TTTGTACGATCAAAGACCAGCAGAGAGCCTGAATAGCCAAAGCAATCCTG 3996
                           ii  i i--   vi - --  i  v  v           i     i  
  L1M4_orf2#LINE/    145 TTCATATGG--AAATGC-A--AGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_32568979_3   3997 AGCAAAAAGAACAAAGACTT--ATGAATCACACT-------------ACT 4031
                          iv  i          --  -- v  v       -------------   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAG--TTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_32568979_3   4032 TG--ACAAA---ACAG----CAAG---GTGT-----TAGAATAAAAACAG 4064
                          i--     ---    ----    ---    ----- i v    ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_32568979_3   4065 ACATATAGAACAATGGAATAGATTAGAGAACTCAGAATTAAATCCATGTA 4114
                                  v            v v    iii     v    i    ii 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_32568979_3   4115 TTTACATACAACTTGTTTTTGACAAAAGCACCAAGAACATGCATTAGGGG 4164
                             iivv   i vi    i     ii ii      v   v  v -    
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGG 386

  chrX_32568979_3   4165 GAAGGACA-CCTTCTT--CAAATGGTGCTGAGA--ATTGGATTGTCAGAT 4209
                         i   i i -i   i i--            i  -- i     v?i  v  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_32568979_3   4210 GCAGAAGTATGAAACTGGATCCCTGTCTCTCACCATATTAGAAAATTCAG 4259
                            i   v     ii    i    ii   v        vvi      - i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AA 485

  chrX_32568979_3   4260 CTCAAGATGGATTAAGGATTTAAAGGTAAGACCTAAAACTG--AAACTAC 4307
                              i      i ?i  ii    v      v        i--     - 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-C 534

  chrX_32568979_3   4308 AT-GAAGCAAACATAGGGA-AAACAGACAGGACCTTGGTCTAGGCAAAGA 4355
                         v -    v         ?i-   ivvv iv        vi       v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_32568979_3   4356 TTTTATGGTTATGACCTCAAAAGCGCAGGCAACAAAAACATAAATAGATA 4405
                            iv i v      vi       i  i         iv v         
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_32568979_3   4406 ATTGGGACTGTAG-AAAATGAAAGAGCTTCTGTAAAACAAAGGA-AGGAT 4453
                          v v     vi v-     v   i -   i   ivvv       - vv  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chrX_32568979_3   4454 TCAACAGAGTGAAGAGACAACCTGCTGAATGGGAGAAAAGATTTGTAAAC 4503
                         -   v i      i        ii v             v     i   i
  L1M4_orf2#LINE/    684 -CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_32568979_3   4504 TAT---TCAGACAAGAGACTAATATCTAGGAAATACGAGGATCCCAAACA 4550
                         i  ---  v  i   i    vi    i  i v   ii i  v i vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_32568979_3   4551 ATTTAACAGTAAAAA----AATAATCACATT-AAAAATGGACAAAGGACA 4595
                          i i  i i      ----     i vv   -        i       iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_32568979_3   4596 ATAATAAGTATTTCTCAAAAGAAGA----CAAATGACCAACGGGTATATG 4641
                         vv    iii       v        ----      i    iii i i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_32568979_3   4642 AAAAAATGCTCAACATCACTAATCAT 4667
                             i             ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (118 / 76)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 2.76 (91 / 33)  


 673 27.35 4.04 1.35  chrX_32717706_32719327        3   225 (1397)    L1M4_orf2#LINE/L1       44   272 (636)  

  chrX_32717706_3      3 TTAAAATGGCCATACTACCCAAAGCAATCTACGAATTAAATGTTATTCCT 52
                             i     v     v      vii      ii   v  i iv  i   
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chrX_32717706_3     53 ATCAAACCACTAACATCATTTTTCACAGAACTGGAAAAAAGCT-ATACTA 101
                               viv i i vv v     ii     v v  v  --   -  v   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTA 141

  chrX_32717706_3    102 AAATTCATATAGAACCAAAAAGGAGCCCA--------AAAGTAATCCTAA 143
                                   i   viiv  i   -    --------   ii    i i 
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGA 190

  chrX_32717706_3    144 GGAAAAAGAACAAAGCCAGAGGCAGCACATTACCCAACTTCAAACTATAC 193
                         ii  i          iii    vvv    i v     i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_32717706_3    194 TATAAGGCTACAGCAACCGAATCAGCATGGTA 225
                           i  i       i  i i iv   ii     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

Transitions / transversions = 1.65 (38 / 23)
Gap_init rate = 0.02 (4 / 229), avg. gap size = 3.00 (12 / 4)  

1838 27.16 3.70 0.93  chrX_32717706_32719327      490  1137 (485)    L1M4_orf2#LINE/L1      243   908 (0)  

  chrX_32717706_3    490 CAAAA--ACAAAAACAAAAACAGCATGGTACTGGCACAAAAACAGACACA 537
                             i--   iv  iv  i    ii           i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_32717706_3    538 TAAACCAATGGAACAAAGTAGAGAACCCAGAAATAAAGCCACACACCTGC 587
                           i i        i i i v    ii           v   i   ii ii
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_32717706_3    588 AGCCATATGATTTTCAACAAAGTTGACAAAAATAAGCAATGGGAAAGGAC 637
                         i i  vv        i    i v  v   i vi vv       i  i  v
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_32717706_3    638 TC-CCTGTTCAATAAATGG----------ACTGGCTAGCCATATGTGGAA 676
                          v-i  v     i      ----------     v  ?   i   iii  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_32717706_3    677 GAATGAAACTGGATCCCTAATTTTCGACATGTATAAAAATTAACCCAAGA 726
                                ii    i     vi iv iv   i  i          i   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_32717706_3    727 TG-ATTAAAGATTTAAATGTAAGACCTCAAACTAGAAGAATTGTAGAAGA 775
                           -  i ?   ii           v  v      v  i v iv       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_32717706_3    776 AAACCTAAGAA-ACATCATTCTGGACATTGGGGTTAGGAAAGCATTTATG 824
                             v  i ?i- v   -   vv   v     -     v  vvi   v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCT- 589

  chrX_32717706_3    825 ACTAAAT----CCTCAAAAGCAATTGGAGCAAAACCAAAAAATTGACAAG 870
                         --  i  ---- vi        vvv v i     v-       v  i  i
  L1M4_orf2#LINE/    590 --TAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAA 636

  chrX_32717706_3    871 CGAGACCTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACTATCAA 920
                         ivi   i v  i   v v    i   i  ii vv    i  v        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_32717706_3    921 CAGAGT-AACAGACAACCTACGGAACAGGAGAAAATCATTACAAACTACA 969
                         v i   -  v        i  i   ii         vv  i    ii i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_32717706_3    970 TATCACACAAAGGTTCAATATCTAGAATTTACAAGGAACTTAAAAAACTG 1019
                             vv i  i  viivi    i     v  i  i     ivv v    v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_32717706_3   1020 AACAAGCAAAATACAA----CGCCATCAAAAAACAGGCAAAGGGCATGAA 1065
                           i  vv    v    ---- v v  i?     ii        iiv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_32717706_3   1066 CAGACACCTCTCAAAAGAAGACATACAAGTAGCCTACAAGCATATGAAAA 1115
                         i     ii    v        i      i i   v i     i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_32717706_3   1116 AATGCTGAATAACATTAATTGT 1137
                         i     v  i v  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (103 / 69)
Gap_init rate = 0.02 (12 / 666), avg. gap size = 2.50 (30 / 12)  


2619 27.48 2.15 1.43  chrX_32992276_32994526.rev      582  1418 (833)    L1M4_orf2#LINE/L1        5   847 (61)  

  chrX_32992276_3    582 AAAACATTTCATGCTCTTGGATTGGAAGAATAAATATTGTTAAAATGGCC 631
                           i i  ii    i  v            v v           i     v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_32992276_3    632 ATACTGCCCAAAGCAATTTACAGATTCAGTGCTAATCTTATCAAACTACC 681
                              v      vii  i          ii  v vi i       v v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_32992276_3    682 AACGTCAATTTTCATTTTTCATTTTCATTAGAAAAGACTAATCC--AAAT 729
                          i ------- v v     iiivvvv   -  v   -  i    --    
  L1M4_orf2#LINE/    105 AGC-------TGCCTTTTTTGCAGAAATT-GACAAG-CTGATCCTAAAAT 145

  chrX_32992276_3    730 TTGTATGGAACCAAAAGAG-CCCATAG-AGCCAAAGCAATCTTAAGCTAA 777
                          ii       viiv   i -    v i-       i       i ivv i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_32992276_3    778 AAGAATAAAGCAAGAGGCATCACACTACCTGACTTCAAGCTATACTATAA 827
                              i    ivi    vv       v  ii i     iviv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_32992276_3    828 GCCTACAGTAACCCAAACAGCATGGTACTGGTACAAAAACAGAC-CATAG 876
                         iv         i v i    ii         i i  ii i    -i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_32992276_3    877 ACCAATGGAACAGAATAGTGAACCCAGAAACAAAGCGACACACCTATAAC 926
                          i        i     v v  ii       i   v v i   ii   iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_32992276_3    927 CATCTGATCTTTGACTAAGTCAACAAAAATAAGCAATGGGGAAAGGACTT 976
                           vi    i  i   v i viiv   i vi vv            i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_32992276_3    977 CCTATTCAATAGATGGTGCTGGGAAAACTGGCTGGCCACATGCAGAAGAT 1026
                         i  v     i i            v      v i?         i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_32992276_3   1027 TGAAATTGGACCTCTACTTTTCATTATATACAAAAATCAACTGACGGTGA 1076
                             i       i    i iv  ii            i    v vii  i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_32992276_3   1077 ACTAAAGGTTTAAATATAAGACCTCATACTGTAAAAAATCCTAGAAGAAA 1126
                          ii ?  iii     i     v  v v   i     v-  i         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAA 544

  chrX_32992276_3   1127 ACCTAGGAAGTACCCTTTTTTACATTGGTCTTGGCAAAGAATTTATGACT 1176
                           v    ?ivv vi   iv v  v    vi v     v iv  iv iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_32992276_3   1177 AAGTCCCCAAAAGC-CATTGCAACAAAAACAAAAATTGACAAGTGGAACT 1225
                          v v v        -  v-         iv      v  i  i v i   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_32992276_3   1226 TGACTAAGCCAAAGAGCTTCTGCAAAGCAAAAGAAAC-ATCAACAAAGTA 1274
                          v ii  iviv  i i   i  iivvv    i  v  -     v     i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_32992276_3   1275 AACAGACGA-----AGAATGGGAGAAAATATTCACAAAATATGCATCTGA 1319
                           v    i -----                  ii    vi  ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_32992276_3   1320 CAAAGGCCTAGTATCCAGAATCTATAAGAAACTT----AAATCAACAAAC 1365
                         i  i  v  v           v     ii    i----  v    i  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_32992276_3   1366 CAAATACAAATACATTCA--TTAAAAATGGGCAAAGTATATGAACAGACA 1413
                         v   v       - ii  -- ?              v  v    i     
  L1M4_orf2#LINE/    794 AAAAGACAAATA-ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_32992276_3   1414 CTTTT 1418
                         i  i 
  L1M4_orf2#LINE/    843 TTTCT 847

Transitions / transversions = 1.40 (132 / 94)
Gap_init rate = 0.02 (15 / 843), avg. gap size = 2.00 (30 / 15)  

 268 19.61 0.00 0.00  chrX_32992276_32994526.rev     1702  1752 (499)    L1M4_orf2#LINE/L1      833   883 (25)  

  chrX_32992276_3   1702 TGAACAGACACTTCTTGAAAGAAGACATACAAGCGGCCAACAAGCATATA 1751
                             i     i    iv        i      ii      i     i  i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_32992276_3   1752 A 1752
                          
  L1M4_orf2#LINE/    883 A 883

Transitions / transversions = 9.00 (9 / 1)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.00 (0 / 0)  


 842 22.04 0.54 0.00  chrX_32998784_33004257     1831  2016 (3458)    L1M4_orf2#LINE/L1        5   191 (717)  

  chrX_32998784_3   1831 AAGATAATCCATATTCATGGATGGGAAGGCTCAATATTTTTATTATGTCA 1880
                               vi    i         v     i  i      v   vv   v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_32998784_3   1881 GTTATTCTCAAATTGATCTATAGACTCAATGTAATCCCAATCAAAATCTC 1930
                         i vv i i            i   i    i i      v         i 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_32998784_3   1931 AG-TAGTTACTTTGCAGATATTAACAAAGAGATTCTAAAAATGATATGGA 1979
                           - ivi vi        v   i    ivv   i      v v       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_32998784_3   1980 AAGGCAAGAAACCTTGAATAGCCAAAACAACATTGAA 2016
                           v     ii   iv               iv     
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

Transitions / transversions = 1.16 (22 / 19)
Gap_init rate = 0.01 (1 / 187), avg. gap size = 1.00 (1 / 1)  

2471 21.19 10.60 0.90  chrX_32998784_33004257     2322  2991 (2483)    L1M4_orf2#LINE/L1      174   908 (0)  

  chrX_32998784_3   2322 AACAAAAACAATATTGAAGGACAAGCACAAAGTCAGAAGATTGAGACTGC 2371
                          i v        v     ii v   v       ii  i  i v v   v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_32998784_3   2372 TCTACTTCAAGACTT------------CGGTAATCAAGACAGTGTCTTAT 2409
                         i v i     i    ------------ i                vv  i
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_32998784_3   2410 TGGCA-AAAGA-AGA------GATCAATGGAACAGAATAGAGAGCCCAGG 2451
                              -  i  -   ------           i     v     i    i
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_32998784_3   2452 AATAAACCCACATAAATATAGTCAACTGACTGATGTTTGATAACGGAGCA 2501
                                   i i vv   i     i   i ----  i  i  v  v  v
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATT----TTCGACAAGGGTGCC 369

  chrX_32998784_3   2502 AAGAC-------------------AACCTTTTCAATAAATGGTGCTGGAA 2532
                              ------------------- ii        i            i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_32998784_3   2533 CAACTGGGCATCCACATGCAAA-------------------------CAC 2557
                                ii ?           -------------------------   
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_32998784_3   2558 CTTTCACAAACATTAACTCAAAATGGATCAGAAACTTAAATGTAAAATGC 2607
                          v vi     v                   ? i  i         i -  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GC 518

  chrX_32998784_3   2608 -AAAACTATAAAGCCCACAGAAGATAACATAGGAGAAAATCT--ATA--- 2651
                         -           i i vi      v        ? v      --i i---
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_32998784_3   2652 -TGGGTCTGGTGATGACTTTTTAGATATAACACCAAAGACATGACCTATG 2700
                         -     iv  ii   ii  i        i        ii  ii v v ii
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_32998784_3   2701 CAAGAAATAATTGATAAGCAGGACTTCATTAATATTGAAAAATTCTATGC 2750
                         v      v   v     iiv         i  v   i    v  i i   
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_32998784_3   2751 TGCAAAAGACATTGTCAAAAGAATGTAAAGACAAGCCACAGAATAGGAGA 2800
                          v    i    i i    i i i  v        v         i     
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_32998784_3   2801 GAATATTTGCAAAAGACATATCAGGTAATGGACTGTTATCCAAAATATAC 2850
                         i            vv i     v i   v     vv      i      i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_32998784_3   2851 AAAGAACTGTTAAAAATCAACAATAAGAAAACAAACAACTCTATTTTAAA 2900
                                 v   v  v    i     i  i     i   i v   ?-   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAA 817

  chrX_32998784_3   2901 AATGGGCAAAACACCTTAACAGATAACTCACCAAAGAAGATATACAGATG 2950
                                   iv ii v  i   i vi  v                i   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_32998784_3   2951 GAAAACAGGCGTATGAAAAGACGCTTCACATCATATGTCAT 2991
                          vv  i i  ii         i   iv      ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (87 / 51)
Gap_init rate = 0.02 (12 / 735), avg. gap size = 6.42 (77 / 12)  

2457 26.40 2.48 4.63  chrX_32998784_33004257     4054  4981 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_32998784_3   4054 TGAAGAAATATATTGTGCTCGTGGATTGAGAGATTCAACACAGT---AAT 4100
                           i i i    viii  i  i       ii   i i  i iv  ---i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_32998784_3   4101 GTCAATTTTACCCAAACTGTTACACAGTTT--ACACAATTTTTATCAAAA 4148
                          v    vi v      i  v vi    v  --  i    iii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_32998784_3   4149 TCTCAGCAATATTTTTGGAATTTAGGTGTAGGAAAAATTTATGTGAAAAG 4198
                           i    viiv     ----------  i  ---     -----  v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT----------TGCAG---AAATT-----GACAAG 132

  chrX_32998784_3   4199 GC-ACTCTAAAATTTATGTGAAAAGGCAATGGATTTAGAATAGCTAAAAC 4247
                         vi- ii        i  i  i   v    v   iii        i     
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chrX_32998784_3   4248 AATGTTGAAAAGGAAGAATGAAGTAAGAGGAATAA-GTCTACCAGACTGA 4296
                            v       i      ii    vi     v v -iii v   ivi v 
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_32998784_3   4297 AGACTTATTAAATAGCTACAGTAATCAAGATAGTGTGGTGTTGGTGTTGG 4346
                          i     i  v v                 i        ii   ii vi 
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_32998784_3   4347 GATAGACACGCAGATTAATGGAACAGAATAGAGACTTCAGAAATAGACCC 4396
                                 iii    i       i     v    v i        i    
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_32998784_3   4397 ACACAAAT-TGCTCAACTGATTTT-GACACAG-TGC-AAAATAATTCAGT 4442
                          i   vv -  v    i       -    vi -   -  i iv     i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_32998784_3   4443 GGAGCAAAGATAGTCTTTTCAACACATGGGTCTTAGAACAAGTGGACAAA 4492
                           i v  ii               v    - vi i i    v    i ?v
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGG-TGCTGGGACAACTGGATAKC 431

  chrX_32998784_3   4493 AATAATG-GAAAGAAAAAAGAAGAAAAAGAACCTTGACATAACTTTACAC 4541
                         v i -  -i      vi   vv -----  v  i ------  i i    
  L1M4_orf2#LINE/    432 CACA-TGCAAAAGAATGAAGTTG-----GACCCCT------ACCTCACAC 469

  chrX_32998784_3   4542 CTTATGCAAAA-TAAAATGCAAATAGATGATGAATTTAAATGTGAAACAC 4590
                          v   i     - v  v vv    i   v ?ii ii       i i vvi
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_32998784_3   4591 AAAATAATAAATATTTTACAAAAACATACAGGAG--AGTCTTCAGGATGA 4638
                             iv     vv i   v  i  v i i   ? -- i     iv  ivv
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_32998784_3   4639 AAGGCTAGG--AGGAGTTCTTAGATTTGACGTTAAAATCGTGTGCCTTAA 4686
                         vi  i    -- v iv         v    iii    v iiiv  vvi  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_32998784_3   4687 AAGACACAATTTGATAAATTTGAC---ATACAAAATTTTAAAATTTTGCT 4733
                             v v   v-        v   ---  -       vv   v     iv
  L1M4_orf2#LINE/    620 AAGAAAAAATA-GATAAATTGGACTTCAT-CAAAATTAAAAACTTTTGTG 667

  chrX_32998784_3   4734 CTGAGAAAGATGCTGCCAAGAGGATGAAGAGACAGGCTGCACATCGAGA- 4782
                           vvi  i  ii  ii     iii    i     iv ii  v vi i  -
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_32998784_3   4783 AAAATACCTGCAAACCATATATCTGACCATGCACTAGTATCTAGACTAAA 4832
                               ii      i           iv v v   v     i   v  v 
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_32998784_3   4833 TGAAGAATTCATGTAACCCAAAAGTAAAAACAAAATAGACACAAAAAAAT 4882
                          i     i  v ii   i   v i      -------    ---  v  i
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAA-------GACA---AATAAC 807

  chrX_32998784_3   4883 CCATTAGAAAAATGGGCAAAAGACATGGA--GACATTTCACCAAAGACAA 4930
                            v v?             i  iv  i --        v       vi 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_32998784_3   4931 CACATAGATGGCGGATAAGCTTGTGAAAAGATGTTCAGCATCATTGGCTC 4980
                         i i i i     vi      vii          i   i     ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_32998784_3   4981 T 4981
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.54 (66 / 26)  


2222 23.47 3.68 8.11  chrX_33006244_33008234.rev      551  1500 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33006244_3    551 TGGAGAGATATACTCTGCTAATGGATTGGAATACTCAACATGGTAAAGAT 600
                             i      v iv  i v           v   i  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33006244_3    601 GTCAATTATCTCCAAATTAATCTATAGTTTTAATGCCATTTCTACTAAAA 650
                          v    vv  i       i     i  v  i  i  v  ii   ii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33006244_3    651 TACCAGCAAGGTCTTTTTAGTAGACTTGGATCAGCTTATTCTAAA-TTTA 699
                          v     --v i      v i   vv v  iv    v  i     -  i 
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_33006244_3    700 TACGGAAAAGTACAAGCCTGATAATAGCTAATACAATCTTGACAAAGAAG 749
                           i     v i vii v iv v      i  v          v       
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_33006244_3    750 AATAAAGTGGAAAGAATCACTCCACTAAATATTAAGGCTTATTATGTAGC 799
                           i     v i i  v    v iv iv   v i  ii    i  iiv   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_33006244_3    800 TACAGTAATCAAGACAGTGTGGAATTGGGGGAGAGATAGACGCATAGTTC 849
                                               v i   viv ii       ii    v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_33006244_3    850 AATGCAATAGAATAGAGATTCCAGAAATAGACCCGCACAAATATGTGCAA 899
                             v        v    v          i    ii   vv    - iv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG-GTCA 347

  chrX_33006244_3    900 ACTCATTTTTTAAAAAGTTGTGAAAGCAATTCCAAGGAGGAATTTTAACA 949
                          i v     iv v  i v  iv  ii v    -  v i    ------- 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTC-AATGGGGAA-------A 389

  chrX_33006244_3    950 GCCTTTCCATTTCTATAGCCTTTTCAACAAATAGTGTGCGTTTTTTCTAA 999
                          ------- -----    i             ------------------
  L1M4_orf2#LINE/    390 G-------A-----ATAGTCTTTTCAACAAAT------------------ 409

  chrX_33006244_3   1000 GTGAGTGGTGTTTGAGCAAGTAGACATCTAAAGGCAAAACAAACAAAG-- 1047
                         ------    i v ii   v i  i ? i v v      -i  ii   --
  L1M4_orf2#LINE/    410 ------GGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAAGTT 452

  chrX_33006244_3   1048 -----CCCACC-CATAA-ATATATAAGTAAATAAATAGAGCCTCAACTTA 1090
                         -----  i   -  i v-     i  --    v  ------     vv i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAA--AAATTAA------CTCAAAATG 494

  chrX_33006244_3   1091 AGTCTTATGCAAAATTATCTCAAATGTCAAATATAAAACATAAAACTACA 1140
                         ii  ------ ? i-- i  --------    i   i vv        i 
  L1M4_orf2#LINE/    495 GATC------AWAG--ACCT--------AAATGTAAGAGCTAAAACTATA 528

  chrX_33006244_3   1141 AATATTTTAGAAAAACATATGGGAGAAAATTTT-GTGAC--TG----AGG 1183
                           vv i      i  v i  i  ? v    i  -     --  ----   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_33006244_3   1184 CAAAGACTTTTTACACTTTACACAAATAGCACAATCCATAAAAAAGAAAA 1233
                            v ii  i   v iv v    v  v       v v i    i -    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAA 627

  chrX_33006244_3   1234 ACTGATAAATTGGACTTCGTTAAAATTAAAA-CTTTTGATCTGAAAAGGA 1282
                          iv               i i          -      vv  vv      
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_33006244_3   1283 TCCTCTTAAGAA-GTGAAA-TACAAGGTACAGAATGGGAGAAAATATTTG 1330
                         iv  v i     -      -v    vvi                      
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_33006244_3   1331 CATATCAGTTG-CAAAAACAGGGACT----------ATATACGAAGAACT 1369
                           v    vv i- vi v -       ----------     ii       
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATA-AGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_33006244_3   1370 TAGAAAACTCAAAAGCAAAAATCCAAAAATAAATTAATTAGGAAATGAGC 1419
                         ivv v       v ii     vv    --   vii    ?ii     i  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAA--TAACCCAATTWAAAAATGGGC 824

  chrX_33006244_3   1420 CAAAGGCACGAAGAGACATTTTACTGAATAGTATATATAAATGAC----A 1465
                         v  i iivi   v        iv ii  v iv     i     i ---- 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_33006244_3   1466 AACATATGGAAAAGATATTAAATATCACTAGACAT 1500
                          i  i   -       ii v  i    ????????
  L1M4_orf2#LINE/    875 AGCACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (118 / 101)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 3.73 (112 / 30)  


1698 23.97 2.37 9.46  chrX_33044037_33046832     1106  1739 (1057)    L1M4_orf2#LINE/L1        2   590 (318)  

  chrX_33044037_3   1106 GAAAAAGCATTCCATGCTCAT----TGGAAGAAACAATATAATTAAAATG 1151
                          i   iii  i     i    ----       vvi     vi    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_33044037_3   1152 GCTATACTGCACAAAACAACTTATAGATTCAATGCTGTCCTTATCAAACT 1201
                           v     v v    vii ii  i        i  vi   i       v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_33044037_3   1202 ACCAAGGTCATTCCTCACAGAATTAGAAAAAACAATTCTAAAATTCATAT 1251
                         v   ivvv v  ii ii     v v  v  ivii  i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_33044037_3   1252 GCAACCAAAAAAAAAAATAAAAGAG-CGCATA-TAGCCGAAGCCATCCTA 1299
                          ------------i    iv   i - v  v -     i  i v   i i
  L1M4_orf2#LINE/    152 G------------GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_33044037_3   1300 AGCAGCAAGAACAAAATTGGAGGCATCACACTACAGTACTTCACCCTACA 1349
                          iv iv         i       vv       ------- i ------  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACT-------TCC------CA 226

  chrX_33044037_3   1350 ATAATTCACACCACAGTACATCACACTATAGAACTTCCAACTATGCTACA 1399
                           --    ----------------------i     --------i     
  L1M4_orf2#LINE/    227 AT--TTCA----------------------AAACTT--------ACTACA 244

  chrX_33044037_3   1400 AGACTACAGTAGCCAATACAGCATAATATTGGTACAGAAACAGACATATA 1449
                          ii        ii   v    ii ii  i   i i iii i         
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_33044037_3   1450 GACCAATGGAACAGAATAGAAAACACAGAAATAAAGCCATACACCT---- 1495
                           i        i     v  i iiv          v       ii ----
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_33044037_3   1496 TCAACCAGCCTTCGACAAGGCTGGCAAAAACAAGCAATGGTAAAAGGACT 1545
                             iiiiii          v  v   i v  vv      vi    i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_33044037_3   1546 TCCTATTCAATAAATGATGCCAGGATCACTGGCTAGCCATATGCAGAAGA 1595
                         vi  v     i     i   ii   iv     v  ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_33044037_3   1596 ATGAAACTTGATCCCTACCTTTTGCCATATACAAAAATAAACTCATGGTG 1645
                              ii v  i        ivii              v      vii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_33044037_3   1646 GATTAAAGATATTAATGTAAGACCTAAAACTACAAA--TCCTAGAAACAA 1693
                            i ?   iv v         v         i   --  i     iv  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_33044037_3   1694 ACCTAGG---AAATGTCCTTCTTGACATTGGCATTGGCAATTTTTTTTT 1739
                           v    ---    ---    v    v    vv v      vv   i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.63 (93 / 57)
Gap_init rate = 0.02 (13 / 589), avg. gap size = 5.77 (75 / 13)  

 640 27.08 19.86 0.00  chrX_33044037_33046832     2027  2303 (493)    L1M4_orf2#LINE/L1      577   908 (0)  

  chrX_33044037_3   2027 GGCAAAGAATTTTTGGCTAAGTCCCCAAAAGTAATTGTAACAAAAATAAA 2076
                              v iv  i  i v  v v v       i vvv i       iv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_33044037_3   2077 AATTGACAAGAGGGACCTAATTAAACTAAAGAGCTTCTGCACAGCCAAAG 2126
                            v  i  ivv    i v  i   v v  i i   i  ii vv v  i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_33044037_3   2127 AAACTATCAACAAAGTAAACAGATAATCTACAGAATGGGAGAAAATATTC 2176
                          v        v     i  v   i  i i                    i
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_33044037_3   2177 ACAAACTGTGCACCTGACAAAAG--------------------------T 2200
                         i    iii ii i    i  ii -------------------------- 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_33044037_3   2201 CT--------AATA---------------------TTAAAAAATGGACAA 2221
                           --------    ---------------------  ?        i   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_33044037_3   2222 AAGACATGAACAAACACTTCTCAAAGGAAGACATGCAAGCGACCAACAAA 2271
                          i  iv    i i   i     v  i     i  i   ii i    i  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_33044037_3   2272 CATACGAAGAAATGCTCATCATCATTAATCAT 2303
                           i i   i i       v     ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (49 / 25)
Gap_init rate = 0.01 (3 / 332), avg. gap size = 18.33 (55 / 3)  


 953 25.50 4.30 4.01  chrX_33057083_33059482.rev      632   980 (1420)    L1M4_orf2#LINE/L1        6   355 (553)  

  chrX_33057083_3    632 AGATACATTATGTTCATGGATTGGAAAACTCACCATAGTAAAGATGTGAA 681
                              ivii                 i   i vi  v  v      vv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_33057083_3    682 TTCTCTCTAAGTTGATCTATT--TTTAAGACAATTCTTACGAAAATTTTA 729
                          v   i i  i        iv--  i  vi    i i  iv     iii 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_33057083_3    730 GCAATGTTTTT----GAACTTACACAGGCTTATTATAAAAATTATATAGG 775
                           viiv     ----   v  i-   i   v  iv     v i    -  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCATAT-GG 153

  chrX_33057083_3    776 ATGTATAGAATGGCACAGGACCTATACTAGCCAAAAC--TATTGAATAAG 823
                          -------    -  vi     i v v          -- v     -  i
  L1M4_orf2#LINE/    154 A-------AATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAA 194

  chrX_33057083_3    824 GAAAAATTAA-TTAGAGAAATCACTCTTACTGTTGTTAAAGTTAATTATA 872
                            i  iv  -  i   i v    v   v iiv v i   ii v i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_33057083_3    873 TAGCAGCAGTATTCTAGACAGTCTGATACTGGT----GGTGTACAGACTC 918
                         v   vi     v  v       v  i      i----  --- i    vi
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG---ATAGACAT 291

  chrX_33057083_3    919 ATATATCAGTGAAACAGAATAGAGAGCCCAGAAATAGATCCACAAAT--A 966
                            v    i  i  i     v     i         i i   i v  -- 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_33057083_3    967 TGCCCAATTTATTT 980
                           vi     v    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTT 355

Transitions / transversions = 1.34 (51 / 38)
Gap_init rate = 0.03 (12 / 350), avg. gap size = 2.42 (29 / 12)  

 465 27.70 22.30 2.03  chrX_33057083_33059482.rev     1135  1430 (970)    L1M4_orf2#LINE/L1      349   704 (204)  

  chrX_33057083_3   1135 TTG-TTTTGGACGAAG----CAGGA--ATCCAGTAAGGAGGGT-TAGCCT 1176
                            -    v   i i ----  i  --  i  i ii   ii v-   i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_33057083_3   1177 TTTTAATAAATGGTGTTGTAGTAATCCAACACCCATAGGCAAAA-AACAA 1225
                            i  i        i  viii  iivi i ?   i v      -  ii 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_33057083_3   1226 A--------------------------CAAAAAACACCTT---------- 1239
                          --------------------------      vi v  i----------
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_33057083_3   1240 ---GATCTAAACATCAGAAGAACTTAAACTGTAAAACTTACTCAAAAATA 1286
                         ---  i     ii ---    i  v     i       --  i i  i- 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGT---AAGAGCTAAAACTATAAAACT--CTTAGAAG-A 542

  chrX_33057083_3   1287 GAACATA----------TTTGGGATCTAACGTTAA--AGTG--TTCTTAG 1322
                         i      ----------  i v  i  viv    i-- i  --       
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_33057083_3   1323 ACTTGACACCAAAGTCGCCATCCATAAAAGGAAATTTTGATAAAGTGAAC 1372
                          iv          iv i v v v i     i   vv v      v  i  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_33057083_3   1373 CTCATTAAAATAAAAAACTTTTGCTATGCAAAATATTCTGTTAAGAAG-- 1420
                         i    i     v           ivv v    iv iv  i i     i--
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_33057083_3   1421 --AAATATAACC 1430
                         --   v i    
  L1M4_orf2#LINE/    693 GAAAAGACAACC 704

Transitions / transversions = 2.00 (54 / 27)
Gap_init rate = 0.04 (14 / 356), avg. gap size = 5.14 (72 / 14)  

 727 20.81 3.62 2.26  chrX_33057083_33059482.rev     1689  1909 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_33057083_3   1689 AAAAAAATGAAA-TACGAGCTACAGACTGGGAGAAAATATTGGCAAACCA 1737
                           i   i     -v  i v i     v              v     i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_33057083_3   1738 TATATCTAGATATCAAGAACTAGTATCAAAACTACATAAAGAGCTCTCAA 1787
                                -    -- i i   v     v i v  i       i    i v
  L1M4_orf2#LINE/    735 TATATCT-GATA--AGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_33057083_3   1788 AACTCAACATTTTAAA-------AATCCAATAAGAAAATGGACAAAAGAC 1830
                                i v vv   -------  i     v?i       i    i  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_33057083_3   1831 AGGCACAGATGTTTCACCAATGAAGATATACAGATGGCATATATAAATGC 1880
                         vv v i   ii    v    v           i     -i -    iii 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC-CA-ATAAGCAC 879

  chrX_33057083_3   1881 ATTAAAAAATGTTCAACATCAACAACCAT 1909
                           v    i   i         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (27 / 18)
Gap_init rate = 0.03 (6 / 224), avg. gap size = 2.17 (13 / 6)  


3341 23.86 1.78 1.78  chrX_33119203_33125031      487  1387 (4442)  C L1M4_orf2#LINE/L1   (0)   908     8  

C chrX_33119203_3   1387 ATGTTCTGTGTTCATGGACTAGAAGGATTAATATTGTTAAAATGTCCATG 1338
                           i i ii          i i    iv             i   v v  i
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

C chrX_33119203_3   1337 CTACTCAAAGCAATTTACAGATTCAGCACAACCTCTATCAAAATGCCAAT 1288
                           v i    vii  i          i i   i i          v   ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

C chrX_33119203_3   1287 AGCATTTTTCATAGAT-TTAAAAAA--AATC-TAAAATTCAAATGAAACA 1242
                         v  v     iii   v-  i v  i--i   -         v   i  vv
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

C chrX_33119203_3   1241 ACAAAAGAAAGAGAATAGCCAAAGCAATCTTGAGAAGGATAAGCAACATT 1192
                         i   ii  vvv            i         i  i  vi i   vi  
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

C chrX_33119203_3   1191 GGAGGTATCACACTTCCTGATTTTGAATTATATGACAAAGCTTTAGTAAT 1142
                              vv          ii    ii  viv  iv        vi      
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

C chrX_33119203_3   1141 CAAAATAATATAGTACTGGCATAAAAGCAGACATATAGACCAATGCAACA 1092
                            i i i i i            iiii           i     v  i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

C chrX_33119203_3   1091 GAATGGAGGGCCCATAAATAAACCCATTCATATATGGTCAACTAAATTTT 1042
                             v   i i   v            v   v         i i v   i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

C chrX_33119203_3   1041 GAGAAGGGCAACAAGAGTACACTATGAGGAAAGGATATTCTCTTTAATAA 992
                           v     iiv     vi iv v   i      i   v   i  i  i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

C chrX_33119203_3    991 ATGGTGTTTGAAAAACTGGATATACACATGCTAAAGAATAAAATTGGACC 942
                               i v i v         ?v       v       i  i       
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

C chrX_33119203_3    941 CTTACATCACAC-A---ACAAAAGTCAGCTAAAAATTGATTAAAGAATTA 896
                          i   v      - ---      i i i  v     v   i ?   vi  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

C chrX_33119203_3    895 AATGTAAGACCTGAAACTACAAAATTCCTAGAAGAAAGTGCATGAAAAAA 846
                                  v  i      i    i  i         i--   -- ii?i
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA--CAT--AGGNG 553

C chrX_33119203_3    845 TAAATTCTCGAAA--TTGGTCTTGGCAATGATTTTTTAGATATGACATGA 798
                              ii   vi --    vi v       i   i            iv 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

C chrX_33119203_3    797 AAAGCACAGACAGTAAAATCAAAATTAAACAAGTTGTACTACGGCAAACC 748
                                 ii  ii    vv    v  i i  i   v   v iv    --
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA-- 651

C chrX_33119203_3    747 AT--AAACCTTCTGTACAGCATAGGAAACAATTAACAGAGTGAAGAGACA 700
                           --   v   i   i vv  v    v  v  i  v i      i     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

C chrX_33119203_3    699 ACT-GTGGAATGGGAGAATATATTAGCAAACCATATGACCAATATGCAGC 651
                           i-iii           v     v     i     iv ii   v vii 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

C chrX_33119203_3    650 TTTCATCCAAAATATATGAGGAACTC--AGAGCTCAAGCAAAACACACAA 603
                           vi     i       i i      -- v i     v---  i -----
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT---AATA----- 793

C chrX_33119203_3    602 ACAAAAAACAAAAAATCTGATT-AAAAATGGTCAAAGCCCCTGAATAGAC 554
                         --    i     v  i ii   -        v     vvii         
  L1M4_orf2#LINE/    794 --AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chrX_33119203_3    553 AGTTCTCCAAAGAAGACATGCAAATGGCCAACAGGTATATGAAAAGATTC 504
                          v              i  i           i i i i          v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

C chrX_33119203_3    503 TCAAAAGCGCTAATCAT 487
                             v v i????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (134 / 78)
Gap_init rate = 0.02 (15 / 901), avg. gap size = 2.13 (32 / 15)  

3049 26.82 1.68 0.34  chrX_33119203_33125031     4446  5336 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_33119203_3   4446 AAACATCCCATGCTCATGGACAGGAAGAATCAACATTGTGGAAATGACTA 4495
                          i i        i       iv      v i  i     vi i   i v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_33119203_3   4496 TACAGCCAAAAGCAATCTGCAGATTCAGTACAATCCC-ATCAAAATACCA 4544
                            vv  v   vii    i        iii       -        v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_33119203_3   4545 TCATCATTCTTCACAGAACTAGAAAAA--AATCCTAAAATTCATATTGAA 4592
                         v vv v  i  ii     v v  v  i--i                v   
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_33119203_3   4593 CAAAAAAAAAGAGCCCACAA-AGCCAAAGCAATAGTAAGCAAAAAGAACA 4641
                         --- viv  i ii    v  -       i    vv i iv  i       
  L1M4_orf2#LINE/    156 ---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_33119203_3   4642 AATCTGGAGGCATCACATTACCCAACTTCAAATTACACTATGTGGCTACA 4691
                           vi      vv     i v     i      vivi    iivi      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_33119203_3   4692 GTTACCAAAACAATG--GTAGTGGTATGAAAATAGGCACGTAGACCAATG 4739
                           v i   i   i  --   v   i  i ii    i  ii    i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_33119203_3   4740 GAACAGAACAGAGAACCTAGAAATGAAGCCAAATACTTATAGCCAACTGA 4789
                            i    iv    ii i      i  v   v i i    i i   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_33119203_3   4790 TCTTTGACAAAGCTTATAAAAGCATAAATTGGGGAAGGGACACCCTATTC 4839
                          i  i     i v vvi  i v   vv v       i i i vi  v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_33119203_3   4840 AATAAATAGTGCTGGGAAAACTAGTAAACCACATGTAGAAGAATGAAACT 4889
                           i    i         v    i vv ?       i i         ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_33119203_3   4890 GGATCCTTATCTCTCACCTTATACAAAAATCAACTCAAGATGAATCAAAG 4939
                            i  i  i   v    v           i       i   i    ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_33119203_3   4940 ACTTAAATCTAAGACCTTAAAGTATAAAAATTCTAGAACATAACATCAGA 4989
                           i     v     v  v   v       v ii     v v     vi ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_33119203_3   4990 AAAACTCTTCTGGGCATTAGCTTAGGCAAATAATTCATAACTAAGGCCCC 5039
                         iv  v     vv i v  i v        vviv   v  iv  v i v  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_33119203_3   5040 CAAAGCAAATGCAACAAAAACAAAAATAAGTAAATTAGACCCAATTAAAC 5089
                         v      v v         iv       ii      i   iiv  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_33119203_3   5090 TAAAAAGCTTCTGTATAGCAAAAGAAATAATCAGCAGAGTAAAGAGACAA 5139
                          v    i   i   iivv    i  v iv    iv i   i  i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_33119203_3   5140 CCCATAGAGTGGGAGAAAATCTTTTCAAGCTCTGCATCCGACAAAGGACT 5189
                             i   i           v   v   iiiv ii   i  i  i     
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_33119203_3   5190 AGTATCCAGAGTCTATGAGGAACTC----AAATCAGCAAGAAAAAAA--- 5232
                         v         i v   i i      ----  v   ii  v     i ---
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_33119203_3   5233 --AGTCTCATCAGAAAGTTATCAAAGGACATGAATAGACATTTCTCAAAA 5280
                         -- ii iv  i?i   i viv       iv                v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_33119203_3   5281 GGAGATATACAAACAGTCAACAAATACATGAGGAAATGCTCAACATCACT 5330
                          i           ii i   i  ii      ii i             ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_33119203_3   5331 AATTAT 5336
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.01 (7 / 903), avg. gap size = 2.57 (18 / 7)  


2636 26.35 2.06 1.49  chrX_33170050_33173398     1984  2856 (493)    L1M4_orf2#LINE/L1       31   908 (0)  

  chrX_33170050_3   1984 AGAATCAATATCAATAAAATGGCAATACTGGCCAAAGCAATTTACAGATT 2033
                            v i     iiv   i           vv     vii  i        
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chrX_33170050_3   2034 CAATACTATTCCTATCAAA-TACCAATGGCATTCTTTA-AATAATTAGAA 2081
                            ii v  i         - v   iiv  v  i   i- iv    i---
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG--- 127

  chrX_33170050_3   2082 AAAAACTG-TTTTACAATTAATATGGAACTA-AAAAGAGCCTGAATAGCC 2129
                          v  i   - ii  v    v        v i-  ii  v  v        
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chrX_33170050_3   2130 AAGAAAATCCTAATCAAAAACAAGAAAGCTGGAGGCATTACATTACCTGA 2179
                           i v    i i vv  i  v  v    i      vv i   i v  ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_33170050_3   2180 CTTCAAAATATACTATAAGGGTATAGTACCCAAAACAGCATGGCACTGGT 2229
                         i       iv     i  i v  i    vi   i    ii   i     i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_33170050_3   2230 AAAGAAACAGACACATAGACAAATGGGACAGAATACAGAACCTAGAAATA 2279
                          v iii i     i     iv     i i     vv   ii i       
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_33170050_3   2280 AGGTCACACACCTACAATCATCTGGTCTTTGACAAACCTGACAAAAACAA 2329
                          ivi  i   ii  iii   vi  i i  i     ivv  v   i v  v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_33170050_3   2330 GCAGTGGGGAAAGGGCTTCCTATTCAATAAATAGTGCTGGGATAACTGGC 2379
                         v  i         iiivvi  v     i    i         i      v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_33170050_3   2380 TAGCCATAGGCAGAAGACTGAAACTAGACCCTTACTT-ACAACATATACA 2428
                           ?   i v   i    v    ii i     i   i -   v        
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_33170050_3   2429 AAAATGAACTCAAGGTGGACTAAAGACTTAAATCTAAAATCAAAAACTAT 2478
                              v       ii    ii ?    i     v   i v v        
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_33170050_3   2479 AAAAACTCT-GGAAGATAACCTAG---TAAATACTATTCTGAACATAGAA 2524
                             -    -i     v   v   ---     -  - iv   v v i i-
  L1M4_orf2#LINE/    528 AAAA-CTCTTAGAAGAAAACATAGGNGTAAAT-CT-TCGTGACCTTGGG- 573

  chrX_33170050_3   2525 CCTGGCAAAGAGTTCAT-GACACAGATGCCAAAAGCAATTGCAACAAAAG 2573
                         iiv     v iv   v -  i i-  ii         vvv          
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAACAAAAG 622

  chrX_33170050_3   2574 CAAAAATTGACAAATGAGACCTAA-CTAAATTAAAGAGCTTCTGCACAAC 2622
                         v      v  i    vi   i v - v        i -   i  ii vv 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTC 671

  chrX_33170050_3   2623 AAAAGAAACTATCAACGGAGTAAACAGACAACCTACAAGATGGGAGAAAA 2672
                            i  v        vii   i  v        i   ii           
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_33170050_3   2673 TTTTTGCAAACTATGCATTGGATAAAGGTTTAATATCCAGAACCCAAAAG 2722
                          v        ii  ii  iv     i  vi vi         ivi v  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_33170050_3   2723 GAACTTAAATTTACAAGAAAAGAAGAAAAGAACAAACAACCCCATCAAAA 2772
                              i----      vvv  v  v    ii     i     v  i?   
  L1M4_orf2#LINE/    772 GAACTC----TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_33170050_3   2773 AGTTGGCAAAG-ACATGAA----CACTTTTCAAAAGAAAACATACACGTG 2817
                          i v       - iv    ----  i  i  v      i i     vi  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_33170050_3   2818 GCCAAAAAGCAAATAAAAA--TGCTCAACATCACTAATCAC 2856
                              v     v  i    --            ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (137 / 90)
Gap_init rate = 0.02 (20 / 878), avg. gap size = 1.55 (31 / 20)  


2449 28.37 5.28 0.12  chrX_33194609_33199532     3579  4431 (493)    L1M4_orf2#LINE/L1       12   908 (0)  

  chrX_33194609_3   3579 CCCATGCTTATGAATTAGAAGAATCATCATTGATAAAATGATCATTCTGC 3628
                               i i   i   i     v i vi    v   i   iiv  v  v 
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chrX_33194609_3   3629 CCAAAGCAATCCATAGATTCAAAGCAATTTCTATCAAATTACCAAAATAA 3678
                              vii   i i        v     ii        v v   ivvvvv
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chrX_33194609_3   3679 TTTTTCACAGAATTAGACAAA--AATCCTAAAATTCATATAGAACCACAA 3726
                              ii     v v     i--i                i   vii   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_33194609_3   3727 AAGAGCCTGAATGGCCAAAACAATCCTAAGCAAAAAGAACAAAGCCA-AG 3775
                         ii  v  v    i            i i iv  i          iii-  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_33194609_3   3776 GTGTTACATTACCTGACTTTAAATTATACCGCAA-GCTATAGTAACCCAA 3824
                          vv i   i v  ii i  i   viv   ii   -    i     i v i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_33194609_3   3825 ACAGCATATTATTGGTACATAAAATAGACACACATAACAATGGAA----- 3869
                             ii iv  i   i i - ii       i i v v        -----
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATA-AGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_33194609_3   3870 ----------AGGAATA--CC--TACA------ATCAACTGACAGTCAAC 3899
                         ----------  i    --  --    ------i    i   ivv  i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_33194609_3   3900 AATGTAGATAAAAATAAACTATGGTGAAAGGACACCTTATTCAATAAATA 3949
                           v vv vi  i vi vv v    v     i i vii v     i    i
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_33194609_3   3950 ATACTGGGAAAATTGGCCAGTTATAGGCAGAAGAATGAAACTTGACCTCT 3999
                         i i      v  i   vi ?ii i v   i         ii v    i  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_33194609_3   4000 ATCTCTCGCCATACACAAATATTAACTCAAGGTAAATTAAAGATTTAAAC 4049
                          i   v i     i     v          ii ii  i ?   ii    i
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_33194609_3   4050 ATAAGACCTGAAACTATAAAAATAATAGAAGAAAACCTAGGA--AAATCT 4097
                         i     v  i           v vv           v    ?--      
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_33194609_3   4098 ACTGGACACTGGCCTAGGCAAAGAATTCATGACTGAGGCCTCAAAAGCAA 4147
                         v vv   vi   vi       v iv   v iiv iv i vi        v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_33194609_3   4148 ATTCAACAAAATCAAAAATAGACAAATGGGACTTAATTCAACTAAAATGA 4197
                          vv        vv         i    v      v  iv  v v   viv
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_33194609_3   4198 TTCTGCACAGCAAAAGAAATAATCAACAGAGTGAATAGTCAACCAGCAGA 4247
                           i  ii vv    i  v iv     v i      v  v     vi    
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_33194609_3   4248 ATAGGAGAAAATATTTGCAAACGGCGCATTTGACAAATGACTAATATTTA 4297
                           i                  iviiii  i   i  iv    vi   ii 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_33194609_3   4298 GTATCTGCAAGAAACTTAAACAAC---------AAGAAATAAATAACCCC 4338
                          v  v ii  ii    ivv     ---------  i i i         v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_33194609_3   4339 ATTACAAAGTGGGCAAAAGACATGAG----CATTTTTCAGAAGAAGACAT 4384
                            ?v   i        i  iv   i----     i  vi       i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_33194609_3   4385 ACAAATGGCTAATAAGCACGTGAAA-TATGCTAAACATCACTAATCAG 4431
                                  i         i     -v     v       ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.01 (12 / 897), avg. gap size = 3.83 (46 / 12)  


2769 23.93 4.39 4.72  chrX_33213671_33218635     3562  4472 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33213671_3   3562 TGGAAATAAATTCTGTGTTCATGGATTTGAAGACTGAATATT---AAAAT 3608
                               v v  i ii            v       v      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33213671_3   3609 GTTCATACTACCCAAAACAATGTACAAATTCAATGCAGTCCTTATTACAA 3658
                          viv     v      vii  v    i      i   i   i   i v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33213671_3   3659 TG--AATAGCATTTTAAAAAGAAATAGGAAAA--------AAAAGACATA 3698
                          v-- iiv  v    vviv      v iv  i--------    vv    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_33213671_3   3699 TGAAACCACAAAGAACCCTGAATAG-----ACACATTTTGAAAAAGAAGA 3743
                           i  vii   i i    v      -----   -  i             
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACA-ATCTTGAAAAAGAAGA 199

  chrX_33213671_3   3744 ACAAAATTAGAGGCCTCATATTTTATGGTTCCAAA---CATCATAAAACT 3790
                              i  i    v    i i  iviii  i    ---i ii i   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_33213671_3   3791 ACAGTTATCAAAACAATATGGTAATGATGTAAAGATAGACCCATAGATCA 3840
                              v     i   i i     v  iii   i       vi        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_33213671_3   3841 ATGGAACATAATAGACAGCCCACAGGTA------TACGTT------CAAC 3878
                               i v   v  v  i   v ii  ------   i  ------   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_33213671_3   3879 TCACGTTTGACAAGAGTGCCAAGACTACAGAATGTGGAAAGAATAATCCC 3928
                          v iv  i      i          i ivv    v          i  --
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-- 397

  chrX_33213671_3   3929 TTTCCACATAAGAATAAACAGTGACAGGA--ATTGTGGATATTCACATGC 3976
                            i  ------- i   ii   vii   -- i  --    ?i       
  L1M4_orf2#LINE/    398 TTTTCA-------ACAAATGGTGCTGGGACAACTG--GATAKCCACATGC 438

  chrX_33213671_3   3977 AAACTAACGATTTTGAACTATGGTGTTGCATTGTACACAAATATTAAATC 4026
                            vv  i  vv   i  iviviiv ii  iii  i     v     v  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_33213671_3   4027 AAAATGGATTAAAGAATTAAACATAAGACCTGAAATTGTAGAACTCCTAG 4076
                                  i ?   vi    ii     v  i   i i  i     i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_33213671_3   4077 TAGAAACC-TAGGGGGAAGGTGTCAAGCCATTGGTCTTGGCAATGATTTC 4125
                         v     v -    ? v  iviv  iv v v    vi v       i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_33213671_3   4126 TTGCATGTGATATCAAAATCACAGGCAATAAAACCAAAAATAGACAAATA 4175
                           iv  i   i i     v    i    i    vv         i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_33213671_3   4176 GGACTACATCAAA-TTAAAAAGCTTCTGCCCAGCAAAGGAAACACTCAAC 4224
                              v       -       -   i  iv vv       v  vv    v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_33213671_3   4225 AGAG--GAAAGGCAGTCTTTGGAATGGGAGAAAATATTTGCAAACTATAT 4272
                          i  --i    i  ii ivii                       ii    
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_33213671_3   4273 ATCTGATAAGG-ACTTAATATGCAAATTTTATAGGCAACTCTTTCAACTC 4321
                                    -    i-   v  i v v    iiv       v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_33213671_3   4322 AATAGCAAAAAAAGGAAGAAAAAGAAAAAGAAAGAAAGAAAAGAAAAGAA 4371
                             ------------ v       v   v  vvv  -------------
  L1M4_orf2#LINE/    787 AATA------------ATAAAAAGACAAATAACCCAA------------- 811

  chrX_33213671_3   4372 AAGATTAAAAAGTGGGCAAAGGACTTGAGTAGACACTTCTCCAAAGAAGA 4421
                         ----  ?    i           i    i      i              
  L1M4_orf2#LINE/    812 ----TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_33213671_3   4422 CATAAAAATGGTCACCAGGTGTAGGAAAGGGTGCTCAACACCAGGAATCA 4471
                         i   v      i  vi i iii v    i i         i  ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_33213671_3   4472 T 4472
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.49 (128 / 86)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.15 (83 / 20)  


2063 22.63 1.09 3.47  chrX_33245437_33249132.rev     1999  2546 (1150)    L1M4_orf2#LINE/L1        4   538 (370)  

  chrX_33245437_3   1999 AAAGACATACCATCTTCTTGAATTGGCAGACTTGATATTATTAGAATGGC 2048
                              i  v    v   v  i     v      i     i   ii     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_33245437_3   2049 AATATTTGCCAAAATGGTACACAACAATTGATCTACAGCAATCAATGCAA 2098
                             i iv     --------------           - v    i    
  L1M4_orf2#LINE/     54 AATACTCCCCAAA--------------TTGATCTACAG-ATTCAACGCAA 88

  chrX_33245437_3   2099 CCCCTATCAAAAATGCTAACCTCAATTTTTTGCAAAAATTGAACTGTTCA 2148
                         i           - v i i iv v-         i       vvv i v 
  L1M4_orf2#LINE/     89 TCCCTATCAAAA-TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA 136

  chrX_33245437_3   2149 TCCTAAAATTAATGTGGAATCACATGGGATCCAAAGTAGTTAAACTAATC 2198
                                   v  i     vii  v    i   i i   ii   vi    
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_33245437_3   2199 TTTTAAAAAGAAAAACAA-GTTGAAGGACTCATAGATTCCAATTTAACAT 2247
                           v-        i     -    i        i vv i       v v v
  L1M4_orf2#LINE/    187 TTG-AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_33245437_3   2248 CTTATTACAATGCTATTATAATCAAGGGAGAGTGGCAGTGGTGTACATGT 2297
                             i     v    ivi        iv  v    i v   ii  vivi 
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_33245437_3   2298 AGGCATATATGCCACTGGAATTGAATTGAGAGTCCAGAAATAAGTCCTCA 2347
                           i      vii  v      v                     ii  vi 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_33245437_3   2348 CATTT-TGGCCAATGGAACTT-GATAAGGG-AACAAGACAATTAAAGTAG 2394
                              -   i    v  vi  -  i     -iv      v   v  vvi 
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_33245437_3   2395 AAATGAAC--TTTGTTTTAATTAATGCTGCTGGGACAATTGTATATTCAC 2442
                         i  v   i-- i -   i  iv    v           i  v   ?i   
  L1M4_orf2#LINE/    386 GAAAGAATAGTCT-TTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_33245437_3   2443 AGGCAAATTAGTGAATTTGCATACTTGCCTCACCTCATATGCAAAAATTA 2492
                          v     vv i    v   v iv i i      vi     i         
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_33245437_3   2493 ACTCTAAAAGAATCAGGGACTGAAATATAAGAACTAAAACTATAAAACTC 2542
                             v   v i    ?i   iv    i     i                 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_33245437_3   2543 TTGG 2546
                           i 
  L1M4_orf2#LINE/    535 TTAG 538

Transitions / transversions = 1.22 (67 / 55)
Gap_init rate = 0.02 (11 / 535), avg. gap size = 2.27 (25 / 11)  

1300 19.14 9.43 0.57  chrX_33245437_33249132.rev     2856  3205 (491)    L1M4_orf2#LINE/L1      528   908 (0)  

  chrX_33245437_3   2856 AAAACTTTTAAGAGAAAA--TAAGTGTAAATGTCCATGACCTTGTTTTAG 2903
                               i   ii      --  i ?      v i i        vv    
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_33245437_3   2904 -------------AGA-ATGACACCAAAAGCA-AA---ACAGAAGAGAGA 2935
                         -------------   -               -  ---   i    i i 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_33245437_3   2936 ATAGCTTAATTAATCTTCATCAAATTTTAAAACTTCTATGTTTAAAAAAA 2985
                             v v    iiv          v  v       i i  i  v   ii 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_33245437_3   2986 ATCACAATGAAGAAAGTCAAATGACAACCCACCGAATGGGAAAAA----- 3030
                         --   v  v        v   v          v        i   -----
  L1M4_orf2#LINE/    678 --CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_33245437_3   3031 TGCAAATTATATATCAGATAGAGGATTTGTATCTAGACCCTGTAAAAAAT 3080
                                i       v    ii   i       i   viv i    i  i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_33245437_3   3081 T-TTACAACTCTATATTAAAAGAACAAATAA------TTAAAAATGA-CA 3122
                          -         v   v     ii        ------ ?       i-  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_33245437_3   3123 ACATATATGAATAGATATTTCTCTAAAACAGGTATACAAATGGCCAGTAA 3172
                          viv  v        i       i   iv  i              i   
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_33245437_3   3173 GTGCATGAAATGATCTGTAACATCATTTTTAAG 3205
                          ii       v   vivi       ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (39 / 26)
Gap_init rate = 0.03 (10 / 381), avg. gap size = 3.50 (35 / 10)  


2887 26.35 2.80 1.01  chrX_33255201_33260117     3533  4424 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33255201_3   3533 TGGAAAAACATTCCATACTCATAGGTGGGAGGGATCAATATTGTTAAAAT 3582
                               i i  i    ii    i i v   i iv i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33255201_3   3583 GACCACAGTGCCCAAAGAAATTTACAGATTGAATGCTATTGCTATCAAAC 3632
                          i v i v v      vvi  i        v  i  v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33255201_3   3633 TACCAGTAACCTTTTTCATAGAA-TT-ATAAAAAAATTCTGAAAATCATA 3680
                          v    ivi       iii    -  - i  ivvi  i  i   v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_33255201_3   3681 TGGAAA---AAAAGAGCT----TAGCCAAAACAATCTTAAGCAAAAAGAA 3723
                               ---  ii  v i----                i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_33255201_3   3724 CAAAGCTGGTTATATCACACTACCTGACTTCAAACTACACTACAAGGCTA 3773
                              i   vvivv       v  ii i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_33255201_3   3774 TAGTAATCAAAATGGCATGGTACTGGTACAATAACAGACATATAGACAAA 3823
                         i         i ii ii         i i  vi i           iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_33255201_3   3824 TGGAATAGGTTGGAGAACCAAGAAATAAGGCTGTACGCCTACAACCATCT 3873
                                 iv v    ii v        iv ii   iii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_33255201_3   3874 GATCTTTGACAAAGCTGATAACAACAAGCAATGGGGAAAGGAC--TCCGT 3921
                            i  i     i v  vi  v v  vv            i i--  -- 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC--T 398

  chrX_33255201_3   3922 ATTAAATAAGTGGTGCTGGGAAACCTAGCAAGCCATATGCTGAAGATTTA 3971
                         v  v  i  i           v v  i vv ?   i    vi    v v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_33255201_3   3972 AATTAGATCTCCTTTCCCTTACCATATACAAAA-TGAACTCAAGATGGAT 4020
                          i  i  i -   vi i vi             - v       i      
  L1M4_orf2#LINE/    449 AGTTGGACC-CCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_33255201_3   4021 TAAAGACTTACATGTAAAGCCTAAAAGTGTTAAGAACCCTAGAAAAATAG 4070
                         i ?    i  v      iiv      v i -  i vi i     i  v v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAAC 546

  chrX_33255201_3   4071 CTAGG---AAATTCCATTTTG-GACATTGGCCCAGGCAATGGTTTCAT-G 4115
                         v    ---    i----  i -   v    vii             v - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC----TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_33255201_3   4116 ATAGAGACTCCAAAAGCA-ATGCAACAAAACAAAAACT-GACAAGTGGGA 4163
                            v-   v         - v         v     v -  i  i v   
  L1M4_orf2#LINE/    593 ATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_33255201_3   4164 CCAAATTAAACTAAAGGGCTCCTGCACAGCAAAAGAAACTATCAACAGAG 4213
                          ivv  i   v v  iii  ii  ii vv    i  v        v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_33255201_3   4214 TATACAGATAACCTACAGAATAGGAGAAAACATTTGTCAATGATGAATCT 4263
                          iv v   i    i       i        i     iv   v  iv    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_33255201_3   4264 GATAAAGGTCTAATATCCAGAATCTATAAGGAACTTAAACAAATCAACAA 4313
                              i  v  vi          v     i     ivv    v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_33255201_3   4314 GCAAAAAACAA----TCCCATTAGAAAATAGACAAAGGACATGAACACAC 4359
                         vv    i    ----i  v   ?i     i i       iv    i v  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_33255201_3   4360 ACTTTTCAAAGGAAACCATACACATTGCCAACAAGCATATAAAAA--TGC 4407
                          i  i  v  i   ivi     v  v     i     i  i    --   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_33255201_3   4408 TCAGCATCACTGATGAT 4424
                            i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.89 (34 / 18)  


 273 29.52 1.90 0.00  chrX_33271107_33273215.rev      405   509 (1600)  C L1M4_orf2#LINE/L1   (0)   908   802  

C chrX_33271107_3    509 AACAATCTGAGTTTGAAATGGGCAAAAGTTTTAAATAGACACTTCACAAA 460
                           i  i ii v ?vi           i v   i        i   v v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

C chrX_33271107_3    459 AG--TACATGCAAATAAATAAAAATCACATGGAAAGCCACTTAAAGTCTC 412
                           --v i  i     iivi  v  v      i    vii  i  vi  v?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

C chrX_33271107_3    411 CAGGCAT 405
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.50 (18 / 12)
Gap_init rate = 0.01 (1 / 107), avg. gap size = 2.00 (2 / 1)  

3225 23.69 5.13 1.71  chrX_33271107_33273215.rev      744  1621 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33271107_3    744 TGAAAAGACATCTCATGTTCATAGACTGAAAAAATTAATATTGTTAAAAT 793
                           i     i   i         i  i  i  i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33271107_3    794 GTCTGTACTACCCAATGTGATCTACAGATTCAA-----TTCCTATCAAAA 838
                          v vi    v     vv                ----- i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33271107_3    839 TCTGAATGACATTTTTTACAGAAATGAACAA-----TTCTAAAATTTATA 883
                           iv iivi v      i       vi    ----- i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_33271107_3    884 TAGAACCACAAA------AGAATAGCCAAAGTCATCTTGATAAAGAAGAA 927
                          i   vii   i------            iiv       v         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_33271107_3    928 CACAGCTGGAGGCATCACAATTCCTGATTTCAAAATATGTTACTGAGCTA 977
                           v  i      vv     v    ii         iv ii   vi     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_33271107_3    978 CAATAATTAAAACAGTGGGATTCTAACATAAAGACAGACACATAGACCAA 1027
                           i    i  i      v i v  ii     i  i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_33271107_3   1028 TGAAACAGAATAGAGATTCCAGAAATAAACCCACAGATATGCAGTCAATA 1077
                           i  i     v    v                i v  v iii      v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_33271107_3   1078 TATCTTTGACAAGGATGTCAAGAACACAAAGTGTGGAAAGAATAGTCTCT 1127
                         v  i  i       i  i     v  ivv i  v              i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_33271107_3   1128 TCAGTGAATGATACTGGGAAGACTAGGTATTGACATGCATA-GTATACAA 1176
                            iii    i i      vi   i i  ?iv       v - v  iv i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_33271107_3   1177 TTGGAACCCTGTCTTACACTGTGCACAAAAATAAACTCAAAATGGATTAA 1226
                              v    ii  i    ii ii        v              i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_33271107_3   1227 AGACTTAAATGTAGGACTTGAAATTGTAAAACTTATTGAAGAAAGCATAA 1276
                             i        i  vi i   i i       iv v       i    i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_33271107_3   1277 AGGAAAACCTTGTTTATGACCTTCTTTATTAGTCTTGGCAATGATTTATT 1326
                         i? v   i   ---ii       -------i vi v       i   v  
  L1M4_orf2#LINE/    551 GNGTAAATCTT---CGTGACCTT-------GGGTTAGGCAATGGTTTCTT 590

  chrX_33271107_3   1327 AGATATGACACCAAAA-CACAAGCAA-AAACCCCAAAATAGAAAAACTA- 1373
                                         -         -   vvvv        v   i i-
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_33271107_3   1374 --------------AAAAACTTCTGCACAGCAAAGGAGACAGTCAACACA 1409
                         --------------        i  ii vv       v  vi    ----
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA---- 686

  chrX_33271107_3   1410 GTAGAGTAAAAAGTCAAGCTCTGTGTTGAAAGTAAATATTAGCAACT-GT 1458
                          - i   i     v   v iviiviv  ii  v       v    v -i 
  L1M4_orf2#LINE/    687 G-AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_33271107_3   1459 GCATCTGATAGGAGATTAATATCCAAAGTATGTAGGAAACTCCTACAACT 1508
                         ii        i i  i vi      i i   i  iii     i       
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_33271107_3   1509 CAGTAGGAAGAA-------AGCCCAATTACAAAATGG-CAAAGGACATGA 1550
                           i  iv  i  ------- i       ?v       -       iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_33271107_3   1551 ATTGAAATTTCTC--AAAAAAACAAACAAATGGCCACGAGATATATGAAA 1598
                           v  v       --  i  i i v           vv iii i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_33271107_3   1599 GGGTGCTCAACACTACTCATCTT 1621
                         i i         ii ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (133 / 71)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.00 (60 / 15)  


2536 28.54 2.70 0.67  chrX_33324318_33331594      492  1381 (5896)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_33324318_3   1381 TGGAAAAACATTCCATGCTTATAAATAGGAAGAATCAATATTGTTAAAAT 1332
                               i i  i     i i  ii  v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_33324318_3   1331 GACAATAATGGCCAAAGTAATATATAGATTCAATGCTATTCCCATTAAAC 1282
                          i     v vv     v i  v  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_33324318_3   1281 TCTCATTGACATTCTTCACAGAACTAGAAAAA--AATTTTTAAATATAAT 1234
                           i  vivi v  i  ii     v v  v  i--i  ii v    - v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT-TCAT 149

C chrX_33324318_3   1233 ATAGAACCAAAAAAGAAGTCGAATAGCCAAGGCAATCCTATGCAAAAAGA 1184
                           i   viiv  ii  vviv          ii     i iviv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

C chrX_33324318_3   1183 ACGAAGCTGGAGGCATCACGCTACTCAACATTAAACTATAATACAGGACT 1134
                           i   i      vv    i  v i   iv i   viv  v    iii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

C chrX_33324318_3   1133 AAAGTAACCAAAACAACATAGTACTGGTACAACAACAGATACTTAGACCA 1084
                          v     i   i   iii i       i i  vi i   i iv    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

C chrX_33324318_3   1083 ATGGATCAGAATACAGAACATAGAAATAAGACCATACACCTGCAACTATC 1034
                              vi     vv   iivi        iv       ii iiiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

C chrX_33324318_3   1033 TGATCTTTGACAAACCTGGCAAAAACAAACCATGGGGAAAGGATTCCCTA 984
                             i  i     ivv  v   i v  vv v          i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

C chrX_33324318_3    983 TGCCATAAATGGTACTGGGATAACTGGGTAGCCATAAGCAGAAGATTGAA 934
                          v v i       i      i      i  ?   i v   i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chrX_33324318_3    933 ACTGGACTCCTTCCTTACACTATATTCAAAAACTAACTCAAGATAGATTA 884
                         ii     i   v   i    i    v      i        i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chrX_33324318_3    883 AAGATTTAAAAGTAAAACCTGAAACTATAAAAAATCCTGGAAGACAACCT 834
                         ?   ii    v    i v  i           v-  i i     v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACAT 548

C chrX_33324318_3    833 CAGCA-ATACCATTCAGGACATATGCATGAG-CAAACATTTCAT-GATGA 787
                         vi ?i- v i -   iv   v -  vi v  -   vvi    v -   - 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGAT-A 595

C chrX_33324318_3    786 AGATAACAAAAGCAATTGCAACAAAAGAAAAAATTGACAAGTGGAATCT- 738
                         v  i v        vvv                 v  i  i v i ii -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chrX_33324318_3    737 -----AGTTAAAGAGCTTCTGCACAGCAAAATAAACTATCAACAGGGTAT 693
                         ----- i     i -   i  ii vv    iv v        v ii  iv
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

C chrX_33324318_3    692 ACAGACAACCTACGGAATGGGAGAAAATTTTTGCAATCTATTCAACTGAC 643
                          v        i  i              v       vii  vi v    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

C chrX_33324318_3    642 AAAGGTCTAATATTTAGCATCTACAAGGAACT--TA-AATTTA-CAAGAA 597
                           i  v  vi   ii  v  v  i  i     --  -  i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

C chrX_33324318_3    596 AAAAA-----AACCCCATT-AAAAATGGTCAAATGACATGAATAGACACT 553
                            i -----     v   -        v    v  iv          i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chrX_33324318_3    552 TCTCAAAAGAAGGCTTACATGCAGCCAACAA--ACATAAAAAAA-ACTCA 506
                             v       iiv    viii     i  --    i    i -i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chrX_33324318_3    505 ACATTACTGATTAT 492
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (151 / 100)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.67 (30 / 18)  

1486 29.50 5.51 0.81  chrX_33324318_33331594     6169  6785 (492)    L1M4_orf2#LINE/L1      263   908 (0)  

  chrX_33324318_3   6169 CAGCATATTATTGATACAAAAACAGATGCGTGGACTAATGGCATAAAATA 6218
                            ii iv  i  ii i  ii i   iiii i  ii     v   i   v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_33324318_3   6219 GTGACCCCATAAAT-----CACATATTTGCAGTCAAAGGATTTTTGACAG 6263
                          v  vi   v    -----  i i    iii     vv      i    i
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_33324318_3   6264 AGGCACCAAGAACATACACTGGGGACAGGATACCCTCTTCAAGAAATGTT 6313
                         i  ii      v   v  v      v  i   vi  i     v     v 
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_33324318_3   6314 GCTGAAAAAA---AATATCCATATGCATAAGATTGAAACTGGACCCATAT 6360
                             ii v  ---i   ?   i     v    v    ii       v  i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_33324318_3   6361 CTC-CACCATAAACAAAAATCAACTCAA-----------GACTTCAACGT 6398
                            -       v        i       -----------   i v  i  
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_33324318_3   6399 AAGACCCAAAACTCTAAAATGACTAGAAGAAAACTTAAGGGAAACACTTC 6448
                             v i      v     ivvi           v  i ? v  vv    
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_33324318_3   6449 AGGACAT-GGCTCTAGGCAAAGACATTATAGCTAAAACCTCAAAAGCACA 6497
                         iv   v -  v -       v iiv iv   v  vi  vi          
  L1M4_orf2#LINE/    563 GTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_33324318_3   6498 GGTAACAAAACCAAAAATAAGAAAAATGAGACTATACTAAACCAAAATGA 6547
                         i i       vv       -  v    vi    vi ii   viv   viv
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATA-GATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_33324318_3   6548 TTCCGCACACCAAAGAAGACAGTCAACACAATAAAGGGACAAACTGTTAA 6597
                           ii ii vi     i v  vi    v v i i  ii     v iiivi 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_33324318_3   6598 ATGCAAGAAAATATTTTCAGAATATTTACTCAATAAGAGACTATTATCTC 6647
                            vi           v  i vi  v  iiii     i    vv    iv
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_33324318_3   6648 AAATGCACGAGGAAATAAAAAAACTCAACAGTAAAATAAAAACAAATAAT 6697
                         i   ii ii i   v vvv v       i i     --- i        i
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAA---AGACAAATAAC 807

  chrX_33324318_3   6698 TCCACT--AAAATGGGCAAAG-----------ACACTTATCAAAGGAAGT 6734
                         i v i --             -----------   i  v  v  i    v
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_33324318_3   6735 CATTCAAATGCAAAACAGGTACATGAAAAAATGTTCACCATCGCTAATCA 6784
                         i  v      vvv  i i i         i   i   v    i???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_33324318_3   6785 T 6785
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.40 (105 / 75)
Gap_init rate = 0.02 (10 / 646), avg. gap size = 3.90 (39 / 10)  


1066 21.76 3.35 2.51  chrX_33334753_33336971.rev      530   768 (1451)    L1M4_orf2#LINE/L1       18   258 (650)  

  chrX_33334753_3    530 TTCACATATTAAAAGA--------TGTTAACATGTCAACACTCCACGTGT 571
                             iiv   ii    --------      v   v   i     v ivi 
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_33334753_3    572 TAATCTATAGATTTGATGTATTCTGTACCATAACCCCAGTTGACTTTTTT 621
                          i     i     ii i i v  iv  i  v  i     i  v       
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_33334753_3    622 TTTTTTGGAGAAATTAACAAACTGATCCTGAAACTCATATGGAGGTACAA 671
                         ------ v       i    i        i   i         ii i   
  L1M4_orf2#LINE/    118 ------GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_33334753_3    672 AGTGCCAAGAATAGCCAAAACAATCTTGAAAGGGAAGAATATAGTTGGAG 721
                         i vi  v                        ii      i v        
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_33334753_3    722 GCCTCACAGTTCCTGGATTTAAAACTTACTAGGAAGTTACAGTAATC 768
                          v      v    iiiv  i           vi   i          
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

Transitions / transversions = 2.06 (35 / 17)
Gap_init rate = 0.01 (2 / 241), avg. gap size = 7.00 (14 / 2)  

2224 18.71 5.24 6.89  chrX_33334753_33336971.rev     1061  1728 (491)    L1M4_orf2#LINE/L1      252   908 (0)  

  chrX_33334753_3   1061 AGTAATCACAGA--GTGTGGTAGTGGCAGAAGGATAGTCGTATAAAT-GA 1107
                                 -   --        v     v        v i    i  -i 
  L1M4_orf2#LINE/    252 AGTAATCA-AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_33334753_3   1108 TGGAGTAGAATTTATAGTCTAGAAATAAACCTTTACATTTATGTTAAGTT 1157
                             i       v v    i           iv          v v i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_33334753_3   1158 GATTTTCAACAAATGTTCCAAGAC-----AATGGGGAAA--ATAACCTTT 1200
                                i    iv  v       -----          --   ii    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_33334753_3   1201 TCAACAAACGGTGCTGAAAAAACTGACAATCCACATGAAAAGGAATAAAA 1250
                                 i       ii v     ivv ?       v   i    i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_33334753_3   1251 TTAGATTTCTACCTCACTCTGTATGCAAAA-----CTTCAAATAAATAAT 1295
                           i  iii         v ii   i     -----  iv    ii  v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_33334753_3   1296 AGATCTAAATGTAAGAGTTAAACTTC---AACACATAGAGTGAAACACAA 1342
                            i             i    vi v---   v v    ivi     i i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_33334753_3   1343 AACTAAGTTTATGTGACTTTAG-TTAGGCAAAGTTTCCTTATATACAATA 1391
                         i?v   i i vi     i  i -        v v  i    v   ii i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_33334753_3   1392 AGAAAAGTCTGAGTGACAAAAAAATAAATAAATAAATTGGACTTCATTAG 1441
                         vv     ivii  ii      i  v     i                i i
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_33334753_3   1442 AATTTAAAACTTTTCTACTGCAAATAGGA-A--ATCAGGAAAGTGAAA-G 1487
                             v         v i  v    --   - --    i          - 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAA--GGACACTATCAAGAAAGTGAAAAG 698

  chrX_33334753_3   1488 ACTACCCACAAAATGAGA-AAAATATTTGCAAAATATGTATCTGATAAGG 1536
                           v       i    i  -              vi  i            
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_33334753_3   1537 GGATATATATTATCTGATAAGGGGATATATGTTATTTATATATTATCTAT 1586
                          -------------------------------- i  i   ----- i v
  L1M4_orf2#LINE/    749 G--------------------------------ACTTGTAT-----CCAG 761

  chrX_33334753_3   1587 TCTTAATATATAAATAACTC--ATGAGTCAATAATAAAAAGAAAAACCAC 1634
                         ----          v     -- ii v               v   iv  
  L1M4_orf2#LINE/    762 ----AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_33334753_3   1635 CTAATT-AAAAAGGAGTCATGGATTTTAAAAGGAATTTCTCCAAA----- 1678
                          i    -     v i iv v      v  v  iv           -----
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_33334753_3   1679 ---ATAAACTGCTTCAATAAGTACATGAAAAGATGCCCAACATCATTTGT 1725
                         --- i   iv  --       i              i        ?????
  L1M4_orf2#LINE/    858 TATACAAATGGC--CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_33334753_3   1726 AAT 1728
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.54 (74 / 48)
Gap_init rate = 0.03 (20 / 657), avg. gap size = 4.05 (81 / 20)  


2228 27.96 1.73 0.67  chrX_33344279_33349791.rev     2646  3396 (2117)  C L1M4_orf2#LINE/L1   (0)   908   150  

C chrX_33344279_3   3396 ATGAAAGTG---GGCATCCTCATATAGCCAAGACAATCCTAAGCAAAAAG 3350
                            i  i  ---  v i  vv -        i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGA-ATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_33344279_3   3349 AACAAAGCTGGAGGCATCACGTTACTCAACTTCAAACTATACTACTGGAC 3300
                                i      vv    ii v i   i      viv      viii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_33344279_3   3299 TACAGTAACCAAAACAGCATGATACTGGTACAAAAACAGACACACAGACT 3250
                                 i   i    ii  i      i i  ii i     i i   ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_33344279_3   3249 AATGGAACAGAATAGAGAACTCAGAAATAAGACCC-TATACCTACAA-CA 3202
                                i     v    iii         -    -  i ii  iii-  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCA 347

C chrX_33344279_3   3201 ATCTGACCTTCAACAAACCTGACAAAAACAAGAAATGCAAAATGGATTCC 3152
                           -   ii   i    ivv  v   i v  vvv    vii  v i  vvi
  L1M4_orf2#LINE/    348 AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_33344279_3   3151 CTATTTAATAAACGGTGCTGGAAGAACTGACTAGCCATGTGCAGAGAATT 3102
                           v  i  i   i        i v     iv  ?   ii    i ii v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_33344279_3   3101 GAAACTGGACCCCTTCCTTACACCTTACACAAAAATCAACTCAAGATAGA 3052
                            ii         v   i     v  i        i       i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_33344279_3   3051 TTAAAGACTTAAATGTGAAACCCAACACTATAAAAACCC-AGAAGAAAAT 3003
                          i ?    i       i i v i  v         vi i-         i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_33344279_3   3002 CTAGGCA-ATACCATTCAGGACATAGGCATGAGCAAAGATTTCAT-GCTG 2955
                         v    ?i- v i -   iv   v v  vv ii    v i    v - v -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

C chrX_33344279_3   2954 AAAACACCAAAGGCAATTGCAACAAAAGCAAAAATTGACAA-TGGGATCT 2906
                          vi        i   vvv          v      v  i  - v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

C chrX_33344279_3   2905 AATTAAACTAAAGGGCTTCTGTACAGAAAAATAGTCTATTATCAGAATGA 2856
                         v  i   v v  iii   i   i vvv   iv vv    i vv i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

C chrX_33344279_3   2855 ACAGACAACCTACAGAATAGGAGAAAATTTTTACAACCTATTCATCTGAC 2806
                          v        i       i         v   i   vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

C chrX_33344279_3   2805 AAAGGTTTAGTGTCAAGCAACTACATGTAACT--TA-AATTTA-CAAGAA 2760
                           i  vi v  i  v  v vv  i viv    --  -  i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

C chrX_33344279_3   2759 AAAAACAAACAACCCTATTAAAAAGTGGGCAAAGGGCATGAACAGACACT 2710
                            i     i     v   ?    i          iiv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chrX_33344279_3   2709 TCTCAAAAGAATATATTTATGCAGCCAACAAACATATGAAAAAAACCTCA 2660
                             v      v    vi viii     i  i  i       i vv    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chrX_33344279_3   2659 ACATCACTGATTAT 2646
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (126 / 80)
Gap_init rate = 0.02 (15 / 759), avg. gap size = 1.20 (18 / 15)  

1821 26.09 5.25 1.93  chrX_33344279_33349791.rev     3785  4355 (1158)    L1M4_orf2#LINE/L1        1   590 (318)  

  chrX_33344279_3   3785 TGGAAAGATATCATGTGTTCATGGATTGGAATCATTAACATCGTTGAAAT 3834
                                     vii                vvv    i  i   i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33344279_3   3835 GTTCATACTATCCAAAGAGATCTGTAGATTCAGTGCAGTCCATACTAAAA 3884
                          viv     vi     vv     ii       ii   i   v  ii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33344279_3   3885 TACCAATGACGTTCTTCACAGAAACAGAAATGACAACCCTAAAATTTACA 3934
                          v   iivi v  i  ii      iv  v v vii i         i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_33344279_3   3935 TGGAACCACAAATGAATGAGCCAGAATAGCTAAAGCAATTCTGAGCAAAA 3984
                              vii   -- i--  v          i   i    ii   iv  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAA--GG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_33344279_3   3985 AGAACAAAGTTGGAGACATCACATTACCTGTCTTCAAAATTGACTAGAAA 4034
                                        ivv     i v  iivi       i v    v   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_33344279_3   4035 GCTATAGTGACTGAAACAGCATAGTGTTGGCATAAAAATAGACACATAGA 4084
                             i   i iii i    ii i  ii        ii       i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_33344279_3   4085 CCAATGCAACA-AAT---GCATCT-GA--------CACACA------GCC 4115
                         i     v  i -   --- vi  i-  --------  i   ------ i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_33344279_3   4116 AACAAATTTTTG-CAATAGGTGACAAGAACACACATTAGTGAAAGAACAA 4164
                           ivi     i -   -i    v     v  iv  v i v       i i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAA-GGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_33344279_3   4165 TCTCTTCAATAAATGATGCTAGGTAAACTGCATATTCACATGCAGA-GAA 4213
                            i     i     i    i  vv     v   ?i        i -   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_33344279_3   4214 TGAAGCTAGACCTCTACCTCGACAT-ATATACAAAAA--AATTTTCCAAA 4260
                              i i    i       -   i-           --  i -- v   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTC-ACACCATATACAAAAATTAACT--CAAAA 492

  chrX_33344279_3   4261 TTAACTA----CTTAAGTGTACAA-CCAAAATTATAAAATCACAAGGATA 4305
                          vi ii ---- i   i    vi - i    i       iiviv  i v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_33344279_3   4306 AAATTTCATGGGTA-AAAGCTCCATGACATTGGCGTAGGCAAGGATTTTT 4354
                            ---   i  ?i-   v  i i    v    vv       v i   i 
  L1M4_orf2#LINE/    543 AAA---CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_33344279_3   4355 T 4355
                          
  L1M4_orf2#LINE/    590 T 590

Transitions / transversions = 2.06 (99 / 48)
Gap_init rate = 0.03 (18 / 590), avg. gap size = 2.28 (41 / 18)  

 975 23.44 1.56 4.38  chrX_33344279_33349791.rev     4703  5022 (491)    L1M4_orf2#LINE/L1      598   908 (0)  

  chrX_33344279_3   4703 ACCTCAAAAGCACAGACAATACAAAAAGCAAATATAGGCAAATGGGATTG 4752
                           vi          ii   i ---    v   v    ii    v   i v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACA---AAAGAAAAAATAGATAAATTGGACTT 644

  chrX_33344279_3   4753 CATCAATCACATCAATCTAAAAAGCTTCTCTACAACAAATGAAACAATCA 4802
                               -------   -      -   i v i vv    v  v  v    
  L1M4_orf2#LINE/    645 CATCAA-------AAT-TAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_33344279_3   4803 ACAGAGCAAAGGGACAACCTAGAGAATGGGAGAAAATATTTGCAAGGTGT 4852
                          v i  ii  ii       i v                       ivii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_33344279_3   4853 GCATCAGACAATGGGTTAACATCCAGAATATTTAAGGAACTCACACAACT 4902
                         ii   v  i  v  ii vii           v   i      vi      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_33344279_3   4903 CAGTAGCAGAAA----AATTATCTAATCAAAAAATGGACAAAAGTCCTCA 4948
                           i  ii i   ----   v i i   i?        i    i vii v 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_33344279_3   4949 TTAGGTATTTTTGTCAAAAAAAGACATATAAGTGGCCAAGCAGTATATGA 4998
                         v   ii    i -- v   i    i   i  i       vv  i i    
  L1M4_orf2#LINE/    836 ATAGACATTTCT--CCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_33344279_3   4999 AAA-ATGCTCAACCTCACTAATCAT 5022
                            -         v   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (47 / 27)
Gap_init rate = 0.02 (7 / 311), avg. gap size = 2.71 (19 / 7)  


2678 26.62 4.10 0.91  chrX_33349932_33354531.rev     3231  4109 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_33349932_3   3231 GGAAAGATATTCCACACTCATGGGTAGGAAGGATCAATATTGTTAAAACG 3280
                                   i   iii      i v     iv i           i i 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_33349932_3   3281 GCCACACTCCTCAAAGCAATTTAAAGATTCAATGTTATTCCTAGCAAACC 3330
                           v i     i    vii  i  v        i iv  i    v    vi
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_33349932_3   3331 ACCAATGACATTTTTCACAGAATTAGAAAAAGCT-ATTTTAAATTTCATA 3379
                         v   iivi v     ii     v v  v  -   -  ii    v      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATA 150

  chrX_33349932_3   3380 TGGAATCAAAAAAGGGCCAGAATAGCCCAAACAATCCTAAGCAAAAAGCA 3429
                              viiv  ii iv           v        i i iv  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_33349932_3   3430 CAAAGCTGGAGCGA-TCCCATTAACCAACTTCAAACAATACTGCAGGGCT 3478
                              i     -  -  v  i vv    i      vvv    i  ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAG-GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_33349932_3   3479 ACAGTAACCAAAACAATATGATACCGCCACAAAAACAGACACATAGACCA 3528
                                i   i   i i  i   i v  i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_33349932_3   3529 ACAACAAAACAAAAT--GGAGCCCAGAAATAATGCCACACACCTACAACC 3576
                          iii---  i i   --i   i          vv   i   ii  iiii 
  L1M4_orf2#LINE/    300 ATGG---AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_33349932_3   3577 ATCTTCTCTTTGACAAAGTTGACAAAA--A--CAACGGGGAAAGGACTCT 3622
                          vi vv i  i     i v  v   i -- --   i        i ivv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_33349932_3   3623 CTATTCAATAAATGGTACAGGCATAACTGGCTAGCCATATGCAGAAGTTT 3672
                           v     i       i v  v i      v  ?   i     i   vv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_33349932_3   3673 GAAACTCGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGA 3722
                            ii v       v   i                 i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_33349932_3   3723 TTCAAAAGTTAAATGTAAAAATGAAAACTATAAAAACCTTGGAAGATAAC 3772
                          iv? i vi         i iiv            vi   i     v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_33349932_3   3773 CCAGG---AAATACCATTCTGGACTTAAGACCCAGTAACGACTTCATGAC 3819
                         vi   ---    -- -   vv   i vi iiivi i  i ii   v iiv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_33349932_3   3820 AAAGACACTATAAGCATG-GCATCAAAAACAAAAATTGATAAGTAGGAAC 3868
                         v v     i v     ii-   v     iv      v     i v   vi
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_33349932_3   3869 T------AACTAAA--CTGGCATGCTTCT--GCACAGTA---AGAGAGTA 3905
                          ------  i    --  vvii      v-- v   v  ---   i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_33349932_3   3906 AACAGACAACCTGAACAATGGGAGAAAATATGTGCAAACTATGCCTCCAA 3955
                           v        iiv v               v      ii  iiv  ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_33349932_3   3956 CAAAGGTATAATATCCAGAATCTATAAGGAACTTCAACAAATTAACAAGC 4005
                         i  i  vv vi          v     i     iiv    v i  i  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_33349932_3   4006 AAAGCACAA----CCCCATTAAAAAGTAGGCAAAGGACATGAA----CAC 4047
                            iv    ----   v   ?    i i         iv    ----  i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_33349932_3   4048 TTTTC-AAAGAAGACATACACGTGGCCAACAA--ACATGAAAAAATTCTG 4094
                           i  -        i     vi       i  --         i  v  v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_33349932_3   4095 AACATCACTGATCAT 4109
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (142 / 89)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 2.20 (44 / 20)  


3025 27.05 2.36 0.45  chrX_33412279_33414180.rev      521  1411 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33412279_3    521 TGGAAAAACATTCCATGCTTATGGATAGGAAGAATCAATATCGTGAAAAT 570
                               i i  i     i i      v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33412279_3    571 AGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTGTCTCCATCAAGA 620
                         i  v     v      v i  i  i        i  vi  i i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33412279_3    621 TACCATTTACTTTCTTCATAGAATTAGAAAAAACT-ACTTTAAATTTCAT 669
                          v   vi i i  i  iii    v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_33412279_3    670 ATGCAACTAAAAAAGTGCCCGGATAGCCAAGACAATCCTGCGTAAAAAGA 719
                            v  v iv  ii vv  v i        i      i  viv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_33412279_3    720 ACAAAGCTGGAGGCATCATGCTTCCTCACTTCAAACAATACTACAAGGCT 769
                               i      vv   ii     iv i      vvv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_33412279_3    770 ACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAAAGATATAGACCA 819
                                i   i    iii        i iv ii i i v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_33412279_3    820 ATGGAACAGAACTGAGGCCTCAGAAATAATGCCATCCATCTACAACCATC 869
                               i    i    ivii         vv    v   i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_33412279_3    870 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTT 919
                             i  i     ivv  v   i v  vv            i  vvi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_33412279_3    920 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 969
                           i  i        i     v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_33412279_3    970 ACTGGACCCTTTCCTTACACCTTATA-AAAAGTTAACTCAAGATAGATTA 1018
                         ii       i v   i     v    -    i         i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_33412279_3   1019 AAGACTTAAACATAAGACCTAAAACCATAAAAACCCCAGAAGGAAGCCTA 1068
                         ?    i    ii     v       i      vi ii     i  i v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_33412279_3   1069 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGGCTAAAA 1117
                           ?i- v i -   iv   v v  vv i     v ii   v i v  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_33412279_3   1118 CACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACCAATGGGATCTAATT 1167
                                    vvi          vv   i v  iv   v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_33412279_3   1168 AAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCA------TCA---G 1208
                            v v  i i   i  ii vv    iv v       ------ v --- 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_33412279_3   1209 GCAACCTACAGAATGGGGGAAAGTTTTTTGCAATCTATCCATCTGACAAA 1258
                         i     i          i    i v   -    vii  vi      i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGATAAG 747

  chrX_33412279_3   1259 GGGCTAATATCCAGAATCTACAAGGAACTTAAATAAATTTACAAGAAAAA 1308
                           i  vi          v  i  i     ivv i  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_33412279_3   1309 CACAA----CCCCATCAAAAAGTGGGTGAAGGATAAGAACAGACACTTCT 1354
                         v    ----   v  i?    i    ii      vv   i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_33412279_3   1355 CAAAAAAAAGACATTTATACAGCCAACAA--ACATGAAAAAAAGCTCA-- 1400
                          v   i  -  i  vi v ii     i  --         i v     --
  L1M4_orf2#LINE/    848 CCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_33412279_3   1401 -TCACTGGTCAT 1411
                         -   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.08 (25 / 12)  


3254 26.57 0.66 0.55  chrX_33417246_33419564      920  1826 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33417246_3    920 TGGAACAACATCCCATGCTCATGGATAGGAAGAATTAATATTGTGAAAAT 969
                              vi i        i        v      v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33417246_3    970 GGCCGTACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1019
                            vi    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33417246_3   1020 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1067
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_33417246_3   1068 TATGGAACTAAAAAAGAGCCCGCATTGCCAAGACAATCCTAGGCCAAAAG 1117
                                v iv  ii  v  v v  v     i      i iiivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_33417246_3   1118 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1167
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_33417246_3   1168 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1217
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_33417246_3   1218 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACTACACACCTACAACC 1265
                                i    i--    i  --        vv i i   ii  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_33417246_3   1266 ATCCAATCTTTGACAAATCTGACAAAAACAAGAAATGGGGAAAGGATTCC 1315
                          viii  i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_33417246_3   1316 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1365
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_33417246_3   1366 GAAACTGGATCCCTCCCTTACACT-TATACAAAAACTAATTCAAGATGGA 1414
                            ii    i    v   i    i-          i   i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_33417246_3   1415 TCAAAGACTTAAATGTTAGACCTAAAGTCATAAAAACCCTAGAAGAAAAC 1464
                            ?    i       v   v     iii      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_33417246_3   1465 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1513
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_33417246_3   1514 AAACACCAAAAGCAATGGCAACCAAAGCCAAAACTGACAAATGGGATATA 1563
                         vi            vvi     v    vv    iv  i    v   iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_33417246_3   1564 ACTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1613
                          ii   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_33417246_3   1614 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 1663
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_33417246_3   1664 AGGGGCTGATATCCAGAATCTACAAAGACCTCAAACAAATTTACAAGAAA 1713
                             i  vi          v  i     v   vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_33417246_3   1714 ACAACAAACAACCCCGTCAACAAGTGGGCGAAGGATATGAACAGACACTT 1763
                          vi     i     vi i? v  i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_33417246_3   1764 CTCAAAAGAAGACATTTATGCAGCCCACAGACACATGAAAAAATGCTCAT 1813
                            v        i  vi viii   v i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_33417246_3   1814 CATCACTGGCCAT 1826
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3000 25.17 2.77 2.11  chrX_33438258_33441709     2061  2962 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33438258_3   2061 TGGAAAGATACTCTGTGTTCAAGGATTAGA-GAATTGATATTGTTTAAAT 2109
                                   ii ii      v     i  -  v  i        v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33438258_3   2110 GTCCATACTATCCAAAGCGATCTGAAGAGTCAATGCAATCTCTATCAAAA 2159
                          v v     vi     vi     iv   v    i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33438258_3   2160 CACTAA-TGGCATCTTCACAGAAATAGG--AGAAAATCTAAATATTTGTA 2206
                         iv i i-  v v i  ii       v i--  vvi   iv  v   ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_33438258_3   2207 TGGAACCACAAAATAACTCA-AATAGCCAAAGTAATCTTGAGTGAAAAGA 2255
                              vii   ii-i  i  -          ii        ivi i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_33438258_3   2256 ACAAAGCTGGAGGCATCACACT-----ATAT---GACTTACTACATAGCT 2297
                               i      vv       -----  v ---i          v    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_33438258_3   2298 ATAGTAACCAAATGAGCATCATATTGGCATAAAAAATAAACATAGAGACC 2347
                          i     i   ivv  ii vi  i        ii -  i     v   i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATC 298

  chrX_33438258_3   2348 AACAGAAGAGAA-----AACACAGAAATAACTCCACACACCTACAGTCAA 2392
                           ii   v    ----- iiv         vi   i   ii  ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_33438258_3   2393 CTGATTTAT-ACAAAAGTGTCAGAAACAGTCAATGAGAAAAGGACAATCT 2441
                         i      vi-    ii   i  ii v  v      i i    i i i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_33438258_3   2442 CTACAATAAATGGTCCTGGGAAAACTGGATATCTGCATGCAGAAGAATGA 2491
                         i v   i       v      v         ? ii      i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_33438258_3   2492 AGCTACATTCCTATCTCTCACCATATAAAAGAATCAACTTAAAATGGATT 2541
                           i iv ii    i   v         v  i   i    i         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_33438258_3   2542 CAAGATTCAAATGTAAGACCTGAAAGTATGAAACTACTAGAAGAAAATAT 2591
                         v?   iii          v  i   v   i     vi          i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_33438258_3   2592 GGGGGAAACTATTCATGACATTGGTCTAGGCAAGGATTTTTTTGATATGT 2641
                         i  ? v  v v   i    v    vi       v i   i  v      v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_33438258_3   2642 CCTTAAAAGCACAGGCAAAAGAAAGCAAAAATAGACAAATGGAATTATAT 2691
                          vii         i    v -    v         i    v i i vi  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_33438258_3   2692 CTTA-CTAAAGAGTCCTGCACAGCAAAGGAAACAAT---GAA--TGAAGA 2735
                          vv -i    i v ii  ii vv       v  v  ---   --    i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_33438258_3   2736 CACAACATACAGAATGGGAGAAAATGCTTGCATAGTATGCATGTGACAAG 2785
                         v     vi                 ii     v vi  ii  v   i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_33438258_3   2786 GGGTTAATAACCAGAATATATAAGAAACTCAATAGCAAAACAAAAAACAA 2835
                           ii vi  v             ii     -- vi   vv   ----i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCAA----TAA 791

  chrX_33438258_3   2836 CAAAAAAAAACAAAAACAAACAAACTCCAATTTAAAAATAGGCCTAAGAC 2885
                         i     i --------    i  --i      ?      i   vv i  i
  L1M4_orf2#LINE/    792 TAAAAAGA--------CAAATAA--CCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_33438258_3   2886 CTGACCTAACATTTCTCAAAAGAAGATATACAAGTGGCCAACAGGTATAT 2935
                         i   vivi         v               i       i i i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_33438258_3   2936 GAAAAATTCCTTAATAAGACTAATCAT 2962
                              iv v  i  i vv ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (141 / 82)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.44 (44 / 18)  


2621 26.47 0.91 0.65  chrX_33459069_33464849.rev     3243  4009 (1772)  C L1M4_orf2#LINE/L1   (0)   908   140  

C chrX_33459069_3   4009 TAAAGTTCATATGGAAC--CAAAAAACAGCCCGCATTGCCAACTCAATCC 3962
                             i           v--   iii  --  v v  v     vv     i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCT 187

C chrX_33459069_3   3961 TAAGCCAAAAGAACAAAGCTGGAGGTATCATGCTACCTGACTTCAATCTA 3912
                          i ivv i          i      vv   ii  v  ii i     vviv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

C chrX_33459069_3   3911 TATTACAAGGCTATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAG 3862
                           i     i    i     i   i    ii         i iv ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

C chrX_33459069_3   3861 AGATACAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCA 3814
                          v   i   i        i    i--    i  --        vv  ii 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATA 335

C chrX_33459069_3   3813 TATCTACAACTATCTGATCTCTGACAAACCTGACAAAAACAAGAAACAGG 3764
                         i  i  iiiii vi    i ii     ivv  v   i v  vvv  ii  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

C chrX_33459069_3   3763 GAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATA 3714
                              i  vvi  v  i  i              v      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

C chrX_33459069_3   3713 TG-GAAAGC-TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAA 3666
                           -i    v-    ii    i    v   i     v              
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

C chrX_33459069_3   3665 TTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCC 3616
                         i    i      i ?    i       v   v       i      vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

C chrX_33459069_3   3615 TAGAAGAAAACCTAAGCA-ATACCATTCAGGACATAGGCATGGGCAAGGA 3567
                                    v  i ?i- v i -   iv   v v  vv i     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

C chrX_33459069_3   3566 CTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCTAAATTGACA 3517
                         i   v ivv  vi            vvi          vvv    v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

C chrX_33459069_3   3516 AATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACC 3467
                            v   ii v  i   v v  i i   i  ii vv    i  v    i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

C chrX_33459069_3   3466 ATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTA 3417
                          vv i      v  i     i                 v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

C chrX_33459069_3   3416 CTCATCTGACAAAGGGCTAATATCCAGAATCCACAAAGAACTCAAACAAA 3367
                         ivi      i  i  i  vi          vi i         vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

C chrX_33459069_3   3366 TTTACAAGAAAAAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATG 3317
                          iv i  v     i     i     v  i? v  i            v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

C chrX_33459069_3   3316 AACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAA 3267
                           i     i     v        i  vi viii     v ii        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

C chrX_33459069_3   3266 AAAATGCTCATCATCACTGGCCAT 3243
                           i       v     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (116 / 83)
Gap_init rate = 0.01 (8 / 769), avg. gap size = 1.50 (12 / 8)  

3440 24.84 0.88 1.10  chrX_33459069_33464849.rev     4381  5290 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33459069_3   4381 TGGAAAAATATTTTGTGTTTATGGATTGGAAGAATCAATATTGTTAAAAT 4430
                               i    iiii    i             v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33459069_3   4431 GTCCATACTACCCAAGGCAATCTACAGATTAAATGCAATCCCTTTCAAAA 4480
                          v v     v     ivii           v  i         v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33459069_3   4481 TACCAATTATATTCTTCATAGAAAATAGAAAAAACAATCCTGAAATTTAT 4530
                          v   ii iiv  i  iii     - v  v  ivii     i     i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCAT 149

  chrX_33459069_3   4531 ATGGAATGACAAAAGACCCAGAATAGCCAAAGCTGTCTTAAGCAAAAATA 4580
                               vvi   ii                 i vi    i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_33459069_3   4581 AGAAAACCGGAGGAGTCACGTTACCTGACTTCAAATGATACTCCAGAGAT 4630
                          v   iii      v    ii v  ii i      vvv    v  i  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_33459069_3   4631 ATGGGAA---AGA-AGCATGGTTCTAGCATAAAAACAGACACATAGACCA 4676
                          ii v  ---   -  ii    v  i      ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_33459069_3   4677 ATGAAGTGGAATAGAGAACCCAGAAACAAATCCATGCACCTACTGTTAAT 4726
                            i i i    v    ii       i   i    i  ii  iv  i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_33459069_3   4727 GCAGTTTTGACAAAGGTGTGAAGAACATACACTGGAGGGAAAGA-CAGTC 4775
                         vv v   i     i    iv    v   v  v   --       -i    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG--GGAAAGAATAGTC 397

  chrX_33459069_3   4776 TCTTCAATGTACAGTGATGGGAAAACTGGATATTCATGTTGCAGAACAAT 4825
                          i     iiv ii   v     v         ?i  ii-    i  v   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGAAT 446

  chrX_33459069_3   4826 GAAATAAGACCCCTATTTCTCATCTTATA-AAAAATCCAAATTAAAATGG 4874
                            i vi        ii  v  i v    -      -i  v i       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAACTCAAAATGG 495

  chrX_33459069_3   4875 ATTAAAAACTTAAATCTAAGACCTCAAACTGTGAAATTCATACAAGAAAA 4924
                           i ? i  i     v     v  v     i i   i  v  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_33459069_3   4925 TATTGGGGGAAGATCTCCAGGATATTGGTCTGGGCAAAAATTTTTGAGCA 4974
                         i  v  ? v  -    i iv  iv    vi i     vii   i v  vv
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_33459069_3   4975 AT-ACCCCACAAGCACAGGCAACAAAAGCAGAAATGGACAAATGGGATCA 5023
                           -  v   v       i          v i    i  i    v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_33459069_3   5024 CATCAA-GTTAAAAAGCTTCTGCACAGCAAATGATACAATCAACAAAATG 5072
                               -i       -   i  ii vv    v  i  v     v   i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_33459069_3   5073 AAGCATCAACTCACAGAATGGGAGAAAATATTTGCAAACTACCTATCTGA 5122
                           iviv    i                           ii iv       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_33459069_3   5123 CAAGAGATTAATAAGCAGAATGTGTAATGAGCTCAAACAGTTCTATAGGA 5172
                         i   i  i vi  vv      i i   v  i   vv   ii  v   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_33459069_3   5173 AAAAAATATATAATAATCCAATCAAAGAATGAGCAAAAGATTTGAATAGA 5222
                             i i ---     i     i?  i    i     i            
  L1M4_orf2#LINE/    794 AAAAGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_33459069_3   5223 CATTTCTCAAAAGAATATATACAAATGGCAAACAGGTATATAAAAAGGTG 5272
                                 v      v             v  i i i i  i     i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_33459069_3   5273 CTCAACATCACTGACCAT 5290
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (140 / 82)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.38 (18 / 13)  


2117 26.16 3.51 0.48  chrX_33520604_33522233.rev      505  1131 (499)    L1M4_orf2#LINE/L1      215   860 (48)  

  chrX_33520604_3    505 TCATGCTACCTGACTGCAAACTATACTGTAGGGCTACAGTAACCAAAACA 554
                            ii  v  ii i v    viv    ii ii          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_33520604_3    555 GCATAGTACTAATACAAAAACAGACACATAGACCAATGGAACAGGATAGA 604
                          ii i     iii i  ii i     i     i        i  i  v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_33520604_3    605 GAACTCAGAAATAAGGCCACACACTTACA--CATATACGATCTCCGACAA 652
                           iii         iv   i   i   ii--  -  -i   i i      
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCA-AT-TGATTTTCGACAA 362

  chrX_33520604_3    653 ACCTGACAAAAACAAGCAATGGGGAAAGGAT-TCCCTTTCAATTAATGGT 701
                         ivv  v   i v  vv            i  -vi i      iv      
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_33520604_3    702 ---------ACTGGCTAGCCATATACACAAGATTGAAACTGGACCCCT-T 741
                         ---------     v  ?   i  i  v    v    ii         -i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_33520604_3    742 TTTACACCATATACAAAAATTAACTCAAGATAGATTAAAGACTTAAATGT 791
                         i i                         i  i   i ?    i       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_33520604_3    792 AAAACCCAAAACTATAGAAGCCT-GGAAGACAACCTAGGCA-ATATCTTT 839
                           i v i         i  vi  -i     v   v    ?i- v     -
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT- 561

  chrX_33520604_3    840 CAGGACATAGGCATAGGCAAATATTTCATGAAGAAGACACCAAAGGCAAC 889
                          iv   v v  vv       vvi    v ii v v         i   vv
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_33520604_3    890 TGCAACAAAACCACAAATTGACAAATGGGATCTAATTAAACT---GAGCT 936
                         v         vv v    v  i    v   ii v  i   v ---i i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_33520604_3    937 TCTGCATAGCAAAGGAAACTATCAAGAGAGTGAGCAGACAACCTACAGAA 986
                          i  iiivv       v          i     iv        i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_33520604_3    987 TGGGAGAAAACTTTTGCAAATTATGCATCTGACAAAGGTCTAATATCCAG 1036
                                   iv         i  ii      i  i  v  vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_33520604_3   1037 AATCTATAAGGAACTTAAGCAAATTCACAAGAAAAAGACAA----CCTCA 1082
                            v     i     ivvi   v iv i  v          ----  iv 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_33520604_3   1083 TTAAAAAGAGGGCAAATTACATGAACAGATACCTTTCAAAAGAAGACAT 1131
                           ?    iv       vv iv    i   i ii i  v        i  
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.62 (99 / 61)
Gap_init rate = 0.02 (11 / 646), avg. gap size = 2.27 (25 / 11)  


 896 31.21 0.00 0.00  chrX_33528178_33532173.rev        2   331 (3665)  C L1M4_orf2#LINE/L1   (146)   762   433  

C chrX_33528178_3    331 ATATGCAGAAAATTGAAAGTGAATCCATTTCTTACACTTTATACAAAAAC 282
                          i     i  i v    iv  i i  v vi  i    iv          i
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

C chrX_33528178_3    281 TAACTCAAGCTGAAAAAAAAACTTAAGTGCAAAACCCAAAACTATAAAAA 232
                                 iv  i vv ? i  i   i  i  i v i            v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

C chrX_33528178_3    231 CCCTAGAAGAAAATCTAGGCATTACCATTCAGGACATAGGCATGGGCAAA 182
                         i i          iv    ?i v viv   iv   v v  vv i     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

C chrX_33528178_3    181 GATTTCATGACAAAAACATCAAAAGCAATTACAACAAAAGCAAAAATTGA 132
                          i    v iivv vi   i        vvvi         v      v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

C chrX_33528178_3    131 CAAACAGAATCTAATTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTG 82
                         i   iv i ii v  i   v v  i i   i  ii vvi   i  v   i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

C chrX_33528178_3     81 TCATCAGAGTGAACACAGAGCCAACAGAATGGGAGAAAATTTTTGCAACC 32
                            vv i      v v v i  v                 v       vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

C chrX_33528178_3     31 TATCCATCTGACAAATGTCTAATATCCAGA 2
                         i  vi      i  iv v  vi        
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGA 762

Transitions / transversions = 1.10 (53 / 48)
Gap_init rate = 0.00 (0 / 330), avg. gap size = 0.00 (0 / 0)  

 218 24.86 13.87 5.78  chrX_33528178_33532173.rev      332   504 (3492)  C L1M4_orf2#LINE/L1   (700)   208    22 *

C chrX_33528178_3    504 TGGATAGGAAGAATCAGTAT-GTTAAAATGGCCATATTGCAAAAACCTAT 456
                              v      v i i   -     i     v   i v vv   iiv  
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGAT 71

C chrX_33528178_3    455 TTGCATATTCAATGCTATCAGTCTACCAATAAT---A------TTCTTCA 415
                         i i  v      i  v   --i   i   -   --- ------  i  ii
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATC--CCTATCAA-AATCCCAGCTGCCTTTTTTG 118

C chrX_33528178_3    414 CACAATTAGAAAAAATGACTATATTAAAATAAATATGGAA---------- 375
                           v  v v  v  iv   --- vi      vv        ----------
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGA---TCCTAAAATTCATATGGAAATGCAAGGGA 165

C chrX_33528178_3    374 CCCAAAAAGAGGCCAAA----TCTCCAAGGCAAAAAGAGCAAAACTG 332
                             i  vi--      ----   iv  i--  i    i    ii  
  L1M4_orf2#LINE/    166 CCCAGAATA--GCCAAAACAATCTTGAAA--AAGAAGAACAAAGTTG 208

Transitions / transversions = 1.26 (24 / 19)
Gap_init rate = 0.05 (10 / 187), avg. gap size = 3.40 (34 / 10)  

1739 26.48 1.97 1.48  chrX_33528178_33532173.rev      503  1110 (2886)    L1M4_orf2#LINE/L1      298   908 (0)  

  chrX_33528178_3    503 CAATGGAAGAGAATAGAGTGCCAAAAAATAATGCTGGACACCCACAAGAA 552
                                 v     v   v i v i      vv iiv   iii iiivv 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_33528178_3    553 GCCGCTCTTCAACAAAATCTACAAAAACAAGCAATACAGAAAGGACTTTC 602
                         iii v i   i    iivivv   i v  vv    ivi     i ivv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_33528178_3    603 TATTTAATAAATGGTGCTGGGATAACTGGTTAGTTATATGCAGAAGATTT 652
                          v  i  i              i      v  ?ii i     i    v v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_33528178_3    653 TAACCGGACTCTTTGCTTATGCCATATACAAAAATCAACTAAAAATGGAT 702
                         v iii    i i vv  i ii              i    v         
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_33528178_3    703 TAAAGACTTACATGTAAAACTTAAAACTATAAAAATCCCTAGAAGATAAC 752
                         i ?    i  v      i vi             v  i-       v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAAC 546

  chrX_33528178_3    753 CTAGA---AAATGCCATTCTGGACATAGGCCTTGGGAAAGATTTCAT-GA 798
                         v   i---    -- -   vv   v v  vi v  v  v i    v -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_33528178_3    799 TGATGATGCCAAAAGCAACTGCAATAGAATAAAAAGGA-ACAAATTAGAC 847
                          -    ii         vvv    i i  v     iv - i     i   
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_33528178_3    848 CTAATTAAACTAAAGACCTTCTGCACATCAAAAC-CATCTATCAACACAG 896
                         i v  i   v v  i v   i  ii v     iv-  -       v v  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGAAAG 691

  chrX_33528178_3    897 TAATCAGGCAACCTACAGAATGGGAGAAAATATTTAAAAAGTATGCATCT 946
                          i vv  i     i                     iv   vi  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_33528178_3    947 GGCAAAGGTTTAATATCCAGAATCTCTAAGGAACATAAACAAATCAACAA 996
                          ii  i  vi vi          v v   i    vivv    v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_33528178_3    997 GCAAAAAACA-----CTGCCATTAAAAAATGGGCAAAG-ACATGAATAGA 1040
                         vv    i   ----- i- v   ?              - iv        
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_33528178_3   1041 CACTTCTCAAAAGAAGACATAAACGTGGCCAACAAGCATATGAAAAAAAT 1090
                           i     v        i   v vi       i     i       i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-T 889

  chrX_33528178_3   1091 GCTTCAACATCACTAATCAT 1110
                            -        ????????
  L1M4_orf2#LINE/    890 GCT-CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (85 / 73)
Gap_init rate = 0.02 (14 / 611), avg. gap size = 1.50 (21 / 14)  

2608 26.36 3.62 0.90  chrX_33528178_33532173.rev     2622  3505 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33528178_3   2622 TGGAAAATAATTCCATGCTCATAAGTGGAAAGAATCAATATCGTTAAAAT 2671
                               ivv  i     i    iii v i    v i     i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33528178_3   2672 GGCCATACTGCCCAAAAGAATTTATAGATTCAATAGTGTTCTCATTAAAC 2721
                            v     v      vvi  i  i        iivvi i ii  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33528178_3   2722 TAC-AGGTGACTTTCTTCACAGAACTAGAAAAAAACT-ACTCTAAAATAC 2769
                          v -  v  v    i  -i     v v  v  i--  - ii       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_33528178_3   2770 ATATGGAACCAAAACAGAGTCCATGTAGCCAAAA-AATCCTACACAAAAA 2818
                                 viiv  vi  vi vivi         -    i iv v  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_33528178_3   2819 GAACAAAGCTGGAGGCATCACAGTACCCAACTTCAAACAATACTACAGGT 2868
                                 i      vv     v v     i      vvv       iiv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_33528178_3   2869 CTGCAGTAACCAAAATAGCATGGTACTGTTACAAGAAAAGATACACTGAC 2918
                           i      i   i i  ii        vi i   i v   i i iv  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_33528178_3   2919 CAATGGAACAGAATAGAGAACATAGAAATAAGACCACACACCTTCAACTA 2968
                                 i     v    iivi        iv   i   ii viiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_33528178_3   2969 TCTGATCTTCAGCAAACCTAACAAAAACAAGCAATGAGGAAAGGATTCCC 3018
                         vi    i   ii   ivv iv   i v  vv     i      i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_33528178_3   3019 TATTCAATACATGGTGCTGGGATAACAGGCTAGCCATATGCACAAGATTG 3068
                          v     i v            i   v  v  ?   i     v    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_33528178_3   3069 AAACTGAACCCCTTCCTTATACCACGTACAAAATTTAACTCAAGATGGAT 3118
                           ii  i      v   i i    ii       v         i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_33528178_3   3119 TAAATACTTAAATGTAAAACCCAACACTATAAAAATCCTAGAAGGCAATC 3168
                         i ? v  i         i v i  v         v  i      iv  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_33528178_3   3169 TAGGCA-ATACCATTCAGGACATAGGCACAGGTAAAGATTTCAT-GATGA 3216
                             ?i- v i -   iv   v v  vvi   i  v i    v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_33528178_3   3217 AGACGCCAAAAGCAATTGCAACAAAAGTAAAAATTGACAAAT-GGA---- 3261
                         v   i         vvv          v      v  i    -   ----
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_33528178_3   3262 AT-AAAACTAAACTAAGCTTCTGCACAGCAAAAGAAAGTATCAACAAAGT 3310
                           -    i    --- i   i  ii vv    i  v v      v     
  L1M4_orf2#LINE/    646 ATCAAAATTAAA---AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_33528178_3   3311 AAA----CAATCCACAGAATAGGAGAAAATTTTTGCAAACTATGCATCTG 3356
                         i  ----   i         i         v        ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_33528178_3   3357 ACAAAGGTCTAATATCCAACATTTATAAGGAAC----A-AATTTA----C 3397
                          i  i  v  vi      iv  v     i    ---- -  i i ----i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_33528178_3   3398 AAAACAACAACTG---CAAT-AAAAAGTGGACAAATGACGTAAAAAGACA 3443
                             vi    v i---    -?    i   i    v  iv i  v     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_33528178_3   3444 CTTATC-AAAGAAGACATACATGCAGCCAACAA--ACATGAAAAAA-GCT 3489
                         i  v  -        i     viii     i  --         i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_33528178_3   3490 CAACATCACTTATCAC 3505
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (134 / 95)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.82 (40 / 22)  


2020 25.27 5.22 7.35  chrX_33533009_33536881.rev     2138  2980 (893)    L1M4_orf2#LINE/L1        1   825 (83)  

  chrX_33533009_3   2138 TGTAAAGACTCATCTC--GCTCATAGATCGGAAAAATTAATTTCATTACA 2185
                           v     i--   i -- i    i   i    i v     v ii   vi
  L1M4_orf2#LINE/      1 TGGAAAGAT--ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_33533009_3   2186 ATAATTATACTGCCCAAAGCAACATACAGATTTAATACAATTCCTATTAA 2235
                           iiiv     v      vii iv        i  ii    i     i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_33533009_3   2236 AA----A--TGTCATCATTTAAACAATTTTTAAGC----CCTAAAATTCA 2275
                           ---- --  i v iv  vv iv    vvi    ----           
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_33533009_3   2276 TAAGAAACTAAAAAAAATGTCTGTGTAGGCAAAGCAATCTTCAGCAAAAA 2325
                           v i  v iv  iii i-i v vi   v    i       v iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_33533009_3   2326 GAACATAAGCTGGAGGCATCACACTACCTGATGTAAAAATAGATTACAAG 2375
                              -   i      vv       v  ii  v v    ivv i     i
  L1M4_orf2#LINE/    198 GAACA-AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_33533009_3   2376 CCTATAGTAACCAAAACATCACGGTATTGGTATAAAAATAGACACATAGA 2425
                         v   i     i   i   viii    i   i    ii       i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_33533009_3   2426 ACAATGAAAGTGAATACAGAACCCAGAAACAAATCCACCAACTTACAGCC 2475
                         v     i  vv    vv   ii       i   i   ivv i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_33533009_3   2476 AGCTGATTTTAGACAAAGGTGCCAAAGATTTCCTTTCCCACTGGGGAAAG 2525
                          ii       v     i        -  ---  v   -- v         
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAA-GA---CCATTC--AATGGGGAAAG 390

  chrX_33533009_3   2526 AATACGCTCCTCAATAAATGATGCTGGGAAAATTAGATATCCATATGCAG 2575
                             vv  ii    i     i        v  i i    ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_33533009_3   2576 AAGAATGAAACTGGAACTCT--CTGACATTATAAACAAAAATCAACTCAA 2623
                                  ii    v i  --  v   ii   v        i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_33533009_3   2624 GATAAATTA-----TTAAACTTAAGAACCAAAACTATTAAATTACCAGAA 2668
                         i  ii  i -----i    iv     i i        v   i vii    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_33533009_3   2669 GGAAACATACATA-AAATACTTCAGGACATTGGTCTAGGCAAAGATTTGC 2717
                          i       vi?i-    -    iv   v    vi       v i   vi
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_33533009_3   2718 TGGCTAAGACCTTAA------------------------TAGACAAATAG 2743
                          i v  v   vii  ------------------------    i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_33533009_3   2744 TATTATACTAAAGTAAAACACTTCAGCACAGCAAAGAAAACAATGCAGAG 2793
                         v i vi ii   i v   v    iv ii vv     i v  v  vv   i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_33533009_3   2794 AGTGAAGAAACAACCTACAGAATGGAAGAAAATATTTGCAAACTATTCAT 2843
                               i i      i         i                ----    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA----TCAT 735

  chrX_33533009_3   2844 CCAAACTATTAAGACAGAATGGAAGAAATATTTGCAAACTATTCATCAAA 2893
                         ---------------------------    i  ----------------
  L1M4_orf2#LINE/    736 ---------------------------ATATCTG---------------- 742

  chrX_33533009_3   2894 CTATTAAGACACTAATATCTGGAATATACAAGGAACTCAAACAACTCAAC 2943
                         --  -   iv   vi    ii       i  i      vv         i
  L1M4_orf2#LINE/    743 --AT-AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_33533009_3   2944 AAATAAATAAACCAATCATTCCATTAAAGGGTGCGCA 2980
                           -    v i  v   v ii v   ?  iii  v   
  L1M4_orf2#LINE/    790 AA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 1.59 (129 / 81)
Gap_init rate = 0.02 (20 / 825), avg. gap size = 5.30 (106 / 20)  

 213 23.23 10.10 2.02  chrX_33533009_33536881.rev     3276  3374 (499)    L1M4_orf2#LINE/L1      787   893 (15)  

  chrX_33533009_3   3276 AATAATAATAAAAAAAATAA---------AAAGTGGGCAGAAGACATGAA 3316
                                 v  i v      ---------   i      i i  iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_33533009_3   3317 AAAGCAATTGGC-AAAGAAGACATACAGATGGCCAACAATTATATATTTA 3365
                         v ii  v  vv -        i     i        i  vi i  iv-- 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA--A 884

  chrX_33533009_3   3366 AAAATGCTC 3374
                           i      
  L1M4_orf2#LINE/    885 AAGATGCTC 893

Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.03 (3 / 107), avg. gap size = 4.00 (12 / 3)  

 264 34.19 1.71 0.85  chrX_33533009_33536881.rev     3754  3870 (3)  C L1M4_orf2#LINE/L1   (629)   279   162  

C chrX_33533009_3   3870 GGAACATAAAATAA--AGAATAAATACTCAGAAAAAAATTCAAAGCTGAA 3823
                           i  vi i    i-- i  i  - vi v i   i  ivv     i  i 
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAACAAAGTTGGA 210

C chrX_33533009_3   3822 GGTATCACATTACCTGACTTCAAACTATACCACAAGACTACAGTAACCAA 3773
                           vv     i v  ii i      viv   i    ii         i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

C chrX_33533009_3   3772 AACATCATCGTGTTGATAT 3754
                         i   vii v  ii  ii  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCAT 279

Transitions / transversions = 2.33 (28 / 12)
Gap_init rate = 0.02 (2 / 118), avg. gap size = 1.50 (3 / 2)  


1004 23.15 11.69 3.82  chrX_33551235_33555338.rev       62   480 (3624)    L1M4_orf2#LINE/L1      382   833 (75)  

  chrX_33551235_3     62 TGAGGAAAGA-----TTTTTCAACATATGATCCTGAAACAAATGCATATC 106
                           i       -----i         v   i v   ii    v  v   ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_33551235_3    107 CACATACAAAATACTGAA--TGTGACACAGGCCTTACAC-AT-TA-AGGA 151
                              i     v v    --  -   v vvi   i    -  -  - ii 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTG-GACCCCTACCTCACACCATATACAAAA 480

  chrX_33551235_3    152 ATTGACTCAAAATGGATCATAGACCTAAATATAA-AGCACAAAGCTTTAA 200
                            i               ?          i   -   -i   i  v   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAA 529

  chrX_33551235_3    201 C-CTCTTCAAAGGTAAATGTAAGA--AAATCTT----ACATTTGGGGTTT 243
                         v-     vi   i-   ii  i ?--       ----  v  --     v
  L1M4_orf2#LINE/    530 AACTCTTAGAAGA-AAACATAGGNGTAAATCTTCGTGACCTT--GGGTTA 576

  chrX_33551235_3    244 GGTGATAAGTTTTTAGATATGTT----------------------GATAT 271
                           ii  iiv  i         vi----------------------  v v
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_33551235_3    272 AATTGATAAGTTGGATTTCATTAAAACTATAAAAAAGTACTTTGTG---- 317
                            v     i     i     i    i  ---    v --      ----
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTA---AAAACT--TTTGTGCTTC 671

  chrX_33551235_3    318 -AAAGAGACTGTTAAAAGCATGAAAAGACAATC-ATAGACCAGGTTAAAA 365
                         -  i  v   i i  i ivi           i - i   vii  vv    
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_33551235_3    366 TGTTTATGAGTTACATATCTGACAAAGTACTTATATCCAGAATATACAAC 415
                          i   iii i i i        i  i v    i             i  v
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_33551235_3    416 ATACACTTAAAATACAATGATAGGAAAGTGTACAAGGAAATCCCCAT--- 462
                         iv  v    v  iv    i   i-    ---    iv  --   v  ---
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAA-AAAG---ACAAATAA--CCCAATTWA 815

  chrX_33551235_3    463 AAAACCATCAGTGGATTT 480
                             iviv  iv      
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTT 833

Transitions / transversions = 1.61 (58 / 36)
Gap_init rate = 0.05 (22 / 452), avg. gap size = 2.95 (65 / 22)  

2377 24.51 13.18 1.35  chrX_33551235_33555338.rev     2802  3613 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33551235_3   2802 TAAAGAGATATTCTACATTCATGGATTGGCAGACTTAATGTTGTTAAAAC 2851
                          ii i      i i ii            v         i       i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33551235_3   2852 AACCATACTACCCAAAGCTATCTAAAGATTCTATGCAATCTCTATCAAAA 2901
                         ii v     v      viv     v      v i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33551235_3   2902 TCTTAATGACATTCTTCACAGAAATAGAAAAAAAAAAACCCAAAGTTTAT 2951
                           ii iivi v  i  ii       v  v  ivvi v-  i   i  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chrX_33551235_3   2952 ATGGAGCCACAATAAAACACCAGAA-AGCCAAACCACTCGAGAGAAAAAA 3000
                              ivii   -iii  -      -       v  v  vv  i   i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAA-GGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_33551235_3   3001 TAATGAAACTGGAGGCATCACACTTCCTGATTAGCAATATATATTACACG 3050
                         v  ii  ii      vv          ii   -v   v iv  i    vi
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATT-TCAAAACTTACTACAAA 246

  chrX_33551235_3   3051 GCTATGTTAATTAAAACAGTAT------------AGGATA--CA------ 3080
                             iiv    i  i     i ------------      --  ------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_33551235_3   3081 -------------------------------------------------C 3081
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_33551235_3   3082 AATTG---------------------------------GGAGAGAATAGT 3098
                              ---------------------------------   i        
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_33551235_3   3099 CTCTTTAATAAATGTTGTTGGGAAAACTGGATATACACACGCAAAAGAAT 3148
                           i  i  i     v  i     v         ?v    i          
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_33551235_3   3149 GAAATTGGACCCTTAACTTACACCACACACAAAAAAATCAACTAAAAATG 3198
                            i        i  v  i      i i       -- i    v      
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAATG 494

  chrX_33551235_3   3199 AATTAAAGACTTAAGTGTAAAACCTCAAATTAGAAATCTACAAGAAGAAA 3248
                         i  i ?    i   i     i v  v   i  v   v  viv        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_33551235_3   3249 ACAGTGAA--AAAGCATCATGACATTAATCTTAGCAATGATTTTATGCAC 3296
                            vv i?--   v v  i    v  iivi vi      i   iv iv i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_33551235_3   3297 ATGAAACCAAAAGCGTAGGCAAAAAAAGCAAAA-TAAACAATTGGGATAT 3345
                             v         ii i    v     v    -  i i  v v   iv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_33551235_3   3346 CATTAAA-CTAAAAGCTTCTGCATTGCAGAGGAAATTATCAACAGATTGA 3394
                            i   -i     i   i  iii v  i    v i      v i v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_33551235_3   3395 AAAGGCAACCTAAAGAATAGGAAAAAAAAATTTGCAAACAATATATCTGA 3444
                             i     i v     i   i    v -        iv          
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATA-TTTGCAAATCATATATCTGA 743

  chrX_33551235_3   3445 TAAGGGTTTAATTTCCAAAACATATAAGGAACTCCTACAACTCAACAGCA 3494
                               vi vi v    i  i      i      i          i ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_33551235_3   3495 AAAAAAAGCTAATCACCCAATTTTTAAAATGGGTTAAAGACTTTTAACAG 3544
                             i -- v   v        ?v-        i-    iv   v  i  
  L1M4_orf2#LINE/    794 AAAAGA--CAAATAACCCAATTWA-AAAATGGGC-AAAGGATTTGAATAG 839

  chrX_33551235_3   3545 ACGTTTATCCAAATAAGACATACAAATGACGAACAGGTTTATGACAAGAT 3594
                           i   v      v    i         i v  i i ivi    v     
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_33551235_3   3595 GCTCAAAGTCACTAATCAT 3613
                               vi   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (121 / 74)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 6.94 (118 / 17)  


2309 25.94 3.30 5.46  chrX_33563153_33565024.rev      503  1381 (491)    L1M4_orf2#LINE/L1       49   908 (0)  

  chrX_33563153_3    503 ATAGCTGTACTCCCCAAAGCAATTTAGAGATTCAACAGTATTCCTATCAA 552
                           i  vi           vii  i  v         ivv  i        
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_33563153_3    553 ACTACCAA-TATCTTCTTCAAAGAATTAGAAAAACT-ATTCTAAAATTCA 600
                          v v   i- ii   i  iiv    v v  v  i  -  i          
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_33563153_3    601 CATGGAACCAAAAAAAGAGGCCCA--ATAGCCAAAGCAATCCTAAGAAAA 648
                         i      --- viv   i i    --         i     i i i   i
  L1M4_orf2#LINE/    149 TATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_33563153_3    649 AGGAACAAAACTGGAGACATTAAACTATTCAACTTCAAATTATACTATAA 698
                          i       ii     ivv i v   vii   i      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_33563153_3    699 GGCTACAGTAATCACAACAGTATGGTCCTGGTACAAAAATGGACACATAG 748
                         i             vi     i    v    i i  ii  i    i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_33563153_3    749 ACCAATGGAACAGAACAGAAATCTCGGAAATAAAGCCACACACCTACAAC 798
                          i        i    iv  i vii i        v   i   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_33563153_3    799 CATCTGATCTCCGACAAGG---CCAAGCAATAGAAAAAGGACCCCCTATT 845
                           vi    i i        ---     -------------   ----   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAG-------------ACC----ATT 378

  chrX_33563153_3    846 AAATAAGTGGTGCAATAGGAAAACTAACTCCTATTCAGTAAATGGCCCTG 895
                         v   ii ---------- i  i v  i-  i -    ii      iv   
  L1M4_orf2#LINE/    379 CAATGGG----------GAAAGAATAG-TCTT-TTCAACAAATGGTGCTG 416

  chrX_33563153_3    896 GGATAACTGGCTGGCCTCACTCAGAAAAATGAAAGTGGACACTTATCTTT 945
                            i      v i?  v  iv  i  i      iv     v i  i  iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_33563153_3    946 CAACATGTACAAAAATAAACTCAAGATGGATT-------TAAATGTAAGA 988
                           v   i         v       i      i-------           
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_33563153_3    989 CTTCAAACTCTAAGAATCCTAGAAGAAACCGTAGG---AAATACCCTTAC 1035
                         vi v     v   i v  i         v i    ---    ---   vv
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCG 563

  chrX_33563153_3   1036 TGGTACTGGCCTTGGCAAATCATTT-TTGGCTAAATCCCTAAAAGCAATT 1084
                           iivi   vi v     - vi   -  i v  viv v i       vvv
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_33563153_3   1085 GGAAGAAAAACAAAATTTGACAAGTGGGATCTAATTAA--CTAAAGAACA 1132
                          v  v    iv    v v  i  i v   ii v  i  --i    -   v
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA-AACT 661

  chrX_33563153_3   1133 TTTGCATAGCAAAAGAAACTATCAACAGAGT--AAACACAACCTACAGAA 1180
                             iiivv    i  v        v i   --   v      i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_33563153_3   1181 TGGAAGAAAAAGTTCACAAACTATGCACGTGACAAAAGTCTTGCATCTGG 1230
                            i      vi  ii    ii  ii iv   i  ii v    i   ii 
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_33563153_3   1231 AATCTATAAGGAACTT----AAATTGACAAGCAAGGAGCAAATACCACCA 1276
                            v     i     i----  v ii i  vv  iiii      v v v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_33563153_3   1277 TTAAAAAATGGGCAGACGAAATGAACAGACACTTGTC---AAAAGACACA 1323
                           ?           i v  vv    i     i  v  --- i    i i 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_33563153_3   1324 TAAGAAGCCAACAAACATATGAAAAAAACATGAAAAAATGCTCACTATCA 1373
                         i  ivi     i  i  -----------        i       vi    
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCA-----------CATGAAAAGATGCTCAACATCA 900

  chrX_33563153_3   1374 CTATCATT 1381
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.72 (143 / 83)
Gap_init rate = 0.02 (21 / 860), avg. gap size = 3.67 (77 / 21)  


2228 27.14 1.18 1.33  chrX_33567545_33572457.rev     3172  3849 (1064)    L1M4_orf2#LINE/L1        1   677 (231)  

  chrX_33567545_3   3172 TGGAAGGATATTCCACGTTTATGGATTAGAAGAATCAAAATTGTTAAAAT 3221
                              i     i   i   i       i     v i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33567545_3   3222 GTCCATATTACCAAAAGCAAGCTACAGACTCAATGTAATCTCTATCAAAA 3271
                          v v   i v  v   vii v       i    i i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33567545_3   3272 TAGCAATTACATTCTTCACAAAAAAAGAAAAAGCAACAATTCTAAAATTT 3321
                          vv  ii i v  i  ii  i   vv  v  -  --ii  i        i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GC--TGATCCTAAAATTC 147

  chrX_33567545_3   3322 ATATGGAACCACAGAAGTCCCAGAGCAGCCGAGCCTATCTTAACAAAAAA 3371
                                 vii  iii v      ii    i iv v     i ----   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA----AAA 193

  chrX_33567545_3   3372 AAAAAAAAAAAAAAGGAGGAATTACATTACCTGACTTCAAT-CATATTAC 3420
                          i  i  v   ivv      v i   i v  ii i     v- v  i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_33567545_3   3421 AGA--TATAGTAACCAAAATAGTATATTACTGCAATAAAAACAGACACGT 3468
                          i --  i     i   i i   i iv     vv    ii i     ii 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_33567545_3   3469 AGATCAACGGCATAGAATAGAGAACCCAGAAACAAATCCACACACCTACA 3518
                                i  v       v    ii       i   i   i   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_33567545_3   3519 GTGAACTTATTTTTGAAAAAGGTACCAAGAAAATACACTGGGGAAATGAC 3568
                           v  i v     i  v  i   i      vv  v  v        vi i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_33567545_3   3569 CGTCTCTTCAATAAACGGTGCTGGGAAAACTGGATAGTTACATGCAAAAG 3618
                         v    i     i   i          v         ?ii           
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_33567545_3   3619 AAGGAAACTAGATCCC-ATATTGC----TATACAAAAATATAAAATCAAA 3663
                           v   ii i  i   - iv ii ----           -   v-     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAAC-TCAAA 491

  chrX_33567545_3   3664 ATGTATTAAAGACTTAAATCTAAGATCTCAAACTGTGGAACTACTACAAG 3713
                            v  i ?    i     v     v  v     i ii    vi  v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_33567545_3   3714 AAAACATTGGGGAAAATCTCCAGGACATTGTTCTGGGCAAAAATTTCTTG 3763
                                v  ? v      i iv   v   vvi i     vii      i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_33567545_3   3764 AGCAATACCCCACAAGCACTAGCAATCAAAGCAAAAATAAACAAATGAGA 3813
                         iii vv  v   v      v     iv    v       i i    vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_33567545_3   3814 TCACATAAAGAGAAAAAGCTTCTGTAAAACAAAGGA 3849
                         iiv   v  i vv    i   i   ivvv       
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

Transitions / transversions = 1.55 (110 / 71)
Gap_init rate = 0.01 (9 / 677), avg. gap size = 1.89 (17 / 9)  

 820 23.45 0.00 0.44  chrX_33567545_33572457.rev     4197  4422 (491)    L1M4_orf2#LINE/L1      684   908 (0)  

  chrX_33567545_3   4197 CAACAAAGTGAAGAGACAGCACAGATAATTAAAGAGAAAATTTGCAAACT 4246
                            v        i     i v  v v   vii   i  v         ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_33567545_3   4247 ACCTATCTGACAAGAAATTAATAACCAGAATATATAAAGAGCTCAAAAAA 4296
                          iv       i   ii i vi  v                i   vv v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_33567545_3   4297 CTTTGTAGAAAACAATCTAATAATCTGATTTTTAAAATGAGTAAAATATT 4346
                           ivi  iv   v iv v     i ii   -?v      i i   iv   
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATT-WAAAAATGGGCAAAGGATT 832

  chrX_33567545_3   4347 TGAATAGACATTTCTCAAAAGAAGACATACAAAAGGCAAATGGCCATATG 4396
                                         v        i       v   v   iiv  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_33567545_3   4397 AAAAGGTGCTCAACATCATTGATCAT 4422
                              i            ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (29 / 23)
Gap_init rate = 0.00 (1 / 225), avg. gap size = 1.00 (1 / 1)  


2301 27.37 8.41 0.83  chrX_33592535_33594876.rev     1008  1851 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33592535_3   1008 TGAAAAAATATTCCATGCTCATTCATAAAAAGAATCAATATTGTTTAAAT 1057
                           i   i    i     i    vv  vii    v i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33592535_3   1058 GGCCACACTTTTCAAAGCAATGTATAGA----AC---------------- 1087
                            v i   iii    vii  v  i   ----  ----------------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33592535_3   1088 ------------------CAGAAA------AACT-ATTTTAAAATTCATA 1112
                         ------------------      ------ i  -  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_33592535_3   1113 TGGAACCAACAAAGAGCCAAAATAGCCAAGGCAATCCTAAGCAAAAGGAA 1162
                              viivv ii  v   i         ii     i i iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_33592535_3   1163 CAAACCTGGAGGCATCATCCCACCTGACTTCAATCTATACTATAGGGCTA 1212
                             vi      vv   iv iv  ii i     vviv     i ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_33592535_3   1213 CAGTAACCAAAACAACATGGCACTGGTACAAAAACAGACACAGAGACCAA 1262
                               i   i   iii   i     i i  ii i     i v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_33592535_3   1263 TGGAACAGGATAGAGAACTCAGAAATAAGACTACATACCTACAACTATCT 1312
                              i  i  v    iii         iv i i i ii  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_33592535_3   1313 GATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAATGATTCCCTTT 1362
                            i  i     ivv  v   i v  vv      i    vi  vvi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_33592535_3   1363 TCAATAAATAGTGCTAAGATAACTGGCTAGCCATATGGACAAGATTTAAA 1412
                             i    i     ii  i      v  ?   i   v v    v v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_33592535_3   1413 CTGGACCCCTTCCTTACACAAGATACAAAAAATAACTCAAGATAGATTAA 1462
                         i         v   i    v v         v        i  i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_33592535_3   1463 AGACGTAAATATAAAACCCAAAACTATAAAAACCTTGGAAGTAAACCTAG 1512
                             v     i   i v i            vi   i    v    v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_33592535_3   1513 CAATA--TCATTCAGGAAAT--AGTCACAGGCAAATGTTTCATGACAAAG 1558
                         v?i  --  -   iv  vv --i  i --     vv     v iivv v 
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATATG 597

  chrX_33592535_3   1559 ATGCCAAAAGCAATTAG-AATAAAAGAAAAAATTGAGAAATGGAATCTAA 1607
                          ii         -iv  -  i            v  v    v i ii v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_33592535_3   1608 TTAAA--CAAAAGTGCTTATGCACAGCAAACAACACTATCAACA----GC 1651
                          i   --i    i--   v  ii vv    vi          v ---- v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_33592535_3   1652 ACAGACAACCTACAAAATGGGAAAAAACATTTA--------------GAC 1687
                          v        i   i       i    i    i--------------  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_33592535_3   1688 AAAGTTCTAAAATCCAGAATCTATAAGGAACTTAAACAGATTTATTAA-A 1736
                           i vv  viv         v     i     ivv   - i i v   - 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCAATAATA 793

  chrX_33592535_3   1737 AAACACCTAACAACCTCTTTAAAAAGTGGGCAAAGGATATGAATAGACAC 1786
                            viv v  i    ivv  ?    i            v          i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_33592535_3   1787 TTTTCAAAAGAAGACATATAGGTGACCAACAATCATATGAAAAAAAGCTC 1836
                           i  v        i   i ii  i    i  v  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_33592535_3   1837 TACATCACTGATCAT 1851
                         v      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.88 (78 / 16)  


3036 26.40 1.90 0.34  chrX_33601786_33607626.rev     4457  5350 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33601786_3   4457 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4506
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33601786_3   4507 GGCCATACTGCCCAAAGTAATTTATAGATTCAAGGCTATTCCCATTAAAC 4556
                            v     v      v i  i  i        v  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33601786_3   4557 TACCATTGACATTCTTCACAGAACTAGAAGAAACT-ATTTTAATATTCCT 4605
                          v   vivi v  i  ii     v v  v-  i  -  ii   v    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_33601786_3   4606 ATGGAACCAAAAAAGAGCTCATATAGCCCCGACAATCTTAAGCAAAAAGA 4655
                               viiv  ii  v iviv      vvi        i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_33601786_3   4656 AGAAAGCTGGAGGCATCACACTACCAAACTTCAAACCACACTCCAAGGCT 4705
                          v    i      vv       v  v  i      v vi   v   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_33601786_3   4706 TCAATAAACAAAACATCATGGTACTGGTACAAAAACAGGAATGTAGACCA 4755
                         v  i   v   i   vii         i i  ii i  iv  i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_33601786_3   4756 ATGGAATAGAATAGAGAAACTACAAATAAAACTGCACATCGACAATCATC 4805
                                     v    iv i v       v iii    iv iii   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_33601786_3   4806 TGATCTTTGACGAAACTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 4855
                             i  i   i iiv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_33601786_3   4856 TTTAATAAATGGTGCTAGGAGAAGTGGCTAACCATATGCAGAAAATTGAA 4905
                           i  i          i   v  v   v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_33601786_3   4906 ACTGGACCCCTTCCTGACACCTTATATGAAAATTAACTCAAGATGGATTA 4955
                         ii         v   v     v    ii             i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_33601786_3   4956 AAGACTTAAATGTAAGACCCAAAACTATAAAAACCTTAGAAGAAAATCTA 5005
                         ?    i           v i            vi            iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_33601786_3   5006 GGC---AAT--TCAGGACATAGGCACGGGCAAATATTTCAT-GATGAAAT 5049
                           ?---   --  iv   v v  vvii     vvi    v -   ivi -
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA- 598

  chrX_33601786_3   5050 CACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCT---- 5095
                                    vvv          v      v  i    v   ii ----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_33601786_3   5096 --AATTAAAGAACTTCTGCACAGCAAAAGAAACTGTCATCAGGGCAAACA 5143
                         --       -     i  ii vv    i  v   i   vv ii ii  v 
  L1M4_orf2#LINE/    649 AAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_33601786_3   5144 GGTAACCTACAGAATGG-AGAAAATCTTTGCAGTCTATCCATTGGACAAA 5192
                          ii    i         -       v      ivii  vi  iv  i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_33601786_3   5193 GGTCTAATATCCAGAATCTACAAGGAACTTACACAAATTTACAAGAAAAA 5242
                           v  vi          v  i  i     ivi    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_33601786_3   5243 ---AAACAAGCCTATTAAAAAGTAAGCAAAGGACATGAACAGACACTACT 5289
                         ---   i  v  v   ?    i ii        iv    i     i v  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_33601786_3   5290 TAAAAGAAGACATTCATGTGGTCAACAAACATATGAAAAAAAGCTCAACA 5339
                         iv        i  v  vi   i   i  i  i       i v        
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_33601786_3   5340 TCACTGATCAT 5350
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.27 (130 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


1204 29.28 0.29 0.58  chrX_33610617_33612777.rev      446   790 (1371)    L1M4_orf2#LINE/L1        1   344 (564)  

  chrX_33610617_3    446 TGGAAAGATATTTCATGTTCATGGATCGCAAGAGTGAATATAGTTAAAAT 495
                                    ii             i v    v v     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33610617_3    496 GTCCATACTGTACAAGGTAATCCACAGATTCAATGCAATGTCTATCAATA 545
                          v v     viv   iv i   i          i     vi       v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33610617_3    546 TACCAATGACATTCTTCACATAAATAAAGAAAAAC-AATCCTACAATTTA 594
                          v   iivi v  i  ii  v    --v  v  i -i      v    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCA 148

  chrX_33610617_3    595 TATGGAATCATAGAAGACCCAGAATAGCCAAAGTTATCCTAAGCAAAAAG 644
                                viii iii                 iiv   i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_33610617_3    645 AATAAAATTGAAGAAATCACATTACATGACTCCAAATTATATAACAGAGC 694
                           i   i   i  i v     i v vii i i    viv  iv   i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_33610617_3    695 TGTAGTAACCAAAATAGCATTGTACTGACATAAAAACATACACATAGACC 744
                          ii     i   i i  ii v      i     ii i v   i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_33610617_3    745 CATGGAGCAGAATAGAGAACTCAGAAACAAATTCACCCACCTACAG 790
                         v     ii     v    iii      i   ii  iv  ii  ii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

Transitions / transversions = 2.16 (69 / 32)
Gap_init rate = 0.01 (2 / 344), avg. gap size = 1.50 (3 / 2)  

2374 22.20 0.36 0.53  chrX_33610617_33612777.rev     1108  1670 (491)    L1M4_orf2#LINE/L1      347   908 (0)  

  chrX_33610617_3   1108 AACTCATTTTTGACAAAGCTGCTAACAACATACACTAGGGAAAAGACAGT 1157
                           i v     i     i v   i  v v   v  v i      ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_33610617_3   1158 CTCTTCAATAAATGGTGCTAGGAAAACTGGATATCCATATGCAAAAGAGT 1207
                           i     i          i   v         ?   i          i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_33610617_3   1208 GAAACTAGACCCCTACCTCTTGACATATACAAAAATGAAACCAAAATGGA 1257
                            ii i            viiv             v  vi         
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_33610617_3   1258 TTAAAGACTTAATTTTAAGACCTCAAACTATGAAACTATTACAAGAAAAC 1307
                          i ?    i   v v     v  v       i     v   v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_33610617_3   1308 TTTGGGTAAAATCTCCAGGACATTGGTCTAGGCAAAGACTTCTTGAGCAA 1357
                         v v  ?vv      i iv   v    vi       v ii     iiii v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_33610617_3   1358 TACCCCATAAGCACAGGCAACCAAAGCAAACATGGACAAATGGGATCACA 1407
                         v  v   v       i     v    v   v  i  i    v   iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_33610617_3   1408 TCAA-GTTAAAAAGCTTCTTCACAGCAAAGGATACAATCAAAAAAGTGAA 1456
                             -i       -   i vii vv       i  v     i        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_33610617_3   1457 AAGACAATTCACAGAATGGGAGAAAATATTTTCAAACTACCTCTCTGCCA 1506
                                ii                      v    ii iv v    vi 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_33610617_3   1507 AAGGATTAATAGCCAATATATATAGGGAGCTCAAACAACTCTATAGGAAA 1556
                          i   i vi  v   iv       ii  i   vv       v   iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_33610617_3   1557 AAAAATCTACTAATCTGATT-AAAAATGGGCAAAAGATTTGAATAAACCT 1605
                           i -- v v   i ii   -             i          i  v 
  L1M4_orf2#LINE/    796 AAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_33610617_3   1606 TTCTCAAAAGAAGACATACAAATGGCAAACAAGCATAGGAAAAGGTGCTC 1655
                              v        i           v  i     i v      i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_33610617_3   1656 AGCATCACTGATCAT 1670
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (67 / 55)
Gap_init rate = 0.01 (4 / 562), avg. gap size = 1.25 (5 / 4)  


2832 27.04 1.32 1.10  chrX_33680160_33682353      796  1701 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33680160_3    796 TGTAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATTAAAAT 845
                           v   i i  i     i        v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33680160_3    846 GGCCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCCACTAAAC 895
                            v     v      vii  i  i        i  v  i  i ii   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33680160_3    896 TACC-TTTGACATTCTT-CAGAGAACTAGAAAAAACT-ATTTTAAGATTC 942
                          v  -vi  v v  i  -    -  i i-- v  i  -  ii   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_33680160_3    943 ATATGGAACCAAAAAAGAGCCAAAATAGCCAAGGCAATCCTAAGCAAAAA 992
                                 viiv  ii  v   i         ii     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_33680160_3    993 GAACAAAGCTGCAAGCATCATCCAAACTGACTTCAAACTATACAGCAGGG 1042
                                 i  v i vv   iv vvv ii i      viv   vi  ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_33680160_3   1043 CTATAGTAAACAAAACAGCATGATAGTGGTACAAGAA----CACATAGAT 1088
                            i     v   i    ii  i  v   i i   i ----  i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_33680160_3   1089 CAGTGGAACAGAACAGAGAACCCAGAAATAAGACCACACAACTACAACTA 1138
                           i     i    iv    ii          iv   i   vi  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_33680160_3   1139 TTTGATTGTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGAATTCCC 1188
                         v      v i     ivv  v   i v  vv               vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_33680160_3   1189 TATTCAATAAATGGTGCTGGGACAACTGGTTAGCCATATGTAGAAAATTG 1238
                          v     i                     v  ?   i   i i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_33680160_3   1239 GAACTAGACCCCTACCTTACACTGTATACGAAAAATCAACTCAAGATGGA 1288
                         i ii i           i    ii     -      i       i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAAATGGA 496

  chrX_33680160_3   1289 TTAAAGACTAAAATATAAAACCCAAAACTATAAAAACTCTC-GAAGAAAA 1337
                          i ?    iv    i   i v i            -    i-        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_33680160_3   1338 CCTAGGCA-ATATCATTCAGGACATAGGCACGGGCAAAGATATCAT-GAT 1385
                          v    ?i- v   -   iv   v v  vvii     v i v  v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_33680160_3   1386 GAAGATGCCAAAAGCAATTGCAACAAAAGCAACAACTGACAAATGGGATC 1435
                         - v  ii         vvv          v  v  iv  i    v   ii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_33680160_3   1436 TAATTAAACTAAAGAGCTTCTGAACAGCAAGGGAACCTATCAACATTGTA 1485
                          v  i   v v  i i   i  vi vv   i   vv       v vv  i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_33680160_3   1486 AACAAGCAACACACAGAATGGGAAAAAA-ATTGTGCAAAGTATGCATCTG 1534
                           v ii    v            i    -   -      vi  ii     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATT-TGCAAATCATATATCTG 742

  chrX_33680160_3   1535 ACAAAGGTTTAATGTCCAGCATCTATATACAATTTAAACAAATATACAAG 1584
                          i  i  vi vi i     v  v    v v  i ivv    v vv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_33680160_3   1585 AAAAAAACCAAACACTCCCATTAAAAAAGTGGGTAAAGAACATGAACAGA 1634
                              i  -   i vi  v   ?     -    i    i iv    i   
  L1M4_orf2#LINE/    793 AAAAAGAC-AAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGA 840

  chrX_33680160_3   1635 CACTTTTCAGAAGAAGGCATACGTGTGGCCAACAAGCGTGTGAAGAAA-G 1683
                           i  i  vi      ii    ivi       i    iii    i i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_33680160_3   1684 CTTAACATCAGTGATCAT 1701
                           i       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.22 (22 / 18)  


1501 29.43 8.51 4.48  chrX_33722679_33724536      496  1365 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_33722679_3    496 AAGGATATC--ATGTTCATGGTTTGGAAGGACCAATATTGTAAAAATGTC 543
                           i      --          v       ivii        v  i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_33722679_3    544 AAATTTTTTTTTTTATAATTTCATGTATACTTTCCATGAAATCCTAATTA 593
                           ------ vi iivi  v  v  v  i vv   v i v     iv  i 
  L1M4_orf2#LINE/     54 AA------TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_33722679_3    594 AATTTACAAAGACCCTTTTTAGTGAAAACTGAAAAGCTAATTCTTCACTT 643
                           v iv  ivvi  i     - iii   i   v     i  i  vv v  
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_33722679_3    644 TATATGAAAATTCGAGTGATGAAGCCTAACAAAAAACAATGT---AGGTG 690
                         i     i    v i  v  ivv  vv  i v    -    v --- iiv 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAG 195

  chrX_33722679_3    691 AAAAATGAAATCGGAAGGATTA-ATTCCACAGGATCCCAAGACTTATTGT 739
                           i  ii  i i   i iv i - i i v  --  ii   i     i ii
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCA--ATTTCAAAACTTACTAC 243

  chrX_33722679_3    740 AAAACCTCAGCAATTGATACAGTGTGTTCTTGGTTCAAGGACAAAAA-AT 788
                            i iv   i   ii v        v vi   ivi     i i v -  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_33722679_3    789 ACACCAGTGGAATAGTATAGAGAGGCAGGAAAC-----------TTT-TG 826
                          v i  i        v  v     v vi    i-----------   -  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_33722679_3    827 GACACTTGCTATATGACAGTGGTTTATGC--AGAGCAT-----GAGGAGA 869
                          v  v   v v vi    iv   ----  --   v   ----- i   i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGT----GCCAAGACCATTCAATGGGGAAA 389

  chrX_33722679_3    870 GTGATATATGTCTTTTCTGTTTGTTTTTAAAATAAATGACAGTGGCTTAC 919
                          -i   ---        -------------  i     iiiv   vvi v
  L1M4_orf2#LINE/    390 G-AATA---GTCTTTTC-------------AACAAATGGTGCTGGGACAA 422

  chrX_33722679_3    920 TTGAAAGCCTATATACAAAACGTAATAAACCTC-ATACCTACATCACACC 968
                         i  i vi? i i  i     - -   i  vi v- iv     v       
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAA-G-AATGAAGTTGGACCCCTACCTCACACC 470

  chrX_33722679_3    969 ATTCACAAAAATCAATATTAGGTGAAGTGTCGATCTAAATGTGAAGGGC- 1017
                           vi        i  iviv ii  i vii?v  i        -   i  -
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCT 519

  chrX_33722679_3   1018 -AAAC---AAGTTTTCTAGGTGAAAAATATTCAAAGGTA--TCT--ATTA 1059
                         -    ---  ivi ii   iv     -i  -- ii?   --   --i v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAA-CAT--AGGNGTAAATCTTCGTGA 566

  chrX_33722679_3   1060 TTTGGGAGTAGGAAAGATTTTTTTATATATGACACAAAATGTATGA---- 1105
                         ii v  iv    v  viv   i   v         v   v i ii ----
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_33722679_3   1106 ---------------ATAATTTAAACTATATTAAAATTAAAAATTTCTAG 1140
                         ---------------    v  ii   vi  i           i  i - 
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT-G 665

  chrX_33722679_3   1141 TATTCCGAATAATA------------TGAAAAAGTAAGTCACACGGTGGA 1178
                          ii i i  vi i ------------      iii  vi    vii   i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_33722679_3   1179 CAAAGATATTTGCAA--CACACATTAAAATAAGGGACTTGTATTTAAAAT 1226
                         vi  i          --  i i  ivi -              ii i   
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGA-TAAGGGACTTGTATCCAGAAT 764

  chrX_33722679_3   1227 ATGTGAAGA-TTCTTGCAAGTCAGT--TAAAAAGTCATATAGCACTGTGT 1273
                           i i    -i    i   v   i --       v  v   i v vi v?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_33722679_3   1274 AAAAATGGTCAAGAGACTTGAACAGGTACTTCACAAACCAGGGAATTCAA 1323
                                 v   ii  i     i  ii i   v v  vv i iv  v   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_33722679_3   1324 CTGGACAATAA--ACATGAAAAGATGCTCCATGTCATTGTTCAT 1365
                         v   v      --                v ii   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (153 / 99)
Gap_init rate = 0.04 (34 / 905), avg. gap size = 3.32 (113 / 34)  


 929 26.73 5.71 3.00  chrX_33725871_33729489     1933  2265 (1354)    L1M4_orf2#LINE/L1       15   356 (552)  

  chrX_33725871_3   1933 ATGCTCATGGACTGGAAGAATTAATATTTTTAAAAGGTCAGT-------- 1974
                            i       i       v        v    i v v  i --------
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_33725871_3   1975 ----GATCTACAGATTTAGGGCAATTATGCAATTATTATAAAAATACCAA 2020
                         ----            i -------- i     ivi   v     v   i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCA--------ACGCAATCCCTATCAAAATCCCAG 106

  chrX_33725871_3   2021 TGATATTCCTTATAGAAATAGAAAAA--AATCATAAAATTAATATAGAAC 2068
                         iviiv  ii  ii      v  v  i--i   v       v    i   v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_33725871_3   2069 --CACGAGTCTCCAAATAGCCAAAATCATCCTGAGCCAAAAGAATAAAGC 2116
                         --  v i v i vi           iv   i   ivv i     i    i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_33725871_3   2117 TGGAGTTATCACACTACTTGATTTCAAAATATACCACAAAGCCATAGCAA 2166
                              vvv       v iii         iv   i       i i  i  
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_33725871_3   2167 TAAAAACAGCACAGTACTATAATATAAAGA--GA-ACATGGATCAATAGA 2213
                          v  i    iiii     i--ii    i  --  - i  i       i  
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTG--GCATAAGGATAGACATATAGATCAATGGA 304

  chrX_33725871_3   2214 CCAGAAAAGAGAACCCAGAAATAAATGCGTAGATTTACAGCCAATTCTTT 2263
                         vi    vv    ii           iv i  v     ii i     vv  
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_33725871_3   2264 TT 2265
                           
  L1M4_orf2#LINE/    355 TT 356

Transitions / transversions = 1.70 (56 / 33)
Gap_init rate = 0.02 (7 / 342), avg. gap size = 4.14 (29 / 7)  

1830 25.44 1.78 1.25  chrX_33725871_33729489     2565  3126 (493)    L1M4_orf2#LINE/L1      344   908 (0)  

  chrX_33725871_3   2565 GCCAATTCATTTTTAACCAAATTGCCAAGAGCATACATTGTGAAAAGG-T 2613
                          i     v     ii  v iiv        v   v  v  v i    i- 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_33725871_3   2614 AATATCTTCACTAAATTGTGCTGGGAAAACTGGATAA--ACATGCAGAAG 2661
                          i v i    vi    v         v         ?--       i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_33725871_3   2662 AATGAAGTTAGGGCATTATTTCTCATCATATACAAAA-CCAAATCAAATT 2710
                                  i iv vi  ii  v  i           -ii  v     v 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_33725871_3   2711 GGATGAAAAACTTAAATTGAAGACCAAAAACTGTGAAACTACTAAAAGTA 2760
                             v ? i  i     vv    v v      i i     vi  i   v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_33725871_3   2761 AACCTTCAGGAAGCA---CTTTGGGATACTGATCTGAGCAAAGATTTTTG 2807
                            v --   ?- i ---   i v  ivi  ivi ii    v i   i v
  L1M4_orf2#LINE/    544 AACAT--AGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_33725871_3   2808 AG-CAAGACCTGAAAAGCACAGGCAACAAAAACAAAAGAAGACAAATGGG 2856
                           -i v   viv         i         iv    iv   i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_33725871_3   2857 ATTATATCATGCTGAAAAGTTTCTGCAAAGCAAAGGACACAATCAACAAA 2906
                          i vi    viv v    ii  i  iivvv          v     v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_33725871_3   2907 GTAAAGAGACAACCTACAGAATGGTAGAAAAAACATTGCAAACTACTCAT 2956
                           i  i        i         v      v i-       ii ivi  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATAT-TTGCAAATCATATAT 739

  chrX_33725871_3   2957 CTGACAAGGGGCTAATAACCAGAATATATGAGGACTGCAAACAACTCAAT 3006
                             i     i  vi  v           i i  viv vv          
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_33725871_3   3007 AGCAAAAACAATTAAATAAATTTGCTTAAACAATGGGCAAATAATTTGAA 3056
                          ii     v --i      -iiiiv  ?  v          vi       
  L1M4_orf2#LINE/    790 AATAAAAAGA--CAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_33725871_3   3057 TAGACATTTCTCAAAAGAAGA-ATGCAAAGGGCCAATAGGTATGTGGAAA 3105
                                     v        -  i    v        i i ii  i   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_33725871_3   3106 -ATGCTCAGTGTCACTAATCAT 3126
                         -       iii   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (80 / 59)
Gap_init rate = 0.02 (12 / 565), avg. gap size = 1.42 (17 / 12)  


 290 28.42 2.11 0.00  chrX_33819595_33821668      500   594 (1480)    L1M4_orf2#LINE/L1      137   233 (675)  

  chrX_33819595_3    500 TTCTACAGTTCATATGGAACTAAAATAGAACTTAAATAGCCAAAGCAGTC 549
                          i   v i           v iv  vi  v ivi          i  i  
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_33819595_3    550 CT-AAGCATAAGAACAA-GCTGGAGGCATCACATTACCTTACCTCAA 594
                         i -  iv v        - i      vv     i v  iv ii    
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.02 (2 / 97), avg. gap size = 1.00 (2 / 2)  

2242 26.33 1.63 1.18  chrX_33819595_33821668      906  1581 (493)    L1M4_orf2#LINE/L1      230   908 (0)  

  chrX_33819595_3    906 TCAAATTATGCTACAAAGCTACAGTGACTGAAACAGCATGGTACTGGGAT 955
                              viv i               i iii i    ii         v  
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_33819595_3    956 GAAAATAGACACACATTTCAATAGAACAGAAGAAGGAACCCAGAAATAGA 1005
                         i ii       i i vv     i   i    vvii  ii         i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_33819595_3   1006 GATACATATTTATAGCCAAATAATCTTTGACAAAGCCAATAAAAGCCCCC 1055
                         vvi i i      i i   v i  i  i     i viivi  i -  vii
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA-CCATT 378

  chrX_33819595_3   1056 CAACATGGAGGAAGGACATCCTTTTCAATAAATGATGCTGGGTAAATTGG 1105
                            --   i i   i i vi        i     i       vv  i   
  L1M4_orf2#LINE/    379 CAA--TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_33819595_3   1106 CTATCTATATGCAGAAGAATGAAGCTGGATACCGATCTGTCACCACATAC 1155
                         v  ? i i     i          i    iv  v i  vv     i    
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_33819595_3   1156 AAAAAATTACTCAAGATGGATTTAAGACTTAAATATAAGACCTGAAACTA 1205
                              v v      i      iv?    i     i     v  i      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_33819595_3   1206 TACAAATACTAGAAGAAAATCTAGGGA-AAATTCTTGTGGACATTGGTCT 1254
                           v  v vi          iv    ?i-    ii i   -  v    vi 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTT 575

  chrX_33819595_3   1255 AGGCAAATAATTCGTGACTAAGACCTCAAAAGCATGAGCAACAACA--AA 1302
                               vviv   v iiv  v   vi        ii        v --  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_33819595_3   1303 AAATAGGCAATTGGGACTT-----AAATGAAAAAGCTCCCTAACAACAAA 1347
                               ii  v v      -----    v     vi iiv i- vv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG-CTTCAAA 674

  chrX_33819595_3   1348 ATACATAATCAACAGAGTGAACAGACAACCTACAGAATGGGAGAAAATAT 1397
                         iv   iv     v i      v        i                   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_33819595_3   1398 TTACAAACTGTATGTCCCACAGGGGACTAATAATCCCTAATTTACAGGGA 1447
                           i    iii   i  iv i i      vi  -   vv   v  i ii  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTA-TCCAGAATATATAAAGA 773

  chrX_33819595_3   1448 ACTCAATAACAAC--AACAACAACAA-ACAAATAACCTCATTATAAAGCA 1494
                             -- v     --  i  i  v  -          iv   ?v   iii
  L1M4_orf2#LINE/    774 ACTC--TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_33819595_3   1495 AGCAAATGACATAAATAGACATTTTTCAAAGGAAGATATGCAAATGGTCA 1544
                         i     v  iv i           i  v  i        i       i  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_33819595_3   1545 TCAAACATATGAAAAAGTGATAAACATCACTAATCAT 1581
                         vi  i  i       ii  v v       ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (109 / 65)
Gap_init rate = 0.02 (11 / 679), avg. gap size = 1.73 (19 / 11)  


2653 26.41 2.93 2.03  chrX_33892988_33895598     1233  2118 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_33892988_3   1233 ATGTACATAAA--GGGAAACTAAAACATTGATGAATAATTAAAGATGTCA 1280
                             v   ii --  i i   v  -i    --------    -    v  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAA-TATTG--------TTAA-GATGGCA 54

  chrX_33892988_3   1281 ACTTTTTCAAAATTG-TCCATAGATTCAATGCATTTCCAATCAAAATTCA 1329
                          ivi ii v      -  i i        i   v i  v        i v
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_33892988_3   1330 AAAT---TGTTTTGTGGA--TTACAGCAAACTGATTCTAAAGTTTATGTG 1374
                          iv --- v     ii  --  i--i   i     i     i  i  i  
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATG 152

  chrX_33892988_3   1375 GAAAGGCAAAAGACCCCAAATAGCCAACACAACATTGAA---GGAGAGCA 1421
                             v    ii     vi         v    iv     --- i   i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_33892988_3   1422 AAATGAGAGGATTAATACTACCCGACTTCAAGACTATATT-----GTTAC 1466
                           i vi     i v i   v   i i     i   -  i ----- i   
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTAC 251

  chrX_33892988_3   1467 AATAATCAACATATTGTGGTATTGGTAAAGAAACAGAAAAATAGATCAAT 1516
                          i       v i v       i   i v iii i   v v          
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_33892988_3   1517 GGAACAGAATAGAAAGTCCAAAAATAGACC--TACATTAATATAACCAAT 1564
                             i     v  i      i     i   --      --   iii    
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAAT 349

  chrX_33892988_3   1565 TTATATTTGACAAATGAGC-AAGAAAGTTCAGTGGAGAAAGAATGCTCTT 1613
                          v  v  i     iv v  -    vvi    i   i        iv    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_33892988_3   1614 TTCAACAAAATGTGCTAGAATAATTGGACATTCATATGCAAAAAAATGAA 1663
                                  vv     i i i  i    i ?i  i        i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_33892988_3   1664 TGTAGACACAGACCTTGCACATTTTACAAGCAATAGCATCAAATGCATTG 1713
                         vv i   v vv    ii   vv v     iv v  i viv     v  ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_33892988_3   1714 TAGACCTAAATGTAAATGCTAAA-CTATAAAACTCCCAGATGATAACATA 1762
                         ?              iv      -           ii   v  v      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_33892988_3   1763 AGAGAAAATATAGGTGGCCTTCGGTTTGGCCAAGACTATTTAGATACAGC 1812
                         i ? v    v vv   i    v    v   v v ii vi       iii 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_33892988_3   1813 ACCATTAGCATAATCTATGGAA--AAAAGGAGATACATTGGAATTCTTTA 1860
                             vv    i  v v iii  --    iv     v      v   v i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_33892988_3   1861 AAATTATAATGTTTTTCTGT---GAAACATCCTGTTACAGAGAATGAAAA 1907
                               v  -ii    v  i---i  iv iv  i i -   i i      
  L1M4_orf2#LINE/    650 AAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCA-AGAAAGTGAAAA 697

  chrX_33892988_3   1908 T-CGAGTCATACAGTGAGACAAAATATTTTCAAAACATACACAGAATGAA 1956
                         v- i vi  i v i  i  v         v    v    i ivvi  i i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_33892988_3   1957 GAATTTGTATTCACAATACATAAAGAATTCTAGAAACTCAACTGTAAGAG 2006
                          i i      i  v    i        i   viv       ivi   i i
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_33892988_3   2007 AAGAAACATCTCAATATTAAAAACAGATAAAATATCTAAACAGACACCTC 2056
                         i v   i v i    - ?     ii ii   iv  i i  i     ii  
  L1M4_orf2#LINE/    798 GACAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_33892988_3   2057 ATGAAAGAAGATCTGCAAATGGAAAATAAGCAAATGAAAACATGCTCAAC 2106
                         viv         v i       vv        v       v         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_33892988_3   2107 AGCATATGTAAT 2118
                          v  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.02 (21 / 894), avg. gap size = 2.10 (44 / 21)  


1711 23.88 13.00 3.25  chrX_33909757_33911902.rev      856  1655 (491)    L1M4_orf2#LINE/L1       31   908 (0)  

  chrX_33909757_3    856 AGATTTCCTATTGTTAACATGCCAATTATCCTCAAATTGATCTATAGATT 905
                            i  vv         v   v    vv   i            i     
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chrX_33909757_3    906 CAACAAAATCCTAATCAAATTCCCAACAGGACTTTTTTTTTTTTTTGACG 955
                             iv     iv      v     i v ------ii      viv  vi
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTG------CCTTTTTTGCAGAAA 124

  chrX_33909757_3    956 TTGACAAACTGACTTTAAAATTTCTATAGAAATTCAAAGGACCTAGGA-- 1003
                                i    iii       iv   i     v   i     i  i --
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chrX_33909757_3   1004 ---AAAACTAACTTTGTAAAAGAA---CATTGTTAAAGGACTAATACAGC 1047
                         ---     -  ii   v       ---  vv   ii      v i  vv 
  L1M4_orf2#LINE/    175 GCCAAAAC-AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_33909757_3   1048 CTAATTTCTAGATTTATTATAAAGCTAAAGTAACCAACAGAATGGGAAAT 1097
                          i      v i i   i  i       v     i   v v i  v iv i
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_33909757_3   1098 TTGTGTGAG---AGA-A---AAATCAATGGAAGAGAAAAGAGTGTCCAGA 1140
                          v ii i  ---   - --- i          v    vv   v       
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_33909757_3   1141 AATTGACCTTCAAAAAACATACA--------CAACTGATATTCTACCAAT 1182
                            vi   ---------      --------   i    v   v  v iv
  L1M4_orf2#LINE/    324 AATAAACC---------CATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_33909757_3   1183 TTCCAAATGTAATTCAGCGGAGAAAAATTTAGTCTTTACAA-AAATAGTT 1231
                         v v v  viiv     ii  i    i v -       v   -    i  v
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAAT-AGTCTTTTCAACAAATGGTG 413

  chrX_33909757_3   1232 CTAAAATTATCAGATAT----ATGTAA------GCAATAGG-----TACA 1266
                           iii iv iii    ?----   i  ------ v i v  -----   v
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_33909757_3   1267 TTTT----TAAATAAAAACT---------TTGATC-TATATCT---TGT- 1298
                          ivi----  v i     i --------- v    -? v i  ---   -
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_33909757_3   1299 ---GCTG-------------TTTACAA--AAAT-TA-----AAACCTT-- 1322
                         ---   i-------------i   v  --   i-  -----   i   --
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_33909757_3   1323 -GACCTTTGGATAGGCCAAGTTTTCATAGATA---CATCAAAAGAAGCAC 1368
                         -      v  v     v v v    v      ---  i      ---   
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG---CAC 610

  chrX_33909757_3   1369 AATCCATAAAAGAACAAACTGATAAATTGGACTTCATCAAA-TTAAAAAA 1417
                           v v i       v   iv                     -       -
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA- 659

  chrX_33909757_3   1418 ACTTCT---CTTT----GACACTGTTAAGACAATGAAAGGGAAAAGCCA- 1459
                         -   i ---   i----      i i    v i     i - v  v   -
  L1M4_orf2#LINE/    660 -CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG-ACAACCCAC 707

  chrX_33909757_3   1460 AGGATGAAGTGAAAA-ATTTGCAAATCATATATCCGATAACCTATTTACA 1508
                           i   i- v     -                  i     vvv i  ii 
  L1M4_orf2#LINE/    708 AGAATGG-GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_33909757_3   1509 TCTAGAACACAGCAAGTATTCTCAAAACTAAATATGATATCCAGA----- 1553
                           i    i i vv   v i   i v    v    --   vvv   -----
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATA--ATAAAAAGACAAAT 804

  chrX_33909757_3   1554 AACACAATTTAAAAATGGGGAAAAAATCC--ACAGAAACTTCAACCAAGG 1601
                            v     ?         v   ii  ii-- i   v i   vv v   i
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_33909757_3   1602 AGAGATAAGGATGGCAAATAAGCAAATATAGAGATGTTCAATATCAGTAG 1651
                            v   vii     v        v  iv i     i    i    ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_33909757_3   1652 TCAT 1655
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.09 (98 / 90)
Gap_init rate = 0.04 (37 / 878), avg. gap size = 3.51 (130 / 37)  


1393 21.77 2.35 20.33  chrX_33931353_33935306.rev     2357  3463 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_33931353_3   2357 TGGAAAAACATTTGATGCTCATGGATAGGAAGAATAAATATTGTTAAAAT 2406
                               i i  iiv   i        v      v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_33931353_3   2407 GGCCATACTGCCCAAAGCAATTTACAGAATCTATGTTATTCCTA---AAA 2453
                            v     v      vii  i      v  v i iv  i    ---   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_33931353_3   2454 GTACA---------TTTATAAAACTATAAAAAA--AATTTTAAAGTTCAT 2492
                         viv  ---------   ii i  v - i v  i--i  ii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_33931353_3   2493 ATGGAACCACAAAAGAGCCCAATTAGCCAAAGCAATCCTAAGCAAAAGAA 2542
                               vii   ii  v  vi v        i     i i iv  i ii 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_33931353_3   2543 ACAAAGCTGGAAATATCATGTTACCTTACTTCAAACTATACTCCAGGGCT 2592
                               i    iivv   iii v  iv i      viv    v  ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_33931353_3   2593 ACAGTAACTAAAAGAACATGGTACTGGTACAAACACAGACACACAGAACA 2642
                                ii  i v iii         i i  iv i     i i   v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_33931353_3   2643 AAGGAACAGAATAGAGAGCCCAGAAATAATGCTGCAAACCTACATACATC 2692
                          v    i     v     i          --------   --       i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAA--------ACC--CATACATT 339

  chrX_33931353_3   2693 TGATCTTCCACAAAGCAGACAAAACAAACAATGAGGAAACAACACCCTAT 2742
                          -------------------------------------------------
  L1M4_orf2#LINE/    340 T------------------------------------------------- 340

  chrX_33931353_3   2743 TTAATAAATGGTGCTGGGATAACGGGCTAGACCTATGCCGATGATTGACA 2792
                         -------     -------------------- v  -----     ----
  L1M4_orf2#LINE/    341 -------ATGGT--------------------CAAT-----TGATT---- 354

  chrX_33931353_3   2793 CTGGACCCGTTCCTTATGCTATATAAAAAAGAAATAATGCTGCAAACTTA 2842
                         ---------   --------------------i i  v v   -------
  L1M4_orf2#LINE/    355 ---------TTC--------------------GACAAGGGTGC------- 368

  chrX_33931353_3   2843 CATACATCTGATCTTCCACAAAGCAGACGAAACAAACAATGAGGAAA-AA 2891
                         ------------------   ----   ----  vv     i     -  
  L1M4_orf2#LINE/    369 ------------------CAA----GAC----CATTCAATGGGGAAAGAA 392

  chrX_33931353_3   2892 CACCCTATTTAATAAACGGTGCTGGGATAACTGGCTAACAATATGCAGAT 2941
                         i vi  v  i  i   i          i      v  ? v i     i v
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_33931353_3   2942 GATTGACACTGAACCCATTCCTCACACACACACACACACACACACACACA 2991
                           v   vii  i    v v        -----------------------
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACAC----------------------- 469

  chrX_33931353_3   2992 CACACACACACACACAAAATTCCTTACACTGTACACTATACTAAAAAACC 3041
                         ------  i i   -      -------------------------   i
  L1M4_orf2#LINE/    470 ------CATATACA-AAAATT-------------------------AACT 487

  chrX_33931353_3   3042 CACAAGATGGATTAAAGACTTAAAGG-AAATCCCCAAACTATAAAAACCC 3090
                           -- i      i ?    i    v -  ivv iv           vi i
  L1M4_orf2#LINE/    488 CA--AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_33931353_3   3091 TGCAAGACAACCTATGC---AATACCAGT---CTGGAATTAGAAACTGGC 3134
                          iv    v   v  v ?---   viiv  ---  v ii    ------  
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG------GC 579

  chrX_33931353_3   3135 AAAGATGTCAT-GATAAAGACACCAATACCAATTGCAACAAAAACAAATA 3183
                           v i v  v -    v-        v v  vvv         iv   v 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_33931353_3   3184 CTGATAAATCAGATCTTATTAGACTAAAGAGTTTCTTCACAGCAAAGGAA 3233
                         iv       ii  ii i  i i v v  i ii  i vii vv       v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_33931353_3   3234 ACTCTCAATAGAATAAACAGGCAACCTACGGAATACAAGAAAATATTTGC 3283
                            v    v i i i  v  i     i  i    ivi             
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_33931353_3   3284 AAACTATGCATCTGGCAAAAGTGTAATATCTAGCATCTGCAAGGAACTTA 3333
                            ii  ii     ii  ii vv vi    i  v  v ii  i     iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_33931353_3   3334 AGCAAATTTACAAGAAAAAAATTAAACAACCCCATT-AAAAATGGGCAAA 3382
                         vi   v iv i  v     i i-   i     v   -             
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_33931353_3   3383 GGACAAGAACAGACACTTTTCAAAAGAAGACATA--AATGCAGCCAACAA 3430
                            ivv   i     i  i  v        i   --    --     i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG--GCCAATAA 875

  chrX_33931353_3   3431 GTACATACAAAGGAGCTCAATATCACTGATCAT 3463
                          i    iv    iv      i    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 8.66 (251 / 29)  


2862 27.52 1.44 1.00  chrX_33990457_33993459     1610  2510 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_33990457_3   1610 AAATACATTTCATGCTCATGGATAGGAAGAATCAATATTATTAAAATGAC 1659
                            v i  ii    i        v      v i      i    i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_33990457_3   1660 CATAGTGACCAAACCAATTTATAGATTCAATGCTATTCCTATTAAACTAC 1709
                         v   v vv     iii  i  i        i  v  i     i   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_33990457_3   1710 CAATGATATTCCTCACAGAAGTAGAAAAAAAGTGCTT-TAAAATTCGTAT 1758
                           iiviiv  ii ii     i v  v  iv--  v i-        i   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCATAT 151

  chrX_33990457_3   1759 GAAACTGAAAAACAGCCTGAATAGCCAACGCAATCTTAAGAAA-AAGAAC 1807
                          i  v  v  iiv v  v          vi       i i   -      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_33990457_3   1808 AAAACTGGGAGCATCATATTACTTAACTTCAAACTATACTACAAGGCTAC 1857
                            ii   ii vv   i i v ii  i      viv        i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_33990457_3   1858 AGTAACCAAAACAGCATGGTACTGGTACAAAGATAGACACATCAACCTAT 1907
                              i   i    ii         i i  i        i  vi i v  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_33990457_3   1908 GGAACACAATAGAGAGCCCAGAAATAGTGCCATACACCAAAAACCATTTG 1957
                             i v   v     i         ivv       iiv viii  v   
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_33990457_3   1958 ATCATCATCAAAATAAACTGAAACAAA-CAATGGAGAGAGGATTCCCTAT 2006
                           iv  iv   ii-ivi ii i  v v-      i  i  i  vvi  v 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_33990457_3   2007 TCAATGAGTGGTGCTGGGAAAACTGGCTAAGCATATGCAGAAGATAGGAA 2056
                             ii i           v      v  ?v  i     i    vv i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_33990457_3   2057 CTGGACCCCTTCCTTGCACCATATACAAAAGTCAACTCAAGATGGATTGA 2106
                         i         v   ii              i i       i      ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_33990457_3   2107 ATACTTAAGTGTAAAACCTAAAACTATAAAAACCCTGGAAGATAACCTAG 2156
                          v  i   i     i v              vi i i     v   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_33990457_3   2157 G---AAATACCATTCTGGACATAGGGCCTGACAAAGATTTCAT-GATGAA 2202
                          ---    -- -   vv   v v   iiv i   v i    v -   - v
  L1M4_orf2#LINE/    551 GNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chrX_33990457_3   2203 GATGCCAAAAGCAATTGAG--ACAAAAGCAAAAATTGAGAAATAGGACCT 2250
                           ii         --ii  --       v      v  v    v    i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_33990457_3   2251 AATCAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTATCAATAGAATAA 2300
                         v      v v  i i   i  ii vvi   i  v        v i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_33990457_3   2301 AGAGACAACCTACAGAATGGGAGAAAACATTTCCAAACTATGCATCCAAT 2350
                          i        i                i    v    ii  ii   ii  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_33990457_3   2351 GAAGGTCCAATGTCCATAATCTATAAGGAACTTAAGCAAATTTACAAGCG 2400
                         i i  v ivi i    v   v     i     ivvi   v iv i  vvi
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_33990457_3   2401 AAAAACAA----CTCCATTACAAATTGGGCAAAGTACATGAACAAACACT 2446
                            i    ---- i v   ?v   v         v iv    i i   i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_33990457_3   2447 TTTCAAAAGAAGACCGACATGCCACCAACAAGCATATGAAAAAATGCTCA 2496
                          i  v        ivv   viivi    i     i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_33990457_3   2497 ACATCATTAATCAT 2510
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (150 / 95)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 1.69 (22 / 13)  


1698 26.14 1.89 3.62  chrX_34051820_34053451.rev      506  1140 (491)    L1M4_orf2#LINE/L1      285   908 (0)  

  chrX_34051820_3    506 TAGATATATAGAACAATGGAACAAAATACAGAACCCAGAAATACAGCCAC 555
                             i       v        i i   vv   ii         v v   i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_34051820_3    556 ATATTTAAAAACAATCAATCTTTTACAAAAGCTGACAAGAACATACATTG 605
                          i     viiv    ii  i  iv    ii -  v     v   v  v  
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGG-TGCCAAGACCATTCAATG 383

  chrX_34051820_3    606 GAGAAAGGACACCTTTTTCAATAAATAGTACTGGATAAATTGGATTGACG 655
                          i     i i vii       i    i  i    ivv  i     v?v i
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_34051820_3    656 TATACAGAAGAATGAAACTGGATATCTATCTCTCACCATACTA-AAATAT 704
                         i  i  i         ii    ivi   i   v       -  -   v  
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA-TACAAAAAT 482

  chrX_34051820_3    705 TAGCTCAAGATGGAATTAAAGAC--AAACATAAGACTCAAAATTATACAA 752
                           i     i     - i ?    --   ii     vii    i    v  
  L1M4_orf2#LINE/    483 TAACTCAAAATGGA-TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_34051820_3    753 GTACTAGAAAAGACAACAGGAAAACATTTTCTGGACATTGGGCTAGGAAA 802
                         v vi     i i vv i   ?iv v  i   vv   v     i    v  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_34051820_3    803 AGAACTTGTGACTAAGACTTCAAAAGCACAAGCAACAAAAATAAAAGTAG 852
                         v ivi iv iiv  v   vi                    iv    i   
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_34051820_3    853 AAAAATGGGACTTAATTACACTAAAAAGCTTCTGAAAAGCAGAAAATATT 902
                          v    v      v  i v v v    i   i  vivvv  i ii i i 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_34051820_3    903 AATCAACAGAGCGAAAAGACAACCTGTAGAAAGAGAGAAAAATATTTTTA 952
                          -    v i  i            iii    v i       -     vi 
  L1M4_orf2#LINE/    682 A-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCA 729

  chrX_34051820_3    953 AATTATACATCTGACAGAAGATGAATATCCAGAATTTACAAGGAGCTCAA 1002
                            i   i      i iii  ivvi          v  i  i  i   vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_34051820_3   1003 ACAACGCCACAGCAAAAA-AGAGATAATCCCATT-AAAAGTGGGCACTTT 1050
                              v v i ii     - v i    i  v   -    i      ----
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA---- 825

  chrX_34051820_3   1051 TTAGTGAAAGGAAACTGTTGTAAAAAAGACA-------AAAGAAGACATA 1093
                         -------     --- -   ---  v     -------        i   
  L1M4_orf2#LINE/    826 -------AAGGA---T-TTG---AATAGACATTTCTCCAAAGAAGATATA 861

  chrX_34051820_3   1094 AAAATGGCCAACAGGTTTATGAAAAAATGCTTAATACCACGAATCAT 1140
                         v          i i ivi       i     i  i i  ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (99 / 64)
Gap_init rate = 0.02 (14 / 624), avg. gap size = 2.50 (35 / 14)  


2188 29.14 5.64 1.53  chrX_34178028_34179885      507  1357 (501)    L1M4_orf2#LINE/L1        1   886 (22)  

  chrX_34178028_3    507 TGGAAAATCATTCTATGCTTATGGACTGAAAGAATCAATATCG------- 549
                               ivi  i i   i i     i  i    v i     i -------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34178028_3    550 ----------CTCAAAGCAATTTATAGATTCTAGGCTATTCCAATCAACC 589
                         ---------- i    vii  i  i      v v  v  i  v     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34178028_3    590 TACCAACATCATTCTTCACAGAACTAGAAAAAAAAAGATTCTAAAATGTA 639
                          v   i vv v  i  ii     v v  v  ivv--   i       vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT--GATCCTAAAATTCA 148

  chrX_34178028_3    640 TATAGAACCAAAAAAAGGGCACT---AATAGC------AATCCTAAGCAA 680
                            i   --- viv     -  i---      ------    i i iv  
  L1M4_orf2#LINE/    149 TATGGAA---ATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_34178028_3    681 AAAGAACAAAGCCAGGAGCATCACACTATC--------GGGCTT----TA 718
                         i          iii ii vv       vi --------iii   ----i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_34178028_3    719 AAGCTACAATAACCAAAATGGCATGGTGCAGACACAAAAACAAACACATA 768
                                 i   i   i ii ii    i v i  i  ii i i   i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_34178028_3    769 GACCAACAAAACAGAACAGAAAACTCAGAAATAAAGCCAAATACATACAA 818
                           i   iii  i    iv  i iii          v   v i iv  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_34178028_3    819 CCACCTTGTCTTCGATGAGGCCAACAAAAACAAGCAATGGGGAAAGGACT 868
                         i  vi vi i     ii   viiv   i v  vv            i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_34178028_3    869 TCCTATTCAGTATATGGTGCTGTGATAGCTGTCTAGCCATACGCAGAAAA 918
                         vi  v    ii v         v  i i   vv  ?   i i   i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_34178028_3    919 ATGAAACTTGATTCTTATACCTCTTATCATACACAAAAATTAACTCAAGA 968
                              ii v  ii i  --    vi i    i                i 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_34178028_3    969 TAGATTAAAGATTTAAATGTAAGACCTCAAACTATAAAAATCCTAGAAGA 1018
                          i   i ?   ii           v  v           v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_34178028_3   1019 AAACCTAGG---AAATGCCCTTCTCAACACTGGCCTTGGCAAAGAATTTT 1065
                             v    ---    ---    vii  vi   vi v     v iv  i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_34178028_3   1066 TGGCTAAGTCCCCAAAAGCAACGGCAATAAAAACAAAAATTGACAAGTGG 1115
                          i v  v v v         vvi    i    iv      v  i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_34178028_3   1116 GACCTAGTTAAACTAAAGAACTTCTGCACAGCAGAAGACAGTATCAACAG 1165
                            i vi i   v v  i     i  ii vv  i i    v      v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_34178028_3   1166 AGTAAACAGATAACCTACAGAATCAGAGAAAACATTTGCAAACTATGAAT 1215
                            i  v   i    i       vi       i         ii  iv  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_34178028_3   1216 CCAACTAAGGTCTGAGATCTAGAATCTATAGGGAACT--TA-AAC-CAAC 1261
                          ii iv i  v  viv   i     v    ii     --  -   -   i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_34178028_3   1262 AAGCAAAA-ACAAAGAACTGCATTGAAAAATGGTCAAAGAACATGAAAAA 1310
                           vv    -     v   ivv   ?        v     i iv    v i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_34178028_3   1311 ACGCTTCTC--AAGAGGACATACAAGCAGCCAACAGAAGCAAATCAAAA 1357
                           ii     --    i  i      iii     i --    v  v    
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATA--AGCACATGAAAA 886

Transitions / transversions = 1.72 (155 / 90)
Gap_init rate = 0.02 (17 / 886), avg. gap size = 3.59 (61 / 17)  


3667 22.38 2.47 0.34  chrX_34187467_34189631      784  1672 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34187467_3    784 TGGAAACAGATTTC----TTATGAATTGGAAGACTTAATATTGTCAAAAT 829
                               v v  ii ---- i   i                    i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34187467_3    830 GTCCTTACTACCCAAAGAGACCTACAGATTCAATGGGATTCTTATCAAAA 879
                          v vv    v      vv  i            i vi  i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34187467_3    880 TCCCAATGGCATTTTTTGCAAAAATAGAAAAGA-AATTCTAAAATGTATA 928
                              iiv  v         i    v  v   v-i  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_34187467_3    929 TGAATTCTCATTGAATCCCAAATAGCCAAAATTATCTTGAGAAAGAAAAA 978
                           i vviv  vv i i  vi           iv       i      i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_34187467_3    979 CAAA-CTGGAGGCCTCATACATCCAAATTTCAAAACATATTACAAAGCTA 1027
                             -i      v    i  v   v           v  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_34187467_3   1028 CTGTAATCAAAACACAATGGAACTGGCATAAAGACAGAGATATAGACCAA 1077
                          v        i   vvi   v          i  i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_34187467_3   1078 -AGCACAGAAT--AGAGTTCAAGAATAAACTGTCATGTAT--ATGGTCAA 1122
                         -i v i     --     i  ii       i--   ii  --        
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCAA 348

  chrX_34187467_3   1123 ATTATCCTTGGCAAAGGTGCCTAGTACA--CAATGGAAAAAGCAAAATTT 1170
                         v v  ii i i   i      v  vv  --      ii    v v i i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_34187467_3   1171 CTTCAACAAATGATCCTGGAAAAACTGGACATCCACATGAAGAATAATGA 1220
                         i           i v    i v       i ?       v i  v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_34187467_3   1221 ACTGTGACTCTTACCTTTTACCATATATAGAAATTAACTCAAAATGGATT 1270
                          v vv   i i     ivi        i i                   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_34187467_3   1271 AACAAGCCAAATGTAAGGGCCAAAACTATAAAACTGTTACAAATAAACAT 1320
                          ?vi v i         i  i              v   v  iv      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_34187467_3   1321 GGAA--AAGGCTTTATGACTCTGAACTTGGCAATGTTTTCTTGAATAAAA 1368
                         i i?--  iv   ii    ii  iii v       v      ii   vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_34187467_3   1369 CACCAAAAGTACAGGCATCAAACACAGAACTACACAAATGAGACTATATC 1418
                                  i   i   v    viv i  v  v i    vi    vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_34187467_3   1419 AAACTTGAAAACTTCTCCATAACAAAGGAAACAATCAACAGAGTAAAAAG 1468
                            v  i       i viiivv       v  v     v i   i     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_34187467_3   1469 GCAACCTATGGAATGAGAGAAAGTATTTGCAAATCCATATATCTGATAAG 1518
                         i     i ii     i      i            -              
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAG 747

  chrX_34187467_3   1519 AGGTTAATATCTAGAATGTATCAAGAACTCTTACAACTCAACAA-AGAAA 1567
                         i ii vi    i     i   v                   i  - i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_34187467_3   1568 ATTAAATAATCCAGTATAAAAATGGACAAAGGACTTGA-----CATTTCT 1612
                         ivi      i   i v?        i       i    -----       
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_34187467_3   1613 CCCAAGATAATATACAAATGACCAACAA-TATATGAAAAGATGCTCAACA 1661
                           v    vi           i    i  -i i                  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_34187467_3   1662 TCACTAACCAT 1672
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (119 / 76)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.92 (25 / 13)  


3296 26.57 0.55 0.44  chrX_34192465_34198694     4831  5737 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34192465_3   4831 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATAGTGAAAAT 4880
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34192465_3   4881 GGCCATACTGCTGAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4930
                            v     v iv  iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34192465_3   4931 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4978
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_34192465_3   4979 TATGGAACCAGAAAAGAGCCCGCATCGCCAAGTCGATCCTAAGCTGAAAG 5028
                                viiv  ii  v  v v  v     iv i   i i ivvii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_34192465_3   5029 AACAAAGCTGGAGGTATCACGCTACCTGACTTCAAACTATACTACAAGGC 5078
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_34192465_3   5079 TACAGTAACCAAAACAGCATGGTAATGGTACCAAAACAGAGATATAGATC 5128
                                 i   i    ii     v   i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_34192465_3   5129 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5176
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_34192465_3   5177 ATCTGATCTTTGACAAACCTGAGAAAAGCAAGCAATGGGGAAAGGATTCC 5226
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_34192465_3   5227 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5276
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_34192465_3   5277 GAAACTGGATCCCTTCCTTACACCTTTTACAAAAATGAATTCAAGATGGA 5326
                            ii    i    v   i     v v         v  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_34192465_3   5327 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCATAGAAGAAAAC 5376
                          i ?   ii    i  v   v       i      vi v           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_34192465_3   5377 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATATCTAA 5426
                         v    ?i v viv   iv   v v  vv i     v ii   v  vv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_34192465_3   5427 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5476
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_34192465_3   5477 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5526
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_34192465_3   5527 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5576
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_34192465_3   5577 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA-AAAA 5625
                         i  i  vi          v  i  v      vv    v iv i  -    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_34192465_3   5626 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5675
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_34192465_3   5676 TCAAAAGAAGACATATATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5725
                           v        i   i viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_34192465_3   5726 ATCACTGGCCAT 5737
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2654 27.87 2.01 0.78  chrX_34220552_34222488      548  1444 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34220552_3    548 TGGAAATAAATCACATGCTTGTTGATGGGTTGAATCAATATTGTGAAAAT 597
                               v v   v    i ii v   v  vv  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34220552_3    598 GATCATACTGCCAAAAGCAATCTATAAATTCAATGCAATTCCCACCAAA- 646
                          iiv     v  v   vii     i i      i     i  i i    -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34220552_3    647 TACCATCATTATTCTTCACAGAACTAGAGAAAACATTCCTAAAATTTATA 696
                          v   v vviv  i  ii     v v  v  iviiv          i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_34220552_3    697 TGGAACCAGAAAAGAGCCCACATAGCCAAAGAAAGACTAAGCAAAACAAA 746
                              viiv  ii  v  viv         iv  vvi i iv  i vi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_34220552_3    747 CAAGTCTGGAGGAATCACACTACCTGATTTCAAGCTATACTGTAAGACCA 796
                            ivi       v       v  ii       iviv    ii  ii i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_34220552_3    797 TAGTCACCAAAACATCATGGTACTGGTATAAAAATAGACACATAGACCAA 846
                         i   v i   i   vii         i    ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_34220552_3    847 TGGAACAGAAAAGACAACCCAAAAAATAAAGCCAGATACTTACAGCCAAC 896
                              i    vv  v ii   i   -    v   v i i   ii i   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGTCAAT 349

  chrX_34220552_3    897 TGTTCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGA------- 939
                           v i   i    i vviv   i v   vv i         i -------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_34220552_3    940 -----CAAATGGTGCTGGAATAATTGGCTAGCCACATGTAGGAGAATGAA 984
                         -----             i i  i   v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_34220552_3    985 ACTGGATGCTCATCTCTCACCTTATACAAAAATTAACTCAAGATGGATTA 1034
                         ii    iv ii i   v    v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_34220552_3   1035 AGGACTTAAATCTAAGACCTGAAACTATACAAATTCT-AGAGCATAACAT 1083
                         ?i   i     v     v  i        -   i   -   iv v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACAT 548

  chrX_34220552_3   1084 TGGAAAACCCCTTCTAAACACTGGCTTAAGGCAAGAATTTCATGACCAAG 1133
                         v  ?iv vvi    vvi  vi   v   -     vii    v iivi v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATATG 597

  chrX_34220552_3   1134 AACCCAAAAGCAAATGCAATAAAAACAAACATAAATAGCTGGGACCTAAT 1183
                          vv         v v    i    iv   v   i   iv v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_34220552_3   1184 TAAACTAAAGAGCTTTTTCATGGCAAAAGGAACAGTCAGCAGAGTAAACA 1233
                         i   v v  i i     viiivv    i iv  vi   iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_34220552_3   1234 GACAACCCACAGAGTGGGAGAAAGTCTTTA-AAATCTATACATCTCACAA 1282
                                      i         i v   i-     -   i    v i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAA 746

  chrX_34220552_3   1283 AGGACTAATATCCAGCATCAATAAA---CTCAAACAAATCAGCAAGAAAA 1329
                         i     vi       v  vv     ---   vv    v   ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_34220552_3   1330 AAAGCAAATAATACCATTCAAAAAGTGTGCTAAGGATATGAATAAACAAT 1379
                          i -       iv v   ?     -  v  v      v      i   v 
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATT 844

  chrX_34220552_3   1380 TATCAAAAGAAGATACATAAATGACCAACAAACATACGAAAAAAATGCTC 1429
                          v  v          i i     i    i  i  i i     i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chrX_34220552_3   1430 AAAATCACTAATGAT 1444
                           v    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (137 / 109)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.08 (25 / 12)  


2366 29.65 3.27 0.90  chrX_34253565_34258944.rev     4003  4889 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34253565_3   4003 TGGAAAAACTTTCAATGCTCATGGACAGGAAGAATAAATATTGTTAAAAT 4052
                               i iv i v   i       iv      v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34253565_3   4053 TGCCATGCTGTTTAAAGCAACTTACAGATTCTATTCTATTCCT--TAAAA 4100
                         v  v  i  viii   vii ii         v iv v  i   --i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34253565_3   4101 T---AAATTCAT--------GAAACTACAAAAC--ATTTTAAAATTTATA 4137
                          --- iv v v --------    i ivv  i --  ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_34253565_3   4138 TGGAACCTCAAAAGAGCTTGAATACCCAGGGCAATCCTAAGCAAAAGGAA 4187
                              viv   ii  v iv     v   iii     i i iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_34253565_3   4188 CAAAGCTGGAAGTATCATA-TACTTGACCTCAAATTATACCCCAGAGCTA 4236
                              i    i vv   i - v iii ii     viv   iv  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_34253565_3   4237 TAGTAACCAAAACAACATGGTACTGGCACAAAAACAGACACATAGAACAA 4286
                         i     i   i   iii           i  ii i     i     v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_34253565_3   4287 AGGAACAGAATGGAGAGCCCGGAAATAATTCTGCAAACCTACATACATCT 4336
                         v    i     v     i  i       vi iii v ii  iivv  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_34253565_3   4337 GATCTTCCACAAAGCAGACAAAACAAG-CAATGAGGAAGTGACACACTAT 4385
                            i   v    i vv v   i  v v-     i    ivi i vv  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_34253565_3   4386 TCAATAAATGGTGCTGAGATAACTGGCCAGCCATAAGCAGATGACTGAAA 4435
                             i           i  i      vi ?   i v   i v  v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_34253565_3   4436 CTGGACCCCTTACTTACACTATGTACAAATATCAACTCAAGATGGATTAA 4485
                         i         vv  i    i  i      v  i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_34253565_3   4486 AGACTTAAAGG-AAAACTCAAAACTATAAGAACCCTGGAAGACAACCTAG 4534
                             i    v -  i vii          i vi i i     v   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_34253565_3   4535 GCA-ATACCTTTCTGGACTTAGAAACT-GGCAAAGATGTCATAATGAAGA 4582
                          ?i- v i   iv  iv   i i--i -     v i v  v  ivv v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGATATGA 598

  chrX_34253565_3   4583 CGCCAATAGCAATTGCAACAAAGACGAATATTGCCAAAT-GGGCCCTATT 4631
                          i    v    vvv        iivi  v  v vi    -  i iii  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_34253565_3   4632 ATACTAAAGAGCTTCTTCACAGCAAAAGAAACTCTCAA-----TAAGCAG 4676
                          v v v  i i   i vii vv    i  v   v    ----- i iv  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_34253565_3   4677 ACAACCTACAGAAAGCAAGAAAATATCTGCAAACTATGCATCTGGCAAAA 4726
                               i      v vi         i      ii  ii     ii  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_34253565_3   4727 GTCCAATATCCAGCATCTATAAGAAACTTAAACAAATTTACAAGAAAAAA 4776
                          v ivi       v  v     ii    ivv    v ---   v  v   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAAA 795

  chrX_34253565_3   4777 AAAATCAAACAACCCCATT-ACAAATGGGCAAATGACATGAACAGATATT 4825
                           i -    i     v   - v           v  iv    i   i   
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_34253565_3   4826 TTTCAAAAGAAGACA--CAGGTGCAGCCAGCAAGCATATGGAGAAAAGCT 4873
                          i  v        i --  ii  --    ii     i   i i i v   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCT 892

  chrX_34253565_3   4874 CAATATCACAGATCAT 4889
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (158 / 102)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.18 (37 / 17)  


 839 25.64 7.87 11.28  chrX_34311817_34313402.rev      164  1103 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34311817_3    164 TGCAGGGGTATATCATGTTTATGGATTGAAAGAGTCAATGATACAAAGAT 213
                           v ii i   vi      i        i    v i   iv iiv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34311817_3    214 ACCAATTATCCTCAAATTTATTTATAGATTCAATGTATTATTATTATTAT 263
                         iv    vv   i      v  i  i        i i --  ivi   i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA--ATCCCTATCAA 98

  chrX_34311817_3    264 TATTTTTAGAGATGAGGGTCTTACTATGTTGTCCAGACTTGTCTCAAACT 313
                         v  iii---  v  ----i   ---- v   --    ---------  i 
  L1M4_orf2#LINE/     99 AATCCC---AGCTG----CCTT----TTTTG--CAGA---------AATT 126

  chrX_34311817_3    314 CCTGAGCTCAAG-TGATCCTCCAGACTCAGCTTCCCAAGTATCTGGAACT 362
                         ---  ---    -       v- i i   ----------   --    v 
  L1M4_orf2#LINE/    127 ---GA---CAAGCTGATCCTA-AAATTCA----------TAT--GGAAAT 157

  chrX_34311817_3    363 ACAGGAGTATGCCATTACAACCAGCCAGAATTTTTATAAAATTTGATATG 412
                         i  i i - i-   ----i vi     i  i--------   --------
  L1M4_orf2#LINE/    158 GCAAGGG-AC-CCA----GAATAGCCAAAAC--------AAT-------- 185

  chrX_34311817_3    413 CTGTTTCTCCATTGCACTTGAAATAGAACAGGCCAGATACAG--AGAGG- 459
                         ----------------       v    v ------ i v  --i    -
  L1M4_orf2#LINE/    186 ----------------CTTGAAAAAGAAGA------ACAAAGTTGGAGGA 213

  chrX_34311817_3    460 -----------CAATTCTAGAAATATAGTTACGAAAA-ATAGTTATTAAG 497
                         -----------     ii -   iv  -i   i  iv- i   v  i   
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCA-AAACTTA-CTACAAAGCTACAGTAATCAAG 261

  chrX_34311817_3    498 TC-------TTTTGGATACAAAGATAGACTAATAGACCAAAAGAACAGAG 540
                         v ------- vi   -i i  i       vv     i   vi   i   i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGG-CATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_34311817_3    541 TACAGAGATCCAGAA-TGA-CTCTTGTATATACAGCTACTTGATTAATGA 588
                          vv    -       - i - i v ii  v  ii ii v      vvi  
  L1M4_orf2#LINE/    311 TTGAGAG-TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_34311817_3    589 CA--GACAC-AGTACTTGCATAAAA-GTGAAAAAAACGGTACTCTT---- 630
                           -- iii - iv  ---   vv  - v i   i  ii  -  i  ----
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGAC---CATTCAATGGGGAAAGAATAGT-CTTTTCAAC 405

  chrX_34311817_3    631 AAATGGTGCTCAGAAACTTGGTTTTCCTTAAGAAATAAAACCAAATGGAA 680
                                   vi  v vi   v v?  vi v v  v i  iv  i v i 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_34311817_3    681 CCCCTACTTCACATAATAAACAAAAATCAATTCCACATAGATTAGTGCTC 730
                                i     iv   v        i  i  v v  i   i ?v vi 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_34311817_3    731 TAAATGTGAAA--TACAAATTAATAAAACTTTAAAAATGTAATATAG-TG 777
                                i i --  -   i  -       i v i  viv  i    -? 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTA-AAACTA-TAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_34311817_3    778 T----CTTCTAGAATTCTGGA--AAGTAAATATATCTTAAATAAGATG-- 819
                          ----    vv  vi -   i-- i i  vvi v     i   v  ii--
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_34311817_3    820 AAATGGCACTGAATACCCAGA-AACAGATTGATAAGTTTGACAATATAAA 868
                            -i    -i ii v v i -  v i  v     i  v   vvi  v  
  L1M4_orf2#LINE/    603 AAA-AGCAC-AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_34311817_3    869 AATTAAGAACTTTTGGTCATTAAAAGATAT-----AAAAAATGAAAAGAT 913
                               i        vv v i   i  i i----- i   i        i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_34311817_3    914 AAGCCACAGAATAGGAAAATAAACTTGCCA--CATATACAACTGGCAATC 961
                           v         i   i  v v i    v --      i--   ii  vv
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT--CTGATAAGG 748

  chrX_34311817_3    962 AATTTGTAT-----------AAAGAACTCTTACAAATTAATTAGAAAAAG 1000
                         i i      -----------               v i   v v      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_34311817_3   1001 ACAA----CTCAATAGAAAAAAATTGGCGAAAT-TTTGAGCAG----TTA 1041
                             ---- i    v--?      v   i  iv-     ii  ----  v
  L1M4_orf2#LINE/    799 ACAAATAACCCAATT--WAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_34311817_3   1042 ATAAAAGAGGAAAT-CAAGTAGCCAGTGAAAATATATTAAG-TGCTTACC 1089
                         viv     i  v  -   i i    i i iv i  ivv   -    i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_34311817_3   1090 TTATTAGTTTCAAG 1103
                         --  i ????????
  L1M4_orf2#LINE/    897 --ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.06 (56 / 908), avg. gap size = 3.21 (180 / 56)  


2299 28.23 1.88 1.63  chrX_34374166_34379563.rev     3692  4488 (910)    L1M4_orf2#LINE/L1        1   799 (109)  

  chrX_34374166_3   3692 TGGAAAAACATTCCATGCTCATGGATAAGAAGAATCAATAGCATTAACAT 3741
                               i i  i     i        vi     v i    vii    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34374166_3   3742 GGCCATACTGCCCAAAGGAATTTACAGATTTAATGCTATTACTATCAAAC 3791
                            v     v      vvi  i        i  i  v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34374166_3   3792 TATCAA-TGCCATTCTTCACAGAACTAGAAAACCT-ATTTTAAAAATTAT 3839
                          vi  i-    -  i  ii     v v  v  v  -  ii     v i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_34374166_3   3840 ATGGAACTGAAACAGAATCTGAATAGCCATG-CAATCCTAAGCAAAGAGA 3888
                               v  v  vi  vi v         vi-     i i iv  ii   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_34374166_3   3889 ACAA-TCTGAAGGCATCATGCCACCTGACTTCAAACTACACTACAGGGCT 3937
                             -vi  i   vv   ii iv  ii i      vivi      ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_34374166_3   3938 ATAAGTCACCAAAACAGCACGGCAGTGGTACAAAAACAGGCATACA--TC 3985
                          i -  v i   i    iii  i v   i i  ii i  i    i --  
  L1M4_orf2#LINE/    250 ACA-GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_34374166_3   3986 AATGGAAAAAAATAGGTAACCCAGAAGTAAAGCCACACATCTGCAACTAC 4035
                                v i   v iv ii      i    v   i    i iiiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_34374166_3   4036 CTGATCTTCAACAAACCAGCAAAAAAAAAAGCAATGGGGAAAAGATTCCC 4085
                         i    i   i    ivvv  v  i vv v-v           ii  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGTC 397

  chrX_34374166_3   4086 TATTCAATAAATGATGCTGCGATAACTGGCTGGCCATATGCAGAAGATTG 4135
                          v     i     i     v  i      v i?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_34374166_3   4136 AAACTGGACTCCTTCTTTACACCATATACAAAAAATCACCTCAAGATGAA 4185
                           ii     i   v i i                - i v     i   i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGA 496

  chrX_34374166_3   4186 TTAAAGTCTTAAATGTAAAACCCAAAACTATAAAAGCTCT-GGAAGACAA 4234
                          i ?  v i         i v i            -    -i     v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_34374166_3   4235 CCTAGGGA-ATACCATTCTGGACATAGAAACTGGCAAAGATTTC------ 4277
                          v    ?i- v i -   vv   v v iiviv     v i    ------
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_34374166_3   4278 ATGACAAAGTCTCCAAAAGCAATTGCAACAAAAGCAAAAGTTGACAAATG 4327
                               ------         vvv          v    i v  i    v
  L1M4_orf2#LINE/    595 ATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_34374166_3   4328 GTATCTAATTAAG-TGAAACAGCTTCTGTATGGCAAAAGAAAGTATCAAC 4376
                          v ii v  i  i- v   - i   i   iivv    i  v v      v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_34374166_3   4377 CAAGCAAACAGACAATATACAGAATGGGAGAAAATATTTGCAAACTATGC 4426
                         v   ii  v      ivi                          ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_34374166_3   4427 ATCTGGCAAAGGCCTAGTATTCAGCATCTTTAAGTAACTTAAACAAATTT 4476
                              ii  i  v  v    i   v  v v   iv    ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_34374166_3   4477 ACAAGAAAAAAA 4488
                          i  v     i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGA 799

Transitions / transversions = 1.39 (129 / 93)
Gap_init rate = 0.02 (17 / 799), avg. gap size = 1.65 (28 / 17)  

 291 15.71 2.86 2.86  chrX_34374166_34379563.rev     4839  4908 (490)    L1M4_orf2#LINE/L1      839   908 (0)  

  chrX_34374166_3   4839 GACGCTTTTTAAAAGAAGACATA--AATGCAGCCAACAAACACATGAAAA 4886
                            ii  i iv        i   --    --     i  i          
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAA 886

  chrX_34374166_3   4887 GAAGCTCAATATCCCTGATCTT 4908
                           v      i   v????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.03 (2 / 70), avg. gap size = 2.00 (4 / 2)  


1510 28.94 7.58 1.06  chrX_34380593_34382239      500  1159 (488)    L1M4_orf2#LINE/L1      206   908 (0)  

  chrX_34380593_3    500 TTAAAGGCTTTACACTACCTAATTTCTAT-CTTTCTATAATGCTACAGTA 548
                           ii   vi i     v  i      v v-   v   i  v         
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_34380593_3    549 ATTGAGATGTTGTGGTATT---ATAAATGGATATACAAATAGCTCAAAAA 595
                           ii   iiv       i ---    --     v   v    v    vii
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAA--GGATAGACATATAGATCAATGG 303

  chrX_34380593_3    596 AACAGAATATAGCATCCAGAAAAAGACTCACATA--------CAATCAAT 637
                           i     vv  vi        v i  i  i i --------    ii  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_34380593_3    638 TTTTAAGAAAGAGCTTAATGCCATTCAAAGAAGAAGT--TAAT---TTGA 682
                            ii v  i ivvii  vi        v ii   iv--  i ---  v 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_34380593_3    683 ACAAATAGGGCTGGAGCAACTTAATAA--ATATAGGGAAAAACTAACCTT 730
                               i v     ii     vi   ?-- i  ivii  i  iv  vi v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_34380593_3    731 GTCCCCT-TTTTAC-CCAGTGCACAAATATTAATTTGAGATGGATTA-AG 777
                          v     -ii i  -   - ii     v     i ii i      i -  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCA-TATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_34380593_3    778 ACCTTAATATAAAAGCTAAAACTGCAAAAGTTTTTAGAAGAAAACATTAC 827
                             v   i   i          ii    -i i              viv
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGG 551

  chrX_34380593_3    828 AGAATATTTTGGGGAACACAGAGTCTGCACAGATTTCTTAGA-GTGGTCA 876
                         ? v v  i  v v  v vii iv vv   vv i         -i  i-  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-CA 600

  chrX_34380593_3    877 CCACAAAAATATATTCAGCATAAAGAAAAAT-GATAAATTGGACTTCATC 925
                            --   ii i vv  i  v  ii      -                  
  L1M4_orf2#LINE/    601 CCA--AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_34380593_3    926 AAAAT-AAAAG--TCTGCTTTTCAGTAATCATCCTTATGAAAATAAAAAT 972
                              -    i-- i  ivi    iviiv  iiv i v    i i    v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_34380593_3    973 GCTAACCACAGAGGGAGTGAAAATTTTAGCAACACACATGTCTG-CAAAG 1021
                         i v v       iv i v      v  v    vv  i  i    -i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_34380593_3   1022 AACTTGTGTCTAGAATATATAAATATCTCTCA------------AAAATG 1059
                         i      i  i            v v    i ------------    v 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_34380593_3   1060 ACTAATAA---------AAAATGGACAAAATACTTGGACAAATACTATAT 1100
                           v     ---------       i    iv i   i i i i i vivi
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_34380593_3   1101 AAAAGAAGATTTGTAAATAGCCAATCAGTGTATGTAAAGATTCGCA-TGT 1149
                         v         v ii    i      v  iii   v      v v  -ii 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_34380593_3   1150 TATTAGTTAT 1159
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.55 (115 / 74)
Gap_init rate = 0.03 (22 / 703), avg. gap size = 2.59 (57 / 22)  


2771 25.22 2.42 2.42  chrX_34600030_34602997     1568  2475 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34600030_3   1568 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 1617
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34600030_3   1618 GACCATACTGCCAAAAGCAATCTATACATTTGATGCAATTCCCATCAAAA 1667
                          i v     v  v   vii     i v   ii i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34600030_3   1668 TATCATCATTATTCTTCCTAGAACTAGAAAAAAACATTCCTAACATTCAT 1717
                          vi  v vviv  i  ivi    v v  v  ivvv  -     v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chrX_34600030_3   1718 ATGTTACCAAAA---AAGAGACT--GCATAGCCAAAGTAAGACTAAGCAA 1762
                            -----i   ---   i   i-- v         ii  vvi i iv  
  L1M4_orf2#LINE/    150 ATG-----GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_34600030_3   1763 GAAGAACAAATCTGGAGGCTTCACATTACCTGACTTCAAACTACATTAGA 1812
                                   vi      vi     i v  ii i      vivi i  v 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_34600030_3   1813 AGGCTATAGTTACCAAAACAGCATGGTACTTGTATAAAAGCAGGGACATA 1862
                          i    i   v i   i    ii       v i    iiii  iv i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_34600030_3   1863 GACCAATGGAATA---TT-ATAG---AGAAATAAAGCCAAGTAC-TTAAC 1904
                           i          ---  - v  ---         v   --   -  v i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTAT 342

  chrX_34600030_3   1905 AGCCAACTGATCTTCGACAAAGCAAACAAAAATATGAAGTGGGGAAAGGA 1954
                         i i   i    i        i vviv   i vi  vv i         i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_34600030_3   1955 CTCCCTATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGCAGAA 2004
                         ivvi  v                    i  i   vv ?         i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_34600030_3   2005 GAATGAAACTAGATCCTCACCTCTCACCTTGTACAAAAATCAACTCAGGA 2054
                                ii i  i  ii     v    v i         i      ii 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_34600030_3   2055 TGGATGAAAGACTTAAATCTAAGACCTGAAACCATAAA--TTCTAGAAGA 2102
                              v ?    i     v     v  i    i     -- ii       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_34600030_3   2103 TAACAGTGGAAAAAGCGTTCTAGACATTGCCTTAGGCAAAGAATTCAT-G 2151
                         v    vv  ?iv  iiv   vv   v   vv        v iv   v - 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_34600030_3   2152 ACCAATAAC-CCAGAAGCAAATGCAACAAAAATAAAAGTAAATAGATGAG 2200
                          i--  i  -   i     v v         iv    i  i   i  vi 
  L1M4_orf2#LINE/    593 AT--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_34600030_3   2201 ACCTAATGAAACTTAAAAGCTTCTGCACAGCAAAAGAAATAATTAGCAAA 2250
                           i v  v   v      i   i  ii vv    i  v iv  i iv   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_34600030_3   2251 GTAAACAGATAACCCACAAAGTGGGAGAAAATATTCTCAAATAATCATCG 2300
                           i  v   i        i i              iv     ---   --
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT---CAT-- 735

  chrX_34600030_3   2301 CAAATATGCATCTGACAAAGGACTAATAGTCAGAATTTATAAGGAAATCA 2350
                         ---    ----    i  i     vi  vi      v     i   v  v
  L1M4_orf2#LINE/    736 ---ATAT----CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_34600030_3   2351 -AAAAATCAGCAAGAAAAAAACAA-T--CTCAGC-AAAAAGTGGGCTAAG 2395
                         - v  v   ii  v     i    - -- i  ii-?    i     v   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_34600030_3   2396 GACATGAACAGACAATTCTCAAAAGAAGATATGCAAACCACCAACAAAGA 2445
                           iv    i     v     v           i    ivi    i  iv 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_34600030_3   2446 TATGAAAAAAGGCTCAACATCATTAATTAT 2475
                         i       i v           ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (128 / 97)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.20 (44 / 20)  


 344 30.41 12.60 2.74  chrX_34607736_34610212       49   413 (2064)    L1M4_orf2#LINE/L1      374   774 (134)  

  chrX_34607736_3     49 CTATT-AGTGGGCAAAGAAAGAGCTATTCAA----TGGTGGTGTGACAAT 93
                          i   - i    v      viiv  v     ----     v  v     i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_34607736_3     94 TTGGCCATCCACTTATAAAACAAATGCTAATTA----TCTACCTCACTTT 139
                          -  vi ?    v ii    -i    v- i  i----i         vii
  L1M4_orf2#LINE/    424 T-GGATAKCCACATGCAAAA-GAATGA-AGTTGGACCCCTACCTCACACC 470

  chrX_34607736_3    140 ATATACAAGAGTATATTTAGG-TAGATTTTAGGCTTAAATA----AATTT 184
                                 i i vv i i ii- i   iv?  i i     i---- ii v
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_34607736_3    185 TTATTATGA-----TTAGATGAAAATACAGGAGAATGTTTTCACCATCTG 229
                         vv i   i -----     v     i i   ? v vi i   iiv i  -
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT- 569

  chrX_34607736_3    230 TAGATT---CAAT------TTAAGT--GATACTCCAAATCTCAAA-GACG 267
                          i i  ---    ------   ii --  i  - v   v v   i-i  i
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACAC-CAAAAGCACAAGCAACA 618

  chrX_34607736_3    268 TAAAGAAAACAAAAAAATAAATTTGACAATATAAAAAGGAACTATTTTTG 317
                         -        --  v i       v   vvi  v    vv  vv i     
  L1M4_orf2#LINE/    619 -AAAGAAAA--AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_34607736_3    318 T-CTGATGAAAACAAAC-ACCAAG----TTAATA-ATTACTTCTAAAGTG 360
                          -  -- v   iv v  - i    ---- v  v - iv  iivi i i  
  L1M4_orf2#LINE/    666 TGCT--TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_34607736_3    361 GAAGAAAATAACTGCAA----CACATTTGGCAAAGGA----TAGTCATAA 402
                          i        vi     ----i i  i  ii  i   ----  vi  v  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_34607736_3    403 TATATTGAGAA 413
                              vi    
  L1M4_orf2#LINE/    764 TATATAAAGAA 774

Transitions / transversions = 1.51 (65 / 43)
Gap_init rate = 0.06 (24 / 401), avg. gap size = 2.33 (56 / 24)  

3163 25.25 2.12 0.89  chrX_34607736_34610212     1090  1984 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_34607736_3   1090 GAAAAACATCCCATGATCATGGATCAGAAGAACAAATATCATTAGAATGA 1139
                             i i        v        ii     viv     ii   ii   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_34607736_3   1140 CCATACCACCCAAAGCAATCTACAGATTCAATGCAATCTCTATCAGAATA 1189
                          v    iv      vii              i      i      i   v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_34607736_3   1190 TCAAAGTCATTTTTCAGAGAAATGGAAAAAATAACCTGAAAATT---ATG 1236
                         i  ivvv v     iiv      v  v  iv i i iv      ---   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_34607736_3   1237 AAACCAAAAAAGAGCCCAAATAGCAAAAGTAATCCTAAGCAAAAAGAACA 1286
                         i  viiv  ii  v  vi      v   ii    i i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_34607736_3   1287 AAGTTGGAGGCAGCACATTACCTGACTTCAAAGTATATTACAAGACTATA 1336
                                   vvv    i v  ii i      iiv  i     ii   i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_34607736_3   1337 GTAACCAAAGCAGCATGGTAGTGGTATAAAAGTAGACACATAGATCAATG 1386
                             i   ii   ii     v   i    iii      i           
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_34607736_3   1387 GAACAGAATAAAAAACCCAGAAATAAAGCCATATATTTATAGCTAACTGA 1436
                            i     vi i ii           v     i      i ii  i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_34607736_3   1437 TCTTTAACATAGCTGACAAGAACATACATTGAGAAAAGGACTTTTTTTTT 1486
                          i  ii   vi v  v     v   v  v  i i    i - vv i    
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTTTT 401

  chrX_34607736_3   1487 CAATAAATTGTGCTGGGAAAATCAGATTACCATATGCAGAAGAATGAAAC 1536
                            i    v         v  iii   v?   i     i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_34607736_3   1537 TGGACCCCTATCTTACACCATATAGAAAAATCAGCTCAAGATGGTTTAAA 1586
                                   i  i          v      i i     i    v i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_34607736_3   1587 GACTTAAATGTAAGACTCAAAACTATAAAAATCCTGTAAGAAGAC----- 1631
                            i           vii            v  i iv     i  -----
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_34607736_3   1632 ------TCTTCCGGACATTGATCTAGGCAAATAACTTATTACAAA-GACC 1674
                         ------     vv   v   ivi       - iii  v   v v -   v
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACA 600

  chrX_34607736_3   1675 TCAAATACACAAGCAACATAAACAAAAATAGACAAATGGGTCTTAATTAA 1724
                         i    vi           v  iv         i    v  v   v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_34607736_3   1725 ACTAAAAAGCTTCTCCATAGCAAAAATAAAC-ATCAACAGACAGAACAGA 1773
                          v v    i   i viiivv    ii- v  -     v i vv   v   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGG-ACACTATCAAGAAAGTGAAAAGA 699

  chrX_34607736_3   1774 CAACCTGCAGA--GGGGAAAAATATGTGCAAATCAAACTATTTACCCAAC 1821
                              ii    --   ii       v         ---   -- i ii i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCA---TAT--ATCTGAT 744

  chrX_34607736_3   1822 AGAGGACA-ATATCCAGAATATAAAAGGAACTCTAACACCTCAACAACAA 1870
                          ii    v-i             v  i       v   v     i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_34607736_3   1871 CAACAACAACAACCTCATTAAAAACTGGGCAAAGGACATGAATAGACATT 1920
                         v  v vv  i    iv   ?    v           iv            
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_34607736_3   1921 TTTCAAAAGAAGACATACAAATGGCCAACAGATATATGAAAAAGTGCTCA 1970
                          i  v        i              i iii i       ii      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_34607736_3   1971 ATATTACTAATCAT 1984
                          i  i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (140 / 83)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 2.45 (27 / 11)  


 830 23.11 1.14 7.20  chrX_34612399_34614590.rev      509   772 (1420)    L1M4_orf2#LINE/L1      286   533 (375)  

  chrX_34612399_3    509 AAACACATAGTCCAATGGAAAAGAATAGAAAACTTATTGTATTAACAATT 558
                          i   i    vi        v     v  i -------  --------ii
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGA-------GT--------CC 320

  chrX_34612399_3    559 ATAATTATAAATTAACACCTTTACAACCAATTAATTTTCAACAAAGGTGC 608
                          v  --     iiv i  v    iiii     i      i    i     
  L1M4_orf2#LINE/    321 AGAA--ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_34612399_3    609 CAAGAACCCA--CATTGGGAAGAGGATAGTCTAGTCAAATCATGATTTTA 656
                              --   --  v    i i  i       vv    vvv   i vi i
  L1M4_orf2#LINE/    369 CAAGA--CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_34612399_3    657 GGAAAATTGGATATCCATATGCAGAAGAATGAAATTAGATCCTTATTTTT 706
                            v  i      ?   i     i         i  i  i  i  ii iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_34612399_3    707 CACCACTTACAAAAATCAACTCAAAATGGATAGGAGACTTACATTTAAGA 756
                              iv         i              vi?    i  v  v     
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_34612399_3    757 CCCAAA-CAATGAAACT 772
                         v i   - v  i     
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACT 533

Transitions / transversions = 1.81 (38 / 21)
Gap_init rate = 0.02 (6 / 248), avg. gap size = 3.67 (22 / 6)  

1156 22.09 9.01 0.87  chrX_34612399_34614590.rev     1358  1701 (491)    L1M4_orf2#LINE/L1      537   908 (0)  

  chrX_34612399_3   1358 AAAAAAACACATAGAAGAAACGCTTCATGATATTGGTCTGGGCAAGGAAT 1407
                          i  i  v      i? v  vv    i   iv    vi i     v -i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GT 585

  chrX_34612399_3   1408 TTTTTGGATACTACCAAAAAAGCACAAACACCAAAAGCAAGAATAGACAA 1457
                           i  i    iv  vvv          i  v      v  i      i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_34612399_3   1458 GTGGAACTATGTCAAAGTAGAAGGCTTCTGCACAGCAAAGTAAACAATTA 1507
                         i v i   vii     i vi  ii   i  ii vv     v v  v  i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_34612399_3   1508 ACAGAGTGAAGAGACAACCCACAGAGTGGGAGAAAAATATTTAAAAACTA 1557
                          v i      i              i      -         iv   ii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAG-AAAATATTTGCAAATCA 734

  chrX_34612399_3   1558 TACATCTGACAAGGGGGTAATATCCAGAATATATAAGAAACTC--A-AAC 1604
                           i      i     iv vi                ii     -- -   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_34612399_3   1605 TCAATAGCAAAAAGA--------------------------AAGG-TCTG 1627
                               ii       --------------------------    - i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_34612399_3   1628 AGTAGACATTTCTCAAAAGAAGACATGCAAATGGCCAACAAGTCTATGAA 1677
                          i            v        i  i           i   ivi     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_34612399_3   1678 AAAAATGCT-AACATCACTAATCGT 1701
                           i -    -       ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (48 / 27)
Gap_init rate = 0.02 (8 / 372), avg. gap size = 4.25 (34 / 8)  


 497 26.83 0.00 0.00  chrX_34622896_34624631.rev       16   138 (1598)  C L1M4_orf2#LINE/L1   (785)   123     1  

C chrX_34622896_3    138 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAACATTGTGAAAAT 89
                               i i  i    vi        v      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_34622896_3     88 GGCCATACTGCCTAAAGTAATTTATAGATTCAAGGCTATTCCCAGCAAAC 39
                            v     v  i   v i  i  i        v  v  i  i v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_34622896_3     38 TACCATTGACATTCTTCACAGAA 16
                          v   vivi v  i  ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA 123

Transitions / transversions = 1.20 (18 / 15)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.00 (0 / 0)  

2501 25.70 1.74 1.61  chrX_34622896_34624631.rev      499  1245 (491)    L1M4_orf2#LINE/L1      161   908 (0)  

  chrX_34622896_3    499 AGGGACCCTGTATAGTCAAGACAATCCTAAGCAAAAAGGACAAAGCTGGA 548
                                 v v    i   i      i i iv  i   i      i    
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_34622896_3    549 GGCATCACGCTACTTGACTTCAAATTATACTACAAGACTATAGTAAGCAA 598
                           vv    i  v iii i      viv        ii   i     v   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_34622896_3    599 AACAGAATGGTATGGGTACTGAAACAGACATATAGACCAATGGAGCAGAA 648
                         i    vi     iv  i iviii i           i       ii    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_34622896_3    649 CAGATATCTCAGAAA--AACACCACACATCTACAGCCTCCTGAGCTTTGA 696
                         iv  v vii      --   -   i    i  ii i vvi   vi  i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAAC-CCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_34622896_3    697 CAAACCTGCCAAAAGTAAGCAATAGGGAAAGGATCTCCTATTCAGTAAAT 746
                            ivv      i vi vv    i       i  vvi  v    ii    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_34622896_3    747 GTTGCTGGGAAAACTGCCTAACCAAATGCAGAAAACCCTGAAACTGGGCC 796
                          v        v     vv  ?   v     i  i v--    ii   i  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--TGAAGTTGGACC 457

  chrX_34622896_3    797 CCTTCCTTACACCTTATGCAAAAATTAACTCAAGATGAATTAAAGACTCA 846
                            v   i     v   i               i   i  i ?    ii 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_34622896_3    847 AATGTAAAACCCAAACCAATAAAAACCCTAGAAGAAAACCTAGGCA-ATA 895
                                i v i   v v      vi i           v    ?i- v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_34622896_3    896 CCATTCAGGACCT---ATCACGGACAAAGACTTC------ATGACAAAAA 936
                         i -   iv     ---i i -- i   v ii   ------      ----
  L1M4_orf2#LINE/    558 TC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATATGACA---- 600

  chrX_34622896_3    937 TGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATTGAATCTAATT 986
                         --         vvv          vv     v  i      i ii v  i
  L1M4_orf2#LINE/    601 --CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_34622896_3    987 AAA-CTAAAGAGCTCTGCACAGCAAAAGAAACTATTATCAGAGTGAACAG 1035
                            -i    i vi i  ii vv    i  v     i vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_34622896_3   1036 GCAACCTACAGAGTGGGAGAAAATGTTTGCAATCTACCCATCTGACAAAG 1085
                         i     i     i           i       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_34622896_3   1086 GTCTAATATCCAGAATCTAAAACAAAGTTAAACAAATTTACAAGATAAAA 1135
                          v  vi          v  v  vi  v ivv    v iv i  v v   i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_34622896_3   1136 ACAAACAATCCCATTAAAAAGTGGGCAAAGGATATGAACAGACATTTCTC 1185
                              i  i  v   ?    i            v    i           
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_34622896_3   1186 AAAAGAAGACATTTATGTGGCCAATAAACATATGAAAAAAAGCTCAACAT 1235
                         v        i  vi vi          i  i       i v         
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_34622896_3   1236 CACTGATCAT 1245
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (112 / 76)
Gap_init rate = 0.01 (10 / 748), avg. gap size = 2.50 (25 / 10)  


2902 27.19 2.92 0.90  chrX_34644730_34650231     4133  5022 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34644730_3   4133 TGGAAAAACATTCTATTCTCATGGGTAGGAAGAATCAATATCATTAAAAT 4182
                               i i  i i  vi      i v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34644730_3   4183 GGTCATACTGCCTAAAGCAATTTACAGATCCAATGCAATTCCTACCAAAC 4232
                           iv     v  i   vii  i       i   i     i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34644730_3   4233 TACCAAGCGACATTCTCCACAGAACTAAACAAACCTACTTTAAATTTGAT 4282
                          v   -  vi v  i iii     v vi    i iv iii    v  v  
  L1M4_orf2#LINE/    101 TCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_34644730_3   4283 ATGGA---GCCAAAAAAGCCCA-AATAGCCAAGGCAATCCTAAGCAAAAA 4328
                              ---  --  iiii    -         ii     i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_34644730_3   4329 GACCAAA-CTGGAGGCATCACACTATGCAACTTCAAACTATACTACAAGG 4377
                           v    -i      vv       viv   i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_34644730_3   4378 CTACAGTAACCAAAACAGCATGGCACTGGTACAAAAACAGGCATATAGAC 4427
                                  i   i    ii   i     i i  ii i  i        i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_34644730_3   4428 CAATGGAATGGAATAGACAGCCCAGAAATAATGTGACACATCTACACCCA 4477
                                  i    v  v  i          vviv i    i  iivi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_34644730_3   4478 TCTGATCTTTGACAAAGCTGACAAAAACAAACAATGTGGAAAGGACACTT 4527
                         vi    i  i     i v  v   i v  vv     v      i i v i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_34644730_3   4528 TATTCAATAAATTGTGCTGGGATAACTGGCTGGCCATAGGCACAAGATTG 4577
                          v     i    v         i      v i?   i v   v    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_34644730_3   4578 AAACTGGACTCCTTCCTTACACTATATACAAAAATAAACTCAAGATGAAT 4627
                           ii     i   v   i    i            v       i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_34644730_3   4628 TAAAGACTTAAATGTAAAAACC----------------TGGAGGACAATG 4661
                         i ?    i         i i i---------------- i  i  v  ii
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_34644730_3   4662 TAGGCAGTAACATTCTGGACATAGGAACTGGCAAAAATTTCAT-GATAAA 4710
                             ?ivv  iv   vv   v v  iviv     vii    v -    v-
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT- 596

  chrX_34644730_3   4711 GATGTTAAAA--ACAATTACAACCAAAGCAAAAATTGACAAATGGGATCT 4758
                           iiii    --    --i    v    v      v  i    v   ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_34644730_3   4759 AATTAAACTTAAAAGCTTCTGCACACCAAAAGAAACTATCAACTGAGTGA 4808
                         v  i   v      i   i  ii vi    i  v        vvi     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_34644730_3   4809 ATAAATAACCTACAGAATGGGAGAAGATATTTGCAAACTGTTTACCCAAC 4858
                          v i i    i              i           iii v  i ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_34644730_3   4859 AAGG--TTAATATCCAGAATTTATAAGGAACTTTAACAAATTTACAAGAA 4906
                             --i vi          v     i     i v    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_34644730_3   4907 AAAAACCAAACAACTTCATTAAAAAGTGGGCAAAGAACATGAAGAGACAC 4956
                            i  -   i   iiv   ?    i         i iv    v     i
  L1M4_orf2#LINE/    795 AAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_34644730_3   4957 TTTTCAAAAGAAGACACACATGCAGCCAAACATAATGTGAAAAAAAAGAT 5006
                           i  v        i i   viii     vv vv ii      i v- v 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCT 892

  chrX_34644730_3   5007 CCATATCACTGATCAT 5022
                          v i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (150 / 88)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.62 (34 / 13)  


2971 22.76 3.36 1.62  chrX_34681763_34683556      503  1306 (488)    L1M4_orf2#LINE/L1       91   908 (0)  

  chrX_34681763_3    503 CCTATCAAAATACCAATGATGC--TCTTCACAGAAAGAGAAAAAA-AATC 549
                                    v   -- v   -- i  ii      vv  v  iv-i   
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chrX_34681763_3    550 CTAAAATTCATATGGAACCACAATAGACCCAGAATAGCCAAATAAGTATT 599
                                          vii   vi                 vv i v  
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chrX_34681763_3    600 GAGCAAAAAGAACAAAGCTAAAGGCATCAATCACATTACCTGACTTCAAA 649
                           iv  i          i ii   ---- v     i v  ii i      
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGG----ACTCACACTTCCCAATTTCAAA 234

  chrX_34681763_3    650 TTATACTG------TATAGTAACCAAAACAGCATGATACTGGCATTAAAA 693
                         viv    i------  i     i   i    ii  i         ---- 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT----A 280

  chrX_34681763_3    694 AAAACA-ACACATAGACCAATGGAACAGAATAGAAAGCCCAAAAATAAAT 742
                          ii i -   i     i        i     v  i  i   i       i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_34681763_3    743 CTACTTATTTATAGTCAATTCTTTTTTGACAAAGTCACCAAGAACATACA 792
                          i ivi      i       vv    i     i vii      v   v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_34681763_3    793 TTGGGGAAAGGACAGTTTCTTTAATCAATGGTGCTGGAGAAACTGGTTAT 842
                         v         i i   i i  i  iv           iiv      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_34681763_3    843 CCATATGCAGAAGAATAAAAGTAGACCCTTATCTCTCACCATATATACAG 892
                            i     i      i  iv i     i  i   v         i v i
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_34681763_3    893 ATCTAA-TCAAAATGGATTA-------AAAT-----ACCTGAAACTATGA 929
                           -   -           i -------    ----- v  i       i 
  L1M4_orf2#LINE/    481 AT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_34681763_3    930 AATTACTGGAAGAAAACATTGGAG-AAATGCTTCCAGACATTGACCTGGG 978
                           i vi i           v  ? -    -    vv   v   ivi i  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGG 578

  chrX_34681763_3    979 CAAAGATTTCTTTAGTAAGAACTCAAAAGCACA-GTAACCAGAGCAAAAA 1027
                            v i      vii  v  vvi          - i   v i  v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_34681763_3   1028 CTTAAAGATGGGATTACATCAAGCTAAAAAGCTTCTGCACAGCAAAGGAA 1077
                         ivv v i  v   i v      iv v    i   i  ii vv       v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_34681763_3   1078 GCAATCAACTAAGTGAAA-GACAACCTACAGAATGATCGAAAATATTTGC 1126
                         i v     vv        -       i        ivv            
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_34681763_3   1127 GTACTATGCATCTGACAAGGGGTTTGTATTTAGAATATATGAGGAACTCA 1176
                         iv ii  ii      i     ii      ii         i i      v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_34681763_3   1177 AACAACTCAATAGCAAAACCCCCAAATAATCCAAT-GAAAAATGGGCAAA 1225
                         v           ii    vvv -      i     -?             
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_34681763_3   1226 AGATATGAATAGACATTTCTCAAAAGATGACATACAAATGGCCAACAAGT 1275
                         i   v                v     v  i              i   i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_34681763_3   1276 ATATGAAAAAATGCTCAATGTTGCTAATCAT 1306
                          i       i        ii ii????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (112 / 68)
Gap_init rate = 0.02 (17 / 818), avg. gap size = 2.35 (40 / 17)  


3149 26.16 1.11 0.44  chrX_34687076_34690371.rev     1904  2805 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34687076_3   1904 TGGAATGTCGTTCCTTGTTCATAGATTGCAAGAATCAATACTGTTAATAT 1953
                              v vii i  v       i     v    v i    i      v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34687076_3   1954 GTATATGCTACCCAAAGCAATCTACAGAGACCATGCAATCCCTATGAAAA 2003
                          vvv  i  v      vii         vv v i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34687076_3   2004 TACCTATGATATTCTTCACAAAAGTAGAAAAAACAATTCTAAAATATATA 2053
                          v  viiviiv  i  ii  i  i v  v  ivii  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_34687076_3   2054 TGGAACCATAAGAGACCCAGAATAGCCAAAGCTATCCTAAGCAACAAGAA 2103
                              viii   i                 i v   i i iv  v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_34687076_3   2104 TGAAACTGGAAGAATCACATTACCTAACTTTAAATTATACTACATTGTTA 2153
                         ii  ii    i  v     i v  i  i  i   viv       vv i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_34687076_3   2154 TAGTAACCCAGACAGCATGGTATTGGCATAAAAACAGACACATAGACCAA 2203
                         i     i v      ii     i        ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_34687076_3   2204 TGAAATAGAATAGAGAACCCAGAAACAA-TGCATAAATTTACAGGGAACT 2252
                           i        v    ii       i  -iv    v     ii vv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_34687076_3   2253 AATTTTTTGACAGAGATGCTAAGAACATATATTGGGGAAA--AGAGTGTC 2300
                         i     -i    ii i   i    v   vi v        -- v   v i
  L1M4_orf2#LINE/    351 GATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_34687076_3   2301 TTCAATAAATGGTGCTAGGAAAACTGGTTATCCATATGCAAAGGAATGAA 2350
                              i          i   v      v  ?   i       i       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_34687076_3   2351 ACTAGACACCTATCTCTCATCATATACAAACATCAAATCAAAATGGACTA 2400
                         ii i   v    i   v  i          v  i  v          ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_34687076_3   2401 AAATCTTAAATCTAAGACTTCAAACTATGAAACTACTACAAGAAAACATT 2450
                         ? iv i     v     vi v       i     vi  v          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_34687076_3   2451 GATGAAAATCTCCAAGACATAGATCTGGGCAAAAATTTCTTGAGCTGT-A 2499
                          i? v      i iv   v v ivi i     vii      -  v i - 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chrX_34687076_3   2500 CCCGACAAGCACAGACAACCATCTCAAAAATGGACAAATGGGATTACA-- 2547
                          v v v       ii    v vvvv      i  i    v   i v  --
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_34687076_3   2548 --AGTTAAAAAGCTTCTGACCAGCAAAGGAAACAGTAAACAAAGAGAAGA 2595
                         -- i       -   i  vv vv       v  vi v  v    v   i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_34687076_3   2596 GATAACCCACAGAATGGGAGAAAATATTGGCAAGCTATCCATCTGATCAG 2645
                           i                         v    iii  vi       v  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_34687076_3   2646 CGATTAATAACCAGAATACATAAGGAGCTCAAACAACCCTATAGAGAAAA 2695
                         v  i vi  v        i    i  i   vv     i v   ivi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_34687076_3   2696 AATATAATAATCCGG-TAAAAAATGGGCAAAAT-TTTGAATAGAGATTTC 2743
                         i i -     i  ii- ?             iv-          v     
  L1M4_orf2#LINE/    798 GACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_34687076_3   2744 TCAATAAAAGACATAGAAATGACAAAGAGGTATATGAAAAGGTGCTCACG 2793
                           v v i    i   v     i v  v i i i        i      vv
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_34687076_3   2794 ATCATTGATCAT 2805
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (130 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


1886 25.33 11.28 2.28  chrX_34718104_34720901     1473  2305 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34718104_3   1473 TGGAAAGATGACCT-TCCTCAGTGG-TCAGAACATTTCATATTGGTAATA 1520
                                  iv  i- vi   -   - ii   v i  v      v   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCA-TGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_34718104_3   1521 TGCCAATTATCCTCAAATTGATCTATAGATTCAACAGAATCCTAATCAAA 1570
                           v    vv   i            i         iv     iv      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_34718104_3   1571 ATCCAAACAGGACTTTTTCTA-AGACATAGACAAGCAGATTTTAAAATTT 1619
                             v i v -- i    i i-   v  v       v   ii       i
  L1M4_orf2#LINE/    100 ATCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_34718104_3   1620 CTATAGAAATTCAAAGGACCTAGAAGAACCAA-----CTTTGTAAAAGAA 1664
                         v   i     v   i     i    v i    -----ii   v       
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_34718104_3   1665 ---CATTGTTAAAGAATTAGTACAGCCTAATTTCTAGATTTATTATAAAG 1711
                         ---  vv   ii  i i vii  vv  i      v i i   i  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_34718104_3   1712 CTAGAGTAACCAAGATAGTGTGAAATTTGTGTGAG---AGA-A---AAAT 1754
                            v     i     i      iv i v ii i  ---   - --- i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_34718104_3   1755 CAATGGAAGAGAAAACAGTGCCCAGAAATTGACC--TTCAA--ATAGACA 1800
                                 v    vvv  v i        vi   -- v  v--  i v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_34718104_3   1801 ACTGATACTCTACCAATTTCCGAATGTAATTCAGTGGAGAAAAGATTGTC 1850
                          i    vi  v  v ivv v v  viiv     i   i    ii  v   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_34718104_3   1851 TTTATAA-AAATAGTTCTGAAATTATCAGATATGCGTAAGCAATAG---- 1895
                            vi  -    i  v   ii iv iii    ?v ii v    v  ----
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_34718104_3   1896 --GT---ACATTT---TTAAA------ATAAAAACT---------TTGAT 1922
                         --  ---  vii --- i v ------ i     i --------- v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_34718104_3   1923 C-TATATCT---TGT----GCTGTTTACAAAAATTATAGCATT--TAAAT 1962
                          -? v i  ---   ----   -------    i    iv i --  i v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCT-------AAAACTATAAAACTCTTAGAA 540

  chrX_34718104_3   1963 GAAAA---------AAATCTTTGTGACCTTTGGATAGGCAA-AGTTTTTC 2002
                              ---------       i        v  v       -i    i -
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT- 589

  chrX_34718104_3   2003 ATAGATA---CATCAAAAGAAGCACAATCCGTAAAAGAACAAATTGATAA 2049
                         -      ---  i      ---     v vii       v    v     
  L1M4_orf2#LINE/    590 -TAGATATGACACCAAAAG---CACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_34718104_3   2050 ATTGGACTTCATCAAATTAAAAAACTTCT---CTTT----GACAC----- 2087
                                         v v        i ---   i----     -----
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_34718104_3   2088 AGACAATGAAAGAGCAAAGCCA-AGGATGAAGTGAAAA-ATTTGCAAATC 2135
                            v i     iii   v-   -  i   i- v     -           
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAAC-CCACAGAATGG-GAGAAAATATTTGCAAATC 733

  chrX_34718104_3   2136 ATGCATCTGATAACCTATTTACATCTAGAACACAGCAAGGATTCTCAAAA 2185
                           ii         vvv i  ii   i    i i vv   i i   i v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_34718104_3   2186 CTAAATATGATAT-----CCAGCAACACAATTTAAAAATGGGGGGAAAAT 2230
                           v    --   v----- v ii   v     ?         vii ii  
  L1M4_orf2#LINE/    784 CTCAATA--ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_34718104_3   2231 CC--ACAGAAACTTCAACCAAGGGGAGATAAGGATGGCAAATAAGCAAAT 2278
                         ii-- i   v i   vv v   ii  v   vii     v        v  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_34718104_3   2279 ATAGAGATGTTCAATATCAGTAGTCAT 2305
                         iv i     i    i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (117 / 91)
Gap_init rate = 0.04 (38 / 908), avg. gap size = 2.97 (113 / 38)  


2478 25.48 1.12 8.56  chrX_34726901_34730953     2580  3560 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34726901_3   2580 TGGAAAAACATTCCATGCTCATGAAAAGGAGGAATCAATATTGTTAAAAT 2629
                               i i  i     i     i vv   i  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34726901_3   2630 CGCCATACTGCCAATATACAGATTTAATGCCATTCCTATCAAATCGCCAT 2679
                         v  v     v  ---------------------------     i ----
  L1M4_orf2#LINE/     51 GGCAATACTCCC---------------------------CAAATTG---- 69

  chrX_34726901_3   2680 ACAAAGCAATATACAGAATCAGTGCTATTCCTATCAAACTACCAATGACA 2729
                         --------  v      v   ii  v  i         v v   iivi v
  L1M4_orf2#LINE/     70 --------ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chrX_34726901_3   2730 TTCTTCTCAGAAACAGATAAAGCT-ATTTTAAAATTCATATGGAACCAAA 2778
                           i  iv      iv  i  -   -  ii                viiv 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_34726901_3   2779 AAAGAGCCTGAATTGCCAAGGCAATCCTAAGCCAAAGGAACAAAGCTGCA 2828
                          ii  v  v    v     ii     i i ivv i i        i  v 
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_34726901_3   2829 GGCATCAAGTTACTCA---TCAAATTATACTACCGAG--ACAGTAACCAA 2873
                           vv   vii v i  ---     viv      vi  --       i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_34726901_3   2874 AACAGCATAGTAGTGGTACAAACACAGACACATAGACCAGTGGAACATAA 2923
                         i    ii i   v   i i  iv i     i     i  i     i v  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_34726901_3   2924 TAAAAAGACCAGAAATAAGGCCACGCACCTACGACCATCTGATCTTCAAT 2973
                          vi i  v          iv   ii  ii  i ii  vi    i   i i
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_34726901_3   2974 AAAGCTGACAAAAACAGGCAATGGGGAAAGGACTTCCTATTCAGTAAATG 3023
                           i v  v   i v  vv            i ivvi  v    ii     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_34726901_3   3024 GTGCTGGGATAACTGACTAGCCATATGCAGAAGATCGAAACTGGACCCCT 3073
                                  i     iv  ?   i     i    vi   ii         
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_34726901_3   3074 TCTTTATACCATATACAAAAATAAACTCAAAATGGGTGAAAGACCTAGGG 3123
                         v i i i               v            i v ?       ---
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA--- 507

  chrX_34726901_3   3124 AGTACCATGGTTTAAATGGTAAGACTTAAATGTAAAACACAAAGCTATAA 3173
                         ----------------------------       i vvi   i      
  L1M4_orf2#LINE/    508 ----------------------------AATGTAAGAGCTAAAACTATAA 529

  chrX_34726901_3   3174 AATCCCTATATGACACTCCTAGGGAGTACCAGGGTTTATG-CCAGGGACA 3222
                           ii i  v v  v v- v    ?-   -- ivv  ii  -  vv  ii-
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAA-CATAGGN-GTA--AATCTTCGTGACCTTGGGT- 574

  chrX_34726901_3   3223 TAAACCCTGGCAAAGATTTCATGAGGAAGACACCAGAA--ACAATTGCAC 3270
                           ------     v i    v iiiv v       i  --    --   v
  L1M4_orf2#LINE/    575 TA------GGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GCAA 616

  chrX_34726901_3   3271 CGAAAACAGAAATTGACAAGTGGGATCTAATTAAACTAAAATGCTTTTGC 3320
                          i   iv i    v  i  i v   ii v  i   v v   vi      i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_34726901_3   3321 ACAGCAAAAGAAACTATCAACAGAGTAAACAGACAACATACAGAACGGGA 3370
                         i vv    i  v        v i   i  v       vi      i    
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_34726901_3   3371 GGAAATATTTGCAAACTATGCATCTGACAAAAGTCTAATATCCAGCATCT 3420
                          i             ii  ii      i  ii v  vi       v  v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_34726901_3   3421 TTAAGGAACAA--ACAAATTTACAAGAAGAAAATTAACAATCCCATTAAA 3468
                         v   i    vv--    v iv i  v  i  i iv  i  i  v   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_34726901_3   3469 AAGCGGGCAAGGGATTCGAATAGATACTTATCAAAAGAAGCCATCCATGC 3518
                           ii      i     i       i i  v  v       vi  v  vii
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_34726901_3   3519 AGTGAATAAGCATATGGGAAGAAGGTCAATATCACCGATCAT 3560
                         i iv        i   ii    v v    i    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 5.94 (95 / 16)  


2574 25.96 7.37 1.17  chrX_34756424_34761775     4005  4859 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34756424_3   4005 TGGAAAAACATATCATGCTTGTGGATAGGAGGAATCAATATCATTAAAAT 4054
                               i i  vi    i ii     v   i  v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34756424_3   4055 GGCCATAGTACCCAAAGCAATTTA-AGATTTAATGATATTCCTATTAAAA 4103
                            v   v v      vii  i  -     i  i vv  i     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34756424_3   4104 TACCCA--------------------TAACA------TTCT-----TCA- 4121
                          -    -------------------- i   ------ i  -----   -
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_34756424_3   4122 ------------------CAGAATG--CAATACAATCCTTAACAAAAACA 4151
                         ------------------      i--   v      i v  v  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_34756424_3   4152 GCAAAGGTGGAGGAATCACATTACCCAACTTTAAACTATCCTATAAGGCT 4201
                         i     v       v     i v     i  i   viv v   i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_34756424_3   4202 ACAGTAATAAAAACAGCATGGTACTGGTACAAAAGCAGGCATTTAGACCA 4251
                                 v  i    ii         i i  iiii  i   v    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_34756424_3   4252 ATGGAACATAGCAGAAAGCCCATAAATAAGGCCACACAACTACAACCATC 4301
                               i v iiv  i  i   v      iv   i   vi  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_34756424_3   4302 TGATCTTTGACAAAGCCGACAAAAACGAGCAACAGGTAAAGGACTCCCTA 4351
                             i  i     i vi v   i v ivv   ii  v    i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_34756424_3   4352 TTCGGTAAATGGTGCTGGGATAGCTGGCTAGCCACATGCAGAACACTGAA 4401
                            iii              i i    v  ?         i  v v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_34756424_3   4402 ACTGTATCCCTTTCTTACACCACATATGAAAATTAACTCAAGATGGATTT 4451
                         ii  v i    vi  i      i   ii             i      i-
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC- 498

  chrX_34756424_3   4452 GAATACAACCCTTAAAAGTAAAACCAAAAACTATAAAAACCTTGGAATAT 4501
                         -- ? -i   --    v    i v v            vi   i   v v
  L1M4_orf2#LINE/    499 --AWA-GACC--TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_34756424_3   4502 AACCTAAG---AAATACCATTCTGGATATAGGACCTGGCAAAGACTTCAT 4548
                            v  i ---    -- -   vv  iv v  iiiv     v ii   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_34756424_3   4549 GACAAAGATGCCAAAAGCAGTTGCAACAAAAACAAAAATTGACAAATGAA 4598
                         iivv v  ii         vvv         iv      v  i    vii
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_34756424_3   4599 ACCTAATTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTATCAACAGA 4648
                           i v  i   v v  i i      ii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_34756424_3   4649 GTAAACAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTGTGTATC 4698
                           i  v        i                          iii i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_34756424_3   4699 TGACAAGGT-CTAATATCACGAATCTATAAACA-----CAAAATTTA-CA 4741
                            i    v-  vi    vv    v      v -----i v  i i -i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_34756424_3   4742 AGCAAAAAACAAACATCCCCATTAAAAAGTGGGCAAAGGACATGAATAGA 4791
                          vv    i     i v   v   ?    i           iv        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_34756424_3   4792 CATTTTTCAAAAGAAGACACACATTTGGCCAACAAGCATATGAAAAAATA 4841
                              i  v        i i   vv       i     i       i  i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_34756424_3   4842 CTCAGCATCATTAATCAT 4859
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (132 / 87)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.56 (73 / 16)  


3266 17.18 3.44 6.16  chrX_34797191_34799031.rev      509  1352 (489)    L1M4_orf2#LINE/L1       88   908 (0)  

  chrX_34797191_3    509 ATCCCTAACAAAATCTCAGATGACATCTTTGCAGAAATTGACAAGCTGAC 558
                                v       i   v  v v i                      i
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chrX_34797191_3    559 TTTAAAATTAATATGGAATTGCAAGAAACACAAAAGAGCCAAAATAATTC 608
                         ii       v        v      ii  v  i  v        i   ii
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chrX_34797191_3    609 CGAAAAATAAGAATAAAGTAAGAGTAATCACTCTCCTCAATTTCAAAACA 658
                         i      v     i     vi   v v    v  i i            v
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_34797191_3    659 TACTACAAAGCAGTGGTAATCAAGACAATGTGGTACTGGCACAAGGAAAA 708
                                    viii            i             i     v i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_34797191_3    709 ACATATAGATGAATGCAGTAGAAT-GGGAGCTTCAGAAATAAACTTATAC 757
                                   v    v i      - i   - i           ii    
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAG-TCCAGAAATAAACCCATAC 336

  chrX_34797191_3    758 ATCTGTGGTCAACTGATTTTCAACAAGGATGCCAAGACCATTTAATGAGT 807
                           i i       i        i      i             i    i -
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG- 385

  chrX_34797191_3    808 AAAAGAAGAGTCTTT-AAGCAAATGGTGCTGGGGCAAGCAGATATCCACA 856
                         i      v       -v i              i   vii    ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_34797191_3    857 AGTAAAA--ATGAAGTTGAACCCTTACTTCATATTATATAAAAAACATTA 904
                         v i    --         i    i   i   i ii     v    -    
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTA 484

  chrX_34797191_3    905 ACTCAAATTGT-TCTAATATCTAAGTCTGAGAGATCAAATTATAAAACTC 953
                                v  v-  v? v i    i v i    v v   i          
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_34797191_3    954 TTAGAAAAAA--------------CTTTGTAACCTT---TTATGTGGCAA 986
                               i   --------------   i  i     ---   ---     
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA---GGCAA 581

  chrX_34797191_3    987 AGAATTCTTAGATACAACACCAAAAGCATCAGCAATAAAAGAAAAAAAGA 1036
                         v iv          ii            iv     i           ---
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA--- 628

  chrX_34797191_3   1037 AATAGAAAAATT----TTCTTATAAAAATTAAAA-CATTCATGCTTCAAA 1081
                         --    v     ----   --  v          - v  ii         
  L1M4_orf2#LINE/    629 --TAGATAAATTGGACTTC--ATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_34797191_3   1082 GGACACCATCAAGAAAGTGAAAAAGTAACCCACAAAATGGGAAAAAATGT 1131
                               i                iii        i       i     i 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_34797191_3   1132 --GTATATCATATATCTGATGTTATTATACATAGATTATCACATATTATA 1179
                         -- i v              i--------- vi  i --------- i  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATA---------AGGGACT---------TGTA 756

  chrX_34797191_3   1180 CCTAGAAGATATAAATAATTCTTAGAACACAGTACTGAGTACTGAATAGA 1229
                         i i    v       v  i     v   v  i  v i ------  -   
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAA------AA-AGA 799

  chrX_34797191_3   1230 CTAATAACACAATGGCCCAAATGAGATTTTTCTTTTGAGAAAAATCTCCA 1279
                          v      v    v?vv-     i ------ ------i  ii  i vv 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAA-AAATGGG------C------AAAGGATTTGAA 836

  chrX_34797191_3   1280 CAGATATTTCTCCAAAGAAGACACACCAGTAGGCCAATAAGCACATGAAA 1329
                         i   i                i i  v i -                   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAAT-GGCCAATAAGCACATGAAA 885

  chrX_34797191_3   1330 ATATGTTCAGCATAATTATTCAT 1352
                          v   i   i   v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (89 / 53)
Gap_init rate = 0.03 (23 / 821), avg. gap size = 3.52 (81 / 23)  


2626 29.48 0.66 1.53  chrX_34884915_34887435     1113  2028 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34884915_3   1113 TGGAAAAACATTCCATGCTCAGGGATTAGAAAAATCAATGTCACGAAAAC 1162
                               i i  i     i   v     i   i v i   i iiiv  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34884915_3   1163 GTCCATATTGCAAAAAGCAACCTCAAGATTCAACACTACTCCCACCAAAC 1212
                          v v   i v vv   vii i  vv         i v ii  i i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34884915_3   1213 TATCAACATCATTTTTCACAGAATTAGAAAAAAACGATTCTAAAATTTAT 1262
                          vi  i vv v     ii     v v  v  iv-i   i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_34884915_3   1263 ATGGAACTGAAAAAGAGCCTGAAGAGCCAAAGTAATCCTAACCACAAAAA 1312
                               v  v  ii  v  v   v       ii    i i ---------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--------- 190

  chrX_34884915_3   1313 AAAAAAAACAACAAAGCTGGAGGTATCACATTACCTGACCTCAAACTCTA 1362
                         -    i  v       i      vv     i v  ii ii     vii  
  L1M4_orf2#LINE/    191 -AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_34884915_3   1363 CCATGAGGCTACAGTAA-CAAAACAACATGGTACTGCTACAAAAAGAGAC 1411
                          i ii i          -   i   iii        vi i  ii v    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_34884915_3   1412 ACGTAGACAAAAGTAACAGAATTGAGAACCTAGAAATAAAGCCATACACT 1461
                          ii    iv  v v  i          ii i         v       i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_34884915_3   1462 GACAATAAGCTGATCTGTGACAAAGTTGACAAAAATATGCAATGGATCAA 1511
                         v iii v ii    i vi     i v  v   i vi  v      ivv  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_34884915_3   1512 GGAC--TCCTTATTCAATAAATGGTACTGGGATAACTAGGTAATCACATA 1559
                          i i--  i  --    i       i      i    i i  ?i     i
  L1M4_orf2#LINE/    390 GAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_34884915_3   1560 CAGAGGAATTAAACTGGACCCCTTCTTATCATCATATACAAAAATTAAGT 1609
                           i i    v  ii         v i vv  i                v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_34884915_3   1610 CAAGATGGGTTAAACACTTAATGGTAAGATCTACAATGCTAAAAATCCAA 1659
                            i    i i ? v  i   vv      v   v  ivv     v  iv 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_34884915_3   1660 GAAGAAAACCTAGGACTTACCCTCTG-GACATTGGCCTTTGCAAAGAATT 1708
                                  v    ?v v vi  ii -   v    vi vv    v iv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_34884915_3   1709 TATGAGTAAGTTTTCAAAAGTAGTTGCAACAAAAGCAAAAATTGACAAGT 1758
                         iv iii  v vivi      i vvv          v      v  i  i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_34884915_3   1759 TGGACTCAATGAAACTAAAGAGCTTCTGCACAGCCAAAGAAGCTATCAAT 1808
                               iv  v   v v  i i   i  ii vv v  i  vi       v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_34884915_3   1809 TGATCAACCAGATTATCTACAGAATGGGAGAAAACGTTCACAAACTATGC 1858
                         vi vii vv   iv i i                ii  ii    ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_34884915_3   1859 ATGTGACAAAGAACTAATATCCAGAATCTATGAAAAATGTAAACAAATAA 1908
                           v   i  i i   vi          v   i  i  ivivv    v v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_34884915_3   1909 ACAAGTAAAAAG-CAAATAACCCCATTAATATGTGGGCAAAGTATGTAAA 1957
                          i  -       -          v   ? v vi         v  v i  
  L1M4_orf2#LINE/    788 ATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_34884915_3   1958 CAGACGCTTCTCAAAGGAAGACATACAGGTGGCCAACAACTATATTAAAA 2007
                         i    ii     v  i     i     ii       i  vi i  v    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_34884915_3   2008 -ATACTCAACAACACTAATCAT 2028
                         -  i       v  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (156 / 110)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


2765 27.77 1.21 1.54  chrX_34910544_34915825.rev     3881  4791 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_34910544_3   3881 TGGAGAAACATTCCATGCACATGTATAGGAAGAATCAATATCGTCAAAAT 3930
                             i i i  i     iv    v  v      v i     i  i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34910544_3   3931 GACTATACTACCAAAAGCAATTTATAGATTCAATGCTATTCCCATTAAAT 3980
                          i v     v  v   vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34910544_3   3981 TACCATTGACATTCTTTACTGAA-TTAGGAAAAACT-ATGTTAAAATTCA 4028
                          v   vivi v  i   i v   -  --  v  i  -  vi         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_34910544_3   4029 TATGGAACCAAAAATGTACCCA-AATAGTCAAGACAATCCTAAGCAAAAA 4077
                                viiv  iv -     -     i   i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_34910544_3   4078 GAAAAAAGCTGGAGACATCACACTACCTAACTGCAAACTATACTACAAGG 4127
                            v    i     ivv       v  i  i v    viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_34910544_3   4128 CTATTTGAGTCAAAACAGCACAGTACTGGCACAAAATCAGACACATAGAC 4177
                            ivvv i    i    iiii         i  iivi     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_34910544_3   4178 CATTAGAACAGAATAGAGAACTCAGAAATGAGGCTGCACATCCACAACTA 4227
                           v i   i     v    iii       i iv iii    ii iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_34910544_3   4228 TCTGATCTTTGACAAACCTGACAAAAGCACGCAATGGAGAAAGGAT--TC 4275
                         vi    i  i     ivv  v   i v  iv      i     i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_34910544_3   4276 CTTGTTTAATAAATGTTGCTGGGAGAACTGGCTAGCCATATGCAGAAAAT 4325
                         i  -- i  i     v        v      v  ?   i     i  i v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_34910544_3   4326 TGAAACTGGACCCCTTCCCTACACC-TATATAAAGGTCAACTCAAGATAG 4374
                             ii         v  ii     -    i   ii i       i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_34910544_3   4375 ATTGAAAACTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGGAAA 4424
                           ii? i  i         i v i            vi i      i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_34910544_3   4425 TCTAGGCA-ATACCATTTAGT-ACATAGGCACAGGCAAAGATTTCATGAC 4472
                         iv    ?i- v i --  v  -  v v  vvi      v i    v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_34910544_3   4473 AAAGTCACCAAAAGCAATAGCAATTGCAACAAAAGCAAAAGCTGACAAAT 4522
                         v v v           ----   --          v    iiv  i    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCA----CAA--GCAACAAAAGAAAAAATAGATAAAT 637

  chrX_34910544_3   4523 -GAAATCTACTTAAACTAAAGAGCCTCTGCACAGCAAAAGAAACTATCAT 4571
                         - i v ii iiv   i    i - i i  ii vv    i  v       v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_34910544_3   4572 CA--GTAAACAGACAACCTACAGAACGAGAGAAAATTTTTGCAATCTATC 4619
                         v --  i  v        i      i i        v       vii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_34910544_3   4620 CATCTAACAAAGGTCTAACATCCAGAGTCTACGAGGAACTTAAACAAATT 4669
                         i    i i  i  v  vii       i v  ii i     ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_34910544_3   4670 TACAAGAAAACAACAAACAACCCCATCAAAAAGTGGGGAAAAGACATGAA 4719
                         v i  v    vi     i     v  i?    i    v   i  iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_34910544_3   4720 CAGACACTTCTCAAGAGAAGACCTATATCTGGCCAACAAACATATGAAAA 4769
                         i     i     v i      iv  i vv       i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_34910544_3   4770 AAAGCTCAACATCACTGACCAT 4791
                         i v           ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (158 / 91)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.56 (25 / 16)  


 771 24.04 0.96 0.48  chrX_34970320_34972811.rev      810  1017 (1475)    L1M4_orf2#LINE/L1        1   209 (699)  

  chrX_34970320_3    810 TGCAAATAAACCCAATGTTCATAGATTAGAAGACTTAATATTATTAAAAT 859
                           v   v v i  v        i    i              i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_34970320_3    860 GTCTATTGCACACAGAACAATCTACAGATTCAATGCAATCTCTACCCAAA 909
                          v v  vviv v  i vii              i      i   i v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_34970320_3    910 TTCCAGAAATA-TTTTTGCAGAAAATAGAAAAATCCATCCTCAAATTCAT 958
                          i    vviiv-            - v  v  iiiv     v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCAT 149

  chrX_34970320_3    959 ATGGAAACTCATGGGATGCAGAATAGCCAAAACAATGGTAAAAAATAAAA 1008
                                iv  v    iv                  vv i     v  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_34970320_3   1009 ATA-GGCTGG 1017
                          i -i i   
  L1M4_orf2#LINE/    200 ACAAAGTTGG 209

Transitions / transversions = 1.00 (25 / 25)
Gap_init rate = 0.01 (3 / 209), avg. gap size = 1.00 (3 / 3)  

2597 20.62 5.47 1.26  chrX_34970320_34972811.rev     1289  2001 (491)    L1M4_orf2#LINE/L1      166   908 (0)  

  chrX_34970320_3   1289 CTCAAAATTATAATAATAATAATAAAAATAAAGATAAAAAAGTTAGAGAT 1338
                          i  i   viiv v  i   vv i    vi    -- v      i   iv
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA--ACAAAGTTGGAGGA 213

  chrX_34970320_3   1339 GTCACATTTCCTGATTTCAAA--T--CTACATAGCTATAGTAATCAAAGC 1384
                         v     i    ii        -- --     v     i         ii 
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_34970320_3   1385 AGTGTGATGCTGTCATAAAGACAGATATATAGATACATGGAATATAATAG 1434
                               i i   v     i  i   i        vv        v   v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_34970320_3   1435 AGAACTCAGAAATAAACCTTTATATATACATTCAAATTGCATTT--GACC 1482
                            iii            iv  i  v  iiv    -   -    --   v
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAA-TTG-ATTTTCGACA 361

  chrX_34970320_3   1483 AAAGTGGCAA-ATGATTCAATGCCAAAAAGAA-------------AAACA 1518
                          ii   v   - iv        v-ii      -------------   ii
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_34970320_3   1519 GTGTTGGAGAAACTGGATAGCCACATGCAAATGAATAAAGTTAGAAACAT 1568
                            i   iiv         ?           v    i     i  vv v 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_34970320_3   1569 ATTTTATTTCATATACAAAACTTTAAC--AAACTGGATCAAAGAGCTAAA 1616
                          ii i ivi           v  -   --   v       ?   v     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATT-AACTCAAAATGGATCAWAGACCTAAA 509

  chrX_34970320_3   1617 CTATAAGATCTAAAGCAATAAAACTC--AGGAGAAAACAGAGGA--AAAG 1662
                         - i     v     i v         --  i        v   ?--   v
  L1M4_orf2#LINE/    510 -TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_34970320_3   1663 CTTCATAATATTGTATTTGGCAATAATTTCTTGAATATGATAACCAAAAG 1712
                             i i iv   vi  v      ii      ii      i -       
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA-CCAAAAG 607

  chrX_34970320_3   1713 CGCAGGAAACAAAAGAAAAAATAAATAAATTGGACTTCATCCAAATTAAA 1762
                          i  i v                i                 v        
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_34970320_3   1763 ATGATTTGTGTGTCAAAATATACTATGAACAGAGTGAAAAAA--ATACAT 1810
                          vvv      iv     iv i     v  v i        i -- iv  i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_34970320_3   1811 AAAATGAGTGAAAATATTTGCAAATTACATATCTGGTAAGAGATTAATAT 1860
                          i    i v                i i       i    i  i vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_34970320_3   1861 CCACCATATATTAAAAACTGCTAAATCTCAAGAAC-------CAAATATA 1903
                            vv      v  i    vi  v v     v  i-------      - 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA-A 806

  chrX_34970320_3   1904 CCCAATTCAAAA-TGGGCAAAGGGCTTAAATAGACATTTCTTCAAAGG-- 1950
                                ?    -          ii  i             i     i--
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_34970320_3   1951 -TATATAAATGTCCAATAAGCACAAGAAAAGATGTTCAACATCATCAATT 1999
                         -    i     v            v         i         ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_34970320_3   2000 AT 2001
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.42 (84 / 59)
Gap_init rate = 0.03 (20 / 743), avg. gap size = 2.40 (48 / 20)  


1358 26.69 4.29 7.88  chrX_35032407_35034084      497  1219 (459)    L1M4_orf2#LINE/L1      212   908 (0)  

  chrX_35032407_3    497 GAC-CACAATATGTAATTTCTACACTCA-TATAAAGCTCCAATAATCAAC 544
                            -    v vivi      v v   i -  i      v  i       v
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_35032407_3    545 ATTGAGTGGAACTGGCATAATGATAGATAGATAGATAGATAGATAGATAG 594
                          iv v    v          v      i v      --------------
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGAT-------------- 297

  chrX_35032407_3    595 ATAGATCGATAGATCGATAGATCTATCAATGAAATAAAATGGAATTTTAA 644
                         --------------------------     i    i   v  ivv iv 
  L1M4_orf2#LINE/    298 --------------------------CAATGGAATAGAATTGAGAGTCCA 321

  chrX_35032407_3    645 GAAATATACTCACACATATTTCAAAAAATAATTTTTGAGAAATATACAAA 694
                               v  i  i    v v vivv  v i     i  v  ivi i v  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_35032407_3    695 GGCAATACAGTGGAGAAGGGAAAATCTATTCAATACATTGTGTGGGCATA 744
                          i v  v  i   i   i i v i   v     i v  v   iv  v i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_35032407_3    745 AATGGTTATCCATATGCCCAA-AGTGGAATTTGATACATACGTTGGGTTA 793
                          v   v  ?   i    vv  - i  i i  v  iv v   v -------
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT------- 464

  chrX_35032407_3    794 CACACGCAGACCTGCACACAAATAGCAACTCAAAATGGATCATA--CCTA 841
                              -  ---- ii   v    --i                ? --    
  L1M4_orf2#LINE/    465 CACAC-CA----TATACAAAAAT--TAACTCAAAATGGATCAWAGACCTA 507

  chrX_35032407_3    842 AATGTGAAATCTAAA-TTGTAAAACTTCTACATGAAAAC----------- 879
                              i i v     -i i       ii  v v      -----------
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_35032407_3    880 -CACTGTGACCTTGGGTTAGACAAATATGTCTCAGTTATGGCACCAAAGG 928
                         - vii               i   vvi v   i  v    i       i 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_35032407_3    929 CATGGTCCACAAAAGAACCAACTGACAATGTGGATGTCATCAAAATGAGA 978
                           iiiv v         vv  iv  i  vv    iv          v i 
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_35032407_3    979 AG--TTCATGCTTAGTGAAATACTCCATTAACAGC-TGAAAAGATAAGCT 1025
                          i--  ii     --ii  iv  v i  i  v iv-        i  v i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_35032407_3   1026 ACAGACCAAGAGAAATCATTTACAAACCACACATTGAACAAGGGGCTTGC 1075
                              viii      vi    i    i  i i  ivi i     i    i
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_35032407_3   1076 ATATAAAATATATAAATAACTCTCAAGAGTAATTGATAAGATATTAAACA 1125
                           vi i          v      i vi v v v i    i vivi   i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_35032407_3   1126 ATTCAATATAAAAGAGGAACAAA---TTAGTACAGACACTTGACTAAAGG 1172
                          ii    - ?   i v ii    ---  v v i     i  vv i    i
  L1M4_orf2#LINE/    806 ACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_35032407_3   1173 AGATA----GAGGGCGAATAATC-CTTCCAGAAATGC--AAAATAAAGCT 1215
                              ----i v   v     v - v vv i i    --  v  v ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_35032407_3   1216 ATAA 1219
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.13 (101 / 89)
Gap_init rate = 0.03 (19 / 697), avg. gap size = 4.63 (88 / 19)  


2074 24.54 6.85 1.71  chrX_35060755_35062447      500  1200 (493)    L1M4_orf2#LINE/L1      172   908 (0)  

  chrX_35060755_3    500 ATGGCCAAAATCAACCTTGAGCAAAAATAATAAAGCCAG-GGTCATCAGA 548
                           i       -   i     iv  i  v  i    iii -  v -   v 
  L1M4_orf2#LINE/    172 ATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC-TCACA 219

  chrX_35060755_3    549 CTACCTGGTTTAAAAATCTACTACAAAGCTATAGTAATCAATACAGCTTG 598
                           v  iii   v    ii             i         v    iv  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_35060755_3    599 GAGCTACTGGCATAAAAACTGACACA---AT---TGGAAGAGAATAGTGA 642
                          ---           ii iv    i ---  ---     v     v v  
  L1M4_orf2#LINE/    270 G---TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_35060755_3    643 GCCCAGAAATATATTCAAATATTTATAGTCAATGGATTTTAG-CAAAAAT 691
                          i         v ii  v i      i      v      v -   iii 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_35060755_3    692 GCCAACAACACACAATAGTGAAATGACAGTCTCTTCAATAGATGGTGCTG 741
                              v v  iv    i v    vi i     i     i i         
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_35060755_3    742 TGAAAACTAGATATTTACAAGCAGAAAAATGAAATAAGAACTTCATCTCA 791
                         v  v    i    ?ii   v   i  i      i vi  v iii i    
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_35060755_3    792 CACCATATATCAAAAA--AATTCAAAATAAAT-----ACTTAAATATAAT 834
                                  -      --  i       ii  -----  i     i   v
  L1M4_orf2#LINE/    467 CACCATATA-CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_35060755_3    835 CCATGAAATTTCAAAACTACTAGACAGAAACATAGGGACGAA-CTCTATG 883
                         vvv i   i vi      vi    vii         ?iii  -  iii  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_35060755_3    884 GCATTGGTCTAGGCAAAGATTTTTTTCATATGACCCGAAAAGCAAAGGCT 933
                         i v    vi       v i   i  vv       v v       v i  v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_35060755_3    934 AGAAAAGAAAAAGTATACAAGTGAGATTACATTACACTTTTAAAAGCTT- 982
                          v          i  v i  i vi  i v   i v v  --    i   -
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT--AAAAACTTT 663

  chrX_35060755_3    983 ----CTTCAAAGCCAACA--ATCAACAAAGTGAAGACACAACCTACTAAA 1026
                         ----        --i   --     v        i v      i  vi  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAG--GACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_35060755_3   1027 TGGGAAAAAATATTTTCAAACCAT-CATCTGATAAGTAGTTAATATCTAA 1075
                              i         v    i   -i          viii vi    i i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_35060755_3   1076 AATATGTGAGGAACTC----AAAT-AATAGTAAGAGAACAATGTGATTTT 1120
                              i i i      ----  v -    i   i ii    -i i iiiv
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA-ATAACCCA 810

  chrX_35060755_3   1121 AT---AAAATG----------------AGACATTTATCACAAGAATACAT 1151
                           ---      ----------------        v  vv     v i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_35060755_3   1152 AAAAATGGACAACAGGTATATGAAGAAAGTACTCAGCATCACTAATTAT 1200
                          v      v   i i i i     i i - i    i     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (108 / 62)
Gap_init rate = 0.03 (22 / 737), avg. gap size = 2.73 (60 / 22)  


2730 26.76 2.80 1.90  chrX_35084043_35086354      927  1819 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_35084043_3    927 ATATTCCATGTTCATCAATTGAAAGAATCAATATTGTTAAAACATTCATG 976
                             i          vi    i    v i           i iiviv  i
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_35084043_3    977 TTACCCAAAGCAATCTATAGATTCCAAGTAATCCATATCAAAATACCAAC 1026
                         i v      vii     i      v v i     v         v   i 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_35084043_3   1027 -GACATCTTCACAGAAATAGAAAAAAATAATCTTAACATTTAT-TACAAA 1074
                         - v v i  ii       v  v  iv- i   i   v   i  - iv   
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATGGAAA 156

  chrX_35084043_3   1075 ACTTTGTATTATTACAAAATACCCACAGTAGCCATAGCTATCTAGAGCAA 1124
                         ------------ i   iiv     v i      v i v    v  iv  
  L1M4_orf2#LINE/    157 ------------TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_35084043_3   1125 AAAGAACAAAACTGCAGGAATCATGTTATCTGACTTCATATGATACCTCA 1174
                         i         ii  v    v   iii vi ii i    v vvv   iv  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_35084043_3   1175 GAGCTATAGTAACCAAAACAGAATGGTA-------GAGG-----CACGCA 1212
                         i     i     i   i    vi     -------i   -----  iii 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_35084043_3   1213 GATCAATGAAACAGAATAGAGAACCCAGAAATAAATCAATACATCTCCGG 1262
                                 i  i     v    ii           i v      i vi  
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_35084043_3   1263 TGATCTCATTTTTGATGAAGGTATCAAGAACATAAATTGGAGAAAGGATA 1312
                          v vi v     i  ii i   ii     v   vv v   i     i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_35084043_3   1313 GTCTCTTTAATAAATTGTGGTAGGAAAACTGGAAATCCACATGCAGAAGA 1362
                             i  i  i    v   v i   v       v ?         i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_35084043_3   1363 ATGAAACTATACCCCTATCTGTTGCCATATGCACAAATCAAATCAAA-TG 1411
                              ii iv       i  vvii      i  v    i  v     -  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_35084043_3   1412 GATTGAAAATTTAAATCTAAGACCTCAAACTATGAAACTACTAAGAAGAA 1461
                            ii? i ii     v     v  v       i     -  v       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAA 543

  chrX_35084043_3   1462 TTCATTAGGAA-AATTCTCTAAGACATTGGTCTGGGCAAAGATTTATTGA 1510
                         vv   -   ?i-  v   iiiv   v    vi i     v i   v  ii
  L1M4_orf2#LINE/    544 AACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_35084043_3   1511 GTA--ACACCCCAAAGCATGGGCAACTAAAACAAAAATGAACAAATAGGA 1558
                         i  --     v-      iii     v   iv      ii i    v   
  L1M4_orf2#LINE/    593 ATATGACACCA-AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_35084043_3   1559 CCACCTTATG-TTAAAAAGCTTCTGCATAGCAAAGGAAAA-ATCAATAAA 1606
                          iv v i vi-       -   i  iiivv       v v-     v   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_35084043_3   1607 GTGAAGAGACA-----CAGAGTAGGAAAAATTATTTGCAAACTTGCCATT 1651
                              i     -----    i i   i   v          iivvvi  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_35084043_3   1652 TGACAAGGGACTAATAACCAGAACATATAGGGAGCTCATACAACTCTATA 1701
                            i        vi  v      i     ii  i   v        v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_35084043_3   1702 GAAAAAAATCTAATAATCTAATTAATAAGAGGGTAAAACATCTGAATAGA 1751
                         iv     iv v     i i    ? v  iv   i   iv  i        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_35084043_3   1752 CATTTCTCAAAGGAATACATACACATGGCAAAGAGGTTTATGAAAAGGTA 1801
                                 v  i   v i     v     v  v i ivi        i i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_35084043_3   1802 TTTAACATTATTGACCAT 1819
                         i i     i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.02 (16 / 901), avg. gap size = 2.62 (42 / 16)  


1803 25.17 7.11 4.78  chrX_35147161_35150174.rev     1676  2533 (481)    L1M4_orf2#LINE/L1       31   908 (0)  

  chrX_35147161_3   1676 AGATTTAGTATTATTAAAATATTGAT-TATCCTAAACTTAT-----GATT 1719
                            i   i    i    i  ivii  -ivi  i   i v  -----    
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chrX_35147161_3   1720 TCAATG-AATTTTAATCAGTGTCCCCACAGGGATTAAGGTTGAAATCAGT 1768
                         -   i -   iiiv    ivi    vi v vvv  vvv iv     iiii
  L1M4_orf2#LINE/     81 -CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chrX_35147161_3   1769 AAGCTGATTTAAGAATACACAGAGAAATCCAAAGAAACTAGAAGTGCCAA 1818
                                 iiv i   v  i vi     v   i i v i    vv     
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_35147161_3   1819 AACAATTATGTTTTTTTTTTAAAAAAGGA-AACAAAGTTGAAGGATGCAC 1867
                               i-----------  i      i -          i    iv   
  L1M4_orf2#LINE/    180 AACAATC-----------TTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chrX_35147161_3   1868 ACTGCCTGATATCCA---TTATTAC-----T---GTGA---AGACAATAT 1903
                            v  ii  v  v ---   i   ----- ---  i ---     i i 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chrX_35147161_3   1904 GA-A--GGTACCAG------CATATAGATCAATTGAACAGAATTGA-AGT 1943
                          i- --  i iv  ------             v   i        -   
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_35147161_3   1944 GTAAAAATAAACCCCAAAATATATAGTAAACTGATTTTTACCAAGG-TAC 1992
                         vi i          vv v  v   i  v  i       iiv     - i 
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_35147161_3   1993 -AATGTCATATCAATGGTTAAAGCATAGTCTTTTCAAAAAATTTTGGTAG 2041
                         -  vii   -       vv    v             v    vv  v i 
  L1M4_orf2#LINE/    369 CAAGACCAT-TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_35147161_3   2042 GACAATTTTATACCCACTATACACTATATGAGGCAACAACAACAACAAAA 2091
                              i vv   ?    ----------   ------------   -  i 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCAC----------ATG------------CAA-AAGA 444

  chrX_35147161_3   2092 AT-AACTTTAATCCAAGCCTTACAGCC---TACAAAAATGTAACTCAAAA 2137
                           -  v  vi i  vvi   i   -  ---         -          
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACA-CCATATACAAAAAT-TAACTCAAAA 492

  chrX_35147161_3   2138 T--ATTATAAATAAAAATGTAAAACACAATACTATAAAATTTCTAGAAAA 2185
                          --  i ? i ivv        i vvi  v         i ii     i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_35147161_3   2186 AAATAT-GTAGAACAATCTTTTTGACCTTGAGGTAGGTAACAG------A 2228
                            i  - v? v -      iv        i v    i  ii ------ 
  L1M4_orf2#LINE/    543 AAACATAGGNGTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_35147161_3   2229 AGTACAGTAGTCAAAGCATAATTCATAAAAGATAAAATTGAGAAATTAGA 2278
                         ii  iiii viv      i  viv i      v     v  v     i  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_35147161_3   2279 CTCTACAAAAATTAAGAATTTTTACTCTTTGAAAGGCACTGTTAACAGAA 2328
                           ii iv        i  i    iiv   ii  i i    i i  v i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_35147161_3   2329 TTAAAAGAGAAGTGACAGACTGGGAGAAAATATTCACAAATCACATATTT 2378
                          v      v  viv     v              ii       i    i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_35147161_3   2379 GTTAAAGGACATATAGTCA---TATAGAAA-AATTCATAAAAATCAATAA 2424
                          v   i    v i  vi  ---    v   -  i  v  v  v       
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_35147161_3   2425 TAAGAATACAAA-----CAAATAGAAAACAGGCAAAATATTTGAAGAGTC 2469
                            i  v     -----   v ?i    ii      iv       v  v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_35147161_3   2470 AATTTCTG-AAAGAAGATATGCAGTTTGGCAAACAAACACATAAAAA--T 2516
                          -     v-           i  iv -   v  i  i     i    -- 
  L1M4_orf2#LINE/    842 A-TTTCTCCAAAGAAGATATACAAAT-GGCCAATAAGCACATGAAAAGAT 889

  chrX_35147161_3   2517 GT--AACATTGATCATTAG 2533
                          i--     ii????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (125 / 87)
Gap_init rate = 0.04 (36 / 878), avg. gap size = 2.83 (102 / 36)  


1672 20.35 2.60 14.43  chrX_35188810_35190495      501  1193 (493)    L1M4_orf2#LINE/L1      298   908 (0)  

  chrX_35188810_3    501 CAATGGAACAAACAGAATAGAGAGAACAGAAATAAATACACATATTTACA 550
                                 i ----    v     vv          iv  i i     ii
  L1M4_orf2#LINE/    298 CAATGGAATA----GAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_35188810_3    551 CTAAATTGAGCTTTGACAAAGGTGCCAAAAACAC---ATGAAGAAATAAT 597
                         v v      vi  i     i        i v  i---   ii    v   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_35188810_3    598 ATTCTCTT--AGAAATGATGTTAGGAAAACTAGATATCCACATGCAAAAG 645
                          v   i  -- v     i  i i   v    i    ?             
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_35188810_3    646 AATGAAATTGCACCTTTATCTCACAATGTACACAAAAACCAACTCAAAAT 695
                               i   v   ii  i      vii  i       ii          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_35188810_3    696 GGATTAAAGACTTAAATG---------GAACTGTTAAACTACTAGAAGAA 736
                             i ?    i      ---------i    i v     vi        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_35188810_3    737 AATGTAGTGAAAAAGTTTCTTGACTTTGATCTGGGCAATGACTTATAAAA 786
                           ii   v?iv   vi   v    i   ivi i       ii  v v i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_35188810_3    787 TATGATATGAAAACCACCGGCAACAAAAGCAGAAATAGACAAATGGGATG 836
                              i iv    v   vi          v i       i    v   --
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA-- 641

  chrX_35188810_3    837 GCATTAAACTAAAAAGTGCCTGCACAGCCAAAGAAGAAATCAACAGAGTA 886
                         -------------------  v  ---------------    -------
  L1M4_orf2#LINE/    642 -------------------CTTCA---------------TCAA------- 650

  chrX_35188810_3    887 ATCTATGGAATGGGAGAAAATATTTGCAAACCAAAATTGACAAATGGGAC 936
                         --------------------------------------------------
  L1M4_orf2#LINE/    651 -------------------------------------------------- 650

  chrX_35188810_3    937 CTAATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 986
                         --       i -   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    651 --AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_35188810_3    987 GACAACCTACAGAATGGGAGAAAATTTTTGCAA-TC---TATCTGACAAA 1032
                                i                 v       -  ---       i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_35188810_3   1033 GGTCTAATATGCAGCATCTACAAGGAATGTAAACAAATATACAAGAGAAA 1082
                           v  vi   v   v  v  i  i   ivivv    v vv i  v i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_35188810_3   1083 AACAAACAGCCCCATTAAAAAGTGTGCAAAGGACATGAACACACACTTCC 1132
                         i     i i   v   ?    i  v        iv    i v   i   i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_35188810_3   1133 CAAAAGAGGACATTTATGCAGCCAACAAACACATGAAAAAAAGCTCAACA 1182
                          v     i  i  vi viii     i  i          i v        
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_35188810_3   1183 TCACTGATGAT 1193
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (81 / 56)
Gap_init rate = 0.02 (10 / 611), avg. gap size = 11.80 (118 / 10)  


1722 27.00 1.22 0.70  chrX_35227846_35231005.rev      502  1075 (2085)    L1M4_orf2#LINE/L1      243   819 (89)  

  chrX_35227846_3    502 CAAAGCTACAGTAGTCAATATGCTGTAATTAATGAGCAAAAGAATAGGCA 551
                                      i    v iiv   ii - v  -   v   i    i  
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGT-ACTG-GCATAAGGATAGACA 290

  chrX_35227846_3    552 -AAAGATTAGTGGAACAGAATAGAGGACCCAGAAATAGACACATATAGTT 600
                         - v    i i     i     v   iii         i  v    i v  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_35227846_3    601 ATAGTCAACTCATCTTTGAAAAAGGATCAAAGTCAATACAATGGGGAAAT 650
                           i     i v  i  i  v  i  vv v   v v  v           v
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_35227846_3    651 GTTTCTCTTTTCAACAAGTG-TGTTGGAACAAATGGAAATTTGTTTGCAA 699
                         iv vv            i  -  i   i    v    v ?iiiiv     
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_35227846_3    700 AAAAATGAATCTAAAGACAGGCCATAGATACTTCACAAAAATTAACTCAA 749
                           i      vi ii vv vvi  vi v ivv vi                
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_35227846_3    750 AGTGGATCACAGACCTAAAAATAAAATGTAAAACAATTGAACACCAAGAA 799
                          i       ?         vi   i vv      v  vi   v iv    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_35227846_3    800 GATAGCATAGAAGAAAAATCTAAATGACCTTAGGTTTGGCAATAATTTTT 849
                           v i     i? v   -   vvi       i    v      ii   i 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_35227846_3    850 TAGATACAACACCAAAGCCATGATTAATAAATAAAATAATTGATAATCTA 899
                               ii        iv  ii vi  i   vi   v   v     vi i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_35227846_3    900 GAATCCATTAATATTAGAAACTTTTTTG-TGCAAAAGACATTGTCAAGAC 948
                           v i   i  v    i        v  - v    i    i i      v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_35227846_3    949 AATGGAAAGACAA-GCACAGATTGAAAAAAAAATATTTGCAAAGGACATA 997
                          i  i        -v      v  ii i    -          vv i   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATA 738

  chrX_35227846_3    998 TCAGATAAAGGCCT--CATCAAAAATATACAAGAAATTATTA-ACTTTCA 1044
                           v     i  v  --i   v i      i  ii  i v   - vi iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_35227846_3   1045 GAATAAGCAAACAAATAACCAGATTTAAAAA 1075
                         v     iv i          vi   ?     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAA 819

Transitions / transversions = 1.19 (82 / 69)
Gap_init rate = 0.02 (10 / 577), avg. gap size = 1.10 (11 / 10)  

 677 24.67 4.85 0.88  chrX_35227846_35231005.rev     1447  1673 (1487)    L1M4_orf2#LINE/L1      673   908 (0)  

  chrX_35227846_3   1447 AAAAACA--ATCAACAGAG--AGAAGACAACCTGAAGAAGGGAAGAAAAT 1492
                           ii   --     v i  -- i         iiv    v  i       
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_35227846_3   1493 ATTTGCAAACTATTAAAGTGACAAGGGATTATTACTCAGAATATACAAGG 1542
                                  ii  vv vv   i      i vv  ii         i  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_35227846_3   1543 AACTT---CATCTCAACAGCAAAATAACAG----TCTGATTTTTAAAACG 1585
                             i---  v     i ii    vi   i----i ii   ?v-    i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATG 821

  chrX_35227846_3   1586 GGCAAAATGTCTGAACAGACATTTCTCAAAGAAAGACTTACAAATAGCCA 1635
                               ivi i    i           v  ii    iv       i    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_35227846_3   1636 AAAAATATATGAAAAAAATGTTAAACATCACTAATCAT 1673
                          v  ii i       i -  i v       ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (38 / 17)
Gap_init rate = 0.03 (6 / 236), avg. gap size = 2.17 (13 / 6)  

 314 27.59 4.02 1.72  chrX_35227846_35231005.rev     2501  2674 (486)    L1M4_orf2#LINE/L1      731   908 (0)  

  chrX_35227846_3   2501 ATTATATGTATTATAATGTCATTGTGTACCCCATAA-ATATGTATAATTA 2549
                           i    i v v    v vvv    i ---   v  -    iv v  i v
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTAT---CCAGAATATATAAAGAACTC 777

  chrX_35227846_3   2550 TTATGGGACAAT--TAAAAA--TAAATTAAAAAAT--AAAAACTACCAAA 2593
                            iiivv    --      --i    v vvv   --     iviv    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_35227846_3   2594 AGACCTGAACCGACATCTCACTGAAGAATATATACAGATGGTAAGTAAGT 2643
                         i  ii    iv     i  v ii     v       i    iv i    i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_35227846_3   2644 ATATGAAAAGATGTTCAAATTCACATGTCAT 2674
                          i           i    vv   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (24 / 24)
Gap_init rate = 0.03 (5 / 178), avg. gap size = 2.00 (10 / 5)  


1693 27.27 1.79 3.43  chrX_35301714_35303711.rev      502  1172 (826)    L1M4_orf2#LINE/L1      217   876 (32)  

  chrX_35301714_3    502 ACACTGTCTGACTTCAAGACTTACTATAAAGCCACTGTAATAAAGA---- 547
                              vi ii i     i        i     i  v     v    ----
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_35301714_3    548 GTTATAAT--CATGAGAGAATAGACAAATAGATTAAATAGAACATGGTAG 595
                           vi  v --   i  i--       v      i  - i   i vii v 
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGG--ATAGACATATAGATCAA-TGGAATAGAATTG 313

  chrX_35301714_3    596 AGATCCCAGAAGTAGACCCTCATAAATATAGTCAATTGCTCTTAGACAAA 645
                            vi      i  i    vi i vv   i        v i  v     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_35301714_3    646 GGAGCAAAGAAAATGCAATGGAACGAAAATAGTCTTTTTAGTGAATGGTA 695
                           v  v    vv  v      iivi i           i iii      i
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_35301714_3    696 TTGGAACACAGGGACATCCACATGCAAAAAGAAAATATATATGAATCCAG 745
                         i   i   vvv   i ?            -   --------    viii 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAA-GAA--------TGAAGTTGG 454

  chrX_35301714_3    746 ATACAGACCTTATCCTTTA---AAAAATTAACCCAAA-TGGATCATAAAT 791
                          iv vv    i iv iv  ---          i    -       ? i i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_35301714_3    792 CTAAATGTAAAATACAAAGATATAAAATTACTA-AATAATAGACAGGAGA 840
                                   i vvi   iv       i vi  -  v  v v i   ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_35301714_3    841 AAACCTAGATGACCACAACTTGGGTATGGAGATGAGTTTTTAGACACAAC 890
                            i  vvi     -----      vv  vi   iv  i     i ii  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACC-----TTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_35301714_3    891 ACCAAAGGCACAATCCATTAAGAAAATAATTGATAAGCTGCACTTCATTA 940
                               i      v v iv  ii   v   v     ii  v       i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_35301714_3    941 AAATTAAAACCTTCTGATATGAAAAATAAAATGTCATGAGAATGAGAAGA 990
                                  v   i  vvv vv   iv v v i   v  i i   i    
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_35301714_3    991 CAAGCCATTTATTTTTGCAAAAATATTTGCAAAAAATGCATGTAATAAAG 1040
                            v   ivv v vv- vi              vv  ii  v i    i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGG-GAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_35301714_3   1041 AACT-GTGATTCAAAATATACAAATACATTTTGAAACTAACTGAACAATA 1089
                         i   -  -  i  i      i   v vv i  ---  -    v  i    
  L1M4_orf2#LINE/    749 GACTTGT-ATCCAGAATATATAAAGAACTCTT---AC-AACTCAATAATA 793

  chrX_35301714_3   1090 AGAAAACACACAACCAGATTAAGAAACGGGCCAAAGATCTTAACAGACAC 1139
                          i  i   v i    vi   ? i   i    v  i   i v  i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_35301714_3   1140 CTCACAAAAGAAGATATAGAGATGACAAATAGG 1172
                         i  v v            v i   i v    i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

Transitions / transversions = 1.21 (98 / 81)
Gap_init rate = 0.02 (15 / 660), avg. gap size = 2.33 (35 / 15)  

 228 16.95 8.47 0.00  chrX_35301714_35303711.rev     1449  1507 (491)    L1M4_orf2#LINE/L1      845   908 (0)  

  chrX_35301714_3   1449 TCTCCAAAAAA-----ATAGGTGACAAATAAGCACAAGAAAAGATGCTGT 1493
                                 i  ----- i ii  i v          v           vv
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_35301714_3   1494 ACATTATATGTTAT 1507
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (6 / 4)
Gap_init rate = 0.02 (1 / 64), avg. gap size = 5.00 (5 / 1)  


2438 26.22 4.77 1.70  chrX_35354090_35356683     1221  2101 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35354090_3   1221 TGGAAAAACATTCTGTGCTCATGGATAGAAAGTATCAATATTGTTAAAAT 1270
                               i i  i ii  i        v i   vv i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35354090_3   1271 GGCCATATTGCCCAAGGCAGTTTACAGATTACCTGCTATACCTATCAAA- 1319
                            v   i v     iviii i        vvvi  v  v         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35354090_3   1320 -TGGAGTT-----------AGAAA---A-AAACT-ATTCTAAAATTCAAA 1352
                         -ivv  i -----------     --- -  i  -  i          v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_35354090_3   1353 TGGAACCAAATAAGAG--TCA-AATAGCCAAAGAAATCCTAAGGAAAAAG 1399
                              -- vii   i --i  -          iv    i i ii  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_35354090_3   1400 AACAAACTGAGAGGCATTACACTACCCAACTTCAA--CCTA-TACAGTGA 1446
                               v vi    vv i     v     i     -- i  -    --- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA---A 245

  chrX_35354090_3   1447 AGCTACAGTAACCAAAACAGCATGGTACTGGTACAAA-ACAGAGACGTTG 1495
                                    i   i    ii         i i  i- i   v ii v 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_35354090_3   1496 ACCAATGGAGTGGAATAGAGCGCCCAGAAACAATGCTGCACACTTAAAAC 1545
                          i       i i    v   v i       i  vv iii   i   viii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_35354090_3   1546 CATTTGATCTTCAACAAAGTTAATGAAAACAAGCAGTGCAGAAAGGACTC 1595
                           v     i   i    i v ivii i v  vv  i  vi     i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_35354090_3   1596 CCTTTCTGCAATCAATGATGCTGCAATAACTGGTGAGCCACATGCAGAAG 1645
                         i    i--   iv    i     vi i      vv ?         i   
  L1M4_orf2#LINE/    396 TCTTTT--CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_35354090_3   1646 ATTGAACTTGGCCCCTTCTCTTTCACCATATACACAAATCAACTCAAGAT 1695
                          v    v    v   i vi  iv           v    i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_35354090_3   1696 AAATTAAAGACTTAAACGTAAAACCTAAAAATACAAAAAC--TAGGAGAA 1743
                         ii  i ?    i    i    i v      v  i    vi--   i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_35354090_3   1744 AATCTAGG--TAATACCATTCTGGACACAGGCCCTAGCAAAGTTTTCATT 1791
                           iv    --   - i -   vv   viv  viivi    v v    -  
  L1M4_orf2#LINE/    544 AACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TT 590

  chrX_35354090_3   1792 ACAAA-GACTGTAAAAGCAATTACAA---ACAAAACAAAAATTA-ACAAG 1836
                          v v -   vvi       ----   ---      v     v  - i  i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCA----CAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_35354090_3   1837 TGGAATCTAATTAACCTAAAGAGCTTCCGCACACTAAAATACATTATCTA 1886
                          v i ii v  i  vv v  i i   ii ii vii   iv   i    v 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_35354090_3   1887 CATAGCAAACAGGCAACTGACACAATTGGAGAAAATATTTACAAAGTATA 1936
                         v v  ii  v  i    iv   v   v             i    vi   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_35354090_3   1937 CCTCTGACAAAGGTCTAATACTCAGAATACATGAGGAACT--TA-AATT- 1982
                         iv     i  i  v  vi  ii       i  i i     --  -  i -
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_35354090_3   1983 ---AACAAAAA-ACAATGAACACTATTAAAAAATAGGCAAAGGACAGGAA 2028
                         ---  i     -    vv   v v   ?      i         ivv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_35354090_3   2029 CAGACATTTCTCAAAAGAAGACATACATGTGACCAACAAGCATATGCAAA 2078
                         i           v        i     vi  i    i     i   -   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAA 885

  chrX_35354090_3   2079 AAATGCTCAACATCAGTAATCAT 2101
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (137 / 91)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.11 (57 / 27)  


3091 25.82 1.10 1.32  chrX_35373485_35376429     1543  2452 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35373485_3   1543 TGGAAACACATCCCATGCTCATGGATGCGTAGAATCAATATTGTAAAAAT 1592
                               v i        i        vv v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35373485_3   1593 GACCATACTGTTAAAAGAAATCCACAAATTCAATGCAATTCTCATTAAAA 1642
                          i v     viiv   vvi   i   i      i     i ii  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35373485_3   1643 TACCACCAGCATTCTTCACAGAACTAGAAAAAAATCAATCCTAAAATTCA 1692
                          v   v v  v  i  ii     v v  v  i--iii             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_35373485_3   1693 CATGGAACCAATAAAGAGCCTGCATAGCCAAAGCAAGATTAAGCAAAAAG 1742
                         i      viivv ii  v  v v         i   vv  i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_35373485_3   1743 AACAAATCTGGAGGCATCACACTACCCAACTTCAAACTATATTATAAGGC 1792
                               vi      vv       v     i      viv  i  i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_35373485_3   1793 CACAGTCACCAAAACAGTATGGTATACTGGTATTAAAATAGGTACATAGA 1842
                         i     v i   i     i     --    i  v ii    ii i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTA--CTGGCATAAGGATAGACATATAGA 296

  chrX_35373485_3   1843 CCAAAGAAACAGAATAGAGTGCCCAGAAATAAAGCCAAATACTTACAGCC 1892
                         i   v i  i     v   v i           v   v i i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_35373485_3   1893 AACTGATCTTCAATAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACC 1942
                           i    i   i i  i vviv   i v   vv i         i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_35373485_3   1943 TTATTCAACAAATGGTTCTGGGATCATTGGCAAGCCACATGTAAATGAAT 1992
                         i v             v      iv i   vv ?       i   v    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_35373485_3   1993 GAAACTGGATCTTCACCTCTCACCTTATACAAAAATGAACTCAAGATGGA 2042
                            ii    i iii     v    v           v       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_35373485_3   2043 TCAAAGACTTAAATTTAAGACCTGAAACAACAAAGATTCTAGAGGATAAA 2092
                            ?    i     v     v  i    v i   iv ii    i  v  v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_35373485_3   2093 ATCAGAAAAAGCCTTCTAGACATTGGCTTAGGCAAAGACTTC------AT 2136
                           vi ?iv  ii    vv   v    v        v ii   ------  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_35373485_3   2137 GACCAAAAACTCAAAAGCAAATGCAACTAAAACAAAGACAAATAGATGGG 2186
                            -----  -        v v     v   iv   i i i   i  v  
  L1M4_orf2#LINE/    597 GAC-----AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_35373485_3   2187 ACTTAATTAAGCTTAAAAGCTTCCGCACAGCAAAGGAAATAATTAGCACA 2236
                             v  i  iv      i   ii ii vv       v iv  i iv v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_35373485_3   2237 GTTAACAAACAACTAACAGAGTGGTAGAAAATCTTCACAATCTATACATC 2286
                           v  v i     iv     i   v       v  ii   vii   i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_35373485_3   2287 TGACAAAGGACTAATATCCAGAATCTACAAAGAACTC----AAATGAACA 2332
                            i  i     vi          v  i         ----  v v  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_35373485_3   2333 GGCAAGAAAAAAAAAAAATCTCATCAAAAAGTGGGCTAAGGACATGAATA 2382
                         i-i  -   i v   v  i iv  i?    i     v     iv      
  L1M4_orf2#LINE/    791 A-TAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_35373485_3   2383 GACAGTTCTCAAAAGAAGATATACAAATGGCCAAGAAGCATATGGAAAAA 2432
                             v     v                       v     i   i   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_35373485_3   2433 TGTTCAACATCACTAATTAT 2452
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (131 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.75 (22 / 8)  


3119 22.60 3.97 3.86  chrX_35397407_35399366      561  1467 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35397407_3    561 TGAAGAGATTTCCCATGGTCATAG-TTGGAAGACTCAATATTTTTAAAAT 609
                           i i    v       v    i -          i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35397407_3    610 GTCCATACTTCCCAAGGAAATTCACAGATTCAATGCAA-AACTATCAAAA 658
                          v v     i     ivvi  ii          i    -vv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35397407_3    659 TCCCAAGATAAAATTTTAAAGATGTAGTAAAAAAATCTTAAAATTTGTAG 708
                              - v ivvv    -----  i  -----    - v v  vi  ---
  L1M4_orf2#LINE/    101 TCCCA-GCTGCCTTTTT-----TGCAG-----AAAT-TGACAAGCTG--- 135

  chrX_35397407_3    709 TGACATTAAATTAAAATTTATATAGA--CCCAAAATACCTCAAATAGCCA 756
                         ----  i---i       i    i  --iv   iiv   ivi        
  L1M4_orf2#LINE/    136 ----ATC---CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chrX_35397407_3    757 AAGTAATCTTGAAGAAGAAGATCAAAGCTGGAAGCTTTG---TTCCTGGT 803
                           ii         i       v     i    i vi ii---    iii 
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_35397407_3    804 TTCAAAGTATGTAACAGAGCTATAGTAATGGAAGTAGCATGTTATTGGCA 853
                               iiv iiv   i     i      vi iii  ii  v  i     
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_35397407_3    854 TAAAAACAGA--TACAGATTCCAATGAAACAGCATAGAGAACCCAGAAAT 901
                            ii i   --  i    --     i  i  v  v    ii        
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGAT--CAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_35397407_3    902 AAACCTATACAGATGTGGTCAAGTGATCTTTGACAGGGGTGCCAAGAATA 951
                              i     vv i       v    i  i    i           vi 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_35397407_3    952 TAAAATATGAAAAAGATAGTCTCCTCAACAAATGATCTTGGGAAAACTGG 1001
                          vv   iv i   ii       ii          i vi     v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_35397407_3   1002 AAATTCACATGCAAAAGAATGAAATTAGACCCTTATTT-ATACGATACAC 1050
                          v ?i                  i  i     i  ii - i  v   i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_35397407_3   1051 AAATAAAATCAACTTGAAGTAGATTAAAAACTTAAACCTAAAACCTAAAA 1100
                            ---   i    ii  i i   i ? i  i    iv   i v      
  L1M4_orf2#LINE/    477 AAA---AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_35397407_3   1101 CTATAAAACTCCCAGCAGAAAACTTAA-TATAAAAGTTTTTGAGA--TTA 1147
                                    ii  v       v  i-?i    -- i  i v  --  i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTG 571

  chrX_35397407_3   1148 TTTTTGGCAATGGTTTTCTGGATATGACAGCAAAAGTACAGACAACAAAA 1197
                         vv  v           ii i         v      i   ii        
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_35397407_3   1198 GCATAAATAGACAAGTGGGACTATATCAAACTAAAAAGCACTTGCACAGC 1247
                          v v       i  i v     vi      v v    i vi   ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_35397407_3   1248 AAAGGAAAATATCAAGAGAATAAAAAGGCAGCCTAGAGA-TTGGAGAAAA 1296
                               v v        i i i     i  i  i v   - v        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_35397407_3   1297 TACTTGTAAACCACATATCTGATA--------------------TATGAG 1326
                           i   i   i  i          --------------------   i i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_35397407_3   1327 AAACTTATACAACTGAGTAGAAAACAATAAAAACAAA--ACCCAATTAAA 1374
                         i    iv       v i  ---- i  -   i     --        ?  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATA----ATAA-AAAGACAAATAACCCAATTWAA 816

  chrX_35397407_3   1375 AAATGGGCAAAGGACCTGAATAGACATTTTTTCTATAGAAGACATACAAA 1424
                                       ii             i i v -      i       
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAA-AGAAGATATACAAA 865

  chrX_35397407_3   1425 TAGTCAAAAGATATATGTTAAGATGCTCAACATCACTAATCAT 1467
                          i i   v iii i   vv                ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (135 / 66)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.09 (71 / 23)  


3098 26.90 0.99 0.88  chrX_35408428_35415091.rev     5267  6173 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35408428_3   5267 TGGAAAAATATTCCATGCTTATGGATAGGAAGGACCAGTATCATGGAACT 5316
                               i    i     i i      v     ivii i   ii vi iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35408428_3   5317 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAATC 5366
                            v     v      v i  i  i        i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35408428_3   5367 TACCA-TTGACTTTCTT-CAGAGAATTAGAATAAACT-ACTTTAAATTTC 5413
                          v   -i  v    i  -    -    i-- i  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_35408428_3   5414 ATATGGAACCAAAAAAGAGCCCTTATAGCCAAGACAATACTAAGCAAAAA 5463
                                 viiv  ii  v  vvv        i     vi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_35408428_3   5464 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTAAACTACAAGG 5513
                                 i      vv       v  ii i      vivv       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_35408428_3   5514 CTACAGTAACCAAAAGAGCATGGTACTGATACCAAAACAGATATATAGAC 5563
                                  i   i v  ii        ii iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_35408428_3   5564 CAATGGAACAGAACAGATGCCTCAGAAATAATGCCGCACATCTACAACCA 5613
                                 i    iv  vivii         vv  ii    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_35408428_3   5614 TCTGACCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5663
                         vi   ii  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_35408428_3   5664 TATTTAATAAACGGTGTTGGGAAAACTGGCCAGCCATATGCAGAAAACTG 5713
                          v  i  i   i    i     v      vi ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_35408428_3   5714 AAACTGGACCCCTTCCTTACACCTTATAGAAAAATTAACTCAAGATGCAT 5763
                           ii         v   i     v    v              i   v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_35408428_3   5764 TAAAGACTTAAGCATAAGACTTAAAACCATAAAAACCCTAGAAGAAGCCC 5813
                         i ?    i   iii     vi      i      vi i        iv v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_35408428_3   5814 TAGGCA-ATACCATTGAGGACACAGGCATGGGCAAAGACTTCATGACTAA 5862
                             ?i- v i v i v iv vii  i- i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT 596

  chrX_35408428_3   5863 AACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5912
                         i    v       vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_35408428_3   5913 TTAAACTAAAGAGCTTCCG-----CAAAAGAAACTATCATCAGAGTGAAC 5957
                          i   v v  i i   ii -----    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_35408428_3   5958 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 6007
                           i     i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_35408428_3   6008 AGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 6057
                         i  i  vi          v  i  i     ivv    v ---   v  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATA 793

  chrX_35408428_3   6058 AAACAAACAAACAATCTCATCAAAAAGTGGGCAAAGGATAAGAACAGGCA 6107
                            - i     i  i iv  i?    i            vv   i  i  
  L1M4_orf2#LINE/    794 AAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_35408428_3   6108 CTTCTCAAAAGAAGATACTTATGTGGCCAATAAGCATATGAGAAGACGCT 6157
                         i     v          ivi vi             i    i    i   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_35408428_3   6158 CATCATCACTGGTCAT 6173
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


2492 26.40 2.73 1.31  chrX_35505662_35511102.rev     3585  4425 (1016)    L1M4_orf2#LINE/L1        1   853 (55)  

  chrX_35505662_3   3585 TGAAAAAGCATTCCATGCTCATGGATAGGAAGGATCAGTATCATTAAAAT 3634
                           i   iii  i     i        v     iv i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35505662_3   3635 GGCCTTACTACCCAAAGCAATTTACAGATTCAAAGCTATTCCCACTAAAC 3684
                            vv    v      vii  i           v  v  i  i ii   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35505662_3   3685 TACCA-CTGACATTCTT-CAAAGAATTAGGAAAAAAT-ATTTTAAAATTC 3731
                          v   -   v v  i  -  i -    --  v  iv -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATT--GACAAGCTGATCCTAAAATTC 147

  chrX_35505662_3   3732 ATATGTTACCAAA---AAAAGAGTTTGAATAGCCAAGGTAATCCTAAGCA 3778
                              v----   ---  ii  viiv          iii    i i iv 
  L1M4_orf2#LINE/    148 ATATGG----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_35505662_3   3779 AAAAGAATAAAGCTGGAGACGTCACACTATCCAACTTCAAATTATACTGC 3828
                          i     i    i     ivv       vi    i      viv    i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_35505662_3   3829 AGGACTACAGTAAACAAAACAGCATGGTACTGGTACAAAAACAGACACAT 3878
                          iii         v   i    ii         i i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_35505662_3   3879 AGACCAATGGAACAGCATAGAGAGTCCAGAAATGAGGCTGAACAGTTAGA 3928
                            i        i  v  v              i iv iiv   v   vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_35505662_3   3929 ACTATCTGATCTTTGACAAGCCTG--AAAACAAG-CAATGGGGAAAAGAT 3975
                         iii vi    i  i      vv  --  i  v v-           ii  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_35505662_3   3976 TCCCTGTTCAATAAATGGTGCTGTGATAACTGGCTAGCCATATGCAGAAA 4025
                         vvi  v     i           v  i      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_35505662_3   4026 AATTAAACTGGACCACTTCATTACATCATATA-AAAAATTAACTCATTAT 4074
                            v  ii      v  v v i   i      -             vv  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_35505662_3   4075 GG-TTAAAGACTTACATGTGAAACCCCAAATAATAAAAACCCTAGAAGAC 4123
                           - i ?    i  v    i i v iv   iv      vi i       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_35505662_3   4124 AACCTAGGCA-ATACCATTCTGGACATAGGAATGGACAAAAATTTTAT-G 4171
                            v    ?i- v i -   vv   v v  iv i i   vii   iv - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_35505662_3   4172 ATGAAGATACCAAAAGTAATTGGAACAAAAGCAAAAAT-TATCAAGTGGT 4220
                           - v  i        i vvv v        v      -v  v  v   -
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG- 640

  chrX_35505662_3   4221 ATATAATTAAA-TGAAAGAGCTTATGCACAACAAAGGAAACTATCAACAG 4269
                          iv v  i   - v   i -   v  ii vv       v        v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_35505662_3   4270 AGTAAACAGACAACCTACAGAATGGGAGAAAATTATTACAAAC--TGCAT 4317
                            i  v        i                 vv  i    i-- ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_35505662_3   4318 CTGACAAAGGTCTAATATCCAGCATCTACAAGAAACT--TA-AATTTA-C 4363
                             i  i  v  vi       v  v  i  ii    --  -  i i -i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_35505662_3   4364 AAAAGAAAAACAAA--ACACCATTAAAATATGGTTAAAGTACATGAATAG 4411
                           v i   i     --  v v   ?   v    vi    v iv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_35505662_3   4412 ACACTTTTCAAAAG 4425
                            i  i  v    
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAG 853

Transitions / transversions = 1.34 (125 / 93)
Gap_init rate = 0.03 (24 / 853), avg. gap size = 1.42 (34 / 24)  


1949 25.88 1.76 1.12  chrX_35525199_35526816.rev      502  1127 (491)    L1M4_orf2#LINE/L1      279   908 (0)  

  chrX_35525199_3    502 TAAAAACAGACACATATACCAATGGAATAAAATAGAGAACCCT----TAA 547
                            ii i     i   v i          i   v    ii  v----   
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_35525199_3    548 ATTCATTTATTTAGAGCCAACTAATTTTCCACAAAGGTGCCCAAAACACA 597
                          ii   vi     vi i   i i      v    i      v i v  iv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_35525199_3    598 CATTGGAGAAATGATAGTTTCTCCAATACATAGGGCTGAAA-AACTGAAT 646
                           v   i    vi     i i i   i v  i v    ii -     i  
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_35525199_3    647 ATCTATATGCAGAAGACATAAA-TTAGACCCCAATATCTCACTGTATAAA 695
                          ? i i     i    -  i  -  i      v iv  v   ii    v 
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGA-ATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_35525199_3    696 AAAATAAACACAAAATGGGTTAAATACTTAAAAGTAAGACCTAAAACTGT 745
                              v   v        i i ? v  i    v      v        i 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_35525199_3    746 GAAACTACTAGAAGAAAATAT-TGTGGAAATGCTTCAGGACATAGGTGTG 794
                         i     vi          i  -v ? v    -    iv   v v  vv i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTA 576

  chrX_35525199_3    795 AGCAAAAAGTTTATGGAGA--ACAC-AAAAGCAAAGGCAAGCAAAGCAAA 841
                         i    viiv  iv i  v --    -       v i    vv    v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_35525199_3    842 AATTGGCAAATGGGATTATATCTAGCTAAAAAACCTCTGCACAGCAATGT 891
                            v ii    v   i vi   v iv v      i i  ii vv   v v
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_35525199_3    892 AAACAATCAAGAAAGTGAAGAGAAAACTTGCAAAATAGGATAAAATATTT 941
                          v  v              i   v   iii  i   i   v         
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_35525199_3    942 GTGAACTATTCATTTAACAAAGGGCTAATATCTAGAATATAAAAGGAATT 991
                          ii  ii  vi  i i i  i  i  vi    i        v  i   i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_35525199_3    992 AAAACAACAGCAAAAA-AACACCAAAAATAAATAATCCAATTTAAAAATG 1040
                         vvv     -v   v  -  ----   i i      i      ?       
  L1M4_orf2#LINE/    777 CTTACAAC-TCAATAATAA----AAAGACAAATAACCCAATTWAAAAATG 821

  chrX_35525199_3   1041 GGCAAATGATCTGAATAGACATTTCTCAAAAGGAGGCATAAAAACAGCCA 1090
                               v   i                v    i  ii   v   ii    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_35525199_3   1091 ATAAGTATAGAAAACAATGCTCAACATCACTAATCAT 1127
                              i i vi   vi             ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (93 / 65)
Gap_init rate = 0.02 (11 / 630), avg. gap size = 1.64 (18 / 11)  


3215 25.17 0.88 0.99  chrX_35534952_35536849.rev      502  1407 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_35534952_3    502 AAAGAGTATTCCATGCCAATGGATTGGAAGAAATAATATTATTAAAATAA 551
                              -   i     iiv             vv       i    i  ii
  L1M4_orf2#LINE/      4 AAAGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_35534952_3    552 CAATACAACCCAAAGACATTTAGAAATTCAATGCAAACCCTATCAAAATA 601
                               vv      vvv  i  v i      i    v            v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_35534952_3    602 CCAACGACATTCTTGACACAAATAGAGAAAAACAATCCTATAACTCATAT 651
                            i vi v  i  vi  v    v  v  iv-ii      v  i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATAT 151

  chrX_35534952_3    652 TGGAACCACAAAAGACCCTGAATAGCCAAAGCAATTATGAGCAAAAAGAG 701
                         -    vii   ii     v           i    iv   iv  i    i
  L1M4_orf2#LINE/    152 -GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_35534952_3    702 CAAAGCTGGAGGCATCACACTACCTGACTTCAAATATAATT-CAAAGCTA 750
                              i      vv       v  ii i      vv v i -        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_35534952_3    751 TAGCAATGATGTAAGTATGGTACTGGCATAAAAATAGACACATAGACCAA 800
                         i  i   v v vv   i              ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_35534952_3    801 TAGAACAGAATGAGGAACCCACATATAAAATCATATATTTACAACCAACT 850
                          i   i     vii  ii   v v     vi    i     iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_35534952_3    851 CTTTCTCAACAAAGGCACCAAGAACATATAACGGGGAAAGGACAATCTCT 900
                         vv  i  i    i  ii      v   vi  i        i i i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_35534952_3    901 TCAATAAATGGTGCTGAGAAAATGGGATATCCATATGCAAAAGAAAAAAA 950
                             i           i  v  iv     ?   i           vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_35534952_3    951 ATAGGTCCCCATTTCTTCACATGTACAAAAAGCAAACCAAAATTGATTAA 1000
                         v i ii   i ii  vivv   i        vi  vi      v   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_35534952_3   1001 AGGCTTAAATCTAAGATCTGAAATTATGAAACTATTAAAAGAGAACAT-- 1048
                           i i     v     v  i   i   i     v   i    i     --
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_35534952_3   1049 -TGCAGATGCTCCAGGATATTGGTCTGGGCAAAGACTTTTTAATATAAGA 1097
                         -? i i  -  i iv  iv    vi i     v ii  i   i-   v  
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-ATATGA 598

  chrX_35534952_3   1098 CCTCAAAAGCATGTGCAACCAAAGCAAAAATACACAAATGAGACTGTATC 1147
                          vi        iiv     v    v       v i    vi    vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_35534952_3   1148 AAGCTATAAAGCTTCTGTGAAGCAAAGGAAATAATGAAAAAAGTGAAGAT 1197
                           iv vv   i   i    vvv       v iv  v  i        i v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_35534952_3   1198 ACAACCCACAGAATGGGAGACAACATTTGCAAACTATCCATCTGACAAGG 1247
                                             v  i         ii  vi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_35534952_3   1248 GATTATTAATCAGAATATATAAGGAGCTCAAACAACTCAATAGCAAAAAG 1297
                           i vv  vi            i  i   vv           ii      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_35534952_3   1298 AAACCTTAATAAACCAATTAAAAAATTGACAAAAAAT----ATAAGCAAT 1343
                          v ----     v      ?      v i    ii  ----   ii  v 
  L1M4_orf2#LINE/    799 ACA----AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_35534952_3   1344 TCTCAAAAGAAGAAATACAAATGGTCAACAGTTATATAAAAAAATGCTTA 1393
                             v        v          i   i ivi i  i    i     i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_35534952_3   1394 ACATCACTAATCAT 1407
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (134 / 90)
Gap_init rate = 0.01 (9 / 905), avg. gap size = 1.89 (17 / 9)  


2416 22.57 8.48 1.92  chrX_35647824_35650836.rev     1095  1825 (1188)    L1M4_orf2#LINE/L1        1   779 (129)  

  chrX_35647824_3   1095 TGAAAAGATATTTTTGTGTTTATGAATTAAGAGACTTAATATT-TTAAGA 1143
                           i        iii-i    i   i   iii            -      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_35647824_3   1144 TG-CAAGTACTACCCAAAGTGATCTTCAGATGCAATGCAATCCTT-TCAA 1191
                           -   -    v      v      v     v   i       i -    
  L1M4_orf2#LINE/     50 TGGCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_35647824_3   1192 AATTCCAATAATGTTTCTTTTTGCA-AAATTAGAAAAAAATCCATCCTAA 1240
                            i   ii--  ii -        -     i--- v  iiiv       
  L1M4_orf2#LINE/     99 AATCCCAGC--TGCCT-TTTTTGCAGAAATTG---ACAAGCTGATCCTAA 142

  chrX_35647824_3   1241 CATACATATGGAATCTCAACAGACTCCAAGTAGACAAAGCAATCTTGAAA 1290
                         v  v         viv   vi   i vi i   v    i           
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_35647824_3   1291 AAGAAGATCAAAATTTGAGGTCTCACACTTCATGATTTCCAAACTTACTA 1340
                                v    i  v    v          vii     v          
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_35647824_3   1341 CAAAGATACACAAAGCAAAACAATGTGGTATTGGCAATATAACAGACATA 1390
                              v    vv  v   i   i       i     vv vi i       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_35647824_3   1391 TATGCCAATGGAATAGAATACAAAGCTTCCA--AATAAATCC-TATTATA 1437
                           vii              vv i  --    --      i  -  i-  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAG--TCCAGAAATAAACCCATAC-ATT 339

  chrX_35647824_3   1438 CAAGATTAAATGGTTTTCAATAAGAGATGTCAAGACAATTCAATAGGGAA 1487
                         i v i i  v  i     i i   i -  i      v       i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGAA 388

  chrX_35647824_3   1488 AGAACAATTTTTTCAACAAATACTGTTGGGAAAATTGGATACCCACA--- 1534
                             i i i            iv  i     v  i      ?     ---
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_35647824_3   1535 -GAAGA-----GTTAGA-----------------AGAGGAGGA------- 1554
                         -i    -----   i  ----------------- v vi ii -------
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_35647824_3   1555 -----GGA-CAAGGA---GAA-GAAGAAGTTGTTGCATCATTA---TCTT 1591
                         -----   -  ?i  ---i  - v ii  i i--iv ii  v ---    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTA--AAACTATAAAACTCTT 536

  chrX_35647824_3   1592 ATAC-----CATA--TATAAAACT--ATGATATGGGATATAGCAATTGTT 1632
                          v v-----    --?i    v  --i   iv v  i vvi     v   
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_35647824_3   1633 TCCTGGATATGACATCAAAAGCACAGGCAACAAAAGAAAAAGTTTATAGG 1682
                           i i         i          i               i vv   ii
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_35647824_3   1683 TTGGGCACCATCAAAAGTAGAAATTTTTGTGCATCAAAGGAAAGTATTAA 1732
                             i vi        v  i   i        v        v v   i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_35647824_3   1733 CAGAGTGAAAAGGCAACCTATGAAATGAGAGAAAACATTTGCAAATTATA 1782
                         v i         i     i iii    i       i          i   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_35647824_3   1783 TATTTGATAAGGATTTAATATACAGAATATATTAAAGATTCCT 1825
                            i        ivi vi   v          v  ii i  i 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

Transitions / transversions = 1.75 (103 / 59)
Gap_init rate = 0.03 (26 / 779), avg. gap size = 2.92 (76 / 26)  

 459 15.50 10.85 2.33  chrX_35647824_35650836.rev     2394  2522 (491)    L1M4_orf2#LINE/L1      769   908 (0)  

  chrX_35647824_3   2394 AAAGTACTCCTACAACTTAACAACAATAACAACACAGATAA--------- 2434
                             v    i       ---   i     v  v   i    ---------
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACT---CAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_35647824_3   2435 -AAATGGGCAAAAGACTTGAATAAACATTTTTCCAAAAA---TATAAAAG 2480
                         -           i  i       i      i      i ---    v  i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_35647824_3   2481 TGGCCTATAAACATATGAAA-GTTGTTTAACAACACTAATCAT 2522
                              v    i  i      - v  i i    v  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.03 (4 / 140), avg. gap size = 4.25 (17 / 4)  


3232 25.91 0.99 0.88  chrX_35682603_35684928.rev      932  1838 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35682603_3    932 TGAAAAAATATTCCATGTTCCTGGATTGGAAGAATCAATATTATTAAAAT 981
                           i   i    i        v            v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35682603_3    982 GTCCATAAGACCCAAAACAATCTGCAGATTCAATGTAATCCCTATCAATA 1031
                          v v   vvv      vii    i         i i            v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35682603_3   1032 TACCAATGACATTCTTCACAGAAACAGAAAAA---ATACTAAAAATTATG 1078
                          v   iivi v  i  ii      iv  v  i---  v      v i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_35682603_3   1079 TGAAACCACAAAAGACCCATAGTAGCCAAAACTATCCTAAGCAAAAAGAA 1128
                           i  vii   ii      v i          v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_35682603_3   1129 GAAAACAGAACAAACCACATTACCTTACTTCAGATTATACTACAGAACTA 1178
                         v   iiv i vi vi    i v  iv i    i viv       i i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_35682603_3   1179 TAGTAACCAAAACAGCATGGTACTGGCATAAAGACAGACACATAGACCAA 1228
                         i     i   i    ii              i  i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_35682603_3   1229 TGGAACAGAAGAGAGAACCCAGAAACAAATCTACATACCTACAGTGAACT 1278
                              i    vv    ii       i   i i i i ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_35682603_3   1279 CATTTTTGACAAGG-TGCCAAGAACATACACTGGGAAAAAGACAATCTCT 1327
                         v     i       -        v   v  v    i   ii i i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_35682603_3   1328 TTAATAAATGGTGCTGGGAAAGCTGAATATCCACATGCAGAAG---GAAA 1374
                          i  i              v i   i   ?         i   ---   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_35682603_3   1375 CCAGCCCCATATATCTCGTCATAAACAAAAATCAAATCAATATGGGTTAA 1424
                         iii v   v  iv  v ii    v        i  v    v    i i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_35682603_3   1425 AAACTTAAATTTAAGACTTCAAACTATAAAACTGCTATTAGAAAGCATTG 1474
                          i  i     v     vi v             vi  vv     i   v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_35682603_3   1475 AGAAAACTCTCCAGGGTACTGTTCTAGGCAAAAACTTTTTGAGTAGTAAG 1524
                         i?iv  v   i iv iivi  vvi       viii  i  iii  - i -
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGA- 598

  chrX_35682603_3   1525 TACCCCACAAGCACA-GCAAGCAAGGCAAAAATTGACAAATAGGATCACA 1573
                         -- v   v       -    vv  i v      v  i    v   iiv  
  L1M4_orf2#LINE/    599 --CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_35682603_3   1574 TTAAG-TTAAAAAGCTTATGTACAGCAAAGGGAACAATCCACAAAGGGAA 1622
                          i  i-       -   v   i vv      iv  v   v v    v   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_35682603_3   1623 GATACAACACACAGCATGGGAGAAAATATTTGCAAACTACCAATCTGACA 1672
                         i v     v     v                     ii ivv      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_35682603_3   1673 TGGGATTAATAACCAGAGTATATAAGGTGCTCAAACAACTCTATAAGAAA 1722
                         v    i vi  v     i       i vi   vv       v    v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_35682603_3   1723 AAAATGTATAATAACCTGATTTAAAAATAGGCAAAATATTTGAATAGACA 1772
                           i ii---       ii   ?      i      iv             
  L1M4_orf2#LINE/    796 AAGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_35682603_3   1773 TTTCTCAAAAGAAGACATACAAATGGCAAACAGGCATATGAAAAGGTGTT 1822
                               v        i           v  i i   i        i  i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_35682603_3   1823 CAATAGTATTGGTCAA 1838
                            i vi ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (141 / 90)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


2379 26.74 3.20 2.87  chrX_35705681_35709477.rev     2402  3306 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35705681_3   2402 TGGAAAGACATAGCACATTCATGTTTGGGGAGAATTACTATAGTAAAGAT 2451
                                 i  vv  ii      vv v  i   v   v   v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35705681_3   2452 GTCTATTTCCCTCAAATTGATCTATAAGCTAAGCTCAATTATTCTCAAAA 2501
                          v v  vii  i            i iii v i v    ivi v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35705681_3   2502 GCCCAGCAAGTTATTTTTTTTTTGCAGGCTCAGA-AAGATTATTCTAAAA 2550
                         v      ------ vii          ivviv  -   v v  i      
  L1M4_orf2#LINE/    101 TCCCAGC------TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_35705681_3   2551 TTTACATGGAAAGGTAGAGATATTTTGA-TAACTAAACTAATGGTGACAA 2599
                           i i       v i -  iv iiiv  -  i i   vi   vv   v  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_35705681_3   2600 AGAAGAATAACACGTGAGGAATTATTCTACATGATATTAAGAATTACTAT 2649
                                i  viivv     v i iv  v vii  v i  i v      i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_35705681_3   2650 ATAGCAAAGGTAATTAAGGTAGCATGATGTTGGCAAACGTATGGATACAC 2699
                          v   v vi     i   ii  ii  i ii     v v v  i  i i i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_35705681_3   2700 AGATGAATGGAAAAAAAATGCAGAACACAGAAATAGACCAATGCAGATTA 2749
                             v       v i  v  -   iiv        i   v  i  v-   
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTG-AGAGTCCAGAAATAAACCCATACAT-TTA 341

  chrX_35705681_3   2750 TGTTGAAGTGATTTTTTTCAAGGGTAC----ACAATTCAATGGAGGAA-A 2794
                           v v  v       ivv       i ----  v         i i  - 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_35705681_3   2795 ATAGCTTTTTCAACAAATTTGGTCAGAGCAATTGAACATCTATAGG--AA 2842
                             ii            vvv iii ii   i  i i ? i i v --  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_35705681_3   2843 ATAATTA----GAACCTCAATGTAAATCACACTTTATACAAAAATTAACT 2888
                          v   v ---- i   i ----  vv      iv                
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCC----TACCTCACACCATATACAAAAATTAACT 487

  chrX_35705681_3   2889 CAAAATATATCATAGACTTAAATGTAAAACTTTAAAAGT-TAAAAAT--- 2934
                               iv    ?    i         i vi -    v -     v ---
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTT 536

  chrX_35705681_3   2935 AGAAGAAAATCT-----TCAACCATTATGATCAAGGATTAGGTAAAGAGT 2979
                                  iv ----- v  i v ii   i vv  i     i  v iv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_35705681_3   2980 TCTTAGACTTAACACTAAAAGCAGTACTAATTAAAGGAAAATT-GATAAA 3028
                                iv i    i       vv vi  iv    i    v -      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_35705681_3   3029 TTGGACATCATTGAACGTTTAAAAAAAAAACCCTTTTGTTCTACAAAATA 3078
                               v    ii  v--       -------       v  v    iv 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAA--TTAAAAA-------CTTTTGTGCTTCAAAGGA 677

  chrX_35705681_3   3079 CCCAGTTAAAAGGATGAAAAGTCAAACCTCAAACTGGGAGAACATATTTG 3128
                          v vi i  i iii       v   v  v  i v        v       
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_35705681_3   3129 CAAGCCACATAACCATCAAAAGACTTGTATCCAGAATATACAAAGAAATT 3178
                            ii  i   v iivi  ii                   i      v i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_35705681_3   3179 GCAAAACTCAATAATAAAGAG-CAATGTAATC--AT---AAAATGAGAAA 3222
                         vi v              i  -   -i   i --  ---      i v  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAA-ATAACCCAATTWAAAAATGGGCAA 826

  chrX_35705681_3   3223 AACACATTAACAGAGATTTCACTAGAGAGGGTACTCAGATGGCAAAGAAG 3272
                          iv iv v  i   v     v i i   i i  iv  i     v  v   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_35705681_3   3273 CACCTGAAAATATGTTGTCAACATCATTATTCAT 3306
                            v      v   i --        ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCT--CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (129 / 111)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.39 (55 / 23)  


2652 23.60 9.65 1.43  chrX_35759541_35766339.rev     5470  6308 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35759541_3   5470 TAGAAAAATATTCTGTGCTCATGAATTGAAAGAATCAATACTGTTAAAAT 5519
                          i    i    i ii  i     i    i    v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35759541_3   5520 GAC---------CAAAGCAATGTACAGATTCAATGCCATTCCTATCACAC 5560
                          i ---------    vii  v           i  v  i       v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35759541_3   5561 TACCA-CTGACATTCTTCACA-AAATTAGAATACT-ATTTTAAAATTCAT 5607
                          v   -   v -  i  ii  -     iiv vi  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_35759541_3   5608 ATGGAACCATAAAAAGAGCCCA-AATAGCCAAGACAATCCTAACCAAAAA 5656
                               --  iv  i ii    -         i      i i vv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_35759541_3   5657 GAACAAACTTGGAGGCATCACATTATCCAACTTCAAACTATACTACAAGA 5706
                                v       vv     i vi    i      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_35759541_3   5707 ATACAGTAATGAAGACAGCTTGGTACTGGTAGAAAAACAGATACATAGAC 5756
                         v         v       iv         i v  ii i   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_35759541_3   5757 CAATGGAACAGACTAGAGAGTCCAGAAATAAAGCCACACATCTACAATGA 5806
                                 i   v v                 v   i    i  iii v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_35759541_3   5807 TCTGATCTTTGACAAAATTGACAAAGACAAGCAATAGGGAAAGGACTCCC 5856
                         vi    i  i     iiv  v   iiv  vv    i       i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_35759541_3   5857 TATTCAACAAATAGTGCTAGGATAATTGGCTAGCCATATGCAGAAAATTG 5906
                          v          i     i   i  i   v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_35759541_3   5907 AAGTTAGACCCTTTCCTTACACAACATACAAAAATCAACTCAAGATGCCT 5956
                              i     i v   i    v i          i       i   vv 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_35759541_3   5957 TACAGATTAAAATGTAAAGCCTAAAACTA-AAAA-TCCTGGAAAATAACC 6004
                         i ?   iiv        iiv         -    -  i i   i v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_35759541_3   6005 TAAG---AAATAGCATTATG-----GAGATAAGCCCTGGCAAAGATTTCA 6046
                           i ---    -- v ii  ----- i v  ------     v i    v
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--CTTCGTGACCTTGGGTTA------GGCAATGGTTTCT 589

  chrX_35759541_3   6047 T-GATGAAGACACCAAAAGCAATTGCAACAAAAATGAAAATTGACAAATG 6095
                          -   - v             vvv         ivi     v  i    v
  L1M4_orf2#LINE/    590 TAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_35759541_3   6096 AGACCTAATTAAACTAAAGAGCTTCTATACAGCAAAATTAACTATCAACA 6145
                         i   i v  i   v v  i i   i i i vv    ivvv        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_35759541_3   6146 GAGTAAAAATACAACCTACAGAATGGGAAAATATATTTTCAAACTACGTA 6195
                         i   i    v      i           i  v      v    ii ii  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_35759541_3   6196 TCTGACAAAAG--------------------------TCT--------AA 6211
                              i  ii --------------------------   --------  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_35759541_3   6212 TA---------------------TTAAAAAATGGGCAAAGGATATGAACA 6240
                           ---------------------  ?                 v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_35759541_3   6241 GACATTTCTCAAAATAAGACATTCATGCAGCCAACAAGCATATAAAAA-- 6288
                                   v   v    i  v  viii     i     i  i    --
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_35759541_3   6289 TTCTCAACATCACTAATCAT 6308
                          v          ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (120 / 75)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 4.89 (93 / 19)  


2683 27.93 0.64 3.84  chrX_35853763_35855942.rev      752  1689 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35853763_3    752 TGGAAAAACATTTTATGCTCATTGATTGGAAGAATCAATATAGTTAAAAT 801
                               i i  iii   i    v          v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35853763_3    802 GGACTTACTGCCCAAAGCAATCTACAGATTCACTGCTATTTCTACCACAT 851
                           vvv    v      vii             vi  v  ii   i  v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35853763_3    852 TACCAA-TGCTATTTTT-CAAAGAATTATAAAAAAAAACTT-TTCTAAAA 898
                          v   i-   iv     -  i -    i----- v  i  v- i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG-----ACAAGCTGATCCTAAAA 144

  chrX_35853763_3    899 TTCATATGTAACCAAAAATAAGCCCAAATAACCGAATGACTCCTGAGCAA 948
                                 v  viiv  ivi v  vi    i  i  vv v  i   ----
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---- 190

  chrX_35853763_3    949 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCTGGAGGCGCT 998
                         ------------------------    i  i  v    i      vvii
  L1M4_orf2#LINE/    191 ------------------------AAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_35853763_3    999 GTATTACCTGACTTCAAACTGTACTATAAGGCTACAGGAACCAAAATTGG 1048
                         ii i v  ii i      viv     i  i       v  i   i iv v
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_35853763_3   1049 ATGGTACTGGTATAAAAACAGACACAAAGACCAACGGAACAGAATAGAGA 1098
                         i         i    ii i     i v   i   i    i     v    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_35853763_3   1099 ATCCAGAAATAAAGCTGTATAGCTACAGCCATCTAATCTTCAACACAGTC 1148
                         i            v ii  i vi  ii i  vi i  i   i   vi vi
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_35853763_3   1149 AACAAAAATAAGCAATGGAGAAAGGATTCTGTATTCAATAAATGATACTA 1198
                         iv   i vi vv      i     i  vv v v     i     i i  i
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_35853763_3   1199 TGATACTTGGCTAGTCATTTGCAGACGATTAAAAGTAGACCCCTAACTTT 1248
                         v  i vi   v  ?i  iv    i v  v i  iv i        v  iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_35853763_3   1249 CACCATATACAAAAATTCACTCAGGATGGATTAAAGATTTAAATATAAAG 1298
                                          v     ii      i ?   ii     i   ii
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_35853763_3   1299 TCCCAATCTATAAGAATTCTAGAGGAAAACCTAGGAATCACCATTCTGGA 1348
                         v iv  v      i v ii    i      v    ?i v viv   vv  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_35853763_3   1349 CATTGGCCTTGGGAAAGAATTTATGTCTAAGTCCTCAAAATCAATTGCAA 1398
                          v    vi v  v  v iv  iv ivv  v v vi     v  vvv    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_35853763_3   1399 CAAAAAGAAAAAAGTGACAAGTGGGAC--CAGTTAAACTAAAGGGCTTCT 1446
                              -       vv  i  i v    --  viv   i    ii-   i 
  L1M4_orf2#LINE/    617 CAAAA-GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTT 664

  chrX_35853763_3   1447 GCACAGCAAAGGAAACTATTAACAGAGTAAACAGACAACCTACAGAATGG 1496
                          ii vv       v     i  v i   i  v        i         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_35853763_3   1497 GAGCAAATATTTGCAAACTATGCATCTGACAAAGGTCTAATATCCATAAC 1546
                            v             ii  ii      i  i  v  vi      v  i
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_35853763_3   1547 CTAGAAGGAACTGAAACAGTTTAAAAGCAAAAA-ACAAATAACCCCATTA 1595
                         v  v  i     vvv   ii i  v ii     -           v   ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_35853763_3   1596 AAAAGTGGGCAAATAACATAAACAGACACTTTTCAAAAGGAGATATATAA 1645
                             i        vi iv i  i     i  i  v    i       i  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_35853763_3   1646 CTGGCCAATGAACATATGAAAAAGTGCTCAACATTACTAAACAT 1689
                         v        i i  i       ii          i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (148 / 110)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 4.20 (42 / 10)  


2538 27.40 2.87 2.54  chrX_35887136_35892767.rev     4237  5141 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35887136_3   4237 TGGAAGAATCATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAA 4286
                              ii  -  i     i        v      v i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_35887136_3   4287 TGACCATATGACCCAAAGCAATTTATACAATCAATGCTATTTCTATAAAA 4336
                           i v   ivv      vii  i  i v v    i  v  ii    v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_35887136_3   4337 CTACCAATGGCATTCTTCACAGAACTAGAAATAACT-ATTTTAAAATTCA 4385
                         v v   iiv  v  i  ii     v v  v - i  -  ii         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chrX_35887136_3   4386 TATGGAACCAAAAAAGATCCCAAATTGCCAAGGCAATCCTAAACAAAAAG 4435
                                viiv  ii  i  vi   v     ii     i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_35887136_3   4436 AACAAAGCTGGAGGCTTCACTGTATCCAACTTCAAA--CTA-TACAAAGG 4482
                                i      vi    vv vi    i      --i  -       -
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG- 247

  chrX_35887136_3   4483 GGCTACAGTAACAAAAAGGGGATG--ACTGGTACAAAAACAGATACATAA 4530
                         --         iv  i vi vi  --     i i  ii i   i i   i
  L1M4_orf2#LINE/    248 --CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_35887136_3   4531 ACCAATGGAACAGAAT--AGAGGTCAGACATAAGGTCGCACACCTACAAC 4578
                          i        i     --    vi    v    ivi ii   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_35887136_3   4579 TATCTAATCTTTGACAAAATTGACAAAAAAAG-CAATGGGGAAAGGACTC 4627
                         i vi i  i  i     iiv  v   i vv v-            i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_35887136_3   4628 CCCATTCAATAAATACTGACAGAATAACTGGCTAACCATATGCAGAAGAT 4677
                         i iv     i    iv  vii i i      v  ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_35887136_3   4678 TGAAACTGGACCCCTTCCTTACACTATATATAAAAATTAATCCAAATTGT 4727
                             ii         v   i    i     i         ii    v  v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_35887136_3   4728 ATTAAAAAGTTAAATGTAAAACCCAAAAGTATAAAAACCCTGGAGGACAA 4777
                           i ? i vi         i v i    v       vi i i  i  v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_35887136_3   4778 CTTTGGCACTACCATTCTTCATG---TAGAAATGAGAAAAAATTTCATGA 4824
                          v v  ?i-  -- v     i  --- v iiv ii v  vii    v ii
  L1M4_orf2#LINE/    546 CATAGGNG-TA--AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_35887136_3   4825 CAAAGACACCAGAAGCAATTGCAACCAAAGAAAAAATTGACAAATGGGAT 4874
                         vv v       i     vvv     v           v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_35887136_3   4875 CT-GTTTAAGCTAATAAGCTTTTGCACAGCAAAAGAAACTACCAACAGAG 4923
                         i -i iv  ii   -  i      ii vv    i  v    i   v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_35887136_3   4924 TAAACGGACAACCTACAGAATGGGAGAAAAGTTTTGCAATCTATGCACCT 4973
                          i  vi       i                vv       vii  ii i  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_35887136_3   4974 GACAAAGGTCTAATATAAGGAATATAAGGTCATCTATAAGGAACTTAAAT 5023
                           i  i  v  vi   vvi       ----------   i     i----
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATA----------TAAAGAACTC---- 777

  chrX_35887136_3   5024 TTACAAGCCAA------AAAGA--AACAACCCA-TTAAAAAGTAGGCAAA 5064
                               vi   ------     --  i      -  ?    i i      
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_35887136_3   5065 GGACATGAACAGACACTTTTC---AAAAGACATACATGCAGCCTAGAAGC 5111
                            iv    i     i  i  --- i    i     viii   v v    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_35887136_3   5112 ATATGAATAAA-GCTTAACATCACTGATCAT 5141
                          i     v i -   i       ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (154 / 90)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.33 (49 / 21)  


2932 26.26 2.57 1.12  chrX_35894777_35899661.rev     3500  4394 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35894777_3   3500 TGGAAAGATATTCCATGTTCATGGGTTGGGGAAATAAATATCTTTTAAAT 3549
                                    i            i    iii v v     iv  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35894777_3   3550 GTCCATACCACCCAAAGCAAACTACAGATTCCATGCAACCCCTATGAAAA 3599
                          v v    iv      vii v          v i    i      v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35894777_3   3600 TACCAAGGGCATTCTCCAAATAAAAAGAAAAAACAATTCTAAAATTTCTA 3649
                          v   ivv  v  i iiiv v   vv  v  ivii  i        iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_35894777_3   3650 ---AAATTTCTAAAAGACCCAGAATAGCCAAAGTTATACTAAACAAAATG 3696
                         ---    vi--  ii                 iiv  vi i  v  i v 
  L1M4_orf2#LINE/    151 TGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_35894777_3   3697 AACAAAACTGGAAGAATCACATTATCTGACTTCAAATTATACTACAGAGC 3746
                               ii    i  v     i vi ii i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_35894777_3   3747 TATAGTAACCAAAATGGCATGGTATTGGCATAAAAACTGACACATAGTCC 3796
                           i     i   i ii ii     i        ii iv    i    vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_35894777_3   3797 AAGGGAACAGAATAGAGAACCCAGAAACAAATCCACATATCTACAGTGAG 3846
                           v    i     v    ii       i   i   i i  i  ii  v i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_35894777_3   3847 CTCATTTTTGAGAAAGGTGTTAAGAAGATACACTGGGGAAAAGAGAGTCT 3896
                         i v     i  v  i    ii    vv  v  v        ii v     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_35894777_3   3897 CTTCAATAAATGGTTCTGAAAAAAGTGGATATCTATATGCAGAAGAATGA 3946
                         i     i       v   ii v  v      ? i i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_35894777_3   3947 AACTTGGACCA--ATCTCTTTTCGTATATAAATATCAAATCAAAATGGAT 3994
                          i-       v-- i   vivi i    i   v  i  v           
  L1M4_orf2#LINE/    449 AG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_35894777_3   3995 TAAAGACTTAAATCTAAGACCTCAAACTATAAAATTACTACAAAAAAACT 4044
                         i ?    i     v     v  v           i vi  v  i     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_35894777_3   4045 TAAGGA-AAACTGTAGAATGCTGATCT-GTGT----CAA-AATTTCTTTA 4087
                           i ?i-   iiv v -----   i  - v  ----   -ii      vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCG-----TGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_35894777_3   4088 TTAATACCCCACAATCACAGGCAACCGAAGCATAA-TGGACAAATAGAAT 4136
                         v  vv  v   v  v    i     vi   v v  - i  i    v i i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_35894777_3   4137 CATATTAAG--TAAAAAAGCTTCTGCACAGCAAAGAAAATAATTCACAAA 4184
                         ivi  i  i--      --   i  ii vv     i v iv  iv v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_35894777_3   4185 GTGAAGAGACAACCCACAGGATGAGAGAAAATGTTTGAAAAATACCCATC 4234
                              i             i   i        i    v   vi ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_35894777_3   4235 TGTTAAGGGATTAATAACCAGAATATATAAGAAGCTCAAACAACTCTATA 4284
                           v       i vi  v             ii i   vv       v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_35894777_3   4285 AGAAAAATG-GAATAATCCAATCAAAAAATGGGCAAAAGGTTTGAATAGG 4333
                          v     vi-i     i     i?             i i         i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_35894777_3   4334 CATTTCTCAAAAGAAAGCATACAAATGGC----AAACA---GAAAATGTG 4376
                                 v      iii           ----  i  ---     vi  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_35894777_3   4377 TTCAATATCATTGATCAT 4394
                         i    i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (140 / 91)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


1722 26.48 13.79 1.97  chrX_35911175_35913256      780  1591 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35911175_3    780 TAGAGAAATATAGCATGCACATGACGTTGGAAAACTAAATGTTGTTA--- 826
                          i  i i    vv    iv    i-i      i   v   i      ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGG-ATTGGAAGACTTAATATTGTTAAGA 49

  chrX_35911175_3    827 -GGCTAT------CAAATTGATCTCTAGATTCAATTCAATTCCAGTGAAA 869
                         -   v  ------           vi        iv    i  vi v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_35911175_3    870 ATACCATC-ACATATTCTTATAGTCAATATCAGTAAGTTGACTCTAAAAT 918
                           v   v -i v -  i  ii  --  -  iiii   i   ii       
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCT-TTTTTGCAG--AA-ATTGACAAGCTGATCCTAAAAT 145

  chrX_35911175_3    919 ATATATATAAAGGCATTG--CCATTAAAATAGCCAAAACAATTTTGAAAA 966
                         vi    iv   v   vv --  --i i               i       
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACC--CAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_35911175_3    967 GG-----------CGGAAGA------------AATTCTGAAACT------ 987
                         i -----------i   i  ------------    iii     ------
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_35911175_3    988 ------ACGATAATTAAGACTGGGTGGTATTGACAAAAGAATAGATGTGT 1031
                         ------  ii    i     v v      i  i  v   i     ii i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_35911175_3   1032 AGATCAAAAGAATAGAATTGAGAGGCAAGGAATATATCTACACAAATATA 1081
                                vi               v v  i    v i i i   vv   i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_35911175_3   1082 ATCAACTGGGTGTTTTTGGTTACAAAAGTGCAAAAGCAATTAAATCAAGT 1131
                         i    i  i---    i ---    ii    v  ii v   v   vii v
  L1M4_orf2#LINE/    344 GTCAATTGA---TTTTCG---ACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_35911175_3   1132 AAGGCTAGTGTTTTCAACAAATATTACTTGAATAATTGGAAGTGCATATG 1181
                            iv    v            iv i  v i i  i    vi?v  i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_35911175_3   1182 TAAAA-AATGAGCATTGG-CCTATACCTCACATCTCGTACTAAAATTATC 1229
                         i    -     i-i    -  iv         i vii   v       v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAA-GTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_35911175_3   1230 TCAAAGTAGATCATAGATCTAAATGTAA-------ACCCACACAACTTTT 1272
                              i i     ?   i          ------- v i i v    i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_35911175_3   1273 ATATACATACATA--TATACA----CGTA---------TATACA-TG--- 1303
                          v viv v     --?i  v ----   i---------  vi  -  ---
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_35911175_3   1304 -------TATA----------CACA--TATC-----------TATTTGTA 1323
                         -------   i----------    --i v -----------  vv iv 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_35911175_3   1324 TTGGACTTTACCATA-TTAAAA---TTTCTGCTTTATGAAAGACTATTAA 1369
                                 i i  v -      ---   v     i viii v     i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_35911175_3   1370 GAGAAAGAAAAGACAAGCTACAGACTGGGGGAAAGTATTTTTGAATAACA 1419
                           i iv          v i     v    i    i     vii   v i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_35911175_3   1420 TATTCCACAAATTTCTTGTATGCAGGATACATAAAGAACTCTCCAAATTC 1469
                            iiv i  ivvv       v   i   i            ivv  i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_35911175_3   1470 AACAACAAGAAAATAAACAACCAAATTTGAAAAATAGTCAAAAGTTCTGA 1519
                           i  i  i  i i   i    v    ?-      i v    i v i   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGA 835

  chrX_35911175_3   1520 AAAGATACATCACCAAAAAAAGATAGAAAGATAGAAAAAAGACATAT-AT 1568
                          v   i iv  v     i  -    v v i  i vv  v ii  i  - v
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAA 884

  chrX_35911175_3   1569 AAGTTGCCCAATA-CAATTACTAT 1591
                            v   i   i -  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (129 / 82)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 4.00 (128 / 32)  


3316 25.99 0.77 0.77  chrX_35948322_35954598.rev     4879  5786 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_35948322_3   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_35948322_3   4929 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_35948322_3   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_35948322_3   5027 TAAGGAACCAAAAAATAGCCCGCATCGCCAAGTCAATCCTGAGCCAAAAG 5076
                           v    viiv  iiv v  v v  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_35948322_3   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATATTACAAGGC 5126
                                i      vv       v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_35948322_3   5127 TACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i     i         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_35948322_3   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAGCT 5224
                                i    i--    i  --        vv   i i  i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_35948322_3   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT--T 5272
                          vi    i  i     ivv  vv  i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_35948322_3   5273 CCTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5322
                          i  -- i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_35948322_3   5323 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5372
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_35948322_3   5373 GATTAAAGACTTAAACGTTAGACCTAAAACCATAACAACCCT-AGAAGAA 5421
                            i ?    i    i  v   v       i    -   i  -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAA 543

  chrX_35948322_3   5422 AACCTAGGCATTACCATTCAGGACACAAGCATGGGCAAGGACTTCATGTC 5471
                            v    ?i v viv   iv   vivi vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_35948322_3   5472 TAAAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATC 5521
                           vi            vvi      i   vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_35948322_3   5522 TAATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5571
                          v  i   v i  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_35948322_3   5572 AACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 5621
                           v  i     i   i             v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_35948322_3   5622 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5671
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_35948322_3   5672 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACGGACAC 5721
                             i     i     v  i?    i           iv    ii    i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_35948322_3   5722 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5771
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_35948322_3   5772 ACCATCACTGGCCAT 5786
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (140 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3258 26.51 0.77 0.88  chrX_36007635_36014039.rev     5006  5914 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36007635_3   5006 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5055
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36007635_3   5056 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5105
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36007635_3   5106 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 5152
                          v   i-       i  -i     -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chrX_36007635_3   5153 AATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAA 5202
                         v        viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_36007635_3   5203 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATATTACAAG 5252
                                  i      vv       v  ii i      viv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_36007635_3   5253 GCTACAGTAACTAAAACAGCATGGTACTGGTACCAAAACAGAGATATTGA 5302
                                   ii  i    ii         i iv ii i   v    v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_36007635_3   5303 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGTCGCATATCTACAA 5350
                                  i    i--    i  --        vvi ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_36007635_3   5351 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT- 5399
                         ii vi    i  i     ivv  vv  i v  vv            i  -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_36007635_3   5400 -TCCTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 5448
                         -  i  -- i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    395 GTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_36007635_3   5449 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 5498
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_36007635_3   5499 TGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGA 5548
                              i ?    i    i  v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_36007635_3   5549 AAACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGT 5598
                             v    ?i v viv   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_36007635_3   5599 CTAAAACACCAGAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5648
                         v  vi      i     vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_36007635_3   5649 CTAATTAAGCTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5698
                         i v  i  iv i  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_36007635_3   5699 GAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCAGCTG 5748
                            v  i     i   i             v       vii ivi v   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_36007635_3   5749 ACAAAGGGCTAATATCCAGATTCTACAATGAACTCAAACAAATTTACAAG 5798
                          i  i  i  vi        v v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_36007635_3   5799 AAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACGTGAACAGACA 5848
                              i     i     v  i?    i    ii     iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_36007635_3   5849 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 5898
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_36007635_3   5899 CATCATCACTGGCCAT 5914
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


1713 27.84 3.29 2.10  chrX_36020599_36024594     2836  3503 (493)    L1M4_orf2#LINE/L1      233   908 (0)  

  chrX_36020599_3   2836 AAACACGCTCTAAGGGTACAGTAACCAACACAGCATAGTACTGATGCAAA 2885
                             vii  vi  i v        i   v    ii i      iiii  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_36020599_3   2886 AACAAACACATAGACCAATGGAACAGAGTAGAAAACCCAGAAATAAAGCC 2935
                         i i i   i     i        i   i v  i ii           v  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_36020599_3   2936 ACACACCTACGATCATCTGATCTTCAAAAAACCCTACAAAAACAAGCAAT 2985
                          i   ii  i i   vi    i   i v  ivvivv   i v  vv    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_36020599_3   2986 AGTAAAAGGACTTCCTATTCAATAAATGGTGCTGAGATAACTGTCTATCC 3035
                         i vi    i ivvi  v     i           i  i     vv  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_36020599_3   3036 ATATGCAGAAGAATGAAACTGGATCCCTATCTTTCACTGTATACAAAAAT 3085
                          i     i         ii    i     i  iv   ii           
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_36020599_3   3086 TAACTCAAGATTGATGAACAATTTAAAGGTAGGACCTCAAACTATTAAAA 3135
                                 i  v   v ?vi ii    v   i  v  v       v   v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_36020599_3   3136 TCCTGGATTT---TATTAGCTTGAGCACCTTTCTCAACATCAGCCTTGGC 3182
                           i i  vvv---i  vi ?v i -- i   iv -i  v ii vi v   
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAA--ATCTTCGT-GACCTTGGGTTAGGC 579

  chrX_36020599_3   3183 AAGGA------AATTATGACTAAGTACCCAAAAGTA-AATTGCAACAAAT 3225
                           v i------ iv      -----   -     i -  --        v
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGAC-----ACC-AAAAGCACAA--GCAACAAAA 621

  chrX_36020599_3   3226 CAAAAATTTTATTAA--GGATCTAATTAAA-TTAAAGAGTATCTGCATAG 3272
                         v     v vv  v  --   ii v  i   -     i v - i  iiivv
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT-TTTGTGCTT 670

  chrX_36020599_3   3273 CAAAATAAATTATCAACAAAAC--AAAGACATCCTACAGAATGGTAGAAA 3320
                             iv v i      v   ii--       v  i         v     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_36020599_3   3321 ATATTCACAATCTGTTCATCCAACAAAGGTCTAAAACCCAGAATCTATAA 3370
                              ii   viii vi   ii i  i  v  viv i       v     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_36020599_3   3371 GGAACTT----AAATCAGCAAGCTTAAAAGA--AATAAGCCTGTT-AAAA 3413
                         i     i----  v   ii  -- v      --     v  vi  -    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAA--TAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_36020599_3   3414 ATTTGCACAGGACGTGAATAAACCCTTCTGAAAAGAAGACATACAAATGT 3463
                           vv   v    iv      i  vi    vv        i         v
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_36020599_3   3464 CCAACAAACATATGAAAAAATGCTCATCATCACTAATCAT 3503
                             i  i  i       i       v     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (108 / 75)
Gap_init rate = 0.02 (16 / 676), avg. gap size = 2.25 (36 / 16)  


3183 23.74 0.52 5.54  chrX_36227617_36230359     1308  2263 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36227617_3   1308 TGGAAAAATATTCCATGTGCATGGATTGAAAGAATCAATATTATTAAAAT 1357
                               i    i      v         i    v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36227617_3   1358 GCCCATACTATCCAAAGCAATCTACAGATTCAATGCAATATCTATCAAAA 1407
                          v v     vi     vii              i     vi         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36227617_3   1408 TACCAATGACATTCTCCACAGAAATAGA-AAACAGAATCTTAAAATTTAT 1456
                          v   iivi v  i iii       v  -  i v  -  i       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_36227617_3   1457 ATGGAACCGGAAAAGACACAGACTAGTCAAAGGAAAGTATACTTAGTACA 1506
                               vi v  ii   v    v   i    -------------------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAA------------------- 180

  chrX_36227617_3   1507 CAAAGTATACAAACTATACAAAGCTTATGCTAAGCAAAAATAATGAAACT 1556
                         --------    v  --------------- i iv  i  v  ii  ii 
  L1M4_orf2#LINE/    181 --------ACAATCT---------------TGAAAAAGAAGAACAAAGTT 207

  chrX_36227617_3   1557 GGAGGAATTACATTAACTAACTTCAAATTATACTATAGAGATATAGTAAC 1606
                               v i   i vv i  i      viv     i i  v  i     i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_36227617_3   1607 CAAAACAGCATGGTACTGGCATAAT-ACAGAGACATAGATCAATGGAGCA 1655
                            i    ii              v- i   v i             ii 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_36227617_3   1656 GAATAGAAAATCCAGAAACAAATCCACACACCTTCAGTGAACTCATTTTT 1705
                             v  i i        i   i   i   ii vii  v  i v     i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_36227617_3   1706 GACAAACCTACTATGGACATGCACCGGGGAACATACAGTCTCTTCAATAA 1755
                              ivv i i v iv   v  vi      viv i     i     i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_36227617_3   1756 ATGGTGCTGGGAAAACTGGATATCTATATGCAGAAGAATGAAACTAGGCC 1805
                                     v         ? i i     i         ii i i  
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_36227617_3   1806 TCTATCTCTCACCATGTACAAAATTCAAATCAAAATGTATTAAAGACTTA 1855
                         i   i   v      i       v i  v        v  i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_36227617_3   1856 AATCTATGACCTCAAACTATGAAACAACTATGAGAAAACATCAGGG-AAA 1904
                            v  v  v  v       i    vvi  vi         vi ? -   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_36227617_3   1905 TCTCCAGAACATTGGTCTGGGAAAAAAAATTCTTGAGCAATATCCCAGAA 1954
                            i ivi  v    vi i  v  viiv-     iiii vv iv   i  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATATGACACCAAAA 606

  chrX_36227617_3   1955 GCACAGGCAACCAAAACAAATATGGACAAATGGAATCACATCAAGCTAAA 2004
                              i     v   iv   v  i  i    v i iiv      iv v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_36227617_3   2005 AAACTTCTGCAAAGCAAAGGATACAATCAAGAAAGTGAAGAGATAACCCA 2054
                               i  iivvv       i  v              i   i      
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_36227617_3   2055 CAGAATGAGAGAAAATATTTGCAAACTACACATCTGACAAGGGATTAATA 2104
                                i                 ii i i      i      i vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_36227617_3   2105 ACCAGAATATATTAGGAGCTTAAACAACTCTACAGGAATAAAATGTAATA 2154
                         v           v i  i  ivv       v i iv  v  i ii-    
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA-AATA 805

  chrX_36227617_3   2155 ACCTAAT--AAAAATGGGCAAAAAATTTGAATAGACATTTGTCAAAAGAA 2202
                            i   --             ii                v  v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_36227617_3   2203 GACATATAAATGGCAAACAGACATACAAAAAAGTGCTCAAAAATTGATCA 2252
                           i   i       v  i ii  i ii    ii       --------  
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA--------CA 897

  chrX_36227617_3   2253 TCAAAGAAATG 2263
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.70 (141 / 83)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 5.80 (58 / 10)  


2510 26.92 4.81 0.80  chrX_36232746_36237972     3864  4736 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36232746_3   3864 TGGAAAAACATTCCATGCTCGTGAATTGGAAAAACCAATACAGCTAAAAT 3913
                               i i  i     i  i  i       i vii    iv i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36232746_3   3914 AACCATTCTGCTCAAAGCAATCTACAGATTCA-TGCAACTCCCATCAAAT 3962
                         ii v  v  v i    vii             -i    ii  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36232746_3   3963 TACCAA-TGCCATTCTTCACATAA--TGCTAAAAAATAATTCTAAATATC 4009
                          v   i-    -  i  ii  v  --  -- v  iv i  i     vv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_36232746_3   4010 AAACCAAAA---AAGAG-CCCA-AATAGCCAAAGCAATCCTAAGCGAAAA 4054
                          v ivi   ---   i -    -          i     i i ivi i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_36232746_3   4055 CAATAAAGTCAGAGACATCCCATTACCTGACTTCAAACTGTACTACAAGG 4104
                         v  i     ii   ivv  v  i v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_36232746_3   4105 CTATAGGAACCAAAACCGAATAA----GGTACAAAAACCAATACATAGAT 4150
                            i  v  i   i  v vi ii----  i i  ii ivi i i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_36232746_3   4151 AAATGAAACAGAATAAAGAACCCAGAAATAAAGCCACACACCCACAGCCA 4200
                         v    i  i     vi   ii           v   i   iii ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_36232746_3   4201 ACTGATCTTTGACAAAGTCAACAAAAATGTACAATAGGGAAAGGAAACCC 4250
                          i    i  i     i viiv   i vii v    i       i v vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_36232746_3   4251 TTTTCAAAAAATGGTGCCGGGATAACTAGCTAGCTATATACAGAAGGATG 4300
                                v         i    i    i v  ? i i  i  i   i   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_36232746_3   4301 AAACTGGACCTCTACCTCTCACCATATACAGAAAGTAACTCAAGATGAAT 4350
                           ii      i       v           i   v        i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_36232746_3   4351 GAAAGACATAAATATGAGACCATAAACT-CAGAA-TCCTAGAAGAAAACC 4398
                         v ?    v     i i   v vv     -i i  -  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_36232746_3   4399 TAGGA--AAATTCTCATGGACATTGGTTTAAGCAAATAATTTAT--GACT 4444
                             ?--    ii  i  -  v    v   i    - ii   v --  - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAA-TGGTTTCTTAGA-T 594

  chrX_36232746_3   4445 AAGACCCCAAATGCAAATGCAACAAAAATAAAATTTGAGAAATGAGACC- 4493
                          v   v     v   v v         iv    v v  v    vi   i-
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_36232746_3   4494 CACTTAAACTAAAGAGCTCTGCACAGCAAAAGAAACAATGAACAGAGT-A 4542
                           iiv   i    i vi i  ii vv    i  v  v  v  v i   - 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_36232746_3   4543 ATAGATAACCTATAGAATAGGAGGAAATATTTGCAAACTATGTGTCTGAC 4592
                          v   i    i i     i    i             ii  i i     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_36232746_3   4593 ATAGGAATAATGCCTAGAATACATGAAGAACT--TA---------AATAA 4631
                          vi   v vi ii i      i  i       --  ---------     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_36232746_3   4632 ACAAAAAAAAAAACCACATTAAAAAGTGGGCAAAGGAC----ATGGACAC 4677
                          v i v   v  v   -   ?    i           i----  i    i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_36232746_3   4678 TTTTT-AAATAAGACATATAAGTAGCCAACAAACA----AAAAG-TGCTC 4721
                           i i-   v    i   i  i i     i  i  ----     -     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_36232746_3   4722 AACATTGCTAATTAT 4736
                              ii????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (155 / 76)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 1.96 (49 / 25)  


3213 27.75 0.44 0.44  chrX_36243186_36249142.rev     4559  5466 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36243186_3   4559 TGGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4608
                              ii i  ii    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36243186_3   4609 GGTCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4658
                           iv     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36243186_3   4659 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4706
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_36243186_3   4707 TATGGAACCGAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 4756
                                vi v  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_36243186_3   4757 AACAAAGCTGAAGGCATCACACTACCTGGCTTCAAACTATACTACAAGGC 4806
                                i  i   vv       v  iiii      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_36243186_3   4807 TACAGTAACTAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4856
                                 ii  i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_36243186_3   4857 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACTGCATATCTACAACT 4904
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_36243186_3   4905 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4954
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_36243186_3   4955 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5004
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_36243186_3   5005 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5054
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_36243186_3   5055 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAAC 5104
                          i ?    i    i  v   v       i      vi i   i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_36243186_3   5105 CTAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAA 5154
                         v    ?i v viv   iv   v v  vv i i   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_36243186_3   5155 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5204
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_36243186_3   5205 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5254
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_36243186_3   5255 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5304
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_36243186_3   5305 ATGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5354
                         iv i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_36243186_3   5355 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5404
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_36243186_3   5405 TCAGAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5454
                           vi       i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_36243186_3   5455 ATCACTGGCCAT 5466
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (154 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 348 18.42 0.00 0.00  chrX_36272192_36273992.rev      410   485 (1316)  C L1M4_orf2#LINE/L1   (0)   908   833  

C chrX_36272192_3    485 TGAACAGACACTTTTCAAAAGAAGACATAAATGTGGTCAACAAGCATATG 436
                             i     i  i  v        i   v vi   i   i     i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

C chrX_36272192_3    435 AATAAAAGCTCAACATCACTGATCAT 410
                           v i v           ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.00 (0 / 0)  

2699 24.57 4.07 1.60  chrX_36272192_36273992.rev      502  1311 (490)    L1M4_orf2#LINE/L1       79   908 (0)  

  chrX_36272192_3    502 TTCAAAG-AACTCCTATTAAAATACCAA-TGTCATTTTTCACAGAAATAG 549
                              v -  ii     i     v   i-  i -     ii       v 
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTG 127

  chrX_36272192_3    550 AAAAAA-AATGCTAAAATTCGTATGAAAACTCAAGACACT-GGAA-AGTC 596
                          v  iv-i  v         i    i   iv    iv  i-i   -  i 
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chrX_36272192_3    597 AAAATGGTTTTGAAAA----TAACAAAGTGGTAGGTCTCACACTTCCTAA 642
                             iii i       ----v        v v   v           i  
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_36272192_3    643 TTTCAAAACATACTACAAAACAGTAATTATTAAGATAGTATGTTACTGGC 692
                                  v         i vii i v  i    i   i  v       
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_36272192_3    693 ATAAATGTAGATGTATAAATTAATCAAATAGAACAAAGAGTCCAGAGATA 742
                             ivi    ii    i  i   vi       ivi          i   
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_36272192_3    743 AATCT------------TCAAATGATGTTTCAACA-GTGTGCCCAGATTA 779
                           i i------------    v    -    i   - v     v   ii 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGAT-TTTCGACAAGGGTGCCAAGACCA 376

  chrX_36272192_3    780 CACAGTAGGGAAAGGCCTGTCTCTTCAACAAATGGTATTGAGAAAAC--A 827
                         iv  i i       iviv    i             ii  i  v   --i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_36272192_3    828 ATATTCAGAAG-AAAAAAATGTAGTTGGACCCTTATTT-ACATCACATAC 875
                            ?i  v v -    i    v          i  ii -   i  i    
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_36272192_3    876 AAAA-CTAATTTAAAATGAACTAAATACTGAAATGTAAGAATTGAATTAA 924
                             -i   i i      i ii ? v  iv          ii -----  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-----AA 521

  chrX_36272192_3    925 AACTATAACATTTGTAGAATCGAACATATGGTAAAATCTTCAGGACATTA 974
                                 v i iv     vvi      v ?vv        iv   v  i
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chrX_36272192_3    975 AATTTGGCAATGATTTATTGGATATGACACCAAAGGCATAGGCAA---AA 1021
                         ii  v       i   v  i              i   i i    ---  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_36272192_3   1022 TATTTTTTTAAATAGCCAAATAAGAATGCAACAAACTTAAACATTTCTGC 1071
                         v vv-----      vi    vi  v v  v    v     v i  i  i
  L1M4_orf2#LINE/    622 GAAA-----AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_36272192_3   1072 ACAGCAAAGGAAACAATGGACATGGTGGGAAGAAAACTTACATAGAGGAA 1121
                         i vv       v  v  vi v vi   ii    v   ii   v iv  i 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_36272192_3   1122 TAAGATACTTGCAAATTACATATGTGATAAAAGGTTGACATCCAGAATAT 1171
                         v  i   i        i i    v      ii ii vii           
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_36272192_3   1172 ATAAGGAAGTCCTATACTTCAATAGCAACAAAACAACTTGATT--ATTTT 1219
                             i   v  i  i vi      ii  v  i    v -i ii--   ?v
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT-AACCCAATTWA 815

  chrX_36272192_3   1220 CAAATGAGCAAAGGATTGAAATAGTCATTTCTCCAAAGAACATGTACAAA 1269
                         v     i          vi     v               v  i      
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_36272192_3   1270 TGGC-AATAAGCATATGAAAAGATGCTCGACATCCCTCATCAT 1311
                             -        i              i     v????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (120 / 75)
Gap_init rate = 0.02 (20 / 830), avg. gap size = 2.30 (46 / 20)  


2068 24.56 4.73 1.33  chrX_36274477_36276143      500  1175 (492)    L1M4_orf2#LINE/L1      210   908 (0)  

  chrX_36274477_3    500 AGGCATCACATTATCTGACATCAAATTATACTTCAAGACTATAGTAACCA 549
                            vv     i vi ii iv     viv    v   ii   i     i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_36274477_3    550 AGGCAGCATGGCACTGGTATAAAAATAGACACATAGAACAATGAAACAGA 599
                           i   ii   i     i    ii       i     v     i  i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_36274477_3    600 AGAGAGAACCCAGAAACGAAGCCACATACCTACAACCAGCTGATCATTGA 649
                          vv    ii       ii  v   i i ii  iiii  ii    iv i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_36274477_3    650 -AATAGT--CAATGAAAATATACACTGGGCAAATGAGAACCTACATAATA 696
                         -  vi  --   ---i vi  v  v    v   vi v ii  vivi  i 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAA---GACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_36274477_3    697 AATGGTGCTGGGAAAATTAGATAGCCATATGCAAAAGAAAGAAA---GAC 743
                                      v  i i    ?   i           v   i---   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_36274477_3    744 TCCTACCTCTCACCATATAGAAATATTAACTCAAGGTGGATTAAAAACCT 793
                         i        v         v   v          ii     i ? i    
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_36274477_3    794 -----------C--AAACTATAAAAATTCTAGAAGAAAACCTAGGATGGA 830
                         ----------- --           v ii           v    ?vvi 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_36274477_3    831 CTCTTTTGGACATTGGCCTAGGGAAAGAATTTAT-GATCAAGTCCTCAAA 879
                         v    ivv   v    vi    v  v iv  iv -   - v v vi    
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAA 605

  chrX_36274477_3    880 AACA-AATTTGCAACAAAACCAAAAATAGATAAAATGGGACTTAATTAAA 928
                          i  -  ---         vv             - v      v  i   
  L1M4_orf2#LINE/    606 AGCACAA---GCAACAAAAGAAAAAATAGATAAA-TTGGACTTCATCAAA 651

  chrX_36274477_3    929 CTAAAGAGCTTCTGTACTGCAAAAGA-ACAATCAACAGAGTAAACAGATA 977
                         v v  i i   i   i  v    i  -  v     v i   i  v   i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_36274477_3    978 ACCTAGAGAATAGGAGAAAATATTTG-AAATCTATGCATCTGACAAAAGG 1026
                            i v     i              -     -  ii      i  ii i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGGGA 750

  chrX_36274477_3   1027 CTAATATCCCGAATCTACAAGGAACTCATACATCTCAACAAGAAAAAAA- 1075
                           vi     v    v  i  i      v    v     i  v     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_36274477_3   1076 -----ACTCCATTAAAAAATGGGCAAATGACATGAACAGACATTTTTCAA 1120
                         -----  i v   ?             v  iv    i        i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_36274477_3   1121 AAGGAAATAAACAAGTTGCCAACAA--ACATAAAAAAAAG-TCAACATCT 1167
                            i i   v    i v     i  --    i    i v -        v
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_36274477_3   1168 CTAAATAT 1175
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.42 (95 / 67)
Gap_init rate = 0.02 (17 / 699), avg. gap size = 2.41 (41 / 17)  


2847 21.02 13.93 1.24  chrX_36298921_36300759.rev      545  1348 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_36298921_3    545 GAAAGAT-TTTCATGTTGATGGATTGGAAGAC--AATATTCTTAAAATGA 591
                                - ii      v              --      v    i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_36298921_3    592 CCATATTGCCCAAAGTCTTCTATAGATTAAATGTAACCTCTATCAAAATT 641
                          v   i v      v vv    i     v  i i  i i          i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_36298921_3    642 TCAATGGCATTTTTTTGCA-AAATAGAGAAA--AATCCTAAAATTCATAT 688
                         i  iiv  -i         -    v  v  i--i                
  L1M4_orf2#LINE/    103 CCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_36298921_3    689 GCTATCTCAAAAGGCCTTAAATAGCCAAAACAATATTGAAAAATAAAAAC 738
                          vv viv   ii i  ivi               v        v  i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_36298921_3    739 AATGTTGGAGGTCTCACACTTCCTGATT-CAAAATATTTTGCAAAGCTAC 787
                           v        v           ii   -     iv vi i         
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_36298921_3    788 AGTAATCAAAACAGTATGGTACTCATATGAAGACCTACATATAGATGAAT 837
                                  i     i       vii  i i  ivv          v   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_36298921_3    838 GAAACAGAATAGAGAGCCTAGAAATCAACCCTGGCATATATGGTCAAATA 887
                          i  i     v     i i      v     vvi   v         v i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_36298921_3    888 ATCTTAGCACAAGGGTGTCAAGCCTACAAAAGGGGAAAACAATAGTTTCT 937
                           i  v -         i    v i ivv  v   i   v      i i 
  L1M4_orf2#LINE/    352 ATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_36298921_3    938 TCAATAAATGATGATTGAA-AACAGAATATCCATATGC-------CGAA- 978
                             i     i  v v i -   v i   ?   i    -------i   -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_36298921_3    979 -TGG---------------------------------------------- 981
                         -   ----------------------------------------------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_36298921_3    982 --------------------------TAAACCTTTTAGAATAAAACCTAG 1005
                         --------------------------    v  i      v     v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_36298921_3   1006 GGGAAAAGCTTCATGACTTTGGATTTAGCAATGATTTCTTGGATATGACA 1055
                          ? v   v    i    i    i  vi      i      i         
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_36298921_3   1056 CCAAAAGCATAGGCCAAGAAAAAAAAAAAGCAAAAATAGGCAAATGAGAC 1105
                                  i i  --------  v     v        ii    vi   
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGC--------AACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_36298921_3   1106 TATGTTAAATTTCAA---TTTTACATAGCAAAGGAAACAATCAACACTGT 1152
                          vii i   v  v  ---    iiiivv       v  v     v vv  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_36298921_3   1153 GAAAATGCAACCTACAGAATGGGACAAAATATTTGCAAAC--TACATTTG 1200
                              vi     i           v              i--  i  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_36298921_3   1201 ACAAAGGATTAATATCTAGAATATA-------------CAACTTGACAAG 1237
                          i  i   i vi    i        -------------     ii i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_36298921_3   1238 GAAAAAA-AAA----CTAATTTAAAAATGATCAAAAGACTTGAATAGGCA 1282
                         i    i -   ---- i    ?       iv    i  i        i  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_36298921_3   1283 TTTCTCCAAAGAAGATATACAAATTGCCAAGAAGCACATTAAAAGATGTT 1332
                                                 v     v        v        i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_36298921_3   1333 TAGCACCACTAATTAT 1348
                         i i  i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (98 / 68)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 7.18 (122 / 17)  


2244 25.06 9.46 2.13  chrX_36309726_36312802.rev     1741  2586 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36309726_3   1741 TGGAAATTCATCCCATGCTCATGGATTGGAAGAATCAATATCTCGAAAAT 1790
                               vvi        i               v i     iviv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36309726_3   1791 CATCATACTTTTCAAAGCAATCTACAGATTTAATGTAATTCATATCAAAA 1840
                         viiv     iii    vii           i  i i   i v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36309726_3   1841 TACCAATAACATTTTTCACAGAA-TT----AG------------------ 1867
                          v   iivi v     ii     -  ----  ------------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_36309726_3   1868 ---------AAGAAAC----AATCACCAAAGCAATTCTAAACAAATAGGA 1904
                         ---------   ii  ----   vi     i    ii i  v  iv  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_36309726_3   1905 CAAATCTGGAGGCATCACACTACCAGACTTCAAATTATACTACAACACAA 1954
                             vi      vv       v  vi i      viv        vi v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_36309726_3   1955 TAGTTACCAAAACACCATGGAAATGGTATAAAAGTAGAC--------CCG 1996
                         i   v i   i   vii   v v   i    iii     -------- vi
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_36309726_3   1997 TAAAACAGAATAGAGAGCCCCAAAATTAAATTAAATATTTACAATCAACT 2046
                          ii  i     v     i  vi    v  vii v i     iii    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_36309726_3   2047 GATCTTTGAGAAATCATAC-AAAATCATAAACTGGAGAGAGGACACGATA 2095
                            i  i  v  iv-i i -  i i   vv v   i  i  i i vvv v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_36309726_3   2096 TTCAATAAATGGTGTTTGTAAAACTGGATAGTCACAGGTTGAAGAGTGAA 2145
                              i        i v v v         ?i    v ivi    i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_36309726_3   2146 ATTGGATCTGTATCTCACACCATATGCAAAAATCAACTCAAGATAGATCA 2195
                         i     i iv  i            i       i       i  i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_36309726_3   2196 AAGACTTAAATCTAAAACCTAAAACCGTACAAATTCT-AGAAGAAACCCT 2244
                         ?    i     v   i v       ii  -   i   -        v v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACAT 548

  chrX_36309726_3   2245 AGGAA-AAACCCT-GTGGACATTGGTTTAGGTATAGAATTTACGACTTAG 2292
                            ?i-   i i -   -  v    v     i - vii   ----     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCA-ATGGTTT----CTTAG 592

  chrX_36309726_3   2293 A-GT----CCAAAAACAAAAGCCACAAAATTAAAA-TAATTAAACTG--- 2333
                          -i ----      i  v    v      vv    -  iv    i  ---
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_36309726_3   2334 ------------AAAAGCTTCCACACAGCAAAAGAAATAATCAACAGAGC 2371
                         ------------    i   iiiii vv    i  v iv     v i  i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_36309726_3   2372 AAACAGACAACCCACAAAATGGGAGAAAATATTTGCAAAGTATGTATCCA 2421
                         i  v            i                      vi  i    ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_36309726_3   2422 ACAAAGGACTAATATCTAGAATCTAAAAGGAACTCA-ACAA---AATTAG 2467
                          i  i     vi    i     v  v  i      v-    ---   ---
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT--- 789

  chrX_36309726_3   2468 AATGAAAAAAACAAAAAATCTG-TCAAAAATTAGGCAAATGAC----ATA 2512
                            -     i     v  i ii- i?    v i      v  i----   
  L1M4_orf2#LINE/    790 AAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_36309726_3   2513 AACATTTCTCAAAAGAAGATATACAAACACAAATGTCCAACAAACATATA 2562
                         i         v                ------  v    i  i  i  i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAA------TGGCCAATAAGCACATG 882

  chrX_36309726_3   2563 AAAA--TGCTCAACATCACTAATCAT 2586
                             --            ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (131 / 77)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.77 (98 / 26)  


2235 24.56 1.44 0.64  chrX_36325624_36327240.rev      504  1126 (491)    L1M4_orf2#LINE/L1      281   908 (0)  

  chrX_36325624_3    504 AAAACAGAGATATAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAA 551
                          ii i   v       i        i    i--    i  --        
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAA 328

  chrX_36325624_3    552 TACCACACATCTACAACCATCTGATCTTTGACAAACCTGACAAAAACAAG 601
                         vv   i    i  iiii  vi    i  i     ivv  v   i v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_36325624_3    602 AAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGAT 651
                         v           i  vvi  v  i  i              v        
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_36325624_3    652 AGCCATATGCAGAAAACTGAAACTGGATCCCTTCCTTACACCTTATACAA 701
                          ?   i     i  i v    ii    i    v   i     v       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_36325624_3    702 AAATTAATTCAAGATGGATTAAAAACTTAAATGTTAGACCTAAAACCATA 751
                                i    i      i ? i  i       v   v       i   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_36325624_3    752 AAAACTCT-AGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATG 799
                            -    -          v    ?i- v i -   iv   v v  vv i
  L1M4_orf2#LINE/    529 AAA-CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTA 576

  chrX_36325624_3    800 GGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAA 849
                              v ii   v ivv  vi            vvi           v  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_36325624_3    850 AATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAG 899
                            v  i    v   ii v  i   v v  i i   i  ii vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_36325624_3    900 AAACTACCATCAGAGTGAACCGGCAACCTACAGAATGGGAGAAAATTTTT 949
                          v    i  vv i      vv i     i                 v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_36325624_3    950 GCAATCTACCTATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACT 999
                             vii iv       i  i  i  vi          v  i  v     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_36325624_3   1000 CAAACAAATTTGCAAGAAAAAAACAA----CCTCATCAAAAAATGG-CGA 1044
                          vv    v ivii  v     i    ----  iv  i?        - i 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_36325624_3   1045 AGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGA 1094
                             iv    i     i     v        i  vi viii     i ii
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_36325624_3   1095 CACATGAAAAAATGCTCATCATCACTGGCCAT 1126
                                   i       v     ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (85 / 64)
Gap_init rate = 0.01 (8 / 628), avg. gap size = 1.62 (13 / 8)  


1947 26.04 2.16 1.00  chrX_36337196_36339117.rev      829  1431 (491)    L1M4_orf2#LINE/L1      299   908 (0)  

  chrX_36337196_3    829 AATGAAACAGAATATAGAGATAAAAAATAAACTCACACATGTGCAGTCAA 878
                             i  i     vv    viv i        i  i    v iii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_36337196_3    879 GTTATCTTTGACAAGGACACCAAGAATACACAATGGACAAAGGATAGTCT 928
                         v v  i  i       iii      vi iv      iv    i       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_36337196_3    929 GTTAAATAAATGGTAG-GGAAAAACTACATATTCACCTACAAAAATAATA 977
                         v  v  i       iv-  i v    iv   ?i   v i     i-   i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AATG 447

  chrX_36337196_3    978 AA-CTGGACACTTACTTTAAACTACATATAAAAAATAACTAGAAATGGA- 1025
                           -i     v i   i i v  i i   i     v     vi       -
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_36337196_3   1026 ----GGTTTAAATATAAGACCTGAAACTA---AACGTCCTAGAAGAAAAT 1068
                         ---- iii     i     v  i      ---   -  i          i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAAC 546

  chrX_36337196_3   1069 ATAGAGAAAAATCTCCCTGTTATTGG-TCATGGCAATGAATTTTCAC-TA 1116
                             i?iv      i v  viv    - i -       iv  i i v-  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATA 595

  chrX_36337196_3   1117 TGACACCAAAAGCA-AAGCAACAAAAACAAAAATAATCACGTAGGACTAC 1165
                                       -           iv       ivi vi v     v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_36337196_3   1166 ATCAAACTAGAAAGCTTTTCCACAGCAAGGGAAATAATCAGCAAAATTCA 1215
                               v vi   i     vii vv   i   v iv    iv   i vv 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_36337196_3   1216 AAAGCTACTTCTGAAATGAGAGAAAATATTTGCAAACTATGTATCTGTTA 1265
                           ii v  iiviii    i                 ii  i      v  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_36337196_3   1266 AGGGGTTAATATCTAAAATATATAAAGAAATCAAACAGCTCAACTGCAAA 1315
                             ii vi    i i             v  vv   i     ivii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_36337196_3   1316 CAAATAAATAAATACTCAAGTAACAAATGGCCTAAGGACCTGAATAGACA 1365
                         v i i      --- i   v ? v      v v     ii          
  L1M4_orf2#LINE/    796 AAGACAAATAA---CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_36337196_3   1366 TTTTTCCAAAGGAGATATGCAACTAGATAACAAGTGTTTGAAAAGATGCT 1415
                            i       i      i   v i vi  i   iiiv            
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_36337196_3   1416 CAGCATCACTAATAAT 1431
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (96 / 58)
Gap_init rate = 0.02 (11 / 610), avg. gap size = 1.73 (19 / 11)  


2306 25.62 7.76 1.76  chrX_36398667_36400851.rev      849  1699 (485)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_36398667_3    849 GACATACCACATTAATGGATTGGAAGATTCAATATT---AAGATGCCTAT 895
                           i  v   ii  v             i i      ---      v v  
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_36398667_3    896 TCTTATCAAATGAACCTATGGAGTCAACACAATTCTAATAAAAACATTGT 945
                         v  ivi     vi i   ii  v     i    i iv  v    iviiiv
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_36398667_3    946 CTAACTTCTTTTGGGGGACACTAATTTACAAGCTGATTCTAAAATGTATA 995
                           iv   -     -----  vv    v          i       vi   
  L1M4_orf2#LINE/    107 CTGCCTT-TTTTG-----CAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_36398667_3    996 TGGAAATACAAAAGA----GATATGATCAAC-CAATCTTGAATGACCAGT 1040
                                i   ii  ----  -  iii   v-          vi vv  v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGA-ATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_36398667_3   1041 -CTAAGTATGGAAGAC---------CTGATTTCACGACTTACTGTAAAGC 1080
                         - v    -    i   --------- ii      vi       ii     
  L1M4_orf2#LINE/    200 ACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_36398667_3   1081 TAGCATAATAAAGACAACGTGATACTAGCTTAAGAATAAACATATAAGTC 1130
                           vvi    v      ii   i    i  v    i   i       ii  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_36398667_3   1131 AATAAAATAGAACTGAGAGTCCAGAAGTATACCTTTACAGTTATGGTCAA 1180
                            ii       i             i  v   iv    v          
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_36398667_3   1181 TTAATTTTTGACAACAATGCCAA--CCAATTCAATGAGGGAAAAGATAAT 1228
                           i     i     vii      --   -       -      ii   i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATG-GGGAAAGAATAGT 396

  chrX_36398667_3   1229 CTTTTCAACAAATGGTGCTAAAACAATTGGATACCCATA---AGAAAAAT 1275
                                            iii    i      ?   i --- i  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_36398667_3   1276 AAACCCACATTGCTCTCTTTCATCATATAGAAATAT--ATTTGTGTTGAA 1323
                         i  viiiv iiv  vi  iv  i      v   v  -- i iiviv  i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_36398667_3   1324 TCACAAATCTAAATATACAAGCTGTAATCATAAACCTTCTTGAA-AAAAC 1372
                            ? i i      i  vi    iv  ii     v  ii v   -     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_36398667_3   1373 AGAGGAGAATATGCTCACGACCTTGAAATTAGCAAAAAGTTCTTAGG-AT 1421
                          v   ? v v  vi  ii       iiv vi    viiv       i-  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_36398667_3   1422 G----CAGAAGC-CACTGATCATAAGAGAAAATAG-T---CTGTATTTTA 1462
                          ----  i    -  vvv v  v    i       - ---i  v i  i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_36398667_3   1463 TTAAAAGTATTTAAAGGCTCT-GTTTATTAAAA-ATACTGTTAAGGAAAT 1510
                          i    ----     ii  i -  viv i   i- i   i i   i  i 
  L1M4_orf2#LINE/    647 TCAAAA----TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_36398667_3   1511 TAAAAAGTAAGTCA-AAAGTGGG-GAAAATATTT-TATTTCACA-A---G 1553
                         v    iii  vi  - i i    -          -i vv   i - --- 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_36398667_3   1554 ACAAAGAACTTATA------ACATATAAATAACTCCTATGAC--AAGAAT 1595
                          i  i i    i  ------ i       v     i  ii  --  v   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_36398667_3   1596 -----GACAAACA-TCTGAT------ATGGGCAATGGTTTCCAATCACCA 1633
                         -----      i -i ii  ------        v  v  iv   viv  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_36398667_3   1634 TTTCTCTAAATAAGATATAGAAATTGCCATTTAGCAAATGAAAGG-TTCT 1682
                               i   v        v    v    v v    v      i - v  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_36398667_3   1683 CAAAAGTCAATAGTCAG 1699
                            v -   ????????
  L1M4_orf2#LINE/    893 CAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.69 (135 / 80)
Gap_init rate = 0.04 (35 / 902), avg. gap size = 2.31 (81 / 35)  


2802 27.28 4.11 0.46  chrX_36402992_36405243.rev      887  1762 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36402992_3    887 TGGGAAAATATTCCATATCCGTGGATTGGAAGAATCAATATTGTTAAACT 936
                            i  i    i    i i i            v i           iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36402992_3    937 GTCCATAC-----------ATCTACATATTCAATGCAATCTCTATCAAAA 975
                          v v    -----------       v      i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36402992_3    976 T----------------ACAGAAATAAAAAAA---ATCCTAAAACTTATA 1006
                          ----------------i       vi v  i---         i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_36402992_3   1007 TGGAACCACAGAAGACCCAGAATAGCCAAAGCTGTACTAAAGAAAAAGAA 1056
                              vii  iii                 i vi vi i  i  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_36402992_3   1057 CAAAACTGAAAAAGCCACATTATCTGTCTTCAATTTATACTACAGAACTA 1106
                             ii  i ii vi    i vi iivi     vviv       i i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_36402992_3   1107 TAATAACCAAAATAGCATGTTACTGTCATAAAAACAGACACATAAACCAA 1156
                         i i   i   i i  ii  v     v     ii i     i   i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_36402992_3   1157 TAGAACAGAATAGATAACTCAGAATCAAATCCATACATATA-AGTAAACT 1205
                          i   i     v  v iii     vi   i        v  -i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_36402992_3   1206 CATTTTTGACAAAAGTGCCATGAACATACT-TAGGTAAAGGACAGCATTG 1254
                         v     i     ii      v  v   v v- i  v    i i  iv  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_36402992_3   1255 TCAATAACCGATGCTCAAA-AACTGGATATTCTTAAGCAGAAAAATACAA 1303
                             i  vi i    vii -         ?i vi v   i  i   iv i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_36402992_3   1304 CTAGACCCTATATCTTTTACCATATACAAAAATCAAATCATAATGGATTA 1353
                         i i     i-  i  ivi               i  v   v       i 
  L1M4_orf2#LINE/    451 TTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_36402992_3   1354 AAGACTTAAATTGATGTCCTCAAACTATGAAACTGCTAAAAGAAAACATT 1403
                         ?    i     vv v vv  v       i     vi  i          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_36402992_3   1404 AGAGAAACTCTCCAGGATATTATTCTGGGCAAACATTTCTTAAGTAATAC 1453
                         i ? v  v   i iv  iv  ivvi i     vvi       ii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_36402992_3   1454 CCCAAA-GCACAGGCAATCAAAGCAAAAATGGACAAGTGGAA--TCATTT 1500
                         v     -     i    iv    v      i  i  i v i --    i-
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC- 648

  chrX_36402992_3   1501 CAAGTTACAAAGCTTCTGCACAGCAAAGAAAACATTTCACAAAATGAAGA 1550
                         v  i   -   i   i  ii vv     i v  vv iv v   i    i 
  L1M4_orf2#LINE/    649 AAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_36402992_3   1551 GACAACCCACAGGATGGGAGAAAATATTTGCAAACTATCCATCTGATAAT 1600
                                     i                     ii  vi         v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_36402992_3   1601 GGATTAATAACTGAAATATATACAGAGTTCAAATAACTATATAGGAAAAA 1650
                            i vi  v iii        v   ii  vv i    vv   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_36402992_3   1651 ATCTAATATTCTGATTAAAAACTGGGCAAAAGCTATGAGTAGGCATTTCT 1700
                         iv v    vi ii   ?    v        i v v   i   i       
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_36402992_3   1701 CAAAAGAAGGCATACAAATGGCATATGAGATATTTGAAAAAGTGCTCAAC 1750
                          v       ii           vv  i  -i iv      ii        
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCAAC 896

  chrX_36402992_3   1751 ATCTTTGAACAT 1762
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (145 / 90)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.33 (40 / 12)  


2807 25.44 2.43 1.99  chrX_36411499_36414097.rev     1205  2108 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36411499_3   1205 TGGAAAAACATCTCATACTCATGGATCAAAATAATTAATATT---AAAAT 1251
                               i i   i   ii        iii  v v        ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36411499_3   1252 TGTGATATTGCCCAAAGCAATCTAAAGATTCAATGCAATCCC-ATCCAAA 1300
                         v ii   i v      vii     v        i        -   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36411499_3   1301 TACCAATACCACATTTTTTACAGAGTTAGAAAAAA-AATCCTAAAATTTT 1349
                          v   i-- ii v      i    iv v  v  iv-i           iv
  L1M4_orf2#LINE/    101 TCCCAG--CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_36411499_3   1350 TACAGAAAAAAAAGAG---CAAAATATTCAAAGGAATCCTGACCAA-AAG 1395
                           ii    viv   i ---  i    vi    iv    i   vv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_36411499_3   1396 AACAAATCTGGAGGCATCATGTTACCTGATTTCAAAATGTATTACAAGGC 1445
                               vi      vv   iii v  ii         iv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_36411499_3   1446 TGTAGGAAACAAAAGAACATGGTATTGGTATAAAAATAGACACATAGACC 1495
                          ii  v  v   i v iii     i   i    ii       i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_36411499_3   1496 AATGGACCAAACTAATGGAAGAGAATAGAGAATCCAGACATAAAGC-ACG 1544
                               --------  -----     v    i      v     v - ii
  L1M4_orf2#LINE/    299 AATGGA--------AT-----AGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_36411499_3   1545 TATTTATAGCCAATTGATCTTTCACAAAGCTGATAAGAACTTACATTTGG 1594
                         i      i i        i  iv    i v  vi    v v v  v v  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_36411499_3   1595 AAAAGGGAATTCTATTTAAGAAATGGTACTCGTAAAATTGGATCACCACA 1644
                         i    iiv v   v  i  v       i  v v v  i     v?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_36411499_3   1645 TGCA---GAATAAAACGTGACCCTTATTTCTCATCATATATAAAAATCAA 1691
                             ---    i  iivv     i  ii  v  i      i      i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_36411499_3   1692 GTAAAAATAGATCAAAGACATAAAGGTAAGGCCCAAAACTTTTAAAATAC 1741
                         v v     i     ?    v    v     iv i      v v   v vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_36411499_3   1742 TGGAAGAAAACCTAGAGAAAACTCTCCTGGATGTTGT-CTAGGCAAATAA 1790
                          i         v   i?iv  v   i vv  iv   v-i       - ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGG 584

  chrX_36411499_3   1791 TGTAT--GACAAGATCTCAAAAGCACATGCAACAAAAACCGAAATAGATA 1838
                          v v --  i v  ivi          v         ivvi         
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_36411499_3   1839 AAT-GTGTTTAATTAAACTAAAAAGCTTCTGAATGCT--AAAAGAAATAA 1885
                            - vii  v  i   v v    i   i  --    --   i  v iv 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTG--TGCTTCAAAGGACACTA 682

  chrX_36411499_3   1886 TCAGCAGATT--AGAGACAACCTATTGAATGGGAGAAAATGTTTGCAAAT 1933
                            iv i v -- i        i iv              i         
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_36411499_3   1934 GATTCATCTGACAGGGGACTATTTTCCAGAATATACAAAGAACTCAAACA 1983
                         v  vi      i i      vv v           i         vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_36411499_3   1984 ATTCAATAGGAAATAC-CAAGTAATTCCATTAAAATGTGGTCAAAGAACA 2032
                          i      iv   v v-   i   ii v   ?   vi   v     i iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_36411499_3   2033 TGAATAGACATTTCTCAAAAGAAGATATACAAATGGTCAACAGATATATT 2082
                                         v                   i   i iii i  v
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_36411499_3   2083 AAAAAATTCTCAAAATCAGTAATCAT 2108
                             i  v     v    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (126 / 100)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.22 (40 / 18)  


1610 18.22 1.98 27.12  chrX_36442382_36446412.rev     2349  3561 (470)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36442382_3   2349 TGGAAAGCTCTCTAGTGTTCATAGATTGGAAGAATTAATATAGTTAAAAT 2398
                                v v  ivi       i          v       v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36442382_3   2399 ATTCATGCTACATAAAGGGGCCTACAGATTCAATGCAGCCCCCATTATAA 2448
                         iviv  i  v vi   vv ii            i   ii   i  i v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36442382_3   2449 TTCCAATGACCCTTTTGTTATAGAAATAGCAAAAGACAATCCTAAAAATT 2498
                          i   iivi  i    -- ii      v - v   vii         v i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT--TGCAGAAATTG-ACAAGCTGATCCTAAAATTC 147

  chrX_36442382_3   2499 GCGTGGAACCCCAAAACACCCCAAATAGCCAAATAAATTCTTAGCAAAAA 2548
                         iii     viv   iiv    vi          vv   ii v iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_36442382_3   2549 GAACAAAGCTGCGGGCATCAAAGTCTCTGATTTCAAAGTGTACTGTGAAG 2598
                                 i  vi  vv   v v ii ii        iiv    iii   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_36442382_3   2599 CTATAGTAACAAAAGCAGAATGGCACTGGTATG----------------- 2631
                            i     iv  ii   vi   i     i  i-----------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_36442382_3   2632 CAACAGAACAGGCTAGAAAGCCCAGAAATAAACCCATTTGTCTATGATAG 2681
                            ii   i  iv v  i  i                vii i    i vi
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_36442382_3   2682 ATTGAATTTCAACAGAGGGGCCAAGAACACATGATGGCGAAAAGACAGTG 2731
                              v    i   ii  v       v  ivii    v    ii i   v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_36442382_3   2732 TCCTTGATAAATTGTATTGGGAAAACTGGCTGTCCAAATACA---GAATG 2778
                          ii ii i    v  ii     v      v i?   v  i  ---     
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_36442382_3   2779 AAATTGGACTCTATACATCCCTTATATAAGAATCAACTTTGGGAGGCCAA 2828
                           i      -----------------------------------------
  L1M4_orf2#LINE/    448 AAGTTGGAC----------------------------------------- 456

  chrX_36442382_3   2829 GGCGGGTGGATAACGAGGTCAAGAGATCGAGACCATCCTGGCCAGCATGG 2878
                         --------------------------------------------------
  L1M4_orf2#LINE/    457 -------------------------------------------------- 456

  chrX_36442382_3   2879 TGAAACCCTGTCCCTACTAAAATACAAAAAATTAGCCAGATGTGGTGGCA 2928
                         -----------      ---------------------------------
  L1M4_orf2#LINE/    457 -----------CCCTAC--------------------------------- 462

  chrX_36442382_3   2929 CGTGCCTGTAGTCCCAGCTACTTGGCAGGCTGAGGCAGGAGAATCACTTG 2978
                         ----------------------------------------------  --
  L1M4_orf2#LINE/    463 ----------------------------------------------CT-- 464

  chrX_36442382_3   2979 AACACACAGGAGGCAGACATTGCAGTGAGCTGAGATTGTGCCACTGCACT 3028
                         --     ----------   ------------------------------
  L1M4_orf2#LINE/    465 --CACAC----------CAT------------------------------ 472

  chrX_36442382_3   3029 CCAGCCTGGTGACAGAGTGAGACTCCATCTCAAAAAAAAAAAAACAAAAA 3078
                         --------------------------  ----------------------
  L1M4_orf2#LINE/    473 --------------------------AT---------------------- 474

  chrX_36442382_3   3079 ACAAAAAACAAAAAAACAAAAAAACAAAAACAGCATCAACTCAAAATGGA 3128
                         -----------------------       ----- i             
  L1M4_orf2#LINE/    475 -----------------------ACAAAAA-----TTAACTCAAAATGGA 496

  chrX_36442382_3   3129 TTAAAGACTGAAATGTAAGACCTGAAACCATAAAATTGCTAGAAGAAAAC 3178
                          i ?    iv          v  i    i      i vi           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_36442382_3   3179 ACAGGGGAAAA-CTTAACATGACATTGGTCTGGCCAATGATTTCTTGCAT 3227
                          i   ? v   -   -- i    v    vi i v     i      iv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTT--CGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_36442382_3   3228 ATGACCCCAAAA--ACAGGCAACAAAAGCAAAAATAGACAAATGAGATTG 3275
                              v      --   i          v         i    vi  i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_36442382_3   3276 CATCAAA-CTAAAAACTTTTGCACAGCCAAGGAAACAATGAAAAGAGTGA 3324
                                -i            ii vv v     v  v  v  i i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_36442382_3   3325 AGAGATAATCCACAGATTGGGAGAAAATATTTGCAAATCATACAACAGGT 3374
                          i   i  i       v                         i v v i 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_36442382_3   3375 AAGGGTTTCATATCCAAAATATATGAGTAACTCCGATTATTCAATAACAA 3424
                              vi ii      i       i iv     iv iv i       i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_36442382_3   3425 AAAAAAAGAAAAAAGAAACAAATAACCCTATTTAGGAAATGGTCAAAAGA 3474
                            i -------------          v   ? i-      v    i  
  L1M4_orf2#LINE/    795 AAAGA-------------CAAATAACCCAATTWAA-AAATGGGCAAAGGA 830

  chrX_36442382_3   3475 CCTGAATAAACATTTCTGAAAAGAAGACGTATAAAAGGCCAACTGATATA 3524
                         ii      i        vv        ii  i   v      iviii i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_36442382_3   3525 TGAAAAAAACATGGTTTTAAAGCCCATCACTTCTAAG 3561
                               i ---  --i i  ----     ????????
  L1M4_orf2#LINE/    881 TGAAAAGA---TG--CTCAA----CATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 17.65 (353 / 20)  


1090 31.90 6.22 3.51  chrX_36448771_36450760.rev      622  1505 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36448771_3    622 TGTAGAGATA---AACATTCATGAATTAAAA-ACACAATATCATAAAGAT 667
                           v i     ---v ii      i   ii  -  vi     ii v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36448771_3    668 ATAAATTCTACTCAAATTGCATTA-AAATGTCAATATAATCCCAGTGGAA 716
                         ivv   v  v i       vvi  - i  -    iii      vi vi  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGAT-TCAACGCAATCCCTATCAAA 99

  chrX_36448771_3    717 ATTCTCACCATCAATTTTGTGGAATTTGATAAGCTGATTCAAAAGTTTAT 766
                           i ivi iii vv     ii   v    i        i v   i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_36448771_3    767 AAGGAATAGAAAAGTGGTAGTAAGGAGGGTCAAGACCAACAT---AAAGA 813
                          v    vv v  ---  v viv  i vi i   i  v v v ---     
  L1M4_orf2#LINE/    150 ATGGAAATGCAA---GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_36448771_3    814 AAAACAAAGT-AAAGG-----TGTTTTCTAACTAGATATCAAGGCTTATT 857
                          i        -ii   -----iii  i i  i -----    ii    i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATT-----TCAAAACTTACT 241

  chrX_36448771_3    858 ATAAAGCTACAGTAATCAAGAATGTTTT-TGTTGGTAAATGGAATGAA-- 904
                          i                   vv  v v- ii   i v v   - ii --
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACA 290

  chrX_36448771_3    905 -GCAGTTCAACAAAACAGAATAGAGAGAACAGACACAGACCCAC----TT 949
                         -ii  v    iii  i     v     vv    v i i     i----  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_36448771_3    950 ATGG-CACTTGATATATTAAAAAAA----CA-GACCTTTGAAGATCAACA 993
                             -  v     v - ii v  ii----  -    v  ------   ii
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTT-TCGACAAGGGTGCCAAGACCATT------CAATG 383

  chrX_36448771_3    994 GGGAA-TAATGGATTTTTTTAAAAAAATGGTGCTGGCTCAATTAGGAATC 1042
                              -v   i -- i    v  v            vv   i i iv ? 
  L1M4_orf2#LINE/    384 GGGAAAGAATAG--TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_36448771_3   1043 CATGGGCAAAAA-------TTCTACCCCAACTTAATATTTTGTG-AAAGA 1084
                           iiv      i-------  vv     v  i v i iiv i i-   i 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_36448771_3   1085 TAAATTCCAGCTAAATTTAAGCCATGTACTATAATACCCAACA-TATGAA 1133
                          v  i  v iv ii  iv?  v v i- v i   v v i  v -   i  
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTA-AATGTAAGAGCTAAAACTATAAA 530

  chrX_36448771_3   1134 ACATTTAGAATACAATAGAGAAGACTGTCAACCTGACTGTAGCATAGGAA 1183
                           vi      v v  i v  i? vvvi  vv v    iv i vv    v 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_36448771_3   1184 AAAACTACT-AAACAAAACATTAAAATCACC--CAGCCAAAGAAAATACT 1230
                          viii v  - i i vi   ii    v   v--  i v        v iv
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_36448771_3   1231 GTTAAATTG-----CATTAAAATGAAAAAAAAGTTTATTAATCAGAAGAC 1275
                          v       -----   i     v     v--v   i vvv   i i   
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAAC--TTTTGTGCTTCAAAGGAC 678

  chrX_36448771_3   1276 -----CAGGGGAAATATTTAAAAAGATTAGTCACCAACTGAAAGGAAAAG 1320
                         -----  i ii i----- i      iv vi   vi v  ii  i   vi
  L1M4_orf2#LINE/    679 ACTATCAAGAAAG-----TGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_36448771_3   1321 TTTTCTTATAGTATAGTTGACAAAGGATTCAAGTACAGAATATATAAA-A 1369
                            v vv  vi    vi   i  i   i iivi v             - 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_36448771_3   1370 GCTTCTACAAATCAATATTAATACTATAGACAACAAAATAGACAAAAGGA 1419
                         i  ii     v      v   v vv i i i   vv   v? v   v  i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_36448771_3   1420 CCAAAAACTTAAACA---ATCTCTCCACAAAAGAAGAAATCCAAATAATC 1466
                          v  ii i  i  i ---  i      ---       v  v     iii 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCA---AAGAAGATATACAAATGGCC 870

  chrX_36448771_3   1467 AATACATTTCTGAATAGGTGTTCAAGTTTCACTGAAATG 1505
                             viiviv    v  i  i    -iv   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (154 / 124)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 2.53 (86 / 34)  


3188 27.12 0.66 0.55  chrX_36478179_36484564.rev     4989  5895 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36478179_3   4989 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5038
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36478179_3   5039 AGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5088
                         i  v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36478179_3   5089 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5136
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_36478179_3   5137 TAGGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5186
                           v    viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_36478179_3   5187 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5236
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_36478179_3   5237 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5286
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_36478179_3   5287 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5334
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_36478179_3   5335 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGAG-AAAGGATTCC 5383
                          vi    i  i     ivv  v   i v  vvv    i -    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_36478179_3   5384 CTATTTAATAAATGTTGCTGGCAAAACTGGTTAGCCATATGTAGAAAGCT 5433
                           v  i  i     v      v v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_36478179_3   5434 GAAACTGGATCCCTTCCTTGCACCTTATACAAAAATTAATTCAAGATGGA 5483
                            ii    i    v   ii    v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_36478179_3   5484 TTAAAGACTTAAATGTTAGACTCAAAACCATAAAAACCCTAGAAGAAAAC 5533
                          i ?    i       v   vii     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_36478179_3   5534 GTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5582
                         i    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_36478179_3   5583 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGGATCTA 5632
                         vi            vvi          vv     v  i   iv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_36478179_3   5633 ACTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5682
                          ii   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_36478179_3   5683 CAGGCAACCTACAGAATGGGAGAAGATTTTTGCAACCTACTCATCTGACA 5732
                         v  i     i              i  v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_36478179_3   5733 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5782
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_36478179_3   5783 AAAACGAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5832
                           i  i  i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_36478179_3   5833 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5882
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_36478179_3   5883 CATCACTGGCCAT 5895
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2494 25.15 6.29 1.90  chrX_36518475_36520314.rev      507  1349 (491)    L1M4_orf2#LINE/L1       29   908 (0)  

  chrX_36518475_3    507 GAAGAATTAATATCATTAAAATGGCCATGTTGCCCAAAGCAATGTACAGA 556
                              v       ii    i     v  ii v      vii  v      
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chrX_36518475_3    557 TTCAATGCTATTCCTATCAAACTACAAACAACATTCTTCACAGAACTAGA 606
                              i  v  i         v v v i vi v  i  ii     v v  
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chrX_36518475_3    607 AAAAATTATTTTAACATCTATATGGAACCA-AAAATAGCCTGATTAGCCA 655
                         v  iv v  ii   v  ii        vii-  iiv v  v  v      
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chrX_36518475_3    656 AGAAAATCCT----------AATA--GCTGGAGGCATGATGTTACCCAAC 693
                          i v    i ----------  i -- i      vv v iii v     i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_36518475_3    694 TTCAAACTATACTACAGTGCTACAGTAACCAAAACAGCATGGTACTAGTA 743
                               viv       iv          i   i    ii       i i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_36518475_3    744 CAAAAACAGGCACTA-AGACCAATGGAACAGAATAGGGAGCCCAGAAATA 792
                         i  ii i  i  -  -   i        i     v i   i         
  L1M4_orf2#LINE/    279 TAAGGATAGACA-TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_36518475_3    793 AGGCCACTCACCTATGACCTATGACCATCTGCTGTTCAACAAAGCTGACA 842
                          iv   iv  ii    ii v  -------  v v   i    i v  v  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAAT-------TGATTTTCGACAAGGGTGCCA 370

  chrX_36518475_3    843 AAAATAAACAATGGGGAAA----AGCCTCCCTAACAATAAATGGTGCTGG 888
                          i vi vv           ----  i  iiii     ---          
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA---ATGGTGCTGG 417

  chrX_36518475_3    889 GATAACTGTCTAGCCATATGCAAAAGATTGAAGCTGGATGCTTTTCTTAC 938
                           i     vv  ?   i          v     i    iv i vi  i  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_36518475_3    939 ACCATATGCAAAAGTCAACTCAAGATGTACTAAAGACTTAAATGTAAAAC 988
                                i     i i       i   v ii ?    i         i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_36518475_3    989 CAAAACACTATAAAAATCCTGGAAGACAATCTAGA---AAATACCATCCT 1035
                          v   -         v  i i     v  iv   i---    -- v  v 
  L1M4_orf2#LINE/    518 CTAAA-ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGT 564

  chrX_36518475_3   1036 GGACATAGGAATGGGCAAAGATTTC------ATGACA---AAGACAC--- 1073
                          -  v v  iv i     v i    ------      ---  ii   ---
  L1M4_orf2#LINE/    565 G-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_36518475_3   1074 ---CAAA--------TTGACAG--TGGTATCTAATCAAACTGAAGAGCTT 1110
                         ---    -------- v  i i--   - ii v      v v  i i   
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGG-ACTTCATCAAAATTAAAAACTT 662

  chrX_36518475_3   1111 CTGCACAGAAAAAGAAACTATCAACAGAGTCAACAGATAACCTACAGCAT 1160
                         i  ii vvv   i  v        v i   v  v   i    i    v  
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_36518475_3   1161 GGGAGAAAATATTTGCAAAGAATGCATTTGACAAAGGTCTAATATCCAGC 1210
                                            vv  ii  i   i  i  v  vi       v
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_36518475_3   1211 ATCTGTAAGGAACT--TACA-CACATTTACAAGA-GAAAAACAATTCCAT 1256
                           v i   i     --    - v  v v i  i -  v   i  ii v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_36518475_3   1257 TAAAAAGTGGACAAAGGATATAAATAG-CAATTTTTCAAAGAAGACATAC 1305
                          ?    i   i        v i     -  v  i i         i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_36518475_3   1306 ATGAGGCCAACAAGAATATGAAA-GA-GCTCAATATCACTGATCAT 1349
                          viv      i   v i      -  -      i    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (123 / 86)
Gap_init rate = 0.03 (24 / 880), avg. gap size = 2.88 (69 / 24)  


3544 18.50 4.41 1.47  chrX_36574085_36575881      500  1315 (482)    L1M4_orf2#LINE/L1       69   908 (0)  

  chrX_36574085_3    500 GATGTATACATTCAATGCAACTTTTATCAAAATCCCAA-TGCCTTATTTT 548
                            v  i v      i    iiii             i-      ---  
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT---TT 115

  chrX_36574085_3    549 TTTAAGAAATGGAAAAGTTGATCCTCAAATTCATATGCTATTGCAATTGA 598
                           vv      v  v   i       v           vv v     vv  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_36574085_3    599 CCCAGAATAG-----ACAAGC-------AGAAGAATAAATTTGGAGGACT 636
                                   -----    v -------       i   v          
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_36574085_3    637 CATGCTTCTTGATGTTAAAACTTATTACAAAGCTA---TAATTAAAACAG 683
                           ii    iii  v i        i          ---    i  i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_36574085_3    684 TATGTTATTGGAATAAATATAAACATAATGATTAATATAATAGAATTAAG 733
                          i  v  i   v    iv   i     vv   i   iv         i  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_36574085_3    734 AATTTTGAAATTAACTCATACATTT---------TGATTTTCCACTAGGA 774
                          i iiv     v   i         ---------        v  v   i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_36574085_3    775 TGCCAACATCATTCAATGGGGAAAGAATAGTATCTTCAACAAATTTTATT 824
                               v i                      v i          vv ii 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_36574085_3    825 AAGACAAATGCATGTCCACATGTAAAACAATGTAGTTGGGCCCTTATGGC 874
                         ii     v  v  i?       i    v    v      i   i  ivv 
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_36574085_3    875 ACACTATATATATAAAACTAATTCAAAATGAGTCAAAGACCTAAGTATAA 924
                             i     i -    i   i        ii   ?        i i   
  L1M4_orf2#LINE/    466 ACACCATATACA-AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_36574085_3    925 GAGCTAAAATTATAAAAATCCTTGAAGAAAACA-AGGA-TAAATTTTTAT 972
                                  i       v  i v          -   ?-     i  ii 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_36574085_3    973 GATCTCGGGTTTGGCAATAATTCTTTAAATATGCCACCAAAAATACAAGC 1022
                           i  i     v      ii  ii   i     v        ii      
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_36574085_3   1023 AACAAAAGAAAACAAAGTCAATACATTTGATCTCATGAAAATTCCAAACT 1072
                                     v v  ---   v   v  ii    v      vv     
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAG---ATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_36574085_3   1073 TTTCC-CATCAAAGTACATTATCTAGAGAATTAAAAGACAACTCACAGAA 1121
                            vi- v      v   i    v   i i v          i       
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_36574085_3   1122 TAGGAGAAAATGTTTGCAAATCATATGTCTGATAAGAGACTAATATGCAG 1171
                          i         i              i         i    vi   v   
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_36574085_3   1172 AATATATGAAGAACTC--ATAACTCAATAA------GACAAATAACTCAG 1213
                                i        -- i          ------          i  i
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_36574085_3   1214 TGAAAAAAAAATGAACAAATGACTTGAATATAAATTTATCCAAAGAAGAT 1263
                          v?     ---  ii    v  i       v v    v            
  L1M4_orf2#LINE/    812 TTWAAAAA---TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_36574085_3   1264 ATACAATTGTCAAATAAGCACATGTAAAGATGCATTAGTCATTAGATAAG 1313
                               v  v v            v        - i i-   i ??????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGC-TCAA-CATCAZZZZZZ 906

  chrX_36574085_3   1314 TA 1315
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.37 (85 / 62)
Gap_init rate = 0.02 (16 / 840), avg. gap size = 3.00 (48 / 16)  


2927 24.97 1.52 1.87  chrX_36587368_36589228      512  1368 (493)    L1M4_orf2#LINE/L1       55   908 (0)  

  chrX_36587368_3    512 ATACAACCCAAAGTGAGCAATATATTAAATGCTATTCCCATCAAAATCCC 561
                             vv      v   v v i v   v  i  v  i  i           
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_36587368_3    562 AATGACATTTATTTAAAATATAGAAGAAAGCT-ATACAGAAATTTACATG 610
                          iivi v   v  vv i v  v  v--     -  v vi     i i   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCATATG 152

  chrX_36587368_3    611 GAACCAGAAAAGAAAAAGACT-AGAATAGCCAAAGTGATTTTAAGAAAGA 659
                            ------ v v  ii   i-            iii  i  i i     
  L1M4_orf2#LINE/    153 GAA------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_36587368_3    660 A---CAAATGTAGAGACATTATATTTCCTGCTTTCAAAACATATTACAAA 706
                          ---    vv i   ivv i i i    iiv         v  i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_36587368_3    707 GCTACAGTATTGAAAATAGTATGGTACCAGCATAAATACAGATGCATAGA 756
                                  v v  i i   i      ii      iv i   iii     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_36587368_3    757 CCAATGAAACCAAATAGAGAGCCCCCAAATAAATCTATGCATCTATGGTA 806
                         i     i  ivi   v     i  vv       i i  i   i      v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_36587368_3    807 AACTGATTTTCAACAACGGTGCCAAGAACACACGATGTGGAAAGGCTAAT 856
                           i        i    v          v  iv i   v      iv  i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_36587368_3    857 CTCTTCAATAAATAGTGATAAAAAAAATGGATATCAAC-CACAAAAGAAT 905
                           i     i    i   v iii v  v      ? v  -ii         
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_36587368_3    906 AAAGTTGAACTCCTAATCTTACATCATACACAGAAATCAACTCAAAATGG 955
                         i      i  i    -i  i   i    i   i    i            
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_36587368_3    956 ATTAGATATCTAAATATGAGACTTGAAACTGTTAAAATTTATAAAAGAAA 1005
                           i ? v i      i i   vi i     i -    i iv  i      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAA 544

  chrX_36587368_3   1006 CTATAAAGG--AAGTTTCTTGACATTGGTCTTGGCAATAGTTTCTGGGAT 1053
                         vi   ii? --  vi   v    v    vi v      i      vi   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_36587368_3   1054 ATGACACTAAAAGCACAGGCAACAGAAACAAGAATAGACAG-TGAGACAA 1102
                                i         i      i  iv  i      i i- vi   vv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_36587368_3   1103 TATCAAACTAAAAAAATGTCTGCACAGAAAAGGAAACAATTAACAGAATG 1152
                         i      v v     v - i  ii vvv      v  v  i  v i i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_36587368_3   1153 AAAAGACAATCTATAGAATGGAATAAAATATTTACAAAGCATTTATGTAT 1202
                                  i i i       i v         i    v   v   v iv
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_36587368_3   1203 TAAGGGGTTAATATCCAAAAAATGTAAGTAACTTCTACAACTGAATAATT 1252
                               ii vi      i  v  i   iv    ii       v      -
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT- 792

  chrX_36587368_3   1253 AACTAAATAAATAAATAATCCAATTTAAAAATGGGAAAAGGATTTGAATA 1302
                         ----   v i i      i      ?         v              
  L1M4_orf2#LINE/    793 ----AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_36587368_3   1303 TACTTTTCTCTAAAGAAGA----CAAATGACCACCAGGTATATGAAAAGG 1348
                         v  v      i        ----      i   vi i i i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_36587368_3   1349 TTCTTAAAGTCACTAATCAT 1368
                          v  i  vi   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (128 / 82)
Gap_init rate = 0.02 (13 / 854), avg. gap size = 2.23 (29 / 13)  


2322 23.21 2.29 2.44  chrX_36611307_36612953      500  1154 (493)    L1M4_orf2#LINE/L1      255   908 (0)  

  chrX_36611307_3    500 AATCAAAACAATGTGGTATTGGCACAAAAAAAAATAGATATAGGGACCAA 549
                               i   i       i     i  ii ----    i   vi  i   
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGA----TAGACATATAGATCAA 300

  chrX_36611307_3    550 TAAAACAGACTAGAGA-TCACAGAAATAAATCCACTCATCTACAGTCAAC 598
                          ii  i   v v    -  -          i   iv   i  ii     i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_36611307_3    599 TGATCTTTGACAAGGGTGCTAAGAAGAC-CAATAGGGAAAGGAGAGTCTG 647
                             i  i           i    vv i-    i       i v     v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_36611307_3    648 TTCAACAAATGTTGTTGAGAAAACTGGATATCCACATAAAGAAAAATGAA 697
                                    v  i  i  v         ?      iv i  i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_36611307_3    698 ATTGGGCCCTTATCTCAT-CCACATAAAAAAAC--ACATTAAAATATGTT 744
                         i    i   i  i    i-   i   v     i--  - i     ivi i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAAC-TCAAAATGGATC 498

  chrX_36611307_3    745 GAAGGCTTATATATAAGACCGCAAACTGTAAAATTACTAGAAGAAAACAC 794
                         i?  i i  v  i     v vv     i     i vi            i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_36611307_3    795 AGGGGAGAAGCTTCTTGACATTGGCCCTGGCAAAGGTTT-TTGGATATGA 843
                            ? vi  v    v    v    viiv     v     -  i       
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_36611307_3    844 C-CCAAGAAACACAGGAAGCATAAGCAAAAATAAACAAACGAGATTGCAT 892
                          -    -  i    i v i  v   v       i i   ivi  i v   
  L1M4_orf2#LINE/    599 CACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_36611307_3    893 CAAACTAAAAAGTTTCTGCACAACAAAAAA-----TCAAAAGTATCAAAA 937
                             v v    ii  i  ii vv    ii -----    i ivi v    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_36611307_3    938 GACAAACTATGGAATGGGAGAGAATATTTGCATACCATATTTCTGTACAA 987
                              v i ii          i          v i     v    - i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG-ATAA 746

  chrX_36611307_3    988 GG--TTAATATCGAATATGTATAAATAATTCAAATGACTCAATAGCAAGA 1035
                           --i vi    v iv  i      v  i  vv ii        ii  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_36611307_3   1036 CAACAAATAACCTGATT-AAAAATGCACAAAGGACCTGAACAGACATTTA 1084
                         vi          ii   -       vi       ii    i        v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_36611307_3   1085 TCAAAAGAAACCATACAACCATACAAATGGCCAACAGATATATGAAAAGG 1134
                           v      i--   ------             i iii i        i
  L1M4_orf2#LINE/    847 TCCAAAGAAG--ATA------TACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_36611307_3   1135 TGCTCAACATCACCAATCAT 1154
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (100 / 49)
Gap_init rate = 0.02 (16 / 654), avg. gap size = 1.94 (31 / 16)  


2558 23.32 2.80 8.81  chrX_36651077_36653238      705  1669 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_36651077_3    705 GGAAATGGAATATTTCATGCTCATGGATTCAAATAATTAATATTGTTAAA 754
                              ---i    ii    i         vi  v v             i
  L1M4_orf2#LINE/      2 GGAAA---GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_36651077_3    755 TTGTTTATATGATCCAAAGAGATTTACAGATTCAATGCAATCCTTATGCC 804
                         v  viv   ivvi     vv   i           i       i   ---
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT--- 95

  chrX_36651077_3    805 TGTATCAAAACATCCCATATACCCCATAAATATATACACCTACTATGTAC 854
                         -----     --     vv i  ----------------- vi v  ---
  L1M4_orf2#LINE/     96 -----CAAAA--TCCCAGCTGCC-----------------TTTTTTG--- 118

  chrX_36651077_3    855 CCAGAAAACTTTAAATTAAAAAAATTTTTAAAAATACTGAGATTCTTCAC 904
                         -      --------  i v  iv -------i  v  i i    v - i
  L1M4_orf2#LINE/    119 -CAGAAA--------TTGACAAGCT-------GATCCTAAAATTCAT-AT 151

  chrX_36651077_3    905 AGAAATAGAAAAAAAATTCTAAAAAGTATCACAAAAGTCCTCAAATAGTC 954
                         i     i------------------------   ii v  ivi     i 
  L1M4_orf2#LINE/    152 GGAAATG------------------------CAAGGGACCCAGAATAGCC 177

  chrX_36651077_3    955 ATACCAAATCTGAGCAAAAAGAACAAAGCAGGAGGCATCACACTATCTGA 1004
                          v v   vii   iv  i          iv     vv       vi ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_36651077_3   1005 CTTCAAAATATAATACAAAGCCATAGTAACCAAAACAGCACTGTACTGGC 1054
                         i       iv  v        i i     i   i    iiiv        
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_36651077_3   1055 ATAAAGACAGACATTTAGACCAATGGAACAGAATAGAATACGCAGAAATA 1104
                             i  i      v    i        i     v  iviiv        
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_36651077_3   1105 TATCCATGCATTTATAGCCAACTCATTTTCTACAAAGATGTCAAGAGTGT 1154
                         v i    i       i i   i v      v    i i  i     vii 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_36651077_3   1155 ATATTGGGGAAAGGACAGTCTCTTTAATAAA------------AACTGGC 1192
                         vi v         i i     i  i  i   ------------      v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_36651077_3   1193 TAACCATATGTAGAAGAATAAAACTAGACCTCTAGCCCTCACCATATAGA 1242
                           ?   i   i i      i  ii i    i   v i v         v 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_36651077_3   1243 AAAATCAAATCAAAATAGGTTAAAGACTAATCAAATCAAAAAACCTGAAA 1292
                              i  v       i i i ?    i---i    vv  i i - i   
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACC---TAAATGTAAGAGC-TAAAA 523

  chrX_36651077_3   1293 CTATGAAACTACGAAACTACGAGATAAAAACAGGGG-AAATGCTCTATCA 1341
                             i     viv i -----   -   v i   ? -    -  iii v 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGA-----AGA-AAACATAGGNGTAAAT-CTTCGTGA 566

  chrX_36651077_3   1342 TGTTGGCCTGGACAAAGAGTTTTTGAGCAAAACCTCAAAAGCACAGGCAA 1391
                         iv    vi i i   v iv  i  iiii vi  vi          i    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_36651077_3   1392 AAAATGTAAAAAAAGACAAATGGCATTACATCAAGATAAAAAGCTTTAGC 1441
                         v   v v     v   i    v v i v      i  v    i    v i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_36651077_3   1442 ACAGCAAAGGATA--A--AACAAAGTGAAGAGACAACCCACAGAATGGAA 1487
                         i vv       i -- --  v        i                  i 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_36651077_3   1488 GAAAATATTTGGAAACTATCCATCTGACAAGAGATCAATAGTCAGAATAT 1537
                                    v   ii  vi      i   i  iivi  vi        
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_36651077_3   1538 ATTAGGAACTC---------AATGGTAAGAAAACAAGTAATCCAATTTTA 1578
                           v i      ---------   ii   i  i    i   i      ?v 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_36651077_3   1579 AAATGGGCAAAAGATCTGAATAGACATTTCTCAAAAGAAGACAAACAA-T 1627
                                    i   i                v        i v    - 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_36651077_3   1628 GGCCAAAGGGTGTATAAAATAATGCTCACCATCACTAATAAT 1669
                               vii iii  i   vi       v     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (140 / 81)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 5.60 (112 / 20)  


3160 25.06 2.57 1.01  chrX_36667450_36671663     2828  3721 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36667450_3   2828 TGGAAAAATGGACCATGTTTATGGAGTGTAAGAATCACTATTGTTAAAAT 2877
                               i  ivv       i     v  v    v i v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36667450_3   2878 GTCCATAATTCACAAGGCAATCTGCAGATTCAATAAAATCCATATCAAAA 2927
                          v v   v i v   ivii    i         iiv     v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36667450_3   2928 TGCCAATGACATTCTT--CAAAAGCGGTTGAAAAAACAATCCTAAAATTT 2975
                          v   iivi v  i  --  i  i---    v  ivii           i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA---TTGACAAGCTGATCCTAAAATTC 147

  chrX_36667450_3   2976 ATATGGAACTACAAAAGATCCA---------AAGCTATCCTAACCAAAAA 3016
                                 v i   ii  i   ---------  i v   i i vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_36667450_3   3017 GAACAAAACAGGAGGAATCACATTACCTAACTT--GAGCTAATATTACAG 3064
                                iiv      v     i v  i  i  --i i  --  i    i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT--TACTACAA 245

  chrX_36667450_3   3065 AGCCATAGTAACCAAAACAGCATAGAACTGGCATAA----AAACAC-TAG 3109
                            i i     i   i    ii i v          ---- i   i-   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_36667450_3   3110 ACCAGTGGATCAGAATTGAGAACTCCAAAATGAATCCATGCATCTATAGT 3159
                          i  i    vi          iii vi    i  i    i   i   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_36667450_3   3160 AAACTCATTTTTTACAAAGACACCAAGAACATATATTGGGGAAAGGCCA- 3208
                         v  i v     iv    i iii      v   vi v         ivi -
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_36667450_3   3209 TCTCTTCTATAACTGGTGCTGGGAAAACTGGATATTCATATGCAGAAGGA 3258
                            i   v i  v           v         ?i  i     i   i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_36667450_3   3259 TGAAACTGGACCCCTATCTCTCACCATATACAAAAATCAAATAAAAATGG 3308
                             ii          i   v                i  v v       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_36667450_3   3309 ATTAAAGACTTAAATCTAAAACCTCACACTATGAAACGACTAAAAGTAAA 3358
                           i ?    i     v   i v  v v     i    vvi  i   v   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_36667450_3   3359 CATTGGGAAAACTCTCCAGGACATTAGATTGGACAAAGGTTTCTTGAGTA 3408
                            v  ?iv  v   i iv   v  i i  i i   v        iii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_36667450_3   3409 ATACCCCACAAGCACAAGCTACCAAAGCAAAAGTGGACAAATGGGATCAT 3458
                         vv  v   v          v  v    v    i i  i    v   iivi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_36667450_3   3459 GTCCAGTTAAAAAACTTCTGCATAGCAAAGGGAACAATAAACAAAGTGAA 3508
                         i  v iv v        i  iiivv      iv  v  v  v        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_36667450_3   3509 GAGACAACCCACAAAATGGGAGAAAATATTTGCAAACTATCCATCTGACA 3558
                         i            i                      ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_36667450_3   3559 AGGGATTAATAACCAGAATA---AAAGAAGATTAAACAACTCTATAGGAA 3605
                              i vi  v        ---      vvi v -      v   iv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATAA 794

  chrX_36667450_3   3606 AAAAATCTCATAATCAGATTTTTTTAATGGGCAATGTGTCTGAATAGACA 3655
                            i - vv    i vi   ?vvv-         v vi i          
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACA 842

  chrX_36667450_3   3656 ATCCTCCAAAGAAGACATACAAATGGC-AATCAGGTACATAAAAAGGGGC 3704
                         v i            i           -   - i i    i     iv  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCACATGAAAAGATGC 891

  chrX_36667450_3   3705 TCAACACCATTGATCAT 3721
                               i  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (130 / 90)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.29 (32 / 14)  


1741 26.82 10.13 1.91  chrX_36784280_36786436      826  1664 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36784280_3    826 TGGGAAAATGTACCTTTTTCAGTGG-TCAGAAGACTTCCTATTTTTAATA 874
                            i  i  i v  v v    -   - ii        vv    v    v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCA-TGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_36784280_3    875 TGTCAATTAC-CCACAAATTTATCTACAGATTCAAAAGAATCCTAATTGA 923
                           v    -  -  v      v              viv     iv  ii 
  L1M4_orf2#LINE/     50 TGGCAAT-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_36784280_3    924 AATCCCAACGGAATTTTTTTTAGACATTGATAAACTGATTTTAAAGTTTC 973
                                i v vv      vi   v     i  i     ii    i  iv
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_36784280_3    974 TGTAGAAATTCAAAGGACCTAGAAGAACCAA-----CTTTGTAAATGAA- 1017
                          i i     v   i     i    v i    -----ii   v   v   -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_36784280_3   1018 --CATTGTTAAAGAACTAATACAGCCTAATTTCTAGGTTTATTTTAAAGT 1065
                         --  vv   ii  i   v i  vv  i      v iii   i vi    i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_36784280_3   1066 TAAAGTAATCAACAGAGGGTGAAATTTGTGTGAG---AGA-A---AAATC 1108
                           v         v v  v   iv i v ii i  ---   - --- i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_36784280_3   1109 --TGGAAGACAAAAGAGTGCCAAGAAATTGACCCACAAAAAAATATACAC 1156
                         --     v v  vv   v i v      vi     i v vv--   ivv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTC 346

  chrX_36784280_3   1157 AGCTGATATTCTACAAATTTCCAAAGGTAATTCAGTGGAGAAAATATAGT 1206
                          ii    v   v    ivv v v   iiv     i   i    iv     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_36784280_3   1207 CTTT------------ACTGAAATTACCAGATATACACAGGCAATAGA-- 1242
                             ------------i   ii iv  ii    ?v    v    v   --
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_36784280_3   1243 ------------------CACATTTTTT-TAAAAAGTA-CT-----TTGA 1267
                         ------------------    iiv v -i     v  -  ----- v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_36784280_3   1268 TC-TATATC---GTGT----GCTGT--TTACAAATCTTTAAACAAATTTA 1307
                           -? v i ---i   ----   iv--i  i   v  i v iv i --- 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA---A 543

  chrX_36784280_3   1308 AATTTAAAA--AAATCTTTGTGACCTTTGGATAGGCAAAGTTTTCACAGA 1355
                           iv  ii?--       i        v  v       v v    vi   
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_36784280_3   1356 TA---CATCAAAAGAAGCACAATCTGTAAAAGAGCAAATTAATAAATTGG 1402
                           ---  i      ---     v vii      iv    vi         
  L1M4_orf2#LINE/    594 TATGACACCAAAAG---CACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_36784280_3   1403 ACTTCATCAAATAAAAAAAAACTTCT---CTTTGATAGACACTGTTAAGA 1449
                                    -- vv        i ---   ii vi      i i    
  L1M4_orf2#LINE/    641 ACTTCATCAAA--ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_36784280_3   1450 CAATGAAAGGGAAAAGCCA-ACGATGAAGAGAAAA-ATTTGCAAATCATA 1497
                         v i     i - v  v   - vi   i-       -              
  L1M4_orf2#LINE/    689 AAGTGAAAAG-ACAACCCACAGAATGG-GAGAAAATATTTGCAAATCATA 736

  chrX_36784280_3   1498 TAGATGATAACGGACTTAGATGTAGAACAGAACAAGAATTTTCAAAACTA 1547
                           vv      v      iv  vi    i v vv     i i i v    v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_36784280_3   1548 AATATGATAT-----CCAGCAACACAATTTAAAAATGGGGGAAAAATCC- 1591
                             --   v----- v ii   v     ?         vi  ii  ii-
  L1M4_orf2#LINE/    787 AATA--ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_36784280_3   1592 -ACAGAAACTTCAACCAAGGAGAGATAAGGATGGCAAATAAGCAAATATA 1640
                         - i   v i   vv v   i   v   vii     v        v  iv 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_36784280_3   1641 GAGATGTTCAATATCAGTAGTCAT 1664
                         i     i    i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.03 (112 / 109)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.06 (101 / 33)  


 313  4.26 8.51 0.00  chrX_36850430_36853081      962  1008 (1644)    L1M4_orf2#LINE/L1        1    51 (857)  

  chrX_36850430_3    962 TAGAATGATATCCCATGTTCATGGATTGGAAGA----ATATTGTTAAGAT 1007
                          i   v                           ----             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36850430_3   1008 G 1008
                          
  L1M4_orf2#LINE/     51 G 51

Transitions / transversions = 1.00 (1 / 1)
Gap_init rate = 0.02 (1 / 51), avg. gap size = 4.00 (4 / 1)  

2639 23.39 2.83 3.47  chrX_36850430_36853081     1382  2159 (493)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_36850430_3   1382 ATCCTAAAATTTGTATGAAAACACAAAAGACATCAAGTAGCAAAACCAAT 1431
                                    ii    i   ii   ii   vivi i    v   v    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_36850430_3   1432 TGAGCAAAAAGAAAGAGAATGAAGCTGGAGATATTGCAATACCTGATTTC 1481
                         ivv -        ---   ii   i     ivv ii  v v  ii     
  L1M4_orf2#LINE/    186 CTTG-AAAAAGAA---GAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_36850430_3   1482 AAAAC-----ATAAAGCAATTGTAATCAAAACAGTACAGTAGTATGGTAC 1526
                              ----- i     v iv        i     i--------      
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTG--------TGGTAC 273

  chrX_36850430_3   1527 TGGCATACAAACAGACTCATTGGTCAATGGAATAGGATAGAAAGCCCAGA 1576
                                vii i    vi  v i            i  v  i  i     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_36850430_3   1577 AAT----CTATGCATTTACAGTTCATTAATTTTTTACAAAGTTACCAAAA 1622
                            ---- i  i      ii  iv   i     iv    i v i    i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_36850430_3   1623 ACATACAATGGGGAAAGGACAGTCTATTCAATAAATGGTACTGAGAAAAC 1672
                         v   v            i i     v     i       i   i  v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_36850430_3   1673 CGGTTATCTATGTGCAGAAGAATGAAATTAGACCCTTTTCTCACATCATG 1722
                         i  v  ? i ii    i         i  i     i vi      i   i
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_36850430_3   1723 CACATACCATGCACAAAATTCAACTCAAAATGGATTAAAGATTTAATCGG 1772
                         i   ----------      -              i ?   ii   vi v
  L1M4_orf2#LINE/    474 TACA----------AAAATT-AACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_36850430_3   1773 AAGACCTGAAACTATAAAATCACTTA-AAGAAAACATAGGAGAAAAGTTC 1821
                             v  i           - v    -             ? v   vi i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_36850430_3   1822 TGTGACACTGGTCTGGGCAAGGACTTTTTAGACACGACCCTGAAAGCTCA 1871
                         i     vi   vi i     v ii  i     i i   v ii     v  
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_36850430_3   1872 AGCAACAATA----AACTA---AAA--GGATTGCA-AGAAATTAAAG-CT 1910
                                 v ----  v  ---   --   i v  -vi        i-  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_36850430_3   1911 TCTCCACAACAAAAGAAATAATTAACAAAATGAAGACATAGCCAAAAGAT 1960
                          i vii vv    i  v iv  i  v   i    i v i i  v v   v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_36850430_3   1961 TGAGAAAAAAAATATTTGCATGCCATACATTTGATAAGGGGTTAATATCC 2010
                           i  i    --        vii    i  i         ii vi     
  L1M4_orf2#LINE/    712 TGGGAGAAAA--TATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_36850430_3   2011 AAAATATATAAGGAACTAAAACACCTGAATCATAGAAA-ACCAATAACCC 2059
                          i         i     vvv   v  v   v   i   -  v        
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_36850430_3   2060 ATTTAAAAAATGGACAAAGAACCTGAACAGGCACTTCTCAAAAGAAGACA 2109
                          v  ?        i     i ii    i  i  i     v        i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_36850430_3   2110 TACAAATGGCCAACAGGTTCATTTAAAAAATGTTCAGCATCATTGATCAT 2159
                                      i i iv   v-    i   i   i     ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (115 / 63)
Gap_init rate = 0.02 (17 / 773), avg. gap size = 2.88 (49 / 17)  


3382 25.19 0.77 0.88  chrX_36937813_36942073     2860  3768 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36937813_3   2860 TGAAAAGATACCCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 2909
                           i       i                      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36937813_3   2910 GTCTATACTACCCAAAGCAACCTACAACTTTAATGCAATCCTTAACAAAA 2959
                          v v     v      vii i     iv  i  i       i  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36937813_3   2960 TACCAATGGCATTCTTCACAGAAATAGTAAAAGC-AATCCTAAAATTTAT 3008
                          v   iiv  v  i  ii       v - v    -i           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chrX_36937813_3   3009 ATAAAGCCACAAAAGGCCCAGAATAGTCAAAGTTATCC-AAGCAAAAAGA 3057
                           ii ivii   ii i          i    iiv   i-i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_36937813_3   3058 ACAAAACTGGAGGAATCATATTACCTGATGTCAAA--TTATTCTACAGAG 3105
                              ii       v   i i v  ii  v     --   --     i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAG 247

  chrX_36937813_3   3106 CTATAGTAAACAACACAGCATGGTGCTGGCATAAAAACAGATACATAGAC 3155
                            i     v   v    ii    i         ii i   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_36937813_3   3156 CAATTGAACACAATAGAGAATACAAAAACAAATTCACACACCTAAAATAA 3205
                             v   i v   v    i v  i   i   ii  i   ii  vii v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_36937813_3   3206 ACTCATTTTAGACAAGGATGCCAAGAACATGTATTGGGGAAAAGTTAGTC 3255
                          i v     v       i        v   vi v        iiv     
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_36937813_3   3256 TCTTCAATAAATGGTGCAGGCACAACTGGATATATCCATATATAGAAGAA 3305
                          i     i         v  v           ?--   i  ii i     
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAK--CCACATGCAAAAGAA 445

  chrX_36937813_3   3306 TGAAAATAGATTCCTATCTCTCACCGTACACAAAAATCAAATCAAAATGG 3355
                             iv i  ii    i   v    i  i        i  v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_36937813_3   3356 ATTAAAAACTTAATTCTAAGACCCAAA-CCATGAACCTACTACAATAAAA 3404
                           i ? i  i   v v     v i   - i  i  v  vi  v  v    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_36937813_3   3405 CATTGGGGAAACTCTCCAGGACACTGGTCTGGGCAAAAACTTCTTGAGTA 3454
                            v  ? v  v   i iv   vi   vi i     viii     iii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_36937813_3   3455 ATACCCCACGAGCACAGGCAACCAATGCAAAAATGGACAAACGGGATCGC 3504
                         vv  v   vi      i     v  v v      i  i   iv   iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_36937813_3   3505 ATCAAGTTTAAAAACTTT-ACACACTAAAGGAAACCATCAACAAAGTAAA 3553
                              iv           -iii vii      v  i     v     i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_36937813_3   3554 GAGACAACCAACTGAATGAGATAATACATTTCCAACT-ACCCATCTGACA 3602
                         i        v  v     i  v  v i    v   v - ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_36937813_3   3603 AGGGATTAATAACCAGAATACATAAGGAGCTCAAACAACTCTGTAGGAAA 3652
                              i vi  v        i    i  i   vv       vi  iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_36937813_3   3653 AAAAAGCTAATAATCTGATTTTTTTAATAGGCAAAAGTTTTGAATAGACA 3702
                           i -- v     i ii   ?vvv-   i      i v            
  L1M4_orf2#LINE/    796 AAGA--CAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACA 842

  chrX_36937813_3   3703 TTTCTCAAAAGAAGGCATACAAATGGCAAACAGGCATACGAAAAGGTGTT 3752
                               v       ii           v  i i   i i      i  i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_36937813_3   3753 CAACATTATTGATCAT 3768
                               i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (141 / 84)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2236 26.82 4.83 2.92  chrX_36958249_36960308.rev      679  1569 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36958249_3    679 TGAAAAAATATATCATGTTCATGGATGAAAAGCTTTAATATTATTAATAT 728
                           i   i    vi             vii   vi        i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36958249_3    729 ATCATTTATCCCAACATTAGTTT-TAGTGTCAACACATTCCCAATTATAA 777
                         iv  v vv    v v   ii i -i  vv     i  v    v  i v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36958249_3    778 TCCAAGCAGACTTTTAAG--GAAGTAGACCAAC-GATATAAGGCATATAG 824
                            v   v v     vv --   i v   v i -   ------ v  ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT------CCTA--- 141

  chrX_36958249_3    825 GAAAATAAAGGCATATAGACATACAAAGGAAGAACCTAGATTATGCAAAG 874
                         --    ----v     i  v  i   i   ----  i   v  vv    i
  L1M4_orf2#LINE/    142 --AAAT----TCATATGGAAATGCAAGGGA----CCCAGAATAGCCAAAA 181

  chrX_36958249_3    875 TAATTTTGAAAAAGAA---CAAACTTAAAGGATTTATAATAATTGCT--T 919
                         i   i           ---    v  ii    i i i v --- v i-- 
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT---TCCCAAT 228

  chrX_36958249_3    920 TTTAAGATCTACTATAACATAATGGCAATCAAGACAGTGTAG------CA 963
                           i  i ii     i  viiv ii i              i ------  
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_36958249_3    964 TAAAAACGAACAAATATGTCAATAGAGTTGAATAGAGAGACTAGAAATGT 1013
                            ii iii   v   vi     i  i v    v     v i      iv
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_36958249_3   1014 CTCTCCACTTATATATTCATTTGATTTTTTGACAAAATAGCCAAGGCAAT 1063
                         vi ivi  v v   iv   v        i-     iivv      i v  
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTC-GACAAGGGTGCCAAGACCAT 377

  chrX_36958249_3   1064 CCATTGGGGACAGAAAAGGCTTTTCCATGAATAGTGCTGGAACAACTGGG 1113
                         i  v      v    v  v      v ii   i       i        i
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_36958249_3   1114 TATCCATATGCAAGGAAATGAAACTCAATTCCTGCCTCATGCAATAAACA 1163
                           ?   i      iii      ii vi ii   i     ii v   v   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_36958249_3   1164 AAAATTAATTTGAGACAGAACAATAGACCTAAATGTAAAAAGTAAAACTA 1213
                                 i ii i ii  v  ?-              i iv        
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAW-AGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_36958249_3   1214 TAAATCTTTTGTATGAAAACATAGAC-TA--TCTTTGTGATTTGGAGATA 1260
                             v  i  iv v          i?-  --    i    ii v i v  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_36958249_3   1261 GACAAAGGTCTCTTAGA----ACAAAGAAAGCAATAATTGTAAATGAAAA 1306
                          i   v   i       ----   vvi      vv iivii   v     
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_36958249_3   1307 A-TAATGAAAAATTAAACTTCATAAACATTTAATACATTTACTCATCAAA 1355
                          -  --  v     ii       v  v   v  v  v   iiv v     
  L1M4_orf2#LINE/    627 AATA--GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_36958249_3   1356 AAACACCATTACAAAAATTAATAAACAAGCCTCAGTGTGGGAGAAAA-AT 1404
                         ii    i  i vi   i v  v i    v  v   vi          -  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_36958249_3   1405 TTGCAAAACATGTATCAGATAAAATACTGGTATC-AAAATATGCACAAAA 1453
                                v   i    v     iiv   v     - i     ii v i  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_36958249_3   1454 TCTTTGGAACTCAACCATAAA--------TAA----ATT-AAAAATTAAC 1490
                         iii  iv       iv     --------   ----   -      vii 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_36958249_3   1491 AAAAACATTGA-TAGAAAATTCAAAAGGGAAAAGATACA----GCCAATG 1535
                            iivv    -    v v   vvv ii   i v     ----      i
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_36958249_3   1536 AATACATGAAAATGTGTCCAACATCATCAGTCAT 1569
                          ii         vi  ii        ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (135 / 101)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.76 (69 / 25)  


2959 21.71 6.97 3.20  chrX_36972947_36976672.rev     2361  3235 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_36972947_3   2361 TGGAAAGATATCCCATGTTCACGAATAGGAAGACTCGATAGTCTCAAGAT 2410
                                              i i  v        ii   v v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_36972947_3   2411 ATCAGTTCTTTCCAACTTGATCTACGAATTCAGTGCAACCCCAATCAAAA 2460
                         iv  i v  ii    v         ii     ii    i   v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_36972947_3   2461 TCCCAGCAAGTGATATTGTGAATTTTTTTTTTTAAAAA---ACAA-CTGA 2506
                                ---------  i-----i      vi i   ---    -    
  L1M4_orf2#LINE/    101 TCCCAGC---------TGC-----CTTTTTTGCAGAAATTGACAAGCTGA 136

  chrX_36972947_3   2507 TTCTAAAGTTTATATGGAGAGGCAGCAGATACAGAATAGCCAAGACAATA 2556
                          i     i  i       i v   ivi  iv            i     v
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_36972947_3   2557 TTGTA---GAACACCAAAGTTGGTGGACTGACACTACCTAATTTCAAGAA 2603
                            v ---   v v         v     v     v  i        i v
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_36972947_3   2604 TTACTATTAAACTACAGTAATAAAGACAGTG--------GCAAAAGAATG 2645
                               iv  i          v         --------   v   i  i
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_36972947_3   2646 GACAAACAGGTAAATGTAACAGAATAGAGAG-------GTATATCCATA- 2687
                             v i  i v    v  i     v     -------i  v i     -
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_36972947_3   2688 -----TCGTCAACTGATCTTTGACAAAGGAGCAAAGGCAAAACAATGAAG 2732
                         ----- v     i    i  i     i  v  v   i v vv     ii 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_36972947_3   2733 ATAGA-----CTTTTCAACAAATGATGCTGGAACAACTGGACATCCACAT 2777
                          v   -----              i      i         i ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_36972947_3   2778 GAAAAAAAAATGAATCTAGA----TATGGCCTTACACCCTTCATAAAAAT 2823
                          v    i  -    vi i  ----  ---   i     v vi i      
  L1M4_orf2#LINE/    437 GCAAAAGAA-TGAAGTTGGACCCCTA---CCTCACACCATATACAAAAAT 482

  chrX_36972947_3   2824 ---CTCAAAATGGATCATATACCTAAATGTAAAATACAAAACTATAAAAC 2870
                         ---              ? v            i vvi             
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_36972947_3   2871 TCCTAGAA-----CATAGGAAAAAATCTACATGACCTCTAATATGGTAAT 2915
                           i     -----      ?iv      v i      ivii vv  i   
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_36972947_3   2916 GAGTT-TTAGTTATAACACCAAAGGTATGATTCATGAAAGGA----CTGA 2960
                          iv  -    v   i        i i ii viv ii    i ----iv  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_36972947_3   2961 TAAGCTGGATTTAAT----ATTATAAACTCCTACTCAGCAAAATACACTG 3006
                            ii    i  v  ----    v     ii iiv vv    iv     i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_36972947_3   3007 TCAAGAATATGAGAAGTCAAGCCACAGACTGTGAGAAAATATTTGCAGAA 3056
                                vi   i   v   v       v  v               i v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_36972947_3   3057 GACATAACATATAAAGTACTATTATCCAAAATATACAAACAACTCTTAAA 3106
                         v i   v vv    i v   vv      i      i   v        v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_36972947_3   3107 ACTCAGCAATGAGAAAAAAAAAAACATGATTTGAAAATGGACTAAATATG 3156
                              ii   i i  i v   v   vii   ?i       i v  iv  v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_36972947_3   3157 TG----GACACCTCACCAAAGAAGATATACAGATGGATACAGATGACAAA 3202
                           ----    ii  v                i    ---------- v  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGG----------CCAA 872

  chrX_36972947_3   3203 TAAACATATGGAAAG---CCCAACATCATATGTCAT 3235
                            i  i   i    --- i        ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (106 / 80)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.45 (89 / 20)  


3131 26.97 1.22 0.44  chrX_37012988_37018838     4458  5358 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_37012988_3   4458 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4507
                              ii i  i   i i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_37012988_3   4508 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4557
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_37012988_3   4558 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4605
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_37012988_3   4606 TATGGAATCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 4655
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_37012988_3   4656 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4705
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_37012988_3   4706 TACAGTACTCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACC 4755
                                v    i    ii         i iv ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_37012988_3   4756 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACTGCATATCTACAACC 4803
                                i    i--    i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_37012988_3   4804 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 4853
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_37012988_3   4854 CTATTTAATAA--GG-GCTGGGAAAACTGGCTAGCGATAAGTAGAAAGCT 4900
                           v  i  i  --  -       v      v  ? v i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_37012988_3   4901 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4950
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_37012988_3   4951 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5000
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_37012988_3   5001 CTAGGCATTACCATTCAGGACATAGGCATAGGCAAGGACTTCATGTCTAA 5050
                         v    ?i v viv   iv   v v  vv       v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_37012988_3   5051 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAA 5100
                         i            vvi          vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_37012988_3   5101 TTAAACTAAAGAGCTTCTGCACAGCAACAGAAACTACCATCAGAGTGAAC 5150
                          i   v v  i i   i  ii vv   vi  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_37012988_3   5151 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5200
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_37012988_3   5201 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTATAAGAAAA 5250
                         i  i  vi          v  i  v      vv    v iv    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_37012988_3   5251 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5296
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_37012988_3   5297 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5346
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_37012988_3   5347 ATCACTGGCCAT 5358
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


3186 24.65 0.64 4.14  chrX_37197481_37203881.rev     4970  5910 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_37197481_3   4970 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5019
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_37197481_3   5020 GGCTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5069
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_37197481_3   5070 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5118
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_37197481_3   5119 ATGGAATCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGG 5168
                               viiv  ii  v  viv  v     iv     i i ivv i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_37197481_3   5169 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5218
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_37197481_3   5219 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATCGATCA 5268
                                i   i    ii         i iv ii i   v    v     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_37197481_3   5269 ATGGAACAGAAC--AGAGCCCTCAGAAATAATACCAGACATCTACAACCA 5316
                               i    i--    i  --        vv   v    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_37197481_3   5317 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5366
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_37197481_3   5367 TATTTAACAAATAGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGGTG 5416
                          v  i       i         v      v  ?   i   i i  iii  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_37197481_3   5417 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5466
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_37197481_3   5467 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5516
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_37197481_3   5517 TAGG--TAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5564
                             --   - i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_37197481_3   5565 AAACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGGATCTA 5614
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_37197481_3   5615 ATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5664
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_37197481_3   5665 CAGGCAACCTACAGAATAAGAGAAAATTTTTGCAATCTACTCATCTGACA 5714
                         v  i     i       ii        v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_37197481_3   5715 AAGGGCTAATATCCAGAATCTACAA-GAACTCAACCAAATTTACTCAAAC 5763
                          i  i  vi          v  i  -      ------------------
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTC------------------ 777

  chrX_37197481_3   5764 AAATTTACAAGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCA 5813
                         ----      ---     ---------i  v     i     i     v 
  L1M4_orf2#LINE/    778 ----TTACAA---CTCAA---------TAATAAAAAGACAAATAACCCAA 811

  chrX_37197481_3   5814 TCAACAAGTGGGTGAAGGATATGAACAGACACTTCTCAAAAGAAGACATT 5863
                          i? v  i    ii      v    i     i     v        i  v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_37197481_3   5864 TATGCAGCCAAAAGACACATGAAAAAATGCTCATCATCACTGGCCAT 5910
                         i viii     v ii          i       v     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 4.09 (45 / 11)  


3218 27.28 0.44 0.55  chrX_37244146_37250539.rev     4995  5903 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_37244146_3   4995 TGGAAGAATATTCCATGCTCATGGGCAGGAAGAATCAATATCGTGAAAAT 5044
                              ii    i     i      iiv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_37244146_3   5045 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5094
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_37244146_3   5095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5142
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_37244146_3   5143 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5192
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_37244146_3   5193 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5242
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_37244146_3   5243 CTACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATCTAGAT 5292
                               i  i   i    ii         i iv ii i   v  v     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_37244146_3   5293 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAAC 5340
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_37244146_3   5341 TATCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAGGATTC 5390
                         i vi    i  i     ivv  v   i vi vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_37244146_3   5391 CCTATTTAATAAATGGTGCTGTGAAAACTGGCTAGCCATATGTAGAAAGC 5440
                         i  v  i  i           v  v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_37244146_3   5441 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5490
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_37244146_3   5491 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5540
                           i ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_37244146_3   5541 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5590
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_37244146_3   5591 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5640
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_37244146_3   5641 ATTAAACAAGAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5690
                           i   vvvi i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_37244146_3   5691 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5740
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_37244146_3   5741 AAGGGCTAATATCCAGAATCTACAGTGAACTCAAACAAATTTACAAGAAA 5790
                          i  i  vi          v  i iv      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_37244146_3   5791 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5840
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_37244146_3   5841 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCCCAT 5890
                            v        i  vi viii     v  i          i    i  v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_37244146_3   5891 CATCACTGGCCAT 5903
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.80 (9 / 5)  


2090 23.96 7.35 0.80  chrX_37339260_37340877      500  1125 (493)    L1M4_orf2#LINE/L1      242   908 (0)  

  chrX_37339260_3    500 ATAAAGCTACAACAATCAAGACAGTGTAGTAGTGGCAAAAGAACAGACAA 549
                          i         ii              i   v     v   i i     v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_37339260_3    550 ATAGATCAATGGAACAGAATAGAGAGCCTATAAATAGACCCACATAAAAA 599
                                       i     v     i i v     i     i i vvv 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_37339260_3    600 CAGTCAACTGATCTTTGACAAAAGAACAAAAACAATACAATGGAGAAATG 649
                         ii     i    i  i     ii vi v  i  v  v      i    vi
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_37339260_3    650 ATAATTTTT--AA--AAT--T----------CTAGA----CACA------ 673
                            i i   --  --   -- ----------  i  ----    ------
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_37339260_3    674 -----GACCTTACACCCTT----CACA--------AAAAATTAACCTGAA 706
                         -----  vv  iv    i ----    --------          iii  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_37339260_3    707 ATGGCTCACAGACCTAAATACAGAATACAAAACTATAAAATTCCTAGAAG 756
                             v   ?          ii ii vvi            i  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_37339260_3    757 ATAACACAGGAGAAAATCTAGGTGACTTTGGATTTGATGATTGCTTTGTA 806
                          v    i   ? v      vv     i    i  v iii  v i  iv  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_37339260_3    807 GATACAACACCAAAGGCATGATCCATAAAAGAAAGAACTAATAATCTGAA 856
                             ii        i   ii v v i        i  ivi    vi  i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_37339260_3    857 CTTCATTAAAATTAAAAATTCCTGCTCTGCAGAAGACGCTCTCAAGAGAA 906
                               i           i ii  iv  v  i i   i  v      i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_37339260_3    907 TAAAAAGACAAACCACAGACTGAAAAAATATATTTGCAAAAGACTTATCT 956
                          i         v       v  ii i  v           vv iv     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_37339260_3    957 GATAAAGGGCTTTTATGCAAAATGTACAAAGAACCCTTAAAACTCAACAA 1006
                              i  i   v   v  i   i  i       i    v       i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_37339260_3   1007 TAAGAAAACAAACAATCAAGTAAAAAAAAAAATGGGCCAAAGACCTTAAC 1056
                            i  i     i  i v i v?     ----     v  i  ii v  i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAA----TGGGCAAAGGATTTGAAT 837

  chrX_37339260_3   1057 AGATACCTTGCCAAAGATGG---ACAAGATGGCAAATAAGCATATGAAAA 1103
                            i ii iv       v i---    -     v        i       
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAA-ATGGCCAATAAGCACATGAAAA 886

  chrX_37339260_3   1104 TATACTCCACATTATATGTTAT 1125
                         v  i   v    i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (96 / 51)
Gap_init rate = 0.02 (11 / 667), avg. gap size = 4.64 (51 / 11)  


3398 25.19 1.10 0.77  chrX_37354233_37358483     2854  3758 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_37354233_3   2854 TGGAAAGACATTCCATGTTTATGGATTGGAAGAATCAATATTGTTAAAAT 2903
                                 i  i       i             v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_37354233_3   2904 GTCCACACTACCCAAAGAAATCTACACATTTAATGTAATCCCTATCACAA 2953
                          v v i   v      vvi       v   i  i i           v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_37354233_3   2954 TACCAATGACATTCTTCAAATAAATAGAAAAAACAGTCC-AAAATTTATA 3002
                          v   iivi v  i  iiv v    v  v  iviii   -      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_37354233_3   3003 TGGAA-CACAAAAAGACCCAGAATAGCCAAAGCTATCCT---AAGGAAAA 3048
                              -ii   ii-                 i v   i ---  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_37354233_3   3049 ATAAAACCGGAGGAATCTCATCACCTAACTTTGAATTACACTGCAGAGAT 3098
                          i   iii      v  v  iiv  i  i  ii  vivi   i  i  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_37354233_3   3099 ATAGTAACCCAAAGGGCACAGTAGTGGCGTAAAAACAGACACATGGATCA 3148
                          i     i v i vi iiii   v    i   ii i     i  i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_37354233_3   3149 GTGGAACAGAATAGAGAATCCAGAAACAAATCCACACACCCACAGTGAAC 3198
                         i     i     v    i        i   i   i   iii ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_37354233_3   3199 TCATTTTTGACAAAGGTGCCAAGAACATACA-CAGGAAAAGA-CAGCCTC 3246
                          v     i     i          v   v  -ii  i     -i  i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_37354233_3   3247 TTCAATAAATGGTGCTGGGATGATTCTACATCCATGTGCAGAAGAATGAA 3296
                              i              ii i vv i ?   ii    i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_37354233_3   3297 ACTAGACTCCCATCTCTCACTATGTATAAAAATCAAATCAAAATGGATAA 3346
                         ii i   i  i i   v   i  i  i      i  v           v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_37354233_3   3347 AAGTCTTAAATCTAATACCTCAAACTATGAAGCTACTAAAAGAAAACATT 3396
                         ?  v i     v   v v  v       i  i  vi  i          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_37354233_3   3397 GGGGAAACTCTTCAGGACACTAGAGTGGGCAAAGATTTCTTGAAAA--AC 3444
                           ? v  v     iv   vi i iv i     v i      ii v --  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_37354233_3   3445 ACCCGACAAGCACAGGCAACCAAAGCAAATATGGACAAATTGGATCTCAT 3494
                            -- v       i     v    v   v  i  i        ii    
  L1M4_orf2#LINE/    600 ACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_37354233_3   3495 CAAG-TTAAAAAGCTTCTGCACAGCAAAGGAAACGATCAACAAAGTAAAG 3543
                            i-       -   i  ii vv       v  v     v     i  i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_37354233_3   3544 AGACAACCCACAAAATGGAAGAAAATATTTACAATCTACCCATCTGACAA 3593
                                     i     i           i   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_37354233_3   3594 GAGATTAGTAACCAGAATATATAAGGAGCTCAAACAACTCTTTAGGAAAA 3643
                          i  i v   v             i  i   vv       vv  iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_37354233_3   3644 AAATTTTATAATCTGATTTTAAAAAGGGCAAAGGATCTTAATAAACATTT 3693
                          i ivv-    i ii   ?v    v           i v    i      
  L1M4_orf2#LINE/    797 AGACAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_37354233_3   3694 GGCAAAAGATAAGACATACAAATTGCAAGCAGACATATGAAAAGGTGCTC 3743
                         vv v     --   i        v  v ii ii  i        i     
  L1M4_orf2#LINE/    846 CTCCAAAGA--AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_37354233_3   3744 AACATCATTGATCAT 3758
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (146 / 78)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


3158 27.06 0.55 0.66  chrX_37383578_37389979     5001  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_37383578_3   5001 TGGAAGAACATTCAATTCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5050
                              ii i  i v  vi        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_37383578_3   5051 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5100
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_37383578_3   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5148
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_37383578_3   5149 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5198
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_37383578_3   5199 AACAAAGCTGGAGGCATCACGCTGCCTGATTTCATACTATACTACAAGGG 5248
                                i      vv    i  v  ii      v viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_37383578_3   5249 TACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5298
                             i   i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_37383578_3   5299 AATGGCACAGAAC--AGAGCCCTCAGAAATAATACTGCATATCTACAACC 5346
                              v i    i--    i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_37383578_3   5347 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACAATTCC 5396
                          vi    i  i     ivv  v   i v  vvv          v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_37383578_3   5397 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCAATATGTAGAAAGCT 5446
                           v  i  i              v      v  ? v i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_37383578_3   5447 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5496
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_37383578_3   5497 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5546
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_37383578_3   5547 CCAGGCA-ATACCATTCAGGACATAGGCATGAGCAAGGACTTCATGTCTA 5595
                         vi   ?i- v i -   iv   v v  vv ii    v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_37383578_3   5596 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5645
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_37383578_3   5646 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5695
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_37383578_3   5696 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5745
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_37383578_3   5746 GAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5795
                         ii  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_37383578_3   5796 AAAAGCAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGATACT 5845
                           i -    i     v  i? v  i            v    i   i i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_37383578_3   5846 TCTCGAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCCCA 5895
                             v        i  vi viii     v ii          i    i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_37383578_3   5896 TCATCACTGGGCAT 5909
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3240 21.59 4.25 2.68  chrX_37712251_37714426      790  1683 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_37712251_3    790 TAGAAACATATTCTGTGTTAATGGATTAGAAGATTCAATATTTTTAAGAT 839
                          i    v    i ii    v       i     i i      v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_37712251_3    840 GGAAATTCTCTCCAAATAAATTTGTAGA--CAATGCAAGCCCAATCAAAA 887
                           v   v   i      vi  i ii   --   i    v   v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_37712251_3    888 TACAAGCAGGATAATTTTGTAGAAATAGA--AATTATTATTCTACCATTT 935
                          v v   v vv v-     i      v  -- ii i--  i   vv   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTC 147

  chrX_37712251_3    936 ATATGAAAATATATGGGACCCAGAATAACAAAATCAATTTTAAA------ 979
                              i    ii v             i v   v    i  i  ------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_37712251_3    980 GAGCAAAGTTGGAAGACTTATACTACTAGATTTAAAAACTTACTCTACAG 1029
                           i          i    i i   v ivi    v          vi v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_37712251_3   1030 TTATAGCTATCAGTACAACACAGTATTGGCATAAGCATTGGCA-----AT 1074
                         i  i  iv    iv   iiiii   i         v  v i  -----  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_37712251_3   1075 CAGTGGAATAGAATTGAGATTCCAGAAAAAAAAAAAAAACTTTATGGCCA 1124
                           i                v        v   vvv v vv       i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_37712251_3   1125 ATTGATTTTTG------GTAC--------TTCAGTGGGGAAAGAATAACC 1160
                                  i ------  i --------    i             ii 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_37712251_3   1161 TTTTCAACAAATCATACTGGGACAACAGGATATCCAAATACCACAAAACA 1210
                                     vi i          v     ?   v  i ---    --
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC---AAAA-- 442

  chrX_37712251_3   1211 TAAAAGAACTTTGACTCTTAACATATACCATG--CAGAAATTAAGCAACG 1258
                         -i  v   v  v   i i  v vi i     i--  i       ---- v
  L1M4_orf2#LINE/    443 -GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA----CT 487

  chrX_37712251_3   1259 CAAAATGGATTATAAACCTAAATGTAAGAACAGAAACCATAAAATTCT-A 1307
                                   i ? i              i vi    i      i   - 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_37712251_3   1308 AAAGAAAACCTAGGAGAAAATCTCCATGACTTTCAGTTAGGCAAAGAATT 1357
                         i        v    ? v      i i    i  vi         v iv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_37712251_3   1358 CTTAAATATGGCACTGAAAGCATGATGCATGTATTCAAGAAAAAAAACTG 1407
                             i     i   ii      ii -   --- --   i i      iv 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAA-GCA---A--CAAAAGAAAAAATAG 631

  chrX_37712251_3   1408 GTAAATTAAATTTCATCAAAATGAAAAATGTTTACACTTCAAAAGACACC 1457
                         i      ii i           v     iv   iii       i     i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_37712251_3   1458 ACTACAGATGTGAAAAGTCAAGCCACAGACTGGAA--AAGTATTTTCAAA 1505
                          ii vii v        v   v       v   i --  i     v    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_37712251_3   1506 TTATATATTTGTTAAAGGACTTGTATCTAGAATATATTTCTTAAA--ACC 1553
                          i      i  v   i           i         -----   --  i
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATAT-----AAAGAACT 776

  chrX_37712251_3   1554 CTTACA-TTCAATATTAAAAAGACAAATAATCATATTAGATAATGGGAAA 1602
                               -i      v               i vv   ?i v      v  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_37712251_3   1603 AAGATTTGGATAGACATTTAATCAA-GAAGATTTACAAATGCCTAATAGC 1651
                          i      i          vvi   -      v        v i    iv
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_37712251_3   1652 TGCATTAAAATATGTTCAGCAACATTAGTTAT 1683
                         ii   v    v   i   i  v  ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (114 / 75)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.95 (62 / 21)  


2901 20.45 1.95 2.11  chrX_37730651_37732306.rev      502  1166 (490)    L1M4_orf2#LINE/L1      245   908 (0)  

  chrX_37730651_3    502 AAACTATAGTAATCAAAACAGCATGGTACTGGCATAAGAACAGATACATA 551
                           i   i         i    ii               i i   i i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_37730651_3    552 ACACCAATGGAACATAATAGAGAGTCCAGAAATAAA--------TTTATG 593
                         i- i        i v   v                 --------      
  L1M4_orf2#LINE/    295 G-ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_37730651_3    594 GTCAATTGATTTTCAACAAAAGTGCCAAAAATACACAATGGGGAAAGGAC 643
                                       i    ii       i vi iv            i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_37730651_3    644 AGTCTCTTTAATAAACAGTATTGGGACAACTGAATATCCACATGCAGAAG 693
                              i  i  i   ii  ii           i   ?         i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_37730651_3    694 AATGAAATTGGACCCTTGTCTCACACCATATACAAAAATCAACTCAAAGT 743
                               i        i ii                    i        i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_37730651_3    744 GGATTAAAGACTTAAGCATGAGACCTGAAACTGTAAAACGACTAGGA-AA 792
                             i ?    i   iii i   v  i     i      vvi   i -  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_37730651_3    793 AACATAGGGGAAAAGCTCCACAACATAGGTCTGGGAAATTTTTTTTTGAA 842
                                 ? v   v  i iii  v v  vi i  v   vv   i  ii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_37730651_3    843 TATGACCCTAAAAGCACAGGAAACAAAAGCAAAAATAGGCAAATAGGACT 892
                               v i         i v        v        ii    v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_37730651_3    893 GCCTCAAACT---GAACTTCTGCAGAGCAAAGAAAACAATCGACAGAGTG 939
                         v v     v ---i     i  iivvv     i v  v   i v i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_37730651_3    940 AAGAGACAATCTGCAGAATGAGAGAAAATAGTTGCAAATCATACATCTGA 989
                           i      i ii       i         v            i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_37730651_3    990 TATAGTTTAAGTTAAATCATTTAATATCGAAGATACATGAGGAACTCAAG 1039
                           -  ----i ------- i  i-    v ii   i  i i      vvi
  L1M4_orf2#LINE/    744 TA-AG----GG-------ACTTG-TATCCAGAATATATAAAGAACTCTTA 780

  chrX_37730651_3   1040 CAATTCAATAGTAAGAAAACAAATAATCCAATTAAATAATGGGGAAAGGA 1089
                            i      i   i  i        i      ?  v      v      
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_37730651_3   1090 TCTTAACAGACATCTCTCAAAAGAAGACATACAAATGGCCAA-AAGTGTG 1138
                          i v  i      i    v        i              -   iiii
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_37730651_3   1139 TGACAAAATGCTCAACATCGCTAATCAC 1166
                            v  i            i????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.57 (95 / 37)
Gap_init rate = 0.01 (9 / 664), avg. gap size = 3.00 (27 / 9)  


2552 21.40 14.65 1.15  chrX_37856138_37858975     1561  2345 (493)    L1M4_orf2#LINE/L1       18   908 (0)  

  chrX_37856138_3   1561 TTCATGGATCTGAAGACTCAATATTTTTAAGATGTCAAGTCTCCCTGAAC 1610
                                  iv       i      v        v   vv     ii  i
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_37856138_3   1611 TGATCTTTACATTCAACTCAGTCCAAATCAAAATCTCAGTAGACTTTTGT 1660
                               vi v       v  i   vv         i   iv v     - 
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT-T 116

  chrX_37856138_3   1661 CATGGAAATTGACAGACAAATTCTAAAATGAATATTGAAATGCAAAGAAC 1710
                         iiii          ii vi  i       vv    v         i i  
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_37856138_3   1711 T-AGAGCAGCAAAAACCACTTTGAAAAAGAAAAATAAATTTGGAGAAATA 1759
                         i-   ii   v     v ii           i  i   v      i v v
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_37856138_3   1760 ACACTCCCTGACTTCAAGATTTATTAAAAAGCTATGTTAATGAAGATAAT 1809
                              i  ii i     i i   i  v       iiv    v    i i 
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_37856138_3   1810 GTGGTGTTGGCATAAAGGTAGACAAACAGATCAATGAAACAGAAGAGAAA 1859
                              ii        i i      v i         i  i    vv  i 
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_37856138_3   1860 GTCCAGAAATAGACCCATGCATATAAGATCAATTAAATTCTGACAAAGGT 1909
                                    i      i   v  v i      i v  ii     i   
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_37856138_3   1910 GCCAAGGCAATACAGTGGCAAAAAGATAGTATTATCAACAAATGATA--- 1956
                               i v  v  i   vi   ii     v  v          i i---
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_37856138_3   1957 ------------------ATGTAA------------------CCATCACA 1970
                         ------------------   i  ------------------ i i v  
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_37856138_3   1971 CATCTATATGC-----------CAA---------------TAAA---AAG 1991
                           i -    i -----------   ---------------    ---   
  L1M4_orf2#LINE/    467 CACC-ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_37856138_3   1992 AGC----ACTTTGATCCACGTCTAGAAGAAAACACAAG---AAATCTTTG 2034
                            ----   v i --v  vii            i i ---       i 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAA--AACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_37856138_3   2035 TGATCTTGGACTAGGCAAAGCTTTCCTAGATATGACACCAAAAGCACAAT 2084
                            i     ii       v v    i                       v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_37856138_3   2085 CTATAAAAGAGGAAAATAATGTGAAATGAACTTCATCAAAATGAAAAAGG 2134
                          v i      i-      i-i i  v  i             v     vv
  L1M4_orf2#LINE/    614 CAACAAAAGAA-AAAATAG-ATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_37856138_3   2135 TATGCTTCTCAAATGATGATGTTAACAAACT-AAAAGACGAGCCACAGGT 2183
                          v  ivii     v  iiv i i  v   v -       i v      iv
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_37856138_3   2184 GAAGAGAAAATATTTGTAAATTATATGTT------------------CAG 2215
                         vii             i    i    i i------------------   
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_37856138_3   2216 AATATATGAAGAACTCC-AAAA-TCAATCATAAGAAAATAAATAAGCACC 2263
                                i        i- v  -     v    i  i i      ---  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA---CC 808

  chrX_37856138_3   2264 CAA------AAT----------TTGGAATAGACACTTCACAAAAGTAGAT 2297
                            ------   ----------  v         i   v v    v    
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_37856138_3   2298 ATACGGATGACAAATAAGCACA--AAAAGATGCTCAACATCATTAGGGAA 2345
                             ii   i v          --                  ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (105 / 63)
Gap_init rate = 0.02 (21 / 891), avg. gap size = 5.90 (124 / 21)  


2480 23.48 1.25 0.18  chrX_38033209_38035701.rev      751  1308 (1184)    L1M4_orf2#LINE/L1        1   564 (344)  

  chrX_38033209_3    751 TGGAATGATATCCCATGTTCATGGATTGAAAGAATTAAT---GTAAAAAT 797
                              v                      i    v     ---  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38033209_3    798 GTCCACACCACCCAAAGTGATCTACAGATTCAATGCAACCCCTATCAAAA 847
                          v v i  iv      v                i    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38033209_3    848 TTCCAA-TGTCATTTTTCACATAAATCAAAAATACAATCCTTAAGTTTGT 896
                          i   i-  i -     ii  v    ii v  vvii     v  i  ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_38033209_3    897 AGGGAACCACAAAGAACCCA-CATAGATAAAGCAATCTTGAACAAAAGGA 945
                          v    vii   i i     -v    vi   i          v  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_38033209_3    946 AGAAAGCTGGCAGCATCACACTCCTTGATTTTAAAACATATTATAAAGAC 995
                          v    i   vi vv       i iii    i     v  i  i    vi
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_38033209_3    996 ATTTTAATAAAAACCACACGGTACTGTCATAAAAACAGACACATTAACCA 1045
                          ivv    v  i  viiii       v     ii i     i  vi i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_38033209_3   1046 ACAAAACAGTAAGGAAAGCCCAGAAATGAACCCATGCATTTATGGTCAAT 1095
                          iii  i  v vv  i  i        i       i              
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_38033209_3   1096 TGCTTTTTGACAGAGGTGCCAAGAACACATAATGGGGAAAGGACAGTCTC 1145
                           v    i    ii          v  ivi           i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_38033209_3   1146 TTCAGCAAATGGTGTTGAGAAAACTGGATATCCACATGCAGAAAAATAAA 1195
                             i         i  i  v         ?         i  i   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_38033209_3   1196 ATTGGACCCTTGTCTCACACCATATA--AAAATCAACTCAAAATGGATTA 1243
                         i        i ii             --     i              i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_38033209_3   1244 AAGACTTAAATATAAGCTCTGAAGCTGTAACACTACTAAAAGAAAACATA 1293
                         ?    i     i    vv  i  i  i   v   vi  i           
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_38033209_3   1294 GGGAAAAAGCTCTGT 1308
                           ?iv   v  ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT 564

Transitions / transversions = 2.05 (86 / 42)
Gap_init rate = 0.01 (5 / 564), avg. gap size = 1.60 (8 / 5)  

1255 22.39 5.37 0.00  chrX_38033209_38035701.rev     1667  2001 (491)    L1M4_orf2#LINE/L1      556   908 (0)  

  chrX_38033209_3   1667 AAGCTCTATGACAT-GAGTCTTGTAATTGTTC---ACATATGACCCTGAA 1712
                           v  iii    v - i  ivv i   v   i--- v       v ii  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_38033209_3   1713 AACACAAGTGATAGAAACAAACATAGACAAATCAAATTGCATCAAAG--- 1759
                          i      ii i i  iv   v     i    iii i v       i---
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_38033209_3   1760 ----CTTCTGCACAGCAAAAGAAACAATTAATAAAGTGAAGAGACAATCC 1805
                         ----   i  ii vv    i  v  v  i  v        i      i  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_38033209_3   1806 ACAGAATGGGACAAAATATTTGTAAACCATACATCTGTTAAGGGATTAAT 1855
                                    v          i   i    i     v       i vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_38033209_3   1856 ATCCAAAATATATAAGGAACTCAAACAACT-AA--AGAGAAAGA-AAACA 1901
                              i         i      vv      -  -- v i     -   i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_38033209_3   1902 ACCTGATTAAAAAATGGGCAAAGGACCTGAACAGGCATTTTTCCAAAGAA 1951
                            ii   ?                ii    i  i     i         
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_38033209_3   1952 GACATACAAAT---CATCAAGTTCATGAAAAAATGCTGAGTATCATTAAT 1998
                           i        ---  vi   iv        i     v ii    ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_38033209_3   1999 CAT 2001
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.08 (50 / 24)
Gap_init rate = 0.02 (7 / 353), avg. gap size = 2.57 (18 / 7)  


1928 19.38 0.33 24.73  chrX_38062273_38065015.rev     1056  2252 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_38062273_3   1056 AAAGATATCCCATTCTCATGGATTGGTAGAATTAATATTATTAAAATGTC 1105
                                      vi           v   v        i    i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_38062273_3   1106 CATACTATCCAAAGTGATCTGTAGATCCAATGCAATTCCTATCAAAATAC 1155
                         v     vi     v      ii    i   i     i           v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_38062273_3   1156 CAATGACATTCTTAATATAAATGGAAAAAAC-ATCCTGAAATCTGTATGA 1204
                           iivi v  i  vii v    v  v  ivi-     i    iii    i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_38062273_3   1205 AACCACAAGAGACTGTGAATAGCTGAAGCAATTCTTAGCAGAAAGAACAA 1254
                           vii    i   ivv       ii  i    ii v iv ii        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_38062273_3   1255 AGCTGGGGCA-TAACACCATTTGACTTAAAAATGTACTACAAAGCAATGG 1303
                           i   i v - v    iviiii i  v    iv           v ii 
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_38062273_3   1304 TAATCAAAACAGCATTGTACTGACATAAAAACAGATACATAGACCAATAG 1353
                                i    ii v      i     ii i   i i     i    i 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_38062273_3   1354 AACAGAGTAGAGAACCCGGAAATAAATCCATGTATTTACAGCTAACTCAT 1403
                           i   i v    ii  i        i    ii     ii ii  i v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_38062273_3   1404 TTCCTGCAAAGGCACCAAAAACTTATATTTGGGAAAAAAAAAACAGTCCC 1453
                           i vi   i  ii    i v v vi v v      i  ----i    ii
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA----TAGTCTT 399

  chrX_38062273_3   1454 TTCAAAAAATGATGCAGGGAAAACTGGATATCCATATGCAAAAGAATGAA 1503
                              v     i   v    v         ?   i               
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_38062273_3   1504 ACTAGACCTCTGTTTCTCATCATATACAAAAATCAACTTAAGTCAGGTGC 1553
                         ii i    i  iii  v  i             i    ------------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACT------------ 487

  chrX_38062273_3   1554 GGTGGCTCATGCCTATAATGACAGCACTTTAGGAGGCCTAGGTGGAAGCA 1603
                         --------------------------------------------------
  L1M4_orf2#LINE/    488 -------------------------------------------------- 487

  chrX_38062273_3   1604 TTACTTGAGTCCAGGAGATTGAGACCACCCTGAGTAATATAGGGAGATCC 1653
                         --------------------------------------------------
  L1M4_orf2#LINE/    488 -------------------------------------------------- 487

  chrX_38062273_3   1654 TGTCTCTACATACAAACACACACAAAATTAAAGTGTTATCCAGGCATGGT 1703
                         ----------------------      ----------------------
  L1M4_orf2#LINE/    488 ----------------------CAAAAT---------------------- 493

  chrX_38062273_3   1704 GGCATGTGCTTGTAGTCCCAGCTACTTGGGAGGCTGAGGTAGGATGCAGT 1753
                         -----------------------------------------    -----
  L1M4_orf2#LINE/    494 -----------------------------------------GGAT----- 497

  chrX_38062273_3   1754 GAGCCATGATCATGCCACTGCACTCCAGCCTGGGTGACAGAGCAAGACGC 1803
                         --------------------------------------------------
  L1M4_orf2#LINE/    498 -------------------------------------------------- 497

  chrX_38062273_3   1804 TGTCTCAAAAAAAAAAAAAATCAACTTAAAATAGATTGACTTAAATGTAA 1853
                         -----  ? ----------------------------   i         
  L1M4_orf2#LINE/    498 -----CAWA----------------------------GACCTAAATGTAA 514

  chrX_38062273_3   1854 GACCTGAAACTATGAAACTACTAGAAGAAAACATTAGAGAAACACTTCTG 1903
                           v  i       i     vi             vi ? v  vv    vv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_38062273_3   1904 GAAATTGATCTGAGTAAAGATTT-TGGGGCAAGACCATAAAAGCACAGAT 1952
                           vv   ivi ii i  v i   - vi ii v   vvi         iii
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_38062273_3   1953 AACAAAAGCAAAAATAGACTAATGGAATTACATCAAACTAAAAAGCTTCT 2002
                                 v         iv   v i i v       v v    i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_38062273_3   2003 GCACAGCATGGAAAACGATCAACAGACTGAAGAGAAAACTTACAGAATGG 2052
                          ii vv  vi i v  v     v i v    i   v   ii         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_38062273_3   2053 AAGAAAATATTTTCAAGCTATCCATTTCGCAAGGGGTTAATAACCAGAAT 2102
                         i           v   iii  vi  i vii     ii vi  v       
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_38062273_3   2103 TTGTAAGAAACTCAAACAACTCAATAGCAAAAACAGAAAACAAAAATAAT 2152
                         v i   ii     vv           ii     -----i     --   i
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAA-----GACAAA--TAAC 807

  chrX_38062273_3   2153 CCAATT-AAAAATGGGCAAATGATCTGAATAGACATTTCTCAAAAGAAGA 2201
                               -             v   i                v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_38062273_3   2202 CATACAAATGGCCAAGAAGCATATGAAAAATTGTTTGATATCACTCATTA 2251
                         i              v     i       iv  i ii i    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_38062273_3   2252 T 2252
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.83 (148 / 81)
Gap_init rate = 0.01 (11 / 905), avg. gap size = 27.27 (300 / 11)  

 253 26.98 0.00 0.00  chrX_38062273_38065015.rev     2678  2740 (3)    L1M4_orf2#LINE/L1        4    66 (842)  

  chrX_38062273_3   2678 AAAAACATTCCATGATCATGAATTGCAAGGATCAATGTAGTTAAAATGGC 2727
                            i i  i     v     i    v   iv i   i v     i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_38062273_3   2728 CATATTGCTTAAA 2740
                         v   i v ii   
  L1M4_orf2#LINE/     54 AATACTCCCCAAA 66

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.00 (0 / 0)  


3261 25.52 0.49 0.12  chrX_38165359_38167174.rev      507  1325 (491)    L1M4_orf2#LINE/L1       87   908 (0)  

  chrX_38165359_3    507 AATTACAATGAAAGCACCAATGACATTCTTCACAGAGATAGAAAAAC-AA 555
                            iv v  v   iiv   iivi v  i  ii    i  v  v  i -i 
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chrX_38165359_3    556 TCCTAAAATTTATATGGAATCACAAAAGACTTAGAATAGCCAAAGCTATC 605
                                   i        vii   ii   ii            i v   
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_38165359_3    606 TTGAGCAAAAAGAATAAAACTGGAGGAATCACATTACCTGACTTCAAATC 655
                             iv  i     i   ii       v     i v  ii i      v 
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_38165359_3    656 ATTCTATAGAACTATAGTAAACAAAACAGCATGGTACTGGCATAAAAACA 705
                         v v   i i i   i     v   i    ii              ii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_38165359_3    706 GACACATAGACCAATGCAACCAAATAGAGAACCCAGAGGCAAATCCATAC 755
                             i     i     v  ivi   v    ii     iii   i      
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_38165359_3    756 ATCTACAGTGAACTAATTTTCAACAAAGTTCCCAAGAACATACACTGGGG 805
                           i  ii  v  i i      i    i v v      v   v  v     
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_38165359_3    806 AAAGGACAGTCTCTTCAATAATTGGTGCTGGGAAAACTGGATATCCCTAT 855
                             i i     i     i  v           v         ?  vi  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_38165359_3    856 GCAGAAGAATGAAACTAGACCCCTCTCTCATACCATATAAAAAAATCAAA 905
                            i         ii i       vi    i        v      i  v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_38165359_3    906 TCAAAATGGATTAAAGAGTCACATCTAAGACCTCGAACTGTGAAACTACT 955
                                    i ?   vii v  v     v  vi    i i     vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_38165359_3    956 AAAAGAAGACATTGGGGAAACTCTCTAAGACACTGGATTGGGCAAAGATT 1005
                          i     i    v  ? v  v   iiiv   vi   i  i     v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_38165359_3   1006 TCTTGAATAATACCTCACAAGCACAGGCCACCAAAGCAAAAATGGACAAA 1055
                             ii   vv  vi  v       i  v  v    v      i  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_38165359_3   1056 TGGGATCACATCGAGTTTAAAAGTTTCTGCACAACAAAGGATACAATCAA 1105
                          v   iiv    i iv      ii  i  ii vv       i  v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_38165359_3   1106 CAAAGTGAAGAGACATCGCACAGAATGAGAGAAAATATTTCTAAACTACT 1155
                         v        i     v v         i            vi   ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_38165359_3   1156 CATCTGCCAAGGAATTAATAGCCAGAATATATAAGGAGCTCTAACAACT- 1204
                         i     vi    i i vi  v             i  i    v      -
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_38165359_3   1205 -ATAGGAAAAAAATATAATGATCTGATC-AAAAATGGGTGAAAGACCTGA 1252
                         -   iv     i i -   i i ii  i-         ii  i  ii   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_38165359_3   1253 ATAGATATTTCTCAAAAGAAGATACCCAAATGGCAAACAGGTATATGAAA 1302
                              i       v          iv        v  i i i i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_38165359_3   1303 AAGTAGTCAACATCATTGATCAT 1325
                          ii iv         ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (135 / 71)
Gap_init rate = 0.00 (4 / 822), avg. gap size = 1.25 (5 / 4)  


 209  9.76 0.00 0.00  chrX_38219635_38222248      448   488 (2126)  C L1M4_orf2#LINE/L1   (0)   908   868  

C chrX_38219635_3    488 GCCAAAAAACACATGAAAAAATGCTCACCATCACTGGCCAT 448
                              v  i          i       v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (2 / 2)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  

3019 27.60 0.47 0.47  chrX_38219635_38222248     1259  2113 (501)    L1M4_orf2#LINE/L1        1   855 (53)  

  chrX_38219635_3   1259 TGGAAGAACATTATATGCTCATGTGTAGGAAGAATCAATATCGTGAAAAT 1308
                              ii i  ivi   i     vi v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38219635_3   1309 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1358
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38219635_3   1359 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1406
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_38219635_3   1407 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1456
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_38219635_3   1457 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1506
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_38219635_3   1507 TACAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGAGATATAGATC 1556
                                 i   i    ii       i i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_38219635_3   1557 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 1604
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_38219635_3   1605 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGTGGAAAGGATTCC 1654
                          vi    i  i     ivv  v   i v  vv     v      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_38219635_3   1655 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1704
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_38219635_3   1705 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1754
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_38219635_3   1755 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1804
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_38219635_3   1805 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1854
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_38219635_3   1855 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAAGGGATCTAA 1904
                         i            vvi          vv     v  i   vv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_38219635_3   1905 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1954
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_38219635_3   1955 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 2004
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_38219635_3   2005 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 2054
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_38219635_3   2055 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 2104
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_38219635_3   2105 TTAAATGAA 2113
                          iv  v   
  L1M4_orf2#LINE/    847 TCCAAAGAA 855

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (5 / 855), avg. gap size = 1.60 (8 / 5)  


3018 26.92 1.22 1.11  chrX_38357341_38359230.rev      501  1399 (491)    L1M4_orf2#LINE/L1        9   908 (0)  

  chrX_38357341_3    501 TATTCCATGCTCATGTCTAGGAAGAATCAATATAGTTAAAATGGCCATAC 550
                            i     i     vv v      v i     v     i     v    
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chrX_38357341_3    551 TGCTCAAAGCAATTTCCGGACTCAATGTA-TTCCTATCAAACTACCAATG 599
                          v i    vii  i v i  i    i i - i         v v   iiv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chrX_38357341_3    600 ACATCTTTCACAGAATTAGAAAAA---ATTCTAAAATTCATATGAAACCA 646
                         i v i   ii     v v  v  i---  i              i  vii
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_38357341_3    647 AAAAAGAGTCTGAGTAGCCAAAGCAATCTGAAGCAAAAGGAACAAAGCCA 696
                         v  ii  vi v  i        i      vi iv  i i        iii
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_38357341_3    697 GAGGCATCACATTACCTGACTTCAAACTATACTACAAAGCTACAGTAA-C 745
                             vv     i v  ii i      viv                   - 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_38357341_3    746 AAAAAAGCATGGTACTGATACAAAGAGAGACATATAAAGCAATAGAACAG 795
                           i v  ii        ii i  i  v         i v    i   i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_38357341_3    796 GCTAGAGAACCCAGAAATAAAGTTGCAGACCTACAAACAGCTGATCTTTG 845
                         iv v    ii           viiii v ii  iiiv  ii    i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_38357341_3    846 ACAAAGTT--CACAATTATAAGCAATGGGGAAAGAACTTCCTATTCAATA 893
                             i v --  vi ii  --v              ivvi  v     i 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_38357341_3    894 AATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGGTTGAAACTCGAC 943
                                      i      v  ?   i     i   iv    ii v   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_38357341_3    944 TCCTTTCTTTCACCTTATACAAAAATAAACTGAAGATGCATTAAAGTCTT 993
                         i   vi  iv    v           v    v  i   v  i ?  v i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_38357341_3    994 AAATATAAGACATGAAGCTATAAAAACCCTAGAAGAAAACCTAGG---AA 1040
                             i     vv i  i        vi i           v    ---  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_38357341_3   1041 ATGCCATTCTCGACACAGGCCCTGGCAAAGATTTCATGACCAAAATGCCA 1090
                           -- -   vi   viv  viiv     v i    v iivi vi ii   
  L1M4_orf2#LINE/    557 AT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_38357341_3   1091 AAATTTTGCAATAAAAACAAAA-ACAAAATTGACAAGTGGGACCTAATTA 1139
                            ----   vv iv       - v     v  i  i v    i v  i 
  L1M4_orf2#LINE/    604 AAA----GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_38357341_3   1140 AACTAAAGAGCTTCTACACAGCAAAAGAAAATATCAACAGGGTAAACAGA 1189
                           v v  i i   i iii vv    i  v v      v ii  i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_38357341_3   1190 CAACCTACAGAACGGGAGAAAATATTTGCAAACTACGCATTTGACAAAAG 1239
                              i      i                   ii iii  i   i  ii 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_38357341_3   1240 TCAAATATCCAGAATCTATAAGGAACTTAAACAAATTGGCAAGCAAAAAA 1289
                         v vvi          v     i     ivv    v iiii  -i     i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAG 798

  chrX_38357341_3   1290 ACAAACAACCCCGTTTAAAAATGGGCAAAGGACATGATCAGACATTTCTT 1339
                              i     vi  ?                iv   vi          i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_38357341_3   1340 GAAAGAAGACATGCACATGGCCAATAGACATATGAAAAAATGCTCAACAT 1389
                         v        i  i  v          ii  i       i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_38357341_3   1390 CACTAGTCAT 1399
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.63 (148 / 91)
Gap_init rate = 0.01 (11 / 900), avg. gap size = 1.91 (21 / 11)  


2021 24.49 3.15 0.74  chrX_38443140_38445861     1029  1567 (1155)    L1M4_orf2#LINE/L1        3   554 (354)  

  chrX_38443140_3   1029 GAAAAAAATCGCATGTTTATGGATTGCAAGTATTAATATCATTAAAATGT 1078
                             i v   v      i        v   vv       ii    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_38443140_3   1079 CCATACAATCCAAAGCAATATACAGATTCAGTGAAATTCCTATCAAAATA 1128
                          v    vvi     vii  v          ii v   i           v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_38443140_3   1129 CCAATGACATTCTTTATGACAAT--AAAAGA-AATCCTAAAATTTGTGTG 1175
                            iivi v  i   iiiiv   -- v   v-i           ii i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_38443140_3   1176 GAACCACATAAGACCCTGAATAGCCAAAGCAATCGTGAACAAAAAGAACA 1225
                            vii  vii     v           i     v    v  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_38443140_3   1226 AAGTTGTAGGCATCTTATTACTTAACTTCAAATTATACTACAAAGCTATA 1275
                               v   vv  vi i v ii  i      viv             i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_38443140_3   1276 ATAACCAAAACACTGTGGTCCTGGCATAAAAACAGGCAC-T-GACCAGTG 1323
                         i   i   i   v      v         ii i  i  i- -  i  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_38443140_3   1324 GAATAGAATAGAGAACCGAGAAATACATTCATGCACCTACAGCTAACTGA 1373
                                  v    ii v       v ii   i  ii  ii ii  i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_38443140_3   1374 ATTTTGACAAAAACACCAAAAACACACATTGGGGAAATGACAGTCTTTTT 1423
                         v   i     iiiii    i v  iv  v        vi i        -
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT- 401

  chrX_38443140_3   1424 CAATAAATGGTTCTGGGA-AA----------ACATGCTGAAGAATGAAAC 1462
                            i       v      -  ----------      vi         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_38443140_3   1463 TAGACCCCTATCTCTTACCATATACAAAAAATCAACTAAAAATGCAT-AA 1511
                          i        i   vi              - i    v      v  - ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAW 500

  chrX_38443140_3   1512 AGGCTTAAATGTAAAACCTAAAGTTATGAAACTACTAGAAGAAAACATAT 1561
                           i i         i v     ii   i     vi              -
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA- 549

  chrX_38443140_3   1562 GGGAGT 1567
                         -  ?  
  L1M4_orf2#LINE/    550 -GGNGT 554

Transitions / transversions = 1.77 (83 / 47)
Gap_init rate = 0.02 (10 / 552), avg. gap size = 2.10 (21 / 10)  

1099 23.45 6.21 1.98  chrX_38443140_38445861     1876  2229 (493)    L1M4_orf2#LINE/L1      540   908 (0)  

  chrX_38443140_3   1876 AGATAACACATGGGAAACAATTCATGACATTGATCTAGG---TGGGATTT 1922
                            v    i v ? v  vvv   i    v   ivi    ---   ---- 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG----T 585

  chrX_38443140_3   1923 TTTTTGGATAGAACCTGAAATGCACAGGCAACAAAAAGCAAGAATAGACA 1972
                           i  i    vi  viv   v     i         - v  i      i 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATA 634

  chrX_38443140_3   1973 AAT-GAATTTACATCAAACCAAAAAGCTTCTACACTGGAAAGGAAACAAT 2021
                            - i i  -       viv    i   i iii  vv      v  v  
  L1M4_orf2#LINE/    635 AATTGGACTT-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_38443140_3   2022 TGATGA-GTGAA--GACAATCTGCAGAATAGGAGAAAATATTTGCAAACT 2068
                         ii vi -     --     i ii      i                  ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_38443140_3   2069 ATGCATCTTGACAAGGGGTTAATACCCACA-TATATAAGGAACTCAAATA 2117
                           ii    -  i     ii vi  i   v -       i      vv i 
  L1M4_orf2#LINE/    734 ATATATCT-GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_38443140_3   2118 ACTCAATAGCAAAAAAACAAATA-TCTGGTTTAAAAATGGGGAAAAGACC 2166
                                 ii     i       -i iii  ?         v   i  ii
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_38443140_3   2167 TG-----------CTCAAAAGAAGACA--CAAATGGCCAACAGGTGTATG 2203
                           -----------   v        i --           i i iii   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_38443140_3   2204 AAAAAATGCTCAATATCACTAATCAA 2229
                             i        i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (55 / 26)
Gap_init rate = 0.03 (12 / 369), avg. gap size = 2.42 (29 / 12)  


2335 26.59 5.47 0.25  chrX_38490591_38492974.rev      716  1501 (883)    L1M4_orf2#LINE/L1        1   827 (81)  

  chrX_38490591_3    716 TGGAAATACATCCCATGCTCATGGGTTGGAAGAATCAATATTGTGAAAAT 765
                               v i        i      i        v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38490591_3    766 AATTGTACTGCCCAAATCAATCTATAG-TTCAATGTAATTTCTATCAAAA 814
                         iiivi    v       ii     i  -     i i   ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38490591_3    815 TACAAACATCGTTTTTCACAGAA-TAGAAAAAA-AATCCTAAAATTCATA 862
                          v v i vv v     ii     - v  v  iv-i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_38490591_3    863 CGGAACCAAAAAGAGCCCA-AATAGCCAAAGCAATCCTCAGCAAAAAGAA 911
                         i    viiv  i ii    -          i     i v iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_38490591_3    912 CAAATCTGGAGGCATCACATTACCCAATTTCACATTATACTACAAGGCTA 961
                             vi      vv     i v          v viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_38490591_3    962 TAGTAAGCAAAACATCACACTACTGATATAAAAGGAGACATATAGAGCAA 1011
                         i     v   i   viiiiv     ii    iiiv           v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_38490591_3   1012 TGGAACAAAATAGAGAACCCAGAAATAAAGCCAAATACTTACAAAAAACT 1061
                              i i   v    ii           v   v i i   iiivv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_38490591_3   1062 GATCTTCGACAAAGCCAACAAAAACATAAACTGGGAAAAGGACACCCTAT 1111
                            i        i viiv   i v   vv v    i    i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_38490591_3   1112 TCAATAAATGGAGATGGGAAAATTGGATAACCA----------AATG--- 1148
                             i      v v     v  i      ?   ----------    ---
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_38490591_3   1149 ---------------------TATACAAAAATTAACCCAAGATGGAATAA 1177
                         ---------------------               i   i     vi ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_38490591_3   1178 ATACTTTAATCTTAAGTCCCAAAACCATACAAATTCT-GTAAGATAACA- 1225
                          v  i v   v -   vv i     i   -   i   -iv    v    -
  L1M4_orf2#LINE/    501 AGACCTAAATGT-AAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACAT 548

  chrX_38490591_3   1226 AGGGAAAAGTCTT-G-GATATCGGCCTAGGTAACGAATTTACAACTAAGA 1273
                            ?iv  i    - -  iv i  vi    i  i iv  ivi iv  v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_38490591_3   1274 TCCCAAAAGCAAATGAAACAAA-GCAAAAATAAATAAATAGTACTTAATT 1322
                         iv         v v v      - v       i      v v    v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_38490591_3   1323 AAACTAAAAAGCTTCTGCACAGCAAAATAAATAATAAACAGAGTAAATAC 1372
                            v v    i   i  ii vv    iv v iv  v  v i   i  v v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_38490591_3   1373 ACAATCTACAGAATGGGAGAAAATACTTGCAAACTGTCTATCTGACAAAG 1422
                             i i                  i       iii v       i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_38490591_3   1423 GATTGATATCCAGAATCTGCAAAAAACTCAAACAAATCTGCAAGAAAAAA 1472
                           i vi          v ii   i     vv    v  vii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_38490591_3   1473 ACAAATGATTCTATTAAAAAGTGGGCAAA 1501
                               i ii v   ?    i        
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAA 827

Transitions / transversions = 1.33 (117 / 88)
Gap_init rate = 0.02 (13 / 827), avg. gap size = 3.46 (45 / 13)  

 428 18.09 1.06 1.06  chrX_38490591_38492974.rev     1800  1893 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_38490591_3   1800 AAAGGTAGGCAAATGACATGAACAGACATTTCTC-AAAGAAGGTATACAA 1848
                            ii i      v  iv    i           -       i       
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_38490591_3   1849 ATGACCAACAGACATGTGAAAAAAATGCTCGATATCACTAGTCAT 1893
                            i    i ii  ii      i -     i i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 7.50 (15 / 2)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.00 (2 / 2)  


 867 28.63 0.41 0.00  chrX_38636822_38638498.rev        9   249 (1428)    L1M4_orf2#LINE/L1        1   242 (666)  

  chrX_38636822_3      9 TGGAGAGACATTCCA-GTAAGTGGATTAGAAGACTCAACATAGTAAAGAT 57
                             i   i  i   -  vvi      i       i  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38636822_3     58 ATCAATTCTCCCCAAATTGGTAAATAGGTTTAATGCAATTCCAATCAACA 107
                         iv    v            i vv i  i  i  i     i  v     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38636822_3    108 TCCCATCAAGATTTTCTGTAGAGATAGACAAACTTATTCTAAAATTTATA 157
                              v vivv    i  i   i  v     i  v  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_38636822_3    158 TGGTAAGTCACAAGCCCTAAAATAGGTAAGACAATTTTGAAGTGAAAGAA 207
                            v  vv  vii v  i i     vi  i     i     ivii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_38636822_3    208 TAAAGTATAAGGAATCACTCTCTGCAGTGTTAAGGCTTATTA 249
                         i     vvi    v    v  iiv  i v i  ii    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

Transitions / transversions = 1.38 (40 / 29)
Gap_init rate = 0.00 (1 / 242), avg. gap size = 1.00 (1 / 1)  

2023 25.46 1.86 4.01  chrX_38636822_38638498.rev      494  1192 (485)    L1M4_orf2#LINE/L1      225   908 (0)  

  chrX_38636822_3    494 CAATTATATTAAAGCTTATTATTTGGCCACAATAATCAGGA--GTGTGGA 541
                              --- i   i    i  ivvi  i   i      i  --      v
  L1M4_orf2#LINE/    225 CAATT---TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_38636822_3    542 CTTGGTGGAAAAATAGACATATAAATTAATGGAACAGAATAGAGAACCCA 591
                         vi   iiv  ii           i  i       i     v    ii   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_38636822_3    592 GAAATAGCCCCACATGAATATGCCCAACTAAATTTTTACTAAGATGTAAA 641
                               iv    i iivv    vi   i i v   iv  v i i  iv  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_38636822_3    642 AGTAATCCAATGGAGAAATATCAGCCTTT-CAATGAATAATGCCAGAGCA 690
                         iiiv  i      i    v vi  i    -   ii   ii   ii ii  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_38636822_3    691 ATTGGACA--CACATGAGTAACAACCACAAAAAAAAATAATAACCTTGAC 738
                          i    i --      -----------     i  -- i -- vi v   
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATG-----------CAAAAGAA--TGA--AGTTGGAC 456

  chrX_38636822_3    739 CTAAACCTCACAGCTTACGGAAAAATTAACTCAAAATGAATCATGGAGTT 788
                          ivv        v v  iiv                  i    ?i  vi 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_38636822_3    789 AAATGTGAAACAAAAAACTATGAAACATTTAGAAAAAGAAA-AGAGAAAA 837
                               i i vvv        i    vi      i  i v -  i?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_38636822_3    838 ATCTCCGAGAACTAGAGAGAGGCAATGAATTCTTAAAAATAACAGAAAAA 887
                             i  v  v  v i vv        iv      i v  i   vv    
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_38636822_3    888 GCACACTCAATAAAATTTTAAAAATTAG-TAAATTGGACCTCATCAATAT 936
                              vv   i    v---     v   -          i       v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAG---AAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_38636822_3    937 GAGCAACTTTTGCTCTGTGAAGTACGCCAT-AAGAGGATGAAAAGACAAG 985
                         v iv        iv  vii   v  i i  -    iii           v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_38636822_3    986 CTACAGAGTGAAAGGAAATATTTGCAGACCACATATTTCACACAAAGGAC 1035
                          i     i  ii  i           i i  i    i v i -- i    
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA--AGGGAC 751

  chrX_38636822_3   1036 TAGTATTTAGAATATATAAAGAACTCTCAGAACTCAATAGTCAAAA-ATG 1084
                          v    ii                   i v         i v    - ii
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_38636822_3   1085 AACAGTCCAATTAGATAATTTGCAAAGTATAAAAAAAGGAAAGACATTTC 1134
                           i ii      ?i v   vv      v  vvi  v  -----       
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG-----ACATTTC 846

  chrX_38636822_3   1135 ATCAAAGAGGATAAACA---GGC-GACAAGCATGTGAAAAGATGTTCAGT 1180
                         vi      i    v   ---   -i i     ii          i   ii
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_38636822_3   1181 TTCATTAGCTAT 1192
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (110 / 65)
Gap_init rate = 0.02 (16 / 684), avg. gap size = 2.56 (41 / 16)  


3215 24.97 2.15 1.13  chrX_38639562_38643735.rev     2799  3683 (491)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_38639562_3   2799 ATGCTCATGAATTAAAAGAATTAATATCATTAAAATGTCCACACTGCCCA 2848
                            i     i   ii    v       ii    i   v v i   v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_38639562_3   2849 AAGAGATCTATTGATTCAATGCAATCTTCGTAAAAAAGAAACAATAATAT 2898
                           vv      iv       i      iiii v    vvv--  iiviiv 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC--CAGCTGCCT 112

  chrX_38639562_3   2899 TCTTTACATAAATAGAAAAAACGATCCTAAATTTTGCATGGAACTACAAA 2948
                          i   i  v    v  v  ivi         v  iii      v i   i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_38639562_3   2949 AGACCCCATACAGCCAAAGCAATTTTGAGAAAATGGAACAAAGCTGAAGG 2998
                         i     viv i       i    i    i   ivi        i  i   
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_38639562_3   2999 CATCACAATATTTGACTTTAAAATATACTACAAAGCTGTAGTAACCTAG- 3047
                         vv     v viiii i  i    iv            ii     i v  -
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_38639562_3   3048 CATTGT--TATTGGCATAAAAACAGACACATAGACCAATGGAACAGAATA 3095
                           v   --  i        ii i     i     i        i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_38639562_3   3096 GAGAGCCCAGAAATAAATGCACGCATTTACAGTCAACTGATTTTTAACAA 3145
                              i           iv  ii      ii     i       ii    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_38639562_3   3146 AAAAGTGCCAAGAATGCACATTT--TGGGGGAAAAA--GTATCTTCAATA 3191
                         ii--         --- -    i--     i  i  --  v i     i 
  L1M4_orf2#LINE/    363 GG--GTGCCAAGA---C-CATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_38639562_3   3192 AATGCTGCTGGGAAAACTGGATATCCATATGCAGAAGAATAAAACTAGAT 3241
                             v        v         ?   i     i      i  ii i  i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_38639562_3   3242 CTTTATCTTTGACTTTATACAAAAAAAAAACCAAAATGAATTAAAAACTT 3291
                          ii  i  ivv  iv          vv  vi       i  i ? i  i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_38639562_3   3292 AAATTTAATACTGAAAACT-TAAAATTACTACAAGAAAACATACGGA-AA 3339
                             v   v viv      -     i vi  v           v ?i-  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_38639562_3   3340 ATGCTTTCTGACATTGGCTTGGGCAAGGGCTT-TTGGATAGAAGCTCAAA 3388
                           -   iv    v    v  i     v  i  -  i    vi vvi    
  L1M4_orf2#LINE/    557 AT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_38639562_3   3389 AGCACAGGCAACAAAAGCAGAAATTGACAAATGGCGTTACATCAAACTAA 3438
                               i          v i    v  i    v vii v       v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_38639562_3   3439 AAGGCTTCTGAACAACAAAGGAAATAAT-----AAGTGAAGGGACAACCT 3483
                           ii   i  vi vv       v iv  -----       ii       i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_38639562_3   3484 ACAGAATGGGAGAAAATATTTACATACTATGCATTTGACAAGTGGTTAAT 3533
                                              i  v ii  ii  i   i   v ii vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_38639562_3   3534 AACCAGAATATACAAGAAACTC----AATGCCATAGGAAACAAAACAAAT 3579
                          v          i  ii     ----  iv v   iv   -  i      
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAAAT 804

  chrX_38639562_3   3580 AATCTGATTTAAAAATGGGCAAAAGATCTGAATAGACATTTCTCAAAAAA 3629
                           i ii   ?             i   i                v   i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_38639562_3   3630 AGACACACAAATGGCCAGCAGGTATATGACAAAATGCTTAGCATCACTAA 3679
                            i i           ii i i i    v  i     i i     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_38639562_3   3680 TCAT 3683
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.89 (142 / 75)
Gap_init rate = 0.02 (15 / 894), avg. gap size = 1.93 (29 / 15)  


2413 28.93 4.59 0.34  chrX_38692844_38697146.rev     2942  3812 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_38692844_3   2942 TGGAGAAACTTTCCATGCTCATGGATAGGAAGAATCAACATGGTTTAAAT 2991
                             i i iv i     i        v      v i  i  v   v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38692844_3   2992 GGGCATATTGACCAAAACAATTTATGTATTCAATACTATTCCTATTAAAC 3041
                           vv   i vv     vii  i  iiv      ii v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38692844_3   3042 TACCA-CTGACAATCTTCACAGAACTAGAGAAAAGTACTTTAAAATTCAT 3090
                          v   -   v v- i  ii     v v  v  ivvv iii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_38692844_3   3091 ATGGAA-T-CAAAAAGCTT-GAATAGCCAAGGCAATCCTAAGCAAAAAGA 3137
                               - -   iiii ii-          ii     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_38692844_3   3138 ACAAAGCTAA---------------CAACTTTAAACTATACTATAGGGCT 3172
                               i ii---------------   i  i   viv     i ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_38692844_3   3173 ACAATAACCACAACAGCATGGTATTGGTACAAAAACAGACACATACACTA 3222
                            i   i  vi    ii     i   i i  ii i     i   v ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_38692844_3   3223 ATGGAACAGAATAGAGAACCCAGAAATATGGCTGCACACCTACAACTATC 3272
                               i     v    ii         viv iii   ii  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_38692844_3   3273 TGATCTTCTCCAAACCTGACAAAA--AAGCAATGGGGAAAGGATTCCCTA 3320
                             i   vv   ivv  v   i -- vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_38692844_3   3321 TTCAATAAATGGTGCCAGGATAAATGGCTAGCCATGTGCAGAAGATTGAA 3370
                              i         ii   i  v   v  ?   ii    i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_38692844_3   3371 ACTAAACCCCTTCCTTACATCATATACAAAAATTAACTCAAGATGGATTA 3420
                         ii ii      v   i   i                     i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_38692844_3   3421 AAGACTTAAACGTAAAACCCAAAAGTATAAAAACCTTGGAAGACTACCTA 3470
                         ?    i    i    i v i    v       vi   i     vv  v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_38692844_3   3471 GGCA-ATACCATTCAGGACATAGGCACAGGCAAAGATTTCATGACAAAGA 3519
                           ?i- v i -   iv   v v  vvi      v i    v iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_38692844_3   3520 TGCCAAAAGCAATTGCAGCAAAAGCAAAAATTGACAACGTGGGTCT---- 3565
                         ii         vvv   i      v      v  i  vv   iii ----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_38692844_3   3566 --AATTAAAGAACTTCTGCAGAGCAAAAGAAACTATCAACAGAATAAACA 3613
                         --       -     i  iivvv    i  v        v i i i  v 
  L1M4_orf2#LINE/    649 AAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_38692844_3   3614 GACAATCTACACAATGGAAGAAAATTTGTGCATACTATAGATCTGACAAA 3663
                              i i   v     i       v v    v ii   v      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_38692844_3   3664 TGTCTAATATCTAGCATCTATGAGGAACT--TAAAAA--AAT--TTACAA 3707
                         v v  vi    i  v  v   i i     --  v  v--   -- v v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_38692844_3   3708 GAAAAAAAACC--ATAAAAACGTGGGCAAATGAC----ACAGACAGTTTT 3751
                           v   v    --  v?   vi        v  i---- i     v  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_38692844_3   3752 CAAAAAAGAACATACATGCAGCCCATAAGCATATTTTAAAAAGCTCAACA 3801
                          v   i ii i     viii   v       i  vvv  i v        
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_38692844_3   3802 TCACTGATCAT 3812
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.69 (43 / 16)  


3204 20.27 5.71 4.03  chrX_38700132_38710806     2917  3809 (6866)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_38700132_3   2917 TGGAAGAACATCC-GTGATTATGAATTGGAAGAC--AGTATTGTTAAAAT 2963
                              ii i    -i  v i   i          -- i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38700132_3   2964 GCTCATACTATTCAAAGTGTTCTACAGATTCAGTGCAATATCTATCAAA- 3012
                          viv     vii    v  v            ii     vi        -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38700132_3   3013 TCCCTATGACTTTTTTTGCAGAAATAAAAAAA---ATTT--AAATTCA-- 3055
                             viivi i              vi v  i---  ii--       --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_38700132_3   3056 ---AAAGGCATCTTTAGAAACCT--------CAAAACAATCTTTAAAAAG 3094
                         ---   v   -----  ii   i--------            v      
  L1M4_orf2#LINE/    151 TGGAAATGCA-----AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_38700132_3   3095 AAGAACAAAGCTTGGGGACTGGCACTTCCTGATTTCAAAACTTACTACAA 3144
                                   i v i     vi       ii                   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_38700132_3   3145 AGCTATAGTAATCAAAGCAGTGTGGTACTGGTATAAG-ATAGATATATAG 3193
                              i         ii              i     -     i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_38700132_3   3194 ACCAATGAAACAGAATAGGTATCCCAGAAATAAATCTTTGCTTTCTTTAT 3243
                          i     i  i     v iv vi           i iv i v  ------
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT------ 339

  chrX_38700132_3   3244 GAGATGGTATGGTCAAATGAGTTTTGACAAGGATGCTTAGACCATTTAGT 3293
                         -------         v   v   i       i   iv        i i 
  L1M4_orf2#LINE/    340 -------TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_38700132_3   3294 GAGGTAAAGACAGTCTTTTCAACAAAGCATGCTGGGAAACCTGGATATTC 3343
                          i  v  ii i               vvi        v v       ?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_38700132_3   3344 ATATTCAAAA-AATGATGTTGAACTCTTACCTAAGAATGTATACAAAAAT 3392
                          i  v     -     v    i  i i     v v vii           
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_38700132_3   3393 AAACTCAAAATGGATCCAATACCTAAAC--AAGATCTAAAACTGTAAAAC 3440
                         v               v? v       i--    v        i      
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_38700132_3   3441 TGTTAGAAGAAAACGTATGGCAAAAGCTTTACAACACTAGATCTGGCAAT 3490
                          v            i  v ?vv   v   iiii  vi i i iv      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_38700132_3   3491 GATTTCTTGGATATGACACCAAGGGCACAGACAATGAAAGAAACAAAGGA 3540
                          i      i             ii     ii   ii       v  vi  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_38700132_3   3541 -AAATTTTTAAAATGCATATGTCAAAATATAAGATCAATAGGGT----AA 3585
                         -     ---ii v v   ----      -   i v vv v v i----  
  L1M4_orf2#LINE/    633 TAAATT---GGACTTCAT----CAAAAT-TAAAAACTTTTGTGCTTCAAA 674

  chrX_38700132_3   3586 AAACATT--CA-GA---TGAGAATACTTTCAAATCATATAGCTGATATGG 3629
                         ii   i --  -  ---   i  v  ----  vi  i -----  -    
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGAC----AACCCACA-----GA-ATGG 714

  chrX_38700132_3   3630 ATGAAAATACTTTCAAATTTTATAGCTGATAAGGAATTGATA-ACAGAGT 3678
                         iv       i  v     iv    v         i i vi  -v    i 
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_38700132_3   3679 GTATAGAAAACTTCTAAAACTCAACAAT-----GACA------TTAATTC 3717
                         i    i i    ii  v       i   -----    ------ii    ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_38700132_3   3718 AAAAATGGGCAAATGACTTGAATAGCCATTTCTCCAAAGAAGACATACAA 3767
                                      v  i        v                 i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_38700132_3   3768 ATGTCCAATAAGCAAAT--AAAGATGTTGAGCGTCACTAATCAT 3809
                            v          v  --       i v i i   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (110 / 67)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.22 (87 / 27)  

3092 26.24 0.99 0.88  chrX_38700132_38710806     9276 10182 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_38700132_3   9276 TGGAAAAACATTCCATGCTCATTGATAGGAAGAATCAATGTTGTGAAAAT 9325
                               i i  i     i    v   v      v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38700132_3   9326 GGCCATACTGCCCAATGTAATTTATAGATTCAATGCTATCCCTATCAAAC 9375
                            v     v     vv i  i  i        i  v            v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38700132_3   9376 TACCA-TTGACTTTCTT-CACACAATTAGAAAAAACT-ACTTTAAATTTC 9422
                          v   -i  v    i  -  v -    i-- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_38700132_3   9423 ATATAGAACCAAAAAAGAGCCCATAG-AGGCAAGACAATCCTAAGCAAAA 9471
                             i   viiv  ii  -    v i-  v   i      i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_38700132_3   9472 AGAACAAAGCTGGAGGCATCAGGCCACCTGACTTCAAACTATGCTACAAG 9521
                                  i      vv   vi iv  ii i      viv i      i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_38700132_3   9522 GCTACAGTAGCCAAAACAGCATGGTACTGGTACCAAGACAGATATGTAGA 9571
                                  ii   i    ii         i iv i  i   i  i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_38700132_3   9572 CCAAAGGAACAGAA--AAGAGGCCTCAGAAATAACGCCACACATCTGCAA 9619
                         i   v    i    --i    v  --        vv   i    i iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_38700132_3   9620 ACATCTGATCCTTGACAAAGCTGATAAAAACAAGAAATGGGGAAAGGAAT 9669
                         v  vi    ii i     i v  vi  i v  vvv           -   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AAT 393

  chrX_38700132_3   9670 C-CCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAA 9718
                         v-i  v  i  i        i     v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_38700132_3   9719 ACTGAAACTGGACCCCTTTCTTACACCTTATACAAAAATTAATGCAAGAT 9768
                          v    ii         vi  i     v              iv   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_38700132_3   9769 GGATTAAAGACTTAAACGTAAGACCTAAAACCATAAAAATACTAGAAGAA 9818
                             i ?    i    i      v       i      v vi        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_38700132_3   9819 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 9867
                            v    ?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_38700132_3   9868 GTCAAACACCAAAAGCAATGGCAAGAAAAGCCAAAATTGACAAATGGGAT 9917
                         i vvi            vvi    v     vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_38700132_3   9918 CTAATTAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTATCACCAGAGT 9967
                         i v  i   v v  i i   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_38700132_3   9968 GAACAGGCAACCTACAAAATGAGAGAAAATTTTTTCAATCTATCCATCTG 10017
                            v  i     i   i    i        v   v   vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_38700132_3  10018 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAG 10067
                          i  i  i  vi          v  i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_38700132_3  10068 AAAAAATTGAACAACCCCATCAAAAAGTGGGCAAACGGTATGTACAGACA 10117
                              ivii  i     v  i?    i        v i v  v i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_38700132_3  10118 CTTCTCAAAAGAAGACATTTATGCGGCCAACAAACATATGAAAAAA-GCT 10166
                         i     v        i  vi vii      i  i  i       i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_38700132_3  10167 CATCATCACTGGTCAT 10182
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.21 (17 / 14)  


2910 26.93 1.66 1.43  chrX_38715480_38717689.rev      814  1719 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_38715480_3    814 TGGAAAAACTTTCCATGCTCATGGTTAGGGAGAATCAGCATCGTTTAAAT 863
                               i iv i     i      v v  i   v i ii  i   v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38715480_3    864 GGCCATATTGCCCAAAGCAATTTATAGATTCAATGCTATTCCTATTAAAC 913
                            v   i v      vii  i  i        i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38715480_3    914 TACCATTGATG--TTCTTCACAGAACTAGAGAAAACT-ACTTTAAAATTC 960
                          v   -- v  --  i  ii     v v  v  i-  - iii        
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chrX_38715480_3    961 ATATGGAATCAAAAAAGAGCCCGAACAGCTAAGGCAATCCTAAGCACAAA 1010
                                 viiv  ii  v  v   i   i  ii     i i iv vi  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_38715480_3   1011 GAACAAAGCTAGAGGCATCACGCTACCCAACTTCAAATTATACTACAGGG 1060
                                 i i    vv    i  v     i      viv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_38715480_3   1061 CTACAGTAACCAAAACAGCATGGTATTGGTACAAAAACAGACACATACAC 1110
                                  i   i    ii     i   i i  ii i     i   v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_38715480_3   1111 TAATGGAACAGAATAGAGAACCCAGAAATAAGGCTGCACACCTACAACTA 1160
                         i       i     v    ii          iv iii   ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_38715480_3   1161 TCTGATCTTTGACAAACGTGACCAAAACAAG-CAATGGAGAAAAGATTCC 1209
                         vi    i  i     iv   -    i  v v-      i    ii  vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_38715480_3   1210 CTATCCAATAAATGATGCCAAGATAACTGGCTAGCCATGTGCAGAAGATT 1259
                           v i   i     i   iii  i      v  ?   ii    i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_38715480_3   1260 GAACCTGGACCCCTTCCTTGCATCATTTACCAAAAAAAAAAAAACTCAAG 1309
                            vi         v   ii  i   v   -----     vv       i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATAC-----AAAAATTAACTCAAA 491

  chrX_38715480_3   1310 ATGGATTAAAGACTTAAATGTAAAACCCAAAAGTATAAAAACTCT-GGAA 1358
                               i ?    i         i v i    v       -    -i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAA 540

  chrX_38715480_3   1359 GACAACCTAGGTAATACAT-TTCAGGACATAGGCACAGACAAAGATTTCA 1407
                           v   v    ?i-  v  -   iv   v v  vvi  i   v i    v
  L1M4_orf2#LINE/    541 GAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_38715480_3   1408 TGGCAAAGATGCCAAAAGCAATTGCAACAAAAGCAAAAATTGACGAA--G 1455
                          i vv v  ii         vvv          v      v  ii  -- 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_38715480_3   1456 AAC---ATCTAA-TTAAATAGCTTCTGCACAGCAAAAAGAAACTATTAAT 1501
                         i  ---   v  -     - i   i  ii vv    i-  v     i  v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAG-GACACTATCAAG 687

  chrX_38715480_3   1502 AGAGTAAACAGACAACCTAAACAATGGGAGAAAGTTTTTGCAAACTATGC 1551
                          i   i  v        i v v           i v        ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_38715480_3   1552 ATCTGACAAAGATTTAATATCCAGCATCTATGAGGAACTTAAACAAATTT 1601
                               i  i ivi vi       v  v   i i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_38715480_3   1602 ACAAGAACAAAGCAAA---CCCCATGATAAAGTGGACAAAGGACATGAAC 1648
                          i  v  v  ii    ---   v  v?v   i   i       iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_38715480_3   1649 AGACACTTTTCAAAAGAAGACATACATGTGGCCAACGAGCATATTTAAAA 1698
                              i  i  v        i     vi       ii    i  vv   i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_38715480_3   1699 AAGCTCAACATCACTGATCAT 1719
                          v           ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (149 / 91)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.65 (28 / 17)  


2222 22.72 5.63 9.24  chrX_38718025_38720788     1330  2271 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_38718025_3   1330 TGGAGAGACAATACCATGTTCATGGATTGGGAGACTAAACATAGTAAAGA 1379
                             i   i - v                 i     v  i  v  v    
  L1M4_orf2#LINE/      1 TGGAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_38718025_3   1380 TGTTATTTCTCCTAAAATTGATCTATAGAGTCAACACAATTTCTATAAAA 1429
                           vi v v    iv           i   v     i    ii    v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_38718025_3   1430 ACGCCAGCAGTATCTTTTGTAGATATAGACAAGCATAATATAAAAATT-A 1478
                          iv     v iv i     i   v  v       - i  viv      - 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chrX_38718025_3   1479 TATGGAAAGACAAAGAAACTAGAATAGCTAAAACGATGTTAAAAAA---- 1524
                                 vi   i i v i        i     i  v  i     ----
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_38718025_3   1525 -ATAAAGTTGGAGGAATCACACTACCAAATTTTAGGACATAGTATATATT 1573
                         - i            v       v  v     i ii  v  v  i v vi
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_38718025_3   1574 TACAGTAACAAAGACAGCGTAGCATTAGTGGAGGGAGAGACAGGCAAACA 1623
                                 iv       i  i i i ----------------    v vi
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACT----------------GGCATAAG 282

  chrX_38718025_3   1624 GATAGATACATACATATGTACATACATACATACATAGATTGATCAGTGGA 1673
                               i i   ----------------------------     i    
  L1M4_orf2#LINE/    283 GATAGACATATA----------------------------GATCAATGGA 304

  chrX_38718025_3   1674 ATAGAATAGAGAACCCCAAAATAATATTCACCAAACATGTGT----AACT 1719
                                v    ii  vi      - i---   v    v i ----  i 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAA-AC---CCATACATTTATGGTCAATT 350

  chrX_38718025_3   1720 AATTTTTG-CAAAGATACAAAAGCAATTCAAGGAAGGAACTATTGTCTTT 1768
                         i     i -   i i i v  ii v      v ii i  vv  v      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_38718025_3   1769 TCAGCATATGTTACTAGAACAATTGGACATCAATGGGCCAAAACACACAC 1818
                            i  v   v i  i i    i    i ? -------------------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKC------------------- 431

  chrX_38718025_3   1819 AAACACACATACAAACACACAGAACAAGCCTTCTACCTCATATTAACATT 1868
                         -----     i    viv iii iivi v ii        i i---   v
  L1M4_orf2#LINE/    432 -----CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC---CATA 473

  chrX_38718025_3   1869 T-------TTATTTCAAAATGGATTA------TAAATGTAA-------AA 1898
                          -------   vi           i ------         -------  
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_38718025_3   1899 CTATAAGATTTATTGAAGAAAACATAAGAAAACATCTTTGT--------- 1939
                               i i iv v            i ?iv v     i  ---------
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_38718025_3   1940 -TAG-CAAGAGAGTTCTTAAATGTGATGCCAAAATACATTATCCATAGAT 1987
                         -   -   vi -v      i  i   ii      -i  iv v v i i v
  L1M4_orf2#LINE/    574 TTAGGCAATGG-TTTCTTAGATATGACACCAAAA-GCACAAGCAACAAAA 621

  chrX_38718025_3   1988 TTAAAAGATCACCCAAATCT-ACTTAATCAAAATGTGAAATTTTTGCTCT 2036
                         v-    i  - vvi    iv-    v        vvi   i     iv  
  L1M4_orf2#LINE/    622 G-AAAAAAT-AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_38718025_3   2037 GTGAG-------ATGAAGAGGATGAAAAGATAAGCCACAGCCTGGGA-AA 2078
                         vii i-------  v    iii        i  v      vv     -  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_38718025_3   2079 AATATTTGTAAATCATATATCTGAGAAAGGAGTCATAACCAGAATATATA 2128
                                 i               v  i   v ii  v            
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_38718025_3   2129 AGGAATTATCTA-AACTCAACAGTAATAAAACAACACGGTCCAGTTAGAA 2177
                          i   i v -  -       i i   v  i    - iiii   i  ?i  
  L1M4_orf2#LINE/    770 AAGAACTCT-TACAACTCAATAATAAAAAGACAA-ATAACCCAATTWAAA 817

  chrX_38718025_3   2178 AACAGACAAAAATATTTGAATAG-CATTTTACCAAAGAAGATATATGGGT 2226
                           ii i    ii-          -     iv              iiii 
  L1M4_orf2#LINE/    818 AATGGGCAAAGG-ATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_38718025_3   2227 GGAAACTAAGTACATTTGAAAAAAGTGTTCACCATCATTAGCCAC 2271
                           vv v    i    --     i -  i   v     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACAT--GAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (130 / 81)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 4.52 (140 / 31)  


3186 25.55 1.33 0.88  chrX_38796089_38802468.rev     4986  5889 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_38796089_3   4986 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAACATCGTGAAAAT 5035
                              ii i  i     i        v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38796089_3   5036 GGACATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5085
                           vv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38796089_3   5086 TACCAATGACTTTCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCA 5133
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_38796089_3   5134 TGTGGAACCAAAAAAGAGC-AGCACTGCCAAGACAATCCTAAGCAAAAAG 5182
                          i     viiv  ii  v -  v iv     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_38796089_3   5183 AACAAAGCTGGAGGCATCACGCTACCAGACTTCAAATGATACTACAAGGC 5232
                                i      vv    i  v  vi i      vvv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_38796089_3   5233 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGACC 5282
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_38796089_3   5283 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 5330
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_38796089_3   5331 ATCTGATCTTTGACAAACCTGACAGAAACGA---AATGGGGAAAGGA--G 5375
                          vi    i  i     ivv  v  - i  v ---           i -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAG 395

  chrX_38796089_3   5376 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5425
                           -- v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_38796089_3   5426 GCTGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGAT 5475
                         iv    ii    i    v   i     v  i           i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_38796089_3   5476 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5525
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_38796089_3   5526 AACCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGT 5574
                            v    ?i- v i -   iv   viv  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_38796089_3   5575 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5624
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_38796089_3   5625 CTAACTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5674
                         i v ii   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_38796089_3   5675 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTCCAATCTACTCATCTG 5724
                            v  i     i                 v   v   vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_38796089_3   5725 ACAAAGGGCTAATATCCAGAAATTACAAAGAACTCAAACAAATTTACAAG 5774
                          i  i  i  vi         vv  i         vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_38796089_3   5775 AAAAAAACAAACAACCCCATC-AAAAACGGGCAAAGGATATGAACAGACA 5823
                              i     i     v  i-     i           v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_38796089_3   5824 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCT 5873
                         i     v        i  vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_38796089_3   5874 CATCATCACTGGCCAT 5889
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (139 / 89)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


1088 28.05 0.33 0.66  chrX_38886833_38897128.rev        2   304 (9992)  C L1M4_orf2#LINE/L1   (606)   302     1  

C chrX_38886833_3    304 TGGCCAAACATTCCATTCTTGTGGATAAGAAGAATCAATACTGTTAAAAT 255
                            vv i i  i    vi ii     vi     v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_38886833_3    254 GTCCATACTGCCCAAAGCAATTTACAGATTCAATGTTATTCCTATCAAAC 205
                          v v     v      vii  i           i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_38886833_3    204 TACCAATGGCATTCTTCACAGAATTAGAATAAAACT-ATTTTAAAATTCA 156
                          v   iiv  v  i  ii     v v  v--  i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

C chrX_38886833_3    155 TGTGGAACCAAAAAAAGGCCTGAATAGCCAAAGCAATCCCAAACAAAAAG 106
                          i     viiv  iiiiv  v           i     iii  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_38886833_3    105 AACAAAGCTGGAGGCATCACATTACTCAACTTCAAACAATACTACAAGGC 56
                                i      vv     i v i   i      vvv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_38886833_3     55 TACAGTAACCAAAATAACATGATACTGATACAAAAACAAACACATAGACC 6
                                 i   i i iii  i     ii i  ii i i   i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_38886833_3      5 AATG 2
                             
  L1M4_orf2#LINE/    299 AATG 302

Transitions / transversions = 2.04 (57 / 28)
Gap_init rate = 0.01 (2 / 302), avg. gap size = 1.50 (3 / 2)  

2976 26.22 1.55 1.11  chrX_38886833_38897128.rev     8902  9805 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_38886833_3   8902 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAGTATTATGAAAAT 8951
                               i i  i     i        v      v i i    i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38886833_3   8952 GGCCATACACCCAAAGTAACTCATAGAATTCATAGATTCAATGCTATCCC 9001
                            v    v   v  -------  v  - ii i        i  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA-------ATTGA-TCTACAGATTCAACGCAATCCC 92

  chrX_38886833_3   9002 CATCAAGCTACCATTGACTTTCTTCACAGAATTGAAAAAACT-ACTTTAA 9050
                         i     iv v   vivi i  i  ii     v vi v  i  - iii   
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_38886833_3   9051 ATTTCATGTGGAACCAAAAAAGAGCCTGTGTAGCCAAGACAATCCTAAGC 9100
                          v     i     viiv  ii  v  v vi       i      i i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_38886833_3   9101 AAAAAGAACAAAACTGGAGGTATCACACTACCTGACTTCAAACTATACTA 9150
                           i         ii      vv       v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_38886833_3   9151 CAAGGCTACAGTAACCAAAACAGCTTGGTACTGGCACCAAGACAGATATA 9200
                            i          i   i    iv           iv i  i   i   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_38886833_3   9201 TAGACCAATGGAACAGAACAGA-AGCCTCAGAAATAATGCCACACATCTA 9249
                             i        i    iv  -  i -         vv   i    i  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTA 341

  chrX_38886833_3   9250 TAACCATCTGATCTTTGGCAAACCTGACAAAAACAAACAATGGGGAAAGG 9299
                          iii  vi    i  i i   ivv  v   i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_38886833_3   9300 ATTTCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAAA 9349
                           vvi  v  i  i        i     v      v  ?   i       
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_38886833_3   9350 AAACTGAAACTGGACCCCTTCCTTACACCTTATA-AAAAATTAACCCAAG 9398
                          i v    ii         v   i     v    -          i   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_38886833_3   9399 ATGGATTAAAGACTAAAACATAAGACCAAAAACCATAAAACCCCTAGAAG 9448
                               i ?    iv   ii     v v     i       i i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_38886833_3   9449 AAAACCTAGGCA-ATACCATTCAGGAAATAGGCATGGGCAAAGTCGTCAT 9497
                              v    ?i- v i -   iv  vv v  vv i     v viv  v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_38886833_3   9498 GACTAAAACACCAAAAGCAATGGCAACAAAAGCCGAAATTGACAAATGGG 9547
                         iiv  vi            vvi          vvi    v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_38886833_3   9548 ATCTAATTAAACTAAAGATCTTCTGCACAGCAAAACAAACTATCATCAGA 9597
                          ii v  i   v v  i v   i  ii vv    iv v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_38886833_3   9598 GCAAACAGGCAATCTACAGAATGGGAGAAAAGTTTTTCAATCTATCCATC 9647
                          ii  v  i   i i                vv   v   vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_38886833_3   9648 TGACAAAGGGCTAATATCCAGAATCTACAAAGAAATCAAACAAATTTACA 9697
                            i  i  i  vi          v  i      v  vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_38886833_3   9698 AGAAAAA---AGA-AACC--ATCAAAAACTGGGCGAAGGATCTGAACAGA 9741
                          v     --- i -    --  i?    v     i      i    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_38886833_3   9742 CGCTTCTCAAAAGAAGACATTTATGTGGCCAAAAAACATATGAAGAAA-G 9790
                          ii     v        i  vi vi       v  i  i     i i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_38886833_3   9791 CTCA---TTAGAGAAATG 9805
                             --- i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (134 / 99)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


3175 26.40 0.44 0.55  chrX_38960897_38966011     3714  4622 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_38960897_3   3714 TGGAAACACATCGCATGCTCATTCATGGGTAGAATTGATATTGTAAAAAT 3763
                               v i   v    i    vv  v  v   v  i       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38960897_3   3764 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAAA 3813
                          i v     v  v   vii       i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38960897_3   3814 TACCACCATCATTCTTCGCATAATTAGAAAAAACAATTCTAAAATTCATA 3863
                          v   v vv v  i  i   v  v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_38960897_3   3864 TGGAACCAAAAAAGAGGCCACATAGCCAAAGCAAGACTAAGCAAAAATAA 3913
                              viiv  ii  vv viv         i   vvi i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_38960897_3   3914 CAAATCTGGAGGCATCACACTACCTGATTTCCAACTACACTATAAGGCCA 3963
                             vi      vv       v  ii     v  vivi    i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_38960897_3   3964 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGACACATAGACCAA 4013
                         i   v i   i    ii         i    ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_38960897_3   4014 TGGAACAGAATAGAGAATCCAGAAATAAACCAAAATACTTGCAGCCAACT 4063
                              i     v    i              v v i i  iii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_38960897_3   4064 GCTCTTCAACAAAGCAAACAAAAAC-TTAAAGTGGGGAAAGGACACCCTT 4112
                          v i   i    i vviv   i v -  v  -         i i vi   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTT 399

  chrX_38960897_3   4113 TTCAACAAATGGTGCTGGGATAATTGGCTAGCCACCTGTAGGAGAATGAA 4162
                                             i  i   v  ?    v  i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_38960897_3   4163 ACTGGATCCTCATCTCTCAATTTATACAAAAATCAACTCAAGATGGATTA 4212
                         ii    i  ii i   v  viv           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_38960897_3   4213 GGGGCTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGATAATCTT 4262
                         ?i i i    iv     v  i           v ii       v  iv v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_38960897_3   4263 GGAAAAACCCTTCTAGACATTGGCTTAGGAAAGGAATTCATGACCAAGAA 4312
                           ?iv  vi    vv   v    v     v  v iv   v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_38960897_3   4313 CCCAAAAGCAAATGCAATAAAAATAAAGATAAATAACTGGTACCTAACTA 4362
                         v         v v    i    iv   i   i    v v v  i v ii 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_38960897_3   4363 AACTAAAGAGCTTTTGCACAGCAAAATGAACA--GTCAGCAGAGT-AAAC 4409
                           v v  i i      ii vv    -- i   --i   iv i   -   v
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAA--GGACACTATCAAGAAAGTGAAAA 697

  chrX_38960897_3   4410 CACAACCCATAGAGTGGGAGAAAATCTTCACAATCTATACATCTGGCAAA 4459
                         v        i   i           v  ii   vii   i     ii  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_38960897_3   4460 GGACTCATATCCAGAATCTACAACGAACTCAAACAAATCAGTGAGAAAAA 4509
                              ii          v  i  v      vv    v   i i v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_38960897_3   4510 AACAAACACTCCCATCAAAAAGTGGGCTAAGGAGATGAATAGACAATTCT 4559
                         i     i vi  v  i?    i     v     vv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_38960897_3   4560 CAAAAGAAGGTATACAAATGGCCAACAAACATACGAAAAAAAATGCTTAA 4609
                          v       i               i  i  i i     i --    i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAA 895

  chrX_38960897_3   4610 CATCACTAATGTT 4622
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (132 / 104)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3129 25.48 2.13 0.22  chrX_38966669_38970842.rev     2793  3683 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_38966669_3   2793 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTTTGAAAAT 2842
                               v i        i        v  v   v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_38966669_3   2843 GACCATAATGCCAAAAACAATCTACAAATTCAATGCAATTCCCATTAAAA 2892
                          i v   v v  v   vii       i      i     i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_38966669_3   2893 TACCACCATCATTTTTCACAGAA-CTAAAAAAAAAATCCCAAAATTCATA 2941
                          v   v vv v     ii     -i i v  ivvi    i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_38966669_3   2942 TGGAA-CAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 2990
                              -iiv  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_38966669_3   2991 CAAATCTGGAGGCATCACAATACCCGACTTTA-----TACTATAAGGCCG 3035
                             vi      vv     v v   i i  i -----     i  i  ii
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_38966669_3   3036 TAGTAACCAAAACAGCATGGTACTGGTATAAAAATAGGCGTATAGACTAA 3085
                         i     i   i    ii         i    ii    i i      ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_38966669_3   3086 TTGAACAGAATAAAGAACATGAAAATAAAGCCAGATACTTATCCCCAACA 3135
                          v   i     vi   iiviii       v   v i i    vvi   iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_38966669_3   3136 GATCTTCAACAAAGCAAACAAAAAC-TTAAAGTGGGGAAAGGACACTCTT 3184
                            i   i    i vviv   i v -  v  -         i i v    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTT 399

  chrX_38966669_3   3185 TTCAACAAATGGTGCTGGGATAATTGGCAAGCCATATGTAGAAGAATGAA 3234
                                             i  i   vv ?   i   i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_38966669_3   3235 ACTGGATCC-----TCTCACCTTATACAAAAATCAACTCAAGATGGATCA 3279
                         ii    i  -----  v    v           i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_38966669_3   3280 AAGACTTAAATCTAAAACCTGAAACCATAAAAATTCTAGAAGATAACATT 3329
                         ?    i     v   i v  i    i      v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_38966669_3   3330 GGAAAAACCCTTCCGGACATTGGCTTAGGCAAAGACTTCATGACCAAGAA 3379
                           ?iv  vi    vv   v    v        v ii   v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_38966669_3   3380 CCCAAAAGTAAATGCAACAAA------GATAAATAGATGGGACTTAATTA 3423
                         v       i v v        ------i   i   i  v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_38966669_3   3424 AACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTAAACAGA 3473
                           v v    i   i  ii vv    i  v iv    iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_38966669_3   3474 CAACCCACAGATGGGGAGAAAATCTTCGCAATCTATGTTTCTGACAAAGG 3523
                                    vv          v  i    vii  i v     i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_38966669_3   3524 ACTAGTGTCCAGAATCTACAAGGAACTCAAACAAATCAGCAAGAAAAAAA 3573
                            v  i        v  i  i      vv    v   ii  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_38966669_3   3574 ACAGATAATCCCAGCAAAAATTGGGATAAGGACATGAATAGACAATTCTC 3623
                         -  i    i  v vi?    v    vv     iv          v     
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_38966669_3   3624 AAAAGAAGATTTACAAATGGCCAACAAACATATGAAAAAATGCTGAATAT 3673
                         v         v             i  i  i       i     v  i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_38966669_3   3674 CACTAATTAT 3683
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.25 (124 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.62 (21 / 8)  


3116 27.45 0.77 0.66  chrX_39156837_39163792     5564  6470 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_39156837_3   5564 TGGAAAAGCATTTCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5613
                               iii  ii    i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_39156837_3   5614 GGCCATATTACCCAAAGTAATTCATAGATTCAATGCTATCCCCATCAAGC 5663
                            v   i v      v i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_39156837_3   5664 TACCATTCACTTTCTTCACAGCATTAGAAAAAACT-ACTTTAAATTTCAT 5712
                          v   viii i  i  ii   v v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_39156837_3   5713 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 5762
                               viiv  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_39156837_3   5763 ACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACGATACTACAAGACT 5812
                               i      vv   vi  v  ii i      vvv        ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_39156837_3   5813 ACAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGATATATAGACCA 5862
                                i   i    ii       i i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_39156837_3   5863 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 5912
                               i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_39156837_3   5913 TGATCTTTGACAAACCTGACAAAAACAAGCAGTGGGGAAAGGATTCCCTA 5962
                             i  i     ivv  v   i v  vv  i         i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_39156837_3   5963 TTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCTGAA 6012
                           i  i              v  i   v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_39156837_3   6013 ACTAGATCCCTTCCTTACATCTTATACAAAAATTAACTCAAGATGGATTA 6062
                         ii i  i    v   i   i v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_39156837_3   6063 AAGACTTAAATGTAAGACCTAAAACCGTAAAAACCCTAGAAGAAAACCTA 6112
                         ?    i           v       ii     vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_39156837_3   6113 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 6161
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_39156837_3   6162 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACACAATCAAATT 6211
                                    vvi          vv     v  i   ivvi iivv  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_39156837_3   6212 AAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAGTGAACAG 6261
                            v v  i i   i  iiivv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_39156837_3   6262 GCAACCTACAGATTGGGAGAAAATTTTTGCAATCTAGCCATCTGACAAAG 6311
                         i     i     v           v       vii vvi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_39156837_3   6312 AGCTAATATCCAGAATCTACAAGGAACTTAAACAAATGTACAAGAAAAAA 6361
                         ii  vi          v  i  i     ivv    v vv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_39156837_3   6362 A-----AACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 6406
                          -----     v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_39156837_3   6407 AAAAGAAGACATTTATGTAGCCAACAGACATATGAAAAAATGCTCACCAC 6456
                         v        i  vi vi i     i ii  i       i       v  -
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA- 897

  chrX_39156837_3   6457 TTGTCATCAGAGAA 6470
                         ---   ????????
  L1M4_orf2#LINE/    898 ---TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.17 (13 / 6)  


3987 16.77 2.30 0.90  chrX_39221895_39223667      500  1280 (493)    L1M4_orf2#LINE/L1      117   908 (0)  

  chrX_39221895_3    500 TGCAGAAATTGACAAGCTGATCCCAATATTC-TGTGAAGATGTAACAGAA 548
                                                i  v    - i  i i   i  vi  v
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_39221895_3    549 CCAGAATAATCAAAATAATTTTGAAAAA-AGGAACAAAGTTAGAGAACCA 597
                                 ii     i   i        - i          i   i  iv
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_39221895_3    598 ATACTTCCTGATTT-AAAGCATACTACAAAGCTACAGTAATCAAATCAGT 646
                          i      ii    -   i v                       iv    
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_39221895_3    647 GTGGTGCTAGTATAAGGGTAGACATTTAGATCAATGGAATAAAATTCAGA 696
                              i  i i      i       v               i    v   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_39221895_3    697 GTCAAGAAAGAGAATCTTACACTTATGATCAATTAATTTTCAACAAGGGT 746
                            v     v i vi v    i     i      i      i        
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_39221895_3    747 GCCAATGCTTTTCAATGGG-AAAGGATATTTTTTTCAATAGATGATGCTG 795
                              vi iv         -    i   v i       i i   i     
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_39221895_3    796 GGACTATTGGATAGCCATATGCAAAAACATGAATTTAGATCCTTATCCTT 845
                             v i      ?   i        iv     v  i  i  i  i iiv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_39221895_3    846 CACTACACACAAAAATTAGCTCAAAATGAATCATAGACCTAAATTTAAGG 895
                            i i i          i         i    ?          v    i
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_39221895_3    896 GC-AAAATTATAAAACTTTT-GAAGAAAGCAT--GAGAAAATCTTTGTGA 941
                           -    i         i  -       i   -- ? v       i    
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_39221895_3    942 CCTTGGATTAGGTAAAG--TTCTTAGTTATGACACCAAAGGTACAATCCA 989
                               i     i  v --       v            i i    v v 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_39221895_3    990 TAAAATGAAAAACTA-ATACATTGGATTATATCAAATTTTAAAACTTTTG 1038
                         i    -      v  -   v      i vi      v  v          
  L1M4_orf2#LINE/    617 CAAAA-GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_39221895_3   1039 CACTTCAAAAGACATCACTAAGAAAGTGAAAAGACAAGCCACAAACTGGG 1088
                         ii       i    ii ii                  v     i v    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_39221895_3   1089 AGAAAATATTTGCAAATCACGTATCTGATAGAGGTCTTGTATCTAGAAAT 1138
                                            ii         ii  v        i    - 
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA-T 764

  chrX_39221895_3   1139 ATATACATTTAAACCCTTACAATTCAATAATGAGGAGACAA----CCCAA 1184
                              v ---i   i       i        i ii      ----     
  L1M4_orf2#LINE/    765 ATATAAA---GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_39221895_3   1185 TTTTTAAAGATGGGCACAAAATTTGAATAGCTATTTCATCAAAGAATATA 1234
                           ?--   i       v ii          vi     vi       v   
  L1M4_orf2#LINE/    812 TTW--AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_39221895_3   1235 TACAAATGGCCAAAAGGCACAT---AAGATGCTCAACATCATTTAGTCA 1280
                                      v i      ---                ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.26 (88 / 39)
Gap_init rate = 0.02 (15 / 792), avg. gap size = 1.67 (25 / 15)  


3206 23.06 3.31 1.53  chrX_40056771_40058982      500  1284 (928)    L1M4_orf2#LINE/L1        2   800 (108)  

  chrX_40056771_4    500 GAAGAGACATACCAGGTTAATGGACTGGGAGACTCAACATGGCAAGGATG 549
                          i i   i  v   v   v     i   i     i  i  v iv i    
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_40056771_4    550 CCAATTCTCTCCCAAGTCAATCTACATATTTACCATAATTTCAATCAAAA 599
                         v    v   -     i ii       v   i v ii   ii v       
  L1M4_orf2#LINE/     52 GCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_40056771_4    600 TCCCATCACAATTTCTTGTAGATAAAGACAGACTGATTCTACAATGTATA 649
                              v vvvv   i   i   v vv    ii     i   v   vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_40056771_4    650 TGGAATGACAAAGAGGCTAGAATAGCCAAAACAATTTTGAAGAAAACAAA 699
                              vvi   i iiv i                 i     i  i vi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_40056771_4    700 TGAAATTGGAGGAATCACATTACCTAATTTTAAGACTTATTACGAAGCTA 749
                         ii  i        v     i v  i     i  i     i   i      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_40056771_4    750 CAATAATCAAGATGATGTGGTATTGGT----GGAGAGATACATAGATCAA 795
                           i         iii       i   i----   v   i i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_40056771_4    796 TGAAATAGAAT--AGAGTCCAGA--------CATA-------GG-CAACT 827
                           i        --          --------    -------  -   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_40056771_4    828 GATTTTTGACAAAAGTGCAAAGGCAATTCAATAGAGAAAGAATAGTCTTT 877
                               i     ii    v   i v       i i               
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_40056771_4    878 TTGACAAACGGTGTTGGAACAATTGGATATCCATACGAAAAACAAAATGA 927
                          ii     i    i   i    i      ?   i i v    --i     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA--GAATGA 448

  chrX_40056771_4    928 ACCTGAACTTAAACTTCACACCTTATACAAAAATTAACTGAAAAATGGAT 977
                          vi  i  iivv  i       v                v    -     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGAT 497

  chrX_40056771_4    978 CATAGGTCTAAATGTAAAATATAAAACTATAAAACTCTTAGGAGAAAACA 1027
                           ?  ii          i vv                    i        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_40056771_4   1028 CAGGGAAAAATTTTCATGACCTAGGATTAGGCA--GAATTCTTAAACATG 1075
                         i   ?iv    i   i      v  i       -- iv      i i   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_40056771_4   1076 AGACCAAATATGTGATCCATAAAG--AAAAATTTATGACTTGGACTTCAG 1123
                          v      viiiii v v i   i--      vv  i v          v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_40056771_4   1124 CAAAATTTAAAAATTAAAAACTTTTGTTCTGTGAAAGACATCATTAAGAC 1173
                                --------            v  vii  i    ii  i    v
  L1M4_orf2#LINE/    648 CAAAATT--------AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_40056771_4   1174 AATTAAAAAGCAACCTATGGACTGAAGAAAAACATTTGTAAATCATATAT 1223
                          i v    ii     i ii  v  iiii    i     i           
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_40056771_4   1224 CCAACAAAAGACTTATATACAGAATATATAAAGAATGTTCAAAACTCAAC 1273
                          ii i  ii     i   v                ivi i v       i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_40056771_4   1274 AGTAAGAAAAC 1284
                          i   i  i  
  L1M4_orf2#LINE/    790 AATAAAAAGAC 800

Transitions / transversions = 2.18 (122 / 56)
Gap_init rate = 0.01 (11 / 799), avg. gap size = 3.45 (38 / 11)  

 270 16.67 8.77 7.02  chrX_40056771_40058982     1606  1719 (493)    L1M4_orf2#LINE/L1      793   908 (0)  

  chrX_40056771_4   1606 AAGAAAACTAACAGCCCAATT-AAAAATGGTCAAAAAGATAACCTCTTTG 1654
                           i  i  v  i i       -        v    i-   -------   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG-GAT-------TTG 834

  chrX_40056771_4   1655 GTTA------TCCTCAAACA-GATAAACAGATGGCAAATAAACAGA--AA 1695
                         iv  ------  ii    v -    v   i     v     i  v --  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_40056771_4   1696 AAGATGTTCCACATCATCAGCCAT 1719
                               i  v      ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (11 / 8)
Gap_init rate = 0.05 (6 / 116), avg. gap size = 3.00 (18 / 6)  


3118 23.15 3.65 3.10  chrX_40366837_40370228.rev     2000  2902 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_40366837_4   2000 TGAAAAAGTATCCCATGTTCATGTAT-GGAAGAATTAATATTGTTAAAAA 2048
                           i   ii               v  -      v             i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_40366837_4   2049 ATGTCCATACTACCCAAAGCAATCTATGGGTTCAGTTAAATCTCTATCAA 2098
                         -  v v     v      vii     ii i    iivv    i       
  L1M4_orf2#LINE/     50 -TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_40366837_4   2099 AATTACAA-TGTCATTTTTCACAGAACTAGAAAAAGCAATCCTAAAATTT 2147
                            iv  i-  i -     ii     v v  v  ivii           i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_40366837_4   2148 GTATGGAACCACAAAAGACCCTGCATAGCCAAAGCAATCTTGAGCAAAAA 2197
                         i       vii   ii     v v         i         --    i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAG 195

  chrX_40366837_4   2198 AACTGGAGCCCAAAGATCAAAAGCAAAAGCTGAAGGCATCATACTACCTG 2247
                           ---  i ----------------    i  i   vv   i   v  ii
  L1M4_orf2#LINE/    196 AA---GAAC----------------AAAGTTGGAGGACTCACACTTCCCA 226

  chrX_40366837_4   2248 GCTTCAAAATCTATTACAAAGCTGTAGTAATCAAAACAGCATGGTACTGG 2297
                         ii       ii  i         ii         i    ii         
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_40366837_4   2298 CATTAAAAAAGATGCATTGACCAATAGAACAGAAT--AGAGCCCAAAAAT 2345
                            v ii v   iii  v  i    i   i     --    i   i    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_40366837_4   2346 AACCCCAAGCACTTACAATCAATTGATTTTTGACAAAGATGCCAAGAACA 2395
                           v    vi  i   iii            i     i i        v  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_40366837_4   2396 CACAATGAG-AAAGGACAATCTCTTCAATAAGGAGTGTTGGGAAAACTGG 2444
                         iv     i -    i i i   i     i  ivi   i     v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_40366837_4   2445 ACATCCACATGCAAAA---TGAGCTTGGACTCTTAT-----ACCATGTAC 2486
                          i ?            ---   iv      i i  i-----     i   
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_40366837_4   2487 AAAAATCAACTCAAAGCGGATTAAAGACTTAAACATAA-AGCTTGAAACT 2535
                               i        ii    i ?    i    ii   -    -i     
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACT 525

  chrX_40366837_4   2536 GTAAAACTACTGGAAGAACACATGGGGGAAAATGCTCCACAACAT-GGG- 2583
                         i       vi i      v    i  ? v    -  i iii  v -   -
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGT 574

  chrX_40366837_4   2584 --GGAAATG-CTCCACA---ATAGCCCCAAAAGCAAAGGCAACAAAAGCA 2627
                         --  v    -i i vi ---  ii v         v i          v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_40366837_4   2628 AAAATAAACAAATGGGATTGGATCAAA-TTAAAAAGCTTCCACACAGCAA 2676
                               i i    v   i vv      -       -   iiiii vv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chrX_40366837_4   2677 AGGAAACCATTAACAGGATGAAGAGACAACTCAAGGACTGGGAGAAAATA 2726
                             v  i  i  v iii    i       i  vi  v            
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_40366837_4   2727 TTTGCAAACCATACATCTGACAAGAAACTAATATCCAAAATA----AGGA 2772
                                 i    i      i   ii   vi      i    ---- i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_40366837_4   2773 ACTCAAACAACTCAATAGCAAGAAAAAAAAACAAACTAGTTAAAACACGG 2822
                             vv           ii  -   i v   i  v i i  ?   v i  
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_40366837_4   2823 ACCAATGACTTGA-----CATTTCTCAAAAACAGATACACCAATGTTCAA 2867
                         i v  v  i    -----        v   iv     i  v    vi   
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_40366837_4   2868 CAGATATATGAAAA-ACACTTATCATCCCTAATCAT 2902
                         i iii i       - ii  i v    v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.36 (144 / 61)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.54 (61 / 24)  


1589 22.51 1.28 2.56  chrX_40400532_40402825.rev       99   489 (1805)  C L1M4_orf2#LINE/L1   (507)   401    16  

C chrX_40400532_4    489 TGGTTATTGATTAGAAGA---AATATTGTTAAAATGTCCATACTGCCCAA 443
                           v i  v    i     ---           i   v v     v     
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

C chrX_40400532_4    442 AGTGATCTACAAATTCAATGTAATCCCTATCAAAATTCTAACGACATTTC 393
                          v         i      i i               i i i vi v   i
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

C chrX_40400532_4    392 TTCACATAAATTTTTAAAA-AATCCTAAAATTCATATGGAACCACAAAAG 344
                           -i  v     vvi  iv-i                    vii   ii 
  L1M4_orf2#LINE/    116 TT-GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

C chrX_40400532_4    343 ACCCTGAATAGCTAAAGCAATCTTGAGCAAAAATAGCAAAGCTAGAGGCA 294
                             v       i   i         iv  i  v i     i i    vv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

C chrX_40400532_4    293 TCATACTAGTTGACTTCAAAATATACTACAAATCTATAGTAATCAAAACT 244
                            i   vviii i       iv         v   i         i  v
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

C chrX_40400532_4    243 GCATGGTACTGACATAAAAACAACACACATAGATCACCAGAACAGAATAT 194
                          ii        i     ii i i-   i        vii   i     vv
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAG-ACATATAGATCAATGGAATAGAATTG 313

C chrX_40400532_4    193 AGGGCCCAGAA-TAAATCCACACATTTACAGTCAATTTATTTGTCAGTTT 145
                           i i      -    i   i       ii       v    --------
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT-------- 355

C chrX_40400532_4    144 TTGACAAAGATGCCAAGAACACACAATGGAGAATGAACAGTCTCTT 99
                          i     i i        v  iv      i   v   i     i  
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

Transitions / transversions = 1.93 (58 / 30)
Gap_init rate = 0.02 (6 / 386), avg. gap size = 2.50 (15 / 6)  

 430 30.65 7.79 4.94  chrX_40400532_40402825.rev      627  1011 (1283)    L1M4_orf2#LINE/L1        6   401 (507)  

  chrX_40400532_4    627 AGAT-TACCACGTTCTTTGATAGAAAAATTTAACAACATAAAAATGTCAA 675
                             - v   i    v v   v i  i i    i vii v  i   v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_40400532_4    676 TTCTTTGTAAGCTAATCTACAGATTTAACACTATCTCAAT-ATAATTTCA 724
                          v  iivi  ii i           i   i v   i v  - v   ii  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_40400532_4    725 TCAGTCTTATTTTCTGGAGCCAGAAAT------GTTGATTATAAAGTTTA 768
                         v v i   ---  i  ----       ------ i    iv    i  i 
  L1M4_orf2#LINE/    106 GCTGCCTT---TTTTG----CAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_40400532_4    769 TTTAGAAGAATAAACAAGTAAGAACAG-----ACATTCCTTAGGAAATAA 813
                          v i   ivii  ivi viv    i  -----   v  -  iii   v  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAAGAA 197

  chrX_40400532_4    814 AAGTGATGA-GGAGGGCTAGC---TCCAAGAGATATGAAAACATATTTAA 859
                         i iii v v-     i  vi ---   v ---  v v     v  i vv 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCA---ATTTCAAAACTTACTACA 244

  chrX_40400532_4    860 AAGTTTTA-TAATTAAATCACTATGATATTGACATATGAATTGACA---- 904
                            i vi -    i  iv  v i  i  i  i    v i  v    ----
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_40400532_4    905 ----AATGGAACAGAATATAAAGCAAGCAAGAAATACATCCACACACACA 950
                         ----       i     vv i  i--- v       v i   i   ivi 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGT---CCAGAAATAAACCCATACATTTA 341

  chrX_40400532_4    951 TGG-AAATATAGTATATGATAAAAG--CTTATTTCAATCA-TGGGGAAAA 996
                            -v   - ii v vi  i  ii -- iv vvi  v   -        i
  L1M4_orf2#LINE/    342 TGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_40400532_4    997 GAAACACGGTTTTTT 1011
                         --  i --  i    
  L1M4_orf2#LINE/    391 --AATA--GTCTTTT 401

Transitions / transversions = 1.46 (70 / 48)
Gap_init rate = 0.05 (19 / 396), avg. gap size = 2.58 (49 / 19)  

 710 31.36 7.54 1.43  chrX_40400532_40402825.rev     1317  1807 (487)    L1M4_orf2#LINE/L1      388   908 (0)  

  chrX_40400532_4   1317 AAGAAACACTTTTTAAATAAGTGGCACTGGAACAACTTGATAGCCATACA 1366
                              vviii    v  i  i   ii    i      v    ?   i ii
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_40400532_4   1367 GAAAAAGATAAGATCCAATTTATTCCTTACACTG-GTA--------AATT 1407
                         v    ii  i ii ivi iiiv v   i    ii-i  --------  i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_40400532_4   1408 CCAGATAGAGAAGAATTCTCAGTGTGAAAAATGAAACTACACAAATAATA 1457
                          v i  i  vv ? ivi  v i   i i iv i      i v  v vv  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_40400532_4   1458 AGAGAAAA--TAAGGGTGAATCC-CTTGAAGTCTGGGAGAGGGAAAACAT 1504
                         ii      --  i ?  i    i- v   vv -    vv   v  vivv 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCT-TGGGTTAGGCAATGGTT 586

  chrX_40400532_4   1505 TCCTAACTATGATTC--AAAGTCCAGAAGCAATAAG-GAAAAA---GATA 1548
                           i  iv     iv --    --  v      i  i-      ---    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAG--CACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_40400532_4   1549 AATTTGATCACATAAAAAT-AAAAACATTTTACATGTCAGAAAACATTAT 1597
                             v  iiv   v     -      -    iiiiv   i ii   i   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTAT 683

  chrX_40400532_4   1598 -ACAAAAGTGAGAAGACAAATGACCAATTGGAAAAAAATATTTGCAACTT 1646
                         - vi       i       viv  vi v   i i             v i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_40400532_4   1647 ATATCAATC-AAGAAGTAA---GCATCTTTAACATATAATGAACTTCTTA 1692
                             --   -i v   vi --- i   ivv  i      v     -    
  L1M4_orf2#LINE/    734 ATAT--ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT-CTTA 780

  chrX_40400532_4   1693 -AATTGAG----AAGAAAAGAAATAG--------AAAAAGTTGTAAGAGA 1729
                         -  i v i----  i  i v     i--------     vvv i  ii  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_40400532_4   1730 TATGTATAGACCATTCACAGAAAAAGAAATGAAAACAGCCTTTAAATATG 1779
                          v  v      vv   v vi  i    v  iv   ii   vv   ii ii
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_40400532_4   1780 TGAAAAGATATCCAACTTTACTTACAGT 1807
                                  iii    v i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (90 / 61)
Gap_init rate = 0.04 (19 / 521), avg. gap size = 2.32 (44 / 19)  


3114 25.56 2.47 0.67  chrX_40410444_40416144     4317  5208 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_40410444_4   4317 TGGAAACACATCC-----------ATTGGGTAGAATCAATATTGTGAAAA 4355
                               v i    -----------     i-   v i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGA-AGACTTAATATTGTTAAGA 49

  chrX_40410444_4   4356 CGACCATACTGCCAAAAGCAATTTACAAATTCAATACAATCCCCATCAAA 4405
                         i i v     v  v   vii  i    i      ii       i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_40410444_4   4406 ATACC-GCCATCATTCTTCACAGAGTTAGAAAAAACAATTCTAAAATTCA 4454
                           v  -  iii -  i  ii    iv v  v  ivii  i          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_40410444_4   4455 TGTGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAG 4504
                          i     viiv  ii  v  viv         i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_40410444_4   4505 AACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGC 4554
                               vi      vv       v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_40410444_4   4555 CATAGTCACCAAAACA---TGGTACTGGTATAAAAACAGGCATATAGATC 4601
                         i i   v i   i   ---         i    ii i  i          
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_40410444_4   4602 AATAGAACAGAATAGAAAACCCAGAAATAAACCCAAATACTTACAGCCAA 4651
                            i   i     v  i ii               v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_40410444_4   4652 CTGCTCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCT 4701
                         i  v i   i    i vviv   i v   vv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_40410444_4   4702 TTTCAACAAATGGTGCTGGGATAATTGGCTAGCTACACGTAGGAGAATGA 4751
                                              i  i   v  ? i   i i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_40410444_4   4752 AACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATT 4801
                          ii    i  ii i   v    v           i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_40410444_4   4802 AAGGACTTAAACCTAAGACCTGAAACTGTGAAGAGTCT-AGAAGATAACA 4850
                          ?i   i    iv     v  i     i i  - v   -      v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chrX_40410444_4   4851 CTGGAA-AAACCTTTCTAGACACTGGCTTAGGCAAGGATTTTATGACCAA 4899
                         iv  ?i-   i   iv -   vi   v        v i   iv iivi v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_40410444_4   4900 GAACCCAAAAGCAAATGCAGTAAAAACAAAGGTAAATAGCTAGGACCTAA 4949
                           vv         v v   ii    iv   ii  i   iv v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_40410444_4   4950 TTAAACTGAAGAGCTTTCGCATGGCAAAAGGAACAGTCGGGAGAGTAAAC 4999
                          i   v v  i i    i iiivv    i iv  vi  ii  i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_40410444_4   5000 AAACAACCCACAGAGTGGGAGAAAA-ATCTTCACAATCTATACATCTGAC 5048
                          i            i          -  i v  -    -   i      i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGAT 744

  chrX_40410444_4   5049 AAAGGACTAATATCCAGAATCTACAACGAACTCAAACAAATCAGTAAGAA 5098
                           i     vi          v  i  v      vv    v   i   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_40410444_4   5099 AAAAACAA----TCCCATAAAAAACTGGGCTAAGGACATGAATAGACAAT 5144
                            i    ----i  v  v?    v     v     iv          v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_40410444_4   5145 TCTCAAAAGAAGATAAACAAATGGCCAACAAACATATGAGAAAATGCTCA 5194
                             v          v            i  i  i    i  i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_40410444_4   5195 ACATCACTAATAAT 5208
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (141 / 83)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.15 (28 / 13)  


3312 23.20 5.92 0.59  chrX_40503116_40505182.rev      724  1568 (499)    L1M4_orf2#LINE/L1        1   890 (18)  

  chrX_40503116_4    724 TGGGGAGCTATTCCATGTTCATGGGTAGTAAGACTCAATATTGTCAAGAT 773
                            ii  v   i            i v v      i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_40503116_4    774 GGCAGTTCTTCCCAACTTGATCTATAGATTTAATGCAATCACAATCAAAA 823
                             i v  i     v        i     i  i      v v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_40503116_4    824 TCCCAGCAATTTATTTTCTAGAGACTGACAAACTAATTCTAAAGTTTATA 873
                                viii v    vi   i i      i  i  i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_40503116_4    874 CAGAGAAACAAAATACCAAGGATAGCCAACCCAGTGTTGAAGGAGAAAAA 923
                         ii  i vi   iiv   v  i        vv  i v     ii    i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_40503116_4    924 CAAAGTTGAAATACTGACACTACCCAACTTAAAGACTTACTATAAAGCTA 973
                                 i iv   v     v     i  v  i        i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_40503116_4    974 CAGTAAGCA------TGTGGTATGGATGAAAGAATAGGCAAATAGATCAA 1017
                               v  ------       iv iiiv   i    i  v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_40503116_4   1018 TGGAACAGAAGAGAGAGTCCAGAAATAGACCCACATAAATA----CAACT 1063
                              i    vv               i     i i vv  ----   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_40503116_4   1064 GATTTTTGA---GGGAGC-AAAAGCACTACAGTGGAGAAAAGGTAAACAT 1109
                               i  ---   v  -  i v  i -  i   i    iii  iv v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAGTCTT 399

  chrX_40503116_4   1110 TTCAACAAATGGTGCTGAAACAACTAGATATCCACATGCAAAAAAATGAC 1159
                                          ii      i    ?            i     v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_40503116_4   1160 TCTAGACACAGACCTTACACTCT---------TCCACTCAAACTGGATCA 1200
                         vi i   v vv    i    iv --------- iv       v       
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_40503116_4   1201 CAAATCTAACTGTAAAATACAAAACTATAAAACTCCTAGAAGATAACTTT 1250
                         ? i i    v     i vvi               i       v   v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_40503116_4   1251 GGAGAAAATCTAAATAACCTTGGATTTGGTGATGACTTTTTAGATACAAC 1300
                           ? v      vvi i       i  v  ii   ii  i       ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_40503116_4   1301 ACCAAAGGCATGACCCATGAAA-----------TAACTTCATGGACTTCA 1339
                               i   ii v v ii   -----------   v  ---        
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT---GGACTTCA 646

  chrX_40503116_4   1340 TTAAAATTAAAAATTCCTGCTCTGCAAAATACACTATCGAAACAATAAAA 1389
                          i           i ii  iv  v    iv        i i v i i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_40503116_4   1390 AGACAAACCACAGACTGGGAGAAAATATTTGCAAAAGGCATATCTGATAA 1439
                               v       v                    vvii           
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_40503116_4   1440 GGGGTTGTTATCGAAAATATACAAGGTAA-----AAAACTCAACAATAAG 1484
                            ii vv    v i      i  i -  ----- v       i     i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAG-AACTCTTACAACTCAATAATAAA 795

  chrX_40503116_4   1485 AA----AAGAACCAGATCAAAAAATAAGTGAAAGACTTTAACTGACACCT 1530
                           ----  v    vi  i?      ii ii  i  i  v  iv    ii 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_40503116_4   1531 CACCAAAGA-------TAGGTGGCAAATAAGCATATGAAAAGATG 1568
                          v       -------i ii    v        i           
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

Transitions / transversions = 1.70 (121 / 71)
Gap_init rate = 0.01 (12 / 890), avg. gap size = 4.58 (55 / 12)  

 930 24.66 4.07 2.98  chrX_40503116_40505182.rev     1698  2066 (1)    L1M4_orf2#LINE/L1      488   860 (48)  

  chrX_40503116_4   1698 CAAAATCCAGATTAAAGATTTAAATCTAAGACCTCAAATTATAAAAATCC 1747
                               --i   i ?   ii     v     v  v   i       v  i
  L1M4_orf2#LINE/    488 CAAAAT--GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_40503116_4   1748 TAGATGAAAACCTAGG---AAATGTTATTCTGGATATCAGCCTTGGCAAA 1794
                             v      v    ---    v  --- vv  iv ii vi v     v
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTT---CGTGACCTTGGGTTAGGCAAT 582

  chrX_40503116_4   1795 GAATT------TATGAC--TAAGTCCTCCAATTGCAACCAAAACAAAAAA 1836
                          iv  ------      --i  ivv -v   --     -    v      
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGC-ACAA--GCAAC-AAAAGAAAAAA 628

  chrX_40503116_4   1837 T-GACAAGCGGGACCTAATTAAA-CTAAAGAGGCTTGGAAAGCAAGAGAA 1884
                          -  i  iiv    i v  i   -i    i vvi   vivvv   ii  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_40503116_4   1885 ACTATCAGCAAAGTAAACAGACAACTCACAGAATGGGAGAAAATATTTGC 1934
                                iv     i  v       i                        
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_40503116_4   1935 AAACTCTGCATCCAACAAAGGCCAAATACCCAGAGTTTATAAGGA--TCT 1982
                            iiv ii   ii i  i  v vvi  i     i v     i  --   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_40503116_4   1983 TAAACAACTCAACAAGCAAAAACCAAATAACCCTATTAAAAATTGGGCAA 2032
                           --        i  vv    iv          v   ?    v       
  L1M4_orf2#LINE/    779 TA--CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_40503116_4   2033 AGGACATTAAGAGACACTTCTCAAAAGACAACAT 2066
                             iv v  v     i     v     vi i  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.02 (45 / 44)
Gap_init rate = 0.03 (12 / 373), avg. gap size = 2.17 (26 / 12)  


4038 13.16 1.06 0.45  chrX_40570965_40573982      983  1643 (1375)    L1M4_orf2#LINE/L1        1   665 (243)  

  chrX_40570965_4    983 TGGAAA--CATCATATATTCATGGGTCAGAAGACCTAATATTGTTAAGAT 1030
                               --i   vi  i       i ii      i               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_40570965_4   1031 AGCAATACTCCCCAAAGCGATTTACAGATTCAGTGCAATGCCTATCAAAA 1080
                         i               vi   i          ii     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_40570965_4   1081 TCCCAGCTTGCTTTTTTGTAGTAATTGACAAGCTGATCCTAAAATTCATT 1130
                                 vv        i  v                           v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_40570965_4   1131 TGGAAATGCAAGAGACTCACAATAGCCAAAGCAATCTTGAAAAAGAA--- 1177
                                     i   i  v          i                ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_40570965_4   1178 CAAAGTTGGAAGACTCACATTTCCTGATTTCAAAACTTACCAAAAAGGTA 1227
                                   i        i    ii              i v    v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_40570965_4   1228 CAGTAATCAAGACCACGTGGTACTGGGATAAAGACAGACATATAGACCAA 1277
                                      vii          v    i  i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_40570965_4   1278 TGAAATAGAATTAAGAGTCCAGAAATAAACCCATTCATTTACGGTCAAAT 1327
                           i         i                     v      i      v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_40570965_4   1328 GATTTTCAACAAGGGTGCTAAGACCATTTAGTGATGAAAGAATAGTCTTT 1377
                                i          i         i i  iv               
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_40570965_4   1378 TCAGCAAGTGGTTCTGGGACAACTAGATATTCAATTACAAAAAGAATGAA 1427
                            i   i    v           i    ?i  vv i     -       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAA 449

  chrX_40570965_4   1428 GTTAGACCCTTACCTCACAATATACACAAAAATTAATTTAAA-TGAATCA 1476
                            i     i         vi   i           i i   -  i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_40570965_4   1477 AAGATC-AAATGTAAGAATTACTGCTATAAAACTCTTAGAAGAAAATAAT 1525
                         ?   i -          ii  vvi                      i - 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-T 548

  chrX_40570965_4   1526 AGGAGTAAATCTTCATGGCCTTGGGTTAAGCAATGAATTCTTAGGTGTGA 1575
                            ?          i  i          i      iv       i i   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_40570965_4   1576 CACCAAAAGCACAAGCAGCAAAAGAAAAAAATACATAAATTAGACTACAT 1625
                                          i            -  v       i    v   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCAT 647

  chrX_40570965_4   1626 CAAAATTTAAAACTTTTG 1643
                                v          
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTG 665

Transitions / transversions = 2.36 (59 / 25)
Gap_init rate = 0.01 (7 / 665), avg. gap size = 1.43 (10 / 7)  

 540 19.23 0.00 2.31  chrX_40570965_40573982     1933  2062 (956)    L1M4_orf2#LINE/L1      649   775 (133)  

  chrX_40570965_4   1933 AAAATTTAAAACTTTTCTGCTACAAGCAATACCATCAAGAAAGTGAGAAG 1982
                               v         v    v   ivi i  i             i   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_40570965_4   1983 ACAACCAAAAAAATGGGAGAAAAATAATTGTGATTCATATACTTAAGAAG 2032
                               v v i            -  v   ii v       ii i v   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAG 747

  chrX_40570965_4   2033 GGATGTATATCCAGAATATGTTTAAAAAAC 2062
                            iv i            i --   i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATAT--AAAGAAC 775

Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.02 (2 / 127), avg. gap size = 1.50 (3 / 2)  

 767 12.95 0.72 0.00  chrX_40570965_40573982     2387  2525 (493)    L1M4_orf2#LINE/L1      769   908 (0)  

  chrX_40570965_4   2387 AAAAACCTCTTATAATTCAATAATAAAAAGGCAAATAACCTAATTTTAAA 2436
                            i v      i  i              i         i    ?v   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_40570965_4   2437 ATGGGCAAAGGATATGAATAGACTTGTCTCCAAAGAAGATGTACAAATG- 2485
                                      v         v v              i        -
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_40570965_4   2486 CCAATAAGAACCTGAAAGGATGCTCGATTTCATTAGTCAC 2525
                                 v  v     i       i iv   ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.01 (1 / 140), avg. gap size = 1.00 (1 / 1)  


1422 26.93 12.08 0.40  chrX_40665320_40667465      489   993 (1153)    L1M4_orf2#LINE/L1      126   689 (219)  

  chrX_40665320_4    489 TGAAAATGTAGTTCTTAAGTTTATATGGAAATGTAAAGGACCAAGAATA- 537
                            v  vv ii i  v  i  i           i  i     v      -
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chrX_40665320_4    538 ------------TGAAAAAGAA---CAAAGTTTGAGAACTTACATTACTT 572
                         ------------          ---       v   i   i   i v ii
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_40665320_4    573 GATTTCAAGGATTATTATAAAACTATTATCATCAACAGAGTATGG----- 617
                         i       iiv   i  i   i   ivi v     v v   i   -----
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_40665320_4    618 -------------CATATAAATTAACA-AGTAGAATAAAAAG-CTAGAAG 652
                         -------------      i  i  ii- i      vi i  - i    i
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_40665320_4    653 TAGACACACACATATATAGTCATGTGATTTTTTACAAAAGCACCAATGCA 702
                           i  v  i    v   i    vv       iv    ii ii    vi v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_40665320_4    703 ATCTAGTGGGGGAAGGAAAGTTGATGCAACAAGTGGTGC----------- 741
                           ii i     i   i v   ivv v      i      -----------
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_40665320_4    742 ------CACATGGAAAAATATGAATCTCAACCTGTGCCTCACACCATATA 785
                         ------      v    iv     vi vi   iv i              
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_40665320_4    786 TGAAAACTAATCTGAGATGGATCACATACCTAAATGGAAATGGTAAAACC 835
                         ii    i   iiii i        ? v         v  iv v      i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_40665320_4    836 ATATGTCTTTCGGAGGAAACCTCAGAAGAGTA--TCTTCATGAT-TTGGG 882
                            viv  i ii  i    v -- v i ?   --     i   i-     
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAAC--ATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_40665320_4    883 ATAGGCAAAGTTTGCTTAG-CAGGTCACAGAAAACAGTAACCATAAAAGA 931
                         v       v v  v     -i v v   vi   i  vv i v i      
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_40665320_4    932 AAACATTGAT----TAGAGTTCATCAAAATTTAAAACTTCCGTTCATCAA 977
                            v  v   ---- i  v            v       ii  v v    
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_40665320_4    978 AAGACAACATTAAGAA 993
                          i    vi  i     
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAA 689

Transitions / transversions = 1.48 (80 / 54)
Gap_init rate = 0.02 (11 / 564), avg. gap size = 5.73 (63 / 11)  

 760 20.77 3.38 0.00  chrX_40665320_40667465     1447  1653 (493)    L1M4_orf2#LINE/L1      695   908 (0)  

  chrX_40665320_4   1447 AAAGCCAAGCCACAGACTGGG-GAAAATATTCATAGAATACATATTTGAC 1495
                             v   v       v    -         iii i vi i    i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_40665320_4   1496 AAAGCACTGCTATACAGAAAATATAAAGAAC-CTGAAAAATCAGTAATAC 1544
                           i v   vv   v     v           -  v v  v   i     v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_40665320_4   1545 TAAGACAAATGGCCCAACTTAAAA-TGGGCAA----TTTGAGTAGACACT 1589
                         v         ii     i ?    -       ----     i      i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_40665320_4   1590 TCCTAAAAGAAAATAAACAAATGAACAATAAGCACATGAAAAAGTGACCA 1639
                           iiv      i   v       iv                 ii  vi  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_40665320_4   1640 AGGTCATTAGTCAC 1653
                          vi   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (23 / 19)
Gap_init rate = 0.02 (4 / 214), avg. gap size = 1.75 (7 / 4)  


4125 16.14 3.98 4.09  chrX_40697294_40699545.rev      882  1761 (491)    L1M4_orf2#LINE/L1       30   908 (0)  

  chrX_40697294_4    882 AAGACTGAAATAAAAGTATTAAGATAGCAATACTCCTCAAATTGATCTAC 931
                               ----   v v i       i          i             
  L1M4_orf2#LINE/     30 AAGACT----TAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chrX_40697294_4    932 AGAGTCAATGCAATCCCTATCAAAATCCCAGCAGGCTTTTTTTTTTTTTG 981
                            v    i                       v v       ------- 
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT-------G 118

  chrX_40697294_4    982 CAGAAATGGACAAGATGATGCTAAAATTCATACAGA----TAAGGAGTTT 1027
                                v      v    v            ii  ----i    i----
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG---- 164

  chrX_40697294_4   1028 CCCCCCCACCTCGCCACTAGCCAAAACAATCTTGAAAAAGGAGAACAATG 1077
                         -------   iv -- v                       i       v 
  L1M4_orf2#LINE/    165 -------ACCCAG--AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_40697294_4   1078 TTGGGAGGGCTCCTACTTCCTGATTTCAAAACTCACTATGAAACT----- 1122
                             -   i   vi      ii           i    ii  i  -----
  L1M4_orf2#LINE/    206 TTGG-AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_40697294_4   1123 ---------------GTACTG-CGTAAGGACAGGTATATATGCCAATGGG 1156
                         ---------------      - i      i  ii     vii      i
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_40697294_4   1157 ATAGAATAAGGAGCTCATAAATAACCCTTAACATATATGATCAACTGATT 1206
                                vii   ii  v      v  ivv    v    i    i     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_40697294_4   1207 TTCCACGAGGGTGCCATGACCATTCAATGAGGGAAAGGATAGTCTTTGCA 1256
                            v  i         v            -       i         v  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTTCA 403

  chrX_40697294_4   1257 ATAAATGGTGCTGGGAAAACTGGATATATATATATATATATATGCAAAAA 1306
                          i              v         ?vi i  ----------      i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACAT----------GCAAAAG 443

  chrX_40697294_4   1307 AATGGAGTTGGATCTTTTCCTCACATAACATACAAAAATTAACTGAAAAT 1356
                             i       i ii v       iv i               v     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_40697294_4   1357 GAATCAAAAACCTAACCATAAGAGGTAAAACTATAAAACTCTTAGAAGAA 1406
                          i    ? i      vii      v                         
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_40697294_4   1407 AACGTGACAGGGAAGTTTCACAACATTGGATTTGGCAATAATTTCTTGGA 1456
                            i iiv? vi  vi   iii  v    i  v      ii      i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_40697294_4   1457 TATGACA---ATAGCACAGGTG------GAAAAAATAGACAAATTGGAGT 1497
                                --- v      i ii------           i        v 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_40697294_4   1498 TCAACAAAATTAAAAACTTTTGTGCATCAAAAGACACTATCAACAGAGTG 1547
                            v                     v     i           v i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_40697294_4   1548 AAAAGGCAACCTACAGAATGGGAGAAAATATTTGCAAATAATATATTTGA 1597
                              i     i                           v      i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_40697294_4   1598 TATGGCATTAATATCCAGAACATATAAAAAACTCCTACAACTCAACT-CA 1646
                           v  v i vi         i       i     i          iv-i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_40697294_4   1647 GCAAAACAAAAAACCCAAGTCAAAAATGGGCAAAGGACTTGCAGAGCCAT 1696
                         iv  i     v       v ?                i   v v  v   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_40697294_4   1697 TTCTTCAAAGAATATATGTAAATATCCAATAAGCACATGAAAAGACACTT 1746
                             i       v    ii    iv                    ii  i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_40697294_4   1747 AACATCATAGTCATT 1761
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (86 / 52)
Gap_init rate = 0.01 (13 / 879), avg. gap size = 5.46 (71 / 13)  


3200 22.57 2.78 5.67  chrX_40793489_40795610.rev      699  1633 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_40793489_4    699 TGGAAAAATATTCTATGTTCATGGGTTGGAAGAACAAATATTGTTAAAAT 748
                               i    i i          i        viv           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_40793489_4    749 GTCCATATTACCCAAAGCAATCTACAGATT-GATGCAATCTCTATTAAAA 797
                          v v   i v      vii           -i i      i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_40793489_4    798 TACCAATTATATTCTTCACAGAAATAGAAAAAACATCCTTTGAGGTGAAT 847
                          v   ii iiv  i  ii       --------------------   --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT--------------------TGA-- 128

  chrX_40793489_4    848 CTGCAAGGTAAAACAAAAAAATACAAAAAACACTCCTAAAATTCATATGG 897
                         ---    v i ----------------------                 
  L1M4_orf2#LINE/    129 ---CAAGCTGA----------------------TCCTAAAATTCATATGG 153

  chrX_40793489_4    898 AACTACAAAAGACTCCAAATAGCCGAATCAATCTTGAGTAAGAAGAACAA 947
                           v i   ii   i vi       i  v         iv           
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_40793489_4    948 AGCTGAAGGCATCA-GCTACTTGACTTCAAAATTTACTATAGAGCAATAG 996
                           i  i   vv   -i  v iii i       i      i i   v i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_40793489_4    997 TAACCAAAACAGCATGGTATTGACACAAAAATAGACACA--GATCAATTG 1044
                            i   i    ii     i  i  i  ii       i --       v 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_40793489_4   1045 AACAGAATAGAGAACCCAGAAATAAATCCACATAATCAGAAACAACTGAT 1094
                           i     v    ii           i   i i v i viiv   i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_40793489_4   1095 TTTCAACAAAGGTGCCAAGAACACACATTGGGGGAAAAGGCAATCTCTTG 1144
                             i    i          v  iv  v     i  i i-i i   i  v
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTTTTC 402

  chrX_40793489_4   1145 AATAAAAATGGTGTTGCAAAAACAGAATATACATATGCAGAAAAATGAAA 1194
                           i   --     i  vi v   v i   ?v  i     i  i      i
  L1M4_orf2#LINE/    403 AACAAA--TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_40793489_4   1195 CTAAACCCCTATTATTCATCATATGTAAAAATAAACTCAAGATGGGTTAA 1244
                         i ii       iiviv  i     ii      v       i    i i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_40793489_4   1245 AAACTTAAATGTAAGACCAGAAACTATAAAACTACTAGAAGAAAACACAA 1294
                          i  i           v vi             vi            i i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_40793489_4   1295 GGG-AAATGTTTCATGTCATTAGTGTGGGCAAGGACTTTTTGGCTAAGAC 1343
                          ? -    -i   i  v v  i vv i     v ii  i  i v  v   
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_40793489_4   1344 TTCAAAAGCACAGGCAACAAACACAAAAACAGACAAACGAAATTACATTA 1393
                         vi          i        viv     i   i   ivii i v   i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_40793489_4   1394 AACTAAAAAGCTTCTACCCAACAAAGGAAAT----AAGACCACAAAAAGA 1439
                           v v    i   i iiv vv       v i----    vviii      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_40793489_4   1440 CAAATCTACAGAATTGGAGAAAATATTTGCAAACTATGCATCTGACAAGG 1489
                            -i i       v                  ii  ii      i    
  L1M4_orf2#LINE/    700 CAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_40793489_4   1490 GGTTAATATCCAGAATATATAAGGAACTC----AAC------------AG 1523
                          ii vi                i      ----   ------------  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_40793489_4   1524 -CAAAAAATCCGATTTTTAAAATGGGCAAAAGACTTGAATAGATATTTCT 1572
                         -    v  i  i   ?v-            i  i         i      
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_40793489_4   1573 CAAAAGAAGACATCCAAATGGCCAACATGTACATGAAAGCACACTCAACA 1622
                          v        i  v           i v i        iv ii       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_40793489_4   1623 TAACTAATCAT 1633
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.18 (142 / 65)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.94 (79 / 16)  


3230 27.09 0.44 0.44  chrX_41042450_41044310.rev      463  1370 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_41042450_4    463 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 512
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_41042450_4    513 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGGCATCCCCATCAAGC 562
                            v     v     iv i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_41042450_4    563 TACCAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 610
                          v   iivi    i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_41042450_4    611 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 660
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_41042450_4    661 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 710
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_41042450_4    711 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGATC 760
                                 i   i    ii         i iv ii i   v  i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_41042450_4    761 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 808
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_41042450_4    809 ATCTGATCTTTGACAAACCTGAGAAAAATAAGCAATGGGGAAAGGATTCC 858
                          vi    i  i     ivv  vv  i vi vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_41042450_4    859 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 908
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_41042450_4    909 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 958
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_41042450_4    959 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1008
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_41042450_4   1009 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1058
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_41042450_4   1059 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1108
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_41042450_4   1109 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1158
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_41042450_4   1159 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 1208
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_41042450_4   1209 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1258
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_41042450_4   1259 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 1308
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_41042450_4   1309 TCAAAAGAAGACATTTATGCACCCAAAAAACACAGGAAAAAATGCTCACC 1358
                           v        i  vi viiiv    v  i    v     i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_41042450_4   1359 ATCACTGGCCAT 1370
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 386 24.29 2.14 5.71  chrX_41104188_41106429        1   140 (2102)    L1M4_orf2#LINE/L1      199   333 (575)  

  chrX_41104188_4      1 AATAAAGTGAGAGGAATCACTCTACATGATACTAAGTCTAACTATATAAC 50
                           i     vi     v    v  v vii  vii  iv  v    i v i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_41104188_4     51 TACAGTAATCATGAC--TGTGGTATGGTCAGAGAGATAGGAACATAGAAA 98
                                    v   --       iv v  v ii     --     ----
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG--ACATA---- 292

  chrX_41104188_4     99 CATAGATCAATG-AACAGAATAGAAAACCCAGACATATGTCCA 140
                         --          -  i     v  i ii     v   vii   
  L1M4_orf2#LINE/    293 --TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

Transitions / transversions = 1.12 (18 / 16)
Gap_init rate = 0.03 (4 / 135), avg. gap size = 2.75 (11 / 4)  

 547 27.50 2.50 0.00  chrX_41104188_41106429      501   660 (1582)    L1M4_orf2#LINE/L1      223   386 (522)  

  chrX_41104188_4    501 CCGGATTTTAAGAC--ATCATCTAGCTACA-TAATCAAGGCTCTGTGGTA 547
                           vi    i  i  -- ii ivv       -        i vv       
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_41104188_4    548 CTGGTAGAGGGATAGACA-ACAGAACAACAGAACAGAGTAGAGAATCTAC 596
                             i v i         - i   v   ii   i   i v    i  i v
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_41104188_4    597 AAATAGAGCCACACAAATATGCCCAGCTGACTTTTGACAAAGGTGCAAAA 646
                              i v   i   vv    vi  ii   i   i     i     v  i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_41104188_4    647 GTAAATCAATGGAG 660
                         iiv v       i 
  L1M4_orf2#LINE/    373 ACCATTCAATGGGG 386

Transitions / transversions = 1.75 (28 / 16)
Gap_init rate = 0.02 (3 / 164), avg. gap size = 1.33 (4 / 3)  

 596 25.53 0.71 0.00  chrX_41104188_41106429      962  1102 (1140)    L1M4_orf2#LINE/L1      378   519 (389)  

  chrX_41104188_4    962 TCAATGGAGAAATGAGAGCCTTTTCAGCAAATGGTGCTGGAGCAATTGAA 1011
                                i    vi v  i       i             ii   i  i 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_41104188_4   1012 CATCCATAGGCAAAAAAATGAACCTTCAACCTAAATTCACACCTTAGATA 1061
                         i ?   i v      i      vi vv v  iv vi       v  v i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_41104188_4   1062 AGAATTATCTCAAAATGAATCATGAAATTAAATGTAGG-GCT 1102
                          i     v         i    ?ii vi        i -   
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

Transitions / transversions = 1.62 (21 / 13)
Gap_init rate = 0.01 (1 / 142), avg. gap size = 1.00 (1 / 1)  

 826 24.14 16.67 0.86  chrX_41104188_41106429     1402  1749 (493)    L1M4_orf2#LINE/L1      506   908 (0)  

  chrX_41104188_4   1402 TAAATGTAAAA--TACAAATTATAAAAC-CTTA--AGTAAAAATAGA--- 1443
                                  i --  -   i        -    --  v   v    i---
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_41104188_4   1444 AAATCTGTAGGCCCTAGGGCTAGACAAATAGTT-CTTAG------CATTG 1486
                               viiv v   v   i   i   - i   -     ------  iii
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCA 603

  chrX_41104188_4   1487 AGGG-----------------AAAATTGACAAATTCTATCTCATCAAAAT 1519
                          ii -----------------     v  i     vv ii          
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_41104188_4   1520 TAAAAAATGTTGTTCTGCAAAAGCCCATGT-AAGTAGGATGAAAAGACAA 1568
                               v v    v  v    i v vv i -   v i -           
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG-TGAAAAGACAA 702

  chrX_41104188_4   1569 GGTATGGCCTGGAAGAAAATATTTGCAAACCGCATATCCCACAGAGGA-- 1616
                         vvi ii vv   i                i ii     iv i ii   --
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_41104188_4   1617 ---ATCTCAAA----------ACTTTT---------TGGTAAAAAAGCCA 1644
                         ---   ivi  ----------   i  --------- ii      ii v 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_41104188_4   1645 ACAATGCAATTAGAAAATGGGCAAAA-ATTACAACAGATATTTCACCGAA 1693
                          i  iv     ?i            i-   vv  i   i     v  i  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_41104188_4   1694 AAGGATACACAGATGGTAATTAAGCACACGAAAAGAGGTTCAGCATCACT 1743
                         i i    i   i    iv v        i       v i   i     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_41104188_4   1744 AGCCAT 1749
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.68 (52 / 31)
Gap_init rate = 0.04 (15 / 403), avg. gap size = 4.07 (61 / 15)  


3190 26.54 0.66 0.66  chrX_41423593_41430011     5019  5926 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_41423593_4   5019 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5068
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_41423593_4   5069 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGGCATCCCCATCAAGC 5118
                            v     v     iv i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_41423593_4   5119 TACCAATGACTTTCTTCAC-GAAATTGGAAAAAACT-ACTTTAAAGTTCA 5166
                          v   iivi i  i  ii -       -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_41423593_4   5167 TATGGAACCAAAAAAGAGCCCGTATTGCCAAGTCAAACCTAAGCAAAAAG 5216
                                viiv  ii  v  v v  v     iv   v i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_41423593_4   5217 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAGCTATAATACAAGGC 5266
                                i      vv       v  ii i     iviv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_41423593_4   5267 TACAGTAACCAAAACAGCAAGGTACTGGCACCAAAACAGAGATATAGACC 5316
                                 i   i    iiv          iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_41423593_4   5317 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5364
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_41423593_4   5365 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATAGGGAAAGTATTCC 5414
                          vi    i  i     ivv  v   i v  vvv   i       v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_41423593_4   5415 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5464
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_41423593_4   5465 GAAACTGGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAGGTGGA 5514
                            ii    i    v   i     v    i         i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_41423593_4   5515 TTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5564
                          i ?    i     i v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_41423593_4   5565 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5613
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_41423593_4   5614 AAACACCAAAAGC-CATGGCAACAAATGCCAAAATTGACAAATGGGATCT 5662
                         vi           -  -i        v vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_41423593_4   5663 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5712
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_41423593_4   5713 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5762
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_41423593_4   5763 AAAGGGCTAATATCCAGAATCTACAAATAACTCAAACAAATTTACAAGAA 5812
                           i  i  vi          v  i   v     vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_41423593_4   5813 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5862
                            i     i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_41423593_4   5863 CCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5912
                         i   v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_41423593_4   5913 TCATCACTGGCCAT 5926
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


 928 22.25 5.92 5.92  chrX_41434238_41437330        1   355 (2738)    L1M4_orf2#LINE/L1      348   702 (206)  

  chrX_41434238_4      1 ATCAAATTTTAACAAAATTGCAAGGGGAAATTCAATGGAGAAAAGATAAT 50
                           ii v   ii    iiv   v i ivv -        i    ii   i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGT 396

  chrX_41434238_4     51 CTTTTCAACAAATGATGCTGGAACAACTATATATATGGAAAAAAAAGACA 100
                                       i      i      iv   ?vi-----------   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC-----------ACA 435

  chrX_41434238_4    101 AGACCAAAAAAA--AAGACAACTTGTATCCAGACTTCAGAAAATATCTAA 148
                         v --     i  --   -----   v i  vv  i   v vv    vi  
  L1M4_orf2#LINE/    436 TG--CAAAAGAATGAAG-----TTGGACCCCTACCTCACACCATATACAA 478

  chrX_41434238_4    149 AAATTAACTCAAAATGGACCAAAGACCTAAATGTAAAACCTAAAACTATT 198
                                           i  ?              i v          v
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_41434238_4    199 AAATTTCTATTAAAAAAA---AGGAGAAAAGCTTTCCAACCTTGGATTAG 245
                            i ii  v-  i    ---   ? v   v   ivii       i    
  L1M4_orf2#LINE/    529 AAACTCTTAG-AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_41434238_4    246 GCAAAGATTTCTTAGA-AGGAGCACCAAAAGTACAATTCATAAAACAATA 294
                             v i         - v  -         i    viv i    v  v 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_41434238_4    295 CGTCGACAAATTGGACTTTATTAAAAC-A---------GTGAT----AGA 330
                         vi v  i           i  i    i- ---------   v ----  i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_41434238_4    331 A-ATTACCCAGAAAATGAACAAACAA 355
                          - i  i v     i    v i    
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAA 702

Transitions / transversions = 1.38 (44 / 32)
Gap_init rate = 0.04 (13 / 355), avg. gap size = 3.23 (42 / 13)  

2259 25.35 10.77 1.14  chrX_41434238_41437330     1804  2592 (501)    L1M4_orf2#LINE/L1       16   880 (28)  

  chrX_41434238_4   1804 TGTTCATGGATTGGAGGACTCAATATGGTTAAGATTTCCATTCTCCCCAA 1853
                                        i    i     v        vv v  v        
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_41434238_4   1854 ATTAATATATAGATTAAAAGTAACACCAATCAAAATCTCA--TGC-TTCA 1900
                            i  v  i     v  v i  iv  v         i  --   -  iv
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_41434238_4   1901 TTGCAGAAATTCACAAATTTACTCTAAATTGTTTATGAAAATTTAAGT-A 1949
                                    v    ii v ii     v viv    i    vi   v- 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_41434238_4   1950 GCTAGAATAGCCTAAACA--C---------AAAATCCTAATTGTAGGATT 1988
                         v i         v     -- ---------  i v vv i   v    i 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_41434238_4   1989 TTGGCTACTGGATTTTAAGACTTAATA------TAGAATAATCTAGACAG 2032
                         ivvi  v ivi    i  i     v  ------  v i     v      
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_41434238_4   2033 TGTGAATCTGATATAAGGATAGACATACAGATCA---GAATAGAA----- 2074
                             ivv   ii               i      ---        -----
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_41434238_4   2075 AGTGCAGAAAATAGACCAACACATT------------ATTTTTGATAAAG 2112
                            v      -  i   v i     ------------     i  i  i 
  L1M4_orf2#LINE/    316 AGTCCAGAAA-TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_41434238_4   2113 GTGCTAAAATAACTCAATAGGG---------TTATTTCAACAAATAGTGC 2153
                             i  i iv i     i   --------- iv           i    
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_41434238_4   2154 TGGAGCGAATGGCTACCCA------------TGAATCTCAACCCTTACAC 2191
                            ii i v   v  ?   ------------    vi vi    i   --
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC-- 462

  chrX_41434238_4   2192 TTCATACGATATACAACTCTTATGCTAAAGTGCATCA------TAAACGT 2235
                         i   i  v        vvv   vvii   i  v    ------    i  
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_41434238_4   2236 A---GCCAAAACTACAA---TTATACAAGAAAATATAAAGA-AAATTTTC 2278
                          ---  i       i  --- iv  v       i   ii?i-    i   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_41434238_4   2279 ACAAATTTGACGTAGGTGAAATTTTCTTAGGT----CACAAAAATCAGGA 2324
                         iii vi   ivv    ii viv        i ----   v    v  vi 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_41434238_4   2325 ACCATGAAGGAAAAAAACTGTAAACTGGACTTCATCAAAATGAAAAACTT 2374
                         i v ii  i       vvvi    i                v        
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_41434238_4   2375 CTACTCTTTTAAAGATTCCATTAAGAATATAAAAGGGAAAGTTACAAACT 2424
                         i iiv   iv  i  iv i  i     vi i   i iv  vii   i v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_41434238_4   2425 GGGAAAACATATTTGCAATATGTATATTTGACCAAGGAAGTGTATCCAGA 2474
                             i  v          vvii     i   iv i   vv          
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_41434238_4   2475 ATATACAAAGAACTCCTACAACTTAATAC--AAAAGACACACACCTCAAT 2522
                              i         i       i    v--        v i v i    
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_41434238_4   2523 -GAAAAATAGACATCGGTGTAAGATCTGAA--GATATA-CTTCAACAAAG 2568
                         -?      i i  v------ i   i    --  i  v-  i   vi   
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAA------AGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_41434238_4   2569 ATATATGAATGGCCAATAAGTGCA 2592
                              ii             ii  
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACA 880

Transitions / transversions = 1.40 (115 / 82)
Gap_init rate = 0.03 (23 / 865), avg. gap size = 4.09 (94 / 23)  


1152 20.68 1.27 0.84  chrX_41456307_41461754.rev     3430  3666 (1782)    L1M4_orf2#LINE/L1        1   238 (670)  

  chrX_41456307_4   3430 TGGTAAGATCTCTCGTGTTTGCCTACTAGAAGACTTAATATT---AAAGT 3476
                            v     v  i i    iiivv i i              ---  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_41456307_4   3477 GAAAATATTTCCCAAATTGATCTATAGATTCAGTGCTATCTCTATCAAAA 3526
                          iv    i i              i       ii  v   i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_41456307_4   3527 TCCCTACTGGCGCTTTTTGCAAAAATTGACAAACTAATCTAAAAATTTAC 3576
                             vi   - vi        i          i  i   iv      i i
  L1M4_orf2#LINE/    101 TCCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_41456307_4   3577 ATGGAAAAGCAAGGTACCCCGAGTAGCCTTAACAATCCTGAAAAACAATG 3626
                                v      v    v  i     vv       i       v  - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-G 198

  chrX_41456307_4   3627 GACAAAGTTGGAGTACTCACATTTTTCAACTTCAGAATTT 3666
                         i            v       i  ii   i    i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

Transitions / transversions = 2.06 (33 / 16)
Gap_init rate = 0.01 (3 / 238), avg. gap size = 1.67 (5 / 3)  

2428 18.59 0.64 0.43  chrX_41456307_41461754.rev     3960  4427 (1021)    L1M4_orf2#LINE/L1      231   699 (209)  

  chrX_41456307_4   3960 CAGAATTTTCTATAAAGCTACATTAATACACATAGTGTAACCCTGGCATA 4009
                           i  i  v   i         v    vv v i     iiiv        
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_41456307_4   4010 AGGATAGACATATAGATTGATGAAATTGAATTAACAATCCAGTAGTAAAT 4059
                                          ii   i   v     i v i     v i    i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_41456307_4   4060 CCATATATTTACAGTCAAATAATTTTCAACTGTGGTGCCAAGACAGTTCA 4109
                              i     ii     v i      i  viv           vi    
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_41456307_4   4110 ATGGAGAAAGAATAGTTTCTTCAAAACAGTGGTATTGGGACAACTGGAGG 4159
                             i           i i     v - i    ii             vi
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACA-AATGGTGCTGGGACAACTGGATA 429

  chrX_41456307_4   4160 CTGACATGCAAAAGTTTGAAGGTGGACCTCTACCCTACACCATATACAAA 4209
                         ?iv           vv     v      i     ii              
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_41456307_4   4210 AATTAACTCAAAGTAGATCAAAGATCTAAATGTATGAGTTAACACCATGC 4259
                                     i i     ?   i         v   i   v  i  iv
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_41456307_4   4260 AATT-TTAAAAGAAAACATAGGCATAAATCTTTGTGACCTTGGATTAAGT 4308
                           i -   i             ?i        i          i   i i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_41456307_4   4309 AGTGGTTTCTTCATTATTACACCTAAAGCACAAGCAACCAAAGAAAAAAA 4358
                          i         viv   v     v              v          -
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA- 628

  chrX_41456307_4   4359 TAGATAA--TGGGATTCATCATAATTTAAAATTTTTATGCTTCAGTAGAC 4406
                                --   iv       v    v    i    i       ivi   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_41456307_4   4407 ACTATCAAGAAAGTAAAAAGA 4427
                                       i      
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGA 699

Transitions / transversions = 1.71 (53 / 31)
Gap_init rate = 0.01 (4 / 469), avg. gap size = 1.25 (5 / 4)  

 930 16.89 3.20 1.37  chrX_41456307_41461754.rev     4739  4957 (491)    L1M4_orf2#LINE/L1      686   908 (0)  

  chrX_41456307_4   4739 AAAAAGGAAAAAGATAATACACAGCATTGGGGGAACTATTTGCAAATCAT 4788
                          i    vi      i  iv     v  v  i i  v              
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_41456307_4   4789 ATATTTGATAAT---CTAGTATCTCAGA-TATACAAAGAACTCTTGAAAA 4834
                             i      v---  v     -    -    i           iv  v
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATC-CAGAATATATAAAGAACTCTTACAAC 784

  chrX_41456307_4   4835 TCAACAATAAACAAAAACAGATAACCTGATT--AAAATGA-TAATGGATT 4881
                             i      --  i   i      ii   --      i-i  v     
  L1M4_orf2#LINE/    785 TCAATAATAAA--AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_41456307_4   4882 TGAATAGACATTTCTTCAAATAATATTTACAAATGGTCAATAAACACATG 4931
                                        i    v  v  v         i      i      
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_41456307_4   4932 AAAAGATATTCAGTGTCATTGGCTTT 4957
                                ii   iii   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (24 / 13)
Gap_init rate = 0.03 (6 / 223), avg. gap size = 1.67 (10 / 6)  


1746 27.43 0.95 1.14  chrX_41619307_41625584        4   528 (5750)    L1M4_orf2#LINE/L1      193   716 (192)  

  chrX_41619307_4      4 AAAAAGAACAAAGCCAGAGGTATCACATTACCCAACTTCAAACTATTCCA 53
                           i          iii    vv     i v     i      viv v i 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_41619307_4     54 CAAGGCTACAGTAACAAAAACAGAATGGTACTGGTACAAAAACAGACACA 103
                            i          iv  i    vi         i i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_41619307_4    104 CAGACCAATGGAACAGAATAGAGAATACAGAAATAAAGCCACACACCTAT 153
                         i   i        i     v    i v          v   i   ii   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_41619307_4    154 AACCATCTGATCTTTGTCAAAGGTGACAATAACAAGCAATGAGGAATGGA 203
                         iii  vi    i  i v   i    v   v v  vv     i    v i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_41619307_4    204 CTCCCTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATAAGCAGAA 253
                         ivvi  v     i              i      v  ?   i v   i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_41619307_4    254 GGTTGAAACTGGACCCCTTCCTTTCACCATATGTAAAAATTAACTCAAGA 303
                          iv    ii         v   iv        ii              i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_41619307_4    304 TGGATTAAAGACTTTAATGTAAGACCTCAAACTATAAAAATCCTAGAAGA 353
                              i ?    i v         v  v           v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_41619307_4    354 AAACCTAGGAAATACTATTCTGGACATCAGCCTTGGCAAAGAATTTATGG 403
                             v    ?ivv v v   vv   v ii vi v     v iv  iv i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_41619307_4    404 CTAAGTCCCCAAAAGCAATTGCAAAAACAACAAAAATTGACAAGTGGGAT 453
                         v  v v v         vvv    v  v iv      v  i  i v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_41619307_4    454 CTAATTAAACGGAAGGGCTTTTGCACAGTAAAAGAAACTAACGGTCGGGG 503
                         i v  i   vvv  iii      ii vvi   i  v    ----  ii i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA----TCAAGA 688

  chrX_41619307_4    504 AAG-GAGCCAAGATGGCC----GAATAGGA 528
                            -  i--    iii  ----    i   
  L1M4_orf2#LINE/    689 AAGTGAA--AAGACAACCCACAGAATGGGA 716

Transitions / transversions = 1.24 (78 / 63)
Gap_init rate = 0.01 (4 / 524), avg. gap size = 2.75 (11 / 4)  

3127 27.28 0.55 0.66  chrX_41619307_41625584     4877  5785 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_41619307_4   4877 TAGAAGAACATTCCATGCTCGTGGGTAAGAAGAATCAATATCGTGAAAAT 4926
                          i   ii i  i     i  i   i vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_41619307_4   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAAC 4976
                            v     v     iv i  i           i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_41619307_4   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_41619307_4   5025 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGTCAAAAG 5074
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_41619307_4   5075 AACAAAGCTGGAGGCATCGCTCTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv  i v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_41619307_4   5125 TACAGTAACGAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATC 5174
                                 iv  i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_41619307_4   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 5222
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_41619307_4   5223 ATCTGATCTTTGATAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i  i  ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_41619307_4   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_41619307_4   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_41619307_4   5373 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAAC 5422
                          i ?    i    i  v   v       i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_41619307_4   5423 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGTACTTCATGTCTA 5471
                         v    ?i- v i -   iv   v v  vv i     vvii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_41619307_4   5472 AAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTA 5521
                         vi            vvi     v    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_41619307_4   5522 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5571
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_41619307_4   5572 CAGGCAACCTACCAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5621
                         v  i     i  vi             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_41619307_4   5622 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5671
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_41619307_4   5672 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5721
                           i -    i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_41619307_4   5722 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5771
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_41619307_4   5772 CCATCACTGGTCAT 5785
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3736 21.32 4.33 1.25  chrX_41748345_41750513.rev      807  1683 (486)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_41748345_4    807 AAGAGATTTTATTTTCACAGATTGGAAGATTCAATATTATTATGATGGCA 856
                             v  iii  v    ii          i i      i   v       
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_41748345_4    857 ATTTTCCCCAAATTGGTCTATAAATTCAATGCAATTCCTATCAAAGTCCT 906
                           vi           i    i i      i     i         i   i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_41748345_4    907 AGCTGCCATTTTTACAGAAACTGAGGGGTT-ATCCTAAAATTCATATGGA 955
                                v     i      i   vii i -                   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_41748345_4    956 AATGCAAAGGCCCTAGAATAGTCAAAATAATTTTGAAAAACAAGAACAAA 1005
                                i  v  i       i     i   i        v         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_41748345_4   1006 GTCAGAGGACTTGTACTTCCTGACTTCAAAACTTACTATAAAGCTACAGT 1055
                           ii       iii      ii i              i           
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_41748345_4   1056 AATGAAGACAATGCGGTACTAGCATAAGGATAGACATATAGATCAATGGA 1105
                            v      i  i      i                             
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_41748345_4   1106 ACAGAATTGAGATTCTAGAAATAAACCCTTACATTTATGGTTAATTGATT 1155
                          i          v  i            v            i        
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_41748345_4   1156 GTTTACAAAGGTGTCAATGCAATATGATACAGAAACAACAATCTTTTCAA 1205
                         v iv    i    i   vi v  vii  ivi    v  i i         
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_41748345_4   1206 CAAACAG--CAGAGACAATTTTTAACAAATGGC-ACATGCAAAAAGTTAA 1252
                             ii -- v i     i ------ii  i? -          iiv i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACT------GGATAKCCACATGCAAAAGAATGA 448

  chrX_41748345_4   1253 ATTTAAACACTTTTCTCACATTATTCACAAAAAGAAAATAACTCAG--CG 1300
                          v  ii  v i vi      ii  vi       v----       i--i 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAAT----TAACTCAAAATG 494

  chrX_41748345_4   1301 CATTGTAAGTCTAAATTTAAAAGCTAAAAGTGTAAAACTTTCCTAAGAAA 1350
                         v  ii? iii      v   i        v i       i ivv      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_41748345_4   1351 AC------------CTTTGTGACCTTGAGTCAGGCA--GAGTTTTTAGAT 1386
                           ------------   i         i  i     -- iv  i      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_41748345_4   1387 ACCATGTCAAAAGCAAAATCCATTTAAAAATACTTA-ATAAATGGAACTT 1435
                          iv iii        v  v v ivv  i  v vv  -      v i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_41748345_4   1436 TACCGAAATTTAAAAACTTT-GCTCTTCAAAAAGCACCTTTAAGAAAATT 1484
                         i i i     -         - iv       iii   iv i      i v
  L1M4_orf2#LINE/    645 CATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_41748345_4   1485 TAAAGACGAGCCAAATAATGAAGACAAATATTTGCAAATCATATATCTAA 1534
                         v      i v   v v    iiiiv                       i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_41748345_4   1535 TAA----------------ATATATAAAGAACTCTTCCAATTCAACAGTA 1568
                            ----------------                 v   i    i i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_41748345_4   1569 AAAAGAAAAACAACCCTGTTAAAATTTTGGCTAAAGATTTGAATAGATGC 1618
                               v   i     vi  ?   vv v   v  i            iii
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_41748345_4   1619 TTCACCAAAGAAAATACCTAAATGGATAATAAATACATGAAAAGATGTTC 1668
                            v        i   ivi      vi     ii             i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_41748345_4   1669 AAACTCATTGTTTAT 1683
                           vv   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (123 / 61)
Gap_init rate = 0.01 (12 / 904), avg. gap size = 4.08 (49 / 12)  


2914 27.86 0.66 0.66  chrX_41772501_41777349.rev     3451  4358 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_41772501_4   3451 TGGAAGAACATTCCATGCTCCTGGATAGGAAGAATCAATATTGGTCAAAC 3500
                              ii i  i     i  v     v      v i       v v i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_41772501_4   3501 GGCCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCTATCAAAC 3550
                            v     v      vii  i  i        i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_41772501_4   3551 TACCAATGATATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 3599
                          v   iiviiv  i  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_41772501_4   3600 ATAGAATAAAAAAAGAGCCTGAATAGCCAAGATAATTCTAAGCAAAAAGA 3649
                           i   vviv  ii  v  v          i i   ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_41772501_4   3650 ATAAAGCTGGAGGCATCACACTAGCTGACTTCAAACTATACCACAGGTTT 3699
                          i    i      vv       vv ii i      viv   i   iivi 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_41772501_4   3700 A-AGTAACCACAACAGCCTGGCACTGGTACAAAAACAGACACATAGACCA 3748
                          -     i  vi    iv   i     i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_41772501_4   3749 ACGGAACAGAATACAAAGCTCAGAAATAAAGCCGCACACCTATAACCCTG 3798
                          i    i     vv i  ii          v  ii   ii   iii vvv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_41772501_4   3799 TGATCTTCAATAAACCAGACAAAAATAAGCAATGGGGAAAGGACTCCCTA 3848
                             i   i i  ivvv v   i vi vv            i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_41772501_4   3849 TTCAATAAGTGGTGCTGGGATAACTGGCTAGCCATAAGCAGAAGATTGAA 3898
                              i  i           i      v  ?   i v   i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_41772501_4   3899 ACTGGACCCCTTCCTTACATGATATACAAAAAATCAACTCAAGACGGATT 3948
                         ii         v   i   iv           - i       i i    i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATC 498

  chrX_41772501_4   3949 AAAGACTTAAGTGTAAAACCCCAAACTATGAACACCCG-GGAAGACAACC 3997
                          ?    i   i     i v iv       i  -  i v-i     v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chrX_41772501_4   3998 TAGGCA-ACACCACTCTGGACATAGGAACAGGCAAAGATTCAT--GATGA 4044
                             ?i- v i -i  vv   v v  ivi      v i  iv --   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_41772501_4   4045 AGACGCCAAAAGCAATTGCAAGAAAAGCAAAATTTGACAAATGGGATTTA 4094
                         v   i         vvv    v     v    v v  i    v   i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_41772501_4   4095 ATTAAACTAAACAGCTTCTGCACAACAAAAGAAACTATCAATAGAGTAAA 4144
                           i   v v  v i   i  ii vv    i  v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_41772501_4   4145 CAGACAACCTACAGAATGGGAGAATATATTTACAAACTATGTATCTGATG 4194
                         v        i              v      i    ii  i        i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_41772501_4   4195 AAGGTCTAATGTCCAGCATCTATCAGGAACTTAAACAAATTTACAAGCAA 4244
                          i  v  vi i     v  v   v i     ivv    v iv i  -i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAA 794

  chrX_41772501_4   4245 AAAAAAAAGAAACTCCATTAACATGTGGGCAAAGGACATGAACAGACACT 4294
                            i v  iv   i v   ? v vi           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_41772501_4   4295 TTTCAAAAGAAAACACACATCTGACCTATATGCACATGTAAGAAAGCTCA 4344
                          i  v      i i i   vv  i  v   v       v  ii v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_41772501_4   4345 ACATCACTGATCAC 4358
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (143 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.09 (12 / 11)  


3263 27.09 0.44 0.44  chrX_41817923_41824190.rev     4870  5777 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_41817923_4   4870 TGGAAGAACATCCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4919
                              ii i        i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_41817923_4   4920 GGCCATACTGCCCATGGTAATTTACAGATTCAATACCATCCCCATCAAGC 4969
                            v     v    viv i  i           ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_41817923_4   4970 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5017
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_41817923_4   5018 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5067
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_41817923_4   5068 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAGCTATACTACAAGGC 5117
                                i      vv       v  ii i     iviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_41817923_4   5118 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5167
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_41817923_4   5168 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5215
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_41817923_4   5216 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5265
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_41817923_4   5266 CTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCT 5315
                           v  i  i              v  i   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_41817923_4   5316 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5365
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_41817923_4   5366 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5415
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_41817923_4   5416 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGTACTTCATGTCTAA 5465
                         v    ?i v viv   iv   v v  vv i     vvii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_41817923_4   5466 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5515
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_41817923_4   5516 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5565
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_41817923_4   5566 AGGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5615
                           i     i   iv            v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_41817923_4   5616 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5665
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_41817923_4   5666 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5715
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_41817923_4   5716 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5765
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_41817923_4   5766 ATCACTGGCCAT 5777
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3080 27.19 0.55 0.99  chrX_41837894_41842453.rev     3158  4069 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_41837894_4   3158 TAGAAAAACGTCCCATGCTCTTGGATATAAAAAAAATTAATATCATTAAA 3207
                          i    i ii       i  v     - ii  i v-       ii    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-TGGAAGAC-TTAATATTGTTAAG 48

  chrX_41837894_4   3208 ATGACCATATTGCC-AAAGCAATCTACAAATTCAGTGCAATCCCTATCAA 3256
                            i v   i v  -   vii       i     ii              
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_41837894_4   3257 AATGCTAATGTGATTCTTCATAGAAGGAATTAGAAAAAACAATCCTAAAA 3306
                            v i ii-  vi i  -- v v  i    -  v  ivii         
  L1M4_orf2#LINE/     99 AATCCCAGC-TGCCTTTT--TTGCAGAAATT-GACAAGCTGATCCTAAAA 144

  chrX_41837894_4   3307 TTCATATGCAACCAAAAAGAGCCCA-AATAACCAAAGCAATCCTGAGCAA 3355
                                 v  viiv  i ii    -    i     i     i   iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_41837894_4   3356 AACAGAACAAAGCTAGGGCA-TCACATCACCTGACTTCAAAATATCTTAC 3404
                         i -         i i i v -     iiv  ii i       iv vi   
  L1M4_orf2#LINE/    195 GA-AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_41837894_4   3405 AGGATGATAGCAACCTAAATAGCATGATGTTGTTATGAAAATACACACAA 3454
                          iiiiv i  i  i v i i  ii  i ii  vi  i ii   v   i v
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_41837894_4   3455 AGATTAATGACTCATAATACAGAACCCAGAAATAATGACACATATTTAGA 3504
                             i    ivvi v   vv   ii          vvv  i i     vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_41837894_4   3505 GCCAACTGATCTTTGACAAAGCCAACAAGAACTTACGTTGGGGAAAGGCC 3554
                          i   i    i  i     i viiv     v v v iv         ivi
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_41837894_4   3555 ACCCTCTTCAAAAAACGGTGCTGAAAATATTGGAAAGCCACTCGCAGAAG 3604
                          vi  i     v   i       ii vv i    v ?    vi   i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_41837894_4   3605 AATGAAACTGGACCCCTATCTCTCACCATACACAAAAATTAACTCAAAAT 3654
                               ii          i   v       i                   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_41837894_4   3655 GGATTAAACACTTAAATGTAAGACCTGAAACCATAAAAATACTAGAAGAA 3704
                             i ? v  i           v  i    i      v vi        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_41837894_4   3705 AATCTAGGGAAAACTCTCTTG-GATATTGGTCTAGGCAAAGAATTTGTGA 3753
                           iv    ?iv  v   - i -  iv    vi       v iv  iv ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_41837894_4   3754 TTAAAATCTCAAAAGCACAGGCGACAAAAACAAAAATAGACAAATGGGAC 3803
                         v  vi ivi          i  i      iv         i    v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_41837894_4   3804 TTAATTAAACTAAAAAGCTTCTGCACAGCAAAATATATAATCAACAGTGT 3853
                           v  i   v v    i   i  ii vv    iv i iv     v iv  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_41837894_4   3854 GAAGAGACAACCTGTTAAATGGGAGAAAATATTTGCAAACTA-ATCACCT 3902
                            i        iiivi                      ii -  - i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCT 741

  chrX_41837894_4   3903 GACAGGGGACTAATATTCAGAATATACAAGGAACTCCAGCAACTCAACAG 3952
                           i i      vi   i         i  i      ivi        i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_41837894_4   3953 GAAAAAAGCAAGTAATCCCATTAAAAAGTAGGCAAATAACATGAATAGAC 4002
                         v     ii   i   i  v   ?    i i      vi iv         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_41837894_4   4003 ATTTCTCAAAAGGAAACATACAAATGACCAACAGGTATATGAAAAAATTC 4052
                                v    i i i         i    i i i i       i  v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_41837894_4   4053 TAAACATCACTAATCAT 4069
                          v       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (161 / 83)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.08 (14 / 13)  


2862 27.40 1.17 0.59  chrX_41922804_41927736     3221  4074 (859)    L1M4_orf2#LINE/L1        1   859 (49)  

  chrX_41922804_4   3221 TGGAAAAACATTCCATGCTCATGG-TAAGAAGAATCAATATCGTGAAAAT 3269
                               i i  i     i      - vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_41922804_4   3270 GGCCATACTGCCCAAAGTAGTTTATAGATTCAATGCTATTTCCATTAAAC 3319
                            v     v      v ii i  i        i  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_41922804_4   3320 TATCATTGAAATTCTTCACAGAAGTAGGAAAAGGT-ATTTTAAATTTCAT 3368
                          vi  vivivv  i  ii     i -v  v   v -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_41922804_4   3369 ATGGAATCAATG-AAG--ACCCTGTATAGTGATGACAATCCTAAGCAAAA 3415
                               ---   -   --    v v    iv vi      i i iv  i 
  L1M4_orf2#LINE/    150 ATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_41922804_4   3416 AGAACAAAGCTGGAGGCATCACTCTACCAGACTTCAAACTATACTACAAG 3465
                                  i      vv    v  v  vi i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_41922804_4   3466 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGA 3515
                                   i   i    ii         i iv ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_41922804_4   3516 CCAATGGAGCAGAACAGAGACCTCAGAAATAACACCACACATCTACAACC 3565
                         i       ii    iv    vii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_41922804_4   3566 ATCTGATCTTCAACAAATTTGATAAAAACAAGCAATTGGGAAAGGATCTC 3615
                          vi    i   i    ivv  vi  i v  vv    v       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_41922804_4   3616 CCATTCAGTAAATGTTGCTGAGAAAACTGGCTAGCCATAGGCAGAAAACT 3665
                          iv    ii     v     i  v      v  ?   i v   i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_41922804_4   3666 GAAAGTGGACTCCTTCCTTACACCTTATGCAAAAATTAACTCAAGATGGA 3715
                            iv     i   v   i     v   i               i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_41922804_4   3716 TTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAAC 3765
                          i ?    i         i v i     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_41922804_4   3766 CTAGGCA-ATACCATTTAGGATATAGGCATTGGCAAAGACTTCATGACAA 3814
                         v    ?i- v i -  iiv  iv v  vv v     v ii   v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_41922804_4   3815 AAACGCCAAAAGCAATTGCAACAAAAGCCAGAATTGACAAATGGGATCTA 3864
                         vi  i         vvv          vv i   v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_41922804_4   3865 ATTAAACTAATGAGCTTCTGTACAACAAAAGAAACTATCATCAGAGTGAA 3914
                           i   v v vi i   i   i vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_41922804_4   3915 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACCCATCTGACA 3964
                         v  i     i                 v      ivii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_41922804_4   3965 AAGGTCTAATATCCTGAATTTATAAGGAACTTAAACAAATTTACAAGATA 4014
                          i  v  vi     v    v     i     ivv    v iv i  v v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_41922804_4   4015 AAAACCA----CCCCATCAAAAAGTGGGCAAAGAATATGAACAGACACTT 4060
                           i  v ----   v  i?    i         i  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_41922804_4   4061 CTCAAAAGAAGACA 4074
                            v        i 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATA 859

Transitions / transversions = 1.25 (128 / 102)
Gap_init rate = 0.01 (9 / 859), avg. gap size = 1.67 (15 / 9)  

 262 16.95 0.00 0.00  chrX_41922804_41927736     4382  4440 (493)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_41922804_4   4382 AAAAAAGACATTCATGTGGCCAATAAACGTATGAAAAAAAGCTCAACATC 4431
                            i    i  v  vi          i ii       i v          
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_41922804_4   4432 ACATCAGAG 4440
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


3026 20.82 9.75 0.48  chrX_41948080_41951314.rev     1914  2744 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_41948080_4   1914 TGGAAAGATATATCATGATCATGCTATTCGCAGACTCAATATAGTTAAAA 1963
                                    vi    v     v-   v v     i     v     i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGG-ATTGGAAGACTTAATATTGTTAAGA 49

  chrX_41948080_4   1964 TGTCAAATCACCGCAACTCGATGTATATATTTTAAGCAATCCCAATGAAA 2013
                           v   vv v  v   v i   v  i v   iv v        v  v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_41948080_4   2014 ATTCCAAA---ATTTTTTGTACATATTGACAAGCTGATTCTAAACATTT- 2059
                           i   iv---v       i v v              i     -   i-
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA-ATTCA 148

  chrX_41948080_4   2060 TATGGAAA-----GTGA-----AATAACCAAAGCATTTTTGAAGAAGAAA 2099
                                 ----- v  -----    i     i  v i     i     i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_41948080_4   2100 AACAAAGCTGAAGGAC--ACACTCCCCAATATTAAGATATACTTTAAACC 2147
                                i  i     --     i      v i  i iv    vi   v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_41948080_4   2148 TATAGAAATCAAGGCAGGGCAGTATTGGCTTAAGGATAGATATATAGACG 2197
                           i  v       i   v ii   i    v          i       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_41948080_4   2198 AATGGAA-AAAATGGTGAGTTCCAAAACAGAGCCATGTAAACATGTTCAA 2246
                                - i   v v    i vi   i i v    ii vvi   v    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_41948080_4   2247 TTGATTTTTTGACAAAGATGTAAAGGCAATTTAATAGAGAAAGGACAGTC 2296
                                 i-     i i  iv   i v   i   i i     i i    
  L1M4_orf2#LINE/    349 TTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_41948080_4   2297 TT--CAACAAATGATGCTGGAACCACTGGACATCCATATG-AAAAAAATA 2343
                           --         i      i  v      i ?   i   -    i   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_41948080_4   2344 AACCTTGACCTATACCTCACATTGTATACCAAAAACAA----AAATGGGT 2389
                           vi v    iv         iii     v    vi  ----      i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_41948080_4   2390 CA---ATTT---T-------CTAAA---------CTCCTAGAAGAAAATA 2417
                           --- ii --- -------     ---------   i          i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_41948080_4   2418 TAGGAA-AACTCTCTGTGACCTTAGGTTAGGTAAAGATTTCTTAGACATA 2466
                             ?i-  v   ii        i       i  v i         i  i
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_41948080_4   2467 ACACCAAAAGCACAATCCATAAAAGAAGAAAT---TGAAGTGTACATCTT 2513
                                        v v i       i    --- i  v  v  v  v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_41948080_4   2514 TTAAATTTAAAAGTTTTGCTCTTTGAAGGACACTGT----AAAGTGAAAA 2559
                         iv     v    v     iv   ii         i ----          
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_41948080_4   2560 GACAAACCACAGACTGGGAGAAA-TAGTTGAAAGTTACATATCCAACAAA 2608
                              v       v         -  v   v  i i i     ii i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_41948080_4   2609 AGACTT-----------ATGTAAAG--CTCT---------ATAATAATAA 2636
                         i     -----------  i     --    ---------       v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_41948080_4   2637 AATAATGTAAT---ATTTAAAACTGGACAAAATATTTGAATAGATATTTC 2683
                         i i  -i   i---   ?    v   i    iv           i     
  L1M4_orf2#LINE/    798 GACAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_41948080_4   2684 ATCAAAGAAAATATATAA-TGGCAAATAATCACATGAAAAGATGCTCAAC 2732
                         vi       i     i  -    v     v                    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_41948080_4   2733 TTCATAAGTCAT 2744
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (100 / 70)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.27 (85 / 26)  


2883 26.86 1.44 0.67  chrX_42023462_42029484.rev     4632  5532 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42023462_4   4632 TGGAAAATCGTTTTATGCTCACAGATAGGAAGAATTAATATCATGAAAAT 4681
                               ivii iii   i   ii   v      v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42023462_4   4682 GGTCATACTGCCCAAAGCAATTTATAGATTCATTGCTATTCCTATTAAAC 4731
                           iv     v      vii  i  i       vi  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42023462_4   4732 TACCA-TTGACATTG--ACATAATTAGAAAAAAACT-ATTTTAAAATTTA 4777
                          v   -i  v v  v--i  v  v v  v  i--  -  ii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_42023462_4   4778 TATAAAACCAAAAAAGAGCCTGAATAGCCAAAACAATCCTAAGCAAAAAG 4827
                            ii  viiv  ii  v  v                 i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_42023462_4   4828 AACAAAGCTGAAGCCATCACTCTTCCCAATGTCAAACTATACTACAAGGC 4877
                                i  i  vvv    v         v     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_42023462_4   4878 TCCAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACATATAGACC 4927
                          v      i   i    ii         i i  ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_42023462_4   4928 AATAGAACAGAACAGAGAACCCAGAAATAAGACAGCACACCTACAA-CAA 4976
                            i   i    iv    ii          iv vii   ii  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_42023462_4   4977 TCTGATCTTGTACAAACCTGACAAAAACAAGCAATAGGTAAAGGATTCCC 5026
                          -    i  vv    ivv  v   i v  vv    i  v    i  vvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_42023462_4   5027 TACTTAATAAATGGTGCTGGAAGAACCGGCTAGCCATATGCAGAAAATTT 5076
                          vi i  i            i v   i  v  ?   i     i  i v v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_42023462_4   5077 AAACTGGACCCCGTCCTTACATCATATACAAAAATCAACTCAAGATGGAT 5126
                           ii        vv   i   i             i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_42023462_4   5127 -AAAAACTTAAATATAAAACCCAAAACTATAAAAACACTAGAAGAAAGCC 5175
                         - ? i  i     i   i v i            vivi         i v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_42023462_4   5176 AAGGAAGTA--CCATTCAGGACATAGGCATAGGCAAAGTTTTCAT-GATG 5222
                         v   ?-   --i -   iv   v v  vv       v v    v -   -
  L1M4_orf2#LINE/    548 TAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chrX_42023462_4   5223 AAGACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAGTGGGATCT 5272
                          v             vvv          v      v  i  i v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_42023462_4   5273 AATTAAACTAAACAGCTTCTGCACTACAAAAGAAACCATCCTCAGAGTAA 5322
                         v  i   v v  v i   i  ii  v    i  v  i   vvv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_42023462_4   5323 ACAGACAACCTATAGAATGGGAGAAAATTTTTGCAAACTATGCACCTGAC 5372
                          v        i i               v        ii  ii i    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_42023462_4   5373 AAAGGCCTAATATCCAGCATCTACAAGAAACTTGAAAAAATTTACAGGAA 5422
                           i  v  vi       v  v  i  ii    ivv v  v iv i iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_42023462_4   5423 AAAATCAA----CCTCATTAAAAAGTGGGCAAAGGATATAAACAGACACT 5468
                            iv   ----  iv   ?    i            v i  i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_42023462_4   5469 TCTGAAAAGAAGGCATACATGCTGCCAATAATCATATGAAAAAAAGCCCA 5518
                            vv       ii     viiv        v  i       i v  i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_42023462_4   5519 ACATCACTGATCAT 5532
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


3309 26.46 0.55 0.44  chrX_42040617_42044310.rev     2297  3203 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42040617_4   2297 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAACAT 2346
                              ii i  i     i      i v      v i     i  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42040617_4   2347 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2396
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42040617_4   2397 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2444
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_42040617_4   2445 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTGAGCCAAAAG 2494
                                viiv  ii  v  v v  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_42040617_4   2495 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2544
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_42040617_4   2545 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2594
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_42040617_4   2595 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 2642
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_42040617_4   2643 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2692
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_42040617_4   2693 CTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCT 2742
                           v  i  i              v  i   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_42040617_4   2743 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 2792
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_42040617_4   2793 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2842
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_42040617_4   2843 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2892
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_42040617_4   2893 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 2942
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_42040617_4   2943 CTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGCGAAC 2992
                         ii   v v  i i   i  ii vv    i  v    i  vv i  i   v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_42040617_4   2993 AGGCAACCTACAAAATGGGAGAAAAT-TTCGCAACCTACTCATCTGACAA 3041
                           i     i   i             -  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_42040617_4   3042 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAGAA 3091
                         i  i  vi          v  i  v      vv    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_42040617_4   3092 AAACAAATAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 3141
                          i           v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_42040617_4   3142 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 3191
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_42040617_4   3192 ATCACTGGCCAT 3203
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2774 23.71 2.90 5.47  chrX_42051172_42056132     3537  4468 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42051172_4   3537 TGGAAAAGCACTATATGCTCATGGATAGGAAGAATTAATATCGTTAAGAT 3586
                               iii iivi   i        v      v       i        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42051172_4   3587 GACCATACTCCCCAAAGCAATTTACAGAATCAATGTTATTCCTATCAAAT 3636
                          i v            vii  i      v    i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42051172_4   3637 TACCAATGACTTTATTTACAGAATTAGAAAAACT-ATTCTAAAATTCATA 3685
                          v   iivi i  v   i     v v  v  i  -  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_42051172_4   3686 TGGAACCAAAAAAAAAAAAAAAAAGAGAGAGAGAGAGAGCCCA-AAGAGC 3734
                              ------------- viv   i  -----------    -  v   
  L1M4_orf2#LINE/    151 TGGAA-------------ATGCAAGGGA-----------CCCAGAATAGC 176

  chrX_42051172_4   3735 CAAAGCAATCCTAAGCAAAAAGAACAAGGCTAGAAGCATCACATTATCCA 3784
                             i     i i iv  i        i i i  i vv     i vi   
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_42051172_4   3785 ACTTCAAACTATACTACAAGGTTACAATAACCAAAA-----TGATA-TAA 3828
                          i      viv        i i    i   i   i -----  i  - ii
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_42051172_4   3829 TAAAAAAAAAGACATGTAGACCAATGGAACAGAATAGAAAGCCCAGAAAT 3878
                         i v  ii v      i    i        i     v  i  i        
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_42051172_4   3879 AAAGCCATACATCTATAGCCATCTGAACTTTGACAAAGCTGACAAGGAAA 3928
                            v        i   i i  vi   vi  i     i v  v    ivv 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_42051172_4   3929 AGCAATAATGAAAGAATTCCCTGTTCAATAAATGATAATAGAATAACTGG 3978
                         vv    iiv        vvi  v     i     i iv i i i      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_42051172_4   3979 CTAGCCATATGCAAAAGATTGAAACTGGCCCCTTTCCTTATATCATATAT 4028
                         v  ?   i          v    ii   v   i v   i i i      i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_42051172_4   4029 ATAA-CCAACTCAAGATAGATTAAAGACTTAAATGTAAAACCTAAAACTA 4077
                          v  -ii       i  i   i ?    i         i v         
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_42051172_4   4078 TAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCCGGACACAGGCTC 4126
                              vi i           v    ?i- v i -   vv   viv  v i
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTT 575

  chrX_42051172_4   4127 CAGCAAAGATTTCATGACCAAGATGTGAAAAGCAAATCCACAGCCAACAA 4176
                         vi    v i    v -----    i   ----------   ---   v i
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTT-----AGATATGA----------CAC---CAAAAG 607

  chrX_42051172_4   4177 CTTACTGAACAGG-AACAAACGCAAAAATTGACAAATGGGAAATAATTAA 4225
                          -------   i -      v v      v  i    v   vv v  i  
  L1M4_orf2#LINE/    608 C-------ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_42051172_4   4226 ACTAAACAGCTTCTGCACAGTAAAG----CTATCAACAGAGTAAACAGAC 4271
                          v v  v i   i  ii vvi    ----       v i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_42051172_4   4272 AACTTGCAGAATGGGAGAAAATATTTACAAACTATGCATCCG-CAAAGGT 4320
                            iii                    i    ii  ii   i -i  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_42051172_4   4321 CTAATATCCAGCATCTATATGGAACT--TACATTTACAATTTTAAAAA-- 4366
                           vi       v  v    vi     --    vi -    vv      --
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACT-CAATAATAAAAAGA 799

  chrX_42051172_4   4367 -----AACC--ATTAAAAAGTGGACAAAGGACATAAACAGACACTTTTCA 4409
                         -----    --   ?    i   i       iv i  i     i  i  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_42051172_4   4410 GAAGACGACATACACATGGCCAACAAGCATATGAAAAAATGCTGAATATC 4459
                         i    v  i     v        i     i       i     v  i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_42051172_4   4460 ACTAATGAT 4468
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.55 (132 / 85)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.90 (78 / 20)  


 626 22.36 0.00 0.00  chrX_42062811_42064811      338   498 (1503)  C L1M4_orf2#LINE/L1   (0)   908   748  

C chrX_42062811_4    498 GGGCTCATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 449
                           i  ii          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

C chrX_42062811_4    448 AACAAACAACCCCATCAAAAAGTGGGCAAAGGAAATGAACAGACACTTCT 399
                         i     i     v  i?    i           vv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

C chrX_42062811_4    398 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 349
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

C chrX_42062811_4    348 TCACTGGCCAT 338
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.50 (21 / 14)
Gap_init rate = 0.00 (0 / 161), avg. gap size = 0.00 (0 / 0)  

2881 25.57 0.62 7.01  chrX_42062811_42064811      539  1508 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42062811_4    539 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 588
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42062811_4    589 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCATCAAGC 638
                            v     v     iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42062811_4    639 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 686
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_42062811_4    687 TGTGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 736
                          i     viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_42062811_4    737 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 786
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_42062811_4    787 TACAGTAACCAA--CAGCATGGTACTGGTACCAAAACAGAGATATAGATC 834
                                 i   --   ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_42062811_4    835 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATGTCTACAACT 882
                                i    i--    i  --        vv  ii ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_42062811_4    883 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 932
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_42062811_4    933 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 982
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_42062811_4    983 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1032
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_42062811_4   1033 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAGCCCTAAAAGAAAAC 1082
                          i ?    i    i  v   v       i      vi i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_42062811_4   1083 CTAGGCCTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1132
                         v    ?v v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_42062811_4   1133 AACACGAAAAGCAATGGCAACAAAAGCCAAAAGTGACAAATGGGATCTAA 1182
                         i    v       vvi          vv    vv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_42062811_4   1183 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1232
                          i   v v  i i   i  ii vv    i  v    i  -----------
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA----------- 685

  chrX_42062811_4   1233 AGGAAACCTTTATTAAAACTAAATTTTTTTCTGTTCTGAAAAAGATACTG 1282
                         -------------------------------------- i    ------
  L1M4_orf2#LINE/    686 --------------------------------------AGAAAG------ 691

  chrX_42062811_4   1283 CTATAAGAATAAAAAGTCAAGGCACATACTGAGAGAAAATATCAGCAAAA 1332
                         --------- i     v   vv    v v  i          iv     v
  L1M4_orf2#LINE/    692 ---------TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_42062811_4   1333 TACATATTTAATGAAGAACTTATGTCTAAAATATACAAAGAACTTTAAAA 1382
                         i i    i i  i i i    i i  i i      i        i v v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_42062811_4   1383 ACTCAATAATAAGAAAACAAACAATTCAATGTAAAAATGGACAAAAGGTC 1432
                                     i  i     i  ii    v?        i    i i i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_42062811_4   1433 TGAACAGATTCCCCACCAAAGAAGGTATACAGATGGCAAAGAAGCCTATG 1482
                             i   iviii v         i      i     v  v    vi   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_42062811_4   1483 AAAAGACACTCGCCATCATTTTTCAA 1508
                               ii   iv     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (151 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 9.25 (74 / 8)  


3308 26.52 0.66 0.33  chrX_42121740_42128427     5291  6195 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42121740_4   5291 TGGAAAAAGCACTCCATGCTCATGGATAGGAAGAATCAATATAGTGAAAA 5340
                               i -i ii     i        v      v i     v  v  i 
  L1M4_orf2#LINE/      1 TGGAAAGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_42121740_4   5341 TGGCCATACTGCTCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAG 5390
                             v     v i    v i  i  i        i  v     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_42121740_4   5391 CTACCATTGACTTTCTTCACATAATTATAATGAACT-ACTCTAAATTTCA 5439
                         v v   vivi i  i  ii  v  v - i ii i  - ii     v    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chrX_42121740_4   5440 TATGGAATCAAAAAAGAGCCTGTATAGCCAAGACAGTCCTAAGCAAAAAG 5489
                                viiv  ii  v  v v        i   i  i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_42121740_4   5490 AACAAAGCTGGAGGCATCACAGTACCTGACTTCAAACTATACTATAAGGC 5539
                                i      vv     v v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_42121740_4   5540 TACAGTAACCAAAACAGTATGGTACTAGTACCAAAACAGATATATAGACC 5589
                                 i   i     i       i i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_42121740_4   5590 AATGGAACAGAACAGAGGCCTCAAAAATAACACCACACATCTACAACCAT 5639
                                i    iv   ivii  i      vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_42121740_4   5640 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5689
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_42121740_4   5690 ATTTAATAAATGGTGTTGGGAAAACTGACTAGCCATATGCACAAAACTGA 5739
                         v  i  i        i     v     iv  ?   i     v  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_42121740_4   5740 AACTGGACTCCTTCCTTACATCTTATACAAAAATTAACTCAAGATGGATT 5789
                          ii     i   v   i   i v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_42121740_4   5790 AAAGACTTAAACATAAAACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5839
                          ?    i    ii   i v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_42121740_4   5840 AGGCA-ATACCATTCAGGACATAGGCATGGACAAAGACTTCATGGCTAAA 5888
                            ?i- v i -   iv   v v  vv i i   v ii   v i v  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_42121740_4   5889 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5938
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_42121740_4   5939 TAAACTAAAGCGTTTCTGCACAGCAAAAGAAACTATCATAAGAGTGAATA 5988
                         i   v v  ivii  i  ii vv    i  v       vi i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_42121740_4   5989 GGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 6038
                          i     i   i             v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_42121740_4   6039 GAGGTAATATCCAGAATCTACAAAGAACT--TA-AATTTA-CAAGAAAAA 6084
                          iiv vi          v  i        --  -  i i -i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_42121740_4   6085 AACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 6134
                         i     i     v  i?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_42121740_4   6135 CAAAAGAAGGCATTTATATGGCCAACAAACATATGAAAAAAAGCTCATCA 6184
                          v       ii  vi v        i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_42121740_4   6185 TCACTGGTCAT 6195
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.62 (146 / 90)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


3072 27.23 0.88 0.77  chrX_42204690_42211066     4978  5884 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42204690_4   4978 TGGAAGAACATCCCATGCTCGTGGGTAGGAAGAATCAATATCATGAAAAT 5027
                              ii i        i  i   i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42204690_4   5028 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5077
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42204690_4   5078 TACCCA--TGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 5123
                          -    --  v    -   i     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTT-TTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_42204690_4   5124 CATATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAA 5173
                                  viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_42204690_4   5174 AGAACAAAGCTGGAGGCATCACGCTACGTGACTGCAAACTATACTGCAAG 5223
                                  i      vv    i  v vii i v    viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_42204690_4   5224 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5273
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_42204690_4   5274 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAA 5321
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_42204690_4   5322 CTATCTGATCTTTGACAAACATGAGAAAAACAAGCAATGGGAAAAGGATT 5371
                         ii vi    i  i     ivi  vv  i v  vv       i    i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_42204690_4   5372 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5421
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_42204690_4   5422 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAAGTAATTCAAGATG 5471
                         v    ii    i    v   i     v          v   i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_42204690_4   5472 GATTAAAGACTTAAACGTTAGACCTACAACCATAAAAACCCTAGAAGAAA 5521
                            i ?    i    i  v   v   v   i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_42204690_4   5522 ACCTGGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5571
                           v i  ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_42204690_4   5572 AAAACATCAAA-GCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCT 5620
                          vi   i    -   vvi     i    vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_42204690_4   5621 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGA 5670
                         v  i   v v  i i   i  ii vv    i  v    i  vv i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_42204690_4   5671 ACAAGCAACCTACAAAATGGGAGAAAAT-TTTCCCAACCGACTCATCTGG 5719
                          v ii     i   i             -   v v  i - ivi     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGA 743

  chrX_42204690_4   5720 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5769
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_42204690_4   5770 AAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACAC 5819
                             i     i     v  i?    i    ii     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_42204690_4   5820 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGGAAAAATGCTC 5869
                              v        i  vi viii     v  i      i   i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_42204690_4   5870 ACCATCACTGGCCAT 5884
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


3122 27.45 0.66 0.55  chrX_42269586_42275634     1127  2033 (4016)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42269586_4   1127 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAATATTGTGAAAAT 1176
                              ii i  i     i    i i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42269586_4   1177 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1226
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42269586_4   1227 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1274
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_42269586_4   1275 TATGGAACCAGAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 1324
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_42269586_4   1325 AACAAAGCTGGAGGCATCATGCTACCGGACTGCAAACTATACTACAAGGC 1374
                                i      vv   ii  v  vi i v    viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_42269586_4   1375 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1424
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_42269586_4   1425 AATGGAACAGAA--AAGAGCCCTCAGAAATAATGCCACATATCTACAACT 1472
                                i    --i    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_42269586_4   1473 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 1522
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_42269586_4   1523 CTATTTAATAAATGGCGCTGGGAAAACTGGCCAGCCATACTTAGAAAGCT 1572
                           v  i  i      i       v      vi ?   i ivi i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_42269586_4   1573 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1622
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_42269586_4   1623 TGAAAGACTTTAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1672
                          v ?    i v     v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_42269586_4   1673 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCACGTCTA 1721
                         v    ?i- v i -   iv   v v  vv i     v ii   viivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_42269586_4   1722 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1771
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_42269586_4   1772 ATTAAACTGAAGAGCTTCTGCACAGCAAAAGGAACTACCATCAAAGTGAA 1821
                           i   v v  i i   i  ii vv    i iv    i  vv        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_42269586_4   1822 CAGGCAGCCTACAGAATGGGAGAAAATGTTTGCAATCTACTCATCTGACA 1871
                         v  i  i  i                 i       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_42269586_4   1872 AAGGGCTAATATCCAGAATCTACAATAAACTCAAACAAATTTACAAGAAA 1921
                          i  i  vi          v  i  vi     vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_42269586_4   1922 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 1971
                           i     i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_42269586_4   1972 CTCATAAGAAGGCATTTATGCAGCCAAAAGACACATGAAAA-ATGCTCAT 2020
                            vv      ii  vi viii     v ii          -       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_42269586_4   2021 CATCACTGGCCAT 2033
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  

2719 27.90 3.53 0.34  chrX_42269586_42275634     4679  5556 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_42269586_4   4679 GAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAATGA 4728
                             v i        i        v  v   v i        v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_42269586_4   4729 CCAGACTGTCAAAAGAAATCTACAAATTCAATGCAATCCGCATCAAAATA 4778
                          v v   vi v   vvi       i      i       vi        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_42269586_4   4779 TCA-CCATCATTCTT-CA------------CCGA-------ATT------ 4801
                         i  - iii v  i  -  ------------ i  -------   ------
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_42269586_4   4802 -AGATACAACAGAGCCCACATAGCCAAAGTAAGACTAAGCAAAAAGAATA 4850
                         - i  i   vi  v  viv         ii  vvi i iv  i     i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_42269586_4   4851 AATCTGGAGGCATCACACTACCTGATTTCAAACTGTATTGTAAGGCCATA 4900
                           vi      vv       v  ii        viv  i ii  i  i i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_42269586_4   4901 GTCACCAAAACAGCAAGGTACTGGTATAAAAACAGGCACATAGACCAATG 4950
                           v i   i    iiv        i    ii i  i  i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_42269586_4   4951 GAACAAAACAGAGAACTCAGAAATAAACCCAAATACTTACAGCTAACTGA 5000
                            i i  iv    iii              v i i   ii ii  i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_42269586_4   5001 TCTTCGACAAAGTAAACAAAAACATAAAGTAGGGAAAGGACACCCTATTC 5050
                          i        i vviv   i v   vv i i       i i vi  v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_42269586_4   5051 AACAAATGGTGCTGAGATAATTGGCTAGCCACATGTAGGAGAATGAAACT 5100
                                       i  i  i   v  ?       i ii        ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_42269586_4   5101 GGATCCTCATCTCTCACCTTATATAAAAATCAACTCAAGATGGATTAAGG 5150
                            i  ii i   v    v    i      i       i      i ?i 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_42269586_4   5151 ACTTAAACCTAAGACCTGACACTATAAAAATTTTAGAAGATAACCTTGGA 5200
                           i    iv     v  i v         v i        v   v v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_42269586_4   5201 AAACCCCCTCTAGACAATGGCTTAGGCAAGGATTTCATGACCAAGAACCC 5250
                         iv vvi i  vv   vv   v        v i    v iivi v  vv  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_42269586_4   5251 AAAAGCAAATGCAATAAAAAAAAAAGCTAAATAGCTGGGACCTAATTAAA 5300
                                v v    i    i     i-  i   iv v    i v  i   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAA 651

  chrX_42269586_4   5301 -TTAAAGAGCTTTTGCATGGCAAAAGGAATAGTCAGCAGAGTAAACAGAT 5349
                         -     i -      iiivv    i iv ivi   iv i   i  v   i
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_42269586_4   5350 GACCCACAGAGTGGGATAAAATCTTCATAATCTATACAACT-ACATAGGA 5398
                         i         i     v     v  iii  vii   i v  - i vi   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_42269586_4   5399 CTAATATCCAGAATCTACAATAAACTCAAACAAATCAGTAAGAAAAAAAT 5448
                           vi          v  i  vi     vv    v   i   v     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA- 799

  chrX_42269586_4   5449 CAAACAAACCCATCAAAAAGTAGGCTAAGGACATGAACAGACAATTCTCA 5498
                             i  v  v  i?    i i   v     iv    i     v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_42269586_4   5499 AAAGAAGATATATAAATAGCCAACAAACATACAAAAAAA-ACTGAGCATC 5547
                                     i    i     i  i  i ii    i -i  v i    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_42269586_4   5548 ACTAACGAT 5556
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 3.09 (34 / 11)  


3407 22.73 3.15 0.82  chrX_42348996_42350987      644  1501 (491)    L1M4_orf2#LINE/L1       31   908 (0)  

  chrX_42348996_4    644 AGACTTGGTATCATTGAGATATGAATTATCCTTAAATTGATCTATAGATT 693
                               ii   ii  i    ivv   vv   ii           i     
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chrX_42348996_4    694 TAACATAATTGTAATCAAAGTCTCAGCAGGCCTTTTTAAATAGAAAATGA 743
                         i   ii   iviv      i  i    v v i     i--i     v   
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG--CAGAAATTGA 128

  chrX_42348996_4    744 AAATTAGATTCTAAAATTTATAAGAAAATGCAAGAGACCTCAAATGGCCA 793
                         v  viv   i        i   v i         i    ivi   i    
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chrX_42348996_4    794 AAACAACTTTGAA---GAGCAACGATTTTGGACGAATTATAGTACCCGAT 840
                               ii     ---  iv   i vv     v  v i i v v   i  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_42348996_4    841 TTCAAAATTTATTATAAAACTGTAGTAATCAAGAGAGTAAGAGATTAACA 890
                                i   i  i   i  ii           v   iv iv i ii  
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_42348996_4    891 TCAAGACAGACAAATAGATCAATGAAATAAAA--AAGAGTTCAAAAATAG 938
                          v i  i     v           i    i  --i     i  i     i
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_42348996_4    939 ACTCATACATATATAGACACCTGATTTTCAACAAACGTGCAATGGCAATT 988
                           i       v   i v  vi        i    iv    v v i v   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_42348996_4    989 CAATGCAGAAAGA-TAG-CATTTTGACAAATAGTGCTGAAACAATTGGAT 1036
                              vi      -   - v   ii      i      ii    i     
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_42348996_4   1037 AGCCTTATGCAAAAAGAAAAAAACTTTGGTCCATAATACCTCATACCATA 1086
                          ?  vi        -   vi  i--    v  vi--       i      
  L1M4_orf2#LINE/    429 AKCCACATGCAAAA-GAATGAAG--TTGGACCCC--TACCTCACACCATA 473

  chrX_42348996_4   1087 TACAGAAATTAATTCAATATTTATCCTAAACCTAAATGTAAAAACTAAAA 1136
                             i       i    v  vv   v? i            i i      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_42348996_4   1137 CTTCAAAACTTCTAGAAGAAAA------------TCTTTGTGACCTTGGA 1174
                           vi      ii          ------------    i          i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_42348996_4   1175 TTAGGCAACGATTTCTTATATACCATATCAATACCATGATCCAT----TA 1220
                                 i i       v   iv i i   v v  ii v v i----v 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_42348996_4   1221 AAAAATTGATGAACTGGACCTCAGCAAAGTTAAAAACATTTGCTCTTCAA 1270
                               v   i  i     i   v    i        v    iv      
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_42348996_4   1271 AAGACACTCCTAAGAGAATAAAAAGAGAAACCACAGACTGGGAGAAAATA 1320
                          i      vii    i i i      v  v       v            
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_42348996_4   1321 TATACAAAGCATATGTCTGACACAATACTTGTACTCAGAATATATAAAGA 1370
                          v i    v     i     i viiv       ii               
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_42348996_4   1371 ACTCTCAAAATTCAATAATAAGAAAACAAATGACC-AATTAAAAAATGGG 1419
                              i v  i          i  i      i   -    ?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_42348996_4   1420 CAAAATATTTTGACAGACACTTCACCAAATA---TATACTGATGACGAAT 1466
                             iv    vi i     i   v     v ---     vi   i v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_42348996_4   1467 AAGCACACAAAAAGATGCTCAATATAATTAGCCAT 1501
                                ii             i  v ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (121 / 71)
Gap_init rate = 0.01 (12 / 878), avg. gap size = 2.83 (34 / 12)  


3312 25.67 1.44 0.56  chrX_42426438_42432959.rev     5132  6031 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42426438_4   5132 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATTAATATTGTGAAAAT 5181
                              ii i  i     i       iv      v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42426438_4   5182 GGCCATACTTCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5231
                            v     i      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42426438_4   5232 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5280
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_42426438_4   5281 TGGAACCAAAAAAGAGCCCTCATAGCCAAGACAATCCTAAGCAAAAAGAA 5330
                              viiv  ii  v  vvv        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_42426438_4   5331 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTGCAAGGCTA 5380
                              i      vv   ii  v  ii i      viv    i   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_42426438_4   5381 CAGTAACCAAAATAGCATGGCACTGGTACCAAAACAGAGATATAGACCAA 5430
                               i   i i  ii   i     i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_42426438_4   5431 TGGATCAGAAC--AGAGTCCTCAGAAATAACACCACACATCTACAACCAT 5478
                             vi    i--       --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_42426438_4   5479 CTGATCTTTGACAAACCTGACAAAAGCAAGCAATGGGGAAAGGATTCCCT 5528
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_42426438_4   5529 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5578
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_42426438_4   5579 AAATGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 5628
                          iv    i    v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_42426438_4   5629 AAAGACTTAAATGTAACACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5678
                          ?    i         v v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_42426438_4   5679 AGGC---AATGCCATTCAGGACATAGGCATGGGCAAAGACTTCATGGCTA 5725
                            ?---   -- -   iv   v v  vv i     v ii   v i v  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_42426438_4   5726 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCCG 5775
                         vi            vvi          vv        i    v   iiiv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_42426438_4   5776 ATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAGTGAA 5825
                           i   v v  i i   i  iiivv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_42426438_4   5826 CAGGCAACCTACAGAATAGGAGAAAATCTTTGCAATCTACCCATCTGACA 5875
                         v  i     i       i         v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_42426438_4   5876 AATGGCTAATATCCAGAATCTACAAAGAACTTAAACAA----AT--TTAC 5919
                          iv i  vi          v  i        ivv    ----  -- v v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_42426438_4   5920 AAGATAAA-AACACCATCAAAAAGTGGGCAAAGGATATGAACAGCCACTT 5968
                             i   -   v v  i?    i            v    i  v  i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_42426438_4   5969 CTCAAAAGAAGACATTTATGCAACCAACAGACATAAGAAAAAATGCTCAT 6018
                            v        i  vi viiii    i ii  i v     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_42426438_4   6019 CATCACTGGTCAT 6031
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (136 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


3258 27.20 0.44 0.44  chrX_42503374_42509624     4851  5758 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42503374_4   4851 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4900
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42503374_4   4901 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4950
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42503374_4   4951 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4998
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_42503374_4   4999 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5048
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_42503374_4   5049 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5098
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_42503374_4   5099 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATGGATC 5148
                                 i   i    ii         i iv ii i   v    i    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_42503374_4   5149 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5196
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_42503374_4   5197 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5246
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_42503374_4   5247 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5296
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_42503374_4   5297 GAAACTGGATCCTTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5346
                            ii    i  i v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_42503374_4   5347 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5396
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_42503374_4   5397 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5446
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_42503374_4   5447 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTAA 5496
                         i            vvi          vv     v  i    v i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_42503374_4   5497 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5546
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_42503374_4   5547 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5596
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_42503374_4   5597 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5646
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_42503374_4   5647 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5696
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_42503374_4   5697 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5746
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_42503374_4   5747 ATCACTGGCCAT 5758
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3473 24.67 0.76 1.64  chrX_42539041_42543295     2847  3762 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42539041_4   2847 TGGAAAGATATCCCGTGTTCTTAGATTGGAAGAATCAATATTGTTAAAAT 2896
                                       i     v i          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42539041_4   2897 GTCCCTAATGCCCAAAGCAATCTACAGATTTAATGCAATCTCTATCAGAA 2946
                          v vv  v v      vii           i  i      i      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42539041_4   2947 TACCAGTGACATCCTTCACAGAAATAGCGAAAAAC-AATCC--AAGTTTA 2993
                          v    ivi v ii  ii       --i  v  i -i    --  i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCA 148

  chrX_42539041_4   2994 TATGGAACCAGAAAAGATCCAGAATATTCAAAGCTAT-TTAAGCAAAAAG 3042
                                viiv  ii  i        vi    i v  -  i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_42539041_4   3043 AACAAAACTGAAGGAATCATGTTACCTTACTTCACATTATACTACACAGC 3092
                               ii  i    v   iii v  iv i    v viv       v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_42539041_4   3093 TATAGTAACCAAAACAGCATGATATTGGCATTACAACAGACATAGACAGA 3142
                           i     i   i    ii  i  i      v vi i       --i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA--TAGA 296

  chrX_42539041_4   3143 CCAATAGAACAGAATAGAGAACCCAGAAACAAATCCATACATCTATAGTG 3192
                         i    i   i     v    ii       i   i        i   i  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_42539041_4   3193 AACCTGTTTTCAATAAAGTTGCCAAGAACATACACTGGGGAAAGGACAGT 3242
                           iivi     i i  i v        v   v  v         i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_42539041_4   3243 CTCTTCAGTAAATGGTGCTGGGAAAACTCCATATCCATATGCAGAAGAAT 3292
                           i    ii              v    vv   ?   i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_42539041_4   3293 GAAATTAGACCC-TATCTCTTGCCATATATAAAAATCAAACCAAGATTGA 3341
                            i  i     -  i   vii       i      i  vi   i  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_42539041_4   3342 TTAAATATTTAAATCTAAGTCCTCAGAATATAACACTACTATAAAAAAAA 3391
                          i ? v ii     v    vv  v i v     v   vi  --------i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA--------G 538

  chrX_42539041_4   3392 AAAAAAACATTGGGG-AAACTATCCCACTCATTGAACTGGGCAAAGATTT 3440
                           i       v  ? -   iiv  viivi -   iii i     v i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTT 587

  chrX_42539041_4   3441 CTTGAGTAATACCCCACAAGCACAGGCAACCAAAGCAAAAATGGACAAAT 3490
                            iii  vv  v   v       i     v    v      i  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_42539041_4   3491 GAGATCATATCAAG-TTAAAAAGCTTCTAGACAGTGAAAGAAATAATCAA 3539
                         vi  iivi     i-       -   i ivi vvii  i  v iv     
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_42539041_4   3540 CAAAGTGAAGGGAAAACCCACAGAATGGGAGAAAATATTTGCAAACTACC 3589
                         v        ii  v                               ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_42539041_4   3590 CATCTGACAAGAGATTAAGTAACCAGAATATATGAGGAGCTCAAACAGCT 3639
                         i      i   i  i v-   v           i i  i   vv   i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTT-GTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_42539041_4   3640 CTGTAGGAAAATATCTAATGATCCAATTAAAAAATGGGCAAAAGATTTGA 3689
                          vi  iv    viv v   i i      ?             i       
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_42539041_4   3690 ATTGACATTTCTCAAAAGAAGACATACAAATGGCAAACAGGTATATGGAA 3739
                           v          v        i           v  i i i i   i  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_42539041_4   3740 AGGTGCTCAACATCACTGATATT 3762
                           i            ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (142 / 80)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


2913 25.88 3.52 0.45  chrX_42660819_42665068.rev     2879  3759 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42660819_4   2879 TGAAAACACGTTCCATGCTCGTGGATAGGTAGAATCAATATTGTGAAAAT 2928
                           i   v ii i     i  i     v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42660819_4   2929 TACCATACTGCCAAAAAGCAATCTACAAATTCAATGCAATTTCCATTAAA 2978
                         vi v     v  v   -vii       i      i     ii i  i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_42660819_4   2979 ATACCACCATCATTCTTCACAGAACTAGAAAAATCAATCCTAAAATTCAT 3028
                           v   v vv v  i  ii     v v  v  iiii              
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_42660819_4   3029 ATGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAACA 3078
                               viiv  ii  v  v v         i   vvi i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_42660819_4   3079 ACAAATCTGTAGGCATCACATTACTTGACTTCAAACTGTACTATAAGGCT 3128
                              vi  v   vv     i v iii i      viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_42660819_4   3129 ATAGTTACCAAAACAGCATGGTACTGGTATAAATATAGGCACATAGACCA 3178
                          i   v i   i    ii         i    iv    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_42660819_4   3179 ATGGAACAGAATAAAGAACCCAGAAATAAAGCCAAATACTTACAGCTAAC 3228
                               i     vi   ii           v   v i i   ii ii  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_42660819_4   3229 TGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACATCCTA 3278
                             i  i     i vviv   i v   vv i         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_42660819_4   3279 TTCAACAAATGGTTCTGGGATAATTGGCAAGCCATATGTAGAAGAAAGAA 3328
                                      v      i  i   vv ?   i   i i     v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_42660819_4   3329 ACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAAATGGATCA 3378
                         ii    i  ii i   v    v           i                
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_42660819_4   3379 AAGACTTAAATCTAAGGCCTAAAACCCTAAAAAATTCT-AGAAGATAACA 3427
                         ?    i     v    iv       --  v    i   -      v    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAAC--TATAAAACTCTTAGAAGAAAACA 547

  chrX_42660819_4   3428 TCAGTAAAACTCTTCTAGACAT-GGCTTAGGCACGGAGTTCATGACCAAG 3476
                          vi ?iv  v     vv   v -  v       vv iv   v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_42660819_4   3477 AACCCTTAAGCAAATGCAACAAAAACAAAAATAAACACATGGGACCTAAT 3526
                          vv  vv     v v         iv       i i v  v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_42660819_4   3527 --AAACTAAAAACTTCTGCACTCTGA------TTA-CAGCAGAGTAAACA 3567
                         --   i         i  ii  iii ------i  -  iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_42660819_4   3568 GACAACCCACAGAGTGGGAGAAAATATTCACAAA---------------- 3601
                                      i              ii    ----------------
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_42660819_4   3602 GGACTAATATCCAGACT---CAGGGAACTCAAAAAAATCTGCAAGAAAAA 3648
                              vi        v ---i ii      vv v  v  vii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_42660819_4   3649 -ACAACTAATCCCATCAAAAAAGTGGGCAAAGGATATTAATAGACAATTC 3697
                         -    v   i  v  i?     -            v v        v   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_42660819_4   3698 TCAAAAGAAGATATATAAATGACCAACAAATATATTTAAAAATGCTCAAC 3747
                           v            i     i    i  ii i  vv   i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_42660819_4   3748 ATCACTAATCAG 3759
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (126 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.18 (35 / 11)  


2926 21.98 5.75 3.38  chrX_42688105_42691212.rev     1732  2618 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42688105_4   1732 TGGAGAGATATACCATGTTCTTTGATTAAAGGACTCAACATCAATCAACA 1781
                             i      v        v v    ii i    i  i  ii-------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTG------- 43

  chrX_42688105_4   1782 TCAATCAATTTACATGAGCAAAGATGTAAATTCTCCCTATATTGATCTAT 1831
                         ---------   ---------     vv   v     i v         i
  L1M4_orf2#LINE/     44 ---------TTA---------AGATGGCAATACTCCCCAAATTGATCTAC 75

  chrX_42688105_4   1832 AAGCTTAACGCAAACCCTATAAAAATGTCAGCAAAGTCTATTGTAGACAT 1881
                          iii i       v      v     vi    vivv i v   i   v  
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chrX_42688105_4   1882 AGACAAGCTTATACTAAAGTT-ATATGGAAGGTGCAC---ACCCTAGAAT 1927
                         v        v  v     i  -        i-    v---    -     
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAA-TGCAAGGGACCC-AGAAT 173

  chrX_42688105_4   1928 AGATAAAACAATCTTGACAAAGAAGAATAAAGTGGGATGAATCACTCTAC 1977
                           vi             v         i     v   v  v    v  v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_42688105_4   1978 CATATACTAAAGCTTACTATATAGCTACATTAATCAAGATAATGTGATAT 2027
                          vv  vii   i       i v       v         i i    i  i
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_42688105_4   2028 TGGTGAAGGGAGAGAGAAATATATAAATGAAACAGAATAGATCACACAGA 2077
                            iiv i   v   v v   v  v    i  i     v  vviiv    
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_42688105_4   2078 AATAGACCCATACAGATATGCTCAACTGATTTTTGGTGAAGATGCAAAGG 2127
                             i         vv    v    i       i iii i i   v   i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_42688105_4   2128 CAATTCAATAGAGGAAGGAGAGCCTTTTCAA-AA-----GC--------C 2163
                          v       i i i   i v  i        -  -----  -------- 
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_42688105_4   2164 TCGA----CATA--------AAT----------------CTCATATCTTA 2185
                          v  ----  i --------   ----------------    i i v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_42688105_4   2186 TACAAAAATTAACTCAATATAGATCAATGGATTTAAATGTAAAATGTAAA 2235
                                          v  i     ?-i  ii         i vv    
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAW-AGACCTAAATGTAAGAGCTAAA 522

  chrX_42688105_4   2236 TCTATAAAACTTTTATAA-AAAACACTGGATAAAATCTTAG-GATTTAAG 2283
                         v          i   v  -      iv  ?vv       v -  ii vi 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_42688105_4   2284 GCTAGGCAAAAAGTTCTTACACTTGACACCAAAAGCACAACCAATAAGAG 2333
                          i       viiv      v iv                 v   i  i  
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_42688105_4   2334 AAAACATTGATAAACTGGACTTCATCAAAATTAAAAACTTTTGTTCTGTG 2383
                             v  v      i                             v  - v
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT-TC 671

  chrX_42688105_4   2384 AAAGTCCAC-ATGAACAGGATGGAAAGACAAGCTACAGACTGGGAGAAAA 2432
                             vv   -  v  v iii  i        v i     v          
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_42688105_4   2433 TATTTCCAAGCCACATATATGACAAACGACTAGTATTTAGAATATATAAA 2482
                              v   ii  i    v   i  iv    v    ii            
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_42688105_4   2483 GAGCTCATAAAACTCAACAGTAAAAATTAAAAAAACTCCAATTAGAAAAT 2532
                           i   v  v       i i      vvv   v   -      ?i     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAAC-CCAATTWAAAAAT 820

  chrX_42688105_4   2533 GATCAAAAGACTTGAAGAGACATTTCACTGCAGACGGCATACAGGTGGCT 2582
                          iv    i  i     v         v iiv   v ii     ii    i
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_42688105_4   2583 AATGAACACAT--AAAGATATTCCACATCGGCATCCAT 2618
                            i i     --      ii  v     i????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.13 (102 / 90)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 4.26 (81 / 19)  

 601 15.20 4.00 1.60  chrX_42688105_42691212.rev     2950  3074 (34)  C L1M4_orf2#LINE/L1   (557)   351   224  

C chrX_42688105_4   3074 CCAAGGTTTCAAAACTTACTATAAAGCTACAGTAATCAAGGCAAT----- 3030
                             --               i                  i  i -----
  L1M4_orf2#LINE/    224 CCAA--TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

C chrX_42688105_4   3029 ACTGGCAAAAGGATAGACACAAAGATTAATGGACTAGAATAGAAAGCCCA 2980
                                v           i v    i      v      v  i  i   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

C chrX_42688105_4   2979 GAAGTAGACACACAAAAATATGGTTAATTG 2950
                            i  i  v  i v vv      i     
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTG 351

Transitions / transversions = 1.38 (11 / 8)
Gap_init rate = 0.02 (2 / 128), avg. gap size = 3.50 (7 / 2)  


2739 23.34 3.17 7.29  chrX_42776008_42778764     1318  2264 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42776008_4   1318 TGGAGAGACATATTATGTTCATGGATTAAAAGATTCACCATAGTAAAGAT 1367
                             i   i  vii             ii    i i vi  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42776008_4   1368 GTCAGTTTTCCCCAACTTGATCTGTAGGTTTATTGCAATTCCTATCAAAG 1417
                          v  i vi       v       ii  i  i vi     i         i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42776008_4   1418 TTTCAGGAAAGTTTTTTTTTTTTTCAAATATAGATAAGTATAGTCTAAAG 1467
                          ii   ------i vii      v  i v  v  i   ivv vi     i
  L1M4_orf2#LINE/    101 TCCCAG------CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_42776008_4   1468 TTTATATAAAGAGGCAAAGGAACTAGAATAGCTATTACAATTTTGACAAA 1517
                           i    ii i v    i   v i        i vv     i    v   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_42776008_4   1518 GAT---TTAAGTGAGAGAA---AC-----CTGAGGTTATGACTTACTATA 1556
                           v---iv    vi   i ---  ----- ii vv i vi        i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_42776008_4   1557 TAGCTACAGCAATCAAGATAGTGTGTTATTGG-AGAAGGAGTAGACACAT 1605
                         v        i        i      v  i   - v     -      i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATAT 293

  chrX_42776008_4   1606 AGATCAATGCAACAGAAAACAGAACCCAGAAATAGACCAACATAAATATA 1655
                                  v  i    vvv   ii         i   v i i vv   i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_42776008_4   1656 CTCAATTGATTTTTGACAAAAGTATAAAAGCAATTCCATGAAGGAAGGAT 1705
                         v            i     ii  iiv  ii v    v   ii i   i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_42776008_4   1706 AGTTTTTTCAACAAATTGTGCTGGAACAATAGGACATCCATAGGCAAAAA 1755
                            i            v       i    iv   i ?   i v      i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_42776008_4   1756 ACAACAACAACAACAACAAAAAAACCCACCTTGATCTAATTCTGTATCAC 1805
                          -------------- ii  i---------   iv i---i  iiv    
  L1M4_orf2#LINE/    444 A--------------ATGAAG---------TTGGACC---CCTACCTCAC 467

  chrX_42776008_4   1806 ACTGTACACAAAAATTAATTCAAAATGGATTATGAATTTAAATGTAAAAG 1855
                           ii  i           i           i ?ii ii         i  
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_42776008_4   1856 ATAAAACTATAAAATTTTTAGAAGAAAACATA--------TCTTTGGGAC 1897
                         v             i i               --------    i v   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_42776008_4   1898 ATAATACTAGGCAAAAAGCTAGTG-CTTAGATAAGACACCAAAAATATAT 1946
                         v vivii       ----- i  v-        v          ii i v
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAA-----TGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_42776008_4   1947 TCCACTT--TAAAAAATGTATAAATTGGACTTCATCAATATTAAAAACTT 1994
                         v v  vv--v       iv                   v           
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_42776008_4   1995 TTTTACTGTTTTGTAAAAACAGTACTGCAAAAGACCCTATTGTGAACATG 2044
                           -------------------  i  v    i   v    iiv   vi  
  L1M4_orf2#LINE/    663 TT-------------------GTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_42776008_4   2045 AAAAGACAAGCTATTGACTGGAAGAAAATATTTGTAAATCTTATATCTGA 2094
                                  v i iv  v   i            i     v         
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_42776008_4   2095 AAAAGGTCTTATATCTAAAATATATAAATAACGCTCAAAACTCAACAGTT 2144
                         v  i  v   i    i i          v   v  i v       i i -
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT- 792

  chrX_42776008_4   2145 TGCTCTTTTACAAATAAATATAGATTTCAATTGCAAAATGGG-AAAAAAC 2193
                         -----------   v i i v v vii     ?v        -   ii i
  L1M4_orf2#LINE/    793 -----------AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_42776008_4   2194 ACGAA-AAATATT-CTACAAAGAGAAGACACAGATGGACA-TAAACACAG 2240
                         vi   - i i   -  v      ii v i   i    v  -   i    v
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_42776008_4   2241 GAAG---TGTTCAAAATCATTATCTGT 2264
                            i---  i    v    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (134 / 84)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.95 (99 / 20)  


2930 27.17 1.67 0.56  chrX_42813565_42817040.rev     2088  2985 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42813565_4   2088 TGGAGAAACAATCCATGGTCATGGATAGGAAAAATCAATATTGTGAAAAT 2137
                             i i i vi     v        v    i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42813565_4   2138 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGTTATTCCCATTAAAC 2187
                            v     v      v i  i  i        i iv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42813565_4   2188 TACCATCAACATTCTTCACAGAATTAGAAAAAAACT-ATTTAAAAATTCA 2236
                          v   v vi v  i  ii     v v  v  i--  -  iiv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_42813565_4   2237 TATAGATCAA-AAAATGAGCCCA-AATAGCCAAGATAATCCTAAGCAATA 2284
                            i  --  -iv  v ii    -         i i    i i iv  v 
  L1M4_orf2#LINE/    149 TATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_42813565_4   2285 AGAACAAAGCTGACGGCATCATGCTACCTGACTTCAAACTATACTGCAAG 2334
                                  i  iv  vv   ii  v  ii i      viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_42813565_4   2335 GTTACTATAACCCAAACAGCATGGTACTGGCACAAGAACAGATACATAGA 2384
                          i   vi   i v i    ii           i   i i   i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_42813565_4   2385 CCGATGGAATAGAATAGAGAACTCAGAAATAAAACCGCAAACTTACAACC 2434
                         i i            v    iii          v  ii v i   iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_42813565_4   2435 ATCTGATCTTTGCCCA---TGACAAAAACAAGCAATGGGGAAAGTACTCC 2481
                          vi    i  i v v ---  v   i v  vv            v ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_42813565_4   2482 CTATTTAATAAATGGTGCTGAGAGAGCTGGCTAGCCATATGCAGAAAATT 2531
                           v  i  i           i  v i    v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_42813565_4   2532 GAAACTGGACCCCTTCCTTACACCATATACAAAAATTAATTCAAGATGGA 2581
                            ii         v   i                    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_42813565_4   2582 TTAAAGACTGAAATGTAAAACCCCAAACTATAAAAACCCTAGAAGAAAAT 2631
                          i ?    iv        i v iv           vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_42813565_4   2632 CTAGGCA-ATATCATTCAGGACAGAAGAATGGGCAAACATTTCATAACCA 2680
                         v    ?i- v   -   iv   vvvi iv i     vvi    v  ivi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_42813565_4   2681 ACATGCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGAATGTA 2730
                         vv ii         vvv          v      v  i    v i iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_42813565_4   2731 ATTAAACTAAAGAGCTTCTGCACAACGAAAGAAATTATCATCAGAGTGCA 2780
                           i   v v  i i   i  ii vv i  i  v i     vv i    v 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_42813565_4   2781 GAGACAACCTACAAAACGGGAGAAAATTTTTGCAATGTATCCATCTGACA 2830
                         i        i   i  i          v       vvi  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_42813565_4   2831 AAGGTCTAATATCTAGAGTCTACAAGGAAAT--TA-AATTTA-CAAGAAA 2876
                          i  v  vi    i   i v  i  i   v --  -  i i -i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_42813565_4   2877 AAAA--AACAACCTCATTAAAAAGTGGGCAAAGGACACAAACAGACACTT 2924
                           i --  i    iv   ?    i           ivii  i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_42813565_4   2925 CTCAAAAGAAGACATAAATGTGGCCAACGA--ACATTAAGAAAAGCTCAA 2972
                            v        i   v vi       ii --    v  i i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_42813565_4   2973 CATCACTGATCAT 2985
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


3070 25.00 1.78 1.11  chrX_42827079_42832490     4020  4919 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_42827079_4   4020 GAAAAAT-TTCTATGCTCATGGATAGGAAGAATCAACATTGTTAAAATGG 4068
                             i  - i i   i        v      v i  i        i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_42827079_4   4069 CCATGCTGCCCAAAGCAAGTTATAGATTCAATGCTATTCCTATCAAACTG 4118
                          v  i  v      vii vi  i        i  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_42827079_4   4119 CCAA-TGTCATTTTTTACAGA--TTAGAAAAAAAACT-ATTC-AAAATTC 4163
                            i-  i -      i    --  i---- v  i  -  i -       
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATTC 147

  chrX_42827079_4   4164 ACATGTAACCAAAAATAGCTCA-AATAGCAAAGGCAATCCTAAGCAAAAA 4212
                          i   v  viiv  ivii i  -      v  ii     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_42827079_4   4213 GAACAAAGCTGGAGGAATCACATTATCCAATTTCAAACTGTACTACAAGG 4262
                                 i       v     i vi           viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_42827079_4   4263 CCACAGTAACCATAATAGCACGGAATTGGTACAAAAATAGACACATAGAC 4312
                          i       i  vi i  iii  v i   i i  ii       i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_42827079_4   4313 CAATTGAACAGG-TTATAAATCCCAGAAATAAAGCTGCACATCTACAACC 4361
                             v   i  i-  ivi i   -         v iii    i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC-AGAAATAAACCCATACATTTATGGTC 346

  chrX_42827079_4   4362 ATCTGATTTTTTACAAAGTTGACAATAACAAACAATGGGGAAAGGACTCC 4411
                          vi       iv    i v  v   v v  vv            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_42827079_4   4412 CTATTCAATAACTGATGCTGGGATAACTAGCTAGCCATATGCAGAATATT 4461
                           v     i  v  i        i    i v  ?   i     i  v v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_42827079_4   4462 AAAACTGGACCCCTTTCTTTCACCACATACAAAAATTAACTGAAGATGGA 4511
                         i  ii         vi  iv     i               v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_42827079_4   4512 TTGAAGACTTAAATGTAAGACCTAAAACTATAGAAACCCTAGGAAAAAAA 4561
                          ii?    i           v           -    i  vi   i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAA 545

  chrX_42827079_4   4562 CCTAGGAA-ATATCATTCTGGACATAGGCCTTGGCAAAGATTTCAT-GAT 4609
                          v    ?i- v   -   vv   v v  vi v     v i    v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_42827079_4   4610 GAAGATGCCAAAAGCAATTGCAACAAAAACAAAAATAGACAATTGGGACC 4659
                         - v  ii         vvv         iv         i  v v    i
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_42827079_4   4660 TAATTAAACTAAACAGCTTCTGCACAACAAAAGAAACTTTCAACAGACTA 4709
                          v  i   v v  v i   i  ii vv    i  v   v    v i v i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_42827079_4   4710 AACAGACAACCTACAGAATGGGAAAAAA-ATTTGCAAGCTACGCATATGA 4758
                           v        i           i    -        iii iii  v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_42827079_4   4759 CGAAGGTCTAATATCCATAATCTATAAGCAACTT----AAATCAGTAAGA 4804
                         ii i  v  vi      v   v     iv    i----  v   i   v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_42827079_4   4805 AAAAACCAAACAACCCTATT-AAAAATGGGCAAAGTACATGAACAGACAC 4853
                             iv    i     v   -              v iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_42827079_4   4854 TTCTCAAAAGAAGACATACATGCAGCCAACAAACACATGAAAATAATTCT 4903
                              v        i     viii     i  i          -i  v  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCT 892

  chrX_42827079_4   4904 CCACATCACTAATCAT 4919
                          v      ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (133 / 89)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 1.37 (26 / 19)  


3679 18.51 5.86 1.72  chrX_42834160_42836143.rev      624  1493 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_42834160_4    624 GAAAAA-ACTCTATGTTCATGGATAAAAAGACTTAATATTATTAACATAG 672
                             i - ii i            vii             i    v  i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_42834160_4    673 ACATACTTCCCAAATCGAT-TACAGATCCA-CACAATTACTAGCAACATT 720
                         vv     i       i   -       i  - i    iv   v   v  i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_42834160_4    721 TCACCAGGCTTCTTTGCAGAAATTGAAGAGCTGATTCTAAAATCAATGAG 770
                         i  v v v   i              vi       i       iv  iv 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_42834160_4    771 GAAATTCACAGGGCCCAGTATAGCTAAAATAAATAAATAAATAAAAACTT 820
                              v  vi  i     v     i    i  --------- -----   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAA---------T-----CTT 188

  chrX_42834160_4    821 GACAAATAAAAACAAATTTGGAGAATTCACACTTTCTGATTTCAAAACTT 870
                           v   v  i      v      i i        i ii            
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_42834160_4    871 ACCACAAAACTCCAGTAATCAAGACAGCATGGTACTGGCAAAAAGATAGA 920
                           i     i  v               ii           v  i      
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_42834160_4    921 AGTATAAATAAACTAAATAGAATTGAGGGTCCAGAAATAAACTCTCACAT 970
                         vi    i  v  ivi            i              i vi    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_42834160_4    971 TTATGGTCAA-------------AAGATGCCAAGACAATGCAATAGGGGA 1007
                                   ------------- i i         v  v    i   i 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_42834160_4   1008 A-AATAGT-TCTTGAATAAATGGTGGTGGTATAATTGAATATTCACACAT 1055
                          -      - i  v  i        v   v i  i  i   ?i    iii
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_42834160_4   1056 AAAAGAAGGAAGAAGAACACTCT-CCTAAATCCACACAAGAAAATTAAAT 1104
                                v    vv i  - i  -   v vv   i i vi        v 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_42834160_4   1105 C----TG-ATCTTAGACCTAAAT--------TAAAATTATACAACTTTTA 1141
                          ----  -   v?          --------     i    v    i   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_42834160_4   1142 GAAGAAAATATAGGAGCAAATCTTCATGACCTTAGGCTAGGCAAAAATTT 1191
                                 i     ? i        i       i  i       vii   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_42834160_4   1192 -TTAGACATGAAAACAAAAGTACAAGCAACAAAAGAAAACATAGATAAAA 1240
                         -     i    v v      i                  v         v
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_42834160_4   1241 TGGACATCATCAAAATGTAAAACTTTAGTCCCTGAAAGAATACTATGAAG 1290
                              v          vv        v  v i v    i i     v   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_42834160_4   1291 AAAATGAAAAGGCAACC-ACA-AATGGGAGGAAATATTTTCAAATCTTAT 1338
                            i       i     -   -        i        v      v   
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_42834160_4   1339 ATTTGATAATGGATTTGTATTCAGGATA-----------CTTACCATTCA 1377
                           i      v   i      i   i   -----------     v i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_42834160_4   1378 ATGATAAAAAGA----TAACTCAATTGAAAAATGGACAAATTATATGAAC 1423
                           i         ----    i     ?        i    vv  v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_42834160_4   1424 AAATAGTTTTCTGAA-AAGATACATAAATGGCCAACAAACACATGAAAAG 1472
                          i i v  i  ii  -      i i          i  i           
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_42834160_4   1473 ATACTCAACATTATTAGCCAT 1493
                           i        i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (97 / 60)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 3.47 (66 / 19)  


2943 27.38 2.36 0.45  chrX_42843865_42847016     1772  2662 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42843865_4   1772 TGAAGAGACTTGCCATGTTCATGAATTGGGAGACTCAACACAGTATAGTT 1821
                           i i   iv v           i     i     i  i iv  vv  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42843865_4   1822 GTCAATCCTCTCCTAATTTATATAGAGAGTTAACAAATTTCCCATCAAAA 1871
                          v    v   i  v    v  v  v   v i   iv v i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42843865_4   1872 TTTAAGCAAGGTGTTTTATAGTCATATAGAAGCTTATTCTAAAACTCATA 1921
                          iiv   vivv v    ii  vv  vv v     v  i      i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_42843865_4   1922 GGGAAAAGCACAGGCCCTGGAATAACTAAGATAACGTTGATAAAGAATAA 1971
                         v     v   vi  v  ii     i i  i i  iv    v      v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_42843865_4   1972 TAAAGTGGGAGGATTTACTCTACCCAATATTAAGACTTACTATATAG-TC 2020
                         i     v      i i  v  v      v i  i        i v  - v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_42843865_4   2021 CAATAATCAAGACAATATGATA-TGGTG-AAGGCACAGATGCATAGATCA 2068
                           i           i i  i  -   ii-    - i   iii        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAGACATATAGATCA 299

  chrX_42843865_4   2069 ATGGAATAGAATAGAGAACACAGAAATTGCTTCCACACAAGTACAACCAC 2118
                                     v    iiv       vivi-   i   vv  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTTATGGTCAA 348

  chrX_42843865_4   2119 TTGATTTTTGACAAAGGTGCAAATACAATTCAATAGAGGAAGGATAGCCT 2168
                                 i     i     v  v  v       i i i   i    i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_42843865_4   2169 TTTCAAGAAATCGTGTGGGAGCAATTGGCCCTCCATAAGCAAAA-AATGA 2217
                               v    v   iv  ii   i   viv?   i v      -     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_42843865_4   2218 ACCTTG--CCCTAAACCTCACACCTTATACAACTATTAACCTAAAATGGA 2265
                          vi v --     --         v       vv      ii        
  L1M4_orf2#LINE/    449 AGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_42843865_4   2266 TAATGGACTTAAGTGTAAAA--TA----TACAGAA------AAAAAAAAC 2303
                          v ?i   i   i     i --  ----  i i  ------i  i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_42843865_4   2304 AAGAGAAAAAATCTTTGGGGTCTAATACTAGACAAAGTTTTATTAGCCTT 2353
                          vii ?iv       i v ii  vivii   i   v v   v    viv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_42843865_4   2354 GACACCAAAAGCATGATTCATAGAAGGAAAAATTGATAAATTGTACCTCA 2403
                                      ii viv i i   i      v         v  i   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_42843865_4   2404 TTAAAACTAGAAACTTTTACTCTGTGAAATCCCGTATGAGGAGGATTAAA 2453
                          i    i  i        iiv  vii  ivv vv   v i  iii v   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_42843865_4   2454 -GACAGTCTACAGACTGGCAGAAATTATTTGCTAACCACATATTTGACAA 2502
                         -    ii i     v   v     v       v  i  i    i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_42843865_4   2503 AGGGCGATTATGTAGGATATA--AAGAAGTCCCAAAACCCAACGGCAAAA 2550
                         i  i vvv   vi  i     --     v  ii v   i   iiii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_42843865_4   2551 CCACAAACAATCCAATTAGAAAATGGGCAAAAGTCTTGAAAAAACATTTC 2600
                         vv     i  i      ?i            i vi     v i       
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_42843865_4   2601 ACCTAAAGGGATACACAGATGGAAAATAAGCACATGAAAAGATGTTCAAC 2650
                         v  v  iii    i   i    vv                    i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_42843865_4   2651 ACTATTAGCTAA 2662
                          ii ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (139 / 101)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.92 (25 / 13)  


2344 23.52 8.39 2.06  chrX_42875543_42877277.rev      518  1244 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_42875543_4    518 ATCCTAAAATTTATACAAAACCACAAAAGACCCAGAATAGCCAAAGCTAT 567
                                    i   iii  vii   ii                 i v  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_42875543_4    568 CCTGGCGGGGGAGGGGCGGGGAGGAAACAAAACTGGAGGAATCACATTAC 617
                          i  iviii i  ------------      ii       v     i v 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAG------------AACAAAGTTGGAGGACTCACACTTC 223

  chrX_42875543_4    618 CTAACTTCAAA--------------TACAG-------------------- 633
                          i  i      --------------     --------------------
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_42875543_4    634 --------------ACACATAGACCAATGAAATAGCATAAAGAACCCAGA 669
                         --------------   i     i     i     v  vi   ii     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_42875543_4    670 AACAAATCCACACACCAACAGGGAACTCATTTTCAACAAAACTGCCAAGA 719
                           i   i   i   iiv ii vv  i v      i    iiv        
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_42875543_4    720 ACATACACTGTTTAAAATAAAGTCTCTTCAATAAATGGTGCTGGGAAAAC 769
                         v   v  v  vvv   iv v     i     i              v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_42875543_4    770 TGGATATACATATGCAAAAGAATGAAACTATACCCCTATCTTTCACCATA 819
                               ?v  i               ii iv       i  iv       
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_42875543_4    820 AATGAAAATCAAATCAAAATAGCTTA-AAACTTAAATCTAAGACTTCAAA 868
                         v ii     i  v       i v i - i  i     v     vi v   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_42875543_4    869 ATATGAAACTATTAAGAGAAAATATTGAGGAAAATCTCTAGGACATTAGT 918
                         v   i     v   ii      i  v i? v      iiiv   v  i v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_42875543_4    919 CTGTGCAAAGATATCTTGAGCAATACCCCACAAGCACAGGCAAAACAAGC 968
                         i iv    v i v    iiii vv  v   v       i    v v   v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_42875543_4    969 ACAAATGGACAAATGGGATCGCATCAAG-TTAAAAAGCTTCTGCACAGCA 1017
                          v    i  i    v   iiv      i-       -   i  ii vv  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCA 672

  chrX_42875543_4   1018 AAGG-CAACATCAATAAAGTGAAGAGACAACCCACAAAATGGGAGAAAAT 1066
                             -  vi     v        i            i             
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_42875543_4   1067 ATTTGCAAACTACCTATCTCACAAGGAATTAATAACCAGAATATATAAGG 1116
                                  ii iv     v i    i i vi  v             i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_42875543_4   1117 AACTCAAACAACTC--T--TGGAAAAATCTAATGATCCAATCAAAAAAAC 1162
                              vv       -- -- ii   i - v   i i     i?     -i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAA-T 820

  chrX_42875543_4   1163 GGGCAAATGATTTGACTCGACATTTCT------AAGACATACAAATGGCA 1206
                                v       v v         ------    i           v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_42875543_4   1207 AACAAGCATATGAAAAGGTGCTTGACATCACTGATCAG 1244
                           i     i        i    ii      ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (103 / 65)
Gap_init rate = 0.02 (12 / 773), avg. gap size = 6.33 (76 / 12)  


2536 26.04 1.89 1.54  chrX_42895580_42901094.rev      511  1355 (4160)    L1M4_orf2#LINE/L1       61   908 (0)  

  chrX_42895580_4    511 CTCAAAGCAATCTACAGATTCAATGAAATTCTTATCACA-TCACCAACAT 559
                          i    vii              i v   i i     v -  -   i vv
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC-CCAGCTG 109

  chrX_42895580_4    560 CATTTTTCACAGAACAATAACAAAAAAAAATTAAAATTAATAC--AAACC 607
                          v     ii     - v i    ivvi vvi       v   i--   iv
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_42895580_4    608 CCAAAAAAGAGCCCA-AATAGCCAAAGGAATCCTAAGCAAAAAGAATAAA 656
                          ----  i ii    -          iv    i i iv  i     i   
  L1M4_orf2#LINE/    159 C----AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_42895580_4    657 TCTGGAGGAATCAAATTACCTGACTTCAAATTATACTACAAGGCTAAAGT 706
                         vi       v   v i v  ii i      viv        i    v   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_42895580_4    707 AACTAAAACAGTATTGTACTGGTACAAAAATAAACACATAGACCAATGGA 756
                           ii  i     i v       i i  ii   i   i     i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_42895580_4    757 ACAGAATAGAGAACCCGAAAGTAAAGCCACATATCTACAACCACCTGATC 806
                          i     v    ii  ii  i    v   i i  i  iiii  vi    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_42895580_4    807 TTTGACAAAGGTGACAAAAGTAAACACTGTGGAAAGGACGTCCTTTTCAA 856
                           i     i    v   i vi vv  v  v      i iivi        
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_42895580_4    857 TAAATAGTGCTGGGAAATTTTTCTAGCCATTTGTAGAAGAATGAAACTGG 906
                         i    i         v vi vvv  ?   iv  i i         ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_42895580_4    907 ACCCCTATCTCTCACCATATACAAACATCAACTAAAGATGAATTAAAAAT 956
                                i   v             v  i    v  i   i  i ? i i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_42895580_4    957 GTAAAT-TACAAAAC-ATAACT-TAAACAATTCTAGAAGAAAATCTAGGA 1003
                         v     -  - i i - v    -    - v ii          iv    ?
  L1M4_orf2#LINE/    505 CTAAATGTA-AGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGN 552

  chrX_42895580_4   1004 AATACTCTT-GTGGACATTGGCCTAGGCAAAAAATTTATGACAAA-GACC 1051
                         ivv v    -   -  v    vi       vii-   v v v v -   v
  L1M4_orf2#LINE/    553 GTAAATCTTCGTG-ACCTTGGGTTAGGCAATGG-TTTCTTAGATATGACA 600

  chrX_42895580_4   1052 CCAAAAGCAAATGCGACAAAA-ACAAAATATACAAATGGGACTTAATTAA 1100
                                  v v  i      - v      v i    v      v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_42895580_4   1101 ACTAAAAAGCTTCT-TACAGCAAAAGAAATAATCAGAAGAGCAAACAGAC 1149
                          v v    i   i - i vv    i  v iv    ii i  ii  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_42895580_4   1150 AACCTACAGAATAGGATAAAATATTTGAAAATTATGGTTCCAACAAAGGA 1199
                             i       i   v          v    i  ivv  ii i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_42895580_4   1200 CTAATATCTAAAATCTATAAGAAACTC----AATTCAACAAGAAGTAAGC 1245
                           vi    i i   v     ii     ----  i    i  v  iv ii 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_42895580_4   1246 AAACAACCTCATT-AACAGTGGACAAAGTACATGAACAGTCATGTCCTCT 1294
                            i    iv   -  v i   i     v iv    i  v   - i   i
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT-TTCTCC 849

  chrX_42895580_4   1295 TAAAGGAAAATATACAAGTGGCCAATAAACACATGAAAAAATGCTCAACA 1344
                         --  i   i        i          i          i          
  L1M4_orf2#LINE/    850 --AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_42895580_4   1345 TTACTAATCAT 1355
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.61 (134 / 83)
Gap_init rate = 0.02 (21 / 848), avg. gap size = 1.38 (29 / 21)  

3120 22.97 3.34 2.12  chrX_42895580_42901094.rev     4128  5024 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42895580_4   4128 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATCTTGTTAAAAT 4177
                               i i  i     i        v      v i   v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42895580_4   4178 GGCTATATGATCCAAAGTAATTCACAGATTCAATGCTATACCTATCAAAC 4227
                            v   ivvi     v i  ii          i  v  v         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42895580_4   4228 AACCAACAACCTTTTTCACAGAA-TTGGAACAAAAGGATTCTCAAATCCA 4276
                         vv   i vi       ii     -   --    ivv   i  v    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_42895580_4   4277 TATGGAACTAAAAGAGAGCCTGAATAGTCAAAGCAATCTTAAGCAAAAAG 4326
                                v iv   i  v  v      i    i       i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_42895580_4   4327 AACAAAGCTGGAGGTATCACACTACTCAACTTCAAATCATACTACAAGTC 4376
                                i      vv       v i   i      v v        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_42895580_4   4377 TACAGTAACTAAAATAGCATGGTACTGGTATAAAAACAAACACATAGACC 4426
                                 ii  i i  ii         i    ii i i   i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_42895580_4   4427 AATGGAACAGG-TT------CCAGAAATAAGGCTGCACACCTACAGCCAT 4469
                                i  i-  ------          iv iii   ii  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_42895580_4   4470 CTGATCTTTGACAAAGGTGACAAAAACAAGCAATGGGGAA----TAGGCT 4515
                         i    i  i     i    v   i v  vv          ----   ---
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG--- 395

  chrX_42895580_4   4516 CTCTATTCAATAAATGGTGGTGAGATAACTGGCTAGCCATATGCAGAAGA 4565
                         -   v     i        v  i  i      v  ?   i     i    
  L1M4_orf2#LINE/    396 -TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_42895580_4   4566 TTGAAGCTGGACCCCTACATTTCACTGTATACAAAAACCAACTCAAAATG 4615
                         v     i           v iv   ii          ii           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_42895580_4   4616 GATTAAAGACTTAAACATAAAATGTAAAACTATAAAGACCCTAGAAGAAA 4665
                            i ?    i    ii   i vv            ivi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_42895580_4   4666 ATCTAGG---AAATACCATTCTGTATATTGGCCCAGGTAAAAA---CTTA 4709
                          iv    ---    -- v iv  - iv    vii   i  vii---    
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--CTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_42895580_4   4710 ATGATGAAGACTCCAAAAGCAATTGAAAAACAAATAAACAAAAATTGA-A 4758
                         --   - v   v         --ii iv      - i -      v  - 
  L1M4_orf2#LINE/    592 --GAT-ATGACACCAAAAGCA--CAAGCAACAAA-AGA-AAAAATAGATA 634

  chrX_42895580_4   4759 AAGTGGGTT--AT---AACTAAACAGCTTCTGCACAGCCAAAAAAAAAAA 4803
                           v   ii --  ---  i    - i   i  ii vv --   ii v vv
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTC--AAAGGACACT 681

  chrX_42895580_4   4804 ATTAAGA--GTAAACAGACAACCTACAGAATGTGATAAAATATTTGCAAA 4851
                           i    --  i  v        i        v  v              
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_42895580_4   4852 CTATGCATGCAACAAAGGTTTAATATCCTGAATCTATAAGGAACCCAAAC 4901
                         ii  ii  vii i  i  vi vi     v    v     i    i vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_42895580_4   4902 AAATCAACAAGCAAAA----AATAACCCCATTACAAAATGGGCAAAGGAT 4947
                           v    i  vv    ----        v   ?v                
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_42895580_4   4948 ATGAGCAGACACTTCTCAAAAGAAGACATACACACGACCAACAAGCATAT 4997
                         v   ii     i     v        i     v i i    i     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_42895580_4   4998 GTAAAAATAGTCAACATCACTAATTAT 5024
                          v   i  iv         ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (125 / 78)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.23 (49 / 22)  


3257 27.09 0.44 0.44  chrX_42921955_42927793.rev     4441  5348 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42921955_4   4441 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4490
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42921955_4   4491 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4540
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42921955_4   4541 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4588
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_42921955_4   4589 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4638
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_42921955_4   4639 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4688
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_42921955_4   4689 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4738
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_42921955_4   4739 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 4786
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_42921955_4   4787 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4836
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_42921955_4   4837 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4886
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_42921955_4   4887 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4936
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_42921955_4   4937 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4986
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_42921955_4   4987 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5036
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_42921955_4   5037 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5086
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_42921955_4   5087 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5136
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_42921955_4   5137 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5186
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_42921955_4   5187 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5236
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_42921955_4   5237 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5286
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_42921955_4   5287 TCAAAAGAAGACATTTATGCAGCCAGAAAACACAGGAAGAAATGCTCATC 5336
                           v        i  vi viii    iv  i    v   i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_42921955_4   5337 ATCACTGTCCAT 5348
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2862 27.40 0.00 3.20  chrX_42936255_42940573.rev     2891  3828 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42936255_4   2891 TGGAAACACATGCCATTGTCCTGGATGGGTAGAATTAGTATTGTGAAAAT 2940
                               v i  v    vv  v     v  v   v   i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42936255_4   2941 GATCATACCACCAAAAGCAATCTGCAAATTCAATGCAATTCCCATGAAAA 2990
                          iiv    iv  v   vii    i  i      i     i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42936255_4   2991 TACCACCATCATTCTTCACAGAACTAGGAAAAACAATCCTAAAATTCATA 3040
                          v   v vv v  i  ii     v v iv  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_42936255_4   3041 TGGAACCAAGAAAGATCCCACATAGCCAAAGCAGGACTAAGCAAAAAGAA 3090
                              viivi ii  i  viv         i  ivvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_42936255_4   3091 CAAATTTGGAGGCATTGCATTACCTGACTTCAAACTATACCAAACATCCA 3140
                             v       vv ii  i v  ii i      viv   i v v v i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_42936255_4   3141 TAGTCACCAAAGCAGCATGGTACTGGTATAAAAATAGGCATACAGACCGA 3190
                         i   v i   ii   ii         i    ii    i    i   i i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_42936255_4   3191 TGAAACAAAAGAGAGAATGCAGAAATAAAGCCAAATACTTACAGCCAACT 3240
                           i  i i  vv    i v          v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_42936255_4   3241 GATCCTTGACAAAGGAAATAAAAACATAAAGTGGGGAAAGGACACCCTAT 3290
                            ii i     i  vivi  i v   vv i         i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_42936255_4   3291 TCAACACATGGTGCTGGAATAATTGACAAGCCACATGTAGGAGAATGAAA 3340
                               v          i i  i  ivv ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_42936255_4   3341 CTGGATCCTCATCTCTTACCTTATACAAAAATCAACTCAAGATGGATCAA 3390
                         i    i  ii i   vi   v           i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_42936255_4   3391 AGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACATCA 3440
                             i     v     v  i    i      v ii       v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_42936255_4   3441 GAAAAACCCTTTTAGATATTGGCTTAGTCAAAGACTTCATGTCCAAAAAC 3490
                          ?iv  vi   ivv  iv    v    v   v ii   v ivvi vi vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_42936255_4   3491 CCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGACTTAATTTA 3540
                                  v v         iv   i   i   i  v      v  iv 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_42936255_4   3541 ACTAAAAACCTTCTGCACAGCAACAAAACAAAAAACAAAAAAACCCCAAA 3590
                          v v    v   i  ii vv   - ii   ----- v -------i   i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAA-AGGACA-----CTA-------TCAAG 687

  chrX_42936255_4   3591 AAACCAGCAGAGTAAGCAGACAACCCACAGAGTGGGAGAAAATATTCACA 3640
                            --------  i iv              i              ii  
  L1M4_orf2#LINE/    688 AAA--------GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_42936255_4   3641 AACTATGCATCCAACAAAGGACTAATATCTGGAATCTACAAGGAACTCAA 3690
                           ii  ii   ii i  i     vi    ii    v  i  i      vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_42936255_4   3691 ACAAATCAGCAAAACAAACAAACAAAAAACAAATAATGCCATCAAAAAGT 3740
                             v   ii  v ---------    i        iv v  i?    i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATA---------AAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_42936255_4   3741 GGGCTAAGGACATGAATAGACAATTCTCAGCAGAAGATATACAGATGGCC 3790
                             v     iv          v     viv            i      
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_42936255_4   3791 AACAAACATATAAAAAAATGCTCAACATCACTAATTAT 3828
                           i  i  i  i    i             ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (151 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 6.00 (30 / 5)  


2694 25.93 4.19 1.36  chrX_42960410_42964127.rev     2345  3227 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_42960410_4   2345 TGGAAAAACATTCAATGCCCACAGATTGAAAGAATTAATATTGATAAAAT 2394
                               i i  i v   ii  ii     i    v         v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_42960410_4   2395 GACCATACTTCCTAAAGCAATCTACAGATTCAACACAATTCCTATCAAAT 2444
                          i v     i  i   vii               i    i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_42960410_4   2445 TACCAACATTATTTTTCACAGAACTAGAAGTAAA--AATTCTAAAATTCA 2492
                          v   i vviv     ii     v v  --i  i--i  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCA 148

  chrX_42960410_4   2493 TATGGAACAAAAAAGAACCT-GAATAGCCAAAGCAGTCCTAAGCAAAAGG 2541
                                vviv  i i   i-           i  i  i i iv  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_42960410_4   2542 AACCAAGCCAAAGCCATCATGTTACCCCACTTCAAGCTATAATACAAGGA 2591
                            v   iiii  vvv   iii v   v i     iviv  v     i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_42960410_4   2592 TATAGTAACCAAAACAGCATGCTGCTAATACAAAAATAAACACATAGATC 2641
                           i     i   i    ii  v i  iii i  ii   i   i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_42960410_4   2642 AATGGCATAGAATAGAGAAACTAGAAATAAATCCACACACTTATAACCAA 2691
                              v       v    iv i         i   i   i    iii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_42960410_4   2692 CTAATGCTTGACGAAG---TCAAGAAAAATAAACAGTGGGGAAAGAACA- 2737
                         i i  vi i   i i ---i     vv v ---  i           i -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAAGAATAG 395

  chrX_42960410_4   2738 TCTTATTCAATAAATGGTGTTGGGAAAGCTGGCTAACTATATGCAGAAGA 2787
                             -     i        i     v i    v  ? i i     i    
  L1M4_orf2#LINE/    396 TCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_42960410_4   2788 ATGAAACTGGACCCCGAC------------ACAAAAACTAACTTAAGATG 2825
                              ii        v  ------------       i     i  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_42960410_4   2826 GATTAAAGAATTAAATGTAAGACCTTAAGTGATAAAAATATAAGGAAAAA 2875
                            i ?   vi           v  v  iiv      v v v  -  i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG-AAGAA 543

  chrX_42960410_4   2876 AAC-TAAGA--AAAACAATTCTGGATATTGGCCTGAAGAAT------TTA 2916
                            -  i ?--   v --   vv  iv    vi iiiv   ------   
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_42960410_4   2917 TGACTAAGACCTTGAAAGCAAATGCAACAAAATAAAACTT-GACAATTGG 2965
                         -  -  v   viii      v v         v    vv -  i  v v 
  L1M4_orf2#LINE/    592 -GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_42960410_4   2966 GACTTAATTAAA-TTAAAGAGCTTCTGCACAGCCAAAGAAACTATCGCCA 3014
                              v  i   -     i -   i  ii vv v  i  v      ivv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_42960410_4   3015 GAGTAAACAGACAACCTTCAGAATGGGAGAAAATATTTGCAATCTATGCA 3064
                         i   i  v        iv                        vii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_42960410_4   3065 TCTGACAAAGGACTAACACCCAGA-TCTGTAAGTAACTTAAACAAATCAA 3113
                              i  i     vii i     - v i   iv    ivv    v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_42960410_4   3114 CAAGAGAAA-ACAAGTAGCCCCATTAAAAAGTAGGCCAAGGAC----ACA 3158
                         i  v i   -    i  i   v   ?    i i   v     i---- i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_42960410_4   3159 GACACTTCTCAAAAGAAGTCAGACAAGCAGCCAACAAATA-ATGAAAACA 3207
                             i     v       vi v    iii     i  ii -       v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_42960410_4   3208 TGTTCAGCATCACTAATCAT 3227
                           i   i     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (143 / 82)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.23 (49 / 22)  


2873 25.51 4.08 1.13  chrX_43025069_43029336.rev     2896  3777 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_43025069_4   2896 TGGAAAGATATTTTAATTTTTATTGATTGGAAAACTCAATATTATTAAAA 2945
                                    iii - v  i  v        i   i      i    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCA-TGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_43025069_4   2946 TATAAATTCTTCCCAACTTGATCCACAGATGCAATGCAATATCAAT-AAA 2994
                          ivv   v  i     v      i      v   i     vi v  -   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_43025069_4   2995 TTCCTAGCAAATTATTTTG-AAATATCTATAAACTGATTGTAAAGTTTAT 3043
                         v   i   vivi v     - i v  iv i  i     iv    i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_43025069_4   3044 ATAAAAA-GCAAAAGATCTAGAATATCCAACATGATAATGAAGAAAAAGA 3092
                           ii   -    ii  i i      v    v ii  vv    i  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_43025069_4   3093 ACAA-GTTGCAACACTCTCGCTACCTGATTTCAAGTCTTAATATAAAACT 3141
                             -    v iv    v i  v  ii       iv    v  i   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_43025069_4   3142 ACAACAATCAAGAAAGCATAGTGTAAGTGAAAGAATAGACACACTGATCA 3191
                            ii        v  ii i  iivi iiv   i       i iv     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_43025069_4   3192 ATGGAACAGAATTGATAGCCCATATACAGACCAATA--TTAATATAGTCA 3239
                               i        v  i   v v i i   v   --  --   i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCA 347

  chrX_43025069_4   3240 GTTGATTTTTGACAAAGAAGCAAAGGCAATTTAATGAAGAAAGAATATTG 3289
                         i        i     i iv  v   i v   i    ii         v v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_43025069_4   3290 TTTTAAACAAATGGTGCCAGAACAATTGGATGTCCCCACCATGGGGGGAG 3339
                             v            ii i    i     i?  v  i-iiiiii i v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAAT 446

  chrX_43025069_4   3340 AAACCT--ACTCATAGACCTTACACCTTTCAGAAAAATGAACTCAATATG 3387
                         i  vi --  i v  --   i     v vi v      v       v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_43025069_4   3388 GATTATAGACCTAAATGAAAATGGCAAAACTATAAAACTCCTAGAAGAAA 3437
                            i ?           v  iv vi               i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_43025069_4   3438 ACATAGGAAGAAATATAAGTGACCTTAGGAT-GATGATGAATTTTTAGAT 3486
                                ?iv    v vv        i  v - iii   iv  i      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_43025069_4   3487 ACAATACCAAAAGCATGATCTATGAAAAAAAAGAAATTGATG--TTGGAT 3534
                          ii i          ii v v ii   i    --   v   i--     i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAA--AATAGATAAATTGGAC 642

  chrX_43025069_4   3535 TTTGTTAAAATGAAAAAAATTTGCTCTGTGAAAGACTATGTTA-GAGAAT 3583
                           ii i     v     vv    iv  vii  i   vv i i -  i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_43025069_4   3584 GAAAAGGCAAGCCATGGTCTGGGAGAAAATATTTTCAAAAAAAA-ATCTG 3632
                               i   v   ii vv               v    vv v -     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_43025069_4   3633 ATAAACGACTTGTACCCAAAATTTATAAATAACACCTAAAACATC----- 3677
                             iv        i   i   v      v   v i  v   -  -----
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAATAA 791

  chrX_43025069_4   3678 --------CA-----CCTAATTTAAAAA-----AAATAGATCTGAACAGA 3709
                         --------  -----  i    ?     -----   -i   i    i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA-GGATTTGAATAGA 840

  chrX_43025069_4   3710 CATCTCATCAAAGAAGACATGCAAATGGCAAATAAATATACAAGAAGATG 3759
                            i  vi         i  i        v     ii i ii i      
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_43025069_4   3760 TTCAACATTATTTGTCAT 3777
                         i       i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (139 / 82)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.30 (46 / 20)  


 979 24.78 0.66 12.61  chrX_43043597_43045256.rev        1   452 (1208)    L1M4_orf2#LINE/L1        4   401 (507)  

  chrX_43043597_4      1 AAAGGTATAACATGGTCATAGTTTGGAAGATTCAACATAGCAGAGATGGT 50
                             i   vv    v    i v        i i  i  v ivi      i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_43043597_4     51 ACTTTTCCTCAAATTGATCTATAGGTTTTAATGCAATTCCTATCAAAAGC 100
                          v vi   i            i  i  i-  i     i          v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTC-AACGCAATCCCTATCAAAATC 102

  chrX_43043597_4    101 CCAGCAAG--TTTTTGTAGACATATTTAAGCTTGTTCCAAGACTTATATG 148
                              viv--      i   v  vvvi     vi i i  i i i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_43043597_4    149 GAGAGCCACAGGCTCAAGTATAGCCAACATCATCTTGAAGAACTATGAGA 198
                           i vv  vi  vi v  v        v iv        i  -------i
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA-------G 195

  chrX_43043597_4    199 AAGTGCTCTACCTAACATTTAGGCCGGATTTATAGCTAGAGTATTTATGT 248
                            ----------    -------------- -  i i   v i i ---
  L1M4_orf2#LINE/    196 AAG----------AACA--------------A-AGTTGGAGGACTCA--- 217

  chrX_43043597_4    249 GTGAACACTCTAGCTATATATTAGTATGATATTGGTGTAGAGATAGATAC 298
                         -----    ii-- i -  v i iv i----  iv ii i  v  ---- 
  L1M4_orf2#LINE/    218 -----CACTTC--CCA-ATTTCAAAAC----TTACTACAAAGCTA----C 251

  chrX_43043597_4    299 AAAGAACAATTGGTATTAGTGTTGTACAGGTGGAGGAATAGATACATAGA 348
                          ivi v   -- ii ---    v    v  iiv i i     i i     
  L1M4_orf2#LINE/    252 AGTAATCAA--GACA---GTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_43043597_4    349 TCATTGGAACAGAATAGAGAGCCCAGAACTGC-TCTATACAAGTATGGCC 397
                            v     i     v     i      v iv-i i     vv     i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_43043597_4    398 AACTGATTTTTGACAAGGGTACAAAGGCAATTCAATGGAGGAAAGATGAT 447
                           i       i         i v   i v         i i  ii  ii 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_43043597_4    448 CTTTT 452
                              
  L1M4_orf2#LINE/    397 CTTTT 401

Transitions / transversions = 1.67 (70 / 42)
Gap_init rate = 0.04 (14 / 398), avg. gap size = 4.29 (60 / 14)  

 202 25.93 0.00 0.00  chrX_43043597_43045256.rev      450   503 (1157)  C L1M4_orf2#LINE/L1   (673)   235   182 *

C chrX_43043597_4    503 CAATGCTAAGCAAAAAGAACAAAGCTGGAGGCATCATGCTACCCAACTTC 454
                             vi i iv  i          i      vv   ii  v     i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

C chrX_43043597_4    453 TAAA 450
                         v   
  L1M4_orf2#LINE/    232 AAAA 235

Transitions / transversions = 1.33 (8 / 6)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.00 (0 / 0)  

1993 27.23 3.18 1.36  chrX_43043597_43045256.rev      501  1161 (499)    L1M4_orf2#LINE/L1      206   878 (30)  

  chrX_43043597_4    501 TTGGAGTCATCACACTATCTGACTTTAAACTATATCACAAGGCTA-AGTA 549
                               vvv       vi ii i  i   viv  ii    i    -    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_43043597_4    550 ACCAAAACTGCATGGTACTGGTACAAAAACAGTCGCATAGACAAATGGAA 599
                          i   i  v ii         i i  ii i  v ii     iv       
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_43043597_4    600 CAGAATAGAAAACTCAGAAATAAGACTGCACATCTACAACCAACTGATCT 649
                         i     v  i iii         iv iii    i  iiii   i    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_43043597_4    650 TCAACAAACCTCACAAAAACAAGCAACAGGGGAAAGGAT-TTCTTATTTA 698
                           i    ivv vv   i v  vv   i-        i  -v    -  i 
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTT-TTCA 403

  chrX_43043597_4    699 ATAAATATTGCTGGGAGAGTGGGCCAGCCATATGCAGAAAATTGAAACTG 748
                          i    iv        v iiv  vi ?   i     i  i v    ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_43043597_4    749 GACCCCTTCCTTACACCTTAAACAAAAATTAACTCAAGATGGATTAAAGA 798
                                v   i     v  v                i      i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_43043597_4    799 CTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGAAAATCTAGGCA 848
                          i         i v i            vi i          iv    ?-
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN- 552

  chrX_43043597_4    849 GTT--TCATTCAGGACATAGGCATGGGCAAAGATTTCAT-GATGAAATCA 895
                           v--  -   iv   v v  vv i     v i    v -   ivi -  
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-CA 600

  chrX_43043597_4    896 CCAAAAGCAAATGCAACAAAAGCAAAAATTGACAAATGGGGCCT------ 939
                                  v v          v      v  i    v  i i ------
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_43043597_4    940 AATTAAAGAGCTTCTGTACAGCAAAAGAAACTATCATCAGAATGAACAGG 989
                                i -   i   i vv    i  v       vv i i    v  i
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_43043597_4    990 CAACCTAGAGAGTGGGAGAAAATTTTTACAATCTATCCATCTTGTAA--- 1036
                              i v   i           v   i   vii  vi    vi   ---
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_43043597_4   1037 --TTTTGTTTAAGTTCCTTGTAGA--TCCTGGATATT--ACAAGAAAAAA 1080
                         --  v i ii iiv viv iv   --  i iv - i -- i  v     i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCAATAATAAAAAG 798

  chrX_43043597_4   1081 ACAAACGACCTCATTAAAAAGCGGGCAAAGGACACATATAGGCACTTCTC 1130
                              ii   iv   ?    ii          iviiv    i  i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_43043597_4   1131 -AAAGATAAGATATTCATGTGGCCAACAAACA 1161
                         -     --      v  vi       i  i  
  L1M4_orf2#LINE/    849 CAAAGA--AGATATACAAATGGCCAATAAGCA 878

Transitions / transversions = 1.63 (109 / 67)
Gap_init rate = 0.03 (17 / 673), avg. gap size = 1.76 (30 / 17)  


 366 29.03 0.00 0.00  chrX_43103127_43108744     3908  4000 (1618)    L1M4_orf2#LINE/L1        1    93 (815)  

  chrX_43103127_4   3908 TGGACAAACATGCCATGCTCCTGGATAGAAAGAATCAATATCATTTAAAT 3957
                             v i i  v     i  v     v i    v i     ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_43103127_4   3958 GGCCATACTGCCCAAAGCAATTTATGGATTCAATACTATTTCT 4000
                            v     v      vii  i  ii       ii v  ii  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.00 (0 / 0)  

2729 25.21 4.14 1.95  chrX_43103127_43108744     4305  5125 (493)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_43103127_4   4305 ATTTATGGATTCAATACTATTTCTATCAAACTATCAATGACATTGTTTAC 4354
                           i  ii       ii v  ii        v vi  iivi v  v   i 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_43103127_4   4355 AGAACTAGAAAAAAAAACTATTTATAAA-TTCACATGTAACCAAAAAAGA 4403
                             v v  v  i----  iv iv    -    i   v  viiv  ii  
  L1M4_orf2#LINE/    120 AGAAATTGACAAG----CTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_43103127_4   4404 GCCCAAATAGCCAAGGCAATCCTAAGCACAAAGAACAAAACTGGAGGCAT 4453
                         v  vi         ii     i i iv vi         ii      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_43103127_4   4454 CATGCTACCTGACTTCAAACTATACTACAAGGCTACACTAGCCAAAACAG 4503
                           ii  v  ii i      viv        i      v  ii   i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_43103127_4   4504 CATGGTACTGGTACAAAAAACAGACACATAGACCAATGGAACAGAATAGA 4553
                         ii         i i  ii -i     i     i        i     v  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_43103127_4   4554 GAACCCAGAAATAAATCTGCACACCTGCAACCATCTGATCTTCAACAAAG 4603
                           ii           i iii   ii iiiii  vi    i   i    i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_43103127_4   4604 CTGACAAGAAAAG-CAATGGAGAAAGGAT--TCCTTATTCAATAAATGGT 4650
                         v  v     vv v-      i     i  --  i  --    i       
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGT 412

  chrX_43103127_4   4651 GCTAGGATAACTGGCTAGCCATATGCAGAAGATTGAAACTGGACCCCTTC 4700
                            i   i      v  ?   i     i    v    ii         v 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_43103127_4   4701 CTTACACCATATACAAAAATTAA-----GATGGATTAAAGACTTAAATGT 4745
                           i                    -----i      i ?    i       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_43103127_4   4746 AAAACCCAAAACTATAAAAA-CTTAGAAGAAAACATAGG---AAATATGA 4791
                           i v i            v-                  ---    v --
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT-- 560

  chrX_43103127_4   4792 TTCTGGACATAGGAATGAACAAAGATTT------TATGACAAAGATGCCA 4835
                         -  vv   v v  iv iii   v i   ------       ------   
  L1M4_orf2#LINE/    561 -TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA------CCA 603

  chrX_43103127_4   4836 AAAGCAATTGCAACGAAAGTAAAAATTGACAAATGGGATCT-------GT 4878
                               vvv     i    v      v  i    v   ii -------i 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_43103127_4   4879 TGATAGCTCCTGCACAGCAAAAGGAGCTATCGACAGAGTAAAGAGACAAC 4928
                          i v i  ii  ii vv    i ivi     i v i   i  i       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_43103127_4   4929 CTGCAGAATGGGAGAAAATATTTGCGAACTGTACATCTGACAAAGGTCTA 4978
                          ii                      i  iii  i      i  i  v  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_43103127_4   4979 ATATCCAGCATCTATAAGGCACTTAAACAAATTTACAAGATAAA----AA 5024
                         i       v  v     i v   ivv    v iv i  v v   ----  
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_43103127_4   5025 TAACCCCATTAAAACGTGGGCAAAAGACATGAA----CTCTTTTCAAAAG 5070
                               v   ?   vi        i  iv    ---- vi  i  v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_43103127_4   5071 AAGGCAGACATGTGGCCAAGAAGCATATGAACAAAAGCTCAACATCACTG 5120
                            ii v   vi       v     i     v i v           ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_43103127_4   5121 ATCAT 5125
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.72 (129 / 75)
Gap_init rate = 0.02 (15 / 839), avg. gap size = 3.33 (50 / 15)  


3310 26.76 0.44 0.44  chrX_43286195_43292598.rev     5006  5913 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_43286195_4   5006 TGGAAGAACATCCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAACC 5055
                              ii i        i      i v      v i        v  ivi
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_43286195_4   5056 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGGCATCCCCATCAAGC 5105
                            v     v     iv i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_43286195_4   5106 TACCAATGACTTTCTTCACATAA-TTGGAAAAAACT-ACTTTAAACTTCA 5153
                          v   iivi i  i  ii  v  -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_43286195_4   5154 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5203
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_43286195_4   5204 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5253
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_43286195_4   5254 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5303
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_43286195_4   5304 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5351
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_43286195_4   5352 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5401
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_43286195_4   5402 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5451
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_43286195_4   5452 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5501
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_43286195_4   5502 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5551
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_43286195_4   5552 CTAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAA 5601
                         v    ?i v viv   iv   v v  vv i i   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_43286195_4   5602 AACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5651
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_43286195_4   5652 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAAC 5701
                          i   v v  i i   i  ii vv    i  v    i ivv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_43286195_4   5702 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5751
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_43286195_4   5752 AGGGCTAATGTCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5801
                         i  i  vi i        v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_43286195_4   5802 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5851
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_43286195_4   5852 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5901
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_43286195_4   5902 ATCACTGGCCAT 5913
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


4401 15.60 3.43 3.54  chrX_43318926_43321872     1551  2454 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_43318926_4   1551 AGGCATCCTGTGTTCATGGA--------CTTAATATTGTTAGGGTGACAA 1592
                           ii    ii          --------             i i  i   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_43318926_4   1593 TACTTCCCAAATTGAACTACGTTTTTAACACAATCCCTTTCAAGATCCTA 1642
                             i          v    ivv  i   i        v    i    i 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_43318926_4   1643 GCTGACAGTTTTTGCAGAAATTGGGAGATTGATCCTAAAATGTATATGTA 1692
                             v -v               iv iii            vi     v 
  L1M4_orf2#LINE/    106 GCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_43318926_4   1693 AATGTGAGAGACCCATAATAGCCAAAGCAGTTTTAAAAGAGAAGAACAAA 1742
                             ii  i      v          i  i i  i   i           
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_43318926_4   1743 TTTGAAGGACCCACACTTCCTGATTTCAAAAATTACTATGAAGCTAGTGT 1792
                         v   i     i         ii         v      ii      ----
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA---- 250

  chrX_43318926_4   1793 GCTAAAACAATGTGTACTTGTATAAAAACAATGTG-TACTTCTATAAGGA 1841
                         -------  ----   -----  v  i   i    -    vvi       
  L1M4_orf2#LINE/    251 -------CA----GTA-----ATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_43318926_4   1842 TAAACATATAGGTAAATGGAGTAGAACTGTGATTTCAGAAATAAACCCTT 1891
                           i        i v      i     i  v  v i             v 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_43318926_4   1892 ACATTTATGCCCAATTGATTTTTGTCAAGGGTAGCAAGACAACTCAGTGC 1941
                                  vi           i v       iv      v i   i  v
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_43318926_4   1942 AAAAAGTAAAATAAGTTATTTCAACAAATGTTGTTGGAACGACTGGATAT 1991
                         ii    ---    -  iv            v  i   i  i        ?
  L1M4_orf2#LINE/    385 GGAAAG---AATA-GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_43318926_4   1992 CCACATGCAAAAGAATGAAGCTGGACTTCT-TCTCACACTATACACAAAC 2040
                                             i     ii  -i       i   i     v
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_43318926_4   2041 ATTAACTCA-------TTTTAGACCTAACTATAAGAGCTAAAAATATAAA 2083
                                  ------- iv?        v i            v      
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_43318926_4   2084 ACTCCTGGAAGAAAAAATAA---TAAATCTCTGTGA------GTTAGGCA 2124
                             i i        v   i---       ii    ------        
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_43318926_4   2125 GTGATTTATTTGAT--GATACTGAAAGCACAAGCAACAGAAGAAAAAATA 2172
                         i  i   v  v   --  i  ii               i           
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_43318926_4   2173 GATAAATTGGTCTTCATCAAAA---AAAGTTTTTGAAGTGTTGTCATTTG 2219
                                   v           ---   ii     ---  i -   vvv 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTG---TGCT-TCAAAGG 676

  chrX_43318926_4   2220 TATACCATCAAGAAACTGAAAAGACAATCCATAGAATGGGAGAAAATATT 2269
                         - i  i         v           i   i                  
  L1M4_orf2#LINE/    677 -ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_43318926_4   2270 TGCAAATCATATATCTGATAAAGGACTTGTATTCCGAACATATAAAGAAC 2319
                                              i          i v   i           
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_43318926_4   2320 TCTAACAACTCAATAATAAAAAGACAAACAACCCAATTCAAAAATGGACA 2369
                            v                        i         ?        i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_43318926_4   2370 AAGGACTTGAATAGATACTTTGCCAAAAAAAAGATATGCACATGATCAAT 2419
                              i         i i  iv     i  --     i  v   ii    
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAA--GATATACAAATGGCCAAT 873

  chrX_43318926_4   2420 AAGCATCTGAAAAGATGATCAATGTTATTAGTTAT 2454
                              iv          v    ii i ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (94 / 44)
Gap_init rate = 0.02 (18 / 903), avg. gap size = 3.50 (63 / 18)  


3144 26.71 1.10 0.88  chrX_43337442_43343949.rev     5112  6017 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_43337442_4   5112 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCACGAAAAT 5161
                              ii i  i     i        v      v i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_43337442_4   5162 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 5211
                            v     v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_43337442_4   5212 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTC 5258
                          v   -   v    i  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_43337442_4   5259 ATATGGAACCAAAAAAAGAGCCC-GCATAGCCAAGACAATCCTAAGCAAA 5307
                                 -- viv  i ii   - v        i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_43337442_4   5308 AAGGACAAAGCTGGAGGCATCACGTTACCTGACTTCAAACTATACTACAA 5357
                            i      i      vv    ii v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_43337442_4   5358 GGTTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAT 5407
                         i i        i   i    ii         i iv ii i   i     -
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA- 294

  chrX_43337442_4   5408 AGACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACA 5457
                         -  i        i    iv   ivii         vv   i    i  ii
  L1M4_orf2#LINE/    295 -GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_43337442_4   5458 ACCATTTGATCTTTGACAAAC-TGACAAAAACAAGCAACAGGGAAAGGAT 5506
                         ii  v     i  i     iv-  v   i v  vv   ii       i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_43337442_4   5507 TCCCTATTTAATAAATAGTGCTGGGAAAACTGGCTAGCCATATGCAGAAA 5556
                         vvi  v  i  i    i         v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_43337442_4   5557 GCTGAAATTGGATCCCTTCCTTACACTTTATACGAAAATTAACTCGAGAT 5606
                         iv    i     i    v   i    iv     i           i i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_43337442_4   5607 GGATTAAAGATTTAAACGTATAACTTAAAACCATAAAAACCCTAGAAGAA 5656
                             i ?   ii    i   vi vi      i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_43337442_4   5657 AACCTAGGCA-ATACCATTCAGGACATAGGGATGGACAAAGACTTCATAA 5705
                            v    ?i- v i -   iv   v v   v i i   v ii   v  i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_43337442_4   5706 CTAAAACACCAAAAGCAATAGCAACAAAAGCCAAAACAGACAAATGGGAT 5755
                         v  vi            vv           vv    i   i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_43337442_4   5756 CTAATTAAACTAAAGAGCTTTGGCACAGCAAAATAAATTATTATCAGAAT 5805
                         i v  i   v v  i i    v ii vv    iv v i   i vv i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_43337442_4   5806 TAACAGGCAGCCTACAGAATGGGAGAAAATTTTTGTAATCTACCCATCTG 5855
                         v  v  i  i  i                 v    i  vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_43337442_4   5856 ACAAAGGGCTAATATCCAGAATCTACAACGAACCTAAACAAATTTACAAG 5905
                          i  i  i  vi          v  i  v    iivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_43337442_4   5906 AAAGAAACAA----CCCTATCAAAAAATGGGCAAAGGATATGAACAGACA 5951
                            i i    ----   v  i?                 v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_43337442_4   5952 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACTTATGAAAAAATGTT 6001
                         i     v        i  vi viii     v  i vi       i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_43337442_4   6002 CATCATCACTGGTCAT 6017
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (149 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


3483 20.57 3.52 4.18  chrX_43503455_43505355.rev      502  1410 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_43503455_4    502 AGGTATCCCTTGTTTATGGATTG-AATAATTAATATTGTCAAAATGTTCA 550
                           i      v    i        -  v v          i  i   viv 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_43503455_4    551 TACTACCCAAAGTGATCTATAGATTCAAGG-AATCCC----AAAGTC--A 593
                             v      v       i        v -      ----   i  -- 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_43503455_4    594 ------TTTTTCAAAGAAATAGAATAAATGATCCTAAAATTCATATGGAA 637
                         ------     iiv      v  vv iv                      
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_43503455_4    638 ACACAAAAGACCCA-AATTGCCAAAACAATCTTGAGAGAGAAGAACAAAG 686
                          ii   ii      -   v                i i            
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_43503455_4    687 CTGGAGGCATCACGCTTCCTGGTTTCAAACTATGTTACAAAGCTATAGTA 736
                         i      vv    i     iii       viv ii          i    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_43503455_4    737 ATCAAAACAGTATGTTACTAGCATAAAAACAGACACACAGACCAATGAAA 786
                              i     i  v    i      ii i     i i   i     i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_43503455_4    787 CGTAGAA--GAGATCCCTGAAATAAACCCATGCATATATAGTCAATTAAT 834
                         --     --    vi  v             i   v   i       i  
  L1M4_orf2#LINE/    306 --TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_43503455_4    835 CTTTGACAAAGGTGCTAAGAAAACACAATCAAGAAAGGGCAGTCTCTTCC 884
                         i  i     i     i    vv iv    vii     iii     i   v
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_43503455_4    885 ACAAATGGTGTTGAGAAAATTGGGTATTCACATGCAAAATAATGAAATTG 934
                                   i  i  v  i   i  ?i           v      i   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_43503455_4    935 CATGCTTATCATGCACTGTATGCAAAAA------------GGAATATAGA 972
                         v iv i  i vii   ii   i      ------------   vi ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_43503455_4    973 CTTCATTAAATATAAGACCTGAAACCATAAAACACCTAGAAGAAAACA-G 1021
                          i ----    i     v  i    i       v i            -i
  L1M4_orf2#LINE/    504 CCT----AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_43503455_4   1022 GAAAAAAAACTCCTTGACATTGGTCTTGGCAGTGTTTCGTTGTTGTTGTT 1071
                          i?iv   v  i v    v    vi v    i  ----------------
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG---------------- 583

  chrX_43503455_4   1072 GTTGTTGTTGTTTTTTGGATATGATACCAAAAGCACAGGCAACAAAATAA 1121
                         ---------    i  i       i            i         v  
  L1M4_orf2#LINE/    584 ---------GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_43503455_4   1122 AAAATAAACAAGA-GGACTACATCAAACTAAGAAGTTTCTGCACAGCAAA 1170
                               i i  iv-     v       v v i  ii  i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_43503455_4   1171 GGAAACAGTCAACACTATGAAAAGGTTACT-ATGGAATAAGATAAAATAT 1219
                            v  vi    v vvi       iiv  i- ii    ii  v       
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_43503455_4   1220 TAGCAAATCATACATCTGATAAAAAGCTGGTATCCAAAATATAAAAGGAA 1269
                          v          i         iiii  v       i      v  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_43503455_4   1270 CTCATACAACTCAACAGTAAAACAAAAAAAATCAAATAACTCAATTAAAA 1319
                            v          i i     ------ i -        i     ?   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAA------AGA-CAAATAACCCAATTWAAA 817

  chrX_43503455_4   1320 AATGAGCAAAGGACCTGAATAGACATTTCTCCACATAAGACATACAAAAA 1369
                             i        ii                  v v    i       vi
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_43503455_4   1370 GCCAACAGACACCTGAAAGGGTGCTCAGCATCACTAATCAT 1410
                              i ii   v     i i      i     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (120 / 63)
Gap_init rate = 0.02 (16 / 903), avg. gap size = 4.38 (70 / 16)  


3256 27.12 0.33 0.22  chrX_43537650_43543385.rev     4339  5245 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_43537650_4   4339 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATTAATATCGTGAAAAT 4388
                               i i  i     i        v      v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_43537650_4   4389 GACCATACTGCCCAAAGTAATTGATAGATTCAATGCCATCCCCATCAAGC 4438
                          i v     v      v i  iv i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_43537650_4   4439 TACTATTGATTTTCTTCACAGAATTAGAAAAACCTACTTTTAATTTCATA 4488
                          v i viviii  i  ii     v v  v  i iv iii v  v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_43537650_4   4489 TGGAACAAAAAAGAGCCCCT--ATAGCCAAGACAATCCTGAGCAAAAAGA 4536
                              - viv   i v   v--        i      i   iv  i    
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_43537650_4   4537 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 4586
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_43537650_4   4587 ACAGTAACGAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 4636
                                iv  i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_43537650_4   4637 ATGGAACAGAACAGAGGCCTCAGAAGTAACACCACACATCTACAACCATC 4686
                               i    iv   ivii     i   vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_43537650_4   4687 TGGTCTTTGACAAACCTGACAAAAGCAAGCAATGGGGAAAGGATTCCCTA 4736
                           i i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_43537650_4   4737 TTTAAAAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 4786
                           i  v        i     v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_43537650_4   4787 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 4836
                         ii    i    v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_43537650_4   4837 AAGACTTAGACGTAAGACCTCAAACCATAAAAACCCTAGAAGAAAACCTA 4886
                         ?    i  i i      v  v    i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_43537650_4   4887 GGCA-ATACCATTCAGGACACAGGCATGGGCAAAGACTTCATGACTGAAA 4935
                           ?i- v i -   iv   viv  vv i     v ii   v iiv ivi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_43537650_4   4936 CACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAACGGGATCTAATT 4985
                                    vvii         vv     v  i   iv   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_43537650_4   4986 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5035
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_43537650_4   5036 GCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTATCCATCTGACAAAG 5085
                         i     i                 v      ivii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_43537650_4   5086 GGCCAATATCCAGAATCTACAAGCAACTTAAACAAATTTACAAGAAAAAA 5135
                          i ivi          v  i  iv    ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_43537650_4   5136 TCAAACAACCCCATCAAAAAGTGGGCAAAGAATAGGAACAGACACTTCTC 5185
                         v    i     v  i?    i         i  vv   i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_43537650_4   5186 AAAAGAAGACATTTATGTGGCCAAAAAACATATGGAAAAAAGCTCATCAT 5235
                         v        i  vi vi       v  i  i   i   i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_43537650_4   5236 CACTGGTCAT 5245
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.25 (5 / 4)  


3237 22.49 1.78 3.08  chrX_43621404_43623995      808  1652 (940)    L1M4_orf2#LINE/L1        1   834 (74)  

  chrX_43621404_4    808 TGAAAACACACCCTGTGTTCATGGACTGGAAGAATTAATGTTGTTAAAAT 857
                           i   v i i  ii          i       v     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_43621404_4    858 GTCCATAGTGTTCAAAAT-ATCTA--GATTCAATGCAATCTCTATCAAAA 904
                          v v   v vii    v -     --       i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_43621404_4    905 TTCCAA-TGTCATTTTTCACAGAAATAGAAAAAACAATCCTTAAATTCAT 953
                          i   i-  i -     ii       v  v  ivii     v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_43621404_4    954 A-GAAACCACACAAGACT--GAATAGCCAAAGCAGTCTTCGGCAAAAG-- 998
                          - i  vii  vii   i--           i  i    -- v     --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--GAAAAAGAA 197

  chrX_43621404_4    999 GAACAAAGCTGGAGGCATCACACTCCCTGGTTTCAAAATATACTATAAAG 1048
                                 i      vv       i  iii        iv     i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_43621404_4   1049 TTATTGTAATCAAAACAGTTATTGTAATCAAAACATGGTACAGGCATAAA 1098
                         i  iv        i     ---------------i      v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGT---------------GTGGTACTGGCATAAG 282

  chrX_43621404_4   1099 AACAGACACATCAATCAATGGAAGATGATAGAAAGCCCAGAAACAAACCC 1148
                         i i     i  vi          v vi  v  i  i       i      
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_43621404_4   1149 ACAACTTTACAGTCAAATGATTTTTGACAAAGGTGCCAAAACACA--CAA 1196
                          i vv    ii     v       i     i        i  -  --   
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAA 381

  chrX_43621404_4   1197 TAAAGAAAGGACAGTCTT--CAAAAAATGTTATTAGGTAACCTGGATATT 1244
                          iii     i i      --   v     v ii i  vv v       ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_43621404_4   1245 CACATGCAGAAGAATGAAAGTGGATGCTCATCTCACATCATATACAAAAA 1294
                                 i         iv    iv ii i      i            
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_43621404_4   1295 AAAAACCTCAAAATGGATTAAAGACTTAAATATAAGACCTGAAACTGTAA 1344
                         vv  --            i ?    i     i     v  i     i   
  L1M4_orf2#LINE/    482 TTAA--CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_43621404_4   1345 AGCTACTAGCAGAACACATAGGTGAAAAGCTTCAATACATTGATCTGGGC 1394
                          i  vi   v    v       ? v   v    ivv  v   ivi i   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_43621404_4   1395 AGTGATTTTTTTTGTATAGGTCCCCAAAAGCACAGGGAACAAAAGTGAAA 1444
                          i  i   i  --iv   v v v           i v        vi   
  L1M4_orf2#LINE/    580 AATGGTTTCTT--AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_43621404_4   1445 ATAGGCAAATAAGACTGCATCAAACTAAACAGCTTCTGCACAGCAAAGGC 1494
                             ii    vi    v       v v  v i   i  ii vv      v
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_43621404_4   1495 CACAATTAACAAAGTGATGAGACAACCCAT-GAGTGGGAGAAAATATTTG 1543
                            v  i  v       vi          i-  i                
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_43621404_4   1544 CAAACCATCCATCTGGTAAAGGGTTAATATACAAAATATCTAAAGCATTC 1593
                             i   vi     i   i  ii vi   v  i     v     v i  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_43621404_4   1594 ATACAGCTCAATGGCAAGA-GACAAATAACCTGATTTTTTTTAAATGGAC 1642
                         v    i      iii  i -           ii   ?vv---      i 
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA---AAATGGGC 824

  chrX_43621404_4   1643 AAAGGACTTG 1652
                               i   
  L1M4_orf2#LINE/    825 AAAGGATTTG 834

Transitions / transversions = 1.66 (116 / 70)
Gap_init rate = 0.02 (17 / 834), avg. gap size = 2.41 (41 / 17)  

 299 22.77 0.00 7.92  chrX_43621404_43623995     1999  2099 (493)    L1M4_orf2#LINE/L1      816   908 (0)  

  chrX_43621404_4   1999 AAAATGGACTAAGACAGACCAGACAAGAACAGATATTTTTCAAGAGAAGG 2048
                                i v   --------  ivv   i   i    i  v i     i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAG--------GATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_43621404_4   2049 CTTACATGTGGCTAACGAGTTTATGATAAAATGCTCAACATCACTAATCA 2098
                         iv    vi    i  ii  ivi    v  i             ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_43621404_4   2099 T 2099
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.01 (1 / 93), avg. gap size = 8.00 (8 / 1)  


3209 27.37 0.44 0.22  chrX_43666622_43669807.rev     1790  2695 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_43666622_4   1790 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 1839
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_43666622_4   1840 GGCCATACTGCCCAAAGTAATTGATAGATTCAATGCTACCCCCATCAAGC 1889
                            v     v      v i  iv i        i  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_43666622_4   1890 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 1938
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_43666622_4   1939 ATGGAACCAGAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 1988
                               viiv  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_43666622_4   1989 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATAAT-CAAGGCT 2037
                               i      vv       v  ii i      viv  v -   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_43666622_4   2038 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATGTAGACCA 2087
                                i   i    ii         i iv ii i   i  i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_43666622_4   2088 ATGGAACAGAACAGAGGCCTCAGAA-TAACGTCACACATGTGCAACCATC 2136
                               i    iv   ivii     -   vvi  i    v iiiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_43666622_4   2137 TGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAGGATTCCCTA 2186
                             i  i     ivv  v   i vi vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_43666622_4   2187 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAGACAGAA 2236
                           i  i        i     v      v  ?   i     i    vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_43666622_4   2237 ACTGTACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 2286
                         ii  v      v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_43666622_4   2287 AAGACTTACATGTACAACCTAAAACCATAAAAGCCCTAGAAGGAAACCTA 2336
                         ?    i  v     vi v       i      vi i      i    v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_43666622_4   2337 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 2385
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_43666622_4   2386 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 2435
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_43666622_4   2436 AAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 2485
                            v v  i     i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_43666622_4   2486 ACAATCTACAGAATGGCAGAAAATTTTTGCAGTCTATTCATCTGACAAAA 2535
                             i i         v       v      ivii  vi      i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_43666622_4   2536 GGCTGATATCCAGAATCTACAAGGAACTTAAATAAATTTACAAGAAAAAA 2585
                          i  vi          v  i  i     ivv i  v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_43666622_4   2586 ACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGGACAGACACTTCTC 2635
                              i     v  i?    i    ii      v  i i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_43666622_4   2636 AAACGAAAACATTTATGTGGCCAACAAACATGTGAAAAAAACCTCATCAT 2685
                         v  v   i i  vi vi       i  i  ii      i vv    v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_43666622_4   2686 CACTGGTCAT 2695
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.00 (6 / 6)  


3609 24.03 1.56 0.56  chrX_43691755_43694315     1170  2068 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_43691755_4   1170 TGGAGAGAGGTTCCATGTTCACAGATAGAAATATTCAATATTGTCAAGAT 1219
                             i   vi i         ii   v i  v i i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_43691755_4   1220 GTCAGTTCTTCTCAACTTGATCTATAGATTTAATATAAACCCAATCAAAA 1269
                          v  i v  i i   v        i     i  iii  v   v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_43691755_4   1270 CCCCAGC--CTGTAATTTTGTAGATATTGACAAA-TGATTCTAACGTTTA 1316
                         i      -- iv --     i   v        i-    i    vi  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_43691755_4   1317 TATGGAGAGGCAAATGACTCGGAATAGCCAATACAATGTTGAAAAAGAAG 1366
                               i v    iv   i i          v     v            
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_43691755_4   1367 AAAAAAGTTGGAGGACTGACACTACCCGACCTCAAGACTTACTATACAAC 1416
                           v              v     v   i ii    i        i v i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_43691755_4   1417 TACAGTAATCAAGACAGTGTAATATTCTCAAAAGAATAGACAAATAGATT 1466
                                             ii  i vv  v   i       v      i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_43691755_4   1467 CATAGAACAGAACAGAGAGCCCAGAAATACAACCACACAAATACAGTCAA 1516
                         v  i   i    iv     i         v v   i   vv  ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_43691755_4   1517 CCAATCTTTGGCAAAGGAACAAAGGCAATAAAATGGAGGAAAGACAGTCT 1566
                         iii  i  i i   i  vi v   i v  vv     i i  ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_43691755_4   1567 TCTCAACAAATGGTGCTGGAAGAACTGAACATTCACGTGCAAGAAAAATG 1616
                          i                 i v     i i ?i   i     -  i    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA-AAGAATG 447

  chrX_43691755_4   1617 AAGCTAGATGCAGGCATTATACCCTTTGCAGATATTAACTCAAAATCAAT 1666
                            i i  iv vvi v i i   v v i  i v             vi  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_43691755_4   1667 CATAGACCAAAGAGTAAGATGC-AAAACTATAAGGCTCCCAGAAGACAAC 1715
                           ?     v  iv      -  -          ii   ii      v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_43691755_4   1716 ACAGGAGAAAATTTAGTTGGCCATGGATTTGGCAATGACTTTTTAGGTAC 1765
                          i   ? v    i vvv  i  v   i  v       ii  i    i  i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_43691755_4   1766 AACACCAAAGGCATAATCCATGAAAGAAATAATTGATGAGATTAAA-TTC 1814
                         i        i   i  v v ii       v   v   i -   ii -   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA-ATTGGACTTC 645

  chrX_43691755_4   1815 ATTAATTTT-----TTTTAATTTTTAAAAAGACA-TGTCAAGAGAATGAG 1858
                           i  vv  -----i   vi vi  v   i    - i      i i   i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_43691755_4   1859 AAGACAATTCACCAACTAGGAGAAAATATTTTCAAAAGACATATCTGATA 1908
                                ii   vi v i             v    vv i          
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_43691755_4   1909 AAGAACTGTTATCCAAAATATAAAGAGAATACTTGAAACTTAACAATAAG 1958
                          i i   vv      i      v i    iv   iv    i  i     i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_43691755_4   1959 AAAATGAACAACCCAACTTAAAAATGGGCAAAAGAACTGAACAGACACCT 2008
                           i ii  i       i ?             i  vi    i     ii 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_43691755_4   2009 CACCAAAGA---TACACAGATGGCAAATGAGCATACAAAAAGATGCTCAA 2055
                          v       ---  i   i     v   i    i ii             
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_43691755_4   2056 CATTATAATGTCA 2068
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (138 / 74)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


2407 27.00 7.67 0.94  chrX_43745709_43747531.rev      485  1332 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_43745709_4    485 AAAAATGTCAGTTGACTATGAACTGGAAGGCTCAATATAATAAAGATGTA 534
                            i  i  vvv  vii   i i      i  i     vi v      vv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_43745709_4    535 AATTCTCCC-AAATTGAAATACAAATATAATGCAATTCCCACTAAAAGTT 583
                            v     -       vv    i  vi  i     i  i ii    vii
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_43745709_4    584 CAGCAACACTTTTTGTAGATATAGACAAGATTATTTTAAAATTTATATGG 633
                             vi vi      i   v  v      v v  ii       i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_43745709_4    634 AAAAAGAATGGAACTAGAAAAGCTAAAATGATTTTGAA---GAAGGTCAA 680
                            viv  v   v i    v   i    ii  i     ---    iv   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_43745709_4    681 AGT-GGAGGAGTCAGTCTATCTGATTTAAATATTTTTATTATATAGCTAC 729
                            -      v   vv  vi ii    v  v i  -- i  i v      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTT--ACTACAAAGCTAC 251

  chrX_43745709_4    730 AATCATCAAGACTGTTTGGCATTGGTAGGAGCATAGAAACATAGATCATT 779
                          i v        v  v   i i   i vi  v     v i        v 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_43745709_4    780 GGAAGTGGATAGAGAACCCAGAAATAGACTCACACAAATATCATCAACTG 829
                             vv i  v    ii         i  i  i   vv   vi    i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_43745709_4    830 ATTTTTGACAAAAATACTAAA-----TCAAT-----------------TT 857
                              i     iii i i  i-----     -----------------  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_43745709_4    858 CACCAAGTGGTGCTGAAGTAACCAAACATTTATAGGCAAAAAGAAAGAAA 907
                           v   i        iiii   iii i ?ii i v      -   v   i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAAG 450

  chrX_43745709_4    908 AGCCTTGACCTAAGCTTCATGCTTTGTACAAATATCACCTCAAAAAGGAT 957
                         ---i v    ivvi i   ii iv i      v  i v       v    
  L1M4_orf2#LINE/    451 ---TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_43745709_4    958 CATGGGCTTAAGGGTAAAATGTAAACAC-GTAAAAGGTGTAGAAAAAAAC 1006
                           ?i i i   iv    i vv    -  -i     vviv     i     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAA-ACTATAAAACTCTTAGAAGAAAAC 546

  chrX_43745709_4   1007 CCAGGAGAAAATACTCAGGATAAAGGGT-AGGTGAAGAGTTCTTAGACTT 1055
                         vi   ? v    vi  iv  ivvv    -   ii v iv        iv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_43745709_4   1056 AACACCAAAAGTGTGATCCATAAAAGAAAAAAATATATAAATTGGACTT- 1104
                         i          iiii v v i           -  v             -
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTC 645

  chrX_43745709_4   1105 -TTAAAATTAAACA--TTTGCTCTGCAAAAGACCCTATTAAGAGGATGAA 1151
                         - i         v --    iv  v    i   v    i    iii    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_43745709_4   1152 GAGACAAGCTACAGACTCAGGGAAAATCTTTGCAAACCATGTATGCAACA 1201
                         i      v i     v vi i      v        i   i   vii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_43745709_4   1202 AAGGATGAGTATCTAGAATATGTAAATAAATCTCAAAACTCAAT------ 1245
                          i   ivv     i       i    v  v   i v        ------
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_43745709_4   1246 ------------CCA-TT---------ACAAAAGACATGAACCAACATTT 1273
                         ------------   -  ---------i    i  iv    ivi      
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_43745709_4   1274 CACCAAGGAGGATATACAGATG---AA-AAGCACATGAAAAGTCATTCAA 1319
                          v    i  i        i   ---  -              viii    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_43745709_4   1320 CATCATTTAACCA 1332
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 3.84 (73 / 19)  


1800 24.90 2.55 2.16  chrX_43821266_43823909      954  1463 (1181)    L1M4_orf2#LINE/L1        1   512 (396)  

  chrX_43821266_4    954 TGGAAAAACATCCCATGCTCATGGATTGTAAGAATCAACATCATTAAAAT 1003
                               i i        i          v    v i  i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_43821266_4   1004 ATCCATACTGCCCAAAGCAATCTACAGATTCAATGCAATTCCTATCAAAT 1053
                         iv v     v      vii              i     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_43821266_4   1054 TACCAATGTCATTTTTTTCACAGAATTAGAAAAAACACATTTCTAAAATT 1103
                          v   -- iiiii     ii     v v  v  i- vv  i-        
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAG-CTGATC-CTAAAATT 146

  chrX_43821266_4   1104 CATATGGAACCAAAAAAGAGCCTCAAAAGCCAAAGTAAACCTAAGCAAAA 1153
                                  viiv  ii  v  vv  v       ii  v i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_43821266_4   1154 ATAACAAAGCCAGAGCCATCACATTACCCAACTTCAAACAATACTACAAG 1203
                          v       iii   vvv     i v     i      vvv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_43821266_4   1204 GCTATAGTAACCAAAACAGCATGGTACTTGTACAAAAAATAGGCACGTAC 1253
                             i     i   i    ii       v i i  ii -   i  i----
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACAT---- 291

  chrX_43821266_4   1254 TAATAGATCAATGGAAAAGAATAGAGAACTCAGAAATAAAGCCACATACC 1303
                         --              v     v    iii          v   i i ii
  L1M4_orf2#LINE/    292 --ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_43821266_4   1304 CACAACCAACTGATCTTTGACAAAGCTGACAAAAATAAACAATAGAGAAA 1353
                         i iiii   i    i  i     i v  v   i vi vv    i i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_43821266_4   1354 GGACACCCTCTTCAATAAATGGTGCTGGGAAAACTGGCTAG--ACATG-- 1399
                          i i vi  i     i              v      v  ?--     --
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_43821266_4   1400 ---------AATTGGATCCCTAACTCTCATTATATACAAAAATGAACTAA 1440
                         --------- i     i     v   v  ii            v    v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_43821266_4   1441 AAATGGATTAAAGACTTAAATGT 1463
                                 i ?    i       
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGT 512

Transitions / transversions = 1.78 (80 / 45)
Gap_init rate = 0.01 (7 / 512), avg. gap size = 3.43 (24 / 7)  

1113 21.74 7.42 2.56  chrX_43821266_43823909     1761  2151 (493)    L1M4_orf2#LINE/L1      499   908 (0)  

  chrX_43821266_4   1761 AAAGGCTTAAATGTAAGACCTAAAACTAT-------------GAAAACCT 1797
                          ?  i i           v          -------------      v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_43821266_4   1798 AGGAAAAATTCTTCTGGACATTTGCCTAGGCAAAGAATT--TATATTGAA 1845
                            ?iv  v     vv   v  v vi       v iv  --  v  -- v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--AT 596

  chrX_43821266_4   1846 GACCTCAAAAGCAAATGTAACAAAACCAAAAATTGACAAACGGGACTTAA 1895
                            vi        v v i       vv      v  i   iv      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_43821266_4   1896 TCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGTCAATGGAGTAAAC 1945
                              v v  i i   i  ii vv    i  v   i    vii   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_43821266_4   1946 AGACAACCCACAGAATGGGAGATAATATTTGCAAACTATGAACCTGACTA 1995
                                               v            ii  iv i    -  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA-TA 745

  chrX_43821266_4   1996 AAGGACTAATATACAGAATCTA-----AACTT----AAATCAACAACAAC 2036
                          i     vi   v      v  -----    i----  v    i  i  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_43821266_4   2037 AACAACAACAACAAC---ATTCGAAAGTGGGCAAAGAACATGAACAGACA 2083
                           -i    -- i   ---   ?i   i         i iv    i     
  L1M4_orf2#LINE/    796 AA-GACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_43821266_4   2084 CTTCTCAAAAGCAGACAGACATAAAAGCAGCCAACAA--ACATGAAAAAA 2131
                         i     v    v   i v   ---- iii     i  --         i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACA----AATGGCCAATAAGCACATGAAAAGA 888

  chrX_43821266_4   2132 TGCTCAGCATCACTAATTGT 2151
                               i     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (43 / 39)
Gap_init rate = 0.03 (11 / 410), avg. gap size = 3.55 (39 / 11)  


 427 33.95 2.69 9.73  chrX_43824300_43827067       24   506 (2262)    L1M4_orf2#LINE/L1      235   683 (225)  

  chrX_43824300_4     24 ACATATCATGATGCTATAGTAATAAATGAAAACAG-ATAATACTGATTTA 72
                           v  ii ii v    i      v  ----i    -i ii     iiv  
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAA----GACAGTGTGGTACTGGCATA 280

  chrX_43824300_4     73 AGAATAGACAAGCAAACAAACTTAATAAAATTGGAGGGCTTAGAAACCAA 122
                           i       vii i iv  ivv    i     -  i iii     iv  
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTG-AGAGTCCAGAAATAAA 329

  chrX_43824300_4    123 TTCATATGGATATGGGTCCAT-GACATATGTCAGATGTATCAGTACAAAC 171
                         ii    iivv     -  v  -  iv vi v  iiv  ii  iv  v vi
  L1M4_orf2#LINE/    330 CCCATACATTTATGG-TCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_43824300_4    172 CACTGGGGAAAGGACAGAC-----AATGCATGATACTGGGTTGATTGGCA 216
                           v         i i  v -----  iiv   i i     vii i   vv
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_43824300_4    217 ATCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 266
                          ? iiii  iiviv vi  vi-----------------------------
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAA----------------------------- 449

  chrX_43824300_4    267 GTGTGTGTGTGTGTGTGTGTTAACCTAGACACAAAAATTAATCTTAGATT 316
                         ----  -  viiviv iiv i vv i v i           iiiv i  v
  L1M4_orf2#LINE/    450 ----GT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_43824300_4    317 AATTTAAGACCCAAATGTGGAAGGCAAATGTTGTAA--CTTTTAGAAGAA 364
                         i  iv?     i      iii  vi   -ii i   --  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAA-ACTATAAAACTCTTAGAAGAA 543

  chrX_43824300_4    365 AATGGAGAAGAATATCTTCATA----TATGTGGGGCATACATAATTTCTT 410
                           iiv  i? v v      i i---- iv  vi    ---  ii      
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA---ATGGTTTCTT 590

  chrX_43824300_4    411 AAACAGAATGCAAAATTCACAAACCCATAAAGGAAAAGATGGACAAATTC 460
                          i i vi ii v   vv     i v- i   i     i  i  i     v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCA-ACAAAAGAAAAAATAGATAAATTG 639

  chrX_43824300_4    461 AAGTATAATTAAAAATTTAAAGCTTTCATGTGACAAAACACACCAT 506
                         i v - v  i    -  v   i    ii  ivv    iv    i  
  L1M4_orf2#LINE/    640 GACT-TCATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

Transitions / transversions = 1.82 (104 / 57)
Gap_init rate = 0.03 (15 / 449), avg. gap size = 4.00 (60 / 15)  

3297 21.76 6.71 1.62  chrX_43824300_43827067     1412  2275 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_43824300_4   1412 TGGAGAGACATACCACGTTCATTAGTCAAAAGGCTCAATATTGT------ 1455
                             i   i  v   i      vii iii   i  i        ------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_43824300_4   1456 ---------CTCCAAATTTATCTGTAGAGTCAATGCAATCTCAATCAAAA 1496
                         --------- i       v    ii   v    i      i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_43824300_4   1497 TCCCAACAGGGTTTGTTATAGAAATTGACAAGCTGATACCAAAGTTCAAA 1546
                              i v vv   v  ii                  v i   i    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_43824300_4   1547 AGAAAATACAAAG-ATCCAGTATAGAGCCAAAATAACTTTGAAAAAGAAG 1595
                         v i    i   i - i    v    --      i  ii            
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAG--CCAAAACAATCTTGAAAAAGAAG 198

  chrX_43824300_4   1596 AACAAAGTTGGAGCACTAACACTATCAGATTTCAAGACTTAC---AAAGC 1642
                                      v   v     vi vi       i      ---     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_43824300_4   1643 TACAGTAATCAAGAAAATGCGGTATTGGTATCAAAATGGACAAATACGTC 1692
                                       v i  i    i   i  v ii  i    v   vi  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_43824300_4   1693 AATTGGACAGAAT--AGAGTCCAGAAATAGGCCCATTCCTACATGGACAA 1740
                            v i i     --              ii     v v vi    v   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_43824300_4   1741 CTGATTTTCAACAAGG----CAA-----TTCAGTGGAGAAAGGATAGTCT 1781
                         i        i      ----   -----    i   i     i       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_43824300_4   1782 TTTCAACAAATGATGCTAAAAAAAATTGCATATCCATGTGCAAACGAGCA 1831
                                     i    iii v  -i  v   ?   ii      v  iii
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATG 447

  chrX_43824300_4   1832 AAACTTTTTAACAAATACTTCACACC-CATACAAAAATTAACTCAAAGTG 1880
                           i---  vi  vvv   i       -i                   i  
  L1M4_orf2#LINE/    448 AAG---TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_43824300_4   1881 GATCATAGCCCTAAATATAAAATCTGAAATGATAATGCTTCTAGAGGAAA 1930
                              ?  v       i   i v  i   iv    vi  ii    i    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_43824300_4   1931 ATACAGTAGAAAAGAAACCTGTGTGGCCTTGGATTAGGCCAAGACTTCTT 1980
                          i i  v? ----v   i  vi   i      i      v v ii     
  L1M4_orf2#LINE/    545 ACATAGGNG----TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_43824300_4   1981 AGATACAATACCAAT-GCATAATCCATAGAAGCAAAAACTGATAAATAGG 2029
                              ii i     v-   i  v v i i   v     iv       v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_43824300_4   2030 ACTTAATCAGAATTTAAAACTTTTGCTCTTTGAAAGACACTTTTAAAAGA 2079
                             v    i    v          iv   ii  i      v i  i i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_43824300_4   2080 ATAAAA------TCCACAGAGAAATAGAAAACATTTGGCAATCATATATC 2123
                         i i   ------i       iviiv      i     vv           
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_43824300_4   2124 TGATAAAGGTCTGGTATCCAGCACATACTTTTAAA--ACTCTCAAAATTC 2171
                               i  v  v        v i   ----    --     i v  i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATA----TAAAGAACTCTTACAACTC 786

  chrX_43824300_4   2172 AGTAATAAGA-GA-----AACT------AAAAATGGACAAAAGGCTTGAA 2209
                          i      i -  -----   i------        i    i ii     
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_43824300_4   2210 TAGGTAGTTCACCA-----GATATATGGATGGCAAATAAGTGAA-GAAAA 2253
                            ii v   v   -----      iii     v      iiv -     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_43824300_4   2254 GATGTTCAACATTATTAATCAT 2275
                             i       i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (121 / 64)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.60 (72 / 20)  


3053 25.47 2.11 1.11  chrX_43867828_43874538     5320  6218 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_43867828_4   5320 TGGAAAAACATTCCATGCCCATAGAT-AGAAGAATCAATATCATAAAAAT 5368
                               i i  i     ii   i   -i     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_43867828_4   5369 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 5418
                            v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_43867828_4   5419 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTACATTTT 5466
                          v   -   v    i  -i     v v  v  i--  - iii  v v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_43867828_4   5467 ATATAGAACCAAAAAAGAGCTCGTATAGCCAAGACAATCCTAAGCAAAAA 5516
                             i   viiv  ii  v iv v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_43867828_4   5517 GAATAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGT 5566
                            i    i      vv       v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_43867828_4   5567 TTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5616
                         i        i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_43867828_4   5617 CAATGGAACAGAAC--AGAGTCCTCAAAAATAACACCACACATCTACAAC 5664
                                 i    i--       -- i      vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_43867828_4   5665 CAACTGATCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGAT-- 5712
                            i    i  i     ivv  v   i v  vv     i      i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_43867828_4   5713 TCCTTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAA 5762
                           i  -- i  i        i     v      v  ?   i     i  i
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_43867828_4   5763 ACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 5812
                          v    ii         v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_43867828_4   5813 GGATTAAAGACTTAAACATAAGACCTAAAATCATAAAAACTCT--AAAGA 5860
                             i ?    i    ii     v      ii      -    --i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGA 542

  chrX_43867828_4   5861 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATG 5909
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_43867828_4   5910 ACTAAAATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5959
                         iv  vi i          vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_43867828_4   5960 TCTAATTAAA-TTAACAAGCTTCTGCACAGCAAAAGAAACTATCATTAGA 6008
                         ii v  i   -    -  i   i  ii vv    i  v       vv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_43867828_4   6009 GTGAACAGGCAACCTACAGAATGGAAGAAAATTTTTGCAATCTATCCAAC 6058
                              v  i     i         i       v       vii  vi v 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_43867828_4   6059 TGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACA 6108
                            i  i  i  vi          v  i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_43867828_4   6109 AAAAAAAAAAAAAT----CAA----AAAGTGGACAAAGGATATGAACAGA 6150
                          v     i v    ----   ----   i   i        v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_43867828_4   6151 CACTTCTCAAAACAAGACATTTATGCAGCCAAGAAACATATGAAAAAAAG 6200
                           i     v   v    i  vi viii     v  i  i       i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_43867828_4   6201 TTCATCATCACTGGTCAT 6218
                         i   v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (140 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.71 (29 / 17)  


 773 19.73 0.90 6.73  chrX_43969868_43971625      164   386 (1372)    L1M4_orf2#LINE/L1       29   238 (670)  

  chrX_43969868_4    164 GAAGACTAAATATTGTTAAGATGGCAATAGCCCCCAAATTGACCTACGCA 213
                                v                     vi           i    iv 
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chrX_43969868_4    214 TTGATTGCAATCCCTACCAAAATCTCAGCTGCCCATTTTTGCAGAAATGG 263
                           v vi          i       i        i-             v 
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCT-TTTTTGCAGAAATTG 127

  chrX_43969868_4    264 ACAAGGTAATCCTAAAATTTATGTAGTAATACATAAT-CCTAAAATTTAT 312
                              v i           i  i i v   i  viiv-  i i   -- -
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT--A- 174

  chrX_43969868_4    313 GTTCTAATACAAGTATTACAAAAGAAGCAGAAACTGGCCGGGCACGGTGG 362
                          -- i  v    - v  iv        v v   v v -- i ------ i
  L1M4_orf2#LINE/    175 G--CCAAAACAA-TCTTGAAAAAGAAGAACAAAGTTG--GAG------GA 213

  chrX_43969868_4    363 CTCACACCTGT-AATCCCAGCACTT 386
                                i vi-   ii  iv    
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTT 238

Transitions / transversions = 1.32 (25 / 19)
Gap_init rate = 0.04 (9 / 210), avg. gap size = 1.89 (17 / 9)  

3599 14.60 1.56 5.74  chrX_43969868_43971625      499  1265 (493)    L1M4_orf2#LINE/L1      174   908 (0)  

  chrX_43969868_4    499 AGCAAAAACCATCTTTAAAAATAA---TAAAGTTAGAGGACTCACACTTC 545
                            v     v     v     v  ---i      i               
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_43969868_4    546 CTGATTTCAAAATTTACTACAAAACTACAGTAATGATGACAATGTGATCC 595
                          ii         i          i          v v    i    i v 
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_43969868_4    596 TGG--TAAGGACACATATATAGATCAAAGGAATAGAATTGCAAGTCCAGA 643
                            --      i v i           v            vi        
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_43969868_4    644 AATAAACTCTTACATTTACTGTCAATTGATTTTTGACAAGAATGCTAAGA 693
                                i v        iv             i      ii   i    
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_43969868_4    694 CAAATCAATGGGGGAAAGCACAGTCTTTTCAACAAATGATA---GGACAA 740
                          v v         -    v i                 i i---      
  L1M4_orf2#LINE/    374 CCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_43969868_4    741 CTGGATATCCACATGCAAAAGAAGGGAATTGTACACCTGCCATACACCAA 790
                                ?               v i i   v  v   i  vi      -
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA- 471

  chrX_43969868_4    791 GACATGGATATCTCACTATATACAATAATTAGGTTGAAATGGACCAGAGA 840
                         ------------------       v     iv ii       i  ?   
  L1M4_orf2#LINE/    472 ------------------TATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_43969868_4    841 CCTAAATGTCAGAGCAAAAACTACAAAACTCTTAAAAGAAAACATAGGAG 890
                                  v     v       i          i             ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_43969868_4    891 TAAATTTTTTTTTGAACTTGGTTTAGGCAATGATTTTTTATATATGACAC 940
                              i  iv --  v     v          i   i   v         
  L1M4_orf2#LINE/    554 TAAATCTTCGT--GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_43969868_4    941 CAAAAGCGCTAACAGCAAAAGAAAAA-CAGATACATTAAACTTCATCAAA 989
                                i v i  i           -i     v   ii           
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_43969868_4    990 ATTTAAAACTTTTGTGCTTCAGAGGAAATCATCAACAAAGTAAAAGGGCA 1039
                            v                 i    v ii     v     i   i i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_43969868_4   1040 ACTCAGAACATGGGAGAAAATGTTTACAAATCATCTATCTAATAAGCAAC 1089
                           i  v iv            i   i        v     i     vi  
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_43969868_4   1090 TGAGTTGTATCTAGAATCTATATGTGAAAAAACTCTTACAATTCAAGAAC 1139
                          ----      i     --    ---   i           i    v  i
  L1M4_orf2#LINE/    752 T----TGTATCCAGAAT--ATAT---AAAGAACTCTTACAACTCAATAAT 792

  chrX_43969868_4   1140 AACTACAAAAAGAAAAACAATAAATAACCCAATTTAAAAGTGGACAAAGG 1189
                           ----------   i    ---           ?    i   i      
  L1M4_orf2#LINE/    793 AA----------AAAGACAA---ATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_43969868_4   1190 ATTTGAGCAGCCATTTTTCCAAAAA---TAAACAAATGACCAGTAAACAC 1236
                               ii  v     i      i ---  v       i   i   i   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_43969868_4   1237 ATGCAAAAATGCTCAGCATCATTAGTAAT 1265
                            v   i       i     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (68 / 40)
Gap_init rate = 0.02 (13 / 735), avg. gap size = 4.31 (56 / 13)  


 625 24.66 0.00 0.00  chrX_44018964_44023596.rev     2874  3019 (1614)    L1M4_orf2#LINE/L1        1   146 (762)  

  chrX_44018964_4   2874 TGGAAATATAGTCCATGTTCATGGGTTGGAAGAATTAATATTGTTAAAAT 2923
                               v   vi            i        v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_44018964_4   2924 GACAATACTTCCCAAAGCAATTTACATATTCAATGTAACCCCTATAAAAA 2973
                          i       i      vii  i    v      i i  i      v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_44018964_4   2974 TACCGATGACATTCTTCACAGAAATAAAAATAATAATCTTAACATT 3019
                          v  iiivi v  i  ii       vi v viv i   i   v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

Transitions / transversions = 1.57 (22 / 14)
Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.00 (0 / 0)  

2815 22.29 0.74 5.54  chrX_44018964_44023596.rev     3331  4142 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_44018964_4   3331 ATCTTAACATTTATATGGAACCACAAATTATCCCAAATAGCCAAG-CAAT 3379
                            i   v   i        vii   ivv i  vi         i-    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_44018964_4   3380 CCTGAGCAAAAAGACCAAAGCTGGAGGCATCACACTGCCTGACTTCAAAA 3429
                          i   iv  i    v     i      vv       v  ii i       
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_44018964_4   3430 TATACTACAAAGTTATAGTAATCAAATCAGCATGGTACTGGCATAAAAAC 3479
                         iv          i  i         iv   ii              ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_44018964_4   3480 AGACACATAGACCAAGGGAACAGAGTAAAGTACCCAGATATAAATCCACA 3529
                              i     i   v    i   i vi  vii     v     i   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_44018964_4   3530 CATTTATAGCCAACTGATTTTTTAT--TGGTGCCAAGAACACTTATTGGA 3577
                                i i   i       iv i--v          v  i i v   i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_44018964_4   3578 GAAAGGACAGTCTCTTCAATAAATAGTGCTGAGAAAACCAGATAACCATA 3627
                              i i     i     i    i      i  v   ii    ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_44018964_4   3628 TCTAGAAGAATGAAACTAGACCCTTATCTTTCACCATATGCAAAAATCAA 3677
                          vi i         ii i     i  i  iv        i       i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_44018964_4   3678 ATCAAAATGGATTAAAGACTTACATCTAAGGCCTGAAACTATGAAACTAC 3727
                         v           i ?    i  v  v    iv  i       i     vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_44018964_4   3728 TAGAAGAAAACATTGAGG-AAATGTTTTCCAGAACACTGGTCTGGGTAAA 3776
                                      v i? -    v  --- ivi  -  ----     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTT---CGTGAC-CT----TGGGTTAG 577

  chrX_44018964_4   3777 AAAAAAAATT-TTGTGTAAGACATAAAATGCACAGACAACAGAAACAAAA 3825
                         iv  viiv  -  ivi  v    iv   v     ii     -   v    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA-AAAGAAAA 626

  chrX_44018964_4   3826 AACAGACAAATGGTATTACATCAAACTAAAAAGCTCCTGTACAACAAAGG 3875
                           i   i    v v i v       v v    i  ii   i vv      
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_44018964_4   3876 AAACAATCATTAAAATGAAGGGACAACC-ATAGAATGGGATAAAATATTT 3924
                          v  v    vv   i    ii       - i         v         
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_44018964_4   3925 GCAAATTATCCATCTGACAAGGGACTGATGACCAGAATATATAAGGAGCT 3974
                               i  vi      i        vi iv             i  i  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_44018964_4   3975 CAAAGAACTCAATAGCAAAACAAAAACAGAAACAAAAACAAAAACAAACA 4024
                          vv v         ii    ------------------------- i   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAA-------------------------AGACA 801

  chrX_44018964_4   4025 AACAAAAAAAAACCCTGACTTTAAAAATGAGCAAAAGATCTGGATAAACA 4074
                           i  -------   -- v  ?       i     i   i  i   i   
  L1M4_orf2#LINE/    802 AATAA-------CCC--AATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_44018964_4   4075 TTACTCAAAAGAAGACACACAAATGGCCAACGGGTATATAAAAAAAAATG 4124
                           v   v        i i            iii i i  i    i --  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TG 890

  chrX_44018964_4   4125 CTCAGTATCACCAATCAT 4142
                             ii    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (116 / 61)
Gap_init rate = 0.02 (13 / 773), avg. gap size = 3.92 (51 / 13)  


2630 25.12 0.37 3.11  chrX_44111364_44113164.rev      507  1310 (491)    L1M4_orf2#LINE/L1      127   908 (0)  

  chrX_44111364_4    507 GAAAAGAAAATCCTAAAGTTCATATGGAACCCCAAAAGGATCT-GAATAG 555
                           v   vvi        i           viv   i-   i i-      
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAG-GGACCCAGAATAG 175

  chrX_44111364_4    556 CCAAAGCAATCCCAAGCAAAAAGAACAAATTTAGAGGCATCACATTGCCT 605
                              i     iii iv  i         v  i    vv     i v  i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_44111364_4    606 GACTTCAAATTATACTACAAGGCAATAGTAACTAAAATAGCATGGTACCA 655
                         i i      viv        i  v i     ii  i i  ii      ii
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_44111364_4    656 ATACACAAAAATAGATACATAGATCAATGAAACAGAATAGAGAACCCAGA 705
                         i--  i  ii     i i           i  i     v    ii     
  L1M4_orf2#LINE/    276 G--CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_44111364_4    706 AATAAAGCTACATGCCTACAACCAACTGATCTTCAACGAAGTCAAACAAA 755
                               v i i iiii  iiii   i    i   i  i i viiv-   i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC-CAAG 372

  chrX_44111364_4    756 AATAAACAATAGGCAAAGGACAACCTTTTCAATAAATGGTGCTGGGAAAA 805
                          vi vv    i  v    i i ii        i              v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_44111364_4    806 CTGGCTAGCCATACGCACGACAATGAAACTGGAACCATACCTCTCACCAT 855
                             v  ?   i i   vi v      ii    v  v      v      
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_44111364_4    856 ATACAAAAATTAACTCCAGATGAATTAAAGGCCTAAACATAAGACCTGAA 905
                                         v i   i  i ?  i      ii     v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_44111364_4    906 ACTATAAAAATCCTATAAGAAAACCAAGGAAAAACCCTTCTGAATATTGG 955
                                  v  i  v        vv   ?iv  vi    vvi iv    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_44111364_4    956 CCTAGGTAAAGAATTTAT-GATGAAGACCCCAGAAGCAAATCCAACAAAA 1004
                         vi    i  v iv  iv -   - v   v   i     v vv        
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_44111364_4   1005 ATAAAAATAGACAAGTGGGACTTAATTAAACTAAAAAGCTTCTGCATAGC 1054
                         iv         i  i v      v  i   v v    i   i  iiivv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_44111364_4   1055 AAAAGAAATAATCAACAGAGTAAACAGATGACCTACAGAAAGGGAGAAAT 1104
                            i  v iv     v i   i  v   ii   i      v        v
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_44111364_4   1105 TATTTGCAAATTATGCATCTGACAAAGGACTAACATCCACAACCTACAAG 1154
                                    i  ii      i  i     vii     v  iv  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_44111364_4   1155 GAACTCAAACACCTTAACAAGAAAAAAACCAAACAGCCCCATTAAAAAGT 1204
                               vv   v  i  i  v     i  -   i i   v   ?    i 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAAT 820

  chrX_44111364_4   1205 GCACATTTTTGGCCCAAATGTTCAAAGAATATGAATAGACATTTTTCAAA 1254
                          ---------   ----------    i  v             i  v  
  L1M4_orf2#LINE/    821 G---------GGC----------AAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_44111364_4   1255 AGAAGACATACAAGCAGCCAACA-GTGCATGAAAAAATGCTCAACATCAC 1303
                               i      iii     i - ii        i             ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_44111364_4   1304 TAATATT 1310
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.79 (127 / 71)
Gap_init rate = 0.01 (10 / 782), avg. gap size = 2.80 (28 / 10)  


2486 25.89 1.57 0.72  chrX_44354035_44355721.rev      498  1196 (491)    L1M4_orf2#LINE/L1      204   908 (0)  

  chrX_44354035_4    498 AGCTGG-GGACATCACGTTACCTGACTGCAAACTACACTACAGGGCTACA 546
                           i   -    -    ii v  ii i v    vivi      ii      
  L1M4_orf2#LINE/    204 AGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_44354035_4    547 GTAACCAAAATAGCATGGTACTGGTACAAAAGCAGACACATAGACTGATG 596
                             i   i i  ii         i i  iiii     i     iii   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_44354035_4    597 GAACAGAATAGGGAGCCCAGAAATAAATCTGCACACCTACTACTATCTGA 646
                            i     v i   i           i iii   ii  iviii vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_44354035_4    647 TCTTTGACAAAGCTGACAAAAACAAGCAATGGGAAAGGACTC-CCTATTC 695
                          i  i     i v  v   i v  vv       i  i  v v-i  v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_44354035_4    696 AATAAATGGTGCTGGGATGACTGGTTAGCCATATGCAGAAGATTGAAACT 745
                           i              ii     v  ?   i     i    v    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_44354035_4    746 GGACCCCT----TACACCATATACAAAAATCAACTCAAGATGGATTAAAG 791
                                 ----i                 i       i      i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_44354035_4    792 ACTTACATGTAAAACCCAAAACTATAAAAACCCTGGAAGACAACGTAGGC 841
                           i  v      i v i            vi i i     v   i    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_44354035_4    842 AATACCATCCTTC---ACACAGGAACGGGCAAAGAATTTATGACAAA-GA 887
                         i-  -- vi    ---  viv  ivii     v i-   v v v v -  
  L1M4_orf2#LINE/    553 G-TA--AATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGA 598

  chrX_44354035_4    888 CACCAAAAACGATCGTAACAAAAGCAAAACTTGACAAATGGGATCTAATT 937
                                 i ivvv i        v    v v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_44354035_4    938 AAACTAAAGAGCTTCTGCACAGCGAAAGAAACTATCAACAGAGTAAACAG 987
                            v v  i i   i  ii vv i  i  v        v i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_44354035_4    988 ACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCTGACAAAG 1037
                               i                          ii  ii      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_44354035_4   1038 GTCTACTATCCAGCATCTATAAGGAATTTAAACACATTTACAAGAAAAAA 1087
                          v  vv       v  v     i   i ivv   vv iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_44354035_4   1088 ACAAACACCCCCATTAAAAAGTGGGCAAAGAACAGGAACAGACACTTTTC 1137
                              i v   v   ?    i         i ivv   i     i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_44354035_4   1138 AAAAGAAGACATACATGGGGTCAACAAGCATATGAAAAAA-GCTCAATAT 1186
                         v        i     viv  i   i     i       i -      i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_44354035_4   1187 CACTGATCAT 1196
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.81 (114 / 63)
Gap_init rate = 0.01 (10 / 705), avg. gap size = 1.60 (16 / 10)  


3113 25.42 2.82 0.23  chrX_44452082_44454603     1145  2029 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_44452082_4   1145 TGCAAATATATCCCATGCTCATGAATTAGAAGAATCAGTATCATGAAAAT 1194
                           v   v          i     i   i     v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_44452082_4   1195 GACCATACTGCCCAAAGCAATCTATAAATTCAATACAATTCCTATGAAAA 1244
                          i v     v      vii     i i      ii    i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_44452082_4   1245 TACCGACATCATTTTTTCACAGAATTAGAAAAA-TGATCCTAAAATTCAT 1293
                          v  ii vv v      -i     v v  v  i-                
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_44452082_4   1294 GTAGAACCAAAAAAGAGC--AAATAGCCAAAGCAATCCGAAGCAAAAAGA 1341
                         i i   viiv  ii  v --i          i     ivi iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_44452082_4   1342 AAAAATCTGGAGGCATCACATTACCACACTTTGAATTATACTGCAAGGCT 1391
                          v   vi      vv     i v  vv i  ii  viv    i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_44452082_4   1392 A------TC--------GTGGTACTGGTATGAAAGTAGATACATAGACCA 1427
                          ------  --------          i  i iii    i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_44452082_4   1428 ATGGAATAGAATGGCGAAGCAAGAAATAAGGCAAAATACTTACAACCAAC 1477
                                     v v  iv v        iv v v i i   iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_44452082_4   1478 TAATCTTTGACAAAGCATATAAAAAC-ATAAACTGAGGAAAGGACACCCT 1526
                          i  i  i     i -i iiv  i  -  vv v  i      i i vi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_44452082_4   1527 ATTCAATAAATGGTGTTGGGAAAACTGGAT-CCCACATGTAGAAGAATGA 1575
                         v     i        i     v        -?       i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_44452082_4   1576 AACTGGATTCATTTCTCTCACCATGTATAAAAATCAATTCAAGATCGATT 1625
                          ii    ii v vi   v      i  i      i  i    i  v   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_44452082_4   1626 AAAGACTTAAATGTAAGACCTGAAGCCATAAAAATTCTAGAAGAAAACCT 1675
                          ?    i           v  i  i i      v ii           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_44452082_4   1676 AGGAA-AGCTCTTCTGGACATTGGTCTAGGCAAAGAATTCATGACTAAGA 1724
                            ?i- iv     vv   v    vi       v iv   v iiv  v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_44452082_4   1725 CCCCAAAAGCAATTGCAACAAAACAAAAA-TAAACAAATAGGATATAATT 1773
                          v         vvv         v     -  i i    v   iv v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_44452082_4   1774 AAATTTATAAGCTTCTGCACAGCAAAAGAAACAATCGCCAGAGTAAACAG 1823
                            v   v  i   i  ii vv    i  v  v   ivv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_44452082_4   1824 ACAACTCACAGAATGGGAGAAAATATTTGCAAACTATGCATTCAACAAAG 1873
                              i                           ii  ii  iii i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_44452082_4   1874 GACTAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAGGAAAAAA 1923
                             vi          v  i  i      vv    v   ii iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_44452082_4   1924 ACA--TAATCTCATTAAAAAGTGGGCAAATGACATGAATAGATATTTCTC 1971
                            --   i iv   ?    i        v  iv        i       
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_44452082_4   1972 AAAAGAAGATATACAAATGCTCAACAA--ACATGAAAAAATGCTCAACAT 2019
                         v                  vi   i  --         i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_44452082_4   2020 CACTAATCAT 2029
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.25 (27 / 12)  


1496 26.18 10.08 1.46  chrX_44505632_44507543.rev      487  1101 (811)    L1M4_orf2#LINE/L1      227   894 (14)  

  chrX_44505632_4    487 ATTTCAAACAAGACCTACTATACAATGACAGTAATTAAGATAATGTGATA 536
                                 ----  i     i v iiv        i    i i    i  
  L1M4_orf2#LINE/    227 ATTTCAAA----ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_44505632_4    537 CTGGTGGAGGAATAAGCACGTAGACAAATCGAACATAATAGAGAACCCAG 586
                             iiv i i   ii  ii    iv   v   i v   v    ii    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_44505632_4    587 AAATAAACCCCTACAAATATATACGCAACTATTTTTTAACAAAGATTCAA 636
                                   v    -- v   ivv   i iv    ii    i i v v 
  L1M4_orf2#LINE/    323 AAATAAACCCATACA--TTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_44505632_4    637 AAGCAATTCAGTGGAGAAAAAATGACCTTTTCAACAAATAATGGTGGAGC 686
                          ii v     i   i    i   iii             ii  v   ii 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_44505632_4    687 AGTTGAACATCTACA-GCAAAA--ACAAAGCTCAACTTCAACCTCACACC 733
                          ii  i i ? i   -      -- ii   i vi  ii v          
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_44505632_4    734 TGATATAAAA-------CA---TGAAT---------AAA----------- 753
                         vv   i    -------  ---  i  ---------   -----------
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_44505632_4    754 AAACTATGAAACTTTTAGAAAAATAAATA--AATAAACCTTAGGGATCTA 801
                                i     i      i  v v   --?i    i   v v  i  v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_44505632_4    802 GGGCCAGGCAACATGTTTTTATACTTCACATCAAGATC-CA-----TAAA 845
                            ii      iivv  i   v iv v   i   i v -  -----i   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_44505632_4    846 ATAAAAATTA-ATACATTGGAC--AAT--AAATTAAAAACCTTTGCACTG 890
                          v     v  -   v       --v  --           i    ii  v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_44505632_4    891 CAAAAGAC--TGTTAAAATCATTCAAAGTTA---TAGAGCGAGCGGGAGA 935
                             i   -- i i  i vvi vv    vi ---i v  -- ii      
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG--AATGGGAGA 718

  chrX_44505632_4    936 AAAT-----CCAACCACGTACCTAACAAGG-ACT-ACACTCTAGAAAATA 978
                             ----- v  i  ii  i  i i    -   -ii -  i    v   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTA-TCCAGAATATA 767

  chrX_44505632_4    979 TAAAGAAATCTCAAAACTGAACAGTTAAAAAAAAAAT---CCAACTAGAA 1025
                                v   i v    v  i i v    i v    ---    i ?i  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_44505632_4   1026 AATGTGCAAAAGACACGAACAGACATTTTACCAAAGATAATATACAGATG 1075
                             v     i  ivi   i        iv       vi       i   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_44505632_4   1076 GAAAATAAGAACATGAAA-GATGTTCA 1101
                          vv      v        -    i   
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.82 (102 / 56)
Gap_init rate = 0.03 (23 / 668), avg. gap size = 3.09 (71 / 23)  


3197 27.42 0.55 0.55  chrX_44599161_44605547.rev     4989  5896 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_44599161_4   4989 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5038
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_44599161_4   5039 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5088
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_44599161_4   5089 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5136
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_44599161_4   5137 TATGGAACCAAAAAAGAGCCCGCGTTGCCAAGTCAATCCTAAGCCAAAAG 5186
                                viiv  ii  v  v vi v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_44599161_4   5187 AACAAAGCTGGAGGCATCACACTATCTGGCTTCAAACTATACTACAAGGC 5236
                                i      vv       vi iiii      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_44599161_4   5237 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 5286
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_44599161_4   5287 AATGGAAAAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5334
                                v    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_44599161_4   5335 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAAGGATTCC 5384
                          vi    i  i     ivv  vv  i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_44599161_4   5385 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5434
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_44599161_4   5435 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5484
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_44599161_4   5485 TTAAAGATCTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5534
                          i ?   i        v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_44599161_4   5535 CTAGGCA-ATACCATTCAGGACACAGGCCTGGGCAAGGACTTCATGTCTA 5583
                         v    ?i- v i -   iv   viv  vi i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_44599161_4   5584 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5633
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_44599161_4   5634 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5683
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_44599161_4   5684 CAGGCAACCCACAAAATGGGAGAAAATTTTTACAATCTACTCATCTGACA 5733
                         v  i         i             v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_44599161_4   5734 AAGGGCTAATATCCAGAATCTACGATGAACTCAAACAAATTTACAAGAGA 5783
                          i  i  vi          v  ii v      vv    v iv i  v i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_44599161_4   5784 AAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACCCTT 5833
                           i     i     v  i? v  i    ii      v    i    vi  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_44599161_4   5834 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5883
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_44599161_4   5884 CATCACTGGCCAT 5896
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (149 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2926 20.92 0.96 13.82  chrX_44737716_44741959.rev     2712  3753 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_44737716_4   2712 TGAAAAGATATTCCATATTCATGGATTAGAAGAATCAATATTGTTAAAAT 2761
                           i        i    i          i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_44737716_4   2762 GTTCATACTACCTAAACCAATCTACAGATTCATTGTAATCCCTATCAAAA 2811
                          viv     v  i   iii             vi i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_44737716_4   2812 TACCAGTAGTATTCTTCACAGAAGTAGAAAAAA-AATCCTTAAATTTATA 2860
                          v    iv iv  i  ii     i v  v  iv-i     v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_44737716_4   2861 TAGAACCACAAAAGACCCAGAACAGCCAAAGCTATTCTAAAGAAAAAGAA 2910
                          i   vii   ii         i       i v  ii i  i  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_44737716_4   2911 CAAAACTGAAGGAATCACATTATCTGACTTCAAATTTTACTACAGAGCTA 2960
                             ii  i    v     i vi ii i      vi        i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_44737716_4   2961 TAGCAACCAAAACAGCATGATATTGGCATAAAAACAGTCACACAGACTAA 3010
                         i  i  i   i    ii  i  i        ii i  v  i i   ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_44737716_4   3011 TGAAACAGAATAGAGAACACATAAATCAATC-ATACATCTACAGTGAACT 3059
                           i  i     v    iiv  v    v  i -      i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_44737716_4   3060 CATTTTTTGACAAAGGTTCCAAGAATATATATTGGGAAAAGGAT------ 3103
                         v     i-     i   v      vi  vi v    i    i  ------
  L1M4_orf2#LINE/    351 GATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_44737716_4   3104 -TTAATAAATGGTGGTGGGAAAACAGGATATCCATATGCAGAAGAATGAA 3152
                         - i  i        v     v   v     ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_44737716_4   3153 ACTAGACCCCTGCCTCTTGCTATATGCAAAAATCAAATCAAAATGGATTA 3202
                         ii i       i    vii i    i       i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_44737716_4   3203 AAGTCTGAAATCTAAGACCTCAAACTCTGGAACTATTACAAGAAAACATT 3252
                         ?  v iv    v     v  v     v ii    v   v          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_44737716_4   3253 GGAGAAACTCTCCACGACATTAGACTGAGCAAAGATTTCTTGCATAATAC 3302
                           ? v  v   i ii   v  i ii ii    v i      iv   vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_44737716_4   3303 CCCGCAAGCACAGACAATCAAAGCAAAAATGGACAAATGGGATCACAT-G 3351
                         v  iv       ii   iv    v      i  i    v   iiv   -i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_44737716_4   3352 AAATTAAAAAGCTTCTGCATACTGGGGCTAGGCGTGGTGGCTCACGCCTG 3401
                                   -   i  -- i  ---------------------------
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTG--TGCT--------------------------- 669

  chrX_44737716_4   3402 TAATTCCAGCAATTTGGGAGGCTGAGATGGAAGGATCGCTCGAGGCCAGG 3451
                         --------------------------------------------------
  L1M4_orf2#LINE/    670 -------------------------------------------------- 669

  chrX_44737716_4   3452 ATTTCAAGACAAGCCTGGGCAACATAGAAAGACCCTATCTGTATAAAAAA 3501
                         ---    --------------------- i   v     -------  i 
  L1M4_orf2#LINE/    670 ---TCAA---------------------AGGACACTATC-------AAGA 688

  chrX_44737716_4   3502 AACTTCTGCATAGCAAAGGGTATAATCAACGAGGTGAAGAGACAACTCAC 3551
                           -------------------------------     i       i   
  L1M4_orf2#LINE/    689 AA-------------------------------GTGAAAAGACAACCCAC 707

  chrX_44737716_4   3552 AGAATGGGAGAAAATGTTTGCAAACTATCCATCTGACAAGGGATTAATAA 3601
                                        i        ii  vi      i      i vi  v
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_44737716_4   3602 CTGGAATACATAAGGAGCTCAAACAACTCTATACAAAAAAAGTATAATAA 3651
                          ii     i    i  i   vv       v   vv     iii -     
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA-AATAA 806

  chrX_44737716_4   3652 TCAGATTAAAAAGCGGGCAAAAGATCTGAACAGACATTTCTCAAAAGAAG 3701
                         i vi   ?    ii       i   i    i           v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_44737716_4   3702 ACATACAAATGGAAAACAGGTATGTAAAAAGGTGCTCAACATCATTGATC 3751
                          i          vv  i i i ii i     i            ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_44737716_4   3752 AT 3753
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.15 (146 / 68)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 12.83 (154 / 12)  


3071 26.27 2.93 0.56  chrX_44830211_44836097     4508  5394 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_44830211_4   4508 TGGAAAAACATTCCATGCTCATGGACACGAAGAATCAACATCATTAAAAT 4557
                               i i  i     i       ivv     v i  i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_44830211_4   4558 GGCCATACAGCCCAAAGCAATTTATAGATTCAATGCTATTCTCACTAAAC 4607
                            v    vv      vii  i  i        i  v  i ii ii   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_44830211_4   4608 TACCATTGACATTCTTCACAGAATTAGAAAAAATTATTTTAAAATTCATA 4657
                          v   vivi v  i  ii     v v  v  iv v  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_44830211_4   4658 TGGAA--GCAAAAAGAGCCTGAATAGCCAAGGCAATCCTAAGCAAAAAGA 4705
                              --    ii-  v  v          ii     i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_44830211_4   4706 ACAAAGCTGGAGGCATCACCCTATTCGACTTCAAGCTGTACTACAAGGCT 4755
                               i      vv    v  vii i i     iviv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_44830211_4   4756 GCAGTAACCAAAGCA---TGGTATTGGTACAAGAACAGACATATAGACTA 4802
                         i      i   ii  ---     i   i i   i i           ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_44830211_4   4803 ATGGAATAGAATAGGGAACCCAGAAATAAGACTGCACACCTACAA-CAAT 4851
                                     v i  ii          iv iii   ii  iii-    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_44830211_4   4852 CTGATCTTCAACAAACCTGATAAAAACAAGTAATGGGGAAAGGATCCCCT 4901
                         -    i   i    ivv  vi  i v  vvi           i  vvi  
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_44830211_4   4902 ATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATG------ATTGA 4945
                         v     i              i      v  ?   i   ------ v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_44830211_4   4946 AACTGGACCCTTTCCTTATACCATATACAAAAATTAACTTACGATGGATT 4995
                          ii       i v   i i                    i vi      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_44830211_4   4996 AAAGACTTAAATGTGAAACCCAAAAGTATAAAACTCT-GGAAGACAACCT 5044
                          ?    i       i i v i    v           -i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_44830211_4   5045 AGGCA-ATACCATTCAGGATTCTGGCACAGGCAAAGATTTCAT-GATGAA 5092
                            ?i- v i -   iv  iii   vvi      v i    v -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chrX_44830211_4   5093 GATGCTGAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTAA 5142
                           ii ii      vvv          v      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_44830211_4   5143 TTAAACTTAAGAGCTTCTGCACAACAAAAGAAACTATCAACAGAATAAAC 5192
                          i   v    i i   i  ii vv    i  v        v i i i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_44830211_4   5193 AGACAACCTATAGAATGTGAGAACATTTTTACAAATTATGCATCCAACAA 5242
                                 i i      v     v  v   i     i  ii   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_44830211_4   5243 AGGTCTAATATTCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAA 5292
                         i  v  vi   i   v  v     i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_44830211_4   5293 A---AGAT--CCCCATTAAAAAGTAGGCAAAAGACATGAA----CACTTT 5333
                          --- i  --   v   ?    i i      i  iv    ----  i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_44830211_4   5334 TCAAAAGCAGACA--CATGTGGCCAACAAGCATATGAAAAAAAAGCTTAA 5381
                           v    v   i --  vi       i     i       i v-   i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAA 895

  chrX_44830211_4   5382 CATCATTGATTAC 5394
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (145 / 84)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.94 (31 / 16)  


2024 22.67 13.01 1.23  chrX_44837755_44839314.rev      502  1070 (490)    L1M4_orf2#LINE/L1      273   908 (0)  

  chrX_44837755_4    502 CTGGCATAAAAACAGATACATAGATCAGTGGGACTCAATAGAGAGTCCTG 551
                                  ii i   i i        i   i ivv   v        v 
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_44837755_4    552 AAATAAATTAACACATTTATGGTCAATTGATTTTTGACAAAGGTGCTAAG 601
                                iiv i                      i     i     i   
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_44837755_4    602 AGCACACAATCAAGAAAGGACAGTGTCTTCAATAAATGGTATTGAGGCAA 651
                          v  iv    vii     i i   v i     i       ii  i i   
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_44837755_4    652 CAATGGTGTTGATATCCACATGCAGAAGAATGA----------------- 684
                          --   -----   ?         i        -----------------
  L1M4_orf2#LINE/    423 C--TGG-----ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_44837755_4    685 ------------------------------------GACTTAAATGTAAG 698
                         ------------------------------------   i          
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_44837755_4    699 ACCCGAAACTATAAAACTACTGGAGGAAAACATTGGGAAAAA-CTCTATG 747
                          v ii             vi i  i        v  ?iv   -  iii  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_44837755_4    748 ACATTGGTCTGGTCAATATTTTTTTTAATATGACCCCAAAAGCACAGGCA 797
                           v    vi i v    iv   i  vi       v           i   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_44837755_4    798 ACGAGCACAAAAATAGACAAATGGGATTGCATCAAACTAAAAAGCCTCTG 847
                           i iviv         i    v   i v       v v    i i i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_44837755_4    848 ------------CAC----AGCAAAGTAAAGAGACAATCTATGGTATGGG 881
                         ------------   ---- iv     i  i      i i ii v     
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_44837755_4    882 AGAATATATTTGCAA-CCATACGTCTGATAAGGGG-TAATATCCAAAATA 929
                             v          -i    ii           i- vi      i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_44837755_4    930 CATAAGGAACTCAAACAAC--AAGAGCAAGAAATCAAATAACTCAATTAA 977
                         i    i      vv     --  v ii  i  iv        i     ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_44837755_4    978 CAAGTGGGCAAAGGACCTGAAAAAACATTTCTTAAAAGAAGGCATATGAG 1027
                         v  i           ii    v i        iv       ii   ii i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_44837755_4   1028 TAGCCAACAGGTATATGTTAAAATGTTCAACATCTCTAATCAT 1070
                          i     i i i i   vv  i   i        v????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.23 (87 / 39)
Gap_init rate = 0.01 (9 / 636), avg. gap size = 9.00 (81 / 9)  


3631 24.19 1.34 0.11  chrX_44859366_44862495.rev     1743  2639 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_44859366_4   1743 TGGAAGAATATTCTGTGTTCGTGCATTGGAAGAATCAATATTGTGAAAAT 1792
                              ii    i ii     i  v         v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_44859366_4   1793 GTCCATACTGCTCAAAGCAATCTACAGATTCATTATAATCCCTACCAAAA 1842
                          v v     v i    vii             viii        i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_44859366_4   1843 TACCAATGACATTCTTCACAGAAATAAAAAAA---ATCATAAGATTTATA 1889
                          v   iivi v  i  ii       vi v  i---   v   i   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_44859366_4   1890 TGGAACCAGAAAAGACCCAGAATAGCGAAAGCTATCCCAAGCAAAAGGAA 1939
                              viiv  ii             v   i v   iii iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_44859366_4   1940 CAAAACTAGAGGAATCACATTACCTGACTGAAAATAATGCCACACAGCTA 1989
                             ii i     v     i v  ii i vv   vvv i i   v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_44859366_4   1990 TCGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACACATAGACCAA 2039
                         iv    i   i    ii              ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_44859366_4   2040 TGGAACAAAATAGACAATCCAGAAACAAATCCACACATCTACAGTGAACT 2089
                              i i   v  v i        i   i   i    i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_44859366_4   2090 CATTTTAGACAAAGGTGCCAAGAACATACACTGGGGAAAAGACAGTCTCT 2139
                         v     v     i          v   v  v        ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_44859366_4   2140 TCAGTA---GATGCTGGGAAAACTGGATATCCATATGCAGAAGAATGGAA 2186
                            ii --- i        v         ?   i     i       i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_44859366_4   2187 CTAGACCTCTATCTCTCATCACATACAAAAACCAAATCAAAATGGATTAA 2236
                         i i    i   i   v  i  i         ii  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_44859366_4   2237 ATACTTAAATCTAAGACCTCAAACCATGAAACTATGACAAGAAAACGTTG 2286
                          v  i     v     v  v    i  i     v v v        i v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_44859366_4   2287 GAGAAAATCTCCAGGACATTGGTCTGAGAGAAAATTTCTTGAGTAATACC 2336
                          ? v      i iv   v    vi ii vi vii      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_44859366_4   2337 CTACAAGCACAGGCAA----AGCAGAAATGGATAAAGGGGATCACATCAG 2382
                          i v       i    ----  v i    i      vv   iiv     i
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_44859366_4   2383 G-TTAAAAAGCTTCTGCACAGCAAAGGATACAATCAACAAAGTAAAATGA 2431
                         i-       -   i  ii vv       i  v     v     i   v  
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_44859366_4   2432 CAACCCACAGAATGGGATAAA-TATTTGCAAGCTACTTATCTGACAAGGG 2480
                                          v   -         iii iv       i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_44859366_4   2481 ATTAATAACCAGAATATATAAGGAGCTCAAACAACTCTATAGGAAAAAAT 2530
                          i vi  v             i  i   vv       v   iv     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_44859366_4   2531 CTAATAATCCAATAAAAAGATGGGCAAAAGATTTGAATAGACATTTCTCA 2580
                          v     i     v?   i         i                    v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_44859366_4   2581 AAAGAAGACACACAAATTGCAAACAAGCATATGAAAAGGTGCTCAACATC 2630
                                 i i      v  v  i     i        i           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_44859366_4   2631 ATTGATCAT 2639
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.66 (133 / 80)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.17 (13 / 6)  


2901 26.37 4.79 1.14  chrX_44864746_44866693.rev      582  1457 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_44864746_4    582 TGGAAAGACATACTGTGTTTATGGATTGGAAGACATTACATAATAAAAAG 631
                                 i  v ii    i              v v i  vi v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_44864746_4    632 GTCAATTCTCCCCCAAATTAATATGCAGATCTAATGTAATTTCTGTCAAA 681
                          v    v      -     i  v i     ii  i i   ii  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_44864746_4    682 ATCCCAACAAGGTTTT--ATAGATATAGATAA--TAGTC-TAAAATTTAT 726
                               i vivv    --ii   v  v  i  -- ii  -       i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_44864746_4    727 ATGGAAATACAAAGGATATAGAATAGCTTAAGACAACTTAGAAAAAGAAG 776
                                 i   i   ivi        i-  i    ii v          
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCC-AAAACAATCTTGAAAAAGAAG 198

  chrX_44864746_4    777 AATAAAATGGAAGGAATTACTCTACCTAATTGTCATACATATTATAGAGC 826
                           i   i v i    v i  v  v  i    viv v  v  i  i i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_44864746_4    827 TACAATAA--AGGCTTGTGTGGTATTGGCAGAGGGATCGACATATAGATC 874
                             i   -- i viv        i     v i    v            
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_44864746_4    875 AATGGAACAAAAGAGAGAACTCAG--------CCAAATACAAGTACAGAC 916
                                i i  vv    iii   --------   --    vv  ii v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTC 346

  chrX_44864746_4    917 AACTGATTTTTGACAGAGATGCAAAAGCAATTCAATGAAGGAAGGATAGT 966
                           i       i    ii i   v  ii v        ii i   i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_44864746_4    967 CCTGTCAACAAATAATGCTGGAGCAATTGGATATTCACAGGCAAAAACAC 1016
                          i v         ii      ii   i      ?i    v      iv i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_44864746_4   1017 ATACATT----TCCTAAACCTCACGTTTTATACAAAAGTAAACTCA---- 1058
                         i- vi  ----i    --      iiiv         i v      ----
  L1M4_orf2#LINE/    447 G-AAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_44864746_4   1059 -----------TTAAATGTAAA--CCATAAATTATAAAATTTTTAAAAGA 1095
                         -----------i         i-- i -   i       i i   i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGA 542

  chrX_44864746_4   1096 CAACATAAGAGAAAATCTTCAGAACCTGAAACTTGATGAAGAATTTTTAG 1145
                         v      i ? v        ivi    viiii v iii v iv  i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_44864746_4   1146 ACATAACACCAAGAGTATGATTCATAAAAGAAAAAAAATTGATG--TTAG 1193
                          i  i       i  i ii viv i           v --   i--  i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGG 640

  chrX_44864746_4   1194 ATTTCATTAAAATTAAAAATGTTTGCTCTTTGAAAGACCTCGTTAAGAAG 1243
                          i     i           iv    iv   ii  i   viii i     i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_44864746_4   1244 ATTAAAAGACAAGATACAGCCTCTAAGGAAATATTTGCAAACCACATATC 1293
                         i v         vvi    vv vvi  i             i  i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_44864746_4   1294 TGACAAAGAACTCACGTCTAGAATATATAAAGAATTCTCAAAGCTCTCAA 1343
                            i  i i   iiii  i               i   i v i   vvv 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_44864746_4   1344 AAAGAAAAACAAAT--CTTATTT--AAAATGGGCAGAAGGCATGAAGGGA 1389
                          v i   i      -- ii v  --          i i iiv    vi  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_44864746_4   1390 AAGTTCACTGAAGAGCATATACAGATGGCAAATAGGCACGTGAAAAGATG 1439
                         v v   v ii    iv       i     v    i    i          
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_44864746_4   1440 TTCAACATTACTATCCAT 1457
                         i       i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (155 / 74)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.89 (52 / 18)  


2451 23.74 7.78 0.68  chrX_44882995_44884716.rev      499  1231 (491)    L1M4_orf2#LINE/L1      124   908 (0)  

  chrX_44882995_4    499 ATTAAAAAAC-AATCCTAAAATTTATATGGAGCAACAAGAGACCCAGTAT 547
                            i v  i -i           i       ivvi    i       v  
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chrX_44882995_4    548 ACCCAAAGCTATCCGAAGAAAAAAGAACAACACTGAGGGAATCACATTAC 597
                          v     i v   ivi i   i        vii  ii   v     i v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_44882995_4    598 CTAACTTCAAATTATACTACACAGCTATTGTAACCAAAATAGCATGGTAC 647
                          i  i      viv       v     iv    i   i i  ii      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_44882995_4    648 TTACATAAAAATACACACACAGACCAATAAAACAGAAGAGACAATCCAGA 697
                          vi     ii   v   i i   i    ii  i    vv  v i      
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_44882995_4    698 AGCAAATCCAGACACCTACAGAAAATCCATTTTCTACAAAGGTGCCAAGA 747
                          ii   i   v   ii  ii vv   iv      v    i          
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_44882995_4    748 ACATACAATGGGGAAAAGACAATCTCT--GATAAATG---CTGGGAAACC 792
                         v   v           ii i i   i --i i     ---      v v 
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_44882995_4    793 TGGATATCCATATGCAGAGGAATGAAACTAGATCCCCATCTCTCACCATA 842
                               ?   i     i i       ii i  i   i i   v       
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_44882995_4    843 TACAAAAATCAAATCAAAATGGATTAAAGACTT-----------CCCACA 881
                                  i  v           i ?    i ----------- iv v 
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_44882995_4    882 TTATAAAGCTACTACAAGAAAAC-------------TT-------TTGGG 911
                         i      i  vi  v        -------------  -------     
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_44882995_4    912 --AAAC-----TCTCC-AG------CAC----AGCACAGGCAACCAAAGC 943
                         -- ii ----- i  i-  ------   ----      i     v    v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_44882995_4    944 ACAACTGGATACATGGGATCACATCAAG-TTAAAAAGCTTCTGCACAGCA 992
                          v  v i    v  v   iiv      i-       -   i  ii vv  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCA 672

  chrX_44882995_4    993 AGGGAAACAATCAACAAAGTGAAGAGCCAACCCACAGAATGGGAGAGAAA 1042
                          i   v  v     v        i  v                   --  
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA--AA 720

  chrX_44882995_4   1043 ATGTTTGCAAACTACCCCTCTGACAAAAGGTTAATAACCAGAGTTT-TAA 1091
                           i        ii iviv     i  ii ii vi  v     i v -   
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_44882995_4   1092 GGAGCTCAAACAACTCTACAGAAAAAAAAATCTAATAATCCAATCAAAAA 1141
                         i  i   vv       v i iv     i -- v     i     i?    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAA 818

  chrX_44882995_4   1142 CTGGGCAAAAGATATGAACAGACATTTTTCAAAAGGAGACATACAAATGG 1191
                         v        i   v    i        i  v    i   i          
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_44882995_4   1192 CAAACAGGCATATGAAAAGGTGCTCAACATCATTGATCAT 1231
                          v  i i   i        i            ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (110 / 61)
Gap_init rate = 0.02 (16 / 785), avg. gap size = 3.88 (62 / 16)  


3249 24.46 1.20 2.50  chrX_44989128_44993449     2910  3829 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_44989128_4   2910 TGGAAATATATTCTACTTTCATGGATTGGAAAAATCAATACTGTAAAAAT 2959
                               v    i i iv              i v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_44989128_4   2960 GTCTATACTATCCAAGGCAATCTACAGATTTAATGCAATACCTATCAAAA 3009
                          v v     vi    ivii           i  i     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_44989128_4   3010 CACCCA--TGACATTCTTCCCAGAAATATAAAAAGCAG-TCCTAAAATTT 3056
                         i-    --  v -  i  iv       - i v    v -          i
  L1M4_orf2#LINE/    101 T-CCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTC 147

  chrX_44989128_4   3057 ATACGGAACCACAAAAGATGCAGAATAGTCAAAAGTATCCTAAGCACAAA 3106
                            i    vii   ii  iv        i     vv   i i iv vi  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_44989128_4   3107 GAA-AAAATTGGAGAAATCACATTATCTGACTTTAA--TTTACACTACAG 3153
                            -   i      i v     i vi ii i  i  --i    --    i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAA 245

  chrX_44989128_4   3154 AACTATAG-AACTAAAATGTCATGACGTGGGTATAAAAACAGACACATAA 3202
                          i   i  -  ii  i iivii  iiiiv  i    ii i     i   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_44989128_4   3203 ATCTGTGGGACAGAGTAGAGAACCCAGACAGAAATCCATTAATCTACAGT 3252
                            vi   i i   i v    ii     v v   i    vv  i  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_44989128_4   3253 TCAAAATGAACTCATTTTTGATAAAGGCGCGAAGAACATACACTGGGGAA 3302
                         i-------  i v     i  i  i  i  v    v   v  v       
  L1M4_orf2#LINE/    346 C-------AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_44989128_4   3303 AGGATAGTCTCTTCAATAAATGGTGCTGAGAAAACTGGATATCCATATGC 3352
                           i       i     i           i  v         ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_44989128_4   3353 AAAAGAATGAAACTAGACCTCTCTCTCTCTCTCCATATACAAAAATCAAA 3402
                                    ii i    i  vi   v v --             i  v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACAC--CATATACAAAAATTAAC 486

  chrX_44989128_4   3403 TCAAAATAGATTAAAGACTTAAATCCAAGATCTCAAACTGTGAAACTCTT 3452
                                i   i ?    i     vi    v  v     i i        
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_44989128_4   3453 GCAAGAAAACATTGAGGAAAATCTCCAGGACATTGG-TCAGTGTGAAAAT 3501
                         iv          v i? v      i iv   v    - i  - ii vii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG-GCAATGGT 585

  chrX_44989128_4   3502 TTCTTCAGTAATACACCACAAGCACAGGCAGCCAAAGTAAAAATGGAGAA 3551
                              vii  vv      v       i   i v    v      i  v  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_44989128_4   3552 ATGAGATCACATTAAG-TTAAAAAGTTTC-TGCATGGCAAAGGGAAAAGA 3599
                           vi  iiv   i  i-       v   i-   v --      ------ 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGG------A 677

  chrX_44989128_4   3600 CACAATCAACAAAGTTAAGAGACAACGCACAGAATGAGACAAAATATTTT 3649
                            v     v     v  i       v         i  v         v
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_44989128_4   3650 CAAACTACCCATCTGAGAAGAGATTAATAACCAGAATACATAAGGAGCTC 3699
                             ii ivi      v   i  i vi  v        i    i  i   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_44989128_4   3700 AAACAACTTTATAGGAAAAAG-CTAATAATACAATTTAACAATGGGGAAC 3748
                         vv      iv   iv      - v     iv     ?  v      v  v
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_44989128_4   3749 AGATCTGAATAGATGTTTTTCAAAAGAAAACATAGAAATGGCAAACAGGT 3798
                         i   i        ii   i  v      i i   v       v  i i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_44989128_4   3799 ATATGAAAAGGTGCTCGACATTATTGAACAT 3829
                          i        i     i    i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (140 / 81)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.89 (34 / 18)  


3128 25.95 0.97 2.81  chrX_45003007_45008134.rev     3713  4637 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45003007_4   3713 TGAAAAGATATTCGATGCTCATGAATTGAAATAATTAATATTGTTAACAT 3762
                           i        i v   i     i    i  v v             v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45003007_4   3763 TTCCTTACCACCCATAGCTATCTACAGAGTCAATGCAATC--TATTAAAA 3810
                         vv vv   iv    v viv         v    i      --   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45003007_4   3811 TTCCAA-TGTAATTTTTCACAAAAATAGAAAAAC-AATTCTAAAATTCAT 3858
                          i   i-  iv-     ii  i    v  v  i -i  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_45003007_4   3859 ATAGTACCACAAAAAAACACAAATAGTAAAGCTAATCTTGCACAGGAA-- 3906
                           i v vii   iii v vvi     iv  ivi       v v i   --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_45003007_4   3907 --AAAGCTAGAGGCATCCCACTGCCTGACTTCTAAGTATATTACAAAACA 3954
                         --    i i    vv  v    v  ii i   v  iiv  i      i v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_45003007_4   3955 ATAGTAATTAAAACAGCATGGTACTGGCATAAAAGTAGACACATCAATAA 4004
                          i      i  i    ii              iii      i  vi  v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_45003007_4   4005 AGGGAACAGAATAAAAAGCCCAAAAGTGAACCCAGGCATTTACAGCAAAT 4054
                          v    i     vi i  i   i  i i      vi      ii iv   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_45003007_4   4055 TGATTTTTCAACAAAAATGGCAAAAATACACAATGGCAGATGGACAGTCT 4104
                                - i    iii  v   i vi iv      vii v i i     
  L1M4_orf2#LINE/    350 TGATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_45003007_4   4105 CTTCAATGAAGGGTATTGGAAAAACTGGATATCTGCATGCAGAAGAATGA 4154
                         i     ii  v   ii   i v         ? ii      i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_45003007_4   4155 GATTGGACTCTTACCTCACACTATATGCAAAAATCAACAAAAAATGGATT 4204
                         ii      i i          i    i       i   vv         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_45003007_4   4205 AAATACTTAAACATA-TACCTGAAACTATAAAACTACTAAGAGAAAGCAG 4253
                          ? v  i    ii  -v v  i             vi  ii     i  -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA- 547

  chrX_45003007_4   4254 TGTGGGGGGGAGGAATTATATGATATTGGTCTGGACAATGATTTTTTGGA 4303
                         -- i  ? vi -- vi vii   iv    vi i i     i   i  i  
  L1M4_orf2#LINE/    548 --TAGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_45003007_4   4304 TTTGACCCCCGAAGCTCAAACAACAAAAACAAAAATAGACAAATGGTATT 4353
                          v    v  vi    v   i        iv         i    v v i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_45003007_4   4354 ACATCAAACCAAAAAGCTTCTGCACAGCAAAGGAAACAGTTAACAGACTG 4403
                         v       viv    i   i  ii vv       v  vi i  v i v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_45003007_4   4404 AGGAGACAACCTATGGAATGAGAGAATATATTTACAAGCCACTCATCTGA 4453
                          ii        i ii     i     v      i   ii  ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_45003007_4   4454 TAAGACATTAATATCCAAAGTATATTTTTAAAAAGTTTAAAAAACTCAAA 4503
                             iv i vi      i i     -------------   i     vv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATAT-------------AAAGAACTCTTA 780

  chrX_45003007_4   4504 CAACTCAATAGTAAGAAAACAAACAACCTGCTTAAAAGATGGGCAAAGGG 4553
                                   i   i  i     i    iiv  ?   i           i
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_45003007_4   4554 TCCAAATATAAATTTCTCAAAAGAAGACATACAAATGGCCAACAGGTATT 4603
                          iii    v v       v        i              i i i i-
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC- 879

  chrX_45003007_4   4604 ATGGAAAAAAAAAATGCTCAACATCACTAGGCAT 4637
                            -----    i             ????????
  L1M4_orf2#LINE/    880 ATG-----AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (154 / 82)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.92 (35 / 12)  


1307 22.07 3.29 2.58  chrX_45073217_45077933.rev       76   501 (4216)  C L1M4_orf2#LINE/L1   (0)   908   480  

C chrX_45073217_4    501 AATTTAATCAAGATGGATTAATGACCTAAATGTAAGACCAGAAACCATTA 452
                             v v    i      i ?v               v vi    i  - 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-A 528

C chrX_45073217_4    451 AAATTCT-AGAAAAAAACCTAGGTTTTCAGAAAAACTTTTCTGAACATTG 403
                            i   -    i     v    ?v ------   ii  iv   v -   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGT------AAATCTTCGTGACC-TTG 571

C chrX_45073217_4    402 GCCTATGCAAATAATTTATTAC-TAAGACCCCAAAAGCAAATGCAATAAA 354
                          vi  v    - ii   v   v-  v   v         v v    i   
  L1M4_orf2#LINE/    572 GGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

C chrX_45073217_4    353 AACAAAAATAAATAAATAGGACCTAGTTAAA--TGAAAAGGCTTCTGCAC 306
                          iv       i      v    i vi i   -- i    --   i  ii 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA--CTTTTGTGC 668

C chrX_45073217_4    305 AGCAAA--ATA--ATCATCAGAGTAAACAGGCAATCCACAGAATGAGAGA 260
                         vv    -- i --    vv i   i  v  i   i          i    
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

C chrX_45073217_4    259 AAATATTTGCAAACTATGCATCTGACAAAGGACTA--ATCCAGAATCTAC 212
                                      ii  ii      i  i     v--         v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

C chrX_45073217_4    211 AAGGAGCGCAAACAAATCAGCAAGAAAAA---AAA-AACCTCATCAAGAA 166
                           i  i v vv    v   ii  v     ---   -    iv  i? i  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

C chrX_45073217_4    165 GTGGACAATTGACATGAATAGACATTTCTCAAAAGAAGATGTAAAAATAG 116
                         i   i   vv  iv                v         i  v    i 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

C chrX_45073217_4    115 CCAACAGCCATATGAAAAAATGCTCAATATCACCAATCAT 76
                             i iv  i       i        i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (52 / 39)
Gap_init rate = 0.03 (13 / 429), avg. gap size = 1.92 (25 / 13)  

2484 26.60 7.00 1.05  chrX_45073217_45077933.rev     3370  4226 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45073217_4   3370 TGGAAAAGCATCCCATGCTCATGGCTTGAAA-----------------AT 3402
                               iii        i      v   i  -----------------  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45073217_4   3403 AGCCATACTGTCCAAAGCAATCTACAGATTCAATGCTATTCCTATCAAAC 3452
                         i  v     vi     vii              i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45073217_4   3453 TACCAA-TGTCATTTTTCATAGAAGTAGAAAAAAAAATTTTTTAATTCAT 3501
                          v   i-  i -     iii    i v  v  ivvi  ii vv       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_45073217_4   3502 TTGGTACCAAAAAAGAGCCTGAATAGTCAAAGCAATCCTAAGCAATAAGA 3551
                         v   v viiv  ii  v  v      i    i     i i iv  v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_45073217_4   3552 ACAAATCCAGAGGCATCACAGTGCCTGACTTCAAACTATGCCAACATGCT 3601
                              viii    vv     v v  ii i      viv i i vv v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_45073217_4   3602 GCAGTAACCAAAACAGCCTCATATTGGTACAAAAATAGATACATAGACCA 3651
                         i      i   i    iv vi  i   i i  ii     i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_45073217_4   3652 ATG----AGA----------CA-------ACC---AC---------CAAA 3668
                            ----   ----------  -------   ---  ---------   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_45073217_4   3669 TGATCTTTAACAAAGTCTACAAAAATAAGCAATGGAAAACGATTC-CCTA 3717
                             i  ii    i vivv   i vi vv      ii  v  v v-i  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_45073217_4   3718 TTAAAAAAATAGTGCTGGGTAAACTGGCTAACCATATGCAGAAGAACGGA 3767
                           v  v    i        vv      v  ?   i     i     i i 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_45073217_4   3768 ACTGGACACCTACCTATCACCATACACAAAAATCAAC--AAGATGGATTA 3815
                         ii     v       vv       i        i   --  i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_45073217_4   3816 AAGACTTAAATTTAAGACCTCAAACTATAAAAATTCTGTAAGAAAACCTA 3865
                         ?    i     v     v  v           v ii iv        v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_45073217_4   3866 GGAAATAGCCTTCTGGACATCGTCTTTGGCAAATAATTTATGACTAAGTC 3915
                           ?ivv ii    vv   v i vv  v     - ii   ----  v  vi
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTT----CTTAGAT 594

  chrX_45073217_4   3916 ATAATTCCTCAAAAGCAATTGTAACAAAAACAAAAATTGGCAAGT-GGTC 3964
                           i -- vi        vvv i       iv      v ii  i -  v 
  L1M4_orf2#LINE/    595 ATGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_45073217_4   3965 CTAATTAAA-TGAAAGAGTTTCTGCACAGTAAATGAAACTATCAAGAGAG 4013
                         i v  i   - v   i v   -  ii vvi   v  v          i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_45073217_4   4014 TAAATAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCC 4063
                          i  v        i                          ii  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_45073217_4   4064 AACAAAAAACTAATATCCAGAATCTATAAGGAAC----ATAATTCAACAA 4109
                         i i  iii   vi          v     i    ---- i  i    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_45073217_4   4110 TCAGAAAACAAACAACCTGATTAAAAAGTGGGCAAAGAACATGAACAGAC 4159
                          v i  i     i    ii   ?    i         i iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_45073217_4   4160 ACCTCTCAAAAGAAGACATACAAGCACCCAACAAACATATGAAAAAATGC 4209
                          ii    v        i      iiiv    i  i  i       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_45073217_4   4210 CCAACATCACGAATCAT 4226
                         i        ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (135 / 89)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.06 (69 / 17)  


2742 20.43 6.30 7.61  chrX_45078385_45081177.rev     1386  2305 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45078385_4   1386 TAGATAGATATACCCTATTCATGAATTGAAAGATTGAATATT-TTAAGAT 1434
                          i  v      v  v i      i    i    i v      -       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45078385_4   1435 GTTATTTCTCCCCTAATTGAACTACAGATTCAATGCAAAC----TCACGG 1480
                          vi v v      v      v            i    v ----   ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA--- 97

  chrX_45078385_4   1481 CAAATTTCTGTAGGCTTTTT-GTAAAAATTGACGA-CTGAATTTTAAAAT 1528
                         -    ii v iv v      - i i        i -    - ii      
  L1M4_orf2#LINE/     98 -AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAAT 145

  chrX_45078385_4   1529 TCAAATGGATATGCAAAGAACTTAAAGTAGCCAAAACAAGTTTAAAAGAC 1578
                            v     v      i i  ii i i            vi  i   i v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_45078385_4   1579 AACAAAAAACTTGGAGAATTTACATCATTTTACTGCAAGACTTATTATAA 1628
                           v  v   v      i i i   iiviiiv i v   i     i  i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_45078385_4   1629 AGCTATAGTAATCAATACAGTGTGGTATTTGTGTAAAGATATACAAATA- 1677
                              i         v           i v ii   i    v   v   -
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_45078385_4   1678 -----TG-AACAG------GAGTCCAGAAATAGACCCACAAATATATGGT 1715
                         -----  -  i  ------             i     i v  v      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_45078385_4   1716 CAACTGAATTTGTTTTTTTTAAGTGTA--GGGGCAATTCAGTGGAGAAAG 1763
                            i   -----    ivvi   v  i--ii i v     i   i     
  L1M4_orf2#LINE/    346 CAATTGA-----TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_45078385_4   1764 AAAAATCTTGTCAACAAATGGTGCTGGAACAATTGGATATCCACATAGAA 1813
                           v i    v                 i    i      ?      iv  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_45078385_4   1814 AAAAAGAGAACTGCAGCCTATATCTCACACCATAATCAAAAGTTAATTCA 1863
                           i  vii ii  v v  i-  i           vv     i    i   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCA 489

  chrX_45078385_4   1864 AAATGGATCATAGACCTAAATGTAAAACTTAAAACTATAAAATTTCTAGA 1913
                                   ?              i vi             i ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_45078385_4   1914 ACAAAAATTTAGAAG-AAAGCCTCATGACCTTGGATTAAGCAAAGATGTC 1962
                          -i    iv   i? -   v i  i         i   i    v i v  
  L1M4_orf2#LINE/    540 A-GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_45078385_4   1963 T---ACATCAC-TTAAAA--ATGATCCATAAAAGAAAAAA-----AAATC 2001
                          --- i  v  -ii    -- ii v v i           -----    i
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_45078385_4   2002 AAATGTCATCAAGGTTTAAA-TTTCTGCTCTTATAAAGACATTGCTAAAG 2050
                         ii iv       ii  v   -i  i  iv   vv  i    i i- v   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAG 687

  chrX_45078385_4   2051 AGAATGAAAAGACAAGATGCATACTGGGAGAAATACATATTATATCAAAT 2100
                          i i           vvii  v v         ---     - i-     
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAA---ATATT-TG-CAAAT 732

  chrX_45078385_4   2101 GTATCATATGTATGCTATATATGTACACACACACACACACACACACACAC 2150
                         ----     i ---  ----------------------------------
  L1M4_orf2#LINE/    733 ----CATATAT---CT---------------------------------- 741

  chrX_45078385_4   2151 ACACACACGATAAAGAATTTGTATCCAGAATATGTAAAGAACTCTGAAAG 2200
                         --------     i i i               i           v v i
  L1M4_orf2#LINE/    742 --------GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_45078385_4   2201 CTCAGTAATTTTAAAAA---------CCCAATTTAAAA----------GA 2231
                             i    ---     ---------       ?    ----------  
  L1M4_orf2#LINE/    784 CTCAATAAT---AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_45078385_4   2232 TTTGAACACATACTTC----AAGAAGATATATAGGTAGCAAATAAGCACA 2277
                               i v i i   ----           i ii i  v          
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_45078385_4   2278 TAAAAAGGTACTCAACAAAATTAGTCAC 2305
                          i     i i       vv ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (119 / 65)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 4.27 (128 / 30)  


3509 23.48 3.16 0.68  chrX_45107736_45111673.rev     2562  3447 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45107736_4   2562 TAAAAAGATAATCCATGTTCATGAATTGGAAGAATCAATATTGTTAAAAT 2611
                          ii       vi           i         v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45107736_4   2612 GTCCATATTACCCAAAGCAACCTGTAGATTCAATGCAATCCCTATCAAAA 2661
                          v v   i v      vii i  ii        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45107736_4   2662 TACCAATAACATTCTTCACAGAAATATA-AAACAGAATCCTAAAATGTAT 2710
                          v   iivi v  i  ii       vv -  i v -          vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chrX_45107736_4   2711 ATGGTACCACAAAATATCCAGAATAGC--------TC-TAAGCAAAAAGA 2751
                             v vii   iiv i          --------  - i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_45107736_4   2752 ACAAAACTGGAGGAATTGCATTACCTGACTTCAAATTATACTACAGAGCC 2801
                              ii       v ii  i v  ii i      viv       i   i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_45107736_4   2802 ATAGTAATCAAAACAGCATGATACTGGCATAAAAAAAGACACATGGACCT 2851
                          i         i    ii  i           ii v     i  i  i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_45107736_4   2852 ATGGAGCAGAATAGAGAACCCAGAAACAGATCCGCACGCTTACAGTAAAC 2901
                              ii     v    ii       i i i  ii  ii   ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_45107736_4   2902 TCATTTTTGACAAAGATGCCAAGAGCATACACTGGGGAAAAGGCAGTCTT 2951
                          v     i     i i        v   v  v        iiii      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_45107736_4   2952 TTCAATAAATGGTGCTGAGAAACCTGGATATCCATATGCAGAAGAATGTA 3001
                              i           i  v v       ?   i     i       v 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_45107736_4   3002 ACTAGACCCCTATCTCTCACCATATATAAAAATCAAATCAAAATGGATTA 3051
                         ii i        i   v         i      i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_45107736_4   3052 AAGACTTAAATCTAAGACCTCAAACT--GAAACTCCTACAAGAAAATATT 3099
                         ?    i     v     v  v     --i      i  v       i  v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_45107736_4   3100 GGGA-AAATCTCCAGGACATTGATCTGGGCTAAGATTACTTAAGCAATAC 3148
                           ?i-      i iv   v   ivi i   v v i  v    iii vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_45107736_4   3149 CCCACAAGTACAGGCAAGCAAAGCAAAA-TGGACAAATGGGATTGCATCA 3197
                         v   v   i   i    vv    v    - i  i    v   i v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_45107736_4   3198 AATTTAAAAGCTCTC-CACAGCAAAGGACACAATCAACAAAGTGAA---- 3242
                           v      i  i i-ii vv          v     v        ----
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_45107736_4   3243 ---------GAATGGGAGAAAATATTTGCAAACTACCCATCTGACTAGGG 3283
                         ---------                       ii ivi      iv    
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_45107736_4   3284 ATTAATAACCAGAATATATAAGGAGCTCAAACAACTCTTCAGGAAAAAAA 3333
                          i vi  v             i  i   vv       -----i v  v  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTC-----AATAATAA 794

  chrX_45107736_4   3334 AAAGTCAAACAATCTGATCAAAAAATGGGCAAAAGATTTTTATAGACATT 3383
                             v    i  i ii  i?             i     vv         
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_45107736_4   3384 TATTGAAAGAAGACATACAAATGGCAAACAGGCATATATAAAAGTGCTCA 3433
                          v iv        i           v  i i   i  iv   ii      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_45107736_4   3434 ACATCATTGATAAT 3447
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (130 / 74)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.40 (34 / 10)  


2259 22.02 16.90 0.64  chrX_45150027_45154430     3131  3911 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45150027_4   3131 TGGAAAGATTATTCCATGTTCATAGATTGGAAGAATCAATATTGTTAAAA 3180
                                  -  i          i          v i           i 
  L1M4_orf2#LINE/      1 TGGAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_45150027_4   3181 TGTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAA 3230
                           v v     v      vii              i               
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_45150027_4   3231 ATAACAA-TGTCATTCTTCACAGAAATAGAAAAAAAAATCCTAAAATGTA 3279
                           vv  i-  i -  i  ii       v  v  ivvi          vi 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_45150027_4   3280 TATGGAACTACAAAATACCCACAATAGCCAAAGCTAT-TTGAGCAAAAAG 3328
                                v i   iiv     v          i v  -    iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_45150027_4   3329 AACAAAACTGGAAGAATCACATTACCTGACTTCAAATTATACTACAGAGC 3378
                               ii    i  v     i v  ii i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_45150027_4   3379 TATAGCAAGCAAAACAACATGGTACTGACATAAAAACAGACACATAGA-C 3427
                           i  i  v   i   iii        i     ii i     i     - 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_45150027_4   3428 ATATGGAACAGAACAGAGATCCCAGAAAAAAAATCCACACACCTACAGTG 3477
                          -      i    iv    vi       v   -i   i   ii  ii  v
  L1M4_orf2#LINE/    299 A-ATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTC 346

  chrX_45150027_4   3478 AACTCATTTTTTACAAAGATGCCAAGAACAT-AAATTGGGC-------GC 3519
                           i v     iv    i i        v   -v   v   v------- i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_45150027_4   3520 CT------CAAATTGTG-----A-AACT------CC---TGCAAGAAAA- 3547
                           ------     v   ----- -    ------  ---     i i  -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_45150027_4   3548 --------------------CACTATG---GAAAAT---CTCCA---GGA 3568
                         --------------------   i  i---i     ---   v ---   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_45150027_4   3569 TATTAG-TCTGA----------TAAAA-TATG----TCTT---------- 3592
                          vv?  -i  i ----------     -   i----    ----------
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_45150027_4   3593 ----GAGTAA-T-------ACC-------AGACAA--------------- 3608
                         ---- ?    - -------   -------  i   ---------------
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_45150027_4   3609 ----------GCACAGACAACCAAAACAAAAATGGACAAATAGGATCACA 3648
                         ----------     ii    v   iv      i  i    v   iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_45150027_4   3649 TCAAGTTTAAAAGCTTCTGCATAGCAAAGGAAACAATCAGCAAAATGAAG 3698
                             iv      i   i  iiivv       v  v    iv   i    i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_45150027_4   3699 AGAAAACTGACACAATGGGAGAAAATATTTGCCAACTACTCATCTGACAA 3748
                            v   iv   v                   v  ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_45150027_4   3749 GGAATTAGTAACCAGAATAATATAAGGAGTCCAAACAGCTCTACAGGAAA 3798
                           i i v   v        -     i  iii vv   i   v i iv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATA-TATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_45150027_4   3799 AAGTCTAATAATTCAATTGAATAATGGGCAAAAGATTTGAATAGACATTT 3848
                            v v     ii     ?  v          i                 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_45150027_4   3849 CTCAAAGGAAGACACACAAATGACAAACAGGCATATGAAAACGTGCTCAA 3898
                            v  i     i i       i v  i i   i       vi       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_45150027_4   3899 CATCACTGATCAT 3911
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (106 / 63)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 4.89 (137 / 28)  


2557 22.35 6.66 4.18  chrX_45164452_45166639      816  1701 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45164452_4    816 TGGAAAGGTATACCATATTTAAAGTTTAGAAGACTCAATTTTGTTAAAAT 865
                                i   v    i  i vi v  i       i   v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45164452_4    866 T-CAGAT-CTCCTCAA-TTGATCTATAGTTTCAAGAAAATTCCATTAAAA 912
                         v-  -  -    i   -        i  v     viv   i  vv v   
  L1M4_orf2#LINE/     51 GGCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_45164452_4    913 ATTTCATCAGGCATTTTTGTAGAAATTGCAAAGCTGATTCTAAAATTAAT 962
                           ii  v v v v      i        vv        i        v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_45164452_4    963 ATGAATTTATAAAGGATG-AAAATAGCCAAAAAAAT-TTGAAAGAGAAAA 1010
                            i vv ii  i   iv- i           v   -      i    i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_45164452_4   1011 ACAAAGTTGAAAGATATACGCTACTTTACTTCAAGACTTACTATAAAGGT 1060
                                  i i  ivi  i  v iiv i     i        i    v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_45164452_4   1061 ACAGTAATCAATACAGTATAATATTGCTATAAAACTATACAAACAGATCA 1110
                                    v     i ii  i  vi    iiv  v   v i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_45164452_4   1111 ATGGAA-AAAATACAGAGTTCAGAAATAGATCCATGTATATATA--CAAC 1157
                               - i   vv     i        i i    ii  v   i--   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_45164452_4   1158 TGATTTTCTATGAAAGTGTGAAGGCAGTACAGTGGACAAAGA-TAGCCTT 1206
                                 v ii ii   iv   i vi v  i   iv     -   i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_45164452_4   1207 TTCAACAAATGGTAC------------ATATCCATTTGAAAAAGAA-GAA 1243
                                      i ------------   ?   iv  v       -   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_45164452_4   1244 CTTTAATCCACACCTCA--------------ATTAACTCAAAGTGGACCA 1279
                         v  vi i  vi      --------------           i    i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_45164452_4   1280 TAGACCTAAATATACAACCTAAAGCTATAAAACTTCTGGAAAGAAATCAT 1329
                         ?          i  vi v     i          ii i   -    v   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA-GAAAACAT 548

  chrX_45164452_4   1330 AA---TCCATCTTAATGACCTTGGGTTAGGCAAAGACATTTTAGATACAA 1376
                          i--- vv     vi                  v iiv i       ii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_45164452_4   1377 ATGTCTTTAATCACCAAAATCACCATCTAATAAATTTCATCTATTTTTTT 1426
                         -----------        v   v v -  i   ---- vvv -------
  L1M4_orf2#LINE/    599 -----------CACCAAAAGCACAAGC-AACAAA----AGAAA------- 625

  chrX_45164452_4   1427 AAATA-ATAAATTTGGACTTCAT---AAGTAAAGGCTGCCACTCTACTTC 1472
                              -       -         ---  v    ii  vi--- v i    
  L1M4_orf2#LINE/    626 AAATAGATAAATT-GGACTTCATCAAAATTAAAAACTTT---TGTGCTTC 671

  chrX_45164452_4   1473 CAAAGACAATACTAAGAGAATGAAAAGACAAACTAAAGACTAGGAGAAAA 1522
                         v  i    v  ii    i i           v i v   v i        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_45164452_4   1523 TGTTACAAAATCACAACTTTTATCTGATTTTAATAACTTCTATATGGAAT 1572
                          i  vvv      i -----        v-- ivi    v   vii    
  L1M4_orf2#LINE/    722 TATTTGCAAATCATA-----TATCTGATA--AGGGACTTGTATCCAGAAT 764

  chrX_45164452_4   1573 ATATTAAGAACTCTCAAAACTCAGTTATAAGAAAATTAAATT-CCCAATT 1621
                             v         i v      i v    i  i i-    v-       
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATT 813

  chrX_45164452_4   1622 -AAAAATGGGCAACGAACTTCAA------------CAAAAAA--TAGGCA 1656
                         -            v i i  v  ------------    i  --  vi  
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_45164452_4   1657 GGTGGTAAATAAGAACATGAAAACATGCTCAGTACCTGTAGTCAT 1701
                         ii   iv      v         v       ii i v????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (112 / 84)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 3.31 (96 / 29)  


 270 25.97 9.09 0.00  chrX_45173548_45177216.rev     1911  1987 (1682)    L1M4_orf2#LINE/L1        1    84 (824)  

  chrX_45173548_4   1911 TGGAAAAACAT-------TTATGAAATGGAAGGATCAATATCATTAAAAA 1953
                               i i  ------- i   i v      iv i     ii    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45173548_4   1954 GGCCATCCTGTCCAAAGCAATCTGCAGATTCAAC 1987
                            v  v  vi     vii    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.01 (1 / 84), avg. gap size = 7.00 (7 / 1)  

2696 27.03 0.96 1.20  chrX_45173548_45177216.rev     2343  3178 (491)    L1M4_orf2#LINE/L1       75   908 (0)  

  chrX_45173548_4   2343 CATATCTAACAATATTCCTATCAAACTACCAA-TGTCATTTTCCACAGAA 2391
                           v  ii   ivv  i         v v   i-  i -    iii     
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAA 123

  chrX_45173548_4   2392 TTGGAAAAAATTATTCTAAAATTATTTTGGAACCAAAAAAGAGCACAAGT 2441
                         v v  v  iv v  i        vv v     viiv  ii  v vvi i 
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chrX_45173548_4   2442 AGCCAAAGCAATCCTATGCAAAGAGAATAAAGTTGGGGGCATTATATCAC 2491
                                i     i iviv  ii    i        i  vv i i iiv 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_45173548_4   2492 CTGACTTCGTACTATACTATAAGGCCAAAGTAACCAAAACAGCATGGTAC 2541
                          ii i   iv viv     i  i  i v     i   i    ii      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_45173548_4   2542 TGGTACAAAAACAGACATATAGACCAATGGAACAGAATAGAGAACCCAGG 2591
                            i i  ii i           i        i     v    ii    i
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_45173548_4   2592 AATAAATCTGCACACTTACATTCATCTGATCTTCAACAATGTCAACAAAA 2641
                               i iii   i   iiv   vi    i   i    v viiv   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_45173548_4   2642 ATAAGCAATTGGGAAAAGATTTCCTATTCAATAAATAGTGCTGGAATAGC 2691
                         vi vv    v      ii  vvi  v     i    i       i i i 
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_45173548_4   2692 TGGCTAGCCATATGCAGAAGATTGAAACTGTATCCCTTCCTTATACCATA 2741
                            v  ?   i     i    v    ii  v i    v   i i      
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_45173548_4   2742 TACAAAAATTA-CTCACGATGAATTAAAGATTGAAATGTAAGACCTCAAA 2790
                                    -    vi   i  i ?   iiv          v  v   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_45173548_4   2791 CTATAAGAATCCTAGAAGATAAAC-TAGG---AAATACCCTTCTGGACAT 2836
                               i v  i       -    -    ---    ---    vv   v 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGA-AAACATAGGNGTAAAT---CTTCGTGACCT 569

  chrX_45173548_4   2837 AGGCCTTGGCAAATAATTTAT--GACTAAGTCCTCAAAAGCAATTGCAAT 2884
                         v  vi v     - ii   v --  -  v v vi        vvv    i
  L1M4_orf2#LINE/    570 TGGGTTAGGCAA-TGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAAC 617

  chrX_45173548_4   2885 AAAAACAATAATTGACAAGTGGCACATAATTAAACTTAAGAGCTTCTGCA 2934
                             iv  v   v  i  i v v  v v  i   v    i i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_45173548_4   2935 CAGCAAAAGAAACTATCAACAGAGTAAACAGAAAACCTACAGAATGGGAG 2984
                          vv    i  v        v i   i  v   v    i            
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_45173548_4   2985 AAAATATTTGCAAACTATGCATCCAACAAAGGTCTAATATCCAGAATCTA 3034
                                       ii  ii   ii i  i  v  vi          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_45173548_4   3035 TAGGGAACTTAAATAAACTATTTGACAAGCAAACACAAATAACCCCATTA 3084
                           ii     ivv i  -  vvv i i  --   v           v   ?
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAA-CTCAATAATAA--AAAGACAAATAACCCAATTW 814

  chrX_45173548_4   3085 TTAAATGGGAAAAAGACATAAACAAACACTTCTCAAAAGAAGACATACGA 3134
                         vv       v   i  iv i  i i   i     v        i    i 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_45173548_4   3135 GTGGCCAACAAACACATGAAAACATGCTCAACATCAGCAGTCAT 3178
                         i       i  i          v             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (131 / 92)
Gap_init rate = 0.01 (12 / 834), avg. gap size = 1.50 (18 / 12)  

2755 12.18 0.85 1.28  chrX_45173548_45177216.rev     3202  3669 (0)    L1M4_orf2#LINE/L1      298   763 (145)  

  chrX_45173548_4   3202 CAGTGGAGTAGAATAGAGAGTACAGAACTAAACACATACATCTATGGTCA 3251
                           i    i      v      v     v     v       i        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_45173548_4   3252 ATTGATTTGCAACAAGGGTACCATGACCATTCAATGGGAAAATAATAGAC 3301
                                 v i        i   v              i   v     v 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_45173548_4   3302 TCTTCAACAAATGATGCTGGGACAACTGTATATCCACACGCAAAAGAATG 3351
                          i           i              v   ?     i           
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_45173548_4   3352 AAGTTGGACTCCTACCTTACACTATATATGAAAGTTAACTAAAAATGGAT 3401
                                  i       i    i     ii   i      v         
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_45173548_4   3402 CAAAGACCTGAATAAATATAAGAGCTAAAACCATAAAACTATTAGAAGAA 3451
                           ?      ----    i             i        v         
  L1M4_orf2#LINE/    498 CAWAGACCT----AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_45173548_4   3452 AACACAGGGGTAAATCATCATGTCCTTGGATTCAGAAAATGGATTTTTAG 3501
                             i   ?       v  i  v      i  -  iv     v  i    
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTT-AGGCAATGGTTTCTTAG 592

  chrX_45173548_4   3502 AT--GACACGAAAAGCATGAGCAACAAAAGAAAAAGTAGATAAATTGAAC 3549
                           --     v       ii                i           i  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_45173548_4   3550 TTCTTCAAAATTAAAAACTTGTTTG--TCAAAGGATACTATCAAGAAATC 3597
                            v                v v  --        i            vi
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_45173548_4   3598 GAAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCACATATCT 3647
                              -                                     i      
  L1M4_orf2#LINE/    693 GAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_45173548_4   3648 AATAAGGATCTAGTATTCAGAA 3669
                         i      iv  v    i     
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAA 763

Transitions / transversions = 1.45 (32 / 22)
Gap_init rate = 0.01 (5 / 466), avg. gap size = 2.00 (10 / 5)  


2201 24.07 10.05 3.97  chrX_45200643_45202615.rev      627  1482 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45200643_4    627 TGAAGAGATATACCATATTCATGACTTGGAAGACTCAGCATAGTAAAAGC 676
                           i i      v    i      iv          i ii  ---------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT--------- 41

  chrX_45200643_4    677 TGTTTAGA--GCAAAGGTTTGCTCTATGACTCTCTTCAAATTGATATACA 724
                             v   --    ----------  -----   ii         v    
  L1M4_orf2#LINE/     42 TGTTAAGATGGCAA----------TA-----CTCCCCAAATTGATCTACA 76

  chrX_45200643_4    725 G-TTTAATGTAACTCCTATTAACATCCCAGCAAGATTTTGTG--GACATA 771
                          -  i  i i  ii     i  v        vivv    v  --  v  v
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

  chrX_45200643_4    772 AACAAGATTATTCTAAAATTTTTATCAAAAGGCAAAATAACTAGAATAGC 821
                         i     v v  i        iv   vi   v    iiv v i        
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chrX_45200643_4    822 TGAAACAATTTTGGAAAAGAAGAATAAAGTGAAAAGAATCACTCTACTTG 871
                         ii       i   i          i     vii i  v    v  v iii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_45200643_4    872 ATACTAAAGTTTTCTATGTAGCTACAGTAAT----ATAGT---------- 907
                           vii   ii  v   iiv            ---- i   ----------
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_45200643_4    908 ---AA--------ATACAG--TAAAGGAATAGAA-----AACTCAGAAAT 939
                         ---  --------   i  --i  v         ----- iii       
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_45200643_4    940 AGTCCCACACAAGTAAGGCGAGTTG--------CAAAAG---CAA----A 974
                          iv    i   vv  v  iv i   --------   ii ---   ---- 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_45200643_4    975 TT-AATGGAGAAAGGATAAACTTTTTAACAAATGATGCTGGAGCAATTGT 1023
                           -     i     i   iv     i        i      ii   i  v
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_45200643_4   1024 ATATCCATTGGCAAAAAAA--AA--TGAACCT-------------TATGC 1056
                            ?   ivv      i  --  --  i   i-------------   i 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_45200643_4   1057 AAAAACTAACTCCACATTGATTATAGATATATATATAAAATGC-AAAACT 1105
                              i      v v  v   i ?   iv  v  i   i -  -      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACT 525

  chrX_45200643_4   1106 ATAAACTTTTTAGATAATAAGAAAGGAGAGAATCTTCAGGGTG----TGG 1151
                              vi i     vi v  v v   ? vi       ---   ----   
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC---GTGACCTTGG 572

  chrX_45200643_4   1152 GTCTAGGCAAAGAGTTCTTAGACTA-GACACCAATAGCATGAT-----GA 1195
                           -       v iv        -  -        v    ii v-----i 
  L1M4_orf2#LINE/    573 GT-TAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAA 620

  chrX_45200643_4   1196 AGACAAATCAAAT---TTGTAAATCTCATCCAAGATTAAAAACCTTTGCT 1242
                            v   vi i  ---   --i ii     -  i         i    iv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTG--GACTTCATC-AAAATTAAAAACTTTTGTG 667

  chrX_45200643_4   1243 CTATGACAGACTTCATTAAGAGGATGCAACAACAAGCTACAGATTGGAAG 1292
                           vii vi   vii  i    iii  v  vi    v i     v   i  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_45200643_4   1293 AAAATAGTTACCA--TATATATTTGACAATGGTTTGGTATCTAGAATATA 1340
                               v  i v --i      i   i  v  vi v     i        
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_45200643_4   1341 TAAAGAACCCTTTAAATTTAACACTAACAAAAAAAAACAGTTTAATTGGA 1390
                                 i   vv  i i  i v   -   i v   i iiii    ?i 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAA-AAAGACAAATAACCCAATTWAA 816

  chrX_45200643_4   1391 AAATTGGTGAAAGATGTGAAGAGACATTTTACCAAATTGGATATATGGAT 1440
                             v  ii  i   v    v        iv     vvi      iii  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_45200643_4   1441 AGCAAATAAACACATGAAAAGATGTTCAACATCACTGGAAAT 1482
                         i  v     i              i         ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (126 / 76)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 3.87 (120 / 31)  


2876 24.32 4.66 1.48  chrX_45221282_45225759.rev     3108  3987 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45221282_4   3108 TGAAAAAACATTCCATGCTTATAGATAGGAAGAATCAATATTATTAAAAT 3157
                           i   i i  i     i i  i   v      v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45221282_4   3158 GGCTATACTGCCCAAAGCAATCTACAGATTCAATGCTATTCC-A-CAGAA 3205
                            v     v      vii              i  v  i  - -  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45221282_4   3206 TT-----------------AGAAA-----AATCTG-TTCTAAAATGTATA 3232
                          i-----------------     -----  v   - i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_45221282_4   3233 TGAAA--GCAAAAAAAGAGTCCA-AATAGCCAAGGCAATCCTAAGCAAAA 3279
                           i  --    iii ----i   -         ii     i i iv  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_45221282_4   3280 AGAACAAAGACGGAGACATCACATTACCCAACTTCAAATTATACTACAAG 3329
                                  vi    ivv     i v     i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_45221282_4   3330 GTTATAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGATACATAGA 3379
                          i  i     i   i    ii         i i  ii i   i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_45221282_4   3380 CCAATGGAATAGAATGGAAAGCCTAGCAATAATGCCATACACTGACAACC 3429
                         i              v  i  i i  v     vv       i v iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_45221282_4   3430 ATCTGATTTTCTACAAGGTCAACAAAACAAG-AAATGGGAGAAGGACTTC 3478
                          vi        v      viiv   i  v v-v      ii   i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_45221282_4   3479 CTATTTCATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAATATT 3528
                           v  iv i              i      v  ?   i     i  v v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_45221282_4   3529 GAAACTGGACCGCTTCCTTACACCATATACAAAAATAAACTATAAAGATG 3578
                            ii      v  v   i                 v    -i   -   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT-CAAA-ATG 494

  chrX_45221282_4   3579 GATTAAAGACATACATATAAAATGTAAAACTATAAAAACCCTGGAAGATA 3628
                            i ?    v  v  i   i vv             vi i i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_45221282_4   3629 ACCTAGG---AAATACCATTCTGGGCATAGGACCTGGTAAAGATTTCAT- 3674
                           v    ---    -- -   vv i v v  iiiv  i  v i    v -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_45221282_4   3675 GATGAAGGTGCCAAAAGCAATTGCAACAGCAACAAAAAAAT-GACAAATG 3723
                            - v iii         vvv      --  vi       -  i    v
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACA--AAAGAAAAAATAGATAAATT 638

  chrX_45221282_4   3724 GGACCTAACTAAACTAAGGAGCTTCTGTACAGCAAAAGAAACTATCAGCA 3773
                             i v ii   v v ii i   i   i vv    i  v       iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_45221282_4   3774 GAGTCACA-GACAATCTACAGAATGAGAGAAAATATTTGTAAACTATCCA 3822
                         i   v v -     i i        i             i   ii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_45221282_4   3823 TCTGACAAAGGTCTAATATCCAACATCCATAAGGAACGTAAACAAATCCA 3872
                              i  i  v  vi      iv  vi    i    vivv    v  v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_45221282_4   3873 CATGTGCAAA-ACAAACTTCCCAATTAAAAAGTGGGCCAAGGACATGAAT 3921
                         i -i iv   -     ivv       ?    i     v     iv     
  L1M4_orf2#LINE/    789 TA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_45221282_4   3922 AGACATTTTTCAAAAGAAGACATACA----GCGAGCAAGCATATGAAAA- 3966
                                 i  v        i     ----  v ii     i       -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_45221282_4   3967 ATGCTCAACATCATTAATTAT 3987
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (128 / 83)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.35 (54 / 23)  


3368 22.86 2.26 1.07  chrX_45227915_45229734      488  1327 (493)    L1M4_orf2#LINE/L1       59   908 (0)  

  chrX_45227915_4    488 TCCCCAAAT--GCC--CAGACTCCCATGCAATTTCTGTCAAAATTGCAAT 533
                                  --ii --    i  v- i     ii  i       iv  ii
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCA-ACGCAATCCCTATCAAAATCCCAGC 107

  chrX_45227915_4    534 GACGTTTTTCACAGAAATAGAAAAAGCT-ATCCTAGAATTCATATATTAA 582
                         vi v     ii       v  v  -   -      i         i----
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATG---- 152

  chrX_45227915_4    583 TAGAACCATAAATAATCT-GAATAGCCAAAGCAATCTTGAGCAAGAAGAA 631
                         --   viii  ivi i i-           i         iv        
  L1M4_orf2#LINE/    153 --GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_45227915_4    632 CAAAGCTAAAGGCATCACACT----AATCTCAAAATATACTACAAAGCTG 677
                              i ii   vv       ----   i      iv            i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_45227915_4    678 TAATCATCAAAGAAGTATGATACTGGTACAAAAACACACATATAAACCAA 727
                         i i v     iiv   i  i      i i  ii i v       i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_45227915_4    728 TGGGACAGAATAGAGAGGCCAGAAATAAGTCCACACATTTAGAGTCAGTT 777
                            i i     v     v          ii   i       vi    i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_45227915_4    778 GATCTTTATCAAAGTTGCCAAGAACATACAATGGG-AAAGAATTGTCTCT 826
                            i  iiv   i v        v   v       -       v    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_45227915_4    827 TCAATAAGTGGTGGTGGGAAAACT--ATATTCACACACAAGAGAATGAAA 874
                             i  i     v     v    --   ?i    ii   i        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_45227915_4    875 CTGGACCCTTATCTCACATCATACACAAAAATCAACTTACAATACATTAA 924
                         i       i  i      i    i        i    i v   iv  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_45227915_4    925 AGACTTAAACGTAAGACCTGAA-CCATAAAACTCCTAGAAGGAAACATAA 973
                             i    i      v  i  - i         i      i       i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_45227915_4    974 GGGAAAAGCTTCTTGACATTGGTATTGGTCATGATGTTTTGAATATGACA 1023
                          ? v   v    v    v    vv v  iv   i v i  ii        
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_45227915_4   1024 CAGAAAGCACAGGAAACAAAAGCAAAAACAGACAATTGAGATTACATCAA 1073
                          vi        i v        v     i   i  v vi  i v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_45227915_4   1074 ACTATAAAGCTTCTGCACAGCAAAGGAAACAACCAACAGGGCTAAGATAC 1123
                          v vv   i   i  ii vv       v  v i   v ii iv  i v  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_45227915_4   1124 AACCTATGGAATGGGAGAAAATATTTTCAAACCATACATCCGATAAAGAG 1173
                             i ii                  v    i    i   i     i ii
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_45227915_4   1174 TTAATATCCAAAATATATAAGGACCTC----AAAT-AATAGAAAGAAAAC 1218
                         i vi      i         i  v   ----  v -    iv  i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_45227915_4   1219 AAATAACCCAATTTAAAAATGGGCAAAGGACCTGAATAGTTATTTCTTAA 1268
                                      ?                ii       vi      iv 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_45227915_4   1269 AAGAAGACATACGAATGGCCAACAGGTAATACGAAAAAGTGCTCAACAAC 1318
                                i    i         i i i -i i     ii         v 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCA-CATGAAAAGATGCTCAACATC 899

  chrX_45227915_4   1319 ACTAATCAT 1327
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.08 (127 / 61)
Gap_init rate = 0.02 (14 / 850), avg. gap size = 2.00 (28 / 14)  


4599 16.74 2.83 0.11  chrX_45231287_45235236.rev     2576  3459 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45231287_4   2576 TGGAATGTCATTCCATGCTCATGATTTCAAAGACTTACTGTTATTAACAT 2625
                              v vi  i     i     iv  vi        v i  i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45231287_4   2626 GGCAATACTCC---AATTGATCTACAGATTTAATACAATCCCTATGAAAA 2672
                                    ---                i  ii          v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45231287_4   2673 TCCTAGCTAGCTTT---GCGGAAATAGGCAAGTTAGTTTTGAAATTCATA 2719
                            i    iv    ---  i     v i    i ii ii i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_45231287_4   2720 TGAAAATTTAAGGTTCTCAGAATGG-TAAAACAATCTTGAAAAAGA---T 2765
                           i    vi    vv i      i -i                   ---v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_45231287_4   2766 CTGAATTAGAGAACCCACTAGTTCCAATCTCAAAACTTACTACAGAGATA 2815
                          vi i  i   i  i   vvv i     i               i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_45231287_4   2816 CAGTAATTACAACAGCATGGTACTGGCATAAAAGTAGATGTACAGATCAA 2865
                                i vi    ii              iii    ii  i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_45231287_4   2866 TAGAATAGAATTGAGAGTCTAAAGA-AAACCT-CACATTTATAGTCAATT 2913
                          i                 i i i -     i-i        i       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_45231287_4   2914 GACTCTTGACAAGGGTGTCAATTCAATTCAACAGGGAAAGTACAGTCTTT 2963
                           i i i          i   vv v      ii       v i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_45231287_4   2964 TTAACAAACGGGACTGGGACAATTGGATATCCATATGCAAAAAAAATGAA 3013
                          i      i  vi         i      ?   i        i  -    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAA 449

  chrX_45231287_4   3014 GTTAGACCTCTCCCTCAAACCATATACAAAAATGAATTCAGAAGGGATCA 3063
                            i    i  v     v               v  i   i  v      
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_45231287_4   3064 CAGACCTAAATGTAAAAGCTAAACCTATAAAACACTTAGAGGAAAATA-A 3112
                         ?              i       v         v      i     i - 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_45231287_4   3113 GGGGTAAATCTTCATTACCTTGGATTAGGGAAAGCCTTCTTAGATATGAA 3162
                           ?          i v       i     v  v vi             v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_45231287_4   3163 ATCACAAGCATAAGCAACAAAAGAA----TAAATAAATTAGATTTCATCA 3208
                          i  v     i              ----  i       i  i       
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_45231287_4   3209 AAATTAAA-TCTTTTGTGCTCCAAAGGACACTATAAAAAAAGTGAAAACA 3257
                                 -v          i             v  i          v 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_45231287_4   3258 TAACCCACTGAATGGTAGAAAGTATTTGCAAATCATATATCTGATAACGA 3307
                         i       v      v     i                         v i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_45231287_4   3308 ACTTGTATCTAGAAAGTATGAATAACTCTTAAAAC-----AACAAAAACA 3352
                                  i    vi   i  v        v   -----  i     v 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_45231287_4   3353 CAAATAACTCAGTTAAAATATGGTAAACAGATTTGAATAAACATTTCTCC 3402
                                 i  i  ?   v    vv  vi          i          
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_45231287_4   3403 AA-GATGATATACAAATGTCCAATAAGCACATGAAAA-ATGCTCAATATC 3450
                           -  v            v                  -        i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_45231287_4   3451 ATTAGCTTC 3459
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.77 (92 / 52)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.00 (26 / 13)  


2841 26.37 2.20 2.42  chrX_45241165_45243116.rev      564  1473 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45241165_4    564 TGGAAAAACATTCAATGTTCATGGATAGGAAGAATCAATATCATTAAAAT 613
                               i i  i v            v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45241165_4    614 GACCATACTCTCCAAGGCAATTTATAGATTCAATGTTATTTCCATTAAAC 663
                          i v      i    ivii  i  i        i iv  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45241165_4    664 TACCA--TGACATTTTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCA 710
                          v   --  v -     ii     v v  v  i-  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_45241165_4    711 TATGAAACCAAAAAAGAGCCCCAATAGCCAAGACAATCCTAAGCAAAAAG 760
                             i  viiv  ii  v  vv         i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_45241165_4    761 --CAAAGCTGGAGGCATCATGCTACCCAACTTCAAACTATTCTGCAGGGC 808
                         --     i      vv   ii  v     i      viv v  i  ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_45241165_4    809 AACAGCAACCAAAAAAGCATGGTACTGGTACAAGAACAGACACATAGACC 858
                         v    i  i   i v  ii         i i   i i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_45241165_4    859 AATGGAACAGAGAAGATAACCCAGAAATAAGACTGCACACCTACAACTAT 908
                                i   ivv  v ii          iv iii   ii  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_45241165_4    909 CTGGTCT--GACAAAAA---CAAG------CAATGGGGAAAGGATTTCCT 947
                         i  i i --     iii---    ------            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_45241165_4    948 ATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGACTGA 997
                         v     i              i      v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_45241165_4    998 AACTGGACCACTTCCTTAAACTGTATAGAAAAGTTAGTTCAAGATGGATT 1047
                          ii      v  v   i v  ii    v    i   ii    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_45241165_4   1048 AAAGACTTAAATGTAAAACCCAAAACTATAAAAGAAAAAACAACAACAAC 1097
                          ?    i         i v i            ------------- --i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-------------C--T 533

  chrX_45241165_4   1098 CCTGGAAGACAACCTAGGCA-ATACCATTCAGGACATAAGCACAGGCAAA 1146
                          i i     v   v    ?i- v i -   iv   v vi vvi      v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chrX_45241165_4   1147 GATTTCATGACAAAGACGCCAAAAGCAATCA--CAACAAAAGCAGACATT 1194
                          i    v iivv v   i         --  --         v i v  v
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATA 630

  chrX_45241165_4   1195 GACAAATGGGATGTAATTAAACTAAAGAACTTCTGCACAGTGAAAGAAAC 1244
                           i    v   iv v  i   v v  i     i  ii vvii  i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_45241165_4   1245 TGT-AAGCAGAGTAAAAAGACAACCTGGGAGAATGGGAGAAAATTTTTGC 1293
                          i -   - i   i           iiv-               v     
  L1M4_orf2#LINE/    681 TATCAAG-AAAGTGAAAAGACAACCCAC-AGAATGGGAGAAAATATTTGC 728

  chrX_45241165_4   1294 AAGCTATGTATCCAACAAAGATCTAATATCCAGCATCTATAAGGAACTTA 1343
                           iii  i    ii i  i iv  vi       v  v     i     iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_45241165_4   1344 AACAAATTTACAAGAAAAAAACAAACAACCCCATTAAAGAGTGATGAAAG 1393
                         v    v iv i  v     i     i     v   ?  i i  ivv    
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_45241165_4   1394 GACATGAATAGACACTTCTCAAAAGAAGACATACATGTGGCCAACAATCA 1443
                           iv          i     v        i     vi       i  v  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_45241165_4   1444 TATGAAAAAAAAACCAACATCTATGTACCC 1473
                         i       i vivi       v????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (150 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.47 (42 / 17)  


2482 25.69 4.53 1.64  chrX_45251659_45255503     2067  2860 (985)    L1M4_orf2#LINE/L1        1   817 (91)  

  chrX_45251659_4   2067 TGGGAAAACATCCCATGCTCATGAATAGGAAGAATCAATATCATTAAAAT 2116
                            i  i i        i     i  v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45251659_4   2117 GTCTATACTGCCCAAAGCAACCTACAGATTCAATGCTATTCCTATCAAAT 2166
                          v v     v      vii i            i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45251659_4   2167 TACGAGCATCATTTTTCACA-AAATTAGAAAAAACT-ATTTTAAAACTCA 2214
                          v v   vv v     ii  -     i-- v  i  -  ii     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_45251659_4   2215 CTTGCAACCAAAAAAGAGCCCAAATAGCCAAAGCAATTCTAATCAAGAAG 2264
                         iv  v  viiv  ii  v  vi          i    ii i vv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_45251659_4   2265 AACAAATCTGGAGGCATCACATTACCCAATATCAAAGC-----------C 2303
                               vi      vv     i v      v     i ----------- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_45251659_4   2304 TATGGTAACCAAAGCAGTGTGGTATGGGCACAAAAACATACATATAGACC 2353
                           ii    i   ii          iv    i  ii i v         i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_45251659_4   2354 AATGGAGTAGAATAGAGGACCCAGAAATAAAGA-ATCACACCTACCACCA 2402
                               i      v   iii           vv-  -   ii  ivii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGGTCA 347

  chrX_45251659_4   2403 ACTGATCTTTGACAAAGTGGACAAAAATAAGCAGTGATGAAAGAACTCCC 2452
                          i    i  i     i vv v   i vi vv  i  iv       ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_45251659_4   2453 TATTCCGTAAATGGTGCTGAGATAACTAAGTAT----ATGCAGAAGAATG 2498
                          v   vii           i  i    iii  ?----     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_45251659_4   2499 AAACTGGACGCCCACCTGTCACCATATACAAAAATTAACTCAAGATGGAT 2548
                           ii     v  i    vv                        i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_45251659_4   2549 TAAAAACTTAAATGTAAGACCTTAA-TTGTAAGAATCCTAGAAGAAAACC 2597
                         i ? i  i           v  v  -i i   i v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_45251659_4   2598 TAGG---AAATACCCTTCTGGACATAAGCTCTGACAAATAGTTT------ 2638
                             ---    ---    vv   v vi v iv i   - i    ------
  L1M4_orf2#LINE/    548 TAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA 593

  chrX_45251659_4   2639 -ATGACCAAATTCTCAAAAGCAATTGCAACAAAAACAAAAATTGACAAGT 2687
                         -     --- i---        vvv         iv      v  i  i 
  L1M4_orf2#LINE/    594 TATGAC---AC---CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_45251659_4   2688 GGGACCTATTTAAGCTGCAGAGCTTCTGCATAGCAAAAGAAACTATCAAC 2737
                         v    i vv i  iv vv i i   i  iiivv    i  v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_45251659_4   2738 AGAATAAACACACAACCTACAGAATGGGGGGAAATATCCACAAACTATGC 2787
                          i i i  v v      i          i i      iii    ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_45251659_4   2788 ATCTGACAAAGGTCTAACATCCAGAATATATAAGGAACTCAAACAA---- 2833
                               i  i  v  vii               i      vv    ----
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_45251659_4   2834 ATAAGCAAAAGACAAC---CCCAATGCAAA 2860
                             vv         v---      v?   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAA 817

Transitions / transversions = 1.45 (119 / 82)
Gap_init rate = 0.02 (16 / 817), avg. gap size = 3.06 (49 / 16)  

 354 23.30 3.88 0.00  chrX_45251659_45255503     3255  3357 (488)    L1M4_orf2#LINE/L1      802   908 (0)  

  chrX_45251659_4   3255 AATAATTT--TTAAAAAGTGGACAAAGGACATGAACGGACATTTCTCAAA 3302
                              iii--  ?    i   i       iv    ii          v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_45251659_4   3303 AGTAGACATACACGCAGCCAAGAA--ATATGAAAAAATGCCCAAATTTAC 3350
                           v   i     viii     v  -- i       i    i   vv i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_45251659_4   3351 TAATCAT 3357
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.02 (2 / 107), avg. gap size = 2.00 (4 / 2)  


2989 27.54 0.88 0.44  chrX_45306226_45308220      605  1508 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45306226_4    605 TGGAAAAACATCCCATGCTCATGGATAGGAAGAATCAATATCATAAAAAT 654
                               i i        i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45306226_4    655 GACCATACTGTCCAAAGCAATTTATAGATTCAATGCAATTCCTATGAAAC 704
                          i v     vi     vii  i  i        i     i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45306226_4    705 TACCATCGAGATTCTTCACATAACTAGAAAAAACT-ATTTCAAAATTTGT 753
                          v   v vivv  i  ii  v  v v  v  i-  -  iii      ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_45306226_4    754 ATGGAAACAAAGAAGAGCCTGAATAGCCCAAGCAATCCTAAGCAGAAAGA 803
                                iiv iii  v  v        v  i     i i iv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_45306226_4    804 ACAAAGCTGGAAACATCATGCTACTCGCCTTCAAATTATACTACAGGGTG 853
                               i    iivv   ii  v i ivi      viv       ii iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_45306226_4    854 AAAGTTACCAAAACAGCATGGTACTAGTACAAAAACAGACACATGGACCA 903
                          v   v i   i    ii       i i i  ii i     i  i  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_45306226_4    904 ATGGAACAGAATAGAGAACCCAGAGATAACCCCACACACTCACAACTCTC 953
                               i     v    ii     i    v    i   i i iiiiivvi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_45306226_4    954 TGATCTTCAGAAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCCCTA 1003
                             i   iiv  ivv  v   i v  vv       i    i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_45306226_4   1004 TTCAGTAAATGGTGTTGGGATAAGTGGCTAGCCATATGCAGAAGATTGAA 1053
                             ii        i     i  v   v  ?   i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_45306226_4   1054 ACTGGACCCCTTCTTTACACCATATACAAAAATTAACTCAAGATGGATTA 1103
                         ii         v i i                         i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_45306226_4   1104 AAGACTTAAATGTAAAACCCAAAACTGTAAAAATCCTGGAAGGCAACCAA 1153
                         ?    i         i v i      i     v  i i    iv   vv 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_45306226_4   1154 GGCA-ATACCATCCTGGACAAAGGAACGGGCAAAGATTTCATGACAAAGA 1202
                           ?i- v i v  v  -  vvv  ivii     v i    v iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_45306226_4   1203 CGCCAAAA--ACAATTGCAACAAAAGCAAAAATAGACAAATGGGAACTGA 1250
                          i      --    --          v         i    v   vi v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_45306226_4   1251 TTAGACTAAAGAGCTTCTGTGCAGCAAAGGTGAGTATCAACAGAGTAAAC 1300
                          i i v v  i i   i     vv      vv v      v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_45306226_4   1301 AGACAACCTAAAGAATGGGAGAAAAAGTTTGCAAACAATGCATCTAACAA 1350
                                 i v              vi        iv  ii    i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_45306226_4   1351 AGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATCTACAAGAAAA 1400
                         i  v  vi       v  v     i     ivv    v  v i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_45306226_4   1401 ---CAAACAACCCCAT-AAAAAGTAGGCAAAGGACATGAACAGACACTTT 1446
                         ---    i     v  -?    i i         iv    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_45306226_4   1447 TCAAAAGAGGACATACATGCAGCCAACAATCACATGATAAAAAGCTCAAG 1496
                           v     i  i     viii     i  v       v  i v      v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_45306226_4   1497 ATCTCTGATCAT 1508
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


 496 29.06 5.66 3.40  chrX_45533064_45535671.rev      630   894 (1714)    L1M4_orf2#LINE/L1        1   271 (637)  

  chrX_45533064_4    630 TAGAGAGGTATGCT-TGTTTGTGGATGAGAAGATTCAATATT-TTAAGGT 677
                          i  i  i   v i-    ii     vi     i i      -     i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45533064_4    678 TGTCAATTCTTACTAAGTTAGTCTCTAAATT-AATGCAACTTCAATTAAA 726
                         v -    v  iv i  i  ii   vi i   -  i    iii v  i   
  L1M4_orf2#LINE/     51 GG-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_45533064_4    727 ATTATACCAGAATAC--TTAATGTATT--TTAACAAACTAATTATCAAAT 772
                           i---    v- i --  vv  i vv--  i    i  i  iv v    
  L1M4_orf2#LINE/    100 ATC---CCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_45533064_4    773 TCATATAGCAGTGTAAA--ACTAATGAAAATCCAAGACATTCCTGAAAAA 820
                               i v i  i  i--  iv -   v v    i   v  i       
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAA 194

  chrX_45533064_4    821 ATATAGGACAA----GGACG-TTTGCTCTGCCGGATATAAAGAATTA-TA 864
                         i- -  i    ----   v -i ii v  v  vi  v v  i v   -  
  L1M4_orf2#LINE/    195 G-A-AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_45533064_4    865 TACAGCTACAGTGATTAGGCCGGGCGTGGT 894
                         i v         i  i i v i -i     
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAG-TGTGGT 271

Transitions / transversions = 1.75 (49 / 28)
Gap_init rate = 0.06 (16 / 271), avg. gap size = 1.50 (24 / 16)  

 592 28.92 12.05 4.58  chrX_45533064_45535671.rev     1181  1595 (1013)    L1M4_orf2#LINE/L1      244   689 (219)  

  chrX_45533064_4   1181 AAAGCTACAGTGATTAAAACAGATTAAAACAGAGTGATATTAGCATGAGA 1230
                                    i  i  i    -- --------   i  i i    i  i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAG--T--------GTGGTACTGGCATAAGG 283

  chrX_45533064_4   1231 ATAAATAAGTAGATTGATGGAATAGAAGAGGAATCCCAGAAACAGAC--- 1277
                            i i vi     ii           vv ii vi       i i  ---
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_45533064_4   1278 TGGATATATGG------GGATTACTACAGAAAT----AGACTTATAAATC 1317
                          iv  v     ------ iv  v v   iiii ----    i-  ---  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC-AT---TC 379

  chrX_45533064_4   1318 ATTAGGGGAAATTCTAAACTATTTAATGACTACTATCAGGAGATTTGATT 1367
                          v -       vvv  iv  v  i  ii v iv iiii   v vi  iv 
  L1M4_orf2#LINE/    380 AAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_45533064_4   1368 ATCCCTACGTGGAAAACAA-AAAATT-----CTTACCTCTTAGTATTGAC 1411
                          ?  --  i  v    v  -i  i  ----- i      vi vi  vv  
  L1M4_orf2#LINE/    429 AKCC--ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_45533064_4   1412 AGAAACCAGATTTTAAATGGAT---GTATCTGACTGTGGAAATCAGAATT 1458
                          i   ii - i iv        ---iv i  i v   iii iii i  i 
  L1M4_orf2#LINE/    477 AAAAATTA-ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_45533064_4   1459 -TAGAAATTATTAGAA--AAATTTTAGAATA--TCTTTGTG--------- 1494
                         -  -   i v      --   iv vi ?i  --    i   ---------
  L1M4_orf2#LINE/    526 ATA-AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_45533064_4   1495 TATGCAGT----------ATACGTCATAAAAAGCACAAGTCACAAAGGGA 1534
                           v   i ----------   i v  iv           iv     i i 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_45533064_4   1535 AATATTGATAAATTGGACTACACTAAAATTTAAAACTTCTGTAT---AAA 1581
                           v  v             v  ii      v       i   ii---   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_45533064_4   1582 AAATAC-ATCACGAA 1595
                         ii i  -    v   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAA 689

Transitions / transversions = 1.88 (77 / 41)
Gap_init rate = 0.05 (21 / 446), avg. gap size = 3.29 (69 / 21)  

 446 25.12 6.98 2.79  chrX_45533064_45535671.rev     1903  2117 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_45533064_4   1903 AAAAAAAAAAAAAGTTGAACAATC----GCTTGGGAGGCTATATTTGCAA 1948
                           i   ivi     ----    i ---- vv      ivv          
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAG----ACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_45533064_4   1949 TGCATATAACTATCACATGGTTGGTATCCAGAATAGATGAAGATATTCTA 1998
                         vv      v  ivi viv ii v            v  i    - i   -
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA-ACTCT- 778

  chrX_45533064_4   1999 TATA--TTGAT--TAGAAA--TAAAT--CAGAA---AAAAATGGGTAAAT 2037
                           i -- ii  --  i   --i    -- vv  ---         i   v
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_45533064_4   2038 GATATGAGCAAGCAATTAATGGAAGAGGGCATACAAATAGCCAATAAACA 2087
                            v   ii ii  v  vvivi    i ii        i        i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_45533064_4   2088 TATAAAAAGAGGCTCAACCTCACAAGTAAT 2117
                         i  i      v       v   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (31 / 23)
Gap_init rate = 0.04 (9 / 224), avg. gap size = 2.33 (21 / 9)  


3658 19.83 1.59 5.30  chrX_45578533_45583721.rev     3756  4698 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45578533_4   3756 TGAAAAGATATCCCCTGTTCATGGATTGGAAGACTTAATAATGTTAAGAT 3805
                           i           v                         v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45578533_4   3806 GTCAATACTACTCAAAGTGATCTACAGATTCAGTATAATCCTTATCAAAA 3855
                          v       v i    v               iiii     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45578533_4   3856 TACCAATGATTTTTTTTACAGAAATAGAAATATCT-ATTCTATAATTCAT 3904
                          v   iiviii      i       v  v - v  -  i   v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_45578533_4   3905 ATAAAATCTCAAGGAACCCTGAACAGTCAAAATAATCTTGGAAAAGAACA 3954
                           ii  viv     i    v   i  i     i       i       v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_45578533_4   3955 ACGAAGTTTAAGGCCTCACACTTCTTGATTTCAAAACTTACAGCAAAATT 4004
                           i     vi   v          iii              vi    ii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_45578533_4   4005 ACAGAAATCAAAACGGTGGAGTATTGCCATAAAGACAGACATATAGATCA 4054
                             v      i  i   vi   i  v     i  i              
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_45578533_4   4055 ATAAAATAGAATAGAGAGCCCCCAAATAAGCTTATA----TATAATCAAA 4100
                           ii        v     i  vv      i ii   ----   ii    v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_45578533_4   4101 TGCTTTTTGCCAATGCCGCAACGACCATTTGAAGGGGGAAAGAATAGTCT 4150
                           v    i v   v vi  v v       i-  v                
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTC-AATGGGGAAAGAATAGTCT 398

  chrX_45578533_4   4151 TCATTCTTTTCCATATGCATATACAGTTTTCCCAACAGTTTGTTGAAAAG 4200
                          -------   v i ------------------  ii  -----------
  L1M4_orf2#LINE/    399 T-------TTCAACA------------------AATGGT----------- 412

  chrX_45578533_4   4201 ACAGTTGGGAAAACTGTGTATGCATATGGAAAAGAATGAAGTTAGAATTT 4250
                         --- i     v     vi  ?v  i   v              i  viii
  L1M4_orf2#LINE/    413 ---GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_45578533_4   4251 TGCCTTATACCAGTCACAAAAATTAACTCAAAATGTATCAAAGACCCAAA 4300
                          i   i i    vvi                    v    ?     i   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_45578533_4   4301 CATTAGAGCTAAAACTGAAGTCTTCTGAAGTCTTAAAATAAAATGTAGGG 4350
                         ii v            iv i-------  v     i  v    ii    ?
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAA-------AACTCTTAGAAGAAAACATAGGN 552

  chrX_45578533_4   4351 GAATACCTTCAATGACATTAGATTTGGCAATGATTTCTTGAATATGACAC 4400
                          v v i    i-    v  i i  v       i      ii         
  L1M4_orf2#LINE/    553 GTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_45578533_4   4401 CAAAAGCAGAGGCAACAACA-AAAAAAT---TAAATTGAATTACATTAAG 4446
                                 v i       v -       ---       i i v   i  i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_45578533_4   4447 ATTAAAAACATATGTGCACTAAAGGGCACTATCAACAGAATGAAAAGGCA 4496
                                  v v     vii     i         v i i       i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_45578533_4   4497 ACCCATGAAATGAGAGAA--TATTTGCAAATAATATATATGATAAAATGT 4544
                              iii    i     --           v      v      iivii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_45578533_4   4545 TAATGTCCAGAAGATACTAAAAAACTCCTACATCTAAAGAACAAAAAAAT 4594
                          vi i       v   -    i     i    v  v  v  i     i i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATA-TAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_45578533_4   4595 CAA--ACCCAATTTAAAACTAGGGAAATGAATTGAATAGATATTTCTCCA 4642
                         v  --        ?    v i  v   v  v         i         
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_45578533_4   4643 AAGAAGACATAGGAATA--CAAAAAGCACTTGAAGATATTCCCAACATCA 4690
                                i   vi   i--   v      v    i v  v i        
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_45578533_4   4691 CTAATTAT 4698
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.47 (109 / 74)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.33 (65 / 15)  


 505 22.05 2.36 0.00  chrX_45614257_45620677.rev       12   138 (6283)    L1M4_orf2#LINE/L1      461   590 (318)  

  chrX_45614257_4     12 ATCTCACACCTTATACAAAAATTAACTCAAAGTAAATCAGTAA-TTAAAT 60
                          i        v                    i ii    ?vi -i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_45614257_4     61 GTAAAATATAAAATTATAAAACTTTTAGA-GAAAAC-TAGGAGAAAATTT 108
                             i vv     i         i     -      -    ? v    i 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_45614257_4    109 GGGGGATCTGGGGCTAGAAAATAGTTCTTT 138
                         vv v  i  v   i   iv   i   ii  
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.60 (16 / 10)
Gap_init rate = 0.02 (3 / 130), avg. gap size = 1.00 (3 / 3)  

 455 20.51 2.56 0.85  chrX_45614257_45620677.rev      386   502 (5919)    L1M4_orf2#LINE/L1      547   665 (243)  

  chrX_45614257_4    386 ACAGGCGTGAGCCACCAC-ACC-TGGCCTA-GCAAAGAGTTCTTAGACAT 432
                          i   ?  i ii vi ii-   -   vi  -    v iv        i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_45614257_4    433 TGATACCAAAAGAACAATCCACAAAAGGAAAAACTGATAAATTGGCCTTC 482
                         -  i        v    v v       i     iv          v    
  L1M4_orf2#LINE/    597 -GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_45614257_4    483 ATCAAAATTTAAAACTTTTG 502
                                  v          
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.03 (4 / 119), avg. gap size = 1.00 (4 / 4)  

3248 26.81 0.44 0.66  chrX_45614257_45620677.rev     5021  5930 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45614257_4   5021 TGGAAGAACATTCCATGTTCATTGATAGGAAGAATCAATATCACAAAAAT 5070
                              ii i  i          v   v      v i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45614257_4   5071 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5120
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45614257_4   5121 TACCAATGATTTTCTTCACAGAA-TTGGAAAAAAAACT-ACTTTAAAGTT 5168
                          v   iiviii  i  ii     -   ---- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chrX_45614257_4   5169 CATATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAATCCAAA 5218
                                  viiv  ii  v  v v  v     i      i i vvv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_45614257_4   5219 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 5268
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_45614257_4   5269 GCTACAGTAACCAAAACAGCAGGGTACTGGTACCAAAACAGAGATATAGA 5318
                                   i   i    iiv        i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_45614257_4   5319 CCAATGTAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAA 5366
                         i     v  i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_45614257_4   5367 CCAACTGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATT 5416
                         i   i    i  i     ivv  v   i v  vv      i     i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_45614257_4   5417 CCCTATTTAATAAATGGTGCTGGGAAAACTGCCTAGCCATATGTAGAAAG 5466
                         vi  v  i  i              v     vv  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_45614257_4   5467 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5516
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_45614257_4   5517 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5566
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_45614257_4   5567 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCC 5616
                           v    ?i v viv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_45614257_4   5617 AAAACACCAAAAGCAATGGTAACAAAAGCCAACATTGACAAATGGGATCT 5666
                          vi            vvi i        vv  v  v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_45614257_4   5667 AATTAAACTAAAGAGCTTCGGCACTACAAAAGAAACTATCATCAGAGTGA 5716
                         v  i   v v  i i   iv ii  v    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_45614257_4   5717 ACAGACAACCTACAGAATGGGAGAAAAGTTTTGCAATCTACTCATCTGAC 5766
                          v        i                vv       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_45614257_4   5767 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5816
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_45614257_4   5817 AAAAACAAACAACCCCATCAAAATGTAGGTGAAGGATATGAACAGACACT 5866
                            i     i     v  i?   vi i  ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_45614257_4   5867 TCTCAAAGGAAGACATTCATGCAGCCAAAAGACACATGAAAAAATGCTCA 5916
                             v  i     i  v  viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_45614257_4   5917 TCATCACTGGCCAT 5930
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.00 (10 / 5)  


 581 32.11 0.00 0.00  chrX_45662348_45666983     2974  3163 (1473)  C L1M4_orf2#LINE/L1   (718)   190     1  

C chrX_45662348_4   3163 TGGAAAAACATTCCATGCTCATGGATAGGAAGAAACAATGTTGTAAAAAT 3114
                               i i  i     i        v      vvi   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_45662348_4   3113 GGCCATACTGCCCAAAGCAATTTATAGATTCAATGATATTTCTATTGAGC 3064
                            v     v      vii  i  i        i vv  ii    ii iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_45662348_4   3063 TACCATCAAGATTCTTCACTGAACTAGAAAAAACTATTTTAAAATTAATG 3014
                          v   v vivv  i  ii v   v v  v  iviv  ii       v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chrX_45662348_4   3013 TAGAACCAAAGAAGAGCCCGAATAGCCAAGGCAATCTTAA 2974
                          i   viiv iii  v  v          ii       i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

Transitions / transversions = 1.35 (35 / 26)
Gap_init rate = 0.00 (0 / 190), avg. gap size = 0.00 (0 / 0)  

3196 24.34 1.49 2.17  chrX_45662348_45666983     3276  4150 (486)    L1M4_orf2#LINE/L1       40   908 (0)  

  chrX_45662348_4   3276 ATTGT---GATATCAGTTCTTCTCAACGTGATCTACAGATTCAATGAAAT 3322
                              ---   iv  i v  i i   vv                i v   
  L1M4_orf2#LINE/     40 ATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

  chrX_45662348_4   3323 CCCAATCAAAATCCCAGCAAATTATTTTTGTGAATACTGAGAAACTGATT 3372
                            v              vivi -      iii v i   v  i     i
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATC 138

  chrX_45662348_4   3373 CTAAAGTTTATATGGAGAAGCAAAAAAAAAAAAATCCAAAAACAGAATAG 3422
                              i  i       i v    iii --------  -----        
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGA--------CC-----CAGAATAG 175

  chrX_45662348_4   3423 CTACA-CAATGTTGAAGAAGAAGAAAAAAATTCGAGAAATGACACTACCC 3471
                          i v -    v     i        v   i  v   i v v     v   
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_45662348_4   3472 AACTTTAAGACT-ACCATAAAGCTACAGTAACCAAGACAGTATAGTGTTG 3520
                           i  i  i   -  i i             i         i i  ii  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_45662348_4   3521 GTAGAAGGATAGACAAATAGGTCAATAGAACAGAATAGAAAGCCCAGAAA 3570
                          i v           v    i     i   i     v  i  i       
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_45662348_4   3571 TAGACTCG--CATCAATAAAATCAACTGATAATTGACAAAAGAACAAAGG 3618
                           i  i i--   iv  ii--    i    vv i     ii vi v   i
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGG--TCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_45662348_4   3619 CAATTCAATGGAGCAGAGAGAGTCTTTTCAACAAATGCTGCTGAAACAAT 3668
                          v         i v iii v                 v     ii    i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_45662348_4   3669 TGGACATCCACATGCAAAAGAAGTTAATCTAGACTCAAACCTTACATTCT 3718
                             i ?               - v  vi i   i vv    i   iiv 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_45662348_4   3719 TCACAAAAATTAA-----AATCAATTAAAGACTTAAATGTAAAACACAAA 3763
                         vi           -----   vi  i ?    i         i vvi   
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_45662348_4   3764 ACTATAAAATTCCTAGAACATAACCTAGGAGAAAATTTAGATGACCTTGG 3813
                                  i  i     v v   v    ? v    i vvi         
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_45662348_4   3814 GTTTGGTGATGACTTTTTAAATATGACACAGAAAGCACACTCCATGGAAG 3863
                            v  ii   ii  i   i         vi        vv v iii   
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_45662348_4   3864 AAAGAATTGATAATTTGGACCTAATTAAAATTAAAATTTTACGTTCTGCA 3913
                            i   v     v      i v  i          vi  vi  v  v  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_45662348_4   3914 AAATATACTATCAAGAGAGTGAAAAGACAAGCCACAGTCTGGGAGAAAAT 3963
                           iv i          i             v      vv           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_45662348_4   3964 ATCTTCAAAAGACATATTTGATAAAGAACTGTTATGTAAAATATACAAAG 4013
                           i v    vv i    i      i i   vv   vi i      i    
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_45662348_4   4014 AACTTTTAAAATTTAACAGTAAGAAAATGAACAACCTGATTTTTAAAAAT 4063
                             i   v  i i  i i   i  i ii  i    ii   ?--      
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW--AAAAAT 820

  chrX_45662348_4   4064 GAGTCAAGACCTTAAA-AGAAACCTTCCCAACAGAGATACATAGATCCCA 4112
                          i iv   ivi  i  -   v ii ii    vii     i i i  vv v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_45662348_4   4113 AATACACACTTGAAAAGATGCTCCATGTAATATGTCTT 4150
                             vi   v             v ii v ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (130 / 79)
Gap_init rate = 0.01 (12 / 869), avg. gap size = 2.67 (32 / 12)  


3141 28.19 0.44 0.44  chrX_45667974_45674638.rev     5267  6174 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45667974_4   5267 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5316
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45667974_4   5317 GGCCTTACTGCCTAAGGTAAGTTATAGATTCAATGCTATCCCCATCAAGC 5366
                            vv    v  i  iv i vi  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45667974_4   5367 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5414
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_45667974_4   5415 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAACCAAAAG 5464
                                viiv  ii  v  v v  v     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_45667974_4   5465 AACAAAGCTGAAGGCATCATGCTACCTGACTTCAAGCTATACTACAAGGC 5514
                                i  i   vv   ii  v  ii i     iviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_45667974_4   5515 TACAGTAACCAAAACAGCAGGGTACTGGTACCAAAACAGAGATATAGACT 5564
                                 i   i    iiv        i iv ii i   v       ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_45667974_4   5565 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5612
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_45667974_4   5613 ATCTGATATTTGACAAACTTGAAAAAAACAAGATATGGGGAAAGGATTCC 5662
                          vi    v  i     ivv  vv  i v  vvvv          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_45667974_4   5663 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATACGTAGAAAGCT 5712
                           v  i  i        i     v      v  ?   i i i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_45667974_4   5713 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5762
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_45667974_4   5763 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5812
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_45667974_4   5813 CTAGGCATTACCATTCAGGACATAGGCATGGGCAACGACTTCATGTCTAA 5862
                         v    ?i v viv   iv   v v  vv i     i ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_45667974_4   5863 AGCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5912
                         ii           vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_45667974_4   5913 TTAAACCAAAGAGCTTCTGCACAGCAAAGGAAACTATCATTAGAGTGAAC 5962
                          i   viv  i i   i  ii vv       v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_45667974_4   5963 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 6012
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_45667974_4   6013 AGGGCTGATATCCAGAATCTACAATGAACACAAACAAATTTACAACAAAA 6062
                         i  i  vi          v  i  v    v vv    v iv i  i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_45667974_4   6063 AAACAAACAACCCCATCAACAAGTAGGTGAAGGATATGAACAGACACTTC 6112
                          i     i     v  i? v  i i  ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_45667974_4   6113 TTGAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 6162
                          iv        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_45667974_4   6163 ATCATTGGCCAT 6174
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (151 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3292 27.20 0.33 0.33  chrX_45690496_45696919.rev     5026  5933 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45690496_4   5026 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATCAAAAT 5075
                              ii i  i     i        v      v i     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45690496_4   5076 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5125
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45690496_4   5126 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5173
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_45690496_4   5174 TATGGAACCAAAAAAGAGCCCATATTGCCAAGTCAATCCTAAGCCAAAAT 5223
                                viiv  ii  v  viv  v     iv     i i ivv i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_45690496_4   5224 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5273
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_45690496_4   5274 TACAGAAACAAAAACAGCATGGTACTGATACCAAAACAGATATATAGACC 5323
                              v  iv  i    ii        ii iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_45690496_4   5324 AATGGAACAGAATAGAGGCCTCAGAAATTATGCCACACATCTACAATCAT 5373
                                i     v   ivii       v vv   i    i  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_45690496_4   5374 CTGATCTTTGACAAAACTGACAAAAACATGCAATGGGGAAAGGATTCCCT 5423
                         i    i  i     iiv  v   i v   v            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_45690496_4   5424 ATTTAATAAATGGTGCTGGGAAAACTGCCTAGCCATATGTAGAAAGCTGA 5473
                         v  i  i              v     vv  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_45690496_4   5474 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGAATT 5523
                          ii    i    v   i     v              i    i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_45690496_4   5524 AAAGACTTAAATGTTCGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5573
                          ?    i       vv  v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_45690496_4   5574 AGGCA-ATACCGTTCAGGACATAGGCATGGGCAAGGACTTCGTGACTAAA 5622
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_45690496_4   5623 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATGTAAT 5672
                                     vvi          vv     v  i    v   iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_45690496_4   5673 TAAACGAAAGAGCTTTTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5722
                         i   vvv  i i      ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_45690496_4   5723 GACAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5772
                                i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_45690496_4   5773 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 5822
                           i  vi          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_45690496_4   5823 AACATACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACCCTTCT 5872
                         i   v i     v  i?    i            v    i    vi    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_45690496_4   5873 CAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGTTCATCA 5922
                          v        i  vi viii     i ii  i       i   i   v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_45690496_4   5923 TCACTTGTCAT 5933
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


2999 27.99 0.88 0.44  chrX_45702018_45708714     5301  6204 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45702018_4   5301 TGGAAAAACATTCCAGGCTCATGGATAGGAAGAATCAATATCGTAAGAAT 5350
                               i i  i   v i        v      v i     i  v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45702018_4   5351 GGCCATACTGCCCATGGTAATATATAGATTCAATGCTATCCCCATCAAGC 5400
                            v     v    viv i  v  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45702018_4   5401 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5448
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_45702018_4   5449 TATGGAACCAAAAAAGAGCCCATATTGCCAAGACAATCCAAAGCAAAAAG 5498
                                viiv  ii  v  viv  v     i      ivi iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_45702018_4   5499 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATACTGCAAGGC 5548
                                i      vv   ii  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_45702018_4   5549 TACAGTAACAAAAACAGCATGGTACTGATACCAAAACAGATATATAGACC 5598
                                 iv  i    ii        ii iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_45702018_4   5599 AATGGAACATAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCAT 5648
                                i v  iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_45702018_4   5649 CTGATCTTTGAGAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5698
                         i    i  i  v  ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_45702018_4   5699 ATTTAATAAATGGTGTTGAGAAAACTGGCTAGCCATATGCAGAAAACTGA 5748
                         v  i  i        i  i  v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_45702018_4   5749 AACTGGACCCCTTCCTTACACCTTATAAAAAAATTAATTCAAGATGGATT 5798
                          ii         v   i     v    v         i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_45702018_4   5799 AAAGACTGAAATGTAAGACCTAAAACTGTAAAAACCCTACAAGAAAACCT 5848
                          ?    iv          v        i     vi i  v        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_45702018_4   5849 AGGCA-ATACCATCCTGGACATAGGCATTGGCAAAGACTTCATGACTAAA 5897
                            ?i- v i v  v  iv v i  i- v     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chrX_45702018_4   5898 ACACCAAAAGCA-ATGTCAACAAAAGCCAAAACTGACAATTGGGATCTAA 5946
                                     - v -         vv    iv  i  v v   ii v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_45702018_4   5947 TTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 5996
                          i   viv  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_45702018_4   5997 AGGCAACCTACAGAATGGGAGACAATTTTTGCAATCTATCCATCTGACAA 6046
                           i     i             v   v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_45702018_4   6047 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 6096
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_45702018_4   6097 AAACAA----CCCCATCAAAAAGTGAGTGAAGGATATGAACAGACACTTC 6142
                          i    ----   v  i?    i  i ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_45702018_4   6143 TCGAGAGAAGACATTTATGCGGCCAGCAAACATGAAAAAAAAAGCTCATC 6192
                           v i      i  vi vii     ii  i  iivi    i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_45702018_4   6193 ATCATTGGTCAT 6204
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


 779 27.32 0.82 9.84  chrX_45716627_45725445        1   366 (8453)  C L1M4_orf2#LINE/L1   (546)   362    30  

C chrX_45716627_4    366 AAGAATCAATATAGTAAAAACGGCCATACTGCCCCAAAC-AATGTATAGA 318
                             v i     v  v  i i   v     -       i-i  v  i   
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACT-CCCCAAATTGATCTACAGA 78

C chrX_45716627_4    317 TTCAATGCTATTCCTATTAAACTGCCATTGAGATTCTTCACAGAACTAGA 268
                              i  v  i     i   v v   vivivv  i  ii     v v  
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

C chrX_45716627_4    267 AAAAAAAAGAAACTTTTAAAATTCGTATGGAACCAAAAAAAAAAAAAAAA 218
                         v  ivvi ----- ii        i       ------------------
  L1M4_orf2#LINE/    129 CAAGCTGA-----TCCTAAAATTCATATGGAA------------------ 155

C chrX_45716627_4    217 AACAAACAAACAAACAAAACAGCCTGAACAGACAAGGCAATCCTAAGCAA 168
                         ----------- vi   iiv v  v   i  v   ii     i i iv  
  L1M4_orf2#LINE/    156 -----------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

C chrX_45716627_4    167 AAAGAACAAAGCTGGAGGCCTCATGCTACCTGACTTGAAATTATGCGACA 118
                         i          i      v    ii  v  ii i  v   viv i v   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

C chrX_45716627_4    117 GGGCTACAGTAACCAAAACAGCATGGTGTT--CATACAAAATAGACACAT 70
                         ii          i   i    ii    ii --    - ii       i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA-AGGATAGACATAT 293

C chrX_45716627_4     69 AGACCAATGGAACAGAGTAGAAAACCCAGAAATAATTCCACAAACCTACA 20
                            i        i   i v  i ii          vi   i v ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

C chrX_45716627_4     19 ACTATCTGAACTTAGACAA 1
                         iii vi   vi  v     
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAA 362

Transitions / transversions = 1.86 (65 / 35)
Gap_init rate = 0.02 (6 / 333), avg. gap size = 6.50 (39 / 6)  

2284 26.63 9.27 1.31  chrX_45716627_45725445      492  1332 (7487)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_45716627_4   1332 TGGAAAAACATTGCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAA 1283
                               i i  i-     i        v      v i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATC-CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

C chrX_45716627_4   1282 TGGTCATACTGCCCAAAGTAATTTGTAGAGTCAATGCTATTCCCATTAAA 1233
                            iv     v      v i  i ii   v    i  v  i  i  i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

C chrX_45716627_4   1232 AGACCATTGACATTTTTCACAGAACTAGAAAAAACT-ATTTTAACATTTA 1184
                          vv   vivi v     ii     v v  v  i-  -  ii   v   i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

C chrX_45716627_4   1183 TATGGAACCAAAAAAGAACTTGTATAGCCAAGACAATGCTAAGCAAAAAG 1134
                                viiv  ii  v iv v        i     vi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_45716627_4   1133 AACAAAGCTGGAAGCATCATGCCACCTGACTTCAGACTATACTGCAAGGC 1084
                                i    i vv   ii iv  ii i    i viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_45716627_4   1083 TACAGTAACTGAAACAGCATGGTAC------AAAAACAGACACATAGACC 1040
                                 iii i    ii      ------  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_45716627_4   1039 AATGGAACAGAATAGAGAACTCAGAAATAAGGCTGCACATCT-T------ 997
                                i     v    iii         iv iii    i - ------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

C chrX_45716627_4    996 ---ATTTTTGCATATGGCTAGCCA------------------------GT 974
                         ---     i - i v  v -    ------------------------  
  L1M4_orf2#LINE/    349 TTGATTTTCG-ACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_45716627_4    973 TCTCCCAACA------------------------CCACATATTAAA-AAT 949
                         ii ii     ------------------------      iiv   -   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_45716627_4    948 GA--TT----CCCTATTTAATAATAACCCTATACAAAAATTAACTCAAGA 905
                           --  ----     ii v i ----  v                   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACA----CCATATACAAAAATTAACTCAAAA 492

C chrX_45716627_4    904 TGCATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGA 855
                           v  i ?    i         i v i            vi i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

C chrX_45716627_4    854 CAACCTAGGCA-ATACCATCCTGGACATAGACATGCACAAAGATTTCATG 806
                         v   v    ?i- v i v  v  iv v i ii- ivi   v i    v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTA 591

C chrX_45716627_4    805 ACAAAGACATCAAAAGCAATCA--CAAGAAAAGCAAAAATTGACAAATGG 758
                         ivv v    i        --  --   v     v      v  i    v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTG 639

C chrX_45716627_4    757 GATCTAACTAAGCTAAAGAGATTCTGCACAGCAAAAGAAACTATCATCAG 708
                           ii v ii  iv v  i iv  i  ii vv    i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

C chrX_45716627_4    707 AGTGAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAGTCTATCCAT 658
                               v        i                 v      ivii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

C chrX_45716627_4    657 GTGACAAAGGTCTAATATCCAAAATCTATAAGGAACTTAAACAAATTTAC 608
                         v   i  i  v  vi      i   v     i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

C chrX_45716627_4    607 AAGAAAAA-ACAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAG 559
                           v     -     i     v   ?    i           iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

C chrX_45716627_4    558 ACACTTCTCAAAAGAAAACATTTATGCAGCCAACAAACAC--GAAAAAAA 511
                            i     v      i i  vi viii     i  i   --     i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

C chrX_45716627_4    510 GCTCAGCATCACTGATCAT 492
                              i     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (137 / 84)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.45 (89 / 20)  

3072 26.64 2.12 0.89  chrX_45716627_45725445     7430  8326 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45716627_4   7430 TGGAAGAACATTCCATGCTCATGGATAGGAAGAGTCAATATCGTGAAAAT 7479
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45716627_4   7480 GGTCATACTGCCCAAGGTAAGTTATAGATTCAATGCCATCCCCATCAAGC 7529
                           iv     v     iv i vi  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45716627_4   7530 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 7577
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_45716627_4   7578 TATGGAAGCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 7627
                                iiiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_45716627_4   7628 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTAGAAGGC 7677
                                i      vv   ii  v  ii i      viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_45716627_4   7678 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAAACC 7727
                                 i   i    ii         i iv ii i   v     i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_45716627_4   7728 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATGTGGCATATCTACAACT 7775
                                i    i--    i  --    i   vvivii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_45716627_4   7776 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 7825
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_45716627_4   7826 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTGTATGTAGAAAGCT 7875
                           v  i  i              v      v  ? iii   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_45716627_4   7876 GAAACTGGATCCCT-------------TACAAAAATTAATTCAAGATGGA 7912
                            ii    i    -------------            i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_45716627_4   7913 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 7961
                          i ?    i       v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_45716627_4   7962 CCTAGGCA-ATACCATTCAGGACATAGGCATAGGCAAGGACTTCATGTCT 8010
                          v    ?i- v i -   iv   v v  vv       v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_45716627_4   8011 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGACCT 8060
                          vi            vvi          vv     v  i    v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_45716627_4   8061 AATTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGA 8110
                         v  i   v v  i i   i iii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_45716627_4   8111 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 8160
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_45716627_4   8161 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 8210
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_45716627_4   8211 AAAAACAAAAACAACCCCATCAAAAAGTAGGCAAAGGATGTGAACAGACC 8260
                            i     --i     v  i?    i i          v    i    v
  L1M4_orf2#LINE/    795 AAAGACAAA--TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_45716627_4   8261 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCT 8310
                         i     v        i  vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_45716627_4   8311 CATCATCACTGGCCAT 8326
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.45 (27 / 11)  


3105 15.48 3.84 12.69  chrX_45737656_45739506.rev      502  1360 (491)    L1M4_orf2#LINE/L1      126   908 (0)  

  chrX_45737656_4    502 TGACAAGCTGATATTAAAACTCATTTGGAATTGCAAGGGACCAAAAATGG 551
                                     vi     i    v     v           v i   i 
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chrX_45737656_4    552 CCAAAAC--TCTTTAAAAAGAAGGACAAAGTCAGAGCATTCACACTTTTC 599
                                --    v         i       ii   v i        ii 
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_45737656_4    600 AATTTCAAAAC-------AATG-----GTATTCAA-ACAGTGTGGTATTG 636
                                    -------  v -----   v    -           i  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_45737656_4    637 GCATAAGATATCTCTATGTCTACCTGTCTATTTATCTATCTATCTATCAT 686
                                i------------------------------------------
  L1M4_orf2#LINE/    276 GCATAAGG------------------------------------------ 283

  chrX_45737656_4    687 CTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCATCTGTCTG 736
                         --------------------------------------------------
  L1M4_orf2#LINE/    284 -------------------------------------------------- 283

  chrX_45737656_4    737 TCTATCTACCTATCTATCTATGTAATCTCAATGCAATAGAAGTGAGAATC 786
                         ---  vv  v   vv   -----------    v       v     i  
  L1M4_orf2#LINE/    284 ---ATAGACATATAGATC-----------AATGGAATAGAATTGAGAGTC 319

  chrX_45737656_4    787 CAGAAATGAGTCCGTCCATCTACAGTCAACTTATTTCTG-CAATGGTGTC 835
                                i ii  i v   i  ii     i v    ii -   v    i 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_45737656_4    836 AAGACCATTTAATAGGGAAAGAATAGTTTTTTCAACAAATGGTGCTAGGA 885
                                  i   i             i                  i   
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_45737656_4    886 CAACTGGATATCCAGGTGCAAAATAATGAAGCTGAACCCCTATATTACAC 935
                                   ?   vi       v       i  i       iv i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_45737656_4    936 CATATACAAAAATTAACCCAAAAAGAATCAGGGACCTAAATGTA-GCACT 984
                                          i     v i    ?i            - vi  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_45737656_4    985 AAAACTACCAAATTCTGAGAAGGAAACATAGATGTATATCTTTGTGAACT 1034
                                iv   i   v     i        i?   v     i    v  
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_45737656_4   1035 TGGACTAAGCAGTGGTTACCTAAATATGACACCAAAACCATATATATCAA 1084
                            ii  i   i     v i  i              v  i vii v   
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_45737656_4   1085 AATAAAAAAATGGATAATTTTTATTTCATCAAAAATTTAAAAG---TTGT 1131
                           -i       i     v  vv i          --      i---    
  L1M4_orf2#LINE/    620 AA-GAAAAAATAGATAAATTGGACTTCATCAAAA--TTAAAAACTTTTGT 666

  chrX_45737656_4   1132 GTATCAAAAGAAACTATTAATTGAGTGAAAAGACAGCCCACACAATGGGA 1181
                          iv     i  v     i  vvi            i      v       
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_45737656_4   1182 GAGAATATTTGCAAATCATATGTCTGCTAAACGTCTAGTATTCCGAATAT 1231
                           i                  i    v   iv v  v    i v      
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_45737656_4   1232 ATAAAGACCTCCTACAACTCAACGATA----GACGAGTAAC---AGTTAA 1274
                                v   i          ii   ----   i i    --- v ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_45737656_4   1275 GAATGGGCAATGCTTTTTAATAAACATTTCTCCAAAGAAGGTAT------ 1318
                         i         v vv   v    i                 i   ------
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_45737656_4   1319 GGCCAGTAAGAACCTGGAGATATGCTCAGCATCATTAGTCAT 1360
                              i    v  v  i i v       i     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (76 / 53)
Gap_init rate = 0.02 (14 / 783), avg. gap size = 10.14 (142 / 14)  


3055 27.89 0.22 1.31  chrX_45789486_45793804.rev     2911  3828 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_45789486_4   2911 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAACATTGTGAAAAT 2960
                               v i        i        v  v   v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45789486_4   2961 GACCATATTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 3010
                          i v   i v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45789486_4   3011 TACTACCATTATTCTTCACAGAACTAAAAAAAAAAAAAAAAAAAAAAATC 3060
                          v i v vviv  i  ii     v vi v  ivvi ------------  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA------------TC 138

  chrX_45789486_4   3061 CTAAAATTCGTATGGAACCAAAAAAGAGCCTGCATTGCCAAAGCAATACT 3110
                                  i       viiv  ii  v  v v  v      i    vi 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chrX_45789486_4   3111 AAGCAAAAAGAACAAATCTGGAGACATCGTATTACTTAACTTCAAACTAT 3160
                         i iv  i         vi     ivv  ii i v ii  i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_45789486_4   3161 GGTATAAGGCCATAGTCACCAAAACAGCATGGCACTAGTATAAAAATAGG 3210
                         iv  i  i  i i   v i   i    ii   i   i i    ii    i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_45789486_4   3211 CACATAGACCAATAGAACAGAATGGAGAACCCAGAAATAAACCCAAATAC 3260
                           i     i    i   i     v    ii               v i i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_45789486_4   3261 TTACAGCCAACTGATCTTTGACAAAGCAAACAAAAACATAAAGTGTGGAA 3310
                            ii i   i    i  i     i vviv   i v   vv i  v    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_45789486_4   3311 AGGACACCCTATTTGACAAATGGTGGGGGGATAATTGGCAAGCCACATGT 3360
                           i i vi  v  ii          vv    i  i   vv ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_45789486_4   3361 AGAAGAATGAAACTGGATCCTCATCTCTTGCTGTATACAAAAATCAACTC 3410
                          i         ii    i  ii i   vii ii           i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_45789486_4   3411 AAGATGGATCAAAGACTTGAATATAAGGCCTGAATCCATAAACATTTTAG 3460
                           i        ?    i i   i    iv  i  v i     vv i    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_45789486_4   3461 AAGATAACGTTGGAAAAACCCTTCTAGATATTGGCTTAGGCAAAGACTTC 3510
                             v   i v  ?iv  vi    vv  iv    v        v ii   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_45789486_4   3511 ATGACCAAGAACCCAAAAGCAAATGCAACAAAAACAAATATAAATAGATG 3560
                         v iivi v  vv         v v         iv   v   i   i  v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_45789486_4   3561 GGACTTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAACCATCA 3610
                               v  i   v v    i   i  ii vv    i  v iv i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_45789486_4   3611 GAGTAAGCAGACAACCCATAGAGTGGGAGAAAATCTTCACAATCTACACA 3660
                         i   i iv          i   i           v  ii   vii i i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_45789486_4   3661 TCTGAAAAAGGACTAATATCCTGAATCTACAAAGAATTGAAATAAATCAG 3710
                              v  i     vi     v    v  i      i vvv i  v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_45789486_4   3711 CAAGAAAAAAACAAACAATCCTATCAAAAACTGAGCTAAGGACATGAATT 3760
                         i  v     i     i  i  v  i?    v  i  v     iv     v
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_45789486_4   3761 GACAT--CTCAAAAGAAGATATACAAACGGTCAACAAGCATATGGAAAAA 3808
                              --   v                i  i   i     i   i   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_45789486_4   3809 TGCTCAACATCACTAAGTAT 3828
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (151 / 101)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 7.00 (14 / 2)  


2820 28.36 0.37 0.25  chrX_45951401_45955085     1663  2466 (1219)    L1M4_orf2#LINE/L1        1   805 (103)  

  chrX_45951401_4   1663 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 1712
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_45951401_4   1713 GACCACACTGCCAAGGACAATCTACAAATTCAATGCAATCCCCATCAAAA 1762
                          i v i   v  v iivii       i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_45951401_4   1763 TACCACCATTATTCTTCACAGAATTAGAAAAAACAATTTTAAAATTCATG 1812
                          v   v vviv  i  ii     v v  v  ivii  ii          i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_45951401_4   1813 TGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAATACTAAGGAAAAAAAA 1862
                              viiv  ii  v  v v         i    vi i ii  i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_45951401_4   1863 AAAATCTGGAGGCATCACACTACCTGGTTTCAAACTATAC-GTAAGGCCA 1911
                         v   vi      vv       v  iii       viv   -ii  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_45951401_4   1912 TGGTCACTAAAACAACATGGTACTGGTGTAAAAATAGGCACATAAACCAA 1961
                         ii  v ii  i   iii         ii   ii    i  i   i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_45951401_4   1962 TGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAACT 2011
                              i     v    ii               v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_45951401_4   2012 GATCTTCGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACATCCTTT 2061
                            i        i vviv   i v   vv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_45951401_4   2062 TCAACAGATGGTGCTGGAATAACTGGCTGGCCATATGTAGGAGAATGAAA 2111
                               i          i i      v i?   i   i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_45951401_4   2112 CTGGATCCTCATCTCTCACCTTATGCAAAAAGCAACTCAAGATGGATTGA 2161
                         i    i  ii i   v    v   i      vi       i      ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_45951401_4   2162 GGACTTAAACCTAAGACCTGAAACTGTAAAAATTCTAGAAGACAACATTG 2211
                         i   i    iv     v  i     i     v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_45951401_4   2212 GAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAAC 2261
                          ?iv  vi    vv   v    v        v i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_45951401_4   2262 CCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTAATTAA 2311
                                  v v    i    iv   i   i   iv v    i v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_45951401_4   2312 ACTAAAGAGCTTTTGCGTGGCAAAATGAACA--GTCAACAGAGTAAACAG 2359
                          v v  i i      i ivv    -- i   --i    v i   i  v  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAA--GGACACTATCAAGAAAGTGAAAAG 698

  chrX_45951401_4   2360 ACAACTCACAGAGTGGGAGAAAATCTTCACAATCTGTACATCTGACAAAA 2409
                              i      i           v  ii   viii  i      i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_45951401_4   2410 AACTAATATCCAGAATCTACAACAAACTCAAACAAATCAGTAAGAACAAA 2459
                         i   vi          v  i  vi     vv    v   i   v  v  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_45951401_4   2460 ACAAACA 2466
                              i 
  L1M4_orf2#LINE/    799 ACAAATA 805

Transitions / transversions = 1.68 (141 / 84)
Gap_init rate = 0.00 (3 / 805), avg. gap size = 1.67 (5 / 3)  

 320 18.60 0.00 1.16  chrX_45951401_45955085     2754  2839 (846)    L1M4_orf2#LINE/L1      787   871 (37)  

  chrX_45951401_4   2754 AAAAAGAAAGAAAAAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAA 2803
                           v  v   i i v   i  i  v  i?    i     v     iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_45951401_4   2804 TAGACAATTCTCAAAAGAAGATATACAAATGGGCCA 2839
                               v     v                   -   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGG-CCA 871

Transitions / transversions = 0.88 (7 / 8)
Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1)  

 307  7.02 3.51 0.00  chrX_45951401_45955085     3136  3192 (493)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_45951401_4   3136 AAAAAAGATATACAAATGGCCAACAA--ACATGAAAAAATGCTCAGCATC 3183
                            i                   i  --         i       i    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_45951401_4   3184 ACTAATGAT 3192
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.00 (4 / 0)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 2.00 (2 / 1)  


3233 24.61 1.68 1.79  chrX_45961746_45965299     2168  3061 (493)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_45961746_4   2168 TGTTCATTGATTAGAATACCCAACAAGGTAAAGTTGTGAGTTTTCCCCCA 2217
                                v    i   v  ii  i vv  v   v  vv i vi     - 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC-A 64

  chrX_45961746_4   2218 AATTACTGTATAGGCTTAATGCAATTCCTATCAAAAGCC-AACAAGGTTT 2266
                             iv v  i  ii i  i     i          v  - i vivv   
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_45961746_4   2267 TTTGTAGACACAGACAAGCTTATTCTAAAATTTATTTGAAAAGGCATAAG 2316
                             i   v iv        v  i        i  v  i   v   vii 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_45961746_4   2317 CCCTAAAATAGCTAAAACAATATTGAAAAAGAAGAATAAAGTGGGAGGGA 2366
                         v  i i      i        v              i     v     iv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_45961746_4   2367 TCATTCTCCCCAACATTAAGACCTACTATATGTCTACAGTAATCAAAACA 2416
                            iv  i     iv i  i  i     i viv             i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_45961746_4   2417 GTATGGTATTGGTGGTGGAATAGACACATAGATAAAGGAAACAGAGTAGA 2466
                           i     i   iivvi i       i      v  v i  i   i v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_45961746_4   2467 GAACCTGGGTTCTCTAGACTCACATAAATATGCTCAACTGATTTTTGACA 2516
                           ii ii iv---v  i  i  i i vv    v    i       i    
  L1M4_orf2#LINE/    315 GAGTCCAGAA---ATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_45961746_4   2517 AAGATGCAAAAGAAATTCAATGAAGGAAGGACAGCCTTTTCAACAAATGG 2566
                          i i   v  iivv        ii i   i i  i               
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_45961746_4   2567 TGCTGGGGAAATTGGACATCCATAGGTTAAAAAACAAAACAAAAACCTTT 2616
                                iv  i    i ?   i v iv   i  ii  iivii -  ii 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA-CCCCT 460

  chrX_45961746_4   2617 ACTAAATCTCATACCTCAAGTA-AAAAATTAACTCAAAATGGATCACAGA 2665
                           -----    i   vi --  -                       ?   
  L1M4_orf2#LINE/    461 AC-----CTCACACCATA--TACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_45961746_4   2666 CATAAATATAAAATGTAAAACTATAAAACTTTTAGAGAAAAACATTATAG 2715
                          v     i   i vv               i     ii       ---  
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT---AG 550

  chrX_45961746_4   2716 GAGAAAATTGTCATGATCTAGGACTAGGCAAAGAGTTCTTAGATTTGACC 2765
                          ? v    iv  i   i  v  ii       v iv         v    v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_45961746_4   2766 CCAAAAGCATGATC--CA---GGAAAACT-GATAAATCAGACCTCATCAA 2809
                                  ii v --  --- i    v -       ii   i       
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_45961746_4   2810 AATTTAAAACTTTGAT-CTGTGAAAGACCCTGTTGAAAACATGGAAAAAC 2858
                             v        vi -  vii  i   v  i ii i  vi  i   i  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_45961746_4   2859 AAGCAACAGACTGGGAGAAAATATTTGCAAACTACATAGCTGACAAAGGA 2908
                           v v     v                    ii i   v    i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_45961746_4   2909 ATAATATCTAGAATATATAAAGAACCCTCAAAAACCCAAAGTTAAAAAAA 2958
                         v vi    i                i  i v  - i   viv      i 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAAAAGA 799

  chrX_45961746_4   2959 -----AATCCA-TAAGAAAATAGGCAAAAGACCTCAACAGACATTTCACC 3002
                         -----  i   - v?i     i      i  ii v  i         v  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_45961746_4   3003 AAAGAGGATATTCAAATGGCAAATAAATGCATGAAAATATGTTAAATATC 3052
                              i     v        v     iii        v   i v  i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_45961746_4   3053 ATCAGCCAT 3061
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.70 (136 / 80)
Gap_init rate = 0.02 (15 / 893), avg. gap size = 2.07 (31 / 15)  


3174 26.85 0.99 0.88  chrX_46025830_46032227.rev     5003  5907 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_46025830_4   5003 GGAAGAAATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGG 5052
                          i    v  i     i      i v      v i     i  v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_46025830_4   5053 CCATACTGCCCAAGGTAATTTATAGATTCATTGCCATCCCCATCAAGCTA 5102
                          v     v     iv i  i  i       vi  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_46025830_4   5103 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 5150
                            iivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chrX_46025830_4   5151 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5200
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_46025830_4   5201 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACTATACTACAAGG 5250
                              i      vv   ii  v  ii i      --   -        i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACT-TACTACAAAG 247

  chrX_46025830_4   5251 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAAAGAG 5300
                                  i   i    ii         i iv ii i   v   v   v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_46025830_4   5301 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5348
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_46025830_4   5349 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5398
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_46025830_4   5399 CCTATTTAATAAATGGTGCTGGGAAAACTAGCTGGTTATATGTAGAAAGC 5448
                         i  v  i  i              v    i v i?ii i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_46025830_4   5449 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCATGATGG 5498
                             ii    i    v   i     v              i   vi    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_46025830_4   5499 ATTAAAGACTTACATGTTAGACCTAAAACTATAAAAACCCTAGAAGAAAA 5548
                           i ?    i  v    v   v              vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_46025830_4   5549 CCTAGGC-TATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCT 5597
                          v    ?-  v i -   iv   viv  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_46025830_4   5598 AAAACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCT 5647
                          vi            vvi     i    vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_46025830_4   5648 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGA 5697
                         v  i   v v  i i   i  ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_46025830_4   5698 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAAGCTACTCATCTGAC 5747
                          v  i     i                 v       iii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_46025830_4   5748 AAAGGGCTAATATCCAGAATCTACAATGAACTC----AAATTTACAAGAA 5793
                           i  i  vi          v  i  v      ----  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_46025830_4   5794 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGGCACT 5843
                            i     i     v  i?    i    ii      v    i  i  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_46025830_4   5844 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5893
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_46025830_4   5894 TCATCACTGGCCAT 5907
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.70 (17 / 10)  


2802 26.17 6.43 0.35  chrX_46095528_46102698.rev     5825  6680 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_46095528_4   5825 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5874
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_46095528_4   5875 GGCCATACTACCCAAGGCAATTTACAGATTCAATGCCATCCCCATCAAGC 5924
                            v     v     ivii  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_46095528_4   5925 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 5969
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_46095528_4   5970 TGGAACCAAAAAAGAGCTTGCATAGCCAAGACAATCCTAAGCAAAAAGAA 6019
                              viiv  ii  v iv v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_46095528_4   6020 CAAAGCTGGAGGCATCACACTACCTGACTTTAAACTATATTACAAGGCTA 6069
                              i      vv       v  ii i  i   viv  i     i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_46095528_4   6070 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 6119
                               i   i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_46095528_4   6120 TGGAACAGAACAGAGGCCTCAGAAATAAAACCACACATCTACAACCATCT 6169
                              i    iv   ivii          v   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_46095528_4   6170 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 6219
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_46095528_4   6220 TTAATAAATGGTGCTGGGAAAACTGACTAGTCATATGTAGAAAGCTGAAA 6269
                          i  i              v     iv  ?i  i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_46095528_4   6270 CTGGATCCCTTCCTTACAACTTATACAAAAATTAA-----GATGGATTAA 6314
                         i    i    v   i   v v              -----i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_46095528_4   6315 AGACTTAAATGTTAGACCTAAAACCGTAAAAACCCTAGAAGAAAACCTAG 6364
                             i       v   v       ii     vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_46095528_4   6365 GCA-ATACCATTCAGGACATAGACATGGGCAAAGACTTCATGACTAAAAC 6413
                          ?i- v i -   iv   v v ivv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_46095528_4   6414 ACCAAAAGCAATGGCAACAAAAGCCAAAATAGACTAATGAGATCTACAT- 6462
                                   vvi          vv        iv   vi  -  v   -
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA-CTTCATC 648

  chrX_46095528_4   6463 -AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA-- 6509
                         -   i    i -   i  ii vv    i  v       vv i      --
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_46095528_4   6510 ---------CAG-----------------GCAAA-------------AAA 6520
                         ---------   -----------------     -------------  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_46095528_4   6521 GG-CTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAGAA 6569
                           -  vi          v  i        ivv    v iv i  v  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_46095528_4   6570 GACAAGCAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 6619
                              ii     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_46095528_4   6620 CAAAAGAAGACATTTATGCAGCCAACAGACATATGGAAAAATGTTCATCA 6669
                          v        i  vi viii     i ii  i   i   i   i   v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_46095528_4   6670 TCACTGCTTAT 6680
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.62 (136 / 84)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 4.83 (58 / 12)  


1145 21.38 6.52 1.45  chrX_46138320_46143560     3365  3640 (1601)    L1M4_orf2#LINE/L1        4   293 (615)  

  chrX_46138320_4   3365 AGAGATA---CATGCTATTCATTAATTGGAAGACTCAATATTGTCAGTAT 3411
                          i     ---    ---     vi           i        i iv  
  L1M4_orf2#LINE/      4 AAAGATATCCCATG---TTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_46138320_4   3412 ATCAAT------------GATCCACAGATTCAGTGTAATCCCATACAAAA 3449
                         iv    ------------    i         ii i      -  iv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC-TATCAAA 99

  chrX_46138320_4   3450 ATCCCTGCGGGCTTTTGTGTACAAATTCACAAGCTGATTCTAAGATTTAT 3499
                              v  v v     v  i v     v          i    i   i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_46138320_4   3500 ATAAAAATACCAAGGACCTAGAATAGGCAAAACA--TTAGGAAAGGAAGA 3547
                           ii    i v i     i       v       --i v i   i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_46138320_4   3548 ACAAAGTTGGAAAACTCATACTTCCTGATTTGAACACTTAATGTTAGGCT 3597
                                    ii     i      ii    v  v     v iiv i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_46138320_4   3598 ACAGTAATTAA-ACAGTGTATTAATGATGTATAGACAGACACAT 3640
                                 i  -       iv  v  iii  vi  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

Transitions / transversions = 1.95 (39 / 20)
Gap_init rate = 0.02 (6 / 290), avg. gap size = 3.67 (22 / 6)  

 992 25.92 10.14 0.56  chrX_46138320_46143560     3998  4352 (889)    L1M4_orf2#LINE/L1      387   775 (133)  

  chrX_46138320_4   3998 AACGAAGAGTATTTTCAA-AACTGCTGCTGGAAAAATTGGATATACATAT 4046
                           v   v   v       -  v  v      i v  i      ?v  i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_46138320_4   4047 GCAAAAA---GCCCCCTGACCCTCACCTCATGTCAGATTTACAAACTTAA 4093
                               i--- vvviiv     ii      iii  v  vi v   -    
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAA 485

  chrX_46138320_4   4094 CTCATTCTTTGTCATAGGTCTAAATTTAAGAGCTAAAATTATAAATCTTC 4143
                             vvv vvi   ?  ii      v            i      v  ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_46138320_4   4144 TGAAAGAAGGCATAGGAGAAAAATCTCCATTGCTCTGAGTCAGA----GA 4189
                          ii     ii      ? v   -   i i vi ii  i  i  i---- i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_46138320_4   4190 TTTGTTAGATAGGATACAAAAGGCATGAACCATAAAAGAAC---TTGATA 4236
                            v       v  i  v   i   ii i v i       v--- v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_46138320_4   4237 AACTCAGCCTTATCAAAATTAAAAACGTCTACTCTACAAAGCACA--GTT 4284
                           i vii i i               v i iiv  v     v   --i i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_46138320_4   4285 AAGAAA---AAAAGA--AGCCATAATCTGGGAG----TA---------CA 4316
                               ---      -- v   i ivv      ----  ---------  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_46138320_4   4317 TA---CT--TAAAGGACTTGCATCAAGAATATATAAAGAAC 4352
                           ---  --   i       i   v                
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

Transitions / transversions = 1.34 (51 / 38)
Gap_init rate = 0.03 (13 / 389), avg. gap size = 2.92 (38 / 13)  

 267 20.97 17.74 0.00  chrX_46138320_46143560     4647  4770 (471)    L1M4_orf2#LINE/L1      763   908 (0)  

  chrX_46138320_4   4647 ATATATAAAGAAC-CTTACAATTTAATAGCAAAGA--------------- 4680
                                      -       i i    ii   i ---------------
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_46138320_4   4681 ---AAAAT-GGCAAAAGATTACAACAAATACTTCCACAAAGAAGATATAA 4726
                         ---     -      i    vv  i i i i   iv             v
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_46138320_4   4727 AGATAGCAAATAAGGGC-TCAACA-ATATTCATCATTAGAAAAATG 4770
                          i  i  v      vi - v  v -  ii   v   i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.03 (5 / 146), avg. gap size = 4.40 (22 / 5)  


3012 22.79 7.91 0.71  chrX_46253572_46256984     2074  2920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_46253572_4   2074 TGGAGAAATATATCATGTTCATGGATTGGAAGATTCAACATAATAAAGAT 2123
                             i i    vi                    i i  i  vi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_46253572_4   2124 GTCAAT-CTCCCCAAAAATTAATGTAAAGGTTTAACATAATTCCTATGAA 2172
                          v    -         --  i  v  v  i  i   ii   i     v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_46253572_4   2173 AGACCCAGCAAGATTTTTTTTACATGTAGACAAATTTATTCCAAAATTTA 2222
                          iv      vivv      vi v vi v     ii v  i i      i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_46253572_4   2223 TATGGAAA------GGAACTAGAATAGCCATAACAAT------------- 2253
                                 ------   v i          v      -------------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_46253572_4   2254 ---AAAGTGGGAGGAATCAC----TCTGATGCTAAGGTTTGCTGCGTAAG 2296
                         ---     v      v    ----i ii  vii  iii  i  i iv iv
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_46253572_4   2297 TATAGTCATCAAGACAGTATGGTCTTGG---AAGGATAGACACATAAACC 2343
                           i   v           i    vi   ---           i   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_46253572_4   2344 AATAGAGCAG---TG------CAGAAAGACACCCCCATGCAT--AGAGAC 2382
                            i  ii  ---  ------      v v    --  i   -- vi v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCC--ATACATTTATGGTC 346

  chrX_46253572_4   2383 AACTGATTTTTGACAAAGGAGCAAAATTAATTCAATGGAGTAGGA-TAGT 2431
                           i       i     i  v  v  iviv         i v i  -    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_46253572_4   2432 CTTTTTAACATATTATGCTAGAACAACTGGATAGCCATTGGCAAATAAA- 2480
                              i    v  vi    i i           ?   ivv     vi  -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_46253572_4   2481 --ACCTCAACCTAAACCTCACATCTTATATAAAAATTAACTCAAAATGGA 2528
                         -- vi vi   ivv        i v    i                    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_46253572_4   2529 TCACAGACTTAAATGTACAGTG-TAAAACTAAAAAGCTTTTAGAAGATAA 2577
                            ?    i        -  v -        v   i  i        v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTA-AGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_46253572_4   2578 CGCAGAAG-AAATCTTCA-GGCCTAAGGCTTGGTG--GAGTCCTTAGACA 2623
                          ii  i? -        i- i   vi  i v  ii-- iv i      i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_46253572_4   2624 TGATACCAAATGCATGACCCATAAAAGAAAAAAAATGATAAATT------ 2667
                            i      v   ii v v i           v -        ------
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTT 644

  chrX_46253572_4   2668 -AT--AAATTAAAA-CTTCTGCTCTATGAAAGACCCTATTAAAAGGATTA 2713
                         -  --         -   i  iv  vii  i   v    i  i iii v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_46253572_4   2714 AAAGACAAGCTACACACTGGGAAAAAATATTTGCAAACCATGTATCTGAC 2763
                                 v i   v v     i              i   i       i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_46253572_4   2764 AAAAGACTACAGTCTAGAATA----AAGAACTCTAAAAACTCAACAA--- 2806
                           ii    vvvi  i      ----         v v       i  ---
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_46253572_4   2807 AGAAACAAACAATCCAATTTAAAAATGGACAAAAGACTTGAACAGATATT 2856
                          i i     i  i      ?        i    i  i     i   i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_46253572_4   2857 TCACCAAAGAAGACATATAAATGGTAAATAAACACATGAAGTCATGCTTA 2906
                           v          i   i      iv     i        ivv     i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_46253572_4   2907 ATATCATTATCTAT 2920
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (119 / 70)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.17 (73 / 23)  


3168 26.55 1.33 0.88  chrX_46270547_46276821     4879  5782 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_46270547_4   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_46270547_4   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_46270547_4   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_46270547_4   5027 TACGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCT----AAGCCA 5072
                           i    viiv  ii  v  v v  v     iv     i ----   vvi
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_46270547_4   5073 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5122
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_46270547_4   5123 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGATC 5172
                                 i   i    ii  i      i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_46270547_4   5173 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5220
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_46270547_4   5221 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5270
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_46270547_4   5271 CTATTTAATAAATGGTGCTGGGAAAACTGCCTAGCCATATGTAGAAAGCT 5320
                           v  i  i              v     vv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_46270547_4   5321 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5370
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_46270547_4   5371 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5420
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_46270547_4   5421 CTAGGCATTACCATTCAGGACATAGGCATGGGTAAGTACTTCATGTCTAA 5470
                         v    ?i v viv   iv   v v  vv i  i  vvii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_46270547_4   5471 AACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTAA 5520
                         i            vvi     i    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_46270547_4   5521 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5570
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_46270547_4   5571 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5620
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_46270547_4   5621 AGGGCTAATAGCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5670
                         i  i  vi  v       v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_46270547_4   5671 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5720
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_46270547_4   5721 TCAAAAGAAGACTTTTATGCA----GCCAAAAAACACATGAAAAAATGCT 5766
                           v        ----   i  ----     v  i          i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_46270547_4   5767 CATCATCACTGGCCAT 5782
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.50 (20 / 8)  


3079 23.15 3.77 3.43  chrX_46355866_46358234      974  1876 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_46355866_4    974 GAGAAATATA--ATGATCATGGATCAGAAAATCCAATACAGTAATAATGT 1021
                           i i    v--   v        ii   i iii    iv  v vi   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_46355866_4   1022 CCATTCTCCTCAAATTGACTAACAGATTCAATACAATTCCAATCAAAGTA 1071
                          v  v    i        iiv          ii    i  v      i v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_46355866_4   1072 CCAGCAAGACATTCCGCAGGTAGAGACAACCTGACTCTAAAATGTATATG 1121
                              vivviv  ii    iv vv     v    ii       vi     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_46355866_4   1122 GAAAGGCAAAGGAACTAGAACAGCTAAAACAATTTTGAGAAAGAG---TA 1168
                             v    i   v i    i   i        i    i     i---i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_46355866_4   1169 AGGTTGGAGGATTCACACTACCCAATTTTAAGACCTTCTATAAAACTGCA 1218
                          i         i       v        i  i  i v   i   i  i  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_46355866_4   1219 GTAAGAAAGATGGTGTGGTATTGGCAAAGAGCTAGATACACAGATCAGTG 1268
                             vv    ii        i     v ii v    i i i      i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_46355866_4   1269 GAATAAAATAGAAAGTCCGGAAATAGATCCACACAAATATGGACAATTGA 1318
                              i   v  i     i      i i   i   vv     v       
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_46355866_4   1319 TTTTTGACAATGTTGTGACAGTA--ATTCAGTGAAGAAAAGATTGTCAAC 1366
                             i     v --   v  iv --     i  ii    ii  -------
  L1M4_orf2#LINE/    353 TTTTCGACAAGG--GTGCCAAGACCATTCAATGGGGAAAGAAT------- 393

  chrX_46355866_4   1367 AACAATCTTTTGGAACAAAAGAACATCAAAAATATTGGAACAATTGAACA 1416
                         --- i      v-      v i---------- ii   i    i  i i 
  L1M4_orf2#LINE/    394 ---AGTCTTTTC-AACAAATGG----------TGCTGGGACAACTGGATA 429

  chrX_46355866_4   1417 TCTATACATAAAAAAAC-----TCAACCTAAACCTCATACCTTCTACAAA 1461
                         ? i i iii    i  i----- vi   ivv      i   v v      
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_46355866_4   1462 CATTAACTCAAAATAAATCATAGATCTAAATATAAAATGC-AAAACCATA 1510
                         v             ii    ?   i      i   i -  -     i   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATA 528

  chrX_46355866_4   1511 AAACATTTAGGAGAAAACATAGGAGAAAATCTTCTCAACCTGGGATTAT- 1559
                             vi    i            ? v        vii    v  i   v-
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_46355866_4   1560 --ATAGTTT--TGGACATGACACCAAAAGCATGATAAATAAAAG------ 1599
                         --  i    -- i  i               ii vv  i     ------
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_46355866_4   1600 TTGATAAATTGGACTGCATCGAAATTTAAAAGTTTTGCTCTCCAAAAGAT 1649
                          v             v    i     v    v     iv  i    i  i
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_46355866_4   1650 ATGGTTAAGATACTGAAAAGAAAAAAAAAACCCCAAAGC-TAGGAGAGAA 1698
                          ivi i    v v        v  -------    v  v- i     i  
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAA-------CCCACAGAATGGGAGAAAA 721

  chrX_46355866_4   1699 TATTTGCAAATTACACATCTAATGAAGTACTTCCATC-AAAGTATATAAA 1747
                                    i i i    i  i i v    vi   - i i        
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_46355866_4   1748 GAACACTCGAAACTC--CAA-AGAAAAACAA-CAGTACAATTTAAAAATG 1793
                             v  iiv     --i  - i   i    -i iiv     ?       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_46355866_4   1794 GGCAAAAGACTC----AGTCATTTCACCAAAAAGGATATATAAATGACAA 1839
                               i  i i----  v      v     i i      i     i v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_46355866_4   1840 ATAAGCACATGAAAATATATTCAACATTAGGGAAATA 1876
                                        v  ii       i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (135 / 70)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 3.25 (65 / 20)  


2997 25.06 3.34 2.23  chrX_46379321_46382439     1729  2626 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_46379321_4   1729 TGAAGAGACATGCCATGTTCATGGATTGAAAGACTAAGCA-----AAGAT 1773
                           i i   i  v                i      v ii -----     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_46379321_4   1774 GTCAAATCTCTCCAAATTGATATACAGATTTAATAAAATTTCCATAAAAA 1823
                          v   vv   i          v        i  iiv   ii i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_46379321_4   1824 TCCCAGCAAAATGTTTGGTGAATATAGCCATGTGAAATATAAAATTAATA 1873
                                vivv v   v iii v  v v  v ivi viv       v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_46379321_4   1874 -GGAAAGTCAAAGTAAC-AGACTAGCCAAAACAATTTTGAAAAAGAAGAA 1921
                         -     vv   i v v -   v             i              
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_46379321_4   1922 TAAAATTGGAGGCCTCACACTATCCAATTT-AAGATGTACTGTAATGCTA 1970
                         i   i       v        vi       -  i iv    ii  v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_46379321_4   1971 CTATGTAAAGTAATAAAGTATAATTAAGGCAGGGTAGCATTGGTGAAGGA 2020
                          -------      ----------i   i   v  i i i   iiv i i
  L1M4_orf2#LINE/    251 C-------AGTAAT----------CAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_46379321_4   2021 ATAGATATATACATCAATGGGACAAAATT-AGAGTCCAGAAATAGGTCTA 2069
                              i     v        i i i    -              iii --
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC-- 331

  chrX_46379321_4   2070 CATACA---A-----AATTGATTTTTCACAAAAGTGCAAAAGCAATTAAA 2111
                               --- -----          iv    ii    v  ii v   v  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_46379321_4   2112 TGGACAAGGTACGTTCTTTTCAATGAATTGT-TTGGAATTATTGGGCATC 2160
                            iv  i v iiv         ii   v  -i   i iv i   ii ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_46379321_4   2161 CATACACAAAAAGAATGAACCTTGAGCTAAATCTTATACCTTGTACAAAA 2210
                           i ii     -       vi v  v ivv i  i i   v i       
  L1M4_orf2#LINE/    432 CACATGCAAAA-GAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_46379321_4   2211 ATGAATTTTATGTAGATTATAGATTTAAATGTAACATACAAAACTGTGAA 2260
                           v  i iv vi i   i ?   ii         v vvi      i i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_46379321_4   2261 ACAGTTACAAAAAAACATAAGA--ACACCTTCCTGATCTTGGATTAAGCA 2308
                           vv   v  i        i ?-- v i    v   i     i   i   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_46379321_4   2309 AAGAGTGCCTAGATATGACACCAAAAGCACAATCCTTATATGAAAAAATT 2358
                          v iv v i                       v vvi v v        v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_46379321_4   2359 GATAA-TTGGACTGCATCAAAATTAAAAGTTTTTGCTCTGCAAAAGACAC 2407
                              -       v              ii     iv  v    i     
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_46379321_4   2408 TTTTAAAGTAATGAAAAGACAAGCTACAGAGTGGGAGAAAATATTTACAA 2457
                          v i  iiv i           v i     i               i   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_46379321_4   2458 A--ACATATTCAACAAAGGACTTATATCCATAGTACATAAGAAATTCTCC 2505
                          -- i    iii i  i      i      v i  i    ii  i   iv
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_46379321_4   2506 AAACT---TAATAAGAAAACAA----CCCAGTTGAAAAATGGGCAGAAGG 2548
                         v    ---      i  i    ----    i  ?           i i i
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_46379321_4   2549 TTTAAACTAACACTTTACAAAAGACGGTATGTGGATGAGAAATCATTACA 2598
                            i  ivi   i  iv v     v i   iiii   ivv   v vi   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_46379321_4   2599 TGAAGAGATGTTTAACACCATTAGCCAT 2626
                             i     i i    i  ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (136 / 85)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.94 (50 / 17)  


3033 24.20 3.77 3.00  chrX_46523252_46526029     1385  2285 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_46523252_4   1385 TGGAGAGATAGACATATCGTGTTCATGGATTGGAAAATTCAATATACAAT 1434
                             i     ---- vi i                i i i     ---- 
  L1M4_orf2#LINE/      1 TGGAAAGATA----TCCCATGTTCATGGATTGGAAGACTTAATAT----T 42

  chrX_46523252_4   1435 AGTAAAGATGTCAATTCACCTTAAACTGATCTATAGGCTTAACACAATTT 1484
                         -  v      v    v v  ii   i       i  ii i   i    ii
  L1M4_orf2#LINE/     43 -GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chrX_46523252_4   1485 CTTTCAAAATCCCAGC-AAGGTTTTCGTAGATACAGAATACACTCATTCC 1533
                           v             -ivvv    i i   v iv  -i vi  v  i i
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCT 140

  chrX_46523252_4   1534 AAAATTTATATGGAAAGGCAAATGACCTTGAATGGCTAAAACAATTCTGA 1583
                               i         v    iv    iv    i  i        ii   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_46523252_4   1584 GAAAGAACAATAAAGTGGGAGGAAGTGCTCTACCCAATGTTAAGGCTTAT 1633
                         i      v  i     v      vvii v  v      v i  ii    i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_46523252_4   1634 TATATAGCTAGAGTAATCAAGAC----TGGTATTCACAGAGGTATAGGCA 1679
                           i v     v            ----     i vi  v i v    i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_46523252_4   1680 CATAGATCGATAGAACAGAATAGCGAACCCAGAAACAGCCCCACACAAAT 1729
                         i       i  i   i     v v  ii       i ----------  -
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA----------AA- 329

  chrX_46523252_4   1730 AGCCCCACACAAATATGCCCAATCGATTTTTT-CAAACGTGCAGAAGCAA 1778
                         ---    i   vv    vi    i      iv-   iv    vi ii v 
  L1M4_orf2#LINE/    330 ---CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_46523252_4   1779 TTCAGTGGAGGAAAAGTAGTCATTTTA-----T----TTGAGCCATC-AG 1818
                             i   i i  i i     v   i ----- ----i  i v  v -i 
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_46523252_4   1819 ACAACCATAGACAAAAATATGAACCTCAACCTTAGGTTTAGATCCTATAT 1868
                          i ?   i vi     iv     vi vi   iivivi i v i v    i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_46523252_4   1869 AAAAAGTAA------ATGAATCATGCACTTAAATGTAAAATATAAAACTA 1912
                              v   ------   i    ?iv  i         i vv        
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_46523252_4   1913 TAACACTTATAGAAGGAAAGATAAGAGAAAATCTTCAGGACCTGGAGCTA 1962
                            v   iv      i   v   i ? v        iv     v i i  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_46523252_4   1963 GATGAAGATGTCTTAGCCATGACAC-AAAAACATGATACATAAATGCAAA 2011
                          iii v i v      vi       -    i  ii vvv i   v v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_46523252_4   2012 AATTGATAAATTGGACATCATCAAAATTTAAAA-TTTGGT-CTGCAAA-- 2057
                            v            v           v    -   v  -  v    --
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_46523252_4   2058 AT-CTCTTAAGAGGATGAAAAGACCAGCTACAAACTGGGA-AAAATATTT 2105
                          i-  v i    iii         v v i   i v     -         
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_46523252_4   2106 GCAGATCACATATCTGACAGAGGACTTGTATCTAGAATGTAGTATACAGA 2155
                            i    i        i ii           i     i  ---  v   
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA---TAAAGA 773

  chrX_46523252_4   2156 ATTCTCAAAATTTAACAGTAGGAA-----ACAATCTGATTAGAAAATGGG 2200
                          i   i v  i i  i i  ii  ----- i  i ii   ?i        
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_46523252_4   2201 CAAAAGACTTGAACGGACATTTCACCAAAGAGGTTATACAGATGGCAAAT 2250
                             i  i     ii        v       i v      i     v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_46523252_4   2251 AAGCACATGAAAAGATGCTCAACAGCATTAGCCAT 2285
                                                 v  ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (133 / 81)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.90 (61 / 21)  


1268 26.51 7.20 0.00  chrX_46774665_46776662      498   844 (1154)    L1M4_orf2#LINE/L1      170   541 (367)  

  chrX_46774665_4    498 GAATAGCCAAAGCAATCCTAAGCAAAAAGAACAAAGCCAGAGGCATCACA 547
                                    i     i i iv  i          iii    vv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_46774665_4    548 TTGTCCAACTTCAAACTATACTGTAAGGCTACAGTAATCAAAATAGCATG 597
                         i vi    i      viv    ii  i              i i  ii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_46774665_4    598 GTCCTGGTGCAAAAACAGACACATAAACCAGTGGAACAGAGTAGAGAACA 647
                           v    iii  ii i     i   i i  i     i   i v    iiv
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_46774665_4    648 CAGAAATAAACCCGCACACATAGAACCATCTGATCTTTGACAAAATCAAC 697
                                      ii   iv  viii  vi    i  i     iiviiv 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_46774665_4    698 AAAAGTAAGCAAGGGGGAAAGGACTCCCTGTTCAATAA---GTGCTGGGA 744
                           i vi vv   v        i ivvi  v     i  ---         
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_46774665_4    745 TAGGTGGCTAGCCATATTCAGAAGAATGAAACCGGACCCTTACCTCTCAC 794
                         i iv   v  ?   i  v  i         iii      i      v   
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_46774665_4    795 CATATACAAAAATTAA----------------------GATGTAAGACCT 822
                                         ----------------------i        v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_46774665_4    823 CAGACTATAAAAATCCTAGAAG 844
                         v i         v  i      
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAG 541

Transitions / transversions = 2.25 (63 / 28)
Gap_init rate = 0.01 (2 / 372), avg. gap size = 12.50 (25 / 2)  

1109 24.25 4.90 1.09  chrX_46774665_46776662     1139  1505 (493)    L1M4_orf2#LINE/L1      528   908 (0)  

  chrX_46774665_4   1139 AAAAATCCTAGAAGAAAACCTAGG---AAATGCCCTCCTCGATACAGGGT 1185
                             v  i           v    ---    ---  i vi  iviv    
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGT 574

  chrX_46774665_4   1186 TTGGCAAAGAATTTATGGCTAAGTCCCCAAAAGCAATTGCAACAAAACCA 1235
                          v     v iv  iv i v  v v v         vvv         vv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_46774665_4   1236 AAAATTGACAATTTGGACCT------AATTAAACAGCTTCTGCACAGCAA 1279
                              v  i  v      i ------       - i   i  ii vv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAA 673

  chrX_46774665_4   1280 AAGAAACTACCAACAGAGTAAATGGACAGCCTACAGAATAGGAGAAAAT- 1328
                          i  v    i   v i   i  vi    i  i       i         -
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_46774665_4   1329 --CATAAGCTACACATCTGACAAAGGTCTAATATCCAGAATCTACAAGGA 1376
                         --iii  iii i i      i  i  v  vi          v  i  i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_46774665_4   1377 AGTT----AAATCAATAGGCAAAAAGCAAAATTTCCAATTAAAAAATGGG 1422
                          v i----  v      ivv    ii    vvvi      ?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_46774665_4   1423 CAAAGGACATGAACAGATACTTCTCAAAAGATAACATACAAGTGGCCAAC 1472
                                iv    i   i i     v     vi i      i       i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_46774665_4   1473 AA--ACATGAAAAAATGCTCATCATCACTAATCAT 1505
                           --         i       v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (49 / 39)
Gap_init rate = 0.02 (7 / 381), avg. gap size = 3.14 (22 / 7)  


1641 24.26 1.69 2.95  chrX_46992971_46996301.rev      501   974 (2356)    L1M4_orf2#LINE/L1       28   495 (413)  

  chrX_46992971_4    501 GGAAGACTCAATACTGTTAACATGTCAATTGTCCCCACCTTGATCAGGAG 550
                                 i    i      v   v    vv      vv      viv  
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chrX_46992971_4    551 ATTCAACATAATCCCAATCAAATTCCCACCAAATTATTTTGTGGCTATCA 600
                                ii      v      v     v vivi v     ii vv  ii
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chrX_46992971_4    601 ACAAACTGATTCTAAAGTTTATATGGAAAGGCAAAA-ATCCAAAGTAGTC 649
                             i     i     i  i         v    ii- i   i i   i 
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chrX_46992971_4    650 AACATAGTACT---AAACAAGAACAAAGTCAGAGGACTGAGACCACCCAA 696
                           v i i vi ---   v           ii       v v  iv     
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_46992971_4    697 CTTCATGACTTACTATAAAACTAGACTAATCAAGACAGAG--GTATTGGT 744
                         i    vi        i   i   v v            v --   i   i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_46992971_4    745 GAAAGAATAGGCAAATAGATCAATGGAATAGAATAGAGAACCTAGAAATA 794
                         iv   i    i  v                    v    ii i       
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_46992971_4    795 TATATACACACAAAAACAGCCAACTGATCATTGACAAAGGAGCAAAAGAA 844
                         - - iv  i   vvv ii i   i    iv i     i  v  v  iivv
  L1M4_orf2#LINE/    328 -A-ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_46992971_4    845 ATTCGGTGAAGAAATAA--GTCTTTTCAACAAATGGTGCTGGAACAACTG 892
                             ii  ii    v  --                       i       
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_46992971_4    893 GACATCCATATGCAAAAAAAAAAAAAAAAAAAGCATCTAGACACAGTCCT 942
                           i ?   i        i  vi  i-----------i i   v vvv   
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAG-----------TTGGACCCCTACCT 464

  chrX_46992971_4    943 TATATGTTTCACAAAAATTAACTCAAAACTGG 974
                         i i ivv vi                  -   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAA-TGG 495

Transitions / transversions = 1.38 (66 / 48)
Gap_init rate = 0.02 (8 / 468), avg. gap size = 2.75 (22 / 8)  

 497 26.67 0.61 1.21  chrX_46992971_46996301.rev     1193  1357 (1973)    L1M4_orf2#LINE/L1      440   603 (305)  

  chrX_46992971_4   1193 AAAGGCTGGAGTGCAGA-CCCTGTCTCAAAAAAAAAAAAAAAAATTAACT 1241
                             iv  i   -ii  -    ii   - v vv v v v           
  L1M4_orf2#LINE/    440 AAAGAATGAAGT-TGGACCCCTACCTC-ACACCATATACAAAAATTAACT 487

  chrX_46992971_4   1242 CAAAATGGATTATAGATCTCTATGTAAAATGAAAAACTATAAAATTTCTA 1291
                                   i ?   i  vv      i vvv            i ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_46992971_4   1292 TAAGATAACAAAGAAGAAAATCCAAGTAACCTTGGGTTTGGTGATGAGTT 1341
                         v    v    v  i? v     ivv  i          v  ii   iv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_46992971_4   1342 TTTAAATACAACACCA 1357
                         i   i   ii      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCA 603

Transitions / transversions = 1.10 (22 / 20)
Gap_init rate = 0.02 (3 / 164), avg. gap size = 1.00 (3 / 3)  

 565 25.00 2.33 1.74  chrX_46992971_46996301.rev     1496  1667 (1663)    L1M4_orf2#LINE/L1      593   765 (143)  

  chrX_46992971_4   1496 ATACAACACCAAAAGTATGACCTGTGAAAGAAAAAAAAAACAGTACGTTG 1545
                            ii          i ii v viii          v i ---  vi   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA---TAAATTG 639

  chrX_46992971_4   1546 TGCATTATTAAAATTAGAAACTTCTCTTCTGTGAAAGACGCTG--ATGAC 1593
                         vi v i  i       i      i v v  vii  i   i  i-- v  v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_46992971_4   1594 AG--AATAGACAAGCCACAGACTGGGAGAAAATATTTGCAAAACACTTAT 1641
                           --  v      v       v                    v  iv   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_46992971_4   1642 CTCATAAAGGACTTGTATTGAAACTA 1667
                           v    i          iv i v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATA 765

Transitions / transversions = 1.26 (24 / 19)
Gap_init rate = 0.02 (3 / 173), avg. gap size = 2.33 (7 / 3)  

 602 19.74 2.63 0.66  chrX_46992971_46996301.rev     2688  2839 (491)    L1M4_orf2#LINE/L1      754   908 (0)  

  chrX_46992971_4   2688 GTATCCAAAACGTACAAAGAACTATTA-AACTCAACAATAAGAAAACAAA 2736
                                i  ii  i        v   -       i     i  i     
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_46992971_4   2737 CTACTCAATTAAAAAGTGGGCAAAAGATCTGAAAAGATGACCTCATCAAA 2786
                         iv  i     ?    i        i   i    v   i- ii  vi    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC-ATTTCTCCAAA 852

  chrX_46992971_4   2787 GA---CATTCAGATGGTAAATAAGCATATAAAAAGGTCCTCAACATCATG 2833
                           ---i  v  i    iv        i  i     i v          ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_46992971_4   2834 TCACTA 2839
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 3.14 (22 / 7)
Gap_init rate = 0.02 (3 / 155), avg. gap size = 1.67 (5 / 3)  


3195 26.98 0.77 0.77  chrX_47399576_47405850.rev     4877  5784 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_47399576_4   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_47399576_4   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCTCCATCAAGC 4976
                            v     v     iv i  i           i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_47399576_4   4977 TACCAATGACTTTATTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  v  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_47399576_4   5025 TATGGAAGCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5074
                                iiiv  ii  v  v v  v     iv     i i ---     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAG 195

  chrX_47399576_4   5075 AAGTGT---GCTGGAGGCATCACACTACCTGACTTCAAACTATACTGCAA 5121
                            vii--- i      vv       v  ii i      viv    i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_47399576_4   5122 AGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 5171
                                    i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_47399576_4   5172 ATCAATGGAACAGAAC--AGATCCCTCAGAAATAACGCCGCATACCTACA 5219
                                   i    i--   vi  --        vv  ii i ii  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_47399576_4   5220 ACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT 5269
                         iii vi    i  i     ivv  vv  i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_47399576_4   5270 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5319
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_47399576_4   5320 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGAT 5369
                         iv    ii    i    v   i     v           i  i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_47399576_4   5370 GGATTAAAGATTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAA 5419
                             i ?   ii    ii v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_47399576_4   5420 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5469
                            v    ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_47399576_4   5470 CAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5519
                         i vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_47399576_4   5520 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5569
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_47399576_4   5570 AACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGA 5619
                           v  i     i   iv            v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_47399576_4   5620 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5669
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_47399576_4   5670 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 5719
                             i     i     v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_47399576_4   5720 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5769
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_47399576_4   5770 ATCATCACTGGCCAT 5784
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  


1017 24.73 0.72 1.08  chrX_47512467_47516017.rev        1   279 (3272)  C L1M4_orf2#LINE/L1   (509)   399   122  

C chrX_47512467_4    279 AAACTGTCAAAGAGATTTAAAAATTTATATGGATATGCAAAAGACCTAGA 230
                            i  v   ivv   iiv      i       v      ii    i   
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

C chrX_47512467_4    229 ATGACCAACACAGTCTTGAGGAAGAAGAA-AAAGTACGGAGGATTGACAC 181
                           ii    v   i      ii        -     -i      i v    
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT-TGGAGGACTCACAC 220

C chrX_47512467_4    180 TACCAAATGTTAAGATTTACTTTAAAGCTATAGCAATCTGGACAGTATGT 131
                          v  v   v i  i i     vi       i  i    vi      i  v
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

C chrX_47512467_4    130 TATTGGTGTAAAGACACACTAATATATAAATGGAACAGAAGGGAAAGACT 81
                           i   ii   i  i v  vv   v  v       i    vv  i  v i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

C chrX_47512467_4     80 AAAAATAGACCCATTAATATATAGACAACTGATTTTTGACAAAGGTGCCA 31
                          i     i      vv  v   i v   i       i     i       
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

C chrX_47512467_4     30 ATGTAATTTGAAGGGAGAAATGAA-AGTCTT 1
                          viiv   i-  v  i    -   -      
  L1M4_orf2#LINE/    371 AGACCATTC-AATGGGGAAA-GAATAGTCTT 399

Transitions / transversions = 1.46 (41 / 28)
Gap_init rate = 0.02 (5 / 278), avg. gap size = 1.00 (5 / 5)  

1195 22.11 3.16 0.35  chrX_47512467_47516017.rev     1647  1931 (1620)    L1M4_orf2#LINE/L1        1   293 (615)  

  chrX_47512467_4   1647 TGCAGAAATATGCCATTTTCATGGGTTAGAAGGCTCAATATTGTTAAGAT 1696
                           v i i    v    v       i  i    i  i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_47512467_4   1697 GTCAATTCTCCTAAAATTGATCTACAGAGTTAACTGAACTCCAAACAAAA 1746
                          v    v    iv               v i   vv  ii  v v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_47512467_4   1747 TCCCAGTAGGCTTTTTTGTAAAAAGT-ACAAACTGATTATAAAATGTATA 1795
                               iv v        i i   v -    i     iv      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_47512467_4   1796 TGAAAATGCAAATGACCTAGAAGAGC-AAAGTAATTTTTAAAAAG----- 1839
                           i        iv    i    v   -   ii   i  v      -----
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_47512467_4   1840 CAAAGTTGAAGGACTTATACTCCCTGATT-GAAGATTTACTGTAAAAACT 1888
                                 i      i i   i  ii   -v  i i     ii   -i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-GCT 249

  chrX_47512467_4   1889 ACAGTAATAAAGATAGTATGGGTTTGCTAAAAGGATA-ACGTAT 1931
                                 v    i   i   vvi  vi v       -  i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

Transitions / transversions = 1.52 (38 / 25)
Gap_init rate = 0.02 (6 / 293), avg. gap size = 1.67 (10 / 6)  

1876 21.82 12.16 0.18  chrX_47512467_47516017.rev     2502  3060 (491)    L1M4_orf2#LINE/L1      283   908 (0)  

  chrX_47512467_4   2502 GACAGACAAATAGATTAATTGAACAGAAATGAGAGACCAGATACAGGCTC 2551
                           i     v      i   v   i    v      v     v i ii i 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_47512467_4   2552 ATACACATAAAGTCAATTGATTTT-GATAAACATACCAAGGAAATTCAAT 2600
                              iv  vi             -  i  ivi i     ivv       
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_47512467_4   2601 AGGAAAAAGAAAGCCCCTTCAACAAATGTTTCTGGAACAATTAGATATC- 2649
                         i  i   ii v  i ii           v v    i    i i    ? -
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_47512467_4   2650 ----------------AGT-----------------------------AT 2654
                         ----------------   -----------------------------  
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_47512467_4   2655 TGA---AAAATGAATCACAGACCTAACTGAAAAAGTTAAAATGATAAAAC 2701
                          i ---      i    ?        v  v  i  i     iv       
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_47512467_4   2702 TTATAGAAGAAAGTAT--GAGAAAATCTTTGTG-CCTTGTGGTAGGCAAA 2748
                          iv         ii  -- ? v       i   -     v v       v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_47512467_4   2749 GATTTCTTAAACAGATCGCAAAAGGTACTAACAATAAAACAGA---T-GA 2794
                          i       i i viv i v   i i  v i   i    v i --- -  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_47512467_4   2795 TAAATTGGACTTCATCAAA-TTAAAA-TGTTTGCTCTTTGATGGGCACCA 2842
                                            -      -iv    iv   ii v  i   i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_47512467_4   2843 AAAAGAAAATGAAATTTCAAGCCACAGATTGGAACAAAATATTAGCAATA 2892
                         vv      i     vvv   v       v   i v        v    vv
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_47512467_4   2893 CATATATCTGGCAAAGGAGTTGTATCCAGTAAATATA--------TTAAA 2934
                                   ii  i   v          v v     --------   v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_47512467_4   2935 ACTCACTAATAAGAAGACAAACAACCTGATTAAAAAATGAG-AAAGATAT 2983
                              v      i        i    ii   ?       i -    i-  
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG-AT 831

  chrX_47512467_4   2984 CTGAGTAGATATTTCACACCAAAAAATGTACAAATGGTCAATAAGCACAT 3033
                         i   i    i     v vvv i  i  i         i            
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_47512467_4   3034 AAAAAGATGCTTAACATCATTATTCTC 3060
                         i          i       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (69 / 49)
Gap_init rate = 0.02 (13 / 626), avg. gap size = 5.31 (69 / 13)  


2475 21.23 6.47 8.62  chrX_47541043_47544310.rev     1850  2777 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_47541043_4   1850 TGGAATGATATGTCCTGTTTATGGATATGAAAAC--AATGTAATTAAGAT 1897
                              v     vi v    i      vv   i  --   i vi       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_47541043_4   1898 GTCAATTCTCTCCATATAGATCTATGAATTCAGTTCAATC----TCAAAA 1943
                          v    v   i   v  v      iii     iiv     ----      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_47541043_4   1944 TCCCAGCAGGCTTTTTTTTAATAGTAACTGACAAGGTGATTCTAAAATTT 1993
                                v v       ---ii  v  i       v    i        i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_47541043_4   1994 ATATAGAAATTCAAAGAAAAACCAGAATAGCCAAAACG--TGTGAAAAAG 2041
                             i     v   i i v--                i--iv        
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_47541043_4   2042 AGGAATAAAGTTAGAGGATTTGCATGATCTGACTTCAAGACTTATGAAGC 2091
                          i   i      i     i ii  ivvi ii i     i     ------
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA------ 239

  chrX_47541043_4   2092 TACAGCAAAGAGTAATGCTACAGTAGTACAGAAGCTACAGTAGTACAGAA 2141
                         -----------------     ---------           i -  -- 
  L1M4_orf2#LINE/    240 -----------------CTACA---------AAGCTACAGTAAT-CA--A 260

  chrX_47541043_4   2142 GCTACAGTAATGGTGTAGTACTGGCAGTAGTGGTACTGGCATA------- 2184
                          --     ------  i         -  iv i  -- i    -------
  L1M4_orf2#LINE/    261 G--ACAGT------GTGGTACTGGCA-TAAGGATA--GACATATAGATCA 299

  chrX_47541043_4   2185 ATAGAA---AACT-AGAG--CAGAAATAGAACCA----------ATCAAT 2218
                           i   ---  i -    --        i v   ----------i     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_47541043_4   2219 TAATTTTTTGATAAATATATCAAGGCAATCCAATGC-------ATTATCA 2261
                          i     i-  i  ivi ii    i v  i     v-------  vi  -
  L1M4_orf2#LINE/    350 TGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chrX_47541043_4   2262 TTTTCAACAAATGGTTCTGGAACAACTGGACAGCCATATGCAAAACAAAA 2311
                                        v    i         i ?   i        --i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA--GAA 445

  chrX_47541043_4   2312 TCAACCTAAATCCTTATCTTTGGAAAGGATTTACATCATATGCAAAA-TT 2360
                          v  vi ii i  i  i  i------------   i     i     -  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTC------------ACACCATATACAAAAATT 483

  chrX_47541043_4   2361 AA-TAAAAATGGATTAGGTAACCAAATATAAGAGCCAATATTATAAAACT 2409
                           - v         i ?iv v i    i       i  v i         
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_47541043_4   2410 TCTAGAAGAAAGCATAAATCTTTTTAAAAACTTTTATCTTAATGACCTTG 2459
                         ii         i    ii?v ------   ------    vi        
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGT------AAA------TCTTCGTGACCTTG 571

  chrX_47541043_4   2460 AGCTTTGCAAAAATTTATTAACCATGACCAAAAAAGCATGAAGTA-TAAA 2508
                         i i vv    vii   v   ivi     vvv       i-   i -i   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC-AAGCAACAAA 620

  chrX_47541043_4   2509 AGAAAACAAAAATGAATTGAGCTT-GTTAACATTAAAAACTTTTGGTCTT 2557
                               v v i  i     ii   -i i  v              vv   
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_47541043_4   2558 C------TGTTATTTAAA---TGAAAAGGCAAACC------TAGAAGAAA 2592
                          ------iii   iv i ---       i   v  ------ i i     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_47541043_4   2593 CTGTTTACAGAATGTACATCCAACAAAGGACATATATCTAGGATATATAA 2642
                         v i   i  i vii  i   ii i  i    v i    i  i        
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_47541043_4   2643 AGAACACTTACAACTCAATAATAA---GACGAACAACTGAGTTTACAAAT 2689
                              v                  ---   i  i   iv i  ? v    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_47541043_4   2690 TGGCAAAATATTTAAGAAGACACATCAACCAAGATGGTATACAGATGGTA 2739
                         v      iv    i iv     iv  vv v    v i      i    iv
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_47541043_4   2740 CATAAACACAAGAAAAGATGCTCAACAGCATTACTTAT 2777
                         v    i    v                v  ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (125 / 68)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 4.12 (140 / 34)  


 850 31.25 12.17 0.82  chrX_47598755_47600335      485  1092 (489)    L1M4_orf2#LINE/L1      232   908 (0)  

  chrX_47598755_4    485 AAAACTAAGTA-AGAG----AATACTTGAGACAATGTCATTATCAGCACA 529
                               v v  - i  ---- i  v ii     i   vi - iii   i 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT-ACTGGCATA 280

  chrX_47598755_4    530 AGGACAGACAAACAGTCCAGTGGAACTAAAA---AGAG----------AA 566
                             i     v i  vi  i     -  i  ---    ----------  
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAA-TAGAATTGAGAGTCCAGAAATAAA 329

  chrX_47598755_4    567 TCCAAACATGTATGGACACCTGATTTATGACAAAGTTGGCACAGTAAAGC 616
                         i   v    v     v  vi      vi     i v  v  viiiv vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_47598755_4    617 AGTAGGGAGAAGATGACCTTTTCAATAGATGTGGATGGGTTA-TTAGATA 665
                          i i    i ii  iii        i i   vv v    vi -i i    
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_47598755_4    666 TCTATATGGAGAA-AATGAAATTTAACCCCT--CT-A-GCCACACATAAA 710
                         ? i i   v i  -      i  vi      --  - -i   i i i   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_47598755_4    711 AATCAGCTACAGGTAAATCGTAAATCTAA-TGTGAGAGGTAAC-CAATTA 758
                            i i  vv ii ii   i? i i    -   i    v   v- v  v 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_47598755_4    759 AGTGTCTATAAAATAATACAGGAAAATGTTTTCATAAGCTTTGGAGTAGG 808
                          iivii  v  i v  i i   ?iv vi i   i i - i    iv    
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA-CCTTGGGTTAGG 578

  chrX_47598755_4    809 GAAACAATTCTATAACAAAACATGAAAAGCACTCCTCATAAAGGAAAA-- 856
                         v  vviv    vvi i vi   iv        vvviv i   i     --
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_47598755_4    857 --GACAAGT-G----TTAT-AAGATCAAAA------GTACTACAA----- 887
                         --  i  i - ---- i  -  i  i    ------  i  v   -----
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_47598755_4    888 -------------TGAAAAGGCAAGCCACAGA-TGGG-GAAATTGCTGGC 922
                         -------------       i   v       -    -    v ii v  
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_47598755_4    923 AATATT-CATGAGGGATAAGGTA-TCGTATGTAGAATATATAAAATAATC 970
                           -  i-i  ivvv       v - i    vi            i-  ii
  L1M4_orf2#LINE/    729 AA-ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG-AACT 776

  chrX_47598755_4    971 CCCTCAAATCAATAAGAAACACACA-------CAA---AAGAATGGATAA 1010
                          iiv   v       v   v v   -------   ---  i     ii  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_47598755_4   1011 GAGAAGTGAATAGGTACTTCACTGAAAAGCAAAACCAAATGATCTATGAA 1060
                         ii  vv       ii i   v ii  i iv v vv      ii v  i i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_47598755_4   1061 CACAAGATAATGTACTCAACCCCATTAGCAAT 1092
                             v  v  vi i      vi  ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (114 / 73)
Gap_init rate = 0.04 (28 / 677), avg. gap size = 2.82 (79 / 28)  

 204 21.05 14.04 0.00  chrX_47598755_47600335     1525  1581 (0)    L1M4_orf2#LINE/L1      529   593 (315)  

  chrX_47598755_4   1525 AAACTC---GAAGA-----TTGAAGAAACTCTTTTTAACCTTGGGTTAGA 1566
                               ---     ----- v i? v  v    iv i            i
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_47598755_4   1567 CAAATATTTCTTAGA 1581
                            vvi         
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGA 593

Transitions / transversions = 0.83 (5 / 6)
Gap_init rate = 0.03 (2 / 65), avg. gap size = 4.00 (8 / 2)  


4411 15.01 4.24 1.95  chrX_47638781_47641403.rev     1269  2141 (482)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_47638781_4   1269 TGTTCGTGGATAATTAAGGAAAACTTAACATTGTTAAGATGCCAATACTC 1318
                              i     --- --    i      i            v        
  L1M4_orf2#LINE/     16 TGTTCATGGAT---T--GGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chrX_47638781_4   1319 CCCAAAGCAACCTACAAATTCAATGTAATCTCTAACAAAATCCCAAATCC 1368
                               vii i     i      i i    i   v          iv v 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_47638781_4   1369 CTTTTGTGCATAAAGGGGAAAGCTAATCCTAAAATTTATATGGAGTTGCA 1418
                              v    v   vv iv     i           i       iv    
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_47638781_4   1419 AGGGTCCCTGGATAGCCAAAACAATCTTGAAAAAGAAGAACAAATTTGGA 1468
                             v   v i                                 v     
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_47638781_4   1469 AGACTCACACTGCCCTATTTCAAAACTTACTGCAAAGGTACAGTAATCAA 1518
                         i          v   v               i     v            
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_47638781_4   1519 AACAGTGTGGTGCTGGCACCAGGATAAACATATAGATCAATGGAATAGAA 1568
                         i          i      iv      i                       
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_47638781_4   1569 TTGAAAGTCCAGAAAAAAAAAACCCATGCA-----GCTCAAATGATTTTT 1613
                             i          v   ---     i  ----- v    v       i
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAA---CCCATACATTTATGGTCAATTGATTTTC 357

  chrX_47638781_4   1614 GATTAGGGTGCCAAGATCATTTAATGGGGAAAGAATAGTCCGTTCAACAG 1663
                           iv            i    i                  iv       i
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_47638781_4   1664 ATG-CACTGGAAAAA-TAGATATCCACATGTAAAAGAATGAAGTTGTACC 1711
                            -ii    i v  - i    ?       i               v   
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_47638781_4   1712 ATGACCCCATACCATATATAAAAGTTAACTCAAAATGGATAAAAGACCTA 1761
                         viv   i  i        i    i                v ?       
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_47638781_4   1762 AATACAATAACTAAAACTGTAAAATAACTAGAAGAAAATGAAGGAATAAA 1811
                            ii  v i        i     ivvi          iiv   ?i    
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_47638781_4   1812 TCTTCACGTCTTTGGACTTGGCAATTGTTTCTTAGATATGATACCAAAAG 1861
                              ii v i    ii v      v               i        
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_47638781_4   1862 CATAAGTAACAGAA-AAAAAATGAATAA-TTGGACTTAATAAAAAT-GAA 1908
                           i   i    i  -       ii    -        v  v     -i  
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_47638781_4   1909 AACTTTTGTGTATCAAATGACATTATCAGGAGAATGAAAAGACAACCCAG 1958
                                   iv     v    i     i  i i               v
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_47638781_4   1959 AGAATGGGA------------AAATTATA-ATCTGATAAGGG-----TAT 1990
                                  ------------    i   -            -----   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_47638781_4   1991 CCAGAATATATAAAGAACTCTTACAATCTAATAACCAAAAAAT------C 2034
                                                   iii     iv    i i------ 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_47638781_4   2035 CCCAGTTAACACTGGGCAAAG-ACTTGAATAGATATTTTTCCAAATAAGA 2083
                           v v ?  v v         - i         i    i      v    
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_47638781_4   2084 TATACATGATATACACATGGCCAATAAGCTCATGAAAAGAT--TTGTCAT 2131
                               -------- -             v           -- iiv   
  L1M4_orf2#LINE/    858 TATACA--------A-ATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_47638781_4   2132 TAGTCATCAG 2141
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.65 (79 / 48)
Gap_init rate = 0.02 (17 / 893), avg. gap size = 3.18 (54 / 17)  


 232 23.53 0.00 10.08  chrX_47676214_47678141       47   165 (1763)    L1M4_orf2#LINE/L1      448   554 (354)  

  chrX_47676214_4     47 AAGTTGGATCCTTAACTCACACCATAACATAAAAATAAATTCTAGATATA 96
                                 i  i  v           -i i      v  i  v i  iv 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATA-TACAAAAATTAACTCAAAATGGA 496

  chrX_47676214_4     97 ACAAAAGTATAAACATGAAAAACCAAAACTATAAAAGAACACACTCTATT 146
                         v  ? iiiv    ii -  i i i            -------    -- 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAA-------CTCT--T 536

  chrX_47676214_4    147 AAAGGAATATCATAAAGGT 165
                          i i   v -    ii?  
  L1M4_orf2#LINE/    537 AGAAGAAAA-CATAGGNGT 554

Transitions / transversions = 2.71 (19 / 7)
Gap_init rate = 0.05 (5 / 107), avg. gap size = 2.40 (12 / 5)  

 427 28.73 12.13 4.66  chrX_47676214_47678141      470  1005 (923)    L1M4_orf2#LINE/L1      260   835 (73)  

  chrX_47676214_4    470 AAACAATGTAAAACCCTGCCATTAGCA-AGA---ATAG-TTAGTGGAACA 514
                          i   i   iiv  --  v   v  v -   ---    - i i     i 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTAC--TGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_47676214_4    515 GAACAGACAGTCTAGAAATAGATACAAATAAAAATGGGAAATTTAATATA 564
                            iv  v    i       i iv  v i vvv    vv    -i  v v
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT-GATTTT 356

  chrX_47676214_4    565 TAATAAAGGT----AG--CATTTTAAACAGGAATGGAAAAACAGACTATT 608
                         ii i  i   ----  --    i--  ii  i ---  i  i  v  v  
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTC--AATGGGGA---AAGAATAGTCTTTT 401

  chrX_47676214_4    609 CAA----------------AACTGGAGAGCTATCAG-AAAAAAATTAA-C 640
                            ----------------       v ? i ivv -    i   v  -i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_47676214_4    641 TGGATTCCCTACCTCACACTATATACAAAAATAAATTCA---TGA--CAA 685
                             i-             i            v  i   ---  i--  ?
  L1M4_orf2#LINE/    452 TGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_47676214_4    686 AAATTTAAATGAAAAAAGAGAAACTATAAAA----TA-AAGACAGGAGAG 730
                          i ii      v  i ivvi           ----  -    v iv v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_47676214_4    731 GTTTTAAAAA-----ATAATCTTTGAGTGGAGAAGACTCTTCTAAGCATG 775
                          ?v ---   -----i i i   v iv i iv  viv i ii  iii   
  L1M4_orf2#LINE/    551 GNGT---AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_47676214_4    776 CC-CCAAAACCCAGATGCCACAAATGAAAACACTGATAAATGTGACT--- 821
                         v -      v - v v  v     v     v iv       vv    ---
  L1M4_orf2#LINE/    598 ACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_47676214_4    822 ------------ACTTTATGTATTACATGGCAAAATA-TATCAAACAAAC 858
                         ------------     -   ii v  ---v ii i -      i-   v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTT-TGTGCTTCA---AAGGACACTATCAAG-AAAG 691

  chrX_47676214_4    859 TCAAAGGATATGACTAACTA---GGGAAAAAATATACACATAACAGATAG 905
                          v   i  i --  iv  vi---    i       vii  v v  v   v
  L1M4_orf2#LINE/    692 TGAAAAGACA--ACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_47676214_4    906 GATGGACAAAGAGTTAATTTCCTCCATGTATAGAGAGAGCTCCTACAAAG 955
                         --iv  i  i iii vi v   vvv  i    i   i--   i     vv
  L1M4_orf2#LINE/    740 --CTGATAAGGGACTTGTATCCAGAATATATAAAGAA--CTCTTACAACT 785

  chrX_47676214_4    956 CAAGAAGAAAAAGACCAATAACTTT-TTAAAAAATGGTTGATATGGTTTG 1004
                            v  v        v      iiv-  ?        vii - v i    
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA-AGGATTTG 834

  chrX_47676214_4   1005 A 1005
                          
  L1M4_orf2#LINE/    835 A 835

Transitions / transversions = 1.17 (81 / 69)
Gap_init rate = 0.06 (32 / 576), avg. gap size = 2.81 (90 / 32)  

 242 28.09 1.12 0.00  chrX_47676214_47678141     1347  1435 (493)    L1M4_orf2#LINE/L1      819   908 (0)  

  chrX_47676214_4   1347 ATGGTCAAGGGACATGACCAT-CATTTCACAGAAAATAAAATGCAAATGT 1395
                             v   i   iv   vi v-      v vi  i vi v  i      v
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_47676214_4   1396 TTTTTAAACATGTAAAAAGATGCTCAACTTCACTCACATG 1435
                         iivv   i  ii i              v   ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.08 (13 / 12)
Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1)  


1479 24.92 8.53 4.68  chrX_47765888_47767890      500  1097 (906)    L1M4_orf2#LINE/L1      173   793 (115)  

  chrX_47765888_4    500 TAGCTAAGACAAGTTTTGAAAAAGAAGAATAAGGTGGGAGGAATGGCTCT 549
                             i  i    - i              i  i  v      v vi v  
  L1M4_orf2#LINE/    173 TAGCCAAAACAA-TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_47765888_4    550 ACCATATTTGAATACTTCTTATATAGCTACAGGAATCAAGAC--TGTAGT 597
                         v  vv    v  v    vi  i v        v         --   i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_47765888_4    598 ATTAGGAGAAGAATAGACACGTAGATCACTGGAACAAAATAGAGAACCTA 647
                          i i v v   i       ii       v     i i   v    ii i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_47765888_4    648 TATAAGAACGTAGAAATAGCCCCACAC-------------TGATTTTTTA 684
                         ------------      iv    i  -------------       iv 
  L1M4_orf2#LINE/    322 ------------GAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_47765888_4    685 CAAAG------AGACAA---AAAGAAGGAAGGATCGTCTGCTTAACAAAT 725
                            i ------    v ---  v ii i   i  v    vi i       
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_47765888_4    726 GGTGCTGGAGCAGTTGCATATTCATAGGCCAAAAAAAAAAAAAAGACCTT 775
                                 ii  ii  v   ?i  i v  v   i  vi  ivvi    ii
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_47765888_4    776 TAT---ACAAAAAAAAAAAAAA--ACCTCAAG-TGAATCATAGATTTAAA 819
                           i---   vv v v v     -- v     i-  i    ?   ii    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_47765888_4    820 TGTAAAATATAAAACTAAAAAAAAACTTTCACAAGAAAACATAGGAG-AA 868
                              i vv        v    ---  i i v             ? -  
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAA---CTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_47765888_4    869 ATGTCTGAGATCTAGGGCATAGCGAACGGTT------------CA--AAA 904
                           v ii v  i  v   i-   vv  i    ------------  --   
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_47765888_4    905 AACATAATC--CATAAGGAAAA-TA--TAAATTAGATTTCATCCAATTTA 949
                          i  i  v --  v   i    -  --      i  i      v  v   
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_47765888_4    950 AAA-CTTTTGCTCTGCAAGAAACCATGTTAAAAGGATGAAAAAACAGGGT 998
                            -      iv  v   iii  vv i i  i iii      i   ivvi
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_47765888_4    999 ATAAACTGGGAGAAAATGTTTGCAAACCATGTTTCCAACAGAGGGCTTAC 1048
                          i i v           i        i   i v  ii i ii  i   ii
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_47765888_4   1049 ATCCAGAATATATAATGGATATGTATACTACTCTCAAAATTCAATGGTA 1097
                                        -i  ----------     i v  i     ii  
  L1M4_orf2#LINE/    756 ATCCAGAATATATAA-AGA----------ACTCTTACAACTCAATAATA 793

Transitions / transversions = 1.61 (90 / 56)
Gap_init rate = 0.03 (20 / 621), avg. gap size = 3.95 (79 / 20)  

 371 23.08 4.27 0.00  chrX_47765888_47767890     1397  1513 (490)    L1M4_orf2#LINE/L1      787   908 (0)  

  chrX_47765888_4   1397 AAAAACAAACAAACAAATAATCCAATTAGAAAATTATGAAAAGATATGAA 1446
                           v  i   v i        i      ?i     vivv   i   v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_47765888_4   1447 CATACATTTCACTGAAGGGGAAATA-----AGCAAATAAGTACATGAAAA 1491
                         i v       v ii   ii  v   -----i  v      i         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_47765888_4   1492 GATGTTCAACACTAATTTGCTT 1513
                             i      ii ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (16 / 10)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 5.00 (5 / 1)  


1766 23.78 7.59 3.37  chrX_47815437_47817461.rev      502  1094 (931)    L1M4_orf2#LINE/L1      172   789 (119)  

  chrX_47815437_4    502 ATAGCTAAGACAATTTTTGAAAAAGAAGAATAAGGTGGGAGGAATGGCTC 551
                              i  i     i  -            i  i  v      v vi v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_47815437_4    552 TACCATATTTCAATACTTCTTATATGGCTACAGGAATCAAGACTGTGTAG 601
                          v  vv       v    vi  i vi       v         v    i 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_47815437_4    602 TACTGGGAGAAGAATAGACACATAGATCACTGGAACAAAATAGAGAACCT 651
                               v v   i       i        v     i i   v    ii i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_47815437_4    652 AGAAATAGCCCCACAC-------------TGATTTTTTACCAAG------ 682
                                iv    i  -------------       iv  v i ------
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_47815437_4    683 AGACAA---AAAGAAGGAAGGATAGTCTGCTTAACAAATGGTGCTGGAGC 729
                             v ---  v ii i   i       vi i               ii 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_47815437_4    730 AGTTGCAGAGCCACAGGCCAAAAAAAAAAA--AAAGCCCTAATCTTCAAA 777
                          ii  v v ?     v  v   i  vi  i--ii v     -- i   v 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA--CCTCACA 468

  chrX_47815437_4    778 CCTTTATACAAAAAAGTAACT-GAAGTCGATCATAGATTTAAATCTAAAA 826
                           v -         -v     -i  i v     ?   ii     v   i 
  L1M4_orf2#LINE/    469 CCAT-ATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_47815437_4    827 TATAAAACTAAAAGAAAACTTTTACAAGAAAATATAAGAG-AAACGTCTG 875
                         vv        ---v      i   v       i   i ? -   iv ii 
  L1M4_orf2#LINE/    517 GCTAAAACTA---TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_47815437_4    876 AGATCTAGGGCATAGTCAATGGTT------------CA--AAAAGCATAA 911
                         v  i  v   i-   v        ------------  --       i  
  L1M4_orf2#LINE/    564 TGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_47815437_4    912 TCCATAAG-GAAAAAA---ATAAATTAGATTTCATCCAATTTAAAA-CTT 956
                         v v i  i-       ---       i  i      v  v      -   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_47815437_4    957 TTGCTCTGCAAGAAATCTTGTTAAAAGGATGAAAAAACAGGGTATGACCT 1006
                            iv  v   iii ivi i i  i iii      i   ivvi iiivv 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_47815437_4   1007 GGGAGAAAATGTTTGCAAACCACATATCCAAGAAAGGACTCACATCCAGA 1056
                                   i        i  i     ii v  i     iii       
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_47815437_4   1057 ATATATAATGGATATATATACTACTCTCAAAACTCAAT 1094
                                 -i  ----------     i v        
  L1M4_orf2#LINE/    763 ATATATAA-AGA----------ACTCTTACAACTCAAT 789

Transitions / transversions = 1.56 (84 / 54)
Gap_init rate = 0.03 (19 / 618), avg. gap size = 3.42 (65 / 19)  

 406 19.84 3.97 4.76  chrX_47815437_47817461.rev     1414  1539 (486)    L1M4_orf2#LINE/L1      784   908 (0)  

  chrX_47815437_4   1414 CTCAATGGTAAAAAATACAAACAAATAATCCAATTAGAAAATCATGAAAA 1463
                               ii      i-----        i      ?i     vivv   i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAG-----ACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_47815437_4   1464 GATATGAGCATACATTTCACTGAAGAGGAAATA-----AGCAAATAAGCA 1508
                            v   ii v       v ii    i  v   -----i  v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_47815437_4   1509 CATGAAAAGATGTTCAGCCCTCATTTGCTTC 1539
                                     i   i v-   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.67 (15 / 9)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 3.67 (11 / 3)  


1552 24.07 9.09 4.55  chrX_47856602_47858615      500  1093 (921)    L1M4_orf2#LINE/L1      173   793 (115)  

  chrX_47856602_4    500 TAGCTCAGACAATTTTTGGAATATAAGAATAAGGTGGGAGGAATGGCTCT 549
                             iv i     i  - i  v v     i  i  v      v vi v  
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_47856602_4    550 ACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTGTGTAGT 599
                         v  vv       v    vi  i v        v         v    i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_47856602_4    600 ACTGGGAGAAAAATAAACACACAGATCACTGGAACAAAATAGAGAACCTA 649
                              v v  ii   i   i i      v     i i   v    ii i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_47856602_4    650 GAAATAGCCCCACAC-------------TGATTTTTTACCAAG------A 680
                               iv    i  -------------       iv  v i ------ 
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_47856602_4    681 GACAA---AAAGAAGGAAGGATTATCTGTTTAACAAATGGTGCTGGAGCA 727
                            v ---  v ii i   i  vi   v  i               ii  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_47856602_4    728 GTTGCAGAGCCATAGGCCAGTAAAAACATGA---------CCTAATCTTC 768
                         ii  v v ?   i v  ----    iv    ---------    -- i  
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGC----AAAAGAATGAAGTTGGACCCCTA--CCTC 465

  chrX_47856602_4    769 ATACCTTTATACAAAAAAACAACTCAAG-TGGATAATAGATTTCAATCTA 817
                          i   v -         v-i       i-     v ?   ii v   v  
  L1M4_orf2#LINE/    466 ACACCAT-ATACAAAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_47856602_4    818 AAATATAAAACTAAGAAAAAGCTTTTACAAGAAAGCATAGGAGAAACATC 867
                          i vv        vi   ---  i   v      i      ? v  -   
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAA---CTCTTAGAAGAAAACATAGGNGTAA-ATC 559

  chrX_47856602_4    868 T--GGGATCTAGGGCATAGTGAACGGTT------------CA--AAAAGC 901
                          -- v  i  v   i-   vv  i    ------------  --      
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_47856602_4    902 ATAATCAATAAGG---AAAACAAATAAATTAGATTTCACCCAATTTAAAA 948
                          i  v   i  ii---    i i       i  i    i v  v      
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_47856602_4    949 -CTTGTGCTCTGCAAGAATCCCTGTTAAAAGGATGAAAAAACAGGATCTT 997
                         -   v  iv  v   iiiv v  i i  i iii      i   -- i iv
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA--ACCCA 706

  chrX_47856602_4    998 --GACTAGGAGAAAATATTTGCAAACCACATATCCAAGAAAGGACTCACA 1045
                         --  v i                  i  i     ii v  i     iii 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_47856602_4   1046 TCCAGAATATATAATGGATATGTATAGTACTCTCAAAACTCAATGGTA 1093
                                       -----------  v     i v        ii  
  L1M4_orf2#LINE/    757 TCCAGAATATATAA-----------AGAACTCTTACAACTCAATAATA 793

Transitions / transversions = 1.46 (83 / 57)
Gap_init rate = 0.03 (21 / 621), avg. gap size = 3.86 (81 / 21)  

 394 19.35 8.39 3.87  chrX_47856602_47858615     1370  1524 (490)    L1M4_orf2#LINE/L1      747   908 (0)  

  chrX_47856602_4   1370 GAGACTCTGTCTCAAAAAAAATAATTAAAAAA-----AC--CTCAATGGT 1412
                          i    -   v  v i  v -  --    i  -----  --      ii 
  L1M4_orf2#LINE/    747 GGGACT-TGTATCCAGAATA-TA--TAAAGAACTCTTACAACTCAATAAT 792

  chrX_47856602_4   1413 AAAAAATACAAATAATCCAATTAGAAAATCATGAAAAGATATGAACATAC 1462
                              i-        i      ?i     vivv   i   v    i v  
  L1M4_orf2#LINE/    793 AAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_47856602_4   1463 ATTTCACTGAAGAG------CAAATAAGCAAATAAGCACATGAAAAGATG 1506
                              v ii    i------     i-  v                    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATG-GCCAATAAGCACATGAAAAGATG 890

  chrX_47856602_4   1507 TTCGACACTAATTTGCTT 1524
                         i  i   ii ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.05 (8 / 162), avg. gap size = 2.38 (19 / 8)  


1735 23.95 8.09 3.37  chrX_47862443_47864485.rev      502  1094 (949)    L1M4_orf2#LINE/L1      173   793 (115)  

  chrX_47862443_4    502 TAGCTCAGACAATTTTTGGAAAAGAAGAATAAGGTGGGAGGAATGGCTCT 551
                             iv i     i  - i          i  i  v      v vi v  
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_47862443_4    552 ACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTGTGTAGT 601
                         v  vv       v    vi  i v        v         v    i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_47862443_4    602 ATTGGGAGAAGGATAGACACATAGATCACGGGAACAAAATAGAGAACCTA 651
                          i   v v           i        vv    i i   v    ii i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_47862443_4    652 GAAATAGCCCCACAC-------------TGATTTTT--------TACCGA 680
                               iv    i  -------------       i-------- i  i 
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_47862443_4    681 GACAA---AAAGAAGGAAGGATCGTCTGCTTAACAAATGGTGCTGGAGCA 727
                            v ---  v ii i   i  v    vi i               ii  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_47862443_4    728 GTTGCAGAGCCATAGGCTAAAAAAAAAAAAAAGACC--TAATCTTCATAT 775
                         ii  v v ?   i v  v   i  vi  ivvi    --  -- i   i i
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA--CCTCACAC 469

  chrX_47862443_4    776 TTTTATACAAAAAATAACTCAAG-TGGATCATAGATTTAAATCTAAAATA 824
                         iv -         v        i-       ?   ii     v   i vv
  L1M4_orf2#LINE/    470 CAT-ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_47862443_4    825 TAAAACTAAAAAAATCTTTTAGAAGAAAGCATAGGA-CAAACGTCTGAGA 873
                                 v    --  i          i      ?-i   iv ii v  
  L1M4_orf2#LINE/    519 TAAAACTATAAAA--CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_47862443_4    874 TCTAGGGCATAGTGAAGGGTT------------CA--AAAAGCATAATC- 908
                         i  v   i-   vv  v    ------------  --       i  v -
  L1M4_orf2#LINE/    567 CCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_47862443_4    909 -CATAAGGAAAA-CAAATAAATCAGATTTCATCCAATTTAAAA-CTTGTG 955
                         -  v   i    -i i      ii  i      v  v      -   v  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_47862443_4    956 CTCTGCAAGAGACCCTGTTAAAAGGATGAAAAAACAGGATCTT--GACTA 1003
                         iv  v   ii   v  i i  i iii      i   -- i iv--  v i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA--ACCCACAGAATG 713

  chrX_47862443_4   1004 GGAGAAAATATTTGCAAACCACATATCCAAGAAAGGACTCACATCCAGAA 1053
                                           i  i     ii v  i     iii        
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_47862443_4   1054 TATATAATGGATATGTATAGTACTCTCAAAACTCAATGGTA 1094
                                -----------  v     i v        ii  
  L1M4_orf2#LINE/    764 TATATAA-----------AGAACTCTTACAACTCAATAATA 793

Transitions / transversions = 1.53 (84 / 55)
Gap_init rate = 0.03 (19 / 621), avg. gap size = 3.58 (68 / 19)  

 408 19.84 3.97 4.76  chrX_47862443_47864485.rev     1432  1557 (486)    L1M4_orf2#LINE/L1      784   908 (0)  

  chrX_47862443_4   1432 CTCAATGGTAAAAAATACAAATAAATAATCCAATTAGAAAATCATGAAAA 1481
                               ii      i----- i      i      ?i     vivv   i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAG-----ACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_47862443_4   1482 GATGTGAATATATATTTCACTGAAGAGGAAATA-----AGCAAATAAGCA 1526
                            v      v i     v ii    i  v   -----i  v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_47862443_4   1527 CATGAAAAGATGTTCAGCCCTCATTTCCTTC 1557
                                     i   i v-   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.67 (15 / 9)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 3.67 (11 / 3)  


1399 24.47 7.22 6.24  chrX_47898605_47900650.rev      502  1110 (936)    L1M4_orf2#LINE/L1      173   787 (121)  

  chrX_47898605_4    502 TAGCTAAGACAATTTTTGGAAAAGAAGAATAAGGTGGGAGGAATGGCTCT 551
                             i  i     i  - i          i  i  v      v vi v  
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_47898605_4    552 ACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTGTGTAGT 601
                         v  vv       v    vi  i v        v         v    i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_47898605_4    602 ATTGAGAGAAGGATAGACACATAGATCACGGGAACAAAATAGAGAACCTA 651
                          i  iv v           i        vv    i i   v    ii i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_47898605_4    652 GAAATAGCCCCACAC-----TGATT------TTTTTTACGAAG------A 684
                               iv    i  -----  i i------    iv  i i ------ 
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_47898605_4    685 GACAA---AATAAGGAA-GTATTGTCTGCTTAACATATGGTGCTAGAGCA 730
                            v ---   ii    - v  v    vi i    v        i ii  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_47898605_4    731 GTTTCATATCCACAGGCCAAAAAAAAAAAAAAAAAAAAAAAGGCCTAATC 780
                         ii vv   ?     v  -------    i  vi  ivvii vv    -- 
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGC-------AAAAGAATGAAGTTGGACCCCTA--C 462

  chrX_47898605_4    781 TTCTTACCTTTATACAAAAAAAAAAAAAAAAAAAACTCAAG-TGGATCAT 829
                         i  vi   v -         vv  -----------     i-       ?
  L1M4_orf2#LINE/    463 CTCACACCAT-ATACAAAAATTAA-----------CTCAAAATGGATCAW 500

  chrX_47898605_4    830 AGACTTAAATCTAAAATATAAAACTAAAAAAAGACTTTTACAAGAAAGCA 879
                             i     v   i vv        v    ---  i   v      i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA---CTCTTAGAAGAAAACA 547

  chrX_47898605_4    880 TAGGAGAAACATCT--GAGATCTAGGGCATAGTGAACAGTT--------- 918
                             ? v  -    -- v  i  v   i-   vv  ii   ---------
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chrX_47898605_4    919 ---CA--AAAAGCATAATC--CATAAGGAAAA-CAAATAAATTGGATTGC 960
                         ---  --       i  v --  v   i    -i i          i v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_47898605_4    961 ATCCCATTTAAAAG-TTTTGCTCTACAAGAAATCTTGTTAAAATGATGAA 1009
                            vv v      i-     iv  v   iii ivi i i  i vii    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_47898605_4   1010 AAAA-AGGGTATGACCTGGGGGAAA-TGTTTGCAAACCACATATCTAAGA 1057
                           i - ivvi iiivv    i    - i        i  i      i v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_47898605_4   1058 AAGGACTCACATCCAGAATATATAATGGATATGTATAGTACTCTCAAAAC 1107
                          i     iii               -----------  v     i v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAA-----------AGAACTCTTACAAC 784

  chrX_47898605_4   1108 TCA 1110
                            
  L1M4_orf2#LINE/    785 TCA 787

Transitions / transversions = 1.32 (83 / 63)
Gap_init rate = 0.04 (23 / 615), avg. gap size = 3.57 (82 / 23)  

 386 17.52 9.49 4.38  chrX_47898605_47900650.rev     1423  1559 (487)    L1M4_orf2#LINE/L1      765   908 (0)  

  chrX_47898605_4   1423 ATAAGAAGAA----TAAACCTCAATGGTAAAAAATATAAACAAATAATCC 1468
                            vi     ----  v v      ii      i-----        i  
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAG-----ACAAATAACCC 809

  chrX_47898605_4   1469 AATTAGAAAATCATGAAAAGATGTGAA----CATTTCACTGAAGAAGGAA 1514
                             ?i     vivv   i   v    ----      v ii      iv 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_47898605_4   1515 TA-----AGCAAATAAGCACATGAAAAGATGTTCAACACTCATTTGCTTC 1559
                           -----i  v                    i      -   ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.03 (5 / 144), avg. gap size = 3.80 (19 / 5)  


1582 24.57 9.22 3.92  chrX_47926152_47928176.rev      502  1087 (938)    L1M4_orf2#LINE/L1      172   788 (120)  

  chrX_47926152_4    502 ATAGCTAAGACAATTTTTGAAAAAGAAGAATAAGATGGGAGGAATGGCTC 551
                              i  i     i  -            i  ii v      v vi v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_47926152_4    552 TTTCATATTTCAATACTTCTTATATAGCTACAGGAATTAAGACTGTGTAG 601
                           i vv       v    vi  i v        v   i     v    i 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_47926152_4    602 TACTGGGAGAAGAGTAGACACATAGATCACTGGAACAAAATAGAGAACCT 651
                               v v   ii      i        v     i i   v    ii i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_47926152_4    652 AGAAATAGCCCCACAC-------------TGATTTTTTACCAAG------ 682
                                iv    i  -------------       iv  v i ------
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_47926152_4    683 AGACAA---AAAGAAGGAAGGATTGTCTGCTTAACAAATGGTGCTGGAGA 729
                             v ---  v ii i   i  v    vi i               -  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG-GA 419

  chrX_47926152_4    730 TG-TTG--TAGACATAGGCCAAAAAAAAATGACCTAATT---TTCTTACC 773
                         ii-i  --  ?v  i v  ---    i     --- i  ---ii i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGC---AAAAGAATGA---AGTTGGACCCCTACC 463

  chrX_47926152_4    774 TT------TATACAAAAAAGTAACTCAAG-TGCATCACAGATTTAAATCT 816
                          i------          -v        i-  v    ?   ii     v 
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_47926152_4    817 AAACTATAAAACTAAAAGAAAACTTTTACAAGAAAATATAGGAG-AAACG 865
                           ivvv        ---v      i   v       i     ? -   iv
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTA---TAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_47926152_4    866 TCTGAGATCTAGGGC---ACAGTGA----------ATGGTCCAAAAAGCA 902
                          ii v  i  v   i---i  i  i----------   iiv v       
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_47926152_4    903 TAATCAATAAG-GAAAAAA---ATAAATTAGATTTCATCCAATTTAAAA- 947
                         i  v   i  i-       ---       i  i      v  v      -
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_47926152_4    948 CTTGTGCTCTGCAAGAAATCTTGTTAAAAGGATGAAAAAACAGGGTATGA 997
                            v  iv  v   iii ivi i i  i iii      i   ivvi iii
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_47926152_4    998 TCTGGGAGAGAATGTTTGCAAACCACATATCCAAGAAAGGACTCACATCC 1047
                         vv       i   i        i  i     ii v  i     iii    
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_47926152_4   1048 AGAATATATAATGGATATGTATACTACTCTCAAAACTCAA 1087
                                    -i  ----------     i v       
  L1M4_orf2#LINE/    760 AGAATATATAA-AGA----------ACTCTTACAACTCAA 788

Transitions / transversions = 1.82 (91 / 50)
Gap_init rate = 0.04 (22 / 617), avg. gap size = 3.50 (77 / 22)  

 397 17.56 3.82 5.34  chrX_47926152_47928176.rev     1408  1538 (487)    L1M4_orf2#LINE/L1      780   908 (0)  

  chrX_47926152_4   1408 ATAACTCAAAGGTAAAAAAAAAAACCCAAATAATCCAATTAGAAAATTAT 1457
                          i       ---   v     i ---       i      ?i     viv
  L1M4_orf2#LINE/    780 ACAACTCAA---TAATAAAAAGA---CAAATAACCCAATTWAAAAATGGG 823

  chrX_47926152_4   1458 GAAAAGATATGAGCATACATTTCACTGAAGAGGAAATA-----AGCAAAT 1502
                         v   i   v   ii v       v ii    i  v   -----i  v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_47926152_4   1503 AAGCACATGAAAAGATGTTCAACACTCATTTGCTTC 1538
                                          i      -   ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.03 (4 / 129), avg. gap size = 3.00 (12 / 4)  


1014 23.65 6.55 3.99  chrX_47976910_47979252.rev      502   852 (1491)    L1M4_orf2#LINE/L1      172   531 (377)  

  chrX_47976910_4    502 ATAGCTAAGACAATTTTTGAAAAAGAAGAATAAGGTGGGAGGAATTGCTC 551
                              i  i     i  -            i  i  v      v ii v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_47976910_4    552 TACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTATATAT 601
                          v  vv       v    vi  i v        v         vi i iv
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_47976910_4    602 TATTGGGAGAAAAATAGACACATAGATCACTGTAACAAAATAGAAATCCT 651
                           i   v v  ii       i        v  v  i i   v  i vi i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_47976910_4    652 AGAAATAGCCCCACAC-------------TGATTTTTTACCAAGA-GACA 687
                                iv    i  -------------       iv  v i i- v  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_47976910_4    688 AAA-------ATAGGGAAAGA-TCATCTGCTTAACAAATGATGCTGGGGC 729
                          i -------  i        - vi   vi i        i       i 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_47976910_4    730 AGTTGCAGAGCCATAGGCCAAAAAGAAAAAAAAAAAACCAAAAAGGCCTA 779
                          ii  v v ?   i v  --       vi  ivvii   -------    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGC--AAAAGAATGAAGTTGGACC-------CCTA 461

  chrX_47976910_4    780 ATCTTCACACCTTTATACAAAAAAGTAAGTCAAG-TGGATCATAGATTTA 828
                         -- i       v -         -v   v    i-       ?   ii  
  L1M4_orf2#LINE/    462 --CCTCACACCAT-ATACAAAAA-TTAACTCAAAATGGATCAWAGACCTA 507

  chrX_47976910_4    829 AATCTAAAATATAAAACTATAAAA 852
                            v   i vv             
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAA 531

Transitions / transversions = 1.25 (45 / 36)
Gap_init rate = 0.03 (11 / 360), avg. gap size = 3.36 (37 / 11)  

 548 27.30 8.88 4.28  chrX_47976910_47979252.rev     1115  1418 (925)    L1M4_orf2#LINE/L1      476   793 (115)  

  chrX_47976910_4   1115 CAAGAATGCATCTCAAAA---AACAAACAAACAAACAAAAAAACTAAAA- 1160
                            i   -i v       --- v  ? v vvi   iiv  i i      -
  L1M4_orf2#LINE/    476 CAAAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_47976910_4   1161 -A-AAAAGTTTTACAAGAAAATATAGGAG-AAGCGTCTGAGATCTAGGGC 1207
                         - -    v i   v       i     ? -  iiv ii v  i  v   i
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_47976910_4   1208 ATAGTGAATGGTT------------CA--AAAAGCATAAT--ACATAAGG 1241
                         -   vv       ------------  --       i  v--   v   i
  L1M4_orf2#LINE/    575 -TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_47976910_4   1242 AAAAA---ATAAATTAGATTTCATCCAATTTAAAA-CTTTTGCTCTGCAA 1287
                              ---       i  i      v  v      -      iv  v   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_47976910_4   1288 GAAATCTTGTTAGAAGGATGAAAAAATATGGTATGATCTGAAAGAAAATG 1337
                         iii ivi i i ii iii      i i vvvi iiivv  ii       i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_47976910_4   1338 TTTGCAAACCACATATCCAAGAAAGGACTCACATCCAGAATATGTAATGG 1387
                                 i  i     ii v  i     iii           i   ---
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA--- 770

  chrX_47976910_4   1388 ATATGTATAGTACTCTCAAAACTCAACAGTA 1418
                         --------  v     i v       i i  
  L1M4_orf2#LINE/    771 --------AGAACTCTTACAACTCAATAATA 793

Transitions / transversions = 1.89 (53 / 28)
Gap_init rate = 0.04 (12 / 318), avg. gap size = 3.33 (40 / 12)  

 397 18.87 6.29 5.66  chrX_47976910_47979252.rev     1698  1856 (487)    L1M4_orf2#LINE/L1      749   908 (0)  

  chrX_47976910_4   1698 GACTCTGTCTCAAGAA-----AAAAAAATAATAAAAACCTCAATGGTAAA 1742
                             -   v  v    -----   i  v vv  v  --      ii    
  L1M4_orf2#LINE/    749 GACT-TGTATCCAGAATATATAAAGAACTCTTACAA--CTCAATAATAAA 795

  chrX_47976910_4   1743 AAATACAAACAAATAATCCAGTTAGAAAATCATGAAAAGATATGAACATA 1792
                           i-----        i   i  ?i     vivv   i   v    i v 
  L1M4_orf2#LINE/    796 AAG-----ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_47976910_4   1793 CATTTCACTGAAGAGGAAATA-----AGCAAATAAGCACATGAAAAGATG 1837
                               v ii    i  v   -----i  v                    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_47976910_4   1838 TTCAACACTCATTTGCTTC 1856
                         i      -   ????????
  L1M4_orf2#LINE/    891 CTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.07 (15 / 14)
Gap_init rate = 0.04 (6 / 160), avg. gap size = 3.17 (19 / 6)  


 819 20.33 7.19 21.99  chrX_47989241_47991375.rev      502  1224 (911)    L1M4_orf2#LINE/L1      173   788 (120)  

  chrX_47989241_4    502 TAACTAAGACAATTTTTGAAAAAGAAGAATAAGGTGGGAGGAATGGCTCT 551
                           i i  i     i  -            i  i  v      v vi v  
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_47989241_4    552 ACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTGTGTAGT 601
                         v  vv       v    vi  i v        v         v    i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_47989241_4    602 ATTGGGAGAAGAATAGACACATAGATCACTGGAACAAAACAGAGAACCTG 651
                          i   v v   i       i        v     i i  iv    ii ii
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_47989241_4    652 GAAATTGCCCCACAC-----TG---------TTTTCCCCAAG-------A 680
                              viv    i  -----  ---------     vv    ------- 
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_47989241_4    681 GAC-----AAAAAG--AAGGATCGTCTGCTTAACAAATGGTGCTGGAGCA 723
                            -----  vii --   i  v    vi i               ii  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_47989241_4    724 GTTGCATATCCATAGACAAAACAACAACAACAACAACAACAACAAACAAA 773
                         ii  v   ?   i vi     v  ii -----------------------
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGA----------------------- 448

  chrX_47989241_4    774 CAAACAACAACAAGAAAACACCTAATCTTCATATATATATACATATATAT 823
                         ----------- ivvii  v    -- i   -------------------
  L1M4_orf2#LINE/    449 -----------AGTTGGACCCCTA--CCTCA------------------- 466

  chrX_47989241_4    824 ATACATATATATACACATATATATATACATATATATACACATATATATAC 873
                         --------------------------------------------------
  L1M4_orf2#LINE/    467 -------------------------------------------------- 466

  chrX_47989241_4    874 ACATATATATACATATATATACACATATATATATACATATATATATACAT 923
                         ---------------------   -----------------i       v
  L1M4_orf2#LINE/    467 ---------------------CAC-----------------CATATACAA 478

  chrX_47989241_4    924 ATATTAAAAACTCAAG-TGGCTCATAGATTTAAATCTAAAATATAACACT 972
                          v     ---     i-   v   ?   ii     v   i vv   v   
  L1M4_orf2#LINE/    479 AAATTAA---CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_47989241_4    973 AAAAAAACTTTTACAAGAAAGAGTAGGAG-AAACGTCTGAGATCTAGGCA 1021
                          v    -  i   v      ivi    ? -   iv ii v  i  v  vv
  L1M4_orf2#LINE/    526 ATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_47989241_4   1022 TAGTGAACGGTT------------CA--AAAAGCATAATCCATAAG-GAA 1056
                            vv  i    ------------  --       i  v v i  i-   
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_47989241_4   1057 AAAA---ATAAATTAGATTTCATCCAATTTAA---CTTTTGCTCTGTAGA 1100
                             ---       i  i      v  v    ---      iv  vi i 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_47989241_4   1101 A-ACCGTGTTAAAAGGATGAAAAAACAGGGTGTAAAGTGGGAGAAAATGT 1149
                         i-  vv i i  i iii      i   ivviii i i           i 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_47989241_4   1150 TTGCAAACCACGTATCCAAGAAAGGACTCACATCCAGAATATATAACGGA 1199
                                i  ii    ii v  i     iii               ----
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA---- 770

  chrX_47989241_4   1200 TACGTATAGTACTCTCAAAACTCAA 1224
                         -------  v     i v       
  L1M4_orf2#LINE/    771 -------AGAACTCTTACAACTCAA 788

Transitions / transversions = 1.44 (85 / 59)
Gap_init rate = 0.03 (21 / 616), avg. gap size = 10.05 (211 / 21)  

 325 24.41 3.94 2.36  chrX_47989241_47991375.rev     1522  1648 (487)    L1M4_orf2#LINE/L1      780   908 (0)  

  chrX_47989241_4   1522 ACAAAACAACGGTAAAAACAAACAAATAATTCAATTAGAAAATTATGAAG 1571
                             vv   iii      --i        ii     ?i     vivv  i
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAA--GACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_47989241_4   1572 ATATATGAACATACATTTCACTGAAGAGGAAATA-----AGCAAATAAGC 1616
                         iv  v    i v       v ii    i  v   -----i  v       
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_47989241_4   1617 ACATGAAAGGCTGTTCAACACTTACTTGCTTC 1648
                                 i v  i      - i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.50 (18 / 12)
Gap_init rate = 0.02 (3 / 129), avg. gap size = 2.67 (8 / 3)  


1750 22.85 7.12 4.97  chrX_47992028_47994082      500  1103 (952)    L1M4_orf2#LINE/L1      172   788 (120)  

  chrX_47992028_4    500 ATAGCTAAGACAATTTTTGAAAAAGAAGAATAAGGTAGGAGGAATGGCTC 549
                              i  i     i  -            i  i  v      v vi v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_47992028_4    550 TACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTGTGTAG 599
                          v  vv       v    vi  i v        v         v    i 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_47992028_4    600 TATTGGCAGAAGAATAGACACATAGATCACTGGAGCAAAATAGAGAACCT 649
                           i     v   i       i        v    ii i   v    ii i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_47992028_4    650 AGAAATAG--CCACACACT-----------GATTTTTTACAAAG------ 680
                                i--   i   i -----------      iv    i ------
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_47992028_4    681 AGACAG---AAAGAAGGAAGGATCGTCTGCTTAACAAATGGTGCTGGAGC 727
                             vi---  v ii i   i  v    vi i               ii 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_47992028_4    728 AGTTGCATATCCATAGGCAAAAAAAAAAAAAAAAAAAAATAAGACC--TA 775
                          ii  v   ?   i v      i  vi  i--------- vi    --  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAG---------TTGGACCCCTA 461

  chrX_47992028_4    776 ATCTTCATAACTTTATACAAAAAAGTAACTCAAA-TGGATCATATATTTA 824
                         -- i   i - iv          -v         -       ? v ii  
  L1M4_orf2#LINE/    462 --CCTCACA-CCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTA 507

  chrX_47992028_4    825 AATCTGAAATATAAAACTAAAAAAAAAAGCTTTTACAAGAAAACATAGGA 874
                            v i i vv        v    -----  i   v             ?
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAA-----CTCTTAGAAGAAAACATAGGN 552

  chrX_47992028_4    875 G-AAACGTCTGAGATCTAGGGC------ATGGT------GA-ACAGTTCA 910
                          -   iv ii v  i  v   i------     ------  - iiiiv v
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_47992028_4    911 AAAAGCATAATC--CATAAGGAAAAAAAG-TAAATTAGATTTCATCCAAT 957
                                i  v --  v   i     v  -      i  i      v  v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_47992028_4    958 TTAAAA-CTTTTGCTCTGCAAGAAACCCTGTTAAAAGGATGAAAAAACAA 1006
                               -      iv  v   iii  v  i i  i iii      i    
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_47992028_4   1007 AGTATGGACTGGGAGAAAATGTTTGCAAACCACATATCCAAGAAAGGACT 1056
                         vvi ii  v           i        i  i     ii v  i     
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_47992028_4   1057 CACATCCAGAATATATAATGGATATGTATAGTACTCTCAAAACTCAA 1103
                         iii               -----------  v     i v       
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAA-----------AGAACTCTTACAACTCAA 788

Transitions / transversions = 1.65 (84 / 51)
Gap_init rate = 0.03 (20 / 617), avg. gap size = 3.65 (73 / 20)  

 418 18.75 3.91 3.12  chrX_47992028_47994082     1439  1566 (489)    L1M4_orf2#LINE/L1      780   908 (0)  

  chrX_47992028_4   1439 ATAACTCAAAGGTAAAAAAAAACCAAATAATCCAATTAGAAAATTATGAA 1488
                          i       ---   v     iv       i      ?i     vivv  
  L1M4_orf2#LINE/    780 ACAACTCAA---TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_47992028_4   1489 AAGATATGAGCATACATTTCACTGAAGAGGAAATA-----AGCAAATAAG 1533
                          i   v   ii v       v ii    i  v   -----i  v      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_47992028_4   1534 CACATGAAAAGATGTTCAACACTCATTTGCTTC 1566
                                       i      -   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.02 (3 / 129), avg. gap size = 3.00 (9 / 3)  


1745 22.81 7.11 5.12  chrX_48031648_48033703.rev      502  1106 (950)    L1M4_orf2#LINE/L1      172   788 (120)  

  chrX_48031648_4    502 ATAGCTAAGACAATTTTTGAAAAAGAAGAATAAGGTAGGAGGAATGGCTC 551
                              i  i     i  -            i  i  v      v vi v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_48031648_4    552 TACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTGTGTAG 601
                          v  vv       v    vi  i v        v         v    i 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_48031648_4    602 TATTGGCAGAAGAATAGACACATAGATCACTGGAGCAAAATAGAGAACCT 651
                           i     v   i       i        v    ii i   v    ii i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_48031648_4    652 AGAAATAG--CCACACACT-----------GATTTTTTACAAAG------ 682
                                i--   i   i -----------      iv    i ------
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_48031648_4    683 AGACAG---AAAGAAGGAAGGATCGTCTGCTTAACAAATGGTGCTGGAGC 729
                             vi---  v ii i   i  v    vi i               ii 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_48031648_4    730 AGTTGCATATCCATAGGCAAAAAAAAAAAAAAAAAAAAAATAAGACC--T 777
                          ii  v   ?   i v      i  vi  i---------- vi    -- 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAG----------TTGGACCCCT 460

  chrX_48031648_4    778 AATCTTCATAACTTTATACAAAAAAGTAACTCAAA-TGGATCATATATTT 826
                          -- i   i - iv          -v         -       ? v ii 
  L1M4_orf2#LINE/    461 A--CCTCACA-CCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCT 506

  chrX_48031648_4    827 AAATCTGAAATATAAAACTAAAAAAAAAAGCTTTTACAAGAAAACATAGG 876
                             v i i vv        v    -----  i   v             
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAA-----CTCTTAGAAGAAAACATAGG 551

  chrX_48031648_4    877 AG-AAACGTCTGAGATCTAGGGC------ATGGT------GA-ACAGTTC 912
                         ? -   iv ii v  i  v   i------     ------  - iiiiv 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_48031648_4    913 AAAAAGCATAATC--CATAAGGAAAAAAAG-TAAATTAGATTTCATCCAA 959
                         v       i  v --  v   i     v  -      i  i      v  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_48031648_4    960 TTTAAAA-CTTTTGCTCTGCAAGAAACCCTGTTAAAAGGATGAAAAAACA 1008
                         v      -      iv  v   iii  v  i i  i iii      i   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_48031648_4   1009 AAGTATGGACTGGGAGAAAATGTTTGCAAACCACATATCCAAGAAAGGAC 1058
                          vvi ii  v           i        i  i     ii v  i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_48031648_4   1059 TCACATCCAGAATATATAATGGATATGTATAGTACTCTCAAAACTCAA 1106
                          iii               -----------  v     i v       
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAA-----------AGAACTCTTACAACTCAA 788

Transitions / transversions = 1.65 (84 / 51)
Gap_init rate = 0.03 (20 / 617), avg. gap size = 3.70 (74 / 20)  

 418 18.75 3.91 3.12  chrX_48031648_48033703.rev     1442  1569 (487)    L1M4_orf2#LINE/L1      780   908 (0)  

  chrX_48031648_4   1442 ATAACTCAAAGGTAAAAAAAAACCAAATAATCCAATTAGAAAATTATGAA 1491
                          i       ---   v     iv       i      ?i     vivv  
  L1M4_orf2#LINE/    780 ACAACTCAA---TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_48031648_4   1492 AAGATATGAGCATACATTTCACTGAAGAGGAAATA-----AGCAAATAAG 1536
                          i   v   ii v       v ii    i  v   -----i  v      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_48031648_4   1537 CACATGAAAAGATGTTCAACACTCATTTGCTTC 1569
                                       i      -   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.02 (3 / 129), avg. gap size = 3.00 (9 / 3)  


 744 19.52 6.82 24.47  chrX_48034357_48036520      500  1247 (917)    L1M4_orf2#LINE/L1      173   788 (120)  

  chrX_48034357_4    500 TAACTAAGACAATTTTTGAAAAAGAAGAATAAGGTGGGAGGAATGGCTCT 549
                           i i  i     i  -            i  i  v      v vi v  
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_48034357_4    550 ACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTGTGTAGT 599
                         v  vv       v    vi  i v        v         v    i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_48034357_4    600 ATTGGGAGAAGAATAGACACATAGATCACTGGAACAAAACAGAGAACCTG 649
                          i   v v   i       i        v     i i  iv    ii ii
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_48034357_4    650 GAAATTGCCCCACAC-------------TGATTTTCCCCAAG-------A 679
                              viv    i  -------------        vv    ------- 
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_48034357_4    680 GAC-----AAAAAG--AAGGATCGTCTGCTTAACAAATGGTGCTGGAGCA 722
                            -----  vii --   i  v    vi i               ii  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_48034357_4    723 GTTGCATATCCATAGACAAAACAACAACAACAACAACAACAACAAACAAA 772
                         ii  v   ?   i vi     v  ii -----------------------
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGA----------------------- 448

  chrX_48034357_4    773 CAAACAACAACAAGAAAACACCTAATCTTCATATATATATACATATATAT 822
                         ----------- ivvii  v    -- i   -------------------
  L1M4_orf2#LINE/    449 -----------AGTTGGACCCCTA--CCTCA------------------- 466

  chrX_48034357_4    823 ATACATATATATACACATATATATATACATATATATACACATATATATAC 872
                         --------------------------------------------------
  L1M4_orf2#LINE/    467 -------------------------------------------------- 466

  chrX_48034357_4    873 ACATATATATACATATATATACACATATATATATACATATATATACACAT 922
                         ---------------------------------------------   --
  L1M4_orf2#LINE/    467 ---------------------------------------------CAC-- 469

  chrX_48034357_4    923 ATATATATACATATATATATACATATATTAAAAACTCAAG-TGGCTCATA 971
                         ---------------i       v v     ---     i-   v   ? 
  L1M4_orf2#LINE/    470 ---------------CATATACAAAAATTAA---CTCAAAATGGATCAWA 501

  chrX_48034357_4    972 GATTTAAATCTAAAATATAACACTAAAAAAACTTTTACAAGAAAGAGTAG 1021
                           ii     v   i vv   v    v    -  i   v      ivi   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAG 550

  chrX_48034357_4   1022 GAG-AAACGTCTGAGATCTAGGCATAGTGAACGGTT------------CA 1058
                          ? -   iv ii v  i  v  vv   vv  i    ------------  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_48034357_4   1059 --AAAAGCATAATCCATAAG-GAAAAAA---ATAAATTAGATTTCATCCA 1102
                         --       i  v v i  i-       ---       i  i      v 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_48034357_4   1103 ATTTAA---CTTTTGCTCTGTAGAA-ACCGTGTTAAAAGGATGAAAAAAC 1148
                          v    ---      iv  vi i i-  vv i i  i iii      i  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_48034357_4   1149 AGGGTGTAAAGTGGGAGAAAATGTTTGCAAACCATGTATCCAAGAAAGGA 1198
                          ivviii i i           i        i   i    ii v  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_48034357_4   1199 CTCACATCCAGAATATATAACGGATACGTATAGTACTCTCAAAACTCAA 1247
                           iii               -----------  v     i v       
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAA-----------AGAACTCTTACAACTCAA 788

Transitions / transversions = 1.42 (84 / 59)
Gap_init rate = 0.03 (20 / 616), avg. gap size = 11.70 (234 / 20)  

 326 24.60 3.97 1.59  chrX_48034357_48036520     1550  1675 (489)    L1M4_orf2#LINE/L1      780   908 (0)  

  chrX_48034357_4   1550 ACAACGGTAAAAACAAACAAACAAATAATTCAATTAGAAAATTATGAAGA 1599
                              v-i  v  i   v i        ii     ?i     vivv  ii
  L1M4_orf2#LINE/    780 ACAACT-CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_48034357_4   1600 TATATGAACATACATTTCACTGAAGAGGAAATA-----AGCAAATAAGCA 1644
                         v  v    i v       v ii    i  v   -----i  v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_48034357_4   1645 CATGAAAGGCTGTTCAACACTTACTTGCTTC 1675
                                i v  i      - i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.31 (17 / 13)
Gap_init rate = 0.02 (3 / 129), avg. gap size = 2.33 (7 / 3)  


1595 23.70 8.74 4.20  chrX_48058422_48060431      497  1091 (919)    L1M4_orf2#LINE/L1      172   793 (115)  

  chrX_48058422_4    497 ATAGCTAAGACACTTTTTGAAAAAGAAGAATAAGGTGGGAGGAATGGCTC 546
                              i  i   v i  -            i  i  v      v vi v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_48058422_4    547 TACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTGTGTCG 596
                          v  vv       v    vi  i v        v         v    v 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_48058422_4    597 TATGGGGCGAAGAATAGACACACAGATCACTGGAACAAAATAGAGAACCT 646
                           iv  vvv   i       i i      v     i i   v    ii i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_48058422_4    647 AGAAATAGCCCCACAC-------------TGACTTTTTACAAAG-CGACA 682
                                iv    i  -------------   i   iv    i -i v  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_48058422_4    683 A--------AAAGAAGGAAGGATTGTCTGCTCAACAAATGGTGCTGGAGA 724
                          --------  v ii i   i  v    vi                 iiv
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_48058422_4    725 AGTTGCAGAGCCATAAGCTAATAAAAAAAA---GACC--TAATCTTCATA 769
                          ii  v v ?   i v  v  vi  vi  i---    --  -- i   i 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA--CCTCACA 468

  chrX_48058422_4    770 CCTTTATACAAAAAAAAAAAAACTCAAG-TGGATCATAGATTTAAATCTA 818
                           v -         vv  ----     i-       ?   ii     v  
  L1M4_orf2#LINE/    469 CCAT-ATACAAAAATTAA----CTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_48058422_4    819 AAATATAAAACTAAAACAGAAACTTTTACAAGAAAACATAGGAGAAACAT 868
                          i vv        v  ----    i   v             ? v  -  
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAA----AACTCTTAGAAGAAAACATAGGNGTAA-AT 558

  chrX_48058422_4    869 CT--GAGATCTAGGGCATAGTAAACAGTT------------CA--AAAAG 902
                           -- v  i  v   i-   vv  ii   ------------  --     
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_48058422_4    903 CATAATC--CATAAGGAAAAA-----AAATTAGATTTCATCCAATTTAAA 945
                           i  v --  v   i     -----     i  i      v  v     
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_48058422_4    946 A-CTTTTGCCCTGCAAGAAACCCTGTTAAAAGGATGAAAAAACAGGGTAT 994
                          -      iv  v   iii  v  i i  i iii      i   ivvi i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_48058422_4    995 GGAATGGGAGAGAATGTTTGCAAACCACATATCCAAGAAAGGACTCACAT 1044
                         i          i   i        i  i     ii v  i     iii  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_48058422_4   1045 CCAGAATGTATAATGGATATGTATAGTACTCTCAAAACTCAACAGTA 1091
                                i     -----------  v     i v       i i  
  L1M4_orf2#LINE/    758 CCAGAATATATAA-----------AGAACTCTTACAACTCAATAATA 793

Transitions / transversions = 1.38 (80 / 58)
Gap_init rate = 0.03 (20 / 622), avg. gap size = 3.85 (77 / 20)  

 422 20.80 4.00 2.40  chrX_48058422_48060431     1396  1520 (490)    L1M4_orf2#LINE/L1      782   908 (0)  

  chrX_48058422_4   1396 AACTCAACGGCAAAAAACAAACAAATAATCCAATTAGAAAATGATCAAAA 1445
                                iiii     i---        i      ?i      iv    i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAG---ACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_48058422_4   1446 TATATGAACATACATTTCACTGAAGAGGAAATA-----AGCAAATAAGCT 1490
                         v  v    i v       v ii    i  v   -----i  v       v
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_48058422_4   1491 CATGAAAAGATGTTCAACACTAATTTGCTT 1520
                                     i      ii ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (17 / 8)
Gap_init rate = 0.02 (2 / 127), avg. gap size = 4.00 (8 / 2)  


2094 12.99 3.95 1.13  chrX_48392033_48395924     1330  1683 (2209)    L1M4_orf2#LINE/L1        1   364 (544)  

  chrX_48392033_4   1330 TGGAAAGACATCACATGTTCATGGATTGGAAGACTTTATAGTGTTAAGAT 1379
                                 i   v                       v   v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_48392033_4   1380 GGCAATACTCCCCAAATTGATCTACAGACTTGATGCAATCCCTATCAGAA 1429
                                                     i ii i             i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_48392033_4   1430 TCCCAGCTTGCTTCTTTGCAGAA-CTGACAAGCTGAT--------TCACA 1470
                                 vv   i         -i            --------   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_48392033_4   1471 TGGGAGTGCTAGGGGCCCAAAATA--CAA--CAATCTTGAAAAAGAAAAA 1516
                            i i   v    i    i    --   --                i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_48392033_4   1517 CAAAGTTAGAGGACTCACACCTTCCAGTTTAAAAACTTACTATACAGCTA 1566
                                i            i i   i   v           i v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_48392033_4   1567 CAGTAATCAAGACCATGTGCTACTGGCATAAAAACATACATATAAATTAA 1616
                                      vi    v           ii i v       i  i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_48392033_4   1617 CGAAATAGAATTGAAAGTCCAGAAATAAATTCATACATT-ATAGGCAACT 1665
                         i i           i              ii        -  i v   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_48392033_4   1666 GATTTTTTTGAGACAGGG 1683
                               i----    i  
  L1M4_orf2#LINE/    351 GATTTTC----GACAAGG 364

Transitions / transversions = 2.83 (34 / 12)
Gap_init rate = 0.02 (6 / 364), avg. gap size = 3.00 (18 / 6)  

1312 11.28 0.00 0.00  chrX_48392033_48395924     1941  2135 (1757)    L1M4_orf2#LINE/L1      346   540 (368)  

  chrX_48392033_4   1941 CAATTGATTTTTGACAAGTGTACCAAGACCATTCAATGGGGAAAGAATGC 1990
                                    i      v  i                          iv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_48392033_4   1991 TCCTTTCAACAAATGGTGCTGAGACAGCTGAGTATCCACATGCAAAAGAA 2040
                           i                  i    i   ii  ?               
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_48392033_4   2041 TAAAGTGGGACCCCTTCCTCATACCATATACAAAAAACAACTCAAAACAG 2090
                          i    v        v     i              vi         ii 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_48392033_4   2091 ATCAAAGACCTAAATGTAAGAGCTAAAACGATAAAACTTTTAGAA 2135
                             ?                        v        i      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.00 (0 / 195), avg. gap size = 0.00 (0 / 0)  

 715 15.08 2.38 0.00  chrX_48392033_48395924     2452  2577 (1315)    L1M4_orf2#LINE/L1      535   663 (245)  

  chrX_48392033_4   2452 TTAGAAGAAAACA--GGCTTAAGTCTTTGTGACCTTGGATTAGGCAATGG 2499
                                      --  ?v   i    i          i           
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_48392033_4   2500 TTTCTTAGACGTGACATCTAAAGCATAAGCAGCCAAAGAAAAA-TAGACA 2548
                                  ii     i v      i     i v         -    i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_48392033_4   2549 CACTGGAGTTCATCAAAACTATAAGCTTT 2577
                         v i    v          i  v  i    
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTT 663

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.02 (2 / 129), avg. gap size = 1.50 (3 / 2)  

 965 11.48 6.56 0.00  chrX_48392033_48395924     2870  3052 (840)    L1M4_orf2#LINE/L1      685   879 (29)  

  chrX_48392033_4   2870 AAAAAAGTGAAAAGACAACCTACAGAA-----GACAATATTTGAAAATCA 2914
                           i                 i      -----  v        v      
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_48392033_4   2915 CATATCTAAAAAGAGTCTAGTATCCAGAATACATAAAGAACTCTTACTAC 2964
                         i      i v   i v  v            i               v  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_48392033_4   2965 TCAACAATAAAAGGACAAATAACCCAATTCAAAA-TGGGCAAAGGATTTA 3013
                             i       i                ?    -              i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_48392033_4   3014 AATAAACACTTCTCCAAAGAAGATA----AATGGGC--TGGGCAC 3052
                             i   i                ----     v -- ii    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.02 (4 / 195), avg. gap size = 3.00 (12 / 4)  

 262 12.73 7.27 0.00  chrX_48392033_48395924     3345  3399 (493)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_48392033_4   3345 AAAGAAGATA----GATGACCAACAAGTTTATGAAAATATGCTCAACATC 3390
                                   ----i   i    i   ivi       v            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_48392033_4   3391 AGTGGTCAC 3399
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 4.00 (4 / 1)  


3240 26.48 0.66 0.88  chrX_48483257_48488536     3878  4787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_48483257_4   3878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_48483257_4   3928 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3977
                            v     v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_48483257_4   3978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT--TCTTTAAAGTTC 4024
                          v   iivi i  i  ii     -   -- v  i  --  i -   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCT-AAAATTC 147

  chrX_48483257_4   4025 ATATGGAACCAAAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGACAAAA 4074
                                 viiv  ii  v  v v  i     iv     i i i v i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_48483257_4   4075 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACCATAAGG 4124
                                 i      vv    i  v  ii i      viv   i i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_48483257_4   4125 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGAC 4174
                                  i   i    ii         i iv ii i   v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_48483257_4   4175 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 4222
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_48483257_4   4223 CATCTGATCTTTCACAAACCTGAGAAAAACAAGCAATGGGGAAATGATTC 4272
                           vi    i  iv    ivv  vv  i v  vv           vi  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_48483257_4   4273 CCTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGC 4322
                         i  v  i  i              v     iv  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_48483257_4   4323 TGAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGG 4372
                             ii    i    v   i i   v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_48483257_4   4373 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4422
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_48483257_4   4423 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 4471
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_48483257_4   4472 AAAACACCAAAAGTAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4521
                          vi          i vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_48483257_4   4522 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 4571
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_48483257_4   4572 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 4621
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_48483257_4   4622 AAAGGGCTAATACCCAGAATCTACAATGAACTCTAACAAATTTACAAGAA 4671
                           i  i  vi  i       v  i  v       v    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_48483257_4   4672 AAAAACAAAAAACCCCATCACAAAAAGTGGGCAAAGGATATGAACACACA 4721
                            i     v     v  i?--    i            v    i v   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_48483257_4   4722 CTTCTCAAAAGAAGACATTTATGTAGCCAAAAGACACATGAAAAAATGCT 4771
                         i     v        i  vi vi i     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_48483257_4   4772 CATCATCACTGGCCAT 4787
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3187 27.59 0.55 0.33  chrX_49088167_49094560.rev     4998  5903 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_49088167_4   4998 TGGAAGTACATTCCATGTTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5047
                              iv i  i            i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_49088167_4   5048 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 5097
                            v     v     iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_49088167_4   5098 TACCAATGACTTTCTTCACAGAATTGGAAAAAAT-ACTTTAAAGTTCATA 5146
                          v   iivi i  i  ii     v v  v  iv - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_49088167_4   5147 TGGAACCAAAAAAGAGCCCTCATGGCCAAGTCAATCCTAAGCCTAAAGAA 5196
                              viiv  ii  v  vvv  i     iv     i i ivvvi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_49088167_4   5197 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5246
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_49088167_4   5247 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAAGATATAGACCAA 5296
                               i   i    ii         i iv ii i i v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_49088167_4   5297 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTAT 5344
                              i    i--    i  --        vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_49088167_4   5345 CTGGTCTTTGACAACCCTGACAAAAACAAGCAATAGGGAAATGATTCCCT 5394
                         i  i i  i     vvv  v   i v  vv    i      vi  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_49088167_4   5395 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5444
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_49088167_4   5445 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5494
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_49088167_4   5495 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5544
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_49088167_4   5545 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5593
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_49088167_4   5594 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5643
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_49088167_4   5644 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAACC 5693
                         i   v v  i i   i  ii vv    i  v  i i  vv i      vv
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_49088167_4   5694 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5743
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_49088167_4   5744 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAAA 5793
                           i  vi          v  i  v      vv    v iv i  vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_49088167_4   5794 -ACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 5842
                         -     i     v  i?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_49088167_4   5843 CAAAAGAAGACATTTATGCAGCCAAAAAACGCATGAAAAAATGCTCATTA 5892
                          v        i  vi viii     v  i i        i       vi 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_49088167_4   5893 TCACTGGCCAT 5903
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (145 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2306 22.49 4.56 1.52  chrX_49108586_49110227.rev      494  1151 (491)    L1M4_orf2#LINE/L1      231   908 (0)  

  chrX_49108586_4    494 CATAACTTA-----AAGTTATAGTAATTAAAAGAGTGTAGTTTTGACATC 538
                           v      -----   i  i      i  i v     i  vi  i   v
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_49108586_4    539 AAGGTAGACAAATAGACCAACGAAACAGAAT--ACAGTCAAGAAATAAAC 586
                          i i      v     i   i i  i     -- v    v          
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_49108586_4    587 CTACACAGATATAGATCACTGATATTTTACAAAGGCACAAAAGAAACACA 636
                          i i   vv   i viv i    v  iv    i  ii v  iivv iv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_49108586_4    637 GTAGAGAAAGGATAATCTCAACAAATAAATGGTAATAAAACAATTGGATA 686
                         i i i     i   i   ivv   -i       iv iii    i      
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAA-CAAATGGTGCTGGGACAACTGGATA 429

  chrX_49108586_4    687 TCCATATGTGAAAAAAAGAACAAAGAACCTCAAGCCATACTTTCTACCAT 736
                         ?   i   i----       ii   ---i vi v  v   i ivi     
  L1M4_orf2#LINE/    430 KCCACATGC----AAAAGAATGAAG---TTGGACCCCTACCTCACACCAT 472

  chrX_49108586_4    737 GTGCATAA-TTACCTCAAA-TGGATCATAGACCTAAACATAAAACCTCAA 784
                         i i  v  -   v      -       ?         ii   i v  v  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_49108586_4    785 ACTATAAAACTTGTAGGACAAAAC------------CTTTGTGATGTTGG 822
                                    iv   i v     ------------   i    iv    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_49108586_4    823 ATTAGGAAAAGTTTTCTTAGACATGACAGCAAAAGAACAAGTCG-AAAAG 871
                         i     v  v v         i      v      v     ivi-     
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_49108586_4    872 AACAAATTAATAAATTTGACTTAATCAAAACTAAAA-CGTTTCTGCTTTT 920
                           v    vi       v     v       i     - v   v     --
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT-- 670

  chrX_49108586_4    921 CAAAAGACAC----AGGAGAATAAACTGACAAGCCGCAGACAAGGAGAAA 966
                             i     ---- i  i i i  vv     v  i    vvi       
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_49108586_4    967 ATATTTGCAAAGCATATATCTGATAAAGGACTTTTATCCAGAATTTATAA 1016
                                    v              i      v          v     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_49108586_4   1017 AGAACGCTTAAAACTGAAAGATGAGAAAACAAGCAACCAAA---AAATAT 1063
                              v    v    v  vi  i i  i    ii    v  ---   v  
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_49108586_4   1064 AGGCAAAGAATTTGAACAGACACTTCACCAAAGGAGACACTCAATTGGCA 1113
                         i       i       i     i   v      i   i iv   v    v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_49108586_4   1114 AAGAAGCACATAAAAAGATGCTCAACATTATTAGTCAT 1151
                           v        i                i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (84 / 62)
Gap_init rate = 0.02 (13 / 678), avg. gap size = 3.08 (40 / 13)  


2873 20.65 2.05 13.21  chrX_49149873_49152513.rev     1129  2150 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_49149873_4   1129 TGGAGTGACATACTGTGTCTGTGGATTGGAAGACTCAAAATAGTGGAGTT 1178
                             iv  i  v ii   iii              i  v  v  vi  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_49149873_4   1179 GTCAAATCTCCCCAAATAGATCTTTAAGTTTAATGCAATTCCCATCAAG- 1227
                          v   vv          v     vi ii  i  i     i  i     i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_49149873_4   1228 -----------TTTTTTGTAGACATAGACAAGCTTATTCTAAAATTCATA 1266
                         -----------       i   v  v        v  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_49149873_4   1267 TGGAAAGGCACAAACCCTAGAATAGCTAAAACAATTTTGAAAA-GAAGAA 1315
                               v   viiiv  i        i        i       -      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_49149873_4   1316 TATATTGGGAGGAATTGCTCTACCTGAT-----GACTTGCCATCTAGCTA 1360
                         i v v v      v ii v  v  ii  -----i    i i ivv     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_49149873_4   1361 TAGTAACCAAAGAAATTATCACATTGTCCAAGAGATAGACATACA--TCA 1408
                         i     i   -  v v i vii i  v vv ii          i --   
  L1M4_orf2#LINE/    251 CAGTAATCAA-GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_49149873_4   1409 ATGGAACAGAATTGAAAACCCATAAATAGACCCACACAACTGATTCTTTT 1458
                               i        i ii   v     i     i   ------------
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA------------ 337

  chrX_49149873_4   1459 TTTGATGGGGTCTTGCTATGTTACCCACACTGGACTTGAACTCCTTGGCT 1508
                            -    ------------------------------------------
  L1M4_orf2#LINE/    338 TTT-ATGG------------------------------------------ 344

  chrX_49149873_4   1509 CAAGTGATCCTCCCACCTTAGCCTTCCATGTAACTAGGATTACAGGCATG 1558
                         --------------------------------------------------
  L1M4_orf2#LINE/    345 -------------------------------------------------- 344

  chrX_49149873_4   1559 CACCACCACATCTAGCTTTTCAACTGATTCTTGACAAAGATGGAAATGCA 1608
                         -------------------    i     i i     i i  vv  vi v
  L1M4_orf2#LINE/    345 -------------------TCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_49149873_4   1609 ATCCAATTTAAAAAGGAGAGCCTTTTCAACAAATTGTGCTGGAACAATTG 1658
                           i    vvii    i v  i             v       i    i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_49149873_4   1659 GACATCCATAAGCAAAAAAAATTAAACCTTGACCTAAACCTCATACCTTA 1708
                           i ?   i v      i  -- i  vi v    ivv      i   v  
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAA--TGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_49149873_4   1709 TACAAAAATTAGTGCAAAATGAATCATGGACTTAA-TGCAAAATGTAAAA 1757
                                    iiv       i    ?i   i   -  i  i vv     
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_49149873_4   1758 CTCTAAGACCTTTAGAAACAAATCATAAGAGAAAAATCTTTGGGTCCTAG 1807
                           v   i  ii      iv   -    i ? v   -    i v v   v 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAA-CATAGGNGTAAA-TCTTCGTGACCTTG 571

  chrX_49149873_4   1808 GACTAGATGAAGAGTTCTTAGATTTGACACCAAAAGCCCAATCCTTAAAA 1857
                          ii   iii v iv         v             v   v vvi    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_49149873_4   1858 GGAAAAATTGATGAATTGGACTTTATCAAAATCAAAGACATTTGTTCTGT 1907
                          i      v   i          i        i   i  v     v  - 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT-T 670

  chrX_49149873_4   1908 GAAAGACCCCTGTTAAGAAGATGAAAAGGCAAGCCATATCACAGACTGGA 1957
                         v    iv v  i i     ii       i   -  ----      v   i
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAA-CC----CACAGAATGGG 715

  chrX_49149873_4   1958 ATAAAATAATTGCCAACCACATATCTGACAAGGGCCCTATAGCTAGAATA 2007
                          v      v    v  i  i        i     v i i  v i      
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_49149873_4   2008 TATAAAGAACTCTCAGAACTCAACAATAAAAAAGCAAACAATCCAATTAG 2057
                                      i v       i        ii    i  i      ?i
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_49149873_4   2058 AAACTGGGCAAAAGACATGAACATATATTTCACCAAAGAGAAGATGTGAA 2107
                            v        i  iv    i v i     v       ii v  iii  
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_49149873_4   2108 TGGCAAATGAGCACATGAAAGGATGTTCAACATCAGTAGCCAT 2150
                             v   i           i    i         ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (126 / 81)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 10.40 (156 / 15)  

1039 19.21 1.97 0.00  chrX_49149873_49152513.rev     2438  2640 (1)    L1M4_orf2#LINE/L1      293   499 (409)  

  chrX_49149873_4   2438 TAGA--AATAGAACAGAATAGAGAACCCAGAAATAAATCCACACATCTTT 2485
                             --   i   i     v    ii           i   i    i v 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_49149873_4   2486 GGTGAACTCATTTTCAACAAAGGTAGCAAGAATATACATTGGGGAATAGA 2535
                            v  i v      i    i   iv     vi  v  v       vii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_49149873_4   2536 CAGTCTCTTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAAA- 2584
                         i     i     i              v         ?   i       -
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_49149873_4   2585 GAATGAAACTAGGCCCCTACCTCTTGCCAT-TACAAAAATCAACTCAAGA 2633
                                ii i i          vii    -         i       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_49149873_4   2634 TGGATTA 2640
                              i 
  L1M4_orf2#LINE/    493 TGGATCA 499

Transitions / transversions = 2.45 (27 / 11)
Gap_init rate = 0.01 (3 / 207), avg. gap size = 1.33 (4 / 3)  


3376 23.65 3.04 0.79  chrX_49238368_49240446.rev      701  1588 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_49238368_4    701 TGTAAAGATATTCCATGTTCATGGAATGGAGGAATAAACATTGCAAAAAT 750
                           v        i             v    i  v v  i    iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_49238368_4    751 GTCCATACTACCCAAAGCAATCTACAGATTTAATGCAATCCCTGTCAAAA 800
                          v v     v      vii           i  i         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_49238368_4    801 TACCAATGACATTGTTAACAAAAATAGAAAAAACAACCCTGAAATTTATA 850
                          v   iivi v  v  vi  i    v  v  ivii i   i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_49238368_4    851 TAGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAGCAAAAAGAA 900
                          i   vii   ii                 i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_49238368_4    901 CAAAACTGGAGGAATCGTATTACCTGACTTCAAATTATACTACAGAGCTA 950
                             ii       v  ii i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_49238368_4    951 TAGTAACCAAAACACCATAGTACTGGCATAGAAACAGATGCATAGCCCAA 1000
                         i     i   i   vii i           iii i   iii    vi   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_49238368_4   1001 -GGAACAGCATACAGAACCCAGAAACAAATCCACACACCTACAACTAACT 1049
                         -    i  v  vv   ii       i   i   i   ii  iiiii  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_49238368_4   1050 AATTTTTGACAAAGGTGCCAAGA-------------AAAGA-CAGTCTT- 1084
                         i     i     i          -------------     -i      -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_49238368_4   1085 -CAATAAATGGTGCTGGGAAAACTGGATATCCATAGGCAGAAGAATAAAC 1133
                         -   i              v         ?   i v   i      i  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_49238368_4   1134 TCG-ACCCGTGTCTCTCGCCATATACAAAAATCAAATCAAAATAGATTAA 1182
                          i -    v ii   v i              i  v       i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_49238368_4   1183 ATATTTAAATCTAAGACCTCAAACTATAAAACTACTACAAGAAAATATTG 1232
                          v ii     v     v  v             vi  v       i  -i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-A 549

  chrX_49238368_4   1233 GGGGGAAATCTCCAGGACATTGGTCTGGGCACAGATTTCTTGAGTAATAC 1282
                           ? v      i iv   v    vi i    vv i      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_49238368_4   1283 CCCACAAGCACA-GTAATACCCCCAAAGCAAAAATAGACAAATGGGATCA 1331
                         v   v       - i  i -----    v         i    v   iiv
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACA-----AAAGAAAAAATAGATAAATTGGACTT 644

  chrX_49238368_4   1332 CATCAAG-TTAAG--CTTCTGCACAGCAAAGGAAACAATCAACAAAGTGA 1378
                               i-    i--   i  ii vv       v  v     v       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_49238368_4   1379 AGAGACAACCCACAGAATGGGGGAAAATATTTGCAAACTACCCATCTGAC 1428
                          i                   i               ii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_49238368_4   1429 AGGGAATTAATAACCAGAATATATAAGGAGCTCAAACAAGTCTATAGGAA 1478
                          i  i i vi  v             i  i   vv    v  v   iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_49238368_4   1479 AAA-ATATACTAATCCAACCAAAATATGC-CAAAAGATTTGAATAGGCAT 1526
                            - i - v   i    ii?   v   v-    i           i   
  L1M4_orf2#LINE/    795 AAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_49238368_4   1527 TTCTCAAAAGAAGACA--CAAATGGCAAGCAGGCGTATGAAAAGGTGC-C 1573
                              v        i --        v ii i  ii        i   - 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_49238368_4   1574 AACATCATTGGTCAT 1588
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (134 / 72)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.27 (34 / 15)  

 207 27.97 3.50 2.80  chrX_49238368_49240446.rev     1937  2079 (0)    L1M4_orf2#LINE/L1      489   632 (276)  

  chrX_49238368_4   1937 AGAATGGAT-AAAGA---AAATGTA-GTACTACCCCAAACTATAAAAACC 1981
                          i       - ?   ---       - vi   ----           vi 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTA----AAACTATAAAACTC 534

  chrX_49238368_4   1982 CTAGAAGAAAATCTAGGCAATACTATTGAGGACATAAACAGAGGCAAAGA 2031
                         i          iv    ?ivv v v  viv   v viivvv      v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_49238368_4   2032 TTTCATGACAAAAACATCAAAAGCAATTGCAACAAAAGCAAAAATTGA 2079
                             v iivv vi   i        vvv          v      v  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

Transitions / transversions = 0.58 (14 / 24)
Gap_init rate = 0.03 (4 / 144), avg. gap size = 2.25 (9 / 4)  


 459 28.03 0.76 0.76  chrX_49362967_49367507.rev      558   689 (3852)    L1M4_orf2#LINE/L1        1   132 (776)  

  chrX_49362967_4    558 TGGAGGGACATATCAGGTTCATGAACTGGTAAATTTAACATAGTAAAGAT 607
                             ii  i  vi  v       i i   v i i    i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_49362967_4    608 GTCAATTCTCCCCCAAGTTAATGTATATACTTAATGCAATTCCTGTCAAA 657
                          v    v      -  i  i  v  i v i i  i     i   i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_49362967_4    658 ATCCAAGC-AATATTTTGGTCAATATTAACAAG 689
                             v   -iviv    v ivi v   i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG 132

Transitions / transversions = 1.47 (22 / 15)
Gap_init rate = 0.02 (2 / 132), avg. gap size = 1.00 (2 / 2)  

2419 26.99 1.99 1.46  chrX_49362967_49367507.rev     2958  3709 (832)    L1M4_orf2#LINE/L1      128   883 (25)  

  chrX_49362967_4   2958 ACAAGGTGATACCAAAATTTATATGAAAAGACAAAAGAATGAGAATAGCT 3007
                              v    v i      i     i   vi   ii  viv        i
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chrX_49362967_4   3008 AAAACAATTTTTAAAA----GAATAAAGCTGAAGTAATGAGACTACCTGA 3053
                                 i  v    ----   i    i  i  v v v v   v  ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_49362967_4   3054 CTGTAAGACTTACTATGAAGTTATAG-AGTCCAGAGAGTGTGGTGTTAGT 3102
                         i vi  i        ii   i  i  - i  v   v        ii i i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_49362967_4   3103 G-AAGGCACACACATGTAGATCAATG---CAGAACAGAGAGTTCAGAAAT 3148
                         i-    - i v    i          ---i    iv      i       
  L1M4_orf2#LINE/    278 ATAAGG-ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_49362967_4   3149 AGCCCCACACCAGTATGGACATTTGATTTTTGATAAAAGTGCAAAGGCAA 3198
                          iv    i  vvv     v  v        i  i  ii    v   i v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_49362967_4   3199 TTCAATGAAGAGAGGATTATATTTTCAACAAATGAATGAATGGTATTGGA 3248
                                ii  i  i  vi v             --------  ii   i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATG--------GTGCTGGG 418

  chrX_49362967_4   3249 ACAACTGTACTTTCATATACAAAAAAAAGAACCTCAACCTTAACTTTACA 3298
                                v iv?i  i  i     i  v   vi vi   iiv  i i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_49362967_4   3299 CCTTATGCAAACATTAATTCAAAATCAACAACATATATAAATGTAAAATA 3348
                           v   i    v     i       vi iv ? v iv         i vv
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_49362967_4   3349 TAATAGTGTGAAACTTTTAGCAGAAAACA--GGAGAAATATCTCTATAAT 3396
                            v v i i     i    v        --  ? v  -    iii i i
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGAC 567

  chrX_49362967_4   3397 CTGGGATTAGGTAA-AATTTTTT-GACATGACGCAAAAAGCATGATCTAT 3444
                           v  i     i  -ii   i  -  i     i v       ii v v i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_49362967_4   3445 AAAAGAAGAAAGATTATAATTTGGACTTCATCAAAACCAAAATCTTTTGT 3494
                                i   v v-    v                ii    v       
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAG-ATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_49362967_4   3495 TCTGTGAAAGACACTGTTCAGAGAAGGATATGAGAAGCTACAGATCAGGA 3544
                         v  vii  i      i iv   i iv  v v  v  v i     vii   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_49362967_4   3545 TAATATACTTTCAAATCACATATCTGACAGAGGACTTCTATCCAGCATGT 3594
                         v  v   i  v       i        i ii      v       v  i 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_49362967_4   3595 ATAAAGAACTCTTACAACTCAGCAGTTAGAAAATTTA-AGCACCATTTTA 3643
                                              ii i v i  i ivv - i v v   ?v 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_49362967_4   3644 AAATGGCCAAAAGACTTCAACAATCACATCAACAAAGAGTGTATATGGAT 3693
                               v    i  i  v  i iv  iv  vv      ivi    iii  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_49362967_4   3694 GAA-AATAAGCACATGA 3709
                          iv-             
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGA 883

Transitions / transversions = 1.49 (119 / 80)
Gap_init rate = 0.02 (13 / 756), avg. gap size = 2.00 (26 / 13)  


3000 26.85 0.91 0.91  chrX_49405336_49407195      489  1367 (493)    L1M4_orf2#LINE/L1       30   908 (0)  

  chrX_49405336_4    489 AAGATATTGATTATTGTGAAAATGGCCATACTGCCCAAGGTAATTTATAG 538
                             i-  i  -     v  i     v     v     iv i  i  i  
  L1M4_orf2#LINE/     30 AAGAC-TTAAT-ATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chrX_49405336_4    539 ATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTCACAGAA-TTG 587
                               i  v     i     iv v   iivi i  i  ii     -   
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chrX_49405336_4    588 GAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCACATTG 636
                         -- v  i  - iii    i           viiv  ii  v  viv  v 
  L1M4_orf2#LINE/    128 --ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chrX_49405336_4    637 CCAAGTCATTCCTAAGCCAAAAGAACAAAGCTGGAGACATCACGCTACCT 686
                             iv  v  i i ivv i          i     ivv    i  v  i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_49405336_4    687 GACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGTATGGTACTG 736
                         i i      viv        i          i   i     i        
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_49405336_4    737 GTACCAAAACAGAGATATAGACCAATGGAACAGAAC--AGAGCCCTCAGA 784
                          i iv ii i   v       i        i    i--    i  --   
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGA 323

  chrX_49405336_4    785 AATAATGCCGCATATCTACAACCATCTGATCTTTGACAAACCTGACGAAA 834
                              vv  ii i  i  iiii  vi    i  i     ivv  v i i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_49405336_4    835 ACAAGCAATGGGGAAAGGATTCCCTAGTTAATAAATGGTGCTGGGAAAAC 884
                         v  vv            i  vvi  vv i  i              v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_49405336_4    885 TGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTA 934
                            v  ?   i   i i  iiv    ii    i    v   i     v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_49405336_4    935 TACAAAAATTAATTCAAGATGGATTAAAGACTTACATGTTAGACCTAAAA 984
                                     i    i      i ?    i  v    v   v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_49405336_4    985 ACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAG 1033
                         - i      vi i           v    ?i- v i -   iv   v v 
  L1M4_orf2#LINE/    524 -CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chrX_49405336_4   1034 GCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAA 1083
                          vv i     v ii   v ivv  vi            vvi         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_49405336_4   1084 GCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGC 1133
                          vv     v  i    v   ii v  i   v v  i i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_49405336_4   1134 AAAAGAAACCCCCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAA 1183
                            i  v  ivi  vv i      v  i     i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_49405336_4   1184 TTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAAT 1233
                          v       vii ivi      i  i  i  vi          v  i  v
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_49405336_4   1234 GAACTCAAACAAAT---TTACAAGAAAACAAGCAACCCCATCAAAAAGTG 1280
                               vv    v --- v i  i  i    ii     v  i?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_49405336_4   1281 ACCGAAGGATATGAACAGACACTTCTCAAAAGAAAACATTTATGCAGCCA 1330
                         iv i      v    i     i     v      i i  vi viii    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_49405336_4   1331 AGAAACACATGAAAAAATGCTCATCATCACTGGCCAT 1367
                          v  i          i       v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (11 / 879), avg. gap size = 1.45 (16 / 11)  


3284 26.98 0.44 0.44  chrX_49487374_49493650.rev     4879  5786 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_49487374_4   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_49487374_4   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_49487374_4   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_49487374_4   5027 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_49487374_4   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_49487374_4   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_49487374_4   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5224
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_49487374_4   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_49487374_4   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_49487374_4   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_49487374_4   5375 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_49487374_4   5425 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_49487374_4   5475 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5524
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_49487374_4   5525 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5574
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_49487374_4   5575 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5624
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_49487374_4   5625 AGGGCTAATAGCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  i  vi  v       v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_49487374_4   5675 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_49487374_4   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5774
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_49487374_4   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2296 29.08 1.28 0.71  chrX_49517608_49520837.rev     1530  2234 (996)    L1M4_orf2#LINE/L1        1   709 (199)  

  chrX_49517608_4   1530 TGAATAAATAGTCAATGTTCATGGGATGTAAAACTCAGTATTATTGAGAT 1579
                           i v i   vi v          iv  v  i   i i    i  i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_49517608_4   1580 TTCAATTCTTCCCAGCTTGATCTATAGATTCAACACAATCCCAACAGAAA 1629
                         vv    v  i    iv        i         i       v ivi   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_49517608_4   1630 CCCAAGCAAGTCATTTTGCAGCTAC-AATAAACTGATTCTAAAGCTTCTG 1678
                         i  v   viviiv        vv i-i i  i     i     ii iv i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_49517608_4   1679 TGGAAAAGCAAAACATCTAGAGTATCCAACACAATGTTGAA---GCTGAA 1725
                               v    iiv i i   i  v    v     v     --- vv   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_49517608_4   1726 CA--GTTGGAAGGCTCACACTACCTCATTTCAAGATTTACCATAAAGCCA 1773
                           --      i i        v  iv       i i    i i     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_49517608_4   1774 TAGTAATCAGGACAGCATGGTATTGTCAAAAGAAAAGATGCATAGACGAA 1823
                         i        i     ii     i  v  v   i v   iii     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_49517608_4   1824 GAGAACAGAATAGAGAGCCCCAAAATAGACCCACACAAATACAGTCAATT 1873
                         vi   i     v     i  vi     i     i   vv  ii       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_49517608_4   1874 AATCTTTAAAGAAGGCGCAAAGGCAAATCAGTGGAGAAAGGACAGTGTTT 1923
                         i  i  ii vi i  i  v   i v v   i   i     i i   v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_49517608_4   1924 TTAACAACCAGTGCTGCAATGACTAGGCATAAGTATGTTAAAAAGAT-AA 1972
                          i     vii      vi ii   i ii ?vvii   i-    ii  -  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-AAAAGAATGAA 449

  chrX_49517608_4   1973 TCTAAACAAAGACTTTCCTCCTTTTATAAAAATTTACACAAAATGTACCA 2022
                         vi ii  vvvv  i iv v  v v  i       v  v       v i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_49517608_4   2023 TTGACCTAAATGTAAAATGC-AAAACTATAAAACTTCTGGAAGATATCAT 2071
                         ?v             i -  -              ii i     v v   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_49517608_4   2072 AGGAGAAAATCTACATGATTTTGGATTCAGTGATGACTTTTTATATACAA 2121
                            ? v      v i   ii    i  vi ii   ii  i   v   ii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_49517608_4   2122 TACAAATAGCATGATCCAGGAAAGAAAAAAAATTAATAAGTTAGACTTCA 2171
                         i  v  v    ii v v vi          v --i    i  i       
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTCA 646

  chrX_49517608_4   2172 CTAAAATTAAAAATTTCTG-GTTTGCAAAAACTACTGTAAAGAGTATAAA 2220
                         ii           i  i  - i  -    iivi   i v    ivi i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTT-CAAAGGACACTATCAAGAAAGTGAA 695

  chrX_49517608_4   2221 AAGACAAGCCACGG 2234
                                v    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAG 709

Transitions / transversions = 1.73 (128 / 74)
Gap_init rate = 0.01 (10 / 709), avg. gap size = 1.40 (14 / 10)  

 835 14.83 8.13 0.96  chrX_49517608_49520837.rev     2531  2739 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_49517608_4   2531 AAAAAAGCCAAGAAGACAAGCCACAGACTAGGATAAGACATTTACAAAAT 2580
                           i    iv  -       v       v i   v  i i    i    vi
  L1M4_orf2#LINE/    685 AAGAAAGTGAA-AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_49517608_4   2581 ATATATCTGATAAAGGACTGGTATCCAAAATACA--AAGAACT---AAAA 2625
                                      i     v       i    i --       --- v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_49517608_4   2626 CTCAACAATAAAAA---AAAT--CCCAATTTAAAAATGGGCAAAAAACCT 2670
                              i        ---    --       ?             ii ii 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_49517608_4   2671 GAAC------CTCACCAAAGAAAGATGTACATATGGCAAATA-GCACGTG 2713
                            i------i  v        -   i    v     v    -    i  
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAA-GATATACAAATGGCCAATAAGCACATG 882

  chrX_49517608_4   2714 AAAAGATGTTCAACATCATTTGTCAT 2739
                                 i         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.04 (8 / 224), avg. gap size = 2.38 (19 / 8)  


3182 27.64 0.44 0.44  chrX_49527337_49533616     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_49527337_4   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_49527337_4   4930 GGCCATACTGCCCCAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v   v iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_49527337_4   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_49527337_4   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_49527337_4   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_49527337_4   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_49527337_4   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCTTACCTACAACT 5225
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_49527337_4   5226 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_49527337_4   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_49527337_4   5326 GAAACTGGATCCCTTCCTTATGCCTTATACAAAAATTAATTCAAGATGGA 5375
                            ii    i    v   i ii  v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_49527337_4   5376 TTAAAGATTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_49527337_4   5426 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_49527337_4   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_49527337_4   5526 TTAAACTAAAGAGCTTCCGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   ii ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_49527337_4   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_49527337_4   5626 AGGGCTAATAGCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi  v       v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_49527337_4   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_49527337_4   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_49527337_4   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3533 22.07 1.71 0.61  chrX_49587283_49589088      494  1313 (493)    L1M4_orf2#LINE/L1       80   908 (0)  

  chrX_49587283_4    494 TCATTGCAATCCCTATCAAAAATTTAATGGAATTTTTCACAGAAATAGGA 543
                            vi                viii iiv vv     ii       v iv
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chrX_49587283_4    544 AAAACAATTCTAAAATTTGTATGAAACCACAAAG-ATCCTGAATAGCTAA 592
                           ivii  i        ii    i  vii   i - i  v       i  
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_49587283_4    593 AGCAGTCTTGAGCAAGAA---CAAAGCTGGAAGCATCACATTTCTTGATT 639
                          i  i      iv     ---     i    i vv     i   iii   
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_49587283_4    640 TCAAATGATATTACAGTGCTATAGTAATCAAAACAGCATGGTACTGGCAT 689
                              vvv  i    iv    i         i    ii            
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_49587283_4    690 AAAAACAGACACATAGACCAAGGGAATAGAACAAAGAGCCCAGAAATAAA 739
                           ii i     i     i   v         ivi    i           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_49587283_4    740 CCCACATATATATAGTTAGCTAATTTTAGACAAAGGCACCAAGAATACAC 789
                             i i  v   i  i ii i     v     i  ii      vi iv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_49587283_4    790 AATGGGGAAAGGATAGTCTCTTTAATAAATGATGTTGGGAAAACTGGATA 839
                                    i       i  i  i     i  i     v         
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_49587283_4    840 TCCACATGCAATAAAAATGAAATTGGATC------TTAGACCATACACAA 883
                         ?          -  i      i     i ------ i v      i    
  L1M4_orf2#LINE/    430 KCCACATGCAA-AAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_49587283_4    884 AAATCAACTCAAAATTGATTAGATACTTAATTATAAGACCTGAAACTGTA 933
                             i          v   i ? v  i   v i     v  i     i  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_49587283_4    934 AAACTCTTAGAAGAAAACTTACGGAAAAAGCTCCTTAACATTGGTCTTGG 983
                                           v  v ?iv   v  i v i  v    vi v  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_49587283_4    984 CAATGACTTTTTGGATTTGACACCAAAAGCACAGGCAACAAAAGTAAAAA 1033
                              ii  i  i   v                i          v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_49587283_4   1034 TAAACAAGTGGGATTACATCAAACTAAAAAGCTTCTTCATGGCAAAGAAA 1083
                           i i  i v   i v       v v    i   i viiivv     i v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_49587283_4   1084 AA-ATCAACAAAAT-AAAAGACAACCTACAGTACAGGAGAAAATATTTGT 1131
                          v-     v   i -           i    v ii              i
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_49587283_4   1132 AAGCCATATATCCAATAAGGGGTTAATATCCAAAATATATAAGGAACTCA 1181
                           ii        ii       ii vi      i         i      v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_49587283_4   1182 TACAACTCAATAG--GAAATACAAAGCTAACAAGCAAACAAAAACTGGGC 1229
                                     i--i   v     --    v--   vi?    v     
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAA--TAACC--CAATTWAAAAATGGGC 824

  chrX_49587283_4   1230 AAAGGATCTGAATGGACATTTTCCCAAAGATGAAATACAAATGGCCAATA 1279
                                i     i       ii       v  v                
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_49587283_4   1280 GGTATATGGAAAGACGCTCAGCATCACTAATCAT 1313
                         i i i   i     i     i     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (119 / 58)
Gap_init rate = 0.01 (9 / 829), avg. gap size = 2.11 (19 / 9)  


3271 26.51 0.55 0.66  chrX_49872416_49878815.rev     5001  5909 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_49872416_4   5001 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5050
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_49872416_4   5051 GGCCATACTGTCCAAGGTAATTTAGAGATTCAATGCCATCCCCATCAAGC 5100
                            v     vi    iv i  i  v        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_49872416_4   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5148
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_49872416_4   5149 ATATGGAACCAAAAAAGAGCCCGCATTGACAAGTCAATCCTAAGCCAAAA 5198
                                 viiv  ii  v  v v  v v   iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_49872416_4   5199 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5248
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_49872416_4   5249 CTATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5298
                            i     i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_49872416_4   5299 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCAACAAC 5346
                                 i    i--    i  --        vv   i    iv iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_49872416_4   5347 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5396
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_49872416_4   5397 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5446
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_49872416_4   5447 TGAAACTGGATCCCTTCCTTTCACCTTATACAAAAATTAATTCAAGATGG 5496
                             ii    i    v   iv    v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_49872416_4   5497 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5546
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_49872416_4   5547 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGATTTCATGTCT 5595
                          v    ?i- v i -   iv   v v  vv i     v i    v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_49872416_4   5596 AAAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCT 5645
                          vi            vvi      i   vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_49872416_4   5646 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGA 5695
                         v  i   v v  i i   i  ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_49872416_4   5696 ACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5745
                          v  iv    i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_49872416_4   5746 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5795
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_49872416_4   5796 AAAAGCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACATT 5845
                            ii    i     v  i?    i    ii      v    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_49872416_4   5846 TCTGAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5895
                            vv        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_49872416_4   5896 TCATCACTGGCCAT 5909
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


 288 15.09 1.89 0.00  chrX_49879072_49883785.rev     1613  1665 (3049)    L1M4_orf2#LINE/L1        1    54 (854)  

  chrX_49879072_4   1613 TAGATAGACAT-CCATATTCATGAATTAGAAAACTTAATATTGTTAAGAT 1661
                          i  v   i  -    i      i   i   i                  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_49879072_4   1662 GTCA 1665
                          v  
  L1M4_orf2#LINE/     51 GGCA 54

Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1)  

 518 19.57 0.00 0.00  chrX_49879072_49883785.rev     1996  2087 (2627)    L1M4_orf2#LINE/L1       49   140 (768)  

  chrX_49879072_4   1996 ATATCAATACTTCCCAAGTTGATCCACAGATCCAAGGCAATTTGTACAAG 2045
                           iv       i     i      i      i   v     iiv  iv i
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_49879072_4   2046 AATCCCAGCTAGCTTGTTTGTAGAAATTGACAAGCTGATTCT 2087
                                   iv   v    i                  i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.00 (0 / 0)  

1970 26.07 0.36 0.54  chrX_49879072_49883785.rev     2827  3386 (1328)  C L1M4_orf2#LINE/L1   (0)   908   350  

C chrX_49879072_4   3386 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATTCCCTA 3337
                             i  i     ivv  v   i v  vvv          vi  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

C chrX_49879072_4   3336 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 3287
                           i  i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chrX_49879072_4   3286 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA 3237
                         ii    i    v   i     v              i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chrX_49879072_4   3236 AAGACTTAAATGTTAGACCTGAAACCATACAAATCCTAGAAGAAAACCTA 3187
                         ?    i       v   v  i    i   v  v  i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

C chrX_49879072_4   3186 GGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 3139
                           ?-   --i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    550 GGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

C chrX_49879072_4   3138 ACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAAT 3089
                                     vvi     v    vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

C chrX_49879072_4   3088 TAAACTAAAAGAGCTCCTGCACAGCAAAAGAAACTACCGTCAGAGTGAAC 3039
                         i   v v   i -  ii  ii vv    i  v    i ivv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_49879072_4   3038 AGGCAACCTAGAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 2989
                           i     i v               v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chrX_49879072_4   2988 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2939
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chrX_49879072_4   2938 AAACAAACAACCCCATCAACAAGTAGGCGAAGGATATGAACAGACACTTC 2889
                          i     i     v  i? v  i i   i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chrX_49879072_4   2888 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATT 2839
                           v        i  vi viii     v ii          i       vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chrX_49879072_4   2838 ATCACTGGCCAT 2827
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (75 / 67)
Gap_init rate = 0.01 (4 / 559), avg. gap size = 1.25 (5 / 4)  

3762 12.79 2.77 8.32  chrX_49879072_49883785.rev     3395  4223 (491)    L1M4_orf2#LINE/L1      126   908 (0)  

  chrX_49879072_4   3395 TGACAAGCTGATTCTAAAATTTATATAGAATTGCAAGGAACCCAAAATAG 3444
                                     i        i    i   v       i     i     
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chrX_49879072_4   3445 TCAAAACAATCTTGAAAAAGAAGAACAAAATTTGGAGGAGTCACACTTCC 3494
                         i                            i  -      v          
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTT-GGAGGACTCACACTTCC 224

  chrX_49879072_4   3495 CAATTTCAAAAC--ACAACATGAAGCTGCAATAATCAAGACAATATGGTA 3542
                                     --  v   --     i  i           i i     
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACA--AAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_49879072_4   3543 CTGGCATAATGATAGTTAATGAGAGACATACAGATAAATGGAATAAAATT 3592
                                  v     ----------     i    v         i    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAG----------ACATATAGATCAATGGAATAGAATT 312

  chrX_49879072_4   3593 GAGAGTCCATATATAAAC----ACATTTATGGTCAACTGATTTCCAAGAA 3638
                                  v v      ----              i      i i v  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_49879072_4   3639 GGGTGCCAAGACAATT-AA----GAAAGGTTAGTTTTCTCAACAAATAGT 3683
                                     v   -  ----     iv    i  i         i  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_49879072_4   3684 GCTGGAAAAACTGGACATCCACACTCAAAACAATGAAGTTAAGGCTCCTA 3733
                              i v       i ?     iv     v         i- i i    
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG-GACCCCTA 461

  chrX_49879072_4   3734 ATACACACCACCAATAAAAATTAACTGAAAATAGATCAAAACCCTAAGT- 3782
                         viv       ivv i           v     i     ? iv     i -
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_49879072_4   3783 TAAGAGCTAAAACTTTAAAATTCTTAGAAGAAAACA--GGTGTAAATTTT 3830
                                       v     i               --  ?      i  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_49879072_4   3831 CTTAACCTGGGATTTGGCAGTGGTTTCTTAGGCATGACATCAAAATCATA 3880
                          v i    v  i  v    i           ii      i     v  i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_49879072_4   3881 AACAACAAAAGAAAAAACA----AATTAGACTTCTTCAGAATTAAAAATT 3926
                          i               i ----    i      v   i         i 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_49879072_4   3927 TCTGTACTTCAAAGGACATCATCAACAAAGTGAAAAGATAACCCAAAAAA 3976
                          i   i            ii     v            i      v i  
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_49879072_4   3977 TGGATGAAAATATTTGCAACTCGTAT--CTGATCAGGGACTTGTATCTAA 4024
                            iv              v  i   --     v             i i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_49879072_4   4025 AATATATAAAGAACTCTTACAACTCAACAATACAAAGACCAACAATTATT 4074
                                                    i    v      v  i  ii---
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC--- 808

  chrX_49879072_4   4075 TACGATTATTATATGTCAATTAAAAATAAAATTAAAAAATTAAGAAATAA 4124
                         ----------------     ?    ------------------------
  L1M4_orf2#LINE/    809 ----------------CAATTWAAAA------------------------ 818

  chrX_49879072_4   4125 AAGCATAAAAAAATGGGCAAAAGATCCAAACAGACATTCCTCCAAAGAAG 4174
                         ------------         i   iii  i       i           
  L1M4_orf2#LINE/    819 ------------ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_49879072_4   4175 -TAC-CAAATAGCCAATAAGTACAT-AAATGATGCTCAACATCATTAGTC 4221
                         -  i-     i         i    -   v              ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_49879072_4   4222 AG 4223
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.09 (69 / 33)
Gap_init rate = 0.02 (17 / 783), avg. gap size = 5.41 (92 / 17)  


 328 23.91 6.52 0.00  chrX_49892732_49897137.rev     2464  2555 (1851)    L1M4_orf2#LINE/L1       86   183 (725)  

  chrX_49892732_4   2464 CAATTCCAATCAAACTCCTAGAAATATTTTT----AAGAT--ATAATCTG 2507
                             i  v      v   i  vviiv     ----i i  -- i  v   
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chrX_49892732_4   2508 ATTCTAAAATTTACATAGAAAGGCAAAGGAACTAGAATAGCTAAAACA 2555
                           i        i i  i    v    i   v i        i      
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.02 (2 / 98), avg. gap size = 3.00 (6 / 2)  

1046 24.78 6.78 1.77  chrX_49892732_49897137.rev     2890  3228 (1178)    L1M4_orf2#LINE/L1      196   551 (357)  

  chrX_49892732_4   2890 AAGAATAGAGTTGAAAATATCACAATACCCAGTTTTAAGACTAACTATAA 2939
                              i i     i iivv     v v    i   i  i   v    i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_49892732_4   2940 AACTACAGAAATAAAGACAGTGTGATATTGGTGAAGGAAGAGACACAGAG 2989
                          i      v   v           i  i   iiv i i v     i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_49892732_4   2990 ATAAAGGAAACAGAATATTG---GT------ATAGACCCACAGA------ 3024
                           v  v i  i     --  ---  ------   i     i v ------
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAAT--TGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_49892732_4   3025 ---AACTG-TTTTTAGCAAGG-TGCAAAAACAATTCCATGAAGAAAGTAT 3069
                         ---  i  -    iii     -   v  i  v    v   ii     v  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_49892732_4   3070 AGTTTTTAATTCCCACACGTGGCATTAGAACAATTAGACACTCATATGCA 3119
                            i   ----i v   vi   iii i i    i i  i ?i  i     
  L1M4_orf2#LINE/    394 AGTCTTT----TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_49892732_4   3120 AAAAAA-GAACCTTGACCTAAATCTCACACCTTATACAAAAATTAACTAA 3168
                            i  -   vi v    ivv i        v                v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_49892732_4   3169 AAATGGACTATAGATTTAA-TGTAACATGTAAAACTATAAACCTTTGAGA 3217
                                ii ?   ii   -     v vv            v  i v   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_49892732_4   3218 -TAAAATATAGG 3228
                         -v    i     
  L1M4_orf2#LINE/    540 AGAAAACATAGG 551

Transitions / transversions = 1.65 (51 / 31)
Gap_init rate = 0.03 (10 / 356), avg. gap size = 2.90 (29 / 10)  

1195 22.94 7.95 0.00  chrX_49892732_49897137.rev     3604  3930 (476)    L1M4_orf2#LINE/L1      556   908 (0)  

  chrX_49892732_4   3604 AATATTCCTGACCTAGGTTTAGGCAAAGAGTCCTTAGAAGT--------A 3645
                            v   v      v  v        v iv i      vi -------- 
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_49892732_4   3646 AGTATAATCCATAAA-GAAGGCATTGATAAACTGGACTTCATCAAAATTA 3694
                           i i  v v i   -   iiv  v      i                  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_49892732_4   3695 AAAACTTTTGCTCTGGGAAAGACACTGGTAAGAGA-----AAGAAAAACT 3739
                                   iv  vvi  i      ivi    i -----    v  v i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_49892732_4   3740 ACAGACTGAGAGGATATATTTATAAATCACATATCCAACAAAGGATTTGT 3789
                              v  i   i v      ii      i     ii i  i   i    
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_49892732_4   3790 ATCCAGAATACATAAAGAACTCTCGTAACTTGACACTAAGGAAACGAACT 3839
                                   i            iii    ii i v   ii i  i  iv
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_49892732_4   3840 ACCTA-TTTATAACTGGGCAAAAGACTTGAATAGACATTTCATCAAAGAG 3888
                            i -  ? v  v        i  i               vi      i
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_49892732_4   3889 GATATATGCATGAC----AAGTA--TG----GTTG-TCAACATTATTAAC 3927
                               iiv   i ----   i --  ---- v  -       i ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_49892732_4   3928 CCT 3930
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.85 (48 / 26)
Gap_init rate = 0.02 (8 / 353), avg. gap size = 3.25 (26 / 8)  


3309 25.61 0.44 0.22  chrX_50134555_50139670     3718  4623 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_50134555_5   3718 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3767
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50134555_5   3768 GACCATATTGCCAAAAGCAATCTACAAACTCAATGCAATCCC-ATCAGAA 3816
                          i v   i v  v   vii       i i    i        -    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50134555_5   3817 TACCACCATCATTCTTCACAGAATTAGAAAAAA-AATTCTAAAATTCATA 3865
                          v   v vv v  i  ii     v v  v  iv-i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_50134555_5   3866 TGGAACCAAAAAATAGCCCACATAAACAAAGCAAGACTAAGCAATAAGAA 3915
                              viiv  iiv v  viv   iv    i   vvi i iv  v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_50134555_5   3916 CAAATCTGGAGGCATCACACTACCTGATTTCAAACTATCCTATAAGGCCA 3965
                             vi      vv       v  ii        viv v   i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_50134555_5   3966 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCAAATACACCAA 4015
                         i   v i   i    ii         i    ii    i  v   v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_50134555_5   4016 TGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCTAACT 4065
                              i     v    ii               v i i   ii ii  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_50134555_5   4066 GATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGATACCCTTT 4115
                            i  i     i vviv   i v   vv i         i   vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_50134555_5   4116 TCAACAAATGGTGCTGGCATAATTGGCTAGCCATATGTAAGAGAATGAAA 4165
                                          v i  i   v  ?   i   i  i        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_50134555_5   4166 CTGGAACCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATGA- 4214
                         i    v  ii i   v    v           i       i      v -
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_50134555_5   4215 AGATCTTAAACCTAAGACCTGAAACTACAAAAATTCTAGAAGATAACATT 4264
                            i  -   iv     v  i      i    v ii       v     v
  L1M4_orf2#LINE/    501 AGACCT-AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_50134555_5   4265 AGAAAAACCCTTCTAGACATTGGCTTCGGCAAGGATTTC-AGGATCAAGA 4313
                         i ?iv  vi    vv   v    v  v     v i    -vi   - v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGA 598

  chrX_50134555_5   4314 CCCCAAAAGCAAATGCAATAAAAATGAAGATAAATATCTGGGACCTAATT 4363
                          v         v v    i    ivi  i   i   vv v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_50134555_5   4364 AAACTGAAGAGCTTTTACATGGCAAATGGAACAGTCAGCAGAGTAAACAG 4413
                            v v  i i     iiiivv    v iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_50134555_5   4414 ACAACCCACAGAGTGGGAGAAAATCTTTACCATCTATACATCTGACAGAG 4463
                                     i           v   i v vii   i      i ii 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_50134555_5   4464 GACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGTAAGAAAAAA 4513
                             vi          v  i  v      vv    v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_50134555_5   4514 ACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAACTCTC 4563
                              i  i  v  i?    i     v     iv          vi    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_50134555_5   4564 AAAAGAAGATATACAAATGGTGAACAAACATATGAAAAAATGCTCAACAT 4613
                         v                   iv  i  i  i       i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_50134555_5   4614 CACTATCAGG 4623
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.25 (127 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.00 (6 / 6)  


2926 20.15 4.24 8.48  chrX_50149818_50152283.rev     1033  1975 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_50149818_5   1033 AGATATGAACCATGTTCATATGTTGGAAGACTCAATATTGTTAAGATATT 1082
                               v--          ivi          i              ivi
  L1M4_orf2#LINE/      6 AGATATC--CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_50149818_5   1083 AATTATCCCAAAATCGATCTATAAATTCAATGCAAACTCAATTAAAATCC 1132
                            vv    v    i      i i      i    v i v  i       
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_50149818_5   1133 CAGCAGGATTTTTTTTCTAGATATTAACGAGGTGATTCTTAAATTCATAT 1182
                             v --ii      vi   v   i  i  v    i  v          
  L1M4_orf2#LINE/    104 CAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_50149818_5   1183 TGAAAGGCAAAGGAACTAGGATATCCAAAATAATTTTCAAAAAGAA---T 1229
                         v    v    i   v i  i   v      i   i  v        ---i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_50149818_5   1230 AAAGTTGGAGGACTCGTAGTATCTTATTTCAAGACTTACTATTAA-CTAT 1278
                                        ii v vi iv       i        iv  -   i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_50149818_5   1279 A----TCAACACAGTGTGGTATTTGGAGGAATTACTCTATTGGATGTTAA 1324
                          ----    v           i ---------------------------
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACT--------------------------- 274

  chrX_50149818_5   1325 GGCTTATTATCCTGCTATAAAAAATAAAGGTAATTATTGTATTGGCAGAA 1374
                         -------------------------------------------    v  
  L1M4_orf2#LINE/    275 -------------------------------------------GGCATAA 281

  chrX_50149818_5   1375 GGATAGACACATAGATCAAGTGAA-AAAATAGAG-GCCAAGAAGTAGTCC 1422
                                  i         vv   - i   v   - i v    i  iv  
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_50149818_5   1423 AACACAAATAGAGTCAACTGATTTTTGACAAAAATTCAAAGGAAA--CAA 1470
                         v i   vv  vi     i       i     iii v v   ivv --   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_50149818_5   1471 --GAGAAAAGGTAGTCTTT-CAATAAATGGTGCTGGAATATTTGGACATC 1517
                         -- i    iii        -   i            i i vi    i ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_50149818_5   1518 CATATATTTTTAAAA---TGAACCCGAAT---TATTTT------TACACA 1555
                           i  ii----    ---    vii i i---  ii i------  i   
  L1M4_orf2#LINE/    432 CACATGC----AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_50149818_5   1556 AAAATAAACTCAAAATGGTTCCTAAGGCTAAATTTAAAATGTAGAATTTA 1605
                              v            v  v? iiv      v   i vv  i  i - 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT-A 526

  chrX_50149818_5   1606 TAATATTTTGAGAAGAAAAAACAGA---ATATCTTTGTGACCTTAGGTTA 1652
                            v i i v         v i  i--- v     i        i     
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_50149818_5   1653 GGCCAAGAGTTCTTACATACCACACCGAAAGCACATGTTATAAAAGAAAA 1702
                            v v iv      v   iv     i        v iv i         
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_50149818_5   1703 AATTTGATAAATTGGGCCTTACCAAAATTAAAAACTTCTTCCCTGTGAAA 1752
                            v-          i i i i               i viv  vii  i
  L1M4_orf2#LINE/    627 AATA-GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_50149818_5   1753 GACAATATTAAGAGAATGAAAAGACAGTATATA---T-----AAAATATT 1794
                             v   i    i i          iivi i --- -----        
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_50149818_5   1795 TGCAAAACTCATATTTGATAAAGGACTTGTATCCA-AACATATAAAGAAC 1843
                               v vi    i      i             -  i           
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_50149818_5   1844 TCTTAAAACTCATCAATAAGAA-ACAAATGACTCAATTTAAAAATGGACA 1892
                              v      vi     i  -      i  i     ?        i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_50149818_5   1893 AAAGATCTTAACAGACAAGTCATCATAGAAGATATACAGATGACAAGTAA 1942
                           i   i v  i     vv  vi  v            i   i v i   
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_50149818_5   1943 GCATAAGAAAAGATGCTCAACATCATATGTCAT 1975
                            i v                   ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (113 / 74)
Gap_init rate = 0.02 (22 / 903), avg. gap size = 5.45 (120 / 22)  


3607 16.75 9.77 0.63  chrX_50165571_50168636.rev     1061  1848 (1218)    L1M4_orf2#LINE/L1        1   860 (48)  

  chrX_50165571_5   1061 TGGAAAGACACTCCATGTTCATGGATTGGAAGACTTAGTATTGTTAAGAT 1110
                                 i ii                         i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50165571_5   1111 GA-AATGTGCCCCAAATTGATCTACAGATTCAATCCAGTGCTTATCAGAA 1159
                          i-   iiv                        iv  i v i     i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50165571_5   1160 TTCCAG-TGGCTTCCTTGTGTAAGTTTACAAGCTGATTCTAAAATTCATA 1208
                          i    -  v   ii   iiv  i  v          i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_50165571_5   1209 TGGAATTACAAGGGACCTGGAACAGTCAAAACAATCTTTAAAAAGAA--- 1255
                              v i         ii   i  i            v        ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_50165571_5   1256 CA--GTTGGAGGGCTCATACATCCCAACTTCAAAACTTACTGCAAAACTA 1303
                           --        i    i  v      i             i    i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_50165571_5   1304 CAGTAATCAAGACAGTGTGGTACAGACACAAGGGTAGGTGTATAAATAAA 1353
                                                v i  i    i   iii    i  v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_50165571_5   1354 TGGAATTAAATTGAGAGTCCAGAAATAAATCCTCATGTATATGGTTAGTT 1403
                               vi                     i  vi ii v      i i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_50165571_5   1404 AATTT-CAACAAGGGTCCCAAGAGAAAT---TGAGGAGAGAATAGTTTTT 1449
                         i    - i        v      vv v ---  i   i        i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_50165571_5   1450 T-AACAAATGATGCTGAGACAACTGGGTATCTACATGGGAAAAAATGAAG 1498
                          -        i     i         i  ? i     vi   i       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_50165571_5   1499 TT-------TTCCTTAAATCACATGCAAGAATCAACTCAAAATGGATTAT 1541
                           ------- v   i v i  i  i   i   i              i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_50165571_5   1542 AGA-----ATGTAAGAGTCAAAATTATAAAATTCTTAGAAGAAAACATTG 1586
                            -----         ii    i       i                v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_50165571_5   1587 TAATAAGTCTTCCTAAT-----GTTAAG--ACGATTT------------- 1616
                         v?i   i     v i i-----    i -- i i   -------------
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_50165571_5   1617 ------GCACAAGTGATACAAGAAATAG-AAATAAATTGGAGTAAATCAA 1659
                         ------       ii i v      v i- i          v vv     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_50165571_5   1660 AATTAAAAACTTTTGTGCT-AAAAATATACCATATAAAAAAGTGAAAAGA 1708
                                            -v   iv i  i  -i  i            
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTAT-CAAGAAAGTGAAAAGA 699

  chrX_50165571_5   1709 CAAGCAACATAATATTAGGAGAAAATATTTGCATATCA-------GATA- 1750
                            v v   v   i---                v    -------    -
  L1M4_orf2#LINE/    700 CAACCCACAGAATG---GGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_50165571_5   1751 ----CTT-----CAAAATATGAAAAGGACTCTTACAACTCAATGATAAAA 1791
                         ----   -----  i     iv    i                i      
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_50165571_5   1792 A------TAACC-AATT-AAAAATGGGTTAACAGATTGTAATAGACATTT 1833
                          ------     -    -         i-  vi    vv           
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGC-AAAGGATTTGAATAGACATTT 845

  chrX_50165571_5   1834 CTTCAAAGAAAATAT 1848
                           i       i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATAT 860

Transitions / transversions = 2.31 (90 / 39)
Gap_init rate = 0.03 (23 / 860), avg. gap size = 3.57 (82 / 23)  

 236 16.98 0.00 1.89  chrX_50165571_50168636.rev     2529  2581 (485)    L1M4_orf2#LINE/L1      857   908 (0)  

  chrX_50165571_5   2529 ATATGCAACTGGCTAGCAAGCACAGGGAAAGATGCTCAAGCACTACTATT 2578
                             i   v    i ii       v i            -  ii ?????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA-CATCAZZZZZ 905

  chrX_50165571_5   2579 CAT 2581
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1)  


3792 22.76 2.02 0.56  chrX_50231544_50234124.rev     1199  2090 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_50231544_5   1199 AAAGATATTCCATGTTCATGGGTTAGAAGAATTACTATCATTAAAATGTC 1248
                                 i            i  i     v   v   ii    i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_50231544_5   1249 CATACTGCTGAAAACAATCTACAGATTGAATGCAATCTCTATCAAAATTC 1298
                         v     v iv   vii           v  i      i          i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_50231544_5   1299 CAACTACATTTTTTCACAGGAAT-AAAAA----ATTCTAAAATTTGTAAG 1343
                           i  i v      -i   i   -i v  ----  i        ii  v 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_50231544_5   1344 GAACCACAAAAGACCCCAAATAGCTAATGAAATATTGAGGAAAAAAAA-A 1392
                            vii   ii     vi      i  viv   v    ii  i  i  - 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_50231544_5   1393 AAGCTGGAGGCATCATACTACCTGATCCCAAA-TATACTACAAAACTATA 1441
                            i      vv   i   v  ii  ii    -iv         i   i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_50231544_5   1442 GTAATCAAAACAGTATGGTACTGGCATAAAAACGGAAATACCATTCAATG 1491
                                 i     i              ii ii  v   iviv      
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_50231544_5   1492 GAACAGAAGAGAGAGCCCAAAAATAAATCCACACATTTACAGTCAACTGG 1541
                            i    vv     i   i       i   i       ii     i  i
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_50231544_5   1542 TCTTCAACAAAGGTGTCAAGAACACATAATGGGGAAAGCACAGTCTCTTC 1591
                          i   i    i    i     v  ivi           v i     i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_50231544_5   1592 AGTAAATGGTGTCATGAAAACTGGATATTCACATGCG---GAATGAAATT 1638
                          ii        iiiv  v         ?i       i---       i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_50231544_5   1639 GGACTCTTATCCTACATCATATATAAAAACCAATTCAAAATTGATTAAAG 1688
                             i i  i ii   i      i     ii  i       v   i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_50231544_5   1689 ACTTAAACATAAGACCTTAAACTCTAAAACTACTACAAGGAAACATATGG 1738
                           i    ii     v  v     v       vi  v   i       v ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_50231544_5   1739 A-AAAGCTTTTTGACATTTGGCTTTGGCAAAGATTTTTTGGCTATGGCCC 1787
                         i-   v   iv    -i    v  v     v i   i  i v    i v 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_50231544_5   1788 TAAAAGCACAGGCAACAAAAGCAAAAATAGGT----TGGATTGCATCAAA 1833
                         i         i          v        i ----    i v       
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_50231544_5   1834 -TTAAAAAGCTTCTGTACAGCCAAGGAAACAATCCACAGAGTAAAGAGAC 1882
                         -       -   i   i vv v     v  v   v v i   i  i    
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_50231544_5   1883 AACCTGCAGGATTGGAGAAAATATTTGCAAATCATAT--TTGATAAGGAG 1930
                             ii   i  v                        --i        ii
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_50231544_5   1931 TTAATATCCAAAACATATAAGGAAATCAAACAAGTCAATAGTAAGAAAAC 1980
                         i vi      i  i      i   v  vv    v      i   i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_50231544_5   1981 AAATAACTTGATTACAAAATGGGCCAAAGATCTGAAGAGACATTTCTCAA 2030
                                iii   ?v         v  i   i    v           v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_50231544_5   2031 AAGAAGATATATAAATGGTCAACAGGTATATTTAAAAAAATGTTTGACGT 2080
                                    i      i   i i i i  --i    i   i ii  i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACAT--GAAAAGATGCTCAACAT 898

  chrX_50231544_5   2081 CACTAATCAT 2090
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.16 (136 / 63)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 1.77 (23 / 13)  


1099 20.85 0.00 2.98  chrX_50307912_50312261     2257  2491 (1859)    L1M4_orf2#LINE/L1        1   228 (680)  

  chrX_50307912_5   2257 TGAAAAACTACACTACATTCATAAATTCAAAGACCTAACATTTTTAAGAT 2306
                           i   iv  iv i ii     ii   vi     i   i   v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50307912_5   2307 GGCAGTACTTCCCAAACTGAGCTATACATTTGAAGCAATTCCTACTAGAA 2356
                             i    i      i   v   i v   ii v     i    ii i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50307912_5   2357 TCTCAGCTGACTTGTTTGTACAAATTGACAAGCTGATTCAAAAATTCATA 2406
                           i      v   v    i v                i v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_50307912_5   2407 TGGGACCCAGAATTACAAGGGACCCAGAATACTGAAAACAATCCAGAAAA 2456
                            -------  v i                viv         iv     
  L1M4_orf2#LINE/    151 TGG-------AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_50307912_5   2457 AGAAGAATAAAGTACGAGGGCTCACACTTCTTGAT 2491
                                i     vv    i          iii  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

Transitions / transversions = 1.88 (32 / 17)
Gap_init rate = 0.00 (1 / 228), avg. gap size = 7.00 (7 / 1)  

3019 18.30 2.93 0.88  chrX_50307912_50312261     3177  3859 (491)    L1M4_orf2#LINE/L1      212   908 (0)  

  chrX_50307912_5   3177 GACTAGTACACTTCCCAATTT-AAAACTTATTTAAAAACAACAGAAAGCA 3225
                             --i              -        i vv   i v    v  v  
  L1M4_orf2#LINE/    212 GACT--CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_50307912_5   3226 AGACAGTCTTGTAATGGCACAAGGATAGACACACAGAGCAATGGAATGGC 3275
                                v v   v     i           i i   v         i v
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_50307912_5   3276 ATTGAGAGTTCAGAAATAGACCGATAAACCTATGTTTAACTGATGTTTGA 3325
                                  i        i   v   v ii    v i  i    v  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_50307912_5   3326 CAAGGGTGCCAAGACAATTCAATAGAAAATGAATCATCTTTTAAACAAAT 3375
                                        v       i ii  v    vi      v       
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_50307912_5   3376 GTTGCAGGGACAATAGGATACCCATATGCAAAAAGACTTAAACTGGATCC 3425
                          v   v       iv     ?   i        -  v v  ii    i  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAAGTTGGACCC 458

  chrX_50307912_5   3426 CTATGTCACACTGTATACAAAAATTCACTCAAAATT-ATCAAAGACTTAA 3474
                            iv      ii            v         v-    ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_50307912_5   3475 ATGTGA--------ACAATAAAACTACTAGAAGAAAAAGCAGG--TAAAC 3514
                             i --------  v        vi          vii   --    i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_50307912_5   3515 CTTAATGACTTTTGATTTGGTACAGGATTCTTAGGTATGATACCAAAAGC 3564
                            vi    i  v i  v  i vv  v       i     i         
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_50307912_5   3565 ATGAGTAGCAAAAGAAAAAATAGATCAATTGGACTGCAT-AAAATGTAAA 3613
                          ii  i i                 v         v   -     vv   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_50307912_5   3614 AGTTTTGAGCTTCAAAAGACACTAT----AAAGTGAAAAGGCAACCCACA 3659
                          v     v        i        ----           i         
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_50307912_5   3660 GAACAGGAGAATTTATTTTAAAACCATATATCTGATAAGGGA-TAGTATC 3708
                            ii      vv     vv   i                  - v     
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_50307912_5   3709 TGGA-TATGTAAAGAAA-ATTAGAACTCAATGATAAAGAGAAAAACAAGT 3756
                         ii  -   i       v-v   v        i     i   v   i  vi
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_50307912_5   3757 CAATGAAAAAAAAACAGACAAAGGATATGAGTAGACATTTATCCAAACAA 3806
                             v?     ---ii i        v   i         v      v  
  L1M4_orf2#LINE/    809 CAATTWAAAAA---TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_50307912_5   3807 TATATATAAATGGCCAACAAACACATGAAAAGATGATTAACGTGGCTGGG 3856
                         v     i          i  i              v i   i vi?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_50307912_5   3857 CGC 3859
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.10 (64 / 58)
Gap_init rate = 0.02 (12 / 697), avg. gap size = 2.17 (26 / 12)  


 651 18.80 0.00 0.00  chrX_50332278_50335585.rev     1603  1719 (1589)    L1M4_orf2#LINE/L1        1   117 (791)  

  chrX_50332278_5   1603 TAGAAAGATATCCCATGTTTGTGAATTAGAAGATATAATATTATTAAAAT 1652
                          i                 ii  i   i     iv       i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50332278_5   1653 GGCTGTACTTCCCAGATGGATCTACAAATTCAATACAATCCCTAGAAAAA 1702
                            vi    i    i  v        i      ii         vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50332278_5   1703 TCTCAGATGACTTTTTT 1719
                           i   v  v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT 117

Transitions / transversions = 2.14 (15 / 7)
Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.00 (0 / 0)  

3393 20.62 1.88 1.38  chrX_50332278_50335585.rev     2018  2817 (491)    L1M4_orf2#LINE/L1      105   908 (0)  

  chrX_50332278_5   2018 AGATGACTTTTTTGTTTCAGAAAATTACAAGCTGATTCTAAAATACACAG 2067
                           v  v        ---      v v          i       v  i v
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTG---CAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_50332278_5   2068 AGAAATGCAAGAAACCCAGAGTAGCCAAAACAGTCTTTAAAAAGAT---C 2114
                         i          ii       i           i    v       v--- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_50332278_5   2115 AAACTTGGAGGACCTACAGTGGCCAATTTCAAAATTTATGACAAGGCCAC 2164
                            v         ii   v vv            i   iv    i  i  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_50332278_5   2165 AATAGTCAAGTCAGTGTGCTACTGGCTTAAGGAAAGACATATAGAT-AAT 2213
                          i  i     v       v       v      v            -   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_50332278_5   2214 GGCAATC-AGTTGAGATCCCAGAAATAAGCCTTTACATGTGTGATCAACT 2262
                           -   v- i      vi          i  iv     v i  i    i 
  L1M4_orf2#LINE/    302 GG-AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_50332278_5   2263 GATTTTGGGCAAACTTGCCAAGAAAATTCAAAGGGAAAGAAATAGTTTTT 2312
                               v i   ivv        vv      v   i  ii      i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_50332278_5   2313 TCAACAATTGGTGTTCAGGCGGTAGAATATTCACATGCAAAATAATGAAT 2362
                                v     i vi i iiiv i   ?i           v      v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_50332278_5   2363 TTGATCTTTGACTTCACACCATACACACCAATTAACTCAAAAGTGTACCA 2412
                            iv iiiv  i          i   vv             -  v i  
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGATCA 499

  chrX_50332278_5   2413 TATACCTAAGTATAAGAGCTTAAACTATAAAACTCTTAGAAGAAAACATA 2462
                         ? v      i i        v                             
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_50332278_5   2463 GGAGTAAATCTCTGTGATCTTGAGTTACACAAAGATTTCTAAGATACAAC 2512
                           ?        ii    i    i    vi   v i     v     ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_50332278_5   2513 AACAAAACCACAAGTCATAAAAACATGATAAGCTGGATGTAAGCTGGACT 2562
                          v     v      iv i    ----  v  iv i   --  ii      
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAA----GAAAAAATAGAT--AAATTGGACT 643

  chrX_50332278_5   2563 T----AAAATTTAAAACCTTCACACTTTAAAG-ATACCATCCAGAAAGTG 2607
                          ----      v     i  iiii   i    - i  i   v        
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_50332278_5   2608 AAATAACACCTCAAAGACTGAGAGACTATACCTATAAATCATATATCATA 2657
                            vi   v i  v   v  i    vv   ii ii            vv 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_50332278_5   2658 CAAAGTCTTTAGATTCAGAAAATATAAAGC-CTCTTACAACTCAGTAATA 2706
                         i  i vvi  iv  i     v        v-             i     
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_50332278_5   2707 A---GACAGATTATACA-TTAAAAAGCAGGATAAGAATTTGAATAGACAT 2752
                          ---    i  v iv  -  ?    iii  vv   i              
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_50332278_5   2753 TTATCCAAAGAATATATATAAATGGCAAATAAACATGTGAACAGATACTC 2802
                           v         v     i       v     i  ii    v    i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_50332278_5   2803 AACATCATTAGTCAT 2817
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (91 / 70)
Gap_init rate = 0.02 (13 / 804), avg. gap size = 2.00 (26 / 13)  


 519 26.39 0.00 1.39  chrX_50358644_50361559      827   970 (1946)    L1M4_orf2#LINE/L1        1   142 (766)  

  chrX_50358644_5    827 TGGAGAGATATACATTGTTCCTAGATTAGAAAAATCAGTACTGCTCAGGC 876
                             i      v vv     v i    i   i v i i  i  i v  ii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50358644_5    877 ATTAATTCTCCTCCAAACTGATCTATAAATACAGCACAAACCCAATCATA 926
                         ivi   v    -     i       i i  v  i i   v   v    v 
  L1M4_orf2#LINE/     51 GGCAATACTCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_50358644_5    927 ATGCCAGCAGCCATTTTAAATAGAAATTGACAAGTCGATTCTAA 970
                           v     v   v    -vii             ii   i    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAA 142

Transitions / transversions = 1.38 (22 / 16)
Gap_init rate = 0.01 (2 / 142), avg. gap size = 1.00 (2 / 2)  

1109 22.78 2.70 0.00  chrX_50358644_50361559     1269  1527 (1389)    L1M4_orf2#LINE/L1      135   400 (508)  

  chrX_50358644_5   1269 GATTCTAAACTTTATATAAAAATTCAA---ACAAGGAATAGCCAAAACA- 1314
                            i     v  i    ii    v   ---  vvi              -
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_50358644_5   1315 CCTTTAAAAAGAA---CAAAGTTGGAGGACTTATACGACTTGATTTCAAA 1361
                         i   v        ---               i i  vv iii        
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_50358644_5   1362 ACATATTATAAAGCTACAGTAATCAAGACAGTGTGGTTTTGGCATAAAGA 1411
                           v  i  i                            vi        i  
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_50358644_5   1412 TAAACATATGGGTTAATGTTACACAACGGCGTCGCCAAAAATAGATCCAT 1461
                           i      i i i    vv i v  iv v vvv   i     i i    
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_50358644_5   1462 ATGTAAAAGGTCAATTGATTTTTGACAAAGGTACCAAAGCAATTAAGTAG 1511
                          ii vv v              i     i   i    ii v   v i i 
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_50358644_5   1512 AAAAAGGATAATCTTT 1527
                         ii    i   i     
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTT 400

Transitions / transversions = 1.68 (37 / 22)
Gap_init rate = 0.01 (3 / 266), avg. gap size = 2.33 (7 / 3)  

 289 22.22 0.00 0.00  chrX_50358644_50361559     1856  1909 (1007)    L1M4_orf2#LINE/L1      384   437 (471)  

  chrX_50358644_5   1856 GGAAAAGGATAATCTTTTAATCAAATAGTGCTGGAACAATTGGATGTTCA 1905
                           i    i   i      v v     i       i    i     i?i  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_50358644_5   1906 TATG 1909
                         i   
  L1M4_orf2#LINE/    434 CATG 437

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.00 (0 / 0)  

1822 20.23 2.92 4.28  chrX_50358644_50361559     1910  2423 (493)    L1M4_orf2#LINE/L1      402   908 (0)  

  chrX_50358644_5   1910 CAACAAATAGTGTTGGAATAACTAGACGTCCATATGCAAAAACAAACAAA 1959
                                 i   i   i i    i  ii?   i        i--  ii  
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG--AATGAA 449

  chrX_50358644_5   1960 ACCCAAAAATCCCTTAG-CTCTTACTTCACAAAACATACA----TTAACC 2004
                         i------------  i - i i   i     vv i     ----     i
  L1M4_orf2#LINE/    450 G------------TTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_50358644_5   2005 CAAAATGGATCCTAAACCCAAGTGCAAGAGCTAAAGTTATATAACTTCTA 2054
                                    v? i   i  i  i          ii    v    ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_50358644_5   2055 GAAGAAAATATAAAAGAAAAATCATAGTTACATCGGTTAAGGCAAAAATT 2104
                                 i   ii? v   -  v v  v  v i  v v      vii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_50358644_5   2105 TCTTAAATAGGACAC-AAATGCAGAAATTATAAAAGAAAAAATCATTAAA 2153
                              i   v     -   v   v  iiv i            viv    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_50358644_5   2154 CTGGACTTTATGAAAATTCAAAATTAAAACATTTTACTTTTCAAAAGTCA 2203
                         i       i  -------           vv    iivi      i v  
  L1M4_orf2#LINE/    637 TTGGACTTCAT-------CAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_50358644_5   2204 CTATTAAGAAA-TGGAAAGGCAAGCCACAGACTGGGAGAAAATATTGGCA 2252
                             i      -  i    i   v       v              v   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_50358644_5   2253 AATCTCATATCCAACAAAGGACTTATATCTTGAATAAA-AAATAACTCTT 2301
                             vi     ii i  i      i    iv     v -   v       
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_50358644_5   2302 ACAACTCAATATTAGTATTACAAG-----CAAT--AAAAATGTACAAAAG 2344
                                    v  iv vv    i-----    --       vi    i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_50358644_5   2345 ATTTAAATAGACACTTCACTAAAGATGATATACATATGGCAAATACACAG 2394
                             i        i   v i     v        v     v    vi  v
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_50358644_5   2395 ATGAAAAGATGCTCAACATCATTAGCCAT 2423
                                              ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (61 / 40)
Gap_init rate = 0.02 (11 / 507), avg. gap size = 3.36 (37 / 11)  


 449 18.87 6.60 0.00  chrX_50364192_50369261     3166  3271 (1799)    L1M4_orf2#LINE/L1        5   117 (791)  

  chrX_50364192_5   3166 AAGACATTC-ATGCTAATGAAT-GCAAGACTTA---TTGTTAAAATGTCC 3210
                             i  i -   i v   i  - v        ---       i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_50364192_5   3211 ATACTACCCAAAGTGATCTA--GAATCAATGTAATCCCTATCAAAATCTT 3258
                              v      v       --  v    i i                ii
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_50364192_5   3259 AATGGCATTTTTT 3271
                          iiv  v      
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTT 117

Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.75 (7 / 4)  

1479 24.66 16.18 0.77  chrX_50364192_50369261     3539  4057 (1013)    L1M4_orf2#LINE/L1      100   698 (210)  

  chrX_50364192_5   3539 ACCCTAGTGGCATTTTTTACAGAAATAGGAAAAAAAAATCTCTACAATTC 3588
                          i  i  iv  v      i       -v  v  ivvi   -   v     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATC-CTAAAATTC 147

  chrX_50364192_5   3589 AGAGGGAATTGCAAAGAACTTCAAATAGCCAAAACAATCTTATAAAAGAA 3638
                          v v    v     i i  iivi                  iv       
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_50364192_5   3639 ----AAAGCTGGA---------TTCCCTGATTTCAA--TTGATATTGCAA 3673
                         ----    i    ---------i i  ii       --i --  i i   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT--TACTACAA 245

  chrX_50364192_5   3674 AGTTATAGTAATCAA--CAGTATG-TAC----------------ATATAG 3704
                           i  i         --    i  -   ----------------      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_50364192_5   3705 AGCAAGGGCACAGAAGAGACAGCCCCAAAATAAACCCACCCATATACGAC 3754
                          v   v  v i    vv  v  i  vi           iv   v  i ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_50364192_5   3755 CAAGTGATCTTTGAGAAGGGTATCAAGACTACAAAATGGGGAAAGTATAG 3804
                            v    i  i  v      ii      i ivv           v    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_50364192_5   3805 TCTCTTCAATGAATGGTA-TGGGAAAACTGGATATC-------AAA---- 3842
                            i     ii      i-     v         ? -------   ----
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_50364192_5   3843 ----------CCACTTTCTTACACCATATGCA------------------ 3864
                         ----------  v  vi  i         i  ------------------
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_50364192_5   3865 ----------TACACATAAGACCTGAAACTGCAAAACTTGTAGAAGAAAA 3904
                         ----------  v ii     v  i     ii      iv          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_50364192_5   3905 TGTGAGGGAAAAGGCTCTTGACATTAGTCTTGGCCATGGGTTCTTGAATA 3954
                         ii ii ? v   vvi  v    v  i vi v   v    v     ii   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_50364192_5   3955 TGATACTAAAAGCACAGGCAACAAAAGCAAAAATAAACAAGTGGGACAAC 4004
                            i  i         i          v       i i  i v    vv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_50364192_5   4005 ATCAAACTAAAAGGCTTCTGCACAACTAACGAATCTTTTAACACAGTGAA 4054
                               v v   ii   i  ii vv v  v  vv  v i  v v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_50364192_5   4055 AAG 4057
                            
  L1M4_orf2#LINE/    696 AAG 698

Transitions / transversions = 1.25 (70 / 56)
Gap_init rate = 0.02 (13 / 599), avg. gap size = 6.77 (88 / 13)  

1032 19.00 1.36 0.00  chrX_50364192_50369261     4357  4577 (493)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_50364192_5   4357 AAAAAAAAGAAAAGGCAGCCTATGGAATGGAAGAAAATATTTGCAAAGCA 4406
                           i   iv      i  i  i ii      i                v  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_50364192_5   4407 TTTATCTGATAAAGGGTTAATATCCAAAACATATAAGGAACTTATACAAC 4456
                          v          i  ii vi      i  i      i     iv      
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_50364192_5   4457 TCAACAGCATAATAACAAA--ATCCAGTT-AAAAATGGGCAAAGGACTTG 4503
                             i ii v  vi     -- i   i  -                i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_50364192_5   4504 AGTAAACATTTCTCCAAATAAGACACATAAACAGCCAACAGGACCATGAA 4553
                          i  i             v    i i i   ii     i i vv      
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_50364192_5   4554 AAGATGCTCAACATCACTAATCAT 4577
                                         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.20 (32 / 10)
Gap_init rate = 0.01 (2 / 224), avg. gap size = 1.50 (3 / 2)  


3487 17.87 1.44 1.30  chrX_50431783_50434670.rev     1200  1893 (995)    L1M4_orf2#LINE/L1        1   695 (213)  

  chrX_50431783_5   1200 TGGAAAGACATCTCATATTCATGGGTAAGAAGACTTAATATTTTTATGAT 1249
                                 i   i   i       i vi              v   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50431783_5   1250 GCCAGTACTACCCAAAGAGACTTACAGATTCAACACAGTATCTACCAAAA 1299
                          v  i    v      vv  ii            i  i vi   i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50431783_5   1300 TTCCAACAGCTCCCCTTTTCTTTACAAAAATGGGAAAGCATATCCTCAAA 1349
                          i   i v  ----     --  i  i    v iv    vv     v   
  L1M4_orf2#LINE/    101 TCCCAGCTGC----CTTTT--TTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_50431783_5   1350 TTCATATGGAGCTGCAAGGG-CCCTGAATAGCCAAAATAATCTTCTAAAA 1398
                                   iv        -   v            i      vv    
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_50431783_5   1399 GAA---CAAAGTTGGAGGACTCACA-TTCCAGACTTCAAATCTGCCTAAA 1444
                            ---                   -    vi i      v  vv   v 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_50431783_5   1445 AGGCTACAGTAATCAAAACAGTGTGCTACTGGCATAATGAGAGAAATATA 1494
                          i              i        v           v  v   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_50431783_5   1495 GATCAATGGAATAGAATTGAGAGCCCATAAATAAACCTATACATCTATAC 1544
                                                i   v         i      i   iv
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_50431783_5   1545 CCAGTTGATTTTTGACAAGGTTGTCAAGCCTATTCAATGGGGAAATAAAT 1594
                         i  i        i       v  i    v i              -i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAAT 393

  chrX_50431783_5   1595 AGTCTCTTCAGTACATGGTGTTGGGACAACTAGATTTCTACATGCGAAGA 1644
                              i    ii v      i          i   v? i      i  - 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-A 442

  chrX_50431783_5   1645 AAAGGGCTTTGCACTCCTACCTCAAACCATGTACAAAAATTAACTCAAAA 1694
                         i  v ivv   v  i         v     i                   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_50431783_5   1695 CTGATCAATGACTTAAATACAAGAGTAAAAAATCATAAAATACTTA---- 1740
                         iv     ?v   i     ii     iv    v -      iv    ----
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTTAGAAG 541

  chrX_50431783_5   1741 -AAACATGGAAGTAAATCTTCATAACCTCAGATTTGGTAATGGATTCTTA 1789
                         -      i i?          i i    ii i  v  i     v      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_50431783_5   1790 GATATGCCACCAAAAGCATGAGCAGCAAAAGAAAAAATTACTAAATTGGA 1839
                               v           ii    i             viv         
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_50431783_5   1840 TTTCCTCAAAATTTAAAACTTTTGTGCATTAAAGGGTGTTATTAAGAAAG 1889
                         i   v        v             v i     iiii   i       
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_50431783_5   1890 TAAA 1893
                          i  
  L1M4_orf2#LINE/    692 TGAA 695

Transitions / transversions = 1.37 (70 / 51)
Gap_init rate = 0.01 (9 / 695), avg. gap size = 2.11 (19 / 9)  

 962 18.14 4.19 0.00  chrX_50431783_50434670.rev     2183  2397 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_50431783_5   2183 AAAAAAGGAAAAAGACAACCTACAGGATGAGAGAAAATATTTGAAAATCA 2232
                           i    vi           i    i   i             v      
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_50431783_5   2233 TATATCTGAGAAGTGTTTGATATTCAGAATATACAAAGAAAACCTACAAC 2282
                                  v   v vi vi   i         i      vv i      
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_50431783_5   2283 TTAACAACA------TAAACAACCCAATTTAAAAATGTGAGAAGGACTTG 2326
                          i  i  i ------i   i         ?       v vi     i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_50431783_5   2327 AGTAGATATTTCCTCAAAGAAGATATATAAATGGC-AACAAACATATAAA 2375
                          i    i     ii             i       -  i  i  i  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_50431783_5   2376 AA--TGTTCAATATCATTAGTCAT 2397
                           --  i    i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.80 (28 / 10)
Gap_init rate = 0.01 (3 / 224), avg. gap size = 3.00 (9 / 3)  


2532 25.94 2.02 0.43  chrX_50466610_50471779     1415  2108 (3062)    L1M4_orf2#LINE/L1        1   705 (203)  

  chrX_50466610_5   1415 TGGAAAGATATCCTATACTCATGGATTGCAAGAGTTAATATTGTTAAAAT 1464
                                      i  ii          v    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50466610_5   1465 GACCATACTACCCAATGTGATTTACAGATTCAATGCAATCCCTATCAAAA 1514
                          i v     v     vv    i           i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50466610_5   1515 TACCAATGACATTCTGCAAAGAAATAGAAAGGGAAATACTAAAATTAATA 1564
                          v   iivi v  i viiv      v  v i vvi  v        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_50466610_5   1565 TGGAAGCACAAAAGACC-ACAATAGCCAAAGCAATACTGAGCAAAAAGAA 1613
                              iii   ii    - v          i    vi   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_50466610_5   1614 TAAAGCTGAAGGCATCACTCTACCTGACTTTAAAAAATATTACAAAGCTA 1663
                         i    i  i   vv    v  v  ii i  i    vv  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_50466610_5   1664 TAGTAATCAAAACAGCATGGTATCAGCATAAA-ACAGACACATAGACCAA 1712
                         i         i    ii     iii      i- i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_50466610_5   1713 TGGAACAGAATAGAGAACCCAGATATAAATCTATGCATTTACAATCAACT 1762
                              i     v    ii     v     i i  i      iii    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_50466610_5   1763 GACTTTCAACAAAGGCACCAAGAACATACATTGGGAAAAGGATACCCTCT 1812
                           i    i    i  ii      v   v  v    i    i   vi  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_50466610_5   1813 TCAAAAAATATCACTGGGAAAACTGCATATTCATATACAGAAGAATAAAG 1862
                             v    ivii      v     v   ?i  i  i  i      i   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_50466610_5   1863 CATGACCCCTATTTAACACTATATGCAAAAATCAACTCCGAATAGATTAA 1912
                         ivv        ii v    i    i       i     vi   i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_50466610_5   1913 AGACTTAAACCTAAGACCAAAAACTATAAAATGACTAGAAGAAAATACAA 1962
                             i    iv     v v            ivvi          i i i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_50466610_5   1963 GGAAACAATTCTGCACA-----GGGTCTAGGCCAAGATTTTATGGGTAAG 2007
                          ?i--i  v   v iii-----    -     v v i   iv i i  v 
  L1M4_orf2#LINE/    551 GNG--TAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chrX_50466610_5   2008 ACTTTAAAAGTATAGGTAACAAAA------ACAGATAAATGGGACTATAG 2051
                           vii     i i i i       ------ i        v     vi v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_50466610_5   2052 CAAACTAAAAAGCTTCTGCACAGCAAAATAAATAATTGAGAAA-TAAAAA 2100
                             v v    i   i  ii vv    iv v iv  ii     - i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_50466610_5   2101 TAAAATCC 2108
                         v v  i  
  L1M4_orf2#LINE/    698 GACAACCC 705

Transitions / transversions = 1.77 (113 / 64)
Gap_init rate = 0.01 (7 / 705), avg. gap size = 2.43 (17 / 7)  

 542 21.62 3.24 6.49  chrX_50466610_50471779     2806  2990 (2180)    L1M4_orf2#LINE/L1      648   826 (82)  

  chrX_50466610_5   2806 CAAATTTAGGAACCTCATGATTCTTCAATTGACATGACCAACAAAG---- 2851
                             v   ii   i -- vi v      vv    iv i   v    ----
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTT--TTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_50466610_5   2852 -AGACAACCTATAGA-TGGGAGAAAATATTTGCAAACTATTCATTCAACA 2899
                         -        i i   -                    ii  vi  iii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_50466610_5   2900 AGGGACTAATAAACAGAATATACAAGGAACTTGCACAACTCAAAAGCAAA 2949
                                vi  vv         i  i     ivi         v -----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA----- 790

  chrX_50466610_5   2950 AAAAAAAAAAAAAACAAATAATCCCATTAAAAAGTGAGCAA 2990
                         ----- v     i        i  v   ?    i  i    
  L1M4_orf2#LINE/    791 -----ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

Transitions / transversions = 1.60 (24 / 15)
Gap_init rate = 0.02 (4 / 179), avg. gap size = 4.50 (18 / 4)  

1365 24.30 1.01 0.76  chrX_50466610_50471779     2991  3385 (1785)    L1M4_orf2#LINE/L1      513   908 (0)  

  chrX_50466610_5   2991 AAGACCTCAAACTATAAAACTACTATAAGAAAACACTGGGGAAAATCTCC 3040
                             v  v             vi  v         iv  ? v      i 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_50466610_5   3041 AGGACATTAGTCTGGGCAAAGACTTCTTAAGCAATACCTCACAAGCACAG 3090
                         iv   v  i vi i     v ii      iii vv  vi  v       i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_50466610_5   3091 GCAAGCAAAGTAAACATGGACAGACGGGATCACACC-AAGTTAAAAAGCT 3139
                             vv    v   v  i  i i iv   iiv  i -  i       -  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CT 661

  chrX_50466610_5   3140 TCTTCACAGCAATGGATACAATCAACAAAGGGAAGAGACAACTCATAAAA 3189
                          i vii vv   v   i  v     v    v   i       i  i i  
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_50466610_5   3190 TGGGAGAAA-TATTTGCAAACTAGCCCTCTGACAAAGGATTAAAAACCAG 3238
                                  -          ii vviv     i  i   i viv v    
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_50466610_5   3239 AATATATAAGGAGCTC-AACAACTCTATAGGAAAAAAAATCTAATAATTC 3287
                                  i  i   -v       v   iv     i -- v     ii 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CAAATAACCC 809

  chrX_50466610_5   3288 AATCAAAAGATGGGCAAAAGATTTGAATAGACATTTATC-AAAAAAGTCA 3336
                            i?   i         i                 v  -   i   vi 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_50466610_5   3337 TATAAATGGCAAACAGGCATATGAAAAGGTGCTCAACACCACTGATCAT 3385
                           i       v  i i   i        i         i  ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (54 / 40)
Gap_init rate = 0.02 (6 / 396), avg. gap size = 1.17 (7 / 6)  

 408 17.65 0.00 2.94  chrX_50466610_50471779     4576  4677 (493)    L1M4_orf2#LINE/L1      810   908 (0)  

  chrX_50466610_5   4576 AATTAAAAAAAGTGAGCAAAGAATGTGAATAGACGTTTCTCAAATGATAA 4625
                             ?     --  i      i  v         i      v  v  vi 
  L1M4_orf2#LINE/    810 AATTWAAAAA--TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_50466610_5   4626 CATAAAAATGGCCAACAGGTATTTGAAAAAAATGCTCAATATCACTAATC 4675
                         i   v          i i i iv      i -       i    ??????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZ 906

  chrX_50466610_5   4676 AT 4677
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.02 (2 / 99), avg. gap size = 1.50 (3 / 2)  


3255 15.73 4.99 0.30  chrX_50495911_50499507      492  1152 (2445)  C L1M4_orf2#LINE/L1   (0)   908   217  

C chrX_50495911_5   1152 ACACTTTCCAATTTCACAACTTACGACATATCTACAATTATAAAGACAGT 1103
                               i         v       v   v v     i v  v        
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

C chrX_50495911_5   1102 ATTGTCCTGGCATAA---TAGACATATGGATCAATGGAATAAACTTGAGA 1056
                         i v  v         ---         i             i v      
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

C chrX_50495911_5   1055 GTACAGAAATAAACTTATA--TTTATGGTCA-----TTTTTTACACATGT 1013
                           v           ii   --          -----    iv   viv  
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

C chrX_50495911_5   1012 GCCAAGAC-----AATGGAGAAAGATTAATCTTTTCAATAAATGATGCCA 968
                                 -----     i      v  i         i     i   ii
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

C chrX_50495911_5    967 GGACAACTATATAACCACATGCAAAAGAATGAAGTTGGACTTTTACCTCA 918
                                 iv   ?                          iii       
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

C chrX_50495911_5    917 CACAGTATGCAAAAATTAACT-AAAATAGATTTAAAACCTAAATATAACA 869
                            vi   i            -     i   iv? i        i   v 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

C chrX_50495911_5    868 GCTAAAACTAGAAAACACTTAGAAAAAAACATAGGCGTAAATTTTCATGA 819
                                   v     v       i          ?      i   i   
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

C chrX_50495911_5    818 CACTTGGATTATTCGATT-TTTCTCCAAT--GATACCAGAAGCACAAGCA 772
                          -     i   vv i  v-     ivi  --  i    i           
  L1M4_orf2#LINE/    567 C-CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

C chrX_50495911_5    771 GCAATAGATAAAAATAGATAAACAGGGCTTCTTCCAAATTAAAAACTTTT 722
                         i   v   -             iv  i    v  v               
  L1M4_orf2#LINE/    616 ACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

C chrX_50495911_5    721 GTG-TTCAAAGAACACCATCAAGAAAGTTAAA---TAATCCACAGAATC- 677
                            -       i    i           v   ---i  i         v-
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

C chrX_50495911_5    676 -AGAAAATATTTGTGTATCATAGCTCTGATAAGAGATTAATATCCAAAAC 628
                         -            iiv      vv         i  i vi      i  i
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

C chrX_50495911_5    627 ATATGAAGAACTTTTACAACACAACAA----GAGACAA----CACAATTT 586
                             i       i       v   i  ----i      ---- v     ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

C chrX_50495911_5    585 TAAACTGGGCAAATGGTTTGAATAGACATTTATCCAAAGATGATGTGCCA 536
                         v   v        v i               v        v   i i v 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

C chrX_50495911_5    535 GTTGCCAATAAGCACATGAAAAGATGCTCCACATCATTAATCCT 492
                         i v                          v      ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (56 / 44)
Gap_init rate = 0.02 (14 / 692), avg. gap size = 2.50 (35 / 14)  

1087 21.40 1.31 0.87  chrX_50495911_50499507     1464  1692 (1905)  C L1M4_orf2#LINE/L1   (678)   230     1  

C chrX_50495911_5   1692 TAAAAAGATGTCTCATGTTTACAGATCAGAAGACTTAA---CGTCAAAAT 1646
                          ii      i  i      i ii   ii          ---i  i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_50495911_5   1645 GGCAATACTATTCAAATTTGTCAGTAGATTCAATGTAGCCCCCATCAAAG 1596
                                  vii      vi  vii        i i ii   i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

C chrX_50495911_5   1595 AAATCCGGCTGGTATTTTTGTAGAAATTGAAGAGTTGACCCTAAAATTAA 1546
                         - vi  i    viv      i         vi  i   i         v 
  L1M4_orf2#LINE/    100 -ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

C chrX_50495911_5   1545 TATGGAAATACAAGTGACTCAGAATAGCCAAAACAATCTTGCTAAAGAAT 1496
                                  i    v   i                      vv      v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_50495911_5   1495 AAAATATTTGGAAGAATCACACTTTCCAATTT 1464
                           v v v     i  v        i       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTT 230

Transitions / transversions = 2.06 (33 / 16)
Gap_init rate = 0.01 (2 / 230), avg. gap size = 2.50 (5 / 2)  

1771 25.52 7.93 0.34  chrX_50495911_50499507     2174  2753 (844)    L1M4_orf2#LINE/L1      232   855 (53)  

  chrX_50495911_5   2174 AATACTTACTTTAAAGTTACAGTAATCAAGGTATTGTAGTATTGGGGAAA 2223
                           v       vi    i             ii v   i   i   viv  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_50495911_5   2224 GAATAAACACATAGATCAATGGAACAGAATAGAAAACCCAAAAAATAGAT 2273
                          i   i   i              i     v  i ii   i   -  i i
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA-TAAAC 330

  chrX_50495911_5   2274 CCACACAAATGCAGTCAATTAATCTTTGACAAAGGAGCAAAGGCAATTCA 2323
                            i   vv iii       i  i  i     i  v  v   i v     
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_50495911_5   2324 ACAGATAAAGAGTAATTTTTTCAACAAATAGTGCTAGAACAA-------- 2365
                          ii iv     i  i i            i     i i    --------
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_50495911_5   2366 --------AAACAAAT----CTAGACAAAGACCTTATACTTTCAATAAGA 2403
                         --------   vi   ----i i   vvvv    i i  iv vv i  i 
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_50495911_5   2404 GTTTATTGAAAATTGATCATAGATATAAATGTCAAA-CACAAACTATAAA 2452
                         i  v i v     v     ?   iv       v i - vv          
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_50495911_5   2453 ACTTCTAGAAGATAACATAGGAGAAAATATAAATAACTTTGAGTTATGTG 2502
                            ii       v        ? v    v vvi i  i   i    v ii
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_50495911_5   2503 ATGACTTTTCTGAGACAAAACCAAAAGCATTATCTAAAAAAGCAAAAATA 2552
                            ii  i iv  v ii v          iv v v v     v       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_50495911_5   2553 ----AGTTGGGCTTTGTTAAAATTAAAG-CTTCTGTTGTGTGAAAG---A 2594
                         ---- i    i   ii i         i-   i   - iv v    --- 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGT-GCTTCAAAGGACA 679

  chrX_50495911_5   2595 CTGTTAAGAATATGAAAAGATAAGCCACAGACTGAAAAAAAAT---TGCA 2641
                           i i     vi        i  v       v  ii i     ---    
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_50495911_5   2642 AA--ACATATTAGATAAGGGGCTTGTATCTAAAATATACAAAGAACTCTG 2689
                           -- i    iv        i        i i      i          v
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_50495911_5   2690 AAAACTCAACAGTAAGAAAAT--------CAATT-AAAAATGGGGAAAAC 2730
                          v       i i   i  i i--------     -         v   iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_50495911_5   2731 ATATGAACAAACA---CCTCAAAAAA 2753
                           v    i i   --- ii    i  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAA 855

Transitions / transversions = 1.81 (94 / 52)
Gap_init rate = 0.02 (13 / 624), avg. gap size = 3.69 (48 / 13)  

 271 13.79 1.72 0.00  chrX_50495911_50499507     3047  3104 (493)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_50495911_5   3047 AAAAAAGGCATATATGTGG-CAATAAGCATATGAAAAGATGCTCAACAAC 3095
                            i   ii   i vi   -         i                  v 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_50495911_5   3096 ATATATCAT 3104
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1)  


2329 12.98 2.45 28.33  chrX_50512686_50516164.rev     1764  2988 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_50512686_5   1764 TGGAAAGATACTCCATTTTCATCAATTGGAACACTTAATATTGTTAAGAT 1813
                                   ii    v     vi       v                  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50512686_5   1814 GGTGCTACTTTTCAAATTGATCTATAGATTTAACACAGTCCCTATCAAAA 1863
                           iiv    iii            i     i   i  i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50512686_5   1864 GAGCAGCTGGTTTTTTTTGGTTTTTTGTTTGTTTGTTTGTTTTGTAGAAA 1913
                         vvv      vi      -------------------------- i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--------------------------GCAGAAA 124

  chrX_50512686_5   1914 CTGTCGACCTGTTCTGAAAACTCTTATGGAAATGCAGGGGAATCTAAATA 1963
                         i  v i v   v  iv    i  v            i    vi vi    
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chrX_50512686_5   1964 TTTTTAAAAATCATGAAAAAGAAGAACAAAATTGGAAAAC-AACACTTCC 2012
                         viivv  v    v                 i     ii  -v        
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_50512686_5   2013 CAATTTTAAAACTTACTACCAAGCTACAATATTCAAGATTGTATGTTAAT 2062
                               i            v        i  v      iv  i  v  v 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_50512686_5   2063 GGAACATGGATAGACATATAGAT-AATGTAATACAATTGAAAGTCCAGAA 2111
                           v i v                -    v    v      i         
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_50512686_5   2112 ATAAACTCATATA------GTAAACTGATTTTCAACAAGGGTGACCTGAC 2155
                               i    i ------  v  i        i         -------
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG------- 367

  chrX_50512686_5   2156 CATTCAATGTGTGAAAGATCTGTCTTTTCCACCAGGCGCGGTGGCTCACG 2205
                         --------------------------------------------------
  L1M4_orf2#LINE/    368 -------------------------------------------------- 367

  chrX_50512686_5   2206 CCTGTAATCCCAGCACTTTGGGAGGTCGAGGTGGGCAGATCACAAGGTCA 2255
                         ---------   --------------------------------------
  L1M4_orf2#LINE/    368 ---------CCA-------------------------------------- 370

  chrX_50512686_5   2256 GGAGAGCAAGACCATCCTGGCTAACACAGTGAAACCCTGTCTCTACTAAA 2305
                         --------       i ---------------------------------
  L1M4_orf2#LINE/    371 --------AGACCATTC--------------------------------- 379

  chrX_50512686_5   2306 AATTAAAAAAAATTTAGCCGGATGTGGTGGCGGGCACCTGTAGTCCCAGC 2355
                         --------------------------------------------------
  L1M4_orf2#LINE/    380 -------------------------------------------------- 379

  chrX_50512686_5   2356 TACTCAGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCT 2405
                         -----------------------     ----------------------
  L1M4_orf2#LINE/    380 -----------------------AATGG---------------------- 384

  chrX_50512686_5   2406 TGCAGTGAGCCGAGATCATGCCACTGCACTCCAGCCTGGGCGACAGAGCA 2455
                         --------------------------------------------------
  L1M4_orf2#LINE/    385 -------------------------------------------------- 384

  chrX_50512686_5   2456 AGACTCTGTCTCAAAAAACAAAAAAAGGAAAGAAAGATCTGTCTTTTCAA 2505
                         --------------------------        vi----          
  L1M4_orf2#LINE/    385 --------------------------GGAAAGAATA----GTCTTTTCAA 404

  chrX_50512686_5   2506 AAAATAGTGCTGGGACAACTAGATATCCACATG-GAAAGAGTGAATTTGG 2554
                         v    i              i    ?       -i     i    v    
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_50512686_5   2555 ACCCCTACCTTACATTCTGTATAGAAATTAACTGAAAGTGGATCATAAAC 2604
                                   i   iiv i  i i         v   i       ? i  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_50512686_5   2605 CTAAATATTGAACCTAAAACTATACAACC--TAGAA-AAAACATAGTGGT 2651
                               i vii v           v   i--     -         v?  
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_50512686_5   2652 AAACCTTTGTAACCTTAGATAAGGTAATAGATTTTTAGATATGACAT-AA 2700
                            i   i  i     i i v   i   i v  i            i-  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_50512686_5   2701 AAATACAAGCAACTAAAGAAAAAATAAGTTGGATAGACTACATTACA-TT 2749
                           ii         v            ii viiv i    v   i v -  
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_50512686_5   2750 AAAAATGTGTGTGCCATAAAGATACAC----AAGACA---AAAA-----C 2787
                              iv v     ivi    i-    ----    v ---    ----- 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGG-ACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_50512686_5   2788 CCATGGAATGAGAGAAAATATTTATAAAT-A-ATATCAGATAATGATCTA 2835
                            ii     i            ii    - -     v     v iv  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_50512686_5   2836 GTATCTAAAATATGTAAAGCATTCTTACAACTCAATAATAAAA-GATAAA 2884
                              i i     i     v i                     -  i   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_50512686_5   2885 TAACCCAATT-AAAAATGGACAAAGGATCTGTATAGATTTTTCTCAAAAG 2933
                                   -        i        i  v     iv      v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_50512686_5   2934 AAGTTATACAAATGACCAATAAGCACAGGGAAAGAAACTCAGCTTCATTA 2983
                            v          i            v i     vi    i v   ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_50512686_5   2984 TTCAT 2988
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.48 (93 / 63)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 17.14 (377 / 22)  


2835 20.00 7.58 1.67  chrX_50551681_50553916.rev      559  1218 (1018)    L1M4_orf2#LINE/L1        1   699 (209)  

  chrX_50551681_5    559 TGGGAAGACATCCAGTGCTCAAAGATAGAAAAACTTAATAATGTTAAGAC 608
                            i    i    vi  i   vi   v i  i        v        i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50551681_5    609 GGTAATACTCTTCAAAGTGATCTATGAATTCAATGGAAATTCTATCAAAA 658
                           i       ii    v       iii      i v  vii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50551681_5    659 TGTCAGTTGACTCCTTTATAGAAATTAACAACATAATACTTAAATTTATA 708
                          vi   i  v  ii   ii       i    vv i  v  v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_50551681_5    709 TGGAAACTCAAGAAACACAGAATAGTCAAAACAATCATGATAAAGGAGAA 758
                               iv    ii  v        i          v   v    i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_50551681_5    759 CGAATTTGGAGGGCTCATAATTCCTGACTTCAAAG-----------GCTA 797
                          i  v       i    i v    ii i      i-----------    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_50551681_5    798 CAGGAAGCAGGACA-TATGATGCCCTGCTTATTGGCATAATGATAGACAT 846
                            v  v  i    - i  i --------- i        v         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGT---------ACTGGCATAAGGATAGACAT 291

  chrX_50551681_5    847 ATAAATCAATAAAATATAACTGAGAGTCTTGAAATGAGTTCTCATATTTA 896
                            i      ii    v  i        iv     i iii vi i     
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_50551681_5    897 CAATAAATCAAGTTTTGACAAGGGTGCTGAGACAATTCAAGGAGAAAATA 946
                         iii v   ii v   i           ii    v      v i i   v 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_50551681_5    947 ATAGTCTTTTCAACAAATGGTGCTAGAACAACTGAATATCCACATTTAAA 996
                                                 i i       i   ?      vi   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_50551681_5    997 CAAAC----TTGAGCCTCAATCTCACACCATATGCAAAAGTTAACTCAAA 1042
                         vi  i----   ii  i v i            i     i          
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_50551681_5   1043 ATGAAT-AAAGATCTAAATACCAGTGTTTACATTATACAAATATTAGAAG 1091
                            i  - ?   i      iiv  v i v v i    v  v v       
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_50551681_5   1092 AAAACATAGGGGTAAATCATAG-------------GGCAATGGTTTCTTA 1128
                                   ?       v v -------------               
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_50551681_5   1129 GA--------------------CAACAAAAGAAAAAAATAGATACATTGG 1158
                           --------------------               -      v     
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGG 640

  chrX_50551681_5   1159 ACTTCATCAAAATTAAGATTTTTTAATGCTTCAAAGGACACTATTAAGAA 1208
                                         i vi    i-                  i     
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAA 689

  chrX_50551681_5   1209 AGTGAAAAGA 1218
                                   
  L1M4_orf2#LINE/    690 AGTGAAAAGA 699

Transitions / transversions = 1.93 (85 / 44)
Gap_init rate = 0.01 (9 / 699), avg. gap size = 6.78 (61 / 9)  

 948 16.88 0.42 5.91  chrX_50551681_50553916.rev     1509  1745 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_50551681_5   1509 AAGAAAGTGAAAAGAAAATTCAAATAATGAGAGATGATATATACATAAAC 1558
                                        v  ii  v v    i    vi    v i  --  i
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA--AAT 732

  chrX_50551681_5   1559 TATATATTGGACAAGGGACTTATATCTGAAATGTACCTAAAATATGTAAA 1608
                         i      iv  i         i    -----------i i     i    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATC-----------CAGAATATATAAA 771

  chrX_50551681_5   1609 GAATGCTTGCAACTCAATGATAAGAAGACAAATCACCCAAATGAAAAAAT 1658
                            iv   i         i    i         v      - v?      
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA-TTWAAAAAT 820

  chrX_50551681_5   1659 AGTCAAATGATTTGAATAGACACTTCT-GAAAGAAGATATACAAATGGTC 1707
                         i v    v              i    -v                   i 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_50551681_5   1708 TATAGGTTCATGAAAAGATGTTTAACATTAGTCACCAG 1745
                         v   i iv            i i     i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (25 / 14)
Gap_init rate = 0.02 (4 / 224), avg. gap size = 3.75 (15 / 4)  


3187 27.43 1.00 0.55  chrX_50588946_50595338.rev     4999  5902 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_50588946_5   4999 TGTAAGAACATTCCATGCTCATGGGTGGGAAGAATCTATATCGTGAAAAT 5048
                           v  ii i  i     i      i v      v iv    i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50588946_5   5049 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5098
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50588946_5   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_50588946_5   5147 TATGGAACCAAAAAAGAGCATGCATTGCCAAGTCAATCCTAAGCCAAAAG 5196
                                viiv  ii  v vv v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_50588946_5   5197 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5246
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_50588946_5   5247 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5296
                           i     i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_50588946_5   5297 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATGTCGCATATCTACAACC 5344
                                i    i--    i  --    i   vvi ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_50588946_5   5345 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5394
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_50588946_5   5395 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGAAAGGT 5444
                           v  i  i              v      v  ?  ii   i i  iii 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_50588946_5   5445 GAAACTGGATCCCTTTCTTACACCTTATACAAAAATTAATTCAAGATGGA 5494
                            ii    i    vi  i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_50588946_5   5495 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5544
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_50588946_5   5545 CTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5593
                         v i  ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_50588946_5   5594 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5643
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_50588946_5   5644 ATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5693
                           iv  v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_50588946_5   5694 CAGGCAACCTACAGAATGGGAAAAAATTTTTGTAATCTACTCATCTGACA 5743
                         v  i     i           i     v    i  vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_50588946_5   5744 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5793
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_50588946_5   5794 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5839
                           i    ----   v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_50588946_5   5840 CTCAAAAGAAGACATGTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5889
                            v        i  ii viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_50588946_5   5890 CATCACTGGCCAT 5902
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (149 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


 336 12.50 3.57 0.00  chrX_50645279_50649765     2759  2814 (1673)    L1M4_orf2#LINE/L1        1    58 (850)  

  chrX_50645279_5   2759 TAGAAAGCTATCTCGTGT--ATGGACTGGAAGACTTAATATTGTAAAGAT 2806
                          i     v    i i   --     i                  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50645279_5   2807 GACAATAC 2814
                          i      
  L1M4_orf2#LINE/     51 GGCAATAC 58

Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 2.00 (2 / 1)  

3945 19.24 0.58 1.39  chrX_50645279_50649765     3132  3994 (493)    L1M4_orf2#LINE/L1       53   908 (0)  

  chrX_50645279_5   3132 CAATACTACCCAAGGCAATCTACAGATTCAATGCAATAGCTATCAAATTA 3181
                                v     ivii              i     vv        v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_50645279_5   3182 GCAATAGGATTTTTTATTTTTGCAGAAATGGAAAAGCCAATCCTAAAATT 3231
                         v  ---- v vii  --            v  v    ii           
  L1M4_orf2#LINE/    103 CCA----GCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_50645279_5   3232 CCCATGGAATTGTAAGGGGCCCCCAATTCTCTCAAACATTCTTGAACAAA 3281
                          vi      v  i     i   vv   -vv iv     v       v  i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAAT-AGCCAAAACAATCTTGAAAAAG 195

  chrX_50645279_5   3282 AAGAAAATAATTAGAAGACTCATATTTCCTGATTTGGAAACTTAATAGAA 3331
                              v v i  i  i      i i    ii    vi       v  v  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_50645279_5   3332 ATCTGCAGTAATCAAAACAGTGTGATACTGGCATATGCATAGACATATAA 3381
                          v  i          i        i          v v           i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_50645279_5   3382 ATCAACAGAATAGAACTGAGATTCCAGAAATAAACACATACATCTACAGA 3431
                              ii        i     v             v       i  ii v
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_50645279_5   3432 CAACTGATTTTTGATGAGTGTGTCAAGTTCATTCAATGGAAAAATAATGC 3481
                            i       i  ii  v   i    vi          ii   v   iv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_50645279_5   3482 TCTTTTTAACAAATGGTGCTGATACAACTGGATAGCCACATGTAAAAGAA 3531
                               i              iv           ?       i       
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_50645279_5   3532 TGAAATTGGACCCCTAC-TCACACTATGTATAAAAGATAACTAAAAAGGG 3580
                             i            -      i  i  i    iv     v    v  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_50645279_5   3581 ATCAACAACCTTAATATAAGAGCTAAAGCTATTAAAATTTTAGAAGAAAA 3630
                             ?vi    v   i           i    v   v i           
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_50645279_5   3631 CATATGGGTAAATATTCATGGCCTAGGATTCAGCAATGGATTCTTAGACA 3680
                             v ?      v   i  i   v  i  vi       v        i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_50645279_5   3681 TGACACAAAAACCATGAGCAACAAAAGAAAAA-CAGATATATTGTACTTC 3729
                               v    v  ii                -i     v    v     
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_50645279_5   3730 ATTAAAATTAAAACCTTTTGTACATCAAAGGTTATTATCAAGAAATTGAA 3779
                           i          v       i v       vi i          v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_50645279_5   3780 AAGAAAAATCTGTAAAATGGGAGAAAATATATGCAAATCATACATTTCTT 3829
                             v  -i iii i               v           i  i vv 
  L1M4_orf2#LINE/    696 AAGACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_50645279_5   3830 ACAAGCATTTATTATCCAGAAGATGTAAAGAACTCCTGCAACTAAACAAC 3879
                          - i v i  i -        v  i          i i     v  i  i
  L1M4_orf2#LINE/    745 A-AGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_50645279_5   3880 AAACAAACAAGCAACCCGATTTTTAAAAATGA-TAGAGGACTTCAATAGA 3928
                            v i    ii     i   ?--       i-i i    i  v      
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_50645279_5   3929 CATTTTTC-AAGGAAGATACAGAAATGACCCATATGCACATGATAAAAC- 3976
                              i  -  i       i v     i  v   v        v  i i-
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_50645279_5   3977 CTCAACATCATTAATCAT 3994
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (93 / 69)
Gap_init rate = 0.01 (12 / 856), avg. gap size = 1.42 (17 / 12)  


3222 26.68 0.66 0.55  chrX_50688514_50693497     3585  4491 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_50688514_5   3585 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3634
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50688514_5   3635 GGCCATACTGCCCAAGGTAACTTATAGATTCAATGCCATCCCCATCAAGC 3684
                            v     v     iv i ii  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50688514_5   3685 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 3731
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_50688514_5   3732 ATATGGAATCAAAAAAGAGCCCGCATAGCCAAGTCAATCCTAAGCCAAAA 3781
                                 viiv  ii  v  v v        iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_50688514_5   3782 GAACAAAGCTGGAGCA-TCACGCTACCTGACTTCAAACTATACTACAAGG 3830
                                 i     v -    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_50688514_5   3831 CTACAGTAAGCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGAT 3880
                                  v   i    ii         i  v ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_50688514_5   3881 CAACGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAAC 3928
                            i    i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_50688514_5   3929 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAACGGATTC 3978
                         i vi    i  i     ivv  vv  i v  vv          v i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_50688514_5   3979 CCTATTTAATAAATGGTGCTGGGAAAACTTGCTAGTCATATGTAGAAAGC 4028
                         i  v  i  i              v    v v  ?i  i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_50688514_5   4029 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 4078
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_50688514_5   4079 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4128
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_50688514_5   4129 CCTAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGCCTA 4178
                          v    ?i v viv   iv   v v  vv i i   v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_50688514_5   4179 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 4228
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_50688514_5   4229 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4278
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_50688514_5   4279 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGATA 4328
                         v  i     i   i             v  ii   vii ivi        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_50688514_5   4329 AAGGGCTAACATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4378
                          i  i  vii         v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_50688514_5   4379 AAAACAAACAACCCCATCAAAAAGCGGGTGAAGGACATGAACAGACACTT 4428
                           i     i     v  i?    ii   ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_50688514_5   4429 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 4478
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_50688514_5   4479 CATCACTGGCCAT 4491
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2793 25.28 2.88 3.88  chrX_50775115_50777214      698  1599 (501)    L1M4_orf2#LINE/L1        1   893 (15)  

  chrX_50775115_5    698 TGGAAAGATATTCCATACTCATGGCTTGGAAGAATTAAGGTTATTAAAAT 747
                                    i    ii      v        v    vi  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50775115_5    748 GACTATAGCACTAAAAGCAATTTACATACTCAGTGCAATCACTATAAAAA 797
                          i v   viv iv   vii  i    v i   ii      v    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50775115_5    798 TACCAATGACATTCTT--CATAAATAGAAAAA--GATACTAAAATACACA 843
                          v   iivi v  i  --  v    v  v  i--   v       v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_50775115_5    844 TGGAATTGCAAGAGACCTCGAATAGCCAAAGCAATCCTGAACAAAAAGAA 893
                              v      i    iv           i     i    v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_50775115_5    894 CAAAGCTGGAGGCATCACACTACCTGACTTCATAATATACTACAAAGCTG 943
                              i      vv       v  ii i    v  iv            i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_50775115_5    944 TAATAACCAAATTAGCATGGTACTGGCAAAAAACAAACAAAAAACACAAA 993
                         i i   i   ivi  ii           ----------------------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA---------------------- 278

  chrX_50775115_5    994 ACAACAACAACAAAAACAGAGACACAGACCAATGGAACAGAATAGAGAAT 1043
                         ----------i  ii i   v i i   i        i     v    i 
  L1M4_orf2#LINE/    279 ----------TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_50775115_5   1044 CCAGAAATAAATCCACACATTTACAGCCAACTCATTTTCAACAAAGGCAC 1093
                                    i   i       ii i   i v      i    i  ii 
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_50775115_5   1094 CAAGTGCATACATTGAGAGATAGGACAGTCTCTTCAATAAGTGATGTGAG 1143
                             vv   v  v  i -  v  i i     i     i  i  i  ivi 
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_50775115_5   1144 GAAAACTAGATGACCATAGGCAGAAGAATGAAACTAGACCTCCTGTCTCT 1193
                           v    i   i?   i v   i         ii i    -   ii   v
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC-CCTACCTCA 466

  chrX_50775115_5   1194 TATTACGTA-AAAAATCAACTCAAAATAAATTAAATATTTAAATCTAAGA 1242
                         i ii ii  -      i          ii  i ? v ii     v     
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_50775115_5   1243 CCTGAAAATATGAAACTAATAAAA-AAAACTTTGGAA-AAATCCTTCAGA 1290
                         v  i   v   i     vv  i  -     v v  ?i-     -   ivi
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTG 565

  chrX_50775115_5   1291 ACATTGGTCTGGGCAATGATATTTTGTGTAAGACCTCAAAAGCACAGGCA 1340
                           v    vi i       i v i  ivi  v   vi          i   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_50775115_5   1341 ACTGAAGTAAAAATAGACAAATGGAATATTATCAAGCTAAAAAGCTTCTG 1390
                           vi   v         i    v i iv i     iv v    i   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_50775115_5   1391 CACAGCAAAGGAAAC-------AAAG-----AGATAAATCATGGAATTG- 1427
                         ii vv       v  -------    -----   i  vi  ii    v -
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_50775115_5   1428 --AAAATATTTTCAAGCTTTCCATCTTACA-TGGATTTATAACCAGAATA 1474
                         --         v   iiiv vi    v i -v   i  i  v        
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_50775115_5   1475 GATAAGGATTTCAAAGAACTCTGTAGCAAAAAAAAAAAAAA---AGTTTT 1521
                         v    i  vi  vv v     vi  ii     i v   v  --- i  ?v
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_50775115_5   1522 AAAATGCGTAAAAGATCTCAATAGACATTTCTCAAAAGCATATACACAAA 1571
                               v i   i   i v              v    v v   i     
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_50775115_5   1572 TGGACAATATGTATATGAAAAAATGCTC 1599
                            v     v i i       i      
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.55 (136 / 88)
Gap_init rate = 0.02 (14 / 893), avg. gap size = 4.36 (61 / 14)  

 999 24.91 0.36 0.00  chrX_50775115_50777214     1690  1970 (130)    L1M4_orf2#LINE/L1      627   908 (0)  

  chrX_50775115_5   1690 AATTGACAAATGGGATCTAATTAAACTTAAGAGCTACTACATAGCAAAAG 1739
                            v  i    v   ii v  i   v    i i  vi iiiivv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_50775115_5   1740 AAACTATCAACAGAGTAAACAGACAACCTACAGAATGGAAGAAAATTTTT 1789
                          v        v i   i  v        i         i       v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_50775115_5   1790 GCAAACTATGCATCTGACAAAGGTCTAATATCCAGAATCTATAAGGAACT 1839
                              ii  ii      i  i  v  vi          v     i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_50775115_5   1840 TAAAGAAATTTACAAGGGAAAAACAAA-AAAAAAATTTAAAAATGGGCAA 1888
                         ivv v  v iv i  vii   i     -  vvv    ?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_50775115_5   1889 AGGACATGAATAGACACTTCTCAAAAGAAGACCTACATGCAGCCAACAAG 1938
                             iv          i     v        iv    viii     i   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_50775115_5   1939 CATATGAAAAAAAGCTCAATGTCATTGATCAT 1970
                           i       i v      ii   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (41 / 28)
Gap_init rate = 0.00 (1 / 282), avg. gap size = 1.00 (1 / 1)  


2281 24.30 2.06 8.55  chrX_50812578_50818074     4034  5004 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_50812578_5   4034 TGGAAGGACATTCCATGCTCATGAATCACAATAATTAATATAGTTAAAAT 4083
                              i  i  i     i     i  iiv  v v       v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50812578_5   4084 GACCACACTGCCCAAAGAAATCTACACACTCAGTGCAATCTTTATCAAAA 4133
                          i v i   v      vvi       v i   ii      ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50812578_5   4134 TACCAATGACATTCCTCACAGAAATAAAAAAA---ATCATAAAATTGATA 4180
                          v   iivi v  ii ii       vi v  i---   v       v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_50812578_5   4181 TGGAACCACAAAATAACCTAAATAGCCAAAACAATCTGAAATGAAAAGAA 4230
                              vii   iiv v  vi                 vi  vi i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_50812578_5   4231 CAAATCTGGAGGCATCACACTACCTGAATTCAAAACATACTACAAAGCTA 4280
                             vi      vv       v  ii v        v             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_50812578_5   4281 TAGTTACCAAAACAGCATGGTATTGGTATAAAAACAGACACATAGAGCAG 4330
                         i   v i   i    ii     i   i    ii i     i     v  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_50812578_5   4331 TGGAACAGAATAGAGAAACCAGAAATGATGCTGGGTGTAGTGGCTCATGC 4380
                              i     v    iv        i --------------i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAA--------------ACCCATAC 336

  chrX_50812578_5   4381 --CTATAATC--TCAGCACTTTGGG--AGGCTGAGCCAGGTGGATCACCT 4424
                         --i   ii  -- ii-- i   v i--   v  --   i --- i  iii
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTG--ATTTTCGACAAGGGTG--CCAAG---ACCATTC 379

  chrX_50812578_5   4425 AAGGTCAGGAATTTGAGAAACCAGAAATGAATTTATGTATTTACAGATAA 4474
                           -----------  i i  --    -------  -  v   v  - i  
  L1M4_orf2#LINE/    380 AA-----------TGGGGAA--AGAA-------TA-GTCTTTTCA-ACAA 407

  chrX_50812578_5   4475 CTGACTTTTGATGAAAGTGTCAAGAACACACATTGGGGAAAGGGCATACT 4524
                         ----------   ---   - vi i   --- i   ---------   -?
  L1M4_orf2#LINE/    408 ----------ATG---GTG-CTGGGACA---ACTGG---------ATA-K 430

  chrX_50812578_5   4525 CCTCA-ATAAATGGAAGAATGAAACTAGGCTTCTTTCTTGCACCATGTAC 4573
                           v  -ii   ----        ii i i ii  vi  ii      i   
  L1M4_orf2#LINE/    431 CCACATGCAAA----AGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_50812578_5   4574 AAATATCAACTCAACTTGAATTA-AAACTTAAGTGCAATACTCAAAACTA 4622
                            v  i       vv  i  i - i  i   i  i  v vii       
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_50812578_5   4623 TAAAACTACTAGGAGAAAACATGTGGGAAACACTTAAAGACATTGG-TTA 4671
                                vi   i         iv ? v  vv   viv   v    -   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_50812578_5   4672 GGTAAAAATTTTATGGCTAAGACTTAAAAAGCACAGTCTACTAAAATAAA 4721
                           i  vii   iv i v  v   viv         iv v  v   iv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_50812578_5   4722 AATAGACAAATGGGGTTATATTAAA-TGAAAAAAAAAGCTTCTGCACAGG 4770
                               i    v  ii vi  i   - v     -----   i  ii vvv
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAA-----CTTTTGTGCTTC 671

  chrX_50812578_5   4771 AAAGGGAAAAAAATAAACACAGTGAGGAGACAAGTTATGCAATGGGAGAA 4820
                              -- v vv  v  v v     ii      vii iiv          
  L1M4_orf2#LINE/    672 AAAGG--ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_50812578_5   4821 AGTATTTACAAATGATTCCTCTGATAAGGGACTAATAGTCAAGATATAGA 4870
                          i     i     v  viv              vi  vi  ii     v 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_50812578_5   4871 AGGAACTCTAAAAACTAAACAGCAAACAAACAAATAATCCACTTAAAAAG 4920
                          i       v v    v  i ii   v i        i   v  ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_50812578_5   4921 TGGGCAAAGAAACTGGACAGCCATTTCTCAAAAGACCAGA------AATG 4964
                                  i vi  i i  v        v     --   ------    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA--AGATATACAAATG 867

  chrX_50812578_5   4965 GCTAATAAATATGTGAAAA-ATGCTCCACATCAGGAAAATG 5004
                           i     ii ii      -      v      ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 3.55 (103 / 29)  


3295 26.22 1.00 0.55  chrX_50837491_50843809     4923  5826 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_50837491_5   4923 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4972
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50837491_5   4973 GGCCATACTGCCCAAGGTAACTTATAGATTCAATGCCATCCCCATCAAGC 5022
                            v     v     iv i ii  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50837491_5   5023 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5069
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_50837491_5   5070 ATATGGAACCAAAAAAGAGCCCGCATAGCCAAGTCAATCCTAAGCCAAAA 5119
                                 viiv  ii  v  v v        iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_50837491_5   5120 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5169
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_50837491_5   5170 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5219
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_50837491_5   5220 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5267
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_50837491_5   5268 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5317
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_50837491_5   5318 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5367
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_50837491_5   5368 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5417
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_50837491_5   5418 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5467
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_50837491_5   5468 CCTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGGCTTCATGTCTA 5517
                          v    ?i v viv   iv   v v  vvii     v  i   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_50837491_5   5518 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5567
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_50837491_5   5568 ATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5617
                           i   v v  i     i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_50837491_5   5618 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5667
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_50837491_5   5668 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5717
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_50837491_5   5718 AAAACAA----CCTCATCAAAAAGTGGGTGAAGGACATGAACAGACACTC 5763
                           i    ----  iv  i?    i    ii     iv    i     i i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_50837491_5   5764 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5813
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_50837491_5   5814 CATCACTGGCCAT 5826
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3880 16.93 4.66 3.30  chrX_50845477_50847854      998  1877 (501)    L1M4_orf2#LINE/L1        1   892 (16)  

  chrX_50845477_5    998 TGAAATGACGTTCCATGTTTGTGGATTTTGAGAC--AGTATTTTTA-GAT 1044
                           i  v  ii i       ii      vvi    -- i    v   -   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50845477_5   1045 GCCAATACTCCCCAAATTTATCTACAGATTTGACACAATACATACCAAA- 1093
                          v                v           ii  i    v v  i    -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50845477_5   1094 TTCCAGCTGAGATTTT-GCAGAGACTGAGAAGCTGATTCTGAAGTCCCTA 1142
                          i       vvv    -     i i   v        i  i  i i v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_50845477_5   1143 TGGAATTGAATATCCAAGTACTTGGTATTCAATATTAATGAAACTTGAAT 1192
                              v  ------    -----  - ii  ---------------    
  L1M4_orf2#LINE/    151 TGGAAATG------CAAG-----GG-ACCCA---------------GAAT 173

  chrX_50845477_5   1193 ACCCAAAAGGATCTTAAATATGAAGAACAAACTTGAAGGACACACACTTC 1242
                          v      vi     i  v v          v   i     v        
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_50845477_5   1243 TCAATTTCAAATCTTACCCCAAAGGTACTGTAATCAAGACTATGAAGTTC 1292
                         i          v     iv     v   v           vi  vi  v 
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_50845477_5   1293 TGGACTACAGATATACATATAGATCAGTGGAATAAAATTAA-AGTCCAAC 1341
                            vv  vi    v            i       i    i -      iv
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_50845477_5   1342 AAGAAACCCTCACATTTCTGGTCAATTGATTTTTGACAAGGGTGCTAA-- 1389
                           v      vi      v               i           i  --
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_50845477_5   1390 -TGTT-AATG---------TTGTCTTTTCAACAAATACTTCTGGAACA-- 1426
                         -ii  -    --------- v               iv v    i   --
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_50845477_5   1427 ------CCCACATGCAAAGGAATAAAATTAGACTTCTACTCCACACTATA 1470
                         ------?           i    i  i  i   ii    ii     i   
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_50845477_5   1471 TTTTAAAA---ACTCAAA-TGGATCAAAGACTTAAATATAAGAGGTAAAA 1516
                          viv    ---       -       ?    i     i      v     
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_50845477_5   1517 CTGTAAAACTCTTAGAAGAAAACA--GGTTGAAATCTTCATGACCTTGAA 1564
                           i                     --  ?vv        i        ii
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_50845477_5   1565 TTAAACCATAATTTCTTAGATATGACACCAAAAGCACAAGTAACAAAAGA 1614
                            ii v  ii                             i         
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_50845477_5   1615 AAAAGATAATTAAATTGAAAGTCATCAAAATTGAAAATGTTTTG-GCTTT 1663
                             -   iv       i vv           i    i-     -    i
  L1M4_orf2#LINE/    624 AAAA-ATAGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTC 671

  chrX_50845477_5   1664 AAAGGACACTATTAAGAAAGTGAAAAGATAACTTACAAAATATGA--AAA 1711
                                     i               i   ii   i   iv  --   
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_50845477_5   1712 TATTTGCAAGTTATATATCCAATAATGATCTAGTATCCAGAATA----AA 1757
                                  i i       ii    v iv  v            ----  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_50845477_5   1758 GATCCCTTACAACTAAATAATAAAAATACAAATAACCCAATT-AAAAATG 1806
                           v i         v           v               -       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_50845477_5   1807 GGCAAAACATCTGAATAGGCAGGTTTCCAACAAAGTTATACAAATGTCAA 1856
                               iv  i       i  vv i     vi   v          v v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_50845477_5   1857 ATAAGCACATGGAGAGATGCT 1877
                                    i i       
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.39 (85 / 61)
Gap_init rate = 0.02 (22 / 892), avg. gap size = 3.18 (70 / 22)  


2962 26.42 1.78 0.56  chrX_50937311_50943450     4751  5647 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_50937311_5   4751 TGGGAAAACATTCCATCCTCATGGACAGGAAGAATCAATATCGTGAAAAT 4800
                            i  i i  i    vi       iv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_50937311_5   4801 GGCCATACAGCCCAAAGTAATTTACAGATTCAGTGTTATTCC---CAAAC 4847
                            v    vv      v i  i          ii iv  i  ---    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_50937311_5   4848 TACCATTGACATTCTTCACAGGATTAGAAAAAACT-ATTTTAAATTTCAT 4896
                          v   vivi v  i  ii   i v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_50937311_5   4897 ATC-AAAT-CAAAGAAGACCCTGTATAGACAAGACAATCCTAAGCAAAAA 4944
                           v-    -   i --     v v    v   i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_50937311_5   4945 GAACAAAGCTGGAGACATCACGCTGCCTGACTTCAAACTATACTACAAGG 4994
                                 i     ivv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_50937311_5   4995 CTATGGAAACCAAAATGGCATGGTACTGGTATCAAAACAGACATATAGAC 5044
                            ii v  i   i ii ii         i  v ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_50937311_5   5045 CAATGGAGCAGAACAGAGACCTCAGAAATAATACCACACATCTACAACCA 5094
                                ii    iv    vii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_50937311_5   5095 TCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT-GTC 5143
                         vi    i   i    ivv  v   i v  vv            i  -   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_50937311_5   5144 CTATTCAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5193
                         i -    ii              v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_50937311_5   5194 GAACCTGGACCCCTTCCTTACACCTTATTCAAAAATTAACTCAAGATGGA 5243
                            vi         v   i     v   v               i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_50937311_5   5244 TT-TAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAAC 5292
                          i-?    i         i v i     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_50937311_5   5293 CTAGGCA-ATGTCATTCAGGACATAGGCGTGTGCAAAGACTTCATGACAA 5341
                         v    ?i- vi  -   iv   v v  vv iv    v ii   v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_50937311_5   5342 AAACACCAAAAGCAATGGCAACAAAAGCCAAATTTGA-AAATGGGATTTA 5390
                         vi            vvi          vv   v v  -    v   i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_50937311_5   5391 ATTAAACTAAAGAGCTGCTGCACAGCAAAAGAAATTATCATCAGAGTGAA 5440
                           i   v v  i i  vi  ii vv    i  v i     vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_50937311_5   5441 CAGGCAACCTACAGAATG--AGAAAATTTTGGCAGTCTACCGATCTGACA 5488
                         v  i     i        --       v  v   ivii ivv      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_50937311_5   5489 AAGTTCTAATAGCCAGAATTTACAAGGAACT--TA-AACATATTAGCAAG 5535
                          i vv  vi  v       v  i  i     --  -   vi v  ii  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_50937311_5   5536 AAAA-AAACAACCCCATCAAAAAGTGAGCAAATGATATGAACAGACACTT 5584
                           i -   i     v  i?    i  i     v   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_50937311_5   5585 CTCAAAAGAAGACATTTACGTGGCCAAGAAACATATGAAAAAAAGCTCAA 5634
                            v        i  vi vi       v  i  i       i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_50937311_5   5635 CTTCACTGATCAT 5647
                          v   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (132 / 101)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.31 (21 / 16)  


3611 22.27 0.76 2.59  chrX_50947620_50950806     1770  2694 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_50947620_5   1770 TGGAAAAATATTTCATGTTCATAGATTGGAAAAATCAATATTGTTATTGG 1819
                               i    ii         i        i v i          --i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA--AG 48

  chrX_50947620_5   1820 AAGAATTAATATTGTCCATGCCACTAAAGCAATCTACAGACTCAATGCAA 1869
                          v i--i    i -------  - i   vii         i    i    
  L1M4_orf2#LINE/     49 ATGG--CAATACT-------CC-CCAAATTGATCTACAGATTCAACGCAA 88

  chrX_50947620_5   1870 TCCCTACCAAACTACCCA--TGACATTCTTCACAGGAATAGAAAGAGC-A 1916
                               i    v -    --  v -  i  ii   i   v  v -   -i
  L1M4_orf2#LINE/     89 TCCCTATCAAAAT-CCCAGCTGCC-TTTTTTGCAGAAATTGACA-AGCTG 135

  chrX_50947620_5   1917 TTCCTAAAATTTATGTGGAACCATAAAAGACCCAGAATAGCCAAAGCTAT 1966
                         v          i  i     viii  ii                 i v  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_50947620_5   1967 CCTAAGCAAAAAGAACAAAACTGGAGGAAGCACATTACCTTACTTCAAAT 2016
                          i i iv  i         ii       vv    i v  iv i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_50947620_5   2017 TATACTACAGAGATACAGTAACCAAAAAAGCATGGTACTAGCATAAAGAC 2066
                         iv       i  v        i   i v  ii       i      i  i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_50947620_5   2067 AGACACATAGACCAATGGAACAGAATAGAGAACCCAGAAACAAGTCCACA 2116
                              i     i        i     v    ii       i  ii   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_50947620_5   2117 CACCTACAATGAACTCAGTTTTGATAAAGGTGTCAAGAACATACACTGGG 2166
                           ii  iii v  i v v   i  i  i    i     v   v  v    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_50947620_5   2167 GAAAACACAGTCTCTTCAATAAATGGTTCTGGGAAAACTGGATATCCATA 2216
                             iv i     i     i       v      v         ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_50947620_5   2217 TGCACAAGAATGAAACTAGACCCTATCTCTCTCTCTCTCCATATACAAAA 2266
                             v         ii i     -----  vi   v v            
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCC-----CTACCTCACACCATATACAAAA 480

  chrX_50947620_5   2267 ATCAAGTTAAGATGGATTGAAGACTTAAATCTAAGACCTGAAACTGTGAA 2316
                           i  v i  i      ii?    i     v     v  i     i i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_50947620_5   2317 ACTACTACAAGAAAACATTGGGAAAAATCTCCAAGATATTGGTCTGGGCA 2366
                            vi  v          v  ?iv      i iv  iv    vi i    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_50947620_5   2367 AAAATTTCTTGAACAATACCCCACAAGCACAGGCAACTAAAGCAAAAATG 2416
                          vii      ii i vv  v   v       i     v    v      i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_50947620_5   2417 GACAAATAGGATCACATCAAG-TTAAAAAGCTTCTGCACATCAAATGATA 2465
                           i    v   iiv      i-       -   i  ii v     v  i 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA 679

  chrX_50947620_5   2466 CAATCAACAATGTTAAAAGACAACCTGCCGAGTGGGAGAAAATATTTGCA 2515
                          v     v  v  v           ii v  i                  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_50947620_5   2516 AACTACCCATCTCACAAGGGATTACTAACCAGAACATATAATGAGCTCAA 2565
                           ii ivi    v i      i vv  v      i      v  i   vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_50947620_5   2566 ACAACTCTAATGGAAAAAAAAAACTAATAATCCTATCATAAAATGGGGAA 2615
                                -   --  v     i  v     i  v  i?v        v  
  L1M4_orf2#LINE/    780 ACAACTC-AAT--AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_50947620_5   2616 AAGATTTGAATAGACACTTCTC---AAAAGACATACAAATGGCAAACAGG 2662
                          i              i     --- i    i           v  i i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_50947620_5   2663 CATATGAAAAGGTGCCCAACATCACTGATCAT 2694
                           i        i   i        ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (129 / 73)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.07 (31 / 15)  


3169 27.53 0.44 0.44  chrX_51003588_51009987.rev     5002  5909 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51003588_5   5002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5051
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51003588_5   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51003588_5   5102 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51003588_5   5150 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51003588_5   5200 AACAAAGCTAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5249
                                i i    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51003588_5   5250 TACAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5299
                                 v   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51003588_5   5300 AATGGAACAGAAC--AGAGCCCTCAGAAAGAACGCCACATATCTACAACT 5347
                                i    i--    i  --     v  vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_51003588_5   5348 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5397
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51003588_5   5398 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5447
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51003588_5   5448 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5497
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51003588_5   5498 TTAAAGACTTAAACGTTAGACCTAAAACCATAAGAACCCTAGAAGAAAAC 5547
                          i ?    i    i  v   v       i    i vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51003588_5   5548 CTAGGCATTACCATTCAGGACATAGGCATGCACAAGGACTTCATGTCTAA 5597
                         v    ?i v viv   iv   v v  vv ivi   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_51003588_5   5598 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5647
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_51003588_5   5648 TTAAACTAAAGAGCTTCTTCGCAGCAAAAGAAACTACCATCAGAGTGAAC 5697
                          i   v v  i i   i vi  vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_51003588_5   5698 AGGCAACCTACAAAATGGGAGAAAATTTTCACAGCCTACTCATCTGACAA 5747
                           i     i   i             v  ii  ivii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_51003588_5   5748 ACGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5797
                         iv i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_51003588_5   5798 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5847
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_51003588_5   5848 TCAAAAGAAGACATTTATGCAGCCAAAAAACATATGAAAAAATGCTCACC 5897
                           v        i  vi viii     v  i  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_51003588_5   5898 ATCACTGGCCAT 5909
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2992 28.05 0.44 0.55  chrX_51088457_51094732.rev     4877  5785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51088457_5   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51088457_5   4927 GGCCATACTGGCCAAGGTAATTTACAGATTCCATGCCATCCCCATCAAGC 4976
                            v     vv    iv i  i         v i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51088457_5   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51088457_5   5025 TATGGAACCAAAGAAGAGTCCGCATTGCCAAGTCAATCCTGAGCCAAAAG 5074
                                viiv iii  vi v v  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51088457_5   5075 AACAAAGCTGGAGGCATGACACTACCTGACTTCAAACTATACTACAAAGC 5124
                                i      vv v     v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51088457_5   5125 TACAGTAACCAATACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                 i   v    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51088457_5   5175 AATGGAACAGAAC--AGAGTCCTCAGAAAGAACGCTGCATATCTACACCT 5222
                                i    i--       --     v  vv iii i  i  iivii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_51088457_5   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGAAAACGATTCC 5272
                          vi    i  i     ivv  vv  i v  vvv      i   vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51088457_5   5273 CTATTTAAAAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  v              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51088457_5   5323 GAAAATGGATCCCTTCCTTACGCCTTATACAAAAATCAATTCAAGATGGA 5372
                            iv    i    v   i  i  v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51088457_5   5373 TTAAAGACTTAAACGTTAGACCTAAAACCCTAAAAACCCTAGAAGAATAC 5422
                          i ?    i    i  v   v       iv     vi i        v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51088457_5   5423 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGAACTTCATGTCTAA 5472
                         v    ?i v viv   iv   v v  vv i     viii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_51088457_5   5473 AACACCAAAAGCAATGGCAACAAAAGCCCAAATTGACAAATGGGATCTAA 5522
                         i            vvi          vvv    v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_51088457_5   5523 ATAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 5572
                         vi   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_51088457_5   5573 AGGCAACCTACAGAATGGGAAAAAATTTTTGCAACCTACTCATCTGACAA 5622
                           i     i           i     v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_51088457_5   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACACGAAAA 5672
                         i  i  vi          v  i  v      vv    v iv i vv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_51088457_5   5673 AACCAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGATACTTC 5722
                          iv    i     v  i?    i     i     iv    i   i i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_51088457_5   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAACATGCTCAC 5772
                           v        i  vi viii     v  i-          v       v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCAA 895

  chrX_51088457_5   5773 CATCACTGGCCAT 5785
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (139 / 112)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3136 27.97 0.44 0.44  chrX_51107712_51113982.rev     4873  5780 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51107712_5   4873 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4922
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51107712_5   4923 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4972
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51107712_5   4973 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTGTAAAGTTCA 5020
                          v   iivi i  i  ii     -   -- v  i  - iiv    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51107712_5   5021 TATGGAACCAAAAAAGAGTCCGCATTGCCAAGTCAATCCTGAGCCAAAAG 5070
                                viiv  ii  vi v v  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51107712_5   5071 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAGCTATACTACAAGGC 5120
                                i      vv       v  ii i     iviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51107712_5   5121 TACAGTAAGCAAAACAGCACAGTACTGGTACCAAAACAGAGATATAGATC 5170
                                 v   i    iiii       i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51107712_5   5171 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5218
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_51107712_5   5219 ATCTGATCTTTGACAACCCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5268
                          vi    i  i     vvv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51107712_5   5269 CTACTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5318
                           vi i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51107712_5   5319 GAAACGGGATCTCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5368
                            iiv   i i  v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51107712_5   5369 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5418
                          i ?    i    i  v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51107712_5   5419 TTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5468
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_51107712_5   5469 AACACCAAAAGCAATGGCAACAAAAGCCCAAATTGACAAATGGAATCTAA 5518
                         i            vvi          vvv    v  i    v i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_51107712_5   5519 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5568
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_51107712_5   5569 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5618
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_51107712_5   5619 AGGGCTAATATCCAGAATCTACAATGAACTCCATCGAATTTACAAGAAAA 5668
                         i  i  vi          v  i  v      ivv i v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_51107712_5   5669 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5718
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_51107712_5   5719 TCAAAAGAAGACATTTATGCAACCAAAAAACACATGAAAAAATGCTCACC 5768
                           v        i  vi viiii    v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_51107712_5   5769 ATCACTGGCCAT 5780
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (149 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3009 26.35 2.80 1.01  chrX_51114183_51120327.rev     2797  3688 (2457)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_51114183_5   3688 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3639
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_51114183_5   3638 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCACCCTCATCCATC 3589
                            v     v     iv i  i           i  v i  ii   v vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_51114183_5   3588 TACCAATGGCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3541
                          v   iiv  i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_51114183_5   3540 TATGGAATCAAAAAAGAGCCTGCATTGCCAGGACAATCCTAAGCCAAAAA 3491
                                viiv  ii  v  v v  v    ii      i i ivv i  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_51114183_5   3490 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATTT--TACAAG 3443
                                i      vv   ii  v  ii i      -- i  --     i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAA 246

C chrX_51114183_5   3442 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 3393
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chrX_51114183_5   3392 TCAATGGAATGGAAC--AGAGCCATCAGAAAGAATACCACACATCTACAA 3345
                                   i   i--    i --      v  vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGG 344

C chrX_51114183_5   3344 CCATCTGATCTTTGACAAACCTGACAAAAACGAGAAATGGGGAAAGGATT 3295
                         i  vi    i  i     ivv  v   i v ivvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

C chrX_51114183_5   3294 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 3245
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chrX_51114183_5   3244 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 3195
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chrX_51114183_5   3194 GATGAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 3145
                            v ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chrX_51114183_5   3144 ACCTAGGCAGTA--CCATTCAGGGCATAGGCATGGGGAAGGACTTC---- 3101
                           v    ?-   --i -   iv i v v  vv i  v  v ii   ----
  L1M4_orf2#LINE/    545 ACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

C chrX_51114183_5   3100 ATGT----CTAAAA-------CAACATAAGCCAAAATTGACAAATGGGAT 3062
                           i ---- i    -------     v   vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

C chrX_51114183_5   3061 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGT 3012
                         i v  i   v v  i i   i  ii vv    i  v  i i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

C chrX_51114183_5   3011 GAACAGGCAACCTATAGAGTAGGAAATAATTTTTGCAATCTACTCATCTG 2962
                            v  i     i i   i i   i v   v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

C chrX_51114183_5   2961 ACAATGGGCTAACATCCAGAATCTACAAAGAACTCAGACAAACTTA-CAA 2913
                          i  v  i  vii         v  i         vv    -  i -i  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAA 791

C chrX_51114183_5   2912 GAAAAAAACAAACAACCCCATCAACAAGTGGGTAA-GGATATGAACAGAC 2864
                         v     i     i     v  i? v  i    i  -    v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chrX_51114183_5   2863 ACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGC 2814
                          i     v        i  vi viii     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

C chrX_51114183_5   2813 TCATCATCACTGGCCAT 2797
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (142 / 89)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.12 (34 / 16)  

2671 25.60 3.52 3.74  chrX_51114183_51120327.rev     4750  5659 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51114183_5   4750 TGGGGAAATATTCCATGTAAATAAATAGGAAGACACAATATTGTCGAGCA 4799
                            ii i    i      vv  ii  v       vi        ii  vv
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51114183_5   4800 ATCAAGTTCTTCCCAACTTGATCTATAGATTCAATGCATTTCCAATCAAA 4849
                         iv   - v  i     v        i        i   v i  v      
  L1M4_orf2#LINE/     51 GGCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_51114183_5   4850 ATCGCAGTTAGTTACTTTGTCAATATTAACAAACTGATTCTAAAGTTTAC 4899
                            v   i ivi vi    ivi v   i    i     i     i  i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_51114183_5   4900 ATAGAAAGACAAAAAATC-AGAATAGCTATGAAAGTATTGAA---GAAGA 4945
                           i    vi   iii i -        i vi v i v     ---     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_51114183_5   4946 ACAAAATTGGAGGACTCACATTACCCAACCTCAAAACTCACTATAAAGCT 4995
                              i              i v     ii        i    i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_51114183_5   4996 ACAGGAGCCAAGATAGTTTAGTATTGGCAAAAGAATAAGTAAATAGATCA 5045
                             v ii     i   v i   i     v   i   iii v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_51114183_5   5046 AGAGAATAGAATAGAGAGCCCAGAAATAGACTCATACAAATACAGATAAC 5095
                          vi         v     i         i  i      vv  ii vi  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_51114183_5   5096 CCATCTTTTACAAAAGAAGAAAGGCAATTCAATGGAGAAAGGACAGACTT 5145
                         iv  i  iv    ii vivv   i v         i     i i  v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_51114183_5   5146 CTCAACAAATGAACTGCTTG--CA--TGCAGTTCTACATGCACAAAAAAA 5191
                         i          i--    v --  --  v vv? i       -   i  v
  L1M4_orf2#LINE/    400 TTCAACAAATGG--TGCTGGGACAACTGGATAKCCACATGCA-AAAGAAT 446

  chrX_51114183_5   5192 GAATCTAGATATAGATCTTATATCTTTTATCAAAAGATCTTTTA--TCAA 5239
                            vi i  ivivv i  i i i v v  iv    ------   --    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA------TTAACTCAA 490

  chrX_51114183_5   5240 AAGATCTTACATCTTTTATCAATTACCCATGTAATTGTTAATATGTAAAA 5289
                           ------------ vv    ?vv   -----------   -      i 
  L1M4_orf2#LINE/    491 AA------------TGGATCAWAGACC-----------TAA-ATGTAAGA 516

  chrX_51114183_5   5290 CACAAAATTATAAAACTTCTAGAAGCTGGCAGGGGAGAAAATCTTGGTGA 5339
                         vvi    i         ii      vvii  vi  ? v       v    
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_51114183_5   5340 TCTTCGGTTTGACTATTATATTTTGGATATAATACCAAAATTACAATCTC 5389
                         i   v    v i v  vi v i  i     i i       vi    v vv
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_51114183_5   5390 TGAAAGAAAAAATTGATT--TCAGGCTTTATTGAAAATAAAAGCT---GC 5434
                         ii           v   v-- ii i   i  ii   v     i  --- i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_51114183_5   5435 ACTACAAAACACACTCTTAA-----TGA---------CCA--GGCTGGGA 5468
                         i  v    iv     v i  -----   ---------   -- iv     
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_51114183_5   5469 GAAAATCTTTGCAAAACACATAACCAATAAAGGACTAGTATCCAAAATAT 5518
                               v        v  i   v ii    i     v       i     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_51114183_5   5519 ACAAACAGCTCCTAAAACTCAACAATAAAAAACTAAACAACC-AACTTAA 5567
                          i   v i   i  v       i        ivi   i    -  i ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_51114183_5   5568 AAACGGGCAAAATATAGGAACAGATACCTCACCAAACAAAATGTACAGAT 5617
                            i       iv  vv   i   i ii  v     v  i  i    i  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_51114183_5   5618 AGCACATAAGCATATAAAAAGATGCTCAATGACATACGTCTT 5659
                         i  vv       i  i             iiv  ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.67 (66 / 18)  


2424 23.88 7.38 2.65  chrX_51122911_51125565.rev     1299  2165 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51122911_5   1299 TGAAGAGATAT---ATCTTAACTGGTTCAAAGACTTGATGTTATTAAGGC 1345
                           i i      ---  v  v iv i  vi       i  i  i     ii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51122911_5   1346 ATCATTTATTCCCAAATTGATGTATACATTCAATGTAATACCAGTCAATA 1395
                         iv  v vv i           v  i v      i i   v  vi    v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51122911_5   1396 TCACAGCTGGCTTTTCTTGCAAAAATTGACAAGAAAATGCTATATGAAAT 1445
                           v      v     -     i           vvi  v   ----    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTA----AAAT 145

  chrX_51122911_5   1446 ATGAAATACGAAAATGAAAAGTACCTAAATTATTCAAAACAACTCTGAAA 1495
                         vi---   i i     v  i v   i i v  vi        iii     
  L1M4_orf2#LINE/    146 TC---ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_51122911_5   1496 AAGAA---CGAAATTGAAGGACTACTACCACTTTATTTCAAATGTTTTTT 1542
                              --- i  i   i      vvi  iv iiv        v--i  vi
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA--CTTAC 240

  chrX_51122911_5   1543 TACAAAGCAACAGTAATCAAAACACCACAGTATTGATGTAAAGATTGATA 1592
                                 v           i   viiii   i  iii   i   v  i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_51122911_5   1593 AATAGATCAGTGGAACAAAATAGAAAGTGCAGA--CAAACCCAAACAGAA 1640
                         v        i     i i   v  i   v    --i       v   vvv
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_51122911_5   1641 ATGGACAACTTATTTTTTGTTTTTGCAAAGGTGCAAAAGAC-----AGTG 1685
                             v   -  iv    i -----i   i     v  -   ----- i  
  L1M4_orf2#LINE/    341 ATGGTCAA-TTGATTTTCG-----ACAAGGGTGCCAA-GACCATTCAATG 383

  chrX_51122911_5   1686 CAGAAATGGATAGACTTTCTTAAACAAA----------ATAATTGGATAT 1725
                         vi    - i    v    -- v      ---------- i  i      ?
  L1M4_orf2#LINE/    384 GGGAAA-GAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_51122911_5   1726 CCATATGCAAAA-ATTAAAGTTGGAGCCATATATCATACCATA----AAA 1770
                            i        - v i        v  v  iv   i      ----   
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_51122911_5   1771 CGCAACTCAGAATAGACCAAAGCTCTAACTGTAAAATCTAAATTTATAAA 1820
                         vvi      i   i  i  ?  vi    v     i v     vi      
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_51122911_5   1821 ATTTCTAGAAGAAATGATGGGAGAAAATCTTCATGATGTTGGTTTATGTG 1870
                          i ii         vv  i  ? v        i   iv    v   v ii
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_51122911_5   1871 AAGATATCTTAGATATGACATAAAAAGCACAATCCACAACATAACAAATT 1920
                          v i v              iv          v v    v v  v    v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_51122911_5   1921 GTTAAATTT-ATTTCACCGATAGTAAAAA-----GTGCTCCTAGAAAAAC 1964
                          v      v- i    i i v v      -----     i --i  ii  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC--AAAGGAC 678

  chrX_51122911_5   1965 AATGATAAAAGAATGGAAAAA-AAGCCACATACTGGGTAAAAACTCTTTT 2013
                          v ivi  i i i  i   i -  v     v v    - i   v v   v
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG-AGAAAATATTTG 727

  chrX_51122911_5   2014 CAAAGCATGTATCTGATAAAGTACATATATCTATAATATATAAAGAGCTC 2063
                             v   i          i v  v i    i v            i   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_51122911_5   2064 TCAAAATACAACAATAAAA---CAAACAACCAAATT-AAAAATGGGCAAA 2109
                          i v  iv   i       ---    i    v    -             
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_51122911_5   2110 TGATTTGAACAGA-------------------------TGTCAAGTAAGC 2134
                         v        i   -------------------------  v v i     
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_51122911_5   2135 ACATCAAAATATGCTCAACATCTTCAGTAAT 2165
                             v    v            v????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (109 / 95)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.62 (87 / 24)  


3174 28.19 0.22 0.22  chrX_51126510_51131439.rev     3532  4439 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51126510_5   3532 TGGAAGAACATTCCATGCTCATGGATCGGAAGAATCAATAATGTGAAAAT 3581
                              ii i  i     i        i      v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51126510_5   3582 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3631
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51126510_5   3632 TACCAATGACTTTCTTCACAGAA-CTGAAAAAAACT-ATTTTAAAGTTCA 3679
                          v   iivi i  i  ii     -i   v  i--  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_51126510_5   3680 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 3729
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51126510_5   3730 AACAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATTCTACAAGGC 3779
                                i      vv   ii  v  ii        viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51126510_5   3780 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGTTATAGACC 3829
                                 i   i    ii         i iv ii i   vv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51126510_5   3830 AGTAGAACAGAACAGAGCTCTCAGAAGTAATGCCGCATATCTACAACTAT 3879
                          i i   i    iv   vvii     i   vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_51126510_5   3880 CTGATCTTTGACAAACCCGAGAAAAACAAGCAATGGGGAAAAGATTCCCT 3929
                         i    i  i     ivvi vv  i v  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_51126510_5   3930 ATTTAATAAATGGTGCCGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3979
                         v  i  i         i    v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_51126510_5   3980 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 4029
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_51126510_5   4030 AAAGACTTACATGTTCCACCTAAAACCATAAAAACCCTAAAAGAAAACCT 4079
                          ?    i  v    vvv v       i      vi i  i        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_51126510_5   4080 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTTTAAAA 4129
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_51126510_5   4130 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 4179
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_51126510_5   4180 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAACAG 4229
                            v v  i i   i  ii vv    i  v  i i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_51126510_5   4230 GCAACCTACAGAATGGGAAAAAATTTTTGCAACCTAGTCATCTGACAAAG 4279
                         i     i           i     v       vii vvi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_51126510_5   4280 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACCAGAAAAAA 4329
                          i  vi          v  i  v      vv    v iv iv v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_51126510_5   4330 ACAAACAACCCCATGAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 4379
                              i     v  v?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_51126510_5   4380 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 4429
                         v        i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_51126510_5   4430 CACTGGCCAT 4439
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (147 / 105)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


2966 26.83 1.44 0.78  chrX_51152365_51157446     3688  4589 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51152365_5   3688 TGGAAAATCATTCCATCTTCATTGATAGGAAGAATCAATATCATGAAAAT 3737
                               ivi  i    v     v   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51152365_5   3738 GGCCATATTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 3787
                            v   i v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51152365_5   3788 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTCAT 3836
                          v   vivi v  i  ii     v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_51152365_5   3837 ATGGAATCAACAAGGTCCCATA-TAGCCAAGATGATCCTAAGCAAAAAGA 3885
                               viivv i  v    v -       i ii   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_51152365_5   3886 ATAAAGCTGGAGGCATCACGCTGCCTGACGTCAAACTATACTACAAGCCT 3935
                          i    i      vv    i  v  ii iv     viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_51152365_5   3936 ACAGTAACCAAAACAACATAGTGCTGGTACCAAAATAGACATATAGACGA 3985
                                i   i   iii i  i    i iv ii             iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_51152365_5   3986 ATGGAGCAGAACAGAGATCTCAGAAATAACACCACACATCTACCACCATC 4035
                              ii    iv    vii         vv   i    i  ivii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_51152365_5   4036 TGATCTTCGACAAACCTGACCAAAAATAG-CAATGGGGAAATGATCTCCT 4084
                             i        ivv  -    i vi v-           vi  vvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_51152365_5   4085 ATTCAGTAAATAGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 4134
                         v    ii    i         v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_51152365_5   4135 ATCTGGATCCCTTCCTTACACATTACACAAAAATTAATTCAAGATGTATT 4184
                          vi    i    v   i    vv  i           i    i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_51152365_5   4185 AAAGACTTAAATTTAAAACCTAAAACCATAAAAACCCTAGAAGAAAACCT 4234
                          ?    i     v   i v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_51152365_5   4235 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACAAAA 4283
                            ?i- v i -   iv   v v  vv i     v ii   v --- i v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT---AGAT 594

  chrX_51152365_5   4284 ATGACA---AAAGCAATTGCAATAAAAGCCAGAATTGACAAATGGGATCT 4330
                               ---      vvv    i     vv i   v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_51152365_5   4331 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCACCAGAGTGA 4380
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_51152365_5   4381 ACAGGCAACCTACAGAATGGGAAAAACAT-TTTGCAGTCTACCGATCTGA 4429
                          v  i     i           i   -  -      ivii ivv      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAA-ATATTTGCAAATCATATATCTGA 743

  chrX_51152365_5   4430 CAAAGAGTTAATATCCAGAATTTACAAGGAACTTAAACAAATTTACAAGA 4479
                         i  i iii vi          v  i  i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_51152365_5   4480 AAAA---AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATAGACAC 4526
                             ---   i     v  i?    i            v          i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_51152365_5   4527 TTCTCCAAAGAAGAAATTTATGCAGCCTACAA--ACATGAAAAAAAGCTC 4574
                                       v  vi viii   v i  --         i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_51152365_5   4575 AACATCACTGATCAT 4589
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


3151 23.63 2.91 1.23  chrX_51158693_51162694.rev     2625  3517 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51158693_5   2625 TAGAAAGACTTTCTATATTCATGGATTCCAAGACACGATGCTGTT----T 2670
                          i      iv i i  i          vv     vii  ii    ---- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51158693_5   2671 GGCAATTTTCCCCAAATTGGTCTATGGATTCAACACAATCCCCATCAAAG 2720
                               vi           i    ii        i       i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51158693_5   2721 TTCCAGCAGGACTTTTTGTAGAAAGTGACTATCCAAT--TAAAA---ATA 2765
                          i     v vvi      i     v    v v ii  --     ---   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_51158693_5   2766 TGGAAA-GCAAAAGATCTAGAATTGGCAAATCAATCTTTAAAAAGAAAAA 2814
                               -    ii  i i     v v    v       v        i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_51158693_5   2815 -ATTGTTGGAGGGTTTCTACTACACAGTTTTAAAACTT-TTATACATCTA 2862
                         - vv        ii ivi   v v  i   i       -i  i v v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_51158693_5   2863 CAGTAATCAAAACACTGTATTAACTGGCATAAGGACAGACATATAGTTCA 2912
                                   i   v   iv  -            i          v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTA-CTGGCATAAGGATAGACATATAGATCA 299

  chrX_51158693_5   2913 ATGGAATATATTTGAAAGTTCAGAAATAACCCCTTATATTTATGATTAAT 2962
                                 v v    i   i         v   v  i       i i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_51158693_5   2963 TGATTTTTTAAACAAAGAAGCCAAAGCAATTCACTGGGATAAAGAGTAGC 3012
                                i--i    i iv     ii v     v    i-     i   i
  L1M4_orf2#LINE/    350 TGATTTTC--GACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGT 396

  chrX_51158693_5   3013 CTTCTCAACAAACAGTGCTGG-ACAGTTGAACATGCACTTGGAAAAAGAC 3061
                            i        ii       -   ii  i i ?v   v  v    ii i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51158693_5   3062 CACTTTAGACATTCACCTCACACTACACA-AAAAATTAACTCTCAACAGA 3110
                         v vv  i   viii         i i i -            vv  ii  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51158693_5   3111 TTGTATCTCTAAATGTAATAGCTAAAACTATAATGCTTTTAGAAGAAAAG 3160
                          ii? vvi          v              vi  i           v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51158693_5   3161 GTAGAATCAAATCTTCATGACCTAAGGTTAGATAAAGATATCTTGCATAC 3210
                         i   i?vi        i      vi      ii  v i v    iv   i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_51158693_5   3211 AACACTAAAAACACAATCTACAAAAGAGAAAAAT-GATATGTTGTGCTTC 3259
                         i    i    i     v v        -      -    vi   vi    
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTC 645

  chrX_51158693_5   3260 ATCTACCCCATA--CTTCCAAACATCAAAAGAC--CATGAAGAAAAAAGA 3305
                            v vvii v --   iiivi v     i   --i  v      iv-  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT-GA 694

  chrX_51158693_5   3306 AGAGACAAGTCCCATACTAGT-GAAAATACATGCAAACCATAT--CTAAT 3352
                          i      vi v  v v i v-       iv      i     --  i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_51158693_5   3353 AAGGG-TTTGTATCCCAAACATATGAACAATTCTTACAACTAAATAGCAA 3401
                              -i        vi  i    i  v  i          v    ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_51158693_5   3402 AAGGTCAAATAAACCAATT-AAAAATGATCAAAACACTGTAATAAA-ATT 3449
                           i v       v      -       iv    iv i vv    i -   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_51158693_5   3450 TTAACAATGAAGATGTACAAATACTACATCCAAAAAGCATAT-AAAAGAA 3498
                          ivv   v      i       iv-----    v     i  -      v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGG-----CCAATAAGCACATGAAAAGAT 889

  chrX_51158693_5   3499 GCTCATCTTTATTTATTAG 3517
                              v v i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (122 / 86)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.61 (37 / 23)  


1486 27.61 1.39 1.39  chrX_51164089_51167060        1   431 (2541)  C L1M4_orf2#LINE/L1   (476)   432     2  

C chrX_51164089_5    431 GGAAGAACATTCCATGCTCATGGATAGGAAGACTCAATATCGTGAAAATG 382
                             ii i  i     i        v        i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

C chrX_51164089_5    381 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 332
                           v     v     iv i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

C chrX_51164089_5    331 ACCAATGACTTTCTTCACC-AAATTGGAAAAAACT-ACTTTCAAGTTCAT 284
                         v   iivi i  i  ii v-      -- v  i  - iii v  i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

C chrX_51164089_5    283 ATGGAACCAAAAAAGAGCACGCATTGCCAAGTCGGTCCTAAGCTAAAAGA 234
                               viiv  ii  v vv v  v     iv ii  i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

C chrX_51164089_5    233 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATTT--TACAAGG 186
                               i      vv   ii  v  ii i      -- i  --     i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAG 247

C chrX_51164089_5    185 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 136
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chrX_51164089_5    135 CAATGAAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 88
                              i  i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

C chrX_51164089_5     87 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAATGATTC 38
                           vi    i  i     ivv  v   i v  vv           vi  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

C chrX_51164089_5     37 CCTATTTAATAAATGGTGCTGGAAAAACTGGCTAGCC 1
                         i  v  i  i            i v      v  ?  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

Transitions / transversions = 1.81 (76 / 42)
Gap_init rate = 0.02 (7 / 431), avg. gap size = 1.71 (12 / 7)  

2725 27.28 4.34 0.68  chrX_51164089_51167060     1609  2484 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51164089_5   1609 TGGGGAAATACTCCATGTAAATAAATAGGAAGACACAATATTGTTGAGCA 1658
                            ii i   ii      vv  ii  v       vi         i  vv
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51164089_5   1659 ATCAAGTTCTTCCCAACTTGATCTATAGATTCAGTGCAATTCCAATCAAA 1708
                         iv   - v  i     v        i       ii     i  v      
  L1M4_orf2#LINE/     51 GGCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_51164089_5   1709 ATCACAGTTAGTTATTTTGTCAATATTAACAAACTGATTCTAAAGTTTAC 1758
                            v   i ivi v     ivi v   i    i     i     i  i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_51164089_5   1759 ATAGAAAGACAAAAAATC-AGAATAGCTATGAAAGTATTGAA---GGAGA 1804
                           i    vi   iii i -        i vi v i v     --- i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_51164089_5   1805 ACAAAATTGGAGGACTCACCTTACCCGACTTCAAAACTTACTATAAAGCT 1854
                              i             vi v   i i              i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_51164089_5   1855 ACAGGAGCCAAGATAGTTTAGTATTGGCAAAATAATAAGCAAATAGTTCA 1904
                             v ii     i   v i   i     v  vi   ii  v    v   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_51164089_5   1905 AGAGAATAGAATAAAGAGCCTAGAAATAGACTCATACAAATATAGATAAC 1954
                          vi         vi    i i       i  i      vv   i vi  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_51164089_5   1955 CCATCTTTTACAAAAGAAGAAAGGCAATTCAATGGAGAAAGGACAGACTT 2004
                         iv  i  iv    ii vivv   i v         i     i i  v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_51164089_5   2005 CTCAACAAATGAACTGCTTG--CA--TGCAGTTCTACATGCACAAAAAAA 2050
                         i          i--    v --  --  v vv? i       -   i  v
  L1M4_orf2#LINE/    400 TTCAACAAATGG--TGCTGGGACAACTGGATAKCCACATGCA-AAAGAAT 446

  chrX_51164089_5   2051 GAATCTGGATATAGATCTTACATCTTTTATCAAAAGTAACCCA---TGTA 2097
                            vi    ivivv i  i   i v v  iv    v    i  ---  -i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG-G 495

  chrX_51164089_5   2098 ATTG-----TTAATATGTAAAACACAAAATTATAAAACTTCTAGAAGCTG 2142
                           ii-----i   -      i vvi    i         ii      vvi
  L1M4_orf2#LINE/    496 ATCAWAGACCTAA-ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_51164089_5   2143 GCAGGGGAGAAAATCTTGGTGACATTGGGTTTGACTATTATATTTTGGGT 2192
                         i  vi  ? v       v     v       v i v  vi v i  i i 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_51164089_5   2193 ATAATACCAAAATTACAATCTCTGAAAGAAAAAATTGATT--TCAGGCTT 2240
                           i i       vi    v vvii           v   v-- ii i   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_51164089_5   2241 TACTGAAAATAAAGGCT---GCTCTACAAAACACACTCTTAA-----TGA 2282
                         i iii   v    ii  --- iv  v    iv     v i  -----   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_51164089_5   2283 CTAGGC-----------TGGGAGAAAGTCTTTGCAAAACACATAACCAAT 2321
                         vv  i -----------         i v        v  i   v ii  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_51164089_5   2322 AAAGAACTAGTATCCAAAATATACAAACAGCTCCTAAAACTCAACAATAA 2371
                           i i   v       i      i   v i   i  v       i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_51164089_5   2372 AAAACTAAACAACC-AACTTAAAAATGGGCAAAATATAGGAACAGATACC 2420
                            ivi   i    -  i ?             iv  vv   i   i ii
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_51164089_5   2421 TCACCAAACAAAATGTGCAGATAGCACATAAGCATATAAAAAGATGCTCA 2470
                           v     v  i  i i  i  i  vv       i  i            
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_51164089_5   2471 ATGACATATGTCTT 2484
                          iiv  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.75 (44 / 16)  


3283 26.87 0.55 0.55  chrX_51198530_51204906     4977  5884 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51198530_5   4977 TGGAAGACCATTCCATGCTCATGGGTAGGAAGAATCAGTATTGTGAAAAT 5026
                              iivi  i     i      i v      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51198530_5   5027 GGCTGTACTTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5076
                            vi    i     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51198530_5   5077 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 5124
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51198530_5   5125 TATGGAACCAAAAAAGAGCACGCATTGCCAAGTCGATCCTAAGCTAAAAG 5174
                                viiv  ii  v vv v  v     iv i   i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51198530_5   5175 AACAAAACTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5224
                               ii      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51198530_5   5225 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5274
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51198530_5   5275 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5322
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_51198530_5   5323 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAATGATTCC 5372
                          vi    i  i     ivv  v   i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51198530_5   5373 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5422
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51198530_5   5423 GAAACTGGATCCCTTCCTTACACCTTATACAAAAGTTAATTCAAGATGGA 5472
                            ii    i    v   i     v         i    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51198530_5   5473 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5522
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51198530_5   5523 TTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5571
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_51198530_5   5572 AAACACCAAGAGCAATGGCAACAAAAGCCCAAATTGACAAATGGGATCTA 5621
                         vi       i    vvi          vvv    v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_51198530_5   5622 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCATCATCAGAGTGAA 5671
                           i   v v  i i   i  ii vv    i  v  i    vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_51198530_5   5672 CAGGCACCCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5721
                         v  i  v  i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_51198530_5   5722 AAGGGCTAATATCCAGAATCTACAATGAACTCCATCGAATTTACAAGAAA 5771
                          i  i  vi          v  i  v      ivv i v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_51198530_5   5772 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5821
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_51198530_5   5822 CTCAAAAGAAGATGTTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5871
                            v         i vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_51198530_5   5872 CATCACTGGCCAT 5884
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1014 25.86 0.38 0.00  chrX_51206667_51211446.rev      132   394 (4386)    L1M4_orf2#LINE/L1      280   543 (365)  

  chrX_51206667_5    132 AAAAACAGACAAATTAGCCAAAGGGACACAATAGAGACCCCGAAAATAAT 181
                           ii i     v  viii   v  i i v   v    vi  ii      v
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_51206667_5    182 ACCAGACTTATATGGTCAAGTGATCTTCAACAACGGTGCCAGGAATACAC 231
                         v   v  v v         v    i   i    v       i  vi iv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_51206667_5    232 AATGGGAAAATGACGGTCTCATCAAAAAACAGTATTAGGAAAACTAGCTA 281
                               i   vi ii    iv    v   ii  ii i   v    i v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_51206667_5    282 TCCACATGCAAAAGAATGAAATTGGATC-TTATCTCACAATATGTACAAA 330
                         ?                   i     i -i  i      vi  i      
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_51206667_5    331 AATAAACTCAAAATGAATTAAAGACTTAAACGTAAGACCCCAAACTTTAA 380
                            v           i  i ?    i    i      v iv     v   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_51206667_5    381 GACTTCTAGAAGAA 394
                         i   ii        
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAA 543

Transitions / transversions = 1.64 (41 / 25)
Gap_init rate = 0.00 (1 / 264), avg. gap size = 1.00 (1 / 1)  

1586 25.20 4.03 4.23  chrX_51206667_51211446.rev     3175  3670 (1110)    L1M4_orf2#LINE/L1        1   495 (413)  

  chrX_51206667_5   3175 TGGTGAAGTACACTGTGTTAGTTGATTGGAAGGCTCAGTACAGTAAAGGC 3224
                            vi ii  iv ii    vi v         i  i i  iv  v   ii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51206667_5   3225 GTCAATTCTCCACAAACTGATCTATAGGTTTAATGTAGTTCCTATCTAAA 3274
                          v    v    v    i       i  i  i  i i i i      v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51206667_5   3275 TCCCAGC-AAAGTTCTTGCAGACATAGACAAGCTTATTCTAAAATTTGTA 3323
                                -ivvv  i       v  v        v  i        ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_51206667_5   3324 TGGAAAGACACAGGTCCTAGAATAGCTTAAATAATCTTGAAAAACAACAA 3373
                               vi  vi  v  i        iv   i            v  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_51206667_5   3374 --AAATTTGAGGAATTAC-CT-----AT-------CTGATAATAAGGCT- 3407
                         --  i  v     v i  -  -----  -------  v iv i  i   -
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_51206667_5   3408 --GTAGTCAAGACAGTGTGGTATTGGGGCAGGTATGGCTGCACAGATCAA 3455
                         --   i                i   vii i v  i viii i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_51206667_5   3456 TGAAACACAATAGAGAATCCAGAAATAGACAGACACAAATATGCTCAACT 3505
                           i  i v   v    i          i  vv i   vv    v    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_51206667_5   3506 GATTTTTGACAATGGTGG-AAGAGCAATTCAGTGGAGAAAGGATAGCTTT 3554
                               i     v    v-    v  -    i   i     i    ii  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCTT 399

  chrX_51206667_5   3555 TTCAATAAAATGGTGCTAAGGAAATTGGACATTCCTATGGGGAAAAAAAC 3604
                              i   -       ii iv  i    i ?i vi   -----------
  L1M4_orf2#LINE/    400 TTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATG----------- 437

  chrX_51206667_5   3605 CAGAAAGTAAGAAAATAAAGGCTTGATCTAAACCTAACACCTTATATAAA 3654
                         -------i  i i   i   -i v  i ivv    v     v    i   
  L1M4_orf2#LINE/    438 -------CAAAAGAATGAAG-TTGGACCCCTACCTCACACCATATACAAA 479

  chrX_51206667_5   3655 AATTAGTTGAAAGTGG 3670
                              ii v   i   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGG 495

Transitions / transversions = 1.64 (77 / 47)
Gap_init rate = 0.02 (11 / 495), avg. gap size = 3.73 (41 / 11)  

 469 19.22 13.17 9.61  chrX_51206667_51211446.rev     4009  4289 (491)    L1M4_orf2#LINE/L1      618   908 (0)  

  chrX_51206667_5   4009 AAAAAAAAACATGAGA-AAATCTGTGTGATT----CAGAACCAAAAA--- 4050
                             i    v  -   -    ---  -  i ----  i  ii     ---
  L1M4_orf2#LINE/    618 AAAAGAAAAAAT-AGATAAAT---TG-GACTTCATCAAAATTAAAAACTT 662

  chrX_51206667_5   4051 --GTTCTC---AGACCATTGTGAAGAGGATGAAAAAATAAAT-ACAGACT 4094
                         --  v  i---  iv  i i v    iii      i i  vi-     v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_51206667_5   4095 AAAAGAAAATATTTACAAGCCATATATCTAACAAAGAAATACTATTCAGA 4144
                         iii           i   ii         i i  i i v vv   i    
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_51206667_5   4145 ATACA--AATAACTCTTA-AACTCAACAGTAAAAATGTGAAATAAACAAA 4191
                            i --  v        -       i i      ---------i     
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAA---------GACAAA 803

  chrX_51206667_5   4192 TAAAAGCCAACAAAAACCCAATTAGAAAATGGGCAAAG-----------A 4230
                            -------------       ?i             ----------- 
  L1M4_orf2#LINE/    804 TAA-------------CCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_51206667_5   4231 CAT-------ACG--GCTGCACAGATGGCATATAAATACTTGAAAAGATG 4271
                            ------- v -- v ii   i     vv    ii  v          
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_51206667_5   4272 CCCAACACCATTAGCAAT 4289
                          i     i  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.53 (38 / 15)
Gap_init rate = 0.05 (15 / 291), avg. gap size = 4.27 (64 / 15)  


3172 27.57 0.78 0.22  chrX_51220350_51226492     4748  5650 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51220350_5   4748 TGGAAGAACATTCCATGCTCATGGGTAGGAGGAATCAATATCGTGAAAGT 4797
                              ii i  i     i      i v   i  v i     i  v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51220350_5   4798 GGCCATACTGCCCAAGGTAACTTACAGATTCAATGCCATCCCCATCAAGC 4847
                            v     v     iv i ii           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51220350_5   4848 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAATTCATA 4892
                          v   iivi i  i  ii     v v  v  i--- --            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_51220350_5   4893 TGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAGAA 4942
                              viiv  ii  v  viv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_51220350_5   4943 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 4992
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_51220350_5   4993 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5042
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_51220350_5   5043 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5090
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_51220350_5   5091 CTGATCTTTGACAAATCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5140
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_51220350_5   5141 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5190
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_51220350_5   5191 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5240
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_51220350_5   5241 AAAGCCTTAAACGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAACCT 5290
                          ?  v i    i  v   v  i    i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_51220350_5   5291 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5340
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_51220350_5   5341 CACCAAGAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5390
                               i    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_51220350_5   5391 CAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5440
                         v  v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_51220350_5   5441 GCAACCTACAAAATGGGAGAAAATTTTCCCAACCTACTCATCTGACAAAC 5490
                         i     i   i             v  iv   vii ivi      i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_51220350_5   5491 GGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAAAA 5540
                          i  vi          v  i  v      iv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_51220350_5   5541 ACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCTC 5590
                              i     v  i?    i    ii     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_51220350_5   5591 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5640
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_51220350_5   5641 CACTGGCCAT 5650
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.25 (9 / 4)  


2250 23.28 13.24 1.96  chrX_51231706_51234156.rev     1145  1960 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51231706_5   1145 TGGATAGTTACGTCATATTTATG---TGGAAGACTCGATTTTGTTAA--- 1188
                             v  v  ivi   i  i   ---         ii  v       ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51231706_5   1189 --------TCCCTGAACTGATCTGAAACACAGATTAAATA-AAT------ 1223
                         --------    ii  i      -----       v  ii-   ------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCT-----ACAGATTCAACGCAATCCCTAT 95

  chrX_51231706_5   1224 ----ACTCCAACAGACTATTTTGTAG-----------CTAATTCTAAATT 1258
                         ---- ii   i v v  v     i  -----------  i  i     v 
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_51231706_5   1259 TCAAATGAAATTACAAAGGATGCAAAATAGCCAAAATGACTTTTAAAAAG 1308
                            v   i  v i   i   iv  i           ii ii  v      
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_51231706_5   1309 AA---CAAATTTGGA--------------CAATTT----AC--AGTAGAA 1335
                           ---    v     --------------      ----  -- v  v  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_51231706_5   1336 AGCTACACTAATAAAGATAGTATAGTAATGGTACCAATATGGGCAAAAAT 1385
                                v    v    i   i i   v   i ----  v  ii i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCA----TAAGGATAGACAT 291

  chrX_51231706_5   1386 ATAGGCAAAAAATG-AATAGAATAGACA--TCAGCAATAGACC-ACACAT 1431
                             --- vv    -        v  v --i   v    i   - i    
  L1M4_orf2#LINE/    292 ATAG---ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_51231706_5   1432 GTATGTCCAATTGTATTTCAACAAAGGTGCAAAGGTAATTCAGTGCAAAA 1481
                         v    vi      vv    i    i     v   iiv     i  vii  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_51231706_5   1482 AGGATA-TCTCTTCAATAACTAGTGCTGGAAGAACCTGCTGTCTATA--- 1527
                           i   -   i     i  v i       i v   iv v i? i i ---
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_51231706_5   1528 -----------------CCCATGCAGCACATGCTATATAAAAATTAATT- 1559
                         -----------------   v i vv    ivv    i         i -
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_51231706_5   1560 -----GGATCACACATGTAAATGTAAAATGC-AAAGCTGTACA-CTTCTA 1602
                         -----      ? v iv         i -  -   i  i  v -  ii  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTA 537

  chrX_51231706_5   1603 GAAGAAAATATGGAA--AAATCTTTGTGACCATACAGTAGGCAACAATTT 1650
                                 i  i i?--       i      v iviv       iii   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_51231706_5   1651 CTTA--TATGAAACTCAAAAAACTTG--ATAAAAGAAAAG-T-GACAAAT 1694
                             --     v  iv   iv  vv -- i         i- -  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_51231706_5   1695 TGGAATTCATTAAAACTAAGAACTTCTGTCCTTCAAAAGACATCATTAAA 1744
                             v     i    i   i     i   v       i    ii  i  -
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA- 686

  chrX_51231706_5   1745 TGAAAG--AAAGGGTAAGCCACAGAACTAGAGGAAGTATTAGAAAATCAC 1792
                         -     --   i ii  v        ivi   i  i    v v      i
  L1M4_orf2#LINE/    687 -GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_51231706_5   1793 ATACCTAATAAAGGACTTGTATCTAGTATACATAAGAAACTATCAAAACT 1842
                            i  i    i           i  v   i    ii    v i v    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_51231706_5   1843 CAATAATAAGAGAACAAGCAATCCAATTTTTTAAATGGG-AAAAAAT--G 1889
                                  i ii    ii  i      ?vv-       -   ii  -- 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTG 834

  chrX_51231706_5   1890 AACAGATGCTTTACTTAAGAAGATATATGAATGGCAAATGAGCACATAAA 1939
                           i   iii  iv iv           ii      v   i       i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_51231706_5   1940 A---TGCTCAACATCATTAGTCAT 1960
                          ---            ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (119 / 67)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 3.88 (124 / 32)  


1337 30.49 1.63 2.00  chrX_51263394_51265963.rev      803  1353 (1217)    L1M4_orf2#LINE/L1        1   549 (359)  

  chrX_51263394_5    803 TGGAGAGAGATGTCATATATACGGACTGGAAGATTTGTAATTGTTAGAAG 852
                             i   v  vi   i vi i   i       i  ivv       --  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA--AG 48

  chrX_51263394_5    853 ATTTCAAATCCTCTGAGACTGATCTATTGTAACATCAGAATCCCAATCAA 902
                           vv   vv ii iv i i       iv vvv  v iv      v     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_51263394_5    903 AATTACAGC-ATTCACTTTGTAGATATCAACATATTGACTCGAAATTTCG 951
                            iv    -iiiivi    i   v  ii   vii   ii v   v   i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_51263394_5    952 TACTGAAGCACAAATGTGCTAGAATAG--AAAAGCCATTCTAAAAAAAGG 999
                           iv   iii   iv vv i       --    --  v   vi      i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAA--CAATCTTGAAAAAGA 196

  chrX_51263394_5   1000 AGAATGGAGTTGCAAAAGTCATAAGATGCGATTCTAAGACCTACTATAAA 1049
                             iii     v ii v   i vvviv i   ii  i  i     i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_51263394_5   1050 ACTACAGTAATCAAGACAGGGTGGCATTTAC-TAAGAATACACACACAGT 1098
                         i                  v    i i vi -    i   v   i i  v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_51263394_5   1099 TCAATGCAACAGACTAGCAAGCCCAATAATCGAACTGCAGAAATAT-TTC 1147
                               v  i   v v vi  i   iv   -i   i-  v v  v - vv
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAAT-AAACC-CATACATTTATGG 344

  chrX_51263394_5   1148 TCAACTGATCCTTGACAAAGGCACGTGCACAATACAATGGGAAAAGGATA 1197
                             i    ii i     i  ii vviv  v  v       i    i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_51263394_5   1198 GCCTTTTCAGTAAATGGTGGTGGGAGATTTCGGGC--CCATATGGAAAAA 1245
                          i       ii        v     v vi -  ii--   i   v    i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACT-GGATAKCCACATGCAAAAG 443

  chrX_51263394_5   1246 ACATTAACCTAGACCAAGAACTTACACTTTA-ACAAAAATTAACTCAAAA 1294
                          -  v  vi i    vvv v  i    iv  -                  
  L1M4_orf2#LINE/    444 A-ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_51263394_5   1295 AGGACCAAAGTCCCGTATGTAAAA-TTCAAATTATAAAGCACATGAAATA 1343
                         v   i  ?  v  iiv      i -i v   i      i v v ii  --
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA-- 540

  chrX_51263394_5   1344 TAAAAATATA 1353
                         -i    i   
  L1M4_orf2#LINE/    541 -GAAAACATA 549

Transitions / transversions = 1.35 (96 / 71)
Gap_init rate = 0.03 (14 / 549), avg. gap size = 1.43 (20 / 14)  

 768 28.17 4.39 3.62  chrX_51263394_51265963.rev     1699  2085 (485)    L1M4_orf2#LINE/L1      519   908 (0)  

  chrX_51263394_5   1699 TAGAAATATAAAACACAGGGAAGAAAACACAGGAAAAACATCAACATGTC 1748
                           i  v        v vvi          i   ?iv  -   vv i  v 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGAC 567

  chrX_51263394_5   1749 TTTGTGTTTCCTGATGGGGTTTTAGTCACAAACCCTACCACAGAGTCTGT 1798
                         i   v   vvvii    vv i    vi ii ----i    - i  iviiv
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGA----CACCA-AAAGCACAA 612

  chrX_51263394_5   1799 G-AACAAAAAGCAA------TTATTTGGAGTTTGTTAAAACTTAAAACTT 1841
                          -       iiv  ------ v v     v  ii i    i v       
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_51263394_5   1842 CTGCTGTGTGGAAG-ACATTACTGTTAAGGAAG---AAAGATAACCTAAG 1887
                         i  -  iv vi   -   i  --- i   i   ---     i    i vi
  L1M4_orf2#LINE/    663 TTG-TGCTTCAAAGGACACTA---TCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_51263394_5   1888 GACTGAAAGAAAATATTTTCAAAG-AGATATCTGAGAAAAGACTTG-ATT 1935
                           v  ii           v    v- v        v  ii      -  i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_51263394_5   1936 CCAAATATTCAAAAAACTGTGGACA-TTCAAAAACCAAACAACCACAAAT 1984
                          vi     vi   i    v v-   -i    v  iv   - i--      
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTT-ACAACTCAATAATAAAA-AG--ACAAAT 804

  chrX_51263394_5   1985 AACCCAATTTAAAAATGAGCTAAAGGTCTGAGCAGACACCTCACCAAAGA 2034
                                  ?       i  v  i i i   ii     ii  v       
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_51263394_5   2035 ---TTTGGAAGTGATAAATGAGCATGTGAAAGAATGTTTACTGTTATTTG 2081
                         --- v iv  i  iiv   i    ii     ii   i i vii i ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_51263394_5   2082 GCAT 2085
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.55 (65 / 42)
Gap_init rate = 0.04 (16 / 390), avg. gap size = 1.94 (31 / 16)  


1415 27.61 6.85 5.72  chrX_51269669_51271797      746  1636 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_51269669_5    746 ATATCGCAC--TTATGGACTGGAAGAC--AATGTCATGAAAGTAAACCGA 791
                              v  i-- i     i        --   i ii v  ii -------
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT------- 50

  chrX_51269669_5    792 AGAGAGAATTCTAATGAAAATGATTTATAGATTCAATGTGACCCCAGTGA 841
                         --- iv   v  vviv   v    i  i        i ii i   vi v 
  L1M4_orf2#LINE/     51 ---GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_51269669_5    842 AATTCCCGGCT-CTTTTTCTGAAAAGGGAAATAAATGGGCACGCCACTTC 890
                           v    i   - i    i  v i --------   v i  v  iiv i 
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGA--------AATTGACAAGCTGATCC 139

  chrX_51269669_5    891 TAAGTTCTATAAGGATGTCCAAG--ATCCAAGAAAAGCCAAGGCCTTCT- 937
                            iv ii   v   vi v    -- i   -   v      ii vv   -
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTT 188

  chrX_51269669_5    938 --AAAGCAAGAACAC-TTTTTAGAACCCTCACAGCCAGATAGCAATACCA 984
                         --   iv       v-v  vv  i  i v   vv  vi  vv   v  iv
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_51269669_5    985 ACCATAAAGGTATCATAATTAAGGAAGTGTGGTACGTGCACAGTAATAGA 1034
                           i i    v  ivi    i   iv          vv   i ivi     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_51269669_5   1035 CAAATAGACCAATAGAGCA-AAGAGAGGGTCCCACAAACACAGGTGCACA 1083
                           v     i    i  ii -  vv   i    - v   i v ---- v  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCC-AGAAATAAA----CCCA 333

  chrX_51269669_5   1084 TACATACGTATATGGTCACGCTCATTTACAAAAAATGTGCCA---CC--T 1128
                              --- -        -ii v    v i v  iv      ---  -- 
  L1M4_orf2#LINE/    334 TACAT---T-TATGGTCA-ATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_51269669_5   1129 CAATGCTCTGGAGGCAAGA-TGGTCTATTAAATAAGTGGAGCTGGACTAA 1177
                              ------i  v    - i    v  v  i  i   v     ivi  
  L1M4_orf2#LINE/    379 CAATG------GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_51269669_5   1178 TTTGGATATCCATATGGAAAAAGATTAACATTGG-CCCCTAAGTTACACC 1226
                         i -     ?   i   v    ii  v  -i    -      vv i     
  L1M4_orf2#LINE/    423 CT-GGATAKCCACATGCAAAAGAATGAA-GTTGGACCCCTACCTCACACC 470

  chrX_51269669_5   1227 ATACACAAAGATTAACTC---------CAGAGGTT---ATG-----GCT- 1258
                            i     i        ---------  ?  iii---   -----   -
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_51269669_5   1259 ----TGTACAA-------AATAATGCATAAGCATA--TCTGCATGACCTT 1295
                         ---- i  v  -------  v  vi    i ?i  --   v i       
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_51269669_5   1296 GGGGGTGAGCAAAGATATCTGAAATAGGACAC-AGAGTCACTAACGATAA 1344
                            v- ii    v i v   v i   v     - i iv   v i i i  
  L1M4_orf2#LINE/    571 GGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_51269669_5   1345 AGGAAAACATTGTTCATCTTTACGTTATCAAAAGGAAGGACCTCTGTTCA 1394
                          i     v  v v v vi vv  v i       vv  ii  i i   v v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_51269669_5   1395 TCAAAAGATGA-ATTTAGAGAATCAAAAGATAAATCTCATGATAGAAGAA 1443
                              i  iiv-  iv   i i v      i  vi v  vi  i i    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_51269669_5   1444 AGATATTTGCAATATACATATGTATATACCACAAATGTCTGATGTACAGA 1493
                          -          -  -     i v i---- i  iv v  vi i v    
  L1M4_orf2#LINE/    720 A-ATATTTGCAA-AT-CATATATCTG----ATAAGGGACTTGTATCCAGA 762

  chrX_51269669_5   1494 ATGTA---ATACCCCCTAAAA-TCAAGAGGGGAAAAGA---ATAATGCAA 1536
                           i  --- v v i i  v  -    v ivi-      ---    iv   
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATA-AAAAGACAAATAACCCAA 811

  chrX_51269669_5   1537 C-AAAACATTGGCAAAATATTTGAACAG-CACCTTCACAAAACAGGACAT 1584
                         i-?   v  v      iv       i  -  i-   v v   v i  i  
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACAT-TTCTCCAAAGAAGATAT 860

  chrX_51269669_5   1585 CCAGCGGACTAATAGACAAACAGACAAACAGCTGCTCAACCTCAGTCACC 1634
                         v  ivv i i    ---- i  v ii  v  v        v   ??????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATA----AGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_51269669_5   1635 AG 1636
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.14 (129 / 113)
Gap_init rate = 0.05 (43 / 901), avg. gap size = 2.60 (112 / 43)  


1046 26.53 7.48 6.46  chrX_51332495_51335324     1460  2341 (489)    L1M4_orf2#LINE/L1       18   908 (0)  

  chrX_51332495_5   1460 TTCTTATATAGGAA-AGTTAACATTATTAAGATG-------TC----AGC 1497
                            v iv  v    - v    i   i        -------  ---- ii
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_51332495_5   1498 TAGTTTATAAACTTAATGAAATCTTAATTAAAAATATGCCAGCAAGTTTT 1547
                          ii i  i i i i  i v    iiv  i    --- v     ---- vi
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAA---TCCCAGC----TGC 110

  chrX_51332495_5   1548 CTTTTCTCTAGAGAAAGACAAGTTGATTCTAAAGTTCCTCTTGAGG-GTG 1596
                              i vi   i vv      i    i     i   v v v  ii- ii
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_51332495_5   1597 AGGGAAACACCATGCAGGAACAGCTACAACAATCTCTGAAAAAATAATAG 1646
                              ----  ---   -  i   i v        -       i-  v i
  L1M4_orf2#LINE/    161 AGGGA----CC---CAG-AATAGCCAAAACAATCT-TGAAAAAG-AAGAA 200

  chrX_51332495_5   1647 CAGTGAGGAAAGACTAACCCAACCAGGAAT---AAAACATGCTATTAAGT 1693
                           iv vv i i    v  v vv  v--   ---     v i   iv   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCC--AATTTCAAAACTTACTACAAAGC 248

  chrX_51332495_5   1694 CTCAATAATTAAAATTGTATGGTACTGGCAC-----T-----------CC 1727
                         iv  i    i  i iv  i           i----- -----------i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51332495_5   1728 AATG-AACAGAATAGAAATGTAT-GAAATACACCCATACACATATGGAAA 1775
                             -  i     v  i -  vi-      v         iv     vv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGA-GTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_51332495_5   1776 ATTCATATATAATAAATGTGACAA---CATATAACTAGGGAACAGAAAAA 1822
                            v  v vii i  iv   v   ---   vi  - i     -    v i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAA-AGAATAG 395

  chrX_51332495_5   1823 CATTTTTAATGAATGCTGTTAGGACAATTGGGTAGCCATTTGGTAAAAGA 1872
                         iv    i  ii    v  i i      i   i  ?   iv  -i      
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGA 444

  chrX_51332495_5   1873 -TAAAATTTGATCCATAACTCG-------TAGAAAGAATAATCTCCATGT 1914
                         - i  i  v  i  v  v   i-------  v   i v   -   v vi 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA-CTCAAAAT 493

  chrX_51332495_5   1915 GGTTTAGAGATCCTCATGTAAAAAATGAAGTTCTTTAATACT---AGAAG 1961
                           v i ?   i ivv      i iv i  i--  v   v   ---     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAA--CTATAAAACTCTTAGAAG 541

  chrX_51332495_5   1962 GGAATACAGA--TAGATTCTGTAATAACCTGGGAGCGT--GGAAAGGACT 2007
                         ii  i i  i--  i  -  - vi i    v  ---  --  v  v ii 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CT-TCGTGACCTTGG---GTTAGGCAATGGTT 586

  chrX_51332495_5   2008 TCT---ATCAAGGAATCCAAATCCAGACACAATCAAATAAAAATT-GATA 2053
                            ---  -- v  vv     vv  v vi   iv   v     v -    
  L1M4_orf2#LINE/    587 TCTTAGAT--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_51332495_5   2054 AATAGCCCCTC--CAGAATAAAGAAGAAGACACATTTTG-GCCTAGCAAA 2100
                            v vv i  --  i   v  i  ------- -     -  i --    
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-------C-TTTTGTGCTT--CAAA 674

  chrX_51332495_5   2101 AAATGAAAACAAAAACAGAGAAATAAACAAATAA-AAAATAATAAATTTG 2149
                         ii iivv v   i  -  v    - i    viv - i   i-------- 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAA-AGTGAAA-AGACAACCCACAGAATG--------G 714

  chrX_51332495_5   2150 GAGAAAATATTTTCAAA--ATATATTTTAAAAAAG-CTAATATCCTCAAT 2196
                                     v    --      i v v  ii -  vi     vv   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_51332495_5   2197 AAATGTAAAGCACTCTTTAAAATCAAATAA-AAAAGGTCATA-AACCCAT 2244
                          -- i     v      vv  v    -   -    i v  v -      v
  L1M4_orf2#LINE/    765 A--TATAAAGAACTCTTACAACTCAA-TAATAAAAAGACAAATAACCCAA 811

  chrX_51332495_5   2245 TACATAAATTGGCAAAAGACCTAAACAAATAGTTTACAAAACAAGCCCAC 2294
                          v? v    v      i  ii i  i i i v  iv v   v   vi- i
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT-AT 860

  chrX_51332495_5   2295 ACAAATGGCCCTGAACTATATCAAAAGATGGTCAA-ATCTACTCATAA 2341
                                   vvv  vi i  v        v    -   v????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (122 / 109)
Gap_init rate = 0.06 (52 / 891), avg. gap size = 2.37 (123 / 52)  


1497 28.29 9.14 2.38  chrX_51382834_51384622.rev      500  1298 (491)    L1M4_orf2#LINE/L1       56   908 (0)  

  chrX_51382834_5    500 TGCTCCCTAAACTGATCTG----TTAGATGGTATCTCAATCAGAATGCCA 545
                          i     i   i      i----  vi i vv   i v    i   v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_51382834_5    546 AGAAGAATGTTTGTAGAAATTGACTAGCT----CTAAAACGTATAAGGAA 591
                         ivvivvv v    i          v    ----      ivi   v    
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_51382834_5    592 A---AAG--ACCAGGAATAACCAAGGCATTATTGAAGAAAAAGAACAAAA 636
                          ---   --   vi     i    ii  v v     i  i         i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_51382834_5    637 GTGTAAGACTCACA-TAACCA--TACATAAGGCATGTTGTGAAGTTACAT 683
                         v  v i        - vv   -- v  v  -- v ii iii   i    v
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAA--CTTACTACAAAGCTACAG 253

  chrX_51382834_5    684 TAATTAAGACAGTG--GTATTCATACAAGGATAGACA----AACCAAACT 727
                             i         --   i vii i           ----i i   -iv
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA-TG 302

  chrX_51382834_5    728 GAACAGAATTCAGAACT---ATATCAAATTATTGATTTATA--TATTTGA 772
                            i      v   iii--- v  v  vii  vv      i--i v    
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_51382834_5    773 GTTAATGAAAAGGATGGCA---CTA--CAAAAGGGAAAGAATGATCTTTT 817
                         v  v-i  v    i  v  --- i --   vi          ii      
  L1M4_orf2#LINE/    353 TTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_51382834_5    818 CAATAAGTGGTTTGGGGTTGACTGAAT-GTCACTTCAACAACAAAAAAAG 866
                            i  i    viv   vii    i  -?i   v -----i     i  v
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACAT-----GCAAAAGAAT 446

  chrX_51382834_5    867 GGCCTTTACATATACCCATAC-TGACAATATACACAAAAATCAATT---- 911
                          ivv  vi-----    v   - v   vi   i        i  i ----
  L1M4_orf2#LINE/    447 GAAGTTGG-----ACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_51382834_5    912 ACAGATTATAAACATAAATATGAAAGGTTAAACAATAACAC--------- 952
                          ii   i ? i  v     i i i  v v    v    v  ---------
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_51382834_5    953 --AGCCTAGGA--AACTATCTTCATGGCCTTGGGAAATATAAAAGTTTCC 998
                         -- i v    ?--  --      i  i       vv vii  vi     i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_51382834_5    999 TAATCAGTACAA-AGAAGCACTAACCATAAATGAAAAAAAATA-ATGAAC 1046
                           ivi vv   v- i      v i v i   -- i        -  i  i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAA--AGAAAAAATAGATAAAT 637

  chrX_51382834_5   1047 GGAATGATATTAGAATTCAGATATTCAGTTCATCAAAAGACACCATGAAG 1096
                         v i ivvi  i i    v i vv  iv  v v     i     i  v   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_51382834_5   1097 AGACTGAAGATACAAGCCAC----TGAGA-------TTTGTAATACATAT 1135
                          i v    i v    v    ----  i  -------    i  vv     
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_51382834_5   1136 ATCTGACAAAGCATTCACATCCTTAATATAGAAAGAGCTCCTATAAATCA 1185
                               i  i v i iii    vv      v     i   i  i  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_51382834_5   1186 ATAAAAAAAAGT----TAGCCCAGGAGAAAAAGTAGTCAAAAGATTTGAA 1231
                             v      v----  i    ivv?     - i v    i        
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chrX_51382834_5   1232 CAGGCA---CCTCATAAAAAATATCCAAAAGACTAACAAACTTATGGAAA 1278
                         i  i  --- ii  v i  i    v    v i i  i  i vi   i   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_51382834_5   1279 G--GTCCATCATCAGAGAAATG 1298
                          -- ii  v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (126 / 96)
Gap_init rate = 0.04 (32 / 853), avg. gap size = 2.88 (92 / 32)  


4085 18.49 3.84 0.23  chrX_51395188_51400288.rev     3751  4610 (491)    L1M4_orf2#LINE/L1       18   908 (0)  

  chrX_51395188_5   3751 TTCATTAATTGTAAGATTTAATATTGTTAAGATGGCAATACTCTCCAAAC 3800
                              vi    v    i                          i     i
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_51395188_5   3801 TGATCTATAGATTCACTGAAATTCCTATTGAAATTCTAAATACCTTCTGT 3850
                                i       vi v   i     ii    i i iv i    i v 
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_51395188_5   3851 GCAGAAACAGACAAGCTGACCCTAAAATTAATACTAAAATGGAAGTAACT 3900
                                iv          i         v   ivi     v   vi  i
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_51395188_5   3901 CAAAATGGTCAAAACACCTTTTGAAAACGTGGAACAAAGTTGGAGGAGTC 3950
                           i   i i       v- i       v vi                v  
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_51395188_5   3951 ATACTTCCCAATATCAAAACTTACTACAAGGCTTCAGTTACTAAGATTCT 4000
                          i          v                i   v    v ii    ivv 
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_51395188_5   4001 AAGGTACTAGAATAATTGTAGACATATAGACTGATG-AACAGAATTGAGA 4049
                         iv      i v    vvi            iii   -  i          
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_51395188_5   4050 GTGTAGATATAAACCCTTATATTTATGGTGAATTGACTTTTGACAAGAGT 4099
                           vi   v        v  i         v      i   i      i  
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_51395188_5   4100 GCCAAG----T--------------ATAGTCTCTCAAACAA-TGGTGCCA 4130
                               ---- --------------       i iv     -      ii
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_51395188_5   4131 GGACAACTGGATATCTATATGCAAA----TGAAACTGGACCCCTATCTCA 4176
                                      ? i i       ----    ii          i    
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_51395188_5   4177 CACCACATACAAAAATAAACTCAAAAGAGATCAAAGATTTACATGTAGAA 4226
                              i          v         vi     ?   ii  v     ii 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_51395188_5   4227 GCTAAAATTATAAAACTCACAGAAGAAAGCATAGGTGTAAATCACTGTGA 4276
                                i          vi        i      ?       vii    
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_51395188_5   4277 ACTTGA-TTAGGTAACAATTT-TTATATAAGACAC-AAAAACACAAGCTA 4323
                         v    i-     i  iii   -   v   v     -    i       v 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_51395188_5   4324 TAAAAGAAAAATTAGACAGCTTGGACTTCACTAAAATGAAAAACTTTTGT 4373
                         i          v    i iv          ii     v            
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_51395188_5   4374 ACT-CAAAAGACACTATCAAGAAAGTGAAAAGACAACCCATAAAATGGAA 4422
                         i  -    i                               i i     i 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_51395188_5   4423 GACAACAATTGAAAATCATGTATCTGTTAGGGACCTAATACCCACAATAC 4472
                           v  i v   v       i      v  i  iv  vi  i   v    i
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_51395188_5   4473 ATAAA-AAGTCATATGACTAAACAATTAAAAATATAAATAATGTAATTTA 4521
                              -  v  v  ii   v  i   -     v i      ivi    ? 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAAT-AAAAAGACAAATAACCCAATTWA 815

  chrX_51395188_5   4522 AAAA-G---AAGGGACTTGAATAGATATTTCTCTAAAGAAGATATACAAA 4567
                             - ---  i   i         i       i                
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_51395188_5   4568 TAGCCGATAAGGACATGGAAATACGTTCAACATCATTAGTCAT 4610
                          i   i     v     i   v i i         ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (100 / 55)
Gap_init rate = 0.02 (14 / 891), avg. gap size = 2.50 (35 / 14)  


2702 21.11 9.76 6.92  chrX_51439363_51441819.rev     1088  1968 (489)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_51439363_5   1088 GAAAAGTATTCTGTGTTCATGGATTGGAAGAATCAATATTGTCAAAATGT 1137
                             ii   i ii                  v i        i  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_51439363_5   1138 CCGTACTAACTAAAGCAATCTGCAGATTCAATAAAACCCCTATTAA---- 1183
                          vi    vv i   vii    i         iiv  i      i  ----
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_51439363_5   1184 -------------------------------------------------- 1183
                         --------------------------------------------------
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_51439363_5   1184 --------------------TAACTAAAAGCAATCTTGAATAAGAAGAAC 1213
                         --------------------  i i    -          v         
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAAC 201

  chrX_51439363_5   1214 AAAGTCAGAGGCATCATACTTCCTGATTTCACA--TTACGTTACAAAGCT 1261
                              ii    vv   i      ii      v --    --         
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGCT 249

  chrX_51439363_5   1262 ATAGTAATCAAAACAACATGGTACTGGCATAAAAACAGACACATAGACAA 1311
                          i         i   iii              ii i     i     iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_51439363_5   1312 ATA-AATAAAAT----AGCCCAGAAACAAATCCATGCATATACAGTCAAC 1356
                           i-    i   ----  i       i   i    i   v  ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_51439363_5   1357 TAATCTTTGACAAAGGCATCAAGAATACATAATGTGGAAAGGATAGTTTC 1406
                          i  i  i     i  iii     vi ivi    v      i     i i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_51439363_5   1407 TTCAACAAATGGTGTTGGAAAAACTGAATGTCCAT-TGCAGAAAAAAATG 1455
                                       i   i v     i  i?   i-    --   i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA--AAAGAATG 447

  chrX_51439363_5   1456 AAATTGGATCATTATCTTACACACACACACACACACACACACACTCTCTC 1505
                           i     i vi  i  i    ---------  i i   v v i -----
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACAC---------CATATACAAAAATT----- 483

  chrX_51439363_5   1506 TCTCTCTCTCTCACACCCCTCAACTCAAATTGGAAATTGGATTAGAGATT 1555
                         ---------------------        ------  -    i ?   ii
  L1M4_orf2#LINE/    484 ---------------------AACTCAAA------AT-GGATCAWAGACC 505

  chrX_51439363_5   1556 TAAATGCAAGTCCTAAAAC-ATACAACTTCTAGAAGAAAACATCGGAAAA 1604
                               i   vv       -   v    ii             v  ?iv 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_51439363_5   1605 GGTCCT--TCACATTGAACATGACAATGATTTTTTTGTTATTACACCAAA 1652
                         ii  i -- v  v   iiivv i     i   i  v v   v        
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_51439363_5   1653 AAGGCAGGTAACAAAAGCAAACATAAACAAGTGGGACTACATCAAACTAC 1702
                          ivi  i i        v   v   i i  i v     v       v vv
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_51439363_5   1703 AAAGTTTCTACACAGCAAGGGAAACAATCAACAAAATGAAAAGGCAACCC 1752
                            ii  i iii vv   i   v  v     v   i       i      
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_51439363_5   1753 ACAGATTAGGAGAAAATATACACAAACCATATATCTGATAAGGGGTTAAT 1802
                              v i           vii    i                 ii vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_51439363_5   1803 ATACAAAATATATAAGGAACTCACATAGTTAACTCAGTAGTTAAAAAAAA 1852
                           v  i         i      vi i ----     i  i ---     i
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACA----ACTCAATAAT---AAAAAG 798

  chrX_51439363_5   1853 ACACACACAAATAACCCAATTTAAAAATGGGCAAAGGACCTGAATAGACA 1902
                            ------            ?                ii          
  L1M4_orf2#LINE/    799 ACA------AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_51439363_5   1903 TTTTTTCCAAGGAAGACATACAAATGCCCAACAGGTATATTGAAAG-TGT 1951
                            i -    i     i         v    i i i i  vi    -  i
  L1M4_orf2#LINE/    843 TTTCT-CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_51439363_5   1952 TAAACATTTCTAATCTT 1968
                          v     iv????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.37 (128 / 54)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 7.74 (147 / 19)  


1688 25.60 7.37 7.97  chrX_51462145_51465021     1187  2014 (863)    L1M4_orf2#LINE/L1        1   823 (85)  

  chrX_51462145_5   1187 TGGAGAAGCACATATCGTCACATTCATGGATTGTAAGAATCAATGTAA-- 1234
                             -   ---     -i  ii           v    v i   i vi--
  L1M4_orf2#LINE/      1 TGGA-AAG---ATATC-CCATGTTCATGGATTGGAAGACTTAATATTGTT 45

  chrX_51462145_5   1235 AAAATGATATTAATTTTCCCTAAATTGATACACAGTTTAAGTGCAGTTCC 1284
                           i   ii v  ---i    i        vi    v  v ii   i i  
  L1M4_orf2#LINE/     46 AAGATGGCAATA---CTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chrX_51462145_5   1285 TATCAAAATCCCTGCAAGATGTTTTGTAGCTATAAATAAGATTATCCCAA 1334
                                     v  vivv v     i  vv  vi i   v v    i  
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_51462145_5   1335 AAT--ATATGGAAAGACAAAAGAACCAGAATAATACATAAAATAATTTTG 1382
                            --         vi   ii  v        ii---i    i   i   
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGC---CAAAACAATCTTG 189

  chrX_51462145_5   1383 AAAAAGAAAGATAAAGTGGGAGAAATCATTCTATTCAAATTTGAGACT-A 1431
                                 ii i     v    i v   iv  vii   v  ii i   - 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_51462145_5   1432 CTG----ACTATTATAATCAAGACTGTAGGAT-TTGATAGATGAACAGAC 1476
                           i----i   ivi          v  iv i -i  ii v v i i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_51462145_5   1477 ACAGAAA---ATAGAATAGAACAGAGAACTCAGAAATTGCCTCACAAAT- 1522
                          i v i ---  i        iv    iii       viv i  i v  -
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_51462145_5   1523 -ATG-CCAGCTGATTTTCGACAAAGGTACAAAAACAATTCAAAGGAAGAA 1570
                         -   -i  ii             i   i v  i  v      v  iii  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_51462145_5   1571 GGATCACCCTTTAATCACCCTGTACTGGCCTGACTGGATATCCATAGCTC 1620
                          i  vii i   v v  vviv  i    vvii        ?   i ----
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA---- 435

  chrX_51462145_5   1621 TGACACCCGCCCCCCTGCCCCCTCCCCGCTGCCAAA---TGAACTTCAGC 1667
                         -----------------------------   v   ---    v  vii 
  L1M4_orf2#LINE/    436 -----------------------------TGCAAAAGAATGAAGTTGGAC 456

  chrX_51462145_5   1668 TTAAACTTCACACCTCAT-TAAAACTTAATCTCAAA-TGGATGACAGACA 1715
                         iivv  i       vi  -i    v    -      -     v ?    v
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAA-CTCAAAATGGATCAWAGACC 505

  chrX_51462145_5   1716 TCAATGTAAAAATTAAAACCATAAAACTTTTAGAAGATATTGTAGGAGAA 1765
                          v       i ii      i        i        v vii    ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_51462145_5   1766 AATT---GTGAGGTACTAGGGCTTGTTGAAGAGTTCTTAGAAATGAAATA 1812
                            i---    v---  v   i v vii v iv        v    v iv
  L1M4_orf2#LINE/    556 AATCTTCGTGAC---CTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_51462145_5   1813 AAACCCACAATCCATAAAAGGAAAAAAAAAAACCAATAAATTGAATTTCT 1862
                            vv     v v i     ------      ivi        i i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAG------AAAAAATAGATAAATTGGACTTCA 646

  chrX_51462145_5   1863 TCAAAATT---------TCCCCTGCAAAAGTCTCTG-------------- 1889
                                 --------- viv  v    i v v  i--------------
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_51462145_5   1890 ---CAATC-------TGGGAGAAAGTATTTGCAAACCATATATCTGACAA 1929
                         ---   i -------         i          i           i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_51462145_5   1930 AAGACTCATACATAAAATACAT---GAACTCTCAATATTCAACAGTAAAA 1976
                         ii    ii  ivi i    i  ---       i vv i    i i     
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_51462145_5   1977 GAGAAAAGAAAGA-AAACAATGCAATTAAGGGTAATGGG 2014
                         ----------   -   i  iv     ? ii--      
  L1M4_orf2#LINE/    797 ----------AGACAAATAACCCAATTWAAA--AATGGG 823

Transitions / transversions = 1.54 (126 / 82)
Gap_init rate = 0.03 (28 / 823), avg. gap size = 4.54 (127 / 28)  

 412 21.21 0.00 0.00  chrX_51462145_51465021     2286  2384 (493)    L1M4_orf2#LINE/L1      810   908 (0)  

  chrX_51462145_5   2286 AATTAAAAAATAGGTAAAAGGCATGAAGAGGCATTTAATCAAAGAGGATA 2335
                             ?      i  i   i iiv    v  i     vvi      i    
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_51462145_5   2336 TATGGATGGCAGAAAAGCACATGTAAAGATGTTCAACATCATTAGCCAT 2384
                           iii     vi v         v       i         ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.00 (0 / 0)  


2030 20.04 8.82 0.20  chrX_51484602_51486569.rev      585  1083 (885)    L1M4_orf2#LINE/L1      266   807 (101)  

  chrX_51484602_5    585 TATGGTACCGGCATA------GACATATAGACCAATGAAATAGAATAGTG 628
                          i      i      ------          i     i        v v 
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_51484602_5    629 AGTCAAGAAATGAACCCTCATATATGTAGTTAAATGATCTTTGACAAGGG 678
                             v      i     vi i  v i i  i  v    i  i        
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_51484602_5    679 TGCCAAGATTACTCAATGGGGAAATGACAATCTT--CAACACATGGTGCT 726
                                 ii i            vi i i    --     v        
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_51484602_5    727 GGGAAAACTGGACATCCATCTGCAAAAAAGTAAAAT-AGACCTTT----T 771
                             v       i ?   iv       i i i  i -i    ii ----i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_51484602_5    772 ACACCATA----AAAATTAAT--AAAATAGTTTGGAGATTTAAATGTAAG 815
                                 ----        i--     i v ii?   ii          
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_51484602_5    816 ACCTAAAATTTAAAAACTCCTAGAAGTAAAGATAGA---AAATCTTCATG 862
                          v      i vv       i      v   v    i---        i  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_51484602_5    863 ACACTGGATTTGGCAAATAATTTCT-GGTTATGACACCAAAAGCA----- 906
                           vi   i  v     - ii     -i v                -----
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_51484602_5    907 ---------AAAAATAGACAAATGGGACTACATCAAA--CAAATACGTTT 945
                         ---------         i    v     v       --i   v  v   
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_51484602_5    946 GTGTATCAGAGGACAAAGTCAACACAGTGAAAAGGCAACATACAGAATGG 995
                            iv   i      vvi    v v         i    vi         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_51484602_5    996 GAGAAGATATTTGCAAAGTATATACCTAATAAGGGATTAATAAGCAGAAT 1045
                              i           vi     i  i        i vi  vv      
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_51484602_5   1046 ATATAAAAAATACT-----CTCCACAACAAAAAATTAAATAAC 1083
                                i  iv  -----   v i  i     ivi       
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

Transitions / transversions = 1.72 (62 / 36)
Gap_init rate = 0.02 (12 / 542), avg. gap size = 3.75 (45 / 12)  

 497 17.80 5.93 0.00  chrX_51484602_51486569.rev     1362  1479 (489)    L1M4_orf2#LINE/L1      784   908 (0)  

  chrX_51484602_5   1362 CTTAA-AAGAAAAACACAAGTAACCCAATTGTAAAATGGACAAAAGA--- 1407
                           i  -  v     v    i          ?v       i    i  ---
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_51484602_5   1408 ---CAGACATTTCCCCAAAGATTATATGCAAATGGCCAGCAAGCATATTG 1454
                         ---i         i       vv    i          ii     i  vi
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_51484602_5   1455 AAAGATGCTAAACATTGCTGATCAT 1479
                                  v     ii????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.02 (2 / 125), avg. gap size = 3.50 (7 / 2)  


 253 26.00 9.00 2.00  chrX_51510402_51515061        6   105 (4555)  C L1M4_orf2#LINE/L1   (546)   362   256  

C chrX_51510402_5    105 ATAAAGAAAATGTG-TACC------AAAACAGAGATATAGATCAATGGAA 63
                           v    v i    -   i------ ii i   v                
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

C chrX_51510402_5     62 CAGAAC--AGAGCCCTCAGAAAGAACGCCATGTATCTACAAGTATCTGAT 15
                         i    i--    i  --     v  vv    ii  i  iiivi vi    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGAT 353

C chrX_51510402_5     14 CTTTGACAA 6
                         i  i     
  L1M4_orf2#LINE/    354 TTTCGACAA 362

Transitions / transversions = 2.25 (18 / 8)
Gap_init rate = 0.04 (4 / 107), avg. gap size = 2.75 (11 / 4)  

 368 14.29 0.00 0.00  chrX_51510402_51515061      492   561 (4099)  C L1M4_orf2#LINE/L1   (0)   908   839  

C chrX_51510402_5    561 GACACTTCTCAAAAGAAGACATACAAGTGGCCAAAGAACATACGAAAAAA 512
                             i     v        i      i       vi i  i i     i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

C chrX_51510402_5    511 TGCTCAACATCACTATCATT 492
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.00 (8 / 2)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.00 (0 / 0)  

1867 28.49 4.52 1.92  chrX_51510402_51515061      889  1618 (3042)  C L1M4_orf2#LINE/L1   (60)   848   100  

C chrX_51510402_5   1618 ATGTCAGC-ATCTTCATTTTACAGACA---AGAAGCTGAGGCATAGACAT 1573
                           vi    -ii   --    i    v --- v       vv -  i -  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCC-TAAA-AT 145

C chrX_51510402_5   1572 ACATAT-----TGCA--TGAACTAGACAAAGCCACAG--AGCTAGTAAAC 1532
                         v     -----    --v  v i   - v     v i-- v  v v   v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGA-ATAGCCAAAACAATCTTGAAAAA 194

C chrX_51510402_5   1531 AAAATTTAAAATTTGGTCCTGGGCAGCACATTCCCCAACTTCAAACCATG 1482
                         i  ivvi   i  v i----  i -v    i i     i      v v i
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGA----GGAC-TCACACTTCCCAATTTCAAAACTTA 239

C chrX_51510402_5   1481 CTATAAGGCTACAGTAACCAAAGCAGTATGGTACTGGTACAAAAACGGAA 1432
                            i  i          i   ii    i         i i  ii ii  v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

C chrX_51510402_5   1431 ACATAAACCAATGGAAGAGAATAAAGAACCCAGAAATGAAGCTTCACACC 1382
                          i   i i        v     vi   ii        i  v ivi   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

C chrX_51510402_5   1381 CACAGCCATCTGATCTTCAACAAAGTTGACAAAAATAAGCAAGGAGGAAA 1332
                         i ii i  vi    i   i    i v  v   i vi vv   v i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

C chrX_51510402_5   1331 GAACTCTCTATTCAATAAATGGTGTTGGGATAACTGGCTAGCCATAAGCA 1282
                            ivv   v     i        i     i      v  ?   i v   
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

C chrX_51510402_5   1281 GAAGATTGAAACTGGACCCCGTTCCTTACACCATATACAAAAATCAGCTC 1232
                         i    v    ii        - v   i                 i i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTC 488

C chrX_51510402_5   1231 AAGATGGATTAAAGATTTAAATACAATACCTTAAACGATAAGAATCCTAG 1182
                           i      i ?   ii     ii  v v  v    v    i v  i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

C chrX_51510402_5   1181 AAGAAAACCTTAAAA-ACACCATTCTGGACGTTGATCTTGGGAAAGAATT 1133
                                 v vii?i- v i -   vv   v   ivi v  v  v iv  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

C chrX_51510402_5   1132 ATTGGCTAAAAGTCCTCAATAGAAATTGCAACAAAACCAAAAATTGACAA 1083
                         v  i v  vi -- vi   v  v vvv         vv      v  i  
  L1M4_orf2#LINE/    588 CTTAGATATGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

C chrX_51510402_5   1082 GTAGGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTATCA 1033
                         i v    i v  i   v v  i i   i  ii vv    i  v i     
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

C chrX_51510402_5   1032 ACGGAGTAAA----CAGCCTACAGAATAGGTGAAAGTATTCTCAAACTAT 987
                          vii   i  ----  i  i       i  v    i    iv    ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

C chrX_51510402_5    986 GCATTCAACAAATGTCTAATATCCAGAATCTACAAGGAACTTAAATAATT 937
                         ii  iii i  iv v  vi          v  i  i     ivv i  i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

C chrX_51510402_5    936 CAACAAGCAAAAAA----------AATTTAAGA-TGGGCAAAGGACATGA 898
                            i  vv    i ----------    ?  i -           iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

C chrX_51510402_5    897 A----CATTTCTC 889
                          ----        
  L1M4_orf2#LINE/    836 ATAGACATTTCTC 848

Transitions / transversions = 1.37 (118 / 86)
Gap_init rate = 0.03 (19 / 749), avg. gap size = 2.47 (47 / 19)  

2284 24.55 17.70 0.52  chrX_51510402_51515061     3396  4169 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_51510402_5   3396 GGAAATATATCCCATGTACATGGATTGGAAGAATTAATATTGTTAAAATG 3445
                              v           v              v             i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_51510402_5   3446 TCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAAT 3495
                         v v     v      vii              i                 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_51510402_5   3496 ACCAA-TGTCATCCTTCACAGAAACAGAAAAAGTAATTCTAAAATGTATA 3544
                         v   i-  i - ii  ii      iv  v  iv i  i       vi   
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_51510402_5   3545 TGGAACCAAAAAAGACCTTGAATAGCCACAGTGATTCTGAGCAAAATGAA 3594
                              viiv  ii    iv         v iii  ii   iv  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_51510402_5   3595 CAAAGCTGGAGACATCACATTATCTGACTTCAAAATATACTCCACAGGTA 3644
                              i     ivv     i vi ii i       iv    v  v  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_51510402_5   3645 ---TAACTAAAACAGCACGGTACTGGCATAAAAACAGCCACATAGACCAA 3691
                         ---   ii  i    iii             ii i  v  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_51510402_5   3692 TGTATCAGAATAGAAAACCCAGAAGTAAATCTATACATTTACAGCTAACT 3741
                           v vi     v  i ii      i    i i         ii ii  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_51510402_5   3742 CATTTTTGACAAAGACATCAAGA--------------------------- 3764
                         v     i     i iiii     ---------------------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_51510402_5   3765 ---ACAAA------------------------------------------ 3769
                         ---     ------------------------------------------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_51510402_5   3770 -------------------------------------------------- 3769
                         --------------------------------------------------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_51510402_5   3770 -GACGTAAATATCAAACCTGAAACTATGAAACTTCTAGAAAAAACACATT 3818
                         -   v     i v i v  i       i     ii     i   -    v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA-ACATA 549

  chrX_51510402_5   3819 GGGG-AAATGCTTCAGGACATTGGTCTTGGTAAAACTTTTGTG--TAGGA 3865
                           ? -    -    iv   v    vi v  i  viv   iv i--  v  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_51510402_5   3866 CCTCAAAAGCACAGGCAGCTAAAGCAAAAATAGACAAATCGAATTATGTC 3915
                          vi          i   i v    v         i    i i i vii  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_51510402_5   3916 AAG-CTAAAACCTTCTGAACAGCGAAAGACAC----AACAGATTGAAGAG 3960
                           i-i     v   i  vi vv i  i     ----  v i v    i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_51510402_5   3961 GCAACCTACAGAATGGGAGAAAATGTTTGCAAACTATTCATGTGACAAGG 4010
                         i     i                 i        ii  vi  v   i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_51510402_5   4011 GATTATTAACCAGAATATATAAGAAACTCAAAGAACTCAACAGTGAAAAA 4060
                           i vv  v             ii     vv v       i i -     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAAAA 797

  chrX_51510402_5   4061 AACAAATAATCTGATCTTAAAATAGGCAAATGATCTGAATAGACATTTCT 4110
                         i        i ii  i?v     i      v   i               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_51510402_5   4111 CAAAAGAAGACATTCAA-TGGCAAACAGATATATTAAAAG-TACTCAACA 4158
                          v        i  v   -    v  i iii i  v     - i       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_51510402_5   4159 TTGCTAATCAT 4169
                          ii????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.85 (122 / 66)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 10.07 (141 / 14)  


3212 27.23 0.55 0.44  chrX_51535749_51540529.rev     3384  4290 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51535749_5   3384 TGGAAGAACATTCCTTGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 3433
                              ii i  i  v  i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51535749_5   3434 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3483
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51535749_5   3484 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3531
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51535749_5   3532 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 3581
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51535749_5   3582 AGCAAAGCTGGATGCATCACACTACATGACTTCAAACTATACTACAAGGC 3631
                          i     i    v vv       v vii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51535749_5   3632 TACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGATGTAGATT 3681
                                 i   i    ii       v i iv ii i   v  i     i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51535749_5   3682 AATGAAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 3729
                             i  i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_51535749_5   3730 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGATTCC 3779
                          vi    i  i     ivv  v   i v  vv     i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51535749_5   3780 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3829
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51535749_5   3830 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3879
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51535749_5   3880 TTA-AGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3928
                          i -    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51535749_5   3929 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 3978
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_51535749_5   3979 AATACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGGATCTAA 4028
                         i i          vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_51535749_5   4029 TTAAACTAGAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4078
                          i   v vi i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_51535749_5   4079 AGGCAACCCACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 4128
                           i         i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_51535749_5   4129 AGGGCTAATATCCAGAATCTACAATGAACTCCATCAAATTTACAAGAAAA 4178
                         i  i  vi          v  i  v      ivv   v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_51535749_5   4179 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 4228
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_51535749_5   4229 TCGAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 4278
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_51535749_5   4279 ATCACTGGCCAT 4290
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2867 23.54 3.67 5.62  chrX_51544713_51548671     2541  3466 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51544713_5   2541 TAGAAAGATATCCTGAGTTATTGAAACAGAAGAATTAACATTGTTACAAT 2590
                          i           iiv   vv  i vii     v    i       vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51544713_5   2591 GTCCATACTACTCAAAGCAATCCGATGAAAATAAATGAAAATCCTATCAA 2640
                          v v     v i    vii   i- i- i v v  i v  vi        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCT-AC-AGATTCAACGCAATCCCTATCAA 98

  chrX_51544713_5   2641 AATTCTAATCTTATTTTTCACAGAAAATAAAAA----ATCCTAAA-TTTG 2685
                            i i iiiviv     ii      v i v  ----        -  ii
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_51544713_5   2686 CATGAAACCACGAAAGACCCTGATT--TCAAAGCAATCTTAAGAAAGACT 2733
                         i   i  vii i ii     v  v --i    i       i i     vv
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51544713_5   2734 AACAAATTTAGAGGCATCACACTTCCTA-TTTCAAGCTGTATTGCAAAGC 2782
                               v  i    vv          i -      iviv  i i      
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51544713_5   2783 TGTAGAAAGCAAAACAGCATGGTACTGGCATAAAAGCAGACACATAGAGC 2832
                          ii  v  v   i    ii              iiii     i     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51544713_5   2833 AATAGAATAGA-----GAGCCCAGAAATATACTCATCCATCTACAGTCAA 2877
                            i       -----   i         v  i   v   i  ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_51544713_5   2878 TTTATCTTTGACAAAGGTGTCAAAACCATGTCATGGGGAAAGG-----CT 2922
                           v  i  i     i    i   i     viv          i-----  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_51544713_5   2923 CTTCAATAAATTGTATTGGGAAAACTGGATATCCACAGGCAAAAAAAAAA 2972
                         i     i    v  ii     v         ?     v      i  vi 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_51544713_5   2973 AAAAAAAAAAGGACCCTTATTTTACACTACTTACAAAAATGAACTCAAAA 3022
                          ivv------      i  ii i    i iv         v         
  L1M4_orf2#LINE/    449 AGTT------GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_51544713_5   3023 TGAATTAAAGACATACATGTAACACTTGAAACCTTAAA-CTCCTACCAAA 3071
                           i  i ?    v  v      v vi i    iv    -   i  vv i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_51544713_5   3072 AAAAACAGGAAAAAGATCTCCTTGACATTGTTCTCAACAATAATTTTTTG 3121
                            v i   ?iv  -    i v    v   vvi vii    ii   i  i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_51544713_5   3122 CACATGACACCAAAAGCA---------------AAAATAAACAAGTGGGG 3156
                         v i               ---------------      i i  i v  i
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_51544713_5   3157 TTACATCAAACTAAAAAGCTTTTGCACAACAATGAAAACAATCAATAAAA 3206
                         i v       v v    i      ii vv   v i v  v     v   i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_51544713_5   3207 TGAAAATGTAACTGACAGAATGGGAGAAAATATTTGTAAACCATATACCT 3256
                               vii   iv                      i   i      i  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_51544713_5   3257 GATAAAGGGTTGATATTTGAAATTTATAAGGAAGTCCTACAACTCCTTAG 3306
                              i  ii vi   iiii   v     i   v  i        -----
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC----- 786

  chrX_51544713_5   3307 CAAAAACAAAACAAGAAAAACAAAACCCAGAAAACAACAAAAAACCCACT 3356
                         ---------  i  v     ---------------i     v      --
  L1M4_orf2#LINE/    787 ---------AATAATAAAAA---------------GACAAATAACCCA-- 810

  chrX_51544713_5   3357 CCTAATAATCCTATTAAAAATGGGCAAAGAAGCTGAATAGACATTTTTGC 3406
                         -------  ---- ?              i vi             i v 
  L1M4_orf2#LINE/    811 -------AT----TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_51544713_5   3407 AAAGAAGATATACAAATGGCCAACAGATATAATGAAAAGTTGCTCAACAT 3456
                                                i iii i -       v          
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACA-TGAAAAGATGCTCAACAT 898

  chrX_51544713_5   3457 TACTAATCAT 3466
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.71 (135 / 79)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 5.06 (86 / 17)  


2078 19.87 1.77 1.55  chrX_51567686_51577854.rev     1156  1608 (8561)    L1M4_orf2#LINE/L1        4   457 (451)  

  chrX_51567686_5   1156 AAAGA-ATCCTGTGTTTTTGGATTAGAAGACTTAATATTGTTTCAACTTC 1204
                              -    ii    iv      i                 vvi ivv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_51567686_5   1205 A-TACTACCCAAAGCAATCTATAGATGTAGTGCAATCCCTATCAAAATCC 1253
                          -    v      vii     i    vi ii                   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_51567686_5   1254 TAGTGACATTTTTTACAGAAATAGGAAAAACC-ATCTTAAAATTCATATG 1302
                         i  ivi v      i       -v  v  i i-   i             
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATG 152

  chrX_51567686_5   1303 AAATTTCAAGG-ACCCTGAATAGCCAAAACAATCTTGAAAAAGAAGAGCA 1351
                         i  v v     -    v                              i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_51567686_5   1352 AAGTTGAAGGTCTCACTTTTCCTGATTTTAAAA--TAC-ACAAAAATGCT 1398
                               i   v     vi    ii    i    --   -     ---   
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA---GCT 249

  chrX_51567686_5   1399 ACAGTAATCAAAACATTGTGGTACTGGTTCAAAGACAGACATATAGGCCA 1448
                                    i   v           ivi  i  i          ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_51567686_5   1449 ATGGAACAGAATATAGAGCCCATAAATAAACTCTTGTGTATATGGCCAAA 1498
                               i     vv    i   v        i v iii v     i   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_51567686_5   1499 TGATTTTCAACAAGAGTGCCAAGACCACATAGTGAAAAAAAAAGAACAGT 1548
                                 i     i            ivi i  iii   ---   i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA---GAATAGT 396

  chrX_51567686_5   1549 CTTTTCAACAAACACTGTTGATAAAACTGAGAACCTACATGCAAAAGAAT 1598
                                     iiv  i  iv v     iiv ? i              
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51567686_5   1599 AAAAT-GGGCC 1608
                         i  i -  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACC 457

Transitions / transversions = 1.97 (59 / 30)
Gap_init rate = 0.02 (10 / 454), avg. gap size = 1.50 (15 / 10)  

 519 16.04 0.94 0.00  chrX_51567686_51577854.rev     1761  1866 (8303)    L1M4_orf2#LINE/L1      439   545 (363)  

  chrX_51567686_5   1761 AAAAGGTTAAAGTGGAATCCTAACCTTAAGCCATATACAAAAATTAACTA 1810
                              iv i    v i i  iv    i vi                   v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_51567686_5   1811 AAAATGGATTAAAGACCTAAACATAAGACCTAAAACTATAAA-CTCTTAG 1859
                                  i ?         ii     v             -       
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_51567686_5   1860 AAGAAAA 1866
                                
  L1M4_orf2#LINE/    539 AAGAAAA 545

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.01 (1 / 107), avg. gap size = 1.00 (1 / 1)  

1214 21.40 1.05 0.35  chrX_51567686_51577854.rev     2213  2497 (7672)    L1M4_orf2#LINE/L1      542   828 (80)  

  chrX_51567686_5   2213 AAAACATAGGGAAAAAGTCTTCATGACACTGGATTTGGTAACGATTTCTT 2262
                                   ?iv   -     i    vi   i  v  i  i i      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_51567686_5   2263 ACATATGACAACAAAAGCACAGGTAACAAAAGCAAAAATAAACAATTGAG 2312
                          v        v          i i        v       i i  v vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_51567686_5   2313 ACTACATACAACTTCAAAACTTCTGTAAATCAAAGGATACAATCAATAGA 2362
                            v   vv  v  v       i   ivv        i  v     v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_51567686_5   2363 ATGGAAAGGCAATGTATGGAATGCAAGAAAATATTTTCAAATCGTA-ATC 2411
                         i  i    i   ivi ii     vi           v      i  -   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_51567686_5   2412 TGATACAGGGTTAATATCCAGAATGTATAAAGAACTTTTTCAGCTCAACA 2461
                              vi  ii vi          i           i  v  i     i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_51567686_5   2462 ACAAAAA--CAAATAACCCCATTTAAAAATAGGCAAAG 2497
                          i     --          v   ?      i       
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.46 (35 / 24)
Gap_init rate = 0.01 (3 / 287), avg. gap size = 1.33 (4 / 3)  

2424 27.43 1.78 1.31  chrX_51567686_51577854.rev     2498  3339 (6830)    L1M4_orf2#LINE/L1       63   908 (0)  

  chrX_51567686_5   2498 CAAAGCAATCTATAGATTCAATGTTATTCCTACCAAATTATCAA-TGTGA 2546
                             vii     i        i iv  i    i    v vi  i-  iv-
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC- 111

  chrX_51567686_5   2547 TTTTTCACAGGATTAGAATAAAACT-ATTCTAAAATTCATATAGAACCAC 2595
                              ii   i v v  v--  i  -  i             i   vii 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_51567686_5   2596 AAAAGAGCCTGAATAGCCAAGGCAATCCTAAGCAAAAAGAACAAAGATGG 2645
                           ii  v  v          ii     i i iv  i          v   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_51567686_5   2646 AGGCATCACATTACCGAACTTCAAACTATACTATAG-GCAATACTAACCA 2694
                            vv     i v  v  i      viv     i i-  v i v   i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_51567686_5   2695 AAACAGTAAAGTACTGGTACAAAAACAGGCACATAGACCGATGGAACAGA 2744
                          i     ivi       i i  ii i  i  i     i i      i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_51567686_5   2745 ATAGAGACCTCTGAAATAAAGCCACACACCTAAAACCAACTGATCTTTGG 2794
                           v    vii v        v   i   ii  viii   i    i  i i
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_51567686_5   2795 CAAAA-TCAAAAAAAAAAACAGTGAGGAAAGAACATGCCATTCAAAAAAT 2843
                            ii- vvv  i vv vv  i  i        i vv iv     v    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_51567686_5   2844 GGAGCTGGAAAAACTGGCTAACCACGTACAGAACAATGAACCGGGACCAC 2893
                           v     i v      v  ?    i i  i  v      viv     v 
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_51567686_5   2894 TATCTCTCACCATAC-------TTAACTTAAGATGGATTAAAGACTTAAA 2936
                           i   v       i-------      i  i      i ?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_51567686_5   2937 TGCAAGACCTTAAACTATAAAAGTCCTAGAAGAAACCCTGGG---AAATA 2983
                           i    v  v           v  i         v v i  ---    -
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT- 558

  chrX_51567686_5   2984 CCCTTCTAGACATCGGCCTAGGCAAAGAATTTATGACTAAGTTCTCAAAA 3033
                         --    vv   v i  vi       v iv  iv iiv  v vivi     
  L1M4_orf2#LINE/    559 --CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_51567686_5   3034 GCAAATGCAAATAAAACAAAAATTGACAAATGAGATCTAATTAAA-TTAA 3082
                            v v    vv   iv      v  i    vi  ii v  i   -    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_51567686_5   3083 ATAGCTTCTCCACAGCAAAAGAAACTATCAACAGAGTATACTGACAACCT 3132
                          - i   i vii vv    i  v        v i   iv vv       i
  L1M4_orf2#LINE/    657 A-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_51567686_5   3133 ATAGAATGGAATGAAGAAAATATTTGCAAACTATGCATCTGACAAAGGAC 3182
                          i       i ----               ii  ii      i  i    
  L1M4_orf2#LINE/    706 ACAGAATGGGA----GAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_51567686_5   3183 TACCATCCAGAATCTATAAGGAACTTGAACAAATCAAAAAGAGTAAAACA 3232
                          vvi         v     i     ivv    v    v  v iv  i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_51567686_5   3233 AATAACATCATTAAGAAACGAGCAAAGTACATGAACAAAAATCTCTCAAA 3282
                               viv   ? i   i i      v iv    i i v  i    v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_51567686_5   3283 AGAAGACAAAAAAGCAGCCAAAAAACATATGAAAAAATGCTCAGCAGTAA 3332
                               i v v  iii     v  i  i       i       i  vi ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_51567686_5   3333 TAATCAG 3339
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.35 (131 / 97)
Gap_init rate = 0.01 (12 / 846), avg. gap size = 2.17 (26 / 12)  

 332 19.42 5.83 0.97  chrX_51567686_51577854.rev     4036  4138 (6031)    L1M4_orf2#LINE/L1      801   908 (0)  

  chrX_51567686_5   4036 AAATAA---AATTTTAAAAACGGAAAAAGGACTTGAATAGACCTTTTTGC 4082
                               ---    ?-     i  iv      i          v   i v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_51567686_5   4083 AAAACTAAT---CAAATGGCCAAAAAGTCTACGAAAAGAAGCTGAACATT 4129
                            ivvi  ---           v   ivi i       v   v     i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_51567686_5   4130 ACTAATCAT 4138
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.03 (3 / 108), avg. gap size = 2.33 (7 / 3)  

3097 28.08 0.44 0.44  chrX_51567686_51577854.rev     8771  9678 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51567686_5   8771 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCATGAAAAT 8820
                              ii i  i     i      i v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51567686_5   8821 GGCCATACTGCCCAATGTAATTTATAGATTCAATGCCATCCCCATCAAGC 8870
                            v     v     vv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51567686_5   8871 TACCAGTGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAACGTTCA 8918
                          v    ivi i  i  ii     -   -- v  i  - iii   vi    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51567686_5   8919 TATGGAACCAAGAAAGAGCCCGCATTGCCAAGTCAATCCCAAGCCAAAAG 8968
                                viivi ii  v  v v  v     iv     iii ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51567686_5   8969 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 9018
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51567686_5   9019 TACAGTAACCAAAACAGCATGGTACTCGTACCGAAGCAGAGATATAGACC 9068
                                 i   i    ii       v i iviiiii   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51567686_5   9069 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACT 9116
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_51567686_5   9117 ATCTGTTATTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 9166
                          vi  v v  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51567686_5   9167 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 9216
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51567686_5   9217 GAAACTGAATCCGTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 9266
                            ii  i i  v v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51567686_5   9267 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 9316
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51567686_5   9317 CTAGGCATTACCATTCAGGACATAGGCATGGCCAAGGACTTCATGTCTAA 9366
                         v    ?i v viv   iv   v v  vv i v   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_51567686_5   9367 AACACCAAAAGCAGTGGCAACAAAAGCCAAAACTGACAAATGGGATCTAA 9416
                         i            vvi          vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_51567686_5   9417 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 9466
                          iv  v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_51567686_5   9467 AGGCAACCTACAGAATGGGGGAAAATTTTTGCAGCCTACTCATCTGACAA 9516
                           i     i          i      v      ivii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_51567686_5   9517 AGGGCTAATATCCAGAATCTACAATGAACTCAAACATATTTACAAGAAAA 9566
                         i  i  vi          v  i  v      vv   vv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_51567686_5   9567 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATAAACAGACACTTC 9616
                          i     i     v  i?    i            v i  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_51567686_5   9617 TCAAAGGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 9666
                           v  i     i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_51567686_5   9667 ATCACTGGCCAT 9678
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (146 / 105)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3200 27.64 0.44 0.44  chrX_51584122_51585984.rev      465  1372 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51584122_5    465 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 514
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51584122_5    515 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 564
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51584122_5    565 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 612
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51584122_5    613 TATGGAATCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 662
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51584122_5    663 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGCC 712
                                i      vv   ii  v  ii i      vivi       iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51584122_5    713 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 762
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51584122_5    763 AATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCACATATCTACAACT 810
                                i    i-- v  i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_51584122_5    811 ATCTGATCTGTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGATTCC 860
                          vi    i vi     ivv  v   i v  vv     i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51584122_5    861 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 910
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51584122_5    911 GAAACTGGATCCCTTCCTTACACCTTATACAGAAATTAATTCAAGATGGA 960
                            ii    i    v   i     v      i       i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51584122_5    961 TTAAAGACTTAAATGTTAGACCTAGAACCATGAAAACCCTAGAAGAAAAC 1010
                          i ?    i       v   v   i   i  i   vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51584122_5   1011 CTAGGCATTACCATTCAGGACATAGGCACAAGCAAGGACTTCATGTCTAA 1060
                         v    ?i v viv   iv   v v  vvi i    v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_51584122_5   1061 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1110
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_51584122_5   1111 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCACCAGAGTGAAC 1160
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_51584122_5   1161 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAGTCTACTCATCTGACAA 1210
                           i     i   i             v      ivii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_51584122_5   1211 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 1260
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_51584122_5   1261 AAACAAACAACCCCATCAAAAAGTGAGCAAAGGACATGAACAGACACTTC 1310
                          i     i     v  i?    i  i        iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_51584122_5   1311 TTAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGTTCAAC 1360
                          iv        i  vi viii     v  i          i   i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_51584122_5   1361 ATCACAGGCCAT 1372
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (152 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1553 30.02 0.20 0.20  chrX_51596815_51603216.rev        1   493 (5909)    L1M4_orf2#LINE/L1      208   700 (208)  

  chrX_51596815_5      1 GGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAAC 50
                              vv    i  v  ii i      viv        i          i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_51596815_5     51 CAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAATGAAACA 100
                            i    ii         i iv ii i   i       i     i  i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_51596815_5    101 GAACAGAGGCCTCAGAATTAATACCACACATCTACAATCATCTGATATCT 150
                            iv   ivii     v   vv   i    i  iii   vi    v ii
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_51596815_5    151 GACAACCCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAA 200
                              vvv  vv  i v  vv            i  vvi  v  i  i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_51596815_5    201 ATGCTGTTGGGAAAATTGGCTAGCCACATGCAGAAAACTGAAACTGGACT 250
                            v  i     v  i   v  ?         i  i v    ii     i
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_51596815_5    251 CCTTCCTTACACCTTATACAAAAATTAACTTGAGATAGATTAAAGACTTA 300
                            v   i     v                ii i  i   i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_51596815_5    301 AACATAAGACCTAAAGCCATAAAATTCCCAGAAGAAAACCTAGGTG-ATA 349
                           ii     v     i i      i  ii          v    ? - v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_51596815_5    350 CCATTCAGGATATAGGCATGGGCAAAGACTACATGTCCAAAACACCAAAA 399
                         i -   iv  iv v  vv i     v ii v v ivvi vi         
  L1M4_orf2#LINE/    558 TC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_51596815_5    400 GCAATGGCAACAGAAGCCAAAATTTTCTAATGGAATCTAATTAAAACAAA 449
                            vvi      i   vv     vvviv   v i ii v  i    iv  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_51596815_5    450 GAGACTCTGCACAGCAAAAGAAACTGTCATCAAAGTGAACAGGC 493
                         i ivi i  ii vv    i  v   i   vv        v  i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

Transitions / transversions = 1.34 (83 / 62)
Gap_init rate = 0.00 (2 / 493), avg. gap size = 1.00 (2 / 2)  

3047 28.16 0.33 0.66  chrX_51596815_51603216.rev     5003  5911 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_51596815_5   5003 GAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGG 5052
                            ii    i     i      i v      v i     i  v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_51596815_5   5053 CCATGCTGCCCAAGGTAATTTATAGATTCAATGCCATCACCATCAAGCTA 5102
                          v  i  v     iv i  i  i        i  v   v i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_51596815_5   5103 CCAATGACTTTCTTCACAGAATTGGAAAAATCTACTTTAAATTTCTTATG 5152
                            iivi i  i  ii     v v  v  iiiv iii    v   v    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_51596815_5   5153 GAACCAAAAAAAGGGCCT-GCATCACCAAATCAATCCTAAGCCAAAAGAA 5201
                            -- viv  i  i  i- v  vi     v     i i ivv i     
  L1M4_orf2#LINE/    153 GAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_51596815_5   5202 CAAAGCTGGAGGCATCACACTACCTGATTTCAAACTATACTACAAGCCTA 5251
                              i      vv       v  ii        viv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_51596815_5   5252 CAGTACCCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5301
                              vi   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_51596815_5   5302 TGGAACAGAAC--AGAGCCCTCAGAAATAACACTGCACATCTACTACTAT 5349
                              i    i--    i  --        vv iii    i  iviii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_51596815_5   5350 CTGATCTTTGACAAACCTGACAAAAAAACAAGCAATGGGGAAAGGATTCC 5399
                         i    i  i     ivv  v   i v--  vv            i  vvi
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGAC--CATTCAATGGGGAAAGAATAGT 396

  chrX_51596815_5   5400 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5449
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51596815_5   5450 GAAACTAGATCCCTTCCTTACACCTTATACAGAAATTAATTCAAGATGGA 5499
                            ii i  i    v   i     v      i       i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51596815_5   5500 TTAAAGACTTAAACGTTATACCTAAACCCATAAAAACCCTAGAAGAAAAC 5549
                          i ?    i    i  v v v     v i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51596815_5   5550 CTAGGCATTACCATTCAGGACAAAGGCACAGGCAAGGACTTCATGTCTAA 5599
                         v    ?i v viv   iv   vvv  vvi      v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_51596815_5   5600 AACACCAAAACCAATGGCCACAAAAGCCAAAATTGACAAATGGGATCTAA 5649
                         i         v  vvi  v       vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_51596815_5   5650 TTAAACTAAAGGGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5699
                          i   v v  iii   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_51596815_5   5700 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAAACTACTCACCTGACAA 5749
                           i     i   i             v        ii ivi i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_51596815_5   5750 AGGGTTAATATCCAGAATCCACAATGAACTCAAACAAATTTACAGGAAAA 5799
                         i  ii vi          vi i  v      vv    v iv i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_51596815_5   5800 AAACAAACAACCCCGTCAGAAAGTGGGCAAAGGACACGAACAGACACTTC 5849
                          i     i     vi i?i   i           ivi   i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_51596815_5   5850 TCAAAAGAAGACATTTATGCAGCCAAAAAGCACATGAAAAAATGCTCACC 5899
                           v        i  vi viii     v             i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_51596815_5   5900 ATCACTGGCCAT 5911
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (147 / 105)
Gap_init rate = 0.01 (5 / 906), avg. gap size = 1.80 (9 / 5)  


3456 23.32 0.88 1.43  chrX_51620488_51623917     2029  2937 (493)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_51620488_5   2029 AAGGTGTCCCTTACACATGGACGGGGAAGACTGTGTATCATTAAAATAGT 2078
                            i i    v iiv      iv  -      vvi   ii    i  i i
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGG-AAGACTTAATATTGTTAAGATGGC 53

  chrX_51620488_5   2079 AACAGTCCACAAGTGGATCTATAGATACAACATACTCACCGTTTCAAATC 2128
                           i v   v   i v      i    v    ii v  -  vv iv     
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATC-CCTATCAAAATC 102

  chrX_51620488_5   2129 CCACCAGGATCTTCTTGCCATAATTGACAATCTGATTCTGACATTCCCTT 2178
                            v v vv i  -    viv         v     i  i v    viv 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_51620488_5   2179 GGCAACGCAAGGGACCCAGAAAAGCCAAAACAATCTTGAAAAAGAG---C 2225
                           v  i               v                       i--- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_51620488_5   2226 AATGATGGAGGACTCACACGTCTCTATTTCAAAACTTACTGCAAAGCTAC 2275
                           v v              v  i v               i         
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_51620488_5   2276 AGTAATCAATGTGTTGTGGTACTGGCATAAATTTAGGCATATATATATCA 2325
                                  viiiv                ivv   -- i     v    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG--ACATATAGATCA 299

  chrX_51620488_5   2326 GTGTCATAAAAATGCAAATTTTAGAAATAAACCTCTTCTTTTAAGTTCAG 2375
                         i  vv   i  v  - i v ii           iv v v    v v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTG-AGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_51620488_5   2376 TTGATTTTCCACAAGTGTATCAAGGCAACTCAAAGTGAGAAAGAATAGCA 2425
                                  v     v  ii    i v i    v - i          iv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTC 397

  chrX_51620488_5   2426 TTTTCCACAAACGGTGCTGGGACAAATGGTTATGCCCATGGAGAAGAATG 2475
                              v     i             v   v  ?v v    v i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_51620488_5   2476 AAGT-GGACCCACCATCTCATGCCATGCCTGAAAATTAATTCAAAATGAA 2524
                             -      - i i    ii    iivii        i        i 
  L1M4_orf2#LINE/    448 AAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51620488_5   2525 TGATAGACATAAACCTAAGGGGAAAAAAACTATGTAACTTTTGGAAAAAA 2574
                          v ?    v    iv    i vv    --    iv    i  i   i   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAA--CTATAAAACTCTTAGAAGAAA 544

  chrX_51620488_5   2575 ACTTTGGGGATAACCTTCATGACCTTGAAATTGGAATTGGCTTTGTAGAT 2624
                           v v  ? vv  i    i        iiv v  v v   i  iv     
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_51620488_5   2625 ATGGTACCCATATCACGGGTGAAAAACATGAAACACAGAGGAATTGTACT 2674
                            ii   v v v   ii ii v   - vi   v i   vi     v   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAA-AGAAAAAATAGATAAATTGGACT 643

  chrX_51620488_5   2675 TCATTAAAATTAAATACTTTTGTGCTTCAAAGCCCACCATCAAGGACAGG 2724
                             i         v                 vv   i      i -  v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA-AGT 692

  chrX_51620488_5   2725 GAA--GACAACTTATGAGATGATTGAAAAGATTGGAAAATCATATATCTC 2772
                            --      ii iiii   ivv     v   v v             v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_51620488_5   2773 ATATTTGACTC-TATTTGCAATATCTACTAAACACTTACGACTGCCTAAT 2821
                            vvv    i-   iiiv     v  vvi   v     i   vvv    
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_51620488_5   2822 AAAAAAGACACACAGCCCAAAT-AAAAGTGGGCAAAGCATTGCAATAGAC 2870
                              -    v i i     v -    i         v   vv       
  L1M4_orf2#LINE/    793 AAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_51620488_5   2871 ATTTCTCTAAAGAACATGTACAAATGGCTAATAAGCTCAAGAAAAGATGC 2920
                                i      v  i          i       v  v          
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_51620488_5   2921 TCAGTGTCATTAGTCAT 2937
                            iii   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.95 (102 / 107)
Gap_init rate = 0.02 (16 / 904), avg. gap size = 1.31 (21 / 16)  


 977 24.22 3.13 3.13  chrX_51648229_51652349.rev      169   519 (3602)  C L1M4_orf2#LINE/L1   (0)   908   558  

C chrX_51648229_5    519 TCTTCATCTTTTTGGTTTTGGCAAAGATTTTCAAAATGAGACACCCAAAC 470
                              i vvii    v  v     v i   iiv i  iv      v   v
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

C chrX_51648229_5    469 CACAAACTATAAAAGAAGAAAAATTAATACATTTGATTCCACCACAATTA 420
                              i v i       --     vi   v   v  i i  i  v     
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAA--AAAATAGATAAATTGGACTTCATCAAAATTA 655

C chrX_51648229_5    419 AAG-TTTTTGGCCTTTAAAAGGCATTCTTTTGAAATTGAAAGAGA-AATC 372
                           i-i     vv   i   i i  i v ivv    v     -   -  i 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA-AGACAACC 704

C chrX_51648229_5    371 CACACTCTGTGATAAAATATTTAGAATTCATATATCTATATCCAACACAG 322
                             vvv  v  v         iv  v          i------ i vi 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTG------ATAAGG 748

C chrX_51648229_5    321 GAC--ACTTCTAGACTATA--AAGAAGTCTTATAACTCAATTATAAGAAG 276
                            --iiv  i   v    --     v     i        v    i   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

C chrX_51648229_5    275 GCAAATA-CTCAACTATAAATATGGAGAAAAGACTTCAACAGACTACCTC 227
                         i      - i   i ?v   -    iv   i  i  v  i    - ii  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAGAC-ATTTC 846

C chrX_51648229_5    226 ACCAAAGAAGATACACAGATGGCTAACAACCACACAAAAAGATAC----C 181
                         v            i   i     i  i  v    ii       i ---- 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chrX_51648229_5    180 ATCATTTATCAT 169
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (47 / 37)
Gap_init rate = 0.03 (11 / 351), avg. gap size = 2.00 (22 / 11)  

2474 27.26 4.69 3.24  chrX_51648229_51652349.rev     2736  3630 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51648229_5   2736 TGGAAAAACATCCCATGCTCATGGATAGGAAGAACCAATATCATTAAAGT 2785
                               i i        i        v      vii     ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51648229_5   2786 GGCTACACTGCCTAAAGCAATTTATAGATTCAATGCTATTCCCATCGAAC 2835
                            v i   v  i   vii  i  i        i  v  i  i   i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51648229_5   2836 TACCAAGGACATTCTTCACAGAGCTAGAAACAATTATTTAAAAATGTACA 2885
                          v   ivvi v  i  ii    iv v  v viv v  iiv     vi i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_51648229_5   2886 TGGAACCAGAAAAGGAGCCCGGATAGCCAAGGCAATCGT----------- 2924
                              vi- v  i   v  v i        ii     v -----------
  L1M4_orf2#LINE/    151 TGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_51648229_5   2925 ---AAGCTAAAAGA---------------------ACTATACTGCAAGGC 2950
                         ---   i ii i  ---------------------   -    i   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_51648229_5   2951 TACAATGACCAAAACAGCATGGTACTGGTACTGGCACAAAAACAGGCACA 3000
                             i i i   i    --  ----           i  ii i  i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAG--TG----TGGTACTGGCATAAGGATAGACATA 292

  chrX_51648229_5   3001 TAGACCAATGGAACAGAATAGAGAGGCCATAAATAATGTCGCACATCTAC 3050
                             i        i     v     v   v      vvi ii    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_51648229_5   3051 AACCAGCTTTTTTCTTTTTTTTTTTTTTTGACAAAGCTGACAAAAACAAG 3100
                         iii  i--------------  vv    i     i v  v   i v  vv
  L1M4_orf2#LINE/    343 GGTCAA--------------TTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_51648229_5   3101 CGGTGGGAAAAAGAC--TCCATATTCTATCAATGGTGCTGTGATAACTGG 3148
                          ii    i   ii i--  -- v   v iv          v  i      
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_51648229_5   3149 CTAGCCGTATGCAGAGGATTGAAGCTGGACCCCTTCCTTACACTATCTAC 3198
                         v  ?  ii     i i  v     i         v   i    i  v   
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_51648229_5   3199 AAAAATCCACATGAGATGGATTAAAGGCTTTAATGTAAAACCCAACACCA 3248
                               iv  vii i      i ?  i i v       i v i  v  i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_51648229_5   3249 TAAAAACCCTGGAAGACAACCTAGGCA-ATACCATCCTGGACATAGGAGC 3297
                              vi i i     v   v    ?i- v i v  v  -  v v  ivi
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTT 575

  chrX_51648229_5   3298 AGGCAAAGATCTCAC-GACAGAGGCACCAAAAGCAATCA--CAGCAAGAG 3344
                               v i i  vi-  i v- i           --  --  i   i  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATAT-GACACCAAAAGCA--CAAGCAACAAAAG 622

  chrX_51648229_5   3345 TAAAAATTGACACATGGGATCTAATTAAACTTAGAG-CTTCTGCACAGCA 3393
                         v      v  i v  v   ii v  i   v   i i-   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_51648229_5   3394 AAAGAAACTATCAACAGAGTAAACAGACAACCTACAAAGTGGGAGAAAAT 3443
                           i  v        v i   i  v        i   i i           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_51648229_5   3444 TTTTGCAACACTATTCATCTAACAGAGGTCTGATATCCAGCATCTATAAA 3493
                         v       - ii  vi    i i ii  v  vi       v  v      
  L1M4_orf2#LINE/    723 ATTTGCAA-ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_51648229_5   3494 AAGCCTAAACAAATGCACAAGAGAAAAACAAACAACCCCATTAATAAGGG 3543
                         i i iivv    v vv i  v i   i     i     v   ? v  iv 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_51648229_5   3544 GGCAAATGACATGAACAGACACTTCTCAAAAGAAGACATACATGTAGCCA 3593
                               v  iv    i     i     v        i     vi i    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_51648229_5   3594 AGAAGTATATGAAAAACAGCTCAATATCACTGATCAT 3630
                          v   i i       ivv      i    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.18 (71 / 17)  


2784 26.95 2.12 1.00  chrX_51659616_51665184.rev     4188  5085 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51659616_5   4188 TGGAAAT-CATTCCATGGGCATGGATAGAAAGAATCAATATTGTGAAAAT 4236
                               v-i  i     vv       v i    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51659616_5   4237 GGCCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCCATTAAAC 4286
                            v     v      vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51659616_5   4287 TACTATTGATATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 4335
                          v i viviiv  i  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_51659616_5   4336 ATGGAACCAAAAAAGAGTCTGAAGAGCCAAGGCAATCTTAAGCAAAAAGA 4385
                               viiv  ii  vi v   v      ii       i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_51659616_5   4386 ACAAAGCTGGAGATAACACGCTACCCGACTTCAAACTATACTACAAGGCA 4435
                               i     ivvv   i  v   i i      viv        i  v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_51659616_5   4436 GTAGTAACCAAACCAGCATGGTACTGGTACAAGAACAGACACATAGACCA 4485
                         ii     i   iv   ii         i i   i i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_51659616_5   4486 ATGGAACAGAATAGGGAACCCGGAAAGGAGACCACACACCTA----CACC 4531
                               i     v i  ii  i    vi iv   i   ii  ----  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_51659616_5   4532 TTATTTTCAACAAACCTGACCAAAAAAAAGCAATGGGGAGAGAAT--TCC 4579
                          v      i    ivv  -    i vv vv         i     --  -
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chrX_51659616_5   4580 ATATTTAATAAATGATGCTGGGAGAACAGGCTAGCCATATGTGGAAAACT 4629
                         - v  i  i     i        v   v  v  ?   i   iii  i v 
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51659616_5   4630 GACACTGGACCCCTTCCTTATACCATATACAAAAATCAACTCCAGTTGGA 4679
                           vii         v   i i               i     v iv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51659616_5   4680 TTAAATACTTAAATGTAAAACCCAAAACTATAAAAAA--TAGAAGAAAAC 4727
                          i ? v  i         i v i            vv--           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51659616_5   4728 CTAG---TCAATCTCATTCAGGACACAGGCACAAGCAAAGATTTCAT-GA 4773
                         v   --- v     ---  iv   viv  vvi i    v i    v -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCT---TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_51659616_5   4774 TAAAGACAACCAAAAGAAATTGCAATAAATACAAAAATTGACAAACGAGA 4823
                           v-    -       v vvv    i   viv      v  i   ivi  
  L1M4_orf2#LINE/    594 TAT-GACA-CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_51659616_5   4824 TCTAATTAAACTAAAGAGCTTCTGCACTGCAAAAGAAATTGTGAACAGAG 4873
                         ii v  i   v v  i i   i  ii  v    i  v i i v  v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_51659616_5   4874 TAAACAGACAACCTACAGAATGGGAGAAAATTTTTGTAAACTATGCATCT 4923
                          i  v        i                 v    i   ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_51659616_5   4924 TACAAAGGTCTAATACCCATTATCTATAAGAAACT--TA-AATTTA-CAA 4969
                         v i  i  v  vi  i   vv  v     ii    --  -  i i -i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_51659616_5   4970 GAAAAAAACAAACAACCCCATTAAAAAGTGAGCAACGGACATGAACAGCC 5019
                         v     i     i     v   ?    i  i    v   iv    i  v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_51659616_5   5020 ACTTCTTAAAAGAAGACGTGCATGTGGCCAACAATCATATTTAAAAA-GC 5068
                          i    iv        ii i  vi       i  v  i  vv   i -  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_51659616_5   5069 TCCACATAACTAATCAT 5085
                           v    v ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (138 / 101)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.65 (28 / 17)  


1690 27.31 5.52 1.49  chrX_51666145_51669087     1272  1941 (1002)    L1M4_orf2#LINE/L1        1   697 (211)  

  chrX_51666145_5   1272 TGGAGAAATTAGCTGTATTCTTAGATTTGTAGACTTAATGTTGTTAAGGT 1321
                             i i  vvv ii i   v i    v v         i        i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51666145_5   1322 ATCAATTTTCTCCAAATTGTTTTATACATTTAATTCAATCACAGTTAAAA 1371
                         iv    vi  i        v i  i v   i  iv     v vi i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51666145_5   1372 CCCCAGAAGGCTTTTTCCATAGAAATTGACAAGGTTATTATAAAATTTAT 1421
                         i     vv v      i-ii             v v  iv       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_51666145_5   1422 CTGATAGTGCAAATGCCTTACAATATAAGAAACAATTTTGACAA----GA 1467
                         v  iv i     iv v ii v    vvvi       i    v  ----  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_51666145_5   1468 GCAAA-TTAAAGAACTTACACTATATGACTTCAAGAGTTATTACAAAGTA 1516
                         i    -  ii  i   i     vivii i     i v   i       iv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_51666145_5   1517 GTAGTAATTAAAACCATGAAATATTG-----AGG-------TATAAAT-- 1552
                         ii      i  i  vi  vii  i  -----   -------    i  --
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_51666145_5   1553 ---GAACAGAAGTAA-AGTT----AATAAAGATACACATAGAAGTTCAAT 1594
                         ---   i    v i -   i----      vvi i    vv v v     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_51666145_5   1595 CAATTTTTGACAAAGTTGACAA-----TTCAATAAATAAAAAATA---TT 1636
                         ii     i     i v  v   -----      iiiv   i    ---  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_51666145_5   1637 TTCAATAAATACTATGAATACAATTGGATTACTATTAACAACATAGTAAA 1686
                              i    iv iiviiv    i     v? i ivvi   v v i i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_51666145_5   1687 TTTCAATCACTACTTCATACAATATACAAAAAGTAACTGAAAA-GGATTA 1735
                         v  vi i v    i   i  v           v     v    -    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_51666145_5   1736 TAAACCTAAATTTAAAAACTAAAACTATAAA-TTATTAGAAGAAAATGTA 1784
                         ? i        v   i i             -i v           ----
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA---- 545

  chrX_51666145_5   1785 AGACATAGAGAAAAGATCTTATTGACATTGTGTTTAGCAATGATTTCTTA 1834
                         ---     i?iv  -     vv    v   v   vi      i       
  L1M4_orf2#LINE/    546 ---CATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_51666145_5   1835 AGTCAGACACAAAAAGAGCAAACTATATAAGAACAATATCAATAAATTGA 1884
                         ii vv     v     vi   i v i v     v  -  vi        i
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGG 640

  chrX_51666145_5   1885 ACTTAATCAAAATTAAAATCATTTGGCTTTCAAAATACACTATTAAGAAA 1934
                             v             v v    vvi      iv       i      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_51666145_5   1935 GTAAAAA 1941
                           i    
  L1M4_orf2#LINE/    691 GTGAAAA 697

Transitions / transversions = 1.25 (100 / 80)
Gap_init rate = 0.02 (15 / 697), avg. gap size = 3.13 (47 / 15)  

 524 25.33 6.11 0.00  chrX_51666145_51669087     2223  2451 (492)    L1M4_orf2#LINE/L1      666   908 (0)  

  chrX_51666145_5   2223 TGTCTCAAAAAAAAAAA--AAGTAAGTAAAAATGCAATTTAAAGAGTATT 2270
                           ii     ii v vv --   v    i    vi   iii v   i ivv
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_51666145_5   2271 A-AAAATACTTGTAGA-CATACATATGATA-----CTTGTATCTAGAATG 2313
                          -      i   i i -    i  v     -----        i     i
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_51666145_5   2314 TGTAGA-AACCTTCACAATTCAAACATAAGAATACAAAACATGCAAT--A 2360
                          i  i -   ii i    i    vv    i  v     vv iv    -- 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_51666145_5   2361 AAAATAGGGAAAATATTTGAAGAGACACTTC-ACAATGCAGATAAACTGA 2409
                              i  v   iv       v     i   -v   v v     v  vi 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_51666145_5   2410 AGGCAAATCAG-ATATGAAAATATGCTCAACATCTTTAGTTAT 2451
                         v   v   v  - i       v            v????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.07 (30 / 28)
Gap_init rate = 0.03 (8 / 243), avg. gap size = 1.75 (14 / 8)  


3008 27.31 0.88 0.88  chrX_51676956_51683381.rev     5028  5935 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51676956_5   5028 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATACTGTGAAAAT 5077
                               i i  i     i      i v      v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51676956_5   5078 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5127
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51676956_5   5128 TACCAAGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5175
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51676956_5   5176 TATGGAACCAAAAAAAGCCCCCA-TCGCCAAGTCAATCCTAAGCCAAAAG 5224
                                viiv  iiii   vv - v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51676956_5   5225 AACACAGCCAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5274
                             v  iii    vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51676956_5   5275 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATCTATAGATC 5324
                           i     i   i    ii         i iv ii i   iv        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51676956_5   5325 AATGGAACAGAAT--AGAGTCCTCAGAAATAATGCTGCATATCTACAACC 5372
                                i     --       --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_51676956_5   5373 ATCTGATCTTTGACAAATCTGAAAAAAAAAAAGCAATGGGGAAAGGAT-- 5420
                          vi    i  i     ivv  vv  i vv v-v            i  --
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAG 395

  chrX_51676956_5   5421 TCCGTATTTATTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5470
                           -- v  i vi              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_51676956_5   5471 GCTGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGAT 5520
                         iv    ii    i    v   i     v  i           i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_51676956_5   5521 GGATGAAAGACTTATATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5570
                             v ?    i  v    v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_51676956_5   5571 AACCTAGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCATGT 5619
                            v    ?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_51676956_5   5620 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5669
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_51676956_5   5670 CTAATTCAACTAAAGAGCTTCTTCACAGCAAAAGAAACCACCATCAGAGT 5719
                         i v  iv  v v  i i   i vii vv    i  v  i i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_51676956_5   5720 GAACAGGCAACGTACAGAATGGGAGGAAATTTTCACAACCTACTCATCTG 5769
                            v  i    vi            i    v  ii   vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_51676956_5   5770 ACAAACGGCTATTATCCAGAATCTACAATGAACTCAAACATATTTACAAG 5819
                          i  iv i  vv          v  i  v      vv   vv iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_51676956_5   5820 AAAAAAACAAACAACCCCATGAAAAAGTGGGCAAAGGATATGAACAGACA 5869
                              i     i     v  v?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_51676956_5   5870 CTTCTCAAAAGAAGACGTTTATGCAGCCAAAAGACACATGAAAAAATGCT 5919
                         i     v        ii vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_51676956_5   5920 CATCATCACTGGCCAT 5935
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3106 27.64 0.55 0.55  chrX_51686755_51693150     4996  5903 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51686755_5   4996 TGGAAGAACCTTCCATGCTCATGGATAGGAATAACCAATATCTTGAAAAT 5045
                              ii iv i     i        v    v vii     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51686755_5   5046 GGCCATACTGCCCAAAGTAGTTTATAGATTCAATGCTATGCTCATCAAGC 5095
                            v     v      v ii i  i        i  v  v ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51686755_5   5096 TACCATTGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   vivi i  i  ii    i-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51686755_5   5144 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAAG 5193
                                viiv  ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51686755_5   5194 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCAA--TACTACAAG 5241
                                i      vv    i  v  ii i     --  --        i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAA--AACTTACTACAAA 246

  chrX_51686755_5   5242 ACTACAGTAACAAAAGCAGCATGGCACTGGTGCCAAAACAGATATATAGA 5291
                         i         iv  ii   ii   i     iiiv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_51686755_5   5292 CCAATGAAACAGAACAGAGGCCTCAGAAATAATGCCACACATCCACAACC 5341
                         i     i  i    iv   ivii         vv   i    ii iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_51686755_5   5342 ATCTGATCTTTGACAAGCCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5391
                          vi    i  i      vv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51686755_5   5392 CTATTTAATAAATGGTGTTGGACAAACGGGCTAGCCACATGGAGAAAACT 5441
                           v  i  i        i   ivv   v  v  ?       v i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51686755_5   5442 GAAACTGGGTCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGG 5491
                            ii   ii    v   i     v                   i    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51686755_5   5492 TTAAAGACTTAAACATAAAACCTAAAACCATAAAAACCCTAGAGGAAAAC 5541
                          i ?    i    ii   i v       i      vi i    i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51686755_5   5542 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5590
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_51686755_5   5591 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5640
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_51686755_5   5641 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5690
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_51686755_5   5691 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTCTCTATCTGACG 5740
                         v  i     i                 v       viiv v       ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_51686755_5   5741 AAGGACTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5790
                          i     vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_51686755_5   5791 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATACGAACAGACACTT 5840
                           i     i     v  i?    i            vi   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_51686755_5   5841 CTCAAAAGAAGACATTTATGCAGCCAAAACACATATGAAAAAATGCGCAT 5890
                            v        i  vi viii     v vi  i       i    v  v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_51686755_5   5891 CATCACTGGTCAT 5903
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3217 26.79 0.66 0.55  chrX_51694782_51701194     5014  5920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51694782_5   5014 TGGAAGAACATTCCCTGCTCATGGATAGGAAGGATCAATATCATGAAAAT 5063
                              ii i  i  v  i        v     iv i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51694782_5   5064 GGCCATACTACTCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 5113
                            v     v i   iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51694782_5   5114 TACCAATGACTTTTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5161
                          v   iivi i     ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51694782_5   5162 CATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTGAGCCAAAAG 5211
                         i      viiv  ii  v  v v  v     i      i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51694782_5   5212 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACCACAAGGC 5261
                                i      vv    i  v  ii i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51694782_5   5262 TACAGTAACCAAAACAGCATGGTACTGGTACCAA-ACAGAGATATAGACC 5310
                                 i   i    ii         i iv i- i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51694782_5   5311 AATGAAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5358
                             i  i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_51694782_5   5359 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5408
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51694782_5   5409 CTATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGTAGAAAGCT 5458
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51694782_5   5459 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5508
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51694782_5   5509 TGAAAGACTTAAATGTTAGACCTAAAGCCATAAAAACCCTGGAAGAAAAC 5558
                          v ?    i       v   v     i i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51694782_5   5559 CTAGGCA-ATACCATTCAAGACATAGGCACGGGCAAGGACTTCATGTCTA 5607
                         v    ?i- v i -   iv   v v  vvii     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_51694782_5   5608 AAACACCAAAAGCAATGGGAACGAAAGCCAAAATTGACAAATGGGATCTA 5657
                         vi            vvi v   i    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_51694782_5   5658 ATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCAAAAGAGTGAA 5707
                           i   v v  i i   i   i vv    i  v    i   i i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_51694782_5   5708 CAGGCAACCTACAGAATGGGAGAAAACTTTTGCAATCTACCCATCTGACA 5757
                         v  i     i                iv       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_51694782_5   5758 AATGGCTAATATCCAGAATCTACAATGAACTTAAACAAATTTACAAGAAA 5807
                          iv i  vi          v  i  v     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_51694782_5   5808 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5857
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_51694782_5   5858 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5907
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_51694782_5   5908 CATCACTGGCCAT 5920
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2671 25.59 3.93 2.02  chrX_51703618_51709420     4427  5317 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51703618_5   4427 TGGAGAAATATTCCATGCTTATGGATTAGAAGATTCAATATTGTTAAATT 4476
                             i i    i     i i       i     i i           iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51703618_5   4477 TGCCATATTGCCCCAAGCAATTTGCAGGTTCAGTGCTATTGCTATCAAAC 4526
                         v  v   i v   v  vii  i i   i    ii  v  iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51703618_5   4527 TGCCAATGACATTTT--GCACTTAATTAGGAAAAAATGATTCTAAAATTC 4574
                          v   iivi v    --   vv-    --  v  iv    i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATT--GACAAGCTGATCCTAAAATTC 147

  chrX_51703618_5   4575 ATATGGAAC--CAA-------AAAAGAGCCAAT-TAGTCCTAAGCAAAAA 4614
                                 v--   ------- i  v      v-i i  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_51703618_5   4615 GAGCAATGTTACAGGCATCACACCACCCAACCTCAAACTATACTACGAGG 4664
                           i   v   iv   vv      iv     ii     viv      i i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_51703618_5   4665 CTACAGTAACCAAAACAGCATGTTTCTGGTCCAAA-ACAGACACATAGAT 4713
                                  i   i    ii  v v    ivi  i- i     i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_51703618_5   4714 CAATGGAATAGGTCAGAGAACGAAAAAATACACCTGCATACCTACAACCA 4763
                                    iviv    iivv i     v   iii i ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_51703618_5   4764 TCTGATCTTTGACAAAGCTGACAAAAATGAACAATGGGGAAAAGACTCCC 4813
                         vi    i  i     i v  v   i viivv           ii ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_51703618_5   4814 TATTCAACAAATGGTGCTGGGATAACTGGCCAGCCACATGCAGATGATTG 4863
                          v                    i      vi ?         i v  v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_51703618_5   4864 AAACTAAACTCCAACCTTTCACCATATACAAAAATCAAGTCAACATGGAT 4913
                           ii ii  i  v    iv                i  v    v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_51703618_5   4914 TAAAGACTTCCATGTAAAACCGAAAATTATAATAACCCTGGAAAAAAAAC 4963
                         i ?    i vv      i v v    i     -   i  vii  i     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAAC 546

  chrX_51703618_5   4964 CTAGG---AAATACCATTCTGAACATAGGCTCTGGCAAAGATTTCATAAT 5010
                         v    ---    -- v iv   v v i  i v-     v i    v  iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--CTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGA 593

  chrX_51703618_5   5011 GAAGACTCCAAAAACA-ATGCTATATAAACAAAAAATTGACAAGTGGGAC 5059
                         v v   v      i  - v  v i -   v       v  i  i v    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAATTGGAC 642

  chrX_51703618_5   5060 CT------AATTAAAGAGCTTTCACACAGCAAAGGAAACTATCAACAGAG 5103
                         i ------       i -    iiii vv       v        v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_51703618_5   5104 TTAACAGACAACCTACAGAATGGTAGAAAATATATGCAATCTATGCATCT 5153
                          v  v        i         v         v     vii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_51703618_5   5154 GACTATAATG---TTCAATATACAGAATCTATA---------TGTAACTT 5191
                           ---   v ---  --i   v      v    --------- ii    i
  L1M4_orf2#LINE/    742 GA---TAAGGGACTT--GTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_51703618_5   5192 AAAAAAATTAGCAAGTAAAAACAACCCCATTATAAAATAGGCAAAGGACA 5241
                           v  ---  iv   - v   i     v   ?v     i         iv
  L1M4_orf2#LINE/    787 AATAA---TAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_51703618_5   5242 TGAACAGATACTTCTCAAAAGAAGACAAACACACGGCCAAAAAACATATG 5291
                             i   i i     v        i v   v i      v  i  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_51703618_5   5292 AAAAAATGCTCCACAGCACTAATAAT 5317
                             i      v   v  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (128 / 97)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.52 (53 / 21)  


 378 16.67 7.14 1.19  chrX_51734361_51741946      404   487 (7099)    L1M4_orf2#LINE/L1        3    91 (817)  

  chrX_51734361_5    404 GAAAGATATCTCGTG---GTG---TGCAAGAATTAATATTGTTATAATGT 447
                                   i i  ---i  ---  v    v            vi   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_51734361_5    448 CCATACTACCCAAAGTGGACCTATAGATTCAATGCAATCC 487
                          v     v      v  - i   i        i       
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTG-ATCTACAGATTCAACGCAATCC 91

Transitions / transversions = 1.00 (7 / 7)
Gap_init rate = 0.03 (3 / 89), avg. gap size = 2.33 (7 / 3)  

2547 25.37 0.59 0.73  chrX_51734361_51741946      490  1171 (6415)    L1M4_orf2#LINE/L1      200   880 (28)  

  chrX_51734361_5    490 ACCAAATTCCAGGCATCACATTTCCTGATTTCAAATTATATTACAAGGAT 539
                           v  i  vv   vv     i    ii        viv  i     i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_51734361_5    540 ATA-TACTCAAAACAGTATTATACTGGCTTAAAAACAGACATATAGACCA 588
                          i -  v    i     i vi       v   ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_51734361_5    589 AGGGAACAAAACAGAGAGCCCTGAAATAAACTCAAGCACATAAGGTCAAC 638
                          v    i i  iv     i  v         i  vi  iv  v      i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_51734361_5    639 TTACCTTTGGCAGGTGTGCCAAGAATACACAATGGGGATGGGAGAGTCTC 688
                          v ii  i i  i v         vi iv         vi i v     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_51734361_5    689 TTCAATAAATGATGTTGGGGAAACTGGACATTCATATGCAAAACACTGAA 738
                              i     i  i    iv       i ?i  i        v v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_51734361_5    739 ATTGAACTCCTATCTTACAGCATACACAAAAACAAACTCAAAATAGTTTA 788
                         i   i  i    i  i   v    i       iv          i v i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_51734361_5    789 AAGGCTTAAATGTAAGACTTAAAACCAGAAACCTCCTAGGAGAAAATATA 838
                         ?  i i           vi      i v   v   i   i      i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_51734361_5    839 AGGGAAAAAGTCCTTGACATTGCTCTTGGCAATTATTTTTTGGCTATGAC 888
                         i ? v   vv i v    v   vvi v      vi   i  i v      
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_51734361_5    889 ACCAAAAGCGAAAAGCAAATAAAACAAAAATAAACAAGTGAGACTTCGGC 938
                                  - v      vv   iv       i i  i vi      iv 
  L1M4_orf2#LINE/    600 ACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_51734361_5    939 AAACTGAGAAGCTTCTGCACAGTAAAGAA-ACAAACAATAGAATTAACAG 987
                            v v i  i   i  ii vvi    i -  v v   v i i v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_51734361_5    988 GCAGACTATAGAATGGGAGAAGATAATTACAAGCCATGTAACTGATAAGA 1037
                         i  iv i i            i   v  i   ii   i  v        i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_51734361_5   1038 AA-TTATCATCCAAAATATATAAGGAACTCATACAATTCAATAGCAAAGA 1086
                         i -  i -     i         i      v     i      ii   i 
  L1M4_orf2#LINE/    749 GACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_51734361_5   1087 AACAAATAACCCAATTTAACAATGGGGAAAGGACCTAAATAGACATTT-T 1135
                         i               ?  v      v      ii i           - 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_51734361_5   1136 CCAAAAAAAATCATAAAAATGTCCAGGCCAGGCACA 1171
                              i  i  -   v     v   i--i i     
  L1M4_orf2#LINE/    848 CCAAAGAAGAT-ATACAAATGGCCAA--TAAGCACA 880

Transitions / transversions = 1.60 (104 / 65)
Gap_init rate = 0.01 (8 / 681), avg. gap size = 1.12 (9 / 8)  

3044 27.73 0.88 0.55  chrX_51734361_51741946     6189  7093 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51734361_5   6189 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 6238
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51734361_5   6239 GGCCATACTGCCCAAGGTAAT-TATAGATTCAATGCCATCCCCATCAAGC 6287
                            v     v     iv i  -  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51734361_5   6288 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6335
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51734361_5   6336 TATGGAACTAAAGAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 6385
                                v iv iii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_51734361_5   6386 AACAAAGCTGGGGGCATCACACTACCTGACTTCAAACTATACTACAAGGA 6435
                                i   i  vv       v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_51734361_5   6436 TACAGTAACCAAAACAGCATGGTACTCTTACCAAAACAGAGATATAGACC 6485
                                 i   i    ii       vvi iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_51734361_5   6486 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCCACAACT 6533
                                i    i--    i  --        vv   i i  ii iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_51734361_5   6534 GTCTGGTCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGACTCC 6583
                         ivi  i i  i     ivv  v   i v  vv     i      i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51734361_5   6584 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6633
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_51734361_5   6634 GAAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGGA 6683
                            ii    i    v   i     v i            i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51734361_5   6684 TGAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 6733
                          v ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_51734361_5   6734 TTAGGCA-ATACCATTCAGGACATAGGGATGGGCAAGGACTTCATGTCTA 6782
                         v    ?i- v i -   iv   v v   v i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_51734361_5   6783 AAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTA 6832
                         vi            vvi      i   vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_51734361_5   6833 ATTAAACTGAAGAGATTCTGCACG-CAAAAGAAACCACCATCAGAGTGAA 6881
                           i   v v  i iv  i  ii v-    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_51734361_5   6882 TAGGCCACCTGCAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 6931
                         v  i v   ii                v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_51734361_5   6932 AAGGGCTAATATCCAGTATCTACGATGGACTCAAACAAATTTACAAGAAA 6981
                          i  i  vi       v  v  ii v i    vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_51734361_5   6982 AAAACAAACAACCCCATC-AAAATTGGGTGAAGGATATGAACAGACACTT 7030
                           i     i     v  i-    v    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_51734361_5   7031 CTCAAAAGAAGACATTTATGCAGCCAAAACACACATGAAAATATGCTCAT 7080
                            v        i  vi viii     v vi          v       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_51734361_5   7081 CATCACTGGCCAT 7093
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3026 26.87 0.99 0.99  chrX_51746410_51752810     5001  5908 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51746410_5   5001 TGGAAGAATATTCCATGCTCATTCAGA--GGAAGAATCAATATCATAAAA 5048
                              ii    i     i    --i  --      v i     ii v  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCAT--GGATTGGAAGACTTAATATTGTTAAG 48

  chrX_51746410_5   5049 ATGGCCATACTGCCCAAGGTAATTTATAGATTCACTGCCATCCTTATGAA 5098
                              v     v     iv i  i  i       vi  v    i   v  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_51746410_5   5099 GCTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 5146
                         iv v   iivi i  i  ii     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_51746410_5   5147 CATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTGAGCCAAA 5196
                                  viiv  ii  v  viv  v     i      i   ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_51746410_5   5197 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATAATACAAG 5246
                                  i      vv    i  v  ii i      viv  v     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_51746410_5   5247 GATACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGATATAGA 5296
                          v        i   i    ii       v i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_51746410_5   5297 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATACCTACAA 5344
                         i        i    i--    i  --        vv   i i ii  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_51746410_5   5345 CTATCTGATCTTTGACAAACTTGACAAAAACAAGCAATGGGGAAAGGATT 5394
                         ii vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_51746410_5   5395 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5444
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_51746410_5   5445 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5494
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_51746410_5   5495 GATGAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5544
                            v ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_51746410_5   5545 ACCTAAGCA-ATACCATTCAGGACACAGGCATGGGCAAAGACTTTATGTC 5593
                           v  i ?i- v i -   iv   viv  vv i     v ii  iv ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_51746410_5   5594 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGCATC 5643
                           vi            vvi          vv    iv  i    v v ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_51746410_5   5644 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA-CAATCAGAGT 5692
                          v  i   v v  i i   i  ii vv    i  v    -   v- i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGT 692

  chrX_51746410_5   5693 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATGTACTCATCTG 5742
                            v  i     i                 v       vvi ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_51746410_5   5743 ACAAAGGCCTAATATCAAGAATCTACAAAGAACTCAAACAAACTTA-CAA 5791
                          i  i  v  vi    v     v  i         vv    -  i -i  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAA 791

  chrX_51746410_5   5792 GAAAAAAACAAACAACTCCATCAAAAAATGGGCAAAGGGTATGAACAGAC 5841
                         v     i     i   i v  i?               i v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_51746410_5   5842 ACTTCTCAAGAGAAGACATTTGTGCAGCCAAAAAACACATGAAGAAATGC 5891
                          i     v i      i  viiviii     v  i        i i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_51746410_5   5892 TCATCGTCACTGCCCAT 5908
                            v i   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.38 (18 / 13)  


 977 24.22 3.13 3.13  chrX_51754010_51758130      167   517 (3604)  C L1M4_orf2#LINE/L1   (0)   908   558  

C chrX_51754010_5    517 TCTTCATCTTTTTGGTTTTGGCAAAGATTTTCAAAATGAGACACCCAAAC 468
                              i vvii    v  v     v i   iiv i  iv      v   v
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

C chrX_51754010_5    467 CACAAACTATAAAAGAAGAAAAATTAATACATTTGATTCCACCACAATTA 418
                              i v i       --     vi   v   v  i i  i  v     
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAA--AAAATAGATAAATTGGACTTCATCAAAATTA 655

C chrX_51754010_5    417 AAG-TTTTTGGCCTTTAAAAGGCATTCTTTTGAAATTGAAAGAGA-AATC 370
                           i-i     vv   i   i i  i v ivv    v     -   -  i 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA-AGACAACC 704

C chrX_51754010_5    369 CACACTCTGTGATAAAATATTTAGAATTCATATATCTATATCCAACACAG 320
                             vvv  v  v         iv  v          i------ i vi 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTG------ATAAGG 748

C chrX_51754010_5    319 GAC--ACTTCTAGACTATA--AAGAAGTCTTATAACTCAATTATAAGAAG 274
                            --iiv  i   v    --     v     i        v    i   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

C chrX_51754010_5    273 GCAAATA-CTCAACTATAAATATGGAGAAAAGACTTCAACAGACTACCTC 225
                         i      - i   i ?v   -    iv   i  i  v  i    - ii  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAGAC-ATTTC 846

C chrX_51754010_5    224 ACCAAAGAAGATACACAGATGGCTAACAACCACACAAAAAGATAC----C 179
                         v            i   i     i  i  v    ii       i ---- 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chrX_51754010_5    178 ATCATTTATCAT 167
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (47 / 37)
Gap_init rate = 0.03 (11 / 351), avg. gap size = 2.00 (22 / 11)  

2474 27.26 4.69 3.24  chrX_51754010_51758130     2734  3628 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51754010_5   2734 TGGAAAAACATCCCATGCTCATGGATAGGAAGAACCAATATCATTAAAGT 2783
                               i i        i        v      vii     ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51754010_5   2784 GGCTACACTGCCTAAAGCAATTTATAGATTCAATGCTATTCCCATCGAAC 2833
                            v i   v  i   vii  i  i        i  v  i  i   i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51754010_5   2834 TACCAAGGACATTCTTCACAGAGCTAGAAACAATTATTTAAAAATGTACA 2883
                          v   ivvi v  i  ii    iv v  v viv v  iiv     vi i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_51754010_5   2884 TGGAACCAGAAAAGGAGCCCGGATAGCCAAGGCAATCGT----------- 2922
                              vi- v  i   v  v i        ii     v -----------
  L1M4_orf2#LINE/    151 TGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_51754010_5   2923 ---AAGCTAAAAGA---------------------ACTATACTGCAAGGC 2948
                         ---   i ii i  ---------------------   -    i   i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_51754010_5   2949 TACAATGACCAAAACAGCATGGTACTGGTACTGGCACAAAAACAGGCACA 2998
                             i i i   i    --  ----           i  ii i  i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAG--TG----TGGTACTGGCATAAGGATAGACATA 292

  chrX_51754010_5   2999 TAGACCAATGGAACAGAATAGAGAGGCCATAAATAATGTCGCACATCTAC 3048
                             i        i     v     v   v      vvi ii    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_51754010_5   3049 AACCAGCTTTTTTCTTTTTTTTTTTTTTTGACAAAGCTGACAAAAACAAG 3098
                         iii  i--------------  vv    i     i v  v   i v  vv
  L1M4_orf2#LINE/    343 GGTCAA--------------TTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_51754010_5   3099 CGGTGGGAAAAAGAC--TCCATATTCTATCAATGGTGCTGTGATAACTGG 3146
                          ii    i   ii i--  -- v   v iv          v  i      
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_51754010_5   3147 CTAGCCGTATGCAGAGGATTGAAGCTGGACCCCTTCCTTACACTATCTAC 3196
                         v  ?  ii     i i  v     i         v   i    i  v   
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_51754010_5   3197 AAAAATCCACATGAGATGGATTAAAGGCTTTAATGTAAAACCCAACACCA 3246
                               iv  vii i      i ?  i i v       i v i  v  i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_51754010_5   3247 TAAAAACCCTGGAAGACAACCTAGGCA-ATACCATCCTGGACATAGGAGC 3295
                              vi i i     v   v    ?i- v i v  v  -  v v  ivi
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTT 575

  chrX_51754010_5   3296 AGGCAAAGATCTCAC-GACAGAGGCACCAAAAGCAATCA--CAGCAAGAG 3342
                               v i i  vi-  i v- i           --  --  i   i  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATAT-GACACCAAAAGCA--CAAGCAACAAAAG 622

  chrX_51754010_5   3343 TAAAAATTGACACATGGGATCTAATTAAACTTAGAG-CTTCTGCACAGCA 3391
                         v      v  i v  v   ii v  i   v   i i-   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_51754010_5   3392 AAAGAAACTATCAACAGAGTAAACAGACAACCTACAAAGTGGGAGAAAAT 3441
                           i  v        v i   i  v        i   i i           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_51754010_5   3442 TTTTGCAACACTATTCATCTAACAGAGGTCTGATATCCAGCATCTATAAA 3491
                         v       - ii  vi    i i ii  v  vi       v  v      
  L1M4_orf2#LINE/    723 ATTTGCAA-ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_51754010_5   3492 AAGCCTAAACAAATGCACAAGAGAAAAACAAACAACCCCATTAATAAGGG 3541
                         i i iivv    v vv i  v i   i     i     v   ? v  iv 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_51754010_5   3542 GGCAAATGACATGAACAGACACTTCTCAAAAGAAGACATACATGTAGCCA 3591
                               v  iv    i     i     v        i     vi i    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_51754010_5   3592 AGAAGTATATGAAAAACAGCTCAATATCACTGATCAT 3628
                          v   i i       ivv      i    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.18 (71 / 17)  


3456 23.32 0.88 1.43  chrX_51782473_51785902.rev     2031  2939 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_51782473_5   2031 AAGGTGTCCCTTACACATGGACGGGGAAGACTGTGTATCATTAAAATAGT 2080
                            i i    v iiv      iv  -      vvi   ii    i  i i
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGG-AAGACTTAATATTGTTAAGATGGC 53

  chrX_51782473_5   2081 AACAGTCCACAAGTGGATCTATAGATACAACATACTCACCGTTTCAAATC 2130
                           i v   v   i v      i    v    ii v  -  vv iv     
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATC-CCTATCAAAATC 102

  chrX_51782473_5   2131 CCACCAGGATCTTCTTGCCATAATTGACAATCTGATTCTGACATTCCCTT 2180
                            v v vv i  -    viv         v     i  i v    viv 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_51782473_5   2181 GGCAACGCAAGGGACCCAGAAAAGCCAAAACAATCTTGAAAAAGAG---C 2227
                           v  i               v                       i--- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_51782473_5   2228 AATGATGGAGGACTCACACGTCTCTATTTCAAAACTTACTGCAAAGCTAC 2277
                           v v              v  i v               i         
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_51782473_5   2278 AGTAATCAATGTGTTGTGGTACTGGCATAAATTTAGGCATATATATATCA 2327
                                  viiiv                ivv   -- i     v    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG--ACATATAGATCA 299

  chrX_51782473_5   2328 GTGTCATAAAAATGCAAATTTTAGAAATAAACCTCTTCTTTTAAGTTCAG 2377
                         i  vv   i  v  - i v ii           iv v v    v v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTG-AGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_51782473_5   2378 TTGATTTTCCACAAGTGTATCAAGGCAACTCAAAGTGAGAAAGAATAGCA 2427
                                  v     v  ii    i v i    v - i          iv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTC 397

  chrX_51782473_5   2428 TTTTCCACAAACGGTGCTGGGACAAATGGTTATGCCCATGGAGAAGAATG 2477
                              v     i             v   v  ?v v    v i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_51782473_5   2478 AAGT-GGACCCACCATCTCATGCCATGCCTGAAAATTAATTCAAAATGAA 2526
                             -      - i i    ii    iivii        i        i 
  L1M4_orf2#LINE/    448 AAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_51782473_5   2527 TGATAGACATAAACCTAAGGGGAAAAAAACTATGTAACTTTTGGAAAAAA 2576
                          v ?    v    iv    i vv    --    iv    i  i   i   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAA--CTATAAAACTCTTAGAAGAAA 544

  chrX_51782473_5   2577 ACTTTGGGGATAACCTTCATGACCTTGAAATTGGAATTGGCTTTGTAGAT 2626
                           v v  ? vv  i    i        iiv v  v v   i  iv     
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_51782473_5   2627 ATGGTACCCATATCACGGGTGAAAAACATGAAACACAGAGGAATTGTACT 2676
                            ii   v v v   ii ii v   - vi   v i   vi     v   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAA-AGAAAAAATAGATAAATTGGACT 643

  chrX_51782473_5   2677 TCATTAAAATTAAATACTTTTGTGCTTCAAAGCCCACCATCAAGGACAGG 2726
                             i         v                 vv   i      i -  v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA-AGT 692

  chrX_51782473_5   2727 GAA--GACAACTTATGAGATGATTGAAAAGATTGGAAAATCATATATCTC 2774
                            --      ii iiii   ivv     v   v v             v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_51782473_5   2775 ATATTTGACTC-TATTTGCAATATCTACTAAACACTTACGACTGCCTAAT 2823
                            vvv    i-   iiiv     v  vvi   v     i   vvv    
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_51782473_5   2824 AAAAAAGACACACAGCCCAAAT-AAAAGTGGGCAAAGCATTGCAATAGAC 2872
                              -    v i i     v -    i         v   vv       
  L1M4_orf2#LINE/    793 AAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_51782473_5   2873 ATTTCTCTAAAGAACATGTACAAATGGCTAATAAGCTCAAGAAAAGATGC 2922
                                i      v  i          i       v  v          
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_51782473_5   2923 TCAGTGTCATTAGTCAT 2939
                            iii   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.95 (102 / 107)
Gap_init rate = 0.02 (16 / 904), avg. gap size = 1.31 (21 / 16)  


3168 27.23 0.66 0.55  chrX_51797769_51806198     4871  5777 (2653)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51797769_5   4871 TGTAAGAACATTCCATGCTCATGGGTAGGAAGAATCACTATCGTGAAAAT 4920
                           v  ii i  i     i      i v      v i v   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51797769_5   4921 GGCCATACTGCCCAAGGTAATTTATAGATCCAATGCCATCCCCATCAAGC 4970
                            v     v     iv i  i  i    i   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51797769_5   4971 TACCAATGGCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 5018
                          v   iiv  i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_51797769_5   5019 TATGGAACAAAAAAGAGGCC--GCATTGCCAAGTCAATCCTAAGCCAAAA 5066
                                - viv   i i  -- v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_51797769_5   5067 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5116
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_51797769_5   5117 CTACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGAT 5166
                                  i   i    ii         i  v ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_51797769_5   5167 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATACCTACAAC 5214
                                 i    i--    i  --        vv   i i ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_51797769_5   5215 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5264
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_51797769_5   5265 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5314
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_51797769_5   5315 TGAAACTGGATCTCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5364
                             ii    i i  v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_51797769_5   5365 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5414
                           i ?   ii    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_51797769_5   5415 CCTAGGCATTGCCATTCAGGACATAGGCATGGGCAAGGCCTTCATGTCCA 5464
                          v    ?i viviv   iv   v v  vv i     v vi   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_51797769_5   5465 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5514
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_51797769_5   5515 ATTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACTACCATCAGAGTGAA 5564
                           i   v v  i i   i vii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_51797769_5   5565 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5614
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_51797769_5   5615 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5664
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_51797769_5   5665 AAAACAAACAACTCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5714
                           i     i   i v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_51797769_5   5715 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTGAT 5764
                            v        i  vi viii     v  i          i     v v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_51797769_5   5765 CATCACTAGCCAT 5777
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  

3388 23.92 2.11 1.11  chrX_51797769_51806198     7039  7937 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51797769_5   7039 TGGAAAAATATTCCATGTTCACAGATTGGAAGAATCAACACTGTTAAAAT 7088
                               i    i         ii          v i  i i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51797769_5   7089 CTTCATACCACCCAAAGCAATTTACAGATTCAATGCAATCCCTATCAAAA 7138
                         vviv    iv      vii  i           i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51797769_5   7139 TACCAATGACATTCTTCACAGAAATAGAAAAAACAATTCTAAAATTTATA 7188
                          v   iivi v  i  ii       v  v  ivii  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_51797769_5   7189 TGAAACCAAAAAAGACCAAGAATAGCCAGCACTATTTGGCTAACAAATAA 7238
                           i  viiv  ii    v          iv  v  i --- i v   v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT---TGAAAAAGAA 197

  chrX_51797769_5   7239 AAATAAAACATTATGAACTTA--------AAGTTTA-----TACTACTGA 7275
                         i  i   ii- viv i   i --------  v  i -----      vi 
  L1M4_orf2#LINE/    198 GAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_51797769_5   7276 GATATAATAACCAAAACAGCATGGTACTGGCATCAAAAGAGACACAGAGA 7325
                          v  i i   i   i    ii            v ii v     i v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_51797769_5   7326 CCAATAGAACAGAATAGAGAACCCATAAACAAATCCACACACCTACACTG 7375
                         i    i   i     v    ii   v   i   i   i   ii  iiv v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_51797769_5   7376 AACTCATTTTCGACAAAGGTGCCAAGTACC-TACAGTAGGAAAAAGACAG 7424
                           i v           i         -   - v  i i  i   ii i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAATAG 395

  chrX_51797769_5   7425 TCTGTTCTATAAATGTTGCTGAGAAAACTGGATATCCATATGCAGAAGAA 7474
                            v   v i     v     i  v         ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_51797769_5   7475 TGAAACTAGGCCCCTATCTGTCACCATATAGAAAAATCAAATCAAAATGT 7524
                             ii i i      i  vv         v      i  v        v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_51797769_5   7525 ATTAATGACTTAAATCTAAGACCTCAAACTATGGGACTACTGCACAAAAA 7574
                           i ?v   i     v     v  v       iii   vi iv vi    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_51797769_5   7575 CATTGGGGAAAATTTCCAGGACATCAGACTGGGCAAAGATTTCTTGAGCA 7624
                            v  ? v    i i iv   v ii ii i     v i      iiii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_51797769_5   7625 ATACCCCACAAGCACAGGCAACCAAAGCAAAAATGGACAAATGAGATCAC 7674
                         vv  v   v       i     v    v      i  i    vi  iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_51797769_5   7675 ATCAAG-TTAAAAGGCTTCTTCTGCACATCAAAGGAAACAATCAAGAAAG 7723
                              i-      i----   i  ii v        v  v          
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA----CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_51797769_5   7724 TGAAAAGACAACCCATAGAATGGGAGAAAATATTTGCAAACTACCCATCT 7773
                                        i                        ii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_51797769_5   7774 GACAAGGGATTAATAACCAGAATATAGAAGGAGGTCAAACAACTC--TA- 7820
                           i      i vi  v          v  i  iv  vv       --  -
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_51797769_5   7821 TAAAACATCTAATGATCCGATCAAAAAATGGACAAAAGATTTGAATAGAC 7870
                              viv v   i i  i  i?        i    i             
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_51797769_5   7871 ATTTCTCAAAAGAAGACATACAAATGACAAA-AAGTCATATGAAAAGGTG 7919
                                v        i         i v  -   -  i        i  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATG 890

  chrX_51797769_5   7920 CTCAACATCACTGATCAT 7937
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (134 / 77)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  


2823 26.43 1.29 0.82  chrX_51865002_51866848.rev      502  1356 (491)    L1M4_orf2#LINE/L1       50   908 (0)  

  chrX_51865002_5    502 TGACCAAACTACCAAAAGTGATCTACAG-TTCAAGGCAATTTTTATTGAA 550
                           i v v   v  v   v          -     v     iii   ii  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_51865002_5    551 ATGTCAATTACATTCTTCACAGAAAT-GAAAAAAACATCCTAAAATTCAT 599
                           vi  ii i v  i  ii       -  v  ivvv              
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_51865002_5    600 ATGGAACCAAAGAAGACCCCAAATAGCCAAAGCCATCCTGGGCAAAAAGA 649
                               viiv iii     vi          i v   i  iiv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_51865002_5    650 AAAAAGCTGGAAACATCACACTACCTGACTTCAAAATATTCCACAAAGCC 699
                          v    i    iivv       v  ii i       iv v i       i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_51865002_5    700 AGAGTAACCAAAACATCATGGTGCTTGCATAACACCATGCCACACACAGA 749
                          v     i   i   vii    i  v      vivi - --   i i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-G--ACATATAGA 296

  chrX_51865002_5    750 CCAGTGGAACAGAATAGAGAATCTGGATTTACATCCACATATTTAAAGCC 799
                         i  i     i     v    i  ii  vv  v i   i i     vi i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_51865002_5    800 AAGTGATTTTTCATGAAAGCAGCAAAAACATTCGGTGGGGAAAGGAAAGT 849
                           v       iv ii ii iiv   i v     ii         i v   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_51865002_5    850 TTCTTCAATAAGTGGTGCAGGGAACACTAGATATTC-CAGTGCAGAAAAA 898
                         i i     i  i      v    vv   i    ?i -  -    i  i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGAA 445

  chrX_51865002_5    899 TGAAACTAGACCCCTATCTCTTACCATATAAAAAAGCCAACTCAAGTTGG 948
                             ii i        i   vi        v    iii       iv   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_51865002_5    949 ATTAAAGAATTTAATATAAGACTTGAAACTAAGAAAATACTAGAAGAAAA 998
                           i ?   vi v   i     vi i      vi   v vi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_51865002_5    999 CACTGGGA-AAATGCTTCAAGACATTGGTCTGGGCAAACATTTTTTGCTT 1047
                           iv  ?i-    -    iv   v    vi i     vvi   i  ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_51865002_5   1048 AAGACCTTAAAAGCA-AA---ACCAAAGCACAAATAGACAAATGGGATTA 1093
                          v   vii       -  ---  v    v v       i    v   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_51865002_5   1094 TATCAAGCTAAAAACCTTCTGCACAGCAAAGGAAACAGTCAACAGAGTGA 1143
                         i     iv v    v   i  ii vv       v  vi    v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_51865002_5   1144 AAAGGCAACCTACAGAATTGGAGAAAATATTTGCAAACTATCCACCTGAC 1193
                             i     i       v                  ii  vi i    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_51865002_5   1194 AAATAATTAATAACCAGAATATATAAGAAACTCAAACAACTCAATAGCAA 1243
                           ivi i vi  v             ii     vv           ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_51865002_5   1244 CAAAACCAAGTAATCCAATT-AAAAATGG-CAAAG-ATCTGAATAGAAAT 1290
                         v  i  -  i   i      -        -     -  i        v  
  L1M4_orf2#LINE/    795 AAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_51865002_5   1291 TTCTCAAAAAAAAGACACACCAACAGCCAACAGGAATATGAAAAAATGCT 1340
                              v   i  -  i i  v  ii     i i v i       i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_51865002_5   1341 CAATATTACAAAATGT 1356
                            i  i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (138 / 85)
Gap_init rate = 0.02 (15 / 859), avg. gap size = 1.20 (18 / 15)  


3145 27.86 0.44 0.44  chrX_51867466_51873862     4997  5904 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51867466_5   4997 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5046
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51867466_5   5047 GGCCATACTGTCAAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     vi v  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51867466_5   5097 TACCAATGACTTTCTTCACAGAATAGGAAAAAAGTACTTTAAAGTTCACG 5146
                          v   iivi i  i  ii     vvv  v  ivvv iii    i    ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_51867466_5   5147 TGGAACTGAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGAA 5196
                              v  v  ii  v  viv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_51867466_5   5197 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATAGTACAAAGCTA 5246
                              i      vv    i  v  ii i      viv  v          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_51867466_5   5247 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5296
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_51867466_5   5297 GGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCGTATCTACAACTAT 5344
                         v    i    i--    i  --        vv  iiii  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_51867466_5   5345 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5394
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_51867466_5   5395 GTTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5444
                         v  i  i       i      v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_51867466_5   5445 AACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGGATT 5494
                          ii    i    v   i     v i            i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_51867466_5   5495 AAAGACTTACATGTTAGATCTGAAACCATAAAAACCCTAGAAGAAAACCT 5544
                          ?    i  v    v   v  i    i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_51867466_5   5545 AGGCA-ATACCATTCA-GGCCATAGGCATGTGCAAGGAGTTCATGTCTAA 5592
                            ?i- v i -   i- i  v i  i- iv    v iv   v ivv  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT 596

  chrX_51867466_5   5593 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5642
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_51867466_5   5643 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 5692
                          i   v v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_51867466_5   5693 AGGCACCCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5742
                           i  v  i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_51867466_5   5743 AGGGCTAATATCCAGAATCTACAATGAACTCCATCAAATTTACAAGAAAA 5792
                         i  i  vi          v  i  v      ivv   v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_51867466_5   5793 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5842
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_51867466_5   5843 TCAAAAGAAGACATTTATGCAACCAAAACACACATGAAAAAATGCTCATC 5892
                           v        i  vi viiii    v vi          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_51867466_5   5893 ATCACTGGCCAT 5904
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (146 / 103)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


1220 26.60 8.74 4.82  chrX_51882824_51884546      472  1238 (485)    L1M4_orf2#LINE/L1      112   908 (0)  

  chrX_51882824_5    472 TTTTTTGACTTGGGGAATAAACCATCTG----TAAAATTTACACAGAAAT 517
                                - ---i i   vi  v v   ----       i i ii     
  L1M4_orf2#LINE/    112 TTTTTTG-C---AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_51882824_5    518 TCAATGGACTACAAACAGCCAAG------CTGAA---GAAGAACACAGGT 558
                         v   v    ivvi  i      i------i    ---        v  v 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_51882824_5    559 GAAGAACTTACAGTACGAAAAT-CAACACTCATTATAAAA-TACGAGTAA 606
                          i  i   i   v v vv  v -   v   i i  i   i-   -     
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC-AGTAA 256

  chrX_51882824_5    607 TTAATACAGTGATGTATTGACACTAGGATAGTAAAAATAAACCAGTGGAA 656
                          i  v      vv   i  i  iv       - v v   i i  i     
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAG-ACATATAGATCAATGGAA 305

  chrX_51882824_5    657 CAGAAT--AGACTCAAGAAATAGTTCCAGTCATAGAAAATCACCTGACTT 704
                         i     --   v  v       ivi   vv   vv vii   vi   i  
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_51882824_5    705 ACTACAAAGG-----AG-CCATTGCAACTAAGGGAAGAA-AG-------- 739
                         v v    i  -----  -     -   - ii  i     -  --------
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATT-CAA-TGGGGAAAGAATAGTCTTTTCA 403

  chrX_51882824_5    740 ---AATGATTCTTGATCA-CTGGATA-CCACATGGAAA----TTAAATCT 780
                         ---    i v  v iv  -       -       v   ---- v  i --
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT-- 451

  chrX_51882824_5    781 TGGGCCTTTGG-TCATATCGGCCACAAAAATCAATTCCTGATGGATCTTT 829
                            i  ii iv-   i i ivvi        i  i  vvi       ---
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC--- 498

  chrX_51882824_5    830 TGACCAAAATTGGTCAAAATATGAAAGTTAAAAC----AAGCT---AGAA 872
                         ------ ? -- ii v    i i i  i      ----  i  ---    
  L1M4_orf2#LINE/    499 ------AWA--GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_51882824_5    873 GTAG-CATAGGAAAATATTCTTATGACTTCAGAATAGGCA-TAGTTTAAA 920
                          v i-      ?iv v  ii ii    i ii iv      - i    vvv
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_51882824_5    921 AAAAAACAGGACATGATGAGCACTAAGAATAAAAGATCGACAATATATAA 970
                          i ---i v    iv vi     v iv  i      --i v    v    
  L1M4_orf2#LINE/    591 AGA---TATGACACCAAAAGCACAAGCAACAAAAGA--AAAAATAGATAA 635

  chrX_51882824_5    971 -TTG------ATTAAAATTAAGATCATCTGTTCATCTCCAAGG-CACCAC 1012
                         -   ------  i        i v v i   v --i  v    -   i i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGC--TTCAAAGGACACTAT 683

  chrX_51882824_5   1013 TGAGAAGATGAAAAAACTAGCCATTGAATGGGA--ATATGTTAGTTCTAA 1060
                         ii    ii      i  v v   iv        -- v  i  v -- v  
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG--CAAA 731

  chrX_51882824_5   1061 TACATATATCCAAAAAAGGACTC--ATGGAGAATATCTAAGGAACTTCCA 1108
                          -        ii v  i     i--  vv       v   i     iii 
  L1M4_orf2#LINE/    732 T-CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_51882824_5   1109 CAAATGACCAAGAAAAAGGCAGACAATCTAGT--AAGAATAGGCAAAAGG 1156
                            v v vi  v      i  i i  i i i --  i   i      i i
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_51882824_5   1157 CTTGGAAAGCCATTTCACAAAAAAACAATAACCAAGTAGAAAATAA--AT 1204
                         i   i v  v      v v   i  -i   vv   i i vv     -- i
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAA-GATATACAAATGGCCAATAAGCAC 879

  chrX_51882824_5   1205 ATGAATATGTGCTCAATAAGTGTTCAAAATCTTT 1238
                              v vi       i -----   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACA-----TCAZZZZZZZZ 908

Transitions / transversions = 1.38 (117 / 85)
Gap_init rate = 0.05 (41 / 797), avg. gap size = 2.54 (104 / 41)  

1063 26.09 0.72 0.72  chrX_51882824_51884546     1448  1723 (0)    L1M4_orf2#LINE/L1      264   539 (369)  

  chrX_51882824_5   1448 AGCATGGTACTGGTACCAAAACAGAGATATAGACCAATGGAACAGAGC-- 1495
                           ii         i iv ii i   v       i        i   ii--
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_51882824_5   1496 AGAGCCCTCAGAAATAATACCACACATCTACAACCATCTGATCTTTGACA 1545
                             i  --        vv   i    i  iiii  vi    i  i    
  L1M4_orf2#LINE/    314 AGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_51882824_5   1546 AACCTGACAAAAACTAGAAATGGGGAAAGGATTCCCTATTGAATAAATGG 1595
                          ivv  v   i v vvvv           i  vvi  v  v  i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_51882824_5   1596 TGCCGGGAAAACGGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTT 1645
                            i    v   v  v  ?   i   i i  iiv    ii    i    v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_51882824_5   1646 CCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTACATG 1695
                            i     v              i    i      i ?    i  v   
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_51882824_5   1696 TTAGACCTAAAACCATAAAAACCCTAGA 1723
                          v   v       i      vi i    
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGA 539

Transitions / transversions = 1.59 (43 / 27)
Gap_init rate = 0.01 (2 / 276), avg. gap size = 2.00 (4 / 2)  


2545 23.70 2.96 6.88  chrX_51908535_51911045.rev     1076  2020 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_51908535_5   1076 TAAAGAGATACTTTATGTTTATGGATAGGAAGGGTCTATATTGTCAAGAT 1125
                          ii i     iiii     i      v     iv iv       i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51908535_5   1126 GTTAGTTCTTCCAAACTTAATGTATAGATTCAACACAATCGTAATGAAAA 1175
                          vi i v  i  v  v  i  v  i         i     viv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51908535_5   1176 TCCCAACAGGTTATTTTGTGGATACCAAAAAACTGATTCTAAAGTTTATA 1225
                              i v vi v     ii  v iii v  i     i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_51908535_5   1226 TGGAGAAACAAAACACCATGAATATCCAAATCAATATTGAAGGAGAAGAA 1275
                             i vi   iiv   vv     v     v    v     ii       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_51908535_5   1276 CAAAATTGGAGAACTGACACTATTCTACTTCAAGACTTACTATAAAGCTA 1325
                             i      i   v     vii v i     i        i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_51908535_5   1326 CAGTAATCAACATGGCATGGTACTGGTGAAAGAATAGATAAGTAGAGCAA 1375
                                   v ii ii         iiv   i     i vi    v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_51908535_5   1376 TAGAACAGAATATAGAGCCCAGAAATAGACTCATATAAATATAGTCAACT 1425
                          i   i     vv    i         i  i    i vv   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_51908535_5   1426 GATCTTTGACAAAGGAGCAAAGGCAATATAGTGGAGAAAAGATAGTCTTC 1475
                            i  i     i  v  v   i v  vi i   i    ii        i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_51908535_5   1476 TCAACAAATGGTGGTGAAA-GACTCTACATTGACATATGAAAAAA-AAAG 1523
                                      v  ii -i   vv i ?iv    iii   i  -i   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_51908535_5   1524 ---AATCC------------AGACACAAAAATTAACTCAAAATATATCAT 1558
                         ---i i  ------------ v i                   iv    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_51908535_5   1559 AGACATAAATGTAAAATGAAAAACTATAAAAACTATAAAACGCCCTGAAG 1608
                             v         i ------i   ---            v iiv    
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA------GCTA---AAACTATAAAACTCTTAGAAG 541

  chrX_51908535_5   1609 AAAACATAGGAGAAAATCTATATGACATTGGGTATGGTGATGACTTTTTA 1658
                                   ? v      vii    v      vv  ii   ii  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_51908535_5   1659 GATATAACACCAAAGACATGATCTATGAAAGAAAGAATTGATCAACTGAA 1708
                              i        ii  ii v v ii       i   v   v  i  i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_51908535_5   1709 CTTAATTAAAATTAAGA-CTTTAATTAATTAAA-----CTTAATTAA--A 1750
                            v  i        i -    vi vvv i   -----  --  i  -- 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT--ATCAAGAA 689

  chrX_51908535_5   1751 ATTAATTATACATACATACATATATATATATATATATATATATATATATG 1800
                          v i vv v   -  vi   v -  iviviv v    v ii v  -i  i
  L1M4_orf2#LINE/    690 AGTGAAAAGACA-ACCCACAGA-ATGGGAGAAAATATTTGCAAAT-CATA 736

  chrX_51908535_5   1801 TATGCCCAGCCTGGGCAACAAGAGCAAAACTCCATCTCTCTCTCTCTCTC 1850
                            -------   ---- i   i ----   -------------------
  L1M4_orf2#LINE/    737 TAT-------CTG----ATAAGGG----ACT------------------- 752

  chrX_51908535_5   1851 TCTCTCTCTCTATATATATATATATATACACACACAGAACTCTTAAAATT 1900
                         ---------- i   vi v -       ----- -          v  i 
  L1M4_orf2#LINE/    753 ----------TGTATCCAGA-ATATATA-----A-AGAACTCTTACAACT 785

  chrX_51908535_5   1901 CAACAATATAAAAATGAACAACCCAAT-AATAAATGGGCAAAA-ACCTGA 1948
                            i    v   i ii  i        -? v           i- ii   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_51908535_5   1949 AGAGACACCTC-ACAAAGAAGTAATACAAATGGCAAATAAGTATATGAAA 1997
                          v     ii  -v        vv           v      i i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_51908535_5   1998 AGATACTTAACATCACTAGGAGG 2020
                             i  i       ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (137 / 83)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 4.04 (93 / 23)  


3006 26.88 1.35 0.79  chrX_51969519_51973890.rev     2984  3872 (500)    L1M4_orf2#LINE/L1        1   894 (14)  

  chrX_51969519_5   2984 TGGAAACACATCCCATGATCATAGATGGGTAGAATCCATATTGTGAAAAT 3033
                               v i        v    i   v  v   v iv       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_51969519_5   3034 GACCATACTGCCAAAAGCAATCTACAAATTCAACGCAATTTCCATCAAAA 3083
                          i v     v  v   vii       i            ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_51969519_5   3084 TACCACCATCATGCTTCACAGAATTAGAAAAA--AATTCTAAAATTCATA 3131
                          v   v vv v vi  ii     v v  v  i--i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_51969519_5   3132 TGGAACCAAAAAAGGAGCCCATG-TAGCCAAAGCAA----GAACAAGCAA 3176
                              -- viv    ii    vi-        i   ----   v   ---
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG--- 195

  chrX_51969519_5   3177 AAAGAACAAATCTGGAGGCATCACATATCT-GATTTCAAACTATACTATA 3225
                         -         vi      vv     iv  i-i        viv     i 
  L1M4_orf2#LINE/    196 -AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_51969519_5   3226 AGGCCATAGTCACCAAAACAGCATAATACTGGTGTAAAAATAGGCACATA 3275
                          i  i i   v i   i    ii ii      ii   ii    i  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_51969519_5   3276 GACCAATGGAACAGAATACAAAACCCAGAAATAAACCCAAATACTTACAG 3325
                           i        i     vv i ii               v i i   ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_51969519_5   3326 CCAACTGCTCTTCAACAAAGCAAACAAAAC-ATAAAGTGGGGAAAGA-CA 3373
                         i   i  v i   i    i vviv   i  -  vv i          -i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_51969519_5   3374 CCCTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGA 3423
                         vi                       i  i   v  ?       i ii   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_51969519_5   3424 ATGAAACTATATCCTCATCTCTCACCTTGTACAAAAATCAGCTGAAGATG 3473
                              ii iv i  ii i   v    v i         i i  v  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_51969519_5   3474 GCTTAAGGACTTAAATCTAAGACCTGAAACTATAAACATTTTAGAAGATA 3523
                          v i ?i   i     v     v  i          vv i        v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_51969519_5   3524 ACATTAAA--AAACCCTCCTAGACATTGGCTAAGGGAAGGATTTCATGAC 3571
                             vii?--   i i  v -   v    v v   v  v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_51969519_5   3572 CAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACT 3621
                         i v  vv         v v    i    iv   i   i   iv v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_51969519_5   3622 TAATTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTTGGCAGATTA 3671
                          v  i   v v  i i      iiivv    i iv  vi iiiv i v i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_51969519_5   3672 AACAGACAACCTATAGAGTGGGAGAAAATCTTCATGATCTATACATCTGA 3721
                           v        i i   i           v  iiii vii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_51969519_5   3722 CAAAGGACTAATATCCAGAATCTACAACAATCTCAAACAAATCAGCAAGA 3771
                         i  i     vi          v  i  vi v   vv    v   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_51969519_5   3772 AAAAATCGAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAA 3821
                             iv i  i  i  v  i?    i     v     iv          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_51969519_5   3822 TTCTCAAAAGAAGATATACAAATGGTCAACAAACATATGAAAAAATGATC 3871
                              v                   i   i  i  i       i   v  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_51969519_5   3872 A 3872
                          
  L1M4_orf2#LINE/    894 A 894

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (10 / 894), avg. gap size = 1.90 (19 / 10)  


3125 27.64 0.55 0.55  chrX_52018544_52020926.rev      985  1892 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_52018544_5    985 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATGTCATGAAAAT 1034
                              ii i  i     i      i v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_52018544_5   1035 GGCCATACTGCCCAAGGTAATTTAGAGATTCAATGCCATCCCCATCAAGC 1084
                            v     v     iv i  i  v        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_52018544_5   1085 TACCAATGATTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1132
                          v   iiviii  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_52018544_5   1133 TATGGAACTAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1182
                                v iv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_52018544_5   1183 AACAAAGCTGGGGGCATCACACTACCTGACTTCAAACTATACTACAAGGA 1232
                                i   i  vv       v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_52018544_5   1233 TACAGTAACCAAAACAGCATGGTACTCTTACCAAAACAGAGATATAGACC 1282
                                 i   i    ii       vvi iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_52018544_5   1283 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCCACAACT 1330
                                i    i--    i  --        vv   i i  ii iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_52018544_5   1331 GTCTGGTCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGACTCC 1380
                         ivi  i i  i     ivv  v   i v  vv     i      i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_52018544_5   1381 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1430
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_52018544_5   1431 GAAACTGGATCCCTTCCTTACAACTTATACAAAAATCAATTCAAGATGGA 1480
                            ii    i    v   i   v v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_52018544_5   1481 TTAAAGACTTAAATGTTAGACCTAAAAACATAAAAATCCTGGAAGAAAAC 1530
                          i ?    i       v   v      vi      v  i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_52018544_5   1531 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1579
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_52018544_5   1580 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1629
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_52018544_5   1630 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTAAA 1679
                           i   v i  i i   i  ii vv    i  v  i i  vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_52018544_5   1680 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 1729
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_52018544_5   1730 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAGGAAA 1779
                          i  i  vi          v  i  v      vv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_52018544_5   1780 AAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTT 1829
                           i     i     v  i? v  i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_52018544_5   1830 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1879
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_52018544_5   1880 CATCACTGGCCAT 1892
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2814 25.75 0.81 3.48  chrX_52064904_52066761.rev      507  1368 (490)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_52064904_5    507 ATCTGCAGATTCAGTGCAATCCCTAAAAAAAAAAAACAAACAACAACAGA 556
                             i        ii          v----------    - v -- ---
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTAT----------CAAA-ATC--C--- 103

  chrX_52064904_5    557 CAGTGACATTTCTCACAGAAATGGATAAAGCAATCACAAAATTCATATGG 606
                            ivi v   i ii       v  i  ivii   vi             
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_52064904_5    607 AACCACAAGTGACCCAGAATAGCCAAGCTATTCTAAACAAAAAAGAACAA 656
                           vii    v                ivi v   vi v   i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_52064904_5    657 ATCTGGAGGACTCACATTACCTGACTTCAAATCATACTACAGAGAGATAG 706
                          vi             i v  ii i      v v       i  vv i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_52064904_5    707 TAACCCAAACAGCACGGTACTGACATTAAAACAGACGTATAGACCCATTG 756
                            i v i    iii       i   v ii i    i      i v  v 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_52064904_5    757 AACAGAATACAGAAAGCAGAAACAAACCCACACACTTACAGTGAACTCAC 806
                           i     vv   ivv      i       i   i   ii  v  i v i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_52064904_5    807 TTTCCACAAAGGTGCCAAGAACATACACTGGGGAAAGA-CAGTCTCATTA 855
                             v    i          v   v  v          -i     iv i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_52064904_5    856 ATAAATGGTACTGGGAAACCTGGATATCCATATGCAGAAGAATGAATCTA 905
                          i       i      v v       ?   i     i         vi i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_52064904_5    906 GACCCCTATCTCTCACCATATACAAAAATCAAATCAGAATGGGTTAAAGA 955
                                 i   v                i  v   i     i i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_52064904_5    956 ----AATCTAAGCTTTCAAACTATGAAACTACTACAATAAAATATTGAGG 1001
                         ----   v    vvi v       i     vi  v  v    i  v i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_52064904_5   1002 AAACTCTACAAGACATTTAGATTGTAGATTTCCCTGGGCGAAAATTTCTT 1051
                         v  v   v iv   -i  i i  i------------   i vii      
  L1M4_orf2#LINE/    554 TAAATCTTCGTGAC-CTTGGGTTA------------GGCAATGGTTTCTT 590

  chrX_52064904_5   1052 GAGTAATGCC-CCACAAGCACAGGCATCCAAAGCAAACACGGGCAAATGA 1100
                         iii  -  v -   v       i   v v    v   v ii ii    vi
  L1M4_orf2#LINE/    591 AGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_52064904_5   1101 GATCACATCAAGTTCAAAAGCTTCTGCACAGCAGAGGATACAATCAACAC 1150
                           iiv      iv i    i   i  ii vv  i    i  v     v v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_52064904_5   1151 ATTGAAGAGACAGCACACAGAATGGGACAAAATATTTGCAAACTACCCGT 1200
                          v    i     i v            v              ii ivii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_52064904_5   1201 CTCACGAGGGATTAATAACCAGAGTATACGGGAAGCTCAAACAATTCTAT 1250
                           v ii     i vi  v     i    iiiii i   vv    i  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_52064904_5   1251 CGGAAAAAATCTAATA-TCTGATCAAGAAATCACCAAAAGATTTGAGTGG 1299
                         viv     iv v    -i ii  i? i    viv    i       i i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_52064904_5   1300 ACATTTCTCAAAGGAAGACATACAAATGGAAAACAGGCATGTGAGAAGGT 1349
                                  v  i     i          vv  i i   ii   i   i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_52064904_5   1350 GCTCAGCATCGCTGATCTT 1368
                              i    i????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (133 / 85)
Gap_init rate = 0.01 (11 / 839), avg. gap size = 3.36 (37 / 11)  


2814 25.75 0.81 3.48  chrX_52098455_52100312      505  1366 (492)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_52098455_5    505 ATCTGCAGATTCAGTGCAATCCCTAAAAAAAAAAAACAAACAACAACAGA 554
                             i        ii          v----------    - v -- ---
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTAT----------CAAA-ATC--C--- 103

  chrX_52098455_5    555 CAGTGACATTTCTCACAGAAATGGATAAAGCAATCACAAAATTCATATGG 604
                            ivi v   i ii       v  i  ivii   vi             
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_52098455_5    605 AACCACAAGTGACCCAGAATAGCCAAGCTATTCTAAACAAAAAAGAACAA 654
                           vii    v                ivi v   vi v   i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_52098455_5    655 ATCTGGAGGACTCACATTACCTGACTTCAAATCATACTACAGAGAGATAG 704
                          vi             i v  ii i      v v       i  vv i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_52098455_5    705 TAACCCAAACAGCACGGTACTGACATTAAAACAGACGTATAGACCCATTG 754
                            i v i    iii       i   v ii i    i      i v  v 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_52098455_5    755 AACAGAATACAGAAAGCAGAAACAAACCCACACACTTACAGTGAACTCAC 804
                           i     vv   ivv      i       i   i   ii  v  i v i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_52098455_5    805 TTTCCACAAAGGTGCCAAGAACATACACTGGGGAAAGA-CAGTCTCATTA 853
                             v    i          v   v  v          -i     iv i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_52098455_5    854 ATAAATGGTACTGGGAAACCTGGATATCCATATGCAGAAGAATGAATCTA 903
                          i       i      v v       ?   i     i         vi i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_52098455_5    904 GACCCCTATCTCTCACCATATACAAAAATCAAATCAGAATGGGTTAAAGA 953
                                 i   v                i  v   i     i i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_52098455_5    954 ----AATCTAAGCTTTCAAACTATGAAACTACTACAATAAAATATTGAGG 999
                         ----   v    vvi v       i     vi  v  v    i  v i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_52098455_5   1000 AAACTCTACAAGACATTTAGATTGTAGATTTCCCTGGGCGAAAATTTCTT 1049
                         v  v   v iv   -i  i i  i------------   i vii      
  L1M4_orf2#LINE/    554 TAAATCTTCGTGAC-CTTGGGTTA------------GGCAATGGTTTCTT 590

  chrX_52098455_5   1050 GAGTAATGCC-CCACAAGCACAGGCATCCAAAGCAAACACGGGCAAATGA 1098
                         iii  -  v -   v       i   v v    v   v ii ii    vi
  L1M4_orf2#LINE/    591 AGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_52098455_5   1099 GATCACATCAAGTTCAAAAGCTTCTGCACAGCAGAGGATACAATCAACAC 1148
                           iiv      iv i    i   i  ii vv  i    i  v     v v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_52098455_5   1149 ATTGAAGAGACAGCACACAGAATGGGACAAAATATTTGCAAACTACCCGT 1198
                          v    i     i v            v              ii ivii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_52098455_5   1199 CTCACGAGGGATTAATAACCAGAGTATACGGGAAGCTCAAACAATTCTAT 1248
                           v ii     i vi  v     i    iiiii i   vv    i  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_52098455_5   1249 CGGAAAAAATCTAATA-TCTGATCAAGAAATCACCAAAAGATTTGAGTGG 1297
                         viv     iv v    -i ii  i? i    viv    i       i i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_52098455_5   1298 ACATTTCTCAAAGGAAGACATACAAATGGAAAACAGGCATGTGAGAAGGT 1347
                                  v  i     i          vv  i i   ii   i   i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_52098455_5   1348 GCTCAGCATCGCTGATCTT 1366
                              i    i????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (133 / 85)
Gap_init rate = 0.01 (11 / 839), avg. gap size = 3.36 (37 / 11)  


3125 27.64 0.55 0.55  chrX_52144290_52146672      983  1890 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_52144290_5    983 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATGTCATGAAAAT 1032
                              ii i  i     i      i v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_52144290_5   1033 GGCCATACTGCCCAAGGTAATTTAGAGATTCAATGCCATCCCCATCAAGC 1082
                            v     v     iv i  i  v        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_52144290_5   1083 TACCAATGATTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1130
                          v   iiviii  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_52144290_5   1131 TATGGAACTAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1180
                                v iv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_52144290_5   1181 AACAAAGCTGGGGGCATCACACTACCTGACTTCAAACTATACTACAAGGA 1230
                                i   i  vv       v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_52144290_5   1231 TACAGTAACCAAAACAGCATGGTACTCTTACCAAAACAGAGATATAGACC 1280
                                 i   i    ii       vvi iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_52144290_5   1281 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCCACAACT 1328
                                i    i--    i  --        vv   i i  ii iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_52144290_5   1329 GTCTGGTCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGACTCC 1378
                         ivi  i i  i     ivv  v   i v  vv     i      i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_52144290_5   1379 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1428
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_52144290_5   1429 GAAACTGGATCCCTTCCTTACAACTTATACAAAAATCAATTCAAGATGGA 1478
                            ii    i    v   i   v v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_52144290_5   1479 TTAAAGACTTAAATGTTAGACCTAAAAACATAAAAATCCTGGAAGAAAAC 1528
                          i ?    i       v   v      vi      v  i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_52144290_5   1529 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1577
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_52144290_5   1578 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1627
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_52144290_5   1628 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTAAA 1677
                           i   v i  i i   i  ii vv    i  v  i i  vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_52144290_5   1678 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 1727
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_52144290_5   1728 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAGGAAA 1777
                          i  i  vi          v  i  v      vv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_52144290_5   1778 AAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTT 1827
                           i     i     v  i? v  i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_52144290_5   1828 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1877
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_52144290_5   1878 CATCACTGGCCAT 1890
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3006 26.88 1.35 0.79  chrX_52190540_52195697     3769  4657 (501)    L1M4_orf2#LINE/L1        1   894 (14)  

  chrX_52190540_5   3769 TGGAAACACATCCCATGATCATAGATGGGTAGAATCCATATTGTGAAAAT 3818
                               v i        v    i   v  v   v iv       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_52190540_5   3819 GACCATACTGCCAAAAGCAATCTACAAATTCAACGCAATTTCCATCAAAA 3868
                          i v     v  v   vii       i            ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_52190540_5   3869 TACCACCATCATGCTTCACAGAATTAGAAAAA--AATTCTAAAATTCATA 3916
                          v   v vv v vi  ii     v v  v  i--i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_52190540_5   3917 TGGAACCAAAAAAGGAGCCCATG-TAGCCAAAGCAA----GAACAAGCAA 3961
                              -- viv    ii    vi-        i   ----   v   ---
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG--- 195

  chrX_52190540_5   3962 AAAGAACAAATCTGGAGGCATCACATATCT-GATTTCAAACTATACTATA 4010
                         -         vi      vv     iv  i-i        viv     i 
  L1M4_orf2#LINE/    196 -AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_52190540_5   4011 AGGCCATAGTCACCAAAACAGCATAATACTGGTGTAAAAATAGGCACATA 4060
                          i  i i   v i   i    ii ii      ii   ii    i  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_52190540_5   4061 GACCAATGGAACAGAATACAAAACCCAGAAATAAACCCAAATACTTACAG 4110
                           i        i     vv i ii               v i i   ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_52190540_5   4111 CCAACTGCTCTTCAACAAAGCAAACAAAAC-ATAAAGTGGGGAAAGA-CA 4158
                         i   i  v i   i    i vviv   i  -  vv i          -i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_52190540_5   4159 CCCTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGA 4208
                         vi                       i  i   v  ?       i ii   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_52190540_5   4209 ATGAAACTATATCCTCATCTCTCACCTTGTACAAAAATCAGCTGAAGATG 4258
                              ii iv i  ii i   v    v i         i i  v  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_52190540_5   4259 GCTTAAGGACTTAAATCTAAGACCTGAAACTATAAACATTTTAGAAGATA 4308
                          v i ?i   i     v     v  i          vv i        v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_52190540_5   4309 ACATTAAA--AAACCCTCCTAGACATTGGCTAAGGGAAGGATTTCATGAC 4356
                             vii?--   i i  v -   v    v v   v  v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_52190540_5   4357 CAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACT 4406
                         i v  vv         v v    i    iv   i   i   iv v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_52190540_5   4407 TAATTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTTGGCAGATTA 4456
                          v  i   v v  i i      iiivv    i iv  vi iiiv i v i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_52190540_5   4457 AACAGACAACCTATAGAGTGGGAGAAAATCTTCATGATCTATACATCTGA 4506
                           v        i i   i           v  iiii vii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_52190540_5   4507 CAAAGGACTAATATCCAGAATCTACAACAATCTCAAACAAATCAGCAAGA 4556
                         i  i     vi          v  i  vi v   vv    v   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_52190540_5   4557 AAAAATCGAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAA 4606
                             iv i  i  i  v  i?    i     v     iv          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_52190540_5   4607 TTCTCAAAAGAAGATATACAAATGGTCAACAAACATATGAAAAAATGATC 4656
                              v                   i   i  i  i       i   v  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_52190540_5   4657 A 4657
                          
  L1M4_orf2#LINE/    894 A 894

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (10 / 894), avg. gap size = 1.90 (19 / 10)  


3125 27.64 0.55 0.55  chrX_52341484_52343866.rev      985  1892 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_52341484_5    985 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATGTCATGAAAAT 1034
                              ii i  i     i      i v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_52341484_5   1035 GGCCATACTGCCCAAGGTAATTTAGAGATTCAATGCCATCCCCATCAAGC 1084
                            v     v     iv i  i  v        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_52341484_5   1085 TACCAATGATTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1132
                          v   iiviii  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_52341484_5   1133 TATGGAACTAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1182
                                v iv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_52341484_5   1183 AACAAAGCTGGGGGCATCACACTACCTGACTTCAAACTATACTACAAGGA 1232
                                i   i  vv       v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_52341484_5   1233 TACAGTAACCAAAACAGCATGGTACTCTTACCAAAACAGAGATATAGACC 1282
                                 i   i    ii       vvi iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_52341484_5   1283 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCCACAACT 1330
                                i    i--    i  --        vv   i i  ii iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_52341484_5   1331 GTCTGGTCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGACTCC 1380
                         ivi  i i  i     ivv  v   i v  vv     i      i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_52341484_5   1381 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1430
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_52341484_5   1431 GAAACTGGATCCCTTCCTTACAACTTATACAAAAATCAATTCAAGATGGA 1480
                            ii    i    v   i   v v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_52341484_5   1481 TTAAAGACTTAAATGTTAGACCTAAAAACATAAAAATCCTGGAAGAAAAC 1530
                          i ?    i       v   v      vi      v  i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_52341484_5   1531 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1579
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_52341484_5   1580 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1629
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_52341484_5   1630 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTAAA 1679
                           i   v i  i i   i  ii vv    i  v  i i  vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_52341484_5   1680 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 1729
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_52341484_5   1730 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAGGAAA 1779
                          i  i  vi          v  i  v      vv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_52341484_5   1780 AAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTT 1829
                           i     i     v  i? v  i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_52341484_5   1830 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1879
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_52341484_5   1880 CATCACTGGCCAT 1892
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2814 25.75 0.81 3.48  chrX_52387844_52389701.rev      506  1367 (490)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_52387844_5    506 ATCTGCAGATTCAGTGCAATCCCTAAAAAAAAAAAACAAACAACAACAGA 555
                             i        ii          v----------    - v -- ---
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTAT----------CAAA-ATC--C--- 103

  chrX_52387844_5    556 CAGTGACATTTCTCACAGAAATGGATAAAGCAATCACAAAATTCATATGG 605
                            ivi v   i ii       v  i  ivii   vi             
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_52387844_5    606 AACCACAAGTGACCCAGAATAGCCAAGCTATTCTAAACAAAAAAGAACAA 655
                           vii    v                ivi v   vi v   i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_52387844_5    656 ATCTGGAGGACTCACATTACCTGACTTCAAATCATACTACAGAGAGATAG 705
                          vi             i v  ii i      v v       i  vv i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_52387844_5    706 TAACCCAAACAGCACGGTACTGACATTAAAACAGACGTATAGACCCATTG 755
                            i v i    iii       i   v ii i    i      i v  v 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_52387844_5    756 AACAGAATACAGAAAGCAGAAACAAACCCACACACTTACAGTGAACTCAC 805
                           i     vv   ivv      i       i   i   ii  v  i v i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_52387844_5    806 TTTCCACAAAGGTGCCAAGAACATACACTGGGGAAAGA-CAGTCTCATTA 854
                             v    i          v   v  v          -i     iv i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_52387844_5    855 ATAAATGGTACTGGGAAACCTGGATATCCATATGCAGAAGAATGAATCTA 904
                          i       i      v v       ?   i     i         vi i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_52387844_5    905 GACCCCTATCTCTCACCATATACAAAAATCAAATCAGAATGGGTTAAAGA 954
                                 i   v                i  v   i     i i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_52387844_5    955 ----AATCTAAGCTTTCAAACTATGAAACTACTACAATAAAATATTGAGG 1000
                         ----   v    vvi v       i     vi  v  v    i  v i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_52387844_5   1001 AAACTCTACAAGACATTTAGATTGTAGATTTCCCTGGGCGAAAATTTCTT 1050
                         v  v   v iv   -i  i i  i------------   i vii      
  L1M4_orf2#LINE/    554 TAAATCTTCGTGAC-CTTGGGTTA------------GGCAATGGTTTCTT 590

  chrX_52387844_5   1051 GAGTAATGCC-CCACAAGCACAGGCATCCAAAGCAAACACGGGCAAATGA 1099
                         iii  -  v -   v       i   v v    v   v ii ii    vi
  L1M4_orf2#LINE/    591 AGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_52387844_5   1100 GATCACATCAAGTTCAAAAGCTTCTGCACAGCAGAGGATACAATCAACAC 1149
                           iiv      iv i    i   i  ii vv  i    i  v     v v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_52387844_5   1150 ATTGAAGAGACAGCACACAGAATGGGACAAAATATTTGCAAACTACCCGT 1199
                          v    i     i v            v              ii ivii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_52387844_5   1200 CTCACGAGGGATTAATAACCAGAGTATACGGGAAGCTCAAACAATTCTAT 1249
                           v ii     i vi  v     i    iiiii i   vv    i  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_52387844_5   1250 CGGAAAAAATCTAATA-TCTGATCAAGAAATCACCAAAAGATTTGAGTGG 1298
                         viv     iv v    -i ii  i? i    viv    i       i i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_52387844_5   1299 ACATTTCTCAAAGGAAGACATACAAATGGAAAACAGGCATGTGAGAAGGT 1348
                                  v  i     i          vv  i i   ii   i   i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_52387844_5   1349 GCTCAGCATCGCTGATCTT 1367
                              i    i????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (133 / 85)
Gap_init rate = 0.01 (11 / 839), avg. gap size = 3.36 (37 / 11)  


2814 25.75 0.81 3.48  chrX_52421427_52423284      505  1366 (492)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_52421427_5    505 ATCTGCAGATTCAGTGCAATCCCTAAAAAAAAAAAACAAACAACAACAGA 554
                             i        ii          v----------    - v -- ---
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTAT----------CAAA-ATC--C--- 103

  chrX_52421427_5    555 CAGTGACATTTCTCACAGAAATGGATAAAGCAATCACAAAATTCATATGG 604
                            ivi v   i ii       v  i  ivii   vi             
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_52421427_5    605 AACCACAAGTGACCCAGAATAGCCAAGCTATTCTAAACAAAAAAGAACAA 654
                           vii    v                ivi v   vi v   i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_52421427_5    655 ATCTGGAGGACTCACATTACCTGACTTCAAATCATACTACAGAGAGATAG 704
                          vi             i v  ii i      v v       i  vv i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_52421427_5    705 TAACCCAAACAGCACGGTACTGACATTAAAACAGACGTATAGACCCATTG 754
                            i v i    iii       i   v ii i    i      i v  v 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_52421427_5    755 AACAGAATACAGAAAGCAGAAACAAACCCACACACTTACAGTGAACTCAC 804
                           i     vv   ivv      i       i   i   ii  v  i v i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_52421427_5    805 TTTCCACAAAGGTGCCAAGAACATACACTGGGGAAAGA-CAGTCTCATTA 853
                             v    i          v   v  v          -i     iv i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_52421427_5    854 ATAAATGGTACTGGGAAACCTGGATATCCATATGCAGAAGAATGAATCTA 903
                          i       i      v v       ?   i     i         vi i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_52421427_5    904 GACCCCTATCTCTCACCATATACAAAAATCAAATCAGAATGGGTTAAAGA 953
                                 i   v                i  v   i     i i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_52421427_5    954 ----AATCTAAGCTTTCAAACTATGAAACTACTACAATAAAATATTGAGG 999
                         ----   v    vvi v       i     vi  v  v    i  v i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_52421427_5   1000 AAACTCTACAAGACATTTAGATTGTAGATTTCCCTGGGCGAAAATTTCTT 1049
                         v  v   v iv   -i  i i  i------------   i vii      
  L1M4_orf2#LINE/    554 TAAATCTTCGTGAC-CTTGGGTTA------------GGCAATGGTTTCTT 590

  chrX_52421427_5   1050 GAGTAATGCC-CCACAAGCACAGGCATCCAAAGCAAACACGGGCAAATGA 1098
                         iii  -  v -   v       i   v v    v   v ii ii    vi
  L1M4_orf2#LINE/    591 AGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_52421427_5   1099 GATCACATCAAGTTCAAAAGCTTCTGCACAGCAGAGGATACAATCAACAC 1148
                           iiv      iv i    i   i  ii vv  i    i  v     v v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_52421427_5   1149 ATTGAAGAGACAGCACACAGAATGGGACAAAATATTTGCAAACTACCCGT 1198
                          v    i     i v            v              ii ivii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_52421427_5   1199 CTCACGAGGGATTAATAACCAGAGTATACGGGAAGCTCAAACAATTCTAT 1248
                           v ii     i vi  v     i    iiiii i   vv    i  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_52421427_5   1249 CGGAAAAAATCTAATA-TCTGATCAAGAAATCACCAAAAGATTTGAGTGG 1297
                         viv     iv v    -i ii  i? i    viv    i       i i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_52421427_5   1298 ACATTTCTCAAAGGAAGACATACAAATGGAAAACAGGCATGTGAGAAGGT 1347
                                  v  i     i          vv  i i   ii   i   i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_52421427_5   1348 GCTCAGCATCGCTGATCTT 1366
                              i    i????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (133 / 85)
Gap_init rate = 0.01 (11 / 839), avg. gap size = 3.36 (37 / 11)  


2814 25.75 0.81 3.48  chrX_52434321_52436178      505  1366 (492)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_52434321_5    505 ATCTGCAGATTCAGTGCAATCCCTAAAAAAAAAAAACAAACAACAACAGA 554
                             i        ii          v----------    - v -- ---
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTAT----------CAAA-ATC--C--- 103

  chrX_52434321_5    555 CAGTGACATTTCTCACAGAAATGGATAAAGCAATCACAAAATTCATATGG 604
                            ivi v   i ii       v  i  ivii   vi             
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_52434321_5    605 AACCACAAGTGACCCAGAATAGCCAAGCTATTCTAAACAAAAAAGAACAA 654
                           vii    v                ivi v   vi v   i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_52434321_5    655 ATCTGGAGGACTCACATTACCTGACTTCAAATCATACTACAGAGAGATAG 704
                          vi             i v  ii i      v v       i  vv i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_52434321_5    705 TAACCCAAACAGCACGGTACTGACATTAAAACAGACGTATAGACCCATTG 754
                            i v i    iii       i   v ii i    i      i v  v 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_52434321_5    755 AACAGAATACAGAAAGCAGAAACAAACCCACACACTTACAGTGAACTCAC 804
                           i     vv   ivv      i       i   i   ii  v  i v i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_52434321_5    805 TTTCCACAAAGGTGCCAAGAACATACACTGGGGAAAGA-CAGTCTCATTA 853
                             v    i          v   v  v          -i     iv i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_52434321_5    854 ATAAATGGTACTGGGAAACCTGGATATCCATATGCAGAAGAATGAATCTA 903
                          i       i      v v       ?   i     i         vi i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_52434321_5    904 GACCCCTATCTCTCACCATATACAAAAATCAAATCAGAATGGGTTAAAGA 953
                                 i   v                i  v   i     i i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_52434321_5    954 ----AATCTAAGCTTTCAAACTATGAAACTACTACAATAAAATATTGAGG 999
                         ----   v    vvi v       i     vi  v  v    i  v i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_52434321_5   1000 AAACTCTACAAGACATTTAGATTGTAGATTTCCCTGGGCGAAAATTTCTT 1049
                         v  v   v iv   -i  i i  i------------   i vii      
  L1M4_orf2#LINE/    554 TAAATCTTCGTGAC-CTTGGGTTA------------GGCAATGGTTTCTT 590

  chrX_52434321_5   1050 GAGTAATGCC-CCACAAGCACAGGCATCCAAAGCAAACACGGGCAAATGA 1098
                         iii  -  v -   v       i   v v    v   v ii ii    vi
  L1M4_orf2#LINE/    591 AGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_52434321_5   1099 GATCACATCAAGTTCAAAAGCTTCTGCACAGCAGAGGATACAATCAACAC 1148
                           iiv      iv i    i   i  ii vv  i    i  v     v v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_52434321_5   1149 ATTGAAGAGACAGCACACAGAATGGGACAAAATATTTGCAAACTACCCGT 1198
                          v    i     i v            v              ii ivii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_52434321_5   1199 CTCACGAGGGATTAATAACCAGAGTATACGGGAAGCTCAAACAATTCTAT 1248
                           v ii     i vi  v     i    iiiii i   vv    i  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_52434321_5   1249 CGGAAAAAATCTAATA-TCTGATCAAGAAATCACCAAAAGATTTGAGTGG 1297
                         viv     iv v    -i ii  i? i    viv    i       i i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_52434321_5   1298 ACATTTCTCAAAGGAAGACATACAAATGGAAAACAGGCATGTGAGAAGGT 1347
                                  v  i     i          vv  i i   ii   i   i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_52434321_5   1348 GCTCAGCATCGCTGATCTT 1366
                              i    i????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (133 / 85)
Gap_init rate = 0.01 (11 / 839), avg. gap size = 3.36 (37 / 11)  


1638 25.75 7.36 3.51  chrX_52526597_52528636.rev      502  1099 (941)    L1M4_orf2#LINE/L1      173   793 (115)  

  chrX_52526597_5    502 TAGCTAAGACAATTTTTGGAAAGGAAGAATAAGGTGGGAGGAATGGCTCT 551
                             i  i     i  - i   i      i  i  v      v vi v  
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_52526597_5    552 ACCATATTTCAATATTTCTTATATAGCTACAGGAATCAAGTCTGTGTAGT 601
                         v  vv       v i  vi  i v        v       v v    i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_52526597_5    602 ACTGGGAGAAGAATAGACACATAGATCACTGGAACAAAATAGAGAACCTA 651
                              v v   i       i        v     i i   v    ii i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_52526597_5    652 GAAATAGCCCCA------------CAAT-GATTTTTTACAGGGA---CAA 685
                               iv    ------------    -      iv   i  i---   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_52526597_5    686 --------AAAGAAGGAAGGGTCATCTGCTTGACAAATGGTGCTGGAGCA 727
                         --------  v ii i   ii vi   vi ii              ii  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_52526597_5    728 GTTGCAGAGCCATAGGCTAAAAAAAAAAAAAAAAAGACCTAATCTTCATA 777
                         ii  v v ?   i v  -    i  vi  ivvii vv    -- i   i 
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGC-AAAAGAATGAAGTTGGACCCCTA--CCTCACA 468

  chrX_52526597_5    778 TTTTTATACAAAAAATAACTCAAG-TGGATCATAGATTTAAATCTAAAAT 826
                         iiv -         v        i-       ?   ii     v   i v
  L1M4_orf2#LINE/    469 CCAT-ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_52526597_5    827 ATAAAACTAAAAAAAAATCTTTTACAAGAAAGCAT-GGGACAAACGTCTG 875
                         v        v    ----  i   v      i   -  ?ii   iv ii 
  L1M4_orf2#LINE/    518 CTAAAACTATAAAA----CTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_52526597_5    876 AGATCTAGGGTATAGTGAATGGTT------------CA--AAAAGCATAA 911
                         v  i  v    -   vv       ------------  --       i  
  L1M4_orf2#LINE/    564 TGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_52526597_5    912 TCCATAAAG---AAAACAAGTAAATTAGATTTCATCCAATTTAAAA-CTT 957
                         v v i   i---    i ii      i  i      v  v      -   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_52526597_5    958 GTGCTCTGCAAGAGACCCTGTTAAAAGGATGAAAAAACTGGGTCTTGACT 1007
                         v  iv  v   ii   v  i i  i iii      i  vivviviv  v 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_52526597_5   1008 AGGAGAAAATGTTTGCAAACCACATATCCAAGAAAGGACTCACATCCAGA 1057
                         i         i        i  i     ii v  i     iii       
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_52526597_5   1058 ATATATAATGGATATGTATAGTACTCTCAAAACTCAATGGTA 1099
                                 -----------  v     i v        ii  
  L1M4_orf2#LINE/    763 ATATATAA-----------AGAACTCTTACAACTCAATAATA 793

Transitions / transversions = 1.56 (92 / 59)
Gap_init rate = 0.03 (17 / 621), avg. gap size = 3.82 (65 / 17)  

 395 20.63 3.97 4.76  chrX_52526597_52528636.rev     1429  1554 (486)    L1M4_orf2#LINE/L1      784   908 (0)  

  chrX_52526597_5   1429 CTCAATGGTAAAAAATACAAACAAATAATCCAATTAGAAAATCATGAAAA 1478
                               ii      i-----        i      ?i     vivv   i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAG-----ACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_52526597_5   1479 GATGTGAACATATACTTCACTGAAGAGGAAATA-----AGCAAATAGGCA 1523
                            v    i v i i   v ii    i  v   -----i  v    i   
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_52526597_5   1524 CATGAAAAGATGTTCAACCCTCATTTCCTTC 1554
                                     i     v-   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.78 (16 / 9)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 3.67 (11 / 3)  


1566 24.20 8.97 3.72  chrX_52570753_52572777.rev      502  1092 (933)    L1M4_orf2#LINE/L1      172   793 (115)  

  chrX_52570753_5    502 ATAGCTAAGACAATTTTTGAAAAAGAAGAATAAGGTGGGAGGAATGGCTC 551
                              i  i     i  -            i  i  v      v vi v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_52570753_5    552 TTTCATATTTCAATACTTTTTATATAGCTATAGGAATCAAGACTGTGTAG 601
                           i vv       v    vi  i v     i  v         v    i 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_52570753_5    602 TACTGGGAGAAGAATAGACGCATAGATCACTGGAACAAAATAGAGAACCT 651
                               v v   i      ii        v     i i   v    ii i
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_52570753_5    652 AGAAATAGCCCCACAC-------------TGATTTTTTACCAAG------ 682
                                iv    i  -------------       iv  v i ------
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_52570753_5    683 AGACAA---AAAGAAGGAAGGATTGTCTGCTGAACAAATGGTGCTGAAGA 729
                             v ---  v ii i   i  v    vi v              i-  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG-GA 419

  chrX_52570753_5    730 TG-TTG--TAGACATAGGCCAAAAAAAAAAG----ACC--TAATTTTCAT 770
                         ii-i  --  ?v  i v  v   i  vi   ----   --  --ii   i
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA--CCTCAC 467

  chrX_52570753_5    771 ACCTTTATACAAGAAAGTAACTCAAG-TGGATCATAGATTTAAATCTAAA 819
                            v -      -   v        i-       ?   ii     v   i
  L1M4_orf2#LINE/    468 ACCAT-ATACAA-AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_52570753_5    820 ATATAAAACTAAAAGAAAACTTTTACAATAAAATATAGGAGAAACATCT- 868
                          vv        ---v      i   v  v    i     ? v  -    -
  L1M4_orf2#LINE/    516 AGCTAAAACTA---TAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTT 561

  chrX_52570753_5    869 -GAGATCTAGGGCATAGTGAACGGTT------------CA--AAAAGCAT 903
                         - v  i  v   i-   vv  i    ------------  --       i
  L1M4_orf2#LINE/    562 CGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_52570753_5    904 AATCCATAAG-GAAAAAA---ATAAATTAGATTTCATCCAATTTAAAA-C 948
                           v v i  i-       ---       i  i      v  v      - 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_52570753_5    949 TTGTGCTCTGCAAGAAATCTTTTTAAAAGGATGAAAAAACAGGTTATGAC 998
                           v  iv  v   iii ivi v i  i iii      i   ivii iiiv
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_52570753_5    999 CTGGGAGAGAGTGCTTGCAAACCACATATCCAAGAAAGGACTCACATCCA 1048
                         v       i i ii       i  i     ii v  i     iii     
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_52570753_5   1049 GAATATATAATGGATATACATACTACTCTCAAAACTCAATGGTA 1092
                                   -i  ----------     i v        ii  
  L1M4_orf2#LINE/    761 GAATATATAA-AGA----------ACTCTTACAACTCAATAATA 793

Transitions / transversions = 1.59 (86 / 54)
Gap_init rate = 0.04 (24 / 622), avg. gap size = 3.12 (75 / 24)  

 435 17.46 3.97 4.76  chrX_52570753_52572777.rev     1413  1538 (487)    L1M4_orf2#LINE/L1      784   908 (0)  

  chrX_52570753_5   1413 CTCAATGGTAAAAAATGCAAACAAATAATCCAATTAGAAAATCATGAAAA 1462
                               ii      i-----        i      ?i     vivv   i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAG-----ACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_52570753_5   1463 GATATGAACATACATTTCACTGAAGAGGAAATA-----AGCAAATAAGCA 1507
                            v    i v       v ii    i  v   -----i  v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_52570753_5   1508 CATGAAAAGATGTTCAACACTCATTTGCTTC 1538
                                     i      -   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 3.67 (11 / 3)  


 912 24.93 6.80 4.82  chrX_52623750_52626109.rev      502   854 (1506)    L1M4_orf2#LINE/L1      172   531 (377)  

  chrX_52623750_5    502 ATAGCTAAGACAATTTTTGAAAAAGAAGAAGAATAAGGTGGGAGGAATTG 551
                              i  i     i  -            ---i  i  v      v ii
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTT-GAAAAAGAAGAA---CAAAGTTGGAGGACTCA 217

  chrX_52623750_5    552 CTCTACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTATA 601
                          v  v  vv       v    vi  i v        v         vi i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_52623750_5    602 TACCATTGGGAGAAAAATAGACACATAGATCGCTGTAACAAAATAGAAAA 651
                          ivi i   v v  ii       i       iv  v  i i   v  i i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_52623750_5    652 CCTAGAAATAG-CCCACAC-------------TGATTTTTTACCAAGA-G 686
                         i i       i-    i  -------------       iv  v i i- 
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_52623750_5    687 ACAAAA-------ATAGGGAAAGA-TCATCTGCTTAACAAATGGTGCTGG 728
                         v   i -------  i        - vi   vi i               
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_52623750_5    729 GGCAGTTGCAGAGCCATAGGCCAAAAAAAAAAAAATAATAATAATAAGGC 778
                          i  ii  v v ?   i v  -------    i   i ---- i vi i 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGC-------AAAAGAATGA----AGTTGGAC 456

  chrX_52623750_5    779 CTAGTCTTCATACCTTTATACAAAAAAGTAAGTCAAG-TGGATCATAGAT 827
                          ivvv i   i   v -         -v   v    i-       ?   i
  L1M4_orf2#LINE/    457 CCCTACCTCACACCAT-ATACAAAAA-TTAACTCAAAATGGATCAWAGAC 504

  chrX_52623750_5    828 TTAAATCTAAAATATAAAACTAAAAAA 854
                         i     v   i vv        v    
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAA 531

Transitions / transversions = 1.39 (50 / 36)
Gap_init rate = 0.03 (12 / 360), avg. gap size = 3.42 (41 / 12)  

 627 25.47 8.99 4.49  chrX_52623750_52626109.rev     1168  1434 (926)    L1M4_orf2#LINE/L1      515   793 (115)  

  chrX_52623750_5   1168 GAACTAAAA--ACAAAGTT-TTACAAGAAAATATAGGAG-AAACGTCTGA 1213
                           i      -- i   ii -   v       i     ? -   iv ii v
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_52623750_5   1214 GATCTAGGGCATAGTGAATGGTT------------CA--AAAAGCATAAT 1249
                           i  v   i-   vv       ------------  --       i  v
  L1M4_orf2#LINE/    565 GACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_52623750_5   1250 --ACATAAGAAAAAA---ATAAATTAGATTTTATCCAATTTAAAA-CTTT 1293
                         --   v         ---       i  i  i   v  v      -    
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_52623750_5   1294 TGCTCTGCAAGAAATCTTGTTAAAAGGATGAAAAAATAGGGTACGATCTG 1343
                           iv  v   iii ivi i i  i iii      i i ivvi  iivv  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_52623750_5   1344 AAAGAAAATGTTTGCAAACCACATATCCAAGAAAGGACTCACATCCAGAA 1393
                         ii       i        i  i     ii v  i     iii        
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_52623750_5   1394 TATACAATGGATACGTATAGTACTCTCAAAACTCAACAGTA 1434
                             i  -----------  v     i v       i i  
  L1M4_orf2#LINE/    764 TATATAA-----------AGAACTCTTACAACTCAATAATA 793

Transitions / transversions = 2.35 (47 / 20)
Gap_init rate = 0.04 (10 / 279), avg. gap size = 3.60 (36 / 10)  

 396 18.12 5.62 5.62  chrX_52623750_52626109.rev     1714  1873 (487)    L1M4_orf2#LINE/L1      749   908 (0)  

  chrX_52623750_5   1714 GACTCTGTCTCAAGAAAAAAAAAATAA----TAAAAACCTCAATGGTAAA 1759
                             -   v  v    v v v   v  ----  v  --      ii    
  L1M4_orf2#LINE/    749 GACT-TGTATCCAGAATATATAAAGAACTCTTACAA--CTCAATAATAAA 795

  chrX_52623750_5   1760 AAATACAAACAAATAATCCAATTAGAAAATCATGAAAAGATATGAACATA 1809
                           i-----        i      ?i     vivv   i   v    i v 
  L1M4_orf2#LINE/    796 AAG-----ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_52623750_5   1810 CATTTCACTGAAGAGGAAATA-----AGCAAATAAGCACATGAAAAGATG 1854
                               v ii    i  v   -----i  v                    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_52623750_5   1855 TTCAACACTCATTTGCTTC 1873
                         i      -   ????????
  L1M4_orf2#LINE/    891 CTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 0.87 (13 / 15)
Gap_init rate = 0.04 (6 / 160), avg. gap size = 3.00 (18 / 6)  


2843 27.38 0.83 0.60  chrX_52639094_52640915      490  1329 (493)    L1M4_orf2#LINE/L1       67   908 (0)  

  chrX_52639094_5    490 TTACTCTGTA-ATTCAATGCCATCCCCATCAAGCTACAAATGACTTTCTT 538
                           iv   ii -      i  v     i     iv v v iivi i  i  
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTT 116

  chrX_52639094_5    539 CACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAAG 586
                         ii     -   -- v  i  - iii    i           viiv  ii 
  L1M4_orf2#LINE/    117 TGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_52639094_5    587 AGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCCAGAGGCA 636
                          v  viv  v     iv     i i ivv i          iii    vv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_52639094_5    637 TCATGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACA 686
                            ii  v  ii i      viv        i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_52639094_5    687 GCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC--A 734
                          ii         i iv ii i   v                i    i-- 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_52639094_5    735 GAGCCCTTAGAAATAATGCCACATATCTACAACCATCTGATCTTTGACAA 784
                            i  --        vv   i i  i  iiii  vi    i  i     
  L1M4_orf2#LINE/    315 GAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_52639094_5    785 ACCTGACAAAAACAGGCAAAGGGGAAAGGATTCCCTATTTAATAAATGGT 834
                         ivv  v   i v  vv   v        i  vvi  v  i  i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_52639094_5    835 GCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTC 884
                                v      v  ?   i   i i  iiv    ii    i    v 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_52639094_5    885 CTTACACCTTATACAAAAATTAATTCAAGATGGATGAAAGACTTAAATGT 934
                           i     v              i    i      v ?    i       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_52639094_5    935 TAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATT 983
                         v   v       i      vi i           v    ?i- v i -  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TT 561

  chrX_52639094_5    984 CAGGACATAGCAT-GGGCAAGGACTTCATGTCTGAAACACCAAAAGCAAC 1032
                          iv   v v vi -i     v ii   v ivv ivi            vv
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_52639094_5   1033 GGCAACAAAAGCCATAATTGACAAATGGGATCTAATTAAACTCAAGAGCT 1082
                         i          vv v   v  i    v   ii v  i   v i  i i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_52639094_5   1083 TCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAGCCTACAGAA 1132
                          i  ii vv    i  v    i  vv i      v  i  i  i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_52639094_5   1133 TGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAG 1182
                                    v  i    vii ivi      i  i  i  vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_52639094_5   1183 AATCTACAATGAACTCAAATAAATTTACAAGAAAAAAACAAACAACCCCA 1232
                            v  i  v      vv i  v iv i  v     i     i     v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_52639094_5   1233 TCAAAAAGTCGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATT 1282
                          i?    i v          v    i     i     v        i  v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_52639094_5   1283 TATGCAGCCAGAAGACACATGAAAAAATGCTCATCATCACTGGCCAT 1329
                         i viii    iv ii          i       v     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.01 (9 / 842), avg. gap size = 1.33 (12 / 9)  


 912 24.93 6.80 4.82  chrX_52656489_52658849      500   852 (1509)    L1M4_orf2#LINE/L1      172   531 (377)  

  chrX_52656489_5    500 ATAGCTAAGACAATTTTTGAAAAAGAAGAAGAATAAGGTGGGAGGAATTG 549
                              i  i     i  -            ---i  i  v      v ii
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTT-GAAAAAGAAGAA---CAAAGTTGGAGGACTCA 217

  chrX_52656489_5    550 CTCTACCATATTTCAATACTTCTTATATAGCTACAGGAATCAAGACTATA 599
                          v  v  vv       v    vi  i v        v         vi i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_52656489_5    600 TACCATTGGGAGAAAAATAGACACATAGATCGCTGTAACAAAATAGAAAA 649
                          ivi i   v v  ii       i       iv  v  i i   v  i i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_52656489_5    650 CCTAGAAATAG-CCCACAC-------------TGATTTTTTACCAAGA-G 684
                         i i       i-    i  -------------       iv  v i i- 
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_52656489_5    685 ACAAAA-------ATAGGGAAAGA-TCATCTGCTTAACAAATGGTGCTGG 726
                         v   i -------  i        - vi   vi i               
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_52656489_5    727 GGCAGTTGCAGAGCCATAGGCCAAAAAAAAAAAAATAATAATAATAAGGC 776
                          i  ii  v v ?   i v  -------    i   i ---- i vi i 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGC-------AAAAGAATGA----AGTTGGAC 456

  chrX_52656489_5    777 CTAGTCTTCATACCTTTATACAAAAAAGTAAGTCAAG-TGGATCATAGAT 825
                          ivvv i   i   v -         -v   v    i-       ?   i
  L1M4_orf2#LINE/    457 CCCTACCTCACACCAT-ATACAAAAA-TTAACTCAAAATGGATCAWAGAC 504

  chrX_52656489_5    826 TTAAATCTAAAATATAAAACTAAAAAA 852
                         i     v   i vv        v    
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAA 531

Transitions / transversions = 1.39 (50 / 36)
Gap_init rate = 0.03 (12 / 360), avg. gap size = 3.42 (41 / 12)  

 627 25.47 8.99 4.49  chrX_52656489_52658849     1166  1432 (929)    L1M4_orf2#LINE/L1      515   793 (115)  

  chrX_52656489_5   1166 GAACTAAAA--ACAAAGTT-TTACAAGAAAATATAGGAG-AAACGTCTGA 1211
                           i      -- i   ii -   v       i     ? -   iv ii v
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_52656489_5   1212 GATCTAGGGCATAGTGAATGGTT------------CA--AAAAGCATAAT 1247
                           i  v   i-   vv       ------------  --       i  v
  L1M4_orf2#LINE/    565 GACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_52656489_5   1248 --ACATAAGAAAAAA---ATAAATTAGATTTTATCCAATTTAAAA-CTTT 1291
                         --   v         ---       i  i  i   v  v      -    
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_52656489_5   1292 TGCTCTGCAAGAAATCTTGTTAAAAGGATGAAAAAATAGGGTACGATCTG 1341
                           iv  v   iii ivi i i  i iii      i i ivvi  iivv  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_52656489_5   1342 AAAGAAAATGTTTGCAAACCACATATCCAAGAAAGGACTCACATCCAGAA 1391
                         ii       i        i  i     ii v  i     iii        
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_52656489_5   1392 TATACAATGGATACGTATAGTACTCTCAAAACTCAACAGTA 1432
                             i  -----------  v     i v       i i  
  L1M4_orf2#LINE/    764 TATATAA-----------AGAACTCTTACAACTCAATAATA 793

Transitions / transversions = 2.35 (47 / 20)
Gap_init rate = 0.04 (10 / 279), avg. gap size = 3.60 (36 / 10)  

 397 18.63 4.97 5.59  chrX_52656489_52658849     1712  1872 (489)    L1M4_orf2#LINE/L1      749   908 (0)  

  chrX_52656489_5   1712 GACTCTGTCTCAAGAAAA---AAAAAAATAATAAAAACCTCAATGGTAAA 1758
                             -   v  v    v ---   i  v vv  v  --      ii    
  L1M4_orf2#LINE/    749 GACT-TGTATCCAGAATATATAAAGAACTCTTACAA--CTCAATAATAAA 795

  chrX_52656489_5   1759 AAATACAAACAAATAATCCAATTAGAAAATCATGAAAAGATATGAACATA 1808
                           i-----        i      ?i     vivv   i   v    i v 
  L1M4_orf2#LINE/    796 AAG-----ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_52656489_5   1809 CATTTCACTGAAGAGGAAATA-----AGCAAATAAGCACATGAAAAGATG 1853
                               v ii    i  v   -----i  v                    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_52656489_5   1854 TTCAACACTCATTTGCTTC 1872
                         i      -   ????????
  L1M4_orf2#LINE/    891 CTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 0.93 (14 / 15)
Gap_init rate = 0.04 (6 / 160), avg. gap size = 2.83 (17 / 6)  


2755 27.01 0.62 0.74  chrX_52748592_52750392      504  1310 (491)    L1M4_orf2#LINE/L1      103   908 (0)  

  chrX_52748592_5    504 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATA 551
                            iivi i  i  ii     -   -- v  i  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chrX_52748592_5    552 TGGAACCAAAAAAGAGCCCACACCTCCAAGTCAATCCTAAGCCAAAAGAA 601
                              viiv  ii  v  viv ivv    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_52748592_5    602 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAAGCTA 651
                              i      vv    i  v  ii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_52748592_5    652 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 701
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_52748592_5    702 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCACATCTACAGCTAT 749
                              i    i--    i  --        vv iii    i  ii ii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_52748592_5    750 CTGATCTTTCACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 799
                         i    i  iv    ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_52748592_5    800 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCTGA 849
                         v  i  i              v      v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_52748592_5    850 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 899
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_52748592_5    900 AAAGACTTACATGTTAGATCTAAAACCATAAAAACCCTACAAGAAAACCT 949
                          ?    i  v    v   v       i      vi i  v        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_52748592_5    950 AGGCA-ATACCATTCAGAACATTGGCATGGGCAAGGACTTCATGTCTAAA 998
                            ?i- v i -   ivi  v    vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_52748592_5    999 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1048
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_52748592_5   1049 TAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAACA 1098
                         i   v i  i i   i  ii vv    i  v    i ivv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_52748592_5   1099 GGCAAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 1148
                          i   -  i                 v       vii ivi      i  
  L1M4_orf2#LINE/    698 GACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_52748592_5   1149 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1198
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_52748592_5   1199 AAACAAACAACCCCATCAACAAGTGGTCAAAGGATATGAACAGACACTTC 1248
                          i     i     v  i? v  i   v        v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_52748592_5   1249 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 1298
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_52748592_5   1299 ATTGCTAGCCAT 1310
                           ii????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (127 / 87)
Gap_init rate = 0.01 (8 / 806), avg. gap size = 1.38 (11 / 8)  


 386 26.09 9.42 0.00  chrX_52755788_52762230.rev       95   232 (6211)  C L1M4_orf2#LINE/L1   (269)   639   489  

C chrX_52755788_5    232 AAAATGCATCATAGAACTAAATGTAAAAGCTAATGTTACAACACTTGTAG 183
                               v    ?   v          i      vii  i  v   iv   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

C chrX_52755788_5    182 AAGAAAATGTATGAGGATGTCT----GACATCATGTTAGACAA------- 144
                                ii  v ? v vi   ----   v iiv     i   -------
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

C chrX_52755788_5    143 --AGACAGGATACAAAAAGCACAGACTATGAAATAAAAAATTCATAAACT 96
                         --   i v  i  v         ii v ii   v       vv     i 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

C chrX_52755788_5     95 G 95
                          
  L1M4_orf2#LINE/    639 G 639

Transitions / transversions = 1.12 (18 / 16)
Gap_init rate = 0.01 (2 / 151), avg. gap size = 6.50 (13 / 2)  

3088 27.61 0.66 0.77  chrX_52755788_52762230.rev     5044  5952 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_52755788_5   5044 TAGAAGCACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5093
                          i   iv i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_52755788_5   5094 GGCCATACTGCCCAAGGCAATTTTTAGATTCAATGCCATCCCCATCAAGC 5143
                            v     v     ivii  i vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_52755788_5   5144 TCCCAATGACTTCCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCA 5191
                              iivi i ii  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_52755788_5   5192 TATGGAACCAAAAAAGAGCCTGCCTTGCCAAGACAATCCTAAGGAGAAGG 5241
                                viiv  ii  v  v vv v     i      i i ii ii i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_52755788_5   5242 AACAAAGCTGGAGAAATCAGGCTACCTGACTTCAAACTATGCTACAAGGA 5291
                                i     i v   vi  v  ii i      viv i      i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_52755788_5   5292 TAAAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGACC 5341
                           v     i   i     i         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_52755788_5   5342 AATGAAACAGAAC--AGAGCCCTTAGTAATAACACTACACATCCACAACT 5389
                             i  i    i--    i  --  v     vv i i    ii iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_52755788_5   5390 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5439
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_52755788_5   5440 CTATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCATATGTAGAAAGCT 5489
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_52755788_5   5490 GAGACTGGATCCCTTCCTTACACCTTATACAGAAATTAATTCAAGCTGGA 5539
                           iii    i    v   i     v      i       i    iv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_52755788_5   5540 TTAAACACTTAAATTGTA-GACCTAAAACCATAAAAACCCTAGAAGAAAA 5588
                          i ? v  i     -   -  v       i      vi i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_52755788_5   5589 CCTAGGCA-ATACCATTCAGGACATTGGCATGGGCAAGGACCTCATGACT 5637
                          v    ?i- v i -   iv   v    vv i     v iii  v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_52755788_5   5638 AAAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAAAGGGATCT 5687
                          vi            vvii         vv     v  i   vv   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_52755788_5   5688 AATTAAACTCAAGAGCTTCTGCACAGGAAAAGAAACTATCATCAGAGCGA 5737
                         v  i   v i  i i   i  ii vvv   i  v       vv i  i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_52755788_5   5738 AAAGGCAACCTAGAGAAAGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5787
                             i     i v    v          v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_52755788_5   5788 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5837
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_52755788_5   5838 AAAAATCAAACAACCCCATCAAAAAGTGGACAAAGGATATGAACAGACAC 5887
                            i -    i     v  i?    i   i        v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_52755788_5   5888 TTTTCAAAAGAAGACATTTATGCAGCCAACAGGCACATGAAAAAATGCCC 5937
                           i  v        i  vi viii     i i           i    i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_52755788_5   5938 ATCATCACTGGTCAT 5952
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (154 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3209 26.32 0.66 1.10  chrX_52789316_52793621     2902  3813 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_52789316_5   2902 TGGAAGAACATTCCATGCTCATGGATAGGAAGAGTCAATATCGTGAAAAT 2951
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_52789316_5   2952 GGCCATACTGCCCAAGGTAATTTATAGAATCAATGCCATCCCCATCAAGC 3001
                            v     v     iv i  i  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_52789316_5   3002 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3049
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_52789316_5   3050 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTTAATCCTAAGCCAAAAG 3099
                                viiv  ii  v  v v  v     ivi    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_52789316_5   3100 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATATATACTACA 3149
                                i      vv    i  v  ii i      ---- iv       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACTTACTACA 244

  chrX_52789316_5   3150 AGGCTGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAACGATATA 3199
                          i   i      i   i    ii         i iv ii i ivv     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_52789316_5   3200 GACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATTTAC 3247
                           i        i    i--    i  --        vv  ii i     i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chrX_52789316_5   3248 AACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGA 3297
                         iii  vi    i  i     ivv  v   i v  vvv           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_52789316_5   3298 TTCCCTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAA 3347
                          vvi  v  v  i              v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_52789316_5   3348 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGC 3397
                         iiv    ii    i    v   i     v              i    iv
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_52789316_5   3398 TGGATTAAACACTTAAATTGTA-GACCTAAAACCATAAAAACCCTAGAAG 3446
                              i ? v  i     -   -  v       i      vi i      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_52789316_5   3447 AAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 3495
                              v    ?i- v i -   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_52789316_5   3496 GTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 3545
                         ivv  vi            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_52789316_5   3546 ATCTAATTAAACTCAAGATCTTCTGCACAGCAAAAGAAACTACCATCAGA 3595
                          ii v  i   v i  i v   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_52789316_5   3596 GTGAACAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATC 3645
                              v  i  i  i                 v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_52789316_5   3646 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCCATCAAATTTACA 3695
                            i  i  i  vi          v  i  v      ivv   v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_52789316_5   3696 AGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGA 3745
                          v     i     i     v  i?    i     i      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_52789316_5   3746 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATG 3795
                           i     v        i  vi viii     v ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_52789316_5   3796 CTCATCATCACTGGCCAT 3813
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3007 26.22 1.09 2.29  chrX_52794886_52797580.rev     1310  2228 (467)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_52794886_5   1310 TGGAAGAACATTCCATGCTCATGGATAGGAAGAGTCAATATCGTGAAAAT 1359
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_52794886_5   1360 GGCCATACTGCCCAAGGTAATTTATAGAATCAATGCCATCCCCATCAAGC 1409
                            v     v     iv i  i  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_52794886_5   1410 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1457
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_52794886_5   1458 TATGGAACCAAAAAAGGGCCCGCATTGCCAAGACAACCCTAAGCCAAAAG 1507
                                viiv  ii iv  v v  v     i    i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_52794886_5   1508 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATATATACTACA 1557
                                i      vv    i  v  ii i      ---- iv       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACTTACTACA 244

  chrX_52794886_5   1558 AGGCTATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 1607
                          i    i     i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_52794886_5   1608 GACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTAC 1655
                           i        i    i--    i  --        vv   i    i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chrX_52794886_5   1656 AACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGA 1705
                         iii  vi    i  i     ivv  v   i v  vvv           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_52794886_5   1706 TTCCCTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAA 1755
                          vvi  v  v  i              v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_52794886_5   1756 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 1805
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_52794886_5   1806 TGGATTAAAGACTTAAATGTTAGACCTAAAACCATTAAAACCCT-AGAAG 1854
                              i ?    i       v   v       i  -     i  -     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAG 541

  chrX_52794886_5   1855 AAAACCTAGGCAATACCTTTCAGGACATAGGCATGGGCAAGGACTTCATG 1904
                              v    ?ivv vii   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_52794886_5   1905 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 1954
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_52794886_5   1955 TCTAATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGCG 2004
                         ii v  i   v i  i i   i  ii vv    i  v    i  vv iv 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_52794886_5   2005 TGAATAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCT 2054
                             v  i  i  i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_52794886_5   2055 GACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAA 2104
                           i  i  i  vi          v  i         vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_52794886_5   2105 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGTCTTCTCAAAAGA 2154
                         v     i     i     v  i?    i         vv  - v  v   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT-TGAATAGA 840

  chrX_52794886_5   2155 CTTCTCAAAAAGTCTTCTCAAAAGAAGACATTTAGGCAGCCATCAGAGAA 2204
                          v -----------     v        i  vi iiii    vi iiv v
  L1M4_orf2#LINE/    841 CAT-----------TTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_52794886_5   2205 ATGCAAA-----TCAAAACCACAATGAGA 2228
                            v   -----    v i  ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.82 (31 / 11)  


2988 26.33 1.09 2.29  chrX_52882495_52885189     1308  2226 (469)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_52882495_5   1308 TGGAAGAACATTCCATGCTCATGGATAGGAAGAGTCAATATCGTGAAAAT 1357
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_52882495_5   1358 GGCCATACTGCCCAAGGTAATTTATAGAATCAATGCCATCCCCATCAAGC 1407
                            v     v     iv i  i  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_52882495_5   1408 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1455
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_52882495_5   1456 TATGGAACCAAAAAAGGGCCTGCATTGCCAAGACAACCCTAAGCCAAAAG 1505
                                viiv  ii iv  v v  v     i    i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_52882495_5   1506 AACAAATCTGGAGGCATCACGCTACCTGACTTCAAACTATATATACTACA 1555
                               vi      vv    i  v  ii i      ---- iv       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACTTACTACA 244

  chrX_52882495_5   1556 AGGCTATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 1605
                          i    i     i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_52882495_5   1606 GACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTAC 1653
                           i        i    i--    i  --        vv   i    i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chrX_52882495_5   1654 AACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGA 1703
                         iii  vi    i  i     ivv  v   i v  vvv           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_52882495_5   1704 TTCCCTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAA 1753
                          vvi  v  v  i              v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_52882495_5   1754 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 1803
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_52882495_5   1804 TGGATTAAAGACTTAAATGTTAGACCTAAAACCATTAAAACCCT-AGAAG 1852
                              i ?    i       v   v       i  -     i  -     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAG 541

  chrX_52882495_5   1853 AAAACCTAGGCAATACCTTTCAGGACATAGGCATGGGCAAGGACTTCATG 1902
                              v    ?ivv vii   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_52882495_5   1903 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 1952
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_52882495_5   1953 TCTAATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGCG 2002
                         ii v  i   v i  i i   i  ii vv    i  v    i  vv iv 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_52882495_5   2003 TGAATAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCT 2052
                             v  i  i  i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_52882495_5   2053 GACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAA 2102
                           i  i  i  vi          v  i         vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_52882495_5   2103 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGTCTTCTCAAAAGA 2152
                         v     i     i     v  i?    i         vv  - v  v   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT-TGAATAGA 840

  chrX_52882495_5   2153 CTTCTCAAAAAGTCTTCTCAAAAGAAGACATTTAGGCAGCCATCAGAGAA 2202
                          v -----------     v        i  vi iiii    vi iiv v
  L1M4_orf2#LINE/    841 CAT-----------TTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_52882495_5   2203 ATGCAAA-----TCAAAACCACAATGAGA 2226
                            v   -----    v i  ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.82 (31 / 11)  


1126 13.76 5.82 0.00  chrX_52925644_52928812      500   688 (2481)    L1M4_orf2#LINE/L1      271   470 (438)  

  chrX_52925644_5    500 TATTGGCATAAGGGTAGATAT----------GGAATAGAACTAAAAATCC 539
                           i          i    i  ----------         i i i i   
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_52925644_5    540 AAAAATAAACACTCACGTTTCTGGTCAACTGATTTTGGACAAGGAGGCCA 589
                          i        v vi  i   v       i       v       iv    
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_52925644_5    590 AAACAATTCAATGG-CAAAGAATATTCTTTTCAACAAATGGTGCTGGGAC 638
                          i  v         -v        v                         
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_52925644_5    639 AACTGGATATCCACATGCAAAACAATGAAGTTAGACCTCTATCTCACACC 688
                                  ?            v         i    i   i        
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

Transitions / transversions = 1.78 (16 / 9)
Gap_init rate = 0.01 (2 / 200), avg. gap size = 5.50 (11 / 2)  

 522 11.34 14.43 0.00  chrX_52925644_52928812     1584  1680 (1489)    L1M4_orf2#LINE/L1      462   572 (336)  

  chrX_52925644_5   1584 CTTCACACCATATACAAAAATTGGCTCAAAATGGATCAAAGA-TTAAA-- 1630
                          i                    ii              ?   -i    --
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_52925644_5   1631 ---GAGCTAAAACT--------CTTAGAAGAAAACATAGGCATGAAACTT 1669
                         ---           --------                  ?i i  v   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_52925644_5   1670 TGTGACCATGG 1680
                         i      v   
  L1M4_orf2#LINE/    562 CGTGACCTTGG 572

Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.03 (3 / 111), avg. gap size = 4.67 (14 / 3)  

 666 17.28 16.46 6.58  chrX_52925644_52928812     2005  2247 (922)    L1M4_orf2#LINE/L1      555   821 (87)  

  chrX_52925644_5   2005 AAACCTTTGTGACCATGGATTAGGCAATGGTCCCTTAAATGTGATAGCAA 2054
                            i   i      v   i            ii    i  i   i v   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_52925644_5   2055 AAAGCCTAAGTAATAAAAGGAAAAAAATAGATAGATTGGTTGTCATCAAA 2104
                           -  vi   i  i     --            i     viv        
  L1M4_orf2#LINE/    605 AA-GCACAAGCAACAAAAG--AAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_52925644_5   2105 ATTAAAA----------------GGACACCATCATGGACGTGAAGAAGCA 2138
                                ----------------      i    v i v     i ii  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_52925644_5   2139 AC--ACAGAATAGGA---ATTTTTTGCAAATTGTATA-CAGAT---GCTC 2179
                           --       i   --- v v         ii    - v   --- ---
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG--- 748

  chrX_52925644_5   2180 CTTGACTTGCA----------ATAAGG-----TTACAACTCAATACATCC 2214
                         ---      i ----------    i -----             -----
  L1M4_orf2#LINE/    749 ---GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA----- 790

  chrX_52925644_5   2215 ATTAAAAGTCAAAAATATCATAAGTTGGAAATG 2247
                           v     v    --  v vi  v ?ii     
  L1M4_orf2#LINE/    791 ATAAAAAGACAAA--TAACCCAATTWAAAAATG 821

Transitions / transversions = 1.73 (26 / 15)
Gap_init rate = 0.04 (12 / 267), avg. gap size = 4.67 (56 / 12)  

 742 14.19 3.23 0.65  chrX_52925644_52928812     2522  2676 (493)    L1M4_orf2#LINE/L1      750   908 (0)  

  chrX_52925644_5   2522 ACCTGATATCTGTATTATAGAGAAAAC----ACAACTCAATAATAAAAAG 2567
                           i  -    iiv v    v i i   ----                   
  L1M4_orf2#LINE/    750 ACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_52925644_5   2568 ATAAATGACCTCATTTAAAAGTGGGCAAAATATATTAATAGACATTTCTC 2617
                          i    i   iv   ?    i        iv  v v              
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_52925644_5   2618 TAAAGAAAATATACAA-TGACCAATATGCACATGAAAAGATGCTCAACAT 2666
                         i      i        -  i      v                       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_52925644_5   2667 CAACAGTCAT 2676
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.02 (3 / 159), avg. gap size = 2.00 (6 / 3)  


 654 17.42 2.27 2.27  chrX_53017083_53020421.rev      648   779 (2560)    L1M4_orf2#LINE/L1        4   135 (773)  

  chrX_53017083_5    648 AAATAAATCCCAAGTTCACAGACTAGAAGAC--AATATTGTTAA-ATGGC 694
                            v v      v     ii  i i      --           -     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_53017083_5    695 AATACTCCCCAAGTTGATATATAGATTCAACATAATCTCTATGAGAATTT 744
                                     i     v  i         ii    i    v i   ii
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_53017083_5    745 CAGCTGTTTTTTTTTTTAAAGAAATTGATAAACTG 779
                               ii      vi---         i  i   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGC---AGAAATTGACAAGCTG 135

Transitions / transversions = 2.83 (17 / 6)
Gap_init rate = 0.02 (3 / 132), avg. gap size = 2.00 (6 / 3)  

1270 11.02 3.47 26.73  chrX_53017083_53020421.rev     1035  1524 (1815)    L1M4_orf2#LINE/L1      120   495 (413)  

  chrX_53017083_5   1035 AGAAATTGGAAAGCTGATCCTAAAATTCCTATGAAAATGCAAGG------ 1078
                                 iv                  v    i          ------
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_53017083_5   1079 --ATAGCCAAAACAATCTTGAAAAAGAA---CAAAGTTGGAAGACTCTCA 1123
                         --                          ---          i     v  
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_53017083_5   1124 CTTCTTGACTTCAAAACTTACTACAA--CTACAGTAATTAAGACAGTGTG 1171
                             iii i                 --          i           
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_53017083_5   1172 GT-CTAGCATAGTGACAGACCTGCAAATCAATGGAATAGAATTAAGAGTC 1220
                           -  i     iv  i    v ii i                 i      
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_53017083_5   1221 CAGAAGTTAACCTTTATGTTTATGTTTTATGGTCAATTATTTTTTTCAGA 1270
                              i v    iv  ii      -------       iv    i-----
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATG-------GTCAATTGATTTTC----- 357

  chrX_53017083_5   1271 GATGGGGTGTCACTATGTTGCCCAGGTTGGCCCTGAACTCCTGGGCTAAA 1320
                         --------------------------------------------------
  L1M4_orf2#LINE/    358 -------------------------------------------------- 357

  chrX_53017083_5   1321 GTGATCCTCCTGCTTCAGCCTCTCTAGTAGCTGGGACTACAGATGGGTGT 1370
                         --------------------------------------------------
  L1M4_orf2#LINE/    358 -------------------------------------------------- 357

  chrX_53017083_5   1371 CACTATGCCTGGTCTATGACAAGGTCGTCAAGACAATCCAATGGTAAAAA 1420
                         -----------------       vi i      v  i      -ii   
  L1M4_orf2#LINE/    358 -----------------GACAAGGGTGCCAAGACCATTCAATGG-GGAAA 389

  chrX_53017083_5   1421 GAATA--TTTTTCAACAAAAGGTGCTCAGAAAACTAGATATCCATGT-CA 1467
                              --i           v      vi  v    i    ?   ii -  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_53017083_5   1468 GAAGAATAAACCTGTACCCCTACTCTCACGCTATACACAAATATTAACTC 1517
                         i      i  vi  v        -     i i   i     v        
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTAC-CTCACACCATATACAAAAATTAACTC 488

  chrX_53017083_5   1518 AAAATGG 1524
                                
  L1M4_orf2#LINE/    489 AAAATGG 495

Transitions / transversions = 2.31 (37 / 16)
Gap_init rate = 0.03 (10 / 376), avg. gap size = 14.80 (148 / 10)  

1318 17.54 2.61 0.37  chrX_53017083_53020421.rev     1803  2070 (1269)    L1M4_orf2#LINE/L1      475   748 (160)  

  chrX_53017083_5   1803 ACAAAAAT-AACTCAAAATGGATCACTGTCCTAAATGTAAGAGCTAAAAC 1851
                                 -                ?v v                     
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_53017083_5   1852 GATAAAATTCCTAGAAGAAAACATAGGAATAAATCTTTGTCACCCTGATT 1901
                         v      i  i                ?i        i  v   i  iv 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_53017083_5   1902 TAGGCGATGATTTATTGGATATAACACCAAATGCCCAAGTGACAACA--- 1948
                              i   i   v  i     i        v  v    ii    v ---
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_53017083_5   1949 -AAATAGGTAAGCTGGACATCACTGAAATTAAAACCTACTGTACATTAAA 1997
                         -      i   ii     v   iii         v  vi   i v i   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_53017083_5   1998 AGATACCATCAATAAAATGAAAAGA--ACCCACAGAATGGGAGAAAATAT 2045
                         i  i  i     v   i        --                       
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_53017083_5   2046 TTATAATTCATATTATCTGGCCAGG 2070
                           ii  v      -     iiv   
  L1M4_orf2#LINE/    725 TTGCAAATCATAT-ATCTGATAAGG 748

Transitions / transversions = 1.81 (29 / 16)
Gap_init rate = 0.01 (4 / 274), avg. gap size = 2.00 (8 / 4)  

 220 10.87 2.17 2.17  chrX_53017083_53020421.rev     2370  2415 (924)    L1M4_orf2#LINE/L1      729   774 (134)  

  chrX_53017083_5   2370 AAAACATATTATCTGACAAAGGACTTATATCCAGA-TACATAAAGAA 2415
                            v    -       i  i      i        -  i        
  L1M4_orf2#LINE/    729 AAATCATA-TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

Transitions / transversions = 4.00 (4 / 1)
Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2)  

 613 14.09 10.07 1.34  chrX_53017083_53020421.rev     2700  2848 (491)    L1M4_orf2#LINE/L1      747   908 (0)  

  chrX_53017083_5   2700 GAGACTCCGTCTCCAAAAAAAAAAAAAGAAGTCCTGCAACTCAATAATAA 2749
                          i    -i  v   - i  v v v      v  i i              
  L1M4_orf2#LINE/    747 GGGACT-TGTATCC-AGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_53017083_5   2750 AAAGACACATAATCCAATT-AAAAATGGGCTAAGAATTTGAATAGACATT 2798
                                v    i      -          v   i               
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_53017083_5   2799 TCTCCAAAGA---TATACAA-----------GCATATAAAAGGACATTCA 2834
                                   ---       -----------   i  i   i  iii   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_53017083_5   2835 ATATCATGAGTTAT 2848
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.03 (5 / 162), avg. gap size = 3.40 (17 / 5)  


 612 22.03 5.76 13.22  chrX_53084535_53087895     1532  1826 (1535)    L1M4_orf2#LINE/L1        6   278 (630)  

  chrX_53084535_5   1532 AGATA--CCATATTCACATGCATAAGCTGCTGAACTCAGTATTACAAGAA 1579
                              --    i    --  v  ----  vvii   i i    iiv ii 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCA--TGGAT----TGGAAGACTTAATATTGTTAAGA 49

  chrX_53084535_5   1580 TGCCAGTTCTCCCCAAGTAGCTCTACAGATTCAATGTGATTCCAATTAAA 1629
                           v  i v        i v v             i ii  i  v  i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_53084535_5   1630 --CCCTGATGGGTGGGTTGGTTGGTTTGTTTCTTTTGGTGGAACTTGAC- 1676
                         --   v ------------------i  ii i     -ii   v     -
  L1M4_orf2#LINE/    100 ATCCCAG------------------CTGCCTTTTTTG-CAGAAATTGACA 130

  chrX_53084535_5   1677 ---TGATTCTAAAATGTATATATTAATAGAAATGAAAAAG-TTAAGAATA 1722
                         ---    i       vi    i------      v  ii -iiv      
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATG------GAAATGCAAGGGACCCAGAATA 174

  chrX_53084535_5   1723 GCCATGAC--TCCTGAA---GAAGAACTATGATGGAGGACTTG-ATCTCT 1766
                             vi  --  i    ---       v v v         ii- ii  i
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_53084535_5   1767 CAGATGTTAAGGGTTTTTTAAAAAAATAAAGCTATAGTAATTAAGA--GT 1814
                           -  v i  iiv  vi ------- i       i      i    --  
  L1M4_orf2#LINE/    225 CA-ATTTCAAAACTTACT-------ACAAAGCTACAGTAATCAAGACAGT 266

  chrX_53084535_5   1815 GTAGTACTGGCA 1826
                           i         
  L1M4_orf2#LINE/    267 GTGGTACTGGCA 278

Transitions / transversions = 2.10 (44 / 21)
Gap_init rate = 0.05 (15 / 273), avg. gap size = 3.73 (56 / 15)  

 367 25.39 3.12 14.06  chrX_53084535_53087895     2117  2372 (989)    L1M4_orf2#LINE/L1      296   523 (385)  

  chrX_53084535_5   2117 ATCAAAAAAAAAGAA--AAAAGAAAAGAAGGATGAATCCATGCATATTCG 2164
                              vii  v    --i i  vvv    --  i  i    i   v vi 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAA--ATAAACCCATACATTTATG 343

  chrX_53084535_5   2165 CATACTTGATTTATCAA-AAATGTGTCTCTGTAGAGCCAT-----GGGAG 2208
                         vvi v       -  i -  iv   i ----- iii    -----   ii
  L1M4_orf2#LINE/    344 GTCAATTGATTT-TCGACAAGGGTGCC-----AAGACCATTCAATGGGGA 387

  chrX_53084535_5   2209 CAGGGCAGTCTTTTCAACAAATGGTGCTGGGACAATTGGGTGCCCAGTTA 2258
                         v  iii                             i   i i?   vv i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_53084535_5   2259 AAAAAATAATAATAAATAACTAAAGCTAAATTGGGTATTTACGTCACATT 2308
                         v    i----   i  -------------i    iivii   v     ii
  L1M4_orf2#LINE/    438 CAAAAG----AATGAA-------------GTTGGACCCCTACCTCACACC 470

  chrX_53084535_5   2309 ATATATTTTTTAAAACTCAAATGATTCCCAGGTAGATTATAGACCTAAGT 2358
                              i-----    v i  v ----- v ii i   i ?        i 
  L1M4_orf2#LINE/    471 ATATAC-----AAAAATTAACT-----CAAAATGGATCAWAGACCTAAAT 510

  chrX_53084535_5   2359 GTGAAAAGCAAAGA 2372
                           -  i   v  i 
  L1M4_orf2#LINE/    511 GT-AAGAGCTAAAA 523

Transitions / transversions = 2.00 (42 / 21)
Gap_init rate = 0.05 (11 / 228), avg. gap size = 4.00 (44 / 11)  

 664 27.74 6.77 2.90  chrX_53084535_53087895     2551  2860 (501)    L1M4_orf2#LINE/L1      568   889 (19)  

  chrX_53084535_5   2551 CCTGGGATGGTAAAAGATTTCTTAAACAAGACACCAAAAGTACAAACCAT 2600
                          i    v i vv  v i       i i v           i    i v i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_53084535_5   2601 GAAAAGAAAGGACTGATAAAATTGACTCCGTCAAAAATAATAACTT---- 2646
                         -        ii iv      v v    i i      v   v     ----
  L1M4_orf2#LINE/    618 -AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_53084535_5   2647 -CTTCACCCAGAGACACCAT--AAATGGTACAAAGGAAAACCACAAAATG 2693
                         -     --- ii     i  -- i vi  iv    iv  v     i    
  L1M4_orf2#LINE/    667 GCTTCA---AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_53084535_5   2694 GGAAAATTTGTTTGCA--TCACTTAAAATCAGAT------TCCATATCCA 2735
                            i  vv i      --   iv  ---  v   ------iiii      
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATA---TCTGATAAGGGACTTGTATCCA 760

  chrX_53084535_5   2736 GATCGTAAGATGAAGTTCTACAATTCAACAAGAGAAAGATAGATAATC-A 2784
                           vii  vi v   v ii     i    i  v i     i i    i - 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_53084535_5   2785 ATAGAAAAATATGTGAAAGAGTTGAACAG----TTTTACAAGAGAG-TAC 2829
                           v?      iv ii  i  v     i  ----  i v   iii  -  i
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_53084535_5   2830 TTGAATGGCCAGTAAAAAAATATGAAAAGGT 2860
                         vii        i   iv --i        i 
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCA--CATGAAAAGAT 889

Transitions / transversions = 1.83 (55 / 30)
Gap_init rate = 0.03 (11 / 322), avg. gap size = 2.73 (30 / 11)  


 366 34.18 1.02 2.04  chrX_53186498_53191479.rev     3075  3270 (1712)    L1M4_orf2#LINE/L1        4   197 (711)  

  chrX_53186498_5   3075 AAAGTTATATCTTGTTCTTGGATGAGAAGAGTCACTGTGGTAAAAATGAC 3124
                             v   vi v     v     vi     v i v i v  v  i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_53186498_5   3125 ATTTTGTTCCTAATTTGGCCAAAACATTCATTGCATTCCTTATTAAAATT 3174
                          v vi- i  i  v   ii v v v     vi   v   i   i     i
  L1M4_orf2#LINE/     54 AATAC-TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_53186498_5   3175 TCAGTGATATTTTCTTTG--GGATTTGAGTGATTGGAGTTTAAAGTTCAT 3222
                         i   i-- iii  i    -- i v    -ii viv  vii    i     
  L1M4_orf2#LINE/    103 CCAGC--TGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_53186498_5   3223 TCAGAAGAGTAAATGTTCATGAATCACTAAGAAAATTTTGAAAAAGAA 3270
                         vii   iv i  iv vi vv    vi i  i v   i           
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

Transitions / transversions = 1.31 (38 / 29)
Gap_init rate = 0.02 (4 / 194), avg. gap size = 1.50 (6 / 4)  

 330 29.10 10.03 7.69  chrX_53186498_53191479.rev     3512  3810 (1172)    L1M4_orf2#LINE/L1      174   479 (429)  

  chrX_53186498_5   3512 AGCCAAGATCTCAGTCTCAAAAAAAAAAAAAAAAAAAAGAATGAGGGCAA 3561
                               i ---  i   ii     i  i  v   iv-----  ii  -- 
  L1M4_orf2#LINE/    174 AGCCAAAA---CAATCTTGAAAAAGAAGAACAAAGT-----TGGAGG--A 213

  chrX_53186498_5   3562 CTTGTTGTTCTGTTAGATAT--AAACTTACCATAAAGCTGCAATAATTTC 3609
                           iiivv   i--i -  v --        i i      i  i    -- 
  L1M4_orf2#LINE/    214 CTCACACTTCC--CA-ATTTCAAAACTTACTACAAAGCTACAGTAAT--C 258

  chrX_53186498_5   3610 AAA----TGT--T-CTATCACAGAAATAGAGGACTACAGAC--ATGAAAC 3650
                           i----   -- -  iv  i iii     vi--  i   i--   i  i
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACA--TATAGATCAATGGAAT 306

  chrX_53186498_5   3651 AAAATAGAGAGTTTAGACACAAACTTATGTTCATATGGGAATTTAATTCA 3700
                          i   v      ii   v i    ii  iiviv     vv v  i   iv
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_53186498_5   3701 TGACAAAAGACATCTCAAA-----TCAGTGGGGAG------------TCA 3733
                         i     ii --- vi   i-----   i      i------------   
  L1M4_orf2#LINE/    357 CGACAAGGG---TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_53186498_5   3734 ATAAATGA-GATGGGACTATTGGTTACCCATTTGGGAAAAAAAATTTAAG 3782
                          i     i- v      v i   v  ?   iv  vi   i  --- v   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA---TGAAG 450

  chrX_53186498_5   3783 TGAAATCCTTGTCTCATATGAAA-ACAAA 3810
                          vii i  i ii    i iv v -     
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAA 479

Transitions / transversions = 2.44 (61 / 25)
Gap_init rate = 0.06 (18 / 306), avg. gap size = 2.94 (53 / 18)  

 469 31.68 4.19 2.36  chrX_53186498_53191479.rev     4115  4496 (486)    L1M4_orf2#LINE/L1      520   908 (0)  

  chrX_53186498_5   4115 AAAGCCATAAAAGTACCAGAAAAAAATCT-GGAATA--TTTTAATAATAT 4161
                            i i      v vii    i    iv -  ?i  -- i  vi i iv 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_53186498_5   4162 TAAGGTGGAGAAAGCCTTCCTGAGCATGAC-TTAAAAACCCATAAGCTAT 4210
                          ii v i iv  v vi   i iiii     -ii    i -- i    v i
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC--ACAAGCAAC 617

  chrX_53186498_5   4211 AACATAAAGAGTA-ATAATTTTGGCTACATTAAAATTTAAAACTTCTGTG 4259
                           v v   i i  -    v  v i  v   i      v       i    
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_53186498_5   4260 TGGAGAAAGATGCTATACACAAAATTAAAACATAA---ACAGGCTAGGAG 4306
                         ivvvi  i  ii    vv v   i v    v i  ---    iv i    
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_53186498_5   4307 AAAGTGTTTACTACACAGATATCAGGCAAAAGGTTAATATCTCTGCCTAT 4356
                            i i   i v vv  v     v ii  ii ii vi    - v vv   
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC-CAGAATAT 766

  chrX_53186498_5   4357 ATCTATATCACCTTCTGGAAACT-AGTAAGAAAAAGATACAAAACCCA-- 4403
                           vv v --  --   viv    - i   v       i v v      --
  L1M4_orf2#LINE/    767 ATAAAGA--AC--TCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_53186498_5   4404 TTCAAAATGGAGAGATAACATGATATGG-CAATTCAGGGAAGAA-ATAGA 4451
                          ?v       iv i vi iv   -  i -  v   vvvi     -   v 
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGA-ATAGACATTTCTCCAAAGAAGATATA 861

  chrX_53186498_5   4452 CAATTAGCTAATAAAGGA---GAAAATATGCCCAAGCTTACTAATAGT 4496
                            v i  i     - v ---     v    i   vv i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAA-GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (63 / 56)
Gap_init rate = 0.04 (16 / 389), avg. gap size = 1.56 (25 / 16)  


2677 17.94 12.90 5.16  chrX_53515090_53516854      498  1272 (493)    L1M4_orf2#LINE/L1       74   908 (0)  

  chrX_53515090_5    498 ACAGATTTAATGCAATCACTATCAAAATTCCAATGCTGTTTTTTGTTTTG 547
                                i  i      v          i   --    ii    ------
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCA--GCTGCCTTTT------ 115

  chrX_53515090_5    548 GTTTTGCAGAAATAGAAAAATCCCTTCTAAAATTTATATGAAATCTTAAG 597
                         ---          v  v  iiivv i        i     i  vivi   
  L1M4_orf2#LINE/    116 ---TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_53515090_5    598 GGACCCCAAATAGCCAAAACAAGTTGGG----GAAAAATT--TTTGGAGG 641
                               vi              vi v i----   i  iv--v       
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_53515090_5    642 TCTCACTCTTTTTGATTTC------TATTACAAAGTTACAGTGATCAAAA 685
                         v     v   iiii     ------  i       i      i     i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_53515090_5    686 C--TGTGATACTGGCATAAAGACAGACGTAAAGACCAATGGAATAGAATA 733
                          --    i           i  i    i  v   i              v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_53515090_5    734 GAGAGCCCAGAATTAAATCTTCACATATATATGGTCAAATGATTTTTGAC 783
                              i      v    i --  i i  v         v       i   
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACC--CATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_53515090_5    784 AAAGGTACCAAGACCATGCAATAGG-AAAGGACAGACTTTT--------- 823
                           i   i          v    i  -    i i  v     ---------
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_53515090_5    824 -------------------------------------------------- 823
                         --------------------------------------------------
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_53515090_5    824 -------ACCATATA-AAAAATCTAA-TCAAAATGGATTAAAGACCTGAA 864
                         -------        -      -   -           i ?      i  
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAAT-TAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_53515090_5    865 TATAAGAGCTAAG-TTATAAAACTCCTAGAAGAAGCCACAGTGGGAAAGC 913
                          i          i-i          i        iv  i  v? v   v 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_53515090_5    914 TGCAAAACATCGGATTTGGCAATGGTTTTGTGGACACGACACCAAAAACA 963
                          v ivi  v i  i  v           iv i  i i          i  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_53515090_5    964 CAGGTGTTTACACAGGCAACAAAAACAAAAAAAGAGAAGCTGAACTTTAT 1013
                           i ------------        iv     v   v  ii  i    i  
  L1M4_orf2#LINE/    610 CAAG------------CAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_53515090_5   1014 CAAGATTAAAAATGTTTGTGAATCCAAAGACA--ACCAAGAAA------A 1055
                            i        iv      vv  v  i    -- i       ------ 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_53515090_5   1056 GGCAACTCACAGAACAGGA-AAAATATATGCAAATCATATACCTGAGAAG 1104
                          i    i       ii   -       v             i    v   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_53515090_5   1105 AAATTAGTATCAGGTATTAATACGTGTACAAGAATACACAACTCTTACAA 1154
                         ii i v     vi ----    -- i  -     -------         
  L1M4_orf2#LINE/    748 GGACTTGTATCCAG----AATA--TATA-AAGAA-------CTCTTACAA 783

  chrX_53515090_5   1155 CTCAACAA------AACAAATAACACGATTAAAAAA-GAACAATGAATTT 1197
                              i  ------i         v i   ?     - ii   v i    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_53515090_5   1198 GAATAGACATTTCTACAAAGAAGATATATACATGGATAACAAGCACATGA 1247
                                       v             i v    vi  i          
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_53515090_5   1248 AAAGATGTTCATTATCACTATGCAT 1272
                                i   vi    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (89 / 47)
Gap_init rate = 0.03 (23 / 835), avg. gap size = 6.09 (140 / 23)  


 697 31.39 5.18 3.17  chrX_53601221_53602810.rev      502  1100 (490)    L1M4_orf2#LINE/L1      298   908 (0)  

  chrX_53601221_5    502 CAATGGAACAGAA----GATTCTACAAATGCATCCCAAAATGTCAGGG-- 545
                                 i    ----  v  i v    iv i  vv v  - i v  --
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-TTATGGTC 346

  chrX_53601221_5    546 AATTTAGTATTTGATAAAGGGGGCATTTTAAGTTAATGAGTGAAATGTCA 595
                             v v -  i  i  i  v v  vvviv v i    i vi  ivi vi
  L1M4_orf2#LINE/    347 AATTGATT-TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_53601221_5    596 ACTATTCAATAATTATGA----AGAACAATTGGATAGATTTTGAGAAAAA 641
                         v  v     i  --   i----i i    i      ?vivivviv    i
  L1M4_orf2#LINE/    396 TCTTTTCAACAA--ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_53601221_5    642 AATAAAGTTGGAATCCTACGTTTGTACTACACGCCAAAATAATACCCACA 691
                            i        vi     -i iii  i i ii v     v -  i  v 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTAC-CTCACACCATATACAAAAATTA-ACTCAAA 491

  chrX_53601221_5    692 -TGAGACAAATATTGAAATGTAATATTCAAAACCATAAAGGCGTTAGAAG 740
                         -  iiv  ? v iiv        v vii     i     iviv       
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_53601221_5    741 AAAACATAGATGAAGAGTTTTCTAGTCTTGAAGTGGGCAA-AGCCTTTCA 789
                                  i? v i vi  iv iii    iiv i     -i ii i i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_53601221_5    790 GAACACAGCACTTAAACCAGCTACTATAAATAAATGAAATGATA-ACAAA 838
                           -i iii   i-   --   -  v vv  i   v    vi   - i   
  L1M4_orf2#LINE/    592 GA-TATGACACC-AAA--AGC-ACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_53601221_5    839 TTTGATTATATAAAGGATGTTAAACTTGTATGTTCTAAGAAACAGCTTT- 887
                           v  i vi  v  i-  vvv      v i  i ii  iii   -  v -
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGACA-CTATC 684

  chrX_53601221_5    888 -ATAAGGTTAAAACACAAACAAAAAAATGA-AGAAAATATTTATGA--CA 933
                         - v  i  v    v    v v v i    i-           iii --  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_53601221_5    934 GGAA---GACAAGAGTATT--ATCCGTGATATAAAAAGAGCTATTCCAAC 978
                         viv ---  i   i vv  --    ivi     v     i  v  v    
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_53601221_5    979 TCAACAACAA---GAC---TA-TTCAACAAAAAACATGGGCAAAATGTAC 1021
                             i  i  ---   ---  -ii   iv?    -         ivi vi
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGGATTT 833

  chrX_53601221_5   1022 AAACAAGCTATACATTTAGAAGAAGAAGA-ATACAAATGGCCAAGAAACT 1070
                         i  -----  v      vvvvi       -              v  i v
  L1M4_orf2#LINE/    834 GAA-----TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_53601221_5   1071 AATTAAAAGATATTCAACCTCGCCAAAAAT 1100
                         v  v       ii     v  i????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (103 / 81)
Gap_init rate = 0.05 (28 / 611), avg. gap size = 1.79 (50 / 28)  


3036 25.90 1.73 0.58  chrX_53649682_53651964.rev      928  1792 (491)    L1M4_orf2#LINE/L1       34   908 (0)  

  chrX_53649682_5    928 CTTAATA-----AAGATAGAAATTTTCCTAAAATTTATATACAGGTTTAG 972
                                -----     i v   vi   iv     v  v     i  i i
  L1M4_orf2#LINE/     34 CTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAA 83

  chrX_53649682_5    973 TGAAATTCTTTTCAAAATCCCAGCAGGATGTTTTGTAGATATAGACAAGA 1022
                         i v   i i v             v vv v     i   v  v      v
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC 133

  chrX_53649682_5   1023 TTATTCTAAAATTTACATGGAAAAGCAAAGGAACTATAATAGCTAAAACA 1072
                          v  i        i i       v    i   v i v      i      
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_53649682_5   1073 ATTTTGGAAAAGAATAATAAAGTAGGAGGACTCACTTCACCTAATTTGAA 1122
                           i   i       v  i     v           viiv  i     v  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_53649682_5   1123 AACATATCATTTGGCTACCATAATCAAGATTGTGAGTTATTGGTAGAAGA 1172
                            v  ii ivvi     vi         iv   v v  i   i v   i
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_53649682_5   1173 ATAGACACATTGATGAATGGAACAGA-TAGAGAACCCAGAAGTGGACCCA 1221
                                i  v   v       i   - v    ii      i ii     
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_53649682_5   1222 CACAAGTCTCAGCAATTGATTTTTGACAAAGACGCAAACATAATTCAATG 1271
                         i   vv v viv           i     i ii  v  v iv        
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_53649682_5   1272 GAGGAA--ACAGCCTTTTCAACAAATGGTGCTGGAGCAATTGGATATACA 1319
                          i i  -- i  i                     ii   i      ?v  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_53649682_5   1320 TAAGCAAATAAATAAACCTCAACCTAAACCTCAAACCTTATACAAAAATT 1369
                         i v     vi   i  vi vi   ivv      v   v            
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_53649682_5   1370 AACTTAAAATTAACTATAGATTGAAACATAAAATGTAAAATTTTAGTCAT 1419
                             i     vi ii ?   iiv   ii   i vv     i v  ivvv 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_53649682_5   1420 CTTAGAAGAACACATAGAAGAAAATCTTCAGAACCTAGGGCTTGTTGAAG 1469
                                   v      i? v        ivi    v   i v -- v i
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG--GCAA 581

  chrX_53649682_5   1470 TGGT--CTTAGACTTGACACCAAAAGCATGATCTGTAAAAGGAAAATATC 1517
                             --      iv              ii v vii     i    -  v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATA 630

  chrX_53649682_5   1518 AACAAATTGCACTTCATCAAAATTTTAAAATTTTTCT-CTGCAAAACACC 1566
                         i i      v              v-    i    v -  v    iv  v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACA 679

  chrX_53649682_5   1567 TTGGCAAGAGGATGAAAAGGTAAGCTATGGACTGGGAGAAAACATTTGCA 1616
                         i iv     iii       ii  v i ii  v          i       
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_53649682_5   1617 AATCACATATCTGCTAAAG-AC--ATATCTAAAATTTATAAAGAAACCTC 1663
                              i       v   i -  --i    i i   v         vi  i
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_53649682_5   1664 AAAACTCAATTGTGCAAA-ATAAACGATTCAATTAGAAGGTAGACAAAAT 1712
                          v        vi iv   - i   ii ii     ?i  ii i i    iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_53649682_5   1713 ATATCAAAGGAGAGTTTCACTAAAGAGGATGTATGGATGGCACATAAGCA 1762
                           v v  vi  v -    v i     i   i  iii     vv       
  L1M4_orf2#LINE/    830 ATTTGAATAGACA-TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_53649682_5   1763 TATGAAAAGACATTCAACGCCATTAAGGAA 1792
                         i         iii     ii  ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (128 / 92)
Gap_init rate = 0.01 (12 / 875), avg. gap size = 1.67 (20 / 12)  


1133 28.42 8.23 2.95  chrX_53654252_53655869.rev      502  1145 (473)    L1M4_orf2#LINE/L1      231   908 (0)  

  chrX_53654252_5    502 CAAGATTTATTTTAAAGCTATAGTGATTAAAACAGTGTGAGTCTGATGTG 551
                            i i   i vi       i   i  i  i        ivv   iii i
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_53654252_5    552 GGAATAGTCAAATGGATTACTGGAAGAGAATAGAAAACCCAGAAACAGGT 601
                         i i    v  v  i   i v     v     v  i ii       i iii
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_53654252_5    602 TCATGGAACT-TAG--AAT--ATT----ATAGAAGTGGCAT-----TTCA 637
                         i   iv vi - i --   --   ---- i iii   v  v-----    
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_53654252_5    638 AACACTAGGGAAAGGAAAGAATATTCAATAAGTGGTGTTGCAAAAAC-AT 686
                          ---- i       i v  vv v     i  i     i  vi v   -iv
  L1M4_orf2#LINE/    381 A----TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_53654252_5    687 ATTTTTACATGGAAAA-AATAAAATTAGATCACTACCTTATATCTTACAC 735
                           v?ii     v    -   i  i  i  i v      i i i v  i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_53654252_5    736 AGAAATAAATTCTAAATATACTAAACCTCCAAATGTGAAAAGC-AACATT 784
                          i    v  i  v    iv ii ? vvi i      -  i   -  v i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACT 525

  chrX_53654252_5    785 TTAAACCTGTTAAAGGAAAATATATGAG--AATTT--ATGACCTTGGAGC 830
                         v    v  v   i i     i   v ? --   i --i         ivi
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_53654252_5    831 AGGAACAAT--TTTCTTATCCAAATTATA--AAAAGCCCAAACCATAAAG 876
                            --    --       v-- v  v i --      v   i v i   i
  L1M4_orf2#LINE/    576 AGG--CAATGGTTTCTTAG--ATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_53654252_5    877 GAAGAGA---ATCGGTTTGACTTTATTAAAATTAATA-TTACTGTAAAAT 922
                            i i ---  vii  v     i  i        v -i vi   ivvvi
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_53654252_5    923 AAAAG-CACCAT-AAGCAGATTAATAAGACAAGTGACAGTCTGGGAAAAG 970
                            i -   i  -   v ii v  -       viv    vv     i  i
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAA-AAGACAACCCACAGAATGGGAGAAA 720

  chrX_53654252_5    971 ATACTCGCAA--CACATATCTTAGACAAAAAAAAACCCC---TCCAGAAT 1015
                            i i    --  i      --  i  iii ---- ii---        
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCT--GATAAGGGA----CTTGTATCCAGAAT 764

  chrX_53654252_5   1016 GTATTAAGAATTCCCGTAACTCAATAAGAAAAAGACAAATGAAACTCAAC 1065
                         i   v     i  iiii          v            --   i   i
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT--AACCCAAT 812

  chrX_53654252_5   1066 AGAGAAAGAAGCCAAGTAAATGAAAAGAC--TATTACAGAAAAGGAAAAC 1113
                         v? i   vii  v   v vv    v    -- vi v  i i   iv v  
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_53654252_5   1114 GAA--------------ATGAAAAGGTACT-AATACTCACTGAATAT 1145
                         i  --------------        i i  -  i -   ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.75 (114 / 65)
Gap_init rate = 0.04 (30 / 678), avg. gap size = 2.40 (72 / 30)  


2469 25.70 0.16 0.49  chrX_53688067_53690068.rev      506  1116 (886)    L1M4_orf2#LINE/L1      159   767 (141)  

  chrX_53688067_5    506 CAAAAGACCCAGAACAGCCAAAGCTATCCTAAGCAAAAATAACAAAACTG 555
                            ii         i       i v   i i iv  i  v      ii  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_53688067_5    556 GAGGAATCACATTACCTGACTTCAATTTATACTACAGAGTTATAGTAACC 605
                              v     i v  ii i     vviv       i  i  i     i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_53688067_5    606 AAAACAGCACGACACTGGCATAGCAACAGACACATAAACCAGTGGAACAG 655
                           i    iii ii         ivi i     i   i i  i     i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_53688067_5    656 AATAGAGAGCCCAGAAACAAATCCACACATCTACAGTGAACTCGCTTTTG 705
                            v     i       i   i   i    i  ii  v  i vii   i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_53688067_5    706 ACAAAGGTGCTGAGAACATATACTGGGGAAAAGACAGTCTCTTCGATAAA 755
                             i     ii   v   vi v        ii i     i   i i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_53688067_5    756 TGGTTCTGGGAAAACTGGATATCCATATGCAAAATAATGAAAGTAGACCT 805
                             v      v         ?   i        v      iv i    i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_53688067_5    806 CTATCTCTTGCCATATA-AAAAATCAAATCAAAATGGATTAAAGATGTAA 854
                            i   vii       -      i  v           i ?   iv   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_53688067_5    855 AACTAAGACCTCAAACTATGAAACTACTACAAGAAAACATTGGGGGAAGA 904
                          vv     v  v       i     vi  v          v  ? v  - 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-A 557

  chrX_53688067_5    905 TCTCCAGGACACTGAGCTGGGCAAAAAATTCTTGAGCACAACAACCCACA 954
                            i iv   vi  i i i     viiv     iiii ii   --   v 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA--CCAAA 605

  chrX_53688067_5    955 AGCACAGGCAACTAAAGCAAAAATGGGCAAATAGGATCATATCAAGATAA 1004
                               i     v    v      i ii    v   iivi     i  v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_53688067_5   1005 AAAGCTTCTGCACAGCAAAGGATACAATCAGCAAAGTGAAGAGGCAATCC 1054
                            i   i  ii vv       i  v    iv        i  i   i  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_53688067_5   1055 ACAGAATGAGAGAAAATATTTGCAAACTACCTGTCTGACAAGGGGTTAAT 1104
                                 i                 ii iv i     i     ii vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_53688067_5   1105 AGCCAGAATACA 1116
                          v        i 
  L1M4_orf2#LINE/    756 ATCCAGAATATA 767

Transitions / transversions = 2.28 (107 / 47)
Gap_init rate = 0.00 (3 / 609), avg. gap size = 1.33 (4 / 3)  

 466 12.09 3.30 0.00  chrX_53688067_53690068.rev     1421  1511 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_53688067_5   1421 AAAAATGGGCAAAAGATTTGCATAGACATTTCTCAAAAGAAGATATACCA 1470
                                      i      v             v             v 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_53688067_5   1471 ATGGCAAACAGGTATATGAAAAGGTGATCA---TCAGAGAAATG 1511
                              v  i i i i        i  v   ---   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (6 / 5)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 3.00 (3 / 1)  


3253 25.38 0.86 2.81  chrX_53692382_53698790     4991  5916 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_53692382_5   4991 TGGAAGAACATTCCATGCTCATGGGTAGGAACAATCAATACCGTGAAAAT 5040
                              ii i  i     i      i v    v v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_53692382_5   5041 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5090
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_53692382_5   5091 TACCAATGACTTTCTTCACAGAA-TTGGAATAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii     -   -- i  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_53692382_5   5139 TATGGAACCAAAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCCAAAAG 5188
                                viiv  ii  v  v v  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_53692382_5   5189 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5238
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_53692382_5   5239 TACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGCATGGTACTGG 5288
                                 i   i    ii        -----------    i-------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTG-----------GCATA------- 280

  chrX_53692382_5   5289 TACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAA 5336
                         ---- ii i   v                i    i--    i  --    
  L1M4_orf2#LINE/    281 ----AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAA 324

  chrX_53692382_5   5337 ATAATGCCACATATCTACAACCATCTGATCTTTGACAAACCTGACAAAAA 5386
                             vv   i i  i  iiii  vi    i  i     ivv  v   i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chrX_53692382_5   5387 CAAGAAATGGGGAAAGGATTCCCTATTGAATAAATGGTGCTGGGAAAACT 5436
                           vvv           i  vvi  v  v  i              v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_53692382_5   5437 GGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTAT 5486
                           v  ?   i   i i  iiv    ii    i    v   i     v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_53692382_5   5487 ACAAAAATTAATTCAAGGTGGATGAAAGACTTAAATGTTAGACCTAAAAC 5536
                                    i    ii     v ?    i       v   v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_53692382_5   5537 CATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCA 5586
                         i      vi i           v    ?i v viv   iv   v v  vv
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_53692382_5   5587 TGGGCAAGGATTTCATGTCTAAGACACCAAAAGCAATGGCAACAAAAGCC 5636
                          i     v i    v ivv  v             vvi          vv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_53692382_5   5637 AAAATTGACAAGTGGGATCTAATTAAACTCAAGAGCTTCTGCACAGCAAA 5686
                              v  i  i v   ii v  i   v i  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_53692382_5   5687 AGAAACTACCATCAGAGTGAACAGGCAACCTATAGAATGGGAGAAAATTT 5736
                         i  v    i  vv i      v  i     i i               v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_53692382_5   5737 TTGCAATCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAA 5786
                               vii ivi      i  i  i  vi          v  i  v   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_53692382_5   5787 CTCCAACAAATTTACAAGAAAAAAACAA----CCCCATCAAAAAGTGGGC 5832
                            iv    v iv i  v     i    ----   v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_53692382_5   5833 AAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 5882
                                v    i     i     v        i  vi viii     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_53692382_5   5883 GACACATGAAAAAATGCTCATCATCACTGGCCAT 5916
                         ii          i       v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 4.25 (34 / 8)  


2523 27.84 0.30 0.75  chrX_53742898_53748481.rev     3883  4550 (1034)    L1M4_orf2#LINE/L1        1   665 (243)  

  chrX_53742898_5   3883 TGGAAAGGTATCCCATGCTCTTGGATCGGAAGAATTAATATCATTAAAAT 3932
                                i         i  v     i      v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_53742898_5   3933 GACCATACTATCCAAAGCAATCTACAGATTTAATGCAATCTTTATCAAAA 3982
                          i v     vi     vii           i  i      ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_53742898_5   3983 TACTAAAGTCATTTTTTTCATAGAAATAGAAAAAACATTTCTAAAACTTG 4032
                          v i -- iiiii     iii      v  v  iviiv i      i ii
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_53742898_5   4033 TATGGAATCACAAAAGACCCCAAATAGCCAAGGAAATCCCAACAAAAAAG 4082
                                vii   ii     vi         iiv    iii v   i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_53742898_5   4083 AACAAAGCTGAAGGCATTACGCTACTTGACCTCAACATATATTATGAGGC 4132
                                i  i   vv i  i  v iii ii    v iv  i  ii i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_53742898_5   4133 TATATTACCCCAAACAGCATGGTATTGGCATAAAAACAGACACACAGACT 4182
                           i v  vi v i    ii     i        ii i     i i   ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_53742898_5   4183 AATGGAGCAGAATCGAGA-CACAGAAATAAATCCACATATTTACAGCCAA 4231
                               ii     i    -iv          i   i i     ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_53742898_5   4232 CTGATTTTCAACAAAGGTGCCAAGAACATACGTTGGGGAAAGAACACTTT 4281
                         i        i    i          v   v iv           i v i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_53742898_5   4282 TCTCTTCAATAAA-GATGCTGGGGAAATTGCATATCCATATGCAGAAAGA 4330
                          ---     i   - i       iv  i  v   ?   i     i  ii 
  L1M4_orf2#LINE/    399 T---TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_53742898_5   4331 TGAAACTGCACCCCTATCTTTCACCATATTAAAAAATTAACTTAAGACGG 4380
                             ii  v       i  iv        vv           i  i i  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_53742898_5   4381 ATTAAATACTTAAACATAAGACCTGAATCTCTATAACCACTAGAAGCAAC 4430
                           i ? v  i    ii     v  i  v  v  v   ivi      v  v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_53742898_5   4431 CATAGGAGGAAAACTTCAGGACATTGGTCTAGACAAAGATGTTATGGCCA 4480
                               ? v   v    iv   v    vi   i   v i v iv i vi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_53742898_5   4481 GGACCTCAAAAGCCTGGGAAACAAAAACAAAAATAGACAAACGGGACTAT 4530
                         v   vi       viii v       iv         i   iv     vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_53742898_5   4531 ATTAAACTAAAAAGCTTCTG 4550
                           i   v v    i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 2.10 (124 / 59)
Gap_init rate = 0.01 (4 / 665), avg. gap size = 1.75 (7 / 4)  

 906 22.87 1.16 0.39  chrX_53742898_53748481.rev     4838  5095 (489)    L1M4_orf2#LINE/L1      649   908 (0)  

  chrX_53742898_5   4838 AAAAAAAAAAGCTTCTACATAGCAAAGGAAACAATCAACAGAGTGAAGAG 4887
                             vv    i   i iiiivv       v  v     v i      i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_53742898_5   4888 ACAAACTGTTAAATGGCAGAAAATATTTGCAAATTATTTATCTGACAAGG 4937
                             v iiivi     v                 i  v       i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_53742898_5   4938 -ACTAATATCAAGAATATACAAGAAACACAAACCATTTAAAAATAACAAA 4986
                         -   vi    v        i  ii   v vv  v i i  v     v  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_53742898_5   4987 A--AATAATCCCATTAAAAAGTGGGCAAAAGACATGCATAGGCATTTTTT 5034
                          --     i  v   ?    i        i  iv  v    i     i i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_53742898_5   5035 AAAAGAAGACATACAAATGGCCAATAATTATATGTAAAAAATGCTCAACA 5084
                         v        i                 vi i   -    i          
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTCAACA 897

  chrX_53742898_5   5085 TTGCTAATTTT 5095
                          ii????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.42 (34 / 24)
Gap_init rate = 0.01 (3 / 260), avg. gap size = 1.33 (4 / 3)  


 346 25.24 6.80 0.97  chrX_53784785_53786616.rev       19   121 (1711)    L1M4_orf2#LINE/L1        1   109 (799)  

  chrX_53784785_5     19 TGGAAAAACATCCCATGCTCATGGATAGGAAGAATCACTATTGCTAC-AT 67
                               i i        i        v      v i v     i  v-  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_53784785_5     68 GGCCATACTACCTGATATAGTCTGGATATTTG------TCCCCATCCAAA 111
                            v     v  ii vv ii   iv v   ii------    i   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_53784785_5    112 TCTCATGTTG 121
                           i  - i  
  L1M4_orf2#LINE/    101 TCCCA-GCTG 109

Transitions / transversions = 1.36 (15 / 11)
Gap_init rate = 0.03 (3 / 109), avg. gap size = 2.67 (8 / 3)  

2697 28.72 1.42 0.47  chrX_53784785_53786616.rev      496  1341 (491)    L1M4_orf2#LINE/L1       55   908 (0)  

  chrX_53784785_5    496 ACATTTCCCAAAGCAATATAAAGATTCAATGCTATTCCTATCAAACTACC 545
                          i i i      vii  v  v        i  v  i         v v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_53784785_5    546 AATGACATTCTACACAGAACTAGAAAAAATTATTTTAAAACTTACATGGA 595
                          iivi v  i vii     v v  v  iv v  ii     i i i     
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_53784785_5    596 A-TG-AAAAAACAGCCCAAATAGCCAAGGCAATCTTAAGCAGAAAGAACA 643
                          -  -  iii  --  vi         ii       i iv ii       
  L1M4_orf2#LINE/    155 AATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_53784785_5    644 AAGCTGGAGGCATCACTCTACCTGACTTCGAACTATACTACAAGGTTACA 693
                            i      vv    v  v  ii i   i  viv        i i    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_53784785_5    694 GTAGCCAAAACAGCATGGTACTGGTACAAAAACAGGCACATAGACCAATG 743
                            ii   i    ii         i i  ii i  i  i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_53784785_5    744 GAAGAGAATAGAAAGCCCAGAGATAAGGCTGCACACCTACAACTATCTGA 793
                            v     v  i  i     i    iv iii   ii  iiiii vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_53784785_5    794 TCTTCCACAAAGATGACAAAAATAAGCAATAGGGAAATGACTCCCTATTC 843
                          i   v    i i  v   i vi vv    i      vi ivvi  v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_53784785_5    844 AATAAATTGTGCTGGTATAACTGGTTAGCCATAGGCAGAAGATTGAAACT 893
                           i    v       v i      v  ?   i v   i    v    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_53784785_5    894 AGACCCCTTCCTTACATCACACATAAAAATCAGCTCAAGATGGATTAAAT 943
                         i       v   i   i  i i i      i i     i      i ? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_53784785_5    944 TCTTAAATGTAAAATCCAAAACTATAAAAACCCTGGAAGACAATCTAGGC 993
                         v i         i v i            vi i i     v  iv    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_53784785_5    994 A-ATACCATTCTGGACATAGGACCTGGCAAAGATTTCATGACAAAGATAC 1042
                         i- v i -   vv   v v  iiiv     v i    v iivv v  i  
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_53784785_5   1043 CAAAAGCAATTGCAATGAAAACAAAAATTGACAAAAGGGACCTAAATAAA 1092
                                 vvv    ii   iv      v  i   vv    i v vi   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_53784785_5   1093 CTAAAGAGCTTCTGCACAGAAAAAGAAACTATCAAAGGAGTAAACAGACA 1142
                         v v  i i   i  ii vvv   i  v        iii   i  v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_53784785_5   1143 GCCTACAGAATGGGAGAAAATATTTGGAAACTATGCCTCAGACAGAGGTC 1192
                         i  i                      v   ii  iiv  v  i ii  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_53784785_5   1193 TAGTATCCAGCATCTGTAAGGAACTT----AAATCTACACACAAAAAG-C 1237
                          v        v  v i   i     i----  v  v i - i      - 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAAAAGAC 800

  chrX_53784785_5   1238 AAACAACCTCATTAAAAAGTGTGCAAAGGACGTGAA----CACTTTTAGA 1283
                            i    iv   ?    i  v        iv    ----  i  i vv 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_53784785_5   1284 GAGAAGACTTACATACGGCCAACAAGTATATGAAAAAATGCTCAACATCA 1333
                         i      iv    v i      i   i i       i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_53784785_5   1334 CTGATCAT 1341
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.66 (149 / 90)
Gap_init rate = 0.01 (9 / 854), avg. gap size = 1.78 (16 / 9)  


 272 29.41 0.00 0.00  chrX_53797866_53803742        7    91 (5786)    L1M4_orf2#LINE/L1       70   154 (754)  

  chrX_53797866_5      7 ATTTACAGAATCAATGCTATTCCTATCAAACTACCAATGACATTCTTCAC 56
                           i      v    i  v  i         v v   iivi v  i  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_53797866_5     57 AGAACTAGAAAAAACTATTTTAAAATCCATATGGA 91
                             v v  v  iviv  ii      i        
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

Transitions / transversions = 1.27 (14 / 11)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.00 (0 / 0)  

3148 27.56 0.66 0.55  chrX_53797866_53803742     4478  5384 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_53797866_5   4478 TGGAAGAACATTCCATGCTCATTCGTAGGAAGAATCAATATCATGGAAAT 4527
                              ii i  i     i    vvi v      v i     ii vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_53797866_5   4528 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4577
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_53797866_5   4578 TACCAATGACTTTCTTCACAGAA-TTGGAATAAACT-ACTTTAAAGTTCA 4625
                          v   iivi i  i  ii     -   -- i  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_53797866_5   4626 TATGGAACCAAAAAAGAGCCCACATGGCCAAGTCAATCCTAAACCAAAAG 4675
                                viiv  ii  v  viv  i     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_53797866_5   4676 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAGCTATACTACAAGGC 4725
                                i      vv   ii  v  ii i     iviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_53797866_5   4726 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4775
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_53797866_5   4776 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 4823
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_53797866_5   4824 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 4873
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_53797866_5   4874 CTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4923
                           v  v  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_53797866_5   4924 GAAACTGGATCCCTTCCTTACGCCTTATA-AAAAATTAATTCAAGATGGA 4972
                            ii    i    v   i  i  v    -         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_53797866_5   4973 TGAAAGACTTAAACGTTAGACCCAAAACCATAAAAACCCTAGAAGAAAAC 5022
                          v ?    i    i  v   v i     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_53797866_5   5023 CTAGGCA-ATACCATTCAGGACATAAGCATGGACAAGGACTTCATGTCTA 5071
                         v    ?i- v i -   iv   v vi vv i i   v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_53797866_5   5072 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5121
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_53797866_5   5122 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5171
                           i   v i  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_53797866_5   5172 CAGGCAACCTATAGAATAGGAGAAAATTTTTGCAATCTACTCATCTGACA 5221
                         v  i     i i     i         v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_53797866_5   5222 AAGGGCTAATATCCAGAATCTACAATAAACTCCAACAAATTTACAAGAAA 5271
                          i  i  vi          v  i  vi     iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_53797866_5   5272 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5321
                           iv    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_53797866_5   5322 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACAAGAAAAAATGCTCAT 5371
                            v        i  vi viii     v ii    v     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_53797866_5   5372 CATCACTGGCCAT 5384
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (152 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3457 23.58 1.25 1.48  chrX_53877883_53884277     1056  1933 (4462)    L1M4_orf2#LINE/L1        1   876 (32)  

  chrX_53877883_5   1056 TGGAAAGATAGCATATGCACATGTATTGGAAGAACTAATATTGCTAAAAT 1105
                                   v vi   iv    v         vi        i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_53877883_5   1106 GTCTATACTACCCAAAAACGATCTATAGATTCCATGCAATCCCTAACAAA 1155
                          v v     v      v-i      i      v i          v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_53877883_5   1156 ATACCAATGACATTCTTCACAGAAATAGAAAAAGCAATCCTAAAATTCAC 1205
                           v   iivi v  i  ii       v  v  ivii             i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_53877883_5   1206 ATAAAACTGCAAAAGATGCCAAATAACTAAAGCAATACTGAGCAGTAAGA 1255
                           ii  v     ii  iv vi    i i   i    vi   iv iv    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_53877883_5   1256 ACAAAGCTGGAAGCCTCATACTACCTGATTTCAAATTATATTACAAAGCT 1305
                               i    i v    i   v  ii        viv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_53877883_5   1306 ACAGTAACCAAAACAGCATGGTACTGGCATTAAAACAGATACATGGGCCA 1355
                                i   i    ii            v ii i   i i  i ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_53877883_5   1356 ACAGAACAGCATAGAGAATCCAGAAATAAATCCACCCACTTATAGCCCAC 1405
                          ii   i  v  v    i            i   iv  i    i i v i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_53877883_5   1406 TCACTTTCCACGAAGGCACCAAGAACATTCACTGGGGAAAGAACAGTCTC 1455
                          v i    v  i i  ii      v      v           i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_53877883_5   1456 TTTAATAAATGGTGTCAGGAAAACCGAATACCCATATGCAAAAGAATGAA 1505
                           i  i        iii   v   i i   ?   i               
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_53877883_5   1506 ACTAGACCTTTATCTCTTGCCATATACAAAAAAATCAATTGAAAATGGAT 1555
                         ii i    ii  i   vii             -- i  i v         
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAATGGAT 497

  chrX_53877883_5   1556 TAAAAGACTTAAATGTAAGACCTGAAACTATGAAACTACTACAAGAAAAT 1605
                         i ? -   i           v  i       i     vi  v       i
  L1M4_orf2#LINE/    498 CAWA-GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_53877883_5   1606 ACTGGGG-AAATGCTATAGGACATTGGTCTGGGCAAAGATTGTTTTGGAG 1654
                          iv  ? -    -  viiv   v    vi i     v i  - i  i  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAGA- 593

  chrX_53877883_5   1655 TAAGAACTCAAAAGCACAGGCAACAAATGCAAGAATACACAAATATAATT 1704
                           v  vvi          i        v v  i    v i    vvi i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_53877883_5   1705 ACATTAAGCCAAAAAGCTTCTGTACAGCAAAGGAAACAATCAACAAAGTG 1754
                         v   i  iviv    i   i   i vv       v  v     v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_53877883_5   1755 CAGAGACAACCCACAGAATGGGAGAAAATATCTGCAAACTATCCATCTGA 1804
                         v i                            i      ii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_53877883_5   1805 CAAGGGATTAGGATTAATAACTAAAATATATAAGGAACTC---------A 1845
                         i      i v v  ------ i i         i      --------- 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTAT------CCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_53877883_5   1846 ATAGCAAAAA-ACAAATAATCCAATTTAAAAATGGGCAAAATACCAGAAC 1894
                            ii     -        i      ?             iv iiv   i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_53877883_5   1895 AGACATTTCTCAAAAAAAGACATAGAAATGGCCAACAGG 1933
                                    v   i    i   v          i i 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

Transitions / transversions = 1.82 (131 / 72)
Gap_init rate = 0.01 (10 / 876), avg. gap size = 2.40 (24 / 10)  

2508 26.04 3.19 1.84  chrX_53877883_53884277     4732  5545 (850)    L1M4_orf2#LINE/L1        1   825 (83)  

  chrX_53877883_5   4732 TGGAAAAATATTCCATGCTCCTGGACAGAAAGAATCAATATCGTGAAAAT 4781
                               i    i     i  v    iv i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_53877883_5   4782 GGCCATGCTGCCCAAAGTAATTTACAGATTCAATGCTATTCCCATTAAAC 4831
                            v  i  v      v i  i           i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_53877883_5   4832 CACTATTGACATTCTTCACAGAATTAGAAGAAACT-ACTTGAAAATTCAC 4880
                         iv i vivi v  i  ii     v v  v-  i  - iiiv        i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_53877883_5   4881 ATTGAA-TGAAAAAAGAGCCCA-AATAGCCAGGACAATCCGAAGCAAAAA 4928
                           v   -  v  i-- ii    -        ii      ivi iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_53877883_5   4929 GAATTAAAGCTGGAGGCATCACGCTACCCGACTTCA-----TACCACAAG 4973
                            i-    i      vv    i  v   i i    -----   i    i
  L1M4_orf2#LINE/    198 GAAC-AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_53877883_5   4974 GCTACAGTAACCAAAACAGCATGCAACTGGTACAAAGACAGACACATAGA 5023
                                   i   i    ii  vv     i i  i  i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_53877883_5   5024 CCAATG-AACAGAATAGAGAACCCAGAAGTTAGACCACACACCTACACAC 5072
                         i     -  i     v    ii      i v iv   i   ii  iivv 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_53877883_5   5073 ATCTAATCTTCGACAAACCTGACAAAAACAAGCAATAGAGAAAGGATTCT 5122
                          vi i  i        ivv  v   i v  vv    i i     i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_53877883_5   5123 CTATTTAATAAGTGGTGCTGGGGAGAACCAGGTAGCCATATGCAGAAAAT 5172
                           v  i  i  i          - v   ii i  ?   i     i  i v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGG-ACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_53877883_5   5173 TAAAACTGGATCCCTTCCTTATACCATATACAAGAATTAACGCAAGATGA 5222
                          i  ii    i    v   i i           i       v   i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_53877883_5   5223 ATGAAGGACCTAAATGTAAAACCCCAAACTATAAAAACCCTAGAAGAAAA 5272
                           v ?i             i v iv           vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_53877883_5   5273 TCTAGGCA-ATACCATTCAGGACATAGGCACAGGCAAAGATTT------T 5315
                         iv    ?i- v i -   iv   v v  vvi      v i   ------ 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_53877883_5   5316 ATGACAAAAATGCCAAAAGCAATTGCAACAAAAGTAAAAATTGACAAATG 5365
                               ------         vvv          v      v  i    v
  L1M4_orf2#LINE/    595 ATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_53877883_5   5366 GGATCTAATTAAA-TTAAAGAGCTTCTGCACATCAAAAGAAACTATAATC 5414
                            ii v  i   -     i -   i  ii v     i  v     v vv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_53877883_5   5415 AGAGTGAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAA--TATAT 5462
                          i      v        i                 v       --i    
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_53877883_5   5463 CCATCTGGCAAAGGTATAATATCCAGAGTCTAAGAGGAACTTAAACAAAT 5512
                         --     ii  i  vv vi        i v  vi i     ivv    v 
  L1M4_orf2#LINE/    738 --ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_53877883_5   5513 ---TTATAAGAAAACAA----CCCCACTAAAAAGAAGACA 5545
                         --- v    i  i    ----   v i ?    ivi i  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 1.54 (126 / 82)
Gap_init rate = 0.02 (19 / 825), avg. gap size = 2.16 (41 / 19)  

 213 14.81 7.41 0.00  chrX_53877883_53884277     5849  5902 (493)    L1M4_orf2#LINE/L1      851   908 (0)  

  chrX_53877883_5   5849 AAGAAGACATTCATGCGGCCA-T---CATATGAAAAAAAGCTCAACATCA 5894
                                i  v  vii     - ---  i       i v           
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_53877883_5   5895 CTGTTCAT 5902
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.03 (2 / 58), avg. gap size = 2.00 (4 / 2)  


3523 14.89 7.16 1.12  chrX_53915581_53917615      831  1542 (493)    L1M4_orf2#LINE/L1      154   908 (0)  

  chrX_53915581_5    831 AAATTCAAGGGGCC-----------AAATAATCCTGAAAAAGAA----AA 865
                             v      i  -----------   i    i          ----  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_53915581_5    866 AGTTGGAGCACTGGCACTTCCCAATTTCAAAACTTACTACAAATGTACAA 915
                                 v   vi                             vv    i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_53915581_5    916 TAATTGAGATGGTGTGACACTGTTAGAAGGAT------------CAACAG 953
                             ii   ii     ii    vi v      ------------   ii 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_53915581_5    954 AATAGAATTCAAGGTCCAGAAATAAACCCTTATCTTT--GGTCAACAGAT 1001
                                  v ii                v  iv   --      iv   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_53915581_5   1002 TTTTGACACAGGTGTCAAGACAATTCAATGGGGAAAGAACAGTCTTTTCA 1051
                            i    vi    i      v                 i          
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_53915581_5   1052 A-AA--GGTTCTGGGACAACTAGA--ACTACATACAAAAGAAAGAAATTG 1096
                          -  --   v           i  --? i    i        v   i   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_53915581_5   1097 GACCCTTACCTCATACCATACACAAAATCAATATAAATCAAAATGGATGA 1146
                              i       i      i      ---  -   v           v 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAA---AT-TAACTCAAAATGGATCA 499

  chrX_53915581_5   1147 AAGATCTAAATGTAAGAACTAAAACTATAAAATGCTTAGAAGAAAACATA 1196
                         ?   i            i              iv                
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_53915581_5   1197 GGCATAAATCTTCATGACCTTGAATTAAGCAA--GCCTCTTAGA-----C 1239
                           ?i         i        ii   i    -- ii       ----- 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_53915581_5   1240 ACCAAAAGCATAAGCAAATAAAGAAAAAAAAATAGATAAATTGGGC---A 1286
                                   i      -i   -- i                  i --- 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAA-CAAA--AGAAAAAATAGATAAATTGGACTTCA 646

  chrX_53915581_5   1287 TCAAAATTTGTAACTTTTGTCCTTCATAGGACACTATCAAAAAAGTGACA 1336
                                 viv         v     v             i       v 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_53915581_5   1337 AGACAACCCCAAGAATGAGAGAAAATATTTGCAAATCACATATCTGGTAA 1386
                                  vv      i                    i       i   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_53915581_5   1387 AAGTCTAGTATCCAAAGTATATAAA---TTCTTGTAACTCAACAATGAAG 1433
                         ii v  v       i i        ---i    ii       i   i  i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_53915581_5   1434 AGACAA----TCTAATTAAAGAATGGGCAAAAGATTTAAATAGATATTTC 1479
                               ----i i    ?  i          i     i      i     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_53915581_5   1480 TCCAAAAAAAACTATACAAGTGTCCAATGAACATTTGGAAAGATGTTAAA 1529
                               i  i -       i  v     i i  iv  i       i v  
  L1M4_orf2#LINE/    847 TCCAAAGAAGA-TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_53915581_5   1530 CATCAAAGGTCAT 1542
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (72 / 30)
Gap_init rate = 0.02 (17 / 755), avg. gap size = 3.47 (59 / 17)  


2820 15.40 8.12 0.85  chrX_54007525_54009893.rev      502  1092 (1277)    L1M4_orf2#LINE/L1      155   788 (120)  

  chrX_54007525_5    502 AATACAA---ACTCAGAATAGCCAAAATAATGTTGAAAAA-AAGAACAAA 547
                            i   ---  i              i   v        -         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_54007525_5    548 -------------CACTGTACAGTTTCAAAATTTACTACAAAAGTATAGT 584
                         -------------    viv  i        i          iv  i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_54007525_5    585 AACCAAAAACAGTG--------GAATAAGGATAGACATATAAATTAATGT 626
                           i   i -     -------- v                 i  i    v
  L1M4_orf2#LINE/    255 AATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_54007525_5    627 AGTTACATTCGAGTGTCCAGAAATAAACTC-TGCTATTTGTGGTCAATTA 675
                          i viv   -   v              i - i -    i         i
  L1M4_orf2#LINE/    304 AATAGAATT-GAGAGTCCAGAAATAAACCCATAC-ATTTATGGTCAATTG 351

  chrX_54007525_5    676 ATTTTTGACAAGGGTGCCAAGATAATTCAATGGGGGAAAAATAGTCTTTA 725
                              i                iv           i  i          v
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_54007525_5    726 CAACAGATGGT-----------TGGATATTAACATGCAAAAGAAT--AGT 762
                              i     -----------      ?iv              --   
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_54007525_5    763 TAGACCTCTACTTCACACTATATACAAAAATTAGCTCAAAATATATCATA 812
                          i    i    i      i              i        iv    ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_54007525_5    813 GACTTAAATGTCAGACTGAAAACTATAAAACACTTAGAAGA---CA-AGA 858
                            i       v   viv             v         ---  -  i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_54007525_5    859 GGTAT-TCTTCACGAACTCAGGTTAGGCAGTGGTTTCTTTGATATGATGC 907
                         ?   v-     ii  v  ii         i         v       ii 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_54007525_5    908 CAGAAGCATAAGTAACAAAAGGAAAAACAGGT----TAGACTAGATCAAA 953
                           i     i   i        i     i  i ---- i    vv      
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_54007525_5    954 ATTTAAAATTTGTGTGCTAGAAACAAGACTACAAATAAAGTGAAAACACA 1003
                            v    i  v      vv   vi v    iv  v          v   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_54007525_5   1004 ACCCACAGAATGAGAGAAAATATTTGCAAACCATGTATCTGATAAGGGCC 1053
                                     i                 i   i             v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_54007525_5   1054 TAGTATCCATAATATATATAAAGAATTCTTACAACTCAA 1092
                          v       v        --     i             
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATA--AAGAACTCTTACAACTCAA 788

Transitions / transversions = 1.59 (54 / 34)
Gap_init rate = 0.02 (15 / 634), avg. gap size = 3.53 (53 / 15)  

 333 21.00 1.00 2.00  chrX_54007525_54009893.rev     1421  1520 (849)    L1M4_orf2#LINE/L1      769   867 (41)  

  chrX_54007525_5   1421 AAAAAAAGCCTACAAGTAAAGCAAT-AAATGATGAATAAATCAATTTTTT 1469
                            i  vv i     v v  -i   -   v  ii     vi   -  ?vv
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAA-TAATAAAAAGACAAATAACCCAA-TTWAA 816

  chrX_54007525_5   1470 AAATGGGTGAAAGATTTGAATAGACATTTCTCCAAAGAACATACGCAAAT 1519
                                ii  i                           v   ii     
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_54007525_5   1520 G 1520
                          
  L1M4_orf2#LINE/    867 G 867

Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.00 (3 / 3)  

 274  7.14 5.36 0.00  chrX_54007525_54009893.rev     1823  1878 (491)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_54007525_5   1823 AAAGAACATATACAAATGTCCAATAAGCACATGAAAAAATGATCA---TC 1869
                               v           v                  i   v   ---  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_54007525_5   1870 AGGGAAATG 1878
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 0.33 (1 / 3)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 3.00 (3 / 1)  


3227 25.17 2.00 0.89  chrX_54013792_54016765     1584  2481 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54013792_5   1584 TGAAAAAACATTTCATGGTCATGGATAGGAAGAATCAATGTCGTGAAAAT 1633
                           i   i i  ii    v        v      v i   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54013792_5   1634 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAAC 1683
                            v     v      v i  i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54013792_5   1684 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAATTTC 1731
                          v   iivi i  i  ii     -   --- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_54013792_5   1732 ATATGGAACCAAAAAGGAGCCCTCATAGCCAAGACAATCCTAAGCAAAAA 1781
                                 viiv  i   v  vvv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_54013792_5   1782 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 1831
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_54013792_5   1832 CTACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 1881
                             i    i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_54013792_5   1882 CAATGCAACAGAACAGAGGCCTTACAAATAACACCACACATCTACAACCA 1931
                              v  i    iv   iviii v      vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_54013792_5   1932 TCTGATCTTTGACAAACCTGACAAAAACAAGCAAAGGGGAAAGAATTCCC 1981
                         vi    i  i     ivv  v   i v  vv   v           vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_54013792_5   1982 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 2031
                          v  i  i        i     v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_54013792_5   2032 AAACTGGATCCCTTCCATATACCTTATGCAAAAATTAACTCAAGATGGAT 2081
                           ii    i    v  vi i   v   i               i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_54013792_5   2082 TAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 2131
                         i ?    i    ii     v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_54013792_5   2132 TAGGC---AATGCCATTCAGGACACAGGCATGGGCAA-GACTTCATGACT 2177
                             ?---   -- -   iv   viv  vv i     - ii   v iiv 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_54013792_5   2178 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 2227
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_54013792_5   2228 AATTAAA-TTAAAAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 2276
                         v  i   -      i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_54013792_5   2277 ACAGGCAACCTACAGAATGAGAGAAAATTTTTGCAATCTATCCATCTAAC 2326
                          v  i     i        i        v       vii  vi    i i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_54013792_5   2327 AAAGGGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTA-TAAGAA 2372
                           i  i  vi          v  i        --  -  i i -   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_54013792_5   2373 AAAAA-----AACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 2417
                            i -----   i v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_54013792_5   2418 TCTCAAAAGAGAAGACATTTATCCAGCCAACAA--ACATGAAAAAATGCT 2465
                             v     --   i  vi vvii     i  --         i     
  L1M4_orf2#LINE/    845 TCTCCAAAGA--AGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_54013792_5   2466 CATCATCAGTGGTCAT 2481
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (136 / 86)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.86 (26 / 14)  


 257 22.64 0.00 18.87  chrX_54028420_54034698.rev      183   288 (5991)    L1M4_orf2#LINE/L1      347   432 (476)  

  chrX_54028420_5    183 AACTGATTATTGACAAAGCTGCAAAAGCACTTCATTGGAGGAAGGATAGT 232
                           i     v i     i v   v  ii vv    v   i i   i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_54028420_5    233 TTTTTTGTTGTTTTTTGTTTCTTTTATATAAATGGTGTTAGATCAACTGG 282
                         i    ii-------------------- i        i i iv       
  L1M4_orf2#LINE/    397 CTTTTCA--------------------ACAAATGGTGCTGGGACAACTGG 426

  chrX_54028420_5    283 ACATCC 288
                          i ?  
  L1M4_orf2#LINE/    427 ATAKCC 432

Transitions / transversions = 2.29 (16 / 7)
Gap_init rate = 0.01 (1 / 86), avg. gap size = 20.00 (20 / 1)  

 660 17.03 5.49 2.20  chrX_54028420_54034698.rev      289   470 (5809)    L1M4_orf2#LINE/L1      721   908 (0)  

  chrX_54028420_5    289 ATAGTTGAACAAGTACCACATATCT-ATA-----CTAGTATCTAAAATAT 332
                            v   --   i --  i      -   -----  v     i i     
  L1M4_orf2#LINE/    721 ATATTTG--CAAAT--CATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_54028420_5    333 ATAAAGAACTCTCAAAACTGAACA-TAACAA---AAACAATTGAATTAGA 378
                                     i v    v  i -   v  ---   i  iiv    ?i 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_54028420_5    379 AAATTGGCAAAAGACATGCACAGACATTTCACTGAAGAAGATATACATAT 428
                             v      i  iv  v i         v ii             v  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_54028420_5    429 GGCAAATAAAGACATGAAAAGATGTTCAACATCAGTAGCCAT 470
                            v     iv             i         ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (17 / 13)
Gap_init rate = 0.03 (6 / 188), avg. gap size = 2.33 (14 / 6)  

3287 26.98 0.44 0.44  chrX_54028420_54034698.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54028420_5   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54028420_5   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54028420_5   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_54028420_5   5029 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_54028420_5   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_54028420_5   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_54028420_5   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_54028420_5   5227 ATCTGATCTTTGACAAACCTGGGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_54028420_5   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_54028420_5   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_54028420_5   5377 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_54028420_5   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGTACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     vvii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_54028420_5   5477 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5526
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_54028420_5   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_54028420_5   5577 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_54028420_5   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_54028420_5   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACACGAACAGACACTTC 5726
                          i     i     v  i?    i     i     ivi   i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_54028420_5   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_54028420_5   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2928 15.47 16.22 1.65  chrX_54150949_54153524      819  1484 (1092)    L1M4_orf2#LINE/L1       17   779 (129)  

  chrX_54150949_5    819 GTTCATGGACAGGAAGACTTAAT-CTGT--------CAACAGTCCACAGA 859
                                  iv            -i   --------   i v   v  i 
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chrX_54150949_5    860 GTGACCTACAGATTCAATGCAATCCCTATCAAAACCCCAATGGCCTTTTT 909
                         v   i            i                i    iiv        
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTT 116

  chrX_54150949_5    910 CACAGGAATAGAAAAGCTTATACTAAAATTCATATGGAATCACAGGGGAC 959
                         ii   i   v  v     v  v                 vii  i     
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_54150949_5    960 TCTGAATAGCCAAAA-AATATTTAAAAAGAA---CAAAGTTGGAGGACTC 1005
                         i v            -   v  v        ---                
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_54150949_5   1006 ACATTTCCTGATTTCCAAATGTACTATAAAACTACAGTAATCAAAACACT 1055
                            i    ii     v   iv     i   i             i   v 
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_54150949_5   1056 GTCATTTTGCTACTGGCATAAGGATAGATATTGGGAGTGATG-AATTGAA 1104
                           ------ v                  i  vvi  vii   -   v   
  L1M4_orf2#LINE/    267 GT------GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_54150949_5   1105 TT---AGTCCAGAAATAAATCCATACATCTATATAGTCAGCTGATTTTTT 1151
                           ---              i        i   i--    ii       iv
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATG--GTCAATTGATTTTCG 358

  chrX_54150949_5   1152 ACAAGAATGCCAAGACCATTAAATGGGGGAAAGAATAGTTTCTTCACCAA 1201
                              ii             v       -          i i    v   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAA 407

  chrX_54150949_5   1202 ATGGTGCTGA-ACAACTGGATATCCAAATGCAAAAGAACGAAGCTGGACC 1250
                                  i-           ?   v           i    i      
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_54150949_5   1251 CTTGTCTCATAC-ATATACAAAAATTAACTCAACATATATCAAAGACGTA 1299
                          i ii    i  -                    v  iv    ?    v  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_54150949_5   1300 ATTATAAGAGCTAA------------------------------------ 1313
                          v i          ------------------------------------
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_54150949_5   1314 --------------------------------------------CAAA-- 1317
                         --------------------------------------------    --
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_54150949_5   1318 -----GCAATACAAGGAAAAGTGGATAA-TCAGACTTCAACAAAATTAAG 1361
                         -----    i v   i    i i     - ii       v         i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_54150949_5   1362 AACTTTTGTGCGTTAAAGGATACCATCAAGACAGTGAAAAGACAAACCTA 1411
                                    v i      i  i       v             -  i 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA-CCCA 706

  chrX_54150949_5   1412 CAGAATGGGAGAAAATATTCACAAATAAAATATCTAATAAAG-ACTTAGC 1460
                                            ii     v v      i    i -    - i
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT-GT 755

  chrX_54150949_5   1461 ATCCAGAATATACAAAGATTTTTT 1484
                                     i     vi i  
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTT 779

Transitions / transversions = 1.81 (65 / 36)
Gap_init rate = 0.02 (17 / 763), avg. gap size = 7.00 (119 / 17)  

 727 11.68 2.19 0.00  chrX_54150949_54153524     1947  2083 (493)    L1M4_orf2#LINE/L1      769   908 (0)  

  chrX_54150949_5   1947 AAAGAATTCTTACAACTCAACAACACAAA--C-AACAACCCAATTAAAAA 1993
                               i             i  i v   -- -  i         ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_54150949_5   1994 ATAGGCAAAGGACTCGAACAGACATTTCTTCAAAGAAGATATACAGATGG 2043
                           i         i i   i          i               i    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_54150949_5   2044 CCAACAAGCACACGAAAAGATTCTCAACACCACTAGCCAT 2083
                             i       i        v       i  ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 6.50 (13 / 2)
Gap_init rate = 0.01 (2 / 140), avg. gap size = 1.50 (3 / 2)  


1567 19.08 6.36 0.29  chrX_54248486_54250701      500   845 (1370)    L1M4_orf2#LINE/L1      279   645 (263)  

  chrX_54248486_5    500 TAAGGACAGACATATAGGTCAAT-----AGAACTGAGAGTCTA-----AA 539
                               i          i     -----    i        i -----  
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_54248486_5    540 AGCCGTAACATTTATGGTCAATTGATTTTCAATACAGAGGTTAAGACCAT 589
                          v  i  -                      i i vi iv ii        
  L1M4_orf2#LINE/    329 ACCCATA-CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_54248486_5    590 TCAATAGGAAAAGAACAGTTATTTCAACCAAACTTG-TGGCATAACTGCA 638
                              i  i      i   iv       v  vvv  -   v i     v 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_54248486_5    639 -ATCCACATGCAAAAGAATGAAGCTGGACCCCGACCTCGTACCATACACA 687
                         - ?                    i        v     ii      i   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_54248486_5    688 GAAATT----TAAAGTGGATCACAGTCCTAAATACAAAAGCTAAAACTAT 733
                         i     ----i   i       ?  v       ii  i            
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_54248486_5    734 AAAACTTTTAGAAGAAAACATTGGAGTAAATCTCAGTAAC-TCGGGTCAG 782
                               i              v  ?        iv  i  - i    i  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_54248486_5    783 ACAAT----TCCCAGCCACAACACTAAAACCACAAGCA-TAAAAGAGAAA 827
                         i    ----  ii  vi ii    i    v        -i      i   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_54248486_5    828 ATTAAGAAGCTGCACCTC 845
                           vi v  ii  v  i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTC 645

Transitions / transversions = 2.32 (44 / 19)
Gap_init rate = 0.02 (9 / 367), avg. gap size = 2.56 (23 / 9)  

 681 19.08 2.89 1.16  chrX_54248486_54250701     1117  1289 (926)    L1M4_orf2#LINE/L1      602   777 (131)  

  chrX_54248486_5   1117 CAAAAAAACAAAAAACCAAA---AAAACAGAGAAGCTTCACCTCATCAAA 1163
                              iv    iv   v   ---    i   v  ii vv  i        
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_54248486_5   1164 ATTTTAAACTTTTGTGCTTCAAAGGATACCTTCAAGAAAGAGGTGAAGAC 1213
                            vv                     i  iv         v i-i     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA-AAAGAC 700

  chrX_54248486_5   1214 AACCTACAGGGGAGGAGAAAGTATGTGCCAAATCATATATGTGATAGGGG 1263
                             i    iivi       i   v   -           v     i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGC-AAATCATATATCTGATAAGGG 749

  chrX_54248486_5   1264 A-TGGTATC-AAACTATATCAAGAACTC 1289
                          - v     - i v     v        
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTC 777

Transitions / transversions = 1.06 (17 / 16)
Gap_init rate = 0.03 (5 / 176), avg. gap size = 1.40 (7 / 5)  

 615 15.75 0.00 0.00  chrX_54248486_54250701     1597  1723 (492)    L1M4_orf2#LINE/L1      782   908 (0)  

  chrX_54248486_5   1597 AACCCAATAATGACAAGACAAATAATCCAATTTTAAAATAGGCAAAAGAT 1646
                            i       i v           i      ?v     i      i   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_54248486_5   1647 CTGAATAGACATTTCTATAAAGAAGAAATCCAAAAGACCAATAAACACAT 1696
                         i               vi        v  v    v i       i     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_54248486_5   1697 AAAAAGTTGTTCCACATCATTACTTAT 1723
                         i     v  i  v      ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (11 / 8)
Gap_init rate = 0.00 (0 / 127), avg. gap size = 0.00 (0 / 0)  


1310 27.45 0.00 0.84  chrX_54499262_54504587.rev     3172  3528 (1798)    L1M4_orf2#LINE/L1        3   356 (552)  

  chrX_54499262_5   3172 GAAAAATATTCCATGTTCATGAATTGGAAGATTCAGTTTTATTAAAATGT 3221
                             i    i           i         i i i v  i    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_54499262_5   3222 CCATATAACCCTAAGCAATCTACAGATTCAATGCAATCTCTATCAGAATA 3271
                          v   ivv   v  vii              i      i      i   v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_54499262_5   3272 CCAATGACATTCTTCACAGAAATAGAAAAAAAAATCCTTAAATTTATATG 3321
                            iivi v  i  ii       v  v  ivvi     v     i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_54499262_5   3322 GAACCACAGAAGACACAGAATAGCCAATGTTATCCTTAGCAAAATAAACA 3371
                            vii  iii   v            viiv   i -- v    v  iv 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--GAAAAAGAAGAA 200

  chrX_54499262_5   3372 CAAAATTGAAGGAATCCCATTACCTGACTTCAAATTATACTACAGAGCTT 3421
                             i   i    v  v  i v  ii i      viv       i    v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_54499262_5   3422 TAGTAACCAAAACAGCATGGTACTAGCATAAAAACACACACATAGACCAA 3471
                         i     i   i    ii       i      ii i v   i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_54499262_5   3472 AGGAACAGAGTAGAGAACTCAGAAACAAATCTACACACCTACAGTGAACT 3521
                         v    i   i v    iii      i   i i i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_54499262_5   3522 CAATTTT 3528
                         -i     
  L1M4_orf2#LINE/    351 -GATTTT 356

Transitions / transversions = 2.06 (66 / 32)
Gap_init rate = 0.01 (2 / 354), avg. gap size = 1.50 (3 / 2)  

 832 22.65 0.55 0.00  chrX_54499262_54504587.rev     3828  4008 (1318)    L1M4_orf2#LINE/L1      344   525 (383)  

  chrX_54499262_5   3828 GTGAACTCATTTTTTACAAAGGTGCCAAAAACATACACTGGGGGGAAGAC 3877
                           v  i v     iv    i        i v   v  v     ii ii i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_54499262_5   3878 AGTCTCTTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGAAGAAG 3927
                              i     i              v         ?   i   v i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_54499262_5   3928 AATGAAACTGGGCCCCAATCTCTCACCATATACAAAAAACAAATCAAAAT 3977
                               ii   i    v i   v               vi  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_54499262_5   3978 GCATTAAAT-TCTAAATCTAAGACCTCAGGCT 4008
                          v  i ? v-i      v     v  v ii  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

Transitions / transversions = 1.29 (22 / 17)
Gap_init rate = 0.01 (1 / 182), avg. gap size = 1.00 (1 / 1)  

1037 16.56 2.73 14.88  chrX_54499262_54504587.rev     4359  4835 (491)    L1M4_orf2#LINE/L1      490   908 (0)  

  chrX_54499262_5   4359 AAATAAAT-AAATACATAAATCTAAGACCTCAAACTATGAAACTACTACA 4407
                             ii  - ? v  v     v     v  v       i     vi  v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_54499262_5   4408 ATAAAACACTGGGGAAAATCT-CAAGCACATTGGTCT-GGTAAAAATTTT 4455
                          v      iv  ? v      - iv -  v    vi -  i  vii   -
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTT- 587

  chrX_54499262_5   4456 CTTGAATAATAC-CCAATAAGTACAGGCAACCAAAGCAAAAATAG----- 4499
                            ii   vv  -    -   i   i     v    v        -----
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_54499262_5   4500 ---GATCACATCAAG-TTAAAAAGCTTCTGTACAGCAAGGGAAATGATCA 4545
                         ---  iiv      i-       -   i   i vv   i   v iv    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_54499262_5   4546 ACAAAGTGAAGAGACAATTCACAGAATGGGAGAAAATTATTTGTAAATTA 4595
                          v        i      ii                  -     i    i 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT-ATTTGCAAATCA 734

  chrX_54499262_5   4596 CCCATCTGACAAGAGATTAAATAATCACAATATATAAAGAGTTCAAACAA 4645
                         ivi      i   i  i vi-  vi  v            --------- 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGA---------A 774

  chrX_54499262_5   4646 CTCTTTCATCAATGGAACCCACCACGTCAACAGACTAAACAAGAAAAATC 4695
                              ---------------  v  -    i i--    -    v    -
  L1M4_orf2#LINE/    775 CTCTT---------------ACAAC-TCAATAA--TAAA-AAGACAAAT- 804

  chrX_54499262_5   4696 ATATAATCATATCAATTGATGCAGGAAAAAAACTAAAAATTTGATCAAAA 4745
                         ----  i ----     ----------------?      ----------
  L1M4_orf2#LINE/    805 ----AACC----CAATT----------------WAAAAAT---------- 820

  chrX_54499262_5   4746 TTGGGCAAAATATTTGAATAGACATTTCTCAAAAGAAGACATATACATGG 4795
                         --       iv                   v        i   i v    
  L1M4_orf2#LINE/    821 --GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_54499262_5   4796 CAAACAAGTATATGAAAAGATGCTCAACATCATTCATCAT 4835
                          v  i   i i                     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (42 / 34)
Gap_init rate = 0.05 (21 / 419), avg. gap size = 4.00 (84 / 21)  


3272 25.33 1.00 0.11  chrX_54518060_54523190.rev     3741  4640 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54518060_5   3741 TGGAAACACATCCCATGCTCATGGATGTGTAGAATAAATATTGTGAAAAT 3790
                               v i        i        vv v   v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54518060_5   3791 GACCATACTGCCAAAAGCAATCTACAAATTCAACACAATCCC-ATCAAAA 3839
                          i v     v  v   vii       i       i       -       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54518060_5   3840 TACCACCATCATTCCACACAGAATTAGAAAAAACAATGCTAAAATTGATA 3889
                          v   v vv v  iivii     v v  v  ivii  v        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_54518060_5   3890 TGGAAACAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 3939
                               iiv  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_54518060_5   3940 CAATTGTGGAGGCATCACACGACCTGATTTTAAACTATACTATAAGGCCA 3989
                            vvv      vv      vv  ii    i   viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_54518060_5   3990 TAGTCACCAAAACAGTGTGGTACTGGTATAAAAATAGGCACATAGATCAA 4039
                         i   v i   i               i    ii    i  i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_54518060_5   4040 TGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAACT 4089
                              i     v    ii               v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_54518060_5   4090 GATCTTCAACAAAGCAAACAAAAACATAAAGCAGGGAAAGGACAGCCTAT 4139
                            i   i    i vviv   i v   vv iii       i i  i  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_54518060_5   4140 TCAACAAATCGTGCTGGAATAATTGGCTAGCCACATGTAGGAGAATGAAA 4189
                                  v       i i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_54518060_5   4190 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCGAGATAAATTAA 4239
                         i    i  ii i   v    v           i     i i  ii  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_54518060_5   4240 GGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATCG 4289
                         i   i    iv     v  i           v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_54518060_5   4290 GAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGGACAAGAAT 4339
                          ?iv  vi    vv   v    v        v i    v i  i v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_54518060_5   4340 CCAAAAGCAAATGCAATACAAACAGAGATGAATAGCTGGGACCTAATTAA 4389
                                  v v    i v  iv i i  ii   iv v    i v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_54518060_5   4390 A-CTAAAGAGCTTTGCAAGGCAAAAGGAACAGTCAGCAGAGTAAACAGAC 4438
                          -i    i vi    iivvv    i iv  vi   iv i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_54518060_5   4439 AACCCACAGAGTGGGAGAAAATTTATACAATGTATACATCTGACAAAGGA 4488
                                   i           v v i   vvi   i      i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_54518060_5   4489 CTAATATCCAGAATCTACAAA--ACTC----AAATCAGTAAGAAAAAAAC 4532
                           vi          v  i   --    ----  v   i   v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_54518060_5   4533 AAATAATCCA-TCAAAACATGGGATAAGGACATGAATAGACAATTCTCAA 4581
                               i   - i?   v     vv     iv          v     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_54518060_5   4582 AAGAAGATATACAAACGGCCAACAAACACATGAAAAAAATGCTCAACATC 4631
                                        i      i  i          i -           
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATC 899

  chrX_54518060_5   4632 ACTAATGAT 4640
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.29 (126 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


 490 20.35 0.88 1.77  chrX_54531112_54534248.rev     1121  1233 (1904)    L1M4_orf2#LINE/L1        1   112 (796)  

  chrX_54531112_5   1121 TGAAAAGACAAGTCCCATGTTAATGGGTAGGAAGATTTAATATTGTTAAT 1170
                           i     i --         v    i v      i             v
  L1M4_orf2#LINE/      1 TGGAAAGATA--TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_54531112_5   1171 ACATCAATACTATCCAAAAGGATGTACAGATATAAAACAATCCCTATCAA 1220
                          iiv       vi     vv   v       vi  vi             
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_54531112_5   1221 AATTTCAAC-ACCT 1233
                            ii  i -i   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCT 112

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.02 (2 / 112), avg. gap size = 1.50 (3 / 2)  

3599 15.71 2.20 1.32  chrX_54531112_54534248.rev     1531  2211 (926)    L1M4_orf2#LINE/L1      100   786 (122)  

  chrX_54531112_5   1531 ATTTCAACATCCTTTTTTTGCAGAAATGGAAAAGCCAATCTTCAAATTCA 1580
                           ii  i - v i              v  v    ii   i v       
  L1M4_orf2#LINE/    100 ATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_54531112_5   1581 TATGGAATTGCAAGGGGCCCTTAATAGTCAAAATGATCTTAAAAAAGAAC 1630
                                v        i   vv     i     ii     i        v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_54531112_5   1631 AACAACATTGGAGGACTCATACTTCCTGATTTCAAAACTTACTAC----- 1675
                              vi            i      ii                 -----
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_54531112_5   1676 TAAAGTGATCCAAACAGTGTGGTACTAGTATAAAGATAGACATATAGACC 1725
                           v   i   v i             i i    i              i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_54531112_5   1726 ATTGGAATAGAATTGAGAGTTCAAAAACAAACCCATACACCTATGACCAA 1775
                          v                  i  i   i           ii    ii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_54531112_5   1776 TTGATTGTTGACAAAGGTGACAAGTCCATTAAATAGGGTAAGAACAGTCT 1825
                               v i     i    v    v     v   i   v     i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_54531112_5   1826 CTTCAACAAATGGTGCTGGGACAACTGAATTTCCACATGCAAAAGAATGA 1875
                         i                          i  v?                  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_54531112_5   1876 AGTCAGACCCCCTACCTCACATCATATACAAAAATTAACTCAAAATTGAT 1925
                            ii      -         i                        v   
  L1M4_orf2#LINE/    449 AGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_54531112_5   1926 CAATGACCTAAATGTAAGAGTTAAAACCATAAAACCCTTAGGAAAATATA 1975
                           ?v                i      i       i     i i  v i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_54531112_5   1976 TATGGGTAAATCTTCCTAACACTGGACTTGGCAATGGTTTCTAGAATAT- 2024
                           v ?          v i  vi   ii v             vii    -
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_54531112_5   2025 --ACCAAAA-CATATGAAACAGCAACAAAAGAAAAAA---ATAGATTAGA 2068
                         --       -  i ------                 ---   i   i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACA------AGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_54531112_5   2069 TTTCATCAGT-TTACAAA-TTTCATGCATGAAAGGGCATTACCAAGAAAG 2116
                         i       iv-   v   -   ii   v v     i  i  i        
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_54531112_5   2117 TGAAAAGACAACCTCACAGAATGGAAGAAAATATTTATAAATTATATATC 2166
                                      -          i           ii    i       
  L1M4_orf2#LINE/    692 TGAAAAGACAACC-CACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_54531112_5   2167 TGATAAGTGTTTAATATTCATAATATTTAAA-AACTCATGCAACTC 2211
                                v vi vi   i  v     v    -     v i      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

Transitions / transversions = 1.89 (68 / 36)
Gap_init rate = 0.02 (11 / 687), avg. gap size = 2.18 (24 / 11)  

 471 16.92 8.46 0.77  chrX_54531112_54534248.rev     2517  2646 (491)    L1M4_orf2#LINE/L1      769   908 (0)  

  chrX_54531112_5   2517 AAAAAATTCCTGCAACTCAACAA---AAAGACAA----CCCAATTTTAAA 2559
                            i  i  i i        i  ---        ----       ?v   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_54531112_5   2560 AGGAGAAAAGGACTT----AGATATTTCTCAACAAAAAGACATACAAATA 2605
                          v i v      i  ----   i       v -  i    i        i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCA-AAGAAGATATACAAATG 867

  chrX_54531112_5   2606 AACAATAAGCAAGTGAAAAAATGCTCAACATTATTAGTCAT 2646
                         iv         vi      i           i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.03 (4 / 140), avg. gap size = 3.00 (12 / 4)  


3912 17.75 4.47 2.52  chrX_54572751_54574573.rev      460  1332 (491)    L1M4_orf2#LINE/L1       19   908 (0)  

  chrX_54572751_5    460 TTATGGAT---AAAGTCTAAAATTGATAAATCAAGAAATAGAAATATACT 506
                          i      ---  iiii   v    ----- i    -- i v    --  
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTG-----TTAAGA--TGGCAATA--CT 59

  chrX_54572751_5    507 CCCCAAACTAAT--ACAGATTCATTGAAATACATATCCAAAACCCCAGCT 554
                                i i  --         vi v   v v    -    i       
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATC-AAAATCCCAGCT 108

  chrX_54572751_5    555 GT------------AATTGCCAAAGCTGATTCTAAAATTCATGTGAAAAT 592
                          i------------     v   -      i           i  i    
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATGGAAAT 157

  chrX_54572751_5    593 ACAAGGAACATAGAATAACCAAGACAACCTTGAAAAAGAAGACCAAAGTT 642
                         i     i  vi      i    i    i              v       
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_54572751_5    643 GGAAGACTCACACTTCTCAATTTTAAAACTTACTAAACAGCTACTGTAAT 692
                            i            i      i           v v      v     
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_54572751_5    693 CAAGACAATGTGGTACAGGCATAATAATAGGCATATAGATCAATGGAATA 742
                                i        v       vi    i                   
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_54572751_5    743 AAAGTTGAG-GTCCAGGAATTAACTTACATATCTGTGATCAATTGGTTTT 791
                         i  -     -      i   v   ii i i  i i  i       i    
  L1M4_orf2#LINE/    308 GAA-TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_54572751_5    792 CAACAAGGATGCCAATACAACTCAATAGG-AAATAATAGTATTTCCAACA 840
                          i      i      v  v i     i  -   v      v   i     
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_54572751_5    841 AATGATGCTGGAGGAATTGGAGATCCGCATTTAAAA--ATGAAGATGTAT 888
                             i      iiv  i    v ?  i   vi    --      v  v i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_54572751_5    889 CTCTACCTCAC--CGCCTTTAAAACTTAATTCAAAGTGGATCAAAGACCT 936
                          i         -- iiv vi    v    i     i       ?      
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_54572751_5    937 AAATGCAAGAGCCAAAACT--------CCCAGAAGAAAACCTGTGCAAGA 978
                              i      i      -------- ii          v iv ?ivi 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_54572751_5    979 ATCTTCATGACTTTGAACTAGGAAATGTTTTCTTAGATATGACACCAAAG 1028
                               i    i   iii    v    v                     i
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_54572751_5   1029 GCAAAAATGACAAAAGTGAGA-TAAATTGCTTGGACTTCATAAAAACTTA 1077
                            v  iii       vi i -  i  viv           v    i v 
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_54572751_5   1078 AAATGTTTGTGATTCAAAGGATACCATCAAGAAAGTGAAAAGATAATACA 1127
                            iv      v         i  i                  i  iv  
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_54572751_5   1128 CAGAATGGGAGAAAATATTTGCAAATTATATATATAATAAGGAATTTGTA 1177
                                                   i      v i      i i     
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_54572751_5   1178 CACAGAATATATAAAGCAC----ATACCTTAACAATGAAAA--CATATCA 1221
                         iv              v  ---- i v  i  i   i    --  v  v 
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_54572751_5   1222 CCCAATTTAAAAATGGGCAAAGAATTTGAATAGACATTTCATCAAAAAAG 1271
                                ?              i                 vi    i   
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_54572751_5   1272 ATACAAAAAGATATCCAAATGGCTA-CAGCCATATAAAAAGACACTCAAT 1320
                            i ----------        i -i iv  i  i      ii     i
  L1M4_orf2#LINE/    857 ATATA----------CAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_54572751_5   1321 ATCATTAAGACA 1332
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (102 / 49)
Gap_init rate = 0.02 (19 / 890), avg. gap size = 3.21 (61 / 19)  

 694 25.23 0.45 1.35  chrX_54572751_54574573.rev     1601  1822 (1)    L1M4_orf2#LINE/L1      588   807 (101)  

  chrX_54572751_5   1601 CTTATACATAAACATCAAAGGCATAATACAGGAAAA-ACATAATTGATAA 1649
                             v i  i -  i    i   i  -i  iv    - v v   v     
  L1M4_orf2#LINE/    588 CTTAGATATGA-CACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAA 635

  chrX_54572751_5   1650 GCTGGTATTTATTAAAATTTAAAAGTTCTGCTCAGTGAAAGAAACTGTCA 1699
                         ii   vv  i  i      v    v  i  iv vvii  i  v   i   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_54572751_5   1700 AGAGAATGAAAAAACAAGCCACAGACTGGAAGAAAATACTTGCAAAAGAC 1749
                            i i      i    v       v   i        i       vv i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_54572751_5   1750 ACATCTGATAAAGGACTGTTATCCTAAATATACAATGAACTCTTTAAAAT 1799
                          i         i     vv     vi      i  v        - v  i
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT-ACAAC 784

  chrX_54572751_5   1800 TCAACTATAAGAAAATAAACAAC 1822
                             iv    i  i i   i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAAC 807

Transitions / transversions = 1.43 (33 / 23)
Gap_init rate = 0.02 (4 / 220), avg. gap size = 1.00 (4 / 4)  


3012 27.72 0.55 0.66  chrX_54584277_54586536      859  1767 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54584277_5    859 TGGAAAAACATTCCATAGTTATGGATAGGAAGAATCAATATCATTACAAT 908
                               i i  i    iv i      v      v i     ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54584277_5    909 GGCCATACTGCCCAAAGCAATTTATAGATTCAACACTATTTCTATTAAAC 958
                            v     v      vii  i  i         i v  ii    i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54584277_5    959 TACCAATGACATTCATTCCAGAAACAGAAGAAGGT-ATTTTAAAATTCAT 1007
                          v   iivi v  iv  v      iv  v-   v -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_54584277_5   1008 GAGGAACCAAAAAGGAGCCCGAATAAGCAAAGCAATCCTAAGCAA-AAGA 1056
                         iv    viiv  i   v  v     iv    i     i i iv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_54584277_5   1057 ACAAAGCTGGAGGCATCACACTATCTGACTTTAGACTATATTACAGAGCT 1106
                               i      vv       vi ii i  i i viv  i    i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_54584277_5   1107 ATGGTAACCAAAACAGCATGGTACTAGTACATAAACAGGCACAAAG-TCA 1155
                          ii    i   i    ii       i i i vii i  i  i v  -   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_54584277_5   1156 AATGAAACAGAATAAAGAACCCAGAAATAAGACCACACACCTACAACTAT 1205
                          -  i  i     vi   ii          iv   i   ii  iiiii v
  L1M4_orf2#LINE/    300 A-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_54584277_5   1206 TGGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAAGACTCCCT 1255
                          v   i  i     i v  v   i v  vv           ii ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_54584277_5   1256 ATTCAATAAATGATGCTGGGATAACTGGCTAGCCACAAGTAGAAGACTGA 1305
                         v     i     i        i      v  ?     v i i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_54584277_5   1306 AACCAGACCCCTTCCTTATACCACATACAAAAATTAACTCAAGATAGATT 1355
                          iiii       v   i i    i                  i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_54584277_5   1356 AAAAACTTAAATGTAAAACCTGAAATTATAAAAACCCTGGAAGGCAACCT 1405
                          ? i  i         i v  i   i       vi i i    iv   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_54584277_5   1406 AGGCAATACAATTCTGGAA--TAGGAACAAGCAAAGATTTCATGACAAAG 1453
                            ?i-  v vi ii vi -- v  ivi i    v i    v iivv v 
  L1M4_orf2#LINE/    549 AGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_54584277_5   1454 ACACCAAAAGCAATTGCAACAAAAGCAAAAATGGACAAATGGGATCTAAT 1503
                                     vvv          v      i  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_54584277_5   1504 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTAACATAGTGAACA 1553
                         i   v v  i i   i  ii vv    i  v     i  v v      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_54584277_5   1554 GATAACTTACAGAATGGGAGAAAAATTTTGCAAGCTATGCATCTGAGAAA 1603
                           i   ii                vv       iii  ii      v  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_54584277_5   1604 GGTCTAATATTCAGCATCCATAAGGAACTTAAACAAATGTACAAGGTAAA 1653
                           v  vi   i   v  vi    i     ivv    v vv i  --    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA--TAAA 795

  chrX_54584277_5   1654 AACCTCAAACAACCCAATTAAAAAGTGGGCAAAGGACGTGAAAAGACACT 1703
                           vv-    i         ?    i           iv    v     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_54584277_5   1704 TTTAAAAAGAAGATATGCATGTGGCCAACAATCATATGAAAAAAAGCTTA 1753
                          i vv           i  vi       i  v  i       i v   i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_54584277_5   1754 ACATCACTGATACA 1767
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (152 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.22 (11 / 9)  


2224 25.76 6.33 0.29  chrX_54587411_54589104.rev      509  1203 (491)    L1M4_orf2#LINE/L1      172   908 (0)  

  chrX_54587411_5    509 ATAGCCAAGACAATCCTAAGCAAAATTAACAAAGCTGGAGGCATCACACT 558
                                 i      i i iv  i vv       i      vv       
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_54587411_5    559 ACCTGACTTCAAATTATACTACAAGGCTACAGCAACCAAAACAGCATGGT 608
                         v  ii i      viv        i       i  i   i    ii    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_54587411_5    609 ACTGGTACCAAAACAGACATACAGACCAATGGAACAGAATAGAGACCTCA 658
                              i iv ii i       i   i        i     v    vii  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_54587411_5    659 GAAATAACACCACACATCTATAA-CAATCTGATCTTCTACAAACCTGACA 707
                                vv   i    i   ii-    -    i   v    ivv  v  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCA 370

  chrX_54587411_5    708 AAAACAAGCAATGGGGGAAGAATTCCCTATTTAATAAATGGTCCTGGAGT 757
                          i v  vv        i      vvi  v  i  i       v    iii
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_54587411_5    758 AACTGGCTAGCCATATGCAGAAAACTGAAACTGGACCTCTTCCTTACACC 807
                               v  ?   i     i  i v    ii      i  v   i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_54587411_5    808 TTATACAAAAATTAACTCAAGATGGATTAAAAGCTTAAATGTAAAACCCA 857
                         v                   i      i ? ii i         i v i 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_54587411_5    858 AAAC---------CCTAGAA---AAC------------------------ 871
                             --------- i     ---   ------------------------
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_54587411_5    872 ---TTAGGCAAAGATTTTAT-GATGAACCGCCAAGAGCAATTACAACAAA 917
                         ---        v i   iv -   iviv i    i    vvvi       
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_54587411_5    918 AACTAAGATTTACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAG 967
                          ivv  i  vv i    v   ii v  i   v v  i i   i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_54587411_5    968 CAAAAGAAACTATCATCAGAGCAAACAGGCAACCTAGGGAATGG-AGAAA 1016
                             i  v       vv i  ii  v  i     i vi      -     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_54587411_5   1017 ATTTTTGCAATCTACCCATCTGACAAATGTTTACTATCCGGAATTTACAA 1066
                           v       vii ivi      i  iv vi vv     i    v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_54587411_5   1067 GGAACTAAAACAAATGTATAAGAAAAAAACAAACAATCCCATTAAAAAGT 1116
                         i     vvv    v vv    v     i     i  i  v   ?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_54587411_5   1117 GGGCAAAGGACATGAACAGACAATTTTCAAAAGAAGACATACATGCAGGC 1166
                                   iv    i     v  i  v        i     vii-   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT-GGC 869

  chrX_54587411_5   1167 CAACAA--ACATGAAAAACAGCTCAATATCACTGATCAT 1203
                            i  --         ivv      i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (103 / 73)
Gap_init rate = 0.01 (9 / 737), avg. gap size = 5.11 (46 / 9)  


3018 25.68 3.83 1.58  chrX_54593485_54596111.rev     1249  2136 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54593485_5   1249 TGAAGAGATATTCCATGCTCTTGGGTAGGAAGACTCAATATTGTGAAGAT 1298
                           i i      i     i  v   i v        i        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54593485_5   1299 GTCATTTCTTCTCAACTAGTTCCATAGGTACAAGGCAGTCCTAATTAAAA 1348
                          v  v v  i i   v v v  i i  i v   v   i   iv  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54593485_5   1349 TCTCAGCATTTTATTTTATGGTTATTACTAAACTTATTCTAAAAATTATA 1398
                           i    vvii v    iii vv   ivi  i  v  i      v i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_54593485_5   1399 AGATGAGGTGAAAGACCCAAAATAGCTAGCATAGTATTGAA---GGAGAA 1445
                         v ivi v ii ii      i      i iv i i v     --- i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_54593485_5   1446 CAAAGTTGGAGTACTGGCGCTACTAGACTTCAAGACTTACTATAAAGCTA 1495
                                    v   vi i  v ivi i     i        i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_54593485_5   1496 TAGTAATCAAGACTGTGTGGTAATGATGAAAAAATAGACAAATAGATTAG 1545
                         i            v        v  iiiv  ii       v      i i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_54593485_5   1546 TGGAATATAATGGAAAGCCCGGAAATAGACCCACA----TATAGTCAACT 1591
                                v   v  i  i  i      i     i ----   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_54593485_5   1592 GATCTTTGACAATGAAGCAAAGGCAATAGAGTGGAGCAAATAGGGCCTTT 1641
                            i  i     v iv  v   i v  vv i   i v  iv vi i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_54593485_5   1642 TAAACAAGTAGTGCTGGAACAACTGGACACCCATATGCACAAAAAACCCA 1691
                          v     i i       i         i ?   i     -   i  iv--
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAATG-- 447

  chrX_54593485_5   1692 CAAATACAGATGCAAACCTTACATCTTTCACAAAAA--AACTCAAAATAA 1739
                         -  i -ii  iv vv    i   i v vi       --          ii
  L1M4_orf2#LINE/    448 -AAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_54593485_5   1740 ATCATAAACCTAAAAATAAAATGCAAATGCAAAACTATAAAACTCCTAGA 1789
                             ? i       vi   i -  -----i               i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA-GC-----TAAAACTATAAAACTCTTAGA 539

  chrX_54593485_5   1790 AGATAACACAGGAGAAAATCTAGGTGACATTGGGTATGGGGATGACCTTT 1839
                            v    i   ? v      vv     v      vv  vi   iii i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_54593485_5   1840 CAGGTACAAAATCAAAGGTATAATACATAAAAGAAATAACCAATAAGCTT 1889
                         i  i  ii v i    i i i  vvv i        v  ivi    ii v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_54593485_5   1890 GACTTCATAAAAATTAAAAACTGCTCTGTG-----GAAGACATTGTCAAG 1934
                                 v             -- i    -----i i    i i     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACT--TTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_54593485_5   1935 AGAATGAAATGACAAGTCACACACTGGGAGAAAATACTTGTAAA------ 1978
                          i i     v     vi    v v            i   i   ------
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_54593485_5   1979 --------AGAGACTGTTATCCAAAATACGCAAAGAACAGTTAAAGCTCA 2020
                         --------  i    vv      i    iii       vv   v i    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_54593485_5   2021 ACTATAAGTAAATGAGTAACCCTACTTTAACAATGGGCAAAATACCTGAA 2070
                          iv    iv i ii i      - v  ?  v          iv ii    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_54593485_5   2071 TATACATCTCACCAACAAAGATAT------GGCAAATAAGCATATGCAAA 2114
                           v    i  v    vi       ------   v        i   v   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_54593485_5   2115 GATGCTCAATATCATAGGTCAT 2136
                                  i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (137 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.69 (48 / 13)  


3272 25.83 0.99 0.77  chrX_54626084_54630755.rev     3276  4181 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54626084_5   3276 TGGAAGAACATTCCATGCTCATGGATAGGAACAATCAATATGGTGAAAAT 3325
                              ii i  i     i        v    v v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54626084_5   3326 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3375
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54626084_5   3376 TACCAAGGACTTTCTTCACAGAA-TTGGAAACAA-CT-ACTTTAGAGTTC 3422
                          v   ivvi i  i  ii     -   ---    -  - iii  i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_54626084_5   3423 ATATGGAAC--CAAAAAAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAA 3470
                                 v--   iii v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_54626084_5   3471 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 3520
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_54626084_5   3521 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGAC 3570
                                  i   i    ii         i iv ii i   v i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_54626084_5   3571 CAATGGAACAGAAT--AGAGCCCTGAGAAATAACACCACACATCTACAAC 3618
                                 i     --    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_54626084_5   3619 CACCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 3668
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_54626084_5   3669 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3718
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_54626084_5   3719 TGAAACTGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 3768
                             ii  i i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_54626084_5   3769 ATTAAAGACTTAAATGTTAGACCTAAAACCTTAAAAACCCTAGAAGAAAA 3818
                           i ?    i       v   v       iv     vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_54626084_5   3819 CCTAGGCA-ATACCATTCAGCACATAGGCATGGGCAAGGACTTCATGTCT 3867
                          v    ?i- v i -   ivv  v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_54626084_5   3868 AAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCT 3917
                          vi            vvi          vv i   v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_54626084_5   3918 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3967
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_54626084_5   3968 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTTATCTGAC 4017
                          v  i     i                 v       vii iv       i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_54626084_5   4018 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAACTTA-CAAGA 4066
                           i  i  vi          v  i         vv    -  i -i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chrX_54626084_5   4067 AAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 4116
                             i     i     v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_54626084_5   4117 TTCTCAAAAGCAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 4166
                              v    v   i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_54626084_5   4167 ATCATCACTGGCCGT 4181
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (137 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3113 27.01 0.77 0.77  chrX_54641169_54645743.rev     3178  4084 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_54641169_5   3178 GGAAGAACATTCCATGCTCATGGGTAGGAACAATCAATATAGTGAAAATG 3227
                             ii i  i     i      i v    v v i     v  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_54641169_5   3228 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 3277
                           v     v     iv i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_54641169_5   3278 ATCAATGACTTTCTTCACGGAA-TTGGAAAAAACT-ACTTTAGAGTTCAT 3325
                         vi  iivi i  i  ii i   -   -- v  i  - iii  i i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_54641169_5   3326 ATGGAACCAAAAAAGAGCCCGCATTACCAAGTCAATCCTAAGCCAAAAGA 3375
                               viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_54641169_5   3376 ACAAAGCTGAAGGCATCACGCTACCTGACTTCAAA--CTACAGTACAAGG 3423
                               i  i   vv    i  v  ii i      --i   --     i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAG 247

  chrX_54641169_5   3424 CTACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGATATAGAT 3473
                                  i   i    ii       v i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_54641169_5   3474 CAATGGAACAGAAC--AGAGCCCTCAGAAATAGTGCCATGCATCTACAAC 3521
                                 i    i--    i  --       ivv    i   i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_54641169_5   3522 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 3571
                         i vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_54641169_5   3572 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGCAGAAAGC 3621
                         i  v  i  i              v      v  ?i  i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_54641169_5   3622 TGAAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 3671
                             ii    i i  v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_54641169_5   3672 ATGAAAGACCTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3721
                           v ?            v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_54641169_5   3722 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTGATGTCT 3770
                          v    ?i- v i -   iv   v v  vv i     v ii  vv ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_54641169_5   3771 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3820
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_54641169_5   3821 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3870
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_54641169_5   3871 TCAGGCAACCCACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 3920
                         vv  i         i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_54641169_5   3921 AAAGGGCTAATATCCAGAATCTACAGTGAACTCAAAGAAATTTACAAGAA 3970
                           i  i  vi          v  i iv      vv v  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_54641169_5   3971 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAAGATATGAACAGACACT 4020
                            i     i     v  i?    i        i   v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_54641169_5   4021 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 4070
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_54641169_5   4071 TCATCACTGGCCAT 4084
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 1.56 (14 / 9)  


3787 21.62 0.88 1.21  chrX_54692076_54694556     1078  1988 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54692076_5   1078 TGGAAAGATATTCCATGTTCATGGATTGGAAGACTCAATATTGTTAAAGT 1127
                                    i                       i           ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54692076_5   1128 GTCCATACTACCCAAAGCAATCTACAGATTCAAAGCAATCCCTATCAAAA 1177
                          v v     v      vii              v                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54692076_5   1178 TCGCAATGACATTCTTCACAGACATTGAAAAAACAATCCTAAAATCTAAA 1227
                           v  iivi v  i  ii    v     v  ivii          ii v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_54692076_5   1228 TGGAACCAGAAAAGACCCAGAATAACCAAAGCTATCCTAAACCAGAAGAA 1277
                              viiv  ii           i     i v   i i  vv       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_54692076_5   1278 CAAAACTGGAGGAATCACATTATCTGACTTCAAATTATACGGCAGAGCTA 1327
                             ii       v     i vi ii i      viv   vi  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_54692076_5   1328 TAGCAACAAAAACAGATTGGTACTGGGATAGAAACAGACACATAGACCGA 1377
                         i  i  iv  i    vv         v   iii i     i     i i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_54692076_5   1378 TGGAAAGGAATAGAGAACCCAGAAACAAATACACTA-ATCTATAGTGAAA 1426
                              vi    v    ii       i   iv  -  -  i   i  v  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTATGGTCAAT 349

  chrX_54692076_5   1427 TGATTTTCAACACAGGTGCCAAGAACATACATTGGGGAAAGAACAGTCGC 1476
                                 i   vi          v   v  v           i    vi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_54692076_5   1477 CTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAATAATGAA 1526
                         i    i              v         ?   i     i  v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_54692076_5   1527 ACTAGACCTCT--CTCTCACCATATACAAAAATCAAATCAAAATTGATTA 1574
                         ii i    i  --   v                i  v       v   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_54692076_5   1575 AAGACTTCAATCTCAGACCTCAAACTATGATACTATTAATACTACAAGAA 1624
                         ?    i v   v v   v  v       i v   v   i------     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG------AAGAA 543

  chrX_54692076_5   1625 AACCTTGGGA-AAATCGCCAGGGCATTGGTTTGGGCAAAAATTTCTTGAA 1673
                            v v  ?i-     vi iv i v    v  i     vii      ii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_54692076_5   1674 TAATG-C-CCAATAAGCACAAGCAACCGTAGTAAAAGTGGACAAATGGGA 1721
                           -  - -    -             viv  v    i i  i    v   
  L1M4_orf2#LINE/    594 TA-TGACACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_54692076_5   1722 TCACATCAAG-TTAAAAAGCTTCTACACTGCAAGGGAAATGATAAACAAA 1770
                         iiv      i-       -   i iii  v   i   v iv  v  v   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_54692076_5   1771 GTGAAGAGACAACCCACAGAATGGGACAAAATATTTGCAAACTACCCATT 1820
                              i                    v              ii ivi  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_54692076_5   1821 TCACAAGGGATTAATAACCAGAATATATAAGGAGCTCAAACAACTCCATA 1870
                          v i      i vi  v             i  i   vv       v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_54692076_5   1871 GGAAAAAAATCTAAAAATCCAATCAAAAAA-GGGCAAAAGATTTGAATAG 1919
                         iv     i - v  v  i     i?     -       i           
  L1M4_orf2#LINE/    791 ATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_54692076_5   1920 ATATTTCTCAAAAGAAGACATACAAATGGCAAACAGACATATGAAAAGGT 1969
                          i       v        i           v  i ii  i        i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_54692076_5   1970 GCTCAACATCACTGATCAT 1988
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (115 / 78)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


2714 27.05 0.26 0.26  chrX_54737531_54739283.rev      505  1273 (480)    L1M4_orf2#LINE/L1      140   908 (0)  

  chrX_54737531_5    505 TAAAGTTCATATGGAACCAAAAAAGAGCCTGCATTGCCAATTCAATCCTA 554
                             i           viiv  ii  v  v v  v     vv     i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_54737531_5    555 AGCCAAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATA 604
                          ivv i          i      vv       v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_54737531_5    605 CTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAG 654
                               i          i   i    ii         i iv ii i   v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_54737531_5    655 ATATAGATCAACGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATA 702
                                    i    i    i--    i  --        vv  ii i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACA 337

  chrX_54737531_5    703 TCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGA 752
                          i  iiiii vi    i  i     ivv  vv  i v  vv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_54737531_5    753 AATGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATG 802
                           vi  vvi  v  i  i              v      v  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_54737531_5    803 TAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATT 852
                         i i  iiv    ii    i    v   i     v           i  i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_54737531_5    853 CAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCCA 902
                            i      i ?    i    i  v   v       i      vi ii 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_54737531_5    903 GAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTT 952
                                  v    ?i v viv   iv   v v  vv i     v ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_54737531_5    953 CATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAAT 1002
                          v ivv  vi            vvi           v     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_54737531_5   1003 GGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATC 1052
                         v   ii v  i   v v  i i   i  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_54737531_5   1053 AGACTGAACAGGCAACCTACAAAATAGGAGAAAATTTTTGCAACCTACTC 1102
                          i v    v  i     i   i   i         v       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_54737531_5   1103 ATCTGACAAAGGGCTAATATCCAGAATCTGCAATGAACTCAAACAAATTT 1152
                               i  i  i  vi          v ii  v      vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_54737531_5   1153 ACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAAC 1202
                          i  v     i     i     v  i?    i     i     iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_54737531_5   1203 AGTCACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAA 1252
                           v  i     v        i  vi viii     v  i          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_54737531_5   1253 ATGCTCATCATCACTGGCCTT 1273
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (117 / 87)
Gap_init rate = 0.00 (2 / 769), avg. gap size = 2.00 (4 / 2)  


3171 27.42 0.44 0.44  chrX_54763637_54772593.rev     1758  2665 (6292)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54763637_5   1758 TGGAAGAACATTCCATGCTCATGGGCAGGAAGAATCAATATCGTGAAAAT 1807
                              ii i  i     i      iiv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54763637_5   1808 GGCCAAATTACCCAAAGTATTTTATAGATTCAATGCCATCCCCATCAAGC 1857
                            v v i v      v iv i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54763637_5   1858 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTCA 1905
                          v   iivi i  i  ii     -   -- v  i  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_54763637_5   1906 TACAGAACCAAAAAAGAGCACGCATTGCCAAGTCAATCCTAAGCCAAAAG 1955
                           ii   viiv  ii  v vv v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_54763637_5   1956 AACAAAGTTGGAGACATCACGCTACCTGACTTCAAACTAAACTACAAGGC 2005
                                      ivv    i  v  ii i      vivv       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_54763637_5   2006 TACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 2055
                                     i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_54763637_5   2056 AATGGAACAGAACAGAGCCTTCAGAAATAATGCTGCATATCTACAACCAT 2105
                                i    iv   vv i         vv iii i  i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_54763637_5   2106 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 2155
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_54763637_5   2156 ATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 2205
                         v  i  i   i          v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_54763637_5   2206 AACTGGATCCTTTCCTTATACCTTATACAAAAATTAATTCAAGATGGATG 2255
                          ii    i  i v   i i   v              i    i      v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_54763637_5   2256 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 2305
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_54763637_5   2306 AGGCAATAAA-ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 2354
                            -?i    -v   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGG-NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_54763637_5   2355 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGAGCTAAT 2404
                                     vvi           v     v  i    v   vi v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_54763637_5   2405 TAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 2454
                         i   v i  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_54763637_5   2455 GGCAACCTACAGAATGGGAGAAAATTTTTGCGATCTACTCATCTGACAAA 2504
                          i     i                 v     i vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_54763637_5   2505 TGGCTAATATCCAGAATCTATGATGAACTCAAACAAACTT-ACAAGAAAA 2553
                         v i  vi          v   i v      vv    -  i- i  v    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAAA 796

  chrX_54763637_5   2554 AAACAAACAATCCCATCAAAAAGTGGGTGAAGGACATGAATAGACACTTC 2603
                          i     i  i  v  i?    i    ii     iv          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_54763637_5   2604 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 2653
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_54763637_5   2654 ATCACTGGCCAT 2665
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  

3200 26.54 1.10 1.10  chrX_54763637_54772593.rev     7559  8466 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54763637_5   7559 TGGAAGAACATTCCGTGCTCATGGGTAGAAAGAATCAATATATTGAAAAT 7608
                              ii i  i  i  i      i v i    v i     vv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54763637_5   7609 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 7658
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54763637_5   7659 TACCAATGACTTTCTTCACAGGA-TTGGAAAAAACT-ACTTTAAAGTTCA 7706
                          v   iivi i  i  ii   i -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_54763637_5   7707 TATGGAACCAAAAAAGAGCCTGCATGGCCAAGTCAATCCTAAGCCAAAAG 7756
                                viiv  ii  v  v v  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_54763637_5   7757 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 7806
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_54763637_5   7807 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 7856
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_54763637_5   7857 AATGGAACAGAAT--AGAGCCCTCAGAAATATTGCCACATATCTACAACT 7904
                                i     --    i  --       vvv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_54763637_5   7905 ATCTGATCTTTGAGAAACCTGACAAAAACAAGCAATAGGGAAAGGA--GT 7952
                          vi    i  i  v  ivv  v   i v  vv    i       i --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_54763637_5   7953 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 8002
                          -- v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_54763637_5   8003 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 8052
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_54763637_5   8053 GATGAAAGACTTAAATGTTAAACCTAAAACCATAAAAACCCTAGAAGAAA 8102
                            v ?    i       v i v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_54763637_5   8103 ACCTAGGCAATACTGTTCAGGACATAGGCATGGGCAAGGACT----AAAT 8148
                           v    ?ivv v v   iv   v v  vv i     v ii ---- i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_54763637_5   8149 GTCTAAAACAGCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 8198
                         i ----i   v        vvi          vv     v  i    v  
  L1M4_orf2#LINE/    595 AT----GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_54763637_5   8199 ATCTAATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 8248
                          ii v  i   v i  i i   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_54763637_5   8249 GTGGACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATC 8298
                            i v  i     i                 v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_54763637_5   8299 TGACAAAGGGCTAATATCCAGAATCTGCAATGAACTCAAACAAATTTACA 8348
                            i  i  i  vi          v ii  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_54763637_5   8349 AGAAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGA 8398
                          v     i     i     v  i?    i    ii      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_54763637_5   8399 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATG 8448
                           i     v        i  vi viii     v ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_54763637_5   8449 CTCATCATCACTGGCCAT 8466
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


2055 26.69 6.90 0.30  chrX_54820838_54822484      488  1154 (493)    L1M4_orf2#LINE/L1      198   908 (0)  

  chrX_54820838_5    488 GAATGAGGTCTCAGGCATCACATTGCCTGACTTCAAACTGTGCTATAAGG 537
                            ii i  ivv   vv     i v  ii i      viv i   i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_54820838_5    538 CCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAAGCATACAAAC 587
                          i i   v i   i    ii         i    ii   ii    i i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_54820838_5    588 TGATGGAACTGAACAGAGAACCCAGAAATAAAGCCAAATACTTAAAAGCC 637
                         ii      iv   iv    ii           v   v i i   vi- i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG-GTC 346

  chrX_54820838_5    638 AACTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACT 687
                           i    i   i    i vviv   i v   vv i         i i v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_54820838_5    688 CTATTCAACAAATGGTGCTGGCATAATTGGGAAGCCACAAGTAGAAAAAT 737
                           v                  v i  i   iv ?     v i i  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_54820838_5    738 AAAACCGGATCCTCATCTCTCATCTTATACAAAAATCAACTCAAA-TGGA 786
                         i  iii   i  ii i   v  i v           i        -    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_54820838_5    787 ACAAAGACTTAAATCTCAGGCCTGAAACCACAAAAGTTTTAAAAGATAAC 836
                         v  ?    i     v v  iv  i    i i    v i   i    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_54820838_5    837 ATTGGGA-AAACATTC------------TAGACA-TGG------GGAAAT 866
                           v  ?i-   iv   ------------   i  -   ------i  v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_54820838_5    867 G----------------CAACAAAAACAAAGATAAATACATGCAACTTAA 900
                          ----------------        iv   i   i   v  vvi    v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_54820838_5    901 TTAAACTAAAAAGCTTCTGCACAGCAAAAGA-ATTAATCAGTAGGGTAAA 949
                          i   v v    i   i  ii vv    i  - i  -   iv ii  i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAA 695

  chrX_54820838_5    950 CAGACAACCCACAGAGTGGGAGAAAATCTTCTCAATCTATATATCCAGCA 999
                         v              i           v  iv   vii       iiii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_54820838_5   1000 AATAACTAATATCCAGAATCTACAAGGAACTGAAACCAATCAGCAAGAAA 1049
                          ivi   vi          v  i  i     vvv  v v   ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_54820838_5   1050 AA-ACAAACAATCCCATCAAAAAGTGGACA-------TGAATAGACAATT 1091
                           -     i  i  v  i?    i   i  -------          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_54820838_5   1092 CTCAAAAGAAGATATACAGATGGCCAACAAACATATGAAGAAATGCTCAA 1141
                            v              i        i  i  i     i i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_54820838_5   1142 CATCACTGATTAC 1154
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (113 / 61)
Gap_init rate = 0.02 (11 / 711), avg. gap size = 4.36 (48 / 11)  


3169 28.22 0.33 0.22  chrX_54826472_54828950     1080  1986 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54826472_5   1080 TGGAAGAACATTCCATGCTCATGGCTAGGAAGAATCAATATCGTGAAAAT 1129
                              ii i  i     i      v v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54826472_5   1130 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 1179
                            v     v     iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54826472_5   1180 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 1228
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_54826472_5   1229 TGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGAA 1278
                              viiv  ii  v  v v  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_54826472_5   1279 CAAAGCTGGGGGCATCTCGCTACCTGACTTCAAACTATACTACAAGGCTA 1328
                              i   i  vv  v i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_54826472_5   1329 GAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGAGATACAGATCAA 1378
                         v     i   i    ii       i i iv ii i   v   i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_54826472_5   1379 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT 1426
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_54826472_5   1427 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 1476
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_54826472_5   1477 ATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1526
                         v  i  i   i          v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_54826472_5   1527 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATG 1576
                          ii    i    v   i     v              i    i      v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_54826472_5   1577 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1626
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_54826472_5   1627 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 1676
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_54826472_5   1677 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAGTGGGATCTAATT 1726
                                    vvi          vv     v  i  i v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_54826472_5   1727 TAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 1776
                         v  v i  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_54826472_5   1777 GCAACTTACAGACTGGGAGAAAATTTTTGCAACCTACTCATCAGACAAAG 1826
                         i    ii     v           v       vii ivi   v  i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_54826472_5   1827 GGCTAACATCCAGAATCTACAATGAACTCAAACAAATTGACAAGAAAAAA 1876
                          i  vii         v  i  v      vv    v ii i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_54826472_5   1877 ACAAACAACCCCATCAAAAAGTAGGTGAAGGACATGAATAGACACTTCTC 1926
                              i     v  i?    i i  ii     iv          i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_54826472_5   1927 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 1976
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_54826472_5   1977 CACTGGCCGT 1986
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (150 / 102)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.67 (5 / 3)  


3233 27.09 0.44 0.44  chrX_54847329_54851608     2880  3787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54847329_5   2880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAGAT 2929
                              ii i  i     i      i v      v i     i  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54847329_5   2930 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2979
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54847329_5   2980 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 3026
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_54847329_5   3027 GTATGGAACCAAAAAAGGGCCCGCATCGCCAAGTCAATCCTAAGTCAAAA 3076
                         i       viiv  ii iv  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_54847329_5   3077 GAACAAAGCTGGGGGCATCATGCTACCTGACTTCAAACTATACTACAAGC 3126
                                 i   i  vv   ii  v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_54847329_5   3127 CTACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGAC 3176
                                  i   i    ii    i    i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_54847329_5   3177 CAATGGAACAGAACAGAGCCTTCAGAAATAATGCTGCATATCTACAACTA 3226
                                 i    iv   vv i         vv iii i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_54847329_5   3227 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGCTTCCC 3276
                         vi    i  i     ivv  vv  i v  vv            iv vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_54847329_5   3277 TATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCTG 3326
                          v  i  i   i          v      v  ?       i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_54847329_5   3327 AAACTGGACCCCTTCCTTACACCTTATTCAAAAATTAATTCAAGATGGAT 3376
                           ii         v   i     v   v          i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_54847329_5   3377 GAAAGACTTAAACGTTAGACCTAAAACCATAAAAACC-CAGAAGAAAACC 3425
                         v ?    i    i  v   v       i      vi -i          v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_54847329_5   3426 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 3475
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_54847329_5   3476 ACACCAAAAGCAATGGCAACAAAAGCCAAAACAGACAAATGGGATCTAAT 3525
                                     vvi          vv    i   i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_54847329_5   3526 TAAAACTCAAGAGCTTCTTCACAGCAAAAGAAACTACCATCAGAGTGAAC 3575
                         i    i -  i i   i vii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    648 CAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_54847329_5   3576 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 3625
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_54847329_5   3626 AGGGCTAATATCCAGAATGTACAAAGAACTGAAACAAATTTACAAGAAAA 3675
                         i  i  vi          i  i        vvv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_54847329_5   3676 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAATAGACACTTC 3725
                          i     i     v  i?    i    ii      v          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_54847329_5   3726 TCAAAAGAAGACATCTATGCAGCCAAAAGACACATGAAAAACTGCTCATC 3775
                           v        i  vi viii     v ii          iv      v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_54847329_5   3776 ATCACTGGCCAT 3787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


3203 27.42 0.44 0.44  chrX_54877474_54886340     3060  3967 (4900)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_54877474_5   3967 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAGAT 3918
                              ii i  i     i      i v      v i     ii v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_54877474_5   3917 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3868
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_54877474_5   3867 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3820
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_54877474_5   3819 TATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 3770
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_54877474_5   3769 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGCC 3720
                                i      vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_54877474_5   3719 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3670
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_54877474_5   3669 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3622
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chrX_54877474_5   3621 ATCTGATCTTTGACAAACCTGAGAAAAATAAGCAATGGGGAAAGGATTCC 3572
                          vi    i  i     ivv  vv  i vi vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_54877474_5   3571 CTATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3522
                           v  i  i     i        v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_54877474_5   3521 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3472
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_54877474_5   3471 TGAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3422
                          v ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_54877474_5   3421 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 3372
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_54877474_5   3371 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3322
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_54877474_5   3321 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGACTGAAC 3272
                          i   v i  i i   i  ii vv    i  v    i  vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_54877474_5   3271 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 3222
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chrX_54877474_5   3221 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATCGACAAGAAAA 3172
                         i  i  vi          v  i  v      vv    v  i i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chrX_54877474_5   3171 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATCAACAGACACTTC 3122
                          i     i     v  i?    i    ii     iv v  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chrX_54877474_5   3121 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 3072
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chrX_54877474_5   3071 ATCACTGGCCAT 3060
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

3269 24.35 2.14 0.34  chrX_54877474_54886340     5967  6853 (2014)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_54877474_5   5967 AGACATACTGTGTTCATGGACTGGAATACTCAATATGGTAAAGATGTCTA 6016
                            i  v ii          i     v   i     v  v      v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_54877474_5   6017 TTCTCCCCAAAGTGACCTATATACGTAACACAATACCAATAAAAACCCTA 6066
                          v         v   i   i v ivi   i    v  v  v    i  i 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_54877474_5   6067 TCAGGATATTTT--AGATATAGACAAGCTGATCCTGAAACTCATATGGAA 6114
                         v v vv v    --   v  v              i   i          
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_54877474_5   6115 GGGCTAAGAAACTACAATGGCCAAAACAAT-TTGCAAAATAAAAACAATG 6163
                         iv  v i i v i v   i           -   v    v  i     v 
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_54877474_5   6164 TTG-----CTGAAACTTC---------AAATTATACTGCAAGGCTATAGT 6199
                            -----  v v     ---------   i -    i   i    i   
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGT 254

  chrX_54877474_5   6200 TACCAAAACAGCATGGTACTGGTATAAAAACAGGCACATAGAGCAATGGA 6249
                         v i   i    ii         i    ii i  i  i     v       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_54877474_5   6250 ACAAAATTCGGAACCCAGAAATAAAGCCAAATACTTACAGCTAACTGATC 6299
                          i i    vi  ii           v   v i i   ii ii  i    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_54877474_5   6300 TTTAACAAAGCATGC-AATAACATAAAGTAGGGAAATGATACCCTATTCA 6348
                           ii    i -i   -  v v   vv i i      vi   vi  v    
  L1M4_orf2#LINE/    355 TTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_54877474_5   6349 ATTAATGATGCTGGGATAATTGGCAAGCCACATATAGAAGAATAAAACTG 6398
                          iv    i        i  i   vv ?      ii i      i  ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_54877474_5   6399 GACCCTCCTCTCTCACTTTATACAAAAATCAACTCAAGATGGATCAAAGA 6448
                              iivi   v   iv           i       i        ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_54877474_5   6449 CCTATACCTCAGACCTGAAATCATAAAAATTTTACAAGATAACATTGGGA 6498
                             v iv v   v  i   ii      v i   v    v     v  ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_54877474_5   6499 AAACTCTTCTAGACATTGGCTTAGGCAAAGAATTCATGACTAAGAGCCCA 6548
                         v  v     vv   v    v        v iv   v iiv  v  vv   
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_54877474_5   6549 AAAGCAAATGCAACAAAAATAAAAATAAATAAATGGGACATAATTAAACT 6598
                               v v         iv       i      v    v v  i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_54877474_5   6599 AAAATGCTTCTGTGCAGTAGAAGAAATAATCAGCAGAGTAAACAGACAAC 6648
                         v   vi   i     vvi i i  v iv    iv i   i  v       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_54877474_5   6649 CAACAGAGTGGGAGAAAATATTCGCAAACTATGCATTTGATAAAGGACTA 6698
                          v     i              i     ii  ii  i      i     v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_54877474_5   6699 ACATCCAGAATATACAAGAAACTCAAAACAACTCAGCAAGAAAAA-ACAA 6747
                         ii            i  ii     vv -       ii  v     -    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATAAAAAGACAA 802

  chrX_54877474_5   6748 ATAATCCCATCAAAAAGTGGGCAAAGGACATGAATATAGAATTCTCAAAA 6797
                             i  v  i?    i           iv      v v v     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_54877474_5   6798 GAAGATATATAAACAGCGAACAAACACATGAAAAAATGCTCAACATCACT 6847
                                  i   ii  v  i  i          i             ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_54877474_5   6848 ATCTTT 6853
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.23 (117 / 95)
Gap_init rate = 0.01 (9 / 903), avg. gap size = 2.44 (22 / 9)  

1902 21.15 4.18 8.75  chrX_54877474_54886340     7609  8374 (493)    L1M4_orf2#LINE/L1      178   908 (0)  

  chrX_54877474_5   7609 AAAATAAA--TAAATAAATAAAACAATGTTGGTGGACTGA-ACTTTACTA 7655
                             i  v-- i  v  iv i     v     v     v -    i- i 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC-CCA 226

  chrX_54877474_5   7656 CATGATTTTGAGACTTATTATAAAGCCACAATACTCAGGACAGTGTGGTA 7705
                         ----    ii i     i  i     i   i  v   i            
  L1M4_orf2#LINE/    227 ----ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_54877474_5   7706 TTGGAAAAAGGATAGCAATCTAGATCAATGAAATAGAATAAAGAGCCCAG 7755
                         i   v v        vv  v          i        vi    i    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_54877474_5   7756 AAATAGACCCACTCAAATTTTGGACAAAGTCAACTAATTTTGGACAAAGG 7805
                              i     iv  ---   ---- vi     i i     v     i  
  L1M4_orf2#LINE/    323 AAATAAACCCATACA---TTT----ATGGTCAATTGATTTTCGACAAGGG 365

  chrX_54877474_5   7806 TACAAAGTCAATTCAATAGAGAAAATAGAGTCTTTTCAACAAATGGTGCT 7855
                          i v   v v       i i    iv v                      
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_54877474_5   7856 AGAACGATTGGAAGTCCAC-TGCAAAA-AATGAACTTGAA----TACTTA 7899
                         i i  i i    vi?    -       -      v   i ----   i v
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_54877474_5   7900 A-ACCTTACCCAAAAAATAATTCAAAGTGGATCATAGGTCTAAATATAAA 7948
                          -   v  iv      v   i     i       ?  ii      i   i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_54877474_5   7949 ATGTAAAACTATAAAACTTCTAAAAAAAGGACTTGGGAGAGAAT----GT 7994
                          vv               ii  i  i  i-  v i  ? vi   ----  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAA-ACATAGGNGTAAATCTTCGT 564

  chrX_54877474_5   7995 AAAATATTGGATATGCCAATTAGTTTTTAGTTACATCACAAAAAGCATTA 8044
                         i --iv    i vv v    viv  i    v  iiv   v       iv 
  L1M4_orf2#LINE/    565 GA--CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_54877474_5   8045 TCCACACAAGAAAAAAATAGATAAATTGAACT--ATAAAAATTTAAACAT 8092
                         v v   v         -           i   --  v      -   v i
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATT-AAAAAC 660

  chrX_54877474_5   8093 TTTTATTTACGAAAAATTTTAAAATAAAAATTGTTAAATATTTACATATT 8142
                             i ---------ii  i   i--------------------------
  L1M4_orf2#LINE/    661 TTTTGT---------GCTTCAAAG-------------------------- 675

  chrX_54877474_5   8143 AACATTTTTTTATCTGTGAAAGACACAAAGGAATGAAAAATGCCACAGAA 8192
                         i   i -----   -----    ---  iv   vii v  i-        
  L1M4_orf2#LINE/    676 GACACT-----ATC-----AAGA---AAGTGAAAAGACAAC-CCACAGAA 711

  chrX_54877474_5   8193 TGAAAGAATATACTTGTACATTATATATCTGGTA---------TATCCAA 8233
                           ii    v   i   i v  i         i  ---------      i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_54877474_5   8234 AATATATAAATAACACTTAAAACTGAACAATAAAA-GATAAA--ATTTAG 8280
                                   v   v    v    v  i       -  i   -- iii i
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_54877474_5   8281 TTTTAAAAATTAGCAAAGCATCTGAACAAACATTTCACCAACCCAAATGT 8330
                           ?-      vi      v  i    i i       v    vvv i  i 
  L1M4_orf2#LINE/    812 TTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_54877474_5   8331 ACAGATGGCAAACAAGTGTATTAAAAGAT----AATATCAATCATTGG 8374
                            i     v  i   iii  v       ----  i    ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (95 / 63)
Gap_init rate = 0.04 (27 / 731), avg. gap size = 3.67 (99 / 27)  


2291 27.21 2.66 1.82  chrX_54956623_54962894.rev     4988  5700 (572)    L1M4_orf2#LINE/L1        1   719 (189)  

  chrX_54956623_5   4988 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5037
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54956623_5   5038 GGCCATACCTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5087
                            v    ii     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54956623_5   5088 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCG 5135
                          v   iivi i  i  ii     -   -- v  i  - iii    i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_54956623_5   5136 TATGGAACTGAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5185
                                v  v  ii  v  v v  vi    iv     i i ---     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAG 195

  chrX_54956623_5   5186 AAG--CA------------TCACGCTACCTGACTTCAAACTATACTACAA 5221
                            --  ------------    i  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_54956623_5   5222 GGCAACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATAAAG 5271
                         i  v       i   i    ii    i    i iv ii i   v   v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_54956623_5   5272 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACA 5319
                          i        i    i--    i  --        vv  ii i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_54956623_5   5320 GCTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT 5369
                          ii vi    i  i     ivv  vv  i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_54956623_5   5370 TCCCTATCTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGTAGAAA 5419
                         vvi  v ii  i           i  v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_54956623_5   5420 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 5469
                         iv    ii    i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_54956623_5   5470 GGAGTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5519
                            vi ?    i  v    v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_54956623_5   5520 AACCTAGGCA-ATACCATTCAGGACATAGGATTGGGCAAGGACTTCATGT 5568
                            v    ?i- v i -   iv   v v  i  i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_54956623_5   5569 CTAAAACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGGAT 5618
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_54956623_5   5619 CTAATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5668
                         i v  iv  v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_54956623_5   5669 GAAACAAACAACCCCATCAAAAAGTGGGCAAA 5700
                             - i       ---- v i i    vi  
  L1M4_orf2#LINE/    693 GAAA-AGACAACCC----ACAGAATGGGAGAA 719

Transitions / transversions = 1.58 (117 / 74)
Gap_init rate = 0.02 (12 / 719), avg. gap size = 2.67 (32 / 12)  

 329 22.22 0.00 0.00  chrX_54956623_54962894.rev     5701  5781 (491)    L1M4_orf2#LINE/L1      828   908 (0)  

  chrX_54956623_5   5701 GGACATGAACAGACACTTCTCAAAAGAAGACATTTGTGCAGCCAAAAGAC 5750
                            iv    i     i     v        i  viiviii     v ii 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_54956623_5   5751 ACATGAAAAAATGCTCATCATCACTGGCCAT 5781
                                  i       v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.00 (0 / 0)  


3293 26.61 0.44 0.22  chrX_54971306_54975516.rev     2821  3722 (489)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_54971306_5   2821 AAGAAATTAAATGTTAATGGATTGGGAAAATCAATATTTTTAA-ATGTCC 2869
                             v  ivv     v         i i v i      v    -   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_54971306_5   2870 ATACTACCCAAAACAATCTACAGATTTGATGCAATCCCTATCAAAATACC 2919
                              v      vii           ii i                 v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_54971306_5   2920 AATGATATTCTTCATATAAATAGAAAAA--AACTCTAAAATTTATATGGA 2967
                          iiviiv  i  iii v    v  v  i--i ii        i       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_54971306_5   2968 ACCACAAAAGACACAGAATAGCCAAAGCTATACTGAGCAAAAAGAACAAA 3017
                          vii   ii   v             i v  vi   iv  i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_54971306_5   3018 CATGGAAGAATCATATTACCTGACTTTAAATTACACTACAGAGCTATAGT 3067
                         vv    i  v   i i v  ii i  i   vivi      i     i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_54971306_5   3068 AACCAAAACAACACAGTACTGGCATAAAAACAGACACACAGACCAATGGA 3117
                           i   i   iiiii            ii i     i i   i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_54971306_5   3118 ACAGTATAGAAAACCCAGAGATAAATTCACACATCTACAGCAAACTCACT 3167
                          i  v  v  i ii     i     ii  i    i  ii iv  i v i 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_54971306_5   3168 TTTGACTAAGTTCTCAAGAACATACACTAGTGAAAGGACAGTCTCTTTAA 3217
                           i   v i v vi     v   v  v i v     i i     i  i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_54971306_5   3218 TACATAGTGCTGTGAAAACTGGATATCCACATGCAAAAGAATGAAACTAC 3267
                         i v  i      v  v         ?                   ii iv
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_54971306_5   3268 ACCCCTATCTCTCACCATATACAAAAATCAAATCAAAATGTATTAAAGAC 3317
                                i   v                i  v        v  i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_54971306_5   3318 TTAAATTATAAGACCTCAGACTATGAAACCACCAAAGGAAAACATTGGGG 3367
                         i     -i     v  v i     i    ivii i i        v  ? 
  L1M4_orf2#LINE/    505 CTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_54971306_5   3368 AACCTCTCTAGGACACTGGACTGCACAAAGATTTCGTGAGCAATATCCCA 3417
                         v vv   iiiv   vi   ii ivi   v i    v iiii vv iv   
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_54971306_5   3418 CAAGCACAGGCAACCAAAGCAAAAATGGACAAATTGAATTACATCAAGTT 3467
                         v       i     v    v      i  i      i i v      iv 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_54971306_5   3468 TAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAAGCGGCAAC 3517
                              i   i  ii vv       v  v     v        iv i    
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_54971306_5   3518 CCACATAATGGGACAAA-CATTTGCAACTTACCCATCTGACAAGGAATTA 3566
                              v       v   -i        v i ivi      i    i i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_54971306_5   3567 ATAATCAGAATACATAAGGAGCTCAAAGAACTCTATAGGAAATAAATCTA 3616
                         i  vi       i    i  i   vv v     v   iv   v i - v 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAA 802

  chrX_54971306_5   3617 ATCGTCTCATTTAAAAATGGGCAAAAGACCTGAATGGACATTTCTCAAAA 3666
                           vii iv   ?             i  ii     i          v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_54971306_5   3667 GAAGACATACAAATAGCAAACAGGTATATGAAAAGATGCTCAATATAATT 3716
                              i        i  v  i i i i                i  v ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_54971306_5   3717 GATCAT 3722
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.65 (147 / 89)
Gap_init rate = 0.01 (5 / 904), avg. gap size = 1.20 (6 / 5)  


3055 26.54 2.58 0.90  chrX_54976757_54982612.rev     4473  5365 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_54976757_5   4473 TGGAAAAACATTCCATGTTCATGGATAGGAAGAATCAATATTGTCAAAAT 4522
                               i i  i              v      v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_54976757_5   4523 GGCCATACTGCCCAAAGTAATTTATAGATTTAATGCTATCCCGATCAAGC 4572
                            v     v      v i  i  i     i  i  v     v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_54976757_5   4573 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTC 4619
                          v   -   v    i  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_54976757_5   4620 GTATGGAACCAAAAAAGAGCCCTCATAGCCAAGACAATCCTAAGCAGAAA 4669
                         i       viiv  ii  v  vvv        i      i i iv ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_54976757_5   4670 GAACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTGTACTACAAGG 4719
                                 i     ivv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_54976757_5   4720 -TACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 4768
                         -        iv  i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_54976757_5   4769 CAATGCAACAGAACAGAGGCCTCAGAAATAATGCCACATATCTACAACCA 4818
                              v  i    iv   ivii         vv   i i  i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_54976757_5   4819 ACTGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 4868
                          i    i  i i   ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_54976757_5   4869 TATTTAATAAATGGTGTTTGGAAAACTGGCTAGCCGC-----------TG 4907
                          v  i  i        i v   v      v  ?  i -----------  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_54976757_5   4908 AAACTGGATCCCTTCCTTACATCTTATACAA-------CTCAAGATGGAT 4950
                           ii    i    v   i   i v       -------     i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_54976757_5   4951 TAAAGACTTAAACGTAAGATCTAAAACCATAAAAACCCTAGAAGAAAGCC 5000
                         i ?    i    i      v       i      vi i         i v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_54976757_5   5001 TAGGCA-ATACCATTCAGGACATTGGCATGGGCAAAGACTTCATGACTAA 5049
                             ?i- v i -   iv   v    vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_54976757_5   5050 AACATCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGAATCTGA 5099
                         i   i        vvi          vv        i    v i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_54976757_5   5100 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGTCATCAGAGTGAAC 5149
                          i   v v  i i   i  ii vv    i  v   i   vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_54976757_5   5150 AGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTATCCATCTGACAA 5199
                           i     i                vv       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_54976757_5   5200 AGGGCTAATATCCAGAATCTACAGAGAACTTAAACAGATTTATAAGGAAA 5249
                         i  i  vi          v  i i      ivv   iv iv    v--  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT--AA 794

  chrX_54976757_5   5250 AAAGAAACAAACAAACCCACCCAAAAGTGAGCGAAGGATATGATCAGACA 5299
                              --    i  v  v ii?    i  i  i      v   vi     
  L1M4_orf2#LINE/    795 AAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_54976757_5   5300 CTTCTCAAAAGAAGACATTTATGCAGCCAACAAACGTATGAAAAGAAGTT 5349
                         i     v        i  vi viii     i  i ii         v i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_54976757_5   5350 CATCATCACTGGTCAT 5365
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


3378 24.50 1.32 1.43  chrX_55144949_55147352.rev     1008  1913 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_55144949_5   1008 AAATATATTTTATGTACATGTATGAGGAGAATCAATATTGTTAAAAATGT 1057
                            v    iii    v    v  vi i   v i           i -  v
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-TGG 52

  chrX_55144949_5   1058 CCATACTAACCAAAGCAATCTACAGATTCAATGCAATCCCTAGCAAAATA 1107
                          v     vv     vii              i          v      v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_55144949_5   1108 CCAATGACATTCTTCAAAGAAATAGAAAAAACAATTCTAAAATTTATATA 1157
                            iivi v  i  iiv      v  v  ivii  i        i    i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_55144949_5   1158 CAACTACAAAAGACCCAGAATAGCCAAAGCTATCCTAAGAAA-AAGAACA 1206
                         v  v i   ii                 i v   i i i   -       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_55144949_5   1207 AAACTGGAGGAATCACATTACCTGACTTCAAATTATACCACAGAGCTATA 1256
                           ii       v     i v  ii i      viv   i   i     i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_55144949_5   1257 GTAACCAAAACAGCATGGTACTGGCATAAAAACACACACATAGACCAATG 1306
                             i   i    ii              ii i v   i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_55144949_5   1307 GAACAGAATAGGGAATCCAGAAGCAAATCCACACATCTACAGTGGAGTCA 1356
                            i     v i  i       ii   i   i    i  ii  vi v v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_55144949_5   1357 TTTTCAACAAAGTTCCCAAGAACATGCACTGGGAAAAAGACAGTCTCTTC 1406
                              i    i v v      v   v  v    i   ii i     i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_55144949_5   1407 AATAAGTTGTGCTGGGAAAACTGGATATCCATATGCAGAAAAAAATATGA 1456
                           i  i v         v         ?   i     i  i  ----   
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA----TGA 448

  chrX_55144949_5   1457 AACTTATACCCCTATCTTTTGCCATATATAAAAATCGAATCAAAATGGAT 1506
                          i-  iv       i  ivii       i      ii v           
  L1M4_orf2#LINE/    449 AG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_55144949_5   1507 TAAAGACTTACAACTAAGACCTTAAAGTATGAAACTATTACAGGAAAACA 1556
                         i ?    i  v vv     v  v   v   i     v   v i       
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_55144949_5   1557 TAAGGAAATATCTCTAGGATATTGGTCTGGACAAAGATTTATTGAGCAAT 1606
                           i ?iv v    iiiv  iv    vi i i   v i   v  iiii vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_55144949_5   1607 ATCCCACAAGCACA-GTAACCAAAGCAAACATGGACAAATGGGATCCCAT 1655
                          iv   v       - i   v    v   v  i  i    v   iii   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_55144949_5   1656 CAA-GTTAAAAAAATTTCTGCACAGTAAAGGATACAATCAATAAAGTGAG 1704
                            -i       --i  i  ii vvi      i  v     v       i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_55144949_5   1705 AAGACAACCCACAGAATGGGAGAAAACTAAATATTAGCAAACAACCCATC 1754
                                                   -----    v     iv ivi   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAA-----TATTTGCAAATCATATATC 740

  chrX_55144949_5   1755 TGACAAGGGATTAATAACCATAATATACGAGGAACTCAAACAACTTTATG 1804
                            i      i vi  v   v      ii i      vv      iv  i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_55144949_5   1805 GGAAAACATCTAATAATCCAACC-AAAAATG--------ATTTGACTAGA 1845
                         iv    viv v     i    ii-       --------      v    
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_55144949_5   1846 TATTTTTTAAAAGAAGACATACAAATGGCAAATAGGCACATGAAAAGGTG 1895
                         i    i iv        i           v    i            i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_55144949_5   1896 CTCGACATCATTGATCAT 1913
                            i      ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (136 / 83)
Gap_init rate = 0.01 (10 / 905), avg. gap size = 2.50 (25 / 10)  


2584 25.40 3.90 0.94  chrX_55161256_55164896      468  1211 (2430)    L1M4_orf2#LINE/L1       96   861 (47)  

  chrX_55161256_5    468 CAAGATTTCAGCTG----------AGAAATC--CA--CTGATAGCC---- 499
                            i  ii      ----------      i--  --     --  ----
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT--CCTAAA 143

  chrX_55161256_5    500 ATTTATGTGAAACCACAAAAGACCCCAAATAACCAAAGCACTCTTGAGAA 549
                            i  i  i  vii   ii     vi    i     i  v      i  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_55161256_5    550 AAAAGAACAAAGCTCAAGGCATTATACTTCCCAATTTCAAACTGCAGTAC 599
                          i          i vi   vv i i                vivi v   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_55161256_5    600 AATGCTATGTTAGTAAAGACAGTATGGTACTTGCATAAAAACA--CACGT 647
                           v    iiv  i v        i       v      ii i --  ii 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_55161256_5    648 AGGACAATAAAACAGAATAGAGAGCCCAGAAATAAATTTAGGCATATATG 697
                           iv    ii  i     v     i           iii vi   v    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_55161256_5    698 TTAAACTAATTTTTGATATGGAAACCAAGAATACATGATAAGGAAAGGAT 747
                         v v  i i     i  i v  ivi      vi ivii  ii      i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_55161256_5    748 ATTCTCTTTAATAAGTGGGGTTGAGAAAACTGGATATCCAAATTCCAAAG 797
                          v   i  i  i  i   v i  i  v         ?   v  v v    
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_55161256_5    798 AATAATATTGGGTCCTTACCTTATACCATACATAAAAATCAAATGAAAAT 847
                            i vi    ii  i     i i      i i      i  v v     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_55161256_5    848 GGATTAAAGACTTAATCAT-TAAGACTTAA---TACAACAC-CTT-GAAG 891
                             i ?    i   --  -     vi   ---  i  v  -   -    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAA--ATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_55161256_5    892 AAAACAAAGAGAATAAA-CTCCTTGACACTGGCCTTTTCAGTAATTT-TT 939
                               v  - ?i    -  i v    vi   vi vvv  i ii   -  
  L1M4_orf2#LINE/    542 AAAACATAG-GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_55161256_5    940 GTATGTGCTACCAAAAACATAGGCAACAAAAGAAAAAAAATTTAAATGGG 989
                         iv  i  vi       i  i i                v vv     v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_55161256_5    990 ACCACACCAAACTAAAAAGCTTCTGTACAGTAATGGAAACAATCAACAAA 1039
                           iv  i    v v    i   i   i vvi  v   v  v     v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_55161256_5   1040 GTGAAAAGGCAGCCTACAGAATGGGATAAAATACT-GTAAACCATATGTC 1088
                                 i  i  i           v      i - i   i     i  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_55161256_5   1089 TGATAAGAAGTTAATATTCAAAATATACAAGGAAATTACGCTACTCAATA 1138
                                iiii vi   i  i      i  i   v ivii v        
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_55161256_5   1139 GCAAGAAAACAAGTAACCCTGTTTTAAAAAATGGGCAATGGACCTGAATA 1188
                         ii  i  i    i      vi  ?--            v   ii      
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATA 838

  chrX_55161256_5   1189 GACATTTTCCCAAAGAAGACATA 1211
                                ii          i   
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATA 861

Transitions / transversions = 1.94 (122 / 63)
Gap_init rate = 0.02 (16 / 766), avg. gap size = 2.25 (36 / 16)  

 941 21.79 9.40 0.00  chrX_55161256_55164896     2065  2298 (1343)    L1M4_orf2#LINE/L1      152   407 (501)  

  chrX_55161256_5   2065 GGAAAAACAATAGAACAAGAATAACCAAAATGATTCTGAA------GAAT 2108
                              vi   vi  v v      i      ii  ii    ------   i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_55161256_5   2109 AATGTTGAAGAACTCACGCTACCTAATTTAAAGACGTAGTGTAAAACTAC 2158
                           v    i  i      i  v  i     v  i  v  v ii   i    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_55161256_5   2159 AGTAATCAAAATAGTGTGGTATTGGT-TAAAAAAA------------AAT 2195
                                  i i         i   i-   ii v ------------   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_55161256_5   2196 GGACCAGAAT--AGAGTCCAGAAATAGACTCATGCATATATGATCAACTG 2243
                            vi     --              i  i   i   v    i    i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_55161256_5   2244 ACTTTCAACAAAGGTGCAAAAACAATTCAATGGAGAGAGAG-AATCTTTT 2292
                          i    i    i     v  i  v         i  i   i- i      
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_55161256_5   2293 TAACAA 2298
                         i     
  L1M4_orf2#LINE/    402 CAACAA 407

Transitions / transversions = 2.64 (37 / 14)
Gap_init rate = 0.02 (5 / 256), avg. gap size = 4.40 (22 / 5)  

1141 22.63 5.35 7.41  chrX_55161256_55164896     2663  3148 (493)    L1M4_orf2#LINE/L1      433   908 (0)  

  chrX_55161256_5   2663 ACAAGCAAACAAACAAAA-------CCAACCTTATTCCACATGCAATAGT 2705
                            v     vi  ii  i-------  v    i iv   i  i   v i 
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_55161256_5   2706 TAACCTAGTGTGTGTCATAGAGTTAAATATAACACCTAAAACTGGAAAAC 2755
                             ii ivi  vi   ?   vi     i   v v        iv     
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_55161256_5   2756 TTCTAGGAAAAAAAAAAATATCAGAAGATATTTTTGGCCTTCTGTGAAGC 2805
                          ii   ---  i    v   vv? v i  v  iv  i    vv  v i  
  L1M4_orf2#LINE/    533 TCTTAG---AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_55161256_5   2806 AAAGATTTCTTGGAT-------TAAAAA---AATCCATTAAAGAAAAACT 2845
                           v i      i   -------i    i---  v v iv         v 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_55161256_5   2846 AGGTACTTTGTACTTCA---AAACTAAAAACATCTTCTGCTCTTCAAAAT 2892
                           i  vv   v      ---   i       ---  i  iv       iv
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAAC---TTTTGTGCTTCAAAGG 676

  chrX_55161256_5   2893 ACATGGTTAGGAGAAAGAAAGACAAGGTACATATCAGGAGAAGATGTTTG 2942
                            ivi i ------      ------------ ---  i    i-----
  L1M4_orf2#LINE/    677 ACACTATCA------AGAAAG------------T---GAAAAGAC----- 700

  chrX_55161256_5   2943 CAAAACATCACATATGGGGAGAAAATATTTGCAAAACACATCTCTTATAA 2992
                         ---   -i    v vv                   v  i  v   v    
  L1M4_orf2#LINE/    701 ---AAC-CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_55161256_5   2993 AGTACTCATTTCCAGAATATAAAAAGTACCCTCAAATCTCAATAA-GAAA 3041
                         i v   ii v           v    v  i  i v v        -i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_55161256_5   3042 TGA-AAATAACTCAATTAAAAAATTGGCTGAAGATTTGAACAGACAC--C 3088
                         v  -       i     ?      v   vi i        i     i-- 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_55161256_5   3089 ACAAAAGAAGACATG--GATGGCTAATAGGCACATAAAAAGATGCTCAGC 3136
                         v v        i  i--i     i    i      i            i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_55161256_5   3137 ATCATAAATTAT 3148
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (59 / 48)
Gap_init rate = 0.03 (15 / 476), avg. gap size = 4.13 (62 / 15)  


3037 26.39 1.55 0.89  chrX_55203293_55213744.rev     4993  5894 (4558)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55203293_5   4993 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATGAATATCATGAAAAT 5042
                              ii i  i     i        v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55203293_5   5043 GGCTGTACTGCCCAAGGTAATTTATCGATTCAATGCCATCCCCATCAAGC 5092
                            vi    v     iv i  i  iv       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55203293_5   5093 TACCAGTGACTTTCTTCACAGAA-TTGAAGAAAATTA--CCTCAAA---G 5136
                          v    ivi i  i  ii     -    v--  ii i--   v   ---i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chrX_55203293_5   5137 TATGGAACCAAAAAAGAGCCCGCATTGCCAATTCAATCCTAAGCCAAAAG 5186
                                viiv  ii  v  v v  v     vv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_55203293_5   5187 AACAAAGATGGAGGCATCATGCTACCTGACTT-GAAACTATACTACAAGG 5235
                                v      vv   ii  v  ii i  -i     -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_55203293_5   5236 CTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGAT 5285
                                  i   i    iii        i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_55203293_5   5286 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5333
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_55203293_5   5334 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5383
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_55203293_5   5384 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5433
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_55203293_5   5434 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGCTGG 5483
                             ii    i    v   i     v              i    iv   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_55203293_5   5484 ATTAAACACTTAAATTGTA-GACCTAAAACCATAAAAACCCTAGAAACAA 5532
                           i ? v  i     -   -  v       i      vi i     iv  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_55203293_5   5533 ACCTAGGCA-ATACCATTCA-GGCCATAGGCATAGGCAAGGACTTCATGA 5580
                           v    ?i- v i -   i- i  v i  i-       v ii   v ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAG 592

  chrX_55203293_5   5581 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5630
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_55203293_5   5631 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5680
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_55203293_5   5681 GAACAAGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTTATCTG 5730
                            v ii     i                 v       vii iv      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_55203293_5   5731 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTGAAACAAATTTACAAG 5780
                          i  i  i  vi          v  i        vvv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_55203293_5   5781 AAACAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATTAACAGACA 5830
                            v i     i     v  i? v  i     i      v v  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_55203293_5   5831 CCTCTCAAAAGAAGACATTTATGCAGCCAACAG--ACATGAAAAAATGCT 5878
                         ii    v        i  vi viii     i i--         i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_55203293_5   5879 CATCATCACTGGCCAT 5894
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.47 (22 / 15)  

2727 28.00 1.67 0.78  chrX_55203293_55213744.rev     9062  9961 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55203293_5   9062 TGGAAAAACACTCAATGCTAATGGATAGAAAGAATTAATAT-G--AAAAT 9108
                               i i ii v   i v      v i    v       - --  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55203293_5   9109 GGCCACACTGCCCAACGTAATTTATAGATTCAGTGCTGTTCCCATCAAGC 9158
                            v i   v     vv i  i  i       ii  vi i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55203293_5   9159 TACCATTGGCTTTCCTCACAGAACCAGAATAAAAAACT-ATTTTAAATTT 9207
                          v   viv  i  ii ii     ---- v i v  i  -  ii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA----ATTGACAAGCTGATCCTAAAATT 146

  chrX_55203293_5   9208 CATATAGAACCAAAAAAGAGCTCGTAGAGCCAAGACAATCCAAGGCAAAA 9257
                              i   viiv  ii  v iv v v      i      iviiiv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_55203293_5   9258 AGAACAAAGCTGGAGGCATCACACTACCTGACTT-GAAACTATACTACAA 9306
                                  i      vv       v  ii i  -i     -        
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chrX_55203293_5   9307 AGCTGCAGAAACGAAAACAGCATGGCCCTAGCACCAAAACAGATATATAG 9356
                             i   v  iv  i    ii   iv  i   iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_55203293_5   9357 ACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAT 9406
                          i        i    iv   ivii         vv   i    i  iii 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_55203293_5   9407 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGATTC 9456
                           vi    i  i     ivv  v   i v  vv     i      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_55203293_5   9457 CCTATTTAATAAATGGTGTTGAGAAAACTGTCTAGCCATATGCAGAAAAC 9506
                         i  v  i  i        i  i  v     vv  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_55203293_5   9507 --AAACTGGACCCCTCCCTTACACCTTATTCAAAAATTAACTCAAGATGG 9554
                         --  ii         v   i     v   v               i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_55203293_5   9555 ATTAAAGACTTAGACGTAAAACCAAAAATCATAAAAACCCTAGAAGAAAA 9604
                           i ?    i  i i    i v v    ii      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_55203293_5   9605 CCTAAGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACT 9653
                          v  i ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_55203293_5   9654 AAAATAACAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 9703
                          vi i v        vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_55203293_5   9704 ------AACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 9747
                         ------  i    i -   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_55203293_5   9748 AACACACAAATTACAGAATGGGAGAAAATTTTTGCAATGTATCCATCTAA 9797
                           v v    vii                 v       vvi  vi    i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_55203293_5   9798 CAAAGGTCTAATATTCAGAATCTAAAACGAACATAAACAAATTTACAAGA 9847
                         i  i  v  vi   i      v  v  v    vivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_55203293_5   9848 AAAA-ACAAACAACCCCAGCAAAAAGTGGGTGAAGGATATGAACACACAC 9896
                             -     i     v vi?    i    ii      v    i v   i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_55203293_5   9897 TTCTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTC 9946
                              v        i  vi vi       i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_55203293_5   9947 ATCATCACTGGTCAT 9961
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (143 / 105)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


3116 26.79 0.55 0.44  chrX_55223577_55226760.rev     1787  2693 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55223577_5   1787 TGAAAACACATCCCATGATCATAGATGGGTAGAATCAATATTGTGAAAAT 1836
                           i   v i        v    i   v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55223577_5   1837 GACAATACTGCCAAAA-CGATCTACAAATTGAATGCAATTCCCATCAAAA 1885
                          i       v  v   -i        i   v  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55223577_5   1886 TACCATCATCATTTTTCCCAGAACTAGAAAAAACAATTCTAACATTCATA 1935
                          v   v vv v     iv     v v  v  ivii  i    v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_55223577_5   1936 CAAAACCAAAAAAGAGCTCACATAGCCAAAGCAAGACTAAGCAGAAAGAA 1985
                         iii  viiv  ii  v iviv         i   vvi i iv ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_55223577_5   1986 TAAATCTAGAAGCAACACATTACCCGACTTCAAACTATACCATAAGGTCA 2035
                         i   vi i  i vvv    i v   i i      viv   i i  i ii 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_55223577_5   2036 CAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACACAGACCAA 2085
                             v i   i    ii         i    ii    i  i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_55223577_5   2086 TGGAACAGAATTGAGAACCCAGAAATAAAGCCAAATACTTACAGCCAACT 2135
                              i          ii           v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_55223577_5   2136 GATCTTTAGCAAAGCAAACAAGAACACAAAGTGGGGAAAGGACACCCACT 2185
                            i  iii   i vviv     v  ivv i         i i vi vi 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_55223577_5   2186 TCAACAAATGGTGCTGGGATAATTGGCAAGTCACATGTAGAAGAATAAAA 2235
                                            i  i   vv ?i      i i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_55223577_5   2236 CTGGATCCTCATCTCTCACCTTATACAAAAATTGATTCAAGATGAATCAA 2285
                         i    i  ii i   v    v            i i    i   i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_55223577_5   2286 AGACTTAAACCTAAAACCTGAAACCATAATAATTCT-AGTAGATAACATC 2334
                             i    iv   i v  i    i    -  i   -  v   v     v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACATA 549

  chrX_55223577_5   2335 AGAA-AAATCCTTCTAGGCATTTGGCTTAGGCAAAGACTTCGTGACCAAG 2383
                         i ?i-     -   vv i -i    v        v ii   v iivi v 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_55223577_5   2384 AACCCAAAAGTAAATGCAACAAAAACAAAGATAAATAGATGGGACTTAAT 2433
                          vv       i v v         iv   i   i   i  v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_55223577_5   2434 TAAACTAAAAACCTTCCGCACAGCAAAAGA-ACTAGTCAGTAGAGTAAAC 2482
                         i   v v    v   ii ii vv    i  -    -   iv i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAAA 696

  chrX_55223577_5   2483 AGGCAACCCACGGAGTGGAAGAAAATCTTTGCAATCTATACCTCTGACAA 2532
                           i        i  i   i       v       vii   iv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_55223577_5   2533 AGGACTAACATCTAGAATCTATAAGGAACTCAAACAAATCAGCAAGAAAA 2582
                         i     vii   i     v     i      vv    v   ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_55223577_5   2583 AAA-AAACAATCCCATCAAAAATTGGGCTAAGGACATGAATAGACAATTC 2631
                          i -   i  i  v  i?    v     v     iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_55223577_5   2632 TCAAATGAAGATACACAAATGGCCAACAAATATATGAAAAAATGCTCAAC 2681
                           v  v       i            i  ii i       i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_55223577_5   2682 ATCACTAATTAT 2693
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (147 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.00 (9 / 9)  


 644 27.31 1.32 3.08  chrX_55227539_55232074.rev       85   311 (4225)    L1M4_orf2#LINE/L1        1   223 (685)  

  chrX_55227539_5     85 TGGAGAGGCATACCATGTCCATGGATTGGAAATCTTAACATAGTGAAGAT 134
                             i  ii  v      i            iv     i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55227539_5    135 GTCAAT-TATCCTAAATATAAAC-ACAGTTTTAATGCAATGCCTGTCAAA 182
                          v    -ivi  i    - i v -    v  i  i     v   i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_55227539_5    183 TTATCAACAAGATTTTTTTCAGATATAGATAAGATTATTCTAAATTATAT 232
                         v vi  i vivv      v    v  v  i   v v  i     v vi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_55227539_5    233 ATGAGAAAGCAAAAGATCTAAAATAGGTTAAACAGTTTTGAAAAAAAGAG 282
                            ii  v    ii  i i i     viv     i i        i ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA--- 196

  chrX_55227539_5    283 GAGGATGCAGTGAGCCAAGA-TCACACCTC 311
                         -  i iiv   vi -- i  -      i  
  L1M4_orf2#LINE/    197 -AGAACAAAGTTGG--AGGACTCACACTTC 223

Transitions / transversions = 1.38 (36 / 26)
Gap_init rate = 0.03 (6 / 223), avg. gap size = 1.67 (10 / 6)  

3195 25.97 1.10 0.77  chrX_55227539_55232074.rev     3141  4045 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55227539_5   3141 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 3190
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55227539_5   3191 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3240
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55227539_5   3241 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3288
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_55227539_5   3289 TATGGAAACAAAAAAGAGCCCGCATTGCCAATTCAATCCTAAGCCAAAAG 3338
                                 iiv  ii  v  v v  v     vv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_55227539_5   3339 AACAAAGATGGAGGCATCACACTACCTGACTTCAAACTATACTACAG-GC 3387
                                v      vv       v  ii i      viv       i-  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_55227539_5   3388 TACAGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGAGATATAGATC 3437
                                 i   i    ii     v   i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_55227539_5   3438 AATGGAACAGAAC--AGAGTCCTCAGAAATAATACCACACATCTACAACC 3485
                                i    i--       --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_55227539_5   3486 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 3535
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_55227539_5   3536 CTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3585
                           v  i  i   i          v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_55227539_5   3586 GAAACTGGAACCCTTCCTTATACCTTATACAAAAACTAATTCAAGCTGGA 3635
                            ii    v    v   i i   v          i   i    iv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_55227539_5   3636 TTAAACACTTAAATTGTA-GACCTAAAACCATAAAAACCCTAGAAGAAAA 3684
                          i ? v  i     -   -  v       i      vi i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_55227539_5   3685 CCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 3733
                          v    ?i- v   -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_55227539_5   3734 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3783
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_55227539_5   3784 AACTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3833
                         v ii   v i  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_55227539_5   3834 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACTATCTATCCATCTGAC 3883
                          v  i     i                 v   i v vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_55227539_5   3884 AAAGGGCTAGTATCCAGAATCTACAAAGAACTCAAACAAATTGACAAGAA 3933
                           i  i  v           v  i         vv    v ii i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_55227539_5   3934 AAAAATCAAACAACCGCATCAAAAAGTGGGCAAACGATATGAACAGACAC 3983
                            i -    i    vv  i?    i        v   v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_55227539_5   3984 TTCTC---AGAAGACATTTATGCAGCCAACAGACGCATGAGAAAATACTC 4030
                              ---      i  vi viii     i ii i     i  i  i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_55227539_5   4031 ATCATCACTGGCCAT 4045
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (137 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


2862 25.33 3.50 1.21  chrX_55257878_55261156.rev     1581  2409 (870)    L1M4_orf2#LINE/L1        1   848 (60)  

  chrX_55257878_5   1581 TGGAAAGATATCCCATATTTCATGGATTACAAGAATTAATATTGTTAAAA 1630
                                         i  -        iv    v             i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTT-CATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_55257878_5   1631 TATGTATACTACCCAAGGTGACCCACAGAGTCAATGCAGTCCCTACCAAA 1680
                          ivvv     v     iv   i i     v    i   i      i    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_55257878_5   1681 ATTTCAA-TGTTTTTATT-CAGGGAAATAGAAAAAA-AATCCTAAAATTC 1727
                           ii  i-  ii   v  -   --    v  v  iv-i            
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAG--AAATTGACAAGCTGATCCTAAAATTC 147

  chrX_55257878_5   1728 ACAGGAAACCACTAAAAATACTAAATGGCCAAGGCAATCATGAGCAAAAA 1777
                          i v i  vii v iii iv vi   i     ii     v   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_55257878_5   1778 GAACAAAGCTGGAGGCATCATTGTACCTGATTTCAAACTATATTACAAAG 1827
                                 i      vv   ivv v  ii        viv  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_55257878_5   1828 CTATAATAAATAAAATAGTATTGCACTGGCA-AAAAACAGACACATTGAC 1876
                            i i   vi  i i   i v i       -  ii i     i  v  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_55257878_5   1877 CAGCAGAGCAGAATAGAGAGCCCAGAACTGAACTCACACATGTACAGTCA 1926
                           iii  ii     v     i      v i   i  i    v  ii    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_55257878_5   1927 ATTGATTTTTTTTAACAAAGTTGCCAAAAATACACAATAAGGAAAGGATA 1976
                                  i---i    i v      i vi iv    ii      i   
  L1M4_orf2#LINE/    348 ATTGATTTTC---GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_55257878_5   1977 GTTTCTTCAATAAATGGTGT---GAAAACTGGATATCCACGTG-AAGATA 2022
                           i i     i        i---  v         ?    i  -  i v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_55257878_5   2023 ATTGTGAAACTGGACCCTTATTTCACACTAGATACAAAAGTCAACTCAGA 2072
                           ---   ii       i  ii      i v        i i      i 
  L1M4_orf2#LINE/    445 AT---GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_55257878_5   2073 GTGGATTAAAAAC------ATAAGACCTGAAACTGCAAAATTACTAGAAG 2116
                         i     i ? i  ------i     v  i     ii    i vi      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_55257878_5   2117 AAAACATAGTGGAAAAACTACAAAACAT-GGTCTAGGCAATGATTTTTTG 2165
                                  v? v   v  v ivi  v -  vi         i   i  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_55257878_5   2166 CATTTGACTGCAAAAGCATAGGCAACAAAAGTAAAAAGAGATAAATGAGA 2215
                         v  v    vv        i i          v     v        vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_55257878_5   2216 TTACAT-AAAATTAAAAAGCTTCTGCACAGCAAAGGAAAC----AAGAGT 2260
                         i v   -           -   i  ii vv       v  ----    iv
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_55257878_5   2261 ATAAAGAAACAACCTAATGATTAAGAGAAAATATTTGGAAACCATACATA 2310
                         i i  i i      i vv  v ii             v   i    i  v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_55257878_5   2311 CAATAAGGGGTTAATATCCAAAATATATCAGTAATTCCAACAATTCAACA 2360
                         ii       ii vi      i       v iv  i  iv    i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_55257878_5   2361 TCAAGAAAA-----AATCTAA----AAAATGGACAAGAAACTTGAATAGA 2401
                         vi  i  i -----  i i  ----       i   iii i         
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_55257878_5   2402 CATTTTTC 2409
                              i  
  L1M4_orf2#LINE/    841 CATTTCTC 848

Transitions / transversions = 2.00 (138 / 69)
Gap_init rate = 0.02 (17 / 848), avg. gap size = 2.29 (39 / 17)  

 319 21.05 0.00 1.32  chrX_55257878_55261156.rev     2713  2788 (491)    L1M4_orf2#LINE/L1      834   908 (0)  

  chrX_55257878_5   2713 GAATAGACATTTTTCAAAAGAAGACATACAAATGATCAACAGATATATAT 2762
                                     i  v        i         ii   i iii i  iv
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_55257878_5   2763 TAAAAATGCTTGATATCACTCATCGT 2788
                         -   i     ii i    ????????
  L1M4_orf2#LINE/    884 -AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 7.00 (14 / 2)
Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1)  


2743 28.00 2.46 0.78  chrX_55266086_55271922     4452  5344 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55266086_5   4452 TGGAAAAATATTCCATGCTCATGGATAGGA-GAATCAATATTGTGAAAAT 4500
                               i    i     i        v   -  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55266086_5   4501 GACCACGTTGCCCAAAGTAATTTACAGATTTAATGCTATTCCCATTAAAC 4550
                          i v iii v      v i  i        i  i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55266086_5   4551 TACCATTGACAATCTTCACAGAATCAGAAAAAACT-ATTTTAAAATTCAT 4599
                          v   vivi vv i  ii     viv  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_55266086_5   4600 ATGGAACCAAAAAAGGGCTTGTATAGCTAAGACAATCCTAAGTGAAAA-A 4648
                               viiv  ii iv iv v     i  i      i i ivi i  - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_55266086_5   4649 ACAAAGCTGGAGACATCACACTGCCAGGCTTCAAGCTATACTGTAAGGCT 4698
                               i     ivv       v  viii     iviv    ii  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_55266086_5   4699 ACAATCACCAAAACAGCATGGTACTGATACAAAAACAGACACATAGACCA 4748
                            i v i   i    ii        ii i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_55266086_5   4749 ATGAAACAGAGTGGAGAACTCAGAAATAAGACTGCACTTCTACAACCATC 4798
                            i  i   i v    iii         iv iii  v i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_55266086_5   4799 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGGAGAGGATTCCCT 4848
                             i  i     ivv  v   i v  vv        i -  i  vvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAATAGTCT 398

  chrX_55266086_5   4849 GGTTAATAAGTGGTCCTGAAAGAACAGGCTATCCATATGCAGAAAATGGA 4898
                         vv i  i  i    v   ii v   v  v  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_55266086_5   4899 ACCTGGACCGCTTCCTCGCACCTTATGCAAAAATTAACTCAAGATGGATT 4948
                          vi      v  v    i    v   i               i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_55266086_5   4949 AAAGACTTAAATGTAAAATTAAAAACTGTAAAAACCCTAGAAGAAAATCT 4998
                          ?    i         i viv      i     vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_55266086_5   4999 CGGCAATACAAT--TCAGGACATAGGCATGGGCAAATATTTCAT-GATAA 5045
                         v  ?i-  -   --  iv   v v  vv i     vvi    v -    v
  L1M4_orf2#LINE/    549 AGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_55266086_5   5046 AATCTCCAAAAGCAATTGCAACAAAAGCAAAAATTTTCAAGTGGGACCTA 5095
                         i - v         vvv          v      vvvi  i v    i v
  L1M4_orf2#LINE/    597 GA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_55266086_5   5096 ATTAAACTAAAGAGCTTCTGTGCAGCAAAAGAAACTATCATCAGAGCAAA 5145
                           i   v v  i i   i     vv    i  v       vv i  ii  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_55266086_5   5146 CAGGCAACCTACAGAGTGTGAGAAAACTTTTGCAA--TATATCCATCTGA 5193
                         v  i     i     i  v       iv       --i    --      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chrX_55266086_5   5194 CAAAGGTCTAATATCCAGAATCTACAAGGAAC------AAATTTACAAGA 5237
                         i  i  v  vi          v  i  i    ------  v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_55266086_5   5238 AAAAAA-----AAC---ATTAAAAAGTGGGCAAAGGACATGAACAGACAC 5279
                             i -----   ---   ?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_55266086_5   5280 TTTTCAAAAGAAGACATTCATGTAGCCAACAGAAATATGGAAAAAAGCTC 5329
                           i  v        i  v  vi i     i iiv i   i   i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_55266086_5   5330 AACATCACTGATCAT 5344
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.93 (29 / 15)  


3143 27.77 0.44 0.11  chrX_55305469_55311886     5022  5925 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_55305469_5   5022 GGAAGAACTTTCGATGCTCATGGATAGGAAGAATCAATATCGTGAAAATG 5071
                             ii iv i v   i        v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_55305469_5   5072 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 5121
                           v     v     iv i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_55305469_5   5122 ACCAAGGACTTTCTTCACAGAATTGGAAATAACT-ACTTTAAAGTTCATA 5170
                         v   ivvi i  i  ii     v v  v - i  - iii    i      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATA 150

  chrX_55305469_5   5171 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAAT--TAAGTCAAAAGAA 5218
                              viiv  ii  v  v v  v     iv    -- i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_55305469_5   5219 CAAAGATGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCCA 5268
                              v      vv       v  ii i      viv        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_55305469_5   5269 CAGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5318
                               i   i v  ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_55305469_5   5319 TGGAACAGAACAGAGCCTTCAGAAATAATACCACACATCTACAACCATCT 5368
                              i    iv   vv i         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_55305469_5   5369 GATCTTTGACAAACTTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 5418
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_55305469_5   5419 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5468
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_55305469_5   5469 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 5518
                         i    i    v   i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_55305469_5   5519 AGACTTAAATGTTAGACCCAAGACCATAAAAACCCTAGAAGAAAACCTAG 5568
                             i       v   v i  i  i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_55305469_5   5569 GCA-ATACCATTGAGGACATAGGCATGGGAAGGACTTCATGTCTAAAACA 5617
                          ?i- v i v i v iv v i  ivv  v  v ii   v ivv  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_55305469_5   5618 CCAAAAGCAATGGCAACAAAAGCCAAGACTGACTAATTGGATCTAATTAA 5667
                                  vvi          vv  i iv  iv       ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_55305469_5   5668 ACTCAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGTGAACAGGC 5717
                          v i  i i   i  ii vv       v    i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_55305469_5   5718 AACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAAAAAGGT 5767
                             i                 v       vii ivi      v  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_55305469_5   5768 CTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAAGC 5817
                           vi          v  i         vv    v iv i  v     ii 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_55305469_5   5818 AAACAACCTCATCAAAAAGTGGGCAAAGTATATGAACAGACACCTCTCAA 5867
                            i    iv  i?    i         v  v    i     ii    v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_55305469_5   5868 TAGAAGACATTTGTGCAGACAACAGACACATGAAAAAATGCTCATCATCA 5917
                         v      i  viiviii v   i ii          i       v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_55305469_5   5918 CTGGCCAT 5925
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.31 (140 / 107)
Gap_init rate = 0.00 (4 / 907), avg. gap size = 1.25 (5 / 4)  


3187 26.66 1.11 0.66  chrX_55335471_55341883     5017  5920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55335471_5   5017 TGGAAGAACATTCCATTTTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5066
                              ii i  i    v       i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55335471_5   5067 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCTTCCCCATCAAGC 5116
                            v     v     iv i  i  i        i  vv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55335471_5   5117 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5164
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_55335471_5   5165 TATGGAACCAAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAA 5214
                                viiv  ii-  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_55335471_5   5215 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5264
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_55335471_5   5265 CTACAGTAACTAAAACAGCATGGTACTAGTACCAAAACAGAGATATAGAT 5314
                                  ii  i    ii       i i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_55335471_5   5315 CAATGGAACAGAAC--AGAGCCCTCAGAATTATGTCGCATA--TCTACAA 5360
                                 i    i--    i  --    v  vii -    -- i  iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACC-CATACATTTATGG 344

  chrX_55335471_5   5361 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5410
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_55335471_5   5411 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5460
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_55335471_5   5461 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5510
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_55335471_5   5511 GATGAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5560
                            v ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_55335471_5   5561 ACCTAGGCATTACCATTCAGGACATAGGCATGTGCAAGGACTTCATGTCT 5610
                           v    ?i v viv   iv   v v  vv iv    v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_55335471_5   5611 AAAACACCATAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5660
                          vi      v  i  vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_55335471_5   5661 AATTAAATTCAAGAGCTTCTGCACAGCAAAAGAAACTACCAACGGAGTGA 5710
                         v  i   v i  i i   i  ii vv    i  v    i   vii     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_55335471_5   5711 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5760
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_55335471_5   5761 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5810
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_55335471_5   5811 AAA---AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5857
                            ---   i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_55335471_5   5858 TCTCAAAAGAAGACATTTATGCAGCCAA-AAACACATGAAAAAATGTTCA 5906
                             v        i  vi viii     -  i          i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_55335471_5   5907 TCATCACTGGCCAT 5920
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3348 26.29 0.34 0.57  chrX_55345262_55349517     2885  3755 (501)    L1M4_orf2#LINE/L1        1   869 (39)  

  chrX_55345262_5   2885 TGAAAACATATTCCATGATCATGGATTAGAAGAATCAATATTACTAAAAT 2934
                           i   v    i     v         i     v i      ii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55345262_5   2935 GTCCATACTACCCAAAGCAATCTACAGATTCAATGTAACCCCTATCATAA 2984
                          v v     v      vii              i i  i        v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55345262_5   2985 TACCAATGACGTTCTTCACGGAAATAGAAAAAAAATTCCTAAAATGTATA 3034
                          v   iivi v  i  ii i     v  v  ivviv         vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_55345262_5   3035 TGGAACCATAAAAAATCCAGCATAGCCAATGCCATCCTGAGCAAAATTAA 3084
                              viii  iii i    v        vi v   i   iv  i vv  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_55345262_5   3085 CAAAACTGCAGGAGTCACATTACCTGACTTCAAATTACACTACAGAGTGA 3134
                             ii  v    v     i v  ii i      vivi      i  iv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_55345262_5   3135 TAGTAACCAAAACAGCATGGTACTGGTATTTAAACAGACACATAGACCAA 3184
                         i     i   i    ii         i  vvii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_55345262_5   3185 TGGAATAAAACAGAGAGCTCAGAAATACATCCATACATCTACAGGGAACT 3234
                                i  iv     ii        v i        i  ii vv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_55345262_5   3235 CATTTTTGACAAAGATGCCTAGAACCTACACTGGAGGAAGTACAGTCTTT 3284
                         v     i     i i    v   v v v  v   i i   v i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_55345262_5   3285 TTAATGAATGGTGTTGGGAGAACTAGATATGCATATACAGAAGAATGAAA 3334
                          i  ii       i     v    i    ?v  i  i  i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_55345262_5   3335 CTAGACTCCTATCTCTCACCATATACAGAAATCAAATCAAAATGGATTAA 3384
                         i i   i    i   v           i    i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_55345262_5   3385 AGACTTAAATCTAAGACCTCAAAGTATATAACTACTAATAGGGAATATTG 3434
                             i     v     v  v   v    v    vi  iv  ii  i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_55345262_5   3435 GGGAAACTCTCCAGGACATTGGTCTGGGCAAGTAATAATTCCTGAGTAAT 3484
                          ? v  v   i iv   v    vi i     ---- ii  i  v  vv  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAA----TGGTTTCTTAGATAT 596

  chrX_55345262_5   3485 AAC-TCACAAGTGCAGGCAACCAAAGCAAAAATGGACAAATACAATCACA 3533
                         i  -i  v   ii  i     v    v      i  i    vvi iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_55345262_5   3534 TCTAG-TTAAACAGTTTCTGCACAGCAAAGGATACAATCAACAAAGTGAA 3582
                           v i-     - ii  i  ii vv       i  v     v        
  L1M4_orf2#LINE/    647 TCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_55345262_5   3583 GAGACAGCCCACAGAATGGGAGAAAATATTTACAAACTGTCCACCTGAAA 3632
                         i     i                        i    iii vi i    v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_55345262_5   3633 AAGGATTAGTAAGCAGAATATCTAAGAAGTTCAAACAACTCAATAG-AAA 3681
                          i   i v   vv        v   ii ii  vv           i-   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_55345262_5   3682 AAGTCTAATAATCTGATTTAAAAATGGACAAAAAATCTGAATAGACATTT 3731
                            v v     i ii   ?        i    ii  i             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_55345262_5   3732 CTCAACAGAAGACATGCAAATGGC 3755
                            v v      i  i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGC 869

Transitions / transversions = 1.62 (139 / 86)
Gap_init rate = 0.01 (5 / 869), avg. gap size = 1.60 (8 / 5)  


3127 27.25 1.45 0.44  chrX_55352198_55358618     5030  5928 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55352198_5   5030 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5079
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55352198_5   5080 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5129
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55352198_5   5130 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5177
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_55352198_5   5178 TATGGAACCAAAAAAGACCCCACATTGCCAAGACAATCCTAAGCAAAAAG 5227
                                viiv  ii     viv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_55352198_5   5228 AACAAAGCTGGAGGCATCATGCTACCTGACTTTA-----TAGTACAAGGC 5272
                                i      vv   ii  v  ii i  i -----  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_55352198_5   5273 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGTCC 5322
                                 i   i    ii         i iv ii i   v   i  vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_55352198_5   5323 AGTGGAACAGAAC--AGAGCCCTCAGAAATAATACCACAAATCTACAACC 5370
                          i     i    i--    i  --        vv   i v  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_55352198_5   5371 ATCTGATCTTTGACAAACCTGACAAAAACAAGTAATGGGGAAAGCATTCC 5420
                          vi    i  i     ivv  v   i v  vvi           v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_55352198_5   5421 CTATTTAATATATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5470
                           v  i  i v            v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_55352198_5   5471 GAAACTGGATCCCTTCATTACACCTTATACAAAAATTAATTCAAGATGGG 5520
                            ii    i    v v i     v              i    i    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_55352198_5   5521 TGAAAGACTTAAATGTTAGACCTGAAACCATAAAAATCCTAGAAGAAAAC 5570
                          v ?    i       v   v  i    i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_55352198_5   5571 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5620
                         v    ?i v viv   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_55352198_5   5621 AACATCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAAT-GGATCTAA 5669
                         i   i        vvi          vv        i    -   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_55352198_5   5670 TTAAACTAAAGATCTTATGCACAGCAAAACAAACTACCATCAGAGTGAAC 5719
                          i   v v  i v   v  ii vv    iv v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_55352198_5   5720 AGGCAACCTACAGAATGGGAGAAAATTTTTACTATCTACCCATCTGACAA 5769
                           i     i                 v   i v vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_55352198_5   5770 AGGGCTAATATCAAGAATCTACAAAGAACTTAAACAAATTTTCAACAAAA 5819
                         i  i  vi    v     v  i        ivv    v ivvi  i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_55352198_5   5820 ---CAAACAACCCCATCAAAAAGTGGGCAAGGGATATGAACAGACACTTC 5866
                         ---    i     v  i?    i       i    v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_55352198_5   5867 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5916
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_55352198_5   5917 ATCACTGGTTAT 5928
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


2662 25.27 1.19 3.56  chrX_55441914_55444527.rev      895  1737 (877)    L1M4_orf2#LINE/L1        2   824 (84)  

  chrX_55441914_5    895 GGCAAAACATCCTATCCTCATGAATCTGAAGAATTAATATCATTAAAATG 944
                           v  i i    i  vi     i  iv     v       ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_55441914_5    945 GCAAAACTGCCTCAAGCAATTGCTTTAGATTGCTACAGATTAAATGCAAT 994
                             v   -  i   ---    ------  --         v  i     
  L1M4_orf2#LINE/     52 GCAATACT-CCCCAA---ATTG------AT--CTACAGATTCAACGCAAT 89

  chrX_55441914_5    995 CCCTTTCAAAATATCAA-TGTCATTTTTCGTAGAACTAAAAAAA--AATC 1041
                             v       vi  i-  i -     i i    v vi v  i--i   
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATC 138

  chrX_55441914_5   1042 CTAAAATTTGCACGGAACCAAAAAAGAGCCCCAATAGCCAGAGTGAGCTT 1091
                                 iii i    viiv  ii  v  vv        i iii v   
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chrX_55441914_5   1092 AAGAAAAAAGAACAAAGCTGGAGGCATCACATTACCTGACTCCAAATTAT 1141
                         i i   i          i      vv     i v  ii i i    viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_55441914_5   1142 ACTACAAGGCTACAGTAAATGAAAAAGCATGATAGTGGTATAAAAATAAA 1191
                                i          vii i v  ii  i  v   i    ii   i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_55441914_5   1192 CATGTAAATCAATGGAACAGAATAAAGAACCCAGAAATAAAGGCACATAT 1241
                            i  i          i     vi   ii           vv  i i  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_55441914_5   1242 TTAAAGCTAACAGATTTTTTACAAAGCCAC-AAGAACATATACTGGAGAA 1290
                            vi ii  iv      iv    i vii -    v   vi v   i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_55441914_5   1291 AGCACACTGGGTTCAATAAATGGTGCCGGGATAACTGGATTGCCATATGC 1340
                           v i v vvv     i         i    i        v?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_55441914_5   1341 AGAAGAATGAAACTGGACCCCTATCTGTCACCATATTAAAAAAAATCAAC 1390
                          i         ii          i  vv        -- v      i   
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATAT--ACAAAAATTAAC 486

  chrX_55441914_5   1391 TCAATAATG-ATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAATAC 1439
                             -    -  i ?    i         i v i            v vi
  L1M4_orf2#LINE/    487 TCAA-AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_55441914_5   1440 TAGAAGAAGGCCTAGGGAAAACTCTCCTGGACTTTGATATAGGCAAAGAA 1489
                                 ii v    ?iv  v   i vv   i   ivv       v i-
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG- 584

  chrX_55441914_5   1490 TTTATGCCTA-ATAT--C-TCAAAAGCATAGGCAACAAAACCAAAAACAG 1535
                            --- i  -    -- -i        i i         vv     i  
  L1M4_orf2#LINE/    585 TTT---CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_55441914_5   1536 ACAAATGGGATTTAGTTACACTGAAAAGCTTCTGCACAGTAAAAGAAGTA 1585
                          i    v   i  vi i v v v    i   i  ii vvi   i  viiv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_55441914_5   1586 ATCAACAGGGTGAACAGAGACAACCTGTAGAATGAGAGAAAATATTAGCA 1635
                              v ii     --i        iii      i           v   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAA--AAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_55441914_5   1636 AACTATGCATCTGACAGGAGTCTAATATTCAGAATTTACAAGGAACTACA 1685
                           ii  ii      i i i v  vi   i      v  i  i     viv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_55441914_5   1686 ATAACTAAA-AATAAATAAATAAATAAATAATAATTCTATTAAAAAAGTG 1734
                          i    v  -      v i i      -------ii v   ?     -  
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAA-------CCCAATTWAAAAA-TG 821

  chrX_55441914_5   1735 GGC 1737
                            
  L1M4_orf2#LINE/    822 GGC 824

Transitions / transversions = 1.75 (133 / 76)
Gap_init rate = 0.02 (20 / 823), avg. gap size = 2.00 (40 / 20)  

 242 19.09 7.27 2.73  chrX_55441914_55444527.rev     2014  2123 (491)    L1M4_orf2#LINE/L1      794   908 (0)  

  chrX_55441914_5   2014 AAAAAATAAAAAAT--AA---AAAAAAAGGCTAAGGACATGATGAATAGT 2058
                             i i   v  i--  ---     vi   v     i- --       v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-T--TGAATAGA 840

  chrX_55441914_5   2059 TATTTTTTAGTAGAAGACAGA--AATGGCCAACAAGCATAGGAAAA-ATG 2105
                         i    i iviv      i v --         i     i v     -   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_55441914_5   2106 GTCAACATCACTAATAAT 2123
                         v         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (12 / 9)
Gap_init rate = 0.05 (6 / 115), avg. gap size = 1.83 (11 / 6)  


2928 25.61 2.78 1.67  chrX_55475769_55481875     4717  5614 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55475769_5   4717 TGGAGAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4766
                             i i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55475769_5   4767 GGCCATACTGCCCAAAGCAATCTATAGATTCAATGCTACTCCCATTAAAC 4816
                            v     v      vii     i        i  v ii  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55475769_5   4817 TACCATTGACATTCTTCACAGAATTAGAAGAAACT-ATTTTAAAATTCAT 4865
                          v   vivi v  i  ii     v v  v-  i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_55475769_5   4866 ATGAAACCAAAAAAGAGCTCATATAGCCAAGACAACTCTGAGCAAAAAGA 4915
                            i  viiv  ii  v iviv        i    iii   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_55475769_5   4916 ACAAAGATGGAGGCATCACGTCACCAGACTTCAAACTATACTACAAGGCT 4965
                               v      vv    iiiv  vi i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_55475769_5   4966 ACAGTAACCAAAACAGCATGGTACTGGTAGAA----AAACACATACACCA 5011
                                i   i    ii         i v  ---- i   i   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_55475769_5   5012 ATGGAATAGAATAGAGAACTCAGAAATAAGACTGCACATTTACAACCATC 5061
                                     v    iii         iv iii       iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_55475769_5   5062 TGATCTTTGACAATCCTGACAAAAACAAGCAATGAGGAAGGGATTCCCTG 5111
                             i  i     vvv  v   i v  vv     i    i i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_55475769_5   5112 TTTAATAAATGGTGCTGGGAGAATTGGCTAGCCATATGCAGAAAATTGAA 5161
                           i  i              v  i   v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_55475769_5   5162 ACTGTACCCCTTCCTTACTCCTTTTACAAAAATTAACTCAAGATGAATGA 5211
                         ii  v      v   i  v  v v                 i   i  v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_55475769_5   5212 AAGATGTAAATATAAAACCCAAAGCTATAAAAACCCTAAAAGAAAATATA 5261
                         ?   iv     i   i v i   i        vi i  i       i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_55475769_5   5262 GGC---AATGCCATTCAGGACATAGGCACAGGCAAAGATTTCATG---AT 5305
                           ?---   -- -   iv   v v  vvi      v i    v i---  
  L1M4_orf2#LINE/    550 GGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_55475769_5   5306 GAAATTGCCAAAAGCAATTGCAACAAAAGCAAAACTTGACAAATGGGATC 5355
                           v ---         vvv          v    v v  i    v   ii
  L1M4_orf2#LINE/    597 GACA---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_55475769_5   5356 TCATTCAACTAAATAGCTTCTGTACTGCAAAAGAAACTTATCATTAGATT 5405
                             iv  v v  v i   i   i  v    i  v   -    vv i v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGAAAGT 692

  chrX_55475769_5   5406 GAACAGGCAACCTACAGAATGGCAGAAAATTTTTGC----CATCTACCCA 5451
                            v  i     i         v       v     ----   v  i --
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC-- 740

  chrX_55475769_5   5452 CGTGACAAGGTTCTAATATCCAGACTCTACAAGGAACTTAAACAAATTTA 5501
                         --   i    vv  vi        v v  i  i     ivv    v iv 
  L1M4_orf2#LINE/    741 --TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_55475769_5   5502 TAGGAGAAAAACAAAACAACCCCATGAAAAAGTGTGCAAAGGACATGAAC 5551
                           iv i   i     -i     v  v?    i  v        iv    i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_55475769_5   5552 AGACACTTCTC------AAATCCATGCA----GTCAACAAACATATGAAA 5591
                              i     ------ i  --  i  ---- i   i  i  i      
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGAT--ATACAAATGGCCAATAAGCACATGAAA 885

  chrX_55475769_5   5592 AGAAGCTCAACATCACTGATCAT 5614
                            v           ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (128 / 98)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  


3162 19.47 3.09 4.24  chrX_55485306_55487170      500  1372 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chrX_55485306_5    500 AAGGTAGCAATACTCCCCAAAGAAATCTATATATTCAATGCAATCCCTAT 549
                            i i               vvi     i v      i           
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_55485306_5    550 CAAAATTCTAG-TGGATTCATTGTTGAAAT--AAAAATAAAATTTCTAAA 596
                               i i  -  vv  iv   iv     -- v  iivi -- i     
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAA 143

  chrX_55485306_5    597 AGTCAAATGGCATTTCAAGAGACACTGAATAGCCAAAAAAATT------- 639
                          v   v    v v v    i   v v            v   i-------
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_55485306_5    640 AGAAAA------TTGAAGGACTCAAAATTTT-AGGTTCAAAACTTACTAC 682
                             i ------   i        v v  ii- iv               
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_55485306_5    683 AAAGTTACAGCAATCAAAAACAACATGGTACTAATGTAAAGATAAAAATA 732
                             i     i      i -  iii       iiii   i    i v   
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_55485306_5    733 CAAATTAATGGGATACAATTGAGATTCCAGAAATAAACCGATAAATCTTT 782
                         i i  i     i   v        v              v   v  i v 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_55485306_5    783 GATCAATTGATTTTTGA-AAGGGCTGCCAAAAACATTCAATGGGGAAACT 831
                          i            i  -     -      i v               vv
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_55485306_5    832 AGAATCACTTCAACAAATGATGTTGGGACAATTGCATAGCCACATGCAAA 881
                          v i  vi           i  i        i  v   ?           
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_55485306_5    882 ACTGTTTACAATGCAGTTGGACCGTTACCTCACACCATATACAAAATATA 931
                          -- -----    v         vi                     ----
  L1M4_orf2#LINE/    442 A--G-----AATGAAGTTGGACCCCTACCTCACACCATATACAAAA---- 480

  chrX_55485306_5    932 TACAAAAATTAAGTCAAAGTTGATCAGAGTTCTCAATATAAGAGACAGAA 981
                         -------     v     i v     ?  vi  v   i      vi i  
  L1M4_orf2#LINE/    481 -------ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_55485306_5    982 ATATAAAACTATTAAAAGAAAACCTAAGGGTCTATTTTGTATGACTTTGG 1031
                         v         v   i        v  i ?  vv  i  -ii    i    
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT-CGTGACCTTGG 572

  chrX_55485306_5   1032 ATTTAATAATGGATTCTTAAATATGACACTAAAAACACAAACAACAAAA- 1080
                         i  viii     v      i         i    i     i        -
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_55485306_5   1081 ----AATAGACAAATTGGACTTCA--AACCTTCAA--CTTTTGCACATGA 1122
                         ----      i             --  vv  v  --      ii v v 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_55485306_5   1123 AAAATATTTTATCAATAAATTTAAAAGAAAAACCACACAATTACAGAAAA 1172
                           ii- ivi      v   v v      v  v     v   viv      
  L1M4_orf2#LINE/    673 AAGG-ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_55485306_5   1173 TATTTGCAAGTCATATATGTGGTTAAGTGTCAAATAACCAGACTTTATAA 1222
                                  i        v  i -   v v vvi  v     v v     
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGAT-AAGGGACTTGTATCCAGAATATATAA 770

  chrX_55485306_5   1223 AGATCTCCTTCAACTTAGCAAAAACAAAACAAAACAAAAAACATCAACTC 1272
                            v   i v     ---   v  i    -- i     ------i   i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACT---CAATAATAAAA--AGACAAA------TAACCC 809

  chrX_55485306_5   1273 TATTAAAAAATGGAGCAAAGGATTTCAGCAGACTTTTACCCAAAGAAGAT 1322
                         v   ?        -           v ii    v   vi           
  L1M4_orf2#LINE/    810 AATTWAAAAATGG-GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_55485306_5   1323 ATATAAATGGCAAATACATACACGAAAAGATGCTCACCATCATTATTCAT 1372
                            i       v    vii   i             v     ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.13 (88 / 78)
Gap_init rate = 0.03 (22 / 863), avg. gap size = 2.91 (64 / 22)  


 607 22.98 0.00 0.00  chrX_55495909_55498984      340   500 (2576)  C L1M4_orf2#LINE/L1   (0)   908   748  

C chrX_55495909_5    500 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 451
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

C chrX_55495909_5    450 AACAAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGACACTTCT 401
                         i     i     v  i?    i     i i   iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

C chrX_55495909_5    400 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 351
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

C chrX_55495909_5    350 TCACTGGCCAT 340
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (21 / 15)
Gap_init rate = 0.00 (0 / 161), avg. gap size = 0.00 (0 / 0)  

2064 23.53 7.49 0.36  chrX_55495909_55498984     2023  2583 (493)    L1M4_orf2#LINE/L1      308   908 (0)  

  chrX_55495909_5   2023 GAATAGAGAACCCAGAAATAAGCTCACACATATACTGTCAACTGATCTTC 2072
                             v    ii          i i  i    v  iv     i    i   
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_55495909_5   2073 AACAAGGGTGCCAAGAATATGTAATGGGTAAAAGATAATCCACTTTTGAT 2122
                         i               vi  vi      v   ii   i  i--   ii i
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT--TTTCAAC 405

  chrX_55495909_5   2123 AC-T--TGCTGGGAAAACTGGA---------------------------- 2141
                          v- --        v       ----------------------------
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_55495909_5   2142 CCCTTATCTTACACTATGTGCAAAATTCAACTCAAAATGAATTAAAGGTG 2191
                            i  i  i    i  i i     v i           i  i ?  iiv
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_55495909_5   2192 TTAACATAAGATTGGAAACTATAAAACTCATGGACTAAAACATAAGGGAA 2241
                          v  ii     vivi              v i  vv        i ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_55495909_5   2242 AATCTTCTTGACATTGTCTGAGCCAATAATTTTTT-----TAAC-CCAAA 2285
                                v    v   vv v  v    ii   i  ----- i  -     
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_55495909_5   2286 AGCACAAACAACAAAAGTAAAAAT-GTCAAATGGAATTACATCAAACTAA 2334
                                i         v      - vi    v i i v       v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_55495909_5   2335 GAAGCTCCTGCACAGCAAAGGAAATAATCAACAAAATGAAAAGTCAAACT 2384
                         i  i  ii  ii vv       v iv     v   i       v   v i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_55495909_5   2385 ACAGAATGAGAGAAAATATTTGCAAACCATATGTCTGATAAAGGGTTAAT 2434
                                 i                 i     i        i  ii vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_55495909_5   2435 ATCCAAAACACATAAGGAGCACCTACAACTTAATAG-AAAAA---AAATC 2480
                              i  i i    i  i v i       i    i-     ---    v
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_55495909_5   2481 ACCTGCTTTAAAAATAGACAAAGAAACTGAATAGATATTTCTCCAAGTAA 2530
                            iiv  ?      i i     i vi        i          iv  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_55495909_5   2531 GACATAGCAATGGCCAACAAGTATATGAAAAGGCATTCGGCATCACTAAT 2580
                           i   vv         i   i i        iiii  ii     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_55495909_5   2581 CCT 2583
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.93 (85 / 44)
Gap_init rate = 0.01 (9 / 601), avg. gap size = 4.89 (44 / 9)  


2898 26.94 1.55 1.22  chrX_55510237_55516044.rev     4416  5317 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_55510237_5   4416 AAAGAC-TTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAATGGC 4464
                              i- i     i        v      v i     ii v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_55510237_5   4465 CATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATTCCCATAA 4514
                         v     v      v i  i  i        i  v  i  i  ---  -  
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT---CA-AA 99

  chrX_55510237_5   4515 AGCTACCAATGACTTTCTTCACAGAACTAGAAAAACCTACTTTAAATTTA 4564
                          v --   iivi i  i  ii     v v  v  i iv iii    v  v
  L1M4_orf2#LINE/    100 ATC--CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_55510237_5   4565 ATATGGAACCAAAAAAGAGCCCGTATAGCCAAGATAATCCTAAGCAAAAT 4614
                                 viiv  ii  v  v v        i i    i i iv  i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_55510237_5   4615 GAA--AAGCTGGAGGCATCACGCCACCTGTCTTCAAACTATACCATGAGG 4662
                            --   i      vv    i iv  iivi      viv   i ii i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_55510237_5   4663 CTACAG-AACCAAAACAGCATGGTACTGGTACCAAAACAGATATGTAGAC 4711
                               -  i   i    ii         i iv ii i   i  i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_55510237_5   4712 CAATGGAACAGAATAGAGGCCTCAGAAATAACACCACACATTTACAACCA 4761
                                 i     v   ivii         vv   i       iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_55510237_5   4762 TCTGGTCTTCGACAAACCTGATGAAAACAAGCAATGGGGAAAGATT--TC 4809
                         vi  i i        ivv  vii i v  vv             v --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_55510237_5   4810 CTATTTAATAAATGGTGCTGGGAAAACGGGCTAGCCATATGCAGAAAACA 4859
                         i -  i  i              v   v  v  ?   i     i  i vv
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_55510237_5   4860 GAAACTGGACCCCTTCCTTACACCTTATACGGAAATTAACTCAAGATGGA 4909
                            ii         v   i     v     ii            i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_55510237_5   4910 TTAAAGGCTTAAAGGTAAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 4959
                          i ?  i i    v    i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_55510237_5   4960 CTAGACA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5008
                         v   i?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_55510237_5   5009 AAACACCAAAAGCAATTGCAA-AAAAGCCAAAATTGACAAATGGGATTTA 5057
                         vi            vvv    -     vv     v  i    v   i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_55510237_5   5058 AACTAAACTAAAGAGCTTCTGCAAAGCAAACTAAACTATCATCAGAGTGA 5107
                          v v   i    i -   i  iivvv    vv v       vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_55510237_5   5108 ATAGGCAACGTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5157
                          v  i    vi                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_55510237_5   5158 AAAGGTCTAGTATCCAGACTCTA-GAGGCA-TCTTAAACAAATTTACAAC 5205
                           i  v  v         v v  -i i v -     --   v iv i  i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAAT 792

  chrX_55510237_5   5206 AGAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACA 5251
                          i   i    ----   v  i?    i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_55510237_5   5252 CTTCTCAAAAGAAGACATTTATGTGGCCAACAAACTTATGAAAAAATGCT 5301
                         i     v        i  vi vi       i  i vi       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_55510237_5   5302 CATGATCACTGGTCAT 5317
                           vv    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 1.56 (25 / 16)  


2428 27.64 4.27 2.25  chrX_55536194_55540964     3418  4260 (511)    L1M4_orf2#LINE/L1        1   860 (48)  

  chrX_55536194_5   3418 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCTTGAAAGT 3467
                              ii i  i     i        v      v i     iv v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55536194_5   3468 GGCCATAATGCCCAAGGCAATTTATAGATTCAATGCCATCGCCATCAAAC 3517
                            v   v v     ivii  i  i        i  v   v i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55536194_5   3518 TACGAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 3565
                          v v iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_55536194_5   3566 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCGAAA 3615
                                 viiv  ii  v  v v  v     i      i i ivvii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_55536194_5   3616 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAATCTATACTACAAGG 3665
                                 i      vv    i  v  ii i     vviv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_55536194_5   3666 CTACAGTAACCAAAACATCATGGTACTGGTACCAAAACAGAGATATAGGC 3715
                                  i   i   vii         i iv ii i   v      ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_55536194_5   3716 CAATGGAACAGAACAGAGGCCTCAGAAATAACAACTCA--CATATACAAC 3763
                                 i    iv   ivii         --  i  --   v  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAA--ACCCATACATTTATGGT 345

  chrX_55536194_5   3764 CACCTG-TCTTTGACAAACCTGTCCATAAAAAGA------AATGGGGAAA 3806
                           vi  - i  i     ivv  i ------    ------          
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCC------AAGACCATTCAATGGGGAAA 389

  chrX_55536194_5   3807 TGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTA 3856
                         vi  vvi  v  i  i              v      v  ?i  i   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_55536194_5   3857 GAAAGCTGAAACTCGATCCCTTCCTTACACCTTATACAAAAATTAATT-- 3904
                         i  iiv    ii v  i    v   i     v              i --
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_55536194_5   3905 -----------------AAACATTAGACCTAAAGCCATGAAAACCCTAGA 3937
                         -----------------   ii v   v     i i  i   vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_55536194_5   3938 AGAAAACCTGGGCA-ATACCATTCAGGACAT-AGGCAAGAGCAAAGACTT 3985
                                v i  ?i- v i -   iv   v -i  iv  -    v ii  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG-GCAATGGTTT 587

  chrX_55536194_5   3986 CATGACTAAAACACCAAAAGAAATGGCAACAAAAGCCAAAATAGACAAAT 4035
                          v iiv  vi          v vvi          vv        i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_55536194_5   4036 GGGATCTAATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATC 4085
                         v   ii v  i   v v  i ii  i  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_55536194_5   4086 AGATTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCC 4135
                          i v    v  i     i                 v       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_55536194_5   4136 ATCTGACATAGGGCTAATATCCAGATCCAGAATCTACAAAGAATTTAAAC 4185
                               i vi  i  -- i ----         v  i      i ivv  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACT--TGT----ATCCAGAATATATAAAGAACTCTTAC 781

  chrX_55536194_5   4186 AAATTTACAAGAAAAAAACAA----CCGCATCAAAAAGTGGGCAAAGGAC 4231
                           v iv i  v     i    ----  vv  i?    i           i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_55536194_5   4232 ATGAATAGACAGTTCTCAAAAGAATACAT 4260
                         v          v     v      v i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.02 (16 / 860), avg. gap size = 3.44 (55 / 16)  


3011 28.45 0.55 0.44  chrX_55578036_55597137.rev     4880  5786 (13316)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55578036_5   4880 TGGTAGAACATTCCATGCTAATGGGCAGGAAGAATCAATATCGTGAAAAT 4929
                            v ii i  i     i v    iiv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55578036_5   4930 GGCCATAGTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4979
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55578036_5   4980 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v    ivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_55578036_5   5028 TATGGAACCAAAACAGAGCCCTCATCGCCAAGTCGATCCTAAGCCAAAAG 5077
                                viiv  vi  v  vvv  v     iv i   i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_55578036_5   5078 AACAAAGCTGGAGGCATCGCACTACCTGACATCAAACTATACTACAAGGC 5127
                                i      vv  i    v  ii iv     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_55578036_5   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5177
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_55578036_5   5178 AATGGAACAGAAC--AGAGCCCTCAGAAACAACGCCGCATATCTACAACT 5225
                                i    i--    i  --     i  vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_55578036_5   5226 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAGAGACTCC 5275
                          vi    i  i     ivv  v   i v  vv          iii ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_55578036_5   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_55578036_5   5326 GAAACTGCATCCCTTCCTTACACTTTACACAGAAATCAATTCAAGATGGA 5375
                            ii  v i    v   i    iv  i   i    i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_55578036_5   5376 TTAAAGACTTAAATGTTAAACCTAAAACCATAAAAATACTAGAAGAAAAC 5425
                          i ?    i       v i v       i      v vi           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_55578036_5   5426 CTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAA 5475
                         v    ?i v viv   iv   viv  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_55578036_5   5476 AACACCAAAAGCAATGGCAACAAAAGACACAATTGACAAATGGGATCTAA 5525
                         i            vvi           v v   v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_55578036_5   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_55578036_5   5576 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5625
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_55578036_5   5626 AGGTCTAATATCGAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  v  vi    v     v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_55578036_5   5676 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGTCACTTC 5725
                          i     i     v  i?    i    ii     iv    i  v  i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_55578036_5   5726 TCAAAAGAAGACATTTATGCAGCCAA-AAACACATGAAAAAATGCTCACC 5774
                           v        i  vi viii     -  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_55578036_5   5775 ATCACTGGCCGT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (150 / 104)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  

2735 27.61 2.11 1.44  chrX_55578036_55597137.rev     8971  9872 (9230)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55578036_5   8971 TGGAGGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 9020
                             iii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55578036_5   9021 GGCCATACTTCCCAAGGTAAGTTATAGATTCAATGCCATCTAGTTAT--A 9068
                            v     i     iv i vi  i        i  v   i--i   -- 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC--CTATCAA 98

  chrX_55578036_5   9069 GATTCAAGCTAC------TAATGGACTTGGAATAAACT-ACTTTAAAGTT 9111
                         i  i v    i ------ ivv i v   -- i  i  - iii    i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_55578036_5   9112 CATATAGAACCGAAAAAAAAAAAAGTCCACATTGGC-AAGACAATCCTAA 9160
                              i   vi v  iii ------i   v v i  -  i      i i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA------CCCAGAATAGCCAAAACAATCTTGA 190

  chrX_55578036_5   9161 GCAAAAAGAACAAACCTGGAAGCATCACGCTACCTGACTTCAAACTATAC 9210
                         iv  i         vi    i vv    i  v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_55578036_5   9211 TACATGGTTACAGTAACCAA-ACAGCATCGTACGGGTACCAAAA-AGA-- 9256
                             vi i        i   -    ii v    v  i iv ii -   --
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_55578036_5   9257 TATAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACAT 9304
                               i        i    i--    i  --        vv   i    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACAT 338

  chrX_55578036_5   9305 CTAAAACCATCTGATCTTCAACACACCTGTCAAAAACAAGAAATTGGGAA 9354
                         i  viii  vi    i   i   vivv  i   i v  vvv   v     
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_55578036_5   9355 ACGATTCCCTATTTAACAAATGGTGCTGGGAAGACTGGCTAGCCATATGT 9404
                          vi  vvi  v  i                 vi     v  ?   i   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_55578036_5   9405 AGAAAGCTGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTC 9454
                          i  iiv    ii    i    v   i     v  i           i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_55578036_5   9455 AAGATGGATTAAAGACTTAAATGTA-GTCCTGAAACCATAAAAACCCCAG 9503
                           i      i ?    i        - vv  i    i      vi ii  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_55578036_5   9504 AATAAAAGCTAGGCA-ATACCATTCAGGACACAGACATGGGCAAGTATTT 9552
                           v    vv    ?i- v i -   iv   viv ivv i     vvi   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_55578036_5   9553 CATGACTGAAACACCAAA-GCAATGGCAACAAAAGCCAAAATAGACAAAT 9601
                          v iiv ivi        -   vvi          vv        i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_55578036_5   9602 AGGATCTAATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATC 9651
                         v   ii v  v   v v  i i   i  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_55578036_5   9652 AGAGCGAACAGGCAACCTACAGAATGGGAGAAATTTTTTGCAATCTACCC 9701
                          i  i   v  i     i               v v       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_55578036_5   9702 ATCTGATAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAGATTT 9751
                                  i  i  vi          v  i         vv   iv iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_55578036_5   9752 ACAAGAAAAAATCAAACAACCCTATCAAAAAGTGGGCAAAGGATATGAAC 9801
                          i  v     iv    i     v  i?    i            v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_55578036_5   9802 TGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACAAATGAAAAA 9851
                         v    i     v        i  vi viii     i ii  v       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_55578036_5   9852 ATGCTCATCATCACTGGTCAT 9872
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.00 (32 / 16)  

1895 22.65 1.03 16.40  chrX_55578036_55597137.rev    12030 13102 (6000)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55578036_5  12030 TGGAAATATGTTTCATATTTATGGATTGGAAGAACTAATATTGTTAAAAT 12079
                               v  i ii   i  i             vi            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55578036_5  12080 GTCCATAATACCCAAAACAGTCTACAGATTCAATGCAATCCCTATCAAAT 12129
                          v v   v v      viii             i               v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55578036_5  12130 TACCAATGACAGTCTCCATTGAAATAGAAAAAAACAATTCTAAAATTTAT 12179
                          v   iivi vv i iiiiv     v  v  iv-ii  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_55578036_5  12180 ATATAACCTCAAAAGACCCAGAATAGCCAAAGCCATCCTAAGCAAAAAGA 12229
                           iv  viv   ii                 i v   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_55578036_5  12230 GCAAAACTGGAGAAATCACATTACCTGACTTATTTTTTCATCTCCAAAAA 12279
                         i    ii     i v     i v  ii i  -------------     -
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTT-------------CAAAA- 235

  chrX_55578036_5  12280 AGTTTATTAGCATGATTAAAAACATTTTTTGAATAATAACAGAAAGAATT 12329
                         --i   i  -----------------------------------------
  L1M4_orf2#LINE/    236 --CTTACTA----------------------------------------- 242

  chrX_55578036_5  12330 TCTAAACATGAAAGAATATCAGCAGCTATACCTTAAAACCAGTATTCCGA 12379
                         --i   ------------------    -----------     v  ---
  L1M4_orf2#LINE/    243 --CAAA------------------GCTA-----------CAGTAATC--- 258

  chrX_55578036_5  12380 ATTGAATGGACAGCTTTATTGCCAGTCTTCAAAAAACAATCCATTGATTG 12429
                         ----  --     -------------------------------  --  
  L1M4_orf2#LINE/    259 ----AA--GACAG-------------------------------TG--TG 269

  chrX_55578036_5  12430 GTCACTGCACAGCTGTAGCCACACAGACTAAGGGAACAGAATAGAGGACA 12479
                           -    ---------------i  ---     -------     ---  
  L1M4_orf2#LINE/    270 GT-ACTG---------------GCA---TAAGG-------ATAGA---CA 290

  chrX_55578036_5  12480 CTGATACAGACACAGACTAATGGAACAGAATACAAGACACAGAAAAAAAT 12529
                         i---------- i   ii       i     vv iiiiv      v   i
  L1M4_orf2#LINE/    291 T----------ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_55578036_5  12530 TCTCACATTTACACTGAACTCATTTTTGACAAAGGCTCAAATAATATACA 12579
                         i vi       iiv v  i v     i     i  iv v  v vi  v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_55578036_5  12580 CTGGGAAAAAGACAATTTCTTCAATAAATTATGCTATAAAAACTAAATAT 12629
                         v    i   ii i i i i     i    vi    ivi v    ii   ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_55578036_5  12630 GAATATGCAGAAGAATGAAACAAGGCCCCTATTTCTCACCATATACAAAA 12679
                         vv i     i         iivi i      ii  v              
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_55578036_5  12680 ACCAAATCAAAATAAATTAAAGAGTT-----TAGGATCTTGAACTATAAA 12724
                          ii  v       ii  i ?   vi -----  i  v  vi         
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_55578036_5  12725 ATTACTACAAGGAAACATCAGA--AAAACTTTATAGGATATTGGTCTGGG 12772
                          i vi  v   i      vi ?--   v   ii --  iv    vi i  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT--GACCTTGGGTTAGG 578

  chrX_55578036_5  12773 CGAAAATTTCTT-GAT-TAATACCTCACAAATACATGCAACTGAAGCAAA 12820
                          i vii      -   - i i   -- v  ii   v     vi   v   
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACC--AAAAGCACAAGCAACAAAAGAAAA 626

  chrX_55578036_5  12821 AATGGACAAGTGGGATCACATCAAG-TTAAAAAGCTTCTGAACAAGAAAG 12869
                            i  i  i v   iiv      i-       -   i  vi vvv    
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAG 675

  chrX_55578036_5  12870 GAAATTACCAACAAAATGAAGAGATACCCCACCAATTTGAAGAAAATATT 12919
                           v i  i   v   i    i   i v     vi v v i          
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_55578036_5  12920 TGCTAACTACCTATCTGACAAGGGATTAATAACCAGAATATAGAAA-AGC 12968
                            v  ii iv       i      i vi  v          v   - i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_55578036_5  12969 TCAAATAACTCCACAGGAAAAAAATCTAGCAAGCCAATTAAAAAGTGGGC 13018
                           vv i     v i iv     i - v ii  v      ?    i     
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGC 824

  chrX_55578036_5  13019 AAAAGATTCAAATAGACATTTCTCAAAAAATAACATGCAAATGGCAAAAA 13068
                            i    ii              v   i vi i  i        v  v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_55578036_5  13069 GGCATATTAAAATGGGCTCAACATCACTGATTAG 13102
                         i   i  v    viv           ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (149 / 90)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 7.19 (187 / 26)  

3009 27.59 0.77 0.55  chrX_55578036_55597137.rev    17706 18611 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55578036_5  17706 TGGAAAAAGAGTCCATGCTCATGGATAGGAAGAATCAATATGGTGAAAAT 17755
                               i v vi     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55578036_5  17756 GGCCTTACAGTCCAAAGTAATTCATAGATTCAATGCCATCCGCATCAAGC 17805
                            vv   vvi     v i  ii i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55578036_5  17806 TACCAATGACTTTCTTCACAGAACTGGAGAAAACT-ACTTTAAAGTTCAT 17854
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_55578036_5  17855 ATGGAACCAAAAAGGAGCCAGCATAGCCAAGACAATCCAGGGCAAGAAGA 17904
                               viiv  i   v    v        i      iv iiv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_55578036_5  17905 ACAAAGCTGGAGGCATCATGGTATCTGACTTCAAACTTTACTACAAAGCT 17954
                               i      vv   iiv vi ii i      vi             
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_55578036_5  17955 ACAGTAAACAAAACAGCATGGTACTGGTACTAAAACAGATATGTAGACCA 18004
                                v   i    ii         i iv ii i   i  i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_55578036_5  18005 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACCACCACC 18054
                               i    iv   ivii         vv   i    i  ivii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_55578036_5  18055 CAATCTTTGACAAAC---CTAACACACACAAGCAATGGGGAAAAGATTCC 18101
                         ii  i  i     iv--- i  v  ---  vv           ii  vvi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAAAGAATAGT 396

  chrX_55578036_5  18102 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 18151
                           v  i  i        i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_55578036_5  18152 GAAACTGGACCCCTTCCTTACACCTTATACTAAAATCAACACAAGATGGT 18201
                            ii         v   i     v     v     i   v   i    v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_55578036_5  18202 TCAGAGACTTATACATAAGACCTAGAACCATAAAAATCCTAGACGAAAAC 18251
                            ?    i  v ii     v   i   i      v  i    v      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_55578036_5  18252 CTAAGCA-ATACCATTAAGGACATTGGCATGGGCAAAAACTTCATGTCTA 18300
                         v  i ?i- v i -  viv   v    vv i     viii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_55578036_5  18301 AAAGACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGAGATCTA 18350
                         vi v          vvi          vv        i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_55578036_5  18351 ATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGAA 18400
                           i   v v  i i   i  ii vv    iv v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_55578036_5  18401 CAGGAAACCTACAGAATGGGAGAAAAT-TTTACAATCTATCTTTCTGACA 18449
                         v  iv    i                 -   i   vii  v v     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_55578036_5  18450 AAGGGCTAATAGCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAA 18499
                          i  i  vi  v       v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_55578036_5  18500 AAAGCAAACAACCCCAT-AAAAAATGGGCAAAATATATGAACAGACACTT 18548
                           ii    i     v  -?             iv  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_55578036_5  18549 CTCAAAAGAAGACATTTATTCAGGCAACAGACATATGAAAAAATGCTCAT 18598
                            v        i  vi vvii v   i ii  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_55578036_5  18599 CATCACTAGTCAT 18611
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (140 / 106)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3077 27.65 0.88 0.44  chrX_55611085_55617792     5312  6215 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55611085_5   5312 TGGAAAAACATTCCATGCTCATGGATGGGAAGAATCAATATCGTGAAAAT 5361
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55611085_5   5362 GGCCATACTGCCCAAAGTATTTTATAGATTCAATGCTATCCCCATCAAGC 5411
                            v     v      v iv i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55611085_5   5412 TACCAACGACATTCTTCACAGAA-TTGGAAGAAACT--TCTTTAAATTTC 5458
                          v   i vi v  i  ii     -   -- v  i  --  i v     - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT-C 147

  chrX_55611085_5   5459 ATATGGAACCAAAAAAGAGCCTGCATAGCCAAGATAATCCTAAGCAAAAA 5508
                                 viiv  ii  v  v v        i i    i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_55611085_5   5509 GAACAAAGCTGGAGGCCTCACACTACCTGACTTCAAACTGTACTACAAGG 5558
                                 i      v        v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_55611085_5   5559 TTACAGTAACCAAAACAGCATGGTACTGGTACCGAAACAGATATGTAGAC 5608
                         i        i   i    ii         i iviii i   i  i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_55611085_5   5609 CAATGGAACAGAACAGAGGCCTCAGAAATACCACCACACATCTACAACCA 5658
                                 i    iv   ivii        vvv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_55611085_5   5659 TCTGATCTTTGACACACCTGACAAAAACAAGCCATGGGGATAGGATTCCC 5708
                         vi    i  i    vivv  v   i v  vv v       v  i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_55611085_5   5709 TATTTAATAAATGGTGTTTGGAAAACTGGCTAGCCATACGCAGAAAACTG 5758
                          v  i  i        i v   v      v  ?   i i   i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_55611085_5   5759 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAATGTGAAA 5808
                           ii         v   i     v                   vi  i v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_55611085_5   5809 TATAGACTTAAACATCAGACCTAAAACCATAAAAACCCTAGAAGAGAACC 5858
                         i ?    i    ii v   v       i      vi i       i   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_55611085_5   5859 TAGGCA-ATACCATTCAGGATATAGGCATGGGCAAAGACTTCATGACTAA 5907
                             ?i- v i -   iv  iv v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_55611085_5   5908 AACAACAAAAGCAATGGCAACAAAAGCCTAAATTGACATAAGGGATCTAA 5957
                         i   v        vvi          vvv    v  i v vv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_55611085_5   5958 TTAAACTAAAGAGTTTCTGCACAGCAAGAGCAACTATCATCAGAATGAAC 6007
                          i   v v  i ii  i  ii vv   ii vv       vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_55611085_5   6008 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCTATCTGACAA 6057
                           i     i                 v       vii  v       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_55611085_5   6058 AGGGCTAATATCTAGAATCTACAAGAAACT--TA-AACATATTTACAAGA 6104
                         i  i  vi    i     v  i  ii    --  -   vi v v i  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_55611085_5   6105 AAAAAAACAACCCCATCTAAACGTGGGCGAAGGATATGAACAGACATTTC 6154
                          i v   i     v  i?   vi     i      v    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_55611085_5   6155 TCAAAAGAAGATATTTATGCAGCCTACTTACATATGAAAAAA-GCTCATC 6203
                           v           vi viii   v ivvi  i       i -     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_55611085_5   6204 ATCACTGGTCAT 6215
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (142 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3187 27.86 0.33 0.33  chrX_55678620_55685002.rev     4985  5892 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55678620_5   4985 TGGAAGAACATTCCATGCTCATGGATAGGGAGAGTCAGTATCGGGAAAAT 5034
                              ii i  i     i        v  i   v i i   i vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55678620_5   5035 GGCCATACTGCCCAAGATAATTTATAAATTCAATGCCATCCCCATCAAGC 5084
                            v     v     iv i  i  i i      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55678620_5   5085 CACCAATGACTTTCTTCACTGAA-TTGAAAAAAACT-ATTTTAAAGTTCA 5132
                         iv   iivi i  i  ii v   -    v  i--  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_55678620_5   5133 TATGGAACCAAAAAAGAACCCACATTGCCAAGACAATCCTAAACAAAAAG 5182
                                viiv  ii  v  viv  v     i      i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_55678620_5   5183 AATAAAGCTGGAGGCATCACAGTACCTGACTTCAAACTATACTACAAGGC 5232
                           i    i      vv     v v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_55678620_5   5233 TACAGTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGACA 5282
                                 i   i    ii        ii iv ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_55678620_5   5283 AATGGAACAGAACAGAGGCCTCAGAAATAATACCACATATCTACAACCAT 5332
                                i    iv   ivii         vv   i i  i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_55678620_5   5333 CTAGTCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5382
                         i ii i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_55678620_5   5383 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5432
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_55678620_5   5433 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5482
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_55678620_5   5483 AAAGACTTAAATATTAGACCTGAAACCATAAAAACCCTAGAAGAAAACCT 5532
                          ?    i     i v   v  i    i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_55678620_5   5533 AGGCA-ATACCATTTAGGACACAGGCATGGGCAAGGACTTCATGACTAAA 5581
                            ?i- v i -  iiv   viv  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_55678620_5   5582 ACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGAGATCTAAT 5631
                                     vvi          vv        i    vi  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_55678620_5   5632 TAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTGTCATCAGAGTGAACA 5681
                         i   v    i i   i  ii vv    i  v   i   vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_55678620_5   5682 GGCAACCTACAGAATGGGAGATAGTTTTTGCAATCTACCCATCTGACAAA 5731
                          i     i             v i v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_55678620_5   5732 GGGCTAATATACAGAATCTACAAAGAACTCAAACACATTTACAAGAAAAA 5781
                           i  vi   v      v  i         vv   vv iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_55678620_5   5782 ATCAAACAACCCTATCAAAAATTGGGCAAAGGATATGAACAGACACTTTT 5831
                         iv    i     v  i?    v            v    i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_55678620_5   5832 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5881
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_55678620_5   5882 TCACTGGCCAT 5892
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (152 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


3203 27.51 0.44 0.11  chrX_55688264_55690189      529  1433 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55688264_5    529 TGGAAACACATCCCATACTCATGGATCAGTAGAATCAATATTGTGAAAAT 578
                               v i       ii        ii v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55688264_5    579 GACCATGCTGCCAAAAGCAATCTACAAATTCAATGCAATCTCCATCAAAA 628
                          i v  i  v  v   vii       i      i      i i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55688264_5    629 TACCACCATCATTCCTCACAAAATTAGAAAAAAAAATTTCTAAAATTCAT 678
                          v   v vv v  ii ii  i  v v  v  ivvi - i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_55688264_5    679 ATGGAACCAAAAAAGAGCCCACATAGCCAAAACAAGACTAAGCAAAAAGA 728
                               viiv  ii  v  viv             vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_55688264_5    729 ACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATGAGGCC 778
                              vi      vv       v  ii        viv     ii i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_55688264_5    779 ATAGTCACCAAAACAGCGTGGTACTGGTATAAAAATAGGCACATAGACCA 828
                          i   v i   i    i          i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_55688264_5    829 ATGGAACAGAATAGAGAATCCAGAAATAAACCCAAATACTTACAGCCAAC 878
                               i     v    i                v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_55688264_5    879 TGATCTTTGACAAAGCAAACAAAAATGTAAAGTGGGGAAAGGACACCCTT 928
                             i  i     i vviv   i vii vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_55688264_5    929 TTCAACAAATGGTGCTGGGATAATTGGCTAGCAACACGTAGGAGGATGAA 978
                                             i  i   v  ? v   i i ii  i     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_55688264_5    979 ACTGGATGCTCATCTCTCACCTTATGCAAAAGCCAACTCAAGATGGATTA 1028
                         ii    iv ii i   v    v   i     iii       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_55688264_5   1029 AGTAGTCGAACCTAAGACAGGAAACTATAAAAATTCTAGAAGATAACATT 1078
                         ?iv viii  iv     vvvi           v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_55688264_5   1079 GGAAAAACCCTTCAAGACATTGGCCTAGGCAAGGATTTAATGACCAAGAA 1128
                           ?iv  vi    iv   v    vi       v i   vv iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_55688264_5   1129 CCCAAACGCAAATGCAATGAAAACAAAGATAAATAGCTGGGATCTAATTA 1178
                         v     v   v v    ii   iv   i   i   iv v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_55688264_5   1179 AACTATAAAGCATTTGCATGGCAAAAGGAACAGTCAGCAAAGTAAACAGA 1228
                           v vv   i v    iiivv    i iv  vi   iv     i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_55688264_5   1229 CAACTCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGG 1278
                             i      i           v  ii   vii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_55688264_5   1279 ACTCATATCCAGAATCTACAATGAACTC----AAGTCAGTAAGAAAAAAC 1324
                            ii          v  i  v      ----  v   i   v     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_55688264_5   1325 CAAACAATCCCATCAAAAAGTGGGCTAAGAACATGAATAGACAATTCTCA 1374
                             i  i  v  i?    i     v   i iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_55688264_5   1375 AAAGAAGATATAGAAATGGCCAACAAACATATGGAAAAATGCTCAACATC 1424
                                     v          i  i  i   i   i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_55688264_5   1425 ACTAATGAT 1433
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.50 (5 / 2)  


3273 26.46 0.66 0.66  chrX_55715756_55722136.rev     4984  5890 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_55715756_5   4984 GGAAGAACATTCCATGCTCATGGGTAGGAAGGATCAATATGGTGAAAATG 5033
                             ii i  i     i      i v     iv i     v  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_55715756_5   5034 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 5083
                           v     v     iv i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_55715756_5   5084 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 5131
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_55715756_5   5132 ATGGAACCAATAAAGAGCCCACATT-GCCAAGTCTATCCTAAGCCAAAAG 5180
                               vii-i  i ii    v v -     iv v   i i ivv i   
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_55715756_5   5181 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGCC 5230
                                i      vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_55715756_5   5231 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACA 5280
                                 i   i    ii         i iv ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_55715756_5   5281 AATGGAACAGAGC--AGAGCCCTCAGAAATAAGGCCGCATATGTACAACT 5328
                                i   ii--    i  --        iv  ii i  v  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_55715756_5   5329 ATCTGATCTTTGACAAACGTGACAAAAACAAGCAATGGGGAAAGGATTCA 5378
                          vi    i  i     iv   v   i v  vv            i  vvv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_55715756_5   5379 CTATGCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5428
                           v v   i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_55715756_5   5429 GAAACTGGATCCCTTCTTTACACCTTATACAAAAATTAATTCAAGATGGA 5478
                            ii    i    v i i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_55715756_5   5479 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5528
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_55715756_5   5529 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5577
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_55715756_5   5578 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5627
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_55715756_5   5628 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5677
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_55715756_5   5678 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5727
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_55715756_5   5728 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5777
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_55715756_5   5778 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5827
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_55715756_5   5828 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5877
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_55715756_5   5878 CATCACTGGCCAT 5890
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 1.33 (12 / 9)  


2155 28.98 1.04 2.22  chrX_55729344_55733533.rev     2376  3141 (1049)    L1M4_orf2#LINE/L1        3   759 (149)  

  chrX_55729344_5   2376 GAAAAACTTTCCATGCTCATGAGTAGGATGAATCAATATTGTTTAAATGG 2425
                             i iv i     i     ii v   v  v i         v i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_55729344_5   2426 CTGTACTGCCCAAAGCATTTTACAGATTTGACCCTATTCCTATCCAACTA 2475
                          vi    v      viiv i        ii  v v  i      v  v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_55729344_5   2476 CCAACATCATTTTTCACAGAATTAGAAAAATACT-ATTCTAAAATTTATA 2524
                            i vv v     ii     v v  v  i--  -  i        i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chrX_55729344_5   2525 TGTAACCAAAAATGAGTCCAAATAGCCAAAGCAATCCTAAGATAAAAGAA 2574
                           v  viiv  iv  vi vi          i     i i i v i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_55729344_5   2575 CAAAGCCAGAGACATCACACTACCCAAATTCAAACTATATTACAAGGCTA 2624
                              iii   ivv       v     v      viv  i     i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_55729344_5   2625 GAGTAACCAAGACAGCATGGTACTGGCACACATGCAAACACATAGACTAA 2674
                         v     i        ii           i vivii i   i     ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_55729344_5   2675 TGAAACATGTTAGAAAAACCCAAAATAAGGCCACACAAATACAACCATCA 2724
                           i  i viv v  i iv  vi      iv   i   vv  iiii  viv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_55729344_5   2725 AATCTTCAACAAAGTTGACAGTAACAAGAAATGAGCA--GAAGACTCCTA 2772
                         i  i   i    i v  v  iv v  vvv    i v --   v v  i v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_55729344_5   2773 TT--CAAATGGTGCCAGGGTAACTGGTTAGCCATATGCGAAAGACTGAAA 2820
                          i--          ii  ii      v  ?   i    i     v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_55729344_5   2821 CTGGATCTTTTCCTTTCACCATATACAAAAATCAACTCAAGATGGATTAA 2870
                         i    i ii v   iv                i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_55729344_5   2871 AGACTTACTTAAATATAAATCTTAAAACTATAAAAAAAAATCCTAGAAGA 2920
                             i  ----   i   ivvi             v----  i       
  L1M4_orf2#LINE/    501 AGACCTA----AATGTAAGAGCTAAAACTATAAAAC----TCTTAGAAGA 542

  chrX_55729344_5   2921 AATCCTAGG---AAATACCATTCTGGACATAGGCCATAGTAAAGATTTCA 2967
                           v v    ---    -- v iv  iv v i  ii -i i  v i    v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTA-GGCAATGGTTTCT 589

  chrX_55729344_5   2968 TGACAAAGACTCCAAAAGCAATTGCAACAAAAACAAAATTTGACAAGTGG 3017
                          iivv v   v         vvv         iv    v v  i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_55729344_5   3018 AACCTAATTAAACTAAAGAGCTCTAGCACAGGAAAAGAAATTATCAACAG 3067
                         i  i v  i   v v  i i  i v ii vvv   i  v i      v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_55729344_5   3068 AGTAAACAGAAAACCTACAGAATGGGAGAAAATGTTTTCAAACTATGCAT 3117
                            i  v   v    i                 i   v    ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_55729344_5   3118 CTGATATGGTTTGGATCTGTGTCC 3141
                               v  ----  ii   i   
  L1M4_orf2#LINE/    740 CTGATAAGG----GACTTGTATCC 759

Transitions / transversions = 1.29 (124 / 96)
Gap_init rate = 0.01 (10 / 757), avg. gap size = 2.50 (25 / 10)  

 461 26.59 0.00 1.16  chrX_55729344_55733533.rev     3533  3705 (485)    L1M4_orf2#LINE/L1      738   908 (0)  

  chrX_55729344_5   3533 ATCAAACAAAGATCTAATATCCAGAATCTATAAGGAATTTAAACAAATCA 3582
                            vi i  i iv  vi          v     i   i ivv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_55729344_5   3583 ACAAGCTAAAGGCAGGCAACCTCATTAACAAATGGACAAAGGACACAAAC 3632
                          i  vvv    i  iii    iv   ? v      i       ivii  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_55729344_5   3633 AGACACTTCTCAAATGAAGACATGCATGTGGCCAACAAACAAATGAAAAA 3682
                              i     v  v     i  i  vi       i  i  v       -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA- 886

  chrX_55729344_5   3683 AGATGCTCAAAAGGAAAAAGAAA 3705
                         -         v vv ????????
  L1M4_orf2#LINE/    887 -GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (25 / 20)
Gap_init rate = 0.01 (1 / 171), avg. gap size = 2.00 (2 / 1)  


3021 28.11 0.55 0.44  chrX_55737531_55742445     3516  4422 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55737531_5   3516 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3565
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55737531_5   3566 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3615
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55737531_5   3616 TACCAATTACTTTCTTCGCAGAATTGGAAAAATCTACTTTAAAGTTCATA 3665
                          v   ii i i  i  i      v v  v  iiiv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_55737531_5   3666 TGCAATGAAAAAAGAGCCTGCATTCCCAAGTCAATCCTAAGCCAAAAGAA 3715
                           v  vviv  ii  v  v v  vv    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_55737531_5   3716 CAAAGCTGGAGGCATCATGCTACCTGAGGTCAAACTATACTACAA-GCGT 3764
                              i      vv   ii  v  ii vv     viv        -  - 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC-T 249

  chrX_55737531_5   3765 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACAA 3814
                                i   i    ii         i iv ii i   v       iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_55737531_5   3815 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTA 3862
                               i    i--    i  --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_55737531_5   3863 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCAC 3912
                         vi    i  i     ivv  v   i v  vvv           i  vvv 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_55737531_5   3913 TATTTAATAAATGGTGCTGGGAAAACTGGCCAGCCATATGTAGGAAGCTG 3962
                          v  i  i              v      vi ?   i   i ii iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_55737531_5   3963 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 4012
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_55737531_5   4013 GAAAGACTTAAATGTTAGTCGTAAAACCATAAAAACCCTAGAAGAAAACC 4062
                         v ?    i       v  vvv      i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_55737531_5   4063 TAGGCA-ATACCATTCAGGAGATAGGTATGGGCAAGGACTTCATGACTAA 4111
                             ?i- v i -   iv  vv v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_55737531_5   4112 AACACCAAAAGCAATGGCAAGAAAAGCCAAAATTGACAAATGGGATCTAA 4161
                         i            vvi    v     vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_55737531_5   4162 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4211
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_55737531_5   4212 AGGCAACCTACAGAATGGGAGAAAAGTTTTGCAGTCTACTCATCTGACAA 4261
                           i     i                vv      ivii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_55737531_5   4262 AGGGCTAATATCCAGAATCGACAATGAACTCAAACAAATTTACAAGAAAA 4311
                         i  i  vi          vv i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_55737531_5   4312 A-ACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACACTTC 4360
                          -     i     v  i? v  i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_55737531_5   4361 TCATAAGAAGACACTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 4410
                           vv       i ivi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_55737531_5   4411 ATCACTGGCTAT 4422
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (142 / 109)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


2916 27.89 0.87 2.07  chrX_55755465_55761871.rev     4999  5916 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_55755465_5   4999 GGAAGAACATTCCATGCTCATGGGAAGGAAGAATCAATATCATGAAAATG 5048
                             ii i  i     i      ivv      v i     ii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_55755465_5   5049 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATGAAGCT 5098
                           v     v     iv i  i  i        i  v     i  v  iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_55755465_5   5099 ACTAATGACTTTCTTCACAGAT-TTGGAAAAAACT-ACTTTAAAATTCGT 5146
                         v i iivi i  i  ii    v-   -- v  i  - iii        i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_55755465_5   5147 ATGGAACCAAAAAAGGGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGA 5196
                               viiv  ii iv  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_55755465_5   5197 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5246
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_55755465_5   5247 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGGGATATAGATCA 5296
                                i   i    ii         i iv ii i  iv          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_55755465_5   5297 ATGGAACAGAAC--AGAGCCCTCAGAAAGAACACCACTTATCTACAACTA 5344
                               i    i--    i  --     v  vv   ivi  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_55755465_5   5345 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5394
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_55755465_5   5395 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCTTATGTAGAAAGCTG 5444
                          v  i  i              v      v  ?  vi   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_55755465_5   5445 AAACTGGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAGATGGAT 5494
                           ii    i    v   i     v    i         i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_55755465_5   5495 TAACGACTTAAAGGTTAGACCTAACGTTTTAGGTCTAAAACCATAAAAAC 5544
                         i ?v   i    v  v   ------------- -       i      vi
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGA-------------G-CTAAAACTATAAAACT 533

  chrX_55755465_5   5545 CCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATTGGGCAAG 5594
                          i           v    ?i v viv   iv   v v  -i  i     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAAT 582

  chrX_55755465_5   5595 GACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCTAAAATTGA 5644
                          ii   v ivv  vi            vvi          vv     v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_55755465_5   5645 CAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA 5694
                         i    v   ii v  i   v v  i i   i  ii vv    i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_55755465_5   5695 CCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCACAATC 5744
                         i  vv i      v  i     i   i             v  ii   vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_55755465_5   5745 TACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACA 5794
                         i ivi      i  i  i  vi          v  i  v      vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_55755465_5   5795 AATTTACAAGAAAAAAACAA----CTCCATCAAAATGTGGGAGAAGGACA 5840
                          v iv i  v     i    ---- i v  i?   vi    vi     iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_55755465_5   5841 TGAGCAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATG 5890
                            ii     i     v        i  vi viii     v  i      
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_55755465_5   5891 AAAAAATACTCACCATCACTGGCCAT 5916
                             i  i    v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (150 / 102)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 3.00 (27 / 9)  


2773 26.98 3.16 0.68  chrX_55787876_55793657     4404  5289 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55787876_5   4404 TGGAAAAACTTTCCATGCTCATGGATAGGAAGAATCAATAT-G--AAAAT 4450
                               i iv i     i        v      v i     - --  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55787876_5   4451 GCCCATATTGCTCAAAGCAATTTATAGTTTCAATGCTATTCCCATTAAAC 4500
                          v v   i v i    vii  i  i  v     i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55787876_5   4501 TGCCATTGACATTCTTCACAGGATTAGAAAAAAAAAT--TAAAATTCAC- 4547
                          v   vivi v  i  ii   i v v  v  ivvi  --         i-
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_55787876_5   4548 TAAAAA------AGATCTCCAATAGCCAAGACAATCCTAAGTAAAAAGAA 4591
                          ii   ------i  i ivv         i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_55787876_5   4592 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 4641
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_55787876_5   4642 CAGTAACCAAAACCGCATGGTACTGCTGCAAGAACAGAAACATAGACAAA 4691
                               i   i  v ii        viii   i i   v i     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_55787876_5   4692 TGAAACTGAATAGAGAACTCAGAAATAAGACTGTCTACCTACAACCATCT 4741
                           i  iv    v    iii         iv ii vi ii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_55787876_5   4742 GATCTTTGACAATCCTGACAAAAACAATCAATGGGGAA-GAAT--TCCTT 4788
                            i  i     vvv  v   i v  v           -    --  i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_55787876_5   4789 ATTTAATAAATGGTGCTGGGAGAATGGGCTAGTTATGTGCAGAAAATTGA 4838
                         -- i  i              v  iv  v  ?ii ii    i  i v   
  L1M4_orf2#LINE/    401 --TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_55787876_5   4839 AACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGATT 4888
                          ii         v   i                 i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_55787876_5   4889 AAAGACTTACATGTAAAATCTAAAACTTTAAAAACTGTAGAAGAAAATCT 4938
                          ?    i  v      i v        v     viiv          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_55787876_5   4939 AGGCA-ATACCATTCAAAACATAGGCACAGGCAAAGATTTCCTG---ATG 4984
                            ?i- v i -   ivi  v v  vvi      v i    i i---   
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_55787876_5   4985 A----AAATGGCAAAAGCAATGAAAGCAAAAATTGACAAATGGGATCTAA 5030
                          ----   -i   v      ii    v      v  i    v   ii v 
  L1M4_orf2#LINE/    598 ACACCAAA-AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_55787876_5   5031 TTAAACTAAAGAGCTTCTGCACAGCAGAAGAAACTATAATCAGGGTGAAC 5080
                          i   v v  i i   i  ii vv  i i  v     v vv ii     v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_55787876_5   5081 A-ACAACCTATAGAATGGGAGAAAATATTTTCAAACTATGCATCTGACCA 5129
                          -      i i                   v    ii  ii      iv 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_55787876_5   5130 AGTTCGAATATCCAGCATCTATAAGAAACT--TA-AACTTA-CAAGAGAA 5175
                         i vv vvi       v  v     ii    --  -    i -i  v -  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA-AA 795

  chrX_55787876_5   5176 AAAACAAACAACCCCATTAAAAAATGGGCAAAAGACATAAACATACACTT 5225
                           i     i     v   ?             i  iv i  i v   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_55787876_5   5226 CTGAAAACAAGACATACATGTGGCCAACAAGCATATGAAAAGAAAGCTGA 5275
                           vv   v    i     vi       i     i         v-   v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCA 894

  chrX_55787876_5   5276 ATATCACTGATTGT 5289
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.79 (34 / 19)  


 268 27.22 7.40 7.40  chrX_55838077_55842848.rev      100   437 (4335)    L1M4_orf2#LINE/L1      380   717 (191)  

  chrX_55838077_5    100 AATGGGTAGAAATGGACTATGTGTTTT----AAATGGTGACTGG-ACAAC 144
                               --    --  v  -  v    ----        -    -     
  L1M4_orf2#LINE/    380 AATGGG--GAAA--GAATA-GTCTTTTCAACAAATGGTG-CTGGGACAAC 423

  chrX_55838077_5    145 CATATAGTCATATGGGAAAAGATAAAATTAAACCTCTTCCTTATGTTACA 194
                         iiv   ?i  i   vi   ii  i  i  ii   i  v   i iii--  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC--CA 471

  chrX_55838077_5    195 TATACAAA---TGAGTCATAGGTACATTAAAG---TA--TG-AAAAGC-A 234
                                 --- i v   - ii iv  i ?  ---  --  -  i   - 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCA-AAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_55838077_5    235 AAATGGCAAATATTTT-GAAGAAAACATAAGA--AAACTCTGATAAAACA 281
                            ivii   vv i  -            i ?--   iii vi i -- v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA--CC 568

  chrX_55838077_5    282 AATCAGAACAAGGAAAGGTTTCTTAAGATGTAA----AAATGTACAA--A 325
                         -- ii ivi i v  v         -   i i ----   v i    -- 
  L1M4_orf2#LINE/    569 --TTGGGTTAGGCAATGGTTTCTTA-GATATGACACCAAAAGCACAAGCA 615

  chrX_55838077_5    326 GCATAAGAAAAAAAAACATCCATTTGAGTATCTCAATAGTTAAAACATTT 375
                         i  v         v i-  vv   v  v viv    v v v     v   
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAG-ATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_55838077_5    376 AAACACTGAAATGACATAAACA-GAATTTTAAAAGAGTGTGCTATTAACA 424
                         ivi -i v   v    iv v  -   vv v      ---------i   v
  L1M4_orf2#LINE/    665 GTGC-TTCAAAGGACACTATCAAGAAAGTGAAAAGA---------CAACC 704

  chrX_55838077_5    425 TAAAAGATGGGAG 437
                         i v ii       
  L1M4_orf2#LINE/    705 CACAGAATGGGAG 717

Transitions / transversions = 1.34 (51 / 38)
Gap_init rate = 0.07 (24 / 338), avg. gap size = 2.08 (50 / 24)  

2869 26.06 1.53 2.51  chrX_55838077_55842848.rev     3365  4281 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55838077_5   3365 TGGAAGAATATTTCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3414
                              ii    ii    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55838077_5   3415 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCAGCATCAAGC 3464
                            v     v     iv i  i  i        i  v   vvi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55838077_5   3465 TACCAATGACTTTCTTCACAGAA-TTAAAAAAAAAACTCTTTAAATTTCA 3513
                          v   iivi i  i  ii     -  i v  ivvi ii  --   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chrX_55838077_5   3514 TATGGAACCAAAAAAGAGCCCGTATAGTCAAGACAATCCTCAGTGGAAAA 3563
                                viiv  ii  v  v v    i   i      i ----------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT---------- 188

  chrX_55838077_5   3564 AAAAAAGAAAAAAAAAAAATCTGGAGGCATCATGCTACCTGACTTCAAAC 3613
                         i        i  v   i---i      vv   ii  v  ii i      v
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAG---TTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_55838077_5   3614 TACACTACATGGCTACAGTAACCAAAACGCCATGGCACTGGCACCAAAAC 3663
                         ivi      vi          i   i  ivii   i       iv ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_55838077_5   3664 TGATATATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACA 3713
                         v  i       i        i    iv   ivii         vv   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_55838077_5   3714 CATCTACAACCATCTGATCTTTGACAAACCTGGCAAAAACAAGCAATGGG 3763
                            i  iiii  vi    i  i     ivv  v   i v  vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_55838077_5   3764 GATAGGATTCCCTGTTTAATAAATGGTGTTGGGAAAACTGGATAGCCATA 3813
                           v  i  vvi  v  i  i        i     v         ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_55838077_5   3814 TTCAGAAAACTGAAACTGGACCACTTCCTTACACCCTATACAAAAATTAA 3863
                          v  i  i v    ii      v  v   i     v              
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_55838077_5   3864 CTCAAGATGGATTAAAGACTTAAACGTAAGATGTAAAACCATAAAAACCC 3913
                              i      i ?    i    i      vv      i      vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_55838077_5   3914 TAGAAGAAATCCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGA 3962
                                  v v    ?i- v i -   iv   v v  vv i     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_55838077_5   3963 CTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACA 4012
                         i   v iiv  vi            vvi          vv     v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_55838077_5   4013 AATGGGATCTAATTCAA-TGAAAGAGCTTCTACACAGCAAAAGAAACTAT 4061
                            v   ii v  iv  - v   i -   i iii vv    i  v     
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chrX_55838077_5   4062 CATCAGAGTGAACAGGCAACCTAAAGAATGGGAGAAAATTTTTAC----C 4107
                           vv i      v  i     i v               v   i ---- 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_55838077_5   4108 ATCTCTCAATCTGACAAACGGCTAATATCCAGAATCTACACAGAACT--T 4155
                           v ----      i  iv i  vi          v  i v      -- 
  L1M4_orf2#LINE/    734 ATAT----ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_55838077_5   4156 A-AAC-CAATTTACAAGAAAAACAAA--ACCCA-TGAAAAAGTGGGCGAA 4200
                          -   -    v- i  -   i     --     - v?    i     i  
  L1M4_orf2#LINE/    780 ACAACTCAATA-ATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_55838077_5   4201 GGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCGGCCAACAAAT 4250
                             v    i     i     v        i  vi vii      i  ii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_55838077_5   4251 ATATGATAAAAAGCTCATCATCATTGGTCAT 4281
                          i    v  i v     v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.18 (37 / 17)  


2935 28.40 1.56 0.56  chrX_55845346_55851732     4997  5894 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_55845346_5   4997 GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATG 5046
                             ii i  i     i      i v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_55845346_5   5047 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAATCT 5096
                           v     v     iv i  i  i        i  v     i     vv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_55845346_5   5097 ACCAATGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTAAAGTTCAT 5144
                         v   iivi i  i  ii    i-   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_55845346_5   5145 ATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGA 5194
                               viiv  ii  v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_55845346_5   5195 ACAAAGCTGGAGG-----CATGACCTGACTTCAAACTATACTACAAGGCT 5239
                               i      -----  ivv  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_55845346_5   5240 ACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATATAAACCA 5289
                                i   i    ii     i   i iv ii i   v     i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_55845346_5   5290 ATGTAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACTA 5337
                            v  i    i--    i  --        vv iii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_55845346_5   5338 TCTTATCTTTGACAAACCTGACAAAAACAAGTAATGGGGAAAGGATTCCC 5387
                         vi v  i  i     ivv  v   i v  vvi           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_55845346_5   5388 TATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATGTGAAGAAAGCTG 5437
                          v  i  i          i   v      v  ?   ii  v i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_55845346_5   5438 CAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGTTGGAT 5487
                         v ii    i    v   i     v              i    iv     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_55845346_5   5488 GAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5537
                         v ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_55845346_5   5538 TAGGCATTACCATTCA-GGTCATAGGCATGGGCAAGGACTTCATGTCTAA 5586
                             ?i v viv   i- ii v i  i- i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT 596

  chrX_55845346_5   5587 AACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTAA 5636
                         i            vvi          vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_55845346_5   5637 TTCAACTAAAGAGCTTCTGCAGAGCAAAAGAAACCACCATCAGAGTGAAC 5686
                          iv  v v  i i   i  iivvv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_55845346_5   5687 AGGCAACCTACAGAATGGGAGAAAACTTTCACAACCTACTCATCTGACAA 5736
                           i     i                iv  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_55845346_5   5737 AGGGCTAATATCCAGAATCTATAATGAACTCAAACAAATTTACAAGAAAA 5786
                         i  i  vi          v     v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_55845346_5   5787 AAACAA----CCCCAGCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5832
                          i    ----   v vi?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_55845346_5   5833 TCAAAAGAAGACATTTATGCAGCCGAAAGACACATGAAAAAATGCTCATC 5882
                           v        i  vi viii   i v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_55845346_5   5883 ATCACTGGCCAT 5894
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (152 / 99)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 2.11 (19 / 9)  


3945 21.82 2.14 0.00  chrX_55865613_55867659.rev      668  1556 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55865613_5    668 TGGAAACACATCTTGTGTTCATAGACTGGAAGACTTAATATTGTTAAGAA 717
                               v i   iii       i  i                       v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55865613_5    718 GCCACTACTACTCAAAGCAATCTACAGATTCAATGCAATCCTTATAAAAA 767
                          v  v    v i    vii              i       i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55865613_5    768 TCCCAACAGTAGTTTTTGCAGAAATAGAAAAATTCTTCCTAAAATTCATG 817
                              i v ivv             v  v  ii vv             i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_55865613_5    818 TGGAATCTCAAGGGACCCTGAATAGTCAAAGCCATTTTCGAGAAGAACAA 867
                              viv          v      i    i v  i  vi i     v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_55865613_5    868 CAAATTTGGAAGCTTCACAGTTCCTGATTTCAAACCTTAATATAG-GTTA 916
                             v     i vi     v    ii        v    v  i i- i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_55865613_5    917 CAGTGATAAAAACACTGTAGTACTGGCATAAAGACAGAAAAATATACCAA 966
                             i  v  i   v   i            i  i   v v   v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_55865613_5    967 TGTAACACAATAGAAAGCCAAGAAATAAACTGTTACATATATGGTTAAAC 1016
                           v  i v   v  i  i v          ivv     v      i  vi
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_55865613_5   1017 GATATTTGCCAGGGGTGCCAAGACCACTCAATGAGGAAAGGACAGTCTCC 1066
                            v  i v  i              i      i      i i     ii
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_55865613_5   1067 TCAACAAATGGCATTAGGGAAACTGAATAACCACATGAAGAAGAATAAAA 1116
                                    iii i  iv     i   ?       v i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_55865613_5   1117 CTGGACCCTTATCTTACACCATATACAAAAATTAATTCAAAATGGATCAA 1166
                         i       i  i  i                    i             ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_55865613_5   1167 AGACCTAAC-----GACCCAAAATTATAAAATTCCTAAAA-AAAACACTG 1210
                                 v-----  v i    i       i  i  i  -      iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_55865613_5   1211 GGGGAAAGTTTCATGACATTGAACTTGACAATGATTTCTTGGATATGTCA 1260
                          ? v   vi   i    v   iii v i     i      i      v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_55865613_5   1261 CCAAAAGCATAGGAAATCAAAACAAAAATGGACAAATGGAAGTACATCAT 1310
                                  i i v  iv   iv      i  i    v i v v     v
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_55865613_5   1311 ACTTAAAAACTTATGTA--TCAAAGGACATGATCCAAAGACTGAAAAGGC 1358
                          v          v   i--          iv   v i i v       i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_55865613_5   1359 AACTTATAAAATGGGATAAAATATTTACAAATAAAATATCAGATAAAAGG 1408
                            ii i i       v         i     v v     v     ii i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_55865613_5   1409 TTAATATTCAGAATCCATAAAAAATTCCTGCAACTCAGCAACAAAATGTG 1458
                         i vi   i      vi     i  i  i i       ii  i    v vv
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_55865613_5   1459 AAATA---CAA-------ATGGGCAACTGACTTGAATAAACATTTCTCCA 1498
                              ---   -------        vv  i       i           
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_55865613_5   1499 AAGATGATAAACAAATGACTAATAAGCATATGGAAAGATGTTCAACACCA 1548
                             v    v       i i        i   i       i      i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_55865613_5   1549 CTAATCAT 1556
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.55 (116 / 75)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 3.17 (19 / 6)  


3175 25.14 1.44 0.89  chrX_55877196_55883559     3184  4086 (2278)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55877196_5   3184 TGCAATGATATTCTATGTTCATGGATTGGAAGAATCAACATTGTTAAAAT 3233
                           v  v     i i                   v i  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55877196_5   3234 GTTCACACTACCCAAAGGTAGTCTGCAGATTAAATGCAATCTCTACGAAA 3283
                          viv i   v      v- ii   i      v  i      i   iv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_55877196_5   3284 ATGCTAATGACATTCTTTACAAAAATAGAACAAA--AATCATAAAATTTA 3331
                           v i iivi v  i   i  i    v  -   i--i   v       i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chrX_55877196_5   3332 TATGGAGTCACAACAGACCTAGAATAGCCAAAGTCATCCTGAGCAAAAAG 3381
                               ivii   vi    i            iiv   i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_55877196_5   3382 AAGAAAACTGGAGGAATCACACTACCATACTT-AAAATTACACTGCAGAG 3430
                           v   ii       v       v  vv i  -    i -i   i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_55877196_5   3431 CTGTAGTAAGCAAAACAACATGGTACTGGCATAAAAATAGGCACATAGCA 3480
                           ii     v   i   iii              ii    i  i    - 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG-A 296

  chrX_55877196_5   3481 CAAATGGAACAGAATGGAGAATTCAAAAATAAATTAATGCATTTACAGTG 3530
                         iv       i     v    i i  i       iiv  i      ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_55877196_5   3531 AACTCATTTTTGACAAAAG--CCAAGAACATACATTGAGGAAAGGACAGT 3578
                           i v     i     ii --      v   v  v  i      i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_55877196_5   3579 CTCTTCAATAAATTGTGCTGGCAAAGCTGGATATTTATAAGCAGACTCAA 3628
                           i     i    v       v v i       ?ii i v   i vvv v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_55877196_5   3629 AAAACTATACCCTTATCTCTTGCCATACACAAAAATCAAATCAAAATTGA 3678
                         i  ii iv    i  i   vii     i        i  v       v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_55877196_5   3679 TTAACGACTTAAATCTAAGACCTCAAACTATGAAACTAGTACAAGAAAAC 3728
                          i ?v   i     v     v  v       i     vv  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_55877196_5   3729 ATTGAGGAAACTCCCCAGAACATTAGAGT-GGCAAAGATTTTTTGAGTAA 3777
                           v i? v  v  ii ivi  v  i iv -     v i   i  iii  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_55877196_5   3778 TACCCCACAAAAACATGCATCTAAAACAAAAATGGAAAAAT-AGATTACA 3826
                         v  v   v  iv   v   v v   iv      i  v    -i  i v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_55877196_5   3827 TCAAT-TTAAAAAGCT--GTACAGCAAAGGAAACAATCAACGAAATGAAG 3873
                             v-       vi --  i vv       v  v     vi  i    i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_55877196_5   3874 AGACAACCCACAAAATGAGATAAAATATTTGCAAACTTCCCATAT--GAC 3921
                                     i    i  v              --  vi    --  i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAA--TCATATATCTGAT 744

  chrX_55877196_5   3922 AAGGGATTAATAACCAGCATA-ATAAGGAGCTCAAACAACTCTATAGGAA 3970
                               i vi  v    v   -    i  i   vv       v   iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_55877196_5   3971 AAAAAATCTAATAATCTGATCAAAACATGGGAAAAAGATTTGAATAGACA 4020
                            i -- v     i ii  i?   v     v   i              
  L1M4_orf2#LINE/    795 AAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_55877196_5   4021 TTTCCCAAAAGAAGACATACAAATGACAGACAAGCATATGAAAAGGTGCT 4070
                             i v        i         i vi i     i        i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_55877196_5   4071 CAATGTCATTTACCAT 4086
                            ii   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (133 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.40 (21 / 15)  

2447 27.15 4.41 1.70  chrX_55877196_55883559     4988  5871 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55877196_5   4988 TGGAAA-ACATTTCATACTCATGGATAGGAAAAATCTATATTGTTAAAAT 5036
                               - i  ii   ii        v    i v iv          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55877196_5   5037 AACCATACTGCCCAAAGCAATTTACAGATCGAATTCTATTTCTATGAAAC 5086
                         ii v     v      vii  i       iv  iv v  ii    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55877196_5   5087 TAACAAGGTTAC--TTTTCACAGAATTTGGAAAAACT-ATTCCAAGAGTC 5133
                          vv  -- i i --    ii     v   - v  i  -  i i  i v  
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTC 147

  chrX_55877196_5   5134 ATATTGAACCAACAAAGAACCT-GAATAGCCAAAGGAATTCTAAGCAAAA 5182
                             v   vii-   i i   i-           iv   ii i --    
  L1M4_orf2#LINE/    148 ATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAA 194

  chrX_55877196_5   5183 GAAG--CAAAGCCAGAGGCATCACACTACTTGACTTCCAACTGTACTACA 5230
                             --     iii    vv       v iii i   v  viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_55877196_5   5231 AGAATACAGTAATTAAAACACCATGGTACTGATACAAAAACAGA-A-ACA 5278
                          iiv         i  i   vii        ii i  ii i   - - i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_55877196_5   5279 GACCAATGGAGCAGATTAGGGAACCTAGAAACAAAGCCACACACCTGCAA 5328
                           i       ii   v v i  ii i     i   v   i   ii iiii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_55877196_5   5329 TCATTTGATCTTCAACAAAATT-TCAATAACAAACAATG-------AATA 5370
                            v     i   i    iiv -i   v v  vv     -------    
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_55877196_5   5371 ACCTTTTCAAGTAGTGGTGATAGCATAACTGGCTAGCCATAAGCAGAAGA 5420
                         ii        vv i     v i v i      v  ?   i v   i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_55877196_5   5421 TTGAAACTGGACTCTTGTCTTTTTTCATATACAAAA-TCAACTCAAGATG 5469
                         v    ii     i i ii  ivivi           - i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_55877196_5   5470 GATTAGAGACTCAAATGTAAGCCCTAAAGCTGTATAAACCCT-AGAAGAA 5518
                            i ?    ii         vv     i  i  -    i  -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAA 543

  chrX_55877196_5   5519 AACCTAAGACATA---CTATTTTGGACATAGGCCATGGCAACGATTTCAT 5565
                            v  i ?-i  ---  - iv  iv v i  ii -     i i    --
  L1M4_orf2#LINE/    544 AACATAGGN-GTAAATCT-TCGTGACCTTGGGTTA-GGCAATGGTTTC-- 588

  chrX_55877196_5   5566 GTCAAA---GACTCCAAAAGCAATATCAACAAAAACATAAATTGACAAGT 5612
                         - i i ---   v         vv v        iv v    v  i  i 
  L1M4_orf2#LINE/    589 -TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_55877196_5   5613 GGGAAGTAATTAAA-TTAAAGAGGTTC-TACCTAGCAAAAGAAATGATCA 5660
                         v   vv v  i   -     i vv  i- i i --    i  v iv    
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCA 685

  chrX_55877196_5   5661 C-AGAGTAAACAGTCAACCTACAAAATGGGAGAAGTTATTTGCAAACTAT 5709
                         v- i   i  v  v     i   i          iv          ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_55877196_5   5710 GCATTTGACAAAGATCTAATATCCAGAATCCATAAGGAACTT----AAAT 5755
                         ii  i   i  i iv  vi          vi    i     i----  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_55877196_5   5756 TAACAAGAAAAA-----ACAACCCCATT-AAAAATGGGCATAAGACATGA 5799
                         i  i  v     ----- i     v   -           v i  iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_55877196_5   5800 ACAGATACCTCTCAAAAGAGGACATACATGCTATCAACAAGCATATGAAA 5849
                          i   i ii    v     i  i     viivii   i     i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_55877196_5   5850 A-ATTCTCAACGTCACTGATTAT 5871
                          -  v      i   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (155 / 82)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 1.80 (54 / 30)  


2458 25.86 3.11 2.33  chrX_55900809_55906493.rev     4294  5194 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55900809_5   4294 TGGAAAAACATTCCATTATCATAGATAGAAAGAATCAGTATTATTAAAAT 4343
                               i i  i    vv    i   v i    v i i    i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55900809_5   4344 GGCCATATTCCAAAAAGCAATTT-CTGATTTCAATGCTATTTCTATCAAA 4392
                            v   i   vv   vii  i - v    -   i  v  ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT-CAACGCAATCCCTATCAAA 99

  chrX_55900809_5   4393 CTACCAATGACATTCTTTACAGAACCAGAAAAAAACT-ATTCTATAATTC 4441
                         v v   iivi v  i   i     -- vvi v  i  -  i   v     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chrX_55900809_5   4442 ATATGGAACAAAAAAGTATCCCAAATAGTCAAACCAATCCTGTGCATACA 4491
                                 vviv  i v i  vi     i    v     i  viv viv 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_55900809_5   4492 GAACAAAACCAGAGGCAC-CACTCTACCTGACTT-AAATGGTATTACAAG 4539
                                iiii    -  -   v  v  ii i  -   vvv  i     i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_55900809_5   4540 GCTACAGTAACCAAAACAGCATGGTACTGGCACAAAAACGGGTTCATAGA 4589
                                   i   i    ii           i  ii ii iivi     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_55900809_5   4590 TGAATGGAACAGGTTAGAGAGCCCAGAAATAAAGCCACATACCTACAGTC 4639
                          v       i  iv v     i           v   i i ii  ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_55900809_5   4640 ATCTGACCTT-GACAAAG---TCAAAAACAAGAAGCAATGGAAAAATGAA 4685
                          vi   ii  -     i ---i   i v  vv---      ii   -   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAA-GAA 392

  chrX_55900809_5   4686 T--TCCTATTCTATAAATGGTACTGGGATAACTGGCTAGACATATGCAGA 4733
                          --  i -   v i       i      i      v  ?v  i     i 
  L1M4_orf2#LINE/    393 TAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_55900809_5   4734 ATATTTGAAGT--GAACCCTATCTTTTCCCCACATACAAAAATAAACTCG 4781
                          v v -     --  v     i  iv- v   i          v     i
  L1M4_orf2#LINE/    442 AGAAT-GAAGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTCA 489

  chrX_55900809_5   4782 ATGTGAATTAAAGACTTAAATGCAAAACCTAAAACTATAAAAACTCT-AG 4830
                          vi  i  i ?    i      i  i v              -    -  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAG 538

  chrX_55900809_5   4831 GAAAAATCCTAGGAATATAAT--TC-TGAACATAGGCCATGACAAATATT 4877
                         i i   v v    ?i  -   --  -   v v i  ii - i   vvi  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTA-AATCTTCGTGACCTTGGGTTA-GGCAATGGTT 586

  chrX_55900809_5   4878 TCAT-GATGAAGACTCCAAAATC-TA--TAGCAAAAACAGAAATGGATAA 4923
                           v -   - v   v      v -i --i i     iv i    i     
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_55900809_5   4924 TTGAGACCTAATTAA--TTAAACATCTT----CTGCAAAGAACAATAAAT 4967
                         v vi   i v  i  --     v ii  ----  v     i   -----i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-----C 680

  chrX_55900809_5   4968 TATCAAGAGAGTAAACAGACCAACTACACAACAGAAGAATATATTTGCAG 5017
                                 i   i  v    v v i   v  ii i    v         i
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_55900809_5   5018 ACTATGAATCCAA-AAAGGTCTAATATCCAGAATCTATAAGGAACTTCAA 5066
                          ii  iv   ii -  i  v  vi          v     i     iiv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_55900809_5   5067 CAAATTAACAAGCAAAAACA-AAACAACCACATTAACAAATGAGCAAAAG 5115
                            v i  i  -i     v -   i    vv   ? v     i     i 
  L1M4_orf2#LINE/    781 CAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_55900809_5   5116 ACATGAACAGACACTTCTCATAAGAAGACATACAAGTGGACAAGAAGCAT 5165
                          iv    i     i     vv       i      i   v   v     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_55900809_5   5166 ATGAAAAAATACTAAGCATCACTAATCAT 5194
                                i  i  v i     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (139 / 90)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 1.53 (49 / 32)  


2037 26.20 3.46 3.06  chrX_55942714_55944451.rev      495  1246 (491)    L1M4_orf2#LINE/L1      154   908 (0)  

  chrX_55942714_5    495 AAATTTAAAA-ACCCA-AATAGCCAAGGCAAACTTCAGCAAAAAGAACAA 542
                             vi  ii-     -         ii   v   v iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_55942714_5    543 AGCTGGAGG-----CACTATCTGATTTCACATTATATTAGAAGGCTATAT 587
                           i      -----    vi ii      v viv  i  v  i    i v
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_55942714_5    588 TCATTAAAACAGCATGGTACTGGCATAACAATAGACACATACA-CAAAGA 636
                          v  i  i    ii              vi       i   v -   v i
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_55942714_5    637 AATGGAATAAAAATTCCAGAAATAAACACATGTGTTTTCATTCAATTGAT 686
                            i    vi i v             v   iii   viiv         
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_55942714_5    687 TTTTGACAAAGATGCCAATAATATACAATGGGAAAAGGACAGTCTTTTTA 736
                            i     i i      v vi  v       i    i i        i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_55942714_5    737 ATAAATGATGTTGGGTAAACTGAATATCCATATGCCGAAGAATGAAATTG 786
                          i     i  i    vv     i   ?   i    vi         i   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_55942714_5    787 GACCTTTATTTCACACTGCACATGAAAATCACCTCACCATGGATTACAAA 836
                             ii  ii      iii i ii     i v    vv      i ? i 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_55942714_5    837 TTTAAAGAAAAGACCTGAAAATGTAAAAATACTAAAAGAAAATATAGCAG 886
                         ii    viv    v  i   v i     v vi  i       i    v? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_55942714_5    887 AAAAAACTACATGAAATTGGTCT-GGCAATGATTCTTTGGG-ATTACATC 934
                         v   v-  v i   vv    vi -       i  ii  i i-  v   - 
  L1M4_orf2#LINE/    554 TAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA-C 601

  chrX_55942714_5    935 CAAAATCTTAGGCAACACGAACAAAAATAGACAAACCTGTTTGTAACAAA 984
                              v vi i      vi iv         i   iiv vi vi v    
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_55942714_5    985 --CAAAAATGATTTTGTAACGCAAAGGAAACAA-CAAATATTTGCAAGCC 1031
                         --i     i--      iviv       v  v -   iv vv  v  i--
  L1M4_orf2#LINE/    652 ATTAAAAAC--TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA-- 697

  chrX_55942714_5   1032 AACATCTGATAAAGATTTGCTATACAAAATAT--GTAAGGTATTCAATAT 1079
                         i   v iv i i -  vv ---- v       -- i  ivi  ---    
  L1M4_orf2#LINE/    698 GACAACCCACAGA-ATGGG----AGAAAATATTTGCAAATCAT---ATAT 739

  chrX_55942714_5   1080 ---GTAAGGTATTCAAACAAAGGTATTCAAAATATGTAAGGTATTCAAAC 1126
                         ---i     v i i--------    i  i     i   i v i  vv  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTT--------GTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_55942714_5   1127 AAATGACTAGCAAGAA-ACAACTA------TTTTAAAACAGACAAAAGAT 1169
                           v v v  ii  i  -    v  ------  ?v    ii i    i   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_55942714_5   1170 CTGAAAAGACATTTCTC-AAAGAAGACATACAAATGGCCAACAGGTACAT 1218
                         i    v           -        i              i i i    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_55942714_5   1219 GAAAAAAATGTTCAGCATTACTAATCAT 1246
                              i -  i   i   i ????????
  L1M4_orf2#LINE/    882 GAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (119 / 74)
Gap_init rate = 0.03 (22 / 755), avg. gap size = 2.23 (49 / 22)  


2391 28.54 1.20 3.05  chrX_55947916_55954159.rev     4836  5753 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_55947916_5   4836 ATATTCCATGCTCATGGATAAGAAAAATCAATATAATAAAAATGGCCACA 4885
                             i     i        vi   i v i     vi v  i     v i 
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_55947916_5   4886 CTATCCAAAGTAATTTATAGACTCAATGTTATTCCCATTAAACTACCA-T 4934
                           vi     v i  i  i   i    i iv  i  i  i   v v   -i
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_55947916_5   4935 TGACATTCTTCTTGGAATTAGAAAAAATGATTCTGAAACTTATATGCAAC 4984
                           v v  i  viv i    -  v  iv    i  i   i i     v  v
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_55947916_5   4985 CAAAAAAGAGCCCAAATAGACAAGACAATCCTAAGCAAACAGAACAAAAC 5034
                         iiv  ii  v  vi     v   i      i i iv  iv        ii
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_55947916_5   5035 TGGGGGCATCATGCTATCTGACTTCAAACTATAGTATAAGGCTACTGTAA 5084
                            i  vv   ii  vi ii i      viv  v  i  i     v    
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_55947916_5   5085 TCAAAACAGCATGATACTGGTACAAGAACAGAAACATTGACCAATGGAAT 5134
                             i    ii  i      i i   i i   v i  v  i         
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_55947916_5   5135 ATAATAGATAACTCTGGAATAGAATAGATACTCAGAAATAAGACTGCACA 5184
                          v   ---------  ----   i ------i         iv iii   
  L1M4_orf2#LINE/    307 AGAAT---------TG----AGAGT------CCAGAAATAAACCCATACA 337

  chrX_55947916_5   5185 CCTATACCCATCTGATCTTTGGCAAACTTGACAAAGACAAGCAATGGAGA 5234
                         ii   ivi  vi    i  i i   ivv  v   iiv  vv      i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_55947916_5   5235 AAGGATTCCCTATTTAATAATTAGTGCTGTGAGTGCTGGCTACCCATAGG 5284
                            i  vvi  v  i  i  v i      v  vvi    v  ?   i v 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_55947916_5   5285 CAGAAAACTGAAATTAGGCCTCTTCCTTACACCATATACAAAAATTAACT 5334
                           i  i v    i  i i  i  v   i                      
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_55947916_5   5335 CAAGAGGGATTAAAGACTTAAATGTAAAACCCAAAACTATAATAACTCT- 5383
                            i v    i ?    i         i v i          -      -
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTT 536

  chrX_55947916_5   5384 AGAAGAAAATCTAGGCA-ATACCATTTAGGACATAGGCATGGGCAAAAAT 5432
                                  iv    ?i- v i -  iiv   v v  vv i     vii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_55947916_5   5433 TTCAT-GACATAAACACCAGAAGCAATTGCAACAAAAGCAAAAATTCAAA 5481
                            v -  i  i -     i     vvv          v      vv v 
  L1M4_orf2#LINE/    586 TTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_55947916_5   5482 AATGAAATCTAACTAAACTAAAGAGCTTCTACACAGCAAAAGTAACTATC 5531
                            vii ii v ii   v v  i i   i iii vv    i vv      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_55947916_5   5532 ATCAGCATGAACAAAGAACCTACAAAATGGTAGAAACTTTTTGCAATGTA 5581
                          vv ivi    v i v    i   i     v     v v       vvi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_55947916_5   5582 TCCCTCTGACAAAACTCTAATATCCAGAATCTATAAGGA--TATTAAACA 5629
                          viv     i  iivv  vi          v     i  -- v   --  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CA 782

  chrX_55947916_5   5630 AATTTACAAGAAAAAGAAAAACCAC---ATTAAAAAGTGGGCAATAAACC 5676
                          v iv i  v       v   iv  ---   ?    i       vii ii
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_55947916_5   5677 TCAACAGCCACTTCTCAAAAGAAGACATA--AATGGGGCCATCAAACATA 5724
                          v  i  v  i     v        i   --     --   vi  i  i 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGG--CCAATAAGCACA 880

  chrX_55947916_5   5725 GGGAAAAAAAGCTCACCGTCACTGATCAT 5753
                         v -    i v     v i   ????????
  L1M4_orf2#LINE/    881 TG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (148 / 110)
Gap_init rate = 0.02 (17 / 901), avg. gap size = 2.29 (39 / 17)  


3063 27.53 0.66 0.66  chrX_55956974_55963234.rev     4865  5772 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55956974_5   4865 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATCATGAAAAC 4914
                              ii i  i     i i    i v      v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55956974_5   4915 GGCCATACTGCCCAAGGTAATTTAAAGATTCAATGCCAACCCCATCAAGC 4964
                            v     v     iv i  i  v        i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55956974_5   4965 TACCAATGACTTTCTTCACAGAATTGGAAATAGCT-ACTTTAAAGTTCAT 5013
                          v   iivi i  i  ii     v v  v -    - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_55956974_5   5014 ATGGAACCAAAAAAGAGCCTGCATTGCCACGTCAATCCTAAGCCAAAAGA 5063
                               viiv  ii  v  v v  v    viv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_55956974_5   5064 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5113
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_55956974_5   5114 ACAGTAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGATATAGACCA 5163
                                i   i    i          i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_55956974_5   5164 ATGGAACAGAAC--AGAACCCTCATAAATAATGCCGCACATCTACAACTA 5211
                               i    i--   ii  -- v      vv  ii    i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_55956974_5   5212 TCTGATGTTTCACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT--TC 5259
                         vi    v  iv    ivv  v   i v  vvv           i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_55956974_5   5260 CTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5309
                         i  -- i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_55956974_5   5310 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5359
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_55956974_5   5360 ATTAAAGACTTACATGTTAGTCCTAAAACCAAAAAAACCCTAGAAGAAAA 5409
                           i ?    i  v    v  vv       i v    vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_55956974_5   5410 CTGAGGCA-ATACCATTCAGGACATAGACATGGGCAAGGGCTTCATGTCT 5458
                          vv   ?i- v i -   iv   v v ivv i     v  i   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_55956974_5   5459 AAAACACCAAAGACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5508
                          vi        ii  vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_55956974_5   5509 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATCATCATCAGAGTGA 5558
                         v  i   v v  i i   i  ii vv    i  v ii    vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_55956974_5   5559 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5608
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_55956974_5   5609 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5658
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_55956974_5   5659 AAAAACAAACAACCCCATCAAAACACGGGCAAAGGATATGAACAGACACT 5708
                            i     i     v  i?   v i           v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_55956974_5   5709 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTTA 5758
                             v        i  vi viii     v  i          i     i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_55956974_5   5759 TCATGACTGGCCAT 5772
                         v   v ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (142 / 104)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3326 22.83 3.15 1.01  chrX_55983003_55985315.rev      934  1822 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55983003_5    934 TAGAAATACTTCTTGCATTCATAGATTGGAAAATGTAA-GTCATTGAAAT 982
                          i    v iv  iiiii     i        i iv   -i ii  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55983003_5    983 GTCAATGCTACCCAAAACAATCTACAGATTCAATGTGATGTTTATTAAAA 1032
                          v    i  v      vii              i ii  vii   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55983003_5   1033 TTCCAACTG----TTTTGCAGAAATGGATAAGCTAACCCTCAAGTTCATA 1078
                          i   i   ----            v  i     i i   v  i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_55983003_5   1079 TGGAATTGAAAGTGGCCTTACATAGCCTGAATAATCATGAAAAAGAA--- 1125
                              v  v   v i  iviv      vi  i    v          ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_55983003_5   1126 CAAAGTTGGAAGATTCATATTTCCCAATTTCAAAACTTACTAAAAAGGTC 1175
                                   i  i   i i                      v    v v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_55983003_5   1176 CAATTATCTAAAGAGTGTGTTACTGGTATAGAAATAAATATATAGACCAC 1225
                           i v   v i v      v      i   iii   i i       i  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_55983003_5   1226 TGAATTAGAATTTATATTTGAGATATAAACCCTTAACATATATAGATAAA 1275
                           i v       v v v iv   v        v  -   v   i - v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGG-TCAA 348

  chrX_55983003_5   1276 CTAATTTT-GACATGGGTTCCAAGGGTATTCAATAGTAAAAAGATAATCT 1324
                         i i     -    v    v     ivi       i vi   ii   i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_55983003_5   1325 TTTCAATAAATGGTACTAAGAAAACTGGACTTCCATAT-TAAAA-AATGA 1372
                               i       i  ii  v       iv?   i  -i    -     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_55983003_5   1373 TGTCAGATCACCATCTGAAA--ACATACAAAAATTAATT-AAAAGAAATC 1419
                         v  ii  i v i i  v v -- i             i -    vii   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_55983003_5   1420 AATCACCTAAATATATAATCTAAAAC-ATAAAACTCTTAGAAGATCACAT 1468
                          ?vv        i  vi v       -                 vv    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_55983003_5   1469 AGAGGTAAAATTTCATGACCTTGGATTTGGCAATGTATTTTTCGATATGA 1518
                           i?     vi   i         i  v       vv  i  v       
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_55983003_5   1519 CACCAAAAGGTGACAAAAGGCAAAAAAAGGAAAAAAATATAAAAGTGGGA 1568
                                  ----  v   -   v     i     v v     -- v   
  L1M4_orf2#LINE/    599 CACCAAAAG----CACAAG-CAACAAAAGAAAAAATAGATAAA--TTGGA 641

  chrX_55983003_5   1569 CTTCATGAAAATTAGAAGCTTCTGTGCATGAAAGTACATTATCAAAAAAG 1618
                               v       i  i   i     v v    v   i      i    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_55983003_5   1619 -GAGAAGACAATCTACAAAA---AAGAGGGTACTTTCAAATCACATATCT 1664
                         -  i       i i   i  ---i   iii  i  v       i      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_55983003_5   1665 GATAAGGCTGTAATATTCAGAATACGTAAATAATACCTACAATTTAATAA 1714
                                vvv vi   i       ii    v  iv i     i i     
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_55983003_5   1715 CAAAAAGACAGA----CCAAT-----AATAGGCCAAAATCTTGAGAAGAT 1755
                         i         i ----     -----   i   v  iivi    iv   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_55983003_5   1756 TTTTTTCCAAAGAAGAAATAAAAATGGCCAAAAAGTTCATGAACAAATGT 1805
                         v   i           v   v          v   iv      v i   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_55983003_5   1806 TAAACATCACTGCCAGG 1822
                          v       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (119 / 81)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.06 (37 / 18)  


3061 28.19 0.55 0.55  chrX_55985846_55991300.rev     4057  4964 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_55985846_5   4057 TGGAAGAACATTCCATGTTCATGGGTAGGAAGAATCAGTATCATGAAAAT 4106
                              ii i  i            i v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_55985846_5   4107 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4156
                            v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_55985846_5   4157 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAACGTTCA 4204
                          v   iivi i  i  ii     -   -- v  i  - iii   vi    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_55985846_5   4205 TATGGAACCAAAAAAGAGCCTGCATCGGCAAGTCAATCCTAAGCCAACAG 4254
                                viiv  ii  v  v v  v v   iv     i i ivv iv  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_55985846_5   4255 AATAAAGGTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4304
                           i    v      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_55985846_5   4305 TACAGTAACCAAATCAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4354
                                 i   iv   ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_55985846_5   4355 AATGGAACAGAAT--AGAGCCCTCAGAAACAATGCTGCATGTCTACAACT 4402
                                i     --    i  --     i  vv iii ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_55985846_5   4403 ATCTGATCTTTGACAAACGTGAGAAAAACAAGAAATGGGGAAAGGATTCC 4452
                          vi    i  i     iv   vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_55985846_5   4453 CTATTTAATAAATGGTGCTGGGAAAACCGGCTAGCCATATGTAGAAAGCT 4502
                           v  i  i              v   i  v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_55985846_5   4503 GAAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGGA 4552
                            ii    i    v   i     v i            i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_55985846_5   4553 TTAAAGACTTAAACGTTATACTTAAAACCAGAAATATCCTAGAAGAAAAC 4602
                          i ?    i    i  v v vi      i v   vv  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_55985846_5   4603 CTAGGCATTACCATACAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4652
                         v    ?i v viv v iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_55985846_5   4653 AACACCAAAAGCAATGGCAACAAAAGCCATAATTGACAAATGGGATCTAA 4702
                         i            vvi          vv v   v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_55985846_5   4703 TTAAA-TTAAATAGCTTCTGCACAGCCAAAGAAACTTCCATCAGAGTGAA 4751
                          i   -     - i   i  ii vv v  i  v   vi  vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_55985846_5   4752 CAGGCAACCTACAAAATGGGAGAAAATTTTTGTAACCTACTCATCTGACA 4801
                         v  i     i   i             v    i  vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_55985846_5   4802 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4851
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_55985846_5   4852 AAAACAAACAACCCCGTCAAAAAGTGGGCAAAGGACATGAACAGACACTT 4901
                           i     i     vi i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_55985846_5   4902 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 4951
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_55985846_5   4952 CATCACTGGCCAT 4964
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (147 / 105)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2036 24.85 9.26 1.18  chrX_56001032_56002703.rev      502  1181 (491)    L1M4_orf2#LINE/L1      174   908 (0)  

  chrX_56001032_5    502 AACCAAAGCAATTCTAAGAAAAAAAAA--AAGCTGGAGGCATCACATTGT 549
                          i     i    ii i i   i  i  --   i      vv     i vi
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_56001032_5    550 CTGACTTCAAAATACATTTCCAGGCTACATTATTCAAAACAGAATAGTAT 599
                          ii i       ivi i v v i      v  v    i    vi i   i
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_56001032_5    600 TAGTATAAA-ACAGACACACAGACAAATGGAACAGAATAGAGAACCAACA 648
                          i i    i- i     i i   iv       i     v    ii v v 
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_56001032_5    649 AATAAAGCTA-------------AAATGATCTCCAGCAAGGATAATAAGA 685
                               v i -------------  v    i i ii     i ivi    
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_56001032_5    686 --ATTTACACTGGGGAAAGGACACCCTCTTAAATAAGTGGTGCTGGGAAA 733
                         --   --  v         i i vi  i  v  i  i           v 
  L1M4_orf2#LINE/    374 CCATT--CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_56001032_5    734 GTTGGATAGTCACATGCATAACAATGAAACTAGACTCTTATCTCTCACCA 783
                         ii      ?i        v  v      ii i   i i  i   v     
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_56001032_5    784 TACACAAAAATCAACCCAAAGTGGATTAAAGACCCAAA------------ 821
                           i        i   i    i     i ?     i   ------------
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_56001032_5    822 -ACTATAAAAATATTAGGAGAAAACATAAAG--AAAACT--GT---CCTG 863
                         -         v v    i          ii?--   v  --  --- i  
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chrX_56001032_5    864 GA-----CATTGGTCT----------ACACAAAAAACATGAGTAAGACCT 898
                          i-----  v    i ----------    v    i  ii  i  -----
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA----- 616

  chrX_56001032_5    899 CAAAAGCAATGACAAAAATATTGGACTTAATTAAA-TTAAAAAGTTTCTG 947
                               v  vi i i v v         v  i   -       v   -  
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TG 665

  chrX_56001032_5    948 CACTGCAAAAGAAATAATCAGCAGAGTGAACAGAAAATCTACAGAATGGA 997
                         ii  v    i  v iv    iv i      v   v  i i         i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_56001032_5    998 AGAAAGTATTTGCAAGTTATTTATCTAACAGGGGACTAATATCTGGAATC 1047
                              i         i i  v     i i i      vi    ii    v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_56001032_5   1048 TACAAGAAACTC----AATTCAACAGGAATAAAACAAATAACCCTATTTA 1093
                           i  ii     ----  i    i iv  v  i           v   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_56001032_5   1094 AAAATGGGCAAAGGACAAGAAAAGACATTTTTCAAGTGAGGACACACAAG 1143
                                        ivv   v        i  v iv  i  i i    i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_56001032_5   1144 CAACCAAGAAACA---AAAAAAA--CTCAACATCAGCAATCAT 1181
                         iii    v  i  ---i    i --          ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (113 / 52)
Gap_init rate = 0.02 (17 / 735), avg. gap size = 4.18 (71 / 17)  


 707 26.26 1.52 1.01  chrX_56010655_56012683.rev        1   198 (1831)    L1M4_orf2#LINE/L1      130   328 (580)  

  chrX_56010655_5      1 AAACT-ACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCACATTGCCAA 49
                           i  - iii    i           viiv  ii  v  viv  v     
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_56010655_5     50 GTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACT 99
                         iv     i i ivv i          i      vv   ii  v  ii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_56010655_5    100 TCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTAC 149
                              viv        i          i   i    ii         i i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_56010655_5    150 CAAAATGGAGATATAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATA 197
                         v ii  i  v       i        i    i--    i  --       
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATA 327

  chrX_56010655_5    198 A 198
                          
  L1M4_orf2#LINE/    328 A 328

Transitions / transversions = 2.25 (36 / 16)
Gap_init rate = 0.02 (3 / 199), avg. gap size = 1.67 (5 / 3)  

2649 27.43 1.53 2.30  chrX_56010655_56012683.rev      624  1538 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56010655_5    624 TAGAAAAACACCCCATGTTCATGAAATGGAAGAACCAATATTGTTAAAAT 673
                          i    i i i            i v       vii           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56010655_5    674 GGCCATACTGCCCAAAGAAATTTATAGATTCATAC-CTATTCCTATCAAA 722
                            v     v      vvi  i  i       -  - v  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCA-ACGCAATCCCTATCAAA 99

  chrX_56010655_5    723 CTAACAACATCATTTTTTTCACAGAATTAGAGGGAAAAAAACT-ATTCTA 771
                         v vv  i --iiii     ii     v v  v------  i  -  i   
  L1M4_orf2#LINE/    100 ATCCCAGC--TGCCTTTTTTGCAGAAATTGAC------AAGCTGATCCTA 141

  chrX_56010655_5    772 AAATACATGCGGAACCAAAATAGAGCCTCAATAGCCAAAGCAATCCTAAG 821
                             v   ii    viiv  vi  v  vv          i     i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_56010655_5    822 GAAAAAGAACAGAACTGGAGTTTTCAAACTACCTGACTTTAAGCTGTATT 871
                         i  i       i ii     vvi   v   v  ii i  i  iviv  i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_56010655_5    872 ACAAGGCTAGAGTAACCAAAATAGCATGGTACTGCTACAAAAGCA-ATAC 920
                             i    v     i   i i  ii        vi i  iiii - i i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_56010655_5    921 ATAAACCGATGGAATAGAATAGAGA-TCCTATAGAAATAAAGCCACATGC 969
                            i i i            v    -   ---         v   i iii
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCC---AGAAATAAACCCATACAT 338

  chrX_56010655_5    970 CTACAACCA-TCTATCTTCAAGAAAGCTGACAAAAACGAGCAATAAGGAA 1018
                         i  iiii  - iv  i   i v  i v  v   i v ivv    ii    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_56010655_5   1019 AGGAC--TCCTTATTTAATAAATGGTGCTGGGATAACTGGCCAGCCATAT 1066
                           i i--  i  -- i  i              i      vi ?   i  
  L1M4_orf2#LINE/    389 AGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_56010655_5   1067 GCAGAAGATTAAAAATAAACACATAGCTTTCACCATAAACAAAAATTAAA 1116
                            i    v i  iv ii  v v  v  iv       v           v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_56010655_5   1117 TCAAGATGGATTAAAGATTTAAATATAAGACTTCAAACTATAAAAATACT 1166
                             i      i ?   ii     i     vi v           v vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_56010655_5   1167 AGAGAAAAACCTAGG---AAATTCCCTTCTTTATACCAGTCTCAGGAAAT 1213
                            ii     v    ---    ---    v v i- iv vv i   v   
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT---CTTCGTGAC-CTTGGGTTAGGCAAT 582

  chrX_56010655_5   1214 AATTT-TTGGCTG-AATTCCTAAAAAACAATAGCAACAAAAACAAAAATT 1261
                         ii   -  i v i-i iv  v   iv    --         iv      v
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATA 630

  chrX_56010655_5   1262 GAGAAGTGGGACCTAACTAAACTAGAGGGGTTCTGCACAGCAAAAGAAGC 1311
                           v  i v    i v ii   v vi iiiv  i  ii vv    i  vi 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_56010655_5   1312 TATCAACAGAGTAAGCAGACAACCTACAGAATGGGAGAAAACATTTGCAA 1361
                               v i   i iv        i                i        
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_56010655_5   1362 ACTATGCATCTGACAAAGGTCCAATATCCA-AATGCATAAGGAAC-CTAA 1409
                          ii  ii      i  i  v ivi      -   ii    i    -  v 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_56010655_5   1410 GCAAATCAAGAAGTAAATATCAAATGAACTTATTAAAAAACAGGCAAAGG 1459
                         -   v    v  vv   viv     i v iv   ?     ii        
  L1M4_orf2#LINE/    781 -CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_56010655_5   1460 ACATGGACAGGCACTTCTCAAAAGAAGACATACAATCAGCCAAGAAGCAT 1509
                          iv  i i  i  i     v        i      vii     v     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_56010655_5   1510 AAGAAAAAATGTTCTCCATCACTAGTCTT 1538
                          v     i   i  vv     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (156 / 92)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.75 (35 / 20)  


2672 27.51 2.21 1.88  chrX_56040565_56049968     2917  3821 (5583)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56040565_5   2917 TGGAAACACATCTCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2966
                               v i   i    i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56040565_5   2967 GACCATACTGCTAAAAGCAGTCTACATATTCAATGCAATTCCCATAAAAA 3016
                          i v     v iv   viii      v      i     i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56040565_5   3017 ATGCCA-CCACTATTCTTCACAGAACTAGAAAAAACAATCTTAAAATTCA 3065
                         - v   - ii i-  i  ii     v v  v  ivii   i         
  L1M4_orf2#LINE/    101 -TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_56040565_5   3066 TATGGAACCAAAAAAAAAATTTTGCATAGCCAAAGTAAAACTAAGCAA-A 3114
                                -- viv  iii iiiv v         ii  vvi i iv  - 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_56040565_5   3115 AGAAAAAATCTGGAGGCATCACATTACCTGACTTCAAACTATCCTATAAG 3164
                             v   vi      vv     i v  ii i      viv v   i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_56040565_5   3165 GCCATAGTCATCAAAACAGAATGGTACTGGTATAAAAATGGCCACATGGA 3214
                           i i   v     i    vi         i    ii  i v  i  i  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_56040565_5   3215 CCAATGGGACAGAAAGGAGAACCCAGAAATAAACCCAAATACTTACAGCC 3264
                         i      i i    vv    ii               v i i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_56040565_5   3265 AACTGATCTTCAACAAAGCAAACAAAAACA--AAGTAGAGAAAGGACACC 3312
                           i    i   i    i vviv   i v  --v i i i     i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56040565_5   3313 CTTTTCAACAAATGGTGCTGAGATAATTGGCAAGCCACATCTAGGAGA-- 3360
                                             i  i  i   vv ?      vi ii   --
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56040565_5   3361 ----CTATATCCTCATCTCTCACCTTATACAAAAATCAAGTCATGATGGA 3406
                         ----i iv i  ii i   v    v           i  v   vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56040565_5   3407 TCAATAACTTAAATGTAAGACCTGAAACTATAAACATTCT-AGAAGATAA 3455
                            ?vi  i           v  i          - i   -      v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chrX_56040565_5   3456 CACTGGAA-AAACCATTCTAGATATTGGCTTGGGCAAAGACTTCATGACC 3504
                           iv  ?i-   i -   vv  iv    v  i     v ii   v iivi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_56040565_5   3505 AAGAACCCAAAAGCAAATGCAACAAAACAAGGA-TAAATAGGTGGAACTT 3553
                          v  vv         v v         v  ii -  i   ii v i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_56040565_5   3554 CACTAAAG-----AACTTCTGAAAAGCAAAAAGAACAGTCAGCAGATTAA 3598
                           ii   i-----     i  vivvv    iiiv  vi   iv i v i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_56040565_5   3599 ACAGACAAACTACAGAGTGGGAGAAAATCTTCACAATTTATACATCTGAC 3648
                          v      v i     i           v  ii   v i   i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_56040565_5   3649 AAG--ACTAATATCCAGAATCTACAAGGGACTCAAACAAATTAGCAGGAA 3696
                            --   vi          v  i  i i    vv    v i ii iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_56040565_5   3697 AAAAGAAAGAAAGAAAAAAAAAATCCCATCAAAAAGTGGGCTAAGGACAT 3746
                            i----------- v   v  i  v  i?    i     v     iv 
  L1M4_orf2#LINE/    795 AAAG-----------ACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_56040565_5   3747 GAATAGACAATCCTCAAAAGAAGATGTACAAATAGCCGGCAAACATATGA 3796
                                  v i   v         i       i   iii  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_56040565_5   3797 AAAAATGCTCAGCATCACTAATGAT 3821
                            i       i     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.47 (37 / 15)  

3108 27.11 0.55 0.88  chrX_56040565_56049968     5003  5913 (3491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56040565_5   5003 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5052
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56040565_5   5053 GACCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5102
                          i v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56040565_5   5103 TACCAA-TGCCTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTAAG 5150
                          v   i-       i  -i     v v  v  i-  - iii    i ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAAT--- 145

  chrX_56040565_5   5151 TTCATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCT-AAGCCA 5199
                         -          viiv  ii  v  v v  v     iv      -i ivv 
  L1M4_orf2#LINE/    146 -TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_56040565_5   5200 AAAGAACAAAACTGGAGGCATCACACTACCTGACTTCAAACTATACTACA 5249
                         i         ii      vv       v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_56040565_5   5250 AGACTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 5299
                          ii         i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_56040565_5   5300 GATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTAC 5347
                                    i    i--    i  --        vv  ii i  i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chrX_56040565_5   5348 AACTATCTGATCTTTGACACACCTGACAAAAACAAGCAATGGGGAAAGGA 5397
                         iiii vi    i  i    vivv  v   i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_56040565_5   5398 TTCCCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATTTAGGA 5447
                          vvi  v  i  i              v      v  ?   i  vi ii 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_56040565_5   5448 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGA 5497
                         iiv    ii    i    v   i     v           i  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_56040565_5   5498 TGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGA 5547
                              i ?    i    i  v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_56040565_5   5548 AAACCTAGGCATTACCATACAGGACATAGGCATGGGCAAGGACTTCATGT 5597
                             v    ?i v viv v iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_56040565_5   5598 CTAAAACGCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5647
                         v  vi  i         vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_56040565_5   5648 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5697
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_56040565_5   5698 GAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCCG 5747
                            v  i     i   i             v  i    vii ivi   i 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_56040565_5   5748 TCAAAGAGCTAATACCCAGAATTTACAATGAACTCAAACAAATTTACAAG 5797
                         vi  i ii  vi  i       v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_56040565_5   5798 AAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGTACATGAACAGACA 5847
                              i     i     v  i?    i         v iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_56040565_5   5848 CTTCTCAAAAGGAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 5897
                         i     v    i   i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_56040565_5   5898 CATCATCACTGGCCAT 5913
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  

2427 27.15 5.08 1.42  chrX_56040565_56049968     8057  8903 (501)    L1M4_orf2#LINE/L1        1   878 (30)  

  chrX_56040565_5   8057 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTTAATGT 8106
                               i i  i     i        v      v i           vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56040565_5   8107 GGCCATACTGC--AAAGCAATTTACAAATACAATGCTATTCCTATCAAAC 8154
                            v     v --   vii  i    i  v   i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56040565_5   8155 TACCAACAATATTTTTCACATACTTAGAAAAATCTCTTTGAAAATTCACA 8204
                          v   i viiv     ii  v vv v  v  iiivv iiv        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56040565_5   8205 TGAAACCAGAAAAGAGCTCGAACGGCCAAAACAATGCTAAGCAA-AAGAA 8253
                           i  viiv  ii  v iv   ii           vi i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56040565_5   8254 CACAGCTAGAGGCATCACAATACCTGATTTCAAAGTATATTACAAGATGA 8303
                           v  i i    vv     v v  ii        iiv  i     iiiv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_56040565_5   8304 CACTAACCAAAATAGCATGGTGCTGGTGCA-AAAAACAAACACATAGACT 8352
                           v   i   i i  ii    i    --  -  ii i i   i     ii
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGG--CATAAGGATAGACATATAGATC 298

  chrX_56040565_5   8353 AATGGAACAGAATGGAGAACCCAGAAATAAAATAGCACACTTACAACCAT 8402
                                i     v    ii           vivii   i   iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_56040565_5   8403 CTGATCTTCAACAAAGTGGAGTAAAACAAG-CAATGGGTAAAGGATTCCC 8451
                         i    i   i    i - vivi  i  v v-       v    i  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_56040565_5   8452 TATTCAATAAATGGTGCTGTGAT-------------------------TG 8476
                          v     i           v  i-------------------------  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_56040565_5   8477 AAATTGGACCTCTTCCTTTCACCATACACAAAAATTAACTCAAGATGGAT 8526
                           i       i  v   iv       i                i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_56040565_5   8527 TA-AGACTTGAATGTAAAACCTAAAACTATAAACACCCT-AAAAGAAAAC 8574
                         i -    i i       i v             -  i  - i        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chrX_56040565_5   8575 CTAGGAAGTGCTGTTC-TGTACATAGGACATGGAAAAAATTTC------A 8617
                         v    ?ivviv v   -  vv v i  vi -  v  vii    ------ 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATA 595

  chrX_56040565_5   8618 TGACAAAGATTCCAAAAACAATACCAAGAAAAGCAAAAACAGGCAAATGG 8667
                              ------      i  vv v   v     v     i  ii    v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_56040565_5   8668 GACCTAATTAAACTAAAGAGCTTCTGCACAACAAAATAAACTATCAACAA 8717
                            i v  i   v v  i i   i  ii vv    iv v        v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_56040565_5   8718 AGTAAACAGGCAACCTACAAAATGGGAGAATACATTTGCAAATTATGCAT 8767
                            i  v  i     i   i          v i          i  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_56040565_5   8768 CTGACAAAGGCCTAATATCCATAATCTGTAAGGAACT--TA-AATTAACT 8814
                             i  i  v  vi      v   v i   i     --  -  i v v 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_56040565_5   8815 GGCAAAAC-ACTAAGAACCATGTTAAAAAAATGGGCAGAGGACATGAACA 8863
                         iii    v-  v  v    vvi  ?     -      i    iv    i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATA 838

  chrX_56040565_5   8864 GACACTTCTCAAAAGAAGACATATATGCAGCCAACAAACA 8903
                             i     v        i   i viii     i  i  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

Transitions / transversions = 1.51 (137 / 91)
Gap_init rate = 0.02 (18 / 878), avg. gap size = 3.06 (55 / 18)  


3217 26.79 0.66 0.55  chrX_56066595_56071256.rev     3265  4171 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56066595_5   3265 TGGAAGAACATTCCATACTCATGGATAGGAAGAATCAATATTGTGAAAAT 3314
                              ii i  i    ii        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56066595_5   3315 GGCCATACTCCCCAAGGGAATTTATAGATTCAATGCCATCCCCATCAAGC 3364
                            v           ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56066595_5   3365 TACCAAGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3412
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56066595_5   3413 TATGGAACCAAAAAAGAGCTCGCGTTGCCAAGTGAATCCTAAGCCAAAAG 3462
                                viiv  ii  v iv vi v     ivv    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56066595_5   3463 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3512
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56066595_5   3513 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 3562
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56066595_5   3563 AATGGAACAGAAC--AGAGTCCTCAGAAATAATGCCACATATCTACAACC 3610
                                i    i--       --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_56066595_5   3611 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAACGATTCC 3660
                          vi    i  i     ivv  vv  i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56066595_5   3661 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3710
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56066595_5   3711 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3760
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56066595_5   3761 TTAAAGACTTAAATGTTAGACCCAAAACCGTAAAAACCCTAGAAGGAAAC 3810
                          i ?    i       v   v i     ii     vi i      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_56066595_5   3811 CTAGGCA-ATACCATTCAGGACATAGGCATGGG-AAGGACTTCATGTCTA 3858
                         v    ?i- v i -   iv   v v  vv i  -  v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_56066595_5   3859 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 3908
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_56066595_5   3909 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3958
                           i   v i  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_56066595_5   3959 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 4008
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_56066595_5   4009 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4058
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_56066595_5   4059 AAAGCAAACAACCCCATCAAAAAGAGGGTGAAGTATATGAACAGACACTT 4108
                           ii    i     v  i?    iv   ii   v  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_56066595_5   4109 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 4158
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_56066595_5   4159 CATCACTGGCCAT 4171
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2185 26.93 2.61 2.09  chrX_56072300_56074056.rev      502  1266 (491)    L1M4_orf2#LINE/L1      140   908 (0)  

  chrX_56072300_5    502 TAAAATTCATATGGAACCAAACGAGAGCCTGAATAGCCAAGCCAGTTCTA 551
                                         viiv v i  v  v          iv  i ii i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_56072300_5    552 AGCAAAAAGAACAAAGCTGGAGGCATTGCACTGC---AT----AAACTAT 594
                          iv  i          i      vv ii    v ---  ----     - 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-T 238

  chrX_56072300_5    595 ACTACAAGTCTACAGTAACCAAAACAGGATGGTACTGGTACAAAGACAGA 644
                                iv         i   i    vi         i i  i  i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_56072300_5    645 GACATAGACCAGTGGAACAGAATAGAGTACCCAGACATAAGACTGCACAC 694
                         v i     i  i     i     v   vii     v    iv iii   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_56072300_5    695 CTACAACTATCTAATCTTTGACAAATATGACAAAAC-AGGCAATGGGTAA 743
                         i  iiiii vi i  i  i     ivi  v   i  - vv       v  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_56072300_5    744 ATAATTTCCTATTAAAGAAGTGGTGCTGGGATAACTGGGTATCCATATTC 793
                          v   vvi  v  v  v  i           i      i  ?   i  v 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_56072300_5    794 AGAAGATCAGAGTTGGTCTCCTTATTTATACCATATACAAAAATTAACTC 843
                          i    viii      v i   vvi i i                     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_56072300_5    844 AAGATGGATTACAGACTTAAATGTAAAACCCTAAACTATAGAAACCCTGG 893
                           i      i ?    i         i v iv        i  vi i i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_56072300_5    894 AAGACAACCTAGACCATACCACTGAG-GACATAGGAGTGGGCAAAGATTT 942
                             v   v   i?-i  vvv  vv -   v v  iv i     v i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_56072300_5    943 AGTGACAAAGAACTATAATTCCTGAAAGCAACTGCAACAAA-TCAAAAAT 991
                         vv -----   --   i iv  -i      vvv        -vv      
  L1M4_orf2#LINE/    588 CTT-----AGA--TATGACACC-AAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_56072300_5    992 CAACTAATGAAATCTCATTAAACTAAAGACCTTCTGCACAGCAACAGAAA 1041
                         vi iv   vii ii    i   v v  i v   i  ii vv   vi  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_56072300_5   1042 CTATCAAGG--GTGTAAACAGAATT-ACAGATTGGGAGAAAATTTTTGTA 1088
                                 i--   v   v v  ii-     v           v    i 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_56072300_5   1089 AACTATGCATCTGACAAAGGTCTAATATCCAATATCTATAAGGAATGC-- 1136
                           ii  ii      i  i  v  vi      iv  v     i   iv --
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_56072300_5   1137 AAAA---AATGTGCAAGAGAAAAACAAACAACTCCATTAAAAAGTGGGCA 1183
                          v  ---   ----  v i   i     i   i v   ?    i      
  L1M4_orf2#LINE/    780 ACAACTCAAT----AATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_56072300_5   1184 AAGGGCATAAAAAGGCACTTTTCAAAAGAAGACATA--AATGCAGCCAAA 1231
                             iiv i  v  i  i  i  v        i   --    --     v
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG--GCCAAT 873

  chrX_56072300_5   1232 AATCATATCAAAAAAACCTCAACATCACTTGTTAT 1266
                           v  i  v    i vv          ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (115 / 87)
Gap_init rate = 0.02 (17 / 769), avg. gap size = 2.12 (36 / 17)  


3034 27.44 1.33 0.44  chrX_56081811_56109451      492  1391 (26249)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_56081811_5   1391 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATTAAAAT 1342
                              ii i  i     i      i v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_56081811_5   1341 GGCCATAATGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 1292
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_56081811_5   1291 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1244
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_56081811_5   1243 TATGGAACCAAAAAAGAGCCCGCATTGCCTAGTGAATCTTGAGCCAAAAG 1194
                                viiv  ii  v  v v  v   v ivv        ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_56081811_5   1193 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1144
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_56081811_5   1143 TACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGACA 1094
                                 i   i     i         i iv ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_56081811_5   1093 AATGGAACAGAACAGAGCCTTCAGAAATAATGCTGCTTATCTACCACTAT 1044
                                i    iv   vv i         vv iiivi  i  iviii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

C chrX_56081811_5   1043 CTGATCTTTGAGAAAC-TGGCAAAAACAAGAAATGGGGAAACAATTCCCT 995
                         i    i  i  v  iv-  v   i v  vvv          v   vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

C chrX_56081811_5    994 ATTTAACAAAAGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 945
                         v  i      v          v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

C chrX_56081811_5    944 AACTGGATCCCTTCCTTACAACTTATACAAAAATTAATTCAAGATGGATT 895
                          ii    i    v   i   v v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

C chrX_56081811_5    894 AAAGACTTAAATGTTAGACCCAAAACCATAAAAACCCTACAAGAAAACCT 845
                          ?    i       v   v i     i      vi i  v        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

C chrX_56081811_5    844 AGGC-CATATCATTCCGGATGTAGGCATGGGCAAGGACTTCATGTCTAAA 796
                            ?-i v   -   vv  iv v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

C chrX_56081811_5    795 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 746
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

C chrX_56081811_5    745 TAAACTCAAGAGCTTCTACACAGCAAAAAAAACTACCATCAGAGTGAACA 696
                         i   v i  i i   i iii vv    ii v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

C chrX_56081811_5    695 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATGTTCT-CATCTGACAA 647
                          i     i                 v       -i iv -i      i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATAA 746

C chrX_56081811_5    646 AGGGTTAATATCCAGAATCTACAAAGAACTCAAACAAAT---TTATAAGA 600
                         i  ii vi          v  i         vv    v --- v    i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chrX_56081811_5    599 AAACCA----CCCCATCAAAAACCAGGCAAAGGACATGGACAGACACTTC 554
                          i  v ----   v  i?    vii         iv  i i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chrX_56081811_5    553 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCGTC 504
                           v        i  vi viii     v ii          i      iv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chrX_56081811_5    503 ATCACTGGCTAT 492
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  

2893 27.89 0.89 0.78  chrX_56081811_56109451     5870  6769 (20871)  C L1M4_orf2#LINE/L1   (0)   908     8  

C chrX_56081811_5   6769 ACATTCCACGCTAATGGATAGGAAGAATCAATATTGTGAAAATGGCCATA 6720
                          i  i   i i v      v      v i        v  i     v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

C chrX_56081811_5   6719 CTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAAG 6670
                           v     iv i  i  i        i  v     i     iv v   iv
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

C chrX_56081811_5   6669 GACTTTTTTCACAGAA-TTGAAAAAAACTGCTT-TAAAAGTCATATGGAA 6622
                         vi i     ii     -    v  i--   v i-     v          
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATATGGAA 155

C chrX_56081811_5   6621 CCAAAAAAGAGCCCACATTGCCAAGGCAATCTTCAACCAAAAGAACAATG 6572
                         viiv  ii  v  viv  v     ii       v  vv i        v 
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

C chrX_56081811_5   6571 CTGGAGGCATCAGGCTAGCTGACTTCAAGCTATAGTACAAGGCGACAGTA 6522
                         i      vv   vi  vv ii i     iviv  v     i  v      
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

C chrX_56081811_5   6521 ACTGAAACAGCATGGTACTGGTACCAAAACAGACATATATACCAATGGAA 6472
                          iii i    ii         i iv ii i         v i        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

C chrX_56081811_5   6471 CAGAAC--AGAGCCCTCAGACTTAATGCCACACATCTACAACCATCTGAT 6424
                         i    i--    i  --   vv   vv   i    i  iiii  vi    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGAT 353

C chrX_56081811_5   6423 CTTTGACAAACCTGACAAAAACAAGAAACGGAGAAAGGATTCCCTATTTA 6374
                         i  i     ivv  v   i v  vvv  i  i     i  vvi  v  i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

C chrX_56081811_5   6373 ACAAAGGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAAATG 6324
                              v          v      v  ?   i   i i  iiv    iv  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

C chrX_56081811_5   6323 GATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGA 6274
                           i    v   i     v              i    i      i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

C chrX_56081811_5   6273 CTTAAAAGTTAGAACTAAAACTATAAAAACCCTAGAAGAAAAC-TGAGC- 6226
                          i    v  v   i              vi i           - ii ?-
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

C chrX_56081811_5   6225 CAATTCCATTCAGGGCATAGGCATGGGCAAGGACTTCCTGACTAAAACAC 6176
                         i  v  --   iv i v v  vv i     v ii   i iiv  vi    
  L1M4_orf2#LINE/    554 TAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

C chrX_56081811_5   6175 CAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAA 6126
                                 vvi           v     v  i    v   ii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

C chrX_56081811_5   6125 CTAAAGAGTTTCTGCACAGCAAAACAAACTACCATCAGAGTGAACAGGCA 6076
                         v v  i ii  i  ii vv    iv v    i  vv i      v  i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

C chrX_56081811_5   6075 ACCTACAGGATGGGAGAAAGTTTTTGCAATCTACCCATGTGACAAAAGGC 6026
                            i    i          i v       vii ivi  v   i  ii i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

C chrX_56081811_5   6025 TAATATCCAGAATCTACAAAGAACTAA-ACAAACTTA-CAAGAAAAAATC 5978
                          vi          v  i        vv-    -  i -i  v     iv 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAAAAGAC 800

C chrX_56081811_5   5977 AAACAACCCCATCAAAAAGTGGGTGAAGGATATCAACAGACACTTCTAAA 5928
                            i     v  i?    i    ii      v v  i     i    vv 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

C chrX_56081811_5   5927 AAGAAGACATTTATGCAGCCAACAGACACAGAAGAAAATGCTCATCATCA 5878
                                i  vi viii     i ii    vi i  i       v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

C chrX_56081811_5   5877 CTGGCCAT 5870
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.01 (11 / 901), avg. gap size = 1.36 (15 / 11)  

3093 26.46 1.21 1.10  chrX_56081811_56109451    16027 16933 (10707)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56081811_5  16027 TGGTAGAACATTCCATGATCATGGGTAGGAAGAATCAATATCATGAAAAT 16076
                            v ii i  i     v      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56081811_5  16077 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 16126
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56081811_5  16127 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 16174
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56081811_5  16175 TATGGAACCAAAAAAGAGACGCA---TCACCAAGTCAATCCTAAGCCAAA 16221
                                -- viv   i   v  --- vi    iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_56081811_5  16222 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAT 16271
                                  i      vv   ii  v  ii i      viv        v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_56081811_5  16272 GCTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGACATATAGA 16321
                                   i   i    iii        i iv ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_56081811_5  16322 TCAATGAAACAGAAT--AGAGCCCTCAGAAATAATGCCACATATCTACAA 16369
                               i  i     --    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_56081811_5  16370 CTATCTGATGTTTGACAATCCTGAGAAAAACAAGCAATGGGGAAAGAAT- 16418
                         ii vi    v  i     vvv  vv  i v  vv               -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_56081811_5  16419 -TCCGTATTTAACAAATGGTGCTGGGAAAACTGGCCAGCCATATGTAGAA 16467
                         -  -- v  i                 v      vi ?   i   i i  
  L1M4_orf2#LINE/    395 GTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_56081811_5  16468 AGCTGAAACTGGATCCCTTCCTTACACTTCATTCAAAAATTAATTCAAGA 16517
                         iiv    ii    i    v   i    ivi  v          i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_56081811_5  16518 TGGATGAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGA 16567
                              v ?    i       v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_56081811_5  16568 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 16616
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_56081811_5  16617 TCTAAAACACCAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGGA 16666
                         vv  vi            vvi          v      v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_56081811_5  16667 TCTAATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 16716
                         ii v  i   v i  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_56081811_5  16717 TGAACAGGCAGCATACAAAATGGGAGAAAATTTTTGCAATCTACTCATCT 16766
                             v  i  i vi   i             v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_56081811_5  16767 GACAAAGGGCTAATATCCAGAATCTACAA-GAACTCCAATAAATTTACAA 16815
                           i  i  i  vi          v  i  -      iv i  v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_56081811_5  16816 GAAAAAAAGCAAACAACCCCATCAAAAAGTGGACGAAGGACATGAACAGA 16865
                         v     i -    i     v  i?    i   i i     iv    i   
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_56081811_5  16866 CACTTCTCAAAAAAAGACATTTATGCAGCCAAAAAACACATGAAAAAATG 16915
                           i     v   i    i  vi viii     v  i          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_56081811_5  16916 CTCATCATCACTGGCCAT 16933
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  

2964 25.39 2.66 2.00  chrX_56081811_56109451    19981 20882 (6758)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56081811_5  19981 TGGAAAGATATTCCATGCTCATGTACTGGAAAAATCAATATT---AATAT 20027
                                    i     i     v i     i v i      ---  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56081811_5  20028 ----ATACTACAAAAAGCAATCTACAGGTTCAATGCAATCTCGATCAAAA 20073
                         ----     v vv   vii        i     i      i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56081811_5  20074 CACTAATGGCACTCTTTAGAGAAATAGAAAACACAATCCTAAAATTTATA 20123
                         iv i iiv  vi i   iv      v  v  vvii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56081811_5  20124 TGGTACCACAAAATACCTAAAATAGCCAAAGCTGTCCTAACGAAAAACAA 20173
                            v vii   iiv   i i          i vi  i i vi  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56081811_5  20174 CAAAACTGAAGGAATCATAATACCTGACTACAAA--TTA-TGCAAAATCT 20220
                             ii  i    v   i v v  ii i v    --   - i    i-  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG-CT 249

  chrX_56081811_5  20221 ATATTAACCAAAACAGCACAGTAATGGCA--GGAAAAGACACATAGACCG 20268
                          i v   i   i    iiii   v     --i i v     i     i i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_56081811_5  20269 GTGGAAAAGAATGCAAAACCTGGAAACAAATCCATA--TCTACAGTGAAG 20316
                         i     v     vv i ii ii    i   i     -- i  ii  v  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_56081811_5  20317 TCATTTTTGACAAAGGTGCCAATAACATAAATTGGGGAATGGAACA-TCT 20365
                          v     i     i        v v   vv v       -i   i -   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAATAGTCT 398

  chrX_56081811_5  20366 CTTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAAAAGCATGA 20415
                         i     i              v         ?   i         v    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_56081811_5  20416 AACCAGACCCCTTTCTCTCACCATATACAAAAGTAAAATCAAAATGGATT 20465
                          iiii       vi   v              i v  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_56081811_5  20466 AAAGACTTGAATCAAACATGTTAAAG-TAAAATGGTAAAGTTAAAGTTTC 20514
                          ?    i i   -------  v i  -     ivi    i--------- 
  L1M4_orf2#LINE/    499 AWAGACCTAAAT-------GTAAGAGCTAAAACTATAAAA---------C 532

  chrX_56081811_5  20515 TATCACAAGAAAACATTGGGGAAAATCTCCAGGACTTTGGCCTGGGCAAA 20564
                          v i v          v  ? v      i iv   i    vi i     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_56081811_5  20565 AATTTCTTA----CTACAC---AAACACAGGTAACCAAAGCAAAAATGGA 20607
                         ii       ----iv    ---  i    i i   v    v      i  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_56081811_5  20608 CAAATGGGATCACAT-GAAGTTAGAAAGCTCTGCACAACAAAGAATACAA 20656
                         i    v   iiv   -i  i   i   vi i  ii vv     i i  v 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_56081811_5  20657 TCAACAAAGTGAAGAAACGACCCACAGAGTGGGAGAAAATCTTTGCAAAC 20706
                             v        i i  i         i           v        i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_56081811_5  20707 TACCTTTCTGACAAGGGTTTGAGAACCAGAATGTGTAAGGGACTCAAACA 20756
                         i iv v     i     vi viv v       i i   i i    vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_56081811_5  20757 ACTCTTTAGGGAAAAATCTTATAATCCAATTAAAGAAAGAGCAAAAAAAT 20806
                             vv  ivi    iv vv    i      ?  i  v i     ii v 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_56081811_5  20807 TAAAAAGACATTTCTCAAAAGAATACATACAAGTGGCAAACAAGCTTATG 20856
                          i  v           v      v i      i    v  i    vi   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_56081811_5  20857 AAAAGGTGCTCAACATCCCTGATCAT 20882
                              i           v????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (137 / 88)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.80 (42 / 15)  

2965 27.46 1.11 0.55  chrX_56081811_56109451    26246 27148 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56081811_5  26246 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 26295
                              ii    i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56081811_5  26296 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 26345
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56081811_5  26346 TACCAAGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTCCA 26393
                          v   ivvi i  i  ii     -   -- v  i  - iii i  i i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56081811_5  26394 TATG-AAATGAAAAAAGAGCCTGCATTGCCAAGACAATTCTAAGTCAAAA 26442
                             -     v  ii-  v  v v  v     i     ii i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_56081811_5  26443 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 26492
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_56081811_5  26493 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAAGAGAGTTATAGAC 26542
                                  i   i    ii         i iv ii v   vv      i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_56081811_5  26543 CAAAGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACCACCA 26592
                            v    i    iv   ivii         vv   i    i  ivii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_56081811_5  26593 TCTTATCTGTGACAATCCTCACCAAAACAAG-AAATGGGGAAAGGATTCC 26641
                         vi v  i vi     vvv -i    i  v v-v           i  vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56081811_5  26642 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 26691
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56081811_5  26692 GAAACTAGATCCCTTCCTTACAGCTTATA-AAGAATTAATTCAAGATGGA 26740
                            ii i  i    v   i   v v    -  i      i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56081811_5  26741 TGAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 26790
                          v ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_56081811_5  26791 CTAGGCA-ATACCATTCAGGAAATAGGCATTGGCAAGGACTTCCTGACTA 26839
                         v    ?i- v i -   iv  vv v  vv v     v ii   i iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_56081811_5  26840 AAACACCAAAAGAAATGGCAACAAAATCCAAAATAGACAAATGGGATCTA 26889
                         vi          v vvi         vvv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_56081811_5  26890 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCTGAGTGAA 26939
                           i   v v  i i   i  ii vv    i  v    i  vvvi      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_56081811_5  26940 CAGGCATCCTACAGGATGTGAGAAGGTTTTTGCAATCTACCCATCTGA-A 26988
                         v  i  v  i    i   v     ii v       vii ivi      - 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_56081811_5  26989 ATGGGCTAATATCCAGAATCTACAAAGAACTCTAACAAATTTACAAGAAA 27038
                          v  i  vi          v  i          v    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_56081811_5  27039 AAAACAAACAACCCCATCAAAAAGTGGACAAAGGTTATGAACAGACACAT 27088
                           i     i     v  i?    i   i      v v    i     iv 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_56081811_5  27089 CTCAAAAGAAGACATATATGCAGCCTACAGACACATGAAAAAATGCTCA- 27137
                            v        i   i viii   v i ii          i       -
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_56081811_5  27138 --TCACTGGCCTT 27148
                         --   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (140 / 104)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


3222 25.40 2.93 0.56  chrX_56183227_56186074.rev     1472  2357 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_56183227_5   1472 GGAAAGATATTCCGTGTTCATGGATTGGTGGAATACATTTTGTTAAAATG 1521
                                   i  i              vi  v vv  v       i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_56183227_5   1522 TTTGTACTACTCAAAGCAATCTACAATATTAATGCAATCTCTATCAAAAT 1571
                         vivi    v i    vii       ivv i  i      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_56183227_5   1572 ATTAACGACAATCCTCTGCATAAATAGAAAAAA-AACCCCAAAATTTACA 1620
                         vii i vi v- ii i    v    v  v  iv-i i  i      i i 
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56183227_5   1621 TGGAACCACAAAA-ACCCAGAATAACCAAAGCTATCTTAAGCAAAAATAA 1669
                              vii   ii-          i     i v     i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56183227_5   1670 TAAAACTGAAGGAATCACATTATGTGACTTTACATTATACTACAGAGGTA 1719
                         i   ii  i    v     i vivii i  i v viv       i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_56183227_5   1720 TAGTAATCAAAATAGTGTGCTGCTGGCATA-TAACAGACACACTGATCAG 1768
                         i         i i      v i        -vi i     i iv     i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_56183227_5   1769 TGGAACAGAATAGAGAACCCAGAGATAAATCTATGCATTTATAGTGAACT 1818
                              i     v    ii     i     i i  i       i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_56183227_5   1819 CATTTTAGACACAGGTGCTGAGATCATACATTGGGGAATGGACTGTCTCT 1868
                         v     v    vi     ii   i   v  v       v i iv    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_56183227_5   1869 TCAATAAAGGGTGCTGGGAAAACTGGATATC-ACAGGTAAAAGAATAAA- 1916
                             i   v          v         ? -   v i        i  -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_56183227_5   1917 CTAGAACCCTATATCTCACCATATACAAACATCAAATCAAAATGGATTAA 1966
                         i i  v     iv  v             v  i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_56183227_5   1967 AGGCTTATGTCTAAGATCTGAAACTAT--------TACAAGAAAATATTG 2008
                           i i  vi v     v  i       --------  v       i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_56183227_5   2009 GGGAAAGTCTCCAGGACATTGAACTGGGCAAAGATTTGTTGAGCAATACC 2058
                          ? v  i   i iv   v   iii i     v i   v  iiii vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_56183227_5   2059 CCACAAGCATAGGCAATAAAAGCAAAAATGGACAAATGGGGTGCCAT-AA 2107
                            v     i i    i     v      i  i    v  iivi   -  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_56183227_5   2108 AGTTAAAAAAATCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAAGA 2157
                          i       ---   i  ii vv       v  v     v        i 
  L1M4_orf2#LINE/    651 AATTAAAAA---CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_56183227_5   2158 GACAACTCACAGAATGGGAGAAAATACCTGCAAACTACCCATC-AACAAG 2206
                               i                   ii      ii ivi   -i i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_56183227_5   2207 GGATTCATAATCAGAACATACAAAGAGTTCAAAAAACTCTATAGGAGAAA 2256
                            i ii  vi     i   i     ii  vv v     v   iv i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_56183227_5   2257 AATCTAATAATCCAATTTAAAAATGGGCAAAAAAGCTGAAAAGACATTTA 2306
                         i - v     i      ?             ii vi    v        v
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_56183227_5   2307 TCAAAAGAAGATA-----------AACAGGCATATGAAAAGGTGCTCAAC 2345
                           v          -----------  i i   i        i        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_56183227_5   2346 ATCACTGATAAT 2357
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (138 / 83)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 2.58 (31 / 12)  


3100 26.14 1.66 1.11  chrX_56201468_56206301     3439  4341 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56201468_5   3439 TGGAAGAACACTGTATCCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3488
                              ii i iivi  vi      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56201468_5   3489 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3538
                            v     vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56201468_5   3539 TACCAATTACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3586
                          v   ii i i  i   i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56201468_5   3587 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATTCTAAGCCAAAAG 3636
                                viiv  ii  v  viv  v     iv    ii i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56201468_5   3637 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3686
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56201468_5   3687 TACAGTAACCAAAACAGCATGGTACTGGTACGAAAACAGAGATATAGATC 3736
                                 i   i    ii         i ii ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56201468_5   3737 CATGGAACAGAAT--AGAGCCCTCAGAAATAATGCTGTGTATCTACAACC 3784
                         v      i     --    i  --        vv ii ii  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_56201468_5   3785 AACTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 3834
                           i    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56201468_5   3835 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3884
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56201468_5   3885 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3934
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56201468_5   3935 TGAAAGACTTAA-TATTAGACCTAAAACCATAAAAACCGTAGAAGACAAC 3983
                          v ?    i   - i v   v       i      vi v       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_56201468_5   3984 CTAG---TCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 4030
                         v   --- v   -- -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_56201468_5   4031 TAAAACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAAT--GACA 4078
                           vi            vvi   i      vv     v  i    --   v
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_56201468_5   4079 TCTAATTAAACTAAATAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 4128
                           --  i   v v  v i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    644 TC--ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_56201468_5   4129 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATGTTCT-CATG 4177
                             v  i     i                 v       -i iv -i  v
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATC 740

  chrX_56201468_5   4178 TGACAAAGGGCTAGTATCCAGAATACACAATGAAGTC--A-AATTCA-CA 4223
                            i  i  i  v            i i  v   v  -- -  i   -i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_56201468_5   4224 AGAAAAAAACAAACGATCCCATCAAAAACTGGGCGAAGGATATGAACAGA 4273
                          v     i     ii i  v  i?    v     i      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_56201468_5   4274 CACTTCTCAAAAGAAGACATTTATGCAGCCAGAAGACACATGAAAAAATG 4323
                           i     v        i  vi viii    iv ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_56201468_5   4324 CTCCTCATCACTGGCCAT 4341
                            vv     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.56 (25 / 16)  


3095 27.26 0.88 0.66  chrX_56234666_56239528.rev     3467  4372 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56234666_5   3467 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3516
                              ii i  i   i i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56234666_5   3517 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3566
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56234666_5   3567 TACCCATTACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 3614
                          v  vii i i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_56234666_5   3615 ATATGGAACCAAAAAAGAGCTTGCATTGCCAAGTCAGGCCTAAGCCAAAA 3664
                                 viiv  ii  v iv v  v     iv  iv i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_56234666_5   3665 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGC 3714
                                 i      vv       v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_56234666_5   3715 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 3764
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_56234666_5   3765 CAATGGAACAGAAC--AGAGCCCTCAGAAACAATGCCGCATATCTACAAC 3812
                                 i    i--    i  --     i  vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_56234666_5   3813 TATCTGATCTTTGACAATCCTGAGAAAAACAAGCAATGGGGAAAGGATTC 3862
                         i vi    i  i     vvv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_56234666_5   3863 CCTATTTAATAA-TGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 3911
                         i  v  i  i  -           v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_56234666_5   3912 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 3961
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_56234666_5   3962 ATTAAAGACTTAAATGTTAGACCTAAAACCAGAAAAACCCTT-GAAGAAA 4010
                           i ?    i       v   v       i v    - i   -       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chrX_56234666_5   4011 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 4060
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_56234666_5   4061 AAAACGCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4110
                          vi  i         vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_56234666_5   4111 AATTAAACTAAATAGCTTCTGCATAGCCAAAGAAACTACCATCAGAGTGA 4160
                         v  i   v v  v i   i  iiivv v  i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_56234666_5   4161 ACAGGCAACCTACATAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 4210
                          v  i     i   v             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_56234666_5   4211 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 4260
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_56234666_5   4261 AAAAA--AACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 4308
                            i --  i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_56234666_5   4309 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 4358
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_56234666_5   4359 TCATCACTGGCCAT 4372
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3054 28.22 0.44 0.33  chrX_56245351_56251743.rev     4996  5902 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56245351_5   4996 TGGAAGAACATTCTATGCTTGTGCGTAGGAAGAATCAGTATCAGGAAAAT 5045
                              ii i  i i   i ii  vi v      v i i   iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56245351_5   5046 GGCCATACTGCCAAAGGGAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v  v  ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56245351_5   5096 TACCAATGATTTTCTTCACAGAATTGGAAAAAACAACTTTAAAGTTCATA 5145
                          v   iiviii  i  ii     v v  v  ivii iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56245351_5   5146 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTCAGCCAAAAGAA 5195
                              viiv  ii  v  v v  v     iv     i v ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56245351_5   5196 CAAACCTGGAGGCATCACACTACCCGACTTCAAACTATACTACAAGTCTA 5245
                             vi      vv       v   i i      viv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_56245351_5   5246 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACCAA 5295
                               i   i    ii         i iv ii i   v   i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_56245351_5   5296 TGGAACAGAAC--AGAGCCCTCAGAAATAAGGCTGCATATCTACAACTAT 5343
                              i    i--    i  --        iv iii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_56245351_5   5344 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTATCT 5393
                         i    i  i     ivv  vv  i v  vv            i  vi   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_56245351_5   5394 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCTGA 5443
                         v  i  i              v      v  ?       i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_56245351_5   5444 AACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGATT 5493
                          ii    i    v   i i   v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_56245351_5   5494 AAAGACTTACATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAACCT 5543
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_56245351_5   5544 AGGCA-ATACCATTCAGGACATAGGCATGCGCAAGGACTTCATGTCTAAA 5592
                            ?i- v i -   iv   v v  vv iv    v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_56245351_5   5593 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAGT 5642
                                     vvi          vv     v  i    v   ii vi 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_56245351_5   5643 TAAACTAAACAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5692
                         i   v v  v i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_56245351_5   5693 GGCAACCTACAGAATGGGAGAAAATTTTTGCTACCTACTCATCTGACAAA 5742
                          i     i                 v     v vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_56245351_5   5743 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5792
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_56245351_5   5793 AAAAAAAAAACCA-TCAAAAAATGGGCAAAGGATATGAACAGACACTTCT 5841
                         i v   v  v   - i?                 v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_56245351_5   5842 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 5891
                          v        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_56245351_5   5892 TCACTGGCCAT 5902
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (145 / 107)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


2848 28.30 1.22 0.44  chrX_56253542_56257639     2706  3606 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56253542_5   2706 TGGAAACACATCCCATGCTCATGGATGAGTAGAATGAATATTGTGAAAAT 2755
                               v i        i        vi v   v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56253542_5   2756 GACCAAACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATTAAAA 2805
                          i v v   v  v   vii       i      i     i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56253542_5   2806 TACCACCATCATTCTTCACAGAATTAGAAAAAACATTTCTAAAATTCATA 2855
                          v   v vv v  i  ii     v v  v  iviiv i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56253542_5   2856 TGGAACCAAAATAAGAG-CCCACA-TAGCCAAATCAAGACTAAGCAAAAA 2903
                              --- vii   i -    v -        v   vvi i iv  i  
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_56253542_5   2904 GAACAAATCTGGAGACAACACACTACCTGATTTCAAACTATAATATAAGG 2953
                                vi     ivvv      v  ii        viv  v  i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_56253542_5   2954 CCATAGTCACCAAAACAGTGTGGTACTGGTATAAAAATAGGGACATAGAC 3003
                          i i   v i   i               i    ii    iv i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_56253542_5   3004 CAATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATATTTACAGT-- 3051
                                 i     v    ii               v i     ii  --
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_56253542_5   3052 -TTCATCTTTGGTGAAGCAAACAGAAACATAAAGTCGGGAAAGGACAACC 3100
                         -  v  i  i iii i vviv  ii v   vv i v       i i ii 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_56253542_5   3101 ATTTCTACAAATGATGCTGAGATAATTGGCTAGCCACACGTAGGAGAATG 3150
                         v    v       i     i  i  i   v  ?     i i ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_56253542_5   3151 AAACTGGATCCTCATCTCTCACTGTATAGAAAAAGCAACTCAAGATGGAT 3200
                           ii    i  ii i   v   ii    v     vi       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_56253542_5   3201 TAAGAACTTAAATCTAAGTCCTGAAACTATACAAATTGTAGAAGATAACA 3250
                         i ?ii  i     v    vv  i        v  v iv       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_56253542_5   3251 TTGGAAAAACCCTTCGAGGCATTGGCTGAGGCAAGGATTTCATGACCAAG 3300
                          v  ?iv  vi     v i v    v v      v i    v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_56253542_5   3301 AACCCCAAAACAAATACAATAAAAACAAAGATAAGCAGTTGGGACTTAAT 3350
                          vv  v   i  v vi   i    iv   i   iii iv v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_56253542_5   3351 TAAACTAAGGAGCTTTTGCACGGCAAAAGGAA-TAGTAAGCAGAGTAAAC 3399
                         i   v v ii i      ii vv    i iv -  vi   - i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAA 696

  chrX_56253542_5   3400 AGACAACCCAGAGAATAGGAGAAAATCTTCACAATCTATACATCTGACAA 3449
                                   v     i         v  ii   vii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_56253542_5   3450 AGGACTGATAGCTGGAATCTACAATGAACTCAAACAAATCAGTAAGAAAA 3499
                         i     vi  v ii    v  i  v      vv    v   i   v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_56253542_5   3500 AAA-----AATCCCATCAAAAACTCGACAAAGGACATAAACAGAAAATTC 3544
                          i -----  i  v  i?    v v i       iv i  i   v v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_56253542_5   3545 TCAAAATAATATATACAATTGGCTAACAAATATATGAAAAAATGTTCAAC 3594
                           v   v  v        v    i  i  ii i       i   i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_56253542_5   3595 CTCCCTAATGAT 3606
                         v  v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (141 / 110)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.14 (15 / 7)  


3172 27.34 0.66 0.55  chrX_56262323_56268726.rev     5007  5913 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56262323_5   5007 TGGAAGAACATTCTATGCTCGTGGGTAGGAAGAATCAATATCGTGAAAAT 5056
                              ii i  i i   i  i   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56262323_5   5057 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5106
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56262323_5   5107 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5154
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56262323_5   5155 TATGGAACCAAAAAAGAGTCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5204
                                viiv  ii  vi v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56262323_5   5205 AACAAAGCTGGAGGCATCACTCTACCAGGCTTCAAACTATACTACAAGGC 5254
                                i      vv    v  v  viii      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56262323_5   5255 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5304
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56262323_5   5305 AATGGAACAGAAC--AGAGCCCTCAGAAAGAACGCCGCATATCTACAACT 5352
                                i    i--    i  --     v  vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_56262323_5   5353 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCT 5402
                          vi    i  i     ivv  v   i v  vvv           i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56262323_5   5403 CTATTTAATAAATGGTTCTGGGAAAACTGGCTAGCCGTATGTAGAAAGCT 5452
                           v  i  i       v      v      v  ?  ii   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56262323_5   5453 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5502
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56262323_5   5503 TTAAAGACTTAAATGCTAGACCTAAAACCAGAAAAACCCTAGAAGAAAAC 5552
                          i ?    i      iv   v       i v    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_56262323_5   5553 CTAGGCA-ATACCATTCAGAAGATCGGTATGGGCAAGGACTTCATGACTA 5601
                         v    ?i- v i -   ivi vv i  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_56262323_5   5602 AAACACCAAAAGCAATGGCAAGAAAAGCCAAAATTGACAAATGGGATCTA 5651
                         vi            vvi    v     vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_56262323_5   5652 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5701
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_56262323_5   5702 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACTCATCTGACA 5751
                         v  i     i                 v      ivii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_56262323_5   5752 AAAGGCTAATATCCAGAATCTATAATGAACTCCAACAAATTTACAAGAAA 5801
                          ii i  vi          v     v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_56262323_5   5802 AAT-CAAATAACCCTGTCAAAAAGGGGGCAAAGGATATGAACAGACACTT 5850
                           v-          vi i?    iv           v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_56262323_5   5851 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5900
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_56262323_5   5901 CATCACTGGCCAT 5913
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2906 23.06 2.64 1.58  chrX_56269296_56271046      500  1258 (493)    L1M4_orf2#LINE/L1      142   908 (0)  

  chrX_56269296_5    500 AAATTCAAATTGAATCACAAAATATTTCACATAGCTAGAGCAATCATGAG 549
                                v  v   vii   iiv iiiviv     i i i     v   i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_56269296_5    550 CAAGAAAAATCAAAGCTGGAGACAATTATAT---CTGATTTCAGATTATA 596
                         v     i  -     i     i- v i i i--- ii      i viv  
  L1M4_orf2#LINE/    192 AAAGAAGAA-CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_56269296_5    597 TTACACAGCTATAGTAAACAAGACAGTATGGTACTGGCATAAAAACAGAC 646
                         i    v     i     v         i              ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_56269296_5    647 ACATAGACCAATGGAACACGATAGAGAGACAAGAAATAAACCCACACATA 696
                          i     i        i vi  v     v v             i    v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_56269296_5    697 TATGGTTAATCAATATTTAACAA---TGCCAAAATACA--CAATGGGGAA 741
                               i   ii  v  ii    ---      i i-  --          
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAA 388

  chrX_56269296_5    742 ATGATAATCTCATCAATACATGTTGTTGGGAAAAGTGGATATCCTCATGC 791
                          vi   i   iv    i v   v  i     v  v      ?  v     
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_56269296_5    792 AAAAGTATAAAATTGGGCCTCTGTCTTACACCATATACTAAGATCAACTA 841
                              v  i  i    i  i  ii  i           v  i  i    v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_56269296_5    842 AACATGGATTTATGGCTTAAATATATGA-CTTAAACCGTAAAATTTCTAG 890
                           v      iv?v i i     i  v  -  v    ii     i ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_56269296_5    891 AAGAAAACATAGGAATAAG-CTCCTTGACACTGATCTTGGCAATGAGTTT 939
                                      ?i   i-  i v    vi  ivi v       iv  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_56269296_5    940 TTGGATATGACACTAAAAGCAGAGGCAACAATAGCAAATATAGTCAAGTG 989
                           i          i       v i       v  v   v    vi  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_56269296_5    990 GGACTCCATCAAACT--AAAACTCTATTGCACAGCAAAGGAAAC----AA 1033
                              i       v --      i --  ii vv       v  ----  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTT--TGTGCTTCAAAGGACACTATCAA 686

  chrX_56269296_5   1034 CAGAATAAAGAGACAACCTGCAGAATGAGACAAAATATTTGCAAACCATA 1083
                         v i i i  i        ii       i  v              i    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_56269296_5   1084 TATCTGATAAGGGATTAGTATCCACAGTATATACGGAAATC----AACTC 1129
                                       i v       v i      vi   v  ----     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_56269296_5   1130 AATAGCAAAAATGTAAATAACAAGTAAACCAACTTACAAATTGGCATAGA 1179
                             ii     vii       -------    i ? v    v    v  i
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAAC-------CCAATTWAAAAATGGGCAAAGG 829

  chrX_56269296_5   1180 ATCCAAATAGACATGTCATGAAAGAAGATATGCAAATGGCCAACAGGTAT 1229
                           iii         v  viv           i           i i i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_56269296_5   1230 AAGAAAAGGTGCTCAACATTACTAATTGC 1258
                          v      i          i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (108 / 63)
Gap_init rate = 0.02 (13 / 767), avg. gap size = 2.46 (32 / 13)  


2884 25.84 1.30 3.14  chrX_56272140_56276420.rev     2866  3790 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56272140_5   2866 TGGAAACACATCCCGTGCCCATGGATGGGTAGAATCAATATTGTGAAAAT 2915
                               v i     i  ii       v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56272140_5   2916 GACCATGCTGCCAAAAGCAATCCAGAAATTCAATACAATCCTCATCAAAA 2965
                          i v  i  v  v   vii   i v i      ii      ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56272140_5   2966 TATCCCCA--T-CATTCTGCACAGAATTAGAAAAAACT-ATTCTAAAATT 3011
                          ---    -- - v  i vii     v v  v  i-  -  i        
  L1M4_orf2#LINE/    101 T---CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chrX_56272140_5   3012 CATCTGGAACAAAAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAA 3061
                            v     -- viv  ii  v  v v         i   vvi i iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_56272140_5   3062 AAAGAACAAATCTGGAGGCCTCACACTACTATACTATAGTATAGTAGCAT 3111
                         i         vi      v        v ---- i ----  -- ---- 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTC----CCA----AT--T----T 230

  chrX_56272140_5   3112 CCAAACTATACTATAGGGCCATAGTCA-CACAAACAGCATGGTACTGATA 3160
                          v     -     i ii  i i   v -  - i    ii        ii 
  L1M4_orf2#LINE/    231 CAAAACT-TACTACAAAGCTACAGTAATCA-AGACAGTGTGGTACTGGCA 278

  chrX_56272140_5   3161 TAAAAATAGGCACATAGACCAATGGAACAGAATAGAGAACCCCAAAATAA 3210
                            ii    i  i     i        i     v    ii  vi      
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_56272140_5   3211 AGCC-TAGTACTTACAGCTAACTGATCTTCGACAAAGCAAACAAAAAACA 3259
                          v  -  -i i   ii ii  i    i        i -ivi v  i v  
  L1M4_orf2#LINE/    329 ACCCATA-CATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCA 376

  chrX_56272140_5   3260 TAAAGTGGGGAAAGGACACCCTTTTCAACAAATGGTGCTGAGATAATTGG 3309
                          vv i         i i vi                    i  i  i   
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_56272140_5   3310 CAAGCTACATGTAGGAGAATAAAACTGGATCCTCATCTCTCATCTTATAC 3359
                         vv ? i     i ii     i  ii    i  ii i   v  i v     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_56272140_5   3360 AAAAACCAACTCAAGATGGATTAAGAACTTAACCCTAAGAACGGAAACCA 3409
                              ii       i      i ?ii  i   viv     i vi    i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_56272140_5   3410 TAAAAATTCTAGAAGATAACATTGGAA-AAACCCTTGTAGACATTGGCTT 3458
                              v ii       v     v  ?i-   i i i  -   v    v  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACCTTGGGTT 575

  chrX_56272140_5   3459 AAGCAAGGATTTCACGACCAAGAATCCAAAAGCAAATGTAATAAAATCAA 3508
                          i    v i    viiivi v  vv         v v i  i    vv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_56272140_5   3509 AGATAAATAGCTGGGGCGTAATTGAA-CTAAAGAGTTTTGCATGACAAAA 3557
                          i   i   iv v  i v v  ii  -i    i v     iiivv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_56272140_5   3558 GGAACAGTCAGCAGAGTAAACAGACAACCTACAGAGTGGGAGGAAATCTT 3607
                          iv  vi   iv i   i  v        i     i      i    v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_56272140_5   3608 CACAATCTATACATCTGACAAAGGACTAATATCTGGAATATACAACAAAC 3657
                         ii   vii   i      i  i     vi    ii       i  vi   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_56272140_5   3658 TT----AAATCAGTAAGAAAAAAAAATTCAAACAATCCCATTAAAAAGTG 3703
                          i----  v   i   v     i ----    i  i  v   ?    i  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGA----CAAATAACCCAATTWAAAAATG 821

  chrX_56272140_5   3704 GACTAAGGACTTGAACAGACAATTCTCAAAAGGACATATACAATTGGCCA 3753
                          i v     i     i     v     v    i v        v      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_56272140_5   3754 ACAAACATATGAAAAAATGCTCAACATCACTAATGAT 3790
                          i  i  i       i             ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (152 / 83)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.95 (41 / 21)  


3045 28.34 0.66 0.55  chrX_56282986_56285482     1098  2004 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56282986_5   1098 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCTTGAAAAT 1147
                              ii i  i     i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56282986_5   1148 GGCCACACTGTCCAAGGTAATTTATAGATTCAATGCCCTCCCCATCAAGC 1197
                            v i   vi    iv i  i  i        i  vv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56282986_5   1198 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACCTTAAAGTTC 1245
                          v   iivi i  i  ii     -   --- v  i  - i i    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_56282986_5   1246 ACATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCTTAAGCCAAAA 1295
                          i      viiv  ii  v  v v  vi    iv       i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_56282986_5   1296 GAAGAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 1345
                            v    i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_56282986_5   1346 CTACAGTTACCAAAATAGCATGGTACTGATACCAAAACAGAGATATAGCT 1395
                                v i   i i  ii        ii iv ii i   v      v 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_56282986_5   1396 CAATGGAACAGAAC--AGAGCCCTCAGAAATAAGGCCGCATATCTACAAC 1443
                                 i    i--    i  --        iv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_56282986_5   1444 TATCTGATCTTTGACAAACATGAGAAAAATAAGCAATGGGGAAAGGATTC 1493
                         i vi    i  i     ivi  vv  i vi vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_56282986_5   1494 CCTATTTAATAAATGGTGCTGGTAAAACTGGCTAGACATATGCAGAAGC- 1542
                         i  v  i  i            v v      v  ?v  i     i   v-
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_56282986_5   1543 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 1592
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_56282986_5   1593 ATTACAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAC 1642
                           i ?    i    ii v   v       i      vi i         v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_56282986_5   1643 CCTGGGCTTTACCATTCAGGACATAGGCATGTGCAAGGACTTCATGTCTA 1692
                          v i  ?v v viv   iv   v v  vv iv    v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_56282986_5   1693 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 1742
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_56282986_5   1743 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAA 1792
                           i   v i  i i   i  ii vv    i  v    i  vv i i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_56282986_5   1793 CAGGCAACCTACAAAATGGGAGAAAATTTTTGTAACCTACTCATCTGACA 1842
                         v  i     i   i             v    i  vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_56282986_5   1843 AATGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAG 1892
                          iv i  vi          v  i  v      iv    v iv i  v  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_56282986_5   1893 AAAACAAGTAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 1942
                           i    i      v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_56282986_5   1943 CTTAAAAGAAGACATTTATGCTGCCAA-AAACACATGAAAAAATGCTCAC 1991
                           iv        i  vi viiv     -  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_56282986_5   1992 CATCACTGGCCAT 2004
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (152 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


2954 28.89 0.88 0.77  chrX_56298186_56304847.rev     5265  6171 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56298186_5   5265 TGGAAGAACATTCCATGCTCATGCGTAGGAAGAATCAATATCGTGAAAAT 5314
                              ii i  i     i     vi v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56298186_5   5315 GGCCATACTGTCCAAGGCAATTTATAGATTCAATGCCATCCCTATCAAGC 5364
                            v     vi    ivii  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56298186_5   5365 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5413
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56298186_5   5414 TGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGAA 5463
                              viiv  ii  v  viv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56298186_5   5464 CAAAGCTGGAGGCATCCCTCTACCTGACTTCAAACTGTATATACTACAAG 5513
                              i      vv  v v  v  ii i      ---- iv        i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACTTACTACAAA 246

  chrX_56298186_5   5514 TCTACAGTAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGATACAGA 5563
                         v         i   i    i          i iv ii i   v   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_56298186_5   5564 CCAATGGAACGGAAC--AGAGCCCTCAGAAATAAGGCCGCATATCTACAA 5611
                         i        ii   i--    i  --        iv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_56298186_5   5612 CTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 5661
                         ii vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_56298186_5   5662 CTCTATTTAATAAATGGTGCTGGGAAAACTGACTAGCAATATGTAGAAAG 5711
                         v   v  i  i              v     iv  ? v i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_56298186_5   5712 CTGAAACTGAATGTCTTCCTTACACCTTATACAAAAATTAATTCAATATG 5761
                         v    ii  i ivi  v   i     v              i    v   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_56298186_5   5762 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAACCCCTAAAAGAAA 5811
                            i ?    i       v   v       i       i i  i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_56298186_5   5812 ACCTAGGCA-ATACCATTCAGGACACAGGCATGGACAAGGACTTCATGTC 5860
                           v    ?i- v i -   iv   viv  vv i i   v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_56298186_5   5861 TAAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGAGATC 5910
                           vi            vvi          vv i   v  i    vi  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_56298186_5   5911 TAATTAAACTAAGGAGCTTCTGCAGAGCAGAAGAAACTATCATCAGAGTG 5960
                          v  i   v v ii i   i  iivvv  i i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_56298186_5   5961 AAGAGGCATCCTACAGAATGGGAGACAATTTTTGCAATCTACTCATCTGA 6010
                           i  i  v  i             v   v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_56298186_5   6011 CAAAGGGCTAATATTCTGCATCTACAATGAACTCAAACAAATTTACAAGA 6060
                         i  i  i  vi   i v v  v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_56298186_5   6061 AAAAAACAA----CCCCATCAAAAAATGGGGGAAGGGTCTGAACAGACAC 6106
                             i    ----   v  i?         vi    i i    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_56298186_5   6107 TTCTCAGAAGAAGACATTTATGCAGCCAAAAGACACATGAAAGAATGCTC 6156
                              vi       i  vi viii     v ii         ii      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_56298186_5   6157 GTCATCACTGGCCAT 6171
                         iv     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (155 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.14 (15 / 7)  


2223 26.88 4.26 2.58  chrX_56322028_56324408.rev      998  1890 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56322028_5    998 TGGAAA---ATCATCATATTCACAGAT----AGAATAAATATTGTTAAAT 1040
                               ---   -i   i    ii   ----   v v           iv
  L1M4_orf2#LINE/      1 TGGAAAGATATC-CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_56322028_5   1041 TGGTGTTACTACCCACAGAAATATACAGATTCAATGCA-TTTCTATCAAA 1089
                            iiv    v    v vvi  v           i   - ii        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_56322028_5   1090 CTGCCAATATTATTTTTCACAGTACTAGAAAAAACT-ATTCTAAAATTCA 1138
                         v v   iivviv     ii   v v v  v  i-  -  i          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_56322028_5   1139 TATGGAACAAAAAATAGACC--AAATAGTCAAG-TAATTCTTAGTGAAAA 1185
                                - viv  vi    --i     i   i-i   ii v ivi i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_56322028_5   1186 GAACAAAGCAAGAGGCATCACACTACCGTACTTCAAAGTATACTACAAGG 1235
                                 ivi    vv       v  vv i      iiv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_56322028_5   1236 TTTGAATAACCAAGACAGCATGGTATTTGCATTGAAACAGACACATAGAC 1285
                         i vv i   i        ii     i v    viii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_56322028_5   1286 CTACGTAACAGAATAAAGAACCCAGAAATAAAGCTCCACACCTACAACCA 1335
                          v i v  i     vi   ii           v ivi   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_56322028_5   1336 TTTGATGTTTGACAAAGCTGACAGAAATGAACAATGGG-AAAGAACTCCC 1384
                         v     v  i     i v  v  ii viivv       -      ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_56322028_5   1385 TACTCAATAAATGATGTCTGGATAACTGGCCAGCCATATGTAGAAGATTG 1434
                          vi    i     i  iiv   i      vi ?   i   i i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_56322028_5   1435 AAAGTGGACCCCTTCCTGTCATCATATACAAAAATCATCTCAAGATGGGT 1484
                           iv         v   vv  i             i v     i    i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_56322028_5   1485 TAAAACTTTAAATGTGAGACCTAAAACTTAAAAAAAAAACT---AGGA-A 1530
                         i ? ivii       i   v        ----- v      ---  i - 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACT-----ATAAAACTCTTAGAAGA 542

  chrX_56322028_5   1531 AAACCTAG-CACATACCATTCCAGACTTAGACCTTGGCAAAGATTTC--- 1576
                             v   -?ii v i -   vv   i v ivi v     v i    ---
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_56322028_5   1577 ---ATGACAAAGTCTCCCAAAATAATCA-CAATAAAAACAAAAATTAACA 1622
                         ---      -------      vv iv -   i    iv      vi i 
  L1M4_orf2#LINE/    592 GATATGACA-------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_56322028_5   1623 AGTGGGATCTAATTAAA--TAAAAAGTTCTACATAGCAAACAACAACAAA 1670
                          i v   ii v  i   --      v  i iiiivv    vi   vi vv
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_56322028_5   1671 AAGAATCAACAGTGCAAAAAACAACTTACAGAATGAGAGAACATATTCAC 1720
                              -----    -    i     ii        i     v     ii 
  L1M4_orf2#LINE/    685 AAGAA-----AGTG-AAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_56322028_5   1721 AAAATATGCATCCAACTAAGGTCTAATATCCAGAATCTATAAGGAAGTCA 1770
                            vi  ii   ii iv i  v  vi          v     i   v  v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_56322028_5   1771 AACAAATCAACAAGCAAAAAACAA----CCCCATTAAAAAACAGGGAAAA 1816
                         v    v    i  vv    i    ----   v   ?     i-   v   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT-GGGCAAA 827

  chrX_56322028_5   1817 GCAT--GAACAAACACTT-TCAAAAGAAGACATACACAT----AATAAGC 1859
                          v  --   i i   i  -  v        i     v  ----       
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_56322028_5   1860 ATTTGAAAAAATGCTCAACATCACTAATCTT 1890
                          iv      i             ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (136 / 100)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.35 (61 / 26)  


 824 29.59 5.33 0.89  chrX_56333762_56340162.rev        3   340 (6061)    L1M4_orf2#LINE/L1       55   407 (501)  

  chrX_56333762_5      3 ATACGGCTCAAATTAATTTCTACATTCAATGCTATTCCCATCAAACTACC 52
                             vv i      i  i vi v      i  v  i  i      v v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_56333762_5     53 ATTGACAATCTTCACAAAATTAGAAAAACT-ATTTTAAATTTTATATGGA 101
                          vivi vv i  ii  i  v v  v  i  -  ii    v  i       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_56333762_5    102 A-T-CAAAGAAGTCCCCATATAACCAAGAGAACACTCAGCAAAAAGAACA 149
                          - -   i i --   viv   i    i v  ivi v iv  i       
  L1M4_orf2#LINE/    155 AATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_56333762_5    150 AAGTTGGAGGCATCATGCTACCTAACTTCAAACTATAGTACAA-GCATAC 198
                                   vv   ii  v  i  i      viv  v     -  -   
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC-TAC 251

  chrX_56333762_5    199 AGTAACCAAAACAGCATGGTACTGGTACCA----AAACAT---------- 234
                              i   i    ii         i iv ---- i    ----------
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_56333762_5    235 GGAGGAGAACTGAGACCTCAGAAATAACACCACACATCTACAAACATCTC 284
                            iv    i     vii         vv   i    i  iiiv  vi v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_56333762_5    285 ATCTGTGACAAATTTGACAAAAACAGGCAATGGGGAAACTATCTCCTTTT 334
                           i vi     ivv  v   i v  vv           vv  vvi     
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_56333762_5    335 CAGCAA 340
                           i   
  L1M4_orf2#LINE/    402 CAACAA 407

Transitions / transversions = 1.17 (54 / 46)
Gap_init rate = 0.02 (8 / 353), avg. gap size = 2.62 (21 / 8)  

3091 27.01 0.77 0.66  chrX_56333762_56340162.rev     5004  5910 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56333762_5   5004 TGGAAGAAAATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5053
                              ii v  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56333762_5   5054 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5103
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56333762_5   5104 TAGCAAAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGCTTA 5151
                          vv  ivvi i  i  ii     -   -- v  i  - iii    ii i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56333762_5   5152 TACCGTACTAAAAAGGAGTCCACATAGCCAAGACAATCCTAAGCGAAAAG 5201
                           iv v v iv  i   vi viv        i      i i ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56333762_5   5202 AACAAAGCTGGAGGCAC-CACGCTACCTGACTT-GAAACTATACTACAAG 5249
                                i      -  -   i  v  ii i  -i     -        i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chrX_56333762_5   5250 GCTAAAGTAACTAAAACAGCATGGTACTTGTACCAAAACAGAGAAATAGA 5299
                             v     ii  i    ii       v i iv ii i   v v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_56333762_5   5300 ACAATGGAACAGAACAGAGGCCTCACAAATAACACCACACATCTACAACC 5349
                         v        i    iv   ivii  v      vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_56333762_5   5350 ATCTGATCTTTGACAAACCTGACAAAAAAAG-AAGTGGGGAAGGGATTCC 5398
                          vi    i  i     ivv  v   i vv v-v i       i i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56333762_5   5399 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5448
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56333762_5   5449 GAAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAA-TCAAAGGTGG 5497
                            ii    i    v   i     v i            -     i-   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGG 495

  chrX_56333762_5   5498 ATTAAAAATTTAAATGTCAGCCCTAAAACCATAAAACCCCTAGAAGAAAA 5547
                           i ? i ii       v  vv       i       i i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_56333762_5   5548 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 5596
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_56333762_5   5597 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 5646
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_56333762_5   5647 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5696
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_56333762_5   5697 ACAGGCAACCTACAGAATAGGAGAAAATTTTTGCAACCTACCCATCTGAC 5746
                          v  i     i       i         v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_56333762_5   5747 AAAGGGCTAATATCCAGAATCTACAAAGAACTTTAACAAATTTACAAGAA 5796
                           i  i  vi          v  i        i v    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_56333762_5   5797 AAAAACAAACAACCCCATCGAAAAGTGGGCAAAGGATATGATCAGACATT 5846
                            i     i     v  i?    i            v   vi       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_56333762_5   5847 TCTCAAAAGAAGACATTTATGCAGCCAACTGACACATGAAAAAATGCTCA 5896
                             v        i  vi viii     ivii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_56333762_5   5897 TCATCACTGGTCAT 5910
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.08 (13 / 12)  


3105 27.31 0.66 0.66  chrX_56340905_56351353      492  1399 (9050)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_56340905_5   1399 TGGAAGAACATTCCATGCTCATGTGTAGGAAGAATCAATATCATGAAACT 1350
                              ii i  i     i     vi v      v i     ii v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_56340905_5   1349 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1300
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_56340905_5   1299 TACCAATGAATTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTCA 1252
                          v   iivivi  i  ii     -   -- v  i  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_56340905_5   1251 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 1202
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_56340905_5   1201 AATAAAGCTGGAGGCATCATGCAACCTGACTTCAAACTATACTACAAGGC 1152
                           i    i      vv   ii vv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_56340905_5   1151 TACAGAAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1102
                              v  i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_56340905_5   1101 AATGGAACAGAAC--AGAGCCCTCAGAAATAG-CGCTGACTGTCTACAA- 1056
                                i    i--    i  --       i- v vv  -i i  iii-
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATAC-ATTTATGGT 345

C chrX_56340905_5   1055 CAATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 1006
                             -    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

C chrX_56340905_5   1005 CCCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 956
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chrX_56340905_5    955 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 906
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chrX_56340905_5    905 GATTAAAGACTTAAACGTTAGACCTATAACAATAAAAATCCTAGAAGAAA 856
                            i ?    i    i  v   v   v   v      v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chrX_56340905_5    855 ACCTAGGCATTGCCATTCAGGACATAGGCACAGGCAAGGACTTCATGTCT 806
                           v    ?i viviv   iv   v v  vvi      v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

C chrX_56340905_5    805 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 756
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

C chrX_56340905_5    755 AATTCAACTCAAGAGCTTCTGCACATCAAAAGAAACTACCATCAGAGTGA 706
                         v  iv  v i  i i   i  ii v     i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

C chrX_56340905_5    705 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACTTACTCATCTGAC 656
                          v  i     i   i             v       v i ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

C chrX_56340905_5    655 AAAGGGCTAATATCCAGAATCTACAATGAACTTCAACAAATTTACAAGAA 606
                           i  i  vi          v  i  v     iiv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

C chrX_56340905_5    605 AAAAACAAACAACCTCATGAAAAAGTGGGCAAAGGGCATGAACAGACACT 556
                            i     i    iv  v?    i          iiv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chrX_56340905_5    555 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 506
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chrX_56340905_5    505 TCATCACTGGCCAT 492
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  

2976 27.10 1.55 1.11  chrX_56340905_56351353     9053  9956 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56340905_5   9053 TGGAAGAACATTCCATGCTCATGTGTAGGAAGAATCAATATCATGAAACT 9102
                              ii i  i     i     vi v      v i     ii v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56340905_5   9103 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 9152
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56340905_5   9153 TACCAATGAATTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTCA 9200
                          v   iivivi  i  ii     -   -- v  i  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56340905_5   9201 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 9250
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56340905_5   9251 AATAAAGCTGGAGGCATCATGCAACCTGACTTCAAACTATACTACAAGGC 9300
                           i    i      vv   ii vv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56340905_5   9301 TACAGAAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 9350
                              v  i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56340905_5   9351 AATGGAACAGAAC--AGAGCCCTCAGAAATAG-CGCTGACTGTCTACAA- 9396
                                i    i--    i  --       i- v vv  -i i  iii-
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATAC-ATTTATGGT 345

  chrX_56340905_5   9397 CAATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 9446
                             -    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_56340905_5   9447 CCCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 9496
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_56340905_5   9497 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 9546
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_56340905_5   9547 GATTAAAGACTTAAACGTTAGACCTATAACAATAAAAATCCTAGAAGAAA 9596
                            i ?    i    i  v   v   v   v      v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_56340905_5   9597 ACCTAGGCATTGCCATTCAGGACATAGGCACAGGCAAGGACTTCATGTCT 9646
                           v    ?i viviv   iv   v v  vvi      v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_56340905_5   9647 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 9696
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_56340905_5   9697 AATTCAACTCAAGAGCTTCTGCACATCAAAAGAAACTACCATCAGAGTGA 9746
                         v  iv  v i  i i   i  ii v     i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_56340905_5   9747 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 9796
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_56340905_5   9797 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 9846
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_56340905_5   9847 AAAAGCAA----CCCCATCAAAAAGTGGGTGAAGGATATAAACAGACACT 9892
                            ii   ----   v  i?    i    ii      v i  i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_56340905_5   9893 TCTCAGAAGAAGACAGTTATGCA----GTCAAAAAACACACGAAAAAATG 9938
                             vi       ----   i  ---- i   v  i    i     i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_56340905_5   9939 CTCACCATCACTGGCCAT 9956
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.00 (24 / 12)  


2949 28.11 0.99 0.88  chrX_56362586_56371202.rev     4900  5806 (2811)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56362586_5   4900 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTAAAAAT 4949
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56362586_5   4950 GGCCATACTGCCCAAGGTAAATTTCAAATTCAATGCCATCCCCATCAAGC 4999
                            v     v     iv i vi v  i      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56362586_5   5000 TACCAATGACTCTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5047
                          v   iivi ii i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56362586_5   5048 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCCAAGCCAAAAG 5097
                                viiv  ii  v  viv  vi    iv     iii ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56362586_5   5098 AAGAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5147
                           v    i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56362586_5   5148 TACAGAAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATC 5197
                              v  i   i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56362586_5   5198 AATGGAACAGAAC--AGAGCCCTCAGAAACAACGCTGCATATCTACAACT 5245
                                i    i--    i  --     i  vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_56362586_5   5246 ATCTGATCTTTGACAACCCTGAGAAAAACAAGCAATGGGGACAGGATTCA 5295
                          vi    i  i     vvv  vv  i v  vv         v  i  vvv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56362586_5   5296 CTACTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5345
                           vi i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56362586_5   5346 GAAACTGGATCCCTTCCTTACACTTTATACAAAAATTAATTTAAGATGGA 5395
                            ii    i    v   i    iv              i i  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56362586_5   5396 TTAAAGACTTACATGTTAGACCTAAAACCAGAAAAACCCTAGAAGAAAAC 5445
                          i ?    i  v    v   v       i v    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_56362586_5   5446 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5495
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_56362586_5   5496 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5545
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_56362586_5   5546 TTCAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATGAGAGTGAAC 5595
                          iv  v i  i i   i  ii vv    i  v    i  v  i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_56362586_5   5596 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTGCTCATTTGACAA 5645
                           i     i   i             v  ii   viiiivi  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_56362586_5   5646 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5695
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_56362586_5   5696 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGAAACTTC 5745
                          i     i     v  i?    i     i     iv    i   v i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_56362586_5   5746 CCAAAAGAAGAGGTTTATGCAA----CCAA-AAACACATGAAAAAATGCT 5790
                         i v        ----   i   ----    -  i          i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_56362586_5   5791 CACCATCACTGGCCAT 5806
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (150 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  

3040 27.69 0.66 0.88  chrX_56362586_56371202.rev     7217  8126 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56362586_5   7217 TGGAGGAACATTCCATGCTCATGGGTAGGAAGAAACAATATTGTGAAAAT 7266
                             iii i  i     i      i v      vvi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56362586_5   7267 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 7316
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56362586_5   7317 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 7364
                          vi  iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_56362586_5   7365 ATGTGAAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 7414
                           i  i  viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_56362586_5   7415 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 7464
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_56362586_5   7465 CTACAGTAACCAAAACAGCATGGTACTGGTAACAAAACAGAGATATACAT 7514
                                  i   i    ii         i vv ii i   v     v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_56362586_5   7515 CAATGGAACAGAAC--AGAGTCCTCAGAAATAATGCCGCATATCTACAAC 7562
                                 i    i--       --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_56362586_5   7563 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT-G 7611
                         i vi    i  i     ivv  v   i v  vvv           i  - 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_56362586_5   7612 CCTTATTTAATAAATGGTGCTGGGAAATCTGGCTAGCCATATGGAGAAAG 7661
                         i   -  i  i              v v    v  ?   i   v i  ii
  L1M4_orf2#LINE/    396 TCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_56362586_5   7662 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 7711
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_56362586_5   7712 CATTAAAGACTTACATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAA 7761
                         v  i ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_56362586_5   7762 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 7810
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_56362586_5   7811 TAAAACACCAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGGATC 7860
                           vi            vvi          v      v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_56362586_5   7861 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 7910
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_56362586_5   7911 AACAGGCAACCTAGAAAATGGCAGAAAATTTTCACAACCTATTCATCTGA 7960
                           v  i     i v i     v       v  ii   vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_56362586_5   7961 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 8010
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_56362586_5   8011 AAAAAAACAAACAACCCCCTCAAAAAGTGGGTGAAGGATATGAACAGACA 8060
                             i -    i     vv i?    i    ii      v    i     
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_56362586_5   8061 CTTGTCAAAAGAGGACATTTATGCAGCCATAAAACACGTGAAAAAATGTT 8110
                         i  v  v     i  i  vi viii    vv  i   i      i   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_56362586_5   8111 CATCACCACTGGCCAT 8126
                           v  i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2007 27.88 2.62 4.00  chrX_56380648_56382380.rev      443  1242 (491)    L1M4_orf2#LINE/L1      120   908 (0)  

  chrX_56380648_5    443 AGAAACTAACA--CTAATGGAAAAA--CATATGTATTTGAATATTAGCGT 488
                              i i   --  i  vvv    --      v ----   iiv  v -
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGA----AATGCAAGGG- 164

  chrX_56380648_5    489 ATGTATTTAAATCAGCTAAAATAATTTTGAAAAAGAAGAATAAAGTGGGA 538
                         ---- iii i vi   i    i   i              i     v   
  L1M4_orf2#LINE/    165 ----ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_56380648_5    539 AGAATCACTCTATGCAAGTTCAAGAG--ATTATATAGCTCCAGTAATCAA 586
                         i  v    v  viv   v     i v-- i  i v    v          
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_56380648_5    587 GACTGTGTGGTATTGGTGAATGGTTAAAGACATAGATCAGTGTAACAGAC 636
                            v        i   iiv v  v  i v i        i  v  i   v
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_56380648_5    637 TAAATAACTTAGAAATAGACCCACACACATATCACCAACTGATTTGTGAC 686
                          vi v iiii       i     i   iv   vii   i      vi   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_56380648_5    687 AAAGACAGCTAGATAGTCTAATTCAGGAAGAATAGTCTTTTTTAACAAAT 736
                           i iiiv v   ivi ii   vvi i              i-       
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC-AACAAAT 409

  chrX_56380648_5    737 TGTGTTAGAGCAATTGGACATTCATAGGCAAAAAAACCCAAAACCTTGAC 786
                         v   i i ii   i    i ?i  i v      i  i---i  vi v   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT---GAAGTTGGAC 456

  chrX_56380648_5    787 TTTAACCTCACACT-CATACAAAAATTAACCAAAAATGGACAATAAACTT 835
                         iiiv         i-i              iv        iv ? i  i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_56380648_5    836 AAATATAAAATATAAACCTAGAAAACATTCAGGAAAAAACAT-GGAGAAA 884
                             i   i vv    v   v     vi i  i i       -  ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_56380648_5    885 ATCTTCAAGGCCTAGGACATGGTGAAGATTTCTTAGAGATAACATCCAAA 934
                               iv i   v  iivv  ii v i         v  i   i v   
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_56380648_5    935 GTACAGTCCATACAAGGAACAATCGATAAATTGGACTTAATCAAAATTAA 984
                          i   iv v i v   i  v   v              v           
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_56380648_5    985 AACCTTTTGCTCTGTGAAACATCCTGTTGAGTGAATGAAAATAT----TA 1030
                           v      iv  vii  iv iv  i ii  vi i      v i----i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_56380648_5   1031 CAGACTAGAAGGAAATATTTGCAAAACACTTAGGCAAAAAAAAA-----A 1075
                             v i i  i             v  iv  vvii v  iii ----- 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_56380648_5   1076 ACC-TACTATTTTAA-AACCCTTAAAATTCAAGAGTAAGTAGACAATCAC 1123
                         v  -v v   v v  -   i    v  i    v i   iv      ----
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA---- 802

  chrX_56380648_5   1124 AAATGAGCATAATTGTCTCTCCAAATAAACA--GGGCAAAAGACTTGAAG 1171
                         --------    i-------    v ?  v --       i  i     v
  L1M4_orf2#LINE/    803 --------ATAAC-------CCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_56380648_5   1172 AGACATTTCATTGAATATGATATAATGGTAGCAAAGAAATGCATGAAAAA 1221
                                  viii  v v      vvii i  v  v  iii        i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_56380648_5   1222 TTGTTCAACATCACTAGCTGT 1242
                         v  i         ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (128 / 91)
Gap_init rate = 0.02 (16 / 789), avg. gap size = 3.31 (53 / 16)  


2651 24.76 10.10 0.96  chrX_56399219_56405546.rev     5006  5837 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56399219_5   5006 TGGAAGAACATTCCATGCTCATGGAAAGGAAGAATCAGTATTGTGAAAAT 5055
                              ii i  i     i       vv      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56399219_5   5056 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5105
                            v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56399219_5   5106 TACCAATGACTTTTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5153
                          v   iivi i     ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56399219_5   5154 TATGGAATCAAAAAAGAGCCCGCATAGCCAAGGCA--------------- 5188
                                viiv  ii  v  v v        ii  ---------------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56399219_5   5189 ----------------TCATGCTACCTGACTT--AAACTATCCTACAAGG 5220
                         ----------------   ii  v  ii i  --     - v      i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_56399219_5   5221 CTATAGTAACCAAAACAGTGTGATACTGGTACCAAAATAGA--TATAGAC 5268
                            i     i   i        i      i iv ii     --      i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_56399219_5   5269 CAGTGGAACAGAA--AAGAGGCCTGAGAAATAGCACCACACATCTACAAC 5316
                           i     i    --i    v  --       ivv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_56399219_5   5317 CATCTGATCTTTGACAAACCTGGCAAAAACAAGAAATAGGGAAAGGATTC 5366
                           vi    i  i     ivv  v   i v  vvv   i       i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_56399219_5   5367 CCTATTTCATAAATGATGCCAGGAAAACTGGCTAGCCATATGTAGAAAAC 5416
                         i  v  iv i     i   ii   v      v  ?   i   i i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_56399219_5   5417 TGAAACTGGATCCGTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5466
                             ii    i  v v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_56399219_5   5467 ATTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5516
                           i ?   ii       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_56399219_5   5517 CCTAGGC---AAT-------ACCTT---TCAGG--------------ACA 5539
                          v    ?---   -------     --- i   -------------- i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_56399219_5   5540 T-ACAC-ATGGGTAATGGCAACAAAAGCCAAAATAGACAAAT-GGA---- 5582
                          -    - vii i vvi          vv        i    -   ----
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_56399219_5   5583 ---------AAGAGCTT--GTGCATGGCAAAAGAAACTACCATCAGAGTG 5621
                         ---------  i i   --    v --    i  v    i  vv i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTG 693

  chrX_56399219_5   5622 AACAGGCAATCTATAGAATGTGAAAAAATTTTTGCAATCTACCCATCTGA 5671
                           v  i   i i i      v  i     v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_56399219_5   5672 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTTAACAAATGTACAAGA 5721
                         i  i  i  vi          v  i        i v    v vv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_56399219_5   5722 AAAGAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATACGAACAGACA 5771
                            - i     i     v  i?    i            vi   i     
  L1M4_orf2#LINE/    794 AAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_56399219_5   5772 CTTCTCAAAAGAAGATATTTATGCAGCCAACAGACACATGAAAAAATGCT 5821
                         i     v           vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_56399219_5   5822 CATCATCACTGGTCAT 5837
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (130 / 72)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.60 (92 / 20)  


2952 26.50 0.87 1.85  chrX_56410206_56413184     1570  2486 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56410206_5   1570 TGTAAAGATATTCTATGTTCATGGATTGGAAGTATCAATATTGTTAAAAA 1619
                           v        i i                  vv i           i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56410206_5   1620 GTCCATACTACCCAAAGCAATCTATAAATTTAATGTAATAACTATCAAAA 1669
                          v v     v      vii     i i   i  i i   vv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56410206_5   1670 TATTAATGACATTCTTCACAAAAATAGAAAAAAAG-TCCTAAAATTTATA 1718
                          vii iivi v  i  ii  i    v  v  ivv -          i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56410206_5   1719 TGGAACCACAAAAGACCGAGAATAGCTAAGACTATCCTAAATAATAACAA 1768
                              vii   ii    v        i  i  v   i i  v  v  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56410206_5   1769 CAAGAAAAGAAAACTGGAGGAATCACATTATCTGACTGGAAATTATACTA 1818
                            -------- ii       v     i vi ii i vv   viv     
  L1M4_orf2#LINE/    201 CAA--------AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_56410206_5   1819 TGCAGCTATAGTAACCAAAATGGCATGGAACTGGCATAAAAACAGACACA 1868
                         iiv     i     i   i ii ii   v          ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_56410206_5   1869 TAGATGAGTGAAACAGAATGAAGAACCCAAAGATAAATCCATACATCTAA 1918
                              v i  i  i     vi   ii   i i     i        i  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_56410206_5   1919 AGTGAGTTCATTTTTCACAAAGGTGTCAAGAACATATATTGAGGGAAGGA 1968
                         i  v i  v     iv    i    i     v   vi v  i  i   i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_56410206_5   1969 CAATTTCTTCACTAAATAGTGGTGGGAAAACGAAATGTCCACATGGAGAA 2018
                         i i i i    vi    i   v     v   vii  i?       v i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_56410206_5   2019 GAATAAAACAAGACCTCTATCTTTCACCATATACAAAAATCAAACCAAAA 2068
                             i  iivi    i   i  iv                i  vi     
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_56410206_5   2069 TGGATTGAAGACTTAAATCTAACACCACAAACTACAAACTTACTAACAGA 2118
                              ii?    i     v   v v vv      i   vi vi  iv   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_56410206_5   2119 AAACATTGAGGAAACTCTCCATAACATTGAAGTGGGCAAAGATTTCTTAA 2168
                               v i? v  v   i i i  v   iiv i     v i       i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_56410206_5   2169 GTAATACCCCACAAGCACAGGAAACCAAAGCAAAAATAAAAGAAATGGAA 2218
                         i  vv  v   v       i v   v    v       i vi  v    v
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_56410206_5   2219 TCATATCAAG-TCAAAAAGCCTCTTCACAGCAATTGACACAAGAAACAAT 2267
                          i-i     i- i     --  i  ---- iiv  --  v i  v  v  
  L1M4_orf2#LINE/    643 TT-CATCAAAATTAAAAA--CTTTT----GTGCTT--CAAAGGACACTAT 683

  chrX_56410206_5   2268 TGACAAAGTGAAGAGACAACTCA--GAATGGGAGAAAATATATTCAAACT 2315
                         ii v        i       i  --                v v    ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_56410206_5   2316 ACTCATATTAGAAGACATTAATAACCAGAATATATAAGGAACTCAAACAA 2365
                          ivi  v v v   iv i vi  v             i      vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_56410206_5   2366 CTTTATAGAAAAAAATCTAACACTCCAATTTAAAAATGGGCAAAATATCT 2415
                           iv   iv     iv v  i vi      ?             iv  i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_56410206_5   2416 GAATAGACATATATC---AAAAGACATACAAATGGCAAACAAGCCTATGA 2462
                                   v v  --- i    i           v  i    vi    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_56410206_5   2463 AAAG-TGCTCCACATCACTGATTAT 2486
                             -     v      ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.50 (25 / 10)  


3137 26.52 0.99 0.66  chrX_56419346_56423322     2580  3484 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56419346_5   2580 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 2629
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56419346_5   2630 GGCCATACTCCCCAAAATACTTTATAGATTCAATGCTATGCCCATCAAGG 2679
                            v            v iv i  i        i  v  v  i     ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56419346_5   2680 TACCATTGACGTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 2727
                          v   vivi v  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56419346_5   2728 TGTGGAACCAAAAAAGACCCTACATAGCTAAGACAATCCTAAACAAAAAG 2777
                          i     viiv  ii     viv     i  i      i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56419346_5   2778 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTGTACTACAAGTC 2827
                                i      vv       v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56419346_5   2828 TACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGATATATAGACC 2877
                                 i   i    ii   i     i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56419346_5   2878 AATGGAACAGAACACAG-GCCACAGAAATAACACCGCACATCTACAACCA 2926
                                i    ivv  - i -         vv  ii    i  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chrX_56419346_5   2927 TCTGATCTTTGACAAACATGACAAAAACAAGAAATGGGGAAATGAT--TC 2974
                         vi    i  i     ivi  v   i v  vvv          vi  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_56419346_5   2975 CTTATTTAATAAATGGTGTTGGGAAAACTGGCTAACCATATACAGAAAAC 3024
                         i  -- i  i        i     v      v  ?   i  i  i  i v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_56419346_5   3025 TGAAACTAGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGG 3074
                             ii i  i    v   i     v i            i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_56419346_5   3075 ATTCAAGACTTAAAAGTAAAACCTAAAACCATAAAAATCCTAGAAGAAAA 3124
                           iv?    i    v    i v       i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_56419346_5   3125 CCTAAGCA-ATACCATTCAGGGCATAGGCATGGGCAAGGACTTCATGTCT 3173
                          v  i ?i- v i -   iv i v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_56419346_5   3174 AAAACACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAGTGGGATCT 3223
                          vi         i  vvi          vv     v  i  i v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_56419346_5   3224 AATTAAACTAAAGAGCTTCTGCACAGCAAAACAAACTATCATCAGAGTGA 3273
                         v  i   v v  i i   i  ii vv    iv v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_56419346_5   3274 ACAG-CAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 3322
                          v  -     i                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_56419346_5   3323 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACCAATTTATAAGAA 3372
                           i  i  vi          v  i        ivv  v v iv    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_56419346_5   3373 AAAAACAAACAACTTCATCAAAAGGTGGGCAAAAGATATGAACAGACACT 3422
                            i     i   iiv  i?   ii        i   v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_56419346_5   3423 TCTCAAAAGAAGACATTTATGCAGCCAACAA--ACATCAAAAAATGCTCA 3470
                             v        i  vi viii     i  --    v    i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_56419346_5   3471 TCATCACTGGTCAT 3484
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


3219 25.30 1.10 0.77  chrX_56450235_56454463     2832  3736 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56450235_5   2832 TGGACAAAGATTCCATGATCATGGATTGGAATAATCAATATTGTGAAAAT 2881
                             v i v  i     v             v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56450235_5   2882 GTCCATACTACCCAAAGGAAT--GCAGATTTAATGCAATCCCTATCAAAA 2929
                          v v     v      vvi  --i      i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56450235_5   2930 TACCAATGACATTCTTCACAGAAATAGAGAAAA-AATCATTAAATTTTTA 2978
                          v   iivi v  i  ii       v  v  iv-i   v v     iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56450235_5   2979 TAAAACCACAAAAGACCCAGAATAGTTAAAGCCATTCTAAGAAAAAAAGA 3028
                          ii  vii   ii            ii   i v  ii i -    i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAGA 199

  chrX_56450235_5   3029 ACAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCT 3078
                              ii       v     i v  ii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_56450235_5   3079 ACAGTAACTAAAACGGTATAGTACTGATATAAAATCAGTCACATAGACCA 3128
                                ii  i  i  i i      ii    iivi  v  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_56450235_5   3129 ATGGAACAGAATAAAGAACTCAGAAACAAGTGCACACACCTACAGTGAAC 3178
                               i     vi   iii      i  iiv  i   ii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_56450235_5   3179 TCATTTTCAAAAAAAGTGCAAAGAACATACACTGGGGAAATGACACTTGC 3228
                          v      i v  ii    v    v   v  v        vi i v ivi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_56450235_5   3229 TTTATTAAATGGTCCTAGGAAAACTGGATATCCATATGCAGAAGAATGAA 3278
                           i vi       v  i   v         ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_56450235_5   3279 TCTATCTAGACACATGTCTCTCACCATATACAAAAATGAAGTCAAAGTTG 3328
                         ---i - i   v v ii   v                v  v     i v 
  L1M4_orf2#LINE/    450 ---GT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_56450235_5   3329 ATTAAATATTTAAATCTAAGACCGCAAACTATGAAACTATTACAAGAAAA 3378
                           i ? v ii     v     v vv       i     v   v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_56450235_5   3379 CTTTGGGGAAAATCTCCAGGACACTAGTTTGGGGAAACATTTCTTGAGCG 3428
                          v v  ? v      i iv   vi i v  i  v  vvi      -  vv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGAT 594

  chrX_56450235_5   3429 AT-ACCCCACAAGCATAGGTAACTAAAGCAAAAATGGACCAGTGGGATTG 3477
                           -  v   v     i i i   v    v      i  iv i v   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_56450235_5   3478 CATCAAG-TTAAAAAGCTTCTGCATGGCAAAAGATAAAGTCAACAAAGTG 3526
                               i-       -   i  iiivv    i  i vvi    v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_56450235_5   3527 AATAGACAACCC-CAGAATGGGAGAAAATATTTGCAAATGACCCATTTGA 3575
                           v         -                          v ivi  i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_56450235_5   3576 CAAAGGATTAATAAGCAGAATATATAAGGAGCTTAAGCAACTCTATAGGA 3625
                         i  i   i vi  vv            i  i  ivvi      v   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_56450235_5   3626 GAAAAATAA-TAATCTAATACAAAAATGG-CAAAATATTTGAATAAACAT 3673
                         i   i i  -   i i   v?        -    iv         i    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_56450235_5   3674 TTCTC-AGAAAAGACATACAA-TGGCAAAAAGGCATATGAAAAGGTGCTC 3721
                              - i i    i      -    v  v i   i        i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_56450235_5   3722 AACATCATTGGTAAT 3736
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (132 / 93)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.21 (17 / 14)  


2489 29.06 1.64 2.19  chrX_56485923_56491172.rev     3848  4759 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_56485923_5   3848 GAAAAAACATTCTATGATTATGGATTGGGAGAACCAATATT---AAAATG 3894
                          i   i i  i i   v i         i   vii      ---  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_56485923_5   3895 GCCATTGTGTCCAAAGCAATCTACAGAGTTAATGCT-TTCCTATCAAACT 3943
                           v  vv vi     vii         v i  i  v- i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_56485923_5   3944 ACCAATATTATTTTTTTTTTCATAAAATTGGACAAAACCATTCTAAAATT 3993
                         v   ii-- iii      v-  -i      -    iviv  i        
  L1M4_orf2#LINE/    102 CCCAGC--TGCCTTTTTTG-CA-GAAATTG-ACAAGCTGATCCTAAAATT 146

  chrX_56485923_5   3994 CCTATGGAACCCAAAAAGAGCCCGAATAGCCAAAGCAATCTTAGGCAAAA 4043
                          v       vivv  ii  v  v           i       iiiv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_56485923_5   4044 AGAACAAGGCCAGAGGCATCATGTTAACCCTCTTCAAA-----CTATAAG 4088
                                i iii    vv   iii vv  vvi      -----   i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_56485923_5   4089 GTTACAGTAACCAAAGCAGCATGAAACTGATACAAAAACATACACATACA 4138
                          i        i   ii   ii  iv    ii i  ii i v   i   v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_56485923_5   4139 CCAATTGAATAGGTTAGAAAGCCCAGAAATAAGGCCTCACACCCAGAGCT 4188
                         i    v      iv v  i  i          iv  vi   iii vi ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_56485923_5   4189 ATCTAATCTTTGGCAGACAAAGTCAACAAATATAATCAATGGAGAACGGA 4238
                          vi i  i  i ----    i viiv   ivvi v       i   v i 
  L1M4_orf2#LINE/    347 AATTGATTTTCG----ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_56485923_5   4239 TTCCCTATACAATAAATGATGCTGAAATAGCTGGCTAACCATAAGAAGAA 4288
                          vvi  v v   i     i     ii i i    v  ?   i v v i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_56485923_5   4289 GGATGAGACTGGACCACACTACCTTTCACCATATAAAAAAAT-AACTCAT 4337
                          i    iii      - -      iv         v      -      v
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACC-C-CTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_56485923_5   4338 GGTGGATTAAAGATTTAAATGTACAACCTCAAACTATAAGAGTCCCAGAA 4387
                         ii     i ?   ii        vi v  v         i v  ii    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_56485923_5   4388 GAAAGCCTGGGAA-ACATGATTCTGGACATGGGCCTTGGGAAA-GAATTC 4435
                             i v i  ?i- v  vv iv  iv v    --  i  v  - iv   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTC 588

  chrX_56485923_5   4436 ATGTCTACATTTTCAAAAGCAATTCCAACAAAACAAAAATTGG-CAAGTG 4484
                         v ivv  iivivi        vvvv        v     v i -i  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_56485923_5   4485 GGGCCTAATTCAACTAAAGAGCTTCTGCATAGTAAAATAAACTATCAACA 4534
                           i i v  iv  v v  i i   i  iiivvi   iv v        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_56485923_5   4535 GAGTAAACAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTACGCA 4584
                         i   i  v        i                          ii iii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_56485923_5   4585 TCCAACAAAGGTCTCATAGCCAGAATCTATAAGGAACTTAAACAATCGAA 4634
                           ii i  i  v  ii  v       v     i     ivv    iiv  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_56485923_5   4635 CAACCAAAAAATAAAATAAAACAAACCCA--TTAAAAAGGGGTAAAAGAC 4682
                         i  iv    i i   -   ------    -- ?     v   i   i  i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAA-TAA------CCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_56485923_5   4683 ATAAACAGACACTTCTCAAAAGAAGATATACAAATGGCTAACAAAGACAT 4732
                         v i  i     i     v                    i  i  iv    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_56485923_5   4733 GAAAAAATGCTCATCATCATGTCAGAT 4759
                              i       v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (161 / 100)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 1.94 (35 / 18)  


3188 28.19 0.22 0.22  chrX_56491228_56497626.rev     5001  5908 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56491228_5   5001 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5050
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56491228_5   5051 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5100
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56491228_5   5101 TACCAATGACTTTCTTCACAGAATTGGAAAAAACAACTTTAAAGTTCATA 5150
                          v   iivi i  i  ii     v v  v  ivii iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56491228_5   5151 TGAAACCAAAAAAGAGCCCGCATCGCAAAGTCAATCCTAAGCCAAAAGAA 5200
                           i  viiv  ii  v  v v  v  v  iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56491228_5   5201 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGATA 5250
                              i      vv   ii  v  ii i      viv        i v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_56491228_5   5251 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5300
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_56491228_5   5301 TGGAGCAGAAC--AGAGCCCTCAGAAATAACACCGCTTATCTACAACTAT 5348
                             ii    i--    i  --        vv  iivi  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_56491228_5   5349 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5398
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_56491228_5   5399 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGACATATGTAGAAAGCTGA 5448
                         v  i  i              v      v  ?v  i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_56491228_5   5449 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5498
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_56491228_5   5499 AAAGACTTAAACGTTAGACCTAAAATCATAAAAATCCTAGAAGAAAACCT 5548
                          ?    i    i  v   v      ii      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_56491228_5   5549 AGGCATTACCATTCACGACATAGGCATGGGCAAATACTTCATGTCTAAAA 5598
                            ?i v viv   ii   v v  vv i     vvii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_56491228_5   5599 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGATCTAATT 5648
                                    vvi          vv     v       v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_56491228_5   5649 AAACTCAAGCGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5698
                            v i  ivi   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_56491228_5   5699 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5748
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_56491228_5   5749 GGCTAATATCCAGAATCTACAATGGACTCAAACAAATTTACAAGAAAAAA 5798
                          i  vi          v  i  v i    vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_56491228_5   5799 ACAAACAACCTCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5848
                              i    iv  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_56491228_5   5849 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5898
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_56491228_5   5899 CACTGGCCAT 5908
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (150 / 102)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


2678 27.40 0.74 5.06  chrX_56501383_56508081.rev     5260  6208 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56501383_5   5260 TGAAAAAGCATTCCATGCTCATGGATAAGAAGAATCAATGTCGTGAAAAT 5309
                           i   iii  i     i        vi     v i   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56501383_5   5310 GGCCATAATCCCCAAAGTAACTTATAGATTCAATGCTATCGCCATCAAGC 5359
                            v   v        v i ii  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56501383_5   5360 TACTATTGACTTTCTTCACAGAATTAGAAAAAAAAAATTACTTTAAATTT 5409
                          v i vivi i  i  ii     v v  v  iv---- v iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC----TGATCCTAAAATT 146

  chrX_56501383_5   5410 CATATGGAACCAAAAAAGAACCCATATAGCCAACACAACCCTAAGCAGAA 5459
                                  viiv  ii  v  viv        v    i i i iv ii 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_56501383_5   5460 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAGCAA--TACTACA 5507
                                  i      vv       v  ii i     --  --       
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA--AACTTACTACA 244

  chrX_56501383_5   5508 ACACTGCAATAACCAAAAGAGCATGGTACGGGTACCAAATCAGATATATA 5557
                          vi  i  i   i   i v  ii      v  i iv iivi   i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_56501383_5   5558 GACCGATGGAACAGAATAGAGGCCTCAGAAATAATGCCACACATCTACAA 5607
                           i i      i     v   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_56501383_5   5608 CCATCTGATCTTTGACAAAACTGACAAAAACAAGCAATGGAGAAATGATT 5657
                         i  vi    i  i     iiv  v   i v  vv      i    vi  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_56501383_5   5658 CTATATTTAATAAATGGTGTTGGGAAAACTGGCTAGCTATATGCAGAAAA 5707
                         v v v  i  i        i     v      v  ? i i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_56501383_5   5708 CTGAAACTGGACCCTTTCCTTACAGCTTATACAAAAATTAAGTCAAGATG 5757
                         v    ii       i v   i   v v              v    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_56501383_5   5758 GACCCTTTCCTTACAGCTTATACAAAAATTAAGTCAAGATGTATTAAAGA 5807
                           ----------------------------------------- i ?   
  L1M4_orf2#LINE/    495 GA-----------------------------------------TCAWAGA 503

  chrX_56501383_5   5808 CTTAAACCTAAGTCCTAAAACCATAAAAACCCTAGAATAAAACCTAGGCA 5857
                          i    iv    vv       i      vi i     v     v    ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_56501383_5   5858 -ATACCATTCAGGACATAGGCATAAGCAATCACTTCATGGCTAAAACACC 5906
                         - v i -   iv   v v  vv  i     vii   v i v  vi     
  L1M4_orf2#LINE/    554 TAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_56501383_5   5907 AAAAGCAATTTCAACCAAAGCCAAAATTGACAAATGGGATCTAATTAAAC 5956
                                vvvv    v    vv     v  i    v   ii v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_56501383_5   5957 TAAAGAGCTTCTGCAGAGCAAAATAAATTATCATCAGAATGAACAGGCAA 6006
                          v  i i   i  iivvv    iv v i     vv i i    v  i   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_56501383_5   6007 TCTACAGAATGGGAGAAAATTTTTGCCATCTATCCATCTGACAAAGGGCT 6056
                         i i                 v     v vii  vi      i  i  i  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_56501383_5   6057 AATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA----TAA 6102
                         vi          v  i        ivv    v iv i  v   ----i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_56501383_5   6103 ACAACCCCATCAAAAAGTGGGTGAAGAATATGAACAGATACTTCTCAAAA 6152
                          i     v  i?    i    ii   i  v    i   i i     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_56501383_5   6153 GAAGACATTTATGTGGCCAACAAACATACGAAAAAATGCTCATCATCACT 6202
                              i  vi vi       i  i  i i     i       v     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_56501383_5   6203 GGTCAT 6208
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.37 (148 / 108)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 7.86 (55 / 7)  


2249 28.45 2.09 1.97  chrX_56513710_56515513      500  1311 (493)    L1M4_orf2#LINE/L1       96   908 (0)  

  chrX_56513710_5    500 CAAAATCCCAAAAAATATTATTAACAGAAATAGA------AATCTTAAAA 543
                                   ivviviv  v  i-       v  ------i   i     
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_56513710_5    544 TTTAGATGGAACCATGGAAG--ACTCAGAATAAGCAAAGCTATCCAAAGC 591
                           i v      --   v   --  i       iv    i v   ivi iv
  L1M4_orf2#LINE/    145 TTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_56513710_5    592 AAAAAGAACAAACCCAGAATAATTACATTACCTGACT-CAGA--TTAAAC 638
                           i         viii  iv v i   i v  ii i -  i --   -- 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--C 240

  chrX_56513710_5    639 TATATAGCGATGGTAATCAAAACAAGATGTTACTGGCATAAATACAAAAA 688
                           i v   v ii        i   ivi  v           iv i i v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_56513710_5    689 CATAGATTAATAAAACAGAATTCAGATCCCAGACATAAATCCACATACCT 738
                         i      i   ii  i      v   vi     v     i   i i ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_56513710_5    739 ACATTGAACTCATTTTTGACAAAAGTGCCACAAACATACACTAAGGAATA 788
                          iiv v  i v     i     ii      vi v   v  v ii    vi
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_56513710_5    789 GACACTCTCTTCAAAATATGGTGGGGGGAAAACTGGATATCCATACACAA 838
                         i i v   i     v v      vv    v         ?   i ii   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_56513710_5    839 AGAAATTAAACTAAACCCCTATCTCTTGCCACATACTACAGTGAAATAAA 888
                          ii   v  ii ii       i   vii   i    v v i v  v v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_56513710_5    889 AACGGATTAAAGACTTAAATCAAGGACCTCAAACTATGAAACTACTACAA 938
                           i    i ?    i     vv i  v  v       i     vi  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_56513710_5    939 GTAAACATTGGGGTAAATCTTCAGGACATTGGTCTCAGCAAGAACTTCAT 988
                          v      v  ?          iv   v    vi vi    viii   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_56513710_5    989 GAGTAATATCTCACAAGTACAGACAA--AGCAAAAAAATGGTCAAATGGT 1036
                         iii  vv ivi  v   i   ii   -- ivi       i vi    v v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_56513710_5   1037 ATCATATCAAG-TGAAAAAGCTTCTGTAGAGCAAAGGAAACAATCAACAA 1085
                          iivi     i- v     -   i   ivvv       v  v     v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_56513710_5   1086 AGTGAAGAGACAACCCACAGAATAGAAGAAAATATTTGCGAACTGCTCCT 1135
                               i                i i             i  iiiiviv 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_56513710_5   1136 TTAACAAAGGATTAATAACCAGACTATATAAAAAGCTCAAGCAATTC--T 1183
                         i i i  i   i vi  v     v        i i   vvi   i  -- 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_56513710_5   1184 A-CAAAACAATTGATAATCAGATTTTAAAATGAGCAAAAGATCTTAATAG 1232
                          -i    vi ivi    i vi   ?v      i     i   -  i ---
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGA--- 835

  chrX_56513710_5   1233 ATCTTAATAGACATTTCTTTAAAGAAGACACACAAGTGGCAAACAGGCAT 1282
                         ------            ii        i i    i    v  i i   i
  L1M4_orf2#LINE/    836 ------ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_56513710_5   1283 ATGAAAAGGTGTTCAACATCATTGATCAT 1311
                                 i  i         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.02 (14 / 813), avg. gap size = 2.36 (33 / 14)  


2791 26.90 3.52 0.45  chrX_56532941_56535271      958  1838 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56532941_5    958 TGGAAAAACATTTCACCCTCATGGACAGGAAGAATCAATATCATGAAAAT 1007
                               i i  ii  ivi       iv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56532941_5   1008 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 1057
                            v     v      v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56532941_5   1058 TACCATTGACATTCTTCACCGAATTAGAAAAACCTATTTTAAATTTCATA 1107
                          v   vivi v  i  ii v   v v  v  i iv  ii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56532941_5   1108 TGAAATCAAAAAAGACCCTGTATAGCCAAGACAATCCTAAGCAAAAAGAA 1157
                           i  viiv  ii     v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56532941_5   1158 CAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACGACAAGCCTA 1207
                              i     ivv   ii  v  ii i      viv   v    iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_56532941_5   1208 CAGTAACCAAAACAGCAAGGCACTGGTACCAAAAGAGATATATAGACCAA 1257
                               i   i    iiv  i     i iv ii v   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_56532941_5   1258 TGGAACAGAAGAGAGACCTCAGAAATAACACCAAACATCTACAACCATCT 1307
                              i    vv    vii         vv   v    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_56532941_5   1308 GATCTTCGACAAACCTGACAAAAACA--AAATAGGAAAAAGGATCTTCTA 1355
                            i        ivv  v   i v  --v   i  i   - i  vv   v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTT 399

  chrX_56532941_5   1356 TTCAGTAAATGCTGCTAGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 1405
                             ii     v    i   v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_56532941_5   1406 ACTGGACTCCTGCCATACACCTTATACAAAAACTAACTCAACATGGATTA 1455
                         ii     i   i  vi     v          i        v      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_56532941_5   1456 AACACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAACCTA 1505
                         ? v  i         i v i     i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_56532941_5   1506 GG---AAATCCATTCAGGACATAGGCATGGGAAAAGATTTCATGGCAAAA 1552
                           ---     --   iv   v v  vv i  v  v i    v i vv vi
  L1M4_orf2#LINE/    550 GGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_56532941_5   1553 ACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACTAATGGGATCTAAT 1602
                                     vvv          vv     v  iv   v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_56532941_5   1603 TAATCTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTAAACA 1652
                         i  vv v  i i   i  ii vv    i  v       vv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_56532941_5   1653 GGCAATCTACAGAAGGGGAGAAAATTTTTG-AAATCTACCCATCTGACAA 1701
                          i   i i      v          v    -     - ivi      i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAA 746

  chrX_56532941_5   1702 AGGTCTGATATTCAGAAT-------------TTACAA---------GAAA 1729
                         i  v  vi   i      -------------      ---------i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_56532941_5   1730 A---AAACAACCCCATCAAAAAATGAGCAAAAGGTATGAACATACACTTC 1776
                          ---   i     v  i?       i     i i v    i v   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_56532941_5   1777 TTAAAAGAAGACATTCACGTGGCCAACAAACATATGAAATAAAGCTCAAC 1826
                          iv        i  v  vi       i  i  i      vi v       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_56532941_5   1827 AACACTGATCAT 1838
                          v  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (131 / 103)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.89 (35 / 9)  


2956 27.40 1.22 0.88  chrX_56539280_56551368      492  1396 (10693)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_56539280_5   1396 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGATAAT 1347
                              ii i  i     i      i v      v i i   i  v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_56539280_5   1346 GATCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAATC 1297
                          iiv     v     iv i  i  i        i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_56539280_5   1296 TTCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1249
                          i   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_56539280_5   1248 TATAGAACCAAAAAAGAGCCCACATGGCCAAGTCAATCCTAAGCCAAAAG 1199
                            i   viiv  ii  v  viv  i     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_56539280_5   1198 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGA 1149
                                i      vv   ii  v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_56539280_5   1148 TACAGTAACCAAAACAGCATAGTACTGGTACCAAAAGAGAGATATAGAAC 1099
                                 i   i    ii i       i iv ii v   v       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_56539280_5   1098 A-TGGAACAGAAC--AGAGCCCTCAGAAATAATGACGCATA--TCTACAA 1054
                          -     i    i--    i  --        --  v    -- i  iii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAA--ACCCATACATTTATGG 344

C chrX_56539280_5   1053 CCATCTGATCTTTGACAAACCTGACCAAAACAAG-CAATGGGAAAATGAT 1005
                         i  vi    i  i     ivv  -    i  v v-       i   vi  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAAT 393

C chrX_56539280_5   1004 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 955
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

C chrX_56539280_5    954 ACTGAAACTGGATCCCTTCCTTACACCTTATAGAAAAATTAATTCAAGAT 905
                          v    ii    i    v   i     v    v         i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

C chrX_56539280_5    904 GGATTAAAGAGTTACATGTTAGACCTAAAACCATAAAAAACATAGAAGAA 855
                             i ?   vi  v    v   v       i      vv v        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

C chrX_56539280_5    854 AACTTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 806
                            v    ?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

C chrX_56539280_5    805 CTAAAACACCAAAAGCAGTGGCAACAAAAGCCAAAAGTGACAAATGGGAT 756
                         v  vi            vvi          vv    vv  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

C chrX_56539280_5    755 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 706
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

C chrX_56539280_5    705 GAACAGGCAATCTACAGAATGGGAGAAAATTTTTGCAACCTACTCAGCTG 656
                            v  i   i i                 v       vii ivi v   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

C chrX_56539280_5    655 ACAAAGGGTTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 606
                          i  i  ii vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

C chrX_56539280_5    605 AAAAAAACAAGCAACCCCATCAAAAAGTGGGTGAAGGAAATGAACAGACA 556
                              i    ii     v  i?    i    ii     vv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

C chrX_56539280_5    555 CTTCTCAAAGGAAGACATTTATGCAGCCAAAAA--ACATGAAAAAATGCT 508
                         i     v  i     i  vi viii     v  --         i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

C chrX_56539280_5    507 CACCATCACTGGCCAT 492
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  

 569 28.57 1.98 0.40  chrX_56539280_56551368     5915  6166 (5923)  C L1M4_orf2#LINE/L1   (0)   908   653  

C chrX_56539280_5   6166 TTAAGAACCTCTACCCAGCAAAAGAAACTATCAGCAGAGTAAACAGACGA 6117
                             i   i i iiv vv    i  v       iv i   i  v    i 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

C chrX_56539280_5   6116 CCTAAAGAATGAAAAAAAAAATTT-CAGACTATGAATCTGGCCAAGTTCG 6068
                           i v      ii i    v    -  i ii  iv     iiv i vv v
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

C chrX_56539280_5   6067 AATATCCAC-ATCTTTAAGAAACTTAAACAAATTTACAAGAGAAAAACAA 6019
                         vi      v-  v v   ii    ivv    v iv i  v i   i    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

C chrX_56539280_5   6018 ACAACTCCATT-AAAAATTTGCAAAGGACATGAACAGACACTTCTC-AAA 5971
                          i   i v   -      vv        iv    i     i     -   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

C chrX_56539280_5   5970 GAAGACAAACTTACAGGCAACAAGCATGTGAAAAACAT-CTCAATATCAC 5922
                              i v  vv ii v   i     ii      i-  -     i    ?
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAG-ATGCTCAACATCAZ 901

C chrX_56539280_5   5921 TAATCAT 5915
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.40 (42 / 30)
Gap_init rate = 0.02 (6 / 256), avg. gap size = 1.00 (6 / 6)  

3152 27.89 0.33 0.22  chrX_56539280_56551368    10690 11596 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56539280_5  10690 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 10739
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56539280_5  10740 GGCCATACTGCCCAAGGTAATTGACAGATTCAATGCCATCCCCATCAAGC 10789
                            v     v     iv i  iv          i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56539280_5  10790 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 10837
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56539280_5  10838 TATGGAACAAAAAAGAGCCCACAAC-GCCTAGTCAATCCTAAGCCAAAAG 10886
                                vviv  i ii    v  i-   v iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56539280_5  10887 AGCAAAACTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 10936
                          i    ii      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56539280_5  10937 TACGGTAACCCAAACAGCATGGTACTGGTACCAAAACAGAGATAGAGATC 10986
                            i    i v i    ii         i iv ii i   v   v     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56539280_5  10987 AATGGAACAGAACAGAGACCTCAGAAATAACACCACATATCTACAACTAT 11036
                                i    iv    vii         vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_56539280_5  11037 TGGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAAGATTCCCT 11086
                          v   i  i     ivv  vv  i v  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_56539280_5  11087 ATTTAATAAATGGTGCTGGGAATACTGGCTAGCCATATGTAGAAAGCTGA 11136
                         v  i  i              vv     v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_56539280_5  11137 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 11186
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_56539280_5  11187 AAAGACTAACACGTTAGACCTAAAACCATAAAATCCCTAGAAGAAAACCT 11236
                          ?    iv v i  v   v       i      ii i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_56539280_5  11237 AGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCTAAAA 11286
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_56539280_5  11287 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 11336
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_56539280_5  11337 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 11386
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_56539280_5  11387 GCAACATACAAAATGCGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 11436
                         i    vi   i    v        v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_56539280_5  11437 GGCTAATATCCAGAATCTACAATGAACTCAAACTAATTTACAAGAAAAAA 11486
                          i  vi          v  i  v      vv  v v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_56539280_5  11487 ACAAATAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 11536
                                    v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_56539280_5  11537 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 11586
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_56539280_5  11587 CACTGGCCAT 11596
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.37 (144 / 105)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.25 (5 / 4)  


2207 30.44 2.32 0.98  chrX_56558475_56564305.rev     4140  4957 (874)    L1M4_orf2#LINE/L1        1   829 (79)  

  chrX_56558475_5   4140 TAAAAAAAAATTCCATGCTCATGGATATAAAGAATCAGTGTCATGAAATT 4189
                          ii   i v  i     i        vvi    v i i i ii v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56558475_5   4190 GGCCATACTGCCCAGAATAATTTATAAATTCCATGTTATTCCCATTAAAC 4239
                            v     v    i v i  i  i i    v i iv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56558475_5   4240 TGTCATTGACAGTTTTCACAGAA-TT-ACAAGAAACT-ATTTTAAAATTC 4286
                          vi  vivi vv    ii     -  -     ---  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_56558475_5   4287 ATATGAAACCAAAAAAGAGTTCATATAACCAAGACAATCCTAAGAAGAAA 4336
                              i  viiv  ii  viiviv   i    i      i i i  ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_56558475_5   4337 GAACAAAGCTGGAGGAATCATGTTACAGGACTTCAAACAATATTACAAGT 4386
                                 i       v   iii v vvi i      vvv  i     iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_56558475_5   4387 CTACAGCAACCAAAAGAACATGGTACTGGTACAAGAACAGACACATAAAT 4436
                               i  i   i v iii         i i   i i     i   i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_56558475_5   4437 ATTTGGAACAGAATAGAGAACTCCGAAATGTACC-ACAAACTTACAAACA 4485
                         vvv     i     v    iii v     iv   - i v i   iiiv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_56558475_5   4486 TATGATCTTCAACAAACCTGATAAAAACAAGCAATGGGGAAATAGTTCTC 4535
                         vv    i   i    ivv  vi  i v  vv           v i vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_56558475_5   4536 TATTTAATAAAGGGTGCTGGGAGAACTGGATATCTATACTTAGAAATTTG 4585
                          v  i  i   v          v         ? i i ivi i  ivv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_56558475_5   4586 AAACTGGGCCCTTTCCTCACACAATATAAAACAATTTAGTTAAGATGGAT 4635
                           ii   i   i v        v     v  v    v v i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_56558475_5   4636 TTAAGACTTAAATGTAAGACCCTTAATTATAAAAACCCTAGAAGTAAACC 4685
                         iv?    i           v ivv  i       vi i      v    v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_56558475_5   4686 TAGGCA-ATGTCATTCAGGATATAGACACAGGCTAAGATTTTATAATGAA 4734
                             ?i- vi  -   iv  iv v ivvi    v v i   iv  ivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_56558475_5   4735 AACATCAAAA---TAAATTGCAACGAAAGCAAAAATTGACATGTGGTATC 4781
                         i   i     ---i  ---     i    v      v  i vi v v ii
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA---GCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_56558475_5   4782 T------AATAAAGAGCTTCTGCACAGCAAAATAAACTATCATGAGCAGT 4825
                          ------   v  i i   i  ii vv    iv v       v  i-   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA-AGT 692

  chrX_56558475_5   4826 G----GACAACCTACAGAATGGGAGAAAATTTTTGCAATCTATACATCTA 4871
                          ----       i                 v       vii   i    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_56558475_5   4872 ACAAAGGTCTAATATCCAGAGTCCATAAGGAACTTAAACAATTTA-CAAG 4920
                          i  i  v  vi        i vi    i     ivv    i i -i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_56558475_5   4921 AGAAAAACAAACAGCCCCATTAAAAAGTGGGCAAAGG 4957
                          i   i     i i   v   ?    i          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.02 (13 / 829), avg. gap size = 2.08 (27 / 13)  

 291 20.00 4.21 1.05  chrX_56558475_56564305.rev     5238  5332 (499)    L1M4_orf2#LINE/L1      784   881 (27)  

  chrX_56558475_5   5238 CTAAATAAATAAATAAACAAATAA---AAT-AAAAAGTGGGCAAAGGACA 5283
                           v     -    v i        ---   -?    i           iv
  L1M4_orf2#LINE/    784 CTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_56558475_5   5284 TAAACAGGCACTTCTCAAAAGAAGACATACAAGCAGCCAACAAAAACAT 5332
                          i  i  i  i     v        i      iii     i  iv    
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.03 (3 / 98), avg. gap size = 1.67 (5 / 3)  


3069 27.43 1.00 0.55  chrX_56582657_56589065     5013  5916 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56582657_5   5013 TGGAAAAACATTTCATGCTCATGGATAAGAAGAATCAATATCATGAAAAC 5062
                               i i  ii    i        vi     v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56582657_5   5063 TGCCTTACTACCCAAATTAATTTATAGATTCAATGCTATCCCCATCAAGC 5112
                         v  vv    v        i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56582657_5   5113 CACCA-CTGACTTTCTTCACAGAATTGTGAAAAACT-ACTTTAAACTTCA 5160
                         iv   -   v    i  -i     v -   v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chrX_56582657_5   5161 TATGGAACCAAAAAAGAGCCCACATAGCCAGGGCAATTTTGGGCAAGAAG 5210
                                viiv  ii  v  viv       iii    i   iiv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56582657_5   5211 AACAAATCTGGAGTCATCATGCTACCTGACTTCAAACTTTACTAGAAGGC 5260
                               vi     vvv   ii  v  ii i      vi      v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56582657_5   5261 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGATACATAGACC 5310
                                 i   i    ii       v i iv ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56582657_5   5311 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACCACCAA 5360
                                i    iv   ivii         vv   i    i  ivii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_56582657_5   5361 CTGATCTTTGACAAACCTGACACACACAAGCAATGGGGAAAAGATTCCCT 5410
                         i    i  i     ivv  v  vivv  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_56582657_5   5411 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAGTGA 5460
                         v  i  i        i     v      v  ?   i     i  i i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_56582657_5   5461 AACTGGACCCTTTCTGTACCCCTTGTACAAAAATTAACTCAAGATGGATT 5510
                          ii       i v ivi  v  v i                 i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_56582657_5   5511 AAAGACTTAAGGGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAACCT 5560
                          ?    i   iv      v   ii  i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_56582657_5   5561 --GAGCAATATCACTCAGGACATAGGCAAGGGCAAAGACTTCATGCCTAA 5608
                         -- ? i  -   -i  iv   v v  vvvi     v ii   v ivv  v
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_56582657_5   5609 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATTGGATCTAA 5658
                         i            vvi          vv     v  i i      ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_56582657_5   5659 TTAAA-TGAAAAAGCTTCTGCACGGCAAAGGAAACTATCAACAGAATGAA 5707
                          i   - v     -   i  ii vv       v        v i i    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_56582657_5   5708 CAGGCATCCTGTAGAATGGGAGAAAATTTTTGCAATCTACTCATGTGACA 5757
                         v  i  v  iii               v       vii ivi  v   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_56582657_5   5758 AAGGGATAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5807
                          i  iv vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_56582657_5   5808 AAATCAA----CCCCATCAAAAAATGGGCAAAGGATATAAACAGACACAT 5853
                           iv   ----   v  i?                 v i  i     iv 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_56582657_5   5854 CTCAAAAGAAGACATTTATGCAGCCGACAGACATATGAAAAAATGCTCAT 5903
                            v        i  vi viii   i i ii  i       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_56582657_5   5904 CATCACTGGTCAT 5916
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2291 29.02 1.42 0.91  chrX_56592367_56599013.rev     4898  5669 (978)    L1M4_orf2#LINE/L1        1   776 (132)  

  chrX_56592367_5   4898 TGGAAAAACATTCCCTCCTCATGGATAGGAATAATTAATCTTGTGAAAAT 4947
                               i i  i  v vi        v    v v     v    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56592367_5   4948 GACAATACTGCCCAAATTAATTCATATATTCAATACTATTCCCATCAAAA 4997
                          i       v        i  ii i v      ii v  i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56592367_5   4998 TACTATTGGCATTCTTCACAGAATTAGAAGAAACTA--CTTAAAAATTTA 5045
                          v i viv  v  i  ii     v v  v-  i  i-- i     -  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAA-TTCA 148

  chrX_56592367_5   5046 TATGGAAATA-AAAAGAGCATGAATAGCCAAGACAATTGTAAGCAAAAAG 5094
                                  i-  ii  v vv          i     iv i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56592367_5   5095 AACAAAGCTGGAGGCATCACCCTACCTCACTTCAAACTATACTACAAGGA 5144
                                i      vv    v  v  iv i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56592367_5   5145 TACAGTAACCAAAACAGCATGGTACTTGCACCAAAACAGACACAGAGACC 5194
                                 i   i    ii       v   iv ii i     i v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56592367_5   5195 AATGGACCAGAATAGGGACCTCAGAAAATAAGGCCACACATCTACAACCA 5244
                               vi     v i  vii      -   iv   i    i  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGTCA 347

  chrX_56592367_5   5245 TCTGATCTTTG-CAAAACCTCACAAAAACAAGCAATGGGGAAAGATT-TT 5292
                         vi    i  i -   iiviv -   i v  vv             v -v 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56592367_5   5293 CTATTTAATAAATGGTGCTGGGAAAACTGTCTAGTCATATGCAGAAAACT 5342
                           v  i  i              v     vv  ?i  i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56592367_5   5343 GAAACTGAACCCCTTCTGTACACCTTATACAAAAATTAACTCAAGATGGA 5392
                            ii  i      v ivi     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56592367_5   5393 TTAAAGGCTTAAATGAAAAACCCAATACCATAAAAATCCCCAAA--AAAT 5440
                          i ?  i i      v  i v i  v  i      v  iivi  --   i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_56592367_5   5441 CTAGGC--AATTCCATTTAGAAAATAGACATGAGCAA-AATTTTATA-AT 5486
                         v    ?--  v  --  iivi vv v ivv ii    -ii   iv  -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_56592367_5   5487 GTAATCGCCAAAAGCAATTGCAGCTAAAGCTAAAATTGACAAGCAGGATC 5536
                         i i - i         vvv   i v    vv     v  i  iiv   ii
  L1M4_orf2#LINE/    595 ATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_56592367_5   5537 TAATTAAACTTAAGAGTTTCTGCACAGCAAAAGAAACTATCATCAGAGCA 5586
                          v  i   v    i ii  i  ii vv    i  v       vv i  ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_56592367_5   5587 AACAGGCAACCTACAGAATAAGAGAAACTTTTTGCAATCTACCTGTCTAA 5636
                           v  i     i       ii      v v       vii iv i   i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_56592367_5   5637 CAAAGGTCTAATATCCAGAATTTTTAAGAAGCT 5669
                         i  i  v  vi          v v   ii i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.43 (130 / 91)
Gap_init rate = 0.02 (14 / 776), avg. gap size = 1.29 (18 / 14)  

 445 22.30 3.38 2.03  chrX_56592367_56599013.rev     6009  6156 (491)    L1M4_orf2#LINE/L1      759   908 (0)  

  chrX_56592367_5   6009 CAGCATTTACAAGCAACT--TAAGCCAATTTA-CAAGAAAATGGCAAACA 6055
                            v  v  i  iv    --  ---   i i -i  v    v i    i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTA---CAACTCAATAATAAAAAGACAAATA 805

  chrX_56592367_5   6056 ACCCTATCAAAAATTGGACAAAGGACATGAACAGACACTTCTCAAAAGAA 6105
                             v  i?    v   i       iv    i     i     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_56592367_5   6106 GACATTTATGCGGCCAACAA--ACATGAAAGAAAGTTCAACATCACTGAT 6153
                           i  vi vii      i  --        ii v i         ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_56592367_5   6154 CAT 6156
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.67 (20 / 12)
Gap_init rate = 0.03 (4 / 150), avg. gap size = 2.00 (8 / 4)  


2248 25.99 1.98 1.27  chrX_56599760_56601462      505  1212 (491)    L1M4_orf2#LINE/L1      196   908 (0)  

  chrX_56599760_5    505 AAGAACAAATCCAGAGGCCTCACTTTACCCAACTTCAGATTATATTACAA 554
                                  viii    v     vi v     i    i viv  i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_56599760_5    555 GGCTATAGTTACCAAAATAGCATGGTACCGGTATAAAGATAGGCACAAAG 604
                         i    i   v i   i i  ii      i  i    i     i  i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_56599760_5    605 GCCATTGGAAGATAATATAGAACCCAGAAATAAAGCTAAATACTTACAGT 654
                         ii  v     v v   vv   ii           v i v i i   ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_56599760_5    655 CAACTGATCTTCAACAAAGCATACAAAAAT-ATAAATTGGGGAAAGGACC 703
                            i    i   i    i -i i v  i i-  vv v         i iv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_56599760_5    704 CCCTATGC------TGGTGCTGGGGAAACGGGCAAGCCACATGTAGAAGA 747
                         vi  v v ------          iv   v  vv ?       i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_56599760_5    748 -TAAAACTGGATCCCCATCTCTCACTTTATACAAAAATCAACTCAAGATT 796
                         - i  ii    i   i i   v   iv           i       i  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_56599760_5    797 GATCAAAGAC-TAAATGTAAGACCTGAAATCATAAAAATTCTAGAAGATA 845
                              ?    -           v  i   ii      v ii       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_56599760_5    846 ACATTGG--TAACATTTCTG-GACATTGGCTTAGGCCAAGAATTCATGAC 892
                             v  --   -  i ii -   v    v      v v iv   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_56599760_5    893 TAAGAC-CCAAAAGCAAATGCAACAAAAATGAAAATAAATAAATGGGACC 941
                           v   -         v v         ivi      i      v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_56599760_5    942 TAACTAACCTATAGAGCTTATGCATAGCAAAAGGAACAGTCAGCAGCATA 991
                          v ii  vv vv i i   v  iiivv    i iv  vi   iv ivi i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_56599760_5    992 CACAGACAACCCACAGAGTGGGAGAAAATATTTA-AAATCTATGCATCTG 1040
                         v v              i               i-     -  ii     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTG 742

  chrX_56599760_5   1041 ACAAAAGACTAGTATCCAGAATCTATAAAAAACTCAAGCAAATCAGCAAG 1090
                          i  ii    v           v      i     vvi   v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_56599760_5   1091 AAATAAACAAATAATCCCATCAAACACTGAGCTAAGGATATCAATAGATA 1140
                            v i        i  v  i?  v v  i  v      v v      i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_56599760_5   1141 TTTCTCAAAAGAAGATACACAAAAAGCCAACAAACACATTTTTTTTAAAA 1190
                               v          i     vi     i  i     v------    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG------AAAA 886

  chrX_56599760_5   1191 AAAGCTCAACATTGTTAATCAT 1212
                         i v         ii????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (104 / 77)
Gap_init rate = 0.02 (12 / 713), avg. gap size = 1.92 (23 / 12)  


3255 27.20 0.44 0.44  chrX_56604839_56611118     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56604839_5   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56604839_5   4930 GGCCATACTGCCCAAGGTAATTGACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  iv          i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56604839_5   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56604839_5   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56604839_5   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56604839_5   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56604839_5   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_56604839_5   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56604839_5   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56604839_5   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56604839_5   5376 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_56604839_5   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_56604839_5   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_56604839_5   5526 TTAAACTCAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v i  i i   i iii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_56604839_5   5576 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_56604839_5   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_56604839_5   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_56604839_5   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_56604839_5   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2721 28.22 1.78 0.89  chrX_56615148_56620968.rev     4442  5341 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56615148_5   4442 TGGATAAACATTCCATTCTCATGATTAGGAAGAATCAATATTGCAAAAAT 4491
                             v i i  i    vi     iv v      v i       iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56615148_5   4492 GGTCATACTGGCCAAAGTAATTTATAGATTTAATGCTATTCCCATTAAAC 4541
                           iv     vv     v i  i  i     i  i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56615148_5   4542 TACCATTGGCATTCTTCACAGAATTAGAAAAAAAAACTTTTAAAATTCAA 4591
                          v   viv  v  i  ii     v v  v  ivvi - ii         v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_56615148_5   4592 ATGGTACTATAAAAGAGCCTGAATAGACCAGACAATCCTAAGCAAAAAGA 4641
                             v v ii  ii  v  v      v v i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_56615148_5   4642 ACAAAGCTGGGGGCATCATTCTACCTGACTTCAAACTATACTGCAAGGCT 4691
                               i   i  vv   iv  v  ii i      viv    i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_56615148_5   4692 ACAGTAACCAAAAGAGCATGGGATTGTTACAAGAACAGACCCATAAATCA 4741
                                i   i v  ii   v i  vi i   i i    vi   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_56615148_5   4742 ATGGAACAGAGTAGATAACTCAGAAATAAGACCACACACCTACAAATATC 4791
                               i   i v  v iii         iv   i   ii  iiivi vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_56615148_5   4792 TGATCTTCAACAAACCTGACAAAACAAG-CAATAGGGAAAGGATTCCCTA 4840
                             i   i    ivv  v   i  v v-    i       i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_56615148_5   4841 TTTAATAAATGGTGCTGGGAGAACTGGCTATCCACATGCAGAAAACTGAA 4890
                           i  i              v      v  ?         i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_56615148_5   4891 ACTGGACCCCTTCCTTACACCATATACAACAATTAACTGGAGATGGATTA 4940
                         ii         v   i             v        vi i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_56615148_5   4941 AAGACTTAAATGTAAAACCCAAAACTGTAAAGACCCTAGAAGAAAATCTA 4990
                         ?    i         i v i      i    ivi i          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_56615148_5   4991 GG---AAATGCCATTTAGGACATAGGTACAGGTGAAAATTTCAT-GATGA 5036
                           ---    -- -  iiv   v v  vvi   ii vii    v -   - 
  L1M4_orf2#LINE/    550 GGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_56615148_5   5037 AAATGCCAAAAGCAATTGCAACAAAAGCAAATGTTGACAAATAGAATCTT 5086
                         vi ii         vvv          v   vi v  i    v i -   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA-CTT 644

  chrX_56615148_5   5087 AATTAAACCAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGCA-GT 5135
                         v  i   viv  i i   i  ii vv    iv v       --  v -  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--AGAAAGT 692

  chrX_56615148_5   5136 GAACAGTCAACCTTCAAAATGAAAGAACATTTTTGCAATCTATCCATTTG 5185
                            v  v     iv  i    ii    v  v       vii  vi  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_56615148_5   5186 ACCAAGGTCTAATACCTAG--TCTACAAGGAACTTAAACAATTTA-TGAG 5232
                          iv i  v  vi  i i  -- v  i  i     ivv    i i - i v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_56615148_5   5233 ATAAAGA--AATAACCATATTAAAAAGTGGGCAAAGGACATGAACAGTCA 5280
                          v     --       vv   ?    i           iv    i  v  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_56615148_5   5281 CTTCTCAAATGAAGACATACATGTGGCCAACAAACATCTGAAGA-----T 5325
                         i     v  v     i     vi       i  i  iv    i ----- 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_56615148_5   5326 CAACACCACTGATCCA 5341
                              i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (144 / 107)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.71 (24 / 14)  


1510 26.30 13.99 0.00  chrX_56623798_56628537     3052  3530 (1210)    L1M4_orf2#LINE/L1        1   546 (362)  

  chrX_56623798_5   3052 TGGAGAAACATTCCATGCTCATGAATAGGAATAATTAATATCATTAAAAT 3101
                             i i i  i     i     i  v    v v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56623798_5   3102 GGCCATACTGTCCAAAGCAATTTATAGATTCAATGCTATTCCTATTAAA- 3150
                            v     vi     vii  i  i        i  v  i     i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56623798_5   3151 ------CTACC------------ATTGAC---TT--TTCT-----TCA-- 3170
                         ------  i  ------------      ---i -- i  -----   --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56623798_5   3171 --------------------------CAAAAC--T--------AGGGGAA 3184
                         --------------------------      -- --------  ii   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56623798_5   3185 AAAAGCTGTAGGCATCTCATTACCTGACTTCAAACTATTCTACAGGGCTA 3234
                         v    i  v   vv  v  i v  ii i      viv v     ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_56623798_5   3235 CAGTAACCAAAAAAGCATGGTACTAGTACAAAAACAGACATATACACCAA 3284
                               i   i v  ii       i i i  ii i         v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_56623798_5   3285 TGGAACAGAATAAAAAACCTAGAAATAAGACTGTACACCTACAACTATCT 3334
                              i     vi i ii i        iv ii    ii  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_56623798_5   3335 GATCTTTGACAAACCTGACAAAAACAAGCAATTGGGAAATGATTCCCTAT 3384
                            i  i     ivv  v   i v  vv    v      vi  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_56623798_5   3385 TCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGATGAAAA 3434
                             i              i      v  ?   i     i    vvi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_56623798_5   3435 CTGGAGCCCTTCCTAGTACCATATACAAAAATTAACTCCAGATGGATTAA 3484
                         i    v    v   vii                     v i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_56623798_5   3485 TGACTTAAATGTAAAACCTAAAACTATAAAAAACCTGGAAAACAAC 3530
                         v   i         i v              vv i i   i v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

Transitions / transversions = 1.82 (80 / 44)
Gap_init rate = 0.01 (8 / 546), avg. gap size = 8.38 (67 / 8)  

 710 29.85 3.69 0.92  chrX_56623798_56628537     3926  4250 (490)    L1M4_orf2#LINE/L1      575   908 (0)  

  chrX_56623798_5   3926 TGGGCAAAGATTTCATAACGAACATGACA---AAAGCAATTGCAATAAAA 3972
                          i     v i    v  i--- i      ---      vvv    i    
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAG---ATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_56623798_5   3973 CAAAAATT-GACAAATGGGATGTAATTAAACTAGAGAGATTCTGCACAGC 4021
                         v     v -  i    v   iv v  i   v vi i iv  i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_56623798_5   4022 AAAAGAAGCTATCA-----GCAAACAGATGACCTACAGAATGAGTGAACA 4066
                            i  vi      ----- ii  v   ii   i        i v   v 
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_56623798_5   4067 TTTTTGCAATCCGTGCTTCTGGCAAATGTCTTCTATCAAGTATCTCTAAA 4116
                          v       vi i iiv    ii  iv v   v    v  v  v v    
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_56623798_5   4117 GAACTTAAACAAATTTACAAGGAAAA---AAACAATCCCATTAAAAAGTG 4163
                              ivv    v iv i  vi    ---   i  i  v   ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_56623798_5   4164 GGCAAAGGACAGGAACAAACACCATTCAAAAGAAGACATGCATGTGGCCA 4213
                                  ivv   i i   iivi  v        i  i  vi      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_56623798_5   4214 GCAAACATATTTTAAAAAGCTCAACAAAAGATTTATA 4250
                         ii  i  i  vvv  i v        vv ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (50 / 46)
Gap_init rate = 0.01 (5 / 334), avg. gap size = 3.00 (15 / 5)  


1812 28.44 0.74 0.00  chrX_56629322_56635047     3960  4497 (1229)    L1M4_orf2#LINE/L1        1   542 (366)  

  chrX_56629322_5   3960 TGGAAACACATCCCAGGATCATGGATGGGTAAAATCAATATTGTGAAAAT 4009
                               v i      v v        v  v i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56629322_5   4010 GACCATACTGCC-AAAGCAA-GTACAAATTCAACGCAATTCCCATCCAAA 4057
                          i v     v  -   vii -v    i            i  i   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56629322_5   4058 TAACACCAACATTCTTCACAGAAA--GAAAAACCAATTCTAAAGTTCATA 4105
                          vv  v vi v  i  ii      --  v  i ii  i     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56629322_5   4106 TGTAACTAAAAAAGAGCCCACATAGCCAAAACAAGACTAAGCAAAAAATA 4155
                           v  v iv  ii  v  viv             vvi i iv  i  iv 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56629322_5   4156 CAAATCCCGAGACATCACATTACCTGACTTCAAACTATACTATAATGCCA 4205
                             viiv   ivv     i v  ii i      viv     i  v  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_56629322_5   4206 CAGTCACCAAAACAGCATGGTACTAGTATAAGAATAGGCACAGAGACCAA 4255
                             v i   i    ii       i i     i    i  i v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_56629322_5   4256 TGGAACAGAATAGAGAATCCAGAAATAAACCCGAATACTTACCCCCAACT 4305
                              i     v    i               iv i i   ivvi   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_56629322_5   4306 GATCTTCGACAAAGCAAACAAAAACATGAAGTGGGAAAAGGGCACCCTAA 4355
                            i        i vviv   i v   vv i    i    iii vi  vv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_56629322_5   4356 TCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAAAGTGGAA 4405
                                            i  i   vv ?       i ii i i  i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_56629322_5   4406 CTGTATCCTCATCTCTCAGGTTATACAAAAATCCAATTAAGATGGATCAA 4455
                         i  v i  ii i   v  vvv           iv v i  i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_56629322_5   4456 GGACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGA 4497
                         i   i     v     v  i           v ii       
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

Transitions / transversions = 1.40 (88 / 63)
Gap_init rate = 0.01 (3 / 542), avg. gap size = 1.33 (4 / 3)  

 289 27.78 1.85 1.85  chrX_56629322_56635047     4803  4910 (816)    L1M4_orf2#LINE/L1      536   643 (265)  

  chrX_56629322_5   4803 TAGAAGGTAACATTGATA-AAATCCGTCTAT-ACTTTGGCTTAGGCAAAG 4850
                               iv     v i?i-     -- iii -  i    v        v 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATG 583

  chrX_56629322_5   4851 AATTCATGACCAAGAATCCAAAAGCAAATGCGACAAAAGCAAAGATAAAT 4900
                         iv   v iivi v  vv         v v  i       v   i   i  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_56629322_5   4901 AGGTTGGACT 4910
                          ii       
  L1M4_orf2#LINE/    634 AAATTGGACT 643

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.03 (3 / 108), avg. gap size = 1.33 (4 / 3)  

 851 26.62 1.02 0.68  chrX_56629322_56635047     4941  5233 (493)    L1M4_orf2#LINE/L1      615   908 (0)  

  chrX_56629322_5   4941 AACAAAAGCCAAGATA-ATAGGTGGGACT--ATTAAACTAAAGAGCCTCT 4987
                                 vv  i   -   ii v     --  i   v v  i i i i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_56629322_5   4988 GCACAGCAAAAGGAAGAGCGAACAGAGTAGACAGACAACCCAGAGAGTGG 5037
                          ii vv    i iv vviiv  v i   ii v          v   i   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_56629322_5   5038 GAGGCAGTCTTCACAATCTATGCATCTGACAATGGACTAATACCCAGAAT 5087
                            iv i v  ii   vii  ii      i  v     vi  i       
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_56629322_5   5088 CTACAATGAAATCAAACAAATCAGTAAGAAGAAATAACAAAAAATCCCAT 5137
                         v  i  v   v  vv    v   i   v  i  i--     v  i  v  
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAG--ACAAATAACCCAAT 812

  chrX_56629322_5   5138 CAAAAAGTGGGCTGAGGACACGAATAGACAATTCTCAAAAGAAGATATAC 5187
                         i?    i     vi    ivi         v     v             
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_56629322_5   5188 AAATGGCCAACAAACATATAAAAAACTGCTCAACATCACTAATGAT 5233
                                   i  i  i  i    iv            ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (44 / 33)
Gap_init rate = 0.01 (3 / 294), avg. gap size = 1.67 (5 / 3)  


3135 26.39 1.33 0.67  chrX_56715525_56722169.rev     5253  6154 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56715525_5   5253 TGGAAGGACATTCCATGCTCATGGATGGGAAGAATCAATATCATGAAAAT 5302
                              i  i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56715525_5   5303 GGCCATACTGCCCAGGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5352
                            v     v    iiv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56715525_5   5353 TACCC--CTGACTCTCTTCACAGAATTAGAAAAAAACT-ACTTTAAAGTT 5399
                          -   --   v  i i  -i     v v  v  i--  - iii    i  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATT 146

  chrX_56715525_5   5400 CAAATGGAACCAAAAAAGAGCCCAAATAGCCAAGACAATCCTAAGCAAAG 5449
                           v      viiv  ii  v  vi         i      i i iv  ii
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_56715525_5   5450 AGAACAAAGCTGGAAGCATCACGCTGCCTAACTTCAAACTACACTACAAG 5499
                                  i    i vv    i  v  i  i      vivi       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_56715525_5   5500 GCTACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATATAAA 5549
                                   i   i    ii  i      i iv ii i   i     i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_56715525_5   5550 CCAATGGAACAGAATGGAGGCCTCAGAAATAACACCACACATCTACAGCC 5599
                         i        i     v   ivii         vv   i    i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_56715525_5   5600 ACCTAATATTTGATGAACCTGGCAATAACAAGCCATGGGGAAGGATT-TT 5648
                          vi i  v  i  ii ivv  v   v v  vv v        i  v -v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56715525_5   5649 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGGT 5698
                           v  i  i              v      v  ?   i     i  iii 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56715525_5   5699 GAAACTGGAACCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGA 5748
                            ii    v    v   i    iv                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56715525_5   5749 TTAAAGACTTAAACCTAAAACCTAAAACCATAAAAAACCTAGAAGAAAAC 5798
                          i ?    i    iv   i v       i      vv i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_56715525_5   5799 CTAGGCA-ATACCATTCAGAATACAGGCGTGGGCAAAGACTTCATGACTA 5847
                         v    ?i- v i -   ivi iviv  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_56715525_5   5848 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATATA 5897
                         vi            vvi          vv        i    v   iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_56715525_5   5898 ATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTATCATCAGAGTGAA 5947
                           i   v v  i i   i   i vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_56715525_5   5948 AAGGCAACCTACAGAATGGGAGAAACTCTTTGCAATCTACCCATCTGACA 5997
                            i     i               v v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_56715525_5   5998 AAGGGCTAATATCCAGAATCTACAAAGAACT--TA-AAC-CAATTTACAA 6043
                          i  i  vi          v  i        --  -   -    v- i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAA 794

  chrX_56715525_5   6044 GAAAA-AAACAACCCCATCAAAAAGTGGGCGAAAGATATGAGCAGAGACT 6092
                         i  i -   i     v  i?    i     i  i   v   ii   v i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_56715525_5   6093 TCTCAAGAGAAGACATTTATGCAGCCAATGAACATATAAAAAA--GCTCA 6140
                             v i      i  vi viii      i i  i  i    i--     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_56715525_5   6141 TCATCACTGGGCTT 6154
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (145 / 89)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.29 (18 / 14)  


2950 20.50 2.89 3.42  chrX_56727523_56729727      497  1257 (948)    L1M4_orf2#LINE/L1       14   770 (138)  

  chrX_56727523_5    497 CAT-TTTATGCATCAGAAGGCACAGTATTATAAAGATGACAACACTCTTC 545
                            -  i   v  ii    i vi i    i v      i   i    ii 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chrX_56727523_5    546 AAAATAATCAAACTATTCAATGCAACCCTTATCAAAATTAAGGTTGCCTA 595
                            v i   v vvv      i    i  i         ivvi i     v
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chrX_56727523_5    596 CTTTGAAGAAATTTATAACCTGATTCTAAAGTTCATATGAAAATGTAATG 645
                         i    v       v i  v     i     i        i     i  v 
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chrX_56727523_5    646 GACCCAGAATAGCCAAAACAATCTTGAAGTATA----CAAAGTTTGAAGA 691
                                                     iv v ----       v  i  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_56727523_5    692 GTCACATTTCCAAATTTTAAAACTTATTACAAAGCTACAATAAACAAGTC 741
                         v     i    v     i        i            i   v    v 
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_56727523_5    742 TATGTGGTACTGGCATA-GGATATAAATATTGATCAATGAAATAGAATCC 790
                         vi               -     v v    v        i        iv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_56727523_5    791 AAAGTCCAGACATAAGCCCTCACAAAAGTTAATTTGCAGCCAATTAACTT 840
                          i        v    i   vi   --------   iii i     i i  
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACA--------TTTATGGTCAATTGATTT 355

  chrX_56727523_5    841 CTGAGAAGGAGGC-AAGACAA---AA-GGGGAAATAAC--TATTTTCAAT 883
                         ii  v    iv  -     v ---  -       v  i-- v       i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_56727523_5    884 AAATGGTACTGGGACAACTTGGTATCTACATGCAAAAAAAAAACAAAAAA 933
                                i           v i  ? i          i  ----------
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA---------- 445

  chrX_56727523_5    934 ACAAAAAACTTCCACCCCTACCTCATGCAAAATACAAAAATTAACTCAAA 983
                         -ii  i---  vv            ii v v                   
  L1M4_orf2#LINE/    446 -TGAAG---TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_56727523_5    984 ATAGGCCAAAGACTCAAATATAAGGGTTACA-CTATAAAACTCTTGGGAG 1032
                           i ii  ?    ii    i    i i  v -             i i  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_56727523_5   1033 GAAATATAGAA-TAAATTTTTGTGACCTTGAATTAAGTATTAGATTTTTA 1081
                         i   i    i?-     i  i         ii   i i v i v  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_56727523_5   1082 ATTCTTACACCAAA-GCACAAGTTAATAAAGGAAAAAAAAGATAAACTGG 1130
                         iv v v        -       i-  i   i       v       i   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGG 640

  chrX_56727523_5   1131 ACATAATTAAAATTGAAAAAAAATTT---GCTTCAGTGAACACAGTCAAG 1177
                           v v  i      ---     v   ---      iv i    vi     
  L1M4_orf2#LINE/    641 ACTTCATCAAAATT---AAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_56727523_5   1178 AAATTTGAAAGACAGCC-ACAG--TGCAAGATTATTTTTGCAAATAATAT 1224
                            v vi       i  -    --  vi   vv  v         v    
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_56727523_5   1225 GTCTCATAAATGACTTGTATCTAAAATATATAA 1257
                         i   v    iv          i i         
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAA 770

Transitions / transversions = 1.55 (93 / 60)
Gap_init rate = 0.02 (18 / 757), avg. gap size = 2.67 (48 / 18)  

 450 18.11 3.94 0.79  chrX_56727523_56729727     1589  1715 (490)    L1M4_orf2#LINE/L1      778   908 (0)  

  chrX_56727523_5   1589 TTACCGCTAAATAATAAAACAAACAA-TAAACCAATTTTATAACG---AA 1634
                             vi  v          - i    -   v      ?v v  i ---  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_56727523_5   1635 AGGATCTGAATAGATTCTTCTGTAAAGAAGACATACAAATCACAAATTA- 1683
                              i        ivi    vi        i        vi v   v -
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_56727523_5   1684 CACATGAGAAGATGCTCAACACTATTAGTCAT 1715
                                i             ii ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (12 / 10)
Gap_init rate = 0.03 (4 / 131), avg. gap size = 1.50 (6 / 4)  


3045 24.25 2.44 1.88  chrX_56737075_56739528.rev     1061  1963 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56737075_5   1061 TGAAAGAACATTCCATGCTCATGGATAGAAAGAATCAACATAGTAAAAAT 1110
                           i  ii i  i     i        v i    v i  i  v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56737075_5   1111 GGCCTTACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATTGAGC 1160
                            vv    v      v i  i  i        i  v     i  ii iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56737075_5   1161 TACCA-CTGACTTTCTT-CACAGATTTGGAAAAAAT-ACACTAAACTTCA 1207
                          v   -   v    i  -  v i   --  v  iv - iv     v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_56737075_5   1208 TATGGAA-TG-AAAAAACAGCTCCCA---TAGCCAAGACAATTCTAAGCA 1252
                                -  -  iii  -----   ---       i     ii i iv 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC-----CCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_56737075_5   1253 AAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCACACTGCACTAC 1302
                          i          i      vv       v  ii i    v vivi     
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_56737075_5   1303 AAGGCTACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGATATAT 1352
                           i      i   i   i    ii         i iv ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_56737075_5   1353 AGACCAAGGGAACAGAAGAGAGGGCTCAGAAATACCACCATACATCTACA 1402
                            i   v    i    vv   i ii        vvv        i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_56737075_5   1403 ACCATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGAAT 1452
                         ii  vi    i  i     ivv  vv  i v  vv               
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_56737075_5   1453 -TTCTTATTTAATAAACAGTGTTGGGAAAACCGGCTAGCCATATGCAGAA 1501
                         -v    -  i  i   ii   i     v   i  v  ?   i     i  
  L1M4_orf2#LINE/    394 AGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_56737075_5   1502 AACTGAAACTGGACCCCTTCCTTACACTTTATACAAAAATTAACTCAAGA 1551
                         i v    ii         v   i    iv                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_56737075_5   1552 TGGATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAATCCTAGAAGA 1601
                              i ?    i           v       i      v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_56737075_5   1602 AAACCTAGGCA-ATACCTTCAGGACATAAGCATGGGCAAAGACTTATGTC 1650
                             v    ?i- v i    iv   v vi vv i     v ii  v ---
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT--- 589

  chrX_56737075_5   1651 TAAA----ACACCAAAAGGTATG-GCAACAAAAGCCAAAATTGACAAATG 1695
                           i ----          -i ii-          vv     v  i    v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_56737075_5   1696 GGATCTAATTAAA-TGAAAAAGCTTCTACACAGCAAAAGAAACTATCATC 1744
                            ii v  i   - v     -   i iii vv    i  v       vv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_56737075_5   1745 AGAGTGAACAGGCAACCTATAGAATGGGAGAACGTTTTTGCAATCCATCC 1794
                          i      v  i     i i            vi v       vi   vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_56737075_5   1795 ATCTGACAAAAGGGCTAATATCCAGAATATACAAAGAACTTAAACAAATT 1844
                               i  i-  i  vi             i        ivv    v i
  L1M4_orf2#LINE/    738 ATCTGATAAG-GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_56737075_5   1845 TACAAGAAAAAT-CAAACTACTCCATCAAATAGTGGGCGAAGGATATGAA 1893
                         v i  v     v-    iv  i v  i?  v i     i      v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_56737075_5   1894 CAGACACTTCTCAAAAGAAGACATTATGCAA----CAAACAAACATATGA 1939
                         i     i     v        ---   i   ---- v  i  i  i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGA---TATACAAATGGCCAATAAGCACATGA 883

  chrX_56737075_5   1940 AAAAA-GCTCATCATCACTGGTCAT 1963
                            i -     v     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (129 / 86)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.77 (39 / 22)  


1330 28.16 1.19 1.19  chrX_56755402_56762509     5393  5811 (1297)    L1M4_orf2#LINE/L1        1   419 (489)  

  chrX_56755402_5   5393 TGGAAAAACATTTCATGCTCATGGATAGGAAGAATCAATACTGTGAAAAT 5442
                               i i  ii    i        v      v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56755402_5   5443 GTCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATTATCATCAAGC 5492
                          v v     v      v i  i  i        i  v  ivii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56755402_5   5493 TCCCAGTGAATTTATTTGCAGAA-TTAGGAAAAACT-ACTTTAAATTTCA 5540
                               ivivi  v         -  --  v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_56755402_5   5541 TATGGAACCAAAAAAGAGCCTGTATAGACAAGATAATCCTAAGCAAAAAG 5590
                                viiv  ii  v  v v    v   i i    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56755402_5   5591 AATAAAGCTGGAGGCATCACACTACCTGACTTCCAAATATACTACAAGGC 5640
                           i    i      vv       v  ii i   v   iv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56755402_5   5641 TACAGAAACCGAAACACCATG-TACTGGTACCAAAGCAGATATATAGACC 5689
                              v  i i i   vii  -      i iv iiii   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56755402_5   5690 AATGCAACAGAACAGA-AGCCTCAGAAATAACACCACACATCTACAACCA 5738
                             v  i    iv  -  i -         vv   i    i  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chrX_56755402_5   5739 TCTGATCTTCAACAAACCTGACAAAAACAAGCAATCAGGTTGAAGATTC- 5787
                         vi    i   i    ivv  v   i v  vv    vi  --i    v v-
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAAGAATAG 395

  chrX_56755402_5   5788 CCTATTTAATAAATGATGCTGGGA 5811
                         i  v  i  i     i        
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGA 419

Transitions / transversions = 1.62 (73 / 45)
Gap_init rate = 0.02 (8 / 419), avg. gap size = 1.25 (10 / 8)  

1376 27.62 3.87 2.39  chrX_56755402_56762509     6073  6615 (493)    L1M4_orf2#LINE/L1      358   908 (0)  

  chrX_56755402_5   6073 GACAAGAGTG---AGACTCCATCTCAA------AAAAATAA------AAA 6107
                               i   ---    --   -    ------  i    i------v  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGAC--CAT-TCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_56755402_5   6108 TAAATGGTGCTGGGAAAACTGGTTTGCCATATGCAGAAAACAGATACTGG 6157
                         i              v      v v?   i     i  i vv  vii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_56755402_5   6158 ACCCCTTCTTTATACCTTATACAAAATTTAACCCAAGATGGATTAAATAC 6207
                               v i i i   v         v     i   i      i ? v  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_56755402_5   6208 TTAAGAGTACAATCCCAAACCGTAAGAACCCTAGAAGAAAACCTAAGCA- 6256
                         i   iv   vi v iv    ii   i vi i           v  i ?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_56755402_5   6257 ATACCATTCATCACATAGGCATGGGGAAAGACTTTGTCACCAAAACACCA 6306
                          v i -   i v  v v  vv i  v  v ii  iv vivi vi      
  L1M4_orf2#LINE/    555 AAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_56755402_5   6307 AAAGCAGTTGCAAATAA--AAAGCCCAAATTGACAAATGGGATCTAAT-A 6353
                               ----   ii  --    vvv    v  i    v   ii v  - 
  L1M4_orf2#LINE/    604 AAAGCA----CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_56755402_5   6354 AACTTAAGAGCTTCTGCACAGCCAAAGAAACTATCATCAGAGTGAACAAG 6403
                           v    i i   i  ii vv v  i  v       vv i      v ii
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_56755402_5   6404 CAATCTTCAAAATAGGAGAAAATTTTTGCAAGCTACCCATCTGACAAAAG 6453
                            i iv  i   i         v       iii ivi      i  ii 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_56755402_5   6454 TCTAATATCCAGAATCTACATGGAACTTAAACGAATTTCAAGAA--AAAA 6501
                         v  vi          v  i vi     ivv  i --i    v  --    
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAA--CTCAATAATAAAAA 797

  chrX_56755402_5   6502 AACAAACCACCCCATCAAATTTTGGGTGAAGTATATGAACAGACACTTCT 6551
                         i     iv    v  i?  vvv    ii   v  v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_56755402_5   6552 CAAAAGAAGACATTTATGTGGCCAAGAAACATATGAAAAAACAAAGCTCA 6601
                          v        i  vi vi       v  i  i       i i---     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT---GCTCA 894

  chrX_56755402_5   6602 TCATCACTGGTCAT 6615
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (81 / 65)
Gap_init rate = 0.02 (13 / 551), avg. gap size = 2.62 (34 / 13)  


3135 26.65 0.99 0.99  chrX_56777957_56784341     4985  5892 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56777957_5   4985 TGGAAGAAGATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5034
                              ii v  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56777957_5   5035 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATACCCATCAAAC 5084
                            v     v     iv i  i  i        i  v  v  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56777957_5   5085 TACCAATGAGTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 5132
                          v   iivivi  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56777957_5   5133 TATGGAAACAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGGCAAAAG 5182
                                 iiv  ii  v  viv  v     iv     i i iiv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56777957_5   5183 AAGAAAGTTGGAGGCATCATGCTACCTGACCTCAAACTATACTACAAGGC 5232
                           v           vv   ii  v  ii ii     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56777957_5   5233 TACAGTAACTGAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5282
                                 iii i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56777957_5   5283 AATGGAACAGAA--GAGACCCCTCAGAAATAATGCTGCATATCTACAACT 5330
                                i    --    vi  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_56777957_5   5331 ATCTGATCTTTGACAAACCTGAGAAAAACAAAAAATGGGGAAAGGATTCC 5380
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56777957_5   5381 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5430
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56777957_5   5431 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5480
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56777957_5   5481 TTAAAAACTTACATGTTAGACCTAAAACCATACAAACCCT-AGAAGAAAA 5529
                          i ? i  i  v    v   v       i   -    i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAA 545

  chrX_56777957_5   5530 CTTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5578
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_56777957_5   5579 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5628
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_56777957_5   5629 AATTCAACTAAAGAGCTTCTGCACAGCAAAAGAATCCACCATCAG---AG 5675
                         v  iv  v v  i i   i  ii vv    i  ---   i    i---  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGA---CACTATCAAGAAAG 691

  chrX_56777957_5   5676 TGAATAGGCAACCTAAAGAATGGGAGAAAATTTTTGCTACCTACTCATCT 5725
                             v  i     i v               v     v vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_56777957_5   5726 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAA 5775
                           i  i  i  vi          v  i  v      iv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_56777957_5   5776 GAAAAAGACAAACAACCCCATCAAAAAGTAGGCAAAGGATATGAACAGAC 5825
                         v           i     v  i?    i i          v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_56777957_5   5826 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAACACACATGAAAAAATGC 5875
                          i     v        i  vi viii     v vi          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_56777957_5   5876 TCATCATCACTCGCCAT 5892
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


2896 28.51 0.99 0.66  chrX_56802886_56809275     4993  5897 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56802886_5   4993 TGGAA---TATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5039
                              ---   i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56802886_5   5040 GGCCATACTGCCCAAGGTAATTTGCAGATTCAA-GCCATCCCCATGAAGC 5088
                            v     v     iv i  i i         -  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56802886_5   5089 TACCAATGACTTTCTTCACAGAA-TTGGTAAAAGCT-ACTTTAAAGTTCA 5136
                          v   iivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56802886_5   5137 TATGGAACCAAAAAAGAGCCTGCATTGTCAAGTCAATCCTAAGCCGAAAG 5186
                                viiv  ii  v  v v  v i   iv     i i ivvii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56802886_5   5187 AACAAAGATGAAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5236
                                v  i   vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56802886_5   5237 TACAGTAACCAAAACAGCATGGTACTGGTATGAAAACAGAGATATAGACG 5286
                                 i   i    ii         i  i ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56802886_5   5287 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5334
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_56802886_5   5335 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5384
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56802886_5   5385 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5434
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56802886_5   5435 GAAACAGAACCCTGTCCTTACACCTTATACAAAAATTAATTCAAGATATA 5484
                            iiv i    ivv   i     v              i    i  iv 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56802886_5   5485 TTAAAGACTTAAATATTAGACATAAAGCCTTGAAAACCCTAGAAGAAATC 5534
                          i ?    i     i v   vv    i iv i   vi i         v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_56802886_5   5535 CTAGGCA-ATACCATTCAGGGCATAGACATGGGCAAGGACTTCATGTCTA 5583
                         v    ?i- v i -   iv i v v ivv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_56802886_5   5584 AAATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATGCA 5633
                         vi i          vvi          vv     v  i    v   iviv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_56802886_5   5634 AATAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5683
                          vi   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_56802886_5   5684 CAGGCAACCTACAGAATGGGAGAACGTTTTTGCAATCTACTCATCTAACG 5733
                         v  i     i              vi v       vii ivi    i ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_56802886_5   5734 AAGGGCTAATATCCAGAATCTACAAAGAACTGAAACAAATTTACAAGAAA 5783
                          i  i  vi          v  i        vvv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_56802886_5   5784 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5833
                           i -    i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_56802886_5   5834 TCTCAAAAGAAGACATTTATGCAGCCAAAACACACATGAAAAAATGCTCA 5883
                             v        i  vi viii     v vi          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_56802886_5   5884 TCATCACTGGCCAT 5897
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (150 / 104)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


 322 26.13 3.02 12.56  chrX_56816548_56823063.rev      328   526 (5990)    L1M4_orf2#LINE/L1        1   180 (728)  

  chrX_56816548_5    328 TGGAAAAACATTCCATGCTCATAGATAGGAAGAATCAATATCACTCAGGA 377
                               i i  i     i    i   v      v i     ---------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT--------- 41

  chrX_56816548_5    378 AGAATCAATATCACTAAAATGTCCATATCACCCAAA--GAACTTTATAGA 425
                         -------- i ---   i   v v   iiv      --  -- i  i   
  L1M4_orf2#LINE/     42 --------TGT---TAAGATGGCAATACTCCCCAAATTGA--TCTACAGA 78

  chrX_56816548_5    426 TTCAGTGCTATTTTTATCAATCTACCAAATACATTTTTCACAGAACTAGA 475
                             ii  v  iii      vv v   iv i v     ii     v v  
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chrX_56816548_5    476 AAAAAAGTATTTTAAACTTTATTTGA----GGAAAGGACAGGCAAGATGG 521
                         v  ivv -  ii    v  i  v  i---- v  i    v--  ii  i 
  L1M4_orf2#LINE/    129 CAAGCTG-ATCCTAAAATTCATATGGAAATGCAAGGGACC--CAGAATAG 175

  chrX_56816548_5    522 CTGAA 526
                          ii  
  L1M4_orf2#LINE/    176 CCAAA 180

Transitions / transversions = 1.60 (32 / 20)
Gap_init rate = 0.04 (7 / 180), avg. gap size = 4.43 (31 / 7)  

2776 27.13 2.10 1.55  chrX_56816548_56823063.rev     5123  6025 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56816548_5   5123 TGGGAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5172
                            i ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56816548_5   5173 CACCATAGTGCCCAAAGTAATGTATAGATTCAATGCTATCCCCATTAAGC 5222
                         vi v   v v      v i  v  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56816548_5   5223 TACCA-CTGACTTTCTTCACAGCATTCGAAAAAACT-ACTGTAAACTTCA 5270
                          v   -   v    i  -i   v v i  v  i-  - iiv    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_56816548_5   5271 TATGAAACCAAAAAGGAGCCCACATAGCTAAGACAATCCTAAGCGAAAAG 5320
                             i  viiv  i   v  viv     i  i      i i ivi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56816548_5   5321 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5370
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56816548_5   5371 TAGAGTAATCCAAATAGCATGGCACTGGTACCACAACAGAGATATAGACC 5420
                           v       v i i  ii   i     i iv vi i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56816548_5   5421 AATGAAACAGAACAGAGGCCTCAGAAATAACACCACACGTCTACAATCAT 5470
                             i  i    iv   ivii         vv   i  i i  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_56816548_5   5471 CTGATCTTTGACAAACCTGATGAAAGCAAGAAATGGGGAAATGATTCCCT 5520
                         i    i  i     ivv  vii i v  vvv          vi  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_56816548_5   5521 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGCAGAAAGCTGA 5570
                         v  i  i              v      v  ?         i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_56816548_5   5571 AACTGGATTCCTTTCTTACACC-TACTACAAAAATTAACTCAAGGTGGAT 5619
                          ii    ii   vi  i     -  -                 ii     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATA-TACAAAAATTAACTCAAAATGGAT 497

  chrX_56816548_5   5620 TAAAGACTTAAACATAAGACCTAAAACCATAAAAAACCCTAGAAGAAACG 5669
                         i ?    i    ii     v       i      v-i i         vv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAAC 546

  chrX_56816548_5   5670 CTA--TGCAATACCATTCAGGACATAGGCATGGGAAAAGACTTCATGACT 5717
                         v  --? i  - i -   iv   v v  vv i  v  v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_56816548_5   5718 AAAACACGAAAA---CAATGGCAGCAAAAGCCAAAATAGACAAAAGGGAT 5764
                          vi    v    ---   --   i      vv        i   vv   i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_56816548_5   5765 AT-ATTTAAACTAAAGATCTTCTGCACAGCAAAATAAACTATCATCAGAG 5813
                         v -  iv   i    i -   i  ii vv    iv v       vv i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_56816548_5   5814 TGAACAGGCAACCTACAGAATGGGAGAAAA-ATTCTGCAATCTGTCTACC 5862
                             v  i     i                -   -     viii v  i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATT-TGCAAATCATATATC 740

  chrX_56816548_5   5863 TGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACA 5912
                            i  i  i  vi          v  i        ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_56816548_5   5913 AGAAATAAACAAACAACTGCATCAAAAAGTGGGTGAGGGGTTTGAACAGA 5962
                          v   v i     i   ivv  i?    i    ii i  i      i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_56816548_5   5963 CACTTCTC-----AAGACCTTTATGCA----GCCAACAAACTTATGAAAA 6003
                           i     -----    ----   i  ----     i  i vi       
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_56816548_5   6004 AATGTTCATTATCACTTGTCTT 6025
                         i   i   vi    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.74 (33 / 19)  


3136 26.02 0.88 0.77  chrX_56847601_56852370.rev     3373  4279 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56847601_5   3373 TGGAAGAACATTCTATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3422
                              ii i  i i   i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56847601_5   3423 GGCCATACTGCCCAAGGTAATTTATAGAGTCAATGCCATCACTATCAAGC 3472
                            v     v     iv i  i  i   v    i  v   v       iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56847601_5   3473 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3520
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56847601_5   3521 TATGGAACCAAAAAAGAGCCCACATCACCAAATCAATCCTAAGTCAAAAG 3570
                                viiv  ii  v  viv  vi     v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56847601_5   3571 AACAAAGCTGGAGGCATCACGCTACCTGACCTCAAACTATACTACAAGGC 3620
                                i      vv    i  v  ii ii     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56847601_5   3621 TACACTAACCAAAACAGCATGGTACTGGTATCAAAAAAGAGATATAGATC 3670
                             v   i   i    ii         i  v ii v   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56847601_5   3671 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCACATATTTACAACC 3718
                                i    i--    i  --    i   vv   i i     iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_56847601_5   3719 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGTATTTC 3768
                          vi    i  i     ivv  v   i v  vv            v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_56847601_5   3769 CTATTTAATAAATGGGGCTGGGAAAACTGGCTATCCATATGTAGAAAGCT 3818
                           v  i  i      v       v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_56847601_5   3819 GAAACTGGATCCCTTCCTTACACCTTATACAAAACTTAATTCAAGATGGA 3868
                            ii    i    v   i     v         v    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_56847601_5   3869 TTAAAGACTTACATGTTAGACCTAAAACCATACAAACCCT-AGAAGAAAA 3917
                          i ?    i  v    v   v       i   -    i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAA 545

  chrX_56847601_5   3918 CCTAGCCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 3966
                          v   v?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_56847601_5   3967 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4016
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_56847601_5   4017 -ACCTAAACTAAAGAACTTCTGCACAGGAAAAGAAACTACCATCAGAATG 4065
                         - i v   i    -     i  ii vvv   i  v    i  vv i i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_56847601_5   4066 AACAGGCTACCTACAGAATGGGAGAAAATTTTTGCAACCCACTCATCTGA 4115
                           v  i v   i                 v       vi  ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_56847601_5   4116 CAAAGGGCTAGTATCCCGAATCTACAATGAACTCAAACAAATTTACAAGA 4165
                         i  i  i  v      v    v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_56847601_5   4166 AAAA-ACAAACAACCCCATCCAAAAATGGGCAAAGGATATGAACAGACAC 4214
                             -     i     v  i?                 v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_56847601_5   4215 TTCTCAAAAGAAGACATTTATGCAGGCAAAAAACACATGAAAAATTGCTC 4264
                              v        i  vi viii v   v  i          iv     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_56847601_5   4265 ACCATCACTGGCCAT 4279
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (129 / 103)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


2983 26.94 1.55 0.89  chrX_56858446_56863064.rev     3227  4128 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56858446_5   3227 TGGAAGAACATTCCATGCTCATGGGTAAGAAGAATCAATATCATGAAAAT 3276
                              ii i  i     i      i vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56858446_5   3277 GGCCATACTGCCTAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 3326
                            v     v  i  iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56858446_5   3327 TACCAA-TGACTTTCTTGACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 3373
                          v   i-  v    i   -     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_56858446_5   3374 ATATGGAACCAAAAAAGAGCCTGCCTCACCAAGTCAATCCTAAGCCAAAA 3423
                                 viiv  ii  v  v vv vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_56858446_5   3424 GAACAAAGCTGGAGGCATCACGCTATCTGACTTCAAACTATACTACAAGG 3473
                                 i      vv    i  vi ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_56858446_5   3474 CAACACTAACCAAAACAGCATGGTACTGCTCCAAAAG---AGAGATATAG 3520
                          v   v   i   i    ii        v--  v   ---   v      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGG--CATAAGGATAGACATATAG 295

  chrX_56858446_5   3521 ACCAATGGAACAGAA--GAGAGCCCTCAGAAATAATGCCACATATCTACA 3568
                          i        i    --     i  --        vv   i i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_56858446_5   3569 ACTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT 3618
                         iii vi    i  i     ivv  v   i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_56858446_5   3619 TCCCTATTTAATAAATGGTACTGGGA-AACTGGATAGCTATATGTAGAAA 3667
                         vvi  v  i  i       i      -         ? i i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_56858446_5   3668 GCTGAAACTGGATCCCTTCCTTATACCTTACACAAAAATTAATTCAAGAT 3717
                         iv    ii    i    v   i i   v  i           i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_56858446_5   3718 GGATTAAAGACTTAAATTTTAGACTTAAAACCATAAAATCCCTAGAAGAA 3767
                             i ?    i     v v   vi      i      ii i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_56858446_5   3768 AACCTAGCCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 3816
                            v   v?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_56858446_5   3817 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 3866
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_56858446_5   3867 TGAATTAAACTAAAGAGCGTCTTCACAGCAAAAGAAACTACCATCAGAGT 3916
                          vv  i   v v  i i v i vii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_56858446_5   3917 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTG 3966
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_56858446_5   3967 ACAAAGAGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 4016
                          i  i ii  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_56858446_5   4017 AAAAAAACAA----CCCCATCCAAAAGTGGGTGAAGGATATGAACAGACA 4062
                              i    ----   v  i?    i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_56858446_5   4063 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAACAATGCT 4112
                         i     v        i  vi viii     v ii         vi     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_56858446_5   4113 CATCATCACTGGCCAT 4128
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


2656 26.47 7.18 0.35  chrX_56864526_56869734     3867  4716 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56864526_5   3867 TGGAAAGATATTCCAGGTTTATGAATTTGAAGAATCCATATTTTTATAAT 3916
                                    i   v   i   i   v     v iv     v   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56864526_5   3917 GTCCATACTACTAAAAGCAATCTATAGATTCAATGCAATTCCCATCAAAA 3966
                          v v     v iv   vii     i        i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56864526_5   3967 TACCAATGACATTAATCACAGAAATAGAAAAAAT-ATCCGAAAATTTATA 4015
                          v   iivi v  vv ii       v  v  iv -    v      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56864526_5   4016 TGGAACCAAAAAATGTTCAGAATAGCCAAAACTATCCTAAGTAAAAAGAA 4065
                              viiv  iiviii               v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56864526_5   4066 CAAAAGTGGAAGAATTACAATACCTCATTTCAAATTATACTACAGAGCTA 4115
                             iv    i  v i   v v  iv        viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_56864526_5   4116 TAGTAGCGGAAACAACACGATACTGGCATAA----ACACATATAGTCCGA 4161
                         i    iivi i   iiii i           ---- v        vi i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_56864526_5   4162 TGGAACAGAATACAGAACCCAGAAATAAATGCACACACCTACAATGAACA 4211
                              i     vv   ii           iv  i   ii  iii v  iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_56864526_5   4212 CATTTTCAGCAAAAGTGCCAATGAC-ATACACTGCAGTAAAGACAGTCTT 4260
                         v      ii   ii       -   -  v  v  vi v  ii i      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_56864526_5   4261 TTCAATAAATGTTGCTGGGAAAACTGGAAATCCATATGAAGAAGAGTAAA 4310
                              i     v        v       v ?   i   v i    i i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_56864526_5   4311 ACTAGACCCCTATCTTTTTCCATATACAAAAATCAAATCAAAATGGATTA 4360
                         ii i        i  iviv              i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_56864526_5   4361 AAGGCTTAAATCTAAAACCCAAACTTATGAAACTACTACAAGAAAGAACT 4410
                         ?  i i     v   i v i   vi   i     vi  v      iv iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_56864526_5   4411 GAGGAAAATCTCCTTGACATTGTTCTGGGCAAAAATTTCTGGAGTCAT-A 4459
                          i? v      i v    v   vvi i     vii     -v  vi  - 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT-TAGATATGA 598

  chrX_56864526_5   4460 TTCCAGAATCACAGGCAGCCAAAACAAAATTGGACAAATGAGATCACATC 4509
                         iv   i  v    i   i v   iv    v i  i    vi  iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_56864526_5   4510 AA-GTTAGAAATCTTTTGCAGAACAAAGAAAACAACCAACCAAGTGAAGA 4558
                           -i   i   -      iivvv     i v  v i   vv       i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_56864526_5   4559 CACAACCTACAGAAT----------------------------------- 4573
                         v      i       -----------------------------------
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_56864526_5   4574 -----------------ATATAAGGAGCTCAAACAACTGTATAGGAAAAA 4606
                         -----------------      i  i   vv      vv   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_56864526_5   4607 ATCTAATAATCTGATC-AAAAATGGGTAAAGAATTTGAATAGACATTTCT 4655
                         iv v     i ii  i-         i    i                  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_56864526_5   4656 CAAAAGGAGACCTACAAATGGCAAACAGGCATATGAAAAGGTGCTCAACA 4705
                          v    i   iv          v  i i   i        i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_56864526_5   4706 TCATTGATCAT 4716
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (130 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 6.40 (64 / 10)  


 775 19.65 3.47 1.73  chrX_56905527_56907224.rev      148   320 (1378)    L1M4_orf2#LINE/L1        1   176 (732)  

  chrX_56905527_5    148 TGGAAA----CTCTGTGTTCATGGATTGTAAGAC--AATATTGTTGAGAT 191
                               ----ii ii             v     --         i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56905527_5    192 AACAATACTTCCCAAGTTTATCTGCAGAGTCAGTGCAACCCTTATCAAAA 241
                         ii       i     i  v    i    v   ii    i  i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56905527_5    242 TCCCAACAGTCCTTTTGTTCAGAAAAGGAAAAGACAATCCTAAAATTCAT 291
                              i v -      v v      vv  v   vii              
  L1M4_orf2#LINE/    101 TCCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_56905527_5    292 ATGAAATTGAAAGGAACTATGAAATTAGC 320
                            i  v  v    i  ivv   --    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAA--TAGC 176

Transitions / transversions = 1.43 (20 / 14)
Gap_init rate = 0.02 (4 / 176), avg. gap size = 2.25 (9 / 4)  

2684 18.99 7.96 3.35  chrX_56905527_56907224.rev      492  1207 (491)    L1M4_orf2#LINE/L1      160   908 (0)  

  chrX_56905527_5    492 AAAGGAGCATGAGTAGCCAATACAATCTT-------AATAATATTTTCAG 534
                           i   v vv  i       v        -------  v  i vvv ii 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_56905527_5    535 AGAAATCACACTTACTGATTTCAAA-CATACTGCACAGTTACAGTAATCA 583
                           i v        v ii        - v    i  v  i           
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_56905527_5    584 AAAAATAAATGTGGTTCTTGCATAAAGATAAATTAAAAACGTGGTTTTTG 633
                          i v ---i      v  v      i    i ------------------
  L1M4_orf2#LINE/    260 AGACA---GTGTGGTACTGGCATAAGGATAGA------------------ 288

  chrX_56905527_5    634 CATAAAATTCTATGAAATAGAATTAAGAGTCCAGATATAAGCCTATACAT 683
                             v iv  v   i         i          v    i  i      
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_56905527_5    684 CTGTACTAAATTGATTTTCAACAAGTATGCCAAGACAATTAAAAAGGCTA 733
                         i i iv v           i     vi         v   v  vi  vv 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_56905527_5    734 AGAATTGTCTCTTCAACAGAAGGTGCTGAGACAACTGGATATCCATGTGC 783
                              v    i       i v       i            ?   ii   
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_56905527_5    784 AAAACAATGAATTTGGTCCCCTTCATCACACCATACATAATAATTAACTC 833
                             v      v    v     v v          i i  v         
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_56905527_5    834 AAAATGGGTCAAAGACATAAATATAAGAGCTAAAAACAAACAAAATTTTA 883
                                i   ?    v     i            vi v -   v i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTA 537

  chrX_56905527_5    884 CAAGAAAATATAGGGGTACATTTTCATGAACTTGGATTTGGCAGTGTTTA 933
                         v       i     ?   v  i   i   v     i  v    i  v  v
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_56905527_5    934 TTTAGGTGTGACTCCAAACGCACAACCAA--------------------- 962
                         i    i i    v     v      v   ---------------------
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_56905527_5    963 --GTTTT------------AAGCTTTTGTGCATCAAAA-ATACTATCAAG 997
                         -- vi  ------------  i         v     i- i         
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_56905527_5    998 AAAGTGAA--GACACCCCACAAAACGGGATAAAATATTTTCATATCATAT 1045
                                 --    v      i  i    v         v  v       
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_56905527_5   1046 ATCTGATAAGGTTCTCTCATCCAGAATTTAAAAAGAACAATTAACAGCCC 1095
                                    vv  ivi         v  v       vv   -  i i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTC 786

  chrX_56905527_5   1096 --TGCTA------CAAACAATTCATTTAAAAAATGAACAAAGCACTTGAA 1137
                         -- iv  ------    i  ii  v  ?       ii     v i     
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_56905527_5   1138 ATAGACATTTCTCCAAAGA---TACACAAATGTCCAACAAGCACACAAAA 1184
                         -                  ---  i       v    i       ii   
  L1M4_orf2#LINE/    837 -TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_56905527_5   1185 AGATGCTCATCCTCATTAGTCAT 1207
                                  v v   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.97 (65 / 67)
Gap_init rate = 0.02 (14 / 749), avg. gap size = 5.79 (81 / 14)  


3015 21.27 3.58 4.05  chrX_56910288_56912138.rev      502  1366 (485)    L1M4_orf2#LINE/L1       48   908 (0)  

  chrX_56910288_5    502 GATGACAATACTACCCAAAGCTG-TCTACAGATTTAATGAATTTCCTATC 550
                             i       v      -i  -          i  i v v i      
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_56910288_5    551 AAAATCTTAATAAGGTTTCAAGGTTTTTAAAGTAATTTAAACACTTGTTA 600
                               ii ii--v ii -----     iv  v    v v vi  vi iv
  L1M4_orf2#LINE/     97 AAAATCCCAGC--TGCCT-----TTTTTGCAGAAATTGACAAGCTGATCC 139

  chrX_56910288_5    601 TAAAAT-CATATGGAACCACGAAACAATAAACAAACAAAACAAAACAAAA 649
                               -         -- i ---   vii  v--  i  i iv-     
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAA--ATG---CAAGGGACC--CAGAATAGC-CAAAA 181

  chrX_56910288_5    650 CAAATTCTTAAAAAAGAA---CAAAG----AGGATTCACACTTCTTGATT 692
                            --    i        ---     ----    i         iii   
  L1M4_orf2#LINE/    182 CAA--TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_56910288_5    693 TCAAA-TTTATTACAAAGCTACAGCACT-AAATCAGTGTGCTGCTGGTAT 740
                              -i   i             i v -  iv       v i    i  
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_56910288_5    741 AAACACACACACATAGACCAATGGAATAAAA--GAGAG-CTATGAAATAG 787
                           iv i v   i     i          i  --     - i -      i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA-GAAATAA 328

  chrX_56910288_5    788 ACTCTTGCTTATTTATG--TAAGTGATTTTTGACAAGAATGCCGTGACCA 835
                           i v i --       --i  v       i      ii    iv     
  L1M4_orf2#LINE/    329 ACCCATAC--ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_56910288_5    836 TTAAATGAGGAAAGAAAAATATTTTTAACAATCAGTGCTGGGAAAACTAC 885
                           v    i        v i v    i     vii         v    iv
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_56910288_5    886 ATGGACACTTGCAAAAGAAGGATATTGGATGCTTATCTTACACCATATAC 935
                           i?v   v          v  vi     iv i  i  i           
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_56910288_5    936 ACTATATACCTTACACCGCGCTGTCTTAAATGAACCAAAGACCTAAACAT 985
                          vv vv  v  i --------------     i i  ?         ii 
  L1M4_orf2#LINE/    477 AAAAATTAACTCA--------------AAATGGATCAWAGACCTAAATGT 512

  chrX_56910288_5    986 AAGAGCTAAAACTGTAAAACTGGTAGAAGGAAACATGAGAGAAAACTTCT 1035
                                      i       vv      i      ii ? v   ii ii
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_56910288_5   1036 ATGAAATTGGATTTTGCAATAATTTATCAGATATGACACAAAGAGCACAG 1085
                         i   vv    i  vv     ii   v i           v  i      i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_56910288_5   1086 G----AATGGAAACAGGAGATACATTGGACTCTATTAAAATTAGAA---T 1128
                          ----  vi    v iv     v        ii  i       i  --- 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_56910288_5   1129 AAATGCATCAAGGGACACCATCAACAGAATGAAAAGACAACTCACAGAAT 1178
                         vvi   v    i      i     v i i            i        
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_56910288_5   1179 GAGACAAAA-ATT-GTAAATTATATATCCAATGAGAAACTAACATCCAGA 1226
                          i  v    -   - i    i       ii  i  ii   vii       
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_56910288_5   1227 ATATACAAAGAATTCCCACAACTTAATGATAATAA-ACAAGCA--CCAAC 1273
                              i      i  ii      i   i    v  -    ii --    i
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_56910288_5   1274 TAAAAAGTGGGCAAATGAATTGAATAGGTATTTCTCCAAAGAG---ATAC 1320
                          ?    i        v  v        ii             i---    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_56910288_5   1321 AAATGGCCAATAAAAGCATAAAAAGATGCTCAGTTTCACTAATCAT 1366
                                      ivi   i            iiv   ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (118 / 62)
Gap_init rate = 0.03 (27 / 861), avg. gap size = 2.44 (66 / 27)  


2450 26.27 3.31 3.09  chrX_56913411_56915493.rev      687  1592 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56913411_5    687 TGGAAAAACATCCCAGGCTCATGAATTGGAAGAATCAATATTGTTAAAAT 736
                               i i      v i     i         v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56913411_5    737 GACCACACTGCCCAAAGTAATTTACAGATTCAATTCAGTTGCTATCAAAT 786
                          i v i   v      v i  i           iv  i iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56913411_5    787 TACCAACATCATTTTTTCACAGAATTAGAATAAAC-AATCCTAAAATTCA 835
                          v   i vv v      -i     v v  -i  i -i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chrX_56913411_5    836 TATGGAAACA-AACAGCCCCA--ACAGCCTAAGCAATCCTAAGCAAAAAG 882
                                 ii-  vi v    -- i    v  i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56913411_5    883 AACAAAGCTGGAAGAATCACATCACCTCACTTCAATTTATACTACAGGGA 932
                                i    i  v     iiv  iv i     vviv       ii v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_56913411_5    933 TATAGTAACCAAGACAGCATGGTACTGGTATAAAAATAGACACACAAATT 982
                           i     i        ii         i    ii       i i i  i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_56913411_5    983 AGTAGAACAGAATAGAGAACCCAGAAGTAAGGTCACATACCTATAACCAA 1032
                          i i   i     v    ii      i   ivi  i i ii   iii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_56913411_5   1033 TTGATCTTCAACAATGCTGACAAATATATACACTGAATAAAAGACACCCT 1082
                              i   i    v v  v   ivvi  v  v  iiv   ii i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_56913411_5   1083 ACTCAGTAAATGTTGCTAGGAGAAGTGAATAGCCA--TGCAGAAGAATGA 1130
                         vi   ii     v    i   v  v  i   ?   --    i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_56913411_5   1131 AA--------------CACACAA---ACAAACAA--AACTCATGACAGAT 1161
                          i--------------     v ---     -  --      vi ii   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAA-AATTAACTCAAAATGGAT 497

  chrX_56913411_5   1162 AAAAGACATAAATGTAAA---TAAAACCATACAAAACCTAGAAAAAAAT- 1207
                         v ?    v         i---      i   v  vv i     i    i-
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_56913411_5   1208 TAGGGAAAGCACTTCTGGACATTGGCCTAGGCAAAGAATTTATGACTAAG 1257
                             ?iv ivv    vv   v    vi       v iv  iv iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_56913411_5   1258 TCCTCAAAAGCTAATGCGACAAAAACAAAAATAGACAAATAGGGCTTAAT 1307
                         v vi       vv v  i      iv         i    v  i   v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_56913411_5   1308 TAAACTAAAAATCCCCTACAAAGCAGAAGAAACAGTCAACAGAGTAAATG 1357
                         i   v v    v iii iiivvv  i i  v  vi    v i   i  vi
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_56913411_5   1358 AACAACCTACAAAATGGGAGAAAATATTTGCAAAGTATTCATCTGACCCA 1407
                         i      i   i                      vi  vi      ivvi
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_56913411_5   1408 GGACTAATATCTAGAATCTAGAAAGAACCCAAGCAACACAGAAAGTAATG 1457
                              vi    i     v  v       i vvi    v  -------  -
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-------AT- 789

  chrX_56913411_5   1458 TAAATAATAATAATAATAATCCC-TTAAAAAGTGGGCCAAGAACATGAAC 1506
                         --     v  v vv     i  v-  ?    i     v   i iv    i
  L1M4_orf2#LINE/    790 --AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_56913411_5   1507 AGACACTTTTCAAAAGAAGATATAGAAACAGCCAACAAACAATACAAAAC 1556
                              i  i  v            v   ii     i  i  ---------
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA--------- 878

  chrX_56913411_5   1557 AAAACAAAAAATAAAATACTCAACATCACTAATCAT 1592
                         ----  vi   -- i  i          ????????
  L1M4_orf2#LINE/    879 ----CATGAAA--AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.41 (58 / 17)  


3118 27.05 2.39 0.00  chrX_56917450_56919964.rev     1145  2024 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_56917450_5   1145 ATATTCTTTGTTCATGAATTGGAAGAATTCATATTATTAATATGTTTGTA 1194
                             i iv        i         v  v     i    v   vivi  
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_56917450_5   1195 CTACCCAAAGCAATCTACAGATTTAATGCAATCTCTATCAAAATACCAAT 1244
                           v      vii           i  i      i          v   ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_56917450_5   1245 GACATTCTTCATAGAAATAAAAAAA---ATCCCAAAATTTATATGGAATC 1291
                         vi v  i  iii      vi v  i---    i      i        vi
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_56917450_5   1292 AAAAAAGACCTAGAATAGTCAAAGCTACTGTAAGCAAAAAGAGCAAAACT 1341
                         iv  ii    i       i    i v iiv i iv  i    i    ii 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_56917450_5   1342 GGAGCAATCACGTTACCTGACTTGAAATGATATTTTAGAGCTATAGTAAT 1391
                             v v    ii v  ii i  v   vvv  i vi i     i      
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_56917450_5   1392 CAAAACAGCATAGTACTGGCATAAAAGCAGACA----GACCAATGAAACC 1437
                            i    ii i            iiii     ----  i     i  iv
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_56917450_5   1438 GAATTGAAAACCCAGAAACAAATCCACTCACCTAAAGTGAACTCATTTTC 1487
                                i ii       i   i   iv  ii  vi  v  i v      
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_56917450_5   1488 AACAAAGGTGTCAAGAATATACACTAGGGAGAAGACAGTGTCTTCAATAA 1537
                         i    i    i     vi  v  v i    i ii i   v i     i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_56917450_5   1538 GTGGTTCTGGGAAAACTAGATA------TGGAGAAGAGTTAATCTAGACC 1581
                         i    v      v    i    ------  v i    i v  vi i    
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_56917450_5   1582 CCCATCTCTTGCCATATACAAAAAC-AAATTGAAATGGATTAAACACTTA 1630
                           i i   vii             i-  v ii        i ? v  i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_56917450_5   1631 AATCTAAGACCTCAAACTATGAGATTCCTACAAGGAAACATTGAGAAAAA 1680
                            v     v  v       i i i  i  v   i      v i?iv   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_56917450_5   1681 TCTCCA-GACATTGGCCTGGACAAAAATTTCTTGAGCAATACCCCACAAG 1729
                            i i-   v    vi i i   vii      iiii vv  v   v   
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_56917450_5   1730 CACAGGCGATGAAAGCATAAATGGACAAATGAGATCACATCAAG-TTAAA 1778
                             i  i ii    v v    i  i    vi  iiv      i-     
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_56917450_5   1779 AAGCT--GCACAGTAAAGTAAACAGTCAACAAAGAGAAAAGACAACCCAC 1826
                           vi -- ii vvi    v v  vi    v    v               
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_56917450_5   1827 AGAATGGGAGAAAATACTTGCACACTATTTATCTGACAAGAGATTAATAA 1876
                                         i     v ii  v       i   i  i vi  v
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_56917450_5   1877 CCAGAATACATAAGGAGTTCAAACAACTGTACAGAAAGAACTCTAATAAT 1926
                                 i    i  ii  vv      vv i iv  i  vv v     i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_56917450_5   1927 TCAATTAAAAACTGGGCCAAAGATTTGAATAGACATA---CAAAAGAAGA 1973
                         i     ?    v     v  i               v--- v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_56917450_5   1974 CATACAAATGGCAAACAGGCATATTAAAAGGTGTTCAACATCATTGTTCA 2023
                         i           v  i i   i  v     i  i         ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_56917450_5   2024 T 2024
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.73 (149 / 86)
Gap_init rate = 0.01 (8 / 901), avg. gap size = 2.62 (21 / 8)  


 450 16.26 7.32 1.63  chrX_56920688_56924571.rev      261   383 (3501)    L1M4_orf2#LINE/L1      779   908 (0)  

  chrX_56920688_5    261 TACAATTT--TAATTGAATAAATAAATAA----AT---AAAATGGGCAGT 301
                              i i--    vi  - i i      ----  ---          iv
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_56920688_5    302 GGTCTTAAATAGACATTTCTTCCAGAAAGATATACAAATCGCCAATAAGC 351
                           vi  i             i v ii             v          
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_56920688_5    352 ACGTGGAAAAAATACTCAAAATCAGAAATGAC 383
                           i  -    i  i     v    ????????
  L1M4_orf2#LINE/    878 ACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.04 (5 / 130), avg. gap size = 2.20 (11 / 5)  

 413 21.69 0.00 0.00  chrX_56920688_56924571.rev     2610  2692 (1192)    L1M4_orf2#LINE/L1        1    83 (825)  

  chrX_56920688_5   2610 TGGAAGAACATCCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 2659
                              ii i        i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56920688_5   2660 GGCCATACTGCCCAAGGTAATTTATACATTCAA 2692
                            v     v     iv i  i  i v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA 83

Transitions / transversions = 1.57 (11 / 7)
Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.00 (0 / 0)  

2530 25.53 0.86 0.71  chrX_56920688_56924571.rev     2693  3393 (491)    L1M4_orf2#LINE/L1      207   908 (0)  

  chrX_56920688_5   2693 TGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTGCACTAA 2742
                               vv    i  v  ii i      viv        i   i  v   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_56920688_5   2743 CCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAATGGAAC 2792
                         i   i    ii         i iv ii i   v       i        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_56920688_5   2793 AGAA--GAGACCCCTCAGAAATAATGCTGCATACCTACAACTATCTGATC 2840
                             --    vi  --        vv iii i ii  iiiii vi    i
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_56920688_5   2841 TTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAA 2890
                           i     ivv  v   i v  vvv           i  vvi  v  i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_56920688_5   2891 TAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGG 2940
                         i              v      v  ?   i   i i  iiv    ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_56920688_5   2941 ATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGAC 2990
                          i    v   i     v              i    i      i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_56920688_5   2991 TTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACGTAGGCA- 3039
                         i  v    v   v       i      vi i           i    ?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_56920688_5   3040 ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCA 3089
                          v i -   iv   v v  vv i     v ii   v ivv  vi      
  L1M4_orf2#LINE/    555 AAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_56920688_5   3090 AAAACAATGGCAACAAAACCAAAATT-GACAAATGGGATCTAATTAAACT 3138
                            i  vvi         vv    v -  i    v   ii v  i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_56920688_5   3139 AAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAAC 3188
                         v  i i   i  ii vv    i  v    i  vv i      v  i    
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_56920688_5   3189 CTACAGAATGGGAGAAAATTTTTGCAACCTATTCATCTGACAAAGGGCTC 3238
                          i                 v       vii  vi      i  i  i  i
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_56920688_5   3239 ATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAA 3288
                         i          v  i  v      vv    v iv i  v     i     
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_56920688_5   3289 CAACCCCATCCAAAAGTGGGTGAAGGATATGAATAGACACTTCTCAAAAG 3338
                         i     v  i?    i    ii      v          i     v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_56920688_5   3339 AAGACATTTATGAA--GCCAAAAAACACATGAAAAAATGCTCACCATCAC 3386
                             i  -- ii  --     v  i          i       v     ?
  L1M4_orf2#LINE/    854 AAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_56920688_5   3387 TGGCCAT 3393
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.43 (103 / 72)
Gap_init rate = 0.01 (7 / 702), avg. gap size = 1.57 (11 / 7)  


2068 25.00 2.25 1.95  chrX_56924915_56926569.rev      497  1164 (491)    L1M4_orf2#LINE/L1      239   908 (0)  

  chrX_56924915_5    497 ACCACAA-TCTACAGTAACCCAAATAGCTAGGTATTGATATAAAGACAGG 545
                           i    -v         i v i i  ivv    i  ii    i  i  i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_56924915_5    546 AACATAGACCA-TGTGAGCAGAATAGAGAACTCAGAAATAAAGGCACATA 594
                         v i     i  -  -  ii     v    iii          vv  i i 
  L1M4_orf2#LINE/    289 CATATAGATCAATG-GAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_56924915_5    595 TTTAGAGCCAACTTATTTTC-ACAAAG-TGCTAAGAATAT--AATTGTGG 640
                             vi i   i v      -    i -   i    vi  --   v -  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GG 386

  chrX_56924915_5    641 AAAAGATA-TCTTATTCAATAAATGGTGCTAGGAAAGCTGGATATCCATA 689
                            ii   -    -     i          i   v i       ?   i 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_56924915_5    690 TAAAGAAGGATAAAACTTGTCACCTATCTCTCACCATATACAAAA-TCAA 738
                          iv i   i  i  ii v v v    i   v              - i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_56924915_5    739 CTCAAAATATATTAAAGCATTAAACATAAGACCCAAAAATATAAAACTAA 788
                                 iv  i ?  vvi    ii     v i    v         vv
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_56924915_5    789 TAAATGAAAACAAAGGAAAAACATTTCAGGACATTGGTATAGGAAAATAT 838
                           i v       v   ?iv  vvi   iv   v    vv    v  vvi 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_56924915_5    839 TTTATGGCTAAGACCTCAAAAGCACAGATATATAAAACAAAAATT-GACA 887
                           iv i v  v   vi          iii - i    v     v -  i 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCA-ACAAAAGAAAAAATAGATA 634

  chrX_56924915_5    888 AATGGAACTATATTAAACTGAAAAGC------ACATCAAAGAAAATAATC 931
                            v i   vi  i   v v    i ------i v      i v iv   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_56924915_5    932 AACAGACTGAAGAGGCATCCTGTTGAATGGAAGGAAATATTTGCAAACTA 981
                           v i v    i  i  v  iiiv      i  i             ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_56924915_5    982 TTGATCTGACACAGGACTAATATCCAGAATAAACAAGGAACTCAAACGAC 1031
                          vv      i vi     vi           v i  i      vv  i  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_56924915_5   1032 TCAATAATAAGATAAAAACAAATAACCCCATTAAAAAGTGGGCAAAAAAT 1081
                                   ---   i           v   ?    i        ii  
  L1M4_orf2#LINE/    785 TCAATAATAA---AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_56924915_5   1082 CTGAATAGGCATTTCTCTAAAGAAGTCTTATAAGTGGCCAAAAGGTATAT 1131
                         i       i        i       viv  i  i       v i i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_56924915_5   1132 GAAAAAAGAAAACAACTCAACATCACTAATCAT 1164
                              i vi------          ????????
  L1M4_orf2#LINE/    882 GAAAAGATG------CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (97 / 66)
Gap_init rate = 0.02 (15 / 670), avg. gap size = 1.87 (28 / 15)  


3189 27.09 0.66 0.66  chrX_56931811_56940585.rev     5617  6524 (2251)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56931811_5   5617 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5666
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56931811_5   5667 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAAC 5716
                            v     v     iv i  i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56931811_5   5717 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCTAATT-TAAAGTTCA 5764
                          v   iivi i  i  ii     -   -- v     i  i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_56931811_5   5765 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGAAAAGAG 5814
                                viiv  ii  v  viv        i      i i i   ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_56931811_5   5815 GACAAAGTTGGAGGCATCACGCTACCTGACTT-GAAACTGTACTACAAGG 5863
                         i             vv    i  v  ii i  -i     -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_56931811_5   5864 CTACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGAC 5913
                                  i   i    ii    i    i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_56931811_5   5914 CAATTGAACAGGACAGAGGCCTCAGAAATAACACCACATATCTACAACCA 5963
                             v   i  i iv   ivii         vv   i i  i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_56931811_5   5964 TCTGATCTTTGACAAACCTGATAAAAATAAAAAATTGGGAAAAAATTGCC 6013
                         vi    i  i     ivv  vi  i vi vvv   v      i   v i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_56931811_5   6014 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 6063
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_56931811_5   6064 AAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTGAAGATGGAT 6113
                           ii    i    v   i i   v              i v  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_56931811_5   6114 TAAAGACTTAAATATTAGATCTGAAACCATAAAAACTCT-AGAAGAAAAC 6162
                         i ?    i     i v   v  i    i      -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chrX_56931811_5   6163 CTAGGCA-ATACCATTCACAACACAGGCATGGGCAAGGACTTCATGACTA 6211
                         v    ?i- v i -   iii  viv  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_56931811_5   6212 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATA-ACAAATCGGATCTA 6260
                         vi            vvi          vv      - i    i   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_56931811_5   6261 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAA 6310
                           i   v v  i i   i  ii vv    i  v    i  vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_56931811_5   6311 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCATTTGACA 6360
                         v  i     i                 v       vii  vi  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_56931811_5   6361 AAGGGCTAATATCCAGAATGTACAATGAACTCAAACAAATTTACAAGAAA 6410
                          i  i  vi          i  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_56931811_5   6411 AAAATCAAACAATACCATCAAAAAGTGAGGGAAGGATATGAACAGACACT 6460
                           i -    i  iv v  i?    i  i vi      v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_56931811_5   6461 TCTCAAAAGAAAACATCTATGCAGCCAACAGACACATGAAAAAATGCTCA 6510
                             v      i i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_56931811_5   6511 TCATCACTGGCCAT 6524
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (156 / 86)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.09 (12 / 11)  

2548 27.46 3.84 1.36  chrX_56931811_56940585.rev     7400  8284 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_56931811_5   7400 GGAAAAACATTCCATGTTCATGGATAGGAAGAATCAATATTGTAAAAATA 7449
                              i i  i              v      v i        v  i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_56931811_5   7450 ATTGTACTGCCCAAAGTAATTTATA--TTCAATGATATTTTCCCTA---A 7494
                         iivi    v      v i  i  i --     i vv  ---     --- 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT---CCCTATCAA 98

  chrX_56931811_5   7495 ACTACCA-CTGACACTCTT-CATAAAATTAGAAATAACT-ATTTTAAAAT 7541
                          v v   -   v vi i  -  -i     -  v - i  -  ii      
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCA-GAAATT-GACA-AGCTGATCCTAAAAT 145

  chrX_56931811_5   7542 TTATATGGAAAGAAAACAGAACCCGAATAGCCAGGACAATCCTAAACAAA 7591
                          i         viv  vi  v  v         ii      i i  v  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_56931811_5   7592 ACGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAC 7641
                          v        i      vv   ii  v  ii i      viv       v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_56931811_5   7642 GGCTACAGTAACCAAAACAGCACTGTTCTGGTACAA----------ATAG 7681
                         i          i   i    iiiv  v    i i  ----------    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_56931811_5   7682 GCCAATAGAACAGAATATAAAACTCAGAAATGAGACCACACACTGAAAAC 7731
                         ii    i   i     vv i iii       i iv   i   i v viii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_56931811_5   7732 CATCTGTTCTTCAACAATCCTGACAAAAACATGCAATGGGGAAAGGATTC 7781
                           vi  v i   i    vvv  v   i v   v            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_56931811_5   7782 CCTATTTAATAAATAATGCTTGGAGAACTGGCTAGCCGTATGCAGAAAAA 7831
                         i  v  i  i    ii    v   v      v  ?  ii     i  i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_56931811_5   7832 AGAAGCTAGGCCGCTTCCTTACACCTTATACAAAAATTAAGTCGAGATGG 7881
                         v    i i i  v  v   i     v              v  i i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_56931811_5   7882 ATTCAAGATTTAGATGGAAAACCAAAAACTATAAAAACCCTAGAAGAAAA 7931
                           iv?   ii  i   v  i v v            vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_56931811_5   7932 TACCA---------CTCAGGACATAGGCATGGGCAAAGATTTCATAATGG 7972
                         i ivi---------i  iv   v v  vv i     v i    v  --- 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA---G 592

  chrX_56931811_5   7973 AGATG---CCAAAAGCATTTGCATCAAAAGCAAAAATTGACAAATAGGAT 8019
                          v   ---         ivv   v      v      v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_56931811_5   8020 CTAATTAAGCTAAAGCACTTCTACACAGCAAAATAAACTATCATCATAGT 8069
                         i v  i  iv v  iv    i iii vv    iv v       vv v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_56931811_5   8070 GGACAGACAATCTACAGAATGGGATAAACTTTTTTTAAATTTATTCACAT 8119
                          i v      i i           v   v v   vi    i-  vi iv 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCT 741

  chrX_56931811_5   8120 GACAATGGTCTAATATCCAGAGTCTGCAAGAAACTT----AAATCTACAA 8165
                           i  v  v  vi        i v ii  ii    i----  v  v i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_56931811_5   8166 GAAAGAAACAAACAACCCCATTAAAAAGTGGGCAAAGAATATGAACAGAC 8215
                         v   i i     i     v   ?    i         i  v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_56931811_5   8216 ACTTCTCAAAGGAAGACATACATGCAGCCCACAAACATATAAAACAAAAA 8265
                          i     v  i     i     viii   v i  i  i  i   -- i v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA--AGAT 889

  chrX_56931811_5   8266 GCTCAATATCACTGGTCAT 8284
                               i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (137 / 103)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 2.88 (46 / 16)  


2566 27.88 2.10 1.66  chrX_56955205_56958798     2198  3101 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56955205_5   2198 TGGAAAAACATTCCATGCTCATGGATAAGAAGAATCAATATCATGAAAAT 2247
                               i i  i     i        vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56955205_5   2248 GGCCATATTGCCCAAAGTAATTTATAGATTCAGTGCTATTCCCACTAACC 2297
                            v   i v      v i  i  i       ii  v  i  i ii  vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56955205_5   2298 TACCA-TAGACTTTTTTTCACAAAATTAGAAAAAAATCTA--CTTAAATT 2344
                          v   -iv v       v  -i     -  v  i---  i-- i    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATT-GACAAG---CTGATCCTAAAAT 145

  chrX_56955205_5   2345 TCATGTGGAACCAAAAAAGAGCCCACATATCCAAGACAATCCTAAGCAAG 2394
                             i     viiv  ii  v  viv   v    i      i i iv   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_56955205_5   2395 AAGAACAAAGCTGAAGGCAACATGCTACCTGACTCCAAACTATACTACAA 2444
                                   i  i   vvv  ii  v  ii i i    viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_56955205_5   2445 GGCTACAGTAACAAAAACAACATGGTACTGATACCAA-ACAGATATATAG 2493
                         i          iv  i   iii        ii iv i- i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_56955205_5   2494 ACCAATGGAACAGAA--GAGAGGCTTCAGAAATTATGCCACACATCTACA 2541
                          i        i    --     -- i       v vv   i    i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAG--TCCAGAAATAAACCCATACATTTATG 343

  chrX_56955205_5   2542 ACCATCAGATCTTTGACAAACCTGACCCAAA--CAAGCAATGGGGAAAGA 2589
                         ii  viv   i  i     ivv  --    i--  vv             
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTG--CCAAGACCATTCAATGGGGAAAGA 391

  chrX_56955205_5   2590 ATTCCCTATTTCATAAATGTTTTTGGAAAAACTGGCTAGCCATATGAAGA 2639
                           vvi  v  iv i     v vi   i v      v  ?   i   v i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_56955205_5   2640 AAACTGAAACTGGATCACTTCCTTATACCTTATACAAAAATTAATTCAAC 2689
                          i v    ii    i v  v   i i   v              i    v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_56955205_5   2690 ATGTATCAAAGACTTAAATCTAAGACCTAAAGTTGTAAAAACACTAGAAG 2739
                            v    ?    i     v     v     ii i     vivi      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_56955205_5   2740 AAAACATAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTC-- 2786
                                   ?i- v i -   iv   v v  vv i     v ii   --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_56955205_5   2787 ----ATGACAAAATAAAAAAACAATGGCAACAGAAACCAAAATTGACAAA 2832
                         ----      v--i    iv    --      i  ivv     v  i   
  L1M4_orf2#LINE/    591 AGATATGACAC--CAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAA 636

  chrX_56955205_5   2833 TGGAATCTAATTAAACTGAAGACCTTCTGCAAAGCAAGATACACTGTCAT 2882
                          v i ii v  i   v v  i v   i  iivvv   iiv     i   v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_56955205_5   2883 CAGGGTGAACAGGCAACCTACAGAATAGGAGAATATTTTTGCAATCTATT 2932
                         v ii     v  i     i       i      v  v       vii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_56955205_5   2933 CATCTGACAAAGGGCTAATACACAGAATCTACAAAGAACTTAAACATATT 2982
                         i      i  i  i  vi  iv      v  i        ivv   vv i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_56955205_5   2983 GACAAGGAAAAAAAAAAACAAACCAA----AAAGTGGGCAGAGGATATGA 3028
                         i i  v-     i v   i  v    ----   i      i     v   
  L1M4_orf2#LINE/    787 AATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_56955205_5   3029 ACAGAAACTTCTCAAAAGAAGACACTTATTCAGCCAACAAACATATGAAA 3078
                          i   v i     v        i ivi vvii     i  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_56955205_5   3079 AAAAGCTAATCATCACTGGTCAT 3101
                          i v   v v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (144 / 105)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


2525 29.23 2.46 0.78  chrX_56962464_56966702.rev     2856  3748 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_56962464_5   2856 TGGAAAAACATTCCATGCTCATGCACAGGAAGAATCAATATCATGAAAAT 2905
                               i i  i     i     v iv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_56962464_5   2906 GGACATACTGCCCAAAGTAATTTAGAGATTCAATGCTATTCCAATCAAGC 2955
                           vv     v      v i  i  v        i  v  i  v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_56962464_5   2956 CACCATTTACTTTCTTCACAGAATTAGAAAACATTATTTTAAATTTTATA 3005
                         iv   vi i i  i  ii     v v  v  vv v  ii    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_56962464_5   3006 TGAAACCAAAAAGAGCAC-GTATAGCCAAGACAATCCTAGGCAAAAGGAA 3054
                           i  viiv  i ii v - v        i      i iiiv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_56962464_5   3055 CAAAGCTGGAGGCATCACACTACCTCACTTCAAACTATACTACAGAACTA 3104
                              i      vv       v  iv i      viv       i i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_56962464_5   3105 TAGTAACCAAAACAGCATGGTATTGATACCAAAACAGATATATACCCCAA 3154
                         i     i   i    ii     i  ii iv ii i   i     vvi   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_56962464_5   3155 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTAAAA-CAATC 3203
                              i    iv   ivii         vv   i    i  vii-    -
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT- 349

  chrX_56962464_5   3204 TGATCATTGACAAACCTGGCAAAAACAAGCAATGAGGAAATGAT--TCCT 3251
                             iv i     ivv  v   i v  vv     i     vi  --  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_56962464_5   3252 TTGTTAATAAATGGTATTTGGAAAACTGTCTAGCCATAAGCAGAAAACTG 3301
                           --i  i       ii v   v     vv  ?   i v   i  i v  
  L1M4_orf2#LINE/    400 TT--CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_56962464_5   3302 AAACTGCACCCCTTCCTTACGCCTTATGAAAAAATTAACTCAAGATAAAT 3351
                           ii  v      v   i  i  v   iv              i  ii  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_56962464_5   3352 TAAAAACTTGAATGTAAGACTTCAAAC---------CCTACAAGAAAACA 3392
                         i ? i  i i         vi v    --------- i  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_56962464_5   3393 T--GAGCAATACCATTCAGGACATAGGCATGGGCAGAGATTTCATGACTA 3440
                          -- ? i  - i -   iv   v v  vv i    iv i    v iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_56962464_5   3441 AAACACCAAAAGCAATTGCAACAACAGCCAAAATTGACAAATAGGATCTA 3490
                         vi            vvv       v  vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_56962464_5   3491 ATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATTATCAGATTGAA 3540
                           i   v v  i i   i  ii vv    iv v     i vv i v    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_56962464_5   3541 CGGGAAACCTACAGGATGGGAGAAAACTTTTGCAATCTATACATTTGAAA 3590
                         vi iv    i    i           iv       vii   i  i   v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_56962464_5   3591 AAGGGCTAATATCCAGAATCTACAAGAAACTTGAGCAAATTGACAAGAAA 3640
                          i  i  vi          v  i  ii    ivvi   v ii i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_56962464_5   3641 AA-----ACAACCCCTTCAAAAAGTGGGTGCAAAGTAT--AAACAGACAC 3683
                           ----- i     vv i?    i    --     v  --i  i     i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGG--CAAAGGATTTGAATAGACAT 843

  chrX_56962464_5   3684 TTCTCAAAAGAAGACATTTATACTGCCAAAAAACATATGAAAAAAAGCTC 3733
                              v        i  vi v iv     v  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_56962464_5   3734 ATCATTACTGGTCAT 3748
                          v   i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (148 / 109)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  


2181 27.92 2.75 2.75  chrX_56988631_56991111     1115  1988 (493)    L1M4_orf2#LINE/L1       35   908 (0)  

  chrX_56988631_5   1115 TCAATATTGATAAG-CGGTCATACTGCCCAAGC-AATTTAAAGATTTAAT 1162
                          i       v    -i  iv     v     ii-i  i  v     i  i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chrX_56988631_5   1163 GTTATTCCCATCAAACTACAATGATG--TTTAATGTAGAATTAGAAAGAA 1210
                          iv  i  i      v v v - v  --   vv  i    v v  v ---
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCA-GCTGCCTTTTTTGCAGAAATTGACA--- 130

  chrX_56988631_5   1211 AACT-ATTCCAAAATTTATATG-AAATAAAAAAATAGCCTAAATTGCCAA 1258
                          i  -  i i      i     -    iv  iii- v  vi   v     
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGG-ACCCAGAATAGCCAA 179

  chrX_56988631_5   1259 AGTA-TTTCTAAGGAAAAGAACAAAGCTGAAGGCATCACACTGTCTGACA 1307
                          ii - i iv  ii i          i  i   vv       vi ii iv
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_56988631_5   1308 T-AAAACTAAAATTCAAGATTACAGTTACCAAAATAGAATGGTATTGATA 1356
                          -      v v- v   iii      v i   i i  vi     i  ii 
  L1M4_orf2#LINE/    230 TCAAAACTTAC-TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_56988631_5   1357 CAAAGACAAAAAATAAAAATAAAAAAGACCAATCAAACTGGTTAGAGAAC 1406
                         i  i  -------  i v   v ---  i    vi  iv iv v    ii
  L1M4_orf2#LINE/    279 TAAGGA-------TAGACATATA---GATCAATGGAATAGAATTGAGAGT 318

  chrX_56988631_5   1407 CCAGAAATAAAGCTGTACACCTACAACCACTTAATCTTCAACAAAATTGA 1456
                                    v ii    ii  iiii  v  i  i   i    iiv  v
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_56988631_5   1457 CAAAATAAG-CAATAGGTAAAGGACCCCCTATTTAACAAATTATGGTAAG 1505
                            i iv v-    i  v    i ivvi  v  i       vi  v ii 
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chrX_56988631_5   1506 ATAGGTAACTAGGCATATGCAAAAGATTCAGGATGGATCATTTTCTTTCA 1555
                          i iv iiv  ?v  i          v v i v    i vi vi  iv  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_56988631_5   1556 ACACATATAAAATTCAACTCAAGGTGGATTAAAGACATAAATGTAAAACT 1605
                         v  i   i    v i       ii     i ?    v         i vi
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_56988631_5   1606 TAAAACTATAAAAACTCT-AGAAGAAAACCCAGAAAACACTATTC-TGTA 1653
                                      -    -          vi  i?ivv v v   -  - 
  L1M4_orf2#LINE/    519 TAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-A 566

  chrX_56988631_5   1654 CATTGGCCTCGCTTAAGATTT------TATGACAAAGAATTCAAAAGCAA 1697
                          v    vi v viv v i   ------       ------i        v
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACA------CCAAAAGCAC 610

  chrX_56988631_5   1698 TTGCAGCAAAACCAAAAATGGACAACTGAGACTTTATTAAACTAAAGAGC 1747
                         vv   i     vv      i  i  v vi     i  i   v v  i i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_56988631_5   1748 TTCTGCACAGTAAAATAAACTATCAACAGAGTAAACAGACAATCAACAAA 1797
                           i  ii vvi   iv v        v i   i  v      i v   i 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_56988631_5   1798 ATGAGAGAA--TATTTATGAACTATGTATCTGACAAAGGACTAATATCCA 1845
                            i     --     iii  ii  i       i  i     vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_56988631_5   1846 GAATCTATAAGAAAC----ATAAGTCAATAAGCAAAAAACAAACCACCCC 1891
                             v     ii   ---- i  v       vv    i     iv    v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_56988631_5   1892 ATT-AAACATGGGCAAAAGATATGAACAGACACTTCTTAAAAGAAGACAT 1940
                            -   v         i   v    i     i    iv        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_56988631_5   1941 ACATGTGGCCAACAAGTATATGAAAAAATGCTCAACATCACCAATTGT 1988
                            vi       i   i i       i             ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.03 (23 / 874), avg. gap size = 2.09 (48 / 23)  


2769 27.30 1.55 0.78  chrX_57003301_57009967     5274  6174 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57003301_5   5274 TGGAAAAA-ATCCCATGCTCATGGACAGAAAAAAATCAATATGGTGAAAA 5322
                               i -        i       iv i  i v- i     v  v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chrX_57003301_5   5323 TGGCCATACTGCCCAAGGTAGTTTGTAGATTCAATGCTATCCCCATCAAG 5372
                             v     v     iv ii i ii        i  v     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_57003301_5   5373 CTACCA-CTGACTTTCTTCAAAGAATTTGAAAAAACTACTTC-AAACTTC 5420
                         v v   -   v    i  -iv    v    v  i-  iv i -   v   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chrX_57003301_5   5421 ATATGAAACCAAAAAAGAACCCACATAGGCAAAACAATCCTTAGCAAAAA 5470
                              i  viiv  ii  v  viv    v          i v iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_57003301_5   5471 GAACAAAGCTGGAGGCATCGCGCTGCCTG-CTTCAAACTATACTACAAGG 5519
                                 i      vv  i i  v  ii-i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_57003301_5   5520 CTACAGTAATCAAAACAGCATGGTACTTGAACCAAAACAGATATATAGAC 5569
                                      i    ii       v v iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_57003301_5   5570 CAATGGAACAGAACAGAGGCTTGAGAATTAACACCACACATATACAA-CA 5618
                                 i    iv   iv iv    v   vv   i    v  iii-  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_57003301_5   5619 ATCTGATATTTGACACACCTGACACAAACAAGCAATGTGGAAAACATTCC 5668
                           -    v  i    vivv  v  vi v  vv     v     iv  vvi
  L1M4_orf2#LINE/    348 AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_57003301_5   5669 CTATTTAATA----GTGTTGGGAAAACTGGCTTGCCATATGCAGAAAACT 5714
                           v  i  i ----   i     v      v v?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_57003301_5   5715 GAAACTGGACCCCTTCCTTACACCTTATATAAAAATCAACTCAAGATGGA 5764
                            ii         v   i     v    i      i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_57003301_5   5765 TTAAAGACTTAAACGTAAGACCTAAAACCATAAAAATCCTAGAAGAAATC 5814
                          i ?    i    i      v       i      v  i         v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_57003301_5   5815 CTTAGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTG 5863
                         v vi ?i- v i -   iv   v v  vv i     v ii   v iiv i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_57003301_5   5864 AAATGCCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTA 5913
                         vi ii         vvi     v    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_57003301_5   5914 ACTAAACTAAAGAGCTTCTATACAGCAAAATAAAGTATCATCAGAGTGAA 5963
                          ii   v v  i i   i i i vv    iv v v     vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_57003301_5   5964 CAGGCAACCTAAAGAATGGGAGAAAATTTTTGCGCTATCA---GTCTGAC 6010
                         v  i     i v               v     iv-    ---i     i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGAT 744

  chrX_57003301_5   6011 AAATGGCTAATATCGAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 6060
                           iv i  vi    v     v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_57003301_5   6061 AAAAACAAATGACTCCAC-AAAAAGTGGGCAAAAGATATCAACAGACACT 6109
                            i      i  i v i-?    i        i   v v  i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_57003301_5   6110 TCTCAAAAGAAGACATTTATGTAGCCAACAAACATATGAAAAAAATGCTC 6159
                             v        i  vi vi i     i  i  i       i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chrX_57003301_5   6160 ATCATCACTGGTCAT 6174
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (131 / 111)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.31 (21 / 16)  


 880 23.42 4.09 3.35  chrX_57047781_57050340.rev      879  1147 (1413)    L1M4_orf2#LINE/L1        1   271 (637)  

  chrX_57047781_5    879 TAGAAAAGTATCC-ATGTTCATGAGTTGGACTAATTAATATTGTTAAAAT 927
                          i    ii     -         ii     vv v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57047781_5    928 GTCCATACTACTCCAAGTT-ATCTACATATACATAAACTCAATCTCTGTC 976
                          v v     - i    i  -       v  v  ---  v     i  i  
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCA---ACGCAATCCCTATC 96

  chrX_57047781_5    977 AAAACACCAAAGACATTCTTTATGGAAACAGAAAATAAACAG-TCCTAAA 1025
                             iv   ivvi v  i   iii    iv  ---i  i v -       
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGA---CAAGCTGATCCTAAA 143

  chrX_57047781_5   1026 ATTCATATGGAGCTACAGAAGGATC-AGAATGGCCAAAGCAATCCTGAAG 1074
                                    iv i  - i   i -     i      i     i    i
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_57047781_5   1075 AAAAAGAACTAAGCTGGGGCA-TCAAATTACCTGACTTCAAATTATACTA 1123
                           i      v   i   i v -   v i v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_57047781_5   1124 TAAACCTATGG------GGACAGGCGTGGT 1147
                         i   v   ii ------i     -i     
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAG-TGTGGT 271

Transitions / transversions = 1.86 (41 / 22)
Gap_init rate = 0.04 (11 / 271), avg. gap size = 1.82 (20 / 11)  

2130 27.13 3.57 0.47  chrX_57047781_57050340.rev     1438  2082 (478)    L1M4_orf2#LINE/L1      244   908 (0)  

  chrX_57047781_5   1438 AAACCTGTGGTAACCAAAACAGCATGGTACTGGCATATGAATAGACA--- 1484
                            v  iii    i   i    ii             v i       ---
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_57047781_5   1485 ----CCACAAAATAGA-----GAACTCATAAATAAATCTATGCATTTATA 1525
                         ---- v iii      -----  iii  v       i i  i       i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_57047781_5   1526 GTCAACTTATTTTCAAAAAAGGAGCCAAGAACACACACTATAGAAAGGAC 1575
                              i v      i v  i  v       v  iv  v ivi     i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_57047781_5   1576 ACTCTCTGTAATAAATGTTGTTGGGAAAACTGGGTATCCATACACAGAAG 1625
                          v   i vi  i     v  i     v      i  ?   i ii  i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_57047781_5   1626 AATGAAACTAGACATATCTATCTCTCACCATATACAACACTCAAATCAAA 1675
                               ii i   vi--   i   v            v v i  v     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCC--CTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_57047781_5   1676 ATGGATTAAAGACATAAATCTAAGACCTGAAATTGTGAAGCTACTAGAAG 1725
                               i ?    v     v     v  i   i i i  i  vi      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_57047781_5   1726 AAAACTTTGGGAAAAAGCTTCAGGACATTGGTCTGAGCAACGATTTCTTG 1775
                              v v  ?iv   v    iv   v    vi ii    i i      i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_57047781_5   1776 AGTAAGACCTCAAA-GCACAGGCAA----AGGAAAAATGGGCAAGTGAAA 1820
                         ii  v   vi    -     i    ----  i      i ii  i vii 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_57047781_5   1821 TCACATCAG--CTAAAAAGCTTCTGCACAGCAAAGGAAACAATCA-TAAA 1867
                         iiv     i--i      -   i  ii vv       v  v    -v   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_57047781_5   1868 ATGAAGAGACAACCTAGGTAACAAGAGAAAATATTTACAAAGTATTCAAC 1917
                         i    i        i viv  iii            i    vi  vi v 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_57047781_5   1918 TGAC--GGGATTAATAATAAAAATATGTAAGAAATTCCAACAACTCAATA 1965
                            i--    i vi  viv i     i   ii  i  iv           
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_57047781_5   1966 GTAAAAAATCAAATAATCTGATTTAAAAATGGGCAAAAGAGCTGAGTAGA 2015
                         i      iv       i ii   ?             i  vi   i    
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_57047781_5   2016 CATTTCTCAAACTAAGACGCACAAATGGACAACAGATATATAAAAAG-TA 2064
                                 v  vv    iii        v   i iii i  i     - i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_57047781_5   2065 TTCTAAATCGCTAATCAT 2082
                         i  v v   i????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (114 / 57)
Gap_init rate = 0.02 (10 / 665), avg. gap size = 2.60 (26 / 10)  


 655 30.61 0.00 0.00  chrX_57054266_57057699.rev        2   197 (3237)    L1M4_orf2#LINE/L1      167   362 (546)  

  chrX_57054266_5      2 CCTGCATCACCAAGTCAATCCTAAGCCAAAAGAACAAAGCCGGAGGCATC 51
                           v v  vi    iv     i i ivv i          ii     vv  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_57054266_5     52 ATGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGC 101
                          ii  v  ii i      viv        i          i   i    i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_57054266_5    102 ATGGTACTGGTACCAAAACAGAGATATAGACCAATGAAACAGAACAGAGC 151
                         i         i iv ii i   v       i     i  i    iv   v
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_57054266_5    152 CCCCAGAAATAATGCCGCATATCTACAACTATCTGATCTTTGACAA 197
                         vi          vv  ii i  i  iiiii vi    i  i     
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

Transitions / transversions = 2.16 (41 / 19)
Gap_init rate = 0.00 (0 / 196), avg. gap size = 0.00 (0 / 0)  

2749 27.63 0.66 1.10  chrX_57054266_57057699.rev     2032  2943 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57054266_5   2032 TGGAAATACATCCCATCCTCATGGATGGGGAAAATCAATATTGTGAAAAA 2081
                               v i       vi        v  i i v i        v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57054266_5   2082 GACCATACTGTTAAAAGCAACCTACAAATGTAATGCAATTCTCATCAAAA 2131
                          i v     viiv   vii i     i  vi  i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57054266_5   2132 TGACACCATCATTCTTCACAGAACTAGAAAAAACAACCCTAAAATTCATA 2181
                          vv  v vv v  i  ii     v v  v  ivii i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_57054266_5   2182 TGGAACCAAAAAAAGAGCCTGCATAACCAAAGGAGGACTAAGCA-AAAAA 2230
                              viiv  ii-  v  v v   i     -----  -  v v-i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAA-----AC-AATCTTGAAAA 193

  chrX_57054266_5   2231 AGAAAAAAAAAAATTTGGAGGCATCACATTACCCAACTTCAAACTATACT 2280
                             i  v   i--       vv     i v     i      viv    
  L1M4_orf2#LINE/    194 AGAAGAACAAAG--TTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_57054266_5   2281 ATAAGGCCATAGTCACCAAAACAGCATGATACTGGTATAAAAACAGGCAC 2330
                          i  i  i i   v i   i    ii  i      i    ii i  i  i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_57054266_5   2331 ATAGACCAATGGAACAGAACAGAGAACCCAGAAATAAACCTAAATGCCTA 2380
                              i        i    iv    ii             i v iiii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_57054266_5   2381 CAGCCAACTGAACTTCAACAAAGCAAACAAAAACATAAAGTGGGAAAAGG 2430
                         ii i   i   vi   i    i vviv   i v   vv i    i    i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_57054266_5   2431 ACAGCCTATTCAACAAATGGTGCTGGCATAATTGGCAAGCCACATGTAGG 2480
                          i  i  v                  v i  i   vv ?       i ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_57054266_5   2481 AGAATGAAACTAGATCCTCATCTCTCACTTTATACAAAAATCAAGTCAAG 2530
                                 ii i  i  ii i   v   iv           i  v    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_57054266_5   2531 GTGTATCAAGGACTTAAATCCAAGACCTGAAAGTGTAAAAATTATAGAAG 2580
                         i  v    ?i   i     vi    v  i   v i     v iv      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_57054266_5   2581 ACAACATTGGAG-AAATCCTTCTAGACATTGGCTTAGGCAAAGACTTCAT 2629
                          v     v  ? -     -   vv   v    v        v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_57054266_5   2630 GACCAAGAACCCAAAAGCGAATGCAACTAAAACAAAAATAAATAAGTGGG 2679
                         iivi v  vv        iv v     v   iv       i    i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_57054266_5   2680 ACTTAATTAAACTAAAATGCTTCTGCACAACAAAAGGAACAGTCATCAGA 2729
                             v  i   v v   vi   i  ii vv    i iv  vi   vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_57054266_5   2730 GTAAACAGACAATGCACAGATTGGGAGAAAATCTTTACAATCTATCCATC 2779
                           i  v      iv      v           v   i   vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_57054266_5   2780 CAACAGAGGACTAATATCCGGAATCTCCTGGGAACTCAAACAAATTAGCA 2829
                         ii i ii     vi     i    v vivii      vv    v i ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_57054266_5   2830 AGAAAAA-ACAAATAACCTCATCAAAAAGCGGGGTAAGGACATAAATACA 2878
                          v     -          iv  i?    ii   vv     iv i    v 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_57054266_5   2879 CAATTCTCAAAAGAAGATATACAAATGGCCAACAA--ACATAAAAA-ATG 2925
                           v     v                       i  --    i    -   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_57054266_5   2926 ATCAACATCACCAATGAT 2943
                         v         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (142 / 106)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3062 26.81 1.78 0.78  chrX_57067555_57073840.rev     4899  5797 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57067555_5   4899 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4948
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57067555_5   4949 GGCCATAATGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4998
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57067555_5   4999 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5046
                          v   iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_57067555_5   5047 TATGGAAC--CAAAAAACAGCCCGCATAGCCAAGTCAATCCTAAGCCAAA 5094
                                v--   iii  --  v v        iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_57067555_5   5095 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 5144
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_57067555_5   5145 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5194
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_57067555_5   5195 CAAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAA 5242
                         iv       i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_57067555_5   5243 CTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAATGGATT 5292
                         ii vi    i  i     ivv  v   i v  vvv         v i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_57067555_5   5293 CTCTATTTAATAAATGGTACTGTGAAAACTGGCTAGCCATATGTAGAAAG 5342
                         v   v  i  i       i   v  v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_57067555_5   5343 CTGAAACTGGATCCCT----TACACCTTATACGAAAATTAATTCAAGATG 5388
                         v    ii    i    ----i     v     i        i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_57067555_5   5389 GATTAAAGACTTACATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAA 5438
                            i ?    i  v    v   v       i      v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_57067555_5   5439 ACCTAGGCA-ATACCATTCAGGACAT-GGCATGGGCAAAGACTTCATGTC 5486
                           v    ?i- v i -   iv   v -  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_57067555_5   5487 TAAAACGCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5536
                           vi  i         vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_57067555_5   5537 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTG 5586
                          v  i   v v  i i   i  ii vv    i  v  i i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_57067555_5   5587 AATAGGCAACCTGCAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5636
                           v  i     ii                v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_57067555_5   5637 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5686
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_57067555_5   5687 AAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5732
                             i    ----   v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_57067555_5   5733 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATTAAAAAGTGCTC 5782
                              v        i  vi viii     i ii     v    ii     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_57067555_5   5783 ATCATGACTGGCCAC 5797
                          v   v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


2314 28.14 4.86 2.26  chrX_57087885_57092423     3162  4046 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57087885_5   3162 TGAAAAAGCATTCCATGCTTAT--ATTTAGGAATAATTAATAT-GTTAAA 3208
                           i   iii  i     i i  --   --    v v       -     i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT--GGAAGACTTAATATTGTTAAG 48

  chrX_57087885_5   3209 AATGGC--TATTTGGCCCAAATTCAT-TAAAGATTCAATGCTCTTCCTAT 3255
                          -    --  i i--        v  -  v        i  vv i     
  L1M4_orf2#LINE/     49 A-TGGCAATACTC--CCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_57087885_5   3256 CAAACTACCAATGACATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAA 3304
                             v v   iivi v  i  ii     v v  v  i-  -  ii     
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAA 144

  chrX_57087885_5   3305 TTTATATGGAACCATAAAAAAGCCTGAATAGCCAAGGCAATCCTAAGCAA 3354
                           i        viii  iii v  v          ii     i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_57087885_5   3355 AAAGCACAAAGCTGGAGCA-TGATGCTACCCAACTTCAAACTATACTATA 3403
                         i   v      i     v - v ii  v     i      viv     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_57087885_5   3404 GGGCTGCAATAATCAAAACTGCATGGTACTGGTACACAAACAAAAACATA 3453
                         ii   i  i       i  v ii         i i vii i i v i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_57087885_5   3454 GACCAATGTAACAGAATAGATAGCTTAGAAGTAACACTGCACACCTTTA- 3502
                           i     v  i     v  v  iii    i   -  i-  i  v    -
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAA-ACC-CATACATTTAT 342

  chrX_57087885_5   3503 -ACCATCTCATCTTTGGCAAAGCTAACAAAAACAAGCAATAGAAAAAAAA 3551
                         -ii  vi v  i  i i   i v iv   i v  vv    i ii   i  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_57087885_5   3552 CCCTCCCTGTTCAATAAATGATGCTGGGATAACTGGCTATCTATATGCAT 3601
                         ivv  -- v     i     i        i      v  ? i i     v
  L1M4_orf2#LINE/    393 TAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_57087885_5   3602 AAAATTGAACCTGGAACCCTTCCTTACACTATATACAAAAATCAACTCAA 3651
                           i v    vi    v    v   i    i            i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_57087885_5   3652 GATTTATTAAAGACTGAAGTGTAAAAACAAACGAACAAAGCTATAAAAAC 3701
                         i  vv  i ?    iv  i     i i -------i   i        vi
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGC-------TAAAACTATAAAACT 533

  chrX_57087885_5   3702 CCTGGGAGACAACCTAGGGA-ATATCATTCTGGGCATAGGAACTT--GCA 3748
                          i i i   v   v    ?i- v   v iv  iv v i  ---  --   
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG---TTAGGCA 580

  chrX_57087885_5   3749 AAGAGTTTATAATGAAGATGCTGAAAGCAATTGCAACAAAAGCAATAATT 3798
                          v iv  iv  ivv v  ii ii      vvv          v  v   v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_57087885_5   3799 GACAAATTAGA-----TCGAAA----GAGCTTTTCCACAGAAAAATAAGC 3839
                           i     i  -----  i   ----i i     vii vvv   iv vi 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_57087885_5   3840 TATCAACAGAGTAAACAGACAATTTATAGAATATTAGAAAATATTTGCAA 3889
                               v i   i  v      iii i     ivv               
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_57087885_5   3890 GTTATGCATCTGGCAAAGGTCTAATATCCAGCATCTGTAAGGA--TCTTA 3937
                         i i  ii     ii  i  v  vi       v  v i   i  --     
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_57087885_5   3938 ---------AACAAATTTACAAGAAA--------AAAAGTGGGCAAAGGA 3970
                         ---------  i   vvv    iv  --------    i           
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_57087885_5   3971 CATTAACAGACACTTTTCAAAACAAAACATGCATGCAGCCAACAAGCATA 4020
                         iv v  i     i  i  v   v  i i  i  viii     i     i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_57087885_5   4021 TAGAAAA--GCTCAATATCACTGATCTT 4046
                          ii   i--      i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (154 / 92)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.62 (63 / 24)  


2664 27.36 3.18 0.68  chrX_57100194_57102607.rev     1043  1923 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_57100194_5   1043 AGAGATTTCATGT----GGATTTGAAGGGCCAATATTGTTAAAATGTCCA 1088
                            v  ii     ----     v    ivii           i   v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_57100194_5   1089 TATTACCCAAAGCAATCTATAGATTTTATGCAATCCCCATCAAAATAACA 1138
                           i v      vii     i     iv i        i        vv  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_57100194_5   1139 ATGACATTCTTCACAGAAATAGAAAAAACAATCCTAGAATTTATATGGAA 1188
                         iivi v  i  ii       v  v  ivii      i    i        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_57100194_5   1189 CCACAAAAGACCAAGAATAGCCTA-----TCCTAAGCAAAAAGAA---AA 1230
                         vii   ii    v         v -----  i i iv  i     --- i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_57100194_5   1231 CTAGAGGAATCACATTACCTGACTTCAAGTTATACTACAGA--CATGGAA 1278
                         i i     v     i v  ii i     iviv       i --i ii v 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_57100194_5   1279 ACCAAAACAGCATGGTTCTTGCATAAAAA--GATGCATAGACCAATAGAA 1326
                          i   i    ii    v  v      ii --  iii     i    i   
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_57100194_5   1327 GAGAATAGAGAACCCCAAAGCAAATCCATTCAGCTAGAGTAAACTCCATT 1376
                         v     v    ii  vi  ii   i    v  vi  vi  v  i vvv  
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_57100194_5   1377 TTGATAAACGTGACAAGAACACACACTGAGGAAAAGACCTTCTCTTCAAT 1426
                          i  i  iv   v     v  iv  v  i     ii ivv   i     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_57100194_5   1427 AAATTGTGCTGGGAAAAT--GATATCCACATGCAGAAGAAGGAAACTAGA 1474
                             v         v  i--    ?         i     v   ii i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_57100194_5   1475 ACCCTATCTCTTACAATTTACAAAA-TCAAATCAAAAGGAACTAAAGACT 1523
                         v     i   vi  v  v       - i  v      v i ii ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_57100194_5   1524 TCAATG--AGACCTCAAACTATAAAACTACTAGAAGAAAACTTTGGGGAA 1571
                          v    --   v  v             vi           v v  ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_57100194_5   1572 ATTCTCCAGGACATTGGTCTGCATGAAAATATTT---GTGTAATACCCTA 1618
                          v   i iv   v    vi iviii vii v i ---i i i i   -- 
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC--A 603

  chrX_57100194_5   1619 CAAGCATAGCCAACCAGAACAAAAATGGACAAATGGGATCACATCAAG-T 1667
                         v     i iv    v i iv      i  i    v   iiv      i- 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_57100194_5   1668 TAAAAAGCTTCTGCACAGCAGCGAAAAAAAATAAAAAATTGAAGAGACAA 1717
                               -   i  ii vv  iv i v vv vi  i   v    i      
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_57100194_5   1718 CCCTGAGAGTGGTGGAAAATATTTGCAAATTACACATCTGACAAGGGATT 1767
                            vv   i   vi                i i i      i      i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_57100194_5   1768 AATAATCACAATATATAAGGAGCTCAAACAA-TCATATAGGAAAGA-ATA 1815
                         vi  vi  v         i  i   vv    -   -   iv   i - i 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCA-ATAATAAAAAGACA 801

  chrX_57100194_5   1816 TAATAATATAATTTTTAAATGAGCAAAATATTTGAATAGACATTTCTCAA 1865
                         -     ivi    ?vv     i     iv                   v 
  L1M4_orf2#LINE/    802 -AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_57100194_5   1866 AAGAAGACACACAAATGGCAAACAGGCATATGAAAAGATG-TCAAGCATC 1914
                                i i         v  i i   i           -    -    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA-CATC 899

  chrX_57100194_5   1915 ATTAATCTT 1923
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.02 (18 / 903), avg. gap size = 1.89 (34 / 18)  


2620 28.44 1.35 0.45  chrX_57104312_57106719.rev     1032  1917 (491)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_57104312_5   1032 ATGTTCATGGATGGGTAGAATCAATATTGTAGAAATGTTCATACTGCCAA 1081
                                     v  v   v i        vi i   viv     v  v 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_57104312_5   1082 AAGCAATCTACAAATTCAATGCAATTCCCATCAAAATACCAACATCATTC 1131
                           vii       i      i     i  i        v   i vv v  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_57104312_5   1132 TTCACAGAACTAGAAAAAACT-ATGCTAAAATTCATATGGAAACAAAAAG 1180
                           ii     v v  v  i-  -  v                  iiv  i 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chrX_57104312_5   1181 GAGCCCACATAGCCTAATCAAGACTATGCCAAA--ACAACAAATCTGCAA 1228
                           v  viv      v  v   v-  -  vv   -- v      vi  v i
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_57104312_5   1229 GCATCACATTACCCAACTTCAAACTATACTATAAGGCTATAACCACCAAA 1278
                          vv     i v     i      viv     i  i    i iiv i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_57104312_5   1279 ATAGCATGGCGCTGGTATAAAAATAGGCACATAGACCAATGGACCAGAAG 1328
                          i  ii   ii    i    ii    i  i     i       vi    v
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_57104312_5   1329 AGAGAA-CCAGAAGTAAAACCAAATGCTTACAGCCAACTGATCTTCAACA 1377
                         v    i-      i    v   v iii   ii i   i    i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_57104312_5   1378 AAGCAAACAGAAACATAAAGTAAGGAAAGGACA-TGCTTTCAACAAATGG 1426
                          i vviv  ii v   vv i ii      i i - vi             
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_57104312_5   1427 TGCTGGGATAATTGGCAAGCCACATGTAGGAGAATGAAACTGGATCTTTA 1476
                                 i  i   vv ?       i ii        ii    i ii  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_57104312_5   1477 TTTCTGATTTTATA-AAATGTCAACTAAACATGGATTCAGGACTTAAACC 1525
                         ii  vv iiv    -   vi i    v  v      iv?i   i    iv
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_57104312_5   1526 TAAGACCTGAAACCCTAAAAATTCTGGAAGATAACATCAGAAAACCTTTT 1575
                              v  i    iv     v ii i     v     vi ?iv vv i  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_57104312_5   1576 CTAGACATTGGCTTAGGCAAAGACTTTAT-GATCAAGAATCCAAAAGTAA 1624
                          vv   v    v        v ii  iv -   - v  vv       i v
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCAC 610

  chrX_57104312_5   1625 ATGCAACAAAAACACAGATAAATTGATGGGACTTAATTAAACTAAAAAGC 1674
                          v         iv v i   i  vi  v      v  i   v v    i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_57104312_5   1675 CTC---ACAGCAAAAGAAATAATCAGCAGAGTAAACAGACAACCCACAGA 1721
                         i i---i vv    i  v iv    iv i   i  v              
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_57104312_5   1722 ATGAAAGAAAATATTTGCAAAC--TGCATCTGAAAAAGGACTAATACCTA 1769
                            ii                i-- ii      v  i     vi  i i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_57104312_5   1770 GAATCCACAAGAAACTCAAACAAATCAGCAAGAATAAAACAAATAATCCC 1819
                             vi i  ii     vv    v   ii  v  v  i        i  v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_57104312_5   1820 GTCAAAAAGTGGGATAAAGACATGAATAGACAATTCTCAAAAGAAGACAG 1869
                         i i?    i    vv  i  iv          v     v        i v
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_57104312_5   1870 ACAAATGGTCAACAAACATGCTATAAAATGCACATCATCACTAATTAT 1917
                                 i   i  i  iiiv v  i    v  v     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (140 / 108)
Gap_init rate = 0.01 (12 / 894), avg. gap size = 1.33 (16 / 12)  


3167 24.26 1.65 1.98  chrX_57125982_57128876.rev     1494  2404 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57125982_5   1494 TGGAAACACATGCCATGCTCATAAATGGGTAGAATCAATATTGTAAAAAT 1543
                               v i  v     i    ii  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57125982_5   1544 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCTCCATCAAAA 1593
                          i v     v  v   vii       i      i      i i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57125982_5   1594 TACCACCATCATTCTTCACAGCATTAGAAAAAACAATTCTAAAATTCATA 1643
                          v   v vv v  i  ii   v v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_57125982_5   1644 TGGAAACAAAAAAGAGCCCATATAGACAAAGCAAGACTAAGCAAAAAGAA 1693
                               iiv  ii  v  viv    v    i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_57125982_5   1694 CAAATCTGCAGGCATCACACTACCTGATTTCAAACTATGCTATAAGGCCA 1743
                             vi  v   vv       v  ii        viv i   i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_57125982_5   1744 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCAA 1793
                         i   v i   i    ii         i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_57125982_5   1794 TGGAACAGAAT-AAGAACCCAGAAATAAACCAAAATGCTTACAGCCAACT 1842
                              i     -i   ii             v v iii   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_57125982_5   1843 GATGTTCGACAAAGCAAATAAAAGCATAAAGTGGGGAAAAGACACCCTTT 1892
                            v        i vvivi  i v   vv i        ii i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_57125982_5   1893 TCAACAAATAGTTCTGGGAAAATTGGCTAGCCACATGTGGCAGAATGAAA 1942
                                  i  v      v  i   v  ?       iiiv        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_57125982_5   1943 CTGGATCCTCATCTCTCACCTTATTCAAAAATCAACTCAGGATGGATTAA 1992
                         i    i  ii i   v    v   v       i      ii      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_57125982_5   1993 AGACTTAAACCTAAGACCTAAAACTATAAAAACTCT-AGAAGATAACACT 2041
                             i    iv     v              -    -      v    iv
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATA 549

  chrX_57125982_5   2042 GGAA-AAACCTTTCTAGACATTGGCTTAGGCAATAATTT------TATGA 2084
                           ?i-   i   iv -   v    v         ii   ------     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_57125982_5   2085 CCAAAAACCCAAAAGCAAATGCAATAAAAAGAAAGATAAATAGCTGGGAC 2134
                          -----   -       v v    i    ii   i   i   iv v    
  L1M4_orf2#LINE/    599 C-----ACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_57125982_5   2135 CTAATTCAACAAAAT----AGCTTTTGAATGACAAAAAAAAAAAAACAGT 2180
                         ----    v      ---- i      viivv    ii v ----- vi 
  L1M4_orf2#LINE/    643 ----TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-----CTAT 683

  chrX_57125982_5   2181 CGTCAAAGTAAACAGACAAC--ACAGAGTGGGAGAAAATCTTCACAATCT 2228
                          ivv     i  v       --     i           v  ii   vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_57125982_5   2229 ATACATCTGACAAAGGACTAATATCCAGACTCTACAACGAACTCAAACAA 2278
                            i      i  i     vi        v v  i  v      vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_57125982_5   2279 ATCAGTAAGGAAAAAAACAATCAATCCCATCAAAAAGTGGGCTAAGGACA 2328
                         v   i   v-     i    vi  i  v  i?    i     v     iv
  L1M4_orf2#LINE/    784 CTCAATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_57125982_5   2329 TGAATAGACAATTCTTAAAAGAAGATATACAAATGGCCAACAAACACATG 2378
                                   v    iv                       i  i      
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_57125982_5   2379 AAAAAATGTTCAACATCACTAATGAT 2404
                             i   i         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (128 / 89)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.54 (33 / 13)  


2391 26.33 5.45 2.32  chrX_57166660_57168629      630  1491 (479)    L1M4_orf2#LINE/L1        1   889 (19)  

  chrX_57166660_5    630 TGAAAATATATCTTGTGGTTCATGGATTAGTAAAATCAATATTGCCAAAG 679
                           i   v     iii  -          i v i v i       ii  ii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATG-TTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_57166660_5    680 TGTCCATATTGTTTAAAGCAA-CTAGAGATTCAATGCTATCTCTATCAAA 728
                           v v   i viii   vii -   v        i  v   i        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_57166660_5    729 ATTCCAAC-ATCATTCTTACAGAAATAGA-AA---------AAAATT--- 764
                           i   i -ii v  i  i       v  -  ---------      ---
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_57166660_5    765 ----AAA---------CCTCAATTATCTGTCTCAATTTTGAACAAGAATA 801
                         ----   ---------  ivi v  v iivvv    i     v     v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_57166660_5    802 ACATAGCTAGTTGCATCCGAGTTGCTGATTTCAAATTATATTATACAATT 851
                            v  i i vv vv  vv v  v ii        viv  i  i v ii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_57166660_5    852 ATAGTAATCAAAACAGCATGGTACTGGCATAAAAACAGACACATAGAACA 901
                          i         i    ii              ii i     i     v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_57166660_5    902 GTGGAACAGAATAGAAAGCCCAGAAATATAACCTAAAC-TCTATGG-CAT 949
                         i     i     v  i  i         -    i v  - i     -  -
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATA-AACCCATACATTTATGGTCA- 347

  chrX_57166660_5    950 ATTGATTTTTCATTAAAGCATCAGGA--ATTGACAATAAGAAAAGGATAG 997
                                  iv iv ii iii  i  --   --    ii i    i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATT--CAATGGGGAAAGAATAG 395

  chrX_57166660_5    998 TGTGACCTATAAGTAGTGATGGGA-AATTGAATATCTATATG-AAAAAAA 1045
                          v vvi v i  i i   v     -  i  i   ? i i   -    i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_57166660_5   1046 TGAAACTGGATCCTTATCACAAACCATACACAAAA-TAAACTCAATATGA 1094
                             ii    i  i  i v  v      i      - v       v   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_57166660_5   1095 ATTAAATATTTAAATGTAAGACCTGAAACCATAAA--TCTTAGAGAAGAA 1142
                           i ? v ii           v  i    i     --       --    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA--AGAA 543

  chrX_57166660_5   1143 AATATAAGATTAAAAACTCCATAATATTGATTT-GGCAATAATTTTTTTA 1191
                           i   i ?v    v-  i i i iv   iv  -      ii   i  vi
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_57166660_5   1192 AGCTAACCCCCAAAGCAAAGGTAACAAGAGCAAAAATAAATAATTGGGAC 1241
                          vv i  v  v      v i i     i  v       i    v v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_57166660_5   1242 TATATCAA--TCAAAAAAGTTTG--CTTCACTGTAAAGGAAACCATCAAG 1287
                          vi     -- i     vv    --     -----     v  i      
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCA-----AAGGACACTATCAAG 687

  chrX_57166660_5   1288 AAAATGAAAAGCCATCCTAGAGGATGAGATAATATATGTGTAAGCCATAT 1337
                            i       v  v  i v  i   i  v  v    v  i  ii     
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_57166660_5   1338 ATGTGATAAAGGGTTAATATTCAAAAAATATGAGGAACTCATACAACTTA 1387
                           v      i  ii vi   i  i  v    i i      v       i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_57166660_5   1388 AAAACAAAAA-AGAAATAATCTGATTTTTTAAAAATGACCAAAAAACCTG 1436
                          v  i     - v      i ii   ?---       iv    ii ii  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTW---AAAAATGGGCAAAGGATTTG 834

  chrX_57166660_5   1437 AGTTGCCATTCTTCCACGGAAAACTTACCAACG----ATGAGCATGACTA 1482
                          i v v    ii    vi   i iv   v  i ----  i    i---- 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC----A 880

  chrX_57166660_5   1483 TAAAAAGGT 1491
                          i     i 
  L1M4_orf2#LINE/    881 TGAAAAGAT 889

Transitions / transversions = 1.72 (141 / 82)
Gap_init rate = 0.03 (27 / 889), avg. gap size = 2.48 (67 / 27)  


 366 30.43 1.09 5.43  chrX_57171370_57174397     1543  1726 (1302)    L1M4_orf2#LINE/L1        1   176 (732)  

  chrX_57171370_5   1543 TAAAGAGATATGCCACATTCACG-ATTGGAAGATTGAACATAGTAAAGAT 1591
                          ii i      v   ii    i -         i v  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57171370_5   1592 GTTAATTC-CTCCAAATTAATATACAAATTTAACACAATTCTTGTAAAAA 1640
                          vi   v - i       i  v    i   i   i    i i i v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57171370_5   1641 CTTTTGCAAGATTTTTTATAACAACAGGTGATAAAAAGTAAATAAATTAT 1690
                         iiiiv  vivv      ii iv  i---   i  ivv -------  iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT---TGACAAGCTG-------ATCCT 140

  chrX_57171370_5   1691 AACATTTATAAGTGAAGGCAAAGAAAATAGAATAGC 1726
                           v   i   v vi  v    i i vvi        
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

Transitions / transversions = 1.55 (34 / 22)
Gap_init rate = 0.02 (4 / 176), avg. gap size = 3.00 (12 / 4)  

1405 26.80 7.60 5.80  chrX_57171370_57174397     1812  2535 (493)    L1M4_orf2#LINE/L1      172   908 (0)  

  chrX_57171370_5   1812 ATACCTAAATAAATCTGGAAAAAAGAAAAGAAGAATAAAACATGAAGAAT 1861
                            v i   vv     v      ------      i   iivv  i  v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAA------GAAGAACAAAGTTGGAGGACT 215

  chrX_57171370_5   1862 CTTTCTACCCAATTGTA----TTACATTATATTGCTCTTGGAATCAAGAC 1907
                          viv  v       vi ----    --  i vv   viv v         
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTAC--TACAAAGCTACAGTAATCAAGAC 263

  chrX_57171370_5   1908 TGTGTGGTATTGGAGGAAGGACAGAAACATAGATAAATGGAACCAAACAC 1957
                         v        i   viv     i   v i      v       ivi  ivv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_57171370_5   1958 AAAACCCAGAA-TACACATATAGAT--ATGCCAAATTGATATTTTATAAA 2004
                          i ii      -  v  vi   v  --   viv       v  iv i  i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_57171370_5   2005 GATGTAAAAGCAATTCAATGGAGAAA--AGAGTCTTTTAAACACATGGTT 2052
                          i  iv  ii v         i    -- v        v    v     v
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_57171370_5   2053 TTGGAGCAATTAGAAATGTATAGGTCAACAAATTAAAATACTGAAATACT 2102
                         i   ii   i i  v ?vi i v -   v i v i  i --  i --- i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATG-CAAAAGAATGAAGT--TGGA---CC 457

  chrX_57171370_5   2103 AAACATACTTAAACATACTTAAAATACTAAACATAAACCCCACTCCTAGA 2152
                         --- v   i ---  i  -------------    v  --------- i 
  L1M4_orf2#LINE/    458 ---CCTACCT---CACAC-------------CATATAC---------AAA 479

  chrX_57171370_5   2153 AATTAATGCAAACTGGATTACAGTCTTAAATGTAA-------AACTATAA 2195
                               iv    v     i ?  v i         -------        
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_57171370_5   2196 TATT-TCAGAAAAAAA--TAGGAGAAAATTTTTAGAATCTAGTGTT-GAC 2241
                         v i - i    i    --    ? v    i  iivi i  v v   - i 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_57171370_5   2242 AAAGAGTTCTTAGAATTGGCATTGAAAACATGATATATAAAAGGAAAAAC 2291
                           v iv        vv  i  iii   i  ii vvv i     i     i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_57171370_5   2292 TGATCAATTGTACCAGACCAACATGAAAAACTTTTGTTTTGTGAACAAAT 2341
                         v   v     v  ivv i   v  v            vi vii  vi vv
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_57171370_5   2342 CTGTAAAAAAGATAAAAATACAAGCTACAGA-------------TTC--- 2375
                           i v  i  ii i    v    v i     -------------  i---
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_57171370_5   2376 ---CACATATCTGGCAAAGGACTGGTTTCTAGATTATATACAGAAATCTT 2422
                         ---  i       ii  i     v  v  i   v      v    v    
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_57171370_5   2423 A----------------AAATAAACAATCCCATTAAAAAGTGGGCAAAAG 2456
                          ---------------- i i   i  i  v   ?    i        i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_57171370_5   2457 ACATGAACAGACACTTTTCAAAAGAAGACGCATATGCGGCCAACAAGCAT 2506
                          iv    i     i  i  v        iii i vii      i     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_57171370_5   2507 ATTAAAAAAAGCTCAATATCATTGATCAT 2535
                           v    i v      i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (105 / 85)
Gap_init rate = 0.03 (20 / 737), avg. gap size = 4.85 (97 / 20)  


2638 26.76 1.17 4.37  chrX_57184364_57188820     3027  3964 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57184364_5   3027 TGGAAGAACATTCCGTGCTCATGGATAGGAAGCATCAATATCGTGAAAAT 3076
                              ii i  i  i  i        v     vv i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57184364_5   3077 GGCCATACTGCACAAGATGATTTATAGATTTAATGCCATCCCTATCAAGC 3126
                            v     v v   iv    i  i     i  i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57184364_5   3127 TCCCAATGACTTTCTTCACAGAA-TTGGAAAAAAACTA---CTTAGTTTC 3172
                              iivi i  i  ii     -   --- v  i  i---  v iv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_57184364_5   3173 CTATGGAACCAAAAAAGAGCCCTCATTGCCATGACAATCCTAAGCAAAAA 3222
                         v       viiv  ii  v  vvv  v    vi      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_57184364_5   3223 GAGCAAAGCTGGAGGCATCACGCTACCTGATTTCAAACTATACTACAAGG 3272
                           i     i      vv    i  v  ii        viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_57184364_5   3273 CTAGAGCATCCAAAACAGCATGGTACTGGTAACAAAGA-AGATATATGGA 3321
                            v  i vi   i    ii         i -i  i  -   i    i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGA 296

  chrX_57184364_5   3322 CCAATGGAACAGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTA 3371
                         i        i    iv  ---   v  --        vv   i    i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGA---GAGTCC--AGAAATAAACCCATACATTTA 341

  chrX_57184364_5   3372 CGGCCATCTGATCTTTGACAAACCTGACAATAACAAGAAATGGGGAAAGG 3421
                         i  i  vi    i  i     ivv  v   v v  vvv           i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_57184364_5   3422 ATTCCCTATTTAATAAATGGTGTTGGGAAAACTGTCTAGCCATATGTAGA 3471
                           vvi  v  i  i        i     v     vv  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_57184364_5   3472 AAGCTGAAACTGGATCCCTTCCTTACACCTTATAGAAGAACTAATTCAAG 3521
                          iiv    ii    i    v   i     v    v  i  i   i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_57184364_5   3522 ATGGATTAAAGATTTAAATGCTAGACCTAAAACCATAAAAACCCTAGAAG 3571
                               i ?   ii      iv   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_57184364_5   3572 AAAAAACCTAGGCA-ATACCATTCAGGATAGAGACATGGGCAAGGACTTC 3620
                             -- v    ?i- v i -   iv  ivvv ivv i     v ii   
  L1M4_orf2#LINE/    542 AAAA--CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_57184364_5   3621 ATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATT 3670
                         v iiv  vi            vvi          vv     v  i     
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_57184364_5   3671 GCATCTAAT-AAAACTAAAGAGTTTCTGCACAGTAAAATAATAATAATAA 3719
                          v ii v  -    i    i v   -  ii vvi   i------------
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAG------------ 675

  chrX_57184364_5   3720 CAATAAAACAAAAAAAAACCTATCATCAGAATGAACTGGCAACCTACAGA 3769
                         ------i   ---------      vv i i    vv i     i     
  L1M4_orf2#LINE/    676 ------GACA---------CTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_57184364_5   3770 ATGGGAGAAAAATTTTTGCAATCTATCCACCTGACAAAGGGCTAAT-T-- 3816
                                    - v       vii  vi i    i  i  i  vi - --
  L1M4_orf2#LINE/    711 ATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_57184364_5   3817 -GAATGTACAAAGAAGTTAAACAAATTTACAAGAAAAAAACAAAAAAACA 3865
                         -    i  i      v ivv    v iv i  v     i     v  v v
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_57184364_5   3866 CATTAAAATTTGGGCAAAGTATAAGAACAGATACTTCTCAAAAGTAGACA 3915
                         v   ?   vv         v  vv   i   i i     v    v   i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_57184364_5   3916 TTTATGCAGCTAAGAGGCATATGAAAAAATGCTCATCATCACTGGTCAT 3964
                          vi viii  i  v i   i       i       v     ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (139 / 108)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.06 (52 / 17)  


3144 27.22 0.55 0.88  chrX_57204441_57210826     4983  5893 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57204441_5   4983 TGGAAGAAAATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5032
                              ii v  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57204441_5   5033 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 5082
                            v     v     iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57204441_5   5083 TACAAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5130
                          v v iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_57204441_5   5131 TATAGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5180
                            i   viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_57204441_5   5181 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5230
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_57204441_5   5231 TACAGTAATCAAAACAGTATGGTACTGGTACCAAAACAGACATATAGACC 5280
                                     i     i         i iv ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_57204441_5   5281 AATGGAACAAAAC--AGAGCCCTCAGAAACAATGCCGCATATCTACAACT 5328
                                i i  i--    i  --     i  vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_57204441_5   5329 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGCGGAAAGGATTCC 5378
                          vi    i  i     ivv  v   i v  vv     v      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_57204441_5   5379 CTATTTAATAAATGGTTCTGTGAAAACCGGCTAGCTATATATGTAGAAAG 5428
                           v  i  i       v   v  v   i  v  ? i i  -- i i  ii
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT--GCAAAAGA 444

  chrX_57204441_5   5429 CTGAAATTGGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5478
                         v    i     i  i v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_57204441_5   5479 GATTAAAGACTTACATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAA 5528
                            i ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_57204441_5   5529 ACCTGGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGTC 5577
                           v i  ?i- v i -   iv   v v  vv i i   v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_57204441_5   5578 TAAAACACCAAAAGCAATAGCAACAAAAGCCAAAATTGACAAATGGGATC 5627
                           vi            vv           vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_57204441_5   5628 TAATTAAGCTAAAGAGCTCCTGCACAGCAAAAGAAACCACCATCAGAGTG 5677
                          v  i  iv v  i i  ii  ii vv    i  v  i i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_57204441_5   5678 AACAGGCAACCTACAAAATGGGAGAAAATTTTTTGCAACCTACTCATCTG 5727
                           v  i     i   i             v   -    vii ivi     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTG 742

  chrX_57204441_5   5728 ACAAAGGGCTAATATCCAGAATCTACAGTGAACTCATACAAATTTACAAG 5777
                          i  i  i  vi          v  i iv      v     v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_57204441_5   5778 AAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATGTGAACAGACA 5827
                              i     i     v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_57204441_5   5828 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 5877
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_57204441_5   5878 CATCATCACTGGCCAT 5893
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2462 28.21 1.53 2.61  chrX_57222145_57230383     3550  4467 (3772)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57222145_5   3550 TGTAAAAACATTTCATGTTCTTGGATTGGAAAAATCAGTATTGATGAAAT 3599
                           v   i i  ii       v          i v i i     v i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57222145_5   3600 CGCCATACATCCAAAAACAGTTTACAGATTTAACGCTATTCCTACCAAAC 3649
                         v  v    vi  v   viii i        i     v  i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57222145_5   3650 TACCAAAGACATTTTTCAAAGAA-TTGGAAAAAACCTATTTTAAAATTCA 3698
                          v   ivvi v     iiv    -   -- v  i iv  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_57222145_5   3699 TATGGAATCTAAAAAGAGCCTGAATAGCCAAAGCAATCCTAAGCAAATAG 3748
                                vivv  ii  v  v           i     i i iv  iv  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_57222145_5   3749 AAGCAGAGATA------TCACACTACCCCACTT-AAAACTATATTATAAA 3791
                           -  i  v i------       v   v i  -      -  i  i   
  L1M4_orf2#LINE/    199 AA-CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chrX_57222145_5   3792 GCTACAGTCACCAAAACAGCATGGTGCTGGTACATAAACAGACACATAGA 3841
                                 v i   i    ii    i    i i vii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_57222145_5   3842 CCAATGGAACAGAACAGAAAACTCAGAAATAAAGTCACACACATACAACC 3891
                         i        i    iv  i iii          vi  i   iv  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_57222145_5   3892 ATCTGATCTTTGTCAAGGCCAACAAAAATAAGCAATGGGGGAAGGACTCC 3941
                          vi    i  i v     viiv   i vi vv        i   i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_57222145_5   3942 CTATTCAATACATGGTGCTGGGATAACTCACTAGCCATGTACAGAAGACT 3991
                           v     i v            i    viv  ?   ii i  i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_57222145_5   3992 GAATCTACACTCTTATCTTTCACCATAGGCAAAAACTAACTCAAAATAGA 4041
                            vi iv  i i  i  iv       vi      i           i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_57222145_5   4042 T-AAATATTTAAATGTAAGACGTCAAACTCTAAAAAAGTTGAGATGAAAA 4090
                          - ? v ii           vv v     v     vvv  -   v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT-AGAAGAAAA 545

  chrX_57222145_5   4091 CCTAAG---AAATACCCTTCTCTATATTGACCCTGTCTCCCCCCACCGCC 4137
                          v  i ---    ---    v------     i  vv ivvv v iv ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT---CTTCG------TGACCTTGGGTTAGGCAATGGTT 586

  chrX_57222145_5   4138 TCCAAAAAAACATGGTCAACTCCCTAAAGCTATTGCAACTAAATGAAAAA 4187
                           iv i ---i   i-  ----  v     vvvv     v   vi     
  L1M4_orf2#LINE/    587 TCTTAGA---TATGA-CA----CCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_57222145_5   4188 TTTACAAGTGGGACTTAATTAAACTAAAGACCTTCTGCACAGCAAAATAA 4237
                          vv i  i v      v  i   v v  i v   i  ii vv    iv v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_57222145_5   4238 ACCATCAACAGAATAAACAGGCAACCTACAGATTGGGAGGAAATATTCAT 4287
                           i     v i i i  v  i     i     v      i       iii
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_57222145_5   4288 AAACTATGCATGCAATAAAGGTCTAATATCCAGAATCTATAAGGAACTTA 4337
                            ii  ii  vii    i  v  vi          v     i     iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_57222145_5   4338 AGCAAATCAACAACTAATAAACAAATAACCCA-TTAAAAAGTGAGCAAGA 4386
                         vi   v    i  iv  v i            -  ?    i  i    ii
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_57222145_5   4387 GACATGATCAGACATCACTCAAAAGAAGACAGACAAGTGGCCAACAAATA 4436
                           iv   vi      iv   v        i v    i       i  ii 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_57222145_5   4437 TTTGAAAA-ATGCTCTCAGGATCAAGTTCACA 4467
                         iv      -      -- iv    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTC--AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (149 / 107)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  

2967 26.99 1.33 0.88  chrX_57222145_57230383     6844  7747 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57222145_5   6844 TGGAAAAACATTTCATGCTCATGGGTAGAAAGAATCAATATTGTGAAAAT 6893
                               i i  ii    i      i v i    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57222145_5   6894 GGCCATACTGCCCAAGT-AATTTATAGATTCAATGCTATCCCCATTGAAC 6942
                            v     v     i -i  i  i        i  v     i  ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57222145_5   6943 TGC-AATTGACTTTTTTCACAGAA-TTGGGAAAAACT-ACTTTAAATTTC 6989
                          v - ii  v       -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_57222145_5   6990 ATATGGAACCAAAAAAGAGCTCCGA-TAGCCAAGACAATCTTAAGCTAAA 7038
                                 viiv  ii  - i v  -       i        i ivv i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_57222145_5   7039 TGACCAAAGCTGGAGGCATCATGTTACCTTACTGCAAAGTATACTACAAG 7088
                         v  v     i      vv   iii v  iv i v    iiv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_57222145_5   7089 GCTACAGTAAACAAAACAGCATAGTAGTGGAACCAAAACAGAGATATAGA 7138
                                   v   i    ii i   v   v iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_57222145_5   7139 CCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTGCAG-C 7187
                         i        i    iv   ivii         vv   i    i iii - 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_57222145_5   7188 AATCTGATCTTTGACAAACCTGGCAAAAACAAGCAATGGGGAAAGGATTC 7237
                            -    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_57222145_5   7238 CCTATTTAA----TGGTGCTGGGAGAAATGACTAGCCATATGCAGAAAAC 7283
                         i  v  i  ----           v  v  iv  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_57222145_5   7284 TGAAACTGGACCTCTTTCTTACACCTTATACAAAAATTAACTCAAGATGG 7333
                             ii      i  vi  i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_57222145_5   7334 ATTAAAGACTTAAACTTAAGACTTAAAACCATAAAAACCCTAGAAGGAAA 7383
                           i ?    i    iv     vi      i      vi i      i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_57222145_5   7384 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGTAAATAATTCATGACT 7432
                          v    ?i- v i -   iv   v v  vv i  i  vviv   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_57222145_5   7433 AAAACATCAAAGAAAAAATGGCAACAAAAGCCAACATTGACAAATGGGAT 7482
                          vi   i    iiv v  --          vv  v  v  i    v   i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_57222145_5   7483 CTAATTAAACTAAAGAGCTTCTGAACAGCAAAAGAAACTATCATCATAGT 7532
                         i v  i   v v  i i   i  vi vv    i  v       vv v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_57222145_5   7533 GAACAGGCAACCTATAGAATGGGAGAACATTTTTGTGATCTATCCATCTG 7582
                            v  i     i i            v  v    ii vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_57222145_5   7583 ACAAAGGG-TAATATCCAGAATCTACAAGAAACTTAAACAAATTTACAAG 7631
                          i  i  i- vi          v  i  ii    ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_57222145_5   7632 AAAAAGACAAACATCCCCATCAAAAAGTGGGTGAAGGATATGAATAGACA 7681
                                    i v   v  i?    i    ii      v          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_57222145_5   7682 CTTCTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCT 7731
                         i     v        i  vi vi       i  i  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_57222145_5   7732 CATCATCCCTGGTCAT 7747
                           v    v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (138 / 102)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.33 (20 / 15)  


3137 25.96 0.99 1.53  chrX_57232539_57238304.rev     4363  5275 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57232539_5   4363 TGGAAGAAAATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4412
                              ii v  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57232539_5   4413 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCGCATCAAGC 4462
                            v     v     iv i  i  i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57232539_5   4463 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4510
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_57232539_5   4511 TGTGGAACCAAAAAAGAGCCCGCATTGCCAAATCAATCCTAAGTCAAAAG 4560
                          i     viiv  ii  v  v v  v      v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_57232539_5   4561 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTA-AAGGC 4609
                                i      vv   ii  v  ii i      viv     -  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_57232539_5   4610 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGACC 4659
                                 i   i    ii         i  v ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_57232539_5   4660 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAAC 4707
                                i    i--    i  --        vv   i i  i  iiiv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_57232539_5   4708 ATATGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 4757
                          vv    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_57232539_5   4758 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAAGCAGAAAGCT 4807
                           v  i  i              v      v  ?   i v   i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_57232539_5   4808 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4857
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_57232539_5   4858 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4907
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_57232539_5   4908 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4956
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_57232539_5   4957 AAACATGAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTA 5006
                         vi   iv       vvi   i      vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_57232539_5   5007 ATCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5056
                               v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_57232539_5   5057 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTGCACATCTGACA 5106
                         v  i     i   i             v       viiii i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_57232539_5   5107 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAGTTTACAA---A 5153
                          i  i  vi          v  i         --------      --- 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTC--------TTACAACTCA 787

  chrX_57232539_5   5154 AAAAAAAAAAAAAAAACAACCCCATCAACAAGTGGGTGAAGGATATGAAC 5203
                          v  v     i v   i     v  i? v  i    ii      v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_57232539_5   5204 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAA 5253
                              i     v        i  vi viii     v ii          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_57232539_5   5254 AATGCTTATCATCACTGTCCAT 5275
                          -    i v     ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


2709 26.85 2.68 1.45  chrX_57245498_57249615     2732  3625 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_57245498_5   2732 AAAAAAATCC-ATGCTCATGGATAGGAAGAATCATTATCGTGAAAATAGC 2780
                            i v    -   i        v      v i v   i  v  i  i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_57245498_5   2781 CATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCTATTAAACTAC 2830
                         v     v      v i  i  i        i  v  i     i   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_57245498_5   2831 CA-TTGACATTTTT-CAGAGAATTAGGAAAAAAAAACCTATTTTAAAATT 2878
                           -i  v v     -    -    i------ v  i iv  ii       
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGA-AATTG------ACAAGCTGATCCTAAAATT 146

  chrX_57245498_5   2879 CACGTGGAGACAAAAAAGAGCCCGAGTAGCCAAGACAATCCTAAGCAAAA 2928
                           ii    i iiv  ii  v  v  i       i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_57245498_5   2929 AGAACAAAGCTGGTGGCATCATGGTACCCAACTTCCAACTATACTACAGG 2978
                                  i   v  vv   iiv v     i   v  viv       ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_57245498_5   2979 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAACACATAGA 3028
                                   i   i    ii         i iv ii i i   i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_57245498_5   3029 CCAATGGAGTAGAATAGACAACTCAGAAATAAGACTGCACAACTACAACC 3078
                         i       i      v  v iii         iv iii   vi  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_57245498_5   3079 ATCTGATCTTCTACAAACCTAACAAAAACAAGCAATGGGGAACGGATTCT 3128
                          vi    i   v    ivv iv   i v  vv          v i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_57245498_5   3129 CTATTTAATAATTCGTGCTGGGAGAACTAGCTAGACATATGCAGAAAGTT 3178
                           v  i  i  v v         v    i v  ?v  i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_57245498_5   3179 GAAACTGGACCCTTTCTTTACACCTTGTACAAAAATTAACTCAAGATGGA 3228
                            ii       i v i i     v i                 i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_57245498_5   3229 TTAAAGACTTAAACCTAAAACACAAAACTATAAAAATTTTAGAAGAAAGT 3278
                          i ?    i    iv   i vvi            v i          ii
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_57245498_5   3279 CTAGGCAGTA--CCATTCAGGACGTAGGCATGGGCAAACATTTCAT-GAT 3325
                         v    ?-   --i -   iv   v v  vv i     vvi    v -   
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_57245498_5   3326 GAAAACACCAAAAGCATTTGCAACAAAAGCAAAAATTGACCAATGGAATC 3375
                         - vi            ivv          v      v  iv   v i ii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_57245498_5   3376 TAGTTAA--CTAACAAGCCTCTGCAAAGCAAAATAAACTATCATCAGAGT 3423
                          vi i  --i   -  i i i  iivvv    iv v       vv i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_57245498_5   3424 GAACAGACAACCTACAGAATGGGAGATAATTTTTGCAATCTATCCATCTG 3473
                            v        i             v   v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_57245498_5   3474 ACAAAGGTCTAATATGCAG--TGTACAAGGAACTTAAACAAATTTACAAG 3521
                          i  i  v  vi   v   -- i  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_57245498_5   3522 AAAAAAACA----------TTAAAAAGTAGGCAAAGGACATGACCAGAGA 3561
                              i   ----------  ?    i i         iv   vi   v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_57245498_5   3562 CTCCTCAAAAGAAAACATT--AATGCAGCCAACAAACAT-TAAAAATA-G 3607
                         i i   v      i i  v--    --     i  i  i- i    v - 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATG 890

  chrX_57245498_5   3608 CTCAACATCACTGATCAT 3625
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.02 (18 / 905), avg. gap size = 2.06 (37 / 18)  


2350 29.42 2.91 1.57  chrX_57252326_57256554.rev     2845  3738 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_57252326_5   2845 GAAAAATATTCCATTATCATGGATTGGAAGAATCAATATCATTAAAATTG 2894
                             i    i    vv               v i     ii    i  v 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_57252326_5   2895 CCATACTTTCCAAAGTAATTTACATATTCAATGTTATCCCTATCGAAAT- 2943
                          v     ii     v i  i    v      i iv         i    -
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_57252326_5   2944 ---ACTGTTATTTTTCACAGAATTTAAAAAAAAAAAAAGCT-ATTCTAAA 2989
                         ---i   ii-     ii     v  i v  --------   -  i     
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAA--------GCTGATCCTAAA 143

  chrX_57252326_5   2990 ACTCATATGGAA---CCAATAATACATCTGAACAGCCAAAGGGATCCT-- 3034
                          i          --- v ivi iv  ---   i       ivi   i --
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCA---GAATAGCCAAAACAATCTTGA 190

  chrX_57252326_5   3035 -AAGGAAACA-AAAGGCAAATAAATCACTTTACCCAACTT-AAAACTGTA 3081
                         -  i   iv -    viii vi v    vi v     i  -      -  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TA 239

  chrX_57252326_5   3082 TTGTACGACTAATGTAACCAAAACCACATGAAGCTGGTATAAAAACAGAT 3131
                         i ii vii   vv    i   i  viii  ivi    i    ii i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_57252326_5   3132 ATATAGACCAATGGAACAGAATGGAGATCCCAGAAATAAAGCTGCAAACC 3181
                                i        i     v    vi           v iii v ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_57252326_5   3182 TACAA-CGATCTGATCTTAGACAAAATTTACAAAAGCA----AGGGTAAC 3226
                           iii- i  -    i  v     iiv vv   i v  ---- v  vi v
  L1M4_orf2#LINE/    340 TATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_57252326_5   3227 AGGACTTCCTATTCAATAAATGGCGCCGGGATAACTGGCCAGCCATATGC 3276
                           i ivvi  v     i      i  i    i      vi ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_57252326_5   3277 AGAAAAATATAACTGGATCCCTACCTTTCACCATATGCAAAAATTAACTA 3326
                          i  i   iv ii    i        iv        i            v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_57252326_5   3327 AATATAAATTAAATATTTAAATGTAAGATCCCAACCTATAAAAATGCTAG 3376
                           v  ii  i ? v ii           v iv  v        v vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_57252326_5   3377 AGGAAAGCCTAGGAGATACCCTTCTCAACACTGGACTAGCAAATAATTTA 3426
                          i    i v    ? vv vi    vii  vi   ii   vv   ii   v
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_57252326_5   3427 T-GGCTAAGTCTCCAAAAGCA---ATTTCAAAG--AAAATTTGGCAAGTG 3470
                          -i v  v v v         ---iivv    i--    v v ii  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_57252326_5   3471 GGACCAAATTAAGCTAAAGAGCTACAGCATAGCGAAAGAAATTATCAAAA 3520
                             ivv  i  iv v  i i  viv iiivv i  i  v i      i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_57252326_5   3521 GAGTAAACATACAGTCTACAGAATGGGAGAAAATATTCAGAAACCATGCA 3570
                         i   i  v v   ii i                    iiv   i   ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_57252326_5   3571 TCCAACATAAGTCTAATATCCAGAATCTATAAGGCACTTAAAGAAATCAA 3620
                           ii i vii v  vi          v     i v   ivv v  v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_57252326_5   3621 CAAGCAAAAAGTAAATAATC-AATTAAAGAGTGAGAAAATGACATGAATG 3669
                         i  vv    iii      i -    ?  i i  i v   v  iv     i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_57252326_5   3670 GACACTTCTCAAAAGAAGATGTACAAGCAGCCAAGAAACCTATAAAAA-A 3718
                             i     v         i     iii     v  i vi  i    - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_57252326_5   3719 TGATCAACATCACTAATCAT 3738
                           v         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (160 / 99)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 2.22 (40 / 18)  


2539 26.44 3.89 3.00  chrX_57259455_57263813     2967  3866 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57259455_5   2967 TGGAAGAACATTCTATGCTCATACGTCAGAAGAATTAATATCATTAAAAT 3016
                              ii i  i i   i    ivi ii     v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57259455_5   3017 GACCATATTACACAAAGAAATCTACAGATTCAGTGCAATTCCTATCAAAA 3066
                          i v   i v v    vvi             ii     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57259455_5   3067 TACCAAC-ATCATTTTCACAGTA-TT-ATAAAA-AAT--TAAAATTTATA 3110
                          v   i -ii v    ii   v -  - i  iv-i  --       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_57259455_5   3111 TGGAACCAAAAAAGAACCCTAATAACTAAAGTGTTCCTGAGCAAAAATAA 3160
                              viiv  ii  v  vv    i i   iiiv  i   iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_57259455_5   3161 AAAAGCTAGAATAGT-GCATTACCTCACTTCGGTAA--TATTATGAGGCG 3207
                         v    i i  iv v -i  i v  iv i   ii-  --  i  ii i  v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAA-AACTTACTACAAAGCT 249

  chrX_57259455_5   3208 ACAGTAAGCAAAACAACATGGTTCTGGTAAAAAAACAGATGCATAGGTCA 3257
                                v   i   iii    v    i v  ii i   iii    i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_57259455_5   3258 ATGGTACAGAATAGAGAACCCAGAAATAAAGCCACATAAATACAGCCAAG 3307
                             v i     v    ii           v   i i vv  ii i   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_57259455_5   3308 TGATCTTTGACAAAGGCAGCAATAATATACATTGTGGAAGTGAATCA-CT 3356
                             i  i     i  iiv   v vi  v  v  v    i-    vi-  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCT 398

  chrX_57259455_5   3357 TTTCAATAAATGGTGCTGGGAAAATTGGATAGTCATATATAAAAGAATGA 3406
                               i              v  i      ?i  i  ii          
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_57259455_5   3407 AACTAGAC---TACTTTATTTTGTCATATACAAAAATCAACTCAAAATTA 3453
                          ii i   ---   i i i---ii             i          vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCAC---ACCATATACAAAAATTAACTCAAAATGG 495

  chrX_57259455_5   3454 ATTAAAAACCTAAACAGAAGACCCCAAATTATTAAAAAAAAAAAAAGAAA 3503
                           i ? i       iiv    v iv   i   ---------------   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTAT---------------AAA 530

  chrX_57259455_5   3504 A-----AAAAGAAAACCAAGGGG-AAATTATTTTG-GACATCTGTCTAGG 3546
                          ----- i        vv   ? -    i--  i -   v iv vi    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGG 578

  chrX_57259455_5   3547 CAAATACTTTAT--GACTAAGACCACAAAAGCACAGTCAATAGAAACAAA 3594
                            - iv   v --  -  v   vv          iv   i i  iv   
  L1M4_orf2#LINE/    579 CAA-TGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_57259455_5   3595 AATGGACAAATGTGACTTAATTAAATTTAAAACCTTTTG--CCTAGCAAA 3642
                            i  i    vv     v  i   v      v      -- i --    
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAA 674

  chrX_57259455_5   3643 G-ATGTAATCAACAGAGTGATGAAACAACCTGTTGAATGGAAGAAAGTAT 3691
                          - iiiv     v i     vi i      iiiv      i     i   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_57259455_5   3692 TTGCAAATTATTCATTCAACTGAAGACTTATATTCAGAATATATAACAAG 3741
                                 i  vi  iii iviii     i   i            vi i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_57259455_5   3742 CTC----AACTCAACAATGATAAAACA-----TTTCATTCACAACTGGGC 3782
                            ----       i   i v  i   -----iiiv   ? v  v     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_57259455_5   3783 AAAGGACATAAACAGACATTTTTCAAATAAAAGATATACAAATGGCCAAT 3832
                               iv i  i        i  v  - i                    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAA-AGAAGATATACAAATGGCCAAT 873

  chrX_57259455_5   3833 ATGTATATGAAAA-ACGCTCAGTATCACTAGCTAT 3866
                          v i i       - i     ii    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (157 / 77)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.30 (62 / 27)  


2593 28.28 2.47 0.56  chrX_57282432_57284970.rev     1158  2048 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57282432_5   1158 TGGAAACACGTCCCATCCTGATAGATGGATAGAATCAATATTGTGAAAAT 1207
                               v ii      vi v  i   v iv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57282432_5   1208 ACCA-TACTGCCAAAAGCAACCTACAAATACAATGCAATCCCCATTAAAA 1256
                         iv  -    v  v   vii i     i  v   i        i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57282432_5   1257 TACCA--TGATCATTCTTCACAGAACTAGAAAAATT---CCCAAAATTCA 1301
                          v   --  -- v  i  ii     v v  v  ii ---  i        
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_57282432_5   1302 TATGGGACCCAAAAAGTATCTGCATAGCCAAAGCAAAGCTAAGCAAAAAG 1351
                              i vivv  ii vvi v v         i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_57282432_5   1352 CATAAACCTGGAGGCAACACATTACCTAATTTCAAACTATACTATAAGGC 1401
                         v i   vi      vvv    i v  i         viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_57282432_5   1402 CATAGTCACCAAAACAACATGATACTGCTGTAAAAATGGGCACATATACC 1451
                         i i   v i   i   iii  i     vii   ii  i i  i   v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_57282432_5   1452 AACGGAACAGAATAGAGAACCCACAAAT----CCAAATATTTACAGCCAA 1497
                           i    i     v    ii   v    ----   v i     ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_57282432_5   1498 CAGATCTTTGACAAAGCAAACAAAAACCTAAAGTGGGAAAAGGACACCCT 1547
                         iv   i  i     i vviv   i v v vv i    i    i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_57282432_5   1548 ATTCAACAAATAAAGCTGGGATAATTGGCTAACCACATCTAGGATAATGA 1597
                         v          iiv       i  i   v  ?      vi ii v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_57282432_5   1598 AACTGGATCCTCATCTCTCACCTTACACAAAAATCAACTCAAGATGGATC 1647
                          ii    i  ii i   v    v  i        i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_57282432_5   1648 AGATACCTAAATCTAAGACCTGAAACTATGAAAATTCTAGAAAATAATAT 1697
                          ? v        v     v  i       i   v ii     i v  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_57282432_5   1698 CGAA--AGACCCTTTTAGACATTGGCTGAAGCAATGATTTCATAACCAAT 1745
                         v i?-- i i i iv -   v    v v i      i    v  ivi - 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATA-T 596

  chrX_57282432_5   1746 AAC-CCAAAAGCAAATGCAATAAAAACAAAGATAAAGAGGTGAGACTTAA 1794
                         i  -         v v    i    iv   i   i v ii vi     v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_57282432_5   1795 TTAAACTAAAGAGCTTTTGCATGGCAAAAGAAAC----AGCAGAGTAAAC 1840
                          i   v v  i i      iiivv    i  v  ---- iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_57282432_5   1841 AGACAACCCACAGAGCAGGAGAAAATCTCCACAGTCTATACATCTGCCAA 1890
                                       iii         v iii  ivii   i     vi  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_57282432_5   1891 AGGACTAATATCCAAAATCTAGAAAGAACTCAAACAAATTAGCGAGAAGA 1940
                         i     vi      i   v  v         vv    v i iii v  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_57282432_5   1941 AAACAA-TG--CCA--TCAAAAATGGGGTAAGGACATGAATAGACAATTC 1985
                          i    - i--   -- ?         vv     iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_57282432_5   1986 TCAAAAGCAGATATACAAATGGCCAACAAACATATGAAAAAAATGCTCAA 2035
                           v    v                  i  i  i       i -       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

  chrX_57282432_5   2036 TTTCACTAATAAT 2048
                         iv   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.93 (27 / 14)  


2805 26.70 2.57 1.12  chrX_57285861_57287996.rev      751  1645 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57285861_5    751 TGGAAAAACATTTCATGCTCATGGATAGCAAGAATCAATACTGTAAAAAT 800
                               i i  ii    i        v v    v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57285861_5    801 GGCCATACTACCCAAAGTAATTTATAGATTCAATACTATCCGTATCAAGC 850
                            v     v      v i  i  i        ii v    v      iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57285861_5    851 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 899
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_57285861_5    900 GTGGAA---CAAAATGAGCCCATT-TAGCCAAGACAATCCAAAGCAAAAA 945
                         i     ---   i-- ii    vv-       i      ivi iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_57285861_5    946 GAACAAAGGTGGAGACATCATGCTACCTGGCTTCAAACAATATTACAAGG 995
                                 v     ivv   ii  v  iiii      vvv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_57285861_5    996 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAGACAGAGATATAGAC 1045
                                  i   i    ii         i iv i  i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_57285861_5   1046 CAAAGGAACAGAAC--AGATCCCTCAGATATAATGCCACACATCTACTA- 1092
                            v    i    i--   vi  --   v    vv   i    i  ivi-
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_57285861_5   1093 CAATCTAGTCTTTGACAAACCTGACAAAAACAAGAAATGGAAAAAGGATT 1142
                             - ii i  i     ivv  v   i v  vvv     ii    i  v
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_57285861_5   1143 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAA 1192
                         vi  v  i  i              v      v  ?   i   iii  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_57285861_5   1193 CTGAAACTGGATCACTTCCT-ACACCTTATACAAAAATTAACTCAACATG 1241
                         v    ii    i v  v   -     v                   v   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_57285861_5   1242 GATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAATCCTGGAAGAAA 1291
                            i ?    i           v       i      v  i i       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_57285861_5   1292 ACCTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAC 1340
                           v i  ?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_57285861_5   1341 TAAAACACCAAAAGCAATGGCAACAGAAGCTAAAATTGACAAATGGGATC 1390
                           vi            vvi      i   vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_57285861_5   1391 T------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGATT 1434
                          ------       i -   i  ii vv    i  v       vv i v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_57285861_5   1435 GAGCAGGCAACCTACAGAATAGGAGAACATTTTTGCAATCTATCCATCTG 1484
                           iv  i     i       i      v  v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_57285861_5   1485 ACAAAGATCTAATATCCAGAATCTACAAGAAACTTAAACAAAT---TTAC 1531
                          i  i iv  vi          v  i  ii    ivv    v --- v i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_57285861_5   1532 AAGAAAACAAA-AAC---ATCAAAAAGTGGGTGAAGGATATGAACAGGCA 1577
                           i  i     -   ---  i?    i    ii      v    i  i  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_57285861_5   1578 CTTTTCAAAAGAAGACATTTATGCAGCCAACAAACATATGCAAAAAAAAG 1627
                         i  i  v        i  vi viii     i  i  i   --    i v 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG--AAAAGATG 890

  chrX_57285861_5   1628 CTCATCATCACTGGTCAT 1645
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.83 (33 / 18)  


2121 26.84 3.79 2.67  chrX_57300029_57302317.rev      901  1798 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57300029_5    901 TAGAAAAAGATCTTATGCTCATGGACTGGAAGTATCACTA--GTTAAAAC 948
                          i    i v   ii   i       i      vv i v  --     i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57300029_5    949 GACCATACTGCCAAGAGCAATCTACAGACTAAACATAACTCCTATCA--- 995
                          i v     v  v i vii         i v   ii  ii       ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57300029_5    996 TTACAAAGATAA-TTTTTCACAGAATTAGAAAAAA-AATCCTAGAATACA 1043
                          iv  -- v iv-     ii     v v  v  iv-i      i   v  
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_57300029_5   1044 TATAAAACAAAAAAAGAGCCTGAAGAGCCAAATAAATTTTTCATAAAAAG 1093
                            ii  vviv  ii  v  v   v       vv   i  vv v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_57300029_5   1094 AAAAAAG----AGGCCCCACATTATCTGACTTCAAAATATACTAAAAAAC 1139
                           v    ----   v i    i vi ii i       iv     v   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_57300029_5   1140 TATAGTAACAAAGACTGTATGGTAATGGTAAAAAAATGGAGACATAGA-- 1187
                           i     iv     v  i     v   i v  ii  i  v i     --
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_57300029_5   1188 -ATGGAACCAAATAGAGAATCAAGAAATAAAGCCACATACCTATAAAAAA 1236
                         -      ivi   v    i  v         v   i i ii   iivv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_57300029_5   1237 CTGAACTTTGACAAAGTTGACAAAAATAAACAGTGAAGAAAGGATATGAA 1286
                         i   vi  i     i v  v   i vi vv  i  ii     ------- 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-------A 391

  chrX_57300029_5   1287 ATATTGCTTTACTGAATAGCAATAAAGAGTTCTGGCAAAATTGGCTAGCC 1336
                            v vi   ---------   i   vi  v    v v  i   v  ?  
  L1M4_orf2#LINE/    392 ATAGTCTTTT---------CAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_57300029_5   1337 ATATTCAGAATAATGAAACTGGACCCCTCTCTCTCACCATATACAAAAAT 1386
                          i  v  i  v      ii         vi   v                
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_57300029_5   1387 GAACTCAAGTTTCATTTATGACTTAAATGTAAGACCTCAAACAAGAAAAA 1436
                         v       iv vv  iv?v   i           v  v    v v    v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_57300029_5   1437 TCCTAAGAAAAAAAAATAGAA--AAAACTTC-TGACATTGAG---GGAAA 1480
                           i  -   i    v    i?--   v    -    v   i ---  v  
  L1M4_orf2#LINE/    533 TCTTA-GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_57300029_5   1481 TAATTTAT--GACTAAGACCTCAAAAGCAAATGCAACGAAAACAAAAGTA 1528
                          ii   v --  -  v   vi        v v     i   iv    i  
  L1M4_orf2#LINE/    582 TGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_57300029_5   1529 CACAAATGGAACATAAACTATTTTAG---CTTCTGTACAGCAAAGGAAAT 1575
                         v i    v i  v v v v vv   i---   i   i vv       v i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_57300029_5   1576 AATCAACAGAGCAAAAAGACAAACTACAGAAGAGAAGAAAATATTTGCAA 1625
                         v     v i  ii         v i      vi i               
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_57300029_5   1626 ATTATGCCTCTGAAAATGGTCTAATATCCACAGTCTACAAGAAACCAAAA 1675
                           i  iiv     v  v  v  vi      v i v  i  ii   ivvv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_57300029_5   1676 CAAATCAACAA-AAAAA--------ACCCCATTAAAAAGTGAGCAAAAAA 1716
                            v    i  -     --------    v   ?    i  i     ii 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_57300029_5   1717 CATGAATAGACATTTCTTAAAATAAGACATGCAATTAGCTACAAAAAAAA 1766
                         iv               iv   v    i  i   v i  --   v  iv 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC--CAATAAGCA 878

  chrX_57300029_5   1767 ATTATGAAAAGGTGCTCAACATCACTAGTCAT 1798
                         --i        i            ????????
  L1M4_orf2#LINE/    879 --CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.06 (122 / 115)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.90 (58 / 20)  


2976 28.16 0.55 0.66  chrX_57321929_57330962.rev     1141  2049 (6985)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57321929_5   1141 TGGAAGAACATTCAATACTCATGGGTAGGAAGAATCAATATCATGAAAAT 1190
                              ii i  i v  ii      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57321929_5   1191 GGCCATACTGCCCAAGGTAAATTATAGATTCGATGCCATCCCCATCAAGC 1240
                            v     v     iv i vi  i      i i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57321929_5   1241 TACCAATGACTGTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 1288
                          v   iivi iv i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_57321929_5   1289 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 1338
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_57321929_5   1339 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGG 1388
                                 i      vv   ii  v  ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_57321929_5   1389 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATATAT 1438
                                  i   i    ii         i iv ii i   v     v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_57321929_5   1439 CAATGGAAAAGAAC--AGAGCCCTCAGAAAGAATGCCACATATCTACAAC 1486
                                 v    i--    i  --     v  vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_57321929_5   1487 TATCTGATCTTTGACAAACCTGAGAAAAACCAG-AAATGGGGAAAGGATT 1535
                         i vi    i  i     ivv  vv  i -   v-v           i  v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATA 394

  chrX_57321929_5   1536 CTCTATTTAATAAATGCTGCTGGGAAAACTGGCTAGCCATATGGAGAAAG 1585
                         v   v  i  i     v        v      v  ?   i   v i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_57321929_5   1586 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 1635
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_57321929_5   1636 GATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 1685
                            i ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_57321929_5   1686 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 1735
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_57321929_5   1736 AAAACACCAAAAGCAATGGCAACAAAAACCTAAATTGACAAATGGGATCT 1785
                          vi            vvi         ivvv    v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_57321929_5   1786 AATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 1835
                         v  i   v i  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_57321929_5   1836 ACAGGCAACCTACAAATTGGGAGAAAATTTTCGCAACCTACTCATCTGAC 1885
                          v  i     i   i v           v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_57321929_5   1886 AAACGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1935
                           iv i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_57321929_5   1936 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATGGGAACAGACACT 1985
                            i     i     v  i?    i     i      vv   i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_57321929_5   1986 TCTCAAAAGAAGACATTTATGCTGCCAAAAAACACACGAAAAAATGCTCA 2035
                             v        i  vi viiv     v  i    i     i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_57321929_5   2036 CCATCACTGGCCAT 2049
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (145 / 107)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  

3031 26.43 2.24 0.56  chrX_57321929_57330962.rev     7651  8543 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57321929_5   7651 TGGAAAAACATCCCATGCTCATGGATAGAAAGAATCAATATCATGAAAAT 7700
                               i i        i        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57321929_5   7701 GGCCATACTGCCCAAAGTAATTTATAAATTCAATGCTATCCCCATCAAGC 7750
                            v     v      v i  i  i i      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57321929_5   7751 TACCA-TTGACTTTATTCACAGAGTTAGA-AAAT--ATTTTAAATTTTAT 7796
                          v   -i  v    -  ii    iv v  -  ii--  ii    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_57321929_5   7797 ATGGAAACAAAAAAGAGCCTGTACAGTCAAGACAATCCTAAGCAAAATGA 7846
                                iiv  ii  v  v v i  i   i      i i iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_57321929_5   7847 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTGCAAGGCT 7896
                               i      vv       v  ii i      viv    i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_57321929_5   7897 ACAGTAACCAAAACAGCATGGTACC------AAAACAGACATATAGATAA 7940
                                i   i    ii      i------ ii i            v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_57321929_5   7941 ATGGAACAGAACAGAG-GTCTCAGAAATAACGCCACACATCTACAACCAT 7989
                               i    iv   -   -         vv   i    i  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_57321929_5   7990 CTGATCTTCGACAAACCTGACA----CAAGCAATGGGGAAAGGATTCCCT 8035
                         i    i        ivv  v  ----  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_57321929_5   8036 ATTAAATAAATAGTGCTGTGAAAACTGGCTAGCCATATGCAGAAAACAGA 8085
                         v  v  i    i      v  v      v  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_57321929_5   8086 AACTGGACTCCTTACTTACACCTTATACAAAAATTAACTCAAGATGGATT 8135
                          ii     i   vv  i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_57321929_5   8136 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACCTTAGAAGAAAACCT 8185
                          ?    i           v       i      vi             v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_57321929_5   8186 AGGCA-ATACCATTCAGGACTTAGGCATGGGCAAGGACTTTATGACTAAA 8234
                            ?i- v i -   iv   i v  vv i     v ii  iv iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_57321929_5   8235 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTAAT 8284
                                     vvi          vv     v  i    v i ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_57321929_5   8285 TAAACTAAAGAGCTTCAGCATAGCAAAGAA-ACTATCATCAGAGAGAACA 8333
                         i   v v  i i   iv iiivv     i -       vv i  v   v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_57321929_5   8334 GGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTCTCCATCTGACAAA 8383
                          i     i       i         v       viiv vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_57321929_5   8384 GGGCTGATATCCAGAATCTACAAGGAACTTAAACAGCTTTACAAGAAAAA 8433
                           i  vi          v  i  i     ivv   i  iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_57321929_5   8434 AACAAA---CCTCACCAAAAAGTGGGTGAAGCATATAAACAGACACTTCT 8480
                         i     ---  iv ii?    i    ii   v  v i  i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_57321929_5   8481 CACTAGAAGATATTTATGCAGCCAACAAACATATGAAATAAAAAGCTCGT 8530
                          vvv         vi viii     i  i  i      -- i v    iv
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA--AGATGCTCAA 895

  chrX_57321929_5   8531 CATTACTGGTCAT 8543
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.92 (25 / 13)  


1994 30.20 2.79 0.38  chrX_57334130_57339403     3584  4371 (903)    L1M4_orf2#LINE/L1        3   809 (99)  

  chrX_57334130_5   3584 GAAAAA-ATCTTATGCTCTTGAATAAGAGGAATGAATATCATTAAAATGT 3632
                             i -   ii   i  v  i  vi  i  v v     ii    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_57334130_5   3633 CTATATTATCTAAAGCAATCTACAGATTCATTTCAATTCTCATCAAAATA 3682
                          v   i vi i   vii             viv    i ii        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_57334130_5   3683 CCAA-TGTAATTTTGCACAGAATTAGAAAAA--AATCACCAAATTCATAT 3729
                            i-  iv-    vii     v v  v  i--i   viv          
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_57334130_5   3730 GGAACCACAAAAGAGCTTGCATAGCCAAAACAATCCTATGCAAAAGGAAC 3779
                             vii   ii  v iv v               i iviv  i i    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_57334130_5   3780 TAAGTCGGATGCATCACATTACCTAATTTCAAATTATATTACAAAGCCAT 3829
                         v    i   v vv     i v  i         viv  i        i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_57334130_5   3830 AGAAACTACAACAGCATGGTATTGGTATAAAAATAGACACATAGATCAAA 3879
                           v  ii vi    ii     i   i    ii       i         v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_57334130_5   3880 AGAATAGAAGAGAGAACCCAGAAATTAAGCCACATAACTACAGCCAACTG 3929
                         i        vv    ii        v  v   i i vi  ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_57334130_5   3930 GTCTTCGATAAAGTCAACAAAAG-ATAGGCTGTGAAAACAACATCCTATT 3978
                         i i     i  i viiv   i v-  vviv  v i   v  i vi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_57334130_5   3979 CAA-AAAGGGTTCTTGGAAAATTAGGTGGCCATACACAGAAGAATAAATA 4027
                            -   v   v  v   v  i i i i?   i ii  i      i  vv
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_57334130_5   4028 TGGACCTGTATCTCTCACCATATGCAAAAATTA--TCACAAATGTATTAA 4075
                               iv  i   v        i         --   -     v  i ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCA-AAATGGATCAW 500

  chrX_57334130_5   4076 AGGCTTAAGTGTAAGA-CCAAAACTATAAAAATACAGGAAGAAAACA--G 4122
                           i i   i       - i            v vivi          -- 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_57334130_5   4123 GGAAAACTATTCTGAACATCATTTTTGGCAAAGACATCATGACAAAGACC 4172
                          ?iv  v v   vvi  v iivv  v     v iiv  v iivv v   v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_57334130_5   4173 TTAAAAACAAATGCA-CAATACCAAAAATAGACAAATGGGACTT-----A 4216
                         ii    i  v v   -   v vv         i    v      ----- 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_57334130_5   4217 AACTAAAGTGCTTCTTTACAACAAAAGAAATTATCAACAAAATAAACAGA 4266
                           i    i-i   i v i vv    i  v i      v   i i  v   
  L1M4_orf2#LINE/    651 AATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_57334130_5   4267 CAACGTGCAGAATGGAATAAACTATTTACAAACAATACATCCAATAAAAT 4316
                             vii        i v   v     i    iv   i   ii    iiv
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_57334130_5   4317 ATTAATAACTAGGTTCCACAAAGAACTCAGACATCTCAACAACAA----- 4361
                          i vi  v i  iv vi i         vv   v     i  i  -----
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_57334130_5   4362 CAAATAATTC 4371
                                ii 
  L1M4_orf2#LINE/    800 CAAATAACCC 809

Transitions / transversions = 1.33 (134 / 101)
Gap_init rate = 0.02 (14 / 807), avg. gap size = 1.79 (25 / 14)  

 379 23.44 2.34 0.00  chrX_57334130_57339403     4654  4781 (493)    L1M4_orf2#LINE/L1      778   908 (0)  

  chrX_57334130_5   4654 TTCCATCTCAAAAA-AAAAAAAAAAA-AATTCTGCTAAAATGTAGGCAAA 4701
                           v  v     v  -     i v   -  ii vii ?   vi i      
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_57334130_5   4702 TGGCATAAACAGAC-TTTTTCAAAAGAAGACATACAAATGGCCAACAAAC 4750
                         v iiv i  i    -   i  v        i              i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_57334130_5   4751 ACATAAAAAACTGCTTAACATTATTAATCAA 4781
                             i    iv    i     i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.02 (3 / 131), avg. gap size = 1.00 (3 / 3)  


3137 27.15 0.77 0.55  chrX_57348307_57354672.rev     4970  5875 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57348307_5   4970 TAGAAGAAGATTCCATGCTCATGGATAGGAAGAATCAATATTTTGAAAAT 5019
                          i   ii v  i     i        v      v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57348307_5   5020 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 5069
                           iv     v     iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57348307_5   5070 TACCAATGACTTTCTTCACAGAACTGGAAAAAACTACTCT--AAGTTCAT 5117
                          v   iivi i  i  ii     v v  v  i-  iv  i--  i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_57348307_5   5118 ATGTAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGA 5167
                            v  viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_57348307_5   5168 ACAAAGCTGGAGGCATCACGCTGCCTGACTTCAAACTATACTACAAGGCT 5217
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_57348307_5   5218 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5267
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_57348307_5   5268 ATGGAAGAGAAC--AGAACCCTCAGAAATAATGCCACATATCTACAACCA 5315
                               v    i--   ii  --        vv   i i  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_57348307_5   5316 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5365
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_57348307_5   5366 TATTTAATAAATGGTGCTGGGAAAAGTGGCTAGCCATATGTAGAAAGCTA 5415
                          v  i  i              v  v   v  ?   i   i i  iiv i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_57348307_5   5416 AAACTGGATCCCTTCCTTACACCTTATGCAAAAATTAGTTCAAGATGGAT 5465
                           ii    i    v   i     v   i         ii    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_57348307_5   5466 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5515
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_57348307_5   5516 TAGGCA-ATACCATTCAGGACATAGGCATGTGCAAGGACTTCATGTCTAA 5564
                             ?i- v i -   iv   v v  vv iv    v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_57348307_5   5565 AACACCAAAAGCAAAGGCAACAAAAGCCAAAAAT-GACAAATGGCATCTA 5613
                         i            v i          v-      -  i    v v ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTC 645

  chrX_57348307_5   5614 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5663
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_57348307_5   5664 CAGGCAACCTACAAAATGGGAGAAAA-ATTTGCAACCTACTCATCTGACA 5712
                         v  i     i   i            -        vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_57348307_5   5713 AAGGGCTAATATCCAGAATCTACAATGGACTCCAACAAATTTACAAGAAA 5762
                          i  i  vi          v  i  v i    iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_57348307_5   5763 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5812
                           i     i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_57348307_5   5813 CTCAAAAGAAGACATTTATGCAGTCAAAAAACACATGAAAAAATGCTCAT 5862
                            v        i  vi viii i   v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_57348307_5   5863 CATCACTGGCCAT 5875
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3131 27.81 0.44 0.44  chrX_57410711_57417094     4986  5891 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_57410711_5   4986 GAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTTTGAAAATGG 5035
                            ii i  i     i        v      v i      v v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_57410711_5   5036 TCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 5085
                         iv     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_57410711_5   5086 CCAATGACTTTCTTCATAGAACTGGAAAAAACT-ACTTTAAAGTTCATAT 5134
                            iivi i  i  iii    v v  v  i-  - iii    i       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chrX_57410711_5   5135 GGAACCAAAAAAGAGCCCACATTGCCAAGACAATCTTAAGCCAAAAGAAC 5184
                             viiv  ii  v  viv  v     i        i ivv i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_57410711_5   5185 AAAGCTGGAGTTATCACGCTACCTGGCTTCAAACTATACTACAAGGCTAT 5234
                             i     vvv    i  v  iiii      viv        i    i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_57410711_5   5235 AGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAAAGACCAAT 5284
                              i   i    ii         i iv ii i   v   v   i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_57410711_5   5285 GGAACAGAAC--AGAGCCCTCAGAAATAATACTACACATCTACAACCATC 5332
                             i    i--    i  --        vv i i    i  iiii  vi
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_57410711_5   5333 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 5382
                             i  i     ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_57410711_5   5383 TTTAAAAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 5432
                           i  v              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_57410711_5   5433 ACTGGATCCCTTCCTTACACCTTATATCAAAATTAATTCAAGATGGATGA 5482
                         ii    i    v   i     v    iv        i    i      v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_57410711_5   5483 AAGACTTAAATATTAGGCCTAAAGCCATAAAAACCCTAGAAGAAAACCTA 5532
                         ?    i     i v  iv     i i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_57410711_5   5533 GGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5581
                           ?i- v   -   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_57410711_5   5582 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5631
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_57410711_5   5632 CAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAA 5681
                         v  v v  i i   i  ii vv    i  v    i  vv i      v i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_57410711_5   5682 GCAACCTACAGAATGGGAGAAAGTTTTTTCAATCTACTCATCTGACAAAT 5731
                         i     i               i v   v   vii ivi      i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_57410711_5   5732 GGCTAATATCCAGAATCTACAAAGACCTCAGACAAATTTACAAGAAAAAA 5781
                          i  vi          v  i     v   vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_57410711_5   5782 ACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTC 5831
                              i     v  i?    i     i      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_57410711_5   5832 AAAAGAAGACATTTATGCAGCCAACAGACACATGAGAAAATGCTCATTAT 5881
                         v        i  vi viii     i ii       i  i       vi  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_57410711_5   5882 CACCGACTTT 5891
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.01 (6 / 906), avg. gap size = 1.33 (8 / 6)  


2303 29.30 2.60 1.24  chrX_57420622_57425672.rev     3677  4560 (491)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_57420622_5   3677 CTATGTTCATGGATAGTAAGAATCAATATTGTTAACATGGTCATACTGCC 3726
                          i            v v    v i           v    iv     v  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_57420622_5   3727 CAATGCAATTTACAGATTCAAGGTTATTTCTA-CAAAGTTACTAATGATA 3775
                            vvii  i           v iv  ii   -    i iv viv  viv
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_57420622_5   3776 TT----CACAAATTAAGAAAAAAACCCTAAAATTCATATGGAACCATAAA 3821
                           ----  v     i v  ivvi i                  viii  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_57420622_5   3822 AAACTCTGAATATCCAAAGCAGTTCTAAACAAACAAACAAACAAAAAGCT 3871
                         ii  i v     v     i  i ii i  -   v  i--      -- i 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAG--AACAAA--GTT 207

  chrX_57420622_5   3872 TGAGGCATTATGCTACCTAACTC---ACCTATACTACAAGACTATAGTAA 3918
                         v    vv i ii  v  i  i i--- v  -        ii   i     
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAA 256

  chrX_57420622_5   3919 CCAAAAAAGCATGGTTCCAGAACAAAAACAGTCACACAGATCAATGGAAA 3968
                         i   i v  ii    v ii v i  ii i  v  i i            v
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_57420622_5   3969 AGAATATAGAACCCAGAAATAATACCTCACACCTACAACCATCTGATCTT 4018
                              vv   ii          vv  vi   ii  iiii  vi    i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_57420622_5   4019 CATCAAAG---TCAATGAAAGAAGCAATGGGAAAAGAA-ACTCGAGTTCA 4064
                          iv   i ---i   --i vv vv       i      - v  v-v    
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAA--GACCATTCAATGGGGAAAGAATAGTCT-TTTCA 403

  chrX_57420622_5   4065 CTAAATGATGCTTAGATAACTGGCTAGCCCTATTCAGAATATTGAAACTG 4114
                         vi     i    vi  i      v  ?  vi  v  i  v v    ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_57420622_5   4115 GACCCATTGCTTATACTATATACAAAAATTAATTCAAAATAAATTAAAGA 4164
                              v vv  i i  i               i       ii  i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_57420622_5   4165 CTTAAATGTAAAA-CTGA---TATAAACTCCCTGAAAGTTAACCTAAGAA 4210
                          i         i -  i ---      vii i ii   vv   v  i ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_57420622_5   4211 -ATATCATTCTGCACATGGGTTCTGGCAAGGATTTCATGAAGGGAATGCC 4259
                         - v   v iv  vv v      v-     v i    v ii vivi ii  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATATGACACC 602

  chrX_57420622_5   4260 AAAAACAATCGCAACAAAAGCAAAAATTGACAAATGAGACCTAATTAAAC 4309
                             i  vvv          v      v  i    vi   i v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_57420622_5   4310 TAAAGAGCTTCTGCAAAGCAAAAGAAACTATCAAAGAA-TCAACAGACAA 4358
                          v  i i   i  iivvv    i  v        ii  - v  v      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_57420622_5   4359 CCTAAAGAATAGGA-AGAGTATTTGCAAAATATGAATCCAACAAAGTTCT 4407
                           i v     i   - i i          vi  iv   ii i  i vv  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_57420622_5   4408 TATACCCGGAATACATAAGGGACTT----AAATTAACAAGCAAAAAGCAA 4453
                          i  i  i     i    i i   i----  v i  i  vv    ii   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_57420622_5   4454 ACAACCGCATTAAAAAGTGGGCAAAGGACACAAATAGACACTTTTCAACG 4503
                          i    vv   ?    i           ivii        i  i  v vi
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_57420622_5   4504 GAAGACATCCATGTGGTCAAGAAGTATTTGAAAAATATGCTGAATATCAC 4553
                              i  v  vi   i   v   i iv      i-     v  i    ?
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAG-ATGCTCAACATCAZ 901

  chrX_57420622_5   4554 TAATCAT 4560
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.43 (150 / 105)
Gap_init rate = 0.02 (19 / 896), avg. gap size = 1.79 (34 / 19)  


 866 27.06 1.96 1.18  chrX_57430799_57435136.rev      278   532 (3806)    L1M4_orf2#LINE/L1      379   635 (273)  

  chrX_57430799_5    278 CAATGGGGAAAGAACTTTTTATTCAATCAATGGTGCTGTAATAACTGGCT 327
                                       ivv i v     iv          vi i      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_57430799_5    328 AGCTATATGTGGAAAAATGAAATTGGATTCCTACTTTACATCGTATACAA 377
                          ? i i   iii  i      i     ii     i i   i i       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_57430799_5    378 AAATAAACTCAAGATGGATTAGATATTTAAATGTAAGACCTTAAAAGATA 427
                             v       i      i ? v ii           v  v   vv   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_57430799_5    428 AAGATCCTAGGAGGAAACA--GG---AAATATCCTTCACAACTTAGGCCT 472
                           iv  i   i  i     --  ---    ---    iii  i v  vi 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTT 575

  chrX_57430799_5    473 TGACAAAGAGTGCTTGACCAAGTCCCCAAAAGCAATTGCAATAAAACCAA 522
                         v i   v iv v   iivi v v v         vvv    i    vv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_57430799_5    523 AAATTAATAA 532
                             vi    
  L1M4_orf2#LINE/    626 AAATAGATAA 635

Transitions / transversions = 1.31 (38 / 29)
Gap_init rate = 0.01 (3 / 257), avg. gap size = 2.67 (8 / 3)  

2882 28.74 0.77 0.77  chrX_57430799_57435136.rev     2940  3847 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57430799_5   2940 TGGAAGAACATTCCATGCTACTGGGTAGGAGGAATCAATATCCTGAAAAT 2989
                              ii i  i     i vv   i v   i  v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57430799_5   2990 GGCCATACTGCCTGAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3039
                            v     v  ii iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57430799_5   3040 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3087
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_57430799_5   3088 TATGGAAACAAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCCAAAAG 3137
                                 iiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_57430799_5   3138 AACGAAGCTGGAGGCATCATGCGACCTGACTTCAAACTATACTACAAGGC 3187
                            i   i      vv   ii vv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_57430799_5   3188 TACAGTAACCAAAACAGCATGGTACTGCTACTCAAACAGAGATGTAGATC 3237
                                 i   i    ii        vi ivvii i   v  i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_57430799_5   3238 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCGCACATCTACAACC 3285
                                i    i--    i  --        vv  ii    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_57430799_5   3286 ATCTGATCATTGACAAACTTGACAAAAACAAGAATTGGGGAAAGGATTCC 3335
                          vi    iv i     ivv  v   i v  vvv v         i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_57430799_5   3336 CTATTTGATAAATGGTGCTTCAAAAACTGGCTAGCCATATGTAGAAAGCT 3385
                           v  ii i          vvi v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_57430799_5   3386 GAAACTGGATCCCTTCCCTGCACCTTCTACAAAAATTAACTCAAAATTGT 3435
                            ii    i    v  iii    v v                    v v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_57430799_5   3436 TTAAAGACTTAAATGTTAAACCTAAAACCATAAAAACTCT-AGAACAAAA 3484
                          i ?    i       v i v       i      -    -    v    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_57430799_5   3485 CCTAGGG--AATTCCATTCAGGATATAGGCATGGGCAAGGACTTCATGTC 3532
                          v    ?--  v  --   iv  iv v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_57430799_5   3533 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 3582
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_57430799_5   3583 TAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTG 3632
                          v  i   v v  i i   i  iiivv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_57430799_5   3633 AACAGGCAGTCTACAGAATGGGACAAAATTTTTGCAATCTACTCATCTGA 3682
                           v  i  ii i           v     v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_57430799_5   3683 CAAAGGGCTAATATCCAGAATTTACAAAGAACTCAAACAAATTTACAAGA 3732
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_57430799_5   3733 GAAAAACAAACAACCACATCAACAAGTGGGTGAAGGATATGAACAGACAC 3782
                         i   i     i    vv  i? v  i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_57430799_5   3783 TTCTGAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 3832
                             vv        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_57430799_5   3833 ATCATCACTGGCCAT 3847
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (149 / 108)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2646 26.49 2.10 1.88  chrX_57452274_57462071     4229  5134 (4664)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57452274_5   4229 TAAAAACATATTCCATATTCCTGGATTGGAAGAATCCAAATTTTTAAAAT 4278
                          ii   v    i    i   v            v iv v   v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57452274_5   4279 GTCCGTACTACCCAAAGCAATCTACAGATTTAATGTCATCCCAATTAAAA 4328
                          v vi    v      vii           i  i iv     v  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57452274_5   4329 CATTAATTACATTTTTTACTAAAACAGAAAAA--AATCACAAAATTTACA 4376
                         ivii ii i v      i vi   iv  v  i--i   vi      i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_57452274_5   4377 TGGAACAAATAAGG-ACTCAGAATAGCCATAGTTATCATAAGGAAAAAGA 4425
                              - vii    -  i           v iiv   v ---        
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTT---GAAAAAGA 196

  chrX_57452274_5   4426 AAAA--AAACTGAAGGACTCGCATTACAGGACTTCAAATTATACTACAGA 4473
                          i  --  ii  i       i  i v vvi i      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_57452274_5   4474 CCTATAGTAACCAAAACAGCATGGCACTCTCATAATAATGGACACATAGA 4523
                         v   i     i   i    ii   i   vv     vi  i    i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_57452274_5   4524 CCAGTGGAGCAGAATAGAGAAGCCAGAAACAAATCCACACTCCTACTATG 4573
                         i  i    ii     v    iv       i   i   i  vii  ivi v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_57452274_5   4574 AACTTGTTTTTCAAT---GGTACCAAGAACATACACTGGTGTAAAGACAG 4620
                           -   v     i i---   i      v   v  v   v v  ii i  
  L1M4_orf2#LINE/    347 AA-TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_57452274_5   4621 TCTCTTCTCTAAATGGTGCTGCAAAAACTGGAAATCCATATGCAGAAGAA 4670
                            i   vvi           vi v       v ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_57452274_5   4671 TGAAACTAGACTTCCATCTCTTACCATATACAAAAATCAAATCAAAGTGG 4720
                             ii i   ii i i   vi               i  v     i   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_57452274_5   4721 ATTAATGACTAAAATATAAAACCCCAAACTTTGGAAATTATAAAAGTAAA 4770
                           i ?v   iv    i   i v iv     v ii  v iv  i   v   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_57452274_5   4771 CATTGTGGAAACTCTTCAGGATATTGTAGT--GGCAAAGATTACGTGAGT 4818
                            v v? v  v     iv  iv   -i  --     v i  v v iii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGAT 594

  chrX_57452274_5   4819 ATTACCACACAAGCACAAGCAACCAAACAAAAATGAAAAAAAAAAT--GA 4866
                           v  vv  v             v   v     --- v i v    --  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAA---ATAGATAAATTGGA 641

  chrX_57452274_5   4867 CATAATACCAAGTTAAAAAGCGTCTACACAGCAAAAGAAGCAATTTTCTA 4916
                          v v  - v  i       - v i iii vv    i  --  -i v  v 
  L1M4_orf2#LINE/    642 CTTCAT-CAAAATTAAAAA-CTTTTGTGCTTCAAAGGA--CA-CTATCAA 686

  chrX_57452274_5   4917 G----TAAAGAGACAACCTAAAAAATGGGAGAAAATATTTGCAAACTACC 4962
                          ---- i  i        i v i                      ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_57452274_5   4963 CATCTGACAAGGGATTAATAACCAGTATATATAAGGAGCTCAAACAGCTC 5012
                         i      i      i vi  v    v        i  i   vv   i   
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_57452274_5   5013 TATAGGAAAAA-ATATAATAATGTGATTTAAAAATGAGCAAAACATTTGA 5061
                         v   iv     - i -     ivii   ?       i     iv      
  L1M4_orf2#LINE/    787 AATAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_57452274_5   5062 ATAGACATTTTTCAAAAAAAACACATACAAATGA--AAGAAGGTATATGA 5109
                                   i  v   i  i- i         i--  v   -i i    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAG-CACATGA 883

  chrX_57452274_5   5110 AAATGTGCTAAAGTTCACTAATCAT 5134
                            vi    v  vv   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.71 (36 / 21)  

2215 26.80 2.29 3.44  chrX_57452274_57462071     8433  9305 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chrX_57452274_5   8433 AAAATGACCATACTTCCAAAAGTGATCTACAGTTTCAATGCAATTTCCAT 8482
                           i   i v     i  v   v          v     i     ii i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_57452274_5   8483 CAAAATACCTTCAACATTCTTCCCAGAACTAGAAAAAGCAATACTAAAAT 8532
                               v  vv vi v  i  iv     v v  v  ivii  v       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_57452274_5   8533 GTATATGGAAC--CAAGAAATTCCCTGCATAGCCAAAGCAAGACTAAGCA 8580
                         vi        v--    ii --   v v         i   vvi i iv 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_57452274_5   8581 AAAAGAACAAATCTGGAGACATTACATTACTTAACTTCAAACTATACTAC 8630
                          i         vi     ivv i   i v ii  i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_57452274_5   8631 AAGGCTATAATA-------CAGCATGGTATTGATA-AAAAATAGGCATGT 8672
                           i    i i  -------   ii     i  ii -  ii    i   i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_57452274_5   8673 AGACCAAGGAAACAGAATAGAGAACCTATAAATAAAGCCAAATACTTACA 8722
                            i   v i  i     v    ii i v       v   v i i   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_57452274_5   8723 GCTAACTGTAAACATTACAAAACAGAACATAAAGGAAAACAAACAAAAAA 8772
                          ii  i  --- iv  - i -------  ---   iviv   --------
  L1M4_orf2#LINE/    344 GTCAATTG---ATTTT-CGA-------CA---AGGGTGCCAA-------- 371

  chrX_57452274_5   8773 GAACAT-AAGCAGAGAAACTACACCCTATTCAACAAATGGTACTAGGATA 8821
                           v   -v iii i    vv i vi  v             i  i   i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_57452274_5   8822 ATTGCCAAGACACACGTCGAAGAAGGAAACTGGATCTTCATCACTCACCT 8871
                          i  vvv ?v    i ivi     v   ii    i iii i v v    v
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_57452274_5   8872 TATACAAAAATCAACTCAAGAAGCATCAAAGATTTAAATCTAAGACATGA 8921
                                    i       i v v    ?   ii     v     vv i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_57452274_5   8922 AACCGTAAAAATGTTAGAAGATAGCAT---GATAAAATCTCTTCTAGACA 8968
                            ii     v v        v i   ---?i    ---     vv   v
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA---TCTTCGTGACC 568

  chrX_57452274_5   8969 TTGGCTTAGGCAATGAGTTCATGACCAAGAACCCAAAAGCAAATGCAA-A 9017
                             v          iv   v iivi v  vv         v v    - 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_57452274_5   9018 AATAAATACATAAATAAATAAGACCTAATTAAACTAAAAAGCTACTGCAC 9067
                           vi  v v   i      vi   i v  i   v v    i  vi  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_57452274_5   9068 AGCAAAAGAAATAATCAACAGAGTAAACAAACAACCCGCAGAGTGGGAGA 9117
                         vv    i  v iv     v i   i  v i       i    i       
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_57452274_5   9118 AAATATTCACAAACGATTCATCTGTCAAAGAAGTAATATTCAGAATCTAC 9167
                                ii    iv  vi     vi  i i v vi   i      v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_57452274_5   9168 AAGGAACT---AAAGCAGTCAGCAAGAAAAAAATCAAATAATCCTATCAA 9214
                           i     --- v i --   ii  v     i -       i  v  i? 
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAAC--TCAATAATAAAAAGA-CAAATAACCCAATTWA 815

  chrX_57452274_5   9215 AAACTGGGCATAGGACATAAATAGACAATTCTCAAAAGAAAATATACAAA 9264
                            v      v    iv i        v     v      i         
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_57452274_5   9265 AGGCCAACAAACAC--GAAAAAATGCTCAACATCACTAATTAT 9305
                         v      i  i   --     i             ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (130 / 100)
Gap_init rate = 0.02 (17 / 863), avg. gap size = 2.94 (50 / 17)  


2953 28.51 0.44 0.88  chrX_57468238_57472734     3093  4004 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57468238_5   3093 TGGAAGAACATTCCGTGCTCATGGATATGAAGAATCAATATCGTGAAAAT 3142
                              ii i  i  i  i        vv     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57468238_5   3143 GGCCATATTGCACAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 3192
                            v   i v v   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57468238_5   3193 TACCAATAACTTTCTTCAATTCACAGAATTGGAAAAAAATACTTTAAAGT 3242
                          v   i---  vi   i--  ii     v v  v  ivvv iii    i 
  L1M4_orf2#LINE/    101 TCCCAG---CTGCCTTT--TTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_57468238_5   3243 TCATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAA 3292
                                   viiv  ii  v  v v  v     iv     i i ivv i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_57468238_5   3293 AAGAACAAAGCGGGAGGCATCATGCTACCTGATTTCAAACTATA-TACAA 3341
                                   iv     vv   ii  v  ii        viv  -     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_57468238_5   3342 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 3391
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_57468238_5   3392 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACA 3439
                          i        i    i--    i  --        vv iii i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_57468238_5   3440 ACTATCTGACCTTTGACAAACCTAACAAAAACAAAAAATGGGGAAAGGAT 3489
                         iii vi   ii  i     ivv iv   i v  vvv           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_57468238_5   3490 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATGTGTAGAAA 3539
                         vvi  v  i  i              v      v  ?i  ii  i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_57468238_5   3540 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 3589
                         iv    ii    i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_57468238_5   3590 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 3639
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_57468238_5   3640 AATCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGAACTTCATGT 3688
                           iv    ?i- v i -   iv   v v  vv i     viii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_57468238_5   3689 CTGAAATACCAGAAGCAATGGCAACAAAAGCCAAAATTGAAATATGGGAT 3738
                         v ivi i    i     vvi          vv     v  v v  v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_57468238_5   3739 TTAATTAAACTAACGAGCTTCTGCACAGCAAAACAAACTACCATCAGAGT 3788
                           v  i   v v vi i   i  ii vv    iv v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_57468238_5   3789 GAACAGACAACTTACAGAATGGGACAAAATTTTTGCAATCCACTCATCTG 3838
                            v       ii           v     v       vi  ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_57468238_5   3839 ACAAAGGGCTAATATCCAGATTCTGCAATGAACTCAAACAAATTTACAAG 3888
                          i  i  i  vi        v v ii  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_57468238_5   3889 AAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACC 3938
                              i     i     v  i?    i     i      v    i    v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_57468238_5   3939 CTTCTCAAAAGAAGATTTTTATGCAGCCAAAAGACACATGAGAAAATGCT 3988
                         i     v         v vi viii     v ii       i  i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_57468238_5   3989 CATCATCACTGGCCAT 4004
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (147 / 109)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


1176 30.04 6.27 5.07  chrX_57497922_57499836      599  1427 (488)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_57497922_5    599 ATCTA-AAATATCAGCACAATATGAATTAGAACCCCAAACTAGCTGTTG- 646
                              - i  -   i i    vivv  i i  i    i-  iv  v  v-
  L1M4_orf2#LINE/     70 ATCTACAGAT-TCAACGCAATCCCTATCAAAATCCCAG-CTGCCTTTTTT 117

  chrX_57497922_5    647 GTTGAAGTTTTTATGATGAGTTTATAATTTAAATGGAATTGAAATGGGCC 696
                          iv   i  vvi v v   vii  v    i v      v  v  v  i  
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_57497922_5    697 AAAAGTAGCCAAGACACTTTTGAAGAA--AGA-------TGTAGAATTTA 737
                         v i i       i   v i     i  --   -------  v  i i i 
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_57497922_5    738 CTGCCTTATCCAAATATCAGAATTGACTATGGATCTGTAGTAATTAAGAC 787
                          --v   --  v   v   i  i v    iii v  ii      i     
  L1M4_orf2#LINE/    218 C--ACTT--CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_57497922_5    788 AGTGTGATATT----T-----CAAACAAATAGGGCCGAGCACT-TAATAG 827
                               i  i ---- -----i i   v    iv viv v v -v   v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_57497922_5    828 CGAGTATAGGAACTAGCCCACATATGGGTAGATACTTGATTTATGGCAC- 876
                         v    vi  i  iv i    i i  vvi i vi v       vi i  v-
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_57497922_5    877 --TGTAAA------TCAGTTGGCAAAAGGCAGACTTTTCAATAAGTGGTT 918
                         --  iv  ------   i v  v   iiii  v        i  i    -
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT- 412

  chrX_57497922_5    919 CACTGAGAAAACTGGATATTCAAACAAATAAATAAATAAATAAATAAATG 968
                         -i   i  v         ?i  --  vii   vi   i  ---i ---  
  L1M4_orf2#LINE/    413 -GCTGGGACAACTGGATAKCCA--CATGCAAAAGAATGAA---GT---TG 453

  chrX_57497922_5    969 GAACCCCACTCAACACAATATACAAACATCAATTGCAGGTGGATTA-AGA 1017
                           v   i  iiv    v         v  i  i vv ii     i -   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_57497922_5   1018 CCTGACTGTGAAGGGCAATAGC-ATACGTATTTTGGAAGAAAATATAGAA 1066
                            i v   -   i  v v i -   vivv i  i        i    i?
  L1M4_orf2#LINE/    504 CCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_57497922_5   1067 A-ACGCTTTCATGGCCCAGGGTTTCTTAAAACAGAAAAGATTTCTTAAAA 1115
                         i- viii   i  i  iv     ----- ii  --- v i       i -
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTT-----AGGCA---ATGGTTTCTTAGA- 593

  chrX_57497922_5   1116 CAGATTTCTTAAAACAAAAACACACTAACCATCAGGAAAAGAAT-GATGA 1164
                         ------ v v v v     i    -- i v iv iii   i   -   i 
  L1M4_orf2#LINE/    594 ------TATGACACCAAAAGCACA--AGCAACAAAAGAAAAAATAGATAA 635

  chrX_57497922_5   1165 ATTTGACTATATTATAATTAAGATCTTCTGTTCA-CAAAACACAGCACAA 1213
                            v    vi  i v      i v   i   v v-    iv   vi iv 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_57497922_5   1214 AGCAATGGGAAATACAA---ACAGAACAAGGGAATATTTTGGCCA--CAG 1258
                           v  vv i   v    ---      iii i   v  v  v  v --  v
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_57497922_5   1259 GTAT--------GGACTAGTATTTAAAATATTTAACAGGCTCAT-TAAGT 1299
                         i   --------     v    ii i     v   viii   v -i  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_57497922_5   1300 CAGTAAGTACTAGATGAACAATAGAATAGAAACATGGGTTAAAAGAGGTA 1349
                           i   vv vv   ii  i  ivv   v?   v     i-   i  ----
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC-AAAGGA---- 830

  chrX_57497922_5   1350 AATTTGAATAGGC-CTTCTTCGGAGTAGACACTCCAAAAGGCTCATAAAC 1398
                         --         i -i    i ii  v   i - v    v   iv    i 
  L1M4_orf2#LINE/    831 --TTTGAATAGACATTTCTCCAAAGAAGATA-TACAAATGGCCAATAAGC 877

  chrX_57497922_5   1399 AC--GAAAATGTGCTAAAGCTTACTAGTAAT 1427
                           --     vi    v  vv i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (137 / 109)
Gap_init rate = 0.04 (36 / 839), avg. gap size = 2.61 (94 / 36)  


3151 26.64 1.44 0.67  chrX_57519541_57529073      492  1392 (8141)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_57519541_5   1392 TGGAAGAATATTCCATGCTCATGGGTAAGAAGAATCAATATTGTGAAAAT 1343
                              ii    i     i      i vi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_57519541_5   1342 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 1293
                            v     v     iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_57519541_5   1292 TACCAA-TGTCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTC 1246
                          v   i-  i    i  -i     -   -- v  i  - iii v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

C chrX_57519541_5   1245 ATATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAA 1196
                                 viiv  ii  v  viv  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chrX_57519541_5   1195 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGG 1146
                                 i      vv   ii  v  ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chrX_57519541_5   1145 CTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATACAGAC 1096
                                  i   i    ii         i i  ii i   v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chrX_57519541_5   1095 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAAC 1048
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

C chrX_57519541_5   1047 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 998
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

C chrX_57519541_5    997 CCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGACATATGTAGAAAGC 948
                         i  v  i  i              v      v  ?v  i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

C chrX_57519541_5    947 TGAAACTGGATCACTTCCTTACACCTTATGCAAAAATCAATTCAAGATGG 898
                             ii    i v  v   i     v   i       i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

C chrX_57519541_5    897 ATTAAAGACTTAAATGT------TAAAACCATAAAAACCCTAGAAGAAAA 854
                           i ?    i       ------      i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

C chrX_57519541_5    853 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 805
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

C chrX_57519541_5    804 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAGTGGGATCT 755
                          vi            vvi          vv     v  i  i v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

C chrX_57519541_5    754 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 705
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

C chrX_57519541_5    704 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 655
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

C chrX_57519541_5    654 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 605
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

C chrX_57519541_5    604 AAAT-CAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 556
                            v-    i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chrX_57519541_5    555 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 506
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chrX_57519541_5    505 CCATCACTGGCCAT 492
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  

2654 25.73 3.82 1.80  chrX_57519541_57529073     8151  9040 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57519541_5   8151 TGGAAAAATATTCAATCCTCGTGGATAGGAATAATCAATATGGTGAAAAC 8200
                               i    i v  vi  i     v    v v i     v  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57519541_5   8201 AGCCATACTGTCCAAAGTAATTTATAGATTCAATACTAATGCC-ATCAAA 8249
                         i  v     vi     v i  i  i        ii -   v  -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAAA 99

  chrX_57519541_5   8250 -------CTGACCTTCTTCACAGAATCAGAAAAAAAAACT-ATTTTAAAT 8291
                         -------   -    i  ii     ---- vvi v  i  -  ii    v
  L1M4_orf2#LINE/    100 ATCCCAGCTG-CCTTTTTTGCAGAA----ATTGACAAGCTGATCCTAAAA 144

  chrX_57519541_5   8292 TTTATATGGAGTCAAACAAG--ACCCCGTATAGAAAAGACAATCCTAAGT 8339
                           i       i-- vi    --    v v    vv  i      i i iv
  L1M4_orf2#LINE/    145 TTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_57519541_5   8340 AAAAGGAACAAACTTGGAGGCATCACACTACCTGACTTTGAACTATACTA 8389
                           i i       v       vv       v  ii i  ii  viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_57519541_5   8390 AAAGACTACAGTAACCAAGACAACATAGTACTGGTACAAAAACAGATGTA 8439
                         v  ii         i       iii i       i i  ii i   ii  
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_57519541_5   8440 TAGACCAATGGAGCAAAAAGGAGACCTCAGAAATAACATCACGTATCTAC 8489
                             i       ii i  vv    vii         vvi  iii  i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_57519541_5   8490 AACCATCTGATCTTCGACAAACCTGACAAAAACAAACAATGGGGAAATGA 8539
                         iii  vi    i        ivv  v   i v  vv           vi 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_57519541_5   8540 TCTCCTATTCAGTAAATGTTGCTGGGAATACTGGCTAGTCATATG-AGAA 8588
                          vvi  v    ii     v        vv     v  ?i  i   - i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_57519541_5   8589 AATTAAAACTGGATCCCTTCTTTACACCTTATACAAAAATTAACTCAAGA 8638
                         i v i  ii    i    v i i     v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_57519541_5   8639 TGGATTAAAGATTGAAATGTAAAACCCAAAACCATAAAAACTCC-AGAAG 8687
                              i ?   iiv        i v i     i      -   i-     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAG 541

  chrX_57519541_5   8688 AAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTTC 8736
                             - v    ?i- v i -   iv   v v  vv i     v i-    
  L1M4_orf2#LINE/    542 AAAA-CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG-TTTC 588

  chrX_57519541_5   8737 TGACATA-AATGCCAAAAGCAATTGCAACATAAGCCAAATT-GACAAATG 8784
                          v v   -i ii         vvv      v   vv   v -  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_57519541_5   8785 GGATTT------AATTAAAGAGCTTCTGCATAGTAAAAGAAACTATCATC 8828
                            i  ------       i -   i  iiivvi   i  v       vv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_57519541_5   8829 ACAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCC 8878
                          v      v  i     i                 v       vii  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_57519541_5   8879 ATCTGGCAAAGGTCTCATATCCAGAATTTACAAGGAACA--TACAGAAAT 8926
                              ii  i  v  ii          v  i  i    v--    --- i
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA---AC 784

  chrX_57519541_5   8927 TTAA-AAGAAAAAAA--AACA--CCAA----AAAATGGGTGAAGGATATG 8967
                          i  -  v     i --  i --    ----        ii      v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_57519541_5   8968 AACAGACACTTCTCAAAAGAAGACATTTATGTGGCCAAGAAACATATGAA 9017
                           i     i     v        i  vi vi       v  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_57519541_5   9018 GAAA-GCTAAACATCACTGGCCAT 9040
                         i i -   v       ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (135 / 91)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 1.92 (50 / 26)  


2899 29.36 0.55 0.33  chrX_57532524_57544620     4987  5892 (6205)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57532524_5   4987 TGGAAGGACATTCCATGTTCATGGGTAGGAAGAATCAATATCGTGAAAAA 5036
                              i  i  i            i v      v i     i  v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57532524_5   5037 GGCCATACTGCCCAAGGTAATTTATAGATTTAATACTATCCCCATCTAGC 5086
                            v     v     iv i  i  i     i  ii v     i   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57532524_5   5087 TACCAATGACTTTCTTCACAGAA-TTGCAAAAAACT-ACTTTCAAGTTCA 5134
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_57532524_5   5135 TATGGCACCAAAAAAAGCCC-GCATCACCAAGTCAATCCTAAGCCAAAAG 5183
                              v viiv  iiii   - v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_57532524_5   5184 AACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTATACTACAAGGC 5233
                                i     ivv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_57532524_5   5234 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5283
                           i     i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_57532524_5   5284 AATGGAACAGAACGGAGCCCTCAGAAATAATGCTGCATATCTACAACTAT 5333
                                i    iv   vvii         vv iii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_57532524_5   5334 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5383
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_57532524_5   5384 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGACATATGTAGAAAGCTGA 5433
                         v  i  i              v      v  ?v  i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_57532524_5   5434 AACTGGATCACTTCCTTATACCTTATACAAAAATTAAGGCACGATGAGTT 5483
                          ii    i v  v   i i   v              vv  vi   ii i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_57532524_5   5484 AAAGACTTAAATGTTAGACCTAAAACCATGAAAACCCTAGAACAAACC-T 5532
                          ?    i       v   v       i  i   vi i     v   v - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_57532524_5   5533 AGGCA-ATACCATTCAGGACATAAGCATGTGCAAGTGCTTCATGTCTGAA 5581
                            ?i- v i -   iv   v vi vv iv    vv i   v ivv ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_57532524_5   5582 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5631
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_57532524_5   5632 TAAACTCAAGAGCTTCTGCACAACAAAAGAAACTACCATCAGAGTGAACA 5681
                         i   v i  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_57532524_5   5682 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5731
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_57532524_5   5732 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTATAAGAAAAA 5781
                           i  vi          v  i  v      vv    v iv    v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_57532524_5   5782 AACAAACAACCCCATCAAAAAGTGGACAAAGTATATGAACAGGCACTTCT 5831
                         i     i     v  i?    i   i     v  v    i  i  i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_57532524_5   5832 GAAAAGAAGACATTTATGCAGCCGAAAAAGACATGAAGAAATGCTCATCA 5881
                         vv        i  vi viii   i v  iv       i i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_57532524_5   5882 TCACTGGCCAT 5892
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (154 / 108)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  

3157 27.59 0.66 0.44  chrX_57532524_57544620    10699 11604 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57532524_5  10699 TGGAAGAATATTCCATGCTCATGGGTAAGAAGAATCAATATCGTGAAAAT 10748
                              ii    i     i      i vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57532524_5  10749 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 10798
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57532524_5  10799 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 10846
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_57532524_5  10847 TATGGAACCACAAAAGAGCCCGCATCGCCAAGTCAATCCTAAACGAAAAG 10896
                                vii   ii  v  v v  v     iv     i i  vi i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_57532524_5  10897 AGCAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 10946
                          i     i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_57532524_5  10947 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 10996
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_57532524_5  10997 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 11044
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_57532524_5  11045 ATCTGATCTTTGGCAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 11094
                          vi    i  i i   ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_57532524_5  11095 CTATTTAATAAATGGTGCTGGGAAAAGTGGCTAGCCATATGTAGAAAGCT 11144
                           v  i  i              v  v   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_57532524_5  11145 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATTGA 11194
                            ii    i    v   i     v           i  i    i  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_57532524_5  11195 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAACC 11244
                          i ?    i    i  v   v       i      vi i         v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_57532524_5  11245 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 11294
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_57532524_5  11295 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTAACAAATGGGATCTAA 11344
                         i            vvi          vv     vi i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_57532524_5  11345 TTAAACTAAAGAGCTTCTGCATAGTAAAAGAAACTACCATCAGAGTGAAC 11394
                          i   v v  i i   i  iiivvi   i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_57532524_5  11395 AGGCAACCTAAAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 11444
                           i     i v i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_57532524_5  11445 AGGGCTAATATCTAGAATCTACAATGAACTCAAACTAATTTACAAGAAAA 11494
                         i  i  vi    i     v  i  v      vv  v v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_57532524_5  11495 AAAAAAA-AACTCA-TCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 11542
                          i v   -   i  - i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_57532524_5  11543 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 11592
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_57532524_5  11593 ATCACTGTTCAT 11604
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2453 30.33 1.22 0.89  chrX_57571281_57574406     1734  2633 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_57571281_5   1734 AAACATTTTATGCTCATGGATAGGAAGAATCAATATCATGCAAATGGACA 1783
                          i i  iii   i        v      v i     ii vv i    vv 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_57571281_5   1784 TACTGTCCAAAGTAGTTTATAGATTCAATGGTAATCTC-ATTAAACTAAC 1832
                             vi     v ii i  i        i -i    i -  i   v vv 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACG-CAATCCCTATCAAAATCCC 104

  chrX_57571281_5   1833 ATTGACATTCTTCATAGGATCAGAAACAAATTAATT-TAAAATTTATATG 1881
                          vivi v  i  iii  i -- vvi    ii i  i-       i     
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_57571281_5   1882 GAACCAAAAGAGAGCCTGTATAGCCAAAACAATCTTAACCAAAAAGAACA 1931
                            viiv   i  v  v v                 i vv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_57571281_5   1932 AAGCTGGAGGCATCACACTACTTGACTTCAAACTATACTACCCGGTTAGA 1981
                            i      vv       v iii i      viv      vvi i  v 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_57571281_5   1982 GTAACCAAAACAGCATGGTACTGGTACAAAACCAGAAACGTAGGCCAATG 2031
                             i   i    ii         i i  iivi   v ii   ii     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_57571281_5   2032 GAACAGAATAGAGATCTCAGAAATAAGACCACACATCTACGACCATCTGA 2081
                            i     v    vii         iv   i    i  i ii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_57571281_5   2082 TCTTCAACAAACCTGACAGAAACAAGCAACAAGAAAATGAT-TTCTTAGT 2130
                          i   i    ivv  v  ii v  vv   iii i   vi  -v    -v 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-TT 401

  chrX_57571281_5   2131 TAATAAATAGGGCTGGGAAAACTGGCTAGCCATATGCAGAAAATTGAAAC 2180
                         i  i    i v       v      v  ?   i     i  i v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_57571281_5   2181 TGGACCCCTTCCTTACATCTTATACAAAAATTAACTCAAGATAAATCAAA 2230
                                  v   i   i v                   i  ii    ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_57571281_5   2231 GACTTAAACTTACAAACCAAAACTATAAAAACCCTAGAAGAAAA--TCGA 2278
                            i    iv  vi i i            vi i          -- v i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_57571281_5   2279 GGCAATACCATTCAGGAAAT-AGGTACAGCCACG-TATTTTATGATGAAA 2326
                         ? i  - i -   iv  vv -i   vvi  v i - v i   -   - vi
  L1M4_orf2#LINE/    552 NGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GAT-ATG 597

  chrX_57571281_5   2327 ATGTCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGAATCTAAT 2376
                          iii        vvv          v      v  i    v i ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_57571281_5   2377 TAAACTAAAGAGCTCCTGCACAGCAAAAGGAACTATCATCAGAGCAAAGA 2426
                         i   v v  i i  ii  ii vv    i iv       vv i  ii  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_57571281_5   2427 GAAAGCCTACAGAATGGGAAAAAAATTTTGCAATCTATCCATCTGGCAAA 2476
                           v i  i           i    vv       vii  vi     ii  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_57571281_5   2477 GGTCTAATATCCAGAGTCTACAAGAAACCTAAACAAATTTACAAGGAAAA 2526
                           v  vi        i v  i  ii   iivv    v iv i  vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_57571281_5   2527 TACAA----CCCCATCAAAAAGTAGGCAAAGGTCATGAACAGACCCTTCT 2572
                         v    ----   v  i?    i i        viv    i    vi    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_57571281_5   2573 CAGAACAACACATTTATGCATTCAAGAAACATATTATAAAAAGCTCAACC 2622
                          vi  v  v i  vi viiivi   v  i  i  v v  i v       v
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_57571281_5   2623 TCACTGATCAT 2633
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (162 / 107)
Gap_init rate = 0.02 (14 / 903), avg. gap size = 1.36 (19 / 14)  


2161 27.13 4.62 1.42  chrX_57592106_57599614      495  1338 (6171)  C L1M4_orf2#LINE/L1   (34)   874     4  

C chrX_57592106_5   1338 AAAGATATCCAGTGTTCATGAATTAGACGA-TTATTATTTTTAAAATGTC 1290
                                   vi        i   i  v  -   v    v    i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

C chrX_57592106_5   1289 CATGCTACAAAAGTT-ACATACAAACTGAATGCAATCCCTATAAAAATTC 1241
                         v  i  v vv  i  - iv    i i v  i           v     i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

C chrX_57592106_5   1240 CAATAGAATATTTCACAGAAATAGAAGACAAA---ATTCTAAAGTTAGTA 1194
                           iiv vv v   ii       v  ---   i---  i     i  vi  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGA---CAAGCTGATCCTAAAATTCATA 150

C chrX_57592106_5   1193 TAAAACTTCAAAATACCGTGAGTAGCCAAATAATTCTTGAGAAAAAGAAG 1144
                          ii  v v   iiv   vv  i        vv v      --        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

C chrX_57592106_5   1143 AATTC----TTGAAGGCAGTACACTTCCTGGTCTCAAAATATGTAACAAA 1098
                           -- ----   i   vvvi        iii i      iv iiv     
  L1M4_orf2#LINE/    199 AA--CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

C chrX_57592106_5   1097 GCTTCTGCAATCT-GAAAGTGAAGTGCCACCACAAAAACAGAGAAATAGA 1049
                            v v i    v-  v    vi  i iiv  i  ii i   v v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chrX_57592106_5   1048 CAAATGAAACAGAATAGAAAAACCAGAAATAAACTGACACATATAGAGAC 999
                         iv    i  i     v  i iv            iv i    v  vi v 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

C chrX_57592106_5    998 CACTAACTCT-GACAAGGGTTCCAAGAACACACAATGGGTAAAACAAACT 950
                         v i i i i -         v      v  iv       v   iv v v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_57592106_5    949 CTCTTCAACAAATTGTCTTGGGAAAACCAGATCTCCACAAACAACATAAT 900
                           i          v  vi     v   ii   v?     vi   v v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_57592106_5    899 TGAATTAGATTATTATCTTATACCATGTATAAAA--TACCTTTAA-TGAA 853
                         vi i  i  iivi  i  i i     i  i    --  v  iv  -  i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_57592106_5    852 CTAAAGACTTAAATATAAAACCTAAAACTGACAAAATCC----------- 814
                         ii ?    i     i   i v        - i    ii -----------
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTTAGAAGAAAA 545

C chrX_57592106_5    813 ---AAGGGGAAGCCT--GGGACATTGG-T----CAATGATATTTGTTAG- 775
                         --- i ? v  ii  -- v   v    - ----     i --  v    -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT--TTCTTAGA 593

C chrX_57592106_5    774 TGCAACCCCAACAGCA-AAGAAGACAAAAGCAAAATTA-ACAAGTTGGAC 727
                          iii  v    v    -   v -       v    v  - i  i      
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCA-ACAAAAGAAAAAATAGATAAATTGGAC 642

C chrX_57592106_5    726 TACATTAAACTAAAAAGCTTCTGCACATAAAAAGAAACAATCAACAGATA 677
                          v   i   v v    i   i  ii v v   i  v  v     v i vv
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

C chrX_57592106_5    676 AAAAAGACAATCTCCATATTGGGATAATATATTTTTAAAGCATATATATG 627
                         i         i iv  v v     v  v      vi   v       v  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

C chrX_57592106_5    626 ATAAGAAGTGAATATCCAGAATATATAAGGAACACATACAATTCAATAAC 577
                              iiiivvi                i    v v     i       i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

C chrX_57592106_5    576 AATAAAGTTAAATAACCCAGTGAAAAAATGAACATAGGATCTAAA-AAAC 528
                           -    vi          i v?       ii  v     i i  - i  
  L1M4_orf2#LINE/    793 AA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chrX_57592106_5    527 ATTTTTCCAAAGAAGACATAGAAGTAACTCATA 495
                             i           i   v  i ii iv   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.21 (123 / 102)
Gap_init rate = 0.03 (23 / 871), avg. gap size = 2.22 (51 / 23)  

2986 28.54 0.77 0.44  chrX_57592106_57599614     6113  7016 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_57592106_5   6113 GGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATGTCGTGAAAATG 6162
                             ii i  ii    i      i v      v i   i i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_57592106_5   6163 GCCATATTGCCCAAGGCAATTTACAGATTCAATGCCATCCCCATCAAGCT 6212
                           v   i v     ivii  i           i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_57592106_5   6213 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCAT 6260
                         v   iivi i  i  ii     -   -- v  i  - iii v  i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_57592106_5   6261 ATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCATAAGCCAAAAGA 6310
                               viiv  ii  v  viv  vi    iv     v i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_57592106_5   6311 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 6360
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_57592106_5   6361 ACAGTAACCAAAACAGCATGGTACTGGTAGCAAAACAGACACACAGACCA 6410
                                i   i    ii         i vv ii i     i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_57592106_5   6411 ATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAGCTA 6458
                               i    i--    i  --        vv   i    i  ii ii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_57592106_5   6459 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 6508
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_57592106_5   6509 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGACATATGTAGAAAGCTG 6558
                          v  i  i              v      v  ?v  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_57592106_5   6559 AAACTGGGTCCCTTTGTTACACCTTATACAAAAATTAATTCAAGATCGAT 6608
                           ii   ii    viv i     v              i    i  v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_57592106_5   6609 TAAATACTTACATGTTAGATCTAAAACAACAAAAACCCTAGAAGAAAACC 6658
                         i ? v  i  v    v   v       v i    vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_57592106_5   6659 TAGGCAACACCTTTCAGGACATAGACATGTGCAAAGACTTCATTTCTAAA 6708
                             ?ivv vii   iv   v v ivv iv    v ii   v vvv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_57592106_5   6709 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAGAAATGGAATCTAAT 6758
                                     vvi          vv     v  v    v i ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_57592106_5   6759 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTAAACA 6808
                         i   v v  i i   i  ii vv    i  v  i i  vv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_57592106_5   6809 GGCAATCTACAGAATGGGAGAAAATTTTTGCAGCCTACTCATCTGACAAA 6858
                          i   i i                 v      ivii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_57592106_5   6859 GGGCTAATATCCAGAATCTACAATGAACTCCAGCAAATTTATAAGAAAAA 6908
                           i  vi          v  i  v      ivi   v iv    v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_57592106_5   6909 GACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGGCACTTCT 6958
                               i     v  i?    i    ii      v    i  i  i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_57592106_5   6959 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAATTGCTCA--- 7005
                          v        i  vi viii     v  i          iv      ---
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_57592106_5   7006 TCAACCCTGGC 7016
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (150 / 104)
Gap_init rate = 0.01 (6 / 907), avg. gap size = 1.83 (11 / 6)  


2899 26.85 2.57 1.01  chrX_57601166_57603264      719  1612 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57601166_5    719 TAAAAATATATCACATATTAATGAATTGGAAGAATGAATATTGTTAAAGT 768
                          ii   v     v   i  v   i         v v           ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57601166_5    769 GTCCATACTAACCAA-TTAACCTACAGATTCATTGCAATCAGTATCAAAA 817
                          v v     vv    -  i i           vi      vv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57601166_5    818 TCCTAA-TGTCATTTTTTCACAGAAATAGCAAAAATAATTATTCTATTTA 866
                            i i-  i --     ii       v vv  iv i  iv vvv   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_57601166_5    867 TATGGAACTCACAAAAGAGCCAGAGTAGCCAAAACAATCTTGAGCAAAGG 916
                                v -i   ii  v     i                  iv  iii
  L1M4_orf2#LINE/    149 TATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_57601166_5    917 GAGCAAAGATGAAGGTTTCACACTTCCTGATTTCAAGACATATTTTAAAA 966
                           i     v  i   vi          ii       i  v  i vi   i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_57601166_5    967 CAGTTGTAATAAAAAAAGCATGATATTGGCATTAAAAACAAACACGTTGA 1016
                          viiv     v  i v  ii  i  i      -  ii i i   ii v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGA 296

  chrX_57601166_5   1017 TCATAGAAAGAGAAGAGAGAGCCCAGGAACAAACCCACATATTTACAGTC 1066
                            vv i  v    vv     i    i  i       i i     ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_57601166_5   1067 AGTTAATTTTTAATGAAGCTACCAATATCACACAATGGAGAAA--ATAGT 1114
                          i  i     ii ii i v i    v i  iv      i    --     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_57601166_5   1115 CTCTTCAATAAATTGTGTTGGAAAAACTGGATGTCCACATGCAGAAGTAT 1164
                           i     i    v   i   i v        i?         i   v  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_57601166_5   1165 AAAATTGGAAACTTGTCTCACATCATATAGAAAAACCAGCTCAAAATGGA 1214
                         i  i     vv i ii      i      v     ii i           
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_57601166_5   1215 GTAAATACTTAAACATAAGATTTGAAATGGTAAAAAACTACTAGGAGAAA 1264
                         vi ? v  i    ii     vi i   i--  v      vi   i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAAC--TATAAAACTCTTAGAAGAAA 544

  chrX_57601166_5   1265 ACATAGGAAAAAACCC-CATGATATTGGTCTAGGCAATAACTTTTT-TAT 1312
                                ?iv   i i- i   iv    vi        iii  i  -v  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_57601166_5   1313 ATGACCCCAAAAGCATAGACAACAAAAGAAAAA-TAGACACATAGAATTA 1361
                              v         i ii              -    i v  v i i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_57601166_5   1362 TGTCACTATACAAAGCTTCTGCACAGCAAAGGAAATAATGAACAAAGTTA 1411
                         ii   vv  vv   i   i  ii vv       v iv  v  v     v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_57601166_5   1412 AAAGACAACTCAGAGAATGAGAAAACATATTTGCAAACTATACATCCAAC 1461
                                  i  v      i  i  v           ii   i   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_57601166_5   1462 AATGAGTTATTT-TATCCAGAATGCATAAAAAACTTTGAT-------TAG 1503
                           - i -- i  -          ii     i    i v i-------  i
  L1M4_orf2#LINE/    745 AA-GGG--ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_57601166_5   1504 CAAGAAAGTAATTGACTAAATC-----ATAGACAAAAGACTTGAATACA- 1547
                         i  i  iii  v i  iv   i-----  i i    i  i       v -
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_57601166_5   1548 ACTTTTTTAAA--AGACAAGCAAATGTCCAACAGACATATTAATAAATGC 1595
                          i  i ii   --   i vi      v    i ii  i  v  v i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_57601166_5   1596 TCAGAATTACTAATTAC 1612
                            iv  i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (156 / 81)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.88 (32 / 17)  


 245 22.37 0.00 3.95  chrX_57604250_57606130      434   509 (1372)  C L1M4_orf2#LINE/L1   (0)   908   836 *

C chrX_57604250_5    509 ATAAACATGGCTCCATAAAAGAAGACATTTATGCAATCAAAAGACACATG 460
                            i    vv     ---       i  vi viiiii   v ii      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCA---AAGAAGATATACAAATGGCCAATAAGCACATG 882

C chrX_57604250_5    459 AAAAAATGCTCATCATCACTGGCCAT 434
                             i       v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.01 (1 / 73), avg. gap size = 3.00 (3 / 1)  

2299 30.37 1.91 1.12  chrX_57604250_57606130      500  1388 (493)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_57604250_5    500 CCATGTTTATATATTGAAAGATTCAATATAGCTA-GTTGCTAGGTTTTCC 548
                                i  iv    i    i i     v i  - v  vi ivvi i  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_57604250_5    549 CACTTTATTTTATAG--TGAACAAAATTTCAATCAAAATTC-AGCAAGGT 595
                           vv  iv i  i  -- v   iv   ii v        i -   vivv 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_57604250_5    596 ATTTTGTAGATGTTATCAGACTTATTCTAAAGTTTGTAGGGAAACGTCAA 645
                         v     i   vi  iv  ii  v  i     i  ii  v     i iv i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_57604250_5    646 AGACCTAGA-CAGTCAACAGAATACT--AAAGGAAGC-CTAATTTAGAAG 691
                         i    i   -i  i   v v   vi --   i    v- v  v  i  i 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_57604250_5    692 ACTCAAGCTTCTCAACTTCTAGAATTACTATAAAACTAAAGTAATTAACA 741
                              vi    i   i   v i v      i   i   v      i  v 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_57604250_5    742 AACTGTGGTATTGGTG-AAGGAGTAAATACATAGATCCATGGAACATAAT 790
                         v v       i   ii-     -  i i i       v      i v   
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAAT 311

  chrX_57604250_5    791 ACAGAGCTCAGATATACATGTGGACTCACACGAGCAGGGTAAACCAATCT 840
                         vv    ii    v   ------i  i  i  ivvi v   v  iii  i 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATA------AACCCATACATTTATGGTCAATTGATTT 355

  chrX_57604250_5    841 ATGACAGAAAAGAAAAGAAAACTTAATAAAGAAAGAATAGTTTTTTCAAC 890
                         vi    iiiiv vv    vv i i   iii           i        
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_57604250_5    891 AAGTGGTGTTGAAAGAACTGGACATTCATGTTACAAAAAAATGAATTTCA 940
                           i     i  ii v       i ?i  ii -i     i      v  vi
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAATGAAGTTGG 454

  chrX_57604250_5    941 ACAGATACATTACAATGTTCACACAAATTATGTTAAAATAAATCATATAC 990
                           vvv   v i   vii vi   v      vv i     ii    ? v  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_57604250_5    991 TTAAATGTTAAATGC-AAAATTATAAAACTAC-AGAATACAA-ACAAGCA 1037
                         i       v i -  -    i         vi-    v v  - i i ?i
  L1M4_orf2#LINE/    505 CTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_57604250_5   1038 AAAATATGATTGGCCATAGGTTTGGTGATGAGTG-TTAGATACAACACTA 1086
                         v    v vvv  i  v i    v  ii   iv v-       ii    i 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_57604250_5   1087 AG-GTACATTTCAAGAAAGAAAAAAATTAATAAGTTGGACTTTACTGAAA 1135
                          i- i   vv-   v   ii       vi    i        i iii   
  L1M4_orf2#LINE/    604 AAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_57604250_5   1136 TTAAAAACATCTGCCCTGTGGAAGTCATTGTTAGCAGGATGAAAAGACAA 1185
                                 v i  iv  viii i v  i i i iv iii           
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_57604250_5   1186 GGCACAGACTAGGAGAAAATATTTATAAAAGACTTACCTGATAAAGGACT 1235
                         vv      v i             ii   vv iv  i       i     
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_57604250_5   1236 TGTGGGCAAAATATACAAATAACTCTTGAAACTCAACAATAAGAAAATAC 1285
                            ivv  i      i   v       iv       i     i  i i v
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_57604250_5   1286 ACAATGCAAATAATAACTTGGCAAAAGACTCAAATAGGCACCTCACCAAG 1335
                          i  iv   v ? v  v v      i  i ii     i  ii  v    i
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_57604250_5   1336 AAATGTATACAGATTTCCAATAAGCA---GAAATGAAGTTCAATATTATT 1382
                         i  vi      i  vv          ---    v  v i    i  i ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_57604250_5   1383 TGTCTT 1388
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.51 (160 / 106)
Gap_init rate = 0.02 (18 / 896), avg. gap size = 1.50 (27 / 18)  


3224 27.75 0.11 0.11  chrX_57617484_57623858     4975  5882 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57617484_5   4975 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5024
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57617484_5   5025 GGCCATACTGCCCAAGGTAAATTATAGATTCAATGCCATCCCCATCAAGC 5074
                            v     v     iv i vi  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57617484_5   5075 TACCAA-TGCCTTTCTTCACAGAATTGGAGAAAACTACTTTAAAGTTCAT 5123
                          v   i-       i  -i     v v  v  iviv iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_57617484_5   5124 ATGGAACCAAAAAGGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGA 5173
                               viiv  i   v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_57617484_5   5174 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5223
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_57617484_5   5224 ATAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGATCA 5273
                          i     i   i     i         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_57617484_5   5274 ATGGAACAGAACGGAGCCCTCAGAAATAACGCCACATATCTACAACTATC 5323
                               i    iv   vvii         vv   i i  i  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_57617484_5   5324 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5373
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_57617484_5   5374 TTTAATAAATGGTGCTGGGAAAACTGGCCAAACATATGTAGAAAGCTGAA 5423
                           i  i              v      vi ?v  i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_57617484_5   5424 ACTGGATCCCTTCCTTACACCTCATACAAAAATTAATTCATTACGGATTA 5473
                         ii    i    v   i     vi             i   vv i    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_57617484_5   5474 AAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5523
                         ?    i    i  v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_57617484_5   5524 GGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTACAAC 5573
                           ?i v viv   iv   v v  vv i     v ii   v ivv  ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_57617484_5   5574 ACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGGATCTAATTA 5623
                                   vvi          vv     v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_57617484_5   5624 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGG 5673
                           v v  i i   i  ii vv    i  v    i  vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_57617484_5   5674 CATCCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAGG 5723
                           v  i   i             v  ii   vii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_57617484_5   5724 GCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAA 5773
                         i  vi          v  i  v      vv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_57617484_5   5774 CAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCA 5823
                             i     v  i?    i           iv    i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_57617484_5   5824 AAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATC 5873
                                 i  vi viii     v  i          i       v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_57617484_5   5874 ACTGGCCAT 5882
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.38 (144 / 104)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 1.00 (2 / 2)  


1310 30.62 3.54 2.08  chrX_57629828_57633284.rev     1752  2231 (1226)    L1M4_orf2#LINE/L1        1   487 (421)  

  chrX_57629828_5   1752 TAGAACAGCATTTCATATTCATGGAT-AAAAGTATGCAATATTGTTACAA 1800
                          i   viii  ii   i         -ii   - ivi          vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGA 49

  chrX_57629828_5   1801 TGGCCATACTACCCA------TTTACAGAATCAGTGCTATTCCCTTTAAA 1844
                             v     v    ------ i      v   ii  v  i  iv i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_57629828_5   1845 CTTCCATTGACATTCTTCACAGAA-TTAGCGAAACCTATTTTAAATTTTA 1893
                         v i   vivi v  i  ii     -  ii -  i iv  ii    v  i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCA 148

  chrX_57629828_5   1894 TATGGGAAAAAAAAGAGCCTA-AGTTGCCA------TTCTAAACAAAAAC 1936
                              i  viv  i ii  i - i v    ------ ii i  v  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_57629828_5   1937 AACAAAGCTGGAGGCATCAC-TTTGTTGATACCTGATTTCAAACTATATT 1985
                                i      vv    -i  -------  ii        viv  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTT-------CCCAATTTCAAAACTTACT 241

  chrX_57629828_5   1986 AAACAGCTACAATAACCAAAACAGCATGGCACTGGTACAAGAACAAATAA 2035
                          v v       i   i   i    ii   i     i i   i i i i v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_57629828_5   2036 ATAGACCACTGGAACAGAATAGAGAACTGAGATTTAAGTCTGCATACCTA 2085
                              i  v     i     v    iiiv   vv   ii iii i ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_57629828_5   2086 TAAACATCTGATCTTCAACAAATCTGATAAAAACAAGCAATGAGGAAAGG 2135
                          iiv  vi    i   i    ivv  vi  i v  vv     i      i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_57629828_5   2136 ATACCCTATTTAATAAATGGTGCTGGGAAAACTGTATAGCGATATGCAGA 2185
                            vi  v  i  i              v     v   ? v i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_57629828_5   2186 AAATTGAAACAGGACCCGTTACTTAAAACT-TATACAAGAACTGGCT 2231
                          i v    iiv      -i   i v v  i-       i  i ii  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACT 487

Transitions / transversions = 2.04 (98 / 48)
Gap_init rate = 0.02 (11 / 487), avg. gap size = 2.45 (27 / 11)  

1091 28.33 3.57 0.24  chrX_57629828_57633284.rev     2547  2966 (491)    L1M4_orf2#LINE/L1      475   908 (0)  

  chrX_57629828_5   2547 ACAAGAACTGCCTCAAGATGGATTAAAGATTTAAATATAAAACCCAGAAC 2596
                             i  i iv     i      i ?   ii     i   i v i i   
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_57629828_5   2597 TATAAAAACCCTAGAAGAAAACCGAGGCA-ATACCATTCAGGACATAGGC 2645
                                vi i           vv   ?i- v i -   iv   v v  v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

  chrX_57629828_5   2646 ATGGGCAAAGATTTCATGGCAAAGGTATCTAAAGCAATTTCATCAAAAGC 2695
                         v i     v i    v i vv v ii i v      vvvv  v      v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_57629828_5   2696 AAACATTGACAAATGGGATATGATTAAACTAAAGAGCTTCTGCACAGCAA 2745
                            v  v  i    v   iv v  i   v v  i i   i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_57629828_5   2746 AAGAAACTATCAAGAGAGTAAGCAGAC---CTACAGAATAGGAGAAAATT 2792
                          i  v          i   i iv    --- i       i         v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_57629828_5   2793 TCTGCAATCTATGCATCTGACAAATGTCTAATATCTAGCATCTATAAGAA 2842
                          i     vii  ii      i  iv v  vi    i  v  v     ii 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_57629828_5   2843 ACT--TA-AATTTA-CAATAAATA---AAACAACCCCATTAAAAAGTGCA 2885
                            --  -  i i -i      v ---   i     v   ?    i  vi
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_57629828_5   2886 CAAAGAACATAAACAGATACGTCTC-AAAAAA---ATTCACGTGGCCAAC 2931
                              i iv i  i   i iv    -   i  ---  v  vi       i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_57629828_5   2932 AAACATATAAAACAAAGCTCAACATCACTGATTGT 2966
                           i  i  i   vi v           ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (66 / 50)
Gap_init rate = 0.02 (9 / 434), avg. gap size = 1.78 (16 / 9)  


2976 26.49 1.24 0.45  chrX_57653646_57659466     4442  5328 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_57653646_5   4442 ATGCTCATGGATAGGAAGAATCAATATCATGAAAATGGCCATACTGCCCA 4491
                            i        v      v i     ii v  i     v     v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_57653646_5   4492 AAGTAATTTGTAGAATCAATACTATCCCCATCAAGCTACCA-CTGACTTT 4540
                           v i  i ii   v    ii v     i     iv v   -   v    
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_57653646_5   4541 CTTGTCAGAACTGGAAATAACT-ACTTTAAATTTCATATGGAACCAAAAA 4589
                         i   -     v v  v - i  - iii    v           viiv  i
  L1M4_orf2#LINE/    115 TTTG-CAGAAATTGACA-AGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_57653646_5   4590 AGAGCCTGCATAGTCAAGACAATCCTAAGCAAGAAGAACAAAGCTGGAGG 4639
                         i  v  v v    i   i      i i iv             i      
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_57653646_5   4640 CATCACACTACCTGACTTCAAACTACACTACAAGGCTGCAGTAATCAAAA 4689
                         vv       v  ii i      vivi       i   i          i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_57653646_5   4690 TATCATGGTAGTGGTACAAAAACAGATACAAAGACCAATGGAACAGAACA 4739
                         i vii     v   i i  ii i   i i v   i        i    iv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_57653646_5   4740 GAG-GTCTCAGAAATAACACCACACATTTACAACTATCTGATCTTAGACA 4788
                            -   -         vv   i       iiiii vi    i  v    
  L1M4_orf2#LINE/    313 GAGAGTC-CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_57653646_5   4789 AACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATTG 4838
                          ivv  v   i v  vv            i  vvi  v  i  i    v 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_57653646_5   4839 TTCTGGAAAAACTGGCTAGCCATATGCAGAAAGCTGAAACTGGGTTCCTT 4888
                          v    i v      v  ?   i     i  iiv    ii   iii   v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_57653646_5   4889 CCTTACACCTTATACAAAAATGAACTAAAGATGGATTAAAGACTTAAATG 4938
                            i     v           v    v  i      i ?    i      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_57653646_5   4939 TAAGACCTAAAATCATAGAAACTCT-GGAAGAAAACCTAGGCAATACTAT 4987
                              v      ii   -       -i         v    ?ivv v v 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_57653646_5   4988 TCAGGACATAGGCATGGGCAAAGTCTTCATGACTAAAACAACAAAAGCAA 5037
                           iv   v v  vv i     v vi   v iiv  vi   v        v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_57653646_5   5038 TTGCAACAAAAGCCAAAATAGACAAATGGGATCTAATTAAACTAAAGAGC 5087
                         vv          vv        i    v   ii v  i   v v  i i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_57653646_5   5088 TTCTGCACAGCAAATGAAACTATCAGCAGAAGGAACAGGCAACCTATAGA 5137
                           i  ii vv    v  v       iv i iv   v  i     i i   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_57653646_5   5138 TTGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCCA 5187
                         v           v       vii  vi      i  i  i  vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_57653646_5   5188 GAATCTACAATGAAAT--TA-AACACATTCACAAGAAAAAAAA-AA---A 5230
                             v  i  v   v --  -   v  v v i  i  i v   -  --- 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_57653646_5   5231 ATCAAAAAATGGGTGAAGGTTATGAACAGACACTTCTCAAAAGAAGACAT 5280
                           i?         ii    v v    i     i     v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_57653646_5   5281 TTATGCAGCCAATAAACTTATGAAAAAATGCTCATCTTCACTGGTCAT 5328
                         vi viii        i vi       i       v v   ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (126 / 105)
Gap_init rate = 0.01 (12 / 894), avg. gap size = 1.25 (15 / 12)  


1780 30.72 3.93 0.56  chrX_57668098_57669802      500  1212 (493)    L1M4_orf2#LINE/L1      172   908 (0)  

  chrX_57668098_5    500 ATAGGTAAACCAATTATGCTCAAAAAGAATGAATCTGGATGCATCACACT 549
                             vi   v    iv  vvv  i     ii  vi    v vv       
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_57668098_5    550 TTTCAATTTCAAACTATATTACAAAGCTATAGAAATCACGACAGTATAGT 599
                          ii          viv  i          i  v     v      i i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_57668098_5    600 ACTGGTATAAAAACAGGCACATAGGCCAATAGATCAGAAT--ACAGTGTG 647
                              i    ii i  i  i    ii    i  vi     -- v   vii
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_57668098_5    648 GAAACA------------TGTGATAAGCTATTCTTTGACAAGACCACCGA 685
                             i ------------ i  i v ii iv i  i      ivii  i 
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_57668098_5    686 TAATATATAATGGGTAAATGATATTTTCTTTAATAAATGGTGGTGAGA-A 734
                         v vi  vi      v   vi   v i i  i  i        v  i  - 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_57668098_5    735 ACATGACA-CCACGTGCAAATGAATGAAATTGAACAGTTTTTATACACTA 783
                           vv  i -    i      v       i   i  vvi viivi    i 
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_57668098_5    784 TATACAAAAATCAATTTAAA-TGTGTTA---ACTTAAAAAAAAGACTTGA 829
                                    i  i i   -  vi i ---  i    viv    vi i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_57668098_5    830 AACAATAAAACTTGTTAAAAATAACTTACAAGAAAACCTCTTTGTCATTG 879
                            v        iv vi  i v   v  vi? v   i  iiv  v v   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chrX_57668098_5    880 GTCTCAGCAATGATTTTTACAAATTTAACACTGAAAGCAGAGGCAA--AA 927
                          vi vi      i   i -i i  v i    ii      v i    --  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCT-TAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_57668098_5    928 AGAACCAAATAAGAAAATGGGGCCACTTCAAACTAGTACGTGTCTGCACA 977
                             v-     iiv    v  i iv v     v viv viiv i  ii v
  L1M4_orf2#LINE/    621 AGAAA-AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_57668098_5    978 GCAAAAGAAACTGTCAACATAATGAAAAGACAATTTAAAGACTAGAGAAA 1027
                         v    i  v   i    v v i           iii v   v i iii  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_57668098_5   1028 AATACTTGTAAAGCACATATCTGATAATGGG-TAATATGTAATATATATA 1076
                             i   i   v  i           v  i- vi   vi iv       
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_57668098_5   1077 TGTAGCTCATACTGGCAAAAAAGAACAAAATTAAAATAACTTGATTTTAA 1126
                         viv i   v   viviv  v  v  v  i i--       iii   ?v  
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGAC--AAATAACCCAATTWAAA 817

  chrX_57668098_5   1127 AATGTGCAAAGGACATAAATAAGC--TTTTCCAAAGG---CATACAAATG 1171
                             v        iv i    ii --  i       i---i         
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_57668098_5   1172 GCTGACAGGTATATGAAAAGGTGCTCAACATTACTAATCAT 1212
                           ii i i i i        i          i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (131 / 86)
Gap_init rate = 0.02 (13 / 737), avg. gap size = 2.46 (32 / 13)  


 415 25.71 0.00 0.00  chrX_57705684_57707878.rev      541   645 (1550)    L1M4_orf2#LINE/L1        1   105 (803)  

  chrX_57705684_5    541 TGGAAAGATATTTTATTTTCCTGTGTAAGAAGATGAAGTAATGTTAAGAT 590
                                    iii  v   v  vi vi     ivv i  v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57705684_5    591 GCTAATACTATTCACAGTGATCTATAGATTCAACACAATCACTATAAAAA 640
                          vi      vii  v v       i         i     v    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57705684_5    641 TTTCA 645
                          ii  
  L1M4_orf2#LINE/    101 TCCCA 105

Transitions / transversions = 1.08 (14 / 13)
Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.00 (0 / 0)  

2640 21.83 7.45 1.31  chrX_57705684_57707878.rev      942  1706 (489)    L1M4_orf2#LINE/L1       97   908 (0)  

  chrX_57705684_5    942 AAAATTTCAAAAGTATTTTTTCCA-AAAT--ACAGTAGC-AATTTTTACA 987
                              ii  ivv iv      v  -    --   --   -i  ii v v 
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA--AGCTGATCCTAAAA 144

  chrX_57705684_5    988 TTCATGTTAAGTTGCAACAGTCCCAAATTA-TCAAAACAATTTTGAAAAA 1036
                              i vi iv     vi v    i v  -i         i        
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_57705684_5   1037 -AAG--TAAA--TGCAGATTATCCACATTTACCAATTTTTAAACTTACTA 1081
                         -   --i   --  v  i-- ii    i  v       iv          
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGG--ACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_57705684_5   1082 CAA-GCAACGGTAATCAAAACATTGCAGGACTCTTATAAAGATAGACATG 1130
                            -  v  i        i   v  ii v   vvi    i         i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_57705684_5   1131 CAAATCCATGGAATAGAATTGAGAGTTCAGATATAAACTCAACCATTAAT 1180
                         i i   v                   i    v      i  vv    v  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_57705684_5   1181 GGCTGATTGGTGTTTGACAAGGGTGTCCAGTAACC--TCAATGGGAAAAA 1228
                           iii    i v  i          i v  --   --        i   i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAG--ACCATTCAATGGGGAAAG 390

  chrX_57705684_5   1229 AATGGTCTCTTCAAAAAATAGTGCTGGGATAGATTAATATTCATATGCAA 1278
                            i    i     v    i         i iv vi   ?i  i      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_57705684_5   1279 AACAA---ATTTGGACCCCCACATTACACCATATA--AAAATTAACTTAA 1323
                           v  --- v         i  v i          --          i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_57705684_5   1324 A--------------------------------CCATGATACATTTAGAA 1341
                          -------------------------------- i  i v  vi      
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_57705684_5   1342 GAACACTTACAGGTAAGTCTTCCTGACCTTGGATTTGGCGATGGACTC-- 1389
                            v  v  vi?    i     v         i  v   i    vi  --
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_57705684_5   1390 --GTTTGCACTCCAAAACCAAAAAGAGTGGAAGAAAAAAAAATAGATAAA 1437
                         --i v  -  v      v  v  iv ii--- i  i              
  L1M4_orf2#LINE/    591 AGATATG-ACACCAAAAGCACAAGCAAC---AAAAGAAAAAATAGATAAA 636

  chrX_57705684_5   1438 TTGAACTTCATTGACATTGAAAACTTTTGTGCCTTAAAGGACATTATCAA 1487
                            i       ii v   i             i i        i      
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_57705684_5   1488 GAAGGTTAAAA-ACAACCTACCAAATTGGACAAAATATTTGCACAACTTA 1536
                            i  v    -      i  vi   v   v            v v v  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_57705684_5   1537 TACCTGATAAGAGTTTGATAGGCAGTAAAAATAAAGAACTTCCAAAA-TA 1585
                           i        i vi vi  vv   v v v          iii v  - v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_57705684_5   1586 AACCACAAATAGACAAATAACTCAATTTAAAAATTG-CATGGGACTTGTT 1634
                           iv i   v           i     ?      v -  vi   i   vv
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_57705684_5   1635 TAGACATATCCGCAAAGAAGATATACAAATTGCCAATAAGTTCAAAAAAA 1684
                                v  iv                  v         iv  vi    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_57705684_5   1685 GATGCTCAAAATAATAAGTTAT 1706
                                  v  v ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (89 / 75)
Gap_init rate = 0.03 (21 / 812), avg. gap size = 3.19 (67 / 21)  


2987 27.56 0.88 0.77  chrX_57714741_57726523.rev     5150  6056 (5727)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57714741_5   5150 TGGAAGAACATTACATGCTCAGGGATAGGAAGAATCAATATTGTGAAAAT 5199
                              ii i  iv    i   v    v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57714741_5   5200 GACCATACTGCCAAAGGTAGTTTATAGATTTAATGACATACCCATCAAGC 5249
                          i v     v  v  iv ii i  i     i  i vv  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57714741_5   5250 TACCA--TGAGTTTCTTCACAGAA-TTGGGGAAAACT-ACTTTAAAGTTC 5295
                          v   --  vv   i  -i     -   iv--  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGAC--AAGCTGATCCTAAAATTC 147

  chrX_57714741_5   5296 ATAGGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAA 5345
                            v    viiv  ii  v  v v  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_57714741_5   5346 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5395
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_57714741_5   5396 CTACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATGGAC 5445
                                  i   i    ii       v i iv ii i   v    i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_57714741_5   5446 CAATGGAAAAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5493
                                 v    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_57714741_5   5494 CATCTGATCTTTGACAAATTTGACAAAAACAAGCAATGAGGAAAGGATTC 5543
                           vi    i  i     ivv  v   i v  vv     i      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_57714741_5   5544 CCTATTTAATAAATGGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5593
                         i  v  i  i      -        v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGG-TGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_57714741_5   5594 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATG 5643
                         v    ii    i    v   i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_57714741_5   5644 GATTAAAGACTTAAATCTTAGACCTAAAACCATAAAACCCATAGAAGAAA 5693
                            i ?    i     v v   v       i       i v         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_57714741_5   5694 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTTATGAC 5742
                           v    ?i- v i -   iv   v v  vv i     v ii  iv iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_57714741_5   5743 TAAAACAACAAAACCAATGGCAACAAAAGCCAAAATAGACAAATGGGATC 5792
                           vi   v     v  vvi          vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_57714741_5   5793 TAATTAAACTAAAGTGTTTCTACACAGCAAAAAA-ACTGCCATCAGAGTG 5841
                          v  i   v v  ivii  i iii vv    ii -   ii  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_57714741_5   5842 AACTGGCAACCTGTGGAATGGGAGAAAATTTTTACAATCTACCCATCTGA 5891
                           vv i     iiii              v   i   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_57714741_5   5892 TAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 5941
                            i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_57714741_5   5942 AAAAATCAAACAACCCCATCAAAAAGTGAGTGAAGGATGTGAACAGACAT 5991
                             iv    i     v  i?    i  i ii      v    i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_57714741_5   5992 TTCTCAAAAGAAGACATTTACACCACCAACAGACACATGAAAAAATGCTC 6041
                              v        i  vi v ivi    i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_57714741_5   6042 ATCATCACTGGCCAT 6056
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  

3025 27.13 1.44 0.89  chrX_57714741_57726523.rev    10390 11292 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57714741_5  10390 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 10439
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57714741_5  10440 GGCCATATGGCCCAAGGTAATCTATAGATTCAACGCCATCCCCATCACGC 10489
                            v   ivv     iv i     i           v     i    viv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57714741_5  10490 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTCA 10537
                          v   iivi i  i  ii     -   -- v  i  - iii i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_57714741_5  10538 TATGGAACCTAAAAAGAGCCCACATT-GCCCAGTCAATCCTAAGCCAAAA 10586
                                v- iv  i ii    v v -   v iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_57714741_5  10587 GAACAAAGCCAGAGGCATCACGCTACCTGACTTCAAACTATACTGCAAGG 10636
                                 iii    vv    i  v  ii i      viv    i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_57714741_5  10637 CTACAGTAACCAAAACAGCAAGGTACTGGTATCAAAACAGAGATATAGAT 10686
                                  i   i    iiv        i  v ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_57714741_5  10687 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 10734
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_57714741_5  10735 TATCTGATCTTTTACAAACCTGACAAAAACAAGCAATGAGGAAAGGAT-- 10782
                         i vi    i  iv    ivv  v   i v  vv     i      i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_57714741_5  10783 TCCATATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 10832
                           -- v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_57714741_5  10833 GCTGAAACTGGATCCGTTCCTTACACCTTATACAAAAATTAATTCAAGAT 10882
                         iv    ii    i  v v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_57714741_5  10883 GGATTAAAGACTTAAATCTTAGACCTAAAACCATAAAAACCCTAGAAGAA 10932
                             i ?    i     v v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_57714741_5  10933 ATCCTAGGCA-ATACCACTCAGGACATAGGCATGGGCAA-GACTTCATGT 10980
                          v v    ?i- v i -i  iv   v v  vv i     - ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_57714741_5  10981 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 11030
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_57714741_5  11031 CTAATTAAACTAAAGAGCTTCTGCAGAGCAAAAGAAACCACCATCAGAGT 11080
                         i v  i   v v  i i   i  iivvv    i  v  i i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_57714741_5  11081 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTG 11130
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_57714741_5  11131 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAG 11180
                          i  i  i  vi          v  i  v      iv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_57714741_5  11181 AAAAAAACAA----CCCCATCAAAATGTGGGCGAAGGATATGAACAGACA 11226
                              i    ----   v  i?   vi     i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_57714741_5  11227 CTTCTCAAAAGAAGGCATTTATGCAGCCAACAGATACATGAAAAAATGCT 11276
                         i     v       ii  vi viii     i iii         i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_57714741_5  11277 CATCATCACTGGCCAT 11292
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


 565 27.40 8.22 1.37  chrX_57748279_57750441.rev      502   720 (1443)    L1M4_orf2#LINE/L1      264   497 (411)  

  chrX_57748279_5    502 AGCATAGTACTCATACAAAAATAGACACATACACTAATTAAACAGAATAC 551
                           ii i     vii i  ii       i   v ii   vi  i     vv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_57748279_5    552 AGA-CCCTGAAATAATGCTGTACACCT----TCAATT-ATCCTTAACAAA 595
                            -i  v       vv ii    ii ----      -  ii ii    i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_57748279_5    596 AA---CAAG--CAT-----GGGGGAAGGAC--TCTATTCAATAAAATAGT 633
                         ii---    --   -----    i   i i--   v     i   - i  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA-TGGT 412

  chrX_57748279_5    634 GCTAGGATAACTGGCAAGCAATATGCAGAAGATTGAAAGTGGACGAGTTC 683
                            i   i      vv ? v i     i    v    iv     vvv v 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_57748279_5    684 CTTACACCATGTAAAAAAAAATCAACTCAAGATGTAT 720
                           i       i  v     -- i       i   v  
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAA--TTAACTCAAAATGGAT 497

Transitions / transversions = 1.95 (39 / 20)
Gap_init rate = 0.04 (9 / 234), avg. gap size = 2.33 (21 / 9)  

1111 25.84 1.35 5.17  chrX_57748279_57750441.rev     1228  1672 (491)    L1M4_orf2#LINE/L1      481   908 (0)  

  chrX_57748279_5   1228 ATTAACCATCACAATGGATTAAAGACTTAAATGTAAAACCTAAAACTATA 1277
                               --   v       i ?    i         i v           
  L1M4_orf2#LINE/    481 ATTAAC--TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_57748279_5   1278 AAATCCCTCAAAGATAATCTAGAAAATACTATTCTGGACATAAGACTTGA 1327
                            ii i vi    v  iv   i?ivv v v   vv   v vi ii v i
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_57748279_5   1328 CAA--GTATTTTATGATGGAGATGCCAAAAGGAATTGCAACCATAATAAT 1375
                            --  v i   -   iv-  ii       ----------  i  --ii
  L1M4_orf2#LINE/    579 CAATGGTTTCTTA-GATAT-GACACCAAAAG----------CACAA--GC 614

  chrX_57748279_5   1376 AACAATAATAATAATAGTAATAAACAAATGGGACCTAAATCAGCTGAAGA 1425
                              -  v  -  ----    i i    v    i v viv iv v  i 
  L1M4_orf2#LINE/    615 AACAA-AAGAA-AA----AATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_57748279_5   1426 ACTTCTGCACAGCAAAAGAAACCATCAGCAGAGTAAACAGACAACCTACA 1475
                             i  ii vv    i  v  i    iv i   i  v        i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_57748279_5   1476 GAGTGGGAGAAAATATTTGCAAGCTATGCATCTGACAAAGGTCTAATATC 1525
                           i                   iii  ii      i  i  v  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_57748279_5   1526 CAGAATCTACAAAGAACTTAAACAGATTTACAAGCAATGAAACAATTAT- 1574
                               v  i        ivv   - i i vv ii  vi i    v  v-
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACA-ACTCAATAATAAAAAGACAAATAAC 807

  chrX_57748279_5   1575 ---ATTAAAAGATGGGCAAAGGACATGAACAGACACTTCCTAAAATAAGA 1621
                         ---   ?   i            iv    i     i   iiv   v    
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_57748279_5   1622 CATACTCGCAGCCAACAAGTATGTGAAAACATTCTCAACATCACTATTTG 1671
                         i    vviii     i   i ii      v  v          ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_57748279_5   1672 T 1672
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.49 (67 / 45)
Gap_init rate = 0.03 (11 / 428), avg. gap size = 2.64 (29 / 11)  


2969 27.41 0.77 1.21  chrX_57750741_57757439     5295  6206 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57750741_5   5295 TGGAAAAACATTCCATTCTCATGGATAGAAAGAATCAATATTATAAAAAC 5344
                               i i  i    vi        v i    v i      i v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57750741_5   5345 GGCCACACTGCCCAAGATAGTTTACAGATTCAATGCTATCCCCATCAAGC 5394
                            v i   v     iv ii i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57750741_5   5395 TACCATTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTCA 5443
                          v   vivi i  i  ii     v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_57750741_5   5444 TATGGAACTAAAATA-AAAAAACCCTGTATAGCCAAGACAATCCTAAGCA 5492
                                -----  i-  iii    v v        i      i i iv 
  L1M4_orf2#LINE/    149 TATGGAA-----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_57750741_5   5493 AAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTAC 5542
                          i          i      vv    i  v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_57750741_5   5543 AAGGTTACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGATATAT 5592
                           i i        i   i    ii i       i iv ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_57750741_5   5593 AGACTAATGGAACAGAAC--AAAGCCCAAAGAAATAACACCACACATCTA 5640
                            ii       i    i-- i  i   --       vv   i    i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCA--GAAATAAACCCATACATTTA 341

  chrX_57750741_5   5641 CAACCATCTGATCTTTGGAAAACCTGACAAAAACAAGCAATGGGGAAAGG 5690
                         iiii  vi    i  i iv  ivv  v   i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_57750741_5   5691 ATTTCCTATTTAATAAATGCTGTTGGAA-AACTGGCTAGCCATGTGAAGA 5739
                           vvi  v  i  i     v  i   i -      v  ?   ii  v i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_57750741_5   5740 AAACTGAAACTGGACCCTTTCGTTATGCCTTATACAAAAATTAACTCAAG 5789
                          i v    ii       i v v i ii  v                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_57750741_5   5790 ATAGATTA-AAACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAG 5838
                           i   i - i  i           v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_57750741_5   5839 AAAATTTAGGCAATACTATTCAGGACATAGGCATGGGCAAAGACTT-TGA 5887
                             iv    ?ivv v v   iv   v v  vv i     v ii  - v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_57750741_5   5888 GAGTAAAACACCAATAGCAGTGGCAACAAAAGCCAAAATCGACACATGGG 5937
                           -  vi       v    vvi          vv     v  i v  v  
  L1M4_orf2#LINE/    592 GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_57750741_5   5938 ATGTAATTAAACCAAAGAGCTTCTGCATAGTAAAAGAAACTATCATCAGA 5987
                          iv v  i   viv  i i   i  iiivvi   i  v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_57750741_5   5988 GTGAACAGGCAACCTACAGAATGGAAGAAAATTTTTGCAATCTATCCATC 6037
                              v  i     i         i       v       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_57750741_5   6038 TGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAGCAAATATACA 6087
                            i  i  i  vi          v  i        ivvi   v vv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_57750741_5   6088 AGAAAAAAACAAAGAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGA 6137
                          v     i     v     v  i?    i    ii      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_57750741_5   6138 TACTTCTCAAAAGAAGACATCTATCCACCCAATAAATATATGAAAAAAAA 6187
                         i i     v        i  vi vviiv       ii i       i v-
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT- 889

  chrX_57750741_5   6188 GCTCATCATCACTGGTCAT 6206
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


 760 25.11 3.08 2.20  chrX_57764509_57772003       93   319 (7176)    L1M4_orf2#LINE/L1        4   232 (676)  

  chrX_57764509_5     93 AAAAACACTTCATGCTCATGAATAGGAAGACTCAATATCATGAGAATGGC 142
                            i i iii    i     i  v        i     ii v ii     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_57764509_5    143 CACACTGCCCAAAACAGTTTACAGATTCAACGCTATTCCTATCAAATTAC 192
                         v i   v      viii i              v  i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_57764509_5    193 CAATGACATTTTT---AGACAATTAGACAAAATTATTCTAAAATTAATAT 239
                           iivi v     ---   -    -     iv v  i        v    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGA-AATT-GACAAGCTGATCCTAAAATTCATAT 151

  chrX_57764509_5    240 --AAATACCATAAGAGTCTTA--ATAGCCAAAGCAATCCTAAGCAAAAAG 285
                         --    i ---   i v ii --         i     i i iv  i   
  L1M4_orf2#LINE/    152 GGAAATGC---AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_57764509_5    286 AACAAAGTCTGAGGCATCACACTATCTGACTTTA 319
                                 iv    vv       vi ii i  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

Transitions / transversions = 2.00 (38 / 19)
Gap_init rate = 0.03 (6 / 229), avg. gap size = 2.00 (12 / 6)  

2584 29.00 0.64 3.11  chrX_57764509_57772003     4425  5355 (2140)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57764509_5   4425 TGGAAAAACATTTCATGTTCATGGATAAGAAGAATCAATATTGTGAAAAT 4474
                               i i  ii             vi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57764509_5   4475 GGCCATATTGCTGAAAGTAATTTATAAATTCAATGCTATCCCCATCAAGC 4524
                            v   i v iv   v i  i  i i      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57764509_5   4525 TACCATTTACTTTCTTCACAGAATTTGAAGAAACT-ACTTTAAATTTCAT 4573
                          v   vi i i  i  ii     v    v-  i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_57764509_5   4574 AAGGAACCACACACACACACACACACACACACACACAAAACCCATA-TAG 4622
                          v    ------------------------ ii  viii     v -   
  L1M4_orf2#LINE/    150 ATGGAA------------------------ATGCAAGGGACCCAGAATAG 175

  chrX_57764509_5   4623 CCAGGAGAATCCTAAGCAAAAAGAACAAAGCTGGACACATCATGCCACCT 4672
                            ii v    i i iv  i          i    vivv   ii iv  i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_57764509_5   4673 GACTTCAAACTATACTACCTGGTTACAGTAACCAAAAAAGCATGGTACTG 4722
                         i i      viv      vvi i        i   i v  ii        
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_57764509_5   4723 GTACCAAAACAGATATATAGACCAATGGAACAGAACAGAGGCCTCAGAAA 4772
                          i iv ii i   i       i        i    iv   ivii      
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_57764509_5   4773 TAACGCCACACATCTACAACCATCTGATCTTTGACAAACCTGACAAAAAC 4822
                            vv   i    i  iiii  vi    i  i     ivv  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_57764509_5   4823 AAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGTTGAGAAAACTG 4872
                          vv            i  vvi  v  i  i        i  i  v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_57764509_5   4873 GCCAGCCATATGCAGAAAACTGAAACTGGACCCATTTCTTGCACTTTATA 4922
                          vi ?   i     i  i v    ii       v vi  ii   iv    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_57764509_5   4923 -AAAAATTAACTCAAGATGGATTAAAATCTTAAATATATGACCCAAA-CC 4970
                         -              i      i ? iv i     i  v  v i   - i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_57764509_5   4971 ATAAAAAAACCTAGAAGAAAACCTTGGCAGCACCATTCAGGACATAGGAA 5020
                               vv- i           v v  ?ivv viv   iv   v v  iv
  L1M4_orf2#LINE/    526 ATAAAACT-CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_57764509_5   5021 TTGGCAAAGACTTCATGACTAACACAGCAAAAGCAATGGCAACAAAAGCC 5070
                          v     v ii   v iiv  vv   v        vvi          vv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_57764509_5   5071 AAAATTGACACATGGTATCTAATTAAA-CTAAAGAGCTCTGCAAAGCAAA 5119
                              v  i v  v v ii v  i   -i    i vi i  iivvv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_57764509_5   5120 ATAAACTATCATTAGAGTGAAAATGCAAATTACAAAATGGAAGAAATTTT 5169
                         iv v       vv i        vi   vii   i     i     v v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_57764509_5   5170 TTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAATGTACAAGGAA 5219
                               vii  vi      i  i  i  vi          i  i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_57764509_5   5220 CTTAAACAAATTTACAAGAAAAAAAAAACGAACAATCCCATCAAAAAGTG 5269
                           ivv    v ---   v  v     i  i  i  i  v  i?    i  
  L1M4_orf2#LINE/    775 CTCTTACAACT---CAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_57764509_5   5270 GGTGAAATATATAAACAGACACTTCTCAGAAGAAGACATTCATGCAGCTG 5319
                           ii  iv  v i  i     i     vi       i  v  viii  ii
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_57764509_5   5320 AGAAACATATGAAAAAA-GCTCATCATCAGTGGTCAT 5355
                          v  i  i       i -     v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (158 / 108)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.50 (35 / 10)  

 892 26.20 3.83 2.24  chrX_57764509_57772003     6087  6399 (1096)    L1M4_orf2#LINE/L1      232   549 (359)  

  chrX_57764509_5   6087 AACACTATACTACAAGGCCACAGCA------------TGGTACTGGTACA 6124
                           v   -        i  i    i ------------         i i 
  L1M4_orf2#LINE/    232 AAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_57764509_5   6125 AAAACAGACAACATAGACCAATGGAACAAAATAGAGAACCCAGAAAGAAT 6174
                          ii i     -i     i        i i   v    ii       v  v
  L1M4_orf2#LINE/    281 AGGATAGACA-TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_57764509_5   6175 GCCACACACCTACCAACACCTGATTTTCAAGAAGTCTGACCAAAAAAAAA 6224
                         v   i   ii  iviv  vi        i v   vv  -    i ----v
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG-CCAAGA----C 374

  chrX_57764509_5   6225 AAAGCAATGGGGCAAGAACTGGCTATTCAATAAATGGTGTTGAAATAACG 6274
                         v vv        v     iv v  v     i        i  ii i   v
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_57764509_5   6275 GGCTAGCAATATCCAGAAGAAATAAACTGGACTCATATATTTCACCACGT 6324
                           v  ? v i  v  i     vv  ii     i v  iv iv     ii 
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_57764509_5   6325 ACAAAAATTAATGCAAAATGGATAAAATATTTAAATGTAAGACCAAGTAC 6374
                                    iv          v ? v ii           v v iv  
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_57764509_5   6375 TATAAAAATCCAAGAATAAAACCTA 6399
                                v  iv    v     v  
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATA 549

Transitions / transversions = 1.11 (42 / 38)
Gap_init rate = 0.02 (5 / 318), avg. gap size = 3.80 (19 / 5)  

 678 26.98 7.08 0.54  chrX_57764509_57772003     6636  7002 (493)    L1M4_orf2#LINE/L1      518   908 (0)  

  chrX_57764509_5   6636 CTAAAACT-TAAAG----TATAATAAAA---AAAAATAA--CCTCTCAAC 6675
                                 -    i----  v  v    --- ii?i   -- i  vii  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_57764509_5   6676 ATCAGCCTTGGCAAAGAATTTTTAGCTA--ATTCTCAAAAGTAATTGCAC 6723
                         v ii vi v     v iv  i    v  -- iv -      i vvv   v
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACAC-CAAAAGCACAAGCAA 616

  chrX_57764509_5   6724 CAAAACAAAAACT-GACATGTGAGATTTAATTAAACTAAAGAGCATTCA- 6771
                              v     v -  i vi vi  i  v  i   v v  i i v  ii-
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_57764509_5   6772 GC---AAAAGAAATAATCAACAGAGTAAACAGA-AA---ACAAAATGGGA 6814
                           ---   i  v iv     v i   i  v   -  ---   i       
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_57764509_5   6815 GAAAATACTTTCAAACTATGCATCTGAAGATGGACTAATATTCGGAATCT 6864
                                i  v    ii  ii      vi v     vi   i i    v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_57764509_5   6865 ATAAGGAACATAAACAAATCAACAAGCAAAAAAACAAC---CCCTTTTAA 6911
                             i    vivv    v    i  -i     i    v---   vv  ? 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWA 815

  chrX_57764509_5   6912 AAAATGGACAAAAGATATGAAAAGAAATTTCTCAAAAGTAGACATACAAG 6961
                                i    i   v    v   v       v    v   i      i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_57764509_5   6962 CAGCCAACAAACACA--AAAAAACGCTTATCATCATCAATCAT 7002
                         ii     i  i    --    i i   i v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (53 / 44)
Gap_init rate = 0.04 (14 / 391), avg. gap size = 2.00 (28 / 14)  


3203 26.96 0.77 0.44  chrX_57772149_57778509     4964  5868 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57772149_5   4964 TGGAAGAACATTCCATGGTCATGGATAGGAAGAATCAATATGGTGAAAAT 5013
                              ii i  i     v        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57772149_5   5014 GGCCATACTCTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAG- 5062
                            v      i    iv i  i  i        i  v     i     i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57772149_5   5063 TTACAAATGACTTTCTTCACAGAATTGGAAAAAACAACTTTAAAGTTCAT 5112
                          iv  iv  v    i  -i     v v  v  ivii iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_57772149_5   5113 ATGGAATCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGA 5162
                               viiv  ii  v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_57772149_5   5163 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAA--CTA-TACAAGGTT 5209
                               i      vv   ii  v  ii i      --i  -     i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_57772149_5   5210 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5259
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_57772149_5   5260 GTGGAACAGAAC--AGAGCCCTCAGAAATAATACCACCCATCTACAACCT 5307
                         i     i    i--    i  --        vv   iv   i  iiii v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_57772149_5   5308 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5357
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_57772149_5   5358 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5407
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_57772149_5   5408 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5457
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_57772149_5   5458 CAAAGACTTAAATATTAGACCTAAAACCATAAAACCCCTAGAAGAAAACC 5507
                           ?    i     i v   v       i       i i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_57772149_5   5508 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5556
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_57772149_5   5557 AACACCAAAAGCAATGGCAACAAAATCCAAAATTGACAAATGGGATCTAA 5606
                         i            vvi         vvv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_57772149_5   5607 TTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTATCCTCAGAATGAAC 5656
                          i   v v  i i   i  iiivv    i  v      vvv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_57772149_5   5657 AGGCAACCTACAGAATGGGAGAAAACTTTTGCAATCTACTCATCTGACAA 5706
                           i     i                iv       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_57772149_5   5707 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5756
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_57772149_5   5757 AAGGAAGCAACCCTATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5806
                          iiv  ii     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_57772149_5   5807 TCAAAAGAAGACATTTATGCAGCCAATAGACAGATGAAAAAATGCTCATC 5856
                           v        i  vi viii       ii  v       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_57772149_5   5857 ATCACTGGCCAT 5868
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2399 26.99 4.67 1.25  chrX_57787882_57789817      566  1443 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57787882_5    566 TGGAAAAACATTCCATGCTCATGAACTGGAAGAAGCAATATTATATAAAC 615
                               i i  i     i     i i       vvi      i vv i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57787882_5    616 GGCCAAAAAGCCCAAAGCAATGTACAGATTTGATGCTATTCCTATCAAAC 665
                            v v vvv      vii  v        ii i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57787882_5    666 TACAAACATAATTCTT---CAGAGAATTAGAAAAA--AA--CTAAAATAT 708
                          v v i - ivi i  ---    -    -  v  i--i --       vi
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGA-AATT-GACAAGCTGATCCTAAAATTC 147

  chrX_57787882_5    709 ATATGGAGCCAAAAAAAAGACCCA-AATAACCAAAGCAACCC-GAAGCAA 756
                                i-- viv  ii      -    i     i   i i-   --  
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--AA 193

  chrX_57787882_5    757 AAAAGAACAAAGGCGGAAGAATCACACTACTTGACTTCAAAAAATACTAT 806
                          i          vi   i  v       v iii i       vv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_57787882_5    807 AAAGCCGCATTAAGCAAAATAGCTTGGTACTG-TACAAAAGCAGACACAT 855
                              ii  v   v   i i  iv        -i i  iiii     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_57787882_5    856 AGACCAATAGAACAGAATATAAAACTCAGAAATAAAGCCATACACCAACA 905
                            i    i   i     vv i iii          v       iiv ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_57787882_5    906 ACCATCTGAACTTCAGCAACACTGACAAAAACAAGCAATGGGGAAAGAA- 954
                         ii  vi   vi   ii   viv  v   i v  vv              -
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_57787882_5    955 -GTCACTATTCAATAAATGGTGCTGGGATAGCTGGCTGGTGACATGCA-- 1001
                         -   -- v     i              i i    v i?iv       --
  L1M4_orf2#LINE/    394 AGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_57787882_5   1002 -GATCGATGCTGGACCCCTACCTTTCACCATATACAAAAA-------AAA 1043
                         -  vi  v i             iv               -------   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_57787882_5   1044 AT-----------TTAAACTTAAGATCTCAAACTATAAAAATCCTAGAAG 1082
                           -----------i    iv     v  v           v  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_57787882_5   1083 ACAACCTAGGAAATACTATTCTCAACATTGGCTTTGGCAA-AATTTTTTG 1131
                          v   v    ?ivv v v   vii  v    v  v     -ii   i  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_57787882_5   1132 GCTAAAACCTCAAAA--ATAATTGCAACAAAAACAAAAATAGACAAGTGG 1179
                          v  vi  vi     -- i  --         iv         i  i v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_57787882_5   1180 GATGTAATTAAACTAAAGAGCTTCTGCACAGCCAAAGAAAGTATCAATAG 1229
                           iv v  i   v v  i i   i  ii vv v  i  v v      v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_57787882_5   1230 AGCAAACAGACAATGTACATAATAGGAGGAGATATCTGCAAACTCTGCAT 1279
                           ii  v      ivi   v   i    i i    i      iiv ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_57787882_5   1280 CCAACAAAGGCCTAATATCCCAAATCTATATGAAACTT----AAATCAGC 1325
                          ii i  i  v  vi     vi   v    vii    i----  v   ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_57787882_5   1326 AAGCAAAAACCAAATAACCCCATGAAAAAGTGGGCAAATTATATGAATGG 1375
                           vv    iv          v  v?    i        vv  v     i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_57787882_5   1376 TCAGTTCTC-AAAAAAGATACAAAAGTGGCCAACAAACATATTAAAAAAT 1424
                         v  v     -   i      i v  i       i  i  i  v    i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_57787882_5   1425 GCTCAGCATCACTAATCAT 1443
                              i     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.48 (52 / 21)  


2615 25.82 4.42 1.59  chrX_57802817_57807792     3601  4483 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57802817_5   3601 TAGAAAAACACTCCATGCTCACAGATCTGAAGAACTAATAGCATTAAAAT 3650
                          i    i i ii     i   ii   iv     vi     vii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57802817_5   3651 TACCATACTGCCTAAAACAGTCTGCAGATTCAATGCAATCCCTATCAAAA 3700
                         vi v     v  i   viii   i         i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57802817_5   3701 TGACA----CCATTTTTAACAGAA-TTAGCAAAAAGAATCCCAAATTTCA 3745
                          vv  ----  v     i-     -  ii   ivv  -   i   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGA-TCCTAAAATTCA 148

  chrX_57802817_5   3746 TATGAAACCCCCCAAAAAATCT-GAATAGCAAAAGCAGTTCTAGCAAA-A 3793
                             i  viv --  iii i i-       v   i  i ii iiv   - 
  L1M4_orf2#LINE/    149 TATGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_57802817_5   3794 AGAACGAAGCTGGAGACATCACTTTACCTTACTT-AAAATTATACTAGAA 3842
                              i   i     ivv    vi v  iv i  -    i -     v  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chrX_57802817_5   3843 GGCTATAGTAACCTAAACAGCATGGTACTCTTATTAAAATAGTAACATGG 3892
                         i    i     i v i    ii       vvi  v ii    vv i  i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_57802817_5   3893 ATCAATGGGACAGGATAGAGAACCCAAAACAAAAAGCCATACAGTTACAG 3942
                                 i i  i  v    ii   i  - v   v       v   ii 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAA-ATAAACCCATACATTTATGG 344

  chrX_57802817_5   3943 CCAATGTATCTTTGAAAA---TGTCAAAAAGAACATACATTGGAGAAAGA 3989
                         i    vv  i  i  v  ---  i   ---  v   v  v   i      
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAA---GACCATTCAATGGGGAAAGA 391

  chrX_57802817_5   3990 ACA---CTTTCAGCAAATGGTGCTGGGAAAATTTGATTTTCATAAGCACG 4036
                          i ---i     i               v  i v   v?i  i v   vi
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_57802817_5   4037 GGAATGTAACTG-----CTATGTCTTACCATACACAAAAATCAACTCAAG 4081
                         i     v ii  -----   iv  vi      i        i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_57802817_5   4082 ATGGATTAAAGATTTAAATGTAAG-GCTGAAAC---AAATATTCT-AGAA 4126
                               i ?   ii          -   i    ---   - i   -    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAA 540

  chrX_57802817_5   4127 CAAAACCTAGGGAAAACTCTTTTGGGCCTCGGTTTAGGCCAATAATTTAT 4176
                         v     v    ?iv  v    ivv i   i  v      -   ii   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC-AATGGTTTCT 589

  chrX_57802817_5   4177 --GACTAAGATCTCAAAGGAACAGGCGACAAAAACTGACATAGACAAATG 4224
                         --  -  v  ivi    i v   i  i      ivvi v     i    v
  L1M4_orf2#LINE/    590 TAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_57802817_5   4225 AGACTTCA-----ACTAAAAAGCTTCTGCACAGCACAGGAAATAATAAAC 4269
                         i       ----- i      -   i  ii vv  v    v iv  v  v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_57802817_5   4270 AAAGTGAACAGACAACCTGTAGAATGGGAGAAAATATGTGTAAAGTATAC 4319
                                 v        iii                 v  i   vi   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_57802817_5   4320 ATCCAACAGGGCACTAGTATTCAGAGTATACAAGGAACTCAGCCAACTCA 4369
                            ii i i  v   v    i    i    i  i      vvv       
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_57802817_5   4370 ACAA-AGAAAGA-AAAT--CCCA-TTAAAAAATGGAAAAATGACATGTAT 4414
                          i  - i     -    --    -  ?        iv   v  iv  v  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_57802817_5   4415 GGAGATTTTTC---AAAAGACCTACAAATGCCCCACAGATACGTGAAAAA 4461
                         i  v    i  --- i    iv        v  v i iii  i      i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_57802817_5   4462 AGTATTCAACATCACTAGTCAT 4483
                          - ii         ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 1.83 (53 / 29)  


1655 27.15 1.76 1.56  chrX_57851847_57856823.rev        1   512 (4465)    L1M4_orf2#LINE/L1      112   624 (284)  

  chrX_57851847_5      1 TTTTCTGCACAGAATTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCA 49
                             i    v -     -- v  i  - iii    i           vii
  L1M4_orf2#LINE/    112 TTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_57851847_5     50 AAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTG 99
                         v  ii  v  viv  v     iv     i i ivv i          i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_57851847_5    100 GAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGTTACAGTAACC 149
                             vv    i  v  ii i      viv        i i        i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_57851847_5    150 AAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAATGGAACAG 199
                           i    ii         i iv ii i   v       i        i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_57851847_5    200 AAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACCATCTGATCTT 247
                           i--    i  --        vv  ii i  i  iiii  vi    i  
  L1M4_orf2#LINE/    309 AATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_57851847_5    248 TGACAAACCTGACAAAACCAAGAAATGGGGAAAGGAT--TCCCT---ATA 292
                         i     ivv  v   i    vvv           i  --  ii --- i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_57851847_5    293 AATCATGCTGGGAAAACTAGCTAGCCATATGTAGAAAGCTGAAACTGGAT 342
                            vi        v    i v  ?   i   i i  iiv    ii    i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_57851847_5    343 CCCTTCCTTAAACCTTATACAAAAATTAATTTGAGATGGATTAAAGACTT 392
                             v   i v   v              i ii i      i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_57851847_5    393 AAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-AT 441
                            i  v   v       i      vi i           v    ?i- v
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_57851847_5    442 ACCATTGAGGACCTAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAA 491
                          i v i -v     v  vv i     v ii   v ivv  vi        
  L1M4_orf2#LINE/    557 ATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_57851847_5    492 AGCAATGGCATCAAGCAAGAA 512
                             vvi   v   --     
  L1M4_orf2#LINE/    606 AGCACAAGCAACAA--AAGAA 624

Transitions / transversions = 1.62 (84 / 52)
Gap_init rate = 0.02 (10 / 513), avg. gap size = 1.70 (17 / 10)  

1755 22.71 2.46 16.56  chrX_57851847_57856823.rev     3432  4488 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57851847_5   3432 TGGAAGAACATTCCATGTTCATGGAAGGGAAGAATCAATATTGGTAAACT 3481
                              ii i  i             vv      v i       v   iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57851847_5   3482 GGCCATACACCTCAAAACAATTTACAGATTCAATTTTATTCCTATCAAAC 3531
                            v    v  i    vii  i           iviv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57851847_5   3532 TACCAATGACATTCTACACAGAAATGGAAATAACT-ACTCAAAAATTCAT 3580
                          v   iivi v  i vii       v  v - i  - ii v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_57851847_5   3581 ATGGAGCTAATAAAAGAG-TCTA-AATACACAAGGCAATCCTAGGCAAAA 3628
                              ---   iv   i -i i -    vv   ii     i iiiv  i 
  L1M4_orf2#LINE/    150 ATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_57851847_5   3629 AGAGCAAAGCTGAAGGAATCACATTGACCAACTTCAAATTGTACTACAAG 3678
                            i     i  i    v     i vv    i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_57851847_5   3679 GATGTAGTAATCAAAACAGCATGGAACTGATACCAAAACAGACACATAGA 3728
                          v ii         i    ii   v    ii iv ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_57851847_5   3729 CCAATGGAACAAAATAGTGAGCACAGAAATAAAGCCACATACCTACAACC 3778
                         i        i i   v v   iv          v   i i ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_57851847_5   3779 ATTGGATCTTTGACAAATCTGACAGAAACAAGCAAGAGGGAAAAGACTCC 3828
                          v v   i  i     ivv  v  ii v  vv   vi      ii ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_57851847_5   3829 CTATTAAATTAATGGTGCTGTGATTACTGGTTAGCCATATGAAGAAAACT 3878
                           v  v  iv          v  iv     v  ?   i   v i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_57851847_5   3879 GAAACTAGACTTATGCCATATATAAAATCCATATGCCGGAAAGCTGAGGC 3928
                            ii i   -------------------------  -------------
  L1M4_orf2#LINE/    447 GAAGTTGGAC-------------------------CC------------- 458

  chrX_57851847_5   3929 AGGAGAATCACTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCA 3978
                         ----------  ---   -----------------------------   
  L1M4_orf2#LINE/    459 ----------CT---ACC-----------------------------TCA 466

  chrX_57851847_5   3979 CACTACTGCACTGCAGCCTAGCGACAGAGTGAGACTCCGTTGCAAAAATA 4028
                            i -------------  -------------------- i       -
  L1M4_orf2#LINE/    467 CACCA-------------TA--------------------TACAAAAAT- 482

  chrX_57851847_5   4029 AATAAATAAATAAATAAATAAATAAATAAATAAATATCAACTCAAGGTGG 4078
                         -------------------------------------i       ii   
  L1M4_orf2#LINE/    483 -------------------------------------TAACTCAAAATGG 495

  chrX_57851847_5   4079 ATTAAAGACCAAAATGTAAAACTCTAAAACTATAAAAACCCTGGAAGATA 4128
                           i ?     v        i v-              vi i i     v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAG-CTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_57851847_5   4129 CCCTAGG---AAATACCATTTTG-GACATAGGAGCTGACAACGATTTTTT 4174
                         v v    ---    ----i  i -   v v  iviv i   i i   i  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_57851847_5   4175 GAA---------AAAAACAC------CAAAAGCAAAAGTTGACAAATAAG 4209
                         ii ---------    i   ------      v    i v  i    vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_57851847_5   4210 ACCTAATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCAACAGA 4259
                           i v  i   v v  i     i  ii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_57851847_5   4260 GTAAATAGGCAACCTGCAGAATGGAGGAAAATATTGACAAACTATATATG 4309
                           i  v  i     ii        ii         vi    ii      v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_57851847_5   4310 TGACAAAGGCCTAATATACAAAATCTACGAGGAACT--TA-AACATA-CA 4355
                            i  i  v  vi   v  i   v  ii i     --  -   vi -i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_57851847_5   4356 AGGAAAAATCAAACAACCCACCTCACTAAAAAGTGGGAAAAGGACATAAA 4405
                          vi    iv    i      ---- i ?    i    v      iv i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCA----ATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_57851847_5   4406 CCGACACGTTTCAAAAGAAGACATACAAGCATATACATACAAGCCAACAA 4455
                         iv    iv i  v        i      --------  i---     i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAA--------ATG---GCCAATAA 875

  chrX_57851847_5   4456 GCATATGAAAAAATGCTCATCATGACTAATCAT 4488
                            i       i       v   v ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 8.38 (201 / 24)  


 399 18.31 17.61 4.23  chrX_57870927_57873228.rev      632   773 (1529)    L1M4_orf2#LINE/L1        1   161 (747)  

  chrX_57870927_5    632 TGGAAA-ACATCACATATTAATGGATTGGAAAGAAGACTC-----TGT-- 673
                               - i   v   i  v           ----    i-----   --
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAA----GACTTAATATTGTTA 46

  chrX_57870927_5    674 -AATGGACCAA--------AAATTGGTCTACAGATTTAAGACAATCTCTG 714
                         -i    --   --------      i          i  vi     i  i
  L1M4_orf2#LINE/     47 AGATGG--CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chrX_57870927_5    715 TCAAAATGCCA-------TTTTTGCCAAAATGAACA-GATGAGTCTAAAT 756
                                v   -------       vi    vi   - v   vi     v
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_57870927_5    757 TTTATATCCAGTTGCAA 773
                           i    vv iv     
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAA 161

Transitions / transversions = 1.17 (14 / 12)
Gap_init rate = 0.05 (8 / 161), avg. gap size = 3.88 (31 / 8)  

2511 21.65 5.59 1.54  chrX_57870927_57873228.rev     1096  1811 (491)    L1M4_orf2#LINE/L1      164   908 (0)  

  chrX_57870927_5   1096 GATCCAGAATATTCATAGCAATCTTGAATGAAAAGAGCAAAGTTGGAGAA 1145
                           i        vi  v i          vi i    i           i 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_57870927_5   1146 TCCACATTTCTTTATTTCAAAACTTACTACAAACCTATTGCTTTCAAGAC 1195
                         ii    i   iiv                    v   iv ivv       
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_57870927_5   1196 AGAGTGACACTGGCATAAGTATAGGCAAATATATCAATGGAATATAACTG 1245
                           v   ii           v    i  v   v            v  i  
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_57870927_5   1246 AAAGCCCAGAAGTAGACTGTCACATTTGTAGTCAACTGACTTTCAAGAAG 1295
                          i  i      i  i  ivvi      i i     i   i    i v   
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_57870927_5   1296 ACTGATGAAAGAATTTAATG---AAAAAATAGTCATTTCAACAAATAGTG 1342
                         iv  vii i vv   i    ---   i       v           i   
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_57870927_5   1343 TTGGGGCAAGTGAGTATCCACGTG-------ATGA-------CTCCTATT 1378
                         i    i   v  ii  ?    i  -------    ------- i    ii
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_57870927_5   1379 TACTACTATACACAAAAATTAACTCAAAGTGTATTATAGACCTCAGTGTG 1428
                          vvi  i   i                 i  v  i ?      v i   i
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_57870927_5   1429 AAAGCTAAAATAATAACACT-TTAAAATAAAAGCAAATGAGTAAATCATT 1477
                          i        iv    v   -   i  v    -  v v ?       v i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGTAAATCTTC 562

  chrX_57870927_5   1478 GTTGTCCTTTG-CTAGTTAATGCTTCCTTAGATATGACACCCACAACACA 1526
                           - v    v -i   vi    v  i               v v i    
  L1M4_orf2#LINE/    563 GT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_57870927_5   1527 AGCAACAA---------TA-ATATAATTTGACTAAATGATAACTAACAAA 1566
                                 ---------  -   -    v    vv  v v  i   v  v
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATA-AATTGGACTTCATCAAAATTAAAAAC 660

  chrX_57870927_5   1567 TTTTAT-TATGAAAAAAGA-TATCAAAAA--TAAATAAAAAAGATACAGA 1612
                             i -iv v   ii v -      i  -- i  v i v  vvi     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_57870927_5   1613 A--GAAG----TGTTTGAAAATCATGAACCTATCAAAGG-CTTGCATCCA 1655
                          -- i  ---- i    v       iv i  ivi  i  -    i     
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_57870927_5   1656 GAATATGTTTTTTAAAAAACCTCTTACAACACAATAAAAAAATAATCAAA 1705
                               i -----   i   -         v      v    vi -    
  L1M4_orf2#LINE/    761 GAATATAT-----AAAGAAC-TCTTACAACTCAATAATAAAAAGA-CAAA 803

  chrX_57870927_5   1706 TTAACACAATTAAAAATTAGGCAAAAGATCTGAATAGACATTTCCCAAAA 1755
                          -   v     ?    v i      i   i              i v   
  L1M4_orf2#LINE/    804 T-AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_57870927_5   1756 TAAGATATACTAACAGCCAATAAGCACATGAAATGGTGCTCAACATTATT 1805
                         v         v  ii                  v i          i ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_57870927_5   1806 AGTTAT 1811
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.36 (87 / 64)
Gap_init rate = 0.03 (20 / 745), avg. gap size = 2.55 (51 / 20)  


 967 28.06 4.81 2.61  chrX_57879243_57882341.rev        2   500 (2599)    L1M4_orf2#LINE/L1      319   828 (80)  

  chrX_57879243_5      2 CCAGAAATTCAATCAAGTATTTATAACCAACTAATTTTCAACAAAGGCAC 51
                                 vv vi  vii      iii   i i      i    i  ii 
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_57879243_5     52 CAAGAACATGTATTTGAAAAATGAAATA-TTTTTTCA-TAATTTTTTCTA 99
                              v   vi v v ii   --i    - i      -i  v vv v  i
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAA--GAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_57879243_5    100 GAAAATTTGGATATTCATATGCAGAAAAATAAAACTAGTCCCCCCATTTC 149
                          i v vi      ?i  i     i  i   i  ii i -v    i ii  
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG-ACCCCTACCTC 465

  chrX_57879243_5    150 TCTCCATAT-CAACAAACTCAACT-GAAATGCACTAAAGACTCAAACATA 197
                         v v      -   -   i -    -i     v ii ?    ii   ii  
  L1M4_orf2#LINE/    466 ACACCATATACAA-AAATT-AACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_57879243_5    198 AT-GCAAAAATCTATAAAAGTACTAAAAAAAAACCACAAG---AAAC--- 240
                          v-  v    -        v vi  i  i     - i i ---   i---
  L1M4_orf2#LINE/    514 AGAGCTAAAA-CTATAAAACTCTTAGAAGAAAAC-ATAGGNGTAAATCTT 561

  chrX_57879243_5    241 ----ACCCCAGGTCACCAGTAGGCAAAGATGTTATGGCTAAGAACTCAAA 286
                         ----   iii   ------       v i v iv i v  v  vvi    
  L1M4_orf2#LINE/    562 CGTGACCTTGGGT------TAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_57879243_5    287 ACCACAGGCAACAAAA-ACAAAATAGAAAAATAAAACTAAATCAAA-CTA 334
                          v    i         - v        v    vii   vv      -i  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_57879243_5    335 AACACTTCTGCACAGCAAAGGAAACAATCTGCAAAATGAAGAGACATCCT 384
                           v    i  ii vv       v  v   viv   i    i     v  i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_57879243_5    385 GCTGAATGAGAGAAAATATTTACAAAT--TTTATCTAACAAGAGGTTAAT 432
                         i v     i            i     -- v     i i   i ii vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_57879243_5    433 ATCCAGAATTTATAATAAACTGAAGCAACACAACAGCAAAAA--TAAAT- 479
                                  v     vi    vvvi    v   i ii     --i    -
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_57879243_5    480 --TCACTTAAAAATTAAGAAAAG 500
                         --i  v  ?    v ii v    
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.49 (82 / 55)
Gap_init rate = 0.04 (19 / 510), avg. gap size = 1.95 (37 / 19)  

 364 26.88 0.00 0.00  chrX_57879243_57882341.rev     1440  1532 (1567)    L1M4_orf2#LINE/L1        1    93 (815)  

  chrX_57879243_5   1440 TAGAAAAATATTCCATATTCATGAATAGAAAGAATGAATATCATTCAAAT 1489
                          i    i    i    i      i  v i    v v     ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57879243_5   1490 GGCCCTACAGCTCAAAGCAATTTACAGATTCAAAGCTATTCCT 1532
                            vv   vv i    vii  i           v  v  i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

Transitions / transversions = 1.27 (14 / 11)
Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.00 (0 / 0)  

1700 26.70 9.24 3.08  chrX_57879243_57882341.rev     1830  2608 (491)    L1M4_orf2#LINE/L1       82   908 (0)  

  chrX_57879243_5   1830 AAAGCTATTTTTATTAAACTACCAAAGACATTCTTCACAAAACTAGAAAA 1879
                           v  v  iii   i   v v   ivvi v  i  ii  i  v v  v  
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

  chrX_57879243_5   1880 ATTTATTTTAAAATTCGTAGGGAACAACAACAACAAAAAGACC--AAATA 1927
                         ii v  ii        i  v    vvi   -------ii    --i    
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAA-------GGGACCCAGAATA 174

  chrX_57879243_5   1928 GAAAAAACAAGCTTAATATAAAGGAAGAAAGCTTTAGGCATTGCATTGCC 1977
                          vv       v   i v v i i   v    i vv   vv ii  i v  
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_57879243_5   1978 TAACTTCAAACCATACTACAAGGCTAGAGTAAACAATACAGCATGACACT 2027
                         i  i      v v        i    v     v   v    ii  ii   
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_57879243_5   2028 GGTA-AAGAA---ACA----------------------GAGA---CATAG 2048
                           i -   i ---   ----------------------    ---  v i
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_57879243_5   2049 ACAAACC------------ATC---TGATCTTTGACAAAGTTGACAGAAA 2083
                          i     ------------i  ---    i  i     i v  v  ii v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chrX_57879243_5   2084 CAAGCAAAGGGGAAAT--TACTCGCTGTTAAAATATTGGTGCTGAAATAA 2131
                           vv   v       v--  v  vi - i  v v  -       ii i  
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTT-TCAACAAAT-GGTGCTGGGACAA 422

  chrX_57879243_5   2132 CAGGCTAGCTATCTG-AGGAGACTGAAACTGAACCTCTTCCTTATATTAT 2180
                          v  v  ? i iv  - ii   v    ii  i   i  v   i i ii  
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_57879243_5   2181 ATACAAAAATTTACTCAATATGGATTAACAACTTAAATTTTAAACCCCAA 2230
                                    v      v      i ?vi  i     v v i v iv  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_57879243_5   2231 ACTATAAAAACTCT--GGGGATAAACCTAGG---AAATACAATTCAGAAC 2275
                                  -    -- ii  -    v    ---    - --   ivi  
  L1M4_orf2#LINE/    523 ACTATAAAA-CTCTTAGAAGA-AAACATAGGNGTAAAT-C--TTCGTGAC 567

  chrX_57879243_5   2276 ATAAAATCCGGCAAAGATTT------TATGACAAAGATGCCAAAAGCAAT 2319
                         v viii iv     v i   ------       ------         vv
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACA------CCAAAAGCACA 611

  chrX_57879243_5   2320 TACAACAAAAGCAAATATTGACAAATGGAAACTAATCAAACTAAAGAGCT 2369
                         vi         v   v  v  i    v i vi v      v v  i i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_57879243_5   2370 TCTGCACAGCAAAAGAAACTATCAACAGAGTAAACAGACAACCTGCAGAA 2419
                          i  ii vv    i  v        v i   i  v        ii     
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_57879243_5   2420 TGGGAGAAAATATTAGCAAACTATGCATCCCACAAATGTTTGATATCCAG 2469
                                       v     ii  ii   iv i  iv vi vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_57879243_5   2470 AGTTTATCAGTTAACTATTTACAA-------GTAAAAA---AAA-AACCC 2508
                          i v   v iv-    -i      -------i      ---   -     
  L1M4_orf2#LINE/    762 AATATATAAAG-AACT-CTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_57879243_5   2509 A-TCAAAAAGTGGGCAAAGGATGGAAACAGACACTTTTCCAAAGAAGACA 2557
                          - i?    i            vvi  i     i  i           i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_57879243_5   2558 TACATGTGGCCAGCGGTCATATAAAATAAGATGCTTAACATTACTAACCA 2607
                             vi      iiiiv  i  i   --       i     i ???????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAA--AGATGCTCAACATCAZZZZZZZ 907

  chrX_57879243_5   2608 T 2608
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.33 (117 / 88)
Gap_init rate = 0.03 (27 / 827), avg. gap size = 3.56 (96 / 27)  


2546 29.42 1.90 0.56  chrX_57902426_57907668.rev     1889  2782 (2461)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_57902426_5   1889 GAGAAATCATTCCATGCTCATGGATAGGAAAAATCAATGTCATGAAAATG 1938
                           i i  -  i     i        v    i v i   i ii v  i   
  L1M4_orf2#LINE/      3 GAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_57902426_5   1939 GACATATTGCTCAAAGCAGTTTATAGATTCAATGCTATTCCCAGTAAACC 1988
                          vv   i v i    viii i  i        i  v  i  i vi   vi
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_57902426_5   1989 ACCATTGATATTCTTCGCAGAATTAGAAAAAAACT-ATTTTTAAATTCAT 2037
                         v   viviiv  i  i      v v  v  i--  -  ii v        
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCAT 149

  chrX_57902426_5   2038 ATGGCA--GAAGAAGACCCTGAATAGCCAAGACACTCCTAAACATAAAGA 2085
                             v -- v iii     v          i   v  i i  v vi    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_57902426_5   2086 ACAAAGACAGAGGCATCACACTACCTGTCTTCAAACTATACTACAAAATT 2135
                               vii    vv       v  iivi      viv         ii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_57902426_5   2136 ACAGTAATCAAAATAGCATGGTACTTGCACAAGAACAGACACATAGACCA 2185
                                    i i  ii       v   i   i i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_57902426_5   2186 ATGAAACAGAATAGAGAACCCAGAAATAAGATTGCACAACTGTGACCATC 2235
                            i  i     v    ii          iviiii   vi i  ii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_57902426_5   2236 TGATCTTTGACAAACTTCATGAAAACAAGCAATGCAAAAAGAATTTCCTA 2285
                             i  i     ivv vvii i v  vv     vii       vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_57902426_5   2286 TTTAATAAATGCTACCAGAAGAACAGGCCAGTCATATGCAGAAAATTGAA 2335
                           i  i     v i ii i v   v  vi ?i  i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_57902426_5   2336 ACTGGACCCCTTCCTTACAACATACACAAAAATCAACTCAGGATGAATTA 2385
                         ii         v   i   v    i        i      ii   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_57902426_5   2386 AAGACTTAAATGTAAAACCCAAATTTATAAAAACCTTGGAAGAAAACCTA 2435
                         ?    i         i v i   vi       vi   i         v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_57902426_5   2436 GACA-ATATCATTTATTACATAGGCATAAGCAAAGATTTTATGACAAAGA 2484
                          i?i- v   -  ii v  v v  vv  i    v i   iv iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_57902426_5   2485 CACCAAAAGAAATTGCATCAAAAGCAAAAATTGATAAATAGGATCTGATT 2534
                                  v vvv   v      v      v       v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_57902426_5   2535 AAACTAAAGAGCTTCAGCACAGCAAAAGAAACTATCAGCAGAGTAAACAG 2584
                            v v  i i   iv ii vv    i  v       iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_57902426_5   2585 ACAATCTGCAGAATGC-----AAT-TTTTCAATCTATCAATCAGACAAAG 2628
                             i ii       v-----   -   v   vii  vv   v  i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_57902426_5   2629 GTCAAATATCCTGCATCTATAAGGAACTTATACAAATTTACAAGAACAA- 2677
                          v vvi     v v  v     i     iv     v iv i  v  v  -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_57902426_5   2678 ---AAGAACCTCATTAAAATGTGGGCGAAGAATGTGATCAAACATTTCTC 2724
                         ---  v    iv   ?   vi     i   i  v   vi i         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_57902426_5   2725 AAAAGAAGACATATA--TGAGGCAATAAACATGTGAAAAAA-GCTTAACA 2771
                         v        i   i --  - v      i  ii      i -   i    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATG-GCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_57902426_5   2772 TCACTGATCAT 2782
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.35 (149 / 110)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 1.83 (22 / 12)  

1284 32.32 7.35 1.63  chrX_57902426_57907668.rev     3896  4752 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_57902426_5   3896 GAGAGATATACCATGTACATTGGCTG-AAGAAATATTATGGTAAAAATGT 3944
                           i      v      v   v ii  -    vv  v   v  v  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_57902426_5   3945 AAACTCTATTAAAATTAATATATAGGTTTAACACAATTTTT--CACAAT- 3991
                         v  iv  viiv     i  v  i  i  i   i    iii --  v   -
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_57902426_5   3992 ---G-------TTTAACAAGAATCTTAAAGACAAGATAAACCTAAGATTT 4031
                         --- -------   vi  ii   i-----      v i v     i   i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATT-----GACAAGCTGATCCTAAAATTC 147

  chrX_57902426_5   4032 ATATTGGAA----AGAAATTTACA-TAACTAAAACCACCTTGAAAA---- 4072
                             v i  ----  ii iii v -  i i     v i        ----
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_57902426_5   4073 ---TAAAGTAAAAGGAATTAGTTTCCCTAATTTTAAGGTCTATTATACAT 4119
                         ---i     vii    v i vvi i  i     i  iiii  i  i v v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_57902426_5   4120 TTATGGTAATAAATATTGTGTGGCATTGTTTCGTGGATACATACATCAGC 4169
                         i  ii     v  v iv      i i  viviiv     v i i  viii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_57902426_5   4170 CACTGGAATAGAATAGAGCAGTC-AGAAACAGACCCATACAAATATGCTC 4218
                           v           v   -    -     i i         vv    v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_57902426_5   4219 AACTGATTTTTTCACAAACTTGTGAAAATTATTCTTTGGAGGGGGGATAG 4268
                           i       iv-    ivv  iv  i ii    vv   i iii i    
  L1M4_orf2#LINE/    347 AATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_57902426_5   4269 CTTCTTCAACAAATTGCACCAAAATAATTAGAAATCCACAGGCAAATAAA 4318
                         ii i          v ii iiii i  i i  v ?     v     vi  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_57902426_5   4319 TAAACTTTAAGCAATGTCCCAACCCTTTTACCCAAATAAATTCAAAAGTA 4368
                          i  v  vi v vv ii i  vv  v v   vv    v  i      vvi
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_57902426_5   4369 AGTATGGATTTAAGTA-AAAAACATTAACAAAAACACTTTTAGAAAAAA- 4416
                          vi ?i  ii   i i-  i i vvv   v v  v   i      i   -
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_57902426_5   4417 --TAGAAGAAACATTTGGTAGATATATGCATAAACAAAATG--TTTTTAG 4462
                         --   i? v  vvi  v  -  iv vv vv  ii   --  --  i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAA--TGGTTTCTTAG 592

  chrX_57902426_5   4463 ACTTGGTATCAAAAACA-GAGTGATAAAA------AT-GATAAATTGGGT 4504
                          iv  ii i     i  -i  ii i    ------  -          ii
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_57902426_5   4505 TTAATCATTGAGATCAAAGACTTTTGTTCAGTGACAGACACTCTTAAAAT 4554
                           v    --- i  i   i        v vvii vi      v i  i v
  L1M4_orf2#LINE/    643 TTCATCA---AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_57902426_5   4555 AATAAATGGATGAGCTACAGACTGGAAGAAAATATTTGCAAGCTGCATGC 4604
                          i i  vi  ii v i     v   i               iiiii  ii
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_57902426_5   4605 TTAA-AAAAGACAAGTATATAGCAGATA-AAACAATTAAAACAACAGAA- 4651
                         i i -  ii   vv    vi  v v   -   v  i vvv     vv  -
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_57902426_5   4652 AATAAAAATATCAAT---TTAATTAGAAAAT----AAATAATTTCA-CAG 4693
                                 v iv   ---ii    ?i     ----   vi    v -i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_57902426_5   4694 A----TC-----AGAAAATA--CAGATTAAAAATAAGTACATAAAAAACT 4732
                          ----  -----    i   --  i  vivv      i    i    iv 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_57902426_5   4733 AGCTTATTATCATCATTAGC 4752
                         -   i vi    ????????
  L1M4_orf2#LINE/    890 -GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (162 / 111)
Gap_init rate = 0.03 (30 / 906), avg. gap size = 2.57 (77 / 30)  


2548 26.00 8.04 1.18  chrX_57911375_57917618     4906  5751 (493)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_57911375_5   4906 AAAATATTCCATGGTCATAAATTCGAAGAGTCAATATTGTTAACATTTCC 4955
                           i    i     v    ii   v     v i           v  vv v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_57911375_5   4956 AGACTACTCAAAGCAATCTACAGATTGAATGCAACCCCTATCAAAATACC 5005
                          v   v i    vii           v  i    i            v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_57911375_5   5006 AATGATATTCTTCACAAAAATATAAAAAATAATCCCAAAATTTGTATGAA 5055
                          iiviiv  i  ii  i    vv v  iv i    i      ii    i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_57911375_5   5056 ACAACAAAAGACCCAGCATAGCCAAAGCTATTCTTAGAAAAAAAAAAAAA 5105
                          vvi   ii       v         i v  -   ii    i  i  v  
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAACAA 203

  chrX_57911375_5   5106 AACTGAAGGAATCACACTACCTGACTTGAAATTATACTACAGTGCTATAG 5155
                          ii  i    v       v  ii i  v   viv       iv    i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_57911375_5   5156 TAACCAAAACAGCATGGTATTTGATGGCATAAACTCAGACACATAGACCA 5205
                            i   i    ii     i ----       ivvi     i     i  
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACT----GGCATAAGGATAGACATATAGATCA 299

  chrX_57911375_5   5206 ATGAAACAGAATGGAGAAGCCAGGAACAAATTCACACACCTGCACTGAAC 5255
                            i  i     v    iv    i  i   ii  i   ii iiiv v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_57911375_5   5256 TCATTTCTGACAAAATTGCCAAAAACCTACTTTGGGGAAAGCACTGTCTC 5305
                          v    ii     iiv      i v v v vv         v iv    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_57911375_5   5306 TTTTATAAATGGTGCT--------------------------AAAATGAA 5329
                           iv i          -------------------------- i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_57911375_5   5330 ATTAGATTCC-ATCTCTCGCCATATA-AAAAAT-----CAAAATGGATTA 5372
                         i  i  ii  - i   v i       -      -----          i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_57911375_5   5373 TAGACTTTAGTCTAAGACCTCAAACTATGAAACTACTGCAATAAAACTTT 5422
                         ?    i v i v     v  v       i     vi iv  v     v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_57911375_5   5423 GGAAAAACTCTTCAGGACATTTGTGTGCGCAAAATTTTTTTGAGCCA-GA 5471
                           ?iv  v     iv   v  v vv iv    viv   i  -  vi -  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chrX_57911375_5   5472 CACCACAAGAACTGGCAACCAAAGCAAACATGGACAAATGGGATCTCAAC 5521
                              v   v  vi     v    v   v  i  i    v   ii   v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_57911375_5   5522 AAA-TTAAAAAAAACTTCTGCACCACAAAGGATATTATCGACAAAGAGAA 5570
                            -       ---   i  ii iv       i i    i v    v   
  L1M4_orf2#LINE/    649 AAAATTAAAAA---CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_57911375_5   5571 AAGGAAACCCAAAGAATGAGAGAAA--------------------TAATA 5600
                            iv      v      i      -------------------- i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_57911375_5   5601 A-----------CCAGGATATATAAGGATCTCAAACAACTC--TAGAGGA 5637
                          -----------    i        i  v   vv       --  ivii 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_57911375_5   5638 AAAACTAATAATCCCACCAAAAAAGTGGGTAAAATATTTGAACAGACATT 5687
                           i  v     i  v ii?     -    i   iv       i       
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATT 844

  chrX_57911375_5   5688 TCTCAAAAGAAGACACGCAAGTGGCAAACAGGCGTATGAAAAGGTGCTCA 5737
                             v        i ii   i    v  i i  ii        i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_57911375_5   5738 ACATTATTGATCAT 5751
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (129 / 88)
Gap_init rate = 0.02 (14 / 904), avg. gap size = 5.57 (78 / 14)  


2501 27.91 1.08 3.23  chrX_57918266_57921342.rev     1659  2586 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57918266_5   1659 TGGAAACACATCCCATGCTCATGGAAGGGTAGAATCAGTATTGTGAAAAT 1708
                               v i        i       vv  v   v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_57918266_5   1709 CACCATACTGCCAAAACCGATCTATAAATGCAGGGCAATTCCCATCAAAA 1758
                         vi v     v  v   ii      i i  v  iv     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_57918266_5   1759 T----ACTGCCATTATTCTTCACAGAACTAGA--AAC-AATGCTAAAATT 1801
                          ----i     ----  i  ii     v v  -- i -i  v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_57918266_5   1802 AATATGAAACAGAAAAGGAGCCCACATACCCAAAGCAAAACTAAGCAAAA 1851
                         v     i  vv v  i   v  viv   v     i   vvi i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_57918266_5   1852 AGGTCAGCTATGAAGGCAC-CACTTTGCCCATCTTCTAATTATACTATAA 1900
                           iv  ivvv  i   -  -   vi v    vi   v  viv     i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_57918266_5   1901 GGCCATAATCACCAAAAGAGCATGGTACTGGTGTAAAGATAGGCGCATAT 1950
                         i  i i i v i   i v  ii         ii   i     i ii   v
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_57918266_5   1951 ACCAATAAAGCGGAATAGAGAACCCAGAAATAAACCAAAATACTTACAGC 2000
                          i    ii iii    v    ii             v v i i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_57918266_5   2001 CAAGTGATCTTCGACAAAGCAAACAAAAACATAAAGTGGAGAAATGACAC 2050
                            v    i        i vviv   i v   vv i   i    vi i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_57918266_5   2051 CTTATTCAACAAATGATGCTGTGATAATTGGCAAGCCACAGTTAGGATAA 2100
                         ii v           i     v  i  i   vv ?     vvi ii v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_57918266_5   2101 TGACACTGGATCCTTATCTCTCACCTTATACAAAAATCAACTCAAGATGG 2150
                            vii    i  i  i   v    v           i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_57918266_5   2151 ATCAAAGACTTAAATCTAAGTCCTAAAAACT-TAAAGATTCTAGAATATA 2199
                             ?    i     v    vv      -  -    iv ii     v v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAA 544

  chrX_57918266_5   2200 ACATTGGAACAACCCTTCTAGACATTGGCTTATGCAAAGACTTCAT-GAC 2248
                             v  ?ii  vi    vv   v    v   v    v ii   v -  i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_57918266_5   2249 CCAAAACCCTAAAGCAAATGCAAAAACAAACAAAGAAACAAAAAACAAAG 2298
                         vii v   v-      ----------   i   -----     i -   i
  L1M4_orf2#LINE/    595 ATGACACCA-AAAGCA----------CAAGCAA-----CAAAAGA-AAAA 627

  chrX_57918266_5   2299 ATAAGTAGATGGGACTTAATTAAACTAAAAAGCTTCTGCAGAGCAAAATA 2348
                            ii  i  v      v  i   v v    i   i  iivvv    iv 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_57918266_5   2349 AATAATCAGCAGAGTAAACAGACAACCCATGGAGTGGGAGAAAATCTTCA 2398
                         v iv    iv i   i  v          ii  i           v  ii
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_57918266_5   2399 GAACCTATACATTTAACAAAGAACTAATATCCAGAATTCACAAAAAAAAA 2448
                         v  vii   i  i i i  i i   vi          vi i   i  ---
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA--- 774

  chrX_57918266_5   2449 CAACCACGAACAATTCATCAAGAAAAAAGCAAATAATTCCAACAAAATGT 2498
                         ---- v vv    i   vi  v     ii       ii v vi?   vi 
  L1M4_orf2#LINE/    775 ----CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_57918266_5   2499 GGGCTGAGGACATGAATAGACAATTCTCAAAAGAAAATATACAATTTGCC 2548
                             vi    iv          v     v      i        v v   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_57918266_5   2549 AATAAACGTATGAAAAAATGCTCACCATCATTAATTTT 2586
                              i ii       i       v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (144 / 111)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.86 (40 / 14)  


2214 27.92 2.38 4.11  chrX_57927628_57932604     3581  4504 (473)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_57927628_5   3581 TAAAATGACATTCCATGCTCTTTGATAAAAAAAAATCAGCACTAATAAAA 3630
                          ii  v  i  i     i  v v   vii  i v- i ii i iv   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chrX_57927628_5   3631 TGGCCATACTGCTCAAAGCAAATCACATATTCAATGCTATTTTTATCAAA 3680
                             v     v i    vii vii   v      i  v  iii       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_57927628_5   3681 TTTCCACTTACATTTTACACAGAAGTTGAAAAACCTATTTGAAAACTTAT 3730
                         v i   vi i v    vii     i    v  i iv  iiv    i i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_57927628_5   3731 ATC-AAATAAAAAG---CCTGAATAATCAAGGCAATCCTTTGCAAAA--A 3774
                           v-    iv  i ---  v     ii   ii     --   v    -- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC--TTGAAAAAGAA 197

  chrX_57927628_5   3775 GAACAAAGCTAGAGGCATCATGTTACCCAACTTCAAACTATGCTACAGGA 3824
                                 i i    vv   iii v     i      viv i     iii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_57927628_5   3825 ATACAGTAACCAAAACAGCATGGTACTAATGCAAACACAGACA-A-AGAC 3872
                         v        i   i    ii       iiiii  iv i     - -   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_57927628_5   3873 CAAGAGAAGAGAATAGAAAGCCCAGAAATAAGGCTACACACCTGCAACCA 3922
                            vi   v     v  i  i          iv i i   ii iiiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_57927628_5   3923 TCTGATCTTTGACAAAGCTGACAAAAACAAGAAATGGCAAAAGAATTTCC 3972
                         vi    i  i     i v  v   i v  vvv     vi       vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_57927628_5   3973 TATTTTATAAATGATACTGGGATAACTTCCCAGCTATATGCAGAAGATTG 4022
                          v  iv i     i i      i    vvvi ? i i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_57927628_5   4023 AAACTGGATCTCTTCCTTTCACTATATACAAAAATTAATTCATGAAAGAT 4072
                           ii    i i  v   iv   i               i   vi vi   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_57927628_5   4073 TTCAGACTTAAATGTAAAACCCCAAATTATAAAAATCCTGAAAGACAACT 4122
                         iv?    i         i v iv   i       v  i ii    v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_57927628_5   4123 TGGCAATA--CCATTCTGGACACAGGAACAGGCAAAGATTTTATGAAGAA 4170
                          i v?i  --i -   vv   viv  ivi      v i   iv ii v v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_57927628_5   4171 GACACCAAAA--ACAATTGCAACAAAAGCAAAAAGTA-ATAAAT--GAGT 4215
                                   --    --          -     i  -      --  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA--GCAACAAAAG-AAAAAATAGATAAATTGGACT 643

  chrX_57927628_5   4216 TC-T---AATTAAAACCTTCTGCACAGCAAAAAAAAAAAAAAAATCAACA 4261
                           - ---        v   i  ii vv    ii v vv -----    v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-----TCAAGA 688

  chrX_57927628_5   4262 GAGTAAAAACACAACCTACAGAATGGGAGAAAATATTTGCAAACTACGCA 4311
                         i   i    v      i                          ii iii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_57927628_5   4312 TCTGACAATGGTCTAATATGTAGCATCCACAGAGAACTTAAACAAATTCA 4361
                              i  v  v  vi   vi  v  vi i i      ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_57927628_5   4362 CAATAAAAAAAAATACTAACCCATTCAAAAGTGGGCAAAGGAGATGAAAA 4411
                         i        i v - v       --------------------  v?   
  L1M4_orf2#LINE/    789 TAATAAAAAGACA-AATAACCCA--------------------ATTWAAA 817

  chrX_57927628_5   4412 AAGTGGGCAAAGGACATGAACACACAGTTTTTAAAAGAAGACATACATGT 4461
                           -           iv    i v   v  i iv        i     vi 
  L1M4_orf2#LINE/    818 AA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_57927628_5   4462 GGCCAACAAGCATATTTTTAAAAAG---TTCAATAATACTGATCAT 4504
                               i     i  ----i     ---i    i vi ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACAT----GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (156 / 98)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.73 (60 / 22)  


2372 22.76 4.35 3.45  chrX_57932625_57934337      439  1220 (493)    L1M4_orf2#LINE/L1      120   908 (0)  

  chrX_57932625_5    439 AGAAATAGACAAATCAATCTT----TT-----GGAATCTCCAGGGACTCT 479
                               v     iiii   i ----  -----    viv v      i v
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_57932625_5    480 --ATAGATCTATAAAAACCTCGAAAAAGAA---CAAAGTTGGAGTACTCA 524
                         --    -- i v  v  i  i         ---           v     
  L1M4_orf2#LINE/    170 GAATAG--CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_57932625_5    525 CATTTTCTGATTTCAAA-CTTACTGCCAAACTACACTAATACAACCAGTG 573
                           i  i ii        -      i v  i     v    vv iv     
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_57932625_5    574 TGGTACTGGCATAAAGACAAACATATAGGCCGATGGA-TACAATCGTGAG 622
                                       i  i i        ii i     -  v   --    
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT--TGAG 315

  chrX_57932625_5    623 AA---GGAAATAAGCTAAGTAGATT-ATGATCAAGTAATTTTTGACAATG 668
                          i---i       i iv -  v   -   i    v i     i     v 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCA-TACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_57932625_5    669 TTTTCCTGATGATTCAATAGAGAAAGAGCAGTTTATTCAAATAATGTTCC 718
                         v vi vv  iv       i i      ii   i v     vv    v v 
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_57932625_5    719 TGAGAAAACT---TATCTACACCTGCAAA-GAATGAAGTTGGACCTTGAC 764
                           i  v    ---  ? i   --      -               iiv  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACA--TGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_57932625_5    765 CTTACACAATAAAAGAAAACCAAAACAAAAAATTGATCAAAGCCCTAAAC 814
                           i    v   v vi    ii  vv     -- v     ?  v      i
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAA--TGGATCAWAGACCTAAAT 510

  chrX_57932625_5    815 ACAAAAACTAAAACTGTCAAAGTCTTAGAAGGAATAATTGTGGAAAATTT 864
                         ii  i i        i v   v         i  vv  v v? v    i 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_57932625_5    865 TCGTGATGCTGGATTTGGAAAATTTTGTTT-TTAGATATAAAACTAAAAT 913
                               ivi   i  v  v  --- v    -        i v  i    v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAA---TGGTTTCTTAGATATGACACCAAAAG 607

  chrX_57932625_5    914 CATAGGTAACAAAAGAAACATTAGATAAATTGGACTTCATTAGTACTAAA 963
                           i i i           v v                   i iv i    
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_57932625_5    964 ATCTTATGTACATGAAA----ACTGTCAATA--GTGAAAACTCAAACTAC 1007
                          v   v   i v v   ----   i    v --       vv   v i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_57932625_5   1008 AGAATGAGAGAAAATATTTGCAAATCAAATATCTGTTAAGAAATTAATAG 1057
                               i                    v       v    ii i vi  v
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_57932625_5   1058 TCATAATATATAAACATCTGTTACAACTCAACAACAACAAAACCCAGGTG 1107
                         i  v          v v  v           i  i  v  i  -- ii -
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC--AAAT- 804

  chrX_57932625_5   1108 AAACGTACAAATATTTGACTATATATTTCGAAGGACTTGAATGAACACTT 1157
                         -   vi -----   ?i vv  ivi--- i     i      ii   i  
  L1M4_orf2#LINE/    805 -AACCCA-----ATTWAAAAATGGG---CAAAGGATTTGAATAGACATTT 845

  chrX_57932625_5   1158 CTCTAAATGAAATATAT---TGCAGCTCAACAAAAACATAAGCAGATGTT 1204
                            i   vi i     i---  --  -   i  iv    i iv     i 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG--GC-CAATAAGCACATGAAAAGATGCT 892

  chrX_57932625_5   1205 AAACATCAGTAATCAT 1220
                         v       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (96 / 78)
Gap_init rate = 0.03 (26 / 789), avg. gap size = 2.35 (61 / 26)  


1894 28.86 7.36 1.75  chrX_57944938_57946977      714  1569 (471)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_57944938_5    714 AAAAAATCTTGTGTTAATTAATTGGGGGAC--AATGTTGTTAAAATGTTC 761
                           i v   iii    v  vi     ii   --   i       i   viv
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_57944938_5    762 ATACTATTGAAAGTGATCTACAAATTTAATGCAATTT-TATGATAATCAA 810
                              viiv   v         i   i  i     ii-   v v    vv
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_57944938_5    811 ATTGGTACTCTTTACAAAAATAAAAATGTATATA-TAAAATTTATTTGAA 859
                          viv ivi i   i  i    vi v v ivv  v-       i  v  i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_57944938_5    860 AACACAAAGGGCCACACTTAGCCAAATCAATCTTCAGTAAACA----AAA 905
                           ii   i  i  vvivv        v       v iv  iv ----   
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_57944938_5    906 GTTAAATGTATCACATTTTATGATGTCAAAATATGTTGTAACACTATAGC 955
                            ii v vv     i  ivii  v      iv ii ii  vi   i  i
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_57944938_5    956 TGTTAAAAGAGTATGGCA-TAAAATAAG-ATAGA----TAGACCAATGGA 999
                         vi i  i v   i   i - iiv     -     ----    i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_57944938_5   1000 ACAAAAC--AGGGCTCAGAAAAAAAAGAATTCATACATGTATGGTCAATG 1047
                          i i  i--  i ii      v   ----ii       v          v
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAA----CCCATACATTTATGGTCAATT 350

  chrX_57944938_5   1048 GATCTTTTATAAGTCTGCCAAGAAAATACAATGAAAAATGA-TAGTCTCT 1096
                            i  iv i   vv        vv  v     iii  v  -      i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_57944938_5   1097 TCAACAAATGCCATTGGAAAAACT---TCCCCCACACATGTGAAAGAAAA 1143
                                   viii   i v    --- v?  ---     ii      vi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCC---ACATGCAAAAGAATG 447

  chrX_57944938_5   1144 AACTTA-ATCTTTATTTTACATCATAATA-AAAAATTAACTCAATATGGA 1191
                           v  i- i ii  ii i   i    -  -              v     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATA-TACAAAAATTAACTCAAAATGGA 496

  chrX_57944938_5   1192 ----------AACTGTAAAAGTT-----T-TAAAACACATTA----AAAT 1221
                         ----------  v     i  i ----- -      v -   ----   v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC-TTAGAAGAAAA 545

  chrX_57944938_5   1222 CAT---------TTTTAACGGTCTTGG------CAATGATTTCTCAGCTA 1256
                            --------- i  vii ii     ------     i     i  v  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_57944938_5   1257 TGGCATGAAAAGTATAGACAACAAAACCAAAAATGAACAAGTGAAACTAC 1306
                           i  iv     i i ii        vv      ii i  i vii   v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_57944938_5   1307 AT-AAAACCAAAAACTTCTGTACAGCAAAGGGAACAATCAACAGAGTGAA 1355
                           -    ii        i   i vv      iv  v     v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_57944938_5   1356 GATGCAACCTACAGAATGAGATG---TATTTGGAAACAATATATTTGATA 1402
                         i vi     i        i  vi---      v   iv      i     
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_57944938_5   1403 AGAGA--TAAACTCAAAAAAAATAAGGAACATCTATAATTCAATAGCAAA 1450
                           i  -- iv ii  i  v v    i    vii  i  i      ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_57944938_5   1451 AAAACTCTAATATTTTGATTTTTAAAAGGGGCTAAGAACATAGGTAGATA 1500
                           i  v--    viiii   ?v-    v    v   i iv iii    i 
  L1M4_orf2#LINE/    796 AAGACA--AATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_57944938_5   1501 TTTGTCTAGAGAAGACATGCAAATGGCCAATAGATATATTTTTAAATGCT 1550
                            v  i i      i  i             iii i  vvvv i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_57944938_5   1551 TACTCACACTAATCATCAG 1569
                         i ---   ii ????????
  L1M4_orf2#LINE/    893 CA---ACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (155 / 90)
Gap_init rate = 0.03 (28 / 904), avg. gap size = 2.79 (78 / 28)  


2077 25.65 1.38 1.54  chrX_57969843_57971473.rev      490  1140 (491)    L1M4_orf2#LINE/L1      259   908 (0)  

  chrX_57969843_5    490 AAAGCAGCATGGTACTGACATAAAAAAACAACACAGGGACCAAGGGAATA 539
                           ii   ii        i     ii v -i   i vi  i   v      
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGATCAATGGAATA 307

  chrX_57969843_5    540 TAATGTAGAACTCAAAAACAAATCCCCACACCTACAGTAAACTCATTTTA 589
                         v   vv   iii  i   i   i  vi   ii  ii  v  i v     v
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_57969843_5    590 TTTATAGTTGCCAATAACATACATTGCAGAAA---T-GTCTTTCTCTTTG 635
                         vvi vi v      v v   v  v  vi    --- -      ---- ii
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT----TCA 403

  chrX_57969843_5    636 AAAAATGGTGCTGGGAAAA-TGAATATCTATATGCAAAAGAATGAAACTA 684
                          v              v  -  i   ? i i               ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_57969843_5    685 GACCTGTATCTCTCACTATATGCAGAAATGAAATCAAAATACATTAAAGA 734
                             iv  i   v   i    i  i    v  v       iv  i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_57969843_5    735 CTTAAACATAACATTTCAAGCTATGAAACCATTACAAAAAAACTTTTGGG 784
                          i    ii   v vi v  i    i    iv   v  i     v vv ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_57969843_5    785 AAACTCTCTAGGATGTTGGTCTGGGCAAGAATTTTT--GATGATTACCCC 832
                         v  v   iiiv  iv    vi i     vii   i --   -  v  v  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACC 602

  chrX_57969843_5    833 ACAAGCACAGGCAACTAAAGCAAAAATAAATAAAAGATACTACATCAAG- 881
                          v       i     v    v       i     vviv   v      i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_57969843_5    882 TTAAAATGCTGCTTCACATCAAAGGTAC-CTATCAAGAAAGTGAAAATAT 930
                               -i  vi vii v       -  -                  v i
  L1M4_orf2#LINE/    653 TTAAAA-ACTTTTGTGCTTCAAAGG-ACACTATCAAGAAAGTGAAAAGAC 700

  chrX_57969843_5    931 AACCCACAAAATGGGATAAAATATTTGGAAAGTACACATCTGACAAGGGA 980
                                 i       v          v   vi i i      i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_57969843_5    981 TTTATAACCAGAATGTATAAGGAGCACAAACAACTTTACTGAAAAAAAAA 1030
                         i  i  v       i     i  i v vv      i- v i v     i 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTC-AATAATAAAAAGA 799

  chrX_57969843_5   1031 TCTAATAATCTGATTTAAAAATGTGCAAAAGATTTGAATAAAAATTTCTC 1080
                         - v     i ii   ?       v     i          i v       
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_57969843_5   1081 AAAAGAAGACATACAAGTAACAAACAGGTATATGAAAAGGTGATCAACAT 1130
                         v        i      i ii v  i i i i        i  v       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_57969843_5   1131 TAGAGATTGA 1140
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (95 / 68)
Gap_init rate = 0.02 (13 / 650), avg. gap size = 1.46 (19 / 13)  


3087 27.23 0.99 0.88  chrX_58001379_58003783     1006  1912 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_58001379_5   1006 TGGAAGAACATTCCTTGTTCATGGGTAGGAAGAATCAATATCATGAAAAT 1055
                              ii i  i  v         i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_58001379_5   1056 GGCCATACGCCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1105
                            v    v      iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_58001379_5   1106 TACCAATGACTTTCTTCACAGAG-TTGGAATAAACT-ACTTTAAAGTTCA 1153
                          v   iivi i  i  ii    i-   -- i  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_58001379_5   1154 TATGGAGTCAAAAAAGAGCCCAGATT-GCCAAGTCAATCCTAAGCCAAAA 1202
                               iviiv  ii  -      v -     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_58001379_5   1203 GAACAAAGCTGGAGGCATCATGCTGCCTGACTTCAAACTATACTACAAGG 1252
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_58001379_5   1253 CTACAGTAACCAAAAGAGCATGATACTGGTACCAAAACAGAGATATAGGC 1302
                                  i   i v  ii  i      i iv ii i   v      ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_58001379_5   1303 AAATGGAAAAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAAC 1350
                         v       v    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_58001379_5   1351 CATCTGATTTTTGACAAACTTGACAAAAACAAGAAATGGGGAAAGGATTC 1400
                           vi       i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_58001379_5   1401 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1450
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_58001379_5   1451 TGAAAT-GGATCCCTTCCTTACACCTTCTACAAAAATTAATTCAAGATGG 1499
                             i -   i    v   i     v v            i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_58001379_5   1500 GTTAAAGACTTAAATGTTAGACTTAAAACCATAAAAACCCTAGAAGAAAA 1549
                         i i ?    i       v   vi      i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_58001379_5   1550 CCTAGACA-ATACCATTCAGGACATATGCATGGGCAAGGACTTCATGTCT 1598
                          v   i?i- v i -   iv   v vv vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_58001379_5   1599 AAAACACCAAAAGCAATGGTAACAAAAGCCAAAATTGACAAATGGGATCT 1648
                          vi            vvi i        vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_58001379_5   1649 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 1698
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_58001379_5   1699 ACAGGCAACCTATAGAATTGGAGAAGATTTTTGCAATCTACTCATCTGAC 1748
                          v  i     i i     v      i  v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_58001379_5   1749 AAAGAGCTAACATCCAGAATCTACAATGAACTCAAACAAATTTACAATAA 1798
                           i ii  vii         v  i  v      vv    v iv i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_58001379_5   1799 AAAACCAAACAACCCCATCAACAAGTGGACAAAGGATATGAACAGACACT 1848
                            iv    i     v  i? v  i   i        v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_58001379_5   1849 TCTCGAAAGAAGACATTTATGAA--GCCAACAGACACATGAAAAAATGCT 1896
                             v        i  -- ii  --     i ii          i     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_58001379_5   1897 CGTGATCACTGGCCAT 1912
                          ivv    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


2910 28.22 0.99 0.88  chrX_58017053_58023456     5005  5911 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_58017053_5   5005 TGGAAGAACATTGCATGCTCATGGGTAGTAAGAAACAATATCGTGAAAAA 5054
                              ii i  iv    i      i v v    vvi     i  v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_58017053_5   5055 GGCCATACTACCCAAGATAATTTATACATTCAATGCGATCCCCATCAAGC 5104
                            v     v     iv i  i  i v      i  i     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_58017053_5   5105 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5152
                          vi  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_58017053_5   5153 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGTCAAAAG 5202
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_58017053_5   5203 AACAAAGGTGGAAGCATCACGCTACCTGACTTCAAACTACACTACAAGGC 5252
                                v    i vv    i  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_58017053_5   5253 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5302
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_58017053_5   5303 AATGGAACAGAAC--AGAGCCCTCAGAAACAGTGCCACATATCTACAACT 5350
                                i    i--    i  --     i ivv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_58017053_5   5351 ATCTGATCTTTGACAAACATGACAAAATTAAGCAATGGGGAAAGGAT--T 5398
                          vi    i  i     ivi  v   i ii vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_58017053_5   5399 CCATATTTAATAAATGGTGCTGGGAAAACTGGCTAACCATATGTAGAAAG 5448
                          -- v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_58017053_5   5449 CTGAAATTGGATCTCTTCCTTACACCTTATACAAAAATTGATTCAAGATG 5498
                         v    i     i i  v   i     v            i i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_58017053_5   5499 GATTAAAGACTTAAATGTTAGA-CAAAAATCCACAAAAACCCTAGAAGAA 5547
                            i ?    i       v   - v    - i i    vi i        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAA 543

  chrX_58017053_5   5548 ACC-TAAGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5596
                          v -  i ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_58017053_5   5597 TAAACCACCAAAAGCAATGATAACAAAAGCCAAAATTGACAAGTGGGATC 5646
                           viv           vviii        vv     v  i  i v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_58017053_5   5647 TAATTAGA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5695
                          v  i i -     i -   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_58017053_5   5696 GAACAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACTCATCTG 5745
                            v  i     i i               v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_58017053_5   5746 ACAAAGGGCTAATACCCAGAATCTACAATGAACTCAAACAAATTTACAAA 5795
                          i  i  i  vi  i       v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_58017053_5   5796 AAAAAAACAAAGTACCCCATCAACAAGTGGACGAAGGATATGAACAGACA 5845
                              i     vv    v  i? v  i   i i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_58017053_5   5846 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCC 5895
                         i     v        i  vi viii     v ii          i    i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_58017053_5   5896 CATCATCACTGGCCAT 5911
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (155 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


 545 22.73 2.60 1.95  chrX_58069259_58070871      347   500 (1113)    L1M4_orf2#LINE/L1        1   155 (753)  

  chrX_58069259_5    347 TGAAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 396
                           i  ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_58069259_5    397 GGCCATACTGCC-AAAGTAATTTATAGATTCAATGTTATCCCCATCAAAC 445
                            v     v  -   v i  i  i        i iv     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_58069259_5    446 TACCA-CTGACTTTCTT-CACATAATTGGAAAAAACT-ACTTTAAACTTC 492
                          v   -   v    i  -  v -     -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_58069259_5    493 ATATGAAA 500
                              i  
  L1M4_orf2#LINE/    148 ATATGGAA 155

Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.04 (6 / 155), avg. gap size = 1.17 (7 / 6)  

1924 27.87 1.15 0.33  chrX_58069259_58070871      511  1120 (493)    L1M4_orf2#LINE/L1      294   908 (0)  

  chrX_58069259_5    511 AGACCAATAGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACA 560
                            i    i   i    iv   ivii         vv   i    i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_58069259_5    561 ACCATCTGAATTT-GACAAACCTGAC--GTTCACAACAATAGGAAAAAGG 607
                         ii  vi   v   -     ivv  v -- vi  iv-    i  i   iii
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAA 392

  chrX_58069259_5    608 CTCTCTACTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATGTGCAGAA 657
                         ivv   vi i  i        i     v      v  ?   ii    i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_58069259_5    658 AAATGAAACTGGACTCCTTCCTTACACCTTATACAAAAATCAACTCAAGA 707
                         i      ii     i   v   i     v           i       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_58069259_5    708 TGGATCAAAGACTTAAAAGTAAGACCTAGGACCATAAAAATTCTAGAAGA 757
                                ?    i    v      v   ii  i      v ii       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_58069259_5    758 AAACCTAGGCA-ATACCATTCAGGATACAGGCATGGGTAAAAACTTCATG 806
                             v    ?i- v i -   iv  iviv  vv i  i  viii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_58069259_5    807 ACTAAAACACCAAAAGCAATGGCAATGAAAGCCAAAATTGACAAATGTGA 856
                         iv  vi            vvi    ii    vv     v  i    vv  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_58069259_5    857 TCTAAGTAAACTAAAGAGCTTCCGCACAGCAAAAGAAACTATTACCAGAG 906
                         ii v vi   v v  i i   ii ii vv    i  v     i vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_58069259_5    907 TGAACCGGCAACCTACAGAATGGGAGAAAAT-TTTGCAACCTATCCATCT 955
                             vv i     i                 -       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_58069259_5    956 GACAAAGGGCTAATATCTAGAATCTACAAAGAACTTAAACAAATTTACAA 1005
                           i  i  i  vi    i     v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_58069259_5   1006 GAAAAAAACAAACAACCCCATCAAAAAATGGGCAAAGGATATAAACAGAC 1055
                         v     i     i     v  i?                 v i  i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_58069259_5   1056 ACTTCTCAAAAGAAGACATTTATGCAGCCAACAG--ACATGAAAAAATGC 1103
                          i     v        i  vi viii     i i--         i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_58069259_5   1104 ACACCATCACCGGTCAT 1120
                         v  v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (100 / 66)
Gap_init rate = 0.01 (7 / 615), avg. gap size = 1.29 (9 / 7)  


3128 28.96 0.00 0.00  chrX_58306183_58310991     3409  4316 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_58306183_5   3409 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 3458
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_58306183_5   3459 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 3508
                            v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_58306183_5   3509 TACCAATGACTTTCTTCACAGAATTGGAAAAAACGACTTTAAAGTTCGTA 3558
                          v   iivi i  i  ii     v v  v  ivi  iii    i   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_58306183_5   3559 TGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGTCAAAAGAA 3608
                              viiv  ii  v  viv  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_58306183_5   3609 CAAAGCTGGAGACATCATGCTACCTGACTCCAAACTATACTACAATGCTA 3658
                              i     ivv   ii  v  ii i i    viv        v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_58306183_5   3659 CAGTAAGCAAAACAGCGTGGTACTGGTACCAAAACAGAGATATAGATCAA 3708
                               v   i    i          i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_58306183_5   3709 TTGAAGAGAACGTAGCCCTCAGAAATAGTGCCACTTATCTACAACCATCT 3758
                          v   v    ivv  vvii        ivv   ivi  i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_58306183_5   3759 GATCTTTGACAAACCTGACAAAAACAAGGAATGGGGAAAGGATTCCCTAT 3808
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_58306183_5   3809 TTAATAAATGCTGCTGGGAAAACTGGCTGGCCATATGTAGAAAGCTGAAA 3858
                          i  i     v        v      v i?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_58306183_5   3859 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 3908
                         i    i    v   i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_58306183_5   3909 AGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 3958
                             i  v    v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_58306183_5   3959 GCAATACTATTCAGGACATAGGCATGAGCAAGGACTTCATGTCTAAAACA 4008
                          ?ivv v v   iv   v v  vv ii    v ii   v ivv  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_58306183_5   4009 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAATTAA 4058
                                  vvi          vv     v  i    vi  ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_58306183_5   4059 ACTCAAGAGCTTCTGCATAACAAAAGAAACTACCATCAGCGTGAACAGGC 4108
                          v i  i i   i  iiivv    i  v    i  vv iv     v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_58306183_5   4109 AACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAGGG 4158
                             i   i             v       vii ivi      i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_58306183_5   4159 CTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAAAC 4208
                           vi          v  i         vv    v iv i  v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_58306183_5   4209 AAACAACCCCATCAAAAAGTGGGCGAAGGGTATGAACAGACACTTCTCAA 4258
                            i     v  i?    i     i    i v    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_58306183_5   4259 AAGACGACATTTATGCAGCCAAGAAACACATGAAAACATGCTCATCATTA 4308
                             v  i  vi viii     v  i          v       v   i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_58306183_5   4309 CTGGCCAT 4316
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.33 (148 / 111)
Gap_init rate = 0.00 (0 / 908), avg. gap size = 0.00 (0 / 0)  


3234 26.21 0.66 0.66  chrX_61519095_61525365     4871  5778 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61519095_6   4871 TGGAAGAACATTCCTTGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4920
                              ii i  i  v  i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61519095_6   4921 GGCCATACTGCCCGAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4970
                            v     v   i iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61519095_6   4971 TACCAA-TGCCTTTCTTCATAGAA-TTGGAAAAAACTACTTC-AAAGTTC 5017
                          v   i-       i  -ii    -   -- v  i  iv i -   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_61519095_6   5018 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCTTAAGCCAAAA 5067
                                 viiv  ii  v  v v  v     iv       i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_61519095_6   5068 GAACAAAGGTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGT 5117
                                 v      vv       v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_61519095_6   5118 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5167
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_61519095_6   5168 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACGTATCTACAAC 5215
                                 i    i--    i  --        vv   iii  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_61519095_6   5216 TATCTGTTCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5265
                         i vi  v i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_61519095_6   5266 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5315
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_61519095_6   5316 TGAAAGTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5365
                             iv    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_61519095_6   5366 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5415
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_61519095_6   5416 CCTAGGCTTTACCATTCAGGACATAGGCATGGGGAAGGACTTCATGTCTA 5465
                          v    ?v v viv   iv   v v  vv i  v  v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_61519095_6   5466 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5515
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_61519095_6   5516 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5565
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_61519095_6   5566 CAGGCAACCTACAAAATAGGAGAAAATTTTCACAACCCACTA-ATCTGAC 5614
                         v  i     i   i   i         v  ii   vi  -  -      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGAT 744

  chrX_61519095_6   5615 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5664
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_61519095_6   5665 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5714
                            i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_61519095_6   5715 TCTCAAAAGAAGACATTTATGCAGTCAAATAACACATGAAAAAATGCTCA 5764
                             v        i  vi viii i   vv i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_61519095_6   5765 CCATCACTGGCCAT 5778
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (132 / 102)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2831 28.30 0.88 0.88  chrX_61557428_61563843     5016  5923 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61557428_6   5016 TGGAAGAACATTCCATTCTCATGGGTAGGAAGAATCAATATTATGAAAAT 5065
                              ii i  i    vi      i v      v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61557428_6   5066 AGCCTTAGTGCCCAAGGTAATTTATAGATTCAATGACATCCCAATCAAGC 5115
                         i  vv  v v     iv i  i  i        i vv     v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61557428_6   5116 TATCAATGACTTTCTTTACAGAA-TTGGAAAAAAACT-ACGTTAAAGTTC 5163
                          vi  iivi i  i   i     -   --- v  i  - ivi    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_61557428_6   5164 ATATGGAA-T-CAAAATACAGCCCGCATCACCAAGTCAATCCTAAGCCAA 5211
                                 - -   iiv  --  v v  vi    iv     i i ivv i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_61557428_6   5212 AAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAA 5261
                                   i      vv       v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_61557428_6   5262 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAGCAGAGATATAG 5311
                         i          i   i    ii         i iv iiii   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_61557428_6   5312 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACA 5359
                          i        i    i--    i  --        vv  ii i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_61557428_6   5360 ACTATCTCATCTTTGAGAAACCTGACAAAAATAAGAAATGGGGAAAGGAT 5409
                         iii vi v  i  i  v  ivv  v   i vi vvv           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_61557428_6   5410 TCCCTATTTAATTTATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAA 5459
                         vvi  v  i  ivv            v      v  ?   ii  i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_61557428_6   5460 GCTGAAACGGAATCCCTTCCTTACACATTATACAAAAATTAATTCAAGAT 5509
                         iv    iiv i i    v   i    vv              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_61557428_6   5510 GGATGAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5559
                             v ?    i    i  v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_61557428_6   5560 AACCTAGACATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTC 5609
                            v   i?i v viv   iv   v v  vv i i   v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_61557428_6   5610 TAAAACACCAATAGTAATGGCAACAAAAGCCAAAATTGACAAACGGGATC 5659
                           vi       v  i vvi          vv     v  i   iv   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_61557428_6   5660 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5709
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_61557428_6   5710 AACAGGCAACCTACAAAATGGGAGAAAATTTTCCCAACTGACTCATCTGA 5759
                           v  i     i   i             v  iv   v v ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_61557428_6   5760 CAAAGGGCTAATATCCAGAAAATACAACGAACTCA-ACAAATTTACAGGA 5808
                         i  i  i  vi         v   i  v      v-    v iv i iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_61557428_6   5809 AAAAAACAAACAACCCA-TCAAAAAGTGGGCAAAGGACATGAACAGACAC 5857
                             i     i      - i?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_61557428_6   5858 TTCTCAAAAGAAGACATTTGTGCAGCCAAAAAACACATGAAAAAAATGCT 5907
                              v        i  viiviii     v  i          i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chrX_61557428_6   5908 CACCATCACTGGCCAT 5923
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (146 / 107)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


2725 29.69 1.10 0.88  chrX_61744580_61750584     4607  5512 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61744580_6   4607 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAATT 4656
                              ii i  i     i      i v      v i     i  v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61744580_6   4657 GGCCATACTGCCCAAGGTAATTTATCGATTCAATGCCGTCCCCATCAAGC 4706
                            v     v     iv i  i  iv       i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61744580_6   4707 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4754
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_61744580_6   4755 TATGGAACCAAAAAAGAACCCTCATTGCCAAGTCAATCCTAAGCCA-AAG 4803
                                viiv  ii  v  vvv  v     iv     i i ivv -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_61744580_6   4804 AACAAAGCTGCAAGCATCAGGCTACCTGACTTTAAACTATACTACAAGGC 4853
                                i  v i vv   vi  v  ii i  i   viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_61744580_6   4854 TACAGTAACCAAAACAGCATGGTACTGGTAGCAAAACAGAGATATAGACC 4903
                                 i   i    ii         i vv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_61744580_6   4904 AATGGAACAGAAT--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 4951
                                i     --    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_61744580_6   4952 ATCTGATCTTTGACAAACCCGACAAAAAGAAGAAGTGGGTAA----TGGT 4997
                          vi    i  i     ivvi v   i vv vvv i    v  ---- i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_61744580_6   4998 TTCCTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAA 5047
                         ---   -  i  i              v      v  ?i  i   i i  
  L1M4_orf2#LINE/    397 ---CTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_61744580_6   5048 AGCTGAAACTGGATCCCTTCCTTATGCCTCATACAAAGATTAATTCAAA- 5096
                         iiv    ii    i    v   i ii  vi       i     i     -
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_61744580_6   5097 TGGATTAAAGACTTAAGTGTTAGACCTGAAGCCATAACAAGCCTAGTAGA 5146
                              i ?    i   i   v   v  i  i i    v vv i   v   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_61744580_6   5147 AAACCTAGGCATTACCTTTCAGGACATAGGCATGGGCAAATACTTCATGA 5196
                             v    ?i v vii   iv   v v  vv i     vvii   v ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_61744580_6   5197 CTAAAACACCAAAAACAATGGCAACAAAAGCCAAAATTTACAAATGAAAT 5246
                         v  vi         i  vvi          vv     vv i    vii i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_61744580_6   5247 CTAATTAAACTAAAGAGCTTCAGCACAGCAAAATAAACTACCATCAGAGT 5296
                         i v  i   v v  i i   iv ii vv    iv v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_61744580_6   5297 GAACAGGCAACCTACAGAATAAGAGAACATTTTTGCAACCTACTCATCTG 5346
                            v  i     i       ii     v  v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_61744580_6   5347 ACAAAGGGCTAATATCCAGAATCTACAATGACCTGGAACAAATTTACAAG 5396
                          i  i  i  vi          v  i  v  v  vvv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_61744580_6   5397 AAAAAAACAAACAACTCCATCAGAAAGTGCGCGAAGGATATGAACAGACA 5446
                              i     i   i v  i?i   i  v  i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_61744580_6   5447 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 5496
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_61744580_6   5497 CATCATCACTGGCCAT 5512
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (156 / 109)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


3101 27.75 0.66 0.66  chrX_61823715_61827987     2873  3780 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61823715_6   2873 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2922
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61823715_6   2923 GGCCATACTGCCCAAGGTAACTTATACATTCAATGCCATCCCCATCAAGC 2972
                            v     v     iv i ii  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61823715_6   2973 TACTAACGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 3022
                          v i i vi i  i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_61823715_6   3023 TGGAACCAAAAAAGAGTCCCCA---TTGCCAAATCAATCCTAAGCCAAAA 3069
                              viiv  ii  ---    --- v      v     i i ivv i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_61823715_6   3070 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTAAAGTACAAGG 3119
                                 i      vv   ii  v  ii i      vivv v     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_61823715_6   3120 CTACAGTACCCAAAACAGCATGGTACTGGTACCAAAAGAGAGATATAGAC 3169
                                 vi   i    ii         i iv ii v   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_61823715_6   3170 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATACCTACAAC 3217
                                 i    i--    i  --        vv   i i ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_61823715_6   3218 TATCTGATCTTTGACAAACCTGAGAAAAACGAGAAATGGGGAAAAGATTC 3267
                         i vi    i  i     ivv  vv  i v ivvv          ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_61823715_6   3268 CCTATTTAATAAATGGTGCTGGGAAAACTAGCTAGCCATATGTAGAAAGC 3317
                         i  v  i  i              v    i v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_61823715_6   3318 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 3367
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_61823715_6   3368 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAATCCCTAGAAGAAAA 3417
                           i ?    i       v   v       i      ii i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_61823715_6   3418 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAACGACTTCATGTCT 3466
                          v    ?i- v i -   iv   v v  vv i     i ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_61823715_6   3467 AAAACACCAAAAGCAATGACAACGGAAGCCAAAATTGACAAATGGGATCT 3516
                          vi            vvii    ii   vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_61823715_6   3517 AATTAAACGAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3566
                         v  i   vvv  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_61823715_6   3567 ACAGGCAACCTACAGAATGGGAGAAAATATTTGCAACCTACTCATCTGAC 3616
                          v  i     i                         vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_61823715_6   3617 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 3666
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_61823715_6   3667 AAAAACAAAGAACCCCATCAAAAGGTAGGCGAAGGACATGAACAGACACT 3716
                            i     v     v  i?   ii i   i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_61823715_6   3717 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 3766
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_61823715_6   3767 TCATCACTGGCCAT 3780
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2715 25.14 6.57 1.96  chrX_61832736_61835371     1296  2162 (474)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_61832736_6   1296 GGAAAGATATCTTGTGATCATGAATTGGAAGGATTAATATTCTTTAAATG 1345
                                    iii  v     i        iv        v  v i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_61832736_6   1346 CCCATACAACCCAAAGTGATCTACATATTCAATGCAATCTCTATCAAAAC 1395
                         v v    vv      v         v      i      i         i
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_61832736_6   1396 TCAAAGTGCATATTTCACATATAAATAGAAAAA--AAACCTGAAATGTAT 1443
                         i v iv   v v   ii  v --   v  v  i--i v   i    vi  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGA--AATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_61832736_6   1444 GTGGAATCACAAAAGACTCCAAGTAGCCAAAGCAATTTTGAATAAGAAGA 1493
                         i     vii   ii   i vi i        i    i     v       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_61832736_6   1494 ACAAAGCTGGAGGTGGAGGGATCACATTACCTGATTTCAAAATATGGTAC 1543
                               i      ------iv     i v  ii         iv iv   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG------ACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_61832736_6   1544 AAAGCTATACTAATCAAGA-GGTCGTGGTACTTGAATAAAAACATACACA 1592
                                i v         -i  -        v v    ii i v   i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGT-GTGGTACTGGCATAAGGATAGACATA 292

  chrX_61832736_6   1593 TAGACCACTGCAACA----TG-------------------------TTGT 1613
                             i  v  v  i ----  -------------------------  i 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_61832736_6   1614 G---ACTTAATTTTCCACAAAGTGGACAAGAACACATTATGGTGAAAGGA 1660
                          --- v  i      v    i vv v     v  iviv    v     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_61832736_6   1661 CAGTCTCTTAAATAAATGATGTTGAGAAAACTGGATATTTATATGCAATG 1710
                         i     i  v  i     i  i  i  v         ?ii i      vi
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_61832736_6   1711 TAATAAAACTAGGCTCTTATCACACATCAAATA-AAAAGTCAACT-AAAA 1758
                         v   i  ii i i i i  i v    i  v   -    i i    -    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_61832736_6   1759 TGGATTAAATAATTAATCATAAGATCTGAAACTGTTAGACAACTAGAAGA 1808
                              i ? v vi   vii     v  i     i v i  vvi       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_61832736_6   1809 AAACATAAGGGGAAAGCATC-TGTACATTGGTCTGGACAATGATTTCTTG 1857
                                i ? v   v v  -  -  v    vi i i     i      i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_61832736_6   1858 GCTATGACCCCAAAAGCACAGTCTCTGAAAGGAAAAATAGACAAATGGGA 1907
                          v      v           iv vvii    i         i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_61832736_6   1908 TTGCATCAAACTGAAAGTCTTCTGCGTGGCAAAAGAAACAATCAGTAGTG 1957
                         i v       v v   iv   i  i ivv    i  v  v    iv iv 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_61832736_6   1958 GGGGAAGACAACGTATGGAATGGGAGAAAATAC-------------ATCT 1994
                         v ii        vi ii               i-------------    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_61832736_6   1995 GTT---GGGTTAATAATCAAAATATATAAGGAACTCAAAGAACTCCATAG 2041
                          v ---  ii vi  vi  i         i      vv v     v   i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_61832736_6   2042 CCAGAA-ACA--TGACTTGATTAAAGAATGGGCAAAGGAGCTGAACAGAC 2088
                         iv i  -   -- i  iii   ?  i             vi    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_61832736_6   2089 ATTTCTCCAAAGAAGATATACAAATGACCAATGGATTTTTGAAAAAAAAA 2138
                                                   i     iiiiviv      i ---
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--- 888

  chrX_61832736_6   2139 ATTCCTTTCAACATCACTTACCAT 2162
                         -- v  --        ????????
  L1M4_orf2#LINE/    889 --TGCT--CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (125 / 89)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 4.11 (74 / 18)  


 262 17.81 13.70 1.37  chrX_61837717_61839985      500   572 (1697)    L1M4_orf2#LINE/L1      120   201 (707)  

  chrX_61837717_6    500 AAAAATTTACAAAC----------ATTCCTATGGAAATGCAATGTAATCA 539
                          i     v    i ----------    v             v v vi  
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_61837717_6    540 GAATAGCCAACACAGTCTTCATAAAAGGAGGAC 572
                                   v   i    v -     i  i  
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGA-AAAAGAAGAAC 201

Transitions / transversions = 0.86 (6 / 7)
Gap_init rate = 0.02 (2 / 82), avg. gap size = 5.50 (11 / 2)  

2575 15.62 10.51 2.70  chrX_61837717_61839985     1113  1778 (491)    L1M4_orf2#LINE/L1      191   908 (0)  

  chrX_61837717_6   1113 AAAAGGAGAGAAATGTTAGAGGGCTCAGATCTGCCAGCAATTTCAAAAAT 1162
                              i   iv  v   i    i    v -  v  --           v 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACA-CTTCC--CAATTTCAAAACT 237

  chrX_61837717_6   1163 TACTACAAAGCTA---------------TGTGGCA--------------- 1182
                                      ---------------     i ---------------
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_61837717_6   1183 -------GACCAATGAAATAGAATTGAGAATCCAGGAATAAAC--ATACA 1223
                         -------  i     i             i     i       --     
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_61837717_6   1224 TTTATGATGACCAGCCAATTTTCAACAAGGATGTCAAGACTATTCAATGG 1273
                               i ---  iiii      i      i  i      i         
  L1M4_orf2#LINE/    338 TTTATGGT---CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_61837717_6   1274 GGAAATAATAGT-TTTTCAATAAATGGTG--GGTAGACAACTGGATATGC 1320
                              v      -       i        --  --            ?v 
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGG--GACAACTGGATAKCC 432

  chrX_61837717_6   1321 ACATGCAAAAGGAAGGAAATTGTACTCCAACATCACAACATATTTAAAAA 1370
                                    -  v   i   v  i  v  v     v     vi     
  L1M4_orf2#LINE/    433 ACATGCAAAAG-AATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_61837717_6   1371 TCATCTCACTATGTGCCAGAGACCTAAATAT--GAGCTTCAAATTAATCA 1418
                          i v    vv   vii  ?          i --     -v   i  - v 
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTA-TAA 529

  chrX_61837717_6   1419 AACTCTTAGAAGAAAACTTTGGTGTAACTGTTCGTGATCATTACTTAGGC 1468
                                          v v  ?    v v       i v viv      
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_61837717_6   1469 AATG-TTTCTCTACA-ATAACAATAAAAGCACAAGCAACAACAACAACAA 1516
                             -     -  v -  i   vi                 ----  v  
  L1M4_orf2#LINE/    580 AATGGTTTCT-TAGATATGACACCAAAAGCACAAGCAACAA----AAGAA 624

  chrX_61837717_6   1517 AAAATAGATAAAGTGGACTTCATCTAAAT-AAAAGCTTTTGTGGTTT--- 1562
                                     v           v    -    i        v  i---
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_61837717_6   1563 ---CAC-----AAAAAG-GAAAA-----CTCACATA-TATGAGAAAATTT 1597
                         ---   ----- i    -     ----- i    v - iv        v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_61837717_6   1598 GTGCAAGTCATA-AGCTGATAAGGGTCTACTATTCAGATTATATAAA-AA 1645
                         v     i     - v          v  vv   i    v        -  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_61837717_6   1646 CTCTAGCAACTCAATAGTTTAAAAATGT---TGATCAAAATAAAAAGCAT 1692
                             vi          i --     vii--- i i v  v ?    iiiv
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAAT--AAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_61837717_6   1693 GAAAATGATTTGAATGAACATTTCTCCAAAGAAGATATACAAATGGCCAA 1742
                          v   v         ii                                 
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_61837717_6   1743 TAAGCACATGAAAAGATTCTCAACATTCTTAGCCAT 1778
                                          v        iv????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (50 / 50)
Gap_init rate = 0.04 (27 / 718), avg. gap size = 3.26 (88 / 27)  


2566 28.59 2.58 0.90  chrX_61889811_61896480     5286  6177 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_61889811_6   5286 GAAAAAAAATTCTATGCTCATGGAGAGGAAGAATTAATATTGTGGAAATG 5335
                          i   i v  i i   i       vv      v          vi i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_61889811_6   5336 GCCAAACTGCCCAAAGTAATATACAGATTCAATGCTATTTCCACCAAGCT 5385
                           v v   v      v i  v           i  v  ii i i   iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_61889811_6   5386 ACCATAGACTTATTTCACAGAACTAGAAAAAACT-ACTTTAAATTTTGTA 5434
                         v   vvvi i v   ii     v v  v  i-  - iii    v  ii  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chrX_61889811_6   5435 TGGAACCAAAAAAGAGCCCATATAGCCAGGACAATCCTAATCAAAAAGAA 5484
                              viiv  ii  v  viv       ii      i i vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_61889811_6   5485 CAGAGCTAGAGGCATCATTCCACTGGACTTCAAACTACACTACAAGGCTA 5534
                           i  i i    vv   iv iv ivi i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_61889811_6   5535 CAGTAACCAATATAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 5584
                               i   v i  ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_61889811_6   5585 TGGGACAGA-----GGCCTCAGTAGTAACACCACACATCTACAACCATCT 5629
                            i i   ----- ivii   v i   vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_61889811_6   5630 AATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGA-ATTCCTA 5678
                         i  i   i    ivv  v   i v  vv            i - v  i -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT- 399

  chrX_61889811_6   5679 GTTAATAAATAGTGTTGGGAAAACTGACTAGCCATATGCAGAAACCTGAA 5728
                         v i  i    i   i     v     iv  ?   i     i  ivv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_61889811_6   5729 ATTAGATCCCTTCCTTACACCTTATACAGTAATTAACTCAAGATGGATTA 5778
                         i  i  i    v   i     v      iv           i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_61889811_6   5779 GAGACTTATATATAAAACCTAAAACTATACAAACCCT-AGGATAAAACCT 5827
                         ?    i  v  i   i v           -    i  -  i v     v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACAT 548

  chrX_61889811_6   5828 AGGCAATACTATTCAGGACAC--AGTCATAGGCAAATACTTCATGAATAA 5875
                            ?ivv v v   iv   vi--i  --       vvii   v ii   v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT--TAGGCAATGGTTTCTTAGATAT 596

  chrX_61889811_6   5876 AACACCAAAAGCAATTGCAACGAAAGACAAAATTGACAAATGAGATTTAA 5925
                         i            vvv     i     v     v  i    vi  i  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_61889811_6   5926 TTAAA-CTAAAGAGTTTC-TGCT-CAGGGAAAGAAACTAACATCAGAGTG 5972
                          i   -i    i v   i-    -  ---  i  v    v  vv i    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCA---AAGGACACTATCAAGAAAGTG 693

  chrX_61889811_6   5973 AATTGGCAACCTACAGAATGGGAGAAAAGTTTTGCAA-TC---TATCTGA 6018
                           vv i     i                vv       -  ---       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_61889811_6   6019 CAAAGGGCTAATATCCAGAATCTACAAGAAACTTAAACAAATTTACAAGA 6068
                         i  i  i  vi          v  i  ii    ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_61889811_6   6069 AAAAAA-----AACCTATTCAAAAAGTGGGTGAAGGACATGAACAGACAC 6113
                             i -----    i v i?    i    ii     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_61889811_6   6114 TTTTAAAAAGAAGACATTTATGCAGCCAACAAACAT-TAAGAAAAAGCTC 6162
                           i vv        i  vi viii     i  i  i- i i  i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_61889811_6   6163 ATAATCACTGGTCAT 6177
                          vv    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (148 / 103)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 1.82 (31 / 17)  


2185 26.92 5.38 1.83  chrX_61897198_61899326.rev      766  1638 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_61897198_6    766 AATACATTTCATGTTCATAAACAGAAAGAATCAACATTGTTAAAATAGCT 815
                           v i  ii         ii iv i    v i  i        i  i  v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_61897198_6    816 ATACTGCCCAAAGCTATTTACAAGTTTACTGCAATTCCTATTATG-TACA 864
                              v      viv  i    ii  i vi     i     i vi- v v
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_61897198_6    865 AATTACATTCTTCACAAAACTAGAAAAAACAATCTTAAAATACATATGGA 914
                          ii i v  i  ii  i  v v  v  ivii   i      v        
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_61897198_6    915 A---CAAAAAAATCCCA-AATAGCCAAGGCAATCCTAAGCAAAAAGGACA 960
                          ---   iii --    -         ii     i i iv  i   i   
  L1M4_orf2#LINE/    155 AATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_61897198_6    961 AAGCTGGAGGCATCATGCTACCCGACTTTAAA-----CTACAGGGGCTAC 1005
                            i      vv   ii  v   i i  i   -----     ii -    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG-CTAC 251

  chrX_61897198_6   1006 AGTAATCAAAACAGTGTGCTACTGGTACTAAA---ACACACATAGACCAA 1052
                                  i        v      i -   i--- v   i     i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATCAA 300

  chrX_61897198_6   1053 TGAAACAGAATAGAGAACTCAGAAATAAGGACACACACCTGCAACTATTT 1102
                           i  i     v    iii         ivv  i   ii iiiiii v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_61897198_6   1103 AATCTTCCACAAACATGATTAAAACAAGCAATGTGGAAATGACTCCCTAT 1152
                         i  i   v    ivi  viv i v  vv     v     vi ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_61897198_6   1153 TCACTAAACTGTGCAAGAATAACTGGCTAGACATATGCAAAAGATTGAAA 1202
                            vi   iv    vi i i      v  ?v  i          v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_61897198_6   1203 CCTGACCCTTTCCTTACACCACATACAAAAATTAACTCAAGATGAATAAA 1252
                         iiv     i v   i      i                  i   i  v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_61897198_6   1253 AGACTTAAATGGAAAACCCAAAACTATAAAGACCCTGAAAGACAACCTAA 1302
                             i      v  i v i           ivi i ii    v   v  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_61897198_6   1303 GCAATATAATCCT-G-GACATAGGAACAGGCAAAGATTTTATA-ACAAAG 1349
                          ?i-  -    i - -   v v  ivi      v i   iv  - i ---
  L1M4_orf2#LINE/    551 GNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA--- 595

  chrX_61897198_6   1350 TTGACAATAGAACTCTTGCACA-GCAA-AACAACAACAACA-ACAA---- 1392
                         -     vi i  -----     -    -  v iv  v  i - i  ----
  L1M4_orf2#LINE/    596 -TGACACCAAAA-----GCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_61897198_6   1393 -----CAACAACAATAACAAC------------AACAACAACTATCAACA 1425
                         -----  v   v v   v   ------------  vi   -       v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGA 688

  chrX_61897198_6   1426 TAGTGAACAGAAAACCTGCAGAATGAAAGAAAATTTTTGCAAACTATACA 1475
                         v      v   v    ii       ii       v        ii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_61897198_6   1476 TCTGACAACAGTCTGATATCCAGCATCCATAAGTA--TCTTA-AACAAAG 1522
                              i  vi v  vi       v  vi    iv --     -   vv i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_61897198_6   1523 TTATAAGACATCAAA-AACCTCATTTAAAT-TGGGCAAAGGACAGGAACA 1570
                          v    i viv    -    iv   ?   v-           ivv   i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_61897198_6   1571 GACCCTTTTCAAAAGAAGACATACACATGGCCAAGAATCA--TGAAAAAA 1618
                            vi  i  v        i     v        v  v  --      i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_61897198_6   1619 AGCTTAACCTCACTTATCAT 1638
                         v   i   v   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (137 / 94)
Gap_init rate = 0.03 (26 / 904), avg. gap size = 2.42 (63 / 26)  


2842 26.53 2.45 1.23  chrX_61900678_61902795.rev      732  1628 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61900678_6    732 TGGAAAGATATTCCATATTCATTGATTAGAAGAATCACTATTGTTAAAAT 781
                                    i    i     v    i     v i v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61900678_6    782 GTCTATATTACTAAAAGCAATCTGTAGATTCAATACAGTCTGTGTCAAAA 831
                          v v   i v iv   vii    ii        ii  i  iv i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61900678_6    832 TGTCAACAACATTCTTTACAGAAAT-GAAAACCTTAAAAATTCTAAAATC 880
                          vi  i vi v  i   i       -  v  v  ----i  i       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT----GATCCTAAAATT 146

  chrX_61900678_6    881 TATAAAGAATTACAAATAAC--AGAACAGCCAAAGGTATTTTGAGCAAAA 928
                         i   vi   v i   ivi  --    i       ivv  i    iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_61900678_6    929 AGAATGAAACGGAAGGAATTACATTATCTGGCTTCAAATTATACTACAGA 978
                             ii  iiv i    v i   i vi iiii      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_61900678_6    979 GCTCTAGTAACCACAACATCCTGGTATT----TTAGTAAAGACTCATAGA 1024
                            vi     i  vi   viv     i ---- v  v v    vi     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_61900678_6   1025 CCAATGGAACAGAATAGAAAACCGAGAAATGAATCCATACATCTGCAGTG 1074
                         i        i     v  i ii v      i  i        i iii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_61900678_6   1075 TACTCATTTTTAACAAAGATGCAAATACACATT----GGTGAAAAGACAG 1120
                         v i v     ii    i i   v  v  -    ----  v    ii i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAG 395

  chrX_61900678_6   1121 TCTCTTCAATAAATGGTGCTGGAAAACCTGGATATACATCTGCAAAAAAA 1170
                            i     i            i v v       ?v  iv       i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_61900678_6   1171 TGAAAGTAGAATCCTATCTCTGGCAATAAACAAAAATAAAATCTAAATAG 1220
                             iv i  vi    i   vvi v   v        v  v  v    i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_61900678_6   1221 ATTAAAGGCTTAAATCTAAGTCCTCAAACAATGAAAGTACTAAAATAAAT 1270
                           i ?  i i     v    vv  v    v  i   v vi  i  v   v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_61900678_6   1271 --TGGGAATA--CTTTCTAGGTAA--TTGGAGTGGACAA-GATTTTTTTG 1313
                         -- i  ?i  --ii   ---  i --    iv i i   - i   i  v 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTC---GTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_61900678_6   1314 A-GTAACACCCCACAAGAACAGGCAATCAAAGCAAAAATAAATAAATGGA 1362
                          -i i     -- v   v   i    iv    v       i      v i
  L1M4_orf2#LINE/    593 ATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_61900678_6   1363 ATCACATCAAG-TTAAAAAGATTCTGCAAGTCAAAGGCGACAATCAACAA 1411
                          iiv      i-       v-  i  iivv       vv  v     v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_61900678_6   1412 AGTGAAGAGACAACCCACAGAATAGAAGAAAATATTTGCAAGCTACCCAT 1461
                               i                i i               iii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_61900678_6   1462 CTGATACGGTATTAATAACTGGAATATATAAGGAATTCAAACATCTCTAT 1511
                               v  v i vi  v ii          i   i  vv   v   v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_61900678_6   1512 AGGAAAAATTTGAATA--TGATTTTTAAAATTGGCAACAGATCAGAATAG 1559
                          iv     vvii    --iv v  ?v     v     vi   iv      
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_61900678_6   1560 ACATTTCTCAAAAGAAGATATACAAATGGCAAATAGGTACATGAAAAGGT 1609
                                  v                    v    i i          i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_61900678_6   1610 GCTCAACATCCTCGAACAT 1628
                                   v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (135 / 99)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.06 (33 / 16)  


3109 27.12 0.99 0.88  chrX_61904019_61910106.rev     4691  5597 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61904019_6   4691 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATACCATGAAAAT 4740
                              ii i  i     i      i v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61904019_6   4741 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4790
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61904019_6   4791 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4838
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_61904019_6   4839 TATGGAACCAAAAAAGAGTCCGCATTGCCAAGTCAATCCTAAGCAAAAAG 4888
                                viiv  ii  vi v v  v     iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_61904019_6   4889 AACAAAGCTAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4938
                                i i    vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_61904019_6   4939 TCCAGTAACCAAAACAGCATGGTACTTGTACGAAAACAGAGATATAGACC 4988
                          v      i   i    ii       v i ii ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_61904019_6   4989 AATGGAACAGAATAGAGCACTCAGAAATAATGCAGCATATCTACAACTAT 5038
                                i     v   viii         vv vii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_61904019_6   5039 CTGTTCTTTGACAAACCTGACAAAAAGAAGAAATGGGGTAAGGAT--TCC 5086
                         i  v i  i     ivv  v   i vv vvv       v   i  --  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chrX_61904019_6   5087 GTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5136
                         - v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_61904019_6   5137 GAAACTGGATTCCTTCCTTACAACTTATACAAAAATTAATTCAAGATGGA 5186
                            ii    ii   v   i   v v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_61904019_6   5187 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5236
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_61904019_6   5237 CTCGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5284
                         v v  ?-   --i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_61904019_6   5285 AAGACACCAAAAGCAATGGCAACACAAGCCAAAATAGACAAATGGGATCT 5334
                          v             vvi      v   vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_61904019_6   5335 AATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA---T 5381
                         v  iv  v v  i i   i  ii vv    i  v    i  --   --- 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--AGAAAGT 692

  chrX_61904019_6   5382 GAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTG 5431
                            v  i     i   i             v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_61904019_6   5432 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 5481
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_61904019_6   5482 AAAAAAATAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 5531
                              i i   i     v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_61904019_6   5532 CTTGTCAAAAGAAGACATTTATGCAGCCAAAAGATACATGAAAAAATGCT 5581
                         i  v  v        i  vi viii     v iii         i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_61904019_6   5582 CATCATCACTGGCCAT 5597
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


1706 29.83 5.66 2.43  chrX_61920708_61924448     2397  3261 (480)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_61920708_6   2397 TGTTCAAAAATTGGAAGGCTTAATATTGTTATAATTTCCATACTGCCAAA 2446
                               vii        i             vi  vv v     v  v  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_61920708_6   2447 A------------------GCAATTTCCA-----ATGTCAG-------TT 2466
                          ------------------     ii i -----  vi   -------  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_61920708_6   2467 TTAAAGATACAGAAAAAATAATTCTAAAA---ACATGGGTAACTACAAAA 2513
                           iv   v iv  v  iv i  i      --- i    --  v i   ii
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG--AAATGCAAGG 163

  chrX_61920708_6   2514 GAAAAGCCA-AATAACCAACGCAATAATGAGCAAAAAGAGCAAAGCTGAT 2562
                           v---   -    i    vi    vv   iv  i    i     i  iv
  L1M4_orf2#LINE/    164 GAC---CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_61920708_6   2563 GGCATCATGCTACCTGATTTTAAATTATACTACAAAGCAATGGTAATTAA 2612
                           vv   ii  v  ii    i   viv           v ii     i  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_61920708_6   2613 AACAGCATAATACTCACATTAAAAAAAACAGGAACATTTAAA--AATTGA 2660
                         i    ii ii    vi   ----  ii i  --    v  i --   v  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCAT----AAGGATAG--ACATATAGATCAATGGA 304

  chrX_61920708_6   2661 ACAGAATAAAGAACACAGATATTAACCCACACATGTAACATCAATTTATT 2710
                          i     vi   iiv    v  v      i    v  vvi      v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_61920708_6   2711 TTTTATAAAAGATTTCAAGAATATCTTGTGGAAAAAGTACAGTTTGTTCA 2760
                           iv i  ii - vi     vi  iivi   ii    v i   i v    
  L1M4_orf2#LINE/    355 TTCGACAAGGG-TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_61920708_6   2761 ATAAATGATGATGTGAAAACTGAATTTTCA--TGCAAAATAATAAAATTG 2808
                          i     i  v  v  v     i  v?i  --       v   i  i   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_61920708_6   2809 ATCCTTTATCTCACACCACATACAAAAAATAACTCAAAATAGATTAAAAA 2858
                         iv  ii  i         i         v           i   i ? i 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_61920708_6   2859 CTTAAACAAAAATCCTGAATTCATAAAAGTACTAGAAGAAAATATATGGA 2908
                          i    iiv  ivv  i  vii      v vi          i   v ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_61920708_6   2909 CCAAAGTACACAACACTGCTCTGGGCATTAAAAAAAAAA-----AAAAAA 2953
                         iv  vv v iii  ----  -    --   iiv  viiv----- i v v
  L1M4_orf2#LINE/    554 TAAATCTTCGTGAC----CT-TGGG--TTAGGCAATGGTTTCTTAGATAT 596

  chrX_61920708_6   2954 GACCTCCAAAGCAGAGGGAA-AAAAACTAAAGTGGACAAAGGGGATTACA 3002
                            vi v      v i v  -    ivv   i i  i   vv   i v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_61920708_6   3003 TCAAAATAAAAAGCTTCTTTAC--AAAAAAATAAATACTCAACAAAGTAA 3050
                                v    i   i v i --v   ii i v-  -    v     i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC-TA-TCAAGAAAGTGA 694

  chrX_61920708_6   3051 AGAATCAGCCTACAGGCTTAGGTAATATATTTGTAAACTAAACATTTGAT 3100
                          i iv  i  i    iv vi iv  v       i   ii v i  i    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_61920708_6   3101 AAGTGATTAATATTTAAAATTTACAAA-AACTCAAGCAACTCTGTAGAAA 3149
                            v  i vi   ii i   v  i   -     vvi      vi  iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_61920708_6   3150 GAAAATAAACACTCTGAT-AAGACATGGGCAAAGGACCTGAACAGACATT 3198
                         i  i i   i vi ii  -? i v            ii    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_61920708_6   3199 TCTCAAAAGAAGACATATGAGCAGCTAACAGATACATTAAAAC-TGCTAA 3247
                             v        i   ii iii  i  i iii    v    v-    v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_61920708_6   3248 ATACTATTAATCAT 3261
                          i ii ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (155 / 99)
Gap_init rate = 0.03 (23 / 893), avg. gap size = 3.04 (70 / 23)  


3047 26.71 0.99 0.77  chrX_61948936_61953964     3631  4536 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61948936_6   3631 TGGAAGAATATTCCATGCTCATGGTTAGGAAGAATCAATATCGTGAAAAC 3680
                              ii    i     i      v v      v i     i  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61948936_6   3681 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 3730
                            v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61948936_6   3731 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3778
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_61948936_6   3779 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 3828
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_61948936_6   3829 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGA 3878
                                i      vv    i  v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_61948936_6   3879 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGATATATAGACC 3928
                                 i   i    ii         i i  ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_61948936_6   3929 GATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAAAC 3976
                         i      i    i--    i  --        vv   i    i  iiiv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_61948936_6   3977 ATCTGATCTTTGACAACAATGACAAAAAAA---AATGGGGAAAGGATTCC 4023
                          vi    i  i     vii  v   i vv ---           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_61948936_6   4024 CTATTTAATTAATGGTTCTGGGAAAACTGGCTAGCTATATGTAGAAAGCA 4073
                           v  i  iv      v      v      v  ? i i   i -    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAA 445

  chrX_61948936_6   4074 -GAAATGGGAACCCTTCCATATGCCTTATACAAAAATTAATTCAAGATGG 4122
                         -   i v   v    v  vi ii  v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_61948936_6   4123 ATTAAAGACTTAAATGTTAGACCTAACACCATAAAAACCCTAAAAGAAAA 4172
                           i ?    i       v   v    v  i      vi i  i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_61948936_6   4173 CCTAGGCAATACTATTCAGGACATAGGGATGGGCAAGGACTTCATGACTA 4222
                          v    ?ivv v v   iv   v v   v i     v ii   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_61948936_6   4223 AAACAACAAAAGCAATGGCAACACAAGCCAAAATAGACAAATGGCATCTA 4272
                         vi   v        vvi      v   vv        i    v v ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_61948936_6   4273 ACTAAACTAAAGAGCATCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4322
                          ii   v v  i i v i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_61948936_6   4323 CAGGCAACCTACAGAATGGGAGAAACTTTTTG-AAATCTACCCATCTGAC 4371
                         v  i     i               v v    -     - ivi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGAT 744

  chrX_61948936_6   4372 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAAAATATTTACAAGAA 4421
                           i  i  vi          v  i         vv v vv iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_61948936_6   4422 AAAAATCAAGCAACCCCATCAAAAAGTGGGCAAATGATATGAACAGACAT 4471
                            i -   ii     v  i?    i        v   v    i      
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_61948936_6   4472 TTCTCAAAAGAAGACATTTATCCAGCCAACAGACACATGAAAAAATGCTC 4521
                              v        i  vi vvii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_61948936_6   4522 AACATCACTGGTCAC 4536
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


2576 27.61 5.04 1.03  chrX_61963461_61965533.rev      710  1582 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61963461_6    710 TGGAAAAACATTTCATACTTATGGACAGGAAGAATAAATATCATGAAAAT 759
                               i i  ii   ii i     iv      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61963461_6    760 GGTCATCCTGCTCAAAGTAATTTA--GATTCTATGCTATCCCCTTTAAGC 807
                           iv  v  v i    v i  i  --     v i  v     iv i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61963461_6    808 TACCA-TTGACTTTCTTCCCTGAACTGGAACAAACT-ACTTTAAATTTCA 855
                          v   -i  v    i  v vvi  i  --    i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_61963461_6    856 TATGGAACCAGAAAGAGCTT-GTATAGCCAAGACAATCCTAAGCAA-AAG 903
                                viiv  i ii ii- v        i      i i iv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_61963461_6    904 AACAAAGCTGGAGG-CATATGCTACCTGACTTTAAAGTATACTACAAGGC 952
                                i      - vi ii  v  ii i  i   iiv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_61963461_6    953 TACAGTATCCAAAACAGCATGGTACTGGTACCAAAACATATATATAGACC 1002
                                vi   i    ii         i iv ii i v i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_61963461_6   1003 AATGGAACAGAACAGAGGCCTCAAAAATAACACCACACATCTACAACCAA 1052
                                i    iv   ivii  i      vv   i    i  iiii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_61963461_6   1053 ATGATCTTTGACAAACCTAGCAAACACAAGCAATGGGGAAAGGAT-TTCT 1101
                         v    i  i     ivv iv   ivv  vv            i  -v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_61963461_6   1102 TATTTAGTAAATTGTGTTGGGAAAACTGGCTAGTCATATGCAGAAAACTG 1151
                          -  i ii    v   i     v      v  ?i  i     i  i v  
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_61963461_6   1152 AAACTGGACCCGTTCTTTACATCTTATACAAAAATTAACACAAGATGGAT 1201
                           ii       v v i i   i v               v   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_61963461_6   1202 TAAAGACTTAAATGTAATACCTAAAACCATTAAAACTCT-AGAAGAAAAC 1250
                         i ?    i         v v       i  -        -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAAC 546

  chrX_61963461_6   1251 CCAGTCAGAACAATACCATTCAGAACATAGGCATGGCCAAAGACTTCATG 1300
                         vi  --- ?ii  - i -   ivi  v v  vv i v   v ii   v i
  L1M4_orf2#LINE/    547 ATAG---GNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_61963461_6   1301 ACTAAAACACCTAAAGCAATGGCAACAAAAGCCAAAATAGATAAATGGGA 1350
                         iv  vi     v      vvi          vv             v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_61963461_6   1351 TGTAATTAAGCTAAAGAGCTTTTG------------CAC----------- 1377
                         iv v  i  iv v  i i      ------------   -----------
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_61963461_6   1378 ------AACAATCTACAGAATGGGAAAAAGTTTTTGCTATTTATCCATCT 1421
                         ------i    i i           i   i v     v v i  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_61963461_6   1422 GACAAAGGGCTAATATCCAGAATCTAACAGAAACTTAAAAAAATTTACAA 1471
                           i  i  i  vi          v  vv ii    ivv v  v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_61963461_6   1472 GAAGAA-ACAAACAACCCCATGAAAAAGTGGGTGAAGGATATGAACAGAC 1520
                         v  i  -     i     v  v?    i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_61963461_6   1521 ACTTCTCAAAAGAAGACATTTATGCAGCCAAGAA----ATAAAAAAA-GC 1565
                          i     v        i  vi viii     v  ----  i    i -  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_61963461_6   1566 TCATCATCACTGGTCGT 1582
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (143 / 94)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.79 (53 / 19)  


3276 25.63 0.77 0.88  chrX_61967663_61969817.rev      756  1664 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61967663_6    756 TGGAGA-ACATTTCATGCTCATGGATAGGAAGAATCAATATCGCAAAAAT 804
                             i - i  ii    i        v      v i     i iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61967663_6    805 GGCCATACTGCCAAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGA 854
                            v     v  v  iv i  i  i        i  v     i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61967663_6    855 TATCAA-TAACTTTTTTGCACGAAATTGGAAAAAACT-ACTTTAAAGTTC 902
                          vi  i- iv          -       -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_61967663_6    903 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCATAAGCAAAAA 952
                                 viiv  ii  v  v v  v     i      v i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_61967663_6    953 GAACAAAGCTGGAGGCATTACACTACCTGACTTCAAATTCTACTACAAGG 1002
                                 i      vv i     v  ii i      vii        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_61967663_6   1003 CTACAGTAACCAAAACAGGATGGTACTGGTGCCAAAACAGAGATATAGAC 1052
                                  i   i    vi         iiiv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_61967663_6   1053 CAATGGAACAAAAC--AGAGCCCTCAGAAATAATACCACACATCTATGAC 1100
                                 i i  i--    i  --        vv   i    i    ii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_61967663_6   1101 CATCTGATCTTTGACAAAGCTGACAAAAACAAGAAATGGGGAAAGGATTC 1150
                           vi    i  i     i v  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_61967663_6   1151 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1200
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_61967663_6   1201 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 1250
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_61967663_6   1251 ATTAAAGACTTAAATGTTAGAATTAAAGCCATAAAAACCCTAGAAGAAAA 1300
                           i ?    i       v   ii    i i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_61967663_6   1301 TCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 1349
                         iv    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_61967663_6   1350 AAAACACCAAAAGCAATGGCAACAGAAGCTAAAATAGACAAATGGGATCT 1399
                          vi            vvi      i   vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_61967663_6   1400 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 1449
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_61967663_6   1450 ACAGGCCACCTACAGAATGGGAGAAAATTTTTGCAACCTA-ATCAACTGA 1498
                          v  i v   i                 v       vii -  - v    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGA 743

  chrX_61967663_6   1499 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 1548
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_61967663_6   1549 AAAAAACAAACAACTCCATCAACAAGTGGGCGAAGGACATGAACACACAC 1598
                             i     i   i v  i? v  i     i     iv    i v   i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_61967663_6   1599 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGGAAAAAATGTT 1648
                              v        i  vi viii     v  i      -    i   i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCT 892

  chrX_61967663_6   1649 CACCATCACTGGCCAT 1664
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


1755 28.67 5.22 4.33  chrX_61970296_61976019     4342  5241 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61970296_6   4342 TGGAAAATCATTC-ATGCTCATGGA---GAAGAATCAATATC---AATAT 4384
                               ivi  i -   i       ---     v i     i---  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61970296_6   4385 GGTCATACTACCCAAAGCCACTTACAGATTCAAGGCTATTGCTATTAAAC 4434
                           iv     v      viv ii           v  v  iv    i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61970296_6   4435 TACCAATGACATTTTTTACAGAACCAGAAGAAACT-ATGTTAAAATTTAT 4483
                          v   iivi v      i     viv  v-  i  -  vi       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_61970296_6   4484 ATGGAACCAAAAAAAAACAAAAAAAAAAAACAACCTAGAA-AGCCAAAAC 4532
                               -------- vi   iii ---------  i    -         
  L1M4_orf2#LINE/    150 ATGGAA--------ATGCAAGGGA---------CCCAGAATAGCCAAAAC 182

  chrX_61970296_6   4533 AATCCTTAGGAAAAAAAAAAAAAGCTAATGCCTTTATACT-----AT--- 4574
                             -  iii   i  i  v    i iiv vvi i i   -----  ---
  L1M4_orf2#LINE/    183 AATC-TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_61970296_6   4575 -------AGTACAAGACTATGGAAACTAAAACAGCATACAGCACTGGTAC 4617
                         ------- v     ii   ii v  ii  i    ii i-- i     i i
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG--GTACTGGCAT 279

  chrX_61970296_6   4618 AAAAACAAACACACAGGCGAACAAAACAGAATAGAGAGCTGAGAAATGAG 4667
                           ii i i   i i  iiv  iii  i     v     iiv      i i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_61970296_6   4668 GCCACATACCTAGAACTGTCTGATCTTTGACAAAATCAACAAAAACAAGC 4717
                         v   i i ii  viiiiivi    i  i     iiviiv   i v  vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_61970296_6   4718 AATGAGAAAA--ATACTTCCTATTCAATAAATGGTGCTAAAATAACTTGC 4765
                             i i   --   v --  v     i          iii i    v v
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGT--CTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_61970296_6   4766 TAACCATAAAGAGAAGATAGAAACTCAACCTTTTCCTTACACCATATACA 4815
                           ?   i viv i    vv   ii vi   ii v   i            
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_61970296_6   4816 AAAATTAACTGAAAATGGATTAAAGACTTAAATGTAAAACTCAAAGCTAT 4865
                                   v         i ?    i         i vii   i    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_61970296_6   4866 AAAAACCAT-GAAGAAAACCTAGGC--AATTCCATTCTGGATTTTAAAAA 4912
                             vi v -         v    ?--  v  --   vv  ii  iiiv-
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGT- 574

  chrX_61970296_6   4913 ATGGGCAAAGTTTTC------ATGACAAAAATGCTAAAAGTAATTGCAAC 4956
                         - i     v v    ------      ------ i     i vvv     
  L1M4_orf2#LINE/    575 -TAGGCAATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAAC 617

  chrX_61970296_6   4957 AAAATCAAAATTTGACAAATGTGATCTGTTTAAACTAAAGAGCTTCTACA 5006
                             vv    v v  i    vv  ii vv i   v v  i i   i iii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_61970296_6   5007 CAGCAAAATAAATTAGCAA-----T----AGACAACCTAGAGTATTAGAA 5047
                          vv    iv v i  v   ----- ----        i v  v  vi  i
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_61970296_6   5048 AAAATTTTTGCAAACTATGCATCTGAAGATGTTCTAATATCCAACACCAA 5097
                              v        ii  ii      vi v vv  vi      iv ivv 
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_61970296_6   5098 TAAGGAACTTAAACAAATTTACAAACAAAACAAAACAAACGACCCAATTG 5147
                            i     ivv    -i i vv  i    -- i     ii        ?
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAA-CTCAATAATAAAA--AGACAAATAACCCAATTW 814

  chrX_61970296_6   5148 AAAAGTTGGCAAAAGACAT-AACAGACACTTTTTTCAAAGAAGACACATA 5196
                             i v      i  iv -  i     -   i i         i i i 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACA-TTTCTCCAAAGAAGATATACA 863

  chrX_61970296_6   5197 AGTGTGGCCAATGAACATACGAAAAAA--ATTAACATCACTAATCAT 5241
                          i  --      i i  i i     i --v i       ????????
  L1M4_orf2#LINE/    864 AATG--GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (160 / 94)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.07 (86 / 28)  


1813 29.82 4.93 3.14  chrX_61978649_61985970.rev     2022  2913 (4409)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61978649_6   2022 TGGAAAAATAAATACATGTTCATGTATTTATGGAAAAATCAATATTGTAA 2071
                               i   vvi-          v   ---    i v i        v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCC-CATGTTCATGGATT---GGAAGACTTAATATTGTTA 46

  chrX_61978649_6   2072 AAATGGGCCAGACTGTCCAAAGCGATTTACAGATTCGATGCTATTCCTAT 2121
                          i    - v v   vi     vi   i         i i  v  i     
  L1M4_orf2#LINE/     47 AGATGG-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_61978649_6   2122 ATACCAATGTAATTCT--CCACCAGAT---CAGAAA---A-AAACTT-TT 2161
                         ----   ---   i i-- ii  vvv ---      --- -  i  v- i
  L1M4_orf2#LINE/     96 ----CAA---AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chrX_61978649_6   2162 CTAAAACTTATGTAGAACAACAACAAAAAGGAGCCATAATAGCCAAAGCA 2211
                               i i  i i   ----- iiv  i   v   v          i  
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAA-----ATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_61978649_6   2212 ATTCTCAGCAAAAACAACAA-GCTATAATTATAACATTACTCAAATTCAA 2260
                           ii v iv  i  v     - i iv ivvv v   i v i   v     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_61978649_6   2261 ACTATTGTATAGAACCACAGTAAAAAAAATAATAACAGCTTTATGTTGTT 2310
                          viv vv  i i i i       vv  i i i i------ vi ii  vi
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTG------TGGTACTGGC 277

  chrX_61978649_6   2311 ACAAAAA-AGATATGTAGACCAATGGAATAGAACAGAG-GTATCAGAAAT 2358
                          i  ii -   i  i    i             iv   -  -i       
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT-CCAGAAAT 326

  chrX_61978649_6   2359 AAATTATTACACCTACGACCATCTGATCTTTGACAAGGCTGACAAAAACA 2408
                            iivv    ii  i ii  vi    i  i       v  v   i v  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_61978649_6   2409 AGCAATGGGAATA---TAACCTTGTATTCAGTAAATTGTGCT-------- 2447
                         vv       i v ---  ii   ---    ii    v     --------
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTT---TTCAACAAATGGTGCTGGGACAAC 423

  chrX_61978649_6   2448 TGTCTACCTATACGGACAAGATTGTAGCTCAGCCCCTACTTTTCGCCATA 2497
                           vv  ? i i i v v    v  v  i vii       i iv i     
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_61978649_6   2498 TACAAAAATTAACTTAAA-TTGATAAAGGTTTTAAATATAAGTTCTAAAA 2546
                                       i   - v   v ?i vii     i    vv      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_61978649_6   2547 CTACAAAAATTTTGAAAGAAAACCTAGAAAATACTCTTCTTGACATTGGT 2596
                            i    v i  ii        v   i?ivv v     v    v    v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_61978649_6   2597 CTCAGCAAAAAATGTTTTGCTGAGTCCCCATGAGCAATTGTGATAAAAAC 2646
                         i vi    viiv vi  v v iv v v   vi    vvv ii i    iv
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_61978649_6   2647 CAAAAATAGAAAAGTGGGACCTAATTAAACTAAAGATCTTTTGCACAGCA 2696
                         -         v  i v    i v  i   v v  i v      ii vv  
  L1M4_orf2#LINE/    624 -AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_61978649_6   2697 AGATAAACTATCAACAGAG--AAAAAA--ACCTACAGAATGGTAGAAGAT 2742
                          iiv v        v i  --    i --   i         v    i  
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_61978649_6   2743 ATTCCCAAGCCATGCACCTGAGAAAGACCCAATATCAAGAATCGATAGAA 2792
                            iv   ii   ii i    v  i iv ivi    v     vv   i i
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_61978649_6   2793 GACTTAAATAAACCCACATGCAGAAAACAAGCAATCCTATTTGAAAGCGG 2842
                         i   ivv i  vi v i vvv i  i    ii  i  v   ?i   ii  
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_61978649_6   2843 GTAAAGGACATGAA---------------AGGAGACGTACAAGTGGCCAA 2877
                          i      iv    ---------------  i   ii     i       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_61978649_6   2878 AAAACATATTAATAAATGCTCAATATTACTAATTAT 2913
                         v  i  i  v  v i        i  i ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (150 / 112)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.00 (72 / 24)  

2321 29.11 2.00 1.11  chrX_61978649_61985970.rev     5945  6844 (478)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_61978649_6   5945 TGGAAAGACATTTCATGTACA--GATTGGAA----TAATATTGTAAAAAT 5988
                                 i  ii     v  --        ----         v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_61978649_6   5989 ATCAATACTGCCCTAAGAAATCTATTAATTTAATTCAATCTCTATCAAAA 6038
                         iv       v   v  vvi     ivi   i  iv     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_61978649_6   6039 TATCAATGAAATATTTAACAGAAATAGAAAAAC-AATCCAAACAATTT-T 6086
                          vi  iivivv v   vi       v  v  i -i    v  -    i- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA-AATTCAT 149

  chrX_61978649_6   6087 ATAAAACCACAAAAAACCCA--ATAGTGAAAGCAACCCTAATCATAAAGG 6134
                           ii  vii   iii     --    iv   i   i i i vv vi   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_61978649_6   6135 ACAAAACTGGAGGCATTACATGAAGTAACTGCAAAAGT-ATCAAAAATCT 6183
                              ii      vv i   ivvvvi  i v     v - ii v   v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_61978649_6   6184 ATAACGACCCTAACAGCATGATACTGGCATAAA-ATAAACACATAGATAA 6232
                          i iii i vvi    ii  i           i-   i   i      v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_61978649_6   6233 ATAGAGAAAAGTAGAGAACCTCGAAATGAATCTTCATATTTACTGCCAAC 6282
                           i  iv i i v    ii iv     i  i ivi i     iv i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_61978649_6   6283 TCAATTTTGATAAAAACACAAAAAT-ATACACTGGGCAAAGTACAATATC 6331
                          v v   i  i  iiiii v  i i-  v  v    v    v i i v i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_61978649_6   6332 TTCAATGAAAGATTCTGAGAAAACTGGATATCCATATGTA---GAATAAA 6378
                              ii  v i v   i  v         ?   i   i ---    i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_61978649_6   6379 ACTAGAACCCTGAACCCTTTCACCATATGCAAAAATCAAAGCAAAATGGA 6428
                         ii i  v    i---   iv        i       i  vv         
  L1M4_orf2#LINE/    450 GTTGGACCCCTA---CCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_61978649_6   6429 TCCAAGACTTAAAACTGAGACCAGAAACTATGAATCTGTTGGAATAAGAC 6478
                           v?    i    vv i   v vi       i  v  v  i   v  i  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_61978649_6   6479 ATTGGGAAAACACTTCAGGACATTGGTCTTGGCAAAGATATATTGAATAA 6528
                           v  ?iv  vv    iv   v    vi v     v i v v  ii   v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_61978649_6   6529 GACCTCAGAAGCAAAAGCAACCAAAGCAAAAACATTGACAAATAAGATTG 6578
                            vi  i     v       v    v     i --  i    vi  i v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTT 644

  chrX_61978649_6   6579 CATCAAGGTAAGAAAGCTTCT-TCCTAGCAAAGGTAACAATCAACACAGT 6627
                               ii v i   -   i - v  -v      vv  v     v v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCT-TCAAAGGACACTATCAAGAAAGT 692

  chrX_61978649_6   6628 GAAGAGACAACCTACAGAATGGGAGAAAATATTTGAAAATTATTCATCTA 6677
                            i        i                      v    i  vi    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_61978649_6   6678 ACAAGGCATGAATAACCAGAATATATGAGGAACTCAAACAACCCAATTGT 6727
                          i    v ivvi  v           i i      vv     i    vi 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_61978649_6   6728 AAAGAAAATAAATAATCTGTTTTTAAAATGGGTAAAA-ACATAAATAGAT 6776
                            -  i i      i iiv  ?v        i   i- iv i      i
  L1M4_orf2#LINE/    793 AAA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_61978649_6   6777 GTTTCTCAAAGAAAGATATAGAAGTGGTTATCACGCATGTGAAAAAAATT 6826
                         i      v  ii        v  i   ii vi v   ii      i - v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chrX_61978649_6   6827 ATTAACAACACTAAATCA 6844
                         v i    v  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (149 / 109)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.56 (28 / 18)  


2062 27.52 4.00 3.77  chrX_62007544_62010031.rev     1098  1998 (490)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_62007544_6   1098 AGATATTTCATGTTCATGGAT-GGTAGAATTCATATTGTTAAAATAATAA 1146
                               ii             -  v   v  v          i  iii  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_62007544_6   1147 TATTACTTAAGGTGATAATCTACAGATTCAATTAAATTCCAATCAAAATA 1196
                           i v ii  iv    ---            ivv   i  v        v
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGAT---CTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_62007544_6   1197 TCAATAACATTCTTCACAGA--TTTAGAAAAAAACT-ATCCTAAAGTTTG 1243
                         i  iivi v  i  ii    --  ----i v  i  -        i  ii
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATT----GACAAGCTGATCCTAAAATTCA 148

  chrX_62007544_6   1244 TATAAAACCACAAATGGGCCCATA-TAGCCAAAGCAATCCTAAATAAAAT 1292
                            ii  vii   i-  i    v -        i     i i  v  i v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_62007544_6   1293 TAACAAAGCTAAGGGTATCACACTACTTGACCT-GAAATATACTTTCATG 1341
                         v       i iii  vv       v iii ii -i   iv    viv v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_62007544_6   1342 CTACAATAAACATATATTGTATGGTACTGGCATAAAAATAGACA----GA 1387
                              i   v  - v iv  i              ii       ----  
  L1M4_orf2#LINE/    248 CTACAGTAATCA-AGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_62007544_6   1388 ACAATAAGAAAGAGTAGAGGAAAAACTATAAACAAATCTATACATTTACA 1437
                         v    iii v   i v   --- iv i v   i   i i         ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAG---AGTCCAGAAATAAACCCATACATTTATG 343

  chrX_62007544_6   1438 GCCAACTAATTTGTAACAAAGGCCACAAAAACATACTTTGGGAAAGAACA 1487
                          i   i i    vii    i  ivv   i v   v vv    i  -----
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA----- 388

  chrX_62007544_6   1488 ATAAGAACAATTTCTTCAATAAATGGTGCTGTGAAAACTGGGTTACCGCA 1537
                         ---    i i i i     i           v  v      i v?  i  
  L1M4_orf2#LINE/    389 ---AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_62007544_6   1538 GGCAGAAAAATAAAAT--GACCTTTATCTGCCACCATATACAAAAATCAA 1585
                         v   i  i   i  i --    ii  i  vv                i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_62007544_6   1586 ATAAAAAT-----AAAGATTTAATTATAAAATCTGAAACTATAAAAATAC 1630
                         v v     ----- ?   ii   v i   i v  i           v vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_62007544_6   1631 TAAAAAAAAA-GTGGAGATA--CCTTCCTGACATTGGCCTTGGTATCGAT 1677
                           i  i    -i i i?i  --i    v    v    vi v  i vi i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_62007544_6   1678 TTTTTCTGT-TGTTGTTTGTACCTCAAAAGT-C---TAACCAAAGAACAA 1722
                           i  vvi -  --------  vi      i- ---i   v      v  
  L1M4_orf2#LINE/    586 TTCTTAGATATG--------ACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_62007544_6   1723 -TAGACAAAT-ATAATATATCATGGTGAAAAACTTCTA--CT--AAGAAA 1766
                         -    i    -iv v vi    vii v        i i--  --  ----
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA---- 673

  chrX_62007544_6   1767 ATAAAACACT-TCAC-ATACTGATGGG-CAATGTACTGAATGGAAGAAAA 1813
                         -- ii     -   v- v v   vii -   ivi  v      i      
  L1M4_orf2#LINE/    674 --AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_62007544_6   1814 TATTTGCAAACTATTTACTGGACAACAAGTTAATAACCAGAATAAATAAA 1863
                                   ii  v  iiv  i  viiii vi  v        v     
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_62007544_6   1864 AAATCCAAACAACTCAACAGCAAAGAAACAAATCATGTCATT-AAAAATG 1912
                         i  ii vv         i ii   i i      v iviv   -       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_62007544_6   1913 GGCAAATGATCTGTGGAAACATTTCTAAAAATAACACATACAAATTGCCA 1962
                               v   i  viv i        vv   v  v i        v    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_62007544_6   1963 ACAGCTATATAAAAAAA-GCTCAACATCCCTAGTCTC 1998
                          i ivi i  i    i -          v????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (152 / 93)
Gap_init rate = 0.03 (30 / 903), avg. gap size = 2.33 (70 / 30)  


2179 24.97 3.54 6.32  chrX_62026625_62033184.rev     5137  6069 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_62026625_6   5137 GAAAAAATATCATATGCTCTTGGATTGGAAGAATCAATATTAT-AAAATG 5185
                          i   i     vi   i  v            v i      i -  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_62026625_6   5186 ACCATACTGCTCAAAACAATCTACGGATTTAGGGCAATATTTATCAAATT 5235
                         i v     v i    vii      i    i iv     vii       v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_62026625_6   5236 ACCAA-TGTCGTATTTTATAGAATTATGAAAAAATG---CTAAAAATTAT 5281
                         v   i-  i v -    ii    v -   v  iv  ---      v i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTT-TTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_62026625_6   5282 ATGCAACCAAATAAAATCCTAAACAACCAAAGCAA-CTC--AACATTAAA 5328
                            v  viiv viii i  vi  i i     i   -  i--  v vv i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_62026625_6   5329 ACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTGTACTACAAGGCA 5378
                               i      vv     i v  ii i      viv        i  v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_62026625_6   5379 GTATTAATCAAAACAGAATGGTACTGGTACAAAAGTAGACATATAGATCA 5428
                         ii v       i    vi         i i  iii               
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_62026625_6   5429 ATGGAATATAAATAGAATAGAATAGAATAGAATAGAATAGAATAGAATAG 5478
                                 ------------------------------------------
  L1M4_orf2#LINE/    300 ATGGAATA------------------------------------------ 307

  chrX_62026625_6   5479 AATAGAATAGAATAGAATGCAAGAAATAAAACCAAATACTTATTCTCAAA 5528
                         ----    v  ---  i v  -        v   v i i    vv    v
  L1M4_orf2#LINE/    308 ----GAATTGA---GAGTCCA-GAAATAAACCCATACATTTATGGTCAAT 349

  chrX_62026625_6   5529 TAATCTTTGACAAAGTCAACACAAATATATAATTGGAAAAGTACATTCCG 5578
                          i  i  i     i viiv  vi vi  vi   v  i    v i v  iv
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_62026625_6   5579 TTCAATAAATGATGCTGAGAAAACAGAAAACCCATATGCAAAAGAATAAA 5628
                              i     i     i  v   v i v ?   i            i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_62026625_6   5629 ACTAAACCC-TCTCTCACACCTTATACAAAAATTAATTCAAGATACATTA 5677
                         ii ii    - vi        v              i    i  iv  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_62026625_6   5678 AAGATTTAAATGTAAGACCTGAACCCGTAAAAATTT----AGAAACTAC- 5722
                         ?   ii           v  i  v ii     v i ----     vi i-
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_62026625_6   5723 --------TCTT-GAAAACTTGC-CTAGGCAACAAATTTGTTAG---TAA 5759
                         --------    - vi v    v-i       iii-   v    --- i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGA 598

  chrX_62026625_6   5760 GACCAAAAAACCAAATGCAACAAACTCATAAATAGACAAATGGTACTTAA 5809
                         v       ivv   --        vvv v       i    v v    v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_62026625_6   5810 TTAAACTCTAAACCTTCTGCACAGCAAAAAAGACAATTATCAAAAAA--- 5856
                          i   v iv   v   i  ii vv    i--    -i      i   ---
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAG--GACA-CTATCAAGAAAGTG 693

  chrX_62026625_6   5857 AGCAGAAAACCTATAAAATGGGAGAAAATATTTGGAAA-CTTAGCATCTG 5905
                          iv   v    i i i                  v   - v  -i     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA-TATCTG 742

  chrX_62026625_6   5906 ACAGATTACTAACATCTATAATCTACAAGGAACCCAAACAACTCAAGAGG 5955
                          i iivv   vii   i v   v  i  i    i vv         v iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_62026625_6   5956 AAAAA-ACAAATAATCTCATT-AAAAGTCGCCAAAGTATATGAAGAGATA 6003
                              -        i iv   -    i v v     v  v    v   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_62026625_6   6004 TTTCTCAAAATTAGACATACAAGCAGGCAAGAAACACATGAGAAAATGCT 6053
                               v   vv   i      iii v   v  i       i  i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_62026625_6   6054 TAACATCACTAATTAT 6069
                         i       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (131 / 100)
Gap_init rate = 0.03 (25 / 907), avg. gap size = 3.68 (92 / 25)  


 847 28.68 7.49 2.58  chrX_62053699_62057435.rev     1780  2166 (1571)    L1M4_orf2#LINE/L1        4   409 (499)  

  chrX_62053699_6   1780 AAAAAAGTCCAATGTCCATAGATTGAAAAA---AATCACGATCATTTAAA 1826
                            i vi   v    i   i     i  i ---   ----  ii  v i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAAT----ATTGTTAAGA 49

  chrX_62053699_6   1827 TAACCACATTGCCCCAAGTT-ATCTACAAATTCAATGTAATTTCTATCAA 1875
                          ii v i i -      i  -       i      i i   ii       
  L1M4_orf2#LINE/     50 TGGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_62053699_6   1876 ACTACCAACATCATTTTTCATGGAATTAGA------------GAAACCCA 1913
                          v v   i vv v     iiii   v v  ------------i   ii  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_62053699_6   1914 ---GAAAAT---AG---CCTA-AATAGACAAAACACTCCTAAGCAAAAAG 1953
                         --- i    ---  ---  i -     v       v  i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_62053699_6   1954 AGCAAAACTGGAGGCATCACTTTACCTGACTTTACATTATGCTACAAGGC 2003
                          i    ii      vv    vi v  ii i  i v viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_62053699_6   2004 TATAGTAAACAAAACAGCATGGGTCTGATATAAAAATAAACACACAGATA 2053
                           i     v   i    ii   vv   ii    ii   i   i i    v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_62053699_6   2054 AATGAAACAGAATAGAAAAGCCAGAAATAAAGCCACATATGTACACTGAA 2103
                             i  i     v  i iv           v   i i  v  iiv v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_62053699_6   2104 CTGATTTTTTTGACAAAGCCAGTG--AAAAT-ATAAACTTGGCAAAGGAC 2150
                         i       i--     i ---   --  i i-  vv v v  v    i i
  L1M4_orf2#LINE/    349 TTGATTTTC--GACAAGG---GTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_62053699_6   2151 GCTTTTTTAAAAAAAT 2166
                         iv i    v  v    
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAAT 409

Transitions / transversions = 1.85 (72 / 39)
Gap_init rate = 0.03 (13 / 406), avg. gap size = 3.00 (39 / 13)  

 935 26.94 5.43 6.01  chrX_62053699_62057435.rev     2731  3246 (491)    L1M4_orf2#LINE/L1      396   908 (0)  

  chrX_62053699_6   2731 TTTTTTCACTAAATAATGGTGGGA-AATTTTATAGACATATGCTGAAGAA 2779
                          i      vi    ii  v     -  i vv   ?v  i    vi     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_62053699_6   2780 TAAAACTGGAACCATATGTCTTAACATATACAAGAGT-AACTCAAGATGA 2828
                          i  ii    v  v  iv  vi v         i i -       i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_62053699_6   2829 GCGAAATACTTAACTGTAATATCTAAAGCTATACAAATTATAAATTAAAA 2878
                         iiv ? v  i   v     v v     i     -   i v ----  i  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCT----TAGAA 540

  chrX_62053699_6   2879 AAAGAAAAACTGAAAAATAAGCAAATCTAGGAGAAACTCCTCTGGACATT 2928
                         -----------     -----  ----    ? v  v  i  vv   v  
  L1M4_orf2#LINE/    541 -----------GAAAA-----CA----TAGGNGTAAATCTTCGTGACCTT 570

  chrX_62053699_6   2929 GAACTATTAA--AATAATTTATGCCTAA----GACCTTGGAAGCAAACAC 2972
                          ii---   i--   ii   --- i  i----   viiii     v vi 
  L1M4_orf2#LINE/    571 GGG---TTAGGCAATGGTTT---CTTAGATATGACACCAAAAGCACAAGC 614

  chrX_62053699_6   2973 AACAAAAACAAAAA-AGACCAATATGACTTAACTAAGCTAACAAGATTTT 3021
                                iv     -   iv   vv     v ii  iv v v  iv    
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_62053699_6   3022 GTGTAGTAAAATATGTAATTAGCAGAGTTAACAAGCATTCTACAGAATGG 3071
                            ivvi   iv iiiv  i iv i   v  v ii  vi i         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_62053699_6   3072 GAGAAAATATTTGGAAATTATGCATTTGACAAAGGGCTAATATCCAGAAT 3121
                                      v    i  ii  i   i  i  i  vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_62053699_6   3122 -CACAAGGAACTC----AACTAAATAA-----AAATAAATAGCTCCATT- 3160
                         -i i  i      ----    v     ----- i i     i i v   -
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_62053699_6   3161 AAAATTGGGCAAAGAACATAAACAAACATTTTT-----AAAGGCAGACAA 3205
                             v         i iv i  i i      i -----i   ii v    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_62053699_6   3206 GAGGCCAA-AA--ACAAGACAAAATTTTCAAAATTACTAATTAT 3246
                         iv      -  --   v  v  i  vi    v  i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (82 / 54)
Gap_init rate = 0.04 (19 / 513), avg. gap size = 3.11 (59 / 19)  


3091 27.45 0.66 0.55  chrX_62094998_62101718      492  1398 (5323)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_62094998_6   1398 TGGAAGAACATACCATGCTCATGGGTAGGAAAAATCAATATCGTGAAAAT 1349
                              ii i  v     i      i v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_62094998_6   1348 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1299
                            v     vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_62094998_6   1298 TACCAATAACTTTCTTCACAGAATTAGAAAAAACT--TCTTTAAAGTTCA 1251
                          v   iivi i  i  ii     v v  v  i-  --  i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCT-AAAATTCA 148

C chrX_62094998_6   1250 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1201
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_62094998_6   1200 AACAAAACTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGGC 1151
                               ii      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_62094998_6   1150 TACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGAGATATAGACC 1101
                                 i   i   iii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_62094998_6   1100 AATGGAACAGAAC--AGAGCCCTCAGAAATAATTCCACTTATCTACAACC 1053
                                i    i--    i  --        vi   ivi  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chrX_62094998_6   1052 ATCTGATCTTTGACAAACCTGACAAAAACAAGCCATGGGGAAAGGATACC 1003
                          vi    i  i     ivv  v   i v  vv v          i   vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_62094998_6   1002 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 953
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_62094998_6    952 GAAACTGGATCCCTTCCTTACAACTTATAGAAAAATTAATTCAAGATGGA 903
                            ii    i    v   i   v v    v         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_62094998_6    902 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGACGAAAAC 853
                          i ?    i  v    v   v       i      vi i    v      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_62094998_6    852 CTAGGCA-ACACCATTCAGGACATAGGCATGGGCAGGGACTTCATATTTA 804
                         v    ?i- v i -   iv   v v  vv i    iv ii   v  vv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chrX_62094998_6    803 -AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 755
                         -i            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chrX_62094998_6    754 ATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACCACCATCATAGTGAA 705
                           i   v v  i i   i  iiivv    i  v  i i  vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chrX_62094998_6    704 CAGGCAACCTACAGAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 655
                         v  i     i                 v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chrX_62094998_6    654 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 605
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chrX_62094998_6    604 CAAACAAACAACCCCATCGAAAAGTGGGTGAAGGACATGAACAGACACTT 555
                         v i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chrX_62094998_6    554 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 505
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chrX_62094998_6    504 CATCACTGGCCAT 492
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  

2096 27.44 3.92 3.92  chrX_62094998_62101718     5336  6228 (493)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_62094998_6   5336 TGTTTATAGATTAGAATTATTTATAGTGTTCAAAATGTCCATACTACCTA 5385
                             i  i    i   vvv  v   v    -  i   v v     v  i 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTT-AAGATGGCAATACTCCCCA 64

  chrX_62094998_6   5386 AAGCAATTTACAGATTCAATCTAATCTCTATTAAAATTCAAACCATATGT 5435
                           vii  i           ivi    i    i     i v i iiiv v 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_62094998_6   5436 TTCAGAGAAATAGAATAA--TAATCTTAAAACATCTCTCTAACCAAA--- 5480
                           iiv      v  -i  -- i   i     -- iiv v ii--   ---
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGA-CAAGCTGATCCTAAAA--TTCATATGG--AAATGC 159

  chrX_62094998_6   5481 AAAAGATCCCAAATAGACAAAGCGATCTTGAACAACAACCAAACCAAACA 5530
                           ii  i  vi     v    i i        ------------------
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAA------------------ 191

  chrX_62094998_6   5531 AAAGAAAAACAAAGTTAAAATAGTCATACTATTTGACTTCAAAATATGCT 5580
                               i         ii iv v   i   viiii i       iv i  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_62094998_6   5581 TCAAAGTCAAGGTAACCAA-ACAGCATGGTACTCGCAAAATAAATAGACA 5629
                         v     ii vi    i   -    ii       v   v  -ii       
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA-GGATAGACA 290

  chrX_62094998_6   5630 CATAGACCAATGAAATAGAATAGGCAGTCTGGAAATATATCTATACATTC 5679
                         i     i     i        v iv    ii      v i i       i
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_62094998_6   5680 AGAGTCAACTCATTTTTGATAGAGACATCAAAAGTAATTCTCAA-----A 5724
                          vi     i v     i  i ii iiii   i vi ---i    ----- 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA---TTCAATGGGGA 387

  chrX_62094998_6   5725 AACCACAGTCTT--CAATAAATGGTGGTAGAAAAAATGAATTTTCACGTG 5772
                           vv i      --   i        v i i v  v  i  v?i   i  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_62094998_6   5773 TAGAAAAATGCAAATAAATCCCTATGTCTCATAATGTACAAAAGTCAAAT 5822
                         i i  i    v iv ii i     iv  v  iv  i       i i  v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_62094998_6   5823 AAAAATGGATGATATTCTTAAATATCAGACCCAAAACTATAAAACTACTA 5872
                         v         v ? vv i     i v   v i              vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_62094998_6   5873 GAAAAAAA-ATTGGGA-AAATGCTGTAGGCTATTTGTTTTGGCGAAAATT 5920
                            i    -  v  ?i-    -  viiv viv  v v  v   i vii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_62094998_6   5921 TTT--GGTAAGTCTTCAAAAGCACAGTTAAATAAATCAAAAATAGACAAA 5968
                          i -- i  v v vi          ivi  vv   vv         i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_62094998_6   5969 CAGGATTGCATCAAG-TTAAAAAGCTTCTCCACATCAAAGAAACCAATTC 6017
                         iv   i v      i-       -   i vii v      i --  -i v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA--CA-CTA 682

  chrX_62094998_6   6018 TCA-------GAAATAGCCAAGCTATATAATGGGAGAAAATATTTGCAAA 6060
                            -------    -  v   v i i v                      
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_62094998_6   6061 CTGT-----TAACAAGAAATTAATAACCACAATATGTAAGGAAGTCATAC 6105
                         iii ----- i i   ii i vi  v   v     i   i   v  v   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_62094998_6   6106 AACTCAACAGCAAAAAAATGAAATAATATGATT-AAAAATGAACAAATGA 6154
                                i ii     i i-      ivii   -       ii    v  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_62094998_6   6155 TCTCAA----CGTATCTCAAAAGATGACACACAAATGGCCAAAACATATA 6200
                          i v  ---- i v    v     v  i i            v vii i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_62094998_6   6201 TGAAAAACTGCTCAACATTACTAATCAT 6228
                               iv          i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (151 / 91)
Gap_init rate = 0.03 (26 / 893), avg. gap size = 2.69 (70 / 26)  


3007 28.22 0.55 0.44  chrX_62104915_62116522     4994  5900 (5708)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62104915_6   4994 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5043
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62104915_6   5044 GGCCATACTGCCCAAGGTAATTCATAGATTCAGTGCCATCCACATCAAGC 5093
                            v     v     iv i  ii i       ii  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62104915_6   5094 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5142
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_62104915_6   5143 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGA 5192
                               viiv  ii  v  v v  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_62104915_6   5193 ACAAAGCTGGAGGCATCACTCTACCTGACTTCAAATTATACTACAAGGTT 5242
                               i      vv    v  v  ii i      viv        i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_62104915_6   5243 ACATTAACCAAAGCAGCATGGTACTGGTTCCAAAACAGAGATGTAGACCA 5292
                            v   i   ii   ii         iviv ii i   v  i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_62104915_6   5293 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGTCACACATCTACAACCA 5340
                               i    i--    i  --        vvi  i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_62104915_6   5341 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATTATTCCC 5390
                         vi    i  i     ivv  v   i v  vvv          vv  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_62104915_6   5391 TATTTAATAAATGGTGCTGGGAAAACTGGCTA-CCATATGTAAAAAGCTG 5439
                          v  i  i              v      v  -   i   i    iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_62104915_6   5440 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5489
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_62104915_6   5490 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAAAAAACC 5539
                         i ?    i  v    v   v       i      vi i     i     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_62104915_6   5540 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5588
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_62104915_6   5589 AACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATATAA 5638
                         i            vvi     i    vv     v  i    v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_62104915_6   5639 CTAAACTAAAGAGCTTCAGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5688
                         ii   v v  i i   iv ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_62104915_6   5689 AGGCAACCTAGAGAATGAGAGAAAATTTTTGCAATCTACCCATCTGACAA 5738
                           i     i v      i        v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_62104915_6   5739 AGGGCTAATATCCCGAATCTAAAATGAACTTAAACAAATTTACAAGAAAA 5788
                         i  i  vi     v    v  v  v     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_62104915_6   5789 AAACAAACAACCCCATCAACAAATGGGTGAAGGATATGAACAGACACTTC 5838
                          i     i     v  i? v       ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_62104915_6   5839 TCAGAAGACGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATT 5888
                           vi    v  i  vi viii     i ii          i       vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_62104915_6   5889 ATCACTGGTCAC 5900
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (146 / 107)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  

2045 29.93 5.62 1.72  chrX_62104915_62116522    10244 11115 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_62104915_6  10244 GAAAAATCATTCCATGCTCATAGTTAGGAAGA----ATA--------ATG 10281
                             i  -  i     i    i v v      ----   --------   
  L1M4_orf2#LINE/      3 GAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_62104915_6  10282 GCTATACTGCCTAAAGCAATTTATAGATTCAATGCTATTGCTGTTCAACT 10331
                           v     v  i   vii  i  i        i  v  iv  i iv  v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_62104915_6  10332 ACCAATGATATTATTCAGAGAACTAGAAAATACT-ATTTTAAAATTCATA 10380
                         v   iiviiv  v  iiv    v v  v  -i  -  ii           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATA 150

  chrX_62104915_6  10381 CAAAACCAAAAAAGAGCCTGAATAGCCAAGGGAATCCTAATTTAAAAAGA 10430
                         iii  viiv  ii  v  v          iiv    i i ---    ii 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAA 197

  chrX_62104915_6  10431 G--------TGGCA---TCATGTTACTCCACTTCAAATTACACTAAACGG 10469
                          --------   vi---   iii v i v i      vivi    v vi 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_62104915_6  10470 CTACAGAAATCAAAACAGCATTATATTGCTGCAAAAACAGTCACATAGAC 10519
                               v      i    ii vi  i  viii  ii i  v  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_62104915_6  10520 CGATAAAACAGTATAGAGAACCAGGAAATAAGGCCACACACTTACAACTA 10569
                          i  ii  i  v  v    ii vi       iv   i   i   iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_62104915_6  10570 TCCGATTTTCAACAAAGCTGGAAAAAGAAAAACAACCAATGGAGAAGGAC 10619
                         vii       i    i v  vv  i v-----  vi      i   i  v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGAC-----CATTCAATGGGGAAAGAA 392

  chrX_62104915_6  10620 TC-CCTATTCGATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAA 10668
                          v-i  v   i i              i      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_62104915_6  10669 GATTGAATTTTGACCCATTTCTTATACCATGCACATAG-TTAACGGAAGG 10717
                           v    v  v     v vi  i i     ii   v i-     vv  ii
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_62104915_6  10718 TGGATTAAAGATTTAAATGTAA-------AACCCTAAACCTT---GAAGA 10757
                              i ?   ii         -------   iv    v  i---     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_62104915_6  10758 CAACCTAG---TCAATACCATTCTGGATAAAGAAATGGGCAAAGATTTTA 10804
                         v   v   --- v   -- -   vv  ivvv iiv i     v i   iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_62104915_6  10805 T-GATGAAGACATTAAAAGCAATTGCAATATAAGCAAAAATGGACAAATG 10853
                          -   - v    ii       vvv    i v   v      i  i    v
  L1M4_orf2#LINE/    590 TAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_62104915_6  10854 GGGTCTAATTAAGCTGAAGAGTTTCGGCACAGCAAAAGAAACTGTCAACA 10903
                           iii v  i  iv v  i ii  iv ii vv    i  v   i    v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_62104915_6  10904 CAGTGAACAGACAACCTACAGAACAGGAAGAAATATTTGCAAACTATGCA 10953
                         v      v        i      ii   ii             ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_62104915_6  10954 TCTGACAAAGGCCTGATATCCAGCATCTATAAGAAACTTAAACAAACTTA 11003
                              i  i  v  vi       v  v     ii    ivv    -  i 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCA 787

  chrX_62104915_6  11004 -CAAGAAAAAAA-----AAC--AGTTTTAAAGTAGGCAAGCAACATGAAG 11045
                         -i  v     i -----   -- i  ?v   i i     ivi iv    v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_62104915_6  11046 AGACACTTTTTGAAAGAAGGCATACACATAGCCAAAAATCATATTTAA-G 11094
                              i  i iv       ii     v  i     v  v  i  vv  - 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_62104915_6  11095 AAGTTCAACATCACTCCTCAT 11115
                          v i         ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (155 / 103)
Gap_init rate = 0.03 (23 / 906), avg. gap size = 2.78 (64 / 23)  


1927 28.17 8.10 1.53  chrX_62118826_62123281     3115  3966 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62118826_6   3115 TGGAAAT-CATTTCATGCTCATGCTTTGGAAGAATCAATATTGTTAAAAT 3163
                               v-i  ii    i     vv        v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62118826_6   3164 GATTATACTTTTCCAAGCAATCTACAGATTCAGTGCAATTCTTATCAAAT 3213
                          iiv     iii v  vii             ii     i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62118826_6   3214 TAACAACATAATATTTTACAGAA--TGACAAAAAAAATCCTAAAACTCAC 3261
                          vv  i vvvv v    i     --      ivvi -        i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_62118826_6   3262 TTGGAACCAAAAATAAAAAGCATA-AATGTTCAAAGCAATCCCAAGCATA 3310
                         v     ---- vii  iiii vi -   ivi    i     iii iv vi
  L1M4_orf2#LINE/    150 ATGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_62118826_6   3311 AAGTACAAGCATGGAGGCAC-CACATTACCTGACTTTGAATTATATTACA 3359
                            v    ivv      -  -    i v  ii i  ii  viv  i    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_62118826_6   3360 AGGCAATAGCAATCAAAACAGCATAATAATGATACAAAAATATATATGGA 3409
                          i  v i  i      i    ii ii  v  ii i  ii   v i  ---
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT--- 291

  chrX_62118826_6   3410 ACAGATCAATGAAACAGAATAGTGAACCCAGGAATAAAGCCACATACCTA 3459
                          i         i  i     v v  ii    i      v   i i ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_62118826_6   3460 CATTCAACAGATCTTCAACAATGTCACCACAAATATATAATGGGAAAAGA 3509
                         iiv    iv   i   i    v vii   vi vi  vi      i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_62118826_6   3510 ACACACTATTCAATAAATTATGCTGGAAAAAATGGATAGTCATATGCGGA 3559
                          i vv  v     i    vi      i v  v      ?i  i    ii 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_62118826_6   3560 AAAATAAAACTGGGCCTTTATTTCTCACCATATACAAAAATTA-CTCACA 3608
                          i   i  ii   i  ii  ii  v                  -    v 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_62118826_6   3609 ATGGATTAATGGCTTAAATGTATGGACTGAAACTACAAAATTCTTAAAAG 3658
                               i ?v i i        v ii  i      i    i     i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_62118826_6   3659 AAAAC------------CTT---GAC--TGAGTT------------CT-- 3677
                              ------------   ---   --  i   ------------  --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_62118826_6   3678 ----------CAATAGCAAATTCAACAGAA-ACAAAATAGACAAATGGAA 3716
                         ----------   v    v vv     i  - v        i    v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_62118826_6   3717 CT------AAATTAAAGAGCT----GCTGCATAGCAAAATA--AACAGAC 3754
                           ------        i vi ----   v  v  v v v  --  v i v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_62118826_6   3755 TATACAGATAACCTATAGTAAGGGAGAAAAATATTTACAAACTATGCATT 3804
                          iv v   i    i i  v v         -     i    ii  ii  i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATC 740

  chrX_62118826_6   3805 TGACAGATGCTTAACATTAAGAACCTACAAGAAACTC--AAAAA--AACA 3850
                            i iiv vi vii  iv    iv  i  ii     -- v  v--  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_62118826_6   3851 AGAAATAAACAAATAAC--AGTTAAAAAGTGAGCAAAGTACATCAACAGA 3898
                          v   v i         -- i  ?    i  i      v iv v  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_62118826_6   3899 TATTTATCAAAAGAAGATCTAGAAGCATCATCCAACAA--ACATGAAAA- 3945
                         i    v  v         v  v  --  vi-    i  --         -
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAA--ATGG-CCAATAAGCACATGAAAAG 887

  chrX_62118826_6   3946 ATGGTCATCACTAGTCATCAG 3966
                            v   v  ii ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (148 / 89)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.15 (82 / 26)  


3118 26.83 0.77 1.31  chrX_62150158_62157599     2842  3754 (3688)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62150158_6   2842 TGGAAGAACATTCCATGCTCACGGGTAGGAAAAATCAATATCGTGAAAAT 2891
                              ii i  i     i   i  i v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62150158_6   2892 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCTTCCCCATCAAGC 2941
                            v     v     iv i  i  i        i  vv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62150158_6   2942 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAAAAACT-ACTTTAAA 2989
                          v   iivi i  i  ii     -   ------- v  i  - iii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-------ACAAGCTGATCCTAAA 143

  chrX_62150158_6   2990 GTTCATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCC 3039
                         i           viiv  ii  v  v v  v     iv     i i ivv
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_62150158_6   3040 AAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTCTACTGC 3089
                          i          i      vv    i  v  ii i      vii    i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_62150158_6   3090 AAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAT 3139
                           i          i   i    ii         i iv ii i   v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_62150158_6   3140 AGACGAATGGAACAGAAC--AGAGCCCTCATAAATAATGCCACATATCTG 3187
                            iv       i    i--    i  -- v      vv   i i  i i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chrX_62150158_6   3188 CAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGG 3237
                         iiii  vi    i  i     ivv  v   i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_62150158_6   3238 A--GTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTA 3285
                          --   -- v  i  i              v      v  ?   i   i 
  L1M4_orf2#LINE/    392 ATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_62150158_6   3286 GAAAGCTGAAACTGGATCCCTTCCTTACACATTATGCAAAAATTAATTCA 3335
                         i  iiv    ii    i    v   i    vv   i          i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_62150158_6   3336 AGATGGATTAAAGACATAAATGTTAGACCTGAAACCATAAAAACCCTAGA 3385
                          i      i ?    v       v   v  i    i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_62150158_6   3386 AGTAAACCTAGGCA-ACACCATTCAGGACATAGGCATGGGCAAGGACTTC 3434
                           v    v    ?i- v i -   iv   v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_62150158_6   3435 ATGTCTAAAACAGCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATG 3484
                         v ivv  vi   v        vvi     i    vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_62150158_6   3485 GGATCTAATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCA 3534
                            ii v  v   v v  i i   i  ii vv    i  v  i i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_62150158_6   3535 GAGTGAACAGGCAACCCACAGAATGGGAGAAAAGTTTTGCAATCTACTCA 3584
                         i      v  i                      vv       vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_62150158_6   3585 TCTGACAAAGGGCTGATATCCAGAATCTACAATGAACTCAAACAAATTTA 3634
                              i  i  i  vi          v  i  v      vv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_62150158_6   3635 CAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACA 3684
                         i  v     i     i     v  i?    i     i      v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_62150158_6   3685 GACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAA 3734
                             i     v        i  vi viii     v ii          i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_62150158_6   3735 TGCTCATCATCACTGGCCAT 3754
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  

2447 28.48 1.71 1.10  chrX_62150158_62157599     5594  6411 (1031)    L1M4_orf2#LINE/L1        4   826 (82)  

  chrX_62150158_6   5594 AAAAATAT---ATGCTCATGGACTGGAAGAATCAATATCATTAAAATGTC 5640
                            i    ---   i       i       v i     ii    i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_62150158_6   5641 AACATGACACAGAGTAATTTACAAATTCAATGCTATTTCTATCAAATGAC 5690
                           i ivv v  i v i  i    i      i  v  ii        vvv 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_62150158_6   5691 CAA-TGTCATTCTCCACAGAATTAGAAAAACTTTTTCTAACATTCAGACA 5739
                           i-  i -  i iii     v v  v  i  vv i    v     v ii
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_62150158_6   5740 GAACCAAAAAAGACCTTAAATAGCCAAAGACA-TCTTAAGCAA-AAGAAC 5787
                            viiv  ii    ivi          -   -    i iv  -      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGAAC 201

  chrX_62150158_6   5788 AAAGCCGGATGCATCACACTACCTGACCTCAAATGATACTACAAAGTTAC 5837
                             ii   v vv       v  ii ii     vvv          i   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_62150158_6   5838 AGTAATGTAAACAGCATGGTTCTGGTACAAAATCAGACACATAGACTAAT 5887
                               vv i    ii    v    i i  iivi     i     ii   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_62150158_6   5888 GGAAAGAAAAGAACAGAAAATTTAGAAATAAAATGAAACACCTACTGCCG 5937
                             v----    iv  i i ii         viv v   ii  iv i i
  L1M4_orf2#LINE/    302 GGAAT----AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_62150158_6   5938 TGTGATCTTCAAGAAGGATGATAAAAACAAGCAATGGGAAAACGAC--TC 5985
                         vv    i   i v    i  vi  i v  vv       i   vi i--  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_62150158_6   5986 TTTATTCAGGAAATGGTGCTGAGATAACTGACTAGCCACAGGCAGG---- 6031
                            --   iv           i  i     iv  ?     v   ii----
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_62150158_6   6032 TAAAGCTGGACCCTTGCTTTTCACCATATACAAAAGTTAACTCAAGATGA 6081
                          i   i       i i i iv              i         i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_62150158_6   6082 GTTAAAGATTTAAATGTAGGACCTCAAACTACAGAAGTCCTAGGAGACAA 6131
                         i i ?   ii        i  v  v      i i  v  i   i   v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_62150158_6   6132 CCCAGGCAATACTCTTCTTGACATTGGCTTTGGCAAAGAATTTTTGGCCA 6181
                          vi   ?ivv v     v    v    v  v     v iv  i  i vi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_62150158_6   6182 AGTCCCCAAAAGCAGTTGCAACAATAACAGAAACAGATATATGAGACCTA 6231
                         v v v         vvv       v iv i   i     v  vi   i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_62150158_6   6232 ATTAAAATAAAGAGCTTATACACAGCAAAAGAAACTATCAACACAGTAAA 6281
                           i     v  i i   v iii vv    i  v        v v   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_62150158_6   6282 CAGACAACATACAGAATGGGAGAAAACATCCACAAACTATGCATTCTACG 6331
                         v       vi                i  iii    ii  ii  iiv ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_62150158_6   6332 ATGGCCTAATATCTAGAATCTATAGAGAACTTTAAAAAAATCATTAAGAA 6381
                          v  v  vi    i     v    i      i v v  v-   v   v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAATAATAA 794

  chrX_62150158_6   6382 GAA-ACAAATAACTCCATT-AAAAATTGGCAA 6411
                         i  -         i v   -      v     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAA 826

Transitions / transversions = 1.37 (133 / 97)
Gap_init rate = 0.02 (13 / 823), avg. gap size = 1.77 (23 / 13)  

 309 20.88 3.30 0.00  chrX_62150158_62157599     6859  6949 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_62150158_6   6859 AAAAATTGGCAATGACATTGAACAGACACTTCTCAGAAGAAGACATATAA 6908
                               v     v ivv     i     i     vi       i   i  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_62150158_6   6909 GCAAC-AA-AAACTCATGGAAA-ATGCTCAGCATCACTAATCAT 6949
                         iiii -  -  i v    i   -       i     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.03 (3 / 94), avg. gap size = 1.00 (3 / 3)  


2157 28.03 2.62 3.60  chrX_62173842_62175911      661  1577 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62173842_6    661 TGGAAAAACCTTAAATGCACATGGATCGGAAGAATCAATATTGCTAAAAT 710
                               i iv ivv   iv       i      v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62173842_6    711 GTCCATTTTGCCCAATGCAACCTACAGAGTCGATGCTATTATTATCAAAG 760
                          v v  vi v     vvii i       v  i i  v  ivi       i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62173842_6    761 TTACCAAGGT-CATTTTTTACAGAATTAGACAAGAACT-ATTCTAAAATT 808
                          --  v  v - v      i     v v      --  -  i        
  L1M4_orf2#LINE/    101 T--CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT 146

  chrX_62173842_6    809 TATATGGAACAAAAAATGAGCATGATTACATAAGGTGAGGCTAAGCAACA 858
                         i        vviv  iv  v vv  ----   -------  i  --    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGA----ATA-------GCCAA--AACA 183

  chrX_62173842_6    859 A----AACAAAACAAAACAAAGCCAGAGGCATCACACTGCCCAACTTTAC 904
                          ----i v   iv i       iii    vv       v     i  i v
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_62173842_6    905 ACTGTACTACAAGGCTACACTAATCAAAGTAGCATGACACCGGTACAAAA 954
                          viv        i      v       iii  ii  ii  i  i i  ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_62173842_6    955 ACAGACACGTACACAAATGGAACAGAATAGAGAACCCAAAAATGAAGCTG 1004
                          i     ii  v iv       i     v    ii   i    i  v ii
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_62173842_6   1005 CAAATGTACAACCAACTGATCTTTGAAAAAGTCAACAAAA--ATTAACAA 1052
                         i v  v  iiii   i    i  i  v  i viiv   i --   --   
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT--CAA 381

  chrX_62173842_6   1053 CGGAGAAAAGACACACTATTCCATGAATGATGCTGGAAAAACTGGCTAAC 1102
                         i  i    ii i vv  v   v ii    i      i v      v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_62173842_6   1103 CATATGCAGAAGAAAGAAACTGGATGCCTACCTCTCACTATATATAGAAA 1152
                           i     i     v   ii    iv        v   i     i i   
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_62173842_6   1153 TTAACTCAAGATGGATTAAAGACCTAAATGTAAGATATCAAATTATATAT 1202
                                  i      i ?                vv v   i    ---
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA--- 528

  chrX_62173842_6   1203 GAAAAAA-----AAAAAAAAACCTAGGAAACACTGCTCTGGGCAGTGGTT 1247
                         ----   ----- i  i     v    ?ivv v vi  vv i vv   v 
  L1M4_orf2#LINE/    529 ----AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_62173842_6   1248 TAGGCCAAGAATTTATAATTATGTTCTAAAAAGC-CAAGGTAACAAAAGC 1296
                              v v iv  iv  iv    viviv      -    -i        -
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG-CAACAAAAG- 622

  chrX_62173842_6   1297 AAAAAAT-GACAATTTGGACCTAATTAAACTAAAGAGCATATTCAGAGC- 1344
                                -  i  v      i v  i   v v  i i ---  iv v  -
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC---TTTTGTGCT 669

  chrX_62173842_6   1345 --AAAACAAACTATGACTAGATTTTTAAAATAACCTGCAGAATACAAGAA 1392
                         --   iv v     v vv i v vvv  i i    ii      ivi    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_62173842_6   1393 AATATTAAAAGACTATGGATCCCACAAAGGACTAATATCTAGAATCTATA 1442
                               viv i ii  iv   iv i  i     vi    i     v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_62173842_6   1443 AGGAAAT--TAATCAAACCAGTAAGAAAATAACACATGATCTCAT-AAAA 1489
                          i   v --  --   vi  i   v    vi   v  i i iv  -?   
  L1M4_orf2#LINE/    770 AAGAACTCTTA--CAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_62173842_6   1490 TGTGGGCAGCAGACATGAGCAGACACTTCTC-AAAAAAGACATAAAAGCA 1538
                         vi      ivi  iv   ii     i     -   i    i   v  iii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_62173842_6   1539 GTCAACAG--ACATGAAAAAATGCTCAGCATCACTAATCAT 1577
                          i   i i--         i       i     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (147 / 106)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.48 (57 / 23)  


2162 28.06 2.62 3.49  chrX_62208427_62210460.rev      628  1543 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62208427_6    628 TGGAAAAACCTTAAATGCACATGGATCGGAAGAATCAATATTGCTAAAAT 677
                               i iv ivv   iv       i      v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62208427_6    678 GTCCATTTTGCCCAATGCAACCTACAGAGTCGATGCTATTATTATCAAAG 727
                          v v  vi v     vvii i       v  i i  v  ivi       i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62208427_6    728 TTACCAAGGT-CATTTTTTACAGAATTAGACAAGAACT-ATTCTAAAATT 775
                          --  v  v - v      i     v v      --  -  i        
  L1M4_orf2#LINE/    101 T--CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT 146

  chrX_62208427_6    776 TATATGGAACAAAAAATGAGCATGATTACATAAGGTGAGGCTAAGCAACA 825
                         i        vviv  iv  v vv  ----   -------  i  --    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGA----ATA-------GCCAA--AACA 183

  chrX_62208427_6    826 A----AACAAAACAAAACAAAGCCAGAGGCATCACACTGCCCAACTTTAC 871
                          ----i v   iv i       iii    vv       v     i  i v
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_62208427_6    872 ACTGTACTACAAGGCTACACTAATCAAAGTAGCATGACACCGGTACAAAA 921
                          viv        i      v       iii  ii  ii  i  i i  ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_62208427_6    922 ACAGACACGTACACAAATGGAACAGAATAGAGAACCCAAAAATGAAGCTG 971
                          i     ii  v iv       i     v    ii   i    i  v ii
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_62208427_6    972 CAAATGTACAACCAACTGATCTTTGAAAAAGTCAACAAAA--ATTAACAA 1019
                         i v  v  iiii   i    i  i  v  i viiv   i --   --   
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT--CAA 381

  chrX_62208427_6   1020 CGGAGAAAAGACACACTATTCCATGAATGATGCTGGAAAAACTGGCTAAC 1069
                         i  i    ii i vv  v   v ii    i      i v      v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_62208427_6   1070 CATATGCAGAAGAAAGAAACTGGATGCCTACCTCTCACTATATATAGAAA 1119
                           i     i     v   ii    iv        v   i     i i   
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_62208427_6   1120 TTAACTCAAGATGGATTAAAGACCTAAATGTAAGATATCAAATTATATAT 1169
                                  i      i ?                vv v   i    ---
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA--- 528

  chrX_62208427_6   1170 GAAAAA-----AAAAAAAAACCTAGGAAACACTGCTCTGGGCAGTGGTTT 1214
                         ---   ----- i  i     v    ?ivv v vi  vv i vv   v  
  L1M4_orf2#LINE/    529 ---AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_62208427_6   1215 AGGCCAAGAATTTATAATTATGTTCTAAAAAGC-CAAGGTAACAAAAGCA 1263
                             v v iv  iv  iv    viviv      -    -i        - 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG-CAACAAAAG-A 623

  chrX_62208427_6   1264 AAAAAT-GACAATTTGGACCTAATTAAACTAAAGAGCATATTCAGAGC-- 1310
                               -  i  v      i v  i   v v  i i ---  iv v  --
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC---TTTTGTGCTT 670

  chrX_62208427_6   1311 -AAAACAAACTATGACTAGATTTTTAAAATAACCTGCAGAATACAAGAAA 1359
                         -   iv v     v vv i v vvv  i i    ii      ivi     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_62208427_6   1360 ATATTAAAAGACTATGGATCCCACAAAGGACTAATATCTAGAATCTATAA 1409
                              viv i ii  iv   iv i  i     vi    i     v     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_62208427_6   1410 GGAAAT--TAATCAAACCAGTAAGAAAATAACACATGATCTCAT-AAAAT 1456
                         i   v --  --   vi  i   v    vi   v  i i iv  -?   v
  L1M4_orf2#LINE/    771 AGAACTCTTA--CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_62208427_6   1457 GTGGGCAGCAGACATGAGCAGACACTTCTC-AAAAAAGACATAAAAGCAG 1505
                         i      ivi  iv   ii     i     -   i    i   v  iii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_62208427_6   1506 TCAACAG--ACATGAAAAAATGCTCAGCATCACTAATCAT 1543
                         i   i i--         i       i     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (147 / 106)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.43 (56 / 23)  


3118 26.83 0.77 1.31  chrX_62226738_62234179.rev     2844  3756 (3686)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62226738_6   2844 TGGAAGAACATTCCATGCTCACGGGTAGGAAAAATCAATATCGTGAAAAT 2893
                              ii i  i     i   i  i v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62226738_6   2894 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCTTCCCCATCAAGC 2943
                            v     v     iv i  i  i        i  vv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62226738_6   2944 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAAAAACT-ACTTTAAA 2991
                          v   iivi i  i  ii     -   ------- v  i  - iii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-------ACAAGCTGATCCTAAA 143

  chrX_62226738_6   2992 GTTCATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCC 3041
                         i           viiv  ii  v  v v  v     iv     i i ivv
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_62226738_6   3042 AAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTCTACTGC 3091
                          i          i      vv    i  v  ii i      vii    i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_62226738_6   3092 AAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAT 3141
                           i          i   i    ii         i iv ii i   v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_62226738_6   3142 AGACGAATGGAACAGAAC--AGAGCCCTCATAAATAATGCCACATATCTG 3189
                            iv       i    i--    i  -- v      vv   i i  i i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chrX_62226738_6   3190 CAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGG 3239
                         iiii  vi    i  i     ivv  v   i v  vv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_62226738_6   3240 A--GTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTA 3287
                          --   -- v  i  i              v      v  ?   i   i 
  L1M4_orf2#LINE/    392 ATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_62226738_6   3288 GAAAGCTGAAACTGGATCCCTTCCTTACACATTATGCAAAAATTAATTCA 3337
                         i  iiv    ii    i    v   i    vv   i          i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_62226738_6   3338 AGATGGATTAAAGACATAAATGTTAGACCTGAAACCATAAAAACCCTAGA 3387
                          i      i ?    v       v   v  i    i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_62226738_6   3388 AGTAAACCTAGGCA-ACACCATTCAGGACATAGGCATGGGCAAGGACTTC 3436
                           v    v    ?i- v i -   iv   v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_62226738_6   3437 ATGTCTAAAACAGCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATG 3486
                         v ivv  vi   v        vvi     i    vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_62226738_6   3487 GGATCTAATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCA 3536
                            ii v  v   v v  i i   i  ii vv    i  v  i i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_62226738_6   3537 GAGTGAACAGGCAACCCACAGAATGGGAGAAAAGTTTTGCAATCTACTCA 3586
                         i      v  i                      vv       vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_62226738_6   3587 TCTGACAAAGGGCTGATATCCAGAATCTACAATGAACTCAAACAAATTTA 3636
                              i  i  i  vi          v  i  v      vv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_62226738_6   3637 CAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACA 3686
                         i  v     i     i     v  i?    i     i      v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_62226738_6   3687 GACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAA 3736
                             i     v        i  vi viii     v ii          i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_62226738_6   3737 TGCTCATCATCACTGGCCAT 3756
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  

2447 28.48 1.71 1.10  chrX_62226738_62234179.rev     5596  6413 (1029)    L1M4_orf2#LINE/L1        4   826 (82)  

  chrX_62226738_6   5596 AAAAATAT---ATGCTCATGGACTGGAAGAATCAATATCATTAAAATGTC 5642
                            i    ---   i       i       v i     ii    i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_62226738_6   5643 AACATGACACAGAGTAATTTACAAATTCAATGCTATTTCTATCAAATGAC 5692
                           i ivv v  i v i  i    i      i  v  ii        vvv 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_62226738_6   5693 CAA-TGTCATTCTCCACAGAATTAGAAAAACTTTTTCTAACATTCAGACA 5741
                           i-  i -  i iii     v v  v  i  vv i    v     v ii
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_62226738_6   5742 GAACCAAAAAAGACCTTAAATAGCCAAAGACA-TCTTAAGCAA-AAGAAC 5789
                            viiv  ii    ivi          -   -    i iv  -      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGAAC 201

  chrX_62226738_6   5790 AAAGCCGGATGCATCACACTACCTGACCTCAAATGATACTACAAAGTTAC 5839
                             ii   v vv       v  ii ii     vvv          i   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_62226738_6   5840 AGTAATGTAAACAGCATGGTTCTGGTACAAAATCAGACACATAGACTAAT 5889
                               vv i    ii    v    i i  iivi     i     ii   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_62226738_6   5890 GGAAAGAAAAGAACAGAAAATTTAGAAATAAAATGAAACACCTACTGCCG 5939
                             v----    iv  i i ii         viv v   ii  iv i i
  L1M4_orf2#LINE/    302 GGAAT----AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_62226738_6   5940 TGTGATCTTCAAGAAGGATGATAAAAACAAGCAATGGGAAAACGAC--TC 5987
                         vv    i   i v    i  vi  i v  vv       i   vi i--  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_62226738_6   5988 TTTATTCAGGAAATGGTGCTGAGATAACTGACTAGCCACAGGCAGG---- 6033
                            --   iv           i  i     iv  ?     v   ii----
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_62226738_6   6034 TAAAGCTGGACCCTTGCTTTTCACCATATACAAAAGTTAACTCAAGATGA 6083
                          i   i       i i i iv              i         i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_62226738_6   6084 GTTAAAGATTTAAATGTAGGACCTCAAACTACAGAAGTCCTAGGAGACAA 6133
                         i i ?   ii        i  v  v      i i  v  i   i   v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_62226738_6   6134 CCCAGGCAATACTCTTCTTGACATTGGCTTTGGCAAAGAATTTTTGGCCA 6183
                          vi   ?ivv v     v    v    v  v     v iv  i  i vi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_62226738_6   6184 AGTCCCCAAAAGCAGTTGCAACAATAACAGAAACAGATATATGAGACCTA 6233
                         v v v         vvv       v iv i   i     v  vi   i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_62226738_6   6234 ATTAAAATAAAGAGCTTATACACAGCAAAAGAAACTATCAACACAGTAAA 6283
                           i     v  i i   v iii vv    i  v        v v   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_62226738_6   6284 CAGACAACATACAGAATGGGAGAAAACATCCACAAACTATGCATTCTACG 6333
                         v       vi                i  iii    ii  ii  iiv ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_62226738_6   6334 ATGGCCTAATATCTAGAATCTATAGAGAACTTTAAAAAAATCATTAAGAA 6383
                          v  v  vi    i     v    i      i v v  v-   v   v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAATAATAA 794

  chrX_62226738_6   6384 GAA-ACAAATAACTCCATT-AAAAATTGGCAA 6413
                         i  -         i v   -      v     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAA 826

Transitions / transversions = 1.37 (133 / 97)
Gap_init rate = 0.02 (13 / 823), avg. gap size = 1.77 (23 / 13)  

 309 20.88 3.30 0.00  chrX_62226738_62234179.rev     6861  6951 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_62226738_6   6861 AAAAATTGGCAATGACATTGAACAGACACTTCTCAGAAGAAGACATATAA 6910
                               v     v ivv     i     i     vi       i   i  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_62226738_6   6911 GCAAC-AA-AAACTCATGGAAA-ATGCTCAGCATCACTAATCAT 6951
                         iiii -  -  i v    i   -       i     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.03 (3 / 94), avg. gap size = 1.00 (3 / 3)  


2535 25.03 5.86 1.95  chrX_62252927_62256139     1850  2720 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_62252927_6   1850 AAAAACAATCTGTGCTTATGTATTGGACCACTTAATATTGTGAAAATGTC 1899
                            i i vi ii  i i   v      vv            v  i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_62252927_6   1900 CAGAATATGTAAAGCAATCTACAGATTCAATTGAATCGCTACCAAAATCT 1949
                         v v v vivi   vii              ivv    v   i       i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_62252927_6   1950 CAATT-TTTTATTATTTTACAGAAAT--ACAAGAAAAAAATCCTAAAATT 1996
                           ii -ii  ----    i       --     vvi ---          
  L1M4_orf2#LINE/    104 CAGCTGCCTT----TTTTGCAGAAATTGACAAGCTGA---TCCTAAAATT 146

  chrX_62252927_6   1997 TATAAGGAA-TGTCAGGAAATCCA-AATAGCCGGAACAGTCTTGTAAAAA 2044
                         i   v    -  -  i ii i   -       ii    i     -     
  L1M4_orf2#LINE/    147 CATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTG-AAAAA 194

  chrX_62252927_6   2045 AAATAATAAAATGAGAGAACTCACACTTCCTGATTTCAAAA--------- 2085
                         i  v  i   i vi   i            ii         ---------
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_62252927_6   2086 AAG------TAATCAAGATAGTAAATAATTTT--TACAAAGTTAGAGA-A 2126
                            ------         i   i-- ii vi --i i  i v    v - 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTG--TGGTACTGGCATAAGGATAGACATA 292

  chrX_62252927_6   2127 TTAATCAGTAATACAAAACAGAGAGCCAAGAAATGAACCT-TGCATATAT 2175
                          vi    i iiv i i  iv     i v      i    i- i   v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_62252927_6   2176 AACCAAATTATTCTTGAGAAGGGTACCAA-ACTACACAATGAGAAAGGAA 2224
                         iii   v v   i i  v      i    -  i iv     i i  i   
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_62252927_6   2225 CAGACTCTTCAATAAATGGTGTTGAGAAAACTGGATATCTACACACAAAA 2274
                         i  v  i     i        i  i  v         ? i   ii     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_62252927_6   2275 GAATAAATGTGGACCCTTAAATTACACCATACAGAAAAGTTAACTGTAAA 2324
                             i  vv       i  vv i        i v    i      vv   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_62252927_6   2325 AGAATTAAAGATCTAAATGCAAGGCCTGATAATATAAAG-TCATAGAAGA 2373
                         v i  i ?   i       i   iv  i v v      i-  v       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_62252927_6   2374 AAACATAGGGATAACTCT-CAAGGCATTAGATTTGGCAATTATTTAATAA 2422
                                  ?i   v   - iv i v  i i  v      vi   vv  i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_62252927_6   2423 AGATGACATGAGAAGCGTAGGTAACAGAAGTTAAAATAGACAAATCAAAC 2472
                          v      iv i    ii i i    i   vv        i    iii  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_62252927_6   2473 TATATCGAACTTAAAAACTTGCACACGTCAAAGAAAA--AACAACATAGT 2520
                          vi   i  v          viiii v      i v -- v   v v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_62252927_6   2521 GAAAAAGACAAC-------ATGGAAGAAAATATTTGCATATTATATATCT 2563
                              -      -------    i              v  i        
  L1M4_orf2#LINE/    693 GAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_62252927_6   2564 GATAAGGAGTTAAAA---AGAATATATAAAAAACTT---CAATTCACCAC 2607
                                iii viv ---            i    i---   i   vi v
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_62252927_6   2608 CAACGACCAAAATAAATTACCCAATTAAGATATAGGTAAAATAACACGAA 2657
                         i  -- --  i i    v        ? i v  i  i   i-i ivi   
  L1M4_orf2#LINE/    792 TAA--A--AAGACAAATAACCCAATTWAAAAATGGGCAAAG-GATTTGAA 836

  chrX_62252927_6   2658 TAGACA---------AATAGGTATACAAATAGTCAACAAACATATGAAAT 2698
                               --------- iv  i         i i   i  i  i      v
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_62252927_6   2699 GATGCCCAACATCACTATCATA 2720
                              i        ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (139 / 75)
Gap_init rate = 0.03 (26 / 905), avg. gap size = 2.62 (68 / 26)  


3201 27.12 0.55 0.44  chrX_62264226_62270327.rev     4705  5611 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62264226_6   4705 TGGAAGAACATTCCATGCTCATGGGCAGGAAGAATCAATATCGTGAAAAT 4754
                              ii i  i     i      iiv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62264226_6   4755 GGCCATGTGTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4804
                            v  iivi     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62264226_6   4805 TACCAATGACTTTCTTCACAAAAGTGGAAAAAGCT-ACTTTAAAGTTCAT 4853
                          v   iivi i  i  ii  i  i v  v  -   - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_62264226_6   4854 ATGGAACCAAAAAAGAGTTCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 4903
                               viiv  ii  viiv v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_62264226_6   4904 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 4953
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_62264226_6   4954 ACAGTAACCAAAACAGCATGGTACTGGTACCGAAACAGAGATATAGAACA 5003
                                i   i    ii         i iviii i   v       v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_62264226_6   5004 ACGGAACAGAA--GAGAGCCCTCAGAAATAATGCCACATATCTACAACCA 5051
                          i    i    --     i  --        vv   i i  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_62264226_6   5052 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATATGGAAAGGATTCCC 5101
                         vi    i  i     ivv  v   i v  vv    iv      i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_62264226_6   5102 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5151
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_62264226_6   5152 AAACTGGATCCCTTCCTTACACCCTATACAAAAATTAATTCAAGATGGAT 5201
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_62264226_6   5202 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5251
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_62264226_6   5252 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5300
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_62264226_6   5301 AACACCAAAAGCA-ATCCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5349
                         i            - vv         vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_62264226_6   5350 TGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 5399
                          v   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_62264226_6   5400 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5449
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_62264226_6   5450 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAGAA 5499
                         i  i  vi          v  i  v      vv    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_62264226_6   5500 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5549
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_62264226_6   5550 TCAAAAGAAGACATTTATGCAGCCAAAAAACACAAGAAAAAATGCTCATC 5599
                           v        i  vi viii     v  i    v     i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_62264226_6   5600 ATCACTGACCAT 5611
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3098 27.09 0.99 0.99  chrX_62289151_62299293      492  1399 (8744)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_62289151_6   1399 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1350
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_62289151_6   1349 GGCCATACTGCCCAAGATAATTTATATATTCAATGCCATCCCCATCAAGC 1300
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_62289151_6   1299 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1252
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_62289151_6   1251 TATGGAATCAAACAAGAG--CCTGCATTGCCATGTCAATCTTAAGCCAAA 1204
                                -- vi    i --  v v  v    viv       i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

C chrX_62289151_6   1203 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 1154
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

C chrX_62289151_6   1153 GGTACAGTAACCAAAATAGCACAGTACTGGTACCAAAACAGAGTGATAGA 1104
                          v        i   i i  iiii       i iv ii i   vvv     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chrX_62289151_6   1103 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATTCCACATATCTACAA 1056
                         i        i    i--    i  --        vi   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

C chrX_62289151_6   1055 CTATCTAATCTTTGACAAATCTGAAAAAAACAAGAAATGGGGAAAGGATT 1006
                         ii vi i  i  i     ivv  vv  i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

C chrX_62289151_6   1005 CCCTATTTCATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 956
                         vi  v  iv i  i           v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chrX_62289151_6    955 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 906
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chrX_62289151_6    905 GATTAAAGACTTAAGTGTTAGACCTAAAACCATAAAAACCCTGGAAGAAA 856
                            i ?    i   i   v   v       i      vi i i       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chrX_62289151_6    855 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGGAAGGACTTC--AAG 809
                           v    ?i- v i -   iv   v v  vv i  v  v ii   -- ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

C chrX_62289151_6    808 TCTAAAACACCAAAAGCAATGGCGACAAAAGCCAAAATTGACAAATGGGA 759
                          v i --           vvi  i       vv     v  i    v   
  L1M4_orf2#LINE/    594 TATGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

C chrX_62289151_6    758 TCTAATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 709
                         ii v  i   v i  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

C chrX_62289151_6    708 TGAACAGGCAACCTACGGAATGGGAGAAAATTTTTGCAATGTACTCATCT 659
                             v  i     i  i              v       vvi ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

C chrX_62289151_6    658 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 609
                           i  i  i  vi          v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

C chrX_62289151_6    608 GAAAACGTCAAACAACCCCATCAATAAGTGGGCAAAGGATATGAACAGAC 559
                         v    v v    i     v  i? v  i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chrX_62289151_6    558 ACTTCTCAAAAGAAGATATTTATTTAGCCAAAAGACACATGAAAAAATGC 509
                          i     v           vi vv i     v ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

C chrX_62289151_6    508 TCATCATCACTGGCCAT 492
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  

1717 28.77 1.93 1.40  chrX_62289151_62299293     7240  7809 (2334)    L1M4_orf2#LINE/L1        3   575 (333)  

  chrX_62289151_6   7240 GAAAAAAATTCCATGTCAATGGATTGGAAGAATAAATATTAATAAAATGG 7289
                             i v  i      iv             v v      iv   i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_62289151_6   7290 CAATACTGACCAAAGCAATTTACAGATTCTGTGCTATTCTTATCAAACTA 7339
                                vv     vii  i         vii  v  i i       v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_62289151_6   7340 TCAACATCATTCTTTATAGAAGTAGGAAAAAAAAGATTCTAAAAGTTACA 7389
                         i  i vv v  i   ii    i v -- v  ivv   i      v i i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chrX_62289151_6   7390 AGGGACAAAAAAGGGCTT-GAACAGCCAAAGCCATCCCAAGTAAAAAGAA 7438
                         v  i vviv  i  i ii-   i       i v   iii iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_62289151_6   7439 CAAAGTTGGAGGAACCAAACTACCCAACTTCAAACTACACTGCAAAGCTA 7488
                                      vi  v   v     i      vivi   i        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_62289151_6   7489 TTATAACCCAAACAGCATGGTATTAGTACAAAATCAGACACATAGACCAA 7538
                         ivi   i v i    ii     i i i i  iivi     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_62289151_6   7539 TGGAAGGCAATAGAAACCTCAGAAATAAAACCACACACTAGCAACCATCT 7588
                              viv   v  i vii          v   i   i viiiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_62289151_6   7589 GTTCATTGACAA---CCTCATAACAACTAGCAGTGAGGAAAAAAAA---T 7632
                          v iv i     ---ivi  vi  v i --  i  i     i  v --- 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATT--CAATGGGGAAAGAATAGTCT 398

  chrX_62289151_6   7633 TGTCAGTAAATAGTTCTGGGATAACTGGTTAGCCACAGGTGGGAGATAGA 7682
                          v   ii    i  v      i      v  ?     v iiii   vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_62289151_6   7683 AATTGGGCCC-TACTTTTTATCATATACAAAAAATTAATTCAAAATGGTT 7731
                          i    i   -   i ivi i            -    i         v 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGAT 497

  chrX_62289151_6   7732 CAAAAATCTAAATGTAAGACCTCAAACTACAAAATTGCTAGAAAACAACC 7781
                           ? i i            v  v      i    i vi     i v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_62289151_6   7782 TAGG---AAATACCCTTCTTAACACTGGCTT 7809
                             ---    ---    v i  vi   v  
  L1M4_orf2#LINE/    548 TAGGNGTAAAT---CTTCGTGACCTTGGGTT 575

Transitions / transversions = 1.57 (99 / 63)
Gap_init rate = 0.02 (9 / 573), avg. gap size = 2.11 (19 / 9)  

2029 27.29 4.35 0.29  chrX_62289151_62299293     7811  8499 (1644)    L1M4_orf2#LINE/L1      192   908 (0)  

  chrX_62289151_6   7811 AAAAAAGCACAAAGCTGAGGGTATCACACTACCTGACTTCAAACTATACT 7860
                            i   v      i  ii  vv       v  ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_62289151_6   7861 ACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACTAGAACAGACAC 7910
                             i          i   i    ii         i iv  i i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_62289151_6   7911 ATAGACCAATGGAACGAAACAGAGAACTCAGAAATAAGACTGCACACCTA 7960
                              i        iii  iv    iii         iv iii   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_62289151_6   7961 CAACCATCTGATCTTGTACAAACCTGACAAAAACAACCAATGAGGAAACC 8010
                         iiii  vi    i  vv    ivv  v   i v  vi     i     vv
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_62289151_6   8011 ATTCTCTATTTAATAAATTGTGCTTGAAGAACTAG----TCATTGGCAGA 8056
                           vv   v  i  i    v     v i v    i ----i  ivv   i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_62289151_6   8057 AAATTGAAACTGGACCCCTTTTTTACACCATATACAAAAATTAACTCAAG 8106
                          i v    ii         vii i                         i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_62289151_6   8107 ATAGATTAAAGCCTTAATTGTAAAACCAAAAACAATAAAAATTCCAGAAT 8156
                           i   i ?  v i   v     i v v     v      v iii    v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_62289151_6   8157 AAAATCTAGGT---AAT-------ACC----ATT---CAA-GTTTTCATG 8188
                             iv    ?---   -------   ----i  ---   - v    v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_62289151_6   8189 AAAAAAACACCAAAAGCAATTGCAACAAAAGAAAAATTTGACAAATGGGA 8238
                         i v vi            vvv               v v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_62289151_6   8239 TCTAAATAAA-TGAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGC 8287
                         ii v vi   - v   i -   i  ii vv    i  v       vv iv
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_62289151_6   8288 ATGAACAGACAACCTACAAAATGG-AGAGAATTTTTGCAATCTATGCATC 8336
                         i    v        i   i     -   i   v       vii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_62289151_6   8337 TGACAAAGGTCTAATATCCAGAGTCTAAGAGGAACATAAACAAATTTACA 8386
                            i  i  v  vi        i v  vi i    vivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_62289151_6   8387 AGAAAAAAACAA----CCCCGTTAAATAGTGGGCTAAGGATATGAGCAGA 8432
                          v     i    ----   vi  ?  v i     v      v   ii   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_62289151_6   8433 CGCTTCTCAAAGGAAGATGTTCATGTGGCCAACAA--ACATGAAAAAAAA 8480
                          ii     v  i      i v  vi       i  --         i v-
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT- 889

  chrX_62289151_6   8481 GTTCAACATCACAGATCAT 8499
                          i         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (108 / 77)
Gap_init rate = 0.02 (12 / 717), avg. gap size = 2.67 (32 / 12)  

 704 27.96 3.95 0.61  chrX_62289151_62299293     9322  9650 (493)    L1M4_orf2#LINE/L1      569   908 (0)  

  chrX_62289151_6   9322 TTGGCTTTGACAAAAAATTTTTGCCCAAGCCCCCAAAAGCAATTGCATCA 9371
                             v  v i   viiv  i  ivvi v v v         vvv   v  
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_62289151_6   9372 GAAACAGAAAATAGACAAGTGAGAACTAATTAAAATAAAGAGCT---ACA 9418
                         -   v i        i  i vi  vi v  i     v  i i  ---iii
  L1M4_orf2#LINE/    619 -AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_62289151_6   9419 CAGCAAAGGAAACTATCCACAGAGTAAATAGACAACATAGAGAATGAAAG 9468
                          vv       v      v v i   i  v       vi v      ii  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_62289151_6   9469 AAAATATTCACAAACTATGCATTCCTACAAAGTCCTATTGTCCAGAATCT 9518
                                 ii    ii  ii  - iv i  i vv  vv i        v 
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATAT-CTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_62289151_6   9519 ATAGA------TGACAAATCAACAAGAAAAA-ACAAACAACCCCATTAAA 9561
                            i ------ v    v    i  v     -     i     v   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_62289151_6   9562 AATTGA--AATTGACATGAACAGACACTTCTCAAAAGAAGACATACAAGC 9609
                           v  i--  vv  iv    i     i     v        i      ii
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_62289151_6   9610 AGCCAA-AAACTTATCAAAAAATTCTCAATATCACTAATCAT 9650
                         i     -  i vi  v    i  v     i    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.07 (47 / 44)
Gap_init rate = 0.02 (7 / 340), avg. gap size = 2.14 (15 / 7)  


 823 25.00 7.61 1.45  chrX_62303974_62309894.rev     2429  2704 (3217)    L1M4_orf2#LINE/L1        1   293 (615)  

  chrX_62303974_6   2429 TGAAAACACATCCCATGCTCATGGATGGGAGGAATCAATATTGTGAAAAT 2478
                           i   v i        i        v   i  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62303974_6   2479 AACCATACTTCCAAAAGCAGTCTACAATTTCAATTCAACTCCCATCAAAA 2528
                         ii v     i  v   viii      iv     iv   ii  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62303974_6   2529 TACGACCATCATTCTTCACAGAACTAGA-AAACTCAGTCCTAAAATTCAT 2577
                          v v v vv v  i  ii     v v  -  i  v -             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_62303974_6   2578 ATGGAA-----------CCAAAACTAGCCAAAGCAA----GACAAAGAAA 2612
                               -----------   i  -        i   ----  v      i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAA-TAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_62303974_6   2613 AAAAAATCTGGAGGCATCACATT-----ATGATTCAAATTATAGTACAAG 2657
                           v   vi      vv     i -----  --      viv  v     i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAAT--TTCAAAACTTACTACAAA 246

  chrX_62303974_6   2658 TCTGTAGTCACCAAAACAGCATGGTACTGCTAGAAAAATAGGCAGAT 2704
                         v  ii   v i   i    ii        vi v  ii    i  v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

Transitions / transversions = 1.23 (38 / 31)
Gap_init rate = 0.02 (7 / 293), avg. gap size = 3.57 (25 / 7)  

1792 25.43 1.73 2.98  chrX_62303974_62309894.rev     3003  3639 (2282)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_62303974_6   3003 AAAAAAAGGCAGATGCACCAATGGACTAAAATAGAAAACCCAGAAATATA 3052
                           ii v  i  v  iv i       v  i   v  i ii         v 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_62303974_6   3053 GCCAAATATATACAAATATATACAGCCAACAGATCTTTGACAAAGCAAAC 3102
                         v   ------    ---- v  ii i   iv   i  i     i -ivi 
  L1M4_orf2#LINE/    330 CCCA------TACA----TTTATGGTCAATTGATTTTCGACAAGG-GTGC 368

  chrX_62303974_6   3103 AAAAACAAAAACATAAAGTGAG-AAAGGACACCCTATTCGACAAATGGTG 3151
                         v  i  -----   vv i  i -    i i vi  v   i          
  L1M4_orf2#LINE/    369 CAAGAC-----CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_62303974_6   3152 C-GGTATAATTGGCAACCCTCATGTAGAAAAATAAAACTGGATCCTCCTC 3200
                          -  v i  i   vv ?  v    i i  i   i  ii    i  iivi 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_62303974_6   3201 TGTCACCTTATAAAAAAAATCAACTCAAGATGGATCAAAGACTTAAATGT 3250
                          vv    v    v     - i       i        ?    i       
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_62303974_6   3251 AAGACCTAAAACCATAAAAATTCTAGAAGATAACATTGAAAAAACTCTTC 3300
                             v       i      v ii       v     v i?iv  v     
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_62303974_6   3301 TAGACATTGGGTTAGGCAAAGACTTCATGACCAAGTACACCAAA-GCAAT 3349
                         vv   v             v ii   v iivi v -        -   vv
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG-ACACCAAAAGCACA 611

  chrX_62303974_6   3350 TGCAAC----GCAAACATAAATATATGGGACTTAATTAAACTAAAAATCT 3395
                         v     ---- v   v   i   v  v      v  i   v v    v  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_62303974_6   3396 TCTGCACAGCTAAAGAAATAATCAGTAAAGTACACAGACAACCCCCAGAG 3445
                          i  ii vv v  i  v iv    iv     iv v         v    i
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_62303974_6   3446 TGG-AGAAAATCTTTGCAAACTATGCATCTGACAAAGGATGAACATCCAG 3494
                            -       v        ii  ii      i  i   ivvii      
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_62303974_6   3495 AATCTATAAGGAATTCAAACAAATCAGCAAGAAAAA---AAATTATTTCA 3541
                            v     i   i  vv    v   ii  v     ---    v iiiv 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_62303974_6   3542 TCAAAAAGTGTGCTAAGGACATAAATAGACAATTCTCAAAAGAGGATATA 3591
                          i?    i  v  v     iv i        v     v     i      
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_62303974_6   3592 CAAATGGCCAACAAACATATTCAAAAAATGCTCAACATCACTGATTAT 3639
                                    i  i  i  v-    i             ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (85 / 73)
Gap_init rate = 0.02 (13 / 629), avg. gap size = 2.31 (30 / 13)  

2538 27.90 4.21 0.80  chrX_62303974_62309894.rev     4521  5398 (523)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_62303974_6   5398 TGGAAAAAT--TTCATGCTCATGGATAGGAAGAATCAATATT---AAAAT 5354
                               i  --ii    i        v      v i      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_62303974_6   5353 GGCCAAACTGCCCAA--TGCTATTTACAGATTCAATGCTATCCCTAACAA 5306
                            v v   v     --  --  i           i  v       v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAA 98

C chrX_62303974_6   5305 ACTATAAGTGACATTCTTCACAGAACTAGAAAAAAACT-ATTTTAAAATT 5257
                          v viv  ivi v  i  ii     v v  v  i--  -  ii       
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT 146

C chrX_62303974_6   5256 CATATGGAACC-CAAAATGCTCA-AGTAGCCAAGGCAATCTTAAGCAAAT 5209
                                  vi-   iivi i  - i       ii       i iv  iv
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

C chrX_62303974_6   5208 AGAACAAAGCTGGAAGTATCACATTACCTAACTTCAAACTATACTAGGGG 5159
                                  i    i vv     i v  i  i      viv     viii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

C chrX_62303974_6   5158 GCTACACTAGCCAAAACAGCATGGTACTGGAACAGAAACAGACACATAGA 5109
                               v  ii   i    ii         v i iii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chrX_62303974_6   5108 CCAATGAAACAGAACAGAGAGCCAAAAAATAAGACCACAC--CTGCAACC 5061
                         i     i  i    iv     i v i      iv   i  --i iiiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

C chrX_62303974_6   5060 ACCTGATCTTTGACAAAGGTGACAAAAAGAAGCAATGGGGAAATGACTCT 5011
                          vi    i  i     i    v   i vv vv           vi ivv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_62303974_6   5010 CTATTCAATAAATGGTGCTGGGATGACTGGTTAGCCATATGCAGAAAATT 4961
                           v     i              ii     v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_62303974_6   4960 GAAACTTGGCCCCTTCCTTACACCATATACAAAATTAAACTCAAGATGGA 4911
                            ii v i     v   i               v v       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_62303974_6   4910 TAAAAGACTTACATGTAAAATCCAAAAGGATAAAAACTTTGGGATGCAAC 4861
                          v ?    i  v      i v i    vv      vii  i i viv   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_62303974_6   4860 CTAGGCAATACTATTCTGGACATAGGCGCTAGCAAATA-TTTCATGACTA 4812
                         v    ?ivv v v   vv   v v  - i   vv   i-    v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATA 595

C chrX_62303974_6   4811 AGACACCAATTGCAC------CAAAAGCAGAAA------AATGGGATCTA 4774
                         v        vv    ------      v i   ------   v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chrX_62303974_6   4773 TTTTAAGTAAAGGGCTT-----CTTCAGAGAAGAGTATCAGTAGAGTAAA 4729
                         v iv  i v  iii   -----     i  i v v     iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chrX_62303974_6   4728 GAGACAACATACAGAATCAGATAAAACATTTGCAAACTATGCATCTGACA 4679
                         i       vi       vi  v    i         ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chrX_62303974_6   4678 AAGTTCTAATATTCAGCATCCATAAGAAACAAATATGTTTACAAGAA--A 4631
                          i vv  vi   i   v  vi    ii   vvv  iivi -   v  -- 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT-CAATAATAA 794

C chrX_62303974_6   4630 AAAAACACAGAACCCCATTAAAAAATGGTCAAAAGCCATGAACAG----- 4586
                            i   v v     v   ?        v    i viv    i  -----
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chrX_62303974_6   4585 TTTTCAAAAAGGACATACATGTGACCAACAAGCATGTGAAAAAAAAGTTC 4536
                          i i    i i  i     vi  i    i     ii      i v- i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTC 893

C chrX_62303974_6   4535 AATATCACTAATCAT 4521
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.44 (44 / 18)  


2946 26.10 0.88 1.76  chrX_62309966_62312601     1236  2143 (492)    L1M4_orf2#LINE/L1        9   908 (0)  

  chrX_62309966_6   1236 TACCTTATGTTCATGCATTGGAAGAACTAATATTGTTAAAATGTTCACAC 1285
                           i ii         v         vi            i   viv i  
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chrX_62309966_6   1286 TACCTAAAAAGATTTACAGATTTAATG-AATCCCTATCTAAACACCAA-T 1333
                          v  i   vv   i        i  i -          v   iv   i- 
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chrX_62309966_6   1334 GCCATTCTTCATAGAAATAGA-AAAC-AATCTTCTGAAATTAATATGAAA 1381
                            -  i  iii      v  -  i -i   --  i     v     i  
  L1M4_orf2#LINE/    109 GCC-TTTTTTGCAGAAATTGACAAGCTGATC--CTAAAATTCATATGGAA 155

  chrX_62309966_6   1382 CCACAAAAGTCCTTAAATAGCCAAATCAATTTTAATAACAACCAAAAAAG 1431
                         vii   ii v  ivi          v    i  i v  vi vv  v    
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_62309966_6   1432 TTAATGGCCTTATACTACAGCCTGACTTCATAGTATACTGCAAAAATACA 1481
                           iiv  v  i i   ---v  ii i    v iiv    i    iv    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACT---TCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_62309966_6   1482 GCAAAGCAAAGAGCATTGCATTGACATAAAATAAGGCATATGGACAAGTG 1531
                          i  vvv i v  ii v i i  i     iivv  i     i  iv i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_62309966_6   1532 GAAAAGAATAGAAAGACCAGAAATAAATTCACACAGTTTACA-CCAACTG 1580
                            v     v  i  v           ii  i   -    ii-i   i  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACA-TTTATGGTCAATTG 351

  chrX_62309966_6   1581 ATGTTTGACAAAGGTGCCAAGAACATGTTATGGGGAAAGGACAGTCTCTT 1630
                           v  i     i          v   viv          i i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_62309966_6   1631 CAACAAATGGTGTTGAGAAAACTAGATATCTACATAGAGAAGAATAAAAT 1680
                                     i  i  v    i    ? i    iv i      i  i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_62309966_6   1681 TAAACCATTATATTTCAGAATCTACAAAAATTAACTCAGAATGTATTAAA 1730
                          ii   vi  iv iv  vv  v                i    v  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_62309966_6   1731 GACTTAAATGTAAGATCTAAAACTATGAAACTTCCAGAAGAAAACATAGG 1780
                            i           v          i     iii               
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_62309966_6   1781 GG-AAATGTTTTATGACTTTTGTATGGGCAA-ATTTTTTTTGATAAAACC 1828
                         ? -    -i  ii    i  v vv i     -iv   i  v    vi  v
  L1M4_orf2#LINE/    552 NGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_62309966_6   1829 TCAAAAGCACTGGTAACAAATGCAAAAATAGACAAATGGAACCATATCAA 1878
                         i         vi i      v v         i    v i  ivi     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_62309966_6   1879 AAT-AAAATCTTCACTGTAACAAAAGAACCAATCAGGAGAGTGAAGAGAC 1927
                            -    v   ivv  ivv    i  vv v    i  i      i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_62309966_6   1928 AACCTACCAAATAAGAAAAAATGTTTGCAAACAATTTATCCAGCAATATA 1977
                             i  vi   ii  i     i        iv  v    iiii  viv 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_62309966_6   1978 CTAATATCCAGAATATACAAGGAACTCAAATAACTCAATAGGAAAAAACA 2027
                           vi             i  i      vv i         iv     i--
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG-- 798

  chrX_62309966_6   2028 AACAAGTAAATAACCTGATGTAAAAATGAAAAAAAAATCTGAATAAAAAT 2077
                         -    ----      ii  v?       iiv   ii  i      i v  
  L1M4_orf2#LINE/    799 -ACAA----ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_62309966_6   2078 TTCTCAATAAAAGACATACAAATGAAGAACAGGTATGTCAAAAAAATGTT 2127
                              v v i    i         ivv  i i i ii -i    i   i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-GAAAAGATGCT 892

  chrX_62309966_6   2128 CAACATCACTGATCAT 2143
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (146 / 87)
Gap_init rate = 0.02 (16 / 900), avg. gap size = 1.50 (24 / 16)  


2937 28.08 0.77 0.77  chrX_62373629_62375850      822  1729 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62373629_6    822 TGGAAGAACATTCCATGCTCATGGGGAGGAAGAATCAATATCCTGAAAAT 871
                              ii i  i     i      ivv      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62373629_6    872 GGCCATACTGCCCAAGATAATTTATAGATTCAATGCCATCCCCGTCAAAC 921
                            v     v     iv i  i  i        i  v     ii     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62373629_6    922 TACCAATGACTTTCTTCACGGAA-TTGGAAAAAACT-ATTTTAAAGTTCA 969
                          v   iivi i  i  ii i   -   -- v  i  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_62373629_6    970 TATGGAGCTGAAAAGGAGCCCGCATTGTCAAGTCAATCCTAAGCCAAAAG 1019
                               iv  v  i   v  v v  v i   iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_62373629_6   1020 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACGAGGC 1069
                                i      vv       v  ii i      viv      i i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_62373629_6   1070 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGTGATATAGACC 1119
                                 i   i    ii         i iv ii i  vv       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_62373629_6   1120 AATTGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAAGT 1167
                            v   i    i--    i  --        vv iii i  i  iiivi
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_62373629_6   1168 ATCTGATCTTTGACTAACCTGACCAAAAAAAG-AAATGAGGGAAGGATTC 1216
                          vi    i  i   v ivv  -    i vv v-v    i  i   i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_62373629_6   1217 CCTATTTAATAAATGGTGCTGGGAAAACTAGCTAGGCCTATGTAGAAAGC 1266
                         i  v  i  i              v    i v  ?v vi   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_62373629_6   1267 TGAAAGTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGG 1316
                             iv    i    v   i     v i            i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_62373629_6   1317 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1366
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_62373629_6   1367 CCTAGGCA-ACACCATTCAGGACATAGGCAT-GGAGATGGACTTCATGTC 1414
                          v    ?i- v i -   iv   v v  vv -  vi    -i   v ivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGA 593

  chrX_62373629_6   1415 TAAAACACCGAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 1464
                           vi     i      vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_62373629_6   1465 TGATTAAACTATAGAGCATCTGCACAGCAAAAGAAACTACTATCAGAACG 1514
                          v  i   v vv i i v i  ii vv    i  v    ii vv i ii 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_62373629_6   1515 AACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTCA 1564
                           v  iv    i                 v       vii ivi    v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_62373629_6   1565 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTGACAAGA 1614
                         i  i  i  vi          v  i  v      vv    v ii i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_62373629_6   1615 AAAAAACAAACAACCCCATCAAAAATTGGGCGAAGTATATGAACAGACAC 1664
                             i     i     v  i?    v     i   v  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_62373629_6   1665 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAATATGCTC 1714
                              v        i  vi viii     v ii          v      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_62373629_6   1715 ATCATCACCGGCCAT 1729
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (144 / 107)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


1215 29.13 2.52 1.83  chrX_62390724_62395180.rev     2453  2888 (1569)    L1M4_orf2#LINE/L1        3   441 (467)  

  chrX_62390724_6   2453 GAGAAATATACTTTGTTAACTAATCAGATGTTTTAATACTGTTAAGGTGT 2502
                           i i    v iv    v ivi  ii  v vi      i       i  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_62390724_6   2503 CATTTCTTTTTAAATTTATGTATAACTTCAATGCAATCCAAGTTAAATTT 2552
                           v v  iiii     v  v  i iv     i       vvi i   v i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_62390724_6   2553 CTGAAGTG---TTTTTATAGAAATCAACAAACTGATTATACAATTTACAT 2599
                          i- iv  ---     ii      ii    i     iv  v    i i  
  L1M4_orf2#LINE/    103 CC-AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_62390724_6   2600 GGAAATGTAAAGCCCCTACAATAATTAAATAAATTTTGAAAAAGAA---C 2646
                                i  i vv  i v    iii   vv   i           --- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_62390724_6   2647 AAAGTTGGAGAGCTAAATCTACTTAATTTCAATAATTATTATAAAGCTAC 2696
                                   ii  v vv  v ii        v v   i  i        
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_62390724_6   2697 AGTTAGCAAAAGTGTATGGGATTAACCTAATGACAGAGAAATAGATCCAT 2746
                            v v   i vv  i   v i ii v   v  i   v v       v  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_62390724_6   2747 GGAATAAAA--AAAAGTCTAGAAATGAACCCACACCTACAGAGACAACTG 2794
                               i  --i i    i      i      i  v vi vi v   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_62390724_6   2795 ATTTTT-ACAAAGATTTAATGGCAATTAACCATTAAATGGAGGAA--ACA 2841
                              i-    i i ----- v   --i      v     i i  -- i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGT-----GCCAA--GACCATTCAATGGGGAAAGAATA 394

  chrX_62390724_6   2842 GTTTTGTAAACAAATAAGGATGGAGTAATTGGATATATCTATGTAAA 2888
                           i  v v       iiv v   iii  i      ?vivi   i   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

Transitions / transversions = 1.47 (75 / 51)
Gap_init rate = 0.02 (8 / 439), avg. gap size = 2.38 (19 / 8)  

 335 23.08 1.10 0.00  chrX_62390724_62395180.rev     3215  3305 (1152)    L1M4_orf2#LINE/L1      445   536 (372)  

  chrX_62390724_6   3215 ATAAACTTTGATCCAC-CCTCATACCATATACAAAAATTCTTCTAAAACA 3263
                           i  v  v  i  vi-     i                vviii    ii
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_62390724_6   3264 GATTACAGACCTAAATGTAAATCCTAAAACTAGAAAACTTTT 3305
                            i ?              ivv         v      i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

Transitions / transversions = 1.50 (12 / 8)
Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1)  

 879 25.27 7.97 0.27  chrX_62390724_62395180.rev     3603  3966 (491)    L1M4_orf2#LINE/L1      517   908 (0)  

  chrX_62390724_6   3603 GCCAAAACTAGAAAACT-TTAGAAGAAAAAA-------AAATCTTTGTAA 3644
                           i       v      -           v -------       i  i 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_62390724_6   3645 CATTGTGTTAGAAAAATATTTTT--GATTCAACAGAAAAAATACAATATA 3692
                          v   v     iv  vvi   i --   vii   vv    ii    vvv 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_62390724_6   3693 TAAAACAAAAATTA-ATATGCTTGACTTTATCAGAATTTAAAATTGTTGC 3741
                         i    v     v  -   vii v     i    i    v    i v   i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_62390724_6   3742 TTTTTGAAAGACAC----AAGAAAATTAAAGCAAAAGCCACAGACTAAGA 3787
                         vi  ii  i     ----      i v   iv v  v       v ii  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_62390724_6   3788 AAAGATCTTTGAAAATTATATAATTGATGAAGGACTTGTATCCAGATTAT 3837
                         i  i  v    v    i     vi    i i               v   
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_62390724_6   3838 ACAGAGAAAAGTAAAAAACTTATCAATAAGAAAACAAACAACCTAGT--A 3885
                          i i    vvv v v  -  i vi     i  i     i    i i -- 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAA-CTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_62390724_6   3886 AAAGTCAG-AAAATATTTGAA---ACA--------AGAAAAATACATAAA 3923
                            i vi -   iv       ---   -------- ii  i   i i   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_62390724_6   3924 TGGCAAACAAGCACCTAAAAAGGTATTCAACATCATTAGGCAT 3966
                             v  i      v i     i ii         ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (53 / 39)
Gap_init rate = 0.03 (10 / 392), avg. gap size = 3.00 (30 / 10)  


 787 22.77 2.48 0.00  chrX_62397810_62400057.rev      563   764 (1484)    L1M4_orf2#LINE/L1        1   207 (701)  

  chrX_62397810_6    563 TGAAATGTCATCCAGAGTTCATGGATTGGAGGACTGAATATTGTTAAGAA 612
                           i  v vi    viv              i    v             v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62397810_6    613 GCCAATACTACCTAAAGTGATCTACAGATCCAATGCAATTTCTATCAAAA 662
                          v       v  i   v            i   i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62397810_6    663 TGCCTGCT--TTTTTTTG-AAAAATACAAAAATACATTCAATAATTCATA 709
                          v  v   --i       - i    vv v  iivv  i v v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_62397810_6    710 TGGAATCATCAGGGATTCC-AATTGCCAAA-CTGTCTTGAAAAACAAAAA 757
                              viiiv     ii v-   v      - vi          v  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_62397810_6    758 CAAAATT 764
                             i  
  L1M4_orf2#LINE/    201 CAAAGTT 207

Transitions / transversions = 0.92 (22 / 24)
Gap_init rate = 0.02 (4 / 207), avg. gap size = 1.25 (5 / 4)  

2560 23.64 1.53 1.67  chrX_62397810_62400057.rev     1053  1771 (477)    L1M4_orf2#LINE/L1      191   908 (0)  

  chrX_62397810_6   1053 AAAATAAATATAAAATTTTAGGTCTCACACTTCCTAATTTCAAAAATTAC 1102
                             v  iv i   i  vv   v           i          v    
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_62397810_6   1103 TACAAAGCTACAATAATCAAAACAATGTGGTACTGGCACAAATACAAAAA 1152
                                     i       i   i             i  iv i i v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_62397810_6   1153 ATACAGACAAATGGAACAGAATAGAGAGCCCAGAAATAAATCCTTTTAT- 1201
                         -  i   iv       i     v     i           i  v vi  -
  L1M4_orf2#LINE/    291 -TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_62397810_6   1202 -ATGTTCTGAAAAGATTTTCAACATGGATGCCAAGATTATTCAATTGGAA 1250
                         -   v  --  vv       i   v  i        ii       v  i 
  L1M4_orf2#LINE/    340 TATGGTC--AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_62397810_6   1251 AATGACCATCTTTTTTAAAAATGGTGCTGGGAATACTAGATATATACATA 1300
                           vi ivi      iv v              vv   i    ?vi    i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_62397810_6   1301 CAAAAGAATAATGGTGGATCCTCATTTTATACAGTATATTACAGTTCACT 1350
                                  i v v    i  ii ii i i  vi    iv v i  v   
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_62397810_6   1351 CAATTTTGATCAAAAGCCTAAGCAGCAGAGATAAAAGTATACATATCTTA 1400
                            vv v     ? ii     iiivv    v     v    v vv     
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_62397810_6   1401 TAAAAAAAAAAAAACCGGGAAAAGCTTCATGCCATTGGAATCGGCAGTGC 1450
                         v  i    v v i--- ? v   v    i  v v    iv v    i  v
  L1M4_orf2#LINE/    538 GAAGAAAACATAG---GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_62397810_6   1451 TTTCCTGGATTTAACACCAAAAAACACAGGCAACAAAAAAAATAATCAAT 1500
                             i i   v i         i-    i         i   v   vi  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_62397810_6   1501 ATATTAGATTTCATCAAAATTCAAAACTTTTGTGCACCAATGACCA-TAT 1549
                          v   i  i            v             vi   v iv  -   
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_62397810_6   1550 TAATAAAGTGAAAAAGCCAACCACATAATGGGAGAAAATGTTTGGAAATC 1599
                         i  v          ii v v     v             i    v     
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_62397810_6   1600 ATATA-------AGAGA-TTATATGCAAAATATTTAAAGAACACTTAAAA 1641
                              -------  i  -  i   v  i     v        v    v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_62397810_6   1642 CTCAACAGCAGCAACAAAGAAATAATTCAGTTTAGAAATAGGTGAGCGAC 1691
                              i ii --  v i v      ii  i  ? i    i  ii iv  i
  L1M4_orf2#LINE/    784 CTCAATAATA--AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_62397810_6   1692 TTAAATAGACATTTCTCCAGATAATATATACAGATGGCTAATAAATACAT 1741
                           i                i v  v       i     i     ii    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_62397810_6   1742 AAAAATATATCATTAAACGTTATGTAAATG 1771
                         i    v  ii--- v   i i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (92 / 74)
Gap_init rate = 0.01 (10 / 718), avg. gap size = 2.30 (23 / 10)  


 306 22.08 2.60 1.30  chrX_62409044_62410696.rev        1    77 (1576)    L1M4_orf2#LINE/L1      173   250 (658)  

  chrX_62409044_6      1 TAGCCAAAGCAATCTTGAGCAAAAGGAAAAAAGCTGAAGACGTCACACTT 50
                                 i         iv  i i   v    i  i  ivv        
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_62409044_6     51 CCTGACTTCAAATAC--ATGACAAGGCTA 77
                           ii i      -  -- iv    i    
  L1M4_orf2#LINE/    223 CCCAATTTCAAA-ACTTACTACAAAGCTA 250

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.50 (3 / 2)  

1910 25.75 2.40 2.25  chrX_62409044_62410696.rev      495  1162 (491)    L1M4_orf2#LINE/L1      240   908 (0)  

  chrX_62409044_6    495 CTAAAACAGCTATAATACTCAAACAAACATCATGGTATTGGTATAAAAAC 544
                            v  -     i i  v    i---   vii     i   i    ii i
  L1M4_orf2#LINE/    240 CTACAA-AGCTACAGTAATCAAG---ACAGTGTGGTACTGGCATAAGGAT 285

  chrX_62409044_6    545 AGACACATTGACCAGTGGACCAGAATAGATGACACAGAAATACATCTATG 594
                              i  v  i  i    vi     v  viiiv        v i i  i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_62409044_6    595 TATATATAGCTAACTAACTTTTGAAGAAGGTGCCAAGAACCA---AAACT 641
                         i  v   i ii  i i i   i  vi i          -   ---  -- 
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAA--T 382

  chrX_62409044_6    642 AAGGAAAGAACACCCTTTTCAATAAACTGTGCTGAAGAAACTGGATGTCC 691
                         ii        i vi        i   iv      iiiv        i?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_62409044_6    692 ATATGCAGAAGAATGAAACTAGACCCC-ATCTGTCATTATATTAAAAAAA 740
                          i     i         ii i      - i  vv  ii    -- v    
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT--ACAAAA 480

  chrX_62409044_6    741 AGCTATTCAAAATGGATTAAAGACTTCAACATAA-AGCTTATAATTGTAA 789
                          viv i           i ?    i v  ii   -    v -  i i   
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA-AACTATAA 529

  chrX_62409044_6    790 AACTACTAAAA-AGAACATAGAGA-AAACACACTAGAACATGAATCCACA 837
                             vi  i  - i       i?i-   iviv vv  v v  ii i- vi
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT-AGG 578

  chrX_62409044_6    838 CAAAGATTTTATAGCTTAGACTGCAAAAGCACCAGCAACAAAAAAAATAC 887
                            v i   iv   v vv   vv         v          i   ---
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA--- 625

  chrX_62409044_6    888 AAATAGA-AAATTGAACT-----AAACTGAAAAGCTTTTGTACAACTAAT 931
                                -      i   -----   v v    i       i vv v  v
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_62409044_6    932 AAAACAATCAAGAGAGTGAACAGACAACCCGATA-AGTGGAAGAAAATAT 980
                         i v  v       i      v         - i - i   i         
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCC-ACAGAATGGGAGAAAATAT 724

  chrX_62409044_6    981 TTGCAATCTATTTATCTGACAAGGGACTAATATCCAGAATACACAAGGAA 1030
                               vii  v       i        vi           i i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_62409044_6   1031 CTTAAACAACTCAACAGCAAGAAATCAAATAAACGCATTAGAAAGTGGCC 1080
                           ivv         i ii  i  iv       v vv   ?i   i   v 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_62409044_6   1081 AAAAAAAT-AAATAGACAATTCTCAAAAGAAGATATGCAAATATCTGTCA 1129
                            ii v -i        v     v           i     iv iivi 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_62409044_6   1130 GATAT-TGGAAAAATGCTCAACATCACTAATCAA 1162
                         iii i-  i   i             ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (107 / 61)
Gap_init rate = 0.03 (19 / 669), avg. gap size = 1.63 (31 / 19)  


2761 19.77 8.22 2.70  chrX_62447616_62449386.rev      502  1280 (491)    L1M4_orf2#LINE/L1       87   908 (0)  

  chrX_62447616_6    502 AATCCCTTTCAAAACCACAATAGTCTTTTCTTTGCAGAAACGTACAAGCT 551
                                v      i v  iiv i     --         ivv       
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTT--TTGCAGAAATTGACAAGCT 134

  chrX_62447616_6    552 AATCATAAAATTG----GAAAATT---GGGGCTCAGTATTGCCAAAACAA 594
                         i   v       v---- i    v---   i i   v  v          
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_62447616_6    595 TCTTGATGGAGCAGAGGAAATTTGGAGAAC-CACACTTCCCGTTTTCACA 643
                               vii  v   iv   v      i  -          iv     v 
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_62447616_6    644 AATTACTACAAAGCTATAGTAGTTAAGACAATGTGCTACTGTCATAAGGG 693
                          v              i    i i      i    v     v       i
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_62447616_6    694 TAGACCTATATAAGGTAATATAATAGAATTCAGAGTGCAGAAATTAACCC 743
                              --     iivi   iv         v     v       v     
  L1M4_orf2#LINE/    285 TAGAC--ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_62447616_6    744 ATGCATTAATATTCAATTGATCTTAAA-AAGGATTGCCAGGACAATTTAA 792
                           i    v  iv         i  vi -    i -    i   v   i  
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGT-GCCAAGACCATTCAA 381

  chrX_62447616_6    793 TGGGGAAGGAATAGCCTTTTCAACAAATGGTCCTGGAACAAATGGATATG 842
                                i      i                v    i    v      ?v
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_62447616_6    843 CACATACAAAATAATGGAGTTG-----------CAC-TCATAT------- 873
                              i     v    i     -----------   -i     -------
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_62447616_6    874 ------------GTATCAAAGACTTGAATGTGAGAGGTAAAAGTATAAAA 911
                         ------------ v    ?    i i     i    v     v       
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_62447616_6    912 TGTTTAGATAAAAA-----ATGAAAATTTTAATGACATTTGATTAGGCAC 956
                         ivi     vi    -----i? v    i  vi    v  v i       v
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_62447616_6    957 C--TTTTTAAAGTATGACAC--AAAGATCAAGCAAGAAATGACAATATAG 1002
                         i--   i v ii        --    vv       v   v  v  v    
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_62447616_6   1003 ATAAATTTGACTTCA--AAATTTA-----TTTTGTACATTGAAGGACACT 1045
                                v       --   v   -----      i v ii         
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_62447616_6   1046 ACCA------TGAAAAGACAATCTACAGAATTAGAGAAAGCCTTTTCAAG 1089
                          i  ------           i i       vi      iiv   v   -
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA- 730

  chrX_62447616_6   1090 CCATCAATATATCTGATTAGAGTCTAGTGTACATAACATATAATGAACAC 1139
                         --    -          v  i v  v  i v  v  i      v    v 
  L1M4_orf2#LINE/    731 --ATCA-TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_62447616_6   1140 TTAAAAC--AACAATAAAAAGAGAAAAACAAAAATAATTTGGTCAGTTAA 1187
                            v   --  i          ------    --   ii----  i  ? 
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGA------CAAA--TAACC----CAATTWA 815

  chrX_62447616_6   1188 AACATAACCAAATTATGTGAATAGATACTTCTCCAAAGAAGACGTATATA 1237
                           v  iiv    vv  v        i i              ii  i v 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_62447616_6   1238 TGACAAATGAACACACAAAAATATGTTCAACATCATTAATCAT 1280
                           i v   i i    ii    v   i         ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (79 / 71)
Gap_init rate = 0.03 (22 / 822), avg. gap size = 3.86 (85 / 22)  


2574 27.26 0.85 0.42  chrX_62449611_62455883.rev     4975  5682 (591)    L1M4_orf2#LINE/L1        1   711 (197)  

  chrX_62449611_6   4975 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATAT-G--AAAAT 5021
                              ii i  i     i        v      v i     - --  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62449611_6   5022 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5071
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62449611_6   5072 TACCAATGACTTTCTTCACACAACTGGAAAAATCTACTTTAAAGTTCATA 5121
                          v   iivi i  i  ii  v  v v  v  iiiv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_62449611_6   5122 TGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAGAA 5171
                              viiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_62449611_6   5172 CAAAGCTGGAGGCATCACGCTCCCTGACTTCAAAGTATACTACAAGGCTA 5221
                              i      vv    i  i  ii i      iiv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_62449611_6   5222 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGACCAA 5271
                               i   i    ii         i iv ii i   v v     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_62449611_6   5272 TGGAACAGAAC--AGAGTCCTCAGAAATAATACCACACATCTACAACCAT 5319
                              i    i--       --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_62449611_6   5320 CTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5369
                         i    i  i     i v  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_62449611_6   5370 ATTTAATAAATGGTGCTGGGAAAACTGGCGAGCCATATGTAGAAAGCTGA 5419
                         v  i  i              v      vv ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_62449611_6   5420 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5469
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_62449611_6   5470 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5519
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_62449611_6   5520 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 5568
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_62449611_6   5569 ACATCAAAAGCAATGGCAACAAAAGCCAAAGTAGACAAATGGTATCTAAT 5618
                            i        vvi          vv   i    i    v v ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_62449611_6   5619 CAAACTGAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGAACA 5668
                             v v  i i   i  iiivv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_62449611_6   5669 GGCAACCTACAAAA 5682
                          i     i   i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAA 711

Transitions / transversions = 1.57 (116 / 74)
Gap_init rate = 0.01 (6 / 711), avg. gap size = 1.50 (9 / 6)  

 430 20.21 0.00 0.00  chrX_62449611_62455883.rev     5689  5782 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_62449611_6   5689 AAAAGTGAGCTAAGGATTTGAACAGACACTTCTCAAAAGAAGACATTTAT 5738
                             i  i  v           i     i     v        i  vi v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_62449611_6   5739 GCAGGCAACAGACACATGAAAAAATGCTCATCATCACTGGCCAT 5782
                         iii v   i ii          i       v     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3164 26.76 0.77 0.77  chrX_62480427_62488917     5301  6208 (2283)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62480427_6   5301 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5350
                              ii    i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62480427_6   5351 GGCCATACTGCCCAAAGTAATTTGTAGATTCAATGTCATCCCCATCAAGC 5400
                            v     v      v i  i ii        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62480427_6   5401 TACCAATTACTTTCTTTACAGAA-TTGGAAAAAACTAATT-TAAATTTCA 5448
                          v   ii i i  i   i     -   -- v  i  i  i-    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_62480427_6   5449 TATGGATCCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGGAAAAAG 5498
                               vviiv  ii  v  v v  v     i      i i ii  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_62480427_6   5499 AACAAAGCTGGAGCCATCACGCTACTGGACTTCAAAGTATACTACAAGGC 5548
                                i     vvv    i  v ivi i      iiv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_62480427_6   5549 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5598
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_62480427_6   5599 ACTGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACC 5646
                          v     i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_62480427_6   5647 ATCTGATCTTTGACAAACCTGATAAA--CATAAGAAATGGGGAGAGGATT 5694
                          vi    i  i     ivv  vi  i--   --vv        i  i  v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAATA 394

  chrX_62480427_6   5695 ACCTATTTAATAAATTGTGCTGGGAAAACTGGCGAGCCATATGTAGAAAG 5744
                         ii  v  i  i    v         v      vv ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_62480427_6   5745 CTAAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5794
                         v i  ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_62480427_6   5795 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAA 5844
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_62480427_6   5845 ACTTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGAC 5893
                           v    ?i- v i -   iv   viv  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_62480427_6   5894 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACTAATGGTATC 5943
                           vi            vvi          vv        iv   v v ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_62480427_6   5944 TAATGAAACTAAAGAGCTTCTGCACAGGAAAAGAAACTACCATCAGAATG 5993
                          v  v   v v  i i   i  ii vvv   i  v    i  vv i i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_62480427_6   5994 AACAGGCAACCTATAAAATGGGAGAAAAGTGTTGCAATCTACCTATCTGA 6043
                           v  i     i i i            vvv      vii iv       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_62480427_6   6044 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAAAAGA 6093
                         i  i  i  vi          v  i  v      vv    v iv v  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_62480427_6   6094 AAAAAACAAACAACCACATCAAAAAGTGGGCAAAGGATATGAACAGACAC 6143
                             i     i    vv  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_62480427_6   6144 TTTTCAAAAGAAGAAATTTATGCAGCCAACACACACATGAAAAAATGCTC 6193
                           i  v        v  vi viii     i vi          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_62480427_6   6194 ATCATCACTGGTCAT 6208
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  

2475 26.57 2.06 4.12  chrX_62480427_62488917     7077  7998 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_62480427_6   7077 AAACACTTCATGCTCATGT-TCAGAAGACTTAATATTATTAAAATGGCCA 7125
                          i i iii    i     v- ii              i    i     v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_62480427_6   7126 TAGCACCTAAAGCAATTGACAGATTCAATGCTATCCCTATTAAACTACCA 7175
                           viv  i   vii  iv          i  v        i   v v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_62480427_6   7176 ACAACATTTTTTCACAGAATTAGAAAAAAAGACTTCTAAAATTCATATGG 7225
                         i vi v      -i     v v  v  ivv  - i               
  L1M4_orf2#LINE/    106 GCTGCCTTTTTT-GCAGAAATTGACAAGCTGA-TCCTAAAATTCATATGG 153

  chrX_62480427_6   7226 AACCAAAAAAAGCATCTGGA-TAACCAAAGCAA-CTCAAAGCAAAAAAAA 7273
                           -- viv  i v i ii  -  i     i   -  ii  ----------
  L1M4_orf2#LINE/    154 AA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA---------- 191

  chrX_62480427_6   7274 AAAAAAAAAAAAAAAAGCTGGAGCAG-CACTTTTTCTGACTTCAAACTAT 7322
                         ---   i  i  v    i     v v-   vi  i ii i      viv 
  L1M4_orf2#LINE/    192 ---AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_62480427_6   7323 ACTAGAAGGCTACAGTAATCAAAACAGCATTGTACTGGTACAAAAAACAA 7372
                             v  i              i    ii v       i i  i------
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG------ 282

  chrX_62480427_6   7373 AAACAAAGAAAGACACATACACCAAGGGAAGAGAAAACGGAACTGAGATG 7422
                         -------  v     i   v i   v    v    vvvi  iiiv   vi
  L1M4_orf2#LINE/    283 -------GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_62480427_6   7423 TAAAGGTGCACACCTACCACCACCTAATCTTCAACAAACTTAAGAAAAAC 7472
                             vviii   ii  ivii  vi i  i   i    ivv ivv  i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_62480427_6   7473 AAGCAATAGGAAAAAGACTACCTATTCAATAAATGGTGCTGTGAGAACTG 7522
                          vv    i  i   ii ivii  v     i           v  v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_62480427_6   7523 GCTATCCATATGCAGAAGAATGAAACTGGACCATTACCTACCACCATATA 7572
                          v  ?   i     i         ii      vi     vv         
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_62480427_6   7573 CAAAAATTAGCTTGAGAAGGATTAAGGACCTAAATGTAAGACCTCAACCT 7622
                                  i  ii i v    i ?i               v  v  v  
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_62480427_6   7623 ATGAAAATCCTGGAAGAAAACCTAGA---AAATGCCCTTCTTGATATTGG 7669
                           i   v  i i         v   i---    ---    v   iv    
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGG 572

  chrX_62480427_6   7670 CCTTGGCAACATATTTATGGCTAAGTCCTCAAAA---TAAATTGCAACAA 7716
                         vi v     iivv  iv i v  v v vi     ---i  ---       
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA---GCAACAA 619

  chrX_62480427_6   7717 AAATAAAAATTGATTAAATAAGACTTAATTAATCTAAAGAGCTTCTGCAT 7766
                           iv      v   -    vi     v  i  vv v  i i   i  iii
  L1M4_orf2#LINE/    620 AAGAAAAAATAGAT-AAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_62480427_6   7767 AGCAAAAGAAACTATCAAGGAAGTAAACAGACAACCTATAGAAGGGGAGA 7816
                         vv    i  v         i    i  v        i i    v      
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_62480427_6   7817 AAATA----CAAACTATGCAGCCAACAAAGGTCTAATATGCAGAATCTAT 7862
                              ----    ii  ii v ii i  i  v  vi   v      v   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_62480427_6   7863 AAGGAATTTAAACAAATCAATAAGCAAAAAACCA----CTCCATTTAAAA 7908
                           i   i ivv    v       vv    i  v ---- i v   ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_62480427_6   7909 TTGGGCAAGGGACATGAACGGACATTTCTGAAAAAAAAGACATACAAGTG 7958
                         v       i   iv    ii         vv   i  -  i      i  
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-GATATACAAATG 867

  chrX_62480427_6   7959 GCCAACAAACATATGAAAATATA-TCATCATTAATCATAAG 7998
                              i  i  i       v  i-   v   i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (140 / 102)
Gap_init rate = 0.02 (18 / 903), avg. gap size = 3.17 (57 / 18)  


3270 26.43 0.55 0.66  chrX_62494493_62500901     5009  5916 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_62494493_6   5009 GGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAATG 5058
                             ii i  i     i        v      v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_62494493_6   5059 GCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGCT 5108
                           v     v     iv i  i  i v      i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_62494493_6   5109 CCCAATGGCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 5156
                             iiv  i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_62494493_6   5157 AAGGCACCAAAAAAGAGCCCGCAATGCCCAAGAAAATCCTAAGCTAAAAG 5206
                          v  v viiv  ii  -   iv   iv    i v    i i ivv i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_62494493_6   5207 AAGAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5256
                           v    i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_62494493_6   5257 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5306
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_62494493_6   5307 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5354
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_62494493_6   5355 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5404
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_62494493_6   5405 CTGTTTAATAAACGGTACTGGGAAAACTGGCTCGCCATATGTAGAAAGCT 5454
                           v  i  i   i   i      v      v v?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_62494493_6   5455 GAAACTGGATCCCTTCATTACACCTTATACTAAAATTAATTCAAGATGGA 5504
                            ii    i    v v i     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_62494493_6   5505 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAAC 5554
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_62494493_6   5555 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5603
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_62494493_6   5604 AGACACCAGAAGCAGTGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5653
                         v       i     vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_62494493_6   5654 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5703
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_62494493_6   5704 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATGTACTCATCTGACA 5753
                         v  i     i                 v       vvi ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_62494493_6   5754 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5803
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_62494493_6   5804 AAAACAAATAAACCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5853
                           i        v  v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_62494493_6   5854 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5903
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_62494493_6   5904 CATCACTGGCCAT 5916
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 1.38 (11 / 8)  


3171 27.65 0.77 0.33  chrX_62521558_62527927     4974  5877 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62521558_6   4974 TGGAACAACATTCCCTGCTCATGGGTAGGAAGAATCAACATCGTGAAAAT 5023
                              vi i  i  v  i      i v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62521558_6   5024 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5073
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62521558_6   5074 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5121
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_62521558_6   5122 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5171
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_62521558_6   5172 AACAAAGCTGGACGCATCACGCTACCTGACTTCAAACTATACTATGAGGC 5221
                                i    v vv    i  v  ii i      viv     ii i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_62521558_6   5222 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5271
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_62521558_6   5272 AATGGAACAGAACAGAGACCTCAGAAATAACGCCGCATATCTACAACTAT 5321
                                i    iv    vii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_62521558_6   5322 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5371
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_62521558_6   5372 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5421
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_62521558_6   5422 AACTGGATCCCTTCATTACACCTTATACTAAAATTAATTCAAGATGGATT 5471
                          ii    i    v v i     v     v        i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_62521558_6   5472 AAAGATTTAAATGTTAGAACTAAAACCATAAAAACCCTAGAAGAAAACCT 5521
                          ?   ii       v   i       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_62521558_6   5522 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5570
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_62521558_6   5571 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5620
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_62521558_6   5621 TAAACTAAAGAGCTTCTGCACAGCAAAATAAACTACCATCAGAGTGAACA 5670
                         i   v v  i i   i  ii vv    iv v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_62521558_6   5671 GGAAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACTCATCTGACAAA 5720
                          iv    i                 v      ivii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_62521558_6   5721 GGGCTAGTATACAGAATCTACAATGAACTCCAACAAATTTACAAGAAAAA 5770
                           i  v    v      v  i  v      iv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_62521558_6   5771 AACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 5816
                         i    ----   v  i?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_62521558_6   5817 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 5866
                          v        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_62521558_6   5867 TCACTGGCCAT 5877
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3088 26.92 0.88 1.10  chrX_62534419_62539201     3381  4290 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62534419_6   3381 TGAAAAAATATTCCAGCTTTACAGATTGGAAGAATCAATATTGTTAAAAT 3430
                           i   i    i   vv  i ii          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62534419_6   3431 GTTCATACTACCCAAAGCAATCT-CACATTCAATGCAATCCCTATCAAAA 3479
                          viv     v      vii    -  v      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62534419_6   3480 TACGAATGACACTATTCACAGAAATAGAAAAAGCAATCCTAAAATTTAAA 3529
                          v v iivi vi v  ii       v  v  ivii           i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_62534419_6   3530 CAGAACCATGAAAAACCTAGAATACCCAAAGCTTTCCTAAGCAAAAAGAG 3579
                         ii   viiii iii   i      v     i vv  i i iv  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_62534419_6   3580 CAAAACTGGAGGAATCACATTACAGTACCTGACATCAAATTATACTCCAG 3629
                             ii       v     i ---- -  ii iv     viv    v  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACT----T-CCCAATTTCAAAACTTACTACAA 245

  chrX_62534419_6   3630 AGCCGTAATAACAAAAACAACATGGTACTGGCATACAAACAAACACATAG 3679
                            iii i   iv  i   iii             vii i i   i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_62534419_6   3680 ACCAATGGGATAGAATAGATAACCCAGTTACAAATCCACATACCTACAGT 3729
                          i      i       v  v ii    vv i   i   i i ii  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_62534419_6   3730 GAACACATTTTTGACAAAGGTACCAAGAACATACACTGGGGAAAAGACAG 3779
                         v  ivv     i     i   i      v   v  v        ii i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_62534419_6   3780 TCTCTTCAATAAATGGTGCTGGGAAAACTGGATATCCTTATGCAGAAGAA 3829
                            i     i              v         ?  vi     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_62534419_6   3830 TGAAACTAGACCCCTATATCTCACCAAATA-AAAAGTCAAATCAAAATGT 3878
                             ii i        iv  v     v   -    i i  v        v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_62534419_6   3879 GTTAAAGACTTAAATCTAAGACCTCAATCCATGAAACTGCTGCAAGAAAA 3928
                         i i ?    i     v     v  v  v i  i     vi iv       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_62534419_6   3929 CATTGGAGGAAATCACCAGGACATTGGTCTGGGCAAAAAAAATTTCTTGA 3978
                            v  ? v     vi iv   v    vi i     ---vii      ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA---TGGTTTCTTAG 592

  chrX_62534419_6   3979 GCACTAC-CCACAAGCGCAGGCAAACAAACAAAAAAATGGACAAATGAGA 4027
                         ii iv  -   v    i  i    -    vi       i  i    vi  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAA-CAAAAGAAAAAATAGATAAATTGGA 641

  chrX_62534419_6   4028 TCACAACGAGTTTAAAAGCTTCTGCATAACAAAGGATACAATAAACAAAA 4077
                         iiv  v i iv      i   i  iiivv       i  v  v  v   i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_62534419_6   4078 TTAAGAGATAACCTACAAAATAGGAGAAAATAACTGCAAACTAC-TATCT 4126
                          v  i   i    i   i   i          vi      ii i-     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_62534419_6   4127 GACAAAGGATTAATAACCAGA----GCAAGGAGCTCAAACAATTCTACAG 4172
                           i  i   i vi  v     ----ii  i  i   vv    i  v i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_62534419_6   4173 GAAAAAAATCTAATAATCTGATTAAAAAATGGGCAAAAGATTTAAACAGA 4222
                         v     i - v     i ii   ?             i     i  i   
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_62534419_6   4223 CATTTCTCAAAAGAAGACCTACAAATGGCAAACAGGGATATGAAAACGTG 4272
                                 v        iv          v  i i v i       vi  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_62534419_6   4273 CTCAACATCATTGATCAT 4290
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (156 / 85)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


 380 34.29 1.14 0.57  chrX_62544654_62550150      159   333 (5164)    L1M4_orf2#LINE/L1       37   212 (696)  

  chrX_62544654_6    159 AATATTGTGAAAATGGCCATACTGTCCAAAGCGATTTATACATGCAATGC 208
                                 v  i     v     vi     vi   i  i v  v   i  
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chrX_62544654_6    209 TATTCTCATTAAATTACCA-CTGACATCCTTCAAAGAATTAGAAAAATCT 257
                         v  i ii  i   v v   -   - v ii  iiv    v v  v  iiiv
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTG 135

  chrX_62544654_6    258 ATG-TAAAATTCATATGGAACCAAAAAATAGCTTGTATAAGCAGGACTAT 306
                           v-                viiv  iiv v iv v   iv  ii  v  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_62544654_6    307 CCTAAGCAAAAAGAGCAGCGTTAAAAG 333
                          i i iv  i    i  iv   ii i 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGG 212

Transitions / transversions = 1.31 (34 / 26)
Gap_init rate = 0.02 (3 / 176), avg. gap size = 1.00 (3 / 3)  

2667 25.96 1.98 2.31  chrX_62544654_62550150     1686  2594 (2903)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_62544654_6   1686 GAAAAATCATTCCATGCTCATGGATAGGAACAATCAACATTGTGAAAATG 1735
                             i  -  i     i        v    v v i  i     v  i   
  L1M4_orf2#LINE/      3 GAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_62544654_6   1736 GCCATACTGCC-AAAGTAATTTATAGATGCAATGTTATTCCCATTAAACT 1784
                           v     v  -   v i  i  i    v   i iv  i  i  i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_62544654_6   1785 ATCA-TTGTCATTCTTCCCAGAATTAGAAGAAATTACTTTAAAATTCATA 1833
                         vi  -i  i -  i  iv     v v  vi iv v iii           
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_62544654_6   1834 TGGAACCAAAAAAGAGCCCATGTAGC-AAGACAATCATTAGCAAAAAGAA 1882
                              viiv  ii  v  vivi    -  i      v v iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_62544654_6   1883 CAAAGCTGGAGGCATCTTGCTACCTGACTT-AAAACTATACTACAAGGCT 1931
                              i      vv  vii  v  ii i  -      -        i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_62544654_6   1932 ACACAGTAACCAAAACAGTGTGGTACTAGTACAA---TAGACCAATGTAC 1978
                            --    i   i             i i i  ---     ------ i
  L1M4_orf2#LINE/    250 ACA--GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC------AT 291

  chrX_62544654_6   1979 ATAGACCAATGGAACAGAATGGAGAACTCAGAAATAAGACTGCGCATCTA 2028
                              i        i     v    iii         iv iiii   i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_62544654_6   2029 CAACCACCTGATCTTGGCCAATC-TGACAAAAACAAGCAATTGGGAAAGA 2077
                         iiii  vi    i  v v   vv-  v   i v  vv    v        
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_62544654_6   2078 ATTCCCTATTTAAAAAATGGTGCTGGGAGAACTGGCTAGCCATAGGCAGA 2127
                           vvi  v  i  v              v      v  ?   i v   i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_62544654_6   2128 ATAGAGAAACTGGATCCCTTCCTTACAC-ATCATACAAAAATTAACTCAA 2176
                          v iv   ii    i    v   i    -  -                  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCAT-ATACAAAAATTAACTCAA 490

  chrX_62544654_6   2177 GATGGGTTAAAGACTTAAATGTAAAA-CTCCAACGTATAAAAACTCC-AG 2224
                         i    i i ?    i         i -  vv   -       -   i-  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAAC-TATAAAA-CTCTTAG 538

  chrX_62544654_6   2225 AAGAAAATCCAGGCA-ATACCATTCA-GAACACAGGCAAGGGCAAAGATT 2272
                                ivi   ?i- v i -   i-  v vii  iv   -   v i  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGG-CAATGGTT 586

  chrX_62544654_6   2273 TCAT-GATGAAAATGCCAAAAGCAATTGCCACAAAAGCCAAAATTGACAA 2321
                           v -   - vi ii         vvv  v       vv     v  i  
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_62544654_6   2322 ATGGGATCCAATTAGACTAAAGAGCTGCTGCACAGCAAAAGAAAGTATCA 2371
                           v   iiiv  i i v v  i i  vi  ii vv    i  v v     
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_62544654_6   2372 TCAGGGTGAAAAGGCAACCTACAGAGTGGAAGTAAATTTTTGCAATCTAT 2421
                         vv ii        i     i     i   i  v    v       vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_62544654_6   2422 CCATCCGACAAAAGTCTAATATCCAGAATCTACAAGGAGCTTAAACAAAT 2471
                         vi   i  i  ii v  vi          v  i  i  i  ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_62544654_6   2472 TTACAAGAAAAAAACAAA---CCCCATTAAAAACTGGGCAAAGGATATGA 2518
                         iv i  v     i     ---   v   ?    v            v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_62544654_6   2519 ACAGACACTTCTCAAAACAAGACATTCATGTGACCAACAAATACATATTT 2568
                          i     i     v   v    i  v  vi  i    i  ii    i---
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG--- 882

  chrX_62544654_6   2569 AAAAAAAT-CTCAACATCAGAGATCAT 2594
                         -    i  -          ????????
  L1M4_orf2#LINE/    883 -AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (134 / 98)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 1.50 (39 / 26)  

2222 25.82 4.14 5.23  chrX_62544654_62550150     4087  5004 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62544654_6   4087 TGGAAAAACATTTCATGCTCATGGAAAGGAATAATCAATATTGTCAAAAT 4136
                               i i  ii    i       vv    v v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62544654_6   4137 GGCCATAGTGTCCTAACCAATTTACAGAGTCAATGTTATCACTGTCAAAG 4186
                            v   v vi  v  iii  i      v    i iv   v  i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62544654_6   4187 TACCAATGACATTGTTCACAGAA-TTAAATCAAAGT-ATTTTAAAATACA 4234
                          v   iivi v  v  ii     -  i --   iv -  ii      v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCA 148

  chrX_62544654_6   4235 TATGGAACAACAACAACAACAAAGAGCTTGAATAGCCAAGGCAATCCCAA 4284
                                vvi   --------ii  v iv          ii     iii 
  L1M4_orf2#LINE/    149 TATGGAAATGCAA--------GGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_62544654_6   4285 GCAAAAAGAACAAGGCTGGCGGCATCACATTACCTGACTTCAAACTATAC 4334
                         iv  i        i i   v  vv     i v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_62544654_6   4335 TACAAGGCTACAGTAATGAAAACAGCATGGCACTGGTACAAAAAAAGACA 4384
                              i           v  i    ii   i     i i  ii v     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_62544654_6   4385 CATAGATCAATGGAACAGAACAGAGAGCCCAAAAATATTGCCACGCACCT 4434
                         i              i    iv     i   i     vvv   ii  ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_62544654_6   4435 ACAATTATCTGATCTTTAAGGAAAATACACAAG--CATAAGAAATGTGGA 4482
                          iii i vi    i  ii vi iii i -    --   --vv    v   
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGC-CAAGACCAT--TCAATGGGGA 387

  chrX_62544654_6   4483 AAGGACTCTCTATTCAATAAATGTTGCTGGGAAAACTGTGTAGCCATATG 4532
                            i ivv   v     i     v        v     vi  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_62544654_6   4533 CAGAAGATTGAAACTGGACCCCT----------------------TAACT 4560
                           i    v    ii         ----------------------     
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_62544654_6   4561 CAAGTTGAATTAAAAACCTAAATGTATAACCGAATACTAGAAAAACTCTG 4610
                            iv  i  i ? i           vi v v  v    v    -    v
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTT 536

  chrX_62544654_6   4611 A-AAGATAACTTAGGAAGTACCATTCTGGACATTCTTGACATAGGACCTA 4659
                          -    v   v    ?-   -- v   ------  v    v v  iiivi
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGN-GTA--AATCT------TCGTGACCTTGGGTTAG 577

  chrX_62544654_6   4660 GCAAAGCCTTCATGACAAAGGCGCCAAAAGCAACTACAACAATAACAAAA 4709
                             v vi   v iivv v i i         vvvi      -  v    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA-AAGAAAA 626

  chrX_62544654_6   4710 AA-----AAATTGTAAGATATCTAATTAAG-TTAAAGAGTTTCTGCACAG 4753
                           -----      ---  iv  --  i  i-     i v   -  ii vv
  L1M4_orf2#LINE/    627 AATAGATAAATTG---GACTTC--ATCAAAATTAAAAACTTT-TGTGCTT 670

  chrX_62544654_6   4754 CAAAATAAACTATTAACACAGTAAA----CAACCTACAGAATAGGAGAAA 4799
                             iv v     i  v v   i  ----     i       i       
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_62544654_6   4800 ATATTTGCAAAGTATACTATCCAGCATCTATATCTAGCATCTATAACAAC 4849
                                    vi   -    ii------   v--i v ii i  v ---
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATA-TATCTG------ATAA--GGGACTTGTATC--- 758

  chrX_62544654_6   4850 ATACAGCATCTATAAGAAACTTAAACAAATTTACAAAAAAAAAACCAAAC 4899
                         ---   v  v     ii    ivv    v iv i  v     i  -   i
  L1M4_orf2#LINE/    759 ---CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC-AAAT 804

  chrX_62544654_6   4900 AACTTTATTAAGAAAGTGGGCAAAGTACATGAACAGACACTTTACAAAAG 4949
                            iiv   ? i   -         v iv    i     i  iv v    
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_62544654_6   4950 AAGACATTCATGTGGCTAACAAGC-TATGGAAAAAATGCTCAATATCACT 4998
                             i  v  vi    i  i    -i   -    i        i    ??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTCAACATCAZZ 902

  chrX_62544654_6   4999 AATCAT 5004
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.07 (86 / 28)  


2564 22.08 4.61 7.29  chrX_62571390_62574477     1663  2595 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62571390_6   1663 TGAAAAGACATTTTATACTCATTTATTGGAAGAATTAATATTTTCAAGAT 1712
                           i     i  iii  ii    vv         v        v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62571390_6   1713 GGTGATTCACCCCAAAAGGATATACAGACTTGACACAATCCCTAACAAAA 1762
                           ii  v v       vv   v      i ii  i         v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62571390_6   1763 TTTCACATTGC-TTCTTTGCAGATATTGGCAAGCTGATGCTAAAATTTAT 1811
                          ii  -ii   -  i        v    i         v        i  
  L1M4_orf2#LINE/    101 TCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_62571390_6   1812 GTGGAATTTTAAGGGTCCCAAAATAGCAAAAATAAGCTTGATAAAGAA-- 1859
                         i     v vi     v    i      v    i  v     v      --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_62571390_6   1860 -CAAAGTTTGAGTACCCACCTGATATACTGATTTCAAAACTAATT-CAAA 1907
                         -       v   v  i   --- iv v ii           v i -    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCAC---ACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_62571390_6   1908 GTTACAGTAACAAAGACAA---GAT----GCA-----------ATTTAAA 1939
                          i        iv      i--- i ----   -----------  v  i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_62571390_6   1940 TCAGAGGAATAGAATTGAGTGTCCAAATATAAGCCTTCACATTT-CAGTC 1988
                            iv              v     i v    i  ivi      -ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_62571390_6   1989 AATTTATATCTAA-----ATGCTCTGAAAACAATTTAGTGGGGGGAAAAG 2033
                             v  v iii -----i   i---  i  v   i i     ii i  v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCC---AAGACCATTCAATGGGGAAAGAAT 393

  chrX_62571390_6   2034 AGTTTTT--AAAAAATGGTGCTAGAGAAACTAGGTATCTATATGCAAAGG 2081
                            i   --  v          i iiv    i i  ? i i       i 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_62571390_6   2082 AATGAAGTTGAGCTCTTACCTCGTACCATATATATGCTTTTAGTAAAAAT 2131
                                   ii i i      ii        i vivv  v v v     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_62571390_6   2132 GGAACATGGACATGTATATAAGGGTTAAAACTATTAAACTCTTTTAAATT 2181
                            v  ?i   v iv  i    i i         v        vv  ivv
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_62571390_6   2182 ATCA-AGGTTGTACAT-TTGGGGTCTTTTGATTAAGGAATGGGTTTATAG 2229
                          v  -   ?-   v  -  v v v i  v i   i v     v  iv   
  L1M4_orf2#LINE/    544 AACATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_62571390_6   2230 ACAACGTGCTAAAAGC-----CAATAAAAGAGAAATTCTAAAGACAGATA 2274
                          i vviii i      -----   i      i   -------- i     
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAA--------ATAGATA 634

  chrX_62571390_6   2275 CATTTGATTTCATAAAAATTAATAACTTGTGTCCATCAAAGGGAATTAGC 2324
                         v   v  i     v        v     v   v v       iv i  v 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_62571390_6   2325 ACAAAAGTAAAATGGCACACCACAGAATGAAAGAAAACATTTGCAAATTA 2374
                          vi     i   v i  vv          ii      i          i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_62571390_6   2375 TATATGTATATATGTGTGTGTATATGTATATTTGTTTGTGTTTGTATATA 2424
                              ------------------------------------i  ----- 
  L1M4_orf2#LINE/    735 TATAT------------------------------------CTG-----A 743

  chrX_62571390_6   2425 TAATGTTATATATGGACTTGTGTCAGGAATATATAAA-AATGGTTAGAAC 2473
                            - --------        i  vi           -  ivv   v   
  L1M4_orf2#LINE/    744 TAA-G--------GGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_62571390_6   2474 TCAATAATTAAAATATAAACTACCAAATACTTAAA--TGTGCAGAA-ATC 2520
                                 v    v i   iv   v   -- ?   --  v   i i-  i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAAT--TWAAAAATGGGCAAAGGATT 832

  chrX_62571390_6   2521 CAAATAGACATATCTCCAAAGAAGATATAAAAATGTTCAA-AAACAAAAG 2569
                         ii         v                 v     vi   -  i  v v 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_62571390_6   2570 AAAAAAATCTCAAAATCATTACATAA 2595
                             i vv     v    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (112 / 90)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 4.27 (111 / 26)  


2333 27.43 9.46 0.72  chrX_62594010_62595936.rev      602  1436 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62594010_6    602 TAGGAAAACATTCCATGCTCATGGATAGAAAGAATTAATATTGTTAAAAT 651
                          i i  i i  i     i        v i    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62594010_6    652 GGCCATAATGCCCGAAGTAATTTATAGATTCAATGCTATTTCTGTCCAAC 701
                            v   v v   i  v i  i  i        i  v  ii  i  v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62594010_6    702 TACCAATGACATTTTTCACAGAACTAGATAAAAACT-ATTTTACAATTCA 750
                          v   iivi v     ii     v v  i  i--  -  ii  v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_62594010_6    751 TATGGAAA---AAGAAAAC-----TAGCCATG-CAATCCTAAGCAAAAAG 791
                                 ---   ii v -----      vi-     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_62594010_6    792 AACAAAGAAGAAGGCATCTTGCTACTTGACTTCAAACTATACTATGGGGC 841
                                vv i   vv  vii  v iii i      viv     iiii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_62594010_6    842 TACAGAAACCAAAACAGTATAGTATTTGTACAAAAACAGACACATAGACC 891
                              v  i   i     i i   i v i i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_62594010_6    892 AATGAAACAGAATAGAGAGCCTAGAAGTAAGGCTATATACCTACAACCAT 941
                             i  i     v     i i    i   iv i   i ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_62594010_6    942 CTAATCTCCAACAAACCTGACAAAAACAAGTAATGGGGAAAGAACTCCCT 991
                         i i  i i i    ivv  v   i v  vvi             ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_62594010_6    992 ATTTAATAAATAGTGCTGGGATAACTGGCTAGTCATATGCAGAAGATCGA 1041
                         v  i  i    i         i      v  ?i  i     i    vi  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_62594010_6   1042 AACTGAATCCCTTCCTTATACCATATACAAAAGT-----CAAGATGGATT 1086
                          ii  i i    v   i i             i -----   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_62594010_6   1087 AAAGAC--AAATGTAAAACCCAAAACTATAAAAACCCTGGAAGTCAACCT 1134
                          ?    --        i v i            vi i i    vv   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_62594010_6   1135 AGGCA-ATATCACTCTGAACATAGGAATGGGCAAAAATTT------TATG 1177
                            ?i- v   -i  vvi  v v  iv i     vii   ------    
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_62594010_6   1178 ACA----AAG---ATGC--CAAAAGAA--------------------CAG 1198
                            ----   --- v  --        --------------------  v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_62594010_6   1199 CAAAA-----------------------GAAATTAACAAGAGATTAAACA 1225
                              -----------------------  v i  v     i v i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_62594010_6   1226 GACAGCCTATAGAATGGGAGAAAATATTTGTAAAGTATGCATCTGACAAA 1275
                             i  i i                    i   vi  ii      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_62594010_6   1276 AGTATAATATTCAGCATCTATAAGGAACTTAAACAAATCTACAA-GAAAA 1324
                         i vv vi   i   v  v     i     ivv    v  v i  -i    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_62594010_6   1325 GTCAAACAACCCCATTAAAAACTGGGCAAATAACACGAATGGACACTTTT 1374
                          v    i     v   ?    v        vi ivi    i    i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_62594010_6   1375 CAAAAGTAGACTTACATGAGACCAACAA--AGGTGAAAACAAAAAGCTCA 1422
                          v    v   iv    viv i    i  -- vi      ---i v     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA---GATGCTCA 894

  chrX_62594010_6   1423 GCATCAGTGATTAT 1436
                         i     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (142 / 83)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.72 (85 / 18)  


3306 26.98 0.44 0.44  chrX_62600346_62602898.rev     1155  2062 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62600346_6   1155 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATCGTGAAAAT 1204
                              ii i  i     i      i v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62600346_6   1205 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCTCCATCAAGC 1254
                            v     v     iv i  i           i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62600346_6   1255 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1302
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_62600346_6   1303 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1352
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_62600346_6   1353 AGCAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1402
                          i     i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_62600346_6   1403 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1452
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_62600346_6   1453 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1500
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_62600346_6   1501 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 1550
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_62600346_6   1551 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1600
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_62600346_6   1601 GAAACTGGATCCCTTCTTTACACCTTATACAAAAATCAATTCAGGATGGA 1650
                            ii    i    v i i     v           i  i   ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_62600346_6   1651 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1700
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_62600346_6   1701 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1750
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_62600346_6   1751 AACACCAAAAGCAATGACAACAAAAGCCAAAATGGACAAATGGGATCTAA 1800
                         i            vvii         vv     i  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_62600346_6   1801 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 1850
                          i   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_62600346_6   1851 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 1900
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_62600346_6   1901 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1950
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_62600346_6   1951 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 2000
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_62600346_6   2001 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 2050
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_62600346_6   2051 ATCACTGGCCAT 2062
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 627 29.58 13.78 3.03  chrX_62653718_62655312      500  1094 (501)    L1M4_orf2#LINE/L1      230   888 (20)  

  chrX_62653718_6    500 TTAAATCTTTCTCAAAATCTACTGTAATTGAAACAGCATAGTCTTGATAC 549
                          i   v   v  vv   v    v     ii i    ii i  vi  ii i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_62653718_6    550 AAGAAATGACAAACAGAAGAGTGGAACAGAATAGAAAGTTTAAAAACACA 599
                            i vv    v i   vv i     i     v  i   ii i   i v 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_62653718_6    600 TCTAAGTATATATGCAGAGTTACT--ATATATGAAAAATGGCATTTAAAC 647
                         i i vii  v    ----  i v --  v vi  v  i-  iiiiv i  
  L1M4_orf2#LINE/    330 CCCATACATTTATG----GTCAATTGATTTTCGACAAG-GGTGCCAAGAC 374

  chrX_62653718_6    648 TGT---GTGGAAAATAAATGATTTATTTAATAAATGATGCAGATGCAACT 694
                         ii ---i   ii  vi   ii i v  i  i     i   v ivi     
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_62653718_6    695 GACTATCCACCTTGAAGAAAAAAATGAGGT----CCCCTTTCTCACATCA 740
                          iv  ?    v ---iv    i     i  ----     vi      i  
  L1M4_orf2#LINE/    425 GGATAKCCACAT---GCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_62653718_6    741 TATAAAAATGTAAATTCCGGATGGATTACTGTTCTAAAAATAAA--CCAA 788
                             v   vi v  i  vii      i ?v vi     vi   i-- i  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_62653718_6    789 AAATATA---TTTTTA---------ATCAGG---AAATTTT-AT-AGTTT 821
                           v    ---i i   ---------  -   ---    i  -i - vi  
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACAT-AGGNGTAAATCTTCGTGACCTT 570

  chrX_62653718_6    822 GGAT--GGCAAGAGATCTTAAGCAAGATGAAACTAGGGGC-CAA-----A 863
                           i --     vi v ii v  -- v    v  i iii  -   ----- 
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAG--ATATGACACCAAAAGCACAAGCAACA 618

  chrX_62653718_6    864 AAAGGAATAATAGATACATT---TTTCA----AAGTAAAAATTTAAATAT 906
                             i  v        v   ---i    ----  v      i  vvi ii
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_62653718_6    907 TTATAGAAGTAGGCAATATAAACAAACTCAAAAGACAAAAAACAGACTGG 956
                           -i -   -- i  v   v  v   v v         vvv     v   
  L1M4_orf2#LINE/    669 TT-CA-AAG--GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_62653718_6    957 T-GAAAACGT--GAAATTCGTG-A-CTGACAAAG----TGTCACATCAAC 997
                         v-     ii -- v  v  i i- -    i  i ----   ---   v v
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT---ATCCAG 761

  chrX_62653718_6    998 AATATA----GAGTCCTTCCAAATTTATGTTAAAAG-------------- 1029
                               ----  iii   v   v iv  iv     i--------------
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_62653718_6   1030 ------AATGAGTAAAGGGTATGA---GGCAATTCACAAAAGAA---ATG 1067
                         ------    i i     i v   --- i  v   v v      ---  i
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_62653718_6   1068 AAAATAGCCATTAAGCATATGAAAAAA 1094
                         v    i    v      i       i 
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.42 (102 / 72)
Gap_init rate = 0.05 (32 / 659), avg. gap size = 3.12 (100 / 32)  


2858 21.81 4.54 6.48  chrX_62683700_62687680     2563  3488 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62683700_6   2563 TAGAAAGATTTCCCATGTGCAAGGATTGGAAGAACCAATATTGTTAAAAT 2612
                          i       v        v  v           vii           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62683700_6   2613 GTCCCTACTACTCAAAGTGATATAGAGATTCAACACAACCCCTATCTAAA 2662
                          v vv    v i    v    v  v         i   i       v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62683700_6   2663 TTCCAATGGCATTTTTCATGGAAATAGACAAAAACATATATAAAATTTCT 2712
                          i   iiv  v     iiii     v     ivvv  vi-       iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC-TAAAATTCAT 149

  chrX_62683700_6   2713 ATGGAAC--CAAACTAGACCCTTGATAGCCAAAGCAACTCTGAGAAATAA 2760
                               v--   i--i     vvi         i   iii   i   v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_62683700_6   2761 AAATAAATCTGGAGGCATCACACTCTTTGATTTCAAACAATATTAGAAAA 2810
                         i  i   vi      vv       iiiii        vvv  i  v   i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_62683700_6   2811 CTATGGAAATCAAAACAGTATGGTACTAGCATAAAAACAGATATAC---- 2856
                            ii v      i     i       i      ii i   i   i----
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_62683700_6   2857 CAATGTAATAGAATAGAGAGTCCAGAAATAAACCGAAGCAAATATAGTGA 2906
                              v        v                   v vi  vv   i  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_62683700_6   2907 ACTAATTTTTGACAAGAGCACCAACAGGACACAATGGGGAACGTATAGTC 2956
                          i i     i      i ii    v vv iv          v v      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_62683700_6   2957 TCTTCAATAAATGTTGTTGGAAAAACTGGATATCTATATGCAAAAGAACA 3006
                          i     i     v  i   i v         ? i i           ii
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_62683700_6   3007 AAATTGGGCCCATATTTTAGACCATACACAAAAATCAACTCAAAATGCAT 3056
                           i    i   v  ii i v      i        i           v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_62683700_6   3057 AAGAGACTGAAACATAAGAGCTGAAATAATAAAACTACTAAAAG----CA 3102
                         v ?    iv   ii        i   iv        vi  i   ----  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_62683700_6   3103 -----------CT-----ACT---------GCTGTGCTTTTTTA--TATG 3125
                         -----------  -----  i---------  vi  v   i   --    
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_62683700_6   3126 ACACCAAAAGCACAGGCAACAAAAGCAAAAAGAAACAAGTGGGACTGCAT 3175
                                       i          v     v i i  i v     v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_62683700_6   3176 CAAA-TTAAAAAGCTGCTATGCAGAAAAAAAAA--GTCAACAACATGCAA 3222
                             -       -  vi i   vvv   ii v --i    v  vi  v  
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_62683700_6   3223 AGGTAGCCTATAGACTGAGTGAAAATATTTGCAAACTGTAAAGTGGTTAA 3272
                           ii i  i i   v  i v               ---------------
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAA--------------- 731

  chrX_62683700_6   3273 TATTCAAAATATACATAAAGTGGTTAATATATATAAAATATATAAAGTGG 3322
                         ---   ---------------------     v i ------   i - i
  L1M4_orf2#LINE/    732 ---TCA---------------------TATATCTGA------TAAGG-GA 750

  chrX_62683700_6   3323 TTAATATTCAAAATATATAAGGAACTCACATCACTTCACAGCAAAAAAAA 3372
                         i vi   i  i         i      vi iv   ---  ii  v     
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAAAAA 797

  chrX_62683700_6   3373 ACAAATAAACAAATAAACTAATTAAGAAATGAGCAAAGAATTTGAATAGA 3422
                         i-------        v i    ? i     i      i           
  L1M4_orf2#LINE/    798 G-------ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_62683700_6   3423 CATTCCTCCAAAAAAGACATAAAAATAGCCAACAGGTATACGAT--GATG 3470
                             i       i    i   v    i     i i i i i  v--    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_62683700_6   3471 CTCAACATCATTAATCAT 3488
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (121 / 78)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 5.37 (102 / 19)  


 431 16.67 4.76 0.00  chrX_62691809_62695871     2588  2671 (1392)    L1M4_orf2#LINE/L1        2    89 (819)  

  chrX_62691809_6   2588 GGAAAGATATCCCATATTGATGGATGGGAAGAATTAATATTGTTAAAATG 2637
                                        i  v      v      v             i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_62691809_6   2638 ----TACTGCCTAAAGCAACCTATAGATTAAATGCAAT 2671
                         ----    v  i   vii i   i     v  i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

Transitions / transversions = 1.33 (8 / 6)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 4.00 (4 / 1)  

3182 25.37 0.92 0.57  chrX_62691809_62695871     2700  3570 (493)    L1M4_orf2#LINE/L1       35   908 (0)  

  chrX_62691809_6   2700 TTAATATTGCTAAAAT----ATACTACCAAAAGCAATCTACAGATTAAAT 2745
                                  i   i  ----     v  v   vii           v  i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chrX_62691809_6   2746 GCAATCTCTATCAAAATACCAATGACATTCACCACAGAAATGGGAAAAA- 2794
                               i          v   iivi v  iviii       v iv  iv-
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chrX_62691809_6   2795 AATCCTAAGGTTCATATGGACCCACAAAAGACCCAGAATAGCCAAAGCAA 2844
                         i       ii          vvii   ii                 i   
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_62691809_6   2845 TCCCGAGCAAAAAGAACAAAGCTGGAGGCATCACACTACCTAACTTCAAA 2894
                           ii  iv  i          i      vv       v  i  i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_62691809_6   2895 ATACACTGTAAAGCTATAGTAACCAAAAAAGCATGGTACTGAAGTAAAAA 2944
                          ivi   ii       i     i   i v  ii        ivi   ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_62691809_6   2945 CAGACACATAGACCAATTGAACAGAATAGAGAATCCCAAAATATACCCAT 2994
                         i     i     i    v   i     v    i   vi     v      
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_62691809_6   2995 GCATTTACAGCCAATTCATTTTCAGTAAAGACACCAAGAACACATATTGG 3044
                         i      ii i     v      iii  i iii      v  ivi v   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_62691809_6   3045 AGAAAGGACAGCCTCTTCAACTTATGTT-CTTGGACAAACTGGATGTCCA 3093
                         i     i i  i  i      vv   v -  v      -      i?   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCA 433

  chrX_62691809_6   3094 TATGCAAAAGAATAAAACTAGACCCCTATCTCTCACCATATGAAAAAATA 3143
                         i            i  ii i        i   v        iv      v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_62691809_6   3144 AAATCAAAATAGATGAACGACTTAAACGTAAGACTTGAAACTATAAAACT 3193
                           v       i   v ?v   i    i      vi i             
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_62691809_6   3194 ACTAGAATAAAACACTGGAA-AAATGCCTCAGGTCATTGATATGCACAAA 3242
                         vi     v      iv  ?i-    - i  iv v v   ivv ivi   v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_62691809_6   3243 GACTCTATTGAGTAATACCTCTAAAGCACAGATAACAAAAGCAGAAATAC 3292
                          ii - v  iii  vv  vi v        iii        v i     v
  L1M4_orf2#LINE/    583 GGTT-TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_62691809_6   3293 CCAAATGGGATTATATCAAGCTAAAAAGCTTCTGCACAGCAAGGGAAACA 3342
                         vi    v   i vi     iv v    i   i  ii vv   i   v  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_62691809_6   3343 ATCAACAGAGTGAAGCAACAACATACAGAATGAGAGAAAATATCTGCAAA 3392
                              v i      ivi     vi        i          i      
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_62691809_6   3393 CTATCCATCTGACAAAACATTAATAGCCAAAATATGTAAGTGACTCAAAC 3442
                         ii  vi      i  iiv i vi  v   i     i   ivi    vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_62691809_6   3443 AACTCAATAGCAAAAAAACACAAATAATCTGATTTAAAAGTGGGCAAATG 3492
                                  ii     i   --     i ii   ?    i        v 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACA--AATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_62691809_6   3493 CTCTGAACAGACATTTCTTAAAAGAAGACATACAAATGGCCAATAGGCAT 3542
                         v i    i          iv        i                i   i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_62691809_6   3543 ATGAAAA-ATGCCCAACATCATTAATCAT 3570
                                -    i        ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.01 (9 / 874), avg. gap size = 1.44 (13 / 9)  


4406 16.80 4.60 0.12  chrX_62712469_62715433     1604  2472 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62712469_6   1604 TAGAAAAACCTCTCCTATTCATGGATTGGAAGATTTAATGGTGCTAATAT 1653
                          i    i iv  i v i                i     iv  i   v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62712469_6   1654 AGCAATACTCCTCAGATTAATT--CAGATTCAACGCAATACCTATCAAAA 1701
                         i          i  i   i  i--               v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62712469_6   1702 TCTCACCTGG--TGTCTGCAGAAAATTGAAAAACTGGTACTAAAACTCGT 1749
                           i  v   v-- v i        -    v  i   i v      i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCAT 149

  chrX_62712469_6   1750 ATGGAATTTCAAGGGACCTAGGATAACCAAAACAATTTTGAAAAAGGAGA 1799
                               v v         i  i   i          i         i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_62712469_6   1800 ATAAAGTTGGAGGACTCACACTTTCTGATTTCAAAACTTACTACAAACCT 1849
                          i                     i ii                    v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_62712469_6   1850 ACAGTAATCAAGAGAATGGGGGACTGGCACAAGAATAGATATAAAGATCA 1899
                                      v i  v  v       i   i     i   v      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_62712469_6   1900 ATGAAATAAAACCAGGAGTCCAGAAATATATCC-TACATTCATGCTGAAT 1948
                            i    i  iiii             v i  -      i   v v   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_62712469_6   1949 TGATATTTGTCAAAGGTGCCAGGATTATTCAAGGGGGAAAATATAGTTTT 1998
                             v  i v   i       i  ii      v       iv     i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_62712469_6   1999 TTCAACAAATGGTGCTGGTACAACTGGATATCCACATGCAGGAGAATGAA 2048
                                           v           ?         ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_62712469_6   2049 CTTTGGCTCCTACTTTACACTATACACAAAAATTAAATCAAAATGGATGA 2098
                         v  v i i     i i    i   i           v           v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_62712469_6   2099 AATATCTGAATGGAA----TCAGATTATAAAAGTCATTAAAGAAAACATA 2144
                         ? v i  i    v  ---- v i i       v  v vi           
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_62712469_6   2145 GAGGAAAATCT--GTAAC-----ATTAGACAATAGTTTCTTAGATATGAC 2187
                          i? v      --  i  -----i    i    i                
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_62712469_6   2188 ACCTAGAACACAAGCAACCAAGCAAAAA-----TAAAGTGGACTTCAACA 2232
                            v i i          v  iv     -----    v         v  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_62712469_6   2233 AAATTAAAAACTTT-GTGCTACAAATGATACCATCAATAAAGTGAAAAGG 2281
                                       -     v    v  i  i     v           i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_62712469_6   2282 CAACCCA-GTAATGGGA-AAAATATCTGCATATCATATATCTGATAAAGA 2329
                                -iv       -       i    v                i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_62712469_6   2330 TGTAGTATTCAGAATATATG-----------TAACTTAACAATAAAGTAA 2368
                         vv v    i          i-----------i    i  i      ivi 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_62712469_6   2369 CAA----CTCGCTT-AAAAATGGGCAAAATATCTGAATAGACATTTCTCC 2413
                            ---- i iv  -             iv  i                 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_62712469_6   2414 AAAGAAGACATATAAATGGCCAATAAATACATGAAAAGATGCTCAATATC 2463
                                 i   i             ii                  i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_62712469_6   2464 ATTAGCCAT 2472
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.75 (91 / 52)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.93 (41 / 14)  


3069 27.78 0.44 0.33  chrX_62799888_62806562     5276  6182 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62799888_6   5276 TGGAAAAACATTCCATGCTCATGGATAGAAAGAATCAATATCGTGAAAAT 5325
                               i i  i     i        v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62799888_6   5326 GGCCATACTGTCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5375
                            v     vi     v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62799888_6   5376 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAAGTTC 5423
                          v   -   v    i  -i     v v  v  i--  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_62799888_6   5424 ACATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATGCTAAGCAAAAA 5473
                          i      viiv  ii  v  viv        i     vi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_62799888_6   5474 GAAGAAAACTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5523
                            v   ii      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_62799888_6   5524 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5573
                                  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_62799888_6   5574 CAATGGAACAGAACAGATGCCTCAGAAATAACACCACACATCTACAACCA 5623
                                 i    iv  vivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_62799888_6   5624 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATAGGGAAAGGATTCCC 5673
                         vi    i  i     ivv  v   i v  vv    i       i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_62799888_6   5674 TATTTAATAAATGGTATTGGAAAAACTGGCTAGCCATATGCAGAAAACTG 5723
                          v  i  i       ii   i v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_62799888_6   5724 AAACTGGACCCCTTCCTTACACCTCATACGAAAACTAACTCAAGATGGAT 5773
                           ii         v   i     vi    i    i        i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_62799888_6   5774 TAAAGACTTAAATGTAAGACCTAAAACGTTAAAAACACTAGAAGAAAACT 5823
                         i ?    i           v       vv     vivi           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_62799888_6   5824 TAGGCAATACTATTCAGGACATAGGTATGGGCAAAGAATTCACGACTAAA 5873
                             ?ivv v v   iv   v v  vv i     v iv   viiiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_62799888_6   5874 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAAATCTAAT 5923
                                     vvi          vv     v  i    vii ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_62799888_6   5924 TAAACTAAAGAGCTTCTGCATAGCAAAATAAACTATCATCAGAGTGAACA 5973
                         i   v v  i i   i  iiivv    iv v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_62799888_6   5974 GGGAACCTACAGAATGGGAGAAACTCTTTGCAATCTATCCGTCTGACAAA 6023
                          iv    i               v v       vii  vii     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_62799888_6   6024 GGGCTAATATCTAGAATCTACAAAGAACTTAAACACATTTACAAGAAAAA 6073
                           i  vi    i     v  i        ivv   vv iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_62799888_6   6074 AACAAACAACCCCATCACAAAGTGGGCAAAGGATATCAACAGACACTTCT 6123
                         i     i     v  i?v   i            v v  i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_62799888_6   6124 CAGAAGAAGACATTTATGCAGCCAACCA--ACATGAAAAAATGCTCATCA 6171
                          vi       i  vi viii     iv --         i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_62799888_6   6172 TCACTGGTCAT 6182
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (143 / 105)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


2641 27.81 1.66 1.43  chrX_62824600_62827559.rev     1564  2469 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62824600_6   1564 TGAAAACATACCCCATGCTCATGGATGAATGGAA---TCAATACTGTAAA 1610
                           i   v   i      i        ---     --- i    i   v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT---TGGAAGACTTAATATTGTTAA 47

  chrX_62824600_6   1611 AATGACCATGCTGCCAAAAGCGATCTACAAATTCACTGCAATTTCCATCA 1660
                         i   i v  i  v  v   vi        i     vi     ii i    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_62824600_6   1661 AAATACTATCATCAGTCTTCACAAAACTAGAAGAAACAATTCTAAAATTT 1710
                             v i v vv vv i  ii  i  v v  vi ivii  i        i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_62824600_6   1711 ACATGGAAC--CAAAACACAGCCCGCATAGCCAAAGCAAGACGAAACAAA 1758
                          i      v--   iiv  --  v v         i   vvivi  v  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_62824600_6   1759 AAGAACAAATCTGGAGGCATCACATTACCCAACTTCAAACTATACTATAA 1808
                                  vi      vv     i v     i      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_62824600_6   1809 GGCTGTAGTCACCAAAACAGCATGGCACTGGTATAAAAATACACACATAG 1858
                         i   ii   v i   i    ii   i     i    ii   v   i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_62824600_6   1859 AAAAATGGAACAGAATAGAGAACCCAGAAGTAAAACAAAATACTTACAGC 1908
                          vv       i     v    ii      i    v v v i i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_62824600_6   1909 CAACTGATCTTTGACAAACCAAACAAAAATATGAAGTAGGGAAAGAATAC 1958
                            i    i  i     ivvviv   i vi  vv i i           v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_62824600_6   1959 CCTATTTAACAAGTTGTGCTGGGATAATTGGCAAGCCACTTATAGAATAA 2008
                         i  v  i     i v         i  i   vv ?    v ii i  v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_62824600_6   2009 TGAAACCAGATCCTCATCTCTCAGCCTATACAAAAATCAACTCAAGATGA 2058
                             iiii  i  ii i   v  v v           i       i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_62824600_6   2059 ATGAAAGACTTAAATCTAAAACCAGAAGGCATAAAAATTATAGAAGATAA 2108
                           v ?    i     v   i v vi  ivi      v iv       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_62824600_6   2109 CATTGAAAAAACTCTTCTAGACATTGGCTTAGGCAAAGACTTTATGACTA 2158
                            v i?iv  v     vv   v    v        v ii  iv iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_62824600_6   2159 AGAACCCAAAAGCAAATGCAACAAAAACTAAGATAAATAGATGGGACTTA 2208
                         v  vv         v v         ivv  i   i   i  v      v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_62824600_6   2209 ATTAAA-TTAAAAAGCTTCTGCACAGCAAAAAATAATAATAATAATCAGC 2257
                           i   -       -   i  ii vv    ii i v  -------   iv
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA-------TCAAG 687

  chrX_62824600_6   2258 AGAGTAAGCAAACAACTCCCAGAGTGGGAGAAAATCTTTGCAACT-ATGC 2306
                          i   i iv i     i v    i           v       v -  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_62824600_6   2307 ATCCAACAAAAGACTAATGTCTGGAATCTACAAGGAACTCAAAAAAATCA 2356
                            ii i  ii    vi i  ii    v  i  i      vv v  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_62824600_6   2357 GCAAGAAAAAAA-----AATCCCATCAAAAAGTGAGCTAAGGGCATGAAT 2401
                         ii  v     i -----  i  v  i?    i  i  v    iiv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_62824600_6   2402 AAACAATTCTCAAAAGAAGATATCCAAATGGCCAACAG--ACATGAAAA- 2448
                          i   v     v           v           i i--         -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_62824600_6   2449 ATGCCCATCATCACTAATGAT 2469
                             i  v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (143 / 105)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.55 (28 / 11)  


1655 25.42 4.24 0.21  chrX_62829235_62831240.rev       30   501 (1505)    L1M4_orf2#LINE/L1      340   830 (78)  

  chrX_62829235_6     30 TACAGCCAACTGATTTTTGACAAAAGTACCAGGAACACACATTGAGGGAA 79
                           ii i   i       i     ii  i   i  v  iv  v  i  i  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_62829235_6     80 AGACAGTCTT--CAATAAATGGTGCTTAAA-AACTGGATATCCACATGTA 126
                         ii i      --   i          vii -         ?       i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_62829235_6    127 TAATAATGAAATTAGACTGTGACCTCCTTTTATATAAAAAAAATCAACTG 176
                         v  v      i  i   iviv     vivii     v     - i    v
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTC 488

  chrX_62829235_6    177 AAAACGGAT-AAAGAATTAAGTATAAGACTCTAAACTATGAAAATACAAG 225
                             i    - ?   vi   i i     viiv       i   v viv  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_62829235_6    226 AAAAAAACATAGGGGGAAGTCTCCATGACATTGG------------TTTT 263
                           i          ? v  i   i i    v    ------------   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_62829235_6    264 TTGGATATGACCCTGAAAGTACAGGCAACAAAAGCAACATTA-ACAAATG 312
                           i        v ii    i   i          v  v v  - i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_62829235_6    313 AGATAGTATCAAATTGAAAAGCTTCTGCACAGCCAAGGAAACAAGCCTGA 362
                         i  ivvi      v v    i   i  ii vv v     v  v v vv  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_62829235_6    363 --GTGAAGAGACAACATATAGAATGGGAGAAAATATCTGTAAATCTTGTA 410
                         --     i       vi i                 i  i     v i  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_62829235_6    411 TCTGATAAGAGGTTGATTTCCATAATATATAAGAAACTCAAACAACTCAA 460
                                  i ii vi v    v         ii     vv         
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_62829235_6    461 TAACAAGAAAACAAATAACATGATT-AAAAATGGGCAAGGAA 501
                            i  i  i         vii   -            i i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.60 (72 / 45)
Gap_init rate = 0.02 (8 / 491), avg. gap size = 2.62 (21 / 8)  

2922 28.56 0.77 0.66  chrX_62829235_62831240.rev      609  1515 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62829235_6    609 TGGAAAAACATTCCGTGTTCATGGATATGAAGGATCAATACCATTAAAAT 658
                               i i  i  i           vv    iv i    iii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62829235_6    659 GGCCATATGGCCCAAAGCAATGTATAGATTCAATGCTATTTCTATGAAAT 708
                            v   ivv      vii  v  i        i  v  ii    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62829235_6    709 TACCAAGAATATACTTCATAGAACTAGAAAAAAAAACT-ATTTTAAAATT 757
                          v   ivviiv vi  iii    v v  v  i----  -  ii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chrX_62829235_6    758 CATGTGGAACTGAAAAAGAGCATGAATAGTCAAGGCAATTCTAAGTAAAA 807
                            i     v  v  ii  v vv      i   ii    ii i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_62829235_6    808 ATAACAAAGCAGGAGGCATCATGCTACCCAACTTCAAACTATACTACAGG 857
                          v       iv     vv   ii  v     i      viv       ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_62829235_6    858 GCTACTGTAACCAAAAAAGCATGGCACTGGTACACAAACAGACACATAGA 907
                              v    i   i v  ii   i     i i vii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_62829235_6    908 CCAATGGAACAGACTAGAAAGCCCAGAAATAAGGCCACACACCTACAACT 957
                         i        i   v v  i  i          iv   i   ii  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_62829235_6    958 ATCTGATTGTTGACAAAGCTGACAAAAACAAGCAACAAGGAGAAGATTCC 1007
                          vi     v i     i v  v   i v  vv   iii   i ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_62829235_6   1008 CTATTCAATAAATAGTGCCTGGGATAACTGGCTAGTCATATGCAGAAGAT 1057
                           v     i    i    -     i      v  ?i  i     i    v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGC-TGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_62829235_6   1058 TGAAACTGAACCCCTTCCTTACACCATATACAAAAATCACCTGAAGATAG 1107
                             ii  i      v   i                 i v  v  i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_62829235_6   1108 ATTA-AGATGTAAATATAAAACCTAAAACTATAAAAATCCTGGAAGACAA 1156
                           i -   iv     i   i v              v  i i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_62829235_6   1157 CCTAGGCA-ATACCATTCTTGACATAGGAATGGGCAAATATTTCATGACA 1205
                          v    ?i- v i -   v    v v  iv i     vvi    v iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_62829235_6   1206 AAGATGCGAAAAGCAATTGCAACAAAAGCAAAAATTGATAAATTGGATAT 1255
                          v  ii v       vvv          v      v           iv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_62829235_6   1256 AATTCAACTAAAGAGCTTCTGTACAGCAAAATAAACTATCAACAGAGTAA 1305
                         v  iv  v v  i i   i   i vv    iv v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_62829235_6   1306 ACAGACAACCTACAGTGTAGGAGAAAATTTTTGCAAACTATACATTTGAC 1355
                          v        i    vi i         v        ii   i  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_62829235_6   1356 AAAGGTCTAATATCCTGCACCTGTAAGAAACTT----AAATGTACAAGAA 1401
                           i  v  vi     v v iv i   ii    i----  v vv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_62829235_6   1402 AAAAACAAACAACCCCATTAAAAAGTGGGCAAAGAACATGAACAGACACT 1451
                            i     i     v   ?    i         i iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_62829235_6   1452 TTTTAAAGGAAGACATACGTGCAGCCAACAAGCATATGAAAAAGAACTCA 1501
                          i iv  i     i    iviii     i     i       iivi    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_62829235_6   1502 ATATCACTGATAAT 1515
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (154 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3152 27.37 0.77 0.55  chrX_62841044_62847439     4998  5903 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62841044_6   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATCGTGAAAAT 5047
                              ii i  i     i      i v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62841044_6   5048 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCATCAAGC 5097
                            v     v     iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62841044_6   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_62841044_6   5146 TATGGAACAAAAAAGAGCCC-GCATTGCCAAGTCAATCCTAAGCCAAAAG 5194
                                vviv  i ii   - v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_62841044_6   5195 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTGCAAGGC 5244
                                i      vv    i  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_62841044_6   5245 TACAGTAACCAAAACAGCATGGTACTGGTACCAGAACAGAGATATAGATC 5294
                                 i   i    ii         i iv  i i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_62841044_6   5295 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATGTCTACAAAT 5342
                                i    i--    i  --        vv   i ii i  iiivi
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_62841044_6   5343 ATCTGATCTTCGACAAACCTGACAAAAACAAGTAATGGGGAAAGGATTCC 5392
                          vi    i        ivv  v   i v  vvi           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_62841044_6   5393 CTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCT 5442
                           v  i  i              v  i   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_62841044_6   5443 GAAACTGGATCCCTTCCTTACAGCTTATACAAAAATTAATTCAAGATGAA 5492
                            ii    i    v   i   v v              i    i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_62841044_6   5493 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5542
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_62841044_6   5543 CAT-GGCATTACCATTCAGGATATAGGAATGGGCAAGGACTTCATGTCTG 5591
                         -  -  ?i v viv   iv  iv v  iv i     v ii   v ivv i
  L1M4_orf2#LINE/    547 -ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_62841044_6   5592 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATGGACAAATGGGATCTA 5641
                         vi            vvi          vv     i  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_62841044_6   5642 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5691
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_62841044_6   5692 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5741
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_62841044_6   5742 AAGGGCTAATATCCAGAATCTACAACGAACTCAAACAAATTTACAAGAAA 5791
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_62841044_6   5792 AA-ACAAACAAGCCCATCAAAAAGTGGGTGAAGGACATGAACAGACAGTT 5840
                           -     i  v  v  i?    i    ii     iv    i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_62841044_6   5841 CTGAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5890
                           vv        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_62841044_6   5891 CATCACTGGCCAT 5903
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (149 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3172 27.31 0.55 0.55  chrX_62863527_62869864.rev     4940  5847 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62863527_6   4940 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4989
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62863527_6   4990 GGCCATCCTGCCCAGGGTAATTTATACATTCAATGCCATCCCCATCAAGC 5039
                            v  v  v    iiv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62863527_6   5040 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5087
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_62863527_6   5088 TATGGAACTTAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5137
                                v vv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_62863527_6   5138 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTGCAAAGC 5187
                                i      vv    i  v  ii i      viv    i      
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_62863527_6   5188 TACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5237
                            i    i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_62863527_6   5238 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5285
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_62863527_6   5286 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5335
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_62863527_6   5336 CTATTTAATAAATGGTGCTGAGAAAACTAACTAGCCATATGTAGAAAGCT 5385
                           v  i  i           i  v    iiv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_62863527_6   5386 GACACTGGATCCTTTCCTTATACCTTATACAAAAATTAATTCAAGATGTA 5435
                           vii    i  i v   i i   v              i    i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_62863527_6   5436 TTAAAGACTTAAATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAAC 5485
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_62863527_6   5486 CTAGGCA-ATACCATTCAGGACATAGGCATGTGCAAAGACTTCATGTCTA 5534
                         v    ?i- v i -   iv   v v  vv iv    v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_62863527_6   5535 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 5584
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_62863527_6   5585 ATTAAACTAAAGAGCTGCTGCACAGCAAAAGAAACTACCCTCAGAGTGAA 5634
                           i   v v  i i  vi  ii vv    i  v    i vvv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_62863527_6   5635 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5684
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_62863527_6   5685 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5734
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_62863527_6   5735 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGTTATGAACAGACACTT 5784
                           i     i     v  i?    i          v v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_62863527_6   5785 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGACAAAATGCTCAT 5834
                            v        i  vi viii     v ii       v  i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_62863527_6   5835 CATCACTGGCCAT 5847
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 653 24.52 1.29 1.29  chrX_62878180_62880903      295   449 (2275)    L1M4_orf2#LINE/L1        1   155 (753)  

  chrX_62878180_6    295 TGGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 344
                              ii i  ii    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62878180_6    345 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 394
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62878180_6    395 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAAAGTTCA 442
                          v   iivi i  i  ii     -   -- v  i  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_62878180_6    443 TATGGAA 449
                                
  L1M4_orf2#LINE/    149 TATGGAA 155

Transitions / transversions = 2.45 (27 / 11)
Gap_init rate = 0.02 (3 / 155), avg. gap size = 1.33 (4 / 3)  

2014 25.58 0.50 3.14  chrX_62878180_62880903      637  1242 (1482)    L1M4_orf2#LINE/L1        1   590 (318)  

  chrX_62878180_6    637 TGGAGACATATTTCATGCTTATAAATACGAATACTCAATATTGTCAAGAT 686
                             i v    ii    i i  ii  vv   v   i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62878180_6    687 GTCAGTTCTTCCCAACTTGATCTACAGATTCAACACAATCCCAATAAAAA 736
                          v  i v  i     v                  i       v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62878180_6    737 TCCCAGCAAGTTGTTTTGTGGATATCAACAATGTGATTCTAAAATTTATA 786
                                vivi v     ii  v  ii    vv    i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_62878180_6    787 TGAAAAAGCAAAAGACTGGGAATAGTCAATTCAATATTGAAAGAGAAGAA 836
                           i   v    ii   ivi      i   vv    v      i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_62878180_6    837 CAAAATCAGAGGACTGACACTATCATACTTTAAGCCATACTATAAGGCTA 886
                             i ii       v     vi vv i  i  iv v     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_62878180_6    887 CAGTAGTGAAAACATTGTGGTACTGAAAACGAAACAAAACAAAACAAAAA 936
                              i v  i   v          i--------  v  --ii i i v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGG--------CATAA--GGATAGACA 290

  chrX_62878180_6    937 AACAGAGTAATGGAACAGAATAGAAGGTGCAGAAATAGACAAACATAAAT 986
                         v i   vi       i     v  ii  v        i  vv i i vv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_62878180_6    987 ATAGTCAACTGAATTTTGACAAGGGAGCAAAAGCAATAGAATAGAGAAAA 1036
                           i     i   v   i        v  v  ii v  vv   i i    i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_62878180_6   1037 GATAATCTTTTCAAAAAGTCGTGCTGGAACAACTAGACATCAACATGACA 1086
                         i   i         v  i v       i      i  i ? v     vv 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_62878180_6   1087 AAAAATGAATCTACACACAAACCTCAGGTCTT---TAACAATTAACTCAA 1133
                           i      vi iv  v vv      vii v ---i  v           
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_62878180_6   1134 AATGGATGAACTTAAAACAGATCTAAATGTAAAACATAACATGATACAAA 1183
                                v ?--------   i          i vv   v iv   v  v
  L1M4_orf2#LINE/    491 AATGGATCAW--------AGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_62878180_6   1184 TCCTAGAAGACAACATAGAAGAAAAATCTAGATCATCGTGGGTTTGGCAA 1233
                           i       v       i? v   -   vvi v i v      v     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_62878180_6   1234 TTTTTTTTT 1242
                          vv   i  
  L1M4_orf2#LINE/    582 TGGTTTCTT 590

Transitions / transversions = 1.08 (79 / 73)
Gap_init rate = 0.01 (5 / 590), avg. gap size = 4.40 (22 / 5)  

 798 29.18 2.14 0.00  chrX_62878180_62880903     1532  1812 (912)    L1M4_orf2#LINE/L1      578   864 (44)  

  chrX_62878180_6   1532 GCGATTACTTTTTAGTTGCAATACTAAGGACACAATCCATGAAAGAAAAA 1581
                           i  vii  i    v iii i  i  iii     v v ii         
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_62878180_6   1582 CGTGATAATCTGGGCTTCATTAAAATTAAAATTTCCTATTCTGCAAATGA 1631
                         vvv     vi   i      i          vi ii i v  v    v  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_62878180_6   1632 CACTGCCAAGAGTATAAAAAGA-AGGCAAAAGACTGAGAGAAAATATTTG 1680
                             ii     ivi i      - iv v v   v  i             
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_62878180_6   1681 CAAA--AGGTATTACATAAAAGACTGTTATCAAACATATGCAAATAACTC 1728
                             -- vi   ivv    ii    vv    v iv    ii   v     
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_62878180_6   1729 TTAAAACTCAATAA---GAATGCAAACAATCAAATTTAAAAATGGCCTAA 1775
                            v          ---i  vi    i  i v    ?        v v  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_62878180_6   1776 AAATCTTAACAGACACTTCATTAAAAAAGACATAGAA 1812
                         ii  i v  i     i   vii   i    i   v  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

Transitions / transversions = 1.45 (48 / 33)
Gap_init rate = 0.01 (3 / 287), avg. gap size = 2.00 (6 / 3)  


2349 27.34 4.63 2.03  chrX_62888301_62893964     4294  5178 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62888301_6   4294 TAGAAAAACATTTCATGTGCATGTGGATAGGATGAATCAATATTGTTAAA 4343
                          i    i i  ii     v    --   v   v  v i           i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATG--GATTGGAAGACTTAATATTGTTAAG 48

  chrX_62888301_6   4344 ATGGACATACTCCCCAAATCAATGTA--GATTCAATAATATTCCTATTAA 4391
                             vv             ii  v  --       iivv  i     i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_62888301_6   4392 ACTACCAATGATATTTTTTCACAGAACTAGAGAAAACT-ATTGTAACATT 4440
                          v v   iiviiv      -i     v v  v  i-  -  iv   v   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chrX_62888301_6   4441 CCCCTGCAATGAAA---AAAGAGCCCA-AATAGCCAAAGCAATTCTAAGC 4486
                          viv  ----    ---  i ii    -          i    ii i iv
  L1M4_orf2#LINE/    147 CATATG----GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_62888301_6   4487 ATTAAAAAGAAAGCTGGAGACATCACATTACCTGATTTTAAACTATACTA 4536
                          vv  i  v    i     ivv     i v  ii    i   viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_62888301_6   4537 CAAAGCTACAGTATCCAAAACAGCATGGTATTTGTGGAAAAAAAAAGAGG 4586
                                      vi   i    ii     i v i---- v  ii v  i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC----ATAAGGATAGA 288

  chrX_62888301_6   4587 CCCAAAGACCCATAGAATGG--TTAGAGAATCCAGAAATAAAACTGCACA 4634
                          vi v   i v  i    i --  -    i            v iii   
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACA 337

  chrX_62888301_6   4635 CCTATGACCATATGAATTTAAATACTGTCTACAAAAACAAGCAATGGGAA 4684
                         ii    ii  vv   v   vi i vv vivv   i v  vv       i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_62888301_6   4685 ATGACT--CCTTATTCAATAAATGGCACTGAGATAACTGGCTAGCCATAT 4732
                          v  v --i   -     i      ii   i  i      v  ?   i  
  L1M4_orf2#LINE/    388 AAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_62888301_6   4733 GCAGAAGACTGAAACTGGACCCCTTCCTTACACTATATAAAGAAATCAAC 4782
                            i    v    ii         v   i    i     v i    i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_62888301_6   4783 TCAACATGAATTAAAGACTTACACATAACACCTATGGGTA----AC---- 4824
                             v   i  i ?    i  v ii   v v   viiv  ----  ----
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_62888301_6   4825 -AAAGGAAATAC---CAT-----TTTG-GACATAAGCCCTGGCAAAGATT 4864
                         -i   i   i i---?i -----  i -   v vi viiv     v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_62888301_6   4865 TCATGACAAAGATGCCAAAAGCAATCA--TAATAAAAACAAAAATTGACA 4912
                           v iivv v  ii         --  --i  i    iv      v  i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATA 634

  chrX_62888301_6   4913 AATGGGAACTAATTAAACCAAAGAGCTTCTGTGCAGCAAAAGAAACTGTC 4962
                            v   vi v  i   viv  i i   i     vv    i  v   i  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_62888301_6   4963 AATAGAGTAAACAGATAACTTA-AAAATGGGAGAAAATATCTGCACTCTA 5011
                           v i   i  v   i   ii - i               i    vvii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_62888301_6   5012 TGCAGCCGACAAAAG--TTGAATATCCAGAATCTATAAGGAACTT----A 5055
                          ii v i  i  ii --   --          v     i     i---- 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTG--TATCCAGAATATATAAAGAACTCTTACA 782

  chrX_62888301_6   5056 AGTCAACAAGCAAAAAACAAACAACCCAATTAAAAAATGAGCAATGGACA 5105
                          v    i  vv    i     i         ?       i    v   iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_62888301_6   5106 TCAACAGACACTTCTCAAAAGAA---ATACATGCAGCCAACAAGCATATG 5152
                          v  i     i     v      ---     viii     i     i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_62888301_6   5153 AAAAAATATTCCATATCACTAATTAA 5178
                             i  ii  v i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.36 (59 / 25)  


3084 25.14 2.93 0.56  chrX_62896414_62900949     3157  4043 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62896414_6   3157 TGAAAAGATTTCCCATAGTTCATGGAATGGAAGAATTAATATTGTTATTA 3206
                           i      v      -         v       v            vv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_62896414_6   3207 GGTCCGTACTTCACAAAGCAATCTGTATATTTG-TGTAATCCTTATCAAA 3255
                         v v vi    i v    vii    ii v   ii-i i     i       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_62896414_6   3256 ATACCAGTGATATTCTTCACAGAAATAGGAAAACAAATCCTAAAATTTGT 3305
                           v    iviiv  i  ii       v iv  i vi           ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_62896414_6   3306 GTGGAACCACAAAGACCCCA-AATAGCCAAAGGAATCCTGAACAAAAAGA 3354
                         i     vii   i iv    -          iv    i    v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_62896414_6   3355 AAAAAGCTGGAAGTTTCACATTACCTGACTTCAATATGTACTACAGAGCC 3404
                          v    i    i vi     i v  ii i     v iv       i   i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_62896414_6   3405 ATAATAACCAAAACAGCCTGATACTGGTGTAAAAACTGACACATAGGCCA 3454
                          i i   i   i    iv  i      ii   ii iv    i    ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_62896414_6   3455 ATAGAACAGACTAGAGAACCAATAAATAAATTCATGCATTTATAGCCAAC 3504
                           i   i   v v    ii v v       ii   i       i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_62896414_6   3505 TTATTTTTGATAAAGTCATCAAGAACTTACACTGAAGAAAGGACAGACTC 3554
                          v     i  i  i viii     v v v  v  ii     i i  v  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_62896414_6   3555 TTCAAGAAATTATGCTGGGAAAACTGGATAATGATATGCAGAAGAATAAA 3604
                              v    vi        v         ?iv i     i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_62896414_6   3605 ATTAGACCCCTATATCTCACCATATA--AAAAT-AA----AAATT-ATTA 3646
                         i  i        iv  v         --     -  ----    v-  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_62896414_6   3647 AAGACTTAAATGTAATACCCCAATCTCTGAAAACACT-AGAAGAAAACAT 3695
                         ?    i         v v iv  v  v -     v  -            
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chrX_62896414_6   3696 -TGAGAAAATGCTTTAGGACATTGGTTTGAGCAAAGACTTTTTAGGTAAG 3744
                         -v ? v    -   iiv   v    v  ii    v ii  i    i  v 
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_62896414_6   3745 ATTTCCAAAGTGCAAGAAACAAA-GAAAAAATAGACAAATGGAATTACAT 3793
                          ivi v    ii    v      -           i    v i i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_62896414_6   3794 CAAG-CTAAAGAGCTCTGTATAGCAAAGGAAACAATCAACA--GTGAAAA 3840
                            i-i    i vi i   iivv       v  v     v --       
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_62896414_6   3841 AGACAACCTACAGAATTGAAGAAAATATTTGCAATCTATCCTTCTGACAA 3890
                         -       i       v i               vii  viv     i  
  L1M4_orf2#LINE/    698 -GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_62896414_6   3891 GGAATTAATAACCAGTATCTATAA-GAA--------ACTTAGCAGCAAAA 3931
                           i i vi  v    v  v     -   --------   i ii ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_62896414_6   3932 AACCAAATAACCCAATTAAAAGA-GGGCAAATGATCTGAATAGACATTTC 3980
                          iv              ?   i -       v   i              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_62896414_6   3981 TAAAAAGAAGACATGCAAATGGCTATCTCGATACATGAAAAAGTACTCAA 4030
                          vv        i  i        i -v viii         ii i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCA-ATAAGCACATGAAAAGATGCTCAA 895

  chrX_62896414_6   4031 CATCACTAATCGT 4043
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (135 / 84)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.63 (31 / 19)  


3022 27.47 0.88 1.10  chrX_62938980_62945819     3705  4614 (2226)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62938980_6   3705 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3754
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62938980_6   3755 GGCCATACTGCCCAAGGTAATTTTTAGATTCAATGCCATCCCTATCAAGC 3804
                            v     v     iv i  i vi        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62938980_6   3805 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACTA---CTGTAAATTC 3850
                          v   ivvi i  i  ii     -   -- v  i  i---  i-      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTA-AAATTC 147

  chrX_62938980_6   3851 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGTCAAAA 3900
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_62938980_6   3901 GAACAAAGCTGGAGGTATCATGGTACCTGACTTCAAACTATACTACAAGG 3950
                                 i      vv   iiv v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_62938980_6   3951 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAATAGAGATGTAGAT 4000
                                  i   i    ii         i iv ii     v  i     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_62938980_6   4001 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACTGCATATCTACAAC 4048
                                 i    i--    i  --        vv iii i  i  iii-
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG- 344

  chrX_62938980_6   4049 TATCTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGG 4098
                         --  v  -    i  i     ivv  v   i v  vv            i
  L1M4_orf2#LINE/    345 --TCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_62938980_6   4099 ATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGA 4148
                           vvi  v  i  i              v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_62938980_6   4149 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAG 4198
                          iiv    ii    i    v   i     v              i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_62938980_6   4199 ATGAATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAG 4248
                            i  i ?    i    i  v   v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_62938980_6   4249 TAAACCAT-GGCATTACCATTCAGGATATAGGAATGGGCAAGGACTTCAT 4297
                         -   v   -  ?i v viv   iv  iv v  iv i     v ii   v 
  L1M4_orf2#LINE/    542 -AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_62938980_6   4298 GTCTGAAACACCAAAAGCAATGGTAACAAAAGCCAAAATGGACAAATGGG 4347
                         ivv ivi            vvi i        vv     i  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_62938980_6   4348 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 4397
                          ii v  i   v v  i i   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_62938980_6   4398 GTGAACAGGCAACCTAGAAAATGGGAGAAAATTTTCGCAACCTACTCATC 4447
                              v  i     i v i             v  i    vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_62938980_6   4448 TGACAAAGGGCTAATATCCAGAATCTACAACGAACTCAAACAAATTTACA 4497
                            i  i  i  vi          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_62938980_6   4498 AGAAAAA-ACAAACAACCTCATCAAAAAGTTTGTGAAGGACATGAACAGA 4546
                          v     -     i    iv  i?    i vv ii     iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_62938980_6   4547 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACGTGAAAAAATG 4596
                           i     v        i  vi viii     v  i   i      i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_62938980_6   4597 CTCACCCTCACTGGCCAT 4614
                             v v   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  

3414 24.50 1.43 1.21  chrX_62938980_62945819     5442  6347 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62938980_6   5442 TGGAAAGATATCCCATGTTCATTTACTAGAGGAACTAACATTGCTAAAAT 5491
                                               vv i i  i  vi   i    i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62938980_6   5492 ATCCATGCTGCTTAAAGCAATCTACAGATTCAGTGCAATCCCTATCAAAA 5541
                         iv v  i  v ii   vii             ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62938980_6   5542 CTCCAATGACATCTTTCACTGAAATAGAGGAAACAAACCTAAGATTCATA 5591
                         ii   iivi v i   ii v     v  vi ivii v     i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_62938980_6   5592 TGAAACCACGAAAGACCCCAAATAGCCCAAACAATCTTGAGTGAAAAGAA 5641
                           i  vii i ii     vi       v            ivi i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_62938980_6   5642 CAACACTGGAAACCTTACCCTACTTGATCTCAAAATCTACTACAAAGCTA 5691
                            vii    iiv  i  v  v iii  i      ii             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_62938980_6   5692 TAGTGATCAAGACAGCATGGTACTGACACAAAAACAAACATATAAACCAA 5741
                         i   i          ii        i  i  ii i i       i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_62938980_6   5742 TGGAACAGAATATAAAGCCCAGAAATAAGTCCATACACTTATGCCCAAGT 5791
                              i     vv i  i          ii       i     vi   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_62938980_6   5792 AATTTTTCAAGAAATGTGGCAATAACACACAATGGGGAAAGGACAGTTTC 5841
                         i     - i v  iv   v   v v  iv            i i   i i
  L1M4_orf2#LINE/    351 GATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_62938980_6   5842 TTCAATAAATGATCTTAAGACAACTGGATATCCACATGCCAAA-AATGAA 5890
                              i     i vi ii            ?        v   -      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_62938980_6   5891 ATTGGACCCTTATCTCACCCCATATACAAAACTTAACTCAAAACTGATTA 5940
                         i        i  i     v            v           iv   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_62938980_6   5941 AAGACTTAAACATAAGACTTGCAACTAC--------TAGAAAAAAACATA 5982
                         ?    i    ii     vi iv     i--------     i        
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_62938980_6   5983 GGGGAAAAGGTTCATGACTTTCATCTTGGCAAAGACTT-TTGAATCTGAA 6031
                           ? v   vv   i    i  vivi v     v ii  -  ii  v   v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_62938980_6   6032 CCCAAAAGCACAGGCAACAAAATTGAAAACAGACACATTGGGCTATATCA 6081
                         v           i         vvi    i   i v     i  vi    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_62938980_6   6082 AACTAAAAAATCTTCTGTACAGCAAAGGAAACAATCAACAGTGTGATGAG 6131
                           v v     -   i   i vv       v  v     v iv    vi  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_62938980_6   6132 ATAACCTACAGAAATAGGAGAAAATATTTAGGAAAT-AGACTTCTGATAA 6180
                          i    i      - i             - v    - v iv        
  L1M4_orf2#LINE/    699 ACAACCCACAGAA-TGGGAGAAAATATTT-GCAAATCATATATCTGATAA 746

  chrX_62938980_6   6181 GAGGTTAGTATCCAAAATATACATGGAAGGAATTCAAATGACTTAAAAGT 6230
                          i ii v       i      i ---- i   i  vv ii   i  v i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATA----AAGAACTCTTACAACTCAATAAT 792

  chrX_62938980_6   6231 AAGAAAACAAATAATCCAGTTTTTAAAATGGGCAAAAGACCAAAAAAGAC 6280
                           i  i        i   i  ?v-            i  iivi  v    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_62938980_6   6281 ATTTCT--AAAGAGGAAATACAATATAACCAACAGATAAAATGAAAAAAT 6328
                               --     i  v      -  ii    i iii v -      i  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAA-ATGGCCAATAAGCACA-TGAAAAGAT 889

  chrX_62938980_6   6329 GCTTAATATCACTAATCAT 6347
                            i  i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (144 / 74)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


4634 16.96 1.66 1.00  chrX_62951358_62955548.rev     2799  3700 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62951358_6   2799 TAGAAGAATATCCTATCTTAACGGACAGGAACTCTTAACCTTGTTAAGAT 2848
                          i   ii      i  v  v i   iv    vv     iv          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62951358_6   2849 GGCAATACTCCCCAACTGAATCTACAGATTCAGTGAAATATATATTATAA 2898
                                        v vi             ii v   viv   i v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62951358_6   2899 GTCTAGCTATTTTTCTGTTAGAAAGAACTAGACAAGCTAATTCTAAAATT 2948
                         vi i    iii   i vvi     ---- v        i  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA----TTGACAAGCTGATCCTAAAATT 146

  chrX_62951358_6   2949 CATATGGAATTTCAAGAGACATAGAATGGCCAAACCATTCCTTAAAACTA 2998
                                  v v    i   vi     i      v  v  -  i   -- 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAA--A 193

  chrX_62951358_6   2999 AAAACAAAAAAGTAGGAGGACCCAAAATTCCTGATTCCTAAATTTACTAC 3048
                          i  v  v     v       i  v v    ii   i v   i       
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_62951358_6   3049 AAAGCAACAGTAATCAGAGACAGTGTGGCACTGGCACAAGGACAGATACA 3098
                              v          -           i       i     i   i i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCA-AGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_62951358_6   3099 TAGATGAATGGAATAGAATTGAGACTCCATAAATGAAAGAATGTATCTAT 3148
                              v                  v    v    i  vvv  ii  i   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_62951358_6   3149 GATCTACTGATTTTCAACAAGGGTGCCAA-ACCAGCCAATGGGG---GAT 3194
                          i  v i        i             -    vi        ---  v
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_62951358_6   3195 TAGTCTTTTCAACAAATTGTGCTGGGACAACTTGATAGCCACATGCAAAA 3244
                                          v              v    ?            
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_62951358_6   3245 GAATGAAGTTGGACCCTTATCTCACACCATTTACAAAAATTAACTAAAAA 3294
                                         i  i          v              v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_62951358_6   3295 TGTATTAAAGACCTCAATGTAAGAGCTGGAAGTCTAAAACTCTTAGAAGA 3344
                           v  i ?      v            ii  v v                
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_62951358_6   3345 AAACATAGGGGTAAGCCTTCATAACTTTAGATTTGGCAAAGGTTTCTGAG 3394
                                  ?    ii    i i  i  i i  v     v       v  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_62951358_6   3395 GTTTGGCACTAAAAACATAAGCAACAAAAGA---------TAAATTGGAC 3435
                         i v  i   i    i  i             ---------          
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_62951358_6   3436 TTCATTAAAATTAAAAACTTTTGTTCTTCAATGAGCAGTATCAAGAAAGT 3485
                              i                  v      v ii  v            
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_62951358_6   3486 GAAAAAACAACTCACAGAATGCGAGAGAGTATTTGCAAAGCATATATCTG 3535
                              i     i         v    i i          v          
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_62951358_6   3536 ATAAGGGAGTTGTATACAGAATATATAAAGAACCCTGGCAACCCAAAAAT 3585
                                 v      v                 i  vi    i   v   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_62951358_6   3586 AAAAAGACAAAGAACATAGTTTTAAATGTAGGCAAAGGATCTGAA--GAT 3633
                                    v   vi i  ?v   -i i          i    --  i
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAGAC 841

  chrX_62951358_6   3634 ATTTCTCCAAGGAAGGTATACAAATGGCCAAAAAGCATATGAAAACGTGT 3683
                                   i    i               v     i       vi  i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_62951358_6   3684 TTTATGTCATTAGTCAT 3700
                          iv ii   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (85 / 64)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  


3182 26.03 0.11 2.05  chrX_62955606_62958902     1879  2804 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_62955606_6   1879 TGAAAACACATCCCATGCTCATGGATAGGTAAAATCAATATGGTGAAAAT 1928
                           i   v i        i        v  v i v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62955606_6   1929 TACCATACTGCCAAAAGCAATCTACAAATGTAATGCAATTCCCATCAGAA 1978
                         vi v     v  v   vii       i  vi  i     i  i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_62955606_6   1979 TACCATCATCATTTTTCACAGAACTAGAAAAAACAATTCTCAAATTTATA 2028
                          v   v vv v     ii     v v  v  ivii  i  v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_62955606_6   2029 TGGAACCAAAAAAGAGCCCACAA-AGCCAAAGCAAGACTAAGCAAAAATA 2077
                              viiv  ii  -    v  -       i   vvi i iv  i  v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_62955606_6   2078 ACAAATCTGGAGGCATCACATTACCTGATTTCAATCTATACTATAAGGCC 2127
                              vi      vv     i v  ii       vviv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_62955606_6   2128 ATAGTCACCAAAACACCATAATACTGGCATAAAAATAGGCATGTAGACCA 2177
                          i   v i   i   vii ii           ii    i   i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_62955606_6   2178 ATGGAACAGAATAGAGAGCTCAGAAATAAACCCTAATACTTACAGCCAAT 2227
                               i     v     ii             vv i i   ii i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_62955606_6   2228 TGATCTTTGACAAAGCAAACAAAAACATAAAGTGAGGAAAGGACACCCTA 2277
                             i  i     i vviv   i v   vv i  i      i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_62955606_6   2278 TTCAACAAATGGTGCTGAGGTAATTGGCAAGCCACATGTAGGAGAATTAA 2327
                                          i ii  i   vv ?       i ii     v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_62955606_6   2328 AGTGGATCCTCATCTCACACCTTATTCAAAAATCAACTCAAGATGGATCA 2377
                         iv    i  ii i        v   v       i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_62955606_6   2378 AGAATTTAAATGTAAGGCCTGAAACTATAAAAATTCTAGATGAGAAGATG 2427
                         ?ii ii          iv  i           v ii    v  i  v  i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_62955606_6   2428 GGAAAAACCCTTCTTGACATTGGCTTAGGCAAGGATTTCATGACCAAGAA 2477
                           ?iv  vi    v    v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_62955606_6   2478 CCCAAAAGCAAAGGCAATAAAAACAAAGATAAATAACTGGAACTTAATTA 2527
                         v         v i    i    iv   i   i    v v i    v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_62955606_6   2528 CACTAAAAAGCTTCTGCATGGCAAAGGGAACAGTCAGCAGAGTAAAAAGA 2577
                         v v v    i   i  iiivv      iv  vi   iv i   i      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_62955606_6   2578 AAACCCACAGAGTGGGAGAAAATATTCACAGTCTATACATCTGACAAAGG 2627
                         v          i              ii  i-------   ---------
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAA-------ATC--------- 733

  chrX_62955606_6   2628 TATACATCTGACAAAGGACTAATTTCCAGAATCTAAAAAGAACTCAAACA 2677
                         -   i      i  i     vi v        v  v         vv   
  L1M4_orf2#LINE/    734 -ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_62955606_6   2678 AATTAGCAAGAAAAAAACCAAACAATCCCATCAAAAAGTGGGCTAAGGAT 2727
                          v i ii  v     i  -   i  i  v  i?    i     v      
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_62955606_6   2728 ATGAATAGACAATTCTCAAAAGATAATATGCAAATAGCCAACAAACATAT 2777
                         v          v     v     vi    i     i     i  i  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_62955606_6   2778 GAAAAAATGCTCAACATCACTAATGAT 2804
                              i             ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 4.00 (20 / 5)  


2205 26.26 9.62 0.99  chrX_62975379_62977281      617  1427 (476)    L1M4_orf2#LINE/L1       10   890 (18)  

  chrX_62975379_6    617 ATCCCATGCACATGCATCAGAAGAATTAATATGATTAAAATGATTATACT 666
                                 iv    v  ii     v       vi    i   iiv     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_62975379_6    667 GCACAAAACAATCTATGAATTAAATGTAATTCCTATCAAAATATCAA-TG 715
                         v v    vii     iii   v  i i   i           vi  i-  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_62975379_6    716 TCATCTTTTATAG---TTAGGAAAATAATTCTAAAATTAATATGGAATCA 762
                         i - i    ii  ---  iiv  iv i  i        v        vii
  L1M4_orf2#LINE/    110 CC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_62975379_6    763 AATAGAGCCCA-AATACCCAAAGCAATCCTCAGAAAGAAAAAAAAAAA-A 810
                         v vi ii    -    v     i     i ------      i  i  - 
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTT------GAAAAAGAAGAACA 202

  chrX_62975379_6    811 AAGCTGAAGGCATCATATTACCTGACTTCAAATTATACTACAAAGCTATA 860
                            i  i   vv   i i v  ii i      viv             i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_62975379_6    861 GTAACCAAAA-A---------------AAGGA-AGACAT-----TCA-TA 887
                             i   i - ---------------     -      -----   - i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_62975379_6    888 GAATAGA--TGA---CCCAGAAATAAAGTCACTTGTTTACAGCCAAATGA 932
                                --   ---i           vi  ivii    ii i   v   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_62975379_6    933 TCGCTGACAAAA-TA--AAAAACATACA-TAGGGAAACGACA-CCCTTTC 977
                          ivii     ii- i--  i v   v  - i      vi i -i i    
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_62975379_6    978 AGTAAATGGTTCTGGGAAATTTGAATTGCCATATGCAGAAGAATGAAACT 1027
                          ii       v      v vi  i  v?   i     i         ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_62975379_6   1028 TGACCCCTATCTCCCACCATATACAAAAATCAACTCAAGATGGATCAAAG 1077
                         v        i   v                i       i        ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_62975379_6   1078 ACTTAAATGTAAAA-----------------CCTAGA-GAAAAT------ 1103
                           i         i ----------------- i    -     i------
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_62975379_6   1104 -----TCTTCTGGACATTGGTCTAGGCAAAGAGTCCATGACTAAGATTTC 1148
                         -----     vv   v    vi       v iv i v iiv  v  ivi 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_62975379_6   1149 AAAAGCAGAGGGAACAAAACAAAAATT-GACAAATACGACTT-----AAG 1192
                                v i v       v     v -  i    vv     -----  i
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_62975379_6   1193 CTAAAAACCTCCTGCACATCAAAAGAAAT----AACACAGTGAAGAAACA 1238
                         i       i i-  ii v     i  v i----  v v      i i   
  L1M4_orf2#LINE/    653 TTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_62975379_6   1239 ACATTTTAAATGGGAGAAAATATTGGCAAGCTATGCATCTGACAGAGAAC 1288
                           vivivi                v    iii  ii      i ii i  
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_62975379_6   1289 TAATATACAAAATTTACAAGGAACTTAAAAAGCTCAATGAAAAATAAACA 1338
                          vi   v  i   v  i  i     ivv v i      i v   v i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_62975379_6   1339 AATAATCCCATTAAAAAGTGGGTAAAAGACATGAATAAACATTTCTCAAA 1388
                              i  v   ?    i    i   i  iv      i         v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_62975379_6   1389 AGAAGACATGCAAACTACCTAGGTGTCCATCAACAGATG 1427
                               i  i    ivi  v viv iv   v  v     
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

Transitions / transversions = 1.73 (133 / 77)
Gap_init rate = 0.03 (24 / 881), avg. gap size = 3.58 (86 / 24)  


2582 25.95 0.71 5.33  chrX_62989330_62994015     2017  2860 (1826)    L1M4_orf2#LINE/L1        1   805 (103)  

  chrX_62989330_6   2017 TGGAAGAAGATTCCATGCTCATGGGTAGTAAGAATCAATATCATGAAAAT 2066
                              ii v  i     i      i v v    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_62989330_6   2067 GGCCCATATTTCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAG 2116
                            v-   i i     iv i  i  i        i  v     i     i
  L1M4_orf2#LINE/     51 GGCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_62989330_6   2117 CTACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCAT 2166
                         v v   iivi i  i  ii     v v  v  iv v iii    i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_62989330_6   2167 ATGGAACCAAAAAAATGGCCT-GCATAGCCAAGACAATCCTAAGCCAAAG 2215
                               -- viv  iv i  i- v        i      i i ivv i i
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_62989330_6   2216 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTATAAGG 2265
                                 i      vv   ii  v  ii i      viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_62989330_6   2266 CTGCAGTAAACAAAGCAACATGGTACTGGTACCAAAACAGATATATAGAC 2315
                           i      v   ii  iii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_62989330_6   2316 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCATACATCTATAACCA 2365
                                 i    iv   ivii         vv        i   iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_62989330_6   2366 TCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 2415
                         vi    i  i     i v  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_62989330_6   2416 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCTG 2465
                          v  i  i              v      v  ?   i     i  -----
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA----- 442

  chrX_62989330_6   2466 AAACTGGATGTCTATATGCAGAAGAATGAAACCAGACCTCTATCTCTTAC 2515
                         -----------------------       iiii    i   i   vi  
  L1M4_orf2#LINE/    443 -----------------------GAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_62989330_6   2516 CATATACAAAAATCAAATAGAAATGAATTAAAGACTTAAATCTAAGATCT 2565
                                      i  v vi     i  i ?    i     v     v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_62989330_6   2566 CAAGCTATGAAACTACTACAAGAAAACATTGAGGAA-AAATCTCCAGGAC 2614
                         v  i    i     vi  v          --   ?i-      i iv   
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACAT--AGGNGTAAATCTTCGTGAC 567

  chrX_62989330_6   2615 ATTGATCTGGGCAAAAATTTTTGAGCAATAAT-CCATAAGCACAGGCAA- 2662
                         v   ivi i     vii   i v  vv  i i-   v       i    -
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_62989330_6   2663 -AAAATAAAAATGGACAAATAGGGTCACATTAAT-TTAAAAGCCTTCTGC 2710
                         -   iv      i  i    v  iiiv   i  v-      i i  -  i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGT 666

  chrX_62989330_6   2711 ACAGAAACAGAAACAATCAACAAAGGGAAGAGACAACTTACAGAATGGTA 2760
                         i vvv  vi  v  v     v    v   i       ii         v 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_62989330_6   2761 GAAAATATCTGCAAACTACCCATCTGACAAGAGATTAATATAACCAGAAT 2810
                                 i      ii ivi      i   i  i vi   --       
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT--CCAGAAT 764

  chrX_62989330_6   2811 ATATGAGGAGCTCAAACAACTCTACAGAAATAAAATGTAATAGAGAAATA 2860
                             i i  i   vv       v i ---      ------   v     
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATA---ATAAAA------AGACAAATA 805

Transitions / transversions = 1.73 (137 / 79)
Gap_init rate = 0.02 (13 / 805), avg. gap size = 3.92 (51 / 13)  

 556  9.09 4.96 4.13  chrX_62989330_62994015     4073  4193 (493)    L1M4_orf2#LINE/L1      787   908 (0)  

  chrX_62989330_6   4073 AATAATTTTTAAAAAGA--AAT----CAATTCAAAAATAGACAAAGGATT 4116
                               ----       --   ----     ?      i i         
  L1M4_orf2#LINE/    787 AATAAT----AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_62989330_6   4117 TGAATAGATATTTCTCTCCAAAAAGATATACAAATGGCCCATAAACACAT 4166
                                 i       - v  i                 v    i     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTC-CAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_62989330_6   4167 GTAATGATGCTTAACATCATTAGTCAT 4193
                          v  v      i       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (6 / 4)
Gap_init rate = 0.03 (4 / 122), avg. gap size = 2.75 (11 / 4)  


 575 28.35 0.00 0.00  chrX_63016408_63022687.rev      307   500 (5780)  C L1M4_orf2#LINE/L1   (0)   908   715  

C chrX_63016408_6    500 GAGAAAAGTTTTCCAACCTATCCATAAGACAAAGGTCTAATATCTAGAGT 451
                                vv   v   vii  vi  vv  i  i  v  vi    i   i 
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

C chrX_63016408_6    450 CTAGAAGGAATTTAAACAGATTTACAAGAAAAAAGCAAACAACCCCATTA 401
                         v  v  i   i ivv   iv iv i  v     ii    i     v   ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

C chrX_63016408_6    400 AAAAGTAGGCAAATGATATGAACAGACACTTCTCAAAAGAAGACATTTAT 351
                             i i      v   v    i     i     v        i  vi v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

C chrX_63016408_6    350 GCAGCCAACAAACATATGAAAAAAAGCTTAACATCACTAATCAT 307
                         iii     i  i  i       i v   i       ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (31 / 23)
Gap_init rate = 0.00 (0 / 194), avg. gap size = 0.00 (0 / 0)  

3256 26.98 0.44 0.44  chrX_63016408_63022687.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63016408_6   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63016408_6   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAATC 4981
                            v     v     iv i  i           i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63016408_6   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_63016408_6   5030 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63016408_6   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63016408_6   5130 TACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i     i         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63016408_6   5180 AAGGAAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5227
                           v i  i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_63016408_6   5228 ATATGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vv    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63016408_6   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63016408_6   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5377
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_63016408_6   5378 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_63016408_6   5428 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_63016408_6   5478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5527
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_63016408_6   5528 TTAAACTAAAGAGCTGCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v v  i i  vi  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_63016408_6   5578 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5627
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_63016408_6   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_63016408_6   5678 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_63016408_6   5728 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5777
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_63016408_6   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2231 27.13 3.58 0.41  chrX_63051335_63055954      505  1230 (3390)    L1M4_orf2#LINE/L1      160   908 (0)  

  chrX_63051335_6    505 AAAAGAGCTTGTATAGCCAAGACAATCCTAAGCAAAAAGAACAAAGCTGG 554
                           ii  v iv v        i      i i iv  i          i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_63051335_6    555 AGGCATCACACTACCCGACTTCAAACTTTACTATAAGGCTACAGTAACCA 604
                            vv       v   i i      vi      i  i          i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_63051335_6    605 AAATAGCATGGTACAGGTACAAAAACAGACACAAAGAACAATGGAACAGA 654
                          i i  ii      v  i i  ii i     i v   v        i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_63051335_6    655 ACAGAAAACTCAGAAATAAGACTACACATCTACAACCATCTGGTCTTTGC 704
                          iv  i iii         iv i i    i  iiii  vi  i i  i v
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_63051335_6    705 CAAACCTGACAAAACAAG-CAATGGGGAAAAGATTCCCTATTTAATAAAT 753
                            ivv  v   i  v v-           ii  vvi  v  i  i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_63051335_6    754 GGTACTGGAAGATCTGGCTAGCCATATGCAGAAAATTGAAACTGGATCCC 803
                            i    i v v    v  ?   i     i  i v    ii    i   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_63051335_6    804 TTCCTTACACCTTATACTAAAATTAATTCAACATACATTAAAGACTCAAA 853
                          v   i     v     v        i    v  iv  i ?    ii   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_63051335_6    854 -----AACCCAAAACTCTAGAAACCATAGAAGAAAATCTAGGCA-ATACC 897
                         -----i v i      v  i  vi v          iv    ?i- v i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_63051335_6    898 ATTCAGGAC-TTATGTATGGGCAAAGATTTCATGACAAAAACATCAAAAG 946
                         -   iv   -  iv  - i     v i    v iivv vi   i      
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_63051335_6    947 CAATAGCAACAAAACCAAAAATAGACAAAATTGGATCTAATTAAACTAAA 996
                           vv          vv         i   -     ii v  i   v v  
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAA-TTGGACTTCATCAAAATTAA 656

  chrX_63051335_6    997 GAGTTTCTGCACAACAAAAGAAAATATCTTCAGAGTGAAG-GACA---TA 1042
                         i ii  i  ii vv    i  v v    vvv i      i-    ---i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_63051335_6   1043 CAGAATGGGAGAAAATTTTTGCAATCTATCAATCTGTCAAAGGTCTAATA 1092
                                         v       vii  vv     vi  i  v  vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_63051335_6   1093 TCCAGAATCTACAAGGAACTTAAACAAATTTATAACAAA----CAAACAA 1138
                                 v  i  i     ivv    v iv    i   ----    i  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_63051335_6   1139 CCCCATTAAATAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAG 1188
                            v   ?  v i           iv    i     i     v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_63051335_6   1189 ATAT-----T-----ATACATTTATGAAAAAAAGTTCAACGTGACTGATC 1228
                             ----- -----   viivi       i v i     i v ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_63051335_6   1229 AT 1230
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.44 (114 / 79)
Gap_init rate = 0.02 (12 / 749), avg. gap size = 2.42 (29 / 12)  

2888 23.21 4.97 1.73  chrX_63051335_63055954     3264  4129 (491)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_63051335_6   3264 ATGCTCATGGGTTGGAAGAATAAATTTT----------CA-TACTACCCA 3302
                            i      i        v v   v  ----------  -    v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_63051335_6   3303 AAGCAATGTACAGATTCAATGGAATTTGTATCAAAATCCCAGTGGCATTC 3352
                           vii  v           i v   iiv              iv  v  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_63051335_6   3353 TTCA-AGAAATTTTTTAAAAGC-----CTAAAATTTGTGTGAAACCATAA 3396
                           ii-       v--- v    -----        ii i  i  viii  
  L1M4_orf2#LINE/    115 TTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_63051335_6   3397 AAGACCCA-AATAGCCAAAAGAATTCTGTGAAAGAAGAATAAAGTTGGAG 3445
                         ii      -           v   ii  vi         i          
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_63051335_6   3446 ACATCAAACTTCCTGATTT-AAAATTGTATTACAAAGCTATAGTAACCAA 3494
                         ivv   v      ii    -    i -  i          i     i   
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAA 260

  chrX_63051335_6   3495 AACAGTATGGTACTGGCATTAAAACCAGGTACATAG-----TGGAACATA 3539
                         i     i            -  iivi  ii i    -----     i v 
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_63051335_6   3540 ATACAGA----AGACATAAATACAAAAATTTATGGTAACTTAATTTTTGA 3585
                           vv   ----   v     iv  v v         v v  i     i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_63051335_6   3586 CAAGGGCATCAAGAGTACACAATGAAGAAAAAATACTCTCTTCAATAAAC 3635
                               iii     vi iv     ii    i    v   i     i   i
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_63051335_6   3636 GGTGCTTGGAAAACTGGATTTCCACATGCAAAATAATAAAAATTTTACCT 3685
                               v   v        v?            v   i  i-  vv   i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG-TTGGACCC 458

  chrX_63051335_6   3686 CTGTCTTACATCATACACAAAC-TCAACTCAAACAGGATAAAAGACTCA- 3733
                           ii  i   i    i     v- i        vv    v ?    ii -
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_63051335_6   3734 -TATAGGA-CAAGAACCTATAAAACTCCTAGAAGGGAAAATAGAGGAAAA 3781
                         - i  i  - v i   -          i      ii  v    i? v   
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAAC-TATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_63051335_6   3782 TCTCCTGGACTTTGGCTTTGACAATATTTTTTTAAAATATCACTGCAAAA 3831
                            i vv   i    v  v i    iv   i   i -   v  vv     
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAA 606

  chrX_63051335_6   3832 GTTCAGACCACAAAAGCAAAAATA----AGTGGGACTAAATCACACACAA 3877
                          iv  ii v       v       ---- i v     vv    v - iv 
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA-ATTA 655

  chrX_63051335_6   3878 AAAACCTT----CTTCACATCAAGGAAACAATTAACAAAATGAAATGGCA 3923
                              i  ----     ----     v  v  i  v   i     v i  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCA----AAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_63051335_6   3924 GCCTATAGA-TGGAAACAAAATTATTTGCAAGCCATATATTTGATAAGGA 3972
                         i  i i   -   i i-     -        ii       i        i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAG-AAAAT-ATTTGCAAATCATATATCTGATAAGGG 749

  chrX_63051335_6   3973 GTTAACAACAAAAAATTATAAAGAACTTATACAACTCAGTAGTGGGAAAA 4022
                         ii vii v v i  vv           iv         i  i iii  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_63051335_6   4023 CAAATAACCCAATTTAAAAATGGCCAAAG-ACATGATT-GATATTTCTCT 4070
                                       ?        v     - iv   v -  i       i
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_63051335_6   4071 AAAGAAAATACAAAATTGGCTAACAGGTGTATGAAAAGGTGCTCAATATA 4120
                               i   i v  v    i  i i iii        i       i  v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_63051335_6   4121 ATTATTCAT 4129
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.59 (121 / 76)
Gap_init rate = 0.03 (26 / 894), avg. gap size = 2.23 (58 / 26)  


3091 27.12 0.88 0.77  chrX_63060655_63066738.rev     4687  5593 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63060655_6   4687 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATAGTGAAAAT 4736
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63060655_6   4737 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 4786
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63060655_6   4787 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAGGTTCA 4834
                          v   iivi i  i  ii     -   -- v  i  - iii   ii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_63060655_6   4835 TATGGAACCAAAAATAGAGCCCGCAACA-CCAAGTCAATCCTAAGCCAAA 4883
                                viiv  i-- ii   iv  i -    iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_63060655_6   4884 AGAACAAAGCTGGAGCTATCACGCTACCTGACTTCAAACTATACTACAAG 4933
                                  i     vvv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63060655_6   4934 GCCACCCTAACCAAAACAGCATGGTACTGGTACCAAAACAGA--TATAGA 4981
                           i  vv   i   i    ii         i iv ii i   --      
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_63060655_6   4982 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAA 5029
                         i        i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_63060655_6   5030 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATC 5079
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_63060655_6   5080 TCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5129
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_63060655_6   5130 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5179
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_63060655_6   5180 TATTAAAGACTTAAGTGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5229
                         v  i ?    i   i   v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_63060655_6   5230 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5278
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_63060655_6   5279 TAAAACACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5328
                           vi    i       vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_63060655_6   5329 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5378
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_63060655_6   5379 AACAGGCAACCTACAGAATGGGAAAAAATTTTTGCAATCTACTCATCTGA 5428
                           v  i     i           i     v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_63060655_6   5429 CAAAGGTCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5478
                         i  i  v  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_63060655_6   5479 AAAAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACAC 5528
                             i     i     v  i? v  i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_63060655_6   5529 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5578
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_63060655_6   5579 ATCATCACTGGCCAT 5593
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2594 26.46 2.43 2.32  chrX_63068682_63072267.rev     2189  3095 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63068682_6   2189 TAAAAAAGCATTCCAGGGTCATGGACCGGAAGAATCAATATCATTAAAAT 2238
                          ii   iii  i   v v       ii      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63068682_6   2239 GGCCATACTGCCCAAAACAATTTATAGATTCAATACTATTCCCATTAGAC 2288
                            v     v      vii  i  i        ii v  i  i  i i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63068682_6   2289 TACCATTGGGATTCTTCACAGAACTAGAAAAA--AATATTTACAAATCCA 2336
                          v   viv vv  i  ii     v v  v  i--i  -ii  -    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTA-AAATTCA 148

  chrX_63068682_6   2337 TAAGGAACAACAACACCAAAAATCCCAGA-TAGCCAAGGCAATCCTAAGC 2385
                           v    ----- ii v iii -      -       ii     i i iv
  L1M4_orf2#LINE/    149 TATGGAA-----ATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_63068682_6   2386 AAAAAGAACAAAGCTGGAGGCATCACACTACCCAACTTCAAACTATGCTA 2435
                           i          i      vv       v     i      viv i   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_63068682_6   2436 CAAGGATACAGTAACCAAAACAGCATGATACTGGTACAAGAACAGGCACA 2485
                            i v        i   i    ii  i      i i   i i  i  i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_63068682_6   2486 TGGATAAATGCAACAGAAGAGAGAACCCAGAAATAAGACTGCACACCTAC 2535
                          i   v    v  i    vv    ii          iv iii   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_63068682_6   2536 AAGTATCTCATCTTCTACCTGA---CTAAAACGAG-CACTGGGGAAAGAA 2581
                         iivi vi v  i   v  vv i--- i  i  v v-  v           
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_63068682_6   2582 TTCCCTATTCAATAAATGATGCTGAGATAACTGGCTAGCCAAAATCAGAA 2631
                          vvi  v     i     i     i  i      v  ?   v vv  i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_63068682_6   2632 GATTGAAACTGGACCCCCTTCCTTACACCATATACAAAAATTAACTCATG 2681
                           v    ii        - v   i                        vi
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_63068682_6   2682 ATGGATTAAAGACTTAAAGGTAAAATCCAAAATGATGAAAACTCT-GGAA 2730
                               i ?    i    v    i v i    iv  -        -i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAA 540

  chrX_63068682_6   2731 GACAACCTAAGCA-AAATCATTTAGGACATAGACACAGGCAAAGATTTCA 2779
                           v   v  i ?i-     -  iiv   v v ivvi      v i    v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_63068682_6   2780 TGACAAAGTCACCAAAAGCAATTAAAGTTGCAACAAAGCAAAT--TTGAC 2827
                          iivv v v           --i  ----        iv   v-- v  i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCA--CAA----GCAACAAAAGAAAAAATAGAT 633

  chrX_63068682_6   2828 AAATTG-ATCTAATCAGACTAAAGAACTTCTGCACAGCAAAAG----CAT 2872
                               - ii v    i v v  i     i  ii vv    i ----i  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_63068682_6   2873 CAACAGAGTAAACAGACAACCTACATAATGGGAGAAAATTTGTGCAAAC- 2921
                            v i   i  v        i   v             v v      i-
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_63068682_6   2922 -TGGATCTGACAAAGGTCTAATATCCAGCTTCTATAAGGAACTTAAACAA 2970
                         - iv      i  i  v  vi       vv v     i     ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_63068682_6   2971 ATTTACAAGAAA----CAAACAACCCCATTAAAAAGGGGGCAAAGGACAG 3016
                         v iv i  v   ----    i     v   ?    iv          ivv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_63068682_6   3017 GAACAGATGCTTCTCAAAAAAAAAAAAATACATGTGGCCAATAATCACAT 3066
                            i   iii     v   i  i v --    vi          v     
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATA--TACAAATGGCCAATAAGCACAT 881

  chrX_63068682_6   3067 AAAAAAAAAAGCTCAACATCACTGATTGT 3095
                         i    i v--           ????????
  L1M4_orf2#LINE/    882 GAAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.95 (43 / 22)  


3132 27.86 0.44 0.44  chrX_63082013_63094412      492  1399 (11001)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_63082013_6   1399 TGAAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAGAAT 1350
                           i   i i  i     i      i v      v i     i  v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_63082013_6   1349 GGCCATACTGTCCAAGGTAATTTATACATTCAATGCCGTTCCCATCAAGC 1300
                            v     vi    iv i  i  i v      i  vi i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_63082013_6   1299 TACCAATGACTTTCTTCACAGAATTGGAAAAACCTACTTTAAAGTTCATA 1250
                          v   iivi i  i  ii     v v  v  i iv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chrX_63082013_6   1249 TGGAACCAAAAAAGAGCCCGCATCTCCAAGTCAATCCTAAGACAAAAGAA 1200
                              viiv  ii  v  v v  vv    iv     i i i v i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chrX_63082013_6   1199 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 1150
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chrX_63082013_6   1149 CAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGAGATATAGACCAA 1100
                               i   i    ii        vi iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

C chrX_63082013_6   1099 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACCTT 1052
                              i    i--    i  --        vv   i i  i  iiii vv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

C chrX_63082013_6   1051 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 1002
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

C chrX_63082013_6   1001 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 952
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

C chrX_63082013_6    951 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATAGATT 902
                          ii    i    v   i     v              i    i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

C chrX_63082013_6    901 AAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 852
                          ?    i    ii v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

C chrX_63082013_6    851 AGGCA-ATACCATTCAGGACTTAGGCATGGGCAAGGAGTTCATGTCTAAA 803
                            ?i- v i -   iv   i v  vv i     v iv   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

C chrX_63082013_6    802 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 753
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

C chrX_63082013_6    752 TAAACTAAAGAGCTTCTGCACAGCGAAAGAAACTACCATCAGAGTGAACA 703
                         i   v v  i i   i  ii vv i  i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

C chrX_63082013_6    702 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTCCT-CAGCTGACAA 654
                          i     i                 v       -v  v -i v    i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATAA 746

C chrX_63082013_6    653 AGGGCTAATATGTAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 604
                         i  i  vi   vi     v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chrX_63082013_6    603 ACACAAAAAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 554
                          v     v     v  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chrX_63082013_6    553 TCAAAAGAGGACATTTATGCAGCCAACAGACCCATGAAAAAATGCTCATC 504
                           v     i  i  vi viii     i ii v        i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chrX_63082013_6    503 ATCACTGGCCAT 492
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (146 / 103)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  

3012 26.00 1.89 1.00  chrX_63082013_63094412    11009 11908 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63082013_6  11009 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGTAAAT 11058
                               i i  i     i        v      v i     i  vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63082013_6  11059 GGTCATACTGCCCAAAGTAATTTATAGAGTCAATGCTATCCCCATCAAGC 11108
                           iv     v      v i  i  i   v    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63082013_6  11109 TACCA-TTGACTTTCATCACAGAATTAGAAAAAAGAACTTTAAATTTCAT 11157
                          v   -i  v    i- ii     v v  v  ivvi iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_63082013_6  11158 ATGGAACCAAAAAAGAGCCTGCATATCCAAGAAAATCCTAAGCAAAAAGA 11207
                               viiv  ii  v  v v   v    i v    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_63082013_6  11208 GCAAAGCTGGAAGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 11257
                         i     i    i vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_63082013_6  11258 ACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 11307
                            i   i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_63082013_6  11308 ATGGAACAGAAC--AGACGCCACAGAAATAATACCACACATCTACAATCA 11355
                               i    i--   - i -         vv   i    i  iii   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGA-GTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chrX_63082013_6  11356 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCCC 11405
                         vi    i  i     ivv  v   i v  vv       i    i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_63082013_6  11406 TATTTAATATATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 11455
                          v  i  i v      i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_63082013_6  11456 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAGCTCAAGATGGAT 11505
                           ii    i    v   i     v             i     i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_63082013_6  11506 TAAAGACTTAAACATAATACCTAAAACCATAAAAACCCTAGAAGAAAACC 11555
                         i ?    i    ii   v v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_63082013_6  11556 CAGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCATGTCTAA 11604
                         i   ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_63082013_6  11605 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTAA 11654
                         i            vvi          vv     v  i    v i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_63082013_6  11655 TTAAA-CTAAAGACT---GT-CTTCATAGCAAAAGAAACTATCATCAGAG 11699
                          i   -i    i   ---  -     -----  i  v       vv i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCA-----AAGGACACTATCAAGAAAG 691

  chrX_63082013_6  11700 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTGTCCATCT 11749
                             v  i     i                 v       viii vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_63082013_6  11750 AACAAAGGGCTGATATCCAAAATCTACAAATAAC----A-AACTAATTTA 11794
                         i i  i  i  vi      i   v  i   v   ---- -    v v v 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_63082013_6  11795 CAAGA-GAAAAACAACCCCATCAAAAAGTGAGTAAAGGATATGAACAGAC 11843
                         i  i -  v   i     v  i?    i  i i       v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_63082013_6  11844 GCTTCTCAAAAGAAGACATTTATGTGGTCAACAA--ACATGAAAAAAAGC 11891
                         ii     v        i  vi vi   i   i  --         i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_63082013_6  11892 TCATCATCTCTGGTCAT 11908
                            v    v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (135 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  


1188 28.27 0.00 0.00  chrX_63109577_63119432.rev     1079  1407 (8449)  C L1M4_orf2#LINE/L1   (201)   707   379  

C chrX_63109577_6   1407 CAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCT 1358
                                     i  vvi  v  i  i              v      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

C chrX_63109577_6   1357 AGTCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAA 1308
                          ?i  i   i i  iiv    ii    i    v   i     v       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

C chrX_63109577_6   1307 AAATCAATTCAAGATGGATTAAAGATTTAAACGTTAGACCTAAAACCATA 1258
                             i  i    i      i ?   ii    i  v   v       i   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

C chrX_63109577_6   1257 AAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCGTGGG 1208
                            vi i           v    ?i v viv   iv   v v  vv i  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

C chrX_63109577_6   1207 CAAGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAAAAGCCAAAA 1158
                            v ii   v ivvi vi            vvi          vv    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

C chrX_63109577_6   1157 TTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAA 1108
                          v  i    v   ii v  i   v v  i i   i  ii vv    i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

C chrX_63109577_6   1107 ACTACCATCAGAGTGAACAGGCAAGTTAC 1079
                             i  vv i      v  i   vii  
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCAC 707

Transitions / transversions = 1.20 (49 / 41)
Gap_init rate = 0.00 (0 / 329), avg. gap size = 0.00 (0 / 0)  

 732 23.32 0.00 0.00  chrX_63109577_63119432.rev     1413  1605 (8251)    L1M4_orf2#LINE/L1      716   908 (0)  

  chrX_63109577_6   1413 AGAAAATTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATC 1462
                                v       vii ivi      i  i  i  vi          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_63109577_6   1463 TACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAA 1512
                           i  v      vv    v iv i  v     i     i     v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_63109577_6   1513 AAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATG 1562
                            i           iv    i     i     v        i  vi vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_63109577_6   1563 CAGCCAAAAAACACATGAAGAAATGCTCATCATCACTGGCCAT 1605
                         ii     v  i        i i       v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (26 / 18)
Gap_init rate = 0.00 (0 / 193), avg. gap size = 0.00 (0 / 0)  

3051 26.79 0.76 2.28  chrX_63109577_63119432.rev     6142  7063 (2793)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63109577_6   6142 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 6191
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63109577_6   6192 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 6241
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63109577_6   6242 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6289
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_63109577_6   6290 TATGGAATCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 6339
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63109577_6   6340 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6389
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63109577_6   6390 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGATC 6439
                                 i   i i  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63109577_6   6440 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTGCAACT 6487
                                i    i--    i  --        vv   i i  i iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_63109577_6   6488 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 6537
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63109577_6   6538 CTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCT 6587
                           v  i  i              v  i   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63109577_6   6588 GAAACTGGATCCCTTCCTTACACCAGGGATAATGGATGAATTTAATCCAT 6637
                            ii    i    v   i      viv i  -----i    --------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAA-----AAATT-------- 483

  chrX_63109577_6   6638 CAATTCAAGATGGATGAAAGACTTAAACGTTAGACCTAAAACCATAAAAA 6687
                         -  i    i      v ?    i    i  v   v       i      v
  L1M4_orf2#LINE/    484 -AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_63109577_6   6688 CCCTAAAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAG 6737
                         i i  i        v    ?i v viv   iv   v v  vv i     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_63109577_6   6738 GACTTCATGTCAAA---AACACCAAAAGCAATGGCAACAAAAGCCAAAAT 6784
                          ii   --- i i ---i            vvi          vv     
  L1M4_orf2#LINE/    583 GGTTTC---TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_63109577_6   6785 TGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAA 6834
                         v  i    v   ii v  i   v v  i i   i  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_63109577_6   6835 CTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCACA 6884
                            i  vv i      v  i     i   i             v  ii  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_63109577_6   6885 ACCTACTCATCTGACAAAAGGCTAATATCCAGAATCTACAATGAACTCAA 6934
                          vii ivi      i  ii i  vi          v  i  v      vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_63109577_6   6935 ACAAATTTACAAGAAAAAAACAAACAACCCCATGAAAAAGTGGGCAAAGG 6984
                             v iv i  v     i     i     v  v?    i          
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_63109577_6   6985 ACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACAC 7034
                          iv    i     i     v        i  vi viii     v  i   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_63109577_6   7035 ATGAAAAAATGCTCACCATCACTGGCCAT 7063
                                i       v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.11 (28 / 9)  

2414 25.68 3.81 5.22  chrX_63109577_63119432.rev     8447  9365 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_63109577_6   8447 GAGAAACATAATGTGTTCATGGGTTGGAAGATTCAGTATCGCTAAGATT- 8495
                           i i i  vvii         i        i i i   i i      v-
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_63109577_6   8496 CAATTCTCTA-AAATTGATCTATAGATATGACACAATTCTGATCAATATC 8544
                             v   iv-           i    vii  i    i iv     v   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_63109577_6   8545 CTAG-TATGATTTTTGTATATATAGACAAGCATATTCTAAAATTTAAATG 8593
                          i  - iivv      i v v  v       vv  i        i v   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_63109577_6   8594 AAAGGACAGAGAAACTAGACTCACC----CAATCTTGATAAAAGAA---- 8635
                         i  ivi  ii i v i   v vi  ----         -       ----
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAGAAC 201

  chrX_63109577_6   8636 AAAGTTGCAGAACTTAAACTACTTGACTCTAAGACTTACTGTAAAGTTAG 8685
                                v  i   i v   v iii i ii  i       ii    i  v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_63109577_6   8686 AGTAATCGAGATAAGATGGTGTTGG--TGACTGGATAAACACATGGAATG 8733
                                i   i ivi    ii   -- i --     i   i  i  vii
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAA--GGATAGACATATAGATCA 299

  chrX_63109577_6   8734 -TGGACCAGAATAAAGAACACAGATATAGTTTCACAAATT-ATGGCCAAC 8781
                         -    vi     vi   iiv    v   ivii  i v   -    i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_63109577_6   8782 TGATTTTTGACAAAATTAA-AAGAACATTTCAATGAAGGAAAGATAACCT 8830
                                i     iiv iv-    v    -     ii i  ii   ii  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAGTCT 398

  chrX_63109577_6   8831 TTTAAAACAAATGATGATAGAGCAATTGTTTACATCCATAAGAAGAAAAA 8880
                            v  -      i  v i ii   i  v-- i ?   i v v i  i  
  L1M4_orf2#LINE/    399 TTTCAA-CAAATGGTGCTGGGACAACTGG--ATAKCCACATGCAAAAGAA 445

  chrX_63109577_6   8881 AAATTTTTAAAG--GAAACAATATAAACCCCACATCTTATACGAATATTA 8928
                         ------- i   -- i v vv  ----  i    i v     i  v    
  L1M4_orf2#LINE/    446 -------TGAAGTTGGACCCCTA----CCTCACACCATATACAAAAATTA 484

  chrX_63109577_6   8929 ACACGAAACAGATCACATATTTAAATATAAAACATAAAACTTTAAAAGTT 8978
                           v i   ii     ? v ii     i   i vv       v     v i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_63109577_6   8979 TGAGAAGAAAACTCAAGAGAAAAATCTTTGGGACCTAGTGCTTTGTGAAG 9028
                          v          vi i ? v   -    i v     v v i vv ii v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_63109577_6   9029 AGTTCTCACACAAGACATCAAAAGCATTGTGAACAGTTCTTAGACAAGAC 9078
                         iv    i v i v    i        ------------------    - 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCA------------------CAAG-C 614

  chrX_63109577_6   9079 ATCAAAAGCGTAATTCATTAAAA-AAATAAATTGGACTTTGTCAAAATCA 9127
                          v      ---  ------    - i             ii       i 
  L1M4_orf2#LINE/    615 AACAAAAG---AA------AAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_63109577_6   9128 AAA-CTTCTACTCTTCAAAAGATCCTATTAAGAGAATGAAAAGATAAGCT 9176
                            -   i iiv       i  iv    i    i i        i  v i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_63109577_6   9177 ATATACTGAGAGAAAATATTTGTAAACCACATATCTGACAAAGAACTAGT 9226
                          i v v  i             i   i  i        i  i i   v  
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_63109577_6   9227 GTCTAAAATA------GAGTGTTCAAAATTCAGCAA---------AAATG 9261
                         i  i i    ------  iivi i v  i   ii  ---------    -
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT- 804

  chrX_63109577_6   9262 AATCCAATTAGAAAACGGGCAAAAGACATGAACAGACATTTCACTAAAAA 9311
                           i      ?i    i       i  iv    i         v i   i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_63109577_6   9312 GAATATACAGATGTTAAATAAACACATGAAAAGAAGTTCAACATCATTAG 9361
                         ii       i   viv     i            v i         ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_63109577_6   9362 CTAT 9365
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.01 (155 / 77)
Gap_init rate = 0.03 (27 / 906), avg. gap size = 3.07 (83 / 27)  


2989 24.59 2.19 2.95  chrX_63120069_63126362.rev      732  1646 (4648)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63120069_6    732 TGCAAATATATCGCATATTTATGGATTGGAGGAATCAATATTGTTAACAT 781
                           v   v     v   i  i          i  v i           v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63120069_6    782 GTCCATACTACCCAAATCAATCTACAGATTCGAAACACTCTCTGTCAAAA 831
                          v v     v       ii            i vi  v  i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63120069_6    832 CACTAATGGCAATCTTCACAAAAACAGAAAAAATAAATCCTAAAATTTAT 881
                         iv i iiv  vv i  ii  i   iv  v  iv i -          i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_63120069_6    882 ATGTAACCACAAAAGACCCAGAATAGCCAAATCTATCCTGAGGGGAAAAA 931
                            v  vii   ii                 v v   i   ---------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--------- 190

  chrX_63120069_6    932 AAAAAAAAAAAAAAACATAAAAAAACTCTAGGAATCACATTACCTAACTT 981
                         -----    i  i    -----  ii vv    v     i v  i  i  
  L1M4_orf2#LINE/    191 -----AAAAGAAGAACA-----AAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_63120069_6    982 CAAATTATATTACAGAACTATAGCAAAAAAAAAAAAAAGACATGGTACTG 1031
                             viv  i    i i   i  i  vv  i v i-----ii        
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAG-----TGTGGTACTG 275

  chrX_63120069_6   1032 ATATAAAAACAGAGACATAGACAAATGGAACAGGATAGAGAACCCAGAA- 1080
                         ii    ii i   v i     iv       i  i  v    ii      -
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_63120069_6   1081 CAAATATATACATCAACAGTAAAGTCATTTTTGACAATGTTGCCAAGAAC 1130
                         i   ivi      iv ii  v  v v     i     v v        v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_63120069_6   1131 ATAAACTGGGGAAAGGACTGTCTCTTTAATAAATGGTACTGGAAAAACTG 1180
                           vv v         i iv    i  i  i       i    i v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_63120069_6   1181 AATATACTTATGCAGAAGAATGAAACTAGACTTCTAC------------- 1217
                         i   ?v vi     i         ii i   ii    -------------
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_63120069_6   1218 -AAAAATCAAATCAAAATAGATTAAGGACTTATATCTAAGACCTTAAACT 1266
                         -      i  v       i   i ?i   i  v  v     v  v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_63120069_6   1267 ATGAAACTACTATAA--AAACATTGGGGAAACTTTCCAGGACATTGAGCT 1314
                           i     vi  v  --      v  ? v  v i i iv   v   i i 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_63120069_6   1315 GGGCAAATATTTCTCAAATAATACCCCACAAGCACCGGCAATCAAAGCAA 1364
                         i     vvi     i i   vv  v   v      vi    iv    v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_63120069_6   1365 AAAT-GATCAAATGGGATTACAT-GAAGTAAAAAACTGTCTGCACAGCAA 1412
                             -   -    v   i v   -i  i v       - i  ii vv   
  L1M4_orf2#LINE/    626 AAATAGAT-AAATTGGACTTCATCAAAATTAAAAACT-TTTGTGCTTCAA 673

  chrX_63120069_6   1413 AGGAAATAATCAACAAAGTGAACAGACAACCCACATAATGGTAGAAAATG 1462
                             v iv     v        v            v     v       i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_63120069_6   1463 TTTGCAAGCTATCTGTTTGACAAGGGATTAATAGCGAGAACATATAAGGA 1512
                                iii  v i i   i      i vi  v v    i      i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_63120069_6   1513 GC-CAAACAACTCTATAGGAATAAATCAAATAATCCAATTTAAAAATGGA 1561
                         i - vv       v   iv  v  iv       i      ?        i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_63120069_6   1562 CAGAAAATATGAATAGACATTTCTCAAAAGAAGACACACAAATGGCAAAC 1611
                           i ii  v                v        i i         v  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_63120069_6   1612 AGGTATATGAAAAGGTGCTCAACATCACTGATCAT 1646
                          i i i        i            ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (128 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.92 (47 / 12)  

2852 27.16 1.55 0.89  chrX_63120069_63126362.rev     4902  5803 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63120069_6   4902 TGGAAAAATATTCCATGCTCATGAGTAGGATGAATCGATATTGTTAACAA 4951
                               i    i     i     ii v   v  v ii          v v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63120069_6   4952 GTCCATACTGCCCAAAGCAATTTACAGATGTAATGCTATCCTTA-CAAAA 5000
                          v v     v      vii  i       vi  i  v    i  -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63120069_6   5001 TTTCCAATGGCATTCTTCACAGAATTAGAAAAACT-ATTTTAAAATTCAC 5049
                          i-   iiv  v  i  ii     v v  v  i  -  ii         i
  L1M4_orf2#LINE/    101 TC-CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_63120069_6   5050 ATGAAAACAAAAAGGAGCCCAAATAGCCAAGGCAATCCTAAGCAA-AACA 5098
                            i   iiv  i   v  vi         ii     i i iv  -  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_63120069_6   5099 ACAAAGTGGGTGACCTAACACTACCTGAATTCAAAATATACTATAGGGAT 5148
                                v  v iv  v     v  ii v       iv     i ii v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_63120069_6   5149 ACAGTAACCAAAGC-GCATGGTACTGGTACAAAAACAGGCACATAAACCA 5197
                                i   ii - ii         i i  ii i  i  i   i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_63120069_6   5198 ATGGAACAGAATAGAGAGCCCAGAAAGGAGGTGGCATGC--CTACAACCA 5245
                               i     v     i       vi ivi--   i --i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCA 347

  chrX_63120069_6   5246 -TAGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGTATTCCC 5294
                         - v   i  i     ivv  v   i v  vv            v  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_63120069_6   5295 TATTTAATAAATGGTGCTGGAAGAGCTGGCTAGCCATATGCTGAAAAATA 5344
                          v  i  i            i v i    v  ?   i    vi  i   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_63120069_6   5345 AAACTGTTCTCCTTCCTTACACCATATACAAAACTTAATTCGAGATGGAT 5394
                           ii  vv i   v   i               v    i  i i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_63120069_6   5395 TAAAGACTTAAATGTAA------AAACCATAAAAACCATAGAAAAAGTTC 5438
                         i ?    i         ------    i      vi v     i  iviv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_63120069_6   5439 TAGGCAATACTATTCATGACATAGGCATGGGCAAAGGTTTCAT-GATGAA 5487
                             ?ivv v v   i    v v  vv i     v      v -   - v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chrX_63120069_6   5488 GACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGACCTAA 5537
                                      vvv          v      v  i    v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_63120069_6   5538 TTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTATTATCATAGTGAAC 5587
                          i   v v  i i   i  ii vv v  i  v     i vv v      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_63120069_6   5588 AGACAACCTACAGAATGGGAGAAATTTTTTTTTCAATCTATCCTTCTGAC 5637
                                 i               v v   v--   vii  viv     i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTG--CAAATCATATATCTGAT 744

  chrX_63120069_6   5638 AAACGTCTAATATCCAGAGTCTAAAAGGAACTTAAACAAATTTACAAGAA 5687
                           iv v  vi        i v  v  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_63120069_6   5688 ACAAGCAAACAGCCCAATTAAAAAGTGGACAAAGGACATGAACAGACACT 5737
                          v ii    i i       ?    i   i       iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_63120069_6   5738 TTTCAAAAGAAGACATCCACGCAGTCAAAAAAACATATGAACAAAACCCT 5787
                          i  v        i  v  viii i   v  i-  i     -  i iv  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAA-AAGATGCT 892

  chrX_63120069_6   5788 CAACATCACTAATCAT 5803
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (136 / 105)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.57 (22 / 14)  


4067 19.62 2.00 1.33  chrX_63130868_63133237      976  1877 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63130868_6    976 TGGAAATTCATCCTGTGTTCATGCATAGGAACACCTAATACTGTAAGGAT 1025
                               vvi    ii        v  v    v  i     i   v i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63130868_6   1026 GACAATA-TCCCCAAAGTGATTGATGGAT-----GCAATCCCTATCAGAA 1069
                          i     -        v    iv ii   -----             i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63130868_6   1070 TTCTAATGGCTTTTTTTTTTTTTTTACAGAAATGGAAAATATGGCCCTAA 1119
                          i i iiv  i      --------i       v  v  vv  ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--------GCAGAAATTGACAAGCTGATCCTAA 142

  chrX_63130868_6   1120 AATTCATATGGAATCTCAAGGGACCCTAAGAAG-TGAAACAATCTTGAAA 1168
                                      viv          vi iv  -ii              
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_63130868_6   1169 AAGAA---CACAGTTGGAGGATTCACACTTTCTGATTTCAAAACCTACTA 1215
                              ---  v          i        i ii          i     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_63130868_6   1216 CAAAGTTACAGTCATCAAAACAGTGTGGCACTGGCCGAAGGACAGACTTA 1265
                              i      v     i         i      vv     i    v  
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_63130868_6   1266 TAGACCTTTAGAATAGAATGGAGATCCCCAAAATAAACCCTCACCTGTGT 1315
                             i vv i         v    vi  vi          vi  v v i 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_63130868_6   1316 GGTCAATTGATTTTTGACAAGGATTCCAAGACCATTCAATTGAGAATGGA 1365
                                       i       i v               v i   v i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_63130868_6   1366 CAGTCTTTTCAATAAATGGTGCTGGAAAAACTGGATATCCATTTCCAAAA 1415
                         i           i            i v         ?   iv v     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_63130868_6   1416 TAATGAAGTTGTACCCTTACCTTACATCACACACAAAAAAAATTAG-TGA 1464
                         v          v    i     i   i  i i       ---   i- v 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA---TTAACTCA 489

  chrX_63130868_6   1465 AAATGGATAAAAAATCTAAATATAAGAGCTAATAGTATAAAACTCAAGGA 1514
                                 v ? i i      i          v v          vvi  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_63130868_6   1515 AAAAAACCATAG---CAAATCTTCACAATATTGATTTTGGCAATGATTTC 1561
                          i     -    ---i        iii iv   iv  v       i    
  L1M4_orf2#LINE/    540 AGAAAAC-ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_63130868_6   1562 TTGGATATGACATTCAAAGCACTAGCAACAAAAGAAAAA-CAGATAAACT 1610
                           i         iiv       v                -i       i 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_63130868_6   1611 GTACTTTATCAAGATTAAAAGTATTTTTTAATCAAAGAACACTGTCAAGG 1660
                          v    i     i       iiv   v vvv      i     i     i
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_63130868_6   1661 AGGT-AAAATATAACCCTCAGAAAGGGAGAAAATATTTGCAAATAATATA 1709
                          i  -    v i     v     v                    v     
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_63130868_6   1710 TCTGACAAGTAATTAATATCCACAATATATGAAGAACTCCTCCAAGTCTA 1759
                              i   vi i vi      v       i        i v   v  v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_63130868_6   1760 TTGTAACAA-CCAAA-AATGCAATTAAATAATGGACAATGAACTTGAACA 1807
                          vi   v  -v    -  iv     ?  v     i   v i i     i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_63130868_6   1808 GACATTTTTCCAAAGAAGACATACAAGTTCTCAATAAGCATATCAAAAGA 1857
                                i           i      i vvi         i  v      
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_63130868_6   1858 TATTCAATGTCACTAGTTAT 1877
                          ii    ii   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (100 / 74)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.31 (30 / 13)  


3250 26.35 0.77 0.66  chrX_63135031_63141308.rev     4881  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63135031_6   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4930
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63135031_6   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATTAAGC 4980
                            v     v     iv i  i           i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63135031_6   4981 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5029
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_63135031_6   5030 TGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTGAGCCAAAAGAA 5079
                              viiv  ii  v  v v  vi    iv     i   ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_63135031_6   5080 CAAAGCTGGAGGCATCACACTACGTGACTTCAAACTATACTACAAGGCTA 5129
                              i      vv       v vii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_63135031_6   5130 CAGTAACCAACACAGTATGGTACTGCAACCAAAACAGAGATATAGACCAA 5179
                               i   v     i        vv iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_63135031_6   5180 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAGCCAT 5227
                              i    i--    i  --        vv   i    i  ii i  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_63135031_6   5228 CTGATCTTTGACAAACCTGAGAAACACAAGCAATGGGGAAAGGATTCCCT 5277
                         i    i  i     ivv  vv  ivv  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_63135031_6   5278 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTTGA 5327
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_63135031_6   5328 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGGTGGATT 5377
                          ii    i    v   i     v           i  i    ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_63135031_6   5378 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAATCT 5427
                          ?    i    i  v   v       i      vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_63135031_6   5428 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTGAAA 5477
                            ?i v viv   iv   v v  vv i     v ii   v ivv ivi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_63135031_6   5478 CACCAAAAGCAATGGCAACAAAAGCCTAAATGGACAAATGGGATCTAATT 5527
                                    vvi          vvv    i  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_63135031_6   5528 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5577
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_63135031_6   5578 GCAACCCACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAG 5627
                         i         i             v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_63135031_6   5628 GGCTAATATCCAGAATCTACATTGAACTCAAACAAATTTACAAGAAAAAA 5677
                          i  vi          v  i vv      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_63135031_6   5678 ACAAACAACCCCATCGAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 5727
                              i     v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_63135031_6   5728 AAAAGAAGACAGTTATGCA----GCCAAAAAACACATGAAAAAATGCTCA 5773
                         v        ----   i  ----     v  i          i       
  L1M4_orf2#LINE/    849 CAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_63135031_6   5774 CCATCACTGGCCAT 5787
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (134 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.60 (13 / 5)  


3079 25.05 1.19 3.13  chrX_63156301_63160995     3277  4202 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63156301_6   3277 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATGTCATGAAAAT 3326
                              ii i  i     i        v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63156301_6   3327 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTGTCTCCATCAAGC 3376
                            v     v     iv i  i  i        i  vi  i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63156301_6   3377 TCC-AACTGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTAAAGTTC 3423
                            - i   v    i  -i    i-   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_63156301_6   3424 ATATGGAACCGAAAAAGACCCTGCATTGCCAAGACAATCCTAAGCAGAAG 3473
                                 vi v  ii     v v  v     i      i i iv ii i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_63156301_6   3474 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 3523
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_63156301_6   3524 CTACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGAGAGGTAGAC 3573
                                  i   i    ii        vi iv ii i   v vi    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_63156301_6   3574 AAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTAGAAC 3621
                         v       i    i--    i  --        vv   i    i  viii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_63156301_6   3622 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAATTATTC 3671
                           vi    i  i     ivv  v   i v  vv           vv  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_63156301_6   3672 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAAC 3721
                         i  v  i  i              v      v  ?   i   i--    -
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC--AAAA- 442

  chrX_63156301_6   3722 TGGCTAGCCATATGTAGAAAGCTGAAACTGGATCACTTCCTTACAACATA 3771
                         ----------------   ---    ii    i v  v   i   v    
  L1M4_orf2#LINE/    443 ----------------GAA---TGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_63156301_6   3772 TACACAAATTAACTCAAGATGAATTAAAGACTTAAATGTAAGACCTAATA 3821
                             v            i   i  i ?    i           v    v 
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_63156301_6   3822 CCATATAAACCCT-AGAAGAAAATCTAGGCA-ATACCATTCAGGACATAG 3869
                          i   -    i  -         iv    ?i- v i -   iv   v v 
  L1M4_orf2#LINE/    524 CTATA-AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chrX_63156301_6   3870 GCATGGGCAAAGCCTTCATGACTAAAACACGAAAAGCAATGGCAATAAAA 3919
                          vv i     v vi   v iiv  vi    v       vvi    i    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_63156301_6   3920 GCCAAAATAGACAAATGGGATCTGATTAAACTAAAGAGCTTCTGCACAGC 3969
                          vv        i    v   ii v  i   v v  i i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_63156301_6   3970 AAAAGAAATTATCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAA 4019
                            i  v i     vv i      v  i     i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_63156301_6   4020 TGTTTGCAATCTACCCATCTGACAAAGGGCTAATATCCAGAATCTAAAAA 4069
                          i       vii ivi      i  i  i  vi          v  v   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_63156301_6   4070 GAACTTAAACAAATTTACAAGAAAAAAACAA----CCCCATCAAAAAGTG 4115
                              ivv    v iv i  v     i    ----   v  i?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_63156301_6   4116 GGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCA 4165
                                   v    i     i     v        i  vi viii    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_63156301_6   4166 ACAGACATATGAAAAAATGCTCATCATCACTGATCAT 4202
                          i ii  i       i       v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (136 / 92)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  


3643 15.24 2.64 10.37  chrX_63170072_63173373.rev     1829  2812 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63170072_6   1829 TGGAAAGCTATCCCATGTTCATGAATTGGAAGACTTAATATTGTTAAGAT 1878
                                v               i                          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63170072_6   1879 AACATTAATCCCCAAATTGATCTACAGATTGCATATGGTCTCTATTAAGA 1928
                         ii  v  v                      vv iiiii  i    i  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63170072_6   1929 TCGCAGTTAAGTTATTTATTTTTTTGGTCTTTTTTAGTTTGTTTTGTTTT 1978
                           v   i ------------------ i       i--------------
  L1M4_orf2#LINE/    101 TCCCAGCT------------------GCCTTTTTTG-------------- 118

  chrX_63170072_6   1979 CCAGAAATTGACAAGTTGATTCTAAAACTCATATGAAAATGCAAGCAATC 2028
                         -              i    i      i       i         vi i 
  L1M4_orf2#LINE/    119 -CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_63170072_6   2029 CAAAA--GCCAAAAAGTTCTTGAAAGAGAAAAACAAATTTGGAAAAGTTA 2076
                           i  --       viv        i    i      v     ii v i 
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_63170072_6   2077 TA-TTCTCAATTTCAGATATGACTATAAAGTTACAGTAATCAAGAATGTG 2125
                         i -   i        i vv v    i    i              vv   
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_63170072_6   2126 TGATTCTGATATAAAGATGTATAGATAGATAGATGTAGATATAGATAAAT 2175
                           i v   ii    i   --------   i --------       v   
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGAT--------AGACA--------TATAGATCAAT 301

  chrX_63170072_6   2176 GGAATAAAACAGAAAGTCTAGAAATAAAACCTTATGTT-ATAGGTTGACT 2224
                               i  iv  i    i         v  v  ii  -  -   ii i 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT-GGTCAATT 350

  chrX_63170072_6   2225 GATTTTTGACAAGGGTGTCAAGATAATTCAGTGAGGAAA-AATAATCTTT 2273
                               i          i     iv     i  i     -    i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_63170072_6   2274 TCAACAAATGGTGCTATGTCAACTGGATTTCCACATACAAAAGAATGAGT 2323
                                        iv v         v?      i           iv
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_63170072_6   2324 TTGGGCCCTTACCTCACACCATATACAAAAATTAACTCAAAATAGATCAG 2373
                             i   i                                  i     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_63170072_6   2374 AGGCATACATGTAAAAGCTAAAACTGTAAAATTCTTATAAGAAAACATAG 2423
                           i v  v      i          i     i     v            
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_63170072_6   2424 GAGTAAATCTTTATGAACTTAGATTGGTATATATATACATATATATATAT 2473
                          ?         ii   v   i i  i ---------i  -----------
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAG---------GCA----------- 580

  chrX_63170072_6   2474 ATATATATATATATATATATATATATATATATATATGACACCATAAAGAG 2523
                         ------------------  i-i v v -  v           -    vi
  L1M4_orf2#LINE/    581 ------------------ATG-GTTTCT-TAGATATGACACCA-AAAGCA 609

  chrX_63170072_6   2524 CAAGCAACAAAACAAAACCAAAAATAGATTAACTGAACTTCATCAAAATT 2573
                                     v    -----       v  i  i              
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAA-----AATAGATAAATTGGACTTCATCAAAATT 654

  chrX_63170072_6   2574 AAAAA----TGTGCATTTAAAAACACTGTAAAGAAA-----AAGACAATA 2614
                              ----     v iv  ii     i v      -----       iv
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_63170072_6   2615 CACA-AATGGGAAAAAATAT----AAATCACGT--CTGATTTACTGTCTA 2657
                             -       i       ----      ii --     v- vv v  v
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA-AGGGACTT 753

  chrX_63170072_6   2658 GTATTCAGAGTATCTAAAGAACT-TTAAAACTCATCAATAAAAAGATAAA 2706
                             i    i   v         -   v      vi          i   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_63170072_6   2707 TAATAAAAAGTTTTAAA--TGGATAGAAAATTTGAATAGACGTTTCTCCA 2754
                            ivv  ---  ?   --   ii i ii            i        
  L1M4_orf2#LINE/    804 TAACCCAA---TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_63170072_6   2755 AAGAAGATATACAAATGGCCAATAAGCA-ATAATAAAATATGTTCAGCAT 2803
                                                     -  i --   v   i   i   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGA--AAAGATGCTCAACAT 898

  chrX_63170072_6   2804 -ATTTATTCA 2812
                         - ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.86 (95 / 51)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 4.74 (128 / 27)  


 553 16.11 6.71 1.34  chrX_63240373_63243013.rev      199   347 (2294)    L1M4_orf2#LINE/L1      672   828 (80)  

  chrX_63240373_6    199 AAAGAGAACCA--AATAAAGTGAAAAGACAACCCACAAAATGGTGGGAAA 246
                             iiv  i --  v                     i     vi i   
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_63240373_6    247 TATTTGACAACT--TTTATCTAATAAGGGTCTACTGTCTCAGA-TATAT- 292
                               -   v -- v     i       v  vv i  -    -     -
  L1M4_orf2#LINE/    722 TATTTG-CAAATCATATATCTGATAAGGGACTTGTATC-CAGAATATATA 769

  chrX_63240373_6    293 --GAACTCCTA-AACTCGACAACAAATAGACAAA-AACCTAATTTAAAAA 338
                         --      i  -     i i  i   v       -    i    ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_63240373_6    339 TGGGAAAAG 347
                             v    
  L1M4_orf2#LINE/    820 TGGGCAAAG 828

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.05 (8 / 157), avg. gap size = 1.50 (12 / 8)  

 217 17.57 2.70 16.22  chrX_63240373_63243013.rev      428   501 (2140)    L1M4_orf2#LINE/L1      214   277 (631)  

  chrX_63240373_6    428 CTCACCATTTCTA--TTCAAAACAGTACTGGAAGTCCGAGACAGAGCTAT 475
                              vv  i i --        -v    -----------   i     i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAAC-TTACT-----------ACAAAGCTAC 251

  chrX_63240373_6    476 AGTAATTAAAACAATGTAGTGCTAGC 501
                               i  i   i   i  i  i  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGC 277

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.05 (3 / 64), avg. gap size = 4.67 (14 / 3)  

 770 21.97 1.16 0.58  chrX_63240373_63243013.rev      502   674 (1967)    L1M4_orf2#LINE/L1      256   429 (479)  

  chrX_63240373_6    502 ATTAAAACAATGTAGTACTAGCATAAAAACAGACATGCAGACCAATGAAA 551
                           i  i   i   i     i      ii i      ii   i     i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_63240373_6    552 CAAAATAGAAATACCAGAAATAAATCCTCACATATATGGTTAAATTATCT 601
                         i i   v  i vv           i  vi    v      i  v v  i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_63240373_6    602 TCCACAAA--TGCTAAGGCCACTCAGTGGGGAAAAGGAGAGTCTTTTCAA 649
                           v    i--   i   i   i   i        - i v           
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTCAA 404

  chrX_63240373_6    650 AAAATGGTTCTGGCAAAACTGGATA 674
                         v       v    v v         
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATA 429

Transitions / transversions = 1.92 (25 / 13)
Gap_init rate = 0.01 (2 / 174), avg. gap size = 1.50 (3 / 2)  

2090 18.07 2.94 1.05  chrX_63240373_63243013.rev     1675  2150 (491)    L1M4_orf2#LINE/L1      424   908 (0)  

  chrX_63240373_6   1675 TAGACATTCACATACAAAAGAA----------CCCTTATCTTATATCATA 1714
                          i  i ?i     i        ----------   i  i  i i i    
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_63240373_6   1715 TACAAAAAATAACTCAAAATGGATTAAAGACCTAAATGTAAGACCCCAAA 1764
                                 v               i ?                v iv   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_63240373_6   1765 ATATAAAACTCCTAGAAGAAAACATAGAC-CAAATCTTCGTGACATGGGA 1813
                         v          i               i?-i             v v  i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_63240373_6   1814 TTTGGAAGTGATTTCATGGCTATGACATGAAATGCACAGGCAACAGAAGC 1863
                           v  v i  i    v i v       iv   v     i      i   v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_63240373_6   1864 AAAAATTGACAAATGGTAATACATCAAACTTAAAAACTTTTGTGCATCAA 1913
                               v  i    v v v v       v                v    
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_63240373_6   1914 AAATTAATATCAACAGAGTGAAAAGGCAACTTATGGAATGGTAGAAAACA 1963
                          iivi v      v i         i    ii ii      v      i 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_63240373_6   1964 TTTACAAATTATATATCTGATAAAGGGTTAATACCCAGAATA-ATAAAGA 2012
                            i     i             i  ii vi  i        -       
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_63240373_6   2013 ACTCCTACAACAAAACAACAATGAAACAAACCAAATAATA-AATTTAAAA 2061
                             i      v---   i   i   - i  -      iv-    ?    
  L1M4_orf2#LINE/    774 ACTCTTACAACT---CAATAATAAAA-AGAC-AAATAACCCAATTWAAAA 818

  chrX_63240373_6   2062 -TGTGCAAAGAACTTGAATAGACATTTCTCCAAAGGTAATATACAAATGA 2110
                         -  v      i i                      ivi           i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_63240373_6   2111 CAAAAAAGCACATGAAAAAATGCTCAATATCATTAATCAT 2150
                          v  v             i        i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (51 / 31)
Gap_init rate = 0.02 (8 / 485), avg. gap size = 2.38 (19 / 8)  


2201 27.19 2.93 4.55  chrX_63245870_63250870.rev     3590  4512 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63245870_6   3590 TGGAAAAACATTCCATCCATGTTCACAGACAGGATGAGTCAATATCTTTA 3639
                               i i  i    ----     ii  iv   v  v i     iv   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT----GTTCATGGATTGGAAGACTTAATATTGTTA 46

  chrX_63245870_6   3640 AAATGTCCATACTTCCCAAAGCAATTTGCAGATTCAATGCTATTTCTATC 3689
                          i   v v     i      vii  i i         i  v  ii     
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_63245870_6   3690 AAACTACCAACGAAATTCTTCACAGAATTAGAAAAACT-ATTTTGAAGTT 3738
                            v v   i vivv  i  ii     v v  v  i  -  ii i  i  
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_63245870_6   3739 TATACCAAAAGAGAGCCCAAATACCTAAGGCAATCCTAAGCAAAAACAAA 3788
                         i   i------i  -----   i --    -i i  --  --------  
  L1M4_orf2#LINE/    147 CATAT------GGA-----AATGC--AAGG-GACCC--AG--------AA 172

  chrX_63245870_6   3789 CAAACAAAACAACAACAACAAACAAAACCAAAGCTGGAGGTATCACGTTA 3838
                         i iv        ivvii v   v  i v     i      vv    ii v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_63245870_6   3839 CCCAATTTCAAACTATACTACAAGGCTACACTAACCAAAACACAAAACAG 3888
                                     viv        i      v   i   i   --iviii 
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA--GTGTGG 270

  chrX_63245870_6   3889 CATATTAGAAAAAACAAAACAGACATGGAAAAC--TGGAACAGAATAGAG 3936
                         --  i i v v  i---i i      iv i v --     i     v   
  L1M4_orf2#LINE/    271 --TACTGGCATAAG---GATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_63245870_6   3937 AACCCCAAAATAATGCTGCAGACCTACAACCATATAATCTTCGGCAAAGT 3986
                          ii  vi      vv iii v ii  iiii  vv i  i    i   i v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_63245870_6   3987 TGACAAAAACAGGTAATGGGAAAAGGA--GTTCCTGTTCAACAAACAGTG 4034
                           v   i v  vvi      i    i --  --  v         ii   
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGT--CTTTTCAACAAATGGTG 413

  chrX_63245870_6   4035 CTAGGATAACTGGCCGGCCATATGCAGAAGACTGCAACGGGATGCCTTCC 4084
                           i   i      vii?   i     i    v  v iiv   iv   v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_63245870_6   4085 ATACACCATATACAAAAATCAACTCAAAATGGATTAAACACTTACATATA 4134
                         vi                 i              i ? v  i  v  i  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_63245870_6   4135 AAACTTAAGACTATAAAAATCTTGGAAAACAACCTAGGAAATAACATTCT 4184
                          i vi   i         v    i   i v   v    ?ivv  iv   v
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_63245870_6   4185 GGACATAAGGTCTTGTAAAGAATTCAT-GATG-AACATGCCAAAAGCAAT 4232
                         v   v vi   ivv i  v iv   v -   i-i   --         vv
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA--CCAAAAGCACA 611

  chrX_63245870_6   4233 AGCAACAAAAACAAAAATTGACAAATGGGATCT------AACTAAAGAGC 4276
                                   iv      v  i    v   ii ------  i    i - 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-C 660

  chrX_63245870_6   4277 TTCTGCCCAGCTAAAGAAACTATCAACATAGTAAATTGACAACCTGCAGA 4326
                           i  iv vv v  i  v        v v   i  vv       ii    
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_63245870_6   4327 ATAGGAGAAAATATTTGCAAACTATGCATCTAACTAAGGTCTAATATCCA 4376
                           i                  ii  ii    i iv i  v  vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_63245870_6   4377 GAATCTACAAGAAACTTAAACAAATTTACAAGTTAAAAAAA------AC- 4419
                             v  i  ii    ivv    v iv i  --      i ------  -
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAA--TAAAAAGACAAATAACC 808

  chrX_63245870_6   4420 --ATTAAAAAGTAG-CAAAGG-TC---ATGGGCACTTTTCAAAAAAAGAT 4462
                         --   ?    i i -      - i---  i i  i  i  v   i     
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_63245870_6   4463 ACACACACAGCCAATAAGCTTATGAAAAAGTGCTCAACATTGCTAATCAC 4512
                          i   v ii          vi       ii          ii????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (151 / 96)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.76 (69 / 25)  


3168 27.42 0.44 0.44  chrX_63255497_63261776.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63255497_6   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63255497_6   4932 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63255497_6   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_63255497_6   5030 TATGGAACCAAAAAAGAGCCCGCATCTCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  vv    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63255497_6   5080 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACCACAAGGC 5129
                                i      vv    i  v  ii i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63255497_6   5130 TACAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 v   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63255497_6   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5227
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_63255497_6   5228 ATCTGATCTTTGACAAACCTGAGAAACACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  ivv  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63255497_6   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63255497_6   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_63255497_6   5378 TTAAATATTTAAACGTTAGACCTAAAACCATAAAAAACCTAGAAGAAAAC 5427
                          i ? v ii    i  v   v       i      vv i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_63255497_6   5428 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_63255497_6   5478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGCGATCTAA 5527
                         i            vvi          vv     v  i    vv  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_63255497_6   5528 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCACCAGAGTGAAC 5577
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_63255497_6   5578 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTCACAA 5627
                           i     i   i             v  i    vii ivi    v i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_63255497_6   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTGACAAGAAAA 5677
                         i  i  vi          v  i  v      vv    v ii i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_63255497_6   5678 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_63255497_6   5728 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5777
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_63255497_6   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 621 20.90 0.00 0.75  chrX_63282719_63291680        1   134 (8828)    L1M4_orf2#LINE/L1      323   455 (453)  

  chrX_63282719_6      1 AAATAAACCATTGCATATACAATGAAGTGATTTTTGATAACAGTGCCAAG 50
                                  vv i   v  iii v  v       i  i  vi        
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_63282719_6     51 ATAATTCAATGCAGAAAGGACAGTCTTTCAAACAAATGGGTGCTGGGAAA 100
                          iv        vi     i i       iv         -        v 
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG-TGCTGGGACA 421

  chrX_63282719_6    101 ACTTTATATCCACATGCAAAAGAATGAAACTGAA 134
                            vv   ?                   ii  i 
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.01 (1 / 133), avg. gap size = 1.00 (1 / 1)  

2425 27.28 1.61 4.08  chrX_63282719_63291680     1244  2174 (6788)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63282719_6   1244 TGGAAAAACATTGCATCCTCATGGATAGGAAGAATCAGTATCACGAAAAT 1293
                               i i  iv   vi        v      v i i   iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63282719_6   1294 GGCCATACTGCCCAAGGTAATTTAGAGATTCAATGCTCTTCCCATCAAAG 1343
                            v     v     iv i  i  v        i  vv i  i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63282719_6   1344 AACTATTGACATTTTACATAGAATTAGAAATAACTA--CTTAAAAATTAA 1391
                         vv i vivi v    viii    v v  v - i  i-- i     -  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAA-TTCA 148

  chrX_63282719_6   1392 TATG-AAAT-CAAAAAACAGCTCATATATCCAAGAAAATCCCAAGCAAAA 1439
                             -    -   iii  -- iviv   v    i v    iii iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_63282719_6   1440 AGAACACAGCTAGAGGTATCACACTACTTGACTTCACACTATACTACAAG 1489
                               v  i i    vv       v iii i    v viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63282719_6   1490 GCTATATAGTAACCAAAACAGCATGGTATTGGTCCCAAAACAGACATATA 1539
                             i --    i   i    ii     i   iviv ii i         
  L1M4_orf2#LINE/    247 GCTACA--GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_63282719_6   1540 GACAAATGAAACAGAATCTAGATCTCAGAAA-AAACACCACACATCTACT 1588
                           iv    i  i     iv   vii      -    -   i    i  iv
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTTATG 343

  chrX_63282719_6   1589 ACCATCTGATCTTCGACAAACCTGACAACAACAAGTAATGGAGAAAGGAT 1638
                         ii  vi    i        ivv  v   v v  vvi     i     i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_63282719_6   1639 --TCCTTATTTAATAAAAGGTGCTGGGAAAACTGGCTAGCCATTTGCAGA 1686
                         --  i  -- i  i   v          v      v  ?   iv    i 
  L1M4_orf2#LINE/    394 AGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_63282719_6   1687 AAACTGAAACTGGACCCCTTCCTTATACCTTATACAAAAATTAACTCAAG 1736
                          i v    ii         v   i i   v                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_63282719_6   1737 ATGGATTAAATACTTAAATACAAAACCCAAAACCATAAAAACCATAGAAG 1786
                               i ? v  i     ii  i v i     i      vi v      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_63282719_6   1787 AAAATCTAGGCA-ATACCATTCAGAAAATAGGCATGGGCAAAGATTTTAT 1835
                             iv    ?i- v i -   ivi vv v  vv i     v i   iv 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_63282719_6   1836 G---ATGAAATTGCCAAAAGCAGTTGCAACAAAAGCTAAAATTGACAAAT 1882
                         i---    v ---         vvv          vv     v  i    
  L1M4_orf2#LINE/    591 AGATATGACA---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_63282719_6   1883 GGGATCTAATTAAACCAAAGAGCTTCCGAATAGCAAAAGAAACTACCATC 1932
                         v   ii v  i   viv  i i   ii viivv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_63282719_6   1933 AGAGTGAA----CAACCTACAAAATGGGAGAAAATTTTTGCAATCTACCC 1978
                          i      ----     i   i             v       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_63282719_6   1979 ATCTGACAAAGTTCTAATATCCAGAATTTACAAGGAACTTAAACAAATTT 2028
                               i  i vv  vi          v  i  i     i--------  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--------TT 779

  chrX_63282719_6   2029 ACAAGGAACTTAAACAAATTTACAAGGAAAAAAACAACCCCATCAAAAAG 2078
                             ----  i  ------ v i  ii i v   i     v  i?    i
  L1M4_orf2#LINE/    780 ACAA----CTCAA------TAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_63282719_6   2079 AGGGCAAAGGACATGAACAGATACTTCTCAAAAAAAAAAAAAAGATATTT 2128
                         v          iv    i   i i     v   i  -------     vi
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-------GATATAC 862

  chrX_63282719_6   2129 ATGCGGCCAACAAACATATGAAAGAAAGCTCAACTTCACTGATCAT 2174
                          vii      i  i  i      ii v       v   ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (148 / 102)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.65 (53 / 20)  

1340 19.29 5.14 0.64  chrX_63282719_63291680     2712  3022 (5940)    L1M4_orf2#LINE/L1      439   763 (145)  

  chrX_63282719_6   2712 AAAAGAATAAAGTTGGACTCTTACTTTACACCATAAACAAAAATTAACTC 2761
                                 i         i i   i i        v              
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_63282719_6   2762 AAAGTGTATAAAAGACCTAAAGGTAAGGGTGAAAATTGTAAAATTATTGA 2811
                            i  v  v ?         v     i iv    i i     i v  ii
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_63282719_6   2812 CAGTGAACACAGGA-TAAAACATCATGATACTGAATTCAGCAAT-----C 2855
                         v  vi    i   ?-    v v  i   ivi  ii  vi     ----- 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_63282719_6   2856 TTA--TAT--CAC---AGATATAAG-ACCAAAAGAATAAAAATGGATAAA 2897
                            --   --   --- iii i   - v        --     i      
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAA--AAAATAGATAAA 636

  chrX_63282719_6   2898 TTGGGCTACATCAAAATTAAA--CTTTTGTGTATCAAAATACACTATCAG 2945
                             i  v             --        iv     iv         i
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_63282719_6   2946 AAGAGTGAAAAGGCAACCTGCAGAATGGGAGAAAATATTTGCAAATCATA 2995
                         i i         i     ii                              
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_63282719_6   2996 TATCTAGTAAGGAGTTAATATCCAGAA 3022
                              ii     iii vi         
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAA 763

Transitions / transversions = 2.41 (41 / 17)
Gap_init rate = 0.02 (8 / 325), avg. gap size = 2.25 (18 / 8)  

2807 25.10 0.94 6.35  chrX_63282719_63291680     7510  8469 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63282719_6   7510 TGGAAGAACATTCCATGCTCATGGATAGGAAGACTCAATATCATGAAAAT 7559
                              ii i  i     i        v        i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63282719_6   7560 GGCCATACTGCCTAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 7609
                            v     v  i  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63282719_6   7610 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 7657
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_63282719_6   7658 TATGGAACCAAAAAAAGAGCCC-GCATTGCCAAGTCAATCCTAAGCCAAA 7706
                                -- viv  i ii   - v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_63282719_6   7707 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTGTACTACAAG 7756
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63282719_6   7757 GCTACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGAGATATAGA 7806
                                   i   i    ii        vi iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_63282719_6   7807 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAG 7854
                         i        i    i--    i  --        vv   i    i  ii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_63282719_6   7855 CTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 7904
                         ii vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_63282719_6   7905 CCCTACTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 7954
                         vi  vi i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_63282719_6   7955 CTGAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATG 8004
                         v    ii    i    v   i   i v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_63282719_6   8005 GATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 8054
                            i ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_63282719_6   8055 ACCTAGACAATACCTTTCAGGACATAGGCATGGGCAAGGACTTGATGTCT 8104
                           v   i?ivv vii   iv   v v  vv i     v ii  vv ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_63282719_6   8105 AAAACACCAAAAGCA-ATGTCAACAAAAGCCAAAATTGACAAATGGGATC 8153
                          vi            - v -         vv     v  i    v   ii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_63282719_6   8154 TAATTAAACTAAAGAGCTGCTACACAGCAAAAAAAAAAAAAAAAAAAAAA 8203
                          v  i   v v  i i  vi iii vv    ii v --------------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-------------- 679

  chrX_63282719_6   8204 AAAAAAAAAAAAAAAAAAAAAAAAAAAACTACCATAAGAGTGAACAGGAA 8253
                         ----------------------------   i  vi i      v  iv 
  L1M4_orf2#LINE/    680 ----------------------------CTATCAAGAAAGTGAAAAGACA 701

  chrX_63282719_6   8254 ACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCCTCTGACAAACGGC 8303
                            i                 v       vii iviv     i  iv i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_63282719_6   8304 TAACATCCAGAATCTA-AAAGAACTCACAAAAATTTACAAGAAAAA-ACG 8351
                          vii         v  -         vi v  v iv i  v     -  i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_63282719_6   8352 AACAACCCCATCAAAAAGTGGGTAAAGGATCTGAACAGACACTTCTCAAA 8401
                           i     v  i?    i    i       i    i     i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_63282719_6   8402 AGAAGACATTTATGCAGCCAACAGCTACATTTATGAGC-CATGAAACAAT 8450
                               ----   i  ---  ii  i -----  i   -       vi  
  L1M4_orf2#LINE/    852 AGAAGA----TATACA---AATGGCCA-----ATAAGCACATGAAAAGAT 889

  chrX_63282719_6   8451 GCTCATCACCACTGGCCAT 8469
                              v  i  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (145 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.38 (70 / 16)  


3173 27.64 0.44 0.44  chrX_63299733_63305992.rev     4862  5769 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63299733_6   4862 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4911
                              ii i  i   i i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63299733_6   4912 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4961
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63299733_6   4962 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5009
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_63299733_6   5010 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5059
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63299733_6   5060 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5109
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63299733_6   5110 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5159
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63299733_6   5160 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCCTACCTACAACT 5207
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_63299733_6   5208 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5257
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63299733_6   5258 CTATTTAATAAATGGTGCTGGGGAAACTGTCTAGTCATATGTAGAAAGCT 5307
                           v  i  i             iv     vv  ?i  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63299733_6   5308 GAAACTGGATCCTTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5357
                            ii    i  i v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_63299733_6   5358 GTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5407
                         vi ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_63299733_6   5408 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5457
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_63299733_6   5458 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5507
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_63299733_6   5508 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5557
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_63299733_6   5558 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5607
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_63299733_6   5608 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5657
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_63299733_6   5658 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5707
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_63299733_6   5708 TCAAAAGAAGACATTTATGCCGCCAAAAAACACATGAAAAAATGCTCATC 5757
                           v        i  vi viiv     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_63299733_6   5758 ATCACTAGCCAT 5769
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2188 26.86 9.71 0.84  chrX_63309434_63311445.rev      699  1532 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63309434_6    699 TGGAGAGGCACATTGCATGTTCGTGGATTGTCAAAATCAACACAGTAAAA 748
                             i  -- i  iv       i       vv i v i  i iv  v  i
  L1M4_orf2#LINE/      1 TGGAAAG--ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_63309434_6    749 ATGTCAGCCCTTCCCAAATTGGTATGCAATTACAATACATTTCCTATGAA 798
                            v  iiv  i         i v i  iv v   ii  v i     v  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_63309434_6    799 AATCGCAGGCAGATTTTTTTTGGAGATGTAGTCAACATTATTCTAAAATG 848
                             v   - v -ii       v   vi v v   vv v  i       v
  L1M4_orf2#LINE/     99 AATCCCAG-CTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_63309434_6    849 TGTATGTAAAGTCAGCGGAGGTAGAATAGCTAAGACAAT-TTGACAAAGA 897
                         ii    v   vv  iv   vvi        i  i     -    v     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_63309434_6    898 AGTATAAGGTGGGAGGAACCATTATACTCAATTTCAAGACAT-TTATATG 946
                           v i  i  v      vi  ivv v i         i  v -i  i vi
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63309434_6    947 GCTATGGTAATCAAGTCTGTGCGGCAGTGGTAGAGGGATAGATACGAAAC 996
                             ii         v v   i  i v   i v i       i iiv iv
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_63309434_6    997 TCAATAGAAGAGAATAGAGAACCCAAAAGCCGACCTGCACAGATACGCCT 1046
                              i   v     v    ii   i  iivi   iii   vv  i vii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_63309434_6   1047 AAATTATT----ACAGAAGTA--------ATTAAATGGGGGAAGGATAGT 1084
                           v v   ----   iii  i--------   v       i   i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63309434_6   1085 CTTTTCAACAAATGATGCTGA-ACAA-TCCATTGCCCTCTCC----GCTC 1128
                                       i     i-    - vv  v?  viv v ---- vvi
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63309434_6   1129 AAAATTA-ACCTTCACCT-ACACCTCATAC-----TTTATACAAAATGGA 1171
                         i  i  i-   iii    -     vi    -----  v iv         
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_63309434_6   1172 TCATAAATTTAAATGTAAAATGCTCAAACTATAAATCTTTTAGAAGAAAA 1221
                            ? i ii         i -   v          v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_63309434_6   1222 CTTAGAA--AAAT-TTC-------------AGGTAA--GTCACTT----- 1248
                          v   i?--    -   -------------   i  --  iv   -----
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_63309434_6   1249 -GATACTAAAAGTATGATTCATAACAGGAAAAGTTGATATATTAGACCTC 1297
                         -  i  i     i ii viv i  v  i    i v    v   i   i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_63309434_6   1298 AATAAAATTAAAAACTTTT---CCTC------TAC-----AGAAGCTACA 1333
                          vi                --- i  ------i  -----    iv iv 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_63309434_6   1334 GAG-----CTACAGACTGGGAGAAAATACT-ACAAATAACGTATCCAGTA 1377
                         i  ----- i     v            i -i     v ii    iii  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_63309434_6   1378 ACAAACTAGTATCTAGAATATATCAAGAACTCTTAACACGTAATAGTAAA 1427
                          vii   v     i         v           vv  vi    i    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_63309434_6   1428 AG--CAAG---CCTAGTT-AAAAATAGGCAAAAGAC----ATAAACATTT 1467
                          i--   i---  i i  -      i      i  i----   i      
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_63309434_6   1468 CACTGAAGAAAATATAACAGATGGAAAATAAGCACATGAAAAGGTGTGCA 1517
                          v ii     i     -  i    vv                 i  iv  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATA-CAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_63309434_6   1518 GAGATTGAGGCCATC 1532
                         - v  ii????????
  L1M4_orf2#LINE/    895 -ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (132 / 89)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.93 (88 / 30)  


3308 22.83 3.82 1.91  chrX_63328175_63330840     1285  2173 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_63328175_6   1285 GAAGGATAGCCCATCTTCATGGACTGGAAGAATTAATATTGTTAAAGTGT 1334
                            i    v     v        i       v             ii  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_63328175_6   1335 CTACACTACCCAAAGTGATCTACAGATTCAACGTAATCTCTAACAAAATA 1384
                          v i   v      v                  i    i   v      v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_63328175_6   1385 CCAATGGCATTCTTCACAGAAATAGAAAAAAGAATCCTAAAATTTGTAAG 1434
                            iiv  v  i  ii       v  v  ivvi           ii  v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_63328175_6   1435 GAACCACAAAAGATCCCGAATAGCTGAGGCAAACTTGTGGGGAAAAAAAA 1484
                            vii   ii  i  v       ii ii   v    ----------   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG----------AAA 192

  chrX_63328175_6   1485 AAGAAGAAAGAAAGCTGAAGATATCACTCTATCTGACTTCAAAATGTACT 1534
                                 v-    i  i  ivv    v  vi ii i       iv    
  L1M4_orf2#LINE/    193 AAGAAGAAC-AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_63328175_6   1535 ACAAAGCTATAGCAACCAAAATAGAATGATACTGATCTAAAAATAGACAC 1584
                                  i  i  i   i i  vi  i     iiv   ii       i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_63328175_6   1585 ACAGACCAATGGAATAGA-----GAGCCCAGAAAAAAA---ATGCATATA 1626
                          i   i            -----   i       v   ---  i   v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_63328175_6   1627 ----CA----------GGCAAAGGTGTGAAGAACAAACATTGGGGAAAAT 1662
                         ----  ---------- i   i    iv    v  vv  v        iv
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_63328175_6   1663 ACAATCTT--CAGTAAATGGTGCTGAAAAAAAAATGGATGCCCATATGCA 1710
                          i i    --  ii           ii v  v--     i?   i     
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAAC--TGGATAKCCACATGCA 439

  chrX_63328175_6   1711 GAAGAATGGAACTAGGTACATATCTCTCATCACATATAAAAATCAACTCA 1760
                         i       i ii i iiv v  i   v  i  i   i      i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_63328175_6   1761 AAATGGATTAAAAACTTAAATGAAAGACCGAAAGCTATGAAACTACTGGA 1810
                                 i ? i  i      v    v v   i    i     vi i  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_63328175_6   1811 AGAAAACATAGGGAAAACACTTCATAATATTGGACTAGGCAACAATTTTT 1860
                                     ?iv  vv    i i iv    ii       iii   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_63328175_6   1861 TGGCTATGACTCTAAAAGCACAGGTAACAAAAGCAAAAGTAGACAAATGA 1910
                          i v      v i         i i        v    i    i    vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_63328175_6   1911 GATTACATCAAACTAAAAAGCTTCTGCTGCACAGTAAAGGAAACAATCAA 1960
                           i v       v v    i   i  -   vi--i      v  v     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTG-TGCTT--CAAAGGACACTATCAA 686

  chrX_63328175_6   1961 CAAAGTGAAGAGATAACCCACAGAATGGAAGAAAATATTTGCAAACTACC 2010
                         v        i   i              i                ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_63328175_6   2011 CTTCTAA-AAAGGATTAATAACCAGAATATATAAGAAACTC----AACTA 2055
                         iv   i -  i   i vi  v             ii     ----    v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_63328175_6   2056 AATAGCAAAG---CAAACAATCTGATTTTAGAACGGGCAAAAGATCTGAA 2102
                             ii   i---    i  i ii   ?v i  i       i   i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_63328175_6   2103 TAGATACTTTTCAAAAGAAGATATACAAATGGCCAATAGGTATATGAAAA 2152
                             i i  i  v                         i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_63328175_6   2153 AAATGC--AACATCACCAATCAT 2173
                         i -   --       ????????
  L1M4_orf2#LINE/    887 GA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (133 / 66)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 3.40 (51 / 15)  


3085 27.69 0.77 0.99  chrX_63366024_63372422     4997  5906 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63366024_6   4997 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5046
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63366024_6   5047 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGA 5096
                            v     v     iv i  i  i v      i  v     i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63366024_6   5097 TACCAATTACTTTCTTCACAGAA-TTGGAAAAAAAACT-ACTGTAAAGTT 5144
                          v   ii i i  i  ii     -   ---- v  i  - iiv    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chrX_63366024_6   5145 CATACGGAATCAAAAAAGAGCCCGCATTGCCAAGACAATCGTAAGCAGAA 5194
                             i    viiv  ii  v  v v  v     i      v i iv ii 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_63366024_6   5195 AGAACAAAGCTGGAGGGGTCACACTACCTGACTTCAAACTATACTTCAAG 5244
                                  i      iv       v  ii i      viv    v   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63366024_6   5245 GCTATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGACAGA 5294
                             i     i   i    ii         i iv ii i   v v i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_63366024_6   5295 CTAATGGAACAGAACAGAGGCCTCAGGAATAACACCACACATCTAGAACC 5344
                         ii       i    iv   ivii   i     vv   i    i  viii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_63366024_6   5345 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATAATTCC 5394
                          vi    i  i     ivv  v   i v  vvv          v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63366024_6   5395 CTATTTAATAAATGGTTCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5444
                           v  i  i       v      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63366024_6   5445 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5494
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_63366024_6   5495 TTAAAGACTTAAATGTTAGACCTAAAGCCATAAAAACCCTAGAAGAAAAC 5544
                          i ?    i       v   v     i i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_63366024_6   5545 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCAGGACTA 5593
                         v    ?i- v i -   iv   v v  vv i     v ii   ----i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC----TTA 591

  chrX_63366024_6   5594 AAT----CACCAAAAGCAATGGCAATGAAAGCCAAAATATACAAATGGAA 5639
                         i  ----           vvi    ii    vv      v i    v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_63366024_6   5640 TCTAATTAAACTAAAGAGCTTCTGCAATGCAAAAGAAACTACCATCAGAG 5689
                         ii v  i   v v  i i   i  iiv v    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_63366024_6   5690 TGAACAGGCAACCTACAGAATTGGAGAAAATTTTTGCAATCTACCCATCT 5739
                             v  i     i       v         v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_63366024_6   5740 GACAAAGGGCTAATATCCAGAATCTACAAATAATTTAAACAAAATTACAA 5789
                           i  i  i  vi          v  i   v  i ivv    vviv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_63366024_6   5790 GAAAAAGTCAAACAACCCCATCAAAAAGTTGGTGAAGGATATGAACAGAC 5839
                         v      v    i     v  i?    i v  ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_63366024_6   5840 ACTTCTCAAAAGAAGACATTTATGCAGTCTAAAGACACATGAAAAATTGC 5889
                          i     v        i  vi viii i v v ii          iv   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_63366024_6   5890 TCATCATCACTGGTCAT 5906
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


1327 27.89 5.61 2.64  chrX_63414058_63419316.rev     4163  4768 (491)    L1M4_orf2#LINE/L1      285   908 (0)  

  chrX_63414058_6   4163 TAGAAATACAGCTAACCAGGGAGGTAAAA--GCGAACCCAGAAATAAAGC 4210
                             v   i  --- i  iv iii  i  -- v  ii           v 
  L1M4_orf2#LINE/    285 TAGACATATAG---ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_63414058_6   4211 TGCACACCTATTACCATCTGAT------CGAAGCTGAAAAAAAGAAGCTA 4254
                         iii   ii   vii  vi    ------ i i v  vv  i vv vv v 
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_63414058_6   4255 TGAGGAAA----AGACTCACGACTCAATAAATGGTGCTGGGTTACA--TA 4298
                           i     ----  v  i----i    i             --   -- i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTT----TTCAACAAATGGTGCTGGG--ACAACTG 425

  chrX_63414058_6   4299 TCTAGCCAAATGCAGAAGGTAGAAACTGAACCCCTTCCTT-CAACATATA 4347
                         vv  ?   v     i   ivv   ii  i      v   i-  v      
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_63414058_6   4348 CAAAAATCAACACAAGATGGATTAAAGATTTAAATGAAAAACCTCAAACT 4397
                                i   v   i      i ?   ii      v  i v  v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_63414058_6   4398 TTGAAATCCCTGGAAGACAACCTATGC----ATCCT-G-GACATAGGAAT 4441
                         v i   ii i i     v   v  v ?----   i - -   v v  iv 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_63414058_6   4442 GGACAATGATTTCATGACGAAGACATCCAAAGCAATCACATAA-AAAAGC 4490
                         i i     i    v iivv v    i v      --  vii  -     -
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCA--CAAGCAACAAAAG- 622

  chrX_63414058_6   4491 AAAAAAAT-GACAAATGGGATGT------AATTAACAGCATCTGCACAGC 4533
                         -       -  i    v   iv ------      v i v i  ii vv 
  L1M4_orf2#LINE/    623 -AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_63414058_6   4534 AAGAGAAACTATCAA-AGAGTAAACAGACAACCTACAGAATGAAAGCAAA 4582
                           ii  v        - i   i  v        i        ii  v   
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_63414058_6   4583 TATTTACAAATTATGCATTCAACAAAGGTCTAATATCCAGTTTCTGTAAG 4632
                              i     i  ii  iii i  i  v  vi       vv v i   i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_63414058_6   4633 GAACTTAAATAAATTTACAAGAGAAAAACAAGCAACCACATTAAAAAGTG 4682
                              ivv i  v iv i  v i   i    ii    vv   ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_63414058_6   4683 GGCAAACAACAAGGACAGACACTTTTC---AAAAGACACACATGTGGCCA 4729
                               vi ivv i i     i  i  --- i    i i   vi      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_63414058_6   4730 ACAACCATATATATAAAAAA-GCTCAACATCACTGATCGT 4768
                          i  v  i  i---    i -           ????????
  L1M4_orf2#LINE/    872 ATAAGCACATG---AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (100 / 65)
Gap_init rate = 0.03 (20 / 624), avg. gap size = 2.50 (50 / 20)  


1909 26.93 2.91 1.89  chrX_63422264_63423936.rev      502  1188 (485)    L1M4_orf2#LINE/L1      215   908 (0)  

  chrX_63422264_6    502 TCATGTTTCTCAACTTCAAACTATACCACAGGGCTACTGTAAGCAAAAGA 551
                            iii   i   i      viv   i   ii     v    v   i v 
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_63422264_6    552 GCATGATACTGCGACAA--ATA--CAAATAGACCAGTGGAACAGAATAGA 597
                          ii  i     vv i  --   --  v     i  i     i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_63422264_6    598 GAGCCCAGAAATAAGGCCACACACTTATGACCATCTGATCTTTTATGAAA 647
                            i          iv   i   i     ii  vi    i  i---  --
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC---GA-- 359

  chrX_63422264_6    648 TCAATGAAAACAATAA-ATTCAAT----ATTCAATA--TTATTCAATAAA 690
                         -   v iviv   v v-       ---- vvv    --i v     i   
  L1M4_orf2#LINE/    360 -CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_63422264_6    691 TAATGCCAGGATAACTGGCTAGCCATATGCAGCAGATAAAAACTGGACCA 740
                          ii   ii   i      v  ?   i     iv   vvi  ii      v
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_63422264_6    741 TTTCTTC-TGCCATATTCAAAAATTAACTCAAGATAGATGAAAGACTTAA 789
                         i v i  -ii      v               i  i   v ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_63422264_6    790 ATGTAGAACCCAAAAGTATAAAAACCCTGGAAGACAACCTAGGCA-ATAC 838
                              ii v i    v       vi i i     v   v    ?i- v i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_63422264_6    839 CATTCTGAACATAGAAACT-GGCAAAGGTTGCATGACAAAGACACCAAAA 887
                          v iv   v v i i--i -     v    v v iivv v          
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_63422264_6    888 GCAATCA--CAACAAAAGCAAAAATTGACAAAT---ATCTCATTAGACTT 932
                            --  --         v      v  i    --- ii    i i v  
  L1M4_orf2#LINE/    607 GCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_63422264_6    933 AAGAGATTCTGCACAGTAAAATAAACTATTAACAGAGTAAAGAGACAACC 982
                           i iv  i  ii vvi   iv v     i  v i   i  i        
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_63422264_6    983 TACAGAATGGGAGAAAA-ATTTAGTGAACTATGCATCTGATAAAGGTCTA 1031
                         i                -    - ii  ii  ii         i  v  v
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGATAAGGGACTT 753

  chrX_63422264_6   1032 ATATCCAGCATCTACAAGGAACTTAAACAAATTTACAATAAAAAATACCA 1081
                         i       v  v  i  i     ivv    v iv i        i-  - 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG-AC-A 801

  chrX_63422264_6   1082 AACAATTCCATTGAAAAGTGGGTAATAGACATGAACATACACTTTTCAAA 1131
                           i  ii v   ?    i    i  vi  iv    i v   i  i  v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_63422264_6   1132 AGAAGACAAACATGTGACTGACAAGCACATGAAAAAAATCTCAATACCAC 1181
                               i v   vi  i ii i             i vv     i i  ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_63422264_6   1182 TGATCAT 1188
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.59 (111 / 70)
Gap_init rate = 0.03 (18 / 694), avg. gap size = 1.83 (33 / 18)  


2578 26.04 1.75 2.74  chrX_63460750_63465529.rev     3376  4289 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_63460750_6   3376 AAAAAAATTCCAAGCTCATAGGTAGAAATAAATCATATTGTTAAAAAGGC 3425
                            i v  i   v i    i i v i  v vv v          i v   
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_63460750_6   3426 CATACTGCCCAAAGTAATTTACACATTCAATGCTTTATTTCTAATAAACT 3475
                         v     v      v i  i    v      i  v--  ii   vi   v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCA--ATCCCTATCAAAAT 101

  chrX_63460750_6   3476 ATCA-TTGCAATTCTTCACAGAACTAGAAAAA--AATCTTAAAATGTATA 3522
                         vi  -i   v-  i  ii     v v  v  i--i   i      vi   
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_63460750_6   3523 TGGAGTCGAAAAAGATCCCAAATAGCCAAGACAATCCTAAGCAAAAAGAA 3572
                             ivi v  ii  i  vi         i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_63460750_6   3573 CAAAGCTGGAGGCATCATGCCACCTGACTTCAAACTATACTACAGGG-TA 3621
                              i      vv   ii iv  ii i      viv       ii -  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_63460750_6   3622 GTATAACCAAAGCAGCATGGTACTGGGACTAAAACAGGCATGTAGACCAA 3671
                         vvi   i   ii   ii         v iv ii i  i   i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_63460750_6   3672 TGGAACAGAATAGAGAA-CCAGAAATAAGATAGCACAACTACAACTACCT 3720
                              i     v    i-          ivivii   vi  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_63460750_6   3721 GATCTTCAAAAAACCTGACAAAAACAGGGAATGGGAAAATAAT-TTCATA 3769
                            i   i v  ivv  v   i v  vvv      i   v   -v  v v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_63460750_6   3770 TTAATAAATGGTGCTAGGATAACTGGCTAGCAATATGCAGAAGATTGAAA 3819
                          i  i          i   i      v  ? v i     i    v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_63460750_6   3820 CTGGACCCCTTCCTTACACCATATACAAAAAATAACTCAAGATGGATTAA 3869
                         i         v   i                v        i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_63460750_6   3870 AGACTTAAGTGTAAGACCCAAAACTAAAAAAAAAGCCTTTA--AGACAAC 3917
                             i   i       v i       v    ---- ii   --   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA----CTCTTAGAAGAAAAC 546

  chrX_63460750_6   3918 CTAGGTAATACAATCCT-G-GACATAGGCACAGGCAAAGATTTCATAACA 3965
                         v    ?i-  -    i - -   v v  vvi      v i    v  ivv
  L1M4_orf2#LINE/    547 ATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_63460750_6   3966 AAGACACAAAAAGCAATTAA--AACAAAAGGAAAAATTGAGAAATGGAAT 4013
                          v     v       --i  --        i      v  v    v i i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_63460750_6   4014 TTAATTAAA--CAAATTAGCTTCTGCACAACAAAAGAAACTATCAACAGA 4061
                           v  i   --i   -- i   i  ii vv    i  v        v i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAA--AACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_63460750_6   4062 GTAAACAGACAACCTACAGAAAGTGAACAAATATTTGCAAACTACACATC 4111
                           i  v        i      v v  iv             ii i i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_63460750_6   4112 CAACAAAGATCTAATATTCAGCATTTATAAGGA--TCTTAAATAAATTTA 4159
                         ii i  i iv  vi   i   v  v     i  --     v --- i i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA---ACTCA 787

  chrX_63460750_6   4160 CAGGAACAAAAAAAAAAAACAAAAAACTCCATTGAAAAGTGGGCAATGGA 4209
                         ------- v  v     i     v   i v   ?    i       v   
  L1M4_orf2#LINE/    788 -------ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_63460750_6   4210 CATGAAGAGACACTTTTCAAAAGAAGACATACAGAAGGCCAAAAAGCGTA 4259
                         iv    v     i  i  v        i     i v      v    ii 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_63460750_6   4260 TGAAAAAAAAAGCTCAACGTCACTGATCAT 4289
                               i v--       i   ????????
  L1M4_orf2#LINE/    881 TGAAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 1.95 (41 / 21)  


 615 24.35 11.07 5.17  chrX_63481522_63487918.rev        1   271 (6126)  C L1M4_orf2#LINE/L1   (450)   458   172  

C chrX_63481522_6    271 ATAACAACAAAACTGTTTGTAAAAACAAG--CAAAA--AGAAAACTAATA 226
                            i --      vi i vv     v   --    i--i  ii   v i 
  L1M4_orf2#LINE/    172 ATAGC--CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

C chrX_63481522_6    225 ------------AAAACT-----CAATGCCTTTACAGTAACCAAAACAGC 193
                         ------------      -----   v  ---        i   i    i
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGC---TACAGTAATCAAGACAGT 266

C chrX_63481522_6    192 TTGCTACTGGTACCAAAACAGAGATATAGACCAATGGAACAGAAT--AGA 145
                         v  v      i iv ii i   v       i        i     --   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

C chrX_63481522_6    144 GCCCCTGGAAATAATACCACCCATCTACAA-CAATCTGATCTTTGACAAA 96
                          i  --i       vv   iv   i  iii-    -    i  i     i
  L1M4_orf2#LINE/    317 GTCC--AGAAATAAACCCATACATTTATGGTCAAT-TGATTTTCGACAAG 363

C chrX_63481522_6     95 CCAGACACAAACAAGA------AATGGGGAAAGGATTCCCTATTTAATAA 52
                         --- iii ---     ------           i  vvi  v  i  i  
  L1M4_orf2#LINE/    364 ---GGTGC---CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

C chrX_63481522_6     51 ATGGTCCTGGGTAATCTGGCTAGCCATATGTAGAATGCTGAAACTGGATC 2
                              v     vv v    v  ?   i   i i  viv    ii    i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

C chrX_63481522_6      1 C 1
                          
  L1M4_orf2#LINE/    458 C 458

Transitions / transversions = 1.83 (42 / 23)
Gap_init rate = 0.05 (13 / 287), avg. gap size = 3.38 (44 / 13)  

3033 27.59 0.99 0.77  chrX_63481522_63487918.rev     5001  5906 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63481522_6   5001 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5050
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63481522_6   5051 GGCCATACCTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5100
                            v    ii     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63481522_6   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5148
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_63481522_6   5149 TATGGAAC--CAAAAAACAGCTGGCATTGCCAAGTCAATCCTAAGCCAAA 5196
                                v--   iii  -- ii v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_63481522_6   5197 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAG- 5245
                                  i      vv   ii  v  ii i      viv       i-
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63481522_6   5246 GCCACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATATAGA 5295
                           i       i   i    ii i       i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_63481522_6   5296 GCAATGGAGTGGAAC--AGAGCCCTCAGAAATAATGCCACTTATCTACAA 5343
                         v       i i   i--    i  --        vv   ivi  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_63481522_6   5344 CTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5393
                         ii vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_63481522_6   5394 CCCTATTTAATAAATGGTGCTGGGAAAACTGGTTAACTATATGTAGAAAG 5443
                         vi  v  i  i              v      v  ? i i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_63481522_6   5444 CTAAAACTGGATCCCTTCCTTACACCTCTTACAAAAATTAATTCAAGATG 5493
                         v i  ii    i    v   i     viv            i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_63481522_6   5494 GATTAAAGACTTAAATGATAGACCTAAAACCATAAAAACCCTAGAAGAAA 5543
                            i ?    i      vv   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_63481522_6   5544 ACCTCGGCA-ATACCATTCAGGATATAGGCATGCACAAGAACTTCATGTC 5592
                           v v  ?i- v i -   iv  iv v  vv ivi   viii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_63481522_6   5593 TAAAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATC 5642
                           vi            vvii         vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_63481522_6   5643 TAATTAAACTAAAGAGCTTCTGCACAGCAAAGAA-ACTACCATCAGAGTG 5691
                          v  i   v v  i i   i  ii vv     i -    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_63481522_6   5692 AACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAACCTACTCATCTGA 5741
                           v  i     i                vv       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_63481522_6   5742 TATAGGGCTAATATCCAGAATCTACAATGAACACAAACAAATTTACAAGA 5791
                           vi  i  vi          v  i  v    v vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_63481522_6   5792 AACAAACAAACAACCTCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5841
                           v i     i    iv  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_63481522_6   5842 TTCTCCAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5891
                                       i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_63481522_6   5892 ATCATCACTGGCCAT 5906
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (150 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3132 27.86 0.55 0.55  chrX_63500363_63511369      492  1399 (9608)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_63500363_6   1399 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAATGTCATGAAAAT 1350
                              ii i  i     i    i i v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_63500363_6   1349 GGCCATACTGTCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1300
                            v     vi    iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_63500363_6   1299 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTAAAGTTCT 1252
                          v   iivi i  i  ii     -   -- v  i  - i i    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_63500363_6   1251 TATGGAACGAAAATAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 1202
                                vviv  vi  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_63500363_6   1201 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1152
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_63500363_6   1151 TACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGATC 1102
                             i   i   i    ii         i iv ii i   v  i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_63500363_6   1101 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 1054
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chrX_63500363_6   1053 GTCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1004
                         ivi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_63500363_6   1003 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 954
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_63500363_6    953 GAAACTGGATTCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 904
                            ii    ii   v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_63500363_6    903 TTAAAGACTTCAAT-TATAGACCTAAAACCATAAAAACCCTAGAAGAAAA 855
                          i ?    i v   -  -   v       i      vi i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTA-AGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

C chrX_63500363_6    854 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 805
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chrX_63500363_6    804 AAACGCCAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 755
                         vi  i      i  vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chrX_63500363_6    754 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 705
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chrX_63500363_6    704 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTGCTCATCTGACA 655
                         v  i     i   i             v  ii   viiiivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chrX_63500363_6    654 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAG 605
                          i  i  vi          v  i  v      vv    v iv i  vi i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chrX_63500363_6    604 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 555
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chrX_63500363_6    554 CTCAAAAGAAGACATTTATGTAGCCAAAAAGCACATGAAAAAATGCTCAC 505
                            v        i  vi vi i     v             i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chrX_63500363_6    504 CATCACTGGCCAT 492
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (151 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

2098 29.37 4.31 1.70  chrX_63500363_63511369     7900  8781 (2226)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_63500363_6   7900 AAAATTATTACATGTTTATAGATAAATAGAATCAATGTGATAACCATGGC 7949
                            iv   iv      i  i   viiv   v i   i vi v vv     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_63500363_6   7950 CACACTGCTCAAAGCAACTTACAGATTTAATGCTATTCCCACTGACCTAC 7999
                         v i   v i    vii ii        i  i  v  i  i iii vv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_63500363_6   8000 TAATGACATGCTTCACAGAATTAGAAAAAAAACT-ATCTTAAAAAAATTC 8048
                         i iivi v vi  ii     v v  v  i---  -   i     ---   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAA---TTC 147

  chrX_63500363_6   8049 ATATGAAACCTCAAACAGCCTA-AATACCCAAGGCAAATTTAAGCAAAAA 8097
                              i  viv   ivii  i -    v    ii   vi  i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_63500363_6   8098 GAACAAAGCTAAAGGCGTCATGCTACCTGACTTTCAA--CTACATTATAA 8145
                                 i ii   vv   ii  v  ii -      --  -i i  i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAA-TTTCAAAACT-TACTACAA 245

  chrX_63500363_6   8146 GACAACAGTAACCAAAAATACATGGCACTGGTACCAAAACAGACACATAG 8195
                         ii v       i   i vviii   i     i iv ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_63500363_6   8196 ACCAATGGAACAGAATAGGGAGCCCAGAAGTAAGGCCCTACACCTGCCTC 8245
                          i        i     v i   i      i   iv  v    ii iivvi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_63500363_6   8246 CATCTGATCTTTGACAAAGTTGACAAAAACAAGAACTAGGGAAA--ACAC 8293
                           vi    i  i     i v  v   i v  vvv v i      -- i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_63500363_6   8294 TCACTATTTAATAAATGGTGCTGGAATAACTGGCTAGCCATATGCAGAAG 8343
                           -- v  i  i            i i      v  ?   i     i   
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_63500363_6   8344 ATTAAAACTGGATTCCTTCCT-ATCCTACATACAAAAATCAACTGAAGAT 8392
                          v i  ii    ii   v   - iv i i          i    v  i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_63500363_6   8393 AGGTTAAAGAAATGAATGTAAAATCTAAAACTATAAAAAACTTAGGCAAT 8442
                         i i i ?   vv i       i v              vv     ivi v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_63500363_6   8443 ACCAT---TCTGAATAT--GGAAACT-------GACAAAGATTTCAT-GA 8479
                          v   ---?v i   v -- vi v  ------- i   v i    v -  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_63500363_6   8480 TGAAGATAGCAAAAGCAATTGCA-CAAAATGAAACATGAGCAAATGGTAC 8528
                          - v  i v        vvv   -     vi   v  iiii    v v  
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_63500363_6   8529 CTAATTAACCTAAAGAGCTCCTG--CAGCAAAAGAAACTATCAACAAAGT 8576
                         i v  i  vv v  i i  ii  -- vv    i  v        v     
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_63500363_6   8577 AAA----CAACCTACAGAAAGGGAGAAAAAATTTTCAAACTATGCATCCA 8622
                         i  ----     i      v         v    v    ii  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_63500363_6   8623 ACAAAAA--TTGGATCCATAATTCATAAGAAACTTAAATTTACAAG-CAA 8669
                          i  iii--   v     v   vi    ii    i----      v-   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTC----TTACAACTCAA 788

  chrX_63500363_6   8670 GAATCAAAA-ACA-----CTCG--TTAAAAATGGGCAAAGGACATGAACA 8711
                         v   v    -   ----- i i-- ?                iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_63500363_6   8712 GACACATTTCCAAAGAAGTCATACATGCAGCCAACAAGCATATGAAATAG 8761
                             iv i          vi     viii     i     i      vii
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_63500363_6   8762 TGCTCAACATCACTAATCAT 8781
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (155 / 100)
Gap_init rate = 0.03 (24 / 905), avg. gap size = 2.21 (53 / 24)  

3031 26.57 1.54 1.43  chrX_63500363_63511369     9608 10514 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63500363_6   9608 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCGTGAAAAT 9657
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63500363_6   9658 GACCATACTGCCCAAGGTAATTTATAGATTCAATGACATCCCCATCAAGC 9707
                          i v     v     iv i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63500363_6   9708 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 9755
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_63500363_6   9756 TATGGAACCAAAACAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 9805
                                viiv  vi  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63500363_6   9806 AACAAAACTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 9855
                               ii      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63500363_6   9856 TACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGAGATATAGACC 9905
                                 i   i    ii        vi iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63500363_6   9906 AATGGAACAAAA--GAGAGCCCCCTGAAATAATACCACACATCTACAAGC 9953
                                i i  --     i  v--       vv   i    i  iiiv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCA--GAAATAAACCCATACATTTATGGTC 346

  chrX_63500363_6   9954 ATCTGATCTTTGATAAACCTGTCAAAAACAAGAAATGGGGAAAGGAT--T 10001
                          vi    i  i  i  ivv  i   i v  vvv           i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63500363_6  10002 CCGTATTTAATAAATGGTACTGGGAAAATTGGCTAGTTGTATGTAAAAAG 10051
                          -- v  i  i       i      v  i   v  ?iiii   i    ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_63500363_6  10052 CTGAAACCGGACCCTT-CCTTACACCTTATACAAAAATTAATTCAAGATG 10100
                         v    iii      i -   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_63500363_6  10101 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 10150
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_63500363_6  10151 ACCTAGGCG-ATACCATTGAAGACATAGGCTTGGGCAAGGACTTCATGTC 10199
                           v    ? - v i v i v-   v v  v  i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_63500363_6  10200 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 10249
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_63500363_6  10250 TAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTT 10299
                          v  i   v v  i i   i  iiivv    i  v    i  vv i   v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_63500363_6  10300 AAGAGGAAACCTACAGAATGGGGAAAAATTTTTGCAATCTACTCATATGA 10349
                           i  iv    i          ii     v       vii ivi  v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_63500363_6  10350 CAAAGGGCTAATATCCAAAGTTTACCAAGAACT--TAACCAAATTTACAA 10397
                         i  i  i  vi      i i v  iv       --  --   v iv i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAA 791

  chrX_63500363_6  10398 GAGAAAATCAAACAACCCTATCAAAAAGTGGACAAAGGATATGAACAGAC 10447
                         v i   iv    i     v  i?    i   i        v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_63500363_6  10448 ACTTCTCAAAAGAAGAGACTTATGCAA----CCAAAAGACACATGAAAAA 10493
                          i     v        ----   i   ----    v ii          i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_63500363_6  10494 ATGCTCATCATCACTGGCCAT 10514
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (145 / 92)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.93 (27 / 14)  


3054 20.06 2.62 0.44  chrX_63533840_63535969.rev      500  1187 (943)    L1M4_orf2#LINE/L1      110   812 (96)  

  chrX_63533840_6    500 CCTTCTTTTTAGAAGT-GACAAGCTAATCCTAAAATTCATATGGAAATGC 548
                             i   vi    i -        i                        
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_63533840_6    549 AAGGGACCCACAATAGCCAAAATAATATTTAAAAAGAGGAGCAAACTGTA 598
                                   v           i   v  v       i  i    v - i
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT-TG 208

  chrX_63533840_6    599 AAGG-CTTATGTGTCCTGATTTCAAAACTTACCACAAAGCTGTAGTAATG 647
                         i   -  i iiiv   ii              i        ii      v
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_63533840_6    648 AAAACGGTGTTGTACTGGCATAAATAAAGACATATAGATTGATGGAACAG 697
                           i  i    v            iv v            ii      i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_63533840_6    698 AAAAGAGAGT-------TAAACCCATACAATTGTCTTCAATTTCTTTTTG 740
                           vv      -------            v  i vv      vv    i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_63533840_6    741 A-AAGGATATCAAGAC-ATTAAATGGAGAAAGAA--ATCTTTGCAACAAA 786
                          -    i ii      -   v     i       --i     v       
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_63533840_6    787 TTGTGTTGAGACAATTAGATACCCATATCTAAAAGAATGGAGTTGAAAAA 836
                          v   i  i     i i    ?   i  vi         i     i vvv
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_63533840_6    837 ATACCTCACACCACACAGGAAAATTAACTCAAAATGAATCACAGACCTAA 886
                         v            i i vi                 i    ?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_63533840_6    887 ATGTAAGTGCTAACACCATAAAACTCTTAGAAAAAAAAACA----TAAAT 932
                                v     v  i               i    v i ----     
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_63533840_6    933 CATTGAAATCTTAGATTAGAAAAAAAATCCTTATATATGATACCATAAGC 982
                          v i vi i   i i    iv  viiv i    v      i    v    
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_63533840_6    983 ACAAGCAACATCAGACAAAAAATAGATAAATAGGCCTTTACCAAGACTGT 1032
                                   -- i v               v  v   i i   i i iv
  L1M4_orf2#LINE/    609 ACAAGCAACA--AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_63533840_6   1033 AAACTTTTGTGCATCAAATGGCATT-CCAAGAAAAAGAAAAGACAAGCCA 1081
                                     v     v i  i -i       iv          v   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_63533840_6   1082 CAAAATGGGAGATAATTTTACCAAATAATGCATCTGATAGGGAACTTGTT 1131
                           i         v   v  vv     v  ii        i  i      v
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_63533840_6   1132 TCCAGGATATATAAGGAATATTTTCAGCTCAACAATAAAAAAGAAAATGT 1181
                              i        i   ivi  v  i     i        iiv    iv
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_63533840_6   1182 CTCAGT 1187
                          i  i 
  L1M4_orf2#LINE/    807 CCCAAT 812

Transitions / transversions = 1.52 (82 / 54)
Gap_init rate = 0.01 (10 / 703), avg. gap size = 2.10 (21 / 10)  

 431 18.92 1.80 2.70  chrX_63533840_63535969.rev     1537  1647 (483)    L1M4_orf2#LINE/L1      799   908 (0)  

  chrX_63533840_6   1537 ACAAATAATTAAATTTTAAAATGAGCAGATGATTTGAATAGTCACTTCTC 1586
                                 iiv    ?v      i   i v           v  i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_63533840_6   1587 CAAGGAAGATATACAAATAGTCAATAA--ATAAGAACAAACACTCAAGCT 1634
                            i              i i      -- i v   v i ii     ---
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA--- 895

  chrX_63533840_6   1635 TGTCAGTAACTAG 1647
                         ii   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.02 (2 / 110), avg. gap size = 2.50 (5 / 2)  


3160 27.64 0.44 0.44  chrX_63546965_63553334.rev     4972  5879 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63546965_6   4972 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5021
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63546965_6   5022 GGCCATACCACTCAAGGTAATTTATAGATTTAATGCCATCCCCATCAAGC 5071
                            v    iv i   iv i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63546965_6   5072 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5119
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_63546965_6   5120 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAGG 5169
                                viiv  ii  v  v v  v     iv     i i ivv i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63546965_6   5170 AACAAAGCTGGAGACATCATGTTACCTGACTTCAAACTATACTACAAGGC 5219
                                i     ivv   iii v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63546965_6   5220 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATA 5269
                                 i   i    ii         i iv ii i   v        v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63546965_6   5270 AATGGAACAGAAC--AGAGTCCTCAGAAATAATGCCACATATCTACAACT 5317
                                i    i--       --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_63546965_6   5318 ATCTGATCTTTGACAAACCTGAGAAACACAAGCAATGGGGAAAGGATTCC 5367
                          vi    i  i     ivv  vv  ivv  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63546965_6   5368 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5417
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63546965_6   5418 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAACATCGA 5467
                            ii    i    v   i     v              i    v  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_63546965_6   5468 TTAAAGACTTAAATGATAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5517
                          i ?    i      vv   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_63546965_6   5518 CTAGGCATTACCATTCCGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5567
                         v    ?i v viv   vv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_63546965_6   5568 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5617
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_63546965_6   5618 TTTAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGATTGTAC 5667
                          iv  v v  i i   i  ii vv    i  v    i  vv i v  v v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_63546965_6   5668 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACACATCTGACAA 5717
                           i     i                 v       vii i i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_63546965_6   5718 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5767
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_63546965_6   5768 AAACAAACAACCCCATGAAAAAGTGGACGAAAGACATGAACAGACATTTC 5817
                          i     i     v  v?    i   i i  i  iv    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_63546965_6   5818 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5867
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_63546965_6   5868 TTCACTGGCCAT 5879
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2962 27.92 1.10 0.88  chrX_63604598_63611013.rev     5020  5925 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63604598_6   5020 TAGAAGAACATTCCATGCTCGTGGACAGGAGAAATCAATATCGTGAAAAT 5069
                          i   ii i  i     i  i    iv   ii v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63604598_6   5070 GGCCATACTGCCCAAGGTAATTTATAAATTCAATGCCATCCCCCCATCAA 5119
                            v     v     iv i  i  i i      i  v     i--     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT--ATCAA 98

  chrX_63604598_6   5120 GCTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 5167
                         iv v   iivi i  i  ii     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_63604598_6   5168 CGTGTGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCGAAA 5217
                          i i     viiv  ii  v  v v  v     i      i i ivi i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_63604598_6   5218 AGAACATAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 5267
                               v  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63604598_6   5268 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGGTCGA 5317
                                   i   i    ii         i iv ii i   v vi v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_63604598_6   5318 CCAATGGAAAAGAAC--AGAGCCCTCCA-AAATAATGCCATACATCTAGA 5364
                         i        v    i--    ---    -      vv        i  vi
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAG---TCCAGAAATAAACCCATACATTTATG 343

  chrX_63604598_6   5365 ACCATCTGATCTTTGACAAACCTGACAAAAACAATAAATGGGGAAAGGAT 5414
                         ii  vi    i  i     ivv  v   i v  v v           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_63604598_6   5415 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5464
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_63604598_6   5465 GCTGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAACTCAAGAT 5514
                         iv    ii    i    v   i     v  i                i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_63604598_6   5515 AGATTAAACACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5564
                         i   i ? v  i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_63604598_6   5565 AACCTAGGCA-ATATCATTCAGGAGATAGACATGGGCAAGGATTTCATGA 5613
                            v    ?i- v   -   iv  vv v ivv i     v i    v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_63604598_6   5614 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGAT 5663
                         v  vi            vvi          vv        i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_63604598_6   5664 GTAATTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5713
                         v v  i   v v  v i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_63604598_6   5714 GAACAGGCAATACACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTG 5763
                            v  i   iv                  v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_63604598_6   5764 ACAAAAGGCTAATATCCAGAGTCTACCAAGAACTTAAACAAATTTACAAG 5813
                          i  ii i  vi        i v  iv       ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_63604598_6   5814 ATAAAAACAA----CCCCATCAAAATGTGGGCAAAGGAAATGAACAGAAA 5859
                          v   i    ----   v  i?   vi           vv    i   v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_63604598_6   5860 CTTTTCAAAGGAAGACATCTATGCAGCCAACAGACATGTGAAAAAATGCT 5909
                         i  i  v  i     i  vi viii     i ii  ii      i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_63604598_6   5910 CATCATCACTGGCTAT 5925
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


2700 25.57 5.22 1.27  chrX_63615912_63619980.rev     2390  3175 (894)    L1M4_orf2#LINE/L1        1   817 (91)  

  chrX_63615912_6   2390 TGGAAAAATATGCCATGCTTATAGATTGGGAGAATTAATATTGTTCAAAT 2439
                               i    v     i i  i      i   v           v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63615912_6   2440 GACAATGCTACCCAAAGCAATTTACAGGTTAAATGTCATCCCAATCAAAA 2489
                          i    i  v      vii  i     i  v  i iv     v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63615912_6   2490 TACCGATGATATTTTTCACAGATATAGGAAAAAAATTGA-----AAATTT 2534
                          v  iiiviiv     ii    v  v --- v  ii   -----     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_63615912_6   2535 ATATGAAACCACAAGAATCTCTAAATACTCAAAGCAATCTTGAGGAAAAA 2584
                              i  vii    iiv i vi    vi    i         i-   i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGA 196

  chrX_63615912_6   2585 ATAACAAAGCTGTAGGCATCACCCTACCTGACTTCAAAATATACAACAAC 2634
                          v       i  v   vv    v  v  ii i       iv   v    v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63615912_6   2635 ATTATAATAACCAAAACAGCATAGTGGTGGTGGCCTAAAAACAGACACAC 2684
                         ii  i i   i   i    i---     iv    v   ii i     i i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGT---GTGGTACTGGCATAAGGATAGACATAT 293

  chrX_63615912_6   2685 AGACCAATGGAATGGAATAGAGAACCCTGAAATAAATCCACACATTTACA 2734
                            i         i    v    ii  v        i   i       ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_63615912_6   2735 GTTAACTTATTTTTGACAAAGGTGCCAAGAACATACACTGGGGAAAGGGT 2784
                           i  i v     i     i          v   v  v         ii 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_63615912_6   2785 ACTCTCTTCAATAAATAATGCTGGGAAAATTAGGTATGCACAGACAAT-G 2833
                          v   i     i    ii        v  i i i  ?v    vi   v- 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_63615912_6   2834 AAGGAAATTGGACCCTTATCTCATATCACATACAAAAATCAACTCAGAAT 2883
                           v   i        i  i    i i  i          i      i   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_63615912_6   2884 G---------------------------AACT-TAAGACT---AAAAGAA 2902
                          ---------------------------    -   i   --- i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_63615912_6   2903 AATGCAGGGAAAAAT----GAAATGACATTGATCTGGGCAATGATTTGTT 2948
                           iii   ?iv    ---- ---    v   ivi i       i   v  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCG---TGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_63615912_6   2949 GGATTTGGCTCCAAAAGATTAGGCAAGAGAAGCACAAATAGTCAAATGCA 2998
                         i   v  i v       vvi i    v i   v v      vi    vvi
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_63615912_6   2999 ATTACATCAAACTAAATAGCTTCTGCATAACAAAAGAAACAATGAACAAA 3048
                          i v       v v  v i   i  iiivv    i  v  v  v  v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_63615912_6   3049 ATGAATAGACAACCTACAGATTAGGAGAAAATATTTGGAAGTAATACATT 3098
                         i    v        i     v i              v  i v   i  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_63615912_6   3099 TTATAAGAGATGAATTTCCAAAATATATAAGGAACTCAAACAACTCAATA 3148
                          v     i  ivvi v    i         i      vv           
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_63615912_6   3149 GCAAAAGAACAAATAACCCAATTTAGA 3175
                         ii    ii               ? i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAA 817

Transitions / transversions = 1.64 (123 / 75)
Gap_init rate = 0.01 (10 / 817), avg. gap size = 5.10 (51 / 10)  

 399 15.62 7.81 3.91  chrX_63615912_63619980.rev     3451  3578 (491)    L1M4_orf2#LINE/L1      776   908 (0)  

  chrX_63615912_6   3451 TCTCAAAACTAAATAAGTAAATCAGTAAATAAATAA---AAT--AAAAAT 3495
                            i v    v     -    -- -- i i      ---   --      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAA-TAAA--A--AGACAAATAACCCAATTWAAAAAT 820

  chrX_63615912_6   3496 GGACAGAGAACCTGAATAGACATTTCTC-----AAGACATACAAATGGCT 3540
                           i  i  i ii                -----    i           i
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_63615912_6   3541 AACAGATATATAAAACAATGCTCAACATCACTAATCAT 3578
                           i iii i  i   vi             ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 5.67 (17 / 3)
Gap_init rate = 0.05 (6 / 133), avg. gap size = 2.50 (15 / 6)  


2621 28.46 2.36 0.22  chrX_63640140_63644171.rev     2653  3541 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63640140_6   2653 TGGAAAAACATTTCATGCTTATGGATTGAAAGAATCAATAT----AAAAT 2698
                               i i  ii    i i        i    v i     ----  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63640140_6   2699 GTCCATACTGCCCAAAGCAATCTACGGGTTCAACAAAATATCTATCAAAA 2748
                          v v     v      vii      i i      iv   vi         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63640140_6   2749 AGACTAATGTCGTTTTTTACAGAATTAGAAGAAACAATCACAAAATTCAT 2798
                         vvv viv  i -      i     v v  vi ivii   vi         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_63640140_6   2799 AAGAAACCAAAAAAGAGCCTGAATAGCCAAAGCAACCATAAGCAAAAAGA 2848
                          v i  viiv  ii  v  v           i   i v i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_63640140_6   2849 AAATAGTTGGAGTAATTACATTACCTGACTTCAAATAATACTAGAAAGCA 2898
                          v v        v v i   i v  ii i      vvv     v     v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_63640140_6   2899 ACAGTGACTTAAATCGTATGGTGCTGGTCCAAAAATAGACACATAGATCA 2948
                              i iiv i iv  i    i    ivi  ii       i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_63640140_6   2949 A--GAACAGA-----GAACCCAGAAATAAAGTTGCATACCTACAACCAAC 2991
                          --   i   -----  ii           viiii i ii  iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_63640140_6   2992 TGATCTTTGACAAGGTTGACAAAACTA---AACGGGAAAA-ACTCATATT 3037
                             i  i       v  v   i  i ---  i   i   - v vi v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_63640140_6   3038 TT-ATTAAATGGTGCTGGAAAAAATTTCTAGCCATATGAAGAAGAATAAA 3086
                           - vi            i v  v vvv  ?   i   v i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_63640140_6   3087 ACTAGATCACTATCTCTCACCATATACAAAAGTTAACTCAAGGTGAATTA 3136
                         ii i  i v   i   v              i         ii  i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_63640140_6   3137 AAGACCTAAATCTAAGACTTAAAACTATAAAG-TCCTAGAAGAAAACCTA 3185
                         ?          v     vi            i-  i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_63640140_6   3186 GGAAATACTTTTTAGGATATTGGTCTAGCCAAAGAATTTATGTCCGTGAC 3235
                           ?ivv v i  iiv  iv    vi   v   v iv  iv ivvii    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_63640140_6   3236 CCCAAAAGAAAATACAAAAGAAGCAAAAATAGACAAATGGAACTTAACCA 3285
                         v       v v vi   v i   v         i    v i    v i  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_63640140_6   3286 AACTAAGAAGCTTCCGCACAGCAAAAAATAATAATCAACAGGGTAAATGG 3335
                           v v i  i   ii ii vv    ii i v  -    v ii  i  vi 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAAAAG 698

  chrX_63640140_6   3336 ACAATGTAAAAAATGGGATAAAATATTTGCAAATTATGCCTCTGACAAAG 3385
                             ivi v i       v               i  iiv     i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_63640140_6   3386 GACTAATATCCAGAGTCTATGATGAACTTCAAAAACTCAACAAGAAGAAA 3435
                             vi        i v   i v     iiv v       i  v  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_63640140_6   3436 ACAAAT--CCCATTTTAAAA-TGGGAAAAGAACATGAACAGACTTTTTAA 3482
                               --    v  ?    -    v    i iv    i    v   ivv
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_63640140_6   3483 AAAATAAGACATACAAGTGGGCAAGAAACCTACTAAAA-ATACTCAACAT 3531
                         v   v    i      i   v   v  i vi iv    -  i        
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_63640140_6   3532 CACTAATAGT 3541
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.39 (145 / 104)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


2477 25.26 6.60 1.62  chrX_63646449_63648497      734  1596 (453)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_63646449_6    734 GAAAAATATTATATGCTCATGGATTGAAAGAATTAATATTGTTAATGTGT 783
                             i    ivi   i          i    v             vi  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_63646449_6    784 CCATACTACCCAAAGCTATATAGAAATTCAATGCAATTCTCACCAAAATT 833
                          v     v      viv  v  v i      i     i ii i      i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_63646449_6    834 CTGGCAAAATTCTTCACAGAAACAGAAAAAAAAAATCCTAACGTTCACAT 883
                          ii  vivv  i  ii      iv  v  ivvi -      vi    i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATAT 151

  chrX_63646449_6    884 GGAACCACAAAAGACCCCAAATAGTCAAAGTAATATGGAGAAAAAAAAA- 932
                             vii   ii     vi     i    ii   v v  i   i  i  -
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_63646449_6    933 --AGTTGGAGTGAGT-ATGCTTCCTGGATT-AAAATTATATTACAAAGCT 978
                         --        -  v - ii     iiiv  -    i -  i         
  L1M4_orf2#LINE/    202 AAAGTTGGAG-GACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_63646449_6    979 GTAGTAATTGAAACAGTGTAGTACTGGCATAAAAACAAAAACATGTAGA- 1027
                         ii      ii i       i            ii i i --   i    -
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA--CATATAGAT 297

  chrX_63646449_6   1028 -AATGAAACAGAATATGA-AGCTAAGAAATAAATCTAAAC-TTAATACAG 1074
                         -    i  i     -   -  iiv         i i v  -  --  ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATT--TATGG 344

  chrX_63646449_6   1075 CCAAT-AATTTTTGGGAAGGGCACTAAGAATAT--AATGAGAAAAAAATG 1121
                         i    -i     i iv     ii i    vi  --    i i   i   i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_63646449_6   1122 ACCTCTTCAATAAATTGTGCTGAGAAAACAACACTTCCACATGCAAAA-- 1169
                         ii  i     i    v      i  v   viv iv?            --
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_63646449_6   1170 ATAAA-------------------------ACAAAA--TAA----AAGTT 1188
                           i  -------------------------      --   ----  i v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_63646449_6   1189 GATAAAAGGCATAAAGGCAATACCTGAAATCACAAAGTTTCTAGAAAGAA 1238
                            v ?  i v    v i  v v  i   ii i   ii ii     ii  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_63646449_6   1239 ACATAGGAG-AAATGCTCCCTAACATTGG-TCATAACAATGAGTTTGTT- 1285
                                ? -    -  i v i  v    - i -ii     -    v  -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTGGGTTA-GGCAATG-GTTTCTTA 591

  chrX_63646449_6   1286 GATATTACACTG---GCT---GCAA-AAAAGAAAAAATAAATAAATGGTA 1328
                              v    ii---  v---    -             i      v v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_63646449_6   1329 CTACATCAAACTAAAATGCTACTGCACTGCAAAGGATACAATCAATAAAA 1378
                           v       v v   vi  vi  ii  v       i  v     v   i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_63646449_6   1379 TGAAAAGACAACCTATACATTGGGA--AAACATTTGCAAACCACTTGTCT 1426
                                      i i v v     --   i         i  iv i   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_63646449_6   1427 GATAAGGGATTAATAGCCAAAATTTATAAAGAACTCTTCCAATATAATAG 1476
                                  i vi  v   i   v              v   ivi    i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_63646449_6   1477 CAGAAAAACAAATAACCCAAATAAAGCAAGGACAAATGACCTAAACTGAC 1526
                         i i   i             v ?  iv v  i    v  ii i  iv   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_63646449_6   1527 ATTATTTTTTCAAAGAAAATATAAAAACGTTCAGCAGCTATATAAGAAGT 1576
                            --- i i       i     v   i vi  ii ivi i  i i   v
  L1M4_orf2#LINE/    842 ATT---TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_63646449_6   1577 TGCTCAACATCCCTAATCAC 1596
                                    v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (142 / 72)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 2.45 (71 / 29)  


2668 28.17 3.03 1.12  chrX_63672776_63676327     2169  3059 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63672776_6   2169 TGAAAAAACATTTTATGCTCATGGATGGAAAGAATCAATATCATTAAAAT 2218
                           i   i i  iii   i        v i    v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63672776_6   2219 AGCTATACTCTCCAAAGC-ATGTATAGATTCCATGCTATCCCTATCAAAA 2267
                         i  v      i     vi-  v  i      v i  v             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63672776_6   2268 TACCAATTACATTCTTCACAGAACTAGAAAAAC-AATTTAAAAATTCATA 2316
                          v   ii i v  i  ii     v v  v  i -i  iiv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_63672776_6   2317 TGGAATCAAAAAAGAGCCTGAATATCCAAGGCAATCCTAAGAAAAAAGAA 2366
                              viiv  ii  v  v     v    ii     i i i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_63672776_6   2367 CAAAATGGGAGGCATCACCTTATCTGACTTCAAA-----CTATAGGGCCA 2411
                             i v     vv    vi vi ii i      -----   i ii  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_63672776_6   2412 CAGTAGCCAAAACAGCACGGTACTGGTAACTAAAAAACAGACACATAGAC 2461
                              ii   i    iii        i --   ii -i     i     i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGA-TAGACATATAGAT 297

  chrX_63672776_6   2462 TAATGAAGCAGAATAGAAAGTTCAGAAATAAGGCTGAACACCTACAAGTA 2511
                         i    i ii     v  i   i         iv iiv   ii  iiivi 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_63672776_6   2512 TCTGATCTTTGACAAAACAGACAATAACAAGCAGTGGGGAAAGGAC--TC 2559
                         vi    i  i     iivv v   v v  vv  i         i i--  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_63672776_6   2560 TTTTTCAATAAATGGTGCTAGGATAACTGGTTAGCCATATGAAGAAGATT 2609
                             -   i          i   i      v  ?   i   v i    v 
  L1M4_orf2#LINE/    398 TTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63672776_6   2610 GGAAATGGACCCTTACCTTACACCACTATTCAAAAATCAATTCAAGATTA 2659
                          i iv       i     i      -   v       i  i    i  vi
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCA-TATACAAAAATTAACTCAAAATGG 495

  chrX_63672776_6   2660 ATTAAATACTTAAATGTAAAACCTAAAGCTATAATAACTCT-GGAAAATA 2708
                           i ? v  i         i v     i      -      -i   i v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAA 544

  chrX_63672776_6   2709 ATGGAGGACATACAATTCTG-GACATAAAACTTGGCAACAATTACATGAA 2757
                          iiv   ?-i  v vi ii -   v viiii v     iii  v v ii 
  L1M4_orf2#LINE/    545 ACATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_63672776_6   2758 ---GAAGTGAAAAGAAATTGCAACAAGAGCAGAAATTGACAAAT-GGATC 2803
                         ---  viiv     v vvv       i  v i    v  i    -   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_63672776_6   2804 TAGTTAAACTACAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTA 2853
                          vi i   v vv i i   i  ii vv    i  v        v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_63672776_6   2854 GTCAGACAACCTACAGAATGAGAGAA------TGTA-----TGTATTTGA 2892
                         ivv        i        i     ------  i ----- i   i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_63672776_6   2893 CAAAGGTCTAATATACAGAATCTATAATCAACTTAAACACATCTACAA-G 2941
                         i  i  v  vi   v      v     vv    ivv   vv  v i  -i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_63672776_6   2942 GAAAGATGAAACAACTTTGTTAAAAAGTGGGCAATGGACACAAGCAGACA 2991
                         i     i-   i   iivi  ?    i       v   ivii ii     
  L1M4_orf2#LINE/    794 AAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_63672776_6   2992 TTTTTTCAAAAGAAGATATACACATGGCCAACAAGCATATGAAAAAAATG 3041
                            i i    -           v        i     i       i -  
  L1M4_orf2#LINE/    843 TTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chrX_63672776_6   3042 CTCAACATCACTAGTCAT 3059
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (162 / 85)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.85 (37 / 20)  


2634 24.73 4.62 4.84  chrX_63676684_63680518     2433  3342 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63676684_6   2433 TGGAAAGACCTCTGGTGTTTATGGATTGAAAGATTTAATATTATTAAAAT 2482
                                 iv  ivi    i        i    i        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63676684_6   2483 GTCCGTAATACTC----AAT------GCAATTCCAGTGGCATTTTTACAT 2522
                          --- i       ----   ------i  iv i  ii vv  iii  ---
  L1M4_orf2#LINE/     51 G---GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA--- 94

  chrX_63676684_6   2523 TTTAAACATCCCAGTGGC------TACAAAA--TAAAAAAAAAATT---A 2561
                         - i   -       iv  ------ i  i  -- i v  ivvi  i--- 
  L1M4_orf2#LINE/     95 -TCAAA-ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_63676684_6   2562 AATTCATGTGAAACTATGAAGGACCTCAAAAAGCCAAATCAAGCTTGGG- 2610
                                i  i  v iii i     ivi  v       v   v    ii-
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_63676684_6   2611 --GAAGAACACAGCTGGAGACATCACACTGC----TTTAAAAATATATTA 2654
                         --        v  i     ivv       v ----   v    iv  i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_63676684_6   2655 CAAAGGTGCAATAATTAAG-CTGTATGGTAGTAGCATAAAGTCAGACATA 2703
                              v i  i    i   - v  i     v i      i vi       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_63676684_6   2704 AAGACCAATAAAATAGAATACAAGGCTCAGAAATAAATCCTTGCATATAT 2753
                         v   i    ii        vv ii ii          i  v i   - - 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-T-T 340

  chrX_63676684_6   2754 ATGTTTAACTAATCTTCTGCAAGGATGCCATGAATACACAGCATGGATGA 2803
                            v i  i i  i   vi     i     v  vi iv  iiiv   vii
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_63676684_6   2804 GATAGTCTCTTCAACATATATTTCTGGGAAAACTAGATATCCATATGCAA 2853
                         i       i       v  iv v      v    i    ?   i      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_63676684_6   2854 AA--------TCTAACCCTTATCTCACAACATATACAGAAA--A--TCCA 2891
                           -------- ivi    i  i      v        i   -- --  v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_63676684_6   2892 AATGGATTAATGCTTTACATCTAGGACCTGTAACTATAAAACTGCTAGAA 2941
                                i ?v vii  v  v  i  v  iv            vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_63676684_6   2942 AAAAAAACATACAATAAAAGCTTTATGACATTGGTCTTGGCAGTGCTTTC 2991
                         i    --    vi?vv   v   ii    v    vi v    i  v    
  L1M4_orf2#LINE/    541 GAAAA--CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_63676684_6   2992 ATGGACATGATACCAAAAGCAAAGGAAAGAGAAGCAAAAATAAGTAAGTG 3041
                         v i  i    i          v i v  v i   v       ii   i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_63676684_6   3042 GGACTACATCAAACTCAGAAGCTTTGATACAGCAAAAGAAACAACCAACA 3091
                              v       v i i  i    vi i vv    i  v  v i   v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_63676684_6   3092 GAGTGAAAAAGCAAACTACAGAATGGGAGACCACACTTACATATTTCTGG 3141
                         i        ii   v i             -------- v      ----
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGA--------AAATATTT---- 726

  chrX_63676684_6   3142 GGATCTTGAAGAATATCATATATCTGAAAAGGAGGTTAATCTCCAAAATG 3191
                         ---------- v v             v    iiv  i- v    i   i
  L1M4_orf2#LINE/    727 ----------GCAAATCATATATCTGATAAGGGACTTG-TATCCAGAATA 765

  chrX_63676684_6   3192 TGTAAGGAACTCCAACAACTCAACAGCAATGAG-CTGATAACCTTATTTT 3240
                          i   i      iv         i ii  vi  - vi      iv   ?-
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW- 814

  chrX_63676684_6   3241 AAAAATAAGCTATAGTAATGGATAGTCATACAGATATTTCTCCAAAGAAG 3290
                               ii  ------  v    -- iiv i   i               
  L1M4_orf2#LINE/    815 AAAAATGGGC------AAAGGAT--TTGAATAGACATTTCTCCAAAGAAG 856

  chrX_63676684_6   3291 ATATATAAATAGCCAATAGGTGTATGAAAAGATGCTCAATGTCATTAATC 3340
                              i    i       i iii                ii   ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_63676684_6   3341 AT 3342
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.63 (137 / 84)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.58 (86 / 24)  


3085 26.41 1.44 1.10  chrX_63693119_63699388.rev     4875  5779 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63693119_6   4875 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4924
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63693119_6   4925 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4974
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63693119_6   4975 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5022
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_63693119_6   5023 TATGGAAACAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5072
                                 iiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63693119_6   5073 AACAAAGCTGGCAGCATCATGATACCTGACTTCAAACTGTACTACAAGGC 5122
                                i   vi vv   iiv v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63693119_6   5123 TACAGTAACCAAAACAGCATGGTACTGGTAAAAACCCAGAGAGATAGACC 5172
                                 i   i    ii         i v  ivvi   v v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63693119_6   5173 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACT 5220
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_63693119_6   5221 ATCTGGTCTTTGACAAACCTCACAAAAACGAGAAATGGGGAAAGGAT--T 5268
                          vi  i i  i     ivv vv   i v ivvv           i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63693119_6   5269 CCTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5318
                          i  -- i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_63693119_6   5319 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5368
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_63693119_6   5369 GATTAAACACTTAAAGATTAGACCTAAA-CCATAAAAACCCTAGAAGAAA 5417
                            i ? v  i    vi v   v     - i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_63693119_6   5418 ACCTAGGCAGTA--CCATTCA-GGTCATAGGCATGGGCAAGGACTTCATG 5464
                           v    ?-   --i -   i- ii v i  i- i     v ii   v i
  L1M4_orf2#LINE/    545 ACATAGGN-GTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTA 591

  chrX_63693119_6   5465 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGA 5514
                         vv  vi            vvi          vv     v       v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_63693119_6   5515 TCTAGTTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5564
                         ii vi i   v i  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_63693119_6   5565 TGAACAGGCAACCTGCAGAATGGGAGAAAATTTTTGCAATCTACTCATCT 5614
                             v  i     ii                v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_63693119_6   5615 GACTAAGGG-CTAATATCCAGAATCTACAAAGAATTCAAACAAATTTACA 5663
                           -      -  vi          v  i      i  vv    v iv i 
  L1M4_orf2#LINE/    742 GA-TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_63693119_6   5664 AGAAAAAAA--AACAAACCCATCAGAAAGTGGGCAAAGGATATGAACAGA 5711
                          v     i --  i  v  v  i?i   i            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_63693119_6   5712 CACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATG 5761
                           i     v        i  vi viii     i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_63693119_6   5762 CTCATCATCACTGGCCAT 5779
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (145 / 90)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.44 (23 / 16)  


2239 28.60 5.54 0.81  chrX_63702412_63709917.rev     6149  7015 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63702412_6   6149 TGGAAAAACATTCCATGCACATGTATAGGAAGAATCAATATCATGAACAT 6198
                               i i  i     iv    v  v      v i     ii v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63702412_6   6199 GGCCATAGTGCCCAAAGCAATTTATGGATTCAATGGTATTCCAATTGA-- 6246
                            v   v v      vii  i  ii       i vv  i  v  ii --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63702412_6   6247 -CCTA----CC------------ACTGACATTCT--TCATAGAATT---- 6273
                         -  i ----  ------------ i     vv  --  v  i    ----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_63702412_6   6274 -AGAAA---AAAAAACT----ATTTTAAAGACAATTCTAAGCAAAAAGAA 6315
                         -i    ---  iii  i----  vviv  i     ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_63702412_6   6316 CAAAGCTGGAGGCATCACACTACCCTACTTCAAACTATACTACAAGGCCA 6365
                              i      vv       v   v i      viv        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_63702412_6   6366 CAATAAACAAAACAGCATGGTACTTGTACAGAAACAGGCACATAGACCAA 6415
                           i   v   i    ii       v i i iii i  i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_63702412_6   6416 TGGAAGAGAATATATAACTCAGAAATAAAACAGCACATCTACAACCATCT 6465
                              v     vv v iii          v vii    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_63702412_6   6466 GATCTTTGACAAACCCCCAAAAAACAAGCAATGGGGAAAGGATTCCCTAT 6515
                            i  i     ivviv v  i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_63702412_6   6516 TTAATAAATGGTGCTGGGAGAACTGGCTAGCAATAGGCAGAAAATTGAAA 6565
                          i  i              v      v  ? v i v   i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_63702412_6   6566 CAGGATCCCTTTCTTACAACTTACACAAAAATTAACTCAAGATGGATTAA 6615
                         iv   i    vi  i   v v  i                i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_63702412_6   6616 AGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAATCTAG 6665
                             i         i v i     i      vi i          iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_63702412_6   6666 GCTGTG--TCATTCAGGATATAGGCATGTGCAAAGAATTTAT-GATGAAA 6712
                          ?-  i--  -   iv  iv v  vv iv    v iv  iv -   ivi 
  L1M4_orf2#LINE/    551 GN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_63702412_6   6713 TTATCGAAAGCAATTGCAACAAAATCAAAAATTGACAAATGGGATCTAAT 6762
                         i- i i      vvv         vv      v  i    v   ii v  
  L1M4_orf2#LINE/    599 C-ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_63702412_6   6763 -AAAACTAAAGAGCTTCTACACAGCAAACAAAACTATTACCAGAGAGAAG 6811
                         -    i    i -   i iii vv    vi v     i vv i  v   i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_63702412_6   6812 AGACAATCTATAGAATGGGGGGAAACTGTTGCAATCTACCCATCTGACAA 6861
                               i i i        i i   ivv      vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_63702412_6   6862 AGGTCTATTATCTGGAATTTACAAGGAAAT-TTACCATTTAA-----AAA 6905
                         i  v  vv    ii    v  i  i   v -    v i i  -----   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_63702412_6   6906 ATACAA----CTCCATT-AAAAAGGAGCAAAAGGACATGAAGAGACACTT 6950
                          v    ---- i v   -     v i     -   iv    v     i  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAA-GGATTTGAATAGACATTT 845

  chrX_63702412_6   6951 CTGAAAAAAAGAGACATACATGCAGCCAACAAACCCATGAAGAATAGTTC 7000
                           vv   i    v i i v   --     i  i v      i ivv i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTC 893

  chrX_63702412_6   7001 AACATCACTGATCAT 7015
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.75 (55 / 20)  


3107 26.95 1.67 0.56  chrX_63716870_63721988     3729  4626 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63716870_6   3729 TGAAAAAACATGTTATGTTTCTGGATTGGAGAAACAAATATTGTTAAACT 3778
                           i   i i  vii     iv         ii viv           iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63716870_6   3779 GACCGTACTATCCAAAGTAATCTACAGATTCAATGAAATTATTTTCAAAA 3828
                          i vi    vi     v i              i v   ivi v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63716870_6   3829 TATCAATGATATTCTTCAGAGAAATACAATAAAG-AATCCTAAAATGTGT 3877
                          vi  iiviiv  i  iiv      -ii i  iv-i          vii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_63716870_6   3878 ATGAAACTGCTATA-ACCCTGAATAGCCAAAGCAATTCTGAGCAAAAAGA 3926
                            i  v   v vi-    v           i    ii   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_63716870_6   3927 ACAAATCTGGAGGTATCACACTATCTGACTTCAAAATATAGTATAAATCT 3976
                              vi      vv       vi ii i       iv  v  i   v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_63716870_6   3977 ACAGCAATAAAGACAACATGGTACGGGCATAAAAA-AGACACACAGCCTA 4025
                             i   v      iii      v       ii -     i i  vii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_63716870_6   4026 ATGGAACAGAATAGGGAACCCCTAAATAAATCCACATATTTACAGCCAAC 4075
                               i     v i  ii  vv       i   i i     ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_63716870_6   4076 TGATTTCTGACAAAGTTGCCAAGAATATACACTAAGAAAAGAACACGCTC 4125
                               ii     i v        vi  v  v ii i      i vv  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_63716870_6   4126 TTCAATAAATAGTGCTGGGAAAACTGGATAACCATGTGCAGAAGAATAAA 4175
                              i    i         v         ?   ii    i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_63716870_6   4176 ACTAGATTGCTATCTCTCACCATATACAAAAAAAAACTCAAAATGAATTA 4225
                         ii i  iiv   i   v               vv           i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_63716870_6   4226 AAAATTTAAATGTAAGATCCCAAACTTTAAAACTACTAGAAAAAAATAT- 4274
                         ? i ii           v iv     v       vi     i    i  -
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_63716870_6   4275 --GGTAAATGATTCACTACATTGATCTGGGAAAAGATTTTATGGTTGAAA 4322
                         --?      v-   iiv  v   ivi i  v  v i   iv i v ivi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_63716870_6   4323 CCTCAAAAGCACAGGAAACAAAAACAAAAATAGACAAATGGAATTATAGC 4372
                          vi          i v       iv         i    v i i vi v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_63716870_6   4373 AAACTCAAAAGCTTCTGCATAGCAAAAGGAACAATCAACAGAATGAATAG 4422
                            v i    i   i  iiivv    i iv  v     v i i    v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_63716870_6   4423 ACAACCTGAAGAATTGGAGAAAATATTTTCAATCTATTCACCTGATAAGG 4472
                               iiv     v             v   vii  vi i         
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_63716870_6   4473 GATTAATATACAAAATATACAAGGAACTC----AATTCAACAGTAAGAA- 4517
                           i vi   v  i      i  i      ----  i    i i   i  -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_63716870_6   4518 ----ACAATCTTAGTAAAATATAGGCATAGACTTCTTTGAATAGACATTT 4563
                         ---- i  i iv v ?   v  i    v  iv  ---             
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATT---TGAATAGACATTT 845

  chrX_63716870_6   4564 CTCAAAAGAAGACATGCAAATGACCAACAAATATATGAAAAGCTGCTCAG 4613
                            v        i  i      i    i  ii i        v      i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_63716870_6   4614 CATCACTAATCAT 4626
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (152 / 86)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


2944 27.29 2.01 0.56  chrX_63730436_63736240.rev     4421  5314 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_63730436_6   4421 GGAGAAACATTCCATGCTCATAGACAGGAAGAATCAATATTGTGAAAATG 4470
                            i i i  i     i    i  iv      v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_63730436_6   4471 GCCATACTGCCCAAAATAATTTACAGATTCAATGCTATTCCCATTAAAAT 4520
                           v     v      v i  i           i  v  i  i  i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_63730436_6   4521 ACCATTGACATTCTTCACAGAATTAGAAAAAATTACATTAAAATTCATAT 4570
                         v   vivi v  i  ii     v v  v  iv v ivi            
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_63730436_6   4571 GAAAC--CAAAGGAGAGCCCATA-TAGCCAAAATGATCCTAAGCAAAAAT 4617
                          i  v--   i   ---    v -         ii   i i iv  i  v
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63730436_6   4618 AACAAAGCTGGAGGCATCATACTACTCAACTTCAAACTGTACTACAAGGC 4667
                                i      vv   i   v i   i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63730436_6   4668 TACGGTAAT-----------GGTACTGGTACAAAAACAGACACATAGACC 4706
                            i     -----------        i i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63730436_6   4707 TATGGAACAGAACAGAAATCTCAGAAATAAGACCACACATCTATAACCAT 4756
                         v      i    iv  i vii         iv   i    i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_63730436_6   4757 TTGATTTTTGGCAAATCTGACAAAAACAACCAATGAA-AAAGGATTCCCT 4805
                                 i i   ivv  v   i v  vi     ii-    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_63730436_6   4806 ATTTATTAAATGGTGCTAGAAGAACTGGCTAGCCATATGCAGAAAATTAA 4855
                         v  i vi          i i v      v  ?   i     i  i v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_63730436_6   4856 AACTGGACCCCTTTCTTACACCTTATACAAAAATGATCTCAACATGGATT 4905
                          ii         vi  i     v           v v     v      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_63730436_6   4906 AAAGTCTTAAGTGTGAAACCCCAAACTCTAAAAACCCTAGAAGAAAATCT 4955
                          ?  v i   i   i i v iv     v     vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_63730436_6   4956 AGGCA-ATATCATTTAGGACATAGGCATGGGCAAACATTTTAT-GATGAA 5003
                            ?i- v   -  iiv   v v  vv i     vvi   iv -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chrX_63730436_6   5004 AACATCAAAAGCAATTGCAACAAACAAAAAACTGG-CAAATGGGATCTAA 5052
                         i   i        vvv        vi     v i -i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_63730436_6   5053 TTAAACTAAAGAGCTTCTGCGCAGCAAAAGAAACTATCATCAGAGTGAAC 5102
                          i   v v  i i   i  i  vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_63730436_6   5103 AGGCAACCTACAGAATGGGAGAAAATTTTGGCAATCTATCCATCTGACAA 5152
                           i     i                 v  v    vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_63730436_6   5153 AGGTATGATATTCGGAATCTCCAAGGAACTTAAACAAATTTACCATACAA 5202
                         i  vv vi   i i    v vi  i     ivv    v iv iv   v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_63730436_6   5203 AATAAAACAACCCTATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5252
                          ivv   i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_63730436_6   5253 TCTAAAGAAGACATTTATGTAGGCAACAAACATATGAAAAAAAGTTCAAC 5302
                           i        i  vi vi i v   i  i  i       i v i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_63730436_6   5303 ATCACTGATCAT 5314
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (138 / 102)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 2.30 (23 / 10)  


2741 27.37 1.79 0.34  chrX_63747615_63752237.rev     3245  4139 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63747615_6   3245 TGGAATCACATCCCATGCTCATGGATGGGTAGAATCAATAATGTGAAAAT 3294
                              vv i        i        v  v   v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63747615_6   3295 GACCGTAGTGCTAAAAGCAATCCACAGATTCAATGCAATTCCCATCAAAA 3344
                          i vi  v v iv   vii   i          i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63747615_6   3345 TACCATCATCATTCTTCACAGAAGTAG-TAAGAGAATCCTAAAATTCGTA 3393
                          v   v vv v  i  ii     i v -i   vvi            i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_63747615_6   3394 TGGAACCAAAAAAGAGCTCACATAGCTGAAGCAATACTAAACAAAAAGAA 3443
                              viiv  ii  v iviv     ii  i    vi i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_63747615_6   3444 CAAATCTGGAGGCATCACATCACCTGACTTCAAA--TTA-TACAAGGCTA 3490
                             vi      vv     iiv  ii i      --   -     i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_63747615_6   3491 CAGTTACCAAAACAACATGGTACTGTTATAAAAATAGGAACATAGACCAA 3540
                             v i   i   iii        vi    ii    iv i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_63747615_6   3541 TGGAACAGGATAAAGAACCTGGAAAAAAATCCAAATATTTACAGCCAAAT 3590
                              i  i  vi   ii ii    v   i   v i     ii i   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_63747615_6   3591 AATCTTTGACAAAGCATACAAAAAT-ATAAATTTGAGAAAGAACACTTTA 3639
                         i  i  i     i -i i v  i i-  vv v v i       i v i v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_63747615_6   3640 TTCAATAAATGGTTCTGGGAAAACTGACAAGCCATATGTAGAAGAATGAA 3689
                              i       v      v     ivv ?   i   i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_63747615_6   3690 ACTGGATGCACATCTTTCACCTTATACAAAAATCAACTCAAGATAAATAA 3739
                         ii    iv vi i  iv    v           i       i  ii  v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_63747615_6   3740 AAAAAATTACATCTAAGACCTAAAACCATAAAAATTCTAGAAGATAACAT 3789
                         ? i v-i  v  v     v       i      v ii       v     
  L1M4_orf2#LINE/    500 WAGAC-CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_63747615_6   3790 AGGAAAAACTTTTCTGGACATTAGGTTAGGCAAATAATTCATTAC-TAAG 3838
                            ?iv  v i   vv   v  i          - ii  iv   v-  v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATG 597

  chrX_63747615_6   3839 TCTCCAAAAGCAAATGCAACAAATCCAAAAATAAATAGATGGGACCTGAT 3888
                         v v         v v        vvv       i   i  v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_63747615_6   3889 TAAACTAAAAGTCTTCTGCATAGCAAAAGAAATAATCACTAGAGTAAAGA 3938
                         i   v v   iv   i  iiivv    i  v iv    vv i   i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_63747615_6   3939 GAGAACTCACAGAATGGGAGAAAATATTCTCAAACTATGCATCTAACAAA 3988
                           v   i                     iv    ii  ii    i i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_63747615_6   3989 AGAATAGTACCCAGAATTTACAAGGAACTCAAACAAATCAGCAAGAAAAA 4038
                         i  v v   i       v  i  i      vv    v   ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_63747615_6   4039 ---AAAT--CCCA-TCAAAAAATAG-CAAAGGACATGAATAGACAATACT 4081
                         ---    --    - i?      i -       iv          v v  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_63747615_6   4082 CAAAAGAAGATATACAAACAGCCAACAAACGTATAAAA---TGCCCCAAA 4128
                          v                ii     i  i ii  i   ---   i v v 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_63747615_6   4129 TTACTAATCAT 4139
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.39 (140 / 101)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


2940 28.42 0.34 0.46  chrX_63762215_63767208.rev     3628  4503 (491)    L1M4_orf2#LINE/L1       34   908 (0)  

  chrX_63762215_6   3628 CTCAAGGTTGTGAAAATGGCCATACTTCCTAAAGTAATTTATAGATTTAA 3677
                           i  vi    v  i     v     i  i   v i  i  i     i  
  L1M4_orf2#LINE/     34 CTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAA 83

  chrX_63762215_6   3678 TGCTCTCCCCATCAAGCTACCATTGACTTTCTTCACAGAATTAGAAAAAA 3727
                         i  vv    i     iv v   vivi i  i  ii     v v  v  i-
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG- 132

  chrX_63762215_6   3728 CT-ACTTTAAATTTCATATGGAACCAAAAAAGAGCCTACATAGCCAAGAC 3776
                           - iii    v           viiv  ii  v  viv        i  
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chrX_63762215_6   3777 AATCCTGAACAAAAAGAACAAAGTTAGAGGCATCACGCTACCTGACTTCA 3826
                             i    v  i            i    vv    i  v  ii i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_63762215_6   3827 AAGTATACCACAAGGCTACGGTAACCGAAACAGCATGGTACTGGTAACAA 3876
                           iiv   i    i     i    i i i    ii         i vv i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_63762215_6   3877 AACAGAGATATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCC 3926
                         i i   v       i        i    iv   ivii         vv  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_63762215_6   3927 ACACATTTACAACTATCTGATCTTTGACAAACCTGACAAAAACAAGCAAT 3976
                          i       iiiii vi    i  i     ivv  v   i v  vv    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_63762215_6   3977 GGGGAAAAAAT--TCCGTATTTAATAAATGGTGCTGGGACAACTGGCTAG 4024
                                i   --  -- v  i  i                     v  ?
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_63762215_6   4025 CCACATGCAGAAAACTGAAACTGGACCCCTTCCATACACCTTATACAAAA 4074
                                  i  i v    ii         v  vi     v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_63762215_6   4075 ATTAACTCAAGATGAATTAAAGACTTAAACCTAAGACCTAAAACCATAAA 4124
                                   i   i  i ?    i    iv     v       i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_63762215_6   4125 AACCCTAGAAGAAAACCTAGGCATTACCATTCAGGAAATAGACATGGGCA 4174
                          vi i           v    ?i v viv   iv  vv v ivv i    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_63762215_6   4175 AAGACTTCATGACTAAAATAACAAAAGCAATGGCAATGAAAGCCAAAATT 4224
                          v ii   v iiv  vi i v        vvi    ii    vv     v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_63762215_6   4225 GACAAATAAGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAAGAAA 4274
                           i    vi  ii v  i   v v  i i   i  ii vv    i-  v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GACA 679

  chrX_63762215_6   4275 CTATCATCAGAATAAACAGGCAACCTACAGAATGGGAGAAAATCTTTGCA 4324
                               vv i i i  v  i     i                 v      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_63762215_6   4325 ATCTACCCATCTGACAAAGGGCTAATATTCAGAATCTACAAGGAACTTAA 4374
                          vii ivi      i  i  i  vi   i      v  i  i     ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_63762215_6   4375 ACACATTTACAAGAAGAAAACAAGCAACTTCACCAAAAAGTGGGTGAAGG 4424
                            vv iv i  v  i  i    ii   iiv ii?    i    ii    
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_63762215_6   4425 ATATAAACAGGCATATCTCAAAAGAAGACATTTATGTGGCCAACAAATAT 4474
                           v i  i  i   v    v        i  vi vi       i  ii i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_63762215_6   4475 ATGCAAAAAAGCTCATCATCACTGGTCAT 4503
                            v   i v     v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.01 (5 / 875), avg. gap size = 1.40 (7 / 5)  


2971 28.10 1.11 0.66  chrX_63773181_63777970.rev     3396  4299 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63773181_6   3396 TAGAAGAACATTCCACGCTCACGGATAGGAAGAATCAACATCATGAAAAT 3445
                          i   ii i  i   i i   i    v      v i  i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63773181_6   3446 GTCCATACTGCTGAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3495
                          v v     v iv   v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63773181_6   3496 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAATTTT 3543
                          v   iivi i  i  ii     -   --- v  i  - iii    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_63773181_6   3544 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCCAAGGAAAAA 3593
                                 viiv  ii  v  v v  v     i      iii ii  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_63773181_6   3594 GAGCAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 3643
                           i     i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_63773181_6   3644 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 3693
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_63773181_6   3694 CACTGGAACAAAAC-AAGGGCTCAGAAATAACACCACACATCTACAATCA 3742
                           v     i i  i-i  i ii         vv   i    i  iii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_63773181_6   3743 TCTGATCTTTGACAAACCTGACAAAAACAAGAAACAGGGAAAGGATTGCC 3792
                         vi    i  i     ivv  v   i v  vvv  ii       i  v i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_63773181_6   3793 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 3842
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_63773181_6   3843 AAACTGGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGAT 3892
                           ii    i  i v   i     v              i    ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_63773181_6   3893 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-ACAAGAATAC 3941
                         i ?    i       v   v       i      -    - v     v  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chrX_63773181_6   3942 CTAGGCA-ATACCATTCAGGACATAGGCATAGGCAAGGACTTCATGATTA 3990
                         v    ?i- v i -   iv   v v  vv       v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_63773181_6   3991 AACCACCAAAAGCAATGAG-AACAAAAGCCAAAATTGACAAATGGGATCT 4039
                         viv           -ii  -        vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_63773181_6   4040 AATTAAACTAAAGAGCTCCTGCACGGCAAAAGAAATTACCATCAGAATGT 4089
                         v  i   v v  i i  ii  ii vv    i  v i  i  vv i i  v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_63773181_6   4090 ACAGGAAATCTACAAAATAGGAGAAAATTTTTGCCATCTACCCATCTGAT 4139
                          v  iv  i i   i   i         v     v vii ivi       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_63773181_6   4140 GAAGGGCTAATATCCAGAATCTACAAAAAACTCAAACAAATTTAGAAGAA 4189
                         i i  i  vi          v  i   i     vv    v iv v  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_63773181_6   4190 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAAGAGACACT 4235
                            i    ----   v  i?    i            v    v     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_63773181_6   4236 TCACAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 4285
                           v v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_63773181_6   4286 TCATCACTGGTCAT 4299
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (154 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


2628 27.79 4.33 0.91  chrX_63780368_63783151.rev     1415  2292 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63780368_6   1415 TGGAGAAACATCCCATACTCATTGATGAAAAGAATTAATATCATTAAAAT 1464
                             i i i       ii    v   vii    v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63780368_6   1465 GACCATATTGCCCAAATCTATATACAGATTCAGTGCAATTCCTATGATAA 1514
                          i v   i v       iv  v          ii     i     v v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63780368_6   1515 TAC-AACATTTTACTTTACAGAATTAGAAAAAACAATTATAAAACTCATA 1563
                          v - i vvii vi   i     v v  v  ivii  iv     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_63780368_6   1564 TG---ATACCAAAAAAAAGCTCAGA-TAGCCAAAGCAATCCTGAGTAA-A 1608
                           ---  i ----  iiii i    -        i     i   iv  - 
  L1M4_orf2#LINE/    151 TGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_63780368_6   1609 AGAGCAAAACTAAAGGCATCATATTAACTGACTTCAATATATATTTCAAG 1658
                            i    ii ii   vv   i i vv ii i     v iv  i v   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63780368_6   1659 GCTATAGTAACCAAAACAGCATGATGTCAG-ATAAAAGT-GACACATAGA 1706
                             i     i   i    ii  i iiii -    iii -    i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_63780368_6   1707 CCAATTAAAAAGAGTAGAAGACCCAGAAATAAAGCCACATGTTTATAATC 1756
                         i    vi  v   i v  iiii           v   i ii     ii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_63780368_6   1757 AACCAATCTTTGTCCAGCCAAACAAAGTTATTT--TGAGGAAAGGGCACT 1804
                           iii  i  i v v  vvviv   iiii   i--  i      iii v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63780368_6   1805 CTTTCTAATAAATGGTACTTGGAACATTGGATAGCCACATGATGAGGAAT 1854
                             ii  i       i  v   vv i      ?       vvi i    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63780368_6   1855 GAAAGTGGATCCTTATCTCTCACCATAGACAAGAATCAACACAAGATGAA 1904
                            iv    i  i  i   v       v    i   i   v   i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_63780368_6   1905 TTAGAGACTTAAACATGAGCCCCAAGATTATGTAGCTACTAGAAGAAAAT 1954
                          i ?    i    ii i  vv i  i i   iv i  vi          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_63780368_6   1955 ATAGGA--AAATCTCTCCTGGACATTGGTCTAGGCAAATGATTTAT--GA 2000
                              ?--      -  v  -  v    vi       -  i   v --  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCT-TCGTG-ACCTTGGGTTAGGCAA-TGGTTTCTTAGA 593

  chrX_63780368_6   2001 CTAAGACCTCAAAAGCACAGACAACAAAAACAGACATAGACAAATGGGAC 2050
                         -  v   vi          ii        iv i v     i    v    
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_63780368_6   2051 TTAAACAAAA---AAAGCTTCTATACAGCAAA-------AT-AATAGATT 2089
                           v v     ---   i   i i i vv    -------  -  v i v 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_63780368_6   2090 GACGAGAT--TTTATTGAGTTGCAGAAAATATTTGCAAGCTATTCATGTA 2137
                           vi   i--iii iv  i v v               iii  vi  v i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_63780368_6   2138 ACAAGGTACTAATATCCAAAATATACAAGCAACTG----AACTCAACGGG 2183
                          i    v   vi      i      i  iv    v----       iiiv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_63780368_6   2184 AAAAAAA-----AATCCCATTAAAAAGTGGGCAAATAATATGAATGGACA 2228
                              i -----  i  v   ?    i        vi  v     i    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_63780368_6   2229 TGTCTCCAAAGAAGATACACAAATGGCCAATATGTGTATAAAAA--TGCT 2276
                          v               i              v iii  i    --    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_63780368_6   2277 CAACATCACGAATCAT 2292
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (159 / 81)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.19 (46 / 21)  


3105 28.02 0.33 0.55  chrX_63810807_63822587     4972  5881 (5900)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63810807_6   4972 TAGAAATACATTACATGTTCATGGATAGGAAGAATCAATATCAAGAAAAT 5021
                          i    v i  iv             v      v i     iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63810807_6   5022 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5071
                            v     v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63810807_6   5072 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAACT-ACTTTAAAGTT 5119
                          v   iivi i  i  ii     -   ---- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chrX_63810807_6   5120 CATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATTCTAAGCCAAA 5169
                                  viiv  ii  v  viv  v     i     ii i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_63810807_6   5170 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTGCAAG 5219
                                  i      vv   ii  v  ii i      viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63810807_6   5220 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5269
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_63810807_6   5270 CCAATGGAACAGAACGGAGCCCTCAGAAATAATACCACACATCTACAACC 5319
                         i        i    iv   vvii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_63810807_6   5320 ATCTGATCTTTGACAAACATGACAAAAACAAGCAATGAGGAAAGGATTCC 5369
                          vi    i  i     ivi  v   i v  vv     i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63810807_6   5370 CTATTTAATAAATGGTGGTGGGAAAACAGGCTAGACATATGTAGAAAGCT 5419
                           v  i  i        v     v   v  v  ?v  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63810807_6   5420 GAAACTGGATCCCTTTCTTACAACTAATACAAAAATTAATTCAAGATGGA 5469
                            ii    i    vi  i   v vv             i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_63810807_6   5470 TTAAAGACTTAAATCTTAGACCTAAATCCATAAAAACCCTAGAAGAAAAC 5519
                          i ?    i     v v   v     v i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_63810807_6   5520 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5568
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_63810807_6   5569 AAACACCAAAAGCAATGGCAACAAAGGCCAAAATTGACAAATGGGATCTA 5618
                         vi            vvi        i vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_63810807_6   5619 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5668
                           i   v i  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_63810807_6   5669 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTGCCCATCTGACA 5718
                         v  i     i                 v   i   viiiivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_63810807_6   5719 AAGGGCTAATATCCAGAATCTACAAAGAACTTTAAAAAATTTACAAGAAA 5768
                          i  i  vi          v  i        i v v  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_63810807_6   5769 AAATCAAACAACCCCTTCAAAAAGTGGTCAAAGGATATGAACAGACACTT 5818
                           iv    i     vv i?    i   v        v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_63810807_6   5819 CTCAAAAGAAGACATTTATGTAGCCAACAGACACATGAAAAAATGCTCAT 5868
                            v        i  vi vi i     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_63810807_6   5869 CATCACTGGCCAT 5881
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (148 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

2606 27.26 1.88 1.66  chrX_63810807_63822587    10383 11288 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63810807_6  10383 TGGCAAAACATTTCATCCTCATGGATAGAAAGAATCAATATCATGAAAAT 10432
                            v  i i  ii   vi        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63810807_6  10433 GGCCATACTGCCCAAAGTAACTTATAGATTCAATGATATTCCCATCAACC 10482
                            v     v      v i ii  i        i vv  i  i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63810807_6  10483 TACCATTGGCATTCTTCACAGAATTAGAAAGAAACT-ACCTTAAAATTCA 10531
                          v   viv  v  i  ii     v v  v -- i  - i i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA--AGCTGATCCTAAAATTCA 148

  chrX_63810807_6  10532 TATGGAACCAAAAAAGAGCCCACAA-AGCCAAGATAATCCTAAGCAAAAC 10580
                                viiv  ii  -    v  -      i i    i i iv  i v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_63810807_6  10581 GAATAATGCTGGAGGCATCACACTACCAGACTTCAAACTATGCTACAAGG 10630
                            i  v i      vv       v  vi i      viv i      i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_63810807_6  10631 CTACAGTAACCAAAACAACATGGTAATGGTACCAAAACAGATATATAGAC 10680
                                  i   i   iii     v   i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_63810807_6  10681 CAATGGAACATAAGAGAGACTTCAGAAATAAGACCACACATCTACAACCA 10730
                                 i v  vv    v i         iv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_63810807_6  10731 TCTGATCTTTGACAAAGCTGACAAAGACAAACAATGCAGAAAGGAT-TTC 10779
                         vi    i  i     i v  v   iiv  vv     vi     i  -v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_63810807_6  10780 ATATTTAATAAATAATGCTAAAAAAAAACTGGCTAGTCATATGCAGAAAA 10829
                         v -  i  i    ii    iii v  --    v  ?i  i     i  i 
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAA--CTGGATAKCCACATGCAAAAGA 444

  chrX_63810807_6  10830 TTGAAAATGGACCTCTTCCTTACACCTTATACAAAAAAATAATTCGAGAT 10879
                         v    iv      i  v   i     v          v-   i  i i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAACTCAAAAT 493

  chrX_63810807_6  10880 GGATTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAA 10929
                             i ?    i         i v i     i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_63810807_6  10930 AGCATAGGCG-ATACCATTCAGGACATAGGCATGGGCAAAGATTTTAT-G 10977
                          i      ? - v i -   iv   v v  vv i     v i   iv - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_63810807_6  10978 ATGAAATAACCAAAA--ACAATTGCAACAAAAACTAAAATTGACAAATGG 11025
                           ivi i -      --    --         ivv     v  i    v 
  L1M4_orf2#LINE/    593 ATATGACA-CCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_63810807_6  11026 GATCTAATTAAA-CAAAGAGGTTCTACACAGCAAAAGAAACTGCTATCAG 11074
                           ii v  i   -iv  i iv  i iii vv    i  v   ---    -
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT---ATCA- 685

  chrX_63810807_6  11075 AGCAAGCGAAAAGGCAACCTACAGAATAGGAGAAATT-TTTGCAATTTAC 11123
                           v   i      i     i       i       v -       v i i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_63810807_6  11124 CCATCTGACAAAGGTCTAATATCCAGAATTTACAAGAAATTTAAACAAAT 11173
                         vi      i  i  v  vi          v  i  ii  i ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_63810807_6  11174 TTACAA-------ACAAACAACCCCATCAATAAGTGGGCAA-GGAAATAA 11215
                         iv i  -------     i     v  i? v  i       -   vv i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_63810807_6  11216 ACAGACACTTCTCAAAAGAAAACATTTATGGGGCAAAGAAACATATGAAA 11265
                          i     i     v      i i  vi viv   v  v  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_63810807_6  11266 AAAAGCTCAACATCACTAATTAT 11288
                          i v           ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.60 (32 / 20)  


2105 24.44 2.39 1.54  chrX_63829946_63832457.rev      502  1086 (1426)    L1M4_orf2#LINE/L1       63   652 (256)  

  chrX_63829946_6    502 CAAATTAATTTACAAATCCAATGGAATCC-TATCAAAATCCAAACATTTT 550
                               i  i    i  i   i v     -           v i vvii 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_63829946_6    551 TTTTTGTGGAAATTGACAAGTGGAATCTAAAATTCATATAGAAATGCAAA 600
                               ii            iv  vi             i         i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_63829946_6    601 GGGCCCAGAATAGCCAAAATTAAACCTGAAGAAGAATAACAAAGTTGGAA 650
                           i                i-  v i    i     v            i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAAC-AATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_63829946_6    651 AACTTATACTACCTGGTTATAGGAATTATTATAAAGGTACAGTAATAAAA 700
                         i   i i   v  iii  vi ii v   i  i    v         v  i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_63829946_6    701 GCAGCAAAGTATTGGCATAAAGATAGACAAATAAATTAATGAAGCAGAA- 749
                         i   iivi   i        i        v   i  i    i ii    -
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_63829946_6    750 ----AGTTCAGAAATAAACATACAAATATATAGACAACTGATCTTTGATA 795
                         ----   i           vi i v  v   i v   i    i  i  i 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_63829946_6    796 AAGGTGCAAAGGCAATGCTGTGGAGAAAGGATAGTTTTTCAAACAAATAG 845
                          i     v   i v  v vi   i     i     i   iv       i 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_63829946_6    846 TTCTGAAACAACTGGACATCCATATGCAAAACAA--ATCTTTAACTCATA 893
                          v   ii         i ?   i        v  -- vv  vi  i v  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_63829946_6    894 TCTGGTACCACATACATGATTTAAGTAAAACTGGATCATAGATCTAAATG 943
                         i  vii    i     vi v    v v   v       ?   i       
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_63829946_6    944 TAAAATTTAAAA--ATAA--CTTTCTGGAAGAAATTTTAGGAGAAAATGT 989
                            i vi     --    --  i - i       viv    ? v    v 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAACATAGGNGTAAATCT 560

  chrX_63829946_6    990 TTGTGACTATGGCTTAGGCAAATAATTTTTTA--TATTGTACAAAAAGTC 1037
                          i     iv   v        - ii   i   --   vii  v     - 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAG-C 608

  chrX_63829946_6   1038 ATTATCCATAAAAGAAAATACTGATGAGTTAGAATGGCGATCATTAAAA 1086
                          iv v v i         v iv   i i  i  v -----    i    
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACT-----TCATCAAAA 652

Transitions / transversions = 1.75 (89 / 51)
Gap_init rate = 0.02 (11 / 590), avg. gap size = 2.09 (23 / 11)  

 654 27.94 3.17 3.81  chrX_63829946_63832457.rev     1713  2027 (485)    L1M4_orf2#LINE/L1      596   908 (0)  

  chrX_63829946_6   1713 TAAAACTTAAAGTATAA-TAAAAAAAGAAAGAAAATACTGATGAATTGGA 1761
                          i v  iv    i i  -i  v        --     --   i       
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAA--AAATA--GATAAATTGGA 641

  chrX_63829946_6   1762 TATTACAAAATCAATATTAAAAACTTTTGCAATTCAATAGACA--GTTAG 1809
                         iv i -----    v              iiv     vi    --i i i
  L1M4_orf2#LINE/    642 CTTCA-----TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_63829946_6   1810 AGGAATAAAAATATAAGTTCCAGACCGGGAGACTGTGTTTGCAAA----G 1855
                         iii i i    v i  viiv    vi      vvi i        ----i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_63829946_6   1856 TGTCTGATGAAGAACTTGTATTTAGAAAATACAAAGAACACTCAAAATTC 1905
                          i      i i i        ii    v   i       v  i v  i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_63829946_6   1906 A-CAAGCAGTAACTAAACAACCAAACTGTAAAACAGGCAAAG--TTTGAA 1952
                          -i  vv iv ivi   i    v  i ?v    ii       --      
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_63829946_6   1953 TATATACATCAACAAAGCAGGTATATGGGTGAAAAATAAAGTCATGAAGA 2002
                           v i iv  vv     v  i    iiii  ivv     ivv      i 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_63829946_6   2003 GATGCTTGACAGGGTTAATCATTAA 2027
                               ii   --- i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACA---TCAZZZZZZZZ 908

Transitions / transversions = 1.81 (56 / 31)
Gap_init rate = 0.03 (9 / 313), avg. gap size = 2.44 (22 / 9)  


1539 25.85 3.41 2.81  chrX_63835415_63839270.rev        1   499 (3357)    L1M4_orf2#LINE/L1      271   772 (136)  

  chrX_63835415_6      1 TACTGGCATAAAGCCAGACACACCAACCAATAAAAAAGTATAGAAAGCCA 50
                                    i vi     i ivi i    ii  v  v  v  i  i v
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_63835415_6     51 AGAAATAAACCCAAGTATTTACAGTCAGTTGATTTTTGACAAAGATGCCA 100
                                      vii     ii    i        i     i i     
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_63835415_6    101 AGAACATCCAGTGGAAAAAGGACAGTCTT--AAATAAAAATGATTTTAGA 148
                            v   i  i   ii    i i      --v  i   --  i vi i i
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA--TGGTGCTGGG 418

  chrX_63835415_6    149 AAAACTTAAATATCCACACGCAGAAGAATAAAGTTGAATCCCTGTCTTAC 198
                          v    -ii   ?     i   i      i      i i    ii  i  
  L1M4_orf2#LINE/    419 ACAACT-GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_63835415_6    199 ACTTTATAGAGAAATGAACACAAAATAGATTAAAGACTTCAAC--AAAAT 246
                           iv    v i    v   v      i   i ?    i v  i--  i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_63835415_6    247 CTTGAAACTGTAAAACTACTAGAATAAGGCA-AAGATCAAAGCACCACAA 295
                           -i     i       vi     v  ii  - i ?vi   v vi iii 
  L1M4_orf2#LINE/    518 CT-AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_63835415_6    296 CATTGGTCTGGTCTGGGCAATGATTTCTTGAATAGGACTCCAAAAGCAGA 345
                          v    ----  - i       i      ii   v   v         v 
  L1M4_orf2#LINE/    567 CCTTGG----GT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_63835415_6    346 GGCAGGAAAAGCAAAAATTGACAAATTGGATTACACCAATATTTCAGAGA 395
                         i   iv     v      v  i        i v  i   v   -----i 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT-----AA 656

  chrX_63835415_6    396 AGA------------AAATAAAATAATTAACAGAGTCAGGAGACATCACA 433
                          i ------------   vi v iv  i  v i   v ii     v v  
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_63835415_6    434 GAGATTGGGAGAAAATACTTGCAATCCATATATCTGATGAGGGGATTATA 483
                         v   v            i      vi            i    iv  i  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_63835415_6    484 TAAAAAATATATGAGG 499
                          vv i       i i 
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAG 772

Transitions / transversions = 1.86 (82 / 44)
Gap_init rate = 0.02 (10 / 502), avg. gap size = 3.10 (31 / 10)  

1434 25.86 0.46 0.46  chrX_63835415_63839270.rev     1132  1568 (2288)    L1M4_orf2#LINE/L1      472   908 (0)  

  chrX_63835415_6   1132 TATACAAAAATTAACTCAAGATGGATTAAAGACTTAAATATAAGACCTAA 1181
                                            i      i ?    i     i     v    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_63835415_6   1182 AACCATAAAAACCATAGAAGAAAACCTAGGCA-ATACCATTCACGACATA 1230
                            i      vi v           v    ?i- v i -   ii   v v
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTT 570

  chrX_63835415_6   1231 GGCCTGGTCAAAGACTTCAT-GACAGAAACACCAAAAGCAATGGCAACAA 1279
                           vi i v   v ii   v -  i vi -           vvi       
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAA 619

  chrX_63835415_6   1280 AAACCAAAATTGACAAATGGCATCTGATTAAACTAAAGAACTTCTGCACA 1329
                           ivv     v  i    v v ii v  i   v v  i     i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_63835415_6   1330 GCAAAAGAAACTATCATCAGAGTGAACAGGCAACCTACGGAATGTGAGAA 1379
                         v    i  v       vv i      v  i     i  i     v     
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_63835415_6   1380 TATTTTTACAGTCTATCTATCTGACAAAGGCTTAATATCCAGAATCTACA 1429
                         v  v   i  ivii  v       i  i  vi vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_63835415_6   1430 AAGAACTTAAACAGATTTACAAGAAAAAAATAAGCAACCCCATCAAAAAG 1479
                                ivv   iv iv i  v     i i  ii     v  i?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_63835415_6   1480 TGGGCAAAGGATATGAACAGACAGTTCTCAAAAGAAGATATTTTTGTAGG 1529
                                     v    i     v     v           vivvi i v
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_63835415_6   1530 CAAAAAACATATGAAAAAAAGCTCGTCATCACTGGTCAT 1568
                            v  i  i       i v    iv     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (58 / 52)
Gap_init rate = 0.01 (4 / 437), avg. gap size = 1.00 (4 / 4)  

2455 27.11 7.63 1.06  chrX_63835415_63839270.rev     2514  3365 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63835415_6   2514 TAGAAAAACATTCCATGTGCATGGATAGGAAGAATCAATATTATTAATAT 2563
                          i    i i  i      v       v      v i      i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63835415_6   2564 GGCCATACTGACTAAAGAAATTTATAGATTCAATGCTATTTCTACTAAAC 2613
                            v     vv i   vvi  i  i        i  v  ii   ii   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63835415_6   2614 TGCCAATCACATTCTTTACAGTACTAGTAAAAAACT-ATTTTAAATCTCA 2662
                          v   iiii v  i   i   v v -- i v  i  -  ii    vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCA 148

  chrX_63835415_6   2663 TATGGAACCA-AAAGAAGCCTGAATAATCAAGGAACTCCTATGCAAAAAG 2711
                                vii-  i i v  v     ii   iiv v  i iviv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63835415_6   2712 GGCAACACTGGAGGCATCATGCTACACAACTTCAAA-----CTACAGGGC 2756
                         ii   vii      vv   ii  v v   i      -----     ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63835415_6   2757 TACAGCAAGCAAAACAGCATGGTACTCGTACAAAAACAGACACATAGACC 2806
                              i  v   i    ii       v i i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63835415_6   2807 AATGGAACAGAACAGAGAACCCAGAATTAAAGCCGCACAGCTACAACTAT 2856
                                i    iv    ii      v    v  ii   vi  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_63835415_6   2857 CTGAACTTTGA-AAAGCTGAAAAAAACAAGTAACGGGGAAAGAATTCCCT 2905
                         i   vi  i  -  i v  vv  i v  vvi  i           vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_63835415_6   2906 ATTCAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGTAGAAGATTGA 2955
                         v     i              v      v  ?   i   i i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_63835415_6   2956 AACTGGACTTTTTCCTTACATCGTATACAAAAATTAACTCAAGATGGATT 3005
                          ii     iii v   i   i i                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_63835415_6   3006 ATAGACTTAAATGTAAAACCCAAAACTATAAAAGCCCTGGAAGACAACCT 3055
                          ?    i         i v i            vi i i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_63835415_6   3056 AAGA------TTTCATGA---TGAA-----------------------GA 3073
                          i ?------i   i   ---  ii-----------------------  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_63835415_6   3074 CACCAAAGAAATTC---CAACAAAAGCAAAAATTGACA-------CT--- 3110
                                -- iiv ---         v      v  i -------  ---
  L1M4_orf2#LINE/    599 CACCAAA--AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_63835415_6   3111 ----AATTAAACAGCTTCTGCACAGCCAAAGAAAC-------AGATTGAT 3149
                         ----       - i   i  ii vv v  i  v  ------- i v   v
  L1M4_orf2#LINE/    647 TCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_63835415_6   3150 CAGAAAGCCTACATTATGGGAGAAAATTTTTGCAAACTATGCTA-CTGAG 3198
                         v   v i  i   vv            v        ii  i-  -    v
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA-TATCTGAT 744

  chrX_63835415_6   3199 AAAGGTCTAATATCCAGCATCTACACAGAACTTAAACATATTTACCACAA 3248
                           i  v  vi       v  v  i v      ivv   vv iv iv i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_63835415_6   3249 AAATCTGAACAACCCCATTTAAAAGTGGGCAAAGGACATGACCAGATAGT 3298
                            vvii  i     v   ?    i           iv   vi   i v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_63835415_6   3299 TCTCAAAAGAAGACATACATGTGGCCAACAATCACTTGAGAAAAAAAAGC 3348
                             v        i     vi       i  v   v   ---   i v  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA---AAAGATGC 891

  chrX_63835415_6   3349 TAAACATCACTGATCAT 3365
                          v       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (135 / 92)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.35 (74 / 17)  


2900 27.46 1.44 0.89  chrX_63841769_63845903.rev     2742  3644 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63841769_6   2742 TGAAAACACATCCCATACTCATGGATGGGTAGAATCAATATTGTGAAAAT 2791
                           i   v i       ii        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63841769_6   2792 GACCGTACTGCCAAAAGCAATCTACAAATTCAACACAATCCCCATCAAAA 2841
                          i vi    v  v   vii       i       i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63841769_6   2842 TATCACCATCATTCCTCACAGAGTTAGAAAAAAAAATTCTAAAATTCACA 2891
                          vi  v vv v  ii ii    iv v  v  ivvi  i          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_63841769_6   2892 TGGAACCAAAAAAGAGCCCACATAGCCAAAGTGAGACTAAGCAAAAAGAA 2941
                              viiv  ii  v  viv         iii vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_63841769_6   2942 CAAACCTGGAGGCATCACACTACCTGATTCCAAACTATACTATAAGGCCA 2991
                             vi      vv       v  ii   i    viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_63841769_6   2992 TAGTAACCAAAACAGCTTGGCACTGCTATAAAAATAGTCACATA-ACCAA 3040
                         i     i   i    iv   i    vi    ii    v  i   - i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_63841769_6   3041 TGGAATGGAATAGAGAACACAGAAATAAATCCAAATACTTACAGCCAGTA 3090
                               i    v    iiv          i   v i i   ii i  i v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_63841769_6   3091 GATATTCAACAAAGTAAACAAAAACATAAAGTGGGGAAAGGACACCCTTT 3140
                            v   i    i vviv   i v   vv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_63841769_6   3141 TGAACAAATGGTGCTAGGATAATTGGCTAGCCACATGTAGGAGAATGAAA 3190
                          v             i   i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_63841769_6   3191 CTGGATCCTCATCTCTCACCTTATACAAAAACCAACTCAAGATGGATTAA 3240
                         i    i  ii i   v    v          ii       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_63841769_6   3241 GGAATTAAACCTAAGAACTGAAA-TATAAAAATTCTAGATGATAACATTG 3289
                         i  vi    iv     i  i   -       v ii    v  v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_63841769_6   3290 GAAAAACCCTCCTTGACATTGGCTTAG-CAAAGATTTC------ATGAC- 3331
                          ?iv  vi  i v    v    v    -   v i    ------     -
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_63841769_6   3332 -CAAAAACCCAAAAGCCATTGTAATAAAAACAAAGATAAATAGCCGGGAC 3380
                         -     i v   -------- i  i    iv   i   i   iviv    
  L1M4_orf2#LINE/    601 CCAAAAGCACAA--------GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_63841769_6   3381 CTAATTAAACTAAAGAGCTTTTGCATGGCAAAAGCAACAGTCAGCAGAGT 3430
                         i v  i   v v  i i      iiivv    i vv  vi   iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_63841769_6   3431 AAACAGACAACCCACAGAATGAGCAAAAATCTTCATAATCTATACATGTG 3480
                         i  v                 i vi     v  iii  vii   i  v  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_63841769_6   3481 ACAAAGAGCTAATATCCAGAGTCTACAATGAACTCAAACAAATCAGTAAG 3530
                          i  i ii  vi        i v  i  v      vv    v   i   v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_63841769_6   3531 AAAAAAA--ACCAATCTCATCAAAAAGTGGGCTAAGGACATGAATAAAGA 3578
                              i -- vi  i iv  i?    i     v     iv      i v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_63841769_6   3579 ATTCACAAAAGAAGATATAAAAATGGCCAACAAACATATGAAAAAATGCT 3628
                         v   v v            v          i  i  i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_63841769_6   3629 CAACATCACTAATAAT 3644
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.00 (21 / 7)  


2415 27.22 0.45 0.45  chrX_63878874_63881245      607  1271 (1101)    L1M4_orf2#LINE/L1        1   665 (243)  

  chrX_63878874_6    607 TGGAAAAATATCCCATGTTCATGGATAGGGATAATCAATATTGTGACAA- 655
                               i                   v  i v v i        v vi -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63878874_6    656 GG-AGTATTCTACCCAAAGCAATCTACAGATTCAGTGCAATCTCTGTCAA 704
                           - i  i  --      vii             ii      i  i    
  L1M4_orf2#LINE/     51 GGCAATACTC--CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_63878874_6    705 GATACCAATAACATTCCTCACAGAAATAGAAAAAACAATCCTAAAATTTA 754
                         i  v   iivi v  ii ii       v  v  ivii           i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_63878874_6    755 TATGGGACCATAAAAGACCCAGCATAGCCAAAGCTATACTGAGCAAGATG 804
                              i viii  ii       v         i v  vi   iv    v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63878874_6    805 AACAAAACAGGAGGAATCACATTACTTGACTTCAAATTATACTACAGAGA 854
                               iiv      v     i v iii i      viv       i  v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63878874_6    855 TATAGTAATCAAAACAACGTGGTACTCACATAAAAACAGACATATAGACC 904
                           i         i   ii        vi     ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63878874_6    905 ATTGAAACAGAATAGAGAACCCAGAAGCAAATCCAAACATCTACAGAGAG 954
                          v  i  i     v    ii      ii   i   v    i  ii vv i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_63878874_6    955 CTCATTTTTCACAAAGGTGCCAAGAACATAAATTGGGGAAAAGAGAGTCT 1004
                         i v     iv    i          v   vv v        ii v     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_63878874_6   1005 CTTCAATAAATGATGCTTGGAAAACTGGATATTCATGTGCAGCAGGATGA 1054
                         i     i     i    v   v         ?i  ii    iv  i    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_63878874_6   1055 AACTAGACCTCTATGTCTTACTACGTACAAAAATAAAACCCAAATAGATG 1104
                          ii i    i   iv  vi  i ii         v  vi v    i   v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_63878874_6   1105 CAAGACTTAAATCTAAGACCTAAAACTATGAAACCACTACAAGGAAACAT 1154
                         v?    i     v     v          i    ivi  v   i      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_63878874_6   1155 TGGGGAAATTCTCCAAGACATTGGTCTGGGCAAAACTTTCTTGTGTCGTA 1204
                         v  ? v  v   i iv   v    vi i     viv      ivi vvv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_63878874_6   1205 TTCCACAAGCACAGGAAACCAAAGCAAAAATGGACAAATAGAATCACAT- 1253
                         iv   v       i v   v    v      i  i    v i iiv   -
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_63878874_6   1254 GAAGTTAAAAAGCTTCTG 1271
                         i  i       -   i  
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTG 665

Transitions / transversions = 1.54 (108 / 70)
Gap_init rate = 0.01 (5 / 665), avg. gap size = 1.20 (6 / 5)  

 999 21.79 1.17 0.00  chrX_63878874_63881245     1623  1879 (493)    L1M4_orf2#LINE/L1      649   908 (0)  

  chrX_63878874_6   1623 AAAA--AAAAGCTTCTGCACAACAAGGGAAACAATAAACAACACTAAGAG 1670
                             --    i   i  ii vv   i   v  v  v  v  viiv  i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_63878874_6   1671 ACAACCCGCAGAATGTGAGAAAATATTTGCAAACTACCCATCTGACAAGG 1720
                                i       v                 ii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_63878874_6   1721 GATTAATAACCAGAATATATAAGGAGCTCAAACAACTCTATAGGAAAATA 1770
                           i vi  v             i  i   vv       v   iv    vi
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_63878874_6   1771 TCTAATAATCTGATCATAAAATGGGCAAAAAGATAGAATAGACATTTCTC 1820
                         v v     i ii  i?v            iiiv v               
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_63878874_6   1821 AAAAGAAGATATACAA-TGGCAAACAGGCACATGAAAGGGTGCTCAACAT 1869
                         v               -    v  i i          i i          
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_63878874_6   1870 CACTGATCAT 1879
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.29 (31 / 24)
Gap_init rate = 0.01 (2 / 260), avg. gap size = 1.50 (3 / 2)  


2745 26.89 2.20 2.52  chrX_63910559_63916416     4455  5365 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63910559_6   4455 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4504
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63910559_6   4505 GGCCATACTGTCCAAAGTAATTCATAGATTCAATGCTATCCCCATCAAGC 4554
                            v     vi     v i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63910559_6   4555 TAACATTAACTTAGTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTTG 4603
                          vv  vivi i vv  ii     v v  v  i--  - iii    v  ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_63910559_6   4604 TATGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCCAAAGAAAAAG 4653
                                viiv  ii  v  v v        i      iii  i  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_63910559_6   4654 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4703
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_63910559_6   4704 TACAGTAATCAAAGCAGCATGGTACTGTTACTAAAACAGATATATAGACC 4753
                                     ii   ii        vi iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_63910559_6   4754 AATGCAACAGAACAGAGGCCTCAGAAATAGCACCACACATCTACAA-CAA 4802
                             v  i    iv   ivii        ivv   i    i  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_63910559_6   4803 TCTGATCTTTCAGAAACCTGATAAAAAGAAGTAATGGGGAA--------- 4843
                          -    i  iv v  ivv  vi  i vv vvi         ---------
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_63910559_6   4844 --TTTAATAATTGTTGTTGGAAAAACTGGCTAGCCATATGTAGAAAGCTG 4891
                         --  i  i  v  v  i   i v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_63910559_6   4892 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACCCAAGATGGAT 4941
                           ii    i    v   i     v               i   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_63910559_6   4942 TAAAGACTTAAATGGAAGACCTAAAACCATAAAAACCATAGAAGAAAACC 4991
                         i ?    i      v    v       i      vi v           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_63910559_6   4992 TAGGCATA--CCATTCAGGACATAAGCATGGACAAAGACTGCATGACTAA 5039
                             ?i  --i -   iv   v vi vv i i   v ii v v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_63910559_6   5040 AAGACCAAAAGCAATGGCAAAAAAAAAAAAAAAAAAAAAACAAAATAAAA 5089
                         i v          ----   iv  v    i      ---------  ---
  L1M4_orf2#LINE/    597 GACACCAAAAGCA----CAAGCAACAAAAGAAAAAA---------TA--- 630

  chrX_63910559_6   5090 TTGACAAATGGGATCTAATTAAACTAAGGAGCTTTGGCACAGCAAAATAA 5139
                         --  i    v   ii v  i   v v ii i    v ii vv    iv v
  L1M4_orf2#LINE/    631 --GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_63910559_6   5140 ACTATCATCAGAGTAAACAGTCAACCTACAGAATGGGAGAATATTTTTGC 5189
                                vv i   i  v  v     i              v  v     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_63910559_6   5190 AATCTATCCATCTCACAAAGGGCTAATATCCAGAATTTACAAAGAAGTTA 5239
                           vii  vi    v i  i  i  vi          v  i      v iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_63910559_6   5240 AATAAATTTACAAGAAAAAAACAA----CCCCATTAAAAAGTGGGCAAAG 5285
                         v i  v iv i  v     i    ----   v   ?    i         
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_63910559_6   5286 GATATGAACAGACATTTCTCAAAAGAAGACATTTATGCAGTCAACAAACA 5335
                            v    i           v        i  vi viii i   i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_63910559_6   5336 TATGAAGAAGA-GCTCATCATCACTGGTCAT 5365
                         i     -    -     v     ????????
  L1M4_orf2#LINE/    879 CATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (140 / 101)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.31 (43 / 13)  


 205 20.00 3.33 0.00  chrX_63942561_63949376.rev     3346  3405 (3411)    L1M4_orf2#LINE/L1      847   908 (0)  

  chrX_63942561_6   3346 TCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAAGCTCATC 3393
                           v        i  vi viii     i  --         i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_63942561_6   3394 ATCACTGGTCAT 3405
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (7 / 5)
Gap_init rate = 0.02 (1 / 62), avg. gap size = 2.00 (2 / 1)  

2962 27.01 2.23 0.89  chrX_63942561_63949376.rev     5430  6325 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_63942561_6   5430 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5479
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63942561_6   5480 GACCATACTGCCCAAAGTAATTCATAGATTCAATGCTATTCCCATCAAGC 5529
                          i v     v      v i  ii i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63942561_6   5530 TACCA-TTGAATTTATTCACAGAA-TTAGGAAAAAGT-ACTTTAAATTTC 5576
                          v   -i  vv   -  ii     -  --  v  iv - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATT--GACAAGCTGATCCTAAAATTC 147

  chrX_63942561_6   5577 ATGTGGAACCAAAAAAGAGCCCGTATAGCAAAGACAGTCCTAAGCAAAAA 5626
                           i     viiv  ii  v  v v     v  i   i  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_63942561_6   5627 GAACAAAGCTGG-GGATATCACGCTACCTGACTTCAAATTATACTACAAG 5675
                                 i   -   i-    i  v  ii i      viv        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_63942561_6   5676 GCTATGGTAACCAAAACACCATGGTACTGGTACCAAAACAGATATATAGA 5725
                             ii    i   i   vii         i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_63942561_6   5726 CCAACGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACC 5775
                         i   i    i    iv   ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_63942561_6   5776 ATCTGATCTTTCACCAGTCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5825
                          vi    i  iv  v  vv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_63942561_6   5826 CCATTTAATATGTAGTGTTGGGAAAACAGGCTAGCCATATGCAGAAAACT 5875
                          iv  i  i vi i   i     v   v  v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_63942561_6   5876 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAGGATGAA 5925
                            ii         v   i     v                  ii   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_63942561_6   5926 TTAAAGACTTAAATGTAAGACCTAAAATCATAAAA-------AAGAAAAC 5968
                          i ?    i           v      ii      -------        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_63942561_6   5969 CCAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAAGACTTCATGACT 6016
                         vi   ?-   --i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_63942561_6   6017 GGAACACCAAAAGCAATTGCAATGAAAGCAAAATT-GACAAATGGGATCT 6065
                         ivi            vvv    ii    v    v -  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_63942561_6   6066 CATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 6115
                            i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_63942561_6   6116 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTATCCATCTGAC 6165
                          v  i     i                 v   i   vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_63942561_6   6166 AAAGGTCTAATATCCAGATCCTACAAGGA--TCTTAAACAAGTT--TACT 6211
                           i  v  vi        viv  i  i  --     --   v i--  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAAT 792

  chrX_63942561_6   6212 AGAAAAA--ACCAACCCCATTAAAAAGTGGGTGAAGGTTATGAACAGACA 6259
                          i   i -- vi     v   ?    i    ii    v v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_63942561_6   6260 ATTCTCAGAAGAAGACATTTATGTGGCCAACAAACATATGAAGAAAAGCT 6309
                         v     vi       i  vi vi       i  i  i     i i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_63942561_6   6310 CGTCATCACTGGTCAT 6325
                          iv     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.75 (28 / 16)  

1131 27.78 0.28 0.83  chrX_63942561_63949376.rev     6445  6804 (12)  C L1M4_orf2#LINE/L1   (172)   736   379  

C chrX_63942561_6   6804 CAATGGGGAAAGGATTCCCTATTTAATAAATGGTGTTGGCAAAACTGGCT 6755
                                     i  vvi  v  i  i        i   v v      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

C chrX_63942561_6   6754 AGCCAGATGCAGAAAACTGAAACTCGACCCCTTACTTACACCTTATACAA 6705
                          ?   v     i  i v    ii v       vv  i     v       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

C chrX_63942561_6   6704 AGATTTACTCAAGATGGATGAAAGACTTAAACATAACACCTAAAATCATA 6655
                          i   v      i      v ?    i    ii   v v      ii   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

C chrX_63942561_6   6654 AAAATCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGTAATGG 6606
                            v  i           v    ?i- v i -   iv   v v viv i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG 577

C chrX_63942561_6   6605 GCACAGACTTCATGTCCAAAACACCAAAAATAATGGCACCAAAAGCAAAA 6556
                            vv ii   v ivvi vi         ii vvi   v      v    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

C chrX_63942561_6   6555 ATTGACAAAAGGGATCTAACTAAACTAAAGAGCTTCTGCACAGCAAAAGA 6506
                           v  i   vv   ii v ii   v v  i i   i  ii vv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

C chrX_63942561_6   6505 AACTATTATCAGTGGGAACAGGCAACCTAAAGAATGGGAGAAAATTTTTG 6456
                         v     i vv iv v   v  i     i v               v    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

C chrX_63942561_6   6455 CAATTATTATA 6445
                            --  i   
  L1M4_orf2#LINE/    728 CAA--ATCATA 736

Transitions / transversions = 0.94 (47 / 50)
Gap_init rate = 0.01 (3 / 358), avg. gap size = 1.33 (4 / 3)  


2565 24.12 11.31 0.75  chrX_63965421_63967071      355  1150 (501)    L1M4_orf2#LINE/L1        1   880 (28)  

  chrX_63965421_6    355 TGGGAAGACATAC-ATGTTCATGGATTGGAAGACTTAA------------ 391
                            i    i  v -                        ------------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_63965421_6    392 --CCATACTACTCAAGGCAATCTACAGATTCAATATAATCCTTATAAAAA 439
                         -- v     v i   ivii              iii     i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_63965421_6    440 TCCCAATGGCATTTTTT-------TTTACA--------------TTCAT- 467
                              iiv  v      -------  v   --------------     -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_63965421_6    468 -------GTAA---ACTCCAAGTAGCCAGAACAATCTT------------ 495
                         ------- i  ---  i vi i      i         ------------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_63965421_6    496 ------------------ATCCCCTGATTTTATAATATATTACAAAGCTG 527
                         ------------------ iii  ii    i v  iv  i         i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_63965421_6    528 CAGTAATTAAAACAGTATGGTACTGCCATAAAAACAGACATAGAGGCCA- 576
                                i  i     i        v     ii i       v  ii  -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_63965421_6    577 TGGGAAAAAACAGAGAGCCCAGAAATGAATCCACCCACATACAGTCACTT 626
                            i v i  iv     i        i  i   iv  iv  ii    v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_63965421_6    627 GATCTTTGACAAAGTTTACAAGAATACACAATGCAAGAAATGATAGTCCT 676
                            i  i     i v vv     vi iv     -ii    vi      i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTT 399

  chrX_63965421_6    677 TTCAATAAATGCTATGGGAAAAACT--ATGTCCACATGCAAACGTATAAC 724
                              i     v iiv  i v    --  i?           v v  i v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_63965421_6    725 ATTGGACCCTTATCTTATACCATACACAGAAATTAACTACAAATGTATTA 774
                         i        i  i  i i      i   i         vv     v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_63965421_6    775 AACAC-TGAACATAACTTCTGAAACTACAAAACTCCTACAAGAAGCCATA 823
                         ? v  - i  ii   vvv  i      i       i  v     iv    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_63965421_6    824 AGAGAAAAACTTCAAGACTTTGCTTGTGGCAATGATTTAATGGATATGAC 873
                         i ? v   v    iv   i   vv vv       i   vv i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_63965421_6    874 ACCAAAAGCACAGGCAACAAAAGCAAAAATGACCAAGTAGGATCACATCA 923
                                     i          v      iivi  i v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_63965421_6    924 AA-TTAAAATGTTTCTGCACAGCAAAGGAAACAATAAACAGAGTAAAATG 972
                           -      -ii  i  ii vv       v  v  v  v i   i   v 
  L1M4_orf2#LINE/    650 AAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_63965421_6    973 GCAAACTGCATAA-AGGATGAAATATTTGCAAATCATATATCTGATAATG 1021
                         i   v ii  v  -i   vi                            v 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_63965421_6   1022 GATTAATTTGTAT--AAAATATA---AGAAATCCTACAAACCAATAGTAC 1066
                           i ----     -- i      ---    v  i     vi     i  v
  L1M4_orf2#LINE/    749 GACT----TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_63965421_6   1067 AAAAGCTATTAACCCGATTGAACACTGGGCAAAGGAGTTCCATAAACATT 1116
                            ii v v      i   ?  v v           v  vv   i     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_63965421_6   1117 ATTCCAAAGAACATAAACA--TGGCCAACAGGTATA 1150
                         vi         v   v   --       i i i i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

Transitions / transversions = 1.47 (112 / 76)
Gap_init rate = 0.02 (18 / 880), avg. gap size = 5.33 (96 / 18)  


1628 23.41 11.98 1.81  chrX_63967508_63969608      500  1050 (1051)    L1M4_orf2#LINE/L1       63   669 (239)  

  chrX_63967508_6    500 CAAACTAATCTACAGATCCAACAAAATCC-TATTAAAATCCCAGTATGG- 547
                             i i          i    iv     -   i          i-  v-
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCC 111

  chrX_63967508_6    548 TTTTTGGTAGAAACTGACAAGGGGAATCTAAAACTCATA--GAAATTCAA 595
                              v i     i       vv  vi      i     --     v   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_63967508_6    596 AGCGCCTAGAATAGTCAAAATTATTTCTGAGGAAGAATAATGAAGTTGGA 645
                         i vi  i       i     iv  i -   ii     v  ii        
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCT-TGAAAAAGAAGAACAAAGTTGGA 210

  chrX_63967508_6    646 GAACCTACATGACCTGGTTTCCGTAATTATTAAAAAGATATAGTAATCAA 695
                          i  ii   ivv  iii    viv v   i  v    v  i         
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_63967508_6    696 ATCAGCAAACTATTGGCATAAAGATACACAAATAAAGCAATGAAGCAGA- 744
                         iv   iiviv  i        i    v   v   i v     i ii   -
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_63967508_6    745 T----AGGTCAGAAATAAACCCACAGATGTAAGG--------------AC 776
                          ----  vi              i v  v  v  --------------  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_63967508_6    777 AAG--------------------------------TCTTTCAAACAAATG 794
                            --------------------------------     iv        
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_63967508_6    795 ATAGTGAAACAGCTGAACATCCAAATGCAAAAGAA---AATCCTTAACCC 841
                         i iv  ii   i   i i ?   v           --- i -- vi    
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT--TGGACCC 458

  chrX_63967508_6    842 GTACCTTGCAACATACAAAAAAATTAAGTGAAAATGGATCATAGACCTAA 891
                         v     ii  v    i v         v v           ?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_63967508_6    892 ACGTGAAACCTAAAA--ATAAAATTTCTGGAAGAAAATATAGGAGAAAAT 939
                          i  i i v      --      i ii i        i     ? v    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_63967508_6    940 CTTTGTGAATACGACTTAGGCAAACATTTCTCCTAAATGGCACAAGAATT 989
                            i    vivi iv        vvi     ivv v   i   v i  v-
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG- 607

  chrX_63967508_6    990 CACAATCCATAAAA-----AATACTGATAAATTGGATTTCTTCATCAACA 1034
                              v v i    -----    --           ---         v 
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATA--GATAAATTGGA---CTTCATCAAAA 652

  chrX_63967508_6   1035 TTAAAAGTTTCTG-GCT 1050
                               ii  i  -   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCT 669

Transitions / transversions = 1.47 (75 / 51)
Gap_init rate = 0.03 (17 / 607), avg. gap size = 4.47 (76 / 17)  

 857 23.13 8.19 0.00  chrX_63967508_63969608     1331  1611 (490)    L1M4_orf2#LINE/L1      605   908 (0)  

  chrX_63967508_6   1331 AAACA-AAGAAGCAAAAAAAAAAA-----AAA------------AAAA-- 1360
                           i  -   v i     i      -----   ------------    --
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_63967508_6   1361 AAAGACATT-GTAATTCAAAAGACACTGTTAAGACAATGAAAAGATAAGT 1409
                            i  v  -  iv      i      i i    v i        i  vi
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_63967508_6   1410 CCCAGACTGGGAGAACATGTTTGCAAATCAAGTGTCTGGTAAAA-ATGTG 1458
                          v    v        v  i           vi i    i   ii- iv  
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_63967508_6   1459 TTTCCAGAAAATGTAAATAACACTCAAAACTCA-CAATCAGTAAACAAAC 1507
                          v       v  i    v   v  i v      -i   v iv i     i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_63967508_6   1508 AGCCCAGTTAAAAAATGAACAAAAGGTTTGAATAAACACTTCACAGAAGA 1557
                          i    i  ?       ii    i i        i   i   v vi    
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_63967508_6   1558 GGATATATGGGTGGCAAATAAACTCATGAAGAGATACTCAACAAGATTGG 1607
                         i      iiii    v     i v      i    i       vv ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_63967508_6   1608 TCAT 1611
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.78 (41 / 23)
Gap_init rate = 0.02 (7 / 304), avg. gap size = 3.29 (23 / 7)  


 233 30.53 1.05 1.05  chrX_63989229_63993188      500   594 (3366)    L1M4_orf2#LINE/L1       46   140 (768)  

  chrX_63989229_6    500 AAAATGTCAATTATCTCCAAATTGACATACAAGTTTAATGGAAACTGATA 549
                           i   v    vv  i         iv    ii  i  i v  v i-v  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC-CTA 94

  chrX_63989229_6    550 TCAAAATCC-AGAAATATTTTCCGTAGACACAGACAAGATAATTCT 594
                                  -  vviiv    ii i   v iv      v i  i  
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.00 (2 / 2)  

1347 26.03 4.34 3.69  chrX_63989229_63993188      906  1366 (2594)    L1M4_orf2#LINE/L1      127   590 (318)  

  chrX_63989229_6    906 GACAAGATAGTTCTAAAATTTATATAGAAAGGCAAGGGAACTGAAATAGC 955
                               v ii i        i    i    v        v iii      
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chrX_63989229_6    956 TAAAAACAATTTTGAAAGAGAA---TAAAGTAGAATAAATCATTCTACCT 1002
                         i    -    i      i    ---i     v i vi v   iv  v  i
  L1M4_orf2#LINE/    177 CAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_63989229_6   1003 GATGTCAACATTTATTAGATAGCTACAGTAATCAAGGCTGTGTAGTATTG 1052
                         i  v    v i   i  v v                i v    i   i  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_63989229_6   1053 GTGGTGGAAAAGACATG--GATCAATGGAATAGAATACAGGACCCAGACA 1100
                          iivvi i v      i--                 vv  iii     v 
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_63989229_6   1101 TAGACTCACACATATATGCCAAACTGGTTTGCT----GGGTTTTTTTTTT 1146
                           i  i  i    v    viv  i  i   v v----    vi-------
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC------- 368

  chrX_63989229_6   1147 TTTTTTC----CCA--CAAAGATGAAAGGATGATCTTTTCAACAAATGAT 1190
                         ------ ----   --   v iv     i  ii               i 
  L1M4_orf2#LINE/    369 ------CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_63989229_6   1191 GGTGGAGAAAGTGAGTATCTGTTAGGAAAAAAA---AATTTTACTCAAAA 1237
                          v   iiv  v  ii  ? iiivv v    i  --- i  vv  i v---
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC--- 459

  chrX_63989229_6   1238 GACCTCATATCTTATGCAAAAATTAACTCAGAATGGATGATGGATTTAAA 1287
                         v      i i v   i              i       v ?i  ii    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_63989229_6   1288 TGTAAAATGTAAACCTATAAAACTTTTAGAAAAAAA-A-AGGAGAAAACC 1335
                              i vv    v          i      i    - -   ? v   i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_63989229_6   1336 TTTTGGATCTAGGACTAAGCAAAGGATTTTT 1366
                           ivv  i  v  ii  i    v  v  i  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.44 (69 / 48)
Gap_init rate = 0.02 (11 / 464), avg. gap size = 3.36 (37 / 11)  

3076 26.04 2.69 0.79  chrX_63989229_63993188     2150  3040 (920)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_63989229_6   3040 TGGAAGAACATTCCATGCTCATGGATAGCAAGAATCAATATCGTGAAAAT 2991
                              ii i  i     i        v v    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_63989229_6   2990 GGCCATACTGCCCAAGGTAATTTATAGATTCATTGCCATCCCCATCAAGC 2941
                            v     v     iv i  i  i       vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_63989229_6   2940 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2893
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_63989229_6   2892 TATGGAACCAAAGAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 2843
                                viiv iii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_63989229_6   2842 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGCC 2793
                                i      vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_63989229_6   2792 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATACATC 2743
                                 i   i    ii         i iv ii i   v     v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_63989229_6   2742 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 2695
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chrX_63989229_6   2694 ATCTGATCTTTGACAAACTTGACAAAAACAATAAACGAGGAAAGGAT--T 2647
                          vi    i  i     ivv  v   i v  v v  i i      i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_63989229_6   2646 CCTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAT---AAAGC 2600
                          i  -- i  i              v      v  ?   i  ---    v
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chrX_63989229_6   2599 -TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 2551
                         -    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chrX_63989229_6   2550 GATTGAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 2501
                            ii?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chrX_63989229_6   2500 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 2452
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

C chrX_63989229_6   2451 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATC 2402
                           vi            vvi          vv     v  i i  v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

C chrX_63989229_6   2401 TAGTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATGAGAGTG 2352
                          vi i   v v  i i   i  ii vv    i  v    i  v  i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

C chrX_63989229_6   2351 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAA--------TCTAC 2310
                           v  i     i                 v       --------   iv
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

C chrX_63989229_6   2309 TCAAGGGCTAATATCCAGAATCTACAATGAATTC----AAATTTATAAGA 2264
                          v i  i  vi          v  i  v   i  ----  v iv    v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

C chrX_63989229_6   2263 AAAAAA-AAACAAACCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 2215
                             i -   i  v  v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

C chrX_63989229_6   2214 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAATTGCTC 2165
                              v        i  vi viii     v ii          iv     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

C chrX_63989229_6   2164 ATCATCACTGGCCAT 2150
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (136 / 92)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.21 (31 / 14)  

 904 23.15 6.71 0.67  chrX_63989229_63993188     3170  3467 (493)    L1M4_orf2#LINE/L1      593   908 (0)  

  chrX_63989229_6   3170 ATTTGACACCAAAAGCATAATCCATAAAAGGAAAAGCTGATAAAATGGAC 3219
                           v              i  v v i     i    iiv      v     
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_63989229_6   3220 TTTATCAAAATTGAAA-TTTTT----TTCTATGTGA-------AAGAAGA 3257
                           i         i   -i    ----   v v -  -------     ii
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAG 691

  chrX_63989229_6   3258 TGAAAAGACAAGGTATACACTAGGAGAAAATATTTGAAAACTACATATTC 3307
                                    vvi i v v i              v   ii i    ii
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_63989229_6   3308 AACAAAAGACTAGCATCTAAAATATATTAATAACCCTCAAAGTTCAACAG 3357
                         i i  ii    v i   i i       v  v   i  i v ii    i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_63989229_6   3358 TAAAAAGTTAA-TA---CAATTTAAACAATTGTCAAAAGATATGAAGAAA 3403
                                vi  -  ---     ?   -   v v    i   v    v i 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGA 840

  chrX_63989229_6   3404 CATTTCACTGAAGAGGTTATACAGATGG----TAACTACATGAAAATTTC 3449
                               v ii    i v      i    ----   vi         vv v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_63989229_6   3450 TTCAACGTCATTAGCCAT 3467
                         i     i   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (41 / 27)
Gap_init rate = 0.03 (8 / 316), avg. gap size = 2.75 (22 / 8)  


3892 21.07 1.67 0.67  chrX_64051328_64053265.rev      551  1447 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_64051328_6    551 GGAATACATCT-GTATTAATGGATTGGAAGACTTAATAATGTTAAAATGT 599
                          i  v i   i-i i  v                    v      i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_64051328_6    600 CCATGTTATCCAAAGCTATCTACAGATTCAATGTGATCCCCATCAAAATC 649
                          v  ii vi     viv              i ii     i         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_64051328_6    650 CCAATGGCATTTTTTACAAAAATAGA-AAAC-AATCCTAAAATTCACATA 697
                            iiv  v      i  i    v  -  i -i             i  i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_64051328_6    698 GATCCACAAAGGACTCCCAATAGCCAAAACAATATTGAGAAAGAGCAACA 747
                           vvii   i    i vv               v    i     iv    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_64051328_6    748 AAGTTGGAGACCTCACACTCCAAGATTTTAAAACATATTACAAAGCTACA 797
                                  iv        i vvi    i     v  i            
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_64051328_6    798 GTAATCAAAACAGTATGAAACTGACATAAAGGCAATCATATA--CCAATT 845
                                 i     i  iv    i     i ii iv      --i    v
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_64051328_6    846 TCGAAAAGAATAGTGAGCCCAAAAACAAACGCACACACATGCAGTCAAAT 895
                         --   v     v v   i   i   i    v  i   iv iii     v 
  L1M4_orf2#LINE/    303 --GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_64051328_6    896 GATATTCAACAATGGTGCCAAGACTACATAATAGGAAAATGATAATCTCT 945
                            v   i    v           i ivi   i  i   vi   i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_64051328_6    946 TTAACAGATGGTGCCGGAAAAACTGGATATCTACATGCAAAAGAATGAAA 995
                          i    i       i  i v         ? i                 i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_64051328_6    996 TTGGACCCTTATCTTATACAATATACAAAAATCAACTCAATATGGATTAA 1045
                                 i  i  i i  v            i       v      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_64051328_6   1046 AGACTTAACTGTAATACCTGAAACTATAAAACTCCTAGAAGAAAACATAA 1095
                             i   v     v v  i              i              i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_64051328_6   1096 GG--AAATAGCTTCATAACATCAGTCTTGGGAATGATTTTTTGGATAAGA 1143
                          ?--    --    i i  v ii vi v  v    i   i  i    v  
  L1M4_orf2#LINE/    551 GNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_64051328_6   1144 CACCAAAAGCACAGGCAACAAAAGGAAAAATAGACAAGTGAGACCAAATC 1193
                                      i          i         i  i vi   ivv   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_64051328_6   1194 AAACTAAAAACCTTCTGCATAGCAAAGGAACAC-ATCAACAGAGTTAAAG 1242
                            v v    v   i  iiivv       -   -     v i   v   i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGA-CACTATCAAGAAAGTGAAAA 697

  chrX_64051328_6   1243 GA-AACCCACGGAATGGGAGAAAATATTTGAAAACCTACACAACTGATAA 1291
                           -       i                   v   i - i i v       
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAA 746

  chrX_64051328_6   1292 GGAGTTAATATCCAAACTATAAAAGGAACTTGTACAACTCAATAG--AAA 1339
                           iii vi      i v    v  i     iv            i--   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_64051328_6   1340 AAATGAA----CTGATTATAATATGAGAAAAGGACTTGAATAGATATTTC 1385
                          i ii  ---- ii   ?v  v   i v      i         i     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_64051328_6   1386 TCCAAAGAAGACATGCAAATGGCTAAGAAGTATATGAAAAGATGCTCAAC 1435
                                    i  i        i  v   i i                 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_64051328_6   1436 ATCACTAATCAT 1447
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (120 / 65)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 1.62 (21 / 13)  


1622 26.17 1.62 1.83  chrX_64056260_64062625.rev        1   493 (5873)    L1M4_orf2#LINE/L1      149   640 (268)  

  chrX_64056260_6      1 TATGGAA-TGAAAAAGAACCAGAATACACAAAGCTATTTTATGTAAAAAT 49
                                -  v  ii  v        vv    i v  i  iviv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_64056260_6     50 CAGAAAATTAGAGGAATCACATTACCTGACTTCAAA-TTATATAATACTA 98
                         v v   i  i     v     i v  ii i      -i ------     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT------TACTA 242

  chrX_64056260_6     99 CAGAGCCATAGTAACCAAAAAACCATGGTACTGGCATAAAAACAGACACA 148
                           i   i i     i   i v vii              ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_64056260_6    149 CAGACCAATGGAACAGAATAGAGAACCCAGAATCAAATCCCCA-ATCCTA 197
                         i   i        i     v    ii      vi   i  vi -  i-  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TA 341

  chrX_64056260_6    198 TACTAAACTCATTTTAAACAAAGGTGCTAAGAACCTACACTGGGTAAG-- 245
                          iv v  i v     vi    i     i    v v v  v    v  i--
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_64056260_6    246 ACAGTCTCTTCCATAAACGGTGCTGGGAAAACTGGATATCCATATGCAGA 295
                          i     i   v i   i          v         ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_64056260_6    296 AAAATGAAACTAGACCTCTAC-TCTTCCCATATACAAAAATCAAATTGAA 344
                          i      ii i    i    -  viv              i  v ii  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_64056260_6    345 ATTGATGAAAGACTTAAATCTAAGACCTCAAAATTTAAAACTACTACAAT 394
                           v   v ?    i     v     v  v   v v       vi  v  v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_64056260_6    395 AAAACATTGGGGAAAATCTCCAGGACACTGGTCTGGGCAAAGATTTTTTG 444
                                v  ? v      i iv   vi   vi i     v i   i  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_64056260_6    445 AGCA--ATACCGCACAAGCGCAGGCAGCCAAAGCAAAAATGAACAAACTG 492
                         iii -- i   -- v    i  i   i v    v      ii i   i  
  L1M4_orf2#LINE/    592 GATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_64056260_6    493 G 493
                          
  L1M4_orf2#LINE/    640 G 640

Transitions / transversions = 1.52 (76 / 50)
Gap_init rate = 0.02 (9 / 492), avg. gap size = 1.89 (17 / 9)  

3082 25.85 3.16 0.68  chrX_64056260_64062625.rev     4990  5875 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64056260_6   4990 TGGAAGAACATTCCATGCTCATGGATAGCAAGAATCAATATCGTAAAAAT 5039
                              ii i  i     i        v v    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64056260_6   5040 GGCCATACTGCCCAAGGTAATTTACAGATTCAACGCCACCCCCATCAAGC 5089
                            v     v     iv i  i              v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64056260_6   5090 TACCAATGACTTTCTTCACAGAA-TTGGAATAAACTAATT-TAAAGTTCA 5137
                          v   iivi i  i  ii     -   -- i  i  i  i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_64056260_6   5138 TATAGAACCAAAAAAGAGCCCGCATTGCCAATTCAACCCTAAGCCAAAAG 5187
                            i   viiv  ii  v  v v  v     vv   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_64056260_6   5188 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAGGC 5237
                                i      vv       v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64056260_6   5238 TACAGTAACCAAAACAG--------------------AGA--TATAGACC 5265
                                 i   i    --------------------   --      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_64056260_6   5266 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5313
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_64056260_6   5314 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5363
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_64056260_6   5364 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5413
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_64056260_6   5414 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5463
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_64056260_6   5464 TTAAAGACCTGAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 5512
                          i ?      i     v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_64056260_6   5513 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5561
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_64056260_6   5562 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5611
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_64056260_6   5612 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTACCATCAGAGTGA 5661
                         v  i   v v  i i   i  ii vv    i  v i  i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_64056260_6   5662 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5711
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_64056260_6   5712 AAAGGGCTAATATTCAGAATCTACAATGAACTCAAATAAATTTACAAGAA 5761
                           i  i  vi   i      v  i  v      vv i  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_64056260_6   5762 AAAAGCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5811
                            ii    i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_64056260_6   5812 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5861
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_64056260_6   5862 TCATCACTGGCCAT 5875
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (134 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.09 (34 / 11)  


3003 26.73 1.67 0.67  chrX_64064319_64070135.rev     4429  5326 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_64064319_6   4429 GGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAATG 4478
                              i i  i     i        v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_64064319_6   4479 GCCACACAGTCCAAAGTAATTTATAGATTCAATGTTATTCCCATCAAG-T 4527
                           v i  vvi     v i  i  i        i iv  i  i     i- 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_64064319_6   4528 CACAATTGACTTTGTTCACAGAATTACAAAAACT-ACTTTAAATTTCATA 4576
                          v  ii  v    -  ii     v vv v  i  - iii    v      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_64064319_6   4577 TGGATCCAAAAAAGAGCTCGTATAGCCAAGACAATCCTAAGCCAAAAGAA 4626
                             vviiv  ii  v iv v        i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_64064319_6   4627 CAAAGCTGGAGGTATCATACTACTTGACCTCAAACTATACTACAAGGCTA 4676
                              i      vv   i   v iii ii     viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_64064319_6   4677 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACATATATATAGACAAA 4726
                               i   i    ii         i iv ii i v i       iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_64064319_6   4727 TGTTACAGAACAGAG-GTCTCAGAAATAACACCACACATCTACAACCATC 4775
                           vv i    iv   -   -         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_64064319_6   4776 TGATCTTTGACCAACCTGACAAAAACAAGCAAAGGGGAAAAGATTCCCTA 4825
                             i  i   v ivv  v   i v  vv   v       ii  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_64064319_6   4826 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 4875
                           i  i              v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_64064319_6   4876 ACTGGAACCTTTCCTTACACCTTAAACAAAAATTACCTCAAGATGGATTA 4925
                         ii    v  i v   i     v  v          v     i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_64064319_6   4926 AAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAGCCTA 4975
                         ?    i    i      v       i      vi i         i v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_64064319_6   4976 GGCA-ATACCATTCA-GGTCATAGCCATGGGCAAAGGCTTCATGGATAAA 5023
                           ?i- v i -   i- ii v i vi- i     v  i   v i    vi
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chrX_64064319_6   5024 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5073
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_64064319_6   5074 TAAACTAAAGAACT-----GCTCAGCAAAGAA-ACTATCATCAGAGTGAA 5117
                         i   v v  i    -----   i--     i -       vv i      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAA 695

  chrX_64064319_6   5118 GAGGCAATCTGCAGATTGGGAGAAAAATTTTGCAATCTATCCATCTGACA 5167
                         i  i   i ii    v          vv       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_64064319_6   5168 ACAGTCTAGTATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAA 5217
                          vi v  v           v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_64064319_6   5218 AAAACAA----CCCCATCAAAAAGTGGACAAAGGATATGAACAGACACTT 5263
                           i    ----   v  i?    i   i        v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_64064319_6   5264 CTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAGAAAAGCTCAT 5313
                            v        i  vi viii     i  i  i     i i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_64064319_6   5314 CATCACTGGTCAT 5326
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 1.62 (21 / 13)  


3533 24.12 0.77 0.88  chrX_64083676_64087919     2844  3751 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_64083676_6   2844 GAAAAAATGTTTCATGCTCATGGATTGGAAGAATCAATATTGTTAAAATG 2893
                          i   i  i ii    i               v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_64083676_6   2894 TCCATACTACTCCCAGTACTCTACAGATTCAATGCAATCCCTATCAAAAT 2943
                         v v     v i vv v iv             i                 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_64083676_6   2944 ACCAATGACATTCTTTACATAAATAGAAAATACAATCCTAAATTTTATGT 2993
                         v   iivi v  i   i  v    v  v  vvii        v  i  i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_64083676_6   2994 GGCATGACAAAAGACCCAGAATATGCAAAGCTATTCTAAGCAAAAAACAG 3043
                           v vvi   ii           vv    i v  ii i iv  i  iv v
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_64083676_6   3044 AAAACTAGAGGAATCACA-TTATTGACTTCAAATTATATTATACTACAGA 3092
                            ii i     v     -  viii i      ---- i -       i 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACT-TACTACAAA 246

  chrX_64083676_6   3093 ACCATAGTAACCAAAACACTGTGATACTAGAATAAAAACAGACACACAGA 3142
                         i i i     i   i   v    i    i v    ii i     i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_64083676_6   3143 CCGATGGAACAGAATAGAGAACCCAGAATTAAATCCACA-ATCTTACACT 3191
                         i i      i     v    ii      v    i   i -  -   iiv 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-TTATGGT 345

  chrX_64083676_6   3192 GAACTCATTTTCAACAAAGATGCTAAGAACATACACTGGGGAAAAGACAG 3241
                         v  i v      i    i i   i    v   v  v        ii i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_64083676_6   3242 TCTCTTCCATTAATGGTGCTGGGAAAACCGGATATCCATATGCAGAAGAA 3291
                            i   v iv             v   i     ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_64083676_6   3292 TGAAACTAGACCCCTAC-TCTTGCCATATACAAAAATCAAATTGAAATGG 3340
                             ii i         -  vii              i  v ii      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_64083676_6   3341 ATGAAAGACTTAAATCTAAGACCTCAAAATATGAAATTATTACAAGAAAA 3390
                           v ?    i     v     v  v   v   i   i v   v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_64083676_6   3391 CATTGGAGAAAATCTGCAGGACATTGGTCTGGGCAAAGATTTTTTGAGCA 3440
                            v  ? v      v iv   v    vi i     v i   i  iiii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_64083676_6   3441 GTACTCCACAAGCACAGGCAGCCAAAGCGAAAACAAACAAAT--GATCAC 3488
                         vv  v   v       i   i v    vi    i i i    --  iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_64083676_6   3489 ATCAAA-TTAAAAAGCTTCTGCACTGCAAAGGATACAACCAACAAAGTGA 3537
                               -       -   i  ii  v       i  v i   v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_64083676_6   3538 AGAGACAATCCACAGGATGGGAGAAAATATTTTCAATGTATGAATCTGAC 3587
                          i      i      i                v   vvi  iv      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_64083676_6   3588 AAGGGATTAATAAGCAGAATATATAAGGAGCTCAAACAACTCTACAG-AA 3636
                               i vi  vv            i  i   vv       v i i-  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_64083676_6   3637 AAAAATATAATAATCTGATCAAAAAATGGGCAAAATATTTTAATAGGCAT 3686
                            i i -     i ii  i?             iv    v     i   
  L1M4_orf2#LINE/    795 AAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_64083676_6   3687 TTCTTAAAAGAAGACATACAAATGGCAAAGAGGCATATGATAAGTTGCTC 3736
                             iv        i           v  v i   i    v   v     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_64083676_6   3737 AACGTCATTGATCAT 3751
                            i   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (131 / 84)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 1.36 (15 / 11)  


2258 23.25 11.81 2.21  chrX_64112458_64114867.rev     1107  1919 (491)    L1M4_orf2#LINE/L1       18   908 (0)  

  chrX_64112458_6   1107 TTCATGGATTGGAATACTTAAAATAGA-AATATGTCAATTTTCCCTAAAT 1155
                                       v      v  v v-  v   v    vi    i    
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_64112458_6   1156 AAATATACAGACTTAACACAATTCCTACAAAAATCCTAGCAAGATATTTG 1205
                         vi  v      i i   i    i    iv       i   vivv v   v
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_64112458_6   1206 GTAGATATAGACAAGATTATTCTAAAATGTATATGGAAAGATAAAGAAAC 1255
                          i   v  v      v v  i       vi         vii  i i v 
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_64112458_6   1256 TAAAACAGTTAAAACAATTTTGAAAA-GAAGAA---AGTGGAAAGAAACA 1301
                         i i  i  ii        i       -      ---   v i i  vv  
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_64112458_6   1302 TTCTTCCTGATT-CGAA----------------CAGTAATCAAGATTGTG 1334
                         iv     ii   - i  ----------------            iv   
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_64112458_6   1335 TGGAATTAATGCTGGAATAGACA----GGCTAGTGGAA------------ 1368
                            v i iiiiivi i       ---- iii i     ------------
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_64112458_6   1369 --CAGAAATAGACCCACATAAATATG-CC---TAATTTTTGACAGAGGTG 1412
                         --        i     i i vv    -i --- i     i    ii    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_64112458_6   1413 C-AA----ATTCAA----------GTTGCCTTTTCAA-AAATGGAATGCT 1446
                          -  ----      ----------i v i        -      --    
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG--TGCT 415

  chrX_64112458_6   1447 GGAGCAATTGTGCATCCATAGGTAA-----------TAAACCTCTATCTG 1485
                           ii   i  vii ?   i v i  ----------- ii   i   i  -
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT- 464

  chrX_64112458_6   1486 ATTCTTATGTCTTATACCAAAGTTA-CTCAAAATGGATCAGAGACTTAAA 1534
                         -----i iii v     v   i   -              ?    i    
  L1M4_orf2#LINE/    465 -----CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_64112458_6   1535 TGTAATA-CAACAAACTATAAAACTTTTAGCAAAAAAAAAAAAAGCAGAA 1583
                              v - v -             i    ------  i    vii  i?
  L1M4_orf2#LINE/    510 TGTAAGAGCTA-AAACTATAAAACTCTTAG------AAGAAAACATAGGN 552

  chrX_64112458_6   1584 GAAAATACATAG-GATCTAGGGCTAGGCA--GAATTTTTAGACTTAACAC 1630
                          v    - v v -  i  v   i      -- iv  i     iv i    
  L1M4_orf2#LINE/    553 GTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_64112458_6   1631 CAAAAGCACAATGCA-TAAAAGAAAAATT-GATAGACTGAATTTTATCAA 1678
                                    -   -i          v -    i i  i i  i     
  L1M4_orf2#LINE/    602 CAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_64112458_6   1679 A--TATAAAATTTTTGTTCTGCAAAATACCCTGTTAAGAAGATGAAA-GA 1725
                          --  -    i      v  v    iv  v  i i     ii     -  
  L1M4_orf2#LINE/    651 AATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_64112458_6   1726 CAAACTACAGGCTAGGAGAAAATATTT---AACTGCATATCCAATAAAGG 1772
                            v i    iv i             ---  iiii     ii    i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_64112458_6   1773 ACCAGTATCTAGAATGTA----G---TCTCAAAACTCAAGAGTAAAAA-- 1813
                           iv     i     i  ---- ---   i v       v i      --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_64112458_6   1814 TAAAT---CAAATTAGAAAGTAAGTAAAAGGCATGAAAATACATTTTAGC 1860
                         i    --- v    ?i   i ii i   i iiv    v v      ivv 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_64112458_6   1861 AAAGAGGATATACAGATGGCAAACACGCACATAAAAAGATGATCAACATC 1910
                              i        i     v  i v      i        v        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_64112458_6   1911 ACTAGCCAC 1919
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.89 (121 / 64)
Gap_init rate = 0.04 (34 / 891), avg. gap size = 3.35 (114 / 34)  

 275  5.77 0.00 3.85  chrX_64112458_64114867.rev     1982  2033 (377)    L1M4_orf2#LINE/L1      859   908 (0)  

  chrX_64112458_6   1982 ATACAAAGTAGTCCAATAAGCACAGGAAAAGATGCTCAGCATCATTGCTC 2031
                                - i -            v             i     ??????
  L1M4_orf2#LINE/    859 ATACAAA-TGG-CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_64112458_6   2032 AT 2033
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.00 (2 / 1)
Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2)  


3087 26.86 1.55 0.78  chrX_64141241_64144738.rev     2107  3007 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64141241_6   2107 TGAAAAGCTATCCTGTATTCATAGATTGAAATCATTAATATTGTTAAAAT 2156
                           i    v     ii i     i     i  vvv             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64141241_6   2157 GTCCATACTACTCAAAGCAATCTATATATTCAATGTAATCCCTATGAAAA 2206
                          v v     v i    vii     i v      i i         v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64141241_6   2207 TTTCAATGACTTTTTTCATAGAAATATTAAAAGG--AATCCTAAAATCCA 2254
                          ii  iivi i     iii      -- i v i --i          i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCA 148

  chrX_64141241_6   2255 TAAGGGACCACAAAAGGTGCCA--ACACCCAAACGAATGTTAAGCAAAAA 2302
                           v  i vii   ii ii-   -- i v     vv   v  i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_64141241_6   2303 TTACAAAGCTGGAGACATCACACTACCTGACTTCAAAATATACCACATAG 2352
                         vv      i     ivv       v  ii i       iv   i   v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_64141241_6   2353 CTATAGCAA-CAAAACAGCATGCTACTGGCATTAAAACAGACATATAGGC 2401
                            i  i  -   i    ii  v         v ii i          ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_64141241_6   2402 CAATACAGAAAAAT--AGA--CTAGAAATAAATCCACACATTTATAGTCA 2447
                             iv iv i   --   -- i         i   i        i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_64141241_6   2448 AATAGTTTCCCATAAAGGTACCAGGA--ATGCAAAATGGAAAAAGGAAAA 2495
                          v ii   i v i  i   i   i  --  v   --   ii    i v i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAG 395

  chrX_64141241_6   2496 TCTCCTCCATAAATGGTGTGGGCAAAATTGCATATCCATACACAGAAGGA 2545
                            ii  v i        iv  v v  i  v   ?   i ii  i   i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_64141241_6   2546 TAAAACTACACTCTTATTTCACACAATATGAAGAAATCAACTCGAA-TGG 2594
                          i  ii iv  i i  ii      v    iv i    i     i  -   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_64141241_6   2595 ATTAAAGATTTAAAGATAAGACAGGAGACTCTAAAAGTAATGGAAGATAA 2644
                           i ?   ii    vi     vvvi i   v     v vv i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_64141241_6   2645 CATAGAAGACTAGTTTCTTGACATTGGTGTT-GGCAATGATTACTTGAAT 2693
                              i? vvv vi   v    v    -   -       i  v   ii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGAT 594

  chrX_64141241_6   2694 GTAATACCAAAAGCACAGCCAACAAAA-ACAAAGTAGACAAATGAAACTA 2742
                         i i i            iv        - v   i    i    vii   v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_64141241_6   2743 TGTCAAACTAAAAAGCTTCTGCACAGCTGAGTAAACAATCAACACAGTGA 2792
                         ii     v v    i   i  ii vv vi  v v  v     v v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_64141241_6   2793 AGAGACAACCTATGAAATGGGATAAAACATTTGTAAACCATAGACCTGAT 2842
                          i        i iii       v    i     i   i    v i     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_64141241_6   2843 GAGAGGATAATATCCAAAATATATAAGAAACTCAAACTACTCAATGGTAA 2892
                         i  i iv vi      i         ii     vv  v       ii   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_64141241_6   2893 AACAAACAAACAATCCAATTTAAAAATGGGCAAAGCATCTCAGTAGACAT 2942
                           - i     i  i      ?              v  i v i       
  L1M4_orf2#LINE/    795 AA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_64141241_6   2943 TTCTCAAAGGAAGGCATTCAGATGGCCAACAGGTACATGAAGAGGTGATC 2992
                              v  i    ii  v  i        i i i       i  i  v  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_64141241_6   2993 TACATCACTAATTGT 3007
                         v      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (153 / 85)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


3133 28.57 0.55 0.00  chrX_64160924_64167323.rev     5007  5909 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64160924_6   5007 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCATGAAAAC 5056
                              ii i  i     i      i v      v i    iii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64160924_6   5057 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGACATCCCCATCAAGC 5106
                            v     v     iv i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64160924_6   5107 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 5151
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_64160924_6   5152 TGGAACCAAAGAAGAGCCCGCATCGCCAAGTCAATGCTAAGCCAAAAGAA 5201
                              viiv iii  v  v v  v     iv    vi i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_64160924_6   5202 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATACTACGAGGCTA 5251
                              i      vv   ii  v  ii i      viv      i i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_64160924_6   5252 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGACCAA 5301
                               i   i    ii         i iv ii i   v i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_64160924_6   5302 TGGAACAGAACAGAGACCTCAGAAATAATGCCGCATATCTACAACCATTT 5351
                              i    iv    vii         vv  ii i  i  iiii  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_64160924_6   5352 GAGCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTAT 5401
                           vi  i     ivv  vv  i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_64160924_6   5402 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGGTGAAA 5451
                          i  i              v      v  ?   i   i i  iii    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_64160924_6   5452 CTGGATCCCTTCCTTACACCTTATACAAAAATTTATTCAAGATGGATTAA 5501
                         i    i    v   i     v            v i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_64160924_6   5502 AGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACTTAG 5551
                             i       v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_64160924_6   5552 GCATTACCATTCAGGACACAGGCATGGGCAAGGACTTTATGTCTAAAACA 5601
                          ?i v viv   iv   viv  vv i     v ii  iv ivv  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_64160924_6   5602 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAA 5651
                                  vvi          vv     v  i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_64160924_6   5652 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 5701
                          v v  i i   i  ii vv    i  v    i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_64160924_6   5702 AATGCATAAAATGGGAGAAAATTTTCGTAACCTACTCATCTGACAAAGGG 5751
                           iv  i i             v  i i  vii ivi      i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_64160924_6   5752 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 5801
                           vi          v  i  v      vv    v iv i  v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_64160924_6   5802 AAACAACCCCATCAAAAAGTGGGTGAAGGACACGAACAGACACTTCTCAA 5851
                            i     v  i?    i    ii     ivi   i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_64160924_6   5852 AAGAAGACATTTATGCAGCCAATAAACACATGAAAAAATGCTCACCATCA 5901
                                i  vi viii        i          i       v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_64160924_6   5902 CTGGCCAT 5909
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.49 (152 / 102)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.50 (5 / 2)  


2606 28.01 1.90 0.56  chrX_64169197_64177289.rev     1316  2211 (5882)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64169197_6   1316 TGGAGAAACATTCTATGCTCATGGACAGGAAGAATCAATAATGTGAAATT 1365
                             i i i  i i   i       iv      v i    v   v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64169197_6   1366 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTACCATCAAAC 1415
                            v     v      v i  i  i        i  v  iv i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64169197_6   1416 TACCA-TTGACTTTGTAAGCAGAATTAGAAAAAACT-ACTTTAAATTTTA 1463
                          v   -i  v    v v-      v v  v  i-  - iii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_64169197_6   1464 AATGGAATAAAAAATGAGCCCATA-TAGCCAAGACAATCCTAAGCAAAAA 1512
                         v      - viv  v ii    v -       i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_64169197_6   1513 GAACAAAGCTGGAGGCATCACACTACCTGATTTTAAAGTATACTACAAGG 1562
                                 i      vv       v  ii    i   iiv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_64169197_6   1563 CTACAGTAATAAAAACAGCATGCTACTCGTACCAAAACAATTATATAGAA 1612
                                   v  i    ii  v    v i iv ii i ivi       v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_64169197_6   1613 CAATGGAACAGAACAGAGGACTCAGATATAATGCCACACATCTA-GAACA 1661
                                 i    iv   iiii    v    vv   i    i  - iv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_64169197_6   1662 ATCTGATCTTTGACAAACCTGACAGAAACAAACAATGTAGAAAGGATTCC 1711
                           -    i  i     ivv  v  ii v  vv     vi     i  vvi
  L1M4_orf2#LINE/    348 AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_64169197_6   1712 CTATGTAATAAATGGTGCTGGAAAAACTGGCAAGCCATATGCAGAAAACA 1761
                           v vi  i            i v      vv ?   i     i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_64169197_6   1762 GAAACTGGACCACTTCCTTACACCTTATAGAAAAATTAACTCAAGATGGA 1811
                            ii      v  v   i     v    v              i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_64169197_6   1812 TTAAAAACTTAAGTGTAAAACCCAAAACCATAAAAATCCTAGAAGAAAAC 1861
                          i ? i  i   i     i v i     i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_64169197_6   1862 TTA-----ATACCATACAGGACATAGGTATGGGCAAAGTCTTCATGACAA 1906
                         v  ----- v i v - iv   v v  vv i     v vi   v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_64169197_6   1907 AAACACCAAAAGCAGTTGCAACAAATGCCAAAATTGACAAATGGGATCTA 1956
                         vi            vvv        v vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_64169197_6   1957 ATTAAACTAAAGCACTTCTCCTCAGCAAAGGAAACTATCATCAGAGTGAA 2006
                           i   v v  iv    i viv vv       v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_64169197_6   2007 CAGGCAACATATAGAATGGAA-AAATTTTTTACCCACCA-------GAAA 2048
                         v  i    vi i       i -   v v   i vv i  -------  v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_64169197_6   2049 AAGGTCTAATATCTAGAATCTACAGGGAACTTAAACAAATTTACAAGGAA 2098
                          i  v  vi    i     v  i ii     ivv    v iv i  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_64169197_6   2099 AAAACAAACAACTCCATCAAAAAGTAGGCAAAGGATATGAACAGACACTT 2148
                           i     i   i v  i?    i i          v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_64169197_6   2149 CTTAAAAGAAAACATTTATGTAGCCAATAAACATATGAAAAAAAGATCGT 2198
                           iv      i i  vi vi i        i  i       i v v  iv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_64169197_6   2199 CATCACTGGTCAT 2211
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (130 / 118)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  

2762 27.97 1.43 1.43  chrX_64169197_64177289.rev     6698  7605 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64169197_6   6698 TGGAAGAACATCCCATGCTCATGGATAGTAAGAATCAATATCATGAAAAC 6747
                              ii i        i        v v    v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64169197_6   6748 AGCCGTACTGCCCAAGGTAATTTATAGATTCAATGCAATCCCCATAAAGC 6797
                         i  vi    v     iv i  i  i        i        i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64169197_6   6798 TACCAATGACTTTCTACACAGAA-TTAGCAAAAACT-ACTTTAAATTTAA 6845
                          v   iivi i  i vii     -  ii   i--  - iii    v  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_64169197_6   6846 CATGGAAC--CAAAGAAGAGCCCACA-TACCCAAGACAATCCTAAGCTAA 6892
                         i      v--   i i ---    v -  v    i      i i ivv i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_64169197_6   6893 AAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAA 6942
                                   i      vv    i  v  ii i      vivi       
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_64169197_6   6943 GGCTACAGTAACCAAAACAGCATGGTACCGGTGCCAAAACAGAGATATAG 6992
                         i          i   i    ii      i  iiiv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_64169197_6   6993 ACCAATAGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACA 7040
                          i    i   i    i--    i  --        vv   i    i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_64169197_6   7041 AACATCTGATCTTTGACAAACCTGACAAAAACCAG-AAATGGGGAAAGGA 7089
                         iv  vi    i  i     ivv  v   i -   v-v           i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAA 392

  chrX_64169197_6   7090 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 7139
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_64169197_6   7140 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAACTAATTCAAGA 7189
                         iiv    ii    i    v   i     v          i   i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_64169197_6   7190 TGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGA 7239
                              i ?    i       v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_64169197_6   7240 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGTACTTCATG 7288
                             v    ?i- v i -   iv   v v  vv i     vvii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_64169197_6   7289 ACTAAAACACCAAAGGCAACGGCAACAAAAGCCAGAAGTGACAAATGCAA 7338
                         iv  vi        i   vvi          vv i  vv  i    vvi 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_64169197_6   7339 TCTAATTAAAATAAAGGGCTTCTGTACAGCAAAATAAACTACGACCAGAG 7388
                         ii v  i     v  iii   i   i vv    iv v    iv vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_64169197_6   7389 TGAACAGGCAACCTATACAATGGGAGAAAATTTTTACAATCTACCCATCT 7438
                             v  i     i i v             v   i   vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_64169197_6   7439 GACAAAGGGCTAATATCAAGAATCTACAAAGAACTTAAACAAATTTACAA 7488
                           i  i  i  vi    v     v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_64169197_6   7489 GAAAAAATCAAATAACTGCATCAAAAAGTGGGCGAAAGACATGAACAGAC 7538
                         v     iv        ivv  i?    i     i  i  iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_64169197_6   7539 ACTTCTCAAAAGAAGACCTTTATGCA----GCCAACAGACATGTGAAAAA 7584
                          i     v        ----   i  ----     i ii  ii      i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_64169197_6   7585 AGCCTCACCACTGGCCATCAG 7605
                          vv    v  iii????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (154 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.86 (26 / 14)  


3151 28.41 0.22 0.22  chrX_64191949_64193808.rev      462  1369 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64191949_6    462 TGGAAGAACATTCCATGCTCATGGGTAAGAAGAATCAATATCGTGAAAAT 511
                              ii i  i     i      i vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64191949_6    512 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 561
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64191949_6    562 TACCAATGACTTTCTTCACAGAATTAGAAAAAAATACTTTAAAGTTCATA 611
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_64191949_6    612 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 661
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_64191949_6    662 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 711
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_64191949_6    712 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 761
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_64191949_6    762 TGGAACAGAAC--ACAGCCCTCAGAAATAATGCCGCATACCCACAACTAT 809
                              i    i-- v  i  --        vv  ii i iii iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_64191949_6    810 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 859
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_64191949_6    860 ATTTAATAAATGGTGCTGGGGAAACTGGATAGCCATATGTAGGAAGCTGA 909
                         v  i  i             iv         ?   i   i ii iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_64191949_6    910 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 959
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_64191949_6    960 AAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAATCT 1009
                          ?   ii    i  v   v       i      vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_64191949_6   1010 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAA 1059
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_64191949_6   1060 CACCAAAAGCAATGGCAACAGAAGGCAAAATTGACAAATGGGATCTAATT 1109
                                    vvi      i   iv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_64191949_6   1110 AAACAAAAGAGCTTCTGCATAGCAAAAGCAACTACCATCAGAGTGAACAG 1159
                            vvv  i i   i  iiivv    i vv    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_64191949_6   1160 GCAACTTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 1209
                         i    ii   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_64191949_6   1210 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 1259
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_64191949_6   1260 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 1309
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_64191949_6   1310 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 1359
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_64191949_6   1360 CACTGGTCAT 1369
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.51 (153 / 101)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


2758 27.76 1.67 0.45  chrX_64207794_64210318     1136  2032 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64207794_6   1136 TGGAAACA----CCATGCTCATGGATGGCTAGAATCAATGTTGAGAAAAT 1181
                               v ----     i        v vv   v i   i   vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64207794_6   1182 AACCATACTGCCAAAAGCAGTCTACAAATTCAATGCAATTTGAAGCAAGA 1231
                         ii v     v  v   viii      i      i     iivv v   i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64207794_6   1232 TAC-AACCATTATTCTTCACACAGCTAGAAAATAATCATCCTAAAATTCA 1280
                          v - i iiii-  i  ii  v iv v  v  -iv v             
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_64207794_6   1281 TGTGGAACCAAAAAAGAACCCGCATAGCCAAAGCAAGACTAAGTAAAAAG 1330
                          i     viiv  ii  v  v v         i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_64207794_6   1331 AACAAATCTGGAGGTATCACAGTACCTGACTTTAAGCTGTAGTATAAGGT 1380
                               vi      vv     v v  ii i  i  iviv  v  i  i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64207794_6   1381 CATAGTCACCAAAACAGCAAGGTACTGGCATAAAAATAGGCACATAAAAC 1430
                         i i   v i   i    iiv             ii    i  i   i v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_64207794_6   1431 AATGGAACAGAATAGAGAACACAGAAATAAAGCCAAACACTTACAGCCAA 1480
                                i     v    iiv          v   v   i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_64207794_6   1481 CTGATCTTTGACAAAG-CAACAAAAACATAAAGTAGGGAAAGGACACCCT 1529
                         i    i  i     i -iiv   i v   vv i i       i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_64207794_6   1530 ATTCAACAAATGGTGCTTGGATAATTGGCAAGCCACATGTAGAAGAATGA 1579
                         v                v   i  i   vv ?       i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_64207794_6   1580 AAC-GGATCCTCATCTCTCACCTTATACAAAAAATCAATTCAAGATGGAT 1628
                          ii-   i  ii i   v    v          - i  i    i      
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGAT 497

  chrX_64207794_6   1629 TAAGGATTTAAATGTAAGACCTGAAACTATAAAGATTCTAGAAGGTAACA 1678
                         i ?i  ii           v  i          iv ii      iv    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_64207794_6   1679 TCAGAA-AAATCCTTCTGGACATTGGCTTAGGCAAAGACTTCATGACCAA 1727
                          vi ?i-     -   vv   v    v        v ii   v iivi v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_64207794_6   1728 GAACCCAAAATCAAACACAACAAAA-ATAAAATAAATAGATAGGACTTAA 1776
                           vv      v  v vi        - v      i   i  v      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_64207794_6   1777 TTAAACTAAAAAGCTTCTGCACAGCAACAGAAACAATCAGCAGAGTTAAC 1826
                          i   v v    i   i  ii vv   vi  v  v    iv i   v  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_64207794_6   1827 AGACAACCCGCAGAGTGGGAAAAAATCTTTGCAATCTGTACATCTGACAA 1876
                                  i    i     i     v       viii  i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_64207794_6   1877 AGGACTAATATCTACAATCTACAAGGAACTC----AAAGAAAT--TAACA 1920
                         i     vi    i v   v  i  i      ----  vvv   --   v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_64207794_6   1921 AGAAAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAAGAGACAATTT 1970
                            v   i  i  v  i?    i     v     iv    v     v  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_64207794_6   1971 GCAAAAGAAGATATAGCAGTGGCCAACAAATACATGAAGAAATACTCAAC 2020
                         v v            vv i       i  ii       i i  i      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_64207794_6   2021 AACACTAATTAT 2032
                          v  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (140 / 105)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


2429 25.33 1.01 9.38  chrX_64222731_64233197     2918  3908 (6559)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64222731_6   2918 TGGAAA--CATCCCATGCTCATGGATGGCTAGAATCAATATTGTGAAAAT 2965
                               --i        i        v vv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64222731_6   2966 GACCATACTGCCAAAGGCAGTCTACAAATTCAGTGCAATTCACATCAAAA 3015
                          i v     v  v  iviii      i     ii     i vi       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64222731_6   3016 TGCCAGCATCATTCTTTACAGAACTAGAAAAAAAAATCATCCTAAAATCC 3065
                          v     vv v  i   i     v v  v  iv--- v          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC---TGATCCTAAAATTC 147

  chrX_64222731_6   3066 ATATGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAA 3115
                                 viiv  ii  v  viv         i   vvi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_64222731_6   3116 GAACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATAGTATAAGG 3165
                                vi      vv     i v  ii i      viv  v  i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_64222731_6   3166 TTATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGAC 3215
                         i  i   v i   i    ii         i    ii    i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_64222731_6   3216 CAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAGCCA 3265
                                 i     v    ii           v   v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_64222731_6   3266 ACTGATCTTTGACAAAGCAAACATAAACATAAAGTAGGGAAAGGACACCC 3315
                          i    i  i     i vviv  vi v   vv i i       i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_64222731_6   3316 TATTCAACAAATGGTATTGGG-TAATTGGCAAGCCACAGGTAGAAGAATG 3364
                          v             ii    -i  i   vv ?     v i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_64222731_6   3365 AAACTGAATCCTAATCTCTCAATTTATACAAAAATCAACTTGGCCAGGCA 3414
                           ii  i i  iv i   v  viv           i    --------  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT--------CA 489

  chrX_64222731_6   3415 TTATGGATCACTGCAGATCACTGCACTCCAGCCTATGTGATAGAGGGAGA 3464
                         vv        ?---   i -------------------------------
  L1M4_orf2#LINE/    490 AAATGGATCAW---AGACC------------------------------- 505

  chrX_64222731_6   3465 CGCCGTCTTAAAAAAAAAAAAAATCAACTCAACACGGCTGAAGGAATTAA 3514
                         -----------------------------------------------   
  L1M4_orf2#LINE/    506 -----------------------------------------------TAA 508

  chrX_64222731_6   3515 ATCTAAGATCTGAAACTGTAAAAATTCTGGGAGATAACATCAGAA-AAAC 3563
                           v     v  i     i     v ii i i   v     vi ?i-   i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_64222731_6   3564 CATTTTAGGCATTGGCTTAGGCAAAGACTTCATGACCAAGAACCCAAAAG 3613
                          v iv - i v    v        v ii   v iivi v  vv       
  L1M4_orf2#LINE/    559 CTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_64222731_6   3614 TAAATGCAACAAAG--ACAGATAAATAGATGGGACTTAATTAAATTGAAA 3661
                         i v v        i-- v i   i   i  v      v  i   v v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_64222731_6   3662 AGCTTCAGCACAGCAAAAGAAATAATCAGCAAAGTTAATAGACAACCCAC 3711
                          i   iv ii vv    i  v iv    iv     v  v           
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_64222731_6   3712 AGAGTGGGAGAAAGTTTTTGTAGTCTATACATCTAACAATCAA----TGC 3757
                            i         i v    i ivii   i    i i  vvi ---- ii
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_64222731_6   3758 TCAGACTCTACAAAGAACTCAAACAAATTAGCAAGAAGTAAACAAACAAT 3807
                         i    v v  i         vv    v i ii  v  iv i     i  i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_64222731_6   3808 ACTATCAAAAAGTGGGCTAAAGACATGAAGAGACAGTTTTCAAAAGAAGA 3857
                         v v  i?    i     v  i  iv    v     v  i  v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_64222731_6   3858 TATAGAAATGGCCAACAAACATATGAAGAAATGCTCAACATCACTAATGA 3907
                             v          i  i  i     i i             ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_64222731_6   3908 T 3908
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.35 (142 / 105)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 10.30 (103 / 10)  

3085 27.53 0.88 0.88  chrX_64222731_64233197     9067  9974 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64222731_6   9067 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATAAGTATCATGAAAAT 9116
                              ii i  i     i      i v      v v i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64222731_6   9117 GGCCATACTGCCTAAGGTAATTTGTAGATTCCATGCCATCCCCATCAAGC 9166
                            v     v  i  iv i  i ii      v i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64222731_6   9167 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 9214
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_64222731_6   9215 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 9264
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_64222731_6   9265 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 9314
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64222731_6   9315 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 9364
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_64222731_6   9365 AATGGAACACAAC--AGAGCCCTCAGAAATAACACCTCATATCTACAACT 9412
                                i v  i--    i  --        vv  vi i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_64222731_6   9413 ATCTGATCTTTGACAAACCTGAGT---AAAACAAG-CAATGGGGAAAGGA 9458
                          vi    i  i     ---- i  ---  i  v v-            i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAA----GGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_64222731_6   9459 TTCCCGATTTACTAAATGGTGCTGGGAAAACTGGCTAGTCACATGTAGAA 9508
                          vvi vv  i vi              v      v  ?i      i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_64222731_6   9509 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGA 9558
                         iiv    ii    i    v   i     v           i  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_64222731_6   9559 TGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGA 9608
                              i ?    i    i  v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_64222731_6   9609 AAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 9658
                             v    ?i v viv   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_64222731_6   9659 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAGTGGGAT 9708
                         v  vi            vvi          vv     v  i  i v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_64222731_6   9709 CCAATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTTCCGTCAGAGT 9758
                         iiv  i   v v  i     i  ii vv    i  v   vi ivv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_64222731_6   9759 GAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTG 9808
                            v  i     i   i             v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_64222731_6   9809 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAAGAAATTTACAAG 9858
                          i  i  i  vi          v  i  v      vv v  v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_64222731_6   9859 AAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACA 9908
                              i     i     v  i?    i    ii     iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_64222731_6   9909 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 9958
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_64222731_6   9959 CATCATCACTGGCCAT 9974
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


2527 29.09 1.22 0.77  chrX_64238702_64244490.rev     4395  5298 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64238702_6   4395 TGGAAGAACATTCCATGCTCATGGATAGGAATAATTGATATTATGAAAAT 4444
                              ii i  i     i        v    v v  i     i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64238702_6   4445 GGCCATATTGCACAAAGTAATTTATACATCCAATGCTATTCCCACTAAAA 4494
                            v   i v v    v i  i  i v  i   i  v  i  i ii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64238702_6   4495 TACCATTGACATTCTTCACAGAATTAGAAGAAACTACTTC-AAAATTCAT 4543
                          v   vivi v  i  ii     v v  v-  i  iv i -         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_64238702_6   4544 ACTGAACCACAAAAGAGCCCAAACAGCCACAGCAATTCTAAGCAAAAAGA 4593
                          iv   vii   ii  v  vi  i     v i    ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_64238702_6   4594 ACAAAGCCAGACACATCATGCTACCCAAAATCAAACTATACTCCAAGGCT 4643
                               iii  vivv   ii  v     vv     viv    v   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_64238702_6   4644 ACAGTAAGCAAAACAACATGGTACTGGTACAAAAACAGACACATAGACTA 4693
                                v   i   iii         i i  ii i     i     ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_64238702_6   4694 ATGGAAGATAATAGAGAACTCAGAAATAAAACAACACACCTACAACCATC 4743
                               v v   v    iii          v v i   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_64238702_6   4744 TGATCTATGACAAACCTGACGAAAATGAGCAATGGGAAGACAATCCCCTA 4793
                             i vi     ivv  v i i viivv       i i v   vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_64238702_6   4794 TTTAATAAATAGTGTTGGGAGAATTGGCTAGCCATATGCAGAAAATTGAA 4843
                           i  i    i   i     v  i   v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_64238702_6   4844 ATTGTAAGCCTTCCTAACATCTTATACAAAAATTAACTCAAGATGGAGTA 4893
                         i   v vv   v   v   i v                   i     vi 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_64238702_6   4894 AAGACTTAAATGTAAAACCCAAAACTATAAAAATCC-AGAAGAAAATCTA 4942
                         ?    i         i v i            v  i-         iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_64238702_6   4943 GG---AAATACCATTCAGGAAATAGGCATGGGCAAAGATTTCATTATAAA 4989
                           ---    -- -   iv  vv v  vv i     v i    -   v v 
  L1M4_orf2#LINE/    550 GGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATA 595

  chrX_64238702_6   4990 -AATGCCAAAAGCAATTGCAATAAAAGCAAAAATTGACAAATGGGACCTA 5038
                         -i ii         vvv    i     v      v  i    v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_64238702_6   5039 GTTAAG-TGAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5087
                         i i  i- v   i -   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_64238702_6   5088 ATAGACAACCTACAGAGAAAGAGAAAATTTTTGCTATCTGTCCATCTGAC 5137
                          v        i     ivii        v     v viii vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_64238702_6   5138 AACAGTCTAATATCTAGATTCTAAAAGGAATTTAAACAAAT--ATAA-AA 5184
                           vi v  vi    i   v v  v  i   i ivv    v --    -  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_64238702_6   5185 GAAAA-AAACAACCCCATTTAAAAGTGGGTAAAAAACATGGACAAACCCT 5233
                         i  i -   i     v   ?    i    i   ii iv  i i i  vi 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_64238702_6   5234 TCTCAAAATAAAACATTCATGTGGCTAAGAAACATATGAAAAAAAAGCTA 5283
                             v   v  i i  v  vi    i  v  i  i       i v-   v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTC 893

  chrX_64238702_6   5284 AACATCAGTGACTGA 5298
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (149 / 111)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.29 (18 / 14)  


2699 28.73 3.17 0.45  chrX_64247417_64250550     1758  2641 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64247417_6   1758 TAGAAAAATGTCTAATGCTCATAGATAGGAATAATCAATATTATTAAAAT 1807
                          i    i  i  iv   i    i   v    v v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64247417_6   1808 GGCTATGCTTCCCAAAGCAATTCATTGATTCAATGCTATTTTTATTAAAC 1857
                            v  i  i      vii  ii iv       i  v  iii   i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64247417_6   1858 CACCATTGACATTCTTCACAGCACTAGAGAAAAGTAATT-TAAAATTCAT 1906
                         iv   vivi v  i  ii   v v v  v  iv- i  i-          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_64247417_6   1907 ATGAAACCAAAAGAGAACCTGAATAGCCAAGGCAATTCTAAGCAAAAAGA 1956
                            i  viiv   i  v  v          ii    ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_64247417_6   1957 ATAAAGCTGGAGGCATAATGCTACCTGACTTCAATCTATACTACAATGCT 2006
                          i    i      vv v ii  v  ii i     vviv        v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_64247417_6   2007 ACAGCAACCAAAACAGCCTGGTACTGGTACAAAAAAAGACATGCAGACCA 2056
                             i  i   i    iv         i i  ii v      ii   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_64247417_6   2057 ATGGAACAGAATAGAGAACCCAGAAATAAGATTGCACACCTGCAACTATT 2106
                               i     v    ii          iviiii   ii iiiiii v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_64247417_6   2107 CAGTCTTCAATAAACCTGACAAAAGCA----ATGGGGAAAAGAT--TCCT 2150
                         iii i   i i  ivv  v   i v  ----         ii  --  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_64247417_6   2151 TGTTCAATAAATAGTGCTGGGG-AACTGGCTAGCAATATGCAGAAGATTG 2199
                          --    i    i        i-      v  ? v i     i    v  
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_64247417_6   2200 AAACTGAACCCCTTCCTTACACCATATACAAAAATTAACTTAAGATGGAT 2249
                           ii  i      v   i                      i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_64247417_6   2250 TGAAGACATAAATGTAAAACCCAAAACTGTAGCAATCCTGAAAGACAATC 2299
                         ii?    v         i v i      i  iv v  i ii    v  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_64247417_6   2300 TAGGCA-ATATCATTCAGGACATAGACACCGGCAAAGATTTCATGACGAA 2348
                             ?i- v   -   iv   v v ivviv     v i    v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_64247417_6   2349 GACACAAAAAGCAATTGCAACAAAAACAAAAATTGACAAATGGGACCTAG 2398
                              v       vvv         iv      v  i    v    i vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_64247417_6   2399 TTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCAACAGAGTGAAC 2448
                          i   v v  i i   i  ii vv    iv v        v i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_64247417_6   2449 AGACAACCTACAGAATGGGAGAAAATGTTTGCAAATTATGCATTTGACAA 2498
                                 i                 i         i  ii  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_64247417_6   2499 AG-------ATC-AGCATCTATAAGGAACTTAAACAAATTTACAAGCAAA 2540
                         i -------   -  v  v     i     ivv    v iv i  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_64247417_6   2541 TAACAAACAACCCCGTTATAAAGTGGGCAAAGAACACCAACAGACA---C 2587
                         vi     i     vi  ?v   i         i iviv  i     --- 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_64247417_6   2588 TTCAA--------TACATGCGACCATCAATCATATGAGAAAAAGCTCAAC 2629
                          i   --------    vii i   vi  v  i    i  i v       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_64247417_6   2630 ATCACTGATTAT 2641
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (155 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.67 (32 / 12)  


2497 29.16 3.42 0.23  chrX_64251234_64253340.rev      739  1616 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_64251234_6    739 GAAACATATCCCATGCTCGTGGATGGCTAGAATGAATATTGTGAAAATGA 788
                             v          i  i     v vv   v v        v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_64251234_6    789 TCATACTGCCAAAAGCAATCAACAAATTCAACACAATTCCCATCAAAATA 838
                         iv     v  v   vii   v   i       i    i  i        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_64251234_6    839 TCA-CCGTCATTCTTCACAGACTTAGAAAAA---ATTATAAAATGAATAT 884
                         i  - i i -  i  ii    vv v  v  i---  iv      vv    
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_64251234_6    885 GGAACCAAAAGTAAGCCCACATAGCCAAAGCAAGACTAAGCAGAAAGAAC 934
                             viiv   vi v  viv         i   vvi i iv ii      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_64251234_6    935 AAAACTGGAGGCATCACATAACCTGATTTCAAAGTATACTATAAGGCCAT 984
                            ii      vv     ivv  ii        iiv     i  i  i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_64251234_6    985 AGTCACCAAAACAGCATGTTACTGGTATAAAAGTACCAAT-TAGACCAAT 1033
                            v i   i    ii  v      i    iii  vvv  -    i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_64251234_6   1034 GGAACAAAGTGGAGAACCCAAAAGTAAA--------------GCCAACTG 1069
                             i i i v    ii   i  i    -------------- i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_64251234_6   1070 ATCTTTGACAAAGCAAACAAAAACATAAAGTAGGGATAGGATACCATTTT 1119
                           i  i     i vviv   i v   vv i i    v  i   viv    
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_64251234_6   1120 CAACAAATAGTGCTGGGATAATTGGCTAGCCGCATGTA---GAATAAAAC 1166
                                 i         i  i   v  ?  i    i ---    i  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_64251234_6   1167 TGGATCCTCATCTCTCACCTTACACAGAAAT-----CAAGATGGCTTAAA 1211
                             i  ii i   v    v  i   i    -----   i    v i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_64251234_6   1212 GACTTTAATATAAGACATGAAACTATAAAAATTCTAGAAGATAACATTGA 1261
                            i v   i     vv i           v ii       v     v i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_64251234_6   1262 AAAACCCCTTCTAGATGTTGGTTTAGGCAAGGATTTTATAATCAGGAATC 1311
                         ?iv vvi    vv  iv    v        v i   iv  ivi v  vv 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_64251234_6   1312 CAAAAGCAAATGCAATAAACACAAAGATGAATTGCTAGGACTTAATTAAT 1361
                                 v v    i   viv   i  ii  viv v      v  i  v
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_64251234_6   1362 CTAAAGAGCTTTTGCACTGCAAAAGGAACAGTCAGCAGAGTAAACAGAAA 1411
                         v v  i i      ii  v    i iv  vi   iv i   i  v   v 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_64251234_6   1412 ACCCACAGAGTGAGTAAAAAACCTTCACGATCTATCCATCTGAGAAAA-A 1460
                                  i  i - i    iv  ii i vii  vi      v  ii- 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGG-AGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_64251234_6   1461 CTAATATCCAGAATCTACAATGAAATCAAACAAATCAACAAGAACAAAAC 1510
                           vi          v  i  v   v  vv    v    i  v  v  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_64251234_6   1511 AAACAATCCCATCAAAAAGTCAGCTAATGATATGAATAGGCAATTTTCAA 1560
                            i  i  v  i?    i vi  v  v   v       i  v  i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_64251234_6   1561 AAGAATATATACAAATGACCAACAA--ACATAAAAGAATGCTTAACATCA 1608
                              v           i    i  --    i   ii     i       
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_64251234_6   1609 CTAATGAT 1616
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.29 (142 / 110)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 3.20 (32 / 10)  

 204 30.23 3.49 1.16  chrX_64251234_64253340.rev     1962  2047 (60)  C L1M4_orf2#LINE/L1   (576)   332   245  

C chrX_64251234_6   2047 AGGCTAAAATACTCAAAA-AATGTAGTCTTGGAATAAGAACTGATGTATT 1999
                          i    v i  v    i - i   i  vi   v     i iv  ii   v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

C chrX_64251234_6   1998 ACTCAATGGATACAATATTTAG--CCCGGATAGAAACCC 1962
                         iv        - i iv   v  --i  i  v v      
  L1M4_orf2#LINE/    295 GATCAATGGA-ATAGAATTGAGAGTCCAGAAATAAACCC 332

Transitions / transversions = 1.36 (15 / 11)
Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.33 (4 / 3)  


 708 29.39 1.22 1.63  chrX_64289165_64293643     2841  3085 (1394)    L1M4_orf2#LINE/L1        1   244 (664)  

  chrX_64289165_6   2841 TGAAAAAATATCCCATGTTTATGGGTCAGAAAAGTTAATGTTATTAAAGT 2890
                           i   i            i    i ii   i v     i  i    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64289165_6   2891 GACCATATTGCCCAAGCT-ATCTACAAGTTCAATGTAATCCCAATCAAAA 2939
                          i v   i v     ii -       ii     i i      v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64289165_6   2940 TAACAGTGGCATTATTCACA-ACGTTAGAAAAAAGAAAATTTAAAAATTC 2988
                          vv   iv  v  v  ii  - vi  i--- v   vvi  iiv       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_64289165_6   2989 ACATGGAA-CACAAACAGAGCCTGAATAGCCAAAGCAATCCTGAGAAAAG 3037
                          i      -ii   i-i  v  v           i     i   i   ii
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_64289165_6   3038 TGAACAAAAATGCAAACATCATATTATCTAACCTGAAAATATATTACA 3085
                         v       iv  v iivv   i i vi i  ii v    iv  i    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

Transitions / transversions = 2.00 (48 / 24)
Gap_init rate = 0.02 (5 / 244), avg. gap size = 1.40 (7 / 5)  

2069 25.22 3.96 1.91  chrX_64289165_64293643     3305  3986 (493)    L1M4_orf2#LINE/L1      213   908 (0)  

  chrX_64289165_6   3305 ATTCATAATATCTAATTTGATA--TTATATATAAAAGCTATAGTAACCAA 3352
                          i   i v vi i     v v --   i-  i   -    i     i   
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTAC-TACAAA-GCTACAGTAATCAA 260

  chrX_64289165_6   3353 AACAGCATGGTATTGGTA-AAAAATAGAGACATTGATCCATGGAACAGAA 3401
                         i    ii     i   i -  ii     v i  v    v      i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_64289165_6   3402 TAGAGAATCAAGAAATAAATTCATACA------GCCAACTATTCTTAGAC 3445
                          v    i  v         ii      ------ i   i iv i  v   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_64289165_6   3446 AAAGCTGACAAGAATTTGCATTAGGGAAAAGGACA--CTCTTCAATAAAT 3493
                           i v  v     viv v  v i      - i i --  i     i    
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAAT 409

  chrX_64289165_6   3494 GGTGCTGGGAATGTTGGACAGTCATATGCAAAAGAATGAAACTTGACTTC 3543
                                   vvii    i ?i  i               ii v   ii 
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_64289165_6   3544 TATCTCACACTATGTGCATAAATCAACCCAAAATG--TTTAAG-TTTAAA 3590
                           i       i  i i  v    i   i       -- iv?  -ii    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_64289165_6   3591 CATAACACCCAAAACTATAATACTATTAGAAGAAAACA--GATA-AAATT 3637
                         ii   v v i          v   v             -- i?i-    i
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_64289165_6   3638 GTCCTGGACATTGTCGTAAGCAAGGGATTTATTATCCAT--CCTCAAGAG 3685
                         v  v  -  v   vvv  i    v  -   v   vvi  -- vi   i  
  L1M4_orf2#LINE/    560 TTCGTG-ACCTTGGGTTAGGCAATGG-TTTCTTAGATATGACACCAAAAG 607

  chrX_64289165_6   3686 TATAGTCAGCAAAAGCAAAAATAGAGAAATGGGGCTT-----AAACTAAA 3730
                         i i iv  i      v         v    v  i   -----   i    
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_64289165_6   3731 AAGCTTCTATGTAGTAAAAAATAATAATAATAATAACAGAATGAAGAGAT 3780
                           -   i i  ivvi   ii i v  vi  v  ------ i    i   i
  L1M4_orf2#LINE/    658 AA-CTTTTGTGCTTCAAAGGACACTATCAAGAA------AGTGAAAAGAC 700

  chrX_64289165_6   3781 AACCTATTGAATGGCAGAAAATATTTCCAACCTATTTATCTGACAGGGGA 3830
                             i iv      v           v   vii  v       i i    
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_64289165_6   3831 CCAATATCCAGAATATAAAACAAACTCAAACAAATCAACAG-GAAAACAC 3879
                          ivi             v  vi     vv    v    i i-i    v  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_64289165_6   3880 AAATAATTCCATTTAATG-TGGGCAAAGAACATGAATAGATATTTCTTAA 3928
                               ii v   ?  vi-         i iv        i      iv 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_64289165_6   3929 AAGGTGATATGCAAAATGGTTAACAGATATATGAAAA-ATGCTGAACATC 3977
                            iv     i    -   ii  i iii i       -     v      
  L1M4_orf2#LINE/    851 AAGAAGATATACAAA-TGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_64289165_6   3978 ACTAATCAC 3986
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.62 (104 / 64)
Gap_init rate = 0.03 (21 / 696), avg. gap size = 1.90 (40 / 21)  


1033 28.78 7.67 0.96  chrX_64306097_64308465      708  1124 (1245)    L1M4_orf2#LINE/L1        1   445 (463)  

  chrX_64306097_6    708 TAGAGAGATCTGTAATACTCTTGGATTAGAAGACTCAATTTTGTTAAAGT 757
                          i  i    v viv  ii  v      i       i   v       ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64306097_6    758 GTCAGTTTTACCCAAGTAGAGATACAGATTGAATGAAATC----TCAAAC 803
                          v  i vi v     i v  vv        v  i v    ----     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64306097_6    804 TTTCAAACAGGTTTTTAAAAAGAAATTCACAAACCAATTTTAAAATTCAT 853
                          ii  i- v vi    vviv       v    i ii  ii          
  L1M4_orf2#LINE/    101 TCCCAG-CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_64306097_6    854 TTGAAATTACACAATATCTAGAGGAGCCAAAACGTTATGTGGAAAATA-G 902
                         v  i  v i  viiv i i   iv         iv v -  i    v - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT-TGAAAAAGAAG 198

  chrX_64306097_6    903 TGTAAAGTTATAGGACTTACAATGTC--AT--CAAGACTTAG---AAATC 945
                         vii      iv      i   v vi --  --   i     v---   v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64306097_6    946 TAACTTATTTAAGACAGTGTGGTATTGACA---ATATAGATGAATAAATC 992
                           vvv  v i              i  i  ---iv     iiv   i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_64306097_6    993 AAAGGAA-------GTGAGTTCAGAAATAGGCTTACATACATACAT---- 1031
                           v    ------- v    i        ii i--       vi  ----
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTC 346

  chrX_64306097_6   1032 -ATCAATTTTCAACCAAA---CCTGAA--ATTTCATGGAGAAAGTATAGT 1075
                         -  ii      i  v ii---  vii --   iv    i     v     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_64306097_6   1076 TTCTTTAACTAATGGTGGTAGAATAATTGAGTAACCATATGCAAAAAAA 1124
                         i i  i   v       v i i i  i  ii  ?   i        i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

Transitions / transversions = 1.43 (70 / 49)
Gap_init rate = 0.03 (13 / 445), avg. gap size = 2.77 (36 / 13)  

 933 24.24 8.94 2.12  chrX_64306097_64308465     1452  1876 (493)    L1M4_orf2#LINE/L1      455   908 (0)  

  chrX_64306097_6   1452 ACCCATATCTCACA--GTGTACAATAATTAAATCCAACCCAGTCATTAAC 1499
                             v  i      --i i     v      v  v  vivii   ?vi  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_64306097_6   1500 CTAAATGTAAAA-CCAAAAATAAAAAAGTACACTTTTAGAAGAAAAAAAT 1548
                                   i - i    v  v    -----  i           v vv
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAA-----CTCTTAGAAGAAAACATA 549

  chrX_64306097_6   1549 GGGGAATAATTTTTGTGTTAATTAGGTTAGACAAAAATTTATTAGGTGCG 1598
                           ? v -   i  i   viv-  i      i   vii   v    i ii 
  L1M4_orf2#LINE/    550 GGNGTA-AATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_64306097_6   1599 ACACCATA-GAATGATCAATAAAG--AAAAATA-ATAAATTGGACTTCAT 1644
                               v - v ii v   i   i--       -                
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_64306097_6   1645 CAAAATTAA---TTTTTCTGCTATTTGAAAGACATTTTAAAAATATTGTA 1691
                                  ---i    v    -- ii  i    i v v  i v v  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_64306097_6   1692 AAGACAAGCTATAGACGTGGAGAAAATATTTACA---------------- 1725
                                v i i   vvv             i  ----------------
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_64306097_6   1726 ------TTGTA-CAAGTGTA-ATAAATA--TTTTA-ATCTCAATAAGAAG 1764
                         ------     - v  vi  -     v -- i   - v        v  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_64306097_6   1765 TA-ATAAAAAAACCAAATAAATAATGGACACAAGCTTTGAACAGGTATTT 1813
                         v - i   v  v    v ?  v     i  v i v      i  ii    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_64306097_6   1814 TATCAATGAAGATATGGAGATGGCAAATAAACACAAGAAACAATGATAAA 1863
                         ivi   v        iv i     v     i    v    vi   v v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_64306097_6   1864 TATTATTTCTCAT 1876
                         i  i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (50 / 50)
Gap_init rate = 0.04 (16 / 454), avg. gap size = 2.94 (47 / 16)  


 441 29.85 0.75 0.75  chrX_64343095_64348364     4000  4133 (1137)    L1M4_orf2#LINE/L1        1   134 (774)  

  chrX_64343095_6   4000 TAGGAAAACATTCCATGCTCATGTTTAGGAAGAATTGATATCGTTAAAAT 4049
                          i i  i i  i     i     vv v      v  i    i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64343095_6   4050 GGCCACAGTGCCCAAAGCAATTTATAGATCCAATGCTATTCCTATCAAAC 4099
                            v i v v      vii  i  i    i   i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64343095_6   4100 T-GCAATGACATTCTTCATAGAACTATAAAAAGCT 4133
                          -v  iivi v  i  iii    v - i v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCT 134

Transitions / transversions = 1.67 (25 / 15)
Gap_init rate = 0.01 (2 / 134), avg. gap size = 1.00 (2 / 2)  

1863 27.95 3.42 0.31  chrX_64343095_64348364     4134  4777 (493)    L1M4_orf2#LINE/L1      245   908 (0)  

  chrX_64343095_6   4134 AGGTTACAGTAACCAAAACAGAATGGTACTGGTACAAAAACAGACACATA 4183
                          i i        i   i    vi         i i  ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_64343095_6   4184 GACCAATGGAACAGAATGGAGATCCCAGAAATAAGGCTGCACACCTA-AG 4232
                           i        i     v    vi          iv iii   ii  -i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_64343095_6   4233 TCATATGATCTTCAGCAAAACTGATAAAAACAAGCTATGGGAAAAGGACT 4282
                            vv    i   ii   iiv  vi  i v  vv v     i    i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_64343095_6   4283 CCCTATTCACCAAATGGTACTTGGATAACTGGCAATCCATATGCAGAAGA 4332
                         vi  v    v        i  v   i      vv ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_64343095_6   4333 TTGAAACTAGAACCATTTCTTACACCATATACAAAA-TCAACTCAAGATT 4381
                         v    ii i  v  v vi  i               - i       i  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_64343095_6   4382 AATTAAAAACTTTAATGTAAAA-CCAAAACTATAAAAATTCTCAAAGACA 4430
                         i  i ? i  i v       i - i            v ii vi    v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_64343095_6   4431 GCCTCAGCATTACCATTCAGGACAAAAGAATGGGAAATGATTTCAT-GAT 4479
                         i v vi ?i v viv   iv   vvvi iv i  v    i    v -   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_64343095_6   4480 GAAGACACCAAAAGTGAATGCAATGAAAGCAAAAACTGA-AAACTGAGAT 4528
                         - v           iiv v    ii    v     iv  -   i  iiv 
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_64343095_6   4529 --AT--AAACTAAAGAGCTTCTGCAAAGCAAAAGAAACTGTCAACAGAGT 4574
                         --  --   i    i -   i  iivvv    i  v   i    v i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_64343095_6   4575 AAACAGACAACCTACA-AATGGGAGAACATTTTTGCAAACTATGCATCTG 4623
                         i  v        i   -          v  v        ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_64343095_6   4624 ACAAAGTTCTAATATCCAGAATCTATCAGAAAC----ATAAATTTACAAG 4669
                          i  i vv  vi          v   v ii   ---- i  v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_64343095_6   4670 GAAAAAACAA----CCTCATT-AAAAGTGGACAAAGGACATGAACAGACA 4714
                         i    i    ----  iv   -    i   i       iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_64343095_6   4715 CTTTTT---AAAAGACATACATGAGGTCAACAAGCATATGAGGAAAAGCT 4761
                         i  i i--- i    i     viv  i   i     i    ii i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_64343095_6   4762 CAACATCACTCATCAT 4777
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (110 / 67)
Gap_init rate = 0.02 (14 / 664), avg. gap size = 1.71 (24 / 14)  


 924 28.70 2.37 0.59  chrX_64349272_64355129        1   338 (5520)    L1M4_orf2#LINE/L1      383   726 (182)  

  chrX_64349272_6      1 GGGGAAAGGA-ATCCTATTCAATAAATTTTGCTGGAATACCTGGTTAGCA 49
                                 i - vi  v     i    vv      i i v    v  ? v
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_64349272_6     50 ATATGCAGAAGAATGAAACTGCACCCCTATCTTTCACTATATACAAAAAG 99
                          i     i         ii  v       i  iv   i           v
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_64349272_6    100 TAACTCAAGATGATTCAAAGATTTAAATGTA-GACCTCAAATTATAAAAA 148
                                 i   iv   ?   ii        -  v  v   i       v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_64349272_6    149 TCCTAGAAAAAAACCCCAAAATTATCATTTT--TTACATTCTGT---ACA 193
                           i     i     vivii?i v --  i  -- v  v  vv  ---i  
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_64349272_6    194 AAAAATTTATGACCAAGTCCTCAAAAGCAATTGTAACAAAACCAAAAATT 243
                          viiv  iv iivi v v vi        vvv i       vv      v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_64349272_6    244 GACAGGTGGGTCCTAATTAAACTAAAGAGCTTTTAGACAGCAAAATAAAC 293
                           i ii v  v i v  i   v v  i i     ivi vv    iv v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_64349272_6    294 TATCAACAGAGTAAATAGACAACCTACAGAAGTGGAGAAAA-ATTT 338
                               v i   i  v        i      vv        -    
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

Transitions / transversions = 0.96 (46 / 48)
Gap_init rate = 0.02 (6 / 344), avg. gap size = 1.67 (10 / 6)  

 508 21.90 0.73 0.00  chrX_64349272_64355129      998  1134 (4724)    L1M4_orf2#LINE/L1      771   908 (0)  

  chrX_64349272_6    998 AGAACACCT-CAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGT 1046
                              v i -   v iv i  v     i     i     v  i?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_64349272_6   1047 GGGCAAAGGATATGAACAGACAGTTCTCAAAAGAAGACATTTATGCAGGC 1096
                                    v    i     v     v        i  vi viii v 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_64349272_6   1097 AACAGACACATGAAAAAATGCTCATCATCACTGGCCAT 1134
                           i ii          i       v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (17 / 12)
Gap_init rate = 0.01 (1 / 138), avg. gap size = 1.00 (1 / 1)  

2921 27.43 1.22 0.77  chrX_64349272_64355129     4462  5365 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64349272_6   4462 TGGAAAAACATTCCATGCTCAAGGATAGAAAGAATCAATATCATGAAAAT 4511
                               i i  i     i   v    v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64349272_6   4512 GGCCATACTGCCTAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4561
                            v     v  i   v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64349272_6   4562 TACCA-CTGACTTTCTTCACAGAATTGGAAAAAAATACT-ACTTTAAACT 4609
                          v   -   v    i  -i     v v  v  i----  - iii    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG----CTGATCCTAAAAT 145

  chrX_64349272_6   4610 TTAAATGGAACCAAAAAAGAGCACGCATAAACAAGACAATCCTGGGCAAG 4659
                          i v      viiv  ii  v vv v   iv   i      i  iiv   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_64349272_6   4660 AAGAAAAAAGCTGGAGGCATCATGCTACCTGACTTCAAAATATACTACAA 4709
                              v    i      vv   ii  v  ii i       iv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_64349272_6   4710 AGCTACTGTAACCAA-ATAGCATGGTACTGGTACCAAAACAGATATATAG 4758
                               v    i   - i  ii         i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_64349272_6   4759 ACAAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAA- 4807
                          iv       i    iv   ivii         vv   i    i  iii-
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_64349272_6   4808 CAATCTGATCTTTGACAAACCTGACAAAAACAAGCAATAGGGAAATCTTT 4857
                             -    i  i     ivv  v   i v  vv    i      vvv v
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_64349272_6   4858 CCCTATTTAATAAAAGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAA 4907
                         vi  v  i  i   v    i     v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_64349272_6   4908 CTGAAACTGGACCCCTTCCTTACACCTTATACAAAGATGAACTCAAGATG 4957
                         v    ii         v   i     v        i  v       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_64349272_6   4958 GAACAATGACTTAAA----AGACCTAGGACTGTAAAA-TCCTAGAAGAAA 5002
                           v  ?v   i    ----   v   ii   i     -  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_64349272_6   5003 GCCTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTC 5051
                         i v i  ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_64349272_6   5052 TAAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTTACAAATGGGATC 5101
                           vi            vvi          vv i   vv i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_64349272_6   5102 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 5151
                          v  i   v v  i i   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_64349272_6   5152 AACAGGCAACCTGCACAACGGGAGAAAAAATTTGCAATCTATCCATCTGA 5201
                           v  i     ii  v  i         v        vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_64349272_6   5202 CAAAGGGCTAATATCCAGAATCTACAAAGGACTTAAACAAATTTACAAGA 5251
                         i  i  i  vi          v  i    i   ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_64349272_6   5252 AAAA-ACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGATAC 5300
                             -     i     v  i?    i    ii      v    i   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_64349272_6   5301 TTCTCAAAAGAAGACATTTATGCAGCTAACAGACGTATGAAAAAATGCTC 5350
                              v        i  vi viii  i  i ii ii       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_64349272_6   5351 ATCATCACCGGTCGT 5365
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


2955 27.58 0.66 0.88  chrX_64396352_64402843      492  1401 (5091)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_64396352_6   1401 TGGAAAAACATTCCATGCTTATGGATAGGAAGAATCAATATCTTGAAAAT 1352
                               i i  i     i i      v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_64396352_6   1351 GGCCATACTCTCCAAAGTAATTTATAGATTCAATTCTATTTCCATCAAGC 1302
                            v      i     v i  i  i        iv v  ii i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_64396352_6   1301 TACCATTGACTTTCCTCACAGAACTAGAAAAAACT-ACTTTAAATTTAAT 1253
                          v   vivi i  ii ii     v v  v  i-  - iii    v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

C chrX_64396352_6   1252 ATGGAACCAAAAAAGGAGCCTGTATAGCCAAGACAATCCTAAGTAAAAAG 1203
                               viiv  i-   v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_64396352_6   1202 AACAAAGCTAGAGGCATTAGGCTACCTGACTTCAAACTATACTACAAGGC 1153
                                i i    vv i vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_64396352_6   1152 TACAGTAACCAAAACAGCATGATACTGGTACCAAATCAGATATGTAGACC 1103
                                 i   i    ii  i      i iv iivi   i  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_64396352_6   1102 AATGGAACCGGACACAGGCCTCAGAAATAACACCACACATCTACAACCAT 1053
                                iv i ivv  ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

C chrX_64396352_6   1052 CTGATCTTTGACAAACCTGACAAAAACAAGCAATAGGGAAAAGATTCGCT 1003
                         i    i  i     ivv  v   i v  vv    i      ii  vvv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

C chrX_64396352_6   1002 ATTTAATAAATGATGTTGGGAAAACTGGCTAGACATATGCAGAAAACAGA 953
                         v  i  i     i  i     v      v  ?v  i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

C chrX_64396352_6    952 AACTGGAGCCGTTCCTTACACCTAATACAAAAATTAGCTCAAGATGGATT 903
                          ii    v  v v   i     vv            i     i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

C chrX_64396352_6    902 AAAGACTTAAATGTAAAACCTAAAACCATAAAAACCTTAGAAGAAAGCCT 853
                          ?    i         i v       i      vi           i v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

C chrX_64396352_6    852 AGGCA-ATACCATTCAAGACAT-AGGCAAGGGAAAAAGACTTCATGGCTA 805
                            ?i- v i -   iv   v -i  iv   v  v-- ii   v i v  
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT--GGTTTCTTAGATA 595

C chrX_64396352_6    804 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGTCAAATGGGATCTA 755
                         vi            vvi          vv     v vi    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chrX_64396352_6    754 ATTAAA-TTAAAGAGCTTCTGCCCAGCAAAAGAAACTATCTCAGA--GTG 708
                           i   -     i -   i  iv vv    i  v      -v   --   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC-AAGAAAGTG 693

C chrX_64396352_6    707 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCAATCTGA 658
                           v  i     i                 v       vii  vv      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

C chrX_64396352_6    657 CAAAGGTCTAATATCTGGAATTGATAAGGAACTTAAACAAATTTACAAGA 608
                         i  i  v  vi    ii    vv    i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

C chrX_64396352_6    607 AAAAAACCAAACAATCTCATTGAAAATTGGGTGAAGGATATGAACAGACA 558
                             i  -   i  i iv   ?    v    ii      v    i     
  L1M4_orf2#LINE/    794 AAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

C chrX_64396352_6    557 CTTCTCAAAAGAAGACATTTAGGTAGCCAACAAGCATATGAAAAAAAGCT 508
                         i     v        i  vi ii i     i     i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

C chrX_64396352_6    507 CATCATCACTGGTCAT 492
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.17 (14 / 12)  

 952 26.17 1.17 0.78  chrX_64396352_64402843     4683  4938 (1554)    L1M4_orf2#LINE/L1        1   257 (651)  

  chrX_64396352_6   4683 TGGAAAGGTATTCTCTGTTTGTGGATAGGAAGAATCCATATTTTTAAAAT 4732
                                i   i iv    ii     v      v iv     v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64396352_6   4733 GTCCATTTTACCCAAAGCAATCTATAGATTTAATGCAATCCCTATCCAAA 4782
                          v v  vi v      vii     i     i  i            v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64396352_6   4783 TACCATTGATAC--TTTTTACAGAAATAGAAAAAC-AATTCTAAATTTTA 4829
                          v   -- v i --     i       v  v  i -i  i     v  i 
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_64396352_6   4830 TGGGGAACCATAACAGACCCAGAATATCCAAAGCTATCCTGAGCAAAAAG 4879
                          iv    viii  vi           v     i v   i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_64396352_6   4880 AACAAAACTGGAGTAATCACATTACCTGATTCCATATTATACTACAGAAC 4929
                               ii     v v     i v  ii   i  v viv       i i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64396352_6   4930 TATAGTGAT 4938
                           i   i  
  L1M4_orf2#LINE/    249 TACAGTAAT 257

Transitions / transversions = 1.39 (39 / 28)
Gap_init rate = 0.01 (3 / 257), avg. gap size = 1.67 (5 / 3)  

2026 27.84 2.21 2.50  chrX_64396352_64402843     5321  5999 (493)    L1M4_orf2#LINE/L1      232   908 (0)  

  chrX_64396352_6   5321 AAAATGTACTA-ATACTTATAGTAACCAAAATA-CATGGTCCTGGCACAA 5368
                             iv     - v vi  i     i   i i -ii    v      i  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_64396352_6   5369 AAACACACAAATAGACCAGTGGAACAGAATAGAGAACTCAGAGATAAGTC 5418
                         ii i v   v     i  i     i     v    iii    i    ii 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_64396352_6   5419 TGTTCACCTGCAGTGGACTCATTTTTGACAAAGGTGCCAAGAACACACTT 5468
                         ii v  ii iii  vi i v     i     i          v  iv vv
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_64396352_6   5469 TGGGGAAAGGACTGTCTCTTCAGTAAGTGGTGTTAAGAAAACCAGATATC 5518
                                  i iv    i    ii  i     i ii  v   ii    ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_64396352_6   5519 CATATGCAGAAGAATGAAATTAGATCCCGGTCTCTCACCATATACAAAAG 5568
                           i     i         i  i  i   vii   v              i
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_64396352_6   5569 TCAAATCCAAACATATTAAAGACGCAAATATAAGACCTCAAATTGTGAAA 5618
                          i  v  v   iiv  i ?    vi    i     v  v   i i i   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_64396352_6   5619 CTACTAAAAGCAAACACTGGAGAAATTCATCAGGACATTGGACTGGGTGA 5668
                           vi  i   v     iv  ? v  v  v  iv   v    ii i  ii 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_64396352_6   5669 AGATTTCTTGAGTAATACACTATTAAGTGCTATTTATTGCACTGGCAACC 5718
                         v i      iii  vv    i --  i-----------    vi     v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCA--AAA-----------GCACAAGCAACA 618

  chrX_64396352_6   5719 AACACACAAATGGACAAATGTGA--TCA-CAAG---------TTTTGCAC 5756
                           viv v    i  i    vv  --   -   i---------     ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_64396352_6   5757 AGCAAAGAAAACAATCAACAAAATGCACAGACAACCTACAGAATTAGAGA 5806
                         vv     i v  v     v   i  v v        i       vi    
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_64396352_6   5807 AAATATTTGCAAACTATTCATATGACAATGGATTAGTAATCAGAATACAC 5856
                                      ii  vi  v   i  v   i v   vi       i i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_64396352_6   5857 AG-GAGCTAAAACACCTCTATAGGAAAGGAAAAATATAATAAGCAGATTT 5905
                          i-  i  vvv   v   v   iv   ---  i i -     v vi   ?
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAA---AAGACA-AATAACCCAATTW 814

  chrX_64396352_6   5906 TAAAATGGGTGAAAGTCCTGAATAGGCATTTCTCAAAAGAGGACATACAC 5955
                         v        ii  i vii       i        v     i  i     v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_64396352_6   5956 ATGGAAAACAGGTGTATGAAAAGGTGCTCAATATCATTGATCAT 5999
                             vv  i i iii        i       i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (116 / 69)
Gap_init rate = 0.01 (10 / 677), avg. gap size = 3.20 (32 / 10)  


4044 17.59 2.88 2.43  chrX_64415446_64417489.rev      650  1553 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64415446_6    650 TGAAATGACATACTGTGTTCATAAAATGGAAGAATTAATATTGTTAAGAT 699
                           i  v  i  v ii       ii v       v                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64415446_6    700 GGTAATAATACTCACCTAAAGTGATCTACAGATTCAATGGAATGTCTACC 749
                           i    ---   -  i   v                i v   vi   i 
  L1M4_orf2#LINE/     51 GGCAATA---CTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_64415446_6    750 AAATTTACAATGATGCCTTTT--GCAGATGTGGAAAAGCTAAACCTCAAG 797
                            v iv  -- v        --     vi v  v     i v   v  i
  L1M4_orf2#LINE/     97 AAAATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_64415446_6    798 TTCATATGGAATCACAAGGGTCCTCAAATAGCCACACACAAAAAAAATCT 847
                                    vii      v  ivi        -------   v     
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCA-------AAACAATCT 187

  chrX_64415446_6    848 TTAAAAAGTAAGAAAAAAGTTGGAGGACTCACACTTTCTGATTTCAAACT 897
                          v      -     v                     i ii        vi
  L1M4_orf2#LINE/    188 TGAAAAAG-AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_64415446_6    898 TTACTATAAAGCTACAATAATCATAACAGCGTGGTACCA-TATAAAACTA 946
                               i         i      vi    i       ii-i    iiv  
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_64415446_6    947 AGCATATAGACCAATGTAACAGAATTGGGAGTACAGAAATAAGTCCATAA 996
                         ii        i     v  i       i    v         ii     v
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_64415446_6    997 ACCTATAGTCAATTGATGTTTGACACAGGTGCCAAGACTATTCGA-AGAG 1045
                          ii   i          v  i    vi           i    i -i i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_64415446_6   1046 AAAAAATAATAGTTTTAACAAATACTGTTAGAACAACTAGATAAAAACAT 1095
                            i    i vv   i       iv  i i i      i    ?vv    
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_64415446_6   1096 G-----GAA--AAGTTTGACCCCTACTTCACACCATAAACAAAAATTAAC 1138
                          -----   --     v         i          v            
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_64415446_6   1139 TTAAA-TGGTTCAATGACCCATATAT--GAGTGAAAACCATAAAACTCTT 1185
                          i   -   v   ?v    i v  i --   iv     i           
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_64415446_6   1186 AGAAGAAAACA--GGGGTAAAATTTCACAACCTTGGATTTTGCAATGGAT 1233
                                    --  ?     vi   iii       i  vv       v 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_64415446_6   1234 TCTTAAATATGAAACCAAAAGAA-AAGCAACAACAAAAAAA-----TAAA 1277
                              i      v        v -         v i     -----    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_64415446_6   1278 TTAGACCTTACAAAAATTAAAACCTTTTGTACTTTAACGAACATGATCAA 1327
                           i   i i iv          v       i   i  v i   iv     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_64415446_6   1328 GAAAGTGAAAAGGCAACCCATAGAATGAGAGAAACCATTTGCAAATCATG 1377
                                     i       i      i      vi             i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_64415446_6   1378 T--CTGATAAGAGACTAGTATCCAGAATATATTTAAAAATGTTTAAAATT 1425
                          --        i    v               v-  i  ivi   v  i 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATA-AAGAACTCTTACAACT 785

  chrX_64415446_6   1426 CAACAACAAAAGGACAAACAGCCCGATTTTTTAAAAAAAATGGGGAAAGG 1475
                            i  i    i      i i   i   ?------         v     
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTW------AAAAATGGGCAAAGG 829

  chrX_64415446_6   1476 ATTTGAAATAGATATTTCTCTACA-AAGATATACAAA-GGCAAACAAGCA 1523
                                -    i       i v -            -   v  i     
  L1M4_orf2#LINE/    830 ATTTGAA-TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_64415446_6   1524 CATGAAAAGATGCTCAACATCATTAGTCAT 1553
                                               ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (96 / 59)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.29 (48 / 21)  


2718 27.54 1.11 0.77  chrX_64426619_64432553.rev     4541  5444 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_64426619_6   4541 GAAAAAACATTCTATGCTCATGAATAGAAAGAATCAATATCATGAAAATG 4590
                          i   i i  i i   i     i  v i    v i     ii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_64426619_6   4591 GCAATACTGCCCAAAGCATTTTATAGAGTCAATGCTATTCCCATTAAACT 4640
                                 v      viiv i  i   v    i  v  i  i  i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_64426619_6   4641 ACCATTGACATTCTTCACTGAATTAGAAACAACT-ATGTTAAAATTCATA 4689
                         v   vivi v  i  ii v   v v  v - i  -  vi           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATA 150

  chrX_64426619_6   4690 TGGAACCAAAATAGAGCCCAAAA-AAACAAGACAATCATAAGAAAAAAGA 4738
                              viiv  vi  -    i  - iv   i      v i i   i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_64426619_6   4739 ACAAAGCTGG-GGTCATCACACTACCCAACTTCAAACTATACTACAAGGC 4787
                               i   -  v -       v     i      viv        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64426619_6   4788 TACAGTAACCAAAACAGCATGGTACTGGTACAACAAT-GACACATAGATC 4836
                                 i   i    ii         i i  vi  -    i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_64426619_6   4837 AATGAAACAGAATAGAGAACCCAGAAATAAGACCACACACGTACAACCAT 4886
                             i  i     v    ii          iv   i   iv  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_64426619_6   4887 CTGATCTTTGACAAACCTGACAAAAAAAG-CAATGGGGAAAGGATTCCCT 4935
                         i    i  i     ivv  v   i vv v-            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_64426619_6   4936 ATACAAAAAATTGTTCTGGGAGAACTGGCTAGCCATATGCAGAAAATTGA 4985
                         v v   v    v  v      v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_64426619_6   4986 AACAGGACCCTCTCCTTACACCATATACAAAAATCAACTCAAGATGGAAT 5035
                          iiv      iiv   i                 i       i     vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_64426619_6   5036 AAATACTTAAATGTAAAATCCAAAAATATAAAAACCCTAGAAGAAAATCT 5085
                          ? v  i         i v i    v       vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_64426619_6   5086 GGGCA-ATACCATTCAGGATATAGACACAGGAAAATATTTCATGACAAAG 5134
                         i  ?i- v i -   iv  iv v ivvi   v  vvi    v iivv v 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_64426619_6   5135 ACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTAAT 5184
                                     vvv          v      v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_64426619_6   5185 TAAACTAAATAGCTCCTGCAGAGCAAAAGAAGCTATCACCAAAGTGAGCA 5234
                         i   v v  v i  ii  iivvv    i  vi      vv       iv 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_64426619_6   5235 GACAACCTACAGAGTGGGAGAAAAATTTTGCAACCTATTCACCTCACAAA 5284
                                i     i          vv       vii  vi i  v i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_64426619_6   5285 AGTCTAACATCTAGCATATACAAGGAACTTAAAAAATTTACAAGAATGGA 5334
                         i v  vii   i  v     i  i     ivv v  i --   v   ii 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--CAATAATAAA 795

  chrX_64426619_6   5335 A---CAAACAACCCCATTAAAAAATAGGCAAAGCACATGAGCAGACACTT 5381
                          ---    i     v   ?      i       v iv   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_64426619_6   5382 CTCAAAAGAAGGTGTATGTACGGCTAACAAACAT-TTAAAAAATACCTCA 5430
                            v       i i  iiv i   i  i  i  i- v    i  i -   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC-TCA 894

  chrX_64426619_6   5431 ATATCACAGATCAT 5444
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 1.21 (17 / 14)  

 613 24.23 0.52 3.09  chrX_64426619_64432553.rev     5741  5934 (1)    L1M4_orf2#LINE/L1      595   783 (125)  

  chrX_64426619_6   5741 ATGACAAAACCCGAAAAGCAATTGCAACAAAAGCCAGAATCGACAAATGG 5790
                               ----  -       vvv          vv i   v  i    v 
  L1M4_orf2#LINE/    595 ATGACA----CC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_64426619_6   5791 GATCTAATTAAACTAAAGAGTTTCTGCACAACCAAAGGA-ACTATCATCA 5839
                           ii v  i   v v  i ii  i  ii v-i       -       vv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGA 688

  chrX_64426619_6   5840 GAGTGAACAGACAACCTACAGAATGAGAGAAAATTTTTGCAATCTATCCA 5889
                         i      v        i        i        v       vii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_64426619_6   5890 TCTGGCAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAA 5934
                             ii  i  i  vi          v  i  i     ivv    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

Transitions / transversions = 1.24 (26 / 21)
Gap_init rate = 0.02 (4 / 189), avg. gap size = 1.75 (7 / 4)  


3057 24.26 5.01 1.71  chrX_64439898_64441852.rev      587  1464 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_64439898_6    587 GGAAAGATATTCCATAT-CATGGATTGGAAGA----ATATTGTGAAAATG 631
                                   i    i -              ----       v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_64439898_6    632 TCCATACTACATCAAGTAAGGTACAGATTCAATGCAATCCCTATCAAAGT 681
                         v v     v viv  v i vv           i               i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_64439898_6    682 ATCAATGACATTCTTCACAGAAATAAAAAAA--AATACTTTAAAAATGTA 729
                         vi  iivi v  i  ii       vi v  i--i  v  ---     vi 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT---AAAATTCA 148

  chrX_64439898_6    730 TATGGAGACACAAAGGACCCAGAATAGCCAAAGCTATCCTAAGCATACAG 779
                               i ii   i                  i v   i i iv viv  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_64439898_6    780 AATGAAACTGAAAGAATCACATTGCCTGACTTCAAAATATACTACAGAGC 829
                           ii  ii  i i  v     i v  ii i       iv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64439898_6    830 TATATTTAAAAAAACAGCATAATACTGCCACA-GAATCAGACACATAGAC 878
                           i v v vv  i    ii ii     v  i - i  -     i     i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGAT 297

  chrX_64439898_6    879 CAATGACACAGAATAGAGAAACCAGAAATAAAACTAGACATTT------- 921
                              iv i     v    iv           v i v      -------
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_64439898_6    922 ----------GACAAAGGTGTCAAGAACATATAATGGGGAAAGGACAATC 961
                         ----------     i    i     v   vi           i i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_64439898_6    962 TCTTCAATAAGAGGTACTGGGAAAACTGGATGTCCATATGCAGAAGAATG 1011
                          i     i  iv   i      v        i?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_64439898_6   1012 AAACTAGACTCTTATCTCTTGCTGCATACAAAAAGGAA---------GAT 1052
                           ii i   i i  i   vii iii         vv  ---------   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_64439898_6   1053 TAAAGACTTAAATATAAGACCTCAAACTATGAAACTATTAAAAGAGAACA 1102
                         i ?    i     i     v  v       i     v   i    i    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_64439898_6   1103 TTGAGGAAACTCTCCAAGACATTGGTCTGGGCAAAGATTTCTTGAGTAAT 1152
                          v i? v  v   i iv   v    vi i     v i      iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_64439898_6   1153 ACCCCATAAGCATAGGCAATAAAAGCAAAAATGGATGAATGGGGTTATTT 1202
                           v   v     i i    i     v      i   i   v  ii viv 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_64439898_6   1203 CAAG-TTAAAAA-------GCTTCCACACAGAAAAAAAAGAAAGAGTCAA 1244
                            i-       -------     -----------   i  v vvi    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTC-----------AAAGGACACTATCAA 686

  chrX_64439898_6   1245 CGAAGTGAAGAGACAACCCATAGAATGAGAGAAAATATTTGAAAAC--TT 1292
                         vi       i          i      i             v   i-- v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_64439898_6   1293 CATCTGACAAGGGATTAATAACCAGAATATATAAGGAGCTCAAACAATTC 1342
                         i      i      i vi  v             i  i   vv    i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_64439898_6   1343 AATAGAAAAAAATCTAAAAATATAATTAAAAATTAGGCAAAAGATTTGAA 1392
                             iv     iv v  v  ivi    ?    v i      i        
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_64439898_6   1393 TAGACATTTCTTAAAAGAAGACATACAAATGCCAAACAGACATATGAAAA 1442
                                    iv        i         v v  i ii  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_64439898_6   1443 TGTGCTTGACATTATTGAAGAT 1464
                         vi    ii    i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (131 / 78)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 4.92 (59 / 12)  


 866 23.08 2.43 3.64  chrX_64474575_64477027.rev      566   812 (1641)    L1M4_orf2#LINE/L1        1   244 (664)  

  chrX_64474575_6    566 TGAAAAGACATCCCATATTTTTGGATTGAAAGAATTAATATTGTTAAATG 615
                           i     i       i  iv       i    v             i--
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-- 48

  chrX_64474575_6    616 TTAAAATGTCCATACTACCCAAAGTGAGCTATAGAGTAAACGTAATCTCT 665
                         -----   v v     v      v   v   i   v v    i    i  
  L1M4_orf2#LINE/     49 -----ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chrX_64474575_6    666 ATCAAAATCC--ATTGACATTCTTTACAGAAATGGAATACACT--CCATA 711
                                   --ii  v -  i   i       v  -i vi  --i v  
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGA-CAAGCTGATCCTA 141

  chrX_64474575_6    712 AA--TCATATGAAACCATAAAAGACCCTGAATAGCCAAAGAAATTTTGGG 759
                           --       i  viii  ii     v           iv   i   ii
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_64474575_6    760 CAAGAGGAACTACGATGGAGGTATCACACATCTTGATTTAAAAATATATT 809
                         v    i    v v v      vv      v  iii    v    iv  i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_64474575_6    810 ACA 812
                            
  L1M4_orf2#LINE/    242 ACA 244

Transitions / transversions = 1.28 (32 / 25)
Gap_init rate = 0.02 (6 / 244), avg. gap size = 2.50 (15 / 6)  

2164 22.39 1.53 6.29  chrX_64474575_64477027.rev     1303  1954 (499)    L1M4_orf2#LINE/L1      243   863 (45)  

  chrX_64474575_6   1303 CAAAGGTATGGTAATCAAAACAGTATGGTACAAGCATAAAAACAAACATA 1352
                              v  ii        i     i      vi      ii i i     
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_64474575_6   1353 --GGCCAAAATAACAGAATTGAAAACAGAGAAATAAATCCACATCATTAC 1400
                         -- ii   viv  i        i iivv         i   i ivv   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_64474575_6   1401 AGTCAATTGATTTTCTACAAAAATGCCAAGAATGCACAATGGGGAAA-AA 1449
                         i              v    iii        viiiv           -  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_64474575_6   1450 CAGTCTCTTCAATAAACAGTTATGGGAAAACTGAATATCCACATGCAGAA 1499
                         i     i     i   ii  vv     v     i   ?         i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_64474575_6   1500 TAATGAAGTTGGACTATTATCTCATAC--TATACAAAAACCAACTCAAAT 1547
                         v             ivi  i    i  --          ii        v
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_64474575_6   1548 TGGATTAAAGACTTAAACATAAGATACAAAACTGCTGAATTTATAGAAGA 1597
                              i ?    i    ii     vvi      iivi  i iv       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_64474575_6   1598 AAACA--GGA--AAAACATCTTGAC-TTGGTCTGGGCAACGATTTTTTGG 1642
                              --  ?--   v v  v    -    vi i     i i   i  i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_64474575_6   1643 GTATGATCCCAGAGGCACAGGCAACAAAACCAAAAGTAGACAAATGGGAT 1692
                         i     iv   i i     i         vv    i    i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_64474575_6   1693 TACGACAAACAAACAAAAACAAACAAACAAACAAACAAAAAAAACAAAAA 1742
                          v -------- v     vi   ---------------------------
  L1M4_orf2#LINE/    643 TTC--------ATCAAAATTAAA--------------------------- 657

  chrX_64474575_6   1743 AAACAACTTCTGTACAGTAAAGGGAACAATCAACAGAGTGAAAAGGCAAC 1792
                         ----     i   i vvi     iv  v     v i         i    
  L1M4_orf2#LINE/    658 ----AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_64474575_6   1793 CTAAAGAAAAGGAGAAAAATATTTGGAAAACATATATCTAATAAAGGATT 1842
                          i v    vi        -      v   v         i    i   i 
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_64474575_6   1843 AACATCCAAAATATATTGAGAACACTTGCAACTCAATAACAATGAAAATA 1892
                         vii     i       vi     v   i           i  -i  i i 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AAAGACA 801

  chrX_64474575_6   1893 AATAACTCAATTTAAAAATGAATAAAGGACCTAAATAGACACTTCTCCAG 1942
                               i     ?       iii      ii i        i       i
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_64474575_6   1943 ATAACACATATA 1954
                          v  v i   i 
  L1M4_orf2#LINE/    852 AGAAGATATACA 863

Transitions / transversions = 2.09 (96 / 46)
Gap_init rate = 0.02 (10 / 621), avg. gap size = 5.10 (51 / 10)  


 666 26.21 4.84 1.21  chrX_64617856_64624135.rev      284   531 (5749)    L1M4_orf2#LINE/L1      461   717 (191)  

  chrX_64617856_6    284 ACTCCACCTCAAAAACAACAAC-AACAGAGAA-GTATCA---ACCAAAAT 328
                           ii   vi  v v    v  i-   vv i  - v    ---   v    
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_64617856_6    329 ATAAGACCTAAAACTGTAAAACTCTCAAAAAAAAAAAAAAGTGAAAATCT 378
                         i     v        i         i i  i    v v i ? v      
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_64617856_6    379 TCATAATCTAGTATTTGACAATGGATCCTTGGAAAGGAAACCAAAAGTA- 427
                           i i i  v vi  v i      v i   i  v v  v        i -
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_64617856_6    428 --ACAAAAGAAAAAAAAATAGGTAAATTGGATTTCATGAAAATTTAAGAC 475
                         --i   v i  i         i         i     v      v  i  
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_64617856_6    476 TTTTATGTATCAAAAAACATCATGGAGGAGGAGGAGCCAAGATGGCC--- 522
                             i  iv     ii   ii  vi  i i v i ---    iii  ---
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA---AAGACAACCCAC 707

  chrX_64617856_6    523 -GAATAGGAG 531
                         -    i    
  L1M4_orf2#LINE/    708 AGAATGGGAG 717

Transitions / transversions = 1.56 (39 / 25)
Gap_init rate = 0.02 (6 / 257), avg. gap size = 2.50 (15 / 6)  

3245 27.64 0.22 0.22  chrX_64617856_64624135.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64617856_6   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64617856_6   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64617856_6   4982 TACCAATGACTTTCTTCACAGAATTGGAAAAAACCACTTTAAAGTTCATA 5031
                          v   iivi i  i  ii     v v  v  iviv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_64617856_6   5032 TGGAACCAAAAAAGAGCCCACATCACCAAAGCAATCCTAAGCCAAAAGAA 5081
                              viiv  ii  v  viv  vi     i     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_64617856_6   5082 CAAAGCTAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5131
                              i i    vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_64617856_6   5132 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5181
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_64617856_6   5182 TGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5229
                              i    i-- v  i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_64617856_6   5230 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGGTTCCCT 5279
                         i    i  i     ivv  v   i v  vv            ii vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_64617856_6   5280 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5329
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_64617856_6   5330 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5379
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_64617856_6   5380 AAAGACTTAAACGTTAGACCTAAAACCACAAAAACCCTAGAAGAAAACTT 5429
                          ?    i    i  v   v       i i    vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_64617856_6   5430 AGGCATTACCATTCAGGACATAGGCATGGGCATGGACTTCATGTCTAAAA 5479
                            ?i v viv   iv   v v  vv i    vv ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_64617856_6   5480 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5529
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_64617856_6   5530 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5579
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_64617856_6   5580 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 5629
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_64617856_6   5630 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5679
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_64617856_6   5680 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5729
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_64617856_6   5730 AAAAGAGGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5779
                         v     i  i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_64617856_6   5780 CACTGGCCAT 5789
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


2792 27.35 0.60 0.72  chrX_64664415_64666744      620  1449 (881)    L1M4_orf2#LINE/L1        1   829 (79)  

  chrX_64664415_6    620 TGAAAAAATATCCCATGCTCATGGATTGGAAGAAGCAATATCATTAAAAT 669
                           i   i          i               vvi     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64664415_6    670 AGCCATACTGCCCAAAGCAATTTACAGATTCAACGTTATTCCCATCAAAC 719
                         i  v     v      vii  i             iv  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64664415_6    720 TACCAA-TGTCATTCTTTACAGAATTAGAAAAAACTG-TTCTAAAATTCA 767
                          v   i-  i -  i   i     v v - v  i   - i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCA 148

  chrX_64664415_6    768 CATGGAACCAAAAAGGAGCCCAAATAGCCAAAACAATCTTAAGCAAAAAG 817
                         i      viiv  i   v  vi                  i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_64664415_6    818 AACAAAGCTTGAGGCATCACACTACACAACATCAAACTATACTATAAAGC 867
                                i v    vv       v v   iv     viv     i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64664415_6    868 TATCAAGACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACC 917
                           ivivi i   i    ii         i i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_64664415_6    918 AATGGAACAGAATATATAGAAAACTCAGAAATCAGGCCTCATACTTATAA 967
                                i     --- -  i iii       v iv  vi i i    ii
  L1M4_orf2#LINE/    299 AATGGAATAGAAT---T-GAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_64664415_6    968 CCATCTGATCTTTGACGAGGTCGACAAAAACAAACAATAGG-AAAGAACT 1016
                         i  vi    i  i   i   vi v   i v  vv    i  -      iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_64664415_6   1017 CCCTATGTAATAAAAGGTGCTGAGATACTTGGCTAGCCATATGCAGAAGA 1066
                         vi  v vi  i   v       i  i vi   v  ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_64664415_6   1067 ATGAAACTAGACCCTTACCTTTCACCATTTACAGAAATTAACTCAATATG 1116
                              ii i     i     iv      v    i            v   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_64664415_6   1117 GATTAAGTATTTAAATTTAAGATCTCAAACTATAAAAATCACAGAATAAA 1166
                            i ?iv ii     v     v  v           v  vi    v   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_64664415_6   1167 ACCTAGGAAACACACTTCTTGACATAGGCCTTGGTGAAAAATTTTTGTCT 1216
                           v    ?ivv vv    v    v v  vi v  ii viiv  i  ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_64664415_6   1217 ACGTCTCAAAAAGAATTA-CAACAAAAGCAAAAATTGGCAAGTGAGACCT 1265
                          i v v v     v iv -         v      v ii  i vi   i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_64664415_6   1266 AATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTATCAACAGAGTAA 1315
                         v  i   v v  i ii  i  ii vv    i  v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_64664415_6   1316 ACAGACAACCTACAGAATGAG-GAAGACATTTGTAAACTATTCAACTGAC 1364
                          v        i        i -   i i     i   ii  vi v    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_64664415_6   1365 AAGGGCTTAACATCTAGAATCTATAGGGCACTTAAACAAATCAATAATCT 1414
                              vi vii   i     v    ii v   ivv    v        vv
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_64664415_6   1415 AAAAATAAATAACCCTATTAAAAAATGAGCAAAGG 1449
                            i i         v   ?       i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.37 (129 / 94)
Gap_init rate = 0.01 (9 / 829), avg. gap size = 1.22 (11 / 9)  

 409 18.56 0.00 3.09  chrX_64664415_64666744     1741  1837 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_64664415_6   1741 AAAAATGAGCAAAGGACGTGAACAGACACTTCTCAGAAAAAGACATACAA 1790
                                i        iv    i     i     vi  i    i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_64664415_6   1791 GTGGCCAACAAATATATGAAAAAAAAATGCCTATCATCACTCACCAT 1837
                         i       i  ii i       i ---   ii v     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGA---TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 5.00 (15 / 3)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 3.00 (3 / 1)  


2778 26.45 0.59 1.65  chrX_64756057_64757899      504  1350 (493)    L1M4_orf2#LINE/L1       71   908 (0)  

  chrX_64756057_6    504 TCTATATATTTGATGCAATTCTCATCAAAATACCATCATCATTCTTCACA 553
                             i v   ii i     i ii        v   v vv v  i  ii  
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chrX_64756057_6    554 GAACTAGAAAAAACAATCCTAAAATTCATATGGATTTTAAAAAGAGCCCA 603
                            v v  v  ivii                   vv vv  ii  v  vi
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chrX_64756057_6    604 CATAGACAAATCAAGATTAAGCAAAAAGAACAAATCTGGAGGCATAACAT 653
                         v    v    v   vv  i iv  i         vi      vv v   i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_64756057_6    654 TACCTGATTTCAAACTATATCACAAGGCTATAGTTACCAAAACAGCATGG 703
                          v  ii        viv  ii    i    i   v i   i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_64756057_6    704 TACTTGTATAAAAATGGGTACATAGACCAATGGAATAGAATAGAGAACCC 753
                             v i    ii  i ii i     i              v    ii  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_64756057_6    754 AGAAATAAAGCCAAATACTTATAGTCAAGTGATCTTTGACAAAG-CACAC 802
                                  v   v i i    i     v    i  i     i -ii - 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC-C 369

  chrX_64756057_6    803 AAAAACATAAAGTGGGGAAATGACATACTATTCAACAAATGGTGTTGGGA 852
                           i v   vv i        vi i vv  v              i     
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_64756057_6    853 TAATTGGCAAGCCATATGTAGAAGAATGAAACTTGATCCTCATCTTTTAC 902
                         i  i   vv ?   i   i i         ii v  i  ii i  ivi  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_64756057_6    903 CTTATACAAAAATAAACTCAAGATGGATCAAAGACTTAAATCTAAGACTT 952
                          v           v       i        ?    i     v     vi 
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_64756057_6    953 GAAACCATCAAAATACTAGAAGATAACACCGGAAAAACTCTTTTAGACAT 1002
                         i    i  v   v vi       v    iv  ?iv  v    ivv   v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_64756057_6   1003 TGACTTAGGCAAAGACTTCAT-GACCAAGGAC-CCAAAAGCAAATGCAAC 1050
                           iv        v ii   v -  i-- v   -         v v     
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGAT--ATGACACCAAAAGCACAAGCAAC 617

  chrX_64756057_6   1051 AAAAACAGAGATAAATTGATGGCATTCAATTGAACT--AAAAGTCTTCTG 1098
                             iv i i   i  vi  v v i iv  ii  v --    v i  v  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_64756057_6   1099 CTCAGCAAAAGAAATAGTCAGCAGAGTATACACACAACCCACCAAGTAGG 1148
                           i--    i  v ivi   iv i   iv v v         vi i i  
  L1M4_orf2#LINE/    668 CTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_64756057_6   1149 AGAAAATCTTCACAAACTATGGATCCGACAAAGGAGTAATATCCAGAATC 1198
                                v  ii    ii  iv   i  i  i   v vi          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_64756057_6   1199 TACAAGGAACTCAAACAAATCATCGAAAAAGAAACAAATAATCCCATCAA 1248
                           i  i      vv    v   vii v   i i        i  v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_64756057_6   1249 AAATTGGGCAAAGGATATGAATAGACAGTTCTCAAAAGAAGATATACAAA 1298
                            v            v          v     v                
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_64756057_6   1299 TGGCCAACAAACATATAAAAACATATAAAAAATGTTCAACATCACTATCA 1348
                                i  i  i  i    ---------i   i         ??????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAA---------GATGCTCAACATCAZZZZZZ 906

  chrX_64756057_6   1349 GG 1350
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.29 (124 / 96)
Gap_init rate = 0.01 (8 / 838), avg. gap size = 2.38 (19 / 8)  


2754 26.68 1.95 3.47  chrX_64762525_64768640.rev     4704  5625 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64762525_6   4704 TGGAAAGATATTCCAGGCTCATGAATAGGAAGA------GTTGTGAAAAT 4747
                                    i   v i     i  v      ------i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64762525_6   4748 GGCCATATTGTCCAAAGTAATTTATAGATTCAATGCTGTCCCCATCAAGC 4797
                            v   i vi     v i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64762525_6   4798 CACCA-CTGACTTTCTTCACAGAATTAGAAATACT-ACTTTAAATTTCAT 4845
                         iv   -   v    i  -i     v v  v vi  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_64762525_6   4846 ATGGACCAAA---AAAGTGCCCACA-TAGCCAAGACAATCCTAAGCAAAA 4891
                              ---  ---  i vi    v -       i      i i iv  i 
  L1M4_orf2#LINE/    150 ATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_64762525_6   4892 AGAACAAAGCTGGAGGCAC-CATGCTACCTGACTTCAAACTATACTACAA 4940
                                  i      -  -  ii  v  ii i      viv        
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_64762525_6   4941 GCCTACAGTAACCAAAACAGCATGGTACTAGTACCAATACAGATATATAG 4990
                         iv         i   i    ii       i i iv iv i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_64762525_6   4991 ACCAATGAAACAGAACAGAGGCTTTAGAAATAATGCCACACATCTACAAC 5040
                          i     i  i    iv   iv ii        vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_64762525_6   5041 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGG-AAAGGGTTC 5089
                           vi    i  i     ivv  v   i v  vv       -    ii vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_64762525_6   5090 TCTATTTAGTAAATGGTATTGGGAAAACTGGCTAGCCATATACAGAAAAC 5139
                            v  i ii       ii     v      v  ?   i  i  i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_64762525_6   5140 TGAAACTGGACCCCTTCCTTACACCTTGCATAAAAATTAATTCAAGATGG 5189
                             ii         v   i     v ii i         i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_64762525_6   5190 ATTAAAGATGTAAAAATAAGACCTAAAACCATAAAAACCCCAGAAAAAAG 5239
                           i ?   iv    vi     v       i      vi ii    i   i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_64762525_6   5240 CCTAGGCAATACCTTTCAGGACATAGGAATGGACAAAGACTTCATGACTA 5289
                          v    ?ivv vii   iv   v v  iv i i   v ii   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_64762525_6   5290 AAACACAAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGAGATCTA 5339
                         vi    v       vvi          vv    iv  i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_64762525_6   5340 ATTGAACTAAAGAGCTTCTGCACAGCAAAAAAAAAAAAATTAAAAAAAAA 5389
                           ii  v v  i i   i  ii ----------------  v   ii v 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGC----------------TTCAAAGGACA 679

  chrX_64762525_6   5390 AAAAAAAAAACTACCATCAGAGTGAACTGGCAACCTACAGAATGGAAGAA 5439
                         ----------   i  vv i      vv i     i         i    
  L1M4_orf2#LINE/    680 ----------CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_64762525_6   5440 AATTTTTGCAATCTATCCATGTGACAAAGGGCTAATATCCAGAATCAACA 5489
                            v       vii  vi  v   i  i  i  vi          vv i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_64762525_6   5490 AAGAACT--TA-AACTTA-CAAGAAAAAAATCATACAACCTCATCAAAAA 5535
                                --  -    i -i  v     i -  v i    iv  i?    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAA 818

  chrX_64762525_6   5536 GTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTGTGCAG 5585
                         i            v    i     i     v        i  viiviii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_64762525_6   5586 CCAAGAAACATATGAAAAAAGGCTCATCATCACTGGTCAT 5625
                             v  i  i       i v     v     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (150 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.12 (50 / 16)  


3928 18.86 5.12 0.47  chrX_64769361_64773991.rev     3282  4140 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_64769361_6   3282 ATTCTATGTCCATGGATTGGAAGACTAAATATTCTTAAGATGGCAATACT 3331
                           i i    i                v      v                
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_64769361_6   3332 ATTCAAATTGAGCTAGAAATTCAAAACAATTCCTAACAGAACCCCAGCTA 3381
                         vii        v   v i      vi    i    v  i  i       i
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_64769361_6   3382 AGTTATTTGTAGAAATTGACAAGCTGATCCTAAAATTCATATGTAAATTC 3431
                         vv  v    i                                 v    v 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_64769361_6   3432 AAAGAGATCAAAATAGTCAAAACAATTTTTAAAAAGAAGAGCAATAATGG 3481
                           i iivi  i     i         i  v          i   viv   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_64769361_6   3482 AATACTAGCACTCCTCAATGTCGAATTTTACTATGCAGGTACTGCAGTCA 3531
                          iv   vi    i i    v  i  vi      iiv  v   v i i   
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_64769361_6   3532 GTGCAGTGTGCTACCTGCATAAGGACAGACATATAAA------------- 3568
                         ivi       v   iv         i         i -------------
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_64769361_6   3569 ATTTTTAGTTCTGAAATAAACCTTCATATTTACAGTCAAT-GATTTTCAA 3617
                            vvv   i v          ivi i     ii      -       i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_64769361_6   3618 CAAAAATGCCAAG-----------GGGAAAAAATAATCTTT--AAAAAAC 3654
                            iii       -----------      i    i     --  v   i
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_64769361_6   3655 AGTGCTAGGATAATTGGATAAACACACATAAAA-AATAGAGTTGAACCCC 3703
                         i     i   i  i      ?v    iii    -   ii     i     
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_64769361_6   3704 CTACTTCACACCATATATAACAATTAACTCAAAATTGGTCAAAGACCTAA 3753
                         -   i            i  v              v i   ?        
  L1M4_orf2#LINE/    460 -TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_64769361_6   3754 ATGTAAGAGCTGAAACTATAACACTCATAGAATAAAATATTAGGAGTAAA 3803
                                    i         v    v     v    i  -   ?     
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AGGNGTAAA 557

  chrX_64769361_6   3804 TCTTTGTAACCTTCTATGAAACAATGATTTCTTAGATATGACACTAAAGG 3853
                             i  i     vvi v ii     i                 i   i 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_64769361_6   3854 CAAAAG-AACAAAATAAAAAATAGGTAAACTGGACATCATCAAAGTTAAA 3902
                           v   -       v         i    i     v        i     
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_64769361_6   3903 ATCTTT-GTGCTTCAAACGATGCTATCAAGAAAGTAGAAAGGCAACCCAT 3951
                          v    -          v  ii             ii    i       i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_64769361_6   3952 AGAATGGAAAAATACATTTGTAAAACATACATCTAATAAGGGACTTAAAT 4001
                                i i  v i     i   v    i    i           iv  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_64769361_6   4002 CTAAAATATATAAAGAAAATTTTAACA--TCAACAATAAAAA-----ACA 4044
                          i i             --i i v   --    i        ----- i 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAA--CTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_64769361_6   4045 ACATAATT-------AGGTAAAGGATCTATATAGACATTTCTCCAAAGAA 4087
                           vi    -------i  i       i iv                    
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_64769361_6   4088 GATATTTAAATGGCCAATAAACATATGAAAAGTTTCCCAACATTATTTTT 4137
                              vi             i  i        v v i      i ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_64769361_6   4138 TAT 4140
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.89 (104 / 55)
Gap_init rate = 0.01 (13 / 899), avg. gap size = 3.69 (48 / 13)  


2397 13.31 2.85 26.86  chrX_64779006_64784109      492  1686 (3418)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_64779006_6   1686 TGAGAAGACATCTTGTGTTCATGGATTGGAAAACTTCATATTGCTGAGAT 1637
                           ii    i   iii                i    v      i i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_64779006_6   1636 GCCAATACTACACAAAGTGACCTAGGATTTCAAAGTAATCCCAATCAAAT 1587
                          v       v v    v   i   viiv     v i      v      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_64779006_6   1586 TTTCAAAGGCGCTTGTTGCAGAAATGAAAAAGCTGATC-TAAAATTCAGG 1538
                          ii  ivv  vi  v          vi v         -         vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chrX_64779006_6   1537 TAGAATTGCAAGGGACCCTGTATAGCCAAAACAATTTAGAGAAAGAAAAA 1488
                          i   v            v v              i v  i      i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chrX_64779006_6   1487 CAAAATTAGAAGACTCACACTTCCCTATTTCAAAACTTACTACAGAGCCA 1438
                             i  i  i              v                  i   i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chrX_64779006_6   1437 CAATAATTAAAATATTCTCATACTAGCATATGGATGGACATATAGATTAA 1388
                           i    i  i i v v vi    i     v    i           i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

C chrX_64779006_6   1387 TGGGATAGAATAGAGATTCCAGAAATAAATACTTACATATGTGGTTCATT 1338
                            i       v    v            iv v     v i    iv   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

C chrX_64779006_6   1337 GATTTTTTATTTTTATTTATTTATTTATTTTTGAGACAGAGTCTTGCCCT 1288
                               i---------------------------    ------------
  L1M4_orf2#LINE/    351 GATTTTC---------------------------GACA------------ 361

C chrX_64779006_6   1287 GTCACCCAGGCTGGAGTATACTGACCTGATCTCAGCTCAGTGCAACCTCC 1238
                         -------   -----------------------------    -------
  L1M4_orf2#LINE/    362 -------AGG-----------------------------GTGC------- 368

C chrX_64779006_6   1237 GCCTCCCAGATTCAAGCTATTCTCCTGCCTCAGCCTCCAGAGCAGCTGAG 1188
                         ------------    ----------------------------------
  L1M4_orf2#LINE/    369 ------------CAAG---------------------------------- 372

C chrX_64779006_6   1187 ATTACAGGCACCTGCCACCACACCCAGCTAATTTTTATATTTTTAGTAGA 1138
                         ----------------    ---------------------  i -----
  L1M4_orf2#LINE/    373 ----------------ACCA---------------------TTCA----- 380

C chrX_64779006_6   1137 GATGGGGTTTTACCATGTTGGTCAGACTGGTCTTGAACTCCTGACCTCAC 1088
                         -      -------------------------------------------
  L1M4_orf2#LINE/    381 -ATGGGG------------------------------------------- 386

C chrX_64779006_6   1087 GTGATCCACCTGCCTCGGCCTTCCAAAGTGCTGGTATTACAGGCATGAGC 1038
                         ------------------------    ----------------------
  L1M4_orf2#LINE/    387 ------------------------AAAG---------------------- 390

C chrX_64779006_6   1037 CACTGCTTCCAGCTGGTCCACTGATGTTTAATAAGGATGTCAAAATCCTT 988
                         -----------------------------    -----   -------  
  L1M4_orf2#LINE/    391 -----------------------------AATA-----GTC-------TT 399

C chrX_64779006_6    987 CAGTATGGAAAAAATATTCAACAAAGAATGCTAGAAAAACTGAATATCTA 938
                         ----------------         vii    i i v     i   ? i 
  L1M4_orf2#LINE/    400 ----------------TTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

C chrX_64779006_6    937 CATGCAAAAAAA----GT-GGACATTCTACCTCACACCATATGCAAAAAT 893
                                  i  ----  -    -ii                i       
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGAC-CCCTACCTCACACCATATACAAAAAT 482

C chrX_64779006_6    892 TAACTCAAAATGAA----AGACCTAAGTGTAAGAGGGAAAAGTATAAAAC 847
                                     i ----        i        vv    v        
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

C chrX_64779006_6    846 TCTTAGAA-AAAATAT-GTAGTGAGTCTTCAAGACCTTGGATTTGGCAAG 799
                                 -    i  - v?  i i     iv        i  v     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

C chrX_64779006_6    798 GAAGTCTTAGGTATG-CGCCAAATGCACAAGAAACAAAA----AAATAGA 754
                          ivv      i    - i     v       v       ----       
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

C chrX_64779006_6    753 TAAATTAG----TGTCAAAATTAAAAATTTTTGTGCATCAAAGGTCACTA 708
                               i ----ii             i        v       v     
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

C chrX_64779006_6    707 CAAAGGAAGTAAAAACACCATCCACAGAATGGGAGAAAATACCTGCAAAT 658
                         iv   i    i    v  v i                    ii       
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

C chrX_64779006_6    657 CACATGCCTGATAAGGTTCTAGTACCCAGAA-----------CTGTTACA 619
                           i  ii         vv  v   i      -----------  v     
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

C chrX_64779006_6    618 ACTCAACAACCAAGTGACATTTGACCAAATTAAAACATAA--AAAGGATT 571
                               i  iv  iv    vv i   v    ?   v  ii--        
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

C chrX_64779006_6    570 AGAATAGACATTTTTCCAAAGAAGAAGACGTGCAAATGATCAGCCAGCAT 521
                         v            i           ---ii i      ii  iiv    i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGA---TATACAAATGGCCAATAAGCAC 879

C chrX_64779006_6    520 ATGAAAATATTTTCAACATCATTAGCTAT 492
                                v  vi         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (92 / 64)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 14.20 (355 / 25)  

3065 26.85 1.55 1.22  chrX_64779006_64784109     3707  4611 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64779006_6   3707 TGGAAGAACATCTCATGCTCCTGGATAGGAAGAATCAATATCGTGAAAAT 3756
                              ii i   i    i  v     v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64779006_6   3757 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3806
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64779006_6   3807 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGCTCATA 3851
                          v   iivi i  i  ii     v v  v  i--- --     ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_64779006_6   3852 TGGAACCAAAAAAGAGCCTGCATTTCCAAGACAATCCTAAGCAAAAAGAA 3901
                              viiv  ii  v  v v  vv    i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_64779006_6   3902 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAAGTATACTACAAGTCTA 3951
                              i      vv    i  v  ii i      iiv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_64779006_6   3952 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 4001
                               i   i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_64779006_6   4002 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCAACAACTATCT 4051
                              i    iv   ivii         vv   i    iv iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_64779006_6   4052 GATCTTTGACAAACCTGACAAAAACAAGAAAGAAGAAAAGGGGAAAGGAT 4101
                            i  i     ivv  v   i v  vvv  v-------        i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAAT-------GGGGAAAGAAT 393

  chrX_64779006_6   4102 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAA 4151
                         vvi  v  i  i              v      v  ?       i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_64779006_6   4152 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAACATTAATTCAAGAT 4201
                         iv    ii    i    v   i     v        v     i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_64779006_6   4202 GGATTGAAGACTTAAATGTTATACCTAAAACCATAAAAACCCTAGAAGAA 4251
                             ii?    i       v v v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_64779006_6   4252 AACCTAGGC--AATTCCATTCAGGACATAGGCATGGGCAAGGACTTCATG 4299
                            v    ?--  v  --   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_64779006_6   4300 ACTAAAACACAAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATAGGA 4349
                         iv  vi    v       vvi          vv        i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_64779006_6   4350 TCTAATTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACTATCAGAG 4399
                         ii v  i   v v  i i   i  iiivv    i  v    ii vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_64779006_6   4400 TGAACAGGCAATCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCT 4449
                             v  i   i i                 v   i   vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_64779006_6   4450 GACAAAGGGCTAATATCCAGAATCTACAAAAA---CTTAAGCAAATTTGC 4496
                           i  i  i  vi          v  i   i ---    --   v ivii
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAAT 789

  chrX_64779006_6   4497 AAGAAAAA---AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAG 4543
                           v     ---   i     v  i?    i            v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_64779006_6   4544 ACACCTCTC-AAATAAGACATTTACACAGCCAACAGGCACATGTAAAAAT 4592
                            ii    -   v    i  vi v ii     i i       v   i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_64779006_6   4593 GCTCATCGTCATTGGTCAT 4611
                              v i   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.78 (25 / 9)  


 370 30.95 3.17 0.00  chrX_64812797_64821131     6627  6752 (1583)    L1M4_orf2#LINE/L1        2   131 (777)  

  chrX_64812797_6   6627 GGAAAAACATTCCATGCTTATGGACAGGAGAAATCAGTATCATTAAAATG 6676
                              i i  i     i i     iv   ii v i i   ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_64812797_6   6677 GCCATACTGCCCAAAGCAATGTACAGAGTCAATACTAT----ATCAAACT 6722
                           v     v      vii  v      v    ii v  ----      v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_64812797_6   6723 ACCAATGACATTTTTCACCAAACTAGAAAA 6752
                         v   iivi v     ii vi  v v  v  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

Transitions / transversions = 1.44 (23 / 16)
Gap_init rate = 0.01 (1 / 130), avg. gap size = 4.00 (4 / 1)  

2372 27.89 1.16 1.03  chrX_64812797_64821131     7071  7848 (487)    L1M4_orf2#LINE/L1      130   908 (0)  

  chrX_64812797_6   7071 AAACT-ATTTTAAGATTCATATGGAACCAAAAAAGATCCCAAATAGCCAA 7119
                           i  -  ii   i            viiv  ii  i  vi         
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_64812797_6   7120 GGCAATTCTAAGCAAAAAGAACAAAGCTGGAGGCATCACATCACCAAACT 7169
                         ii    ii i iv  i          i      vv     iiv  v  i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_64812797_6   7170 TCAAACTATACTACAGGGCTACAACAACCAAAATAGCATGGTACTCATAG 7219
                              viv       ii      ii  i   i i  ii       vii v
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_64812797_6   7220 AAAAACAGACACATAGACCAATTAAACAGATTAGAGAGCCCAGAAATAAG 7269
                           ii i     i     i    vi  i   v v     i          i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_64812797_6   7270 GACACACACCTACAACCATCTGAACTTTGACAAAGCTGACAAAAGCA--- 7316
                         vv  i   ii  iiii  vi   vi  i     i v  v   i v  ---
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_64812797_6   7317 -ACAGGAAAAGGACTCCCTATTCAATAAATGGTGCTGAGATAACTGGCTA 7365
                         - ii  i    i ivvi  v     i           i  i      v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_64812797_6   7366 GCACTATGCAGAAGATTGAAACTGGACCTCATCCTTATACAATATATAAA 7415
                         ? vvi     i    v    ii      i vv   i i  v     i   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_64812797_6   7416 AATCAACTCTAGATGGATTGAAGACTTAAATGTAAATCCCAGAACTATAA 7465
                            i     v i      ii?    i         ivv i i        
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_64812797_6   7466 AAACCCTGGAAGACAACGTAGGCA-ATACCATTCTGGACATAAGAACTAG 7514
                           vi i i     v   i    ?i- v i -   vv   v vi ivivi 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGG 578

  chrX_64812797_6   7515 CAAAGAGTTCATG---ATGAATCCACCAAAAGCAACTGCAACAAAAGCAA 7561
                            v iv   v i---    ---           vvv          v  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGA---CACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_64812797_6   7562 AAATTGACAGATGGGAAATAATTAAACTAAAGAGCTTTTGCACAGCAACA 7611
                             v  i i  v   vv v  i   v v  i i      ii vv   vi
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_64812797_6   7612 GAAACTATCAACAGAGTAAACAGACAACCTACAGAACAGGAGAAAATATT 7661
                           v        v i   i  v        i      ii            
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_64812797_6   7662 TGCAAACTATGCAACATACAAAGGTCTAACATCCAGCATCTATAAGAAAC 7711
                               ii  ii v vv i  i  v  vii      v  v     ii   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_64812797_6   7712 TTTAACAAATTTCCAAGAAAAAAACAAACAAACAACCCTATTAAAAAGTG 7761
                          i v    v ---   v  v    - i     i     v   ?    i  
  L1M4_orf2#LINE/    776 TCTTACAACT---CAATAATAAAA-AGACAAATAACCCAATTWAAAAATG 821

  chrX_64812797_6   7762 GGCAGAGAACATTAATAGACATTTATCAAAAGAAGACATACATGTGGCCA 7811
                             i  i iv v           v  v        i     vi      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_64812797_6   7812 ACATGCATATGAAATAAAGCTCAATATTCCTGATGAC 7848
                          i v   i      vi v      i  iv????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (128 / 85)
Gap_init rate = 0.01 (8 / 779), avg. gap size = 2.12 (17 / 8)  


2899 27.03 1.78 0.78  chrX_64853813_64860153.rev     4952  5850 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64853813_6   4952 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5001
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64853813_6   5002 GGCCATACTGCCCAAGGTAATTTATAAATTCAATGCCATCCCCATCGAGC 5051
                            v     v     iv i  i  i i      i  v     i   i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64853813_6   5052 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGCTCA 5099
                          v   iivi i  i  ii     -   -- v  i  - ii     ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_64853813_6   5100 TATGGAACCCAAAAACAGCCTGCATTGACAAGACAATCCTAAGCAAAAAG 5149
                                vivv  iiv v  v v  v v   i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_64853813_6   5150 AACAAAGC-GGAGGCATCACACTATCTGACTTCAAACTAAACTACAAGCC 5198
                                i-     vv       vi ii i      vivv       iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64853813_6   5199 TACTGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGATATAAAGACC 5248
                            v    i   ii   ii         i iv ii i   i   v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_64853813_6   5249 AATGGAACAGAAC--ACAGCCCTCAGAAATAATACCACACATCTACAACC 5296
                                i    i-- v  i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_64853813_6   5297 ATCTGATCTTTGACAAACCTGATGAAAACAAGAAATGGGGAAAGGATTCC 5346
                          vi    i  i     ivv  vii i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_64853813_6   5347 CTATTGAATAAGTGGTGCTGGGAAAACTGGTTAGCCATATGTAGAAAGCT 5396
                           v  v  i  i           v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_64853813_6   5397 GAAACTGGATTCCTTCCTTACACCTTATACAAAAATTAATTCACGATGGA 5446
                            ii    ii   v   i     v              i   vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_64853813_6   5447 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 5495
                          i ?    i       v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_64853813_6   5496 CCTAGGCA-ATACCATTCAGGATATAGGCATGGGCAAGGACTTCATGACT 5544
                          v    ?i- v i -   iv  iv v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_64853813_6   5545 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 5594
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_64853813_6   5595 AATTAAACTAAAGAGCTTCGGCACAGCAAAAGAAACTTCCATCTGAGTGA 5644
                         v  i   v v  i i   iv ii vv    i  v   vi  vvvi     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_64853813_6   5645 ATAGGCAACCTACAGAATGGGAGAAAATTTTTAC---CCAT----CTGAC 5687
                          v  i     i                 v   i ---i   ----    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_64853813_6   5688 AAAGGGCTAACATCCAGAATCTACAAAGAACTTAAACAAATTTA-AAGAA 5736
                           i  i  vii         v  i        ivv    v iv -  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_64853813_6   5737 AAAAATCAAAACACCCCATC-AGAAGTGGGCAAAGGGTATGAACAGACAC 5785
                            i -    vv    v  i- i  i          i v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_64853813_6   5786 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5835
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_64853813_6   5836 ACCATCACTGGCCAT 5850
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.53 (23 / 15)  


4326 17.55 2.81 0.67  chrX_64869497_64871824      947  1835 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64869497_6    947 TGGAAAGACATTTTAAGCTCATGGATTGGAAGACTTTAATATTATCGAGA 996
                                 i  iii v i                  -      i ii   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTT-AATATTGTTAAGA 49

  chrX_64869497_6    997 CGTCAATACT--ATAAAATGATCTATAGTATCGATGCAATCATGGTCAAT 1044
                         i v       --vi   v       i  vv  i i      vivi    v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_64869497_6   1045 ATCTCAATGATGTTTTTTGCAGAAATAGGAAAGTCTATGTGAAAATTTAT 1094
                            i  iiviiv              v iv   iiv  viv      i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_64869497_6   1095 ATGAAATCTCAAGGAATTGCAAATAACCAAAACAATCTTTAAAAAGAACA 1144
                            i  viv     i iivvi    i             v        v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_64869497_6   1145 GCAAAATTGGAGGACTCACACTTCCTGGTTTCAAAACTTACTGCAAAGAT 1194
                         i    i                   iii              i     v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_64869497_6   1195 ACAATAATCAA-ACAATGTGGTTCTGGTATACGGATAGGCATATATATCA 1243
                            i       -   i      v    i   v      i      v    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_64869497_6   1244 GTGGACTACAACTAAGAATCCAGAAATAAACCCATATATCT----TCAAT 1289
                         i    v  v  i i   i                  i  i ----     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_64869497_6   1290 ACTGATTTTTGATAAGACTGTCAAAAC-ATGTTAATGGGCAA-GCATAGT 1337
                         --       i  i   iv  i   i  -  - i      v  - v     
  L1M4_orf2#LINE/    350 --TGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGT 396

  chrX_64869497_6   1338 CTTTTAAACAAATGGTGCCGAGGCAACAACATAGCCACATACAAAAGAAT 1387
                              v            i i i    viv   ?      i         
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_64869497_6   1388 AAATTTGGGGCCCTACCTCAAACCACATACAAAAATTAACTCAAAATAGA 1437
                         i  v    iv          v    i                     i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_64869497_6   1438 TCAAAGAACTAAATGTAAAAGCTAAAACTATGAAACTCTTAAAAGAAAAT 1487
                            ?   v          i            i         i       i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_64869497_6   1488 ACACGGGTAAATCTTAATGA-ATTGGGTTTGGCAATAGATTCTTAGATAT 1536
                          i v ?         vi   -v       v      i v           
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_64869497_6   1537 GACGCAAAAAGCACAAGATTAA-AAAGGAAAAAA-AGATAAGTTGAATTC 1584
                            i v           --i  -   i       -      i   i i i
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAG--CAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_64869497_6   1585 AATTAAAATTAAAAACCTTTGTGCCTCAAAGGATACTATCAAGAAAGTGA 1634
                         v  i            i       i        i                
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_64869497_6   1635 AAAGACAACCTA-AGAGTGGGAGATAATATTTGCAAATAATAAATCTGAT 1683
                                   i -   i       v             v   v       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_64869497_6   1684 AAGGGTCACGTATTTAGAATATATAAAGAACTCTTATAATTCAA------ 1727
                              v vi    ii                     i  i    ------
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_64869497_6   1728 -----CACACAACCCAATT-AAAAATGGGCAAGTAACTTGAATAGAAATT 1771
                         -----  v i         -            ivi i         v   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_64869497_6   1772 TCTCCAATGATGACATACAAGTGGTCAATGAACACATGAAAAGATGCTAA 1821
                                v  v  i      i   i    i i                v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_64869497_6   1822 ACATCACTAATCAT 1835
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (97 / 56)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.07 (31 / 15)  


3291 26.00 1.00 0.55  chrX_64878439_64880583.rev      751  1654 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64878439_6    751 TGGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 800
                              ii i  ii    i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64878439_6    801 GGCCATACTACCCAAAGTAATTTACAGATTCAATGCCATCCCCATCAAGC 850
                            v     v      v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64878439_6    851 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 898
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_64878439_6    899 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 948
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_64878439_6    949 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 998
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64878439_6    999 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1048
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_64878439_6   1049 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAACT 1096
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_64878439_6   1097 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 1146
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_64878439_6   1147 CTATTGAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1196
                           v  v  i       i      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_64878439_6   1197 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1246
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_64878439_6   1247 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAAAAGAAAAC 1296
                          i ?    i       v   v       i      vi i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_64878439_6   1297 CTAGGCATTACTATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1346
                         v    ?i v v v   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_64878439_6   1347 AACACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGACCTAA 1396
                         i            vvi          vv   i v  i    v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_64878439_6   1397 TTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1445
                          i   -     i -   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_64878439_6   1446 TAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 1495
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_64878439_6   1496 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTCACAAGAAA 1545
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_64878439_6   1546 AAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 1591
                           i    ----   v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_64878439_6   1592 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 1641
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_64878439_6   1642 CATCACTGGCCAT 1654
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2845 27.65 1.78 0.56  chrX_64917681_64921083.rev     2016  2912 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64917681_6   2016 TGGAAACACATCCCATGCTCATAGATGGGTAGAATCAATATTGTGAAAAT 2065
                               v i        i    i   v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64917681_6   2066 GACCATACTGCCAAAAGTAATTTATAAACATAATGCAATTTCCATCAAAA 2115
                          i v     v  v   v i  i  i i ivi  i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64917681_6   2116 TTCCATCATCATTTTTCACAGAACTATAAGAAAC-AATTCTAAAATTTAT 2164
                          i   v vv v     ii     v - i v  i -i  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_64917681_6   2165 TTGGAACTAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGA 2214
                         v     v iv  ii  v  viv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_64917681_6   2215 GCAA-GTATGGAGGCATCACATTACCCAAATTCAAACTATACTACAAGGT 2263
                         i   -  -      vv     i v     v      viv        i i
  L1M4_orf2#LINE/    200 ACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_64917681_6   2264 TATAGTCACCAAAAAAGCATAGTACTGGCACAAAAATAGGCACATAGACC 2313
                           i   v i   i v  ii i         i  ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_64917681_6   2314 AATGGAACAGAATAGAGAACCCAAAA---------TAC--TTACAGCCAA 2352
                                i     v    ii   i  ---------   --   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_64917681_6   2353 TTGATCTTCAACAACACAAACAGAAACATAAAGTGAGGAAAGGATGCCCT 2402
                              i   i    vivviv  ii v   vv i  i      i  ivi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_64917681_6   2403 ATTTAACAAATGGTGCTGAGATAACTGGCAAGCCACATGTAGAAGAACGA 2452
                         v  i              i  i      vv ?       i i     i  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_64917681_6   2453 AACTGGATCCTCATATTTCACCTTATACAAAA-TCAACTCAAGAGGGATC 2501
                          ii    i  ii iv iv    v         - i       i v     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_64917681_6   2502 AAAGACCTAAATCTAAGACCAGAAGCCATAAAAATTCTAGAAGATAATAT 2551
                          ?          v     v vi  i i      v ii       v  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_64917681_6   2552 TTAAAAAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCATGACCA 2601
                         -- ii?iv   i -   vv   v    v        v ii   v iivi 
  L1M4_orf2#LINE/    549 --AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_64917681_6   2602 GGAACCCAAAAGTAAATGCAACAAAAACAAAGATAAATAGATGGAACTTA 2651
                         v  vv       i v v         iv   i   i   i  v i    v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_64917681_6   2652 ATTAAACTAAAATACTCCTACACAGCAAAAGAAATAATCAGCAGATTAAA 2701
                           i   v v   v   ii iii vv    i  v iv    iv i v i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_64917681_6   2702 GAGACAACACACCAAGTGGGGGAAAATCTTTGCAAACTATGCATCCAACA 2751
                         i       v   vi i    i      v        ii  ii   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_64917681_6   2752 AAAGAGTAATATCTAGATTCTACAAGGAACACAAACAAGTCAGCAAGAAA 2801
                          ii  v vi    i   v v  i  i    v vv    v   ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_64917681_6   2802 AAAA--AACAATCCCATCAAAAAGTGGGCTAAGGGCATGAATAGACAATT 2849
                           i --  i  i  v  i?    i     v    iiv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_64917681_6   2850 CTCAAAAGAAGGTATACAAATGGCCAACAAATATATGAAAAAATGTTCAA 2899
                            v       i               i  ii i       i   i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_64917681_6   2900 CATCACTAATTAT 2912
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


2753 27.09 1.52 2.72  chrX_64945277_64949888.rev     3203  4121 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_64945277_6   3203 TAGAAAAATACTCTGTGTTCATAAATAAGAGAAATCAGTATTGTTAAAAT 3252
                          i    i   ii ii       ii  vi  ii v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_64945277_6   3253 GGTCATACTTCCCAAAGCAATTCAAATGTTTAATGCTGTTCCTATCAAAC 3302
                           iv     i      vii  ii v vi  i  i  vi i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_64945277_6   3303 TACCAATTACATTCTTCACATAATTAGAAAAA--------AAAATTTAAA 3344
                          v   ii i v  i  ii  v  v v  v  i--------      i --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA-- 148

  chrX_64945277_6   3345 TGTATGTAAA-GCCAAAAAAGAGCCTGAATAGCCAAAACAATCCTAAGAA 3393
                         --    v   -  ---  ii  v  v                 i i i  
  L1M4_orf2#LINE/    149 --TATGGAAATGC---AAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_64945277_6   3394 AATAGAACAAAGCTGGAGGCAC-CACATTACCTGACTTCAATCTATATTA 3442
                          iv         i      -  -    i v  ii i     vviv  i  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_64945277_6   3443 CAAAACTACAGTAGTTAAAACAGCATGGTATTGGTACAAAAATAGACACA 3492
                             i        i i  i    ii     i   i i  ii       i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_64945277_6   3493 TAGACCAATGGAACAGCATAGAGCGCCCAGAAATAAAGCTGCACTTCTCT 3542
                             i        i  v  v   v i           v iii  v i v 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_64945277_6   3543 AACCATCTGATCTTTGACAAAGTGGACAAAAAGAAGCAATGGGGAAAGGA 3592
                         iii  vi    i  i     i vv v   i vv vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_64945277_6   3593 CTCCCTATTCAATAAATGGTGCAGTGATAACTGGCTAGCTATATGAAGAA 3642
                         ivvi  v     i         v v  i      v  ? i i   v i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_64945277_6   3643 TATTAAAACTGGACCTCTTCCTTATATCATATACACAAATCAGCTCAAGA 3692
                         v v i  ii      i  v   i i i        v    i i     i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_64945277_6   3693 TAGATTAAAGACTTAAATATAAAACCTAAAGGTATAAATGCCCTGAAAGA 3742
                          i   i ?    i     i   i v     iv      vvi i ii    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_64945277_6   3743 TAACCTAGGAGATACTACTTCA-GACATAGGACTTGGCAACGATTTTGT- 3790
                         v   v    ? vv v -    i-   v v  ii v     i i   iv -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_64945277_6   3791 GATGAAGACACCAAAAGCAATTGCAAAAAAATAAAAATAAAAATAAAATA 3840
                            - v             vvv    v    v     ----------   
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAA----------ATA 630

  chrX_64945277_6   3841 AATAAATGAGACATAATTAAACT--AAAGTTTTTCTGCACAGCAAAAGAA 3888
                         i      vi   v v  i   v --   ii    v   vi--    i  v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGAC 678

  chrX_64945277_6   3889 CCTATCAACAGAATAAACAGACAACCTACAGAATGGGAGAAAATATTTTC 3938
                         v       v i i i  v        i                     v 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_64945277_6   3939 AAACCATGAATTGAAAAAGGGTCTAATATCCATAATCTATAAGGAAATTA 3988
                            i   iv  ivi v     v  vi      v   v     i   v iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_64945277_6   3989 AACAAATTAACAAGCAAAAACCAAACAACTCCATTAAAAAGCAAGCAAAA 4038
                         v    v i  i  vv    iv    i   i v   ?    iiii     i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_64945277_6   4039 GACTTGAACAGGGAGTTTTCAAAAAAAAAGACATACGTGCGGCTAACAGG 4088
                           i     i  iv v  i  v   i  --  i    ivii   i  i i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAA--GATATACAAATGGCCAATAAG 876

  chrX_64945277_6   4089 CATATGGAAAAAATGCTCAACATCACTAATCAT 4121
                           i   -    i             ????????
  L1M4_orf2#LINE/    877 CACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (149 / 96)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.60 (39 / 15)  


2789 26.85 4.21 0.91  chrX_65091107_65095647.rev     3172  4050 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65091107_6   3172 TGGAAACACATCCCATGTGCATGAATGGATAGAATCAATATCATGAAAAT 3221
                               v i         v    i  v iv   v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65091107_6   3222 GACCACGCTGCCAAAAGCAGTCTACAAATTCAATGCAATTCCCCTCAATA 3271
                          i v ii  v  v   viii      i      i     i  iv    v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65091107_6   3272 TACCA-CCATCATTCTT-----------CAAAC-AATTCTAAAATTCATA 3308
                          v   - iii v  i  -----------   i -i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_65091107_6   3309 TGGAAA-----------CAAAATAGAGCCAAAGCAAGACTAAGCAAAAAG 3347
                               -----------  i     --     i   vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAG--CCAAAACAATCTTGAAAAAGAAG 198

  chrX_65091107_6   3348 AACAAATCTGAAGGCATTACATTACCTGATTTTAAACTATACTATAGGGC 3397
                               vi  i   vv i   i v  ii    i   viv     i ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65091107_6   3398 TATAGACACCAAAACAGTATGGTACTGGCATAAAAATAGGCACATAGCCC 3447
                           i  vv i   i     i              ii    i  i    vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_65091107_6   3448 AACAAAACAGAACAGAGAACTCAGAAATAAACCCAAA----TACAGCCAG 3493
                           iii  i    iv    iii              v ----  ii i  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_65091107_6   3494 CTGGTCTTTGACAAAGCAAACAAAAATATAAAGTGGGGAAAGGACACCCT 3543
                         i  i i  i     i vviv   i vi  vv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_65091107_6   3544 TTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAAGATAATGA 3593
                                              i  i   v  ?       i  i v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_65091107_6   3594 AACTGAGTCCTCTTCTCTAACTTTATACTC---TTTCAACTCAAGATGGA 3640
                          ii  iii  iivi   vv  iv     vv---  --       i     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATT--AACTCAAAATGGA 496

  chrX_65091107_6   3641 TTTAGGACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGATAAC 3690
                          iv?i   i     v     v  i           v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_65091107_6   3691 ATTGGAAAAAACCTTATAAACATTGGCTTAGGCAAGGATTTTATGACCAA 3740
                           v  ?iv   i   vvvi  v    v        v i   iv iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_65091107_6   3741 GAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAACTAGGACTTTA 3790
                           vv         v v    i    iv   i   i    v v      i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_65091107_6   3791 TTAAACTAAAGTGCTTTTGTGTGGCAAAAGGAGCAGTCAGCAGAGTACAC 3840
                          i   v v  ivi        ivv    i ivi vi   iv i   iv v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_65091107_6   3841 AGACAACCCACAGAGTGGGAG----TCTTCACAATCTATACATCTGACAA 3886
                                       i      ---- v  ii   vii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_65091107_6   3887 AGTACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGCAAGAAAA 3936
                         i v   vi          v  i  v      vv    v   ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_65091107_6   3937 AACAAACAAATAATACCA--TCAAAAATGGGTTAAGGACATAAATAGAAA 3984
                          i---        i-   -- ?         iv     iv i      v 
  L1M4_orf2#LINE/    797 AG---ACAAATAAC-CCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_65091107_6   3985 ATTCTCAAAAGAAGATATACAAATAGCCAACAAACATATGAAAAAATGCT 4034
                         v     v                 i     i  i  i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_65091107_6   4035 CAAAATCACTAATAAT 4050
                            v    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (140 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.75 (45 / 12)  


2611 28.10 2.43 1.99  chrX_65096677_65099636     1564  2467 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65096677_6   1564 TGGAAAAACATTTCATCCTCATGTATAGGAAGAATCAATATCATGAAAAT 1613
                               i i  ii   vi     v  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65096677_6   1614 GACCATACTGCCCAAAGTAATTTGTAGATTCAGTGCTATTCCCATCAAAC 1663
                          i v     v      v i  i ii       ii  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65096677_6   1664 TACCATTAACATTGTTCACAGAATTAGAAAAAAAAAATACTTTAAGTTTC 1713
                          v   vivi v  v  ii     v v  v  ivvi ---iii   iv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA---TCCTAAAATTC 147

  chrX_65096677_6   1714 ATGTGGAATTAAAGAAGACCATGTATAGCCAAGACAATCTTAAGCAAAAA 1763
                           i     v iv iii    vv v        i        i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_65096677_6   1764 GAACAAAGCTGGAGGTATCATGCTACCTGACTTCAAACTATACTCCAAGG 1813
                                 i      vv   ii  v  ii i      viv    v   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_65096677_6   1814 CTACGGTAAACAAAACAGCATGGCACTGGTACCAAAACAGACATATAGGC 1863
                             i    v   i    ii   i     i iv ii i          ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_65096677_6   1864 CAATTGAACAGAACAAAGACCTCAGAAATAACACTACACATCTACA-CCA 1912
                             v   i    ivi   vii         vv i i    i  ii-i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_65096677_6   1913 TCTGATTTTCTACAAACCTGGCAAAAACAAGCAATGGGGAAAGGATCTCC 1962
                         vi        v    ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_65096677_6   1963 TATTCAATAAATGGTGCTGGGAAAACTGGTTAGCCACATTCAGAAAATGG 2012
                          v     i              v      v  ?      v  i  i vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_65096677_6   2013 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 2062
                           ii    i    v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_65096677_6   2063 TAAATACTTAAA--------------CCACAAAAACCCTAGAAGAAAACC 2098
                         i ? v  i    -------------- i i    vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_65096677_6   2099 TAGGCAATAGCTTTCAGGACATAGGCATGGACAAAGACTTCAT-GATGAA 2147
                             ?ivv iii   iv   v v  vv i i   v ii   v -   - v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chrX_65096677_6   2148 AATGCCAAAAGCAATTTCAACAAAAGTCAAAATTGACAAATGGGATCTAA 2197
                         i ii         vvvv         vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_65096677_6   2198 CTAAACTAAAGAGCTTCTGCACAGCAAAAGAGTGAACAGGCAACCTACAT 2247
                         ii   v v  i i   i  ii vv    i  ---------  --   -- 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGA---------CA--CTA--T 683

  chrX_65096677_6   2248 CATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAAGTTTTTCAATCT 2297
                           vv i      v  i     i                vv   v   vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_65096677_6   2298 ACCCATCTGACAAAGGTCTAATATCCAGAATTTACAAGACACTTAAACAA 2347
                          ivi      i  i  v  vi          v  i  iiv   ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_65096677_6   2348 ATGTACAACAAAAAAA------ACCCCATCAAAAAGTGGGCAAAGGATAT 2391
                         v vv i  i     i ------    v  i?    i            v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_65096677_6   2392 GAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAAATATATGG 2441
                            i     i     v        i  vi viii     i  ii i   -
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG- 882

  chrX_65096677_6   2442 AAAAAAAACTCAAAATCACTGATATT 2467
                             i vi     v    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (142 / 108)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 4.00 (40 / 10)  


3374 25.27 0.44 0.66  chrX_65105407_65111802.rev     4996  5905 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65105407_6   4996 TGGAAGAACATTCCATGGTCATGGATAGGAAGAATCAATATCATGAAAAT 5045
                              ii i  i     v        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65105407_6   5046 GGCCATACTGCCCAAAATAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65105407_6   5096 TACCAA-TGACTTTCTTCAACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 5142
                          v   i-  v    i  --i     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--GCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_65105407_6   5143 CATATGGAACCAAAAAGGAGCCCGCATTGCCAAGACAATCCTAAGCCAAA 5192
                                  viiv  i   v  v v  v     i      i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_65105407_6   5193 AGAACAAAGCTGGAGGCATCACACTACCCTGACTTCAAACTATACTAAAA 5242
                                  i      vv       v   -i i      viv     v  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCC-AATTTCAAAACTTACTACAA 245

  chrX_65105407_6   5243 GGCTACAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 5292
                         i          v   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_65105407_6   5293 ATCAATGGAACAAAACAGAGGCCTCAGAAATAACGCCACACATCTACAAC 5342
                                   i i  iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_65105407_6   5343 CATCTGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5392
                           vi    i  i i   ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_65105407_6   5393 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5442
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_65105407_6   5443 TGAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAACTCAAGATGG 5492
                             ii    i    v   i     v     v             i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_65105407_6   5493 ATTAAAGACTTAAATGTTAGCCCTAAAACCATAAAAACCCTAGAAGAAAA 5542
                           i ?    i       v  vv       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_65105407_6   5543 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5591
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_65105407_6   5592 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 5641
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_65105407_6   5642 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5691
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_65105407_6   5692 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5741
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_65105407_6   5742 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 5791
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_65105407_6   5792 AAATTCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5841
                            vv    i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_65105407_6   5842 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5891
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_65105407_6   5892 TCATCACTGATCAT 5905
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (129 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


 659 25.89 3.12 3.12  chrX_65122530_65131040.rev     5311  5534 (2977)    L1M4_orf2#LINE/L1        1   224 (684)  

  chrX_65122530_6   5311 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5360
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65122530_6   5361 GGCCATAATTCCCAAAGTAATTTGTAGAT-CAATGCTATTCCCATTAAGC 5409
                            v   v i      v i  i ii    -   i  v  i  i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65122530_6   5410 TAC--ATTGACTTTCCCTGCAGAATTAGGAAAAAAAAAACTACTAC-AAA 5456
                          v --ii  v    ii-       v v ------ v  i  iv v -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTG------ACAAGCTGATCCTAAA 143

  chrX_65122530_6   5457 ATTAATATGGAAC--CAAAAAAGTTTGTATAGCCAAAACCATCCTAAGCA 5504
                            v        v--   iii viiv v           v   i i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_65122530_6   5505 A-AAGAACAAAGCTGGAGGCATCACACTGCC 5534
                          -          i      vv       v  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCC 224

Transitions / transversions = 1.32 (33 / 25)
Gap_init rate = 0.03 (7 / 224), avg. gap size = 2.00 (14 / 7)  

3000 26.34 2.12 0.78  chrX_65122530_65131040.rev     7125  8020 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65122530_6   7125 TGGAAACACATCCCATGCTCATAGATGAGTAGAATCAATATTGTGAAAAT 7174
                               v i        i    i   vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65122530_6   7175 GACCATACTGCCAAAAGCAGTCTACAAATTTAATGCAATTCCCATCAAAA 7224
                          i v     v  v   viii      i   i  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65122530_6   7225 TACCGTCATCATTCTTCATGGAACTAGAAAAAA-AATCCTAAAACTCATA 7273
                          v  iv vv v  i  iiii   v v  v  iv-i         i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_65122530_6   7274 TGGAACCAAAAAAGAGCCTGTGTAGCCAAAGAAAGACTAAGCAAAAAGAA 7323
                              viiv  ii  v  v vi        iv  vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_65122530_6   7324 CAAATCTGGAGGCATCACATTAGCCAACTTCAAACTTTACTGGAAGGCCA 7373
                             vi      vv     i vv    i      vi     iv  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_65122530_6   7374 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCAA 7423
                         i   v i   i    ii         i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_65122530_6   7424 TGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTCACAACCAACT 7473
                              i     v    ii           v   v i i i iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_65122530_6   7474 CAGCTTTGACAAAGCAAACAAAAACATAAAGTGGGGATAGGACACCCTGT 7523
                         v vi  i     i vviv   i v   vv i      v  i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_65122530_6   7524 TCAACAAATGGTACTCAGATAATTGGCAAGCCACATGTAGGAGAATGAAA 7573
                                     i  vi  i  i   vv ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_65122530_6   7574 CTTGATCCTCATCTCTGAACTTTTACAAAAATCAACTCAAGATTGATCAA 7623
                         i v  i  ii i   vv v v v         i       i  v     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_65122530_6   7624 AGACTTAAATCTAAGACCTAAAACCATAAGGATTCTAGAAGATAACATTG 7673
                             i     v     v       i    iiv ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_65122530_6   7674 GAAAAACTCTTCTAGACATTAGCTTAGGCAAAGATTTC------ATGACC 7717
                          ?iv  v     vv   v  i v        v i    ------     -
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC- 599

  chrX_65122530_6   7718 AAAGAGCCAAAAGCAAATGCAACAAAAACGAAGATAAATAGATGGGAATT 7767
                         -----i         v v         ivi  i   i   i  v   v  
  L1M4_orf2#LINE/    600 -----ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_65122530_6   7768 AATTAAA-TTAAAAATCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTT 7816
                         v  i   -       -   i  ii vv    i  v iv    iv i   v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_65122530_6   7817 AAGAGACAACTCACAGAGTGGGAGAAAAT---TACAATCTATACATCCAA 7863
                           i       i      i           --- i   vii   i   ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_65122530_6   7864 CAAAGGAGTAATATCCATAATCTACAAAGAACTCAAACAAGTCAGCAAGA 7913
                         i  i   v vi      v   v  i         vv    v   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_65122530_6   7914 AAAAAACAAACAATCCCACTAAAAAGTGGGCTAAGGATATGAATAGACAA 7963
                             i     i  i  v i ?    i     v      v          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_65122530_6   7964 TACTCAAAAGAAGATATATAAATTGCC--------TATGAAAAGATGCTC 8005
                          v   v            i    v   --------i              
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_65122530_6   8006 CACATCACTAATGAT 8020
                         v      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (132 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.71 (26 / 7)  


3206 27.31 0.44 0.44  chrX_65183813_65190091.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65183813_6   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65183813_6   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65183813_6   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_65183813_6   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_65183813_6   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACGATACTACAAGGC 5128
                                i      vv       v  ii i      vvv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65183813_6   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_65183813_6   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_65183813_6   5227 ATCTTATCTTTGACAAACCTGAGAAAAACAAGCAATGGGAAAAGGATTCC 5276
                          vi v  i  i     ivv  vv  i v  vv       i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_65183813_6   5277 CTATTTAATAAATGGTGCTGTGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i           v  v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_65183813_6   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_65183813_6   5377 TTAAAGATTTAAACTTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    iv v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_65183813_6   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_65183813_6   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_65183813_6   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_65183813_6   5577 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_65183813_6   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_65183813_6   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_65183813_6   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_65183813_6   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2512 26.41 4.38 2.42  chrX_65214457_65216369.rev      556  1422 (491)    L1M4_orf2#LINE/L1       25   908 (0)  

  chrX_65214457_6    556 ATCAAAAGAATTAATATCATTAAAATGACCATATTGTCCAAAGCAATCTG 605
                           iii    v       ii    i   i v   i vi     vii    i
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chrX_65214457_6    606 CAGAATCAATGCAATTCCTCTCAAAATATCAA-TGTCATTCTTCACAAAA 654
                             v    i     i   v       vi  i-  i -  i  ii  i  
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAA 123

  chrX_65214457_6    655 CTTTTTAAA--AATTTGAAAATTTATATGACACCAAAAAAGAGCCCAAAT 702
                         v  vvi  i--i  iiv      i     iv viiv  ii  v  vi   
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chrX_65214457_6    703 AGCCAAAGCAGTCCTGAGCCATAAACAAATAAATAAATAAATAAACCACT 752
                                i  i  i   -----   vi  ---------i  i   --ii 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGA-----AAAAGAA---------GAACAAA--GTT 207

  chrX_65214457_6    753 GGAGGCATTACATTACCTGACTTCAAAATATATTAAAAGGCTATGGTAAT 802
                              vv i   i v  ii i       iv  i  v  i    ii     
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_65214457_6    803 CAAAACAGCATGGTA------TAAAAATAGACAAATAGACCAATGAAACA 846
                            i    ii     ------   ii       v     i     i  i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_65214457_6    847 GAATAGAAAATCCAAAAATATTGCCACATATTTACAGTCAACAACTGATC 896
                             v  i i    i     vvv   i i     ii     i---    i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT---TGATT 354

  chrX_65214457_6    897 TTTGACAAAACTGACAAAAACTTACATTGGAGAAAGAACATCCTCTTTAA 946
                           i     iiv  v   i v v v  v   i       i vi  i  i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_65214457_6    947 TAAATAGTGCTGAGAAAACTGCACAGCCACATGCAGAAGAATAAAACTGG 996
                         i    i      i  v     v i ?         i      i  ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_65214457_6    997 ACCTATATCTCTCACCATATACAAAA-TTATCTCACGATGGAT------- 1038
                            iv  i   v              -   v    vi      -------
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_65214457_6   1039 ----ATGTGA-------AGCTATAAAAATACTAGAAGAAAAC-TGGAGGG 1076
                         ----    i ------- i        v vi           - i i? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_65214457_6   1077 AAACTCTCCTGAACATTGGTTGAGGCAAAGAATT------TATGACCTCA 1120
                            iii  v   v -    v v      v iv  ------      vi  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_65214457_6   1121 AAAATACAGTTAATAAAACCAAAAATAGGCACACGGGACTATATTTAACT 1170
                            ii   ivi  i    vv        ii v iv     vi  iv  v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_65214457_6   1171 AAATAGCTATTGCACAGCAAAGGAAATAATCAACAGAGTGAAAAGACAAC 1220
                         v  v i  v   ii vv       v iv     v i              
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_65214457_6   1221 CTGCTGAATGGGAAAAAAAAATTACAAAGTATTCATTTGACAGGAGACTA 1270
                          ii v        i    v v  i    vi  vi  i   i i i    v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_65214457_6   1271 ATA-CTAGAATAC-CAAGAAACTCAAGCAAGTTAAGAGGAAAAAAAAAAA 1318
                         i  - i      i-i  ii     vvi   v i  v iv     i v   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_65214457_6   1319 AAACACA-TTAAAAAGTGGGTAAAGGACATGAATAGACATTTCTCAAAAT 1367
                         v   v  -  ?    i    i      iv                v   v
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_65214457_6   1368 AAGACATACAAATGGCCAACAGGTATATGAAAAAATGCTCAACATTACTA 1417
                             i              i i i i       i           i ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_65214457_6   1418 ATTAT 1422
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.72 (143 / 83)
Gap_init rate = 0.02 (17 / 884), avg. gap size = 3.47 (59 / 17)  


1147 28.00 1.71 0.00  chrX_65228665_65232150     1821  2170 (1316)  C L1M4_orf2#LINE/L1   (482)   426    71  

C chrX_65228665_6   2170 TTTACA--TTCAATGCAATTTCCATCAAAATACCAACATTATTCTTCATA 2123
                          i    --     i     ii i        v   i vviv  i  iii 
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

C chrX_65228665_6   2122 GAACTAGAAAAAA-AATCCTAAAATTCATATGGAACCAAAAAAGATCCCA 2074
                            v v  v  iv-i                    viiv  ii  i  vi
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

C chrX_65228665_6   2073 CATAGCCAAAGCAAGGTGAAGCAAAAAGAAGAAATCTGGAGGAATCACAT 2024
                         v         i   vv vi iv  i     v   vi       v     i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

C chrX_65228665_6   2023 TACCCAACTTTAAACTATACTATAAGGCCATAGTCACCAAAACAGCATGG 1974
                          v     i  i   viv     i  i  i i   v i   i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

C chrX_65228665_6   1973 TACTAGTATAAAAAAAGGCACATAGAGCAATGGAACAGAATAGAGAA-CC 1925
                             i i    ii v  i  i     v        i     v    i-  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

C chrX_65228665_6   1924 AGAAATAAAGCCAAATGTTTACAGTCAACTAATCTTCAACAAAGCAAACA 1875
                                  v   v ii    ii     i i  i   i    i vviv  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

C chrX_65228665_6   1874 AAAACATAAAGTGTAGAAAGAATACCCTATTCAACAGAAGGTGCTGGGT- 1826
                          i v   vv i  vi         vi  v       i v         v-
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

C chrX_65228665_6   1825 -ACTGG 1821
                         -     
  L1M4_orf2#LINE/    421 AACTGG 426

Transitions / transversions = 1.51 (59 / 39)
Gap_init rate = 0.01 (4 / 356), avg. gap size = 1.50 (6 / 4)  

1280 25.17 2.47 0.90  chrX_65228665_65232150     2549  2993 (493)    L1M4_orf2#LINE/L1      457   908 (0)  

  chrX_65228665_6   2549 CCATATCGCTCACCTTATATAAAAATCAACTCAAGATGGATCAAAGTCTT 2598
                           v  i v v    v    i      i       i        ?  v i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_65228665_6   2599 AAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACATTGGAA-AA 2647
                             v     v  i    i      v ii       v     v  ?i-  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_65228665_6   2648 ATCCTTCTAGACATTGGCTTGTGCCAAGATTTTAT-GATCAAGAACCCAA 2696
                            -   vv   v    v  iv  v v i   iv -   - v  vv    
  L1M4_orf2#LINE/    557 ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAA 604

  chrX_65228665_6   2697 AAACAAATGTATCAAAATCAAAGATAAATAGATGGGACTTAAATAAACT- 2745
                           i  v v i v     vv   i   i   i  v      v vi   v -
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_65228665_6   2746 -AAAGTTACTGCACAGCAAAAGAAATAATCAGTAGAATAAACAGACATCC 2794
                         -   ii vi  ii vv    i  v iv    iv i i i  v     v  
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_65228665_6   2795 CAGAGAGTGAGATAAAATCTTCATAATCTATACATCTGACAAAGTATTAA 2844
                           v   i  i  v     v  iii  vii   i      i  i v i vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_65228665_6   2845 TATCTGGAATCTACAAGGAACTCAAACAAATCAGCAAGAAAAA---AAAT 2891
                             ii    v  i  i      vv    v   ii  v     ---    
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_65228665_6   2892 --CCCA-TCAAAATGTGGGCTAAGGACATGAATAGACAATTCTCAAAAGA 2938
                         --    - i?   vi     v     iv          v     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_65228665_6   2939 AGATATACAAATGGCCAA-AAACATATGGAAAAAAATGCTCAACAGCACT 2987
                                           -  i  i   --    i          v  ??
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATG--AAAAGATGCTCAACATCAZZ 902

  chrX_65228665_6   2988 AAGGAT 2993
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 0.98 (54 / 55)
Gap_init rate = 0.02 (10 / 452), avg. gap size = 1.50 (15 / 10)  


2466 28.00 2.13 2.46  chrX_65237325_65239238.rev      549  1441 (473)    L1M4_orf2#LINE/L1       19   908 (0)  

  chrX_65237325_6    549 TCATGAATAGACAGAATCAATATCACTAAAATGGCCATACAGTCCAAAGC 598
                              i  v iv   v i     iii   i     v    vvi     vi
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chrX_65237325_6    599 AATGTATAGATTCAATGCTATTCCTATCAAACTAC-AGATGCCATTTTTC 647
                         i  v  i        i  v  i         v v -  v    -     i
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTT 117

  chrX_65237325_6    648 AAATAAATAGAAAATACT-ATTTTAAAATTCATGTGGAACCAAAAAGAGC 696
                         iv v    v  v  -i  -  ii          i     viiv  i ii 
  L1M4_orf2#LINE/    118 GCAGAAATTGACAA-GCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_65237325_6    697 CCA-AATAGTTCACCAAAGCAA----------AAAGAGCAAAGCTGGAGG 735
                            -     ----     i   ----------i    i     i      
  L1M4_orf2#LINE/    167 CCAGAATAG----CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_65237325_6    736 CATCACAATACCTGATTTCAAACTATACTAACAAGCTACAGTAACCAAAA 785
                         vv     v v  ii        viv     vv            i   i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_65237325_6    786 CAGCATGGTACTGGTACAAAAATAGACACATAGACCAATATAACAGGATA 835
                            ii         i i  ii       i     i    iv  i  i  v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_65237325_6    836 ATGAGCCCAAAAAGAAGGCCACATACCTACAACTATCTGATCTTCAACAA 885
                         iv   i   i   v  iv   i i ii  iiiii vi    i   i    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_65237325_6    886 AGCTAAAAATGAAACAGGCAGTGGGGAAACAAACAATCCCCTAATTGAAT 935
                         i v ivv  --i v  vv  i        -i  i i  ii----  v  i
  L1M4_orf2#LINE/    363 GGGTGCCAA--GACCATTCAATGGGGAAA-GAATAGTCTT----TTCAAC 405

  chrX_65237325_6    936 AAATGGTGCTAGGATAACTCACTAGCCATATGCAGAAGACTGAAACTGGA 985
                                   i   i    viv  ?   i     i    v    ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_65237325_6    986 CCCCTTCCTTACGCCTTATTCAAAAATCAACTCAATATGGATTAAAGACT 1035
                              v   i  i  v   v       i       v      i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_65237325_6   1036 TAAATGTGAAATCCAAAAGTATAAAAATACTGGAAGAAAACTTAGGCA-A 1084
                                i i v i    v       v vi i         v    ?i- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_65237325_6   1085 TACCATCCTGGATCTACAAAAAGGCAATGATTTCATGACGAAGACACAGG 1134
                         v i v  v  - i  vviivv        i    v iivv v     vii
  L1M4_orf2#LINE/    556 AATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_65237325_6   1135 AAGTAATTGCAACAAAAGCAAAAATTGACAAATGGCATCTAGTTAAACTA 1184
                            i vvv          v      v  i    v v ii vi i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_65237325_6   1185 AAGAGTTTCTACACAGTGAAAGAAACTATCAATTGAGTGAACTGAAAACC 1234
                           i ii  i iii vvii  i  v        vvi      vv  v    
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_65237325_6   1235 TACAGAATTGAAAAAAGT-TTTGCAAACTATGCATCCAAGAAGGGTCTAA 1283
                         i       v i i   i -        ii  ii   ii v     v  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_65237325_6   1284 TATTCAATATCTATAAGGAACTTAAACAAATTTACAAGGTAAAAACAA-- 1331
                            i  iv  v     i     ivv    v iv i  viv   i    --
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_65237325_6   1332 --CCCCATTTAAAAGTGGGCAAAGGACATGAACAGACCCTTCTCAAAAGA 1379
                         --   v   ?    i           iv    i    vi     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_65237325_6   1380 AGACATACATGCAGCCAACAATCATATAGGAAAAAAAAAACTGCTCAATG 1429
                            i     viii     i  v  i  --     i -----       ii
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACAT--GAAAAGA-----TGCTCAACA 897

  chrX_65237325_6   1430 GCCAGGTGTGGT 1441
                         -i  ????????
  L1M4_orf2#LINE/    898 -TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.02 (17 / 890), avg. gap size = 2.41 (41 / 17)  


2504 28.24 2.33 1.77  chrX_65244115_65246136      627  1529 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65244115_6    627 TGGAAGAGGATTCCATGCTCATGGGTAGAAAGAATCATTATTGTTAAAAT 676
                              iiiv  i     i      i v i    v i v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65244115_6    677 GACCATACCACCCAAAACAATTTGTAGATTCAATGGTATTCCTATCAAAC 726
                          i v    iv      vii  i ii        i vv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65244115_6    727 CACTAAGGACATTCTTCACAGAATTAGAAAAAAAACT-ATTTTAAAATAT 775
                         iv i ivvi v  i  ii     v v  v  i---  -  ii      vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_65244115_6    776 ATATG---AGCCAAAAAATAGCTTGAGTAGGCAAGACAATCCTAAGCAGA 822
                              --- vv   iii i-- iv  i   v   i      i i -- i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGA--AAA 193

  chrX_65244115_6    823 AAAAAAAAAAAACTGAAGGCATCACATTACCCAACTTTAAACTATACTAC 872
                          i  i  v   ii  i   vv     i v     i  i   viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_65244115_6    873 AAGGCTATATTAACCAAAACAGTGGGGTATTGGTACAAAAGCAGACACAT 922
                           i    i v   i   i      v    i   i i  iiii     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_65244115_6    923 AGACCAATATAACAGGTTAGAGAATGAAGAAATAAAGCTGCACATGTAGA 972
                            i    iv  i  iv v    i vv         v iii    v  vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_65244115_6    973 ACCATCTGATCTTTTTTAAATATGACAAAAGCAAGGAATGGGAAAAGAA- 1021
                         ii  vi    i  ivvi  ivi  v   i v  vvv      i      -
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_65244115_6   1022 -GTTCCTAATCAATAAATGATGCTGGGATAAATGACTAGCAATATGCAGA 1070
                         -  iii --    i     i        i  v  iv  ? v i     i 
  L1M4_orf2#LINE/    394 AGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_65244115_6   1071 AGATTGAAACTGGACCCTTTCTTTA-ATCATATACAAAAATCAACTCAAA 1119
                            v    ii       i v i i - i             i        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_65244115_6   1120 ATTGATTAAAGACTTAAATGTAAAACCTAAAACTATAAAGACCCTAGAAG 1169
                           v   i ?    i         i v             ivi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_65244115_6   1170 AAACC-TAGGA-CATATCATTATGCACATAGGCCTTGGCAAGATTTTATG 1217
                            v -    ?-i v   v ii  -  v v  vi v     viv   v v
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_65244115_6   1218 AGAAAT-ACTCCAAAATCAATTGTAGCAAAAACAAACATTGTCAAGTAGA 1266
                            v  -  v      v  vvv i i     iv   v  v vi  i v i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_65244115_6   1267 ATCTAATTAAACTAAAAAGCTTCTGTAC--CAAATAA-ACTACCAACAAA 1313
                          ii v  i   v v    i   i   i --    vi -    i   v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_65244115_6   1314 GGAAACAGACAGCCTACAGAATGGGAGAAAATATTTTCAAACTATGCATC 1363
                          vi  v     i  i                     v    ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_65244115_6   1364 CAACAAAGGTCTAATATCCAGAATCTATAAAGAACTTAAACAAATCAACA 1413
                         ii i  i  v  vi          v           ivv    v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_65244115_6   1414 AGCAAGAATCAAACAACCC--T------ATGGACAAAAGACACGAACAGA 1455
                          vv  i iv    i     -- ------    i    i  ivi   i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_65244115_6   1456 TACTTCTTGAAGACATAGACGTTATATTCTGTGGCCAACAAGCATATGAA 1505
                         i i    iv  -----   v v    ivv-i       i     i     
  L1M4_orf2#LINE/    841 CATTTCTCCAA-----AGAAGATATACAA-ATGGCCAATAAGCACATGAA 884

  chrX_65244115_6   1506 AAAATTCTCAACAACACTAATTAT 1529
                           i  v       v  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (150 / 102)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.06 (37 / 18)  


3682 14.38 3.12 3.12  chrX_65255003_65256729      500  1236 (491)    L1M4_orf2#LINE/L1      172   908 (0)  

  chrX_65255003_6    500 ATAGCCAAAACAATGTTAAAAAAGAACAACAAAGTTGGAGAACTCATACT 549
                                       v  i        v             i     i   
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_65255003_6    550 TACTGGTTTCTAAACTTACTACAAAGC-ATAGAATTCAAGATTGTGTGGC 598
                          v iii    v                - i  v v      iv      i
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_65255003_6    599 ATTGGCATAAGGATAGACAGATAGATCAATAGAATAGAATTGAAGATCCA 648
                          i                 v          i            iii    
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_65255003_6    649 GAAATAAACCCTCTA-ATTTTTGGTCAATTGATTTTCAACAAAAGTGCCA 697
                                    -v  -    v                i    ii      
  L1M4_orf2#LINE/    322 GAAATAAACCC-ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_65255003_6    698 AGACCTTTCAATGGAAAAA-AATAGTCTTTTCAATAAATTGTGCTGAGGC 746
                              v        ii   -              i    v      i i 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_65255003_6    747 AATTGGATATCCACATGCAAAACTATGAAGTTGGACCTCTAACTCACAAC 796
                           i      ?            vv             i   v      v 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_65255003_6    797 ATACAGAAAAATCAACTCAAAATGGGTCAAAGACCTAAATATAAAAGCTA 846
                            i v      i            i   ?          i   i     
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_65255003_6    847 AAGCTATAAAACTTTTAGAAGAAAACAAAGGAGCAAACCTTCATAACCTT 896
                           i          i             v   ? i   i    i i     
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_65255003_6    897 GGATTAGGCAATGGTTTCTTATATACAACACTAAAAGCACAAGTGAACAA 946
                           i                  v   ii    i           i-     
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC-AACAA 619

  chrX_65255003_6    947 A------------TAAATTGAAATACCTTAAAATTTGAAA----TATGCT 980
                          ------------       i v v v i      vi   ---- i    
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_65255003_6    981 TTAAAGGACACCAT-AAAAAAGTGAAAAGACAATCCACAGGATGTGAAAC 1029
                          i         i  -  i               i      i   v  i v
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_65255003_6   1030 AAT--TTGACAATCATATATCTGATAAGGGACTTGTATCCAGAATCCATA 1077
                            --   vv                                   vi   
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_65255003_6   1078 AGGAACTATTGCTTGATGTCATTGTTATTTGACAATGCTATTATCAAAAA 1127
                          i     ----   -----------------    iv v  v  v    i
  L1M4_orf2#LINE/    770 AAGAACT----CTT-----------------ACAACTCAATAATAAAAAG 798

  chrX_65255003_6   1128 ACCCATAACCCAATTTAAAA-TGGGCAAAGGATTTGAATAAACATTGCTC 1176
                           vv           ?    -                   i     v   
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_65255003_6   1177 CCAAGAAGATGTTAAAATGGATATTAAGCACAAGAGAAGATTCTCAACAT 1226
                          v        i vv      vi v        v  i     v        
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_65255003_6   1227 GGTTAACCGT 1236
                         vi????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.37 (59 / 43)
Gap_init rate = 0.02 (12 / 737), avg. gap size = 3.83 (46 / 12)  


2703 26.61 3.52 0.49  chrX_65271339_65273161      508  1330 (493)    L1M4_orf2#LINE/L1       61   908 (0)  

  chrX_65271339_6    508 CCCAAAGCAATCTATAGATTCAGTACAATCCCTATCAAAATACTAATGAC 557
                               vii     i       iii                v i iivi 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_65271339_6    558 ATTCCTCACAGAAATTAAAAAAAAAATCCTAAAATTCATACAGAACCACA 607
                         v  ii ii        i v  ivvi               ii   vii  
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_65271339_6    608 AAAGACACAGAATACCCACAGCTATCCTGAGGAAAAAGAA---AACTGGG 654
                          ii   v       v   v i v   i   ii  i     --- ii   i
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_65271339_6    655 GGAATTACATTACCTGATTTCAAATTATACTGCAGAGTTATAGTAACAAA 704
                            v i   i v  ii        viv    i  i  i  i     iv  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_65271339_6    705 AACAGCACAGTACTGGAATAAAAGTAGTCACATAGACCATTGGAAAAGAA 754
                         i    iiii       v    iii   v  i     i  v     v    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_65271339_6    755 TAGAGAACTCAGAAATAAATCCACACACCTACGGTGAACTCACTTTC-AT 803
                          v    iii          i   i   ii  i   v  i v i    - i
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_65271339_6    804 AAAGGTGCCAATAACACACACTGGGAAAAAGAAAGTCTCTTCAATAAATG 853
                           i        v v  iv  v    i   ii v     i     i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_65271339_6    854 GTGCTGGGGAAACTGGATATCCCTATGTGGAAGAATGAAACTAGTTCC-- 901
                                 iv         ?  vi   iii         ii i vi  --
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_65271339_6    902 ACTGTCACTGGCCATATACAAAAATCAAATGAAAATGGATTAAATACTTA 951
                           i-    --i              i  v v         i ? v  i  
  L1M4_orf2#LINE/    461 ACC-TCAC--ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_65271339_6    952 AATTTAAGA-C--------------------AAGAAAAAATTAGGGAACA 980
                            v     - --------------------       v  vi ? v v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_65271339_6    981 CCTCCAGGACATTGGTCTGGGCAGAAATACCTCAAGGAATACCCCACAAG 1030
                         i  i iv   v    vi i    ivii vi  i iiv vv  v   v   
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_65271339_6   1031 CGCAGGCAACCAAAGCCAAAATGGACAAATGAGATCACATCAAG-TTAAA 1079
                          i  i     v    vv     i  i    vi  iiv      i-     
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_65271339_6   1080 AAGCCACTGCAAAGCAAAGGAAATAATCAACAAAGTGAAGAGACACCAAA 1129
                           - ivi  iivvv       v iv     v        i     v vv 
  L1M4_orf2#LINE/    658 AA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_65271339_6   1130 CAGAACGGGAGAAAATATTTGCAAACTACCCATCTGACAAGGGATTAATA 1179
                              i                   ii ivi      i      i vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_65271339_6   1180 ACTAGAATATATAAGGAGCTCAAACAAATCTACAGGAAAAAATCTAGTAA 1229
                         v i           i  i   vv    v  v i iv     iv v i   
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_65271339_6   1230 TCTAATC-AAAAATTGGCAAAATATTTGAATAGACATGCCTCAAAAGAAG 1278
                         i i   i-      v      iv              vi   v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_65271339_6   1279 ACATACAAATGGCAAACAGTCATATGAAAAGGTGCTCAACATCATCAATC 1328
                          i           v  i iv  i        i            ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_65271339_6   1329 AT 1330
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.67 (135 / 81)
Gap_init rate = 0.01 (10 / 848), avg. gap size = 3.30 (33 / 10)  


2020 27.15 11.27 1.58  chrX_65274023_65278815     3487  4311 (482)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_65274023_6   3487 AAAAAAATCCCATGCTCATGAATAGGAAGAGTAAATAAATAAATATTATT 3536
                            i v        i     i  v      v -------   -    i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACT-------TAA-TATTGTT 45

  chrX_65274023_6   3537 AAAATGGTCATAGTTCCCAAAGCAATTTACAGATTTAATGCTGTTTCTAT 3586
                           i    iv   v i      vii  i        i  i  vi ii    
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_65274023_6   3587 GAAACTACCATAGACATTATTTACATAACTAGAAAAAAAACTG-TTTTGA 3635
                         v   v v   vvvi v  v   i  v  v v  v  i---   - ii i 
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAA 142

  chrX_65274023_6   3636 AATTCATATGAAACCAAAAAAGAGCCTAAATAGCCAAGGCAGTTCTAAGC 3685
                                   i  viiv  ii  v  vi         ii  i ii i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_65274023_6   3686 AAAAAGAACAAAGCTGGAGGCCTCATGTTACACTACTTCAAACTATACTA 3735
                           i          i      v    iii v v v i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_65274023_6   3736 CAAGGCTACAGTAACCAAAACAGCATGGTACTGGTATAAAAACAGGAACA 3785
                            i          i   i    ii         i    ii i  iv i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_65274023_6   3786 GAGATCAATATAACGGAATAGTGAGCCCAGAAATAAGGTCACACATCTAT 3835
                         v        iv  ii    v v   i          ivi  i    i   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_65274023_6   3836 GACCATCTAATCTTCAACAAAGCTTACAAAAACAAGCAATGGGGAAACGA 3885
                          ii  vi i  i   i    i v vv   i v  vv           vi 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_65274023_6   3886 CTCCCTATTCAATAAATGGTGCTGTGATAGCTGGCTAGCCATATGCAGAA 3935
                         ivvi  v     i           v  i i    v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_65274023_6   3936 GACTGAAGCTG-ACCCCTTCCC---------TATAAAAAC---CT----- 3967
                           v     i  -      v  i---------  i     i---  -----
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_65274023_6   3968 TGGATGACA-ACCTCA--------GC-AATATTAT-----TCT------- 3995
                              v ? -    v --------  -  v i   -----   -------
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_65274023_6   3996 GGACATAAGAATG---------------------GGCAAAGATTTCATGA 4024
                         ii     i ?i i---------------------     v i    v ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_65274023_6   4025 CAAAGAAACCAAAACCTGTCA--CAACAAAAGCAAAAATTGGCAAGTGGG 4072
                         vv v  v       v v--  --         v      v ii  i v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_65274023_6   4073 ATATAATTAAA-CTAAAGA-----GCACAGCAAAAGAAACTATCAACAGA 4116
                          iv v  i   -i    i ----- ii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_65274023_6   4117 GTAAACAGACAGCCTACAGAA--------ATTATTTGCAAATTCTGCACC 4158
                           i  v     i  i      -------- v           iv ii i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_65274023_6   4159 TGACAAAGGTCTAACATCCAGCATCTATAT-GAACTT----AACTTTACA 4203
                            i  i  v  vii      v  v    v-     i----    iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_65274023_6   4204 AGAGAAA-ACA------CCA-TTAAAAAGAAGGTAAAAGACTTGTACTGG 4245
                          v i   -   ------   -  ?    ivi  i   i  i   v iv i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_65274023_6   4246 CACTTTTCCAAAGAGGACATACATGTGGCCAGCAAGCATATAAAAA-AT- 4293
                           i  i        i  i     vi      ii     i  i    -  -
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_65274023_6   4294 TTTAGTATCACTGGTCAT 4311
                         i i ii    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (135 / 85)
Gap_init rate = 0.03 (26 / 905), avg. gap size = 4.08 (106 / 26)  


 530 14.29 0.00 0.00  chrX_65322826_65327506     1818  1908 (2773)  C L1M4_orf2#LINE/L1   (803)   105    15  

C chrX_65322826_6   1908 ATGTTCATGAATTGGAAGAATTAATATTATTAAGATGCAAATATTACCCA 1859
                                  i         v        i        vv    i v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

C chrX_65322826_6   1858 AAGCAATCTACAGATTCAATGCAATCCTTATCAAAATACCA 1818
                           vii              i       i         v   
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

Transitions / transversions = 1.17 (7 / 6)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.00 (0 / 0)  

2984 24.31 0.85 4.86  chrX_65322826_65327506     3243  4188 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65322826_6   3243 TGGAAAGACATTCCATGTTCATAAATTGTTAAGAATCAATATTATTAAAA 3292
                                 i  i          ii    v-    v i      i    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGG-AAGACTTAATATTGTTAAGA 49

  chrX_65322826_6   3293 TGTCCATATTACCCAAAGCAATCTACAGATTCAATGCAATCCATATCAAA 3342
                           v v   i v      vii              i       v       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_65322826_6   3343 ATCCCAGAGACTTTCTAAACAGAAATAGAATAAACACTTTCTAAAATTTA 3392
                                vvi i  i vvi       v  -i  i vvv i        i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chrX_65322826_6   3393 TATGGAACCGCAAAAGATCCAGAATAGATAAAACTATCCTAAGCAAAAAG 3442
                                vi    ii  i         vi     v   i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_65322826_6   3443 AACAAAACTGGAGGAATCGCATTACCTGACTTCATATACTATATGTTATA 3492
                               ii       v  i  i v  ii i    v ------------- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-------------A 235

  chrX_65322826_6   3493 CTACATATAACATGTAGTATAACATATACTACAGAGGTATAGTAATCAAG 3542
                           ------------------------       i  v  i          
  L1M4_orf2#LINE/    236 CT------------------------TACTACAAAGCTACAGTAATCAAG 261

  chrX_65322826_6   3543 GCAGCATGGTACTGGCATAAAAACAGACACATAGACAAATGGAACAGAGT 3592
                         i   ii              ii i     i     iv       i   i 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_65322826_6   3593 AGAGAACCAAGAAACAAATCCACACACCTACACTGAACACATTTTTGACA 3642
                         v    ii v     i   i   i   ii  iiv v  ivv     i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_65322826_6   3643 AACGTGCCAAGAATATAC--TGGGGAAA-AACAGTCTGTTCAATAAATGG 3689
                          iv         vi  v --        -  i     v     i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_65322826_6   3690 AGCTGGGAAAACTGTGTATCTATATGCAGAAGAATAAAACTAGACCATTT 3739
                         v       v     vi  ? i i     i      i  ii i    vi v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_65322826_6   3740 TCTCTCACCTTGTTCAAAAATCAAATCACTATGGATTAAATACTTAAATC 3789
                         i   v    v i v       i  v   vv      i ? v  i     v
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_65322826_6   3790 TAAGACCTCAAACTATGAAACTACTACAAAATAATCCATTGGGGAAAACT 3839
                              v  v       i     vi  v  i v  --   v  ? v   ii
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATC 559

  chrX_65322826_6   3840 TCCAGGGCATAGGTCTGGGCAAAAATATCTTGAGTAATATTGCAC---AA 3886
                          i iv i v v  vi i     vii v    -  --    vi   ---  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AG--ATATGACACCAAAA 606

  chrX_65322826_6   3887 GCACAGGCAACCAAAGCAAAAATGAACAAATGAAATCACATCAAG-TTAA 3935
                              i     v    v      ii i    vii iiv      i-    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_65322826_6   3936 AAGGCTTCTGCACAAAAAAGAAAACAATAAACAAAGTGAAGAGACAACCT 3985
                           i-   i  ii vvv    i v  v  v  v        i        i
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_65322826_6   3986 ACAGAGTGGGAGACAATATTTTTAAACTCCCTATCTGATGAGTGATTAAT 4035
                              i       v       vi   iiviv        i  v  i vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_65322826_6   4036 AATTAGAACAAATAAGGAGCTCAAACATCTCTATAGAAATAAAATCTAAT 4085
                          vii    i v    i  i   vv   v   v   iv  v  i - v   
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAAT 804

  chrX_65322826_6   4086 AATCCGACT-AAAAATGGGCAAAATATTTGAATAGACATTTTGCAAAATA 4134
                           i  i i -             iv                iv v   v 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_65322826_6   4135 AGCCATACGAATGGCAAACAGGCATATGAAAAGGTGTTAAACAACATTGA 4184
                           vi    i      v  i i   i        i  i v    v  ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_65322826_6   4185 TCAT 4188
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.86 (54 / 14)  


2424 26.54 4.14 2.69  chrX_65335122_65339642.rev     3151  4043 (478)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_65335122_6   3151 GAAAAACATTCCACGCTTATGAATAAGAAGAATCAATATTGTTAGAATGG 3200
                             i i  i   i i i   i  vi     v i          ii    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_65335122_6   3201 CCATACTTCCTAAAACAATGTACAAATTCAGTGCTATTTCTATCAAACTA 3250
                          v     i  i   vii  v    i     ii  v  ii        v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_65335122_6   3251 TGAATGATATTTTTCACAGAATTTGAAAAAAAATCATTCTAAAATTCATT 3300
                         iv iiviiv     ii     v    v  iv-- v  i           v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCATA 150

  chrX_65335122_6   3301 TGGAACCAAAAAAGGAACT--GGATATCCAAGGCAATCCTAAGCAAAAAG 3348
                              -- viv    i  i-- i   v    ii     i i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_65335122_6   3349 AACAAAGCTGGAGGTATCACGTTACCCAACTTCAAACTATACTGCAAGGC 3398
                                i      vv    ii v     i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65335122_6   3399 TACAGTAACCAAAACAGCATGCTGTTGGTATAAAAATAGACACATATATC 3448
                                 i   i    ii  v ii   i    ii       i   v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_65335122_6   3449 AATA-AATAGGACAGAGAATCCAGAAGTAAATCTATAAACCTACAA-CAA 3496
                            i-     i iv    i       i    i i   v ii  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_65335122_6   3497 TCAGATCTTCGACAAAGCTGACAGTAAAGAGCA----ATGGGAAAA--AT 3540
                          i-   i        i v  v  ----   v  ----     i   --  
  L1M4_orf2#LINE/    349 TT-GATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGAAAGAAT 393

  chrX_65335122_6   3541 ACTCCCTATTCAGTAAATGGTTCTGTGATAACTCACTAGCCACATGCAGA 3590
                          v  -- v    ii       v   v  i    viv  ?         i 
  L1M4_orf2#LINE/    394 AGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_65335122_6   3591 AGATTGAAATGTGG-CGCCTTCTTTTTATCATACTCAAAAAGCAACTCAA 3639
                            v    i -   - v   v i ivi i    iv      vi       
  L1M4_orf2#LINE/    442 AGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_65335122_6   3640 TGTGGATTAAAGACTTAAATGTAAAACCTAAAACTATAAAAGTGATACAA 3689
                         vi     i ?    i         i v              v vv  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_65335122_6   3690 GGAAATCTAGAAAATATTATTCTGGACAGGGGCCCTGGCAAAG---CCTT 3736
                          i   iv   i?ivv v v   vv   vvv  viiv     v ---i   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_65335122_6   3737 A---ATGACAAAGACTCCAAAAGC-CATTTCAACATAAACAAAAATTGAC 3782
                          ---      ------        -  vv-     v  iv      v  i
  L1M4_orf2#LINE/    591 AGATATGACA------CCAAAAGCACAAG-CAACAAAAGAAAAAATAGAT 633

  chrX_65335122_6   3783 ACGTGGAACCTTAATTAAACTAAAAATCTTCTGCACAGCAAA----ACTA 3828
                          vi v i  i i viv   i      -   i  ii vv    ----    
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA 682

  chrX_65335122_6   3829 ACAAGAAAATAAACA---AACTTACAGAATGAGAGAAAATATTTGCAAGC 3875
                         v       i i  v ---   ii        i                ii
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_65335122_6   3876 TA-GCATCCAACAGAGGTCTAATATCCACAATCTGTA--GGACGCTTAAG 3922
                         i -ii   ii i ii  v  vi      v   v i  -- i  v    --
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA-- 780

  chrX_65335122_6   3923 CAAATCAACAAGCAAGAACCAAAAAACACCA---------TGGACAAAGG 3963
                            v    i  vv  i iv    v   -   ---------   i      
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAAC-CCAATTWAAAAATGGGCAAAGG 829

  chrX_65335122_6   3964 ATATGAACAGATACTTGTTAAAACAAGACATACATGTGACCAGCAAGCAT 4013
                           v    i   i i  v iv   v    i     vi  i   ii     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_65335122_6   4014 ATGAAAAAAATGGTACATATCACTAATTGT 4043
                                i -  v vv i    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 2.35 (61 / 26)  


3013 27.57 1.33 0.78  chrX_65349649_65356480     3677  4579 (2253)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65349649_6   3677 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3726
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65349649_6   3727 GGCCATACTTCCCAAAGTAATTTATAGATTCACTGCCATCCCCATCAAGC 3776
                            v     i      v i  i  i       vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65349649_6   3777 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3824
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_65349649_6   3825 TTTGGAACCAAAAAAGAGCCCATATCACCAAGTCAATCCTAAGCCAAAAG 3874
                          v     viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_65349649_6   3875 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGT 3924
                                i      vv   ii  v  ii i      viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65349649_6   3925 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATGGATC 3974
                                 i   i    iii        i iv ii i   v    i    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_65349649_6   3975 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCAGATATCTACAACT 4022
                                i    i--    i  --        vv   v i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_65349649_6   4023 ATGTGATCTTTGTCAAACCTGAGAAAAACAAGCAATGGAGAAAGGATTCC 4072
                          vv    i  i v   ivv  vv  i v  vv      i     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_65349649_6   4073 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4122
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_65349649_6   4123 GAAACTGGATCCCTTCTTTACACCTTATACAAAAATTAATTCAAGATGGA 4172
                            ii    i    v i i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_65349649_6   4173 TTAAAGACTTAAAAGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAAC 4222
                          i ?    i    v  v   v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_65349649_6   4223 CTAGGCATTACCATTCAGG--CATAGGTATGGGCAAGGACTTCACATCCA 4270
                         v    ?i v viv   iv -- v i   - i     v ii   vi vvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chrX_65349649_6   4271 AAACACAAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATCTA 4320
                         vi    v       vvi          vv   i v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_65349649_6   4321 ATTAGACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4370
                           i i v i  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_65349649_6   4371 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 4420
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_65349649_6   4421 AAGGGCTAATATCCAGAATCTAAAATGAACTCAAACAAATTTACAAGAAA 4470
                          i  i  vi          v  v  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_65349649_6   4471 AAAACAA----CCCCAT--AAAAACTTGGGCAAAGGACATGAACAGACAT 4514
                           i    ----   v  --     --           iv    i      
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATAGACAT 843

  chrX_65349649_6   4515 TTCTCAAAAGAAGACATTTATGCAGACAAAAAACACATGAAAAAATGCTC 4564
                              v        i  vi viii v   v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_65349649_6   4565 ACCATCACTGGCCAT 4579
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  

3317 23.33 2.57 1.23  chrX_65349649_65356480     5444  6339 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65349649_6   5444 TGGAAAACCATCCCATTTTTGTAGATTATAAGAC--AATATTGCTAAGAT 5491
                               ivi       v  ii i    iv     --       i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65349649_6   5492 GTCAATGTTATCCAAAGAAATCTACAGATTTAATAAAA--CTTGTCAAAA 5539
                          v    ii vi     vvi           i  iiv  -- i i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65349649_6   5540 TTTTAATGACCTATTTTTTTGTAGAAATACACAATTTTATTCTAAAATGT 5589
                          iii iivi   ---      i      vv    vi v  i       vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT---TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_65349649_6   5590 ATATA-AATTTCATGGGGTAGTGAATAGTCAAAACAATTTTGATGAAGAA 5638
                             i-  v v  v   iivvv      i         i    vi     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_65349649_6   5639 GAA---AGTTAGATGACTTACACTTTCTGATTTCAAAAGTCATTTCAAAG 5685
                            ---    i  v    i      i ii         v i i v     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_65349649_6   5686 CTACAGTAATCAAAACAGTGTGGTACTAACATAAAGACAGACATACAGAC 5735
                                      i             ii     i  i       i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_65349649_6   5736 CAATAAAATAGAATACATGACCTGGAAATAG-CCCTCAAATATATGGCCA 5784
                             ii        vv viii ii      i-   vi v  v     i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_65349649_6   5785 AATAATTTTTGACATGGGTGCTAAGA---TTTTATTAAGAAAGAACAGTC 5831
                          v i     i    v      i    ---  iv  vii       i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_65349649_6   5832 T---CAACAAACAATTTCTGGAAAAACTGAATATCCACATGCAAAAAAAT 5878
                          ---       iii v-    i v     i   ?            i   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTG-CTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_65349649_6   5879 GAAGTAGGAGCTTTACCTTATACCACATGCAAAAATT----CAAAGTAGA 5924
                              v   v ii     i i    i  i        ----    i i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_65349649_6   5925 TCAAAGAACAAGTTATAAGACCTAAAACTGTAAAATACTTAGAGAGAAAA 5974
                            ?   v v iv i     v        i     iv      -      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA-AGAAAA 545

  chrX_65349649_6   5975 -GTAGAGGGAAAGCTTCAAGACTTTAGAAATAACAATATTTTTATTGGAT 6023
                         -i   i? v   v    iv   i  i ivvvii    iv   i-  i   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGAT 594

  chrX_65349649_6   6024 ATGACACCAAAAATAAAGGCAACAAAAGCAAAAATAGGTAAATTGGACTA 6073
                                     ii v i          v        i           v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_65349649_6   6074 CATCAAAAGAAAACAATTATCTGTATCAAAGGACATAATTAGTAGAGTAA 6123
                                 vv   v v  v v  iv          iv  i iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_65349649_6   6124 AATGGCAATCTATGGAATGGTGGAAAATATTTTCAAGCCATGATATATGT 6173
                           v i   i i ii      vi          v   ii   -    v  v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT-ATATCTGA 743

  chrX_65349649_6   6174 TAAGGGGTTGGTAGCTAAAATATATAAAGAACTCCTACAACTCAACAGTA 6223
                               ii v   v i i                i          i i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_65349649_6   6224 AAAAACTCACAAA--ACCTATTTTTTTAAATGGGCAAATAATTTGAAAAG 6271
                             i---     --   i v  ?vv-           vi       v  
  L1M4_orf2#LINE/    794 AAAAG---ACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAG 839

  chrX_65349649_6   6272 ACACTTCTCCAAACAGTATATGCATAAGGCCAATAAATATAT-AAAAGAT 6320
                            i         v iv    i  v v         ii i  -       
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_65349649_6   6321 GCTCATCATCACTTATTAT 6339
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (126 / 79)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.89 (34 / 18)  


2309 27.70 4.99 1.93  chrX_65358297_65361631     1962  2842 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65358297_6   1962 TGCAAAAACAATCCACACTCTTGGGTAGGAATAATTAATATTGTTAAAAT 2011
                           v   i i vi   iii  v   i v    v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65358297_6   2012 GGCCATACTGCCCAAAGCAATTTATTGATTCAATGCTGTCCCCATTAAAC 2061
                            v     v      vii  i  iv       i  vi    i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65358297_6   2062 TACCA-CTGACATTATTCACAGAATTAGAAAAAACT-ATTTCAAAATTCA 2109
                          v   -   v v  -  ii     v v  v  i-  -  iii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_65358297_6   2110 TATGTAAC--CAAATGAGCCCAAACAGACAAGATAATACTAAGAAAAAAC 2157
                             v  v--   iv  v  vi  i  v   i i   vi i i   i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_65358297_6   2158 AACAAAGCTGGAGGCATCAGGCTACTCAACTCCAAAGTATACTACAGGGT 2207
                                i      vv   vi  v i   i i    iiv       ii i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65358297_6   2208 AACAGTAACAAAAACAGCATGGTATTGGTACTGGTACAAAAACAGACACA 2257
                         v       iv  i    --  ----         i i  ii i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAG--TG----TGGTACTGGCATAAGGATAGACATA 292

  chrX_65358297_6   2258 TAGACCAATGGAACAGAATAAGGAACCCAGAAATAAAACCATCCACCTGC 2307
                             i        i     vii  ii           v    v  ii ii
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_65358297_6   2308 AACTATCTGATCTTTGGCAAACCTGACAAAAGCAAGCAATGGCAAATGTA 2357
                         iiii vi    i  i i   ivv  v   i v  vv      vi  v v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_65358297_6   2358 TTCCCTATTCAATAAATGGTGCTGGGATA---------------GCAGAA 2392
                          vvi  v     i              i ---------------   i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_65358297_6   2393 GATAGGAACTAGACTCCTCCCTTACACCATATACAACAATCAACCCAAGA 2442
                           vv i ii i   i   v   i             v   i   i   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_65358297_6   2443 TGGATTAAAGATTTAAATATCAAACCCCAAAGTATAAAAACCCTGGAAGA 2492
                              i ?   ii     i v i v iv   v       vi i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_65358297_6   2493 CAACTTAGACA-ATACCATTCAGGACATAGCCATGGGCAAAGATTTCAT- 2540
                         v   v   i?i- v i -   iv   v v vvv i     v i    v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_65358297_6   2541 GATAAAGATGCCAAAA--ACAATTGCAACAAAATCAAAAATTGACAAATG 2588
                             v-  ii      --    --         vv      v  i    v
  L1M4_orf2#LINE/    592 GATAT-GACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATT 638

  chrX_65358297_6   2589 GGATCTAGTTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTGTCAACA 2638
                            ii vi i   v v  i i   i   i vv    i  v   i    v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_65358297_6   2639 GAGTATGCAGACAACCTACACAACGTGAGAAAATTTTAGCAAATTATGCA 2688
                         i   iviv        i   v  i v        v  v      i  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_65358297_6   2689 TCTAATAAAAGTCTAATATGCAACATCTATAAGAAACT------------ 2726
                            i    ii v  vi   v  iv  v     ii    ------------
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_65358297_6   2727 ---TAAAAAAAT---TTACCCCATTAAAAAAGTGGACAAAAGACATGAAC 2770
                         ---      i i--- v    v   ?     -   i    i  iv    i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAAT 837

  chrX_65358297_6   2771 AGACGCTTCTC---AAAAGACATACATGCTGCCAACAATCATATGAAAAA 2817
                             ii     --- i    i     viiv     i  v  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_65358297_6   2818 AAAAAAACTCAACATCACTGATCAT 2842
                          vi----          ????????
  L1M4_orf2#LINE/    888 ATG----CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.21 (61 / 19)  


 487 24.76 0.00 0.00  chrX_65401883_65407518.rev     3735  3839 (1797)    L1M4_orf2#LINE/L1        1   105 (803)  

  chrX_65401883_6   3735 TAGGAAAACATTCCATGGTCATGAATAGGAAGAATTAGTATAGTTAAAAT 3784
                          i i  i i  i     v     i  v      v   i   v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65401883_6   3785 GGCCATATTCCCTAAAGTGATTTATAGATTCAATGCTATTCCCACTAAAC 3834
                            v   i    i   v    i  i        i  v  i  i ii   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65401883_6   3835 TACCA 3839
                          v   
  L1M4_orf2#LINE/    101 TCCCA 105

Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.00 (0 / 0)  

2266 26.52 3.79 1.26  chrX_65401883_65407518.rev     4354  5145 (491)    L1M4_orf2#LINE/L1       97   908 (0)  

  chrX_65401883_6   4354 AAAACCTACCATTGACATTCTTCACAGAATTAGATAAAAACT-ATTTTAA 4402
                             i --   vivi v  i  ii     v v  i  i--  -  ii   
  L1M4_orf2#LINE/     97 AAAATC--CCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAA 142

  chrX_65401883_6   4403 AATTCAGATGGAATCATACAGGAG-CCTA-AATAGCCAAGGCAATCCTAA 4450
                               v      --  i  i i -  i -         ii     i i 
  L1M4_orf2#LINE/    143 AATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_65401883_6   4451 GCAAAAAGAACAAAGCTAAAGGCATCATGCTACACAACTTCAAACTGTAC 4500
                         iv  i          i ii   vv   ii  v v   i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_65401883_6   4501 TACAGGGCCACAGTAACCAAAACAGCATGGTACTGGTCCAAGAACAGACA 4550
                             ii  i       i   i    ii         ivi   i i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_65401883_6   4551 CATAGAACAATGAAATGGAAGAGAGAAGCCAGAAATAAAACCACAC--CT 4598
                         i     v     i   i   vv    iv           v   i  --i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_65401883_6   4599 ACAA-CTATCCATTCTTCAACAAACCTAGCAAAAACAAGCAATGGGGAAA 4647
                          iii- v  iv   -   i    ivv iv   i v  vv           
  L1M4_orf2#LINE/    341 ATGGTCAATTGATT-TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_65401883_6   4648 TGACTCCCTATTCAATAAATGGTTCTGAGAAAACTGGATAGCGATATGCA 4697
                         vi ivvi  v     i       v   i  v         ? v i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_65401883_6   4698 GAAAATTGAAACTGGACCTCTTCCT-------TAAACAAAAATCAACTCA 4740
                         i  i v    ii      i  v   -------  v        i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_65401883_6   4741 AGATGGATTA-AAACTTAAATGTAA-ATCTCAAAACTATGAAAATCCTGG 4788
                          i      i - i  i         - v  -        i   v  i i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAG 538

  chrX_65401883_6   4789 AAGACAACCTAGGC-TATACCATTCAGAATATAGGCATAGGCAAAGATTT 4837
                             v   v    ?-  v i -   ivi iv v  vv       v i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_65401883_6   4838 CAT-GATGAAGATGCTAAAAGCAATTGCAACACAAGCAAAAATTGACAAA 4886
                          v -   - v  ii i       vvv      v   v      v  i   
  L1M4_orf2#LINE/    588 CTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_65401883_6   4887 TGGGATTTAATTAAACTAAAGGGCTTCTGCACAGCAAAAGAAACTATCAT 4936
                          v   i  v  i   v v  iii   i  ii vv    i  v       v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_65401883_6   4937 CAGGGTAAACAGACAACCTACGTAATGGAAGAAAAATTTTGCAAACTATG 4986
                         v ii  i  v        i  iv     i      vv        ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_65401883_6   4987 TATCTGACAAATGTCTAATATCCAGCATCTATCAGGAACTTAAACAATTT 5036
                                i  iv v  vi       v  v   v i     ivv    i i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_65401883_6   5037 -----TCAAAAAA-----AACT--ATTAAAATGTGAACAAATGACATGAA 5074
                         ----- v    i -----   i--   ?   vi  ii    v  iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_65401883_6   5075 CAGACAATTTTC-AAAGAAGACATACATGCAGCCAACAAGCATACTAAAT 5123
                         i     v  i  -        i     viii     i     i iv   v
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_65401883_6   5124 AAAGCTCAACATCATTGACTAT 5145
                         i v           ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (121 / 86)
Gap_init rate = 0.03 (21 / 812), avg. gap size = 1.90 (40 / 21)  


 354 24.10 1.20 0.00  chrX_65420895_65427509.rev     4990  5072 (1543)    L1M4_orf2#LINE/L1        1    84 (824)  

  chrX_65420895_6   4990 TGGAAGAACATTCCATGCTCATGGATAGGAAAAATCAATATCATGAAAAT 5039
                              ii i  i     i        v    i v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65420895_6   5040 GGCCATACTGCCCAAGGTAATCTATA-ATTAAAC 5072
                            v     v     iv i     i -   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1)  

 551 25.44 1.18 0.00  chrX_65420895_65427509.rev     5111  5279 (1336)  C L1M4_orf2#LINE/L1   (0)   908   738  

C chrX_65420895_6   5279 ATCTGGCAAAGGGCTAATATCCAGAGTCTACAAACAATTCAAACAAATTT 5230
                              ii  i  i  vi        i v  i   v  i  vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

C chrX_65420895_6   5229 ACAAGAAAAAAACAAACAACCCCATCAACAAGTGGATGAAGGATATCAAC 5180
                          i  v     i     i     v  i? v  i   iii      v v  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

C chrX_65420895_6   5179 AGACACTTCTCAAGAGAAGACATTTATGCAGCCAA-AAG-ACATGAAAAA 5132
                              i     v i      i  vi viii     -   -         i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

C chrX_65420895_6   5131 ATGCTCATCATCACTGGCCAT 5111
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (26 / 16)
Gap_init rate = 0.01 (2 / 171), avg. gap size = 1.00 (2 / 2)  

2633 28.08 1.10 0.49  chrX_65420895_65427509.rev     5306  6124 (491)    L1M4_orf2#LINE/L1       85   908 (0)  

  chrX_65420895_6   5306 GCCATCCCCATCAAGCTACCAATGACTTTCTTCACAGAATAGGAAAAACA 5355
                           v     i     iv v   iivi i  i  ii     vvv  v  i v
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chrX_65420895_6   5356 CTTCTTTAAAGTTCATATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCA 5405
                         vv  i -   i           viiv  ii  v  v v  v     iv  
  L1M4_orf2#LINE/    135 GATCCT-AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_65420895_6   5406 ATCCTAAGCCAAAAGAACAAAGCTGGAGACATCACTCTACCTGAGTTCAA 5455
                            i i ivv i          i     ivv    v  v  ii v     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_65420895_6   5456 ACTATACTACAAGGCTACAGTAATCAAAACAGCATGGTGCTGGTACCAAA 5505
                          viv        i              i    ii    i    i iv ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_65420895_6   5506 ACAGTGTTATAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGC 5553
                          i  vvv      i        i    i--    i  --        vv 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACC 331

  chrX_65420895_6   5554 CACACATCTACAACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAA 5603
                           i    i  iiiii vi    i  i     ivv  v   i v  vvv  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_65420895_6   5604 TGGAGAAAAGATTCCCTATTTAATAAATGATGCTGGAAAAACTGGCTAGC 5653
                            i    ii  vvi  v  i  i     i      i v      v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_65420895_6   5654 CATATGTAGAAAGCTAAAACCGGATCCCTTCCTTACACCTTATACAAAAA 5703
                           i   i i  iiv i  iii   i    v   i     v          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_65420895_6   5704 TTAATTCAAGATGGATTAAAGATTTAAATGTTAGATCTAAAACCATAAAA 5753
                             i    i      i ?   ii       v   v       i      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_65420895_6   5754 ACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCA 5802
                         vi i           v    ?i- v i -   iv   v v  vv i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chrX_65420895_6   5803 AGGACCTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT 5852
                          v iii  v ivv  vi            vvi          vv     v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_65420895_6   5853 GACAATTGGGATCTAATTAAACTAAAGAGCTTCTG-----CAAAGAA-AC 5896
                           i  v v   ii v  i   v v  i i   i  -----     i -  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_65420895_6   5897 TATCATCATAGTGAAAAGGCTACCTACAGAATGGAAGAAAAGTTTTGCAA 5946
                              vv v         i v   i         i      vv       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_65420895_6   5947 TCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAA 5996
                         vii ivi      i  i  i  vi          v  i         vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_65420895_6   5997 CAAATTTACAAGAAAAAAACAAACAATCCCATCAAAAAGTGGGCAAAGGA 6046
                            v iv i  v     i     i  i  v  i?    i           
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_65420895_6   6047 TATGAACAGAGACTTCTCAAGAGAAGAGATTTATGCAGCCAAAAGACACG 6096
                          v    i   v i     v i      v  vi viii     v ii   i
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_65420895_6   6097 TGAAAAAATGCTTATCATCACAGGCCAT 6124
                               i     i v     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (128 / 98)
Gap_init rate = 0.01 (7 / 824), avg. gap size = 1.86 (13 / 7)  


2967 26.51 1.43 1.54  chrX_65456205_65462606     5001  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65456205_6   5001 TGGAAGAACATTTCGTGCTCATGGGTAGAAAGAATCAATATCGTGAAAAT 5050
                              ii i  ii i  i      i v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65456205_6   5051 GGTCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5100
                           iv     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65456205_6   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5148
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_65456205_6   5149 ATATGGA--CCCAAAAAATAGCCCACATT-GCCAAGTCAATCCTAAGCCA 5195
                                --iv   iii ---    v v -     iv     i i ivv 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_65456205_6   5196 AAAGAAGAAAGCTGGAGGCATCACTCTACCTGACTT-GAAACTATACTAC 5244
                         i     v    i      vv    v  v  ii i  -i     -      
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTAC 243

  chrX_65456205_6   5245 AAGGCTACAGTAACCAAAACAGCATGGAACTGGTACCAAAACAGCGATAT 5294
                           i          i   i    ii   v     i iv ii i  vv    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_65456205_6   5295 AGACCAATGGAACAGAAC--AGAGCCCTGAGAAATAATGTCACATATCTA 5342
                            i        i    i--    i  --        vvi  i i  i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chrX_65456205_6   5343 CAACCATCTGGTGTTTGACAAACCTGTCAAAAACAAGAAATGGGGAAAGG 5392
                         iiii  vi  i v  i     ivv  i   i v  vvv           i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_65456205_6   5393 CATC-CCTTTTTAATAAATGGTGCTGGGAAAAATGGCTAGCCATATGTAG 5441
                         -  v-i     i  i              v  v   v  ?   i   i i
  L1M4_orf2#LINE/    392 -ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_65456205_6   5442 AAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTGAA 5491
                           iiv    ii    i    v   i     v              i v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_65456205_6   5492 GATGCATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAAACCTAGAA 5541
                         i   v  i ?    i       v   v       i      vv i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_65456205_6   5542 GAAAACCTAAGC---AATGCCATTGAGATCATAGGCATGGGCAAGGACTT 5588
                               v  i ?---   -- v i v  i v i  i- i     v ii  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGT-TAGGCAATGGTTT 587

  chrX_65456205_6   5589 CATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACATAT 5638
                          v ivv  vi            vvi          vv i   v  i v  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_65456205_6   5639 GGGATGTAATTAAACTAAAGAGCTTCTGCACAACAAAGGAAACTACCATC 5688
                         v   iv v  i   v v  i i   i  ii vv       v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_65456205_6   5689 AGAGTGAACAGGCAACATACAGAATGGGAGAAAAGTTTTGCAATCTACTC 5738
                          i      v  i    vi                vv       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_65456205_6   5739 ATCTGACAAAGGTCTAATATCCAGAATCTACAATGTACTCAAACAAACTT 5788
                               i  i  v  vi          v  i  v v    vv    -  i
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTC 786

  chrX_65456205_6   5789 A-CAAGAAAAAACCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAA 5837
                          -i  v     iv    i     v  i?    i            v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_65456205_6   5838 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAA 5887
                         i     i     v        i  vi viii     v  i          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_65456205_6   5888 AATGCTCACCATCACTGGCCAT 5909
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.59 (27 / 17)  


2941 26.18 1.54 1.65  chrX_65491268_65498314     5646  6554 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65491268_6   5646 TGGAAAAACTTTCCATGCTCTTGGATAGGAAGAATCAATATCGTGAAAAT 5695
                               i iv i     i  v     v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65491268_6   5696 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCTGCATCAAGC 5745
                            v     v      v i  i  i        i  v   ivi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65491268_6   5746 TACCA-CTGACTTTCTTAACAGAA-TTGGAAAAAACT-ACTTTAAACTTC 5792
                          v   -   v    i  i-     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_65491268_6   5793 ATATGGAACCAAAAAAGACCCTGCATAGCCAAGACATTCCTAAGCAAAAA 5842
                                 viiv  ii     v v        i   v  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_65491268_6   5843 GAACAAAGCTGGAGGCATCACACTACCTGTGTGAAAGTATTTCAAACTAT 5892
                                 i      vv       v  ii---------        viv 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCA---------ATTTCAAAACTT 238

  chrX_65491268_6   5893 ACTACAGGGCTACTGCAACCAAAACAGCATGGTACTGGTACCAAAACAAA 5942
                               ii     v i  i   i    ii         i iv ii i i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_65491268_6   5943 TATATAGACCAATGGAACAGTACAGCGGCCTCAGAAATAACACCACACAT 5992
                         i       i        i  v iv v ivii         vv   i    
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_65491268_6   5993 CTACAACCATCTGATGTTTGACAAACTTGACACAAATAAGCAATGGGGAA 6042
                         i  iiii  vi    v  i     ivv  v  vi vi vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_65491268_6   6043 AAGATTCCCTGTTTAATAAGTGGTGTTGGGAAAACTGGCTAGCCATATGC 6092
                          ii  vvi  v  i  i  i     i     v      v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_65491268_6   6093 AGAAAACTGAAACTGGACACCTTCCTTACACCTTATACAAAAATCAACTC 6142
                          i  i v    ii     v   v   i     v           i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_65491268_6   6143 AAGATTGATTAAATAATTAAACGTAAGACCTAAAACCATAAAAGTCTTAG 6192
                           i  v   i ? v vi    i      v       i      v      
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_65491268_6   6193 AAGAAAACCTGGGCAATAACACTCAGGATATAGGCATGGGCAAAGATTTC 6242
                                 v i  ?ivv  ivi  iv  iv v  vv i     v i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_65491268_6   6243 ATGTCTAAAACACCAAAAGTAATGGCAACAAAAGCCAGAATTGACAAATT 6292
                         v ivv  vi          i vvi          vv i   v  i     
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_65491268_6   6293 AGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTACCA 6342
                         i   i v  i   v v  i i   i  ii vv    i  v     i vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_65491268_6   6343 GAGTGAACAGACAACCTACAGAATAGTAGAAAATTTTTGCAATCTATCCA 6392
                         i      v        i       i v       v       vii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_65491268_6   6393 ATTGACAAAGGGCTAATAGCCAGAATCTACAAAGAACA--TA-AACACAT 6439
                         vi   i  i  i  vi  v       v  i       v--  -   v  v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_65491268_6   6440 TTACAAGAAAAGAAA--ACC--ATCAAAAAGTGGGCAAAGGATATGAACA 6485
                          v i  i  i v   --   --  i?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_65491268_6   6486 GACACTTCTCAAAATAAGACATT--AATGCAGCCATCAA--ACATGAAAA 6531
                             i     v   v    i  v--    --    vi  --         
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAA 886

  chrX_65491268_6   6532 AAATGTTCATCATCACTGGTCAT 6554
                         i -  i   v     ????????
  L1M4_orf2#LINE/    887 GA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (130 / 104)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.07 (29 / 14)  


1613 29.50 2.76 1.46  chrX_65511301_65516889.rev     3489  4105 (1484)    L1M4_orf2#LINE/L1        1   625 (283)  

  chrX_65511301_6   3489 TGGATAAACATTCTATGCACATTGATAGGAAGAATCAACATTATTAAAAT 3538
                             v i i  i i   iv   v   v      v i  i   i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65511301_6   3539 GGCCTTACTGCATAAAATAAGTTGCAGTCTCAATAATGTCCCTATCTAAT 3588
                            vv    v vi   v i vi i   vi    iivvi        v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65511301_6   3589 TACCAACGAAATTTATTACAGAATTAGAAAAATACT-ATTCTAAAATTCA 3637
                          v   i vivv   v  i     v v  v  i--  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_65511301_6   3638 TGTGGAAGAGGAAGACAGCCCAAATAGCCAGAGCAATCCTAAGGAAAAAA 3687
                          i     iv v   iv v  vi        i i     i i i-   i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAA 197

  chrX_65511301_6   3688 CAGCAAAGCTAGAGAAACCACACTACCCATCTTCAAACTATACTACAAAT 3737
                         v i     i i   i vi      v    vi      viv         v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_65511301_6   3738 CAACAGTAACTGAAACAGCATGGTACTA--ATAA--ACACACACATAAAC 3783
                          v       iii i    ii       i--    -- i v   i   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_65511301_6   3784 CAGTGGAACAGG-TTGGGTAACCCAGAAATAAAGCCACATACCTACAGCC 3832
                           i     i  i-   i - ii           v   i i ii  ii i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_65511301_6   3833 ATCTGATCTTTGACAAAATCAATAATAAGAAGCAATGGGAAAAGAACTCT 3882
                          vi    i  i     iiviivi  v vv vv       i      ivv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_65511301_6   3883 GTATTTAACAAACAGTGCTAGGATAACTAGCTAGTCATATGCAGAAGATT 3932
                         v v  i      ii     i   i    i v  ?i  i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_65511301_6   3933 GAAGGTGGACCCCTTTGTTGCAGCATATAAAAAAATCAACTCAAGATAAA 3982
                             v         viv ii  v      v      i       i  ii 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_65511301_6   3983 TTAAAGACTTAAATGCAAAACCTAAAGCAATAAAAACTGTGGAAGATAAC 4032
                          i ?    i      i  i v     i v      viiv i     v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_65511301_6   4033 CTAGG---AAATACCATTCTGGACATAGGCCCTGCAA-AGTTTTT----- 4073
                         v    ---    -- v iv  iv v i  iivv    -i    i -----
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_65511301_6   4074 ATGATG--AAAACTGGAAAAACAACTGAAAGAAA 4105
                             ii--    -- v v  i    -i       
  L1M4_orf2#LINE/    595 ATGACACCAAAA--GCACAAGCAAC-AAAAGAAA 625

Transitions / transversions = 1.50 (108 / 72)
Gap_init rate = 0.02 (14 / 625), avg. gap size = 1.86 (26 / 14)  

 732 25.09 4.66 1.79  chrX_65511301_65516889.rev     4820  5098 (491)    L1M4_orf2#LINE/L1      622   908 (0)  

  chrX_65511301_6   4820 GAAACAAAT-GAGAAATGTGATCTAATT-ATATTAAAGAGCTACTGCACA 4867
                             -    -  v    vv  ii v  i- v      i -  vi  ii v
  L1M4_orf2#LINE/    622 GAAA-AAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCT 669

  chrX_65511301_6   4868 GCAAAAGAAATCATCAACAGAGTAAGCCACCACCCTACAGAGTGGGAAAA 4917
                         v    i  v ii     v i   i ivviv  v  i     i     i  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_65511301_6   4918 AATATTTTCAAACTATGCATCTAAAAAAAGGTCTACTATCCAGAGTCTAT 4967
                                v    ii  ii    i v  ii iii i-        i v   
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTG-TATCCAGAATATAT 768

  chrX_65511301_6   4968 ATAGAACT---------TAAAAAGCAAAATACAAACAACCCCATTCAAAA 5008
                          v      ---------i  v  vv    v     i     v   ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_65511301_6   5009 ATGGGCAAAGAACATGAACAGACACTTCTCAAAAGAAGACATA--AATGC 5056
                                   i iv    i     i     v        i   --    -
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG- 867

  chrX_65511301_6   5057 AGCCAACAATCATATGAACAAATGTTCAGCAGCACCTATCAT 5098
                         -     i  v  i     v i   i   i  v  ????????
  L1M4_orf2#LINE/    868 -GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (41 / 28)
Gap_init rate = 0.03 (8 / 287), avg. gap size = 2.25 (18 / 8)  


2865 27.41 1.66 0.89  chrX_65524300_65527214.rev     1524  2424 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65524300_6   1524 TAGAAACACATCATGTGCTCACGGATGGGTAGAATCCATATTGTGAAAAA 1573
                          i    v i   vii  i   i    v  v   v iv       v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65524300_6   1574 GGCCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAACA 1623
                            v     v  v   vii       i      i     i  i     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65524300_6   1624 TACTACCATTCTTCTTCACAGAAGTAGAAAAAACAATCCTAAGATTCATA 1673
                          v i v vvi   i  ii     i v  v  ivii       i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_65524300_6   1674 TGGAACCCAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 1723
                              vivv  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_65524300_6   1724 CAAATCTGAAGGCATCACATTACCTGATTCCAAACTATACCATAAGGCCA 1773
                             vi  i   vv     i v  ii   i    viv   i i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_65524300_6   1774 TAGTCATCAAAACAGCATGTTACTGGTATAAAAATAGGCACATAGACCAA 1823
                         i   v     i    ii  v      i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_65524300_6   1824 TGGAACAGAATAGAGAACTCAGAAATAAACCCAAATACTTACAGACAACT 1873
                              i     v    iii              v i i   ii v   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_65524300_6   1874 GGTCTTTGACAAATCAAACAAAAACAGT--GTGAGTAAAGGACATCTTTT 1921
                          i i  i     ivvviv   i v  v --i  i v    i i vii   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_65524300_6   1922 TCAAAAAATGATGCTGGGATAATTGGCTAACCACATGTAGGAGAATGAAA 1971
                             v     i        i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_65524300_6   1972 CTGGATGCTCATCTCTTACCTTATACAACAATCAACTCAAGATGGATTAA 2021
                         i    iv ii i   vi   v       v   i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_65524300_6   2022 AGACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGGTAACATTG 2071
                             i     v     v  i           v ii      iv     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_65524300_6   2072 GAAAAACTCTTCTAGACAGTGGCTTAGGTAAAGATTTC------ATGACG 2115
                          ?iv  v     vv   vv   v     i  v i    ------     -
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC- 599

  chrX_65524300_6   2116 AAGAACTCAAAAGCAAATGCAACAAAAACAAAGAAAAATAAGTGGGACTT 2165
                         ----  -        v v         iv   i v i    i v      
  L1M4_orf2#LINE/    600 ----AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_65524300_6   2166 AATTAAACTAAAGAGCTTTTGCATGTCAAAAGGAACAGTCAGCATAGTAA 2215
                         v  i   v v  i i      iiiv     i iv  vi   iv v   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_65524300_6   2216 ACAGACAACCCACAGAATAGCAAAAAATCTTCACAATCTATGCATCCAAC 2265
                          v                i v i     v  ii   vii  ii   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_65524300_6   2266 AAAAGACTAATCTCCAGAATCTACATGGAACTC----AAATTAGCAAGAA 2311
                           ii    vi v        v  i vi      ----  v i ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_65524300_6   2312 AAA-ACAAACCATCTCATTTTAAAAACTCAGCTAAAGATATAAATAGACA 2360
                            -     iv i -  v  ?     - vi  v  i   v i        
  L1M4_orf2#LINE/    795 AAAGACAAATAACC-CAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chrX_65524300_6   2361 ATTAACAAAAGAAGATACACAAATGGCCAATAA--ACATGATAAAAAGCT 2408
                         v  vv v          i               --      v  i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_65524300_6   2409 CAATATTACTAATGAT 2424
                            i  i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.56 (23 / 9)  


2791 28.27 1.00 0.33  chrX_65528057_65531573     2123  3024 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65528057_6   2123 TGGAAACACACCTCATGCTCATGGATGCGTAAAATCAATATTGTGAAAAT 2172
                               v i i i    i        vv v i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65528057_6   2173 TATTATACTGCTAAAAGTAATCTACAAATTCAATCCAATTCCCATCAACA 2222
                         viiv     v iv   v i       i      iv    i  i     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65528057_6   2223 TACCACCCTTACTCTTCACATAATTTGAAAAAGCAATTCTAAAATTAATA 2272
                          v   v ivivi i  ii  v  v    v  ivii  i        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_65528057_6   2273 TGGAACCATAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 2322
                              viii  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_65528057_6   2323 CTAATCTGTAGACATCACATTGCCTGATTCCAAACGATGCTATAAGGACA 2372
                          v  vi  v  ivv     i v  ii   i    vvv i   i  i vi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_65528057_6   2373 TAGTTACCAAAACAGGATAGTACTGATATAAAAATAGGCACATAGACCAA 2422
                         i   v i   i    vi i      ii    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_65528057_6   2423 TAGAACAAAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAGCT 2472
                          i   i i   v    ii               v i i   ii i  ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_65528057_6   2473 GATCTTTGACAAAGCGAACAAAAACGT-AAATGGGGAAAAGACATCCTTT 2521
                            i  i     i vviv   i v i -v          ii i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_65528057_6   2522 TCAACAAATGGTACTGGGATAATTGGCTAACCACATGTAGGAGAATGAAA 2571
                                     i      i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_65528057_6   2572 CTGAATCCTCATATCTCCCCTTATACAAAAATCAACTCAAGATGCATTAA 2621
                         i  i i  ii iv  v v  v           i       i   v  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_65528057_6   2622 GGACTTGAATCTAAGACCTGAAACTA-AAAATTCC-AGAAGATAACATTG 2669
                         i   i i   v     v  i      -    i  i-      v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_65528057_6   2670 GAAAAACTCTTCTAGACATTGGCTTAGGCAAGGATTTTATTACCAAGAAC 2719
                          ?iv  v     vv   v    v        v i   i-   vvv vi  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGAC 599

  chrX_65528057_6   2720 -CCACAAGCAAATGCAATAAAACAAAGA-TAAATAGCTGGCACTTAATTA 2767
                         -   v     v v    i    v   i -  i   iv v v    v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_65528057_6   2768 AACTAAAGAGATTTTATGGGCAAGAGGA-ACAGTCAGCAGGGTAAACAGA 2816
                           v v  i iv    i  vviv i    -  vi   iv ii  i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_65528057_6   2817 CAACACACAGAGGAGGAAAAAAGGTCTTCATAATGTAAACATCTGACACA 2866
                             v      ivi   i    vi i v  -   -i v i      i vi
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCA-AAT-CATATATCTGATAAG 747

  chrX_65528057_6   2867 GAACTAATATCCAGAATCTACCACAAACTCAAAGAAATCAACAAGAAAAA 2916
                          i   vi          v  iv vi     vv v  v    i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_65528057_6   2917 ---AAACAACCCCATTAAAAAGTGGGCTAAGGACATGAATAGACAATTCT 2963
                         ---   i     v   ?    i     v     iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_65528057_6   2964 CAAAAGAAGATACACAAATGGCCAACAAACATATGAAAAAAAGCTCAACA 3013
                          v          i            i  i  i       i v        
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_65528057_6   3014 TCACTAGTGAT 3024
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.32 (143 / 108)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.20 (12 / 10)  


2315 27.34 0.58 0.44  chrX_65549477_65551152      500  1183 (493)    L1M4_orf2#LINE/L1      224   908 (0)  

  chrX_65549477_6    500 CTGACTTCAAACTATAATACAAGGCTACAGTAACCAAAACAGCATGGTAG 549
                          ii i      viv  v     i          i   i    ii     v
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_65549477_6    550 TGGAACCAAAACAGAGATATAGACCAATGGAACAGAAC--AGAGCCCTCT 597
                            v iv ii i   v       i        i    i--    i  v--
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA-- 321

  chrX_65549477_6    598 GAAATAATGCCGCGTATCTACAACTATCTGATATCTGACAAACCTGACAA 647
                                vv  iiii  i  iiiii vi    v ii     ivv  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_65549477_6    648 AAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAA 697
                         i v  vvv           i  vvi  v  i  i              v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_65549477_6    698 ACTGGCTAGCCATATGTATAAAGCTGAAACTGGATCTCTTCCTCACACTT 747
                              v  ?   i   i v  iiv    ii    i i  v        iv
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_65549477_6    748 TATACAAAAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGCCCTAA 797
                                       i    i      i ?    i       v  vv    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_65549477_6    798 AACCATAAAATCCCTAGAAGAAGACCTAAGCA-ATACCATTCAGGGCATA 846
                            i      ii i        i  v  i ?i- v i -   iv i v v
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTT 570

  chrX_65549477_6    847 GGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAA 896
                           vv i     v ii   v ivv  vi            vvi        
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_65549477_6    897 AGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGTACAG 946
                           vv     v  i    v   ii v  i   v v  i i   i   i vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_65549477_6    947 AAAAGAA-ACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAA 995
                         v    i -    i  vv i      v  i     i               
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_65549477_6    996 AGTTTTGCCATCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAA 1045
                          vv     v vii ivi      i  i  i  vi          v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_65549477_6   1046 AGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAACAAGT 1095
                                vv    v iv i  v     i     i     v  i? v  i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_65549477_6   1096 GGGCAAGGGATATGAACAGACACTTCTCAAAAGAAGACATCTATGCAGCC 1145
                               i    v    i     i     v        i  vi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_65549477_6   1146 AAAAAACACATGAAAAAATGTTCGTCATCACTGGCCAT 1183
                           v  i          i   i  iv     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (105 / 78)
Gap_init rate = 0.01 (5 / 685), avg. gap size = 1.40 (7 / 5)  


 230 15.79 3.51 0.00  chrX_65555861_65562634      352   408 (6366)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_65555861_6    352 AAAGAAGACATGTAAGTGGCCAAAAA--ACATGAAAAAATTCTTCACATC 399
                                 i  ii  i       v  --         i  v  iv     
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_65555861_6    400 ACTAATCAT 408
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.00 (6 / 3)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 2.00 (2 / 1)  

2779 27.96 0.99 0.66  chrX_65555861_65562634     5377  6281 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65555861_6   5377 TGGAAAAACATTCCATGCTCGTGGATAGGAAGAATCAGTGTTGTGAATAT 5426
                               i i  i     i  i     v      v i i i    v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65555861_6   5427 GGCCATACTCCCCAAAGTAATTCATAGATCCAATGTTATTCCCATCAAGC 5476
                            v            v i  ii i    i   i iv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65555861_6   5477 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACATACTTTAAATTTCA 5525
                          v   vivi i  i  ii     -   -- v  i vv iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_65555861_6   5526 CATGGAACCAAAAAGGAGGCCACATAGCCAAGACAATCCTAAGCAAAAAG 5575
                         i      viiv  i   vv viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_65555861_6   5576 AACAAAGCTAGAGGCATCACGCTACCTGACTTCAACCTATACTAGAAGCC 5625
                                i i    vv    i  v  ii i     vviv     v  iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65555861_6   5626 TACAGTAACAAAAACAATATGGTACTGGTAACAAAACAGATATATAGACC 5675
                                 iv  i   i i         i vv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_65555861_6   5676 AATGAAAAAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5725
                             i  v    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_65555861_6   5726 CTGATCTTTGATAAACTTGACAAAAACAAGCAATGGGAAAGGATT--CCT 5773
                         i    i  i  i  ivv  v   i v  vv       i  i  v --i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_65555861_6   5774 TATTTAATAAAATGGTGTTGGGAAAACAGGCTAGCCATATGCAGAAAGAT 5823
                          -  i  i   -     i     v   v  v  ?   i     i  ii  
  L1M4_orf2#LINE/    399 T-TTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_65555861_6   5824 GAAACTGGATCCCTCCCTTACACCTTATACAAAAATTAACTAAAAATGTA 5873
                            ii    i    v   i     v                v      v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_65555861_6   5874 T-AAAGACTTAAACGAAAGACCCTAAAAC-ATAAAAACCCTAAAAGAAAA 5921
                          - ?    i    i v    v -      -      vi i  i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_65555861_6   5922 CCAAGGCG-ATACCATTCAGAACATAGGCATGGGCACAGACTTCACGACT 5970
                          vv   ? - v i -   ivi  v v  vv i    vv ii   viiiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_65555861_6   5971 CAAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGCGATTT 6020
                         vvi    v       vvi          vv     v  i    vv  i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_65555861_6   6021 AATCAAACAAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 6070
                         v      vvv  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_65555861_6   6071 ACAGACAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAT 6120
                          v        i                 v       vii  vi       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_65555861_6   6121 GAAGGGCTAATATCCAGAATCTACAAA-AACTTAAACAAATTTACAAGAA 6169
                         i i  i  vi          v  i   -    ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_65555861_6   6170 AAAAA--AAGAACCCCATCAAAAAGTGGACAAAGTATTTTACCAGACAGT 6217
                            i --  v     v  i?    i   i     v    v vi     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_65555861_6   6218 TCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAATAAAAGCTCA 6267
                             v        i  vi viii     i  i  i     v i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_65555861_6   6268 TCATCACTGGTCAT 6281
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (139 / 110)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


2343 28.10 2.41 3.07  chrX_65591167_65596077.rev     3512  4422 (489)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_65591167_6   3512 AGAAACATCCCATTCTCATGGATGGGTATACTCGATATTGTGAAAATGAC 3561
                          i i i       vi        v  v v   ii       v  i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_65591167_6   3562 CATACTGCCAAAAGGAAGCTACAAATTCAATGTAACTCTCATCAAAATAC 3611
                         v     v  v   vvi v     i      i i  ii ii        v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_65591167_6   3612 -AACCATCGTTCTTCACAGAATTCAAAAAAAT--TTCTAAAATTCATATG 3658
                         - i iii -  i  ii     v ii v  iv -- i              
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_65591167_6   3659 GAACCAATAGAGAGATAGCATAGCCAAAGAAAGACTAAGCAAAAAGAACA 3708
                            viivv  i  vvi  v         iv  vvi i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_65591167_6   3709 AATCTGGAGGCATTACATGCCCTGATTTTAAACTATACAATAAGGCTATA 3758
                           vi      vv i   ivi  ii    i   viv   v i  i    i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_65591167_6   3759 GTCAAAAAAACAGCATGGTACTGGTATAAAAACAGGCACATAGACCAATG 3808
                           v vv  i    ii         i    ii i  i  i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_65591167_6   3809 GAACAGAATAGAGAACTCAGAAATAAACCCAAA----TACAGCCAACTGA 3854
                            i     v    iii              v ----  ii i   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_65591167_6   3855 ACTTTGACAAGCAAACAAAAACATAATC--TGGGGAAAGGACACCCTTTT 3902
                         vi  i      vivi v  i  -i v  --         i i vi     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_65591167_6   3903 CAACAAATG-TGCTGGGATAATTGGCAAGCCACATGTAGGAGAATGAAAC 3951
                                  -        i  i   vv ?       i ii        ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_65591167_6   3952 TGGGTCATCACCTCTCACGTTATATAAAAATCAACTCAAGATGAATTAAG 4001
                            ii vii     v   vv    i      i       i   i  i ?i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_65591167_6   4002 GACTTAAATTTAATACTTGAAACTGTAAAAAGTTTAGAAGATAACACTGG 4051
                            i     v   v vi i     i     vvi        v    iv  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_65591167_6   4052 AAAAACCCCTCTAAACATTGGCTTGGGCAAGGATTTTATGACCAAAACCC 4101
                         ?iv  vi i  vvi  v    v  i     v i   iv iivi vi  v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_65591167_6   4102 CCCTCCCCCCAAAAAAGAAAAACAACAACAACAACAAAAAAAAGATAAAT 4151
                          ----------    iv v  i      ----  v      v        
  L1M4_orf2#LINE/    602 C----------AAAAGCACAAGCAACAA----AAGAAAAAATAGATAAAT 637

  chrX_65591167_6   4152 GGCTGGAATTTA-----ATTAAA--CTTTAGTTTAGTTTAAACTGCCA-T 4193
                         ---    v  i -----      --    v  --- i  v  vv v  - 
  L1M4_orf2#LINE/    638 ---TGGACTTCATCAAAATTAAAAACTTTTGT---GCTTCAAAGGACACT 681

  chrX_65591167_6   4194 GCCAGTTGTGCATGGCAAAAGAAACAGCGAGCAGAGTGGCAGAAAATCTT 4243
                         ii  i---- v v vv      --  i vvi    i   v       v  
  L1M4_orf2#LINE/    682 ATCAA----GAAAGTGAAAAGA--CAACCCACAGAATGGGAGAAAATATT 725

  chrX_65591167_6   4244 CACAATCTATACATCTAACAAAGGACTGATATCCAGAATCCACAAGGAAT 4293
                         ii   vii   i    i i  i     vi          vi i  i   i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_65591167_6   4294 TCAAACAAATCATCCAGAAACAAACAAACAATCCCATCAAAAAGCGTGTT 4343
                           vv    v   viv v   v i     i  i  v  i?    ii v iv
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_65591167_6   4344 AAGGACATGAGCAGACAATTCTTAAAAGAAGATATATAATTGTCCAAAAA 4393
                              iv   ii     v    iv            i  v  v    v  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_65591167_6   4394 GCATA-AAAAAG---CTAAACATGACTAATGAT 4422
                            i -i     ---  v     v ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (146 / 106)
Gap_init rate = 0.02 (18 / 905), avg. gap size = 2.78 (50 / 18)  


2877 27.54 1.00 0.55  chrX_65629618_65633963     2951  3854 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65629618_6   2951 TGGAAA--CATCCCATGCTCATGGATGGGTAGAAACAATATTGTGAAAAT 2998
                               --i        i        v  v   vvi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65629618_6   2999 GACCATACTGCCAAAAGCAATCTAGAAATTCAACACAATTCACATCAAAA 3048
                          i v     v  v   vii     v i       i    i vi       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65629618_6   3049 TACCACCATCATTCTTCACAGAATTACAAAAAAAAAATCTAAAATTCATG 3098
                          v   v vv v  i  ii     v vv v  ivvi vi           i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_65629618_6   3099 TGGAACCAAAAAAGAGCCCACATAACCAAAACAAGACTATGCAAAA--AG 3146
                              viiv  ii  v  viv   i         v-  -  v    --  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGAAG 198

  chrX_65629618_6   3147 AACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGC 3196
                               vi      vv       v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65629618_6   3197 CATAGTCACCAAAACAGCATGGTACTGGTATATAAATAGGCACATAGACC 3246
                         i i   v i   i    ii         i   vii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_65629618_6   3247 AATGGAACGAAATCAAAAACCCAGAAATAACCCCAAATACTTGCAGCCAA 3296
                                iii   ii i ii          v    v i i  iii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_65629618_6   3297 CTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGAAAAGGACACCAT 3346
                         i    i  i     i vviv   i v   vv i    i    i i viv 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_65629618_6   3347 TTTCAACAAATGGTGCTGGGATAATTAGCAAGCCACATGTAGGAGAACGA 3396
                                              i  i i vv ?       i ii    i  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_65629618_6   3397 AACTGGAATGTCATCTCTCACATTACACACAAATCAATTCAAGATAGATT 3446
                          ii    vivii i   v   vv  i   v    i  i    i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_65629618_6   3447 AAGGACTTAAATCTAAGACCCGAATCTATAAAAGTTCTAGAAGATAACAT 3496
                          ?i   i     v     v ii  v        v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_65629618_6   3497 TGAAAAAACCCTTCGAGACATTGGCTTAGGCAATGATTTCATGACCAAGA 3546
                         v i?iv  vi     v   v    v          i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_65629618_6   3547 ACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCCGGGACCTAATT 3596
                         vv         v v    i    iv   i   i   iviv    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_65629618_6   3597 AAACTAAAGAGCTTTTGCATGGCAAAAGAATCAGTCAGCAGAGTAAACAG 3646
                            v v  i i      iiivv    i  vv vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_65629618_6   3647 ACAAACCACAGGGTGGGAGAAAAT--CTGCACAATATATACATCTGACAA 3694
                             v      ii           --i    -   -i   i      i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCA-AAT-CATATATCTGATAA 746

  chrX_65629618_6   3695 AGGACTAATATCCAGAATCCACAATGAACTCAAAAAAATCAG--GTAGAA 3742
                         i     vi          vi i  v      vv v  v   i--i  i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_65629618_6   3743 AAATCAAACAATCCCACCAAAACGTGGGCTAAGGACATAAATAGACAATT 3792
                          i -    i  i  v ii?   vi     v     iv i        v  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_65629618_6   3793 TTC-AAAAAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAA 3841
                         i  -   i                   i  i  i       i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_65629618_6   3842 CATCTCTAATGAT 3854
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


3083 26.96 1.10 0.77  chrX_65647946_65653716.rev     4376  5280 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65647946_6   4376 TGGAAGAACATTCCATGCTCATGGATAGAAAGAATCAATATCATGAAAAT 4425
                              ii i  i     i        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65647946_6   4426 GGCCATACTGCCCAAGGTAATTCATAGATTCAATGCCATCCCCATCAAGC 4475
                            v     v     iv i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65647946_6   4476 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4523
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_65647946_6   4524 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAGA 4573
                                viiv  ii  v  viv  v     iv     i i i--     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--AAAGA 196

  chrX_65647946_6   4574 AGAA---AGCTGCAGGCATCATGCTACCTGACTTCAAACTGTACTACAAG 4620
                             ---  i  v   vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_65647946_6   4621 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 4670
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_65647946_6   4671 CCAATGGAATAGAAC--AGAGCCCTCAGAAATAATACGACACATCTATAA 4718
                         i             i--    i  --        vv v i    i   ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_65647946_6   4719 TTATCTGATCTTTGACAAACCTGATAAAAACAAGAAATGGGGAAAGGATT 4768
                          i vi    i  i     ivv  vi  i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_65647946_6   4769 CCCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAG 4818
                         vi  v  i  i              v      v  ?   i   iii  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_65647946_6   4819 CTGAAACTGGACCTCTTCCTTACACCTTATACAAAAATTAATTCAAGACG 4868
                         v    ii      i  v   i     v              i    i i 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_65647946_6   4869 GATTAAAGACTTAAATGTTAAACCTAAAACCATAAAAACCCTAGAAGAAA 4918
                            i ?    i       v i v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_65647946_6   4919 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGTC 4967
                           v    ?i- v i -   iv   v v  vv i i   v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_65647946_6   4968 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAATTTGACAAATGGGATA 5017
                           vi            vvi          vv   v v  i    v   iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_65647946_6   5018 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGCAACTTCCATCAGAGTG 5067
                          v  i   v v  i i   i  ii vv    i vv   vi  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_65647946_6   5068 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5117
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_65647946_6   5118 CAAAGGCCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5167
                         i  i  v  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_65647946_6   5168 AAAAT-CAGACAACCCCATC-AACAATGGGCGAAGGATATGAATAGACAT 5215
                             v-  i i     v  i-  v       i      v           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_65647946_6   5216 TTCTGAAAAGAAGACATTTATGCAGCCAACAGAGGCATGAAAAAATGCTC 5265
                             vv        i  vi viii     i iivi        i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_65647946_6   5266 ATCATCACTGGCCAT 5280
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (140 / 101)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


2950 26.76 1.78 0.56  chrX_65656889_65660719     2442  3338 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65656889_6   2442 TAGAAAGATATCC-ATGTTCATAAATTAGAAGAATCAATATTGTTAAAAT 2490
                          i           -        ii   i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65656889_6   2491 GTCCATACTACCCAAGGCAATCTACAGATTTAACCCAACCACTATCAAAA 2540
                          v v     v     ivii           i   v   i v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65656889_6   2541 TATCAAGAACATTCTTCACAGAAATAGAGAAAATAATCCTGAAATTTATA 2590
                          vi  ivvi v  i  ii       v  v  iv i     i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_65656889_6   2591 TGGAACCATAAAAGATGCACTATATCCAAATCTATCACAAGCATAAAGAA 2640
                              viii  ii  iv  vv   v     v v   vii iv vi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_65656889_6   2641 AAAAGCTGGAGAAATCAAATTAACTGACT---AAGTTATACCACAGAGCA 2687
                         v    i     i v   v i vv ii i ---  ii -   i   i   v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_65656889_6   2688 ATAGTAACCAAAAAAGCACGGTACTGGAATAAAAATAGACACATAGACCA 2737
                          i     i   i v  iii        v    ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_65656889_6   2738 ATGAAACAGAATAGAAAACCCAGAAATAAATCTATACACCTACAATTAAC 2787
                            i  i     v  i ii           i i     ii  iii i  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_65656889_6   2788 TCATTTTCAAGAAAGATTTTAAGAGCATACATTAGAATAAGGACAATCTC 2837
                          v      i v  i i vii    v   v  v i iiv   i i i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_65656889_6   2838 TTCAACAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAA 2887
                                             v         ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_65656889_6   2888 ACTAGACCCCTATCTCTAGAC-ATATACAAA-------TCAAAATGAATG 2929
                         ii i        i   - v  -         -------        i  v
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTC-ACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_65656889_6   2930 AAAGACTTAA-TGCTAAGACCCCAAACTATGAACCTACTACAA-AAAACT 2977
                          ?    i   -  -     v iv       i  v  vi  v  -     v
  L1M4_orf2#LINE/    499 AWAGACCTAAATG-TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_65656889_6   2978 TTTGGGAAACTCTCCAGGACATGGAAGTGGACAAAAACCTTTTGAGCAAT 3027
                          vv ? v  v   i iv   v v iiv i i   viiii i  iiii vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_65656889_6   3028 ATCCCACAGACACAGGCAACAAAAGAAAAA-TAGAAAAATGAGATCATAT 3076
                          iv   v ii    i               -    v    vi  iivi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_65656889_6   3077 CAACATAAGAAGCTTCTGCACAGCAAAGGCAACAATCAACACAGTGAAGA 3126
                            v  v i  i   i  ii vv      vv  v     v v      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_65656889_6   3127 GACAATCCACAGAATGAGAGAAAAATATTTGCAAACTACCCATTTAACAA 3176
                              i          i       -          ii ivi  i i i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAA 746

  chrX_65656889_6   3177 GAGATCAACAACCAGAATATATAAGGAGCTTAAACAGTTCTATAAGAAAA 3226
                          i  iivii v             i  i  ivv   ii  v    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_65656889_6   3227 AAATATAATAATATTATTTTAAAATGGGCAAAAGATCTGAATAGACATTA 3276
                          i i -     iviv   ?v            i   i            v
  L1M4_orf2#LINE/    797 AGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_65656889_6   3277 CTC-AAAAAAGACATACAAATGGCAAAGAGGTATATGAAAAGGTGCTCAA 3325
                            -   i    i           v  v i i i        i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_65656889_6   3326 CATTACTGATCAT 3338
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (149 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


1162 29.76 3.41 0.98  chrX_65672646_65675574.rev     1279  1688 (1241)    L1M4_orf2#LINE/L1       18   437 (471)  

  chrX_65672646_6   1279 TTCATGGATTGGAAGACTCAGCATTATAAAGATGTCAGCTCTCCCCAAAT 1328
                                           i ii   i v      v  iiv          
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_65672646_6   1329 TAACAAATACATTTAACAGAATCTTAAGCAAAA----AG-TA--TTTTTG 1371
                          i ivv i v   i   iv    iiv v     ----  - i--     v
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_65672646_6   1372 ACCAAAATTTTCAAGCTTACTCTAAAAGTCATTTAGAA-TTCAAAAGGGC 1420
                         i vi     vv      v ii      v    v i   - v   ii iv 
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_65672646_6   1421 AAGAAATAACCAAGGCAATCTTTAA---GATGAACAAAGCTGGAAGACAT 1467
                         v    -  i    ii       v  ---  v        i    i   vi
  L1M4_orf2#LINE/    168 CAGAA-TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_65672646_6   1468 ATACTACCAGATTTCA---TTTTCTTTTACAAAGCTATGATAAATATGAC 1514
                          i   v  vi      ---i  v  ---         iii   vi v   
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACT---ACAAAGCTACAGTAATCAAGAC 263

  chrX_65672646_6   1515 TGTTTGATACTGGTTCAAGGATAAACAAACGGACCAATTGAGCATAATAT 1564
                         v  v  i      ivi       i   v ii  i    v  ii v   vv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_65672646_6   1565 AAAATTCAGAAACAGATCGACACATTTATAGTCAACTGATTTATGCTGAA 1614
                          i i i      i i i v i        i     i      vi vii i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_65672646_6   1615 GGTAACACTGCAGTGCAACAGAGAAATAATGATCTTTTAAATAAATGGTT 1664
                            iv  vvi vi v   ii i    v   ii      v  i       v
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_65672646_6   1665 TTATGTGAATTGGGTTGCCATATG 1688
                         i iv vv  i   i v?   i   
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATG 437

Transitions / transversions = 1.42 (71 / 50)
Gap_init rate = 0.02 (8 / 420), avg. gap size = 2.25 (18 / 8)  

 969 25.88 8.49 4.14  chrX_65672646_65675574.rev     1969  2451 (478)    L1M4_orf2#LINE/L1      405   908 (0)  

  chrX_65672646_6   1969 CAAA--GTGGTGGGATTACAGGTGTGAGCCACCATGCCCAACTGAAAACT 2016
                             --   v     iv  v  -i - ?    -    --  ---  i v 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGG-AT-AKCCAC-ATGC--AA---AAGAAT 446

  chrX_65672646_6   2017 ACATCTTAATTTCTA--TCACACCATAACTGAAAACCGACTCCAGATATA 2064
                         iv vi vi iii   --          vvii    iii    v i  iv 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_65672646_6   2065 T-ACAGATCTAAA-GTAAAGGGCAAAACAATACATCTTTTTAAA---AAC 2109
                          - ?   i     -    ii vi     v   v v  i  vi  ---   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_65672646_6   2110 AT----GTAAAACATTTTTATGACCTTGGAGTAGGCAAAGATTTCTAAAA 2155
                           ----     --- i  ii         iv       v i     v i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_65672646_6   2156 CAGGACAC-AAAAGCCCCATTCTTAAAGGTAAAATTTATCACACAAACTA 2204
                         i v     -      v v vivvi   i v    ---  - v i   i i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAA---AT-AGATAAATTG 639

  chrX_65672646_6   2205 AATT-----AAAATCAGGAACTTCTACTCTTTAAAAGATGTTATGCCAAG 2249
                         i i -----     i ii     i iiv   i   i  iii   --    
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT--CAAG 687

  chrX_65672646_6   2250 AGAG--AAAAGGCAACTCACCAACTTGGAGAGGATATTTGCAA----TAC 2293
                          i  --     i    i   vi v v     ii          ----  i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_65672646_6   2294 ATCCAGCAAAGGACTCATATGCAGAATATATAAATAACTTATACAAATTA 2343
                            iiii  i     ii   v             v    iv     v i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_65672646_6   2344 GTAC--AAAAGACAA-----CTTATTAGGAAAATAGACAAGAGACTTGAA 2386
                         i  v--         ----- iv   ?i-     i i   ii  i     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAA 836

  chrX_65672646_6   2387 --GATATTTGACTTAAATG----TATTCAAATACCCAATAAGCATATGAA 2430
                         --  i    --  iv  v ----   v     iv          i     
  L1M4_orf2#LINE/    837 TAGACATTT--CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_65672646_6   2431 G---TGCCCAGTTTCATTAGTAAT 2451
                         i---   i  iiv   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (80 / 42)
Gap_init rate = 0.05 (26 / 504), avg. gap size = 2.35 (61 / 26)  


2730 24.04 2.62 3.50  chrX_65683564_65686056.rev     1088  2002 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_65683564_6   1088 GAAAAAACATTCCATGCTTGTGGATAGGAATAATCAATATCATTAAAATG 1137
                          i   i i  i     i ii     v    v v i     ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_65683564_6   1138 TCTATACTGCCCAAAGCAATTTAAAGATTCAATGATACAAATAACACTA- 1186
                         v v     v      vii  i  v        i ---   - -- v   -
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACG---CAA-T--CCCTAT 95

  chrX_65683564_6   1187 CAAATAATCAAACTACAAATAACACTCCTCT-CAGAACTAGAAGAAAAAC 1235
                             - vi v i  i --------  ii i -     v v  v---  i 
  L1M4_orf2#LINE/     96 CAAA-ATCCCAGCTGC--------CTTTTTTGCAGAAATTGAC---AAGC 133

  chrX_65683564_6   1236 T-ATTTTAAAATTCATATGGAACAAACAAACAGCCCA-AATAGACAAGGC 1283
                          -  ii                - vi   ivii    -     v   ii 
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAAC 182

  chrX_65683564_6   1284 AGATCT-AAGCAAAAACAACAA-GCAGGAGGCATCACATTACTCAACTTC 1331
                          -    -i iv  i  v     - iv     vv     i v i   i   
  L1M4_orf2#LINE/    183 A-ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_65683564_6   1332 AAACTATACTACAGGGCTACAGTAATCTA-ACAGCATGGTACTGATACAA 1380
                            viv       ii            v -    ii        ii i  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_65683564_6   1381 AAACAGACAAATAGACCAATAGAACAGAATAGAGAGCACAGAAATAATTC 1430
                         ii i     v     i    i   i     v     iv         vi 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_65683564_6   1431 TGCACACCTACGGCCATCTGGCCTTCAACAAAGCTGACAAAAACAAGCAA 1480
                         iii   ii  i  i  vi  iii   i    i v  v   i v  vv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_65683564_6   1481 TAGGGAAAGGA----CTCCCCAATAAATGGTGCTGAGATAACTGTCTAGC 1526
                          i       i ----  iii   i           i  i     vv  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_65683564_6   1527 CGTAGGCAGAAGATTGAAAGTGAACCCCTTCCTTATACCATATACAAAAA 1576
                          ii v   i    v    iv  i      v   i i              
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_65683564_6   1577 TTAAATCAAGATGGATAAAAGACTTAAATGTAAAATCTAAATCTATACAA 1626
                             v    i      v ?    i         i v     v     -  
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AA 530

  chrX_65683564_6   1627 ACCCT-GGAAGAAGAGCCAGGACATACCATTTTG-GACATTTGAACT-GG 1673
                           i  -i      i vvi   ?-i  vvvi  i -   -i   iii -  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGN-GTAAATCTTCGTGAC-CTTGGGTTAGG 578

  chrX_65683564_6   1674 CAAAGATTT------TATGACAAAGATGCCAAAAGCAATTGCAACAAAAG 1717
                            v i   ------       ------         vvv          
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAACAAAAG 622

  chrX_65683564_6   1718 CAAAAATTGATAAATGGGA-TACAGTTAAACTAAAGAGCTTTTGTACAGC 1766
                         v      v       v   - v  viv   i    i -       i vv 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTC 671

  chrX_65683564_6   1767 AAAATAAACTATCAAACAGAGTAAACAGACAACCCACAGAATGGGAGAAA 1816
                            iv v        i- i   i  v                        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAG-AAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_65683564_6   1817 ATTTTTGCAAAGTGTACTTCTGA-AAAAGTCTAATATTCAGAATCTA-AA 1864
                           v        vii  iv     -  ii v  vi   i      v  -  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_65683564_6   1865 AGAACATAAACAAATTTGCATGCAAGAAG-CAAACAACTCCATTAAAAAG 1913
                              vivv    v ivii -ii  i   -    i   i v   ?    i
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_65683564_6   1914 TGGGCAAAGGACATGAACAGACGTTTTTCAAAAGAAGATATGCATGCAGC 1963
                                    iv    i    i   i  v           i  viii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_65683564_6   1964 CAACAAGCATATGAAAAAGTGGTCAACATCACTAATCAT 2002
                            i     i       ii  v         ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (134 / 82)
Gap_init rate = 0.03 (31 / 907), avg. gap size = 1.81 (56 / 31)  


3112 26.73 0.88 0.99  chrX_65690104_65693808.rev     2306  3214 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65690104_6   2306 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2355
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65690104_6   2356 GGCCATACTGCCCAAGGTAATTCATAGATTCAATGCCATCCCCATCAAGT 2405
                            v     v     iv i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65690104_6   2406 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2453
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_65690104_6   2454 TATGGAAC--CAAAAAACAGCCCCCATTGCCAAGTCAATCCTAAGCCAAA 2501
                                v--   iii  --  vvv  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_65690104_6   2502 AGAAGAAAGCTGGAGGCATCACACTACCTGACTTCAAACTACACTACAAG 2551
                             v    i      vv       v  ii i      vivi       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_65690104_6   2552 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 2601
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_65690104_6   2602 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACGTATCTACAA 2649
                                  i    i--    i  --        vv   iii  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_65690104_6   2650 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGAAT- 2698
                         ii vi    i  i     ivv  vv  i v  vv               -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_65690104_6   2699 -TCCGTATTTAATAAATGGTGCTGGGAAAACTGGCTTGCCATATGTAGAA 2747
                         -  -- v  i  i              v      v v?   i   i i  
  L1M4_orf2#LINE/    395 GTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_65690104_6   2748 AGCTGTAACTGGATCCCTCCCTTACACCTTATACAAAAATCAATTCAAGA 2797
                         iiv  v ii    i    v   i     v           i  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_65690104_6   2798 TGGATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGC 2847
                              i ?    i    ii v   v       i      vi i      v
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_65690104_6   2848 AAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 2897
                             v    ?i v viv   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_65690104_6   2898 CTAAAACACCAAAAGCAACGGCAACAAAAGCCAAAATTGACAAATGGGAT 2947
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_65690104_6   2948 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCCGAGT 2997
                         i v  i   v v  i i   i  ii vv    i  v    i  vvvi   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_65690104_6   2998 GAACAGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTG 3047
                            v  i         i             v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_65690104_6   3048 ACAAAGGGCTAATATCCAGAATCTATAATGAACTCAAACAAATTTACAAG 3097
                          i  i  i  vi          v     v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_65690104_6   3098 AAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATTAACAGACA 3147
                              i     i     v  i?    i     i     iv v  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_65690104_6   3148 CTTCTCAAAAGAAGACATTTGTGCAGCCAAAAAACACATGAAAAAAATGC 3197
                         i     v        i  viiviii     v  i          i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chrX_65690104_6   3198 TCACCATCACTGGCTAT 3214
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


 432 25.00 0.00 0.00  chrX_65702820_65704501.rev        1   100 (1581)  C L1M4_orf2#LINE/L1   (808)   100     1  

C chrX_65702820_6    100 TGAAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 51
                           i   v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_65702820_6     50 GACCAGGCTGCCAAAAGCAATCTACAAATTCAGTGCAATTTCTATGAAAA 1
                          i v vi  v  v   vii       i     ii     ii    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

Transitions / transversions = 1.27 (14 / 11)
Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.00 (0 / 0)  

2056 25.40 2.47 3.34  chrX_65702820_65704501.rev      502  1190 (491)    L1M4_orf2#LINE/L1      226   908 (0)  

  chrX_65702820_6    502 AATTT--AAACTATGCTATAAGGCCATAGTCACCAAAACAGCATGGTACT 549
                              --     - i   i  i  i i   v i   i    ii       
  L1M4_orf2#LINE/    226 AATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_65702820_6    550 GGCAAAAAAAAAATAAAAAAAATAAAAATAAATAGACCAGTGGAACAGAA 599
                             ---------   ii ---  i v   --    i  i     i    
  L1M4_orf2#LINE/    275 GGCA---------TAAGGA---TAGACATA--TAGATCAATGGAATAGAA 310

  chrX_65702820_6    600 TAGAGAACTCAGAAATGAATCCAAATACTTATA------TGATCTTTGAC 643
                          v    iii       i  i   v i i    i------    i  i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_65702820_6    644 TTAGCATACAAAAAC-ATAAAGTGGGAAAAGGACATCCTATTTAACAAAT 692
                         v-  vi i v  i  -  vv i    i    i i vi  v  i       
  L1M4_orf2#LINE/    361 A-AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_65702820_6    693 GCTGCTGGGATAATTGGCAAGCCACATGTAGGCAAATGAAACTGGATTCT 742
                          v        i  i   vv ?       i iivi      ii    ii i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_65702820_6    743 CATCTCTCACCTTATACAAAAATCAACCAAAGATGGATCATGAACTTAAA 792
                         i i   v    v           i   iv  i        ?ii  i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_65702820_6    793 TCTAACACCTGAAACTGTAAAAATTCTAGAAGATAACATTGGAAAAACCC 842
                          v   v v  i     i     v ii       v     v  ?iv  vi 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_65702820_6    843 TTCTAGACATTGGCTTAGGCAATAATTTTATGACCAAGAAACCAAAAGCA 892
                            vv   v    v         ii   iv iivi v  v          
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_65702820_6    893 AATATAATAAAAACGACGGGAAGTAGTTGAA----ACTTAATTAAACTAA 938
                         v vii  i    ivi ----  i   v i  ----    v  i   v v 
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAA----AAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_65702820_6    939 AGAGATTTTGCACAGCAAAAGGAACAGTCAGCAGAA---GAAACAGGCAA 985
                          i iv     ii vv    i iv  vi   --    ---    -  i   
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCA--AGAAAGTGAAA-AGACAA 702

  chrX_65702820_6    986 CCCACAGAGTGGGAGAAAGTCTTCACAATGTATACATCTGGAAAAGGACT 1035
                                 i         i v  ii   vvi   i     iv  i     
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_65702820_6   1036 AATATCCAGAATCAACAACAAACTCAAACAAAT-AGCAAGGAGAAAACAA 1084
                         vi          vv i  vi     vv    v - ii  vi i  i    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_65702820_6   1085 ACAATTCCATCAAAAAGTGGGCTATGGACATGAATAGACAATTCTCAAAA 1134
                          i  ii v  i?    i     v v   iv          v     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_65702820_6   1135 GAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCACT 1184
                                             i  i  i       i             ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_65702820_6   1185 AATGAT 1190
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.67 (107 / 64)
Gap_init rate = 0.02 (14 / 683), avg. gap size = 2.86 (40 / 14)  


2939 27.73 1.22 0.56  chrX_65720662_65727360     5309  6206 (493)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_65720662_6   5309 AAAAAATTCCAAGCTCATGGGTAGGAAGAATTAATATCATGAATATGGCC 5358
                           i v  i   v i      i v      v       ii v  v     v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_65720662_6   5359 ATACTTCCTAAAGTAATTTATAGATTCAACGCTATCCTCATCAAGATAAC 5408
                              i  i   v i  i  i           v    ii     i  vv 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_65720662_6   5409 ATTGAATTTCTTCATAGAATTAGATAAAACT-ACTTTAAATTTCATATGG 5457
                          vivivi  i  iii    v v  i  i-  - iii    v         
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGG 153

  chrX_65720662_6   5458 AACCAAGAAACAGACC--GTATAGCCAAGACAATCCTTAGCAA-AAGAAC 5504
                           -- v v  vi    -- v        i      i v iv  -      
  L1M4_orf2#LINE/    154 AA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_65720662_6   5505 AAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATGCTACAAGGCTAC 5554
                             i      vv   ii  v  ii i      viv i      i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_65720662_6   5555 AGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGGCCAAT 5604
                              i   i    ii         i iv ii i   i      ii    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_65720662_6   5605 AGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCTG 5654
                         i   i    iv   ivii         vv   i    i  iiii  vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_65720662_6   5655 ATCTTTGACAAAGCTGACAAGAACAAGCAATGGGGAATGGATTCCCTATT 5704
                           i  i     i v  v     v  vv          v i  vvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_65720662_6   5705 TAATAAATAGTGTTGGGAAAACTGTCTAGTCATATACAGAAAACTGAAAC 5754
                         i  i    i   i     v     vv  ?i  i  i  i  i v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_65720662_6   5755 TGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATTGATTAAA 5804
                                  v   i     v                   i  v   i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_65720662_6   5805 GACTTACATGTGAGACCTGAAATTATAAAAAACCCTAGAAGAAAACCTAG 5854
                            i  v    i   v  i   i       v-i i           v   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACATAG 550

  chrX_65720662_6   5855 GCA-ATACCATTCAGGACATAGGCATGGGCAAAGTCTTCATGACTAAAAT 5903
                          ?i- v i -   iv   v v  vv i     v vi   v iiv  vi i
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_65720662_6   5904 ACCCAAAGCAATGGCAACAAAAGACAAAATTGACAAATCAGACCTAATTC 5953
                            v      vvi           v     v  i    ii   i v  iv
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_65720662_6   5954 AACTAAAGAGCTTCTGCACAGCAAAAGAAGCTGTCATCAGAGTGAACAGG 6003
                           v v  i i   i  ii vv    i  vi  i   vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_65720662_6   6004 CAACCTACAGAACAGGAGAAAATTTTGGCAATCTCTCCATCTGACAATGG 6053
                              i      ii         v  v    viiv vi      i  v  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_65720662_6   6054 GCTAATAGCCAGAATCTTCAAAGAAA----AAAAATTTACAGGAAACAAA 6099
                         i  vi  v       v vi      v---- v  v iv i iv   v i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_65720662_6   6100 CAAACAGCCCCAT-AAAAAGTGGGTGAAGGATATGAA-AGACACTTCTCA 6147
                             i i   v  -?    i    ii      v    -     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_65720662_6   6148 AAAGAAGACATTTATGCAGCCAATAAACATATGAAAAAAAGCTCATCATC 6197
                                 i  vi viii        i  i       i v     v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_65720662_6   6198 ACTGGTCAT 6206
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.01 (11 / 904), avg. gap size = 1.45 (16 / 11)  


1428 26.28 1.78 4.55  chrX_65738800_65742325.rev     1897  2402 (1124)    L1M4_orf2#LINE/L1        1   492 (416)  

  chrX_65738800_6   1897 TGAAAATATAGTCTATGTTCATGGACTTGAAGAAATAACAT-ATTAAAAT 1945
                           i   v   vi i           i v     vv   i  -i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65738800_6   1946 AACCATACTACCCAAAACAATCTACAGATTCAATGCAATCGCTATCAAAC 1995
                         ii v     v      vii              i      v        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65738800_6   1996 TACCAATAACATTCTTCACAGAAATAGAAGAAAAACATTTCTAAATTTC- 2044
                          v   iivi v  i  ii       v  v--  iviiv i     v   -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chrX_65738800_6   2045 T-TGAAACTACAAAAGACACTGAATAGCCTTAGAAATCCTGAACAAAAAA 2093
                          -  i  v i   ii   v v        vv iv    i    -   i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAA 197

  chrX_65738800_6   2094 CAAACAAACAAAAACAAAACAAAGGTGGAGGCATCGCATTACCAGGTATC 2143
                         ----------------i       v      vv  i  i v  vii v  
  L1M4_orf2#LINE/    198 ----------------GAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_65738800_6   2144 AAAATATATTATAAAGCTATAGTAACTACAACAGCACAGCACTGTCATAA 2193
                             iv  i  i       i     ii vi    iiii i    v     
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_65738800_6   2194 AAAAACCAGACATA--GGCCAACAAAATAAAATACAGAACCCAGAAATAA 2241
                         ii ---i       -- ii   iii    i   vv   ii          
  L1M4_orf2#LINE/    282 GGA---TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_65738800_6   2242 ACCCATGTAGTTACTACTAAATGACTTTCGAAAAAGGTGTCAAGAACCTT 2291
                               ii v   iviii  v   i      v  i    i     v v  
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_65738800_6   2292 CATTAGGAAAAAGACAGTCTCTTCAATAAATGGTGCTGAAA-AATTGGTT 2340
                           v i  i   ii i     i     i           ii -  i   v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_65738800_6   2341 ATCCACACATAGAAAAAATGAAACTAGACC--TACCTTTTACCTTATA-A 2387
                          ?     iii -   i      ii i    --     ivi   v    - 
  L1M4_orf2#LINE/    429 AKCCACATGCA-AAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_65738800_6   2388 AAAATCAATTCAAAA 2402
                              i  i      
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAA 492

Transitions / transversions = 1.93 (87 / 45)
Gap_init rate = 0.02 (12 / 492), avg. gap size = 2.67 (32 / 12)  

 928 23.91 4.04 3.42  chrX_65738800_65742325.rev     2735  3056 (470)    L1M4_orf2#LINE/L1      585   908 (0)  

  chrX_65738800_6   2735 TTTTATAAATATGACCTCAAA-GCACAGGCAACAAAAACAAGAATAGACA 2783
                            iv  i       vi    -     i         iv  i      i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_65738800_6   2784 AATAGAATTCTATCAAA-CTATAAGTTTTCTTCACTACAAAGAAAACAAT 2832
                            v i i ii      -i  v  ii   iv -i  v     i v  v  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGT-GCTTCAAAGGACACTAT 683

  chrX_65738800_6   2833 CATTAGAGTGGAGA----------AGAATGAAAGAAAATGTTTGCAAACT 2872
                           vv i    i i ----------      ii       i        ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_65738800_6   2873 ATTCATTCAACAAGGTAGTCATATCCAGAATATAGAAGGAACTCAAACAA 2922
                           vi  iii i    v v ii             v  i      vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_65738800_6   2923 TTCCAAAGCAAATAATAATAATAATTCAATTTAAAA-TGGGCAAGTAATC 2971
                         i  v v ii   -  v vv     ii     ?    -       ivi  i
  L1M4_orf2#LINE/    784 CTCAATAATAAA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_65738800_6   2972 TGAATGGACATTTCTCTAAAGAAGACATCCAAATGGACAACAAATATATG 3021
                              i          i        i  v       v   i  ii i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_65738800_6   3022 AAAAAAAAAAAAACCTCTTCAACATCATTAATCAT 3056
                             i --------- vi         ????????
  L1M4_orf2#LINE/    883 AAAAGA---------TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (50 / 26)
Gap_init rate = 0.02 (7 / 324), avg. gap size = 3.43 (24 / 7)  


2931 19.13 2.17 2.90  chrX_65757851_65759754.rev      502  1191 (713)    L1M4_orf2#LINE/L1      144   828 (80)  

  chrX_65757851_6    502 ATTCATGTGAGAATTCAAAAGAGCCAGCATAGCAAAAACAACTTTAAAAA 551
                               i  ii   v   ii  v    v     v       ii  i    
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_65757851_6    552 AGAAAAA--ATTTTTGAGGACTCACACTTCTTGATCTCAAAACATGCTAC 599
                             i  -- vv  v               iii  i       v i    
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_65757851_6    600 AAGGTTAAAGTAATCAAAACGTTGTGATTCTGGTTTAAGATTTGACATAT 649
                           i i  v         i  iv    i v    iv    iv v       
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_65757851_6    650 AAATCAGTGGAACACAGTTGACAGAGTCCAAAAGTAAGCTCTTACACTTA 699
                          i    i     i v i    --       i  i   i i v    i   
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGA--GAGTCCAGAAATAAACCCATACATTTA 341

  chrX_65757851_6    700 AGAACAGTTGACTTTCAGCAAAGGTGCAAAGACTATTGAAGGTAAAAAGA 749
                         v iv  i    i    ii   i     v     i   v  v vii     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_65757851_6    750 ATAGTCTTTT-GATA--TGTGTGCTGGGACAACTGGATATTTACTTGCAA 796
                                   -i i --  -                   ?ii  v     
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATG-GTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_65757851_6    797 AATAATAAATTTGGATCTATACCTTACACCATACACAAAAATTAACTCAA 846
                           v   i  v     i iv     i        i                
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_65757851_6    847 AATGGATCAAATACCTAAATGCAAAAGACTTCAGTGATAGAAAATAAAAC 896
                                  ? v         i  i  -  ---------------     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAG-CT---------------AAAAC 524

  chrX_65757851_6    897 AATAAA-CTCTTAGAAGAAAATATAGGTGTAAATATTTGTGTCCTTACAT 945
                         v     -              i     ?      v  i   v    ivi 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_65757851_6    946 TAAGGAATAGTTTCTTAAATATGACACCAACAGCACAA----CTGAAAAG 991
                           i v   i        i            v       ---- vi  i i
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_65757851_6    992 TAAACAGATAAACTTTATATAATCAAAATTAAAGATGTTTGTGTTTAAAA 1041
                         v   i       i vv iv v            i iv      i  v   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_65757851_6   1042 GGGCACCATCAAGAAAGTGTAAAGGTAACCCACAGAATGC-AGAAAAT-T 1089
                           i   i            v    ii             v-       - 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_65757851_6   1090 TTGAAAATCATACATCTGATAAAAAAACTTGTAACTA-AATACATAAAGA 1138
                            v        i         iii -      v i -    i       
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGA-CTTGTATCCAGAATATATAAAGA 773

  chrX_65757851_6   1139 ACTTTGAAAATTCAACAATAAAAAGACAAATAATTCAAT--ACAAATGGG 1186
                            i v v  i    i                 ii    -- v       
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_65757851_6   1187 CAAAG 1191
                              
  L1M4_orf2#LINE/    824 CAAAG 828

Transitions / transversions = 1.69 (81 / 48)
Gap_init rate = 0.02 (14 / 685), avg. gap size = 2.50 (35 / 14)  

 403 18.68 0.00 0.00  chrX_65757851_65759754.rev     1323  1413 (491)    L1M4_orf2#LINE/L1      818   908 (0)  

  chrX_65757851_6   1323 AATAGGAAAACACTTTGAGTAGACAATTATCTATGGAACATATTTAAATG 1372
                            i  v   viv     i      v  v  i vi   v    vi     
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_65757851_6   1373 CCCAATAAGCATATAAAAAGATGCTCAACATCATTAGCCAT 1413
                         v          i  i                  ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.89 (8 / 9)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.00 (0 / 0)  

 504 29.01 0.00 0.00  chrX_65757851_65759754.rev     1743  1904 (0)    L1M4_orf2#LINE/L1      473   634 (274)  

  chrX_65757851_6   1743 ATACAGAAATCAATTCCAGATGGATCAAGGACTTAAATCTAAGACCTGAA 1792
                              i    i  i  v i        ?i   i     v     v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_65757851_6   1793 ACTATAGAAATTCTAGAAAATAACATTAGAAAAACCCTTCTAGACATTGG 1842
                               i  v ii     i v     vi ?iv  vi    vv   v    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_65757851_6   1843 CTTAGGCGAGGATTTTATGACCAAGAACCCAAAAGCAAATGCAATAAAAA 1892
                         v      i v i   iv iivi v  vv         v v    i    i
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_65757851_6   1893 CAAAGATAAATA 1904
                         v   i   i   
  L1M4_orf2#LINE/    623 AAAAAATAGATA 634

Transitions / transversions = 1.14 (24 / 21)
Gap_init rate = 0.00 (0 / 162), avg. gap size = 0.00 (0 / 0)  


2339 26.99 1.70 5.21  chrX_65764165_65770082.rev     4487  5427 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65764165_6   4487 TGGAAAAAAACGTTTTTCATGCTCATGGATAGGAAGAATCAATTTCATGA 4536
                               i v ---- ii    i        v      v i   v ii v 
  L1M4_orf2#LINE/      1 TGGAAAGATA----TCCCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chrX_65764165_6   4537 AAGTAGTCATACTGCCTAAAGTAATTTTTAGATTCAAATCTATCCCCATC 4586
                          ii i iv     v  i   v i  i vi        vv v     i   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_65764165_6   4587 AAGCTACCA-TTGACTTTCTT-CACATAATTAGAAAAAACT-ACTTTAAA 4633
                           iv v   -i  v    i  -  v -    i-- v  i  - iii    
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAA 143

  chrX_65764165_6   4634 TTTCATATGGAACCAAAAAAGAGCCCGTATACCCAAGACAATCCTAAGCA 4683
                         v           viiv  ii  v  v v   v    i      i i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_65764165_6   4684 AATAGAACAAAGCTGGAAGCAC-CATGGTACCTGACTTCAAACTATACTA 4732
                          iv         i    i -  -  iiv v  ii i      viv     
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_65764165_6   4733 AAAGGCTACAGTAACCAAAAGAGCATGTTATTGATACCAAAACAGATATA 4782
                         v  i          i   i v  ii  v  i  ii iv ii i   i   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_65764165_6   4783 TACACCAAATGAAACAGAACAGAGACCCCAGTAATAACACCACACATCTA 4832
                           v i   -  i  i    iv    vi    v     vv   i    i  
  L1M4_orf2#LINE/    293 TAGATCAA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_65764165_6   4833 CAACCATCTGATCTTTAACAAACCTGACAAAAACAATCAATGGGGAAAAG 4882
                         iiii  vi    i  ii    ivv  v   i v  v            ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_65764165_6   4883 AT--TCCACAGTTAACAAGTGGTGCTGGGAAAACTGGCTAGCCATATGCA 4930
                           --  ivi-- i     i           v      v  ?   i     
  L1M4_orf2#LINE/    392 ATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_65764165_6   4931 GAAAACTGAAACTGGACCACTTCCTTATACCTGATACAAAAATCGACTCA 4980
                         i  i v    ii      v  v   i i   vv          ii     
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_65764165_6   4981 AGATGTATTAAAGACTTGTAAATGTAAAGCCCCAAACCATAAGCCACTTG 5030
                          i   v  i ?    i ---------------------------------
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCT--------------------------------- 506

  chrX_65764165_6   5031 TAAATATAAAACCCAAAACCATAGAAACCTTAGAAGAAAACCTAGGC--- 5077
                         -    i   i v i     i   i  vi             v    ?---
  L1M4_orf2#LINE/    507 -AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_65764165_6   5078 AATTTCATTCAGGACATAGGCACAGGCA--GACTTCATGACTAAAACACC 5125
                            i ---  iv   v v  vvi     -- ii   v iiv  vi     
  L1M4_orf2#LINE/    556 AATCT---TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_65764165_6   5126 AAAAGCAATTGCAACAGAAGCCAAAATTGAAAAATGGGATCTAATCAAAC 5175
                                vvv      i   vv     v  v    v   ii v      v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_65764165_6   5176 TAAAGAGCT---GCACAGCAAAAGAAACTATCATCAGAGTGAACAGGTAA 5222
                          v  i i  --- ii vv    i  v       vv i      v  ii  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_65764165_6   5223 CCTACAAAATGGAAAAAAAAAT--GACAATCTATCCATCTGACAAAAGTC 5270
                           i   i     i i    v  -- vv    -  vi      i  ii v 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGGGAC 751

  chrX_65764165_6   5271 TAATATCCAGAATCTACATGGAATTTAAACAAATTTACAAGAAAAAGACA 5320
                          vi          v  i vi   i ivv    v iv i  v         
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_65764165_6   5321 AACAACCCCATCAAAAAGTGGATGAAAGATATGAACAGACACTTCTCAAA 5370
                           i     v  i?    i   iii  i   v    i     i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_65764165_6   5371 AGAAGACATTTATACAGCCAACAAACATATGAAAAAAAGCTCATAATCAC 5420
                               i  vi v ii     i  i  i       i v     vv    ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_65764165_6   5421 TGGTCAT 5427
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.40 (146 / 104)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.61 (65 / 18)  


 708 26.44 2.40 0.96  chrX_65773181_65777803.rev     2905  3112 (1511)    L1M4_orf2#LINE/L1        1   211 (697)  

  chrX_65773181_6   2905 TGGAAATATATTCCATTGTTCTTGGATTGAAA----TAATATTGTTAGAG 2950
                               v    i    -    v       i  ----           iii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_65773181_6   2951 TGTCCATATTCCTCAAAGAAATCTACAGATTCAATACAATCCCTATCAAC 3000
                           v v   i   i    vvi              ii             v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_65773181_6   3001 ATACCAATGACATTCTTCATAGAAATGGA-AATAAAATCCTAAAACGTAT 3049
                           v   iivi v  i  iii      v  -  vvvi         ivi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_65773181_6   3050 ATGAAAGCCCAAAAGGCCCAGAACAGGCAAAGATATCCTAAAGAAAAAAA 3099
                            i  iiv   ii i       i  v    ivv   i i  -   i  i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAG 198

  chrX_65773181_6   3100 AAAAAAACTGGGG 3112
                           v   ii   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAG 211

Transitions / transversions = 1.75 (35 / 20)
Gap_init rate = 0.02 (4 / 211), avg. gap size = 1.75 (7 / 4)  

2119 26.26 2.11 1.40  chrX_65773181_65777803.rev     3422  4133 (490)    L1M4_orf2#LINE/L1      192   908 (0)  

  chrX_65773181_6   3422 AAAAAATAACAAAACTGGAAGAATCACATTACTTGATGTCAAATTATACT 3471
                            i  v      ii    i  v     i v iii  v     viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_65773181_6   3472 ACAGAGCTCTAGTAA-AAAAACAGCATAGTACTGGCACGAAAACAGACAC 3520
                            i    vi     -v  i    ii i         ii ii i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_65773181_6   3521 GTAGTCCACTGGAACAGAATCAA-AGTCTCAGAAGCAAATCTACACACTG 3569
                         i   vi  v     i     ii -    -     ii   i i i   i v
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTT 340

  chrX_65773181_6   3570 ACCATGAACTCATTTTCAACAAAGGTTTCAAAAACATACACTGGGGAAGA 3619
                          ivi v  i v      i    i   vi   i v   v  v       ii
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_65773181_6   3620 TACAGTATCCTCAATAAATGTTGCTGGGGAAACTGGATATAAATATGCAG 3669
                         v i   v ii    i     v       iv         ?vv i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_65773181_6   3670 AACAATGAAACTAGTCCCCTATCTCTCACCATATACAAAACTGAAATGAA 3719
                           v      ii i v      i   v              v v  v v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_65773181_6   3720 AATGGATTAAAGACCTAAGTCTAAGTCTTCAAACTATAAAACTACTACAA 3769
                                i ?        i v    vvi v             vi  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_65773181_6   3770 GAAAATATTTGGGAAACTCTGCAGGAAATTAGACTGTGCAAAAATTTCTT 3819
                              i  vv ? v  v   v iv  vv  i ii iv    vii      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_65773181_6   3820 CAGCAAT-AC-CCACAATCA-AGGCAACCAAAGCAAAAATGAACAAATGG 3866
                         -  vv  -  -   v  v  - i     v    v      ii i    v 
  L1M4_orf2#LINE/    591 -AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_65773181_6   3867 GATCACATTAAG-TTAAAACGCTTCTGCACACCAAAGGA-------AAGA 3908
                           iiv   i  i-      -i   i  ii vi       -------    
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_65773181_6   3909 A-GCGAAGAGACAACATACAGCATACAGAATGGGAGAAATTATTTCTAAA 3957
                          - i   i       ------ -i               v     vi   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAAC------C-CACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_65773181_6   3958 CTACCCATCTGACAAGGGATTAATTAACATAATATATAACGAGCTCAAAC 4007
                         ii ivi      i      i vi vvv  v         v  i   vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_65773181_6   4008 CAATCTATAGGAAAAAATCTAATAATACACTCAAAAAATGGGCAAAAGAT 4057
                         v v  v   iv     iv v     iv  v i?             i   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_65773181_6   4058 TTGAAAAGAAATTTCTCAAAAGAAAACACACAAATGTAAAACAGGCATAT 4107
                              v   v       v      i i i       vvv  i i   i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_65773181_6   4108 GAAAACGTGCTCAACAT-AGTTGATCA 4133
                              vi          - ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (101 / 82)
Gap_init rate = 0.02 (14 / 717), avg. gap size = 1.79 (25 / 14)  


3033 27.01 1.10 0.99  chrX_65785501_65787422      523  1429 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65785501_6    523 TGGAAACACATTCCATGCTTATTGATAGGAACAATCAATATCATGAAAAT 572
                               v i  i     i i  v   v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65785501_6    573 GGCCATACTGCTCAAAGTAATTTATAGATTCAATGTGATCCCCATCAAGC 622
                            v     v i    v i  i  i        i ii     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65785501_6    623 TAC-AATTGACTTTCTTCACAGAATTAGGAAAAAAAAAC--ACTTTAAAT 669
                          v - ii  v    i  -i     v v ----- v  i -- iii    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG-----ACAAGCTGATCCTAAAA 144

  chrX_65785501_6    670 TTCATACAGAACCAAAAAAAGAGCCCATA-TAACCAAGACAATCCTAAGG 718
                               ii   -- viv  i ii    v -  i    i      i i ii
  L1M4_orf2#LINE/    145 TTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_65785501_6    719 AAAAATAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTA 768
                           i  v       i      vv       v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_65785501_6    769 CAAGGCTATAGTAACCAAAGCAGCATGGTACTGGAACCAAAACAGATATA 818
                            i    i     i   ii   ii         v iv ii i   i   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_65785501_6    819 TAGACCAATGGAACAGAAC-GAGGGCTCAGAAATAACACCACACTTCTAC 867
                             i        i    i-   i ii         vv   i  v i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_65785501_6    868 AACCATCTGATCTTTGACAAACCTGACAAGAAAGGGCAATGGGGAAAGGA 917
                         iii  vi    i  i     ivv  v     vvivv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_65785501_6    918 TTCCCTATTTAATAAATGGTGTTGGGAAAACTGTCTAGCTATATGCAGAA 967
                          vvi  v  i  i        i     v     vv  ? i i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_65785501_6    968 AACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGG 1017
                         i v    ii         v   i     v                   ii
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_65785501_6   1018 TGGATTAAAGACTTAAA-GTAAGACCTAAAATCATAAAAACCCTAGAAGA 1066
                              i ?    i    -      v      ii      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_65785501_6   1067 AAACCTAGGCA-ATACCATTCAGGACATAGGCAT-GGAAAAGACTTCATG 1114
                             v    ?i- v i -   iv   v v  vv -  v  v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_65785501_6   1115 ACTAAAACACAAAAAGTGATGGCGATAAAAGCCAGAATTGACAAATGGGA 1164
                         iv  vi    v     iivvi  i i     vv i   v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_65785501_6   1165 TCT-ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAG 1213
                         ii -  i   v v  i i   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_65785501_6   1214 TGAACAGGCAATCTACAGAATGGGAGAAAATGTTTGCAATCTATCCATCT 1263
                             v  i   i i                 i       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_65785501_6   1264 GACAAAGGGCTAATATTCAGAATCTACAAGGAACTTAAACAAATTTACAA 1313
                           i  i  i  vi   i      v  i  i     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_65785501_6   1314 GAAAAAAACAAACAACCTCATC-AAAAATGGGCAGATGATATGAACAGAC 1362
                         v     i     i    iv  i-           i v   v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_65785501_6   1363 ACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACACATGAAAAAAAGC 1412
                          i     v        i  vi viii     i  i          i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_65785501_6   1413 TCATCATCACTGGTCAT 1429
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


3061 28.32 1.00 0.55  chrX_65792155_65798531.rev     4983  5886 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65792155_6   4983 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5032
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65792155_6   5033 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5082
                            v     vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65792155_6   5083 TACTGATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5130
                          v iiiivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_65792155_6   5131 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5180
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_65792155_6   5181 AACAAAGCTGGAGGCATCACACTACTTGACTTTAAACTATACTACAAGGC 5230
                                i      vv       v iii i  i   viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65792155_6   5231 TACAGTAACCAAAAGAGCATGGTACTGTTACCAAAACAGAGATATAGATC 5280
                                 i   i v  ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_65792155_6   5281 AATGGAACAGAAC--AGAACCCTCAGAAATAATGCTACATATCTACAACT 5328
                                i    i--   ii  --        vv i i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_65792155_6   5329 ATCTGATCTTTGACAAACCTGACAAAAACAAACAATGGGGAAAGGATTCC 5378
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_65792155_6   5379 CTATTTAATAAATGGTGCTGGGAAAAGTGGCTAGCCATATGTAGAAAGCT 5428
                           v  i  i              v  v   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_65792155_6   5429 GAAACTGGATCCCTTCCTTACACCTGATACAAAAATTAATTCAAGATGGA 5478
                            ii    i    v   i     vv             i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_65792155_6   5479 TTAAAGACTTAAATGTTAGAACTAAAACCATAAAAACCCTAGAAGAAAAC 5528
                          i ?    i       v   i       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_65792155_6   5529 CTAGGCA-ATACCATTCAGGACATAGGCATGTGCAAGGACTTCATGTCTA 5577
                         v    ?i- v i -   iv   v v  vv iv    v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_65792155_6   5578 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATGAATGGGATCT- 5626
                         vi            vvi          vv     v   i   v   ii -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_65792155_6   5627 ---AAACTCAGGAGCTTCTGCACAGCAAAAGCGACTACCATCAGATTGAT 5673
                         ---   v i ii i   i  ii vv    i vv    i  vv i v   v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_65792155_6   5674 CAGGCAACCTATAAAATGGGGGAAAATTTTTGCAATCTACTCATCTGACA 5723
                         v  i     i i i      i      v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_65792155_6   5724 AAGGGTTAATAGCCAGAATCTACAAAGAACTCAAACAAATTTACGATAAA 5773
                          i  ii vi  v       v  i         vv    v iv ii     
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_65792155_6   5774 TAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATAAACAGACACTT 5823
                         v i     i     v  i? v  i    ii      v i  i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_65792155_6   5824 CTCCAAAGAAGACATTTATTCAGCCAACAGACACACGAAAAAATGCTCAT 5873
                                     i  vi vvii     i ii    i     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_65792155_6   5874 CATCACTGGCCAT 5886
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (155 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2765 28.46 1.11 0.55  chrX_65813752_65815848.rev      704  1606 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65813752_6    704 TGAAAACACATCTTATGTTCATGGATGCATAGAATCAATATTGTGAAAAT 753
                           i   v i   ii            vviv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65813752_6    754 GACTGTACTGCCAAAAGCAATCTACAAATTTAATGCAATTCCCATCAAAA 803
                          i vi    v  v   vii       i   i  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65813752_6    804 TAC-AACGATTATTTTTTACAGAACTAGAAAAAAATAATCCTAAAATTCA 852
                          v - i viii-      i     v v  v  iv- i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chrX_65813752_6    853 TATGGAACCAAAAAAGAGCCTGCATAGCCAAAACAAGATGAAGCAAAAAG 902
                                viiv  ii  v  v v             vv vi iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_65813752_6    903 AACAAATCTGGAGGCATCACATTACCTGACTTCAAATTATACCATAAGGC 952
                               vi      vv     i v  ii i      viv   i i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65813752_6    953 CATAGTCACCAAAACAGCATGGTAGTGGTATAAAAATAGGCACATCAACC 1002
                         i i   v i   i    ii     v   i    ii    i  i  vi i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_65813752_6   1003 AATAGAGCAGAATAGAGAACCCAGAAATAAACTCAAA----TACGATCAA 1048
                            i  ii     v    ii            i  v ----  i i    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_65813752_6   1049 CTGGACTTTGAAAAAGCAGC---AACAATGAAGTTGGGAAAGGGCACCCT 1095
                         i  ivi  i  v  i vv  ---i  v  vv i v       iii vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_65813752_6   1096 ATTCAACAAATACTGCTGGGATAATTGGCAAACCACATGTAGAAGAAAAA 1145
                         v          iv        i  i   vv ?       i i     vi 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_65813752_6   1146 AATTGGATCCTCATCTCTCACCTTATACAAAAATTAACTCAAGGTGGATC 1195
                          i     i  ii i   v    v                   ii      
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_65813752_6   1196 AAAGACTTAATTTTAAGACCTGAAACCATAAAAATTCCATAAGATAACAC 1245
                          ?    i   v v     v  i    i      v iii v    v    i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_65813752_6   1246 CAGAAAAACCCTTTTAGACATTGGTATAGGCAAAAACTTTATGACCAAGA 1295
                         vi ?iv  vi   ivv   v    vv       viii  iv iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_65813752_6   1296 ACCCGAAAGCAAATGCAACAAAACAATGA-TGAATAGATGGGACTTAATT 1344
                         vv  i      v v         v  vi - ii   i  v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_65813752_6   1345 ACA-TGAAAAAGCTTTTCCACAGCAAAAAAGATAATCAGCAGAGTAAACA 1393
                          v - v     -     vii vv    ii v iv    iv i   i  v 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_65813752_6   1394 GACAAACCACAGAGTGGGAGTAAATCTTTGCAATCTATACATCCATCAAA 1443
                              v       i      v    v       vii   i   iivi  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_65813752_6   1444 GGACTAATGTCCAGAGTCTACTAAGAACTCAAACAAATTAGCAAGAAAAA 1493
                              vi i      i v  iv        vv    v i ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_65813752_6   1494 CAAACAAACAATTCCATAAAAAAGTGGGTTAGGAATATAAATAGACAATT 1543
                         --i     i  ii v  v?    i    iv i i  v i        v  
  L1M4_orf2#LINE/    798 --GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_65813752_6   1544 CTCAAAAGAAGATTTACAAATGGTCAAGAAACATATGAAACAATGCTCAG 1593
                            v         v         i   v  i  i      vi       i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_65813752_6   1594 CATCACTAATAAT 1606
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (145 / 108)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2837 27.23 0.95 0.95  chrX_65840834_65846579     4413  5253 (493)    L1M4_orf2#LINE/L1       68   908 (0)  

  chrX_65840834_6   4413 TAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTC 4462
                          i  i  i        i  v     i     iv v   iivi i  i  i
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_65840834_6   4463 ACATCA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAAGA 4510
                         i  vv -   -- v  i  - iii    i           viiv  ii  
  L1M4_orf2#LINE/    118 GCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_65840834_6   4511 GCCCACATCACCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCAT 4560
                         v  viv  vi    iv     i i ivv i          i      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_65840834_6   4561 CACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAG 4610
                               v  ii i      viv        i          i   i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_65840834_6   4611 CATGGTACCGGTACCAAAACAGAGATATAGATTAATGGAACAGAAC--AG 4658
                         ii      i  i iv ii i   v        i       i    i--  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_65840834_6   4659 AGCCCTCAGAAATAACGCCACATATCTACAACTATCTGATCTTTGACAAA 4708
                           i  --        vv   i i  i  iiiii vi    i  i     i
  L1M4_orf2#LINE/    316 AGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_65840834_6   4709 CCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTG 4758
                         vv  vv  i v  vv            i  vvi  v  i  i        
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_65840834_6   4759 CTGGGAAAACTGGCTAGCCATATGTAGAGAGCTGAAACTGGATCCCTTCC 4808
                               v      v  ?   i   i i iiiv    ii    i    v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_65840834_6   4809 TTACACCTTATACAAAAACTAACTCAAGATGGATTAAAGACTTAAACGTT 4858
                          i     v          i        i      i ?    i    i  v
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_65840834_6   4859 AGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCACTACCATTCA 4908
                            v       i      vi i           v    ?iiv viv   i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_65840834_6   4909 GGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGG 4958
                         v   v v  vv i     v ii   v ivv  vi            vvi 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_65840834_6   4959 GAACAAAAGCCAAAATTGACAAATGGGACCTAATTAAACTAAAGAGCTTC 5008
                         v        vv     v  i    v    i v  i   v v  i i   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_65840834_6   5009 TGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAACATG 5058
                           ii vv    i  v    i  vv i      v  i     i   iv   
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_65840834_6   5059 GGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAA 5108
                                  v  i    vii ivi      i  i  i  vi         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_65840834_6   5109 TCTACAATTAACTCCCACAAATTTACAAGAAAAAAACAAACAACCCCATC 5158
                          v  i  vv     ii    v iv i  v     i     i     v  i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_65840834_6   5159 AAAAAGTGGGTGAAGGACATGAACAGACACTTCTCAAAAGAAGACAATTA 5208
                         ?    i    ii     iv    i     i     v        ----  
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA----TA 859

  chrX_65840834_6   5209 TGCA----GCCAAAAAACATATGAAAAAATGCTCACCATCACTGGCCAT 5253
                          i  ----     v  i  i       i       v     ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.01 (7 / 841), avg. gap size = 2.29 (16 / 7)  


1882 25.34 6.38 0.50  chrX_65849344_65850912      481  1076 (493)    L1M4_orf2#LINE/L1      278   908 (0)  

  chrX_65849344_6    481 ATAATGATAAACAAGT-GATCTAATGGAACATAATAAAGA-TCACAGAAA 528
                             v    i   vi -    -       i v   vi   -  -      
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATC-AATGGAATAGAATTGAGAGTC-CAGAAA 325

  chrX_65849344_6    529 CAAATCTCCACCCCTACACTAAACTCATTTTTGACAAAAGAGCCAAGAAC 578
                         i   i ivi  vii  iiv v  i v     i     ii v       v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_65849344_6    579 ATACACTAGGGAATCAACATTCTCTTCAATAAATGGTGCTGAGAAAACTG 628
                           v  v i     vv  i v   i     i           i  v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_65849344_6    629 GATATCCATATGAAGAAGAATGAAACTAGACCCCTGTCTCTTACCATATA 678
                             ?   i   v i         ii i       ii   vi        
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_65849344_6    679 CAAAAATCAAACTAAAATGGATTAAATACTCACATCTAAGACCTCAATCT 728
                                i  vii         i ? v  ii v  v     v  v  v  
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_65849344_6    729 ATGAAACTACTACAATAAAACTTTGGCAAAAATCTCCAGGACATTGGTTT 778
                           i     vi  v  v     v v  ?iv      i iv   v    v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_65849344_6    779 AGACAATGATTTCTTGAGCAATACTCCATAAGCACAGGCAACCAAATCAA 828
                           i     i      iiii vv  v   v       i     v   vv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_65849344_6    829 AAGTGGACAAATGAGAGCACATCAAG-TTAAAACGTTTCTGCACAGTAAA 877
                           i i  i    vi  viv      i-      -ii  i  ii vvi   
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAA 674

  chrX_65849344_6    878 ATATACTATCAACAAAGTGACAAGACAACACCCAGAATGGGAGAAGATAT 927
                         iv i        v       v        v v             i    
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_65849344_6    928 GTAAAAACTACTCAGCTGA--------------CTGGAACATATAAGGAG 963
                         v iv   ii ivi v    -------------- ii   i      i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_65849344_6    964 CTCAAACAACTCTATAG------GAAAAATAA---GATCAAAAATTTGGC 1004
                            vv       v   i------  v      ---i  i?    v v   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_65849344_6   1005 AAAAGATTTGCATAGATGTTTC------------ATAAAAATGGCAAACA 1042
                            i      v     ii    ------------   v       v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_65849344_6   1043 GGCACATGAAAAGGTGTTCAACATCACTGATCAT 1076
                         i            i  i         ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (82 / 65)
Gap_init rate = 0.02 (10 / 631), avg. gap size = 4.10 (41 / 10)  


4103 16.57 8.82 0.60  chrX_65923376_65925284.rev      582  1420 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65923376_6    582 TGAAAAAGCATCCTACATTCATTTCTCAGAAGACTTAACATTGTTAAAAT 631
                           i   iii    i ii     vvv ii          i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65923376_6    632 GGCAATATTCCTTATACTGATCTACAATTTCAACATAATCCTTATCAGAA 681
                                i   ii v i         iv      ii     i     i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65923376_6    682 TTCCAACTGAGTTATGTTTAGAAATTGACAAGGTGGTTCTAAAATTCATA 731
                          i   i   vv  v v vi             v  i i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_65923376_6    732 TGGAATTGTA-TAGACTCAAGATAGCCAAAACAATTTT-AAAGTGAAAAA 779
                              v  i -vi   i  ii              i  -   iv   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_65923376_6    780 GGAAGTAGGAGGACTCACACTTCCCAATTTCTCAGCTTACTACAAAACAA 829
                         vi    v                        vv i           i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_65923376_6    830 CTGTAATCAAGACAGTATGGTAGTAGTAGAAAGATAGGCATATAGATCAA 879
                          v              i     v i i v  i     i            
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_65923376_6    880 TGGAATATTATATAATTGAGAGAAAAGGAATAAACTGGTACATCTATGGT 929
                                v-----         vvv  i       ivi     i      
  L1M4_orf2#LINE/    301 TGGAATAG-----AATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_65923376_6    930 CAACTAATTTTTGACAAGAGTGCCAAGACCATTTAATGGAGAAAGAATAA 979
                            i i     i      i              i     i         i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_65923376_6    980 TCTTTTCAACAAGTGGTGTTGGAACAAATGGATAGCCATATGCAAAAGAA 1029
                                     i     i   i    v      ?   i           
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_65923376_6   1030 TTAGGTTGGA-----------------------------ACTCAAAATGG 1050
                          v i      -----------------------------           
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_65923376_6   1051 ATCAAAGGCCTAAATGCAAGAGACAAATCTATAAAACTCTTAGAAGAAAA 1100
                             ?  i        i     vi   v                      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_65923376_6   1101 CATAGGAGTAAATCTTCATGACCTTGGATTTGGCAAAGGATT-------- 1142
                               ?          i         i  v     v  v  --------
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_65923376_6   1143 TG---CCAAA-----------------------TGGATAAACTGGACTTT 1166
                           ---     ----------------------- i      i       i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_65923376_6   1167 ATCAAAATTTAAGA-TTTTGTGTTTCAAAGGACATCACTAAGAAAGTGGA 1215
                                  v  i -       i           ii ii         i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_65923376_6   1216 AAGACAAAGCAAAGAATGAAAAACAAT-TTTG--AACCATATATCTGATA 1262
                                vv  v      ii i v   -    --  i             
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_65923376_6   1263 AGCGACATGTATCTAGAATATATAAGGAACTCTTACAAATCAACAATAAA 1312
                           v   v      i           i            v    i      
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_65923376_6   1313 AGGACAAATAAGCCAATT--AAAATGGGCAAAGTACCTGAGTAGACATTT 1360
                          i         v      --             v ii   i         
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_65923376_6   1361 CTCTACAGA---TATATAAATGGTCAATAAACACATGAAAAGATACTAAA 1407
                            i v   ---    i      i      i             i  v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_65923376_6   1408 CATTGTTAGTCAC 1420
                            ii????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (90 / 46)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 6.58 (79 / 12)  


3214 28.30 0.00 0.00  chrX_65927965_65934237.rev     4875  5782 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65927965_6   4875 TGGAAGAACATTCCATGCTCATGAGTAGGAAGAATCAATATCGTGAAAAT 4924
                              ii i  i     i     ii v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65927965_6   4925 GGCCATACTGCCCAAGTAAATTTACAGATTCACTGCCATCCCCATCAAGC 4974
                            v     v     i vi  i          vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65927965_6   4975 TACCAATGACTTTCTTCACAGAATTGGAAAAATCTACTTTAAAGTTCATA 5024
                          v   iivi i  i  ii     v v  v  iiiv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_65927965_6   5025 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5074
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_65927965_6   5075 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5124
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_65927965_6   5125 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5174
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_65927965_6   5175 TGGAACAGAACAGAGCACTCAGAAATAACGCCACATACCTACAACTATCT 5224
                              i    iv   viii         vv   i i ii  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_65927965_6   5225 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 5274
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_65927965_6   5275 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5324
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_65927965_6   5325 CTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAC 5374
                         i    i    v   i     v           i  i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_65927965_6   5375 AGATTTAAACCTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5424
                            ii    iv v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_65927965_6   5425 GCATTACCATTCAGGACATAGGCACATGCAAGGACTTCATGTCCAAAACA 5474
                          ?i v viv   iv   v v  vvi v    v ii   v ivvi vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_65927965_6   5475 CCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAATTAA 5524
                                  vvi     v    vv     v  i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_65927965_6   5525 ACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 5574
                          v i  i i   i  ii vv    i  v    i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_65927965_6   5575 AACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGG 5624
                             i                 v  i    vii ivi      i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_65927965_6   5625 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 5674
                           vi          v  i  v      vv    v iv i  v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_65927965_6   5675 AAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGACACTTCTCAA 5724
                            i     v  i?    i     i i   iv    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_65927965_6   5725 AAGGAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 5774
                            i   i  vi viii     v  i          i       v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_65927965_6   5775 CTGGCCAT 5782
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.46 (150 / 103)
Gap_init rate = 0.00 (0 / 908), avg. gap size = 0.00 (0 / 0)  


3130 27.73 0.77 0.44  chrX_65935631_65940963.rev     3938  4842 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65935631_6   3938 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATCATGAAAAT 3987
                              ii i  i     i      i v      v i  i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65935631_6   3988 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4037
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65935631_6   4038 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4085
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_65935631_6   4086 CATGGAACCAAAAAAGAGCCCGCATCGGCAAGTCAATCCTAAGCCAAAAG 4135
                         i      viiv  ii  v  v v  v v   iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_65935631_6   4136 AACAAACCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4185
                               vi      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65935631_6   4186 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGATC 4235
                                 i   i    ii         i iv ii i   i         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_65935631_6   4236 AATGGAACAGAAC--AGAGCCCTCAGAAATAACCCCATATCGCTACAACT 4283
                                i    i--    i  --        v      ivvi  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_65935631_6   4284 ATCTGATCTTTGATAAACCTGAGGAAAACAAGCAATGGGGAAAGGATTCC 4333
                          vi    i  i  i  ivv  vvi i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_65935631_6   4334 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4383
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_65935631_6   4384 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4433
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_65935631_6   4434 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4483
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_65935631_6   4484 CTAGGGATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4533
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_65935631_6   4534 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTAACAAATGAGATCTAA 4583
                         i            vvi          vv     vi i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_65935631_6   4584 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4633
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_65935631_6   4634 AGGCAGCCTCCAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4683
                           i  i  iv  i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_65935631_6   4684 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAA--GAA 4731
                         i  i  vi          v  i  v      vv    v iv i  --i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_65935631_6   4732 AGA-AAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 4780
                            -   i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_65935631_6   4781 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 4830
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_65935631_6   4831 ATCACTGGCCAT 4842
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3094 27.23 0.77 0.66  chrX_65945156_65951429     4875  5781 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65945156_6   4875 TGGAAGAACATTCCATTCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4924
                              ii i  i    vi      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65945156_6   4925 GGCCATACTGCCCAAGTAAATTTACAGATTCAATGCCATCCCCATCAAGC 4974
                            v     v     i vi  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65945156_6   4975 TACAAA-TGCCTTTCTTCACAGGATTGGAAAAACT-ATTTTAAAGTTCAT 5022
                          v v i-       i  -i   i v v  v  i  -  ii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_65945156_6   5023 ATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5072
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_65945156_6   5073 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACTAGGCT 5122
                               i      vv       v  ii i      viv      v i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_65945156_6   5123 ACAGTAAACAAAAAAAAATGGTACTGGTACCAAAACAGAGATATAGATCA 5172
                                v   i v ivi         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_65945156_6   5173 ATGGAACAGAAC--AGAGCCCTCAGAAACAATGCCGCATATCTACAACTA 5220
                               i    i--    i  --     i  vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_65945156_6   5221 TCTTATCTTTGACAAACCTGACAAAAACAATCAATAGGGAAATGATTCCC 5270
                         vi v  i  i     ivv  v   i v  v     i      vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_65945156_6   5271 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5320
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_65945156_6   5321 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5370
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_65945156_6   5371 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5420
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_65945156_6   5421 TAGGCATTACCATTCAGGACATAGGCACGT---GCAAGGACTTCATGTCT 5467
                             ?i v viv   iv   v v  ---  ---    v ii   v ivv 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGG---GTTAGGCAATGGTTTCTTAGAT 594

  chrX_65945156_6   5468 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGGTCT 5517
                          vi            vvi          vv     v  i    v  iii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_65945156_6   5518 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5567
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_65945156_6   5568 ACAGGCAACCTACAAAATTGGAGAAAATTTTCACAACCTACTCATCTGAC 5617
                          v  i     i   i   v         v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_65945156_6   5618 AAAGGGCTAATATACAGAATCTACAATGAGCTCAAACAAATTTACAAGAA 5667
                           i  i  vi   v      v  i  v  i   vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_65945156_6   5668 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5717
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_65945156_6   5718 TCTCAAAAGAAGACATTTACGCAGCCAAAAAACACATGAAAAAATGCTCG 5767
                             v        i  vi viii     v  i          i      i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_65945156_6   5768 CCATCACTGGCCAT 5781
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3079 27.30 0.68 0.46  chrX_65955230_65958414     1806  2684 (501)    L1M4_orf2#LINE/L1        1   881 (27)  

  chrX_65955230_6   1806 TGGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1855
                              ii i  ii    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65955230_6   1856 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1905
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65955230_6   1906 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTCAATTTCATA 1954
                          v   iivi i  i  ii     v v  v  i  - iii v  v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_65955230_6   1955 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTGAGCCAAAAGAA 2004
                              viiv  ii  v  v v  v     iv     i   ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_65955230_6   2005 CAAAGCTGGAGGCATCACAGCACCTGAGTTCTAACTATACTACAAGACTA 2054
                              i      vv     viv  ii v   v  viv        ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_65955230_6   2055 CAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 2104
                            i  i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_65955230_6   2105 TGAAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACTAT 2152
                           i  i    i--    i  --        vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_65955230_6   2153 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT--TCC 2200
                         i    i  i     ivv  v   i v  vvv           i  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_65955230_6   2201 TTATTTAATAAAAGGTGCTGGGAAAACTGGCTAGCAATATGTAGAAAGCT 2250
                           -- i  i   v          v      v  ? v i   i i  iiv 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_65955230_6   2251 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAAATGGA 2300
                            ii    i    v   i     v           i  i          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_65955230_6   2301 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2350
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_65955230_6   2351 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2400
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_65955230_6   2401 AACACCAAAAGCAAGGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 2450
                         i            vii          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_65955230_6   2451 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2500
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_65955230_6   2501 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 2550
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_65955230_6   2551 AGGACTAATATCCAGAATCTATAATGAACTCAAACAAATTTACAAGAAAA 2600
                         i     vi          v     v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_65955230_6   2601 A-ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 2649
                          -     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_65955230_6   2650 TCAAAAGAAGACATTTATGCAGCCAAAAAACACAT 2684
                           v        i  vi viii     v  i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.01 (6 / 881), avg. gap size = 1.67 (10 / 6)  


2661 29.48 0.44 1.31  chrX_65979266_65981789     1116  2031 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_65979266_6   1116 TGGAAA-ACATTTCATGCTCATAGATAGGAAGAATCAATATCTTGAAAAT 1164
                               - i  ii    i    i   v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_65979266_6   1165 GGCCATACTGCCCAAGATAATTTATAAATTCAAAGCTATCCCCATCAAGC 1214
                            v     v     iv i  i  i i      v  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_65979266_6   1215 TACCATTGACTTTCTTCACAGAATTTGAAAAAAACT-ATTTTAAATTTCA 1263
                          v   vivi i  i  ii     v    v  i--  -  ii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_65979266_6   1264 TATGGAACTAAAAAAGAGCTTGCATAGTCAAGAGAATTCTAAGCACAAAG 1313
                                v iv  ii  v iv v    i   i v   ii i iv vi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_65979266_6   1314 AACAATGCTGGAGGCATCACACTACCTGACCTCAAACTATACTACAAGGC 1363
                              v i      vv       v  ii ii     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_65979266_6   1364 CACTGTAACCAAAACAGCATGGTACTTGTACCAAAACAGATATATAGAAC 1413
                         i  v    i   i    ii       v i iv ii i   i       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_65979266_6   1414 AGTGGAACAGAACACAGACCTCAGAAGTGACACCACACTTCTACAACCAT 1463
                          i     i    ivv   vii     i i vv   i  v i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_65979266_6   1464 CTGATCTTTGACAAACCTGACAAAAACAAGCAAGGGGGAAATGATTTACT 1513
                         i    i  i     ivv  v   i v  vv   v       vi  vvv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_65979266_6   1514 ATTTAATAAGTGGTGTTATGAAAACTTTGTGGCCATATGCAGAAAACTGA 1563
                         v  i  i  i     i iv  v    vvi i?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_65979266_6   1564 AACTGGAACCCTTCTTTATACCTTATACAAAAGTTAACACAAGATGGATT 1613
                          ii    v    v i i i   v         i     v   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_65979266_6   1614 AAAGGCTTAAACATAAGACCTAAATCCATAAAAATCCTAGAAGAAAACAT 1663
                          ?  i i    ii     v     v i      v  i             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_65979266_6   1664 AGGCA-ATACCATTCAGGACATAGGCACGGGCAAAAACATCGTGACTAAA 1712
                            ?i- v i -   iv   v v  vvii     viiiv  v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_65979266_6   1713 ACACCAAAAACAATGACAACAAAAACCAAAATTGACAAGTGTGGTCT-AA 1761
                                  i  vvii        ivv     v  i  i -   v  -v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT-TGGACTTCA 646

  chrX_65979266_6   1762 TTAAGCTAACGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGTAC 1811
                          i  iv v vi i   i  ii vv    i  v       vv i    v v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_65979266_6   1812 AGGAAACCTACAGAATGGGAGAAAAATTTTGCAATCTATCCTTTTGACAA 1861
                           iv    i                vv       vii  viv i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_65979266_6   1862 GGTACTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 1911
                           v   vi          v  i        ivv    v i-------  v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC-------AAT 789

  chrX_65979266_6   1912 AATAAACAAAACAAACAGCCCCCTCAAAAATTGGGTAAAGGATATGAAAA 1961
                               -  i     i i   vv i?    v    i       v    v 
  L1M4_orf2#LINE/    790 AATAAA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_65979266_6   1962 GACACTTCTCAAAAGAAGACATTTATGCAGCCAACAAATGTATAAAAAAA 2011
                             i     v        i  vi viii     i  iiii  i    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_65979266_6   2012 TGCTCATCATCACTTGTCGT 2031
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (151 / 115)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


2901 21.81 1.67 1.67  chrX_65993594_65995298.rev      495  1214 (491)    L1M4_orf2#LINE/L1      189   908 (0)  

  chrX_65993594_6    495 GAAAATAAAGGACCAAGTTGAAGGACTTGCACTTTTTGATTTGAAATCTT 544
                              vi   i  v      i      ii     iiii    v   v   
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_65993594_6    545 ACTACAACGCAATGATAATCAAGACAGTGTGGTGCTTGTACAAAATTAAA 594
                                v  v iii                  i  v i i  iiv  i 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_65993594_6    595 CATAAAGATTAATGAAATATAATTAAGAGTCTG---ATAAATCCCATACA 641
                             v    i    i    v    i      ii---     -        
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACA 337

  chrX_65993594_6    642 TCTATGGCAAACTAATTTTCAACAAAGTTGTCAAGACTATGCAATGGGGA 691
                          i     iv  i i      i    i v  i      i  v         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_65993594_6    692 AAACATTGTTCTTTCAACAAAATGTGCTGGGAGAACGGCATAGCCACATC 741
                           iv  v  ii          vv         v   v v   ?      v
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_65993594_6    742 TAAAAGAATGAATTTGAACTCTTACCTCACATTTTACATGAAAAATTAAC 791
                         i           v   i  i i         iiv  i i-          
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC-AAAAATTAAC 486

  chrX_65993594_6    792 TCAAAATTGATGAACAAGCTACCTAAATGAAAGAGCTAAAACTATCAATC 841
                                v   v ?--  --         v               v  v 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAW--AG--ACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_65993594_6    842 TCTGAGAAGAAAAAATAGGGGCAAATATTTATGACTTTAGATTTGTAAAA 891
                            v         v     ? i    v  ii    i  i i  ---- ii
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT----AGG 578

  chrX_65993594_6    892 CAAT----TATTAGCTATTACACCAGAAGTGTGAATAACAAGAGCAATAA 937
                             ---- v    v   v      i   iiii ii     i  v  -  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA-AA 627

  chrX_65993594_6    938 ACAAATTAGTTAAAATTCATAAAAATTAAAAA-TTTTGCGTTTAAAAGAA 986
                          i i  v i  ii v     v           -     i i  v    i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_65993594_6    987 CACCATCAAGAAAGTGAAAACACAACCCATGGGATGGCA-AACATATTTG 1035
                            i                v        ii i    v -  v       
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_65993594_6   1036 CTAATTATAAATCTTATAAGAAACCTGTATCTAAGGTTTATGAAGATCTC 1085
                          v   i   v    v     ii  i      i iii v   i    v   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_65993594_6   1086 TTGCAAATCAATTAATAGAAAGACAAATATCCTA-TT--AATCTGGAAAA 1132
                           i   v     -    i           v  i -  --  vv   iv  
  L1M4_orf2#LINE/    778 TTACAACTCAAT-AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_65993594_6   1133 ATAATCTGAACAAGCATTTCTTCAAGTGAGATATACACATATCCAACAAG 1182
                          vi  i    i ii       i   ivi         v  iv    i   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_65993594_6   1183 TGCATGAAAACATGTTCAACATTATTAGTCAT 1214
                         ii        v   i       i ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (97 / 57)
Gap_init rate = 0.02 (13 / 720), avg. gap size = 1.85 (24 / 13)  


2055 25.35 15.72 0.89  chrX_66013772_66017642     2596  3384 (487)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_66013772_6   2596 GAAATGCATCCCATTCTCATAAATAGGCAGAATCAATATCATTAAAATGG 2645
                             vii       vi    ii  v  v   v i     ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_66013772_6   2646 CTATACTGCTCAAAGCAATTTACAAATTCAATGCTATTCTTATCAAA--- 2692
                          v     v i    vii  i    i      i  v  i i       ---
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_66013772_6   2693 ----CTACT-----------AAT-GACA--------------TT------ 2706
                         ----  i i-----------   -    --------------  ------
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_66013772_6   2707 ------------ACTCAGA-TAACTA----------GAAAAA----AACT 2729
                         ------------  i    -  i i ----------      ----   v
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_66013772_6   2730 A--TT-------TTACAATT----ATTT------TCACTACAGGGCTACA 2760
                          --  ------- i   v  ----    ------ i      ii      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_66013772_6   2761 GTAACTAAAACAGCATGGTACTGGTACAAAAACAGACACATAGCCCAATG 2810
                             ii  i    ii         i i  ii i     i    vi     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_66013772_6   2811 AAACAGAATAGAGAGTCCAGAAACAAGGCCACACAACAACAACGTC--CT 2858
                         i  i     v             i  iv   i   viv ii--   --i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG--GTCAATT 350

  chrX_66013772_6   2859 GATCTTTGACAAAAGCTACAAAAGCA---AAGGGGAAAAGCCT-TTCTAT 2904
                            i  i     ii ivv   i v  ---  v   i    vv -v   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_66013772_6   2905 TCAATAAGTAGTGCTGGGATAACTGGCTAGCTATATGCAGAAGACTGAAG 2954
                             i  i i         i      v  ? i i     i    v     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_66013772_6   2955 CTGGACCCCTTCCTTACACCATATTCAAAAATCAACTCAAGATGGATTGA 3004
                         i         v   i         v       i       i      ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_66013772_6   3005 AGATTTACATGTAAAACTGAAAACTATGAAAACCCTGGTAGACAACATAG 3054
                            ii  v      i viv        i   vi i i v   v       
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_66013772_6   3055 GCA-ATACCATCCTAAACACAGGAATGGGCAAAGATTTCATGACAAAGAC 3103
                          ?i- v i v  v i v vii  v- i     v i    v iivv v   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGAC 599

  chrX_66013772_6   3104 AACAAAAGCAATCGCAATAAAAAGCAAAAATTGACAAATGGGA------- 3146
                          v        vvv    i    - v      v  i    v   -------
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATC 648

  chrX_66013772_6   3147 ----------GCTTCTGCACAGCAAAAGAAACTATCAACAGAGTAAACTC 3186
                         ----------i   i  ii vv    i  v        v i   i  vvv
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_66013772_6   3187 ACAACCTACAGAATGGGAGAAAAATATTTGAAAACTATGCATCTGACAAA 3236
                               i                -      v   ii  ii      i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAG 747

  chrX_66013772_6   3237 GGTCTAACATCTAGCATCTATAAGGAGCT--TA------AACAATTACCA 3278
                           v  vii   i  v  v     i  i  --  ------  i   v -- 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA--A 795

  chrX_66013772_6   3279 AAGGTAAACAACCCCATTAAAAAGTGGATAAAGAACATGAAC------TT 3322
                            ii   i     v   ?    i   ii    i iv    i------  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_66013772_6   3323 TTCAAAAGAAGATACACATGTGGCCAGCAGTCATATAAAAAAA-GCTCAA 3371
                         i  v          i   vi      ii iv  i  i    i -      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_66013772_6   3372 TGTCACTGATCAT 3384
                         ii   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (126 / 70)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 5.04 (131 / 26)  


3251 23.99 1.85 2.84  chrX_66025241_66027528.rev      881  1797 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66025241_6    881 TAAAAAGATACCCTGTATTCATTGGCCAGAAGACTTAGAAATGTTTAAAT 930
                          ii       i  ii i     v iiii         iv v    v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66025241_6    931 GTCTGTATTTTGCAAAATGATCTACAAATTCAATGCAATCTTTATCAAAA 980
                          v vi  i iiv    v         i      i      ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66025241_6    981 TTGTAGTGACTTTTTTTCACAGGAAT--AAAAGTAGAATCCCAAAATTCA 1028
                          ivi  ivi i      -i   i   -- v   iv  -   i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGA-TCCTAAAATTCA 148

  chrX_66025241_6   1029 TATG-AAATGACAAAACATCCTAAATATCCATAGCAATCTTGA----GAA 1073
                             -     -   iiv i  vi    v   v i         ----   
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_66025241_6   1074 AAACAAGGCTGGAGGAATCACAGTTTCTGGAGTT---AAATTATATTTCA 1120
                         i     i i       v     v  i i-- i  ---   i -  i v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCC--AATTTCAAAACT-TACTACA 244

  chrX_66025241_6   1121 AAGCTATAGTAATCAAGGCAGTATGATGCTAATATTAAAAAAAAACCACA 1170
                               i          i    i  i i  iii  -  ii v i  - i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGAC-ATA 292

  chrX_66025241_6   1171 TAGACCAATATAATAGATTGGAGAGCCCCAAAATAAATCCACACATATAT 1220
                             i    iv      v v     i  vi       i   i    v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_66025241_6   1221 GGTCAACTGATATTTGACAAGGACACCAAGAATATTCAATAGGGAAAAGT 1270
                               i    v  i       iii      vi       i      iiv
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_66025241_6   1271 TAGTCTCTTCAATAAATGATGCAGGGGAAACGGGGTGTTCACAGACAAAA 1320
                               i     i     i   v   iv   v  i i?i    vi     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_66025241_6   1321 TAACAAAATTAGACCCTTGTCTTACATTATATACAATAATGAACTCAAAC 1370
                         v  ii  i  i     i ii  i   ii        v   v        v
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_66025241_6   1371 TGGTTGAAAGACTTAAATGTAAGACTTGAAACCATAAAACTACTGGAAGA 1420
                            v v ?    i           vi i    i        vi i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_66025241_6   1421 AAACA--GGAAAAATATCTCCTTGGCATTGGTCTTGACAATGATTTTTTC 1468
                              --  ?iv  -    i v  i v    vi v i     i   i  v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_66025241_6   1469 AATATGAGACCAAAAGCCCAAGCAAGAAAATAAA---TAAACAAGT-GGC 1514
                         i      v         v       v    v   ---  i i  i -  v
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_66025241_6   1515 CTGCACCAAACTAAAAAGCTTCTGCACAGCAAAGAAAACAATCAACAACA 1564
                           v  i    v v    i   i  ii vv     i v  v     v  vi
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_66025241_6   1565 TGAAAAGGCAATTCACAGAATGGAAGAAAATAGTTTCAAACCATGTATCA 1614
                                i   ii          i        v  v    i   i    v
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_66025241_6   1615 GATACGAG-TTAATATCCAAAATTTATAAGAAACTGTCACAACTCAAAGA 1663
                             v i -i vi      i   v     ii    v i         vi 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_66025241_6   1664 CAAAATGAAATAATAGGTAACTAAATTTATAAATTTGAATTGAATGAGCA 1713
                         i    -- i i  ---i    iv    ? -   ----------   i   
  L1M4_orf2#LINE/    792 TAAAA--AGACAA---ATAACCCAATTWA-AAA----------ATGGGCA 825

  chrX_66025241_6   1714 AAGGGCTTGAATAAACATTTTTTCCAAAGAGGATATACAAATGGCCAACA 1763
                             ii       i      i -       i                 i 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCT-CCAAAGAAGATATACAAATGGCCAATA 874

  chrX_66025241_6   1764 GCTATATAAAAAGGTGCACAGTGTCACTAATCAT 1797
                         ivi i  i     i   v  iii   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (145 / 71)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.05 (43 / 21)  


3088 26.79 1.21 1.10  chrX_66028541_66034942     5003  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66028541_6   5003 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATAC-GTGAAAAT 5051
                              ii i  i     i      i v      v i    i-  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66028541_6   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCTTCCCTATGAAGC 5101
                            v     v     iv i  i  i        i  vv       v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66028541_6   5102 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_66028541_6   5150 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66028541_6   5200 AATAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5249
                           i    i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_66028541_6   5250 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 5299
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_66028541_6   5300 AATGGAACAGAAC--AAAGCCCTCAGAAATAATGCCACATATCTACAACC 5347
                                i    i-- i  i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_66028541_6   5348 ATCTGTTCTTTGACAAACCTGACCAAAACAAG-AAATGG----AGAACTG 5392
                          vi  v i  i     ivv  -    i  v v-v     ----    iv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_66028541_6   5393 TTTCCCTATTTAATAAATGGTGCTGGGATAACTGGCTAGCCACATGTAGA 5442
                          ----  v  i  i              i      v  ?       i i 
  L1M4_orf2#LINE/    396 T----CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_66028541_6   5443 AAGCTGAAACTGGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAG 5492
                          iiv    ii    i    v   i     v    i         i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_66028541_6   5493 ATGGATTAAAGACTTAAATGCTATACCTAAAACCATAAAAACCCTAGAAG 5542
                               i ?    i      iv v v       i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_66028541_6   5543 AAATCCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGAGTTCAT 5591
                            v v    ?i- v i -   iv   v v  vv i     v iv   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_66028541_6   5592 GTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 5641
                         ivv  vi            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_66028541_6   5642 ATCTAATTAAACTAAAGAGTTTCTGGACAGCAAAAGAAACTACCATCATA 5691
                          ii v  i   v v  i ii  i  vi vv    i  v    i  vv v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_66028541_6   5692 GTGAACAGGCATCCTACAGAATGGGAGAAAATTTTCACAACCTACTCATC 5741
                              v  i  v  i                 v  ii   vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_66028541_6   5742 TGACAAAGGGCTAATATCCAGAATCTACAACGAACTCAAACAAATTTACA 5791
                            i  i  i  vi          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_66028541_6   5792 AGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATGTGAACAGA 5841
                          v     i     i     v  i?    i            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_66028541_6   5842 CACTTCTCAAGAGAAGACATTTATGCAGCTAACAGACACATGAGAAAATG 5891
                           i     v i      i  vi viii  i  i ii       i  i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_66028541_6   5892 CTCATCATCACTGGCCAT 5909
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


3032 27.96 0.88 0.55  chrX_66063121_66069497.rev     4982  5886 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66063121_6   4982 TGGAAGAACATTCAATGCTCATGGGTAGGAAGAATCAATAC-GTGAAAAT 5030
                              ii i  i v   i      i v      v i    i-  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66063121_6   5031 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5080
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66063121_6   5081 TACCAATGACTTTCTTTACAGAATTGGAGAAAACTAATT-TAAAGTTCAT 5129
                          v   iivi i  i   i     v v  v  i-  i  i-    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_66063121_6   5130 ATGGAACCAAAAAAGAGCTCGCATTGTCAAGTTAATTCTAAGCCAAAAGA 5179
                               viiv  ii  v iv v  v i   ivi   ii i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_66063121_6   5180 ACAAAGCTGGAGGCATCATGCTACCTGACTT-GAAACTATACTACAAGGC 5228
                               i      vv   ii  v  ii i  -i     -        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_66063121_6   5229 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGA--TATAGACC 5276
                                 i   i    ii         i iv ii i   --      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_66063121_6   5277 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5324
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_66063121_6   5325 ATCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAAGTATTCC 5374
                          vi    i  i     ivv  v   i v  vv            v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_66063121_6   5375 CTATTTAGTAAACGGTACTGGGAAAACTGGCTATCCATATGTAGAAAGAT 5424
                           v  i ii   i   i      v      v  ?   i   i i  ii  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_66063121_6   5425 GAAACTGGACCCCTTCCTTAAACCTTATAGAAAAATAAATTCAAGACGGA 5474
                            ii         v   i v   v    v      v  i    i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_66063121_6   5475 TTAAAGACTTACATGTTAGACCTAACACCATAAAAACCCTAGAGGAAAAC 5524
                          i ?    i  v    v   v    v  i      vi i    i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_66063121_6   5525 CTTGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5573
                         v v  ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_66063121_6   5574 AAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCTT 5623
                         vi            vvi          vv i   v  i    v   ii i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_66063121_6   5624 ATTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTACCAGCAGAGTGAA 5673
                           i   v v  v i   i  ii vv    i  v    i  iv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_66063121_6   5674 TAGGCAACCTAGAGAAGGGGAGAAAATTTTCACAACCTACTCATCTGACA 5723
                         v  i     i v    v          v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_66063121_6   5724 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5773
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_66063121_6   5774 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACGTGAACAGACACTT 5823
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_66063121_6   5824 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5873
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_66063121_6   5874 CATCACTGGCCAT 5886
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (150 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2499 28.46 3.40 0.45  chrX_66071342_66076724     4009  4890 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66071342_6   4009 TGGAAAGACATTGCATGTCAATGGATAGGAAGAATCAATATT---AAAAT 4055
                                 i  iv     iv      v      v i      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66071342_6   4056 TACCTTACTTGTCAAATCAATATATAGATTTGGTGCTATTCCCAATTAAA 4105
                         vi vv    ivi     ii  v  i     iiii  v  -   v  i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT-CCCTATCAAA 99

  chrX_66071342_6   4106 CTACCATTGAAATTCATCACAGAACTAGAAAAAA-GATTTAAAAATGTAT 4154
                         v v   vivivv  iv ii     v v  v  iv-   iiv     vi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_66071342_6   4155 ATGGAACCAAAAAAGAGCTCAAATAGCCAAAA--AT-------------A 4189
                               viiv  ii  v ivi           --  ------------- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_66071342_6   4190 ACAAATCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACTGGGCT 4239
                              vi      vv    i  v  ii i      viv      vii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_66071342_6   4240 ACAGTAAACAAAGCAGCATCGTGCTGGTA-AAAAATAGACACATAGACCA 4288
                                v   ii   ii v  i    i -  ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_66071342_6   4289 ATGAAACAGAATAGGGAACCCAGAAATAAGACTGCATATCTACAAGTATC 4338
                            i  i     v i  ii          iv iii i  i  iiivi vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_66071342_6   4339 TGGACTTCAACAAATCTGACAAAAACAAGCGATGGGGAATGGAAT--TCC 4386
                           ivi   i    ivv  v   i v  vv i        -i    --  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAATAGTCT 398

  chrX_66071342_6   4387 TATTCAATAAGTGATGCTGGGATAACTAGCTAACCATAAGCAGAAGATTG 4436
                          -     i  i  i        i    i v  ?   i v   i    v  
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_66071342_6   4437 AAACTGGACCCCTTCCTTACACCATATACAAAAATTAGCTCAGTGTGGAT 4486
                           ii         v   i                   i    ivi     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_66071342_6   4487 TACACACTTAAATGTAAAACCCAAAACTATAAAAACTCT--GCAGACAAC 4534
                         i ? v  i         i v i            -    -- v   v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chrX_66071342_6   4535 -TAGGGAATATTATTCATGACATATGCATGGGCAAACATTTTATGACAAA 4583
                         -    ?ivv v v   i    v vv vv i     vvi   iv iivv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_66071342_6   4584 GACACAAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGAGTCTAA 4633
                              v       vvi          v      v  i    v iiii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_66071342_6   4634 TTAAACTAAAGAGCTTCTGCACAGAAAAGGAAACTATCAACAGAGTAAGC 4683
                          i   v v  i i   i  ii vvv      v        v i   i iv
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_66071342_6   4684 AGATAACCTACAGAATGAAAGAAAATTTTTGCAAGCTATGCATCTAACAA 4733
                            i    i        ii       v       iii  ii    i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_66071342_6   4734 AGGTCTAATATACAGCATCCAAAAGGAACTTTAACAAATTTACAAGAAAA 4783
                         i  v  vi   v   v  vi v  i     i v    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_66071342_6   4784 AAA--ACTAACCCAATT-AAAAGTGGGCAAAAGACATAAA--GACACTTT 4828
                          i -- v          -    i        i  iv i  --    i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_66071342_6   4829 TCAAAAGAAGACATACAAATGGCCAAGAATTATATGTTAAAAAGCTCAAC 4878
                           v        i              v  vi i   vv  i v       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_66071342_6   4879 ACCACTGATCAT 4890
                          i  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (142 / 106)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.27 (34 / 15)  


2942 25.50 3.79 2.67  chrX_66086274_66090520.rev     2860  3757 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66086274_6   2860 TGGAAATATATTCCATGCTCATGGATCAGAAGAAGTAATATTGTTAAAAT 2909
                               v    i     i        ii     vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66086274_6   2910 GACCATACTACTCAAAGCAATCTGTGGATTCAATGCCATCCCTGTCAAAA 2959
                          i v     v i    vii    iii       i  v      i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66086274_6   2960 TTCCAGTGATGTTCTTCACAGAAGTAGA-AAATAAATCCTCAAATTTGTA 3008
                          i    iviiv  i  ii     i v  -  iivi     v     ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_66086274_6   3009 TGG----------GTCCCCAAATAGTCAATGCAGTCCTCAGCAAAAAGAA 3048
                            ---------- v   vi     i   vi  i  i v iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_66086274_6   3049 CCAAACTGGAAGCAC-CACACTGCCTGACTTCAAAATATACTACAAAGCT 3097
                          v  ii    i -  -      v  ii i       iv            
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_66086274_6   3098 ATAGTAA-CAAAACCAGTGTAGTATTAGTATTGAAAATAGACACTCAAAC 3146
                          i     -   i  -     i   i i i  -i ii       ivi i i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGAC-AGTGTGGTACTGGCAT-AAGGATAGACATATAGAT 297

  chrX_66086274_6   3147 CAATGGAACGGAATAGAGAAACCAGAAATAAGTCCATGTATTTACAGTCA 3196
                                 ii    v    iv          ii    ii     ii    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_66086274_6   3197 ACTCATTTTTGAAAAAGGTGCCAAGAACACTCATTACGGAATGGACAACT 3246
                          i v     i  v  i          v  i   v iv    v i i iii
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_66086274_6   3247 TCTTCAATAAATGGTGTCGGGAATATTGGATATTCATATGCAGAAGAATA 3296
                          i     i        ii    vv i      ?i  i     i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_66086274_6   3297 AAACTGGTTGCCTATCTCTCACCA-ATATAAAAATCAATT-AAAATATAA 3344
                           ii   viv    i   v     -   i      i  i -     iv v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_66086274_6   3345 TA-AGACTTAAACATAAAATCCAAA-CTGTAAAACTACTAGGAAAAAAAC 3392
                         i -    i    ii   i v i   -  i       vi   -  i     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG-AAGAAAAC 546

  chrX_66086274_6   3393 ATATGAG-AAGTGCTTCAGGACTTTGGTCTAGGCACAAATTT------TA 3435
                            v ? -  i -    iv   i    vi      vvii   ------  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_66086274_6   3436 TGGCTTCCAAAGCATAG------AAAAAATAATTAGACAAAAGGGACTAT 3479
                           i vi v      i i------   i  v  v    i   vv     vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_66086274_6   3480 ATTAAACTAAAAAGCTTCTATGCTGCAAAATAAACAATCAACAAAGTGAA 3529
                           i   v v    i   i i    v    iv v  v     v        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_66086274_6   3530 GAGATAATCTGTGGAATAAGAGAAAATATTTCCAAACTATTCATCTGACA 3579
                         i   i  i iiii    ii            v    ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_66086274_6   3580 AGAGACTAATATCCAGAATATACAAGGAACTCAAGCAACTCAACAGCAGT 3629
                           i    vi             i  i      vvi        i -----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA----- 790

  chrX_66086274_6   3630 CATCATCATCATCATCATAGTATCATCATCTCA--TTAAAAATGGGCAAA 3677
                         -------------  v v iv iv vi v i  -- ?             
  L1M4_orf2#LINE/    791 -------------ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_66086274_6   3678 AGACCTGAATGGAAATTTTTC--AAAAAGACATACAAATGATCAACTCGT 3725
                         i  ii     i  v    i  --  i    i         ii   ivv i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_66086274_6   3726 ATATTTAAAAAATGCTCAACATCTCTAATCAT 3757
                          i  v-    i            v????????
  L1M4_orf2#LINE/    878 ACATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (153 / 73)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.90 (58 / 20)  


 256 23.73 1.69 0.00  chrX_66147897_66149720.rev      427   485 (1339)    L1M4_orf2#LINE/L1       28    87 (821)  

  chrX_66147897_6    427 GGAAAA-TCAGTATTGTAAAAATGGCCGTACTGCCCAAAGTCATTTATAG 475
                             i - i i      v  i     vi    v      v v  i  i  
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chrX_66147897_6    476 ATTCAATGTA 485
                               i i 
  L1M4_orf2#LINE/     78 ATTCAACGCA 87

Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1)  

2463 29.25 0.85 0.61  chrX_66147897_66149720.rev      502  1325 (499)    L1M4_orf2#LINE/L1       63   888 (20)  

  chrX_66147897_6    502 CAAAGTCATTTATAGATTCAATACTAATCCTATCAAACTACCA-CTGCCA 550
                             v v  i  i        ii v vi         v v   -     -
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC- 111

  chrX_66147897_6    551 TTCTTCACAAAATTAGAAAAAATTACTTTAAATTTCAAATGAAACAAAAA 600
                           i  ii  i  v v  v  iv v iii    v    v   i  vviv  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_66147897_6    601 AAGAGCCTGTATAGTCAAGATAATCCTAAGCAAAAAGAACAAAGCTGGAG 650
                         ii  v  v v    i   i i    i i iv  i          i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_66147897_6    651 ACATCACGCTACCTGACTTCAAACTATACTACAAGGCTAGAGTAACCAAA 700
                         ivv    i  v  ii i      viv        i    v     i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_66147897_6    701 ACAGCATGGTACTGGTACCAAAACAGATATATAGACCAATGGAATGGAAC 750
                             ii         i iv ii i   i       i         i   i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_66147897_6    751 AGACACTTTAGAAATAATACCC-TACATCTACAATCATCTG--CCTCAAC 797
                         v  v v ii        -    -     i  iii   vi  --ii  i  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_66147897_6    798 AAACCTGACAAAAACAAGCAATGGAAAAAGGATTCCCTATTTAATAAACA 847
                           ivv  v   i v  vv      ii    i  vvi  v  i  i   ii
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_66147897_6    848 GTGTTGGGAAAACTGTCTAGCCACATGCAGAAAACTGAAATTGGACCCCT 897
                            i     v     vv  ?         i  i v    i          
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_66147897_6    898 TCCTTGCACCTTATACAGAAATTAATTCAAGATGGATTAAAGACTTAAAT 947
                         v   ii    v      i       i    i      i ?    i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_66147897_6    948 GTAAAACCTAAAGTCATTAAAACCCT-AGCAGAAAACCTTAGCA-ATACC 995
                             i v     iii  -     i  -  v       v vi ?i- v i 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_66147897_6    996 ATTAAGGATATAGGCATAGACAAAGATTTCATGACGAAAACGCCAAAAGC 1045
                         -  viv  iv v  vv   i   v i    v iivv vi  i        
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_66147897_6   1046 AAATGCAACAAAAGCTACAATTGACAAATGGTATCTAATTAAGCTAAAGA 1095
                          v v          vv v   v  i    v v ii v  i  iv v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_66147897_6   1096 GCTTCTGCAGAGCAGAAGAAACTATCATCAGAGTGAACAGGCAACCTATA 1145
                         i   i  iivvv  i i  v       vv i      v  i     i i 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_66147897_6   1146 GAATGAGAGTAAAAT-TTTGCAATCTACCTATCTGACAAATGTCTAATAT 1194
                              i   -     -       vii iv       i  iv v  vi   
  L1M4_orf2#LINE/    709 GAATGGGAG-AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_66147897_6   1195 CCAGAATCTACAAGGAGCTTAAGCAAATTTACAAGAAAAAAATAAACAAC 1244
                                v  i  i  i  ivvi   v iv i  v     i i   i   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_66147897_6   1245 CCTATCAAAAAGTGAGCCAAGGGTATGAACAGACACTTCTCAAAAGAAGA 1294
                           v  i?    i  i  v    i v    i     i     v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_66147897_6   1295 CATTTATGCAGCCAACAAACATATGAAAAAA 1325
                         i  vi viii     i  i  i       i 
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (11 / 826), avg. gap size = 1.09 (12 / 11)  


2715 25.82 2.29 3.70  chrX_66163871_66169970     2955  3872 (2228)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_66163871_6   2955 AAAAAAATCC-ATGTTCATGAACTGGAAGAATCAATAGTGTTAAAATG-- 3001
                            i v    -         i i       v i    v      i   --
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_66163871_6   3002 ------TCCCAAAC-GATATACCGATTCAATATAATCTCTTTCAAAATGT 3044
                         ------i      i-   v   v       iii    i  v       vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_66163871_6   3045 CAGTAATATTCTTTACAGAAAT--AAAAGATG-TCCTAGGATTTATATGA 3091
                            iviiv  i   i       -- v   v  -     ii   i     i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_66163871_6   3092 GACCACAAAAGGCCAAGAATAGCCAAAGCTGTCTTAAGCAAAAAGAACAA 3141
                         i vii   ii i  v            i vi    i iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_66163871_6   3142 AACTGAAAGAATCACATTACCTGACTTCAAATTATACTACAGATCTACAG 3191
                          ii  i i  v     i v  ii i      viv       i v      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_66163871_6   3192 TAACCAAAACAGCATGGTACTGGCAATGAAAAAACAGACTCATAGAACAA 3241
                            i   i    ii           - --  ii i    vi     v   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCA-T--AAGGATAGACATATAGATCAA 300

  chrX_66163871_6   3242 TAGAACAGAATAGAGAACACAGAAACTAATCCACACACTTACAGCAAACT 3291
                          i   i     v    iiv      iv  i   i   i   ii iv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_66163871_6   3292 CATTTTTCACAAAGGTGCCAAGAATACACACTAGGCAAG----AGTCTCT 3337
                         v     iv    i          vi iv  v i  v  i----     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_66163871_6   3338 TACATAAATGGTTCTGGGAAAACTGGATATCCATATGCAGAAGAATGAAA 3387
                          vv i       v      v         ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_66163871_6   3388 TTAGACCCCTATCTCTTACTGTATACAAAAATGAAATCAAAATGTATTAA 3437
                           i        i   vi  ii           v  v        v  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_66163871_6   3438 AGACTTAAGCCTAAGCCCTCAATATATGAAACTACTACTACCACTACTAC 3487
                             i   iiv    vv  v  vv   i     -----------------
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACT----------------- 533

  chrX_66163871_6   3488 TACTACTACTACTACTACTACAAAA-ATAGGGGAAAATACTCAAGATATT 3536
                         -----------  --  vv v    -     ? v    vi  iv  iv  
  L1M4_orf2#LINE/    534 -----------CT--TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_66163871_6   3537 GGTGTGGGAAA--ATTTCTTAGGCAATCCCTCACAAGCTCAGGCAATCAA 3584
                           vv i  v  --i        ii vvv vi  v    v  i    iv  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_66163871_6   3585 AACAAAAATAGAGAAATGGGATCACATCAAG-TTACAAAGCTTCTGCACA 3633
                          iv         v    v   iiv      i-   -   i   i  ii v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCT 669

  chrX_66163871_6   3634 ACAAAGTACACAATCAACCCAGTGAAGTGGCTTACTACAGAATGGAAGAA 3683
                         v     v    v     vvv      iv i vvv i         i    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_66163871_6   3684 AATATTTTCAAACTACCCTTCTGAAAAGAGATCAATAACTAGAATATATA 3733
                                v    ii iviv     v   i  iivi  v i          
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_66163871_6   3734 AGGAGCACAAACAACTCTATAGGAAAAAATCTAATAATCAGATCAAAAAC 3783
                          i  i v vv       v   iv     iv v     i vi  i?    v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_66163871_6   3784 TGGGCAAAGTATTTGAATAGACGTTTCTCAAAAGGAAACATAGAAAAGGG 3833
                                  v            i      v    i i i   v   v  v
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_66163871_6   3834 AAACAGACATATGAAAAGGTACTAATTATCATTGATTAT 3872
                         v  i ii  i        i i  v vi    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (132 / 101)
Gap_init rate = 0.02 (14 / 905), avg. gap size = 3.93 (55 / 14)  

2550 21.61 11.33 1.04  chrX_66163871_66169970     4847  5614 (486)    L1M4_orf2#LINE/L1       62   908 (0)  

  chrX_66163871_6   4847 CCAAACTGATCTACAGATTCAGCAAAATATTCTATCAATAACCCACCTAC 4896
                              i               i iv   -ii       v v    v  i 
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAAT-CCCTATCAAAATCCCAGCTGC 110

  chrX_66163871_6   4897 ATTTTACTTTTTCAGAAATGGGCATACCGATCCTAAAATTCTCATGGAAA 4946
                         v    ----  v       v i  vi i             vi       
  L1M4_orf2#LINE/    111 CTTTT----TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_66163871_6   4947 TGCAAAAAAAATGCAA-AGTCAAAATGATTTTGAAAA----GAACAAACT 4991
                              iii vviiv  -  i     ii  i       ----       v 
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_66163871_6   4992 TGGAGGAATCTCACTTCCTGATTTCCAACCCTACTACAAAGC---AGAAG 5038
                                v  v       ii     v  v i           ---  v i
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_66163871_6   5039 TCAAGACAG--------------------------------------AAT 5050
                                  --------------------------------------   
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_66163871_6   5051 AAAATTTAGAGTCAAAAAATAATCCTTTACATTTATAATTAATTGATTTT 5100
                          i    v      v i      v  iv         ii i          
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_66163871_6   5101 TGACAAGGGTGCTAAGACAATTCAATGGGTAAA-AACATTCTTTTCAACA 5149
                         i           i     v          v   -  i v           
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_66163871_6   5150 A-TAGTGCTTGAAAAACTGGATATCCACATGCAGA-TAATGTATGTGAAT 5197
                          - i     v i v         ?         i -v    v vv  i i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_66163871_6   5198 ACTTTCTTCATAATATCCACAAAAGTTAGCTCAAA-TGGATTATAGATCC 5246
                         v i v i   i vi  vi      i   i      -     i ?   i i
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_66163871_6   5247 AAATGTAACAATTCAAGTGATAGAATT-TTAAAAGAAAACAATTGAGTAA 5295
                                 v ii v  iiv   i  i -   i         vvv ?    
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_66163871_6   5296 ATGTTTGTGAGCTTGGTTTAGGCAGTGGTTT-TTAGAC-TAA-ACTCAGA 5342
                           v  i    v     v       i      -     i- i -  iv i 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_66163871_6   5343 GCA-AAGCAACAAAATGAAAT-CAGATAAAGTGTACCTTA---AAATTAA 5387
                            -           vi   v-i       v  v  i i ---       
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_66163871_6   5388 AACCTTTTTTGTTTCTCAGGCCGCTATCAA-------------------- 5417
                           v     v  i   vv   v i       --------------------
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_66163871_6   5418 -ATAATGACAGAAAATACTTGCAAATGCTGTATCTGATAAAAATTTTGTA 5466
                         - v    iv        i        vv i          iiivi     
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_66163871_6   5467 TCCAAAATATATAAAGAACGGTT-CAAATTAACAACAACAACAAAAAAAG 5515
                             i              vv  -   v i  i  i  v  v v   v i
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_66163871_6   5516 CCCAATTTTAAAAATCAGCAAAAGAATTGATTT----TTTTTCCCAAGGA 5561
                                ?-      vi     i  v    v v----   i   v   i 
  L1M4_orf2#LINE/    807 CCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_66163871_6   5562 GATA--CAAATAGTTTATAAGCATATGAAAAGCTTCTCAAGTCTTTAGGG 5609
                             --     i iiv       i        v v     -- v i ???
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA--CATCAZZZ 903

  chrX_66163871_6   5610 AAATG 5614
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.16 (87 / 75)
Gap_init rate = 0.03 (23 / 847), avg. gap size = 4.13 (95 / 23)  


2422 23.57 1.64 7.79  chrX_66175459_66177333      471  1382 (493)    L1M4_orf2#LINE/L1       53   908 (0)  

  chrX_66175459_6    471 CAATAGTTTCAAAAAGCTTTGATTTCTTCCTTCAGATTCAATGCAATTCC 520
                              v ii v   ----     ------  v         i     i  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAA----TTGAT------CTACAGATTCAACGCAATCCC 92

  chrX_66175459_6    521 CATAAAAGTGCTATCATCATTCTTCACGGAACTAGAAAAAA-AATCCTAA 569
                         i  v   i v i v vv v  i  ii i   v v  v  iv-i       
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_66175459_6    570 AATTCATATGGAACCAAAAAGAGCCC-TCATAGCCAAAGCAAGACTAAGC 618
                                      viiv  i ii   -vv         i   vvi i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_66175459_6    619 AGAAAGAGCAAATCTGGAAGCATCACACTGCCTGACTTCTAACTATACTA 668
                          ii    i    vi    i vv       v  ii i   v  viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_66175459_6    669 CAAGACTGTTGTTATAAAAACAGCATA-TACTGGTATAAAAATAGGCATG 717
                            ii  iiv  v  v  i    ii i-      i    ii    i   i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_66175459_6    718 TACATCAACAGAACAGGATAGAGAACCCGGAAAGAAAGCCAAATACTTAC 767
                           v     ii   i  i  v    ii  i    v   v   v i i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_66175459_6    768 AGCCAACTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGA 817
                         i i   i    i  i     i vviv   i v   vv i         i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_66175459_6    818 CACTCTATTCAACCAATGGTGCTGCAATAATTGGCAAGCCACACGTAGAA 867
                         i v   v      v          vi i  i   vv ?     i i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_66175459_6    868 GAATGAAACTGGATCCTCATCTGTCACTTTATACAAAAATCAACCCAAGA 917
                                ii    i  ii i  vv   iv           i   i   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_66175459_6    918 TAGAATAAATACTTAAATATAAGAACTAAAAGCATAAAAACTCA-AGAAT 966
                          i  vi ? v  i     i     i      vi      -   v-    v
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAG 541

  chrX_66175459_6    967 ATAACATTGAAGAAACTCTTC-TGTACATTGGATTAGGCA--GAGTTC-- 1011
                          v     v i? v  v     -  -  v    i       -- iv   --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_66175459_6   1012 ----ATGACCAACAAACCCAAAGCAAATGCAACAAAAACAAAAAATAAAT 1057
                         ----     ------   v      v v         i-        i  
  L1M4_orf2#LINE/    591 AGATATGAC------ACCAAAAGCACAAGCAACAAAAG-AAAAAATAGAT 633

  chrX_66175459_6   1058 AGATGGTACTTAATTAAA-CTAAATGTTTCTGCACAGCAAAATAAATGAT 1106
                          i  v v    v  i   -i    vii  i  ii vv    i-----  -
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-----GA- 677

  chrX_66175459_6   1107 CAGCACATGTATCTCATTTTTTAAAGAAGAAATAAAGAAAAAAGAAATAA 1156
                         ---   ---    ----------------------------      ---
  L1M4_orf2#LINE/    678 ---CAC---TATC----------------------------AAGAAA--- 690

  chrX_66175459_6   1157 ACAGCAGAGTAAACAGACAACCCATAGAATGGGAGAAAATATTTGCACGC 1206
                         --------  i  v          i                      vii
  L1M4_orf2#LINE/    691 --------GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_66175459_6   1207 TATACATCCAACAAAGGACTAGTATCCAGAATCTACAAGGAACTCAAACA 1256
                         i   i   ii i  i     v           v  i  i      vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_66175459_6   1257 AATCAGCACTAAAAA-ACAAATCATCCCATCAAAAAAGTGGGCAAAGGAC 1305
                          v   ii v      -      v i  v  i?     -           i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGAT 831

  chrX_66175459_6   1306 ATAAATAAACAATTCTGAAAAGAAGATATACAAATGGCCAACAAACGTAT 1355
                         v i    i   v    vv                       i  i ii  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_66175459_6   1356 GAAACAATGCTCACCATCACTAATTAT 1382
                             vi       v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (125 / 86)
Gap_init rate = 0.02 (21 / 856), avg. gap size = 4.10 (86 / 21)  


2830 27.56 1.32 1.21  chrX_66189574_66193808.rev     2838  3744 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66189574_6   2838 TGGAAGAACATTCCATGCTCATGGGTAGCAAGAATCAATATCATGAAAAT 2887
                              ii i  i     i      i v v    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66189574_6   2888 GGCCATACTGCCCAAGGTGATGTATAGATTCAATGCCATCCCCATCAATC 2937
                            v     v     iv    v  i        i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66189574_6   2938 TACCAATGACTTTCTTCACAGCA-TTGGAAAAAACT-ACTTTAAAGTTCA 2985
                          v   iivi i  i  ii   v -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_66189574_6   2986 TATGGAAGCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 3035
                                iiiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66189574_6   3036 AACAAAGCTGGAGGCATCATGCTACCTGGCTTCAAACTATACTACAAGGC 3085
                                i      vv   ii  v  iiii      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_66189574_6   3086 TACAGTAACCAAAACAACAGGGTACTGGTACCAAAACAGAGAGATAGACC 3135
                                 i   i   iiiv        i iv ii i   v v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_66189574_6   3136 AATGGAGCAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 3183
                               ii    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_66189574_6   3184 ATCTGATCTTTGACTAACCTGACAAAAACAAGAAATGGAGAAAGGAT-TT 3232
                          vi    i  i   v ivv  v   i v  vvv     i     i  -v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_66189574_6   3233 CTATTTAACAAATCGTGTGGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3282
                           v  i       v   iv    v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_66189574_6   3283 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGACGGA 3332
                            ii    i    v   i     v              i    i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_66189574_6   3333 TTAAAGACTTACATGTTAGACCCAAAACCATAAAAACCCTAGAAGAAAAC 3382
                          i ?    i  v    v   v i     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_66189574_6   3383 CTAGGCA-ATACCATTCAGGACATAGGTATGGGCAAGGACTTCATGTCTA 3431
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_66189574_6   3432 AAACACCAAAAGCAATGGCAACAAAAGCCAAATTTAACAAATGGGATCTA 3481
                         vi            vvi          vv   v vi i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_66189574_6   3482 ATTCAACTCAAGAGCTTCTGCATAGCAAAATAAACTACCATCAGAGTGAA 3531
                           iv  v i  i i   i  iiivv    iv v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_66189574_6   3532 CAGGCAACCTACAGAATGGGAGAAAAATTTTTGCAATCTACTCATCTGAC 3581
                         v  i     i                - v       vii ivi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGAT 744

  chrX_66189574_6   3582 AAAGGGCTAATAAGCAGAATCTACAAAGAACTCAAATAAATTTACAAGAA 3631
                           i  i  vi  vv      v  i         vv i  v ---   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAA 791

  chrX_66189574_6   3632 -AAAAAAACAAACAACCCCATC-AAATGTGGGCGAAGGACATGAACAGAC 3679
                         -     i     i     v  i-   vi     i     iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_66189574_6   3680 ACTTCTCAAAAGAAGACTCATGCA----GCCAACAGACACATGAAAAAAA 3725
                          i     v        i--  i  ----     i ii          i v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGAT--ATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_66189574_6   3726 ACTCATCATCACTGGCCAT 3744
                         i    v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (145 / 102)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


2592 27.91 3.03 1.23  chrX_66223351_66225316      581  1472 (494)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66223351_6    581 TGGAAACACATTTCATGTTCATGGATAGGAAGACTCAATATCATGAAAAA 630
                               v i  ii             v        i     ii v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66223351_6    631 GGCCATAATGCCCAAAGTAACTAATATATTTAATGCTATCCCCATCAAGC 680
                            v   v v      v i iiv i v   i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66223351_6    681 TACCA-TTGACTTTCTT-CACGGAGTTAGGAAAAACT-ACTTTAAATTTT 727
                          v   -i  v    i  -  - i i  --  v  i  - iii    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATT--GACAAGCTGATCCTAAAATTC 147

  chrX_66223351_6    728 ATAAGGAACCAAAAATGTGTTTGTACAGGCAACACAAGCCTGAGTAAAAA 777
                            v    viiv  iv vviiv v i  v   v    v i   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_66223351_6    778 GAACAAAGCTGGAGACATCACACTACCTGACTTCAAACTATACTACAAGG 827
                                 i     ivv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_66223351_6    828 CTAAAATAACCAAAAGATCATGGTACTGGTACCAAAACAGATGTATAGAC 877
                            v i   i   i v vii         i iv ii i   ii      i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_66223351_6    878 TAATGGAACAGAGC--AGAGGCCTGAGAAATAATGCCACACATCTACAAT 925
                         i       i   ii--    v  --        vv   i    i  iii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_66223351_6    926 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 975
                           vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_66223351_6    976 TCTATTTAATAA-TTGTGTTGGGAAAACTGGTTAGGCATATGCAGAAAAC 1024
                            v  i  i  - v   i     v      v  ?v  i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_66223351_6   1025 TGAAA------------CTTACACCTTACACAAAAATTAACTCAAGATGG 1062
                             i------------  i     v  i                i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_66223351_6   1063 ATTAAAGACTTAAATGTAAGACCTTAAACTATAGAAACCCTAGAAGAAAA 1112
                           i ?    i           v  v        i  vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_66223351_6   1113 CCTAGGCAATAGCATTCAGAACATTGGCATGGGCAAAGACTTCATGACTA 1162
                          v    ?ivv iiv   ivi  v    vv i     v ii   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_66223351_6   1163 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAAAAA--GG---TG 1207
                         vi            vvi          vv     v  v   --  --- v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_66223351_6   1208 AT-AAAATTAAACTAAAGATCTTCTACACAGCAAAAGAAGCTATCGTTGG 1256
                           -         ---  ---   i iii vv    i  vi     ivvii
  L1M4_orf2#LINE/    646 ATCAAAATTAAA---AA---CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_66223351_6   1257 AGTAAACAGGCTACCTACAGAATGGGAGAAGATTTTTGCAATCTATCCAT 1306
                            i  v  i v   i              i  v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_66223351_6   1307 CTGACAAAGGGCTAATATCCAGAATTTACAAGGAACTTAAACAAATTTAC 1356
                             i  i  i  vi          v  i  i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_66223351_6   1357 AAGAAAAAAGCAAACAAACCCATCAGCAAGTGGAAGAAGAATATGAACAG 1406
                           v     ii    i  v  v  i?iv  i   ivi   i  v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_66223351_6   1407 ACACTTCTCAAAAGAAGATATTGATATGGTCAACAAATATACAAAAAAAA 1456
                            i     v           vv v    i   i  ii i ii    i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_66223351_6   1457 GC---GCATCATTTCTGGT 1472
                           ---i     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (140 / 105)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.53 (38 / 15)  

 717 28.26 0.43 0.00  chrX_66223351_66225316     1737  1966 (0)    L1M4_orf2#LINE/L1      652   882 (26)  

  chrX_66223351_6   1737 ATTATAAGCTTCTGCACAGAAAAAGAAACCACCATCAGAGTGAACAGGCA 1786
                             v  i   i  ii vvv   i  v  i i  vv i      v  i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_66223351_6   1787 ACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAGAGC 1836
                            i   i             v       vii ivi      i  i ii 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_66223351_6   1837 TAATTTCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA-ACA 1885
                          vi v        v  i  v      vv    v iv i  v     -   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_66223351_6   1886 AACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCTCAAA 1935
                           i     v  i?    i    ii      v    i     i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_66223351_6   1936 AGAAGACATTTATGCCGCCAGAAAACACACG 1966
                               i  vi viiv    iv  i    i 
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATG 882

Transitions / transversions = 1.37 (37 / 27)
Gap_init rate = 0.00 (1 / 231), avg. gap size = 1.00 (1 / 1)  


3219 24.38 3.85 0.91  chrX_66226094_66229627     2160  3041 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66226094_6   2160 TGGAAAGTCATACTTTGTTCGTGGATTGGAAGAAATAATATAATTAAAAT 2209
                                vi  v iv     i            vv      vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66226094_6   2210 GT--ACATTCAACCTAAAGTGATCTACAGATTTAATAAAATCCCTATGGA 2257
                          v-- i i  --  i   v             i  iiv         v- 
  L1M4_orf2#LINE/     51 GGCAATACTC--CCCAAATTGATCTACAGATTCAACGCAATCCCTATC-A 97

  chrX_66226094_6   2258 AAACTCCAA-TGCCATTTTTCACATAAGTAGAAAAAC-AATTTCAAAATT 2305
                            ii   i-    -     ii  v  i v  v  i -i  iii      
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_66226094_6   2306 CTTATAGAACCACAAAG-ACCTCGAACAGCCAAAGCAATCTTGAGAATGT 2354
                          v   i   vii   i -   iv   i       i         i  v v
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_66226094_6   2355 AGCACAAGTCTAGAGGCATCACACTTCCTGGTATCAAACTATACTAAAGA 2404
                           v    ivi i    vv          iii v     viv     v i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_66226094_6   2405 GCTGTAACAATCAAAACAGTATGATTGTGGCATAAAAACA---AT-TATA 2450
                            ii ii      i     i  i vv        ii i ---  -  v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_66226094_6   2451 CCAATGGAACAGAGTTGAAATCCCAGAAATAAACCCACACATATACAGTC 2500
                         i        i   i    i vi               i    v  ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_66226094_6   2501 AATTAATTGTTGACAAGGGTGCTGAGAATAAACAATAAGGAAAGGATATT 2550
                             i   v i           ii   vi vv    ii      i   v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_66226094_6   2551 CCCTTCAATAAATGGTGTAAAGAAAACTGGATATTCACATG-GAAAGAAT 2599
                          ii     i        ivii  v         ?i      -i       
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_66226094_6   2600 GAAATTGGAGTTTCATCTTACACTGTATACCAAAATTAACTCAACATAGA 2649
                            i     viiii i  i    ii     v             v  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_66226094_6   2650 TTAAGGACTTAAATATAAGACTTGAAATCATAAAACTCCTAAAAGACAAC 2699
                          i ?i   i     i     vi i   ii         i  i    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_66226094_6   2700 A--GGGAAAAACTTTC-TGACATTTGTCTTGGCAATGTTTTTCTGGATGT 2746
                          --  ?iv   ii   -    v  v vi v       v   ii i   i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_66226094_6   2747 GACATCAAAAGCACAGGCAACAAAAGCAAAAACAAATAAGTCATACTACA 2796
                             i          i          v     i i    i iiv   v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_66226094_6   2797 TCAAACTAAAATGCTTCTACACAACAAAAGAAAT----AACACAGTGTAG 2842
                              v v   vi   i iii vv    i  v i----  v v    v i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_66226094_6   2843 AGACAATCTA-AAAATGGGAGAAAATAATTGCAAACTATATATCTGATAT 2891
                               i i - i              v       ii            v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_66226094_6   2892 GGGGTTAGTATTCAAATTATTTAAAGAACTCATCCAAATCCATAA----- 2936
                            ii v    i  i v   v          v v   v  v    -----
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_66226094_6   2937 ---CAAATA-------TTAAAAATTGGCACAGGCTTTGA-TAGAAATTTC 2975
                         ---      ------- ?      v    v   v     -    v     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_66226094_6   2976 TCCAGAGAAGATATTTAAGTAAATAGTCAACAGTTATATGGAAAGGTGTT 3025
                             i         ----ii    i i   i ivi i   i    i  i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATAT----ACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_66226094_6   3026 CAACATCACTAATCAT 3041
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (136 / 75)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.33 (42 / 18)  


1367 27.47 1.93 1.45  chrX_66237264_66243170     4194  4608 (1299)    L1M4_orf2#LINE/L1        1   417 (491)  

  chrX_66237264_6   4194 TGGAAGAACACTCCATGCTTATGGATAGCAAGAATCAATATTGTGAAAAT 4243
                              ii i ii     i i      v v    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66237264_6   4244 GAACATACTGCCCAAAGTAATTTATAG-TTTAATGCTGTCCCCGTCAATC 4292
                          ivv     v      v i  i  i  -  i  i  vi    ii    vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66237264_6   4293 TCCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4340
                              iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_66237264_6   4341 TATGGAACCAAAAAAAGG---CAGCATTGACAAGACAACACTAAGCCAAA 4387
                                -- viv  i  ---   v  v v   i    ivi i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_66237264_6   4388 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 4437
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_66237264_6   4438 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 4487
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_66237264_6   4488 CCAATAGAACAGAAT--AGAGCCCTCAGAAATAATACCACACATCTGCAA 4535
                         i    i   i     --    i  --        vv   i    i iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_66237264_6   4536 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 4585
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_66237264_6   4586 CCCTATTTAATAAATGGTGCTGG 4608
                         vi  v  i  i            
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGG 417

Transitions / transversions = 1.78 (73 / 41)
Gap_init rate = 0.02 (8 / 417), avg. gap size = 1.75 (14 / 8)  

1620 28.12 0.40 0.20  chrX_66237264_66243170     4910  5414 (493)    L1M4_orf2#LINE/L1      403   908 (0)  

  chrX_66237264_6   4910 AAAAATTGTTGCTGGGAAAACTGACTAGCCATATTTAGAAAGCTGAAACT 4959
                           v  v  v        v     iv  ?   i  vi i  iiv    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_66237264_6   4960 GAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAA 5009
                          i i    v   i     v              i    i      i ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_66237264_6   5010 ACTTACATGTTAGACCTAAAACCATAGAAACCCTAGTAGAAAACCTAGGC 5059
                           i  v    v   v       i   i  vi i   v       v    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_66237264_6   5060 A-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACAC 5108
                         i- v i -   iv   v v  vv i     v ii   v ivv  vi    
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_66237264_6   5109 CAAAAGCAATGGCAACAGAAGTCAAAATAGACAAATGGGATCTGATTAAA 5158
                                 vvi      i   vv        i    v   ii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_66237264_6   5159 CTAAAGTGCTTCTGCACAGCAAAAGAAACTACCATTAGAGTGAACAGGCA 5208
                         v v  ivi   i  ii vv    i  v    i  vv i      v  i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_66237264_6   5209 ACCTACAGAATGGGAGAAAGCTTTTCCAATCTGCTCATCTGAAAAAGGGC 5258
                            i               iiv   v   viiiivi      v  i  i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_66237264_6   5259 TAATATCCAGAATCTACAAAGAGCTCAAAGAAATTTAGAAGAAAAAAA-A 5307
                          vi          v  i     i   vv v  v iv v  v     i - 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_66237264_6   5308 AACAACCCCATAGAAAAGCGGGTGAAGTATATGAACAGACACTTCTCAAA 5357
                           i     v  v?    ii   ii   v  v    i     i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_66237264_6   5358 AGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGTTCATCATCAC 5407
                               i  vi viii     i ii          i   i   v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_66237264_6   5408 TGGCCAT 5414
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.19 (75 / 63)
Gap_init rate = 0.01 (3 / 506), avg. gap size = 1.00 (3 / 3)  


1959 21.96 1.09 18.69  chrX_66252293_66260913     5264  6365 (2256)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66252293_6   5264 TGGAAAAATATTTCATGTTCATGGATAGGAAGAATCAATATCATGAAAAT 5313
                               i    ii             v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66252293_6   5314 TGTCATGCTGCCCAAAGTAATTTATAGATTCAATACTATTCCCATCAAGC 5363
                         v iv  i  v      v i  i  i        ii v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66252293_6   5364 TACCATTGACTTTCTTCACAGAACTAGAAAAAACT-ATTGTAAATTTCAT 5412
                          v   vivi i  i  ii     v v  v  i-  -  iv    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_66252293_6   5413 ATGGAACAAAAAAAAACCTCATATAGACAAGACAATCCTAAGCAAAAA-- 5460
                               vviv  iii   iviv    v   i      i i iv  i  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_66252293_6   5461 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTGCAAGGCT 5510
                               i      vv    i  v  ii i      viv    i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_66252293_6   5511 ACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5560
                            i   i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_66252293_6   5561 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCGGCATATCTACAACCG 5608
                               i    i--    i  --        vv vii i  i  iiii i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_66252293_6   5609 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5658
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_66252293_6   5659 TATTTAATAAATGGTGCTGGAA-AACTGGCTAGCCATATGTAGAAAGCTG 5707
                          v  i  i            i -      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_66252293_6   5708 AAACTGGATCCCTTCCTTACACCTTATACAAAAATGAAAACAGATATATA 5757
                           ii    i    v   i     v           -------------  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAAT-------------TA 484

  chrX_66252293_6   5758 AACCAATGGAACAAAACAGAGGCCTCAGAAATAATGCCACACATCCACAA 5807
                          ----------------------    -----------------------
  L1M4_orf2#LINE/    485 A----------------------CTCA----------------------- 489

  chrX_66252293_6   5808 ACATCTGACCTTTGACAAACCTGACACAAACAAGCAAAGAGAAATGGATT 5857
                         -----------------------------------------        i
  L1M4_orf2#LINE/    490 -----------------------------------------AAATGGATC 498

  chrX_66252293_6   5858 TCCTATTTAATAAACGGTGTTGGAAATCTGGCTAGCCATATGCAGAAAAC 5907
                         --------- ? i  ----------------   i----   i - i i 
  L1M4_orf2#LINE/    499 ---------AWAGAC----------------CTAA----ATGTA-AGAGC 518

  chrX_66252293_6   5908 TGAAACTGAACCCCTTTCTTACAGCTATTACAAAAATTAACTCAAGATGC 5957
                          i     -------------------------------------------
  L1M4_orf2#LINE/    519 TAAAACT------------------------------------------- 525

  chrX_66252293_6   5958 ATAAAGACTTATACATAATTCCTAACACTGTAAAAACCCTAGAAGAAAAC 6007
                              ---------------------   -------- i           
  L1M4_orf2#LINE/    526 ATAAA---------------------ACT--------CTTAGAAGAAAAC 546

  chrX_66252293_6   6008 CTAGGCA-ATACCATTCAGGACACATACAT-GGGCAAAGACTTCATGACT 6055
                         v    ?i- v i -   iv   - v ivi -i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_66252293_6   6056 AAAACACCAAAAGCAATAACAACAAAAGCCAAAATTGACAAATGGGATCT 6105
                          vi            vv i         vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_66252293_6   6106 AATTAAAAT----AACTTCTGCACAGCAAAATAAATTATCATCAGAGTGA 6151
                         v  i     ----     i  ii vv    iv v i     vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_66252293_6   6152 ACAGGCAACCTACAGAATGGGGGAAAATTTTTGCAATCTATCCATCTGAC 6201
                          v  i     i          i      v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_66252293_6   6202 AAAGGGCTAATATCCAGAATGTACAAAGAACTTAAATAAATTTATAAGAA 6251
                           i  i  vi          i  i        ivv i  v iv    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_66252293_6   6252 AAAAGCAAACAGCCCCATCAAAAAGTGGGCAAAGGATATGAAAAGACACT 6301
                            ii    i i   v  i?    i            v    v     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_66252293_6   6302 TCTCAAAAGAAGACATTTATGTAGCCAACAAATATATGAAAAAGACTTCA 6351
                             v        i  vi vi i     i  ii i       iivvi   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_66252293_6   6352 TCATCACTGTTTAT 6365
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (149 / 89)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 10.38 (218 / 21)  

 858 30.31 1.25 1.56  chrX_66252293_66260913     6935  7254 (1367)    L1M4_orf2#LINE/L1        4   322 (586)  

  chrX_66252293_6   6935 AAAAAAATCCT-TGTTCATAAATTTGAAGAATCAATAATGTTAAAATGTC 6983
                            i v    i-       ii   v     v i    v      i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_66252293_6   6984 CATATGACTCAAAGCAATCTACAAAATCAATGCATTTTCTATCAAAATGC 7033
                         v   ivv i    vii       i v    i   v ii          v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_66252293_6   7034 CAATGACATTTTTCACA-AAACAGAAAAA--AATTACTAAAATTTACATA 7080
                           iivi v     ii  -   iv  v  i--i  i-        i i  i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-CTAAAATTCATATG 152

  chrX_66252293_6   7081 GAATTAAAAGAAAAAAACATAGAGTAGCAAAAGCTACCCTGAGCAGAAAT 7130
                            v iv   ii ---- vi   i    v   i v i i   iv ii  v
  L1M4_orf2#LINE/    153 GAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66252293_6   7131 AACAAAACTGGAGAAATCACGTTACCTGACTTCAAATTATACTACAGAGC 7180
                               ii     i v    ii v  ii i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_66252293_6   7181 CATAGCATATAAAACAGCATAGTCCTGGCATAAAAATAGAGACATGAAGG 7230
                         i i  i vvi  i    ii i  v         ii     v i  ii vv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_66252293_6   7231 AATGGAATAGAATACAGAACCCAG 7254
                                      vv   ii    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAG 322

Transitions / transversions = 1.77 (62 / 35)
Gap_init rate = 0.02 (5 / 319), avg. gap size = 1.80 (9 / 5)  

1837 26.13 0.97 2.26  chrX_66252293_66260913     7509  8128 (493)    L1M4_orf2#LINE/L1      297   908 (0)  

  chrX_66252293_6   7509 TCAATATAATACTAATAATACAGAACCCAGAAAAAAAATCCACACACCTA 7558
                              iv    v----   vv   ii       v   -i   i   ii  
  L1M4_orf2#LINE/    297 TCAATGGAATAG----AATTGAGAGTCCAGAAATAAA-CCCATACATTTA 341

  chrX_66252293_6   7559 TAGT-AACTCCTTTTTGACAAAGATGCTAGGAGCATATGTTTGAAAAAAA 7607
                          i  -  i vv    i     i i   i i  v   viiv v ii   i 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_66252293_6   7608 AGAGTCTCCTCAAAAAAAAATGATGCTGGGAAAACTGGATATCAATATGT 7657
                          v     ii    v   ---  i        v         ? v i   i
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAA---TGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_66252293_6   7658 AGAAGAATGAAACTAGACCCCTCTGTCTCACCATATA-AAAAATAAAATA 7706
                          i         ii i       viv  v         -      v  v v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_66252293_6   7707 AAAATGCAATAAATACTTGAATCTAAGACCTCTAACTATGAAACTACTAC 7756
                               v vi ? v  i i   v     v  vv      i     vi  v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_66252293_6   7757 ATGAAAATATTGGAGAAAATCTTCAGGGCATTTTTCTGGGCAAAAATTTC 7806
                          v     i  v  ? v        iv i v  vvvi i     vii    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_66252293_6   7807 TTGAGCAATAA-ACCACAAGCACCGGCAACCAAAGCAATAAAATGGACAA 7855
                           -  vv  i -    v      vi     v    -  -     i  i  
  L1M4_orf2#LINE/    589 TT-AGATATGACACCAAAAGCACAAGCAACAAAAG-AA-AAAATAGATAA 635

  chrX_66252293_6   7856 GTGGGATTACATTAAG-TTAAAAAGCTCTTGCACAATAAAAGTAACAATT 7904
                         i v   i v   i  i-       -  i   ii vvi   i vv  v  i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chrX_66252293_6   7905 GACAAAGTAAAGAGACAGCCCATGTAATGGGAGAAAATATTTCCAAACTA 7954
                         i v     i  i     i    iiv                 v    ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_66252293_6   7955 CCCATCTGACAAGCGATTAATAACTAGAATATATTAGGAGCTCAAACAAC 8004
                         ivi      i   v  i vi  v i         v i  i   vv     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_66252293_6   8005 TGTATA-TGAAAAACCTCTCATAATCTGGTCAAAAGATGGGCACAAGATT 8053
                          vv   - i    iv vv--    i iii i?   i       v i    
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAA--ATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_66252293_6   8054 TGAATAGATGTTTCTCAAGAGAAGACATACTACTGGCAAACAGGCATATG 8103
                                 ii      v i      i    v v    v  i i   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_66252293_6   8104 AAA-GATGCTCAACATCATTGATTAT 8128
                            -              ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (87 / 71)
Gap_init rate = 0.02 (14 / 612), avg. gap size = 1.43 (20 / 14)  


2926 26.70 0.88 1.53  chrX_66265332_66269566.rev     2831  3744 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66265332_6   2831 TGGAAAGATATTTCATGTTCATGGATTGGAAGAATCATTATATTTAAAAT 2880
                                    ii                    v i v   vv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66265332_6   2881 GTCTATACTACTCAAAGCAATCTACTGATTCAATGCATTCTCTATCAAAA 2930
                          v v     v i    vii      v       i   v  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66265332_6   2931 TACCAATGACATTTTTTACCAAAATAGAAAAAACAATCCCAAAATATATA 2980
                          v   iivi v      i vi    v  v  ivii    i     vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_66265332_6   2981 CAATACCACAAAAGACCCAGAATAGTGAAAGCTATCCCAAGCAAAAAGAA 3030
                         iiiv vii   ii            iv   i v   iii iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_66265332_6   3031 CAGAACTGGTGGAATCACATTACCTGACTTCAAATTATACTACAGAGCTA 3080
                           i ii   v   v     i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_66265332_6   3081 CAATAACCAAAATAACATGGTACTGGCATAAAAACAGACACATACACTAC 3130
                           i   i   i i iii              ii i     i   v ii v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_66265332_6   3131 TGAAATATATTAAAGAACCCCAAAACGAATCCTTGCATATACAGTGAACT 3180
                           i    v v vi   ii  vi   ii  i  v i   v  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_66265332_6   3181 CATTTTTGACAAAGGTTCTAAAAACATACATTTGGGAATAGACT-GTCTT 3229
                         v     i     i   v i  i v   v  v v     -   v -     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAATAGTCTT 399

  chrX_66265332_6   3230 TTCAATAAGTGGTGCTGAGAAAACCGGATTTGAATATGCAAAATAATAAA 3279
                              i  i        i  v   i    v?vv i        v   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_66265332_6   3280 ACTAGTTCCCTATCTCACATCACATACAAAAATCAAATAAAAATGGGTTA 3329
                         ii i vi     i      i  i          i  v v       i i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_66265332_6   3330 AAGAC-TAAATCTAAGATCTCCCACTATTAAACTACTAAAAGAATAC--- 3375
                         ?    -     v     v  vvv     v     vi  i     v  ---
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_66265332_6   3376 -GGATAAACTCTTCAGAACATTAAACTGAGCAAGGATTTCTTGAGTAATA 3424
                         - ?i    -     ivi  v  iiii ii    v i      iii  vv 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_66265332_6   3425 TCCCACAAGCACAGGAAACCAAAGAAAAAATGGACAAATGTTCATGGACA 3474
                         iv   v       i v   v           i  i    -----     v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT-----TGGACT 643

  chrX_66265332_6   3475 AATGATCACAAACAGTTAAAAAAATTCTGCATGGAAAAGGACATAATCAA 3524
                         -- v    -   ---       v-  i  iiivvv        iv     
  L1M4_orf2#LINE/    644 --TCATCA-AAA---TTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_66265332_6   3525 CAAAGTGAAG-GAAAAACCAAAAAATGGGACAAAATATTTGCAAACTATT 3573
                         v        i-  v  v   v i       v              ii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_66265332_6   3574 CATACGACAAGAGATCAATAACAAGAATATATAAGAAGCTCACACAACTC 3623
                         i  vi  i   i  iivi  v v           ii i   vi       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_66265332_6   3624 CATAGAAAAAAATCTAATAATTTGGTT-AAAAATGGGCAAAATATTTGAA 3672
                         v   iv     iv v     iiiii  -             iv       
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_66265332_6   3673 TATACATTTTTCAAAGGAATACACACAAATAGCAAACAGATATATAAAAA 3722
                           v      i  v  i   v i i      i  v  i iii i  i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_66265332_6   3723 GATGCTCAACATCATTGATCAT 3744
                                       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


2567 28.38 1.64 2.51  chrX_66269648_66275181      492  1407 (4127)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_66269648_6   1407 TGCAAAAACATTCTATGTTGATGGATTCAAAAAATCAATATTGTTTTAAT 1358
                           v   i i  i i     v       vi  i v i         vvi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_66269648_6   1357 GTCCGTAACCACCCAAAGCAATCTATGCATTCAATGCAATCCCGGTCAAA 1308
                          v vi  vi -      vii     iiv      i        vi     
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

C chrX_66269648_6   1307 GTACCAATGACATTAATCACAG----TAATAAA-TAATCTTAAAATATAT 1263
                         i v   iivi v  vv ii   ---- i i  i- i   i      vi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

C chrX_66269648_6   1262 ATG--AATCCAAAAAACCCAGAATAGCTAAAGCTATACTAAGGAAAAAAA 1215
                            --   v   iii            i   i v  vi ---      i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT---GAAAAAGA 196

C chrX_66269648_6   1214 ATGAAAATAAAACAAAACACAACAGGAAAAATCACATTCCCTGACTT-AA 1166
                          --------i      iiv-----   ii v     i i  ii i  -  
  L1M4_orf2#LINE/    197 A--------GAACAAAGTT-----GGAGGACTCACACTTCCCAATTTCAA 233

C chrX_66269648_6   1165 AATTATACTACAGCATTTTAATAACAAAAAAAAAAGCATGGCAGTGGCAT 1116
                           i -       ivii vi i   iv  i v --- ii   i v      
  L1M4_orf2#LINE/    234 AACT-TACTACAAAGCTACAGTAATCAAGACA---GTGTGGTACTGGCAT 279

C chrX_66269648_6   1115 ATAAACTGATACATAGACCAATGGAACAGAATAGAAAACCCAGAAATAAA 1066
                          vii iv  i i     i        i     v  i ii           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

C chrX_66269648_6   1065 TCCACACACCTAGTGTGCACTCATTTTTGACAAAGTTGCCAAGAACATAA 1016
                         i   i   ii  vv  vv i v     i     i v        v   vv
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

C chrX_66269648_6   1015 ACTGGGGAAAATAAAGTGTCTTCAATAAATGATGTCAAAA-ATCTATATA 967
                          v        iv v   v i     i     i  iiiii - v  iv   
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

C chrX_66269648_6    966 TCCATATGCAGAAGAATGAAACTAGATTACTATCTCTCACCATGTACAAA 917
                         ?   i     i         ii i  iiv   i   v      i      
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

C chrX_66269648_6    916 ACTAAAATCAAAATGGATTAAACACTTAAGTATAAGACTTCAAACTATAA 867
                          v v  v           i ? v  i   i i     vi v         
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

C chrX_66269648_6    866 AACTACTACAAGCAAATATTTGGGAAATTCTCCAAGACATTGGACTGGGC 817
                             vi  v   v   i  vv ? v  v   i iv   v    ii i   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

C chrX_66269648_6    816 CAGAATTTCTCGAGTAATACCCTACAAACCCAGGCAACCAAAGCAAAAAT 767
                         v vii     iiii  vv  v i v  i v  i     v    v      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

C chrX_66269648_6    766 GGACAAATGGAATCACATTCAG-TTAAAAATGTCAGCACAGAAAAGGATA 718
                         i  i    v i iiv   iv i-       iv iv ii vvv      i 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

C chrX_66269648_6    717 AAATCAA--AAGTGAAGAGACAACCCATAGAATGGGAGAAAATATTTCTA 670
                         vv     --       i          i                   vi 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

C chrX_66269648_6    669 GACTACCCATCTGACAAGGATTTAACGGCCAGAATGTATAAGGAGTTTAA 620
                         i ii ivi      i    ivi viiiv       i     i  ii ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

C chrX_66269648_6    619 AAAACTCTACAG-AAAAAAAAAATTATAATTCAATCAAAAGATAGGCACG 571
                          v     v i i-     i v  --    ii    i?   i  i    vi
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAA--ATAACCCAATTWAAAAATGGGCAAA 827

C chrX_66269648_6    570 AGATTTGAATAGACATTTCTCAAAAGAAGGCATACAGAAGGCAAAT--GT 523
                         i                    v       ii     i v   v   -- i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

C chrX_66269648_6    522 GCATGAAAAGGTGCTCAACATCATTGATTAT 492
                         i         i            ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (160 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.38 (38 / 16)  

3017 26.80 1.33 0.78  chrX_66269648_66275181     4139  5041 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66269648_6   4139 TGGAAGAACATTCCATGCTCATGGCTAAGAAGAATCAATATCATGAAAAT 4188
                              ii i  i     i      v vi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66269648_6   4189 GGCCATACTGCCCAAGGTAATTCATAGATTCAATGCCATCCCCATCAAGC 4238
                            v     v     iv i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66269648_6   4239 CACCAA-TGACTTTCTT-CAAAGTATTGGAAAAAACT-ACTTTACAGTTC 4285
                         iv   i-  v    i  -  i i-    -- v  i  - iii  v i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_66269648_6   4286 ATATGGAATCAAAAAAGAGCCCGCATTGACAAGACAACCTTAATCCAAAA 4335
                                 viiv  ii  v  v v  v v   i    i   i vvv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_66269648_6   4336 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 4385
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_66269648_6   4386 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 4435
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_66269648_6   4436 CAATGGAACAGAAC--AGAGCCCTCCGAAATAATGCCACATATCTACAAC 4483
                                 i    i--    i  --v       vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_66269648_6   4484 CATCTGATCTTTGACAAACCTCAAAAAAACAAGCAATGGGGAAAGGATTC 4533
                           vi    i  i     ivv vvv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_66269648_6   4534 CCTATTTAATAAATGGTGTTGGAA-AACTGGCTAGCCATATGTAGAAAGC 4582
                         i  v  i  i        i   i -      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_66269648_6   4583 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGG 4632
                             ii    i    v   i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_66269648_6   4633 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCGTAGAAGAAAA 4682
                           i ?    i       v   v       i      vi v          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_66269648_6   4683 CTTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGGCTTCATGTCT 4731
                          v    ?i- v i -   iv   v v  vv i     v  i   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_66269648_6   4732 AAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCT 4781
                          vi            vvi          vv i   v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_66269648_6   4782 AATTAAACTAAAGAGCTTCAGCACAGCAAAAGAAACTACCATCAGAGTAA 4831
                         v  i   v v  i i   iv ii vv    i  v    i  vv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_66269648_6   4832 ACAGGCAAGCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 4881
                          v  i   v i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_66269648_6   4882 AAAGGGCTAATATCCAGAATCTACAACGAACTCAAACAAATTTACAAGAA 4931
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_66269648_6   4932 AAA-----ACAACCCCATTCAAAAAGTGGGTGAAGGATATGAACAGACAC 4976
                            ----- i     v   ?     -    ii      v    i     i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACAT 843

  chrX_66269648_6   4977 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACACGAAAAAATGCTC 5026
                              v        i  vi viii     v ii    i     i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_66269648_6   5027 ACCATCACTGGTCAT 5041
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


2407 28.60 2.68 1.23  chrX_66282719_66286620     2515  3409 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66282719_6   2515 TGAAAAAACAGTTCATGCTCATGGATAGGAAGAATTAGTAACTTTAAAAT 2564
                           i   i i vii    i        v      v   i  viv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66282719_6   2565 GGTCATAGTTCCCAAAGCAGTTCATAGATCTAATGCTATTCCTATTAAAC 2614
                           iv   v i      viii ii i    ii  i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66282719_6   2615 TACCA-TTGAGATTCTT-CAGAGCAGTAGAAAAAAATATTTTAAAATTCA 2662
                          v   -i  vvv  i  -    -- i v  v  ivvv  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA--AATTGACAAGCTGATCCTAAAATTCA 148

  chrX_66282719_6   2663 CAGGGAACCA-AAAAGAGCCTGAATAACCAAGGTAATCCTAAGCAATAAG 2711
                         i v    vii-  ii  v  v     i    iii    i i iv  v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66282719_6   2712 AACAAAGTTAGAGGCATCACCCTAACTGACTTCAAA-CTAATCTGCAGGA 2760
                                  i    vv    v  vv ii i      -  v -  i  iii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAAAG 247

  chrX_66282719_6   2761 CTATAGAAACCAAAACAGCATAGTAGTAGTATGAATACAGACACATAGAC 2810
                            i  v  i   i    ii i   v i i  i iv i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_66282719_6   2811 CAATGGAACAGAATAGAGAACCCAGAAATAAGACCGCAAACCTACAACTA 2860
                                 i     v    ii          iv  ii v ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_66282719_6   2861 TTTGATCTTCAACACACCTGATAAAAACAATCACTGGGGAAAGTATTCCC 2910
                         v     i   i   vivv  vi  i v  v   v         v  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_66282719_6   2911 TATTCAATAACTGGTGCTGGGATAACTGGATAGCCATAGGCAGAAGA-TT 2959
                          v     i  v           i         ?   i v   i    - v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_66282719_6   2960 AAATTGGACTCCTTCATTACACCATATACAAAAATTAACTCGAGATAGAC 3009
                           i      i   v v i                       i i  i  i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_66282719_6   3010 TAAAGACTCAAATGTAAAACTCAAAACTATAAAAGCCCTGAAAGACAACC 3059
                         i ?    ii        i vii            vi i ii    v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_66282719_6   3060 TA--TGCAATGCCATTCA-AACCATAGGCACTGGCAACAATTTCAT-GAT 3105
                           --? i  vv --   i-i   v i  i-iv     iii    v -   
  L1M4_orf2#LINE/    548 TAGGNGTAAATC--TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_66282719_6   3106 GAAGATGTCAAAAGCAGTTGCAAAAAAAAACGAAAATTAACAAATGTGAT 3155
                         - v  iii        vvv    v    i -i     vi i    vv  i
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGAC 642

  chrX_66282719_6   3156 GTAATTAAACTAAAGAGCTTTTACACAGAAAAAGAAAATATCAACAGAGT 3205
                         v v  i   v v  i i     iii vvv   i  v v      v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_66282719_6   3206 AAACAGACAACATACAGAATGGGAGAAGTT-TTTGAAAACGATGCATCTG 3254
                         i  v       vi              iv -    v   iv  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_66282719_6   3255 ACAAA-------TATCCAGGATCTATAAGGAACTTTAACAAATTTACAAG 3297
                          i  i-------       i  v     i     i v    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_66282719_6   3298 AAAAAAAACAAAGAACCCA-TGAAAAAGGGGGCAAAAGAC----ATAAAC 3342
                              i -    v      - v?    iv       i  i----   i  
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_66282719_6   3343 --TTTTCAAAAGAAGACATACCTGCAGCCAACATTCACATGAAAAAAAAA 3390
                         --  i  v        i    vviii     i vv          i vi-
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG- 890

  chrX_66282719_6   3391 TCTCAACATCACTGATCAT 3409
                         -          ????????
  L1M4_orf2#LINE/    891 -CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (152 / 100)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.67 (35 / 21)  


1083 26.55 0.73 0.73  chrX_66311753_66318358.rev     2000  2274 (4332)  C L1M4_orf2#LINE/L1   (633)   275     1  

C chrX_66311753_6   2274 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2225
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_66311753_6   2224 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2175
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_66311753_6   2174 TACCGATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2127
                          v  iiivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_66311753_6   2126 TATAGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 2077
                            i   viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_66311753_6   2076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTCTACTACAAGGC 2027
                                i      vv       v  ii i      vii        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_66311753_6   2026 TACAGTAACCAAAACAGCATGGTACTG 2000
                                 i   i    ii        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTG 275

Transitions / transversions = 2.04 (49 / 24)
Gap_init rate = 0.01 (3 / 275), avg. gap size = 1.33 (4 / 3)  

1885 26.10 0.20 0.00  chrX_66311753_66318358.rev     2355  2856 (3750)    L1M4_orf2#LINE/L1      406   908 (0)  

  chrX_66311753_6   2355 AAATGGTGTTAGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGA 2404
                                 i i   v      v  ?   i   i i  iiv    ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_66311753_6   2405 TCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGACT 2454
                         i    v   i     v           i  i    i      i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_66311753_6   2455 TAAACGTTAGATCTAAAACCATAAAACCCT-AGAAGAAAACCTAGGCATT 2503
                             i  v   v       i       i  -          v    ?i v
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_66311753_6   2504 ACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAA 2553
                          viv   iv   v v  vv i     v ii   v ivv  vi        
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_66311753_6   2554 AGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTCA 2603
                             vvi          vv     v  i    v   ii v  i   v i 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_66311753_6   2604 AGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCT 2653
                          i i   i  ii vv    i  v    i  vv i      v  i     i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_66311753_6   2654 ACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAGGGCTAAT 2703
                            i             v  ii   vii ivi      i  i  i  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_66311753_6   2704 ATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACA 2753
                                  v  i  v      vv    v iv i  v     i     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_66311753_6   2754 ACCTCATCAAAAAGTGGGTGAAGGATATGAACAGACATTTCTCAAAAGAA 2803
                            iv  i?    i    ii      v    i           v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_66311753_6   2804 GACATTTATGCAGCCAAAAGACACATGAAAAAATGCTTATCATCACTGGC 2853
                           i  vi viii     v ii          i     i v     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_66311753_6   2854 CAT 2856
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.40 (74 / 53)
Gap_init rate = 0.00 (1 / 503), avg. gap size = 1.00 (1 / 1)  

3060 27.31 0.55 0.55  chrX_66311753_66318358.rev     5208  6115 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66311753_6   5208 TGGAAACACATCCGATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 5257
                               v i    v   i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66311753_6   5258 GACCATACTGCCAAAAGCAATCTACAAATTTGACACAATTCCCATCAAAA 5307
                          i v     v  v   vii       i   ii  i    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66311753_6   5308 TACCACGAT-CTTTTTTTACAGAGTTAGAAAAAACAATTCCCAAACTCAT 5356
                          v   - v - i      i    iv v  v  ivii  i iv   i    
  L1M4_orf2#LINE/    101 TCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_66311753_6   5357 ATGGAACCAAAAAATGAGCCTGCATAACCAAAGCAAGACTAAGTAAAAAG 5406
                               viiv  ii-  v  v v   i     i   vvi i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66311753_6   5407 AACAAACCTGGAGGTATCACACTACCTGATTTCAAACTATACTATAAGGC 5456
                               vi      vv       v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_66311753_6   5457 CATAGTCACCAAAACATCATGGTACTGGTATAAAAATAGGCACATAGACC 5506
                         i i   v i   i   vii         i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_66311753_6   5507 AATGGAACAGAATAGAGAACCCAGAAATAAACCAAAATGCTTATGGCCAA 5556
                                i     v    ii             v v iii      i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_66311753_6   5557 CTGATCTTTGACAAGGCAAAGAAAAAAACA---AATTGAGGAAAGGACAC 5603
                         i    i  i       --iv vv  i v  ---   - i      i i v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG--GTGCCAAGACCATTCAAT-GGGGAAAGAATAG 395

  chrX_66311753_6   5604 CTGTTTCAACAAATAGTGCTGGGATAATTGACTAGCCACATGTAGGAGAA 5653
                         iiv           i         i  i  iv  ?       i ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_66311753_6   5654 TGAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTTAAGATAA 5703
                             ii    i  ii i   v    v           i    i  i  ii
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_66311753_6   5704 ATTAAAGACTTAAATCTAAGACTTGAAACTGTAAAAATTCTAGAAGATAA 5753
                           i ?    i     v     vi i     i     v ii       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_66311753_6   5754 CTTTGGAAAAACCCTTCTAAACATTGGCTTATGCAAGGATTTCATGACTA 5803
                          v v  ?iv  vi    vvi  v    v   v    v i    v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_66311753_6   5804 AAAACCCAAAAGCAATTGCAATAAAAACAAAGATAAATATCTGAGACCTA 5853
                         vi vv         vvv    i    iv   i   i   vv vi   i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_66311753_6   5854 ATTAGA-CTAAAGAGTTTTGCATGGCAAAAGGAACAGACCACAGAGTAAA 5902
                           i i -i    i v     iiivv    i iv  viv v v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_66311753_6   5903 AAGACAACCCACATAGTGGGAGAAAATCTTCACAATCTATACACCCAACA 5952
                                      v i           v  ii   vii   i i ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_66311753_6   5953 AAAGAATAATATCCAGGATATACAACTAACTCAAACAAATCAGTAAGAAA 6002
                          ii  v vi       i     i  vv     vv    v   i   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_66311753_6   6003 AAAACAATCAATCCCATCAAAAAGTGGGCTAAGAACATGAATAGACAATT 6052
                           i    vi  i  v  i?    i     v   i iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_66311753_6   6053 CTCAAAATAAGATACACAAATGGCCAACAAACATATGAAAAACTGCTCAA 6102
                            v   v      i            i  i  i       iv       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_66311753_6   6103 CATCACTAATGGT 6115
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2996 28.43 0.88 0.44  chrX_66324430_66330126.rev     4303  5206 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66324430_6   4303 TGGAAGAACATTCCACGCTCATGGGAAGCAAGAATCAATATCATGAAAAT 4352
                              ii i  i   i i      ivv v    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66324430_6   4353 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4402
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66324430_6   4403 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4450
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_66324430_6   4451 TATGGAACCAAAAAATAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 4500
                                viiv  iiv v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66324430_6   4501 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4550
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_66324430_6   4551 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4600
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_66324430_6   4601 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 4648
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_66324430_6   4649 CTCTGATCTTTGACATACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4698
                         vvi    i  i    vivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_66324430_6   4699 CTATTTAATAAACGGTGCTGGGAAAACTGTCTAGCCATTTGTAGAAAGCT 4748
                           v  i  i   i          v     vv  ?   iv  i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_66324430_6   4749 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4798
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_66324430_6   4799 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4848
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_66324430_6   4849 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4898
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_66324430_6   4899 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4948
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_66324430_6   4949 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4998
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_66324430_6   4999 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5048
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_66324430_6   5049 AGGGCTAATTTCCAGAATCTACAATGAGCTCAAACAAATTTACAAGAAAA 5098
                         i  i  vi v        v  i  v  i   vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_66324430_6   5099 AAACAA----CCCCATCAAAATGTGGGTGAAGGACATGAACAGACACTTC 5144
                          i    ----   v  i?   vi    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_66324430_6   5145 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5194
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_66324430_6   5195 ATCACTGGCCAT 5206
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (150 / 103)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


1917 25.17 4.30 0.66  chrX_66332144_66333733      495  1098 (492)    L1M4_orf2#LINE/L1      283   908 (0)  

  chrX_66332144_6    495 GGTAG-CATATAAACCAATGGAACAGAATAGAGAACCCAGAAATAAAGCC 543
                          i   -      i i        i     v    ii           v  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_66332144_6    544 AAATACTTACATCCAATTGATCTTTGACAAAGCATACAAAAAC-ATATAG 592
                          v i i   iivi        i  i     i -i i v  i  -  vi i
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAA 381

  chrX_66332144_6    593 TGAAGAAAGGACACCCTATTCAATAAATGATGCTGGGAAAATTGGCAAGC 642
                           ii     i i vi  v     i     i        v  i   vv ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_66332144_6    643 CACCTGAGGAAGAATGAAATTGGATCCCCATCTCTCACCTTATACAAAAA 692
                            v  vii         i     i   i i   v    v          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_66332144_6    693 TCAACTCAA----GACCAAAGACTTAAGTCTAAGACCTGAAACCATAAAA 738
                          i       ----  i  ?    i   i v     v  i    i      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_66332144_6    739 ATTATAGCAGATAACATTGGAA-AACTCTTCTAGACATTGGCTTAGGTGA 787
                         v iv   v   v     v  ?i-  v     vv   v    v     ii 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_66332144_6    788 AGACTTCAT-GACTTAGCACCCAAAAGCAAATGCAACACAAACAAAAATA 836
                         v ii   v -  iv ii    -       v v      v  iv       
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACC-AAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_66332144_6    837 AATAAGTGGGACCTAACTAAAATAAAAAGCTTCTGCACAGCAAAAGAGAT 886
                         i    i v    i v ii     v    i   i  ii vv    i  v i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_66332144_6    887 AATCA------------GACAACCCACAGAATGGGAGAAA-TATTTGCAA 923
                         v    ------------                       -         
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_66332144_6    924 CCTATGCATTTGACAAATGACTAATATCCAGAATCTACAAGAAACTCAAA 973
                         vii  ii  i   i  iv    vi          v  i  ii     vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_66332144_6    974 CAAATCAGCAAGAAAAAAA-----AATCCCATCTAAACATGGTCAAATGA 1018
                            v   ii  v     i -----  i  v  i?   v    v    v  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_66332144_6   1019 CATTAACAGACAATTATCAAAAGAAGATATACAAACAGCCTGCCAATATA 1068
                         iv v  i     v  v  v                ii   viiv ii i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_66332144_6   1069 TGAAAAAAAATGCTCAAAATCTCTAATCAT 1098
                               i --       v   v????????
  L1M4_orf2#LINE/    881 TGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (86 / 62)
Gap_init rate = 0.02 (11 / 626), avg. gap size = 2.73 (30 / 11)  


1164 27.15 2.87 1.10  chrX_66359812_66367607     3648  4100 (3696)    L1M4_orf2#LINE/L1      448   908 (0)  

  chrX_66359812_6   3648 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGCTGAAT 3697
                           ii         v   i     v                   iv  i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_66359812_6   3698 TAAATATTTAAATGTAAGACATAAAACCACAAAAACTCT-AGAAGAAAAC 3746
                         i ? v ii           vv      i i    -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chrX_66359812_6   3747 CTAGGCA-ATACCATTCAGGAAATAGGCATGGGCAAAGACTTCATGACAA 3795
                         v    ?i- v i -   iv  vv v  vv i     v ii   v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_66359812_6   3796 AAACACCAAATGC-CATGGCTACAAAACCCAAAATTGACAAATGGGATCT 3844
                         vi        v  -  -i  v      vvv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_66359812_6   3845 -ATTTAAACTAAAGAGCTTCTGCAAAGCAGAAGAAACTATCATCAGATTG 3893
                         -  iv   i    i -   i  iivvv  i i  v       vv i v  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_66359812_6   3894 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCATCTGA 3943
                           v  i     i                 v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_66359812_6   3944 CAAAGCACTAATACCCAGCATCCACAAAGAGCTTAAACAAATTTACAGGA 3993
                         i  i v   vi  i    v  vi i     i  ivv    v iv i iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_66359812_6   3994 AAAA-----ACAACCCCATCAAAAAGTGGGTGCAGAATATGAACCGACAC 4038
                             ----- i     v  i?    i    iiv  i  v    iv    i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_66359812_6   4039 TTCTCAAAAGACATTTATGCA----GCCAAGAACCATGTAATAAAAAGCT 4084
                              v     - vv   i  ----     v  v  ii i v  i v   
  L1M4_orf2#LINE/    844 TTCTCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_66359812_6   4085 CATCATCACTGATCGT 4100
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.03 (61 / 59)
Gap_init rate = 0.02 (11 / 461), avg. gap size = 1.64 (18 / 11)  

1848 28.26 3.18 1.00  chrX_66359812_66367607     6565  7162 (634)    L1M4_orf2#LINE/L1        1   611 (297)  

  chrX_66359812_6   6565 TAGAGAAACATTCCCTGCTCATGGATAGGAAAAATCAGTATCAT-AAAAT 6613
                          i  i i i  i  v  i        v    i v i i   ii -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66359812_6   6614 GGCCATACTGTCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 6663
                            v     vi     v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66359812_6   6664 TACCATAGACTTCCTTCACAGAA-TT-AGAAACTCTTCTTTGAATTTCAT 6711
                          v   vvvi i ii  ii     -  - v  i  vv  i vi    -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT-CAT 149

  chrX_66359812_6   6712 ATGGAA---CCAAAAACCGTATGTATAGCCAAGACAATCTTAAGCAAAAA 6758
                               --- v iii   -i - v        i        i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACC-CA-GAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_66359812_6   6759 GATCAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAAA 6808
                           v     i      vv    v  v  ii i      viv         i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_66359812_6   6809 TTACCATAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 6858
                         i   vi   i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_66359812_6   6859 AAATGGAACAGAACAAAGGCCTCAGAAATAACACCAAACATCTACAGCCA 6908
                         v       i    ivi  ivii         vv   v    i  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_66359812_6   6909 TCTGATCTTTGCCAAAACTG--AAAAACAAGCAATGATGAAAGGATTTCC 6956
                         vi    i  i v   iiv  --  i v  vv     iv     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_66359812_6   6957 TATTTAATAAATGGTTTTGGAAAAACTGACTAGTCATGTGCAGAAAACTG 7006
                          v  i  i       vi   i v     iv  ?i  ii    i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_66359812_6   7007 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAATATGGAT 7056
                           ii         v   i     v                   v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_66359812_6   7057 TAAATATTTAAATGTATGACTTAAAACCACAAAAACCCTAGAGGAAAACC 7106
                         i ? v ii        v  vi      i i    vi i    i      v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_66359812_6   7107 TAGGCA-AGACCATTCACAACAT--AGTCATGGGCAAAGACTTC------ 7147
                             ?i- i i -   iii  v --i  i --     v ii   ------
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGAT 594

  chrX_66359812_6   7148 ATGACA--AAAAACACA 7162
                               --    i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACA 611

Transitions / transversions = 1.86 (108 / 58)
Gap_init rate = 0.02 (14 / 611), avg. gap size = 1.79 (25 / 14)  

 439 20.71 5.71 0.00  chrX_66359812_66367607     7163  7302 (494)    L1M4_orf2#LINE/L1      761   908 (0)  

  chrX_66359812_6   7163 GAATCTACAAGGAACT--TA-AATTTA-CAAGAAAAAAACAAACAACCCA 7208
                             v  i  i     --  -  i i -i  v     i     i      
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_66359812_6   7209 -TCAAAAAGTGGACAAAGTATATGAACAGACACTTCTCAAAAGAAGACAT 7257
                         - i?    i   i     v  v    i     i     v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_66359812_6   7258 TTATGTGGCAAAAAAACACATGAAAAACAGCTCA---TCATGTCTGGT 7302
                         vi vi    v  v  i          ivv     ---   ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (17 / 11)
Gap_init rate = 0.03 (5 / 148), avg. gap size = 1.60 (8 / 5)  


 456 33.53 0.00 0.00  chrX_66388927_66394997      136   302 (5769)  C L1M4_orf2#LINE/L1   (718)   190    24  

C chrX_66388927_6    302 GATAGGAAGAAACAATATTGTGAAAATGGCCATACTGCCCAAGATAATTT 253
                            v      vvi        v  i     v     v     iv i  i 
  L1M4_orf2#LINE/     24 GATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCT 73

C chrX_66388927_6    252 ATAGATTCAATGTTATCACCATGAAGCTACCATTGACTTTCTTCACAGAA 203
                          i        i iv   v i  v  iv v   vivi i  i  ii     
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAA 123

C chrX_66388927_6    202 CTAGAAAAAACTACTTTAAATTTCATATGGAACCATAAAATAGCCCATAT 153
                         v v  v  iviv iii    v           viii  iiv v  viv  
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

C chrX_66388927_6    152 AGCCAAGATAATCCTAA 136
                               i i    i i 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGA 190

Transitions / transversions = 1.24 (31 / 25)
Gap_init rate = 0.00 (0 / 167), avg. gap size = 0.00 (0 / 0)  

 594 30.32 0.00 0.53  chrX_66388927_66394997      303   490 (5581)    L1M4_orf2#LINE/L1      207   393 (515)  

  chrX_66388927_6    303 TGGAGGCACCATGCAACCTGACTTCAAACTATACTACAAGGCTACAGTAA 352
                               vvi  ii vv  ii i      viv        i          
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_66388927_6    353 CCAAAACAGCGTTGGTACTGGTACCAAAACAGATATATAAACCAATGGAA 402
                         i   i    i  -        i iv ii i   i     i i        
  L1M4_orf2#LINE/    257 TCAAGACAGTGT-GGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_66388927_6    403 CAGAACAGAGGCCTCAGAAATAATGACACACATCTACAACCATCTGATCT 452
                         i    iv   ivii         vvv  i    i  iiii  vi    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_66388927_6    453 TTGACAACCCTGATAAAAACAAGCAATAGGGAAAGGAT 490
                          i     vvv  vi  i v  vv    i       i  
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

Transitions / transversions = 1.85 (37 / 20)
Gap_init rate = 0.01 (1 / 187), avg. gap size = 1.00 (1 / 1)  

3082 27.28 0.66 0.77  chrX_66388927_66394997     4670  5578 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66388927_6   4670 TAGAAAAACATTCCATACTCATGGATAGGAAGAATCAACATCGTGAAAAT 4719
                          i    i i  i    ii        v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66388927_6   4720 GGCCATACTGCCCAAGGTAATTTATAGATTCAACGCTATCTCCATCAA-- 4767
                            v     v     iv i  i  i           v   i i     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66388927_6   4768 TCTGCAATTGACTTTCTTCACAGAA-TTGGAAAAAAAAGACTTTAAATTT 4816
                           i-  ii  v    i  -i     -   -- v  ivv  iii    v  
  L1M4_orf2#LINE/    101 TCC-CAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_66388927_6   4817 CATATTGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAA 4866
                              v   viiv  ii  v  viv        i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_66388927_6   4867 AGAACAAAGCTGGAGGCATGATGCTATCTGACTTCAAGCTATACTACAAG 4916
                                  i      vv v ii  vi ii i     iviv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_66388927_6   4917 GCTACAGTAATAAAAACAGCATGGTACTGGTACCAAAATAGATATATAGA 4966
                                    v  i    ii         i iv ii     i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_66388927_6   4967 CTAATGGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACAACC 5016
                         ii       i     v   ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_66388927_6   5017 ACCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGCAAGGATTCC 5066
                          vi    i  i     ivv  v   i vi vv        v   i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_66388927_6   5067 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 5116
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_66388927_6   5117 GATACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 5166
                           vii    i    v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_66388927_6   5167 TTAAATACTTAAATGTGAGACCTAAAAAGCATAAAAACTCT-GGGGGAAA 5215
                          i ? v  i       i   v      v-i      -    -i ii    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAAC-TATAAAA-CTCTTAGAAGAAA 544

  chrX_66388927_6   5216 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAC 5264
                           v    ?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_66388927_6   5265 TAAAACACCAAAAATAATAACAACAAAAGCCAAAATAGACAAATGGGATC 5314
                           vi         ii vv i         vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_66388927_6   5315 TAATTAAA-CTAAAGAGCACTGCACGGTAAAAGAAACTATAATCAATGTG 5363
                          v  i   -i    i vivi  ii vvi   i  v     v vv  v   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_66388927_6   5364 AACAGGCAACTTACAAAATGGGAGAAAATTTTTGCAATCTATCCATCTGG 5413
                           v  i    ii   i             v       vii  vi     i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_66388927_6   5414 CAAAGGGCTAACATGCAGACTCTATAAAGAACTTAAACAAATTTACATGA 5463
                         i  i  i  vii  v    v v           ivv    v iv i vv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_66388927_6   5464 AAAAAACAAACAATCCCATCAAAAAGTGGGCAAAGTATATGAACAGACAC 5513
                             i     i  i  v  i?    i         v  v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_66388927_6   5514 TTCTCAAAAGAAGATTTTTATGCAGCCAACAAACATATGAAAAGATGCTC 5563
                              v         v vi viii     i  i  i              
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_66388927_6   5564 ATCATCACTGGTCAT 5578
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.18 (13 / 11)  


2198 28.09 3.03 1.24  chrX_66396784_66398952.rev      789  1678 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_66396784_6    789 GAAACACTTCCCATGCTCATGAAAGGGTAAAGTCAATATTGTGAAAATGA 838
                             v iv       i     i vv  v i v i        v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_66396784_6    839 CCATACTGCCAAGAGCAAACTAGAAATTGAATAAAATTCCCATGAACATA 888
                          v     v  v i vii v   v i   v  iiv   i  i  v  v  v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_66396784_6    889 CCA-TTATTATTCTTCACAGAACTAGAAAAAA-AATCCTAAAATTCATAT 936
                            -i iii-  i  ii     v v  v  iv-i                
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_66396784_6    937 GGAACCAAAAAAGAGCCCACATAGCCAAAGCAATACTAAGCAAAAAGAAC 986
                             viiv  ii  v  viv         i    vi i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_66396784_6    987 AAATCTGGAGGTATCACATTACCTGACTTCAAACTATACAACAAGTCTAT 1036
                            vi      vv     i v  ii i      viv   v    iv   i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_66396784_6   1037 AGTCATCATAATAGCACAGTATTGGTATAAA-ATAGGCACATATACCAAT 1085
                            v    vi i  iiii   i   i    i-    i  i   v i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_66396784_6   1086 GGAATAGAATAGTAAGACTAGAAATAAAGGCAAATACTTACAGCCAACTG 1135
                                   v vi  v i         vv  v i i   ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_66396784_6   1136 -TTTTTGAGAAAGCAAACAAAAAC-TTGAAGTGGAGAAGTGACACCCTAT 1183
                         -    i  v  i vviv   i v -  v  -   i   ivi i vi  v 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTTT 400

  chrX_66396784_6   1184 TCAATAAATTTTGTCGGTAAAATTGGTAAGCCACATGTAAAATAATAAAA 1233
                             i    vv  ii  v v  i   vv ?       i    v   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_66396784_6   1234 CTGGATCTTCATCTTTTGCCTTATA-AAAAAT-AACTAAAAATGGATAAA 1281
                         i    i iii i  ivii  v    -      -    v         v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_66396784_6   1282 AGACTTAAATCTAAGACCAGAAATCATAAAAACTCT-AGAAGATAACATT 1330
                             i     v     v vi   ii      -    -      v     v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATA 549

  chrX_66396784_6   1331 GGAAAAACTCTT-GTAGACATTGGCTTAGGCAAAGAATTCATGACTAAGA 1379
                           ?iv  v    -  -   v    v        v iv   v iiv  v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_66396784_6   1380 TCCCAAAAGCAAATGCAACAAAAACAATAATAATTAAAGCAGACCTAATT 1429
                         iv         v v         iv  v    iv    vii   i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_66396784_6   1430 CA--CTACAAAGCTTCTGCACATCAAAATAAATAATCATCAGAGTAAACA 1477
                         v --i  -   i   i  ii v     iv v iv    vv i   i  v 
  L1M4_orf2#LINE/    649 AAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_66396784_6   1478 GACAACCCACAGAATGGAAAAAAAAAATCTTTGCAAACTACACAACTGAC 1527
                                          i i    --- v        ii i i v    i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAA---TATTTGCAAATCATATATCTGAT 744

  chrX_66396784_6   1528 AAAGGACTAGTATTGATAATCTACAAAGAACTC----AAATCAACAAGAA 1573
                           i     v    iv v   v  i         ----  v    i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_66396784_6   1574 AAAAACAACAAATGATTCCATC-AAAATTGGGCAAAA-ATATGTACAGAC 1621
                            i    ---  i ii v  i-    v        i-  v  v i    
  L1M4_orf2#LINE/    795 AAAGACAA---ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_66396784_6   1622 AATTCTT-----AAGATATA--AATG--CAACAAATATAGGAAAA-ATGT 1661
                          v    i-----        --    --   i  ii i v     -   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_66396784_6   1662 TCAATATTACTAATTAT 1678
                             i  i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (137 / 110)
Gap_init rate = 0.03 (24 / 906), avg. gap size = 1.58 (38 / 24)  


2691 20.20 1.95 13.37  chrX_66407292_66409870     1062  2086 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66407292_6   1062 TAGAAAAACATCTCATGCCCATTGGTTAGAAAACT--GTATTGCTAAAAC 1109
                          i    i i   i    ii   v i  i   i   --i     i   i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66407292_6   1110 AGCAATGCTCCCCAAATTCATGTACAGATTTGAGGCAATTGTTATGGGAA 1159
                         i     i           v  v        ii v     ivi   vii  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66407292_6   1160 ATGCAGGTGACTTAGTTGCAGAAATTAAAAAGCTGGTTCTAAAATTTATA 1209
                         viv   v  v   vv           i v      i i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_66407292_6   1210 CATAAATGCAAAGGACCCAATATTACCAAAACAATCTTGAAAAAGAA--- 1256
                         iiv        i       iv  vi                      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_66407292_6   1257 CAATGTGGAAAAACTTACACTTCCAGGTTTCAAAATTACAAAATTTACTG 1306
                            v  v i ii   i        ------   --  v     i     i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCC------CAA--TTTCAAAACTTACTA 242

  chrX_66407292_6   1307 CATATCTGAACATGTATAGATTTCAAGGCCTGGGTAATCAAGACTGTGTG 1356
                           v v  --   ---------------------           v     
  L1M4_orf2#LINE/    243 CAAAGCT--ACA---------------------GTAATCAAGACAGTGTG 269

  chrX_66407292_6   1357 GTACTGGCATAAGAACAGACGTACAGATTAATGTAATAGAACTGAGAGAC 1406
                                      i i    i  i    i    v       i      v 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_66407292_6   1407 CAGGAGTAAATCTTCACCATTGTATTCAGTTGATTTTAGACAAAGGTACC 1456
                            i i    i ivi  vv  i iv   i        v     i   i  
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_66407292_6   1457 AATAAAATTAAAGGAGAAAAAAATCATCTTT-CAACAAACAGTGCTGTGA 1505
                           v vv   v  v i i   i   vi     -       ii      v  
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_66407292_6   1506 CAACTGGGTAACGGCATGTTAAAAAATGAAGTTGTACTCCTAGCTTACA- 1554
                                i  ? vi    iv   i          v  i    v  i   -
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_66407292_6   1555 ----TACAAAA-TTAACTGAAAATGCATTTACAACCTAGATGTAAGAACT 1599
                         ----       -      v      v  iv?vi     i        i  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_66407292_6   1600 AAAACCATAAAACT--TAAAAGAAAACACGAATATAAATGTTTATAACCT 1647
                              i        --  i         iiii?i     v  ii i    
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_66407292_6   1648 AGAATTGAGCATTGGTTTCTTTTATTATTATTATTATTGTTAACTTTTCT 1697
                         v ii  ii   v         -----------------------------
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTT----------------------------- 590

  chrX_66407292_6   1698 AGCTGCATAGTAGCTGTATATATTTATGTGTTACAGGAGATATTTTGACA 1747
                         -------------------------------------      ---    
  L1M4_orf2#LINE/    591 -------------------------------------AGATAT---GACA 600

  chrX_66407292_6   1748 CAGGCATGCATTGCTTTCTTAGCTATGACACCCATTTGCAAGAAACAAAA 1797
                          -------  -------------- vii   --------   v       
  L1M4_orf2#LINE/    601 C-------CA--------------AAAGCAC--------AAGCAACAAAA 621

  chrX_66407292_6   1798 -AAAAAGTAGTTAAACTGGAAGTCACCAACATTTTAAAAA-TATTGTTCT 1845
                         -     i   v    i    vv   i   v   --     - v    v  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATT--AAAAACTTTTGTGCT 669

  chrX_66407292_6   1846 TCAAAATATATCATCAATAAAGTGAAAAGACATCTTCCAGAATGGGAGAT 1895
                              iv i ii     v              v iiv            v
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_66407292_6   1896 AATGCC-ACAAATCCTATATCTCATGTGAAACTTGTCTCTAGAATATAGA 1944
                            iii-i      v       v  iv ii      v  i        v 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_66407292_6   1945 ATGTACTACTATG-TTCTATATTTTTTTAAGAAAACAGA-AACCTAACTT 1992
                          v v   vi  ii-i  v   v -----  i  i   i -    i  i ?
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAAT-----AAAAAGACAAATAACCCAATTW 814

  chrX_66407292_6   1993 TTAAATAGGCAAAAGGTCTTATTAAACAGTTTTACAATGTAGATATACAA 2042
                         vv    i      i i i v v  i   v  i v   v v          
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_66407292_6   2043 CATAGCTAATTAGCACATGGAAATA-GTACAATATCATTAGCCAC 2086
                         -  i  i   v        i   v - iv   i    ????????
  L1M4_orf2#LINE/    865 -ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (122 / 81)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 6.54 (157 / 24)  


1683 30.78 1.88 0.31  chrX_66415419_66418582.rev      502  1141 (2023)    L1M4_orf2#LINE/L1      207   856 (52)  

  chrX_66415419_6    502 TGGAGGCATCAGATTACCTGACTTCAAACTATACTATAAGGCTATAGTCA 551
                               vv   v i v  ii i      viv     i  i    i   v 
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_66415419_6    552 CCAAAACAGCATGGTACTTGTATAAAAATAGACACAGAGACAAATAGAAC 601
                         i   i    ii       v i    ii       i v   iv   i   i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_66415419_6    602 AGAAGAGACAACCCAAAAATGCACCCAAACACTGACAGCCAACTTGTCTT 651
                             vv  v ii   i    iv     v   i v ii i   i vi i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_66415419_6    652 TGACAAAGGAAACAAAAACATAAAGTGAGTAAATGATACCCTATTCAACG 701
                         i     i  viv   i v   vv i  i v   vi   vi  v      i
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_66415419_6    702 AACAGTGCTTACATAATTGGGAAGCCACATGTA---GAATGAAACTGGAT 748
                           ii     viv i  i   iv ?       i ---       ii    i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_66415419_6    749 TCTCATCTCTCATCTTATACCAAAATCAACTAAAGATAGATCAGAGACTT 798
                         i ii i   v  i v     v     i    v  i  i     ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_66415419_6    799 AAATCTAAGACGTGAAATTATAAGAACTCT-AGAAGATAACATTGGAA-A 846
                             v     vv i   i     -      -      v     v  ?i- 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_66415419_6    847 AACCCTTATAGAGATTGACTTAAATAAAGCCTTCATGACCAAAATCCCAA 896
                           i i ii -  vv   iv   iii  v vi   v iivi vi iv    
  L1M4_orf2#LINE/    556 AATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_66415419_6    897 AAGCAAATGCAACAAAAACAAAGATAAATAGCTGAGACTAAATTAATCTA 946
                              v v         iv   i   i   iv vi    vv  i  vv v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_66415419_6    947 AAGAGTTTTTGCATGGCAAAAGGAACAGTCAGCAGAGT--AAAGA--ATC 992
                           i ii     iiivv    i iv  vi   iv i   --     -- i 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_66415419_6    993 CACAGAGTGGGAGAAAATTTTCACAACTTATACAAATGACAAAGCACTAA 1042
                               i           v  ii   v i   i vv   i  i v   vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_66415419_6   1043 TATCCGGCATCTACAAGGCACACAAAGAAATTAGTAAGAAAAA---AAAC 1089
                              i v  v  i  i v  v vv v  v i i   v     ---   i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_66415419_6   1090 AATCCCATCAAAAAATAGGCTAAGGACATGAATAGACAATTCTCAAAAGA 1139
                           i  v  i?      i   v     iv          v     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_66415419_6   1140 AG 1141
                           
  L1M4_orf2#LINE/    855 AG 856

Transitions / transversions = 1.35 (111 / 82)
Gap_init rate = 0.01 (8 / 650), avg. gap size = 1.75 (14 / 8)  

2527 27.17 0.66 0.79  chrX_66415419_66418582.rev     1142  1903 (1261)    L1M4_orf2#LINE/L1      148   908 (0)  

  chrX_66415419_6   1142 ATATACAAATGACCAACAAACATATGAA-AGCCAAGTCAATCCTAAGCCA 1190
                             iv     --   vii  vi -   -      iv     i i ivv 
  L1M4_orf2#LINE/    148 ATATGGAAATG--CAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAA 194

  chrX_66415419_6   1191 AAAGAACAAAGCTGGAGGCGTCATGCTACCTGACTTCAAACTATACTACA 1240
                         i          i      vv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_66415419_6   1241 AGGTTACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGAGTTGTA 1290
                          i i        iv  i    ii         i iv ii i   vv i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_66415419_6   1291 GATCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTAC 1338
                                    i    i--    i  --        vv  ii i  i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chrX_66415419_6   1339 AACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGA 1388
                         iiii vi    i  i     ivv  v   i v  vvv           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_66415419_6   1389 TTCCCTATTTAATAAATGGTGCGGGGAACACTGGCTAGCCACATGTAGAA 1438
                          vvi  v  i  i         v    vv     v  ?       i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_66415419_6   1439 AGCTGAAACTGGATCCCTTCCTTACACCTTTTACAAAAATTAATTCAATA 1488
                         iiv    ii    i    v   i     v v            i    v 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_66415419_6   1489 TGGAATAAGGACTTACATGTTAGACCTAATACCATGAAAACCCTAGAAGA 1538
                             vi ?i   i  v    v   v    v  i  i   vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_66415419_6   1539 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 1587
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_66415419_6   1588 TCTAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGA 1637
                         vv  vi            vvi           v     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_66415419_6   1638 TCTAATTCAACTAAAGAGCTTCTGCACAGCAAAGGAAACCACCATCAGAG 1687
                         ii v  iv  v v  i i   i  ii vv       v  i i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_66415419_6   1688 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACTCATCT 1737
                             v  i     i                 v      ivii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_66415419_6   1738 GACAAAGGGCTAATATCCAGAATCTACAATGAATTCCAACAAATTTACAA 1787
                           i  i  i  vi          v  i  v   i  iv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_66415419_6   1788 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 1837
                         v     i     i     v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_66415419_6   1838 ACTTCTCAGAAGAAGACATTTATGCAGCCAAAGAACACATGAAAA-ATGC 1886
                          i     vi       i  vi viii     vi i          -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_66415419_6   1887 TCATCATCACTGGTCAT 1903
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (116 / 87)
Gap_init rate = 0.01 (8 / 761), avg. gap size = 1.38 (11 / 8)  


2576 25.83 2.91 5.17  chrX_66424489_66431186.rev     5279  6207 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66424489_6   5279 TGTAAAAACATTCCATGCTCATTGATGGGAAAAATCAATATTGTGAAAAT 5328
                           v   i i  i     i    v   v    i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66424489_6   5329 GATCATAATGTCCAAAGTAATTTATGGATTTCATGCTATTCCCATCAATC 5378
                          iiv   v vi     v i  i  ii    iv i  v  i  i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66424489_6   5379 TACCATTGACTTTCTTCACAGAATTGGAAGAAAACT-ACTTTAAATTTCA 5427
                          v   vivi i  i  ii     v v  v--  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chrX_66424489_6   5428 TATGGAACCAAAAAAGAGCTTGTATAACCAAGACAACCCTAAGCAAAAAC 5477
                                viiv  ii  v iv v   i    i    i i i iv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66424489_6   5478 AGCAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5527
                          i     i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_66424489_6   5528 TACAGTAACCAAAACAGCATGGTACTGGTACCTAA--ACAGATATATAGA 5575
                                 i   i    ii         i --   -- i   i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATAGA 296

  chrX_66424489_6   5576 CCAATGGAACAGAACAGAGGCCTCAGAAATAATGCAACACATCCACAACC 5625
                         i        i    iv   ivii         vv v i    ii iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_66424489_6   5626 ATCTGATCTTTGAGAAACCTGGCAAAAAAAAAAAAAAAAAAACAATGAGG 5675
                          vi    i  i  v  ivv  v   i vv vv----------     i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATT----------CAATGGGG 386

  chrX_66424489_6   5676 AAAGGATATTCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAT 5725
                             i   v   v  i  i        i     v      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_66424489_6   5726 GCAGAAAACTGAAACTAGACCTGTTCATTACACCTTATACAAAAATTAAC 5775
                            i  i v    ii i    iv v v i     v               
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_66424489_6   5776 TCAAGATGGTTTAAAGATCTAAATGTAAGACCTAAAACCATAAAAACCCT 5825
                             i    v i ?   i            v       i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_66424489_6   5826 AGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGAC 5874
                                   v    ?i- v i -   iv   v v  vv i     v ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_66424489_6   5875 TTCATGACTAAGTCACCAAAAGCAATGGTAACAAAAGACAAAATTGACAA 5924
                            v iiv  v v           vvi i         v     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_66424489_6   5925 ATGGGATCTAATTAAACTAAAGAGCTTCTGTATGGCAAAAACAAAACAAA 5974
                           v   ii v  i   v v  i i   i   iivv    ii---------
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG--------- 676

  chrX_66424489_6   5975 ACAAAACAAAAACAAAAAACAAAAACACCATCAACAGAGAGAACAGGCCA 6024
                         ------------------------    i     v i  v   v  i v 
  L1M4_orf2#LINE/    677 ------------------------ACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_66424489_6   6025 CCCAAAGAATGAGAAAAAATTTTTGCAATCTATCCATCTGACAAAGGGCT 6074
                             v      i  i     v       vii  vi      i  i  i  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_66424489_6   6075 ---------AATATACA--GAACT-TAACAAATCTACAAGAAAAA-ACAA 6111
                         ---------      i --     - v    v  v i  v     -    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_66424489_6   6112 ATAACCCCATCAAAAAGTGGGAGAAGGATATGAACAAGTACTTCTCAAAA 6161
                                v  i?    i    vi      v    i iii i     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_66424489_6   6162 GAAG-TG---AGGTGGACAA-----ACATGAAAAAA-GCTCATCATCACT 6201
                             - i--- ii   v   -----         i -     v     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_66424489_6   6202 GGTCAT 6207
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.69 (75 / 16)  


2603 28.45 1.75 2.41  chrX_66459448_66465228     4375  5288 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66459448_6   4375 TGGAAAAATATTCCATCCTTATGGATATGAAGAATCAATATTGTGAAAAT 4424
                               i    i    vi i      vv     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66459448_6   4425 TGCCATATTGTCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 4474
                         v  v   i vi     v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66459448_6   4475 TACCATTGACATTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTTA 4523
                          v   vivi v  i  ii     v v  v  i--  - iii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_66459448_6   4524 TATGAAATTAAAGGAAACCCCATATAGCCAAGACAATCCTAAGCATGATG 4573
                             i  v iv i ii    viv        i      i i iv v  v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66459448_6   4574 AACAAAGCTGAAGGCATCAGGTTACCTGACTTCAAATTATACTACAAGGC 4623
                                i  i   vv   vii v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_66459448_6   4624 TGCAGTGACCAAAACAGCATGGTACTTGTACCAAAACAGATATATAGGCC 4673
                          i    i i   i    ii       v i iv ii i   i      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_66459448_6   4674 AATGGAACAGAACAGAGACCTCAGAAATAATACCACACATCTACAACTAT 4723
                                i    iv    vii         vv   i    i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_66459448_6   4724 CTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGAATCTCCT 4773
                         i    i   i    ivv  v   i v  vv               vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_66459448_6   4774 ATTCAGTTTAATGGTGCCAGGAAAACTGGCTAGCCAGATGCTGAAAAGTA 4823
                         v    iiv-        ii   v      v  ?   v    vi  i i i
  L1M4_orf2#LINE/    399 TTTCAACA-AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_66459448_6   4824 AAACTGGACCCCTTTCTTGCACCTTATACAAAAATTAACTCACAATGAAT 4873
                           ii         vi  ii    v                  v    i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_66459448_6   4874 TAAAGACTTAAATGTATAACCCAAAACCATAAAAACCTTAGAAGGGAACC 4923
                         i ?    i        vi v i     i      vi        ii   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_66459448_6   4924 TAGGCAATAGTATTCAGGACATACTCA---TGGGCAAATACTTC------ 4964
                             ?ivv i v   iv   ---  ii--- i     vvii   ------
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGAC---CTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_66459448_6   4965 ATGACAAAAATGTCAAAAGCAAGTACAACAAAAGCCATAATTGACAAAAT 5014
                               ------i        vivi         vv v   v  i   v 
  L1M4_orf2#LINE/    595 ATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_66459448_6   5015 ---CT--ATTTAAACTAAAGGGTTTCTGCACAGCCAAAGAAACTATCATC 5059
                         ---  --  iv   i    iiv   -  ii vv v  i  v       vv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAG 687

  chrX_66459448_6   5060 AGCATGAACAAGA-AATCTACAGAATGAGAGAAAATTTTTGTGGGCTACC 5108
                          ivi    -    -  i i        i        v    iiiiii iv
  L1M4_orf2#LINE/    688 AAAGTGAA-AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_66459448_6   5109 CATGTGACAAAGGTCTAATATCCAGAATTTAAATGAAACTTAAACAAATT 5158
                         i  v   i  i  v  vi          v  v vii    i-------- 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--------T 778

  chrX_66459448_6   5159 TACAAGAAAAAAACAAACAAACAAACAATCCCATCAAAAAGTGGGCAAAA 5208
                              vvv  v  i   v i     i  i  v  i?    i        i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_66459448_6   5209 AATACGAACAGACACCTCTCAAAAGAAGACCTTTACATGGCCAACAAACA 5258
                         i  vi   i     ii    v        iv vi v        i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_66459448_6   5259 TACAAAAAGAAGCTCAACACCACTGATCAT 5288
                         i ii      v        i  ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (154 / 102)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.92 (38 / 13)  


 311 22.37 0.00 0.00  chrX_66490697_66497121        2    77 (6348)    L1M4_orf2#LINE/L1      833   908 (0)  

  chrX_66490697_6      2 TGAACAGACACTTCTCAAAAGAAAACATTTATGCAGCCAACAAACTTATG 51
                             i     i     v      i i  vi viii     i  i vi   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_66490697_6     52 AAAAAATGCTCATCATCACTGGTCAT 77
                             i       v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.00 (0 / 0)  

3091 27.17 0.66 0.77  chrX_66490697_66497121     5024  5932 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66490697_6   5024 TGGAAGAACATTCTATGCTCATGGGGAGGAAGAATCAATATCGTGAAAAT 5073
                              ii i  i i   i      ivv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66490697_6   5074 GGCCATACTGCCCATGGTAATTTATAGATTCAATGCCATCCCCTTCAAGC 5123
                            v     v    viv i  i  i        i  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66490697_6   5124 TACCAATGACTTTCTTAACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5171
                          v   iivi i  i  vi     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_66490697_6   5172 TATGGAACCAAAAAAAGAGCCC-GCATTGCCAAGTCAATCCTAAGCCAAA 5220
                                -- viv  i ii   - v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_66490697_6   5221 AGAACAAAGCCAGAGGCATCACTCTACCTGACTTCAAACTATACTACAAG 5270
                                  iii    vv    v  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_66490697_6   5271 GCTGCAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGA 5320
                            i      i   i    ii  i      i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_66490697_6   5321 TCAATGGAACAGAAC--AGAGTCCTCAGAAATAATGCCACCTATCTACAA 5368
                                  i    i--       --        vv   ivi  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_66490697_6   5369 CCATCTGATCTTTGACAAACCTGACAAAAATAAGAAATGGGGAAACAATT 5418
                         i  vi    i  i     ivv  v   i vi vvv          v   v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_66490697_6   5419 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5468
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_66490697_6   5469 GTGAAAATGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5518
                         i    iv  i i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_66490697_6   5519 GATTCAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5568
                            iv?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_66490697_6   5569 ACCTAGGCA-ATACCATTCAGAACATAGGCATGGGCAAGGACTTCATGTC 5617
                           v    ?i- v i -   ivi  v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_66490697_6   5618 TAAAACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGGGATC 5667
                           vi            vvi         ivv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_66490697_6   5668 TAATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTT 5717
                          v  iv  v v  i i   i  ii vv    i  v    i  vv i   v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_66490697_6   5718 AACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAAACTACTCATCTGA 5767
                           v  i     i   i             v        ii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_66490697_6   5768 CAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGA 5817
                         i  i  i  vi          v  i  v      iv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_66490697_6   5818 AAAATTCAAACAACCCCACCAAAAAGTGGGCAAAGGATATGAACAGACAC 5867
                             vv    i     v ii?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_66490697_6   5868 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5917
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_66490697_6   5918 ACCATCACTGGCCAT 5932
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2832 27.36 3.63 0.57  chrX_66508028_66510355.rev      962  1842 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66508028_6    962 TGAAAAGATATCCCATGTTCATGGATTGAAA----CAATATTTTTTAAAT 1007
                           i                         i  ----i      v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66508028_6   1008 GGCCATACTATCCAATGCAATTTACAAATTCAACACAATCTCTATCAAAA 1057
                            v     vi    vvii  i    i       i     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66508028_6   1058 TACCAATGACATTCTTCATAGTAAAATAAAAAAAACAATTTAAAAATTTG 1107
                          v   iivi v  i  iii  --    vi v  ivii  iiv      ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG--AAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_66508028_6   1108 TAGGGAACCAAAAAAGACTCTGAATAGCCAAAGCAATCCTGAATAAAATG 1157
                           v    viiv  ii   i v           i     i    v  i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66508028_6   1158 AACTAAGCTGAAAGCATCACACTATCTGACTTTAACATATACTACAAAGC 1207
                            v   i  i i vv       vi ii i  i  v iv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_66508028_6   1208 TATAGTAATCAAAACATCATGGTACTGGCACAGAAACAGACACATAATCC 1257
                           i         i   vii           i iii i     i   ivi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_66508028_6   1258 AATGGAACAAAATAGAGAACTGAGAAATAAATCTACATACTTACAGCCAA 1307
                                i i   v    iiiv         i i i i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_66508028_6   1308 CTGGCTTTTCACAAAGGTGCCAAGAACATATATTGGGGAAAG--TAGTCT 1355
                         i  ii   iv    i          v   vi v         --      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_66508028_6   1356 CTTCAATAAATGGTGCCATGAAAATTGAATAAGCATATAGAGAAGAATTA 1405
                         i     i         iiv  v  i  i   ?v  i  iv i      v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_66508028_6   1406 AATTAGACATCTATCTCTCACCATATACAAACATCAAATCAAAATGGATT 1455
                          i  i   vi   i   v             v  i  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_66508028_6   1456 AAATACTTAAATCTAAGACCTGAAATTATGAAACTACTGAGAGAAAACTT 1505
                          ? v  i     v     v  i   i   i     vi iii       v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_66508028_6   1506 TGAGAGATCA--CTTCAGTACGTTGGTCTGGGCAAAGATTTTTCAGATAA 1553
                         --  i?i v --    ivv  v    vi i     v i   i i     v
  L1M4_orf2#LINE/    549 --AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_66508028_6   1554 AATCTCGAAAGCACAGGCAACAGAAACAAATATAAACTTGTGGAATTATA 1603
                         i ivi i        i      i  iv   v   i ivvi v i i vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_66508028_6   1604 TCAAG-TTAAAAAGCTTCTGAGAAGCAAAGAAAGCAATCAATAAAGGGAA 1652
                             i-       -   i  v vvv     i vi v     v    v   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_66508028_6   1653 TACACAACTTACAGATCACAAGAAAATGTTTTCAAATTATTCATCTGATA 1702
                         v v     ii     viivi       i   v     i  vi        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_66508028_6   1703 ATG-ATTAATAACCAGAAT---TACGTGATTCATGTCA-TCAATT-TG-- 1744
                          v - i vi  v       ---  vivi i  v iiv -     v- i--
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_66508028_6   1745 --GACAAAT----CAA-------ATGGGCAAAAGATCTGAATAAACATTT 1781
                         --       ----   -------         i   i      i      
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_66508028_6   1782 TCTTA--GAAGACATACAAATGGCCAAAAAGTGTATGAAAACATTCTCAA 1829
                         iiii --     i              v   iii       v  v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_66508028_6   1830 TGTTAGTAATCAT 1842
                         ii i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (152 / 86)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.47 (37 / 15)  


2936 27.04 1.32 1.10  chrX_66516878_66521095     2835  3740 (478)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66516878_6   2835 TGGAAAAAAATTCCATGCTCTTGAATAGGAAGAATCAATATTGTGAAAAT 2884
                               i v  i     i  v  i  v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66516878_6   2885 GGCCATACTGTCCAAACTAATTTATAGATTAAATGCTATCCCCATCAAGC 2934
                            v     vi     i i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66516878_6   2935 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAAAAGCT-ACTTTAAATT 2982
                          v   -   v    i  -i     v v  v  ----   - iii    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA----GCTGATCCTAAAAT 145

  chrX_66516878_6   2983 TCATATGGAACGAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAA 3032
                                   vviv  ii  v  v v        i      i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_66516878_6   3033 AAGAACAAAGCTGGAAGCATCACGCTACCTGACTTCAAACTATACTACAA 3082
                                   i    i vv    i  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_66516878_6   3083 GGCTACAGTAACCAAAACATCATGGTACTGGTAGCAAATCAGGTATGTAG 3132
                         i          i   i   vii         i vv iivi  ii  i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_66516878_6   3133 ACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAC 3182
                          i        i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_66516878_6   3183 CACCTGATTTT-GACAAATCTGACAAAAGCAAGCAATGGCGAAAGGACTC 3231
                           vi       -     ivv  v   i v  vv      v     i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_66516878_6   3232 CCTATTTAATAAATGGTGTTGAGAAAACTGGCTAACCATATGCAGAAAAC 3281
                         i  v  i  i        i  i  v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_66516878_6   3282 TGAAACTGGAACCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 3331
                             ii    v    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_66516878_6   3332 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3381
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_66516878_6   3382 CCTAGGCAATACTTTTCAGGACACAGGCATGGGCAAGGACTTCATAACTA 3431
                          v    ?ivv v i   iv   viv  vv i     v ii   v  iv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_66516878_6   3432 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTA 3481
                         vi            vvi          vv     v  i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_66516878_6   3482 ATTAAACTAAAGACCTTCTGCACAGCAAAAGAAATTTTCATCAGTGTGAA 3531
                           i   v v  i v   i  ii vv    i  v i v   vv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_66516878_6   3532 CAGGAAACCTACAGAATGGGAAAATATTTTTGTAATCTATCCATCTGACA 3581
                         v  iv    i           i  v  v    i  vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_66516878_6   3582 AAGT-CTAATATCCATAATATACAATAAACT--TA-AATTTACAAGAACA 3627
                          i v-  vi      v      i  vi    --  -  i --   v  i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--CAATAATA 793

  chrX_66516878_6   3628 AAAA-----ACAACCCCATCAAAAAGTGGGCAAAGGGTATGAACAGACAC 3672
                             ----- i     v  i?    i          i v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_66516878_6   3673 TTCTTGAAAGAAGACATTTCTGTGGCCAACAAACATACAAAACAACCGTG 3722
                             iv        i  vivvi       i  i  i ii   vi ---  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA---TG 890

  chrX_66516878_6   3723 TTCCACTCCAATGTTAAA 3740
                         i  v  vi  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (135 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


4313 15.70 3.16 4.14  chrX_66555156_66557272.rev      710  1626 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66555156_6    710 TGGGAAGACATCGCATATTTATGGATGAAAATAACTTAACGTTGTTGAGA 759
                            i    i   v   i  i      vii  -i      ii     i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAA-GACTTAATATTGTTAAGA 49

  chrX_66555156_6    760 TGACAATGCTCCCCAAATTGGTTTACAGATTTAATATAGTTCCTGTGAGA 809
                           i    i            i i        i  iii i i   i v i 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_66555156_6    810 ATCCTAGCTGACTTCTTCGTAGAAATTGACAAGCTTATCCCAA--TTCAT 857
                             i     v   i  i i               v    i  --     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_66555156_6    858 TTGAAAATTCAAGGGACCCACAAGAGCCAAAGCAATCTTGAAAAAGAAGA 907
                         v  i    v           v  v       i                  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_66555156_6    908 CCAAAGTTGAAGAGTTCAAAATTCCTAATTTCAAAACTCACTAAAAACCT 957
                         v        i  iii   v v    i            i    v   v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_66555156_6    958 ACAATAATCAAGATAACGTGGTACCGGCATAGGAATAAACATATAGATCA 1007
                            i         i ii       i      i i   i            
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_66555156_6   1008 ACTGAATATAGTTGAGAGTCCACAATTAAACCCTCACATTTACGGTCAAC 1057
                          iv     v i           v  v       vi       i      i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_66555156_6   1058 TGATTTTACACAAAGGGTGCCAAGACAGTTAAGTGAGGAAAGA------- 1100
                                vv    -            vi  v i  i       -------
  L1M4_orf2#LINE/    350 TGATTTTCGACAA-GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_66555156_6   1101 -TTCAACAA-CAATATTGTGAGAACTGAATATCTACATGCAAAAGAATGA 1148
                         -        -iii ii  v  v     i   ? i                
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_66555156_6   1149 AGTTGGACCCCTACCTCA-GTCATATATAAACATTACATCAAAACTGATG 1197
                                           -ii      i   v    vv      iv   v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_66555156_6   1198 AAAGACCTAAATGTAAATAGCGAAAACTATAAAACTCTTAGAAGGAAACA 1247
                          ?              i-   v                      i     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAG-AGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_66555156_6   1248 TA--TGTAAATCTTTGTGATCTTGGATTAGGCAAAGACTTCTTAGATACG 1295
                           --?         i    i     i        v ii          i 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_66555156_6   1296 ACGCCAAAATCATAAGCCAAAACAGAAAATAAATAGATGAATTGGACTTC 1345
                           i      v  i    v v  v      --       i           
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAA--AATAGATAAATTGGACTTC 645

  chrX_66555156_6   1346 ATCAAACTTAAAAACATTTTTGTGCTTCAATCTAGATACCATTAAGAACG 1395
                               v        --             v--i  i  i  i     --
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAAC--TTTTGTGCTTCAAA--GGACACTATCAAGAA-- 689

  chrX_66555156_6   1396 TAAAAAGAAAAAAAAGGAAAGTAAAAAAGACAACTCACAGAATGTGAAAA 1445
                         -------------------   i    -      i         v  i  
  L1M4_orf2#LINE/    690 -------------------AGTGAAAA-GACAACCCACAGAATGGGAGAA 719

  chrX_66555156_6   1446 AATATCTACAAATCACA-ATCTATTAAAGGACATGTATCCAGAATATATT 1494
                              i i       i -    iv   i    v                -
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT- 768

  chrX_66555156_6   1495 TTTTAAAAA--TCTTAAAACTCAATAATAAAAA--------ACCCAACTA 1534
                         ----   i --     v                --------      i ?
  L1M4_orf2#LINE/    769 ----AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_66555156_6   1535 AAAACTGAGCAAAGGATCCAAATAGATATTTCTCAAAAAAGAAGATATAC 1584
                             v  i         iii      i       v   --          
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA--GAAGATATAC 862

  chrX_66555156_6   1585 AAATGGCCAATAAGAACATG----GATACTGAACATTATTTGTTAT 1626
                                       v     ----   i  v     i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (94 / 46)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.53 (67 / 19)  


1387 11.44 7.75 0.00  chrX_66629745_66636024.rev      232   502 (5778)  C L1M4_orf2#LINE/L1   (0)   908   617  

C chrX_66629745_6    502 CAGAAAAAAAAATTGTTAAATTGGACTTCATCAAATTTGAAA-TTTTTGT 454
                           i  i       v v                   v  i   -i      
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

C chrX_66629745_6    453 GCTGCAAATGATACCATCAAGAAAGTGAAAATCTCACCCACAGAATGAGA 404
                            v    v  i  i                vviv            i  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

C chrX_66629745_6    403 GAAAGTATTTGCAAATCATATATCTGATAAGGGTATTGAATTTAGAATAT 354
                             i                            vv   v  ii       
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

C chrX_66629745_6    353 ATAAAGAACTCTTGCAACTCAATA-TAAAAAGACAA----CCCAATTTTA 309
                                      i          -           ----       ?v 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

C chrX_66629745_6    308 AAATGGGCAAAGTATTTGAATAGAAATTTCTTGATAGAAGATATACAAAT 259
                                     v           v      iv v               
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

C chrX_66629745_6    258 --------------TTAAAA-ATGCTCAACATCATTAGTCAT 232
                         -------------- v    -             ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.76 (13 / 17)
Gap_init rate = 0.02 (5 / 292), avg. gap size = 4.20 (21 / 5)  

3095 27.38 0.66 1.20  chrX_66629745_66636024.rev     4877  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66629745_6   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66629745_6   4927 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66629745_6   4977 TACTGATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v iiiivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_66629745_6   5025 TATGGAACCAAAAAAGAGCCCACATCCCCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  viv  vv    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66629745_6   5075 AACAAAGCTGGAGGCATCACACTCCCTGACTTCTAACTATACTACAAGGC 5124
                                i      vv       i  ii i   v  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_66629745_6   5125 TACAGTAATCAAAACAGCATGGTACTGGTACCAAAAGAGAGATATAGATC 5174
                                     i    ii         i iv ii v   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_66629745_6   5175 AATGAAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5222
                             i  i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_66629745_6   5223 ATCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGCAAGGATTCC 5272
                          vi    i  i     ivv  v   i vi vv        v   i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_66629745_6   5273 CTATTTAATAAATGGTGCTGGAAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i            i v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_66629745_6   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCGAGATGGA 5372
                            ii    i    v   i     v           i  i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_66629745_6   5373 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_66629745_6   5423 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5472
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_66629745_6   5473 AACACCAAAAGCATGTCTAAAACACCAAAAGTCAAAATTGACAAATGGGA 5522
                         i            i-----  i  v      vv     v  i    v   
  L1M4_orf2#LINE/    597 GACACCAAAAGCAC-----AAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_66629745_6   5523 TCTAATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAT 5572
                         ii v  iv  v v  i i   i  ii vv    i  v    i  vv i v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_66629745_6   5573 TGAACAGGCAACCTACAAAATGAGAGAAAATTTTCGCAA--CGTACTCAT 5620
                             v  i     i   i    i        v  i    -- i  i--  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--AT 739

  chrX_66629745_6   5621 CTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAC 5670
                             i  i  i  vi          v  i  v      vv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_66629745_6   5671 AAGAAAAAAACAAACGACCCCATCAAAAAGTGGGCGAAGGATATGAACAG 5720
                           v     i     ii    v  i?    i     i      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_66629745_6   5721 ACACTTCTAAAAAGAAGACATTTATGCACCCAAAAAACACATGAAAAAAT 5770
                            i    vv        i  vi viiiv    v  i          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_66629745_6   5771 GCTCACCATCACTGGCCAT 5789
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


3208 26.05 0.99 0.77  chrX_66662329_66668615.rev     4891  5796 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66662329_6   4891 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4940
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66662329_6   4941 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCATCAAGC 4990
                            v     v     iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66662329_6   4991 TACCCA--TGACTTTCTTCACAGAAATGGAAAAAACT-ACTTTAAAGTTC 5037
                          -    --  v    i  -i       v  v  i-  - iii    i   
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chrX_66662329_6   5038 ATATGGAACCAAAAAAGAGCCTGAATCGCCAAGTCAACCCTAAGCCAAAA 5087
                                 viiv  ii  v  v    v     iv   i i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_66662329_6   5088 GAACAGAGCTGGAGGCATCACGCTATCTGACTTCAAACTATACTACAAGG 5137
                              i  i      vv    i  vi ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_66662329_6   5138 CTACAGTAGCCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5187
                                 ii   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_66662329_6   5188 CAATGGAACAGAAC--AGAGCCCTGAGAAATAATGCCGCATATATACAAC 5235
                                 i    i--    i  --        vv  ii i  v  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_66662329_6   5236 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5285
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_66662329_6   5286 CCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGACAGC 5335
                         i  v  i  i        i     v      v  ?   i   i i viiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_66662329_6   5336 TGAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGG 5385
                             ii    i    v   i     v     v        i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_66662329_6   5386 ATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5435
                           i ?    i  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_66662329_6   5436 CCTA--CGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5483
                          v  --? i  - i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_66662329_6   5484 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5533
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_66662329_6   5534 TAATTCAACTAAAGAACTTCTGCATAGCAAAAGAAACTACCATCAGAGTG 5583
                          v  iv  v v  i     i  iiivv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_66662329_6   5584 AACAGGCAACCTACAGAATGGGAGAAAACTTTTGCAATCTACTCATCTGA 5633
                           v  i     i                iv       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_66662329_6   5634 CAAAGGG-TAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 5682
                         i  i  i- vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_66662329_6   5683 AAAAAACAAACAACCCTATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5732
                             i     i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_66662329_6   5733 GTCTC-AAAGAAGACATTTACACAGCCAACAGACACATGAAAAAATGCTC 5781
                         v    -        i  vi v ii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_66662329_6   5782 ATCATCACTGGCCAT 5796
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


 642 31.27 14.75 3.03  chrX_66682070_66683758.rev      400  1192 (497)    L1M4_orf2#LINE/L1        1   886 (22)  

  chrX_66682070_6    400 TGCAAAGTTGTACCATATTCCTGGCTAAGAAGAAGCAATATT-TCAAGGA 448
                           v    v i v    i   v   v vi     vvi      - i   - 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-A 49

  chrX_66682070_6    449 TTTCAGTTCTTTCCCAATGAAATCTAAAAATTTAAAACAA-CTCAAACAA 497
                          vv  i v  ii  v   vi -    v i   i  vi   - i v v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGA-TCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_66682070_6    498 AATC----------------------TTGACAAAATAATCCCAAAATTTA 525
                             ----------------------       iv i    i      i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_66682070_6    526 TCTGAAGGAATAAAACATGAGAC----AAT-GCCAAGATATTTGTGAAAA 570
                          v  i --   iv  --- i   ----   -     i i v iv      
  L1M4_orf2#LINE/    149 TATGGA--AATGCAA---GGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_66682070_6    571 ATAAGAGTAA---TAAGACATTCCCTGCTGTACA--TTTAAAGTAT-CTA 614
                          v    ii  --- iiiiv i  v -i  viv  --  i   iiv -   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTTACTA 242

  chrX_66682070_6    615 -AAGGC-ATAATGATTACAACAGTTTGATACTGGCTCCAGCTTAGG---- 658
                         -  i  - i i i  i vi     v  i       viv  vv   i----
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_66682070_6    659 TTGATCAGTGGAAGAGATCAGAAAAGCCAAAACCAGACACA---GTATAT 705
                          v     i     v   viv  i iv   i  vi i  v  ---i v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_66682070_6    706 GG--AAT---------------ATGCCATTCCAATTCAGTGAAGAAAGGA 738
                           --   ---------------i     vvv v     i  ii     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_66682070_6    739 TGAATTATTCACTAAATAATGTCAGAACAACTAGTGAATCATTTGGAGAA 788
                          iivi v    vi    ii  iii i      i vv ?i  iv  v i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_66682070_6    789 GAAAATAAAGTTAAATTACTAGTTAAAATCA-------AAATAAATTCCA 831
                            -- i     ii iiv   vi v v i  -------    v  i  v 
  L1M4_orf2#LINE/    443 GAA--TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_66682070_6    832 AATGGATTAAATATGTCAATTTAAAAGAGGAAATCATGTAAGTACTATTA 881
                                i ? v iv v   v   i  vvi   ii  iv  v vi  vv 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_66682070_6    882 GACAATACAGAGGAAAAT-TTCAAAATTTTTAAAGGTAGAAAA-GGTCAT 929
                           v  i i  i? v    -   ivi ii  --ii v   iv  -   -- 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTT--GGGTTAGGCAATGGT--T 586

  chrX_66682070_6    930 TTTAAGTTATTGACAATGAAGAAAACATAAGTGA----AGACAGACTTGA 975
                          i v  v   -    vii  --- i  i   ii ----   v i v v  
  L1M4_orf2#LINE/    587 TCTTAGATAT-GACACCAAA---AGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_66682070_6    976 TAAATT-----TCATTAGAAAACATTTATAATTTCTTATG--TGAAATAA 1018
                               -----    i i  -----   v  vi i  i  -- v   -ii
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAA-----TTAAAAACTTTTGTGCTTCAAA-GG 676

  chrX_66682070_6   1019 ACACCATTATAAAACTCAAA-GACAAACCATAAACTAAGAATAATTATTA 1067
                             i  i vi   v v   -     v   i i v ii  iv  v    v
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_66682070_6   1068 GCA--TCAAGTATGTAA-----AACCAATGGTCA--ATATAT-------- 1100
                            --   vi   v i -----i  ivi ivi  --      --------
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_66682070_6   1101 --------TCGATA-TATAAAAATAAACAGCACAATAGAAAAATGGGCAA 1141
                         --------  i   -  v   i i   i i v    v?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_66682070_6   1142 CAGACAGGAGAAAGCAGTT------AGAAG---TACAAATGACCAATAAG 1182
                         vi  ivv  iv ii  v  ------     ---        i        
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_66682070_6   1183 CATATGAAGA 1192
                           i     i 
  L1M4_orf2#LINE/    877 CACATGAAAA 886

Transitions / transversions = 1.35 (140 / 104)
Gap_init rate = 0.05 (40 / 886), avg. gap size = 3.52 (141 / 40)  


3130 27.67 0.55 0.44  chrX_66706760_66713139.rev     4983  5889 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66706760_6   4983 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5032
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66706760_6   5033 GGCCATACTGCCCAAGGTAATTCATAGATTCAATGCCATCCCCATCAAGC 5082
                            v     v     iv i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66706760_6   5083 TATCAATGACTTTCTCCACAGAATTGGAGAAAACT-ACTTTAAAGTTCAT 5131
                          vi  iivi i  i iii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_66706760_6   5132 ATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAGA 5181
                               viiv  ii  v  v v  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_66706760_6   5182 ACAAAGCTGGAGGTATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5231
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_66706760_6   5232 ACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGATCA 5281
                                i   i    ii  i      i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_66706760_6   5282 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCGTATCTACAACCA 5329
                               i    i--    i  --        vv iiiii  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_66706760_6   5330 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATTGGGAAAAGATTCCC 5379
                         vi    i  i     ivv  v   i v  vvv   v      ii  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_66706760_6   5380 TATTTAACAAATGGTGCTGTGAAAACTGGTTAGCCATATGTAGAAAGCTG 5429
                          v  i              v  v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_66706760_6   5430 AAACTGGATCCCTTCCTTACACCTTATAGAAAAATTAATTCAAGATGGAT 5479
                           ii    i    v   i     v    v         i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_66706760_6   5480 TCAAGACTTAAATGTTAGACCTAAAACCATAAAACCCT-AGAAGAAAACC 5528
                         iv?    i       v   v       i       i  -          v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_66706760_6   5529 TAGGCA-ATACCATTCATGACATAGGCACCGGCAAGGACTTCATGTCTAA 5577
                             ?i- v i -   i    v v  vviv     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_66706760_6   5578 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5627
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_66706760_6   5628 TTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGAAC 5677
                          i   v v  i i   i iii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_66706760_6   5678 AGGCAACCTACAGAATGGGAGAAAATTTTTTCCATCTACTCATCTGACAA 5727
                           i     i                 v   v v vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_66706760_6   5728 AGGGCAAATACCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5777
                         i  i vvi  i       v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_66706760_6   5778 AAACAAACAACCCCATCAAAAAGTGGGCAGAGGATATTAACAGATACTTC 5827
                          i     i     v  i?    i      i     v v  i   i i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_66706760_6   5828 TCAAAAAAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5877
                           v   i    i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_66706760_6   5878 ATCACTGGCCAT 5889
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


4138 18.07 3.52 0.34  chrX_66742079_66744073.rev      628  1507 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66742079_6    628 TGCAAAGACATTATGTGTTCATGGATTG------TTAATGTTGTTAAGAT 671
                           v     i  ivii             ------     i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66742079_6    672 GGCAATACCTCCTACATTGAGCTACATATTTAGGGCAATC----TCAAAA 717
                                 ii  i v     v     v   i iv      ----      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66742079_6    718 TCCAAGCTGTCATTTTTCTTGAAATTGATAGGCTTATTCTGAAATTCATA 767
                            v     i v     viv        i i   v  i  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_66742079_6    768 TGGAATTACAAGGGATCCAAAATAGCCAAAACAACATTGAAAAA--AGAA 815
                              v i       i   i              iv        --    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_66742079_6    816 CAACGATGGAGGACTCACAATTTCCAATTCCAAAACTTACCACAAAGCTA 865
                            v v             v  i      i          i         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_66742079_6    866 CAGCAATCAAGAGAATGTGGGACTGGAGTAGTGATAGACGTAAAGAAGAA 915
                            i        v i     v     vi  iv       i  v   vv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_66742079_6    916 TGGAATATAATTGAG--TCTAAAACTAAATTCTTACACTGAGTGTCAATT 963
                                v       --  i i  v    ii v    i v vv       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_66742079_6    964 GGTTTTTGACATGTTTGCTAAGAAAATTCAGTGGGAGATAGAATAATCTT 1013
                          i    i    v vv   i    vv     i    -  v      i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTT 399

  chrX_66742079_6   1014 T-CAACACATAATGCTGAGACAACTTGATATCCACGTGCAAAAGAATAAA 1062
                          -     v  ii     i       v    ?    i           i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_66742079_6   1063 GTTGGACCTCTATTTTACACAATATATAAAAATTAATTCAAAATGGGTCA 1112
                                 i   ii i    v     i         i         i   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_66742079_6   1113 AAAAC-TAAATGTAAACAGCTAAAAGTGAAAAATTCTTACAAGAAAACAT 1161
                         ? i  -         i-        v iv    i     v          
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAG-AGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_66742079_6   1162 AGGTGTCAATTTCTGTGACCTTAGATTAG-CAATGGTTTCTTAGCTATGA 1210
                            ?  v   i ii        i i    -              v     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_66742079_6   1211 CTCCAAAGGCAAAAGCAGCAAAA--AATAATA-ACAAAGTGAACATTATC 1257
                          v     i   v     i     --  v    - i   v  i  v i   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_66742079_6   1258 AAAATGAAAAACTTT-GTACTTCAAAGGACATCATGAAGAAAGTGAAAAG 1306
                              v         -  i            ii  v              
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_66742079_6   1307 ATATCCTACAGAATGGAGGAAATTTTTTTCAAATCACATA----AT---G 1349
                          i v  i         ii    v v   v       i   ----  --- 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_66742079_6   1350 GTCTTCTTTCTTGAATACAAAAAGA--TGCTA-AACTTGATAATAAAAAA 1396
                          v   v v  iv     i v     -- vi  -    ii          -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA- 797

  chrX_66742079_6   1397 GATAAATAACCCATTTTGGAAATGGGCGAATTATCTGAATGGGAATTTCT 1446
                           i          v  ?ii        i  vv  i     i iv      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_66742079_6   1447 CCAAAGAAGATATACAAAGTGCCAATAGGCACATGAAAATATGCTCCACA 1496
                                           vv       i           v      v   
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_66742079_6   1497 ATATTAGCCAT 1507
                         vi ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.25 (86 / 69)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


2977 24.78 2.57 1.23  chrX_66797635_66799866      844  1739 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66797635_6    844 TGGAAATACACCCCATGCTCATGGATTGGAAGAATCAATATCATGAAAAT 893
                               v i i      i               v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66797635_6    894 GGCCATACTGCTCAAAGCGATCTACAGATTCAAAGTAATTCTTATCAAAC 943
                            v     v i    vi               v i   i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66797635_6    944 TACAAACATCATTATTCACAGAATTAGAAAAAAACAATCCTACATTTCAT 993
                          v v i vv v  v  ii     v v  v  iv-ii      v v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_66797635_6    994 ATGG---TGC-------CAAAAATAGAGCCCAAATGGCAATCCTAAGCAA 1033
                             ---   ------- v i     ---     --i     i i iv  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAG---CCAAA--ACAATCTTGAAAAA 194

  chrX_66797635_6   1034 -AAGAACAAATCTGGAGGCATCACATTACCAAACTTCAAATTATACTATG 1082
                         -         vi      vv     i v  v  i      viv     ii
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_66797635_6   1083 AGGCTATAGTACACAAAACAGCATGGTACTGATATAAAAGTATATATATA 1132
                          i    i    vv   i    ii        ii    iii  v i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_66797635_6   1133 GACCAATAGAACAGGATAGAGAACCCTGAAGTAAAGCCAAATACTTACAA 1182
                           i    i   i  i  v    ii  v   i    v   v i i   iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_66797635_6   1183 CCAACTGATCTTTGACAAAGCATATGAAAAC-AT--AATGTGGGGAAACG 1229
                         i   i    i  i     i -i iiv  i  -  --    --      vi
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATG--GGGAAAGA 391

  chrX_66797635_6   1230 ACACCCTCTTTAATAAATGGTGTTGGGAAAACTGGATAGCCACATGTAGA 1279
                          i vi  i  i  i        i     v         ?       i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_66797635_6   1280 AGAATGAAAGTGGAGCCCTGTCTCTCACCATATACAAAAATTAACTCTAA 1329
                                 iv    v    ii   v                      v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_66797635_6   1330 ATGGATTAAAGACTTTATTCTAAGTACTGAAACTATAAAAATTCTACAAG 1379
                               i ?    i v v v    vi  i           v ii  v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_66797635_6   1380 AAAATCCAGGCA-AACTCTTCTGGACATTGGCCTAGGCAAAGAATTTATG 1428
                             ivi   ?i-  v     vv   v    vi       v iv  iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_66797635_6   1429 ACTAAGACCCCAAAAGCAAATTCGACAAAAACAAAAATAAATAAATGGGA 1478
                         iv  v   v         v vv i      iv       i      v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_66797635_6   1479 CCTAATGAAACTAAAAAACATCTTTACAGCAAAAGAAATAATCATCAGAG 1528
                          i v  v   v v      v i v i vv    i  v iv    vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_66797635_6   1529 TAAATAGATAACCTAGAGAATGGGAGAAAATATTTGCAAACTATGTATCC 1578
                          i  v   i    i v                        ii  i    i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_66797635_6   1579 AACAGAAGACTAACATCCAGAATCTACAAGGAATACAAACAAATCAGCAA 1628
                         i i iii    vii         v  i  i   iv vv    v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_66797635_6   1629 GAAAAAAA--AAT--CCT--TTAAAAAATGGGTAGATGTCATGAATAAAC 1672
                         v     i --   --  i--  ?         i i v viv      i  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_66797635_6   1673 ATTTCTCAAAATAATATATACAAATGGCCAAGAA--ACATAAAAAAATGC 1720
                                v   v  v                v  --    i    i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_66797635_6   1721 TCACTACATCAAACATTAC 1739
                            --      ????????
  L1M4_orf2#LINE/    892 TCA--ACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (123 / 95)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.12 (34 / 16)  


2240 27.90 3.64 0.40  chrX_66800951_66802680      510  1251 (479)    L1M4_orf2#LINE/L1      130   895 (13)  

  chrX_66800951_6    510 AAACT-ATTTTAAAATTCATATGGAACCAAAAAAGAGCCCAAATATCCAA 558
                           i  -  ii                viiv  ii  v  vi    v    
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_66800951_6    559 GGTAATCCCTAGGCAAAAAGAACAAAGCTGGAGGCATTACACTACCTGAC 608
                         iii    i- iiiv  i          i      vv i     v  ii i
  L1M4_orf2#LINE/    180 AACAATCT-TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_66800951_6    609 TTCAACCTATACTACAAAGTTACAGTAACTAAAACAGCACTGTACTGGTG 658
                              vviv          i        ii  i    iiiv       ii
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_66800951_6    659 TAAGGACAGACACATAGACTGGTGGAAGAGCA--GAGAACCCGGAAATAA 706
                               i     i     iiii     v  v --    ii  i       
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_66800951_6    707 GACCTCGCTCCTACAGCTATCTGATCATCAACAAACCTGGCAAAAACAAG 756
                         iv  vii vii  ii ii vi    iv  i    ivv  v   i v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_66800951_6    757 CAATGGGAAAAAGATTCTCTATTTTATAAATGGTGCTTGGATAACTGGCT 806
                                i   ii  vv   v  iv i          v   i      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_66800951_6    807 AGCCACGTGCAGAAAATTGAAACTGGACCCTGTCCTTACACCTTACACAA 856
                          ?    i    i  i v    ii       ivv   i     v  i    
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_66800951_6    857 AAATTAACTCAAGATAGAGTAAGGACTTAAATATAAAACCCAAAACTATA 906
                                     i  i  vi ?i   i     i   i v i         
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_66800951_6    907 AAAACCCTAGAAGAAAACCTGGGCA-ATACCATTCAGGACATAGGCATGG 955
                            vi i           v i  ?i- v i -   iv   v v  vv i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG 577

  chrX_66800951_6    956 GCAAAGATTTCAT-GATGAAGATGCCAAAGGCAATTGCAACTACAGCAAA 1004
                             v i    v -   - v  ii     i   vvv     v v  v   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_66800951_6   1005 AACTGACAGATGGGATCT-ATTAAACTAAAAAGCTTCTGCACAGCAAAAG 1053
                           iv  i i  v   ii -  i   v v    i   i  ii vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_66800951_6   1054 AAACTATTAACAGAGTAAACAGACAACCTACAGAATGGGAGAAAAGTTTT 1103
                          v     i  v i   i  v        i                vv   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_66800951_6   1104 GCCAA--------CTGACAGAAGTCTAATATCCAGCATCTATAAGAAACT 1145
                           v  --------    i iii v  vi       v  v     ii    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_66800951_6   1146 TAAACAAATTAACAAGAAAAAAACAA----CCCCATAAAAAAGTGGGCAA 1191
                         ivv    v i  i  v     i    ----   v  v?    i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_66800951_6   1192 AG-ACATGAACAGAAACTTCTCAAAAGAAGACATACA--TG-----TGAG 1233
                           - iv    i   v i     v        i     --  ----- i  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_66800951_6   1234 C-CAGGAAAGGTGGCTCAA 1251
                          -  v    i vv      
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.45 (120 / 83)
Gap_init rate = 0.02 (14 / 766), avg. gap size = 2.14 (30 / 14)  


 729 29.97 1.89 0.63  chrX_66832940_66838689        1   317 (5433)    L1M4_orf2#LINE/L1      477   797 (111)  

  chrX_66832940_6      1 AAAAATCAACTCAAGATGGATGAAATAATTAAATGTAACAGAAGAAACTA 50
                               i       i      v ? v vi         v  vvi      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_66832940_6     51 TAAAAATACTAGAAAAAAGC-TAGATAAAACTTCTCTTGGCTTTGGTCTA 99
                              v vi     i   i -   i?iv  v ii  v  i i    vi  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_66832940_6    100 GGCAAAAAACTCCT-GACAAAGTGCTCAAAAGCAGAGACAACAAAA-ACA 147
                              viivi  i -  i viiii -        v ii        - v 
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACAC-CAAAAGCACAAGCAACAAAAGAAA 625

  chrX_66832940_6    148 AAATAGGCAAGTGAGACTTAATTAAA-TTAAAAAGCTTCTACACAGTGCA 196
                               ii  i vi     v  i   -       -   i iii vviiv 
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAA 674

  chrX_66832940_6    197 TGAAATAATCAACCCACTGTACAGACAACCTGCAAAATGGGAGAAAATAT 246
                         v  v iv     vvv v  v v        ii  i               
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_66832940_6    247 TTGCAAGCTATGCAACTGA--AGGAAATGACATTCAGGATTTACAAGGAA 294
                               iii  ii v    --   i v vii  i   i  v  i  i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_66832940_6    295 CTCAAGAAACTCAACAAGAAAAA 317
                            vviv       i  v     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAA 797

Transitions / transversions = 1.38 (54 / 39)
Gap_init rate = 0.02 (7 / 321), avg. gap size = 1.14 (8 / 7)  

2860 27.01 1.21 1.10  chrX_66832940_66838689     4351  5257 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66832940_6   4351 TGGAATAACATTCGATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4400
                              vi i  i v   i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66832940_6   4401 GGCCCTACTGCCCAAAGTTATTTACAGATTCAGTGCTATCCCCAAGAAGC 4450
                            vv    v      v v  i          ii  v     i vv  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66832940_6   4451 TACCA-CTGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAACTTCA 4498
                          v   -   v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_66832940_6   4499 TATGGAACCAAAAAAGAGCCCGCATAACCAAGACAATCCTAAGCAAGAAG 4548
                                viiv  ii  v  v v   i    i      i i iv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66832940_6   4549 AACAAACCTGGAAGCATCACACTACCTGACTTCAA--CTCTACTAGAAGT 4596
                               vi    i vv       v  ii i     --  -     v  iv
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_66832940_6   4597 CTACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGATGTATAGAC 4646
                                  iv  i    ii         i iv ii i   ii      i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_66832940_6   4647 CAATGGAACACAACGGAGGCCTCAGAAATAACACCACACAACTACCACCA 4696
                                 i v  iv   ivii         vv   i   vi  ivii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_66832940_6   4697 -TCGGTTATTTGACAAACCTGACACA--CATAAGCAATGGACAAAAGATT 4743
                         - i i  -  i     ivv  v  vi--   --v      iv   ii  v
  L1M4_orf2#LINE/    348 ATTGATT-TTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAATA 394

  chrX_66832940_6   4744 CCCTATTTAATAAATCGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAA 4793
                         vi  v  i  i    v   i     v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_66832940_6   4794 CTGAAACTGGATCCCTTCCTTACACCTTATA-AAAAAGCAACTCAAGATG 4842
                         v    ii    i    v   i     v    -     vi       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_66832940_6   4843 GATCAAAGACTTAAATGTAAGACTTAGGACCATAAAAATCCTAGAAGAAA 4892
                              ?    i           vi  ii  i      v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_66832940_6   4893 ACCTCGGCA-ATACCATTCAGGACATACACATGGGCAAAGACTTCATGTC 4941
                           v v  ?i- v i -   iv   v vvivv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_66832940_6   4942 TAAAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGAGATC 4991
                           vi            vvi      i   vv     v  i    vi  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_66832940_6   4992 TAATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGGG 5041
                          v  i   v i  i i   i  ii vv    i  v       vv i  v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_66832940_6   5042 AAAGAAGCAAATTACAGAATGGGAGAAAATTTTTGCAATCTATTCATCTG 5091
                            ii -   vii                 v       vii  vi     
  L1M4_orf2#LINE/    694 AAAAGA-CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_66832940_6   5092 TCAAAAGGCTAATATCCAGAATCTACAAAGAACT--TAATCAAATTTACA 5139
                         vi  ii i  vi          v  i        --  --   v iv i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATA 790

  chrX_66832940_6   5140 AGAAAAACACAAACAACCCTATCAAAAAATGGGCAATGGATGTGAACAGG 5189
                          v     v     i     v  i?            v    v    i  i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_66832940_6   5190 CACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAACTG 5239
                           i     v        i  vi viii     i ii  i       iv  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_66832940_6   5240 CTCATCATCACTGGTCAT 5257
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (135 / 106)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.31 (21 / 16)  


2755 24.81 3.54 4.10  chrX_66878443_66881095     1262  2164 (489)    L1M4_orf2#LINE/L1       11   908 (0)  

  chrX_66878443_6   1262 TCCTTTGTTCATAAATTGGAAAA-TAAATATTGTTAAAATGTTCATAATT 1310
                            iv       ii       i - v           i   viv   v i
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chrX_66878443_6   1311 CCCAAAGTGATATATGGACTCAGTACAATTCCTATCAAAATTTCAATGGC 1360
                               v    v  ii  i   iii    i           ii  iiv  
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_66878443_6   1361 ATTTTTCACAGAACTAGAATAAAC-AATTCTAAAATTAGTATGGAAACCA 1409
                         v     ii     v v  -i  i -i  i        vi        i-i
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATATGGAAAT-G 158

  chrX_66878443_6   1410 CAAAAGATCTCAAAGACTCAAAGCAATCTTGAGAAAGAG----AAAGCTA 1455
                            ii  i ivi  v vi    i         i     i----    i i
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_66878443_6   1456 GAGCCTTCACACTTCCTGATTACAAATTATATTACAAAGCCACAGTAATC 1505
                            vvi          ii   v    viv  i        i         
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_66878443_6   1506 AAAATAATATGATATTGGCATTAAAAGCT-GACACATAGACCAATGAAAC 1554
                           i i i i  i  i      --  i v -    i     i     i  i
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGATCAATGGAAT 306

  chrX_66878443_6   1555 AGAACTAAGAGCCCAGAGATAGATCCGCACATACACTGTTAACTAATATT 1604
                             i i    i     i   i i  ii    vi iv  i  i i  v  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_66878443_6   1605 TGATAAGGATACCAAGA--ATGCACCACGGCAAAAAGATAACCTT--CAA 1650
                         i  i    i i      --  v  -- i  vi   ii   ii   --   
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_66878443_6   1651 TAAATGGTATTTGGAAAACTGTATATCCACAGGCAAGTTAATAAACTTGG 1700
                         i       ii v   v     v   ?     v    ivv   i  v    
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_66878443_6   1701 ACTC-TA----AAACT---CACAAAAAGCAACTAGAAATAAATTAAAAAT 1742
                           i -  ---- v  i---i       vi    vi    ii  i ? i i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_66878443_6   1743 ATAAACATAAGACCAAGAACCATAAAACTTTTGGAAGA---CATTGGGTG 1789
                         v    ii     v v i   i        i  i     ---   ------
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT------ 548

  chrX_66878443_6   1790 GAGGGAAACACCTTC---ACATTGAGTT-GGCAATTATTT-TCGGATCCA 1834
                         -   ?iv v i    ---  v   i   -      vi   - ii   vii
  L1M4_orf2#LINE/    549 -AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_66878443_6   1835 ACAGCAAAAGCACAAGCAGCAAGACAAAAA-TAAACAAGTGTAACTACAT 1883
                            v              i   i v     -  i i  i vvi   v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_66878443_6   1884 CAAACTAAAAAGCTTCTGCATAGCAAAGGAAAC-AGCA-GAA--TGAAAA 1929
                             v v    i   i  iiivv       v  - v  -   --      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_66878443_6   1930 AGTAGCATATGAAATGGGAGAGAATATTTATGAAGCATATATCTGATAAG 1979
                         iii i vi iii         i       iii  v               
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_66878443_6   1980 CAGTCAATATTCAAAATATATAAGAAACTCAAACATCTCAATAGCAAAAA 2029
                         viiiivi   i  i         ii     vv   v       ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_66878443_6   2030 AACAAACAAACAAACAGACAAACAAAAAAACAAATGATTTAAAAAATGGA 2079
                         i     i  v -------------------   -----  ?        i
  L1M4_orf2#LINE/    798 GACAAATAACC-------------------CAA-----TTWAAAAATGGG 823

  chrX_66878443_6   2080 CAAAGGGGCTGAATAGACATTTCTCTAAAGAAGACATAAAAATGGCCAAT 2129
                               ivi                i        i   v           
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_66878443_6   2130 AGATACATGAAAAGGTACTCAACTTTACTAATCAT 2164
                          iii          i i      v i ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (154 / 66)
Gap_init rate = 0.03 (24 / 898), avg. gap size = 2.88 (69 / 24)  


3113 27.34 0.99 0.88  chrX_66887062_66893454.rev     4996  5902 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66887062_6   4996 TGGAAGAACATTCCATGCTCACGGATAGGAAGCATCAATATGGTGAAAGT 5045
                              ii i  i     i   i    v     vv i     v  v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66887062_6   5046 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66887062_6   5096 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTGAAGTTCA 5143
                          v   iivi i  i  ii     -   -- v  i  - i i i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_66887062_6   5144 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5193
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_66887062_6   5194 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5243
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_66887062_6   5244 TACAGTAGCCAAAACAGCATGGTACTGGTACCAATACAGAGATATAGACC 5293
                                ii   i    ii         i iv iv i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_66887062_6   5294 AATGGAACACAAC--AGAGCCCTCAGAAATAATACCACCCATGTACAATC 5341
                                i v  i--    i  --        vv   iv   v  iii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_66887062_6   5342 GTCTGATTTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGCTTCC 5391
                         ivi       i     ivv  v   i v  vv            iv vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_66887062_6   5392 CTATTTAATAAATGGTGCGGGGA-AACTGGCTAGCCATATGTAGAGAGCT 5440
                           v  i  i         v    -      v  ?   i   i i iiiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_66887062_6   5441 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 5490
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_66887062_6   5491 TTAAAGACTTAAATGTTAGACCTAAAATCATAAAAACCCTAGAAGAAAAC 5540
                          i ?    i       v   v      ii      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_66887062_6   5541 TTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5589
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_66887062_6   5590 AAACACCAAAAGCATTGGCAACAAAAGCCAAAATTGACAAATAGGATCTC 5639
                         vi            ivi          vv     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_66887062_6   5640 AGTCAA--CTAAAGAGCTTCTGCATAGTAAAAGATACTACCATCAGAGTG 5687
                          -    --i    i -   i  iiivvi   i  i    i  vv i    
  L1M4_orf2#LINE/    646 A-TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_66887062_6   5688 AATAGGCAACTTCCAGAATGGGAGAAAGTTTTTACAATCTACCCATCTG- 5736
                           v  i    iiv              i v   i   vii ivi     -
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_66887062_6   5737 TAAAGGGCTAATATCCAGAATCTACAAAGAGCTTAAACAAATTTACAAGA 5786
                            i  i  vi          v  i     i  ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_66887062_6   5787 AAAAAATCAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGTCA 5836
                             i -    i     v  i?    i    ii     iv    i  v  
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_66887062_6   5837 CTTCTCAAAAGAAGACATTTGTGTAGCCAACAGACACATGAAAAAATGCT 5886
                         i     v        i  viivi i     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_66887062_6   5887 CATTATCACTGGCCAC 5902
                           vi    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (150 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.31 (17 / 13)  


3104 27.03 0.66 0.88  chrX_66944892_66951301     5008  5917 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66944892_6   5008 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCGTGAAAAT 5057
                              ii i  i     i      i v      v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66944892_6   5058 GGCCATACTGCCCAAGGTAACTTATAGATTTAATGCCATCCCAATCAAGC 5107
                            v     v     iv i ii  i     i  i  v     v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66944892_6   5108 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5155
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_66944892_6   5156 ATATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCCAAGCCAAAA 5205
                                 viiv  ii  v  viv  vi    iv     iii ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_66944892_6   5206 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATATTACAAGG 5255
                                 i      vv       v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_66944892_6   5256 CCACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5305
                          i       i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_66944892_6   5306 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAAC 5353
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_66944892_6   5354 TCTCTGATCTTTGACAAACCTGACAAAAGCAAGCAATGGGGAAAGGAATC 5403
                         ivvi    i  i     ivv  v   i v  vv            -   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATA 394

  chrX_66944892_6   5404 -CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAG 5452
                         -i  v  i  i              v      v  ?       i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_66944892_6   5453 CTGAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATG 5502
                         v    ii    i    v   i     v     v        i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_66944892_6   5503 GATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5552
                            i ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_66944892_6   5553 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGAAAGGACTTCATGTC 5601
                           v    ?i- v i -   iv   v v  vv i  v  v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_66944892_6   5602 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5651
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_66944892_6   5652 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAATACCATCAGAGTG 5701
                          v  i   v v  i i   i  ii vv    i  v v  i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_66944892_6   5702 AACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTATTCATCTGA 5751
                           v  i     i                 v   i   vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_66944892_6   5752 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5801
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_66944892_6   5802 AAAAAACAAGCAACCCCACCAAAAAGTGGGCAAAGGATATGAACAGACAC 5851
                             i    ii     v ii?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_66944892_6   5852 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAAAATGCT 5901
                              v        i  vi viii     v  i-          i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCT 892

  chrX_66944892_6   5902 CATCATCACTGGACAT 5917
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2189 28.12 10.30 0.24  chrX_66970796_66973201     1089  1913 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66970796_6   1089 TGGAAACACAGGCCATGCTCATGGATGGGTAAAATCAATATTGTGAGAAT 1138
                               v i vv     i        v  v i v i        v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66970796_6   1139 AATCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATTAAAA 1188
                         iiiv     v  v   vii       i      i        i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66970796_6   1189 TACCACCATCATTCTTCACAGAGTTATGAAAAAC-AATTCTAATATTCAC 1237
                          v   v vv v  i  ii    iv -   v  i -i  i    v     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_66970796_6   1238 ATGGAACCAAGAAGAGCCCACAG-AGCCAAAGAAAGACTAAGCAAAAAGA 1286
                               viivi i ii    v i-       iv  vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_66970796_6   1287 ACAAATCTGGAGGCATCACACCAATTGATTTCAAA-CTATTTATAAGGCC 1335
                              vi      vv      ivviii        -  vvi  i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_66970796_6   1336 TTACTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCA 1385
                         vi v v i   i    ii         i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_66970796_6   1386 ACGGAACAGAATAGAGAACCCAGGACTAAACCCAAATACTTACAGCCAAC 1435
                          i    i     v    ii    i v        v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_66970796_6   1436 TGATCTTTGACAAAGCAAACAAAAACATAAAATGGGGAAAGGACA-CCTT 1484
                             i  i     i vviv   i v   vv           i i -i   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_66970796_6   1485 TTTAA--------------------------------------------- 1489
                           i  ---------------------------------------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_66970796_6   1490 ----------------ACAC-------------------AAGATGGATCA 1504
                         ----------------    -------------------  i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_66970796_6   1505 ATGTCTTAAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGACAACAT 1554
                         ?v v i    - v     v  i           v ii       v     
  L1M4_orf2#LINE/    500 WAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_66970796_6   1555 TGAAA-AACCCTTCTAGATATTGGCTTAGGCAAGAATTTCATGACCAAGA 1603
                         v i?i-  vi    vv  iv    v        vii    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_66970796_6   1604 ACCCAAATGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATT 1653
                         vv     v   v v    i    iv   i   i   iv v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_66970796_6   1654 AAACTAAAGAGCTTTTGCACAGCAAAAAGAACAGTCAGCAGAGCAAACAG 1703
                            v v  i i      ii vv    iiiv  vi   iv i  ii  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_66970796_6   1704 ACAACCCACAGAGTGGGAGAAAATCTTCACAATTTATACATCTGACAAAG 1753
                                     i           v  ii   v i   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_66970796_6   1754 GAATAATATCCAGAATCTACAATGAACTTAAACAAATCAGTAAGAAAAAA 1803
                           v vi          v  i  v     ivv    v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_66970796_6   1804 ATGAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGAAAATTCTC 1853
                          ii  i  i  v  i?    i     v     iv        v v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_66970796_6   1854 AAAAGAGAATACACAAATGGCCAACAAACATATGAAAAAATGTTCAGCAT 1903
                         v     ii   i            i  i  i       i   i   i   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_66970796_6   1904 CACTAATGAT 1913
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 9.67 (87 / 9)  


2922 26.31 2.23 1.00  chrX_66986197_66991785     4200  5096 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66986197_6   4200 TGGAAAAACATTCCATGCTCATCGATTCAAAGAGTTAATATTGTGAAAAT 4249
                               i i  i     i    v    vi    v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66986197_6   4250 GACCATACTGCCCAAAGCAATCTA-AGATTCAATGCAATTTTTATCAAAA 4298
                          i v     v      vii     -        i     iii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66986197_6   4299 TACAAATATCATTTTTCACAGAATTAGAAAAAA-AATTCTAAAATTTGTA 4347
                          v v iivv v     ii     v v  v  iv-i  i        ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_66986197_6   4348 TGGAATAGAAAAGAGCGCACA-CAGTGAAAGTAATCCTAAGCAAAACAAA 4396
                              vv v  i ii v  v -i  iv   ii    i i iv  i vi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_66986197_6   4397 CAAATAAATATGGAAGCATCACAATACCTGACTTCAAATTATGCTACACA 4446
                             ---i -    i vv     v v  ii i      viv i     v 
  L1M4_orf2#LINE/    201 CAAA---GT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_66986197_6   4447 GCTACAGTAACCAAAATAGCATGGTACTAGTATAAAAGTAGACACATAGA 4496
                                   i   i i  ii       i i    iii      i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_66986197_6   4497 CCAATGAAACAGAATAGAGAACCCAGAAATGAAGCTAAATGCCTACAACC 4546
                         i     i  i     v    ii        i  v i v iiii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_66986197_6   4547 AACTGATCTTCAACAAAGCAGACAAAAACATAAACAGGGAAAAGGACACA 4596
                           i    i   i    i vv v   i v   vv vv   i    i i vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_66986197_6   4597 CTATCCAATAAATGGTGCTGGAAAAATTGGATAGCCACATGCAGAAGAAT 4646
                           v i   i            i v  i      ?         i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_66986197_6   4647 GAAACTTGATCCACGTCTTTCACCATATACAAAAATTAACTCAAGATGGA 4696
                            ii v  i  viii  iv                        i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_66986197_6   4697 TTAAATACTTAAATCTAAGACCTGAAACCCTA----TCT-AAAAGAAAAC 4741
                          i ? v  i     v     v  i    iv  ----   - i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_66986197_6   4742 CTAGGTA-AAACTTTTGTAGACGTTGGCCTAGGCAAAAAATTTATGAAAA 4790
                         v    ?i-   ii  i  -   v    vi       viiv  iv ii v 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_66986197_6   4791 AGACCCCAAAAATAAATGCAACAAAAACAAAAATAGATGAATGGGACTT- 4839
                         v   v      ii v v         iv          i   v      -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_66986197_6   4840 ----AAACTAAAAAGCTTCTGCATAACAAAAGAAATAATCAACACAGTAA 4885
                         ----   i      -   i  iiivv    i  v iv     v v   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_66986197_6   4886 ACAGACAACCTACAGAATGGGAGAGAATACTCACAAACTATGCATCTGAG 4935
                          v        i             i    i ii    ii  ii      v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_66986197_6   4936 AAAAGAGTAATATCCAGAATTTACAAGGAAGTCAAACAAATCAACAAGAA 4985
                           ii  v vi          v  i  i   v  vv    v    i  ---
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA--- 791

  chrX_66986197_6   4986 TAAAAAG-CAAATAATTCCATTAAAAACTGGGTAAGTGACATGAATAAAT 5034
                                -       ii v   ?    v    i  iv  iv      i i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_66986197_6   5035 ATTTCCT-----AAGTTATACGGATGGCCAACAAGCATACGAAACAATGC 5079
                              ii-----   v     ii        i     i i    vi    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_66986197_6   5080 TCAACATCACTAATTAC 5096
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (145 / 87)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.07 (29 / 14)  


2566 27.67 2.43 2.32  chrX_66997665_67003429.rev     4368  5274 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_66997665_6   4368 TGCAAAAACATTTCATGCTCAAGGATAGGAAGAGTCAATATTGGTAAAAT 4417
                           v   i i  ii    i   v    v      v i       v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_66997665_6   4418 AGTCATATTGCCCAAAACAAGTTATATATTCAATACTATTCCTGTCAAAC 4467
                         i iv   i v      vii vi  i v      ii v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_66997665_6   4468 TACCAATGACGTTTTTCACAAAATTAGAAAAACT-ATTTTAAAATTCATA 4516
                          v   iivi v     ii  i  v v  v  i  -  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_66997665_6   4517 TGGAACAAATAAAGAGCCCA-AATAGCCAAGAGCCTATTGCAAAAGAGCC 4565
                              - vii  i ii    -         i vvv v   v      ---
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA--- 196

  chrX_66997665_6   4566 TAAGCAAAAAGGATAAAGCTAGAGGTATCACCATTAACTGACTTCAGACT 4615
                         ---------  i i    i i    vv    - i vv ii i    i vi
  L1M4_orf2#LINE/    197 ---------AGAACAAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAAC 236

  chrX_66997665_6   4616 ATACCACAAGGCTGCAGTAACTGAAACATCATGGTACTGGTACAAAAGCA 4665
                         v   i    i   i      iii i   vii         i i  iiii 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_66997665_6   4666 GATAGATAGACTGATGAAACAGAATAGAGAATCCAGAAATAAAGATGAAC 4715
                           i v     iii   i  i     v    i            vviiv  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_66997665_6   4716 ATCTACAACCATCTGATCTTTCACAAAGTCGACAAAAACAAGAAATGAAG 4765
                           i  iiii  vi    i  iv    i vi v   i v  vvv    ii 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_66997665_6   4766 AAAGGACTCCCTATTAAATAAATGGTTCCGGGATAACTGGCTACCCATAT 4815
                             i ivvi  v  v  i       v i    i      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_66997665_6   4816 GCAA--GATTAAAACTG-ACCCTTTCCTTACACCATCTACAAAAATCAAT 4862
                             --  v i  ii  -    i v   i       v         i  i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_66997665_6   4863 TCAACATGGGTTAAAGACTTAAATGTAAAATCTACAACTATAAAAACCCT 4912
                             v    i i ?    i         i v   v          vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_66997665_6   4913 GGAAGAAAACCTAGG---AAATACCATTCTGGACATAGGCCTGGCAAAGA 4959
                         i         v    ---    -- v iv  iv v i  iiv     v i
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_66997665_6   4960 GTTCATGACGAAGT-TGGCAT---AAGCAATTGCAACAAAAACAAAAGTT 5005
                         v   v ---- ii -  i  i---     vvv         iv    i v
  L1M4_orf2#LINE/    585 TTTCTT----AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_66997665_6   5006 GAAAAAC-AGACTTAATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAAG 5054
                           v   i-i     v  v   v v  i i   i  ii vv    i  v v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_66997665_6   5055 TATGAACAGAGTAAACAGACAATCTACAGAATGAGAGAAAATATTTGCAA 5104
                            v  v i   i  v      i i        i                
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_66997665_6   5105 GCTATGCATCCTACTAAGGTCTAATATCCAGAAACCATAAAGAACTT--- 5151
                         iii  ii   iv iv i  v  vi         vvi          i---
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_66997665_6   5152 -AAATTAATAAGCAAGAAGCAAAGCAACCCA-TTTAAAAGTGAGCAAAGA 5199
                         -  v i     vv  i ii    -i      -  ?    i  i      i
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_66997665_6   5200 ACATGAACAGACACTT-TCCAAA--AGACATACATGTGGCCAACAGGCAT 5246
                          iv    i     i  -      --   i     vi       i i   i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_66997665_6   5247 ATAAAAA-ATGCTCAACATCACTAGTCAT 5274
                           i    -             ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (154 / 94)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.26 (43 / 19)  


2832 21.74 7.67 4.35  chrX_67077668_67079592      559  1432 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_67077668_6    559 AGATATATTTTGTTTGCAGGTATAAAGACTCAATAGTGTTAAGATGTAAA 608
                               viiv    iiii i vvi      i    v          vv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_67077668_6    609 TTCTCACAAAATTGATCTACAGACTGAACACAACCC------AAATACCA 652
                          v   v v               i v   i   i  ------    v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_67077668_6    653 GTAAGCTTGTATGTAGACATTGACAAGCTGATTCAAAAATGTATAAGGAC 702
                          iviv   v v  i   v              i v     vi   v   v
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_67077668_6    703 ATGCAAAGAACCTAGAATAGCCAAAACAATCTTGAAAAAGAAAAACAAAG 752
                               i i   i                             i       
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_67077668_6    753 TTGGAAAGCTAACACTACCTGATTTCAAGTCTTATTATAAAGCTACAACA 802
                              iii  v     v  ii       iv    i  i         ii 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_67077668_6    803 ATTAAGACAGTGTGGCACTGATGTCAAGATAGGTGAATAGATCAATGGAA 852
                           i            i    iii v i     iiiv              
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_67077668_6    853 CAAAATAGAAAGCCCAGAAATAGACCCA--CATCTATACAGATAAATTTA 900
                         i i   v  i  i         i     --   i   --- i v    v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT---GGTCAATTGA 352

  chrX_67077668_6    901 TTTATTTATTTTACAAAGG---CAA-----TTCAGTGGAGAAAGGACAGC 942
                            ------ iv    i  ---   -----    i   i     i i  i
  L1M4_orf2#LINE/    353 TTT------TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_67077668_6    943 ----------AATGGTACTGGAACAATGTGATATACATAGGCAAAAAAAA 982
                         ----------      i    i    ivv    ?v  i v      i  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_67077668_6    983 AAAAAAAAAAAAAACTTCAATTCGTATCTTATACCACAGAAGAAAACTAA 1032
                         i  i-----------  vi ii v  i  i i    i v vi    i   
  L1M4_orf2#LINE/    447 GAAG-----------TTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_67077668_6   1033 CTCAGAATGGGCTATA-ATC-AAATTTAAAAGCTGAAACTATAAAATTTC 1080
                             i     iii ? - i -    v   i    i           i ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_67077668_6   1081 GAGGAGAAAA-----------ATCTTTGTAATCTTAGGTTAGCCAAAGAT 1119
                         v  i      -----------     i  i i   i      v   v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_67077668_6   1120 ATCTTAGATACAATGATT-----CATAA-----------AATAATCAATA 1153
                         v         ii i- ii-----  i  -----------  v   vi   
  L1M4_orf2#LINE/    586 TTCTTAGATATGAC-ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_67077668_6   1154 AACTGAAC---ATCAAATTTGAAAACTCATGATTTTCTAAAAGACACTGT 1200
                           i  i  ---      v  i      iv  vvi   -   i      i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC-AAAGGACACTAT 683

  chrX_67077668_6   1201 TAAGAA--TGAAAAGAAAAACCACAGACTGAGTTAAAATATTTGTAAATC 1248
                         i     --        v  v       v  i vv          i     
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_67077668_6   1249 ATATGTCTGATAAAGAACTTGTATTATATATATATTATATAAAGAACTCC 1298
                             i        i i        i-----i v v              i
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATC-----CAGAATATATAAAGAACTCT 778

  chrX_67077668_6   1299 CAAAACTCAATAACTCAATAATAAGAAAACAAGTAAATCAGTTTTTAAAG 1348
                         i --------i             i  i    i   vi  i  ?---  i
  L1M4_orf2#LINE/    779 TA--------CAACTCAATAATAAAAAGACAAATAACCCAATTW---AAA 817

  chrX_67077668_6   1349 AATAAGCAAAATATTTGAATAGACACTTTACCAAAGAAAACATACAAATG 1398
                            ii     iv             i  iv        i i         
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_67077668_6   1399 GC-AA-----ACATAAAAAAA-GTTCAACATCATTAAGTCA 1432
                           -  -----    i    i - i         ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (127 / 60)
Gap_init rate = 0.03 (23 / 903), avg. gap size = 4.57 (105 / 23)  


2153 26.94 5.39 3.70  chrX_67096043_67097957.rev      534  1424 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_67096043_6    534 GAGATACATACTGTGTTCATGGAGTGGAAGACTCAACATGATAAAGATGT 583
                           i v i  v ii          v         i  i  vi v      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_67096043_6    584 CAAT--TCTTTAAA--AAT-TATAAGTTTAAGGTAATCAATATCAAAATC 628
                             --  iii   --i  -  i ii  i  v i    vv          
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_67096043_6    629 CCAGCAAGAGCTTTTGTAGATAAAGACAAGATAATACTAACATATATGTA 678
                              vivvvi     i   v vv      v i  v    v  vi  i i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_67096043_6    679 GAAATGGAAAGGAACTGTAAGGGCTAATACAATTTTGAAAAATAA---TA 725
                               v  i   v iiv  vi  i  v     i        v  ---i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_67096043_6    726 AA-CTGGAGGTAGGTA---TTAATAATATTAATGCTTACTGTATTGCTTC 771
                           -i      - vvi ---  vvi   v i  vi      ii vv   v 
  L1M4_orf2#LINE/    203 AAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_67096043_6    772 AGTAGTCAAGACAGTGTACAATTGGCAGAGGTAACCCGATAAGTCCTCTT 821
                             i            ivv i     v i ------    i--------
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAG------GATAG-------- 287

  chrX_67096043_6    822 GTCTACTTCTTACATAAACAAATAGAACAGAATAGAGAATCCACAAATAG 871
                         ----  ----- i   i iv   i   i     v    i    v     i
  L1M4_orf2#LINE/    288 ----AC-----ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_67096043_6    872 CCCTACAGAGT-ATGGCCTGATTATTTTTC-ATGAAGGTAC-AAAAGCAT 918
                         v  i i v v -    i -i   iv     - ii i   i -  i v   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTC-AATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_67096043_6    919 TTCAAGGGAGAGAGGGTAGTCATTTCAATGAATTGTATTGGAGCAATTGC 968
                          -   v  i  i  ii     v      ii   v  ii   ii   i  v
  L1M4_orf2#LINE/    378 T-CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_67096043_6    969 AGCTCTATAGGTAATGAAAGTGAACCTCAACCTAAACCTCTCATTTTATA 1018
                          vv? i i v i  -i i i    vi vi   ivv     v  iiv    
  L1M4_orf2#LINE/    427 ATAKCCACATGCAA-AAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_67096043_6   1019 TAAAAATGAGCTCACAAAGGATCATACATTTACATATAAATCATAAAACT 1068
                         i      v i    v  v      ? v ii  v  i   ivvv       
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_67096043_6   1069 A--AAACTTGTAGAAGATAATATAGA---AAACTGTTAGAGCCTAGGACT 1113
                          --     iv       v  i    i---   iiv iivii   v  ii 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_67096043_6   1114 TATTGA-GG------AGACATGATACCAAAAGCATAATCCATTAAAGAAA 1156
                         vivii -  ------   i    i          i  v v iv       
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_67096043_6   1157 AAAAATCAATAAATTG-ACTTCATCAAAATTAAAAATTTTTGCTCTGTGA 1205
                            -- vi        -                   i     iv  vii 
  L1M4_orf2#LINE/    626 AAA--TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_67096043_6   1206 ATGACCCTATTAATAAGATGGAAAAAAAAGCTACCGAGATTTGGAGAAAA 1255
                          v   v    i  v  ii  i   i v  v i  --   v v        
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCAC--AGAATGGGAGAAAA 721

  chrX_67096043_6   1256 TATTTGCAAACCACGTATCTGACAAAGGATTAATATCTAGACTATACAAA 1305
                                   i  ii       i  i   i vi    i   v    i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_67096043_6   1306 GAACTCTCAAAGCTCAACAGCACAAA----AATTCAATCTAATTAGAAAG 1351
                                i v i     i ii v   ----   --  i i    ?i   i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAAT--AACCCAATTWAAAAA 819

  chrX_67096043_6   1352 TGGGCAAAAGACATGAA----CAT---------GACG-TATGCG--TGGC 1385
                                 i  iv    ----   ---------  v -   i i--    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_67096043_6   1386 AATTAAGTATATGAAAAGATGTTCAAGATCACTAGCCAT 1424
                         v v    i i           i    v    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 2.79 (81 / 29)  


3410 22.57 1.87 1.87  chrX_67122689_67124729      678  1532 (509)    L1M4_orf2#LINE/L1        1   855 (53)  

  chrX_67122689_6    678 TGAAAAAATAGTCCATGTTCATGGATTAGGAGAACTAATCTTGTTAAAAT 727
                           i   i   vi               i i   vi    v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67122689_6    728 GTCCATACTTCCCAAAGCTT--TCTCTGGGTTCAATGCAATTCCTATCAA 775
                          v v     i      --  --   vii i     i     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_67122689_6    776 AATTCCAA-TGTCATTTTTCACAGAAATAGA--AGATAATCATAAAATTC 822
                            i   i-  i -     ii       v  --  v i   v        
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_67122689_6    823 ATATG-AAATGACAAAAGACCCTGAATAGTCAAAGCAATCTTTAGCAAAA 871
                              -     -   ii     v      i    i       v iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_67122689_6    872 GGAAAAAACATGAAGGTATCACATTCTCTGACTTCAAAATATATTATGAA 921
                         i   v   vv  i   vv     i ii ii i       iv  i  ii  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_67122689_6    922 GTTATTATAATCACATATAAACAGCATGGTACTGGCATAAAAACAGACCA 971
                          i  ivi      ----- i    ii              ii i    vv
  L1M4_orf2#LINE/    247 GCTACAGTAATCA-----AGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_67122689_6    972 ATCAACCAATAGTACAGAACAGAAAGTCCAGACGTAAACCCAAGTACTTA 1021
                           vi i    i v i    iv  i        vi        vii i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_67122689_6   1022 GAGTTAATTGATTTTTTGACAAAGGTGTCAAGAACACTCAACAGGGAAAG 1071
                         vi  i          i-     i    i     v  i    ii       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_67122689_6   1072 GATACTCTATTCAGTAAATGGTGCTGGAAAAACTGGATATCCTCATACGG 1121
                         i   v   v    ii            i v         ?  v   i ii
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_67122689_6   1122 AAG---GAAATTGGACTC-TATCTTACACTGTATACAAAAATCAACACAA 1167
                            ---   i      i -  i  i    ii           i   v   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_67122689_6   1168 AATGAAT-AAAGACTTAAATGTAAGACCAGAAACCATAAAACTACTAGAA 1216
                             i  - ?    i           v vi    i        vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_67122689_6   1217 GAAAACATAGGTGAAAAGCTCCATGACATTTGTCTGGGCAATGATTTCTT 1266
                                    ? v   v  i i    v  v vi i       i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_67122689_6   1267 GGATCAGACTCTAAAGACACAAGCAACAAATGCTAACGTAGACAAATGGA 1316
                         i   vv   v i   ii             v vv  vi    i    v i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_67122689_6   1317 ATTGCACCAAACTAAAAAGCTTCTG-----CAAAGAAATGGAAACAATTA 1361
                          i v  i    v v    i   i  -----     -----  v  v  i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-----GACACTATCA 685

  chrX_67122689_6   1362 ACACAGTGAGGGGACAACCCACGGATTGGGTAAAAACATTGGCAAACCAT 1411
                          v v     iii          i  v    vi    i   v     i   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_67122689_6   1412 AAATCTGATAAGGGGCTGATATCCAAAATATAGAAGTAACTCAAACAACT 1461
                          v            i  vi      i      v  iv     vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_67122689_6   1462 AAATAACAAGAAAACAAATAACCCAAGTAAAAAATGGGTAAGAAAATATG 1511
                         v     i  i  i             v ?         i  - ii  v  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA-AGGATTTG 834

  chrX_67122689_6   1512 AGCAAACATTTCTCCAAAAAA 1532
                          ii i             i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAA 855

Transitions / transversions = 1.78 (121 / 68)
Gap_init rate = 0.02 (15 / 855), avg. gap size = 2.13 (32 / 15)  


 426 27.70 0.68 2.03  chrX_67168950_67170620        7   154 (1517)    L1M4_orf2#LINE/L1      529   674 (234)  

  chrX_67168950_6      7 AAATTTTTACAAGAAAACATATTGGTAAAAATCTTTCAGATGTTGGGTTA 56
                            i i   v           --  ?iv       ivv  iv        
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATA--GGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_67168950_6     57 GGCAAAGATTCATTAGATATGAAACCAAGGGTGTAGTGAATACTAGAAAG 106
                              v i  iv          v     ii iii ivv  i vv     -
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA- 625

  chrX_67168950_6    107 AAATA-ATAAATTATGTCTTGTCAAAATTCAAAACTTTCACACCTAAAA 154
                              -       iviii ii        v        iiii i v   
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

Transitions / transversions = 1.67 (25 / 15)
Gap_init rate = 0.02 (3 / 146), avg. gap size = 1.33 (4 / 3)  

2476 23.70 7.15 0.60  chrX_67168950_67170620      508  1178 (493)    L1M4_orf2#LINE/L1      194   908 (0)  

  chrX_67168950_6    508 AAAAGAACAAAACTGGAAGAATCATA-TACCTGACTTCAAATTATACTAC 556
                          i         ii    i  v   i - v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_67168950_6    557 ACAGCTATAGTAACCAAAATAGCAAGGTGCTGGTGTAAAAACGGACACAC 606
                          v     i     i   i i  iiv   i    ii   ii ii    i i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_67168950_6    607 AGGTCAGTGGAACAGAATTGAGAACCTGGAAACAAATCCATACATCTACA 656
                           i   i     i          ii ii    i   i        i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_67168950_6    657 GTGAACTCATTATTGATAAAGGTTTCAAGAACATACATTGGGGAAAGGAC 706
                           v  i v   v i  i  i   vi     v   v  v         i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_67168950_6    707 AGTCTCTCCAACAAATGGTGCTAGGAAAACTGGATATCCATATGCAGAAG 756
                              i i              i   v         ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_67168950_6    757 AATGAAACTAGAACCCTATCTCTTGCC-TA------AATCAAATTAAAAT 799
                               ii i  v     i   vii  -  ------   i  v i     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_67168950_6    800 GTATTACAGACTTAAATCTAAGACCTCAAACTATAAAACTACTAAAAGAA 849
                          v  i ?    i     v     v  v             vi  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_67168950_6    850 AACATTGGGGACATTCTCCAGGACACTGGACTGGGCAAATATTTCTTGAG 899
                              v  ? vv v   i iv   vi   ii i     vvi      iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_67168950_6    900 TA--ACATTCCACAAGCACAGGCAACCAAAGCAAAAATGGACAAATGGGA 947
                           --   --   v       i     v    v      i  i    v   
  L1M4_orf2#LINE/    594 TATGACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_67168950_6    948 TCACAT-AAAGTTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAA 996
                         iiv   -   i       -   i  ii vv       v  v     v   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_67168950_6    997 GCAAAGAGACAACCTACAGAATGGGAGAAAATATCTGCAAACTATGCATT 1046
                          ii  i        i                   i      ii  ii  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_67168950_6   1047 TGACAAGGGATTAATAGTCAGGGTATATAAGGAGCTCAAACTACTGTGTA 1096
                            i      i vi  vi   ii       i  i   vv  v   vvi  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_67168950_6   1097 GAAAAAAAGTCTAATAA--------------------------TGAACAG 1120
                         - v      v v     --------------------------    i  
  L1M4_orf2#LINE/    791 -ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_67168950_6   1121 ACATTTCTCAAAAGAAGA----CAAATGG-------GTATATGAAAAGGT 1159
                                  v        ----       ------- i i        i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_67168950_6   1160 GCTTAATGTCACTGATCAT 1178
                            i  ii   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (105 / 51)
Gap_init rate = 0.02 (11 / 715), avg. gap size = 4.73 (52 / 11)  


1205 23.27 4.09 1.28  chrX_67219279_67225553       93   483 (5792)    L1M4_orf2#LINE/L1      507   908 (0)  

  chrX_67219279_6     93 AAATGTTAGACCTGAAACCATAAAACTTCTAGACTAAAACACAGAA--AA 140
                               v   v  i    i        ii    vv      i  i?--  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_67219279_6    141 ATGCTTCTAGGAATTGGCCTAATAAAAAAAAATTACTAAGA-----CACC 185
                           -    vv ivv    ---iv  iiv  vii  v  v   -----    
  L1M4_orf2#LINE/    557 AT-CTTCGTGACCTTGG---GTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_67219279_6    186 TAAAGCAAATGCAACAGAAACAAAAATAAATAAATGAGACTTAATTAAA- 234
                         v      v v      i  iv       i      vi     v  i   -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_67219279_6    235 CTAAAATCTTTCTGCACAACAAGATAAATAATCAACAGAGTAAATAGGCA 284
                         i     v    -  ii vv   iiv v iv     v i   i  v  i  
  L1M4_orf2#LINE/    653 TTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_67219279_6    285 ACTTACAGAATGGGAGAAAATATTCACAAACTGTACAGCTGACAAAGGGC 334
                           ii                    ii    iii  i v    i  i  i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_67219279_6    335 TAGTGTCCAGAATCTACAAGGAACTCCAACAAATCAGCAAGAAAAAAA-- 382
                          v  i        v  i  i      iv    v   ii  v     i --
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_67219279_6    383 ---AATCCCATTTAAAAGTGGGCAAACGACATGAACAGACATTTTTCAAA 429
                         ---  i  v   ?    i        v  iv    i        i  v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_67219279_6    430 AGAAGATGCACAAATGGCCAATAA---CATGAAAAAATGCTCAACATCAC 476
                                ii               ---        i             ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_67219279_6    477 TAATCAT 483
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.41 (52 / 37)
Gap_init rate = 0.02 (8 / 402), avg. gap size = 2.62 (21 / 8)  

3186 27.23 0.55 0.44  chrX_67219279_67225553     4876  5782 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67219279_6   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4925
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67219279_6   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAATC 4975
                            v     v     iv i  i           i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67219279_6   4976 TCCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                              iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_67219279_6   5024 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_67219279_6   5074 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAAGC 5123
                                i      vv    i  v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_67219279_6   5124 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGACC 5173
                                 i   i    ii         i iv ii i   v v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_67219279_6   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATACCTACAACT 5221
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_67219279_6   5222 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAACGATTC-C 5270
                          vi    i  i     ivv  v   i v  vvv         v  v v-i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_67219279_6   5271 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5320
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_67219279_6   5321 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTGAAGATGGA 5370
                            ii    i    v   i     v           i  i v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_67219279_6   5371 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5420
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_67219279_6   5421 CTAGGTATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5470
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_67219279_6   5471 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5520
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_67219279_6   5521 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGCAAAC 5570
                          i   v v  i i   i  ii vv    i  v    i  vv i  ii  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_67219279_6   5571 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5620
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_67219279_6   5621 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5670
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_67219279_6   5671 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTCC 5720
                          i     i     v  i?    i     i     iv    i     i i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_67219279_6   5721 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCGTC 5770
                           v        i  vi viii     v  i          i      iv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_67219279_6   5771 ATCACTGGCCAT 5782
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3166 27.75 0.55 0.55  chrX_67227116_67233538     5023  5930 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67227116_6   5023 TGGAAGTACATTCCATGCACATGGATAGGAAGAATCAATATCGTGAAAAT 5072
                              iv i  i     iv       v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67227116_6   5073 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 5122
                            v     v i   iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67227116_6   5123 TACCAATGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTAAAGTTCA 5170
                          v   iivi i  i  ii    i-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_67227116_6   5171 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5220
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_67227116_6   5221 AGCAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATACTACAAGGC 5270
                          i     i      vv   ii  v  ii        viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_67227116_6   5271 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5320
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_67227116_6   5321 AATGGAACAGAAT--AGATCCCTCAGAAATAATACTACACATCTACAACC 5368
                                i     --   vi  --        vv i i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_67227116_6   5369 ATCTGATCTTTGAGAAACCTGACAAAAACAAGCAATGGGGAAACGATTCC 5418
                          vi    i  i  v  ivv  v   i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_67227116_6   5419 CTTTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5468
                              i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_67227116_6   5469 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAAGGA 5518
                            ii    i    v   i     v              i    i v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_67227116_6   5519 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5568
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_67227116_6   5569 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5617
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_67227116_6   5618 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5667
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_67227116_6   5668 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTGTCAGAGTGCA 5717
                           i   v v  i i   i  ii vv    i  v    iiivv i    v 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_67227116_6   5718 CAGGCAACCTACAGAATGAGAGAAAATTTTTACAATCTACCCATCTGACA 5767
                         v  i     i        i        v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_67227116_6   5768 AAGGGCGAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5817
                          i  i vvi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_67227116_6   5818 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGAATATGAACAGATGCTT 5867
                           iv    i     v  i?    i         i  v    i   iii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_67227116_6   5868 CTCAAAAGAAGACATTTATGCAGTCAACAGACACAGGAAAAAATGCTCAT 5917
                            v        i  vi viii i   i ii    v     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_67227116_6   5918 CGTCACTGGTCAT 5930
                          i   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (151 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1740 25.36 0.42 0.42  chrX_67266907_67273363        2   482 (5975)    L1M4_orf2#LINE/L1      428   908 (0)  

  chrX_67266907_6      2 TACCCATATGTAGGCAGCTGAAACTGGATCCCTTCCTTACATCTTATACA 51
                           ?   i   i iiviiv    ii    i    v   i   i v      
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_67266907_6     52 AAAATTAATTCAAGATGGATTAAAGACTTACATGTTAGACCTAAAACCAT 101
                                 i    i      i ?    i  v    v   v       i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_67266907_6    102 AAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATG 150
                             vi i           v    ?i- v i -   iv   v v  vv i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTA 576

  chrX_67266907_6    151 GGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGACAA 200
                              v ii   v ivv  vi            vvi           v  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_67266907_6    201 AATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAG 250
                            v  i    v   ii v  i   v v  i i   i  ii vv    - 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA-G 675

  chrX_67266907_6    251 GAC-CTATCATCAGAGTGAACAGGCACCCTACAGAATGGGAGAAAATTTT 299
                            -      vv i      v  i  v  i                 v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_67266907_6    300 TGCAATCTACTCATCTGACAAAGGGCTAATATCTAGAATCTACAAAGAAC 349
                              vii ivi      i  i  i  vi    i     v  i       
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_67266907_6    350 TCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGAGCA 399
                           vv    v iv i  v     i     i     v  i?    i  i   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_67266907_6    400 AAGGATATGAACAGACACTTCTCAAGAGAAGACATTTATGCAGCCAAAAG 449
                               v    i     i     v i      i  vi viii     v i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_67266907_6    450 ACACATGAAAAAATGCTCATCATCACTGGCCAT 482
                         i          i       v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (67 / 51)
Gap_init rate = 0.01 (4 / 481), avg. gap size = 1.00 (4 / 4)  

3076 27.97 0.55 0.55  chrX_67266907_67273363     5057  5964 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67266907_6   5057 TGGAAGAACATTCCATCCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5106
                              ii i  i    vi      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67266907_6   5107 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 5156
                            v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67266907_6   5157 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTCA 5204
                          v   ivvi i  i  ii     -   -- v  i  - iii i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_67266907_6   5205 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5254
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_67266907_6   5255 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5304
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_67266907_6   5305 TTCAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATATAGACC 5354
                          v      i   i    ii     i   i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_67266907_6   5355 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATATACAACC 5402
                                i    i--    i  --        vv   i i  v  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_67266907_6   5403 ATATGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACGATTCC 5452
                          vv    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_67266907_6   5453 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5502
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_67266907_6   5503 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5552
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_67266907_6   5553 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5602
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_67266907_6   5603 TCAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5651
                         vi   ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_67266907_6   5652 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5701
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_67266907_6   5702 ATTAAACTCAAGAGCTGCTGCACAGCAAAAGAAACTACCATCAGAGCGAA 5751
                           i   v i  i i  vi  ii vv    i  v    i  vv i  i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_67266907_6   5752 CAGGCAACCTACAGAATGGGAGAAAAATTTTGCAGTCTACTCATCTGACA 5801
                         v  i     i                vv      ivii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_67266907_6   5802 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5851
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_67266907_6   5852 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGAATATGAACAGATGCTT 5901
                           i     i     v  i?    i         i  v    i   iii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_67266907_6   5902 CTCAAAAGAAGACATTTATGCAGTCAACAGACACAGGAAAAAATGCTCAT 5951
                            v        i  vi viii i   i ii    v     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_67266907_6   5952 CGTCACTGGTCAT 5964
                          i   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (149 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2620 24.09 5.91 2.73  chrX_67283210_67285185      606  1485 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67283210_6    606 TGGAGAGATAACCCACGTTTATAATTAGGAAAAGTCAATATTTTTAAGAT 655
                             i     v    i   i  iiv v    i v i      v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67283210_6    656 ATCAGTTTTTCCC----TGGT----AGCTTAAAAGCAAATCCTAATCAAA 697
                         iv  i vi i   ----  i ----  v  v  v    vi    -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAAA 99

  chrX_67283210_6    698 ATCAAAAAGATATCTCT-----AGGATCTTAAAAGC-AATCCCAG---TC 738
                            vv -- v ii  i -----  i vi v v    -i    i i---  
  L1M4_orf2#LINE/    100 ATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_67283210_6    739 A-----AAAT--------CCCAGCA-AGTTA------TTTTGTGGA-TAT 767
                          -----    --------     v -  ii ------ i   vii -v v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_67283210_6    768 GAACAAACTGATTCTTAAG--CTTATACCTGACTTCAATGCTTTTTACTA 815
                                v ----- vi  --  i i  i ---ii    ----  i vv 
  L1M4_orf2#LINE/    198 GAACAAAGT-----TGGAGGACTCACACTT---CCCAAT----TTCAAAA 235

  chrX_67283210_6    816 CAGTGCAATTACTACCATGCTAAAGTAATGAAGATAGTGTGGTATTTGTG 865
                          -------       v v    v      v    i         i v ii
  L1M4_orf2#LINE/    236 C-------TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_67283210_6    866 AAAGAATAGATAAATAGATCAATGCAACAGAAATAGAGAGCCCAGATACA 915
                         v   i     i v           v  i    v -     i     v i 
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATT-GAGAGTCCAGAAATA 327

  chrX_67283210_6    916 GACCCATATAAATATAGTCAAGTGATCTTTGATAAAGGACAAAAGGTAAT 965
                         i       i vv   i     v    i  i  i  i  vvvv   iiv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_67283210_6    966 TCAA-GGAGAAAGAATAGTATTTTCAAAAAACAGTGTTGGAGCAACTGGA 1014
                             -  i           v       v   ii   i   ii        
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_67283210_6   1015 TATCCACATGCAAAACAGTGAATCTAGACACAGACCTTATATCCTTCATA 1064
                           ?            v i    vi i   v vv    i i i v vi i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_67283210_6   1065 AAAATTAATTCAAAATGAATCATTGACCTAAATGTAAAA-CAAAAAGCTA 1113
                                 i        i    ?v             i - v    -   
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTA 526

  chrX_67283210_6   1114 AAAAATTCCAAAAATATAACATAGGAGAAAATCTGGGTGACCTTGGATTT 1163
                         v    i  iv i  v v        ? v      vv          i  v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_67283210_6   1164 GGAAAAGACTTTTTAGATATAACACCAAAAGTATGATCCATTAAAGCAAA 1213
                           v  v ii  i        i          i ii v v iv    v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_67283210_6   1214 AATGTGTAAGTTGGACTTCATTAAAATTAAAAACCTATGCAATGCAAAAG 1263
                            ivi   i           i            i v  iiv v    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_67283210_6   1264 AGACTATTAAGAAAATAAAAAGACAAGCCACAGACGAGGAGAAAATCTTT 1313
                          v     i      i i         v       vvi         v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_67283210_6   1314 GCAAAT-GCCTATTGGATAAAGGTCTGGAATCTAAAATATACAAAGAACT 1362
                               -iiv   iv     i  v  v v   i i      i        
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_67283210_6   1363 CTTAAAACTTAACAA----AAGA-AAAT----CAATTTAATAATAGGCAA 1403
                             v    i  i  ----    -    ----     ?  v   i     
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_67283210_6   1404 AAGAACTGAACAAATACCTCACCAGAAAGGATATACCGATGGCAGTTAAG 1453
                          i  vi    i i i ii  v   i i i       vi     viv    
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_67283210_6   1454 CATATGGAAAGATGCTCTGCATGATATGTGAT 1485
                           i   i          vi   v ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (117 / 91)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.04 (76 / 25)  


3175 26.99 0.88 0.44  chrX_67527602_67534283.rev     5288  6191 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67527602_6   5288 TGGAAAAACATTCCATGCTGATGGATAGGAAGAATCAATATCATGAAAAT 5337
                               i i  i     i v      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67527602_6   5338 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATCCCCGTCAAGC 5387
                            v     v      v i  i           i  v     ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67527602_6   5388 TACCATTGACTTTCTTCACAGAAGTAGAAAAAACT-ACTTTAAATTTCAT 5436
                          v   vivi i  i  ii     i v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_67527602_6   5437 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAACAAAAAGA 5486
                               viiv  ii  v  viv        i      i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_67527602_6   5487 ACAAAGCTGGAGTTATCACTCTATCTGACCTCCAACTATACTACAAGGCT 5536
                               i     vvv    v  vi ii ii  v  viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_67527602_6   5537 ATGGTAACCAAAACAGCACAGTACTGGTACCAAAACAGATATATAGACCG 5586
                          ii    i   i    iiii       i iv ii i   i       i i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_67527602_6   5587 ATGGAACAGAACAGAGGCCTCAGAAATAATGCCTCCCATCCAAAATCATC 5636
                               i    iv   ivii         vv  viv   ii vii   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_67527602_6   5637 TGATCTTTGACAAGCCTGATAAAAACCAG-CAATGGGGAAAGGATTCCCT 5685
                             i  i      vv  vi  i -   v-            i  vvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAGTCT 398

  chrX_67527602_6   5686 AGTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5735
                         vv i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_67527602_6   5736 AACTGGACCCTTTCCTTATACCTTATACAAAAATTAACTCAAGATGGATT 5785
                          ii       i v   i i   v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_67527602_6   5786 AAAGACTTAAATGTAACACCTAAAACCATAAAAACCCTACAAGAAAACCT 5835
                          ?    i         v v       i      vi i  v        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_67527602_6   5836 AGATAGTA--CCATTTAGGACATAGGCATAGGCAAAGACTTCATGACTAA 5883
                           i?-   --i -  iiv   v v  vv       v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_67527602_6   5884 AACACCAAAAGCAATAGCAACAAAAGCCAAAACTGACAAATGGGATCTAA 5933
                         i            vv           vv    iv  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_67527602_6   5934 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAT 5983
                          i   v v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_67527602_6   5984 AGGCAACCTACAGAATGGGAAAAAATTTTTGCAATCTATCCATCTGACAA 6033
                           i     i           i     v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_67527602_6   6034 AGGGCTAATATCCAGAATCTACAAAGAACCTAAACAAATTTACAAGAAAA 6083
                         i  i  vi          v  i       iivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_67527602_6   6084 AGACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 6129
                               ----   v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_67527602_6   6130 TCAAGAGAAGACATTTATGCGGCCAACAAACATATGAATAAAAGCTCATC 6179
                           v i      i  vi vii      i  i  i     v i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_67527602_6   6180 ATCACTGCTCAT 6191
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


1983 22.16 4.71 8.59  chrX_67553010_67554698.rev      477  1198 (491)    L1M4_orf2#LINE/L1      215   908 (0)  

  chrX_67553010_6    477 TCATGCTTCCCAATTTCAGG------------GTTACA---ATCAAGAAG 511
                            ii             ii------------ i    ---       vi
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_67553010_6    512 ATTAGGTTGTATTAGCAAAAGTATAGACATAGAAATCAATGGAACCAATT 561
                         i ---  v   i i   v   v         v i          ivi v 
  L1M4_orf2#LINE/    265 GT---GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_67553010_6    562 TGAG--TCTAGAAGTAGATAACATAACAACATATATGGCCAATTAATTTT 609
                             --  i    i  i iv-    ----   v     i     i     
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACC-CATA----CATTTATGGTCAATTGATTTT 356

  chrX_67553010_6    610 TGATAAAGTTATAAAGACAAATTCTACAGAGAAAGGGCAGTCCTTTCAAC 659
                         i  i  i v iiv     v -   v ii i     iii    i       
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_67553010_6    660 AAATA-TATTGGAACAACTGGACCTTCACATACAAAAGAATGAAACTTGA 708
                             i- ii   i         iv?i     i            ii v  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_67553010_6    709 CCTAAAACTGACACCTTACACAAAA-TTAATTCAAAGTGTACCATACATC 757
                           ivv v  v     v  i      -    i     i  v i  ? ----
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA---- 501

  chrX_67553010_6    758 TAAATCCTTCCTGACCCAGGCAAAATTGCACCTGGTTAACAACCACTGAT 807
                         -----------------------------------------------  i
  L1M4_orf2#LINE/    502 -----------------------------------------------GAC 504

  chrX_67553010_6    808 CTAAATATAAAACACAAAACTATACAACTTTTACCAGAAAAAATA----- 852
                               i   i vvi         v    i   vv      v   -----
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_67553010_6    853 AAATATTCATGACCTGTGGTTATGCAAATAGTT-CTTAGACATTACACAA 901
                             v   i      vv     v    - i   -      i  v    v 
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCA 603

  chrX_67553010_6    902 AAAGCATGATTGATAAAA-----AAT-GATGATTTGGACTTCATCAAAAC 945
                               ii vii i    -----   -   i v                i
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_67553010_6    946 TAAAAATCTTTACCCTGCAAGAGATATTGTTGAAAGGGTAAAAAGACAAG 995
                               ii   iiv  v   ii  i i i ii i ii  i         v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_67553010_6    996 CTAGAGACTGGGAGATAATATTTGTAAATTACACATCAGACAATTGACTT 1045
                          i v   v       v        i    i i i   v  i  vv     
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_67553010_6   1046 TCGTGAAGAACATATAAAGAACTGTCAAAACTGAACAG-AAAAAGTACAA 1094
                         vii vv    i            v i v    v  i i-      -    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG-ACAA 802

  chrX_67553010_6   1095 GCAATCCAATTAGGAAATGGGCTA--GACATGAAAAGATGTTTCACAGAA 1142
                         ii  i      ?ii        v --  iv    v   ii    v vi  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_67553010_6   1143 GAAGATATATGGATGGCAAATGAGCACATGAAAAGATGTTAAACATCACT 1192
                                  iii     v   i                i v       ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_67553010_6   1193 AGCCAT 1198
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.75 (100 / 57)
Gap_init rate = 0.03 (18 / 694), avg. gap size = 5.33 (96 / 18)  


3198 26.95 0.44 0.55  chrX_67562891_67568116.rev     3827  4735 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67562891_6   3827 TGGAAGAATATTCCATGCTCATGGATAGGAAAAATGAATATCATGAAAAT 3876
                              ii    i     i        v    i v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67562891_6   3877 GTTCCGTACTGCCCAAAGTAATTTAGAGATTCAATGCAATCCCCATCTAG 3926
                          v- vi    v      v i  i  v        i        i   v i
  L1M4_orf2#LINE/     51 GG-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_67562891_6   3927 CTACCAATGACTTTTTTCACAGAA-TTGGAAAAAAACAACTTTAAAGTTC 3975
                         v v   iivi i     ii     -   -- v  ivii iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_67562891_6   3976 GTGTGGAACCAAAAAAGAGCCCTCATTGCCAAGGCAATCCTAAGCAAAAA 4025
                         i i     viiv  ii  v  vvv  v     ii     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_67562891_6   4026 GAACAAAGCTGGAGGCATCACGTTACCTGACTTCAAACTATACTACAAGT 4075
                                 i      vv    ii v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_67562891_6   4076 CTACAGTAATCAAAACAGCATGGTACTGGTACCAACACAGATATACAGAC 4125
                                      i    ii         i iv iv i   i   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_67562891_6   4126 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 4175
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_67562891_6   4176 TCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCC 4225
                         vi    i  i     ivv  vv  i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_67562891_6   4226 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4275
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_67562891_6   4276 AAACTGGAACCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 4325
                           ii    v    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_67562891_6   4326 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAATC 4375
                         i ?    i       v   v       i      vi i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_67562891_6   4376 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCA-AGACTA 4423
                             ?i- v i -   iv   v v  vv i     v ii   v-   -  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TA 595

  chrX_67562891_6   4424 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4473
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_67562891_6   4474 ATTAAA-CTAAAAAGTTTTGCATGGCAAAAGAAACTACCATCAGAGTGAA 4522
                           i   -i      v     iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_67562891_6   4523 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCACCTGACA 4572
                         v  i     i                 v       vii ivi i    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_67562891_6   4573 AAGGGCTAATACACAGAATCTACAAATAATTCAAACAAATTTACAAGAAA 4622
                          i  i  vi  iv      v  i   v  i  vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_67562891_6   4623 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATAGACACTT 4672
                           i     i     v  i?    i            v          i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_67562891_6   4673 CTCAAAAGAAGACATTTATGCAGTCAACAGACACATGAAAAAATGCTCAT 4722
                            v        i  vi viii i   i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_67562891_6   4723 CATCACTGGTCAT 4735
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


3170 26.19 1.44 1.10  chrX_67579387_67583076.rev     2295  3199 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67579387_6   2295 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 2344
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67579387_6   2345 GGCCATACCGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2394
                            v    iv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67579387_6   2395 TACCAATGACTTTTTTCACAGGA-TTGGAAAAAACT-ACTTTAAAGTTCA 2442
                          v   iivi i     ii   i -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_67579387_6   2443 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCAAAAAG 2492
                                viiv  ii  v  v v  v     iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_67579387_6   2493 AACAAAGCTGGGGGCATCACGCTACCTGACTTCAAACTATACTACAAGTC 2542
                                i   i  vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_67579387_6   2543 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 2592
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_67579387_6   2593 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATAACTACAACC 2640
                                i    i--    i  --        vv   i i vi  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_67579387_6   2641 ACCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATGCC 2690
                          vi    i  i     ivv  v   i v  vvv          vi  ivi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_67579387_6   2691 CTATTTAATAAATGGTGCTGGCAAAACTGGCTAGCCATATGTGGAAAGCT 2740
                           v  i  i            v v      v  ?   i   iii  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_67579387_6   2741 GAAACTGGATCCCTTCCTTACACCTTTTACAAAAAATTAATTCAAGATGG 2790
                            ii    i    v   i     v v        -    i    i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGG 495

  chrX_67579387_6   2791 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2840
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_67579387_6   2841 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 2889
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_67579387_6   2890 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 2939
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_67579387_6   2940 AATTAAACTAAAGAGCTTCTGCACGGCAAAAGAGACCACCATCAGAGCGA 2989
                         v  i   v v  i i   i  ii vv    i  v  i i  vv i  i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_67579387_6   2990 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACTCATCTGAC 3039
                          v  i     i                 v      ivii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_67579387_6   3040 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAGTTTACAAGAA 3089
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_67579387_6   3090 AAAAACAA----CCCCATCAAAAAGTGGGCGAAGGAGATGAACAGACACT 3135
                            i    ----   v  i?    i     i     vv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_67579387_6   3136 TCTCAAAAGAAGACAATTATGCA----GCCAACAGACACATGAAAAAATG 3181
                             v        ----   i  ----     i ii          i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_67579387_6   3182 CTCATCATCACTGGCCAT 3199
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


3260 26.76 0.77 0.77  chrX_67604638_67613047     5032  5939 (2471)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67604638_6   5032 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCGTGAAAAT 5081
                              ii i  i     i      i v      v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67604638_6   5082 GGCCATACCGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5131
                            v    iv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67604638_6   5132 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5179
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_67604638_6   5180 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5229
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_67604638_6   5230 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5279
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_67604638_6   5280 TACAGTAACCAAAACAGCATGGTACTGGTACCATAACAGAGATATAGATC 5329
                                 i   i    ii         i iv vi i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_67604638_6   5330 AATGGAACAGAACAGAGCGCTCAGAAATAATGCCGCATATCTACAACTAT 5379
                                i    iv   v ii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_67604638_6   5380 CTGATCTTTGACAAACCTGATAAAAACGAGCAATGGGGAAAGGATTCCCT 5429
                         i    i  i     ivv  vi  i v ivv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_67604638_6   5430 ATTTAATAAATGGTGTTGGGAAAACGGGCTAGCCATATGTAGAAAGCTGA 5479
                         v  i  i        i     v   v  v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_67604638_6   5480 AACTGGATCCCTTCCTTACACCTTTTACAAAAATTAATTCAAGATGGATT 5529
                          ii    i    v   i     v v            i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_67604638_6   5530 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5579
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_67604638_6   5580 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTGAA 5628
                            ?i- v i -   iv   v v  vv i     v ii   v ivv ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_67604638_6   5629 ACACCAAAAGCAATGGCAACAAAAGCTAAAATTGACAAATGGGATCTAAT 5678
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_67604638_6   5679 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5728
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_67604638_6   5729 GGCAACCTACAGAATGGGAGAACATTTTTGCAACCTACTCATCTGACAAA 5778
                          i     i              v  v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_67604638_6   5779 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5828
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_67604638_6   5829 AACAAACAACTCCATCAAAAAGTGGGCCAAGGATATGAACAGACACTTCT 5878
                         i     i   i v  i?    i     v      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_67604638_6   5879 CAAAAGAAGACAATTATGCA----GCCAACAGACACATGAAAAAATGCTC 5924
                          v        ----   i  ----     i ii          i      
  L1M4_orf2#LINE/    848 CCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_67604638_6   5925 ATCATCACTGGCCAT 5939
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  

3356 21.09 4.42 1.47  chrX_67604638_67613047     7036  7917 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67604638_6   7036 TGGAAA-ACATTACATGTTCCTGTATTGGAAGAATTAATATT---AAGAT 7081
                               - i  iv       v  v         v        ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67604638_6   7082 ----AT-----CCAAAGCAATCTACAAGCTCAATGCAATCCCTACCAAAA 7122
                         ----  -----     vii       iii    i          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67604638_6   7123 TACCA-TGGGATTTTAAATGAAAATAGAAAAAC-AAGCCTAAAATTCATA 7170
                          v   -iv vv    vviiii    v  v  i -i v             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_67604638_6   7171 TGGAACCACGAAACACCCCAAATAGCCAAAACAATCTTGAGAAAGAAAAA 7220
                              vii i iiv    vi                    i      i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_67604638_6   7221 --AAGCACAAGGCCTCATACTTCCTGACTTCAAAATATATTACAAATCTA 7268
                         --   ivvi   v    i      ii i       iv  i      v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_67604638_6   7269 CAGTAATCAAAACAGTATGGTACCTGCATAAAGACAGACATATAAACCAT 7318
                                   i     i      iv      i  i         i i  -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA- 299

  chrX_67604638_6   7319 ATA-AACAGAATAGAGAACCCAGAAATAAACACAGGC-TATACAGTCAAA 7366
                           i-  i     v    ii            v  vi - v  ii     v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_67604638_6   7367 TGATCTTTGGTGGGGGTGCCAAGACTATACAAAAGAGAAAGAATAGTCTC 7416
                             i  i iiii            i  v   vi i             i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_67604638_6   7417 TTTAACAAATGGTGTTGGTAAAACTGAATATCCACATGCAAAAGAGGAAA 7466
                           i           i   v v     i   ?              ivi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_67604638_6   7467 ATTGCACCCTAATCTTATAGTATATATAAAAA--AACTGAAAATAGATGA 7514
                         i   v    iv i  i i vi     i     --    v     i   v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_67604638_6   7515 AAAACATAATTGTAA-ACCTGAAACTA--AAACTCCTAGAAGAAAACATG 7561
                         ? i  v   v     - v  i      --      i             i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_67604638_6   7562 GGG--AAAGCTTTGTAATACTGGTCTTGGCAATGATTTCTTAGATATGAC 7609
                           ?--   v   i  i ivi   vi v       i               
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_67604638_6   7610 ACTAAA-GCACCAGCACCAAAACCAAAACTAGACAAGTGGGACTGCATTA 7658
                           i   -    v    v     vv    v    i  i v     v   i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_67604638_6   7659 AA-CTAAACATTTTCTGTATAGCAAAAGAAACAAACAAGA--GTGAAAAG 7705
                           -i    v i   -   iivv    i  v  v v     --        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_67604638_6   7706 GCAACCTACAGAATGGGAGAACATGTTTGCAAACCA-ATATATGATAAGA 7754
                         i     i              v  i        i  -    v       i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_67604638_6   7755 GAACATTATCCAAATATATCCAACATATATAAAGAACTCCTACAACTCAG 7804
                           ---i ------- i      iv               i         i
  L1M4_orf2#LINE/    749 GA---CT-------TGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_67604638_6   7805 CAA--AAATCTCAAATAACTCAATTTAAAGAATCACCAAGGGACTTGAAT 7852
                         i  --   vvv        i     ?   -   viv   i   i      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAAT 837

  chrX_67604638_6   7853 ------TTTTCCAAAGACGACACACAAATAGCAAACAGATATATGAAAAG 7896
                         ------  i        v  i i      i  v  i iii i        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_67604638_6   7897 ATGTTCAATATCATTAATCAT 7917
                            i    i    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (114 / 68)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.17 (52 / 24)  


2250 26.79 8.81 0.71  chrX_67619844_67622045.rev      872  1711 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67619844_6    872 TGGAAAGAAATATTGTGCTGATGGATTGGAAGATTTAACAGAGTAAAGAC 921
                                 v  viii  i v             i    i vv  v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67619844_6    922 ATCAATTCTCCCTAAACTGATTTATAGGTTAGTTGACAATTT-TGTTGAG 970
                         iv    v     i   i    i  i  i  vivi -    ii- i ii i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACG-CAATCCCTATCAAA 99

  chrX_67619844_6    971 ATT-----TGACAATTTTATA---AT---CAAGCTTATTCTAAAATTTAT 1009
                           i-----  v vv    ii ---  ---      v  i        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_67619844_6   1010 --------GCACAAGCCGTAGAAGAGCTAAAACAATCTTGACAAAGAAGA 1051
                         --------   vii v vi    v   i             v        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_67619844_6   1052 ATAAAATAGGAGGAAGTATTCTACCCAATTGTAAGGCTTACAATATAGCT 1101
                          i   i v      vvi iv  v       vi  ii     v i v    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_67619844_6   1102 AGAGGAATCAAGAGAGTGTGGTGCTTGCAGAGGGAGACGCATATAGATGA 1151
                          v  v        v        i  v   v i   v vi         v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_67619844_6   1152 ATGGAACAAAACAGGGAACCCATAAATAGAAGTGAAAAATTATGCTCAAC 1201
                               i i  iv i  ii   v     i vviiv v v     v    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_67619844_6   1202 TGATTTTTGAAAAAGGTGCAAATAT-ATTTAATGGAGGAAGGATAGCATT 1250
                                i  v  i     v  v i-   i     i i   i    iv  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_67619844_6   1251 TTCAATAAATGATGCTGGAACAACTGCATATCCATAGGCAAAA-AATAAA 1299
                              i     i      i       v   ?   i v      -   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_67619844_6   1300 A------------CTCACAC-AT-CATAAAACTGAATTCAAAATAGATCA 1335
                         i------------       -  -i i    v v  i       i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_67619844_6   1336 -AGATTTAAATACA-GAACATAAAGCTATCAA--TC-------------- 1367
                         -   ii     ii -  i -    i    v  --  --------------
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_67619844_6   1368 --------ATCTTTGGGACCTAGTGATTGATGAAGAATTTTTT-GACATG 1408
                         --------     i v     v - i  iivv  vii   i  -  i   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_67619844_6   1409 ACACAAAAAGCACAATCTAT----TTAAAAATGTATAAATTGGACTTAAT 1454
                             v          v v i----vv      iv             v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_67619844_6   1455 TAAAGTTTAAAACTTTTAGTCTGTGA--GACATTCTGCTAAGAGGATTAA 1502
                         i   i  v         ivv  vii --    --  iii    iii v  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACA--CTATCAAGAAAGTGAA 695

  chrX_67619844_6   1503 GAGATAAGTTA-AAACTGGGAGAAAATGCTTGCAAGACGCAAATCTCGCA 1551
                         i   i  vii - i v           ii      iv ii v    vii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_67619844_6   1552 AAGATCTCATATGTAGGGTATATAAAGATCTCTCAAAACTGAACAAGAAA 1601
                          i iv  ii   vi  ii          v    i v    v  i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_67619844_6   1602 A---CAAATA-TCCAATTTGAAAATGGGCAAACGATTTGAACAAATGCTG 1647
                          ---      -i      ?i            v        i i iii v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_67619844_6   1648 AAATAAACAAGGTAAGCAGATGGCAAAAAACCTACATGAAAATATATTTA 1697
                         vvvi   v   i  vi  i     v  v  v -         v  ii i 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGC-ACATGAAAAGATGCTCA 894

  chrX_67619844_6   1698 ACTTCACTAGCTAT 1711
                           v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (131 / 92)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.20 (80 / 25)  


3840 23.81 0.44 0.33  chrX_67623322_67627868.rev     3150  4056 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67623322_6   3150 TGGAAAGATATTCTGTGTTCATAGATTGGAAGAATCAATATTGTTAAAAT 3199
                                    i ii       i          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67623322_6   3200 GTTCATACTACCCAAAGCAATCTACAGATTCAATGCAATTCCTATCAAAA 3249
                          viv     v      vii              i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67623322_6   3250 TGTCAATGACATTCTTCACAGAAATAAAAGAAAGTAATCCTAAAATTTAT 3299
                          vi  iivi v  i  ii       vi v-  iv i           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_67623322_6   3300 ATGGAACCACAAAAGACCCAGAATTGCCAAAGTTATCCTGAGCAAAAAGA 3349
                               vii   ii          v      iiv   i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_67623322_6   3350 ATAGAACTGGGGGAATCACATTACCTGACTTCAAATTATACTGAAGAGCT 3399
                          i i ii   i   v     i v  ii i      viv    iv i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_67623322_6   3400 ATAAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACACATAGACC 3449
                          i -    i   i    ii              ii i     i     i 
  L1M4_orf2#LINE/    250 ACA-GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_67623322_6   3450 AATGGAACAGAATAGAGAACCCAAAACCATATACACACACCTACAGTGAA 3499
                                i     v    ii   i  vi v iv  i   ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_67623322_6   3500 CTCATTTTCAACAAACTTGCCAAGAATATACATCGGGGAAAAGATAGTCC 3549
                         i v      i    ivv        vi  v  vi       ii      i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_67623322_6   3550 CTTCAATAAATGGTGCTGGGAAAACTCGATATCTATATGCAGAAGAATGA 3599
                         i     i              v    v    ? i i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_67623322_6   3600 AATTAGACTCCTATCTCCCACCATATACAAAAATCAAATCAAAATGTATT 3649
                          i  i   i    i   v                i  v        v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_67623322_6   3650 AAAGACTTAAATCTAAGACCTCACACCATGAGACTACTAGAAGAAAACAT 3699
                          ?    i     v     v  v v  i  i i   vi             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_67623322_6   3700 TGGGGAAACTCTCCAGAACATTGGTCTGGGCAAAAATTTCTTGAGTAATA 3749
                         v  ? v  v   i ivi  v    vi i     vii      iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_67623322_6   3750 CCCCACAAGCCCAGGCAATCAAAGCAAAAATGGACAAATGGGATCACATC 3799
                          v   v    v  i    iv    v      i  i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_67623322_6   3800 AAG-TGAAAAAGCTTCTGTACAGCCAAAGATACAATCAGCAAAGTGAAGA 3848
                           i- v     -   i   i vv v  i  i  v    iv        i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_67623322_6   3849 GACAACCCACAGAATGGGAGAAAATATTTGCAAACTATGTATCTGATAAA 3898
                                                           ii  i          i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_67623322_6   3899 GGATTAATAACCAGAATATAGAAGGAGCTCAAACAACTCTATAA--AAAA 3946
                            i vi  v          v  i  i   vv       v    --    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_67623322_6   3947 ATCCAATAGTCCAATTAAAATCTGGGCAAAAGGTTTGGATTGACATTTCT 3996
                         iv v    ii      ?   vv        i i    i  v         
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_67623322_6   3997 CAAAAGAAGGCCTACAAATGGCAAACAGGCATATTAAAGG-TGTCTAACA 4045
                          v       iiv          v  i i   i  v   i -  iii    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_67623322_6   4046 TCAATGATCAC 4056
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.72 (134 / 78)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


 957 20.60 2.01 0.00  chrX_67628431_67630372.rev        3   201 (1741)    L1M4_orf2#LINE/L1       76   278 (630)  

  chrX_67628431_6      3 AGATTAGATGCAATCCTTATAAAAATCCTGGCTGCCTTTATTACAGAAAT 52
                              vi i       i   v       ii         v  i       
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chrX_67628431_6     53 TGACAAGCTGATTTGAAAATTCATGTGAAAATGGAAGAG--TCAGAATAG 100
                                     iiv         i  i     v   i --i        
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chrX_67628431_6    101 CTAAAGTGTTCTTGAAAAAGAATAA-AAAGTTACAGAAATTGGACTTCCT 149
                          i   iiiv             v  -      iv  i v iiv      i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_67628431_6    150 GATTTTGAAACTTACTACAAAGCTATAGTAATAAAGATAGTATTGGAC-G 198
                         i    ii                  i      v    i   i v v  - 
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_67628431_6    199 GTA 201
                          i 
  L1M4_orf2#LINE/    276 GCA 278

Transitions / transversions = 2.15 (28 / 13)
Gap_init rate = 0.01 (3 / 203), avg. gap size = 1.33 (4 / 3)  

3068 17.18 2.27 0.32  chrX_67628431_67630372.rev      835  1451 (491)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_67628431_6    835 AAAAACAGCTACATAGACCAATGTAATATAATTGAGATACCAGGAATAAA 884
                           ii i  vi i     i     v    v        vv    i      
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_67628431_6    885 GCCTTCTATTTATGGTCAATTGATTTTAGACAAAGGTGCCAATAATATTC 934
                         v  v vi                    v     i        v vi    
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_67628431_6    935 AATGGAGAAAAAGTGGTCTTTTCAACAACTATTGCAGGCACAAATGGATA 984
                              i    i i i             v iv   v  v    v      
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_67628431_6    985 TCCACATGCAAAAGAATTAAGTTGAATCTTTAGCTCACACC-TATGCAAA 1033
                         ?                v      i i ii  v        -   i    
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_67628431_6   1034 AATTAAATCAAAAT-AATCAAAGATTTAAATGTAAGAGCAAAAACTATAA 1082
                               v       -i    ?   ii             v          
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_67628431_6   1083 AACTCTCAGAAGAATACATAGATGTAAATCTGAGTGTCCTTGGATCAGGC 1132
                               i       v      i?        vv   v      i i    
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_67628431_6   1133 AATAGTTTCTTAGATATGACACCAAAAGCACAAGGAACCAAAGGAAAACA 1182
                            i                              v   v    i    - 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-A 628

  chrX_67628431_6   1183 TAAATGAATTCAGTATTATCAAAATTTAAAACTTTTATGCATCAAAAGAC 1232
                           i  i    viiiv i         v         i   v     i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_67628431_6   1233 ACTATCAAGATAGTGA-----CAACACACAGAATGGAGGA---TACTAGC 1274
                                   v     -----    v          ii  ---  i v  
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_67628431_6   1275 CAATCATAT--TGGATAAG--ATCTACTATCCAGCATATATAAAGAACTC 1320
                         v        --iv      -- ii i-       v               
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTC 777

  chrX_67628431_6   1321 TTACAACTCAACAACAAAAATACAAATAATCTACCATAAAAATGGGCAAA 1370
                                    i  i     v        i i viv?             
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_67628431_6   1371 GGATTTGAATAGGTGTTCCTTCAAAGAAAATATATGAATGGCCAATAAAC 1420
                                     iii  i  i       i     ii            i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_67628431_6   1421 ATATAGAAAGAGGCTTAACATCATTAGTCAT 1451
                          i  ii     v   i       ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (62 / 40)
Gap_init rate = 0.01 (8 / 629), avg. gap size = 2.00 (16 / 8)  

 212 19.44 0.00 0.00  chrX_67628431_67630372.rev     1907  1942 (0)    L1M4_orf2#LINE/L1      431   466 (442)  

  chrX_67628431_6   1907 CTACATCCAGAAGAATGAAATTAGACCCTTATCTCA 1942
                          i    v  i         i  i     i  i    
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

Transitions / transversions = 6.00 (6 / 1)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.00 (0 / 0)  


1663 25.35 2.43 0.61  chrX_67738614_67745015        1   493 (5909)    L1M4_orf2#LINE/L1      328   829 (79)  

  chrX_67738614_6      1 AAGCCAAGTACTTATAACCAATTGATCTTTGACAAATCATACAAAAAC-A 49
                           v   vii i    iii        i  i     iv-i i v  i  - 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCA 376

  chrX_67738614_6     50 TAAATTGGGGAAAGGACACCATATTCAATAAATGTTGCTGGGAAACCTGG 99
                          vv v         i i viv v     i     v        v v    
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_67738614_6    100 CAAGCCACACGTAGAAGAATGAAGCTGGATCCTTATCTCCCATCTTATAC 149
                         vv ?     i i i          i    i  i  i   v  i v     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_67738614_6    150 AAAAATCAACTCGAGATGGATCAAGGATTTAAATCT--GACCTGAAACCA 197
                               i     i i        ?i  ii     v --  v  i    i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_67738614_6    198 TAAATATTCT-AGAAGAAAACCTAGGAAAAACTCTTCTTGACATTGGCTT 246
                             - i   -          v    ?iv  v     v    v    v  
  L1M4_orf2#LINE/    527 TAAA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_67738614_6    247 AGGCAAAGAATTTGT-GATGAAGACCCCAAATGCGAATGTAACAAAAACA 295
                               v iv  iv -   - v   v     v  iv v i       iv 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_67738614_6    296 AAAATAAATAAATGGGATCT-ATTGAACTACAAAGTTTCTGCACAGCAAA 344
                               i      v   ii -  ii  v vv   ii  i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_67738614_6    345 AGAAATAATCATCAGAGTAAACAGACAACCCACAGAATGAGAGAAAATAT 394
                         i  v iv    vv i   i  v                 i          
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_67738614_6    395 TTGCAAACTGTGTATCTGACAAAGGACTAGTATCCCGAATCTACAAGAAA 444
                                iii i       i  i     v      v    v  i  ii  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_67738614_6    445 CTCAACCAAATCAGCAAGAAAAA---AAAT--CCCG-TTAAAATGTGGGC 488
                            vvv   v   ii  v     ---    --   i-  ?   vi     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_67738614_6    489 AAAGG 493
                              
  L1M4_orf2#LINE/    825 AAAGG 829

Transitions / transversions = 1.24 (67 / 54)
Gap_init rate = 0.02 (11 / 502), avg. gap size = 1.36 (15 / 11)  

3272 26.65 0.55 0.55  chrX_67738614_67745015     5002  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67738614_6   5002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5051
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67738614_6   5052 GGCCATACTGCACAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v v   iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67738614_6   5102 TACCAATGACTTTCTTCACAGAT-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i  i  ii    v-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_67738614_6   5150 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTGAGCCAAAAG 5199
                                viiv  ii  v  viv  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_67738614_6   5200 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5249
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_67738614_6   5250 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5299
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_67738614_6   5300 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAA-C 5346
                                i    i--    i  --        vv  ii i  i  iii- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_67738614_6   5347 AATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5396
                            -    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_67738614_6   5397 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5446
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_67738614_6   5447 TGAAACTGGATCCCTTCCTTACACCTTTTACAAAAATTAATTCAAGATGG 5496
                             ii    i    v   i     v v            i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_67738614_6   5497 ATTAAAGACTTAAACGTTAGACCTGAAAGCATAAAAACCCTAGAGGAAAA 5546
                           i ?    i    i  v   v  i   vi      vi i    i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_67738614_6   5547 CCTAGGCATTACCATTCAGGACATAGGTATGGGCAAGGACTTCATGTCTA 5596
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_67738614_6   5597 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5646
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_67738614_6   5647 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGCGTGAA 5696
                           i   v v  i i   i  ii vv    i  v    i  vv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_67738614_6   5697 CAGGCAACCTACAAAATGGGAGAAAATGTTTGCAACCTACTCATCTGACA 5746
                         v  i     i   i             i       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_67738614_6   5747 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5796
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_67738614_6   5797 AAAACAAACAACTCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5846
                           i     i   i v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_67738614_6   5847 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5896
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_67738614_6   5897 CATCACTGGCCAT 5909
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3157 26.91 1.22 0.66  chrX_67778649_67784449     4406  5308 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67778649_6   4406 TGGAAGAACATTCTGTGCTCATGGATAGAAAGAATCAATATCATGAAAAT 4455
                              ii i  i ii  i        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67778649_6   4456 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCAACAAGC 4505
                            v     v     iv i  i  i        i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67778649_6   4506 TACCA-CTGACTTTCTTCACAGAATTGGAAAAAACAACTTTAAAGTTCAT 4554
                          v   -   v    i  -i     v v  v  ivii iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_67778649_6   4555 CTAGACCAA---AAAAGAGCCTGCATAGCCAAGACAATGCTAAGCAAAAA 4601
                         v i  --  ---  ii  v  v v        i     vi i iv  i  
  L1M4_orf2#LINE/    150 ATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_67778649_6   4602 GAGCAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATGCTACGAGG 4651
                           i     i      vv   ii  v  ii i      viv i    i i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_67778649_6   4652 CTACAGTAACCAAGACAGCATGGTATTGGTATCAAAACAGATATATAGAC 4701
                                  i        ii     i   i  v ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_67778649_6   4702 CTATGGAACGGAAC--AGAGTCCTCAGAAATAACACCACACATCTACAAT 4749
                          v      ii   i--       --        vv   i    i  iii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_67778649_6   4750 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 4799
                           vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_67778649_6   4800 CCTATTTAATACATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAGC 4849
                         i  v  i  i v            v      v  ?   ii  i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_67778649_6   4850 TGAAACTGGATCCCTTCCTTACACCATATACAAAAATTAACTCAAGATGG 4899
                             ii    i    v   i                         i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_67778649_6   4900 ATTAAAGACTTAAATGTAAGACCTAACACCATAAAAACCCTAGAAGAAAA 4949
                           i ?    i           v    v  i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_67778649_6   4950 TCTAGGCA-ATACCATTCAGGACATAGGCATGGACAAAGATTTCATGACT 4998
                         iv    ?i- v i -   iv   v v  vv i i   v i    v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_67778649_6   4999 AAAACACCAAAAGCAATGACAACAAAAGCCAAAATAGTCAAATGGGATCT 5048
                          vi            vvii         vv       vi    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_67778649_6   5049 AATTAAACTAAAGGGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5098
                         v  i   v v  iii   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_67778649_6   5099 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5148
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_67778649_6   5149 AAAGCGCTAATATCCAGAATCTACAAAGAAGTTAAACAAATTTACAAGAA 5198
                           i vi  vi          v  i      v ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_67778649_6   5199 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGTATACGAACAGACACT 5244
                            i    ----   v  i?    i         v  vi   i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_67778649_6   5245 TCTCAAAAGAAGAAATTTGTGCAGCCAACAGACATAGGAAAAAATGCTCA 5294
                             v        v  viiviii     i ii  i v     i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_67778649_6   5295 TCATCACTGGTCAT 5308
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


3541 17.30 2.27 0.99  chrX_67807863_67809516      471  1175 (479)    L1M4_orf2#LINE/L1      195   908 (0)  

  chrX_67807863_6    471 GAAAAATAA-TTTGACAAAATTCAACAC--CC---TTTCAAAACTTACTA 514
                            i  i  -v   i- ii i   -   --  ---               
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGG-AGGACTCA-CACTTCCCAATTTCAAAACTTACTA 242

  chrX_67807863_6    515 GAAAGCTACAGTATTTACAACAGTCTGGTCCTGGCCTAAGGATAGATACA 564
                         v            v i vi     v    v     v          i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_67807863_6    565 TTGATGATTGGAATCAAATTTAAAGTCCAGAAATAAACCCAAATGTCTAT 614
                          v   v v      vi    v i                  v ii i   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_67807863_6    615 GGTCAACTAATTTTTGACAAAGGTGTCAACACTACTCAACAGGGAAGAAA 664
                               i i     i     i    i   v  i i    ii     ii  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_67807863_6    665 GA-TCTTTTCAACAAATGATGCTGGGGCAGCTAGATATCTACATGCAAAA 713
                         v -               i       i  i  i    ? i          
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_67807863_6    714 GAATGAAGTTGGACCCTTACCTCAAACCGAATACAAAAATTAACTAAAAA 763
                                         i       v   iv               v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_67807863_6    764 TGGATCAAATACCTAAATATAAGAGTGAAGATTATTTTTTAAAACTCTCA 813
                                ? v        i      iv  i i   -----        i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-----AAAACTCTTA 537

  chrX_67807863_6    814 GAAGAAAACACAGAAGTAAATTTTTATGAC--TGGATTTGGCAATGTTTT 861
                                   i  i?      i  ii    --   i  v       v   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_67807863_6    862 TTTAGATGTGACACTAAAAGCACAAGCAGTAAAATAAAAAATAGATTAAT 911
                         i      i      i             ii    v           v   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_67807863_6    912 AGAATTTCATCAAAATTAAAAACTGTTGTGCATCAAGGAATACTATCAAG 961
                         v i i                   v      v    i i i         
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_67807863_6    962 AGAGTAAAAAGACATTCCACACAGTGGGAGAAAATACTTGTGAATCATGT 1011
                          i   i        vi     v i            i   ii      i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_67807863_6   1012 GCCTG-TAAGGGTCT---ATCTGGACTATATGAAGAACTCTTACAACTCA 1057
                         ii   -      v  ---   ii  v     i                  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_67807863_6   1058 AGAG---AAAGACAAACAACCCAATTTAAAAATGGACAAAGCACTTGAAT 1104
                          v i---         i         ?        i     v i      
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_67807863_6   1105 AGACATTTCTCCAAATAAGACATACAAATGGTCAACATGTACATTAAAAA 1154
                                        v    i          i   i v i    v    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_67807863_6   1155 TTTGTCAGTGTCACTAATCAT 1175
                         v vv   iii   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (79 / 39)
Gap_init rate = 0.02 (11 / 714), avg. gap size = 2.09 (23 / 11)  


4114 15.38 2.37 4.73  chrX_67813414_67816161     1340  2269 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67813414_6   1340 TGGAAAGTCATCCTCATTATTCATAAAATGGAAAACTTAATATT-TTAA- 1387
                                vi    -   -i     ii v     i          -    -
  L1M4_orf2#LINE/      1 TGGAAAGATATCC-CAT-GTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_67813414_6   1388 ATG----TAATCTCCAAATTGAACTACAGATTCAATGCAATCCCTATTAA 1433
                            ----  v  i         v            i           i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_67813414_6   1434 AATCCCAGATGGCTTGTGTTTTGCAGAT-TTAATAAGCT------AAAAT 1476
                                 v  v   ---         v-  i i     ------     
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTT---TTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_67813414_6   1477 TTATATGGAA-TGCAAGGAACCCTGAATAAGCAAAACAATCTTGAAAAAG 1525
                          i        -       i    v     iv                   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_67813414_6   1526 AAAATCAAAATTGGAGGCCTCTCACATCCTGATTTCAAAACTTACTATAA 1575
                           i v    i       v   v   v   ii                i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_67813414_6   1576 AGCCATAGTAATCAAGATAGTGTCATATACACTTAAAGACAGATATATAG 1625
                            i i           i     vi  ----  -------- ii   -  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTA----CT--------GGCATA-AG 282

  chrX_67813414_6   1626 TACAGATGTATAGATGTAAAGTGGAATACAATTGAGAGTCCAGAAATAAA 1675
                         v i   ii       -i  --       v                     
  L1M4_orf2#LINE/    283 GATAGACATATAGAT-CAA--TGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_67813414_6   1676 CCTTCATACTTATGGTCAACTGATTTTCAACAAGTATGCTAAAACAATTC 1725
                           ivi i i          i        i     vi   i  i  v    
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_67813414_6   1726 AATGGAGTAAGAAAAGTCTTTCCAACAAA-GGTGCTGGGACATCTGTATT 1774
                              i v     v       i       -            v   v  v
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_67813414_6   1775 TCCACATGTAAAGAAATGAAGTTGGATCTCTACCTCACACTATATACAAA 1824
                         ?       i   ii            i i           i         
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_67813414_6   1825 CATTAACTCAAAATGGAACAAAGACCTAAATGTAAGAGCTAAAACTATAA 1874
                         v                v  ?                             
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_67813414_6   1875 AACTCTGAGAAGAAAATATAGGGGGAAATATGCATGACCTCATATTTGGC 1924
                               v         i     ? v    v v i      iivi  v   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_67813414_6   1925 AATGGATTCTTATATATAATACCAAA-GCATAAA-AACAAAAAAGAAAAT 1972
                              v      v    i i      -   i  i-       i i     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_67813414_6   1973 AGATAAATTCAACTTCATCAAAATTTAAAATTTTCATGCTTTAAAATGAC 2022
                                  vi              v    i   ii     i   i-   
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GAC 678

  chrX_67813414_6   2023 ACTATCAAACAAGTGAAAA----ACTCATACAACAGAAGAAAATATTTGC 2068
                                 iv         ----  i  i v  ii i             
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_67813414_6   2069 AAATAATATACCTGATAAGGAACTTGTATCCATAAAGTATTAAAAACACT 2118
                             v     i         i           v  vi   v  i   v  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_67813414_6   2119 TACAACTCAACAATTAAAAACTGAGTTAAAAATTAAAATAAATTAGAGTA 2168
                                   i   -     --  v----------      vii ---- 
  L1M4_orf2#LINE/    779 TACAACTCAATAAT-AAAAA--GAC----------AAATAACCCA----A 811

  chrX_67813414_6   2169 TTAAATTAATAATTCAGTAAAATATTTCA-TAGACGCTTCTCCAAGGAAG 2217
                           ?  -----  v vi i   iv    v -     ii        i    
  L1M4_orf2#LINE/    812 TTWAA-----AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_67813414_6   2218 ATATAAAAATGGCCAATAGGTACATGAAAACTTTCTAAATGTCATTATCA 2267
                              v            i i         vv v  v  ii   ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_67813414_6   2268 GG 2269
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.57 (85 / 54)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.64 (66 / 25)  


3049 27.51 0.33 0.00  chrX_67816240_67821339     3703  4607 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67816240_6   3703 TGATAACACATCCCGTGCTCATAGATGGGTAGAATCAATATTGTGAAAAT 3752
                           iv  v i     i  i    i   v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67816240_6   3753 GACCATAATGCCAAAAGTAATCTACAAGTTCAATGCAATTCCCATCAAA- 3801
                          i v   v v  v   v i       ii     i     i  i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67816240_6   3802 TACCACCATCATTCTTCACAGAACTAGAAAAAAGAATACTAAAATTTATA 3851
                          v   v vv v  i  ii     v v  v  ivvi  v        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_67816240_6   3852 TGGAACCAAAAAAGAGTCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 3901
                              viiv  ii  vi viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_67816240_6   3902 CAAATATGGAGGCATCACATTACCTGACTTTAAACTATACTATAAGGCCA 3951
                             vv      vv     i v  ii i  i   viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_67816240_6   3952 TAGCCACCAAAACAGCATGGTACTGGTATAAAAA-AGGCACTTAGACCAA 4000
                         i  iv i   i    ii         i    ii -  i  iv    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_67816240_6   4001 TGGAACAAAATAGAGAACCCAAAAACAAAGTCAAATACTTAGAGCCAACT 4050
                              i i   v    ii   i   i   vi  v i i   vi i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_67816240_6   4051 GAAGTTCGACAAAGCAAACAAAAATATAAAGTAGGGAAAGGATACCCTAT 4100
                           vv        i vviv   i vi  vv i i       i   vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_67816240_6   4101 TCAAGAAATAGTGCTGGGATAATTGGCAAGCCACATGTAGAAGAATGAAA 4150
                             v    i         i  i   vv ?       i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_67816240_6   4151 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATCAA 4200
                         i    i  ii i   v    v           i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_67816240_6   4201 AGACTTAAATCTAAGACCTAAAACCATAAAAATTCTAGAAGATAGCATTG 4250
                             i     v     v       i      v ii       v i   v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_67816240_6   4251 GAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCATGACCAAGAAC 4300
                          ?iv  vi    vv   v    v        v ii   v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_67816240_6   4301 CCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGACTTAATTAA 4350
                                  v v         iv   i   i   i  v      v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_67816240_6   4351 ACTAAAAGGCTTCCACACAGTAAAATAAATAATCATCAGAGTAAACAGAC 4400
                          v v   ii   iiiii vvi   iv v iv    vv i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_67816240_6   4401 AACCCACAGAGTGGGAGAAAATTTTCACAAACTAGGCATCCGACAAAGGA 4450
                                   i           v  ii    ii vii   i  i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_67816240_6   4451 CTAATATCCAGAATCTACTAGGAGCTCAAACAAATCAGCAAGAAAAA-AC 4499
                           vi          v  iv i  i   vv    v   ii  v     -  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_67816240_6   4500 AAACAACCCCACGAAAAAGTGGGCTAAGGACGTGAAGAGACAATTCTCAA 4549
                            i     v iv?    i     v     iv    v     v     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_67816240_6   4550 AAGAAGGTATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCA 4599
                               i               i  i  i       i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_67816240_6   4600 CTAATAAT 4607
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.31 (139 / 106)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.00 (3 / 3)  


4597 13.58 2.35 5.24  chrX_67960328_67962367      613  1547 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_67960328_6    613 TGGAAAGACATCCCATGTTCCTGGATAAGAAGAC--AATATTGTTAAGAT 660
                                 i           v     vi      --              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67960328_6    661 GGCAATAATCACCAAATTGATATACAGATTCAACATAATCCCTATCAAAA 710
                                v  v          v            ii              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67960328_6    711 TCCTAGCTACCAATTTTTATTTTTTGCAGATATTGACAAACTGGTCCTAA 760
                            i    i  --------           v        i   i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--------TTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_67960328_6    761 AATTCAACTGGAAACACAAAGAAACAAGAATAGCCAGAACAATCTGG--- 807
                               vv      ii   i i v v          i        v ---
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_67960328_6    808 --GAGGGAAAAAGTGTTGATTATTTGAAACTTTCCAATGTCAAAACTTGC 855
                         --  i i v     - v  vv i i- v    i     v         i 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGT-TGGAGGACTC-ACACTTCCCAATTTCAAAACTTAC 240

  chrX_67960328_6    856 TACAAAGCTACAGTAAATCAAGAT-TTGTGCTACTGGCATAAAGATAGAC 904
                                         -      i-v    v           i       
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAA-TCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_67960328_6    905 ATACAGATGAATCAAATAGAATTCAGAGTCTAGAAATAGACCCATACATG 954
                            i    v   vi         v      i       i          v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_67960328_6    955 TATGTTCAATTGATTTTCAACAAAGATGACAAGACCATTCAATGGGGAAT 1004
                             v             i    i i  v                    v
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_67960328_6   1005 GAATAATCTTTTCAACAAATGGTTCTGGCACAAATGGATAGCCACATGCA 1054
                              i                 v    v    v      ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_67960328_6   1055 AAAGAAT----TTGGATCTCTACCTCACACCATATACAAAAATTAAGTCA 1100
                                ----     i i                           v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_67960328_6   1101 AAATGGATCAAAGAC-TAAATTTAAGAGCTAAAACTATAAAACTCTTAGC 1149
                                   ?    -     v                           v
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_67960328_6   1150 AGAAAACATAGATGTAAAACTTCTTGATCTTGGATTAGATGACAGTTTCT 1199
                                    i?     v    v   i     i    iii ii      
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_67960328_6   1200 TAGACAAGACACCAAAAGGACAAGCAACAAAAGGAAAAAGCAGACAA-TT 1248
                             i v           v              i     -i   i  -  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATT 638

  chrX_67960328_6   1249 GTACTTTTTCCAAATAAAGAGCTCT-ATGCTTCAAAGAATACTATTAGGA 1297
                          v    iv  v    v  i i  i -i          i i     i i  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_67960328_6   1298 AAGTGAAAAGACAATTCACAGATTGTGAGAAAATGTTTACATATCATATA 1347
                                       ii      v  v        i   i  v        
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_67960328_6   1348 CCTGATAAGGGCCTACCATCCAGAATATATAAA-AACTTTTAAAAGTCAA 1396
                         i          v  vvi                -    i   v  v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_67960328_6   1397 CAATAAAAAGGC------CACAGGTTTTAAATGGGCAAAGAATTTGAACA 1440
                         i         i ------ v  iv ?vv            i       i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_67960328_6   1441 CATACACACACCATACACACACACACACACACACACACACACTTCTCCAA 1490
                         v -------------------------------------  i        
  L1M4_orf2#LINE/    839 GA-------------------------------------CATTTCTCCAA 851

  chrX_67960328_6   1491 AGAATATATACACATGACCGATAAGCATATGAAAAGATGCTCAACATCAT 1540
                             v       v   i  i       i                     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_67960328_6   1541 TCGTCAT 1547
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.24 (68 / 55)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.73 (71 / 15)  


1840 24.42 5.96 0.77  chrX_67962648_67965122.rev      792  1311 (1164)    L1M4_orf2#LINE/L1        1   547 (361)  

  chrX_67962648_6    792 TGGAGAGGCA--CAGTGTTCATAGATTCTAAGACTCAACATAGTAAAGAT 839
                             i  ii -- vi       i    vv      i  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67962648_6    840 GTCAATTCTTACCAAATTGAAAT-TAGATTCAATGCAATTTCTATCAAAA 888
                          v    v  iv         vv -i        i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67962648_6    889 TACCAGAAAGATTTTTTGTAAATATAAAAATATTG-TCTTAAAATTCATA 937
                          v    vvivv       i i v  vi v vii  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_67962648_6    938 TGGAAAGGCCAAGGAGTTACAATAGCTA---TAATTT------AGAAGAA 978
                               v  v i   vii v      i ---i   i ------       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_67962648_6    979 --------------TCACTCCACCCGACCTCAAGATTTATTATACAGGTA 1014
                         --------------    v iv   i ii    i i   i  i v  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_67962648_6   1015 TAGTAATCAAAAACATGTGGTATTGGTGAAGAAATAGACATATACATCAA 1064
                         i         i vvi       i   iiv iii           v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_67962648_6   1065 TGAAACAGAATAGAGAACCCAGAAATAGACACACAAAT--ATGCCCAACT 1112
                           i  i     v    ii         i  v  i v  --   vi   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_67962648_6   1113 GATTTTTGATGAAGATGC-AAAAGCATTTCAGTGGAGGAAAGATTA-CCT 1160
                               i  ii i i   -  i v    -  i   -       v  -i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATT-CAATGG-GGAAAGAATAGTCT 398

  chrX_67962648_6   1161 TTTCAACAAATGGTGTTGAAGCAACTGAACATTCATAGGCAAAAAAAGAT 1210
                                        i  iii      i i ?i  i v      i  -- 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--T 446

  chrX_67962648_6   1211 AAACCTTGACCTAAACCTCACACTTTACACAAAAATTAACTCAAAATGGA 1260
                         i  vi v    ivv         iv  i                      
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_67962648_6   1261 CCACAGACTTAAGTGTAAAATGTAAAACTGTACAACTTTTAAAAGAAAAC 1310
                         i  ?    i   i     i vv       i  v    i   i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_67962648_6   1311 A 1311
                          
  L1M4_orf2#LINE/    547 A 547

Transitions / transversions = 1.72 (79 / 46)
Gap_init rate = 0.02 (12 / 547), avg. gap size = 2.92 (35 / 12)  

1147 22.41 6.40 2.22  chrX_67962648_67965122.rev     1579  1984 (491)    L1M4_orf2#LINE/L1      486   908 (0)  

  chrX_67962648_6   1579 CTCAAAATAAAT-AAAAA--TAAAT--AAAA--TGAAA---TAAA----- 1613
                                 ii  - ? i --     --  i -- i   ---    -----
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_67962648_6   1614 TAAGAGAAAACATAGGAAAAAATCTACAGTAAC-TTGGGCT---TAAAAG 1659
                           ii            ?iv      v -  i  -     i ---i  vi 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGG 584

  chrX_67962648_6   1660 TT-CTTAAAAGCAACATCAAAAGCACAATTCATTACAGAAAACATGGACA 1708
                           -    i viii   i           viv iv v      v  i  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_67962648_6   1709 AATTGAACTTCATCAAAATTAAAATATTTTGCTCAACAAAATCC-CTGTA 1757
                              i                  vv     iv vv    ivv -  i v
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_67962648_6   1758 AAGAGGACTAAAGAACAAGTTCCACTGG--GAGAGAAAATATTTGCAAGC 1805
                             iiiiv   ii    --i    v i-- i                ii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAA--CCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_67962648_6   1806 CATATATGTGACAAAGGACTCATATCTAGAATATATTAAGAAGTCTCAAA 1855
                                v   i  i     ii    i         v     v   i v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_67962648_6   1856 ACTCAATAGTAAAACTAAAAAAAAAAAAAGTCCACTTAGAAAATAGGCAA 1905
                                 i     ------ i v   v ii   v  ?i     i     
  L1M4_orf2#LINE/    783 ACTCAATAATAAAA------AGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_67962648_6   1906 AAGACATGAAGAAACATTGCACT---GGAGAGATACAGATGGCAAATAAG 1952
                          i  iv    v i     v v i--- i   v     i     v      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_67962648_6   1953 CACATGAAAAGATGTTCAACATTAGTAGCCAT 1984
                                       i       i ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (56 / 32)
Gap_init rate = 0.04 (15 / 423), avg. gap size = 2.33 (35 / 15)  


1619 25.36 2.84 0.95  chrX_67965963_67970846.rev     2384  2805 (2079)    L1M4_orf2#LINE/L1       13   442 (466)  

  chrX_67965963_6   2384 CTATATACGTAGATAGGAAGACCCAGTATTGTCAAGATGTCAGTTCTTCC 2433
                          i  i v i i   v       ii i      i      v  i v  i  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_67965963_6   2434 CAACTTGATCTGTAGATTAAAAGCATTCCCAATCAAA-TCTCATCAAGTT 2482
                            v       ii     v  v   v    v      -  i  v vivi 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_67965963_6   2483 ATTTTGTGGATATTGACAAACTGATTCTAAAGTGTATATGGAGAGGCAAA 2532
                         v     ii  v        i     i     i vi       i v    i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_67965963_6   2533 AAACTCCGAATAGTCAACACAATATTAAAGGAGAAGAACAAAGTTTAAGG 2582
                         ii  i v      i   v     v  i  ii              vi   
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_67965963_6   2583 ACTTATACCATTTGACTTTAAGAC--ACTATAAAACTATAGTGATTAAGA 2630
                            i i  iviiii i  i  i  --    i   i   i   i  i    
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_67965963_6   2631 CTGTGTGATATTGGCAAAAGAACAGACATATAAATCAATGGAACAGAGTG 2680
                          v     i  i     v   i i         i          i   i v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_67965963_6   2681 GAGAGCCAAGAAATTGACTTCCCCATAAAT--ATAGTGAGCTGATCT--- 2725
                              i v      vi  ----     v  --  i  v ii    i ---
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAAC----CCATACATTTATGGTCAATTGATTTTCG 358

  chrX_67965963_6   2726 ATA---TTGCAGAGGCAATACAATGGAGAATACATAGT-TTTACAACAAA 2771
                          i ---v   vi  i v  v      i   viv     -   v       
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_67965963_6   2772 TTGGGCTGAAACAACTGGACATCTACATACAAAA 2805
                          v v    ii         i ? i    i     
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

Transitions / transversions = 1.86 (69 / 37)
Gap_init rate = 0.02 (7 / 430), avg. gap size = 2.29 (16 / 7)  

1487 21.33 4.27 1.42  chrX_67965963_67970846.rev     3972  4393 (491)    L1M4_orf2#LINE/L1      475   908 (0)  

  chrX_67965963_6   3972 ATAAAAA---ACCCAAA-TATATCACATACCTAAATGTAAAATGC-AAAA 4016
                          i     ---  i    - iv    ? v            i -  -    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAA 523

  chrX_67965963_6   4017 CTATAAATATCTTAGAAAATAACATTGGAGAAAATCTAGATGACCTTGAG 4066
                                vv        i v     v  ? v      vvi        i 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_67965963_6   4067 TTTGATAAC-----TTTAGATACAACACCAAAGGCATGATCCTTGAAAGA 4111
                           v ii  i-----i       ii        i   ii v vvii     
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_67965963_6   4112 AAGAAAT-GATAAGCTGGATTTCATTAAAATTTAAAATTTCTGCTCCGTG 4160
                           -    -     ii    i     i      v    i  i  iv ivii
  L1M4_orf2#LINE/    624 AA-AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_67965963_6   4161 AAAGACACTGTCAAGAGAATGAAAAGACAAGCCACCAACTGTGAAAAAAT 4210
                           i      i      i i           v    vi v  v  i     
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_67965963_6   4211 ATTTGCA--TTAGGCATCTCTGATAAAGGACTGTTATCCAAAATATACAA 4258
                                -- i --i  v        i     vv      i      i  
  L1M4_orf2#LINE/    723 ATTTGCAAATCA--TATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_67965963_6   4259 AGAACTCTTAAAACTCGAAAATAAG----CAAACAACCCAACTAAAATTA 4304
                                   v     i v     i----    i       i ?   v- 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA-A 819

  chrX_67965963_6   4305 TAGGCCAAATGTCTGAACAGATACTTCATCAAAGAAGACATACAGGTGGC 4354
                          i   v  ivi i    i   i i   vi         i     ii    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_67965963_6   4355 AAATAAGCATGAT-AAAAGATGCCCTACATCATATATCAA 4393
                         v        i-  -         i v      ????????
  L1M4_orf2#LINE/    870 CAATAAGCAC-ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (56 / 31)
Gap_init rate = 0.03 (13 / 434), avg. gap size = 1.85 (24 / 13)  


2332 23.50 1.09 1.46  chrX_67971286_67976020     3106  3654 (1081)    L1M4_orf2#LINE/L1        1   547 (361)  

  chrX_67971286_6   3106 TAGAAAACTATCCTATGTTTATGGATTGGAATAATTAATATTGTTAAAAT 3155
                          i    iv     i     i           v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_67971286_6   3156 GTCTATACTACCCAAAGCAATCTATAGATTCAATGCAATCCCTATCAAAA 3205
                          v v     v      vii     i        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_67971286_6   3206 TTCCAATGACACTTTTCACAGAAATAGAAAATACAATTCTAAAACTTATA 3255
                          i   iivi vi    ii       v  v  vvii  i      i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_67971286_6   3256 TCAAACCTCAAAAGACCCCAAGTAGATAAAGCAATCTTGTGAAAGACGAA 3305
                          vi  viv   ii     vi i   vi   i        vi     v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_67971286_6   3306 CAAAGCTGAAGG---TATCTTTTTTTATTTCAAATTATATTACAAAGCTA 3352
                              i  i   ---i ivi  iiiv        viv  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_67971286_6   3353 TAGTAATAAAAACAGTATGGTACTAGCAAATTAAAAAAAATACAGACACG 3402
                         i      v  i     i       i   ---   ii -----i     ii
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA---TAAGGA-----TAGACATA 292

  chrX_67971286_6   3403 GAGAACAATGGGACAGAATAGAGAGCCTAGAAATAA-CCCATACAT--AT 3449
                         v   v      i i     v     i i        -         --  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_67971286_6   3450 GGTCAACTATTCTTTAACAAAAGTACCAAGAATATACAATGGGGAAAGGA 3499
                               i iv i  ii    ii  i      vi  v            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_67971286_6   3500 TAATCCGTTTAACATATTGTGCTGGGAAAACTGGCTAGCCACATGCACAA 3549
                           i  iv  i    v  v         v      v  ?         v  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_67971286_6   3550 GAATGAAATTGGGCCCTTGTTTTACACTGTACAGAAAAATCAACTAAAAA 3599
                                i    i   i iii i    ii  i v      i    v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_67971286_6   3600 TGGATTAAAGACTGAAATGTAAGACCTGAAAGTGTAAAATTCCTAGAAGC 3649
                              i ?    iv          v  i   v i     i  i      v
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_67971286_6   3650 AATCA 3654
                           v  
  L1M4_orf2#LINE/    543 AAACA 547

Transitions / transversions = 1.89 (83 / 44)
Gap_init rate = 0.01 (5 / 547), avg. gap size = 2.80 (14 / 5)  

 422 26.43 0.00 1.43  chrX_67971286_67976020     3657  3796 (939)    L1M4_orf2#LINE/L1      688   825 (83)  

  chrX_67971286_6   3657 AACATGAAAAGGTAAACTACAGAATTGGAGAAAAAAATTGCAAACCACAT 3706
                           vi       ii  v i       v        v v       i  i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_67971286_6   3707 ATCCAATAAAGGATTAATATCGAATGTATATAAGAAACTTATACAACTCA 3756
                            ii    i   i vi    v ivi       ii    iv         
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_67971286_6   3757 ATTGCAAAGAAAACAAATAGCTAGATTTTTAAAATGAGTA 3796
                           vii   -  i       i ivi   -?v      i i 
  L1M4_orf2#LINE/    788 ATAATAAA-AAGACAAATAACCCAATT-WAAAAATGGGCA 825

Transitions / transversions = 2.00 (24 / 12)
Gap_init rate = 0.01 (2 / 138), avg. gap size = 1.00 (2 / 2)  

 428 24.18 0.00 0.00  chrX_67971286_67976020     4152  4242 (493)    L1M4_orf2#LINE/L1      818   908 (0)  

  chrX_67971286_6   4152 AATGAGCAAAGAACCTGAATAGACATTTTTCCAAAGAAGAGACATGAGTA 4201
                             i      i ii             i           v i ii i i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_67971286_6   4202 ACCAACAGGTGTGTGAAAAAGTGTTCAATATCATTAATCCC 4242
                         i    i i iiii      ii  i    i    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 21.00 (21 / 1)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.00 (0 / 0)  


3210 23.34 1.69 5.81  chrX_68008715_68011988.rev     1837  2783 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68008715_6   1837 TGGAAAG-TATGCTGTGCTCATTGAATGAAAGACTCAATGGTGTTAAGAT 1885
                                -   v ii  i    v  v  i      i   iv         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68008715_6   1886 GTCAATTCTTCCAAATTTGATCTGCAGATTTAACACAATCTTAACGAACA 1935
                          v    v  i  v  v       i      i   i     iiv iv  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68008715_6   1936 TCCCTGCAAGGTATTTTGTATA----GACAAGTTGGCCCTACAGTTTATA 1981
                             v  vivv v     i v ----      i  ii    v i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_68008715_6   1982 TGAAAAGGCAAAAGACTTACAATGATCAACACAATACC---AAAGAAGAA 2028
                           i   v    ii   ii v   iii   v     vii---         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_68008715_6   2029 CAAAGTTGAAGGATCCACATGATCCAATTCCATGACTGATTATAAAACTA 2078
                                 i    ii    ivvi      i  vi   v i  i   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_68008715_6   2079 CAGTAATCAAGAAAGTGTAGTATTGGTATAAGAATAGACACACAGATCGA 2128
                                     v     i   i   i     i       i i     i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_68008715_6   2129 TAGAACAGAATTAGGAGCCCAGAAATAGACCCATGCAAATATAGTCAACT 2178
                          i   i      ii   i         i      i  vv   i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_68008715_6   2179 GATCTTTGATAAAGGAGTAAAGGCAATTCAATAGAAAGGGGACAGTTTTT 2228
                            i  i  i  i  v iv   i v       i ii ii i i   i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_68008715_6   2229 TCAATAAATTGTGCTAGAACAATTGTATGCTCACAAGCAAAAAAACAAAA 2278
                             i    v     i i    i  v  i?i    v      i  ii  -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA- 449

  chrX_68008715_6   2279 GTAAAAATAAAAATAAAAATTCCAAAGCAAACCAAAACTAAAATAGCCCT 2328
                           ----------------------------------------- i v  -
  L1M4_orf2#LINE/    450 GT-----------------------------------------TGGACC- 457

  chrX_68008715_6   2329 AAAACCTAAACACAGACCTTAAACCTTTCACAAAAATTAACTCAATATAA 2378
                         ----    --------   i v   v vi                v  ii
  L1M4_orf2#LINE/    458 ----CCTA--------CCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_68008715_6   2379 GTCATAGACATAAATGTAAAACACGAAACTATACAACTTCTAGAAGAAAA 2428
                         i   ?    v         i vvii        v    ii          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_68008715_6   2429 CATATGAGAAAATCAAGGTGACCTTCAGTTCG-TAGTGAGTTTTTAGATA 2477
                             v ? v     vvv        vi   v -i i  iv  i       
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_68008715_6   2478 TAACACCAAATGCACAATTCATGAAAGAAAAAATGGATG--TTACACTTG 2525
                          i        v      viv ii           i   i--  iv    v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_68008715_6   2526 ATTAAAATTGAAAACATCTACTTTGTGAAAGACACTGTTAGGAGAATCTA 2575
                           i      i     v i iivi vii  i      i i i  i i vv 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_68008715_6   2576 AAGATAAGCCTCATATTGGGAGAAAATATTTGAAAAACACATATCTGATA 2625
                             i  v  v  v v                v   v  i          
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_68008715_6   2626 AAGGACTTATATCCAAAATATAAAAAAAATT--TA-AATGCAAAAATAAG 2672
                          i      i      i      v   i  i --  -  iv   v     i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_68008715_6   2673 AAAACAAATAACCCAATTTAAAACTGGGTGAAAGAGTTAAAAAGACAACA 2722
                           i               ?    v    ii  i  v  i  v     viv
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_68008715_6   2723 CATTAAAGAAGATGTGCAAATGACAAACAA--ACATGAAAAGATGTTCAG 2770
                          vii         i i      i v  i  --             i   i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_68008715_6   2771 CATCAGTTTTCGT 2783
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 5.92 (71 / 12)  


2230 26.63 6.63 3.54  chrX_68041237_68044154.rev     1556  2430 (488)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_68041237_6   1556 GATAAACCATATCTGTGATTTAGAAAAAATTAATATTCCCAAGAAGTCAG 1605
                             vv    i iii  iv  i   i v-        vii    v v  i
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGATGGCAA 55

  chrX_68041237_6   1606 TTCTCTCCAAATTAATCCATACAGTCAATGTGATTTCATGCAAAAATCCC 1655
                          v   i       i   i i v v    i ii  ii - iiv        
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCC-TATCAAAATCCC 104

  chrX_68041237_6   1656 AGCAAGTGCTTTTTTAAATTG--AAAATGGTCAAATTGGTTCTAAAATTC 1703
                            ---   i     ----  --i    v v   ii  i i         
  L1M4_orf2#LINE/    105 AGC---TGCCTTTTT----TGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_68041237_6   1704 AGATGGGAATGCAAAGGGCCAGGAATTTCCCAGGTAATATTAAAGGAGAA 1753
                          v    i       i  i  vi    vv  v iii   v  i  ii    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_68041237_6   1754 GAATATAGCTGGAGAACTCTTACTACCAGATATCAAGAC--A-TAGAAAG 1800
                            i v  i     i    vi   v  vi  v    i  -- -  v    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_68041237_6   1801 CTATAGTAGTTAAGACATTGTGGTACTGGCACAAGGATATAGAAACTGCC 1850
                            i    i i      v             i       v v v iv vi
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_68041237_6   1851 AAATGGAA-AGAAGAGAAAATTCAAACACAAAGCCACACATATATGATTA 1899
                         v       -    vv  i i i  i v i   v   i    v    i i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_68041237_6   1900 CTTAATTTATGACAAAAATGACACTGCAGTACATTGGAGGTTCTTTTTTA 1949
                         v  i    vi     iii  v  vvi vi v  v   i -----------
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG----------- 386

  chrX_68041237_6   1950 AAAAAAATAAA----TAAATAAATGGTGTTGGATCAGTTGGATAGCCATA 1995
                         -   i    iv---- v  i        i   iv  ii      ?   i 
  L1M4_orf2#LINE/    387 -AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_68041237_6   1996 GGGAAACAAAAATCTGTATCTTGACCC-TGCCTCACACCATACACAGAAG 2044
                         v v   -- i   -- v vi v     - i            i   i  i
  L1M4_orf2#LINE/    436 TGCAAA--AGAAT--GAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_68041237_6   2045 TCAGTTCCAGATAGATTGCAAACATAAATGTGAAAGGCAACACAATAAAG 2094
                          i ii  v i  i   ii? i  v       i i  vi  v  v     i
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_68041237_6   2095 CTTTTAGAAGAAAATATAGGAGAACAACTTTGTCCCCTTGGAGTATACAA 2144
                           i           i     ? v v v   i  vv      iv  vi   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_68041237_6   2145 ATATTTCT-----------CTAAAAATGCTATCCATGAAAAGGAAATTTG 2183
                         vvi     ----------- i    iii v v v ii   iii   v v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_68041237_6   2184 ATAATTTGGACTATATTAAAAT-AAAAACATACTGGTCATCAAAAGGT-- 2230
                             v       vi  i     -      v -i  vv v     i ii--
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTT-TTGTGCTTCAAAGGACAC 680

  chrX_68041237_6   2231 TATGGTAGGAGAATGAAAAGACAACCCACGGAATGTGAGAAAATATTTGC 2280
                            --i i  i i                i     v              
  L1M4_orf2#LINE/    681 TAT--CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_68041237_6   2281 AATAGATATATCTGACAAAGGAGTCATAATTCAGAATGTATTA------- 2323
                           vvv          i  i   v ii  - i      i   v -------
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTA-TCCAGAATATATAAAGAACTC 777

  chrX_68041237_6   2324 -TGCAACCCAATAG-----------------------AAAAATGTGCAAA 2349
                         - i    i     i-----------------------       v     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_68041237_6   2350 GGACTTTGACAGGCACTTCACAAAAATAGA-ATATCAAGATAGACAATAA 2398
                            i  vi i  i  i   v v   iv   -   -   -  i v      
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATA-CAA-ATGGCCAATAA 875

  chrX_68041237_6   2399 ATATATGAAGAGGTGCTCCAC-TTAGTCAAAAA 2430
                         ii i     i  i     v  - i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.03 (25 / 902), avg. gap size = 3.56 (89 / 25)  


1383 23.63 0.55 3.02  chrX_68044717_68048302.rev     1855  2218 (1368)    L1M4_orf2#LINE/L1        2   356 (552)  

  chrX_68044717_6   1855 GGAGAAACATACCCAGGAGTTCATGGATTGGAAGATTCAACATAGTAAAG 1904
                            i i i  -    v --                i i  i  v  v   
  L1M4_orf2#LINE/      2 GGAAAGATAT-CCCATG--TTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_68044717_6   1905 ATGTCAGTTCTCTC-AAACTACTATGCAAGTTTAGTGTTGTTCTTATCAA 1953
                            v  i v   i -   i iv v i  ii  i ii ivi i i      
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_68044717_6   1954 AATTCCAACAAGCATTTTTGTAGACATAGACAAGATTATTCTAAAATTTA 2003
                            i   i viv v      i   v  v      v v  i        i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_68044717_6   2004 TATGAAAAGGCAAAGGAACTAGAATAGCTAATACAATTTTGCAAAAGAAG 2053
                             i   v    i   v i        i  v     i   v        
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_68044717_6   2054 AACACAGTGGGAGGAATCACACTACCTGATTTTAAGACTTATTACATAGC 2103
                             v   v      v       v  ii    i  i     i    v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_68044717_6   2104 TACTGTCATTAAGACTGTGTGGCACTGGCAGAGAGAGAGAGAGAGAGAGA 2153
                            v  v  i     v      i       v -------  -  v   v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATA-------AG-GATAGACA 290

  chrX_68044717_6   2154 CATAGATCAATGGA-CAGAATAGAGAACTCAGAAGCAGATCTACAAAAAT 2202
                         i             -i     v    iii     ii i i i i v vv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_68044717_6   2203 ATGCTCAACTGAATTT 2218
                            v    i   v   
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTT 356

Transitions / transversions = 1.39 (50 / 36)
Gap_init rate = 0.02 (6 / 355), avg. gap size = 2.17 (13 / 6)  

2177 23.06 2.16 0.72  chrX_68044717_68048302.rev     2541  3095 (491)    L1M4_orf2#LINE/L1      346   908 (0)  

  chrX_68044717_6   2541 CAACTGATTTTTGACCAAGGTAC-AGAAGCATCTCAATGGAGGAAAGACA 2589
                            i       i   v i   i - ii v   -       i i  ii i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATA 394

  chrX_68044717_6   2590 GCCTTTTCAACAAATTAGGCTGGAACAATTGGAAATTCATAAACAAAAGG 2639
                          i             viv     i    i    v ?i  i vi      i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_68044717_6   2640 ACAAACCTCAACCTAGACTTCACACCTTACACAAAAATTAACTGAAAATG 2689
                          ii  vi vi   ivv  i       v  i             v      
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_68044717_6   2690 AGTCATAGATTTAAATATAAAACATAGAACTACAAATTATTTAGAAGAAA 2739
                         ii   ?   ii     i   i vv  i     i   vivi          
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_68044717_6   2740 ACATGGGAGAAAATCTTCAGGACCTAGGCATTAGTGAA-GAAGTCTTAGA 2788
                             i  ? v        iv     v  -i    vv  - ivv       
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGA 593

  chrX_68044717_6   2789 CTTGATATCAAAAGCATGATTCATACAAGAAAAGATGGATAAATTAGACT 2838
                         iv   i i        ii viv i v       i  i        i    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_68044717_6   2839 TCATCAAA-TTAAATACTTACATTCTGCAA-------TA--AAATAGATG 2878
                                 -     v    vii v  v   -------  --  iv ii  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_68044717_6   2879 AAAAGTTAAACTATAGACTGGGAGAGAATATTTGCAAAACATGTATTTGA 2928
                              vi  v i i   v       i            v   i   i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_68044717_6   2929 CATAGGACTTGTATCTAGAATATATGAAGAACTCTTAAGACTCAACAGTA 2978
                         i vi           i         i           vi      i i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_68044717_6   2979 AAACAAAACAAACAATCCAGTGAGAAAATGGGCAAAAGACATGAAGAGAC 3028
                            -- i     i  i   i v?i            i  iv    v    
  L1M4_orf2#LINE/    794 AAA--AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_68044717_6   3029 ATTTCACCACAGAAGATCTACAGATGGCAAATAAGCACATGAAAAGTTAG 3078
                              v   v       v    i     v                 v iv
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_68044717_6   3079 TCAACATCATCAGTGCA 3095
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (77 / 47)
Gap_init rate = 0.01 (8 / 563), avg. gap size = 2.00 (16 / 8)  


3350 26.46 0.55 0.55  chrX_68055465_68057663      800  1706 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_68055465_6    800 GGAAGAACATTCCATGTTCATGGACAGGAAGAATCAATATCATGAAAATG 849
                             ii i  i             iv      v i     ii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_68055465_6    850 GCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGCT 899
                           v     v     iv i  i ii        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_68055465_6    900 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 947
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_68055465_6    948 ATGGGACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAAGA 997
                             i viiv  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_68055465_6    998 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 1047
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_68055465_6   1048 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 1097
                                i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_68055465_6   1098 ATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACCA 1145
                               i    i--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_68055465_6   1146 TTTGATCTTTGACAAACCTGACAAAAACAAGCAATAGAGAAAGGATTCTC 1195
                         v     i  i     ivv  v   i v  vv    i i     i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_68055465_6   1196 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 1245
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_68055465_6   1246 AAACTGGATCCCTTTCTTACACCTTATACAAAAATTAATTTAAGATGGAT 1295
                           ii    i    vi  i     v              i i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_68055465_6   1296 TAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1345
                         i ?    i           v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_68055465_6   1346 TAGGCA-ATACCATTCAGGAAATAGGCATGGGCAAGAACTTCATGACTAA 1394
                             ?i- v i -   iv  vv v  vv i     viii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_68055465_6   1395 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1444
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_68055465_6   1445 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1494
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_68055465_6   1495 AGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCGATCTGACAA 1544
                           i     i                 v   i   vii ivv      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_68055465_6   1545 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 1594
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_68055465_6   1595 AAGCAAACAACCCCATCAAAAAGTAGGCAAAGGATATGAGGAGACACTTC 1644
                          ii    i     v  i?    i i          v   iv     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_68055465_6   1645 TCAAAAGAAGACATTTATGCAGCCAACAGATATATGAAAAAATGCTCATC 1694
                           v        i  vi viii     i iii i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_68055465_6   1695 ATCACTGGCCAT 1706
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (149 / 87)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 1.43 (10 / 7)  


3103 26.62 1.90 0.34  chrX_68246323_68248282.rev      576  1469 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68246323_6    576 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATTAATATCGTGAAAAT 625
                               i i  i     i        v      v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68246323_6    626 GGCCATACTGTCCAAAGTAATTTATACATTCAATGCTATTCCCATCAAGC 675
                            v     vi     v i  i  i v      i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68246323_6    676 TACCATTGACCTTCTTCACAGAATTAGAAAAAAATACTTTTAGTTTCATA 725
                          v   vivi    i  ii     v v  v  ivvv iii v iv      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_68246323_6    726 TGGAACCAAAAAAGAGCCTTTATAGCCAAGACAATCCTAAGCAA-AAGAA 774
                              viiv  ii  v  vvv        i      i i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_68246323_6    775 CAAAGCTGGAGGTGTCATGCTACCTG-CTTCAAACTATACTACAAGTCTA 823
                              i      vv   ii  v  ii-i      viv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_68246323_6    824 CAGTAACCAAAAGAGCATGGTATTGGTACCAAAACAGATATATAGACCAA 873
                               i   i v  ii     i   i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_68246323_6    874 TGGAACAGAACAGAGGCCTCAGAAATAACGTCACACATTTACAACCATCT 923
                              i    iv   ivii         vvi  i       iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_68246323_6    924 GATCTTTGACAAACCTGACAAAAACAAGCAATTGGGGAAAGGATTCCCTA 973
                            i  i     ivv  v   i v  vv    -        i  vvi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTT 399

  chrX_68246323_6    974 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAGGCAGAAAACTGAA 1023
                           i  i        i     v      v  ?   i v   i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_68246323_6   1024 ACTGGACCCCTTCCT-------TATACAAAAATTAACTCAAGATGGATTA 1066
                         ii         v   -------                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_68246323_6   1067 AAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 1116
                         ?    i    ii     v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_68246323_6   1117 GGCA-ATACCAGTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAAAA 1165
                           ?i- v i -v  iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_68246323_6   1166 CACCAAAAGCAATGGCAACAAAAGACAAATT-GACAAATGGGATCT---- 1210
                                    vvi           v   v -  i    v   ii ----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_68246323_6   1211 --AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 1258
                         --       i -   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_68246323_6   1259 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCACCTGACAAA 1308
                          i     i                 v       vii ivi i    i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_68246323_6   1309 GGGCTAATATCCAGCATCTACAAGGAATTTAAACAAATTTACAAGAAAAA 1358
                           i  vi       v  v  i  i   i ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_68246323_6   1359 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 1408
                         i     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_68246323_6   1409 CAAAAGAAGACATTTATGCGGCCCACAAACATATGAAAAAAAGCTCATCA 1458
                          v        i  vi vii    v i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_68246323_6   1459 TCACTGGTCAT 1469
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (135 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.22 (20 / 9)  


3617 18.28 2.99 4.18  chrX_68345822_68349336.rev     1483  2319 (1196)    L1M4_orf2#LINE/L1        3   829 (79)  

  chrX_68345822_6   1483 GAAGGATATCT-GTGGTCATGGATTGGAAGACT----------GAGATGA 1521
                            i      i-i  v                 ----------i     i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_68345822_6   1522 TAGTACTACCCAAAGAGATCCATAGATTTAATGCAATCCCTATCAAAATA 1571
                         i i    v      vv    i i     i  i                 v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_68345822_6   1572 GCA-TTATTTTTTTTTCAGAAACAGAAAAACTCATCCTCAAATTCATATG 1620
                         v  -i iii      v      iv  v  i  v     v           
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_68345822_6   1621 GAATCTCAAGGGACCT-GAATAGCCAAAACATTCTTGAAAAAGAAGAAAA 1669
                            viv         i-              v                v 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_68345822_6   1670 AAGATGGAGAATTCACACTTTTTGATAGTAAAACTTACTACAAATCTACA 1719
                            v     i i        iiii  vvi               v     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_68345822_6   1720 GTAATCAAAACCATGAAGTACAGACTGGCATAAAGACAGACATACAGACC 1769
                                 i  vi  vi    ----        i  i       i   i 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTAC----TGGCATAAGGATAGACATATAGATC 298

  chrX_68345822_6   1770 AATGGAATAGA-------GCTCAGAAGTAAATCTTCACAGACATGGTCAA 1812
                                    ------- ii     i    i ivi   vvi        
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_68345822_6   1813 ATGATTTTTTACAAGAGTGCTGAAACCATTCAATGGGGAAAGTACAGTAT 1862
                         v       iv     i    ii i                  v i   v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_68345822_6   1863 TTTCAACAAATGGTTCTGAGAAAACTAAATATCCACATGCAAAAGAATAA 1912
                                       v   i  v    ii   ?                i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_68345822_6   1913 AGTTAGATCATTATCTAACATCATATACAAAAATTAACTCAAAATGAATC 1962
                             i  i vi  i  v   i                         i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_68345822_6   1963 AAAGGCCTAAACATAAGAGCTAAAACTATAAAACTCATGTAAGAGAACGT 2012
                          ?  i      ii                       v iv    i   i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_68345822_6   2013 GTGGAGAGGGAAAAATCTTCAATG-CATTGGATTTAAAAATAATTTCTTG 2061
                         ------   ?iv        i-  - v    i  viiv   ii      i
  L1M4_orf2#LINE/    549 ------AGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_68345822_6   2062 GATATGACACCAAAAGCGCA-GCAGCAAAAGAAAAAAAAAAGACAAGTTG 2110
                                          i  -   i            v --  i  i   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTG 639

  chrX_68345822_6   2111 GACTTCACCAAAATTAGAAA-TTTTCTGCATTACAGGACACTATTAACTC 2159
                                i        i   -    v   v i v          i  ---
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA--- 686

  chrX_68345822_6   2160 AGTAAAAAGGAAAGGGAAAAATATTTTGTGAC--TCTATGGAATGGGTGA 2207
                         ---------     v     ---------   --i i ii       v  
  L1M4_orf2#LINE/    687 ---------GAAAGTGAAAA---------GACAACCCACAGAATGGGAGA 718

  chrX_68345822_6   2208 AAATATTTGTAAGTCACGTATTTAATAACGAATTACTATCCAGAATATAT 2257
                                  i  i   ii   i i    v i i vv              
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_68345822_6   2258 AAGTAACTCCTAAAACTCAACAACAACAACAACAACCAACCCAGTTCAAA 2307
                           iv     i  v       i  i  v  -i    vi      i  ?   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAA-GACAAATAACCCAATTWAAA 817

  chrX_68345822_6   2308 AATGAGCAAAGG 2319
                             i       
  L1M4_orf2#LINE/    818 AATGGGCAAAGG 829

Transitions / transversions = 1.92 (98 / 51)
Gap_init rate = 0.02 (16 / 827), avg. gap size = 3.75 (60 / 16)  

 507  9.65 9.65 1.75  chrX_68345822_68349336.rev     2903  3016 (499)    L1M4_orf2#LINE/L1      773   895 (13)  

  chrX_68345822_6   2903 AACTC---CATCTCAA--ACAAAATAAAACAAA--AC--AAT--ATAAAT 2941
                              ---  v     -- i    -- i     --  --   -- v    
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAA--AGACAAATAACCCAATTWAAAAAT 820

  chrX_68345822_6   2942 GAGCAAAGGACTTGAATAGACATTTCTCCAAAAAAGATATACAAATGGCT 2991
                          i        i                     i                i
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_68345822_6   2992 AATAGGCACATAAAAAGATACTCAA 3016
                             i      i       i     
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.05 (6 / 123), avg. gap size = 2.17 (13 / 6)  


3148 27.21 0.88 0.44  chrX_68353122_68359511     4994  5897 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68353122_6   4994 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5043
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68353122_6   5044 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5093
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68353122_6   5094 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5141
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_68353122_6   5142 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5191
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_68353122_6   5192 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5241
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_68353122_6   5242 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGACC 5291
                                 i   i    ii         i iv ii i   v  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_68353122_6   5292 AATGGAACAGAACAGAGCCTTCAGAAATAACACCACACATCTACAACCAT 5341
                                i    iv   vv i         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_68353122_6   5342 CTGATCTTTGACAAACCTGACAAAAACAAGAAATTGGGAAAGGATTCCCT 5391
                         i    i  i     ivv  v   i v  vvv   v       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_68353122_6   5392 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTACAAAGCTGA 5441
                         v  i  i              v      v  ?   i   i v  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_68353122_6   5442 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5491
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_68353122_6   5492 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5541
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_68353122_6   5542 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5590
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_68353122_6   5591 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5640
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_68353122_6   5641 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5690
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_68353122_6   5691 GGCACCCTACAGAGTGGGAGAAAATTTTTACAATCTACCCATCTGACAAA 5740
                          i  v  i     i           v   i   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_68353122_6   5741 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5790
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_68353122_6   5791 AGTCAAACAACCCCATCAAAAAGTGGCCGAAGGATATGAACAGGCAT--- 5837
                         - v    i     v  i?    i   v i      v    i  i   ---
  L1M4_orf2#LINE/    798 -GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_68353122_6   5838 --AAAAGAAGACATTTATGCATCCAACAGACATATGAAAAAATGCTCATC 5885
                         --v        i  vi viiiv    i ii  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_68353122_6   5886 ATCACTGGCCAT 5897
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (141 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


3355 24.42 1.44 1.10  chrX_68439736_68445708.rev     4592  5496 (477)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68439736_6   4592 TGGAAAAATATCCCATGCTCATGGATTGGAAGA----ATATCATTAA-AT 4636
                               i          i               ----    ii    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68439736_6   4637 GGCTATACTGCCCAAAGCAATTTACAGATTCAATGTTATTCCTATCAAAT 4686
                            v     v      vii  i           i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68439736_6   4687 TACCAATAACATTTTTTACAGAACTAGAAAAAATTATTTTAGAATTTATA 4736
                          v   iivi v      i     v v  v  iv v  ii  i    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_68439736_6   4737 TGGAACCAAGAAATAGACC--GAATAGCCAAGGCAATGCTAAGCAAAAAG 4784
                              -- v v  vi    --          ii    vi i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_68439736_6   4785 AACAAAATAGGAGGAAATACATTACCTGACTTCAAACTATACTACAAGGC 4834
                               i v      vvi   i v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_68439736_6   4835 CACAGTGACCAAAATAGTATGGTACTGGTACTAAAACAGGCACATGGAAC 4884
                         i     i i   i i   i         i iv ii i  i  i  i  v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_68439736_6   4885 AATGGGATAGAATAGAGGGTCCAGAAATAAGGCTGCACATCTATGACCAT 4934
                              i       v   i            iv iii    i    ii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_68439736_6   4935 CTGATCTTTGACAAAGCTGACAAAAACAAGCAAGGGAGAAAAGACTTCCT 4984
                         i    i  i     i v  v   i v  vv   v  i    ii ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_68439736_6   4985 ATTCAATAAATGGTGCTGGGATAACTGGCTAGTCATATGCAGAAGATTGA 5034
                         v     i              i      v  ?i  i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_68439736_6   5035 GGATGGACCCCTTCCTTACACCATACACAAAC-TCAACTCAAGATGGATT 5083
                         i v         v   i        i     v- i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_68439736_6   5084 GAAGACTTAAATGTAAAATCCAAAACTATAAAAACCCTGGAAGACAACCT 5133
                         i?    i         i v i            vi i i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_68439736_6   5134 AGGCTGTGCCATCCT-G-GACCTAGGAATGGGCAAAGATTTCATGACCAA 5181
                            ?-  iv-   i - -     v  iv i     v i    v iivi v
  L1M4_orf2#LINE/    549 AGGN-GTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_68439736_6   5182 GACACCAAAA--ACAATTGCCACAAAAGCAAAAATTGACAAATGGGATCT 5229
                                   --    --  v       v      v  i    v   ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_68439736_6   5230 AATTAAACTTATGAGCTTCTGCAGAGCAAAATAAACTATCAACAGAGTAA 5279
                         v  i   v   vi i   i  iivvv    iv v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_68439736_6   5280 ACAGACAACCTACAGAATGGAAGAAAATATTTGCAAACTATGGATCTGAC 5329
                          v        i         i                ii  iv      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_68439736_6   5330 AAAGGTCTAATATCCAGCATTTATATGGTGTTTAAACAAACTTA-CAAGA 5378
                           i  v  vi       v  v    vi vii ivv    -  i -i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chrX_68439736_6   5379 GAAAAACAAAAAACCCCATTTAAAAAGTGGGCAAAGGCCATGAACAGACA 5428
                         i   i     v     v   ?     -          viv    i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chrX_68439736_6   5429 CTTCTCAAAAGACAACATACACATAGCCAATAAGCATATGAAAAAAAAAG 5478
                         i     v     vi i     v  i           i       i v-- 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT--G 890

  chrX_68439736_6   5479 CCCAATATCACTGATCAT 5496
                          i   i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (131 / 86)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.53 (23 / 15)  


3293 26.87 0.44 0.44  chrX_68450736_68457004     4869  5776 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68450736_6   4869 TAGAAGAACATTCCATGCTCATGGGGAGGAAGAATCAATATCGTGAAAAT 4918
                          i   ii i  i     i      ivv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68450736_6   4919 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4968
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68450736_6   4969 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5016
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_68450736_6   5017 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTGAGCCAAAAG 5066
                                viiv  ii  v  v v  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_68450736_6   5067 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTAGGAGGC 5116
                                i      vv       v  ii i      viv     vi i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_68450736_6   5117 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5166
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_68450736_6   5167 AATGGAACAGAAT--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5214
                                i     --    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_68450736_6   5215 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5264
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_68450736_6   5265 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5314
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_68450736_6   5315 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5364
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_68450736_6   5365 TTAAAGACTTATATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5414
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_68450736_6   5415 CTAGGCTTTACCATTCAGGACATAGGCATGGGCACGGACTTCATGTCTAA 5464
                         v    ?v v viv   iv   v v  vv i    vv ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_68450736_6   5465 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5514
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_68450736_6   5515 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5564
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_68450736_6   5565 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5614
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_68450736_6   5615 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAGTTTACAAGAAAA 5664
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_68450736_6   5665 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5714
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_68450736_6   5715 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5764
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_68450736_6   5765 ATCACTGGCCAT 5776
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3269 26.96 0.55 0.22  chrX_68461655_68465533.rev     2484  3388 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68461655_6   2484 TGGAAGAACATTCCATGTTCATGGGTAAGAGGAATCAATATCGTGAAAAT 2533
                              ii i  i            i vi  i  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68461655_6   2534 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGACATTCCCATCAAGC 2583
                            v     v     iv i  i  i        i vv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68461655_6   2584 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2631
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_68461655_6   2632 TATGGAACCAAAAAGGAGCCCTCATCGCCAAGTCAATCCTGAGCCAAAAG 2681
                                viiv  i   v  vvv  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_68461655_6   2682 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2731
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_68461655_6   2732 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2781
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_68461655_6   2782 AATGGAACAGAACAGAGCCTTCAGAAATAACACCGCATATCTACAACTAT 2831
                                i    iv   vv i         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_68461655_6   2832 ATGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 2881
                         v    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_68461655_6   2882 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 2931
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_68461655_6   2932 AACCGGATCCCTTCCTTACACCTTATACAAAA-TCAATTCAAGATGGATT 2980
                          iii   i    v   i     v         - i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_68461655_6   2981 AAAGACTTATATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3030
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_68461655_6   3031 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 3080
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_68461655_6   3081 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 3130
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_68461655_6   3131 AAA-TTAAAGAGTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 3179
                            -     i v  i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_68461655_6   3180 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 3229
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_68461655_6   3230 GGCTAATATCCAGAATCTACAATGAACTCAAACAAGTTTACAAGAAAAAA 3279
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_68461655_6   3280 ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGATACTTCTC 3329
                              i     v  i?    i            v    i   i i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_68461655_6   3330 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAA-ATGCTCACTGT 3378
                         v        i  vi viii     v  i          -       vii 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_68461655_6   3379 CACTGGCCAT 3388
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


 975 20.00 1.33 2.67  chrX_68475473_68482309     1321  1545 (5292)    L1M4_orf2#LINE/L1        1   222 (686)  

  chrX_68475473_6   1321 TAGCAAGACATCTGGTTATCATGGATTGGAAGATTTAAGATT---AAGAT 1367
                          i v    i   ivi vv               i    v   ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68475473_6   1368 GACAATAATACTCAAAGCTATCTACAGATTCAATGCAATCCTCATCAAAA 1417
                          i     v v i    viv              i       ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68475473_6   1418 ATCCTAATTGAGGTTTTTTTTCACATAAATAGAAAAACCCATCCTAAACT 1467
                         -   i ii  ----ii     ii  v    v  v  i iv        v 
  L1M4_orf2#LINE/    101 -TCCCAGCTG----CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_68475473_6   1468 TCATATGGAATCTCAAGGGACCCCAAATAGTCAAAACACCCTTGAAAAAG 1517
                                   viv          vi     i       vi          
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_68475473_6   1518 AAGGAAAAAAGTCAGAGGACTCACACTT 1545
                            -  v     ii              
  L1M4_orf2#LINE/    196 AAG-AACAAAGTTGGAGGACTCACACTT 222

Transitions / transversions = 1.37 (26 / 19)
Gap_init rate = 0.02 (4 / 222), avg. gap size = 2.25 (9 / 4)  

3322 15.18 4.61 1.19  chrX_68475473_68482309     1837  2508 (4329)    L1M4_orf2#LINE/L1      214   908 (0)  

  chrX_68475473_6   1837 CTCACACCTCTGGATCTCAAAACTTACTACAAATCTACAATAATGAAAAC 1886
                                i  ivi  i                 v     i    v  i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_68475473_6   1887 AGTATGGTACTGACATAAGGACAGACATATAGATGAATGGAATAGAATAG 1936
                            i        i        i            v             v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_68475473_6   1937 AGAGCCCAGATATAAACATTCACCTATATAGTCAACATTTTATTTTTGAC 1986
                             i     v      vivi  v v   i     ---  v     i   
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAA---TTGATTTTCGAC 360

  chrX_68475473_6   1987 AAAGGTACAAAGACCATTCAATGGGGGAAAGAAATACCTTTTCAACAAAT 2036
                           i   i v                 -      vvii             
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAAT 409

  chrX_68475473_6   2037 GGTGGTAGGAAGACTGAATATCTACATTTAAAAGAATGAAGTTGGATCCT 2086
                             v i   vi    i   ? i    vi                 i  i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_68475473_6   2087 TAC-TCAGCACCGTATACAAAAATTAATTCAAAATGGATCAAATACCTGT 2135
                            -   -    i              i             ? v    iv
  L1M4_orf2#LINE/    460 TACCTCA-CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_68475473_6   2136 ACATAAGATCTAAAACTATAAAATTCTTAGAACA---CATGGG------- 2175
                          ii     v              i        v ---   i  -------
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_68475473_6   2176 -------ACATTGGATGTGGCA----TTT----GATATGACAACAAAAAC 2210
                         -------  v    i vv    ----   ----         v     i 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_68475473_6   2211 ACAGGCAACAAAAGAAAAAAATAGATAAATGAGGCTTCAACAAA-TCAAA 2259
                            i                -         vi i     v    - i   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_68475473_6   2260 AACTTTTGTGCATCAAAGGACACTAACAAAA----GAAAAGACAACCCAC 2305
                                    v             v   i ----               
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_68475473_6   2306 AGAATGAAAGAAAAGCTTTACAAATCATGTATCTGATAAGGAATTAATAT 2355
                               ii      vv   i        i            i i vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_68475473_6   2356 TCAGAATATATAAAGAACTTCTACCATTCAATAACAGAAGAAACAAACAA 2405
                         i                  ii   v i       i i  - i     i  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA-AGACAAATAA 806

  chrX_68475473_6   2406 CCCAATTTGAAAATGGGCAAATAACTTGAGTAAAACATTTCTCCAAAGAA 2455
                                ?i            vi i    i  i -               
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGA-CATTTCTCCAAAGAA 855

  chrX_68475473_6   2456 GATGTACAGATGGCCAACAATCATATGAAAAGATGCTCAACTTCACTAAT 2505
                            i    i        i  v  i                 v   ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_68475473_6   2506 TAG 2508
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.75 (63 / 36)
Gap_init rate = 0.02 (13 / 695), avg. gap size = 3.00 (39 / 13)  

3324 23.46 4.23 0.57  chrX_68475473_68482309     5471  6344 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_68475473_6   5471 GAGAGAGGTTCTGTGTTCATGGATTAGAAGGCTTGATATTGTTAA-ATGT 5519
                           i   vi i ii            i    i   i          -   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_68475473_6   5520 CAATTCTTCCCAATTTAATCTAAAGATTCAATGCAATTCTGATCAAAATC 5569
                             v  i     v  i     v        i     i iv         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_68475473_6   5570 TCAGCAAGTTATTTTCTAGATATCAACAAACTGATTCTAAAGATTATATG 5619
                         i    vivi v    vi   v  ii    i     i     iv i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_68475473_6   5620 GAAAAGCAAAATTCCCAGAATAGCCAACAAAATACTGGAGAAGGAGAATA 5669
                             v    iivv              v v   vi  i i   i    i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_68475473_6   5670 AAGTTAAAAGATTGACACTATCCAACTTCAAGACTTATTATAAAGCTACA 5719
                              ii i  i v     vi    i     i     i  i         
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_68475473_6   5720 GTAATGGAAACAGTGTGCCACTGGTG-AAAGATGGACAAGTAGATCAACG 5768
                              vi i        vi     ii-  i   i    vi        i 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_68475473_6   5769 GAACAGAATAGAGACCCCAGAAAACAGACCCACACATATATAGGTAACTG 5818
                            i     v    vi       -i i     i    v   i vi  i  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGTCAATTG 351

  chrX_68475473_6   5819 ATCTTTGACAAGGA-GCAAAGGCAATTCTATATAGAAAGGATAGTTTTTT 5867
                           i  i       i-  v   i v    v  ivi     i     i    
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_68475473_6   5868 CAACAAA------------------ACATCCATATGCAAAA-AATGACTG 5898
                                ------------------ i ?   i        -     vvv
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_68475473_6   5899 TAGACACAGACTTTAAACCTTTCACAATAATTAACTCAAAGGGAATCATA 5948
                          i   v vv  i i v   v vi    v            iv i    ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_68475473_6   5949 GACCTAAACATAAAGTGC-AATACTATAAAAGTTCTAGAAGATAACACAA 5997
                                 ii   - v  -  v         v ii       v    i i
  L1M4_orf2#LINE/    502 GACCTAAATGTAA-GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_68475473_6   5998 GAGAAAATCCATGTGACCTGGGATTTGGCAATTAGTTTTTAAATA-AACA 6046
                          ? v     ivi       v  i  v      viv  i   i   -i   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_68475473_6   6047 CCAAA-GTGCAACCCATGAAAGAAAAAAT-GATAAACTGGACTTTACTAA 6094
                              - ii   v v ii           -      i       i ii  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_68475473_6   6095 AATTAAAA-TTTCTCTGT-------GACACTGTTTAGAGAATCAAAAGAC 6136
                                 -i  i v  i-------      i iv   i i v       
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_68475473_6   6137 AAGCTACACTCTGGGAGAAAATATTTGCAAACCACATACGTGATGAAAAA 6186
                           v i   vvv                    i  i   iv    --  ii
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT--AAGG 748

  chrX_68475473_6   6187 AACTTGTATTCAAAATATACCATGAAGTCTTTAAACTCAACAATGAGAAA 6236
                         i        i  i      iv v   v    vv       i   i i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_68475473_6   6237 ACAAATAATTCAATTAAGAAATAGGCAAAAAGAT--GAACAGATATC-CA 6283
                                 ii     ? i    i      i-   --   i   i  i- v
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAG-GATTTGAATAGACATTTCT 847

  chrX_68475473_6   6284 CCTAATCAGATATACAGATATCAAATAAACATATGAAAAGATACTCAACA 6333
                           v  vv         i  iv v     i  i          i       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_68475473_6   6334 TTATATGTCAT 6344
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.75 (128 / 73)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 2.47 (42 / 17)  


3158 23.08 0.93 3.61  chrX_68489678_68491527.rev      502  1359 (491)    L1M4_orf2#LINE/L1       74   908 (0)  

  chrX_68489678_6    502 ACAGACTCAATGCAATACCTATCAAAATACCAATGACATTATTCACAAAA 551
                              i    i     v           v   iivi v  v  ii  i  
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAA 123

  chrX_68489678_6    552 ATAGAAAAAC-AATCTTAAAATTTATATGGAAAAGCAGAAGATCCCCGAT 600
                           v  v  i -i   i       i         v   iii  i  vvi  
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chrX_68489678_6    601 A-CCAAAGCAATTTCAAGCAAAAAAGAACAAAGCTGGAGGTATTACAATA 649
                          -     i    i ii i-   i          i      vv i   v v
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAA-AAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_68489678_6    650 CCTGACTTCAAAATATACTACAAAGCTATAGCAACCAAAATAGCCCAGTA 699
                           ii i       iv             i  i  i   i i  ivii   
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_68489678_6    700 CTGGCATAGAAACAGGCACATAAACCAATGGAACAGAATAGAGAACCCAG 749
                                 iii i  i  i   i i        i     v    ii    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_68489678_6    750 GAATGAACCCATGCATTTATAGCTCACGGACTTTTGGCAAAGGCTTCAAG 799
                         i   i       i       i iiv iv  i   i i   i  ivi    
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_68489678_6    800 AACACACATTGGGGAAAGGGCAGTATCTTCAATAAATGGTGTTGGGAAAA 849
                          v  iv  v         iii   v i     i        i     v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_68489678_6    850 CTGGACATACACTTACGTAAGCATGAAACTAAACCGCTATCTCTCACCAT 899
                              i ?v   v i iv   v     ii ii   v   i   v      
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_68489678_6    900 ATATAAAAATCAACTCTAAATGGATTAAATATTTAAATGTAGGATCCCCA 949
                            i      i     v        i ? v ii        i  v iv- 
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-A 521

  chrX_68489678_6    950 AACTATGAAACTACTAGAAGAAAATATGGGGG-AAGTACTTAAGCCCAGA 998
                               i     vi          i  i  ? -  i -   ---- vv  
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTT----CGTGA 566

  chrX_68489678_6    999 CATTGGACTAGGCATGGATTTTTAAAATAAGACCTCAAAAGAACAGGCAA 1048
                          v    ii      vv i   i v i   v   vi      v   i    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_68489678_6   1049 CAAAAGCAAACATAGACAAATGGGATTACATCAAACTTAAAAGCTTCTGC 1098
                               v   v     i    v   i v       v      i   i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_68489678_6   1099 ACAGCAAAGGAAACAATCAATAAAGTGAAAACAGCAGTCTACAGAACGAG 1148
                         i vv       v  v     v          v -  ii i      i i 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGA-CAACCCACAGAATGGG 715

  chrX_68489678_6   1149 AGAAAGTATTTGCAAACCATGCATCTGGCA-GGGAGTTACTACCCAGAAT 1197
                              i          i   ii     ii -    v  i-  i       
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG-TATCCAGAAT 764

  chrX_68489678_6   1198 ATATAAGGAACTC----AACTCAATAGCAAAAACAAAACAAAACAAAAAC 1243
                               i      ----         ii     --------------i  
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAA--------------GAC 800

  chrX_68489678_6   1244 AAATAATCAAATTAATTTTTGCCATTTTTGGCAAAAGACTTTAATAAACA 1293
                               i v    ? vvvv  --------      i  i  v    i   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATG--------GGCAAAGGATTTGAATAGACA 842

  chrX_68489678_6   1294 TCTCTCAAAAGAAGACATACAAATGGCCAACAGATATATGAAAAAATGCT 1343
                          i    v        i              i iii i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_68489678_6   1344 CAACATCACTAATTAT 1359
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (130 / 64)
Gap_init rate = 0.02 (13 / 835), avg. gap size = 3.00 (39 / 13)  


 954 20.73 2.59 0.52  chrX_68595901_68598057      291   483 (1674)    L1M4_orf2#LINE/L1        1   197 (711)  

  chrX_68595901_6    291 TGGGGAGATATATTATATTTGTGGGTCAGAAGATTCAACATTATTAAAGT 340
                            ii      vii  i  ii   i ii     i i  i   i    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68595901_6    341 GTCAATTCTCCCCAGATTGATCTATGGATTTAAATGCAATCCCAATCAAA 390
                          v    v       i         ii    i  -i        v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAA 99

  chrX_68595901_6    391 ATCCCTGAAGGCTT----GTAGAA-TTGACAAGCTGATTCTAAAATTCAT 435
                              v vv v   ---- i    -             i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_68595901_6    436 ATGGAAATGCAAAGGACATAGAATAGTTAAAGCAACTTTGAAGAAGAA 483
                                     i    vi       ii   i   ii     i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

Transitions / transversions = 3.44 (31 / 9)
Gap_init rate = 0.02 (3 / 197), avg. gap size = 2.00 (6 / 3)  

 967 27.82 4.93 0.00  chrX_68595901_68598057      488   771 (1386)    L1M4_orf2#LINE/L1       25   322 (586)  

  chrX_68595901_6    488 ATTAGAGGGCT-AGTA-----AAAATGCCCATACTACCCAAAGCAATCTA 531
                            i  i i  - i  -----  i   v v     v      vii     
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chrX_68595901_6    532 CAGATTAAATACAATCCCTATGAAAATTTCAACATCATTCATTACAGAAA 581
                               v  ii          v     ii  i vv v  iv  i      
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chrX_68595901_6    582 TTTTTAGA--AATCTTAAAATTCATATGGAACCACAAAAAATCTTGA--- 626
                           vvi ii--i   i                vii   iii i iv  ---
  L1M4_orf2#LINE/    125 TTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chrX_68595901_6    627 -CTAAGGCAATTGTGAGGAAAAAGGG-AAAGCTGGAGGCATCACACTACT 674
                         - i  ii    iv   ii  i   ii-    i      vv       v i
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_68595901_6    675 GGATTTCAAA-TATATTACAAAGCTGTAGTAATTCAGACAGCATACTATT 723
                         vi        -iv  i         ii      iv      ii iv  i 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_68595901_6    724 GGCATAAAAACAGATACATCAACCAATGGAATAGAATAGAGAGCCCAG 771
                                ii i   i i  vi i              v     i    
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

Transitions / transversions = 2.29 (55 / 24)
Gap_init rate = 0.02 (6 / 298), avg. gap size = 2.33 (14 / 6)  

2254 23.65 3.38 1.69  chrX_68595901_68598057     1074  1665 (492)    L1M4_orf2#LINE/L1      307   908 (0)  

  chrX_68595901_6   1074 AGAATCAAGAGCCCAGGGA--AATCCACACATCCATGGTCAACTGATTTT 1121
                              ii    i    ii --  i   i    ii        i       
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_68595901_6   1122 TCACAAAGATGCCAACAACTCCTAATGGAGAAAGAAAAAGAGAATAGTCT 1171
                         iv    i i      v v viii     i       --------      
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA--------TAGTCT 398

  chrX_68595901_6   1172 CTTCAATAAATAGCATTGAATAAACTGGACATCCATATACAGAAAAATGA 1221
                         i     i    i iii  iivv       i ?   i  i  i  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_68595901_6   1222 GAATGGACCCTTGTCTCACCTCTTATACACGAATCAACTCAAAATGGATT 1271
                         iiv       i ii     vi v      vi   i              i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_68595901_6   1272 AAAGACTTAAACGTAAAACCTGAAAATATAAAATCACTGAAAGGAAACAT 1321
                          ?    i    i    i v  i   v       iivi ii   i      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_68595901_6   1322 -GAGGTAAATCTCCATGACGTTGGTCTGGGCAGAGACTTCTTGGATATGA 1370
                         - i?        i i    v    vi i    iv ii     i       
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_68595901_6   1371 CATCAAAC-CACAGGCAA---------AAATAGACAAACAGGATTGTATC 1410
                           i    v-    i    ---------       i   iv   i vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_68595901_6   1411 AAAATAAAAAGCTGCTGCACAGCAAAGGAAACAATTAATAGAATGAAGAG 1460
                              v    i  vi  ii vv       v  v  i  v i i    i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_68595901_6   1461 ACAACACAGGGATTGGGAGAAAATATTTGCAAATCATACATCGAATAAGG 1510
                              v  vi  v                         i   vi      
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_68595901_6   1511 GGCTAATAT-------ATACAAGGGACTCAAACTGCTCAAGAACAAAGAA 1553
                          i  vi   -------   i  i i    vv  vi     v  i   -  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AA 797

  chrX_68595901_6   1554 AACAAATAACCCTATTTAAAAATGGGCAAAGGATTTGAATAGAAATTTTT 1603
                         i           v   ?                          v    i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_68595901_6   1604 CAAAAGAAGACGTAAAAGTGGCCAACATATATATGAAAAAAATCTTCAAT 1653
                          v        ii  v  i       i vii i       i - vi    i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAAC 896

  chrX_68595901_6   1654 ATCTCTAATCAT 1665
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (94 / 42)
Gap_init rate = 0.01 (8 / 602), avg. gap size = 3.75 (30 / 8)  


2681 21.02 1.74 5.09  chrX_68598219_68599946      491  1237 (491)    L1M4_orf2#LINE/L1      187   908 (0)  

  chrX_68598219_6    491 TTAAAAATTAAAAAGAACAAAGTTAGAGGGCTAATACTACCTGATTTTAA 540
                           i    --- i            i    i  v i   v  ii    i  
  L1M4_orf2#LINE/    187 TTGAAAA---AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_68598219_6    541 GACTTCCTTTAAAGCTACAGTAATATAGACAGCATGGTATTGGTGTGAAG 590
                         i    v  vi              vv      ii     i   ii i i 
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_68598219_6    591 ATAGATAAATAGATCAGTGGAATAGAATAGAAAAACCATAAATAGACTTT 640
                              i v        i           v  i iv   v     i  iiv
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_68598219_6    641 TACATGTAAGGACAACTGATTTTTGACAAAGGTGAAGAGGCAATTTAGTT 690
                              v  v  v   i       i     i    vvi  i v   i i v
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_68598219_6    691 GAGAAAGGATACTGTTTTCAATAAATGATGCTAGAGCAATTAGATAGATA 740
                          i     i   v v       i     i    i ii   i i    ?vi 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_68598219_6    741 TGTATATGTCAAAAAAGAGAGAACATAAATCCATACCTTGCATC---TAA 787
                         i----   i---      iv   vv ii i  v     ii  i ---  v
  L1M4_orf2#LINE/    434 C----ATGC---AAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_68598219_6    788 AAAAAT--GCTCAAAATGGATCATAGACTTAAATGTAATACTTCTAGATA 835
                               --i              ?    i         ------------
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA------------ 514

  chrX_68598219_6    836 GAATAGCATAGAGCATAGATGTAAATATAAATTTCT-AGAAGAAAACATA 884
                         ----------    -  i ---- v      vi   -             
  L1M4_orf2#LINE/    515 ----------GAGC-TAAA----ACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_68598219_6    885 GAAAAAAACCTTTGTGAACTAGGATTAGGCAAAAATGTCTTAGATATGAC 934
                          i?iv   i   i    v  v  i        vii v             
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_68598219_6    935 ACCAAAAACACAAT--ACATAA----AAATGTGATAAATTGGACTTCATT 978
                                i     v--   v  ----    i-                 i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTCATC 648

  chrX_68598219_6    979 AAAATTTAAAACATCTGTTCTTCAAAAGACATGGTGAAGAAAAGAGTAAG 1028
                               v     v i   v       i    ivi v      iviiv   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_68598219_6   1029 ATGACCCACAAAATGAGAGAAAATATGTGCAAACCATATATCTTATAAAG 1078
                          ii       i    i          v      i         v    i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_68598219_6   1079 GACATGCACTCAGAATATATAGAGAACTGCCAAAACTTATCACTAAGAAA 1128
                            v  i ii           i      vii v    i vi v   i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_68598219_6   1129 ATAAATAACTAAATT-AAAAATGGGCAAAAAATATGAAAAGATATTTCAC 1177
                          i       iv    -             ii  v    v   i     v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_68598219_6   1178 TAAAGAAGATATCTGAATGGCAAATAAGCACGTGAAAATATGCTCAACAT 1227
                         i           vii      v         i      v           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_68598219_6   1228 TGATAGTCCT 1237
                         ii????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.75 (98 / 56)
Gap_init rate = 0.02 (13 / 722), avg. gap size = 3.92 (51 / 13)  


2656 23.33 5.77 1.28  chrX_68600377_68602128      480  1259 (493)    L1M4_orf2#LINE/L1       94   908 (0)  

  chrX_68600377_6    480 ATTAAATGATCCTGGCAACATTTTTTTATGGCCATAGACAAGCTTATTCT 529
                           i   --    ii  vi -i      iii vv  v        v  i  
  L1M4_orf2#LINE/     94 ATCAAA--ATCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chrX_68600377_6    530 AAAATTTATATTGAAAGGTACAGGACCTAGAATAGCTAAAGCA-TCTTTA 578
                               i    v    v i vi     i        i   i  -    v 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_68600377_6    579 AAAAGAAGAATAAAATGGGAGGAATGAGTCTACCCAATATGAAGTCCTGC 628
                                   i   i v      v v vv  v      v v  iv i i 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_68600377_6    629 TACATAGCCACAGTAATCAAAATAGTGTCACGTTGG---AAGGATAGACA 675
                             v   i           i i     viiii   ---           
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_68600377_6    676 CATAGATCAATAAAATGGGATAGAGAACCTAGAAATAGACACACACAAAT 725
                         i          ii   i i  v    ii i       i  v  i   vv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_68600377_6    726 ATGCCCAATTGATTTTTGACAAAGGTGT-AAAACCAATTCAATTGAGGAA 774
                            vi           i     i    i-  i    -      v i i  
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAA 389

  chrX_68600377_6    775 GCATAGACTTTTCAATAAACGGTCCTGGAGCCACTGAGCATCTATAGGCA 824
                          v    v        i   i   v    ii v    iii ? i i v   
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_68600377_6    825 GAAAAATGAACATCTATCTAAACCTTATACCTTATA---AAATTAACTCA 871
                         i  i      vv vv i ivv    i i   v    ---           
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_68600377_6    872 AGGTGAATTACAGACTTAACA---AAGAACTATTATT-TAAAAGT-TTAG 916
                          ii  i  i ?    i   - ---    i   vv i -     v -    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAA-ATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_68600377_6    917 AAAAA----TAGGGGGAAATCTTTTGGATATAGGGCCAGGCA--GAATTT 960
                           i  ----    ? v       ivv  iv v   ii     -- iv  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_68600377_6    961 GTAGACTTTATACCAAAAGCATGATCCATAAAAGAAAAAAT-TATAAATT 1009
                         v    iv v i          ii v v i            -v       
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_68600377_6   1010 GGACTTTATCAAAGTTAAAAACTTTTG--CTTTGTGAAAAAACA-TGTTA 1056
                               i      i             --   i---   ii   - i i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTC---AAAGGACACTATCA 685

  chrX_68600377_6   1057 AAGGAG-GAAAAGATAAGCTACACACTGGGAGAAAATATTTGTACAACAC 1105
                          iii  -       i  v i   v v                i v v  i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_68600377_6   1106 ATATTTGATAAAGGATTTGTATCTCATATACTACAAAGAGCTCTTAAAAC 1155
                             i      i   i       iviv   -  i     i      v   
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATA-TATAAAGAACTCTTACAAC 784

  chrX_68600377_6   1156 TCAACAATAAAAAAGCAA----TCCTATTAGAAAATGGGCAAAAGACATG 1201
                             i        ii   ----i  v   ?i            i  iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_68600377_6   1202 AAGAAAC-------CAA-GAA------CA--TGGTCAAATAAGCTTATGG 1235
                           v i  -------   -   ------  --   i   -     vi   i
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGA 883

  chrX_68600377_6   1236 AAGTATG-TCAACACCATTAGCCTT 1259
                           iv   -      i  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (112 / 66)
Gap_init rate = 0.03 (26 / 815), avg. gap size = 2.12 (55 / 26)  


2344 26.77 6.84 1.30  chrX_68624830_68626669.rev      502  1349 (491)    L1M4_orf2#LINE/L1       14   908 (0)  

  chrX_68624830_6    502 CATGTTCATGGATTGGAAAACTGAATACCAT-AAAATGGTGAGTTCCCTC 550
                                           i   v    iii -  i    ii - v i i 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA-TACTCCC 62

  chrX_68624830_6    551 TAAATTGATTTTTAGATGCAATGCAATCCCAATAAAAATCTCAGCACGTT 600
                         i        i vi    v   i        v  v      i    --- v
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC---TG 109

  chrX_68624830_6    601 TCTTTTTTGTGGAACATGACAAGCTGATTCTAAA-------------TGC 637
                         i        ii   vv            i     -------------   
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_68624830_6    638 AAAGGGCCAAGAATATCCAAGATACTTTTAAATAAGAGGAACAAGGTGAA 687
                           i  i  v      v    i i v i  i  v    i      i  vii
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_68624830_6    688 AGGAGTTGC-TTTACCAGGT--AA----TA--ATAAAG-TCCAGTAATTA 727
                             v ii -i  v   iv --  ----  -- i    - v       i 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_68624830_6    728 AGAT--TGTGGTAGTGATGTAA---T-GACAAAGAGACCAACAGAATAGA 771
                            i--       v  iii   --- -    v v   i   ii       
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_68624830_6    772 ATAAACAGTTCAGAAACAATCTTGCATATATACAGGCACCTGATTTATGA 821
                           vi v   i      i  v iiii i  v  ii v  vi      vi  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_68624830_6    822 CAAAGGTGATGCTATAGAGGACT----GGGGGAAAGACAGTCCTTATAAT 867
                            i    --- i -   vv i ----    i  ii i    i  vi  i
  L1M4_orf2#LINE/    360 CAAGGGTG---CCA-AGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_68624830_6    868 TAATGGTACTGGATCAGTTGGATATCTATATTTTAAAAAATGAAGCTTAG 917
                         v      i    iv  ii      ? i i  viv   i       i vii
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_68624830_6    918 TTTCTGTATCTTAGCATACACAAAAATCGATTTCAAGTGGAGTATAGACC 967
                         iii  iiv  vi v    i        ii i iv  i    vi ?     
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_68624830_6    968 TAAATGTAAATGTCAAAAACATAAAGCTTCTAGAAGATAATATGGGAGAA 1017
                                  iv ii    vi     i  ii       v  i  i  ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_68624830_6   1018 TATCTACA--ATTTCAAGGTAAGAAAATATTTCTTAAATGGGACACAGAA 1065
                         v    v i-- ii iii v  i v  vvi       i  iv     vi  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_68624830_6   1066 AACACTATCCATAAAGGAAAATACTAAA-AAATTAAACA-CATTAAAATT 1113
                          i   v v v i   i     - v  i -     ii  v-   i      
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAATT 654

  chrX_68624830_6   1114 AAAAACTTCTGTTCATCAAAGGATACCATAAAGAAAG-GTAAA------T 1156
                                 i   v v        i  i  v       - v   ------i
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_68624830_6   1157 CACAGATTTGGG---AATGGCTTACAACATAAAAAATACAAAAATAG-TT 1202
                               v v  i---   i-i  i   -  v v v  vii v  vi -i 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATA-TTTGCAA-ATCATATATCTGATAAGGGACT 752

  chrX_68624830_6   1203 CATATTCAGAGTATATAAAGAATTCCTACAAATCTATAAGAAAAAGACAG 1252
                         ii   i    i           i  i     v  v    v         i
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_68624830_6   1253 A----CTAATAGAAAAATGGGCAAAAAACTTGTATAGGCATTTCAC---A 1295
                          ---- i   v?             ii i   v    i      v --- 
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_68624830_6   1296 GAAGATATGCAAATGCATAATAA--ACATGAAAAAGAGCACAACCTCATC 1343
                                 i      vvi     --         iiv  v    v   ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_68624830_6   1344 AGTCTT 1349
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.75 (142 / 81)
Gap_init rate = 0.03 (28 / 895), avg. gap size = 2.46 (69 / 28)  


2333 21.80 4.27 2.44  chrX_68627794_68629441      500  1155 (493)    L1M4_orf2#LINE/L1      241   908 (0)  

  chrX_68627794_6    500 TATGAAGCTACTATTATCAAGACAGGGTGGTTCTGGCATGAGGACAGGCA 549
                           ii       vi v          v     v       i    i  i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_68627794_6    550 TATATATCAATGGAACAGGACTGAGAGGTCAAAAATAAACTCTTATATTT 599
                             v          i  i i      vi  i        i v  i    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_68627794_6    600 ATAATCAATTGATTTTTGACAAAAGTACCAAGATGATT-AGTTGGGGGGA 648
                           ii            i     ii  i      iv   - i ---     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT---GGGGA 387

  chrX_68627794_6    649 AAAGATACCCTGTTCAATAAATGATGTTGGGAAAATTGGATATCCACATG 698
                           ii   vi  v     i     i  i     v  i      ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_68627794_6    699 CAAAAAAGATGAACTTAGATACTCACTAGAGACCATACCCCAAAAATGAA 748
                              i -     v  i  iv ii  ivv v      iv -      v  
  L1M4_orf2#LINE/    438 CAAAAGA-ATGAAGTTGGACCCCTACCTCACACCATATAC-AAAAATTAA 485

  chrX_68627794_6    749 CTCAAAATGGATCATAGGCTTAAATGTAAGTACCAAAACAATAAAATGTT 798
                                       ?  i i          vi i     v      ivi 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_68627794_6    799 TAGAAGAAAACATAGA---AAATCCTTAAGATCTTG---CAGAGCAAAGA 842
                                        i---     i iiv  i    ---i  -    v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG-GCAATGG 584

  chrX_68627794_6    843 TTTATTAGATATGACACCAAACACATAGTCTAAAAAAGAAA--------- 883
                            v                 vi  i iv v v        ---------
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_68627794_6    884 ---TGAACCGTTTTGGAA--AGAAACTTTTTTTTTTTTTCAAAAGAAAAC 928
                         ---  i  iviv iii  -- i        v vi  ---    i  v vi
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT---CAAAGGACACT 681

  chrX_68627794_6    929 CTTGAAAAA-TGAAAAGAAATGCAACAGACTAGGAGAAAATCTTTGGAAA 977
                         v ii i   -        v vv v     v i         v    v   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_68627794_6    978 ACATATATCTGGTAAATAACTTATATTCAAAGGAATTTACAAAGGATTCT 1027
                         v          i   ivi    i   i  ---    v  i    i i   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCA---GAATATATAAAGAACTCT 778

  chrX_68627794_6   1028 TGGAATGTAATAATAA---GACAAA---CCAAACAAAAAAATGAGCAAAA 1071
                          iv  ivi        ---      ---  v  iv?       i     i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_68627794_6   1072 GATATGAACAGATATTATACCACAAATGAAGATACACAAATGGCTAAATA 1121
                            v    i   i   - vi -    -       i         i  -  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATT-TCTC-CAAA-GAAGATATACAAATGGCCAA-TA 874

  chrX_68627794_6   1122 AATACATGAAAACATGTTCGACATCATTATCCAT 1155
                          ii         v   i  i      ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (88 / 52)
Gap_init rate = 0.03 (18 / 668), avg. gap size = 2.44 (44 / 18)  


3003 24.40 4.58 0.92  chrX_68659615_68661853.rev      876  1748 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_68659615_6    876 AAAAGCATTCCATGCTCATGGGCTAGAAGAATCAATATTGTTAAAATGTC 925
                            iii  i     i      ii i     v i           i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_68659615_6    926 CACAGTGCCCAAAGCAATCTACAGAGTCAATGCTATTCCTATCAAATTAC 975
                         v i v v      vii         v    i  v  i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_68659615_6    976 CAATATCATTTTTCACAGAATTAGAAAAAAAGCT-ATTCAAAGCTTCATA 1024
                           iivv v     ii     v v  v  ---   -  i v  iv      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAA---GCTGATCCTAAAATTCATA 150

  chrX_68659615_6   1025 TGGAAC--CAAAAAACAGCTTGAATAGCCAAGGCAATCCTAAGCAAAAAG 1072
                              v--   iii  -- iv          ii     i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_68659615_6   1073 AA---AGCTAGAGGCATCACATTACCTGACTT-AAAACTGTACTACAAAG 1118
                           ---  i i    vv     i v  ii i  -      -          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_68659615_6   1119 CTACAGTAACCAAAACAGCATGGTAC------AAAAACAGACCCACAGGC 1162
                                  i   i    ii      ------  ii i    vi i  ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_68659615_6   1163 CAATGGAACAGAATAGAGACCCCTGAAATGAAGCTGCATACCTACAACCA 1212
                                 i     v    vi  v     i  v iii i ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_68659615_6   1213 ACTGATCTTTGACAAAGTTGACAAAAGTAAACAGGAGAGAAAGGATACCC 1262
                          i    i  i     i v  v   i vi vv  ivi i     i   vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_68659615_6   1263 TATTCAATAAATGGTGCTGGGACAACTGGCTAACCATATGCAGAAGAATG 1312
                          v     i                     v  ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_68659615_6   1313 AAACTTGACTCCCTACCTTTCACCATGTACAAAAATTAAATCAAGATGGC 1362
                           ii v   -        iv      i            v    i    v
  L1M4_orf2#LINE/    448 AAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_68659615_6   1363 TTAAAGACTTAAATGTAAGATGTCCCACTATAAAA-TCCTAGAAGAAAAC 1411
                          i ?    i           vv vvv         -  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_68659615_6   1412 CTAGGAAATACTCTTCTAGACATTGGCCTAGGCAAGGAATTTAT-GATGA 1460
                         v    ?ivv v     vv   v    vi       v iv  iv -   - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_68659615_6   1461 AGATCCCAACAGCAAATGCAACAAAATGAAAAATAGACACATGAGACTTA 1510
                         v  iv    v    v v         vi         i v  vi     v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_68659615_6   1511 AACAAAA----GAGCTTCTGCACAGTGAAAGAAACTACCAACAGAGTAAA 1556
                          v     ----i i   i  ii vvii  i  v    i   v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_68659615_6   1557 CAGACAACCTACAGAATGAGAGAAAATATCTGCAAAATATGCATCCAACA 1606
                         v        i        i          i      vi  ii   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_68659615_6   1607 AAAGACTAATATCTAGAATCCATAAGGAATTT---------AAGAA-AAG 1646
                          ii    vi    i     vi    i   i i---------  v  -  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_68659615_6   1647 AAAACAAGTAACTCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTT 1696
                           i    i    i v   ?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_68659615_6   1697 CTCAAAAGAAG---------TAGCCAATAA--ACATGAAAAAATGCTCAA 1735
                            v       --------- i        --         i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_68659615_6   1736 CATCACTAATCAC 1748
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (129 / 80)
Gap_init rate = 0.02 (17 / 905), avg. gap size = 2.82 (48 / 17)  


3752 22.66 1.10 1.21  chrX_68667428_68672673.rev     3847  4755 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68667428_6   3847 TGGAAAGATATCCCATGCTCATCGATTGGAAAAATTAATATTGATGAAAT 3896
                                          i    v        i v         v i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68667428_6   3897 GTCCATACTATCCAAAATAATATACTGATTCAGTGCAATCCCAATCAAAA 3946
                          v v     vi     v i  v   v      ii        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68667428_6   3947 TCCCAATGGCATTGTTCACAGAAATAGCAAAAACT-ATCCTAAAATTTGT 3995
                              iiv  v  v  ii       v - v  i  -           ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chrX_68667428_6   3996 ATGGAAACATAAAAGACCTTGAATAAACAAAACAATTCTGAGAAAGGAAA 4045
                                iii  ii    iv     iv         ii   i    i i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_68667428_6   4046 ACAAAATTGGAGGCATCATACTTCCTGATTATATTATATAATTTATTATA 4095
                              i       vv   i      ii   --- i - -  i   i  --
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATT---TCA-A-AACTTACTA-- 242

  chrX_68667428_6   4096 TTACAAACCTATAGTAATCAAAATGGTATTGTTCTGGCATAAAAACAGAC 4145
                         ---    v   i         i ii  i v  v         ii i    
  L1M4_orf2#LINE/    243 ---CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_68667428_6   4146 ACATAGACCAGTGAAACAGAATAGAGCGCCCAGGAAAAAATCCAAACATA 4195
                          i     i  i  i  i     v   v i    i  v   i   v    v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_68667428_6   4196 TACAGTCAATTACTTTGTGACAACGGCACCAAGAGAACACAATGGGGAAA 4245
                           ii       iv   vi     v  ii      vv iv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_68667428_6   4246 GGGTAGTCTCTTCAATAAATGGTGCTAGAAAAACTGGATTTCCACGTGCA 4295
                          ii      i     i          i i v        v?    i    
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_68667428_6   4296 AAAGAATAAAATTGAATCTTTAGCTTATACCATA-------ATAAATTCA 4338
                                i  i   i i ii  v  i i      -------  v  i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_68667428_6   4339 AA-TGGATAAAAGACCTAAATGTAAGACCAGAGATTATAAAACTTTTTGA 4387
                           -     v ?                v vi i i         i  v  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_68667428_6   4388 AGGGAATATAAGAGAAAAGCTCCTGGATGTTGGCCTTGACAATGATTTTT 4437
                           ii  i   i ? v   v  i vv  iv    vi v i     i   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_68667428_6   4438 TACATATCACACTAAAAGCTCAAGCCACAAAAGGAAAATTAAATAAATGA 4487
                           v    v    i      v     v       i    v  i      vi
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_68667428_6   4488 GACTACAACAAACTAAAAAGCTTCTGCACAGAAAAGGAAACAATCAACAA 4537
                             v  v    v v    i   i  ii vvv      v  v     v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_68667428_6   4538 AATGAAATGGCAGTCTATGTATTGGGAGAAAATATTTGCAAATCATATAT 4587
                          i     v i  ii i iiv v                            
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_68667428_6   4588 CTGACAAGAGATTAACATCCAAAATGTATAAAGAACTCATACAACTCAAT 4637
                             i   i  i vii     i   i            v           
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_68667428_6   4638 AGCAGAAAAACAAACA-CCTAACTACAAAATGGTCAGAAGACCTGAATAG 4686
                          ii i   i     i -  i  i ?v       v  i i  ii       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_68667428_6   4687 ACATTTCTTTAAAGAATACATAAAAATCTCCAATGAGCATATGAAAAAAT 4736
                                 ii      v i   v    vv     i    i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_68667428_6   4737 GCTCTACATCATTAGTCAC 4755
                             v      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (126 / 76)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.33 (21 / 9)  


3138 27.11 1.33 0.44  chrX_68679945_68686213.rev     4879  5778 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68679945_6   4879 TGGAAGAACATTACATGCTTATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  iv    i i    i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68679945_6   4929 GGCCATACTGTCCAAGGTAATTTACAGATTCAATGTCATCCCCATCAAGC 4978
                            v     vi    iv i  i           i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68679945_6   4979 TACCAATGACTTTCTTCACAGTA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii   v -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_68679945_6   5027 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_68679945_6   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_68679945_6   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_68679945_6   5177 AATGGAACAGAAC--AGAGCCCTCAGGAATAACGTCGCATATCTACAACT 5224
                                i    i--    i  --  i     vvi ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_68679945_6   5225 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_68679945_6   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_68679945_6   5325 GAAACTGGGTCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii   ii    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_68679945_6   5375 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_68679945_6   5425 CTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5474
                         v    ?v v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_68679945_6   5475 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5524
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_68679945_6   5525 TTAAACTAAAGAGCT---GCACAGCAAAAGAAACTACCATCAGAGTGAAC 5571
                          i   v v  i i  --- ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_68679945_6   5572 AGGCAACCTACAGAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5621
                           i     i                 v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_68679945_6   5622 AGGGCTAACATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5671
                         i  i  vii         v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_68679945_6   5672 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5717
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_68679945_6   5718 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAA-ATGCTCACC 5766
                           v        i  vi viii     v  i          -       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_68679945_6   5767 ATCACTGGCCAT 5778
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


2852 25.78 2.68 1.34  chrX_68716533_68722639.rev     3056  3951 (2156)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68716533_6   3056 TGTAAAACCATTCCATGCTCATGGATAAGAAGAATCAATATCATTAAAAT 3105
                           v   ivi  i     i        vi     v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68716533_6   3106 GGCCATACTGCCCAAAGCAATTTAGAGATTCAATGCTATTCCTATCAAAC 3155
                            v     v      vii  i  v        i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68716533_6   3156 TATCAATGACATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 3204
                          vi  iivi v  i  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_68716533_6   3205 ATGGAAC--CAAATAACAGCCCAAGTAGCCAAGGCAATCCTAAGGAAAAA 3252
                               v--   ivi  --  vi i       ii     i ---      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTT---GAAAAA 194

  chrX_68716533_6   3253 AAAAAAATAAGCTGAAGGCATCATATTACCTGACTTTAAACTATATTACA 3302
                         i  i  vv   i  i   vv   i i v  ii i  i   viv  i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_68716533_6   3303 GGGTGACAGTAACCAAAACAGCATGGTAATGGAACAAA-ACAGATGCATA 3351
                         ii iv       i   i    ii     v   v i  i- i   iii   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_68716533_6   3352 GATCAATGGAACAGAATAGAGAGCCTAGAAATAAAGCCACACACCTACAA 3401
                                    i     v     i i         v   i   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_68716533_6   3402 CTATCTGATCTTTGACAAAGTCAACAAAAACAAGCAATGGTGAAAGGAAT 3451
                         ii vi    i  i     i viiv   i v  vv      v     -   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AAT 393

  chrX_68716533_6   3452 CCCTCTATTCAATAAA-GGTGCTGGGAAAACAGGCTAGCCATATGCAAAA 3500
                         vv-   v     i   -          v   v  v  ?   i        
  L1M4_orf2#LINE/    394 AG-TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_68716533_6   3501 GATTGAAACTGGATCCCTTCCTTACAACATATACAAAAGTTAACTCAAGA 3550
                           v    ii    i    v   i   v           i         i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_68716533_6   3551 ACGAGTAAAGACTGAAATGTAAAACCCCAAACTATAAAAACCCTAGAAGA 3600
                         vv  vi ?    iv        i v iv           vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_68716533_6   3601 AAATCTAGGCA-ATACCACTCAGGATATAGGCACAGGCAAAGATTTCAT- 3648
                            iv    ?i- v i -i  iv  iv v  vvi      v i    v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_68716533_6   3649 GATGAAGATGCCAAAAGCGATTGCAACAAAAGCAAAAATGGACAAATGGG 3698
                            - v  ii        ivvv          v      i  i    v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_68716533_6   3699 ATCT------AATTAAAGAGCTTCTGTACAGCAAAAGAAACTATCAGCAG 3742
                          ii ------       i -   i   i vv    i  v       iv i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_68716533_6   3743 ATTAAACAAATAACCCATAGAATAGGAGAAAATATGTGTAAACTATGCAT 3792
                          v i  v i i      i     i           v  i   ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_68716533_6   3793 CTGACAAAGGTCTAATATCCAGCATCTATGAGGAACTG----AAATCTAC 3838
                             i  i  v  vi       v  v   i i     v----  v  v i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_68716533_6   3839 AAGAAAA---CAAA---CCCA-TTAAAAAGTAGGCAAAGGACATGAACAG 3881
                           v    ---    ---    -  ?    i i         iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_68716533_6   3882 ACACTTTTCAAAAGAATATATACATGCAGCCAACAAGCACATGAAAAAAA 3931
                            i  i  v      v       viii     i             i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_68716533_6   3932 AACTCAATATCACTGATCAT 3951
                         i-     i    ????????
  L1M4_orf2#LINE/    890 G-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (138 / 89)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.80 (36 / 20)  

2866 24.71 5.38 1.49  chrX_68716533_68722639.rev     4743  5616 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68716533_6   4743 TAGATAGATATATTGTGTTCATTGATTGGAAGAC--AACATTGTAAAGAT 4790
                          i  v      viii       v           --  i     v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68716533_6   4791 GTCAATTTTCCCCATATTGATCCACAGGTTTACTATAATTCCTATAAAAA 4840
                          v    vi      v       i    i  i viii   i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68716533_6   4841 TCCTAACAAGGATTTTTGTAGACATAGGCAAGCTTATTTTAAG--TTATA 4888
                            i i vivvv      i   v  v i      v  ii   i-- i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_68716533_6   4889 TGGAAAGGCACAGGCCCCAGAATAGGTAGAACAACCCTGGAAAAGAGAAA 4938
                               v   vi  v          vi i     i i  i      ii  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_68716533_6   4939 AAAAGGAGAAGGAATCACTCTAGCACATATTAACACTTAACATATATAGC 4988
                         v    vv i    v    v  vv vv  v i  v     - -  i v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-C-TACAAAGC 248

  chrX_68716533_6   4989 TACCGTAATCAAAACAGCATGGTATTAGTG-GAGGGTAGACATACAGCTC 5037
                            v        i    ii     i i ii-i   i        i  v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_68716533_6   5038 CATGAGACAAAACAGAGAACTCAAAAATATGTTCATATAAATATG--CA- 5084
                         v   ii i i  iv    iii  i     viii    i vv    --  -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_68716533_6   5085 --------TGACTAAAGT--CAAACCCAATTCAATGGAGGAAGCATAGCC 5124
                         --------i   v ii  --   iv   -        i i   v    i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTC 397

  chrX_68716533_6   5125 TTTTCAACAAATGATGCTGGAGCAATTGGATATCCCCAGGCAAG----TA 5170
                                      i      ii   i      ?  v  v    i---- i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_68716533_6   5171 AAGT--AACCCTGAAATAATCTTCACAATTTATATAAAAGTTAACTCAAA 5218
                             --i    i----  -- i     viv    i    i          
  L1M4_orf2#LINE/    448 AAGTTGGACCCC----TA--CCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_68716533_6   5219 ATGTATCATAGACTTAAATATAAAAG-TAAAATTATAAAACCTTTTTTA- 5266
                            v    ?    i     i   i  -     i        --- i   -
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC---TCTTAG 538

  chrX_68716533_6   5267 ---AAAACA--GGAGAAAATCTTTGGGAACTAGGGTGAGGCAAAGAGTTC 5311
                         ---      --  ? v       i v  v  v    v      v iv   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_68716533_6   5312 TTAGACTTGACACAAAAAGTATGATCTATAAAAGAAAAAATTGATAAATT 5361
                              iv      v     i ii v v i            v        
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_68716533_6   5362 GGACCTTACCAAAATTTAAAACCCTTGCTCTGTGAAAGCCTATGTGAGCA 5411
                             i i i       v     ii   iv  vii  i v vv i v iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_68716533_6   5412 CAACAAAAAGATAAGCTTATAGACTACGAGAAAATATTTCCAAACCACAT 5461
                         v iii      i  - ii i   v iv            v    i  i  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_68716533_6   5462 ATTTGAAAATGAACTTATATCTAGAATATATAAAGAACTCTCAAAACTCA 5511
                           i   v  v i    i    i                   i v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_68716533_6   5512 AGAGTAAAC---TAAA------AAT--AAAA-----CAAAAGACATGAAG 5545
                          v i    v---i   ------   --    -----    i  iv    v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_68716533_6   5546 AGACACTTAACTAAAGAGGACACAGAGATTGCAGATCAATACATGAAAAG 5595
                              i  vv i     i  i i v i  v  vi  v ii          
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_68716533_6   5596 ATGTTCAATATTATTAGCCAT 5616
                            i    i  i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (129 / 84)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.73 (60 / 22)  


3299 25.82 0.77 0.99  chrX_68753139_68759551.rev     5012  5921 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68753139_6   5012 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5061
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68753139_6   5062 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5111
                            v     vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68753139_6   5112 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5159
                          v   iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_68753139_6   5160 TATGGAACCAAAAAAGGAGCCCACATT-GCCAAGACAATCCTAAGCAAAA 5208
                                -- viv    ii    v v -     i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_68753139_6   5209 AGAACAAAGCTGGAGGCATCGCGCTACCTGACTTCAAACTATACTACAAG 5258
                                  i      vv  i i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_68753139_6   5259 GCCACCGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5308
                           i  v    i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_68753139_6   5309 CCAATGGAACAGAAT--AGAGCCCTCAGAAATAATACCACACATCTACAA 5356
                         i        i     --    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_68753139_6   5357 CCATCTGATCTTTGACAAACCTGACAAAAAACAAGAAATGGGGAAAGGAT 5406
                         i  vi    i  i     ivv  v   i v-  vvv           i  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAAT 393

  chrX_68753139_6   5407 TCCCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5456
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_68753139_6   5457 GCTGAAACTGGATCCTT-CCTTACACCTTATACTAAAATTAATTCAAGAC 5505
                         iv    ii    i  i -   i     v     v        i    i i
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_68753139_6   5506 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAACCCCTAGAAGAA 5555
                             i ?    i       v   v       i       i i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_68753139_6   5556 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 5604
                            v    ?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_68753139_6   5605 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5654
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_68753139_6   5655 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5704
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_68753139_6   5705 GAACAGGGAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTG 5754
                            v  iv    i                 v   i   vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_68753139_6   5755 ACAAAGGGCTAATATCCAGAATCTATGAAGAACTTAAACAAATTTATAAG 5804
                          i  i  i  vi          v   i       ivv    v iv    v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_68753139_6   5805 AAAAAAATCAAACAACCCCATCTAAAAGTGGGCGAAGGATATGAACAGAC 5854
                              i -    i     v  i?    i     i      v    i    
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_68753139_6   5855 ACTTCTCAAAAGAAGACATTTATGCAGCCCACAGACACATGAAAAAATGC 5904
                          i     v        i  vi viii   v i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_68753139_6   5905 TCATCATCACTGGCCAT 5921
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (142 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


2499 26.11 2.80 1.66  chrX_68770316_68772090.rev      502  1286 (489)    L1M4_orf2#LINE/L1      115   908 (0)  

  chrX_68770316_6    502 TTTGTAGAAATTGACAATTGGGTTCTAAAATTTGTAAGAAAATGTAAAGC 551
                             i            viv i i        ii  v i     i  i v
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_68770316_6    552 ACCTAGATGAGTCTAAATAACTTCAAAAAAGAACAATTA---TGGAGGAC 598
                            i   vv  i v   i  ii ii        v  iv ---        
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_68770316_6    599 ATATGTTACTT--TTTTGGGACTTAATATAAAACTATAATAATCAAGACA 646
                         vi iii v ii--   iiii     v  i   i   i i           
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_68770316_6    647 GTATATTATTG-TGTAAA-ACAGGCAAATTTATTAATGATACATAAT--A 692
                           i iv  i  -ii   i- i  i  v  vv  i    iv i v   -- 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_68770316_6    693 GAACCGAGAAATAGATCTGCTCTTATATCATCAACTGATTTTCAATAAAG 742
                           ii v       i i iiiv v v   vi    i        i i  i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_68770316_6    743 ATGTCAATGCAATACATTGGGAAAAGAACTGTCTATTCAACAAACCATGC 792
                         i  i   vi v  v  v    i      iv    v         ivi   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_68770316_6    793 TGAAACAAGTGGATATCCATATGCAAAAAAATAAATAAAGACACCTTGG- 841
                           ii    v      ?   i        i   i  ---- -----    -
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAA----G-----TTGGA 455

  chrX_68770316_6    842 CACTTACTACACATTGTATA-AAACATTAAGTCAATATGGATCATGGACC 890
                          v i   iv    iii    -   v     v    v        ?i    
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_68770316_6    891 TAAATGTACGAGCTAAAATTATAAAACTTTTTGATGAAAACAGAAGA--A 938
                                 v         i         i  v  v       v i ?-- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_68770316_6    939 AATCTCAATGTACTTAGGTTTGTCAAAGATTTCTTAATTATTACA---AA 985
                              ivi  vv   i    v v   v i       iv   v   ---  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_68770316_6    986 ACTCCAGAAATTACAAAAGGGGAAAAATCATTACATTGGATTTCATGAAC 1035
                          v--  v  iiv       i--      viv  v      i     v  v
  L1M4_orf2#LINE/    606 AG--CACAAGCAACAAAAGA--AAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_68770316_6   1036 ATTAAAGATGTTCACTCTTCAGAAGACATCACTGTGAAAATGTAAAGTCA 1085
                               i iv  iiiv     i i    ii iiiv    i  v    v  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_68770316_6   1086 AGCCACAGA-TGGGGAAAACTATTAACAGAACGTATATGTGACAAAGGAC 1134
                          v       -    ii   v    vi  i v i     v   i  i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_68770316_6   1135 TTGCACCTAGAATATATAAGGAACTCTTACAACTCAATAATAAGATGAGA 1184
                            i i i           i                       i v  v 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_68770316_6   1185 AAGAAC-----TTAAAATTCAGCAAAATACTTGAATGAATGCTTCATCAA 1229
                           v   ----- ?    v vi     iv i      ii iii   vi   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_68770316_6   1230 ATAATATATTCAGATGCCAAATAAGCACATGAAAAGATGTTCAATATAAT 1279
                          v  v    v  i   v v                    i    i  v ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_68770316_6   1280 CTGCCAT 1286
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.54 (122 / 79)
Gap_init rate = 0.02 (15 / 794), avg. gap size = 2.33 (35 / 15)  


3314 26.68 0.44 0.33  chrX_68786408_68792683.rev     4879  5785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68786408_6   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68786408_6   4929 GGCCATGCTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v  i  v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68786408_6   4979 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5027
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_68786408_6   5028 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5077
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_68786408_6   5078 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5127
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_68786408_6   5128 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5177
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_68786408_6   5178 ATGGAACAGAAC--AGAGCCCTCAAAAATAACGCCACATATCTACAACTA 5225
                               i    i--    i  -- i      vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_68786408_6   5226 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5275
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_68786408_6   5276 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5325
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_68786408_6   5326 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5375
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_68786408_6   5376 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5425
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_68786408_6   5426 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5475
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_68786408_6   5476 ACTCCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5525
                           v         vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_68786408_6   5526 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5575
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_68786408_6   5576 GGCAACCTACAGAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAA 5625
                          i     i                 v  ii   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_68786408_6   5626 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5675
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_68786408_6   5676 AACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCT 5725
                         i     i     v  i?    i    ii     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_68786408_6   5726 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAA-ATGCTCACCA 5774
                          v        i  vi viii     v  i          -       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_68786408_6   5775 TCACTGGCCAT 5785
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


2859 27.07 1.31 2.18  chrX_68818420_68824013     4186  5101 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68818420_6   4186 TGGAGAAACATTCCATGCTCATGGATAGGAAGAATCAATATCTTGAAAAT 4235
                             i i i  i     i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68818420_6   4236 GGCCTTGCTGCCCCAAAGTAATTTATAGAGTCAATGCTATTCTCGTTAAA 4285
                            vv i  -       v i  i  i   v    i  v  i iii i   
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_68818420_6   4286 CTACCA-CTGACATTCTTAACAGAATTAGAAAAA--ACTTTTAAAAAATT 4332
                         v v   -   v v  i  i-     v v  v  i--iv ii     --  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAA--TT 146

  chrX_68818420_6   4333 CATGTGGAAGCAAAAAAAAAAAAAAACAAAAAACACCCAAATAGCCAAGA 4382
                            i     -------------- vi   iii  -  vi         i 
  L1M4_orf2#LINE/    147 CATATGGAA--------------ATGCAAGGGAC-CCAGAATAGCCAAAA 181

  chrX_68818420_6   4383 TAATCCTAAACAAAATGAACAAAGATGGAGGCATCAGGCTACCCGACTTC 4432
                         i    i i  v  i v        v      vv   vi  v   i i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_68818420_6   4433 AAACCGTGCTACAAGGTTACAGTAACCAAAACAGCATGGTAGTGGTACAA 4482
                            v v i      i i        i   i    ii     v   i i  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_68818420_6   4483 GACCAGACACATAGACCAATGGAACAGAATAGGGAATTCAGAAATAATAC 4532
                          ivi     i     i        i     v i  i i         vv 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_68818420_6   4533 TGCACACCTACAACCATTTGATCTTTGACAAACTTGACAAAAACTAGCAA 4582
                         iii   ii  iiii  v     i  i     ivv  v   i v vvv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_68818420_6   4583 TGGGAAAATGACTCCCTATTTAGTAATTGGTGCTGAGAGTTCTATCTAGC 4632
                             i   vi ivvi  v  i ii  v        i  vvv  ivv  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_68818420_6   4633 CATATGTGGAAATTTGAAACTAGACCCCTTCGTTACACCATATACAAAAA 4682
                           i   iii  ivv    ii i       v v i                
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_68818420_6   4683 TTAACTCAAGATGAATTAAAGACTTAAATGTGAAACCCAAAACTATAAAA 4732
                                  i   i  i ?    i       i i v i            
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_68818420_6   4733 ACCCCAGAAGAAAATCTAGGCTGTAA-CATTCAGGACATTGGCACGGGTA 4781
                         vi ii         iv    ?-    -iv   iv   v    vvii  i 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_68818420_6   4782 AAGATTTCATAACAAAAACACCAAAAGCAATTGCAACAAAAGCAAAAATT 4831
                          v i    v  ivv vi            vvv          v      v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_68818420_6   4832 GACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAATGAAAC 4881
                           i    v   ii v  i   v v  i i   i  ii vv    v  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_68818420_6   4882 TACCAACAGAGTAAACAGATAACCTACAGAATGGGAGAAAAGTTTTGCAA 4931
                           i   v i   i  v   i    i                vv       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_68818420_6   4932 TGTATCCATCTGACAAAGCTCTGATATCCAGCATCTATAAGGAATTTAAA 4981
                         vvi  vi      i  i vv  vi       v  v     i   i ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_68818420_6   4982 CAAATTTACAAGAAAAAAACAA----CCCCATTAAAAGGTGGTCAAAGGA 5027
                            v iv i  v     i    ----   v   ?   ii   v       
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_68818420_6   5028 CATGAACAGACACTTCTCTAA-GAAGACATACATGCGGCCAACAA--ACA 5074
                         iv    i     i     i  -     i     vii      i  --   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_68818420_6   5075 TAAAAA-ATGTTCAACATCACTGATCAT 5101
                          i    -   i         ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.46 (32 / 13)  


3370 26.21 0.44 0.44  chrX_68825813_68830173.rev     2963  3870 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68825813_6   2963 TGGAAGAACATTCCATGCTCATGCGTAGGAAGAATCAATATCGTGAAAAT 3012
                              ii i  i     i     vi v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68825813_6   3013 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCAATCCCCATCAAGC 3062
                            v     v     iv i  i           i        i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68825813_6   3063 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3110
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_68825813_6   3111 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTGAGCCAAAAG 3160
                                viiv  ii  v  v v  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_68825813_6   3161 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3210
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_68825813_6   3211 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3260
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_68825813_6   3261 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 3308
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_68825813_6   3309 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3358
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_68825813_6   3359 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3408
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_68825813_6   3409 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 3458
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_68825813_6   3459 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3508
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_68825813_6   3509 CTAGACATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAA 3558
                         v   i?i v viv   iv   viv  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_68825813_6   3559 AACTCCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTAA 3608
                         i  v         vvii         vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_68825813_6   3609 TTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAAC 3658
                          i   v v  i i   i   i vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_68825813_6   3659 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3708
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_68825813_6   3709 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3758
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_68825813_6   3759 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 3808
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_68825813_6   3809 TCAAAAGAAGACATTTATGCAGCCAAAAAACATATGAAAAAATGCTCACC 3858
                           v        i  vi viii     v  i  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_68825813_6   3859 ATCACTGGCCAT 3870
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2987 25.93 1.43 1.65  chrX_68874730_68879255     3124  4033 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68874730_6   3124 TGGTAACACATTCCATGCTCATGGATGGGTAGAATTAATATTACGAAAAT 3173
                            v  v i  i     i        v  v   v        iiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68874730_6   3174 AACCATACTGCCAAAAGCAATCTACAAGTTCAA-----TTCTCATCACAA 3218
                         ii v     v  v   vii       ii     ----- i ii    v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68874730_6   3219 TACCATCATCATTCTTCATATAACTAGAAAAAACAATCCTAAAATTCATA 3268
                          v   v vv v  i  iii v  v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_68874730_6   3269 TGGAAGCAAAAAAGAGCCCACACAGCCAAAGCAAGATGAAGCAAAAAGAA 3318
                              iiiv  ii  v  viv i       i   vv vi iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_68874730_6   3319 CAAATCTGGAGGCCTCACAATACCTGACTTTGAACTATACTATAAGGCTA 3368
                             vi      v      v v  ii i  ii  viv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_68874730_6   3369 TAGTCACCAAAACAGCATGGTGCTGATATAAAAATAGGCACATAGATCAG 3418
                         i   v i   i    ii    i   ii    ii    i  i        i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_68874730_6   3419 CAGAACAGAATAGAGAACCTAGAAATAAAGTCAAACACTTAGAGCCAACT 3468
                         ii   i     v    ii i         vi  v   i   vi i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_68874730_6   3469 GATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGAACACCCTAT 3518
                            i   i    i vviv   i v   vv i           i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_68874730_6   3519 TCAACAAATGCTGCTGGGATAATTGGCAGGCCACATGCAGGAGAATGAAA 3568
                                   v        i  i   vvi?         ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_68874730_6   3569 CTGGATCCTCATCTCTCACTTTATACAAAAAATCAACTCAAGATGGATCA 3618
                         i    i  ii i   v   iv          - i       i        
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCA 499

  chrX_68874730_6   3619 AGGACTTAGAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACA 3668
                         ?i   i  --   v     v  i           v ii       v    
  L1M4_orf2#LINE/    500 WAGACCTA--AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_68874730_6   3669 TCAGAAAAACCCTTCTAGACATTGGCTTAGGCAA--ATTTACTT---CAT 3713
                          vi ?iv  vi    vv   v    v        --i   -   ---i  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-CTTAGATAT 596

  chrX_68874730_6   3714 GACCAAAAACCTAAAAGCAAATGCAACAAAAACAAAGATAAATAAGTGGG 3763
                            -----   -       v v         iv   i   i    i v  
  L1M4_orf2#LINE/    597 GAC-----ACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_68874730_6   3764 ACTTAATTAA--CTAAAGAGCTTTTGCATGGCAAAAAGAACAGTCAGCAG 3811
                             v  i  --i    i -      iiivv    iiiv  vi   iv i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_68874730_6   3812 AGTAAACAGACAACCCACAGAGAGGAAGAAAATCTTTACAAACTATGCAT 3861
                            i  v              iv  i       v   i    ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_68874730_6   3862 CTGACAAAGGACTAATATCCAGAATCTATAAAGAACTCAAACACATCAGC 3911
                             i  i     vi          v            vv   vv   ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_68874730_6   3912 CCCCCAAAAAACCAAAGAATCCCATCAAAACATAGGCTAAGGACATGAAT 3961
                         vvi--     iv    v  i  v  i?   v  i   v     iv     
  L1M4_orf2#LINE/    790 AAT--AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_68874730_6   3962 AGACAGTTCTCAAAAGAAGATATATATAAACAGCCAACAAACATATGAAA 4011
                              v     v            i --  ii     i  i  i      
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACA--AATGGCCAATAAGCACATGAAA 885

  chrX_68874730_6   4012 A-ATGCTCAACATCACAAATTAT 4033
                          -             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.15 (28 / 13)  


2293 20.74 5.26 2.01  chrX_68879822_68881427.rev      502  1147 (459)    L1M4_orf2#LINE/L1      242   908 (0)  

  chrX_68879822_6    502 ACAAAGTTAGAGGAGAGAATCAAGTC--TGTGTTACTGGCAACAGAATGA 549
                               i  v  v ----      v --    v        vv  i  ii
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTA----ATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_68879822_6    550 ACACATAGATCAAGGGAACAAA---GAGAGCATCCAGAAATAGACCTACA 596
                            i         v    i i ---     --          i   i i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAG--TCCAGAAATAAACCCATA 335

  chrX_68879822_6    597 CATATATGGTCAATTGCTTTTTGACAAAGATGTCAAAGTAATTCAATAGG 646
                            v            v    i     i i  i   iiiv       i  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_68879822_6    647 GAAAGAATAGTCT---CAACAAATGGTGCTTGAACAACTGT-TATCTATA 692
                                      ---              v i       v-  ? i i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_68879822_6    693 TGCAAAAAAGATGAACCTCAGCTCATGCTTTGCACCATATACAAAAATTA 742
                                i -     vi vii i v i i ii                  
  L1M4_orf2#LINE/    436 TGCAAAAGA-ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_68879822_6    743 ACCCAAAATAAATCAAAGATATAAATGTAATA-C-----CTATAAAATAT 786
                           i      ii    ?   iv         v - -----        ivi
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_68879822_6    787 CCAGAAGGAAAAATAAGAGAAAATCTCTGTAACCTTGGGTTTGGGAGAGA 836
                         ii     i   v   i ? v      ii  i          v  v iv i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_68879822_6    837 TTTCTTAGATATGACACCAAAAGCACAATCTATAATAGAACAAACTTGAT 886
                                                     v v i  v    v   - v   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGAT 633

  chrX_68879822_6    887 AAATTGGACTTCA--AAATTT-----CTGCTGTGT---GAAAGACACTGG 926
                                      --   v  -----  vi    i---i  i      iv
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_68879822_6    927 TAAGAAAGCAATAAGACAACTCACAGACTGAGAAAAAATATTTACAAATC 976
                         i       ii v        i      v  i  i         i      
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_68879822_6    977 ACATGTCTTATAAAGAACTTCTATACAAAAAATATAAAGGACTCTCAAAA 1026
                          i  i   v    i i    v   v  i  v        i     i v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_68879822_6   1027 GTCA-TAATAAAAAAACAAAAAA---AAG-AAAAAATGGGTAACAGGTTT 1071
                         v   -         i     v  ---  v-?         i  vi i   
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_68879822_6   1072 AAACTGACACTTTACTACATTATAAAAGATATTCAACT--TTATTAATCA 1119
                         i  iv    i  --  v  -- - i       v   v --ii v   v  
  L1M4_orf2#LINE/    834 GAATAGACATTT--CTCCA--A-AGAAGATATACAAATGGCCAATAAGCA 878

  chrX_68879822_6   1120 T-TAAAGAAAT-CTAAATTTCAATGGAATT 1147
                         i- i  i i  -  v  iv   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (80 / 50)
Gap_init rate = 0.03 (22 / 667), avg. gap size = 2.14 (47 / 22)  


2883 28.08 1.22 0.44  chrX_68926277_68931125.rev     3458  4358 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_68926277_6   3458 TGGAAAAACATTCCATCCTCAAGGATAGGAAGAATCAGTATCATGAAAAT 3507
                               i i  i    vi   v    v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_68926277_6   3508 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGTTATTTCCATCAAAC 3557
                            v     v      v i  i  i        i iv  ii i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68926277_6   3558 TACCATTGACATTCCTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 3606
                          v   vivi v  ii ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_68926277_6   3607 GTGGAA-T-CAAAGACAACCCTGTATAGCCAAGACAATCCTAAGTAAAAA 3654
                         i     - -   i i--    v v        i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGG--ACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_68926277_6   3655 GAACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAAGG 3704
                                 i      vv     i v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_68926277_6   3705 CTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGACATATAGAC 3754
                                  i   i    iii        i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_68926277_6   3755 CAATGGAAGAGAACAGAGACCTCAGAAGTAACACCACACATCTACAACCA 3804
                                 v    iv    vii     i   vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_68926277_6   3805 TCTGATTGTCGACAAGCCTGACAAAAAGAGGCAATGGGAAAATGACTCCC 3854
                         vi     v        vv  v   i vv vv       i   vi ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_68926277_6   3855 TATTTAATAAATTGTGTTGAGAGTTCTGTCCAGCCACATGCAGAAATTTG 3904
                          v  i  i    v   i  i  vvv   vvi ?         i  ivv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_68926277_6   3905 AAACTGGACCCCTTCCCTACACCACATACAAAAATTAACTCAAGATGGAT 3954
                           ii         v  ii      i                  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_68926277_6   3955 TAAGGACTTACATGTAAAACCCAGAACCATAAAAACCCTAGAAGAAAACC 4004
                         i ?i   i  v      i v i i   i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_68926277_6   4005 TAGGCA-ATACCATTCAGGACACAGGCATGGGCAAAGACTTCATGACGAA 4053
                             ?i- v i -   iv   viv  vv i     v ii   v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_68926277_6   4054 AATGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAACGGGATCTAA 4103
                         i ii         vvv          vv     v  i   iv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_68926277_6   4104 TTAAACTAAAGAGCTTCTGCACAGCAAAACAAAGTATCATCAGAATGAAC 4153
                          i   v v  i i   i  ii vv    iv v v     vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_68926277_6   4154 AGGCAACCTACAGAATGGGAGAAAACTTTTGCGATCTACCCATCTGACAA 4203
                           i     i                iv     i vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_68926277_6   4204 AGGTCTAATATCCAGAATTTACAAGGAACT---GAAATTTG-CAAGAAAA 4249
                         i  v  vi          v  i  i     ---iv  i ii-i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_68926277_6   4250 AAACAAC---CCCAATCAGAAAGTGGGCAAACGATATGAACAGACAATTC 4296
                          i    v---      i?i   i        v   v    i     v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_68926277_6   4297 TCAAAAGAAGACATTTACATAGCCAACAAACATATGAAAAAAAGCTCAAC 4346
                           v        i  vi v  i     i  i  i       i v       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_68926277_6   4347 ATCACTGATAAT 4358
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (146 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3430 23.82 2.25 0.34  chrX_68940730_68945169.rev     3060  3949 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_68940730_6   3060 GAAAAGATAGTCCATGTTCATGGATTAGAAAAATCAATATTGTTAA-ATA 3108
                          i       vi               i   i v i           -  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_68940730_6   3109 TTCATAGTACCCCAAGCT-ATCTACTGATTCAATGCAATCCCTATCAAAA 3157
                         viv   v -      ii -      v       i                
  L1M4_orf2#LINE/     52 GCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_68940730_6   3158 TATCAATGACATTCTTCATGGAAATAAAAAAA---ATTCTAAAATGTATA 3204
                          vi  iivi v  i  iiii     vi v  i---  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_68940730_6   3205 TGGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAAAGAA 3254
                              vii   ii                 i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_68940730_6   3255 CAAAACTGGAAGAATCACATCACCTGACTTCAAATTGTAATACAGAGCTA 3304
                             ii    i  v     iiv  ii i      viv  v    i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_68940730_6   3305 TAGCAACCCAAACAGCATGGTACTAGCATTAAAAGAGACACATAGA-CTA 3353
                         i  i  i v i    ii       i    v ii v     i     - v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_68940730_6   3354 TGGAACAGAATACAGAACCCTGGAATAAATCCATACATCTACAGTGAACT 3403
                              i     vv   ii  v i      i        i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_68940730_6   3404 CATGTTTGATAAAGGTTCCAAGAACATACATTTGGAAAAGA-CAGTCTCT 3452
                         v  v  i  i  i   v      v   v  v v  i     -i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_68940730_6   3453 TCAGTAAATGGTGCTGGGAAAACTGGATATCCATTTGCAAAAGAATGAAA 3502
                            ii              v         ?   iv              i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_68940730_6   3503 CTAGACTCCTATCTCTCACTGTAAACAAAGATAAAATTAAAATGGATTAA 3552
                         i i   i    i   v   ii  v     i  v  v i         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_68940730_6   3553 AGACTTAAATCTAGGACCTCAAACTATGACACTAATAGAAAAAAATTGAG 3602
                             i     v  i  v  v       i v   vv     i    ivv  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_68940730_6   3603 GG--AA--CTCCAGGAAATTGGACTGGGCAAAAATTT----AATAT--C- 3641
                          ?--  --  i iv  vv    ii i     vii   ----i    -- -
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_68940730_6   3642 CCACAAGCACAGGCAACCAAAGTAAAAATGGACAAATGGGAGCATATCAA 3691
                            v       i     v    v      i  i    v   vivi     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_68940730_6   3692 A-TTAAAAACTTCTACATAGCAAAGGAAACAATCCACAAAGTTAAGAGAT 3740
                          -          i iiiivv       v  v   v v     v  i   i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_68940730_6   3741 AATCCACAGAATGGGAGAAAATATTTGCAAAGTACTCATCTGACA-GAGA 3789
                           i                            vi ivi      i - i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_68940730_6   3790 TTAATAACCAGAATATATAAGGAGCTCAAACCACTTCATAGGAAAAAAAA 3839
                         i vi  v             i  i   vv  v   iv   iv     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA- 799

  chrX_68940730_6   3840 TCTAATAATTCGATTTTAAAATGAGCAAAAGATCTGAATAGACATTTCTC 3889
                         - v     ii i   ?v      i     i   i                
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_68940730_6   3890 AAAAGAAGACATACAAATGGCAAAGAAGCATATTAAAAGGTACTCAACAT 3939
                         v        i           v  v     i  v     i i        
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_68940730_6   3940 CATCTATCAT 3949
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.57 (127 / 81)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 1.64 (23 / 14)  


2695 25.61 3.34 2.34  chrX_69017231_69022475     3855  4752 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_69017231_6   3855 GAAAAAACATTCCATGTTTATGCGTCAGAAGAATCAATATTGTCAAAATG 3904
                          i   i i  i       i   vi ii     v i        i  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_69017231_6   3905 GTCATAATACCCAAAGAAATTTACAGATTCAATGCTATTGTTATCAAACT 3954
                          iv   v v      vvi  i           i  v  ivi       v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_69017231_6   3955 ACCAATGACATTCTTCACAAAACTAGAAAAAACT-ATTTTAAAATTCATA 4003
                         v   iivi v  i  ii  i  v v  v  i-  -  ii           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chrX_69017231_6   4004 TGGAACCAAAAAAGAGCCTGAATAGCCAAGGCAATCCAAAGCAAGTAGAA 4053
                              viiv  ii  v  v          ii     ivi iv   v    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_69017231_6   4054 CAAAGCTGGAGGCATCATATTACCTGACTTCAAACTATATGTTAAGGCTG 4103
                              i      vv   i i v  ii i      viv  ivvi  i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_69017231_6   4104 CAATACCCAAAACAGTATGGTAC------------AGA----TCGAACAA 4137
                           i  vi   i     i      ------------   ---- v  v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_69017231_6   4138 TGGAATAGAATAGGTAGCCCAGAAATAATGTCACACACCTATGACCATCT 4187
                                    v iv  i          vvi  i   ii    ii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_69017231_6   4188 GATCTTTGACAAAATTAACAAAAACAAACGATCTAGAAAGGACTTA--CT 4235
                            i  i     iiv iv   i v  vv i  vvi     i --  --  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA--TAGTCT 398

  chrX_69017231_6   4236 ATTCAATAAATGGTGCTGGGATAGCTGGCTAGCCATAAGCAGAGATAATT 4285
                         v     i              i i    v  ?   i v   i - v   -
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-AGAAT- 446

  chrX_69017231_6   4286 GAAACTGGGCCCCTTCCTTACACCATATACAAAAATTAACTCAAGGTGGA 4335
                            ii   i     v   i                         ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_69017231_6   4336 TTAAATCCTTAAATTTAAAACCCAAAACTATAAAAACCCTT-GAGGAAAA 4384
                          i ? vv i     v   i v i            - i   -  i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_69017231_6   4385 TCTAGGAAATACCATTCTAGACATAGACCCTGGA--AAAAAAT---TTAT 4429
                         iv    ?i-  -- v   v-- i -    i   i-- iiv   ---  v 
  L1M4_orf2#LINE/    546 CATAGGNG-TA--AATCTT--CGT-GACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_69017231_6   4430 GACAGA-GACATGAAAAGCAATTGCAACAAAAACAAAAATTGACAAATGG 4478
                         v v v -    iv       vvv         iv      v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_69017231_6   4479 GACCTAATTAAACTAAAGAGCTCCTGCATAGCAAAACAGCAAAAGAAGCT 4528
                            i v  i   v v  i i  ii  ii-------- vv    i  vi  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTG--------CTTCAAAGGACACT 681

  chrX_69017231_6   4529 ATCAACAGAGTAAACAGACAACCCAAAGAATGG-AGAAAATATTTGCAAA 4577
                              v i   i  v          v       -                
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_69017231_6   4578 CAATGTATCTGACAAAGA---TATATCCAGTATCTATAAGAAACTTAAAC 4624
                         iv  i       i  i i--- i       v  v     ii    ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_69017231_6   4625 AAATATACAAGCAAAAAAACAAGCAACCCCATTAAAGAGTGGGCAAAGGA 4674
                           v vv i  -i     i    ii     v   ?  i i           
  L1M4_orf2#LINE/    782 AACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_69017231_6   4675 CATAAACAGACACTTTTCAAAAGAAGACATATACATGAGCAGTAAGCACA 4724
                         iv i  i     i  i  v        i   i v   iv  i        
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_69017231_6   4725 TGAAAAAATGCTCAGCATCACTGATCAT 4752
                               i       i     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (135 / 91)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 2.43 (51 / 21)  


3230 27.01 0.55 0.44  chrX_69102477_69106877     3002  3908 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69102477_6   3002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3051
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69102477_6   3052 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3101
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69102477_6   3102 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3149
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69102477_6   3150 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3199
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69102477_6   3200 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3249
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69102477_6   3250 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3299
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69102477_6   3300 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3347
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_69102477_6   3348 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3397
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_69102477_6   3398 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAAAAAGCT 3447
                           v  i  i              v      v  ?   i   i    iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_69102477_6   3448 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAGATGGA 3497
                            ii    i    v   i     v  i        i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_69102477_6   3498 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3547
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_69102477_6   3548 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 3597
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_69102477_6   3598 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3647
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_69102477_6   3648 TTAAACTAAAGAGCTTCTCCACAGCAAAAGAAACTACCATCAGAGTGAAC 3697
                          i   v v  i i   i vii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_69102477_6   3698 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3747
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_69102477_6   3748 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3797
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_69102477_6   3798 A-ACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 3846
                          -     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_69102477_6   3847 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 3896
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_69102477_6   3897 ATCACTGGCCAT 3908
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3986 21.64 1.22 0.67  chrX_69194940_69198523     2191  3091 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_69194940_6   2191 GAAAGATATCCTGTGTTCATGGACTGGAAAAATTAACATTATTAACATGT 2240
                                    ii          i     i v    i   i    v   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_69194940_6   2241 CTATACTACTCAAAGTGAGCTATAGATCCAATACAATCCCTATGAAAATT 2290
                          v     v i    v   v   i    i   ii          v     i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_69194940_6   2291 CCAATGACATTTTTAAAAGAAAC--ATAAAAAAATCCTAAAATTTGTATG 2338
                            iivi v     viv     i-- i  ivvi           ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_69194940_6   2339 AGACAACAAAAGACCCTGAATAGCCAAAGTAATCTTGAGAAAGAAAAACA 2388
                         ii vvi   ii     v           ii        i      i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_69194940_6   2389 AAGCTAGAGGCATCACACTTCCTGATTTCAAACTATATTACAAAGCCATA 2438
                            i i    vv          ii        viv  i        i i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_69194940_6   2439 GTAATCAAAACACTATGGTACTGACATAAAAACAGACACAGAAACCAATG 2488
                                 i   v i        i     ii i     i v i i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_69194940_6   2489 AAATAAGATAGATAGCCCAGAAATAATCCCATGCATTTATAGTCAACTAA 2538
                         i    ii  v  v  i          v     i       i     i i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_69194940_6   2539 TCTTTGAAATGGGTCCCAAGAATACACAATGGGAAAAGGATAGTTTCTTC 2588
                          i  i  v v    v      vi iv       i    i     i i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_69194940_6   2589 AATAAATGGTGTTG----AACTAGACATCCTCATGCAAAATAATGAAACT 2634
                           i        i  ----    i  i ?  v         v      ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_69194940_6   2635 AGACTCTTACCTTATGACATACACAAACATTAACTCAAAATGGATTAAAG 2684
                         i   i i     i iiv    i     v                 i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_69194940_6   2685 ACTTAAATGTAAGACCTGAAATCACTAAACTCCTAAAAGAAAATATAGGG 2734
                           i           v  i   ii iv      i  i       i     ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_69194940_6   2735 AAAAAGCTCCTTGACATTGGCCTTGACAATGATTTTTTGGATATGACAAC 2784
                         iv   v  i v    v    vi v i     i   i  i         v 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_69194940_6   2785 AAAAGCACAGGCAACAAAAGCAAAAATAAACAAGCAGGAGTACCTCAAA- 2833
                                  i          v       i i  iiv   v v v     -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_69194940_6   2834 CTAAAAA-TCTTCTGCCTAGCCAAGGAAACAATCAACAAAATGAAAAGGC 2882
                         i      - i  v   i -- v     v  v     v   i       i 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_69194940_6   2883 AACCCACAGAATGGAAGAAAATATTTGCAAACCATATCTCTTATAAGGGG 2932
                                       i                i     v   v       i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_69194940_6   2933 TTAATCTCTAAAATATATAAAGAACTCATACCACTCAATAGAAAAAAATA 2982
                         i vi v  i i                v   v        iv     ivv
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_69194940_6   2983 AAATAACATAAACTTTTTAA---TAGGCAAAGGACTTGAATAGACATTTT 3029
                                vi  ----  ?  --- i         i              i
  L1M4_orf2#LINE/    801 AAATAACCCAA----TTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_69194940_6   3030 TCCAAAGAAAACATACAAATAGCCAAAGGGTATATGAAAAGGGGCTCAAC 3079
                                  i i        i     vii i i        iv       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_69194940_6   3080 ATTATTAGTCAT 3091
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (125 / 66)
Gap_init rate = 0.01 (7 / 906), avg. gap size = 2.43 (17 / 7)  


3014 14.55 4.91 0.36  chrX_69208774_69210646      500  1049 (824)    L1M4_orf2#LINE/L1      293   867 (41)  

  chrX_69208774_6    500 TATATCAATAGAATGGAATTGAGAACACAGAG------------------ 531
                           v      i    i         iiv    i------------------
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_69208774_6    532 GGTCAATTGATTTTCACCTAGGGTGCCAAGACAATTCAATGTGGGAAAGA 581
                                        iv v             v        -        
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGA 391

  chrX_69208774_6    582 ATAGTCTT--CAACAAACAATACTGAAACAACTGGACATCCACATGCAGA 629
                                 --       iii i   ii         i ?         i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_69208774_6    630 AAAATAAAGTTGGACCT-TACCTCATATCATATACAAAAATTAACTCAAA 678
                          i   i          i-       i i                      
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_69208774_6    679 -TGGATCAAAGACCTAAA-GTGAAAGTCAAAACTATTAAACTCATGGAAG 726
                         -       ?         -  i i  ii        v      v i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_69208774_6    727 AAAACATAGGTGTAAAGCTTCATAATCTTGGATTAGGCAATGGCTTCTTA 776
                                   ?     v    i i i     i           i      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_69208774_6    777 TATATGACATCAAAAGCACAAACAACAAAATAAAAAATTGATAAGTTGGG 826
                         v        i           i        v       v     i    i
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_69208774_6    827 CTCCATTATAATTAAACACTTTTGTGCTTCAAAGGACACCATTAAGAAAG 876
                           i   i v       v                      i  i       
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_69208774_6    877 TGAAAAGACAACCCACAGAATGGGAGAAAATACCTACAAATCATGTATCT 926
                                                         ii i        i     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_69208774_6    927 CATAAGAGTCTAGGAGCCAGAATAGATAAATAATTCTTATAACTCAACAA 976
                         v     i v  v v v        v     v  i     i       i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_69208774_6    977 CTGAAAGGCAA----TTCAATTTTAAAAATAAGCAAAAGATTTAAATAGA 1022
                         ivi    i   ----ii     ?-      ii     i     i      
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_69208774_6   1023 CATTTCTCCAAAGAAGCTATACAAATG 1049
                                         v          
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATG 867

Transitions / transversions = 2.45 (54 / 22)
Gap_init rate = 0.01 (8 / 575), avg. gap size = 3.62 (29 / 8)  


3163 26.74 0.99 0.66  chrX_69213525_69219910.rev     4991  5895 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69213525_6   4991 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5040
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69213525_6   5041 GGCCATACTGCCCAAGGTAACTTACAGATTCAATGCCATCCCCATCAAGC 5090
                            v     v     iv i ii           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69213525_6   5091 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69213525_6   5139 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5188
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69213525_6   5189 AACAAAGCTGGAGGCATCACACTACCTGACTTTAAACTATACTACAAGGC 5238
                                i      vv       v  ii i  i   viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69213525_6   5239 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACCGA--TATAGACC 5286
                                 i   i    ii         i iv ii iv  --      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69213525_6   5287 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5334
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_69213525_6   5335 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5384
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_69213525_6   5385 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGGAGAAAGCT 5434
                           v  i  i              v      v  ?   ii  v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_69213525_6   5435 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5484
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_69213525_6   5485 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5534
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_69213525_6   5535 CCAGGCAATACAAT--TCAGGGCATAGGCATGGGCAAGGACTTCATGTCT 5582
                         vi   ?i-  -   --  iv i v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_69213525_6   5583 AAAACACCAAAAGCAATGGCCACAAAAGCCAAAACTGACAAATGGGATCT 5632
                          vi            vvi  v       vv    iv  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_69213525_6   5633 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGA 5682
                         v  i   v v  i i   i  ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_69213525_6   5683 ACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5732
                          v  i     i                 v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_69213525_6   5733 AAAGGGCTAATATCCAGAATCTACAATGAGCTCAAACAAATTTACAAGAA 5782
                           i  i  vi          v  i  v  i   vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_69213525_6   5783 AAA-ACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACATT 5831
                            -     i     v  i?    i     i      v    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_69213525_6   5832 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTGA 5881
                             v        i  vi viii     v ii          i     v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_69213525_6   5882 TCATCACTGGCCAT 5895
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3272 26.62 0.55 0.66  chrX_69366362_69372768.rev     5008  5916 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69366362_6   5008 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5057
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69366362_6   5058 GGCCATACTGCCCAAGGTTATTTATAGATTCAATGCCATCCCCATCAAGC 5107
                            v     v     iv v  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69366362_6   5108 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5155
                          v   iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69366362_6   5156 TATGGAAACAAAAAAAGAGCCTGCATTGCCAAGTCAATCCTCAGCCAAAA 5205
                                 iiv  ii-  v  v v  v     iv     i v ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_69366362_6   5206 GAACAAAGTTGGAGGTATCATGCTACCTGATTTCAAACTATACTACAAGG 5255
                                        vv   ii  v  ii        viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_69366362_6   5256 CTACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5305
                               i  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_69366362_6   5306 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5353
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_69366362_6   5354 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5403
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_69366362_6   5404 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5453
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_69366362_6   5454 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5503
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_69366362_6   5504 ATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5553
                           i ?    i  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_69366362_6   5554 CCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAAGACTTCATGTCT 5602
                          v    ?i- v i -   iv   viv  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_69366362_6   5603 AAAACACGAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5652
                          vi    v       vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_69366362_6   5653 AATTAAACTAAGGAGCTTCTGCACAGCAAAAGAAATTACCATCAGAGTGA 5702
                         v  i   v v ii i   i  ii vv    i  v i  i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_69366362_6   5703 AGAGGCAACCTACAGAATGGCAGAAAATTTTCGCAACCTACTCATCTGAC 5752
                          i  i     i         v       v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_69366362_6   5753 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5802
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_69366362_6   5803 AAAAACAAACAACCCCATCAACAAGTGGTCAAAGGATATGAACAGACATT 5852
                            i     i     v  i? v  i   v        v    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_69366362_6   5853 TCTCAAAAGAAGACATTTATGCAGCCACAAGACACATGAGAAAATGCTCA 5902
                             v        i  vi viii    vv ii       i  i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_69366362_6   5903 TCATCACTGGCCAT 5916
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1183 24.48 9.73 0.00  chrX_69391017_69393977.rev     1092  1430 (1531)    L1M4_orf2#LINE/L1        1   372 (536)  

  chrX_69391017_6   1092 TAAAGAGATATACTGCATTCGTGTAT-------CTAAATATTCTTAACAT 1134
                          ii i      v iiii   i  v  -------  v      v    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69391017_6   1135 GTTGATTCTCCTTGAATTGATTTGTAAATTCTATGCAATCTTAATCCAAC 1184
                          vii  v    iii       i ii i    v i      iiv   v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69391017_6   1185 TCCCAGCAAGCTGTTTTGTAGAAATTAACAAGATAATTCTAAAATGTATA 1234
                                viv  v     i       i     v i  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_69391017_6   1235 TGGAAATGCAAAGGACCCAGTTTTCCCAAAACAATTTTGACAAAGAACAA 1284
                                    i        vv vv          i    v      v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_69391017_6   1285 CAACTTTGGA---CTTACACT----GATTTCAGGATTTCTTAAAAAGCAA 1327
                            vv     ---  i     ----i      ii i  vi  v     v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_69391017_6   1328 CTGCATTCAAGACTTTTTGGTATTGGCATAAAAATAGACATATAGATCAA 1377
                          v i v       vv v     i        ii                 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_69391017_6   1378 TGAAACAA---------TCT-GAAATAGA--------TGTATGGATATTT 1409
                           i  i i---------  i-      i -------- v     vi v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_69391017_6   1410 AATTTT-GACAAAGGTGTCCAG 1430
                         i     -     i    i v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAG 372

Transitions / transversions = 1.31 (47 / 36)
Gap_init rate = 0.02 (7 / 372), avg. gap size = 4.71 (33 / 7)  

 444 16.84 1.05 1.05  chrX_69391017_69393977.rev     1431  1525 (1436)    L1M4_orf2#LINE/L1      487   581 (327)  

  chrX_69391017_6   1431 TCAAAATGAATCAAAGACGTAAATGTAA-AGCTTAAAAATATGTAACTTC 1479
                                 i    ?    v         -    -    v   iv    ii
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCT 535

  chrX_69391017_6   1480 TAGAAGAAAACTTAGGGGGAAATCTTAGCGACCATGGGTTTGACAA 1525
                                    v    ? v       v i    v      v i   
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

Transitions / transversions = 0.75 (6 / 8)
Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.00 (2 / 2)  

1085 19.76 3.59 3.89  chrX_69391017_69393977.rev     2137  2470 (491)    L1M4_orf2#LINE/L1      576   908 (0)  

  chrX_69391017_6   2137 AGCCAA-GATTTCTTAAGCAAGATATGAAAACTGTTTAAGTA-TAAAGAA 2184
                           v   - i       iii v  i iv    -- ivi   i -i   ii 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAA--GCACAAGCAACAAAAGA 623

  chrX_69391017_6   2185 AAAAATATCAATAAATTGGATGGCATTAACATAATAAATGTTTGCTCTTC 2234
                                --i          ivv   i  v  v v   iv    iv    
  L1M4_orf2#LINE/    624 AAAAATA--GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_69391017_6   2235 AAAAGACACTGTTAC-AAATTGAAAAGGGCAAGCCACAGCCAGGGAGAAA 2283
                            i      i i v-   v       i-   v      vvv        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGA-CAACCCACAGAATGGGAGAAA 720

  chrX_69391017_6   2284 ATATTTGTAAAACACAGAAGTCCTCTGTTAAA-----TATATCTAGAATA 2328
                                i   v  i v -----    v   i----- i    i      
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATA-----TCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_69391017_6   2329 TATAAAGAATTTT---AATTCAATAATAAGAAAAAGATAAACAACCCAAT 2375
                                  i i ---  i          ---     i   i        
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAA---AAAGACAAATAACCCAAT 812

  chrX_69391017_6   2376 TTAAAAATGGGGACAG-ATTTGAACACATATTTCACAAAAGAAAACATAC 2424
                          ?         v v  -       i v i     v v      i i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_69391017_6   2425 ATATGGCAAATAAGCACATGAAAGGATGTCCAACATCATTAGTCAT 2470
                          v     v               i    ii        ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (38 / 27)
Gap_init rate = 0.03 (11 / 333), avg. gap size = 2.27 (25 / 11)  


3209 27.45 0.44 0.33  chrX_69518243_69524642.rev     5003  5909 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69518243_6   5003 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5052
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69518243_6   5053 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5102
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69518243_6   5103 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5150
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69518243_6   5151 TATGGAACCAAAAAAGAGCCCGCATTGCTAAGACAATCCTAAGCAAAAAG 5200
                                viiv  ii  v  v v  v  i  i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69518243_6   5201 AACAAAGCTTGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5250
                                i v    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69518243_6   5251 TACGGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGTTATAGACC 5300
                            i    i   i    ii i       i iv ii i   vv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69518243_6   5301 AATGGAATAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAT 5350
                                     iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_69518243_6   5351 CTGATCTTTCACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCTCT 5400
                         i    i  iv    ivv  v   i v  vvv           i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_69518243_6   5401 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5450
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_69518243_6   5451 AACTGGATCCCTTCCTTACACCTTATATAAAA-TTAATTCAAGGTGGATT 5499
                          ii    i    v   i     v    i    -    i    ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_69518243_6   5500 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5549
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_69518243_6   5550 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 5598
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_69518243_6   5599 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5648
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_69518243_6   5649 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5698
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_69518243_6   5699 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCTTCTGACAAA 5748
                          i     i   i             v  i    vii iviv     i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_69518243_6   5749 GGGCTAATATACAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5798
                           i  vi   v      v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_69518243_6   5799 ATCAAACAACTCCATCAACAAGTGGGCAAAGGATATGAACAGACACTTCT 5848
                         iv    i   i v  i? v  i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_69518243_6   5849 CAAAGGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5898
                          v  i     i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_69518243_6   5899 TCACTGGTCAT 5909
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


1411 14.17 1.62 1.21  chrX_69559205_69562190     1280  1526 (1460)    L1M4_orf2#LINE/L1        1   248 (660)  

  chrX_69559205_6   1280 TGGAAACATATCCCATGTTCATGGATTTGATGATTTA---TCATTAAGAT 1326
                               v                    v  v  i   --- ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69559205_6   1327 GATAACACTCCCCAAAATTATCTATAGATTCAACACAATCCCTATCAGCA 1376
                          ii  i          v v     i         i            iv 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69559205_6   1377 TCCCAGCTCAGTTATTTTTTTCAGAAACTGACA-GTTGATCTTGAAACTC 1425
                                 -- ii-      v      i     - i     i i   i  
  L1M4_orf2#LINE/    101 TCCCAGCT--GCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_69559205_6   1426 GTATGGAAATTCAAGGGACCCAGAATAACCAAAACAATCTTGAAAACCAA 1475
                         i         v                i                  vv  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_69559205_6   1476 GAATAAAGTTGTAGGACTAACACTTCCTGATTTCAAAGCTTACTAGAAAG 1525
                            i       v      v        ii        i       v    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_69559205_6   1526 C 1526
                          
  L1M4_orf2#LINE/    248 C 248

Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.02 (4 / 248), avg. gap size = 1.75 (7 / 4)  

3306 16.90 2.76 0.15  chrX_69559205_69562190     1843  2493 (493)    L1M4_orf2#LINE/L1      241   908 (0)  

  chrX_69559205_6   1843 TAGAAAGCAATGGTAATCAAGACAGCATGGTACTGACATAAGGATATATA 1892
                           v     v ii             ii        i          v i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_69559205_6   1893 TATATAT--ATGGAACAGAATTGACAACCCAGAAATAAAACAATGTGTCT 1940
                             v  --      i        v ii           v v  iii i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_69559205_6   1941 GTGGTCAACTGATTTTCCAAAAGGG-GCAAAGACCATCCAATGAGGGAAA 1989
                         i       i        v v     -  v        i     -      
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAA 389

  chrX_69559205_6   1990 GGATAGTCTTTTAATCAAATAGTTCTGGGACAACTGGATAGCCACATGAT 2039
                          i          v v     i  v                ?       vv
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_69559205_6   2040 AAAGAATGAAGTTAGACCCTCACCTCATAGCATATACAAGAATTAACTCG 2089
                                      i     ii      i v         i         i
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_69559205_6   2090 AAATAGATCAAATATTTAAAGATAAGAGCTAAA-CTATAAAACTCATGGA 2138
                             i     ? v ii    vi           -           v i  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_69559205_6   2139 AGAAAACAGAGGGGTAAACCTTCATAACTTTTGATTTGGCAATGGATTCT 2188
                                 v   ?     i    i i  i  v i  v        v    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_69559205_6   2189 TAGATATGATATCAAAAGCATAAGCAATGAAAGAAAAA-TAGATAAACTG 2237
                                  i i        i      ii         -        i  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_69559205_6   2238 GACCTCCTCAAAGTTAACGAATTTTGTATTTCAAAGGACATGATCAAGAA 2287
                            i  v     i    vi v      ii           iv        
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_69559205_6   2288 AGAGAAAAGACAATTGACAGAGTGGGGCAAAAT-----CAAGGCATATAT 2332
                           v          iiv     i    iv     -----   iv       
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_69559205_6   2333 CTGATCAAAGACATGTATCTAGAATACATAAATAACTCTTGCTATTCAAT 2382
                              v ii   v      i      i     v       i v i     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_69559205_6   2383 AATAAAAGG-----CAGCCTAATGAAAAATTGGG-AAAGGGTGTGAATAG 2426
                                i -----i i  i   v?    v    -     i v       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_69559205_6   2427 ATACT-CTCCAAAGAAGATATACAA-TGGCCAATAACCATCTGAAAAGAT 2474
                          i i -                   -          v  iv         
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_69559205_6   2475 GCTCAACACCATTGGTCAT 2493
                                 i  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (66 / 40)
Gap_init rate = 0.01 (10 / 668), avg. gap size = 1.90 (19 / 10)  


3171 26.93 0.88 0.66  chrX_69567527_69573929.rev     5007  5912 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69567527_6   5007 TGGAAGAACATTCCATGCTCATGGGTAGGAGGAATCAATATCGTGAAAAT 5056
                              ii i  i     i      i v   i  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69567527_6   5057 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5106
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69567527_6   5107 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5154
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69567527_6   5155 TATGGAACCAAAAAAGAGCCTGCATCTCCAAGTCAATCCTAAGCCAAAAG 5204
                                viiv  ii  v  v v  vv    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69567527_6   5205 AACAAAGTTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAGGC 5254
                                       vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69567527_6   5255 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5304
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69567527_6   5305 AATGGAACAGAAC--AGAGCCCTCAGAAATAAAGCCGCATATCTACAACT 5352
                                i    i--    i  --         v  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_69567527_6   5353 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5402
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_69567527_6   5403 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5452
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_69567527_6   5453 GAAACTGGATCCCTTCCTTACCCCTTATACAAAAATCAATTCACGATGGA 5502
                            ii    i    v   i  v  v           i  i   vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_69567527_6   5503 TTAAAGACTTAAACGTTAGACCTAAAACCGTAAAAACTCT-AGAGGAAAA 5551
                          i ?    i    i  v   v       ii     -    -   i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_69567527_6   5552 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5601
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_69567527_6   5602 AAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTA 5651
                         vi            vvi     v    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_69567527_6   5652 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5701
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_69567527_6   5702 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5751
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_69567527_6   5752 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5801
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_69567527_6   5802 AA---AAAAAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5848
                           ---   v     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_69567527_6   5849 CTCAAAAGAAGACATTTATGCAGCCAATAAACACATTGAAAAAATGCTCA 5898
                            v        i  vi viii        i     -     i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-GAAAAGATGCTCA 894

  chrX_69567527_6   5899 CCATCACTGGCCAT 5912
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2939 11.13 1.80 27.50  chrX_69586305_69589956     1939  3160 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69586305_6   1939 TGAAAAGACAGCCTACATTTATGGATTGGAAGACTTAATATTGTTAAGAT 1988
                           i     i v  i ii  i                              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69586305_6   1989 GTCAACATTTCAAAACTTATATC-ACG----CTAAGCGATCCCTATCAAA 2033
                          v   i i i vv  v  i-   -  i---- v v  i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG-ATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_69586305_6   2034 ATTCCACCAGCCTCTTTTTACAGAAATGAAAAAGTCAATTCTCAAATTTA 2083
                           i   v v    -     i       vi v   iii  i  v     i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_69586305_6   2084 TATGGAATTGTAAGGTGCCCC-AATAGTTCAAAATGAATCTTGAAAAATA 2132
                                v  i    vi   v-     i-     i-            v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGC-CAAAAC-AATCTTGAAAAAGA 196

  chrX_69586305_6   2133 A---CAAAGTTGGAGGGCCAACACTTCTCTGTTTCAAAGCTTATTAGAAA 2179
                          ---            i iv       i vi       i    i  v   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_69586305_6   2180 GCTACAGTAAT-AAAACAGTGTGGTACTACCATACAGATAGACATATAGA 2228
                                    -  i             iv    vi              
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_69586305_6   2229 CCAATAGAATAGAACTGAGAGTTAAGAAATAAACCCATACATCTATGGCT 2278
                         i    i        i       iv                  i     ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_69586305_6   2279 GACTGATTTTCAACAAGGGTGTCAAGACCATTATATGGGACAAAGAATAG 2328
                         i i        i         i          vv     i-         
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAG 395

  chrX_69586305_6   2329 TCTCTTCAGGCCGGGTGTGGTGGCTTACACCTGTAATCCCAGCACTTTGG 2378
                            i    ------------------------------------------
  L1M4_orf2#LINE/    396 TCTTTTCA------------------------------------------ 403

  chrX_69586305_6   2379 GAGGCCGAGGTGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTG 2428
                         --------------------------------------------------
  L1M4_orf2#LINE/    404 -------------------------------------------------- 403

  chrX_69586305_6   2429 ACCAACATGGTGAAACCCTACCTCTACTAAAAATACAAAATTAGCCAGGC 2478
                         ----------------------------------     -----------
  L1M4_orf2#LINE/    404 ----------------------------------ACAAA----------- 408

  chrX_69586305_6   2479 ATGGTGGTGCATGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGAAG 2528
                         ----      ---------------------     --------------
  L1M4_orf2#LINE/    409 ----TGGTGC---------------------TGGGA-------------- 419

  chrX_69586305_6   2529 AATCACTTGAACCAGGGAGGAGGAGGTTGTAGTGAGCCAAGGTTGTGCCA 2578
                         --------------------------------------------------
  L1M4_orf2#LINE/    420 -------------------------------------------------- 419

  chrX_69586305_6   2579 TTGCACTCCAGCCTGGGCAACAAGCAAAACTCCGTCTCAAAACAAACAAA 2628
                         --------------------------------------------------
  L1M4_orf2#LINE/    420 -------------------------------------------------- 419

  chrX_69586305_6   2629 CAAACAAAAAATAATAGTCTCTTCAACAAATGGCATGGTGGCAACTGGAT 2678
                         -----------------------------------------         
  L1M4_orf2#LINE/    420 -----------------------------------------CAACTGGAT 428

  chrX_69586305_6   2679 TTCCACAGGCAAAAGAATGAAGTTGGATGCCTACT--ACACCATTGAATA 2726
                         v?     v                   iv     i--       ---   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT---ATA 475

  chrX_69586305_6   2727 TAAAAATGAACTCAAAATGGATCAATTACCCAAACATATAAGCTAAAACC 2776
                         i      v                ?vv   i   ii  vi         i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_69586305_6   2777 ATAAAACTCTTAGAAGAATTTATAGGAATAAATCTTCATGACTTTGGATT 2826
                                           vvi     ?i         i    i    i  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_69586305_6   2827 TGGCAATGGATTCTTTGACATGACACTGAAAGCACAAGCAACAAAAGAAA 2876
                         v        v     v  i       ii                      
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_69586305_6   2877 AGGTAGATAAATTGGACTTCATCAAAGTTAAAAACTTTTTTACATCAAAG 2926
                          ii                       i            v i v      
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_69586305_6   2927 GACATTATCAAGAAAGTGAAAAGAAAACATGCAG-----GAGAAAATATT 2971
                             i                   v   vii   -----           
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_69586305_6   2972 TGCAAATCATATACCTGATAAGGGTTTAATATACAGAATATATAAAGAAA 3021
                                      i          vi vi   v                v
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_69586305_6   3022 TCCTAAAACGCAACACCAAAAA-----ACAACCCAATTTTAAATATGGGC 3066
                           i  v   v   i vi     ----- i         ?v   -      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA-ATGGGC 824

  chrX_69586305_6   3067 AAAGAACTTGAATAGACAAGTCCTTTCCCTCCCTCAAAGATGAAATACAA 3116
                             i i           -----    i -----      v  v      
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACA-----TTTCTC-----CAAAGAAGATATACAA 864

  chrX_69586305_6   3117 ATAACCAATAAGCACATGAAAAGATGCTCAACATCTTTAGTCAT 3160
                           ii                               v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (81 / 51)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 17.05 (358 / 21)  


3831 15.79 8.09 0.77  chrX_69599462_69601646      573  1351 (834)    L1M4_orf2#LINE/L1        1   836 (72)  

  chrX_69599462_6    573 TGGAAAGATATTCCATGTTCATGAATCAGAGGCTTTAATATT-------- 614
                                    i           i  ii  i vi        --------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69599462_6    615 -------CTCCCTAAACTGATTTACAGTTTCAATGCAACCCCTATCAAAA 657
                         -------     i   i    i     v     i    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69599462_6    658 TCACAGCTGGCTTTTTTGCAGAAATCAACAAGTTGGTCCTAA-------- 699
                           v      v               ii     i  i      --------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_69599462_6    700 TGGAAATTCCAGGGACCTAGAATAGCCAGAACAATCTTTAAAAAGAAGAA 749
                                v v       i          i         v           
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_69599462_6    750 CAATGAGGGGGGACTAACACCTCCCTATTTCAAAATGTACTACATAAAGC 799
                            v vv  i     v    i    v         iv       --    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA--AAGC 248

  chrX_69599462_6    800 TATAATTATCAAGGCAATGTGGTATTGCCCTGAGGATAGACATAGATGTC 849
                           i i v      i  i       i  v v i            v vi  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69599462_6    850 AATGGAATAGAATTGAGA--------ATAAACCTTCTCATTTGTGGTCAA 891
                                           --------       iviv     i       
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_69599462_6    892 GTGATTTTCAACAATGGCACGAAGATAATTCAA-GGGGAAAAAACAGTCT 940
                         v        i    v  ii v    iv      -       i  i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_69599462_6    941 T--CAACAAATAGTACTAGGACAAATGGATATTCAAATGCAAAACAATAA 988
                          --        i  i  i      v      ?i  v        v   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_69599462_6    989 AGTTGGACCCCTATCTCACACCATACACAAAAATTAACTCAAAATGGATC 1038
                                      i           i                        
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_69599462_6   1039 ACAGATCTACATGTAAGAGCTGAAAATATAAAAAACCTTACAAGAAAACA 1088
                          ?   i   v           i   v       v-i    v         
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACA 547

  chrX_69599462_6   1089 TTGAGGTAAACCTTCATGACTTTGGATTAGAAAATGGT--CTTAGATATG 1136
                          v i?     i    i    i    i    iv      --          
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_69599462_6   1137 ATA---------------ACAAAA-------TAAATAAAATGGATATCAT 1164
                          i ---------------      -------  i     v    iv    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_69599462_6   1165 CAAAATTAAAAA----TGTATTTCAAAGGGCACTAGCAAGAAATGGAAAA 1210
                                     ----   ii        i     v       vv     
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_69599462_6   1211 GACAAACCACAGAACAGGAGAAAATAATTGCAAATCATGTATTTGATAAG 1260
                              v        ii          v           i   i       
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_69599462_6   1261 AGTATAGTATAAAGAATATATAAAGAATTATTACAACTCAGTGGTAAAAA 1310
                         i vv v    vv               i v          i ii      
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_69599462_6   1311 GACAAATAGGCTAATTTAAAA-TGAGCATGAAGCACTTTGGA 1351
                                 iv i    ?    -  i   --   v -    i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCA--AAGGA-TTTGAA 836

Transitions / transversions = 1.48 (71 / 48)
Gap_init rate = 0.02 (14 / 836), avg. gap size = 4.93 (69 / 14)  

 494  8.89 2.22 0.00  chrX_69599462_69601646     1603  1692 (493)    L1M4_orf2#LINE/L1      817   908 (0)  

  chrX_69599462_6   1603 AAATGCA-AAAAGATTTCAATAGATATTT-TCCAAAGAAGATATACAAAT 1650
                              vi-   i     v      i    -                    
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_69599462_6   1651 GGCCAATAAACACACGAAAAGATTCTCAACATCATTAGTCAT 1692
                                  i    i        v          ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.00 (2 / 2)  


2950 28.06 0.80 0.80  chrX_69604574_69607292     1363  2235 (484)    L1M4_orf2#LINE/L1        1   873 (35)  

  chrX_69604574_6   1363 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1412
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69604574_6   1413 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1462
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69604574_6   1463 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1510
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69604574_6   1511 TATGGAACCAAAAAGGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1560
                                viiv  i   v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69604574_6   1561 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1610
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69604574_6   1611 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1660
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69604574_6   1661 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 1708
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_69604574_6   1709 CTCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1758
                         vvi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_69604574_6   1759 CTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1808
                           v  i  i   i          v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_69604574_6   1809 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1858
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_69604574_6   1859 TTAAAGACTTAAACATTCGACCTAAAACCATAAAAACCCTA-AAGGAAAC 1907
                          i ?    i    ii vv  v       i      vi i  -   i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_69604574_6   1908 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1957
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_69604574_6   1958 AACACCAAAAGCAGTGGCAACCAAAGCCAAAATTGACAAATGGGATCTAA 2007
                         i            vvi     v    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_69604574_6   2008 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2057
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_69604574_6   2058 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 2107
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_69604574_6   2108 AGGGCTAATATCCAGAATCTACAAGGAACTCCAACAAATTTACAAGAAAA 2157
                         i  i  vi          v  i  i      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_69604574_6   2158 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAAGTATT-C 2206
                          i     i     v  i?    i     i     iv    i iii   - 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_69604574_6   2207 TTTAGAGA-GACAGAGTACCACTGTCCGAT 2235
                          ii i   -  i ---   v v  v  i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATA---TACAAATGGCCAAT 873

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (9 / 873), avg. gap size = 1.56 (14 / 9)  


3246 26.98 0.44 0.44  chrX_69641274_69647554     4881  5788 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69641274_6   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69641274_6   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69641274_6   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69641274_6   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69641274_6   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69641274_6   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69641274_6   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 5226
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_69641274_6   5227 CTCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                         vvi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_69641274_6   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_69641274_6   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCACGATGGA 5376
                            ii    i    v   i     v           i  i   vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_69641274_6   5377 TTAAAGACTTAAACATTCGACCTAAAACCATAAAAACCCTAGAAGAAATC 5426
                          i ?    i    ii vv  v       i      vi i         v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_69641274_6   5427 CTAGGCATTACCATTCAGGACGTAGGCATGGGCAAGGACTTCATGTCTAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_69641274_6   5477 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5526
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_69641274_6   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_69641274_6   5577 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATATGACAA 5626
                           i     i   i             v  i    vii ivi  v   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_69641274_6   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_69641274_6   5677 AAAAAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAATAGACACTTC 5726
                          i v   i     v  i?    i           iv          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_69641274_6   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5776
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_69641274_6   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3053 25.41 6.18 0.35  chrX_69647624_69650009     1036  1893 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69647624_6   1036 TGGAAAGATATCCCAGGTTCACGGATTGGAAAA----ATATTGTTAA-AT 1080
                                        v     i         i ----          -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69647624_6   1081 GTCCATACTACCCAAGGCAATCTACAGATGCAATGCAATCCCTATTAAAA 1130
                          v v     v     ivii          v   i           i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69647624_6   1131 TTCCAGTGACATTTTTTCCCAGAAATAAAAAAAAAAATACTGACGTTTCC 1180
                          i    ivi v      v -      vi v  ivvi  v  i vi  ivi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGC-AGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_69647624_6   1181 ACGGAA--GCAAAAAGACCCTGACTAGCTATCGCAATCTTGAGCAAAAAT 1228
                          i    --    ii-     v  v    i vvi         iv  i  v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69647624_6   1229 AAGAAAGCTGAAGTCAC-CATACTATGTGAAGTCAAAATAAACTACAAAG 1277
                           v    i  i  v-  -  i   vivii vv      ivv         
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_69647624_6   1278 CTATACTAATCAAAACAGCATGGTATTGGCAGAAAAACAGATACATAGGC 1327
                            i v       i    ii     i     v  ii i   i i    ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_69647624_6   1328 CAATGGAAGGAAATAGAGAGCCCAGAAATAAATCCACACATTTACAGTCA 1377
                                 vii   v     i           i   i       ii    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_69647624_6   1378 ATTGGTTTTCAATAAAGGTGTCAAGAACACACAATGAGAAAAGGACAGTT 1427
                             i     i i  i    i     v  iv     i i    i i   i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_69647624_6   1428 TCTTCAACCAATAGTGTTGGTAAAACTGGATACCCACATGCAGAAGAATA 1477
                          i      v   i   i   v v         ?         i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_69647624_6   1478 AAATTTGACCCTTTTCTCACAATATATAAAAAAGCTA-TTCAAAATAGAT 1526
                           i  v     i vi      vi     v    ii  -i       i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_69647624_6   1527 TAAAGATTTAAACGTAAGACATGAAACTGTAGAACTACTAAAAGAAAACA 1576
                         i ?   ii    i      vv i     i  i    vi  i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_69647624_6   1577 TAGAGGAAAAGTTCCACGACATTG-------------------------- 1600
                            i? v   vi i ii   v   --------------------------
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_69647624_6   1601 ---CTAAA--CACAA-------------AAATAGACACATGGGATTACAT 1632
                         --- i   --     -------------       i v  v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_69647624_6   1633 CAAACTAAAAAGCTTCCACACAGCAAAAGAAACCATCAACAGAGTGAAGA 1682
                             v v    i   iiiii vv    i  v  i     v i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_69647624_6   1683 CACAATGTATGGAATGGGAGAATATATTTACAAACCAGGCATTTGAGAAG 1732
                         v    ivi ii           v      i    i  vii  i   v   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_69647624_6   1733 GGGTTAACATCCAAAATATATAAGAAATTCAAACAATTCAATAGGAAGGA 1782
                           ii vii     i         ii  i  vv    i      iv  ii 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_69647624_6   1783 AACAAATAACCTGATTTTAAAATGGGCAAATGACCTGACAAGACACTTCT 1832
                         i          ii   ?v            v  ii   vv     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_69647624_6   1833 CAAAAGGAGATGAGCAAGTGGTCCACAAGTATATGAAAAAATGTCTAACA 1882
                          v    i    ivi   i   i v i   i i       i   iii    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_69647624_6   1883 TCACTACTCAT 1893
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.89 (140 / 74)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 5.09 (56 / 11)  


3636 17.35 8.99 1.25  chrX_69661055_69662835      488  1288 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chrX_69661055_6    488 AAAATGAAGATAC---CCAAAGTGATCTACAGATTCAATGTAATCCCTAT 534
                           i   ivi    ---     v                i i         
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_69661055_6    535 GACAATTCCAAGGGCATTTTTTTTTCATAAATAAAAAAACCCATCCTAAA 584
                         v v   i   ivv  --i      v  v    vi v  i iv        
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_69661055_6    585 ATTCATATGAAGTTTCAAGGGA---------------------------- 606
                                  i iv v       ----------------------------
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_69661055_6    607 ----------------------------TCCTGATTTCAAGACTTAGCTA 628
                         ----------------------------   ii       i     -   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTA 242

  chrX_69661055_6    629 TGAAGATATAGTAATCAAAACAGTATAGTACTGAGATAAGGACTGACATA 678
                         ii   v  i         i     i i      iv       iv      
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_69661055_6    679 TAGACCAATGGCATATAATAGAGAGCCCAGAAATGAACCCTCACATATAT 728
                             i      v   v   v     i        i     vi    v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_69661055_6    729 GGTGAAATGGTTTTTGACAAGGGTTCCCAAACTATTCAATGGGAAAAGGA 778
                            v  v  i    i         v  v i  i          i    i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_69661055_6    779 CAGTCTTTTCAACAAATGGTGCTGGGAAACCAGGATATCCACATGCAAAA 828
                         i                          v v v     ?            
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_69661055_6    829 GAAAGAAGCTGGATCTTTACCTTATATCACACATAAAAATTAACTCAACA 878
                            v    i    i ii     i i i  i i i              v 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_69661055_6    879 TGGATTAAAGGTGTAAACATAAGAGCTAAAACTATACAAGTCTTAGAAGA 928
                              i ?  iiv    ii                 v  v          
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_69661055_6    929 AAACACATGCGAAAATCTTCATGACATCGGATTTGCAAATGACTTCTTGG 978
                              i v ? v        i    v i  i  v vv    ii     i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_69661055_6    979 ATATGACACCCAAAGCACAGTCAACAAAAGAAAAATCAGATAAAT-GGGC 1027
                                   v        iv              vi        -  i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_69661055_6   1028 CTCATCAAAAATTTTTTAAAATCTACTGTTCTTCAAAAGACACTA---AG 1074
                         i         -----      v  vi   v       i       ---  
  L1M4_orf2#LINE/    643 TTCATCAAAA-----TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_69661055_6   1075 AAA-----AAGACAACCCACAGAATGGGAAAACATATTTGCTAATCATAT 1119
                            -----                     i  v        v        
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_69661055_6   1120 -TTTGGTAAGGGGTTAATATCTGAAATATATAAATAATTCCTACAATTCA 1168
                         - i  i      ii vi    iii          v  i  i     i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_69661055_6   1169 ACCACTATAAAATACAAAT--CCCAATT-AAAAATGGGTAAAGGACTTCA 1215
                          iv -  -    v      --       -         i      i  v 
  L1M4_orf2#LINE/    788 ATAA-TA-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_69661055_6   1216 ACAGATGTTTCTCCAAAGAAGATACACAAATGGCCAATAAGCACATGAAA 1265
                          i   ii                 i                         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_69661055_6   1266 ATATGTTCAACATCACTGGTCAT 1288
                          v   i         ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (83 / 53)
Gap_init rate = 0.02 (13 / 863), avg. gap size = 6.31 (82 / 13)  


3179 26.87 0.77 0.77  chrX_69713911_69720299.rev     4991  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69713911_6   4991 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5040
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69713911_6   5041 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCAATCCCCATCAAGC 5090
                            v     v     iv i  i  i        i        i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69713911_6   5091 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 5138
                          v    ivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69713911_6   5139 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTGAATCCTCAGCCAAAAG 5188
                                viiv  ii  v  viv  v     ivv    i v ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69713911_6   5189 AACAAAACTGGAGGCATCACTCTTCCTGACTTCAAACTATACTACAAGGC 5238
                               ii      vv    v     ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69713911_6   5239 TACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATACAGACC 5288
                                 i   i    ii i       i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69713911_6   5289 AATGGAAAAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5336
                                v    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_69713911_6   5337 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT--T 5384
                          vi    i  i     ivv  v   i v  vvv           i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_69713911_6   5385 CCCAATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5434
                          ii--  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_69713911_6   5435 CTGAAATTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATG 5484
                         v    i     i    v   i     v     v        i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_69713911_6   5485 GTTTAAAGATTTGAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5534
                          v i ?   ii i     v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_69713911_6   5535 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5583
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_69713911_6   5584 TAAAACAGCAAAAGCAATGGCAACAAAAGCCAAAAGTGACAAATGGGATC 5633
                           vi   v        vvi          vv    vv  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_69713911_6   5634 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5683
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_69713911_6   5684 AACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5733
                           v  i     i   i             v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_69713911_6   5734 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 5783
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_69713911_6   5784 AAAAAACAAAGAACCCCATCAACAAGTTGGCAAAGGATATGAATGGACAC 5833
                             i     v     v  i? v  i v          v     i    i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_69713911_6   5834 TTCTCAAAAGAAGACATTTGTGCAGCCAAAAGACACGTGAAAAAATGCTC 5883
                              v        i  viiviii     v ii   i      i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_69713911_6   5884 ATCATCACTGGCCAT 5898
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3133 27.25 0.77 0.99  chrX_69730550_69736937     4986  5895 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69730550_6   4986 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5035
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69730550_6   5036 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5085
                            v     v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69730550_6   5086 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCC 5133
                          v   iivi i  i  ii     -   -- v  i  - iii    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69730550_6   5134 TATGGAACCAAAATAGGGCCTGCATTGCTAAGACAATCCTAAGCCAAAAG 5183
                                viiv  vi iv  v v  v  i  i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69730550_6   5184 AACAAAGCTGGAAGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5233
                                i    i vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69730550_6   5234 TACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATACAGACA 5283
                                 i   i    ii i       i iv ii i   v   i   iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69730550_6   5284 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACT 5331
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_69730550_6   5332 ATCTGACCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAAGGAT--T 5379
                          vi   ii  i     ivv  v   i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_69730550_6   5380 CCCAATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5429
                          ii--  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_69730550_6   5430 CTGAAACTGGATCCCTTCCTTACACTTTATACTAAAATTAATTGAAGATG 5479
                         v    ii    i    v   i    iv     v        i v  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_69730550_6   5480 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5529
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_69730550_6   5530 ACTTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5578
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_69730550_6   5579 TAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATC 5628
                           vi            vvi           v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_69730550_6   5629 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATGAGGGTG 5678
                          v  i   v v  i i   i  ii vv    i  v       v  ii   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_69730550_6   5679 AACAGGCGACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5728
                           v  i i   i   i             v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_69730550_6   5729 CAAAGGGCTAATATCCAGAATCTACAATGAACTGAAACAAATTTACAGGA 5778
                         i  i  i  vi          v  i  v     vvv    v iv i iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_69730550_6   5779 AGAAAACAAACAACCCCATCAACAAGTTGGTGAAGGATATGAACAGACAC 5828
                          i  i     i     v  i? v  i v  ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_69730550_6   5829 TTCTCAAAAGAAGACATTTATACAGCCAAAAAAAACACATGAAAAAATGC 5878
                              v        i  vi v ii     v  i--          i    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAG--CACATGAAAAGATGC 891

  chrX_69730550_6   5879 TCATCATCATTGGCCAT 5895
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (150 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3054 27.83 1.11 0.44  chrX_69757988_69764392     5011  5912 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69757988_6   5011 TGGAAGAACATTCCATGCTCATGGATAGGAATAATCAATATCATGAAAAT 5060
                              ii i  i     i        v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69757988_6   5061 AGCCATACTGCC-AAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5109
                         i  v     v  -  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69757988_6   5110 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTTA 5157
                          v   iivi i  i  ii     -   -- v  i  - iii    i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69757988_6   5158 TATGGAACCAAAAAAGAGCCCACATTA-CCAAGACAATCCTAAGCAAAAA 5206
                                viiv  ii  -    v v  -    i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_69757988_6   5207 GAACAAAGCTGCAGGCATCATGCTACCTGACTTCAAACTATATTACAAGG 5256
                                 i  v   vv   ii  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_69757988_6   5257 CCACAATAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGAC 5306
                          i   i   i   i    ii  i      i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_69757988_6   5307 CAATGGAACAGAACAGAGGCTTCAGACA-----CCACACATCTACAACCA 5351
                                 i    iv   iv i    v -----   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_69757988_6   5352 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5401
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_69757988_6   5402 TATTTAATAATTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5451
                          v  i  i  v           v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_69757988_6   5452 AAACTGGATCCCTTCCTTATAGCTTATAGAAAAATTAACTCAAGATGGAT 5501
                           ii    i    v   i i v v    v              i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_69757988_6   5502 TAAAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5551
                         i ?    i    i      v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_69757988_6   5552 TAGGCA-ATACCATTCAGGACATAGGCATGCGCAAAGACTTCATGACTAA 5600
                             ?i- v i -   iv   v v  vv iv    v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_69757988_6   5601 AACACCAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGGATCTAA 5650
                         i            vvi          v      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_69757988_6   5651 TTGAACTAAAGAGCTTCTGCACGGCAGAAGATACTATCATCAGAGTGAAC 5700
                          ii  v v  i i   i  ii vv  i i  i       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_69757988_6   5701 AGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 5750
                           i  i  i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_69757988_6   5751 AGGGCTAATGTCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5800
                         i  i  vi i        v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_69757988_6   5801 ACAGCAACAACCCCATGAAAAAGTAGGCAAAGGATATGAACAGACACTTC 5850
                          v vv  i     v  v?    i i          v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_69757988_6   5851 TCAAAAGAAAACATTTATGCAGCGAACAGACATATGAAAACATGCTCATC 5900
                           v      i i  vi viii  v  i ii  i       v       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_69757988_6   5901 ATCACTGGCCAT 5912
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (152 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2623 24.88 5.50 2.51  chrX_69776585_69778929     1009  1844 (501)    L1M4_orf2#LINE/L1        4   864 (44)  

  chrX_69776585_6   1009 AAAGATATCCCATGTTCATGGGTCAGAAGAGTGTATATTATTAAAGTGAC 1058
                                              i ii     v vv     i    ii  i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_69776585_6   1059 CAAACTGTCCAAAGTAATC---AGATTTAATGCAATCCCTATCAAAATAC 1105
                         v v   vi     v i   ---     i  i                 v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_69776585_6   1106 CAA-TGTCATTTTTCACAGAATTAGAAAAAATAATCCTAAAA-------- 1146
                           i-  i -     ii     v v  v  iv i         --------
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_69776585_6   1147 --------AAGAACTT-GAATAGCCAAAGCAATCCTGAGCAAAAACAACA 1187
                         -------- i i  ii-           i     i   ---    v  --
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAA-- 197

  chrX_69776585_6   1188 ACAACAACAACAAACAAAGCTGGCAGCATCATATTACCTGACT-CAAAAT 1236
                         -----------i       i   vi vv   i i v  ii i -     i
  L1M4_orf2#LINE/    198 -----------GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_69776585_6   1237 ATATTACAAACCTGTATTAACCAAAACAACATGATATTGGTATAAAAACA 1286
                         v  i      v  ii v   i   i   iii  i  i   i    ii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_69776585_6   1287 -ACACATAGACCAATGGAACAAAACAGATAATCCAGAAATAACTCCACAT 1335
                         -   i     i        i i  iv  v i           vi   i i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_69776585_6   1336 ATTTACAGCCAACTAATTTTTGACAAAGCAATCAAGAACAT--------- 1376
                              ii i   i i     i     i vvii     v   ---------
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_69776585_6   1377 --AAATTGGTCTCTTCAATAAATGGTGCTAGGAAAATTAGATATCCATAT 1424
                         -- i v i    i     i          i   v  i i    ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_69776585_6   1425 GCAGGAGAAAAAAATTGAACCCCTGTCTCTCACCATATACAAAAATCAAC 1474
                            ii    vi  i   i      ii   v                i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_69776585_6   1475 CCAAGATAGATTAAAGACTTAAATGTAAGACCTAAAACTATAAAACTACT 1524
                         i   i  i   i ?    i           v                vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_69776585_6   1525 AGAAGAAAACATAGGGA-AAATGCTTCAGGACATTGGTCTAGGCAAAGAT 1573
                                        ?i-    -    iv   v    vi       v i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_69776585_6   1574 GATATGGCTACAACCTCAAAA----AGACAACAAAAACACGAATAGACAA 1619
                         vviv i v  ii  vi     ---- ii        iv vi      i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_69776585_6   1620 ATGGTACCATATTAAA-TTAAAAGGCTTCTACACAGCAAAAGAAACAAT- 1667
                           v v  ivi  i   -      i-   i iii vv    i  v  v  -
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chrX_69776585_6   1668 AACAAATTAAAGAGACAACCTGTTGAATAGGACAAAAATATTTGCAAACT 1717
                           v   v i  i        iiiv    i   -i              ii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGA-GAAAATATTTGCAAATC 733

  chrX_69776585_6   1718 ATTCATTCTACAAGGGACTAATATCTGGAATATACAACATATTCAAACAC 1767
                           vi  iiv i        vi    ii       i  viv i  vv   v
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_69776585_6   1768 CTCAACAATTAAAAAA-----AATCTCATTAAAAAGTGAGGTAAAGGACA 1812
                              i   v    i -----  i iv   ?    i  -  i      iv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG-GGCAAAGGATT 832

  chrX_69776585_6   1813 TGAACAGACATTATTCAAAAGAAGACATACAA 1844
                             i       vi  v        i      
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAA 864

Transitions / transversions = 2.09 (138 / 66)
Gap_init rate = 0.02 (19 / 861), avg. gap size = 3.53 (67 / 19)  

 238 18.33 0.00 1.67  chrX_69776585_69778929     2091  2150 (195)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_69776585_6   2091 AAAAAAGGCATACAAATGGCCAAACAAGTATATGAACAAATTTTCAATAT 2140
                            i   ii              -i   i i     v i  vi    i  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGATGCTCAACAT 898

  chrX_69776585_6   2141 CACTAATCAT 2150
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1)  


2925 28.36 1.45 0.44  chrX_69782719_69789101     4992  5890 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69782719_6   4992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCGTGAAAAT 5041
                              ii i  i     i      i v      v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69782719_6   5042 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 5091
                            v     v     iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69782719_6   5092 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTTA 5139
                          v   iivi i  i  ii     -   -- v  i  - iii    i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69782719_6   5140 TATGGAAACAGAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAAG 5189
                                 iiv  ii  v  viv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69782719_6   5190 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGTC 5239
                                i      vv       v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69782719_6   5240 TACAGTAACCAAAACAGCATGACACTGGTACTAAAG-CAGATATATAGAC 5288
                                 i   i    ii  ii     i -   i -i   i       i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGAT 297

  chrX_69782719_6   5289 CAATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATGTACAACCA 5338
                                 i    iv   ivii         vv   i    v  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_69782719_6   5339 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGG-AAAGGATTCCC 5387
                         vi    i  i     ivv  v   i v  vvv      -    i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_69782719_6   5388 TATTTAATAAATAGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAGCTG 5437
                          v  i  i    i         v      v  ?   i   iii  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_69782719_6   5438 AAACTGGATCCCTTCCATACAGCTTATACAAAAATTAATTCAAGATGGAT 5487
                           ii    i    v  vi   v v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_69782719_6   5488 --------TAAATGTTAGACCTGAAACCATAAAAAACCTAGAAGAAAATC 5529
                         --------       v   v  i    i      vv i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_69782719_6   5530 TAGGCA-ATACCATTCAGGGCATAGGCACTGGCAAAGACTTCATGACTAA 5578
                             ?i- v i -   iv i v v  vviv     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_69782719_6   5579 AACACCAAAAGCTATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5628
                         i           vvvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_69782719_6   5629 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAG 5678
                          i   v v  i i   i  ii vv    i  v  i i  vv i      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_69782719_6   5679 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5728
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_69782719_6   5729 AGGGCTAATACGCAGAATCTACAATGTACTCAAACAAATTTACAAGAAAA 5778
                         i  i  vi  iv      v  i  v v    vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_69782719_6   5779 AATCAAACAGCCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 5828
                          iv    i i   v  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_69782719_6   5829 TCAAAAGAAAACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5878
                           v      i i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_69782719_6   5879 ATCACTGGCCAT 5890
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (155 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


2095 22.27 3.04 0.61  chrX_69821227_69824663     1577  2070 (1367)    L1M4_orf2#LINE/L1        1   506 (402)  

  chrX_69821227_6   1577 TGGAAATACATCCCACATTCACAGATTGGAATAATTAATATTGTTAAAAT 1626
                               v i      ii    ii        v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69821227_6   1627 GTCCATACTACCTAAAATGATCTACAGATTCAATGTAATAC-TATCAAAA 1675
                          v v     v  i   v                i i   v -        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69821227_6   1676 TCTGAATGGCATTCTTTACAGATAG-GAAAAAC-AATCCTAAAATTCATA 1723
                           iv iiv  v  i   i    v v-  v  i -i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_69821227_6   1724 TAAAATCATA-AAAGAATCCA-AATAGCCAAAGAAATCTTGCGCAAGAAG 1771
                          ii  --  i-  i i i   -          iv       viv      
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69821227_6   1772 TACAAACCCAGGAGCATCATGCTTCCTCATTTCAAAATTTATTACAAAGC 1821
                         v     viii ii vv   ii     iv         i   i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69821227_6   1822 TATAGTAATCAAAACAGTATGGTACTAGAATAAGAACAAACATATACACT 1871
                           i         i     i       i v     i i i       v ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69821227_6   1872 AATGGAATAGAATAGAAGAG-CCAGAAATAAATCCACACATTCACAGGCA 1920
                                      v  -   -           i   i     i ii v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_69821227_6   1921 ACTGATCTTCAACATGAGTGCCAAGAACACACAATGAAGAAAAGACAGTC 1970
                          i    i   i   v i         v  iv     ii    ii i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_69821227_6   1971 TCTTCAGTCA---GTGTTGA------TGGATATCAACATGCAAAATAATG 2011
                          i    iiv ---   i  i------      ? v          v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_69821227_6   2012 AAATTGGACCCTTATATCACACTGTATACAAAAATCAACTCAGAATAAGT 2061
                           i        i  iv      ii           i      i   iii 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_69821227_6   2062 TAAAGACTT 2070
                         i ?    i 
  L1M4_orf2#LINE/    498 CAWAGACCT 506

Transitions / transversions = 2.27 (75 / 33)
Gap_init rate = 0.02 (10 / 506), avg. gap size = 1.80 (18 / 10)  

1526 20.80 0.47 6.62  chrX_69821227_69824663     2522  2944 (493)    L1M4_orf2#LINE/L1      512   908 (0)  

  chrX_69821227_6   2522 TAATACCTGAAACCGTAAAACTTTTAGAAGAAAACA-AGGGA-AAAGCTT 2569
                            v v  i    ii       i             -   ?i-   v   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_69821227_6   2570 CTTGACATTCATCCTGGCAATGAGTTTTTGTATATGACTCTAATAGCACA 2619
                          v    v  viviiv       iv  i  iv       v i  v      
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_69821227_6   2620 GGCACCAAAAACAAAAATAGACAAGTGGGATTGCATCAAACTAAAATGCT 2669
                         i   v     iv         i  i v   i v       v v   vi  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_69821227_6   2670 TCTGCACAGCAAAGAAACCCCATCAACAGAGTGAAAAAGCATCCTACAAA 2719
                          i  ii vv     i - v i     v i        ii  v  i   i 
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGA-CACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_69821227_6   2720 ATGAGACAAAATATTTGCAAACCATATATCTGATGAGGAATTAATGTGCA 2769
                            i  v              i            i   i i vi i v  
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_69821227_6   2770 AGATATGTAAGGAACTCATACAACTCAATAGCAAAACAAAAAACAAAACA 2819
                         ii    i   i      v            ii    --------------
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAA-------------- 796

  chrX_69821227_6   2820 AAACAAAACAAAAACCAGATAGCTCAATTTAAAAATGGGCAAATGATCTG 2869
                         ----- i     -------  i i     ?             v   i  
  L1M4_orf2#LINE/    797 -----AGACAAA-------TAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_69821227_6   2870 AATAGACCATTTCTTCAAAGAAAATATACAAATGGCCAACAGGTGTATGA 2919
                                -      i       i                i i iii    
  L1M4_orf2#LINE/    835 AATAGAC-ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_69821227_6   2920 AAAAGTGTTGAACATTACTAATTGA 2944
                            ii  i v     i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (56 / 30)
Gap_init rate = 0.02 (6 / 397), avg. gap size = 5.00 (30 / 6)  


3010 26.55 3.04 0.90  chrX_69840870_69847244     4994  5882 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69840870_6   4994 TGGAAGAACATTCCATGCTCATGGGTAGAAAGAATCAATATCGTGAAAAT 5043
                              ii i  i     i      i v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69840870_6   5044 GGCCATACTGCCCAAGGTAATTTATAGTTTCAATGCCATCCCCATCAAGC 5093
                            v     v     iv i  i  i  v     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69840870_6   5094 TACCAACAACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5141
                          v   i vi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69840870_6   5142 TACGGAACCAAAAAGAGCCCACATT-GCCAAGACAATCCTAAGCCAGAAG 5190
                           i    viiv  i ii    v v -     i      i i ivv     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69840870_6   5191 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5240
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69840870_6   5241 TACAGTAACCAAAACAGCATGGTACTGGTAC------------------C 5272
                                 i   i    ii         i i------------------ 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69840870_6   5273 AA---AACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5317
                           ---  i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_69840870_6   5318 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5367
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_69840870_6   5368 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5417
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_69840870_6   5418 GAAGCTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5467
                             i    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_69840870_6   5468 TTAAAGACTTAAACATTAGACCTAAAACCATAAAACCCCTAGAAGAAAAC 5517
                          i ?    i    ii v   v       i       i i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_69840870_6   5518 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5566
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_69840870_6   5567 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCCA 5616
                         vi            vvi          vv     v  i    v   iiiv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_69840870_6   5617 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGGAACTACCATCAGAGTGAA 5666
                           i   v v  i i   i  ii vv    i iv    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_69840870_6   5667 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5716
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_69840870_6   5717 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5766
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_69840870_6   5767 AAAACTAACAATACCATCAACAAGTGGGCGAAGGATATGAAGAGGAGACA 5816
                           i  v  i  iv v  i? v  i     i      v    v  ---   
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG---ACA 842

  chrX_69840870_6   5817 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 5866
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_69840870_6   5867 CATCATCACTGGCCAT 5882
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (141 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.18 (35 / 11)  


2973 27.36 0.55 0.77  chrX_69865497_69871659     4761  5670 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69865497_6   4761 TGGAAAAAAATTCCATGCTCATGGATAGGAAAGATTAATATCATGAAAAT 4810
                               i v  i     i        v    iiv       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69865497_6   4811 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 4860
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69865497_6   4861 TACCA-CTGACTTTCTTCACAGAACTAGAAAAAACT-ACTTTAAATTTCA 4908
                          v   -   v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_69865497_6   4909 TATGGAACCAAAAAAGAGCCCGTGTAGCCAAGACAATCCTAAGCAAAAAG 4958
                                viiv  ii  v  v vi       i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69865497_6   4959 AACAAAACTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5008
                               ii      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69865497_6   5009 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAAATATATATACA 5058
                                 i   i    ii  i      i iv ii i i i     v i-
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT- 297

  chrX_69865497_6   5059 CCAATGGAACAGAACAGAGGCTTCAGAAATAACACCACCCATCTACAACC 5108
                         -        i    iv   iv i         vv   iv   i  iiii 
  L1M4_orf2#LINE/    298 -CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_69865497_6   5109 ATTCGATCTTCAACAAACTTGACAAAAAAAAAGCAATGGGGGAAGGATTC 5158
                          v i   i   i    ivv  v   i vv v-v        i   i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAG 395

  chrX_69865497_6   5159 CCTATTTAATAAATG-TGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 5207
                         i  v  i  i     -  i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_69865497_6   5208 AGAAACTGGATTCTTTCCTTACACCTTATAAAAAAATTAACTCAACATGG 5257
                         v   ii    ii i v   i     v    v              v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_69865497_6   5258 ATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5307
                           i ?    i    ii     v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_69865497_6   5308 TGTAGGCA-ATACCATTCAAGACATGGGCATGGGCAAAGACTTCATGACT 5356
                         ii    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_69865497_6   5357 AAAACACCAAAAGCAATTGCAGCAAAAGCCAAAATTGAAAAATGGGATCT 5406
                          vi            vvv   i      vv     v  v    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_69865497_6   5407 AATTAAACTAAAGAGCTTCTGCACAGGAAAAGAAACTATCGTCAGGGTGA 5456
                         v  i   v v  i i   i  ii vvv   i  v      ivv ii    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_69865497_6   5457 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCCATCTATCCGTCTGAC 5506
                          v  i     i                 v     v vii  vii     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_69865497_6   5507 AAAGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAA 5556
                           i  v  vi          v  i  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_69865497_6   5557 AAAAACAAACAACCCCATCAAAAAGTAGGCGAAGGATATGAACAGCCACT 5606
                            i     i     v  i?    i i   i      v    i  v  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_69865497_6   5607 TCTCAAAAGAAGACATTTTTGAGGCCAAAAAAACATATTAAAAAA-GCTC 5655
                             v        i  vivviv      v  i-  i  v    i -    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTC 893

  chrX_69865497_6   5656 ATCATCACTGGTCAT 5670
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (140 / 105)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.09 (12 / 11)  


2965 28.24 0.89 0.33  chrX_69892596_69899651     5661  6563 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69892596_6   5661 TGGAAAAAAATTCCATGCTCATGGATAAGAAGAATAAATATCATGAAAAT 5710
                               i v  i     i        vi     v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69892596_6   5711 GGGCATACTGACCTAAGTAATTTATAGATTCAATGCTATTCCTACTAAGC 5760
                           vv     vv  v  v i  i  i        i  v  i    ii  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69892596_6   5761 TATCATTGACTTTCTTTGCAGAATTAGAAAAACT-ACTTTAAATTTCATA 5809
                          vi  vivi i  i         v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_69892596_6   5810 TGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGAA 5859
                              viiv  ii  v  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_69892596_6   5860 CAAAGCTGGAGGCATCACGCTGTCTTACCTCAAATTATACTAATAGGCTA 5909
                              i      vv    i  vi iv ii     viv     vv i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_69892596_6   5910 CAATAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 5959
                           i   i   i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_69892596_6   5960 TGGAACAGAACAGAAGCTTCAGAAATAACACCACACATCTACAACCATCT 6009
                              i    iv  iiv i         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_69892596_6   6010 GATCTTCAACAAACTTGACAAAAGCAAGCAATGGGGAAAGGATTCCCTAT 6059
                            i   i    ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_69892596_6   6060 TTAATAAATGGTGCCAGGAAAACTGGCTAGCCATACGCAGAAAACAGAAA 6109
                          i  i         ii   v      v  ?   i i   i  i vv   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_69892596_6   6110 CCGGATCCCTTCCCTACACCTTATACAAAAATTAACTCAAGATGGATTAA 6159
                         ii   i    v  ii     v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_69892596_6   6160 AGACTTAAATGTAAAACCTAAAACCATAAAAGCCCTAGAAGAAAACCTA- 6208
                             i         i v       i      vi i           v  -
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_69892596_6   6209 -CACAATACCACTCAGGACATGGGCATGGGCAAAGACTTCATGACTAAAA 6257
                         -?ii  - i -i  iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    551 GNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_69892596_6   6258 CACCAAA-GCAATGGCAAGAAAAGCCAAAATTGACAAATTGAATCTAATT 6306
                                -   vvi    v     vv     v  i      i ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_69892596_6   6307 AAACTAAAGAGTTTCTGCACAGCCAAAGAAACTACCATCAGAGTGAACAG 6356
                            v v  i ii  i  ii vv v  i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_69892596_6   6357 GCAACCTACAGAATTGGGAGAAAATTTTTGCAATCTATCCATCCGACAAA 6406
                         i     i       -          v       vii  vi   i  i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAAT-GGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_69892596_6   6407 GGTCTAATATCCAGAATCTACAAGGACCTTAAACAAATTTACAAGAAAAA 6456
                           v  vi          v  i  i  v  ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_69892596_6   6457 AACAA----CCCCATCAAAAAGTGGGCAAAGGATATAAACAGACACTTCT 6502
                         i    ----   v  i?    i            v i  i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_69892596_6   6503 CAAAAGAAGACATTTATGCGGCCAGCAAACATATGAAAAAAAGTTAATCA 6552
                          v        i  vi vii     ii  i  i       i v i v v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_69892596_6   6553 TCACTGGTCAT 6563
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (148 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


1193 24.57 1.04 1.04  chrX_69921095_69923316.rev      491   779 (1443)    L1M4_orf2#LINE/L1      245   533 (375)  

  chrX_69921095_6    491 AAACTATAGCAGTAATCAAG-CAGCATGATATTAGGATAAAAACAGATGC 539
                           i   ---           -   ii  i  i i v    ii i   iii
  L1M4_orf2#LINE/    245 AAGCTA---CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_69921095_6    540 ATTGACCAGTGGAATTAGATAGAGAGCCCAGAAATAAACCCACAAATCTA 589
                           v  i  i      vii  v     i               i v  i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_69921095_6    590 TGGTGAATTAATTTGCAACA--GGTACCAAGAACACAAAAAGGGGAAAGG 637
                             v    i    v i   --   i      v  ivv  v        i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_69921095_6    638 GCAGTCTCTTTAATAAATTGAGTTGAGAAAACTGGATATCTACATACAGA 687
                         ii     i  i  i    v v i  i  v         ? i    i  i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_69921095_6    688 AGAGTAAAAATGGACCGTTATCTCATCCGTTATATAAGAATCAACTCAAA 737
                            i i  iv      vi  i    iv vv    i  i   i        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_69921095_6    738 ATGGATTAAAGACTTAAATGTAAGGCTTAAAATTATAAAATT 779
                               i ?    i          ivi     i       i 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

Transitions / transversions = 2.45 (49 / 20)
Gap_init rate = 0.01 (3 / 289), avg. gap size = 2.00 (6 / 3)  

 377 25.45 3.64 0.00  chrX_69921095_69923316.rev     1106  1215 (1007)    L1M4_orf2#LINE/L1      513   626 (282)  

  chrX_69921095_6   1106 AAGAAGCAAAATTA--AAACTACCAGAAGAAAACAGAGGA--AAAGTTCC 1151
                             ivi    i  --     vii           v   ?--   vi i 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_69921095_6   1152 ATGACATTAGTCTGGGCAGAGATTTTTTTGATATGACCTCAAAAGCACAG 1201
                         i    v  i vi i    iv i   i  v        vi          i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_69921095_6   1202 ACAACAAAAGCAAA 1215
                         i         v   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAA 626

Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.02 (2 / 114), avg. gap size = 2.00 (4 / 2)  

 600 22.07 15.32 0.90  chrX_69921095_69923316.rev     1502  1723 (499)    L1M4_orf2#LINE/L1      610   863 (45)  

  chrX_69921095_6   1502 CAAAAAAAAAAAAAAAAAAGAAAAGCAAATGGGATTGCCTCAAACTAAAA 1551
                            iv  v    i      v i --i    v   i v v     v v   
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGA--TAAATTGGACTTCATCAAAATTAAA 657

  chrX_69921095_6   1552 AA-------ACT-------GCACTA------GAGTGGA--GACAACCCAT 1579
                           -------i  -------i     ------i    i --         i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_69921095_6   1580 -GAACTGGAAAAAATATTTGCAAATTATACATTGGGTAAGGGGCTAATAT 1628
                         -   iv   i               i   i  iv i      i  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_69921095_6   1629 CTAAAATATACAAGGAGCTCCAACTGCTTAATAATAAGAAAACAAACAAC 1678
                          i i      i  i  i   iv  vi  i        i  i     i   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_69921095_6   1679 TCTATT-AAAAGTGGGCAAAGCAT----------ATTTCTCAAAAGAAGT 1717
                         i v   -    i         v  ----------       v       v
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_69921095_6   1718 CATACA 1723
                         i     
  L1M4_orf2#LINE/    858 TATACA 863

Transitions / transversions = 1.88 (32 / 17)
Gap_init rate = 0.03 (8 / 254), avg. gap size = 4.50 (36 / 8)  


3201 26.27 0.99 0.77  chrX_69941082_69947482.rev     5005  5910 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_69941082_6   5005 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5054
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69941082_6   5055 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5104
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69941082_6   5105 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5152
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_69941082_6   5153 TTTGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAACCCTAAGCCAAAAG 5202
                          v     viiv  ii  v  v v  v     iv   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_69941082_6   5203 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAAGC 5252
                                i      vv    i  v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_69941082_6   5253 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5302
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_69941082_6   5303 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5350
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_69941082_6   5351 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5400
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_69941082_6   5401 CTATTTAATAAATGGTGCTGGGAAATCTGGCTAGCCATATGTAGAAAGCT 5450
                           v  i  i              v v    v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_69941082_6   5451 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5500
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_69941082_6   5501 TTAAAGACTTAAACGTTAGACCTAAAACCGTAAAAACTCT-AGAGGAAAA 5549
                          i ?    i    i  v   v       ii     -    -   i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_69941082_6   5550 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5599
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_69941082_6   5600 AAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTA 5649
                         vi            vvi     v    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_69941082_6   5650 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5699
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_69941082_6   5700 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5749
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_69941082_6   5750 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5799
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_69941082_6   5800 AAAA-AAACAACCCCATCAAAAAGTGGGCAAAGGATATGA-CAAACACTT 5847
                           i -   i     v  i?    i            v   -i i   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_69941082_6   5848 CTCAAAAGAAGACA--CTGATGCAGCCAAAAGACACGTGAAAAAATGCTC 5895
                            v        i -- vi   --     v ii   i      i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTC 893

  chrX_69941082_6   5896 ATCATCACTGGCCAT 5910
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3822 15.50 0.60 0.75  chrX_69956974_69960784     1340  2010 (1801)    L1M4_orf2#LINE/L1        1   670 (238)  

  chrX_69956974_6   1340 TGGAAAAATATGACATGTTCATGGATCAGAAGACTTGATATTGTTAAGAT 1389
                               i    vv             ii        i             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69956974_6   1390 GGCAATACTCCCTAAATTGATCTACAGACTTAGAGCAACAGCCATCGAAA 1439
                                     i               i i iv    ivv i   i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69956974_6   1440 TTCCAATTGGCTTCTTTGCAGAAACTGGTAAAGTGATCCTAAAATTTGTT 1489
                          i   ii  v   i          i  ii  iv             ii v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_69956974_6   1490 TGGAAATTTGAGAGCCCCAGAATAGTCAAAACAGTTTTGAAAAATATGAA 1539
                                vii  i v          i       i i        v v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_69956974_6   1540 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 1589
                                                                           
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_69956974_6   1590 CAGTAATCTATACAATGTGATACTACCATAAGGACAGACA----GATCAA 1635
                                 v v   i    i    iv        i     ----      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_69956974_6   1636 CGGAATACAGTTCAGAGTCCAGAAATAAACGCTCTCATTTAGAGTCAATT 1685
                         i      v i  v                 v viv      vi       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_69956974_6   1686 GGTTTTTGACAAGGGTGCCAAGACAATGCAATAGGAGAAAGAGTAACCTT 1735
                          i    i                 v  v    i  -      i  ii   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTT 399

  chrX_69956974_6   1736 TTAAACAAATGGTGGTGGGACAATTAGATCTCCACATAAAAAAGAATGAA 1785
                           v           v        i i   v?      iv           
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_69956974_6   1786 GCTGGACCCCCTTACCTCACACTGTATACAAAAACTAACTGAAAATGGAT 1835
                          i        --          ii          i     v         
  L1M4_orf2#LINE/    450 GTTGGACCCC--TACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_69956974_6   1836 CAAAGACCTAAATATAAGCACCAGAAGTATAAAACTTTTATAAGCAAACA 1885
                           ?          i    vi i i  v         i   v   v     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_69956974_6   1886 TAGGTATAAATCTTCATGACCTTGGATTTGGCAATGGATTCTTAGATATG 1935
                             ?i         i         i  v        v            
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_69956974_6   1936 ACACCAAAACCACAAGCAACAGAATTTAAACAATAGATAAACTGGACATC 1985
                                  v           i  --v   v          i     v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAA--GAAAAAATAGATAAATTGGACTTC 645

  chrX_69956974_6   1986 ATGAAAATTTAAAACTTTTTTATTT 2010
                           v      v         v ii  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTT 670

Transitions / transversions = 1.46 (60 / 41)
Gap_init rate = 0.01 (4 / 670), avg. gap size = 2.25 (9 / 4)  

 646 13.16 5.26 0.00  chrX_69956974_69960784     2306  2419 (1392)    L1M4_orf2#LINE/L1      649   768 (140)  

  chrX_69956974_6   2306 AAAATTAAAAACTTTTGTTCTTCAAAGAATATCATCAAGAAA------AG 2349
                                           v        i i ii         ------  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_69956974_6   2350 ACAACCCATGGAATAGGAGAAAATATTTGCAAATGATATATCTGATCAGA 2399
                                 ii    i                   v           v  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_69956974_6   2400 GATGTGTCTCTAGAATATAT 2419
                           iv   v  i         
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATAT 768

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.01 (1 / 120), avg. gap size = 6.00 (6 / 1)  

 534 17.50 0.83 0.00  chrX_69956974_69960784     3199  3318 (493)    L1M4_orf2#LINE/L1      788   908 (0)  

  chrX_69956974_6   3199 ACAATAAAAATA-AGATGATGCAATTTTAAAATAGGCAAAGCATCTAAAT 3247
                          i        v - i  i iv     ?v     i       v  i i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_69956974_6   3248 AGACATTTCTTCAAAGAAGATATGCAAATAACCAACAAGAACAGGAAAAG 3297
                                   i            i     ii    i   v   v      
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_69956974_6   3298 ATGGTCAATATCACTAGTCAA 3318
                            v    i    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.01 (1 / 121), avg. gap size = 1.00 (1 / 1)  


1073 24.51 0.00 1.17  chrX_69994316_69998770.rev     2380  2636 (1819)    L1M4_orf2#LINE/L1        1   254 (654)  

  chrX_69994316_6   2380 TAGAAAGATATTCCATGTTCATGGACTGAAAGAATCAATATTGTTAAAAT 2429
                          i         i             i  i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_69994316_6   2430 GGTCATACTACGAAAAGCAATCTGAAGATTCAATGTAATCCTTATCAAAA 2479
                           iv     v vv   vii    iv        i i     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_69994316_6   2480 TACCAATGACATTCTTCGCAGAAATAGAAAAAACAATCCTAAAATTTATG 2529
                          v   iivi v  i  i        v  v  ivii           i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_69994316_6   2530 TGGAACCACAAAAGACCCTGAATAGCCAAAGCTATCCTAAGCAAAAAGAA 2579
                              vii   ii     v           i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_69994316_6   2580 CAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGGCCAG 2629
                             ii       v     i v  ii i      viv       i---  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA---AG 247

  chrX_69994316_6   2630 GCACAGT 2636
                         vi     
  L1M4_orf2#LINE/    248 CTACAGT 254

Transitions / transversions = 1.86 (41 / 22)
Gap_init rate = 0.00 (1 / 254), avg. gap size = 3.00 (3 / 1)  

1445 22.74 0.62 0.31  chrX_69994316_69998770.rev     2927  3247 (1208)    L1M4_orf2#LINE/L1      232   553 (355)  

  chrX_69994316_6   2927 AAAATTATACTACAGAGCTATAGTAACCAAAACAGCATGGTACTGGCATA 2976
                             i -       i     i     i   i    ii             
  L1M4_orf2#LINE/    232 AAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_69994316_6   2977 AAAACAGACATA--GACCAATGGAACAGAATAGAGAACCCAGAAACAAAT 3024
                          ii i       --  i        i     v    ii       i   i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_69994316_6   3025 CCATACAACTATAGTAAACTAATCTTCAACAAAAGTGTCCAGAACATACA 3074
                                vi   i  v  i i  i   i    ii   i v   v   v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_69994316_6   3075 AAGGGGAAAGGACAGTCTCTTTAATAAATACTGCTGAGAAAACTGGCTAT 3124
                          v        i i     i  i  i    iv     i  v      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_69994316_6   3125 CCATATGCAGAAGAATGAAACTAGATCCCTTTATCTTGCCATATACAAAA 3174
                            i     i         ii i  i    viv  vii            
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_69994316_6   3175 ACCAAATCAAAATGGATTAAAGACATAAACCTAAGACCTCAAACTATGAA 3224
                          ii  v           i ?    v    iv     v  v       i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_69994316_6   3225 ATTACTAAAAGAAAATATTGGGG 3247
                          i vi  i       i  v  ? 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNG 553

Transitions / transversions = 2.50 (50 / 20)
Gap_init rate = 0.01 (2 / 322), avg. gap size = 1.50 (3 / 2)  

1540 21.67 1.39 0.00  chrX_69994316_69998770.rev     3605  3964 (491)    L1M4_orf2#LINE/L1      544   908 (0)  

  chrX_69994316_6   3605 AATATAGG---AACTCTCCAGGACGTTGGGCTGGGCAAAGATTTCTTGAA 3651
                           i     ---  v   i iv   v     i i     v i      ii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_69994316_6   3652 GAATACCCCACAAGCACAGTCAACCAAAGCAAAAATGGACTAATGGGATC 3701
                         v vv  v   v       iv    v    v      i  iv   v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_69994316_6   3702 ACATCAAG-TTAAAAACTTCTGTACAGCAAAGGACACAATCAACAAAGTG 3750
                         v      i-          i   i vv          v     v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_69994316_6   3751 AGGAGAGAACCCACGGAATGGGAGAAAATATTTGCAAACTATCTGTCTGA 3800
                          ii   v       i                       ii  v i     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_69994316_6   3801 CGAGGAGTTAATAATCAGAATATATAAGAAGCTCAAATAACTCTATAGAA 3850
                         ii   iii vi  vi            ii i   vv i     v   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_69994316_6   3851 AAAAATCTAATAATCCGATTTAAAA-TGGGCAAAAGATCTGAATAGACAT 3899
                             iv v     i  i   ?    -        i   i           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_69994316_6   3900 TTCTCAAAAGAAGACATACAAATGGCAAACAGGTATATGAAAAGATGTTC 3949
                              v        i           v  i i i i           i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_69994316_6   3950 AACGTCAATCATCAG 3964
                            i   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (46 / 31)
Gap_init rate = 0.01 (3 / 365), avg. gap size = 1.67 (5 / 3)  


3050 22.73 5.40 1.72  chrX_70036599_70038855      894  1764 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_70036599_7    894 AGATATACCATGATCATGAGTTAGAAGACACAATATTGTTAAGATGTAAA 943
                               v     v     ii  i      vi               vv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_70036599_7    944 TCCTCCCAGAATTCTTCTATAGATTCAATACAAGAGCAGTCATAATACTA 993
                          v     vi    vv    i        ii   vvv vi   v   v i 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_70036599_7    994 CCAGGTTTTTTAAAGAGAAATGGACAAACTGATTCTAAAATGTATATGGA 1043
                         v v vi     viv-      v     i     i       vi       
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGC-AGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_70036599_7   1044 AATGGAAAGGATCTAAAATATCCAAAACGATCTTGAAAAACAACAGCAAA 1093
                             v  i   i i i    v       i           v  v i    
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_70036599_7   1094 GTTGGAAGACCTATA-TTCCTGACATTAAGACTTACTATAAAACTACAGT 1142
                               i   ii i -    ii iv i  i        i   i       
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_70036599_7   1143 ACTTAA------------------------TAGATAAATAGATCAATGGC 1168
                          v i  ------------------------    i v            v
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_70036599_7   1169 ACAAAATACAGAGCCCAGAAATAAACTTGCACATATAAAGTCA-TTGATT 1217
                          i i   vv    i            iiii    v  vi    -      
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_70036599_7   1218 TTTGATCAAG-----CAA---TGTTGAATTGGGGAAAGGAAAGTCTTTTC 1259
                           i  -    -----   ---ii  v   -        i v         
  L1M4_orf2#LINE/    355 TTCGA-CAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTTTTC 402

  chrX_70036599_7   1260 AACAAATGGTGCTAGAATAACTGGATATTCATTTGGGAAA-AATAAACCT 1308
                                      i i i         ?i  iv  vi   -   i  vi 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_70036599_7   1309 CAACCCCAACCCCACATCACACCCAAAAACCAACTGAAGATGGATCATGA 1358
                         vi     v   i    i  i iv      ii    v  i        ?--
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW-- 500

  chrX_70036599_7   1359 CACTAAACATATAATATAAATGCTAAAACTCTAAAGCTTCTAGAAGAAAA 1408
                         ---- i  v  -   i   iv         v    i  ii          
  L1M4_orf2#LINE/    501 ----AGACCTA-AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_70036599_7   1409 TCCAGAAGAGAATCTTTGGGACTTAGGGATAAACAAAGATCTTTTAGA-- 1456
                         ivi  i? vi      i v   i v   v  ii   v i i i     --
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_70036599_7   1457 --ACACAGAAAGCTATAGTCATAAAAGAAAAAAAAATGATAAATTAGAAT 1504
                         --    vi     vvv  iv i           v --        i  v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACT 643

  chrX_70036599_7   1505 TCACTGAATTTTAAAATCTTCT---CATGAAAAACTACTATTAAGAAAAT 1551
                            iii  v  v    -   i --- v v   iivi     i      i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_70036599_7   1552 GAATAGGCAAGC-ACAGACTAAGAGAAAATACTTGAAAAACATATATCTG 1600
                            v  i   v -     v ii         i   v   v          
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_70036599_7   1601 ACAAAGGACTTGTAAGCAGAATATATAAAGAACTCTTACAAATCAATCAT 1650
                          i  i         vv                         v     v  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_70036599_7   1651 TTAAAAATGGATTTAATCCAACTTTAAAATGGACAAAAGATTTGAATAGA 1700
                         vv   i iii  --  i    i ?v       i    i            
  L1M4_orf2#LINE/    793 AAAAAGACAAAT--AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_70036599_7   1701 TATTT----AGCAAAGATATTTGAATGGTCAATAAGCACATGAAAAAGTG 1746
                         i    ---- ivi       vii     i                 ii  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_70036599_7   1747 CTTGACATCATTAATACT 1764
                           ii      ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (116 / 78)
Gap_init rate = 0.02 (18 / 903), avg. gap size = 3.44 (62 / 18)  


2071 21.91 8.32 9.79  chrX_70277623_70280749.rev     1422  2238 (889)    L1M4_orf2#LINE/L1        2   806 (102)  

  chrX_70277623_7   1422 GGGAGAACACCTGATGATTGTGGATCACAAGGCCTAATGTTGTTAAAATG 1471
                           i ii i i iv   v ii     iiv   i i    i       i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_70277623_7   1472 ACAATCTTCCCCAAGTTAACCAACAAATTCAATGCAATCCCTATCAGAAT 1521
                         i    vi       i  i i v   i      i             i   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_70277623_7   1522 CCTAA--G--TTATTTGTAGAATTTGACAAGCTGATTCTAAAATTCATAT 1567
                           i i-- --  v    i    v             i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_70277623_7   1568 GGAATTCCCAGGGACCTAGATTAGCCAAAACAACTTTGATAAAACAAGAG 1617
                             v v v       i   v            ii    -    v    i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAGAA 200

  chrX_70277623_7   1618 CAAAATTGGAGGACTCACACTTCTTTTTTTT----TTTTCTCTTTCGCTC 1663
                             i                  iivv   i----i  v  vivvv   v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_70277623_7   1664 TCTCTCTCTCTTTTTTTTTTTTTAA-CAAGCTCTTGT----CAGGC-CGA 1707
                         ivv-------------------   -    vivv   ---- v   -ii 
  L1M4_orf2#LINE/    251 CAG-------------------TAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_70277623_7   1708 GGACTCACATTT---TCTAATTTTTTTTTTTTTTGAGATGGAGTCCTGAG 1754
                            ivv    v ---  -   ------------- ii  i  i --    
  L1M4_orf2#LINE/    282 GGATAGACATATAGATC-AAT-------------GGAATAGAAT--TGAG 315

  chrX_70277623_7   1755 TAGCTGGGATTACAGGCATGCACCACAACGCCCGGCTAATTTTTG----- 1799
                         viv ii i v  v vv   i  iiv-- i vi iii i     i -----
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTT--ATGGTCAATTGATTTTCGACAAG 363

  chrX_70277623_7   1800 --TATT-------TTTAGTAGAGATGGGGT------TTCACCA-----TG 1829
                         -- iii-------  i i i i  vi ii ------    v  -----  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_70277623_7   1830 TTGG-------------CCA---------GGCTGGTCTCGAACTCTTGAC 1857
                         i   -------------   --------- iv  ivv i i  i i -  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT-AC 462

  chrX_70277623_7   1858 CTCAAGTGATCCACCCACCTCTGCCTCCCAAAGTGCTGGGATTACAGGCG 1907
                             viiv  vi  vv vv - iv   --   i  ----   i ?  i v
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAAT-TAACTC--AAAATG----GATCAWAGACC 505

  chrX_70277623_7   1908 TGA--GCCACTGCGCCTGGACTATAAAACTGTTAGAAGAAAACATAAAGA 1955
                          i -- iv -- v  ivii           v               ii?i
  L1M4_orf2#LINE/    506 TAAATGTAA--GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_70277623_7   1956 TAAATCTTCATGACCTTGAATTTGGCAATGAATTCTTAAATATAACACCC 2005
                                  i        ii  v       iv      i    i     v
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_70277623_7   2006 AAAGCAAAGACATCAAAAGAAAAAATAGATAACTTGGACCACATCAAAAT 2055
                               v ii  v                   v      iv         
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_70277623_7   2056 GAAAACTTTTGGGGGGGGTGTCCTAAAAAAATTAAAACTTTTATGCTTCA 2105
                         -----------------------      --------     i       
  L1M4_orf2#LINE/    654 -----------------------TAAAAA--------CTTTTGTGCTTCA 672

  chrX_70277623_7   2106 AATTACATTATTAAGAAAATGAAAATTTCAAC--ACTGAATGGGAAAAAA 2153
                           vv   i   i      i      vv-    --  v        i    
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGA-CAACCCACAGAATGGGAGAAAA 721

  chrX_70277623_7   2154 TATTTGTAAATCATACATCTGATAAGGGGCTTGTATCCAGGATATACAAA 2203
                               i        i            i           i     i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_70277623_7   2204 GAACTCTTACAACTCAATAATAAAAAGACAAATAA 2238
                                                            
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

Transitions / transversions = 1.64 (110 / 67)
Gap_init rate = 0.04 (29 / 805), avg. gap size = 5.10 (148 / 29)  

 582 13.18 5.43 0.00  chrX_70277623_70280749.rev     2508  2636 (491)    L1M4_orf2#LINE/L1      773   908 (0)  

  chrX_70277623_7   2508 AACTC---CATCTCAA-AA-AAAAAGACAACTAGCCCAATTCAAAAATGG 2552
                              ---  v     -  -          v  i       ?        
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_70277623_7   2553 ACAAAAT-TTTAAATATACATTTCTCCAAGGAAGATATACAAAAGGTTCA 2601
                         i    iv-   i    v            i             v  iiv 
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_70277623_7   2602 -AGGTACATGAAAAGATGCTCAACATTATTAGTCAT 2636
                         - i i                     i ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.04 (5 / 136), avg. gap size = 1.40 (7 / 5)  


3101 27.49 1.00 0.33  chrX_70444788_70447049.rev      870  1771 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_70444788_7    870 TGGAAGAAGATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 919
                              ii v  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_70444788_7    920 GGCCATAGTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 969
                            v   v v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_70444788_7    970 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACTACTTC-GAAGTTCA 1017
                          v i iivi i  i  ii     -   -- v  i  iv i -i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_70444788_7   1018 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAGAG 1067
                                viiv  ii  v  viv  v     i      i i ivv ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_70444788_7   1068 AACAAAGCTGGAGGCATCATGCCACCTGACCTCAAACTATAATACAAGGC 1117
                                i      vv   ii iv  ii ii     viv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_70444788_7   1118 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGA--TACAGACC 1165
                                 i   i    ii         i iv ii i   --  i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_70444788_7   1166 AATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATCTACAACCAT 1215
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_70444788_7   1216 TTGACCTTTGACAAACCTAACAAAAACAAGAAATGGGGAAAGGATTCCCT 1265
                             ii  i     ivv iv   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_70444788_7   1266 AATTTAATAAATGGTGCTGGGAAAACTGTCTAGCCGTATGTAGAAAGCTG 1315
                         -v  i  i              v     vv  ?  ii   i i  iiv  
  L1M4_orf2#LINE/    399 -TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_70444788_7   1316 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 1365
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_70444788_7   1366 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1415
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_70444788_7   1416 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 1465
                             ?i v viv   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_70444788_7   1466 ACACCAAAACCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAAT 1515
                                  v  vvi          vv     v  i    vi  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_70444788_7   1516 TAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1565
                         i   v    i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_70444788_7   1566 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 1615
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_70444788_7   1616 GAGCTAATATCCAGAATCTACAAAAAACT--TACA--TTTACAAGAAAAA 1661
                          ii  vi          v  i   i    --    -- iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_70444788_7   1662 ATCAAACAACCCCATCAAAAAGTGGGCAAATGATATGAACAGACACTT-T 1710
                         iv    i     v  i?    i        v   v    i     i  - 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_70444788_7   1711 CAAAAGAAGAAATTCATGCAGCCAACAGACACATGAAAAAATGCTCATCA 1760
                          v        v  v  viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_70444788_7   1761 TCACTGGCCAT 1771
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3770 22.80 2.60 0.11  chrX_70736752_70738948.rev      821  1706 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_70736752_7    821 TGGAAAGCTATCCAATGATTATGGATTGGAAGAATCAATATTGTTAAAAT 870
                                v     v   v i             v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_70736752_7    871 GTCCATACTACTCAAAGCAATCAACAGACTCACTGCAATCCCTATCAAAA 920
                          v v     v i    vii   v     i   vi                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_70736752_7    921 TTCC-GATGCTATTTTTACATAACAGAAAAAGC-AATCCTAAAATTCGCA 968
                          i  - v   iv     i  v  vvvi v    -i            ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_70736752_7    969 GAGAACCACAAAAGACTCCAGT-TACCCAAGGCAATCTTGAGCAAGAAGA 1017
                         vi   vii   ii   -    v-  v    ii         iv       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_70736752_7   1018 ACAAAGCTGGAGGAATCACAA--CCTGATCTCAAAATATAATA-AAAGCT 1064
                               i       v     v--  ii  i      iv  v  -      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_70736752_7   1065 AGAGTAATCAAAACAGCATGGTACTGGCATACAAACAGACACATGGACAA 1114
                          v         i    ii             vii i     i  i  iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_70736752_7   1115 ATATAATAGA---------CTAGAAA-AAATCCATGCACTTATGGTCAAG 1154
                           iv      --------- i     -   i    i  i          v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_70736752_7   1155 TGACTTTCAACAAAGATGCTAAGAACACACAATGTAGAAAGGACTGTCTC 1204
                            i    i    i i   i    v  iv     vi     i iv    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_70736752_7   1205 TTCAATAAATGGTCTTGGGAAAACGGAGTATCCACATGCAGAGGAATAAA 1254
                              i       vi     v   v ii  ?         i i    i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_70736752_7   1255 ATGGGACCCTTGTCTCACATCATATACAAAAATCAAGTCAAAATGGACTC 1304
                         i v      i ii      i             i  v          iiv
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_70736752_7   1305 CGGATTTAATCGTAAGATCTGAAACTGTAAA-CTGCCAGAAGAAAACATA 1353
                         ?i  ii   vi      v  i     i    -  vii             
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_70736752_7   1354 GCGAGAAACATCCATGGCATTGACCTGGGCGATAATCTTTCCGCTATGAC 1403
                          v?iv   iv i i  i v   ivi i   i  ii i i iv v      
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_70736752_7   1404 CCCAAAAGCATGAGCAACCAAAGAAAGAATAGAGAAATGGGATTACGTCA 1453
                         v         ii      v       i      v    v   i v i   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_70736752_7   1454 AACTGAAAGGCTTCTGCACAACAAAGGAAACGATCAACAGAGTGAAGAGG 1503
                           v v   ii   i  ii vv       v  v     v i      i  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_70736752_7   1504 CAACCTACAGAATGGGAGAAAATATTCACAAACTATACATCTGATAAGGA 1553
                              i                    ii    ii   i           i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_70736752_7   1554 GTTAATATCCAAAATACATAAGGAACTC----AACTCAATAACAAGAAAA 1599
                         ii vi      i    i    i      ----          i  i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_70736752_7   1600 CAAATCACCTGATTTTAAAACGTGCAAAGGATCTGAATAGACATTTCTCC 1649
                              v   ii   ?v    i v         i                 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_70736752_7   1650 AAAGAAGACATACAAATGGTCAACAGTTGTATGAAAA--TGCTCGACATC 1697
                                 i          i   i iviii       --     i     
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_70736752_7   1698 ACTTATCAT 1706
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.91 (130 / 68)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.18 (24 / 11)  


3135 26.90 0.55 0.66  chrX_70819077_70825457     4982  5888 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_70819077_7   4982 GAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAATGG 5031
                             i i  i     i        v      v i     ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_70819077_7   5032 CCATACTCCCCAAGGTAATTTGCAGATTCAATGCCATCCCCATCAATCTA 5081
                          v           iv i  i i         i  v     i     vv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_70819077_7   5082 CCAATGAGTTTTTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTCAT 5129
                            iivivi     ii     -   --- v  i  - iii    i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCAT 149

  chrX_70819077_7   5130 ATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAGAAGA 5179
                               viiv  ii  v  v v  v     i      i i ivv      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_70819077_7   5180 ACAAAGCTGGAGGCATCACGCTATCTGAGTTCAAACTATACTAAAAGGCT 5229
                               i      vv    i  vi ii v      viv     v  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_70819077_7   5230 ACAGTAACCAAAACAGCATGGAACTGCTACCAAAATAGAGATATAGACCA 5279
                                i   i    ii   v    vi iv ii     v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_70819077_7   5280 ATTGAACAGAAC--AGAGCCCTCAGAAATAACACTGCACATCTACAACCA 5327
                           v   i    i--    i  --        vv iii    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_70819077_7   5328 TCTGATCTTTGGCAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5377
                         vi    i  i i   ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_70819077_7   5378 TATTTAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTG 5427
                          v  i ii              v      v  ?   i   v i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_70819077_7   5428 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 5477
                           ii    i    v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_70819077_7   5478 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5527
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_70819077_7   5528 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGCACTTCATGACTAA 5576
                             ?i- v i -   iv   v v  vv i     vvii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_70819077_7   5577 AACACCAAAAGCAATGGCAACAGAAGCCAAAATTGATAAATGGGATCTAA 5626
                         i            vvi      i   vv     v       v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_70819077_7   5627 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5676
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_70819077_7   5677 AGGCAACCTACAGAATGGGAGAAAAGTTTTACAATCTACCCATCTGACAA 5726
                           i     i                vv   i   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_70819077_7   5727 AGGGCTAATATCCAGAATCTACGAAGAACTCAAACAAATTTACAAGAAAA 5776
                         i  i  vi          v  ii        vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_70819077_7   5777 AATGAAACAACCCCATCAAAAAGTGGGGAAAGGATATGAACAGACACTTC 5826
                          ivv   i     v  i?    i    v       v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_70819077_7   5827 TCAAAAGAAGACATTTATGCAACCAAAAGAAACATGAAAAAATGCTCATC 5876
                           v        i  vi viiii    v iiv         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_70819077_7   5877 ATCACTGGCCAT 5888
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (137 / 103)
Gap_init rate = 0.01 (7 / 906), avg. gap size = 1.57 (11 / 7)  


2968 23.84 3.66 3.44  chrX_70832044_70838729     5292  6193 (493)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_70832044_7   5292 AAAACATTCCATGCTCATGGACAGGAAGAATCAATATCGTGAA------- 5334
                           i i  i     i       iv      v i     i  v  -------
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_70832044_7   5335 ---------------------AGATTTTATGCTATCTCCAACAAGCTACC 5363
                         ---------------------     iv i  v   i i v   iv v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_70832044_7   5364 AG-TGCCTTTTTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCATATG 5411
                           -          -i     v v  v  i-  - iii    v        
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCATATG 152

  chrX_70832044_7   5412 GAACAAAAAAGGAGCCCATA-TAGCCAAGACAATCCTAAGCAAAAAGAAC 5460
                            - viv    ii    v -       i      i i iv  i      
  L1M4_orf2#LINE/    153 GAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_70832044_7   5461 AAAGCTGGAGGTATCACGCTACCTGACTTTAAACTATACCACAAGGCTAC 5510
                             i      vv    i  v  ii i  i   viv   i    i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_70832044_7   5511 AGTAACCAAAACAGCATGGTAGTGGTACCAAAAGATATATATATATATAT 5560
                              i   i    ii     v   i i--  i    v -----------
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGA----------- 288

  chrX_70832044_7   5561 ATATACATACATACATATATATCAATGGAACAAAACAGAGGCTTCCAAAA 5610
                         -------------      v          i i  iv   iv i vi   
  L1M4_orf2#LINE/    289 -------------CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_70832044_7   5611 TAATGCCACACATCTACAACCATCTGATCTTTGACAAACCTGACAAAAAC 5660
                            vv   i    i  iiii  vi    i  i     ivv  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_70832044_7   5661 AAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGTTGGGAAAACTG 5710
                          vv            i  vvi  v  i  i        i     v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_70832044_7   5711 GCTAGCCGTATGCAGAAAACTGAAACTGGACCCCTTCCTTACACCTTATA 5760
                          v  ?  ii     i  i v    ii         v   i     v    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_70832044_7   5761 CAAAAATTAACTCAAGATGGATTAAAGACTTAAACGTAAGACCTAAAACT 5810
                                        i      i ?    i    i      v        
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_70832044_7   5811 ATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCA 5859
                               vi i           v    ?i- v i -   iv   v v  vv
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT 574

  chrX_70832044_7   5860 TGGGCAAAGACTTCATGACTAAAACACCAAAAGCAATAGCAACAAAAGCC 5909
                          i     v ii   v iiv  vi            vv           vv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_70832044_7   5910 AAAACAGACAAATGGGATTTAATTAAACCAAAGAGCTTCTGCACAGCAAA 5959
                             i   i    v   i  v  i   viv  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_70832044_7   5960 AGAAACTATCATCAGGGTGAACAGGCAACCTACAGAATGGGAGAAAATTT 6009
                         i  v       vv ii     v  i     i                 v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_70832044_7   6010 TTGCAATCTCTCCATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAA 6059
                               viiv vi      i  i  i  vi          v  i      
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_70832044_7   6060 CTTAAACAAATTTACAAGAAAAAAACAAACAACCCCATAAAAAAATTGGG 6109
                           ivv    v iv i  v     i     i     v  v?      -   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT-GGG 823

  chrX_70832044_7   6110 CAAAGGATATGAACAGACACTTCTC-AAAGAAGACATTTATGTGGCCAAC 6158
                                 v    i     i     -        i  vi vi       i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_70832044_7   6159 AAACATATGAAAAAAAGCTCATCATCACTGGTCAT 6193
                           i  i       i v     v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (122 / 89)
Gap_init rate = 0.01 (13 / 904), avg. gap size = 4.92 (64 / 13)  


 367 27.78 6.11 1.11  chrX_70841049_70847435.rev      312   491 (5896)    L1M4_orf2#LINE/L1        9   197 (711)  

  chrX_70841049_7    312 TATACTTTGTTTATGAATGGGAACACTCAATA-----AATATG--AGTTC 354
                            v iv    i   i  v    v   i    -----  v   -- i v 
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chrX_70841049_7    355 TCCTTGTATTCATCTATAGATATAACACAATACA-ATTAAACTGATAGTA 403
                            iiiv   v     i    vi   i    v v-  i   v vvi  i-
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC- 107

  chrX_70841049_7    404 TGA-TTTTTTGTAGACATACACAACATGATTCTGTAATTTATACTGAAAA 452
                           v-       i   v  vv    vv    i  iv    i   -  i   
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA-TGGAAA 156

  chrX_70841049_7    453 T-CAAAAGAACTACAATGATTAAAACAATTTT-AAAAAGAA 491
                          -   ii  v i v   iiii        i  -        
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

Transitions / transversions = 1.17 (27 / 23)
Gap_init rate = 0.04 (8 / 189), avg. gap size = 1.62 (13 / 8)  

3226 26.65 0.55 0.55  chrX_70841049_70847435.rev     4989  5896 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_70841049_7   4989 TGGAAGAGCATTCCATGCTCATGGTTAGCAAGAATCAATATCGTAAAAAT 5038
                              iiii  i     i      v v v    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_70841049_7   5039 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5088
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_70841049_7   5089 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5136
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_70841049_7   5137 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5186
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_70841049_7   5187 AACAAAGCTGGAGACATCACACTACCCGACTTCAAACTATACTAGGAGGC 5236
                                i     ivv       v   i i      viv     vi i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_70841049_7   5237 TACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5286
                              i  i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_70841049_7   5287 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5334
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_70841049_7   5335 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5384
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_70841049_7   5385 CTATTTAATAAATGGTGCTGGGAAAACTGGATAGCCATATGTAGAAAGCT 5434
                           v  i  i              v         ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_70841049_7   5435 GAAACTGGATCCCTTTCTTACACCTTATACAAAAATTAATTCAAGATGGA 5484
                            ii    i    vi  i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_70841049_7   5485 TTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5534
                          i ?    i     i v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_70841049_7   5535 ATAGGCA-ATATCACTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5583
                              ?i- v   -i  iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_70841049_7   5584 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAAGGGATCTA 5633
                         vi            vvi          vv     v  i   vv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_70841049_7   5634 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAATACCATCAGAGTGAA 5683
                           i   v v  i i   i  ii vv    i  v v  i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_70841049_7   5684 CAGGCAAACTACAGAATGAGAGAAAATTTTTGCAATCTATTCATCTGACA 5733
                         v  i   v i        i        v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_70841049_7   5734 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5783
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_70841049_7   5784 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5833
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_70841049_7   5834 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5883
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_70841049_7   5884 CATCACTGGCCAT 5896
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3006 26.41 0.88 0.77  chrX_70888035_70889931.rev      502  1406 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_70888035_7    502 GAAACACATCCCATGCTCATGGATGGGTAGAATCATTATCGTGAAAATGA 551
                             v i        i        v  v   v i v   i  v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_70888035_7    552 CCCTACTGCCAAAAGCAATCTCCAAATTCAATGGAATTCCCCTCAAAATA 601
                          vv    v  v   vii    v  i      i v   i  iv       v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_70888035_7    602 CCACCATCATTCTTCACAGAACTAGAAAAACCAATTCCAAAATTCATATG 651
                            v vv v  i  ii     v v  v  i ii  i i            
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_70888035_7    652 GAACCAAAAAAGAAGAGCCCACA-TAGTCAAAGCAAGACTAAGCCAAAAG 700
                            viiv  ii  ----    v -   i    i   vvi i ivv i   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_70888035_7    701 AACAAATCTGGAGGCATCACATTACCCAACTTCAAACTATGCTATAAGGC 750
                               vi      vv     i v     i      viv i   i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_70888035_7    751 CATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAACGACATAGACC 800
                         i i   v i   i    ii         i    ii   ivv i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_70888035_7    801 AATGGAACAGAATAGCGAACCCAGAAATAAAGTCAAACACTTACAGCCAA 850
                                i     v v  ii           vi  v   i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_70888035_7    851 CTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCT 900
                         i    i  i     i vviv   i v   vv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_70888035_7    901 ATTCAACAAATGGTGCTGGGGAAATTGGCAAGCCACATGTAGAAGAATGA 950
                         v                   iv  i   vv ?       i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_70888035_7    951 AACTTGATCCTCATCTTTCATTTTATACAAAAATCAACTCAAGATGGATC 1000
                          ii v  i  ii i  iv  iiv           i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_70888035_7   1001 AAGGACTTAAATCTATGACCTGAAACCGTAAATATTCT-AGAAGATAACC 1049
                          ?i   i     v  v  v  i    ii    - i   -      v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chrX_70888035_7   1050 TCAGAA-AAACCTTCCTGGACATTGGCTTAGGCAAAGACTTCATGACCAA 1098
                          vi ?i-   i    v  -  v    v        v ii   v iivi v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_70888035_7   1099 GAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGATTTAA 1148
                           vv         v v         iv   i   i   i  v   i  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_70888035_7   1149 TTAAACTGAAAAGCTTCCACATAGCAAAAGAAACAATCAGCAGAGTAAAC 1198
                          i   v v    i   iiiiiivv    i  v  v    iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_70888035_7   1199 AGACAA---A-AAAGTGGGAGAAAATCTTCACAATCTATGCATCTGACAA 1244
                               --- - i i           v  ii   vii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_70888035_7   1245 AGGACTAATATCCAGAATCTACAAGGAACTCAAACAAAACAGCAAGAAAA 1294
                         i     vi          v  i  i      vv    vv  ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_70888035_7   1295 A-ACAAACGACCCCATCAAAACATGGGCTAAGGACATGAATAGACAATTC 1343
                          -     ii    v  i?   v      v     iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_70888035_7   1344 TCAAAAGAAGATATACAAATGGCCAACAAGCATATGAAAAAAATGCTCAA 1393
                           v                       i     i       i -       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

  chrX_70888035_7   1394 TATCACTAATGAA 1406
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 1.50 (15 / 10)  


3164 27.20 0.55 0.55  chrX_70900194_70906582.rev     4991  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_70900194_7   4991 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 5040
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_70900194_7   5041 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 5090
                            v     v     iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_70900194_7   5091 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAAGTTCA 5138
                          v   iivi i  i  ii     -   -- v  i   v i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_70900194_7   5139 TATGAAACCAAAAAAGAGCCCGCATTGCCAAGTCAACCCTAAGCCAAAAG 5188
                             i  viiv  ii  v  v v  v     iv   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_70900194_7   5189 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5238
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_70900194_7   5239 TACAGTAACCATAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5288
                                 i  vi    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_70900194_7   5289 AATAGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5336
                            i   i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_70900194_7   5337 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5386
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_70900194_7   5387 CTATTTAATAAATGGTGCTGGGAAAACTGGCTACCCAGATGTATTAAGCT 5436
                           v  i  i              v      v  ?   v   i vv iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_70900194_7   5437 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5486
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_70900194_7   5487 TTAAAGACTTAAATGTTAAACCTAAAACCATAAAATCCCTAGAAGAAAAC 5536
                          i ?    i       v i v       i      ii i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_70900194_7   5537 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5585
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_70900194_7   5586 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5635
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_70900194_7   5636 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5685
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_70900194_7   5686 CAGGCAACCTACAGAGTGGGAGAAAATTTTTGCAACCTAGTCATCTGACA 5735
                         v  i     i     i           v       vii vvi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_70900194_7   5736 AAGGGCTAATATCCCGAATCTATAATCAGCTCAAACAAACGTACAAGAAA 5785
                          i  i  vi     v    v     vv i   vv    vivv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_70900194_7   5786 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5835
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_70900194_7   5836 CTCAAAAGAAGACATTTATGCAGCCAAACAACACATGAAAAAATGCTCAT 5885
                            v        i  vi viii     vv i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_70900194_7   5886 CATTACTGGCCAT 5898
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


4062 14.81 1.23 3.46  chrX_70933496_70935290.rev      500  1309 (486)    L1M4_orf2#LINE/L1      117   908 (0)  

  chrX_70933496_7    500 TGCAGAAATGAAGAAACTGATCCTACAAATCATGTGGAAATTCAAAGGTC 549
                                  vi v  i         v  v    i       v   i  v 
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_70933496_7    550 CCAGAATAGCCAAAACAATCTTGAAAATAAAAAACTAAGTTGGAGGACTA 599
                                                    vi  i   v             v
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_70933496_7    600 ACACGTCCCAATTTCAAAACTTACTACAAAGTAATCAAAAGTAATTAAAG 649
                             v                          ---- v v      -----
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAG----CTACAGTAAT----- 257

  chrX_70933496_7    650 CAATCAAAGTTTTCAAAACTATGTGCTACTGGCATAAGGATACACATATA 699
                         -------------   i  vi    v                v       
  L1M4_orf2#LINE/    258 -------------CAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_70933496_7    700 GATCAAAGTAATAGAATTGACAGTCCAGAAATAAACCCATTCACCTACAG 749
                               v v           v                   v  ii  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_70933496_7    750 TCAATTGATTTTTCACAAGGATACCAATGCCATTCAATGGAGGAAGGAAT 799
                                     iv      i i    vi           -    i    
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAAT 393

  chrX_70933496_7    800 AGTCTCTTTAACAAAAGGCGCTAAAACAAGTGGATATCCAAGAACATGCA 849
                              i  i      v  i   iii    v      ?   ----      
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA----CATGCA 439

  chrX_70933496_7    850 AA-GAATGAAGTTGGACCACTACTTCACACCGTATACAAAAATTAACTCA 898
                           -               v    i       i                  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_70933496_7    899 AAATGGATCACAAACCAAAATATAAGAGCTAAAACTATAAAACTCCTAAA 948
                                   ? i   v    i                       i  i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_70933496_7    949 AGTAAACAT----GTAAATTTGCACGTTCTTAGATTAGACAATGGTCTCT 994
                           v      ----      i v ii vi   i i    i       i   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_70933496_7    995 TACGTATGATGGCAAAAGGACAAGCAACCAAAGAAAAAATAGGTAACTTG 1044
                           vi     iiv      v         v             i   v   
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_70933496_7   1045 GACATCATCAAATTTAAAAAACTTCTGTGCATCAAAGGACACTGTTAAGA 1094
                            v        v       -   i     v            i i    
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_70933496_7   1095 AAGTGAAAAGGCAACTCACAGAATGAGAGAAAATATTTACAAGTCATATA 1144
                                   i    i         i            i   i       
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_70933496_7   1145 CCTGACCAGGGATTAATATACGGAATACATAAAGAACT---ATAATTCCA 1191
                         i    iv     i vi   v i     i          --- i  i  v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_70933496_7   1192 CAACAAAATAATAAACAACCCAATTCAAAAACGGGCAAAAGACTCGAATA 1241
                         i  i    vi i   i         ?     i       i  i i     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_70933496_7   1242 GACATTTATCTAAA-AAGACATACAAATGGCCACTAGGCACATGAAAAGA 1290
                                v  i   -    i             v  i             
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_70933496_7   1291 TGTTTAGT-CCACAATGAGA 1309
                           i i ii-i  ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (74 / 43)
Gap_init rate = 0.01 (10 / 792), avg. gap size = 3.80 (38 / 10)  


4358 16.34 2.07 3.38  chrX_70962486_70964744.rev      851  1768 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_70962486_7    851 GAAATACAGTCTAAGTTCATGGACTGGAAGACTTAGTATTGTTAAGATGT 900
                             v i vi i v         i           i             v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_70962486_7    901 CAATACTACCGAAAACAATCTACAAATTTAATGCAATTCCCATTAAAATC 950
                                v  v   vii       i   i  i     i  i  i      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_70962486_7    951 CCAATATCCCTTTTTGCATAAATGGAAGAGCCAATTCTAAAATTCACATG 1000
                            iivv  i        v    v  vi   ii  i          i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_70962486_7   1001 GTCTTCCAACAGACCCCAAATAGACAAATTACTCTTAGAAAAGAAGAGCA 1050
                          vvv v   vi     vi     v    vi v    ii         i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_70962486_7   1051 CAGTTGGAAGACACACACTTCCAGATTTCTAGTTATACTACAAAGCTACA 1100
                         v       i   v         vi     v iviv               
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_70962486_7   1101 GTAATCAAAACCATATGGTACTGGCATAAAGAAAGACATAAACA--AATG 1148
                                 i  vi i              i  v       v v --    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_70962486_7   1149 GAATAAATTGGACAGTGAAGAAATAAACCCATGCATCTACAGAAAATTGA 1198
                              i v v  v   vv              i   i  ii vv      
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_70962486_7   1199 TTTTCTACAAGAGTGTCAACACCATTCAATGGGAAAAGAACAGTCTCTTC 1248
                              v     i   i   v             i      i     i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_70962486_7   1249 AACAAATGGTGCTGGGACAACTGGATAGCCACATGCAAAAGGATAAAGTT 1298
                                                    ?             i  i     
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_70962486_7   1299 GGATTCCTACCCTA----ATA---AAAGA-------GAAATGGATCAAAG 1334
                            ii      ii ----   ---   i -------i          ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_70962486_7   1335 ACCAAAACGTAAGAACTAAACCAATAAATTTCTTAGAAGAAAATATAGGA 1384
                            v   i      i     v v     vi             i     ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_70962486_7   1385 GTCAATCATCATGATCTTGGATTTGGCAATGCTTTCTTAGATATAATACC 1434
                           v    v  i   i     i  v       v            i i   
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_70962486_7   1435 AAAAGCATAAGCAACAAAAGAAGTAAAAAGCATAAGCAACAAAAGAAATA 1484
                                i              ------------------    ------
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAA------------------AAAA------ 628

  chrX_70962486_7   1485 CATAGTAGCTATAAATTTGACTTCATAAAAATTAAAAACTTTTGAGCATT 1534
                         -----   --       v        v                 v  v i
  L1M4_orf2#LINE/    629 -----TAG--ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_70962486_7   1535 AGTAGATAATATCAAGAGAGTGAAAGGACAACTCA--GAATGGGAGAAAA 1582
                          ivi  i v        i       i      i  --             
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_70962486_7   1583 TATTTGTAAATCAGATATCTGATAAGGGCCTAGTATCCAGAATATATCAA 1632
                               i      v              v  v               v  
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_70962486_7   1633 GAATAATTATAACTCAACAATAAAAAGACAAATCACCCAATT-ACAAATG 1681
                            ivv   i       i               v        - v     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_70962486_7   1682 GGCAAAGGATTTGAAAAGATATTTCTCCAAAGAAAATATACAAAGTGCCA 1731
                                        v   i              i         vv    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_70962486_7   1732 ACTAACACATCAAAAGATGTTTAACATCATGAGTCAT 1768
                          iv i     v        i i       ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (80 / 67)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 5.56 (50 / 9)  


1614 28.64 6.19 2.91  chrX_71018112_71019933.rev      509  1332 (490)    L1M4_orf2#LINE/L1       58   908 (0)  

  chrX_71018112_7    509 CTCCCTAAATTAATCTATAATCTCATTGCTATTTCAATCAAATCTCCAGA 558
                              i     i     i ivi   vi  v  ii v      vii    v
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_71018112_7    559 GGAATTTTTCACAGAACCTGACAAACTGATTCTAAAATCCATGTGAAAAA 608
                         v vv     ii     vi      i     i       i   i  i   v
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_71018112_7    609 GAATATGTATAAGAAGAGCCAAAACAATTTTTTTGGGGAA-AAGAACAAA 657
                          v viv vviv    v            i  --- iii  -         
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTT---GAAAAAGAAGAACAAA 204

  chrX_71018112_7    658 --TGAAGGA-TGACATT-----AT---ACAAGGTAT--CAAATCTACAGT 694
                         --  i    - v   i -----  --- v  vv  i--    v       
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_71018112_7    695 AATTAACAGGGTGTGGCATTGGCACAGAAGTAGACA----AATGAGTGAA 740
                            i  v vi      i i     i iiii      ----i  v i  i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_71018112_7    741 AGAGAACAGAGAGCTCTCAAGCCAACTCATGTAAAGGTGTTAAATAAAAT 790
                          v    iv     ii vv  iiv   i   ii vvvi  v v   vi v 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_71018112_7    791 ---AATAAAAGCTGCATTTATAAG-----TCAGTGGTGAAAGAATGGACT 832
                         ---i i  ii -   -----i   -----   i   v        i v  
  L1M4_orf2#LINE/    355 TTCGACAAGGG-TGC-----CAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_71018112_7    833 ATTCAACGAATAGTGCTGAAGTAACTAGCTTTCCATTTG-ATAAAAATTA 881
                         v      i   i      iiii    i v v?   iv  - v  i   v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_71018112_7    882 AATGAGATCCCTACCTCATACTATACACACACAT--ATTCCACATAGCTC 929
                          i vi  i          i  i   i   v v  -- i  v v  i v  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_71018112_7    930 AAACAACTAAATATAAAA---AAGAATAGAAACCTGTAATGGGAAAAATA 976
                          ? v v      i   i ---  i v  v   v  v v - iii    i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA-GAAGAAAACA 547

  chrX_71018112_7    977 GAGATTTATATATTTGTGACTTTGGTATGGAGAAAGTCATTTTAAACA-- 1024
                         v  i?v  v  v  i     i    vv i iv  v viv i   i i --
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_71018112_7   1025 ACAC-ACAAACACAACC--CAAAAGCCAGGAGGGAGTGGTTGACAAATTT 1071
                             - v  i     v --      ----- iii i i --- i     v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAG-----AAAAAATAG---ATAAATTG 639

  chrX_71018112_7   1072 GAATCTACA-CAAAAG-AATAATTTTTTT--TTAGGCAAAAGACACCATC 1117
                           --  v  -     v-  v  i    v --  ---    i     i   
  L1M4_orf2#LINE/    640 GA--CTTCATCAAAATTAAAAACTTTTGTGCTT---CAAAGGACACTATC 684

  chrX_71018112_7   1118 AATAAAGTTAAAAGACAAATAATAAACTGGGGAAATATATTTG-AAATGT 1166
                           v     v         viv i i v    ii  v       -    -i
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT-C 733

  chrX_71018112_7   1167 ATGTATTAGACAAAGAACA-ATA---AAAATATATAGAGAATTTCTGTAA 1212
                           i   iv  i  i i  v-i  --- i        i    i ii ii  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_71018112_7   1213 ATCAATAA---AAAGGTAAACAACTCAAAATAAATATGGGCAAAGTATAT 1259
                         v       ---    ii   i   i   vv?   v          v  v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_71018112_7   1260 GGACAGGTAATTC--AAAAGGAGAGTTACAGATGGCCAACAGACATTTGA 1307
                          i i  ii v   --v    i   vv    i        i ii  iv   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_71018112_7   1308 AAAGATATTCAGCCTCTGGGAATCA 1332
                               ii   i v  v????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (135 / 97)
Gap_init rate = 0.04 (32 / 851), avg. gap size = 2.34 (75 / 32)  


3715 15.63 2.75 0.87  chrX_71120594_71123977.rev     1696  2386 (998)    L1M4_orf2#LINE/L1        1   704 (204)  

  chrX_71120594_7   1696 TGGAAAGA-----CATGTTCATGGATCAAAATACTTAATATTGTTAAGAT 1740
                                 -----             iii  v                  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71120594_7   1741 GGCAATATTCCTCAAATTGATCTACAGATTCAATGCAATCCCTATCAAAA 1790
                                i   i                     i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_71120594_7   1791 TTCCAATT----TCTTTGTAGAAATTGACCACCTGATCCTAAAATCCATA 1836
                          i   ii ---- i    i          v v             i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_71120594_7   1837 TGGAAATTAAGGGGACCCAGAACAGTCAAAGCAATCTTTAAAAAGAA--- 1883
                                vv i           i  i    i       v        ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_71120594_7   1884 CAGAGTTGGAGGACTCACAATTCCCAATGTCAAACTTTA-TACAATGCTA 1932
                           i                v        v     vi   -     v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_71120594_7   1933 TAGTAATCAAAATAGTGTGTTGCTAACATAAGGATAGACATATAGATCCA 1982
                         i         i i      v i  ii                      --
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC-- 298

  chrX_71120594_7   1983 TATAGTGGAAAGAAATTGAGAGTCCTGAAATAAATCCATACATATATGGC 2032
                         --- i     vii            v        i        v     i
  L1M4_orf2#LINE/    299 ---AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_71120594_7   2033 TGATGGATTTTTGACAAGGGTGCCAATTCCATTCAATGCTGAAAAGAATA 2082
                         ii  v      i              vv          v- i        
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATA 394

  chrX_71120594_7   2083 ATCTTTTCAGTAAGTGGCGCTGGGACAACTGAATATCCAAATGCCAAAGA 2132
                         i        ii  i   i             i   ?   v    v     
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_71120594_7   2133 ATGAAGTTGGAATTCATTCTCATAT-ATAGACAAAATTAAACTCAAAATG 2181
                                    vii vvi    i i-   v      v v           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_71120594_7   2182 GGTCAAAGACCCACATGTAATGGCTAAAACTATAAAACA--TAGAAGGAA 2229
                          i   ?     i v      vi                v--      i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_71120594_7   2230 ACACAGGTATAAATCTTTAAGGCCTTAGATTAGGCAGTGGTTTCTTAGAT 2279
                            i   ?i        iiv i    i i       i             
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_71120594_7   2280 ATGACATTAGTAGCACAAATAACATAAGAGAAAA-ACACAAATTTGACTT 2328
                               ii iv       ii    v    i    - v i     v     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_71120594_7   2329 CATCAAAATTAAAAACTTTTGTTCA-CAAATAATGCCATCAAGAAAGTGT 2377
                                               v v-    vi ii i            v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_71120594_7   2378 AAAGA-AACC 2386
                              -    
  L1M4_orf2#LINE/    695 AAAGACAACC 704

Transitions / transversions = 1.76 (67 / 38)
Gap_init rate = 0.02 (11 / 704), avg. gap size = 2.27 (25 / 11)  

1163 12.30 0.82 5.33  chrX_71120594_71123977.rev     2650  2893 (491)    L1M4_orf2#LINE/L1      676   908 (0)  

  chrX_71120594_7   2650 GACTCTATCTCAAGAAAAAAGCGAAAAGGCAGCCTACAAAATAAGAGAAA 2699
                            v     -----  i    i      i  i  i   i   ii      
  L1M4_orf2#LINE/    676 GACACTATC-----AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_71120594_7   2700 ATATTTGCACATCATATGTTTGATAAGAGACTTGTGTCC-GAACATATAA 2748
                                  v       i i       i       i   -   i      
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_71120594_7   2749 AAATATCTTACAAATCAA-AGGAGAAAGACAAATAATAATCCAAATCAAA 2797
                          i vv        v    - iv i            i---    v ?   
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAAC---CCAATTWAAA 817

  chrX_71120594_7   2798 AATGGGCAAAGGATCTGAACAGACATTTCTCAAAAGATAGTACTATATAC 2847
                                       i    i           v     -  ----      
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA-AG----ATATAC 862

  chrX_71120594_7   2848 AAATGGCCAACAAGCACATGAAAAGATGCTCGACATCATTAGTTAT 2893
                                   i                    i      ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.62 (21 / 8)
Gap_init rate = 0.03 (6 / 233), avg. gap size = 2.50 (15 / 6)  


2862 24.25 5.40 1.03  chrX_71419498_71421815      956  1825 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_71419498_7    956 TGGAAAAACATTCCATGCTCA--GATAGGAAGACTCAATATTTTTAAAAT 1003
                               i i  i     i   --   v        i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71419498_7   1004 GGCCATACTGCCCAAAGCAATTTACTGTTTCAATGCTATTTCTATCAAAT 1053
                            v     v      vii  i   v v     i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_71419498_7   1054 TGCCAA-TGTCATTTTTCACAAAATTATAAAAACACTG-TTCTAAAATTC 1101
                          v   i-  i -     ii  i  v - i v  -i   - i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAA-GCTGATCCTAAAATTC 147

  chrX_71419498_7   1102 ATGT--AAATCCAAAAAGGAGCCCGAATAGCCAAAGCAATCCTAAGCCAA 1149
                           i --    v   i--   v  v           i     i i ivv i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_71419498_7   1150 AAGAACAATGCTGAAGGCATCACATTATCCAACTTCAAACTATACTACAA 1199
                                 v i  i   vv     i vi    i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_71419498_7   1200 GGATATAGTAACCAAAACAGCATGGTACTGGTATAAAAACAGACATATAG 1249
                         i v  i     i   i    ii         i    ii i          
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_71419498_7   1250 ACCAATGAAACAGAATACAAACCCCTGAAATACAGCTGCACAACTACAAC 1299
                          i     i  i     vv i vi  v      v v iii   vi  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_71419498_7   1300 CAACTAATTTTTTACAAAGTTGACAAAAATAAACAATGGGGAAAGCATA- 1348
                            i i     iv    i v  v   i vi vv            v   -
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_71419498_7   1349 TCTTATTCAATAAGTGGTGCTGGGAAAACT--------ACTTGCAGAAGA 1390
                             -     i  i           v    --------  v    i    
  L1M4_orf2#LINE/    396 TCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_71419498_7   1391 ATAAAATTGGACCCCTATCTGTCACCATATACAAAAATTAACTCAAAATG 1440
                           i  i           i  vv                            
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_71419498_7   1441 CATTAAATATTTAAATGTAAGA-TTCACACTATAAAAATCCTAGAAGAGA 1489
                         v  i ? v ii           -i v v         v  i       i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_71419498_7   1490 ACCTAGAAAGTAGTCTTC-TAGTCATAGGCCTACACAAAGATTTCATGAC 1538
                           v   i?ivv i     - iii v i  i-  vi   v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGA 593

  chrX_71419498_7   1539 AAAGATGCCAAAAGCAATTGCAATGAAAACAAAAAATTGACAAGGTGGAA 1588
                         v v  ii         vvv    i-    v       v  i  iv    -
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGGA- 641

  chrX_71419498_7   1589 CCTAATTAAACCAAAGAGTTTCTGCACAGCAATAGAAACTATCAACCAAA 1638
                          i v  i   viv  i ii  i  ii vv   vi  v        vv  i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_71419498_7   1639 TAAACAGACAACTTACAGAATGGGAGGAAATATTTGCAAACTATGCATCT 1688
                          i  v       ii            i             ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_71419498_7   1689 -ATAAGGAACTTAAA--CA-AATAAGCAAAAAAC-------ACCCAA--- 1724
                         -      i    iv --  -    vii   i   -------  i   ---
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_71419498_7   1725 --------------ACCCA-TTAAAAAGTGGGCAGAG-ACATGAACAGAC 1758
                         --------------     -  ?    i      i  - iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_71419498_7   1759 ACTTTTCAAAAGAAGACATACTAATGGCTAACAAACATAGGAAAAAATGC 1808
                          i  i  v        i    v      i  i  i  i v     i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_71419498_7   1809 TCCACATCACTAATCAT 1825
                           v      ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (128 / 80)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.43 (56 / 23)  

1217 18.37 2.86 0.82  chrX_71419498_71421815     2074  2318 (0)  C L1M4_orf2#LINE/L1   (319)   589   340  

C chrX_71419498_7   2318 TATAACCAATTGTTTTTTGACAAGGGTATCAAGTCCATTCAATGGGGAAG 2269
                            iii      v    i         ii    v               i
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

C chrX_71419498_7   2268 GAATCATCTCTTCAACAAATGGTGCTTGGACAACAGGATATCCACATGCA 2219
                             vi   i                v       v     ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

C chrX_71419498_7   2218 AAAGAATTAAGTTGCACCCCTACTTCACACCATATACAAAAAAATTAACT 2169
                                v      v        i                  --      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACT 487

C chrX_71419498_7   2168 GACAATAAATCAACAATCTACATATAAGAGCTAAAACCATAACAATCCTA 2119
                         v v   ii    ?vi i   v  i             i    v v  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

C chrX_71419498_7   2118 GAAGAAAACA-----ATGAATGCATGTGTCTTTATGGAAG--AATGATTT 2076
                                   -----i i   vivi   v i  iv vv  --    i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

C chrX_71419498_7   2075 CT 2074
                           
  L1M4_orf2#LINE/    588 CT 589

Transitions / transversions = 1.26 (24 / 19)
Gap_init rate = 0.01 (3 / 250), avg. gap size = 3.00 (9 / 3)  


3322 26.62 0.44 0.55  chrX_71442965_71449317     4952  5860 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_71442965_7   4952 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5001
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71442965_7   5002 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5051
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_71442965_7   5052 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5099
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_71442965_7   5100 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5149
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_71442965_7   5150 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5199
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_71442965_7   5200 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5249
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_71442965_7   5250 AATGGAACAGAAC--AGAGCCCTTAGAAATAATGCCGCATATCTACAACT 5297
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_71442965_7   5298 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5347
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_71442965_7   5348 CTATTTAATAAATGGTGCTGGAAAAACTGGCTAACCATATGTAGAAAGCT 5397
                           v  i  i            i v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_71442965_7   5398 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5447
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_71442965_7   5448 TTAAAGACTTAAATGTTAGAGCTAAAACCATAAAAACCCTAGAGGAAAAC 5497
                          i ?    i       v           i      vi i    i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_71442965_7   5498 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5547
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_71442965_7   5548 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGATCTAA 5597
                         i            vvi          vv     v       v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_71442965_7   5598 TTAAACTAAAGAGCTTCTGCACAGCAAAAAGAAACTACCATCAGAGTGAA 5647
                          i   v v  i i   i  ii vv    i-  v    i  vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGAA 695

  chrX_71442965_7   5648 CAGTCAACCTACAAAATGGGAGAAAATTTTCACAACCTGCTCATCTGACA 5697
                         v  v     i   i             v  ii   viiiivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_71442965_7   5698 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5747
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_71442965_7   5748 AAAATAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5797
                           i i   i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_71442965_7   5798 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5847
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_71442965_7   5848 CATCACTGGCCAT 5860
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2761 11.11 1.16 29.07  chrX_71473979_71476067.rev      478  1602 (487)    L1M4_orf2#LINE/L1       98   908 (0)  

  chrX_71473979_7    478 AAATCACAGCTGACTTCTCTTCACAAATTGACATATCTGATCCTAAAATG 527
                              v      v   i i v  v         - v             v
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATT 146

  chrX_71473979_7    528 TATCCAGAAATTCAA----CCCAGAATAGCAAAAGCAATCTCGAAACAGA 573
                         i  vii     v   ----           v   i      i    v   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_71473979_7    574 AGGACAAAGTTAGAAAACTCAAACTTCTCAACTTTAAAACTTACAACAAA 623
                           i        i  ii     v     i   i  i         v     
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_71473979_7    624 ACTACAGTAATCAAAGCTGCATCTTGCTGGCATGAGGACAGACATATAGA 673
                         i             ii v ii vv i       i    i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_71473979_7    674 TTAATGGAA--GAGTTCAGAGTCCAGAAATTAACCCCCACAATTATAGTC 721
                          i       --  i  v             v     vi   v    i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_71473979_7    722 AATTGATTTTACACAAAGGGGCCAAGACCATTCAATGGGGGAGAGGACAG 771
                                   vv    i  v                    i -  i i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAATAG 395

  chrX_71473979_7    772 TCTTTTCAATAAATGATGATAGGACAACTGGATGTATCAATATACAAAAG 821
                                  i     i  v i            -- ? v i  i      
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGAT--AKCCACATGCAAAAG 443

  chrX_71473979_7    822 AATAAAGTTGGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTT 871
                            i       ---------------------------------------
  L1M4_orf2#LINE/    444 AATGAAGTTGG--------------------------------------- 454

  chrX_71473979_7    872 GGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCG 921
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chrX_71473979_7    922 GCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGG 971
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chrX_71473979_7    972 GCATAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGG 1021
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chrX_71473979_7   1022 AGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGC 1071
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chrX_71473979_7   1072 CACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAA 1121
                         --------------------------------------------------
  L1M4_orf2#LINE/    455 -------------------------------------------------- 454

  chrX_71473979_7   1122 AAAATAAATAAAATAAAATAAAAAATAAAGTTGGACCCTTACCTCGCACC 1171
                         ----------------------------------    i      i    
  L1M4_orf2#LINE/    455 ----------------------------------ACCCCTACCTCACACC 470

  chrX_71473979_7   1172 ATATATAAAAATTAATTTAAAATAGATCAAAGACTTAAATGTAAGAGCTA 1221
                              i         i i     i     ?    i               
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_71473979_7   1222 AAACTATAAAACTCTTAGATGAAAACATAGATGTAAATTTTCATGATGTT 1271
                                            v          i?      i   i   iv  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_71473979_7   1272 GAAATAGGAAGTGGTCTCTTGGATATGACACCAAAAACATAAGCAAAAAA 1321
                          iiv    v i    i    i               i  i      v   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_71473979_7   1322 AGAAGAAATAGATAAATTGAATTTCGTCAAAATTTAAAAC-TTTGTGCTG 1370
                             i              i i   i        v     -        v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_71473979_7   1371 CAAAGGACACTATCAAGAGAGTGCAAAGATAACCCACAGAATGGGAGTAG 1420
                                           i    v     i                 v i
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_71473979_7   1421 ATATTTGCAAATCATGTGTCTGATAAGAGAC--ATATTTAGAATATTTTA 1468
                                        i i         i   --i   ii       v v 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_71473979_7   1469 AGAACTCTTACAACTCCATATTAAAAAGACAA----CCCGGTTTGAAAAT 1514
                                         v   v           ----   ii  ?i     
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_71473979_7   1515 GGGCAAAGGGTTGAAATAGATATTATTTCAAAGAAGATACACAAATATCC 1564
                                  i  vi      i   vi i           i      iv  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_71473979_7   1565 AATAAGCACATGAAAAGATATTCAACTTTATTACTAAT 1602
                                            ii     v i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (80 / 41)
Gap_init rate = 0.01 (9 / 811), avg. gap size = 37.78 (340 / 9)  


3244 26.38 0.66 0.44  chrX_71501650_71505402     2355  3260 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_71501650_7   2355 TGGAAAAACATCCCATGCTCATGGATAGGAGGAATCAATATAATTAAAAT 2404
                               i i        i        v   i  v i     vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71501650_7   2405 GGCCATACTGCTCAAGGCAACTTACAGATTCAATGCTATACCTATCAAAA 2454
                            v     v i   ivii ii           i  v  v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_71501650_7   2455 TACATGTGACATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAATTCAT 2503
                          v vv ivi v  i  ii     v v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_71501650_7   2504 ATGGAACCAAAAAAGAGCCCAAATGGCCAAGACAATCCTAAGCAAAAAGA 2553
                               viiv  ii  v  vi   i     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_71501650_7   2554 ACAAAGCTTGAAGCATCATGTTACCCAACTTTGAACTACACTACAG-GCT 2602
                               i v  i vv   iii v     i  ii  vivi      i-   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_71501650_7   2603 GACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGATACATAGACC 2652
                         -       i   i    ii         i i  ii i   i i     i 
  L1M4_orf2#LINE/    250 -ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_71501650_7   2653 AATGGAACAGAATAGAGAGCCCAGAAATAAGGCTGCACACCTATCACCAT 2702
                                i     v     i          iv iii   ii   vii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_71501650_7   2703 CTGATCTTCAACAAAGCTGACAAGAGCAAGCAATGGGGGAAAGACTCCCT 2752
                         i    i   i    i v  v     v  vv        i  ii ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_71501650_7   2753 ATTTAGTAAATGGTACTGGGATAACTAGCTAGCCATATTCAGAAGATTGA 2802
                         v  i ii       i      i    i v  ?   i  v  i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_71501650_7   2803 AGCTGGACCCCTTTCTTATAGGATATACAAAAATCAACTCAAGATGGATC 2852
                           i         vi  i i vv            i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_71501650_7   2853 AAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGACAACCT 2902
                          ?    i         i v i            vi i i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_71501650_7   2903 AGG--TAATACCATTCTGAACATAGGAACGGGCAAAGATTTCATGACAAA 2950
                            --   - i -   vvi  v v  ivii     v i    v iivv v
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_71501650_7   2951 GACAACAAATGCAATTTCAACAAAAGCAAAAGTTGACAAATGGGATCTAA 3000
                             v    v   vvvv         v    i v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_71501650_7   3001 TTAAACTTCAGAGCTTCTGCACAGCAAAATAAACTATCAACAGAGTAAAC 3050
                          i   v  v i i   i  ii vv    iv v        v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_71501650_7   3051 AGACAACCTACAGAATAGGAGAAAATATTTGCAAACTATGCATCTGACAA 3100
                                 i       i                  ii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_71501650_7   3101 AGGTCTAATATCCAGCATCTTTAAGGAACT-TAACAAGTTTACAAGAGAA 3149
                         i  v  vi       v  v v   i     - v    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_71501650_7   3150 AAACAAA-AACCCAATTAAAAAGTAGGCAAGGGATATGAACAGATACTTT 3198
                          i     -         ?    i i     i    v    i   i i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_71501650_7   3199 TCAAAAGACGACATACATGCGGCCAACAAGCATAGGAAAAAAAGCTCAAT 3248
                           v     v  i     vii      i     i v     i v      i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_71501650_7   3249 ATCAATGATCAT 3260
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


4588 14.09 6.40 1.05  chrX_71519550_71521397.rev      499  1357 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_71519550_7    499 AATGAGATCTCATGTTCATGGATCAGAAAACTTAATATTGTTAAGATGGC 548
                           v  v   i             ii   i                     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_71519550_7    549 AATACTCCC-GAATTGACCTAAAGATTCAACACAATCTCTATCAAAATTC 597
                                  -i      i   v         i     i          i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_71519550_7    598 CAGCTGGCTTGTT-GTAGAAATTGACAGGCTGATCCTAAAATTCATATGG 646
                               v   v  - i           i                      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_71519550_7    647 AAATGCAAGAGACCCCAAAACAACTAAAATAATCTTGAAAAAGAA---CA 693
                                  i     - i  i i i    i               ---  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCC-AGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_71519550_7    694 AATTTGAAGGACTCACACT------------------------------- 712
                           v   i            -------------------------------
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_71519550_7    713 GTAATCAAGACCATGTGGTCCTGGCATATGGATAGACACGCAGACCAGTG 762
                                    vi      v        v         iii   i  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_71519550_7    763 GAATAGAATTGGGAGTCCAGAAATAAACCCTCACATTTATGATCAACTGA 812
                                    i                  vi         i    i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_71519550_7    813 CTTTCAACAAAAGTACTAAGACAATTCA-TAAGGGAAGAACAGTCTTTTC 861
                         i    i    ii  i i     v     - ii  i     i         
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_71519550_7    862 CACAAATGGTACTAGGAT----------CTACATGCAAAAGAATGAATTT 901
                         v         i  i   i---------- i                 v  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_71519550_7    902 CAATCCCTACCTCAAGCCATACATAAAAATGAATTCCAAATGGATCATAG 951
                         vi i          vi     i i      v  i  v          ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_71519550_7    952 GCCAAAATGTAAGAGCTAAAACTGTGAAAGTCTTACAAGAAAGCATAGGA 1001
                         i  v                   i i   v     v      i      ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_71519550_7   1002 GTAAGTCTTCATGACCTTGGGTGAGGCAAAGCTTTCTCAGATATGTCACA 1051
                             i     i           v      v v     i       v   v
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_71519550_7   1052 GAAAGTACAA--AAAAAAAGAAAATATAGATAAATTG-AC--CATCAAAA 1096
                         i    i    --  v         v            -  --        
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_71519550_7   1097 CTAAAAGCTTTTGGGCTTCAAAGAAAGTGAGAAAAACATCAAGAAAGTGA 1146
                         i     i      v         i v-------- vi             
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGAC--------ACTATCAAGAAAGTGA 694

  chrX_71519550_7   1147 AAATACAACCAATAGAATGGGAAAAAGCATTTGCAAATTATATTTCTGAT 1196
                            v      v i         i   ii          i    v      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_71519550_7   1197 CAGAGA--TGTGTCCAGAATATATAAATAATTCTTACAACTCAATGATGA 1244
                         v  i  --   i               v  i              i  i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_71519550_7   1245 AAAGACAAATAACCTAATTCAAATATAGGCAGAAGATTTGAATAGATGTT 1294
                                       i    ?   v  i    i i            ii  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_71519550_7   1295 TATCCAAAAAAAA-ATATAAATGGCCAATAAGCACTTGAAAAGATGCTCA 1343
                          v      i  i -   i                 v              
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_71519550_7   1344 ACATCATTAGTCAT 1357
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (80 / 38)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 4.92 (64 / 13)  


4370 13.94 2.94 0.90  chrX_71534993_71536770.rev      506  1287 (491)    L1M4_orf2#LINE/L1      111   908 (0)  

  chrX_71534993_7    506 CTTTCTTGCAGAAATTGATATGATGATTCTAAAATTCATATGGAAATGCA 555
                             i             i v v    i                      
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_71534993_7    556 AGGGACCCAGAATAGCCAAAACAATCCTGAAAAAGAA---TAAAGTTGGA 602
                                                   i          ---i         
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_71534993_7    603 GGACTCACAATTCCCAATTTCAAAACTTACCATAAAGCTACAGTAATCAA 652
                                  v                    i i                 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_71534993_7    653 AATAGTCTGTTACTGGCATAAGGATAGATACATAGATCAATGGGATAGAA 702
                         i i   v  v                  i i            i      
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_71534993_7    703 CTGAGAATTGACAAATAAACCCCACACATCCATGGTCAATT----TTTGG 748
                         i     i iv v          - i    ii          ----  i i
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCC-ATACATTTATGGTCAATTGATTTTCGA 359

  chrX_71534993_7    749 CAAGAGAACCAAGACCACTCAATGGGAAAAGAATAGCCTCTTCAACAAAT 798
                             i vi         i        i         i  i          
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_71534993_7    799 GGTGCTGGGATAACCTGATAACCACCTTCAAAAGAGTGAAGTTGGACCCC 848
                                   i   iv    ?    v v       i              
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_71534993_7    849 TACTTCACTCCATATTTAAAAGTTAAGTCAAAATAGATCAAAGACTTAAA 898
                            i    v      vi    i    v       i     ?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_71534993_7    899 TGTAAGAACTAAAACTATAAAACTCTTTGAAGACAATTTAGAAGTAAATC 948
                                i                   v     v  iv   i?       
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_71534993_7    949 TTTGTGACCT-GGGTTAGGC------TTCTTAGATATAATACCAAAAGCA 991
                           i       -         ------           i i          
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_71534993_7    992 CAAGTAACAAAA----AAATAGAT----TGAATTTCATCAAAGTTAAAAA 1033
                             i       ----        ----  i i         i       
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_71534993_7   1034 CTTGTGTGCTGCAAATGATTTATCTTCAAGTAAGTAGAAAGATAATCCAT 1083
                            v      v    v  --i iiv     v    ii     i  i   i
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGA--CACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_71534993_7   1084 AGAATGGGAGAAAATATTTGAAAATAATATATCTAAGAAGGGTCTTTTAT 1133
                                             v    v        i v     v   v   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_71534993_7   1134 CCAGAATATATGTGTATAGAACTCTTGCAACTTAACAATAAAAAGAGCAA 1183
                                    ---- v         i     i  i          vv  
  L1M4_orf2#LINE/    758 CCAGAATATAT----AAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_71534993_7   1184 TGACTCAATTGAAAAATGTATAAAGGATTCAAATAGATGTTTCTCAAAAA 1233
                          i  i     ?       vii        ii      ii      v   i
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_71534993_7   1234 AAGATATACAAGTAGTCAATAAGAGCATTAAA-GATGTTCAGCATCATTA 1282
                                    i i i       vi   v   -    i   i     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_71534993_7   1283 GTCAT 1287
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.09 (71 / 34)
Gap_init rate = 0.01 (10 / 798), avg. gap size = 3.00 (30 / 10)  


3013 27.18 2.13 0.56  chrX_71587826_71594192     4983  5876 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_71587826_7   4983 TGGAAGAACATTCCATGCTCATGGATAGGAAGAACCAATATCATGAAAAT 5032
                              ii i  i     i        v      vii     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71587826_7   5033 GGCCATACTGCTCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 5082
                            v     v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_71587826_7   5083 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5130
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_71587826_7   5131 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGAAA-AA 5179
                                 viiv  ii  v  v v  v     iv     i i i   -  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_71587826_7   5180 GAAGAAAGCTGGAGGCATCACGCTACCTGACATCAAACTATACTACAAGG 5229
                            v    i      vv    i  v  ii iv     viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_71587826_7   5230 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5279
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_71587826_7   5280 CAATGGGACAGAA--GAGAGGCCTCAGAAATAACACTACACACCTACAAC 5327
                               i i    --     v  --        vv i i   ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_71587826_7   5328 CATCTCATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5377
                           vi v  i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_71587826_7   5378 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5427
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_71587826_7   5428 TGAAACTGGATCCCTTCTTTACACCTCATACAAAAATTAATTCAAGATGG 5477
                             ii    i    v i i     vi             i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_71587826_7   5478 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAA 5527
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_71587826_7   5528 CCTAGGC---AATAGGCATG----TG-------CAAGGACTTCATCACTA 5563
                          v    ?---   vvv i  ----  -------   v ii   v viv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_71587826_7   5564 AAACACCAAAAGCAATTGCAACAAAAGCCTAAATAGACAAATGGGATCTA 5613
                         vi            vvv          vvv       i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_71587826_7   5614 ATTAAACTAAAGAGCTTATGCATAGCAGAGGAAACTACCATCAGAGTGCA 5663
                           i   v v  i i   v  iiivv  i    v    i  vv i    v 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_71587826_7   5664 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5713
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_71587826_7   5714 AAGGGCTAATATCCAGAATCTACAAATAATTTAAACAAATTTACAAGAAA 5763
                          i  i  vi          v  i   v  i ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_71587826_7   5764 AAATGAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5813
                           ivv   i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_71587826_7   5814 CTCAAAAGAAGACATTTATGCAGGCAACAGACATGTGAAAAAATGCTCAT 5863
                            v        i  vi viii v   i ii  ii      i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_71587826_7   5864 CATAACTGGTCAT 5876
                            v ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  


1898 26.53 1.00 4.71  chrX_71749086_71750778.rev      502  1202 (491)    L1M4_orf2#LINE/L1      234   908 (0)  

  chrX_71749086_7    502 AACTACACTATAAAGCCACAGGAACCAAAACAGCTTGATACTGATAAAAA 551
                             -i    i     i    v  i   i    iv  i     ii v  i
  L1M4_orf2#LINE/    234 AACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_71749086_7    552 AAAAAAAAAAAAAGACACATAGACCAATGGAACAGAATGGAAAACTCAGA 601
                         i v ---------    i     i        i     v  i iii    
  L1M4_orf2#LINE/    283 GATA---------GACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_71749086_7    602 AATAGAGCTGCACACCTACAACCATCTGAACTTTGACAAGGCTGGCAAAC 651
                             i v iii   ii  iiii  vi   vi  i       v  v   iv
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_71749086_7    652 ACATGCAATGAGGAAAGGACTCGACTCCCTATTCAATAAATGATGGTGGG 701
                         v   v     i      i - v v  i----     i     i  v    
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAA-TAGTCTT----TTCAACAAATGGTGCTGGG 418

  chrX_71749086_7    702 ATAACTGGCTAGCCACTTGCAGAAAATTGAATCTGGACCCCCCCACTTTT 751
                          i      v  ?    v    i  i v    vi        i--  i iv
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT--ACCTCA 466

  chrX_71749086_7    752 CACCACATACAAAAATAAACACAAGGTGGATCAAAGATTCAAATGTAACA 801
                              i          v   v   ii       ?   iii        v 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_71749086_7    802 CCCCAAACCATAAGAATCCTGGAGGACAACTTAGGAAACACTCTTCTGGA 851
                         v iv    i    i v  i i  i  v   v    ?ivv v     vv  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_71749086_7    852 CATCAGCCTTGGCAAAGAATTTTTGACTAAGTCTCCAGA--TTTAATTGC 899
                          v ii vi v     v iv  i  iiv  v v v   i --ivi  --  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GC 614

  chrX_71749086_7    900 AACAAAAACAAAAATTGACACCCCAA---GACCGAATTAAACTGAAGAGC 946
                                iv      v  i ----  ---   ivv  i   v v  i i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATA----AATTGGACTTCATCAAAATTAAAAAC 660

  chrX_71749086_7    947 TTCTACACAGCAAAAGAAGCCAGCACCAGAGTAAACAGACAGCCTACAGA 996
                           i iii vv    i  vi i v  vv i   i  v     i  i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_71749086_7    997 ATGAGAGAAGATATTAGCAAACAATGCATGTGACAACGGCCTAATATCCA 1046
                            i     i     v     iv  ii  v   i  v  v  vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_71749086_7   1047 GAATCTATAGGGAACTTAAACAAATCAACAAGTAAAACACAAATAGCCCC 1096
                             v    ii     ivv    v    i  vv    v       i   v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_71749086_7   1097 ATTTAAAAAAAAAAAAAAACAGGCAAAGGACATGAACAGACACTTCTCAA 1146
                            ?     ----------ii         iv    i     i     v 
  L1M4_orf2#LINE/    811 ATTWAAAAA----------TGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_71749086_7   1147 AGGAAGATGTATAAGCGGCCAACAA--ACATGAAAACATGCTCAGCATCA 1194
                          i      i  i  ii      i  --         v       i     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_71749086_7   1195 CTAATCAT 1202
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.46 (108 / 74)
Gap_init rate = 0.02 (11 / 675), avg. gap size = 3.64 (40 / 11)  


2699 27.50 3.14 1.23  chrX_71797840_71802179.rev     2959  3849 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_71797840_7   2959 TGGAAAGAGATCCCACATTCATGGAC--GAA---TTAATATTGTTACAAT 3003
                                 v      ii        i--   ---            vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71797840_7   3004 GTCCATATTAACCAAAGTGATCTCCATGTTCGACATTTGACATCCCTGTC 3053
                          v v   i vv     v      v  vi   i  ii--- -      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC---A-ATCCCTATC 96

  chrX_71797840_7   3054 AAAATACCAATGACAGTCCGGATAGAAA--AAAAAA---ATCCTAGA-TT 3097
                              v   iivi vv iivvii     --i v  i---      i -  
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_71797840_7   3098 TGTATGGAGCCACAAAAGATGCTGA-TAGCCAAACCAATCCCAAGCAGGA 3146
                         ii      ivii   ii  iv v  -        v     iii iv i  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_71797840_7   3147 AGAACAAAGCTGGAGACAACACACTACCTGACCTCGAAA--TA-TACAAA 3193
                                  i     ivvv      v  ii ii  i   --  -      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_71797840_7   3194 -----AGCAACCAATACAACAGGGCACTGACATAAAATCAGATACATAGA 3238
                         -----  i  i   v   iiiv  i    i     iivi   i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_71797840_7   3239 CCAATAAAACATTATAGGGAACCCAGATATAAATCCAAGCATTAACAGCC 3288
                         i    ii  i vv  v i  ii     v     i   vi    v ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_71797840_7   3289 AACTGATTTTCTACAAAGGAGCCAAGAACATACATGGAGGATAAGACAGT 3338
                           i        v    i  v       v   v  vv i   v ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_71797840_7   3339 CTCCCCAATAAATGGTGCTGGACAAACTGTACGTTCACAATCAGAAGAAT 3388
                           iii   i            ivv     v ii?i    vv  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_71797840_7   3389 GAAACCAGACCCCTATCTCTCACCATATACAAAAGTCAAATCAAAATGAC 3438
                            iiii        i   v              i i  v        iv
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_71797840_7   3439 TTAAAGACTGCAATGTCAGACCTGAAACTGTGAAACTTCTAGAAGAAAAC 3488
                          i ?    ivv     v   v  i     i i     ii           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_71797840_7   3489 ATAGGGGAAACGTTTCACGAAATTGAACTGGGCAACGATTCTTTTCTTCA 3538
                              ? v  vvi   ii  vv   iii i     i i  ----    vi
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT----TCTTAG 592

  chrX_71797840_7   3539 GTAAGGCCTCGAAAGCATAGGCAACAAAAACACAAATAGACCAATAGGAT 3588
                         i  v i vi i      i i         iv v       iv   v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_71797840_7   3589 TATATCAGACTATAAAGCATCTGCACAGCAAAAGAAACAATCAGTAGAGT 3638
                          vi    i v vv   i v i  ii vv    i  v  v    iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_71797840_7   3639 AAAGAGACAGCTTACAGAATGAGAGAAATAGTATTTTCAAACTATGCATC 3688
                         i  i     i ii        i      --i     v    ii  ii   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAA--ATATTTGCAAATCATATATC 740

  chrX_71797840_7   3689 TGACAAGGGGTTAATATCCAGAATATATAAGGAGCCC--A-AAC--AATA 3733
                            i     ii vi                i  i i -- -   --    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_71797840_7   3734 GCAAAATT-CATAATAATTCAATTAAAAATTGGGAAAAATGCCTGAATAG 3782
                         ii    vv-  -     ii     ?    v    v   iviii       
  L1M4_orf2#LINE/    791 ATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_71797840_7   3783 ACCTTTCTCAAAAGAAGATGTGCAAATGGCCAACGGATATATGAAAACA- 3831
                           v      v         i i           iiiii i       v -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_71797840_7   3832 G-TCAACATCACCAATCAT 3849
                          -         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (156 / 85)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.95 (39 / 20)  


2492 21.30 9.13 10.43  chrX_71818510_71822422.rev     2503  3422 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_71818510_7   2503 TGAAAAGCTATTCCATGTTCATTGATTGGAAGAATTATTATTGTTAAAAT 2552
                           i    v   i          v          v   v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71818510_7   2553 ATTCATACTATCCAAAACAATCTACAGATT----GC---------CAAAA 2589
                         iviv     vi     vii           ----  ---------     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_71818510_7   2590 -------------------------------------------------- 2589
                         --------------------------------------------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_71818510_7   2590 --GAAGAGCAAAGG-----------------CTATCCTGAGCAAAAAGAA 2620
                         --   iv    i  ----------------- v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_71818510_7   2621 CAAAACTGGAGGAATCATATTACCTGACTTCAAATTATACTACAGAGCTA 2670
                             ii       v   i i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_71818510_7   2671 TAGTAACCAAAAAGGCACGGTACTGGCATAGAAACAGACACATAGATCAA 2720
                         i     i   i vi iii            iii i     i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_71818510_7   2721 TGGAACAGAATAGAGAGCCCAGAAACAAATCCACACACCTGCAGTGAACT 2770
                              i     v     i       i   i   i   ii iii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_71818510_7   2771 CATTTTCCACAAAGGTGCCAAAAACATGCACTAGAGAAA--AGAGTCTCT 2818
                         v      v    i        i v   v  v i i    -- v     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_71818510_7   2819 TCAATAAATGGTGCTGGGAAAACTGGATATTCACATGCAGAAGCATGAAA 2868
                             i              v         ?i        i   v     i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_71818510_7   2869 CTGGACCTCTATCTTTCAACTTACACAAAAATCAAATTAAAATAGATTAC 2918
                         i      i   i  iv  v v  i        i  v i     i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_71818510_7   2919 AGACTTAAATCTAAGACTTCAAACTATGAAACTACTAAAAGAAAACATTA 2968
                             i     v     vi v       i     vi  i          - 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-A 549

  chrX_71818510_7   2969 GGGGAAACTCTCCAGTATATTGCACTGGGCAAAGATTTCTTGAGTAATAC 3018
                           ? v  v   i ivv iv   vii i     v i      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_71818510_7   3019 CCCGCACACACAGGCAACCAAAGCAAGAAAAAAAAATAGACCAATGGGAT 3068
                         v  iv vi    i     v    -------          iv   v   i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAG-------AAAAAATAGATAAATTGGAC 642

  chrX_71818510_7   3069 CACATCAAGTTGAAAAGCTTCTGCCACAGCAAAGGAAACCGTCAACATTG 3118
                         iv      iv v    i   i  i-i vv       ---------  i -
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGT-GCTTCAAAGGA---------CACT- 681

  chrX_71818510_7   3119 AAAACAAAATAGAGAATAGAAAACCATGGGGGCAAAATCAATGAAACTAG 3168
                         --------------------------------------------------
  L1M4_orf2#LINE/    682 -------------------------------------------------- 681

  chrX_71818510_7   3169 GAGTCTCAAGTGGAATCCTTTGTTCATCAACAAAGTAAAGAGGCAAACCC 3218
                         -------------------------     v     i  i  i   -   
  L1M4_orf2#LINE/    682 -------------------------ATCAAGAAAGTGAAAAGACAA-CCC 705

  chrX_71818510_7   3219 ACAGAATGGGAGAAAATATTTGCAAACTACCTGTCTGACAAGAGATTAAT 3268
                                                   ii iv i     i   i  i vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_71818510_7   3269 AACCACAATACATAAGGAGCTCAAACAACTCTATAGGGAAAAAATGTAAT 3318
                          v   v    i    i  i   vv       v   ivi    i ii-   
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA-AAT 804

  chrX_71818510_7   3319 AATCCGATTAAAAAATAGGCAAAGGATCTGAATAGACACGTCTCAAAAGA 3368
                           i  i   ?      i          i          iv    v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_71818510_7   3369 AGACACATATATGGCAAACAGACATACGGAAAGGTACTCAACATCATTGA 3418
                            i i i v     v  i ii  i i i    i i          ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_71818510_7   3419 TCAT 3422
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.87 (125 / 67)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 15.00 (180 / 12)  

 948 17.52 1.71 2.99  chrX_71818510_71822422.rev     3457  3690 (223)    L1M4_orf2#LINE/L1      631   861 (47)  

  chrX_71818510_7   3457 GATAAACAGGACTTTCATTAAAATTAAAAACTTTT-TGCTGCAATTAATA 3505
                               iv    -     i                -    v   --- vi
  L1M4_orf2#LINE/    631 GATAAATTGGAC-TTCATCAAAATTAAAAACTTTTGTGCTTCAA---AGG 676

  chrX_71818510_7   3506 ATACCATCAAGAATGTGAAAAAAGAAGCCCCAGAATGGGAGAAAGTATTT 3555
                          i  i        v       i v  v  v              i     
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_71818510_7   3556 GCAAATCATATAACTTATAAGTGACTTGTATCTAGATTACAGAAATTAGT 3605
                                     v  v     v          i   v  i v   vv v 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_71818510_7   3606 TTTAGAAATTAATAATAAAA---CATATAACCTCATTGAGAAATGGGCAA 3652
                         i   v  v i          ---  v      iv   ? i          
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_71818510_7   3653 AAGATGTGAACAGCCATTTCTCCCCCCAAAAAAATACA 3690
                          i   v    i  v         ---v  i  i   i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCC---AAAGAAGATATA 861

Transitions / transversions = 0.82 (18 / 22)
Gap_init rate = 0.02 (5 / 231), avg. gap size = 2.20 (11 / 5)  


2927 26.92 2.00 1.00  chrX_71828322_71830173.rev      463  1361 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_71828322_7    463 TGGAAGAGCATTCCATGTTCATGGATAGGAAGAATCAATATTGTGAAAAT 512
                              iiii  i              v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71828322_7    513 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATTGA-- 560
                            v     v      v i  i  i        i  v     i  ii --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_71828322_7    561 ---------CTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGCTCA 599
                         --------- i  i  ii     -   -- v  i  - iii    ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_71828322_7    600 TGTGGAACCAAAAAAGAGGCCACATAGCCAAGACAATCCTAAGCCAAAAG 649
                          i     viiv  ii  vv viv        i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_71828322_7    650 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTACATTACAAGGC 699
                                i      vv   vi  v  ii i      vivi i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_71828322_7    700 TACAGTAACCAAAACAGCGAGGTACTGGTAGCAAAACAGATATATAGAAC 749
                                 i   i    i v        i vv ii i   i       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_71828322_7    750 AATGGAACAGAAC--AGAGGCCTCCA-AAATAACACCACGCATCTACAAC 796
                                i    i--    ---    -      vv   ii   i  iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAG---TCCAGAAATAAACCCATACATTTATGGT 345

  chrX_71828322_7    797 CACCTGATCTCTGACAACCCTGACAAAAACAAGCAATGGAGAAAAGATTC 846
                           vi    i ii     vvv  v   i v  vv      i    ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_71828322_7    847 CCTATTTAATAAATGGTGTTGGGAAAATTGGCTAGCCATATGCAGAAAGC 896
                         i  v  i  i        i     v  i   v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_71828322_7    897 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGG 946
                             ii    i    v   i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_71828322_7    947 ATTAAAAAGTTAAACATAAGACCTAAAACCATAAAAATCCTAGAAGAAAA 996
                           i ? i vi    ii     v       i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_71828322_7    997 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATCTCACGACT 1045
                          v    ?i- v i -   iv   v v  vv i     v i i  viiiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_71828322_7   1046 AAAACAGCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 1095
                          vi   v        vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_71828322_7   1096 AATTAAA-TGAAAGAGCTTCTGCACAGCAAAAGGAACTATCATCAGAGGG 1144
                         v  i   - v   i -   i  ii vv    i iv       vv i  v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_71828322_7   1145 AACAGGCAACCTACAGAAAGGGAGAAAATTTTTGCACTCTATCCATCTGA 1194
                           v  i     i      v          v      vvii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_71828322_7   1195 CAAAGGGCTAATATCCAGGATCTACAAATAAGTTAAACAAATTCACAAGG 1244
                         i  i  i  vi       i  v  i   v  v ivv    v iv i  v-
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT- 792

  chrX_71828322_7   1245 AAAAAAACAAACTTCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 1294
                              i     ivv   v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_71828322_7   1295 CTTCTCAAAAGAAAACATTTATGCAGCCAACAAACATATGAAAAAAATGC 1344
                         i     v      i i  vi viii     i  i  i       i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chrX_71828322_7   1345 TCATCATCACCGATCAT 1361
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.08 (27 / 13)  


2927 26.92 2.00 1.00  chrX_71891776_71898224     5058  5956 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_71891776_7   5058 TGGAAGAGCATTCCATGTTCATGGATAGGAAGAATCAATATTGTGAAAAT 5107
                              iiii  i              v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71891776_7   5108 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATTGA-- 5155
                            v     v      v i  i  i        i  v     i  ii --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_71891776_7   5156 ---------CTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGCTCA 5194
                         --------- i  i  ii     -   -- v  i  - iii    ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_71891776_7   5195 TGTGGAACCAAAAAAGAGGCCACATAGCCAAGACAATCCTAAGCCAAAAG 5244
                          i     viiv  ii  vv viv        i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_71891776_7   5245 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTACATTACAAGGC 5294
                                i      vv   vi  v  ii i      vivi i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_71891776_7   5295 TACAGTAACCAAAACAGCGAGGTACTGGTAGCAAAACAGATATATAGAAC 5344
                                 i   i    i v        i vv ii i   i       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_71891776_7   5345 AATGGAACAGAAC--AGAGGCCTCCA-AAATAACACCACGCATCTACAAC 5391
                                i    i--    ---    -      vv   ii   i  iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAG---TCCAGAAATAAACCCATACATTTATGGT 345

  chrX_71891776_7   5392 CACCTGATCTCTGACAACCCTGACAAAAACAAGCAATGGAGAAAAGATTC 5441
                           vi    i ii     vvv  v   i v  vv      i    ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_71891776_7   5442 CCTATTTAATAAATGGTGTTGGGAAAATTGGCTAGCCATATGCAGAAAGC 5491
                         i  v  i  i        i     v  i   v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_71891776_7   5492 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGG 5541
                             ii    i    v   i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_71891776_7   5542 ATTAAAAAGTTAAACATAAGACCTAAAACCATAAAAATCCTAGAAGAAAA 5591
                           i ? i vi    ii     v       i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_71891776_7   5592 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATCTCACGACT 5640
                          v    ?i- v i -   iv   v v  vv i     v i i  viiiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_71891776_7   5641 AAAACAGCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5690
                          vi   v        vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_71891776_7   5691 AATTAAA-TGAAAGAGCTTCTGCACAGCAAAAGGAACTATCATCAGAGGG 5739
                         v  i   - v   i -   i  ii vv    i iv       vv i  v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_71891776_7   5740 AACAGGCAACCTACAGAAAGGGAGAAAATTTTTGCACTCTATCCATCTGA 5789
                           v  i     i      v          v      vvii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_71891776_7   5790 CAAAGGGCTAATATCCAGGATCTACAAATAAGTTAAACAAATTCACAAGG 5839
                         i  i  i  vi       i  v  i   v  v ivv    v iv i  v-
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT- 792

  chrX_71891776_7   5840 AAAAAAACAAACTTCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 5889
                              i     ivv   v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_71891776_7   5890 CTTCTCAAAAGAAAACATTTATGCAGCCAACAAACATATGAAAAAAATGC 5939
                         i     v      i i  vi viii     i  i  i       i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chrX_71891776_7   5940 TCATCATCACCGATCAT 5956
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.08 (27 / 13)  


2492 21.30 9.13 10.43  chrX_71904124_71908030     2495  3414 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_71904124_7   2495 TGAAAAGCTATTCCATGTTCATTGATTGGAAGAATTATTATTGTTAAAAT 2544
                           i    v   i          v          v   v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71904124_7   2545 ATTCATACTATCCAAAACAATCTACAGATT----GC---------CAAAA 2581
                         iviv     vi     vii           ----  ---------     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_71904124_7   2582 -------------------------------------------------- 2581
                         --------------------------------------------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_71904124_7   2582 --GAAGAGCAAAGG-----------------CTATCCTGAGCAAAAAGAA 2612
                         --   iv    i  ----------------- v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_71904124_7   2613 CAAAACTGGAGGAATCATATTACCTGACTTCAAATTATACTACAGAGCTA 2662
                             ii       v   i i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_71904124_7   2663 TAGTAACCAAAAAGGCACGGTACTGGCATAGAAACAGACACATAGATCAA 2712
                         i     i   i vi iii            iii i     i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_71904124_7   2713 TGGAACAGAATAGAGAGCCCAGAAACAAATCCACACACCTACAGTGAACT 2762
                              i     v     i       i   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_71904124_7   2763 CATTTTCCACAAAGGTGCCAAAAACATGCACTAGAGAAA--AGAGTCTCT 2810
                         v      v    i        i v   v  v i i    -- v     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_71904124_7   2811 TCAATAAATGGTGCTGGGAAAACTGGATATTCACATGCAGAAGCATGAAA 2860
                             i              v         ?i        i   v     i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_71904124_7   2861 CTGGACCTCTATCTTTCAACTTACACAAAAATCAAATTAAAATAGATTAC 2910
                         i      i   i  iv  v v  i        i  v i     i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_71904124_7   2911 AGACTTAAATCTAAGACTTCAAACTATGAAACTACTAAAAGAAAACATTA 2960
                             i     v     vi v       i     vi  i          - 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-A 549

  chrX_71904124_7   2961 GGGGAAACTCTCCAGTATATTGCACTGGGCAAAGATTTCTTGAGTAATAC 3010
                           ? v  v   i ivv iv   vii i     v i      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_71904124_7   3011 CCCGCACACACAGGCAACCAAAGCAAGAAAAAAAAATAGACCAATGGGAT 3060
                         v  iv vi    i     v    -------          iv   v   i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAG-------AAAAAATAGATAAATTGGAC 642

  chrX_71904124_7   3061 CACATCAAGTTGAAAAGCTTCTGCCACAGCAAAGGAAACCGTCAACATTG 3110
                         iv      iv v    i   i  i-i vv       ---------  i -
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGT-GCTTCAAAGGA---------CACT- 681

  chrX_71904124_7   3111 AAAACAAAATAGAGAATAGAAAACCATGGGGGCAAAATCAATGAAACTAG 3160
                         --------------------------------------------------
  L1M4_orf2#LINE/    682 -------------------------------------------------- 681

  chrX_71904124_7   3161 GAGTCTCAAGTGGAATCCTTTGTTCATCAACAAAGTAAAGAGGCAAACCC 3210
                         -------------------------     v     i  i  i   -   
  L1M4_orf2#LINE/    682 -------------------------ATCAAGAAAGTGAAAAGACAA-CCC 705

  chrX_71904124_7   3211 ACAGAATGGGAGAAAATATTTGCAAACTACCTGTCTGACAAGAGATTAAT 3260
                                                   ii iv i     i   i  i vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_71904124_7   3261 AACCACAGTACATAAGGAGCTCAAACAACTCTATAGGGAAAAAATGTAAT 3310
                          v   v i  i    i  i   vv       v   ivi    i ii-   
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA-AAT 804

  chrX_71904124_7   3311 AATCCGATTAAAAAATAGGCAAAGGATCTGAATAGACACGTCTCAAAAGA 3360
                           i  i   ?      i          i          iv    v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_71904124_7   3361 AGACACATATATGGCAAACAGACATACGGAAAGGTACTCAACATCATTGA 3410
                            i i i v     v  i ii  i i i    i i          ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_71904124_7   3411 TCAT 3414
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.87 (125 / 67)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 15.00 (180 / 12)  

 948 17.52 1.71 2.99  chrX_71904124_71908030     3449  3682 (225)    L1M4_orf2#LINE/L1      631   861 (47)  

  chrX_71904124_7   3449 GATAAACAGGACTTTCATTAAAATTAAAAACTTTT-TGCTGCAATTAATA 3497
                               iv    -     i                -    v   --- vi
  L1M4_orf2#LINE/    631 GATAAATTGGAC-TTCATCAAAATTAAAAACTTTTGTGCTTCAA---AGG 676

  chrX_71904124_7   3498 ATACCATCAAGAATGTGAAAAAAGAAGCCCCAGAATGGGAGAAAGTATTT 3547
                          i  i        v       i v  v  v              i     
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_71904124_7   3548 GCAAATCATATAACTTATAAGTGACTTGTATCTAGATTACAGAAATTAGT 3597
                                     v  v     v          i   v  i v   vv v 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_71904124_7   3598 TTTAGAAATTAATAATAAAA---CATATAACCTCATTGAGAAATGGGCAA 3644
                         i   v  v i          ---  v      iv   ? i          
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_71904124_7   3645 AAGATGTGAACAGCCATTTCTCCCCCCAAAAAAATACA 3682
                          i   v    i  v         ---v  i  i   i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCC---AAAGAAGATATA 861

Transitions / transversions = 0.82 (18 / 22)
Gap_init rate = 0.02 (5 / 231), avg. gap size = 2.20 (11 / 5)  


2717 27.38 3.14 1.23  chrX_71924359_71928693     2952  3842 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_71924359_7   2952 TGGAAAGAGATCCCACATTCATGGAC--GAA---TTAATATTGTTACAAT 2996
                                 v      ii        i--   ---            vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_71924359_7   2997 GTCCATATTAACCAAAGTGATCTCCATGTTCGACATTTGACATCCCTGTC 3046
                          v v   i vv     v      v  vi   i  ii--- -      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC---A-ATCCCTATC 96

  chrX_71924359_7   3047 AAAATACCAATGACAGTCCGGATAGAAA--AAAAAA---ATCCTAGA-TT 3090
                              v   iivi vv iivvii     --i v  i---      i -  
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_71924359_7   3091 TGTATGGAGCCACAAAAGATGCTGA-TAGCCAAACCAATCCCAAGCAGGA 3139
                         ii      ivii   ii  iv v  -        v     iii iv i  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_71924359_7   3140 AGAACAAAGCTGGAGACAACACACTACCTGACCTCGAAA--TA-TACAAA 3186
                                  i     ivvv      v  ii ii  i   --  -      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_71924359_7   3187 -----AGCAACCAATACAACAGGGCACTGACATAAAATCAGATACATAGA 3231
                         -----  i  i   v   iiiv  i    i     iivi   i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_71924359_7   3232 CCAATAAAACATTATAGGGAACCCAGATATAAATCCAAGCATTAACAGCC 3281
                         i    ii  i vv  v i  ii     v     i   vi    v ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_71924359_7   3282 AACTGATTTTCTACAAAGGAGCCAAGAACATACATGGAGGATAGGACAGT 3331
                           i        v    i  v       v   v  vv i   v  i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_71924359_7   3332 CTCCCCAATAAATGGTGCTGGACAAACTGTACGTTCACAATCAGAAGAAT 3381
                           iii   i            ivv     v ii?i    vv  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_71924359_7   3382 GAAACCAGACCCCTATCTCTCACCATATACAAAAGTCAAATCAAAATGAC 3431
                            iiii        i   v              i i  v        iv
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_71924359_7   3432 TTAAAGACTGCAATGTCAGACCTGAAACTGTGAAACTTCTAGAAGAAAAC 3481
                          i ?    ivv     v   v  i     i i     ii           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_71924359_7   3482 ATAGGGGAAACGTTTCACGAAATTGAACTGGGCAACGATTCTTTTCTTCA 3531
                              ? v  vvi   ii  vv   iii i     i i  ----    vi
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT----TCTTAG 592

  chrX_71924359_7   3532 GTAAGGCCTCGAAAGCATAGGCAACAAAAACACAAATAGACCAATAGGAT 3581
                         i  v i vi i      i i         iv v       iv   v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_71924359_7   3582 TATATCAGACTATAAAGCATCTGCACAGCAAAAGAAACAATCAGTAGAGT 3631
                          vi    i v vv   i v i  ii vv    i  v  v    iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_71924359_7   3632 AAAGAGACAGCTTACAGAATGAGAGAAATAGTATTTTCAAACTATGCATC 3681
                         i  i     i ii        i      --i     v    ii  ii   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAA--ATATTTGCAAATCATATATC 740

  chrX_71924359_7   3682 TGACAAGGGGTTAATATCCAGAATATATAAGGAGCCC--A-AAC--AATA 3726
                            i     ii vi                i  i i -- -   --    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_71924359_7   3727 GCAAAATT-CATAATAATTCAATTAAAAATTGGGAAAAATGCCTGAATAG 3775
                         ii    vv-  -     ii     ?    v    v   iviii       
  L1M4_orf2#LINE/    791 ATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_71924359_7   3776 ACTTTTCTCAAAAGAAGATGTGCAAATGGCCAACGGATATATGAAAACA- 3824
                           v      v         i i           iiiii i       v -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_71924359_7   3825 G-TCAACATCACCAATCAT 3842
                          -         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (155 / 85)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.95 (39 / 20)  


1903 26.57 1.00 4.57  chrX_71975758_71977449      500  1199 (493)    L1M4_orf2#LINE/L1      234   908 (0)  

  chrX_71975758_7    500 AACTACACTATAAAGCCACAGGAACCAAAACAGCTTGATACTGATAAAAA 549
                             -i    i     i    v  i   i    iv  i     ii v  i
  L1M4_orf2#LINE/    234 AACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_71975758_7    550 AAAAAAAAAAAAAGACACATAGACCAATGGAACAGAATGGAAAACTCAGA 599
                         i v ---------    i     i        i     v  i iii    
  L1M4_orf2#LINE/    283 GATA---------GACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_71975758_7    600 AATAGAGCTGCACACCTACAACCATCTGAACTTTGACAAGGCTGGCAAAC 649
                             i v iii   ii  iiii  vi   vi  i       v  v   iv
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_71975758_7    650 ACATGCAATGAGGAAAGGACTCGACTCCCTATTCAATAAATGATGGTGGG 699
                         v   v     i      i - v v  i----     i     i  v    
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAA-TAGTCTT----TTCAACAAATGGTGCTGGG 418

  chrX_71975758_7    700 ATAACTGGCTAGCCACTTGCAGAAAATTGAATCTGGACCCCCCCACTTTT 749
                          i      v  ?    v    i  i v    vi        i--  i iv
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT--ACCTCA 466

  chrX_71975758_7    750 CACCACATACAAAAATAAACACAAGGTGGATCAAAGATTCAAATGTAACA 799
                              i          v   v   ii       ?   iii        v 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_71975758_7    800 CCCCAAACCATAAGAATCCTGGAGGACAACTTAGGAAACACTCTTCTGGA 849
                         v iv    i    i v  i i  i  v   v    ?ivv v     vv  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_71975758_7    850 CATCAGCCTTGGCAAAGAATTTTTGACTAAGTCTCCAGA--TTTAATTGC 897
                          v ii vi v     v iv  i  iiv  v v v   i --ivi  --  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GC 614

  chrX_71975758_7    898 AACAAAAACAAAAATTGACACCCCAA---GACCGAATTAAACTGAAGAGC 944
                                iv      v  i ----  ---   ivv  i   v v  i i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATA----AATTGGACTTCATCAAAATTAAAAAC 660

  chrX_71975758_7    945 TTCTACACAGCAAAAGAAGCCAGCACCAGAGTAAACAGACAGCCTACAGA 994
                           i iii vv    i  vi i v  vv i   i  v     i  i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_71975758_7    995 ATGAGAGAAGATATTAGCAAACAATGCATGTGACAACGGCCTAATATCCA 1044
                            i     i     v     iv  ii  v   i  v  v  vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_71975758_7   1045 GAATCTATAGGGAACTTAAACAAATCAACAAGTAAAACACAAATAGCCCC 1094
                             v    ii     ivv    v    i  vv    v       i   v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_71975758_7   1095 ATTTAAAAAAAAAAAAAACAGGCAAAGGACATGAACAGACACTTCTCAAA 1144
                            ?     ---------ii         iv    i     i     v  
  L1M4_orf2#LINE/    811 ATTWAAAAA---------TGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_71975758_7   1145 GGAAGATGTATAAGCGGCCAACAA--ACATGAAAACATGCTCAGCATCAC 1192
                         i      i  i  ii      i  --         v       i     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_71975758_7   1193 TAATCAT 1199
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.46 (108 / 74)
Gap_init rate = 0.02 (11 / 675), avg. gap size = 3.55 (39 / 11)  


3054 28.15 0.44 0.44  chrX_71983075_71989504     5032  5937 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_71983075_7   5032 GAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAATGG 5081
                            ii i  i     i        v      v i        v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_71983075_7   5082 CCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTA 5131
                          v     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_71983075_7   5132 CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCACA 5179
                            iivi i  i  ii     -   -- v  i  - iii    v    i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chrX_71983075_7   5180 TGGAACCAAAAAAGAGCCCGCATAGCCAAGAAAATCCTAAGTAAAAAGAA 5229
                              viiv  ii  v  v v        i v    i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_71983075_7   5230 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5279
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_71983075_7   5280 CAGTAAACAAAACAGCATGGTCCTGGTACTAAAACAGATATGTAGACTAA 5329
                               v   i    ii    v    i iv ii i   i  i    ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_71983075_7   5330 TGGAACAGAACAGATGCCTCAGAAACAACATCACACATCTACAACCATCT 5379
                              i    iv  vivii      i  vvi  i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_71983075_7   5380 GATCTTTGACAAACTGGACAAAAAGAAACAATGGGGAAATGATTCCCTAT 5429
                            i  i     ivvv v   i vv vv           vi  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_71983075_7   5430 TTAATAAATGGTGCTTAGAAAACTGGCTAGCCATGTGCAGAAAGCTGAAA 5479
                          i  i          vi  v      v  ?   ii    i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_71983075_7   5480 CTGGATCCCTTCTTTACACTTTCTACAAAAATTAATTCAAGATTGATTAA 5529
                         i    i    v i i    iv v            i    i  v   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_71983075_7   5530 ACACTTAAATGTATAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5579
                          v  i        vi v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_71983075_7   5580 GCA-ATACCATTCAGGACATAGGCATGGGGAAGGACTTCATGACTAAAGC 5628
                          ?i- v i -   iv   v v  vv i  v  v ii   v iiv  vii 
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_71983075_7   5629 ACCAAAAGCAATGGCAACAGAAGCCAAAATAGACAAATGGGATCTAATTA 5678
                                   vvi      i   vv        i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_71983075_7   5679 AACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAATGAACAGG 5728
                           v v  i ii  i  ii vv    i  v    i  vv i i    v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_71983075_7   5729 CCACCTATAGAATGGGAGAAAATTTTTGCAATATTCTCC-TCTGACAAAG 5777
                          v   i i               v       -  iv vi-     i  i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATAAGG 748

  chrX_71983075_7   5778 GGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAA 5827
                          i  vi          v  i         vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_71983075_7   5828 ACAAACAACCCTATCAAAAAGTGGATAAAGGACATGAACAGACACTTCTC 5877
                              i     v  i?    i   ii      iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_71983075_7   5878 AAAAGAAGACATCTATGCTGCCAACAGACACATGAAAAAATGCTCATCAT 5927
                         v        i  vi viiv     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_71983075_7   5928 CACTGGTCAT 5937
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.49 (150 / 101)
Gap_init rate = 0.01 (7 / 906), avg. gap size = 1.14 (8 / 7)  


2836 26.69 2.29 0.92  chrX_71991726_71993732      642  1514 (493)    L1M4_orf2#LINE/L1       24   908 (0)  

  chrX_71991726_7    642 GATTGGAGGAATCAATATCATTAA-ATCGCCACACCACTCAAAGCAATCT 690
                                i  v i     ii    -  v  v i  iv i    vii    
  L1M4_orf2#LINE/     24 GATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCT 73

  chrX_71991726_7    691 ACACATTCAACACAATTCCTATAAAGTTACCAA-TGTCATTCTCCACTGA 739
                            v       i    i     v  iv v   i-  i -  i iii v  
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGA 122

  chrX_71991726_7    740 A-TTAAGAAAAAACCTATTCTACAATGCATTTGGA--TCCAAAGAAAGAG 786
                          -  i v  i--- iv  i   v   v   v    -- v   i ---  v
  L1M4_orf2#LINE/    123 AATTGACAAG---CTGATCCTAAAATTCATATGGAAATGCAAGG---GAC 166

  chrX_71991726_7    787 CCTGAATAGCCAAACCAATTCTGAAA-----GAATAAAGCTGGAGGCATC 831
                           v           v    ii     -----   i    i      vv  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_71991726_7    832 ACATTACTGGACTGCAAACTATACTACAAGGCTACAGTAACCAAAGCAGC 881
                            i v ivi i v    viv        i          i   ii   i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_71991726_7    882 ATGGTATTGGTACAAAAACGGATATATAGAACAATGGAACAGAATGGAGA 931
                         i     i   i i  ii ii  i       v        i     v    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_71991726_7    932 ACCCAGAAACAAAGCCACACACTTAGACCCAACTGATCTTTGACAAAGTT 981
                         ii       i   v   i   i   vivi   i    i  i     i v 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_71991726_7    982 GACAAAAATAACCA-TGGTGAAAGGACACCCTAGTCAATAAATGGTGCTG 1030
                          v   i vi vi  -   v     i i vi  vv    i           
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_71991726_7   1031 GGATAGCTGGCTAGCTACATGCAGAAGAATGAAACTGGATCAATACCTCT 1080
                            i i    v  ? i       i         ii    i vv      v
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_71991726_7   1081 CACTATATACAAAAATGAAGTCAAGACGAGTTAAACATTTAAATGTAAGA 1130
                            i            v  v    i i ii i ? v ii           
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_71991726_7   1131 CCTCAAACTATAAAAATCTTAGAAGAAAACCTAGGAA-AATTCTTCTGGA 1179
                         v  v           v              v    ?i-  v     vv  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_71991726_7   1180 CATTGGCCTAGGTAAAGAATTCATGACTAAGACCTCAGAAGCAAATGCAA 1229
                          v    vi    i  v iv   v iiv  v   vi  i     v v    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_71991726_7   1230 CCAAAACAAAAATTGACAAGTGGGACCTGATTAAGCCAAAGATCTTCTGT 1279
                          v   iv      v  i  i v    i v  i  iviv  i v   i   
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_71991726_7   1280 ATAGCAAAAGAAATCATCAACAGAATAAACAGACAACGTACAGAATGGGA 1329
                         iivv    i  v ii     v i i i  v       vi           
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_71991726_7   1330 GAAAATATTTGCAAACTGTGCATCCGACAAAGGACAAATATCCTGAATCT 1379
                                        iii ii   i  i  i    vvi     v    v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_71991726_7   1380 ATAAGGAAACTAAACAAATCAATGAGAAAAAT-----CAGCCCCATTAGA 1424
                             i   viivv    v     i v     v-----i i   v   ?i 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_71991726_7   1425 GTGTGGGCAAAGGACATGAACAGACACTTCTC--AAAAAGGCAAAAAAGT 1472
                         ivi           iv    i     i     --  i   ii v v  i 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_71991726_7   1473 GGCCAA-AAAAATATGAAAAAAATTCTTAACATCACTAATCAT 1514
                               -  iv i       i - v  i       ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.02 (14 / 885), avg. gap size = 2.00 (28 / 14)  


2904 21.91 4.12 5.64  chrX_72020455_72023542.rev     1676  2597 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72020455_7   1676 TGGAAAGATATCCTGTGTTAATGGACTGGAAGAATTAATATTGTGAAAAC 1725
                                      ii    v     i       v          v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_72020455_7   1726 ATTCTATTTTAACTACCAAATTGACTACCCAAATCAATCTACGGATTCAA 1775
                         --------- ii -----   --   v       ii      i       
  L1M4_orf2#LINE/     50 ---------TGGC-----AAT--ACTCCCCAAATTGATCTACAGATTCAA 83

  chrX_72020455_7   1776 TGCAAAACCTATCAAA-TACCAA-TGTCATTTTT-CATAAATATGGGAAA 1822
                         i    vv         - v   i-  i v     -  v    -  -- v 
  L1M4_orf2#LINE/     84 CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT-TG--ACA 130

  chrX_72020455_7   1823 AAACAATCTTAAAATTTACATAGAATCACAAAA-ATCCATGAATAGCCAA 1871
                          ivii   i       i i  i   vii   ii- i   -          
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA-GAATAGCCAA 179

  chrX_72020455_7   1872 GACAATCATAAGTAAAAACAAAGCAGAACAATGACAAGAACAAAAAGCTT 1921
                         i      v i --    i-----------------         i---  
  L1M4_orf2#LINE/    180 AACAATCTTGA--AAAAG-----------------AAGAACAAAG---TT 207

  chrX_72020455_7   1922 GGAGGCATCACATGACCTCACTTCAAACTACACTACAAAACAATAATAAT 1971
                              vv     ivv  iv i      vivi        i v i i    
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_72020455_7   1972 TAAAACAGCATGATACTGGCATAAAAATAGACCCACACTGACCAATGGAA 2021
                         i  i    ii  i           ii      vi i --  i        
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATA--GATCAATGGAA 305

  chrX_72020455_7   2022 CAGAATTGATAGCCCAGAAATGAGCCCATGCATTTACAGTCAACTGATAT 2071
                         i        v  i        i i     i      ii     i    v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_72020455_7   2072 TGGACAAAAGTAGCAGGAATATAGAATGAGAAAAAGACAGTGTCTTCAAT 2121
                          v     ii  iv  i  vi  vv    i i   ii i   v i     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_72020455_7   2122 AGATGGTTTTGGGAAAACTGGATATCCATCTGCAGAAAAGAAAAATGAAA 2171
                          i     vi     v         ?   iv    --      ---    i
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCA--AAAGAA---TGAAG 450

  chrX_72020455_7   2172 TTGGACCCTTTTCTCACATCATATACAAAAATCAACACAAGATGAATTAA 2221
                                 i vi      i             i   v   i   i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_72020455_7   2222 AGAA-TAAACATAAAACCTGAAACTGTTAAACTACTATAAAAAAATCATA 2270
                            v-    ii   i v  i     i v     vi  v  i    -    
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATA 549

  chrX_72020455_7   2271 GAGGAAAAAC---ATTACATTGGTCTCAGCAATGCTTTTTTATATTTGAC 2317
                          i? v   v ---i v  v    vi vi      v   i   v  v    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_72020455_7   2318 CCCAAAAGTGCAAGCAACTAAAGTGAAAATAGACCAATGGGATTACATCA 2367
                         v       ii        v    vi        iv   v   i v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_72020455_7   2368 AAATAAAAAGCTTCTGCACAACAAAGGAAACAATTAACAGAGTAAAGAAA 2417
                             v    i   i  ii vv       v  v  i  v i   i  i i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_72020455_7   2418 CAATGTACAGAATGAGAGAAAATATTTGCAAACTATACATCTAACAAGGG 2467
                            ivi        i                 ii   i    i i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_72020455_7   2468 GTTAATATCCAAAATACATAAGGAACT------AGTC--TGATAAGAA-- 2507
                         ii vi      i    i    i     ------ v  -- i    i  --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_72020455_7   2508 -------------------ATGGTCAAAGGACATTGA-TAGAAAATTCTC 2537
                         -------------------    v       i-    -    v v     
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGACATTTCTC 848

  chrX_72020455_7   2538 AAAAGAAGACATACAAATGGCTAACAGATACATACAAAAATGCTTGACAT 2587
                         v        i           i  i iii    iv   i     ii    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_72020455_7   2588 CACTGATTAT 2597
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.88 (130 / 69)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.75 (90 / 24)  


1862 21.95 5.38 0.62  chrX_72034795_72041196.rev        1   483 (5919)    L1M4_orf2#LINE/L1      301   806 (102)  

  chrX_72034795_7      1 TAGCACAGAATAGAGATCTCAGAAAGAAATTCTTGCATATAAGATCAAAT 50
                          i v i     v    vii      v   ii v i   v  v i    v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_72034795_7     51 AAATTTTGACAAGGGTATCAAGACCATTTGATATAGGGAGTACAGTCTTT 100
                         i v   i         ii          ii  ivi ii  v i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_72034795_7    101 CCAACAAATGGTGTTTGGAAAACTGGATATCCACATACTAAACAATGAAG 150
                         i            i v   v         ?      i v   v       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_72034795_7    151 TT----------CTTAAGCCATGTACAAAAATTAACTCAAAATGGATTAA 190
                           ----------  i vi    i                        i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_72034795_7    191 CAACATAAATGTAAAAGCAGAAACTATAAAACTCCTAGAAGAAAATAGAA 240
                         vi  v         i   vi              i          i v i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_72034795_7    241 AAGAAAAGCTTCATAACATTGGATTTGGCAGTAATTTCTTGGCTAAGACA 290
                         i? v   v    i i  v    i  v    i ii      i v  v    
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_72034795_7    291 CCAAAAGCACAGGCAGCCAAA--AAAAATCGGTAAGCTGCAC---ATTAA 335
                                    i   i v   --      v i   ii  v  ---  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_72034795_7    336 AATTTTAAAAA---TTATTCATCAAAGTACACAAGCAATGTGGTGAAA-- 380
                             --     ---  i v v      v    v v   vivi      --
  L1M4_orf2#LINE/    651 AATT--AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_72034795_7    381 ----CCCACAGAAGGGAAGGAAATATCTGCAAATCATATATCTGATAA-- 424
                         ----         v  i  i      i                     --
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_72034795_7    425 AATTTAGTATGAAGACTATATAAGGAACTCCTACAACTCAACAAAAACCA 474
                         i i  -    vv   v       i      i          i  v  vv 
  L1M4_orf2#LINE/    749 GACTT-GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_72034795_7    475 GCTAAAGAA 483
                          vi   v  
  L1M4_orf2#LINE/    798 GACAAATAA 806

Transitions / transversions = 1.29 (58 / 45)
Gap_init rate = 0.02 (8 / 506), avg. gap size = 3.62 (29 / 8)  

3192 27.15 0.66 0.44  chrX_72034795_72041196.rev     5006  5911 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72034795_7   5006 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5055
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72034795_7   5056 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5105
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72034795_7   5106 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5153
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72034795_7   5154 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5203
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72034795_7   5204 AACAAAGCTGGAGACGTCACACTACCTGACTTCAAACTATACTACAAGGC 5253
                                i     ivv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72034795_7   5254 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5303
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72034795_7   5304 AATGGAACAGAAC--AGAGCCCTCAGAAATAGCACCGCATATCTACAACT 5351
                                i    i--    i  --       ivv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_72034795_7   5352 ATGTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGG-AAAGGATTCC 5400
                          vv    i  i     ivv  vv  i v  vv       -    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72034795_7   5401 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5450
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72034795_7   5451 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGA 5500
                            ii    i    v   i     v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72034795_7   5501 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5550
                          i ?    i       v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_72034795_7   5551 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5600
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_72034795_7   5601 AACACCAAAAACAATGGCAACAAAACTCAAAATTGACAAATGGGATCTAA 5650
                         i         i  vvi         vvv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72034795_7   5651 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5700
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_72034795_7   5701 AGGCAACCTA-AAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5749
                           i     i - i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_72034795_7   5750 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5799
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_72034795_7   5800 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAAGAGACACTTC 5849
                          i     i     v  i?    i    ii     iv    v     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_72034795_7   5850 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5899
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_72034795_7   5900 ATCACTGGCCAT 5911
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2876 27.25 1.89 0.89  chrX_72055497_72061112     4225  5123 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72055497_7   4225 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4274
                               i i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72055497_7   4275 GGCCACATGGCCCACAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 4324
                            v i ivv    v v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72055497_7   4325 CACCA-TTGACTTTCTT-CACAGATTTAGAGA-AAACT-ACTTTAAATGT 4370
                         iv   -i  v    i  -  v i   ----  -  i  - iii    vv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT----GACAAGCTGATCCTAAAATT 146

  chrX_72055497_7   4371 CATGTGGAACCAAAACAGAGCCCATATAGCCAAGACAATCCTAAGCAAAA 4420
                            i     viiv  vi  v  viv        i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_72055497_7   4421 AGAACAAAGCTGGAGGCATCACCCTACATGACTTCATACTATACTACAAG 4470
                                  i      vv    v  v vii i    v viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_72055497_7   4471 GCTGCAGCAACTAAAACAGCATGGTACTGGTACCAAAACAGACATGTAGA 4520
                            i   i  ii  i    ii         i iv ii i      i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_72055497_7   4521 CTAATGGAGCAGAACAGAGACCTCAGAAATAACACCACAAATCTACAGCC 4570
                         ii      ii    iv    vii         vv   i v  i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_72055497_7   4571 ATCTGATCTTTGACTAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4620
                          vi    i  i   v ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72055497_7   4621 CTATTTAACAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 4670
                           v  i           i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72055497_7   4671 GAAACTAGACCCCTTCCTTACACCTTATACAAAACATAACTCGAGATGGA 4720
                            ii i       v   i     v         vv      i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72055497_7   4721 TGAAAGACTTAACCATAAGACCTAAAACCATTAAAACCCT-AGAAGAAAA 4769
                          v ?    i   vii     v       i  -     i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chrX_72055497_7   4770 CCTAAGTG-ATACCATTTAGGTCATAGGCATGGGCAAAGATTCCATGAAT 4818
                          v  i ? - v i v ivv ii v i  i- i     v i  i v ii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_72055497_7   4819 A-AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGGATCT 4867
                          -i            vvi          vv     v  i   iv   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_72055497_7   4868 AATTAAAACTAATGAGTTTCTCTACAGCAAAAGAAACTATCATCAGAGTG 4917
                         v  i    i   -i ii  i v i vv    i  v       vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_72055497_7   4918 AACAGGCAACCTACAGAATGGCACGAAAGT-TTTGCAATCTATCCATCTT 4966
                           v  i     i         v -    i -       vii  vi    v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGA-GAAAATATTTGCAAATCATATATCTG 742

  chrX_72055497_7   4967 ACAAAAGGCTAATATCCAGAATCTACAAGGAGCT--TA-AACTTA-CAAG 5012
                          i  ii i  vi          v  i  i  i  --  -    i -i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_72055497_7   5013 AAAAAAA-----AATCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 5057
                              i -----  i  v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_72055497_7   5058 CTTCTCAAAAGAAGACATTTATGTGCCCAACAAACATATGAGAAAAAGCT 5107
                         i     v        i  vi vi  v    i  i  i    i  i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_72055497_7   5108 CATCATCACTGGTCGT 5123
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.47 (25 / 17)  


3131 27.86 0.44 0.44  chrX_72062024_72068432     5009  5916 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72062024_7   5009 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5058
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72062024_7   5059 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72062024_7   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72062024_7   5157 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5206
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72062024_7   5207 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGAC 5256
                                i      vv       v  ii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72062024_7   5257 TACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5306
                                 i v i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72062024_7   5307 AATGGAATAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAACT 5354
                                     i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_72062024_7   5355 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5404
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72062024_7   5405 CTATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5454
                           v  i  i     i        v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72062024_7   5455 GAAACTGGATCCCTTCCTTATAGCTTATACCAAAATCAATTCAAGATGGA 5504
                            ii    i    v   i i v v     v     i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72062024_7   5505 TTAAAGACTTAAACTTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5554
                          i ?    i    iv v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_72062024_7   5555 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5604
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_72062024_7   5605 AGCACCAAAAGCAATGGCAACAAAACTCAAAATTGACAAATGGGATCTAG 5654
                         ii           vvi         vvv     v  i    v   ii vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72062024_7   5655 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5704
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_72062024_7   5705 AGGCAACCTACAAGATGGGGGAAAATTTTCGCAACCTACTCATCTGACAA 5754
                           i     i   ii     i      v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_72062024_7   5755 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5804
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_72062024_7   5805 AAACAAACAACCCCATCAAAAAGTGGGCAATGGTCATGAAGAGACACTTC 5854
                          i     i     v  i?    i       v  viv    v     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_72062024_7   5855 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5904
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_72062024_7   5905 ATCACTGGCCAT 5916
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (146 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 660 21.97 1.52 0.00  chrX_72076563_72078221.rev       98   229 (1430)  C L1M4_orf2#LINE/L1   (771)   137     4  

C chrX_72076563_7    229 AAAGACAATCCATGTTCATAAGTTGGAAAAC--AGTATTTTTAAGATGAT 182
                              i vi          iii      i  -- i    v        ii
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

C chrX_72076563_7    181 AATAGTACACAAATCGATCTATATATTTCACACAATCCTCATCAGAATTC 132
                             v v v     i      i v   iv  i      ii    i   i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

C chrX_72076563_7    131 CAGCTGTCTTCTTTGTAGAAATTGACAGACTGAT 98
                               i   i    i           ii     
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

Transitions / transversions = 3.14 (22 / 7)
Gap_init rate = 0.01 (1 / 134), avg. gap size = 2.00 (2 / 1)  

2353 23.35 3.29 2.69  chrX_72076563_72078221.rev      501  1168 (491)    L1M4_orf2#LINE/L1      237   908 (0)  

  chrX_72076563_7    501 TTATTACAAAGCTATAGTAATCAAAACAGTATGATACTGGCATAGAAACA 550
                            i          i         i     i  i          iii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_72076563_7    551 GACACATAGACCAGTGGAACAGAATAGACAG---AAAAAAAAACCTAGGC 597
                             i     i  i     i     v  v  --- i   v     i vi 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_72076563_7    598 ATATATGGTCAACTAATCATCAATAAAGGCACAAAGAATACACAACAGAA 647
                           v         i i  iv  i i  i  ii v    vi iv   ii ii
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_72076563_7    648 AAAGGATAGCCTCTTCAATAAATGGTGTTGGGAAAACTGGATATGTGAAT 697
                             i    i  i     i        i     v         ?viiv  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_72076563_7    698 GCAAAA--ATC---TTGGATGCTTATGTTACACCATACAGAAAAATCAAC 742
                               --  v---     iv i  iv i        i v      i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_72076563_7    743 TCAAAATAGACTAAAGATTTAAACATAAGACCTGAATCCATAAAACTCTC 792
                                i  ii ?   ii    ii     v  i  v i          i
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_72076563_7    793 AGAAGAAAACATAGAGGGAAAC-----TG-CTTTGGTCTTGGCAATGATT 836
                                       i? v   i-----  - i    vi v       i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_72076563_7    837 TCATGGACATGACACCTAAAGCATAGACAATAAAAGCAAAAATAAACAAG 886
                           v i  i        v      i ii   i     v       i i  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_72076563_7    887 TGGGAATACTTCACA-TTAATAAGTTTCTATGCAGCATAAAATA--A--A 931
                          v   v v v   v -    -  ii  i i   vv  v ii i -- -- 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_72076563_7    932 AAAAAACGAAAAGGCAACCTAAGGAATGAAAAAAA---TTTGGAAAACAT 978
                          i   ii      i     i vi     ii i   ---    v   v   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_72076563_7    979 ATATCCAATATGGAGTTAATATCCAAAATATATAAGGAACTCACACAATT 1028
                              ii   v  iii vi      i         i      vi    i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_72076563_7   1029 CAATAGCATAAAAAACAAAACAAAATGAAACAAAACAACCTGAATTAAAA 1078
                              --       i--------------     -i    ii v ?    
  L1M4_orf2#LINE/    786 CAATA--ATAAAAAG--------------ACAAA-TAACCCAATTWAAAA 818

  chrX_72076563_7   1079 ATGGGCAAAAGACCTAAATGGACATTTTTCCAAGGAAGACTTATAAATCA 1128
                                  i  ii i   i       i     i     iv  i    vi
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_72076563_7   1129 CCAACAAGTACATGTAAAGATGCTCAACACCACTAATCAT 1168
                             i   i     v              i  ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.62 (110 / 42)
Gap_init rate = 0.02 (13 / 672), avg. gap size = 3.08 (40 / 13)  


3041 27.32 1.22 0.77  chrX_72097046_72102898.rev     4459  5362 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72097046_7   4459 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4508
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72097046_7   4509 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4558
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72097046_7   4559 TACCAATTACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4606
                          v   ii i i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72097046_7   4607 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 4656
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72097046_7   4657 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAA--CTACAATAAAAG 4704
                                i      vv   ii  v  ii i      --i   v i   --
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-- 246

  chrX_72097046_7   4705 GCCAAAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 4754
                           i v     i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_72097046_7   4755 CCAATGGAACAGAA--AAGAGCCCTCAGAAATAATGCTGCATATCTACAA 4802
                         i        i    --i    i  --        vv iii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_72097046_7   4803 CTACCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 4852
                         ii vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_72097046_7   4853 CCCTATTTAATAAATGGTGCTGGGAAAACTCGCTAGCCATATGTAGAAAG 4902
                         vi  v  i  i              v    v v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_72097046_7   4903 CTGAAAC--GATATCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 4950
                         v    ii--  ivi  v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_72097046_7   4951 GATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5000
                            i ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_72097046_7   5001 ACATAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5049
                                ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_72097046_7   5050 TAAAACACCAAAAGCAATGGTAATAAAAGCCAAAATTGACAAATGGGATC 5099
                           vi            vvi i  i     vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_72097046_7   5100 TAATTAAACTAAAGAGCTTCTGCAAAGCAAAAGAAACTACCATCAGAGTG 5149
                          v  i   v v  i i   i  iivvv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_72097046_7   5150 AACAGGCAGCCTGCAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 5199
                           v  i  i  ii                v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_72097046_7   5200 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5249
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_72097046_7   5250 AAAAAA--AACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5297
                             i --  i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_72097046_7   5298 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5347
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_72097046_7   5348 ATCATCACTGGCCAT 5362
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


3311 26.76 0.44 0.44  chrX_72108503_72114782     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72108503_7   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72108503_7   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72108503_7   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72108503_7   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72108503_7   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72108503_7   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72108503_7   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5225
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_72108503_7   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72108503_7   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGATAGCCATATGTAGAAAGCT 5325
                           v  i  i              v         ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72108503_7   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72108503_7   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_72108503_7   5426 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_72108503_7   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5525
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72108503_7   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_72108503_7   5576 AGGCAACCTACAACATGGAAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i     i   iv    i       v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_72108503_7   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_72108503_7   5676 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_72108503_7   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5775
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_72108503_7   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 223 18.06 0.00 8.33  chrX_72119270_72125548       53   124 (6155)    L1M4_orf2#LINE/L1      843   908 (0)  

  chrX_72119270_7     53 TTTTTCAAAAGCCTTAAAGATCATTTATGCAGCCAAAAAACACATGAAAA 102
                            i  v    -----     -  vi viii     v  i          
  L1M4_orf2#LINE/    843 TTTCTCCAAAG-----AAGAT-ATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_72119270_7    103 AATGCTCGCCATCACTGGCCAT 124
                         i      iv     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.03 (2 / 66), avg. gap size = 3.00 (6 / 2)  

3204 26.10 1.10 1.10  chrX_72119270_72125548     4879  5786 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72119270_7   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72119270_7   4929 GGCCATACTGCCCAAGTTAATTTATAGATTCAATGCCATCCCCAACAAGC 4978
                            v     v     i  i  i  i        i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72119270_7   4979 TACCAA-TGACTTTCTT-CAGAGAGTTGGAAAAAAGT--ACTTTAAAGTT 5024
                          v   i-  v    i  -    i -   --- v   i-- iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA-TTG---ACAAGCTGATCCTAAAATT 146

  chrX_72119270_7   5025 CATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAA 5074
                                  viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_72119270_7   5075 AGAACGAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 5124
                              i   i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_72119270_7   5125 GCTACAGTAACCAAAACAACATGGCACTGGTTCCAAAACAGAGATATAGA 5174
                                   i   i   iii   i     iviv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_72119270_7   5175 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTAGGA 5222
                         i        i    i--    i  --        vv  ii i  i  v i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_72119270_7   5223 CTATCTGATCTTTGACAAACCTGAGAAAAGCAAGCAATGGGGAAAGGATT 5272
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_72119270_7   5273 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5322
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_72119270_7   5323 CTGAAACTGGATCCCTTTCTTACATCTTATACAAAAATTAATTCAAGGTG 5372
                         v    ii    i    vi  i   i v              i    ii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_72119270_7   5373 GATTAAAGACTTAAATGTTAGATGTAAAACCATAAAAACCCTAGAAGAAA 5422
                            i ?    i       v   vv      i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_72119270_7   5423 ACCTAGGC---AATGCCATTCAGGACATAGGCATGGGCAAGGACTTCATG 5469
                           v    ?---   -- -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_72119270_7   5470 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5519
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_72119270_7   5520 TCTAATTAAACTAAAGAGCTTCTGCACTGCAAAAGAAACTACCATCAGAG 5569
                         ii v  i   v v  i i   i  ii  v    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_72119270_7   5570 TGAACAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATGTACTCATCT 5619
                             v  i  i  i                 v       vvi ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_72119270_7   5620 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAACTTA-CA 5668
                           i  i  i  vi          v  i  v      vv    -  i -i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATA 790

  chrX_72119270_7   5669 AGAAAAAAACAAACAACCCCAACAAAATGTGGGCAAAGGATATGAACAGA 5718
                          v     i     i     v vi?   vi            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_72119270_7   5719 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATG 5768
                           i     v        i  vi viii     v  i          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_72119270_7   5769 CTCATCATTACTGGTCAT 5786
                             v   i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


3367 24.36 1.56 0.56  chrX_72147410_72151660.rev     2862  3760 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72147410_7   2862 TGGAAAAGTATTCCATGTGCATAAATTGGAAGAATAAATATTGGTAAAAT 2911
                               ii   i      v   ii         v v       v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72147410_7   2912 GTCCATACTACCCAAGGAAATCTGCACATTCAATGCAATCCCTATCAAAA 2961
                          v v     v     ivvi    i  v      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72147410_7   2962 TGTCAATGATACTCTTCACAGAAATAGAAAAA---ATTATAAAATTCATA 3008
                          vi  iiviivi i  ii       v  v  i---  iv           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_72147410_7   3009 TGAAACAAGAAAAGACCCACAATAACCATGACTCTGTCTTAAGCAAAAAG 3058
                           i  vviv  ii      v    i   vi  v--i    i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACA--ATCTTGAAAAAGAAG 198

  chrX_72147410_7   3059 AACAAAACTGAAGAAATCACATTACCTGACTTCAAATTATACTACAGAGC 3108
                               ii  i  i v     i v  ii i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72147410_7   3109 TATCGTAACCAAAACAGCATGGTACTGGCATATAAACAGATGCATAGACC 3158
                           iv    i   i    ii             vii i   iii     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72147410_7   3159 AAAGGAAAAGAATAGAAAACCCAGAAAAAAATTCACACACTTACAGTGAA 3208
                           v    v     v  i ii       v   ii  i   i   ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_72147410_7   3209 CTCATTTTTGATAGAGGTGCCAAGAGCATACACTGGGGAGAAGACAATCA 3258
                         i v     i  i ii          v   v  v      i ii i i  v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_72147410_7   3259 TTTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGA 3308
                               i              v         ?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_72147410_7   3309 AACTAGACCC-----TCTTGCCATATACAAAAATCAAATAAAAATGGATT 3353
                          ii i     -----  vii              i  v v         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_72147410_7   3354 AAAGACTTAAATCTAATACTTCAAACTATAAAACTACTACAAGAAAACAA 3403
                          ?    i     v   v vi v             vi  v         v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_72147410_7   3404 TGGGGAAAATCTTCAGGACATTGGTCTGGGCAAAAATT-CTTGTGTAATA 3452
                         v  ? v        iv   v    vi i     vii  -   ivi  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_72147410_7   3453 CACCAGAAGCACAGGCAACCAAAGCAAAAATGGACAAATTGGATCACATC 3502
                              i       i     v    v      i  i        iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_72147410_7   3503 AAG-TTAGAAAGCTTTTGCACAGCAAAAGAAACAATTAACAATATGAAGG 3551
                           i-   i   -      ii vv    i  v  v  i  v  vi    ii
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_72147410_7   3552 GAAAACCCACAGAATGGGAGAAAATATTTGCAAACCACCCATCTGACAAG 3601
                           v                               i  ivi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_72147410_7   3602 GGATTAATAAGCAAAATATA-AGCGAAGTTCAAAGAACTCTATA-CAAAA 3649
                            i vi  vv  i      - iv   -i  vv v     v   -i    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATAATAAAA 796

  chrX_72147410_7   3650 AATTGAATAATCCAATTGAAAAAATGTGCAAAAAATTTGAA--AACATTT 3697
                          ivii     i      -?       v     ii       --i      
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_72147410_7   3698 ATCAAAAGAAGGCATACAAATGGCAAACAGGCACATGAAAAGGTGGCCAA 3747
                         v  v       ii           v  i i            i  vi   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_72147410_7   3748 CGTCACTGGTCAT 3760
                          i   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (131 / 84)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


2647 28.23 0.68 0.91  chrX_72166620_72168809.rev      814  1695 (495)    L1M4_orf2#LINE/L1        1   880 (28)  

  chrX_72166620_7    814 TAGAAACACATTCCATGCTCATGGATTGGTTGAAAC--AATATTGTAAAA 861
                          i    v i  i     i           --i i  --        v  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGG--AAGACTTAATATTGTTAAG 48

  chrX_72166620_7    862 ATGACCACACTGACAAAAGCAATCTACAAATTCAATGCAATTTCCATCAA 911
                            i v i   vv v   vii       i      i     ii i     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_72166620_7    912 AATACCACCATAATTTGTCACAGAACTAGAAAAAACAATGCTAAGGTTTA 961
                            v   v vvvv   v ii     v v  v  ivii  v    ii  i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_72166620_7    962 CATGAAACTAAAAAAGAGCTCACGTAGCCAAAGCAAGATTAAGCAAAAAG 1011
                         i   i  v iv  ii  v ivivi        i   vv  i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72166620_7   1012 AACAAATCTGGTGGCATTACATTACCCAACTTCAAGCTATACTATAAAGC 1061
                               vi   v  vv i   i v     i     iviv     i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72166620_7   1062 CATAGTCACCAGAACAGCATGGTACTGGTATAAAAATAGGCATATAGACC 1111
                         i i   v i  ii    ii         i    ii    i        i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72166620_7   1112 AATGGAACAGAATAGAGAATGCAGAAATAAAGCCATATACTTACAGTCAA 1161
                                i     v    i v          v     i i   ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_72166620_7   1162 CTGATCTTCAACAAAGCAAACAAAAACATAAAGTGAGGAAAGGACACCCT 1211
                         i    i   i    i vviv   i v   vv i  i      i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_72166620_7   1212 ATTCATCAAATGGTGCTGGGGTAATTCGCAAGCTACATACAGATGAATAA 1261
                         v    v              ii  i v vv ? i    i  i v    i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_72166620_7   1262 AACTGGAACCTTGTCTCTCATCTTATACAAAAATCAACTCAAGATGGGTC 1311
                          ii    v  i ii   v  i v           i       i    i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_72166620_7   1312 ACAAACTTAAGTCTAAGACACAAAACCATAAAAAATCTAGAATATAACAT 1361
                          ? i  i   i v     vvi     i      vvii     v v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_72166620_7   1362 TGGAA-AAATACTTCTAGACATTGGCTTATGCAAAGGCTTTAT-GACCTG 1409
                         v  ?i-    -    vv   v    v   v    v  i  iv -  iv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_72166620_7   1410 GAACACAAAAGCAAATGCAACAAAAACAAAGATAAATAGGTAAGCCCTTA 1459
                         iv  -        v v         iv   i   i   ii vi v i i 
  L1M4_orf2#LINE/    598 ACAC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72166620_7   1460 ATTAAACTAAAAGCCTTCTGTCCAGTGAAAGAAATAATCAGCAGATTAAA 1509
                         viv   i     i i  -   v vvii  i  v iv    iv i v i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_72166620_7   1510 CAGACAACCCACAGAGTGGAAGACAATCTTTGCAGTCTATATGTCAAACA 1559
                         v              i   i   v   v      ivii    i  vi i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_72166620_7   1560 AAGGACTAATACCCAGCATCTACAAGGAACTCAAACAAATCAGCAAGCAA 1609
                          i     vi  i    v  v  i  i      vv    v   ii  -i  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAA 794

  chrX_72166620_7   1610 GAAAGAAAAA-AATCCCATCAAAAAGTGGGCTAAGGACATGAATATACAA 1658
                         -     v   -  i  v  i?    i     v     iv      v   v
  L1M4_orf2#LINE/    795 -AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_72166620_7   1659 TTCTC-AAAGAAGATACACAAATGGCAAAAAAACCACA 1695
                              -          i         v  v  i -   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGC-ACA 880

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.01 (12 / 880), avg. gap size = 1.17 (14 / 12)  


3053 27.85 0.66 0.33  chrX_72187258_72193365     4711  5615 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72187258_7   4711 TGGAAGAACATTCCATGTTCATGGATAGGAAGAATCAATATGATGAAAAT 4760
                              ii i  i              v      v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72187258_7   4761 GGCCATGCTGTCCAAAATAATTTATAAATTCAATGCTGTTCCCATCAAGC 4810
                            v  i  vi     v i  i  i i      i  vi i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72187258_7   4811 T-ACAACTGAGTTTCTTCACAGTATTAGAAAAAATTACTTTAAACTTTAT 4859
                          -v  i   vv   i  -i   v v v  v  iv v iii    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_72187258_7   4860 ATGGAACCAAAAAAGATCCTATATAGCCAAGACAATCCTAAGCAAAAAGA 4909
                               viiv  ii  i  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_72187258_7   4910 ACAAAGCTGTAGGCATCATGCTACCTGACTT-GAAACTATACTACAAGGC 4958
                               i  v   vv   ii  v  ii i  -i     -        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_72187258_7   4959 TACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5008
                                     i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72187258_7   5009 AATTGAACAGAACAGAGGCCTCAGAAATAATGCCACCCATCTACAACCAT 5058
                            v   i    iv   ivii         vv   iv   i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_72187258_7   5059 CTGATATTTGACAAAGCTGACAAAAACAAGCAATGAGGAAAGA-TTCCCT 5107
                         i    v  i     i v  v   i v  vv     i       - vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_72187258_7   5108 ATTTAATAAATGGTGTTGGAA-AACTGGCTAGGCATATACAGAAAACTGA 5156
                         v  i  i        i   i -      v  ?v  i  i  i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_72187258_7   5157 AGCTGGACCCCTTCCTTACACGTTATACAAAAATTTACTCAAGGTGGACT 5206
                           i         v   i    vv            v      ii    ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_72187258_7   5207 AAAGACTTAAACTGAAGATCTAAAACCATAAAAACCCTAGAAGAAAACCT 5256
                          ?    i    ivv    v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_72187258_7   5257 AGGCG-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 5305
                            ? - v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_72187258_7   5306 ACACAAAAAGCA-ATGCAACAAAAGCCAAAATTGACAAATGGAATCTAAT 5354
                             v       - v          vv     v  i    v i ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_72187258_7   5355 TAAACTAAAGAGCTTCTGTACAGCAAAAGGAACTATCATCAGAGTGAACA 5404
                         i   v v  i i   i   i vv    i iv       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_72187258_7   5405 GGCAACCTACAGAATGGGAGCAAATTTTTGCAATCTATCCATCTGACAAA 5454
                          i     i            v    v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_72187258_7   5455 GGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAGAA 5504
                           i  vi          v  i  i     ivv    v iv i  v  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_72187258_7   5505 AACAAACAACCCTATCAATAGGTAGACAAAAGATATGAACAGACACTTCT 5554
                         i     i     v  i? v ii i i    i   v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_72187258_7   5555 CAAGAGAAGACGTTTGTACAGCCAACAAACATATGAAAAAAAGCTCATCA 5604
                          v i      ii viiv ii     i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_72187258_7   5605 TCACTGGTCAT 5615
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.00 (9 / 9)  


3046 27.31 1.78 0.56  chrX_72232202_72238336     4746  5642 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72232202_7   4746 TGGAAGAACACTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4795
                              ii i ii     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72232202_7   4796 GGTCATACTGCCCAAGGTAATTTATAAATTCAATGCCATCCCCATCAAGC 4845
                           iv     v     iv i  i  i i      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72232202_7   4846 TACCAATGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTAAAGTTCA 4893
                          v   iivi i  i  ii    i-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72232202_7   4894 TATGGAAC--CAAAGAATGGCCTGCATTGCCAAGACAATCCTAAGCAAAA 4941
                                v--   i i i--  v v  v     i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_72232202_7   4942 AGAACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTGCAAG 4991
                                  i     ivv   ii  v  ii i      viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_72232202_7   4992 GCTACAGTAACCAAACCAGCATGGTACTGGTACCAAAACAGATATATAGA 5041
                                   i   iv   ii         i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_72232202_7   5042 CCAATCGAATAGAACAGAGGCCTCATAAATAACATCACACATCTACAGCC 5091
                         i    v        iv   ivii  v      vvi  i    i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_72232202_7   5092 ATCTGATCTTTGACAAGCCTGACAAAAACAAGAAATGAGGAAAGGATTCC 5141
                          vi    i  i      vv  v   i v  vvv    i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72232202_7   5142 CTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGTTGAAAGCT 5191
                           v  i  i           i  v      v  ?   i   ivi  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72232202_7   5192 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAAATCAAGATGGA 5241
                            ii    i    v   i     v              v    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72232202_7   5242 TTAAAGACTTAAATGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5291
                          i ?    i       v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_72232202_7   5292 CTAGGCA-ATACCATTCAGGACATAGCCATGGGCAAGGACTTCATGACTA 5340
                         v    ?i- v i -   iv   v v vvv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_72232202_7   5341 AAACACCAAAAGCAATGGCAACAAAAGCCAAAAGAGACAAATGGGATCTG 5390
                         vi            vvi          vv    v   i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_72232202_7   5391 ATTAAAG-----AGTTTCTGCACAGCAAAAGAAACTACCATCAGAATGAA 5435
                           i   i----- ii  i  ii vv    i  v    i  vv i i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_72232202_7   5436 CAGGCAACCTGTAGAATGGGAGAAAATTTTTACAATTTTCTTCTGTGACA 5485
                         v  i     iii               v   i   v iviv v v   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_72232202_7   5486 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACGAGAAA 5535
                          i  i  vi          v  i         vv    v iv ii v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_72232202_7   5536 AA---AAA-AACTCA-TTAAAAAGTGGGCAAAGGATATGAACAGACACTT 5580
                           ---   -   i  -  ?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_72232202_7   5581 CTC-AAAAAAGACATCTACGCCACCAACAGACACATGAAAAAATGCTCAT 5629
                            -   i    i  vi viivi    i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_72232202_7   5630 CATCACTGGTCAT 5642
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


2893 23.59 3.64 3.53  chrX_72242141_72244329.rev      795  1701 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72242141_7    795 TGAAAAGATATTGTATATTCGTGCATTGTAAGACTTAATATT---AAGAT 841
                           i        ivi  i   i  v    v             ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72242141_7    842 GACAGTACTAGCCAAAGTAGTCTACAAATTTAATGCAATCA-TATCAAAA 890
                          i  i    vv     v ii      i   i  i      v-        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72242141_7    891 ATTCCAATAATGTTTTTT-CATAAATAGAAAAG--AAT--TAAAATTTAT 935
                         - i   iiviiv      -  v    v  v   --i  --       i  
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_72242141_7    936 ATGGAACCACAAAGGACCACAAAATATTTTGGCTGCATATAACCAAAGCA 985
                               vii   i     -  i    ---------------i     i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACC-CAGAATA---------------GCCAAAACA 183

  chrX_72242141_7    986 ATTTTGAGCAAGAA---TAAAGCTGGAAGCATCATACCTCTGGATTTTAA 1032
                           i    iv     ---i    i    i vv   i  i  ivi    i  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_72242141_7   1033 TATATGTTATAAAGGTACAATAATCAAAACAGTATAATATTGATGTAAAA 1082
                         v iv ii  i    v    i       i     i ii  i  iii   ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_72242141_7   1083 ATAGAGACATAGATGAATGGAACAAATTAGAGAACCCAGAAATAAATCCA 1132
                              v i      v       i i v v    ii           i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_72242141_7   1133 CAGAAATATGATCAACTGAT-------------GCCAAGAATACACAATG 1169
                         i v vv    i    i    -------------       vi iv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_72242141_7   1170 GAGAAATGATAGTCTCTTCAATAAATGATGTTGAAACAACTAGATATCCA 1219
                          i    vi       i     i     i  i  ii      i    ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_72242141_7   1220 TATGCAAAAGAATGAACTTGGACCATTATCTCACACCATACACAAAAATA 1269
                         i               v       vi  i           i        v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_72242141_7   1270 AATCCAAAATTAATAAAAGACTTAAATGTAAGGCTTGAAACTGTAAAACT 1319
                           ii      vi  v ?    i          ivi i     i       
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_72242141_7   1320 CCTAGAAACGAGATAAAGAAAAAAA-CTTCTGGGCATTGGTCTTGGCAAT 1368
                          i     i-i i i v  i?iv   -    vv i v    vi v      
  L1M4_orf2#LINE/    534 CTTAGAAG-AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_72242141_7   1369 GATGTCTTGAATATGACACCAAAAGCACACACAACAAAAGCAAAAATAGA 1418
                          i v    ii                   vi         v         
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_72242141_7   1419 CAAGTAGGAATATGTCAATCTAAAAAGCTTCTG-----CAAAGCAAGCAA 1463
                         i  i v   v vii    vv v    i   i  -----     v --  -
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA--CA- 679

  chrX_72242141_7   1464 CCAACCAACAAAATGAAAAGGCAACCTA-AGTAATGAGAGAAGCTATTTG 1512
                         - v i   v   i       i     i -  -    i     iv      
  L1M4_orf2#LINE/    680 -CTATCAAGAAAGTGAAAAGACAACCCACAG-AATGGGAGAAAATATTTG 727

  chrX_72242141_7   1513 TAAACAATATATTATATCTGATAAAGAGTTAATATCCAAAACAAAAGAGA 1562
                         i   iv      -----       i iii vi      i  i v vi ii
  L1M4_orf2#LINE/    728 CAAATCATATAT-----CTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_72242141_7   1563 AACTCTTTCAAATCAACCACACATACACACAAAAATATTCTA-TTAAAAA 1611
                                v   v    iv i v v v   ----    vi i -  ?    
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACA----AATAACCCAATTWAAAA 818

  chrX_72242141_7   1612 GTGGGCAAAAGAAATAAAGATACATTGCTCCAAAGAAGATAAACCAATAG 1661
                         i        i  vv i  v v     v              v  v   i 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_72242141_7   1662 CCAAGAGATATATGAAAAGATATTCAACAACTCTAATCTT 1701
                             v iii i          ii      v v????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (133 / 77)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.25 (65 / 20)  


 693 31.43 2.86 1.79  chrX_72246748_72253290     2835  3114 (3429)    L1M4_orf2#LINE/L1        1   283 (625)  

  chrX_72246748_7   2835 TGGAAAGATATTTTACATTCATGGATTGGAAGA----ATATT-TTAAAAT 2879
                                    iii ii                ----     -    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72246748_7   2880 GTTCATACAACCCAAAGCATTAAATCTCTGGACTTAATGCAATGCCTGTC 2929
                          viv    vv      ---  -i    vii  i i  i     v   i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA---TT-GATCTACAGATTCAACGCAATCCCTATC 96

  chrX_72246748_7   2930 AAAATACTTATGACATTCTTCACAAAAATAGAAAAAGCAATCCTAAGATT 2979
                              v iviivi v  i  ii  i    v  v  ivii       i   
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_72246748_7   2980 CATATCAAACCACAAAGAGAC--AGAACAGCCAAAGCTATACTAAGCAAA 3027
                              vi  vii   i -   --    i       i v  vi i iv  i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_72246748_7   3028 AAGTATGAAACTTAAGGAATTGCATTATCTTACTTCAAATTATACTAAAG 3077
                            v ii  ii vi    v ii  i vi iv i      viv     v i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_72246748_7   3078 CACTTTAGTAACCATAATGGCATGGTACTTG-ATATGG 3114
                         vi  vi     i  vi ii ii       v -   v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

Transitions / transversions = 1.84 (57 / 31)
Gap_init rate = 0.02 (7 / 283), avg. gap size = 1.86 (13 / 7)  

1892 26.48 3.83 1.91  chrX_72246748_72253290     5424  6050 (493)    L1M4_orf2#LINE/L1      270   908 (0)  

  chrX_72246748_7   5424 GTACTGGCATAAAAAGAAACACACAAACCAGTGCACCAAAATAGAGAATC 5473
                                     ii v i   i i i i  i  v vi i   v    i  
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_72246748_7   5474 CAGATGTCAATCCATACATCTACAGTGAACACATTTTTGACACAGCTTCC 5523
                             vi v  i        i  ii  v  ivv     i    vi v v  
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_72246748_7   5524 ATGAACATACATTGGGGAAAGAAGAGTTTCCTCAATAAGTGGTGCTGGGA 5573
                          v  v   v  v           v   i ii    i  i           
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_72246748_7   5574 AAACTAGATATTTATATGTGGAATAATAAAACTAGACCCTTATGTTTCAC 5623
                         v    i    ?ii i   iii  v   i  ii i     i  iv iv   
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_72246748_7   5624 TATATACAAAAATCAA-----------------------ATATAAAACCT 5650
                         i            i  -----------------------  i   i v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_72246748_7   5651 CAGACTTTGAAACAACTACAAGAAAACTTTGGGGAAACTCTCCAGGAGAT 5700
                         v i   v i    vvi  v        v v  ? v  v   i iv  vv 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_72246748_7   5701 TGATCTGGGTGACAATTTACTGAGTAATACTCTACAAACACAGGCAACCA 5750
                           ivi i  ii iii   vi iii  vv  v i v  i    i     v 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_72246748_7   5751 AAGCAAAAATAGACAAATGGAATTACATCAAGTTAAATTATATCAAGTTA 5800
                            v         i    v i i v      ----     v --  v  v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAA----AATTAAA--AACTTT 663

  chrX_72246748_7   5801 AATGGACACAGCAAAGGAAAAAAATCAACAAAGTGAAGGGGCAACCCACA 5850
                         vi  ---- vv       v vv -    v        ii i         
  L1M4_orf2#LINE/    664 TGTG----CTTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_72246748_7   5851 GAATGGGAGAAAATATTTGCAAACTACCTATCTGACAAGGGATTAGTAAG 5900
                                                ii iv       i      i v   vv
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_72246748_7   5901 CAGAATATAAAAAGAGCTCAAACAACTCTATAGGAAAATCATCTAATAAT 5950
                                  v     i   vv       v   iv    vv - v     i
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAAC 807

  chrX_72246748_7   5951 CTGATT-AAAAATGGGCAAAATATTTGCATAGACATTTCTCGAAGAAAGA 5999
                          ii   -             iv     v             v  ii    
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_72246748_7   6000 CAAACAAATGAAAAACAGACATATAAGAAGGTGTTCAACATCATTGATCA 6049
                         i v       ivv  i ii  i  i i   i  i         ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_72246748_7   6050 T 6050
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.28 (92 / 72)
Gap_init rate = 0.01 (7 / 639), avg. gap size = 5.14 (36 / 7)  


2848 26.16 1.88 1.22  chrX_72272138_72277243     3712  4613 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72272138_7   3712 TAGAAACACAACTCATATGCATGGATTAGAAGAATCAATATTATGAAAAT 3761
                          i    v i v i   i v        i     v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72272138_7   3762 GACCATACAGCCCAAAGCAAACTGCAGATTCAATGTAATTTCTATCAAAA 3811
                          i v    vv      vii v  i         i i   ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72272138_7   3812 TACAAAC-ATTTTTTCCTCACAGAATTAGAAAAAAAACAATCCTAAAATT 3860
                          v v i -iii    -- ii     v v  v  iv--ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT--TTGCAGAAATTGACAAGC--TGATCCTAAAATT 146

  chrX_72272138_7   3861 CACATGGAACCAAATAAGAG-CCTA-AATGGCAAAAGCAATCCTAAGCAA 3908
                           i      -- vii   i -  i -   i  v   i     i i iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_72272138_7   3909 AAATAACTAATTTGGAGGCATCACATTACCTGACTTCAAATTACACTGCA 3958
                         i  v   v  v       vv     i v  ii i      vivi   i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_72272138_7   3959 AAGCTATAGTTACCAAAACAACATGGTACTGGTATAAAAGTCAATACATA 4008
                               i   v i   i   iii         i    iii vi i i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_72272138_7   4009 GACTAATGGAACAGAATATATAACCCAGAAATAAAGCCAAATACTTACAA 4058
                           ii       i     vv v ii           v   v i i   iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_72272138_7   4059 GCA--TGATCTTTGACAAAGCATAC-AAAAGCATAAATTGGGGAAAAGAC 4105
                         v  --    i  i     i -i i -  i v   vv v        ii i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_72272138_7   4106 A-TCTTACTTAATAAATTGTGCTGAGAAAACTGGATTTTCACATGTAGAA 4154
                          -    -i i  i    v      i  v        v?i      i i  
  L1M4_orf2#LINE/    394 AGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_72272138_7   4155 GAATGAATCTGGATCCCTATCTCTCATCTTATTAAAAAAATCAACTCAAA 4204
                                vi    i     i   v  i v   - v      i        
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAA 491

  chrX_72272138_7   4205 CTGAATCAAAGATTAAAATCTAAGACATGAAACAATAAAATTTTTAGAAG 4254
                         v  i    ?   iiv    v     vv i    v      i i       
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_72272138_7   4255 AAAATCTAGGAAAAACTGTTCTGGACATTGGCCTAGGCAAGGAGTTTATG 4304
                             iv    ?iv  v v   vv   v    vi       v iv  iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_72272138_7   4305 ACTAAGACCCCAAAAGCA--AGTG-CAAAAGTAAATAAATAAATAAATAG 4351
                         iv  v   v         --  ii-      -   -     i      v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAG-AAA-AAATAGATAAATTG 639

  chrX_72272138_7   4352 GACCTAATTCAACTAAAAATCTTCTGCACAGAAAAAGAAATAATCAGCAG 4401
                            i v  iv  v v    v   i  ii vvv   i  v iv    iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_72272138_7   4402 AGTAGACAGAAAACCCACAGAGTGGGAGAAAATATTTGCGAAGCATACAT 4451
                            ii v   v          i                 i  v    i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_72272138_7   4452 CTGACAAAGGATTAATATTCAAAATCTACAAGGAACACAAACAAATCAGC 4501
                             i  i   i vi   i  i   v  i  i    v vv    v   ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_72272138_7   4502 AA-GAAAAGA------ATCCCATTAAAAAGTAGGCAAATGACATCAATAG 4544
                           -i      ------ i  v   ?    i i      v  iv v     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_72272138_7   4545 GCATTTCTCAAAATAAGATATACGAATGGCCAATGAACATATGAAAGAAT 4594
                         i        v   v         i          i i  i      ii  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_72272138_7   4595 GCTCAACATCACTAATCAT 4613
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.56 (28 / 18)  


1116 26.28 2.68 1.95  chrX_72283735_72290114        1   411 (5969)    L1M4_orf2#LINE/L1      409   822 (86)  

  chrX_72283735_7      1 TGGTGTTGGGAAAACTGACAAGCCACATGTAGAAGAATGAAACTGCATCC 50
                              i     v     ivv ?       i i         ii  v i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_72283735_7     51 CCATCTCTCACCTTATACAAAAATCAACTCATGATGGATCAAAAACTTAA 100
                          i i   v    v           i      vi        ? i  i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_72283735_7    101 ATCTAAGAAAGACGTGAAACTGTAGAAATTCTAGAAGATAACCCTAGAAA 150
                           v     i--- - i     i  i  v ii       -  v v   i?i
  L1M4_orf2#LINE/    509 ATGTAAGAG---C-TAAAACTATAAAACTCTTAGAAGA-AAACATAGGNG 553

  chrX_72283735_7    151 TAC-TTTTCTGGAGAC--TGGCTTAGGCAAAGAATTCATAGCTAAGACAC 197
                           v- i   -- v   --   v        v iv   v   v  v     
  L1M4_orf2#LINE/    554 TAAATCTTC--GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_72283735_7    198 -AGCAGCAAATTCAATAGAAAGAAAAAGAAAGTTAATGAAAACTAATTAA 246
                         - iv    v vv   i -         iv ii v   vii vi v  i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_72283735_7    247 ACTAAAAACCTTCTGCACAGCAAAAGAAATAATTTGCAGAATAAACAGAC 296
                          v v    v   i  ii vv    i  v iv  iviv i i i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_72283735_7    297 AAACCAAAGAGTGGGAGAAAATATTTGTAAACTATGCATCCAAAAAAGGA 346
                           v   v   i                i   ii  ii   ii v  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_72283735_7    347 CTAGTATCTAGAATCTACAAGGAACTCACACAAATCATGAAGAAAAA--- 393
                           v     i     v  i  i      vi    v   vv  v     ---
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_72283735_7    394 AAAT--CCCCAT--GAAAATGG 411
                             --   v  --i       
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGG 822

Transitions / transversions = 1.14 (56 / 49)
Gap_init rate = 0.03 (11 / 414), avg. gap size = 1.73 (19 / 11)  

3236 25.96 0.77 0.88  chrX_72283735_72290114     4979  5887 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72283735_7   4979 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAACCAATATCGTGAAAAT 5028
                              ii i  i     i      i v      vii     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72283735_7   5029 GGCCATACTGCCCAAGGAAATTTATAGATTCAATGCCATCCCCATCAAGC 5078
                            v     v     ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72283735_7   5079 TACCAA-TGACTTTCTT-CAGAGAATTGGAAAAAAGT--ACTTTAAAGTT 5124
                          v   i-  v    i  -    -     --- v   i-- iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAGCTGATCCTAAAATT 146

  chrX_72283735_7   5125 CATACGTAAC--CAAAAAACAGCCCGAATTTCCAAGACAATCCTAAGTAA 5172
                             i v  v--   iii  --  v    vv    i      i i iv  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_72283735_7   5173 AAAGAGCAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACA 5222
                         i    i     i      vv   vi  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_72283735_7   5223 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATA 5272
                          i          i   i    ii         i iv ii i   i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_72283735_7   5273 GACCAATGGAACAGAACAGAGACCTCAAAAATAATACCACACATCTGCAA 5322
                           i        i    iv    vii  i      vv   i    i iiii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_72283735_7   5323 CCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGATAGGATT 5372
                         i  vi    i  i     ivv  v   i v  vv         v  i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_72283735_7   5373 CCCTATGTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5422
                         vi  v vi  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_72283735_7   5423 CCGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5472
                         vi   ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_72283735_7   5473 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5522
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_72283735_7   5523 ACATAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5571
                                ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_72283735_7   5572 TAAAACACCAAAAACAATGGCAACAAAAGACAAAATTGACAAATGGGATC 5621
                           vi         i  vvi           v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_72283735_7   5622 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5671
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_72283735_7   5672 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 5721
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_72283735_7   5722 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGA 5771
                         i  i  i  vi          v  i         vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_72283735_7   5772 AAAAAACCAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACA 5821
                             i  -   i     v  i? v  i     i      v    i     
  L1M4_orf2#LINE/    794 AAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_72283735_7   5822 CTTCTCAAAAGAAGACATTTATGTAGCCAAAAGACACATTAAAAAATGCT 5871
                         i     v        i  vi vi i     v ii     v    i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_72283735_7   5872 CATCATCACTGGCCAT 5887
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3092 26.90 0.99 0.88  chrX_72302738_72309025.rev     4891  5797 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72302738_7   4891 TGGAAGAACATTCCATGCTCATGAGTAGGAAGAACCTA-TATCATGAAAA 4939
                              ii i  i     i     ii v      - i  -   ii v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA-CTTAATATTGTTAAGA 49

  chrX_72302738_7   4940 TGGCCATACTGCCCAAGGTAATTTATAGATTCAAAGCCATCCCCATCAAG 4989
                             v     v     iv i  i  i        v  v     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_72302738_7   4990 CTACCAATGACTTTCTTTACAGAA-TCGGAAAAAACT-ACTTTAAAGTTC 5037
                         v v   iivi i  i   i     - i -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_72302738_7   5038 ATATGGAACTAAAAAAGAGCCCACATTGCCAAGTCCATCCTAAGCCAAAA 5087
                                 v iv  ii  v  viv  v     iv v   i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_72302738_7   5088 GAACAAAGCTGGAGGCATCACGCTACCTGATTTCAAACTATACTATAAGA 5137
                                 i      vv    i  v  ii        viv     i  ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_72302738_7   5138 CTACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGAC 5187
                                  i   i    ii       v i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_72302738_7   5188 CAATGGAACAGAAC--AAAGCCCTCAGAAATAATGCCGCATATCTACAAC 5235
                                 i    i-- i  i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_72302738_7   5236 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5285
                         i vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_72302738_7   5286 CCTATTTAATAAATGGTGCTTGGGAAAACTGGCTAGCCACATGGAGAAAG 5335
                         i  v  i  i          -    v      v  ?       v i  ii
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_72302738_7   5336 CTGAAACTGGATCCCTTTCTTACACCTTATACTAAAGTTAATTCAAGATG 5385
                         v    ii    i    vi  i     v     v   i    i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_72302738_7   5386 GATTAAAGACTTCAATGTTAAACCTAAAACCATAAAAACCCTAGAAGAAA 5435
                            i ?    i v     v i v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_72302738_7   5436 ACATAGGCAATACAAT--TCAGGACATAGGCATGGGCAAGGACTTCATGT 5483
                                ?i-  -   --  iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    545 ACATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_72302738_7   5484 CTAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGAT 5533
                         v  vi            vvi           v     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_72302738_7   5534 CTAATTGGACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5583
                         i v  iii v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_72302738_7   5584 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCCACCCATCTG 5633
                            v  i     i                 v       vi  ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_72302738_7   5634 ACAAAGAGCTAATATCCAGAATCTACAAAGAACTCAAACAAATGTACAAC 5683
                          i  i ii  vi          v  i         vv    v vv i  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_72302738_7   5684 AAAAAAACAAACAACCACATCAAAAAGTGGGCGAAGGATATGAACAGATG 5733
                              i     i    vv  i?    i     i      v    i   ii
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_72302738_7   5734 CTTCTCCAAAGAAGACATTTATGCAGCCAAAAA--ACATGAAAAAATGCT 5781
                         i              i  vi viii     v  --         i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_72302738_7   5782 CATCATTACTGGTCAT 5797
                           v   i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


 480 13.83 0.00 0.00  chrX_72316649_72320402      492   585 (3169)  C L1M4_orf2#LINE/L1   (0)   908   815  

C chrX_72316649_7    585 AAAAGTGGGCTAAGAACATGAATAGATAAATCTCAAAAGAAGATATACAA 536
                             i     v   i iv        i vv    v               
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

C chrX_72316649_7    535 ATGGCCAACAAGCATATGAAAAAATGCTCAGCATCACTAATAAT 492
                                 i     i       i       i     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  

2374 29.92 0.39 0.26  chrX_72316649_72320402      814  1575 (2179)  C L1M4_orf2#LINE/L1   (80)   828    66  

C chrX_72316649_7   1575 ATTGATCTAAAAATTCAACACAACTTCCATCAAAACACCACCATCATTCT 1526
                                  v i       i   iii i       iv   v vv v  i 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

C chrX_72316649_7   1525 TCACAGAACTAGAAAAAGCAATCCTAAAATTCACATGGAACCAAAATCAA 1476
                          ii     v v  v  ivii             i      viiv  vvi 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

C chrX_72316649_7   1475 GCCCGTATAGCCAATGTAAAACTAAGCAAAAAGAATACATCTGGAGGCAT 1426
                         v  v v        vii  vvi i iv  i     i v vi      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

C chrX_72316649_7   1425 CACATTCCCTGATTATAAACTATACTCTAAGGTCATAGTCATTAAAACAG 1376
                             i i  ii   vi   viv    vi  i ii i   v  i  i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

C chrX_72316649_7   1375 CATGGTACTGGTATGAAAATAAGCAAATAGACCAATGGAACAGAATAGAA 1326
                         ii         i  i ii   ii  v     i        i     v  i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

C chrX_72316649_7   1325 AACCCAGAAATAAACCCAAATACTTGCAGCCAACTGGTCTTTGACAAAGC 1276
                          ii               v i i  iii i   i  i i  i     i v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

C chrX_72316649_7   1275 AAACAAAAACATAAAGTGGAGAATAGATACCCCATTCAACCAATGGTGCT 1226
                         viv   i v   vv i   i   vii   vi iv      v         
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

C chrX_72316649_7   1225 GAGTTAATCGGCAAGCCACATGTAGGAGAATGAAACTGGATCCTCATCTC 1176
                          i vi  ii  vv ?       i ii        ii    i  ii i   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

C chrX_72316649_7   1175 TCTCCTTATACAAAAATCAAATCAAGATGGATTAAGGACCTAAATGTAGG 1126
                         v v  v           i  v    i      i ?i            i 
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

C chrX_72316649_7   1125 AACTGAAACTATAAAAATTCTGGAAGATAACGTTGGAAAAACCCTTCTAG 1076
                          i  i           v ii i     v   i v  ?iv  vi    vv 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

C chrX_72316649_7   1075 ACATTGGCTTAGGCAAGGATTTCATGACCAAGAACCCAAAAGCAAATGCA 1026
                           v    v        v i    v iivi v  vv         v v   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

C chrX_72316649_7   1025 GTAAAAACAAAGATAAATAGCTTGGACTTAATTAAACTAAAGCGCTTTTG 976
                         ii    iv   i   i   iv        v  i   v v  ivi      
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

C chrX_72316649_7    975 CACATCAAAAGAAATGGT-AAGCAGAGTAAACAGAAAACCAACAGAGTGG 927
                         ii v     i  v ivi -   - i   i  v   v    v     i   
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAG-AAAGTGAAAAGACAACCCACAGAATGG 714

C chrX_72316649_7    926 GAGAAAATCTTCACAAATTGTACATCTGACAAAGGACTAATATCCAGAAT 877
                                 v  ii     ii  i      i  i     vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

C chrX_72316649_7    876 CTACAACAAACTCAAACAAATTAGCAGGTAAAAGAAAAAGAATCACA--T 829
                         v  i  vi     vv    v i ii ivv      v   v  i -  -- 
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC-CAATT 813

C chrX_72316649_7    828 AAAAAGTGGGCTAAG 814
                         ?    i     v   
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAG 828

Transitions / transversions = 1.46 (133 / 91)
Gap_init rate = 0.01 (4 / 763), avg. gap size = 1.25 (5 / 4)  

3171 28.41 0.33 0.33  chrX_72316649_72320402     2354  3261 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72316649_7   2354 TGGAAGAATATTCCATGTTCATAGATAGGAAGAATCAATATCATGAAAAT 2403
                              ii    i          i   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72316649_7   2404 GGCCATACTTCCTGAGGTAATTTATGGATTCAATGCCATCCCCATCAAGC 2453
                            v     i  ii iv i  i  ii       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72316649_7   2454 TACCAATGACTTTCTACACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCT 2501
                          v   iivi i  i vii     -   -- v  i  - iii    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72316649_7   2502 TATGGAAGCAAAAAAGAGCCTGAATTGCCAAGACAATCCTAAGTAAAAAG 2551
                                iiiv  ii  v  v    v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72316649_7   2552 AGCAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 2601
                          i     i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72316649_7   2602 TACAGTAACCAAAACAGCATGGCACCGGTACCAAAACAGATATATAGACC 2651
                                 i   i    ii   i  i  i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72316649_7   2652 AATGGAACAGAACAGAGACCTCAAAAATAATACCACACATCTGCAACCAT 2701
                                i    iv    vii  i      vv   i    i iiiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_72316649_7   2702 CTGATCTTTGACAAACCTGAGAAAAACAAGAAATAGGGAAAGGATTCCCT 2751
                         i    i  i     ivv  vv  i v  vvv   i       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_72316649_7   2752 ATGTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 2801
                         v vi  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_72316649_7   2802 AACTGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 2851
                          ii  i i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_72316649_7   2852 AAAGACTTAAATGTTAGACTTAAAACCATAAAAACCCTAGAAGATAACCT 2901
                          ?    i       v   vi      i      vi i       v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_72316649_7   2902 AGGCA-ATACCATTCAGGACATAGGCATGGGCGAGGACTTCATGAATAAA 2950
                            ?i- v i -   iv   v v  vv i   i v ii   v ii   vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_72316649_7   2951 ACACCAAAAGCAAAGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 3000
                                     v i          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_72316649_7   3001 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 3050
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_72316649_7   3051 GGCAACCTACAGAATGGGAGAAAGTTTTTACAATCTAGTCACGTGACAAA 3100
                          i     i               i v   i   vii vvi iv   i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_72316649_7   3101 GGGTTAATATCCACAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 3150
                           ii vi      v   v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_72316649_7   3151 ATCAAACAACCCCATCAAAAAGTGGGCAAAGGGTATGAACAGATACTTCT 3200
                         iv    i     v  i?    i          i v    i   i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_72316649_7   3201 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 3250
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_72316649_7   3251 TTACTGGTCAC 3261
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.73 (161 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


2659 26.01 2.69 0.90  chrX_72328442_72330173.rev      350  1241 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72328442_7    350 TGAAAACACATCCCATGCTCATGGATGGGTAGAATTAATATTGTAAAAAT 399
                           i   v i        i        v  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72328442_7    400 GCCA-CACTGCC-AAAGCAATCTACAAATTCAATGCAATTTTCATCAAAA 447
                          v  -i   v  -   vii       i      i     iiii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72328442_7    448 TACCACCATCTTTCTTCACATAACTAGAAAAA--AATTCCTACAATTCAT 495
                          v   v vv i  i  ii  v  v v  v  i--i  -    v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chrX_72328442_7    496 ATAGAACCCCAAAAGAAGCCCACA-TAACCAAAGCAATACTAAGCAAAAA 544
                           i   viv   ii  --    v -  i     i    vi i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_72328442_7    545 GAACATATCTGGAAGCATCACATTACTCGACTTCAAACTATTCTATAAAG 594
                              v vi    i vv     i v i i i      viv v   i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_72328442_7    595 GCCTAC--TTACAAAGACAGCATGGTACTGATATAAAAATAGGCACATAG 642
                         --    -- v iv       ii        ii    ii    i  i    
  L1M4_orf2#LINE/    248 --CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_72328442_7    643 ACCAATGGAAGAGAATAGAGAACCCAGAAATAAATCCGAATACTTTTAGC 692
                          i        v     v    ii           i  iv i i  v i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_72328442_7    693 CAATTGATCTTCAACAAAGCAAACAAAAACA--AAGTAGGGAAAGGACAC 740
                                 i   i    i vviv   i v  --v i i       i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_72328442_7    741 TCTATTGAAGAAATGG--CTGGGATAATTGGCAAGCAACAGGCACAAGAA 788
                            v  v  v      --      i  i   vv ? v   v   v     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_72328442_7    789 GTAAATTCGATACTTATCTCTCACCTTATACTAAAATCAACTCAAAATGG 838
                         vv  i  v  iv i  i   v    v     v     i            
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_72328442_7    839 ATCAAGGCCTTAAATTTAAGTCCTGACACCATAATAGCTCT-ATAAGACA 887
                             ?i v i     v    vv  i v  i    - i    - v    v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAA 544

  chrX_72328442_7    888 ACATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTTATGAGC 937
                             v  ?iv  vi    vv   v    v        v ii  iv iiii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_72328442_7    938 AAGAACCCAAAAGCAAACTCAACAAAAACAAAGATAAATAGATGAGACTT 987
                          v  vv         v vv        iv   i   i   i  vi     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_72328442_7    988 -----AAACTAAAAATCTTCTGCACAGCAAAAGAAACTATCAGGAGAGTA 1032
                         -----   i      -   i  ii vv    i  v       i  i   i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_72328442_7   1033 AACAGACAACTTACACAATGAGATAAAATCTTCATAATCTATACACCTGA 1082
                           v       ii   v    i  v     v  iii  vii   i i    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_72328442_7   1083 CAAAGGTCTAATATCCAGAGTCTACAAAGAACTCAAACATATCAGCAAGA 1132
                         i  i  v  vi        i v  i         vv   vv   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_72328442_7   1133 AAAA-ACAA-T--CCCA--TCAAAAATGGGCTAAGACCATGGAATAGGCA 1176
                             -    - --    -- ?          v   ivi- v      i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGACA 842

  chrX_72328442_7   1177 ATTCTCAAAAGTAGACATACAAATGGCCAACAAACATATTAAAA-ATGAT 1225
                         v     v    v   i              i  i  i  v    -   v 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_72328442_7   1226 TAACATCACTAATTAT 1241
                         i       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (123 / 105)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.60 (32 / 20)  


2832 26.06 2.67 0.36  chrX_72338869_72340686      500  1324 (494)    L1M4_orf2#LINE/L1       20   863 (45)  

  chrX_72338869_7    500 CATGGACTGGAAGAATTCATATTGTTAAGATGGCCATACTATCCAAAATA 549
                               i       v  v                v     vi     v i
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chrX_72338869_7    550 ATCTACAGATTTAATAAAATCGATATCAAAATGTCAATGACATTTATTAC 599
                                    i  iiv    vv         vi  iivi v   v  i 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_72338869_7    600 AGAAATAGAAAAAC--ATCCTAAAATTTATATGGAACCA-AAAAAATCCT 646
                               v  v  i --           i        vii-  iii i  v
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_72338869_7    647 GAATAGCCAAAGCAATCCTGAACAATAATAACAAAGTTTGAGGCATCACA 696
                                    i     i    v  v  v         v    vv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_72338869_7    697 CTTCCACGTTTCAAAATATAACACAAGGCTATAGTAACCAAAACAGCATG 746
                              vvi        iv  vi    i    i     i   i    ii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_72338869_7    747 GTACTTGCATAAAAACAGACACATAGACCAATGGTACAGAATAGATAACC 796
                              v      ii i     i     i      v i     v  v ii 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_72338869_7    797 CAGAAATAAATCCAGATATTTACAGCCACATGATTTTGGACAAAGATGCC 846
                                   i   v i     ii i  vv       v     i i    
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_72338869_7    847 AAGAACATTTATTGGGAAATGGTTAATCTCTACAATAAAGGGTTCTAAGA 896
                             v    i v    i  v iv  i   i v   i   v   v  ii  
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_72338869_7    897 AAACTGGATATCCACATAAAGAAGAATTAAACTAGATCTCCATGTCTCTC 946
                         v         ?      iv i      v  ii i  i i i iv  v v 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_72338869_7    947 CCTATGTTAATGTCAACTCAAAATGAATTAAAGGTTTAAATGTAAGACCC 996
                          v   iiv  vi i           i  i ?  iii           v i
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_72338869_7    997 AAAACTATAAATCTATGAGAAGAAAATATAGGAAAAACACTTCAGGATAT 1046
                                    v  v v         i     ?iv  vv    iv  iv 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_72338869_7   1047 TAGCCTGGG-AATATTTTAT--GACTAAGACCTCAAAAGCACACTTAACA 1093
                          i vi i  -   iv   v --  -  v   vi          vvi    
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACA 618

  chrX_72338869_7   1094 AAAGTAAAAATAGGCAAAGGGGACTCTATCAAA-CTGAAAAGTTTTG-GC 1141
                             v        ii   vv     ii      -i i    v     -  
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_72338869_7   1142 A-CAAAGAAGAAATAACCAACAGCATGAAACG------TACAGAATGGAA 1184
                         v-     --  v iv i   v ivi     v ------i         i 
  L1M4_orf2#LINE/    669 TTCAAAG--GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_72338869_7   1185 GAAAATATTTGCAAACTATGCATCTGACAGAGGATTAATGTCTAGAGTAC 1234
                                        ii  ii      i ii   i vi i  i   i  i
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_72338869_7   1235 ACAAGGAACACAAACAATGCAATAGCCAAAA--TAAATG---TGATTTTT 1279
                          i  i    v vv    iv     iiv    --i    i---ii   ?vv
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_72338869_7   1280 AAATGGCCAAAGGATCTTAATAGGC--TTTTTAAAAAAAATTATATA 1324
                               v        i v     i --  i iv   i  iv    i 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.40 (123 / 88)
Gap_init rate = 0.02 (13 / 844), avg. gap size = 1.92 (25 / 13)  


2513 26.81 1.38 4.79  chrX_72348998_72351437.rev     1010  1949 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72348998_7   1010 TGGAAAAACATTCCCATGTTTA-GGATAGGAAGAATCAATGTTGTAAAAA 1058
                               i i  -        i -    v      v i   i    v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATAT-CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_72348998_7   1059 TGGCCACACTACCCAAAGAAATTTACAGATTCAACGCCATTTCTATCAAA 1108
                             v i   v      vvi  i              v  ii        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_72348998_7   1109 CTACCAATGACATTCTTCACTGAA-TTAAAAACAAAATTATTCTAAAATT 1157
                         v v   iivi v  i  ii v   -  i ---   iv v  i        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGA---CAAGCTGATCCTAAAATT 146

  chrX_72348998_7   1158 CATGTGAAACTAAAAAGGAGCCCAAGTAGCCACAGCTATTGTAAGCAAAA 1207
                            i  i  v iv  i   v  vi i      v i v  iv i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_72348998_7   1208 AGAACAAAGCAGGAAGCATCACATTAACTGACTTTAAACTATACTACAAG 1257
                                  iv   i vv     i vv ii i  i   viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_72348998_7   1258 GCTGCAGTAAACAAAACAGCATGGTACTGGTACAAAAAGAGACACAGGAA 1307
                            i      v   i    ii         i i  ii v     i vii 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_72348998_7   1308 CCAATGCAACAGGTTACAGAGGCCAGAAATAAAGTGACACCTGTAAAACC 1357
                         i     v  i  iv vv    v           viv i  v v  viii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_72348998_7   1358 ATCTGATCTTTGACAACATTGACAGAAGCAAGCCATGAGGAAAGGACTCC 1407
                          vi    i  i     viv  v  ii v  vv v   i      i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72348998_7   1408 CCATTCAATAAAGAGTGCTGGGATGATTGGTTAGCCATATGCAGAAGATT 1457
                          iv     i   vi         ii i   v  ?   i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72348998_7   1458 GAAACTGGACTCCTTCTTTACATCATATACAGAATTCAACTCATGATGGA 1507
                            ii     i   v i i   i        i  v i      vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72348998_7   1508 TTAATGTCTTAAATGTAAAACGTAAAATTATAAAAACTCTT-GAAGAAAA 1556
                          i ?v v i         i vv     i       -     -        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_72348998_7   1557 CCTAGAAAATACCAATCT--G-GACTTAAGCTCTGGCAAAGATTTCAT-G 1602
                          v   i?i-  --     -- -   i vi v iv     v i    v - 
  L1M4_orf2#LINE/    546 CATAGGNG-TA--AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_72348998_7   1603 ATGAAGATACCTAAAGCAATTATAACAAAAACAAAAACTGACAAATGGGA 1652
                           - v  i   v      vvvii       iv     iv  i    v   
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_72348998_7   1653 CCTAATTTAACCAAAGAGCTTCTGTGCATTGACTGTTTACTCTGTCAATA 1702
                          i v  -----    ------------   i --------------  - 
  L1M4_orf2#LINE/    642 CTTCAT-----CAAA------------ATTAA--------------AA-A 659

  chrX_72348998_7   1703 GTTTCTTCTGTGCAGCAAAAGAAGCTATTGACAGAGTAAACAGTCAACAC 1752
                         ----   i     vv    i  vi    ii v i   i  v  v    v 
  L1M4_orf2#LINE/    660 ----CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_72348998_7   1753 ACAGAATAGGTAAAAATATTTGCAAACTAAACACCTGACAAAGGTCTAAT 1802
                                i  vi              ii v i i    i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_72348998_7   1803 ATTTAGAATTTATAAGAAATT-----AAATAAATTATCAAGCAATAAACA 1847
                           ii     v     ii  i -----  v v   v  v  ivi i   i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_72348998_7   1848 ATCACATTAAAAAGTGGGCAAAGGACATAAACAGATGCTTCTCAAAAGAA 1897
                          i vv   ?    i           iv i  i   iii     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_72348998_7   1898 GACATACCTGCAGCCAATAAACATATAAAAA-ATGATTAACATCAACAAT 1946
                           i    vviii        i  i  i    -   v i       ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_72348998_7   1947 CAT 1949
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.05 (58 / 19)  


2388 27.97 2.06 1.69  chrX_72363973_72368571.rev     2894  3719 (880)    L1M4_orf2#LINE/L1        1   829 (79)  

  chrX_72363973_7   2894 TAGAAACACATCCCATGCTCATAAATGGGTAGAATCAATATTATGAAAAT 2943
                          i    v i        i    ii  v  v   v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72363973_7   2944 AACGACACTGCCAAAAGCAATCTACAAATTCAGTGCAATTTCCATCAAAA 2993
                         ii i i   v  v   vii       i     ii     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72363973_7   2994 TTCCACCATCTTTCTTCACAGAACTAGA--AATAAATCCTAAAATTTATA 3041
                          i   v vv i  i  ii     v v  -- iivi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_72363973_7   3042 TGGAACAAACAAACAAACAAAAG-CCCACA-CAGCCAATGCAAAACTAAG 3089
                              --------- vi   ii -    v -i      vi   vvi i i
  L1M4_orf2#LINE/    151 TGGAA---------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_72363973_7   3090 CAAAAATAACACATCTGGAGG---CATATTACCTGATTT-GAAACTGTGC 3135
                         v  i  v    v vi      ---  i i v  ii    -i     - i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TAC 240

  chrX_72363973_7   3136 TATAAGGCCATAGTCACCAAAACAGCATGCTACTGGTATAAAAATAGCCA 3185
                           i  i  i i   v i   i    ii  v      i    ii    v  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_72363973_7   3186 CATAGACCAATGGAACAGAATGAAGAACACAGAAATAAAGCCAAATACTT 3235
                         i     i        i     vi   iiv          v   v i i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_72363973_7   3236 ATGGCCAACTTATTTTTGACAAAGCGAACAAAAACATAAAGTGGGAAACG 3285
                             i   i v     i     i vviv   i v   vv i    i  v 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_72363973_7   3286 GATACCCTATTCAACAAATGGTGCTGGAATAATTGGCAAGCCAT-TGTAG 3334
                         i   vi  v                  i i  i   vv ?   i-  i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_72363973_7   3335 AATAATAAAACTCGATACTTATCTCTCATCTTATATAAAAATCAACTCAA 3384
                           v   i  ii v  iv i  i   v  i v    i      i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_72363973_7   3385 AATGGATCAAAGACTTAAATCTAAGTCCTAATACTATAAAAATTCCATAA 3434
                                  ?    i     v    vv    v         v iii v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_72363973_7   3435 GATAACAT---CACAAATACCCTTCTAGACATTGGCTTAGGCAAAGACTT 3481
                           v     ---?ii    ---    vv   v    v        v ii  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_72363973_7   3482 CATTACCAAGAAC-CCAAAATCAAATGCAACAAAAACAAAAATAAACAGA 3530
                          -   vvv vi  -      v  v v         iv       i i i 
  L1M4_orf2#LINE/    588 C-TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_72363973_7   3531 TGGGACATAATTAAACTAAAAAGCTTCTGCACGGCAAAAGAAACAATCAG 3580
                          v    v v  i   v v    i   i  ii vv    i  v  v    i
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_72363973_7   3581 CAGAATAAACAGACAAGCCACAGAGTGGGAAACAATTTTCACAATCTATA 3630
                         v i i i  v      v       i     i v   v  ii   vii   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_72363973_7   3631 CATCAGACAAAAGACTGATATCCAGAATCTACAAGAAACTT----AAATC 3676
                         i   v  i  ii    vi          v  i  ii    i----  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_72363973_7   3677 AGCAAGAAAACAACAAAGAATCTCATAAAAAAGTGAGCTAAGG 3719
                          ii  v    vi     v  i iv  v?    i  i  v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.44 (134 / 93)
Gap_init rate = 0.02 (13 / 829), avg. gap size = 2.38 (31 / 13)  

 337 13.68 12.82 1.71  chrX_72363973_72368571.rev     3992  4108 (491)    L1M4_orf2#LINE/L1      779   908 (0)  

  chrX_72363973_7   3992 TACATCTCAA-AA-AAAAAAAAAAA-----------AAAAGTGGGCTAAG 4028
                             v     -  -     i v   -----------    i     v   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_72363973_7   4029 GACATGAATAGACAATTCTCAAAAAAAAAGATATGCAAATGGACAACAAG 4078
                           iv          v     v   i  --     i       v   i   
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAA--GATATACAAATGGCCAATAAG 876

  chrX_72363973_7   4079 CA--TGAAAACATGCACCACATCACTAATTAT 4108
                           --      v    v v      ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.60 (6 / 10)
Gap_init rate = 0.04 (5 / 130), avg. gap size = 3.40 (17 / 5)  


2573 26.20 2.02 5.32  chrX_72377593_72389619     4443  5381 (6646)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72377593_7   4443 TGGAAAAATATTCCATGCTCACGGATAGGAAGAATCAATATTGTGAAAAT 4492
                               i    i     i   i    v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72377593_7   4493 GGCCGTACTGCCCAAAGTAATTTATAGATTCAGTGCTATTCCCATCAAGC 4542
                            vi    v      v i  i  i       ii  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72377593_7   4543 TACCA-CTGACTTTCTTCACAGAAGTAGAATAAAACT-ACTTTAAATTTC 4590
                          v   -   v    i  -i     i v  v--  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGAC--AAGCTGATCCTAAAATTC 147

  chrX_72377593_7   4591 ATATGAAAACAAAAAAGAGCCTGTACAGCCAAA-CAATCCTAAGCAAAAA 4639
                              i   iiv  ii  v  v v i       -     i i -------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------- 190

  chrX_72377593_7   4640 ACAAACAAACAAAAAACAAAAACAAAAGCACAACAAAACAAAACAAAGCT 4689
                         ----------    i ----------------------- i       i 
  L1M4_orf2#LINE/    191 ----------AAAAGA-----------------------AGAACAAAGTT 207

  chrX_72377593_7   4690 GGAGGCATCACGCTACCTGACTTCAAACTATGCTACAAGGCTACAGTAAC 4739
                              vv    i  v  ii i      viv i      i          i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_72377593_7   4740 CAAAACAGCATGATACTGGTACCAAAACAGATATATCAACCAATGGAACA 4789
                            i    ii  i      i iv ii i   i    vi i        i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_72377593_7   4790 GGACAGAGGCCTCACAAATAACACCACACATCTACAACCATCTGACCTTT 4839
                          i iv   ivii  v      vv   i    i  iiii  vi   ii  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_72377593_7   4840 GACAAACCCAACAAAAACAAGCAATGGGGAAAGGACTACCTATTTAAAAA 4889
                              ivviiv   i v  vv            i ivii  v  i  v  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_72377593_7   4890 ATGGTGCTGGAAGAACTGGCTAGCTGTATGCAGAAAATTAAAACTGTAAC 4939
                                   i v      v  ? iii     i  i v i  ii  v v 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_72377593_7   4940 TCTTCCTTACATTTTATACAAAAAGTAACTCAAGATGGATTAAAGACTTA 4989
                         i  v   i   iiv          v        i      i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_72377593_7   4990 AATGTAAAACCCCAT-TTATAAAAACCCTAGAAGAAAATCTAGGCA-ATA 5037
                                i v iv v-i       vi i          iv    ?i- v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_72377593_7   5038 CCGTTCAGGACATAGACATGGTCAAAGATTTTAT-GATGAAATCGCTGAA 5086
                         i -   iv   v v ivv i v   v i   iv -   ivi - i ii  
  L1M4_orf2#LINE/    558 TC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-CACCAAA 605

  chrX_72377593_7   5087 AG---AAATTTCAACAAAAGCAAAAATTGACAAAT--GATATCCAGTTAA 5131
                           ---  i---         v      v  i    --  i- i  viv  
  L1M4_orf2#LINE/    606 AGCACAAG---CAACAAAAGAAAAAATAGATAAATTGGAC-TTCATCAAA 651

  chrX_72377593_7   5132 ACTAAAGAGCTTCTACACCACAAAAGAAACTATCATCAGAGTGAACAGAC 5181
                          i    i -   i iii iv    i  v       vv i      v    
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_72377593_7   5182 AACCTACAGAGTGGGAGAAAATCTTTGCAATCTATCCATCTGACAAAGGG 5231
                             i     i           v       vii  vi      i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_72377593_7   5232 CTAATATCCAGAATCTACAAGGAACTTAAGCAAATTTACAAGAAAAAAA- 5280
                           vi          v  i  i     ivvi   v iv i  v     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_72377593_7   5281 ----AAC---ATTAAAAAGTGGGCATAGGACATGAACAGACACTTCTCAA 5323
                         ----   ---   ?    i      v    iv    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_72377593_7   5324 AGGGACACATACATGTGACCAAAAATCATATGAAAAAAAGCTCAACATCA 5373
                          i i v i     vi  i    v  v  i       i v           
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_72377593_7   5374 CTGATCAT 5381
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.72 (153 / 89)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.63 (69 / 19)  

3254 27.20 0.44 0.44  chrX_72377593_72389619    10627 11534 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72377593_7  10627 TGGAAGAACATTCCATGCTCTTGGGTAGGAAGAATCAATATCGTGAAAAT 10676
                              ii i  i     i  v   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72377593_7  10677 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 10726
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72377593_7  10727 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 10774
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72377593_7  10775 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTACGCCAAAAG 10824
                                viiv  ii  v  v v  v     iv     i ivivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72377593_7  10825 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 10874
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72377593_7  10875 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 10924
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72377593_7  10925 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 10972
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_72377593_7  10973 ATCTGATCTTTGACAAACCTGAGAAAACCAAGCAATGGGGAAAGGATTCC 11022
                          vi    i  i     ivv  vv  i    vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72377593_7  11023 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 11072
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72377593_7  11073 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 11122
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72377593_7  11123 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 11172
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_72377593_7  11173 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 11222
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_72377593_7  11223 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 11272
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72377593_7  11273 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 11322
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_72377593_7  11323 AGGTAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 11372
                           ii    i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_72377593_7  11373 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 11422
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_72377593_7  11423 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGATCAGACACTTC 11472
                          i     i     v  i?    i     i     iv   vi     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_72377593_7  11473 TCAAAAAAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 11522
                           v   i    i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_72377593_7  11523 ATCACTGGCCAT 11534
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2696 26.88 4.67 1.25  chrX_72403434_72410091     5288  6165 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72403434_7   5288 TGGAAAAACATTCCATACTCATGGATAGGAAGAATCAATATTGTGAAAAT 5337
                               i i  i    ii        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72403434_7   5338 GGCCATACTGCCCAAAGTAATTTGTAAATTCAATGCTATCCCCATCAATC 5387
                            v     v      v i  i ii i      i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72403434_7   5388 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5435
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72403434_7   5436 TATGGAACCAAAAAAGAGCCTGCATAGCCCAGACAATCCTAAGCAAGAAA 5485
                                viiv  ii  v  v v      v i      i i iv     i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72403434_7   5486 AATAAACCCGGAGGCATCATGCTACCTTATTTCAAACTATACTACAAGGC 5535
                           i   vii     vv   ii  v  iv        viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72403434_7   5536 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACACATATATAGGCC 5585
                                 i   i    ii         i iv ii i v i      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72403434_7   5586 AATAGAACAGAATGGA-AGCCTCAGAAATAACACCACACATTTACAACCA 5634
                            i   i     v  -  i -         vv   i       iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chrX_72403434_7   5635 TCTCATCTTTGGCAAACCTGACACAAAAAAAGCAATGGGGAACAGATTCC 5684
                         vi v  i  i i   ivv  v  - i vv vv          vii  vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72403434_7   5685 CTATTTAATAAATGTTGTTGGGAAAAACTGGCTAGCCATATGCAGAAAAC 5734
                           v  i  i     v  i     v  -    v  ?   i     i  i v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAA 445

  chrX_72403434_7   5735 GGAAACTGGACCCTTTCCTTACACCTGATACAAAAGTCAACTCAAGATGG 5784
                         v   ii       i v   i     vv        i i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_72403434_7   5785 ATCAAAGACTTAAACATAAGACCTAGGACCATAAAAATTCTAGAATAAAA 5834
                             ?    i    ii     v   ii  i      v ii     v    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_72403434_7   5835 CCTGGGC---AATGCCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 5881
                          v i  ?---   -- -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_72403434_7   5882 GCAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCTGAT 5931
                         ii vi            vvi          vv     v  i    iv  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_72403434_7   5932 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 5981
                         i v  i   v v  i i   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_72403434_7   5982 GAACAGGCAA----------AGG-----------------------TCTG 5998
                            v  i   ----------i  -----------------------    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_72403434_7   5999 ACAAAGGTCTAATATCCAGAATCTACAAAGAACTTCAACATATTTCCAAG 6048
                          i  i  v  vi          v  i        iiv   - i --   v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACT--CAAT 789

  chrX_72403434_7   6049 AA--AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAG 6096
                           --    i     i     v  i?    i            v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_72403434_7   6097 ACACTTCTCAAAAGAAGACATTTGCACAGCCAACTGACATATGAAAAAAT 6146
                            i     v        i  viiv ii     ivii  i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_72403434_7   6147 GCTCATCATCACTGATCAT 6165
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (140 / 92)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.47 (52 / 15)  


2810 27.07 2.21 1.88  chrX_72425107_72430029     3532  4436 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72425107_7   3532 TGGAAAAACCACCCATGCTCATGGATAGGA-GAATCAATATCATTAAAAT 3580
                               i ivv      i        v   -  v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72425107_7   3581 GGCTATACTGGCCAAAGAAATTTACAGATTTAATGTCATTTTTATCAAAT 3630
                            v     vv     vvi  i        i  i iv  iii       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72425107_7   3631 TATTGACAACATTCTTCACAAAACTAGAAAAA-TGGTTTTAAAATTCCTA 3679
                          viiii vi v  i  ii  i  v v  v  i-  i ii        v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_72425107_7   3680 TGGAACCAAAAAGGGACCCA-AATACCCAAGGCAATCCTAAGGAAACAGA 3728
                              viiv  -        -    v    ii     i i ii  iv   
  L1M4_orf2#LINE/    151 TGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_72425107_7   3729 ACAAAGCTGGAGGCATTACCTTACCCAACTTCAAACTATACTACAAGGCT 3778
                               i      vv i  vi v     i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_72425107_7   3779 ACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCA 3828
                                i   i    ii         i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_72425107_7   3829 TTGGGACACAACAGAGAGCCCAGAAATAAGGCCACACATCTGCAACCCTC 3878
                         v   i i v  iv     i          iv   i    i iiiii vvi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_72425107_7   3879 CAATCTTTGACAGAAA---CAAG------TAATGAGGAAAAGACT--TCT 3917
                         ii  i  i    iiii---    ------i    i     -  v --   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCT 398

  chrX_72425107_7   3918 TATTCAATAAATGGCATTGGGGTAACTGGCTAGCCATATGCAGAAGATTG 3967
                          -     i      iii    ii      v  ?   i     i    v  
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_72425107_7   3968 AATCTGGATCCCTTTCTTATACCATATACAAAAATCAACTGAAGATAGAT 4017
                           vi    i    vi  i i               i    v  i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_72425107_7   4018 TAAAGACTGAAATGTCTTAAAATTAAAGCCCAAAACTATGAAGAAAACCA 4067
                         i ?    iv      ---------  iiv i        ----     iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGT---------AAGAGCTAAAACTAT----AAAACTC 534

  chrX_72425107_7   4068 T--GAAGACAACCTAGGCA-ATACCATTCTGTACATAGGGATGGGCAAAG 4114
                          --     v   v    ?i- v i v iv  -  v v   v i     v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATG 583

  chrX_72425107_7   4115 ATTTTATGACAAAGACACCAAAAGCAATAGCAACAAAAGCAAAATT-GAC 4163
                         i   iv iivv v             vv           v    v -  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_72425107_7   4164 AATTGGGATCTAATTAAACTTAAGACCCTCCACAGTGCAGAAGAAACTAT 4213
                           v v   ii v  i   v    i v i iiiiiv v  i i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_72425107_7   4214 CAACAGAGTAAACAGACAACCTACAGAATGTGAGAAAATTTTTGCAAACT 4263
                            v i   i  v        i        v        v        ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_72425107_7   4264 ATGCATCCAACAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAATAA 4313
                           ii   ii i  i  v  vi       v  v     i     ivv i  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_72425107_7   4314 ATCTAGAAGAAAAAAA-AAACAACCCCAT-AAAAAGTGTGCAAAGGATAT 4361
                         v  v v  v     i -   i     v  -?    i  v         v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_72425107_7   4362 GAACAAACACTTCTCAAAAGAAGATATACATGCAGTCAACAAGAATTTGA 4411
                            i i   i     v              viii i   i   v iv   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_72425107_7   4412 AAAGGAGCTCAATATTCCTGATCAT 4436
                             iv      i  iv????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (150 / 91)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.18 (37 / 17)  


3153 26.83 0.66 1.20  chrX_72431730_72438108.rev     4976  5888 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72431730_7   4976 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5025
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72431730_7   5026 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5075
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72431730_7   5076 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5123
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72431730_7   5124 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5173
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72431730_7   5174 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5223
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72431730_7   5224 TACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGAGATATAGACC 5273
                                 i   i   iii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72431730_7   5274 AATGGAACAGAACAGAACAGAGCCCTCGGAAATAATGCCACATATCTACA 5323
                                i    iv  ---   i  --i       vv   i i  i  ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGA---GAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_72431730_7   5324 ACTATCTGATCTTTGACAAACCTGACAAAAGCAAGCAATGCG-AAGGGAT 5372
                         iii vi    i  i     ivv  v   i v  vv     v -  i i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_72431730_7   5373 --TCCATTTTTAATAAGTGGTGCTTGGGAAAACTGGCTAGCCATATGTAG 5420
                         --  --    i  i  i       -    v      v  ?   i   i i
  L1M4_orf2#LINE/    394 AGTC--TTTTCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAA 440

  chrX_72431730_7   5421 AAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAA 5470
                           iiv    ii    i    v   i     v              i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_72431730_7   5471 GATGGATTAAAGACTTACATGTTAGACCTAAAACCATAAAAATCCTAGAA 5520
                         i      i ?    i  v    v   v       i      v  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_72431730_7   5521 GATAACTTAGGCA-ATACCATTCAGGACATAGGCAAGGGCAAGGGCTTCA 5569
                           v   v    ?i- v i -   iv   v v  vvvi     v  i   v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_72431730_7   5570 TGTCTGGAACACCAAAAGCAATTGCTGCAAAAGCCAAAATTGACAAATGG 5619
                          ivv ivi            vvv  vi      vv     v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_72431730_7   5620 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAG 5669
                           ii v  i   v v  i i   i  ii vv    i  v  i i  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_72431730_7   5670 AGTGAACAGGCAACCTACAGAATGGGAGAAGATTTTTGCAACCTACTCAT 5719
                               v  i     i              i  v       vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_72431730_7   5720 CTGACAAGGGGCTAATATCCAGAATCTACAGTGAACTCAAACAAATTTAC 5769
                             i     i  vi          v  i iv      vv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_72431730_7   5770 AAGAAAAAAACAAACAGTACCATCAAAAAGTGGGCAAAGGATATGAACAG 5819
                           v     i     i iiv v  i?    i            v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_72431730_7   5820 ACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAAT 5869
                            i     v        i  vi viii     v  i          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_72431730_7   5870 GCTCATCATCACTGGCCAT 5888
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


3040 26.23 3.76 0.23  chrX_72465589_72469764.rev     2809  3685 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72465589_7   2809 TGGAAATACACTCCATGGTCATAGATTGAAAAAATCAATACTGTTAAAAT 2858
                               v i ii     v    i     i  i v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72465589_7   2859 GTCCATACTACCCAAAGAAATCTACAGATTCAATGCAATTCCTATGAAAA 2908
                          v v     v      vvi              i     i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72465589_7   2909 TACCAATTACATTCCTCACAGAAATAGAAAAAGCAATC-TAAAATTTATA 2957
                          v   ii i v  ii ii       v  v  ivii   -       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_72465589_7   2958 TGGAACCAAAACAGACCCAGAATAGCCAAAGCTATCCTAAGCAAAAAGAA 3007
                              viiv  vi                 i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_72465589_7   3008 CAAAACTAGATAAATCACATTAACTGACTTTA-----TATTACAGAGGTA 3052
                             ii i  vi v     i vv ii i  i -----  i    i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_72465589_7   3053 TAGCAATGAAAACTGAATGGTACTGTCATGAAAACATACACATAGACCAA 3102
                         i  i   v  i  v vi        v   i ii i v   i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_72465589_7   3103 TAAAACAGGACAGAGAACCCAGAAATAAATTCACACGTCTACAGAAAACT 3152
                          ii  i  i iv    ii           ii  i  i i  ii vv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_72465589_7   3153 CCTTTTTGACAAAGACGTCAAGAACGTACACTGGAGAAAGAACAGTCTCT 3202
                         vv    i     i ii i     v i v  v   i       i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_72465589_7   3203 TCAATAAGTAGTACTGGGAAAACTGAATACCCATATGCAGAAGAATGAAA 3252
                             i  i i  i      v     i   ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_72465589_7   3253 CTAGACTCTTGTCTTTCACAATATACAGAAATGAAACCAAAATGGATTAA 3302
                         i i   i i ii  iv   v       i    v  vi          i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_72465589_7   3303 AGACTTAAAT-------CTAAGAC-ATGAAACATT---GAGGAAAC---- 3337
                             i     -------    i  -  i    vi ---i  i    ----
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_72465589_7   3338 -------TCTCCAGAATATTTGTCTGGACAGCAATTTCTTGAGTAAGACC 3380
                         -------   i ivi iv  v vi i i  iiii      iii  v   v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_72465589_7   3381 TCAAACACACAGGCAACAAAAGCAAAAATCGACAAATGGGATCACATCAA 3430
                         i    vi    i          v      v  i    v   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_72465589_7   3431 GCTAAAAAGCTTCTGCACAGCAAAGAAAACAATGAACAAAGTGAAGAGAC 3480
                         iv v    i   i  ii vv     i v  v  v  v        i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_72465589_7   3481 AACCCACAGATTGGAAGAAAATATTTGCAATCTAACCATCTGACAACGGA 3530
                                   v   i               vii vvi      i  v   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_72465589_7   3531 TTAAGAACCAGAAATTATAAGGAGCTCAAACAACTTGACAG--AAAAAAT 3578
                         i viv v      vv     i  i   vv      ii i i--    i i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_72465589_7   3579 AAATAATCCAATTTTAAAAATAGGCAAAAGACCTGAATAGACATTTCTGA 3628
                               i      ?-      i      i  ii               vv
  L1M4_orf2#LINE/    801 AAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_72465589_7   3629 AAAGAAGACATACAAATTGCCAA---GCATATGAAAAAAATGCTCAACAT 3675
                                 i        v     ---   i       i -          
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACAT 898

  chrX_72465589_7   3676 CATTAATCAT 3685
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.95 (150 / 77)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.50 (35 / 10)  


2517 26.35 0.93 6.85  chrX_72479359_72485990.rev     5178  6141 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_72479359_7   5178 GAAAAAAAATCCCATGTTCATGGATAGAGAGAATCACTATCTTGAAAATG 5227
                          i   i v                 v ii   v i v   iv v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_72479359_7   5228 ACCATACTGCC-AAAGTCATTTATAGATTCAATGCTATTCCCATCAAGCT 5276
                         i v     v  -   v v  i  i        i  v  i  i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_72479359_7   5277 AGCA-CTGACTTTCTTCACAGAATTAGAAAAAAACACTATAAATTTTGCA 5325
                         vv  -   v    i  -i     v v  v  ivvv iiv    v  iii 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_72479359_7   5326 TGGAAACCAAAAAGAGCCCGTATAGCTAGA-CAATCCTAAAGAAAAAGAA 5374
                               ivv  ii  v  v v     i i -     i i  i  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_72479359_7   5375 CAAAGCTGGAGGCATCGGGCTACCTGACTTCAAACTATACTACAAGGCTG 5424
                              i      vv  ivi  v  ii i      viv        i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_72479359_7   5425 CAGTAACCAAAACAGTATCTGCTTGGTACCAGTACCAAAACAGTATCTGC 5474
                               i   i     i --------------------------------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGT-------------------------------- 268

  chrX_72479359_7   5475 TTGGTACCGGTACCAAAACAGTATCTGTTTGGTACCGGTACCAAAACAGA 5524
                         ------------------------------     i  i iv ii i   
  L1M4_orf2#LINE/    269 ------------------------------GGTACTGGCATAAGGATAGA 288

  chrX_72479359_7   5525 TATATAGACTAATGGAACAGATCAGAGACCTCAGAAATAACACCATATAG 5574
                         i       ii       i   viv    vii         vv     i v
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_72479359_7   5575 CTACAACCATCTGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGGAA 5624
                         i  iiii  vi    i  i i   ivv  v   i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_72479359_7   5625 AGGCT--TCCTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAT 5672
                           iv --  i  -- i  i              v      v  ?   i  
  L1M4_orf2#LINE/    389 AGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_72479359_7   5673 ACAGAAAACAGAAACTGG-CCCCTCTTTTACACCTTATACAAAAATTAAG 5721
                         i  i  i vv   ii   -     vii i     v              v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_72479359_7   5722 TCAAGATGGATTAGGGACTTAAATGTCAAATCCAAAACCATAAAAACCCT 5771
                             i      i ?i   i       v i v i     i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_72479359_7   5772 AGAAGAAAACCTAAGCAATAGCATTCAGGACACATGCAT-GGGCAAAGAC 5820
                                   v  i ?ivv iiv   iv   - v  vi -i     v ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGT 585

  chrX_72479359_7   5821 TTCATAACTA-AAAACCAAAAGCAATTGCAACAAAAGCCAAAATAGACAA 5869
                            v  iv  -i v          vvv          vv        i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_72479359_7   5870 ATGGGATCTAATTGAACTAAAGTGCTTCTGCACAGCAAAAGAAACTATCA 5919
                           v   ii v  ii  v v  ivi   i  ii vv    i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_72479359_7   5920 TCAGAGTGAATAGGAAACCCACAGAATGGGAGAAAATTTTTGCAATCTAC 5969
                         vv i      v  iv                      v       vii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_72479359_7   5970 CCATCTGACAAAGGTCTAA-ATTCAGAATTTATAAGGAACTTAAACAAAT 6018
                         vi      i  i  v  vi-  i      v     i     ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_72479359_7   6019 TTATAAGAATAAAACAAACAACTCCATCAAAAAGTAGGCAAAGAATATGA 6068
                         iv    v  v  i     i   i v  i?    i i       i  v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_72479359_7   6069 ACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAAATATATGAAA 6118
                          i     i     v        i  vi viii     i  ii i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_72479359_7   6119 AAAAGCTCATCATCACTAGTCAT 6141
                          i v     v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (144 / 106)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 6.25 (75 / 12)  


2779 28.52 0.87 1.64  chrX_72495145_72501925.rev     5376  6290 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72495145_7   5376 TGGTAGAACATTCCATGCTCATGGATTGAAGGAATCAGTATCATGAAAAT 5425
                            v ii i  i     i          i i  v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72495145_7   5426 GGCCATACTGCCTAAAGTAATTCAAAGATTCAATACTATTCCCACCAAGC 5475
                            v     v  i   v i  ii v        ii v  i  i i   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72495145_7   5476 TACCATTGACTTTCTTCATAGAA-TTAAGAAAAACT-ACTTTATATTTCA 5523
                          v   vivi i  i  iii    -  --  v  i  - iii  v v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_72495145_7   5524 TATGGAACCAAAAAAAAAAAAAAAAAGCCTGTATAGCCAAGACAATCCTA 5573
                                --------- viv  iii v  v v        i      i i
  L1M4_orf2#LINE/    149 TATGGAA---------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_72495145_7   5574 AGGGAACAGAACAAAGCTGGAGGCCTCATGCTACCTGATTACAAACCATA 5623
                          iii iv         i      v    ii  v  ii   v    v v  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_72495145_7   5624 CTATGAGACTACAGTAAACAA-ACATGCATGGTACTGGTACCAAAACAGA 5672
                            ii ii         v   -   - ii         i iv ii i   
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACA-GTGTGGTACTGGCATAAGGATAGA 288

  chrX_72495145_7   5673 CATGTAGACCAATGGAGAAGAACAGAGACCTCAGAAATAATACCACAAAT 5722
                            i    i       iv    iv    vii         vv   i v  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_72495145_7   5723 CTACAGCCATCTGATCTTTGACAAACCTGACAAAAATGAGCAATGGGAAA 5772
                         i  ii i  vi    i  i     ivv  v   i viivv       i  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_72495145_7   5773 AGGATC-TCGTATTCAGTAAATGGTGCTGGGAAAACATGCTAGCCATATG 5821
                           i  v-  v -    ii              v   vv v  ?   i   
  L1M4_orf2#LINE/    389 AGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_72495145_7   5822 CAGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACT 5871
                           i  i v    ii         v   i     v                
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_72495145_7   5872 CAAGATGAATTAAAGACTTAAAAGTAAAACCCAAAACCATGAAAACTCT- 5920
                            i   i  i ?    i    v    i v i     i  -        -
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTT 536

  chrX_72495145_7   5921 AGAAGAAAACCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAAGAC 5969
                                   v    ?i- v   -   iv   v v  vv i     v ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_72495145_7   5970 TTCATGACTAAAACACCAAAAACAATGGCAACAGAAGCCAAAATTGACAA 6019
                            v iiv  vi         i  vvi      i   vv     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_72495145_7   6020 ATGGGATCTAATTAAACTAAAGTGCTTCTGCACAGCAAAAGAAGCTATCA 6069
                           v   ii v  i   v v  ivi   i  ii vv    i  vi      
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_72495145_7   6070 TCAGAGTGGACAGGCAACCTACAGAGTGAGAGAAAATGTTTGCAATCTAT 6119
                         vv i    i v  i     i     i  i        i       vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_72495145_7   6120 CCACCTGACAAAGGTCTAATATCCAGAATCTACAAGGAGATTAAAGAAAT 6169
                         vi i    i  i  v  vi          v  i  i  iv ivv v  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_72495145_7   6170 TTAGAAGCAAAAAACAAACAACCCCATCAAAATGTGGGGGAAGGGTATGA 6219
                         iv v  vv    i     i     v  i?   vi    vi    i v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_72495145_7   6220 ATAGACACTTCTCAAAAGAAGACATGTATGTGGGCAGCAAACATTTAAAA 6269
                                i     v        i  ii vi   v  ii  i  iv i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_72495145_7   6270 AAA--CTTATCACCACTGGTCGT 6290
                          i --  i v  i  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (155 / 102)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


 846 27.58 1.57 7.85  chrX_72513372_72519678       50   495 (5812)    L1M4_orf2#LINE/L1      329   746 (162)  

  chrX_72513372_7     50 ATCTGTATATTTTGGATTAGTCAATTGATTTTTATTAAGTTGCAAAGGCA 99
                          i ii  i    ---  -i             ii-------i   i  ii
  L1M4_orf2#LINE/    329 ACCCATACATTT---AT-GGTCAATTGATTTTCG-------ACAAGGGTG 367

  chrX_72513372_7    100 ACTCAATGCAACTTAATGAAGAAAGGATTGTATTTTCAATAAA-GATCAC 148
                         --i   vi v i i    ii     i  v  v       i   - i -i 
  L1M4_orf2#LINE/    368 --CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT-GC 414

  chrX_72513372_7    149 TGAAACTACTGGACATCTGTATGCAAACAGATAAATGAAAGTCCTCTCAT 198
                           ii  v      i ? iii       -   ---     iv vvv i v 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAA-AGA---ATGAAGTTGGACCCCT 460

  chrX_72513372_7    199 AATTTACACTTCATA-ACTAATTAACTCAAAGTATATTATAAATCTAAAT 247
                          vi i    ivi   - vv            i iv  i ? i i      
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_72513372_7    248 GTAACACTGGAAAGTACAAAACTTCTAAAAGTATATATGAGAGAAAAAAC 297
                             v vivi   v  i      ii  i   v v i  -  i?iv   v 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AGGNGTAAATC 559

  chrX_72513372_7    298 TTT-TGGCCTTGCATTAAGCAAATATTCCTTAGAAATGACACCAAAAGAA 346
                           i-  i     vi   i    vvi  i      v             v 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_72513372_7    347 TGACC--CATAAGAAAAAAT-GATAAATTAGACTTTATCAAACTTTTCAA 393
                         ii v --  v          -        i     i      v  -----
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT----- 654

  chrX_72513372_7    394 AAGAAAAACAATATATTTCTTCTCTGTGAAATACATGGTTAATAGAATAA 443
                         ---      -------  i viv  vii  iv   ivi i  v i i i 
  L1M4_orf2#LINE/    655 ---AAAAAC-------TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_72513372_7    444 GAAGCTAAGCCATAGACTTCAGTGAAATCATT-GAAAATCACACATCTGA 492
                         i   vi  v   i   v v-i v    vi   - v      i i      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATG-GGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_72513372_7    493 AAA 495
                         v  
  L1M4_orf2#LINE/    744 TAA 746

Transitions / transversions = 1.67 (75 / 45)
Gap_init rate = 0.04 (17 / 418), avg. gap size = 2.47 (42 / 17)  

3087 27.53 0.55 0.55  chrX_72513372_72519678     4907  5814 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72513372_7   4907 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATAACATGAAAAT 4956
                              ii i  i     i      i v      v i    vii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72513372_7   4957 GGCCAAATCGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5006
                            v v iiv     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72513372_7   5007 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5054
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72513372_7   5055 TATGGAACCAAAAAAGAACCCGCATCACCAAGTCAATCCTGAGCCAAAAG 5104
                                viiv  ii  v  v v  vi    iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72513372_7   5105 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTCCAAGGC 5154
                                i      vv       v  ii i      viv    v   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72513372_7   5155 TACAGCAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGATACAGATC 5204
                              i  i   i    i          i iv ii i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72513372_7   5205 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5252
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_72513372_7   5253 ATCTGATCTTTAACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5302
                          vi    i  ii    ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72513372_7   5303 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCT 5352
                           v  i  i              v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72513372_7   5353 CAAACTGGATCCCTTCCTTACACCTTGTACAAAAATCAATTCAAGATGGA 5402
                         v  ii    i    v   i     v i         i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72513372_7   5403 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5452
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_72513372_7   5453 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTGA 5502
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_72513372_7   5503 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAG 5552
                         i            vvi          vv     v  i    v   ii vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72513372_7   5553 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAACATCAGAGTGAAC 5602
                          i   v v  i i   i  ii vv    i  v    v  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_72513372_7   5603 AGGCAACCTACAAATTGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5652
                           i     i   i v           v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_72513372_7   5653 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAACTTA-CAAGAAA 5701
                         i  i  vi          v  i  v      vv    -  i -i  v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAA 795

  chrX_72513372_7   5702 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5751
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_72513372_7   5752 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5801
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_72513372_7   5802 CATCACTGGCCAT 5814
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2790 27.94 1.44 0.78  chrX_72543831_72553697     3988  4889 (4978)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72543831_7   3988 TGGAAAGACATTCCATATTCATGGATAGGAAGAATCAATATCCAGAAAAT 4037
                                 i  i    i         v      v i     ivvv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72543831_7   4038 GGCCATACTATCCAAAGTAATTCATAGAGTCAATGCTTTCCCCATCAAG- 4086
                            v     vi     v i  ii i   v    i  vv    i     i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72543831_7   4087 --CTAGCATTGACTTTATTCACAGAA-TTGGAAAAAACT--TCTTTAAAC 4131
                         -- i   --  v    -  ii     -   -- v  i  --  i -   v
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTT-TTTGCAGAAATTG--ACAAGCTGATCCT-AAAA 144

  chrX_72543831_7   4132 TTCATATGGAACCAAAAGAGAGCCTGTATAGCCAAGACAATCCTAAGCAA 4181
                                    viiv   i  v  v v        i      i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_72543831_7   4182 AAAGAACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTAAACTACA 4231
                         i          i      vv   vi  v  ii i      vivv      
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_72543831_7   4232 AGGCTACAGTAACCAAAACAGCTTGACACTGGTACCAAAAGAGATATATA 4281
                          i          i   i    iv  ii     i iv ii v   i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_72543831_7   4282 GATGAATGGAAGAGAACAGAGGCTTCAGACATAAAACCACACATCTACAA 4331
                            v       v    iv   iv i    v     v   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_72543831_7   4332 CCATCTGATCTTTGACAAACATGACAAAAACAAGCTATGGGGAAAGGATT 4381
                         i  vi    i  i     ivi  v   i v  vv v          i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_72543831_7   4382 CCCTATTTATTAAGTGGTGTTAAGAAAACTGGCTAGCCATATGTAGAAAA 4431
                         vi  v  i vi  i     i ii  v      v  ?   i   i i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_72543831_7   4432 CTGAAAATGGACTCCTTCCTTACACCTTACATAAAAATTAACTAAAGATG 4481
                         v    iv     i   v   i     v  i i           v  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_72543831_7   4482 GATTAAAGACTTAAACATAAGGCCTAAAAGAATAAAAATTCTAGAAGAAA 4531
                            i ?    i    ii    iv      vv      v ii         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_72543831_7   4532 ACCTAGGCA-ATACCATTCAGCACATAGGCATAAGCAAAAACTTTATGTC 4580
                           v    ?i- v i -   ivv  v v  vv  i    viii  iv ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_72543831_7   4581 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCAGATC 4630
                           vi            vvi          vv     v  i    ii  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_72543831_7   4631 TAATTAAACTAAAGAGCTTCTGCACAGCAAGAGAAACTATCATCAGAATT 4680
                          v  i   v v  i i   i  ii vv   ii  v       vv i i v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_72543831_7   4681 AACAGGCAACCTACAAAATGACAGAAAATTTTTGCAATCTGTCTGTCTGA 4730
                           v  i     i   i    iv       v       viii v i     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_72543831_7   4731 CAATCGGCTAATATGCAGAATCTACAAAGAACTT---CAACATATTTACA 4777
                         i  vv i  vi   v      v  i        i---    vi v v i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_72543831_7   4778 AGAAAA-AAACAACCCCATCAAACAGTGGGACAAGGATATGAACAGACAC 4826
                          i  i -   i     v  i?  v i    vv      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_72543831_7   4827 TTCTCAAAAGAAGACATTTATGCAGCCAGCAA--ACATGAAAAAAAGCTC 4874
                              v        i  vi viii    ii  --         i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_72543831_7   4875 ATCATCACTGGTCAT 4889
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (140 / 108)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  

2715 27.96 2.13 0.56  chrX_72543831_72553697     8481  9374 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72543831_7   8481 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAACATCATGAAAAT 8530
                               i i  i     i        v      v i  i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72543831_7   8531 GCCA-TACTGCACAAAGGAATTTATAGATTCAAGGCTATTCCTATCAAGC 8579
                          v  -    v v    vvi  i  i        v  v  i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72543831_7   8580 TACCATTGACTTTCTTTGCACAATGTGAAAAAGCT-ACATTAAATTTCAT 8628
                          v   vivi i  i      v  vv   v  -   - ivi    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_72543831_7   8629 ATGGAACCAAAAAGAAGCCCATATAGCCAAGAGAATACTAAGCAAAAAGA 8678
                               viiv  i i v  viv        i v   vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_72543831_7   8679 ACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTATACTACAAGTCT 8728
                               i     ivv    i  v  ii i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_72543831_7   8729 GCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGATTA 8778
                         i      i   i    ii         i iv ii i   i        i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_72543831_7   8779 ATTGAACAGAACAGAGACCTCAGAAATAACATCACACATCTACAA-CAAT 8827
                           v   i    iv    vii         vvi  i    i  iii-    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_72543831_7   8828 CTGATCCTCAACAAAACTGACAAAAACAAGTAATGGGGAAAGGATTCCCT 8877
                         -    ii  i    iiv  v   i v  vvi           i  vvi  
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_72543831_7   8878 ATTAAATAA-TGGTGCTGAAATAACTGGCTAGCCATATGCAGAAAATAGA 8926
                         v  v  i  -        ii i      v  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_72543831_7   8927 AACTGGACACCTTCCTTACACCTTATACAAAAATTAA-----GATGGATT 8971
                          ii     v   v   i     v              -----i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_72543831_7   8972 AAAGACTTAAATATAAAATCCAAAACCATGAAAATCCTGGAAGAAAACCT 9021
                          ?    i     i   i v i     i  i   v  i i         v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_72543831_7   9022 AGGCA-ATACCATTCAGGACACATGCAT-GGGCAAAGACTTCATGACTAA 9069
                            ?i- v i -   iv   - v  vi -i     v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_72543831_7   9070 AACCCCAAAACCAATTTCAACAAAACCCAAAACTGACAAATGGAATCT-- 9117
                         i  v      v  vvvv        vvv    iv  i    v i ii --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72543831_7   9118 ----AATTAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAGTTAA 9163
                         ----       i -   i  iiivv    i  v       vv i   v  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_72543831_7   9164 CAGGCACCCTACAGAATGGGAGAACATTTTTGCAATCTAACCATCTGACA 9213
                         v  i  v  i              v  v       vii vvi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_72543831_7   9214 AAGGTCTAATATCCAGAATTTACAAGGAACTTACACAAATTTACAAGAAA 9263
                          i  v  vi          v  i  i     ivi    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_72543831_7   9264 AAAA--AACAACACCATCAAAAAGTGGGTGCAGGGTATGAACAGACACTT 9311
                           i --  i   v v  i?    i    iiv   i v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_72543831_7   9312 CTCAAAAGAAGACATTCATGTGGCCAACAAACATATGAAGAAAAGCTCAA 9361
                            v        i  v  vi       i  i  i     i i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_72543831_7   9362 CATCACTGTTCAT 9374
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (141 / 105)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.71 (24 / 14)  


2629 28.54 3.88 0.23  chrX_72575060_72578314.rev     1889  2764 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72575060_7   1889 TGGAAAGACATTTCACGCTTACGGATTGGAAGAATCAA------------ 1926
                                 i  ii  i i i i           v i  ------------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72575060_7   1927 --CAACAT-----AAAGCAATCTGAAGATTCAATGCTATACCTATCAAAC 1969
                         --   i i-----   vii    iv        i  v  v         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72575060_7   1970 TACAAACATCATTCTTCACGGAATTAGAAACAACT-ATTCTACAATTTAT 2018
                          v v i vv v  i  ii i   v v  v - i  -  i   v    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_72575060_7   2019 ACAGAAACAAAAAAGGACCTA-AATAGCCAAAGCAATCCTAAGCAAAAAT 2067
                          ii    iiv  i-     i -          i     i i iv  i  v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72575060_7   2068 AACAAAGCCAGAGGCATCATATTACCTGACTTCAAACTATACTACAAGGG 2117
                                iii    vv   i i v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72575060_7   2118 TACAGTAACCAAAACAGCATGGTACTGGCACAAAAACA--CACATAGACC 2165
                                 i   i    ii           i  ii i --  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72575060_7   2166 AATGGAACAGAAT--AGACCACAGAAATAAAGCTGCGCACCTACTACCAT 2213
                                i     --   viv          v iiii  ii  ivii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_72575060_7   2214 CTGATCTTTGACAAAACTGACAAATCTGAGTAATGGAGAAGGGCCCCTCT 2263
                         i    i  i     iiv  v   iv iivvi     i   i ivivv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_72575060_7   2264 ATTCAATAAATGGAGCTGGGATAACTGGCCAGCCATATGCAGAAGAATTA 2313
                         v     i      v       i      vi ?   i     i      v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_72575060_7   2314 AGCTGGAACACTACCTGTCATGATATACACAAATTAACTCAAGACGGATT 2363
                           i    v v      vv  iv       v            i i    i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_72575060_7   2364 AAGTACTTAAATGTAAGACTTCAAATTATAAAAATCCTAGAAGAAAACCT 2413
                          ?iv  i           vi v   i       v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_72575060_7   2414 GGGAAACACCCTTCTCAACATTGGCCTTGGCAAAGGATTCATGACTAAGT 2463
                         i  ?ivv vi    vii  v    vi v     v  v   v iiv  v v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_72575060_7   2464 CCTTAGAAGCAACTGCAACAAAAACAAAAATTGATTAA---GACCTAGTT 2510
                          vii i     vvv         iv      v   v  ---   i vi i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_72575060_7   2511 AAACTAAAGAGCTTCTGCACAGCAAAAGAAATTATCAA-----TCAACAG 2555
                            v v  i i   i  ii vv    i  v i      ----- v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_72575060_7   2556 ACAACATACAGAATGGGAGAAAATATCCACGATCTATGTATC-AACAAAG 2604
                              vi                   iii i vii  i    -i i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_72575060_7   2605 GTATAATATACAGAATCTATTAGGAATTTAAATAATTCAATAGGCAATAA 2654
                          vv vi   v      v   v i   i ivv i  i      ivv  v i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_72575060_7   2655 ACAAATAGCCCCATCAAAAAGTGGGCAAAGGGCATGAATATACATTTCTC 2704
                                i   v  i?    i          iiv      v         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_72575060_7   2705 AAAAAAACACATGTAAGTGGCCAACAAACATATGAAAAAATGCTCATCAT 2754
                         v   i  v i  ii  i       i  i  i       i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_72575060_7   2755 CACTAATCAT 2764
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.27 (36 / 11)  


3294 26.98 0.44 0.44  chrX_72601440_72604147.rev     1310  2217 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72601440_7   1310 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1359
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72601440_7   1360 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1409
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72601440_7   1410 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1457
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72601440_7   1458 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCACTCCTAAGCCAAAAG 1507
                                viiv  ii  v  viv  v     iv  v  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72601440_7   1508 AACAAAGCTGGAGGCATCACACTACCTGACTTCTAACTATACTATAAGGC 1557
                                i      vv       v  ii i   v  viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72601440_7   1558 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1607
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72601440_7   1608 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 1655
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_72601440_7   1656 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTTC 1705
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72601440_7   1706 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCT 1755
                           v  i  i              v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72601440_7   1756 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1805
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72601440_7   1806 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1855
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_72601440_7   1856 CTAGGCATTACCATTCAGGACATTGGCATGGGCAAGGACTTCATGTCTAA 1905
                         v    ?i v viv   iv   v    vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_72601440_7   1906 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 1955
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72601440_7   1956 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2005
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_72601440_7   2006 AGGTAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 2055
                           ii    i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_72601440_7   2056 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAGATTTACAAGAAAA 2105
                         i  i  vi          v  i  v      vv   iv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_72601440_7   2106 AAACAAACAACGCCATCAAAAGGTGGGCGAAGGACATGAACAGACACTTC 2155
                          i     i   v v  i?   ii     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_72601440_7   2156 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 2205
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_72601440_7   2206 ATCACTGGCCAT 2217
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1960 22.11 3.04 0.41  chrX_72604628_72611310.rev        1   493 (6190)    L1M4_orf2#LINE/L1       93   598 (310)  

  chrX_72604628_7      1 TATCAGAATCTCAA-TGACTTTTTCATAGAAATAAAAAAA---ATCCTAA 46
                              i    i  i-  v      iii      vi v  i---       
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_72604628_7     47 AATTCACAGGAAAACTCAAGATACCCCTATTAGCCAAG-CAATCTTAAAA 95
                               i v i   iv    iv    vv v       i-       i   
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_72604628_7     96 ATGAGAAAAAAAATGTTGGAAGACTCACATCTTCTGATTTAATAATTTAC 145
                          --    i  v  v      i        ii i ii    v v  i    
  L1M4_orf2#LINE/    193 A--AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_72604628_7    146 TACAAAGCTCAAGTGATCAAAAAAGTGTGGTACTGGCATAAAGACAGACA 195
                                  vv   i     i v                  i  i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_72604628_7    196 TATAAACAAATGAAATAGAACACCGAGCCTAGAAGTAAAGTCTCAAATAC 245
                             i iv    i       ivvv   i i    i    vi vi v  vi
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_72604628_7    246 GTGGTCAACT-ATATTCAACAAGAGTATCAAA--CATTTGAAGGAGAAAG 292
                         i       i -  v   i     i  ii   i--    ii v  i     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_72604628_7    293 TAT-GTCTTCTCAACAAATGCTACAGGGAAACCTGGATATCCCCATGCAA 341
                         v  -     i          v i v    v v       ?  v       
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_72604628_7    342 AAGAGTGAAGTAGGATGCTGACCTCACA---TAGATAAAAATTAACTCAA 388
                             i      v   iv iv        ---  v i              
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_72604628_7    389 G-TGTATCAAAGCACTAAATGTAAGAGCTACAACTATAAAACACTCAGAA 437
                         i-  v    ?  vv                v           v  i    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_72604628_7    438 GAAAACA-AGAAG-AAATCGTCATGACACTGGATTTTGCTATGATTTCTA 485
                                -  i? -     v  i    vi   i  vv  v   i     v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_72604628_7    486 AGATATGA 493
                                 
  L1M4_orf2#LINE/    591 AGATATGA 598

Transitions / transversions = 1.26 (59 / 47)
Gap_init rate = 0.02 (11 / 506), avg. gap size = 1.55 (17 / 11)  

2900 27.22 1.56 0.67  chrX_72604628_72611310.rev     5293  6192 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72604628_7   5293 TGGAAAAACATTCCATGCTCATAAATAGGAAGAATCAATATCGTGAAAAT 5342
                               i i  i     i    ii  v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72604628_7   5343 GGCCATACTGCCCGAAGTAATTTATAGATTCAATGATATCCCTATCAAGC 5392
                            v     v   i  v i  i  i        i vv           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72604628_7   5393 TACCATTAACATTCTTCACAGAAGTAGAAAAAACT-ACTTTAAATTTCAT 5441
                          v   vivi v  i  ii     i v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_72604628_7   5442 ATC-AAAT-CAAAAAACAGCCCATATACCCAAGACAATCCT---AAGCAA 5486
                           v-    -   iii  --  viv   v    i      i ---  iv  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_72604628_7   5487 AAACAAAGCTGGAGGCATCACGCTATCTGACTTCGAATTATACTACAAGG 5536
                         i       i      vv    i  vi ii i   i  viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_72604628_7   5537 CTATAGTAACCAAAACAGCATTGTACTAATACCAAAACAGATATATAGAT 5586
                            i     i   i    ii v     iii iv ii i   i        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_72604628_7   5587 CAATGGAACAGAACAGA-AGCCTTATAAATAAACACCACACATCTACAAC 5635
                                 i    iv  -  i i- v        -   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC-AGAAATAAAC-CCATACATTTATGGT 345

  chrX_72604628_7   5636 CACCTGATCTTTGACAAACCTGCCAGAAACAAGCAATGGGGAAAGGATTC 5685
                           vi    i  i     ivv     ii v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_72604628_7   5686 CCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAAGCAGAAAAC 5735
                         i  v  i  i        i     v      v  ?   i v   i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_72604628_7   5736 TGAAACTGAACCCCTTCCTTACACCTTGTACAAAA-CTAACTCAAGATGG 5784
                             ii  i      v   i     v i       -i        i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_72604628_7   5785 ATTAAAGACTTAAACGGAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5834
                           i ?    i    i v    v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_72604628_7   5835 CCTAGGTG-ATACCATTCAGGAGATAGGCATGGGCAAAGACTTCATGACT 5883
                          v    ? - v i -   iv  vv v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_72604628_7   5884 GAAACACCAAAACCAATGGCAACAAAAGCCAAAATAGACAAATGAGATCT 5933
                         ivi         v  vvi          vv        i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_72604628_7   5934 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5983
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_72604628_7   5984 ACAGGCAACCTACAGATTGGGAGAAAATGTTTGCAATCTATCCATCTGAA 6033
                          v  i     i     v           i       vii  vi      v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_72604628_7   6034 AAAGGGCTAATCTCCAGAATCTACAAGAAACTTAAACAAATTTACAAGAA 6083
                           i  i  vi v        v  i  ii    ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_72604628_7   6084 AAA---AAACAAGCCCCTCAAAAAGTGGGTGAAGGATATGAACTGACACT 6130
                            ---   i  v  vv i?    i    ii      v    iv    i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_72604628_7   6131 TTTCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAAGCTCA 6178
                          i  v        i  vi viii     i  --         i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_72604628_7   6179 TCATCACTGGTCAT 6192
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.43 (20 / 14)  


2823 24.23 5.97 2.07  chrX_72631432_72635835.rev     3043  3913 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_72631432_7   3043 AAAGATATCTCAT--TCATGGACTGGAAGAATTTATATGGCTAAAATGTC 3090
                                  i   --       i       v  v    v i   i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_72631432_7   3091 CATACTACCCAAAGCAATCTACAGATTCAATGCAATCC-TATGAAAATTC 3139
                         v     v      vii              i       -   v     i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_72631432_7   3140 CAATGGCATTTTCTTCCCACAGAAATAGAAAAAAACAATCCTAAAATTTA 3189
                           iiv  v    i ----i       v  v  iv-ii           i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTT----GCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chrX_72631432_7   3190 CATGGAACCACAGAAGATCTTGGATAGCCAAAAGAATCTTGAGAATAAAG 3239
                         i      vii  iii  i iv i          v        i  vi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72631432_7   3240 AACAAAGCTGGAGTCCCTAATCTTCCTGATTTCAAACTATACTTTCAAGC 3289
                                i     vv ii vv     ii        viv    viv    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72631432_7   3290 TATAGTAATCAAAACAGTATGATACTGACATAAAAGTAGACAAATACACC 3339
                           i         i     i  i     i     iii      v   v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72631432_7   3340 AAC------------AGAGCCCAGAAATAAACTCATGCATATATGGTCAA 3377
                           i------------    i            i   i   v         
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_72631432_7   3378 CTAATTTTTGAAAAGGAAAACAAGCATACACATTGGAAAAAGGATAATCT 3427
                         i i     i  v    iviv    vvi iv  v   ii    i   i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_72631432_7   3428 TTTCAATACATGGTGTTGGGG-AACTGTATATCCATTTGCAAAGGAATGA 3476
                               i v      i    i-     v   ?   iv      i      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_72631432_7   3477 AACTGTACACTTGTCTTATACCATA--CAAAAATTAACTAAAAATAAATT 3524
                          ii  v  v i ii  i i      --            v     ii  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_72631432_7   3525 AAACATTTAAACAT--GACTTAAAAATGTAAAACTCCTAAAAGAAAACTT 3572
                          ? v ii    ii --  vi     v i        i  i        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_72631432_7   3573 AGGGAATAAGCCCAC-TAACATTGCTATTGACAATGATTTTTGAGTTGTG 3621
                            ?i-   ii iv - i  v   vvv v i     i   i v  v i  
  L1M4_orf2#LINE/    549 AGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_72631432_7   3622 ATTTTAAAAAACACAGGCAACAAAAGCAACAATAAGACA-----GACAAC 3666
                          ivii    i-    i          v  v    -  i -----   vv 
  L1M4_orf2#LINE/    598 ACACCAAAAG-CACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTC 645

  chrX_72631432_7   3667 ATCAAACTAAAAAGCCTCTGCACAGCCAAGGAGACAATCAACAAAATAAA 3716
                               v v    i i i  ii vv v     v  v     v   i i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_72631432_7   3717 AAGGCAATCTATGGAATGTGAGAACATAAATGCCAACAATATATCTGATA 3766
                            i   i i ii     v     v   vv   v  iv            
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_72631432_7   3767 TGAGGTTAACATCCAAAATATATAA-GAACATCATGAAAGAAAAATAACT 3815
                         v i ii vii     i         -    -  v --------- i    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAAC-TCTT---------ACAACT 785

  chrX_72631432_7   3816 GAATAGAAAAAA---AAAT--CCTGATTAAAAAATGAGCAAAAGA----- 3855
                         v    iv     ---    --  ii   ?       i     i  -----
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_72631432_7   3856 ---------------AAAAAGACATATAAATGGCCAACAGGTATATGAAA 3890
                         ---------------  i    i   i          i i i i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_72631432_7   3891 ACGTGCTCAACATCACTGATCAC 3913
                          vi            ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (129 / 78)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 3.68 (70 / 19)  


 996 25.71 1.27 3.81  chrX_72648018_72650171.rev      198   512 (1642)    L1M4_orf2#LINE/L1      330   636 (272)  

  chrX_72648018_7    198 CCCACCTCCATTCA--GCCAACTGACTTTCAATGAAGGCACCAAAGACAT 245
                             -- v    i -- i   i   i    i ii i  ii    iiv   
  L1M4_orf2#LINE/    330 CCCA--TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_72648018_7    246 ACCATGGGTAAAGTGTATCCTCTTCAATAAATGGTACTGGGAAAACTGGA 295
                         v v     v    vi  vi  i     i       i      v       
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_72648018_7    296 TATCCATATGCAGAAGAATGAAACTAGAATCCTATCTCTCACCATATACA 345
                           ?   i     i         ii i  vi    i   v           
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_72648018_7    346 AAAATCAAATAGAAATGTATTTTAGACTTAAATGTAAGACCTGAAACTAT 395
                              i  v vi     v  iv?    i           v  i       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_72648018_7    396 GAAACTACTATAGGAAAA-GTTGGAG-AAATGCTTCAAGGTATTGGTCTG 443
                         i     vi  v i     -i v  ? -    -    iv iiv    vi i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTA 576

  chrX_72648018_7    444 GGTCAAAGATTTTATGGATAAAACTTTGAAAGTAAAAATAGACAAACGGA 493
                           -   v i   iv i    vi  viii    i v  ii -     v i 
  L1M4_orf2#LINE/    577 GG-CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA-ACAAAAGAA 624

  chrX_72648018_7    494 ATTACAACAAAGAAATAAA 512
                          -------   v i     
  L1M4_orf2#LINE/    625 A-------AAATAGATAAA 636

Transitions / transversions = 1.79 (50 / 28)
Gap_init rate = 0.03 (8 / 307), avg. gap size = 2.00 (16 / 8)  

3083 23.15 3.69 2.22  chrX_72648018_72650171.rev      852  1663 (491)    L1M4_orf2#LINE/L1       85   908 (0)  

  chrX_72648018_7    852 GCAATTCCTATGAAAATTCCAATTTTATATTTCACAAAAATAGAAAAAGC 901
                              i     v     i   ii viv v   ii  i    v  v  -  
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GC 133

  chrX_72648018_7    902 ATTTCCTAAAATTCACTTGGAACCACAAAAGATTGCAAATAGCCAAAACA 951
                         vvv            iv     vii   ii  iivvi             
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_72648018_7    952 GTCTTGAGAAAAAAGAACAAAGCTGGAGACCTCACACTACCTGATTTCAA 1001
                         i      i   i          i     iv        v  ii       
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_72648018_7   1002 AATATATTACAAAGCTATAAAAATCAAAACTGCATGGTAACAGCATAAAT 1051
                           iv  i          i iv      i  v ii     vii      iv
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_72648018_7   1052 ACAGACACACTGGA-CAATAGAACAGGATAGAGTGCCCAGAAATAAACCT 1100
                          i     i - i  -    i   i  i  v   v i             i
  L1M4_orf2#LINE/    284 ATAGACATA-TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_72648018_7   1101 ATGTTTACTCATGGTCAAACCATGGTCAATTGGTTTGACAAAGTTGCTAA 1150
                           ii-- i i        ------- ii   --  i     i v   i  
  L1M4_orf2#LINE/    333 ATAC--ATTTATGGTCAA-------TTGATT--TTCGACAAGGGTGCCAA 371

  chrX_72648018_7   1151 GAACACACAATACAGAAAGGACAGTCTCTTTAATAAATGATATTGGAACA 1200
                           v  iv    ivi     i i     i  i  i     i ii   i   
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_72648018_7   1201 ACTGAATATCCACATGCAGAGGAATAAAATTGGACCCTTACCTCATACCA 1250
                             i   ?         i i    i  i        i       i    
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_72648018_7   1251 TACATAAAAATCAGCTCAAAATTGATTGAAGACTTAAATGCAAGACCTGA 1300
                           i i      i i        v   ii?    i      i    v  i 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_72648018_7   1301 AAATATAAAACTACTAGAAGAAAACATAGGGTAAAAACTCCATGACACTG 1350
                           v         vi                ?vv   v  i i    vi  
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chrX_72648018_7   1351 GTCTGGGTAGTAATTTCTTGG---------TAAAAGCGCAGGCAACAAAA 1391
                          vi i  i i ii      i ---------i      i  i         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_72648018_7   1392 GCAGAAATAAATGAACAGGACTGCATGAAACT----ATTTCCTTTGCTTT 1437
                          v i     i  i  iv     v   v   v ---- vi ii v     -
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT- 670

  chrX_72648018_7   1438 GCAAAGGAAATAATTAACAGAGTGAAGAGACAATTGCATGGATTGGGAGA 1487
                         -       v iv  i  v i      i      ii-  ii  v       
  L1M4_orf2#LINE/    671 -CAAAGGACACTATCAAGAAAGTGAAAAGACAACC-CACAGAATGGGAGA 718

  chrX_72648018_7   1488 AAATATTTGCAAACCATACATCTGACAAGG--CTAATATCCAAAACATA- 1534
                                      i    i      i    --  vi      i  i   -
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_72648018_7   1535 -AGAAACTC--A-AACT--GTAGTAAAA-------CAATCCAATTACCAA 1571
                         - ii     -- -    --i  i     -------i  i      ?--  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW--AA 816

  chrX_72648018_7   1572 AAATAGGTGGAGGATCTGAATAGATACTTCTCAAAAGAAGACATACAGGT 1621
                             i  iii     i        i i     v        i     ii 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_72648018_7   1622 AGCCAACAGGTATATAAAAAGGTGCTCAACATCACTAATCAT 1663
                         i     i i i i  i     i            ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.83 (136 / 48)
Gap_init rate = 0.02 (17 / 824), avg. gap size = 2.82 (48 / 17)  


2782 27.17 2.12 1.00  chrX_72650384_72655997     4224  5121 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72650384_7   4224 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAACAT 4273
                               i i  i     i        v      v i     ii v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72650384_7   4274 GGCCGTACTGCCCATAGTAATTTATAGATTTAATGCTCTTCCCATCAAAC 4323
                            vi    v    v v i  i  i     i  i  vv i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72650384_7   4324 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCGT 4372
                          v   vivi v  i  ii     v v  v  i-  - iii    i   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_72650384_7   4373 ATGGAAC--CAAAGAAGAGTGCATA-TAGCCAAGACAGTTCTAAGCAAAA 4419
                               v--   i i ---iv  v -       i   i ii i iv  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_72650384_7   4420 AGAACAAAGCTGGAGGCATCACACTACCTGACTTTAAACTGTAATGCAAG 4469
                                  i      vv       v  ii i  i   viv  v i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_72650384_7   4470 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAGACAGACA----GA 4515
                                   i   i    ii         i iv i  i     ----  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_72650384_7   4516 CCAATGGAACAGAACAGAGACCTTAGAAATAACACCACACATCTACAACC 4565
                         i        i    iv    viii        vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_72650384_7   4566 A-TCCATTCTTCGATGAACCTGACAAAAACAAGCAACAGGGAAAGGATTT 4614
                          - iv   -     ii ivv  v   i v  vv   ii       i  vv
  L1M4_orf2#LINE/    347 AATTGATT-TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_72650384_7   4615 TCTATTCAATAAATGGTGCCGGGAGAACTGGCTAGCCCATATGCAAAAAG 4664
                            v     i         i    v      v  ?  - i        ii
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC-ACATGCAAAAGA 444

  chrX_72650384_7   4665 CAGAAACTGTACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATG 4714
                         vv   ii  v      v   i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_72650384_7   4715 GAATAAAGACTCAAATGTAAATCCCAAAACCATAAAAGCCTTAGAAAAAA 4764
                           vi ?    ii        ivv i     i      vi       i   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_72650384_7   4765 ACCTAGGCAATAACATTCAGGACATAGGCATGGGCAAAGACTTCAT-GAC 4813
                           v    ?ivv  iv   iv   v v  vv i     v ii   v -  i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_72650384_7   4814 ATAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATC 4863
                           i -           vvv          vv     v  i    v   ii
  L1M4_orf2#LINE/    595 ATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_72650384_7   4864 TAATGAAACTAAAGAGCTTCTTCACAGCAAAAGAAACTATCATCAGAGTG 4913
                          v  v   v v  i i   i vii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_72650384_7   4914 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACCCACCTGA 4963
                           v  i     i                 v      ivii ivi i    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_72650384_7   4964 CCAAGGTCTAATACCCAGAATCTACTAGGAACT--TA-AATTTA-CAAGA 5009
                         iv i  v  vi  i       v  iv i     --  -  i i -i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_72650384_7   5010 TAAAAACAATGTCATCCAAAT-----GTGGGCAAAGTATATGAACAGACG 5054
                         v   i    -i v i    v -----i         v  v    i    i
  L1M4_orf2#LINE/    794 AAAAGACAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_72650384_7   5055 CTATTCAAAAGAAGACATTTATGTGGCCAACAAACATATGGAAAAAAAGC 5104
                         i vi  v        i  vi vi       i  i  i   -    i v  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGC 891

  chrX_72650384_7   5105 TCAACATCACTGATCAT 5121
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.65 (28 / 17)  


2639 26.45 2.90 1.56  chrX_72658418_72662225.rev     2422  3317 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72658418_7   2422 TGGAAAAA-ATTCCAGGCTCACGGATAGGAAGAATCAATATTGTGAAAAT 2470
                               i -  i   v i   i    v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72658418_7   2471 AACCACACTGCCCAAAGCAATTTATAAATGCAATGCTATTCCCATTAAAC 2520
                         ii v i   v      vii  i  i i  v   i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72658418_7   2521 TACCA-CTGACATTCTTCACAGACTTAGAAAAACT-ATTTTAAAATTCAT 2568
                          v   -   v -  i  ii    vv v  v  i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_72658418_7   2569 ATGACACAAA---AAAAGAGCTTGAATGGCCAAGGCTATCCTAAGCAAAA 2615
                            i---   ---  ii  v iv    i     ii v   i i i-   i
  L1M4_orf2#LINE/    150 ATGG---AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAG 195

  chrX_72658418_7   2616 AACAATAAAGCTGAAGGCATCACGCTACCTGACT-CTGAACTATACTACA 2664
                           v  i    i  i   vv    i  v  ii i - vi    -       
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACA 244

  chrX_72658418_7   2665 AGGCTACAGTAATCAAAACAGCATGGTACTGGTAAAAGAACAGACACACA 2714
                          i              i    ii         i v   i i     i i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_72658418_7   2715 GACCATTGGAACAGAATAGAGAACCCAGAACTAAGACTGCACACCTACAA 2764
                           i  v     i     v    ii      v   iv iii   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_72658418_7   2765 CCAACTGATGTTTGACAAACCTGAGAAAAACAAGCAATGGG-AAAGGAT- 2812
                         i   i    v  i     ivv  vv  i v  vv       -    i  -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_72658418_7   2813 -TCCATGTTTAAGAAATGGTGCTGGGAGAACTGGCTAGCCATATGCAAAA 2861
                         -  -- v  i  v              v      v  ?   i        
  L1M4_orf2#LINE/    395 GTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_72658418_7   2862 AACTGAAAAATAGACCTCTTCCTTATACCATATATAAAAATCAACTCAAG 2911
                         i v    iv- i    i  v   i i        i      i       i
  L1M4_orf2#LINE/    443 GAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_72658418_7   2912 ACTGATGAAAGACTTAAATATAAAACCCCAAACTATAAAATCCCTAAAAG 2961
                          iv   v ?    i     i   i v iv           ii i  i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_72658418_7   2962 AAAATCTAGGCA-ACACCATTCAGGAAATAGA--CAGGAACAAACATTTC 3008
                             iv    ?i- v i -   iv  vv v i--i   --   vvi    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGG--CAATGGTTTC 588

  chrX_72658418_7   3009 AC-GATGAAGATGCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAAT 3057
                         vi-   - v  ii         vvv          v      v  i    
  L1M4_orf2#LINE/    589 TTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_72658418_7   3058 GGGATCTAGTTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATTATC 3107
                         v   ii vi i   v v  i i   i  ii vv    iv v     i vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_72658418_7   3108 AGGGTGAACAAAAAATCTACAGAATAGGAGAAAATTTTTGCAATCCATCC 3157
                          ii     v i v  i i       i         v       vi   vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_72658418_7   3158 ATCTGA-AAAGGTCTAATATCTAGCATCTACAAGGACCTTAAACAAACTT 3206
                               -  i  v  vi    i  v  v  i  i  v  ivv    -  i
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTC 786

  chrX_72658418_7   3207 AACAAGAGAAA-------AATCCA-TTAAAAAGTGGGCAAAAGACATAAA 3248
                           i  v i   -------  i   -  ?    i        i  iv i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_72658418_7   3249 CAGACACCTCTCAAAGGAAGACATACAAATGCCTAACAA--ACATAAAAA 3296
                         i     ii    v  i     i         v i  i  --    i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_72658418_7   3297 -ATGCTCAATATCACTGATCAT 3317
                         -        i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (144 / 89)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 1.60 (40 / 25)  


3011 25.73 3.16 0.68  chrX_72674876_72681243.rev     4992  5877 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72674876_7   4992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCGTGAAAAT 5041
                              ii i  i     i      i v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72674876_7   5042 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5091
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72674876_7   5092 TACCAAGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5139
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72674876_7   5140 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5189
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_72674876_7   5190 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5239
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_72674876_7   5240 TACAGTAACCAAAACAGCATGGTACTGGTAACAAAACAGA--TATAGATC 5287
                                 i   i    ii         i vv ii i   --        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_72674876_7   5288 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCACATCT----CC 5331
                                i    i--    i  --        vv  ii    i ----i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_72674876_7   5332 AACT-ATCT--GAGAAAAA---CAAA------CAATGGGGAAAGGATTTC 5369
                           i -  i --  v  iii---   i------            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_72674876_7   5370 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5419
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72674876_7   5420 GAAACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5469
                            ii    iv   v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72674876_7   5470 TTAAAGACTTACATGTTAGACCTAAAACCATAGAAACCCTAGAAGAAAAC 5519
                          i ?    i  v    v   v       i   i  vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_72674876_7   5520 CTAGGGA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5568
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_72674876_7   5569 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5618
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_72674876_7   5619 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA-CAATCAGAGTGA 5667
                           i   v v  i i   i  ii vv    i  v    -   v- i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGA 694

  chrX_72674876_7   5668 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5717
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_72674876_7   5718 AAAGGGCTAATATCCAGAATCTACATTGAACTCAAACAAATTTACAAGAA 5767
                           i  i  vi          v  i vv      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_72674876_7   5768 AAA-ACAAACCAC---ATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5813
                            -     iv  ---  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_72674876_7   5814 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACTTGAAAAAATGCTCA 5863
                             v        i  vi viii     v  i   v      i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_72674876_7   5864 TCATCACTGGCCAT 5877
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (134 / 90)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


2811 28.28 2.47 0.56  chrX_72695152_72703853     2864  3754 (4948)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72695152_7   2864 TGGAAAAA-ATTCCATGCACATGAATAGGAAAAATCAATATCATGAAAAT 2912
                               i -  i     iv    i  v    i v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72695152_7   2913 GGCCCTACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 2962
                            vv    v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72695152_7   2963 TACCATTTACTTTCTTCACAGAATTAGAAACAACT-ACTTTAAATTTCAT 3011
                          v   vi i i  i  ii     v v  v - i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_72695152_7   3012 ATGGAACCAAAAAAGAGCTCATATAGTCAACACAATCCTAAGCAAAAAGA 3061
                               viiv  ii  v iviv    i   v      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_72695152_7   3062 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 3111
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_72695152_7   3112 ATAGTAACTAAAACAGCTTGGTATTG-TATTAAAACAGA--TATAGACCA 3158
                          i     ii  i    iv     i  -i  v ii i   --      i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_72695152_7   3159 ATGGAGCAGAACAGAGGCTTCAGAAATAATGCTGCACATCTACAACTATC 3208
                              ii    iv   iv i         vv iii    i  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_72695152_7   3209 TGATCTTTGACAAACCTGCCAAAAATAAGCAATGGGGAAA---TTGTTCC 3255
                             i  i     ivv      i vi vv           --- v  ---
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT--- 396

  chrX_72695152_7   3256 CCATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCGTATGCAGAAAACA 3305
                          iv  i  i        i     v      v  ?  ii     i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72695152_7   3306 GAAACTGGATTCCTTCCTTACACTTTATACAAAAATTAACTCAGT-TGGA 3354
                            ii    ii   v   i    iv                  iv-    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72695152_7   3355 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 3404
                          i ?    i           v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_72695152_7   3405 CTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAAGACTTCATGACTA 3453
                         v    ?i- v i -   iv   viv  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_72695152_7   3454 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAGAAATGGGATCTA 3503
                         vi            vvi          vv     v  v    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_72695152_7   3504 ATTAAACTAAAGAGTATCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3553
                           i   v v  i iiv i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_72695152_7   3554 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCTATCTGTCTATTTGACA 3603
                         v  i     i                 v     v viii v   i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_72695152_7   3604 AAGTGCTAATACCAAGAATCTACAAAGAACT--TA-AATTTA-CAAGAAA 3649
                          i vi  vi  i v     v  i        --  -  i i -i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_72695152_7   3650 AA--------ACCCCATCAAAGAGTGGGCAAAGGATATGAACAGACACTT 3691
                           --------    v  i?  i i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_72695152_7   3692 TTCAATAGAAGACATTTATGCACCCAACAAACATATGATAAAAAGCTCAT 3741
                         i  v v      i  vi viiiv    i  i  i    v  i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_72695152_7   3742 CATCACTGGTCAT 3754
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.93 (27 / 14)  

3151 27.45 0.77 0.66  chrX_72695152_72703853     7303  8209 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72695152_7   7303 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 7352
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72695152_7   7353 GGCCATACTGCCCAAGTTAATTTATAGATTCAATGCCATCCCCATCAAGC 7402
                            v     v     i  i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72695152_7   7403 TACCAATGACTTTCTTCACAGAATCAGAAAAAACT-ACTTTAAAGTTCAT 7451
                          v   iivi i  i  ii     viv  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_72695152_7   7452 ATGGAACCAAAAAAGAGTCCACATTGCCAAGTCGATCCTAAGCCAAAAGA 7501
                               viiv  ii  vi viv  v     iv i   i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_72695152_7   7502 ACAAAGCTGGAGGCATCACGCTATCTGACTTCAAACTATACTCCAAGGCT 7551
                               i      vv    i  vi ii i      viv    v   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_72695152_7   7552 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 7601
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_72695152_7   7602 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACTA 7649
                               i    i--    i  --        vv iii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_72695152_7   7650 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 7699
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_72695152_7   7700 TATTTAATAAATGGTGCTGGGAAAACTGC-TAGCCATATGTAGAAAGCTG 7748
                          v  i  i              v     v-  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_72695152_7   7749 AAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCCAGATGGAT 7798
                           ii    i    v   i i   v              i  v i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_72695152_7   7799 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCGTAGAAGATAACC 7848
                         i ?    i    i  v   v       i      vi v       v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_72695152_7   7849 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 7898
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_72695152_7   7899 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 7948
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_72695152_7   7949 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAAACACCATCAG---AGTGA 7995
                         i   v v  i i   i  ii vv    i  ---   i    i---     
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGA---CACTATCAAGAAAGTGA 694

  chrX_72695152_7   7996 GCAGACAACGTACACAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 8045
                         iv       vi   v             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_72695152_7   8046 AAAGGACTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 8095
                           i     vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_72695152_7   8096 AAAAACAAACAACCACATCAAAAAGTGGGCGAAGGATATGAACAGATGCT 8145
                            i     i    vv  i?    i     i      v    i   iii 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_72695152_7   8146 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 8195
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_72695152_7   8196 TCATCACTGGCCAT 8209
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3056 27.10 1.11 0.66  chrX_72704312_72710154     4447  5350 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72704312_7   4447 TAGAAGGATATTCCATTCTCATGGATAGGAAGAATCAATATCATGAAAAT 4496
                          i   i     i    vi        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72704312_7   4497 GGCCATACCGCCCAAAGTAGTTTATAGATTCAATGCCATCACCATCAAGC 4546
                            v    iv      v ii i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72704312_7   4547 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4594
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72704312_7   4595 TATGCAACCAAAAACTAGCCCACATTA-CCAAGACAATCCTAAGCAAAAA 4643
                             v  viiv  ivv -    v v  -    i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_72704312_7   4644 GAACAAAGCTGGAGGCATCATGCCACCTGACTTCAAACTATACTACAAGG 4693
                                 i      vv   ii iv  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_72704312_7   4694 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 4743
                                  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_72704312_7   4744 CAATGGAACAGAACAGAGGCCTCAGAAATAACATCACACATCTACAACCA 4793
                                 i    iv   ivii         vvi  i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_72704312_7   4794 TCTGATCTTTGACAAAACTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 4843
                         vi    i  i     iiv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_72704312_7   4844 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4893
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_72704312_7   4894 AAACTGGATCCCTTCCTTACACCTTATACAAAAATAAATTCGAGATGGAT 4943
                           ii    i    v   i     v           v  i  i i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_72704312_7   4944 TAAAGACTTAAATGTTAGACCTAACACCAGAAAAACCCTAGAAGAAAACC 4993
                         i ?    i       v   v    v  i v    vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_72704312_7   4994 TAGGCA-ATACCATTCAGGACATAAGCATGGACAAGGACTTCATGACTAA 5042
                             ?i- v i -   iv   v vi vv i i   v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_72704312_7   5043 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 5092
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72704312_7   5093 TTTAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAGTGCAC 5142
                          iv  v v  i i   i  iiivv    i  v    i  vv i    v v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_72704312_7   5143 AGGCAGCCTGCGGAATGAGAGAAAATTTTTGCAATCTACCCATCTGACAA 5192
                           i  i  ii i     i        v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_72704312_7   5193 AGGGCTAATATCCAGAATCTAAAAAGAACTCAAACAAATTTACAAGAAAA 5242
                         i  i  vi          v  v         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_72704312_7   5243 AAACAA----CCCCATCAAAAAGTGGGCAAAGTATATGAACAGACACTTC 5288
                          i    ----   v  i?    i         v  v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_72704312_7   5289 TCAAAAGAAGACAT-CAG-TGCAGCCAAAAAACACATGAAAAAATGCTCA 5336
                           v        i  -  i-  --     v  i          i       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_72704312_7   5337 TCATCACTGGCCAT 5350
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


1637 25.65 3.81 0.60  chrX_72736062_72738908.rev        1   499 (2348)    L1M4_orf2#LINE/L1      323   837 (71)  

  chrX_72736062_7      1 AAACAAAGCAATGCATTTATAGCCAACTGATTTTTGAGAGAAATGTCAAG 50
                            i   v v  i       i i   i       i  v iiii  i    
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_72736062_7     51 AAAATGCATAGGGGAAAGGACACCCTCTTCAACAAATGGTGCAGGGAAAA 100
                          vv  v  vv        i i vi  i               v    v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_72736062_7    101 TTT-ATATACATATGCAGAAAAATGAAACTGGACCTCTATCTTTCACCAT 149
                         i v-   ?v  i     i  i      ii      i   i  iv      
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_72736062_7    150 ATACAAAAATAAAATCAAGATATGTTAAAGACTTAAATGTGAGACCCAAA 199
                                   v  v    i  ivi i ?    i       i   v i   
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_72736062_7    200 ACTATAAAACTCT-AGAAGAGACCATGGGCAAAACACTATAGGACATTCG 248
                                      -      i v   i  ?iv  vv  viiv   v  v 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_72736062_7    249 TATAGGCAAAGATTTTATGGCTGAGACCTCAAAAGCACAGTTAACACAAA 298
                         vv       v i   iv i v iv   vi          ivi    v  i
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_72736062_7    299 CAAAAATAGAGAAATGGGACTATATTAAACTAAAAAGCTTCTGTACAGCA 348
                         v         v    v     vi  i   v v    i   i   i vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_72736062_7    349 AAGGAAACAATCGAGAA--TGAAGAGACAACCTATAGAATTGGAGAAAAT 396
                              v  v   i    --    i        i i     v         
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_72736062_7    397 ATTTGCAAACTATCAATTTAACAAGGGACTAATATCCAGAACA---AAAC 443
                                  ii  vv  i i i        vi         i ---   -
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA- 771

  chrX_72736062_7    444 TGGACT-TTAT--CTCACCATATACAAAAAT---TAACTCAA------GA 481
                         - i   -   i--    vi -   v   i i---    i   ------i 
  L1M4_orf2#LINE/    772 -GAACTCTTACAACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_72736062_7    482 TGGATCAAAAACTTAAAT 499
                            iiv  ii i  i   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAAT 837

Transitions / transversions = 1.40 (73 / 52)
Gap_init rate = 0.02 (10 / 515), avg. gap size = 2.20 (22 / 10)  

2812 27.42 2.47 0.45  chrX_72736062_72738908.rev     1474  2363 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72736062_7   1474 TAGAAAAACATTGTATGCTCATGGATTAGAAGAATCAATATCAAAAAAAT 1523
                          i    i i  ivi   i         i     v i     iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72736062_7   1524 GATCATGCTGCCCAAAGCAATATATGCATTCAATACAATTCCTATCAAAC 1573
                          iiv  i  v      vii  v  iiv      ii    i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72736062_7   1574 TGTCAA-TGTCATTTTTCACAGAATTAGAAAAAATTATTTGAAAATTTGC 1622
                          vi  i-  i -     ii     v v  v  iv v  iiv      iii
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_72736062_7   1623 ATGGAACGAAAAAAGAGTCCAAATGACCAAAGCAATCCTAAGTAAAAAGA 1672
                               vviv  ii  vi vi   ii     i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_72736062_7   1673 ACATAGCTAGAGGCATAACACTACCTGACTTCAAACCATATTACAAGCCT 1722
                            v  i i    vv v     v  ii i      v v  i     iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_72736062_7   1723 ACAGTAACCAAAACAGCATGGTACTGGTA---GAACAGACATATATACCA 1769
                                i   i    ii         i --- i i         v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_72736062_7   1770 ATG-AACAGAATAGAGAACCTGGGAATAAAGCTTCACATCTACAGCCATT 1818
                            -  i     v    ii ii i      v ivi    i  ii i  v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_72736062_7   1819 TGATGTTTGACAAAGTTGACAAAAATAAGCAATGGGGAAAAGATTCCCTA 1868
                             v  i     i v  v   i vi vv           ii  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_72736062_7   1869 TTTAGTAAATGGTGGTGGGATAGCTGGCTAGCCATATGCAGAAGAATCAA 1918
                           i ii        v     i i    v  ?   i     i      v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_72736062_7   1919 ACTGGTTTCCTATGTTTCAACATATACAAAACTTAAATCAATATGGACTA 1968
                         ii   vii    iv iv  v           v    v    v     ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_72736062_7   1969 AAGATTTAAATGTAAGACCTCATACTATAAG-----TAGAAGAAAACCTA 2013
                         ?   ii           v  v v       i-----           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_72736062_7   2014 GGAA-ACATCATTCTGAAAATTGGTTTTGGGAAATCATTTAT--GACTAA 2060
                           ?i- v   -   vvi vv    v  -i  v   vi   v --  -  v
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTT-AGGCAATGGTTTCTTAGA-TAT 596

  chrX_72736062_7   2061 GTCCCCAAAAGCAACTGCAACAAAAACAAAAATTGAAAAGTGGGACCTAA 2110
                          v v         vvv         iv      v  v  i v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72736062_7   2111 TTAAACTAAAGAGCTTCTGAACAGCAAAACAAACTATCAACAGAGTAAAC 2160
                          i   v v  i i   i  vi vv    iv v        v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_72736062_7   2161 AGACAACCTACATAATGGGAGAAAATATTTGTAAGTTATGTATC-AACAA 2209
                                 i   v                  i  i i  i    -i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_72736062_7   2210 AGATCTACTATTCAGAATCTATAAGGAAGTTAAACAATTCAACAAGCAAA 2259
                         i iv  vv   i      v     i   v ivv    i    i  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_72736062_7   2260 AAACAA----CCCCATT-AAAAGTGGGCAAAGG-CATGAACACGTATTTC 2303
                          i    ----   v   -    i          -iv    i vii     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_72736062_7   2304 TCCAAAGAAGACGTACAAGTGGCCAATAA--ACATGAAAAAATGTTCCGT 2351
                                    ii     i          --         i   i  vii
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_72736062_7   2352 ATAACTAATCAT 2363
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (138 / 103)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  


3315 25.83 0.89 0.55  chrX_72746190_72752916.rev     2813  3714 (3013)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_72746190_7   2813 AAAAATATTCCATATTCATTGATGGGAAGAATAAATATTATTAAAGTGCT 2862
                            i    i    i     v   v      v v      i    ii  vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_72746190_7   2863 CAGACTACCCAAAGTGACCTACAGATTCAATGCAATCCCTATAAAAATAC 2912
                         v v   v      v   i            i           v     v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_72746190_7   2913 CAATAGTATTAATCACAGAAATGGGGAAAAAAGCT----CTAAAATTTAT 2958
                           iiv iv  vv ii       v ---- v     ----        i  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATTCAT 149

  chrX_72746190_7   2959 ATGGAACCACAAAAGACCTAGAATAGCCAAAAGTATCCTAAGCAAAAAGA 3008
                               vii   ii    i             vv   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_72746190_7   3009 ACAAAACTGGAAGAATCACATTGCCTGACTTCAAATTATATTACAGAGCT 3058
                              ii    i  v     i v  ii i      viv  i    i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_72746190_7   3059 ATACTAACCCAAACATCATGGTCCTGGCATAAA-ACAGACACATATAACA 3107
                          i v   i v i   vii    v         i- i     i   v v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_72746190_7   3108 ATGGAACAAAATAGAGAACCTGGAAACAAATTCACATACCTACAGTGAAT 3157
                               i i   v    ii ii    i   ii  i i ii  ii  v   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_72746190_7   3158 TAACTTTTGACAAAGGTGCCAAGGACATACACTGCAGAAAATACAGCCTC 3207
                          i i   i     i         iv   v  v  vi    iv i  i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_72746190_7   3208 TTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCACAGGAATAAA 3257
                              i              v         ?   i     v i    i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_72746190_7   3258 ACTAGACCCCTATCTCTCACTGTATACAAAAACCAATGCAAAATGGATTA 3307
                         ii i        i   v   ii          ii  iv          i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_72746190_7   3308 CAGACTCAAATCTAAAACTTCAGACTATGAAACTACTACAATAAAACATT 3357
                         ?    ii    v   i vi v i     i     vi  v  v       v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_72746190_7   3358 GGGAAAAATCTCCAGGACATTGG-TCAGGGCAAAGATTTCTTAAGCAATA 3406
                           ?iv      i iv   v    - i   -   v i       iii vv 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTAGATATGA 598

  chrX_72746190_7   3407 CCCCACAAAGATAGGAAACTAAAGCAGAAATAAACAAATGGGATTACATC 3456
                          v   v  iv i i v   v    v i     i i    v   i v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_72746190_7   3457 AAGTTAAAAAACTTGGGCACAGCAAAAGATATAAACAACAAAGTAAAGGG 3506
                           iv v        vv ii vv    i  i iv v   v     i  ii 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_72746190_7   3507 ACAATCCACAGAATGGGAGGAAATATTTGCAAACTACCCATCTGACAAGG 3556
                             i              i             ii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_72746190_7   3557 GATTAATAACCAGAATATATAAGGAGCTCAAACAGCTCTATAGGAAACCA 3606
                           i vi  v             i  i   vv   i   v   iv   vvi
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_72746190_7   3607 TCTGGTAATCTGATCCAAAA-TGA-CAAAATACTTGAATAGACATTTCTC 3654
                         v vii   i ii  i?    -  i-    iv i                 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_72746190_7   3655 AAAAAAAGACATACAAATGGCAAACAGGCATATGAAAAGGAGTTCAACAT 3704
                         v   i    i           v  i i   i        iv i       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_72746190_7   3705 CACTGACCAT 3714
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.63 (142 / 87)
Gap_init rate = 0.01 (7 / 905), avg. gap size = 1.86 (13 / 7)  

3175 24.34 4.25 0.00  chrX_72746190_72752916.rev     5366  6236 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72746190_7   5366 TGAAAAGATACCCCATGTTCATGAATTGGAAGAATTAATA-----AAG-T 5409
                           i       i            i         v      -----   - 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72746190_7   5410 ATCCATACTATCCAAAGTGATCTACAGATTTAATGTAATTCCTAACAAAA 5459
                         iv v     vi     v             i  i i   i    v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72746190_7   5460 TTCCAA-TATCATTTTTCAAAAAAATAGCAAAA-AATCCTAAAATTAGTA 5507
                          i   i- ii v     vv i   v ii   iv-i           vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_72746190_7   5508 TGTAACCACAAAAGTCCCCAAATAGCAAAACCAATCTTGAGCAAAAAGAA 5557
                           v  vii   ii v   vi      v   v         iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_72746190_7   5558 CAAAGCCGAAGGCATCATACTTCATGATTTCAAACTATATTGCAAAGCTA 5607
                              ii i   vv   i     vii        viv  i i        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_72746190_7   5608 C-GTAATCAGAATAGTATCATACTGGCATAAGAACAGACAAATAGACCAA 5656
                          -       ii i   i vi            i i     v     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_72746190_7   5657 TGGAAGAGAATAGTGAGTCCAGTAATGAACTCACATATATATGGTCAACT 5706
                              v     v v        v   i   i  i i  v         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_72746190_7   5707 AATCTTTGACAAGGATGCCAAGAATGCACAATTGGTAAAAGATAGTCTTT 5756
                         i  i  i       i        viiiv    v  v   ii         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_72746190_7   5757 TCAATAACTGGTGTTGAGA-AACAGCATATCCAGACTCAAAAGGATGTAA 5805
                             i  v     i  i  -   v v   ?   v iv      i   v i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_72746190_7   5806 TTTCACCCTTAGCATATACCATAAGAAAAAATTAACTCAGAACAGATTA- 5854
                           vv    i  v vi i      viv             i  ii   i -
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_72746190_7   5855 -AACTTACATGTAAGTTCTGAA--CA-AAAACTTCTAAAAGAAAATATAG 5900
                         -i  i  v       vv  i  --i -      ii  i       i    
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_72746190_7   5901 AGAAAAAGCTCCTTGACATTGGTCTTGG-AATGATTTGTTAAATATGATG 5949
                         i?iv   v  i v    v    vi v  -    i   v   i      ii
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_72746190_7   5950 GTGAAAACACAGGCAACAACAAAAAAAA---ACAAGTGGGACTGTATCAA 5996
                         vii   i    i       v i      --- i  i v     vi     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_72746190_7   5997 A-CTAAAAAGTTT----CTGCAAAA--------CAACAAAATGAAAAGGC 6033
                          -i      v   ----  v    i--------   v   i       i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_72746190_7   6034 AAACCCCAGAAATAGAGAAAATATTTTCAAGTCAAACATTCCACAAGTGG 6083
                           v  v     vvi            v   i   v i  iiv i   v i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_72746190_7   6084 TTAATGTCTA-AATATATAAGGAACTCCTACAAGTCAAAAGTAAAAAAGA 6132
                         i vi i  i -         i      i     v    v i      iiv
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_72746190_7   6133 AAAT---CTGATTAAAAAATGATCAGAGGACCTGAATAGATATTTTTC-A 6178
                             --- ii   ?       iv  i    ii        i    i  - 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_72746190_7   6179 AAGAGGACATACAAATGGCCAACAAGTATGTAAAAAGGTGCTCAGCATCA 6228
                             i  i              i   i ii i     i      i     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_72746190_7   6229 ATAATCAT 6236
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.71 (132 / 77)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.18 (37 / 17)  


2723 26.64 2.44 1.66  chrX_72758563_72761525.rev     1572  2472 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72758563_7   1572 TGGAAATACATTCCATGCTCATGAGTTGGAAGAATCAATATTGTAAAACT 1621
                               v i  i     i     ii        v i        v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72758563_7   1622 GACCACACTGCCTAAAGTAATCTACAGATTTAATGCAATTCCTAACAAAA 1671
                          i v i   v  i   v i           i  i     i    v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72758563_7   1672 TACCAACATCAATTTTCACAGAATTAGAAAAAACAACCCTAAAATTCACA 1721
                          v   i vv vv    ii     v v  v  ivii i           i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_72758563_7   1722 TGGGATCAAAAAAGAGCATGAATAGCCAAAGCAATCCTAGGAAAAAAGAA 1771
                            i viiv  ii  v vv           i     i iii   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_72758563_7   1772 AAAATCTGGAGGCATCACATTACCTGACTTTAAATTATACTACAAGGTTG 1821
                         v   vi      vv     i v  ii i  i   viv        i i i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_72758563_7   1822 TAGTAATAAAAACAGCATGGTACTGGTATAAAAGTAGATATATCAGCCAG 1871
                         i      v  i    ii         i    iii    i    viii  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_72758563_7   1872 TAGAACAGAATAGAGAATGAATACAGAAATAAAGTCAAACAAACACTTAC 1921
                          i   i     v    i v----          -i ---  v   i   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC----CAGAAATAAA-CC---CATACATTTAT 342

  chrX_72758563_7   1922 AATCAAGCGATCTTTGACAAAGCATGCAGAAAC-ATAAATTGAGGAAAGA 1970
                         ii    vi   i  i     i -i   vi i  -  vv v  i       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_72758563_7   1971 AAACCCTGTTCAATAAATGGTGCTGGGAAAACTGGATAGCTACATGTAGA 2020
                          v vi  v     i              v         ? i     i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_72758563_7   2021 ATAATAAAACTGGTTCTCCATCTT----CATATACAAAAACCAACTGAAG 2066
                          v   i  ii   vi i i i  i----            ii    v  i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_72758563_7   2067 ATGAGTTAAAGACTTAAATCTAAGACCTGAACCCATAAAAATTCTAGAAG 2116
                            ii i ?    i     v     v  i  v i      v ii      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_72758563_7   2117 AAATGCTTAGAAA-AACTCTTC-TGTACATTTACCTGGGCAAATAATTAA 2164
                            -i v   i?i-  v     -  -  v  vivi i     - ii  vv
  L1M4_orf2#LINE/    542 AAA-ACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAA-TGGTTTC 588

  chrX_72758563_7   2165 T--GACTAAGACCTCAAAAGCAAATGCAACAAAAACAAAAATAAATAAAT 2212
                          --  -  v   vi        v v         iv       i      
  L1M4_orf2#LINE/    589 TTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_72758563_7   2213 GTGACCTAATGAAACTAAAAAGCTTCTGCAC---AAAGAA-ATAATCATC 2258
                         vv   i v  v   v v    i   i  ii ---    i - iv    vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_72758563_7   2259 ACAGTAAACAAACACCCCTCAGAATGGGAGAAAATTTTTACAAACTATGC 2308
                          v   i  v i   v   v                v   i    ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_72758563_7   2309 ATCCAACAAAGGACTAATGTGCAGAATCTACAAGGAACTC----AAATCA 2354
                            ii i  i     vi i v      v  i  i      ----  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_72758563_7   2355 GCAAGAAGAAAACAAATAATCCCATCAAAAAGTGAAAAAATGACATGAGT 2404
                         ii  v  i  i        i  v  i?    i  iiv   v  iv   i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_72758563_7   2405 AGATACTTCTC-AAAAAA----TACAAATGGCCAACAAATATATGAAAAA 2449
                            i i     -   i  ----             i  ii i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_72758563_7   2450 AAATTCTCAATACCATTAATCAT 2472
                          -- v     i i  ????????
  L1M4_orf2#LINE/    888 A--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (150 / 86)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.95 (37 / 19)  


3050 27.44 1.33 0.44  chrX_72773859_72779195     3946  4845 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72773859_7   3946 TGGAAGAATATTCCGTGCTCATGCATAGGAAGAATCAATATCGTGAAAAT 3995
                              ii    i  i  i     v  v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72773859_7   3996 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATTACCATCAAGC 4045
                            v     v     iv i  i  i        i  v  iv i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72773859_7   4046 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4093
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_72773859_7   4094 TATGGAACCAAAAAAGAGTCCACATTA-CCAAGACAATCCTAAGCAAAAA 4142
                                viiv  ii  -i   v v  -    i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_72773859_7   4143 GAACAAAACTGGAGGCATCATGCTACCTGACTTCAAACTATACTATAAGA 4192
                                ii      vv   ii  v  ii i      viv     i  ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_72773859_7   4193 CTACAGTAACCAAAACAGCATGGTAATGGTACCAAAACAGATATATAGAA 4242
                                  i   i    ii     v   i iv ii i   i       v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_72773859_7   4243 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 4292
                                 i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_72773859_7   4293 TCTGATCTTTGATGAAACTGACAAAAACGAGAAATGGGGAAAGGATTCCC 4342
                         vi    i  i  ii iiv  v   i v ivvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_72773859_7   4343 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4392
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_72773859_7   4393 AAAGTAGATCCCATCCTTACACCATATGCAAAAATTAACTCAAGATGGAT 4442
                           iv i  i   vv   i         i               i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_72773859_7   4443 TAAAGACTTAAATGTTAGACCTAACACCATAAAAACCCTAGAAGAAAACC 4492
                         i ?    i       v   v    v  i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_72773859_7   4493 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAGTAA 4541
                             ?i- v i -   iv   v v  vv i     v ii   v iii  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_72773859_7   4542 AACACCAAAAGCAAAGGCAATAAAAGTCAAAATTGACAAATGGGATCTAA 4591
                         i            v i    i     vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_72773859_7   4592 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4641
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_72773859_7   4642 AGACAACCTACAGAATGGGAGAAAATCTTTGCAATCTACCCATCTGACAA 4691
                                 i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_72773859_7   4692 AAGACTAATAACCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 4741
                         ii    vi  v       v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_72773859_7   4742 AAA-----AACCCCATCAAAAAGTAGGCAAAGGATATGAACAGACACTTC 4786
                          i -----     v  i?    i i          v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_72773859_7   4787 TCAAAAGAAGACATTTATGCAGCCAACAG--ACATGAAAAAA-GCTCATC 4833
                           v        i  vi viii     i i--         i -     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_72773859_7   4834 GTCCCTGGTCAT 4845
                         i  v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (151 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3218 26.18 0.77 0.88  chrX_72889496_72893905     3009  3917 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72889496_7   3009 TGGAAAAACATTCCATGCTCAGGGGGAA--GGAAGAATCAATATCGTGAA 3056
                               i i  i     i   v  --- --      v i     i  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGG---ATTGGAAGACTTAATATTGTTAA 47

  chrX_72889496_7   3057 AATGGCCATACTGCCCAAGGTAAATTACAGATTCAATGCCATCCCCATCA 3106
                         i     v     v     iv i vi           i  v     i    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_72889496_7   3107 AGCTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGT 3154
                          iv v   iivi i  i  ii     -   -- v  i  - iii    i 
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAAT 145

  chrX_72889496_7   3155 TCATATGGAACCAAAAAAGAGCTCACATTGCCAAGTCAATTCTAAACCAA 3204
                                   viiv  ii  v iviv  v     iv    ii i  vv i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_72889496_7   3205 AAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAA 3254
                                   i      vv       v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_72889496_7   3255 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 3304
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_72889496_7   3305 ATCAATGGAACAGAAC--AGAGCCCTCAGAAATAA-CGCAGCATATCTAC 3351
                                   i    i--    i  --        - v  -i i  i  i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCA-TACATTTAT 342

  chrX_72889496_7   3352 AGCTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGA 3401
                         i ii vi    i  i     ivv  vv  i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_72889496_7   3402 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 3451
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_72889496_7   3452 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATGAATTCAAGA 3501
                         iiv    ii    i    v   i     v           v  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_72889496_7   3502 TGGATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGA 3551
                              i ?   ii    i  v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_72889496_7   3552 AAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 3601
                             v    ?i v viv   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_72889496_7   3602 CCAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGAC 3651
                         vi vi            vvi           v     v  i    v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_72889496_7   3652 CTAGTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 3701
                         i vi i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_72889496_7   3702 GAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTG 3751
                            v  i     i   i             v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_72889496_7   3752 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 3801
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_72889496_7   3802 AAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACA 3851
                              i     i     v  i?    i           iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_72889496_7   3852 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 3901
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_72889496_7   3902 CATCATCACTGGCCAT 3917
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2128 23.50 3.00 13.60  chrX_72910307_72913452.rev     1648  2647 (499)    L1M4_orf2#LINE/L1        1   894 (14)  

  chrX_72910307_7   1648 TGGAAAAGTATTCCATGCTCATGGGTTGGAGGAATTAGTATCATTGAAAT 1697
                               ii   i     i      i     i  v   i   ii  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72910307_7   1698 GTCCATATTGCCCAAGGCAATATAGAGATTCAACACTATTCCTATCAAAT 1747
                          v v   i v     ivii  v  v         i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72910307_7   1748 AGCCAA-TGTCGTTTTTACAGAA-TCAGGAAAAACCTATTCTAAAATTCA 1795
                         vv   i-  i v     i     - i--  v  i iv  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_72910307_7   1796 TATGGAACCAAAAAAGAGCTGGAATAGCCAAGCCAATTCTATGAAAAAGA 1845
                                viiv  ii  v ii          iv    -  -         
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGA 196

  chrX_72910307_7   1846 ATAAAGCCGGAGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGTGCCACTG 1895
                          -------------------------------------------------
  L1M4_orf2#LINE/    197 A------------------------------------------------- 197

  chrX_72910307_7   1896 CCCTTCAGCCTGGGCGACAGAGTGAGACTCCGTCTCACACAAAAAAAATA 1945
                         --------------------------------------------------
  L1M4_orf2#LINE/    198 -------------------------------------------------- 197

  chrX_72910307_7   1946 AATAAATAAAATAAAAAGAATAAAGCTGGAGGGATCACACTACCCAACTT 1995
                         -----------------   i    i      iv       v     i  
  L1M4_orf2#LINE/    198 -----------------GAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_72910307_7   1996 CAAACAATACTACAA-------GTAACCAAAAACAA-ATGGTACTGGTAC 2037
                             vvv        -------    i   i -  i-i         i i
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCAT 279

  chrX_72910307_7   2038 GAAAATAGACACATGGACCAATAGAACATAATAGAGAACCCGGAAATAAA 2087
                         i ii       i  i  i    i   i v   v    ii  i        
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_72910307_7   2088 GTCACATAGCTACAACCAACTGATCTTTGACAAACTCAACATGTATAAAC 2137
                         vi  i i vi  iiii   i    i  i     ivviiv  v vvi vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_72910307_7   2138 AATGGGGAAAGGACACCCTATTCAATAAATGGTGTTGGAAAAACTGGGTA 2187
                                    i i vi  v     i        i   i v      i  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_72910307_7   2188 GCCATATGCAGAAGATTGAAACTGGACCCCTATCTATCAGCATGTATGAA 2237
                         ?   i     i    v    ii          i  vv  v   i  ii  
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_72910307_7   2238 AATTAGCTCAAGATAGATTAAATACTTCAATATAAGATCTAAAATTATAA 2287
                              i     i  i   i ? v  i v   i     v      i     
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_72910307_7   2288 AAATCCTGGAAGAAAACCTAGGAAATACTCTCTTTGATATTGGTCTAGGC 2337
                           v  i i         v    ?ivv v   iiv   iv    vi     
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_72910307_7   2338 AAAAAAAAAAAAAAAATTATCACTAGGT----TCTTAAAAACAAATGCAA 2383
                           vii-----------  -  -i   i ----ivii    i  v v    
  L1M4_orf2#LINE/    580 AATGG-----------TT-TC-TTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_72910307_7   2384 TAAAACCAAAAATTGAACAAGTGGGACCTAATTAAACTAAAGAGCTTCTG 2433
                         i    vv      v  -i  i v    i v  i   v v  i i   i  
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGA-TAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_72910307_7   2434 CACAGCAAAATAAATTACCAACAGAGTAAACAGAAAA-------AATGGG 2476
                         ii vv    iv v i  i   v i   i  v   v  -------      
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_72910307_7   2477 ATAAAATATTTACAAACTATGAT-TCTGGCAAAGGACTAATATCCAGGAT 2525
                          v         i    ii  -  -    ii  i     vi       i  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCAT-ATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_72910307_7   2526 CTATAAGAAACTT----AAATCAACAAGTAAAAGACAA----CCCCATTA 2567
                         v     ii    i----  v    i  vv         ----   v   ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_72910307_7   2568 AAATGTGGGCAAAAAACATGAACAGACCCTTCTCAAAAGAATACATTCAA 2617
                            vi        ii iv    i    vi     v      v i  v   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_72910307_7   2618 GTGGCCAGCAAACATATTAAAAAAAGTTCA 2647
                         i      ii  i  i  v    i v i   
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.69 (145 / 86)
Gap_init rate = 0.02 (19 / 894), avg. gap size = 8.74 (166 / 19)  


1679 16.60 7.71 13.04  chrX_72938852_72942228     1302  1807 (1570)    L1M4_orf2#LINE/L1       10   488 (420)  

  chrX_72938852_7   1302 ATCGCATGTTCATGAATTTAAAGACTTAATATTGTTATAATGTCAAAGGT 1351
                            v          i   vi                 vi   v   viv 
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_72938852_7   1352 TTCCAAATTTATTTATAGACTCAACACAATCCCTATCAAAATCCCAGCT- 1400
                         ii       v  i  i   i     i                       -
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_72938852_7   1401 TGATTACTACAGACATCGACAAGCTGATGCTAAAACTCATATGAGACTGC 1450
                         ivv  vi i    v  i           v      i       ii v   
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_72938852_7   1451 AAGGG-TCCAGAATAGTGAAAATCATCC---------AGAATAAAGTTGG 1490
                              -i         iv    iv   i---------    i        
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_72938852_7   1491 AGGTTGAAGCATTCATGTTTCTTTTTTTTTTTTCTTTTTCGTTTCCAGTG 1540
                            ------- i   iii   -----------------------   ---
  L1M4_orf2#LINE/    210 AGG-------ACTCACACTTC-----------------------CCA--- 226

  chrX_72938852_7   1541 GGGTCAGATACTCATGGTTTTTTATCTTAAAATTTACTTCAAAGCTACAG 1590
                         -----------------------  i i    i     v           
  L1M4_orf2#LINE/    227 -----------------------ATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_72938852_7   1591 TAATCAAGAC--TGTGGGATTGGTATAAAGTTACATTTATAAATATATAT 1638
                                   --     v i   i    i --------   i i     -
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGG--------ATAGACATATA- 294

  chrX_72938852_7   1639 AAATCAAAGGAATAGAGTTGGGAGTTTAGAAATAAACCCTTACATTTATG 1688
                         -i     v        i   i    ii            v          
  L1M4_orf2#LINE/    295 -GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_72938852_7   1689 GTCAATTA----TAAACAAAGAAGC----------------------AAC 1712
                                i---- vi    i iv  ----------------------  i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_72938852_7   1713 ACTCTTTTAAACACATGGTGCTGGGAAAACTGGGTATCTATATGCAAAAG 1762
                          v      v    v            v      i  ? i i         
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_72938852_7   1763 AAAGAAGTTAGATTACTATTGCTCATCACATACAAAAATTAACTC 1807
                           v      i  iiv   iiv v  i  i                
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

Transitions / transversions = 1.86 (54 / 29)
Gap_init rate = 0.02 (11 / 479), avg. gap size = 9.55 (105 / 11)  

1667 13.38 11.87 2.78  chrX_72938852_72942228     2489  2884 (493)    L1M4_orf2#LINE/L1      477   908 (0)  

  chrX_72938852_7   2489 AAAAA--AACTCAAAATGTATCAAAGACCTAAATGTAAATGCTTAAACTA 2536
                              --           v    ?              iv   v      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_72938852_7   2537 TAAAACTCATATAAGAAAA------------TCTTCATGCCCTTAGGTTA 2574
                                 v  v       ------------     i  v    i     
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_72938852_7   2575 GACAATGTGGCTTTTTTTTTTTTTTAGTTATGACATTAAAAACACAAGGT 2624
                          i     -- ---------   i    v       ii    i      vv
  L1M4_orf2#LINE/    577 GGCAATG--G---------TTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_72938852_7   2625 ACAAAAGAAAAAGTA----AGTTGTACTTAGTGAAAATAAAAAACTTTTG 2670
                                     i  ---- i   v    vi v     v           
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_72938852_7   2671 TGCTTTAA-GAACGC-ATCAAGAAACTGAAAAAA--ACTTACGAAATAGG 2716
                              i  - i  i -         v      i --  ii  ii   i  
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_72938852_7   2717 AGAAAATATTTGCAAATCATATATCTGATAA------TGTA--------- 2751
                                                        ------    ---------
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_72938852_7   2752 ------AAACTCCTACAACTCAATAA----ATGACCAATAACCTGATTGA 2791
                         ------i     i             ---- v   v       ii   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_72938852_7   2792 AAAATAGGCCAAGTATTTGAATAGATATTTATCCAAAGAGGATATATAAA 2841
                              i   v   v           i    v        i      i   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_72938852_7   2842 AGGCCAATATGCACATAAAAAGATGCTCTACATCATTAGCTAC 2884
                         v        v      i           v      ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (29 / 22)
Gap_init rate = 0.03 (11 / 432), avg. gap size = 5.27 (58 / 11)  


2720 26.09 5.03 1.14  chrX_72955554_72958524     1605  2478 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_72955554_7   1605 TGAAAAGACTTATCATGTTCATGACTTGGGAAACTCAACATAGTAATGAT 1654
                           i     iv vi          iv    i i   i  i  v  v v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72955554_7   1655 GTCAATTCTCCACAAATTGAT----AGGTTTAATGGAATTTCCATTTAAA 1700
                          v    v    v         ----  i  i  i v   ii i  iv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72955554_7   1701 TCCTAGTATG---TTTTTGTAGATATAGAAAAGCTTATTTTAAAATGTAT 1747
                            i  i-  ---      i   v  v  v     v  ii      vi  
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_72955554_7   1748 GTGGAAAGGCACAGGCCTTAAAATAGCTAAAACCATCTTGAAAAATA-GT 1796
                         i      v   vi  v ii i      i     v           v - v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_72955554_7   1797 ACA---TTGGTAGAATCATTAACTTGACA---TTAATGCCTACTATATTC 1840
                            ---    vi  v   i--    vv  --- i  vi i     i vvv
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCAC--ACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_72955554_7   1841 CTATA----TTAAGACAGTGTTGTATTGGTG-GAGGATAGACACATAAAT 1885
                            i ---- i          v   i   ii-i          i   i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_72955554_7   1886 CAGTGTAACATAATTGAGAACTGAGAAATAGACATATACAATTAGGCCCG 1935
                           i  v  i v        iiiv       i  vi     v   v vi i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_72955554_7   1936 ACTGAATTTTGTCAAACGTGG-AATAGCAGTTCAGTAATGAAAGAA-AGC 1983
                          i   v   i v   iv   v-  v v  -    i iiv       -  i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGT 396

  chrX_72955554_7   1984 CTTTTTAACAA-TGGTGCTTGACCAATTGTCCATCTGTAGGCAAAAAGAT 2032
                              i     -       v iv   i  vvi ? iii v      ii  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_72955554_7   2033 GAACCTGAGTC------TCATATCTAATACAAAAATGTACTCAAAATGAA 2076
                            vi  iii ------   i i vv          vv          i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_72955554_7   2077 TTAGAGACTTAAATGTAAAACTTAAAACTATAAAACTTTTAGAAGAAAAC 2126
                          i ?    i         i vi               i            
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_72955554_7   2127 ATAGGAGGAAATCTTC---AGTTTGTGCTAGGCAAGGAGTTCTTACTCTT 2173
                              ? v        --- vi   v i       v iv      -----
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA----- 591

  chrX_72955554_7   2174 AATATG-C-TTAAAAGGATGATCTGTAAAAGGAAAAATTGATGAATTAAA 2221
                         i     - -ii     v ii v vii     i      v   i    ii 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_72955554_7   2222 TTTTATTGAAGTTAGAAACTCTTGTTCTGCTAAAGACTCTGTTAAGAGAA 2271
                         i  i  ii  i   i     i    v  v v  i   v  i i    i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_72955554_7   2272 TGAAGAGAGG--CTACAGAGTAGGATAATTTATTTGTAAACCACATATCT 2319
                             i   vi-- i     i i   v  vv      i   i  i      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_72955554_7   2320 TGCAAATTAATTGTATTTAGAATACATAAA---CTCTGGAAACTCAGTAA 2366
                         vii  ivv v      ii      i     ---    viv      i   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_72955554_7   2367 --AAAAG-CAACCAGTCCAATTAGAACATGAGCAAAAGACATGAAGAGAT 2413
                         --     -   vi ii      ?i  v   i     i  iv    v   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_72955554_7   2414 TATTTCATGGAAGAAGATACACAGATGGCAAATAAA---ATAAAAGGATG 2460
                         -     vivi         i   i     v     i---  i   i    
  L1M4_orf2#LINE/    842 -ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_72955554_7   2461 TTTAACATTATTAACCAT 2478
                         i i     i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.25 (54 / 24)  


 714 25.89 5.08 0.51  chrX_72960976_72964433.rev     1815  2011 (1447)    L1M4_orf2#LINE/L1        1   206 (702)  

  chrX_72960976_7   1815 TGGAGAGATATTCTATGTTTGTGGATACAAAGAC--AATACTGTCAAGAT 1862
                             i      i i     ii     vvi     --    i   i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_72960976_7   1863 GTCACTTCTTCCCAACTTCATCTACAGATTTCATGCAATTCC----AAAC 1908
                          v  v v  i     v  v           iv i     i  ----   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_72960976_7   1909 TCCCAGCA----TATTTGTGGATATCAGCAAACTGATTGTGAATTTTATA 1954
                                v---- v    ii  v  iii   i     iv i  v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_72960976_7   1955 TGGAGAGCCAAAAGACTCAAAATATCCATCACAATATTGAAGGGGAAATA 2004
                             i vv   ii   i  i    v   vv     v     iii   i- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG-A 199

  chrX_72960976_7   2005 ATAAAGT 2011
                          i     
  L1M4_orf2#LINE/    200 ACAAAGT 206

Transitions / transversions = 1.55 (31 / 20)
Gap_init rate = 0.02 (4 / 206), avg. gap size = 2.75 (11 / 4)  

1767 26.47 7.79 0.88  chrX_72960976_72964433.rev     2292  2971 (487)    L1M4_orf2#LINE/L1      182   908 (0)  

  chrX_72960976_7   2292 CAGTCTCAAAAAAAAAAAAAAAAA---AAGAATAGTCACTGCTTGACTTC 2338
                           i   ii     i  i  v   i---i  i ivvv    v iii i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_72960976_7   2339 AAGACTTAATAAAAAGCTATGGTAATCCAGACAGTGTGAAATTGGTGAAG 2388
                           i     v  v       ii      v          iv i   iiv i
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_72960976_7   2389 GAATGGATAAATGGATCAATGGAACAGAATAAAGAGCCCAGA--TAGAGA 2436
                          i  i  i v  i           i     vi    i     --  i vv
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_72960976_7   2437 CATAAAT--ATAGTCAACTAATCGTTGAGAAAGAAGCAAAGGCAATACAA 2484
                             v  --  i     i i  iv i  v  i iv  v   i v  v   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_72960976_7   2485 TGGAG---------------CAACAAATAGTGTTGGAATAGCTGAATATC 2519
                            i ---------------        i   i   i i i   i   ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_72960976_7   2520 CAAATGCCAAAAAATGAATCTA-ATACAAACTTTACACCCTTCACAAATA 2568
                           v    v   i      vi i- iv vv  i i     v vi     v 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_72960976_7   2569 TTAATTCAAAATGGATGCCAGACCTAAATGTAAAATGC-AAAACTGTAAA 2617
                             i           vv?              i -  -      i    
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAA 530

  chrX_72960976_7   2618 -----TAGAACTCCAACATTTGAGAAAATCTAGACATCAC--TGGGTATG 2660
                         -----     v-vv     vv ? v      v-- i v  --     vv 
  L1M4_orf2#LINE/    531 ACTCTTAGAAG-AAAACATAGGNGTAAATCTT--CGTGACCTTGGGTTAG 577

  chrX_72960976_7   2661 GCAATTACTTTCTAGATACAATACCAAAAGCATAATCCATAAAAGAAATC 2710
                              vii  ii      ii i          i  v v i        vv
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_72960976_7   2711 ATTGACAAGCTAAATGTTATTAAAATTAAAAAAAAATTACTCCACAAAAG 2760
                           v  i  ii ii iv i  i           vvv-  iiv iv    i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTT-TTGTGCTTCAAAGG 676

  chrX_72960976_7   2761 ACACCATTAAAATA-TGAAACGATAAGTCA---------AAAAAA-ATCT 2799
                             i  i  i v -     v  i  vi  --------- i    -  i 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_72960976_7   2800 GCAAAACACATAACTGATAAAGGACTGTTACCTAAAACATACAGACAGCA 2849
                              v  i   v       i     vv  i i i  i   i i v i v
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_72960976_7   2850 CTTAAAACTCAATAA-----------ATAGCCCAATTTTTAAAATGGACA 2888
                             v          -----------   i       ?v-       i  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCA 825

  chrX_72960976_7   2889 AAAGATGTCAACAGAAATCTCGCCAGAGAACATATACAGATGGTAAATAA 2938
                           i   v v  i   v  i  v   i    v       i    iv     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_72960976_7   2939 GAACATGAAAACATGCTCAACTTTGTATGTCAT 2971
                          v         v         v ii????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (102 / 74)
Gap_init rate = 0.02 (17 / 727), avg. gap size = 3.47 (59 / 17)  


2113 24.07 2.53 1.52  chrX_72974867_72976493.rev      543  1136 (491)    L1M4_orf2#LINE/L1      309   908 (0)  

  chrX_72974867_7    543 AAATGAGAATT-ACAAATAAACCCAGACATTTACGTTAAAGTGGCTTTTG 591
                           v     i i- v           v       i v v  v  ii   i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_72974867_7    592 ACAAAGGTACCAAGAACGTACAATGGAGAAAGGACAGCCTCTTCAGTAAA 641
                             i   i      v i v      i     i i  i  i    ii   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_72974867_7    642 TGGTGTTGGGAAAGTTGTATATCCACATATAGAAGAATCAAATCAGACCT 691
                              i     v ii  v   ?      ii i      v  i ii    i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_72974867_7    692 TTGTCTCATACCATATACAGAAAAGAACTCAAAATGAATTAAAGAC---- 737
                         i ii    i          i   vv           i  i ?    ----
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_72974867_7    738 --ATTAGACCAGAAACTGTAAAACTACTAGAATAAAACATAGGGA-AAAT 784
                         --i v   v vi     i       vi     v          ?i-    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_72974867_7    785 GCTCCACAACATTGGTCTGTGCAAAGATTTCATAAATATGACCTCCAAAA 834
                         -  i iii  v    vi iv    v i    v  i       v-      
  L1M4_orf2#LINE/    559 -CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA-CCAAAA 606

  chrX_72974867_7    835 GCACAGACAACTAAAACAAAAATTTTAATTTAAAATGGGATTGCATCAAA 884
                              ii    v   iv      --- iv --    v   i v       
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAAT---AGAT--AAATTGGACTTCATCAAA 651

  chrX_72974867_7    885 -CTAAAAAGTTAACTACACAGCAAAGGAAACAATTGAG----TAAAGCAA 929
                         -i      v  --i iii vv       v  v  ii  ---- i  ivi 
  L1M4_orf2#LINE/    652 ATTAAAAACTT--TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_72974867_7    930 CAACCCACAAACTGGGATAAAATATTTGCAAATCACATATGAAATAATGA 979
                                  i v     v                 i    vvi    v i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_72974867_7    980 GCTAATATTCAAAATATATG--GAACTCCAACAATTCAATAGCAAGAAAA 1027
                         i  vi   i  i       i--      iv    i      ii  i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_72974867_7   1028 CCAAGAACCCAATTTAAAAATGGGCAAGGGACCTAAACATACATTTCTCA 1077
                          v  v         ?            i   ii i  i v         v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_72974867_7   1078 AAAGAAAACATACAAATGGTCAATGGACATATGAAAAACTGTTCATTATC 1127
                               i i          i    iii  i       iv  i   vi   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_72974867_7   1128 ACTTGCAAA 1136
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.90 (91 / 48)
Gap_init rate = 0.02 (11 / 600), avg. gap size = 2.18 (24 / 11)  


1579 30.12 5.85 1.55  chrX_73004689_73009434     2324  2904 (1842)    L1M4_orf2#LINE/L1       16   621 (287)  

  chrX_73004689_7   2324 TGTACATGGATTGGGAAATTTA-TATTGTTATAATTTTCATACTGCCAAA 2372
                            v          i i i   -        vi  vviv     v  v  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_73004689_7   2373 AGAAACATACAGATTCTGTGTAATCAATATTTCAATGTCCTTTTTATTTT 2422
                          vvi iv         vii i    vv   --   vi   i---- vi -
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTAT--CAAAATCCC----AGCT- 108

  chrX_73004689_7   2423 TATTTTTTTTACAGAAAT--ACAAAAAAAATTCTAAAACTTGTATGGAAC 2470
                         -iii      i       --    ivvi - i      i ii       v
  L1M4_orf2#LINE/    109 -GCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATATGGAAA 156

  chrX_73004689_7   2471 TACAAAAGACATTAAATAATCAAAGTAATCTTGAGCAACAAGGACACAGC 2520
                          i   ii   vivi    ii    ii        iv  v   i   v  i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_73004689_7   2521 TGGAGGCATCACTCTACCTGATTTTGTAATCCATTA-------------- 2556
                               vv    v  v  ii    iiv  iii i  --------------
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_73004689_7   2557 TCAAAAAACTGTGGTACCAGCATAAAAACAGATTCACTGACCAGTGGAAC 2606
                             i v v        ii      ii i   ivi iv  i  i     i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_73004689_7   2607 AG----GAAAGCCCAGACATAA-CTCATACATTTCCATCCAATTGATTTT 2651
                           ----  i  i     v    - i         viivi           
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_73004689_7   2652 TGACAAAAGTGGCA----CACAGAATGGGGAGAGGACAAATAAATAAATA 2697
                         i     ii   v  ----  ivv        i  i i ivivvv v  i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_73004689_7   2698 AATTGTTTTGAGATATCTGTATATCTATATG--------TGAAATTGAAC 2739
                            v  vi  i  i v   v   ? i i   --------    i   i  
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_73004689_7   2740 CATTTTCTCATAGCATATAGAAAAATCAACTCAAAATGGATTAAAGCCTG 2789
                          vi vi    i v      v      i              i ?  v iv
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_73004689_7   2790 AAATGTTGCCTTTGAAACTGTAAAACTACTAGTAGAAAATATAGGGGAAA 2839
                               vivvvi i     i       vi   v      i     ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_73004689_7   2840 AGCTCTATGATGTTGTTCTGGGCAATGATTTCTTGGATACATCCTTAAAA 2889
                          v  iii   iv   vvi i       i      i    iiv vii    
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_73004689_7   2890 GCATGGGCAGCAAAA 2904
                            iii   i     
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAA 621

Transitions / transversions = 1.61 (106 / 66)
Gap_init rate = 0.02 (11 / 606), avg. gap size = 3.91 (43 / 11)  

 710 26.10 5.88 2.21  chrX_73004689_73009434     3983  4254 (492)    L1M4_orf2#LINE/L1      627   908 (0)  

  chrX_73004689_7   3983 AACAGACAACTTGAGTTGCATCAAACTAAAAAGCATCTGCACTGCAAAGG 4032
                           i   i  v   iii v       v v    i v i  ii  v      
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_73004689_7   4033 GTACAGTTAACAGAATGAAGA-------CACGGGTTTTGAGAAACCATTT 4075
                         ii  vi i  v i i    i -------   i iv vv      vi    
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_73004689_7   4076 TCAAATCATATATCTGATAAGGGGCTAATATCCAAAATGTATTAAGAAAC 4125
                         v                      i  vi      i   i   v     vi
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_73004689_7   4126 C---CAAGCCCAATAGCAAGAAAACAACTGTC----TTTAAAAGGGGGAA 4168
                          ---   - i     ii  i  i    v iv ----  ?    iv   v 
  L1M4_orf2#LINE/    777 CTTACAA-CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_73004689_7   4169 AAGGACCTCAACTTAAATTTTTCAGAGGAAGACATG--AGTGGCCAATTG 4216
                              ii v  ivv v    i  vi i     i  i-- i        -i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT-A 874

  chrX_73004689_7   4217 ATTGATACATGAAAAAAATGCTCAACATCTCTAATCAT 4254
                          ---ii         i -           v????????
  L1M4_orf2#LINE/    875 A---GCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (44 / 26)
Gap_init rate = 0.03 (8 / 282), avg. gap size = 2.75 (22 / 8)  


1894 29.52 6.14 1.18  chrX_73021858_73026141     2945  3791 (493)    L1M4_orf2#LINE/L1       20   908 (0)  

  chrX_73021858_7   2945 CACAAATAGGAAGAAATGACATTGTTAAAATGGCCATAATCCCCAAAGCA 2994
                           iii  v      vv i i        i     v   v        vii
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chrX_73021858_7   2995 ATTTATACATT------AATTGCTATTCAAACTACCAATGACATTCTTTG 3038
                           i  i v   ------   iv    -    v v   iivi v  i    
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTAT-CAAAATCCCAGCTGCCTTTTTTG 118

  chrX_73021858_7   3039 CAGAA-TTAATA---CAACCTTTAAAAATTCATATGGAG-TGAAAAAGTC 3083
                              -  i i ---ii i i --              i-  v  ii v 
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCT--AAAATTCATATGGAAATGCAAGGGAC 166

  chrX_73021858_7   3084 CTA--ATAGCCAAGGCAATTCTAGACAAAAA--ACAAACTTGGAAGCATA 3129
                          i --        ii    ii ii v  i  --     v     i vv v
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_73021858_7   3130 ACATTACCTGAATTTGAAAGTATTCTACAAGATTACAGTAACCATAACAG 3179
                            i v  i-     v   iiv v      iii        i  vi    
  L1M4_orf2#LINE/    217 ACACTTCCC-AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_73021858_7   3180 CATGGTACCGGTATAAAAGTAGACATGGAGGCCAATGGAGCAGAATATAG 3229
                         ii      i  i    iii       iv  ii       ii     vv  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_73021858_7   3230 A------ACACAAAGCTGTACACCAACAGTCATCTGCTTCTCAACAAAGT 3273
                          ------ v i   v ii    iiv ii    vi  v  i  i    i v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_73021858_7   3274 TGACAAAACAAG-CAATGAAGACAGGACTTCCTGTTCAATAAATGGTGCT 3322
                           v   i  v v-     ii  v  i ivvi  v     i          
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_73021858_7   3323 GGCATAACTGACTACGTATATATTCAAGGTTGACACTGGACCGCTTCCTT 3372
                           v i     iv  ?vi i  iivv   iv   vii      v  v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_73021858_7   3373 ACATTACATATAA----TGACTCAATATAGATTAAGGGCTTAAATGTAAA 3418
                            ii i   i  ---- i      v  i   i ?i i i         i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_73021858_7   3419 ATATAATACCATAAAAATGCTAAAATATAACTTAGG---AAATACCATGC 3465
                          vv   v  i      v vi  i  v v   v    ---    - ivi -
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCG- 563

  chrX_73021858_7   3466 TGAACATAGGTTCTGAAA-AATATTTATGATGAAGACTCCAAATGCAATT 3514
                            v v i    vv v  -ii v i vv   - v   v     v   vvv
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAA 612

  chrX_73021858_7   3515 ACAGCAAAAACAAAAATTGACAAATAGAACCTAGTTAAACTATAGAGA-T 3563
                         i  i     iv      v  i    v i  i vi i   v -  i i - 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACT 661

  chrX_73021858_7   3564 TCTGCACAGCAAGAGAATCTATCAATG--GTGAACA--CAATGTACAGAA 3609
                          i  ii vv   ii  vv       vi--     v --   ivi      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_73021858_7   3610 TGGGAGAAA-TATCTGCAAATTATGCATCTGACAAAGTTCTAATATCCAG 3658
                                  -   i       i  ii      i  i vv  vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_73021858_7   3659 AATTTATAAG---CTACTTA-AATTCA----TGGGGAGA-AAA----CCA 3695
                            v     i---  -    -  i   ---- iiii   -   ----   
  L1M4_orf2#LINE/    762 AATATATAAAGAACT-CTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_73021858_7   3696 CATTGAAAATATGAAAAAG---TACATAGACATTTTTTCAAAGGAAGACA 3742
                         vv ?i     iv v   i --- iv          i i     -    i 
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG-AAGATA 859

  chrX_73021858_7   3743 TGCATACAGCTAGGAGTCATATGACAAAATGCTGAACATCACTAATCTA 3791
                          i  v ii  i iv iv  i    v  i     v       ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.03 (30 / 889), avg. gap size = 2.07 (62 / 30)  


1139 31.21 11.86 1.00  chrX_73028331_73030156      533  1333 (493)    L1M4_orf2#LINE/L1       21   908 (0)  

  chrX_73028331_7    533 ATGAAATGGGAAA-TTATTCATAATTAAAATATCATTACTGCCTAAAGCA 581
                            i v   i i -   v -  vi    i  iv  v    v  i   vii
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAAT-ATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chrX_73028331_7    582 GTCTGCAGATTCA-TTCTTTTTGTATCAAAA-ATCAATGATATTCCTCAT 629
                         i   i        -iv vv iiv        -vi  iiviiv  ii iii
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_73028331_7    630 AGAAATAGAAAAA--GAATTCATAAAATTCAT--GAGACCACAGGAGATA 675
                               v  v  i--  --  v          -- ii vii  i i  iv
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGA--TCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_73028331_7    676 CTGAGTATCAAAAGTAATCCTGAG---GAAAAGCAAAGATGAAGACATCA 722
                          v  i  v v   ii    i   i---   i i     v  i  ivv   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_73028331_7    723 TACT-----ACTTCAAAAGATACTACAATGTCATTGTAAACACAAT-GTG 766
                         i   ----- i       vv        v ii iv    v  vi i-   
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_73028331_7    767 ATGATATTGGCAT---GATATACACGTAGATCAGTGGGATGAAATCAAGA 813
                         -  i  i      ---    v   ii       i   i  ii   ii   
  L1M4_orf2#LINE/    268 -TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_73028331_7    814 ACCCAGTGATAAATACAGACATTTACAAAAAATTCATTTTTAA--AAATC 861
                         ii    vi     iv  v       iiivv    v     ii -- iivi
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_73028331_7    862 ACCATAAATATATGTTGTGGAAAGGATAGTGCTTTCAATGAAAGTTGCTG 911
                         i   vi vi  viiv  v      i     vi      ii  v v     
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_73028331_7    912 GGAAAACTTGGTAATCATATGCAGAAGAATGAA--------------TCT 947
                            v    v i  ?i  i     i         --------------  v
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_73028331_7    948 TACCATATGTAAAAATAAAATTAATATGGGTTAAGTGCTTA--TGT---- 991
                         i       ii      v  v i  v    i i ?ivi i  --   ----
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_73028331_7    992 -CTGAAACTATAAAAAGTGGTAGA-TAAAATCTTTGTATAAATGCTTCTG 1039
                         -  i           v- vv    -v    iv vv ?i     -    vv
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAAC-TCTTAGAAGAAAACATAGGNGTAAAT-CTTCGT 564

  chrX_73028331_7   1040 GATATTTGTCTAGGCAAAGATATTTTGG-TAAGCTCTGAAAAGCAGAGGC 1088
                           iv  v vi       v i v i  i -  v viviv       v i  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_73028331_7   1089 AACAAAAGCAAAAATAGACATAAGTTCA--TACATCTAGCTAAAATGCTT 1136
                                 v         --   i  vi-- v    v iv v   vi   
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGA--TAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_73028331_7   1137 TTGCACAATAGAGG----TAACAAAATAGTGAAACCAAAATT---ATAAT 1179
                            ii vvi i   ----  v   i v       vv v  ii--- v   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_73028331_7   1180 GGGAAAAAAC--CTGATAACTATGTTTTTTACA-GCGA--TG-----AGA 1219
                             i    i--i  vv  ii  i v i v i - v  --  -----   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_73028331_7   1220 ATATATA-----TTCATA----TCATCAGAAGGCAAGCAAATAATCTGAT 1260
                                -----i  v  ----   vi iv iiv ii       i ii  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_73028331_7   1261 TT---------TAAAGGAT------AGA------TTAAAAGAAGGCATA- 1288
                          ?---------i       ------   ------ iv       ii   -
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_73028331_7   1289 -AGTTGCCAACAGGTATATGTAAAATTTTTCATCATCACTAATCAT 1333
                         - i v     i i i i   v   iv vi   v     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (143 / 103)
Gap_init rate = 0.04 (34 / 888), avg. gap size = 3.03 (103 / 34)  


 635 24.34 1.97 0.66  chrX_73037050_73043431.rev        1   152 (6230)    L1M4_orf2#LINE/L1      342   495 (413)  

  chrX_73037050_7      1 TGGTTAATTAACATACAGACAAAGGTGCCAAAGCAATCCAATGGGAAAAG 50
                             i    i iv v -     i        ii v  i       i    
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_73037050_7     51 AA-AGTCTTTTTAACAAATGGTGTTG-AACAACTAGACATCAGTATGGAA 98
                           -        i           i  -i      i  i ? vii   v  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_73037050_7     99 AATAACAATGTTGT-CTCCTACCTTATACCATAGACAGAAGTTAATTTGA 147
                           v  ii v    v- i       i i      v   i  i    i ii 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_73037050_7    148 GTTGG 152
                         iv   
  L1M4_orf2#LINE/    491 AATGG 495

Transitions / transversions = 2.60 (26 / 10)
Gap_init rate = 0.03 (4 / 154), avg. gap size = 1.00 (4 / 4)  

3115 25.11 1.99 1.55  chrX_73037050_73043431.rev     4988  5891 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73037050_7   4988 TGGAAGAACATTTCATGCAAATGGATGGGAAGAATCAATATCCTGAAAAT 5037
                              ii i  ii    ivv      v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73037050_7   5038 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5087
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73037050_7   5088 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAACGTTCA 5135
                          v   iivi i  i  ii     -   -- v  i  - iii   vi    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_73037050_7   5136 TATGGAACCAAAAAAGGG-CCCACATT-GCCAAGTCAATCCTAAGCCAAA 5183
                                -- viv     -    v v -     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_73037050_7   5184 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 5233
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_73037050_7   5234 GCCACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5283
                           i       i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_73037050_7   5284 CCAATGGAACAGA-TTG-GAGCCCTCAGAAATAATACCACACATCTACAA 5331
                         i        i   -   -   i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_73037050_7   5332 CCATCTGATCTTTGACAAACCTGACAAAAAACGAGCAATGGGGAAAGGAT 5381
                         i  vi    i  i     ivv  v   i v- ivv            i  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAAT 393

  chrX_73037050_7   5382 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5431
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_73037050_7   5432 GCTGAAACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 5481
                         iv    ii    iv   v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_73037050_7   5482 GGATTAAAGACTTAAATGTTAGACCTAAAGCCATAAAAACCCTAGAAGAA 5531
                             i ?    i       v   v     i i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_73037050_7   5532 ATCCTAGG---AAATACCATGCAGGACATAGGCATGGGCAATGACTTCAT 5578
                          v v    ---    -- - v iv   v v  vv i       ii   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_73037050_7   5579 GTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGG 5628
                         ivv  vi            vvi          vv     v  i i  v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_73037050_7   5629 ATCTAATTAAACTAAAGAGCTCCTGCACAGCAAAGGAAACTACCATCAGA 5678
                          ii v  i   v v  i i  ii  ii vv       v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_73037050_7   5679 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATC 5728
                              v  i     i                 v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_73037050_7   5729 TGACAAAGGGCTAATACCCAGAATCTACAAAGAACTCAAACCAATTTACA 5778
                            i  i  i  vi  i       v  i         vv  v v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_73037050_7   5779 AGAAAAAAACAA----CCCCATCAAAAAGTGG-CAAAGGATATGAACAGA 5823
                          v     i    ----   v  i?    i   -        v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_73037050_7   5824 CACTTCTCTAAAGAAGACTTTTATGCA----GCCAACAGACATATGAAAA 5869
                           i     i        ----   i  ----     i ii  i       
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_73037050_7   5870 AATGCTCATCATCACTGGCCAT 5891
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (133 / 91)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.88 (32 / 17)  


3173 25.31 2.81 0.67  chrX_73043710_73050338.rev     5250  6138 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73043710_7   5250 TGGAAAAACATTCCATGCTCCTGGATAAGAAGAATCAATATTGTGAAAAT 5299
                               i i  i     i  v     vi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73043710_7   5300 GGCCATACTGACCAAAGTAATTTATAGATTCAATGTTATCCCCATCAAGC 5349
                            v     vv     v i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73043710_7   5350 TACCATGTACTTTCTTCACAGAATTAGAAAAAATTACTTTAAATTTCATA 5399
                          v   vv i i  i  ii     v v  v  iv v iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_73043710_7   5400 TGGCAGCAGAAAAGAGCCCATATAGCCAAGACAATCCTAAAAAAAAAGAA 5449
                            v iiiv  ii  v  viv        i      i i     i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_73043710_7   5450 TAAAGCTGGAGACATCACACTTCCTGACTTTAAACTATACTGCAAGTCTA 5499
                         i    i     ivv          ii i  i   viv    i   iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_73043710_7   5500 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5549
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_73043710_7   5550 TGGAACAGAA--AAGAGGCCTCAGAAATAA--CCACACATCTACAACCAT 5595
                              i    --i    v  --        --   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_73043710_7   5596 CTGATCTTTGACAAACTTGACAAAAACAAGCAATGGGGAAAGGAT--TCC 5643
                         i    i  i     ivv  v   i v  vv            i  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_73043710_7   5644 ATATTTCA-TAAATGGTGTTGGGAAAGCTGGCTAGCCATATGCAGAAAAC 5692
                         ---     -i        i     v i    v  ?   i     i  i v
  L1M4_orf2#LINE/    399 ---TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_73043710_7   5693 TGAAACTGGACCCTTTCCTTACACCTTATACAAAAATTAACTCAATATGG 5742
                             ii       i v   i     v                   v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_73043710_7   5743 ATTAAAGACTGAAACGGAAGACCTAAAACCCTAAAATCCCTAGAAGAAAA 5792
                           i ?    iv   i v    v       iv     ii i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_73043710_7   5793 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTC--AGG- 5838
                          v    ?i- v i -   iv   v v  vv i     v ii   --  i-
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_73043710_7   5839 -----ACTAAA-------GCAACAAAAGCCAAAATTGACAAATAGGATCT 5876
                         -----  i   -------          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_73043710_7   5877 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5926
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_73043710_7   5927 ACAGGCAACCCACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 5976
                          v  i                       v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_73043710_7   5977 AAAGGGCTAATATCCAGGATCCACAAAGAACTTAAACAAATTTACAAGAA 6026
                           i  i  vi       i  vi i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_73043710_7   6027 AAAAAGGAACAAGCCCATCAAAAAGTGGGCAAAGGATATGAACAGGCACT 6076
                            i vi  i  v  v  i?    i            v    i  i  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_73043710_7   6077 TCTCAAAAGAAGACATTTACACAGCCAACAA--ACATGAAAAAAAGCTCA 6124
                             v        i  vi v ii     i  --         i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_73043710_7   6125 TCATCACTTGTCAT 6138
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (132 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


1885 23.33 29.16 0.00  chrX_73070688_73072559.rev      679  1381 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73070688_7    679 TGAAAAAATATTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 728
                           i   i    i                     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73070688_7    729 GTCCATACTACCCAAAGCAATCTACAGATTCAGTGCAATCCCTATAAAAA 778
                          v v     v      vii             ii           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73070688_7    779 TACCAATGACATTCTTCACAGAAAT--A-----TGATCCTAAAATGTATA 821
                          v   iivi v  i  ii       -- -----            vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_73070688_7    822 CAGAACCACAAAG-ACCCAGAATAGCCAAAGCTATCCTAAGCAAAAAGAA 870
                         ii   vii   i -                i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_73070688_7    871 CAAAACTGGAGGAATCACATTACCTGACTTTAAATAATACTACAGAGCTG 920
                             ii       v     i v  ii i  i   vvv       i    i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_73070688_7    921 TTGTAACCAAAACAGCATGGTACTGGCATAAAAGCAGACACACAGACCAA 970
                         iv    i   i    ii              iiii     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_73070688_7    971 TGGAACAGTACAGACAACCCAGAAACAAATCCACACACAAACAGTGAACC 1020
                              i  v iv  v ii       i   i   i   ivv ii  v  ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_73070688_7   1021 CATTTGTGACAAAGGTGCCAAGA--------------------------- 1043
                         v    vi     i          ---------------------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_73070688_7   1044 --------------------------------ATATGCA----------- 1050
                         -------------------------------- i     -----------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_73070688_7   1051 ------------CTC----------------------------GG----- 1055
                         ------------   ----------------------------  -----
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_73070688_7   1056 ----------------------------------------GAAAACACAG 1065
                         ----------------------------------------       i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_73070688_7   1066 -------TCTTT-----------------------------------ACT 1073
                         -------    i-----------------------------------  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_73070688_7   1074 CCACAAGCACAAGCAACCAAAGCAAAAATGGACAAATGGGATTACGTCAA 1123
                            v             v    v      i  i    v   i v i    
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_73070688_7   1124 GTTTAAAAGCTTCTACACAGCAAAAGATACTATCAACCAAGTGAATAGAC 1173
                         iv      i   i iii vv    i  i        vv       v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_73070688_7   1174 ACCCCAAAGAATGGGAGAAAATATTTGCAAACTACCCATCTGACAAGGGA 1223
                          v    v                        ii ivi      i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_73070688_7   1224 TTCATAACCAGGATTTATAAGGAGCTCAAAGAACTCTACTGGAGAAAATC 1273
                         i ii  v    i  v     i  i   vv v     v iviv i   iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_73070688_7   1274 TAGTAATTCCAGTCAAAAATGGGCAAAATATTTGAATAGGCATTTCTCAA 1323
                         v i   ii v v ?             iv          i        v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_73070688_7   1324 GAGAAGACATACGTATTGCAAAGAGGCATATGAAAATGTGCTCAACATCA 1373
                         i      i    iv  v  v  v i   i       vi            
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_73070688_7   1374 TTGATCAT 1381
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.67 (102 / 61)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 22.78 (205 / 9)  


3246 26.44 0.77 0.33  chrX_73075108_73081861.rev     5360  6263 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73075108_7   5360 TGGAAAAACTTTCCATGGTCATGGATAGGAAGAATCAATATCGTGAAAAT 5409
                               i iv i     v        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73075108_7   5410 GGCCATACTGCCCAAAGTAATTTATTGATTCAATGCTATTCCCATCAAGC 5459
                            v     v      v i  i  iv       i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73075108_7   5460 TACCATTGACTTTCTTCACAGAATTAGAAAAAGCT-ACTTTAAATTTCAT 5508
                          v   vivi i  i  ii     v v  v  -   - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_73075108_7   5509 TTGGAACCAAAAGAGATCCCATATAGCCAAGACAATCCCAAGCAAAAAGA 5558
                         v     viiv   i  i  viv        i      iii iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_73075108_7   5559 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5608
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_73075108_7   5609 ACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATATAGACCA 5658
                                i   i    ii  i      i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_73075108_7   5659 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAATGATC 5708
                               i    iv   ivii         vv   i    i  iii v vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_73075108_7   5709 TGACCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAAAATTCCCTA 5758
                            ii  i     ivv  v   i v  vv           i   vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_73075108_7   5759 TTTAATAAGTGGTGCTGGGAAAACTGGCTACCCATATGCAGAAAACTGAA 5808
                           i  i  i           v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_73075108_7   5809 ACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATAGATTA 5858
                         ii         v   i     v                   i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_73075108_7   5859 AAGACTTAAATGTAAAACCTAAAACTATCAAAACCCT-AGAAGAAAACCT 5907
                         ?    i         i v          -     i  -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chrX_73075108_7   5908 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 5956
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_73075108_7   5957 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGCAATCTAAT 6006
                                     vvi          vv     v  i    vvi ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_73075108_7   6007 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAAATATCATCAGAGTGAACA 6056
                         i   v v  i i   i  ii vv    i  v v     vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_73075108_7   6057 GGCAACCTACAGAATGGGAGAAGCTTTTTGCAATCTATCCAGCTGACAAA 6106
                          i     i              iv v       vii  vi v    i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_73075108_7   6107 GGTCTAATATCTAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 6156
                           v  vi    i     v  i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_73075108_7   6157 AACAA----CCCCATGAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 6202
                         i    ----   v  v?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_73075108_7   6203 CAAAAGAAGGCATATATATGGCAAACAAACATATGAAAAAAAGCTCATCA 6252
                          v       ii   i v     v  i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_73075108_7   6253 TCACTGTTCAT 6263
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.35 (135 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 444 25.89 0.89 0.00  chrX_73177313_73181150     1801  1912 (1926)    L1M4_orf2#LINE/L1        1   113 (795)  

  chrX_73177313_7   1801 TGGAAAGATACCTTGTGTTCATGAATTATAAAAATTAATATTGTTAAGAC 1850
                                   i iii        i   iv  i v               i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73177313_7   1851 ATCCATAATACTCTAGGTGATGTACAGATTCAATGAAATCTCTATTAAAA 1900
                         iv v   v v i v iv    v           i v    i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73177313_7   1901 TTCTAA-TATCTT 1912
                          i i i- ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT 113

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.01 (1 / 113), avg. gap size = 1.00 (1 / 1)  

 459 25.81 1.08 3.76  chrX_73177313_73181150     2224  2409 (1429)    L1M4_orf2#LINE/L1      113   293 (615)  

  chrX_73177313_7   2224 TCTTAACATAAATAGAAAAAACAATCCTATAATTTGTATAGAACCATAAA 2273
                          i  vi  v    v  v  ivii      v    ii   i   --  iv 
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA--ATGCA 160

  chrX_73177313_7   2274 AAAAAACTA-AATAGCCAAAACACTGTTGACCAAAAACAACAAAGCTAGC 2322
                          iii v i -             v v    vv  i  v       i i -
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG- 209

  chrX_73177313_7   2323 TAGAGGCAC-CACACTACCAGATTTCAAAATATATTATAAATCTATAGTA 2371
                         ---   -  -      v  vi         iv  i  i   v   i    
  L1M4_orf2#LINE/    210 ---AGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_73177313_7   2372 ATTAAAACAACATGCTACTGGCATAAAAACAGACACAT 2409
                           i  i   iii  v           ii i     i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

Transitions / transversions = 1.67 (30 / 18)
Gap_init rate = 0.03 (5 / 181), avg. gap size = 1.80 (9 / 5)  

2491 23.51 0.97 0.64  chrX_73177313_73181150     2727  3347 (491)    L1M4_orf2#LINE/L1      286   908 (0)  

  chrX_73177313_7   2727 AGACATATCAATCAGTGGAATAAGAAAGATAGACATCCCAGAAATAAACC 2776
                                 vi    i       -   --- v  v vi             
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATA-GAA---TTGAGAGTCCAGAAATAAACC 331

  chrX_73177313_7   2777 TATGCATCTATGGTCAATTGGTTTTGAACAAAAGTACCAAGAACATGCAA 2826
                         i  i   i            i    vi    ii  i      v   v   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_73177313_7   2827 TGGGTAAAGGACAGTTGCTTCAATAAATGCCACTGAAAAAACTAGACATC 2876
                             v    i i   ivi     i     vii   ii v    i  i ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_73177313_7   2877 CACATAAAAAAGAATGAAAATGAGCCACTATCTCACTCCTTATACCAGAA 2926
                              iv           iv  ii  v   i     v  v     v i  
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_73177313_7   2927 TCAACTCAAAATGGATTA--GACTTAAACATAAAACCTGAAACTATATAA 2974
                          i              i --   i    ii   i v  i        v  
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_73177313_7   2975 CTACTAGAAGAAAACGTAGGAGAAAATTTCCATGACATTGACGTGAGCAG 3024
                           vi           i    ? v    i i i    v   ivv ii   i
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_73177313_7   3025 AGATTTCTTGGATATGACTCCAAAAGCACAAGTAACAAAAGCAAAATTAG 3074
                         v i      i        v             i        v    v   
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_73177313_7   3075 ACAAACAAGATTGCATCAAGCTAAAAAGCTTCTGTACTGCAAAGGAAACA 3124
                          i   ivi  i v      iv v    i   i   i  v       v  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_73177313_7   3125 ATTGAGTGAGGGAAAA----ATCCAGGGACTGGGAGAAAATATCTGCAAA 3170
                           ii  vi  v     ---- i   vi  v             i      
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_73177313_7   3171 TTATACATTCAATAAGAAAGTAATATCCAAAACCTACAAGGAACTCAAAC 3220
                          i   i  iii     ii v vi      i  iv  i  i      vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_73177313_7   3221 TACTCAATAACAAGAAAACAAATAACCCTTTTAGAAAATGGGTAAAGGAC 3270
                         v         i  i  i           vv  ?i        i      i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_73177313_7   3271 TTGAATAAACATTTCTCAAAAGAAGACATAAAAATGGACATCAGATATAT 3320
                                i         v        i   v      v  vi iii i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_73177313_7   3321 TTTAAAATGCTCAACATTTCTAATCAT 3347
                         vvv  i           iv????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (88 / 55)
Gap_init rate = 0.01 (4 / 623), avg. gap size = 2.50 (10 / 4)  


 326 20.75 1.89 0.94  chrX_73199621_73201911.rev      397   502 (1789)  C L1M4_orf2#LINE/L1   (0)   908   802  

C chrX_73199621_7    502 AATAA-CTGATTTTTAAATGTACAAAC-ATCTGAAAAGGACACCTCACCA 455
                              - ii   ?vv     vi    v-  i    v -    ii  v   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA-GACATTTCTCCA 850

C chrX_73199621_7    454 AAGAAGATATACATATGGAAAATAGGCATATGAAAAGAAGCTCAAGGTGA 405
                                      v    vv    i   i         v      vi v 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

C chrX_73199621_7    404 TATGAGTT 397
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 0.75 (9 / 12)
Gap_init rate = 0.03 (3 / 107), avg. gap size = 1.00 (3 / 3)  

3437 22.47 4.20 1.14  chrX_73199621_73201911.rev      920  1800 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73199621_7    920 TAAAACGATATTCCATGCTCATAGATTGGAAGAATTAATGTTGTTAAAGT 969
                          ii  v     i     i    i          v     i       ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73199621_7    970 GTCCATACTACCCAAAGCAATATATAGATTCAATGCAATCCCTATCAAAA 1019
                          v v     v      vii  v  i        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73199621_7   1020 TCTCATCAGCATTCTTCACAGAAATAGAAAAA--AATCATACAATTTCTG 1067
                           i  v v  v  i  ii       v  v  i--i   v  v    iv i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_73199621_7   1068 TGGATCCACAAAAGATCCCAAATAACCAAAGCAATTCTGAGAAAAAAAAA 1117
                             vvii   ii  i  vi    i     i    ii   i   i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_73199621_7   1118 TC---CTGGAGGCATCATACTTCCCAATTT--AAATTTATATTACAAAAC 1162
                         iv---i      vv   i            --   i   i--      i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGC 248

  chrX_73199621_7   1163 GAGAGTAATCAAAACAATACAGTATTGGCATAAG---AGATACACAGGAC 1209
                         v v         i   i iii   i         ---   i i i  iv 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_73199621_7   1210 AGTGAAATAG----------CCAGAAATAAATCCAAACATGTATGGTTAA 1249
                          i  i     ----------           i   v    v      i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_73199621_7   1250 TGAATTTTTGACAAGAGCACCAAAAAGACAAAATGAGAAAAGGGTAGTCT 1299
                          vi     i      i ii    i vv ivv    i i    ii      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_73199621_7   1300 CTTCAATAAATAGGTGCTGG---AATT-----TCCACATGCAAAAGAATG 1341
                         i     i    -        ---  i -----?                 
  L1M4_orf2#LINE/    399 TTTCAACAAAT-GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_73199621_7   1342 AAATTAGACTCTTACATTACACCATACACAAAAATCAATCCAAAATGGAT 1391
                           i  i   i i   v i        i        i  ii          
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_73199621_7   1392 AAAAGATCTGAATGTAAGACCTGAAGCCATAAA--TCT-AGAAGAAAACA 1438
                         v ?   i  i         v  i  i i     --   -           
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_73199621_7   1439 TAAGGGAAAAGCTCCTTGACACTGGCTTTGGCAATGTTTCCTTGGATATC 1488
                           i ? v   v  i v    vi   v  v       v  i   i     v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_73199621_7   1489 ACACCAAAACCTCAGGCTACAAAAGCAACAATAAATAAATGAAATTATAT 1538
                                  v v  i  v       v  v    i      vii i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_73199621_7   1539 CAATCTAAAAAACTT-----CTACACAGAACGAAAACAATCAACAAAATG 1583
                            vv v        -----  v  v  i  ----  v     v   i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGAC----ACTATCAAGAAAGTG 693

  chrX_73199621_7   1584 AAAAGGCAATGTACAGATAAGGAGAAAATATTTGCAAACCATATATCAGG 1633
                              i   ivi     vvi                  i        v i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_73199621_7   1634 CAAGGTTTTAATATTCAGGATTTAGGAAGAACTCATACAACTCAATAGCA 1683
                         i    vvi vi   i   i  v  vi        v            ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_73199621_7   1684 AGACAACATATAACCTGATTAAAAAAAAGTGGGGAAAGGACTTGAATAGA 1733
                          i vi   v      ii   ?     ---    v      i         
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA---TGGGCAAAGGATTTGAATAGA 840

  chrX_73199621_7   1734 CATTTCTTCAAAGATGACAGA-AAATGACCAACAGGTATATGAAATGGTG 1782
                                i      v  i v -     i    i i i i      v i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_73199621_7   1783 CTCAATATCACCAGTCAT 1800
                              i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (122 / 72)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.13 (47 / 15)  


2141 25.22 10.50 1.02  chrX_73212317_73214263      666  1446 (501)    L1M4_orf2#LINE/L1        6   860 (48)  

  chrX_73212317_7    666 AGCTATATCATGTTTGTGGCCTA-AAGACAAAATATTGTGAGGATGTAAA 714
                           v   vi      ii   vi i-     vv        v i    vv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_73212317_7    715 TTTTCTTCAAATTCATCTATAGTTCTAACTCAA-------CAGATATACT 757
                          vi  ii      v     i  v ii   v   -------  i -  v i
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA-ATCCC 104

  chrX_73212317_7    758 AGCAGAATTTTTTATAGAAAGCAACAA-----TTCTAAAATT--TCTGGA 800
                            v vv      ii     vii    ----- i        -- v    
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_73212317_7    801 AAAGCAAAG----TAG--TAATCAACACGATTTTTGA---GACGGACGAA 841
                           v    i ----i  --  ii   v  i  i  vi ---  v i  i  
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_73212317_7    842 GTTGTA-----CACACTATCTAATTTTAAGACTTCCTA-----------T 875
                             v -----      vi i     i  i    v   ----------- 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_73212317_7    876 GATTAGGAAAGTGTGGTATTTGTGAATGGATAA----------CAATGGA 915
                         i  i i  v         i v iiv v     i----------       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_73212317_7    916 ACAGAATAGGCAGCCCAGAATTAGACCCAAACAAATATAATCAATTGATT 965
                          i     v iv  i      v  i     v   vv   ii          
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_73212317_7    966 TTTTGACAGAAGTGCAAAAGCAATGCAATAAAAAAGAAACAATCTTTTCA 1015
                           i-    iii    v  ii v  v    iiii  ii  i i        
  L1M4_orf2#LINE/    355 TTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_73212317_7   1016 ACAAATGGTACTAGAACAATTAGATAGCCATATTTTAAAAACTGAACCTT 1065
                                  i  i i    i i    ?   i  viv   i v    vi v
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_73212317_7   1066 GACCCATAGCTAA-ACTTTATACAAACCTTTATTCAAAAAGTATCATAGA 1114
                              v  v  v -  iv        vv  v i      v v    ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_73212317_7   1115 TATAAATGTAAAACTTAAAACTATAAAATTCCTGGATGAAAATA---ATA 1161
                         iv         i vi             i  i i  v     i ---i?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_73212317_7   1162 TATAATCTTCATGACATTGGGTTAGACAA--GTGTTCTTACAT-TGCACA 1208
                           -       i    v         i   --  -      v  -  -   
  L1M4_orf2#LINE/    554 TA-AATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATATG-ACA 600

  chrX_73212317_7   1209 TCAAAAGTA-------------AAAAAATTGATAAAGTGAATTGTATCAA 1245
                         i      i -------------       v      v  i i vi     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_73212317_7   1246 AATTAAAA--TTTT-TGCTCTAAAAAAGTCAGTGTTCAAAGAATGAAAAG 1292
                                 --    -    ii   ii --  v i iv i i i       
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGA--CACTATCAAGAAAGTGAAAAG 698

  chrX_73212317_7   1293 ACAAGTCACAGACTAGGAAAATCTATTTCCAAATAATGTATCTGACAAAG 1342
                             vi      v i   i  vv     v     v  i       i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_73212317_7   1343 GATTTGTATC---AATATATTAAAAAACA--TATAAA--AACAGTAAGAA 1385
                           i       ---       -   i   v--  i  v--  i i   i  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATAT-AAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_73212317_7   1386 AAGGAATAATCCAATAAAAAGGGGAGCAAAAGATCTGAACAGACACTTTG 1435
                         i vi     i     v?   iiv i     i   i    i     i  iv
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_73212317_7   1436 C--AAGAATATAT 1446
                          --     v    
  L1M4_orf2#LINE/    848 CCAAAGAAGATAT 860

Transitions / transversions = 1.57 (118 / 75)
Gap_init rate = 0.03 (28 / 855), avg. gap size = 3.21 (90 / 28)  


3818 18.30 8.61 0.00  chrX_73231240_73233623     1060  1895 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73231240_7   1060 TAGAAAGGTATCTATTGTTAATGGATTGGGAATATTAATATTTCTAACAT 1109
                          i     i    ivv    v         i ivv        vi   v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73231240_7   1110 GGCAATACTCCACAAATTGATCTACAGATTAAATGCTTTCCTTAGCAAAA 1159
                                    v                  v  i  vv   i  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73231240_7   1160 TTCTGGCA-----TTTTCTAGAAATTTACAAGCTGATCCTAAAATTCATA 1204
                          i ii  v-----    vi       v                       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_73231240_7   1205 TGGAAATTCAAAGCCTTCAGAATAATCAAGGC---C---AAAGCAAAGAA 1248
                                v   i vvii       ii   ii --- ---   ivi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_73231240_7   1249 CAAAGCTGGAGAACTCATACTTCCAGATTTTGAAATTTACTCCAAAGCTA 1298
                              i     i     i      vi    ii   i     v        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_73231240_7   1299 CAATAATCAATACTGTGTAGTACAGGCATAAGGATAGATATAGAGATAAA 1348
                           i       v  v    i    v              i   v    v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_73231240_7   1349 TAAAATAAAATTGAGAGTCCA-AAATAAACTCTTATATTTAGAATCAACT 1397
                          ii    i             -        i v  i     vii    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_73231240_7   1398 GATGTTCAACAAGGGTACCAAGACAATTCAATGATGAAG---TAGTCTTT 1444
                            v   i        i       v        iv   i---        
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_73231240_7   1445 TCAACAAATGGTGCTGAGAAAACTGGATATCCATATGCAAAGGGACTAAG 1494
                                         i  v         ?   i       i i iv   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_73231240_7   1495 TTGGACTTCTTCCTTAAACTATATACAAAAGTAAATTCCAAATGAATCAC 1544
                               ii  v   i v  i          i v  i  v     i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_73231240_7   1545 ACACCTAAATGTAAGAGCTACAACT------------------------- 1569
                          v                  v    -------------------------
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_73231240_7   1570 -------------------TAGGTCAGGTAATGGTTTCTTTGTTATGACA 1600
                         ------------------- i   i   i           v v       
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_73231240_7   1601 CTAAAATCACAACTAACAAAA--AAAAATAGATAAATTAGATTTCATCAA 1648
                          i    v     vi       --               i  i        
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_73231240_7   1649 TATTAAAAACTTCTGTGCTATAAACAATGTCATCAAAAAGGTGGAAAGGC 1698
                         v           i      vi   vi iiii     i  i   i    i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_73231240_7   1699 AATACAAAGAATGGAAGAAAATAATTGTAAATCATGTATCCAATAAGAGT 1748
                           iv  v       i        v   i       i    ii     i v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_73231240_7   1749 CTGTTATCCAGATTATATAAAGAACTCTGATAAC-----AACAAAACCAC 1793
                           vv        v               v i   -----  i    vv  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_73231240_7   1794 ATATAACCCAATTCTAA--TGAGCAAAGGATTAGAACAGACATTTCTCCA 1841
                          v           ?v  --  i          v   i             
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_73231240_7   1842 AAGA---TACACAAATTACCACTAAGCACATGAAAAGTTGCTCAATG-CA 1887
                             ---  i      vi   v               v       ii-  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_73231240_7   1888 GAAATACA 1895
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.42 (88 / 62)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 6.55 (72 / 11)  


2044 19.57 3.26 0.65  chrX_73471932_73476016.rev      502   961 (3124)    L1M4_orf2#LINE/L1      189   660 (248)  

  chrX_73471932_7    502 GAAAAATGAACAACAAAGTTGGGAGATTCACACTTCCTAATTTCACATCT 551
                               -   v           ii  i          i       v v  
  L1M4_orf2#LINE/    189 GAAAAA-GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_73471932_7    552 -ACTACAAAGGTACAGTAATAAAAACCGTGTGGTACTTGCATAAGAATGA 600
                         -         v         v  i  v          v       i  ii
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_73471932_7    601 ACGTACAGATTAATGAAACAAAATTGAGAGTCCATTTAAAAACCCCTTTA 650
                           i  i    i    i  i i             vvv v      v -- 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT--A 335

  chrX_73471932_7    651 TATTTCCTGTGAATTGATTAATAGCAAGGTTGCCAAGATAATTCAATATA 700
                         i    viv  v        vviii     v        iv       ivi
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_73471932_7    701 GATAAAATAGTCTTTTCAGCAAATGGTGATGAGTCAACTAGATATTCACA 750
                           v i             i         v  i v     i    ?i    
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_73471932_7    751 TACAAAAGAATGAAGCTGAATTCCTACATGACACCATATATAGAAATTAG 800
                          i             i  i ii     v v          i i      i
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_73471932_7    801 CTCAAAATGAAGTACATACCTACATATAAGAATTAAAAATATAGAAGTCT 850
                                  i vi ? v     v  i     ii     v    i  v   
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_73471932_7    851 TAGAAGAAAGCATAGAAGTAAAT------------AGAATAGGCAATAGT 888
                                  i     i?      ------------i iv        i  
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_73471932_7    889 TT-TTAGAAATAATTTTAAAAGCACAAGCAACAAAA-AAACACTAGATAA 936
                           -     v  i ivii                   -   v v       
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_73471932_7    937 ATTGGAGTTCATAAAAATTAAAAAC 961
                               v     v            
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAAC 660

Transitions / transversions = 1.35 (50 / 37)
Gap_init rate = 0.01 (6 / 472), avg. gap size = 3.00 (18 / 6)  

 882 12.22 3.89 2.22  chrX_73471932_73476016.rev     1528  1707 (2378)    L1M4_orf2#LINE/L1      651   833 (75)  

  chrX_73471932_7   1528 AATGAAAAACTT--GTGCTTCAAGGGGCACCAGTAAGATAGTGAAAAGAT 1575
                            v        --         i  i   i vi    v          i
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_73471932_7   1576 AACACACAGAATGAGAGAAAATATTTTCAAATCATTTATCTGATAAGGG- 1624
                            v         i            v        v             -
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_73471932_7   1625 -TTGAGTATCCAGAATATATATTTAAAACTTTAATAATTCAACAATAAAA 1673
                         -   --               v-- i    i v i  i    i       
  L1M4_orf2#LINE/    751 CTTG--TATCCAGAATATATAA--AGAACTCTTACAACTCAATAATAAAA 796

  chrX_73471932_7   1674 AGACAAATAAC---ATTGACAAATGGGCAAAGGTTTT 1707
                                    ---   ? v             v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

Transitions / transversions = 1.10 (11 / 10)
Gap_init rate = 0.03 (5 / 183), avg. gap size = 2.20 (11 / 5)  

1186 22.46 5.99 0.90  chrX_73471932_73476016.rev     1881  2214 (1871)    L1M4_orf2#LINE/L1      463   813 (95)  

  chrX_73471932_7   1881 CTTACACCCTTCACAAAAATTCACACAAAACTAATCATAGACCTAAATGT 1930
                           i     v vi         v  v     ivi    ?            
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_73471932_7   1931 AAAATGC-AAAACTCTAAAATTCCTAGAAGATAATATAAAAGCAAATTTC 1979
                           i -  -      v     i  i       v  i   ii? i    i i
  L1M4_orf2#LINE/    513 AAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_73471932_7   1980 AATGACCTTGGGT--GGTAATTGTTTAT---GTATAACAACAAAGGCACA 2024
                         vi           --  i   v    v ---i   i   v    i     
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_73471932_7   2025 ATCCATAAAAGATATAATTTGTAAACTGGACTTAATTAAAATTAAGAATC 2074
                          v v i      v v   vvi    i       v  i        i  ii
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_73471932_7   2075 TCTGCTCTGTGAAAGACACTATCAAGTGAATGAGAAGAT----------- 2113
                          i  iv  vii  i            vi i   i    i-----------
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_73471932_7   2114 TGGGAGAAAATACTTGCAAATGACATATCTGATAAAGAA-TTGTTAAT-- 2160
                                     i        v i           i i -    --  --
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT--ATCC 759

  chrX_73471932_7   2161 AATATATACAAAGAACTCTTAAAATTCAACAAAAAGAAAATAAATAACTT 2210
                          iv     i            v  i    i  v  i  i i       ii
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_73471932_7   2211 GATT 2214
                         i   
  L1M4_orf2#LINE/    810 AATT 813

Transitions / transversions = 1.92 (48 / 25)
Gap_init rate = 0.02 (8 / 351), avg. gap size = 2.88 (23 / 8)  

 332 22.62 3.57 0.00  chrX_73471932_73476016.rev     2516  2599 (1486)    L1M4_orf2#LINE/L1      822   908 (0)  

  chrX_73471932_7   2516 GGCAAA---TCTAAATGAACACCTCACCAGAAAATATATATGTATGGTGA 2562
                               --- i i   ii   ii  v   i i  v     iiv    iv 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_73471932_7   2563 ATGTGCATATGAAAAGATGCTCAATATCATATGTCAT 2599
                           iv   i                i    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.80 (14 / 5)
Gap_init rate = 0.01 (1 / 87), avg. gap size = 3.00 (3 / 1)  

 508 17.02 0.00 0.00  chrX_73471932_73476016.rev     3502  3595 (490)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_73471932_7   3502 AAAAGCAGGCCAAGAGTTTCAATAGACATTTCTTTAAAGAAGATATACAA 3551
                             iii   v   ii   v             ii               
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_73471932_7   3552 ATGGCCAATGAACACATGAAAAGATACCTAATATCTTTAGTCGT 3595
                                  i i             i ii  i   v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.33 (13 / 3)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3225 27.75 0.33 0.33  chrX_73477587_73483987.rev     5003  5910 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73477587_7   5003 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5052
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73477587_7   5053 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5102
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73477587_7   5103 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5150
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_73477587_7   5151 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5200
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_73477587_7   5201 AGCAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAGGGC 5250
                          i     i      vv    i  v  ii i      viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_73477587_7   5251 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5300
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_73477587_7   5301 AATGGTACAGAGCAGAGGCCTCAGAAATAATGCCACATATCTACAACTAC 5350
                              v i   iiv   ivii         vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_73477587_7   5351 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5400
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_73477587_7   5401 ATTTAATAAATGGTGCTGGGAAAACTGCCTAGCCATATGTGGAAAGCTGA 5450
                         v  i  i              v     vv  ?   i   iii  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_73477587_7   5451 AACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGATT 5500
                          ii    i    v   i     v     v        i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_73477587_7   5501 AAAGATTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAACCT 5550
                          ?   ii       v   v       i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_73477587_7   5551 AGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAAA 5599
                            ?i- v i -   iv   viv  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_73477587_7   5600 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5649
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_73477587_7   5650 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5699
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_73477587_7   5700 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5749
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_73477587_7   5750 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5799
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_73477587_7   5800 AACAAACAACTCCATCAACAAGCGGGCGAAGGATATGAACAGACACTTCT 5849
                         i     i   i v  i? v  ii    i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_73477587_7   5850 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 5899
                          v        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_73477587_7   5900 TCACTGGCCAT 5910
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


3665 23.10 2.01 0.67  chrX_73563666_73573423     3512  4407 (5351)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73563666_7   3512 TGGGAAGATATTCCATGTTGATGGGTTGGAAGAATCAATATTTTTAAAAT 3561
                            i       i       v    i        v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73563666_7   3562 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTACCAAAA 3611
                          v v     v      vii              i          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73563666_7   3612 TACCAA-TGTCATTCTTCAATAAACAGAAAAAA-AATCCTAAAATTTATA 3659
                          v   i-  i v  i  vv v   iv  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_73563666_7   3660 TGGAACCACAAAAGACCCAGAATAGCCAAAGCTATTCTGAGCAAAAAGAA 3709
                              vii   ii                 i v  ii   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_73563666_7   3710 CAAAACTGAAAGAATCACATTACCTGACTTTGAATTATACTATAGAGCTA 3759
                             ii  i i  v     i v  ii i  ii  viv     i i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_73563666_7   3760 TAGTAACCAAAATGGCATGGTACTGGCTTAAAAACAGACACACA--TCAG 3807
                         i     i   i ii ii          v   ii i     i i --   i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_73563666_7   3808 TGGAATAGAATAGAGAACCCAGAGATAAATCCATACATCTATAGTGAACT 3857
                                    v    ii     i     i        i   i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_73563666_7   3858 CATTTTTGACAAAGGTGCTAAGAACACACATTAGGGAAAGGACAATCTTT 3907
                         v     i     i     i    v  iv  v i       i i i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_73563666_7   3908 TCAATCAAAGGTGCTGGGGAAACTGAATATCCATTTGCCAAAGAATGAAA 3957
                             iv  v         iv     i   ?   iv   v          i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_73563666_7   3958 CTAGACCCCTATCTCTCGCTATGTACAAAAATCAAATAAAAGTGGATTAA 4007
                         i i        i   v i i  i         i  v v   i     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_73563666_7   4008 ACACTTAAGTCTAAGACCTCAACCTATGAAACTACTACAAGAAAACATTG 4057
                          v  i   i v     v  v  v    i     vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_73563666_7   4058 GGGAAAATCTCCAGGACATTATCCTAGGCAAAAATTTCTTGAGTAATACC 4107
                          ? v      i iv   v  ivvi       vii      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_73563666_7   4108 TCACAAGCACAGGCAACCAAAGCAGAAATGGACAAATC-----------A 4146
                         i  v       i     v    v i    i  i    i----------- 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_73563666_7   4147 AGTTAAAAGGCTTCTGCACAGCAAAGGAAACAACAAACAAAGTGAGGAGA 4196
                          i      i-   i  ii vv       v  v iv  v       ii   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_73563666_7   4197 CAACCCACAGAATGGGAGAAAATATTTGCAAACTACCCATCTGACAAAGG 4246
                                                         ii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_73563666_7   4247 ATTAGTAAGCAGAATATATAGAG--TTCAAACAACTCTATAGGAAAAAAA 4294
                          i v   vv           i  --i  vv       v   iv     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_73563666_7   4295 TCTAATTTAAAATCCAATT-AAAAATGGGCAATAGATTCAAATAGACATT 4343
                         - v   ----  i      -            vi    ii          
  L1M4_orf2#LINE/    800 -CAAAT----AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_73563666_7   4344 TCTCAAAAGAAGACATACCAATGGCAAACAGGCATATGAGAAGGTGCTCA 4393
                             v        i    v      v  i i   i    i   i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_73563666_7   4394 ACATCACTGATCAT 4407
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (128 / 76)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  

 483 28.28 11.62 2.02  chrX_73563666_73573423     6277  6474 (3284)    L1M4_orf2#LINE/L1        1   217 (691)  

  chrX_73563666_7   6277 TGGAAAGATATTCTGTGTTCATAGACTGGAAGACTCAACA-----AAGAT 6321
                                    i ii       i  i         i  i -----     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73563666_7   6322 ATCAAT----------TTGG---AAAAAACTGACATA--CGCTATCAAAA 6356
                         iv    ----------   i--- v i viii  ii -- v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73563666_7   6357 TACTAGCATTATATTTTTTTGGTAAGCATAAATGAGATTATTCTAAAATT 6406
                          v i   ---- iii     v i iiv  vi ii  v v  i        
  L1M4_orf2#LINE/    101 TCCCAGC----TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_73563666_7   6407 TATATGGAAAGGTAACAATACTAGAATAGTTACATTGATTTTGCA---GA 6453
                         i         v i  viivv i       ii v vii  i   v ---  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_73563666_7   6454 AGAATAAAGTGGGAGGAATCA 6474
                             i     v      v   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCA 217

Transitions / transversions = 1.95 (37 / 19)
Gap_init rate = 0.03 (6 / 217), avg. gap size = 4.50 (27 / 6)  

1553 21.72 8.83 0.95  chrX_73563666_73573423     6622  7040 (2718)    L1M4_orf2#LINE/L1      224   675 (233)  

  chrX_73563666_7   6622 CTGATTTTAAGAATTATTATT--GTTATAGTAATTAAGACTGTGTGGTAT 6669
                          ii    i  i v   i  iv-- i  i      i     v        i
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_73563666_7   6670 TAGTAGAGGAATAGATATATAGAACAATGGAATAGAATAGAGAAGCTTGA 6719
                          i i v i i     i       v              v    iv iv  
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_73563666_7   6720 CATAGTATGGCACACAATTATGACCAACTGATGTTTCACAAATGTGCAAA 6769
                         v   i- iv-  i   v     ii   i    v  iv    iv    v  
  L1M4_orf2#LINE/    324 AATAA-ACC-CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_73563666_7   6770 ATCAATTTGATTGAGAAATGATAAACTTTTCAACAAATGGTGCTGGAGTA 6819
                         iv v   ii  v i    vi   iv                     iii 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_73563666_7   6820 ATTGGCTATCCATAGGCAAAAA----------GAC--------------- 6844
                          i   v  ?   i v      i----------   ---------------
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_73563666_7   6845 ---ACAAAAATAAATTCAAAATGGATCATAGACTTAAATGTAAAATGTAA 6891
                         ---        v  i             ?    i         i vv   
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_73563666_7   6892 AACTACAACACTTTTAAAAGAAAACA--GGAGAAAATCTTCAGGACCTAG 6939
                              i  v   i   i         --  ? v        iv     v 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chrX_73563666_7   6940 AGCTTGGAGCAG-AGTTTCTTAGACATGACACCAAAAGCACAATTCACA- 6987
                         i -  i -   i-i          i                  viv   -
  L1M4_orf2#LINE/    572 GG-TTAG-GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_73563666_7   6988 --GTAAAAATA-ATAAACTGGACTTCACCAAAAGTAAAAACTTTTGTTTT 7034
                         -- v       -     i         i     v             vi 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_73563666_7   7035 GCAAAG 7040
                         v     
  L1M4_orf2#LINE/    670 TCAAAG 675

Transitions / transversions = 1.51 (53 / 35)
Gap_init rate = 0.02 (11 / 452), avg. gap size = 3.73 (41 / 11)  

 699 20.90 8.46 1.49  chrX_73563666_73573423     9057  9257 (501)    L1M4_orf2#LINE/L1      681   895 (13)  

  chrX_73563666_7   9057 TGTTAAGATGATAAAAAGACAAGCTACAC--TTGGAGAAAATATTTGCAA 9104
                          i i    vii i         v i   v-- v                 
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_73563666_7   9105 ATCACATACCTAACAAAAAACTCATATCCAGAATAT-TAAAAAA------ 9147
                             i   i  i i  iii   ii            -    i  ------
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_73563666_7   9148 -AA-------ATGGAAAAACCTCAAATAACCCAATTTAAAAGTGGGCAAA 9189
                         -  -------  ii   i  ---             ?    i        
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGAC---AAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_73563666_7   9190 AGACATAAAGAGACATTTCATTAAAGACAATATATGTATGGCACATAATC 9239
                         i  iv i  v         vii     vi     iiv     vv    v 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_73563666_7   9240 ACATGAAAAGATGTTCAA 9257
                                      i    
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAA 895

Transitions / transversions = 2.42 (29 / 12)
Gap_init rate = 0.02 (5 / 215), avg. gap size = 4.00 (20 / 5)  


2952 26.66 2.59 0.45  chrX_73640462_73645439     3597  4485 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73640462_7   3597 TGGAAACACACCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3646
                               v i i      i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73640462_7   3647 GACCATACTGCCATAAGTGATCTACAAATTCAATGCAATCCCCATTAAA- 3695
                          i v     v  vv  v         i      i        i  i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73640462_7   3696 TACCA-CTATCATTCTTCACAGAATTAGAAAAAACAGTTCTAAAATTCAT 3744
                          v   -  ii -  i  ii     v v  v  iviii i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_73640462_7   3745 GTGGAACGAAAAAAGAGCCTGCGCGATCAAAGCAAGACTAAGCAAAAAGA 3794
                         i     vviv  ii  v  v viiiii    i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_73640462_7   3795 ACAAATCTGGAGGCATCACACTACCTGATTTCAAAGTATACTATAAGGCT 3844
                              vi      vv       v  ii        iiv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_73640462_7   3845 ATAGTCACTGAAACAGCATGGTAGTGGTATAAAAATAGGCACATATACCA 3894
                          i   v iii i    ii     v   i    ii    i  i   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_73640462_7   3895 ATGGAACAGAATAAAAAAATGAGAAATAAACCCAAA----TACAGCCAAC 3940
                               i     vi i iviv             v ----  ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_73640462_7   3941 TGATCTTCGACAAAGCGAACAAAAATATCAAATGGAGAAAGGACATCCTT 3990
                             i        i vviv   i vi  iv     i     i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_73640462_7   3991 TTCAACAAATGGTGTTGGGAGAATTGGCCAGCCACATGTAGA-GAATGAA 4039
                                       i     v  i   vi ?       i i -       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_73640462_7   4040 ACTGGATCCTCGTCTCTCACCTTAGACAAAAATCAACTCAAGATGTATTA 4089
                         ii    i  iiii   v    v  v        i       i   v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_73640462_7   4090 AGGACTTAAACTTAAGACCTGAAACTATAAACATTCT-AGAAGATAACAT 4138
                         ?i   i    iv     v  i          - i   -      v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACAT 548

  chrX_73640462_7   4139 TGGAAAACCCCTTCTAGACATTGGCTCAGGCAAGGATTTCATGACCAAGA 4188
                         v  ?iv vvi    vv   v    v i      v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_73640462_7   4189 ACCCAAAAGCAAATGCAATAAAA--ACAAATA--TTAATTAAACT----- 4229
                         vv         v v    i    -- v     -- v    ii   -----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_73640462_7   4230 AAAG---AGATCCTCCACGGCAAAAGGAACAGTTATCAG---AGTAAACA 4273
                            i--- i v i iiii vivv  i i   -i     i---   i  v 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGAAAGTGAAAA 697

  chrX_73640462_7   4274 GAAAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAA 4323
                           v          i           v  ii   vii   i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_73640462_7   4324 GGACTAATATCCAGAATCTACAACAAACTCAAACAAATCAGTAAGGAAAA 4373
                              vi          v  i  vi     vv    v   i   vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_73640462_7   4374 AACCAAACAATCCCATCAAAAAGTGGGCTAAGGACATTAATAGACAATTC 4423
                         i  -   i  i  v  i?    i     v     iv v        v   
  L1M4_orf2#LINE/    798 GAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_73640462_7   4424 TCAAAAGAAAATATATGAATGGTCAACAAACATATGAAAAAATGCTCAAC 4473
                           v      i     ii     i   i  i  i       i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_73640462_7   4474 ATCACTAATGAC 4485
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.93 (27 / 14)  


3091 27.42 0.66 0.66  chrX_73690438_73693808.rev     1973  2880 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73690438_7   1973 TGGAAGAACATTCCATGCTCATGAGTAGGAAGAATCAATATCGTGAAAAT 2022
                              ii i  i     i     ii v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73690438_7   2023 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGACATACCCATCAAGC 2072
                            v     v     iv i  i  i        i vv  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73690438_7   2073 TACCAATGACTTTCTTCACAGAA-TTGGAAACAA-CT-ACTTTAAAGTTC 2119
                          v   iivi i  i  ii     -   ---    -  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_73690438_7   2120 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 2169
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_73690438_7   2170 GAACAAAGCTGGAGTCATCATGGTACCTGACCTCAAACTATACTACAAGG 2219
                                 i     vvv   iiv v  ii ii     viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_73690438_7   2220 CTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGAC 2269
                                  i   i    iii        i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_73690438_7   2270 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 2317
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_73690438_7   2318 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 2367
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_73690438_7   2368 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2417
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_73690438_7   2418 TGAAACTGGATCCCTTCCTTACAACTTATACAAAAATTAATTCAAGATGG 2467
                             ii    i    v   i   v v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_73690438_7   2468 ATTAAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2517
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_73690438_7   2518 CCTAGGCA-ATACCATTCAGGACATAGGCACAGGGAAGGACTTCATGACT 2566
                          v    ?i- v i -   iv   v v  vvi   v  v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_73690438_7   2567 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 2616
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_73690438_7   2617 AATTCAACTAAAGAGCTTCTGCACAGTGAAAGAAACCACCATCAGAGTGA 2666
                         v  iv  v v  i i   i  ii vvii  i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_73690438_7   2667 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 2716
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_73690438_7   2717 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 2766
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_73690438_7   2767 AAAAACAAACAACCACATCAAAAAGTGGGCAAAGGACATGAACAGACACT 2816
                            i     i    vv  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_73690438_7   2817 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 2866
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_73690438_7   2867 CCATCACTGGCCAT 2880
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3089 28.21 0.88 0.44  chrX_73698071_73704474     5008  5911 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73698071_7   5008 TGGAAGAACATTCCATGCTCATGAGTAGGAAGAATCAATATCGTGAAAAT 5057
                              ii i  i     i     ii v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73698071_7   5058 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCACCATCAAGC 5107
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73698071_7   5108 TGCCAATGACTTTCTTCACAGAA-TTGGAAACAA-CT-ACTTTAAAGTTC 5154
                          v   iivi i  i  ii     -   ---    -  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_73698071_7   5155 ATATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAA 5204
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_73698071_7   5205 GAACAAAGCTGGAGTCATCATGGTACCTGACTTCAAACTATACTACAAGG 5254
                                 i     vvv   iiv v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_73698071_7   5255 CTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGAC 5304
                                  i   i    iii        i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_73698071_7   5305 CAATGGAACAGAACAGAGGCTTCAGAAATAACACCACACATCTACAACTA 5354
                                 i    iv   iv i         vv   i    i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_73698071_7   5355 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5404
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_73698071_7   5405 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCTG 5454
                          v  i  i              v      v  ?   v   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_73698071_7   5455 AAACTGGATCCCTTCCTTATGCCTTATATAAAAATTGATTCAAGATGGTT 5504
                           ii    i    v   i ii  v    i       i i    i    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_73698071_7   5505 TAAAAACTTAAAAGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5554
                         i ? i  i    v  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_73698071_7   5555 TAGGCA-ATACCATTCAGGACATAGGCACGGGGAAGGACTTCATGACTAA 5603
                             ?i- v i -   iv   v v  vvii  v  v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_73698071_7   5604 AACACCAGAAGCAATGGCAACAAAAGCCAAAATAGATAAATGGGATCTAA 5653
                         i      i     vvi          vv             v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_73698071_7   5654 TTAAACTAAAGAGCTTCTGAATGGCAAAAGAAACTACCATCAGAGTGAAC 5703
                          i   v v  i i   i  viivv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_73698071_7   5704 AGGTAACCTATAGAATGGGAGAAAAGTTTTGCAATCTACCCATCTGACAA 5753
                           ii    i i              vv       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_73698071_7   5754 AGGGCTAATGTCTAGAATCTGCAAAGAACTCAAACAAATTTACAAGAAAA 5803
                         i  i  vi i  i     v ii         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_73698071_7   5804 AAACAAA---CCCA-TCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5849
                          i     ---    - i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_73698071_7   5850 TCTAAAGAAGACATGTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5899
                           i        i  ii viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_73698071_7   5900 GTCACTGGCCAT 5911
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (155 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


2965 27.01 3.05 0.45  chrX_73715063_73720693     4254  5138 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73715063_7   4254 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4303
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73715063_7   4304 GGCCATACTGCCCAAGGTAATTTATAGGTTCAATGCCATCCCCATCAAGC 4353
                            v     v     iv i  i  i  i     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73715063_7   4354 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4401
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_73715063_7   4402 TATAGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCA-AAG 4450
                            i   viiv  ii  v  viv  v     iv     i i ivv -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_73715063_7   4451 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4500
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_73715063_7   4501 TACAGTAACCAAAACAG--------------------AGA--TATAGATC 4528
                                 i   i    --------------------   --        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_73715063_7   4529 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 4576
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_73715063_7   4577 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATTGGGAAAGGATTCC 4626
                          vi    i  i     ivv  vv  i v  vv    v       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_73715063_7   4627 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCT 4676
                           v  i  i              v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_73715063_7   4677 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4726
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_73715063_7   4727 TTAAAGAGTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4776
                          i ?   vi    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_73715063_7   4777 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4826
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_73715063_7   4827 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4876
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_73715063_7   4877 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAAC 4926
                          iv  v v  i i   i  ii vv    i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_73715063_7   4927 AGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4976
                           i         i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_73715063_7   4977 AGGACTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 5026
                         i     vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_73715063_7   5027 AAACAAACAACCACATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5076
                          i     i    vv  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_73715063_7   5077 TCTAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5126
                           i        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_73715063_7   5127 ATCACTGGCCAG 5138
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.88 (31 / 8)  


3242 27.09 0.44 0.44  chrX_73792082_73798356.rev     4877  5784 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73792082_7   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATTGTGAAAAT 4926
                              ii i  i     i      i v      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73792082_7   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73792082_7   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_73792082_7   5025 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_73792082_7   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTGTACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_73792082_7   5125 TACAGTAACCAAAACATCATGGTACTGTTACCAAAACAGAGATATAGATC 5174
                                 i   i   vii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_73792082_7   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5222
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_73792082_7   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_73792082_7   5273 CTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_73792082_7   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_73792082_7   5373 TTAAAGAGTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?   vi    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_73792082_7   5423 CTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAA 5472
                         v    ?i v viv   iv   viv  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_73792082_7   5473 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5522
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_73792082_7   5523 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5572
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_73792082_7   5573 AGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5622
                           i         i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_73792082_7   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 5672
                         i  i  vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_73792082_7   5673 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5722
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_73792082_7   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5772
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_73792082_7   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2868 25.08 3.11 2.55  chrX_73820226_73822220      602  1502 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_73820226_7    602 GAAAAACATTCCATGCTCATGAATAAGAAGACTCAATAATGTTAAAATGG 651
                             i i  i     i     i  vi       i    v      i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_73820226_7    652 CTATACTGCCCAAAGTAATTTAAAGATTCAATGCTATTCCTATGAAACCA 701
                          v     v      v i  i  v        i  v  i     v   viv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_73820226_7    702 CCAATGACATTTTTCACAGAATTAAAAAAAAATTATAAAAAAAATTATAA 751
                            iivi v     ii     ----------   ivv  ivvi  iv   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAA----------ATTGACAAGCTGATCCTAA 142

  chrX_73820226_7    752 AAAAAACTTATAAAATTCAGAACCAAAAAAGAGCCCAAATAGCCAATGCC 801
                           ----i i   -----ii   viiv  ii  v  vi         vi v
  L1M4_orf2#LINE/    143 AA----TTCATA-----TGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_73820226_7    802 ATCCTAAGCAAAAAGAACAAAGCTGGAGGTATCACACTACCTGATTTCAA 851
                            i i iv  i          i      vv       v  ii       
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_73820226_7    852 ACTATACTACAAGGTTACAGTAACCAAAACA---TGGTACTGGTACAAAA 898
                          viv        i i        i   i   ---         i i  ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_73820226_7    899 ACAGACACATAGACCAA-GGAATCAGGTTAAAGAACCTAGAAATAAAGCC 947
                          i     i     i   -     -  iv vi   ii i         v  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAAT-AGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_73820226_7    948 GCACACCTACAACCATCTGATCTTCAACAGTGTCAACAAGAACAAGCAAT 997
                         ii   ii  iiii  vi    i   i   iv viiv     v  vv    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_73820226_7    998 GGGGAAAGGACTCCCTATTCAAAAAATGGTGATGGGATAACTGGCTAGCC 1047
                                 i ivvi  v     v        v     i      v  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_73820226_7   1048 ATGTGCAGAAGATTAAAACTGGACCTCTTCCTTTCACCATATACAAAAAT 1097
                          ii    i    v i  ii      i  v   iv                
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_73820226_7   1098 CAACTCAAGATGGATTAAAGACTTAAATGTAAATCCTAAAACTATAAAAA 1147
                         i       i      i ?    i         ivv              v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_73820226_7   1148 CCC-AGAAAATACCAT---------TCT----GAACACAGGTCCTGGCAA 1183
                         i i-    i v v   ---------   ----  v vii   iv-     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA-GGCAA 581

  chrX_73820226_7   1184 AGATTTCAT-GATGAAGACCTCAAAAGGAATTATAACAAAAACAAAAATT 1232
                         v i    v -   - v   vi      v vvvii       iv      v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_73820226_7   1233 GACATGTGGGACCTAATTAAA-CTAAAGATTTTCTGCACAGCAAAAGAAA 1281
                           i vi v    i v  i   -i    i i   -  ii vv    i  v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACA 679

  chrX_73820226_7   1282 CTATTAACAAAGTAAACAGACAACTCACAGAATGGGATAAAATATTTGCA 1331
                             i  v     i  v       i            v            
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_73820226_7   1332 AACTATGCATCTGACAAAGGTCTAATATCTAGCATCTATAAGGAACTT-- 1379
                           ii  ii      i  i  v  vi    i  v  v     i     i--
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_73820226_7   1380 --AAATCAATGAGCAAAAAACAA----CCCCATTAAAAAGTAGGCAAAGA 1423
                         --  v     i vv    i    ----   v   ?    i i       i
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_73820226_7   1424 ACATGAAGAGACACTTTTCAAAACAAGACATGCATGTGGCCAACAAGCAT 1473
                          iv    v     i  i  v   v    i  i  vi       i     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_73820226_7   1474 ATGAAAAAATGCTCAACATCACTAATCAT 1502
                                i             ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 3.19 (51 / 16)  

1344 28.86 0.25 0.50  chrX_73820226_73822220     1594  1995 (0)    L1M4_orf2#LINE/L1      268   668 (240)  

  chrX_73820226_7   1594 TGGTACTGGTACCAAAACAGATATATAGACCAACGGAACAGAACAGAGGC 1643
                                  i iv ii i   i       i   i    i    iv   iv
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_73820226_7   1644 CTCAGAAATAACACCACACATCTACAACCATCTGATCTTTGACAAACCTT 1693
                         ii         vv   i    i  iiii  vi    i  i     ivv v
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_73820226_7   1694 ACAAAAACAAGAAATGGGAAAAGGATTCCCTATTTAATAAATGGTGTTGG 1743
                         v   i v  vvv      i    i  vvi  v  i  i        i   
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_73820226_7   1744 AAAAACTGGCTAGCCGTATGTAGAAAGCTGAAACTGGATCCCTTCCTTAC 1793
                         i v      v  ?  ii   i i  iiv    ii    i    v   i  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_73820226_7   1794 ACCTTGTACAAAAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGAC 1843
                            v i            i    i      i ?    i       v   v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_73820226_7   1844 CAAAAACCATAAAAACCCCAGAAGAAAACCTAGGCA-ATACCATTCAGGA 1892
                          v     i      vi ii          v    ?i- v i -   iv  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGA 566

  chrX_73820226_7   1893 CATAGGCATGGGCAAGGACTTCATGACTAAAACACCAAAAGCAATGGCAA 1942
                          v v  vv i     v ii   v iiv  vi            vvi    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_73820226_7   1943 CAAAAGCCAAAATAGACAAATGAGATCTAATTAAACTTAAAGAGCTTCTG 1992
                               vv        i    vi  ii v  i   v     i -   i  
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTG 665

  chrX_73820226_7   1993 CAC 1995
                         ii 
  L1M4_orf2#LINE/    666 TGC 668

Transitions / transversions = 1.57 (69 / 44)
Gap_init rate = 0.01 (3 / 401), avg. gap size = 1.00 (3 / 3)  


3632 23.90 1.10 1.10  chrX_73832158_73836952.rev     3397  4304 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73832158_7   3397 TGGAAAGATATTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 3446
                                    i                     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73832158_7   3447 GTTTGTAGTACCCAAAGCAATCTGTAGATTCAATGCAATCCTTATCAAAA 3496
                          vivi  v v      vii    ii        i       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73832158_7   3497 TACCAGTGACATTTTTCACATAATTTTTTTTTAA----AACCTAAAGTTT 3542
                          v    ivi v     ii  v  v  vvi---  ---- v      i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC---AAGCTGATCCTAAAATTC 147

  chrX_73832158_7   3543 ATTTGGAACCACAAAAGTCTCAGAATTGCCAAGGCTATCTGGAGCATAAA 3592
                           v     vii   ii v i      v     ii v    v  iv vi  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_73832158_7   3593 GGACAAAACTGAAGGAATCACATTACCTGAGTTCTTCAAGTTATACTATA 3642
                          i     ii  i    v     i v  ii ---i     iviv     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAA---TTTCAAAACTTACTACA 244

  chrX_73832158_7   3643 GAGCTATGGTAACCAAAACAGCAAGGTACTGGCATGAAAACAGACACATT 3692
                         i     ii    i   i    iiv           i ii i     i  v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_73832158_7   3693 GATCAATGGAACAGAATAGAGAACCCAGAAATAAATCCATACACCTATGA 3742
                                    i     v    ii           i       ii    i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_73832158_7   3743 TGAGCTCGTGTTCGACAAAGATGCCAAGAACATACAATGGAGAAAGGACT 3792
                          v ii vi v        i i        v   v      i     i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_73832158_7   3793 GTCTTTTCAATGAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGA 3842
                                   ii             v         ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_73832158_7   3843 ATGAAACTTGATCCCCATCTCTTGCCATATACTAAAATGAAATCAAAATG 3892
                              ii v  i   i i   vii        v     v  v        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_73832158_7   3893 GATTAAAGACTTAAATCTTAGACCTCAAACTATGAAACTACTACAAGAAA 3942
                            i ?    i     v v   v  v       i     vi  v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_73832158_7   3943 ACATTGGAGAAACTCTCCAGGACATTGGTCTGGGCAAAAATTTCTTGAGT 3992
                             v  ? v  v   i iv   v    vi i     vii      iii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_73832158_7   3993 AATACTCCACAAGCATAGGCAACCAAAGCAAAAGTGGACAAATGGGATCA 4042
                          vv  v   v     i i     v    v    i i  i    v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_73832158_7   4043 TATCAAG-TTAAAAAGATTCTGTACAGCAAAGGAAACAATCAACAAAGTG 4091
                         i     i-       v-  i   i vv       v  v     v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_73832158_7   4092 AAGAGACAACTCACGGATTAGGAAAAAATATTTGCAAACTACCCATCTGA 4141
                           i       i   i  v i   i              ii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_73832158_7   4142 CAAGGGATCAATAACCAGAATA-----AGAAGCTCAAACAACTCCATAGG 4186
                         i      iivi  v        -----    -   vv       v   iv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATAAT 792

  chrX_73832158_7   4187 AAAAAAAATCTAATAATCAGATTTAAAAACTGACAGAAGATTTGAACAGA 4236
                              i -- v     i vi   ?     iv i  i i        i   
  L1M4_orf2#LINE/    793 AAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_73832158_7   4237 CATTTCCAAAAAGAAGAAATATAAATGGCAAACAGGAATATGAAAAGGTG 4286
                               ivv        v   i       v  i i v i        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_73832158_7   4287 CTCAACATTATTGATCAT 4304
                                 i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (129 / 84)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.50 (20 / 8)  


2606 24.85 1.44 7.94  chrX_73842522_73847736.rev     3755  4724 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_73842522_7   3755 GGAAAAACATCCCATGCTCA--GCTGGGAAGAATCAATGTCATTAAAATT 3802
                              i i        i   -- v v      v i   i ii    i  v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_73842522_7   3803 ATCATACTGCCCAAAGCAACTTACAGATTCAATTCTATTCCTATCAAACT 3852
                         iiv     v      vii ii           iv v  i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_73842522_7   3853 ACCAATGACATTCTTCACAGAATTAGAAAAAACT-ATTTTAAAATTCATA 3901
                         v   iivi v  i  ii     v v  v  i-  -  ii           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chrX_73842522_7   3902 TGGAACCAAAATAGAGCCTGAATATCCAAGACAATACTAAGCAAGAAGAA 3951
                              viiv  vi  v  v     v    i     vi i iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_73842522_7   3952 CAAACCTGGAGGTATCACATTATCTGACTTCAAACTATACTACAGGGCTA 4001
                             vi      vv     i vi ii i      viv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_73842522_7   4002 CAGTAACCAAAACAGCATGATACTGGTACAAA-ACAGGCACATAGAACAG 4050
                               i   i    ii  i      i i  i- i  i  i     v  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_73842522_7   4051 TGGAACAGAATAGAAAGCCCAGAAGTGAGGCCTTTCACCTACAACCATCT 4100
                              i     v  i  i      i i iv  v v  ii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_73842522_7   4101 GATCTTGGACAAACCTGACAAAAACAAGCAATTGGGAAAAGACT--TCCT 4148
                            i  v     ivv  v   i v  vv    -   i     v --  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTT 399

  chrX_73842522_7   4149 ATTCAATAAATAGTGACGAGATAACTGGCTAGCCATATACAGAAGATTGA 4198
                         -     i    i   vi i  i      v  ?   i  i  i    v   
  L1M4_orf2#LINE/    400 -TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_73842522_7   4199 AACTGGACACCTTCCTTACACCATATACAAAA-CTAAC--AAGATGGATT 4245
                          ii     v   v   i               -i    --  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_73842522_7   4246 AAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGACAACCT 4295
                          ?    i         i v i            vi i i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_73842522_7   4296 AGGCA-ATACCATCCTAGACATAGGAATGGCCAAAGATTTCATAACAAAG 4344
                            ?i- v i v  v -   v v  iv i v   v i    v  ivv v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_73842522_7   4345 ACACCAAAGGCAATTCCAACAAATGCAAAAATTGACAAGTGGGATCTAAT 4394
                                 i   vvvv       v v      v  i  i v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_73842522_7   4395 TAAACTTAAGGGCTTCTGCACCACAAAAGAAACTATCAACAGAGTAAAGA 4444
                         i   v    iii   i  ii iv    i  v        v i   i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_73842522_7   4445 AACAACCTGCAGCTGAGCATCCCAGCGGAGCATGGGATGTTTTTCCCTTT 4494
                         i      i------------------------------------------
  L1M4_orf2#LINE/    698 GACAACCC------------------------------------------ 705

  chrX_73842522_7   4495 ATTTGTGTCCTCTCTGATTTTTTTGCAACCTACAGAATGGGAGAACATAT 4544
                         -------------------------------              v    
  L1M4_orf2#LINE/    706 -------------------------------ACAGAATGGGAGAAAATAT 724

  chrX_73842522_7   4545 TTGCAAACCATGCATCTGACAAAGGTCTCATAATCAGCATCTATAGGGAA 4594
                                i   ii      i  i  v  ii  vi   v  v    ii   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_73842522_7   4595 CTTACACAAATTTACAAGAGAAAAACAA----CCCCACTTAAAAGTGGGC 4640
                           ivi    v iv i  v i   i    ----   v i ?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_73842522_7   4641 AAAGGATATGAACAGACAGTTCTCAAAAGAAGACATACATGCAGCCAACA 4690
                                v    i     v     v        i     viii     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_73842522_7   4691 AGCATATGAAAAATAGCTCAAAATCACTGATCAT 4724
                             i       ivv      v    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 7.00 (91 / 13)  


2913 26.50 1.77 1.11  chrX_73863401_73874080     6598  7499 (3181)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73863401_7   6598 TGAAAAAACATTCCATGCTCATGGATAGAAAGAATCAATATCATGAAAAT 6647
                           i   i i  i     i        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73863401_7   6648 GGCCACACTGCCCAAAGTAATTTATAGATTCCACGCTATTACCATTACAC 6697
                            v i   v      v i  i  i      v    v  iv i  i v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73863401_7   6698 TACCATTGACATTCTTCACAAAAGTAGAAAAAACT-ACTTTAAAATTCGT 6746
                          v   vivi v  i  ii  i  i v  v  i-  - iii        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_73863401_7   6747 ATGGAACCAAAAAAGAGCCCGTATAGCCATGACAATCCTAAGCAAAAAGA 6796
                               viiv  ii  v  v v       vi      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_73863401_7   6797 GCAAAGCTGGAGGCATCACATCATGCCACCCAACTTCAAACTATACTACA 6846
                         i     i      vv     ----- iv     i      viv       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACA-----CTTCCCAATTTCAAAACTTACTACA 244

  chrX_73863401_7   6847 AGGCTACAGTAACCAAAGCAGCATGGTACTGGTACAAAAACAGACACATA 6896
                          i          i   ii   ii         i i  ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_73863401_7   6897 GACCAATGGAACAGAATAGAGATCTCAGAAATAAGACCACACATCTACAA 6946
                           i        i     v    vii         iv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_73863401_7   6947 CCATCTGATCTTCAACAAACTTGACAAAAACAAGCAATGAAGAAAGGA-A 6995
                         i  vi    i   i    ivv  v   i v  vv     ii     i - 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_73863401_7   6996 TCCTTATTCAATAAATGGTGCTGAGATAACTGGCTAGCCATGTGCAGAAG 7045
                         vi   -     i           i  i      v  ?   ii    i   
  L1M4_orf2#LINE/    395 GTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_73863401_7   7046 ATAGAAACTGGACCCCTTCCTTACACCATATACAAAA--TATGCTGAAGA 7093
                          vv   ii         v   i               --  -i  v  i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA-ACTCAAAA 492

  chrX_73863401_7   7094 TGGACTAAAGACTTAAATGTAAAACCCAAAACTATATAAAACCTGGAAGA 7143
                             ii ?    i         i v i         v  vv i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_73863401_7   7144 CAACCTAAGCA-ATACCATTCAGGAC-TTGGACACAGGCAAAGATTTAAT 7191
                         v   v  i ?i- v i -   iv   -    ii-i      v i   vv 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTT 590

  chrX_73863401_7   7192 GACAAAGACATCAAAAGCAATGGCAACAAAAGTAAAAATTGACAAGTGTG 7241
                         iivv v    i        vvi          v      v  i  i vv 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_73863401_7   7242 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGA 7291
                          ii v  i   v v  i i   i  ii vv    iv v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_73863401_7   7292 GTGAAGAGACAACCTACAGAATGGGAGAAATTTTTTGCAATCTCTCCATC 7341
                              i        i               v v       viiv vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_73863401_7   7342 TGACAAAGGTCTAATATCCAGAGTCTACAAGGAACTTAAACAAATTTATA 7391
                            i  i  v  vi        i v  i  i     ivv    v iv   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_73863401_7   7392 AGAAACAGA-AAAT--CCCG-TTAAAAAGTGGGCAAAGAAC----ATGGA 7433
                          v   v   -    --   i-  ?    i         i i----  i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_73863401_7   7434 CACTTCTTAAAAGAAGACACTCACATGGCCAA-GAG-ACATGAAAAAAAG 7481
                           i    iv        i iv  v        -i  -         i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_73863401_7   7482 CTCAATAGCACTGATCAT 7499
                              i v  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.53 (26 / 17)  

3230 24.94 1.55 0.89  chrX_73863401_73874080     9286 10187 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73863401_7   9286 TGGAAAGATATATCCATGTTAATGGATTGCAAGAATCAATAATGTTAAAA 9335
                                    -i       v        v    v i    v      i 
  L1M4_orf2#LINE/      1 TGGAAAGATAT-CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_73863401_7   9336 TGTCTATACTACCCAAATAAATCTACAGATCCAATGCAATCCCTATCAAA 9385
                           v v     v       vi          i   i               
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_73863401_7   9386 ATACCAATGACATTATTCACAGAAATAGAAAAAAAAATCCTAAAGTTTAT 9435
                           v   iivi v  v  ii       v  v  ivvi        i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_73863401_7   9436 CTGGAACCAAAACAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAAAGA 9485
                         v     viiv  vi                 i v   i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_73863401_7   9486 ACAAATCTGAAGGAATCACATTATATTAATTTCTCAAATTATACTACAGA 9535
                              vi  i    v     i - vii      -v   i -       i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACT-TCCCAATTTC-AAAACT-TACTACAAA 246

  chrX_73863401_7   9536 GCTATAGTAACCAAAAGAGCACTGTATTGTCATAAAAAACAGATACATAT 9585
                             i     i   i v  iiiv   i  v     ii -i   i i   v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAG 295

  chrX_73863401_7   9586 ATCAGTGGAACAGAATAGAGAACCTCAAGA-AAATCCATACATCCACAGT 9634
                             i     i     v    ii ivi i -   i        ii ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_73863401_7   9635 GAACTCATTTTTGACAAAGGTGCCAAGAATATACATTGGAGAAAGGAGAG 9684
                         v  i v     i     i          vi  v  v   i     i v  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_73863401_7   9685 TATCCTCAATAAACGGTGCGGGGA-AACTGGATATCCATATACAGAAAAA 9733
                          v ii    i   i     v    -         ?   i  i  i  i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_73863401_7   9734 GGAAACTTGACCCCCCATCTCTCATCATATACAAAAATCAAATCAAAATA 9783
                         v   i-   iv    i i   v  i             i  v       i
  L1M4_orf2#LINE/    446 TGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_73863401_7   9784 GATTAAAGACTGAAATCTAAGACCTCAAGCTATGAATCCACTA----AAA 9829
                            i ?    iv    v     v  v  i    i  v ivi  ----   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_73863401_7   9830 ACCTTGAGGAAACTCTCCAGGACATCAGTCTGTGCAAGGATTTCT-AGAG 9878
                           v v i? v  v   i iv   v ii vi iv    v i     -   -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA- 593

  chrX_73863401_7   9879 TAATACCCCACAAGCACTGACAACCAAAGCAAAAATGGACAAATGGGGTC 9928
                           vv  v   v      vii    v    v      i  i    v  iii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_73863401_7   9929 ACATCAAGCTGAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTG 9978
                         v      iv v    i   i  ii vv       v  v     v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_73863401_7   9979 AAAGGGTAACCCACAGAACAGGAGAAAATATTTGCAAAATACCCATCTGA 10028
                            i ii           ii                  vi ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_73863401_7  10029 CAAGGGATTAATAACCAGAATATATAAGGAGCTCAATCGACTTTACAGGA 10078
                         i      i vi  v             i  i   vvv i   iv i iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_73863401_7  10079 AGAAATCTAATAATCTGAATAAAAAATGGGCCATAGATCTGAACAGACAT 10128
                          i  iv v     i ii v ?          v vi   i    i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_73863401_7  10129 TTCTCAAAACAAGACATACAAATGGCAAACAGGTACAATG-------GCT 10171
                              v   v    i           v  i i i   -  -------   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA-TGAAAAGATGCT 892

  chrX_73863401_7  10172 CAACATCATCAATCAT 10187
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (129 / 92)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


3257 26.98 0.44 0.44  chrX_73876099_73882371.rev     4875  5782 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73876099_7   4875 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4924
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73876099_7   4925 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4974
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73876099_7   4975 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 5022
                          v   iivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_73876099_7   5023 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCTAAAAG 5072
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_73876099_7   5073 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5122
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_73876099_7   5123 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5172
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_73876099_7   5173 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5220
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_73876099_7   5221 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5270
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_73876099_7   5271 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCT 5320
                           v  i  i              v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_73876099_7   5321 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5370
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_73876099_7   5371 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5420
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_73876099_7   5421 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5470
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_73876099_7   5471 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5520
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_73876099_7   5521 TTCAACCAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5570
                          iv  viv  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_73876099_7   5571 AGGCAGCCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5620
                           i  i  i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_73876099_7   5621 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5670
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_73876099_7   5671 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACATTTC 5720
                          i     i     v  i?    i    ii     iv    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_73876099_7   5721 TGAAAAAAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5770
                          vv   i    i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_73876099_7   5771 ATCACTGGCCAT 5782
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3193 27.21 0.88 0.44  chrX_73884518_73890914     5001  5904 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73884518_7   5001 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGACAAT 5050
                              ii i  i     i      i v      v i     ii v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73884518_7   5051 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5100
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73884518_7   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5148
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_73884518_7   5149 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5198
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_73884518_7   5199 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5248
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_73884518_7   5249 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5298
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_73884518_7   5299 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCGTATGTACAACT 5346
                                i    i--    i  --        vv  iiii  v  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_73884518_7   5347 ATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5396
                          vi    i  i     i v  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_73884518_7   5397 CTATTTAATAAATGGTGCTGGAAAAACTGGCTAGCCAGATGTAGAAAGCT 5446
                           v  i  i            i v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_73884518_7   5447 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5496
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_73884518_7   5497 TTAAAGACTTACAGGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5546
                          i ?    i  v v  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_73884518_7   5547 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCGAA 5596
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_73884518_7   5597 AACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTAA 5646
                         i            vvi   i      vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_73884518_7   5647 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 5696
                          i   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_73884518_7   5697 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5746
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_73884518_7   5747 AGGGCTAATATCCAGAATCTACAATGAACTC----AAATTTACAAGAAAA 5792
                         i  i  vi          v  i  v      ----  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_73884518_7   5793 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATTAACAGACACTTC 5842
                          i     i     v  i?    i     i      v v  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_73884518_7   5843 TCAAAAGAAGACATTTATTCAGCCAAAAAACACATGAAGAAATGCTCATC 5892
                           v        i  vi vvii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_73884518_7   5893 ATCACTGGCCAT 5904
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2999 28.89 0.22 0.11  chrX_73940653_73945094.rev     3045  3951 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73940653_7   3045 TGGAAAAACATTCCATGCCTATGGATAGGAAGAAGCAATATATTAAAAAT 3094
                               i i  i     iii      v      vvi     vv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73940653_7   3095 TGCCATGCTGCCCAAAGAAATTTACAGATTAAATGCTATTC-TATCAAAC 3143
                         v  v  i  v      vvi  i        v  i  v  i -       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73940653_7   3144 TATCAATGACATTCTTCAAAGAATTAGAAAAATCTATTTTAAAATTGATA 3193
                          vi  iivi v  i  iiv    v v  v  iiiv  ii       v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_73940653_7   3194 TGGAACCAAAAAAGAGCCAGAATAGCCCAGGCAATCCTAAGTAAAAAGAA 3243
                              viiv  ii  v           v ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_73940653_7   3244 CGAAGCTGGAGGTATCACATTATCTAACTTCAAACTGTACTAAAAGGCTG 3293
                          i   i      vv     i vi i  i      viv     v  i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_73940653_7   3294 TAGTTACCAAAACAGAATGATACTGGTACAAAAACAGACACATAGACCAA 3343
                         i   v i   i    vi  i      i i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_73940653_7   3344 TGAAACAGAACAGAGAACCCAGAAATAAGGCCACACACCTACAACCATAT 3393
                           i  i    iv    ii          iv   i   ii  iiii  vv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_73940653_7   3394 GATCTTTGACACAGCAGGCAAAACCAGACAATAGGGAAAGAATGCTCTAT 3443
                            i  i    vi vv v   i    vv    i          iv   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_73940653_7   3444 TCAATAAATGGTGGTGAGATAACTGGCTAGCCATATGCAAAGGATTGAAG 3493
                             i        v  i  i      v  ?   i       i  v     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_73940653_7   3494 CTGGACCTCTTTCTTACACCATACAATGAAATAAACTAAAGATGGATTAA 3543
                         i      i  vi  i        i vvi    v    v  i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_73940653_7   3544 AGACTTAAATGTAAAACCTACAAGTATAAAAATCCTGGAATATGACCTAG 3593
                             i         i v   v  v       v  i i   v vi  v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_73940653_7   3594 GAA-ATACCATTCTTGACATAGGATCTGGCAAAGATTTCATGTGGAAGAT 3642
                          ?i- v i -   v    v v  i iv     v i    v iviv v  i
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_73940653_7   3643 GCCAAAAGCAATTGCAACAAAAACAAAATTTGACAAATAGGATCTAATTA 3692
                         i         vvv         iv    v v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_73940653_7   3693 AACTAAAGAGTTTCTGCATAGCAAAAGAAACTATCAACAGATTAAACGGA 3742
                           v v  i ii  i  iiivv    i  v        v i v i  vi  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_73940653_7   3743 CAGCCTACAGAATGGGAGAAAATATTAGCAAACTATGCATGTGACAAAGG 3792
                           i  i                    v     ii  ii  v   i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_73940653_7   3793 TCTAATATCCAGAATCTGTAAGGAATTTAAACAAATTTGCAGGCAAAGAC 3842
                         v  vi          v i   i   i ivv    v ivii ivv   iiv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_73940653_7   3843 CAAACAACCCCATTAAAAGATAGGCAAAGGACATGAAAAAACACTTTTCA 3892
                             i     v   ?   i  i         iv    v i   i  i  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_73940653_7   3893 AAAGAAGACATACACACAGCTAACAAGCATATGAAATAATGCTCAACATC 3942
                                 i     v ii  i  i     i      vi            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_73940653_7   3943 ACTAATTAT 3951
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.41 (151 / 107)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.00 (3 / 3)  


3923 17.22 8.97 0.36  chrX_73945784_73947855.rev      746  1581 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73945784_7    746 TGAAAAGACATCCCATGTTCATGGATCAAGAATTTTAGTATTGTTAAGGT 795
                           i     i                 iiii ivi   i          i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73945784_7    796 GGCAATACTCCTCAAATTGATCTATAGA-----------CCCCATCAAAA 834
                                    i            i   -----------   i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73945784_7    835 TTCCAGCTGGATTCATTACATGAATTGACAAGCTGATCATAAAATTTATA 884
                          i       vv  iv  i  vi                v       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_73945784_7    885 AGAAAATTCAAG--------AAT--CCAAAACATTCTTGAAAAAGAAAAA 924
                         v i    v    --------   --        v             i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_73945784_7    925 ---AGCTAGAGGATGCACACTTCCTGATTTCAAAATTTACTACAAAGATA 971
                         ---  i i     iv         ii         i           v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_73945784_7    972 CAGTAATCAAGACAGTGTGGTACTGGTTTAAAAATAGAAATATAAATCAG 1021
                                                   iv   ii     v     i    i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_73945784_7   1022 TGGAATGCAATTGAGAGTC-----------------ATTT---------- 1044
                               iv           -----------------    ----------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_73945784_7   1045 GCTTTTCAATAAGAGTACCAGGACAATCTGATGGAGAAACAA--GTCTTT 1092
                          v     i i   i  i   i   v  iii    i    v  --      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_73945784_7   1093 TTCTCAACACATGGTACTGGGACAACTGGATATTCATCTGCAAAATAATG 1142
                          ---     v     i                ?i  iv       v    
  L1M4_orf2#LINE/    401 T---CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_73945784_7   1143 TGGCTGGATGCCTACCTCACCCCTTGTAAAAACATTAAGTCGAA-TCGAT 1191
                         vi i    iv          v  v i  v   v     v  i  - v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_73945784_7   1192 CATAGACTTACATGTAAGTGCTAAAGCTATAAAACTCTTAGAAGAAAACA 1241
                           ?    i  v       v      i                        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_73945784_7   1242 TATACATAAATCTTTGTG------GATTAGACAATAGTTTCTGAGATATG 1285
                           vi?i        i   ------ i    i    i      v       
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_73945784_7   1286 ACATCAATAGCACAAGGGGAGAAAGCAGAAATAGATAAATTGGACTTCAT 1335
                            i   v        viivi    v i                      
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_73945784_7   1336 AAAAATTAAGGTCTTTTGTGTGT----------TGTCAAGAAAGTAAAAT 1375
                         v        iiv        iv ---------- i          i   v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_73945784_7   1376 GAGAACCTAAAGAATGGGAGAAAATATTGGCAAATTACATTTTTGCCAAA 1425
                           v    i v                  v      i i  v i  vi  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_73945784_7   1426 AGAATTTAATGTAGAATATATAA-GAACACTTTCAGCTCAATAATAAGAA 1474
                         i  v  vv  vi           -    v   v  i           i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_73945784_7   1475 GACA--TAAGTCAATT--AAAATGCAAAAAGAATCTGAATAAACATTTTT 1520
                             --   vi     --      viv    i  i      i      i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_73945784_7   1521 CCAAAGAATATATACAAATGGCCAATAAATACATAAAAAGATGCTCAACA 1570
                                 v                   ii    i               
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_73945784_7   1571 TCATTATCCAC 1581
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.56 (86 / 55)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 5.57 (78 / 14)  


3212 27.23 0.55 0.44  chrX_73962395_73965088     1296  2202 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_73962395_7   1296 TGGAAGACGATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1345
                              iivv  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_73962395_7   1346 GGCCATACTACCCAAGGTAATTTGTGGATTCAATGCCGTCCCCATCAAGC 1395
                            v     v     iv i  i iii       i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_73962395_7   1396 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1443
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_73962395_7   1444 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 1493
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_73962395_7   1494 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1543
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_73962395_7   1544 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1593
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_73962395_7   1594 AATGGAACAGAAC--AGACCCCTCAGAAATAATGCCGCATATCTACAACT 1641
                                i    i--   vi  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_73962395_7   1642 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATTCC 1691
                          vi    i  i     ivv  v   i v  vv      i     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_73962395_7   1692 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCT 1741
                           v  i  i              v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_73962395_7   1742 GAAACTGGATCCCTTCCTAACACCTTATACTAAAATTAATTCAAGATGGA 1791
                            ii    i    v   v     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_73962395_7   1792 TTAAAGACTTAAATGTTAGACCTAAGACCATAAAAACCCTAGAAGACAAC 1841
                          i ?    i       v   v    i  i      vi i       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_73962395_7   1842 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1891
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_73962395_7   1892 AACACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1941
                         i    i       vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_73962395_7   1942 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1991
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_73962395_7   1992 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 2041
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_73962395_7   2042 AGGGCTAATATCCAGAATCTACAATGAACTCTAACAAATTTACAA-AAAA 2090
                         i  i  vi          v  i  v       v    v iv i  -    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_73962395_7   2091 AACCAAACAACCACATCAAAAAGTGGGCAAAGGATATGAACAGACATTTC 2140
                          iv    i    vv  i?    i            v    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_73962395_7   2141 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 2190
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_73962395_7   2191 ATCTCTGGCCAT 2202
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2933 28.43 0.66 0.66  chrX_73997141_74003524.rev     4990  5893 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_73997141_7   4990 AAGACCATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGC 5039
                             i-  i     i      i v      v i     i  v  i     
  L1M4_orf2#LINE/      5 AAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_73997141_7   5040 CATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTAC 5089
                         v     v     iv i  i           i  v     i     iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_73997141_7   5090 CAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATAT 5137
                           iivi i  i  ii     -   -- v  i  - iii    i       
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATAT 151

  chrX_73997141_7   5138 GGAATCAAAAAAGAGCCCGCATCACAAAGTCAATCCTAAGCCAAAAGAAC 5187
                             viiv  ii  v  v v  vi v  iv     i i ivv i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_73997141_7   5188 AAAGCTGGAGGCATCATGCTACCTGTCTTCAAACTATACTACAAGGCTAC 5237
                             i      vv   ii  v  iivi      viv        i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_73997141_7   5238 AGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAAT 5287
                              i   i    ii         i iv ii i   v            
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_73997141_7   5288 GGAACAGAAC--AGAACCCTCAGAAATAATGCCGCATATCTACAACCATC 5335
                             i    i--   ii  --        vv  ii i  i  iiii  vi
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_73997141_7   5336 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAAGATTCCCTA 5385
                             i  i     ivv  v   i v  vv      i    ii  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_73997141_7   5386 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCTGAA 5435
                           i  i              v      v  ?   v   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_73997141_7   5436 ACTGGATCACTCCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA 5485
                         ii    i v  v   i     v              i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_73997141_7   5486 AAGACTTACAGGTTAGACCTAAA-CCATAAAAACCCTAGAAGAAAACCTA 5534
                         ?    i  v v  v   v     - i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_73997141_7   5535 GGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAAAA 5583
                           ?i- v i -   iv   v v  vv i i   v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_73997141_7   5584 CACCAAAAGCAATGGCATCAAAAGCCAAAATTGACAAATGGGATCTAATT 5633
                                    vvi   v      vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_73997141_7   5634 CAACTAAAGAGCTTCTGCACAGCAAAAGAAGCTACCATCAGAGTGAACAG 5683
                         v  v v  i i   i  ii vv    i  vi   i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_73997141_7   5684 GCAACCTATGAAATGGGAAAAAATTTTCGCAACCTACTCACCTGACAAAG 5733
                         i     i iii       i     v  i    vii ivi i    i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_73997141_7   5734 GGCTAATATTCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5783
                          i  vi   i      v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_73997141_7   5784 ACAAACAACCCCATCAAAAAGTAGATGAAGTATATGAACAGACACTTCTC 5833
                              i     v  i?    i i iii   v  v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_73997141_7   5834 AAAAGAAGACATTTATGCAGCCGAAAAACACATGAAAAAATGCTCATCCT 5883
                         v        i  vi viii   i v  i          i       v v 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_73997141_7   5884 CACTGTCTGT 5893
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (151 / 102)
Gap_init rate = 0.01 (9 / 904), avg. gap size = 1.33 (12 / 9)  


2961 24.84 1.30 3.24  chrX_74029971_74032258.rev      872  1797 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74029971_7    872 TGGAAAGATATTCTGTGTTCATGTATTAGAAGAATCAATGTTGTTAAAAT 921
                                    i ii        v   i     v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74029971_7    922 CTCCATACTACATAAAAGAACCTGCAAATTCAATGCATCCTTTATCAAAA 971
                         vv v     v vi   vvi i  i  i      i   vi ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74029971_7    972 TACCAATAACATTCTTCACAGAAGTAGA-AAAT--ATTCTAAAACTTATT 1018
                          v   iivi v  i  ii     i v  -  ii--  i      i i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_74029971_7   1019 TGAAACCACAAAAGACCCAGAGTAGCCAAAGCTATCCTGAACAAAAGGAA 1068
                           i  vii   ii        i        i v   i    v  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_74029971_7   1069 AAAAACTGGAAAA-TCACACTATCTGACTTTAGATTATACTACAGAGCTA 1117
                         v   ii    ii -       vi ii i  i i viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_74029971_7   1118 TAGTAACCAAAACAGCATGATACTGGTATAAAAACAGACACATAGACCAA 1167
                         i     i   i    ii  i      i    ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_74029971_7   1168 TGGAAGAGAATAGAGAACTTAGAAATAAATTCATATATCTTCAATGAACT 1217
                              v     v    iiii         ii    i  i viii v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_74029971_7   1218 CAGTTTCAACAAAGGTGCCAAGAACATATATTGGGTAAAGTACCATCTCT 1267
                         v v    i    i          v   vi v    v    v ivi   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_74029971_7   1268 TCAATAAATTGTGTTGTGAAAACTGGATATCCATATGCAAAAGAATGAAG 1317
                             i    v   i  v  v         ?   i                
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_74029971_7   1318 ATAGACCCCTATCTCTTGCCATATACAAAAATCCAATGAAAATATATTAA 1367
                         v i        i   vii              iv v v     iv  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_74029971_7   1368 AGACTTAACTCTAAAA-CTGCAAACTATGAATCTACTAAAAAAATAAAAT 1416
                             i   v v   i -  i-       i  v  -  -------  i  v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTA-AAACTATAAAACT-CT-------TAGAAG 541

  chrX_74029971_7   1417 AAAACATTGGGG-AAATTATCCAGT-ACATTGGAGTGAGCAAAGATTTTT 1464
                                v  ? -    iv  --  -  v    iv ii    v i   i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTC--GTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_74029971_7   1465 TAAGTAATACCCCATAAGCATAGGCAACCAAAGCGAAAATGAACAAATGG 1514
                           ii  vv  v   v     i i     v    vi     ii i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_74029971_7   1515 AATCACTTCAAGTAAAAAAAAAAAAAAAAAACTTATTCATAGT--GAAGC 1562
                         i ---     -- v    vv     ------   -- ii iv --i   v
  L1M4_orf2#LINE/    640 GA---CTTCA--TCAAAATTAAAAA------CTT--TTGTGCTTCAAAGG 676

  chrX_74029971_7   1563 AAACAATCAACAAAGTGAAGAGAAAATCCCATAGAATGGGAGCGAAAT-T 1611
                          v  v     v        i   v  -    i          -i    - 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAA-CCCACAGAATGGGAG-AAAATAT 724

  chrX_74029971_7   1612 TTGCAAACTATCCATCTGACAAGGGATTCATAACCAAAAGATATGATAAG 1661
                                ii  vi      i      i ii  v   i  v    i --  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA--AG 772

  chrX_74029971_7   1662 AAGCTCAGACAACTCAATGAGAAGTAATATAA-TAATGTGATT-AAAAAT 1709
                           -   vv          i v  i-  v i  -   ivii   -      
  L1M4_orf2#LINE/    773 AA-CTCTTACAACTCAATAATAAA-AAGACAAATAACCCAATTWAAAAAT 820

  chrX_74029971_7   1710 GAGCCAAAGATCTGAATAGACATTTATCAAAAAAAGACATGCAAATGGAA 1759
                          i  v  i   i             v  v   i    i  i       vv
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_74029971_7   1760 AATGGGTATAAGAAAAGGTGCTCAGCATTATTGATCAT 1797
                            ii i i v      i      i   i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (145 / 82)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.83 (42 / 23)  


3446 23.24 2.46 1.01  chrX_74092149_74096179     2644  3538 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74092149_7   2644 TGGAGAGATACTCCATGTTCATGTATGGGAAGACTCAATATTGTTGAGAT 2693
                             i     ii           v  v        i         i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74092149_7   2694 GTCAGTTTTCTCCAGCTTGATCTATAGATTCAATGTGACCCCAATCAAAA 2743
                          v  i vi  i   iv        i        i ii i   v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74092149_7   2744 TCCCAGTAAGTAATTTTGTGGATATGGACAAACTGATCCTAAAGTTTATA 2793
                               ivivivv     ii  v  v     i           i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_74092149_7   2794 AAGAAAGGCAAAAAACTCAAAACAGCCAACAGAATACTGAAGAAGAA-AA 2842
                         vi    v    iii  i  i  i      v v   vi    i     -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_74092149_7   2843 CAATACTGGAGGTCTGACACTACCTGACTATAAGACTTACTCTATGAAGC 2892
                            vii      v  v     v  ii i vi  i       -- ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT--ACAAAGC 248

  chrX_74092149_7   2893 TACAGTAATCCTGACAGTATGGTACTGGTCAAAAAATAGACAAATAGATC 2942
                                   vv      i         ivv  ii       v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74092149_7   2943 AATGGAAATAGAAGAGACAGCACAAAAATGGACTCACAAAAATATAGTCA 2992
                                -     vv  v  iv  i    ii  i  i v vv   i    
  L1M4_orf2#LINE/    299 AATGGAA-TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_74092149_7   2993 ACTGATCTTTCACAAAGGAGCAAAGGCAACCCAATGGGAAAGAGACAGCC 3042
                          i    i  iv    i  v  v   i v ii       i  iii i  i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_74092149_7   3043 TTTTCAATAAATGATGCTGGAGCAACTGGACATGCCA-ATGGAAAAAAAA 3091
                                i     i      ii        i -?   -   v    i  -
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATA-KCCACATGCAAAAGAA- 445

  chrX_74092149_7   3092 AGGAATCCAAACACAGACCTTACAT-ATTTCATAAAAATTAACTCTAAAT 3140
                         -v   viiii  v vv    i   i-  v - i            v    
  L1M4_orf2#LINE/    446 -TGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAAT 493

  chrX_74092149_7   3141 AGATCATAGACCAAAATGTAGAAGATGAAACTATAAATCATCTAGAAGAT 3190
                         i     ?     v       ii  v i          v vii       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_74092149_7   3191 AACGTAAGATAAAATCCAGGTAACCTTGGGTTTGGCAATGA---CTTAG- 3236
                            i  i ?vv     ivv  i          v       i---     -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_74092149_7   3237 -----CACCAAAAACATGATCCATGAAAGA-----CTGGTAAGTAGGACT 3276
                         -----        i  ii v v ii     -----iv i   i v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_74092149_7   3277 TCATTAATATTAAGAACTTCTGCTTTACAAAAGACACTGTCAAGAGAATA 3326
                             i  v     i     i  ivi v    i      i      i i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_74092149_7   3327 AGATGACAAGCCACAGACTGAGACAAAGTATTTGCAAAAGACTTAACTGA 3376
                          i v     v       v  i  v   i          vv iv  v    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_74092149_7   3377 TAAAGTATTTGTATCCAAAAT-TACAAAAGAACTCTTAAATCTCAACAAT 3425
                            i v i         i   -  i   -         v v     i   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAA-GAACTCTTACAACTCAATAAT 792

  chrX_74092149_7   3426 AAGAAAACAA----TCAAATTTAAAAATGGGCAAAAGAACTGATCAGACA 3471
                           i  i    ----i v    ?             i  vi   vi     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_74092149_7   3472 CTTCACCAAAGAAGATATACAAATGACAAAAAAAGCATATGAAAAGATGC 3521
                         i   v                    i v  v  -   i            
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAA-GCACATGAAAAGATGC 891

  chrX_74092149_7   3522 TCAACATCATATGTCAT 3538
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (124 / 80)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.07 (31 / 15)  


2441 27.20 6.92 0.47  chrX_74106603_74109726     1779  2631 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74106603_7   1779 TGGAAAAA-----CAAACTCAAGGATTGAAAGAATCAATATGGTTAAAAA 1823
                               i -----  vii   v      i    v i     v     i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74106603_7   1824 GACCATACTGTCCAAAGCAATTTACAGATTCAACACTATTCCTATCAAAC 1873
                          i v     vi     vii  i            i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74106603_7   1874 TACTAA-TGTCATTTTTCACAGAATTAGAAAAAACTG-TTCTAAAATTCA 1921
                          v i i-  i -     ii     v v  v  i-   - i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_74106603_7   1922 TATTGAACCAAAAAAGAGGCAGAATACCCAAAGCAATCCTAAGCAAAAAG 1971
                            v   viiv  ii  vv       v     i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74106603_7   1972 AATAAAGCAAGAGGTAC-CACATTATCTGACTTCAAATTATACTACAAGG 2020
                           i    ivi    -  -    i vi ii i      viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_74106603_7   2021 CTACAATAACCAAAACAGCCTG-TACTGGTATAAAAATACACACATAAAT 2069
                              i   i   i    iv  -      i    ii   v   i   i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_74106603_7   2070 CAAT------------------CAGAAAGCAAGCCACATATGTACAACTA 2101
                             ------------------      vv  v   i i  v  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_74106603_7   2102 ACAGATCTTTGACAAAGTTGACAAAAGTATATACTGGGGAAAGGACAATC 2151
                          iv   i  i     i v  v   i vi  vi v         i i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_74106603_7   2152 TATTCAATAAATACTGCTGGGAAAATCAGATAGTCACATACAGAATAATG 2201
                          v     i    iv        v  iii    ?i     i  i  v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_74106603_7   2202 ACACTGGACCCATATCTCTCACTAAAAACAAAAATTAACT---------- 2241
                          vii       v  i   v   i v v             ----------
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_74106603_7   2242 --AAGATCTAA---------------CTATAAAAAGCCTAGAAGAAAACC 2274
                         --?   i    ---------------        vv i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_74106603_7   2275 TAGAAAAAACTTTTCTAGACATTGGCCTAGGTAAAGAATTTATGACTAAG 2324
                            i?iv  v i   vv   v    vi    i  v iv  iv iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_74106603_7   2325 ACTGCAAAAGCACAGATAACAAAAGTAAAAACAGACAAATGGGACTC--- 2371
                           vv          iii        v     i   i    v     i---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_74106603_7   2372 --AAATGAAAAAGATTCTATACAGCAAAATAAATAATTAACAGATTAAAT 2419
                         --    v     v-  i i i vv    iv v iv  i  v i v i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_74106603_7   2420 AGAAAACTTACAGAATGGGAGAAAATATCTGCAAACTATGCACCCAATAA 2469
                            v   ii                   i      ii  ii i ii    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_74106603_7   2470 AGAACTAATATCCAGGATCTAAAAGGAACTCAAAGAACTCAACAAGAAAA 2519
                         i i   vi       i  v  v  i      vv v       i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_74106603_7   2520 AAACAAGTAACTCCATCAAGAAGCGAGCTAAAGACATGAACAGATAGTTT 2569
                          i    i    i v  i? i  ii i  v  i  iv    i   i v  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_74106603_7   2570 TCAAAAGAAGACATATAAGCAGCCAACAAACATATGAAAAAATGTTCAAC 2619
                           v        i   i  iii     i  i  i       i   i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_74106603_7   2620 ATCAATAATCAT 2631
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (141 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.85 (63 / 13)  


3369 21.79 3.91 2.46  chrX_74125127_74127150.rev      639  1533 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74125127_7    639 TGGAAAGAT-TTTAATATCTTTGGATTTATGGAAAGATATTTTAATATTA 687
                                  - iiv  i iiv      ---- i    i---        i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT----GGAAGAC---TTAATATTG 43

  chrX_74125127_7    688 TAAAAAT-------TTCCACA-------CTAC----CCAACACAATCCCT 719
                          v  i  -------i   v  -------    ----i    i        
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chrX_74125127_7    720 ATAAAAATTTCAACAGCATTTTTCACAGCAATAGAAAAA--AGTCATAAC 767
                           v     ii  i v  v     ii   v   v  v  i--ii  v   v
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_74125127_7    768 ATTAACATGGAA---CAATCGACCCCAAATAGCCAAAGCAATCTTGAGAG 814
                            v i      ---   vv     vi          i         i i
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_74125127_7    815 AGAGGAACAAAGTTGGAGGCATCACAGTTCCTAATTTCAAA-----TTAC 859
                            i               vv     v    i         -----i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_74125127_7    860 AAAGCTGTATTAATCAAAACAGTATGGTACTGGCATAAAAACAGACACAT 909
                               ii v       i     i              ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_74125127_7    910 AGACCAATGGAACAGAATATAGAGCCCAGAAATAAACCCATCCATATACA 959
                            i        i     vv    i                v   v  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_74125127_7    960 TTCAACTAAACTTCTACAAGGGTGCCAAAAGTACAAAATGTGGAAAAGAT 1009
                         v    i i vi   v             i vi ivv    v     ii  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_74125127_7   1010 AGTCTTTTCAATAAATCATGTTGGGAAAACAGGATATCCACATGCAAAAG 1059
                                    i    vi  i     v   v     ?             
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_74125127_7   1060 AATGAAACTGGACCATTATCTTAT-TCATACAAAAGAACCC-CTCAAAAT 1107
                               ii      vi  i  i i-i    i v  i  iiv-        
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_74125127_7   1108 GGATAAGAGGCTTACACATAAGCCTTAAACCCTCAAAACTCCTAGAAGAA 1157
                             v ?  i i  v ii    vvi    v ivi       i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_74125127_7   1158 AACATAGGGA-AAGGCTCCTTGACATTACCCTTGGCAATGATTTTTTGGA 1206
                                 ?i-  iv  i v    v  ivvi v       i   i  i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_74125127_7   1207 TATGACACCAAAAGCTCAAGTCAGTGGAAGCAAAAATAAACAAGTAGGTC 1256
                                        v    -  iiii   v       i i  i v  v 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_74125127_7   1257 TAAATCAAACTGAAAAGCTTTTGTACAGCAAAGGAAACAGTCATCAAAAC 1306
                          vv      v v    i       i vv       v  vi   vv   ii
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_74125127_7   1307 TATAAAGCAACCCATGGAATGGGAGAAAATATTTGCAAATCACATATCTG 1356
                         v v  ii       ii                          i       
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_74125127_7   1357 ATAAGGGGTTAATATCCAAAATACAGAAGGAACTCACACAACTTACACAC 1406
                                ii vi      i    i v  i      vi      i -----
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA----- 787

  chrX_74125127_7   1407 ACACACACACACACACACACACACACACCCCAATTTTAAAATGGGCAAAG 1456
                         -------- i - i v v v   v i v       ?v             
  L1M4_orf2#LINE/    788 --------ATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_74125127_7   1457 GACTTGAATAGACACTTTTC-AAAGAAGACATACAAATTGTCAATAGGTA 1505
                           i           i  i  -        i        v i     i i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_74125127_7   1506 --TGAAAAGGTGGTCAACATCACTAATGAC 1533
                         --       i  v         ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (115 / 76)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.35 (57 / 17)  


2507 25.93 1.70 5.21  chrX_74135654_74140646     3560  4500 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74135654_7   3560 TGGAAAAATATCCCATGCTCATGGATATGAAGAATCAAAATTGTTAAAAT 3609
                               i          i        vv     v i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74135654_7   3610 CGCCATACTGCCCAAAGCAATTTA--GATTCAATGCTATTCCTATTCAAA 3657
                         v  v     v      vii  i  --       i  v  i     -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-CAAA 99

  chrX_74135654_7   3658 CTACCAAC-G--TTTTTCAAAGAATCTGAAAAAAACATTCTAAAATTAAT 3704
                         v v   i - --     iiv    vi   v  ivvv  i        v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_74135654_7   3705 TCGGAACCAAAAAGTAGCTCAAATAGCCAAAACAATCCTAAGCAAAAGCA 3754
                         vi    viiv  i v v ivi                i i --     --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAG-- 195

  chrX_74135654_7   3755 AAAACAGAAACAAAAACAAAACAACAACAACAACAACAAAAAAGCTGGAG 3804
                         -----------  i      ----------------------- i     
  L1M4_orf2#LINE/    196 -----------AAGAACAAA-----------------------GTTGGAG 211

  chrX_74135654_7   3805 GCATGGAGGCATCACAATACTTGACTTCAAACTATACTACAAGGCTATAG 3854
                          - i-------     v v iii i      viv        i    i  
  L1M4_orf2#LINE/    212 G-AC-------TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_74135654_7   3855 TAACTAAAAAAGCATGGTACTGGTATAAAAACAGACAGACTGACCATTGG 3904
                            ii  i v  ii         i    ii i     v iv  i  v   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_74135654_7   3905 AACAGGTTAGAGGACCCAGAAATAAAGCTGCACACCAACAGCCATCTGAT 3954
                           i  iv v   iii           v iii   iiv ii i  vi    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_74135654_7   3955 GTTCAACAAAGCCAACAGTAACAAGCAATGGGGAAAGGATTTTCTATTCA 4004
                         v   i    i viiv  iv v  vv            i  vv   v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_74135654_7   4005 ATAAATGCTGCTGGGGTAACTGGCCAGCCATATGCAGAAGA-TGAAAATG 4053
                          i     v       ii      vi ?   i     i    -    iv  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_74135654_7   4054 GGCCCCTATCTTTAACCATTGACAAATATAAATTCAACATCAATTAAAGA 4103
                          i      i  ivv     vv     v  v  i    v  vi  i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_74135654_7   4104 CTTAAACGTAAAACCCAAAACTATAAA-CTCT-GGAAGACAACCTAGG-- 4149
                          i    i    i v i           -    -i     v   v    --
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_74135654_7   4150 -AAATACCATCTGGATATGGGACCTGGCAAAGACTTCAGGAGGAAGACAC 4198
                         -    -- v  vv  iv v  iiiv     v ii   vviiiv v     
  L1M4_orf2#LINE/    554 TAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_74135654_7   4199 CAAAAGCAATTTTAACAAAAACAAAAATTGACAAATGGGACCTAATTACA 4248
                                 vvvvi       iv      v  i    v    i v  i v 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_74135654_7   4249 CTAAAGAGCTGCTGTACAGCAAAAGAAACAACCAACTGAGTAAATAGACA 4298
                         v v  i i  vi   i vv    i  v  v i   vvi   i  v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_74135654_7   4299 ACCTACAGAATGGGGGGTAATATTTGCAAACTATGTATCCGACAAAGGTC 4348
                            i          i iv            ii  i    i  i  i  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_74135654_7   4349 TAATATCCAGTATCTATAAGGAAC----ATAAACCAACAAGCATAAACCA 4394
                          vi       v  v     i    ---- i  vi   i  vv v  iv  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_74135654_7   4395 ACCAACCCCATT-AAAAATGCGCAAAGGACATGAACAGACACTTCTCAAA 4443
                          vi     v   -       v        iv    i     i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_74135654_7   4444 TGAAAACAAACACATGGCTAACAAGCATATTAACGAATACTCAACATCAT 4493
                         v   i i v   v     i  i     i  v  vii  i          ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_74135654_7   4494 TTATCAT 4500
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.18 (131 / 111)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.06 (65 / 16)  


3261 25.41 1.32 1.43  chrX_74186130_74192399.rev     4871  5779 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74186130_7   4871 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4920
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74186130_7   4921 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4970
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74186130_7   4971 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 5017
                          v   i-       i  -i     -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

  chrX_74186130_7   5018 CATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAA 5067
                                  viiv  ii  v  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_74186130_7   5068 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5117
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_74186130_7   5118 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5167
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_74186130_7   5168 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 5215
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_74186130_7   5216 CTATCTGGTCTTTGACAAACCTGACGAAAACAAGCAATGGGGAAAGGATT 5265
                         ii vi  i i  i     ivv  v i i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_74186130_7   5266 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCAAGCCAGATGTAGAAAG 5315
                         vi  v  i  i              v      vv ?   v   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_74186130_7   5316 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5365
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_74186130_7   5366 GATTAAAGACTTAAACGTTCGACCTAAAACCATAAAAACCCTAGAAGAAA 5415
                            i ?    i    i  vv  v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_74186130_7   5416 ACCTAGGCATTA-TCATTCAGGACATAGGCATGGGCAAGGACTTC--AGG 5462
                           v    ?i v -  -   iv   v v  vv i     v ii   --  i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_74186130_7   5463 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5512
                          v i --           vvi          vv     v  i    v   
  L1M4_orf2#LINE/    594 TATGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_74186130_7   5513 TCTAGTTAAACTAAAGTGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5562
                         ii vi i   v v  ivi   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_74186130_7   5563 TGAACAGGCAACCTACAAAATGGGAGAAAGTTTTCGCAACCTACTCATCT 5612
                             v  i     i   i           i v  i    vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_74186130_7   5613 GACAAAGGGCTAATATCCAGAATCTACAAAGAACTC----AAACCAATTT 5658
                           i  i  i  vi          v  i         ----  vi    --
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-- 789

  chrX_74186130_7   5659 GCAAGAAAAAAACAAACAACCCCATCAATAAGTGGGCGAAGGATATGAAC 5708
                         --  v     i     i     v  i? v  i     i      v    i
  L1M4_orf2#LINE/    790 --AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_74186130_7   5709 AGATATTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAA 5758
                            i       v        i  vi viii     i ii          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_74186130_7   5759 ATGCTCATCATCACTGGTCAT 5779
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.92 (25 / 13)  


3103 28.45 0.33 0.22  chrX_74237264_74244692     1904  2810 (4619)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74237264_7   1904 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATGAATATTGTGAAAAT 1953
                              ii i  i     i      i v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74237264_7   1954 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2003
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74237264_7   2004 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2051
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74237264_7   2052 TATGGAACCAAAAAGGAGCCCGCATTGCCAAGTCAATCCTGAGCCAAAAG 2101
                                viiv  i   v  v v  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74237264_7   2102 AACAAAGCTGGAGGTATCGCACTACCTGACTTCAAACTATACTACAAGGC 2151
                                i      vv  i    v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74237264_7   2152 TACAGTAACCAAAACAGTATGATACTGGTACCAAAAAAAAGATATAGATC 2201
                                 i   i     i  i      i iv ii v i v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74237264_7   2202 AATGGAACAGAACCGAGCCCTCTGAAATAATGCTGCATATCTACAACTAT 2251
                                i    ii   vvii v       vv iii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_74237264_7   2252 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGTAAGGATTCCCT 2301
                         i    i  i     ivv  vv  i v  vv        v   i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_74237264_7   2302 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCTGA 2351
                         v  i  i              v      v  ?   v   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_74237264_7   2352 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 2401
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_74237264_7   2402 AAAGACTTAAACGTTTGACCTAAAACCATAGAAACCCTAGAAGAAAACCT 2451
                          ?    i    i  vv  v       i   i  vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_74237264_7   2452 AGGCATTACCATTCAGGACATAGGCAT-GGCAAGGACTTCATGTCTAAAA 2500
                            ?i v viv   iv   v v  vv -     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_74237264_7   2501 CACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATCTAATT 2550
                                    vvi          vv   i v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_74237264_7   2551 CAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGCGTGAACAG 2600
                         v  v v  i i   i  ii vv    i  v    i  vv iv     v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_74237264_7   2601 GCAACCTACAAAATGGGAGAAAATTTTCTCAACCTACTCATCTGACAAAG 2650
                         i     i   i             v  iv   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_74237264_7   2651 GGCTAATATTCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAAAA 2700
                          i  vi   i      v  i  v      vv    v iv i  vi    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_74237264_7   2701 ACAAACAAACCCATCAAACAGTGAGTAAAGGACATGAACAGATACTTCTC 2750
                              i  v  v  i?  v i  i i      iv    i   i i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_74237264_7   2751 AAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCACCAT 2800
                         v        i  vi viii     v ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_74237264_7   2801 CACTGGCCAT 2810
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.35 (146 / 108)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.25 (5 / 4)  

2411 29.06 3.75 0.68  chrX_74237264_74244692     6056  6936 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74237264_7   6056 TGGAAACACATCCCATGCTCATGGATGGGGAG-C---ACACTGCTGAAA- 6100
                               v i        i        v  i  - --- i i  i i i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74237264_7   6101 -GCAA-ACT--------------ATAAATTCAATGCAATTCCCATCAAAA 6134
                         -    -   -------------- i i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74237264_7   6135 TGCCACCATCATTCTTCACAGAGCTAGCAACAA--CAATTCTAAAATTTA 6182
                          v   v vv v  i  ii    iv v --    --ii  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74237264_7   6183 TATGGAA---CAAAGAAAGAGCCCGCATAATCAAAGCAAGACTAAGCAAA 6229
                                ---   i ---  v  v v   ii    i   vvi i iv  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG---GACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_74237264_7   6230 AAGAACAAATCTGGAGGTATCACATTACTTGACTTCAAAGTATACTACAA 6279
                                  vi      vv     i v iii i      iiv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_74237264_7   6280 GGCTGTAGTTGCCAAAACAACATGGTATTTGTTTAAAAATAGGCACATAG 6329
                         i   ii   vii   i   iii     i v iv   ii    i  i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_74237264_7   6330 ACTAATGCAGCATAATAGGGAACCCAGAAATAAAGCCAAATACTTAACAT 6379
                          ii    v ii v   v i  ii           v   v i i   vvi 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_74237264_7   6380 CAACTCATATTTAACAAAGCAAACAAAAACTA--AAGTGGGGAAAGGACA 6427
                            i v  v  ii    i -ivi v  i  i --v i         i i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_74237264_7   6428 CCCTATTCAACAAATGGTGCTGGCATAATTGGCAATCCAAAACTAGAAGA 6477
                         vi  v                  v i  i   vv ?   v vvi i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_74237264_7   6478 ATGAAACTGAATTTTCATCTCTCACCTAATACAAAAATCAACTCAAGATA 6527
                              ii  i iiiii i   v    vv          i       i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_74237264_7   6528 GATCAAAAACTTAAATCTAAGACCTGACACCAAAAAATTCT-AGAAGATA 6576
                              ? i  i     v     v  i v  i v    i   -      v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_74237264_7   6577 ACATCAGAAAAACTCTTCTAAACATTGGCCTAGGCAAAAAATTTATGACC 6626
                             vi ?iv  v     vvi  v    vi       viiv  iv iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_74237264_7   6627 AAGAACCCAAAAGCAAATGGAACAAAAATAAAGATAGATG----GAACTT 6672
                          v  vv         v v v       iv   i      i---- i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_74237264_7   6673 AATTAAAGTAAAAAGCTTCTGCACAGAAAAAAAAAAAATCAGCAGAGTTA 6722
                         v  i   i v    i   i  ii vvv   ii v vv    iv i   v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_74237264_7   6723 ACAGACAACCCACAGAGTGGGAGAAAATCTTCACAAGCTATGCATCCAAC 6772
                          v              i           v  ii   iii  ii   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_74237264_7   6773 AAAGGACTAATATCCAGAATCTCCAAGGAGCTCAAACAAATCAGCAAGAA 6822
                           i     vi          v vi  i  i   vv    v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_74237264_7   6823 TAAAATGAACAACTCCATCAAAAAGTGGGCTAAGAACATGACTAGACAAT 6872
                         v  i ii  i   i v  i?    i     v   i iv   v      v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_74237264_7   6873 TCCCAAAAGAAGATATACAAATGTCTAGCAAACAGGAAAAAAAATGCTCA 6922
                           i v                  v i ii  i  vivi    i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_74237264_7   6923 ACATCACTAATGAT 6936
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (154 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.00 (39 / 13)  


 226 22.03 0.00 0.00  chrX_74249494_74255809      208   266 (6050)  C L1M4_orf2#LINE/L1   (0)   908   850  

C chrX_74249494_7    266 AAATAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCATC 217
                            v    i  vi viii     i ii          i       v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

C chrX_74249494_7    216 ACTGATCAT 208
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  

2909 27.43 2.93 0.45  chrX_74249494_74255809     4938  5823 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74249494_7   4938 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATGAATGTCGTGAAAAT 4987
                              ii i  i     i      i v      v v   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74249494_7   4988 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATTAAGC 5037
                            v     v     iv i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74249494_7   5038 TACCAATGACTTTCTTCACAGAATTGGAAAATCT-ACTTTAAATTTCATA 5086
                          v   iivi i  i  ii     v v  v  v  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_74249494_7   5087 TAGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAGAA 5136
                          i   viiv  ii  v  v v  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_74249494_7   5137 CCAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5186
                          v   i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_74249494_7   5187 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5236
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_74249494_7   5237 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT 5284
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_74249494_7   5285 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5334
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_74249494_7   5335 ATTTAATAAATGGTGCTGGGAAAACTGGCTATCCAGATGTAGAAAGCTGA 5384
                         v  i  i              v      v  ?   v   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_74249494_7   5385 AACTGCATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGTATT 5434
                          ii  v i    v   i     v              i    i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_74249494_7   5435 AAAGACTTACATGTTAGACCTAAAACCATAAAAATGCTAGAAGAAAACCT 5484
                          ?    i  v    v   v       i      v vi           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_74249494_7   5485 AGGCAGTA--CCATTCAGGACATAGGCATGTGTAAGGACTTCATGTCTAT 5532
                            ?-   --i -   iv   v v  vv iv i  v ii   v ivv   
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_74249494_7   5533 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5582
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_74249494_7   5583 TTCAACTAAAGAGCTTCTGCACAACAAAAGAAACTACCATCAGAGTGAAC 5632
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_74249494_7   5633 AGGTAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5682
                           ii    i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_74249494_7   5683 A--------------AAT---TAA----CTCAAACAAATTTACAAGAAAA 5711
                         i--------------   ---   ----   vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_74249494_7   5712 AAACAAACAACCCCATCAAAAAGTGAGGGAAGGACATGAACAGACACTTC 5761
                          i     i     v  i?    i  i vi     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_74249494_7   5762 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5811
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_74249494_7   5812 AACACTGGCCAT 5823
                          v  ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (137 / 102)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.33 (30 / 9)  


3272 25.85 0.91 0.57  chrX_74282399_74284718.rev      944  1821 (499)    L1M4_orf2#LINE/L1        1   881 (27)  

  chrX_74282399_7    944 TGGAAACACATCCCATGCTCATGGATGGGTAGAGTCAATATTGTGAAAAT 993
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74282399_7    994 GATCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 1043
                          iiv     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74282399_7   1044 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 1093
                          v   v vv v  i  ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_74282399_7   1094 TGGAACCACAAAAGACCCCACACAGCCAAAGCAAGACTAAGCAGAAAGAA 1143
                              vii   ii     viv i       i   vvi i iv ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_74282399_7   1144 CAAACCTGGAAGTGTCACACTACCTGATTTCAAACTATACTATAAGGCCA 1193
                             vi    i vv       v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_74282399_7   1194 CAGTCATCAAAACAGCATGGCACTGGTACAAAAATAGGCACAAAGACCAA 1243
                             v     i    ii   i     i i  ii    i  i v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_74282399_7   1244 TGGAACAGAACAGAGAACTCAGAAATAAACCCAAATACTTATAGCCAACT 1293
                              i    iv    iii              v i i    i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_74282399_7   1294 GATCTTCGACAAAGCAAACAAAAATATGAAGTGGGGAAAGGACACCCTTT 1343
                            i        i vviv   i vi  vv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_74282399_7   1344 TCAACTAATGTTGCTGGGATAATTGGCTAACCACATGTAGGAGAATGAAA 1393
                              v    v        i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_74282399_7   1394 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTAA 1443
                         i    i  ii i   v    v           i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_74282399_7   1444 GGGCTGAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACTTTG 1493
                         i i iv    v     v  i           v ii       v   v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_74282399_7   1494 GCTTACAT-------ACATTGGCTTAGCCAAAGATTTCATGACCAGGAAC 1536
                          ?v  v  -------  v    v    v   v i    v iivi v -  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG-AC 599

  chrX_74282399_7   1537 A-CAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATTA 1585
                          -        v v    i    iv   i   i   iv v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_74282399_7   1586 AACTAAAGAGCTTTTGCACAGCAAAAGAAACAGTCAGCAGAGTAAACAGA 1635
                           v v  i i      ii vv    i  v  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_74282399_7   1636 CAACCCATATAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGG 1685
                                i v i           v  ii   vii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_74282399_7   1686 ACTAATATCCAGAATCTACGAGGAACTCAAACAAATCAGCAAGAAAAAAA 1735
                            vi          v  ii i      vv    v   ii  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_74282399_7   1736 AAAACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATT 1785
                         ----    i  i  v  i?    i     v     iv          v  
  L1M4_orf2#LINE/    800 ----CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_74282399_7   1786 CTCAAAAGAAGATATACAAATGGCCAACAAATATAT 1821
                            v                       i  ii i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 1.48 (133 / 90)
Gap_init rate = 0.00 (4 / 881), avg. gap size = 3.25 (13 / 4)  


2914 28.60 1.22 0.55  chrX_74310945_74323013.rev     4993  5894 (6175)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74310945_7   4993 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5042
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74310945_7   5043 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5092
                            v     vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74310945_7   5093 TACCAATGACTTTCTTCACAGAATTGGAGAAAACT-ACTTTAAAGTTCAT 5141
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_74310945_7   5142 ATGGAACCAAAAAAGAGCCCACAGT-GCCAAGTCAGTCCTAAGCCAAAAG 5190
                               viiv  ii  -    v i -     iv  i  i i ivv i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74310945_7   5191 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5240
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74310945_7   5241 TACCGCAAGTAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5290
                            v i  vi  i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74310945_7   5291 AATGGAACAGAAC--AGAACCCTCAGAAATAATGCTGCATATCTACAACC 5338
                                i    i--   ii  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_74310945_7   5339 ATCTGATCTTTGACAAACCTGAAAAAAACAAGCAATGGGGAAAGGATTCC 5388
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_74310945_7   5389 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5438
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_74310945_7   5439 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAATATGGA 5488
                            ii    i    v   i     v              i    v     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_74310945_7   5489 TTAAAGACTTACATGGTAGACCTGAAACCATAAAAACCCTAGAAGAAAAC 5538
                          i ?    i  v   vv   v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_74310945_7   5539 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCACAGACTTCATGTCTA 5587
                         v    ?i- v i -   iv   v v  vv i    vv ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_74310945_7   5588 AAACACCAAAAGCAATGGCAATGAA-GCTAAAGTTGACCATTGGGATCTA 5636
                         vi            vvi    ii  - vv   i v  iv v v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_74310945_7   5637 ATTAAACCAAAGAGCTTCTTCACAGCAAAAGAAACTACCATCAGAGTGAA 5686
                           i   viv  i i   i vii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_74310945_7   5687 CAGGCAACCTACAGAATGGGAGAAAATTTTTCCAATCTACTTATCTGACG 5736
                         v  i     i                 v   v   vii iv       ii
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_74310945_7   5737 AAGGGCTAATATCCTGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5786
                          i  i  vi     v    v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_74310945_7   5787 AA-----ACAATCCCATCAAAAAGTAGGCAAAGGATATGAACAGACACTT 5831
                           ----- i  i  v  i?    i i          v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_74310945_7   5832 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5881
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_74310945_7   5882 CATCACTGGCCAT 5894
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (151 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  

2921 27.42 1.21 1.21  chrX_74310945_74323013.rev    10671 11578 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74310945_7  10671 TGGAAGAACATTCCATGCTCATGGATCGGAGGAATCAATATTGTGAAAAT 10720
                              ii i  i     i        i   i  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74310945_7  10721 GGCCATACTACCCAAAGTAATTTATAGATTCAATGCTATCCCCTTCAAGC 10770
                            v     v      v i  i  i        i  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74310945_7  10771 TACCATTGACTTTCTTCACAGAATTAGAAAAA---A--CTAAATTTCATA 10815
                          v   vivi i  i  ii     v v  v  i--- --     v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_74310945_7  10816 TGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAACCAAAAAGAA 10865
                              viiv  ii  v  v v        i      i i vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_74310945_7  10866 CAAAGCTGGAAGCATCACCCTACCTGACTTCAAACTATACTACAAGGCTA 10915
                              i    i vv    v  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_74310945_7  10916 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 10965
                               i   i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_74310945_7  10966 TGGAACAGAACAGAGACTTCAGAAATAATACCACACAACTACAACCATCA 11015
                              i    iv    v i         vv   i   vi  iiii  viv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_74310945_7  11016 GATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAATGGATTCCCTAT 11065
                            i  i     ivv  vv  i v  vv          v i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_74310945_7  11066 TTAATAAATGGTGTTAGGAAAACTGGCTAACCATATGCAGAAAACTGAAA 11115
                          i  i        i i   v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_74310945_7  11116 CTGGACCCGTTCCTTACACCTCATATAAAAATTAACTCAAGATGGATCAA 11165
                         i       v v   i     vi   i              i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_74310945_7  11166 AGACTAAAATGTAAGACCTAAAACCATAGAAACCCTAGAAGAAAACCTAG 11215
                             iv          v       i   i  vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_74310945_7  11216 G--TAATACCATTCAGGACATACGCGTGGGCAAAGACTTAATGACTAAAA 11263
                          --   - i -   iv   v vv vv i     v ii  vv iiv  vi 
  L1M4_orf2#LINE/    551 GNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_74310945_7  11264 TGCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 11313
                         ii         vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_74310945_7  11314 AAACTAAAGAGCTTCTGCACAGAAAAAAAAAAACAAAAAACTATCATTAG 11363
                            v v  i i   i  ii vvv   ii ----  -----      vv i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGA----CA-----CTATCAAGAA 689

  chrX_74310945_7  11364 AGTGAACAGGCTACCTTTTGAATGGGCAAAAATTTTTGCAATCTATCTAT 11413
                               v  i v   iviv       vi     v       vii  v   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_74310945_7  11414 CTGACAAATGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTAC 11463
                             i  iv v  vi          v  i  i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_74310945_7  11464 AAGAAAAAAACAG----CCCCATCAAAAAGTGGGTGAAGGATATGAACAG 11509
                           v     i   i----   v  i?    i    ii      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_74310945_7  11510 ACACTTCTCAAAAGAAGACATTTATGCAACCAGCAAACATTGGAAAAAAA 11559
                            i     v        i  vi viiii   ii  i  ivv     i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_74310945_7  11560 GCTCATCATCACTGGTCAT 11578
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (138 / 108)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.75 (22 / 8)  


2868 28.51 0.99 0.66  chrX_74403692_74407994     2906  3810 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74403692_7   2906 TGGAAAAATATCCCATGCTGATGGACAGGTAGAATCAATATCATTAAAAT 2955
                               i          i v     iv  v   v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74403692_7   2956 GGCTATACTGCTGGAAGCAATGTACAGATTCCATGCTATTCCTATCAAAT 3005
                            v     v ivi  vii  v         v i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74403692_7   3006 TACCAG-TGTCATTTTTCACTTAACTAGACAAA-TG-TTTTAAAATTCTC 3052
                          v    -  i -     ii vv  v v     i-  - ii        vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_74403692_7   3053 ATGGAAGCAAAAACGAGCCTGAATAGCCAAGGCAATCCAAAGCAAAAAGA 3102
                               iiiv  iv  v  v          ii     ivi iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_74403692_7   3103 ACAAAGCTGGAGGAATCATGTTAGCCAACTT-GAAACTATACTACAAGGA 3151
                               i       v   iii vv    i  -i     -        i v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_74403692_7   3152 TACAGTGACAAAAACAGCATAGTACTGGTACAAAAACAGGCACATAGACC 3201
                               i iv  i    ii i       i i  ii i  i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74403692_7   3202 AAAGGAACACAATAGAGAGCCCAGAAATAAGGCTGCACATCTATGAACAT 3251
                           v    i v   v     i          iv iii    i    iv  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_74403692_7   3252 GTGGTCTTTGACAAAGCTGACAAAAATAAACAATGGGGAAAAGACTCCCT 3301
                         v  i i  i     i v  v   i vi vv           ii ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_74403692_7   3302 ATTCAATAAATGGTGCTGGGATAACTGGTTCACCATATTCAGACAGTTAA 3351
                         v     i              i      v v?   i  v  i viiv i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_74403692_7   3352 AGCTGGACCCCTTCCTTACACCATATACAAAAATCAATTCAAGATGGATT 3401
                           i         v   i                 i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_74403692_7   3402 AAAGAATTAAGTATAAAACCCCAAACTACAAAAACCCAGGAAGACAATCT 3451
                          ?   vi   i i   i v iv      i    vi ivi     v  iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_74403692_7   3452 AAGCAGTA--TTATCCTGGACACAGGAATGGATAAAGAGTTCATGACAAA 3499
                          i ?-   -- iv  v  -  viv  iv i ii  v iv   v iivv v
  L1M4_orf2#LINE/    549 AGGN-GTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_74403692_7   3500 GACACTGAAAGCAATCA--CAACAATAGCAAAAATTGACAAATAGTATCT 3547
                              ii      --  --      v  v      v  i    v v ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_74403692_7   3548 AATTAAACCTAAGAGCTTCTGCCCAGCAAAGGAGAATATCAACAGAGTAA 3597
                         v  i   vi   i i   i  iv vv       v v      v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_74403692_7   3598 ACAGACAACCTACAAAATGGAGGAAAATATTTGCAAGCTGTGCATCTGAC 3647
                          v        i   i     ii              iiii ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_74403692_7   3648 AAAGGTCTAATATCTATCATGTATAAGGAACTTAGGTAAATTTACAAGAG 3697
                           i  v  vi    i vv  i     i     ivvii  v iv i  v i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_74403692_7   3698 AGAAACAAACAACCCCATTAAAAAGTAGGCAAAGGACATGAGCAGATGCT 3747
                          i i     i     v   ?    i i         iv   ii   iii 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_74403692_7   3748 TCTCAAAAGAAGACATACATGCAGCAAACAAACATATAAAAAAA-GCTCA 3796
                             v        i     viii  v  i  i  i  i    i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_74403692_7   3797 ATATCACTGATCAT 3810
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (158 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  


1978 28.12 2.16 0.33  chrX_74420914_74423572      480  1080 (1579)    L1M4_orf2#LINE/L1      208   819 (89)  

  chrX_74420914_7    480 GAATGACCTACAACCGCAAATT---AAACTATACTACAAGGCTACAGTAA 526
                          i v   ii   viiv v    ---     -        i          
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAA 256

  chrX_74420914_7    527 CAAAAATAGCATGGTACTGATATGAAGACAGATATATAGGCCAATGGAAC 576
                         iv  i i  ii        ii  i i  i   i      ii        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_74420914_7    577 AGAACAGAGGCCTCAGAAATAACGTCACAAATCTACAACCATCTGACCTT 626
                             iv   ivii         vvi  i v  i  iiii  vi   ii  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_74420914_7    627 TGACAAAAA---CAAG------CAATGGGGAAAGGATTCCCTATTTAACA 667
                         i     iii---    ------            i  vvi  v  i    
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_74420914_7    668 AATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAGCTGAAACTGGAT 717
                                i     v      v  ?   i     i  iiv    ii    i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_74420914_7    718 ACCTTCCTTACACGTTATACAAAAATTAACTCAAGATGGATTAAAGATTT 767
                         v   v   i    vv                   i      i ?   ii 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_74420914_7    768 AAATGTAAGACATAAAACCATAAAAACCTTAGAAGAAAACCTAGGCA-AT 816
                                   vv      i      vi             v    ?i- v
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_74420914_7    817 ACCATTCAGGACATAGACATGGGCAAAGACTTCATGAACAAAACATCAAA 866
                          i -   iv   v v ivv i     v ii   v ii i vi   i    
  L1M4_orf2#LINE/    557 ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_74420914_7    867 AGCAATGGCAACAAAAGCCAAAATTGGCAAATGGGATTTGATTATACTAA 916
                             vvi          vv     v ii    v   i  v  i v v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_74420914_7    917 AGAGTTTCTACACAGCAAAAGAAACTCTCATTAGAGTGAAGAGGCAACCT 966
                          i ii  i iii vv    i  v   v   vv i      i  i     i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_74420914_7    967 ATAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAAT 1016
                          i               v       vii  vi      i  i  i  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_74420914_7   1017 ATCCAGAATCTACAAATAACTTAAACATATTTACAAGAGAAAAACAAACA 1066
                                  v  i   v    ivv   vv iv i  v i   i     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_74420914_7   1067 ACCCCATCAAAAGA 1080
                             v  i?   i 
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAA 819

Transitions / transversions = 1.62 (102 / 63)
Gap_init rate = 0.01 (6 / 612), avg. gap size = 2.50 (15 / 6)  

 921 23.04 0.00 0.00  chrX_74420914_74423572     1082  1311 (1348)    L1M4_orf2#LINE/L1      679   908 (0)  

  chrX_74420914_7   1082 ACTACCATCAGAGTGAACAGACAATCTACAGAATGGGAGAGAATTTTTGC 1131
                             i  vv i      v      i i             i   v     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_74420914_7   1132 AATCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCA 1181
                           vii ivi      i  i  i  vi          v  i  v      v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_74420914_7   1182 AACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAG 1231
                         v    v iv i  v     i     i     v  i?    i     i   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_74420914_7   1232 GATATGAACAGACACTTCTCAAAAGAAGACATTTATACAGCCAAAAGACA 1281
                            v    i     i     v        i  vi v ii     v ii  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_74420914_7   1282 CATGAAAAAATGGTCATCATCACTGGCCAT 1311
                                 i   v   v     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (30 / 22)
Gap_init rate = 0.00 (0 / 230), avg. gap size = 0.00 (0 / 0)  

 425 21.68 2.80 4.20  chrX_74420914_74423572     2024  2166 (493)    L1M4_orf2#LINE/L1      768   908 (0)  

  chrX_74420914_7   2024 TAAAG----CTTAAAGTATAATAAAAAAAAGAAAAAACCAAACAACCCCA 2069
                              ----    v iivi     v       ------    i     v 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGA------CAAATAACCCAA 811

  chrX_74420914_7   2070 TCAAAAAGTGGGCAAAGGATATGAACAGACACTTCCCAAAATAAGACATT 2119
                          i?    i            v    i     i   i v   v    i  v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_74420914_7   2120 TATGTGGCCAACAAACATATTAAAAAAAGCCCATTATCACCGGTCAT 2166
                         i vi       i  i  i  v    i v  i  vi    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (18 / 12)
Gap_init rate = 0.01 (2 / 141), avg. gap size = 5.00 (10 / 2)  


3116 26.77 1.22 0.77  chrX_74494003_74502892     3150  4053 (4837)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74494003_7   3150 TGGAAGAACATTCCATGCTCATGGGTACGAAGAATCAATATCGTGAAAAT 3199
                              ii i  i     i      i vv     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74494003_7   3200 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3249
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74494003_7   3250 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3297
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74494003_7   3298 TATGAAAGAAAAAAGAGCCCACATT-GCCAAGTCAATCCTAAGCCAAAAG 3346
                             i  iviv  i ii    v v -     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74494003_7   3347 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3396
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74494003_7   3397 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGATATATAGACC 3446
                                 i   i    ii       v i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74494003_7   3447 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCTTATCTACAACC 3494
                                i    i--    i  --        vv  iivi  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_74494003_7   3495 ATCTGATCTTTGACAAACCTGACAAAAACAGGAAATTGGAAAAAGATTCC 3544
                          vi    i  i     ivv  v   i v  vvv   v  i   ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_74494003_7   3545 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCT 3594
                           v  i  i              v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_74494003_7   3595 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3644
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_74494003_7   3645 TTAAAGACTTAAATGTCAGACCTAAAACCATAAAAATCCTAGAAGAAAAC 3694
                          i ?    i       v   v       i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_74494003_7   3695 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3743
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_74494003_7   3744 AAACACCGAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3793
                         vi     i      vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_74494003_7   3794 ATTCAACTAAAGATCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3843
                           iv  v v  i v   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_74494003_7   3844 CAGGCAACCTACAGAATGGGAGAAAAGTTTTGCAA--TATACTCATCTGT 3891
                         v  i     i                vv       --i   i--     v
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chrX_74494003_7   3892 CAAAGGGCTAATATCCAGAATCTACAATGAACTTAAACAAATTTTCAAGA 3941
                         i  i  i  vi          v  i  v     ivv    v ivvi  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_74494003_7   3942 AAAA---AAACAACCCCATCAAAAAGTGGGCAAAGGATTTGAATAGCCAC 3988
                             ---   i     v  i?    i                    v  i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_74494003_7   3989 TTCTCAAAAGGAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTT 4038
                              v    i   i  vi viii     v ii          i     i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_74494003_7   4039 ATCATCACTGGCATT 4053
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  

3065 24.58 2.12 0.67  chrX_74494003_74502892     7503  8397 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74494003_7   7503 TAGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 7552
                          i    v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74494003_7   7553 GACCATACGACA-AAAGCAATCTACAGATTCAATGCAATTCCCATTAAAA 7601
                          i v    vv v-   vii              i     i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74494003_7   7602 TATCATCATCATTCTTCACAGAACTAGAAAAA--AATTCCTGAAATTTGT 7649
                          vi  v vv v  i  ii     v v  v  i--i  -   i     ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chrX_74494003_7   7650 ATGAAACCAAAAAAGAGCCCACATAGCCAAAGAAAGGCTATGCAAAA--A 7697
                            i  viiv  ii  v  viv         iv  v-  -  v    -- 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGAA 197

  chrX_74494003_7   7698 GAACAAATCTGGAGATATCACATTACCCAATTTCTAAATATACTACCAGG 7747
                                vi     ivv     i v         v   iv      v i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_74494003_7   7748 CTATAGTCAACAAAACAGCATGGTACTTGTATAAAAACAGGCACACAGAC 7797
                            i   v v   i    ii       v i    ii i  i  i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_74494003_7   7798 CAATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTAGAGCCA 7847
                                 i     v    ii           v   v i i   vi i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_74494003_7   7848 ACTGATCTTTGAGGAAGAAAACAAAACACA--AAATGGGGAAAGGACACC 7895
                          i    i  i  vi i iviv   i  -  --v           i i vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGT 396

  chrX_74494003_7   7896 CGATTCAACAAATGGTGCTGGGATAGTTGGCAAGCCATATGCAGAAGAAT 7945
                          vv                    i ii   vv ?   i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_74494003_7   7946 GAAACTGAAGCCTCATCTCTCATCATATACAAAAATCAACTCAAGATGGA 7995
                            ii  i v  ii i   v  i             i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_74494003_7   7996 TCAAAGACTTAACC-TAAGACCTGAAATCATAAAAATTCCAGAAAATAAC 8044
                            ?    i   vi-     v  i   ii      v iii    i v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_74494003_7   8045 AT-GGGGAAACTCTTCTAGACTTTGGTTTAGGCAAAGAGCTCATGACCCA 8093
                           -  ? v  v     vv   i    v        v ivi  v iivivv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_74494003_7   8094 GAC-CCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATCGGACTT-- 8140
                            -         v v         iv   i   i   i  i      --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_74494003_7   8141 ---AAACTAAAAAGCTTCTGCACAGCAAAATAAA-TATTCAGCAAAGTAA 8186
                         ---   i      -   i  ii vv    iv v -   iv  -     i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGA 694

  chrX_74494003_7   8187 ACAGAAAATCTACAGAATGGGAAAAAATATTCTTAAACTATGCATCTGAT 8236
                          v   v  i i           i        ivi   ii  ii       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_74494003_7   8237 AAGGGACTAATATCCAGAATCTACAAGGAACTCAAACAAATCATCAAGAA 8286
                                 vi          v  i  i      vv    v   vi  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_74494003_7   8287 AAA-ACAAATAATCCCATTAAAAAGTGAGCTAAAGACATGAATAGACAAT 8335
                            -        i  v   ?    i  i  v  i  iv          v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_74494003_7   8336 TCTAAAAAGAAGATATACAAATGGCCAACAA--ACATGAAAAAATGCTGG 8383
                            vv                       i  --         i     vi
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_74494003_7   8384 ACATCACTAATGAT 8397
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (125 / 91)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.47 (25 / 17)  


1800 17.27 2.26 26.15  chrX_74528860_74532142.rev     1603  2795 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74528860_7   1603 TGGAAAGGTGTTCCATGTTCATGGATAGGAAGACCCAATATTATCACGAT 1652
                                i i i              v       ii      i i v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74528860_7   1653 GTCAGTTCTTCCCAA-----TCCATAGATTCAATGCAATCCCAATCAAAA 1697
                          v  i v  i     -----  i i        i        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74528860_7   1698 TCCCAGCAAATTACTTTGTGGATATCAACAAACTCGTTCTAAAGTTTTTA 1747
                                vivi vi    ii  v  ii    i  vi i     i  iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_74528860_7   1748 TGGAGAGGCAAAATAACCAGAACA-CCA---CAATATTGAAAAAGAA--- 1790
                             i v    iiv v      i -   ---    v           ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_74528860_7   1791 CAATGTTAGAGGACTGACACTAGCCAATTTCAAGACTTACTATAAAGCAA 1840
                            v   i       v     vv          i        i     v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_74528860_7   1841 CAATAATCAAGACACTGTGATATTGATGAAATAATAGACAAACAGATCAG 1890
                           i           v    i  i  iiiv  vi       v i      i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_74528860_7   1891 TGGAA-AAAATAGAGAACCTGGAAATAGAAATAGACCTACATAAATAAAA 1939
                              - i   v    ii i------       i   i i i -------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC------AGAAATAAACCCATACA------- 337

  chrX_74528860_7   1940 TCTCCTGATCTTTGACAAAGGGGTAAATGCAATACCATGGAGAAAAGACC 1989
                         --------------------------------------------------
  L1M4_orf2#LINE/    338 -------------------------------------------------- 337

  chrX_74528860_7   1990 TTGTTTGTTTTGTTTTGTTTTGTTTTGTTTTATTTTGTTTTTAAAGACGG 2039
                         ----------------------------     -----------------
  L1M4_orf2#LINE/    338 ----------------------------TTTAT----------------- 342

  chrX_74528860_7   2040 AGTCTTGCTCTGTCTCCCAGGCTGGAATGCAGTGATGCAATCTTGGCTCA 2089
                         --------------------------------------------------
  L1M4_orf2#LINE/    343 -------------------------------------------------- 342

  chrX_74528860_7   2090 CTGCAACCTCCACCTCCTGGGTTCAAGCAATTTTCCTGCCTCAGCCTCTT 2139
                         -------------------   -   vii      ---------------
  L1M4_orf2#LINE/    343 -------------------GGT-CAATTGATTTTC--------------- 357

  chrX_74528860_7   2140 GAGTAGCTGGCATTACAGGCGCATGTCATCACACCTGGCTAGTTTTTGTA 2189
                         --------------------------------------------------
  L1M4_orf2#LINE/    358 -------------------------------------------------- 357

  chrX_74528860_7   2190 TTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAAGCTCGTCTCGAACT 2239
                         -----------    i  ---------  --      -------------
  L1M4_orf2#LINE/    358 -----------GACAAGG---------GT--GCCAAG------------- 372

  chrX_74528860_7   2240 CCTGACCTCAGGTGATCCACTGGCCTCGGCCTCCCGAAGTGCTAGGAAGG 2289
                         ----   -------  i  v   --------------------i i   i
  L1M4_orf2#LINE/    373 ----ACC-------ATTCAATGG--------------------GGAAAGA 391

  chrX_74528860_7   2290 ATCATCATTTTTACAAATGGTTCTGGAACAAATGGATATCCACATGCAAA 2339
                           vi  v   iv         v    i    v      ?           
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_74528860_7   2340 AAATATAAATCTAGACACAGACCTTACACCCTTCATAAAAATTAACTCAA 2389
                          i -  i  vi i   v vv    i     v vi i              
  L1M4_orf2#LINE/    442 AGA-ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_74528860_7   2390 AATGGATTACACACCTAAATATAAAACACAAAACTGTATAACTCCCAGAA 2439
                                i ? v        i   i vvi      i  v     ii    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_74528860_7   2440 TGTAACATATGTGAAAATCCAGATAACCTTGGGTTTGGTGATGGCTTTTT 2489
                         viv      v ? v     ivvi i          v  ii    i  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_74528860_7   2490 AGATGGAACACCAAAGACACAATCCATGAAAGAAAGAATTAATAAGCTGG 2539
                             ivi        ii     v v ii       i   vi    ii   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_74528860_7   2540 ACTTCATTAAAATAAAAAAGTTGCTCTGCT---AAAGACACTATCAAGAG 2586
                                i     v     v  -i v    ---  i             i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTT-TTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_74528860_7   2587 AATAAAAAGGC----CACATGCTGAAAGAAAATATTTGCAAA--AGACAC 2630
                          i i     i ----    viv  ii                -- v i i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_74528860_7   2631 ATGATAAAGAGCT-GTAATCTAAAATACACAAAAATTATTTAAAATTAAA 2679
                         v      i ii  -   -  i i    i i   i vivi   v  i v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTA-TCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_74528860_7   2680 CAATAAGAAAGCAAGCATCTCAA---AAAAA-GGGCTAAAGACCTGAACA 2725
                         i     i  ii   ii v i   ---     -    v  i  ii    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_74528860_7   2726 GACACCTCACCAAAGAAGATATATAGATGGCAAATAAACATACAAAAAGA 2775
                             ii  v              i i     v     i  i ii      
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_74528860_7   2776 TGCTCCACACTATATGTCAT 2795
                              v   ii ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (134 / 69)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 14.12 (339 / 24)  


3165 27.67 0.33 0.22  chrX_74556527_74570659.rev     4885  5791 (8342)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74556527_7   4885 TGGAAGAACATTCCCTGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4934
                              ii i  i  v  i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74556527_7   4935 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGTCATCCCCATAAAGC 4984
                            v     v i   iv i  i  i        i iv     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74556527_7   4985 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5032
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74556527_7   5033 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTGAGCCAAAAG 5082
                                viiv  ii  v  v v  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74556527_7   5083 AACAAAGCTGGAGGCATCACACTACCTGGCTTCAAACTATACTACAAGGC 5132
                                i      vv       v  iiii      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74556527_7   5133 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5182
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74556527_7   5183 AATGGAACAGAACAGAGGCCTCAGAAATAACGCCACATAACTACAACTAT 5232
                                i    iv   ivii         vv   i i vi  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_74556527_7   5233 GTAATGTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5282
                         v i  v  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_74556527_7   5283 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCTGA 5332
                         v  i  i              v      v  ?   v   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_74556527_7   5333 AACTGGACCCCTTCCTTACACCTTATACAAAAATCAATTCGAGATGGATA 5382
                          ii         v   i     v           i  i  i i      v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_74556527_7   5383 AAAGACTTAAACTTTAGACCTAAAAATATAAAAACCCTAGAAGAAAACCT 5432
                          ?    i    iv v   v      v       vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_74556527_7   5433 AGGCATTACCACTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5482
                            ?i v vivi  iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_74556527_7   5483 CACCAAAAGCAATGGCAACAAAGGCAAAA-TAGACAAATGGGATCTAATT 5531
                                    vvi        i v    -    i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_74556527_7   5532 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5581
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_74556527_7   5582 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5631
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_74556527_7   5632 GGCTAATATCCAGAATCTACAATGAACTCCAACAGATGTACAAGAAAAAA 5681
                          i  vi          v  i  v      iv   iv vv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_74556527_7   5682 ACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCTC 5731
                              i     v  i?    i           iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_74556527_7   5732 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5781
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_74556527_7   5782 CACTGGCCAT 5791
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.25 (5 / 4)  

3204 27.42 0.44 0.44  chrX_74556527_74570659.rev    10996 11903 (2230)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74556527_7  10996 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 11045
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74556527_7  11046 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGTCATCCCCATCAAGC 11095
                            v     v     iv i  i           i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74556527_7  11096 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 11143
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74556527_7  11144 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 11193
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74556527_7  11194 AACAAAGCTGGAGGCATCACACTACCTGACTTCAGGCTATACTACAACGC 11243
                                i      vv       v  ii i    iiviv        v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74556527_7  11244 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 11293
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74556527_7  11294 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 11341
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_74556527_7  11342 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 11391
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_74556527_7  11392 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCT 11441
                           v  i  i              v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_74556527_7  11442 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCGAGATGGA 11491
                            ii    i    v   i     v           i  i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_74556527_7  11492 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 11541
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_74556527_7  11542 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 11591
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_74556527_7  11592 AACACCAAAAGCAATGGCAACCGAAGCCAAAATTGACAAATGGGATCTAA 11641
                         i            vvi     vi   vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_74556527_7  11642 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGTGTGAAC 11691
                          iv  v v  i i   i  ii vv    i  v    i ivv iv     v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_74556527_7  11692 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 11741
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_74556527_7  11742 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAACA 11791
                         i  i  vi          v  i  v      vv    v iv i  v  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_74556527_7  11792 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 11841
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_74556527_7  11842 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 11891
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_74556527_7  11892 ATCACTGGCCAT 11903
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

2572 23.94 4.12 6.18  chrX_74556527_74570659.rev    12729 13651 (482)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_74556527_7  12729 AAGATATTCCATATCCATGAAATGTAAGAATTAATGCTGTTAAACTGTCC 12778
                                i    i i    i v  v    v     ii      iv  v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_74556527_7  12779 ATACCACCTTAAGATG-TTTACAAATTC---GTGTTCCCCATCAAAATTC 12824
                             i-  ii  iv  - i    i    --- iiv    i        i 
  L1M4_orf2#LINE/     55 ATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_74556527_7  12825 CAATGGCATTTTTCACAGAAAGAGAAAAACCAATCTTAGTCGTCATATGA 12874
                           iiv  v     ii      vv  v  i ii   i  ivvv       i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_74556527_7  12875 AACTACAAAAGACTCTGAATAGCCAAAATGATCTTGAAAAAGTATATCAA 12924
                           v i   ii   i v            ii            v v v   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_74556527_7  12925 ATCTGGC---CTCACACTTCTTGATTTCAAATTTCAAAGTATATTACAAA 12971
                          vi   v---          ------- v         iiv  i      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTC-------CCAATTTCAAAACTTACTACAAA 246

  chrX_74556527_7  12972 TCTATAGTAATAAAAACAGTATGATACTGCCATAAAAACAGACACAAAGA 13021
                         v   i      v  i     i  i     v     ii i     i v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_74556527_7  13022 ACAATGGAAAAACATAGGGAGCCCAGAAATAAACCCATAAATACACAGCC 13071
                         v        v iv  v i   i                 v  vi ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_74556527_7  13072 AACTGCTCTTCCACAAGATTGCCAAGAATACAAAATGTTCAAAGAACAGT 13121
                           i  v i   v     iv        vi -------     v ii----
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCA-------TTCAATGGG---- 385

  chrX_74556527_7  13122 CTCAATACACTGTATTAGAAAAACTTAATATATTGCTTTTCAGCCTTTTG 13171
                         -----------------    i ------   v -       i ------
  L1M4_orf2#LINE/    386 -----------------GAAAGA------ATAGT-CTTTTCAAC------ 405

  chrX_74556527_7  13172 GCTAAGATGAGGTATAGGAAATCTAGATTATCTCCATGCAAAATAATTAG 13221
                         ---- i   iv i- i   v v  i   - ? iv         v   v i
  L1M4_orf2#LINE/    406 ----AAATGGTGC-TGGGACAACTGGAT-AKCCACATGCAAAAGAATGAA 449

  chrX_74556527_7  13222 ATTGAACACTTATCTTACACCATTCACCAAAAACAATTCAAAATGGATTA 13271
                         i   i  v i  i  i       vi  v    vi  i           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_74556527_7  13272 AAGACTTAAACATAAAAAATGAAAACATAAAATTCT-------------- 13307
                         ?    i    ii   i iv i   vi      i   --------------
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_74556527_7  13308 GGTG-AAAGCTCCGTGACATTGGTCTTCACAGTTATTTCTTGGATCGGAC 13356
                           ? -   v  i      v    vi vvi  i vi      i   vv   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_74556527_7  13357 AC-AAAAACAGTGAG-AATAAAAGTAAAA-TAAACAAGTGGGATTACATC 13403
                           -    i  -ii  -  i     v    -  i i  i v   i v    
  L1M4_orf2#LINE/    600 ACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_74556527_7  13404 CACCTAAAAAGCTTCTGCACTGCAAAGGAAAT----AACACAGTGAAACG 13449
                         v vv v    i   i  ii  v       v i----  v v       v 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_74556527_7  13450 GCAGTTTACAGAATGGGAGAAACTGTTTGGAAACTATACATCTGGTAAAG 13499
                         i  iiii               v i    v   ii   i     i   i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_74556527_7  13500 TGTTAATATCCAAAATATATAAGGAACTCACACAACTCAAAAGCAAATAA 13549
                         vii vi      i         i      vi         v ii   -  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AA 797

  chrX_74556527_7  13550 GGAAAA----CCAGATTAAAAATGGGCAAAAAACTTGAATAGACATTTTT 13595
                          iv   ----   iv ?             ii i              i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_74556527_7  13596 CCAAAGAAGACATACAAACAGGCAACAGGTATATGAAAA--TGC--AA-A 13640
                                   i       ii v   i i i i       --   --  - 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_74556527_7  13641 TCAAATATTCA 13651
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.65 (135 / 82)
Gap_init rate = 0.03 (24 / 904), avg. gap size = 3.96 (95 / 24)  


3007 24.00 3.54 3.32  chrX_74575442_74579520.rev     2690  3593 (486)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_74575442_7   2690 GAAAGATATTCAATGTTCATGTATTGGAAAAAT-AGTATTTTTTAAACGT 2738
                                  i v         v       i v - i    v  v i i v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_74575442_7   2739 TCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCTTATCAAACTA 2788
                         iv     v      vii              i       i       v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_74575442_7   2789 CCAATGACATTCTTCACAGCAATAGAAAAA--AATTCTAAAACTTATATG 2836
                            iivi v  i  ii   v   v  v  i--i  i      i i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_74575442_7   2837 GAATAACAAAAGACCCAGAATAACCAAAGCTATCCAAAGAAAAATGAACA 2886
                            vvi   ii           i     i v   ivi i   i v     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_74575442_7   2887 GAATCGGAGGAATCACATTATCTGACTCAAATTATACTACATAACTATAT 2936
                         i i i      v     i -  i----   v  ------  v    ----
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACT-TCC----CAATTT------CAAAACT---- 237

  chrX_74575442_7   2937 GACTCAAATTATACTACATAACTATAGTAACCCAAATAGCATGGTACTGG 2986
                         -----------       v i   i     i v i i  ii         
  L1M4_orf2#LINE/    238 -----------TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_74575442_7   2987 CATAAAAACAGACATGCAGACAAATGGAACAGAATACAGAACCCAGGCAC 3036
                              ii i      ii   iv       i     vv   ii    iv i
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_74575442_7   3037 ACATCCACCCACCCATCATTGAAGTCATTTTTGACAAAGTTACCAAGAGC 3086
                          v i   iv  iii  vi i-  v v     i     i v i      v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTC-AATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_74575442_7   3087 ATACACTGAGGGAAAGACAATCTTTTTGATAAATGGTGCTGGGAAAACTG 3136
                           v  v  i  i  ii i i      ii i              v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_74575442_7   3137 GATACCCATATGACAAAAAATAAAACTAGACCCCTATCTCCTGCCATATA 3186
                             ?   i   vv   i   i  ii i        i   vii       
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_74575442_7   3187 CAAAAATCAAATCAAAATGGATTAAATACTTAAATCTCAGATCTCAAACT 3236
                                i  v           i ? v  i     v v   v  v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_74575442_7   3237 ATGAAGCTACTACAAGAACACAT-TGAATAAGATCTCTAGGACATTGGTC 3285
                           i  i  vi  v     v    -v ?i   -    iiiv   v    vi
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGT 574

  chrX_74575442_7   3286 TGGGCAAAGTCTTCTTCAGCAAT-ACCCCACAAGCACAGGCAACCAAGTC 3334
                          i     v vi     -  vv  -  v   v       i     v  ivv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_74575442_7   3335 AAACATGGACAAA---AGCTTCTTCACAGT------------------AA 3363
                            v  i  i   ---ii    v   v i ------------------  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_74575442_7   3364 AGGATATGATCAACAGAGTGAATAGACAACCCACAGAATGGGAGAAAATA 3413
                             i iv     v i      v                           
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_74575442_7   3414 TTTGCAAACTACCCATCTGACAAAGGATTTATAACCAGAATATATAAGAA 3463
                                 ii ivi      i  i   i  i  v             ii 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_74575442_7   3464 GCTCAAACAAATCTACCGGAAAAAAATCTAATAATCCCATCAAAAAATGG 3513
                         i   vv    v  v iviv     i - v     i  v  i?        
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGG 822

  chrX_74575442_7   3514 GCAAAATATTTGGATAGACCTTTCTCAAAAGAAGACATACAAATGGCAAG 3563
                              iv     i      v      v        i           v i
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_74575442_7   3564 TAGGCATACGAAAAGAT------CATTAGAGCAATG 3593
                           i   i i        ------   i ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (128 / 85)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 4.13 (62 / 15)  


3073 27.77 0.88 0.44  chrX_74588885_74595119     4839  5742 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74588885_7   4839 TGGAAGAACATTCCATGCTCGTGGATAGGAAGAATCAATATCGTGAGAAT 4888
                              ii i  i     i  i     v      v i     i  v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74588885_7   4889 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4938
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74588885_7   4939 TATCAATGACTTTCTTCATAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 4986
                          vi  iivi i  i  iii    -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74588885_7   4987 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTGAGCCAAAAG 5036
                                viiv  ii  v  viv  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74588885_7   5037 AACAAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGGC 5086
                                i      vv   i   v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74588885_7   5087 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5136
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74588885_7   5137 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCAAATCTACAACT 5184
                                i    i--    i  --        vv  ii v  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_74588885_7   5185 ATGTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5234
                          vv    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_74588885_7   5235 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAACT 5284
                           v  i  i              v      v  ?   i   v i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_74588885_7   5285 GAAACTGGATCCCTTCCTTACACCTTATACGAAAATCAATTCGAGATGGA 5334
                            ii    i    v   i     v     i     i  i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_74588885_7   5335 TAAGAGACTTAAACATTAGACCTAAAAACGTAAAAACCCTAGAAGAAAAC 5384
                          v ?    i    ii v   v      vii     vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_74588885_7   5385 CTAGGCATTACCACTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5434
                         v    ?i v vivi  iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_74588885_7   5435 AACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGGTCCAA 5484
                         i            vvi     v    vv     v  i    v  iiiiv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_74588885_7   5485 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAAC 5534
                          i   v v  i i   i  ii vv    i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_74588885_7   5535 AGGCAACCTACAAAATTGGAGAAAATTTTCGCAACCTACTCCTCTGACAA 5584
                           i     i   i   v         v  i    vii iviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_74588885_7   5585 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATGTACAAGAAAA 5634
                         i  i  vi          v  i  v      iv    v vv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_74588885_7   5635 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5680
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_74588885_7   5681 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5730
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_74588885_7   5731 ATCACTGGCCAT 5742
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (145 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3092 26.65 0.99 0.99  chrX_74599611_74602898.rev     1890  2797 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74599611_7   1890 TGGAAGAACATTCCATGCTCATGGGTACGAAGAATCAATATCGTGAAAAT 1939
                              ii i  i     i      i vv     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74599611_7   1940 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1989
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74599611_7   1990 TACCAATGACTTTTATCACAGAA--TGGGAAAAAACT-ACTTTAAAGTTC 2036
                          v   iivi i   v ii     --  --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_74599611_7   2037 ATATGGAACCAAAAAGAGACCACATT-GCCAAGTCAATCCTAAGCCAAAA 2085
                                 viiv  i iiv   v v -     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_74599611_7   2086 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 2135
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_74599611_7   2136 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 2185
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_74599611_7   2186 CAACGGAACAGAA--AAGAGCCCTTAAAAATAATGCCACATATCTACAAC 2233
                            i    i    --i    i  -- i      vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_74599611_7   2234 TATCTGATCTTTGACGAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 2283
                         i vi    i  i   i ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_74599611_7   2284 CCTATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGGAGAAAGC 2333
                         i  v  i  i     i        v      v  ?   i   v i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_74599611_7   2334 TGAAACTGGATCCCTTCCTTACAACTTACACAAAAATTAATTCAAGATGG 2383
                             ii    i    v   i   v v  i           i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_74599611_7   2384 ATTAAAGACTTAAATGTTAGACCTAAAACCTTAAAAACCCTAGAAGAAAA 2433
                           i ?    i       v   v       iv     vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_74599611_7   2434 CCTAGGCA-ATACCATTCAGTACATAGGCATGGGCAAGGACTTCATGTCT 2482
                          v    ?i- v i -   ivv  v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_74599611_7   2483 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGATCT 2532
                          vi            vvi          vv     v       v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_74599611_7   2533 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGA 2582
                         v  i   v v  i i   i  ii vv    i  v  i i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_74599611_7   2583 ACAGGCAACCTACAGAATGGGAGAAAATTTTTG--AATTCTACGCATCTG 2630
                          v  i     i                 v    --   iv  i--     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTG 742

  chrX_74599611_7   2631 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAG 2680
                          i  i  i  vi          v  i         vv    v iv i  -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA- 791

  chrX_74599611_7   2681 CAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAAGAGAC 2730
                         i     i     i     v  i?    i     i      v    v    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_74599611_7   2731 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACGCAAGAAGAAATGC 2780
                          i     v        i  vi viii     v ii i  v   i i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_74599611_7   2781 TCATCATCACTGGCCAT 2797
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


2910 27.85 0.88 0.55  chrX_74615520_74617624.rev      710  1614 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74615520_7    710 TGAAAAAACACTCGATGCTAATGGGTAGGAATAAACAATATCATGAAAAT 759
                           i   i i ii v   i v    i v    v vvi     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74615520_7    760 GGCCATACTGCCCAAAGTAATGTATACATTCAATGCTATCCCCATAAAGC 809
                            v     v      v i  v  i v      i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74615520_7    810 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 857
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74615520_7    858 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 907
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74615520_7    908 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTAGAAGGC 957
                                i      vv       v  ii i      viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74615520_7    958 TACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAAAGATATAGACC 1007
                                 i   i    ii        vi iv ii i i v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74615520_7   1008 AATGGAACAGAACAGAGGCCTCATAAATAACACCACACATCTACAA-CAA 1056
                                i    iv   ivii  v      vv   i    i  iii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_74615520_7   1057 TCTGACCTTTGACAAACCTGACAAAAACAAGTAATGGGCATAGGATTTCC 1106
                          -   ii  i     ivv  v   i v  vvi      v v  i  vvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_74615520_7   1107 TATTTAATAAATGGTGTTGGGAAAACTTGCTAGCCATATGCAGAAAACTG 1156
                          v  i  i        i     v    v v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_74615520_7   1157 AAACTGGACCCCTTCCTTATGCTTTACACAAAAATTAACTCAAGTTGGAT 1206
                           ii         v   i ii iv  i                iv     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_74615520_7   1207 TAAAGACTTAAATGCTAAGACCTAAAACCATAAGAACCATAGAAGAAAAC 1256
                         i ?    i      -     v       i    i vi v           
  L1M4_orf2#LINE/    498 CAWAGACCTAAATG-TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_74615520_7   1257 CTAGGCA-AGACCATTTAGGACATAGGCATGGGCAAAGACTTCATGACTA 1305
                         v    ?i- i i -  iiv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_74615520_7   1306 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATACA 1355
                         vi            vvi          vv     v  i    v   iviv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_74615520_7   1356 ATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGAA 1405
                           i   v v  i i   i  ii vv    iv v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_74615520_7   1406 CAGGCAACCTACAGAATGGGAGAAAACTTTTGCAATCTATCTATCTGACA 1455
                         v  i     i                iv       vii  v       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_74615520_7   1456 AAGGACAAGTATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 1505
                          i    vv           v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_74615520_7   1506 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATAAACAGACACTT 1551
                           i    ----   v  i?    i    ii      v i  i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_74615520_7   1552 CTCAAAACAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTCAT 1601
                            v   v    i  vi vi       i  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_74615520_7   1602 CATCACTGATCAT 1614
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (141 / 107)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


 805 22.75 4.71 2.35  chrX_74618756_74625143       32   286 (6102)    L1M4_orf2#LINE/L1      648   908 (0)  

  chrX_74618756_7     32 CAAAGTTGAG--TTCTTACTCTACAAAAGACCCTGT----GAAGTGAACA 75
                             i  i i--i i  iiv  v    i   v  i ----i       --
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA-- 695

  chrX_74618756_7     76 GTAAAACAAGCTACAGACTGGGAGAAAATATTTATAAAACAAATATCTCA 125
                         --  i    v i     v               ii   v  v      v 
  L1M4_orf2#LINE/    696 --AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_74618756_7    126 CAAAGGAATAATTTCCAGAATATTTAAAGAACTCTCATTACTTAATAGTA 175
                         i  i   v vi v          v           i iv   i    i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_74618756_7    176 AAAG--CAAACTATCTGAGAATAAAATATGG---AAAGACATGAACA-AT 219
                            i--    iv i ii v-- ?   v    ---  i  iv    i - i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAAT--TWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_74618756_7    220 ACTTTACCAAAGAGGATATACAAATGGCAAATGAGCATATGAAAAGATGT 269
                          i  iv       i              v   i    i           i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_74618756_7    270 TCAAAATTATTCGCCAT 286
                             v  i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (37 / 20)
Gap_init rate = 0.03 (7 / 261), avg. gap size = 2.57 (18 / 7)  

3196 26.87 0.66 0.66  chrX_74618756_74625143     4988  5895 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74618756_7   4988 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAGTCAATATCATGAAAAT 5037
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74618756_7   5038 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 5087
                            v     v i   iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74618756_7   5088 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5135
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74618756_7   5136 TATGGAACCAAAAACGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5185
                                viiv  iv  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74618756_7   5186 AACAAATCTGGAGGCATCACACTCCCTGACTTCAAACTATACTACAAGGC 5235
                               vi      vv       i  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74618756_7   5236 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5285
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74618756_7   5286 AATAGAAGAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5333
                            i   v    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_74618756_7   5334 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5383
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_74618756_7   5384 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 5433
                           v  i  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_74618756_7   5434 GAAATTGGATCCCTTCCTTACACCCTATACAAAAATTAATTCAAGATGGA 5483
                            i     i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_74618756_7   5484 TTAAAGAATTAAAAGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5533
                          i ?   vi    v  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_74618756_7   5534 CTAGGCA-ATACCATTCAGGACATGGGCATGGGTAAGGACTTCATGACTA 5582
                         v    ?i- v i -   iv   v v  vv i  i  v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_74618756_7   5583 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5632
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_74618756_7   5633 ATTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5681
                           i   -     i -   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_74618756_7   5682 ACAAGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTAGTCATCTGAC 5731
                          v ii     i                 v      ivii vvi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_74618756_7   5732 AAAGGGCTAATATCCAGAATCTACAGTGAACTGAAACAAATTTACAAGAA 5781
                           i  i  vi          v  i iv     vvv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_74618756_7   5782 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGAATATGAACAGACACT 5831
                            i     i     v  i?    i         i  v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_74618756_7   5832 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5881
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_74618756_7   5882 TCGTCACTGGCCAT 5895
                         v i   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2864 28.72 1.68 0.22  chrX_74629175_74633767.rev     3208  4102 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74629175_7   3208 TGGAAACACATCCCATGCCCATGGATGGGTAGAATCAATGTTGTGAAAAT 3257
                               v i        ii       v  v   v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74629175_7   3258 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAAA 3307
                          i v     v  v   vii       i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74629175_7   3308 TAA-AACCATCATTCTTCACAGAGCTAGAAAAAACAATTCTGAAATTCAT 3356
                          vv- i iii -  i  ii    iv v  v  ivii  i  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_74629175_7   3357 ATGGAACCAAAAAATAGCCCACACAGCCAAAGCAAGATTAAGCAAAAAGA 3406
                               viiv  iiv v  viv i       i   vv  i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_74629175_7   3407 GTAAATCTAGAGGCGTCACACTACCTGGTTTCAAATTATAATATAAGGCC 3456
                         ii   vi i    vv       v  iii       viv  v  i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_74629175_7   3457 GTAGTA-CCAAAACAGTATAGCACTGGTATAAAAATAGGCACATAGACCA 3505
                         ii    -i   i     i i i     i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_74629175_7   3506 ATGGAACAGAAGAGAGAACAAAGAAATAAACCCAAATACTTATAGCCAAC 3555
                               i    vv    iivv             v i i    i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_74629175_7   3556 TGATGTTTGACAAAGGAAACAAAAATAT----------AAGGACGCCCTT 3595
                             v  i     i  viv   i vi  ----------   i iivi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_74629175_7   3596 TTCAACTAATGGTGCTGGGATACTTGGCTAGCCACATGTAGGAGAATGAA 3645
                               v             i vi   v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_74629175_7   3646 ACTGCATCCTTATCTATCACCTTATAGAAAAATCAACTCAAGATGGATTA 3695
                         ii  v i  i  i  vv    v    v      i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_74629175_7   3696 AGAACTTAAACCTAAGACCTGAAGCTATAAATATTTTAGAAGATAACACT 3745
                         ?ii  i    iv     v  i  i       vv i        v    iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_74629175_7   3746 GGAA-AAACCTTTCTAGGTATTGGCTTAAGCAAGGATTTCATGACCAGGA 3794
                           ?i-   i   iv - iiv    v   i    v i    v iivi v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_74629175_7   3795 -ATCCAAAGGAAATGCAATAAAAACAAAGATAAATAGTTGGGACCTAATT 3843
                         - i v    v v v    i    iv   i   i   iv v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_74629175_7   3844 AAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAA 3893
                            v v  i i      ii vv    i iv  vi   iv i   i  v i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_74629175_7   3894 ACAGCCCACAAAGTGGGAGGAAATCTTCACAATCTATACATCTGACAAAG 3943
                            i      i i      i    v  ii   vii   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_74629175_7   3944 GCCCAATATCCAGAATCTACAATGAAGTCAAACAAATCAGCAAGAAAAAA 3993
                          v ivi          v  i  v   v  vv    v   ii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_74629175_7   3994 ACAAACGATCTCATCAAAAAGTGGGCTAAGGACATGAATAGATAATAATC 4043
                              ii i iv  i?    i     v     iv        i v vv  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_74629175_7   4044 AAAAGAAGATATACTAATGGCCACCAAACATATAAAAA-ATGCTCAACAT 4092
                         v             v        vi  i  i  i    -           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_74629175_7   4093 CACTGAAGAT 4102
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.58 (155 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


2114 26.31 6.72 3.30  chrX_74664780_74667209.rev     1062  1939 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74664780_7   1062 TGGAAGAACATTTAATGCTCATAAACTAGAAAAATCAATATAATTAAAAT 1111
                              ii i  iiv   i    ii i i   i v i     vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74664780_7   1112 AACCATACTGGCCAAAGCAATTTACAGAATCAACATTATTCTTATCAAAC 1161
                         ii v     vv     vii  i      v     iiv  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74664780_7   1162 TACCAA-TGTCATTTTTCACATAATTTAAAAAA--AATTCTAAAATTCGC 1208
                          v   i-  i -     ii  v  v  i v  i--i  i         ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_74664780_7   1209 GTGAAACCTAAAAAGAGCCCAAATACCTAAAAGGAGCCCA-AATAGCTAA 1257
                         i  i  ----------------  i ----    ii    -      i  
  L1M4_orf2#LINE/    150 ATGGAA----------------ATGC----AAGGGACCCAGAATAGCCAA 179

  chrX_74664780_7   1258 AACAATCTTAATATAAACGAAAAA-AAAGCTGGTGGTATCACATTACCCA 1306
                                  i ---   v   i  -    i   v  vv     i v    
  L1M4_orf2#LINE/    180 AACAATCTTGA---AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_74664780_7   1307 ATGTCAAACTATACTGTAAGCCTACAGTAACCAAAACAGCATGGTACTGG 1356
                           v     viv    ii  iv         i   i    ii         
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_74664780_7   1357 TATAAAAACAGACACATAGACCAATGGAACAAAAT----AACCTAGAAAT 1402
                         i    ii i     i     i        i i   ---- ii i      
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_74664780_7   1403 AAAGCTGCACACCTTCAGCCATCTGGTCTTTGACAAAGTTCACAAAAATA 1452
                            v iii   ii vii i  vi  i i  i     i v vv   i vi 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_74664780_7   1453 AACAATGAGGAATGAAT--TCATTACTCAATAAATGGTTCTGGAATAACT 1500
                         vv     i    v    --  v  --    i       v    i i    
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACT 424

  chrX_74664780_7   1501 GGCTATCAACATGTAGAAGAATTAAACTGTATCCCTACCTTTCACTGTAT 1550
                           v  ? v     i i      v  ii  v i        iv   ii   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_74664780_7   1551 ACAGAAATGAACTCAA-----------GACCTAAACTATAAGAATT---- 1585
                            i    v       -----------        - i     ii ----
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAA-TGTAAGAGCTAAAA 523

  chrX_74664780_7   1586 CTATAAACAACGCT-ATAA-ACACCAT-TCTGTATAT-----TGGTCTTA 1627
                                --  v  - v  - v v   -vv?   v  -----  ii   i
  L1M4_orf2#LINE/    524 CTATAAA--ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chrX_74664780_7   1628 G---AAATAA--ATTTATGACTTATTCC-TCAAAAGCAATTGCAACAAAA 1671
                          --- iii  --i   v v vv   vv -i        vvv         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_74664780_7   1672 ATAAAAATTGACAAATGTGACCTAATTAAAA---AGAGCATCTGCACAGT 1718
                         iv      v  i    vv   i v  i    --- i i v i  ii vvi
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_74664780_7   1719 AAAAGAAACAATCTACAGATTAAA----CAAACTGAAGAATGAGAGAAAA 1764
                            i  v  v   v v i v i  ----   v iiv      i       
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_74664780_7   1765 TATTCACAAA--------CTAACAAAGGCCTAATATCTAGAAACTATAAT 1806
                             ii    --------  i i  i  v  vi    i    vv     v
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_74664780_7   1807 GAACTTAAACAAGTGAACAAGCAAAAAACAAAGAACCCCATTAACAAGTG 1856
                              ivv    v v  i  vv    i     v     v   ? v  i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_74664780_7   1857 GGCAAAAGAC----ATAAACACTTTTCAAAAGAAGACATACAAACAGCCA 1902
                               i  i----   i   i  i  v        i       ii    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_74664780_7   1903 ACAAACATATGAAAACATGCTCCACATCACTAATCAT 1939
                          i  i  i       v      v      ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (139 / 89)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.38 (88 / 26)  


2175 28.31 5.32 2.49  chrX_74729634_74736305.rev     5299  6181 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74729634_7   5299 TGAAAAAATATTCTATGCTCACAGATAGGAAGAATAAATATCATTAAAAT 5348
                           i   i    i i   i   ii   v      v v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74729634_7   5349 GGCCACACTGCCTAAAGAAATTTACAGATGCAATGCTACTCCTATAAAAC 5398
                            v i   v  i   vvi  i       v   i  v ii     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74729634_7   5399 TACAAATAACATTCTTTTTAGAACTAGAAAAAAACT-ATTTAAAAATTTA 5447
                          v v iivi v  i   vi    v v  v  i--  -  iiv      i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_74729634_7   5448 AATGAAAATGAAAATAAAAAGAGCCTGAATAGCCAAGGCAATCCTAAGCA 5497
                         v   i     v  i-----i  v  v          ii     i i iv 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG-----GGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_74729634_7   5498 AAGAGAGCAAACCTGGAGACATCACATTACTCAATTTCAAACTATACTGC 5547
                          ii   i    vi     ivv     i v i          viv    i 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_74729634_7   5548 AAGGCTACAATAATCAAATCAGCATGGTACTGGTACAAGAACAGACACAT 5597
                           i      i       iv   ii         i i   i i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_74729634_7   5598 AGACCAATGGAACAAAATAGAAAGCCCAGAAGTAAGGCCACACACCTGTG 5647
                            i        i i   v  i  i      i   iv   i   ii i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_74729634_7   5648 ATTATCCTATGTTTGACATATCTGACAAAAACAAGTAATTAGGAAGGGAC 5697
                         i i viiv  v  i    vivv  v   i v  vvi   vi    i i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_74729634_7   5698 TCCCTGTTCAATAAATGATGCTGAAATAACTGGCTAGCCATATGCAGAAG 5747
                         vvi  v     i     i     ii i      v  ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_74729634_7   5748 ATTCAAATTGGACCCCTTACCTAA-ACCATAAACAAAAATCCACTTAAGG 5796
                          v v  i          -    v -      v        iv   i  ii
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_74729634_7   5797 TAGATTAAAGACTTAAATGCAAAACCCAGAACTATGAAAATCCTGAAAGA 5846
                          i   i ?    i      i  i v i i      i   v  i ii    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_74729634_7   5847 CAACCTAGGCATATGAACTGGCAAAAATGTGAACATATGAACT-GGCATA 5895
                         v   v    ?i  --  iivv ------    v - -  iii -    vv
  L1M4_orf2#LINE/    543 AAACATAGGNGTA--AATCTTC------GTGACC-T-TGGGTTAGGCAAT 582

  chrX_74729634_7   5896 AATTTTATAACCAAGATGCTGAAA--ACAATTGAACCAAAAGCAAAAATT 5943
                         ii   iv  ivi v  ii ii   --    -- v v      v      v
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATA 630

  chrX_74729634_7   5944 TACAAATAGG--TTC-T---AATTAAA----------------------- 5964
                         v i    v  --   - ---       -----------------------
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_74729634_7   5965 --TCAAGAGAGTAAACAGAATAACTACGAAATGGGAGAAAAGTTTTGCAA 6012
                         --      i   i  v   vv v i  ii            vv       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_74729634_7   6013 CT-ATGCATCTGACAAAGGCCTAGTATTCAACATCTATAAGAAACTTAGT 6061
                         v -  ii      i  i  v  v    i  iv  v     ii    i-- 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--T 778

  chrX_74729634_7   6062 TAC----CAA-----AACAACCAAAAAACCACGTTAAAAAGGGAGCAAGA 6102
                            ----   -----  v iv    v    vvi  ?    iv i    ii
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_74729634_7   6103 GAAATAAAAAGACACTTTTCAAAAAAGGACATGAATTTGGCCAAAGAACA 6152
                           vv i  v     i  i  v   i i  i  iv vv       vi i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_74729634_7   6153 TATGAAAAAA-GCTCAGTATCACTGATTAG 6181
                         i       i -     ii    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.29 (69 / 21)  


1585 28.19 5.07 5.07  chrX_74792234_74794145.rev      528  1435 (477)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74792234_7    528 TGAAGGGGTACACCATATTAAGGGATTGTAAGACTTGATATTTTAAAAAT 577
                           i ii i  iv    i  v v      v       i     v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74792234_7    578 ACTGA--CTCTCTTAAATTGG------GA---AATG-A--------CAAA 607
                         ivii --   i i-      i------  ---  i - --------    
  L1M4_orf2#LINE/     51 GGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_74792234_7    608 ATTCCAAG-GCTTCTCAAGTATGAATGTTGATAA-TAAATTCTAAAATTT 655
                           i   iv-  i i ivv i -   -i    i  -ivi  i        i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCA-GAA-ATTGACAAGCTGATCCTAAAATTC 147

  chrX_74792234_7    656 AAATA-AAATGCAATGGGGCATGAATAGTCAATGCAATATTTAATAAGAA 704
                          v  i-        v  iv vv      i   vi    v  v  v     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_74792234_7    705 --------CTAGAAAACTAACATTACCATATAGTAATAC---CTATCAAA 743
                         --------i i  ii   v   i v  vv  vvi  v  ---   iv  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_74792234_7    744 TTAAAACAATTAAGACAGTGTGGTATTATTGCAAG-ATAAACAACCTGAG 792
                         i  v ii   i              i iviii   -   i   vviv  v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_74792234_7    793 AAATGGAACAACATTGAGAAGATATAAAAAAGCCCATACATATTTGATCA 842
                         v       i iv       ivvi v   v  i         v v  i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_74792234_7    843 CCTGATTTACGATAAGCATGATACTACAATGCCATGATGAAAGC-TGGGT 891
                         vi      v   i   vi  vi vv  v  v v   iv     v- i --
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG-- 395

  chrX_74792234_7    892 TTTCTTTTTTGCAATAATGGTGCTTCATAAATTGAAAATTGGTGTGGTAT 941
                         --      ivi   --        -----ii--  v  i   ----i  ?
  L1M4_orf2#LINE/    396 --TCTTTTCAACAA--ATGGTGCT-----GG--GACAACTGG----ATAK 430

  chrX_74792234_7    942 TTTACCATTTACCATGTGGTGGAAATAAAATGAAAATTCGACCTCTTACC 991
                         ----   -----    i-----   - i      i-  v    i  -   
  L1M4_orf2#LINE/    431 ----CCA-----CATGC-----AAA-AGAATGAAG-TTGGACCCCT-ACC 463

  chrX_74792234_7    992 TTACATCATACTCAAAAATAAATTCCAGATAATTTTTACATCTCAAAATA 1041
                          i   i    iv       v  i  v i  iiv iv? v i  v  vi  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_74792234_7   1042 AAAGGTAAAACAATAAATCGTATTTGAAGAAGGCACAGAAATACCTCATT 1091
                          i  v      v     v - v  v      ii  i  i?i  vv  v i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_74792234_7   1092 GTCACCTTGGTATACACAAAGATTTTTTAAACATAGCTCATAAAGCACTA 1141
                           v       vv  vi   v i   i   i i  ii v vv       v 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_74792234_7   1142 ATCACATAGGAAATTAATTGATAATGTGGACTACA-CAATGACTAAGAAC 1190
                         iiv   v i    v-   v     vv      v  -   -i i   i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAA-AATTAAAAAC 660

  chrX_74792234_7   1191 TTCTGCTCATTGAAAGATAACATTAAGACTGTGAAAATGTAACCAATATA 1240
                           i  iv v ii  i  i vi  i    vv       vii    v i v 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_74792234_7   1241 -TGAGATAAAACATTTGCAGTACATATATTTGACAAAAGACTTGTATCTA 1289
                         -  i  v    i       ivv       i   i  ii          i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_74792234_7   1290 TAAAGTACAAA--ACT-TTACAAGTCAACAAGAAAAGAAAGACAGAT--- 1333
                         v  vi  i   --   -      v    i  v    ---     i  ---
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAA---AGACAAATAAC 807

  chrX_74792234_7   1334 -CAGTTGAAAAAAATGGGCAAAACACTTGAACAAGTATCTCACAAAAGAG 1382
                         -  i  --?             iv i     i iii  i  v v     i
  L1M4_orf2#LINE/    808 CCAATT--WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_74792234_7   1383 AATATCCAAGTGGCTGATAAACACATAAAAATGAGG-TCAGTGTTATTTG 1431
                         i    v   i    ii    i     i    -  v -   iii i ????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZ 904

  chrX_74792234_7   1432 TTAC 1435
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.33 (144 / 108)
Gap_init rate = 0.04 (38 / 908), avg. gap size = 2.42 (92 / 38)  


2607 26.21 2.09 2.09  chrX_74796555_74802148.rev     4196  5103 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74796555_7   4196 TGGAAAAACATTCCATCCTCATGGATAGAATGAATCAATATCATTAAAAT 4245
                               i i  i    vi        v i v  v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74796555_7   4246 GACCTTACTGCTCAAAGTAACTTATAGATTCCATGCTATTCCCATCAAAC 4295
                          i vv    v i    v i ii  i      v i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74796555_7   4296 TACCATTGATATTCTTCACAGAATTTAAAAAA--ACTCCTTTAAATTTCA 4343
                          v   viviiv  i  ii     v  i v  i--iv    --   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chrX_74796555_7   4344 TAGAGAA---CAAAAAAAACCAGTATAGCCAAGACAATCCTAAGGAAAAA 4390
                           vi   ---   iii v-    v        i      i ---      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTT---GAAAAA 194

  chrX_74796555_7   4391 AAAAATGAAACAAAGCTGGAGGCATCACGCTACCAAACTTCAAACTATAC 4440
                         i  i ----      i      vv    i  v  v  i      viv   
  L1M4_orf2#LINE/    195 GAAGA----ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_74796555_7   4441 CATAAGGCTACAGTAACCAAAATGGCATGTTATGGGTACCAAAACTGACA 4490
                         i i  i          i   i ii ii  v  iv  i iv ii iv    
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_74796555_7   4491 TATAGATCAATGGAACAAAACAGAGACCACAGAAATATCACCACACATCT 4540
                                        i i  iv    viv        vvv   i    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_74796555_7   4541 ACAAACATCTGATTTTCAACAAACCTGACAAAA--ATTAGCAATGGAAAA 4588
                          iiiv  vi        i    ivv  v   i --   --      ii  
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT--CAATGGGGAA 388

  chrX_74796555_7   4589 AGAAT--TCCTTATTTAACAAATGGCGCTGGGAAAACTGGCTGGCCATAT 4636
                              --  i  -- i         i       v      v i?   i  
  L1M4_orf2#LINE/    389 AGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_74796555_7   4637 GCAGAAAACTGAAACTGGACCTCTGCCCTAGACATTATACAAAAATTAAC 4686
                            i  i v    ii      i  i  ii v  vv               
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_74796555_7   4687 TCAAGATGGAATAAAGACTTAAATGTAAAATGC-AAAACCATAAATACCC 4735
                             i     vi ?    i         i -  -     i     -  i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAA-ACTC 534

  chrX_74796555_7   4736 T-AGAAGAAAACCTAGGTA-AAACCATTCAGGACATAGGCATTGGGAAAT 4783
                          -          v    ?i-   i -   iv   v v  -i  i  v   
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGG-GTTAGGCAAT 582

  chrX_74796555_7   4784 A-TTTCTT-GACAAAACGCCCAAAGAAATTGCAACAAAAGCCAAAATTGA 4831
                         i-      -  i vi  i  v    v vvv          vv     v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_74796555_7   4832 CAGAT-GAAATACAATTAAACTAAAGAGCTTCTTCACAGCAAAATAAACT 4880
                         i i  - i v v  - i   v v  i i   i vii vv    iv v   
  L1M4_orf2#LINE/    633 TAAATTGGACTTCA-TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_74796555_7   4881 ATCATCAGAGTGAACAAGCAACCTACAGAATGGGAGAAAATTTTCTCAAT 4930
                             vv i      v ii     i                 v  iv   v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_74796555_7   4931 CTACCTATCTGACAAAGGTCTAATCTCCAGAATCTACAAAGTACATAAAC 4980
                         ii iv       i  i  v  vi v        v  i    v  vivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_74796555_7   4981 AAATGTATA-TGAAAAAACAAACAACCCTGTCAAGAAGTAGGCAAAGGCT 5029
                           v vv   - i    i     i     vi i? i  i i        v 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_74796555_7   5030 ATCAATAGACATTTCTCAAAAGAAGACATTTATGCAGCCAACAA--ACAT 5077
                         v v              v        i  vi viii     i  --    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_74796555_7   5078 GAAAAAA-GCTTAACATCACTGATAGT 5103
                              i -   i       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.58 (38 / 24)  


2811 28.62 0.99 0.66  chrX_74807914_74814293.rev     4985  5889 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74807914_7   4985 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5034
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74807914_7   5035 GTCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGT 5084
                          v v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74807914_7   5085 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5132
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74807914_7   5133 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5182
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74807914_7   5183 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5232
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74807914_7   5233 TACAGTACCCAAAACAGCATAGTGCTGGTACCAAAACAGAGATATAGACC 5282
                                vi   i    ii i  i    i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74807914_7   5283 AATGGAACAGAAC--AGAGCCCTCAGAAATGATGCCACATATCTACAACT 5330
                                i    i--    i  --      i vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_74807914_7   5331 TTCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5380
                         vvi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_74807914_7   5381 CTATTGAATAAATGGTGCTGGAAAAACTGGCTAGCCAGATGTAGAAAGCT 5430
                           v  v  i            i v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_74807914_7   5431 GAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGA 5480
                            ii    i    v   i     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_74807914_7   5481 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5530
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_74807914_7   5531 CTAGA--TAATACCATTCAGGACACAGGCATGGG-AAGGACTTCATGTCT 5577
                         v   i--   - i -   iv   viv  vv i  -  v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_74807914_7   5578 AAAACACCAAAAGCAATGAAAACAAAAGCCAAAATTGACAAATGGGATCT 5627
                          vi            vviiv        vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_74807914_7   5628 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGGGA 5677
                         v  i   v v  i i   i  ii vv    i  v    i  vv i  v  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_74807914_7   5678 ACAAACAACGTACAGAATGGGAGAAATT-TTCACAATCTACTCATCTGAC 5726
                          v i     vi               v -  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_74807914_7   5727 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5776
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_74807914_7   5777 AAAAACAA-CAACCCCATCAACAAGTGAGCGAAGGATATGAACAGACACT 5825
                            i    -i     v  i? v  i  i  i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_74807914_7   5826 TCTCAAAAGAAGACACTTATGCAGCCAAAACACACATGAAAAAATGCTTA 5875
                             v        i ivi viii     v vi          i     i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_74807914_7   5876 TCGTCACTGGCCAC 5889
                         v i   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (152 / 104)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2828 27.90 2.12 0.78  chrX_74816814_74822934     4733  5628 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74816814_7   4733 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATAGAAAT 4782
                              ii i  i     i      i v      v i     ii vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74816814_7   4783 GGCCATAGTGCCCGAAGTAATTGATAGATTCAATGCTATCCACATCAAGT 4832
                            v   v v   i  v i  iv i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74816814_7   4833 TATCATTGATTTTCTTCATAGAATTAGAAAAAAACT-ACTTTAAATTTTA 4881
                          vi  viviii  i  iii    v v  v  i--  - iii    v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_74816814_7   4882 TATGGACCCAAAAAAGAGCTTGTATAACCAAGACAATCCTAAGAAAAAGG 4931
                               vviiv  ii  v iv v   i    i      i i i   i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74816814_7   4932 AACAAAGCTGGAGTCATCACACTACTTTACTTCAAAGTATACTACAAGGC 4981
                                i     vvv       v iiv i      iiv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74816814_7   4982 TACAGTAGCCAAAACAGCTTGGTATTGGTACCAAAACAGATATATAGATC 5031
                                ii   i    iv     i   i iv ii i   i         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74816814_7   5032 AATGGAACAGATCCGAGGCCTCAGAAATAATGCCAAACATCTACAA-CGA 5080
                                i   vii   ivii         vv   v    i  iii- i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_74816814_7   5081 TCTGATCTTTGACAAACCTGACAAGAAAAG-CAATGGTGAAAGAATTCCC 5129
                          -    i  i     ivv  v     vv v-      v        vvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_74816814_7   5130 TATTTAATAAATGATGTTGGGAAAACTGGGTAGCCATATGCAGAAAACTG 5179
                          v  i  i     i  i     v      i  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_74816814_7   5180 AAACTGGACCCCTTCCTTACAACATATACAAAAATTAACTCAAGATGTAT 5229
                           ii         v   i   v                     i   v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_74816814_7   5230 TAAAGACTAAAACGTAAGACCTAAAACCATAAAAGCCCTAGACGAAATCC 5279
                         i ?    iv   i      v       i      vi i    v    v v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_74816814_7   5280 TAGGCA-ACACCAGTCAGGACAT--AGTCATGGGCAAAGAGTTCATGACT 5326
                             ?i- v i -v  iv   v --i  i --     v iv   v iiv 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGAT 594

  chrX_74816814_7   5327 AATGG-ACGAAAAGCAGTGGCAACAAAAGCTAAAATTGACAAACGGGATC 5375
                          -  i-  v       vvi          vv     v  i   iv   ii
  L1M4_orf2#LINE/    595 A-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_74816814_7   5376 TAACTAAACTAAAGAGCTTCTGCACACCAAAAGAAACTATCATCACAGGG 5425
                          v ii   v v  i i   i  ii vi    i  v       vv v  v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_74816814_7   5426 AACAGGCAACCTACAGTATGGGAGAAAATTTTTGCAATCTATCCATCTGA 5475
                           v  i     i    v            v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_74816814_7   5476 CAAAGGGCTAATGTTCAGAATCTACAA-GAA-----ACAAATTTACAAGG 5519
                         i  i  i  vi i i      v  i  -   -----    v iv i  vi
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_74816814_7   5520 AAAAAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 5565
                             i    ----   v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_74816814_7   5566 TTCTCAAAAGAAGACATTTATGTGACCAGCAA--ACATGAAAAAAAGCTT 5613
                              v        i  vi vi  i   ii  --         i v   i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_74816814_7   5614 ATCATCACTGGTGCT 5628
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  


3043 27.83 0.44 0.55  chrX_74836371_74842228.rev     4459  5367 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74836371_7   4459 TGGAAGAACATTCTATGCTCATGGGTAGGAAGAATCAATATCGTAAAAAT 4508
                              ii i  i i   i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74836371_7   4509 GGCCATACTGCCCAAAGTAATTTATAGATTCAATCCCATCCCCATCAAGC 4558
                            v     v      v i  i  i        iv v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74836371_7   4559 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4606
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74836371_7   4607 TACGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCTTAAGCCAAAAG 4656
                           i    viiv  ii  v  v v  v     iv       i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74836371_7   4657 AACAAAGACAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4706
                                vii    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74836371_7   4707 TACAGTAACCAAAACAGGATGGTACTGGTACCAAAACAGAGATATAGATC 4756
                                 i   i    vi         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74836371_7   4757 AACGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 4804
                           i    i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_74836371_7   4805 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4854
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_74836371_7   4855 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCT 4904
                           v  i  i              v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_74836371_7   4905 GAAACTGGATCACTTCCTTACACCTTATACAAAAATTAATTCAAGATTGA 4954
                            ii    i v  v   i     v              i    i  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_74836371_7   4955 TTAAAGTCTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5004
                          i ?  v i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_74836371_7   5005 CTAGGCATTACCATTCAGGACATAAGCATGGGCAAGGACTTCATGTCTAA 5054
                         v    ?i v viv   iv   v vi vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_74836371_7   5055 ATCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATATAA 5104
                         iv           vvi          vv     v  i    v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_74836371_7   5105 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5154
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_74836371_7   5155 AGGCAACCTAAAAAAATGAGAGAAAATTTTCGCAACCTACTCATCTGACA 5204
                           i     i v i  -  i        v  i    vii ivi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_74836371_7   5205 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5254
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_74836371_7   5255 AAAACAAACAACCCCATGAAAAAGTGGGCAAAGGATATGAACAGACACTT 5304
                           i     i     v  v?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_74836371_7   5305 CTCAAAAGAAGACATTTTTGCAGCCAAAAGACACGTGAAAAAATGCTCAT 5354
                            v        i  vivviii     v ii   i      i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_74836371_7   5355 CATCACTGGCCAT 5367
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (142 / 107)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2136 27.71 5.82 2.28  chrX_74842825_74846644.rev     2453  3329 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74842825_7   2453 TGGAAAAGCATTTCATGCCCATAGAT----AGAATCAATATTATAAAAAT 2498
                               iii  ii    ii   i   ----   v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74842825_7   2499 GACCATACTGCCCAAA-------GCA-ATTTAACGCTATTTCTATCAAAT 2540
                          i v     v      -------i  -   i     v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74842825_7   2541 TACCAA-TGTAATTTTTCACAAAGCTAGAAAAAACTAGTC-TACAATTCA 2588
                          v   i-  iv-     ii  i iv v  v  i-  ii  -  v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_74842825_7   2589 TATGGAAC--CAAAGAAAAACACA-AATAGCCAAGGCAATCCTAAAAATA 2635
                                v--   i i --- v  -         ii     i i    - 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAA-A 194

  chrX_74842825_7   2636 AAGGAATAAAGTTAAAGACATCAAACTTACCCAACTTCAAACTATACTAC 2685
                         i i   i      ii  ivv   v    -     i      viv      
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTAC 243

  chrX_74842825_7   2686 AGAGAAACAGTAACCAAAGCAGCATAGTACTGGAAAAAAAAAAACAGATA 2735
                          i  vv       i   ii   ii i       v v  ii ---i   i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA---TAGACA 290

  chrX_74842825_7   2736 TGTAGATCAATGAAACATAATAGAGAGCCCAGAAATAA------------ 2773
                          i          i  i v   v     i          ------------
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_74842825_7   2774 --GGTTATCTAATCTTCAACAAAGTTGACAAAAACAAGCACTGAGGAAAA 2821
                         --   i vi i  i   i    i v  v   i v  vv  v  i     i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_74842825_7   2822 GCTTTCCTCTACAATAAGTAGTGCTGGGATAACTGGCTAGCCATAAGCAG 2871
                         iv vvi  i v   i  i i         i      v  ?   i v   i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_74842825_7   2872 AAGATTGAAACAGGGTCCCTTCCATATACTGTATAAAAAAAA-AACTCAA 2920
                             v    iiv  ii    v  vi i  ii    v     v-       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_74842825_7   2921 GATGGATTAAAGACTTAAGTGTAAAACCCAAAACTATAAAAACCCTGAGA 2970
                         i      i ?    i   i     i v i            vi i iii 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_74842825_7   2971 GACAATGTCCAGCCAATACCATTCTAGACATAGGAACTGATGAAGATTTT 3020
                           v  ii vvi?vi  - i -   vv   v v  iviv iii v i   i
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_74842825_7   3021 ATGACGAAGACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATG 3070
                         v iivv v             vvv          v      v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_74842825_7   3071 GTATGT------AATTAAAGAGCTTCTACACAGCAAAATAAACTACCAAC 3114
                          v iv ------       i -   i iii vv    iv v    i   v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_74842825_7   3115 AGAGTAAACAGACAACCTACAGGA--------AATATTTGTGAAATATGC 3156
                          i   i  v        i    i --------        ii  vi  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_74842825_7   3157 ATCTGACAATTGTGTAATATCC-GCATCTATAAGGAACTTAAACAAAT-- 3203
                               i  vv vv vi     - v  v     i     ivv    v --
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_74842825_7   3204 -TTACAAGGAAACACACAATCCCCTTAAAAAGTGGGCAAAGGACATGAAC 3252
                         - v i  ii i   v i  i  vv  ?    i           iv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_74842825_7   3253 AGAC-TGTTTCAAAAGAAGACATACATGTGGCCAACAAGCATTCTTTTCC 3301
                             - v i  v        i     vi       i     ------- v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA-------CA 880

  chrX_74842825_7   3302 TAAAAAAAAGCTCAATATCACTGATCAT 3329
                          i    i v      i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.96 (71 / 24)  


 765 22.56 2.05 1.54  chrX_74866355_74869291.rev     1305  1499 (1438)    L1M4_orf2#LINE/L1        1   196 (712)  

  chrX_74866355_7   1305 TGTAAAGATATTCAATACTCATGGATCAAAAGAATTAATATTGTTAAAAT 1354
                           v        i v  ii        iii    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74866355_7   1355 GACAATACTACCCAAAGCAATTTGCAGATTCAATGCCATCCCTATCAAAA 1404
                          i       v      vii  i i         i  v             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74866355_7   1405 TTCCAACAGCATTCTTCACAGAAATATTTTTAAA---ATCCCAAAATGTA 1451
                          i   i v  v  i  ii       -- vvi  i---    i     vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCA 148

  chrX_74866355_7   1452 TATGGAACTACAAATGAACACA-AATAGTCAAAGCAATTCTGAATAAAA 1499
                                v i   i- i  v  -     i    i    ii    v  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

Transitions / transversions = 2.14 (30 / 14)
Gap_init rate = 0.02 (4 / 196), avg. gap size = 1.75 (7 / 4)  

2060 28.55 1.41 0.42  chrX_74866355_74869291.rev     1738  2448 (489)    L1M4_orf2#LINE/L1      191   908 (0)  

  chrX_74866355_7   1738 AAAAGGAAAA-AAAGCTGGAAGCATCAAACTACTTGACTTCAAAATTTAC 1786
                              i i  -    i    i vv   v   v iii i       i    
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_74866355_7   1787 TACGAATTTCTAGTAA-CAAAATTAGTATAGTACTGGTATAAAAACACAC 1835
                            i  vi vi     -   i i-   i i       i    ii i v  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGAC-AGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_74866355_7   1836 ATATGTATCAATGGAAAAGAAGAGACAACCCAGATATATATCCACACATT 1885
                             iv          v    vv  v ii     v   v i   i     
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_74866355_7   1886 TACAAACAACTCATCTTTGACAAAGGCACT-----TATACAATGAGAAAA 1930
                           iiiv   i v  i  i     i  ii i-----i  v     i i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_74866355_7   1931 GAACAGTCTCTTCAATAAATGTTGCTGAGAAAATTGAATAACTATATGCA 1980
                            i     i     i     v     i  v  i  i   ? i i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_74866355_7   1981 GAAGAATGAAGCTAGATTCCTATATATCTCCCCAAACAAAA-TCAAGTAA 2029
                         i          i i  ii    iv vv v  vi v      - i  v v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_74866355_7   2030 AAACAAATTAAAAACTTAAATCTAAGACCTAAAACAAGAAAACTACCAGA 2079
                            iii  i ? i  i     v     v       v v      vii   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_74866355_7   2080 AAAACAACATTGGGAAAAGACTCTAAGACATTTGTCTTGACAAATATTT- 2128
                          i  -     v  ?iv  iv  iiiv   v  v vi v i   vvi   -
  L1M4_orf2#LINE/    540 AGAA-AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_74866355_7   2129 TTGTGTAAGACCTCAAAAGCATAGGCAACCAAAGCAAAATTAAA-AAATG 2177
                           ivi  v   vi        i i     v    v    v  i -    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_74866355_7   2178 ATATTACATCATGCTACAGGGGTTATGCACAGCAAAGGAGACAACCAAAA 2227
                         iv i v     viv vv iiiv  v  ii vv       v  v i   i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_74866355_7   2228 AAATAAAGAGACAATCCACAGGACGAGAGAATAATATTTGCAAACCTTCT 2277
                           i i  i      i      i i i     -            i v v 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCATAT 737

  chrX_74866355_7   2278 ATCTGTCAAAGAATTAATAACTGGAATATATAAGGAGCTCAAACAAGTTA 2327
                              vi  i i i vi  v ii          i  i   vv    v i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_74866355_7   2328 ATAGCAAAAATATAAATAATACAATTTTTAAATGGGCAAAAGATCTGAAT 2377
                            ii     v i      iv     ?vv           i   i     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_74866355_7   2378 AGACATTTTTCAAAATAATACATACAAATTGCCAATACATATATCAAATA 2427
                                 i  v   v  v i        v       vii i  v   vi
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_74866355_7   2428 GTGCTCAACATAACTAATGAT 2448
                         i          v ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (118 / 81)
Gap_init rate = 0.01 (9 / 718), avg. gap size = 1.44 (13 / 9)  


2914 28.03 2.00 1.00  chrX_74878774_74884909.rev     4747  5645 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74878774_7   4747 TAGAAAAACATTTTATGCTCATCGATAGGAAGAATCAATATTGTGAAAAT 4796
                          i    i i  iii   i    v   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74878774_7   4797 GGCCATACTGCCCAAAGCAATTTATAGATCCAATGCTATTCCCATTGAGC 4846
                            v     v      vii  i  i    i   i  v  i  i  ii iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74878774_7   4847 TACCATTGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAATTTCA 4894
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_74878774_7   4895 TATGGAACCAAAAAAGACCTCGTATAGCCAAGACAATCCTAAGCAAAAAG 4944
                                viiv  ii    iv v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74878774_7   4945 TACAAAACTTGAGGCATCGTGCTACCTGATTTCAAACTATATTACAGGGC 4994
                         v     ii v    vv  iii  v  ii        viv  i    ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74878774_7   4995 TACAGTAACAAAAACAGGATGGTACTGCTACCAAAACAGATATATAGACC 5044
                                 iv  i    vi        vi iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74878774_7   5045 AATGGAATAAAACAGAGGCCTCTGAAATAATGCCGGACATTTACAACCAT 5094
                                  i  iv   ivii v       vv  iv       iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_74878774_7   5095 CTGATCTTTGACAAACCTGACAAAA--AATAAAAAGCAATGGCAAAAGGA 5142
                         i    i  i     ivv  v   i -- v ------      vi    i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATT------CAATGGGGAAAGAA 392

  chrX_74878774_7   5143 TCTCCTATTTAATATATGGTGCTGGGAGAACTGGCTAGCCATATGCAGAA 5192
                          vvi  v  i  i v            v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_74878774_7   5193 AACTGAAACTGGACCCCTTCCTTATACCTTATACAAAAATTAACTCAAGA 5242
                         i v    ii         v   i i   v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_74878774_7   5243 TTGATTAAAGACTTAAATGTAATACCTAAACCCATAAAA---------GA 5283
                          v   i ?    i         v v     v i      ---------  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_74878774_7   5284 AAACCTAGGCAATACTATTCAGGACAGAGGCATGGGCAAAGACTTCATAA 5333
                             v    ?ivv v v   iv   vvv  vv i     v ii   v  i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_74878774_7   5334 GTAGGACACCAAAAGCAATGGCAATGGAAGCCAAAATTGACAAATGGGAT 5383
                         i  v             vvi    iii   vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_74878774_7   5384 CTAATTACACTAAAGAGGTTCTGCACAGCAAAAGAAACTATCATCAGAGT 5433
                         i v  i v v v  i iv  i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_74878774_7   5434 GAACAGGCAATCTACAGAATAGG-GAAAATATTTTGCAATCTATCCATCT 5482
                            v  i   i i       i  -          -    vii  vi    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCT 741

  chrX_74878774_7   5483 GTCAAAGGGCTAATATCCAGAACCTACAAAGAACTTAAACAAATTTACAA 5532
                          vi  i  i  vi         iv  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_74878774_7   5533 GAGAAAAACAA----CCCAATCAAAAAGTGGGCAAAGAATATGAACAGAC 5578
                         v i   i    ----      i?    i         i  v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_74878774_7   5579 GTTTCTTAAAAGAAGACATTTATATGGCCAACAAATATATGACAAAAAGC 5628
                         i     iv        i  vi v        i  ii i    v  i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_74878774_7   5629 TCATCATCACTGGTCAT 5645
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.00 (27 / 9)  


2959 27.10 1.33 0.88  chrX_74897064_74899501.rev     1043  1946 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74897064_7   1043 TGGAAGAGCATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 1092
                              iiii  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74897064_7   1093 GGCCATAGAGCCCAAAGTAGTGTATAGATTCAATGCTATCCCCATCAAGC 1142
                            v   vvv      v ii v  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74897064_7   1143 TACCATTGACTTTCTTCACAGAATTAGAAAAAAAACCTACTTTAAATTTC 1192
                          v   vivi i  i  ii     v v  v  i--- iv iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_74897064_7   1193 ATATGGAACCAAAAAGGAGCCTGCATAGCCAAGACAATCCTAAGCAGAAA 1242
                                 viiv  i   v  v v        i      i i iv ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_74897064_7   1243 GAACAAAGCTGGAGGCAC-CATGCAACCTGACTTCAAACAATACTACAAG 1291
                                 i      -  -  ii vv  ii i      vvv        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_74897064_7   1292 CCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGA 1341
                         v         i   i    ii         i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_74897064_7   1342 CCAATAAAACAGAATAGAGATCTCAGAAATAATGACACACATCTACAA-C 1390
                         i    ii  i     v    vii         vvv  i    i  iii- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_74897064_7   1391 AATCTGATATTTGACAAACCTGACAAAAACAAGCAATGCAGAAAGGATTC 1440
                            -    v  i     ivv  v   i v  vv     vi     i  vv
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_74897064_7   1441 CCTATTTAATAAATGGTATTAGGAAAACTGGCTAGTTATATGCAGAAAAC 1490
                         i  v  i  i       ii i   v      v  ?ii i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_74897064_7   1491 TGAAACTGGACCCCTTCCTTACACCTTACACAAAAAAATAACTCAAGATG 1540
                             ii         v   i     v  i       v-        i   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAACTCAAAATG 494

  chrX_74897064_7   1541 GATTAAAGACTTAAATGTAAGAAATAAAACCATAAATACCCT-AGAAGAA 1589
                            i ?    i           iv      i     -  i  -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAA 543

  chrX_74897064_7   1590 AACCGAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 1638
                            vv   ?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_74897064_7   1639 CTAAAACACCCAAATCAATGGTAACAAAGGCGAAAATTGTCAAGTGGGAT 1688
                         v  vi     v   v  vvi i      i vi     v vi  i v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_74897064_7   1689 CTAATTAAACTAAAGAGCTTCTGCATAGCAAAAGACACTATCATCACAGT 1738
                         i v  i   v v  i i   i  iiivv    i          vv v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_74897064_7   1739 GAGCAGGCAACCTACAGCATGGGAGAAAATTTTTGCAATCCATCCATCTG 1788
                           iv  i     i    v            v       vi   vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_74897064_7   1789 ACAAAGGGCTAATATCCAGAATCTACAAGGAACTTTAACAAATTTACAAG 1838
                          i  i  i  vi          v  i  i     i v    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_74897064_7   1839 AAAAAGA------ACCCCATCAAAAAGTGGGCAAAGGATATAAACAGACA 1882
                                ------    v  i?    i            v i  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_74897064_7   1883 CTTCTCAAAAGAAGACACTTATGCAGCCAACAAGCA--TGAAAAAAAGCT 1930
                         i     v        i ivi viii     i     --      i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_74897064_7   1931 CATCATCACCGGTCAT 1946
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (140 / 101)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


1162 25.84 1.82 2.13  chrX_74926385_74928282      120   448 (1450)    L1M4_orf2#LINE/L1        1   328 (580)  

  chrX_74926385_7    120 TGGAAGAACAATCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 169
                              ii i vi     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74926385_7    170 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 219
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74926385_7    220 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACCTTAAAGTTC 267
                          v   iivi i  i  ii     -   --- v  i  - i i    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_74926385_7    268 ATATG--AATGCAAAAAAGAGCCCGCATTGCTAAGTCATTCCTAAGCCAA 315
                              --       ii--  v  v v  v  i  iv  v  i i ivv i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_74926385_7    316 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAA 365
                                   i      vv   ii  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_74926385_7    366 GGCTACAGTAACCAAAAGAGCATGGTGCTGGTACCAAAACAGAGATATAG 415
                         i          i   i v  ii    i    i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_74926385_7    416 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAA 448
                          i        i    i--    i  --        
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAA 328

Transitions / transversions = 2.04 (57 / 28)
Gap_init rate = 0.02 (7 / 328), avg. gap size = 1.86 (13 / 7)  

2239 29.43 4.20 1.25  chrX_74926385_74928282      526  1405 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_74926385_7    526 GAAAATCATTCCATGCTCATGGATAGGAGGATTTAATACTGTTAAAATGA 575
                             ivi  i     i        v   i  i      i      i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_74926385_7    576 CCACACTGCCCAAAGCAATTTACAGATCCAGTGTTGTTCCTATCAAACTA 625
                          v i   v      vii  i       i  ii ivi i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_74926385_7    626 CTAAAACTG--TTTTTCACAGAATAAGAAAATTCCATTTTAAAATTTATT 673
                          i i--   --     ii     vvv  v  viiv  ii       i  v
  L1M4_orf2#LINE/    103 CCAG--CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_74926385_7    674 TTTAAGAAAAAACA---GCCCCA---TATCCATAGCAATGCTATACAGAA 717
                          ---- i   vi  --- v    ---  v   v i    vi iv v ii 
  L1M4_orf2#LINE/    151 T----GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_74926385_7    718 AGAACAAAGCTGGAAGCATCTCATGACCCAATTTGAAATTATACTGCAAG 767
                                  i    i vv  v  ivv        v   viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_74926385_7    768 ACTACAGCAACAAAAAGCAACATGGTACAGATACAAAAACAGACAAATAG 817
                         i      i  iv  i -  iii      v ii i  ii i     v    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_74926385_7    818 ACAAAGGGAAGAGATTACAGAACTCAGAAATAAAACTGAACATCTACAAC 867
                          iv  v    v   v vv   iii          v iiv    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_74926385_7    868 CATCTGATCTTTGACAAAGCTGTCAATAAGA---AATGGTGAAACTACTC 914
                           vi    i  i     i v  i   v vv ---     v    vv ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_74926385_7    915 CCTATTCAATAAATACTGCCAGAATAACTGGCTAGCCATATGCAGAAGAT 964
                         i  v     i    iv   ii i i      v  ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_74926385_7    965 TGAAACTGAACCCCTTCCTTTCACCATATACAAATATCAACTCAAGATGG 1014
                             ii  i      v   iv             v  i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_74926385_7   1015 ATTAAAGACTTAAATGTAAAACTTAAAACTATAAAGC-CTTAGAAGACAA 1063
                           i ?    i         i vi            i -         v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_74926385_7   1064 CCT---TGTCAATGTCATTCTGGACATAGGAACTGGCAA-AATTTTATGA 1109
                          v ---?  v   -- -   vv   v v  iviv     -ii   iv ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_74926385_7   1110 CCAAGATACCAAAA-CATTTGCAA-AAAGGCAAAAATTGATAAGTGGGAC 1157
                         vi v  i       -  ivv    -   i v      v     i v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_74926385_7   1158 CCAATTAAA-TGAAACAGTTTCAACACAGCTAAAGAAACTATCAACAAAG 1206
                         iiv  i   - v   v v   ii-ii vv v  i  v        v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_74926385_7   1207 TAAAGGGACACTCTATTAAATGAAAAAAAATATTTTCAAGCTATTCATCT 1256
                          i  ii    vi i ivi    ii i         v   iii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_74926385_7   1257 GACAAT---CTCATACTCAGAATCTGTATGGAGCTCTAACAAATCAACAA 1303
                           i  v---  ii  ii      v i  vi  i    v    v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_74926385_7   1304 GCAAAAATCAAACAACCCCATT-AAAAATGGGCATAGGAC----ATAAGC 1348
                         vv    iv    i     v   -           v    i----   ii 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_74926385_7   1349 A----------GAAAACATGCACGCAGTCAGCAAGCATATGCAAAAAAAT 1388
                          ----------   i i  i  viii i  ii     i   v   i vii
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_74926385_7   1389 TCAGTATCACTGATCAT 1405
                            ii    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (154 / 102)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 2.40 (48 / 20)  


2232 29.77 1.73 3.78  chrX_74941182_74943204.rev      606  1532 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74941182_7    606 TGGAAAACCGTCCCATGCTCATGAATTGGAAAAATCAACATTGTTTAAAT 655
                               ivii       i     i       i v i  i      v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74941182_7    656 GACCATGCTGCCCAAAGCACAATTTA--GATTCCATCCA-TTTTTGTTAA 702
                          i v  i  v      vii--  i  --     v iv  - iii i i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_74941182_7    703 TTTGTCAA-TGCCATTTCTCACAGAATTAGAAAAAGCAATCCTAAAATTA 751
                         vv vi  i-    -   i ii     v v  v  ivii           v
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_74941182_7    752 ATATAGGACCAAA---AAAGAACCCA-AAGAGTGAAAGAAGTCCTAAGCC 797
                             i ----   ---  i i     -  v  iv   iv i  i i ivv
  L1M4_orf2#LINE/    148 ATATGG----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_74941182_7    798 AAAAGAACAAAGATGGCAACATTACATTACCTGACTCCAGGTTATACCAC 847
                          i          v   viivv i   i v  ii i i  iiviv   i  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_74941182_7    848 AAGGCTA-----ACCAAAGCAGCATGGAACTGGTATAAAAATAGACACAT 892
                           i    ----- i   ii   ii   v     i    ii       i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_74941182_7    893 AGATCAATGGAACAAAATAGCGCACCCAGAAATAATGCAACATACCTAAA 942
                                     i i   v v vii          vv v i i ii  vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_74941182_7    943 ACTAACTGATCTTTGGCAAAGCGGACAAAAATATACACTGGGGAAATGAC 992
                         iii  i    i  i i   i vv v   i vi  v  v        vi i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_74941182_7    993 ACCCTATTTAATAAATGGTGCTGTGATAATTGGATAGTCATAGGCAGAAG 1042
                          vi  v  i  i           v  i  i      ?i  i v   i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_74941182_7   1043 AATGAGACTGGACTCCCATCTTTCACCATATACTGAAATTAACTCAAGAA 1092
                              iii     i  i i  iv          vi            i v
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_74941182_7   1093 GAGTTAAAGGCTTAAAGGTAGTACTTACCACTATAAAAATTATAGAATAC 1142
                          ii i ?  i i    v   iv vi  vv         v iv     v v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_74941182_7   1143 AATCTAGAAAAAACTTTTCCAGATACTCACCTAGGCAAAGAATTTATAAA 1192
                           iv   i?iv  v i   vv  ivi vivi       v iv  iv  i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_74941182_7   1193 TAAAATCTTAAAAGCAAATGCAAGAAAAAGAAAAATAG-TCAAGTGGATC 1241
                           vi ivii       v v    v    ii        - v  v    - 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA-C 642

  chrX_74941182_7   1242 TTAATTAAACTAAAAATCTTCTACACAGCTTCTGATTGAAGCTGTGAAAT 1291
                           v  i   v v    v   i ii---     -----i   ---------
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGT---GCTTC-----AAAG--------- 675

  chrX_74941182_7   1292 AATCTGCTGAAATAATCAACAGCATAAACTGGCAACCTACAGAATGGGAG 1341
                         --------  v iv     v ivi i  vv i     i            
  L1M4_orf2#LINE/    676 --------GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_74941182_7   1342 AAAATATTTGTAAGCCATGCATTTGCCAATTAACTAATATCCATAATTTA 1391
                                   i  ii   ii  i  vi  vvi   vi      v   v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_74941182_7   1392 CAAGAAACTCAAACG-CTCTACAAGAATATAAACAAATAACTCCATT-AA 1439
                         i  ii     vv  i-   v i  v  v - i         i v   -  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAA-AGACAAATAACCCAATTWAA 816

  chrX_74941182_7   1440 AATTGGGTAAAGGATAAGAGCAGATATTTTTCAAAAAAAAGACATACAAG 1489
                           v    i       vv  ii   i    i  v   i  -  i      i
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-GATATACAAA 865

  chrX_74941182_7   1490 CAGCCAACAAACATATTAGAAACTGCTCAGTGTCACTAATCAG 1532
                         ii     i  i  i  v i  iv      iii   ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (168 / 105)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.83 (51 / 18)  


2512 26.23 2.52 2.85  chrX_74945651_74949938.rev     2896  3806 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74945651_7   2896 TGAAGACACATCCCATGCTCATGGATGGGTATAATTGATATAGTGAAAAT 2945
                           i i v i        i        v  v v v  i    v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74945651_7   2946 GACCATACAGCCTAAAGCAATCTACACATTCAATGCAATTCCCATCGAAT 2995
                          i v    vv  i   vii       v      i     i  i   i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74945651_7   2996 TATCAACATAATTCTTCACAGAACTAGAAAAAACAATCCTAACAT--ATA 3043
                          vi  i vvvv  i  ii     v v  v  ivii       v  --   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_74945651_7   3044 TGTAACAAAAATGAGCCCACA-TA-CCAAAAGGAATACTAAGCAACAAC- 3090
                           v  vviv  v ii    v -  -      v-   vi i iv  v  v-
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AATCTTGAAAAAGAAGA 199

  chrX_74945651_7   3091 -CAAAATTCTGGAGGCAAAACATTACCTGACTTCAAACTATACTTTAAGG 3139
                         -    i  --     vvvv   i v  ii i      viv    vi  i 
  L1M4_orf2#LINE/    200 ACAAAGTT--GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_74945651_7   3140 CCATAGTCACCAAAACAGCACGGTACCAGTATAAAAATAGGCACATAGAC 3189
                          i i   v i   i    iii     ii i    ii    i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_74945651_7   3190 TAACAGAACAGAATAAAGAACCCAGAAATACACCCAAATACTTACAGCCA 3239
                         i  ii   i     vi   ii         v     v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_74945651_7   3240 ACTGATCTTCGACAAA-----CAAAAAATAACAT--AACGTGAGGAAAGG 3282
                          i    i        i-----   i v----   --  --  i      i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGAC----CATTCAA--TGGGGAAAGA 391

  chrX_74945651_7   3283 ACACCCTTTTAAACTAATGGTGCCGGGATAATTGACAAGCCACATGCAGA 3332
                          i vi     v   v        i    i  i  ivv ?         i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_74945651_7   3333 AGTATGAAACTGGATCCTTATCTCTCACCTTATACAAAAATCAACTCAAG 3382
                           v     ii    i  i  i   v    v           i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_74945651_7   3383 GTGGATTAAGGACTTTAACCTAAGACCTGAAACTATAAAAATTCTAGAAG 3432
                         i     i ?i   i v  iv     v  i           v ii      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_74945651_7   3433 TTAACATTGGAA-AAATCCATCTAGACATTGGCTCAGGCAATAATTT--- 3478
                         vv     v  ?i-     i-  vv   v    v i       ii   ---
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_74945651_7   3479 -GATGACTAACAACCCAAAAGCAAATGCAAGAAAAACAAAGATAAATAGC 3527
                         -   i-- i   --         v v    v    iv   i   i   iv
  L1M4_orf2#LINE/    591 AGATA--TGACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_74945651_7   3528 TGGGACCTAATTAAA-CTAAAGAGCTTTGCATGGCAAGAGGA-ACAATCA 3575
                          v    i v  i   -i    i vi    iiivv   -    -  v    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACTATCA 685

  chrX_74945651_7   3576 GCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTGT 3625
                         iv i   i  v              i           v  ii   viii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_74945651_7   3626 ACATCTGACAAAG-ACTAATATTCAGAATTTGCAATGAACTGTAACAAAT 3674
                          i      i  i -   vi   i      v ii  v     v v    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_74945651_7   3675 CAGTAAGAAAAAAAAAAAACAATTTCATCAAAAAGTGGGCTAAGGACATG 3724
                           i   v     i v   -i  iiiv  i?    i     v     iv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_74945651_7   3725 AATAGACAATTTACAAAAAAAAAAAAAGATACACAAATGGCCAAAAA--A 3772
                                 v  iv v   i  ------    i            v  -- 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAA------GATATACAAATGGCCAATAAGCA 878

  chrX_74945651_7   3773 CATGAAAAAATGCTCAATCAACATCACTAATGAT 3806
                                 i        ----     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAA----CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.13 (49 / 23)  


1934 26.61 7.32 6.65  chrX_74954528_74958812.rev     2893  3794 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_74954528_7   2893 TGGAAACACATCCCATGCTTACAGATGGGTAGAACCAATATTGTAAAAAT 2942
                               v i        i i ii   v  v   vii        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74954528_7   2943 GATCATACTGACAAGAGCAATCTACAAATTCAATGCAAT----------- 2981
                          iiv     vv v i vii       i      i     -----------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74954528_7   2982 ---------------------------------------------TCATA 2986
                         ---------------------------------------------     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_74954528_7   2987 TGGAACAATAAAAAGGGCCCACA-TAGCCAAAGCAAAATTAAAAATAAAA 3035
                              --  iv  i  i    v -        i   vv  i    vi  i
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_74954528_7   3036 AAT----CTGGAGGCATCACGTCACCCGACTTCAAACTATACTATGAGGC 3081
                           i----i      vv    iiiv   i i      viv     ii i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_74954528_7   3082 CACAGTCACCAAAACAACATGGTACTGTTA-AAAAATAGGCACATAGATG 3130
                         i     v i   i   iii        vi -  ii    i  i      v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_74954528_7   3131 AATGGAACACAATAAATAACTCAGACATAAAGCCAAATTCTTACAAACAA 3180
                                i v   vi v iii    v     v   v ivi   iiiv   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_74954528_7   3181 CGGATCTTCAACAAAGCAAACAAAAAACATAAAGTTTTTAA--AAGAACT 3228
                         iv   i   i    i -ivi v  i v   ------- i  --ii   --
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCAT-------TCAATGGGGAA-- 388

  chrX_74954528_7   3229 TTATTGTCTATATATTTATATATATATAATATCTATATATTTGTTGAATG 3278
                         ------------------------- v    ------------------ 
  L1M4_orf2#LINE/    389 -------------------------AGAATA------------------G 395

  chrX_74954528_7   3279 TATCCTATTCAACAAATGGTACTGAGATAATGGGCAAGCCACATGTTGGA 3328
                          ---  v             i   i  i  iv  vv ?       ivii 
  L1M4_orf2#LINE/    396 T---CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_74954528_7   3329 GAATGAAACTGGAGCCTCATCTCTCACCTTATACAAAAATCAATTCAAGA 3378
                                ii    v  ii i   v    v           i  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_74954528_7   3379 TGGATTGAGGACTTAAATCTGAGAACTGAAACCATAAAAATTCTAGAAGA 3428
                              ii?i   i     v i   i  i    i      v ii       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_74954528_7   3429 TAACTTTGGAAAAACCCTTCTCAATATTGGCTTAAGCAAAGACTTCATGA 3478
                         v   v v  ?iv  vi    vii iv    v   i    v ii   v ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_74954528_7   3479 CCAAGAACAC-AAAAGCAAATGCAACAAAAACAAAGATAAATAGATAGGA 3527
                         vi v  -   -       v v         iv   i   i   i  v   
  L1M4_orf2#LINE/    593 ATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_74954528_7   3528 CTTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGGG 3577
                            v  i   v v    i   i  ii vv    i  v iv    iv ii 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_74954528_7   3578 TAAAGAGACAACCCACACAGTGGGAGAAAAATATTCATGAACTACGCATC 3627
                          i  i            v i          -    iiii  ii iii   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATC 740

  chrX_74954528_7   3628 TGACATAGGACTAATATCCAGAATCTACAACGAACTCAAAAAAATCCACA 3677
                            i vi     vi          v  i  v      vv v  v  v i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_74954528_7   3678 AAAAAATCGCAA-CAATCCCATCAAAATGTGGGGTAAGGACCTGAATAGA 3726
                          v    vvi   -i  i  v  i?   vi    vv     ii        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_74954528_7   3727 CAATTTTGAAAAGAAGATATACAAATGGCCAACAAACATATTTAAAAATG 3776
                           v  i vv                       i  i  i  vv   i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_74954528_7   3777 CTCAACACCACTAATTAC 3794
                                i  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 8.40 (126 / 15)  


2367 27.18 3.88 0.40  chrX_74974386_74976985     1010  1756 (844)    L1M4_orf2#LINE/L1        1   773 (135)  

  chrX_74974386_7   1010 TGGAAAATCACCTTGTGTTTGTGGCTTGTAAGATCTAATATTGTTAATAT 1059
                               ivi i iii    ii   v   v    ii            v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_74974386_7   1060 GTTTATATTACTCAAAAAGATCTACAAATTGAATGCAATCCATATCAAAA 1109
                          viv   i v i    vv        i   v  i       v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_74974386_7   1110 TCTCAATGGCATTTTTTACAGAAA----CAGAACAATTTTAAAATTTATA 1155
                           i  iiv  v      i      ----  iivii  ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_74974386_7   1156 TAGAACCACAAAAGACTATAAATAGCCAAATCAACCATGAGAAAGAA--- 1202
                          i   vii   ii   ivvi          v   i v   i      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_74974386_7   1203 CAAAGCTAGAATCATCACCCTTTCTGATTTAAAAATATAATACAAATACA 1252
                              i i  ivvv    v   i ii    v    iv  v      vvi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_74974386_7   1253 CGATAAACAAAAGAGTATGGTTCTGAAATAAAAACAGACACAAAGAACAA 1302
                          ii   v   i v   i    v   iv    ii i     i v   v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_74974386_7   1303 TGGAACAGAATACAGAGCCCAGAAATAAATGCACACATATAAAGTGAACT 1352
                              i     vv    i           iv  i    v  vi  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_74974386_7   1353 GATCTTCAACAGGGGCACAAAGAATATACAATGAGGAAA----------- 1391
                            i   i   i   ii v    vi  v     i     -----------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_74974386_7   1392 --AGCAATTGGTGTCGGGAAAACAGGATATTCACATGCAAA-GAATGAAA 1438
                         -- i   v     ii    v   v     ?i          -       i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_74974386_7   1439 CTGAATTTTCATCTT-CAACA-ATTCAGAAAAAATGAACTCAAAATGGAT 1486
                         i  i iiiii i  i-  v  -  v  ---     v              
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACA---AAAATTAACTCAAAATGGAT 497

  chrX_74974386_7   1487 TAAAGACTTAAACAGAAGACTGAAAACTATAAAATTCTTAGAAGTAAACA 1536
                         i ?    i    iiv    viv            i         v     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_74974386_7   1537 --GGAAAAAA-CTATAGGACATTGGTCTTCACAATGATTTCGTGGATATG 1583
                         --  ?iv   -  viiv   v    vi vvi     i    v i      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_74974386_7   1584 ACACCGAAAGCAAAGGCAAAAAAAAATAAATTAAA-GAATGGTACGATAT 1632
                              i      v i    v    i v   v  i -i   v v  vvi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_74974386_7   1633 TAAACTAAAAATCTTCTGCACTACAAAGGAAACAATCAACA--GTGAATA 1680
                         i   v v    v   i  ii  v       v  v     v --     v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_74974386_7   1681 GGCAACATGTGACATTAGAGAAAATATTTGTAAACCATATATCTGACAAG 1730
                          i    viiiiiv  vi             i   i           i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_74974386_7   1731 AGGTTTATCTCCAAAATGTATAATGA 1756
                         i ii  i v    i   i     v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGA 773

Transitions / transversions = 1.44 (118 / 82)
Gap_init rate = 0.01 (11 / 773), avg. gap size = 2.91 (32 / 11)  

 377 25.00 5.71 0.71  chrX_74974386_74976985     1972  2111 (489)    L1M4_orf2#LINE/L1      762   908 (0)  

  chrX_74974386_7   1972 AATAAATAAGAAAATCCTACAACTCAGTAGTAAAAAATTTAAAAATCTCA 2021
                             v    ii  v  i         i  i      iviv  v  i iv 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_74974386_7   2022 TTAAAAACTGGTTAA-GAACTTGAATAGACGTTTTCCCAAAGAAGTCAGA 2070
                           ?    v   vi  - i i          i   ii         vi v 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_74974386_7   2071 GAA--GGCCAACAGGTATACTTTAAAAATGC-----ATCAGGGGAATG 2111
                         v  --      i i i i - vv   i    -----    ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACA-TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (21 / 13)
Gap_init rate = 0.03 (4 / 147), avg. gap size = 2.25 (9 / 4)  


2418 28.73 1.12 1.24  chrX_74977280_74983500.rev     2776  3579 (2642)    L1M4_orf2#LINE/L1        4   806 (102)  

  chrX_74977280_7   2776 AAAGATACTCCATGTTCATGGATTTTAAAAATCTAATATTTTTTAAATGT 2825
                                ii               v-i  i ii       v  v i   v
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTG-GAAGACTTAATATTGTTAAGATGG 52

  chrX_74977280_7   2826 CAATAATACCCAAAGCAATTTACAGATCCAACACATTCCCTATCAAAATG 2875
                              v v      vii  i       i    i  v             v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_74977280_7   2876 CCAATAACATTTTTCACAGATGTAGAAGAAAGTAATCCTAAAATTTATAT 2925
                            iivi v     ii    vi v  v-  iv i           i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCATAT 151

  chrX_74977280_7   2926 GGAACCACAAAAGACCCCTAACAGACAACGTACTCTTGAGCTAATAAATA 2975
                             vii   ii     vv  i  v   vii v      ------   - 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------AAA-A 194

  chrX_74977280_7   2976 AACAAACAAAGCAGGAAGCATCACATGATCTGGCTCCAAAATACATTACA 3025
                         i vi       iv   i vv     ivvi iiii i     ivi i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_74977280_7   3026 AAGCTGTAGTAATAAAATCAGCATGGTATTGCCCTAAAAATTGACATATA 3075
                              ii      v  iv   ii     i  v v   ii  v        
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_74977280_7   3076 GACCAATGAAACAGAAAAGAAAAACCAAATATAAATCCACACATTTACAG 3125
                           i     i  i    vv  i iv   i v     i   i       ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_74977280_7   3126 CCCACTTACTTTAGACAGAGATACCGGGAGCATTCAATGGGAAAAGGACA 3175
                         i v i v i   v    ii i i  ii  v           i    i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_74977280_7   3176 ATCTCTTCAATAAATGGGGCTCAGAAAAC--------CATATGCAGAAAA 3217
                         i   i     i      v   vi  v   --------  i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_74977280_7   3218 ATAAAACCAGAACCCTATGTCTCACCATATACAAAAATTAAATAAAAATG 3267
                           i  iiii  v     iv  v                   v v      
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_74977280_7   3268 GACTGAAGAATTAAATACAAGACATGAAACTATGAAACTGCTACAAGAGA 3317
                           iii?   vi     ii    vv i       i     vi  v    i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_74977280_7   3318 ACTTTGGGA-AAATCCTCTGGAACATTGGTCTGAGTAAAGATTTTTTGAG 3366
                           v v  ?i-     i  - vi  v    vi ii i  v i   i  iii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_74977280_7   3367 TAAGACTGCAAAATCACAGGCAACCAAAGTAAAAATACACAAACGGTGTT 3416
                           v   vv     v    i     v    v       v i   iv vii 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_74977280_7   3417 ACATCAAGGTAAAAAGCTTCTGCACAGCAAAGAAAACAATCGATGAAGTA 3466
                         v      ii v    i   i  ii vv     i v  v   i vi    i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_74977280_7   3467 GAGAAACAATGCACTGAATGGGAGAAAATATTTACAAACTATCCGTCTGA 3516
                         i i i    iv   v                  i    ii  vii     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_74977280_7   3517 CAAGAGAATAATAACCAGAATATACCAGGAGCTCAAACAAATAAATAGCA 3566
                         i   i  v vi  v          iv i  i   vv    v v    ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_74977280_7   3567 AAAAAAAAAAAAA 3579
                             i v   v  
  L1M4_orf2#LINE/    794 AAAAGACAAATAA 806

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.01 (7 / 803), avg. gap size = 2.71 (19 / 7)  

 403 18.10 9.52 0.00  chrX_74977280_74983500.rev     4169  4273 (1948)    L1M4_orf2#LINE/L1      794   908 (0)  

  chrX_74977280_7   4169 AAAAAATAAATAA----AT------ATGGGCAAATGGTCTGAATAGATAT 4208
                             i i      ----  ------         v i i        i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_74977280_7   4209 TTATCAAAGGAAGACCTACGAATGACCAAAAGGTATATGAAATAATGCTC 4258
                           v  v  i     iv   i    i    v i i i      vi      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_74977280_7   4259 AACATCACTAATTAT 4273
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.02 (2 / 115), avg. gap size = 5.00 (10 / 2)  

2136 26.11 1.37 1.22  chrX_74977280_74983500.rev     5068  5722 (499)  C L1M4_orf2#LINE/L1   (51)   857   202  

C chrX_74977280_7   5722 AAAGCTGGAGTCATCTTGCTACCTGACTTCAAACTATACTACAAGGCTAC 5673
                             i     vvv  vii  v  ii i      viv        i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

C chrX_74977280_7   5672 AGTAACTAAAACAGGATGGTACTGGTACCAAAACAGATATATAGACCAAT 5623
                              ii  i    vi         i iv ii i   i       i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

C chrX_74977280_7   5622 GGAACAGAA--GAGAGGCCTCAGAAA-AAACACCACACATCTACAACCAT 5576
                             i    --     v  --     -    -   i    i  iiii  v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCC--AGAAATAAAC-CCATACATTTATGGTCAA 348

C chrX_74977280_7   5575 CTGGTTTTTGAAAAACCTGACACAAACAAGCAATGGGGAAAAGAT-TTCT 5527
                         i  i    i  v  ivv  v  vi v  vv           ii  -v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

C chrX_74977280_7   5526 TATTTAATAAATGTTGTTGAGAAAACTGGCTAGCCATATGCAGAAAACTG 5477
                          -  i  i     v  i  i  v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chrX_74977280_7   5476 AAACTGGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGATGGAT 5427
                           ii         v   i     v           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

C chrX_74977280_7   5426 CAAAAACTTAAACGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAACC 5377
                           ? i  i    i      v   ii  i      v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

C chrX_74977280_7   5376 T-GGAAAATACCATTCAGGACTTAGGCATGGGTAAAGACTTCATGTCTAA 5328
                          -  ?iv v i -   iv   i v  vv i  i  v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_74977280_7   5327 AACACCAAAAGCA-ATGTCAAAAAAAGCCAAACTTGACAAATGGGATCTA 5279
                         i            - v -   v     vv   v v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chrX_74977280_7   5278 ATTAAACTAAAGAGTTTCTGCAGAGCAAAAGAAACTATCATCACAGTGAA 5229
                           i   v v  i ii  i  iivvv    i  v       vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chrX_74977280_7   5228 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCAATCTGATA 5179
                         v  i     i                 v       vii ivv        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chrX_74977280_7   5178 AAGTTCTAATATCCGGAATCTACAGGGA--TCTTAAACAAATGTACAAGA 5131
                          i vv  vi     i    v  i ii  --     --   v vv i  v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATA 793

C chrX_74977280_7   5130 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACATCCAC 5081
                             i     i     v  i?    i            v    i vv  i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

C chrX_74977280_7   5080 TTC-CCAAAAGAGA 5068
                            -     ii   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGA 857

Transitions / transversions = 1.26 (93 / 74)
Gap_init rate = 0.02 (13 / 656), avg. gap size = 1.31 (17 / 13)  


3147 27.12 0.77 0.66  chrX_75001865_75011195.rev     3608  4514 (4817)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75001865_7   3608 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3657
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75001865_7   3658 GGCCATACTGCCTAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3707
                            v     v  i  iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75001865_7   3708 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3755
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75001865_7   3756 TATGGAACCAAAAAAGAGCCCGCATCGCCAAATCAATCCTAAGCCAAAAG 3805
                                viiv  ii  v  v v  v      v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75001865_7   3806 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3855
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75001865_7   3856 TACAGTTACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3905
                               v i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75001865_7   3906 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCTTACCTACAACT 3953
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75001865_7   3954 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT--T 4001
                          vi    i  i     ivv  vv  i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75001865_7   4002 CCATATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 4051
                          -- v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_75001865_7   4052 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 4101
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_75001865_7   4102 GATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 4151
                            i ?   ii    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_75001865_7   4152 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCC 4201
                           v    ?i v viv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_75001865_7   4202 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4251
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_75001865_7   4252 AATTCAACTAAAGAGCTTCTGCACAACAAAAGAAACTACCATCAGAGTGA 4301
                         v  iv  v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75001865_7   4302 ACAGGCAACCTACAACATGGGAGACAATTTTCGCAACCTACTCATCTGAC 4351
                          v  i     i   iv        v   v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75001865_7   4352 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 4401
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75001865_7   4402 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 4451
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75001865_7   4452 TCTC-AATGAAGTCATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 4500
                             -  v    vi  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75001865_7   4501 TCATCACTGGCCAT 4514
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  

2250 28.83 1.70 1.05  chrX_75001865_75011195.rev     7608  8370 (961)    L1M4_orf2#LINE/L1        1   768 (140)  

  chrX_75001865_7   7608 TGGAAAAACATTTTACACTCATAGATACAAAGAATCAATATTGCTAAAAT 7657
                               i i  iii iii    i   vvi    v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75001865_7   7658 GGCCATACTGCCCAAGC-AATTTATAGATTCAATGGTATTCTGATTAAAC 7706
                            v     v     ii-i  i  i        i vv  i iv  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75001865_7   7707 TACCA--TGATTTTCTTCACAGGACTAGAAAAAACTG-TTTTAAAATTTA 7753
                          v   --  vi   i  -i   i v v  v  i-   - ii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_75001865_7   7754 TATGGA--TCCAAAAATGTGCCCA-AATAGCTAAGGCAATCCTCAGCAAA 7800
                               -- v   i--- vi    -      i  ii     i v iv  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG---GGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_75001865_7   7801 AAGAACAAAGTTGAAGGCATCAAGCTACCCAACTTCAAACTATACTACAG 7850
                                      i   vv   vi  v     i      viv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_75001865_7   7851 GGCTAGAGTAACCAAAACAGCATGGTACTGGTACAAGAACATACATATAG 7900
                         i    v     i   i    ii         i i   i i v        
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_75001865_7   7901 ATCAATGGAAGAGAATAGAGAACCTAGAAATAAGACCACACACCTACAAC 7950
                                   v     v    ii i        iv   i   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_75001865_7   7951 TATCTGATTTGTGATCAATTTGGCAAAAACAAGCAATGGGGAAAGGAT-- 7998
                         i vi      vi  iv ivv  v   i v  vv            i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_75001865_7   7999 TCCTTATTCAGTAAATGGTGCTGAGATAACTGGCTAGCCATATTCAGAAA 8048
                           i  --   ii           i  i      v  ?   i  v  i  i
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_75001865_7   8049 ATTGAAACTGTACCCCTTTCTTAAACCACATACAAAAATTAACTCAAGAT 8098
                          v    ii  v      vi  i v    i                  i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_75001865_7   8099 TTATTAATAACTTAAATGTAAAAACTCAA-CTATAAAAACCCTGGAAGAC 8147
                         vv  i ?vi  i         i i  v  -        vi i i     v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_75001865_7   8148 AACCTAAGC-CATACCATTCAAGACATAGGCATGTGCAAAGATTTCCTGA 8196
                            v  i ?-i v i -   iv   v v  vv iv    v i    i ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_75001865_7   8197 GGAAGAAGCCACAAGCAATTGTAACAAAAGTAAAAATTGTCAAATGGTAT 8246
                         iv v  vi   v     vvv i        v      v vi    v v i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_75001865_7   8247 TGAATTAAACTAAAAAGCTTCTGTACAGCAAAATAAAATATCAACAGGGT 8296
                          vv  i   v v    i   i   i vv    iv v v      v ii  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_75001865_7   8297 AAACAGACAACCTAGAGAATTGAA-AAAAT-TTTGCAAACTAAGCCTTTG 8344
                         i  v        i v     v i -     -        ii viiv i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_75001865_7   8345 ACAAAGGTGTAACATCTAGCATTTAT 8370
                          i  i  vv vii   i  v  v   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATAT 768

Transitions / transversions = 1.38 (126 / 91)
Gap_init rate = 0.02 (15 / 768), avg. gap size = 1.40 (21 / 15)  

 375 23.97 1.37 0.68  chrX_75001865_75011195.rev     8695  8840 (491)    L1M4_orf2#LINE/L1      762   908 (0)  

  chrX_75001865_7   8695 AATTTAT-AAGAACTTAAACCAATTTAA-AAGAAAAAAACAAACAACTCT 8742
                            v   -       ivv -   i i  -  v     i     i   i v
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTA-CAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_75001865_7   8743 ATTAAAAATTGAGGAATGTACATGAACAGACAATTTTCAAAGGAAGACAA 8792
                            ?    v  i v  v v iv    i     v  i  v  i     i v
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_75001865_7   8793 ACACATAGGCAACAAGCATATGAAAAAAAGCTGAATATCACTGATTAT 8840
                            v  i v   i     i       i v   v  i    ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (17 / 17)
Gap_init rate = 0.02 (3 / 147), avg. gap size = 1.00 (3 / 3)  


2562 27.57 2.23 0.89  chrX_75018817_75023067     2863  3758 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75018817_7   2863 TGGAAACACATCCCATGCTCATGGACGGGTAGAATTAATAGTGTGAAAAT 2912
                               v i        i       iv  v   v      v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75018817_7   2913 GACCATACTGCAAAAAGCAATCTACAAATTCAATGCAACTCTCATAAAAA 2962
                          i v     v vv   vii       i      i    ii ii  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75018817_7   2963 TACCATCATCATTCTTCACAGAACT--ACAAAAAAAAGTCCTAAAATGTA 3010
                          v   v vv v  i  ii     v --    ivvi --         vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chrX_75018817_7   3011 TATGAAACCAAAAAAAAGCCCGCATAGCCAAACTAAATCTAAGCAAAATG 3060
                             i  viiv  iii v  v v         vi  vii i iv  i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75018817_7   3061 AACAAATCTGGAGGCATCACAACACCTGACTTCAAACTATATTATAAGGC 3110
                               vi      vv     viv  ii i      viv  i  i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75018817_7   3111 CATAATCACCAAAACAGCATGGTACAGGTATAAAAATAGGCATATATATA 3160
                         i i i v i   i    ii      v  i    ii    -- i     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG--ACATATAGA 296

  chrX_75018817_7   3161 TCAATGGATCAGAGTATAGAACCCAGAAATAAACCCAAATACTTACAGCC 3210
                                 vi   i vv   ii               v i i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_75018817_7   3211 AAT-GATCTTGGAGAAAGCAAACAAAACCATAAAGTGGGGAAAAAACACC 3259
                            -   i  v  v  i vviv   i     vv i        i  i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75018817_7   3260 CTATTCAACAAATGGTGCTGGGATAATCGGCAAACCACATGTAGGACAAT 3309
                           v                    i  ii  vv ?       i ii v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75018817_7   3310 AAATCTGGATCCTCATCTCTCACTTTATAGAAAAATCAACTCAAGGTGGA 3359
                         i  vi    i  ii i   v   iv    v      i       ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75018817_7   3360 TCAAGGACTGAACTCCAAGACCTGAAACCATAAATATTCC-AGAAGATAA 3408
                            ?i   iv  v vi    v  i    i     - i  i-      v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chrX_75018817_7   3409 CATCAGAA-AGATCTTTCTAGAAATTGGCTTAGGCAAGGATTTCAT-GAC 3456
                            vi ?i- i     iv -  vv    v        v i    v -  i
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_75018817_7   3457 CAATAAC-CCAAAAGCAAATGCAACAAAAACAAAGATAAATAGGAGGGAT 3505
                         --  i  -         v v         iv   i   i   iivv   i
  L1M4_orf2#LINE/    595 --ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_75018817_7   3506 TTAATTAAACGAAAGAGCTTCTGCACAGCAAAGAA-AC----AGCAGAGT 3550
                           v  i   vvv  i i   i  ii vv     i -  ---- iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_75018817_7   3551 AAAAAGACAACCCACAGAATGGGAGA---TCTCAACAATCTACACATCTG 3597
                         i                         --- v ivi   vii i i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_75018817_7   3598 -CAAAGGACTAATACCCAGAATCTACGACGAACTCAAACAAATCACCAAG 3646
                         -i  i     vi  i       v  ii v      vv    v   vi  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_75018817_7   3647 AACAAAACAA----TCCCATCAAAAAATGGGCTTAGGACATGAATAGACA 3692
                           v  i    ----i  v  i?          vv    iv          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_75018817_7   3693 ATTCTCAAAAGAAGATATACAAATGGTCCACTAGAAAAAGAAAAAGTTCT 3742
                         v     v                   i v iv  v v v     ii v  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_75018817_7   3743 CAACATCACTAATGAT 3758
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (135 / 108)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.75 (28 / 16)  


 820 27.88 3.64 2.73  chrX_75036318_75043084.rev        1   330 (6437)    L1M4_orf2#LINE/L1      351   683 (225)  

  chrX_75036318_7      1 GATTTTCAACAAAGTTGACAAAAGTAAACAATGGGGAAAGGACCCCCTAT 50
                                i    i v  v   i vi vv            i ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_75036318_7     51 TCAACAAACCATGCTGTAATAACCAGTTAACTATATGCAGAAGAAAAAAA 100
                                 ivi     vi i   ii v  ? i i     i     vi  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_75036318_7    101 TTGGACCCCTACTTTTAACCATATACAAAAACTAATTCATGGTAAATTTA 150
                                     i ivv              i   i   vii ii  iv?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_75036318_7    151 ATACTTAAAGATAATACCTAAAACTATAAAAATCC---GGGAAAACATTT 197
                          v  i    vi   v v              v  i---ii        --
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-- 548

  chrX_75036318_7    198 AGGAA-ACACCATTCTGGACATTGGCCGT--GGCAACTAATTTATGACTA 244
                            ?i- v i -   vv   v    --  --     - ii   v ---  
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGG--GTTAGGCAA-TGGTTTCT---TA 591

  chrX_75036318_7    245 AGTGT----CCAAA-GCAGTAGCAATGGAA-AAAAAATTGTCAAGTGGGA 288
                         ii i ----     -   vv     iii  -       v vi  i v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_75036318_7    289 CCTAATTAAACTTACGAGCTTCTGCACAGCAAAAGAAACTAT 330
                          i v  i   v   vi i   i  ii vv    i  v     
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

Transitions / transversions = 1.41 (52 / 37)
Gap_init rate = 0.03 (11 / 333), avg. gap size = 1.91 (21 / 11)  

2731 28.31 0.43 1.95  chrX_75036318_75043084.rev     5355  6276 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75036318_7   5355 TGGAAAAACATTCCATGCTCTACGGATAGGAAAAATCGACATCATGAAAA 5404
                               i i  i     i  - i    v    i v ii i  ii v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTC-ATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_75036318_7   5405 TGGCCATACTGTCTGAAGTAATTTATAGGTTCAGTGCAATTTCCATTAAA 5454
                             v     vi ii  v i  i  i  i    ii     ii i  i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_75036318_7   5455 CTACCC--TTGACTTTCCTCACAGAATCAGACAAAAACT-ACTTTAAATT 5501
                         v -   --i  v    ii -i     viv     i--  - iii    v 
  L1M4_orf2#LINE/    100 AT-CCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAAT 145

  chrX_75036318_7   5502 TCATATAGAACCACAAAAGACCCTGTATACCCATGACAATCCTAAGCAAA 5551
                               i   vii   ii     v v   v   vi      i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_75036318_7   5552 AACAACACAACTGGAGGCATCACACTACCTGACTTCAAAGTATACTACAA 5601
                           v    v ii      vv       v  ii i      iiv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_75036318_7   5602 GCCTACAGTAAACACAACAGCATGGTACTGGTACCAAAACAGATATATAG 5651
                         iv         v  vi    ii         i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_75036318_7   5652 ACCAATGGAAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAA 5701
                          i        -i    iv    vii         vv   i    i  iii
  L1M4_orf2#LINE/    296 ATCAATGGAA-TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_75036318_7   5702 CCATCTGATCTTCAACAAACCTGACAAAAACAAGCAATGAGAAAACGATT 5751
                         i  vi    i   i    ivv  v   i v  vv     i i   vi  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_75036318_7   5752 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAA 5801
                         vi  v  i  i              v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_75036318_7   5802 CTGAAACTAGACCCTTTCCTTAACACCTTACACAAAAATTAACTCAAGAT 5851
                         v    ii i     i v   i -    v  i                i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAAT 493

  chrX_75036318_7   5852 GGATTCAAGACTTAAATGTAAACCCTATAATTTTAAAATCTCTAGAAGAA 5901
                             iv?    i         ivv   v  i v     iiii        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_75036318_7   5902 AACCTAGGCA-ATACCATTCAGAACAAAGGCATGAGCAAATAATTCATGA 5950
                            v    ?i- v i -   ivi  vvv  vv ii    vviv   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_75036318_7   5951 CTATATCACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGAT 6000
                         v   iv           vvv          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_75036318_7   6001 CTAATTAAACTAAGGAGCTTCTGCACAGCAAGAGAAACTAGCATCAGATT 6050
                         i v  i   v v ii i   i  ii vv   ii  v    v  vv i v 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_75036318_7   6051 GAACAGGCAACCTAAAAAATGCGAGAAAATTTTTGCAATCTATCCATCTG 6100
                            v  i     i v i    v        v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_75036318_7   6101 ACAAAGGTCTAATATCCAGAATCTACAAGAAACTTAAACAAATTTACAAA 6150
                          i  i  v  vi          v  i  ii    ivv    v i----  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC----AA 788

  chrX_75036318_7   6151 AAACAAAACAAAACAAAGAAATAATCCCATCAAAAAGTGAGCAAAGGATA 6200
                         v  i    -- i     ----   i  v  i?    i  i         v
  L1M4_orf2#LINE/    789 TAATAAAA--AGACAAA----TAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_75036318_7   6201 TGAACAGACACTTCTTAAAAGAAGACATTTATGTGGCCAACAAACATATG 6250
                             i     i    iv        i  vi vi       i  i  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_75036318_7   6251 AAAAAAAGCTCATCATCACTGGTCAT 6276
                             i v     v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (154 / 103)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


2917 28.57 0.55 0.77  chrX_75049557_75055949.rev     4993  5902 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75049557_7   4993 TGGAAGGACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5042
                              i  i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75049557_7   5043 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5092
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75049557_7   5093 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5140
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75049557_7   5141 TATATATGGAACCAAAAAAGACCCCGTATAGCAAAGTCAATCCTAAGGCA 5190
                            ----    viiv  ii     v v     v  iv     i i iiv 
  L1M4_orf2#LINE/    149 TAT----GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_75049557_7   5191 AAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACA 5240
                         i          i      vv    i  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_75049557_7   5241 AGGCTACAGTAACCAAAACAGCATGCTACTAGTACCAAAACAGAGATATA 5290
                          i          i   i    ii  v    i i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_75049557_7   5291 GACCAATGAAACAGAACAGAGGCCTCAGAAATAATGCCTCATATCCACAA 5340
                           i     i  i    iv   ivii         vv  vi i  ii iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_75049557_7   5341 CTATCTGATCTTTGACAAACCTGACTAAAACAAGCAACGGGGAAAGGATT 5390
                         ii vi    i  i     ivv  v v i v  vv   i        i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_75049557_7   5391 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAG 5440
                         vi  v  i  i              v      v  ?   i   v i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_75049557_7   5441 CTGAACGTGGATCTCTTCCTTACGCCTTATAGAAAAATTAATTCAAGATG 5490
                         v    vv    i i  v   i  i  v    v         i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_75049557_7   5491 CATTAAAGACTTACACGTTAGACCTAAAACCAAAAAACC--TAGAAGGAA 5538
                         v  i ?    i  v i  v   v       i v     i--      i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_75049557_7   5539 ACCTAGGCA-ATACCATTTAGGACATAGGCATGGGCAAGGACTTCATGTC 5587
                           v    ?i- v i -  iiv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_75049557_7   5588 TAAAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATC 5637
                           vi            vvii         vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_75049557_7   5638 TAATTAAACTAAAGTGCTTCTGCACAGCAAAAGAAATCACCATCAGAGTG 5687
                          v  i   v v  ivi   i  ii vv    i  v ii i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_75049557_7   5688 AACAGGCAACCAACAAAATGGGAGAAAAGTTTTGCAATCTACTCATCTGA 5737
                           v  i     v   i            vv       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_75049557_7   5738 CAAAGGGCTAAGATCCATAATCTACAATGAACTCAAACAAATTTACAAGA 5787
                         i  i  i  viv     v   v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_75049557_7   5788 AAAAAACAAACAAACCCATCAAAAAGTTGGCGAAGGATATGAACAGACAC 5837
                             i     i  v  v  i?    i v   i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_75049557_7   5838 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAGCACATGAAAAAATGCTC 5887
                              v        i  vi viii     v             i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_75049557_7   5888 GTCATCACTGGCCAT 5902
                         iv     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (148 / 108)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


1106 26.97 4.39 2.19  chrX_75057246_75059428.rev       32   487 (1696)  C L1M4_orf2#LINE/L1   (63)   845   380  

C chrX_75057246_7    487 AATGAGGAAAGGAC--TCCTTATTCAATAAATGGTGCTGAGATAACTGGC 440
                             i      i i--  i  --    i           i  i      v
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGA 427

C chrX_75057246_7    439 CATCCATATACA---GATTAACACTGAACTTGTTTCCTACATCGTATACA 393
                         i ?   i  i  ---  v i vii  i  iiv vi ii   i i      
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

C chrX_75057246_7    392 AAAATCAACTCAAGATGGATTCAAGACTTAA-TGTAAAGCCGAAAACTAT 344
                              i       i      iv?    i   -     iiv v        
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

C chrX_75057246_7    343 AAAAACCCTGGAACACAACCTAGGC---AATGCCATTCTGGACATAGGAA 297
                             vi i i   v v   v    ?---   -- -   vv   v v  i-
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGG- 573

C chrX_75057246_7    296 CTGGAGAATA-TTTCAT-GATGAAGACACCAAAATCAATTGCAACCAAAA 249
                         i i iv   i-    v -   - v          v  vvv     v   i
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAG 622

C chrX_75057246_7    248 CAAAAATTGACAAGTGGGACCTAATTAAACTAAAGAGTTTCCACACAGCA 199
                         v      v  i  i v    i v  i   v v  i ii  iiiii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

C chrX_75057246_7    198 AAAGAAACTATACACAAAGTAAACAGACAATCTACAGAAAAGAAGAAA-T 150
                           i  v     vv v     i  v      i i      vi i     - 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

C chrX_75057246_7    149 -TTTGCAAACTATGCATCT--TAAAAAAGTCAATATCCAACATCTATAAG 103
                         -        ii  ii    --   iii v ii-      iv  v     i
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTG-TATCCAGAATATATAAA 771

C chrX_75057246_7    102 GAACTTAAACAA----ATATACAAGAAAA-AAATAAGTCCATTAAAAAAT 58
                              ivv    ----   - i  i  i -      vi v   ?      
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAAT 820

C chrX_75057246_7     57 GGGTAAAGAATATGAACAGACGATTT 32
                            i    i  v    i    -    
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGAC-ATTT 845

Transitions / transversions = 1.59 (73 / 46)
Gap_init rate = 0.04 (19 / 466), avg. gap size = 1.58 (30 / 19)  

2729 28.54 1.22 0.77  chrX_75057246_75059428.rev      789  1692 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75057246_7    789 TGGAAACATATCCCATGCTCGTGAATGGGTAGAATCATTATTGTAAAAAT 838
                               v          i  i  i  v  v   v i v      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75057246_7    839 AATCATATTGCCAAAAGCAATCTATAAATTCAATGCAATTCCCATCAAAA 888
                         iiiv   i v  v   vii     i i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75057246_7    889 TACCACCATCATTCTTCAAAGAACTAGAGAAAACAATCCTAAAATTCATA 938
                          v   v vv v  i  iiv    v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75057246_7    939 TGGAAC--CAAAAAATCCTCTGCATTGCCAAAGCTAGACTAAGCAAAAAG 986
                              v--   iii i  v-- v  v      i v vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCA--GAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75057246_7    987 ATCAAATCTGTAGGCATCACATTACCCGACTTCAAGATGTACTACAAGGC 1036
                          v    vi  v   vv     i v   i i     i iv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75057246_7   1037 TATAGTTTCCAAAACGGCATGGGCCTGGTATAAAGATAGGCACAAAGACC 1086
                           i   vvi   i  i ii   vv    i    i     i  i v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75057246_7   1087 AATGGAACAGAATGGAGAACCCAGAAATAAAGCCAAATACTTATAGCTAA 1136
                                i     v    ii           v   v i i    i ii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_75057246_7   1137 CTGATCTTCAAAAAAACATACAAAAAC-ATAAAGTTGGGAAAAGACA-TC 1184
                         i    i   i v  ii-i i v  i  -  vv i v      ii i -  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_75057246_7   1185 ATATTCAACAAACTGTGCTGGGATAATTGGAAAGTCACATGTAGAAGTAT 1234
                         v -         iv         i  i    v ?i      i i   v  
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75057246_7   1235 AAAAGTGAATCTCTATTTCTCACCTTACACAAAAATCAACACAAGATGAA 1284
                         i  iv  i i i   ii  v    v  i        i   v   i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75057246_7   1285 TTAAAGACTTAGACCTAAGACCAGAAACCATAAACCTTCTAGAAGATAAC 1334
                          i ?    i  i iv     v vi    i     v  ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75057246_7   1335 ATTAGAAAAACTCTTTCAGATGTTGGCACAGGCAAAGAATTTAT-GACCA 1383
                           vi ?iv  v    ivv  iv    vvi      v iv  iv -  i--
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-- 594

  chrX_75057246_7   1384 ATAAC-CCAGAAGCAAATGCCATGAAAACAAAAAGAAATAAATAGGACTT 1432
                           i  -   i     v v  v ii   iv     v i      v      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_75057246_7   1433 GATTAAACTAAAAAGCTTCTGCACAGTAAAAGAAATAATCAGCAGAGTAA 1482
                         v  i   v v    i   i  ii vvi   i  v iv    iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75057246_7   1483 ATAGACAATCCATGAAGTGGAGGAAATTCTTTGCAAACCATGCATTTAAC 1532
                          v      i   iii i   ii    v v        i   ii  i i i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75057246_7   1533 AAAGTACTAACATCCAGAATCTACAAGGAACTCAAACAAATCAG-----A 1577
                           i v   vii         v  i  i      vv    v   i----- 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75057246_7   1578 AAAAAGAAATAATCCCATCAAAGAGTGGGCAAGGGACATGGATAGACAAT 1627
                            i v      i  v  i?  i i       i   iv  i       v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75057246_7   1628 TCTCAAAAGAAGATACACAAGAGGCCAAAAAGCATATGAGAAAAATGCTG 1677
                             v          i    iv      v     i    -   i     v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTC 893

  chrX_75057246_7   1678 AACCTCACTAAATAT 1692
                            v   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (150 / 104)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


3166 27.01 0.77 0.66  chrX_75070818_75077092     4876  5782 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75070818_7   4876 TGGAAGGACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                              i  i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75070818_7   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75070818_7   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75070818_7   5024 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75070818_7   5074 AACAAAGCTGGAGGCATCACACTATCTGACTTCAAACTATACTACAAGGC 5123
                                i      vv       vi ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75070818_7   5124 TACAGTAACCAAAACAGCATGGTGCTGGTACCAA-ACAGAGATATAGATC 5172
                                 i   i    ii    i    i iv i- i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75070818_7   5173 AATGGAACGGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5220
                                ii   i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75070818_7   5221 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT--T 5268
                          vi    i  i     ivv  vv  i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75070818_7   5269 CCATATTTAATAAATGGTGCTGGGAAAACTGGCTGGCCATATGTAGAAAG 5318
                          -- v  i  i              v      v i?   i   i i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_75070818_7   5319 CTGAAACTGTATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5368
                         v    ii  v i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_75070818_7   5369 GATTAAAGACTTAAACGTTAGACCTAAAACTATAAAAACCCTAGAAGAAA 5418
                            i ?    i    i  v   v              vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_75070818_7   5419 ACTTATGCATTACCATTCCGGACATAAGCATGGGCAAAGACTTCATGTCT 5468
                           v  v ?i v viv   vv   v vi vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_75070818_7   5469 TAAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCT 5518
                         vvi            vvi     v    vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_75070818_7   5519 AATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5568
                         v  iv  v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75070818_7   5569 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5618
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75070818_7   5619 AAAGGGCTAATATCCAGAATCTACAATGAATTCAAACAAATTTACAAGAA 5668
                           i  i  vi          v  i  v   i  vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75070818_7   5669 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5718
                            i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75070818_7   5719 TCTCGAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5768
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75070818_7   5769 CCATCACTGGCCAT 5782
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2109 23.07 10.99 1.70  chrX_75081649_75086699.rev      457  1102 (3949)    L1M4_orf2#LINE/L1      203   908 (0)  

  chrX_75081649_7    457 AAACTAGAAGAATCACTTTACTTCACTTCACTTCACTTCAAATTGTACTA 506
                           ii i  i  v    ---     ---i  ---- i      viv     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCAC---ACTTC---CCA----ATTTCAAAACTTACTA 242

  chrX_75081649_7    507 CAGAGCTATAGTAACCAAAACAGCATGGCACTGGAATTAAAACAGACACA 556
                           i     i     i   i    ii   i     v  v ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_75081649_7    557 TAGACCAATGGAACCACATAGAGAGCTCAAAACTAAATTCATACACTTAC 606
                             i        iviv  v     ii  i  v    ii      i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_75081649_7    607 AGTGAACTCATTTTCAACAGAGGTACCAAGAATATACATTGGAGAAAGGA 656
                         i  v  i v      i   ii   i      vi  v  v   i     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_75081649_7    657 CAGTCTCTTCAATAAATTGTGCTAGGAAAACTGGATATCCATATGCAGAA 706
                         i     i     i    v     i   v         ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_75081649_7    707 GATTAAAACTTGACCATTGTCTCTCACTGTATACAAAAAT-----CAAAT 751
                           v i  ii v    vi ii   v   ii           -----    v
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_75081649_7    752 TGGATTAAAAACTTAAATCTAAAACCTCATACTATAAAACCACAACAAGA 801
                              i ? i  i     v   i v  v v          iviv v    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_75081649_7    802 AAACGT-----TGAGTTTT--------------------TGGTTGC---- 822
                             i ----- i i i  --------------------     v ----
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_75081649_7    823 --------CCGTAAGCACAGGAAACCAAAGAAAAAAATGGACAAATGGGA 864
                         --------  iv       i v   v          - i  i    v   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGA 641

  chrX_75081649_7    865 TCACATCAAG-TTAAAGGCTTCTGCACAGCAAATGATATCATCAACAAAG 913
                         iiv      i-     ii   i  ii vv    v  i ii     v    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_75081649_7    914 -----AAACAACCCACAGAATGAGAGAAAACA---GAAGA--------CT 947
                         ----- i               i       i --- v i --------  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_75081649_7    948 AATAAG-----------CAGAATATATAAGGAGCTCAAACAACTCCATAG 986
                         i     -----------            i  i   vv       v   i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_75081649_7    987 GAAAAAATCTAATAATCCAAT-AAAAAATGGACAAAATCTTTGAATAGAT 1035
                         v     iv v     i     -?        i    ivv          i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_75081649_7   1036 ATTTCTCAAGAGAAGACACACAAATGGCAAACAAGTGTATGAAAAGGTGC 1085
                                v i      i i         v  i   iii        i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_75081649_7   1086 TCAACATCATTGATTAT 1102
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (97 / 49)
Gap_init rate = 0.02 (14 / 706), avg. gap size = 5.86 (82 / 14)  

2481 29.84 2.76 0.92  chrX_75081649_75086699.rev     1952  2819 (2232)  C L1M4_orf2#LINE/L1   (22)   886     3  

C chrX_75081649_7   2819 GAAAAACATTCCATGCTGATGGATAGGAAGAATCAATATTGTTAAAGTGG 2770
                             i i  i     i v      v      v i           ii   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

C chrX_75081649_7   2769 CAACACTGCCCAAAGCAATCTACAGATAAAATGCTATTCCAATCACATTA 2720
                            i   v      vii          vv  i  v  i  v    v v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

C chrX_75081649_7   2719 CTAATGACATTCTTCCCAGAACAAGAAAAATCTATTTTCAAATTCATATG 2670
                          i iivi v  i  iv     vvv  v  iiiv  ii v           
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

C chrX_75081649_7   2669 GAACCAAAAAGGAGCTCTAACAGCCAAGGCAATTCTAAGCAAAAGACATA 2620
                            viiv  i   v ivv  i      ii    ii i iv  i iiv i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

C chrX_75081649_7   2619 AAGTTGAAGGCATCATGTTACCCGACTTCAAACTATACTGCAGGGCTACA 2570
                               i   vv   iii v   i i      viv    i  ii      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

C chrX_75081649_7   2569 GTAACCTAAACAGCATGGTACTGGTACAAAAAGAGACATATAGACCAATA 2520
                             i v i    ii         i i  ii v           i    i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

C chrX_75081649_7   2519 GAATAGAATAAAAAGCCCAGACATAAGGCCACACATCTACAACCATGTAG 2470
                                  vi i  i     v    iv   i    i  iiii  vv ii
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

C chrX_75081649_7   2469 TCTTTGACAAAGCTGACAAAAACTAGCAATGGGAAAGGACT---CTATTC 2423
                          i  i     i v  v   i v vvv       i  i  v ---  v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

C chrX_75081649_7   2422 AATAAATGATTCTTAGATAACTGGCTAGTCATATGCAAAAGATTAAAACT 2373
                           i     i v  vi  i      v  ?i  i          v i  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

C chrX_75081649_7   2372 GAACACCCCTCTTATACCATTTACAAAAGTTAACTCAAGATGAATTGAAA 2323
                          i  v  ivi  i i     v       i         i   i  ii? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

C chrX_75081649_7   2322 ACTTAAAGGTAAAACCTAGAGCTATAAAAACTCT-GGACTACGACCTAGG 2274
                           i    v    i v   i i        -    -i  vv vi  v    
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGG 551

C chrX_75081649_7   2273 CAATAACATTTTG-AACATAGGATTGGGCGAAGATTCATGAGGAA-GATG 2226
                         ?i-   vvi  i -i  v v  i  i   i v i  iv v  iv -  ii
  L1M4_orf2#LINE/    552 NG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

C chrX_75081649_7   2225 CCAAAAGCAATTGTAACAAAAGCAAAAATTGACAAACCTATTGAATT--- 2179
                                  vvv i        v      v  i   ----   i i ---
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA----TTGGACTTCA 646

C chrX_75081649_7   2178 ---AAACTAAAGGCTTCTACACAGCAAAAAATAATTATAAACAGAGTAAA 2132
                         ---   i    ii   i iii vv    ii i -i   v  v i   i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGAAAGTGAA 695

C chrX_75081649_7   2131 ----CAGCCTACAAAATGGGAGAACCTATTTTCAAACTATGCATCTGACA 2086
                         ----  i  i   i          vv     v    ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chrX_75081649_7   2085 GAGGTCTAATATCCAACATCTATAAGAAACTTAAGCAAATTTACAAGAAA 2036
                         ii  v  vi      iv  v     ii    ivvi   v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chrX_75081649_7   2035 AAGA--AACAACCCCATTAAAAAGTGGGAAAAGAACATAAGCAGACATTT 1988
                             --  i     v   ?    i    v    i iv i ii        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chrX_75081649_7   1987 TTGAAAAGAAGACATACATGTGG---ATGAAGC---TGAAAA 1952
                         i vv        i     vi   ---  -    ---      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAAT-AAGCACATGAAAA 886

Transitions / transversions = 1.66 (159 / 96)
Gap_init rate = 0.02 (14 / 884), avg. gap size = 2.29 (32 / 14)  


2919 26.89 1.78 0.89  chrX_75092025_75099331.rev     5917  6816 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75092025_7   5917 TGGAAAAACCTTCAATGCTCGTGGATATGAAGAATCAATATTGTGAAAAT 5966
                               i iv i v   i  i     vv     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75092025_7   5967 GACCTTAGTGCCCAAAGTAATTTATAGATTTAATGCCATTCTCATCAAGC 6016
                          i vv  v v      v i  i  i     i  i  v  i ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75092025_7   6017 TACCATTGAATTTTTTCACAGAATTAGAAAAACCTACTTTAAATTTCATA 6066
                          v   vivivi     ii     v v  v  i iv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75092025_7   6067 TGTAACCAAAAAGGAGCCTGTATAGCCAAGACAATCTTAAGCAAAAAGAA 6116
                           v  viiv  i   v  v v        i        i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_75092025_7   6117 CGAAGCTGGAGGTATCATGCTACGTGGCTTCAAACTATACTACAAGGCTA 6166
                          i   i      vv   ii  v viiii      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_75092025_7   6167 CAGTAACCAAAATAGCATGGTACTGGTACCAAAACTGATATATAGACCAA 6216
                               i   i i  ii         i iv ii iv  i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_75092025_7   6217 TGGAACAGAAC--AGAGGCCTGACAAAAAACACTACACATCTACAACCAT 6264
                              i    i--    v  v  -  v    - i i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGA-AATAAAC-CCATACATTTATGGTCAA 348

  chrX_75092025_7   6265 CAGATCTTTGACAAACCTGACAAAACAAG-CAATGGGGAAAGGATTCACT 6313
                         iv   i  i     ivv  v   i  v v-            i  vvv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_75092025_7   6314 GTTTAATTAATTGTGTTGGGAAAACTGGATAGCCATATGCAGAAAACTGA 6363
                         v  i  iv   v   i     v         ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_75092025_7   6364 AACTGGACCCCTTCCTTACACCTTATATAAAAATTAACTCAAGATGGATT 6413
                          ii         v   i     v    i              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_75092025_7   6414 AAAGACTAAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 6463
                          ?    iv          v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_75092025_7   6464 AG---CAAATACCATTCA-GGTCATAGGCATCAGCTAA-GACTTCACGAC 6508
                           ---i    -- -   i- ii v i  -- i  vi  - ii   viiiv
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGA 593

  chrX_75092025_7   6509 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 6558
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_75092025_7   6559 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAGAGTG 6608
                          v  i   v v  i i   i  ii vv    i  v    v  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_75092025_7   6609 AACAGACAACCTACAGAATGGGAGAAAATTTTTACAA-TCAATTCATTTG 6657
                           v        i                 v   i   -   - vi  i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTG 742

  chrX_75092025_7   6658 ACAAAGGGCTAATATCCAGAATCTGCAAGGAACTTAAACAAATTTACAAG 6707
                          i  i  i  vi          v ii  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_75092025_7   6708 ACAAAACCAAACAATCCCATCGAAAAGTGGGCAAAGGATATGAA----CT 6753
                          v   iv    i  i  v  i?    i            v    ---- v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_75092025_7   6754 CTTCTCAAAAGAAGACATTTATGTGACCAACAA--AAATGAAAAAA-GCT 6800
                         i     v        i  vi vi  i    i  -- v       i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_75092025_7   6801 CATCATCACTTATCAT 6816
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (138 / 101)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.60 (24 / 15)  


2836 25.47 2.21 1.66  chrX_75101783_75105822.rev     2649  3551 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75101783_7   2649 TGGAAACATATTCTATGTTCATACATTGGAAAAATCAATGTTGCCAAAAT 2698
                               v    i i        iv       i v i   i   ii  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75101783_7   2699 GTCCACACTACCCAAAGCGATCTACATATTCAATACAATCTCTGTCAATA 2748
                          v v i   v      vi        v      ii     i  i    v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75101783_7   2749 TACCAACAACATTCTTCACAAAAATTAAAAAAA-AATTT--AAATTTATA 2795
                          v   i vi v  i  ii  i     i v  iv-i  ii--     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75101783_7   2796 TGAAACTACAAAAGACCCAAAATTGAGCAACAACAACAACAACAACAACA 2845
                           i  v i   ii      i   --   --   -     i-- vvv  v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAAT--AGC--CAA-AACAAT--CTTGAAAA 193

  chrX_75101783_7   2846 ACAACAAACCAAAATGGAAGCAATCACA--------TTACAAGACTTTAA 2887
                          v  v  --    i v i  v v     --------  v   i    ---
  L1M4_orf2#LINE/    194 AGAAGAA--CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT--- 238

  chrX_75101783_7   2888 ACTACACAGCGATTGTCATCAAAACAGTAGAGTACTGGCATAAAAACAGA 2937
                               v   v iv  v     i     ivi            ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_75101783_7   2938 CACATAGACAAATGAAACAAAATAGAGAACTCAGAA-CAAATCCATACAT 2986
                           i     iv    i  i i   v    iii     -i   i        
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_75101783_7   2987 CTACAGTGAACTCATTTTCAACAAAGTTACCGAGAACATACATTGGGGAA 3036
                         i  ii  v  i v      i    i v i  i   v   v  v       
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_75101783_7   3037 AAGACAGTTTCTTCAATAATTGGTGCCTGGAAAACTGGATATCCATATGC 3086
                          ii i   i i     i  v      iv   v         ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_75101783_7   3087 AAAAGAATAAAACTAGACCCCTGTTTCTTGCCATATACAAAAGTCAAATC 3136
                                 i  ii i       iii  vii            i i  v  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_75101783_7   3137 AAAATGAAG-ACATACATAAACCTAATACCTAAAACTATAAGACT---AC 3182
                               i v- ? v  v    iv   v v            i   --- v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_75101783_7   3183 AAGAAAGCATTGGGGAAACTCTTCAGGACATTGGTCTGTACAAATATTTA 3232
                               i   v  ? v  v     iv   v    vi ivi   vvi   v
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_75101783_7   3233 TTAAGAAAT-ACACCACAGACATGGGCAACCTAAGTAAAAGTGGACAAAT 3281
                            -  v  -      v ii  iii     vv   v    i i  i    
  L1M4_orf2#LINE/    589 TTA-GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_75101783_7   3282 TTGATCAAATCAAG-TTAAAAGTCTTCCGTATAGCAAAGGACACAATCAA 3330
                          v  iivv     i-      i-   ii  iivv          v     
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_75101783_7   3331 CAAAGTGAAGAGACAGTCCACAAAATGAAAGAAAGTATTAGCAAACTACC 3380
                         v        i     ii     i    ii     i    v     ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_75101783_7   3381 CATGTTACAAGGGATTAATAACCAGAATATATAAGAAGTTCAAACAACTC 3430
                         i  v v i      i vi  v             ii ii  vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_75101783_7   3431 AATAG-AAGAAGTCAAATAATCCAATTAAAAAATGAGAAAAATATCTGAA 3479
                             i-  i   v       i      ?       i v   iv  i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_75101783_7   3480 TAGACATTTCTCAAAAGAAAATATACAGATTGC-AATCAGGTATATATAA 3528
                                     v      i       i  v  -   - i i i  iv  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCACATGAAA 885

  chrX_75101783_7   3529 AGGTACTAAACATTTATCATTAG 3551
                           i i  v     iv????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (138 / 88)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.84 (35 / 19)  


2976 27.63 0.22 1.95  chrX_75116969_75121563     3180  4102 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_75116969_7   3180 GAAAAAATATTCTATTCTTTATGTAATGGAAAAATCAATGTTGCCAAAAT 3229
                          i   i    i i  v-  i   v v     i v i   i   ii  i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATG-TTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75116969_7   3230 GTTCATACTACTCAAAGCAATCCACAGAGTCAGTGCAATCTCTATCAAAA 3279
                          viv     v i    vii   i     v   ii      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75116969_7   3280 TACCAATGGCATTCTTCATAGATATAAAACAAAATAATTCTAAAATTTAT 3329
                          v   iiv  v  i  iii   v  vi -   iv i  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_75116969_7   3330 ATGAAACCATAAAAGACTTAGAATAGCCAAAGCAATTTTGACCAATCCTG 3379
                            i  viii  ii   ii            i    i    --  -----
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AA----- 192

  chrX_75116969_7   3380 AGCAAAAAGAACAAAACTGAAGGAATTACATTTCCTGACTTCAAATTATA 3429
                         ---  i         ii  i    v i   i    ii i      viv  
  L1M4_orf2#LINE/    193 ---AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_75116969_7   3430 CTTCAAATTAACTTCAAATTAAACCATAACAGTATGTTACTGTCATAAAA 3479
                           v    ---i  v  i--   -i  vi     i  v     v     ii
  L1M4_orf2#LINE/    240 CTACAAA---GCTACAG--TAA-TCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_75116969_7   3480 ACAGACACATAGACAAATGGAACAGAATATAGAACTCAGAAACAAATTTG 3529
                          i     i     iv       i     vv   iii      i   iiii
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_75116969_7   3530 TACATCTACAGTGAACTCATTTTCAATGAAGTTGCCAAGAACATACGTTG 3579
                              i  ii  v  i v      i ii i v        v   v iv  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_75116969_7   3580 GGAAAAGAACAGTTTCTTCAATAATTAGTGCTGAGAAAACTGAATATCTA 3629
                           i      i   i i     i  v i      i  v     i   ? i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_75116969_7   3630 TATGTAGAAGAATAAAACTACACCCCTATCTCTCACCATATACAAAAATC 3679
                         i   i i      i  ii iv       i   v                i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_75116969_7   3680 AAATCCCAATGCATTGAAGACATAAATCTAAGACCTCAAACTATGAAAAT 3729
                           v  vv    v  ii?    v     v     v  v       i   v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_75116969_7   3730 AT-ACAAGAAAATACTGAGGAAGCTCTTAATGACATTGACCTGGGCAAAG 3778
                         v - v       i iv i? v iv    vi    v   ivi i     v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_75116969_7   3779 ATTTCTTGAATAGTACCCCACAAGCACACACAACCAAAGCAGAAATGAAC 3828
                         i      ii   vv  v   v       vi    v    v i    ii i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_75116969_7   3829 AAATAGAATCACACCAAGTTGAAAAGATTCTGCACGATGAGGCAAACAAT 3878
                             v i iiv  i   iv v    iv  i  ii vvii i v v  v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_75116969_7   3879 CAACGAATTGAAAAGACAACCTTCAGAATGGGAGAAAATATTTGCAATCT 3928
                            vi  v             iv                        vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_75116969_7   3929 ACCCATCTTACAAGGGATTAATAATGATAACATATAAGAAGCTAAAACAA 3978
                          ivi    v i      i vi  viv v  i      ii i  vvv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_75116969_7   3979 TTCTACAG-AAAAAAATTAATAATCTGATTTTAAAATGGGCAAAAGATCT 4027
                         i  v i i-     i iv     i ii   ?v            i   i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_75116969_7   4028 GAATAGGCATTTTTCAAACAAAGACATACAAATGGCAAACAAGTATATGA 4077
                               i     i  v  vi    i           v  i   i i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_75116969_7   4078 AAATGTGCTCAACATCATTAATCAT 4102
                            vi            ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (159 / 92)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 2.22 (20 / 9)  


2904 26.83 3.04 0.68  chrX_75129710_75136206     5118  6004 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75129710_7   5118 TAGAAA-ATATTCCATGCTCATGAGTAGGAAGAATCAATATTGTGAAAAT 5166
                          i    -    i     i     ii v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75129710_7   5167 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATTTCCATTGAGC 5216
                            v     v      v i  i  i        i  v  ii i  ii iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75129710_7   5217 TACCA-CTGACATTCTTGACAGAATTAGAAAAAACTT-TTTTAAAATTTA 5264
                          v   -   v v  i   -     v v  v  i-  v- ii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_75129710_7   5265 TATGGAACCAAAAAAGAGTCTGAATAGCTATAAACAATTCTAAGCAAAAA 5314
                                viiv  ii  vi v       i -       ii i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCA-AAACAATCTTGAAAAAGAA 197

  chrX_75129710_7   5315 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATTCTATAAGG 5364
                                 i      vv       v  ii i      viv v   i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75129710_7   5365 CTACAGTAACTAAAACAGCATGGTACTGGTACAAGAACAGACAGACAGAC 5414
                                  ii  i    ii         i i   i i     v i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75129710_7   5415 CAATGGAACAGAATGGAGAACTCAGAAATAAGACTGCACACCTACAACCA 5464
                                 i     v    iii         iv iii   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_75129710_7   5465 TCTGTTCTTTGACAAACCTGACAAAAGCA----ATGGAGGAAATATTGCC 5510
                         vi  v i  i     ivv  v   i v  ----    i i  iv  v i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_75129710_7   5511 TATTTAATAAATGGTGCTGGGAGAACTAGCTAGCCATATGCAGAAAATTT 5560
                          v  i  i              v    i v  ?   i     i  i v v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_75129710_7   5561 AAACTGGACCCCTTCCTTACATCATATACATAAATTAACTCAAGATAGAT 5610
                           ii         v   i   i        v            i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_75129710_7   5611 TAAAGACTTAGATGTAAAACACAAAACTATAAAAAACCTAGAAGAAAATC 5660
                         i ?    i  i      i vvi            vv i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_75129710_7   5661 TAGGCA-ATACCATTCAGGACATAGGAACAAGCAAAGATTTCATAATAAA 5709
                             ?i- v i -   iv   v v  ivi i    v i    v  ivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75129710_7   5710 AATGCCAAAAGCAATTGTAACAAAAGCAAAAATTGGCAAATGAGATCTAA 5759
                         i ii         vvv i        v      v ii    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75129710_7   5760 TTAAACTAAAGAACTGCTGCACAGCAAAAGAAACTGTCATCAGAAAG--A 5807
                          i   v v  i    vi  ii vv    i  v   i   --      -- 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--AGAAAGTGA 694

  chrX_75129710_7   5808 ACAGACAGCCTACAGAATGGAAGAAAATTTGTGCAATCTATGCACCTGAC 5857
                          v     i  i         i       v v     vii  ii i    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75129710_7   5858 CAAGGTCTAATATCCAGAGTCTACAAGGAACTTAAACAAATT-----TAC 5902
                         v i  v  vi        i v  i  i     ivv    v i-----  v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75129710_7   5903 AAAGAAAAA------AATTAAAAAGTGGGCAAAGGACATGAACAGACACT 5946
                              v   ------    ?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75129710_7   5947 TCTC-----AAAACATACATGTGGCCAAGAATCGTG-GAAAAAAAGCTCA 5990
                             -----  i i     vi       v  v iii-     i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75129710_7   5991 ACATCACTGATCAT 6004
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (144 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


3058 25.89 0.76 2.80  chrX_75161065_75167775     5292  6218 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75161065_7   5292 TGTAAAAATATTCCATGCTCATGGCTAGGAAGAATCAATATCGTCAAAAT 5341
                           v   i    i     i      v v      v i     i  i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75161065_7   5342 GGCCATATTGCCCAAAGTAATTCATAGATTCAATGCTATGCCCATCAAGC 5391
                            v   i v      v i  ii i        i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75161065_7   5392 TACCA-TTGACTGTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAATTTC 5438
                          v   -i  v  - i  ii     -   -- v  i  - iii v  v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_75161065_7   5439 ATATGGGACCAAAAAAGAGTCCGTATAGCCAAGACAATCCTAAGCAAAAA 5488
                               i viiv  ii  vi v v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75161065_7   5489 CAACAAAGCTGGAGGCATCACATTACCTAACTTCAAACTATACCATAAGG 5538
                         v       i      vv     i v  i  i      viv   i i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75161065_7   5539 CTACATTAACCAAAACAGCATGGTACTGCTACCAAAACAGATATATAGAC 5588
                              v   i   i    ii        vi iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75161065_7   5589 CAATGGAACAGAACAGAGGCCTCAGAAATAACTCCACATGTGTACAGCCA 5638
                                 i    iv   ivii         vi   i ii v  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_75161065_7   5639 TCTGATCTTTGACAAATCTGACAAAACAAG-CAACGGGGAAAGGATTCCC 5687
                         vi    i  i     ivv  v   i  v v-   i        i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_75161065_7   5688 TACTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATACGCAGAAAGCTG 5737
                          vi i  i        i     v      v  ?   i i   i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_75161065_7   5738 AAACTGGATCCTTTCCTTACACGTTATACAAAAATTAACTCAAA-TGATT 5786
                           ii    i  i v   i    vv                    -  iv 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_75161065_7   5787 TAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5836
                         i ?    i           v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_75161065_7   5837 TAGGCA-ATATCACTTAGGACATAGGTATGGGCATAGACTTCATGACTAA 5885
                             ?i- v   -i iiv   v v  vv i    vv ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75161065_7   5886 AACACCAAAAGCAATGGCAACAAAAGTAAAAATTAACAAATGGGATCTAA 5935
                         i            vvi          v      vi i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75161065_7   5936 TTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAATTATCATCAGAGTGAA 5984
                          i   -     i -   i  ii vv    i  v i     vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75161065_7   5985 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCGATCTATCCATCTAACA 6034
                         v  i     i                 v     i vii  vi    i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75161065_7   6035 AGGGTCTTATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAAAAA 6084
                             v   i          v  i        i--------      ----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTC--------TTACAA---- 783

  chrX_75161065_7   6085 ACCCAAAAACCAAAAAAAAAAAAACCAAACAACCTTATCAAAAAGTGGGC 6134
                         - i   v  i-------     i  -   i    iv  i?    i     
  L1M4_orf2#LINE/    784 -CTCAATAAT-------AAAAAGAC-AAATAACCCAATTWAAAAATGGGC 824

  chrX_75161065_7   6135 AAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 6184
                                v    i     i     v        i  vi viii     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_75161065_7   6185 AACATATGAAAAAAAGTTAATCATCACTGGTCAT 6218
                          i  i       i v i v v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (145 / 91)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


2475 28.43 3.51 1.13  chrX_75189411_75191640.rev      863  1745 (485)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_75189411_7    863 AAAACATTACATGCTCATTGATTAGAAGAATCAATGTTGTTAAAATGGCT 912
                           i i  iv    i    v    i     v i   i       i     v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_75189411_7    913 ATACTACACAAAGCAATCTACAGATTCAATGC------TATCAAACTACC 956
                              v v    vii              i  ------       v v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_75189411_7    957 AACATCATTTTTCACAAAAATAGAAAAA--------AAAATTCCAAATGA 998
                          i vv v     ii  i    v  v  i--------       - v   i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC-ATATGG 153

  chrX_75189411_7    999 AGCCAAAAAAGAGCTGGAATAGTCAAAGCAATCCTAAGCAAAAATAAAAA 1048
                          iviiv  ii  v ii      i    i     i i iv  i  v  v  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_75189411_7   1049 AGCTGTAGGCATCACATTACACAACTTCTAACTATACTACAAGGCTACAG 1098
                           i  v   vv     i v v   i   v  viv        i       
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_75189411_7   1099 TAAGCAAAATAGCATGATAATGGTACAAAAACAGACATATAGACCAATGA 1148
                            v   i i  ii  i  v   i i  ii i           i     i
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_75189411_7   1149 AAGAGAGTAAGAGAACCCAGAAATAAAGCTGCACACCTACAACCAACTGA 1198
                           v   i v-    ii           v iii   ii  iiii   i   
  L1M4_orf2#LINE/    304 AATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_75189411_7   1199 TCTTCAATAAATTTGATAAAAATAAGAAATGGGGAAAGAA--GTTTCTAG 1246
                          i   i i  ivv  vi  i vi vvv             --  i i --
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT-- 400

  chrX_75189411_7   1247 TTAGTAAATGGTGCTGGAATAGCTGGCTAGCCCTATGCAGAAGAATGAAA 1296
                          i ii            i i i    v  ?  vi     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_75189411_7   1297 C--AACCCCTTCCTTTTACCACATACAAAAATTAAC--ATGCTGGATAAA 1342
                         i--i      v   ivi    i              -- viv     v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_75189411_7   1343 ACATTTAAATTTAAGATCTCTTACTATAAAAATCTTAAAAGAAAATCTAG 1392
                          v ii     v     v  vvv         v     i       iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_75189411_7   1393 G---AAATTCCCTTCTAGATATCAGCTTTGGCAAAGAATTTATGACTAAG 1439
                          ---    ---    vv  iv ii v  v     v iv  iv iiv  v 
  L1M4_orf2#LINE/    551 GNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_75189411_7   1440 TCCTCAAAAGCAATTGCAACAAAAACAAAAATTAACAAATGGGACCT--- 1486
                         v vi        vvv         iv      vi i    v    i ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_75189411_7   1487 ---AATTAAAGAGTTTCTGCACACCAGAAGAAACTATTAACAGAGTAAAC 1533
                         ---       i v   -  ii vi  i i  v     i  v i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_75189411_7   1534 AGACAGCCTACAGGATGGAAGAAAATATTAACAAAC--TGCATCTGACAA 1581
                              i  i    i    i          vi    i-- ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_75189411_7   1582 AGGTGTAATATCCAGAGTCTATAAGTAACTTAAATAATTGAACAGGCGAA 1631
                         i  vv vi        i v     iv    ivv i  i v  i ivvi  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_75189411_7   1632 AAACCAATAACTTCATGAAAACGTGGGCAAAAGACATGAACAGACACTTC 1681
                          i  v      iiv  v?   vi        i  iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_75189411_7   1682 TTAGAAAAAGACATACAAGTAGCCAACAAATATATTTTTAAAAATGCTCA 1731
                          ivi  i    i      i i     i  ii i  vv--   i       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGA--AAAGATGCTCA 894

  chrX_75189411_7   1732 TCTTTAATCATCAG 1745
                         v v i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.02 (14 / 904), avg. gap size = 2.93 (41 / 14)  


2935 23.71 5.29 0.81  chrX_75191939_75193807.rev      510  1378 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75191939_7    510 TAGAAAGATATACCATGTTCATGGATTGGAAGAATTAATATTGTTAAAAA 559
                          i         v                     v             i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75191939_7    560 ATCCATATTACTGAAAGTGGTCTACAGATTCAATGCAATCCCTGTCAAAA 609
                         iv v   i v iv   v  i             i         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75191939_7    610 CTCCAA-TGAAATTTTCACAGAAATAGCAAAAGAAATTATAAAATTCACA 658
                         ii   i-  vvv    ii       v vv  ivvi  iv         i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75191939_7    659 TGGAACCACAAAAGATCT-GAATAGCCAAAGCAATCTTGAACAAAAA--- 704
                              vii   ii  i i-           i          v  i  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_75191939_7    705 -----TTTAAAAACTG----TTTCTAATT--A-----TATTACAAAGCAA 738
                         -----  vi ii   v----  i i    -- -----  i        v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_75191939_7    739 CAGTAATCAAAACAGCATGGTACTGATATAAAAACAGATACATAGATCAA 788
                                   i    ii        ii    ii i   i i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_75191939_7    789 TGGAAGAAAAGAGAGAGACCAGAAATAAATCCA-ACAGTTTATGGTAATT 837
                              v i  vv     v           i   -   -        v v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA-TTTATGGTCAAT 349

  chrX_75191939_7    838 TGATCT--AAAAAAAAAGCCAAGAAAACACAAGGGGGATATGACAGTCTC 885
                             i --i v  iiiv       vv iv   v     v vi i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_75191939_7    886 TTCAATAAATACTGTTGGCAAAAGTAGATATCCACATGCTGATGAATGAC 935
                              i    iv  i   v v  v i    ?        vi v      v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_75191939_7    936 ATTGGACCCTTAT-TCACCTCATATACAAAAATCAACTCAAAATAGATCA 984
                         i        i  i-    vi             i          i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_75191939_7    985 AAGATTCAAATGTAAGATTTGAAAGCATAAAATTACCAGAAGAAAATA-A 1033
                         ?   iii          vi i   vi      i vii         i - 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_75191939_7   1034 GGC-CAAAGCTTTATGACATTTGTCTTGGCAGTAATTTTTTTTTAATGGC 1082
                           ?-i   v   ii    v  v vi v    i ii   i  vvvv   i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_75191939_7   1083 ACCAGAAGCACAGGGAACAAAAGGAAAAATATACAACTGAGACTTCATCA 1132
                             i       i v        i       v i  v vi          
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_75191939_7   1133 ATCT----AATGTTT---CTCCATAG--CA--AAGAAAAAAATGAAAT-- 1169
                          vv ----  iv   ---  i  v  --  -- vv  i   i     v--
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_75191939_7   1170 CAATGGAAGCGTAGGTAATGAGAAAAAATATTTGCAAGTCATATATCTGA 1219
                            iv---- ii  --    i  i             i            
  L1M4_orf2#LINE/    700 CAACC----CACAG--AATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_75191939_7   1220 TTGGAGGTTAATATCCAAAA-ATATAAGAAATTCATACAACTCAATAGCA 1268
                          vi i ii vi      i  -      ii  i  v            ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_75191939_7   1269 AAAAAAAAAAGAA---AA--GAAAAATTATCAAAGACCCTGAATAGAAAT 1313
                             i v   v  ---  --?      viv     ivii        v  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_75191939_7   1314 TTTTTCAAAGAAGAAATGCAAATGGCCAACAGGTATGTGAAAAAATGTCC 1363
                           i i         v  i           i i i ii      i   ii 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_75191939_7   1364 AACATCACCAATCAC 1378
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (124 / 78)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.41 (53 / 22)  


2007 20.51 1.90 19.96  chrX_75194719_75200625.rev     4310  5416 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_75194719_7   4310 GAAAAGA-ATTTTATGTTTATAAATCAGAAAAAAATCAATATTGTTAAAA 4358
                          i     -  iii     i  ii  ii   i v-- i           i 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGAC--TTAATATTGTTAAGA 49

  chrX_75194719_7   4359 TGTCCATACTACTCAAAGCAATCTATAGATTCAATGCAATCCCCAACAAA 4408
                           v v     v i    vii     i        i        i v    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_75194719_7   4409 ATACCAATTACATTCCTCACAGAAATGGAAAAATCAGACCTACAATTTAT 4458
                           v   ii i v  ii ii       v  v  iiiiiv    v    i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_75194719_7   4459 ATGGAACCACAAAAGACCTAGAATAGCCGAAGCTATCCTAAGCAAAAATG 4508
                               vii   ii    i         i  i v   i i iv  i  vi
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75194719_7   4509 ACAAGACTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCT 4558
                             iii       v     i v  ii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_75194719_7   4559 ACAGTAAGCAAAACAGCATGGCACTGGAATAAAAAGGAGTCAGACGGACC 4608
                                v   i    ii   i     v    ii v-  v  v ii  i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGATC 298

  chrX_75194719_7   4609 AATGGAACAGAATAGAGAACCTATAAATGAATCCATTTATCTAGAGTGAA 4658
                                i     v    ii i v    i  i    vi  i  -------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA------- 341

  chrX_75194719_7   4659 CTTTTTTTTTTTTTGAGATAGAGTCTTGCTCTGTTGCCCAGGCTGGAGTA 4708
                         --------------------------------------------------
  L1M4_orf2#LINE/    342 -------------------------------------------------- 341

  chrX_75194719_7   4709 CAGTGGTGTAATCTTGGCTCACTGCAACCTCCACCTCCTGGGCTCAACTG 4758
                         ---    -------------------------------------   i  
  L1M4_orf2#LINE/    342 ---TGGT-------------------------------------CAATTG 351

  chrX_75194719_7   4759 ATTCTGTATTTTTAGTAGAGACAGGTTTTCACCATGTTGGCCAAGCTTGT 4808
                            -------  i------    i -------------  -------  i
  L1M4_orf2#LINE/    352 ATT-------TTC------GACAAG-------------GG-------TGC 368

  chrX_75194719_7   4809 CTCAAACTCCTGACCTCAAGAGATCCATTTGCCTGGCCCCCCAAACTGCT 4858
                          ----------------    ---     ------------   --  --
  L1M4_orf2#LINE/    369 C----------------AAGA---CCATT------------CAA--TG-- 383

  chrX_75194719_7   4859 GGGATTACAAGTGTGAGCCTCCTAACTTATTTTTATAAAGGAGCCAAGAA 4908
                             ----   vi -  i  ----------   i ---------------
  L1M4_orf2#LINE/    384 GGGA----AAGAAT-AGTCT----------TTTCA--------------- 403

  chrX_75194719_7   4909 CATACACGAGGAAAAAGTCTTAGATTAATGATGCTGAGAAAACTGGATAT 4958
                         ---   --------------------    i     i  v         ?
  L1M4_orf2#LINE/    404 ---ACA--------------------AATGGTGCTGGGACAACTGGATAK 430

  chrX_75194719_7   4959 CGATATGCAAAAGAATGAAACTAAACCTCTATCTTCCACCATATACAAAA 5008
                          v i               ii ii   i   i  iv              
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_75194719_7   5009 ATCAAATTAAAATGCATTAAAGACTTTAATCTGAGACCTCAAACTATGAA 5058
                           i  v i      v  i ?    i v   v i   v  v       i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_75194719_7   5059 ACTACTACAAGAAAATATTGGAGAAAATCTCCAGGACATTGATCTGGGCA 5108
                            vi  v       i  v  ? v      i iv   v   ivi i    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_75194719_7   5109 AAGATTTTCTGAGTAATACCCCACAAGCACCGGTAATCAAAGCAAACATG 5158
                          v i   ii iii  vv  v   v      vi i  iv    v   v  i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_75194719_7   5159 GACAAATGAGATTACATCCAGTTAAAAAACCTCTGCACAGCAAATAATAC 5208
                           i    vi  i v    v iv v      i i  ii vv    vi i  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_75194719_7   5209 AATCAA-------------CAATGCACAGAATAGGAGAATATATTTGCAA 5245
                         v     -------------   iv        i      v          
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_75194719_7   5246 ACTACCCCTCTGACAAGGGATTAATAAGCAGAATATATAGGGAGCTCAAA 5295
                          ii iviv     i      i vi  vv           ii  i   vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_75194719_7   5296 CAATTCAA-AAGAAAAAAATA--TGATCCAATCAAAAAGTGAGCAAAAGA 5342
                            i    -  v     i i -- i i     i?    i  i     i  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_75194719_7   5343 TCTGAATAGACATTGATCAAAAGAAGACATAGAAGTGAC-AAT---CATA 5388
                          i            vv  v        i   v  i  i -   ---  i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_75194719_7   5389 TGAAAAGGTGCTCAACATCATCGATCAT 5416
                                i            ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (146 / 77)
Gap_init rate = 0.03 (24 / 907), avg. gap size = 10.08 (242 / 24)  


2758 25.97 1.52 3.25  chrX_75211862_75217580      491  1414 (4305)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_75211862_7   1414 TAGAAACACCTCCCATGCTCATGGACAGGTAGAATCAATATTGTGAGAAT 1365
                          i    v iv       i       iv  v   v i        v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_75211862_7   1364 GACCATACTGCCACAAGCAATCTACAAATTTAATGCAATCCCCATCAAAA 1315
                          i v     v  vv  vii       i   i  i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_75211862_7   1314 TACCACCATCTTTCTTCACAGAATTTTAAAAA--AAATCTAAAATTTACA 1267
                          v   v vv i  i  ii     v  v v  i--i vi        i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chrX_75211862_7   1266 TGCAAC--CAAAAAACAGCCCGCATAGCCAAAGCAAGACTAAGAAAGAAG 1219
                           v  v--   iii  --  v v         i   vvi i i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_75211862_7   1218 AACAAATCTGGAGGCATCACACTACCTGATTTCAAATTATATTGTAAGAC 1169
                               vi      vv       v  ii        viv  i ii  ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_75211862_7   1168 AATAGTCACCGAAACATCGTGGTACTGGTGTAAAAATAGGCACAAAGACC 1119
                         v i   v i i i   vi          ii   ii    i  i v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_75211862_7   1118 AAGGGAACACAATAGAGAAGCCAGAAATAAACCCAAACATTTACAGCCAA 1069
                           v    i v   v    iv               v       ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

C chrX_75211862_7   1068 CTGACCTTCACCTTCGACAAAGCAAAAAAAATAAATAAATAAATAAAAAA 1019
                         i   --  ----        i vvivv  i iv v v   ----------
  L1M4_orf2#LINE/    349 TTGA--TT----TTCGACAAGGGTGCCAAGACCATTCAAT---------- 382

C chrX_75211862_7   1018 TAAAGTGGGGGGAAAGGACACACTTTGCAACTAATGGTGCTGGGATCATT 969
                         --------        i i vv    v    v             iv i 
  L1M4_orf2#LINE/    383 --------GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

C chrX_75211862_7    968 GGCCAGTCACATGTAGGAGAACAAAACTGGATCCTCATCTTTCACTTTAT 919
                           vi ?i      i ii    ii  ii    i  ii i  iv   iv   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

C chrX_75211862_7    918 A-GTAAATCAACTCAAGATGGATTAAGGACTTAACC-TAAGATCTGAAAC 871
                          -iv    i       i      i ?i   i   vi-     v  i    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

C chrX_75211862_7    870 TATAAAAATTCTAGAAGATAACATTGGCAAAAACCCTTCTAGACATTGGC 821
                                v ii       v     v  ?iv   i -   vv   v    v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

C chrX_75211862_7    820 TTAGGCAA-GGTT-CTAATGACCAAGAACCCAAAAGCAAATGCAATAAAA 773
                                 -    -  v -  i- v  vv         v v    i    
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTA-GAT-ATGACACCAAAAGCACAAGCAACAAAA 621

C chrX_75211862_7    772 CAAAAAATAAATAGCTGGGACCTAATTAAGCTAAAGAGCTTTTGTACAGC 723
                         v        i   iv v    i v  i  iv v  i i       i vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

C chrX_75211862_7    722 AAAAGGAGCAGTCAGCAGAGTAAATAGACAACCCACAGAGTGGGAGAAAG 673
                            i ivi vi   iv i   i  v              i         i
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

C chrX_75211862_7    672 TCTTCACAATCTATACATCTGACAAAGGACTAATATCCAGAATCTACGAG 623
                          v  ii   vii   i      i  i     vi          v  ii i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

C chrX_75211862_7    622 AAACTCAAACCAATCAGTAAGAAAAAAA-----AATCCCATAAAAAAGTG 578
                         i     vv  v v   i   v     i -----  i  v  v?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

C chrX_75211862_7    577 GTCTAAGGACATAAATAGACAACTCTC-AAAGCAAGATATACAAACGGCC 529
                          v v     iv i        vi    -    -            i    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAG-AAGATATACAAATGGCC 870

C chrX_75211862_7    528 AACAAACATATGAAAACATACTCAACATCTCTGATGAT 491
                           i  i  i       v  i         v????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (135 / 101)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.75 (44 / 16)  

3170 27.50 0.55 0.66  chrX_75211862_75217580     4318  5226 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75211862_7   4318 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4367
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75211862_7   4368 GGCCATACTGCCCAAGGTAATTTATGAATTCAATGCCATCCCCATCAAGC 4417
                            v     v     iv i  i  iii      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75211862_7   4418 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4465
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75211862_7   4466 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 4515
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75211862_7   4516 AACAAAGCTGGAGGCATCATGCTACCTGACTT-GAAACTGTACTAGAAGG 4564
                                i      vv   ii  v  ii i  -i     -     v  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_75211862_7   4565 CTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGAC 4614
                                  i   i    ii         i i  ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75211862_7   4615 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 4662
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_75211862_7   4663 TATTTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGTTTC 4712
                         i v     i  i     ivv  vv  i v  vv            iv vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_75211862_7   4713 CCTTTTTAATAAATGATGCTGGGAAAACTGGCTAGCAATATGTAGAAAGC 4762
                         i     i  i     i        v      v  ? v i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_75211862_7   4763 TGAAACTGGATCCCTTCCTTACACCTTATATAAAAATCAATTCAAGATGG 4812
                             ii    i    v   i     v    i      i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_75211862_7   4813 ATTAAAGACTTAAATGTTAGACCTAAAACCACAAAAACCCTGGAAGAAAA 4862
                           i ?    i       v   v       i i    vi i i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_75211862_7   4863 CTTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4912
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_75211862_7   4913 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4962
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75211862_7   4963 ATTAAACTAAAGAGCTTCTGCACAGCAAAAAGAAACTACCATTAGAGTGA 5012
                           i   v v  i i   i  ii vv    i-  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGA 694

  chrX_75211862_7   5013 AGAGGCAACCCACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5062
                          i  i         i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75211862_7   5063 AAAGGGCTAATATCCAGAATCTACAATGAACTCAATCAAATTTACAAGAA 5112
                           i  i  vi          v  i  v      vvv   v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75211862_7   5113 AAAAACCAACAACCTCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 5162
                            i  v  i    iv  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75211862_7   5163 TCTCAAAAGAAGACATTTATACAGCCAAAAGACACATGAAAAAATGCTCA 5212
                             v        i  vi v ii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75211862_7   5213 CCATCACTGGCCGT 5226
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (151 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2614 29.69 1.90 0.56  chrX_75237266_75242665     4012  4907 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75237266_7   4012 TGAAAATA-ATTTCACGCTGGTGTATAGAAAGAATCAATATTTCAAAAAT 4060
                           i   v -  ii  i i vi  v  v i    v i      viv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75237266_7   4061 GGCCATACTGCCCAAAGTGATTTGTAGATTTAATGCCATTCCCATGAAAC 4110
                            v     v      v    i ii     i  i  v  i  i  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75237266_7   4111 TATCATTGGCTTTCTTTGCAGAATCAGAAAAAACGACCTTAAATTTCATA 4160
                          vi  viv  i  i         viv  v  ivi  i i    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75237266_7   4161 TGGAAACAAAAATGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGAG 4210
                               iiv  iv  v  v v        i      i i iv  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_75237266_7   4211 CAAATCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGGCTG 4260
                             vi      vv    v  v  ii i      viv        i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_75237266_7   4261 CAGTAACCAAAACAGCATGGTACTGGTCCAAAG-CAGATATATAGACCAA 4309
                               i   i    ii         ivi  i -i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_75237266_7   4310 TGGAACAGAACATAGGCCTCAGAAATAACACCACACATCTACAACCATCT 4359
                              i    ivv  ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_75237266_7   4360 GATCTTCAACAAACCTGACAAAAACAG-CAATG------------TTTAT 4396
                            i   i    ivv  v   i v  v-     ------------ i v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_75237266_7   4397 TTAATAAACAGTGCTGGAAAAACTGCCTAGCTATATGCAGAAAATTGAAA 4446
                          i  i   ii       i v     vv  ? i i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_75237266_7   4447 ATAGATCCCTTCATTACAACTTATACAAAAATTAACTTAAGGCAGATTAA 4496
                         v i  i    v v i   v v                i  iiii   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_75237266_7   4497 ACACTTAAATGTAAAACCTAAAACTATAAAAACCCTAGAAGAAAACCTAA 4546
                          v  i         i v              vi i           v  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_75237266_7   4547 GCA-ATACCATTGAGGACATAGGCATGGGCAAGGACTTAATTACTAAAAC 4595
                          ?i- v i v i v iv v i  i- i     v ii  vv viv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGAC 599

  chrX_75237266_7   4596 ACAAAAAGCAATTACAACAAAAGCCAAAACTGACAAATGGGGTCTTATTA 4645
                           v       vvvi         vv    iv  i    v  iii i  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_75237266_7   4646 AACTAAAAAGCTTCCGTAAAGCAAAAGAAACTGTCAGCAGAGTGAACAGG 4695
                           v v    i   ii  ivvv    i  v   i   iv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_75237266_7   4696 CAACCTATAGAATAGGATAAAAGTTTTGCAGTCTATCCATCTGACAAAAG 4745
                              i i     i   v    vv      ivii  vi      i  ii 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_75237266_7   4746 GTTAATATCCAGAATCTACAAGGAATTTAAACATATTTATAAGAAACAAA 4795
                         ii vi          v  i  i   i ivv   vv iv    ----i   
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA----TAAA 795

  chrX_75237266_7   4796 CAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACATACACTT 4845
                         v i     i     v  i?    i            v    i v   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_75237266_7   4846 CTCAAAAGAAGACATTTATGTGGCCAAAAAACATATAAAAA-AGGCTAAT 4894
                            v        i  vi vi       v  i  i  i    - v   v v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_75237266_7   4895 CATCACTGGTCAT 4907
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (152 / 110)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.75 (22 / 8)  


3086 26.54 0.99 0.99  chrX_75258720_75276280      492  1399 (16162)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_75258720_7   1399 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 1350
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_75258720_7   1349 GGATATACTGCTCAAAGTAATTTATGGATTCAATGCCATCCCCATCAAGC 1300
                           vv     v i    v i  i  ii       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_75258720_7   1299 TACCAATGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1252
                          v   iivi i  i   i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_75258720_7   1251 TATGGATCCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 1202
                               vviiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_75258720_7   1201 AACAAAGCTGGAGGCATCACACTAGCTGACTTCAA--CCTACACTAAAAG 1154
                                i      vv       vv ii i     -- i   --  v  i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAA 246

C chrX_75258720_7   1153 GTTACAGTAACCAAAACAGGATGATACTTGTACCAAAATAGAGATATAGA 1104
                          i        i   i    vi  i    v i iv ii     v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chrX_75258720_7   1103 CCAATGGAACAGAGC--AGAGCCCTCAGAAATAATACCACACATCTACAA 1056
                         i        i   ii--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

C chrX_75258720_7   1055 CCATCGGATCTTTTACAAACTTGACAAAAACAAGAAATTGGGAAAGGATT 1006
                         i  viv   i  iv    ivv  v   i v  vvv   v       i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

C chrX_75258720_7   1005 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 956
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chrX_75258720_7    955 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 906
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chrX_75258720_7    905 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 856
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chrX_75258720_7    855 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 807
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

C chrX_75258720_7    806 TAAAACACCAAAAGCAAGAGCAACAAAAGACAAAATTGACAAATGGGATC 757
                           vi            vi            v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

C chrX_75258720_7    756 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 707
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

C chrX_75258720_7    706 AACAGGCAACATACAGAAATGAGAGAAAATTTTTGCAATCTACCCATCTG 657
                           v  i    vi      -  i        v       vii ivi     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATATATCTG 742

C chrX_75258720_7    656 ACAAAAGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAG 607
                          i  ii i  vi          v  i         vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

C chrX_75258720_7    606 AAAAAAAACAAACAACCCCATCAAAAAGTGAGCAAAGGAAATGAACAGAC 557
                              i -    i     v  i?    i  i        vv    i    
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chrX_75258720_7    556 ACTTCTCTAAAGAAGACATCTATGCAGCCAACAG--ACATGAGAAAATAC 509
                          i     i        i  vi viii     i i--      i  i  i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

C chrX_75258720_7    508 TCATCATCACTGGTCAT 492
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  

2703 26.17 2.68 1.34  chrX_75258720_75276280     6905  7798 (9763)  C L1M4_orf2#LINE/L1   (0)   908     3  

C chrX_75258720_7   7798 GAAAAATATTCCATGCTCATGGATAGAAGGAATCAATATCATGAAAATGG 7749
                             i    i     i        v i i  v i     ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

C chrX_75258720_7   7748 CCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCACCATCAAGCTC 7699
                          v     v      v i  i  i        i  v   v i     iv  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

C chrX_75258720_7   7698 C-AACTGACTTTCTTCACAGAATTTTAAAAAACT-ACTCTAAATTTCATA 7651
                          - i   v    i  -i     v  -i v  i  - ii     v      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT-GCAGAAATT-GACAAGCTGATCCTAAAATTCATA 150

C chrX_75258720_7   7650 TGGATCCAAAAAAGAGCCCACACAGCCAACAGAATCCTAAGCAAAAA-AG 7602
                             vviiv  ii  v  viv i      v v    i i iv  i  - i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chrX_75258720_7   7601 CAAAGCTGGAGGCATCACACCATCTGACTTCAAATTATACTACAAGGCTA 7552
                              i      vv      ivi ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chrX_75258720_7   7551 AAATAATCAAAACAGCATGGTACTGGTACAAA-ACAGATATATTGACCAA 7503
                         v i       i    ii         i i  i- i   i    v  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

C chrX_75258720_7   7502 TGTAACAGAACAGAGGCCTCAGAAATAACACCACACATATACAATCCTCT 7453
                           v  i    iv   ivii         vv   i    v  iii  vvi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

C chrX_75258720_7   7452 GGTCTTTGACAAACCTGACAAAAACAAGCAATGTGGAAATAATTTCCTAT 7403
                          i i  i     ivv  v   i v  vv     v     v   vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

C chrX_75258720_7   7402 TTAATAAATGGTGTTTGGA-AACTGGCTACCCATATGCAGAAAACTAAAA 7354
                          i  i        i v   -      v  ?   i     i  i v i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

C chrX_75258720_7   7353 CTGGATCACTTTCTTACACCTAATACAAAAATTAACTCAAGATGAAT--- 7307
                         i    i v  vi  i     vv                  i   i  ---
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

C chrX_75258720_7   7306 -----------TAAGACCTAAAACCATAAAAAAACATAGAAGAAAAACTA 7268
                         -----------     v       i      vv- v          vv  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATA 549

C chrX_75258720_7   7267 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTGAGA 7219
                           ?i- v i -   iv   v v  vv i     v ii   v iiv iv  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

C chrX_75258720_7   7218 CATCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTAATT 7169
                           i        vvii         vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

C chrX_75258720_7   7168 AAACTAAAGAGCTTTTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 7119
                            v v  i i      ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

C chrX_75258720_7   7118 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCATCTGACAAAG 7069
                         i     i                 v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

C chrX_75258720_7   7068 GGCTAATA-CCACGAATCTACAAAGAACTCAAAGAAATTTACAAGAAAAA 7020
                          i  vi  -   -    v  i         vv v  v iv i  v     
  L1M4_orf2#LINE/    749 GACTTGTATCCA-GAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

C chrX_75258720_7   7019 AACAAACAACCCCATCAAAAAGTTGGCAAAGGATATGAACAGACGTTTCT 6970
                         i     i     v  i?    i v          v    i    i     
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

C chrX_75258720_7   6969 CAAAAGACGACATTTACCA---GCCAAGAAACATATGAAGAAAATAAAAG 6923
                          v     v  i  --  v ---     v  i  i     -  i  ---- 
  L1M4_orf2#LINE/    848 CCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAA-AAGAT----G 890

C chrX_75258720_7   6922 CTCATCATCACTGATCAT 6905
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (126 / 105)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 2.12 (36 / 17)  

3330 26.54 0.44 0.44  chrX_75258720_75276280    16161 17068 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75258720_7  16161 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 16210
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75258720_7  16211 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATGAAGC 16260
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75258720_7  16261 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 16308
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75258720_7  16309 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGGCAATCCTAAGCCAAAAG 16358
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75258720_7  16359 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 16408
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75258720_7  16409 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 16458
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75258720_7  16459 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 16506
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75258720_7  16507 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 16556
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75258720_7  16557 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 16606
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75258720_7  16607 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATCAATTCAAGATGGA 16656
                            ii    i    v   i   i v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75258720_7  16657 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 16706
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75258720_7  16707 ATAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 16756
                              ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75258720_7  16757 AACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGGTTCTAA 16806
                         i            vvi          vv     v  i    v  vii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75258720_7  16807 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 16856
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_75258720_7  16857 AGGCAACCTAGAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 16906
                           i     i v i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_75258720_7  16907 AGGGCTATTATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 16956
                         i  i  vv          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_75258720_7  16957 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACGCTTC 17006
                          i     i     v  i?    i           iv    i    ii   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_75258720_7  17007 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 17056
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_75258720_7  17057 ATCACTGGCCAT 17068
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2824 26.79 2.09 1.98  chrX_75285551_75290109.rev     3162  4068 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75285551_7   3162 TAGAAATACATTTCATGTTTATGGAATGGAAGATTCAATATTTTTAAAAT 3211
                          i    v i  ii      i     v       i i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75285551_7   3212 GTCCTTACTACTTACAGCAATCTCCAGATTCAATGCAATTCTTATCAAAA 3261
                          v vv    v ii v vii    v         i     i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75285551_7   3262 TACTAAAGACATTCTT--CAGGTAAATAAAAAAC--ATTCTCAAATTTAT 3307
                          v i ivvi v  i  --   i-  v i v  i --  i  v     i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_75285551_7   3308 ATGGAACTACAAAA-ACACAGCATAGCCAAAGCTATCCTAAGCAGAAATA 3356
                               v i   ii-  v   v         i v   i i iv ii  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75285551_7   3357 ATAAAACTGGAGCAGTCACATTACCTGACTTCAAATTATACTACAGAGCT 3406
                          i   ii     v v     i v  ii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_75285551_7   3407 ATAGTAACCAAAACAGCAAGGTGCTGGCATAAAAACAGACA----GACCA 3452
                          i     i   i    iiv   i         ii i     ----  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_75285551_7   3453 ATGGAACAGAATAGAGAAGCAAGAAATAAATACATACACCTACAGCAAAT 3502
                               i     v    iv v         iv      ii  ii iv   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_75285551_7   3503 TCACTTTTAATAAAGGTGCCAAAA--ATACACTGGGGAAAAGACAGTGTA 3550
                          v i   ii i  i        i --  v  v        ii i   ---
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT--- 396

  chrX_75285551_7   3551 TGTTTATTGTTTTTCAATAAATGGTGA-AGAAAAACGGGATCTCCATATG 3599
                         ---------i       i        v-i i v   v    v?   i   
  L1M4_orf2#LINE/    397 ---------CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_75285551_7   3600 CAGAAGAATAAAACTAGTCCTCTATCTTTCACCCTACACAAAAACTAGAT 3649
                           i      i  ii i v  i   i  iv    v  i       i  iv 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_75285551_7   3650 CAAAATGAATCAAAGACTTCAGTCTAACACTTCAGTTTATAAAACTACTT 3699
                                i    ?    i v i v   v vi v ivi         -   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTT 536

  chrX_75285551_7   3700 C-AAGAAAATGTTCAGGA--AAATCTCCAGAACATTACTCTGGGCAAAGA 3746
                         v-       ii --   ?--      i ivi  v  ivvi i     v i
  L1M4_orf2#LINE/    537 AGAAGAAAACAT--AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_75285551_7   3747 TTTGTCAAGCAATG-CACCACAAGCACAGGCACGCAAAGCAAACATCAAC 3795
                            v i iii -  -     v       i   vvv    v   v  vi i
  L1M4_orf2#LINE/    585 TTTCTTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_75285551_7   3796 AAATTGGATCACATCATG-TTAAAGAGCTTCTGCAAAGCAAATGATACAA 3844
                                 iiv     vi-     i -   i  iivvv    v  i  v 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA 682

  chrX_75285551_7   3845 TCAACAAAGTGAAGAGACAGTTCACAGAATGGAAGAAAATATTTGCAAAC 3894
                             v        i     iii          i                i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_75285551_7   3895 TACCCATATAACAAGGGATTAATAATCAGAATATGCATGGAGCTCAAACA 3944
                         i ivi  v i i      i vi  vi        ii vi  i   vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_75285551_7   3945 ACTCTATAGGGAAAAATTTAATAATTCAATCAAAAAGTGCACAAAG-ATT 3993
                             v   ivi    iviv     ii    i?    i  vi     -   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_75285551_7   3994 GGTATACACATTTCTCAAAAGAAAATATAGAAATGAC-AACAGGCATATG 4042
                         v v   v         v      i     v     i -  i i   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_75285551_7   4043 AAAAGGTGCTCAACACCATTCACGAT 4068
                              i         i  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (149 / 90)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.06 (37 / 18)  

 499 26.56 0.00 0.00  chrX_75285551_75290109.rev     4431  4558 (1)  C L1M4_orf2#LINE/L1   (431)   477   350  

C chrX_75285551_7   4558 TGATCTTTGAGAACTCTGACAAAAACAAGCAATGCAGAAAGCATTCCCTA 4509
                             i  i  v  vvv  v   i v  vv     vi     v  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

C chrX_75285551_7   4508 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 4459
                           i  i              v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chrX_75285551_7   4458 ACTGGACCACTTCCTTACACCTTACACA 4431
                         ii      v  v   i     v  i   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACA 477

Transitions / transversions = 0.74 (14 / 19)
Gap_init rate = 0.00 (0 / 128), avg. gap size = 0.00 (0 / 0)  


1965 24.68 19.61 1.69  chrX_75290597_75304075.rev     6162  6931 (6548)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75290597_7   6162 TGGAAAAATATTCCATGCTCATGGATAGTAAAAATTAATATCATGAAAAT 6211
                               i    i     i        v v  i v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75290597_7   6212 GGCCTTCCTGCGCATAGTAATTTACAGATTCAATGCTATCCTCATCAAGC 6261
                            vv v  v v  v v i  i           i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75290597_7   6262 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTC 6308
                          v   -   v    i  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_75290597_7   6309 ATATGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATTCTGGGCAACAA 6358
                                 viiv  ii  v  v v        i     ii  iiv  v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75290597_7   6359 GAACAAAGCTGGAGGTATCACGCTACCTGACTTCAAACTATACTACAAGG 6408
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75290597_7   6409 CTATATTAACCAAAACAGCATGGTACTGGTACAAAAACAGATATTCAGAT 6458
                            i v   i   i    ii         i i  ii i   i  vi    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75290597_7   6459 CAATGGAACAGAATGGAG-GTCTCAAAAATAACACCACACAGCTACAACC 6507
                                 i     v   -   -  i      vv   i   vi  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTC 346

  chrX_75290597_7   6508 ATCTGATCTTTGACAAAACTGACACACACAAGCACTGGGGAAAAGATTCC 6557
                          vi    i  i     iiv  v  vivv  vv  v        ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75290597_7   6558 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAGGCAGAAAACT 6607
                           v  i  i        i     v      v  ?   i v   i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75290597_7   6608 GAAACAGGACCCCTTCCTTACACCTT-T-------TCAACTCAAGATGGA 6649
                            iiv        v   i     v - ------- i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75290597_7   6650 TCAAATACTTAAACGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAAC 6699
                            ? v  i    i      v   ii  i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75290597_7   6700 ---------------------------CTGGGCAAT-------------- 6708
                         ---------------------------i i      --------------
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75290597_7   6709 -AC----------------------------------------------- 6710
                         -  -----------------------------------------------
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75290597_7   6711 --------------------------------------------GTGAAC 6716
                         --------------------------------------------     v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_75290597_7   6717 AGCCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 6766
                           v     i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_75290597_7   6767 TAGGCTAAGATCAAGAATCTACAAAGAACTTAAACAAATTTAAAAGAAAA 6816
                         vi i  viv   v     v  i        ivv    v i-------  v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC-------AAT 789

  chrX_75290597_7   6817 AACAAACAAACAAACAACCCCATCAAAAAATGGGCAAAGGATATCAACAG 6866
                           i   v i     i     v  i?                 v v  i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_75290597_7   6867 AC---TCTTCAAAGAGAAGACATTTATGCAGCCAGCAG--ACCTGAAAA- 6910
                           ---   i      --   i  vi viii    ii i--  v      -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGA--AGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_75290597_7   6911 ATGCTCATCATCACTGGTTAT 6931
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (108 / 79)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 9.65 (164 / 17)  

3128 27.89 0.55 0.44  chrX_75290597_75304075.rev     7702  8608 (4871)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_75290597_7   8608 TGGAAGAACATTCCATGCTCATGGGTAGGTCGAATCAATCTTGTGAAAAT 8559
                              ii i  i     i      i v  vv  v i   v    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_75290597_7   8558 GGCCATACTTCCGAAGGCAATTTACAGATTGAATGCCATCCTCATGAAGC 8509
                            v     i  v  ivii  i        v  i  v    ii  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_75290597_7   8508 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 8461
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_75290597_7   8460 TATGGAACCAAAAAGAGCCCACA-TCACCAAGTCAATCCTACGCCAATAG 8412
                                viiv  i ii    v - vi    iv     i ivivv iv  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_75290597_7   8411 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 8362
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_75290597_7   8361 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 8312
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_75290597_7   8311 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTACGTATCTACAACT 8264
                                i    i--    i  --        vv i iii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chrX_75290597_7   8263 ATCTGATCTTTTACAAACCTGAGAAAAACAAGCAATGGGAAAAGGATTCC 8214
                          vi    i  iv    ivv  vv  i v  vv       i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_75290597_7   8213 CTATTTAATAAATGGTGCTGGGAAAACTGGCTGGCCATATGTAGAAAGCT 8164
                           v  i  i              v      v i?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_75290597_7   8163 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATCAATTCAAGATGGA 8114
                            ii    i    v   i   i v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_75290597_7   8113 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 8064
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_75290597_7   8063 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 8014
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_75290597_7   8013 AACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGGATCTAA 7964
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_75290597_7   7963 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 7914
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_75290597_7   7913 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 7864
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chrX_75290597_7   7863 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 7814
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chrX_75290597_7   7813 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 7764
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chrX_75290597_7   7763 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 7714
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chrX_75290597_7   7713 ATCACTGGCCAT 7702
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3101 27.64 0.77 0.77  chrX_75314327_75320709.rev     1218  2125 (4258)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75314327_7   1218 TGGAAGAACATTCCGTGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1267
                              ii i  i  i  i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75314327_7   1268 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 1317
                          i v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75314327_7   1318 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1365
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75314327_7   1366 TATGGAACCAAAAAGGAGCTCACATTGCCAAGTCAATCTTAAGCCAAAAG 1415
                                viiv  i   v iviv  v     iv       i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75314327_7   1416 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1465
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75314327_7   1466 TACAGTAACCAAAACAGCATGCTACTGGTACCAAAACAGAGATATAGACC 1515
                                 i   i    ii  v      i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75314327_7   1516 AATGGAACAGAAC--AGAGCCCTCAGAAATTGTGTCACATATCTACAACT 1563
                                i    i--    i  --      vivvi  i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75314327_7   1564 ATCTGATCTTCGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGAT--T 1611
                          vi    i        ivv  vv  i v  vvv           i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75314327_7   1612 CCTTATTTAATAAATGGTGTTGATAAAACTGGCTAGCCAGATGCAGAAAG 1661
                          i  -- i  i        i  iv v      v  ?   v     i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_75314327_7   1662 CTGAAACTGGGTCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 1711
                         v    ii   ii    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_75314327_7   1712 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAGCCCTGAAAGAAA 1761
                            i ?    i       v   v       i      vi i ii      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_75314327_7   1762 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 1810
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_75314327_7   1811 TAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATC 1860
                           vi            vvi           v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_75314327_7   1861 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 1910
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_75314327_7   1911 AACAGGCAACATACAGAACGGGAGAAAATTTTTGCAATCTACTCATCTTT 1960
                           v  i    vi      i          v       vii ivi    vv
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_75314327_7   1961 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAGCAAATTTACAAGA 2010
                         i  i  i  vi          v  i  v      vvi   v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_75314327_7   2011 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 2060
                             i     i     v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_75314327_7   2061 TTCTCAAAAGAAGATATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 2110
                              v           vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_75314327_7   2111 ATTACCACTGGCCAT 2125
                          vi i  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  

2786 27.25 1.43 1.65  chrX_75314327_75320709.rev     4983  5892 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75314327_7   4983 TGGAAACACATTCCATGCTCATGGACCATTAGAATCAATATTGTAAAAAT 5032
                               v i  i     i       iiivv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75314327_7   5033 GACCATACTTCTGAAAGCAATCTACAGATTCAATTCAATCCCCATCAAAG 5082
                          i v     i iv   vii              iv       i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75314327_7   5083 TAACACCATCATTCTTCACAGA----GACAAA--GA--ATACAATTCATA 5124
                          vv  v vv v  i  ii    ----     i--  --v  v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75314327_7   5125 TGGAATAAAAGAAAAAGAGCCTGCAAAGCCAAAGCAAGGTTAAGCAAAAA 5174
                              --- v v  ii  v  v v v       i   vv  i iv  i  
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75314327_7   5175 GAACAAAACCGGAGGCATCACACTACCTGGTTTCAAACTATACTCTAAGG 5224
                                iii     vv       v  iii       viv    vi  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75314327_7   5225 CCATAGTCACCAAAACAGAGTGGCACAGGTATAAAAATAGGCACTTAGAC 5274
                          i i   v i   i    v    i  v  i    ii    i  iv    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75314327_7   5275 CAATGGAACAGAATAGAGAACCCAGAAATAAGCCCAAATACTTACAGCTA 5324
                                 i     v    ii          i    v i i   ii ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_75314327_7   5325 ACTGATCTTTGACAAAGCAAACAAAAACAAAAAGTGGGGAAAGGACACCC 5374
                          i    i  i     i vviv   i v  vvv i         i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_75314327_7   5375 TTTTCAACTAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGTATG 5424
                                 v             i  i   v  ?       i ii  v   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_75314327_7   5425 AAACTGGACCCTCATCTCTCACCTTATACAAAAATCAACACAGGACGGAT 5474
                           ii       ii i   v    v           i   v  ii i    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_75314327_7   5475 TAGAGACTTAAACGTAAGAGCTGAAACTATAAAAATTCTAGAAAATATCA 5524
                         i ?    i    i         i           v ii     i v v  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_75314327_7   5525 CTGGAAAAACCCTTCTAGACATTGGCTTAGCCAAGGATTTTGTGACCAAA 5574
                         iv  ?iv  vi    vv   v    v    v   v i   iv iivi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_75314327_7   5575 ATCCCCAAATCAAATTCAATAAAAACAAAGATAAATAGCTGGGACCCAAT 5624
                          iv  v   v  v vv   i    iv   i   i   iv v    iiv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_75314327_7   5625 TAGACTAAAGAGCTTTTGTATGGCGAAAGGA-ACAGTCAGCAAAGTAAAC 5673
                         i i v v  i i       iivv -      -  vi   iv     i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTC-AAAGGACACTATCAAGAAAGTGAAA 696

  chrX_75314327_7   5674 AGAAAACCGGCAAAGTGGGAGAAAATCTTCACAATCTATACAATCTATAC 5723
                            v    vi  i i           v  ii   --------   -   i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAA--------ATC-ATAT 737

  chrX_75314327_7   5724 AATCTGACAAAGGACTAATATTCAGAATCTACAACAAACTC----AAACC 5769
                          -     i  i     vi   i      v  i  vi     ----  vi 
  L1M4_orf2#LINE/    738 A-TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_75314327_7   5770 AATCAAAAAAAAAATGAACAATCTCATTAAAAAGTGGGCTAAGTACACAA 5819
                            -  v     i ii  i  i iv   ?    i     v   v ivii 
  L1M4_orf2#LINE/    787 AAT-AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_75314327_7   5820 ATAGACAATTCTCAAAACAAGATAGAAAAATGTCCACCAAACATATGAAA 5869
                                v     v   v      v v     v   vi  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_75314327_7   5870 AAATGATCAACATCACTAATGAT 5892
                          i   v         ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (140 / 104)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.55 (28 / 11)  


3313 26.76 0.44 0.44  chrX_75326137_75330173.rev     2639  3546 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75326137_7   2639 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2688
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75326137_7   2689 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2738
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75326137_7   2739 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2786
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75326137_7   2787 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 2836
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75326137_7   2837 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2886
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75326137_7   2887 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2936
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75326137_7   2937 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 2984
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75326137_7   2985 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 3034
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75326137_7   3035 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3084
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75326137_7   3085 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 3134
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75326137_7   3135 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3184
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75326137_7   3185 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 3234
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75326137_7   3235 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3284
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75326137_7   3285 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3334
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_75326137_7   3335 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 3384
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_75326137_7   3385 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3434
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_75326137_7   3435 AAACAAACAACCCCATCAAAAAGTGGACGAAGGACATGAACAGACACTTC 3484
                          i     i     v  i?    i   i i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_75326137_7   3485 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 3534
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_75326137_7   3535 ATCACTGGCCAT 3546
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2394 28.55 1.62 0.62  chrX_75331603_75333394      498  1299 (493)    L1M4_orf2#LINE/L1       99   908 (0)  

  chrX_75331603_7    498 AATATCAACTATATTCTTCACATAAATAGAAAAGCT--TCTATAAAATTT 545
                            vi  i  iiv  i  ii  v    v  v     --  i-       i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC-TAAAATTC 147

  chrX_75331603_7    546 TTATGAAATCATTAAAAATCCAGAATTGTCAATGTTATCCTAAGCAAAAA 595
                         v    i  viiiv iii i       v i   viiv   i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75331603_7    596 GAATAAAATGGGAAGAGTCACATTATCTGACTTCAAATTATATTACAGAG 645
                            i   i v   i  v     i vi ii i      viv  i    i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75331603_7    646 CTACAGTAACCAAAATAGCATGATCCTGCCATAAAAACAGACACATATAC 695
                                  i   i i  ii  i v   v     ii i     i   v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75331603_7    696 CAATGCAACAGAATACAGAACTCAGAAACAATTCCATGCATTTTTAGTGA 745
                              v  i     vv   iii      i  vi    i     v i  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_75331603_7    746 CTTCATTTTCAAGAAAGGTGTCAATAGCATACACTGGGGAAAAGACAATC 795
                         v  v      i v  i    i   v v   v  v        ii i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_75331603_7    796 TCTTCAATAAATAGTGCTGGAAAAACTGAATATCTATATGCAGAATGATA 845
                          i     i    i       i v     i   ? i i     i  vi  i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_75331603_7    846 AAACTAGACACCTATGTCTCACCATATACAAAAATCAAATCAAAATGGAT 895
                           ii i   v    iv  v                i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_75331603_7    896 T-------TAAATTTAAGATCTCAAAATGTGAAAAATTAGTATAAGAAAA 938
                         i-------     v     v  v   v i --    i vv  v       
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT--AAAACTCTTAGAAGAAAA 545

  chrX_75331603_7    939 CTTTAGGA--AAAGTTTCCAGGGCAAAGGTAGGGGAAAAATTTCTCAAGC 986
                          v -   ?--   vi   vv iv vvi   vi  v  vii     i iii
  L1M4_orf2#LINE/    546 CAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_75331603_7    987 AACACCCCACAAGCACAGTGAACCAAAACAGGAATTGATAAATAAGATTT 1036
                          vv  v   v       ivv   v   iv ii   v       vi  i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_75331603_7   1037 TACCAAGCTAAATAACTTCTGAACAATGAATGATACAGTCAACAAAATGC 1086
                         i i   iv v  v     i  vi vvii  v  i  vi    v   i  v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75331603_7   1087 AGAGACAACTTA-AGATTGGAGGAAAATATTTTGAAACTACTCATGTGAC 1135
                          i       ii -   v   ii          vv   ii ivi  v   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75331603_7   1136 AAGGAATTAACAACCACAATATATAAGAAGCTCAAACAACTCTATAG-AA 1184
                             i i vii v   v         ii i   vv       v   i-  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75331603_7   1185 AAAATCTAATAATCCAGTTTAGAAAATGGGCAAAAGATTTGAATAGACAT 1234
                            iv v     i   i  ? -            i               
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_75331603_7   1235 TTATCAAAAGAAGACATATAAATGCCAAACAGACACATGAAAAGTTGCTC 1284
                           v  v        i   i     v v  i ii           v     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_75331603_7   1285 AACATCATTGATCAT 1299
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (132 / 94)
Gap_init rate = 0.01 (9 / 810), avg. gap size = 2.00 (18 / 9)  


 469 28.57 1.95 1.95  chrX_75338791_75342058     1539  1692 (1576)    L1M4_orf2#LINE/L1        1   154 (754)  

  chrX_75338791_7   1539 TGGAAAAATGTCCCATACTCATCAATTAGAAGAATAAATATTATTAAAAT 1588
                               i  i      ii    vi   i     v v      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75338791_7   1589 GACCACACTGCCCAAAGCAGTCTATGGATTCAATGCAGTTAATATCAATT 1638
                          i v i   v      viii    ii       i   i ivv      vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75338791_7   1639 TACTAATGACATTTTT--CACAACTTTAGAATAAAC-AATTCTAAAGTTT 1685
                          v i iivi v     --  v  v  ---i i  i -i  i     i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chrX_75338791_7   1686 ATATGGA 1692
                                
  L1M4_orf2#LINE/    148 ATATGGA 154

Transitions / transversions = 1.93 (29 / 15)
Gap_init rate = 0.02 (3 / 154), avg. gap size = 2.00 (6 / 3)  

2036 29.10 2.65 0.93  chrX_75338791_75342058     2020  2775 (493)    L1M4_orf2#LINE/L1      140   908 (0)  

  chrX_75338791_7   2020 TAAAGTTTATATGGGATCAAAAAAGAGTACAAATAGCCAAAGCAATCCTA 2069
                             i  i      i viiv  ii  vivvi          i     i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_75338791_7   2070 AGCAAAACACACAAAGCTAGAGCCATTACATAGCCTGACATCAAATCATA 2119
                          iv  i viv      i i   vvv i   ivv  ii iv     v v  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_75338791_7   2120 CTACAAGGTTATAGTAACTAAAACGGCATTGTACTAGTACCAAAATAGAC 2169
                               i i  i     ii  i  i ii v     i i iv ii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_75338791_7   2170 ACACAGATCAATGGAACGGAATAGAAAATCCCGAAATAAAGCCACACACC 2219
                          i i            ii    v  i i   v        v   i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_75338791_7   2220 TATGACCAACTGACCTTCAACAAAACCAGCATAAATAAGCAATAAAGAAA 2269
                             ii   i   ii   i    iiviiv  vi vi vv    iii    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_75338791_7   2270 GAACTCCTTTTTCAATAATTGGTGCTGAATAAATTGGCCAGCCATATGCA 2319
                            ivvii       i  v        iivv  i   vi ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_75338791_7   2320 GAAGAATAAATCTGGACCTTCACCTATCATGATATACAAAAATTAACTCA 2369
                         i      i  vi      iii    vv  iv                   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_75338791_7   2370 AAATGGATTAAAGACCTAAATGTAAAGCCTGAAACTATAAAAATTCCAGA 2419
                                 i ?              iiv  i           v iii   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_75338791_7   2420 AGAAAATCAAGGAGAAACTCTTC-TGGTCATTGATTTAGGAAAATAATTT 2468
                               ivv   ? v  v     -  ii -   iv     v  - ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAA-TGGTTT 587

  chrX_75338791_7   2469 AT-AAATAAGACCTCAAAAGTGAATACAAAATAAAAACCCAAAATAGACA 2517
                         v - i   v   vi      iiv vi   v v  i  ---        i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA---AAAATAGATA 634

  chrX_75338791_7   2518 AAAGGGACCAAACTAAACTAAGAAGGTTCTGCACAGCAATAGAAATATTC 2567
                           vv    ivv ii   v v i  iv  i  ii vv   vi  v ivv  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_75338791_7   2568 AACAGAGTAAACAGACAACCTACAAAGTGGGAGAAAATATTTGCAAATTA 2617
                           v i   i  v        i   i i                     i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_75338791_7   2618 -ATCCTCTGACAAAA-------AT----AATCTTCAAGGAACTCAAACAA 2655
                         -  v-     i  ii-------  ----   v vi  i      vv    
  L1M4_orf2#LINE/    735 TATA-TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_75338791_7   2656 CTCAACAAGAAAAA-ACAAACAACTTCATTAAAAAGTGGACAAAGAACAA 2704
                              i  v     -     i   iiv   ?    i   i     i ivv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_75338791_7   2705 GAATGAGCATTTTTTTAAAAGACGACATACAAGCAGCTAAGAA--ACATG 2752
                             iii     i ii   -  v  i      iii  i  v  --     
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_75338791_7   2753 AAATAATGC---ACATCAGTAATAAT 2775
                            vi    ---      ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (137 / 79)
Gap_init rate = 0.02 (13 / 769), avg. gap size = 2.08 (27 / 13)  


1940 28.82 0.64 0.16  chrX_75361019_75362631.rev      495  1122 (491)    L1M4_orf2#LINE/L1      278   908 (0)  

  chrX_75361019_7    495 ACAAAAACAGACACACTGTCTAATAGAACAGAATATAGAATTCCAAATAA 544
                          i  ii i     i iv vii   i   i     vv   i i vi  vv 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_75361019_7    545 AATCGATACATCTACAGTGAACTCATTTTTGACAAACATGCCAAAAACAT 594
                           i v      i  ii  v  i v     i     ivi      i v   
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_75361019_7    595 ACATAGAAGAAAGGACAGTTTCTTTGGTTAATAGTGCTGGGAAAACTGGA 644
                         v  vv ii     i i   i i  iiiiv   i         v       
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_75361019_7    645 TATCCATAATCAGAGGGAAGAAAGTAGACTCTTATCTCTCACTATATATA 694
                           ?   i vv  i i i v   iv i   i i  i   v   i     i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_75361019_7    695 AAAGCAAAATAAAAATGGATTAAACTCTTACATTAAAGACCTCAAACTAT 744
                            iiv  v v         i ? vv i  v  vv    v  v       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_75361019_7    745 GAAACTATTGAAAGAAGACGTTGGAGAAACTCTCCAGGAAATTAGACTGG 794
                         i     v  ii     i  i v  ? v  v   i iv  vv  i ii i 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_75361019_7    795 GCTAAAATTTTCTGAGTAATACCCCACAAACACAGCCAACCAAAGCAAAA 844
                           v vii   ii iii  vv  v   v  i    iv    v    v    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_75361019_7    845 ATGGACAAATGGGATACCATCAA-GTTAAAAATCTTCTGCACAGCAAAAG 893
                           i  i    v   ivi      -i       -   i  ii vv    i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGG 676

  chrX_75361019_7    894 AAATAATCAAAAAAGTGAAGAACAAACCCACAGAATAGGAGAAAACGTTG 943
                          v iv     i        i ivv            i        ii  v
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_75361019_7    944 GCAAATTATCCATCTGAAAAGGCATTAATAACCAGAATATATAAGGAACT 993
                               i  vi      v    v i vi  v             i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_75361019_7    994 CAAAC-ACTCAATA-TGAAAGAATTTATTTCTCTAATTAAAAATGGGCAA 1041
                          vv  -        - i   ii ivv  vv i v v ?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_75361019_7   1042 AAAATCTGAATAGACATTTCTC-AAAGAAAACATACAAATGGCAAACAGG 1090
                          ii  i                -      i i           v  i i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_75361019_7   1091 TATACCAAAAGGTGCTCAACATCACTAATCAT 1122
                         i i iv     i            ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (105 / 72)
Gap_init rate = 0.01 (5 / 631), avg. gap size = 1.00 (5 / 5)  


3335 25.88 0.66 0.66  chrX_75376897_75382179.rev     3885  4792 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75376897_7   3885 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATCTTGTGAAAAT 3934
                              ii i  i     i      i v      v i   v    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75376897_7   3935 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3984
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75376897_7   3985 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4032
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75376897_7   4033 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4082
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75376897_7   4083 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4132
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75376897_7   4133 TACAGTAACCAAAACAGCATGGTACTGGTACCAGAACAGAGATATAGATC 4182
                                 i   i    ii         i iv  i i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75376897_7   4183 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 4230
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75376897_7   4231 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGCATTCC 4280
                          vi    i  i     ivv  v   i v  vv            v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75376897_7   4281 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4330
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75376897_7   4331 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4380
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75376897_7   4381 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4430
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75376897_7   4431 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4480
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75376897_7   4481 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4530
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75376897_7   4531 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4580
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_75376897_7   4581 AGGCAACCTACAAAATGGGAGAA--TATTTTCACAGCCTACTCATCTGAC 4628
                           i     i   i          --     v  v v v  i--      i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGAT 744

  chrX_75376897_7   4629 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 4678
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75376897_7   4679 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 4728
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75376897_7   4729 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAGTGCTCA 4778
                             v        i  vi viii     v  i          ii      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75376897_7   4779 TCATCACTGGCCAT 4792
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (133 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2743 28.41 1.44 0.67  chrX_75382569_75388686     4725  5625 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75382569_7   4725 TAGAAAAATATTCCATGCTCATGGATAGTAAAAATTAATATCATGAAAAT 4774
                          i    i    i     i        v v  i v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75382569_7   4775 GGCCTTCCTGCCCAAAGTAATTTATAGATTCACTGCTATTCCCATCAATC 4824
                            vv v  v      v i  i  i       vi  v  i  i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75382569_7   4825 TACCA-CTGACTTTCTTAAAAGAATTAGATAAAACT-ACTTTAAATTTCA 4872
                          v   -   v    i  iv ii    -  i  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAG-CTGATCCTAAAATTCA 148

  chrX_75382569_7   4873 TATGGAACCAAAAAAGAGCCCGTAGAGCCAAGAAAATCCTAAGCAAAAA- 4921
                                viiv  ii  v  v v v      i v    i i iv  i  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75382569_7   4922 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAAGTATACTGCAAGGC 4971
                                i      vv   ii  v  ii i      iiv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75382569_7   4972 TACAGTAACCAAAACAGTATAGTACTAGTACCAAAAGTGATATATAGACT 5021
                                 i   i     i i     i i iv ii vv  i       ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75382569_7   5022 AATAGAACAGAACAGAGGCCTCAGAAATAGTGCCACACATGTACAACCAT 5071
                            i   i    iv   ivii        ivv   i    v  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_75382569_7   5072 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGATT--CCT 5119
                         i    i  i     ivv  v   i v  vv             v --i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_75382569_7   5120 TATTTAATAAACGGTGTAGGGAAAACTGGCTAGCCTTATGTGAAAAAATG 5169
                          -  i  i   i    iv    v      v  ?  vi   ii   i    
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_75382569_7   5170 AAACTGGGCCTATTCTTTACAATTTATA-AAAAAGTAACTCAAGACGAAT 5218
                           ii   i  iv v i i   viv    -     v        i i i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_75382569_7   5219 TAAAGACTTAAATGTAAGGCCTAAAACCATAAAAGCTCT-AGAAGAAATC 5267
                         i ?    i          iv       i      -    -        v 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chrX_75382569_7   5268 TTAGGCA-ATACCATTCAGGACATAGGAATGGGCAAAGACTTCATGACTA 5316
                         v    ?i- v i -   iv   v v  iv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_75382569_7   5317 AAACATCAAAAGTAATGGCAACAAAAGCCAAAATTGACAAATGGGA-TCG 5365
                         vi   i      i vvi          vv     v  i    v   - iv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75382569_7   5366 ATTTAAACTAAAGAGCTTCTGCACAGCAAGAGAAACTATCATCAGAATGA 5415
                           iv   i    i -   i  ii vv   ii  v       vv i i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75382569_7   5416 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATTTATCCACCTGAC 5465
                          v  i     i                 v       v i  vi i    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75382569_7   5466 AAAGGGCTAAGATCCAGAATCTAAGACAAAATTAAACAAATTTACAAGAA 5515
                           i  i  viv         v  vi vi  v ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75382569_7   5516 AAAAACAA----CCCCATCAAAAAGTGAGAGAAGGATATGACCAGACATA 5561
                            i    ----   v  i?    i  i vi      v   vi      v
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75382569_7   5562 TCTCAAAAGAAGACATTTATGCTGCCAACAAACATATGAAAAAAAGCTCA 5611
                             v        i  vi viiv     i  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75382569_7   5612 TCATCACTGGTCAT 5625
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (147 / 105)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.27 (19 / 15)  


2930 27.73 1.67 0.56  chrX_75391593_75400186.rev     3868  4765 (3829)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75391593_7   3868 TGGAAGACCATTCCATGCTCTTGGGTAAGAAGAAATCAATATCATGAAAA 3917
                              iivi  i     i  v   i vi     v- i     ii v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chrX_75391593_7   3918 TGGCCATACTGATCAAGGTAATTTGTAGATTCAGTGCCATCCCCATCAAG 3967
                             v     vvi   iv i  i ii       ii  v     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_75391593_7   3968 CTACCAATTACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCAT 4012
                         v v   ii i i  i  ii     v v  v  i--- --     i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_75391593_7   4013 ATGGAACCATAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 4062
                               viii  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75391593_7   4063 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCTATACTACAGGGCT 4112
                               i      vv    i  v  ii i     iviv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_75391593_7   4113 GCAGTAACCAAAACAACATGGTACTGGAACCAAAACAGAGATATAGACCA 4162
                         i      i   i   iii         v iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_75391593_7   4163 ATGGAACAGGA--AAGAGCCCTCAGAAATAATGCTGCATATCTACAACCA 4210
                               i  i --i    i  --        vv iii i  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_75391593_7   4211 TCTGACTTT-GACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 4259
                         vi   i   -     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_75391593_7   4260 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4309
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_75391593_7   4310 AAACTGGATCCCTTCCTTACACCTTATA-AAAAATGAATTCAAGACGGAT 4358
                           ii    i    v   i     v    -      v  i    i i    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_75391593_7   4359 TAAAGACTTAAATGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4408
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_75391593_7   4409 TAAGCA-ATACCATTCAGGACATAGGCATGGGAAAGGACTTCATGTCTAA 4457
                           i ?i- v i -   iv   v v  vv i  v  v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75391593_7   4458 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAGTGGGATCTAA 4507
                         i            vvi          vv     v     i v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75391593_7   4508 TCAAACTAAAGAGCTTCTGCACAGCAAAAGCAACTACCATCAGAGTGAAC 4557
                              v v  i i   i  ii vv    i vv    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_75391593_7   4558 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTCCT-CATCTGAGA 4606
                           i     i                 v       -v  v -i      v 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATA 745

  chrX_75391593_7   4607 AAGGGCTAATATCCAGAATCTACAATGAACTGAAACAAATTTACAAGAAA 4656
                          i  i  vi          v  i  v     vvv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_75391593_7   4657 GAAACAA----CCCTATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 4702
                         i i    ----   v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_75391593_7   4703 CTCAAAAGAAGACATTTATGCAGCCAAAGGACACATGAAAAACTGCTCAT 4752
                            v        i  vi viii     viii          iv      v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_75391593_7   4753 CATCACTGGCCGT 4765
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  

2554 27.73 3.49 1.13  chrX_75391593_75400186.rev     7224  8110 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75391593_7   7224 TGAAAACACATTCCATGCTCATGGATGAGTAGAGTCAATATTGTGAAAAT 7273
                           i   v i  i     i        vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75391593_7   7274 GACCATACTGTCAAAAACAATCTACAAATTCAATACAACTCTCACCTAAT 7323
                          i v     vi v   vii       i      ii   ii ii i v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75391593_7   7324 TACCAACATCGTTCTTCACGGAAGTAGAAGAAACAATCCTAAAATTCATA 7373
                          v   i vv v  i  ii i   i v  vi ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75391593_7   7374 TGGAACCATAAAGAGCCT-GAAAAGCCAAAGTAA----GACGAAGCCAAA 7418
                              viii  i ii  i-   v       ii  ----  vi   ---  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG---AA 197

  chrX_75391593_7   7419 GAAACAAATTTGGAGGCATCACATTACCTGACTTCAAACAATACTATAAG 7468
                            -    v       vv     i v  ii i      vvv     i  i
  L1M4_orf2#LINE/    198 GAA-CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_75391593_7   7469 GCTATAGTCACCAAAACAGCACAGTACTGGTATAAAAATAGGCATGTAGA 7518
                             i   v i   i    iiii       i    ii    i   i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_75391593_7   7519 CCAATGGAACTAAATAGAGAACTCAAAAATGAAGGCAAA----TACAGCC 7564
                         i        ivi   v    iii  i    i  vv  v ----  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_75391593_7   7565 AACTGATCTCTGACAAAGCAAGCAAAAATCATAAAGTGGGAAAAGGACA- 7613
                           i    i ii     i -iv  v  i i   vv i    i    i i -
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_75391593_7   7614 CCCTTTCAACAAATGATGCTAGGATAATAGGCAAGCCATATGTACAAGAA 7663
                         i i            i    i   i  iv  vv ?   i   i v     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_75391593_7   7664 TGAAACTGGATCCTCATCTATCACCTTATACAACAGTCAATGCAAGATGG 7713
                             ii    i  ii i  vv    v       v i i  iv   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_75391593_7   7714 ATCAAATACTTAAATCTAACACCTGAAACCATAAGAATTCTAGAAGATAA 7763
                             ? v  i     v   v v  i    i    i v ii       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_75391593_7   7764 GATAGG---AAATATCCTTCTAGACATTGACTTAGGCAAAAACTTTATGA 7810
                         v     ---    ---    vv   v   iv        viii  iv ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_75391593_7   7811 CCAAGAATCCAAAAGTAAATGCAACAAAAACAAAATTAAATAGATGAGGC 7860
                         vi v  vv       i v v         iv    v  i   i  vi i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_75391593_7   7861 ATAATTAAACT--AAAATTTT----CTGCACAGAAAATAATCA-----GT 7899
                         v v  i   v --    i   ----  v  v  i v iv    -----  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_75391593_7   7900 AAACAGACAATCCACAGAGTGGGAGGAAATCTTTGCAAACTCA-GTATCC 7948
                         i  v      i       i      i    v        -   -i    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCT 741

  chrX_75391593_7   7949 AACAAAAAAACTAATATCCAAAATCTACAAGGAACTCAAACAAATCAGCA 7998
                         i i  iii -  vi      i   v  i  i      vv    v   ii 
  L1M4_orf2#LINE/    742 GATAAGGGA-CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_75391593_7   7999 AGAAAAA---AAAT--TTCA-TCAAAAAGTGAGCAAAGGACATGAATAGA 8042
                          v     ---    --ii  - i?    i  i        iv        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_75391593_7   8043 CAATTCTCAATAAAAGATATAGAAATGGTCAGCAAACATATGAAAAAATG 8092
                           v     v v i        v      i  ii  i  i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_75391593_7   8093 CTCTACACCACCAATGAT 8110
                            v   i  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (153 / 90)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.28 (41 / 18)  


2987 28.48 0.77 0.55  chrX_75419084_75423744     3263  4168 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75419084_7   3263 TGGAAGAATATTCCATGCTCATGTGTAGAAAGAGTCAATATCGTGAAAAT 3312
                              ii    i     i     vi v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75419084_7   3313 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCACCATCAAGC 3362
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75419084_7   3363 TACAAATTACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGCTCA 3410
                          v v ii i i  i  ii     -   -- v  i  - iii    ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75419084_7   3411 TATGGAACCAAAAAAGAGCTCACATTGCCAAGTCAATCCTAAGCCAAAAG 3460
                                viiv  ii  v iviv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75419084_7   3461 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCTATACTACAAGAC 3510
                                i      vv    i  v  ii i     iviv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75419084_7   3511 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGGTACAGACC 3560
                                 i   i    ii         i iv ii i   vi  i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75419084_7   3561 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 3608
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75419084_7   3609 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGTGGAAAGGATTCC 3658
                          vi    i  i     ivv  v   i v  vvv    v      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75419084_7   3659 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 3708
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75419084_7   3709 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCTAGATGGA 3758
                            ii    i    v   i     v  i           i  v i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75419084_7   3759 TTAAAGACTTAAATATTAGACCTACAACCATAAAAACCTTAGAAGAAAAC 3808
                          i ?    i     i v   v   v   i      vi             
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75419084_7   3809 CTAGGCA-ATACCATTCAGGACATAGGCATGGGTAAGAACTTCATGTCTA 3857
                         v    ?i- v i -   iv   v v  vv i  i  viii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_75419084_7   3858 AAACACCAAAAGCAGTAGCAACAAAAGCCAAAATTTACAAATGGGATCTA 3907
                         vi            vv           vv     vv i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75419084_7   3908 AATAAACTAAAGAGCTTCTGCACTGCAAAAGAAATTACCATCAGAGTGAA 3957
                          vi   v v  i i   i  ii  v    i  v i  i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75419084_7   3958 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 4007
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75419084_7   4008 AAGGGCTAACATCCAGAATCTGCAATGAACTCAAACACATTTACAAGAAA 4057
                          i  i  vii         v ii  v      vv   vv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_75419084_7   4058 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 4107
                           i     i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_75419084_7   4108 CTCAAAAGAAGACATTTATGCAGTCAA-AAG-ACATGAAAAAATGTTCAT 4155
                            v        i  vi viii i   -   -         i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_75419084_7   4156 CATCACTGGCCAT 4168
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (154 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2815 26.31 1.86 3.49  chrX_75440311_75445023.rev     3307  4222 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_75440311_7   3307 ACACCCCATGCTCATAAATCAGAAGAATTGATATTGTTAAGATTACCATA 3356
                          i i      i    ii  ii     v  i             vi v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_75440311_7   3357 CTACCTAAAGGAATGTACAGATTTAATGCAATCCCTATCAAAATACCAGT 3406
                           v  i   vvi  v        i  i                 v    i
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_75440311_7   3407 GACATTTCTTACAAATATAGAAAAAA-AATCCTAAAATTTGTATGGAACC 3455
                         vi v   i  i  i v  v  v  iv-i           ii       vi
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_75440311_7   3456 AAGAAAGAGCCTGAATAACCAAAGCAACCCTGAACAA----AGCAAAGCT 3501
                         ivi ii  v  v     i     i   i i    v  ---- i     i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_75440311_7   3502 GAAGGCATCACACTACCTGACTTCAAAA-----TATAAGTCTATAGTAAC 3546
                          i   vv       v  ii i       -----  i  iv   i     i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_75440311_7   3547 CAAATCAGCATGGTATTAGGATTAAAGCAGACACATAGACCAATGAAAGA 3596
                            iv   ii     i i v  v iiii     i     i     i  v 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_75440311_7   3597 GTATACGTAACCCAAAAATAATTCCATGTGTTTATAGACAACTGATTTTT 3646
                          v  vviv ii   i      vi    iii     i v   i       i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_75440311_7   3647 GACAAAGGCACCAAGAATATACTTTAAGAGGAGTACCCAATACTTCCCCC 3696
                              i  ii      vi  ----------------i    ---------
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCAT----------------TCAAT--------- 382

  chrX_75440311_7   3697 TTGGGAAGAGGGAAGTATACCCTCTTCAATAAGCCGTTCTGGAAAAATAG 3746
                         ------- i  i   v   vi  i     i  iiv  v    i v  iv 
  L1M4_orf2#LINE/    383 -------GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_75440311_7   3747 GATATTCATATGCAGAAGAATGAAA--GGACCCTGATCTCTTACCTTATA 3794
                             ?i  i     i         i--      iv i   vi   v    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_75440311_7   3795 -AAAAATTAACTCAATATGAATTGAAGACTTAAATGTAAGATTCAAAACT 3843
                         -              v   i  ii?    i           vii      
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_75440311_7   3844 ATAAAACTATTATAAGAAAATATAGGAGAAACCCACTAGGATATTGTTCT 3893
                                 v   v       i     ? v  vi viiiv  iv   vvi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_75440311_7   3894 ATGCAAAGAGTTGATGGCTAAGACCCCAAAAGCACAGATAACCAAATAAA 3943
                          v    v iv  vv i v  v   v           iii   v   v   
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_75440311_7   3944 AAATAGACAACTGGAAAAATATTAAGCTAAAAATCTTCTGCACAGCAAAG 3993
                                i  v v i vvvi  i  iv v    v   i  ii vv     
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_75440311_7   3994 GAAACAATCAGCAAAGTGAAGAAATAACCTGCTGAATAGGAGAACATATT 4043
                           v  v    iv        i i i    ii v    i      v     
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_75440311_7   4044 TCCAAAATATTCATCTGACAAGGGACTAATGTCCAGAATATACAAGGAAT 4093
                          v    vi  vi      i        vi i           i  i   i
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_75440311_7   4094 TCAAACAACTCAAAAATCAAAA-ACAATCTATCCTATTGGAAAGTGGGCA 4142
                           vv         v   v    -    viv i  v   ?i   i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_75440311_7   4143 AAGGATCTAAATAGACATTATTT--AAACATACATGCAAATAGCCAAACA 4190
                               i i          vi i--  iv v i  i     i     vv 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_75440311_7   4191 GTATGTAAAAA-ATGCTCAACATCACTAATCAT 4222
                          i ii i    -             ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (10 / 901), avg. gap size = 4.90 (49 / 10)  


 219 18.39 0.00 11.49  chrX_75446171_75450398.rev        1    87 (4141)    L1M4_orf2#LINE/L1      759   835 (73)  

  chrX_75446171_7      1 CAAAATACATAGAAAATTCAAATAACTCAGTAGTTAAAAAAAAAAAAAAA 50
                           i    i   i i  i  vv i      i  i ---------     i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAAT---------AAAAAGA 799

  chrX_75446171_7     51 GAAATAACCAAATTCTAAAATGGGCAAAGGACCTTGA 87
                         v        v    ?v               i-    
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGA 835

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.03 (2 / 77), avg. gap size = 5.00 (10 / 2)  

 235 26.32 0.00 0.00  chrX_75446171_75450398.rev      433   508 (3720)    L1M4_orf2#LINE/L1      833   908 (0)  

  chrX_75446171_7    433 TGAACAGAAATTTCTTAAAAACAGACATACATTTGGCCAACAGGTATATT 482
                             i   v      iv   iv   i     vv       i i i i  v
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_75446171_7    483 AACAAATATTTAATATCAAATATCAA 508
                           v i  ii i  i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.00 (0 / 0)  

3215 25.59 2.24 0.34  chrX_75446171_75450398.rev     2852  3742 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75446171_7   2852 TAGATGAATATTCCATGTTCATTGATTGGAAGAATTAATATTGTTAAGAT 2901
                          i  vii    i          v          v                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75446171_7   2902 GTCCATACTACCCAAAGCAATCTACAGATACAATGCAATCTCTATCAAAA 2951
                          v v     v      vii          v   i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75446171_7   2952 TACCAATGACATTCCTCACAGAAATGGAAAACACAATTTTAAAAT----- 2996
                          v   iivi v  ii ii       v  v  vvii  ii      -----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75446171_7   2997 ------------AGACGCAGAATAGCCAAAGCTATTCTAAGCAAAATGAA 3034
                         ------------i   v             i v  ii i iv  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_75446171_7   3035 CAAAACTTCAAGAATCACATTACCTGACTT-AAAATTATACTAC-CAGCT 3082
                             ii vv i  v     i v  ii i  -    i -      -v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_75446171_7   3083 ATAATAACCCAAACAAGATGGTACCAGCATAAAAACAGAAACATAGACCA 3132
                          i i   i v i   ivi      ii      ii i   v i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_75446171_7   3133 GTGGAGCAGAATAGAGAACCAACAAACAAATTCATACATCTACAGTGATC 3182
                         i    ii     v    ii v v   i   ii       i  ii  v vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_75446171_7   3183 TCATTTTTGACAAAGGCTTCAAGAACATATACTGAGGAAAATACAGTATC 3232
                          v     i     i  ivi     v   vi v  i     iv i   v i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_75446171_7   3233 TTCAATAAATGGTGCTAGGAAAACTGGATGTCCACATGCAGAAGAAGGAA 3282
                              i          i   v        i?         i     v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_75446171_7   3283 ACTAGACCCTTATTTCTCATCATATACAAAAATCAAACCAAAATGTATTA 3332
                         ii i     i  ii  v  i             i  vi       v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_75446171_7   3333 AAAACTTAAATCTAAGACCTCAAACTATAAAACTACTACAAGAACACATT 3382
                         ? i  i     v     v  v             vi  v     v    v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_75446171_7   3383 GGAGAAAATCTCCATGATATTGGTCTGGGCAAACATTTCTTGAGTAATAT 3432
                           ? v      i i   iv    vi i     vvi      iii  vv i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_75446171_7   3433 CCCCCAAGCACAGGCAACCAAAGCAAAAATGGACAAATGAGATCACACCA 3482
                         v  vv       i     v    v      i  i    vi  iiv  i  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_75446171_7   3483 AA-TTAAAAAGCTTCTGCACAGTAAAGGAAACAATCAGCAAAGTGAACAC 3531
                           -       -   i  ii vvi      v  v    iv        v v
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_75446171_7   3532 ACAACCCAAAGATTGGGAAGAAATATTTGCAAACTACCCAACTGACAAGA 3581
                                 v   v     ii             ii ivi v    i   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_75446171_7   3582 GATTAATAACCTAAATATATAAGGAAATCAAACAACTCTATAGGAAAAAA 3631
                           i vi  v  vi         i   v  vv       v   iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_75446171_7   3632 CCCTAATAATCTGATTAAGAAATGGGCAAAAGATTTGAATAGACATTTCT 3681
                         v v-     i ii   ? i           i                   
  L1M4_orf2#LINE/    799 ACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_75446171_7   3682 CAAAAGAAAACATACAAATGGCAAATAAATATATGTAAAAGTGCTCAAAC 3731
                          v      i i           v     ii i   v   ii       vv
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_75446171_7   3732 TCATGGATCAT 3742
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (133 / 91)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.29 (23 / 7)  


 348 25.00 0.00 0.00  chrX_75451636_75453958.rev        8    91 (2232)    L1M4_orf2#LINE/L1      549   632 (276)  

  chrX_75451636_7      8 AGGAGAAAACCTTCATGAAATTGATCTTGACAAAGATTTCTTGGATTTGA 57
                            ? v   i    i   vv   ivi v i   v i      i   v   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_75451636_7     58 CCCCAAAAGCACGGGCAGCAAAAGCAAAAATAAA 91
                          v          ii   i      v       i 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.00 (0 / 0)  

2697 24.73 2.68 5.46  chrX_75451636_75453958.rev      899  1832 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75451636_7    899 TGAAAATGTAGCCCACATTTAAGAATTTTAAAA---AATTATTGTTAT-- 943
                           i   vi  v    ii  i v i   vv  i ---   -       v--
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT-ATTGTTAAGA 49

  chrX_75451636_7    944 TTTCCACACTATCCAAAGCTG-TCTAAACATTTAATGCAATTTTT-TCAA 991
                          vv v i   vi     -i  -    v v   i  i     iii -    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_75451636_7    992 AATTCTAA-TGTCATTTTTCACAGAAATTTTAAAAAAACT---CCTAGAA 1037
                            i i i-  i -     ii        ---i v  i  ---    i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATT---GACAAGCTGATCCTAAAA 144

  chrX_75451636_7   1038 AT--TATGGAACCACAGAAGACCCAGTATAGCCAAAGAAATCTTTTGTAA 1085
                         v --       vii  iii       v         iv      -- v  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--GAAA 192

  chrX_75451636_7   1086 ATGAAAAAT---GTCAGAAAGCATCACATACTCTGATTTCAAAATATACC 1132
                          v   i  i---  ii  iii -     ivii ii         iv   i
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACT 241

  chrX_75451636_7   1133 ATAAGGTGATTGTAATCAGAGTAGCATAGTACTAATATAAAGACAGACAC 1182
                          i  i iv iv       iiii  ii i     iii    i  i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_75451636_7   1183 ACCAATAAATAAAACAGGATAGAGAGCCAAGAAATAAATCCATGCTTTTA 1232
                          ivi  v   ii  i  i  v     i v         i    i v    
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_75451636_7   1233 TATTCAATTGATCTTTGACACAGATCCCAAAACACA--CAATGAAGAATG 1280
                          iv         i  i    vi i v    i  -  --     ii   v 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAG 390

  chrX_75451636_7   1281 GACAGTCTCTTGAACAAATGGTGCTGGGAAAACCAGATATCCACATA-AA 1329
                         i i     i  v                 v   ii    ?      i-  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_75451636_7   1330 GAGAATGAAATTAGATGCTCATCTCACTCCATATACAAAAATCAACTTAA 1379
                         i        i  i  iv ii i     v              i    i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_75451636_7   1380 ACTAGATTAAGGGATTAA-TATGGAACCTGAAATTGTATAATTAATAGCA 1428
                          v i   i ?i ivi   - i iii v  i   i i  v  i vv   v 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_75451636_7   1429 GAAAACATAAGTGAAAAACTCTTTCACATTGGTCTGGGCAACGATTTCCT 1478
                                  i ? v   v  iiv v  v    vi i     i i    i 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_75451636_7   1479 GGATATGAACCCAAAAACACATGCAAAAGAAAAAAAAAAAAAAACTAAGT 1528
                         i       vv      i    v    v i  i      v i ---   i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA---TAAAT 637

  chrX_75451636_7   1529 GGAATTGCATCAAACTGAAAAGCTTCTG-----CAGAGAAGAGAAACCAA 1573
                         v i i v       v v    i   i  -----  i  ----  v  i -
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG----GACACTA- 682

  chrX_75451636_7   1574 TCAATGGGGTGAAGAGGCAACCCATAGATTGGAAGAATATATGTGCAAAC 1623
                             viii     i  i       i   v   i    v    v      i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_75451636_7   1624 CATACATCTGATATGGAACTAGTATTCAAAATATATAAGGAACTAAACTC 1673
                             i        v  i   v    i  i         i     ---  i
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT---CTT 779

  chrX_75451636_7   1674 AGCAAAAAAGTTTAAATTTTAATTTTAAATTAAATTAATTTTAATTTTAA 1723
                          -   ------------i i   ----   v   vv ----------i  
  L1M4_orf2#LINE/    780 A-CAA------------CTCAAT----AATAAAAAGA----------CAA 802

  chrX_75451636_7   1724 ATTTTAACCCAATTTAAAAATGAGCAAAGGACCTGAATAAACATTTCTCA 1773
                           ---         ?       i        ii      i         v
  L1M4_orf2#LINE/    803 AT---AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_75451636_7   1774 AAAGCAGACCTACAAATGGTCATTAAATATATAAATAAATGCTCAACATC 1823
                             v   iv         i  v   ii i  i  v i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_75451636_7   1824 ACTTAATAC 1832
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.11 (154 / 73)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.71 (76 / 28)  


2349 28.04 3.49 1.24  chrX_75458744_75463473     3361  4248 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75458744_7   3361 TGAAAAAAAATT--ATGCTAATGGATTGAAAGAGTCAATATTCTTAAAA- 3407
                           i   i v  i--   i v        i    v i      v    i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75458744_7   3408 GGCCATACTGCCTAAACCAATCTACATATCTAATGCTATTCTTACCCAAA 3457
                            v     v  i   iii       v  ii  i  v  i i  i v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75458744_7   3458 TACCA-TTGTTGTTCTT-CAAAGATTTAGAAAAATTTATTCTAAAATTTA 3505
                          v   -i  iiv  i  -  i i   --  v  ii v  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_75458744_7   3506 TGTGGAACCAAAAAGGAGACTGGATAACCAAAACAATTCTAAGCAAAAAG 3555
                          i     viiv  i   vv v i   i          ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75458744_7   3556 AACAAACCTTGAGACATTACACTACCCAACTT-ACAACTATACTATAAGG 3604
                               vi v   ivv i     v     i  - v    -     i  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_75458744_7   3605 CTGTGGTAATCAAAACAACGTGGTACTTGCACAGAAACAGACACATAGAC 3654
                           iii        i   ii        v   i iii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75458744_7   3655 CAATGGAAGATAATAGAAAACACAGAAATAAAGCTGTACACCTCCAGCCA 3704
                                 v v   v  i iiv          v ii    ii vii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_75458744_7   3705 TCTAACCATCAAGAAGGCTGACAAAA--A--CAATGGGTGAAGGACT--T 3748
                         vi i iiv  i v    v  v   i -- --       -   i  v -- 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGT 396

  chrX_75458744_7   3749 CCTATTCAATAAACAGTGCTGAGATGACTGC-TATGCTATAGACAGGAGA 3797
                          i -     i   ii      i  ii    v-  -? i i vi  ii   
  L1M4_orf2#LINE/    397 CTT-TTCAACAAATGGTGCTGGGACAACTGGATA-KCCACATGCAAAAGA 444

  chrX_75458744_7   3798 ACGAAACTGGACCCTTACCTTTCAGTATACACAAAA-TTAACTGAAAATT 3846
                          i   ii       i     iv  vi   i      -      v     v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_75458744_7   3847 GATTAAAGATTTCAAGGTAAGACCTCAAACTGCAAACATCCTACAAGACA 3896
                            i ?   ii v  v      v  v     ii   vv  i  v    v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_75458744_7   3897 ACTTGGG---AAATACCATTCTTGACACTGGACTTAGCAAATAGTTT--- 3940
                           v i  ---    -- -   v    vi   i-    vv   i    ---
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT--C-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTT 590

  chrX_75458744_7   3941 --GTAAGTCCCCGAAAGCAATTGCAATGAAACAAAAATT-GACAAGTGGG 3987
                         --i  v v v  i      vvv    ii   v     v -  i  i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_75458744_7   3988 ACCTAATTAAACTAAAAAACATTTGAACATCAAAAGAAACTCTCAACAGA 4037
                           i v  i   v v      v    vi v     i  v   v    v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_75458744_7   4038 GTAAACAGGCAATCTACACAGTACCAGAAACTATTCATAAATTATGTATC 4087
                           i  v  i   i i   v i ivv     v    iii    i  i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_75458744_7   4088 CAACAAAGGTCTATTATCCAGAATCTAGAAAGACCTTAAACAATTAAACA 4137
                         ii i  i  v  vv          v  v     v  ivv    i v  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_75458744_7   4138 ATAAGAAC-CAATTAATCCTAAT--AAAAATGGTCAAAAG----GCATGG 4180
                             i  v-   v   i  -   --        v    i ---- v  i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_75458744_7   4181 ACACTACTCAAAAGAAGTCCTACAAGCATCCAGCAATCATATGAAAAAA- 4229
                            i v   v       viv     iiiv   ii  v  i       i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_75458744_7   4230 GTTCTAAATCACTAATCAT 4248
                          i  v v    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 1.62 (42 / 26)  


2464 27.47 0.42 5.93  chrX_75465176_75469509.rev     2883  3843 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75465176_7   2883 TGGAAACACATCTTATACTCATGGATGGGTAGAATCAACATTTTGAAAAT 2932
                               v i   ii  ii        v  v   v i  i   v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75465176_7   2933 AACCACACTACCAAAAGCAATCTACAAATTCTATGCAATTCTCATCAAAA 2982
                         ii v i   v  v   vii       i    v i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75465176_7   2983 TACCACCATCATTCTTCACAGAACTAGAAAAAAAAATCCTAAAATTCATA 3032
                          v   v vv v  i  ii     v v  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75465176_7   3033 GGAAACCAAAAAAGACCCTTCACGGCCAAAGCAACACTAAGCATAAGGAA 3082
                         v i  viiv  ii     vvv ii      i   ivi i iv vi i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_75465176_7   3083 CAAATCCGGAGGCATCACATTATCTGACTTCAAACTATACTATAAGGCCC 3132
                             vii     vv     i vi ii i      viv     i  i  iv
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_75465176_7   3133 TAGTCACCAAAACAGCATGGGACTGGTATAAAAATAGGCATATATACCAA 3182
                         i   v i   i    ii   v     i    ii    i      v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_75465176_7   3183 TGGAACAGAATTGAGGATTCAGAAGTAAACCAAAATACTTATAGCCAACT 3232
                              i         ii i     i      v v i i    i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_75465176_7   3233 GACCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTAT 3282
                           ii   i    i vviv   i v   vv i         i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_75465176_7   3283 TAAACAAATTGTGCTGAGATAATTGACAAGCCACATATAGAAGAATGAAA 3332
                          v       v      i  i  i  ivv ?      ii i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_75465176_7   3333 CTGGATCCTCATCCCCCACCTTATACAAAAATCAACTCAAGATGGATCAA 3382
                         i    i  ii i i v    v           i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_75465176_7   3383 AGACTTAAATCTAAGACCCAAGACCATAAAGATCCTAGAATATAACATCA 3432
                             i     v     v i  i  i     iv  i     v v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_75465176_7   3433 GAAAAACCCTTCTAGATGTTGGATTTGGCAAAGACTTTATGACCAAGAAC 3482
                          ?iv  vi    vv  iv    i  v     v ii  iv iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_75465176_7   3483 CCGAAAGCA-ATACAATAAAAACAAAGATAAATAGATGGGACTTAATTTA 3531
                           i      - vi   i    iv   i   i   i  v      v  iv 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_75465176_7   3532 ACAAAAAAGCTTCTGCACAACAACAAAAAAAGTAATAATAATCATCATCA 3581
                          vvv    i   i  ii vv   -------  v --------------  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAA-------AGGA--------------CA 679

  chrX_75465176_7   3582 TCATCAGCAGCAGCAGAGTAAACAGACAACCCACAGAGTTGGAGAAAATC 3631
                         ii    -----  - i   i  v              i v         v
  L1M4_orf2#LINE/    680 CTATCA-----AG-AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_75465176_7   3632 TTCACAATCTACCGT---TCTGACAAAGGACTAATATCTGACTAATATCT 3678
                           ii   --- i i ---     i  i     vi    ------------
  L1M4_orf2#LINE/    724 TTTGCAA---ATCATATATCTGATAAGGGACTTGTATC------------ 758

  chrX_75465176_7   3679 GACAAAGGACCAGAATCTACAAGGAATCCAAACAAATCATCAAGAAAATA 3728
                         ----------      v  i  i   ii vv    v   vi  v    vi
  L1M4_orf2#LINE/    759 ----------CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_75465176_7   3729 ATAATAATAATAATCTGATCAAAAAGTGAGCAAACGACATGAATAGAAAA 3778
                          i  -----    i ii  i?    i  i     v  iv        v v
  L1M4_orf2#LINE/    799 ACAA-----ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_75465176_7   3779 TTCTCAAAAGAAGATAAACAAATGGGCCACAAACATATGAAAAAGTGCTC 3828
                              v          v        v v i  i  i       ii     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_75465176_7   3829 AACGTTACTAATTAT 3843
                            i i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (156 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 6.78 (61 / 9)  


2620 29.30 1.55 0.78  chrX_75474411_75480233     4430  5330 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75474411_7   4430 TAGAAAAATTTTCTATGCTTATGGATAGGAAGAATCAATATCGTGAAAAT 4479
                          i    i  v i i   i i      v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75474411_7   4480 GGCCATACTGCCCAAAGTAATTTATAGAATCAGTGCTATCCCCTTCAAGT 4529
                            v     v      v i  i  i   v   ii  v     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75474411_7   4530 GACCATTGACTTTCTTCACAGAATTAGAAGAAACT-ACTTTAAATTTCAT 4578
                         vv   vivi i  i  ii     v v  v-  i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_75474411_7   4579 ATGGAACCAAAAAGAGCCCATAA-AGCCAAGGCAATTCTAAGCAAAAAGA 4627
                               viiv  i ii    v  -      ii    ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75474411_7   4628 ACAAAGCTAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 4677
                               i i    vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_75474411_7   4678 AATGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGATATATAGACCA 4727
                          vv    i   i v  ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_75474411_7   4728 ACGGAACAGAAC-AATGGCCTCAGAAATAATGCCACACATCTACAACCAT 4776
                          i    i    i-i vi i -         vv   i    i  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_75474411_7   4777 CTGACCTTTGACAAACCTGACAAAAACAAGTAATGGGGAAAGGATTCCCT 4826
                         i   ii  i     ivv  v   i v  vvi           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_75474411_7   4827 ATTTAATAAATGGTGTTGGAAAAACTGGCTAGCCATATGCAGAAAACTGA 4876
                         v  i  i        i   i v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_75474411_7   4877 AACTGGACCCCTTCCTTACACCTTATAGAAAAATTAACTTAAGATGGATT 4926
                          ii         v   i     v    v           i  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_75474411_7   4927 AAAGACCTATACATAAGACCTAAAACCATAAAAACTCT-AGAAGAAAACT 4975
                          ?       v ii     v       i      -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chrX_75474411_7   4976 TAGCC---AATACTAGTCAGGACATAGACATGGACAAAGACTTTATGACT 5022
                            v?---   -  --  iv   v v ivv i i   v ii  iv iiv 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_75474411_7   5023 AAAATCCCAAA-GCAATGGCAACAAATGCCAAAATTGACAAATGAAGTCT 5071
                          vi iv     -   vvi        v vv     v  i    viiiii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_75474411_7   5072 AAGTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAATATAATCAGAGTAA 5121
                         v vi   v v  i i   i  ii vv    i  v v   v vv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75474411_7   5122 GCAGGCAACCTACAGAATGGGAGAAAAATCTCTGCAATCTGTCCATCTGA 5171
                         iv  i     i                - v i     viii vi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGA 743

  chrX_75474411_7   5172 CAAAGGGCTTAGATTCAGAATCCGCAAGAAACTTAAACAAAT---TTACA 5218
                         i  i  i   iv  i      viii  ii    ivv    v --- v i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_75474411_7   5219 CGAAGA-AAACAACCCCAT-AAAAAGTGGATGAAGGATATGAACAGACAC 5266
                         vi    -   i     v  -?    i   iii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_75474411_7   5267 TTCTCAAAAGAAAACATTTATGCATTCAACAAACATATGAAAAAA-GCTC 5315
                              v      i i  vi viiivi   i  i  i       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_75474411_7   5316 ATCATCACTACTCAT 5330
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (159 / 101)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.31 (21 / 16)  


1264 31.80 1.05 0.42  chrX_75483199_75487121.rev      995  1472 (2451)    L1M4_orf2#LINE/L1        1   481 (427)  

  chrX_75483199_7    995 TGGAAACACATCCAATGCTCATAGATGGGTAAA-TGAATATAATAAAAAC 1043
                               v i    v   i    i   v  v i - v     vi v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75483199_7   1044 GATCATTCTGTCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 1093
                          iiv  v  vi v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75483199_7   1094 TATCATAATCATTCTTTACAGAACTAGAAAAAAAAATCTTAAAATACATA 1143
                          vi  vvvv v  i   i     v v  v  ivvi   i      v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75483199_7   1144 TGAAACTAAAAATGAATCCGCATAGCCAAGGCAAGACTAAGCAAAAAGAA 1193
                           i  v iv  iv  vi v v        ii   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_75483199_7   1194 CAAATCTCGAGGCATAGCATTACCAGATTTCAAACTATACTATGAGGGCA 1243
                             vi v    vv vi  i v  vi        viv     ii i vi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_75483199_7   1244 TAGTCACCAAAATGGCATG-TACTGGTTTAAAAATAGGCACGTAGACCAA 1292
                         i   v i   i ii ii  -      iv   ii    i  ii    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_75483199_7   1293 TGTAAGAGAATAAAGAACACAGAAATAAACTTAAATACATATAT--CCAA 1340
                           v  v     vi   iiv           ii --     v   --i   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAA 348

  chrX_75483199_7   1341 GTGATCTTTGACAAAGCAAGCAAAAACATTAAGTGGGGAAAGAGCACCTT 1390
                         v    i  i     i vviv   i v    v i          ii vii 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_75483199_7   1391 ATACAACAAATGGTACTGTGATAATTGACAAGCCACATGTAGAAAAGTAA 1440
                         v v           i   v  i  i  ivv ?       i i  i i i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_75483199_7   1441 AACTGGATCTC-ATCTCTCATCTCATACAAAAA 1472
                          ii    i i - i   v  i vi         
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAA 481

Transitions / transversions = 1.36 (87 / 64)
Gap_init rate = 0.01 (5 / 481), avg. gap size = 1.40 (7 / 5)  

2744 27.23 0.38 0.38  chrX_75483199_75487121.rev     1473  2269 (1654)    L1M4_orf2#LINE/L1      112   908 (0)  

  chrX_75483199_7   1473 TTTTTCACAGAATAGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAA 1521
                              ii     - vvi v  i  - iii    i           viiv 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_75483199_7   1522 AAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGAACAAAGCAGGA 1571
                          ii  v  v v  vi    iv     i i ivv i          iv   
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_75483199_7   1572 GGCATCACGCTACCTGACTTCAAACTATACTACAAGCCTACAGTAACCAA 1621
                           vv    i  v  ii i      viv        iv         i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_75483199_7   1622 AACAGCATGGTACTGGCACCAAAACAGAGATATAGATCAACGGAATAGAA 1671
                         i    ii           iv ii i   v           i         
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_75483199_7   1672 C--AGAGCCCTCAGAAATAATGCCACATATCTACAACTATCTGATCTTTG 1719
                         i--    i  --        vv   i i  i  iiiii vi    i  i 
  L1M4_orf2#LINE/    311 TTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_75483199_7   1720 ACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAA 1769
                             ivv  vv  i v  vv            i  vvi  v  i  i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_75483199_7   1770 TGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCC 1819
                                    v      v  ?   i   i i  iiv    ii    i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_75483199_7   1820 CTTCCTTACACCATATACAAAAATTAATTCAAGATGGATTAAAGACTTAA 1869
                           v   i                    i    i      i ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_75483199_7   1870 ATGCTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACC 1919
                            iv   v       i      vi i           v    ?i v vi
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_75483199_7   1920 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGC 1969
                         v   iv   v v  vv i     v ii   v ivv  vi           
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_75483199_7   1970 AATGGCAACAAAAGTCAAAATTGACAAATGGGATCTAATTCAACTAAAGA 2019
                          vvi          vv     v  i    v   ii v  iv  v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_75483199_7   2020 GCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTAGA 2069
                         i   i  ii vv    i  v    i  vv i      v  i     i v 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_75483199_7   2070 AAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATC 2119
                         i             v  i    vii ivi      i  i  i  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_75483199_7   2120 CAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACC 2169
                               v  i  v      vv    v iv i  v     i     i    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_75483199_7   2170 CCATCAAAAATTGGGTGAAGGATATGAACAGACACTTCTCAAAAGAAGAC 2219
                          v  i?    v    ii      v    i     i     v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_75483199_7   2220 ATTTATGCAGTCAAAAGACACATGAAAAAATGCTCATCATCACTGGCCAT 2269
                           vi viii i   v ii          i       v     ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (122 / 91)
Gap_init rate = 0.01 (4 / 797), avg. gap size = 1.50 (6 / 4)  

1013 26.94 1.37 1.60  chrX_75483199_75487121.rev     2995  3432 (491)    L1M4_orf2#LINE/L1      472   908 (0)  

  chrX_75483199_7   2995 TATAAAAAAAA-AACTCAAGATGGATTAAAGACATAAATCTAAGACCCGA 3043
                             v     v-       i      i ?    v     v     v ii 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_75483199_7   3044 AACCATAAACATTCT-AGAAAATAACATCAGAA-AAATCCTTCTAGAAAT 3091
                            i     - i   -    i v     vi ?i-     -   vv  vv 
  L1M4_orf2#LINE/    522 AACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT 569

  chrX_75483199_7   3092 TAGCTTGTGCAAAGACATCACGACCAAAAC-CCAAAAGCAAATGCAAACA 3140
                          i v  iv    v iiv  viiivi vi  -         ----   i  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA----CAAGCA 615

  chrX_75483199_7   3141 AAAAATAAATAAATAAATAGATGGGACTTAAATAAACGAAAAATCTTCTG 3190
                          v   vi  v     i   i  v      v vi   vvv    v   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_75483199_7   3191 CACAACAAAAGAAATAATCAGCAGAGTAAACAGACAACCCACAGAGTGGG 3240
                         ii vv    i  v iv    iv i   i  v              i    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_75483199_7   3241 AGAAAATTTTCATAATGTATACTTCCAACAAAGGACTAATATTTAGAACC 3290
                                v  iii  vvi   iv  ii i  i     vi   ii    iv
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_75483199_7   3291 TACAAAGATCTCAAACATATCAACAAGAAAACAA--AACAATCCCATCAA 3338
                           i     v   vv   vv    i  v    vi --  i  i  v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_75483199_7   3339 AAAGTGGGCTAAGGACATTAATAGGGAAGTCTCAAAAGAAGATATACAAA 3388
                            i     v     iv v     iv vv    v                
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_75483199_7   3389 TGGCCGAAAAGCATACGAAAAAAATGCTCAACGTCACTAATGAT 3432
                              i v     i i     i -        i   ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.05 (59 / 56)
Gap_init rate = 0.02 (9 / 437), avg. gap size = 1.44 (13 / 9)  


2712 27.55 2.02 0.56  chrX_75495826_75501625     4415  5307 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_75495826_7   4415 GAAAAACATTCCGTGCTCATGGATTGAAAAAAGCAATATCGTGTAAATGG 4464
                             i i  i  i  i          i  i vvi     i  vv i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_75495826_7   4465 CCATACAGCCCAAAGTAATTTATAGATTCAACACTATTCCCATCAAGCTA 4514
                          v    vv      v i  i  i         i v  i  i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_75495826_7   4515 CTA-TTGACTTTCTTAACAGAACTAGAAAAAACT-ACTTTAAATTTTATA 4562
                          i -i  v    i  i-     v v  v  i-  - iii    v  i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTG-CAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chrX_75495826_7   4563 TGGAACCAAAAAAGAGCCTGTATAGTCAAGACAATACTAAGCAAAAAGAA 4612
                              viiv  ii  v  v v    i   i     vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_75495826_7   4613 CAAAGCAGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGGCTA 4662
                              iv     vv    v  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_75495826_7   4663 CAGTAACCAAAACAGCATGGTAATGGTACCAAAACAGATACATGGACCAA 4712
                               i   i    ii     v   i iv ii i   i i  i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_75495826_7   4713 TTGTACAGAACAGACACTGCAGAAATAACACCACACATCTACAACCATCT 4762
                          v v i    iv  v v v         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_75495826_7   4763 GATCTTTGACAAACCTGACAAAAACAAGCAGTGGG-AAATCATTCCCTAT 4811
                            i  i     ivv  v   i v  vv  i    -   vv  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_75495826_7   4812 TTAATAAATGGTGCTGGGA-AACTGGCTAACTATATGCAGAAAACTGAAA 4860
                          i  i              -      v  ? i i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_75495826_7   4861 TTG-ACCCCTTCCTTACACCTTATACAAAAATTAA-----AATGGATTAA 4904
                            -      v   i     v              -----       i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_75495826_7   4905 TGACTTAAATGTAAAACCTAGAACCATGAAAACCCTAGAAGAAAACCTAG 4954
                         v   i         i v   i   i  i   vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_75495826_7   4955 GCA-ATACCATTCAGGACATAGGCATGGGAAAAGACTTCATGACTAAAAC 5003
                          ?i- v i -   iv   v v  vv i  v  v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_75495826_7   5004 ACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTA 5053
                                   vvi          vv     v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_75495826_7   5054 AACTAAGGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAGG 5103
                           v v ii i   i  ii vv    i  v       vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_75495826_7   5104 CAACCTACAGAATGGGAGAAACTTTTTACAATCTATCCATCTGACAAATG 5153
                              i               v v   i   vii  vi      i  iv 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_75495826_7   5154 TCTAATATCCAGAATCCACAAGGAACT--TA-AACTAATTTACAAGAA-A 5199
                         v  vi          vi i  i     --  -    v v v i  i  - 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_75495826_7   5200 CAAA---CCCCATCGAAAAATGGACGAAGGATATGAACCGACATTTCTCA 5246
                             ---   v  i?        i i      v    iv          v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_75495826_7   5247 AAATTAGACATTTATGCGGCCAAAAAAAACACATGAAAAAAAGCTCGTCA 5296
                            vv   i  vi vii      v  i--          i v    iv  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAG--CACATGAAAAGATGCTCAACA 897

  chrX_75495826_7   5297 CCACTGGTCAT 5307
                         i  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.24 (134 / 108)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 1.53 (23 / 15)  


1579 29.74 0.00 0.41  chrX_75502418_75505600.rev     1486  1976 (1207)    L1M4_orf2#LINE/L1        1   489 (419)  

  chrX_75502418_7   1486 TAGAAACACATCCCATGCTCATGAATAGGTAAAATCAGTACTGTGAAAAT 1535
                          i    v i        i     i  v  v i v i i  i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75502418_7   1536 GGCCATACTGCAAAAAGTAATCCACAAATTTAACAAAATCCCCATCAAAA 1585
                            v     v vv   v i   i   i   i   iv      i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75502418_7   1586 TACCACCATCATTCTTCACAGAATTAGAAAAAAAAATTCTAAAATTCATA 1635
                          v   v vv v  i  ii     v v  v  ivvi  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75502418_7   1636 TGGAACCAAAAAATAGCCTGCAAAACTAAAGCAAGAATAAGCAAAAGGAA 1685
                              viiv  iiv v  v v v i i   i   vvv i iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_75502418_7   1686 CAAATCTGGAGGTATCACGCTACCTGATTTCAAACTATACTATAAGGCCA 1735
                             vi      vv    i  v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_75502418_7   1736 TCGTCACCAAAACAGCATGGTACTGGTATCAAAATAGGTATTTATACCAA 1785
                         iv  v i   i    ii         i  v ii    ii  v  v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_75502418_7   1786 TGGAACAGAAGCGCAAACCCAGAAATAAAACCAAATACTTAAAGCCAACT 1835
                              i    vi vi ii           v   v i i   vi i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_75502418_7   1836 GATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGGGAAAGGACACCCT 1885
                            i  i     i vviv   i v   vv i     --    i i vi  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAAGAATAGTCT 398

  chrX_75502418_7   1886 TTTCAAAAAATGGTGCTGAGATAATTGGCTAGCCGCCTGTAGGACAATGA 1935
                               v           i  i  i   v  ?  i v  i ii v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_75502418_7   1936 AAGTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCA 1976
                          iv    i  ii i   v    v           i      
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

Transitions / transversions = 1.34 (83 / 62)
Gap_init rate = 0.00 (1 / 489), avg. gap size = 2.00 (2 / 1)  

1047 24.06 4.95 3.07  chrX_75502418_75505600.rev     2269  2692 (491)    L1M4_orf2#LINE/L1      477   908 (0)  

  chrX_75502418_7   2269 AAAAATCAACTCAAGATGGATTAAGGACTTAACC-TAAGAACTGAAACTA 2317
                               i       i      i ?i   i   vi-     i  i      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_75502418_7   2318 TAAAAATCCTAGAAAATTACATGGAAAAAAAACCCTTCTAGACATTGGCT 2367
                              v  i     i vv    i i?iv   --i    vv   v    v 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGT 574

  chrX_75502418_7   2368 TAGGCAAT-------TA---ATGACCAACAACTCAAAAACAAATGCAATA 2407
                                 -------  ---     -----  -     i  v v    i 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGAC-----AC-CAAAAGCACAAGCAACA 618

  chrX_75502418_7   2408 AAACAAAGATAAATAG-TAAA---GATCTAATTAAACTAAAAAGCTTTCA 2453
                            v   ---      -    ---  ii v  i   v v    i    ii
  L1M4_orf2#LINE/    619 AAAGAAA---AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_75502418_7   2454 CACGGCAAAAGGAACAGTCA-----GCAAACAGACAACCCACGGAGTGGG 2498
                         ii vv    i iv  vi   ----- ii  v           i  i    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_75502418_7   2499 AGAAAA-ATCTTCACAATCTATAGAACTGGCAAAGGACTAATATCAACAA 2547
                               -  i v  -    -   v v   ii  i     vi    v v  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCA-AATC-ATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_75502418_7   2548 TCAACAACAAACTCAAATGAATCTGTAAGAAGGAAATAAACAATCCCATC 2597
                          vv i  vi     vv ii v  vi   v  ii i i   i  i  v  i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_75502418_7   2598 AAAAAGTGAGCTAAGAACATGAATAGACAATTCTCAAGGGAAGATAAACA 2647
                         ?    i  i  v   i iv          v     v ii       v   
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_75502418_7   2648 AATGGCCAACAAACATATGAAAAAATGCTCAACACCAGTAATGAT 2692
                                  i  i  i       i          i  ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (59 / 40)
Gap_init rate = 0.03 (13 / 432), avg. gap size = 2.62 (34 / 13)  


3142 26.97 0.66 1.10  chrX_75525182_75531609.rev     5026  5937 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75525182_7   5026 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATTAATATCCTGAAAAT 5075
                              ii    i     i        v      v       iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75525182_7   5076 GGCCATACTGCCCAAGTTAATTTATAGATTCAATGCCATCCCCATCAAGC 5125
                            v     v     i  i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75525182_7   5126 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 5170
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75525182_7   5171 TGGAACCAAAAAGGAGCTCACATAGCCAAGGCAATCCTAAGCAAAAAGAA 5220
                              viiv  i   v iviv        ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_75525182_7   5221 CAAAGCTGGAAGCATCACACGACCTGACTTCAAACTATACTACAAGACTA 5270
                              i    i vv      vv  ii i      viv        ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_75525182_7   5271 CAGTAACCTAAACAGCATGGTACTGGTAACAAGACAGATATATACACCAA 5320
                               i v i    ii         i vv i  i   i     v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_75525182_7   5321 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5370
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_75525182_7   5371 GTTCTTTGACAAACTTGACAAAAATGAGAAATGGGGAAAGGATTCCCTAT 5420
                          v i  i     ivv  v   i viivvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_75525182_7   5421 TTAATAAATGGTGCTGGGAAAAGTGGCTAGCCAGAAGTAGAAAGCTGAAA 5470
                          i  i              v  v   v  ?   v v i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_75525182_7   5471 TTGGATCCCTTTTTTACACCTTATGTAAAAATTAACTCAAGATGGATTAA 5520
                              i    vii i     v   ii              i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_75525182_7   5521 AGACTTAAATGTAAGTCCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5570
                             i          vv       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_75525182_7   5571 GCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAAC 5619
                          ?i- v i -   iv   v v  vv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_75525182_7   5620 ACCAAAACCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTA 5669
                                v  vvi          vv     v  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_75525182_7   5670 AACTAAGGAGCTTCTGCACAGAAAAAGAAGCTATCATCAGAGTGAACACA 5719
                           v v ii i   i  ii vvv   i  vi      vv i      v v 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_75525182_7   5720 CAACCTACAAATTGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGG 5769
                              i   i v           v       vii  vi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_75525182_7   5770 GCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAATAAATAA 5819
                         i  vi          v  i        i--------      v v     
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTC--------TTACAACTCAATAA 791

  chrX_75525182_7   5820 ATAAATAAATAAACAACCCCATCAAAAAGTGGGCAAAGGATATAAACAGA 5869
                         -    v i i   i     v  i?    i            v i  i   
  L1M4_orf2#LINE/    792 -TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_75525182_7   5870 CACTACCCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATG 5919
                           i v i v        i  vi viii     i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_75525182_7   5920 CTCATCATCACTGGCCAT 5937
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (141 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.67 (16 / 6)  


2763 27.26 0.53 3.83  chrX_75545936_75551359.rev     3995  4933 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75545936_7   3995 TGGAAAAACATTCCATGCTCATGGATAGCAACAATCACTATTGTGAAAAT 4044
                               i i  i     i        v v  v v i v      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75545936_7   4045 GGCCATATTGCCAAAAGTAATTTATGGATTCAATGATATTCCCATCAAGA 4094
                            v   i v  v   v i  i  ii       i vv  i  i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75545936_7   4095 TACCATTGATTTTCTTCACAGGGATTAGAAAAAAACT-ACTTTAAATTTT 4143
                          v   viviii  i  ii   ii   i--- v  i  - iii    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_75545936_7   4144 ACATGGAACCAAAAAAGGGTCC--GTATAGCCAAGACAATCCTAAGCAAA 4191
                          i      -- viv     v  -- v        i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_75545936_7   4192 AAGAACAAAGCTAGAGGCATCATGCTACCTGACTTCAAACAATACTACAA 4241
                                   i i    vv   ii  v  ii i      vvv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_75545936_7   4242 GCCTACAGTAACCAAAACATCATGGTACTGCTACCAAAACAGATATATAC 4291
                         iv         i   i   vii        vi iv ii i   i     v
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_75545936_7   4292 ATCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAAC 4341
                                   i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_75545936_7   4342 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGATTC 4391
                           vi    i  i     ivv  v   i v  vv     i      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_75545936_7   4392 CCTATTTAATAAATGATGTTGGAAAAACTTACTTGCCATAAGCAGAAAAC 4441
                         i  v  i  i     i  i   i v    viv v?   i v   i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_75545936_7   4442 TAAAACTGGACCCCTTCCTTACACCTTATACAATAATTAACTCAAGATGG 4491
                          i  ii         v   i     v       v           i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_75545936_7   4492 ATTAAAGACTTAAATGTAAGACATAAATCTATAAAAATCCTAGAAGAAAA 4541
                           i ?    i           vv    v        v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_75545936_7   4542 CTTAGGCA-ATACCATTCAGGATATAGGCATGGGCAAAGACTTCATGACT 4590
                          v    ?i- v i -   iv  iv v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_75545936_7   4591 AAAACACCAGAAGCTATGGTAACAAAAGCCAAAATTGACAG-TTGGAATC 4639
                          vi      i    vvvi i        vv     v  i i-     v -
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT- 643

  chrX_75545936_7   4640 TAATTAAACTAAAGAGCTTCTGCAAAAATAAATAAATAAATAAATAAATA 4689
                          v  i   v v  i i   i  ---------------------- ivv -
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTG----------------------TGCTT- 670

  chrX_75545936_7   4690 AATAAATAATAAAAACTATCATCAGAGTGAACAGGCAACCTACAGAATGG 4739
                         --i   vi i ----      vv i      v  i     i         
  L1M4_orf2#LINE/    671 --CAAAGGACA----CTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_75545936_7   4740 GAGAAAATTTTTGCAATCTATCTATCTGACAAAGGGCTAATATTCAGGAT 4789
                                 v       vii  v       i  i  i  vi   i   i  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_75545936_7   4790 CTACAAAGAACTTAAACAAATTTACAAGAAGAAAACAAACAACTCCATCA 4839
                         v  i        ivv    v iv i  v  i  i     i   i v  i?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_75545936_7   4840 AAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAAACATTTAT 4889
                             i            v    i     i     v      i i  vi v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_75545936_7   4890 GAGGCCAACAAACATATGAAAAAAGACTCATTATCACTGGTCAT 4933
                         iv      i  i  i       i vi    vi    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (147 / 105)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.73 (41 / 11)  


2995 27.83 0.77 0.88  chrX_75562158_75568563     5005  5913 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75562158_7   5005 TGGAAGAGCATTCCATGCTCCTGGATAGGAAGAGTCAATATCATGAAAAT 5054
                              iiii  i     i  v     v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75562158_7   5055 GGCCATTCTGTCCAAGGTAATTTATAGATTCAATGTCGTCCTCATCAAGC 5104
                            v  v  vi    iv i  i  i        i ivi   ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75562158_7   5105 TGCCAATGATTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAATTC 5152
                          v   iiviii  i  ii     -   --- v  i  - iii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_75562158_7   5153 ATATGGAACCAAAAAAGAGCCTGCATTTCCAAGACAATCCTAAGCCAAAA 5202
                                 viiv  ii  v  v v  vv    i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75562158_7   5203 TAATAAAGCTGGAGGTATCACGCTACCTGACTTCAAACTATACTACAAGG 5252
                         v  i    i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75562158_7   5253 CTACACTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGAC 5302
                              v   i   i    ii         i iv ii i   v  i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75562158_7   5303 CAATGGAACGGAAT--AGAGCCCTCAGAAATAATACCACACATCTATAAC 5350
                                 ii    --    i  --        vv   i    i   iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_75562158_7   5351 CATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5400
                           vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_75562158_7   5401 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGAAGAAAGC 5450
                         i  v  i  i              v      v  ?   i   v i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_75562158_7   5451 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5500
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_75562158_7   5501 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACAATACAAGAAAA 5550
                           i ?    i    i  v   v       i      vivv  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_75562158_7   5551 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGAATTCATGTCT 5599
                          v    ?i- v i -   iv   v v  vv i     v iv   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_75562158_7   5600 AAAACACCAAATGCAATGGCAGGAAAAGCCAAAATTAACAAATGGGATCT 5649
                          vi        v   vvi   iv     vv     vi i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_75562158_7   5650 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5699
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75562158_7   5700 ACAGGCAACCCACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5749
                          v  i                       v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75562158_7   5750 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAG 5799
                           i  i  vi          v  i  v      vv    v iv i  v i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75562158_7   5800 AAAAACAAACAACCCCATCAACAAGTGGGTAAAGAAGATGAACAGACGCT 5849
                            i     i     v  i? v  i    i    i vv    i    ii 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75562158_7   5850 TCTCAAAAGAAGACATTTATGAA--GCCAACATACACATGAAGAAATGCT 5897
                             v        i  -- ii  --     i vi        i i     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_75562158_7   5898 CATCATCACTGGCCAT 5913
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (145 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


 656 31.01 1.94 2.71  chrX_75570639_75577050       44   301 (6111)  C L1M4_orf2#LINE/L1   (652)   256     1  

C chrX_75570639_7    301 TGGAAAAACATTTTATGTTCATGGATAGAAAAAAT-ACTATTTTTAAATT 253
                               i i  iii            v i  i v - v    -----i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-----GTT 45

C chrX_75570639_7    252 AAAATTGCCATACTGTCATAAGAAATTTATAGATTCAATGCTATTCCCAT 203
                           i  v  v     vi vv  vvi  i  i        i  v  i  i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

C chrX_75570639_7    202 TAAA--CTAATCAACATTCTTCATAGAA--TCATAAAATACTATTTTAAA 157
                         i   -- iv v vi v  i  iii    -- v i  iv i--  ii    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAA 143

C chrX_75570639_7    156 ATTCATGTGGAACCAAGAAAGAGCCTAAATAGCCAAGGTGGTCCTAAGCA 107
                               i     viivi ii  v  vi         iiiii  i i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

C chrX_75570639_7    106 AAAAGAACGAAGCTGGAGGCATTACACTACCTGAATTCAAACAATACTAC 57
                          i      i   i      vv i     v  ii v      vvv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

C chrX_75570639_7     56 AGGGCTACAGTAA 44
                          ii          
  L1M4_orf2#LINE/    244 AAAGCTACAGTAA 256

Transitions / transversions = 1.76 (51 / 29)
Gap_init rate = 0.02 (5 / 256), avg. gap size = 2.40 (12 / 5)  

2888 26.75 0.86 3.33  chrX_75570639_75577050     4989  5919 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75570639_7   4989 TGGAAGAACAGTCCATGCTCATGGATAGGAAGAATCAATATTGGGAAAAT 5038
                              ii i vi     i        v      v i       vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75570639_7   5039 GACCATACTGCCCAAGGTAATTTTTAGATTCAATGCTATCCCCATCAAGC 5088
                          i v     v     iv i  i vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75570639_7   5089 TACCATGGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5136
                          v   vvvi i  i   i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75570639_7   5137 TATGGAACCGAAAAAGAGCCCACATAGCCAAGACCATCCTAAGCAAAAAG 5186
                                vi v  ii  v  viv        i  v   i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75570639_7   5187 AACAAAGCTAGAGGCATCACACTACCTGACTTCAAACAATATACTACAAA 5236
                                i i    vv       v  ii i      --------------
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-------------- 234

  chrX_75570639_7   5237 CTATACTTTGGTTACTATACTGTAAGCCTACAGTAACCAAAACAGCATGG 5286
                         ----    -----    i ----    -        i   i    ii   
  L1M4_orf2#LINE/    235 ----ACTT-----ACTACA----AAGC-TACAGTAATCAAGACAGTGTGG 270

  chrX_75570639_7   5287 TACTTGTAGCAAAACAGATACATAGACCAATGGAACAGAATGGATGCCTC 5336
                             v i vv ii i   i i     i        i     v  vivii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_75570639_7   5337 AGAAATAAAACCACATATCTAAAACCATCTGATCTTTGACAAACTTGACA 5386
                                  v   i i  i  viii  vi    i  i     ivv  v  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_75570639_7   5387 AAGACAACCAATGGGAAAAGA-TCTCCTATTTAATAAATGGTGCTGGGAA 5435
                          iiv  vi       i     - vvi  v  i  i              v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_75570639_7   5436 AACTGGCTAGCCATATGTGGAAAGCTGAAACTGCATCCCTTCCTTACATC 5485
                               v  ?   i   iii  iiv    ii  v i    v   i   i 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_75570639_7   5486 ATGTACAAAAATTAACTCAAGATGGATTAAAGACTTAAATGTAAGACCTA 5535
                           i                 i      i ?    i           v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_75570639_7   5536 AAACCATAAAAATCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACAT 5584
                             i      v  i           v    ?i- v i -   iv   v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT 569

  chrX_75570639_7   5585 AGGCATGGGCAAATACTTCATGTCTAAAACTCCAAAACCAATGGTAACAA 5634
                         v  vv i     vvii   v ivv  vi  v      v  vvi i     
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_75570639_7   5635 AAGTCAATATAGACAAATGTGATCTAATTAAACTAATGGGCTTCTGCAGA 5684
                            vv  v     i    vv  ii v  i   v v viii   i  iivv
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_75570639_7   5685 GCAAAAGAAAATATCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAA 5734
                         v    i  v v     vv i      v  i     i              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_75570639_7   5735 AATCCTTGCAATCTACCCATCAGACAAAGGGCTAATATCCAGAATCTACA 5784
                            vi      vii ivi   v  i  i  i  vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_75570639_7   5785 AAGAACCCAAACAAATTTACAAGATAAAAACAA----CTCCATCAAAAAG 5830
                               i vv    v iv i  v v   i    ---- i v  i?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_75570639_7   5831 TGGGTAAAGGATATGAACAGACACTTCTCAAAAGAAGACATCTATGCAGC 5880
                             i       v    i     i     v        i  vi viii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_75570639_7   5881 CAACAGACATACGAAAAAATGCTCATCATCACTGGTCAT 5919
                            i ii  i i     i       v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.55 (39 / 11)  


 438 28.29 1.97 1.97  chrX_75581171_75587574.rev       11   162 (6242)    L1M4_orf2#LINE/L1       70   221 (687)  

  chrX_75581171_7     11 ATCTACAGATTCAATGCAAACCTTATCAAAATACAAATGATAGTTTTCAC 60
                                       i    v  i         v v iiviivv    ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_75581171_7     61 AGAAAT-AAAAA--TAATTTTAAAATTTACATGAAAACAAAAAAGACTCA 107
                               -i v  -- i  ii       i i   i   iiv  ii   i  
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_75581171_7    108 GCATAACCCAAGCTATCCTGCCCAATAAGAACAAAATGGGAGGGCCAGGC 157
                          v   i  v  i v   i  vvv  v         i v     i i--- 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT---C 216

  chrX_75581171_7    158 ACATT 162
                            i 
  L1M4_orf2#LINE/    217 ACACT 221

Transitions / transversions = 1.69 (27 / 16)
Gap_init rate = 0.02 (3 / 152), avg. gap size = 2.00 (6 / 3)  

3064 27.17 0.66 0.77  chrX_75581171_75587574.rev     5005  5913 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75581171_7   5005 TGGAAGAAAATTTCATGCTCATGGGTAGGAAGAATCAATATGGTGAAAAT 5054
                              ii v  ii    i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75581171_7   5055 GGCCTTACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5104
                            vv    v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75581171_7   5105 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTC 5151
                          v   i-       i  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_75581171_7   5152 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATGCTAAGCCAAAA 5201
                                 viiv  ii  v  v v  v     iv    vi i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75581171_7   5202 GAACAAAGCTGGAGACATCACACTACCTGACTTCAAACTATACTACAAGG 5251
                                 i     ivv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75581171_7   5252 CTACACTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGATATAGAT 5301
                              v   i   i    ii           iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75581171_7   5302 CAATGGAACAGAAC--AGAGCCCTCAGAAATAA-CGCAGCATATCTACAA 5348
                                 i    i--    i  --        - v  -i i  i  iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCA-TACATTTATGG 344

  chrX_75581171_7   5349 CTATTTTATCTTTGACAAACCTGAGAAAAACAAGCAATGTGGAAAGGATT 5398
                         ii v  v  i  i     ivv  vv  i v  vv     v      i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_75581171_7   5399 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5448
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_75581171_7   5449 CTGAAACTGGATCTCTTCCTTACACCTTTTTACAAAAATCAACTCAAGAT 5498
                         v    ii    i i  v   i     v v -        i       i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAAT 493

  chrX_75581171_7   5499 GGATTAAAGATTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAA 5548
                             i ?   ii    ii v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_75581171_7   5549 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5598
                            v    ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_75581171_7   5599 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5648
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_75581171_7   5649 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTG 5698
                          v  i   v v  i i   i  ii vv    i  v    ii vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_75581171_7   5699 AACAGGCAACCTATAAAATGGGAGAAAATTTTCACAACCTACTCATCTGA 5748
                           v  i     i i i             v  ii   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_75581171_7   5749 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5798
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_75581171_7   5799 AAAAAACAAACAACCCCATCCAAAAGTGGGTGAAGGACATGAACAGACAC 5848
                             i     i     v  i?    i    ii     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_75581171_7   5849 TTCTCAAAAGAAGACATTTATGCAGCCAAAATACATATGAAAAAATGCTC 5898
                              v        i  vi viii     v vi  i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_75581171_7   5899 ATCATCACTGGCCAT 5913
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2319 26.50 1.80 6.97  chrX_75588895_75595483.rev     5152  6098 (491)    L1M4_orf2#LINE/L1       11   908 (0)  

  chrX_75588895_7   5152 TTCTATGCTCATGGCTATG--AGCCATCGATATTGTGAAAATAACCATAC 5199
                          i i   i      v -  --  v - ii       v  i  ii v    
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGAT-TGGAAGAC-TTAATATTGTTAAGATGGCAATAC 58

  chrX_75588895_7   5200 TGCCCAAAGTAGTTTATAGACTCAATGCTATCCCCATCAATCTACCATTG 5249
                          v      v ii i  i   i    i  v     i     vv v   viv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chrX_75588895_7   5250 ACTTTCTTCACAGAATTAGAAAAAAAAACTAATT-TAAATTTCATACAGA 5298
                         i i  i  ii     v v  v  i----  i  i-    v      ii  
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATTCATATGGA 154

  chrX_75588895_7   5299 ACCAAAAAAGAGCCCGTATAACTGAGGCAATCCTAAACAAAGAGAACAAA 5348
                          viiv  ii  v  v v   i ii ii     i i  v  ii        
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_75588895_7   5349 GCTGGAGGCATCATGCTACCTGACTTCAAACTGTAGTACAAGGCTACAGT 5398
                          i      vv   ii  v  ii i      viv  v     i        
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_75588895_7   5399 AACCAAAACAGCATGGTACTGGAACCAAAACAGATATATAAACTAATGGA 5448
                           i   i    ii         v iv ii i   i     i ii      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_75588895_7   5449 ACAGAACAGAGGCCTCAGAAATAACAACCAAAACAGATATACAAACTAAT 5498
                          i    iv   ivii         --   --------i     --i v  
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAA--ACC--------CATACA--TTTAT 342

  chrX_75588895_7   5499 GGAACAGAACAGAGGCCTCAGAAATAACACTACACTGCTACAACCATCTG 5548
                           ---------------   -------------------------  -  
  L1M4_orf2#LINE/    343 GG---------------TCA-------------------------AT-TG 351

  chrX_75588895_7   5549 ATCTTTGACAAATCTGACAAAAAGAAGCAATGAGGAAAGGGT--TCCATA 5596
                           i  i     ivv  v   i vv vv     i      ii --  -- v
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC--TT 399

  chrX_75588895_7   5597 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAGGCAGAAAACTAAA 5646
                           i  i        i     v      v  ?   i v   i  i v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_75588895_7   5647 ACTGAACCATTTTCTTACACAGTATGCAAAAATTACCTCAAGATGGATTA 5696
                         ii  i   vi vi  i    vi   i         v     i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_75588895_7   5697 AAGACTTAAATGTAAGATCTAAAACCATAAAAACCCTA-AAGAAAACCTA 5745
                         ?    i           v       i      vi i  -        v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_75588895_7   5746 GGCA-ATACCATTCAGGACATAGGCATAGGCAAAGACTTCATGAATAAAA 5794
                           ?i- v i -   iv   v v  vv       v ii   v ii   vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_75588895_7   5795 CGCCAAAAGCTATGACAAGC--CAAAA-------TTGACAAATAGGATCT 5835
                          i        ----      --     ------- v  i    v   ii 
  L1M4_orf2#LINE/    599 CACCAAAAGC----ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_75588895_7   5836 AAATAAACTAAAGAGTTTCTGCATAGCAAAAGAAACTATCATCAGAGTGA 5885
                         v vi   v v  i ii  i  iiivv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75588895_7   5886 ACAGGAAACATACAGAACAGGAGAAAATTTTTGCAATCTATCCATCAGAC 5935
                          v  iv   vi      ii         v       vii  vi   v  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75588895_7   5936 TTTGG-CTAATATTTAGAATCTACAAGGAACTTAAACAAATCTACAGGAA 5984
                         vvv  -  vi   ii     v  i  i     ivv    v  v i iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75588895_7   5985 AAGTAAAAACGACCCCATCAAAAAGTGCACAAAGGATATGTACAGACATT 6034
                           iv v   ii    v  i?    i  vi        v  v i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75588895_7   6035 TGTCAAAAGAAGACATTTATATGGCCAACAAACATATGAAAAAAAGCTCA 6084
                          v  v        i  vi v        i  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75588895_7   6085 TCATTACTGGTCAT 6098
                         v   i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.02 (20 / 898), avg. gap size = 4.15 (83 / 20)  


3143 27.61 0.44 0.55  chrX_75600440_75602898.rev     1060  1968 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75600440_7   1060 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1109
                               i i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75600440_7   1110 GGCCATACTGCCCAAGGTAATTGATAGATTCAATGCCATCCCCATGAAGC 1159
                            v     v     iv i  iv i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75600440_7   1160 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTAAAGTTCA 1207
                          v   iivi i  i  ii     -   -- v  i  - i i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75600440_7   1208 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1257
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75600440_7   1258 AACAAAGTTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1307
                                       vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75600440_7   1308 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATC 1357
                                 i   i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75600440_7   1358 AATGGAACAGAAC--AGATCCCTCAGAAATAATGCCACATTATCTACAAC 1405
                                i    i--   vi  --        vv   i i-  i  iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATAC-ATTTATGGT 345

  chrX_75600440_7   1406 TATCTGATCTTTGACAAACCTGAGAAAAACAGGCAATGGGGAGAGGATTC 1455
                         i vi    i  i     ivv  vv  i v  vv         i  i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_75600440_7   1456 CCTATTTAATAAATGGTGCTGGGAAACCTGGCTAGCCATATGGAGAAAGC 1505
                         i  v  i  i              v v    v  ?   i   v i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_75600440_7   1506 TGAAACTGGATCCCTTCCTTACACTTTATGCAAAAATTAACTGAAGATGG 1555
                             ii    i    v   i    iv   i            v  i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_75600440_7   1556 ATTAAAGACTTAAACGTTAGACGTAAAACCATAAAAATCCTAGAAGAAAA 1605
                           i ?    i    i  v   vv      i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_75600440_7   1606 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1655
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_75600440_7   1656 AAACACCAAAAGCAATGACATCAAAAGACAAAATTGATAAATGGGATCTA 1705
                         vi            vvii  v       v     v       v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75600440_7   1706 ATTCAACTAAGGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGAA 1755
                           iv  v v ii i   i iii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75600440_7   1756 CAGGCAGCCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 1805
                         v  i  i  i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75600440_7   1806 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAA 1855
                          i  i  vi          v  i  v      vv    v iv i  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_75600440_7   1856 AAAACAAACAACCCCATCAAAAAGTGGGTAAAGGGCATGAACAGACACTT 1905
                           i     i     v  i?    i    i     iiv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_75600440_7   1906 CTCAAAAGAAAATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 1955
                            v      i    vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_75600440_7   1956 CATCACTGGCCAT 1968
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2537 27.20 2.68 1.56  chrX_75611299_75615809     3122  4018 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_75611299_7   3122 GAAAAGATATTCCATGTTCGTGGATTGAAAGAATGAATATTGGTAAAATG 3171
                          i        i        i       i    v v       v   i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_75611299_7   3172 TCCATACTGCCCAAAGCAATATGCTGATTCAATGCAATCTCTATCAAAAT 3221
                         v v     v      vii  v i v       i      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_75611299_7   3222 ACCAATGACATTTTTCACAGAAACAAAAAAAA-AATTCTAAAATTTATCT 3270
                         v   iivi v     ii      ivi v  iv-i  i        i  v 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_75611299_7   3271 GAAACCAAAGAAGACCCCCAATAGCCAAAGTTATTCTAAGCAAAAAGAAC 3320
                          i  viiv iii     vv          iiv  ii i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_75611299_7   3321 AAAACTGGAGAAATCACATAACCTGACTTCAAATTATACTACAGATCTAT 3370
                            ii     i v     ivv  ii i      viv       i v   i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_75611299_7   3371 AGTAGCAAAAGAAGCATGGTTGTTACTGGCATAAAAACAGACACATAGTT 3420
                             iiv  iiv  ii    ----          ii i     i    v 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGT----ACTGGCATAAGGATAGACATATAGAT 297

  chrX_75611299_7   3421 CATAGGAAAAGAAT-AACAACCCAGAAACAAATCCACATACCCAAAGTGA 3469
                           vv    v     -i v ii       i   i   i i iii vi  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_75611299_7   3470 AGTCATTTTTGACAAATAGT-CCAAGAACATATACTGAGAAAAAGACAGT 3518
                          v v     i     i-i  -      v   vi v  i i   ii i   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAG-GGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75611299_7   3519 GCCTTCAATAAATGGTGCTGAAAAAATTGAAAGTTCGTATTCATAAGAAT 3568
                         vii     i           ii v  i  i vi?i ii  v  v      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75611299_7   3569 CAAAATAGATACTCACTTCTTGCCATGTACAAAAATGAAATCAAAAT--- 3615
                         v  iv i  iv ii  i  vii    i         v  v       ---
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75611299_7   3616 --AAAGACTTAAATTTAAGACCTTAAACTGTGAAACTATTACAAGAAAAC 3663
                         -- ?    i     v     v  v     i i     v   v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75611299_7   3664 TTTGTGGAGGTAC-TCTCCAGGACATTGGTCTAGGCAAAAAAATTCTT-G 3711
                         ---i i i?   v-   i iv   v    vi       viiv-     - 
  L1M4_orf2#LINE/    547 ---ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAG 592

  chrX_75611299_7   3712 AT-TAATACCCAACAAGCACAGGCAAACAAAGCAAAAATGGACAAGTGGA 3760
                           - i i   -  -       i    vv    v      i  i  i v i
  L1M4_orf2#LINE/    593 ATATGACACC-AA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_75611299_7   3761 A--TAATAAGAAGTTAAAAAACTTATGTATAACAAAGGAAACAGTCAACA 3808
                          -- v  v i  -       -   v   iivv       v  vi    v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAA-TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_75611299_7   3809 AAGATGCAA---CAAACC---GAATGAAAGAAAATATTTACAAACCACCC 3852
                            -  v  ---   v  ---     ii           i    i  ivi
  L1M4_orf2#LINE/    689 AAG-TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_75611299_7   3853 GTCTGACAAAAAGTTAATAACCAGAATACATAAGGAGCTCAAAAAACTCT 3902
                         i     i  iiiii vi  v        i    i  i   vv v     v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_75611299_7   3903 ATAACAAAT---CTGACAATCTGATCAAAAAGTGGGTAAAATAATTGAAT 3949
                             i   v--- vi i  i ii  i?    i    i   iv v      
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_75611299_7   3950 AGAAATTT-TCAAAAGAAGACATACAA-TGGCCAACAGGTACATAAAAAG 3997
                            v    -  v        i      -       i i i    i     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_75611299_7   3998 GTGCTCAACATCATTAATCTT 4018
                         i            ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (149 / 91)
Gap_init rate = 0.02 (22 / 907), avg. gap size = 1.73 (38 / 22)  


2493 29.73 1.53 0.59  chrX_75622052_75626845     3440  4290 (504)    L1M4_orf2#LINE/L1        1   859 (49)  

  chrX_75622052_7   3440 TGGAAAAACATTTCTTGTTTATGGGTAGAAAGAATCAATACCACTAAAAT 3489
                               i i  ii v    i    i v i    v i    iiii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75622052_7   3490 GGCTATACTGCCCA--TTGAAATTTACAGATTCAGTGCTATTCCTATGAA 3537
                            v     v    --    -- i          ii  v  i     v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGA--TCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_75622052_7   3538 ACAGCAAGTGACATTCTTCACAGAACTAGAAATAACT-ATTTTAAAATTC 3586
                          vvv v  ivi v  i  ii     v v  v - i  -  ii        
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTC 147

  chrX_75622052_7   3587 ATATGGAACTGAAAAAGAGCCTTAATAGCCAAAGCAATCATAAGCAAAAA 3636
                                 v  v  ii  v  vv          i     v i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75622052_7   3637 GAGCAGGGT-GGAGA---TATGCTACCTGACTTCAAACTATACTACAAGA 3682
                           i  ii  -    i---i ii  v  ii i      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75622052_7   3683 CTACAGTATCCAAAACAGCACGGTACTGGTACAAAAACAGGTCAATAGAC 3732
                                 vi   i    iii        i i  ii i  iivv     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75622052_7   3733 CCATTGAACACAATAGAGAGTCCAGAAATAAGGTGACAAATTGATGATGA 3782
                          v  v   i v   v                iviv i v   v   i v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_75622052_7   3783 TCTGATCATCAACAAAGCTGACAAAAACAAGCAATGGGGAAAAGACTCCC 3832
                         vi    iv  i    i v  v   i v  vv           ii ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_75622052_7   3833 TACTCAATAAATGGTGCTGGGATGACTGGTTAGCCATATACAGAAAATTG 3882
                          vi    i              ii     v  ?   i  i  i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_75622052_7   3883 AAGCAGGACAGCTTTTTTTACACCATATACAAAAATCAACTCAGTATAAA 3932
                            iv    v- i vii i                 i      iv  ii 
  L1M4_orf2#LINE/    448 AAGTTGGACC-CCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75622052_7   3933 TTAAATACTTCATTGTAAAACCCAAAATTATAAAAATCCTGGAAGACAAC 3982
                          i ? v  i v v     i v i    i       v  i i     v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75622052_7   3983 CTAGGCA-ATACCATCCTGGATATAGGAAAGGGCAAAGATTTCATGACAA 4031
                         v    ?i- v i v  v  iviv i  vv   -   v i    v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTAGATA 595

  chrX_75622052_7   4032 AGACACCAAATGCATTTGCAATACAAGCGGAACTTGACAAGTGGGATTAA 4081
                         v         v   ivv    i v   vii  v v  i  i v   i vv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75622052_7   4082 ATTATACTTAAGAGCTTCTGTGCAGAAAAAGAAGTTATCAACAGAATAAA 4131
                           i v v    i i   i     vvv   i  vii      v i i i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75622052_7   4132 CAGAAAACCTACAGAATGGGAAAAAATATTGGCAAACTATGCATCTGACA 4181
                         v   v    i           i        v     ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75622052_7   4182 AGGGTCTAATATCCACCATCTTTAAAGAGCTTAAACACATTTACAAGAGA 4231
                             v  vi      vv  v v      i  ivv   vv iv i  v i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_75622052_7   4232 AAAACAAACAACCCCATTAAAAAGTGG-CAAAAGAC----ATGGACACTT 4276
                           i     i     v   ?    i   -    i  i----  i    i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_75622052_7   4277 TTCAAAAGAAGACA 4290
                         i  v        i 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATA 859

Transitions / transversions = 1.33 (142 / 107)
Gap_init rate = 0.01 (11 / 859), avg. gap size = 1.64 (18 / 11)  


2974 27.64 0.66 0.66  chrX_75634374_75642224.rev     4204  5111 (2740)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75634374_7   4204 TGGAGA-ACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4252
                             i - i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75634374_7   4253 GGCCATACTGCCCAAGGTAATTTAGAGATTCAATGCCATTCCCATCAAGC 4302
                            v     v     iv i  i  v        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75634374_7   4303 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4349
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_75634374_7   4350 ATATGGAGCCAAAAAAGAGCCCACATTGCCAAGTCAACCCTAAGCCAAAA 4399
                                iviiv  ii  v  viv  v     iv   i i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75634374_7   4400 GAACAAAGCTGGAGGCAGCATGCTACCTAACTTCAAACTATACTACAAGG 4449
                                 i      vvv  ii  v  i  i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75634374_7   4450 CTACAGTAACCAAAACAGCATGGTACTGGCACCAAAACACAGATATAGAC 4499
                                  i   i    ii           iv ii i v v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75634374_7   4500 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 4547
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_75634374_7   4548 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACGATTC 4597
                         i vi    i  i     ivv  v   i v  vvv          vi  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_75634374_7   4598 CCTATTTAGTAAATGGTGCTGAGAAAACTGGCTAGCCATATGTAGAAAGC 4647
                         i  v  i ii           i  v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_75634374_7   4648 TGAACCTGAAACCCTTCCTTACATTTTATACAAAAATTAATTCAAAATGG 4697
                             vi  i v    v   i   iiv              i         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_75634374_7   4698 ATTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4747
                           i ?    i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_75634374_7   4748 CCTAGGCATTACCATTCAGGACATAGACATGGTCAAGGACCTCATGTCTA 4797
                          v    ?i v viv   iv   v v ivv i v   v iii  v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_75634374_7   4798 AAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4847
                         vi    v       vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75634374_7   4848 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4897
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75634374_7   4898 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 4947
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75634374_7   4948 ATGGTCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4997
                          v  v  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_75634374_7   4998 AAAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACT 5047
                           i -    i     v  i? v  i     i      v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75634374_7   5048 TCTCAAAAGAAGACATTTATGCAGCCAAAAGATACATGAAAAAATGCTGG 5097
                             v        i  vi viii     v iii         i     vi
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75634374_7   5098 CCATCAGACAAATG 5111
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (141 / 106)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  

2544 29.68 1.11 0.55  chrX_75634374_75642224.rev     6458  7360 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75634374_7   6458 TAAAAACACATCTCATGCCCATGGATGGGTAGAATCAATATTGTGAAAAT 6507
                          ii   v i   i    ii       v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75634374_7   6508 GACCATATGGCCAAAAGCAATCTAAAAATTCAGTGCAATTCCCATGAAAG 6557
                          i v   ivv  v   vii     v i     ii     i  i  v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75634374_7   6558 TGCCATCATCATTCTTTACAAAATTAGATAAAAACAATCCTAAAATTCAC 6607
                          v   v vv v  i   i  i  v v  i  iv-ii             i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_75634374_7   6608 ATGGAACCA-AAGAGAGCCCACATAACCAAAGCAGTATTAAGCAAAGAGA 6656
                               vii-   i  v  viv   i     i  i v  i iv  ii   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75634374_7   6657 ACAAATCTGGAGGCATCACATTACCTGACTTCAAACGATACTGTAAGGCA 6706
                              vi      vv     i v  ii i      vvv    ii  i  v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_75634374_7   6707 CTAGTTACTAAAACAGTATGGTACTAGTGTAAAAATAGGCACATTGACAA 6756
                         vi   v ii  i     i       i ii   ii    i  i  v  iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_75634374_7   6757 ATAGAACAGAACAGAGAATCCAGAAATTAAGCCAATTATTTACAGCCAAC 6806
                           i   i    iv    i         v  v   vvi     ii i   -
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA- 348

  chrX_75634374_7   6807 TTGATCCTTGACTAAGCAAACAAAAACATAAAGTGGAGAAATAACACCCT 6856
                              ii i   v i vviv   i v   vv i   i    v  i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_75634374_7   6857 ATTCAACAACTGGTGCTGGAATAATTGGCAAGCCACATGTAGAAGAATAA 6906
                         v        v         i i  i   vv ?       i i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_75634374_7   6907 AACTGTATCCTCATCTCTTACTTTTTGCAACAATCAACTCAAGATGGATC 6956
                          ii  v i  ii i   vi  iv v i   v   i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_75634374_7   6957 AAGGGCTGAAATCTAAGATCTGAAACCATAAAGATTCTAGAAGATAACTT 7006
                          ?i i iv    v     v  i    i     iv ii       v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_75634374_7   7007 CGGA--AAACCCTACAAGACATTGGCTTAGGCAAAGACCTCATAACCAAA 7054
                         v  ?--   i i - iv   v    v        v iii  v  ivi vi
  L1M4_orf2#LINE/    549 AGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_75634374_7   7055 AACCCAAAAACAAATGCAATAAAAACAAAAATAAGTAGATGAGACTTAAT 7104
                          vv      i  v v    i    iv       ii  i  vi     v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_75634374_7   7105 TAACCAA--AAAAGCTTCTGCACAACAAAAGAAATAATCACTAGATTAAA 7152
                         i  --  --    i   i  ii vv    i  v iv    vv i v i  
  L1M4_orf2#LINE/    648 CAA--AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75634374_7   7153 CTGACAACCCACAGGGTCGGAGAAAATCTTCACAATCTATACATTCAACA 7202
                         vv            ii v         v  ii   vii   i  iii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75634374_7   7203 AAATA-TAATATCAAGAATCTACAAGGAACTCTAACAAATCAGAAAGAAA 7251
                          iiv - vi    v     v  i  i       v    v   iv  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_75634374_7   7252 AAAACA--T--CCCCATCAAAAAGTGGGCTAAAGACATGAATACAAAATT 7297
                           i   -- --   v  i?    i     v  i  iv      v v v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_75634374_7   7298 CTCAGAAAAAGATATACAAACGGCCAATAAACATAGGAAAAAATGCTCAA 7347
                            vi  i            i         i  i v     i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_75634374_7   7348 CATCACTAATGAT 7360
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (154 / 110)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3020 26.99 1.55 1.11  chrX_75654198_75656514.rev      923  1826 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75654198_7    923 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 972
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75654198_7    973 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1022
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75654198_7   1023 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1070
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75654198_7   1071 TATGGAACCAAAAAAGAGCCTGTATTGCCAAGTCAATCCTAAGCCAAAAG 1120
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75654198_7   1121 AACAAAGCTGGACGCTTCACGCTACCTGACTTCAAACTATACTACAAGGC 1170
                                i    v vi    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75654198_7   1171 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1220
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75654198_7   1221 ACTGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCCACAACT 1268
                          v     i    i--    i  --        vv   i i  ii iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75654198_7   1269 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATTCC 1318
                          vi    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75654198_7   1319 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTATATGTAGAAAGCT 1368
                           v  i  i              v      v  ? i i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75654198_7   1369 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAAATGGA 1418
                            ii    i    v   i     v              i          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75654198_7   1419 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1468
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75654198_7   1469 CGAGGCA-ATACCATTCAGGACACAGGTATGGGCAAGGACTTCATGTCTA 1517
                         vv   ?i- v i -   iv   viv  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_75654198_7   1518 AAATACCAAAAGCAATGGCAACAAAAGCCTAAATTGACAAATGGGATCTA 1567
                         vi i          vvi          vvv    v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75654198_7   1568 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAACCCACCATCAG---AGT 1614
                           i   v v  i i   i  ii vv    i  ---   i    i---   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGA---CACTATCAAGAAAGT 692

  chrX_75654198_7   1615 GAACAGGCAAACTACAGAATGGGATAAAATTGTTGCAA--TATACTCATC 1662
                            v  i   v i           v     vv      --i   i--   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATC 740

  chrX_75654198_7   1663 TGACAAAAGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACA 1712
                            i  ii i  vi          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_75654198_7   1713 AGGAAAAAACAA----CCTCATCAACAAGTGGGCGAAGAATATGAACAGA 1758
                          vi    i    ----  iv  i? v  i     i   i  v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_75654198_7   1759 CACTTCTCAAAAGAAGACATTTATGCAGCGAAAAAACACATGAAAAAATG 1808
                           i     v        i  vi viii  v  v  i          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_75654198_7   1809 CTCATCATCACTGGTCAA 1826
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.00 (24 / 12)  


2989 28.22 0.55 0.44  chrX_75663624_75670013.rev     4993  5899 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75663624_7   4993 TGGAAAAACATTCCATGCTCATGGGCAGGAAGAATCAATATCGTGAAAAT 5042
                               i i  i     i      iiv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75663624_7   5043 GGCCATACTGCCCAAGGTAATTTATAGATTCAATACCATCCCCATGAAGC 5092
                            v     v     iv i  i  i        ii v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75663624_7   5093 TACCAATAACTTTCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCA 5140
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75663624_7   5141 AATGGAACCAAAAAAGGGCCTGAATCGCCAAGTCAACCCTAAGCCAAAAG 5190
                         v      viiv  ii iv  v    v     iv   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75663624_7   5191 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGCC 5240
                                i      vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75663624_7   5241 TACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5290
                              i  i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75663624_7   5291 AATGGAACAGAGC--AGAGTCCTCAGAAATAACACTGCATATCTACAACT 5338
                                i   ii--       --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75663624_7   5339 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGATTC-C 5387
                          vi    i  i     ivv  vv  i v  vvv            v v-i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75663624_7   5388 CTATTTAATAAATGGTACTGGGAAAACGGGCTAGCCATGTGGAGAAAGCT 5437
                           v  i  i       i      v   v  v  ?   ii  v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75663624_7   5438 GAAACTGGATCCCTTCCTTACTCCTTATACCAAAATTAATTCAAGATGGA 5487
                            ii    i    v   i  v  v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75663624_7   5488 TTAAAGACTTAAACGTTAGAGATAAAAGCATAAAAACTTTAGAAGAAAAC 5537
                          i ?    i    i  v    v     vi      vii            
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75663624_7   5538 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAA 5587
                         v    ?i v viv   iv   v v  vvii     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75663624_7   5588 AACACCAAAAGCAATCGCAACAAAAGCCAAAATTGACAAATGTGATCTGA 5637
                         i            vvv          vv     v  i    vv  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75663624_7   5638 TTAAACTAAACAGCTTCTGCACAGCAAAAGAAACTACCTTCAGAGTGAAC 5687
                          i   v v  v i   i  ii vv    i  v    i vvv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_75663624_7   5688 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5737
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_75663624_7   5738 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAGAAGAAAA 5787
                         i  i  vi          v  i  v      vv    v iv v  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_75663624_7   5788 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGAGATGAACAGACACTTC 5837
                          i     i     v  i?    i           vv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_75663624_7   5838 TCAAAAGAAGACATTTATGTAGCCAAAAAACACATGAATAAATGCTCACC 5887
                           v        i  vi vi i     v  i        v i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_75663624_7   5888 ATCACTGGCCAT 5899
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (142 / 110)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2599 28.44 3.05 1.02  chrX_75686703_75689700.rev     1622  2507 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_75686703_7   1622 AATACATTCCATGTTCATGGATTGGAGAAA--AAAATCACTAAGATTACC 1669
                           v i  i                  ii v--  v  iii      vi v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_75686703_7   1670 ATACTGCTCAAAGCAATTTACAGATTCAATAAAATTCCTATCAGAATACC 1719
                              v i    vii  i           iiv   i       i   v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_75686703_7   1720 AACATCATTTTTAACATGATTTGAAAAA-TGATCCTAAAATTCACATGGA 1768
                          i vv v     vi  vi v    v  i-               i     
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_75686703_7   1769 ACAACAACAACAAAAAGCCTGAATAGCCAAAACAATCTTAAGCAAAAAGA 1818
                          vvi   -----iii v  v                   i iv  i    
  L1M4_orf2#LINE/    155 AATGCAA-----GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75686703_7   1819 ACAAAGCTGGAAGCATCACATTACCTGACATCAAATTATACTACAACACT 1868
                               i    i vv     i v  ii iv     viv        vi  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_75686703_7   1869 ATAGTAATGAAAACACCATGATACTCGTATAAAAATAAAGATATAGATTT 1918
                          i      v  i   vii  i    v i    ii   i v        iv
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_75686703_7   1919 AAAAAACAGGATAGATAATGAAGAAATAAAGTGACATACCTACAACCAAC 1968
                          vii  i  i  v  v i vv         viv i i ii  iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_75686703_7   1969 TGATGTTTCACAAATTCAACAAAAACATGCACTGGG-----AACACCCTC 2013
                             v  iv    ivviiv   i v   v  v    -----  i vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_75686703_7   2014 TTCAATAATTGGTGCTGGGAAAATTGGATTGCCATGTGCAGAAGAATAAA 2063
                              i  v           v  i     v?   ii    i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_75686703_7   2064 ACTGGACCACTATTCCTCACCATATACAAAAATTAACTCAAGATTGATTA 2113
                         ii      v   iii v                        i  v   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_75686703_7   2114 AAGACTTAAATATAAGACTTGAAACTATAATAATACTCAAAAATAATCTG 2163
                         ?    i     i     vi i         -  iv  i i  iv  v --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAAC-- 546

  chrX_75686703_7   2164 GTAAAAGT---TCTTCCGGACATGGGCTCTGACAAAAAATTCATGACTAA 2210
                         i  ii?  ---     vv   v v  v iv i   viiv   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75686703_7   2211 GATCTCAAAAGCAAATGCAACAAAA-----AATAGAAAAATGAGAC---A 2252
                           ivi        v v         -----      v    vi   --- 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75686703_7   2253 ATGAAACTAAAAAGCTTTTGCATAGCAAGAGAAATAATCAACAATATGAA 2302
                         vii   i      -      iiivv   ii  v iv     v  vi    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75686703_7   2303 GAGATAATCTGCAGGATGGGAGAAAATATCTTTAAACTATGCATCTGATG 2352
                         i   i  i ii   i              i vi   ii  ii       i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75686703_7   2353 AAGAGCCAGCATCCGGAATCTATGAGGAACTCAAGCAAATCAACAACAA- 2401
                          i ii iv i    i    v   i i      vvi   v    i  i  -
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_75686703_7   2402 ----CAAAAAGCCCCACTAAAAAGTAGGTAAAAGACACTAATAGACATTT 2447
                         ----    v i   v i ?    i i  i   i  iviv           
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_75686703_7   2448 T---GAAAAAGACATGTAAATGGCCAAGAAGCATATGAAAAAATGCTCCA 2494
                         i---i  i    i  ii          v     i       i      v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_75686703_7   2495 CGTTACTAATTTT 2507
                          i i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (154 / 94)
Gap_init rate = 0.01 (12 / 904), avg. gap size = 3.00 (36 / 12)  


3207 25.52 1.44 1.10  chrX_75702302_75709314     3235  4139 (2874)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75702302_7   3235 TAGAAAAATAGTCCATGTTCACAGATTGAAAGAATCAATATTGTTAAAAT 3284
                          i    i   vi         ii     i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75702302_7   3285 GTCCATTCTACCCAAAGCAGCCTCCATATTCAGTGCAATCCCTATCAAAA 3334
                          v v  v  v      viiii  v  v     ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75702302_7   3335 TACCAATGGCATTCTTCACAGAAATAGAAAAAGTAATTCTAAAATATATA 3384
                          v   iiv  v  i  ii       v  v  iv i  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75702302_7   3385 CAAAACCACAAAAGACCCAGAGTAGCCAAAGTTATCCTAATCAGAAAGAA 3434
                         iii  vii   ii        i        iiv   i i vv ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_75702302_7   3435 CAAAACTGGATGAATCACACTACCTGACTTCAAATTATGCTACACAGCTC 3484
                             ii    v  v       v  ii i      viv i     v    v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_75702302_7   3485 TAGTAACCAAAATAGTACAGTATTGGCATAAAAACAGACACATAGACCAA 3534
                         i     i   i i   iii   i        ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_75702302_7   3535 TGGAAGAGAATAGAGAACCCAGAAATGAATTCACTCACGTACAGTGAACT 3584
                              v     v    ii        i  ii  iv  iv  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_75702302_7   3585 CATTTTAAACAAAGGTGCAAATAACATACACTACAGA-----CAGTCTCT 3629
                         v     vi    i     v  v v   v  v ivi  -----i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_75702302_7   3630 TCAATAAATGATGCTGGGGAAACTGGATATCCACATGCAGATAAATAAAA 3679
                             i     i       iv         ?         i vi   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_75702302_7   3680 CTTGACCCCTCTCTTTCAGCACCATATACAAAAATCAAATCAAAGTGGTT 3729
                         i v       vi  --  -                i  v     i   v 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCT--CA-CACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_75702302_7   3730 TAAAGACTTAAATCTAAGACTTCAAACTATGAAACTACTTC-AAGAAAAC 3778
                         i ?    i     v     vi v       i     -   v-        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAAC 546

  chrX_75702302_7   3779 ATTAGGAA-AAACCTCCAGGACATTGGTCTGGGCAAAGATTTCTTGAGCT 3827
                           -   ?i-   i  i iv   v    vi i     v i      -  v 
  L1M4_orf2#LINE/    547 AT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGAT 594

  chrX_75702302_7   3828 GT-ACCTCACAAACACAAGCAACCAAAGCAAAGATGGACAAATAGGATCA 3876
                         i -  vi  v  i          v    v   i  i  i    v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_75702302_7   3877 CATCAAGTTCATCAATTTCTGCACAGGAAAGAATAGAAACAACAAAGTAA 3926
                               iv i vv  i  i  ii vvv    i i vv v   v     i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75702302_7   3927 AAAGACAACCCACTGAATTAAAAAAAAACTATTTGCAAACCAGCCATCTG 3976
                                      v    vii i    --          i  vvi     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAA--TATTTGCAAATCATATATCTG 742

  chrX_75702302_7   3977 GCAAGGGATTAATAACCAGAATATATAAAAAGCTCAAACAACTTTATGGA 4026
                         ii      i vi  v              i i   vv      iv  iiv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_75702302_7   4027 AAAGAGTTTAATAATCTGATTTTTAAAAATGGGCGAGTGATTTGAGTA-- 4074
                            i  viv     i ii   ?--          i iv       i  --
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_75702302_7   4075 --TGTCTCAAAAGAAGACATATAAATCGA-AACAAGCATATGAAAAGGTG 4121
                         -- v    v        i   i    v v-  i     i        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_75702302_7   4122 CTCAACATCATTGATTGT 4139
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  

2986 25.57 3.39 0.68  chrX_75702302_75709314     5637  6520 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75702302_7   5637 TGGAAAGTCATTCTATGTACATGAATTAGAAGAATTAATATTATTAACAT 5686
                                vi  i i    v    i   i     v        i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75702302_7   5687 GGCCATACTACCCAAAGCGATCTACAGATTGAATGCAATCCCTAT-GAAA 5735
                            v     v      vi            v  i           -i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75702302_7   5736 TCACCAAAGAAAATTTTCACATAAATAGAAAAACC-ATTCTAAAATTTGT 5784
                           -   ivvivvv    ii  v    v  v  i i-  i        ii 
  L1M4_orf2#LINE/    101 TC-CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_75702302_7   5785 ATGGAACCAGGAAAGACCCCAAATAGCCAAAGCAATGTTAAGCAAAAAGA 5834
                               viivi ii     vi          i    v  i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75702302_7   5835 AAAAAAGCTAGATGCATCACACTATCTCACTTCATAATATCTTACTACA- 5883
                          v   - i i  v vv       vi iv i    v  ---         -
  L1M4_orf2#LINE/    200 ACAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAA---CTTACTACAA 245

  chrX_75702302_7   5884 --CAATAGTAAGCAA-ATAGCATGGTATTGATATAAAAGCAGACACATAG 5930
                         -- v i     v   - i  ii     i  ii    iiii     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_75702302_7   5931 TTCAATGGAAAAGAATAGAGAACCCAGAAATTAATCCACACATTTATGGC 5980
                         v         v     v    ii        v  i   i          i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_75702302_7   5981 CAGCTCATTTTCAACAAAGGTGCCAAGAACATACATTGGGGAAAGAATAC 6030
                           ii v      i    i          v   v  v             v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_75702302_7   6031 CCTCTTCAATAAATGGTGCTAGGAAAACTGGATATTCATATGCACAATAA 6080
                         i  i     i          i   v         ?i  i     v  v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_75702302_7   6081 TGCAACTAGATCATTGTCTCCTACCA-------AAATCAACTTAAAATAG 6123
                           v ii i  i vi ii   vi    -------    i    i     i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_75702302_7   6124 ATAAAAGACTAAAACGTAAAACCCAAAACTATACAACTACTAGAAGAAAC 6173
                           v ?    iv   i    i v i         v    vi         v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_75702302_7   6174 CTTTGAAGAAAGGCTTCTTGATGTTGGTCTAGGCAAATATTTTATGGGTA 6223
                          v v i? v  iv    v   iv    vi       vvi   iv i i  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_75702302_7   6224 AGTTTTCAAAAACACAGGCAACAAAAACAAAAATATGTAAATGAGACTAT 6273
                         v vivi     i    i         iv       vi     vi    vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75702302_7   6274 ATCAAAATAAAAACCTTCTGTACAGCAAAGAAAACAATAAACAGAGTGAA 6323
                                 v    v   i   i vv     i v  v  v  v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75702302_7   6324 GAGACAACCTGTAAAATGGGAGAAGATATTTGCAAACTATTCATCCAACA 6373
                         i        iii i          i           ii  vi   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75702302_7   6374 GGGACCTAATAGCCAAGCTATACAAAAAACTCAAACAACTGAACAGCTAA 6423
                         i  iv  vi  v   iiv    i   i     vv      v  i iiv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_75702302_7   6424 AACATAAACAA-------------TGGCCAAAATATCTGAATATACATTT 6460
                           v i   i  -------------   v    iv  i      v      
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_75702302_7   6461 TTTCTTAAAAATATAAACAAATGGCCAA-ATGTATGTAAAA---TGATCA 6506
                         i i -v  i  v   v            - v i ii i   ---  v   
  L1M4_orf2#LINE/    846 CTCC-AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75702302_7   6507 ACATCACTAATCAT 6520
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (129 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.00 (36 / 12)  


3075 27.50 0.55 0.66  chrX_75723389_75736147      492  1400 (11359)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_75723389_7   1400 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1351
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_75723389_7   1350 GACCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1301
                          i v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_75723389_7   1300 TACCAAA-GCCTTTCTTCATAGAA-TTGGAAAAAAACT-ACTTTAAAGTT 1254
                          v   iv-      i  -ii    -   --- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG---ACAAGCTGATCCTAAAATT 146

C chrX_75723389_7   1253 CATATGGAACCAAAAAAGAGTGTGCATTGCCAAGTCAATCCTAAGCCAAA 1204
                                  viiv  ii  vivv v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

C chrX_75723389_7   1203 AGAACAAAGATGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 1154
                                  v      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

C chrX_75723389_7   1153 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 1104
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chrX_75723389_7   1103 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATAGCTACAA 1056
                                  i    i--    i  --        vv  ii i vi  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

C chrX_75723389_7   1055 CTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGTGGAAAGGATT 1006
                         ii vi    i  i     ivv  v   i v  vvv    v      i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

C chrX_75723389_7   1005 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAG 956
                         vi  v  i  i              v      v  ?   ii  i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chrX_75723389_7    955 CTGAAACTGAATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 906
                         v    ii  i i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chrX_75723389_7    905 TATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 856
                         v  i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chrX_75723389_7    855 ACCTAGACATTACCATTCAGGACATAGGCATGGGGAAGGACTTCATGTCT 806
                           v   i?i v viv   iv   v v  vv i  v  v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

C chrX_75723389_7    805 AAAACACGAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 756
                          vi    v       vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

C chrX_75723389_7    755 AATTAAACTAAAGAGCTCCTGCACAGCAAGAGAAACTACCATCAGAGTGA 706
                         v  i   v v  i i  ii  ii vv   ii  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

C chrX_75723389_7    705 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 656
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

C chrX_75723389_7    655 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 606
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

C chrX_75723389_7    605 AAAAACAAACAACCCCATCCAAAAGTGGGCGAAGGACATGAACAGACACT 556
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chrX_75723389_7    555 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 506
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chrX_75723389_7    505 CCATCACTGGCCAT 492
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (145 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  

2787 26.43 3.15 1.24  chrX_75723389_75736147     5797  6685 (6074)  C L1M4_orf2#LINE/L1   (0)   908     3  

C chrX_75723389_7   6685 GAAAAACATTTCATGTTTACAGAT----AGAATCAATATCATTAAAATGG 6640
                             i i  ii      i ii   ----   v i     ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

C chrX_75723389_7   6639 TCATACTTCCCAAAGCTATTTACAGATTCAA-GCTATTTCTATCAAACTA 6591
                         iv     i      viv  i           -  v  ii        v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

C chrX_75723389_7   6590 CCAATGACATTCTTCAAAGAACTAGAAAAAGCT-ATTTTAAAATTTATAT 6542
                            iivi v  i  iiv    v v  v  -   -  ii       i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATAT 151

C chrX_75723389_7   6541 TAAAA---AAA--ACCCTGAATAATCAAGGCAATCCTAAGCAAAAAAAAC 6497
                         vi   ---  i--    v     ii   ii     i i iv  i  i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

C chrX_75723389_7   6496 AAAACTGGAGGCATCATACTACTCAACTTCAAAGTATACTACACGGCTAC 6447
                            ii      vv   i   v i   i      iiv       vi     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

C chrX_75723389_7   6446 AATATACAAAACAGCATGGTACTAGTACAAAAGCAGACACATAGACCAAT 6397
                          i  vv   i    ii       i i i  iiii     i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

C chrX_75723389_7   6396 GGAAAAGAATAGCGAGACCAGAAATAGTGCTGCACACCTACAACCAACTG 6347
                             v     v v   v         ivv iii   ii  iiii   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

C chrX_75723389_7   6346 TTCTTCGACAAAGATGACAAAAACAAGCAATGAGGAAAAGAC--TCCATT 6299
                         v i        i i  v   i v  vv     i     ii i--  --  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC--TT 399

C chrX_75723389_7   6298 TTAAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGATGACTGAT 6249
                           v  i              i      v  ?   i     i v  v   v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chrX_75723389_7   6248 GCTGGACTGCTCTCTTGTATCATATACAAAAACCAAGTCAAGATAGATTA 6199
                          i     iv  vi  iii i            ii  v    i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chrX_75723389_7   6198 AAGATTTAAATGTAAAACCCAAAGCTGTAAAAACTCTGAAAA-AAGACCT 6150
                         ?   ii         i v i   i  i     -    v i  -  i  v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

C chrX_75723389_7   6149 ATGCAT---TCCATTCTGGACATAGGAATGGGCAAATATTTCACAATGAA 6103
                          v ?i ---  --   vv   v v  iv i     vvi    vi ivv v
  L1M4_orf2#LINE/    549 AGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_75723389_7   6102 GACACCAAAAGCAATCA--CAACAAAAGCAAAAATTGGCAAATTTGATCT 6055
                                      --  --         v      v ii     v  ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

C chrX_75723389_7   6054 AATTAAACTATAGATCTTCTATACAGCAATAGAAGCTATCAACAGATT-A 6006
                         v  i   v vv i v   i i i vv   vi  vi       v i v - 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

C chrX_75723389_7   6005 ATCGACAACCCACAGAATGGGAGAAAATATTTGCAAACTATGAAGCTGAA 5956
                          vv                                  ii  iv v    v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

C chrX_75723389_7   5955 AA---ATTTTAATATCCACCATATATAAAGAACTTACAGCAGCTTA-CAA 5910
                           --- i  --i      vv              ivi -  i  i -i  
  L1M4_orf2#LINE/    745 AAGGGACTT--GTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAA 791

C chrX_75723389_7   5909 GAAAGAAACAA----CCCCATTAAAAACTGGGCAAGGGACATTAACGGAC 5864
                         v   i i    ----   v   ?    v       i   iv v  ii   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chrX_75723389_7   5863 ATTTTTCAAAAGAAGACATACATGTGGCCAAGAAGCGTATGAAAAAAACC 5814
                             i  v        i     vi       v    ii       i vv 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

C chrX_75723389_7   5813 TCAATATCACTGATCAT 5797
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (142 / 89)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 1.95 (39 / 20)  

2686 28.34 1.32 1.21  chrX_75723389_75736147    11360 12266 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75723389_7  11360 TGGAAAAACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 11409
                               i i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75723389_7  11410 GACCATACTGCCAAAAGCAATCTAAAAATTCAAGGCAATTCTCATTAAAA 11459
                          i v     v  v   vii     v i      v     i ii  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75723389_7  11460 TACCACCATCATTCTTCACAGAACTAAAAAAAAAAAAATCCTAAAATTCA 11509
                          v   v vv v  i  ii     v vi v  ivvi --            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chrX_75723389_7  11510 TATGGAACAAAAATGAGTCCACA-TAGCCAAAGCAAGACTAAGCAAAAAG 11558
                                vviv  v iii   v -        i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75723389_7  11559 AACAAACTTGGAGGCATCCCATTACTCAACTTTTAACTATACTATAAGGC 11608
                               v       vv  v  i v i   i  iv  viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75723389_7  11609 CATAGTCACCAAAACAGTGTGGTACTGGTATAAAATTAAGCATGCAGACC 11658
                         i i   v i   i               i    iiv  ii   ii   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75723389_7  11659 AATGGAACAAAATAGAGAATCCGAAAATAAACCCAAATACTTAACGCCAA 11708
                                i i   v    i   ii           v i i   vv i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_75723389_7  11709 TTTATTTTTGACAAAGCAAATAAAAACGTAAACTGAGGAAAACACATCCT 11758
                           v     i     i vvivi  i v i vv v  i     iv i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_75723389_7  11759 ATTTAACAAATGTTGCTCGGATAATTGGCAAGTCACATGGAGAAAAATGA 11808
                         v  i        v    v   i  i   vv ?i      v i  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_75723389_7  11809 AACTGGATTCTCATCTCTCAACTTATACAAAAATCAACTCAAGCTGCATC 11858
                          ii    ii ii i   v  v v           i       iv  v   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_75723389_7  11859 AAAAACTTACATCTAAGACTTGAAATTATAAAAATTTTACAAGATAACAT 11908
                          ? i  i  v  v     vi i   i       v i   v    v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_75723389_7  11909 ---CATAAAAACTTTTCTAGACATTGGCTTAGGCAAAGACTTCATGGCCA 11955
                         ---?i    --- i   vv   v    v        v ii   v i vi 
  L1M4_orf2#LINE/    549 AGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_75723389_7  11956 AGAACCTAAAAGCAAATGTAACAAAAACAAAGATAAATAGATGTGACTT- 12004
                         v  vv i       v v i       iv   i   i   i  vv     -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75723389_7  12005 ----AAATAAAACGCTCCTGCACAGCTAAAGAAATAATGAGCAGAGTAAA 12050
                         ----    v   vi  ii  ii vv v  i  v iv  v iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75723389_7  12051 CAGACAACCCACAGTGTTGGAGAAAATTGTCACAATCTGTACATCCTTCA 12100
                         v             vi v         vv ii   viii  i   ivvi 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75723389_7  12101 GAGGACTAATATCCAGAATCTACAAGAAGCTCAAGGAAATTAGCAAGATA 12150
                         ii     vi          v  i  ii i   vviv  v i ii  --  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA--TA 793

  chrX_75723389_7  12151 AAAAAAGAAAAGAGTGAC---ATCAAAAAATAGGCTAAGGACATGAATAG 12197
                             i v   ---- i  ---  i?      i   v     iv       
  L1M4_orf2#LINE/    794 AAAAGACAAA----TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_75723389_7  12198 ACAATTCTTAAAGGAAGATGTACAAATAGCCAACAAGCATGTGAAAAAAT 12247
                            v    iv  i      i       i     i     ii      i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_75723389_7  12248 GCTCAACATCATTAATGAT 12266
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (141 / 112)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.88 (23 / 8)  


2696 28.72 1.23 0.11  chrX_75745200_75750155     3569  4463 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_75745200_7   3569 AAAAAAATTCTATGCTCATGGATAGGTAGAATCAATATTATGAAAATGAC 3618
                            i v  i i   i        v  v   v i      i v  i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_75745200_7   3619 CACACTGCCAAAAGAAATCTACAAATTCAATGCAATTCCCATCAAAATAC 3668
                         v i   v  v   vvi       i      i     i  i        v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_75745200_7   3669 CACCATCATTCTTCATGGAACTAGGAAAAACAATTCTAAAATTCATATTG 3718
                           v vv v  i  iiii   v v iv  ivii  i             v 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_75745200_7   3719 AACAAAAAATGAGCCTGCATAGTCAAAGCAAGACTAAGCAAATAGAACAA 3768
                           vviv  iv  v  v v    i    i   vvi i iv  iv       
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_75745200_7   3769 ATTTGGAGGTATCACAATACTCGACTTCCAACTATACTATAACGCCATAG 3818
                          v       vv     v v i i i   v  viv     i  v  i i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_75745200_7   3819 TCACCAAAACAGCATGATACTGGTATAAAAATAAGAACACAGACCAATGG 3868
                          v i   i    ii  i      i    ii   iiv i i   i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_75745200_7   3869 AACAGAATAGAAAACCCAGAAATAAACTCAAATACTTACAGACAACTGAT 3918
                           i     v  i ii            i  v i i   ii v   i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_75745200_7   3919 CTTTGACAAAGCAATCTGAAACATAAAGTGGGGAAATGACACCCTACTCA 3968
                         i  i     i vvii vii v   vv i        vi i vi  vi   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_75745200_7   3969 ACAAATGGTGCTGGGATAATAGGCAAGCCACATGGAGAAGAATGAACCTG 4018
                                         i  iv  vv ?       v i         vi  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_75745200_7   4019 GATCTTCATCTCTCACTTCATACAAAAATCAACTCAAGATGGATCAAAGA 4068
                           i iii i   v   ivi          i       i        ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_75745200_7   4069 CTTAAATCTAAGACCTGGAACCATAAAGATTATAAAAGATAACATCCGAA 4118
                          i     v     v  ii   i     iv iv  i    v     vv ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_75745200_7   4119 AAACCCTTCTAGACATTGGCTTAGGCCAGAACTTTATGACCAAGAACCCA 4168
                         v  vi    vv   v    v      v viii  iv iivi v  vv   
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_75745200_7   4169 AAAGTAAATGCAGCAAAACCAAATATAAATAGATGTGACTT-----AAAC 4213
                             i v v   i     vv   v   i   i  vv     -----   i
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_75745200_7   4214 TAAAAAGCTCCTGCACAGCTAACGAAATAATCAGCATAGTAAACAGACAA 4263
                               -  ii  ii vv v  v  v iv    iv v   i  v      
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_75745200_7   4264 CCCAGAGAGTGGGAGAAAATCTTTACAATCTATACATCTGACAAAGGA-T 4312
                             v   i           v   i   vii   i      i  i   - 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_75745200_7   4313 AATATCCAGAATCTACAAATAACTCAAACAAATTAGCAAGAAAAAAA--A 4360
                         vi          v  i   v     vv    v i ii  v     i -- 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_75745200_7   4361 ATCAC---ATCAGAAAGTCGGCTAAGGACATGAATAGACAATTCACAAAA 4407
                           v  ---  i?i   i v   v     iv          v   v v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_75745200_7   4408 GAAGGTATACAAAGGGCCTACAAGCATATGGAAAAATGCTCAACATCACT 4457
                             i        v    v i     i   i   i             ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_75745200_7   4458 AATTAT 4463
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.18 (137 / 116)
Gap_init rate = 0.01 (5 / 905), avg. gap size = 2.40 (12 / 5)  


3002 27.49 1.33 0.67  chrX_75758215_75767582     5720  6621 (2747)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75758215_7   5720 TGGAAGAACATTCCATGCTCATGGGTAGAAAGAATCAATATCATGAAAAT 5769
                              ii i  i     i      i v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75758215_7   5770 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 5819
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75758215_7   5820 TAGCAATGACTTTCTTTCCAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5867
                          vv  iivi i  i   v     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75758215_7   5868 TATGGAAC--CAAAAAAGCCCACATCGCGAAGTCAATCCTAGGCCAAAAG 5915
                                v--   iii v  viv  v  v  iv     i iiivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75758215_7   5916 AACAAAGTCGGAGGCATCAGGCTACTTGACTTCAAACTATACTACAAGGC 5965
                                 i     vv   vi  v iii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75758215_7   5966 TATAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGACC 6015
                           i     i   i    ii  i      i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75758215_7   6016 AATGGAACAGAACAGAGCTCTCAGAAATAATGCCACATATCTGCAACCAT 6065
                                i    iv   vvii         vv   i i  i iiiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_75758215_7   6066 CTGATCTTTGACAAACCTGACAAAAGCAAGCAATGGAGAAAGGAT--TCC 6113
                         i    i  i     ivv  v   i v  vv      i     i  --  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chrX_75758215_7   6114 GTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATATAGAAAGCT 6163
                         - v  i  i              v      v  ?   v  ii i  iiv 
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75758215_7   6164 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 6213
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75758215_7   6214 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 6263
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75758215_7   6264 CTAGGC--AATTCCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 6311
                         v    ?--  v  --   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_75758215_7   6312 AATACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 6361
                          vv            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_75758215_7   6362 AATTAAACTAAAGAGCTTCTGCACAGGAAAAGAAACTACCATCAGAGTGA 6411
                         v  i   v v  i i   i  ii vvv   i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75758215_7   6412 ACAGGCAACCTACAAAATGGGAGAAAACTTTCACAACCTACTCATCTGAC 6461
                          v  i     i   i            iv  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75758215_7   6462 AAAGGGCTAATATCCAGAATCTAAAATGAACACAAACAAATTTACAAGAA 6511
                           i  i  vi          v  v  v    v vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75758215_7   6512 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAGT 6557
                            i    ----   v  i?    i            v    i     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75758215_7   6558 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 6607
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75758215_7   6608 TCATCACTGGCCAT 6621
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  

2525 26.83 6.86 0.71  chrX_75758215_75767582     8055  8900 (468)    L1M4_orf2#LINE/L1        1   898 (10)  

  chrX_75758215_7   8055 TGGAATGGCATACCATGGTCATGAATTGAAAGAATTAATATT--TAA-AT 8101
                              v ii  v     v     i    i    v        --   -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75758215_7   8102 GTCCATATTGCCCAAAGCTATTTACAGATTTAATGCAATCCCTATCAAAG 8151
                          v v   i v      viv  i        i  i               i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75758215_7   8152 TACCAA-TGTCATTTTTCAAATACATAGAAAAAATAATTCTACAATTCAT 8200
                          v   i-  i -     iiv v v  v  v  iv i  i   v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_75758215_7   8201 ATGAAACCAAGAAAAAGCCAGAATAGCCAATGCAATCTTAAGCAAAAAGA 8250
                            i  viivi iii v             vi       i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75758215_7   8251 ATAAAGGTGAAGGCATCACGCTATCTGACTTCAAAATATATTACAAGGCT 8300
                          i    v  i   vv    i  vi ii i       iv  i     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_75758215_7   8301 GTAGTA------------------TGGTATAAAAATAGACCTACAGGCCA 8332
                         ii    ------------------   i    ii      v  i  ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_75758215_7   8333 ATAAAACAGTATAGAGAATGCAGAAATAAATCCACATACCTA-ACCCAAC 8381
                           ii  i  v  v    i v          i   i i ii  -ivi   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_75758215_7   8382 TTATCTTTGATAAAGCCATCAGGAATATATATTGGGAAAAAGAAACACTC 8431
                          v  i  i  i  i viii  i  vi  vi v    i   ii v vv  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_75758215_7   8432 TTCAATAAATTGTG-TAGGAAAACTGGATAACCATATGAAGAAGAATGAA 8480
                              i    v   - i   v         ?   i   v i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_75758215_7   8481 ACTGGACCCATATATATCACGGTATACAAAAGTCAATTCAAGAAGGATTA 8530
                         ii       v  iv vv   vi         i i  i    i v    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_75758215_7   8531 AAGACTTAAATGAGAGACCCAAAATTGTAAAACTACTAAGAGAAAACG-- 8578
                         ?    i      vi   v i    i i       vi  ii       i--
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_75758215_7   8579 ---------CTTCAGGACAGTTAGTCTAGGGAAGGATATTACAGATAAGA 8619
                         ---------    iv   v-  i vi    v  v i v ivi     v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_75758215_7   8620 CCTTAAAAGCACAGGCAACAAAAACAAAAATAGACAAATGGGACTATATT 8669
                          vii         i         iv         i    v     vi  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_75758215_7   8670 AAA-TTAAAAAGCT----GCTGCAGAACAAAAACATTG-------AGTGA 8707
                            -       vi ----   v  ----  ii   i i-------     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCA----AAGGACACTATCAAGAAAGTGA 694

  chrX_75758215_7   8708 AGAGACACCCTCTTGAATGGGAGGAAATATTTGCAAACTACTCATCCAAC 8757
                          i     v  iviv         i             ii ivi   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_75758215_7   8758 AGGGGACTAATA---AGAATGTACAAGAAACTCAAGCAACTCAACAACAA 8804
                          i      vi  ---     i  i  ii     vvi        i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_75758215_7   8805 CAAAA-AAAT---CCTATT--AAAATGGGCAAAGAGCATGAATAAACATT 8848
                         v  i -    ---  v   --             iiiv      i     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75758215_7   8849 TCTAAAATGAAGACATGTAAATGAC-ACTAGGTATATTAAAA-ATGCTCA 8896
                            vv  v     i  ii     i - v  i i i  v    -       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_75758215_7   8897 ACAT 8900
                             
  L1M4_orf2#LINE/    895 ACAT 898

Transitions / transversions = 1.78 (144 / 81)
Gap_init rate = 0.02 (19 / 898), avg. gap size = 3.37 (64 / 19)  


2259 27.99 4.63 2.14  chrX_75775496_75777398      527  1412 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75775496_7    527 TGGTGAAATTTCCCAAGCTCATGGGTTGGAAGAATCAATATCATTAAAAT 576
                            vi i  v     v i      i        v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75775496_7    577 G--AATACATGGCACAAAGCGATCTACAGA--CAATGCAGTGCTTATCAA 622
                          --     vi-- v    vi          --   i   i v i      
  L1M4_orf2#LINE/     51 GGCAATACTC--CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_75775496_7    623 TATATTA-----TTATTTTACACAGTTAGAAAAA-TAATCCAAAAATAAA 666
                         v  vii -----i v    i  v iv v  v  i- i    v     v--
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT-- 146

  chrX_75775496_7    667 AACATAACCAGAAAATAAAAGAG-TCCA-AATAGCCA------TCCTAAG 708
                         --    v--- i    iv   i -i   -        ------  i i i
  L1M4_orf2#LINE/    147 --CATAT---GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_75775496_7    709 CACAAATAGCACAACTGGAAGCATCATATTACCTTACTTCAAATTATACC 758
                         v vi  v i  v ii    i vv   i i v  iv i      viv   i
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_75775496_7    759 ACAAGATTATAGGAACCAAAACAACATGGTACTGAAATAAAAATAGACAC 808
                             iii  i  v  i   i   iii        iv    ii       i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_75775496_7    809 ATGAGATAAATAAAACAGAAGAGAGAACCCAGACATTAAGCCACATACCT 858
                           -    v   ii  i    vv    ii     v  v  v   i i ii 
  L1M4_orf2#LINE/    292 AT-AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_75775496_7    859 GCAACCAACTGATTTTT-ATAAAGTTGACAATAAAACATACACTGTGGCA 907
                         iiiii   i       i- i  i v  v   --i v   v  v  v  v 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAA--GACCATTCAATGGGGAA 388

  chrX_75775496_7    908 AGGACACCCTATTCAATAAATAGTGCTGTGAAAATTGGATAGCCATATGC 957
                           i i vi  v     i    i      v  v  i      ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_75775496_7    958 AGAAGAATGACACTAAGCTCCTATGTCTCACCATGTATAAAAATTAACTC 1007
                          i        vii iii i    iv  v      i  i            
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_75775496_7   1008 AAGATGGATTAAATACTTAAATTATAATACCTGTAATTATAAAAACTTTA 1057
                           i      i ? v  i     -i   v v  iv  i       vii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_75775496_7   1058 TTTAAAGAAAGCTTTGGAAAAAGTTCTCTCGACATTAGCCTTGGCAAAGA 1107
                         ---i      i v v  ?iv  i ii  vi   v  i vi v     v i
  L1M4_orf2#LINE/    538 ---GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_75775496_7   1108 GTTTATAACTAAGACCTCAAAAGCAAATGCAACAAAAACAAAAGTAGGCT 1157
                         v  iv  iv  v   vi        v v         iv    i   iiv
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_75775496_7   1158 AATGGGA-TTCAATGAAACTAAAAAGCTTCTGCATGGCAAAAGATAC--- 1203
                            v   -    vii   i      -   i  iiivv    i  i  ---
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chrX_75775496_7   1204 --AGAGAG--AACAGACAGCATACAAAATGGGAGAAAGTATTTGCAAACT 1249
                         --   i  --  v     i vi   i           i          ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_75775496_7   1250 ATGCATTTGACAAAGGAGTAAGATCCAGA---CACAAA---------CAA 1287
                           ii  i   i  i   v viv       ---i i   ---------   
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_75775496_7   1288 CTGAAGAGATAAAAG--CAAATAACCCCATTAAAAAGTGGTCAAAAGACA 1335
                           v  v -      i--          v   ?    i   v    i  iv
  L1M4_orf2#LINE/    784 CTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_75775496_7   1336 TTAGTAGACATTTTTCACAAGAAGATGTACAAATGGTCAACAAGCATGTT 1385
                          v i         i  vv        i         i   i     ii -
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT- 881

  chrX_75775496_7   1386 AAAAAAAAGTTTGACATAACTAATCAT 1412
                         i    i v i ii    v ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (152 / 92)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.50 (60 / 24)  


2733 27.14 2.34 1.33  chrX_75789584_75791802      828  1726 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75789584_7    828 TGGAAAAACATTCCATGCTCATGGATTGGAAAAATAAATATT---AAAAT 874
                               i i  i     i             i v v      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75789584_7    875 GGCCATACTGCCCAAAGTAATTTACAGATTGAATGCTATTTCTATTAAAC 924
                            v     v      v i  i        v  i  v  ii    i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75789584_7    925 TACCA--TGTCATTCCTCACAGGATTAGAAATAAATCTACTCTAAAATTC 972
                          v   --  i -  ii ii   i v v  --i  iiiv ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTC 147

  chrX_75789584_7    973 ATATGGAACCAAAAAATACCCCAAATAGTCAAAGCAATCATAAGAAATAA 1022
                                 viiv  iiv    vi     i    i     v i i   v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75789584_7   1023 AAA---AGCTGTAGGCATCACACTACCTGACTT--AAACTATACAGTAAT 1067
                         i  ---  i  v   vv       v  ii i  --     -   vii  v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chrX_75789584_7   1068 GCTAGAGTAATCAAAACAGCATGGTACTC-CTCAAAAACAAACACATAAA 1116
                             v         i    ii       v- vi  ii i i   i   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_75789584_7   1117 CCAATGTAACAGAATAGAAAACTCCAAAATAAAGCCACGTATGTACTATC 1166
                         i     v  i     v  i iii vi       v   iii  v  ivi  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_75789584_7   1167 ATCTGATCTTTGACAAGGCTGACAAAAGCAAGCAATGGGGAAAGG---GT 1213
                          vi    i  i       v  v   i v  vv            i---  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75789584_7   1214 CTATTCGATAGATTGTGCTGAGATAACTGGCTAGCCATAGGCAGAAGAAT 1263
                           v   i i i  v      i  i      v  ?   i v   i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75789584_7   1264 GAAGCTAAAGCCTTATCTTTCACCATATAGAAAAATTAACTCAAGATGAA 1313
                             i ii v  i  i  iv         v              i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75789584_7   1314 TTAGAAATTTAAATGTAAGACCTCAAACTATAAAAATCCCAGAAGTCAAC 1363
                          i ? i ii           v  v           v  ii     vv   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75789584_7   1364 CTAGGG---AATTCCCTTCTTGACATGAACCTTGACAAAGAATATGTGGC 1410
                         v    ?---   ---    v    v viivi v i   v iv viv i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_75789584_7   1411 TAAGGCCCCAGAA--ACAATTGCAACAGAAACAAATATTGACAAGTGGAT 1458
                           v i v   i  --    --      i  iv   v  v  i  i v iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_75789584_7   1459 CCTAATTAAACTAAAGACCTTCTGCACAGCAAAAGAAACGATCAACAGAG 1508
                          i v  i   v v  i v   i  ii vv    i  v  v     v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_75789584_7   1509 TAAACAGAAAACCAGCGGAATGAGAGAAAATATTCTCAAAGTATGCATCC 1558
                          i  v   v    vi i     i           iv    vi  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_75789584_7   1559 AACAATGGTCTAATATGAAGAATCTATGCAAAACTTAAACAAATCAACAA 1608
                         i i  v  v  vi   vv     v   iv i    ivv    v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_75789584_7   1609 GCAAAAAGCAAA-AGCTCCATT-AAAAATTGGCAAAGGATATGAATAGAC 1656
                         vv    ii    - i i v   -      v          v         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_75789584_7   1657 ACTTCTCAAAAGAAGGTATACATGCGACCAACAAGCATATGAAAAAAAAA 1706
                          i     v       i      vii i    i     i       i ---
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--- 888

  chrX_75789584_7   1707 TGGTCAGCAGCACTAACTAT 1726
                           v   i  v  ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.06 (33 / 16)  


2783 24.64 8.53 0.95  chrX_75809500_75811972     1137  1980 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75809500_7   1137 TGGAAA-ATATTTTATGTTCATGGATTAGAAGAATCAATATTGTTAAAAT 1185
                               -    iii             i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75809500_7   1186 GTCCATACTACCCAAAGCAATCTGCAGATTCAATGTAATTTCTATCAAAA 1235
                          v v     v      vii    i         i i   ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75809500_7   1236 TACCAATGACATTCTTCACAAAAATAGAAACAAAAAGAATTCTCAAATTT 1285
                          v   iivi v  i  ii  i    v  --   ivv  - i  v     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGA-TCCTAAAATTC 147

  chrX_75809500_7   1286 ATATGGAATGACAAAAGACCCCAGATAGCCAAAACCATTCTAAGCAAAAG 1335
                                 vvi   ii     vii           v  ii i iv  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75809500_7   1336 GAACAAAACTGGAAGAATCACATTACCTGACTTCAAATTATGTTACAGAG 1385
                                ii    i  v     i v  ii i      viv ii    i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75809500_7   1386 CTATAGTAACCAAAACAACATGGTACTGACATGAAAACAGACACATAGAC 1435
                            i     i   i   iii        i   i ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_75809500_7   1436 CAATGGAACAAAACAGAGAGCTCAGAAACAAATCCACACACCTACAGTGA 1485
                                 i i  iv     ii      i   i   i   ii  ii  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_75809500_7   1486 ACTCATTTTTTGACAAAGGTGCCA----------------------TAGG 1513
                          i v     i-     i       ----------------------   v
  L1M4_orf2#LINE/    348 ATTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75809500_7   1514 CTCTTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAAAAT 1563
                           i     i              v         ?   i     i  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75809500_7   1564 AAAACTAGACCGC-ATCTC----------------TCAAATCAAAATAGA 1596
                         i  ii i    v - i   ---------------- i  v       i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75809500_7   1597 TTAAAGACTTAAATCTAAGATTTCAAACCATGAAACTTATACAAGAAAAC 1646
                          i ?    i     v     vi v    i  i     iv  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75809500_7   1647 ACTGGGGGAAATCTCCA-GAACATGGGTCTGGGCAAGGACTTCTTGAGCA 1695
                          iv  ? v      i i-  v v     - i     v ii     -  vv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTT-AGAT 594

  chrX_75809500_7   1696 ATGCC-CCACAAGCACAGGCAACCAAAGCAAACATGAACAAATGGGATCA 1744
                            v -   v       i     v    v   v  ii i    v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_75809500_7   1745 CTTCAAG-TTCATAGCTTCTGCACAGGAAAGAACAGAAACAACAAAGTGA 1793
                          v    i-  v v i   i  ii vvv    i   vv v   v       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_75809500_7   1794 AGAAACAACCCACACAATGGGAAAAAAATATTTGCAAATGAC----CTGG 1839
                          i i          v       i    -           v i----   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGA 743

  chrX_75809500_7   1840 CAAGTGATTAATAACCAGAATGCACAAGGAGCTCAAACAACTC--TAA-A 1886
                         i   v  i vi  v       ii i  i  i   vv       --   - 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_75809500_7   1887 AAAAAACTAATAATCTGATCAACATCTGAGCAAAAGATT----------- 1925
                             i  v     i ii  i? v vv  i     i    -----------
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_75809500_7   1926 --------AGAAAA---ACAAATGGCAAACAGGCATAATGAAAAGATGCT 1964
                         --------    i ---         v  i i   i -            
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA-TGAAAAGATGCT 892

  chrX_75809500_7   1965 GAATATCATTGATCAT 1980
                         v  i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (134 / 70)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 4.21 (80 / 19)  


2849 22.94 2.92 4.65  chrX_75812080_75816213     2718  3641 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75812080_7   2718 TGGAAAGATATTTCATGTTTAGGAATTTGAAGAATCAATATTGTTAAAAT 2767
                                    ii      i v i   v     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75812080_7   2768 ----ATAGTACCCAAACAAATCTAGAG-TATAATGCAACCCCTATCAAAA 2812
                         ----   v v      ivi     v  - vi  i    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75812080_7   2813 TACCAA-TGCCATCCTTCACAAAAATAGAAAAAAAAAATCCCCAAATTTA 2861
                          v   i-    - ii  ii  i    v  v  ivvi -   iv     i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCA 148

  chrX_75812080_7   2862 TACGGAACCACAAAAGACCCCTAATAGCCAAAGTTATCCTAAGCAAAAAG 2911
                           i    vii   ii     vv          iiv   i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75812080_7   2912 AACAAAACTGGAGAAATCACATTACCTGATTTCGAATTCTACTATAGACC 2961
                               ii     i v     i v  ii     i  ----   -  --- 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACT-TA---C 240

  chrX_75812080_7   2962 TATAGAGCTACCTGATTTCAGATTTTACTATAGAGCTGTAAGCAAAACAA 3011
                           i i      ----------------------  ---   v   i   i
  L1M4_orf2#LINE/    241 TACAAAGCTAC----------------------AG---TAATCAAGACAG 265

  chrX_75812080_7   3012 CATTGTACTGGCATAAAAACAGACTCATCATAGACCAATGGAACAGAATA 3061
                         ii v            ii i    --  -     i        i     v
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGAC--AT-ATAGATCAATGGAATAGAATT 312

  chrX_75812080_7   3062 GAGAATCCACGAACAAATCCACACACCTGTAGTGAAATCATTTCTGACAA 3111
                             i    vi  i   i   i   ii i i  v  v v    ii     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_75812080_7   3112 AGGTGACAGAAACATAGACTGGGGAAAAA---GTCTCTGCAATAAATGGT 3158
                         i    v  ii v   vv v        i ---    i v   i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_75812080_7   3159 GCTA-------TGAAT--CCATATGCTGAAGAATAAACCTAGACACCTAT 3199
                            i-------  i  --   i    vi      i  vi i   v    i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_75812080_7   3200 CTCTTGCCATATACAAAAATCAAACCAAAATGGATTAAAGCCTTAAATCT 3249
                            vii              i  vi          i ?  v i     v 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_75812080_7   3250 AATACCTCAAACTATTTAACCACTACAACAAAACATTGGAGAAAACCTTC 3299
                           v v  v       vv   ivi  v  v       v  ? v   i    
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_75812080_7   3300 AAGGCATTGGTCTTGGCAAAAATTTCTTAAGTA--ATATCCAACAAGCAC 3347
                         iv i v    vi v     vii       ii  -- i -    -      
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA-CCAA-AAGCAC 610

  chrX_75812080_7   3348 AGGCAACCAAAGCAAAAATGGAAAAATGGGAGCACATTGAG-TTATAAAT 3396
                          i     v    v      i  v    v   viv   ii i-   v   i
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_75812080_7   3397 TTTCTGCACAGCAAAGTAAACAATGAACAAAGTGAAGAAACAACCCACAG 3446
                            -  ii vv     v v  v  v  v        i i           
  L1M4_orf2#LINE/    661 TTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_75812080_7   3447 AATGAGAGAAAATATTTGCAAACTATCCATCTGACCAGGGATTAATAATC 3496
                             i                 ii  vi      iv     i vi  vi 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_75812080_7   3497 AGAATATATAAGGAGCTCAAACAACTCTACAGAAAAATAATCTAATAATC 3546
                                    i  i   vv       v i iv    vi - v     i 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACC 808

  chrX_75812080_7   3547 CAATATAAAAAATGAGCAAAAGATTTGAATAGATATTTCTCAAAAGAA-- 3594
                             - ?       i     i            i       v      --
  L1M4_orf2#LINE/    809 CAAT-TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_75812080_7   3595 ----CACATCGCAAATAGGCATATGAATAGATGTTCAATATCAATGATCA 3640
                         ----  v  v  v    i   i     v     i    i    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_75812080_7   3641 T 3641
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.46 (124 / 85)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.04 (70 / 23)  


3163 27.53 0.44 0.44  chrX_75843255_75850573     5919  6826 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75843255_7   5919 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5968
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75843255_7   5969 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCTATCAAGC 6018
                            v     v     iv i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75843255_7   6019 TACCAGTGACTTGCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCT 6066
                          v    ivi i vi  ii     -   -- v  i  - iii    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75843255_7   6067 TATGGAACCAAAAAAGAGCCCTCATCGCCATGTCAATCTTAAGCCAAAAG 6116
                                viiv  ii  v  vvv  v    viv       i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75843255_7   6117 AACAAAGCCGGAGGCATCACACTACCTGACTTCAAACTATATTACAAGGC 6166
                                ii     vv       v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75843255_7   6167 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 6216
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75843255_7   6217 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 6264
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75843255_7   6265 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 6314
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75843255_7   6315 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCT 6364
                           v  i  i              v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75843255_7   6365 CAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 6414
                         v  ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75843255_7   6415 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 6464
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75843255_7   6465 CTAGGAATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 6514
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75843255_7   6515 AACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTAA 6564
                         i            vvii         vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75843255_7   6565 TTAAACTAAAGAGCTTCTGGACAGCAAGAGAAACTACCATCAGAGTGAAC 6614
                          i   v v  i i   i  vi vv   ii  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_75843255_7   6615 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTCACAA 6664
                           i     i   i             v  ii   vii ivi    v i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_75843255_7   6665 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 6714
                         i  i  vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_75843255_7   6715 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 6764
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_75843255_7   6765 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 6814
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_75843255_7   6815 ATCACTGGCCAT 6826
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (143 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2618 26.59 1.97 2.63  chrX_75873629_75876011      977  1890 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75873629_7    977 TAGAAAAGCATTCCGTGCTCATGGATAGGAAGAATCAATA-----AAAAT 1021
                          i    iii  i  i  i        v      v i    -----  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75873629_7   1022 GGCCATATTGCCCAAAGTCAATTATAGATTCAATGCTATTCCCTTCAAGC 1071
                            v   i v      v v vi  i        i  v  i  iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75873629_7   1072 TAT-AATTGATTTTCTACACAGAATTAGAAAAAACT-ACTTTAAGTTTCA 1119
                          vi- ii  vi   i -ii     v v  v  i-  - iii   iv    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_75873629_7   1120 TAGGGAACCAAAAAAAGAGCCTGCATAGCCAAGACAATTCTAAGCAAAAA 1169
                           v    viiv  ii-  v  v v        i     ii i ---    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGA---AAAA 194

  chrX_75873629_7   1170 CAAACAAACAAACAAAGCTGGAAGCATCACGCTACCTGACTTCAAACTAT 1219
                         v  i------       i    i vv    i  v  ii i      viv 
  L1M4_orf2#LINE/    195 GAAG------AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_75873629_7   1220 ACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGA 1269
                                i          i   i    ii         i iv ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_75873629_7   1270 TATACAAACCAATGGAACAGAACAGAGACCTCAGAAGTAACACCACACAC 1319
                         i   i i i        i    iv    vii     i   vv   i   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_75873629_7   1320 CTAACACCATCTGATCTTGGACAAACCAAACAAAAAGAAGCAACGGGGAA 1369
                         i  vvii  vi    i  v     ivvviv   i vv vv   i      
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_75873629_7   1370 AGGAT--TCCATATTTAATAAAAGGTGCTCGGAAAACTGGCTGGCCAAAT 1417
                           i  --  -- v  i  i   v      v   v      v i?   v  
  L1M4_orf2#LINE/    389 AGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_75873629_7   1418 GCAGACAACTGAAACTGGACCCCTTCCTTACACCTTATAGAAAAATTAAC 1467
                            i vi v    ii         v   i     v    v          
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_75873629_7   1468 TCAAGATGAATTAAAGACTTAAATGTAAGACCCAAAACTATAAAAACCCT 1517
                             i   i  i ?    i           v i            vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_75873629_7   1518 AGAAGAAAACCTAGGCA-ATACCATTTAAGAC---AGGCATGGGTAAAGA 1563
                                   v    ?i- v i -  iiv   ---i  i- i  i  v i
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGG 584

  chrX_75873629_7   1564 CTTCATTACTAAAACACCAAAAGCAATTGCATCAAAAGCAAAAATTGACA 1613
                         i   v viv  vi            vvv   v      v      v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_75873629_7   1614 AATGGGATCTAAT-AAAACTAAAGAGCTTCTGCAAAGCAAAAGAAACTAT 1662
                            v   ii v  -    i    i -   i  iivvv    i  v     
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chrX_75873629_7   1663 CATTAGAGTGAACAGGCATCCTACAGAATGGGAGAAAATTTTTGC----T 1708
                           vv i      v  i  v  i                 v     ----i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_75873629_7   1709 ATATACTCATCTGAAAAAGGTCTAATATCCAGAATCTACAAGGAACTTAA 1758
                              ----     v  i  v  vi          v  i  i     ivv
  L1M4_orf2#LINE/    734 ATATA----TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_75873629_7   1759 ACAAATTTACAAGAAAAAAAATCAAACAAGCCCATCAAAGAGTGGGGAAA 1808
                             v iv i  v     i --    i  v  v  i?  i i    v   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_75873629_7   1809 GGATATGAACAGATGCTTCTCAAAAGAAGACATTTATGTGGCCAACAAGC 1858
                             v    i   iii     v        i  vi vi       i    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_75873629_7   1859 ATATGAAAAAAAATCTCATCATCACTGCTTAT 1890
                          i       i vi-    v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATG-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (138 / 101)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.10 (42 / 20)  


2969 27.31 0.77 0.77  chrX_75884829_75895189     4993  5900 (4461)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75884829_7   4993 TGGAAGAACATTCCATGCTCATGGTTAGGAAGAATCAATATGGTGAAAAT 5042
                              ii i  i     i      v v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75884829_7   5043 GGCCATACAGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5092
                            v    vv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75884829_7   5093 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5141
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_75884829_7   5142 TGGAACCAAAAAAGAGCCCTCAACA-CCGAGTCTATCCTAAGCCACAAGA 5190
                              viiv  ii  -   vv  i -  i iv v   i i ivv v    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75884829_7   5191 ACAAATCCAGAGGCATCACACTAGCTGACTTCAAACTATGCTACAAGGTT 5240
                              viii    vv       vv ii i      viv i      i i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_75884829_7   5241 ACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGAGATACAGATCA 5290
                                i   i    ii        vi iv ii i   v   i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_75884829_7   5291 AAGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTA 5338
                          v    i    i--    i  --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_75884829_7   5339 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5388
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_75884829_7   5389 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCTG 5438
                          v  i  i              v      v  ?   v   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_75884829_7   5439 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5488
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_75884829_7   5489 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5538
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_75884829_7   5539 TAGG--TAATACCATTCAGGACATAGGCATGTGCAAGGACTTCATATCTA 5586
                             --   - i -   iv   v v  vv iv    v ii   v  vv  
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_75884829_7   5587 AAACACCAAAAGCGATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5636
                         vi           ivvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75884829_7   5637 ATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5686
                           iv  v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75884829_7   5687 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGGCA 5736
                         v  i     i   i             v  i    vii ivi     ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75884829_7   5737 AAGGGCTAATATCCAGAAACTACAAAGAACTCAAACAAACTTA-CAAGAA 5785
                          i  i  vi         vv  i         vv    -  i -i  v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAA 794

  chrX_75884829_7   5786 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATACGAACAGACACT 5835
                            i     i     v  i?    i            vi   i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_75884829_7   5836 TCTCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAAAATGCTC 5885
                             v        i  vi viii     v  i-          i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTC 893

  chrX_75884829_7   5886 ATCGTCACTGGCCAT 5900
                          v i   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  

2937 26.39 2.00 1.33  chrX_75884829_75895189     8967  9868 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75884829_7   8967 TGGAAGAACATTCCATCCTCATGGATAGGAAGAATCAATATCGTGAAAAT 9016
                              ii i  i    vi        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75884829_7   9017 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCTCATCAAGA 9066
                            v     v      v i  i  i        i  v    ii     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75884829_7   9067 TAATGATGACTTTCTTCACAGAA-TTGGAAAGAACT-ACTTTAAAGTTCA 9114
                          vviiiivi i  i  ii     -   iv   --  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_75884829_7   9115 TATGGAACCA-AAAAGAGCCTGCATAGCCAAGTCAATCCTAAGCCAGAAG 9163
                                vii-  ii  v  v v        iv     i i ivv     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75884829_7   9164 AACAAAGCTGGAGGCATCACGCTACCTGACTTTGAACTACACTACAAGGC 9213
                                i      vv    i  v  ii i  ii  vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75884829_7   9214 TACAGTAAGCAAAACAGCATGGTTATGGTACCAAAACAGATATATAGACC 9263
                                 v   i    ii    vv   i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75884829_7   9264 AATGGAACAGAA--AAGAGCCCTCAGAAATAACACCACACATCTACAACC 9311
                                i    --i    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75884829_7   9312 ATCTGATCATTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 9361
                          vi    iv i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75884829_7   9362 CTATTTGATAAATGGTGCTGGGAAAACTGGCTAGCCATACATAGAAAACT 9411
                           v  ii i              v      v  ?   i iii i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75884829_7   9412 GAAACTGGATCCCTTCCTTACACCTTATAAAAAAATTAACTCAAAATGCA 9461
                            ii    i    v   i     v    v                  v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75884829_7   9462 TTAAAAATTTAAATGTAAGGCCTAAACTCGTAAAAACCCCAGCAGAAAAT 9511
                          i ? i ii          iv     viii     vi ii  v      i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75884829_7   9512 CTAGGCA-ATACCATTCAGTACAT--GGTCATGGAAAAAACTTCATGACT 9558
                         v    ?i- v i -   ivv  v --   i -  v  viii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGAT 594

  chrX_75884829_7   9559 AAAACACCAAA--TACAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 9606
                          vi        --i    --          vv     v  i    v   i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_75884829_7   9607 GTAATTAAACTAAAGAGCTTTTACATGGCAAAAGAAACTACCATTAGAGT 9656
                         v v  i   v v  i i     iiiivv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_75884829_7   9657 GAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACCCATCTG 9706
                            v  i     i   i             v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_75884829_7   9707 ACAAAGGACTAATATCCAGAATCTACAAAGAAC-ATAACAAATTTACAA- 9754
                          i  i     vi          v  i       -v v    v iv i  -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_75884829_7   9755 AAAAACAAAAAAAACCC--TTCAAAAATGGGCAAAAGATATGAACAGACA 9802
                              v v   v     --  ?             i   v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_75884829_7   9803 CTTCTCAAAAGAAGATAATTGTGCA----GTCAACAGACACATGAAAAAA 9848
                         i     v          ---- i  ---- i   i ii          i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATA----TACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_75884829_7   9849 TGCTCATCATCACTGGTCAT 9868
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (143 / 91)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.76 (30 / 17)  


2717 27.65 1.77 1.33  chrX_75895989_75899117     1733  2636 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75895989_7   1733 TGGAAAAGCATCCCAGGCTCACAGATACGAAGAATCAATATT---AAAAT 1779
                               iii      v i   ii   vv     v i      ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75895989_7   1780 GGCCATACTGCCCAAAGCAGTTGACGTATTCAATGCTATTCCTATCAAAC 1829
                            v     v      viii iv  iv      i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75895989_7   1830 TACCA-CTGACATTCTTCACAGAACTAGAAAAAAATATTTTAAAATTTAC 1878
                          v   -   v -  i  ii     v v  v  ivvv  ii       i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_75895989_7   1879 ATGCAACCCAAAAAGAGACT--GAATTGCCAAGGCAATCCTAAGCAAAAA 1926
                            v  vi--iv   i   i--    v     ii     i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAAT--GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_75895989_7   1927 GCACAAAGCTGGAGGCATCACACTACTTGACTTCAAACTATACAACAAGG 1976
                          v      i      vv       v iii i      viv   v    i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_75895989_7   1977 CTACAGTAACTTCAA--CAGCATTGTACTTGTACAAAAGCAGGCACACAG 2024
                                  --    --   ii v     v i i  iiii  i  i i  
  L1M4_orf2#LINE/    248 CTACAGTAA--TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_75895989_7   2025 ACCAATGGAACAGAATAGAGAGCCCAGAAATAAGGCCACACACCTATGAC 2074
                          i        i     v     i          iv   i   ii    ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_75895989_7   2075 CATCTGATCTTCGACAAAGCTGACAAAAACAAGCAATGG----AGGATAG 2120
                           vi    i        i v  v   i v  vv      ----  i    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_75895989_7   2121 ACTCCGTATTCAATAAATCATGCTGGGATAACTGGCTAGCCATATGCAGA 2170
                         v  i----     i    vi        i      v  ?   i     i 
  L1M4_orf2#LINE/    396 TCTT----TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_75895989_7   2171 AAATTGAAGCTGGACCCCTTTCTTACGCCATATACAATAATCAACTGCAG 2220
                          i v     i         vi  i  i          v   i    vv i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_75895989_7   2221 ATGTATTCAATACTTAAATGTAAAATCCAAAGCTATAAAAATCCTGGAAG 2270
                            v  iv? v  i         i v i   i        v  i i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_75895989_7   2271 ATAACCTAGGCG-ATACCATCCTGGACATAAGAACAGGCAATGATTTCAT 2319
                          v   v    ? - v i v  v  -  v vi ivi        i    v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_75895989_7   2320 GACAAAAACACCAAAAGCA--ATCTAAACAAAAGCAAAAATGGACAAATG 2367
                         iivv vi            -- v --        v      i  i    v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGC--AACAAAAGAAAAAATAGATAAATT 638

  chrX_75895989_7   2368 GAATCTAATTAAACTTAAGAGATTCTGCACAGCAAAATAAACTCTCCACA 2417
                          i ii v  i   v    i iv  i  ii vv    iv v   v  v v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_75895989_7   2418 GAGTAAACAGAAAACATACAGAATGGGA-AAAATATCTGTAAACTATGCA 2466
                         i   i  v   v   vi           -       i  i   ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_75895989_7   2467 TCTGACAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTA 2516
                              i  i  v  vi       v  v     i     ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_75895989_7   2517 CTGGAGAAAACTAAACAACCCCATTAAAAAGTAGGCAAACAACATGAACT 2566
                         iviv i   ivi   i     v   ?    i i      vi iv    iv
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_75895989_7   2567 GACACTTTTCAAAAGAAGTCATATATGTGGCCAACAACTATATTTTAAAA 2616
                             i  i  v       vi   i vi       i  vi i  vvv  i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_75895989_7   2617 AGCTCAATATCACGGATCAT 2636
                         v      i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (141 / 105)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  


 247 24.00 0.00 0.00  chrX_75911680_75918511     3363  3437 (3395)  C L1M4_orf2#LINE/L1   (0)   908   834  

C chrX_75911680_7   3437 GAACACACACTTCTTAAAACAAGACATTTATGCTGCCAACAAACATATGA 3388
                            i v   i    iv   v    i  vi viiv     i  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

C chrX_75911680_7   3387 AAAAAAGCTCAACATCACTGATCAT 3363
                            i v           ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (11 / 7)
Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.00 (0 / 0)  

2625 27.23 2.46 1.45  chrX_75911680_75918511     5452  6347 (485)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_75911680_7   5452 AAAAATCATTTCATGCTCATGTATCGGAAGAATCAATATCACTAA-ATTG 5500
                            i  -  ii    i     v  i      v i     iii   -  v 
  L1M4_orf2#LINE/      4 AAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_75911680_7   5501 CCATACCGCCCAAAGCAATTTAAAGATTCAACGCTATTTCTATCAAACTA 5550
                          v    iv      vii  i  v           v  ii        v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_75911680_7   5551 CCAA-TGTCATTTTTCACAGAATTAGAAAACATTATTCTAAAATGTATAT 5599
                            i-  i -     ii     v v  v  vv v  i       vi    
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_75911680_7   5600 GGAATCAAAAAAAGAGCACA-AATAGTCAAAGCCATCCTAAGCAAAAAGA 5648
                             -- viv  i ii v  -     i    i v   i i iv  i    
  L1M4_orf2#LINE/    152 GGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75911680_7   5649 ACAAAGCCAG-----TCACA--TCACA-TT----AGCTGACTTCAAA-CT 5685
                               iii -----     --  v  -  ---- i  v   v    -  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_75911680_7   5686 ATAAGTAGCCAAAACAGCATGGTACTGGTATGAAAATGGACACATAAGCC 5735
                          i -   ii   i    ii         i  i ii  i    i   iii 
  L1M4_orf2#LINE/    250 ACA-GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75911680_7   5736 AATGGAACAGAATTGAGAACCCAGAAGTAAAGCTACACACCTGCAGCCAT 5785
                                i          ii      i    v i i   ii iii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_75911680_7   5786 ATGATCCTCGACAAAGTCAACAAAAACAAGCAATGAGGAAAGGAT--TCC 5833
                         v    ii       i viiv   i v  vv     i      i  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_75911680_7   5834 TTATTCAATAAGTGGTTCTGGGATAGCTGGCTAGCCATATGCAGAA-ATT 5882
                           --    i  i    v      i i    v  ?   i     i  - v 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75911680_7   5883 AAACGTGGTCCCCTACCTTTCACCATATACAAAAATTAACTCAAACTAGA 5932
                         i  vv   v         iv                         v i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75911680_7   5933 TTAGAGGTTTAAATGTAAAACCTCAAGTTATAAGAATCT-AGAAGAAAAC 5981
                          i ?  iii         i v  v  ii     i v   -          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75911680_7   5982 CTAGGAACTACCATTCTAGGCATTGGTCTTGAGAA-AGTGTCTGTGACTA 6030
                         v    ?iiv viv   vv i v    vi v iv  -i  v   vv  -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TA 595

  chrX_75911680_7   6031 GGCCCTCAATAGCAATTGCAAAGAAAACATAAATTGACAAGTGAGACCTA 6080
                         v v vi   v    vvv    vi   iv v    v  i  i vi   i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75911680_7   6081 ATTAAACTAAAGAGCTTCTGCACAACAATAGGA-ATCATCAATCGAGTGA 6129
                           i   v v  i i   i  ii vv   -    - ii     vvi     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACTATCAAGAAAGTGA 694

  chrX_75911680_7   6130 ACAGAAAATTTACCCAATGAGATAAAATATTTGCGAATTATGCATCCTGA 6179
                          v   v  iii  vv    i  v           i   i  ii   -   
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC-TGA 743

  chrX_75911680_7   6180 CAAGGGTCTAATATCCAGAATCTATAAAGAACTTAAACATTTCAACAACA 6229
                         i     v  vi          v           ivv   vi    i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_75911680_7   6230 ACAATAACAAAGAAAACCCTATTAAAAAGTAGGCAAAAGACATGAACAGA 6279
                          v  -i     v  --   v   ?    i i      i  iv    i   
  L1M4_orf2#LINE/    794 AAAA-GACAAATAA--CCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_75911680_7   6280 CACTTCTTAAAAGAAGACACACAAGCCACCAACAAACACACAAAAAAATG 6329
                           i    iv        i i    iivi    i  i    ii    i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_75911680_7   6330 TTTTATATCACTAACCAT 6347
                         i iv i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.03 (23 / 905), avg. gap size = 1.52 (35 / 23)  


2927 28.67 0.66 0.55  chrX_75926982_75933378     4998  5904 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75926982_7   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAATAATCAATATTGTGAAAAT 5047
                              ii i  i     i      i v    v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75926982_7   5048 GGCCATACGGACCAAGGTTATTTATAGATTCAATACCATCCCCATCAAGC 5097
                            v    vvv    iv v  i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75926982_7   5098 TACCAATGACTTTCTTCATAGAC-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  iii   v-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75926982_7   5146 CATGGAACCAAAAAAGAGCCCGCATCGTCAAGTCAATCCTAAGCCAAAA- 5194
                         i      viiv  ii  v  v v  v i   iv     i i ivv i  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75926982_7   5195 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGAC 5244
                                i      vv    i  v  ii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75926982_7   5245 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATATATC 5294
                                 i   i    ii  i      i iv ii i   v     v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75926982_7   5295 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 5342
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75926982_7   5343 ATCTGATCTTTGACATACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5392
                          vi    i  i    vivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75926982_7   5393 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGCT 5442
                           v  i  i              v      v  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75926982_7   5443 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGTTGGA 5492
                            ii    i    v   i     v           i  i    iv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75926982_7   5493 TTAAAGACTTAATCGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5542
                          i ?    i   vi  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75926982_7   5543 TTAGGCATTACCATTCAGGACATAGGCATGGGCAA-GGTCTTCATGTCTA 5591
                         v    ?i v viv   iv   v v  vv i     -   -   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATA 595

  chrX_75926982_7   5592 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTA 5641
                         vi            vvi          vv     v  i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75926982_7   5642 ATTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGAA 5691
                           i   v v  i i   i iii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75926982_7   5692 CTAGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5741
                         vvii     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75926982_7   5742 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5791
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_75926982_7   5792 AAAATAAACAACCCCATCAAAAAGTGGGTGAAGGAAATGAGCAGACACTT 5841
                           i i   i     v  i?    i    ii     vv   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_75926982_7   5842 CTTAAAAGAAGACATTTATGCAGCCAAAAAGCACATGAAAAAATGCTCAT 5891
                           iv        i  vi viii     v             i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_75926982_7   5892 CATCACTGGCCAT 5904
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (149 / 107)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3091 26.62 0.99 1.10  chrX_75953019_75959172     4753  5661 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75953019_7   4753 TGGAAGAACATTCCATGCTCATGGATAGGAAGAAACAATATCGTGAAAAT 4802
                              ii i  i     i        v      vvi     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75953019_7   4803 GGCCATACTGCCCAAGGTAATTTATAGATTAAATGCCATCCCCATCAAGC 4852
                            v     v     iv i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75953019_7   4853 TACGAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 4901
                          v v iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_75953019_7   4902 ATGGAATCAAAAAAGATCTTGCATTGTCAAGACAATCCTAAGCCAAAAGA 4951
                               viiv  ii  i iv v  v i   i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_75953019_7   4952 ACAAAGCTGGAGGCATCATGCTACCTGCCTTCAAACTATACTACAAGGCT 5001
                               i      vv   ii  v  iivi      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_75953019_7   5002 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAGCAGAGATGTAGACCA 5051
                                i   i    ii         i iv iiii   v  i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_75953019_7   5052 ATGGAACAGAA--GAGAGCCCTCAGAAATAACACCACACATCTACAA-CA 5098
                               i    --     i  --        vv   i    i  iii-  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_75953019_7   5099 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5148
                           -    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    348 AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75953019_7   5149 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAATCT 5198
                           v  i  i              v      v  ?   i   i i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75953019_7   5199 CAAACTGGATCCCTTCCTTACACCTTATACAACAATTAATTCAAGATGGA 5248
                         v  ii    i    v   i     v       v      i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75953019_7   5249 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5298
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75953019_7   5299 CAAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATATCTA 5347
                         vv   ?i- v i -   iv   v v  vv i     v ii   v  vv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_75953019_7   5348 AAACACCAAGATCAATGGCAACAAAAGCCAAAATTGACAAATGGGATTTA 5397
                         vi       i v  vvi          vv     v  i    v   i  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_75953019_7   5398 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGGGAA 5447
                           i   v v  i i   i  ii vv    i  v    i  vv i  v   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_75953019_7   5448 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTGCCCGTCTGACA 5497
                         v  i     i                 v   i   viiiivii     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_75953019_7   5498 AAGGGCTAATATCCAGAATCTACAAAGAAATTAAACAAATTTACAAGAAA 5547
                          i  i  vi          v  i      v ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_75953019_7   5548 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5597
                           iv    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_75953019_7   5598 CTCAAAAGAAGACAATTTATGCA----GCCAAAAGACACATGAAAAAATG 5643
                            v        -----   i  ----     v ii          i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGA-----TATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_75953019_7   5644 CTCATCATCACTGGCCAT 5661
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


3083 28.41 0.44 0.44  chrX_75981224_75987625     5002  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_75981224_7   5002 TGGAAGAACATTCCATGCTCATGTGTAGGAAGAATCAATATCGTGAAAAT 5051
                              ii i  i     i     vi v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_75981224_7   5052 GGCCATACTGCCCGAGGGAATTTATAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v   i ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_75981224_7   5102 TACCAATGACTTTCTGCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i  i vii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_75981224_7   5150 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_75981224_7   5200 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGTC 5249
                                i      vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_75981224_7   5250 TACAGTAACTGAAACAGCATAGTACTGGTACCAAAACAGAGATATAGATC 5299
                                 iii i    ii i       i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_75981224_7   5300 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAACT 5347
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_75981224_7   5348 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5397
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_75981224_7   5398 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5447
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_75981224_7   5448 GAAACTGGATGCTTTTCTTACACCTTATACAAAAATTAATTAGAGATGGA 5497
                            ii    iv i vi  i     v              i vi i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_75981224_7   5498 TTAAAGACTTAAACGTCAGACCTAAAACCATAGAAACCCTAGAAGGAAAC 5547
                          i ?    i    i  v   v       i   i  vi i      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_75981224_7   5548 CTAGGCATTACCATTCAGGACATAGGCACAGGCAAGGACTTCATGTCTAA 5597
                         v    ?i v viv   iv   v v  vvi      v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_75981224_7   5598 GACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTAA 5647
                                      vvi   i      vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_75981224_7   5648 TTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTACCATCAGAGTGAAC 5697
                          i   v v  i i   i  ii vvi   i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_75981224_7   5698 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5747
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_75981224_7   5748 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5797
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_75981224_7   5798 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5847
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_75981224_7   5848 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5897
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_75981224_7   5898 ATCATGGGCCAT 5909
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (153 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3026 28.08 0.66 0.66  chrX_76039559_76046563     2656  3563 (3442)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76039559_7   2656 TAGAAAACCATTCCATGCTCCTGGGTAGGAAGAATCAATATCGTGAAAAT 2705
                          i    ivi  i     i  v   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76039559_7   2706 GGTGATACAGTCGAAGGTAATTTATAGATTCAATGCCATCCGCATCAAGC 2755
                           ii    vvi v  iv i  i  i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76039559_7   2756 TACCAACGACTTTCTTCACAGAATAGGAAAAAACT-ACTTTAAAGTTCAT 2804
                          v   i vi i  i  ii     - vvi v  i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_76039559_7   2805 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 2854
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_76039559_7   2855 ACAAAGCTGGAGGCATCACGCCACCTGACTTCAAAGTATGCTACAAGGCT 2904
                               i      vv    i iv  ii i      iiv i      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_76039559_7   2905 ACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATATAGACCA 2954
                                i   i    ii     i   i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_76039559_7   2955 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATGTCTACAACCA 3002
                               i    i--    i  --        vv  ii ii i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_76039559_7   3003 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATACCC 3052
                         vi    i  i     ivv  v   i v  vvv           i   vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_76039559_7   3053 TATTTAATAAATGTTGCTGGGAAAACTCGCTAGCCAGATGTAGAAAGCTG 3102
                          v  i  i     v        v    v v  ?   v   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_76039559_7   3103 AAACTGGATCCCTTCCTCACACCTTATACAAAAATTAATTCAAGATGGAT 3152
                           ii    i    v         v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_76039559_7   3153 TAAAGACTTAAATGTTAGACCTAAAACCATGAAAACCCTAGAAGAAAACG 3202
                         i ?    i       v   v       i  i   vi i           i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_76039559_7   3203 TAG---TCAATACCATTCAGGACATAGGCATGTGCAAGGACTGCATGTCT 3249
                            --- v   -- -   iv   v v  vv iv    v ii v v ivv 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_76039559_7   3250 GAAACACCAAAAGCAATGACAACAAAAGACAAAATTGACAAATGGGATCT 3299
                         ivi            vvii          v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_76039559_7   3300 AATTAAACTAAAGAGCATCTGCACAGAAAAAGAAACTACCAGCAGAGTGA 3349
                         v  i   v v  i i v i  ii vvv   i  v    i  iv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_76039559_7   3350 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 3399
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_76039559_7   3400 AAAGGGCTAATATCCAGAATCTGCAATGAACTCCAACAAATTTACAAGAA 3449
                           i  i  vi          v ii  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_76039559_7   3450 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 3499
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_76039559_7   3500 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAACTGCTCA 3549
                             v        i  vi viii     i ii          iv      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_76039559_7   3550 TCATCACTGGCCAT 3563
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (152 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  

2772 29.06 0.88 0.55  chrX_76039559_76046563     5608  6512 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76039559_7   5608 TGGAAAAACATTCTATATTTATGGATTGGAAGAATCAATATTGTTAAAAT 5657
                               i i  i i  i  i             v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76039559_7   5658 GGCCATACTGACCAGAGCAATCTATGGATTTGACACTGTTCCTATCAAAC 5707
                            v     vv   i vii     ii    ii  i vi i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76039559_7   5708 TACCAA-TGTCATTTTT--AGCAATTGAAAAAACT-ATTTTAAAATTCAT 5753
                          v   i-  i v     --  v      v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_76039559_7   5754 ATGGAACTAAAAAAAGAGCCTGAATAGCCGAAGAAATCCTAAGCAAAAAG 5803
                               v iv  ii-  v  v        i  iv    i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76039559_7   5804 AACAAAGCTGAAAGTATAACATTACCTGACTTCAAACTATATTACAAGGC 5853
                                i  i i vv v   i v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76039559_7   5854 TAAAGTAACCAAAATAGCATAGTACCAGTGCACAAACAGACACACAGAAC 5903
                           v     i   i i  ii i    ii iii vii i     i i   v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76039559_7   5904 AATGGAACAGAATAGATATCCCAGAAATAAAGCTACACACATAAAACCAG 5953
                                i     v  v vi           v i i   iv  viii  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_76039559_7   5954 CTGAACTTTCATAAAGTTTATATAAACAAGCAATGGGGAAAGGGCTCACT 6003
                         i   vi  iv i  i v vvi vi v  vv            iiivvv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_76039559_7   6004 ATTCAATGAATTGTACTGGGATAACTGGCTAGCCACAGGCAGAATATTAA 6053
                         v     ii   v  i      i      v  ?     v   i  v v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_76039559_7   6054 AGCTGGTCTCCTTCATTACATCATATATAAAAATCAACTCAAA-TGGGTT 6102
                           i   v i   v v i   i      i      i        -   i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_76039559_7   6103 TAAGACTTAAATGTAAAACCTACAAATATAGAAACCCTGAAAGCTAACCT 6152
                         v?    i         i v   v  v    i  vi i ii   vv   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_76039559_7   6153 AGGCA-ATACCATTCTAGACATAGGACCTGGCAAAGATTTTAT-GATGGG 6200
                            ?i- v i -   vv   v v  iiiv     v i   iv -   iv 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_76039559_7   6201 TTGCCAAAAGTAATTTCAACAAAACAAAAATT-GATAAAAGGGATCTAAC 6249
                         vii       i vvvv        v     v -      vv   ii v i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_76039559_7   6250 TAAACTAAAAAAAATTTCCTCACAACAAAATAAGCTATCAACAGAGTAAG 6299
                         i   v v     --i  iivii vv    iv vi       v i   i i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_76039559_7   6300 TAGACAACATACGGAATGGGAGAAAATATTTGCAAACTACAAGTCTGACA 6349
                         v       vi  i                       ii i vi     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_76039559_7   6350 AAGGTCTGACATCCAGAATCTATAAGATACTTAAATGAATTAACAAGCAA 6399
                          i  v  vii         v     iiv   ivv ii v i  i  vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_76039559_7   6400 AAAACAAACAATCCCACTAAAAAGTGGGCAAAGGATGTGAGCAGACACTT 6449
                           i     i  i  v i ?    i            v   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_76039559_7   6450 TTCAAAAGAAGACATACATGTGGCCAACAAGCATATGAAAAAATGCTTAA 6499
                         i  v        i     vi       i     i       i     i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_76039559_7   6500 CATCACTAATCAT 6512
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (155 / 104)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.18 (13 / 11)  


3066 27.78 0.66 0.55  chrX_76048839_76056809     4878  5784 (2187)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76048839_7   4878 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4927
                              ii    i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76048839_7   4928 GGCCATACTGCCCAAGGGAATTTATAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76048839_7   4978 TACTAA-TGACTTTCT-ACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v i i-  v    i -i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76048839_7   5024 TATGGAACCATAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5073
                                viii  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76048839_7   5074 AACCAAGCTGGAGGCATCACACTACCCGACTTCAAACTATACTACAAGGC 5123
                            v   i      vv       v   i i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76048839_7   5124 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5173
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76048839_7   5174 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5221
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_76048839_7   5222 ACCTGATCTTTGACAAACCTGAGAAAAGCAAGCAAAGGGGAAGGGATTCC 5271
                          vi    i  i     ivv  vv  i v  vv   v      i i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_76048839_7   5272 CTATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATAGGTACAAAGCT 5321
                           v  i  i     i        v      v  ?   i v i v  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_76048839_7   5322 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGTTGGA 5371
                            ii    i    v   i     v           i  i    iv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_76048839_7   5372 TTAAAGACTTAAACGTTAGACCTGAAATCATAAAAACCCTAGAAGAAAAC 5421
                          i ?    i    i  v   v  i   ii      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_76048839_7   5422 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5471
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_76048839_7   5472 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACACATGGGATCTAA 5521
                         i            vvi          vv     v  i v  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_76048839_7   5522 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5571
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_76048839_7   5572 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5621
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_76048839_7   5622 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5671
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_76048839_7   5672 AAAACAAACAACACCGTCAAAAAGTGGGTGAAGGACACGAACAGACACTT 5721
                          i -    i   v vi i?    i    ii     ivi   i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_76048839_7   5722 CTCAAAAGGAGACATTTATGCAGCCAGAAAACACATGAAAAGATGCTCAT 5771
                            v    i   i  vi viii    iv  i                  v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_76048839_7   5772 CATCACTGGCCAT 5784
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  

3302 22.57 2.68 2.01  chrX_76048839_76056809     6584  7478 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_76048839_7   6584 ATATTCCATACTCAATGATCAAAAGAAGAAATATTGTTAAAATGTTTATA 6633
                             i    ii   vv   iii    vvv           i   viv   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_76048839_7   6634 CTACCTAAAGCAATATAAAAATTCAATGCAATCTGTATCAACATTCCAAT 6683
                           v  i   vii  v  v i      i      iv      v  i   ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_76048839_7   6684 GGCATTCCTCACAGAAATAGGAAAAGC-AATCCTAAAATTCAAATGGAGC 6732
                         v  v  ii ii       -v  v    -i             v     --
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGA-- 154

  chrX_76048839_7   6733 CACAACACAAAAGACTTCAAATAGCCAAAATAATTTTAAGAAGAAAAAAC 6782
                         ---  ii   ii   iivi           i   i  i i  ii  i   
  L1M4_orf2#LINE/    155 ---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_76048839_7   6783 GAAGTTGGAGGCATCACACTTCCTGATTTCAAGTTATATTACAAAATTGT 6832
                         i          vv          ii       iviv  i      ii ii
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_76048839_7   6833 AATAATCAAAACAATGTGGTACTTGTATAAAAACAGACACATAGATCAGT 6882
                          i       i   i         v i    ii i     i        i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_76048839_7   6883 GGAATAAAATAGAGAGACCAGAAATAAATTTTAAAAA---ATCATCAACT 6929
                               i   v     v           iii- v v ---  vi    i 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCC-ATACATTTATGGTCAATT 350

  chrX_76048839_7   6930 AATTT-CAACAAGGGCACCCAAAAGAC-A--CAATGAGAAAAGGATAGTC 6975
                         i    - i       ii  ---     - --     i i    i      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCC---AAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_76048839_7   6976 TCTACAATAAATGGTGCTGAGAAAACTGGATTTCCATACACAAAAAAAAT 7025
                          i v   i           i  v        v?   i ii     i  - 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-T 446

  chrX_76048839_7   7026 GAAATTAAACCTTTATCACTCACCATATACAAAAGTTAATTCAAAATGGA 7075
                            i  ii   ii  i v v              i    i          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_76048839_7   7076 TAAGAGACCTAAATGTGAGACCTGAAACCATAAAATTCTTAGAAGAAAAC 7125
                          v ?            i   v  i    i      i              
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_76048839_7   7126 ATAGGAGAAAATCTCCTTGACATTGGTCTTGGCAACAATTTCTTGGATAT 7175
                              ? v      i v    v    vi v     iii      i     
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_76048839_7   7176 CACACCAAAATCTGAAGCTACAAAACAAAAA-TAAATAAATAGGTCTATA 7224
                         v         v vv    v      v     -  i      v  v  vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_76048839_7   7225 TCAAACT---AACCTTCTGCATAGCATCAAAA-ACA--GCCAAAAAAATG 7268
                              v ---  v   i  i---  v     i-   --ii   i   i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGT---GCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_76048839_7   7269 AAAGGGCAACCTATATATTTGAAGAGAAATATTTGTAAACCATAAGTAAA 7318
                            i i     i i v v v i   -         i   i    vi vvi
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGA-AAATATTTGCAAATCATATATCTG 742

  chrX_76048839_7   7319 ATGAGG--TTAATAGTCATGATTTATAAAGAACACATGCAACTCAATA-- 7364
                           i   --i vi  vi  vi  v          v v i          --
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_76048839_7   7365 -----GACAATATATAACCAAATTTTAAAATGGGCAAAGAACTTAAATAG 7409
                         -----     ---      v    ?v             i i  i     
  L1M4_orf2#LINE/    793 AAAAAGACAA---ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_76048839_7   7410 ACATTTTTCCAAAGACGACATAGAAATGGTCAACAGGTACATGAAAAGAT 7459
                               i        v  i   v      i   i i i            
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_76048839_7   7460 GCTCACTATTATTCATTAT 7478
                              vi  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (128 / 70)
Gap_init rate = 0.02 (19 / 901), avg. gap size = 2.21 (42 / 19)  


2957 27.49 1.66 1.00  chrX_76091879_76098266     4994  5895 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76091879_7   4994 TGGACGAATATTTCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5043
                             vii    ii    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76091879_7   5044 GGCCATACTGCCCAAGTTAATTTATAGATTCAATGCCATCCCCATCAAGC 5093
                            v     v     i  i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76091879_7   5094 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTCA 5141
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76091879_7   5142 TATGGAACCAAAAAATAGCCCACATTGCCAAGTCAATCCTAAACCATAAG 5191
                                viiv  iiv v  viv  v     iv     i i  vv v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76091879_7   5192 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATGCTACAG-GC 5240
                                i      vv    i  v  ii i      viv i     i-  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76091879_7   5241 TAC-GTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5289
                            -    i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76091879_7   5290 AATAGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5337
                            i   i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_76091879_7   5338 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5387
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_76091879_7   5388 CTATTTAGTAAATGTTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCT 5437
                           v  i ii     v        v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_76091879_7   5438 GAAACTGGATCCCTTCCTTACACCTTATACGAAAATTAATTCAAGATGGA 5487
                            ii    i    v   i     v     i        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_76091879_7   5488 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5537
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_76091879_7   5538 CTAGGCA-ATACCATTCAGGACGTAGGCATGGGCAAGGACTTCATGTCTA 5586
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_76091879_7   5587 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5636
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_76091879_7   5637 ACTAAACTAAAGAGCTTCTGCACAGGAAAAGAAACTTCCATCAGAGTGAA 5686
                          ii   v v  i i   i  ii vvv   i  v   vi  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_76091879_7   5687 CTGGCAATCTACAGAATGGCAGAAAATTTTTGCAATCTACTCACCTGACA 5736
                         vv i   i i         v       v       vii ivi i    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_76091879_7   5737 AAGGGCTAATATCCACAATCTACAATGAACTCCAACAAATTTACAAGAAA 5786
                          i  i  vi      v   v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_76091879_7   5787 AAAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGATACTT 5832
                           i    ----   v  i?    i     i      v    i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_76091879_7   5833 CTCAAAAGAATACTTTTATACA----GCCAAAAGACACATGAAAAAATGC 5878
                            v      v ----      ----     v ii          i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_76091879_7   5879 TCATCATTACTGGCCAT 5895
                            v   i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.00 (24 / 12)  


3045 26.37 1.10 1.32  chrX_76108099_76112637     3137  4046 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76108099_7   3137 TAAAAAGATATCTCATGTTCATAGTTCAGAAAAATCAATAGTATCAAAA- 3185
                          ii         i         i v ii   i v i    v i i  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76108099_7   3186 ATCCATACTTCCCAAAGCACACTACAGATTCAATGCAATTCCTATCAAAA 3235
                         iv v     i      viivv            i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76108099_7   3236 TTCCAATGGCAATTATTACAGAAGCAGAAAAATCAATCCTAAAATTTGTA 3285
                          i   iiv  vv  v  i     iiv  v  iiii           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_76108099_7   3286 TGGAATTATGATCACTACCAAG--TAGCTAAAGCAATCTTGAGCAAGAAG 3333
                              v iii vvi--   v  --    i   i         iv      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG--ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76108099_7   3334 GAAAAAGGCTGGAGGCATCATAGTTCT-GATTTCAAACTATATTACAAAG 3382
                         i v    -i      vv   i v   i-i        viv  i       
  L1M4_orf2#LINE/    199 AACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_76108099_7   3383 TTATAGTAATTGAAACAGTATGGTAGTGGT-TAAAAGCACACATACAGAT 3431
                         i  i      ii i     i     v   i-   iiii v     i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_76108099_7   3432 CAGTGAAACAGAATAAGAAGACCAGAAATAAATTGACTCATATGTGGTCA 3481
                           i  i  i     viii  v           iiv iv   v i      
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_76108099_7   3482 AATAATCTTTGAAAAAGATGCCAAAAATATAGAGTGGATAAAAGATAGTC 3531
                          v i  i  i  v  i i      i vi  vv i   iv   ii      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_76108099_7   3532 TCTTCAATAAATTGTACTGAGAAAACTGAATATCCACTTGCAATAGAATA 3581
                          i     i    v  i   i  v     i   ?    v     v     i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_76108099_7   3582 AAACTGGACATTTATCTTACTCTATACACAAAAATTAACTCAAACTGGAT 3631
                           ii     vii  i  i  v i   i                 v     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_76108099_7   3632 TAAAAGTTTAAACCTAAGACCTAAAACTGTAAAAACTCCTTGAAAAAAAA 3681
                         i ? iiii    iv     v        i     -   i v   i    -
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA- 545

  chrX_76108099_7   3682 TCATAGGGAAAAATCTCCTTGACATTGCTCTTAGA-AATAATTTTTTA-A 3729
                         -      ?iv      i v    v   vv-    i-   ii   i   - 
  L1M4_orf2#LINE/    546 -CATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGA 593

  chrX_76108099_7   3730 TATAACATCAGAAGCAAAACAAACAAAAGTAAAAATAGACAAGTGAAACT 3779
                            i   i  i     v  vv        v         i  i vii   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_76108099_7   3780 ACATCAAA-CCAAAAAGTTTC-TGCTCAACAAAAGAAACAACCAACAAAA 3827
                         v       -ii     v   i-    i--    i  v  v i   v   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAG 691

  chrX_76108099_7   3828 TGAAAAAGGCAACCTATGGAATGAAAGAAAATATTTGCAAGCCATATATA 3877
                               - i     i ii     ii               ii       v
  L1M4_orf2#LINE/    692 TGAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_76108099_7   3878 CAGTAAGGAGTTAATATTCAAAATACGTCAGGAACTCAGGCAATTAAATA 3927
                         iii     iii vi   i  i    ii v i      vvi   i v    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_76108099_7   3928 GCATAATAA-ATAAATAACCCAATTTTAAAATAAGCAAAAGACCCAAACA 3976
                         --    v  - i             ?v     ii     i  iiii  i 
  L1M4_orf2#LINE/    791 --ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_76108099_7   3977 GGCATTTTTCCAAAATAGTCATAAATATGACCAACAGGTATAAGAAAAGA 4026
                          i     i      iv  vi   v v   i    i i i i v       
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_76108099_7   4027 TGCTCAGCATCATTAATCAT 4046
                               i     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (160 / 76)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.29 (22 / 17)  


2927 27.21 1.77 1.33  chrX_76135376_76141775.rev     5006  5909 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76135376_7   5006 TGGAAGAATATTCCATGCTTATGGATAGGAAGAATCAATATCATGAAAAT 5055
                              ii    i     i i      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76135376_7   5056 GTCCATACTGCCCAAGGTAATTTATAGATTTGATGCCATCCCCATCAAGC 5105
                          v v     v     iv i  i  i     ii i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76135376_7   5106 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5153
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76135376_7   5154 TATGGAACCAACAAAGAGCGT-GCATTGCCAAGTCAATCCTAAGCCAAGA 5202
                                vii-   i ii vi- v  v     iv     i i ivv ii 
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_76135376_7   5203 AAACAAAGCTGGAGGCATCATGCTACTGGACTTCAAACTATACTACAAGG 5252
                         i       i      vv   ii  v ivi i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_76135376_7   5253 CTCCAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGAC 5302
                           v      i   i    ii         i i  ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_76135376_7   5303 CAATGAAACAGAAC--AGAGTCCTCAGAAATAATGCCGCATGTCTACAAC 5350
                              i  i    i--       --        vv  ii ii i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_76135376_7   5351 CATCTGGTCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGATTCC 5400
                           vi  i i  i     ivv  v   i v  vvv            v v-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA- 394

  chrX_76135376_7   5401 GTATTT--AATAAAT--TG-TGGGAAAACTGGTTAGCTATATGTAGAAAG 5445
                           v   --  i    --  -     v      v  ? i i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_76135376_7   5446 ATGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5495
                              ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_76135376_7   5496 GATTAAAGACTTCAATGTCAGACTTGAAACCATAAAAACCCTAGAAGAGA 5545
                            i ?    i v     v   vi i    i      vi i       i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_76135376_7   5546 ACCTAGACA-ATACCATTCAGGACAT--AGTCATGGGCAAGGACTGCATG 5592
                           v   i?i- v i -   iv   v --i  i --     v ii v v i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTA 591

  chrX_76135376_7   5593 TCTGAAACACCAAAAGCAATGGCAACAAAAGCCAAAATCGACAAATGGGA 5642
                         vv ivi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_76135376_7   5643 CCTAATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5692
                          i v  iv  v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_76135376_7   5693 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCT 5742
                             v  i     i                 v  i    vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_76135376_7   5743 GACAAAGGGCTAATACCCGGAATCTGCAATGAACTCCAATAAATTTGCAA 5792
                           i  i  i  vi  i  i    v ii  v      iv i  v ---   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAA 788

  chrX_76135376_7   5793 GAA--AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACA 5840
                         v  --    i     i     v  i?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_76135376_7   5841 GACACTTCTCAAAAGAAGACATTTATGTAGCCAA-AGACACATGAAAAAA 5889
                             i     v        i  vi vi i     - ii          i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_76135376_7   5890 TGCTCATCATCACTGGCCAT 5909
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (153 / 89)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.56 (28 / 18)  


2994 25.95 0.98 1.96  chrX_76173210_76175447      853  1769 (469)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76173210_7    853 TGGAAAGACATCCCATGTTCATGGATCACAAGAATTA-TATTTTTAAAAT 901
                                 i                 iiv    v   -    v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76173210_7    902 GACCATACTACTCAAAGAAATCTG--GATTCAAGGTAATCTCTATCAAAA 949
                          i v     v i    vvi    i--       v i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76173210_7    950 TACTAATGACATTCTTCACAGAAATAGGAAAAAAAATCCTAAAAATTTTT 999
                          v i iivi v  i  ii       v iv  ivvi         -  iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCAT 149

  chrX_76173210_7   1000 GTGGAACCACAAAAGACCCAGAATAGCCAAAGCCATCCTGAGCAAAAAGA 1049
                         i     vii   ii                 i v   i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_76173210_7   1050 ACAA-GCTGGAGTTATCACACTACCATGTTTCAAAATGTACTGCAAAGCT 1098
                             - i     vvv       v  vvi        iv    i       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_76173210_7   1099 ACAGTAA-CAAGCACAGCATGGTACTGGTATAAAAATAGACACACAGACC 1147
                                -    -    ii         i    ii       i i   i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAG-ACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76173210_7   1148 AATGAAAGAGAGGAAATAACCCAGAAATTAATATAAGAATCTACAGCCAA 1197
                             i  v   ivvi v ii        v  ivi viv  i  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_76173210_7   1198 CTTGTGTTTTACAAAAGTGCCAAGAACATTCATTGGGGAAAGAATAGTCT 1247
                         i vi v  iv    ii         v      v                 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_76173210_7   1248 CTTCAATAAATGGTGCTTTCA-AACTAGGTATCCATGTGTAGAAATATAA 1296
                         i     i          vvv -    i i  ?   ii  i i  iv  i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_76173210_7   1297 GACTAGACCCACACCTCTCATCCTACAGAAAAATCAACTCAAAATGAATC 1346
                         iii i     vi     v  i v  i v      i           i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_76173210_7   1347 AAAGACATAAATGTAAGACCCAAGACTACAAAACTACTAGAAGAAAACCC 1396
                          ?    v           v i  i    i      vi           vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_76173210_7   1397 AGGGGAAACAGTCT--AGGATATTGGTCTGGAAAAATACTTTTTGAATAA 1444
                            ? v  --i   --iv  iv    vi i iv  vvii  i  ii   v
  L1M4_orf2#LINE/    549 AGGNGTAA--ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_76173210_7   1445 GACCACGAAAGCACAGACAACCAAAGTAAAAATAAACAAATGGGATTATA 1494
                            vv i        ii    v    v       i i    v   i vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_76173210_7   1495 TCAAACTGCAAAGCTCCTTCATAGCAAAAGAAACAATCAACAGAGTGAAA 1544
                              v vv   i  ii viiivv    i  v  v     v i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_76173210_7   1545 ATACAACCTACAGAATGGGAGAAAACATTTGCAAACTACTCATCTGGCAG 1594
                          v      i                i         ii ivi     ii i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_76173210_7   1595 GGGATCAATACCCAGAATATA-AAAGACATTCAAATATCTCAACAGCAAA 1643
                             iivi  i          -     - i  vv i v     i -----
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGA-ACTCTTACAACTCAATA----- 790

  chrX_76173210_7   1644 AAAAAAAAAAAAAAAAAAATCTGATTTTAAAATGAGAAAATTATCTGAAC 1693
                         --- v     i v   v  i ii   ?v      i v   vv  i    i
  L1M4_orf2#LINE/    791 ---ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_76173210_7   1694 ATACATTTCTCAAAAGAAGACATACAAGTGGCCTAGAAATATATTTTAAA 1743
                          v         v        i      i     v v  ii i  ---i  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT---GAA 884

  chrX_76173210_7   1744 AATTGATGATCGTTATTACTAATGAT 1769
                           --    v  ivi  i ????????
  L1M4_orf2#LINE/    885 AA--GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.93 (27 / 14)  


3177 27.18 0.66 0.33  chrX_76187118_76193512     4998  5902 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76187118_7   4998 TGGAAGAACATTCCATGCTCCTGGGTAGGAAGAGTCAATATCGTGAAAAT 5047
                              ii i  i     i  v   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76187118_7   5048 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCATGC 5097
                            v     v     iv i  i  i        i  v     i    viv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76187118_7   5098 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76187118_7   5146 TATGGAACCAAAAAAGAGCCGGCATCGCCAAGGCAATCCTAAGCCAAAAG 5195
                                viiv  ii  v  i v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76187118_7   5196 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76187118_7   5246 TACAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGA--TATAGACC 5293
                                 v   i    ii         i iv ii i   --      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76187118_7   5294 AATGGAAGAGAACAGAGCACTCAGAAATAACACCACACATCTACAACCAT 5343
                                v    iv   viii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_76187118_7   5344 CTGATCTT-GACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5392
                         i    i  -     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_76187118_7   5393 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGACAGTTGA 5442
                         v  i  i              v      v  ?   i   v i viiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_76187118_7   5443 AATTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5492
                          i     i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_76187118_7   5493 AAAGACTGAAATGTTAGACCTAAAACCATAAAATCCCCAGAAGAAAACCT 5542
                          ?    iv      v   v       i      ii ii          v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_76187118_7   5543 AGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAAA 5591
                            ?i- v i -   iv   v v  vv i i   v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_76187118_7   5592 CCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5641
                         v           vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_76187118_7   5642 TAAACGAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5691
                         i   vvv  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_76187118_7   5692 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACCAA 5741
                          i     i                 v       vii ivi      iv i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_76187118_7   5742 GGCGTAATATCCAGAATCTACAATGAACACCAACAACTTTACAAGAAAAA 5791
                           vv vi          v  i  v    v iv      iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_76187118_7   5792 AACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 5841
                         i     i     v  i?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_76187118_7   5842 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCCTCA 5891
                          v        i  vi viii     v ii          i      vv  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_76187118_7   5892 TCACTGGCCAT 5902
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


2781 28.62 1.22 0.88  chrX_76194892_76198937.rev     2651  3555 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76194892_7   2651 TGGAAAAAGATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 2700
                               i v  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76194892_7   2701 GGCCATATGGCCCAAAGTAATTTATAGATTCAATGGTATCCCCATTTAGC 2750
                            v   ivv      v i  i  i        i vv     i  iv iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76194892_7   2751 TACC-TTTGTCTTTTTTTATGGAATTAGAAAAAACT-ACGTTAAATTTCA 2798
                          v  -vi  i       vvv i    i-- v  i  - ivi    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76194892_7   2799 TATATAACCAAAAAAGAGTCCACATAGCCAAGACAATCCTAAGCAAAAAG 2848
                            iv  viiv  ii  vi viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76194892_7   2849 AACAAATCTGGAGGCATCACACTACTTGACTTCAAACTATACTACAAGGC 2898
                               vi      vv       v iii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76194892_7   2899 TCCAGTAAGCAAAACAGCATGGTACTGCTACTAAAACAGATATATAGAAT 2948
                          v      v   i    ii        vi iv ii i   i       vi
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76194892_7   2949 GATGGAACAGAACAGAGGCCTCAGAAATCACACCACACATCTACAACCAT 2998
                         i      i    iv   ivii       v vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_76194892_7   2999 CTGATCTT-GACAAACCTGACAAAAACAAGAAATGGGGAAAATATTCCCT 3047
                         i    i  -     ivv  v   i v  vvv          iv  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_76194892_7   3048 ATTTAATAAATATTGTTGGGAAAACTGGCTAGCCATATGCAGACAACTGA 3097
                         v  i  i    iv  i     v      v  ?   i     i vi v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_76194892_7   3098 AACTGGACCCCTTCCTTACACCTTATACAAAAGTTAACTCAAGATAAATT 3147
                          ii         v   i     v         i         i  ii  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_76194892_7   3148 AAAGACTTAGGCATAAGACCTAAAACCATAAAAATCCTAGAGGAAAACTT 3197
                          ?    i  iiii     v       i      v  i    i      v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_76194892_7   3198 AG---TCAATACGATTCAGGACATAGGAATGGACAAAGACTTCATGAATA 3244
                           --- v   - --   iv   v v  iv i i   v ii   v ii   
  L1M4_orf2#LINE/    549 AGGNGTAAAT-C--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_76194892_7   3245 AAACACCAAA--CACAATGGCAACAAAAGCCACAATAGACAAATGGGATC 3292
                         vi        --     --          vv v      i    v   ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_76194892_7   3293 TAATTAAACTAAGGAGCTTCTGAACAGCAAAATAAACTATCATGAGAGTG 3342
                          v  i   v v ii i   i  vi vv    iv v       v  i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_76194892_7   3343 AACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACTCATCTGA 3392
                           v  i     i                vv       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_76194892_7   3393 CAAAGGGCTAATATGCAGAATCTATAAA-AATGTAAACAAATT--TACCA 3439
                         i  i  i  vi   v      v      -  ivivv    v i--  vi 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_76194892_7   3440 GAGAAACCAAACATCTTCATTGAAAAGTGGGTGAGGGATACGAACAGGCA 3489
                         i i i  -   i v iiv   ?    i    ii i    vi   i  i  
  L1M4_orf2#LINE/    794 AAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_76194892_7   3490 GTTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCT 3539
                         v     v        i  vi viii     i ii  i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_76194892_7   3540 TATCATCACTGGTCAT 3555
                         i v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (149 / 107)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


 554 28.99 0.97 2.90  chrX_76200115_76203055.rev      298   504 (2437)    L1M4_orf2#LINE/L1       30   232 (676)  

  chrX_76200115_7    298 AAAACTTAAAGTATAATAAAAAAATGGCTACATTACCTAAAGCAATGTAC 347
                           i      --   vi v  i --    v i i v  i   vii  v   
  L1M4_orf2#LINE/     30 AAGACTTAA--TATTGTTAAGA--TGGCAATACTCCCCAAATTGATCTAC 75

  chrX_76200115_7    348 AGATTCAATGCTATTCCTATCAAACTACCAATGACATTCTTTACAGACCT 397
                                 i  v  i         v v   iivi v  i   i    vv 
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chrX_76200115_7    398 AGAAAAATTG-TTTTAAAATTTATATGGAATTAATAAATCACCT-GAATA 445
                         v  v  ii  - ii       i        v i-i  ivv   i-     
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATG-CAAGGGACCCAGAATA 174

  chrX_76200115_7    446 GCCAAGGCAATCCAAAGCAAAAAGGAACAAAGCTGGAAGAATCATGTTAC 495
                              ii     ivi i-   i i        i    i  v   iii v 
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAA-AAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_76200115_7    496 CTGACTTCA 504
                          ii i    
  L1M4_orf2#LINE/    224 CCAATTTCA 232

Transitions / transversions = 1.86 (39 / 21)
Gap_init rate = 0.03 (6 / 203), avg. gap size = 1.33 (8 / 6)  

1307 22.25 3.06 19.20  chrX_76200115_76203055.rev     1412  2458 (483)    L1M4_orf2#LINE/L1       10   887 (21)  

  chrX_76200115_7   1412 ATTTCATGGTCATGCATTGGAAGATACAATATCATAAAAATGTTTCTACA 1461
                           ii    v     v         ivi     ii v  i   vivv   v
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_76200115_7   1462 AGCCAAAGCAATCTACAGACTCAGTGCTATTTCTATCAAATTACCACATG 1511
                         vv     vii         i   ii  v  ii        v v   vv  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_76200115_7   1512 GTTTTTATTCACAGAATTAGAGAAAACT-ATTCTAAAACTTATATGAAAC 1560
                         vi    -- ii     v v  v  i-  -  i      i i     i  v
  L1M4_orf2#LINE/    110 CCTTTT--TTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAA 156

  chrX_76200115_7   1561 CAAAAAAGAATACAAATAGCCAAAGCAATTTTAAAA-----GAACAAAAT 1605
                         iiv  ii  vivvi          i    i  i   -----       i 
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_76200115_7   1606 TGGAGGCATCACATTACCTGACTTCGAACTATACTATAAGACTACAGTAA 1655
                               vv     i v  ii i   i  viv     i  ii         
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_76200115_7   1656 CCAAAACAGCATGGTACTGGTACCAAAATAAGCAGATGGAACAATGGAAT 1705
                         i   i    ii         i iv ii   ii  v  i  v         
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_76200115_7   1706 AGAGTAGAGAA-CCAGAAATAAAC-------------------TGATCTT 1735
                            i v    i-            -------------------    i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_76200115_7   1736 CAACAAAC-TACACAAAAATAAACAATCGAGGAAGGAT-TTCTTATGTAA 1783
                          i    iv- i -   i vi vv    v i i   i  -v    - vi  
  L1M4_orf2#LINE/    357 CGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCTT-TTCAA 404

  chrX_76200115_7   1784 TAAATGTTTCTGAGAAAAGTAGCTAACCATAAGCAGAATAATGAAAC--A 1831
                         i     v v   i  v  v i v  ?   i v   i  v      ii--i
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_76200115_7   1832 ATTTCTACGTTTCTTCCATATAGAAAAATTAACTCTACATGGATTAAAGA 1881
                          iii    -i iviv       v            v v      i ?   
  L1M4_orf2#LINE/    455 ACCCCTAC-CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_76200115_7   1882 CTTAACAATAAACCCTCAAACTATAAAAATCCTAGAAGTAAACCTATGAA 1931
                          i   vvi   ivv  v           v  i      v    -------
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC------- 546

  chrX_76200115_7   1932 ATACCCTTCTTTTTATTTATTTCTTACTTTTTTTTTTTTTTTATAGACAC 1981
                         ------------------------------------------    ----
  L1M4_orf2#LINE/    547 ------------------------------------------ATAG---- 550

  chrX_76200115_7   1982 TGGGTCTCACAATGTTGCCTAGCCTGGGCTTGAACTTCTGGGCTCAGGTA 2031
                         - ?  --- -   v  ------------ v   v   --   i -   i 
  L1M4_orf2#LINE/    551 -GNGT---A-AATCTT------------CGTGACCTT--GGGTT-AGGCA 580

  chrX_76200115_7   2032 ATCCACCGGCCTCAGCCTCCTAAATTGCTAGAATTACAGTCATGAGCCAC 2081
                           -----------i ii  i  i  ----------------    -----
  L1M4_orf2#LINE/    581 AT-----------GGTTTCTTAGAT----------------ATGA----- 598

  chrX_76200115_7   2082 TGCACCTTGCCTGTAAATATTCTTGAAATCAGCCTTGGCCAGAATTTCTT 2131
                         --    --------------------------------------------
  L1M4_orf2#LINE/    599 --CACC-------------------------------------------- 602

  chrX_76200115_7   2132 TTGGCTAAGTCCCCAAAAGCA-ATACAACAAAACCAAAAATTGACAAGTT 2180
                         --------------       - vi        vv      v  i  i  
  L1M4_orf2#LINE/    603 --------------AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_76200115_7   2181 GAACCTAATTTACCTAAAGATCTTCTGTAACCAAATTAACTGAAAGAACT 2230
                          i  i v  --------------------- v       ------i    
  L1M4_orf2#LINE/    639 GGACTTCAT---------------------CAAAATTAA------AAACT 661

  chrX_76200115_7   2231 TCTGCACAGCAAAAGGAACTATCAGCAGAGCAAACAGACAACCTACAGAA 2280
                          i  ii vv    i iv       iv i  ii  v        i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_76200115_7   2281 TGGGAGAAAATATTTGCCACCTATGCATCGAAAAAAACGACTAATACTCA 2330
                                          v vii  ii   vi v  ii-    vi  ii  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGG-GACTTGTATCCA 760

  chrX_76200115_7   2331 GAATCTATAAAATACTTACACAAATCAACAAGAAAAA-ACAAATAATGCC 2379
                             v      iv   ivi    v    i  v     -        iv v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_76200115_7   2380 ATTAAAAAGTGGGTCAAAGGACAAAAACAGATCCTTCTGAAAAGATGTTA 2429
                            ?    i    -       ivvi  i   ivi    vv     v v  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGG-CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_76200115_7   2430 TAGAAGTGGCTAATGTAAAAAATGGAAAG 2458
                           v  i    i   i- iv v   i    
  L1M4_orf2#LINE/    860 TACAAATGGCCAATA-AGCACATGAAAAG 887

Transitions / transversions = 1.39 (133 / 96)
Gap_init rate = 0.03 (30 / 878), avg. gap size = 7.77 (233 / 30)  


2813 28.30 0.99 0.99  chrX_76229993_76234202     2810  3717 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76229993_7   2810 TGGAAAAACATTCCATGCTCATGGATAGGAAGAAGCAATATCGTGAAAAA 2859
                               i i  i     i        v      vvi     i  v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76229993_7   2860 GGCCATACAGCCCAAAATAATTCATAGATCTGGTGCTATTCCCATCAAAC 2909
                            v    vv      v i  ii i    iiiii  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76229993_7   2910 TACCATTGACACTCTTCACAGAATTAGAAAAATCT--TCTTTAAATTTTA 2957
                          v   vivi vi i  ii     v v  v  i-  --  i v     i- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC-A 148

  chrX_76229993_7   2958 TATGGAATCTTAGGTGACCCCATAGAGCAAAGACAATCCTAAGCAAAAAG 3007
                                vivi i v     viv v   v  i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76229993_7   3008 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3057
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76229993_7   3058 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATACAAACC 3107
                                 i   i    ii         i iv ii i       i i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76229993_7   3108 AATTGAACAGAACAGAGACCTCAGAAGTAACACCACACATTTACAACCAT 3157
                            v   i    iv    vii     i   vv   i       iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_76229993_7   3158 CTGATCTTTGACAAACCTGGCAAAAACAAGCAATGGGGAAAGGATCTTCT 3207
                         i    i  i     ivv  v   i v  vv            i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_76229993_7   3208 ATTAAATTAGTGGTGCTGGGAACACTGGCTAGCCATATGCAGAAAACAGA 3257
                         v  v  iv i           vv     v  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_76229993_7   3258 AACTGGACCTTTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 3307
                          ii      ii v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_76229993_7   3308 AAAGACTTAAACGTAAAACCCAAAACCATAAAAACTATAGAAGAAAATTT 3357
                          ?    i    i    i v i     i      viiv          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_76229993_7   3358 AGGCA-ATACCATTCTGGACATAGGCATGGGCAAAGACTTCCT-GATGAA 3405
                            ?i- v i -   vv   v v  vv i     v ii   i -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chrX_76229993_7   3406 AATGCCAAAAGCAATTGCAACAAAAGCCAAAATCGACAAATGGTATCTTG 3455
                         i ii         vvv          vv     v  i    v v ii ii
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_76229993_7   3456 TTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTGTCATCAGAGTGAAC 3505
                          i   v v  i i   i iii vv    i  v   i   vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_76229993_7   3506 AGGCAACTTACAGAATGGGAGAAAAATTTTGCAATCTACCCATCTGACGA 3555
                           i    ii                vv       vii ivi      ii 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_76229993_7   3556 AGGGCTAATATCCAGAATTTACGAGGAACATTAACAAATTTACAAGGAAA 3605
                         i  i  vi          v  ii i    vi v    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_76229993_7   3606 CAAACAAACAACACCATCAAAAAAGGGGCAAAGAATATGAACAGACACTT 3655
                         - i     i   v v  i?     v        i  v    i     i  
  L1M4_orf2#LINE/    797 -AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_76229993_7   3656 AGCAAAAGAAGACCTTTTTGCA----GCCAACAAATATATGACAAAA-GC 3700
                         vv v        ---- v i  ----     i  ii i    v  i -  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_76229993_7   3701 TCAACATCACTGCTCAT 3717
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (147 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  

 270 21.74 0.00 0.00  chrX_76229993_76234202     3740  3808 (402)    L1M4_orf2#LINE/L1      840   908 (0)  

  chrX_76229993_7   3740 ACACTTTTCAAAAGAAGACATTTACATGGTCAACAAACATATGAATAAAA 3789
                            i  i  v        i  vi v    i   i  i  i     v i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_76229993_7   3790 GCTCAACAGCACTGATCAT 3808
                                 v  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.00 (0 / 0)  


2938 25.88 2.21 2.21  chrX_76240365_76245256     3496  4399 (493)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_76240365_7   3496 AATATATTCCATGCTCACATATTGGAAAAAAATCAATAGTGTTAAGATAT 3545
                           v    i     i   iiv       i v-- i    v         iv
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGAC--TTAATATTGTTAAGATGG 52

  chrX_76240365_7   3546 TTATACCACCCAAAGCAATCTACAGATTTCATACAATGCCTATCAAAATA 3595
                         iv    iv      vii           iv ii    v           v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_76240365_7   3596 CCGAGGT-CATTCTTCATAAAAATATTAATAGAAAAAACAATTCTAAAAT 3644
                           -  v - v  i  iii i    ----- -  v  ivii  i       
  L1M4_orf2#LINE/    103 CC-AGCTGCCTTTTTTGCAGAAAT-----T-GACAAGCTGATCCTAAAAT 145

  chrX_76240365_7   3645 TGATATGGAACCACAAAAACCCCAGAGTCACCAAAGTTATCCTAAGTGAA 3694
                          v        vii   iiiv      i vi     iiv   i i ivi i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_76240365_7   3695 CAGAACAAACCTGGAAAAATCACATTATCTGACTTCAAACTATACTACAA 3744
                         v        vi    ii v     i vi ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_76240365_7   3745 AGCTACAGTAACCAAGACAGCATGGTACTGGCATAAAAACAGACATGTAA 3794
                                    i        ii              ii i      i  i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_76240365_7   3795 ACCAATGGAACAGAACGGAGAACCCAAAAACAAACCTACAGACCTGCAGT 3844
                          i        i    iv    ii   i   i     i i v ii iii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_76240365_7   3845 GAACTGATTTTGTACAAAGGTGCCAAGAACATACACTGGGGAAAAGACAG 3894
                         v  i       vv    i          v   v  v        ii i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_76240365_7   3895 TCTTTTCAATAAGTGATGCTGAAAAAAAACTGTATATTCATATGCAGAAG 3944
                                  i  i  i     ii v  --   v   ?i  i     i   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAA--CTGGATAKCCACATGCAAAAG 443

  chrX_76240365_7   3945 AATGAAACCAGACACCTGTCTCTCACCATATATAAAAATCAAATCCAAAT 3994
                               iiii   v   ii   v         i      i  v  v    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_76240365_7   3995 GGATTGATGACTGAAATATAAAATCTCAAACTGTGAAACTACTACAAGAA 4044
                             ii?v   iv    i   i v  v     i i     vi  v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_76240365_7   4045 AGCATTGGG--AAACTTCTCCA-GATCATTGGTCTGGTCCAAAAATTTTT 4091
                          i   v  ?--   --   i i-  i v v   iv  --   vii   i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGG--CAATGGTTTCT 589

  chrX_76240365_7   4092 TTAGTA-ATCACC-----CACAATTTA----AGTAAAAATGGACAAATGG 4131
                          vii  -iv    -----     viv ----  v      i  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_76240365_7   4132 AATCACATTGAG-TTAAAAATCTTCTGTACAGCAAATAATACAATCAATG 4180
                         i iiv   ii i-       -   i   i vv    vi i  v     vi
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_76240365_7   4181 ATGTGAAGAGACAACCAACAGAATGGGAGAAAATATTTGCAAACTACCTA 4230
                          v     i        v                          ii iv  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_76240365_7   4231 TCTGACAAGGGATTAATAACTGGAATATATCAGCAGCTCAAACAGCT--G 4278
                              i      i vi  v ii        v iv i   vv   i  --i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_76240365_7   4279 TAG--AGAAAACTCTTTAATAATCCAATCAAAAAATTGGCTAAAATTTTT 4326
                           i-- i  i  v----     i     i?      v   v  iiv   v
  L1M4_orf2#LINE/    789 TAATAAAAAGACA----AATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_76240365_7   4327 AATAGACAGTTTTCAAAAGAAGACATA-AAATGGTAAACAGGCATATGAA 4375
                                 v  i  v        i   -      iv  i i   i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_76240365_7   4376 AAGCTGCTCAACATCACTGATCAT 4399
                            v            ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (148 / 82)
Gap_init rate = 0.02 (19 / 904), avg. gap size = 2.11 (40 / 19)  


3262 27.09 0.44 0.44  chrX_76246911_76253189     4879  5786 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76246911_7   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76246911_7   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATTCCCATCAAGC 4978
                            v     v     iv i  i           i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76246911_7   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76246911_7   5027 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76246911_7   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTGCAAGGC 5126
                                i      vv       v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76246911_7   5127 TACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGACATAGATC 5176
                                 i   i    ii   i     i iv ii i   v i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76246911_7   5177 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCACATATCTACAACT 5224
                                i    i--    i  --    i   vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_76246911_7   5225 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_76246911_7   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTACAAAGCT 5324
                           v  i  i              v      v  ?   i v i v  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_76246911_7   5325 GAAACTGGATCCCTTTCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    vi  i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_76246911_7   5375 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAATCCCTAGAAGAAAAC 5424
                          i ?    i    i  v   v       i      ii i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_76246911_7   5425 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_76246911_7   5475 ATCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5524
                         iv           vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_76246911_7   5525 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5574
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_76246911_7   5575 AGGCAACCTACAGAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5624
                           i     i                 v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_76246911_7   5625 AGGGCTAATATCCAGAATCTACAATAAACTCAAACAAATTTACAAGAAAA 5674
                         i  i  vi          v  i  vi     vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_76246911_7   5675 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_76246911_7   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5774
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_76246911_7   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 692 23.87 10.70 3.70  chrX_76270799_76277006      244   486 (5722)    L1M4_orf2#LINE/L1      272   531 (377)  

  chrX_76270799_7    244 ACTAGCAGTGAAAAAAAACAGACAAAGACCAATGGAAGAGAGGAGAGAAC 293
                            i   - i ii v i   v i --  i        v   ivv    ii
  L1M4_orf2#LINE/    272 ACTGGCA-TAAGGATAGACATATA--GATCAATGGAATAGAATTGAGAGT 318

  chrX_76270799_7    294 CCAGAAA-AAAGCCACACACCTACAATCATCTGATCTTTGACAAAG---T 339
                                -   v   i   ii  iii   vi    i  i     i ---i
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_76270799_7    340 CAAGAGTAACAAGCAATGTGGCAAGGATTCTCTATTCAACAAATGGTCCT 389
                              v---  vv     v  v   i  vv   v             v  
  L1M4_orf2#LINE/    369 CAAGAC---CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_76270799_7    390 GGGATAACTGGCTAGCCATATACAGAAGATTGAAACTGGACCCCT----- 434
                             i      v  ?   i  i  i    v    ii         -----
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_76270799_7    435 -----------------TAACTCAAGACAGATCAAAGACTTAAATACAAA 467
                         -----------------        i ii     ?    i     ii  i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_76270799_7    468 ACCTTTAAAAGCTATGAAA 486
                          v  ---   i    i   
  L1M4_orf2#LINE/    516 AGCT---AAAACTATAAAA 531

Transitions / transversions = 1.95 (37 / 19)
Gap_init rate = 0.03 (7 / 260), avg. gap size = 5.00 (35 / 7)  

3168 25.88 1.66 1.22  chrX_76270799_76277006     4818  5721 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76270799_7   4818 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4867
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76270799_7   4868 GGCCATACTACCCAAAGTAATTTATAGATTCAATGCCTTCCCCATCAAGC 4917
                            v     v      v i  i  i        i  vv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76270799_7   4918 TACCAATGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTGAAGTTCA 4965
                          v   iivi i  i  ii    i-   -- v  i  - iii i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76270799_7   4966 TATGGAACCAAAAAAGGG-CCCA-AATTGCCAAGACAATCCTAAGCCAAA 5013
                                -- viv     -    -   v     i      i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_76270799_7   5014 AGAACAAAGCTGGAAGCCTCACGCTACCTGACTTCAAACTATACTACAAG 5063
                                  i    i v     i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_76270799_7   5064 GCTATAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5113
                             i     v   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_76270799_7   5114 CCAATGGAACAGAGC--AGAGCCCTCAGAAATAACATCACACATCTACAA 5161
                         i        i   ii--    i  --        vvi  i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_76270799_7   5162 CCATCTTATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 5211
                         i  vi v  i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_76270799_7   5212 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACAGGTAGGAAG 5261
                         vi  v  i  i              v      v  ?     v i ii ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_76270799_7   5262 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5311
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_76270799_7   5312 GATTAAGGACTTACATGTTAGACCTAAAACCATAAAATTTCTAGAAGAAA 5361
                            i ?i   i  v    v   v       i      i ii         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_76270799_7   5362 ACCTAGGCA-ATACCATTCAGGACATAGGCATGTGCAAGGACTTCATGTC 5410
                           v    ?i- v i -   iv   v v  vv iv    v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_76270799_7   5411 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5460
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_76270799_7   5461 TAATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5510
                          v  i   v i  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_76270799_7   5511 AACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACTCATCTGA 5560
                           v  i     i                vv       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_76270799_7   5561 CAAAGGGCTAATATCCAGAATCTACAATGAACTC--A-AATTTAA-AAGA 5606
                         i  i  i  vi          v  i  v      -- -  i i  -  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_76270799_7   5607 AAAAAACAGACAATCCCATCAATAAGTGGGTGAAGGATATGAACAGACAC 5656
                             i   i i  i  v  i? v  i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_76270799_7   5657 TTCTCAAAAGAAGAGGTTTATGCA----GCCAACAGACACATGAAAAAAT 5702
                              v        ----   i  ----     i ii          i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_76270799_7   5703 GCTCAACCTTCCTGGCCAT 5721
                                v iv????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (142 / 88)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  


 242 27.19 3.51 3.51  chrX_76285163_76291854      152   265 (6427)    L1M4_orf2#LINE/L1       42   155 (753)  

  chrX_76285163_7    152 TGTGAAAATAGACTAATACACTTCCCAAAGAAATCTACAGATTCAATGCC 201
                            v  i  i --i     -- i      vvi              i  v
  L1M4_orf2#LINE/     42 TGTTAAGATGG--CAATAC--TCCCCAAATTGATCTACAGATTCAACGCA 87

  chrX_76285163_7    202 ATTCCTATCAAATTAGCAATGACATTATTCCCAGAGTTAGA-AAG---AA 247
                           i         v vv  iivi v  v  iv    iv v  -   --- v
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chrX_76285163_7    248 ACTATAATTTATATAAAA 265
                         v   v    i    ii  
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAA 155

Transitions / transversions = 0.94 (15 / 16)
Gap_init rate = 0.04 (4 / 114), avg. gap size = 2.00 (8 / 4)  

2523 26.35 5.29 3.04  chrX_76285163_76291854     5312  6199 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76285163_7   5312 TGGAAAAACATTCCATCCTCATCGACAGGAAAAATCAATGTCATGAAAAT 5361
                               i i  i    vi    v  iv    i v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76285163_7   5362 AGCCATACTGCCCAAAGTAATTCATAGATTCAATGCTATTCCCATCAAAC 5411
                         i  v     v      v i  ii i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76285163_7   5412 TACCATTGACATTCTTCACAGAATTAGAAAAAATTTAAATTTCATATGGA 5461
                          v   vivi v  i  ii     v v  -------i  ii -------  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-------CAAGCT-------GA 136

  chrX_76285163_7   5462 TCAAAGAAAAATTTAAATTTCATATGGA--T-CAAAGAAAATCTCGTATA 5508
                           ----------i    v          -- -   i i --i iv v   
  L1M4_orf2#LINE/    137 TC----------CTAAAATTCATATGGAAATGCAAGGGA--CCCAGAATA 174

  chrX_76285163_7   5509 GCCAAGACAATCCTCACCAA-AAGAACAAAGCTGGAGGCATCACGCTACA 5557
                              i      i v vv  -          i      vv    i  v v
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_76285163_7   5558 TGACTTCAAACTATATTACAAGGCTACA---------------------- 5585
                         ii i      viv  i     i      ----------------------
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_76285163_7   5586 ----------------CATAGATCAATGGAATAAAATAGAGACCTCAGAA 5619
                         ----------------i                i   v    vii     
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_76285163_7   5620 ATAACACCACACATCTACA-CCATCTGATCTTTGACAAACATGACAAAAA 5668
                             vv   i    i  ii-i  vi    i  i     ivi  v   i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chrX_76285163_7   5669 CAAGCAATGGGGAAGGA-TCTCCTGTTCAACAAATGGTGCTGGTAAAACT 5717
                           vv          i  - vvi  v                  v v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_76285163_7   5718 GGCTAGCCATATGCAGAAAACTGAAACTGGACCCCTTCCTTACATCTTAT 5767
                           v  ?   i     i  i v    ii         v   i   i v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_76285163_7   5768 ACAAAAATTAACTCAAGATGGACTGAAGACTTAAATATACACCCCAAAAC 5817
                                         i     iii?    i     i  vivv i     
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_76285163_7   5818 CATAAAACCCT-AAAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGC 5865
                         i       i  - i        v    ?i- v i -   iv   v v  v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

  chrX_76285163_7   5866 ATGAGAAAAGACTTCATGACTAAAACACCAAAAGCGATGGCAACAAAAGC 5915
                         v ii v  v ii   v iiv  vi           ivvi          v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_76285163_7   5916 CAAAGTTGACAAATGGGATCTAACTAAACTAAAGAGCTTCTGGACAGTAA 5965
                         v   i v  i    v   ii v ii   v v  i i   i  vi vvi  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_76285163_7   5966 AAGAAACTATCATCAGAGTGAACATGCAACCTACAGAATGGGAGAAAATT 6015
                          i  v       vv i      v vi     i                 v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_76285163_7   6016 TTTGCAAGCTACCCATCTAACAAAGGTCTAATATCCAGAATTTACAAGGA 6065
                                iii ivi    i i  i  v  vi          v  i  i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_76285163_7   6066 ACATAAACATATTTACAAGGAAAAAACAAACAACCCCATCAAAAAGTGGG 6115
                           vivv   vv iv i  vi    i     i     v  i?    i    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_76285163_7   6116 CAAAGGATATGAACAGACACTTATCAAAAGAAGACATTTAGATGGTCAAC 6165
                                 v    i     i  v  v        i  vi i    i   i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_76285163_7   6166 AAATATATGAAAAAA-GCTCAACATCACTGATCAT 6199
                           ii i       i -           ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 5.29 (74 / 14)  


3079 27.78 0.66 0.55  chrX_76307358_76313471     4715  5621 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76307358_7   4715 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4764
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76307358_7   4765 GGCCATACTGCCCAAGGTAATTTATACATTCAATGTCATCCCCATCAAGC 4814
                            v     v     iv i  i  i v      i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76307358_7   4815 TGCCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4862
                          v   iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76307358_7   4863 TATGGAACCAAAAATGAGCCCACATTTCCAAGACAGTCCTAAGCCAAAAA 4912
                                viiv  iv  v  viv  vv    i   i  i i ivv i  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76307358_7   4913 AACAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATACTGCAA-GC 4961
                                i      vv   ii  v  ii        viv    i   -  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76307358_7   4962 TACAATAACCAAAACAGCATGGTACTGTTACCAAATCAGAAATATAGACC 5011
                             i   i   i    ii        vi iv iivi   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76307358_7   5012 AATGGAACAGAAC--AGAGCCCTCAGAAGTAACACTGCACATCTACAACC 5059
                                i    i--    i  --    i   vv iii    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_76307358_7   5060 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCC 5109
                          vi    i  i     ivv  v   i v  vv       i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_76307358_7   5110 CTATTTAATAAATAGTGCTGGGAAAACTGGCTAGCCACATGTAGGAAGAT 5159
                           v  i  i    i         v      v  ?       i ii ii  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_76307358_7   5160 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGA 5209
                            ii    i    v   i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_76307358_7   5210 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5259
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_76307358_7   5260 CTAGGCA-ATACCATTCAGGAAATAGGCATGGTCAAGGACTTCATGTCTA 5308
                         v    ?i- v i -   iv  vv v  vv i v   v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_76307358_7   5309 GAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGATCTA 5358
                         vi            vvi          vv     v       v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_76307358_7   5359 ATTAAAGTAAACAGCTTCTGCACAACAAAAGAAACTACCATCAGAGTGAA 5408
                           i   i v  v i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_76307358_7   5409 CAGGAAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5458
                         v  iv    i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_76307358_7   5459 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5508
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_76307358_7   5509 AAAACAAACAACCCCATCAAAAAGTAGGCAAATGATATGAACAGACACTT 5558
                           i     i     v  i?    i i      v   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_76307358_7   5559 CTCAAAAGAAGACGTTTATGCAGCCAAGAGACACATGAAAAAATGCTCAT 5608
                            v        ii vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_76307358_7   5609 CATCACTGGCCAT 5621
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


 669 28.36 2.49 0.50  chrX_76321534_76329370      300   500 (7337)    L1M4_orf2#LINE/L1        1   205 (703)  

  chrX_76321534_7    300 TGGAAAGACATCTCATGATCATGGATTAGAA---TTAATATTGTTTAAAT 346
                                 i   i    v         i   ---           v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76321534_7    347 TCCCATACTATCCAGGGCAATCTCTAGATTCATTACAACCCCTATCAAAA 396
                         vv v     vi   iivii    vi       vii   i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76321534_7    397 TACCAATGGCATTCTTCACAGAAATAGAAAAAACAATTT--AAATCTGTA 444
                          v   iiv  v  i  ii       v  v  ivii  ii--    iii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_76321534_7    445 TGGAACCAAGAAAGATCCCAAATAGCCAAACCAATTCTGAGCAACAAAGA 494
                              viivi ii  i  vi          v    ii   iv  -i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA-GAAGA 199

  chrX_76321534_7    495 ACAAAG 500
                               
  L1M4_orf2#LINE/    200 ACAAAG 205

Transitions / transversions = 1.85 (37 / 20)
Gap_init rate = 0.01 (3 / 205), avg. gap size = 2.00 (6 / 3)  

3220 26.26 0.66 0.88  chrX_76321534_76329370     4981  5890 (1947)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76321534_7   4981 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5030
                              ii    i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76321534_7   5031 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCTATCAAGC 5080
                            v     v     iv i  i           i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76321534_7   5081 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5128
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76321534_7   5129 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5178
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76321534_7   5179 AACAAAGCTGGAGGCATCACTCTACCTGATTTCAAACTAGACTACAAGGC 5228
                                i      vv    v  v  ii        vivv       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76321534_7   5229 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5278
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76321534_7   5279 AATGAAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5326
                             i  i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_76321534_7   5327 ATCTGATCTTTGACAAACCTGACAAAAACTAGAAATGGGGAAATGATTCC 5376
                          vi    i  i     ivv  v   i v vvvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_76321534_7   5377 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5426
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_76321534_7   5427 GAAGCCGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5476
                             ii   i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_76321534_7   5477 TTAAAGACTTACATGTTAGACCTAAAACCATAAAACCCCTAGAAGAAAAC 5526
                          i ?    i  v    v   v       i       i i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_76321534_7   5527 CTAGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCATGTCTA 5575
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_76321534_7   5576 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5625
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_76321534_7   5626 ATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 5675
                           iv  v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_76321534_7   5676 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5725
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_76321534_7   5726 AAGGGCTAATATCCACAATCTACAATGAACTCAAACAAATTTACAAGAA- 5774
                          i  i  vi      v   v  i  v      vv    v ---   v  -
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAAT 792

  chrX_76321534_7   5775 AAAAAAACAAACAACCCCATCAAAAAGTAGGCAAACGATATGAACAGACA 5824
                              i     i     v  i?    i i      v   v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_76321534_7   5825 CTTCTCAAAAGAAGACGTTTATGCAGCCAAGAGACACATGAAAAAATGCT 5874
                         i     v        ii vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_76321534_7   5875 CATCATCACTGGCCAT 5890
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  

2213 25.55 2.35 1.66  chrX_76321534_76329370     6621  7344 (493)    L1M4_orf2#LINE/L1      180   908 (0)  

  chrX_76321534_7   6621 AATAATTT---AAAAAAAGAACAAAGCTGGAGGCATCACACTACTGGACT 6667
                           i   i ---    i          i      vv       v ivi i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_76321534_7   6668 TAAAAATATACTAAAAAACACTAGTAATTAAAACAGCTTAATGCTGGTAC 6717
                          v    iv     v   i vvi      i  i    iv ii i    i i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_76321534_7   6718 AAAGACAGATGCACAGACTCATGTACCAAAATACGGAACACAGAAATAAT 6767
                           i  i   iii i   iiv   v vi i   vvi  iiv         v
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_76321534_7   6768 GCCATATGTTTACAGCCAACTGATTTTCCAAGAAGGTGCTGAGAGCATAC 6817
                         v     ii    ii i   i        v vi i     ii   v   v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_76321534_7   6818 ATTGGGCAAAGGACATTTTCTTCAATAAGTGGTGCTGAGAAAACTGTACA 6867
                          v    v    i i v i i     i  i        i  v     v i 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_76321534_7   6868 TCCATATGCAAAATAATGAAACAAGACCACCATCTCTCGCCATTTACAAA 6917
                         ?   i        v      iivi    v i i   v i    v      
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_76321534_7   6918 AGTCAACCCAACAT-----AAAGGCTTAAACATAAG-GCCAGAAACTAGA 6961
                          i i   i   v  ----- ?  i i    ii    -  i -      v 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATA 528

  chrX_76321534_7   6962 AAACTACTTTAAGAAGAAAATAAAAGAG-AAATGCTTCAGGTAA--TTGG 7008
                              -   --         i v i ? -    -    --  i --    
  L1M4_orf2#LINE/    529 AAACT-CTT--AGAAGAAAACATAGGNGTAAAT-CTTC--GTGACCTTGG 572

  chrX_76321534_7   7009 TCTAGGCAAAGAT--CTTATGCTAAGACTACAAAAGCACAGGGAACAAAA 7056
                         vi       v i --    - v  v   vv          i v       
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTA-GATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_76321534_7   7057 ACAAAAATAGACAAACGGGACTATATTAAACTGAAAATCTTCTACACAGC 7106
                         iv         i   iv     vi  i   v v    v   i iii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_76321534_7   7107 AAAGAAAGCAATGAAATCAGT--AGAGACAATCCCTTCTGAATGGGAGAA 7154
                             i vi v  v  ivv   -- i      i  v-- v           
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCA--CAGAATGGGAGAA 719

  chrX_76321534_7   7155 AAGAGCTGTAAACTATTCCTCTAAGAGGGGACTAATATCCAAAATACACA 7204
                           v vi  i   ii  viv   i v i      vi      i    i i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_76321534_7   7205 AGGAACTCAAATGACTCAACAACAAATAAAAAAATTAATCCCATTAAAAA 7254
                          i      vv ii      i  i   v i v    -  i  v   ?    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAAT-AACCCAATTWAAAA 818

  chrX_76321534_7   7255 GTGGGCAAAGGATCTGAATACAGATTTGTCAAAAAGAAGATACATAAATG 7304
                         i            i      v v    v  v   -       i i     
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAA-GAAGATATACAAATG 867

  chrX_76321534_7   7305 GCCAAAAAGCATGTGAAAA-ATGCTCAACATCACTAATCAT 7344
                              v     ii      -             ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (108 / 73)
Gap_init rate = 0.02 (17 / 729), avg. gap size = 1.71 (29 / 17)  


2465 23.56 2.12 10.31  chrX_76329705_76335617.rev     4441  5429 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76329705_7   4441 TGGAGAAACATTTCATGCTCATGGATGGGAAGTATCAATATCATGAAAAT 4490
                             i i i  ii    i        v     vv i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76329705_7   4491 GACCATGCTTCCCAAAGTAATTTATTGATTCAATGCTATTCCCATTAAAA 4540
                          i v  i  i      v i  i  iv       i  v  i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76329705_7   4541 TACCATTGGCATTCTTCACAGAATTGGAAAAACT-ATTTTAAAAGTTATA 4589
                          v   viv  v  i  ii     v v  v  i  -  ii     v i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_76329705_7   4590 TGGAACTAAAAAAGATCCCAAATAGCCAAGTGAACCCTAAGCTAAAAGAA 4639
                              v iv  ii  i  vi         ivv  i i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_76329705_7   4640 CAAA--CGGAGACATCACACTACCTGACTTCAAACTATACTACAAAGCTA 4687
                             --i    ivv       v  ii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_76329705_7   4688 CAGTAACCAAAACAGAGTGGTACTGGTACAAAAACAGACACATAGACCAA 4737
                               i   i    v          i i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_76329705_7   4738 TGGAACAGAAT-GAGAACCCAGAAATAAGACTGCACACCTACAACCATCT 4786
                              i     -    ii          iv iii   ii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_76329705_7   4787 GATCTTTGACAAACCTGACCAAAAGGAG-CAATGGGGAAAGTATTTCCTA 4835
                            i  i     ivv  -    i vv v-            v  vvi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_76329705_7   4836 TTTAA--AATGGTGCTGGGAGAACCAGCTAGCCACTGGCTAGCTGAAAAC 4883
                           i  --             v   ii v  ?    ---------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCAC--------------- 434

  chrX_76329705_7   4884 TGAAAACTGGAACCCTTCCTTACATCATATACAGAAAACTGAAACTGGAA 4933
                         --------------------------------------------------
  L1M4_orf2#LINE/    435 -------------------------------------------------- 434

  chrX_76329705_7   4934 CCCTTCCTTACATCATATACAGAAAATTGAAACTGGAACCCTTCCTTACA 4983
                         ----------------  i  i  i v    ii    v    v   i   
  L1M4_orf2#LINE/    435 ----------------ATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_76329705_7   4984 TCATATACAAAATTTAACTCAAGAAGGATTAAAGACTGAAATATAAAACC 5033
                         i           v         i v    i ?    iv    i   i v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_76329705_7   5034 CCAAACTATAATAACCCT-AGAAGAAAATCTAGGCA-ATATCATTTGTGA 5081
                         iv         -   i  -         iv    ?i- v   -  i    
  L1M4_orf2#LINE/    519 TAAAACTATAA-AACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGA 566

  chrX_76329705_7   5082 TGTAGGCATGGGCAAAGATTTC------ATGACAA-AAAAGCCAAAGCAA 5124
                         iv v  vv i     v i    ------      v-      vv      
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_76329705_7   5125 TTGATACAAAAGCCAAAATTGACAAATGGGATCTAGTTAAAGTGA----- 5169
                         ------      vv     v  i    v   ii vi i   i v -----
  L1M4_orf2#LINE/    617 ------CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_76329705_7   5170 TTCTGTGCAACAGAAGAAATGATCATCAGAGTGAACAGACAACTTACAAC 5219
                           i     vv  i i  v iv    vv i      v       ii   iv
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_76329705_7   5220 ATAGGAGAAATTTTTTGCAATCTATCCATCTGACAAAGGTCTAATGTCCA 5269
                           i       v v       vii  vi      i  i  v  vi i    
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_76329705_7   5270 GAATCTAGAAGGAGCTTAAACAAATCTACAAGAAAAAAAAAACAAACAAC 5319
                             v  v  i  i  ivv    --  -   v  v     i     i   
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAA--CT-CAATAATAAAAAGACAAATAAC 807

  chrX_76329705_7   5320 AACAAGCCTATTAAAAAGTGGGTAAAGAACATGAACAGACACTTCTCAAA 5369
                         ------  v   ?    i    i    i iv    i     i     v  
  L1M4_orf2#LINE/    808 ------CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_76329705_7   5370 AGAAGACACACATGTGGCCAACAAACACGAAAAGAAAAAAAGCTCCACAT 5419
                               i i   vi       i  i   --- v     i v    v    
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCAC---ATGAAAAGATGCTCAACAT 898

  chrX_76329705_7   5420 GACGGATCAT 5429
                         v ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 6.47 (123 / 19)  


3075 27.48 0.88 0.66  chrX_76336599_76342995     4999  5904 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76336599_7   4999 TGAAAGAACATTCCCTGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5048
                           i  ii i  i  v  i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76336599_7   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCACCCCCATCAAGC 5098
                            v     v     iv i  i  i        i  v i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76336599_7   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76336599_7   5147 TATGGAACCA-AAAAGAGCCTGCATTGCCAAGGAAATCCTAAGCAAAAAG 5195
                                vii-  ii  v  v v  v     iiv    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76336599_7   5196 AAGAAATCTGGAGGCATCACACTACCTGACTTCATACTATACTACAAGGC 5245
                           v   vi      vv       v  ii i    v viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76336599_7   5246 TACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5295
                                 i   ii   ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76336599_7   5296 AATGGAACAGAAC--AGAGCCCTCAGAAATAACATCATACATCTACAACC 5343
                                i    i--    i  --        vvi       i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_76336599_7   5344 ATCTGATCTTTGACAAATCTGACTAAAACGAG-AAATGGGGAAAGGATTC 5392
                          vi    i  i     ivv  - i  i  v v-v           i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_76336599_7   5393 CCTATTTAATAAATGGTGCTGGGAAAACAGGCTAGCCATATGTAGAAAGC 5442
                         i  v  i  i              v   v  v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_76336599_7   5443 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5492
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_76336599_7   5493 ATTAAAGACTTAAATGTTAGACTTAAACCCATAAAAACCCTAGAAGAAAA 5542
                           i ?    i       v   vi    v i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_76336599_7   5543 CTTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGAAT 5591
                          v    ?i- v i -   iv   v v  vv i     v ii   v ii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_76336599_7   5592 AAAACACCGAAAGCAATGGCAATAAAAGCCAAAATTGACAAATGGGATCT 5641
                          vi     i      vvi    i     vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_76336599_7   5642 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTTA 5691
                         v  i   v v  i i   i  ii vv    i  v    i  vv i   v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_76336599_7   5692 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCTATCCACCCATCTGAC 5741
                          v  i     i                 v     v vi  ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_76336599_7   5742 AAAGGGCTAATATCCAGAATCTACAAGGAACTTAAAAAAATTTACAAGAA 5791
                           i  i  vi          v  i  i     ivv v  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_76336599_7   5792 AAAATCAAACAACCCCAT-AAAAAGTAGGTGAAGGATATGAACAGACACT 5840
                            iv    i     v  -?    i i  ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_76336599_7   5841 TCTCAAAAGAAGACATTTATGCAGCAAACAGACACATGAAAAAATGCTCA 5890
                             v        i  vi viii  v  i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_76336599_7   5891 TCTTCATTGGTCGT 5904
                         v v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3041 26.43 1.21 1.21  chrX_76350378_76356556     4779  5686 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76350378_7   4779 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4828
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76350378_7   4829 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4878
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76350378_7   4879 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4926
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_76350378_7   4927 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4976
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_76350378_7   4977 AACGAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATACTACAAGGC 5026
                            i   i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_76350378_7   5027 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAAATATATAGGCC 5076
                                 i   i    iii        i iv ii i i i      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_76350378_7   5077 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATGTACAACAAA 5126
                                i    iv   ivii         vv   i    v  iiiiv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_76350378_7   5127 CTGCTCTTT-ACTAACCTGACAAAAACAAGCAATGGGGAAATGACT--CC 5173
                         i  v i  i-  v ivv  v   i v  vv           -  v --i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTC 397

  chrX_76350378_7   5174 TTATTTAACAAATCGTGTTGGGAAAACTGGCTAGCCATAAGCAGACAACT 5223
                           -  i       v   i     v      v  ?   i v   i vi v 
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_76350378_7   5224 GACACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 5273
                           vii         v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_76350378_7   5274 TTAAAGACTTAAATGTAAGACCTAAAACTATAAAAAACCTAGAAGAAAAC 5323
                          i ?    i           v              vv i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_76350378_7   5324 CTAGGCA-ATATCATTCAGGACATACGCATGGGCAAAGACTTCACAAATA 5372
                         v    ?i- v   -   iv   v vv vv i     v ii   vi i   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_76350378_7   5373 AAACACCAAAAGCAATGGCAAAAAAAGCCAAAATTGACAAACGGTATCTA 5422
                         vi            vvi    v     vv     v  i   iv v ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_76350378_7   5423 ATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAGCTATCATCAGAGTGAA 5472
                           i   v v  i i   i   i vv    i  vi      vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_76350378_7   5473 CAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTATCCATCTGACA 5522
                         v  i     i                vv       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_76350378_7   5523 AAGGGCTAATATCCAGAATCTACAAGGAACT--TA-AACTGATTTACAAG 5569
                          i  i  vi          v  i  i     --  -    ------   v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT------CAAT 789

  chrX_76350378_7   5570 AA--AAAAAACAAACATCCCCTTCAAAAAGTTGGTGAAGGATATGAACAG 5617
                           --    i     i v   vv i?    i v  ii      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_76350378_7   5618 GCACTTCTCAAAAGAAGACATTTATGTGGGCAACAAACATATGAAAAAAA 5667
                         i  i     v        i  vi vi   v   i  i  i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_76350378_7   5668 ACTCATCATCACTGGATAT 5686
                         i    v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


3092 27.02 1.79 0.00  chrX_76370894_76373134      857  1748 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76370894_7    857 TGGAAACACATCTCATGCTCATGGATGGGTAGAATCATTATTGTGAAAAT 906
                               v i   i    i        v  v   v i v      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76370894_7    907 GAACACAGTGCCAAAAGCAATCCACAAATTCAACACAATCCCCATCAAAG 956
                          ivv i v v  v   vii   i   i       i       i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76370894_7    957 TACCACCATCATTCTTCACAGAGTTAGAAAAAACAATTCTAAAAGTCATA 1006
                          v   v vv v  i  ii    iv v  v  ivii  i      v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_76370894_7   1007 TGAAAGCAAAAAAGAGCCCACATAGCCAAAACAAGACTAAGTGAAAAGAA 1056
                           i  iiiv  ii  v  viv             vvi i ivi i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_76370894_7   1057 CAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTGTAAGGCCA 1106
                             vi      vv       v  ii        viv    ii  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_76370894_7   1107 TAGTCACCAAAACAGCATGGAACTGGTATAAAAATAGGCACATAGATCAA 1156
                         i   v i   i    ii   v     i    ii    i  i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_76370894_7   1157 TGGAACAGAATAGAGAACTCAGAAACAAACCCAAATACTTACAGCCAACT 1206
                              i     v    iii      i       v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_76370894_7   1207 GATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGGAAGGACACTCTAT 1256
                            i   i    i vviv   i v   vv i     i   i i v   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_76370894_7   1257 TCAACAAATGGTGCTGGTATAATTGGCTAGCCACATGTAGGAGAATGAAA 1306
                                          v i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_76370894_7   1307 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTAA 1356
                         i    i  ii i   v    v           i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_76370894_7   1357 GAACTTTAACATAAGACCTGAAACTATAAAAATTCTAGAAGATAACATTG 1406
                         ii  i v  ii     v  i           v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_76370894_7   1407 GA--AAAACTTCTAGACATTGGCTTAGGCAAGGATTTCATGGTCAAGAAC 1454
                          ?--   v    vv   v    v        v i    v i vi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_76370894_7   1455 CCAAAAGCAAATGCAATAAAA--ACAAATAGCTG----GGACCTAATTAA 1498
                                  v v    i    -- v      v i----    i v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_76370894_7   1499 ACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAACAGGC 1548
                          v v  i i      iiivv    i iv  vi   iv i   i  v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_76370894_7   1549 AACCCACCAAATGGGAGAAAATCTTCACAATCTATACATCTTACAAAGGA 1598
                                vi             v  ii   vii   i    v i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_76370894_7   1599 CTAACAACTAGAATCTACAACAAATTC----AAATCAGTAAGAAAAAAAC 1644
                           vii v i     v  i  vi  i  ----  v   i   v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_76370894_7   1645 AA----TCCCATCAAATAGTGGGCTAAGAACATGAATAGACAATTCTCAA 1690
                           ----i  v  i?  v i     v   i iv          v     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_76370894_7   1691 AAGAAGATATACAAATGGCCAACAAACATATAAAAAAATACTCAGCATCA 1740
                                               i  i  i  i    i  i    i     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_76370894_7   1741 CTAACAAT 1748
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 3.20 (16 / 5)  


2839 25.31 3.25 1.57  chrX_76379904_76384156     2868  3760 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76379904_7   2868 TGGAAATACATTCCATGCTCATGAATGGGTAGAATCAATATTGTGAAAAT 2917
                               v i  i     i     i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76379904_7   2918 GACCATACTGACCATACTGACAAAAGCAATCTACAAATTCAGTGCAATCC 2967
                          i v     vv   v i   ---------      i     ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGA---------TCTACAGATTCAACGCAATCC 91

  chrX_76379904_7   2968 CCATCAAAATGCCACCATCATTCTTCACAGAATTAGAAAAAACT-ATTCT 3016
                          i        v   v vv v  i  ii     v v  v  i-  -  i  
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCT 140

  chrX_76379904_7   3017 AAAATTCATATGGAAACAAAAAAAGAGCCCACA-CAGCCAAAGCAAGACT 3065
                                         iiv  i-- ii    v -i       i   vvi 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTT 188

  chrX_76379904_7   3066 AAGCAAAAAGAACAAATCTGGAGGCATCACACTACCTGATTTCAAACTAT 3115
                         i iv  i         vi      vv       v  ii        viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_76379904_7   3116 AATAAAAAGCCATAGTCACCAAAACAGCTTGTTACTGGTATAAAAATAGG 3165
                          v  v     i i   v i   i    iv  v      i    ii    i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_76379904_7   3166 CACATAGACCAACGGAACAGAATAGAGAACCCAGCAATAAACCCAAATAC 3215
                           i     i   i    i     v    ii    v          v i i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_76379904_7   3216 TTACAGACAACAGATCTTCCACAAAGCAAACAAAAACATAAAGTGGGGAA 3265
                            ii v   iv   i   v    i vviv   i v   vv i       
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_76379904_7   3266 AGGACACTCTATTCAACAAATGGTGCTGGGATAATTGACAAGCCACATGT 3315
                           i i v   v                    i  i  ivv ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_76379904_7   3316 AGAAGAATAAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTC 3365
                          i      i  ii    i  ii i   v    v           i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_76379904_7   3366 AAAATGGATTAAGGACTTAAATCTAAGACCTGAAACCATAAAAACTGTAG 3415
                                  i ?i   i     v     v  i    i      viiv   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_76379904_7   3416 AAGATAACATTGGACAAACCCTTCTAAACACTGGCTTATGCAAAGACTTC 3465
                             v     v  ?vv  vi    vvi  vi   v   v    v ii   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_76379904_7   3466 ATGACCAAGAACCCAAAAGCAAATGCAACAAAAACAATGATAAATAGGTA 3515
                         v iivi v  vv         v v         iv  vi   i   ii v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_76379904_7   3516 GGACTTAATTAAA-CTAAAAA-------GC-------AACA--ATCAGCA 3548
                               v  i   -i      -------  -------i   --    iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_76379904_7   3549 AAGTAAACAGACAACCCAGCGAGGGGGAGAAAATCTTCACAATCTACACA 3598
                             i  v          vv  iv          v  ii   vii i i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_76379904_7   3599 TTCAACAAAGGACTAATATCCAGAATCTACAAGGAACTCAAACAAATTAG 3648
                          iii i  i     vi          v  i  i      vv    v i i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_76379904_7   3649 CAAGAAGGAAACAAACAAATCTCATCAAAAAATGGATA-------TGAAT 3691
                         i  v  ii i     i  -i iv  i?        ii -------     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_76379904_7   3692 AGACATTTCTC---AAAAGGTACACAAATGGCCAAAAACCATATGAAAAA 3738
                                    --- i   i  i            v  v  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_76379904_7   3739 AATGCTCAACATCACTAATGAT 3760
                          -            ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (129 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.31 (43 / 13)  


3254 27.29 0.55 0.33  chrX_76388489_76392729     2844  3748 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_76388489_7   2844 GAAAAGATATTTTATGTTCATGGATTGGAAGAATCAATATTGTTAAGATA 2893
                          i        iii                   v i              i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_76388489_7   2894 TCCATGC-CACAAAAGCAATCTACAAATACAATGTAATCCCTATCAAAAT 2942
                         v v  i - v v   vii       i  v   i i               
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_76388489_7   2943 ACCTATGACATTCTTCACAGAAATATAAGAAAC-AATCCTATAATTTATA 2991
                         v  viivi v  i  ii       - i v  i -i      v    i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATA 150

  chrX_76388489_7   2992 TAGAACCACAAAAGATCCAGAATAGCCAAAGCTATCCTAAGCTAAAATAA 3041
                          i   vii   ii  i              i v   i i ivv i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_76388489_7   3042 AAAAACTGGAGAAGTCACATTACCTGACTTTAAATTATACTACAGAGCCA 3091
                         v   ii     i v     i v  ii i  i   viv       i   i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_76388489_7   3092 TAGTCATCAAAATGGCATAGGGCTGACATAAAAACAGACACATAGACCAG 3141
                         i   v     i ii ii i vi   i     ii i     i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_76388489_7   3142 TGGAACAGAATAGAAAACCCAGAACAAAATCCGCACATTTACAGTGGACT 3191
                              i     v  i ii      vv   i  ii       ii  vi i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_76388489_7   3192 CATTTTTGACAAAGCTTTCAAGAACACACGCTGAAGAAAAGACAG-CTCT 3240
                         v     i     i v vi     v  iv iv  ii    ii i  -  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_76388489_7   3241 TCAATAAATGGTGCTAGAAAAACTGGACATCCATATGCAGAAGAATGAAA 3290
                             i          i i v       i ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_76388489_7   3291 CTAGACCACTATCTCTCACCATATATAAAAATCAAATCAACGTGAATTAA 3340
                         i i    v   i   v         i      i  v    vi  i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_76388489_7   3341 AGATTAAAATCTAAAACCTCAATCTATGAAACTACTACAAGAAAACATTG 3390
                            iiv    v   i v  v  v    i     vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_76388489_7   3391 GGGAAACTCTCCAGGACATTGGTCTGGGCAAGGACTTTTTGAGTGATGTC 3440
                          ? v  v   i iv   v    vi i     v ii  i  iii -   v 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGAC 599

  chrX_76388489_7   3441 -CCACATGCACAGGCAACCAAAGCAAACATGAACAAATAGGATCACATCA 3489
                         -   v v     i     v    v   v  ii i    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_76388489_7   3490 A-GTTAAAAAGCTTTTGTCCAGCAAAGAAAACAATCAACAAAGTGAAGAG 3538
                          -i       -       v vv     i v  v     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_76388489_7   3539 ACATCCCAAAGAGTGGAAGAAAATATTTACAAACTGCCTGGCTGGCAAAG 3588
                            v    v   i   i           i    iiiiv iv   ii  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_76388489_7   3589 CATGAATAACCAGAATATACGAGGAGCTCAAACAACTCTACAGGAAAAAA 3638
                         v ivvi  v          ii i  i   vv       v i iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_76388489_7   3639 CTGAATAATCTGATCAAAAGTTGGGCAAAAGATTTGAATAGACATTTCTC 3688
                         vii     i ii  i?   iv        i                    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_76388489_7   3689 AAAAGAAGACTTACCAATGGCAAACAGACATGGGAAAAGCTGTTCAACAT 3738
                         v        iv   v      v  i ii  iiv      v  i       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_76388489_7   3739 CACTGATCAT 3748
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.76 (155 / 88)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 1.00 (8 / 8)  


2782 27.13 3.75 0.68  chrX_76392830_76399497     5295  6175 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76392830_7   5295 TGGAAAAACACTCCATGCTCATGTATAGGAAGAATGAATATGGTGAATAT 5344
                               i i ii     i     v  v      v v     v  v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76392830_7   5345 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5394
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76392830_7   5395 TACCATTGACTTTCTTCACAGAATTGGAAAAAAT-ACTTTAAACTTTATA 5443
                          v   vivi i  i  ii     v v  v  iv - iii    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_76392830_7   5444 TGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTGGGCAAGAAGAA 5493
                              viiv  ii  v  viv        i      i  iiv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_76392830_7   5494 CAAAGCTGGACGCATCACGCTGCCTGACTTCAAACTATACTACAAGACTC 5543
                              i    v vv    i  v  ii i      viv        ii  v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_76392830_7   5544 CAGTAACCAAAACAGCACAATACTGGTACCAGATCAGATGTATTGACCAA 5593
                               i   i    iiiii      i iv  ivi   ii   v  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_76392830_7   5594 TGGAATAGAATGGAG-GCCTAAGAAATAACTCTACACATCTACAACCATC 5642
                                    v   - i i -       vi i i    i  iiii  vi
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATGGTCAAT 349

  chrX_76392830_7   5643 TGATCTTTTACAAACCTAACACAAACAAACAATGGGGAAAAGATTCCCTA 5692
                             i  iv    ivv iv  vi v  vv           ii  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_76392830_7   5693 TTTAATAAATG---TTGGGAAAACTGGCTAGCCATATGCAGAAAACTAAA 5739
                           i  i     ---i     v      v  ?   i     i  i v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_76392830_7   5740 ACTGGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGATGGATCA 5789
                         ii         v   i     v           i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_76392830_7   5790 AAGACTTAAATGTAAGACCTAGGACCATAAAAATTCCAGAAGAAAACC-- 5837
                         ?    i           v   ii  i      v iii          v--
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_76392830_7   5838 GGGGCAATACAATTCAGGACAT--AGTCATGGGCAAAGACTTCATGTCTA 5885
                           ? i  vv --   iv   v --i  i --     v ii   v ivv  
  L1M4_orf2#LINE/    550 GGNGTAAATC--TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATA 595

  chrX_76392830_7   5886 AAACACCAAAAGCAATGGCAACTAAAGCCAAAATTGACAAATGGGATCTA 5935
                         vi            vvi     v    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_76392830_7   5936 ATTAAACTAAAGAGCTTCTACACAGCAAAAGAAATTATCATCAGAGTGAA 5985
                           i   v v  i i   i iii vv    i  v i     vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_76392830_7   5986 CAGGCAAGCTACAGAATGGGAGAAAAAATTTTGCAATCTATCCATCTGAC 6035
                         v  i   v i                v    -    vii  vi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGAT 744

  chrX_76392830_7   6036 AAAGGTCTAATATCCAGAATCTACAAAGAACT--TA-AACTAATTTACAA 6082
                           i  v  vi          v  i        --  -    v v v i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_76392830_7   6083 GAAAA-AAACAACCCCATCAAAAAGTGTGCAAAGGTTATGAACAGACACT 6131
                         i  i -   i     v  i?    i  v       v v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_76392830_7   6132 T-----------ATGTA------GCCAACAGACATATGAGAAAATGC--- 6161
                          -----------  i  ------     i ii  i    i  i    ---
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_76392830_7   6162 GCATCACTGCTCAT 6175
                         i     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.60 (39 / 15)  


2772 25.92 5.16 1.03  chrX_76409491_76416409.rev     5557  6428 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76409491_7   5557 TGGAAAAACATTCCCTGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5606
                               i i  i  v  i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76409491_7   5607 GGTCACATTGCTCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5656
                           iv i i v i    v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76409491_7   5657 TACCA-CTGACTTTCTTCACAGAATTAGGAAAAAACTACTTC-AAATTTC 5704
                          v   -   v    i  -i     v v -- v  i  iv i -   v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_76409491_7   5705 ATATGGAACCAAAAAATAGTCCGTATAGTCAAGACATTCCTAAGCAAAAA 5754
                                 viiv  iiv vi v v    i   i   v  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_76409491_7   5755 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAAACT---------- 5794
                                 i      vv       v  ii i         ----------
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_76409491_7   5795 ---------------------GGTACC------AAAACAGATATATAGAC 5817
                         ---------------------     i------ ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_76409491_7   5818 CAATGGAACAGAACAGA-AGCCTCAGAAATAATGCCACACCTCTACAACC 5866
                                 i    iv  -  i -         vv   i  v i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTC 346

  chrX_76409491_7   5867 ATCTGATCTTTGACAAACCTGAGAAAAACAAACAATGGGGAAAGGAT--T 5914
                          vi    i  i     ivv  vv  i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_76409491_7   5915 CCTTATTTAATAAATGTTGTTGGGAAAACTGGCTAGCCATATGCAGAAAA 5964
                          i  -- i  i     v  i     v      v  ?   i     i  i 
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_76409491_7   5965 CTTGAAAATGGACCCTTTCCTTACACCTTATACAAAAATTAACTCAAGAT 6014
                         v -   iv       i v   i     v                   i  
  L1M4_orf2#LINE/    445 AT-GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_76409491_7   6015 AGATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAA 6064
                         i   i ?    i           v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_76409491_7   6065 AACCTAGGCA-ATACCATTCAGGACAT-AGGCAAGGACAAAGACTTCATG 6112
                            v    ?i- v i -   iv   v -i  iv   -   v ii   v i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGG-CAATGGTTTCTTA 591

  chrX_76409491_7   6113 ACTAAAACATGAAAAGCAAAGGCAACAAAAGCCAAAATTGACAAATGGGA 6162
                         iv  vi   iv       v i          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_76409491_7   6163 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAG 6212
                         ii v  i   v v  i i   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_76409491_7   6213 TGAACAAGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 6262
                             v ii     i i               v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_76409491_7   6263 GACAAAGGGCTAATATCAAGAATCTACAAGGAACTTAAATATATTTACAA 6312
                           i  i  i  vi    v     v  i  i     ivv i vv iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_76409491_7   6313 GAAAAAAA-AAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGAC 6361
                         v     i -   i     v  i?    i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_76409491_7   6362 ACTTCTCAAAAGAAGACATTTATGTGGCCAACAAATATATGAAAAAAAGC 6411
                          i     v        i  vi vi       i  ii i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_76409491_7   6412 TCATCATCACTGTTTAT 6428
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (131 / 91)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.38 (54 / 16)  


2908 24.46 5.70 0.76  chrX_76526275_76529132.rev      730  1518 (1340)    L1M4_orf2#LINE/L1        1   828 (80)  

  chrX_76526275_7    730 TAAAAATGTATCCCATGTTCATGGATCAGAAGAATTAATATTCTTAAAAT 779
                          ii   vi                  ii     v        v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76526275_7    780 GGCCATACTACCCAAAGCAATAGACAGATTCAATGCAACCACTATCAAAA 829
                            v     v      vii  vv          i    i v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76526275_7    830 TTCCAATATTAGTTTTCACAGAAATAGAAAAAAAAATCCTTAAATTCATA 879
                          i   iivvivv    ii       v  v  ivvi     v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_76526275_7    880 TGGAACCACAAAATACCCCCAAAAACCAAAACAATCTTGAGCAAAATGAA 929
                              vii   iiv    vv  v i               iv  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_76526275_7    930 CAAAGTTGGAGGCATAACACTCCCTGATTTCAAACTATATTATAAGGTGA 979
                                     vv v     i  ii        viv  i  i  i iv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_76526275_7    980 TGGTGATTAAAACAGCATGGTACTGGCATAAAAA-AGACACATCAACCAA 1028
                         ii  i  i  i    ii              ii -     i  vi i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_76526275_7   1029 CGGAACAGGATAGAAAGCCCAGAAATAAACTAATGAATTTATAGTCAATT 1078
                         i    i  i  v  i  i            iv  iv      i       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_76526275_7   1079 GCTTTTCAACAAAGGTGCCAAGGACACACAATGAGGAAATTAAAAGT--- 1125
                          v     i    i         iv  iv     i     v-  v   ---
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTT 399

  chrX_76526275_7   1126 ------AAATGATGTTGGGAAAATTGAATAGCCACATGCAGAAGAATGAA 1169
                         ------     i  i     v  i  i   ?         i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_76526275_7   1170 ATTTGATCCTTATTTCACCCCATGTACAAAAACCAACCCGAAATTATTTG 1219
                         i  v  i  i  ii    v    i        ii   i i    viv ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_76526275_7   1220 AAGACTTAAATATAAGACCTGAAACTATAAAACTACTAGAAGAAAACATA 1269
                         ?    i     i     v  i             vi              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_76526275_7   1270 AGGG-AAACATTCAACAATACTGGTCTGAGCAATGATTTTTTTTTTTTAT 1318
                         i ? -   iv   i-ii ivi   vi ii      i   i  vv----  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAG----AT 594

  chrX_76526275_7   1319 ATGATCCTGAAAACACAGGCAGCAAGAGAAAAAATAGGCAAAGGGAATTA 1368
                             iv ii   i    i   i   i           ii   vv i i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_76526275_7   1369 CATCAAACTTAAAGGTTTTTGCACAACAAAGGAAACAATTAACAAAG--- 1415
                                v     iii     ii vv       v  v  i  v    ---
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_76526275_7   1416 --AGACAACC-ATGGAGTGGGAGAA-------------------TCTGAT 1443
                         --        - ii  i        -------------------      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_76526275_7   1444 AAAGGATTAATATACAAAATATATA--GAA-------AACTCAATAGCAA 1484
                           i   i vi   v  i        --   -------         ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_76526275_7   1485 GAAAACAAACAACCTGATTAAAAGATGGGTAAAG 1518
                         i  i     i    ii   ?   i     i    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.95 (125 / 64)
Gap_init rate = 0.01 (11 / 828), avg. gap size = 4.64 (51 / 11)  

 307 25.00 0.00 0.00  chrX_76526275_76529132.rev     2292  2367 (491)    L1M4_orf2#LINE/L1      833   908 (0)  

  chrX_76526275_7   2292 TGTACAGGTATTTCTTAAAGGAAGACATACAAATAGCCAACCGGCTCATG 2341
                           v i  ii      iv  i     i        i     ivi  v    
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_76526275_7   2342 AAAAATTGTTTAGTATCACTAATCAT 2367
                             iv  i i ii    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.80 (14 / 5)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.00 (0 / 0)  


3250 27.65 0.66 0.22  chrX_76531786_76538168     4987  5890 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76531786_7   4987 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5036
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76531786_7   5037 GGCCATACTGCCCAAGGTAATTTATAAATTCAGTGCCATCCCCATCAAGC 5086
                            v     v     iv i  i  i i     ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76531786_7   5087 TACCAATGACTTTCTTCACAGAATTGGAAAAATCTACTTTAAAGTTCATA 5136
                          v   iivi i  i  ii     v v  v  iiiv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_76531786_7   5137 TGGAACCAAAAAAGACCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5186
                              viiv  ii     v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_76531786_7   5187 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5236
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_76531786_7   5237 CAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGACCAA 5286
                               i   i    ii         i i  ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_76531786_7   5287 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACCAT 5334
                              i    i--    i  --        vv iii i  i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_76531786_7   5335 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5384
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_76531786_7   5385 TTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTGA 5434
                            i  i              v      v  ?   i   v i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_76531786_7   5435 AACTGGATCCCTTCCTTACAAATTATACAAAAATTAATTCAAGATGGATT 5484
                          ii    i    v   i   vvv              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_76531786_7   5485 AAAGACTTAAACGTTAGACCTAAAGCCATAAAAACCCTAGAAGAAAACCT 5534
                          ?    i    i  v   v     i i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_76531786_7   5535 AGGCATTACCATTCAGGACATACGCATGGACAAGGACTTCATGTCTAAAA 5584
                            ?i v viv   iv   v vv vv i i   v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_76531786_7   5585 CACCAAAAGCAATGGCAACAAAGGCCAAAATTGACAAATGGGATCTAATT 5634
                                    vvi        i vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_76531786_7   5635 CAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5684
                         v  v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_76531786_7   5685 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAG 5734
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_76531786_7   5735 GGCTAATATCCAGAATCTACAATGAACTC----AAATTTACAAGAAAAAA 5780
                          i  vi          v  i  v      ----  v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_76531786_7   5781 ACAAAAAACCCCATCAAAAAGTGGGCGAGGGATATGAACAGACACTTCTC 5830
                              v     v  i?    i     i i    v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_76531786_7   5831 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 5880
                         v        i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_76531786_7   5881 CACTGGCCAT 5890
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 2.67 (8 / 3)  


2980 25.62 1.85 3.26  chrX_76543905_76550583     5266  6186 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76543905_7   5266 TGGAAAAACTTTCCATGCTCATGGATAGGAAGAATCAATATTATTAAAAT 5315
                               i iv i     i        v      v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76543905_7   5316 GGCCATACTGCACAAAGCAATTTATACCTTCAATGCTATTCCTATCAAAC 5365
                            v     v v    vii  i  i vv     i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76543905_7   5366 TACCAATGAAATTCTTCACAGAA-TT----AGCT-ATTTTAAAATTCATA 5409
                          v   iivivv  i  ii     -  ----    -  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_76543905_7   5410 TGGAACAAAAAAGAACCCA-AATAGCCAAGGCAATCCTAAGCTAAAAGAA 5458
                              vviv  i i     -         ii     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_76543905_7   5459 CAAAGCTGGAGGTATTACATTACCTGACTTCAAACTATACTACAGGGCTA 5508
                              i      vv i   i v  ii i      viv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_76543905_7   5509 CAGTAACCAAAACAGCATGGTACTGGTACAAA-ACAGGCACATAGACCAG 5557
                               i   i    ii         i i  i- i  i  i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_76543905_7   5558 TGGAACAGAATAGAGAGCCTAGGAGTAATGTTGCACACCCACAACCATCT 5607
                              i     v     i i  i i   vviiii   iii iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_76543905_7   5608 GATCTTCAAGAAAGCTGACAAAAACAAGCAATGGGGAAAAGGC--TCCTT 5655
                            i   i v  i v  v   i v  vv           iiii--  i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_76543905_7   5656 ACTCAATAAATGGTGGTGGGATAACTGGCTAGCCATATGCAGAAGATTGA 5705
                         --    i        v     i      v  ?   i     i    v   
  L1M4_orf2#LINE/    401 --TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_76543905_7   5706 AACTGGACCCCTTCCTTACACGATATACAAAAATCAACTCAAGATGGATT 5755
                          ii         v   i    v            i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_76543905_7   5756 AAATACTTAAATATAAAACCTAAAATCATAAAAACCCTGGAAGATAACAT 5805
                          ? v  i     i   i v      ii      vi i i     v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_76543905_7   5806 ATG---AAATACCATTCTGGACATAGGACCTGGCAAAAATTTCATGAAGA 5852
                          v ---    -- -   vv   v v  iiiv     vii    v ii v 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_76543905_7   5853 AGATGCCAAACGCAAGTGCAACAAAAACAAAGATTGATAAAAGGGTCCTA 5902
                         v  ii     v   viv         iv   i  v      vv  v i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_76543905_7   5903 ATTAAACTAAAGAGCTTCTGCATAGCAAGAAAAGGTAAGTTGTTTCCTTA 5952
                           i   v v  i i   i  --------------------  i   --- 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTG--------------------TGCTTC---A 672

  chrX_76543905_7   5953 GAAGAAACTATCAACAGAGTAAACAGATAACCTACAGGATAAGAGAAAAT 6002
                         i i  v        v i   i  v   i    i    i  ii        
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_76543905_7   6003 ATTTGCAAACTATACATCTAAAAAAGGTCTAATGTCCAGAATCTATAAGG 6052
                                  ii   i    i v  i  v  vi i        v     i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_76543905_7   6053 AACATAAACAAATTTAGAAGCAAAAAACAA----CCCCATTAAAAAGTGG 6098
                            vivv    v iv v  vv    i    ----   v   ?    i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_76543905_7   6099 GCAAAGGACAAGAACAGACACTTTTCAAAAGAAGACCTATATGTGGCCAG 6148
                                 ivv   i     i  i  v        iv  i vi      i
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_76543905_7   6149 CAAGCATATGGAAAAAAAGGCTGAACATCACTAATCAT 6186
                         i     i   --    i v   v       ????????
  L1M4_orf2#LINE/    873 TAAGCACATG--AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (145 / 88)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.36 (47 / 14)  


3021 26.27 1.44 0.78  chrX_76555924_76562091     4774  5675 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76555924_7   4774 TGGAAAAACATTCCATGCTCATGGAATGGAAGAATCAATATTGTGAAAAC 4823
                               i i  i     i       v       v i        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76555924_7   4824 GGCTATACAGCCCAAATTAACTTATAGATTCAATGCTATTCCCATCAAAC 4873
                            v    vv        i ii  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76555924_7   4874 TAC-AATTGCCTCTTC-ACAGAATTAGAAAAAAACT-ACTTTAAATTTCA 4920
                          v - ii     i  i-i     v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_76555924_7   4921 TATGGAG-TGAAAGAAGACCCAGGATAGAAAAGACAATCCTAAGCAAAAA 4969
                               i-  v   i-       i    vv  i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_76555924_7   4970 GAACAAAGCTGGAGATATCACACTACCTGACTTCAAACTATGCTACAAGA 5019
                                 i     ivv       v  ii i      viv i      ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_76555924_7   5020 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGAC 5069
                                  i   i    ii         i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_76555924_7   5070 CAATGGAACATAACAGAGACCTCAGAAATAACACCGCATATCTACAACCG 5119
                                 i v  iv    vii         vv  ii i  i  iiii i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_76555924_7   5120 ACTGATCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGATCTCC 5169
                          i    i  i     ivv  v   i v  vv     i      i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_76555924_7   5170 TATTCAATAAATGGTGCTGGTAAAACTAGCTAGCCATAGGCAGAAAACTG 5219
                          v     i            v v    i v  ?   i v   i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_76555924_7   5220 AAACTGGACCACTTCCTTACACCTTTTACAAAAATTAACTCAAGATGGAT 5269
                           ii      v  v   i     v v                 i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_76555924_7   5270 TAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAACC 5319
                         i ?    i         i v i     i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_76555924_7   5320 TAGGCA-ATACCATTCAGGACATAGACATGAGTAAAGACTTCATAACAAA 5368
                             ?i- v i -   iv   v v ivv ii i  v ii   v  ivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_76555924_7   5369 AACTCCAAAAGCAGTTGCAATAAAAGCCAAAATTGACAAGTGGGATCTAA 5418
                         i  v         vvv    i     vv     v  i  i v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_76555924_7   5419 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAGAGTGAAC 5468
                          i   v v  i i   i  ii vv    i  v    v  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_76555924_7   5469 AGGCAACTTACAGAGTGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 5518
                           i    ii     i           v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_76555924_7   5519 AGGTCTAATATC-AGAATTTCCAAGGAACTT----AAATGAATTTACAAG 5563
                         i  v  vi    -     v vi  i     i----  v v   v- i  i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAA 795

  chrX_76555924_7   5564 AAGA-AAACAACCATATCAAAAAGTGGGCAAAGGATTCGAACAGACACTT 5612
                             -   i    vv  i?    i             i   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_76555924_7   5613 CTCAGAAAAAGACATTTACGA--GGCCAAAAAACATATGAAAAGAAGTTC 5660
                            vi  i    i  --  i --      v  i  i         v i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_76555924_7   5661 AACAACACTGATCAT 5675
                             v  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.43 (20 / 14)  


2866 25.99 1.98 1.98  chrX_76574758_76577143      986  1893 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76574758_7    986 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTTGAAAT 1035
                               i i  i     i        v      v i         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76574758_7   1036 GGTCATACTGCCCAAAGCAATTTATACATTCAATGCTATTCCTATCAAAC 1085
                           iv     v      vii  i  i v      i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76574758_7   1086 TACTAATGATATTCTT--CATAAACTAGACAAAACT-ATTTTAAAATTCA 1132
                          v i iiviiv  i  --  v   i -     i-  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAG-CTGATCCTAAAATTCA 148

  chrX_76574758_7   1133 TATGGAACAACAAAAAAAAGGTTGAATAGCCAAGGCAATCGTAAGCAAAA 1182
                                -- iiv  iii vviv          ii     v i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_76574758_7   1183 TGAACAAAGCTGGAGGCATTATGCTATACAACTTCAAACTATACTACAGA 1232
                         v        i      vv i ii  viv   i      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_76574758_7   1233 GCTACAGTAACCAAAACAGTGTGGTACTGGTACAAAAA--GACACACAGA 1280
                                   i   i               i i  ii --    i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_76574758_7   1281 CCAATGGAACTGAATAGACAGCTCAGAAATAAGGCCACACACCTACAACC 1330
                         i        iv    v  v  ii         iv   i   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_76574758_7   1331 ATCTGATCTTTGACAAAGTTGACAAAAACAAGTAATGGGAAAAGGACTCC 1380
                          vi    i  i     i v  v   i v  vvi      i    i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_76574758_7   1381 CTACTCAATAAACAGTGCTGGGGTAATTGGCTAGCCACAGGGAGAAGATT 1430
                           vi    i   ii        ii  i   v  ?     v v i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_76574758_7   1431 GAAACTGGACCCCCTCCTTACACACCATATACAAATATCAACTCAAGATG 1480
                            ii        iv   --               v  i       i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCT--CACACCATATACAAAAATTAACTCAAAATG 494

  chrX_76574758_7   1481 CATTCAATACTTAAATGTAAACCCGAAAACTATAAAAACCCTGGAAGACA 1530
                         v  iv? v  i         ivv v            vi i i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_76574758_7   1531 ACCTAAGCAATATAATTCT--G-GATATAGGAATGGGCAAAGATTTCAT- 1576
                           v  i ?i---   v   -- -  iv v  iv i     v i    v -
  L1M4_orf2#LINE/    545 ACATAGGNG---TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_76574758_7   1577 GATGAAGATGCCAAAAGCAATTGCAACAAAAGCAAAAATGGACAAATGAG 1626
                            - v  ii         vvv          v      i  i    vi 
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_76574758_7   1627 A-TCCAACTAAACTCTGCACAGCAGAGCTTCTGCACAGCAAAGGAAACTA 1675
                          - i  v v   i ------ -- i i   i  ii vv       v    
  L1M4_orf2#LINE/    641 ACTTCATCAAAATT------A--AAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_76574758_7   1676 TCAACAGAGTAGAGAGACAACCTACAGAATTGCAGAAAAGTTTTGCAAAC 1725
                             v i   ii i        i       v v      vv        i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_76574758_7   1726 TATCCATCT----AGCAACTAATATCCATTATCTATAAGGAACTTAAAGA 1771
                         i  vi    ----  vi   vi      vv  v     i     ivv v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_76574758_7   1772 AAT--ATAG-AAGAAAATAA-CAACCCCATTAAAAAGTGGGCAAAGGACA 1817
                          v --   i-  i  i i  -i     v   ?    i           iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_76574758_7   1818 TGAACAGACACTTTGCAAAAGAAAACACACACGTGGCCAACAATCATATG 1867
                             i     i  iv v      i i i   vi       i  v  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_76574758_7   1868 AAAAAAAGCTGAACATCACTGATCAT 1893
                             i v   v       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.89 (36 / 19)  


3298 25.33 1.00 0.55  chrX_76577367_76581537     2775  3678 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76577367_7   2775 TGAAAAGATCTTCCATGTTCATGGATTGGATAAATTAATATTGTTAAAAT 2824
                           i      v i                  vi v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76577367_7   2825 GCCCATACTACCCAAAGCAATCCATAGATACAATGCA-TCCTTATCAAAA 2873
                          v v     v      vii   i i    v   i   -   i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76577367_7   2874 TACCAATGACATTCTTCACAGAAACAAAAAAAA-AATTCTGAACTTTTCA 2922
                          v   iivi v  i  ii      ivi v  iv-i  i  i  v  ivi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_76577367_7   2923 TGGAACCACAGAAGACCCACAATAGGCAAAGCTGTAGTGAGCAAAAAGAA 2972
                              vii  iii      v     v    i vi vv   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_76577367_7   2973 CAAAACTGGAGGAATCACATTACCTGACTTCAAATGATACTACAGAGCTA 3022
                             ii       v     i v  ii i      vvv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_76577367_7   3023 CAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACACACAGACCAA 3072
                               i   i    ii              ii i     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_76577367_7   3073 GAGAACAGAAGTGAGAACCCAGAAACAAATCCACACACC---AGTAAACT 3119
                         vi   i    v     ii       i   i   i   ii---i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_76577367_7   3120 CATTTTTTGCACAGGTGCCATGAACATGCATTGAAGAAAGGACAGTCTCA 3169
                         v     ivi  vi       v  v   v  v  ii     i i     iv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_76577367_7   3170 TTAATAAATGGTGCTGTGGA-AGCTGGATATCCATACGCAGAACAATGAA 3218
                          i  i           -   - i       ?   i i   i  v      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_76577367_7   3219 AGAAGACCCCAAGCTCTTGCCATATACAACATTCAAATCAAAATGGATTA 3268
                         ivvi      v v   vii          v v i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_76577367_7   3269 AAGACTTAAATCTGAGACCTCAAACTATGAATCTACTACAGAAAAACACT 3318
                         ?    i     v i   v  v       i  v  vi  v ii      iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_76577367_7   3319 GG-GCAAACTGTCCAGGACATTGAACT-GGCAAAGATTTCTTGAGTAATA 3366
                           - i   - v i iv   v   iii -     v i      iii  vv 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_76577367_7   3367 TCTCACAAGTACAGGCAACCAAATAAAAAATGGACAAACAGGATACCA-C 3415
                         ivi  v   i   i     v   v       i  i   iv   ivi  - 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_76577367_7   3416 TAAGTTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAGGCGAAGA 3465
                         v  i       -   i  ii vv       v  v     v  i i   i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_76577367_7   3466 GACAACCCACAGAATGCGAGAAAATATTTGCAAGCTATCCAACTGACAAG 3515
                                         v                iii  vi v    i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_76577367_7   3516 GGATTAATAACCAGAATATATAAGGAGCTCAAACAACTGCATAGGAAAAA 3565
                            i vi  v             i  i   vv      vv   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_76577367_7   3566 AAATCTAATAATCAGATTTAAAAATGGGCAAAATATCTGAATAGATATTT 3615
                         i -- v     i vi   ?             iv  i        i    
  L1M4_orf2#LINE/    798 GA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_76577367_7   3616 CTCGAAAGAAGACATACAAATGGCAAACAGGCATAGGAAAAGGCACTCAA 3665
                            v        i           v  i i   i v      iii     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_76577367_7   3666 CATCATCAGTCAT 3678
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (137 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3028 26.79 1.79 0.45  chrX_76600705_76605344     3252  4147 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76600705_7   3252 TGGAAAAACATTCCATGCTGAAAGATAGGAAGAATCAATATCGTGAAAAT 3301
                               i i  i     i v vi   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76600705_7   3302 GGCCATACTGACCAAAGTAATTTATAGATTCAATGCTGTCCCCATCAAGC 3351
                            v     vv     v i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76600705_7   3352 TACCA-CTGACTTTATTCACAGAA-TTGGAAAAAACT-ACTCTAAACTTC 3398
                          v   -   v    -  ii     -   -- v  i  - ii     v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_76600705_7   3399 AAATGGAACCAGAAAAGAGCCTGCAAAGCCAAGACAATTCTAAGCAAAAA 3448
                          v      viiv  ii  v  v v v      i     ii i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_76600705_7   3449 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACCACAATG 3498
                                 i      vv   ii  v  ii i      viv   i    v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_76600705_7   3499 CTCCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 3548
                           v      i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_76600705_7   3549 CAATGGAACAAAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 3598
                                 i i  iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_76600705_7   3599 TCTGATCTTTGACAAACCTGACACAAAGAAGCAATGGGGAAAGGACTCCC 3648
                         vi    i  i     ivv  v  vi vv vv            i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_76600705_7   3649 TATTTAATAAATGGTGTTGGGAAAACTGGTTGGCCATATGCAGAAAACTG 3698
                          v  i  i        i     v      v i?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_76600705_7   3699 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAAGTCAATATGGAT 3748
                           ii         v   i     v              v    v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_76600705_7   3749 TAAAGACTTAAACATAAGACCTAAAACCATAAAAATCCTAGAAGAAAACC 3798
                         i ?    i    ii     v       i      v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_76600705_7   3799 TAGGCA-ATACCATTCAGGACAT------GGGCAAAGACTTCATGTCTAA 3841
                             ?i- v i -   iv   v ------i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_76600705_7   3842 AAAACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAATGGGATGTAA 3891
                         i v          vvi          vv     v       v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_76600705_7   3892 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3941
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_76600705_7   3942 AGGCAACCTACAGAACAGGAGAAAATTTTTGCAATCTACTCATCTGACAA 3991
                           i     i      ii         v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_76600705_7   3992 AGGGCTAATATCCGGAATCTACAAAGAATTTAAACAAATTTACAAGAAAA 4041
                         i  i  vi     i    v  i      i ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_76600705_7   4042 AAACAA----CCCTATCAAAAAGTGGGCAAAGTATATGAACAGACACTTC 4087
                          i    ----   v  i?    i         v  v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_76600705_7   4088 TCAGAAGAAGACATATATGCAGCCAACAG--ACATGAAAAAATACTCATC 4135
                           vi       i   i viii     i i--         i  i    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_76600705_7   4136 ATTACTGCTCAT 4147
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


 924 27.60 7.12 1.78  chrX_76628368_76633079     3083  3419 (1293)    L1M4_orf2#LINE/L1       48   402 (506)  

  chrX_76628368_7   3083 GATATCAATTCTCTACAAATTAGTA-ATAGGTTTAATACAATACCTATTA 3131
                            iv    v   iv      ii v- i  i  i  ii    v     i 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_76628368_7   3132 AAATT---ATTGCAAAACTTTT--GTAGGTCTAGACAAGATTATTCTAAA 3176
                             i---ii   ----     -- i  ivv v      v v  i     
  L1M4_orf2#LINE/     98 AAATCCCAGCTGC----CTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_76628368_7   3177 ATTCATATAAAAAT----------------AGCTAAAACAATCTGTGAAA 3210
                                 ii    ----------------   i          -     
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT-TGAAA 192

  chrX_76628368_7   3211 G-GTAGAACAAAGTGGGAAGAATCATTCAATGTGATATTAAGGCTTAGTA 3259
                         i- v          v   i  v   iv vvivii  v i  ii    v  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_76628368_7   3260 CACAGCTACAGTAATCAAGACTATGTAGTAATGATGCAGAGAAAGACATA 3309
                           v                  vi   i   v  iiii ii  v       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_76628368_7   3310 TGGAATAAAGGAATAGAATAGCAAACTGAAAAACAGCCCAAAACAAGTAT 3359
                          i  vi  v          v vi iiiv i   i iv  v v   vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_76628368_7   3360 AGCCAACTGATTTTTCACAAAGGTGC-AAAACCAATTCAGTAAAGGAAGT 3408
                         i i   i       iv    i     -  i    -    i iii i   v
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGA 391

  chrX_76628368_7   3409 ATGGTTTTTTC 3419
                           i  i     
  L1M4_orf2#LINE/    392 ATAGTCTTTTC 402

Transitions / transversions = 1.66 (58 / 35)
Gap_init rate = 0.03 (9 / 355), avg. gap size = 3.33 (30 / 9)  

1797 22.16 2.70 3.08  chrX_76628368_76633079     3703  4221 (491)    L1M4_orf2#LINE/L1      392   908 (0)  

  chrX_76628368_7   3703 ATAGTTTTTTTCAACAAATGATGCTGCAGCAATTGAACATCCACAGCCAA 3752
                              i    -         i     vii   i  i i ?     vv   
  L1M4_orf2#LINE/    392 ATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_76628368_7   3753 AAATATGAA------CCTTTAAACTTCACACCTTATACAAAAATTAACTC 3796
                           iv     ------  ii  -- i       v                 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTC 488

  chrX_76628368_7   3797 AA--TACAACATGGACTTAAACATAAAAGGTAAAATTATAAAACTTGTAA 3844
                           -- iv v  ?i   i    ii   i  v     i         iv  i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_76628368_7   3845 AATACAACACAGGACAAAGTCTTCAAGACCTAGGGCTTTGAGGAAGAGTT 3894
                           v v    i   ?vv  i     iv     v   --  ii v  vi   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTT 586

  chrX_76628368_7   3895 -CTTAGACTTGACATCAGAACCATGATCAAAACAAAGAAACAAACATTGA 3943
                         -      iv     i  i  v  ii v   v -       -   i --  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACA-AAAGAAA-AAATA--GA 632

  chrX_76628368_7   3944 CAAACTAGATTTCATCAAAATTAAAATCTTT-GTTCTCTGAAAGACCCTG 3992
                         i   i i  i                v    -  v  iii  i   v  i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_76628368_7   3993 TGAAGGGGATGAAAAGACAAGCCATAAACTGGCAGGAAGTATTTGCAAAC 4042
                          v   iiii           v   i i v   v  i  i          i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_76628368_7   4043 CATATATCTGACAAAGGACACATATCTAGATTATATAAAGAACTCTCAAA 4092
                                    i  i    vii    i   v               i v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_76628368_7   4093 ACCCTACAATAAAAAAACAAGCAATCCAATAAGAAAATGGACAAAAAGAC 4142
                           i v i        i    ii  i     v?i       i    i-  i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG-GAT 831

  chrX_76628368_7   4143 ATAAAGAGAT-TTTCACCCAAGAGGATATACAATATTTGATGGCAAATAA 4191
                         v i  v   i-    v  v    i         ------     v     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAA------ATGGCCAATAA 875

  chrX_76628368_7   4192 ACACAT---AAGATGTTCAATATAACTGGTTGT 4221
                         i     ---      i    i  v ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (72 / 39)
Gap_init rate = 0.03 (14 / 517), avg. gap size = 2.14 (30 / 14)  


3309 24.22 2.47 0.67  chrX_76642319_76647176     3474  4365 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76642319_7   3474 TAGAATGATATTCCAGGTTCAGGGATTGGAATAATCGATATTATTAAAAT 3523
                          i   v     i   v     v         v v ii     i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76642319_7   3524 GTCCATACTACCCAAAGCAATCTACAGATTCATTACAATCTGTAT-AGAA 3572
                          v v     v      vii             vii     iv   - i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76642319_7   3573 TACCAGTGACATTCTTCACAGAAATACAAAAAACAACCCTAAAAATTTAT 3622
                          v    ivi v  i  ii       vv v  ivii i       -  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCAT 149

  chrX_76642319_7   3623 ATGGAACCACAAAAGACCCAAAATAGCCAAAGCTATACTAAGCCAAAAGA 3672
                               vii   ii      i          i v  vi i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_76642319_7   3673 ACAAAAGTGTAAGAATCACATTACCTGACTTTA-----TACTACAGAACT 3717
                              iv  v i  v     i v  ii i  i -----       i i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_76642319_7   3718 ATAGTAACCAAAACACTATGGTACTGGCATAA----AAACACATAGATCA 3763
                          i     i   i   v i              ---- i   i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_76642319_7   3764 ACACAATAGA-----GAACCCTGAGATAAATGTATAAATCTGCAGTGAAC 3808
                          iiv      -----  ii  v  i     ivi   v  i iii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_76642319_7   3809 TCATTTTTGACAAAGTTGCCATGAATATACCCTGGGGAAAAGACAGTCTC 3858
                          v     i     i v     v  vi  v vv        ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_76642319_7   3859 TTCAGCAAATGGTGCTGGGGAAAACTGGATATACATATTCAGGAGAAAAA 3908
                             i              - v         ?v  i  v  ii    vi 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGG-ACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_76642319_7   3909 AACTAGACCCCTATCTCTCGCCATATATAAAAATCAAGTCAAAATGGATT 3958
                          ii i        i   v i       i      i  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_76642319_7   3959 AAAGATTTAAATCTTAGACCTCAAACTGCAAATCTACTACAAGAAAACAT 4008
                          ?   ii     v v   v  v     ii   v  vi  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_76642319_7   4009 TGGGGAAACTCTCCAGGACATTGGACTAGGCAAAGATTTTTTGAGTAATA 4058
                         v  ? v  v   i iv   v    ii       v i   i  iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_76642319_7   4059 C-CCAACAAGCAGAGGCAACAAAAGCAAAAACAGACAAATGTGATTTCAT 4107
                          -    -     v i          v     i   i    vv  i     
  L1M4_orf2#LINE/    599 CACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_76642319_7   4108 CAAG-TTAAAAAGCTTCTGCGCAACAAAGGACACAGTCAACAAAGTGAAG 4156
                            i-       -   i  i  vv          vi    v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_76642319_7   4157 AGACAACCCACAGGATGGGAGAAAATATATGAAAACTACCCATCTGACAA 4206
                                      i              v  v   ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_76642319_7   4207 GCGATTAATAACCGGAATATATAAAGAACTCAAACAACTCTACAGGAAAA 4256
                          v  i vi  v  i                 vv       v i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_76642319_7   4257 AAAATTTAATAATCTGATTTTAAAATGGACAAA--AT---AATAATCATT 4301
                          i --iv     i ii   ?v       i    --  ---    iv    
  L1M4_orf2#LINE/    797 AGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_76642319_7   4302 TCTCAAAAGAAGACATACCAATGGCAAACAGGTATAGGAAAAGGTGCTCA 4351
                             v        i    v      v  i i i i v      i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_76642319_7   4352 ACATCATTCATTAT 4365
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (126 / 86)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.15 (28 / 13)  


 627 21.34 4.27 3.05  chrX_76767019_76769972      106   269 (2685)    L1M4_orf2#LINE/L1       53   218 (690)  

  chrX_76767019_7    106 CAATACTCCACAAACTAATCTACAGACACGCTGCAATCTCTGTCAGAATC 155
                                  v    i i         iv ivi      i  i   i    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_76767019_7    156 CCAGCTGACTTCTTTGTAAAAATTGACAAGCTCATTCCAAAATTCATATG 205
                                v   i    i i             v  i i            
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_76767019_7    206 GACCAGGCATGGTGGCTCAGACCTATAATCCCAGCACT-TTG-----GGA 249
                           v- v   v  - i i    ---   ii vv i  v -   ----- i 
  L1M4_orf2#LINE/    153 GAA-ATGCAAGG-GACCCAGA---ATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_76767019_7    250 GGCCAAGGTGGAAGGA-TCAC 269
                          iv   i  v i    -    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCAC 218

Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.04 (6 / 166), avg. gap size = 2.00 (12 / 6)  

 466 12.84 8.95 24.51  chrX_76767019_76769972      343   599 (2355)    L1M4_orf2#LINE/L1      140   356 (552)  

  chrX_76767019_7    343 TAAAATTCATAGGGAATTG-AAAACATTCAGAATAGGCAGA-TAATTTTG 390
                                    v    v  -  iiv ii        v  i -i   i   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_76767019_7    391 AAAAATGA----AAAGTATGAAGACTCACACTTCCTAATTTTGCCAGTAC 436
                              vi ----     vv  i             i     ---------
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT--------- 230

  chrX_76767019_7    437 TGCACAGACTTGATTGCCAGTTTTGCAAAACTACACAACAACTTTGGTGC 486
                         -------------------------       --------------- --
  L1M4_orf2#LINE/    231 -------------------------CAAAACT---------------T-- 238

  chrX_76767019_7    487 AACTTTGCACAAAACTGTAAAACAATGCAATCAAGACCGTGGAGTACTGG 536
                         -   ----     i  -----   i --         v   vi       
  L1M4_orf2#LINE/    239 -ACT----ACAAAGCT-----ACAGT--AATCAAGACAGTGTGGTACTGG 276

  chrX_76767019_7    537 TAAAAGGACAAACA-----------------GAATTAAGAGTCCAGAAAT 569
                         i v     i i   -----------------     i             
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_76767019_7    570 AAACCCATATATCTATGACCAGCTGATTTT 599
                                  i  i    ii  ii       
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 2.30 (23 / 10)
Gap_init rate = 0.05 (10 / 217), avg. gap size = 8.60 (86 / 10)  

1770 16.89 2.18 1.91  chrX_76767019_76769972      865  1231 (1723)    L1M4_orf2#LINE/L1      312   679 (229)  

  chrX_76767019_7    865 TGGGATTACAGACATGAGCCACCATGC-CCAACAGTCCCACTGATTTCTG 913
                           i  v v    v  i i  --   i -iiv ii   v- i      ii 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACC--CATACATTTATGGTCA-ATTGATTTTCG 358

  chrX_76767019_7    914 ACAAGGGTGGCAAGACCATTCAATGAAGAAAGAATTGTCTTT-CAATAAA 962
                                  v               ii        v      -   i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_76767019_7    963 TGGTGCTGAGACAACTGGTTAGAAACCTACAAAA-AATGAAGCTGGACCC 1011
                                 i         v  ?vv  v i     -       i       
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_76767019_7   1012 CTACTTCGCAACATATACAAAACATTAACTCAAAGTAGATCAAAGACCTA 1061
                             i  i  v           -           i i     ?       
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAA-ATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_76767019_7   1062 AATTTAAGAACTAAATCTATAAAACTTTTAGAAGAAAACATGGGGGTAAA 1111
                            v     i     v          i              i  ?     
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_76767019_7   1112 TCTTCATTACCTTCAATTTGGTAATGGATTCTTAAA---GACACCAAAAG 1158
                              i v     vii  v  i     v      i ---           
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_76767019_7   1159 AATGAGCAACAAAAGGAAAAACAGATAAATAAAAGTTCATCAAAATTAGT 1208
                         v ii           i     i        vii v             iv
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_76767019_7   1209 AACTT--GTGCTTCAATTAAAGACA 1231
                              --         --- i    
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAA---AGGACA 679

Transitions / transversions = 1.68 (37 / 22)
Gap_init rate = 0.02 (9 / 368), avg. gap size = 1.67 (15 / 9)  

 253 13.98 3.23 9.68  chrX_76767019_76769972     1522  1614 (1340)    L1M4_orf2#LINE/L1      688   774 (134)  

  chrX_76767019_7   1522 AAAATAAATAAAGACAACTCAAAGAATAGGGGAAAATATTTCCAAATTAT 1571
                            i i  --        i  v     i  i          v     i  
  L1M4_orf2#LINE/    688 AAAGTGAA--AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_76767019_7   1572 ATATCTTATCCAAGTGTCCATTGAAATAT---GAATAGATAAACAA 1614
                               v  --   v v --   ---   ---     v     v  
  L1M4_orf2#LINE/    736 ATATCTGAT--AAGGGAC--TTG---TATCCAGAATATATAAAGAA 774

Transitions / transversions = 0.86 (6 / 7)
Gap_init rate = 0.06 (5 / 87), avg. gap size = 2.40 (12 / 5)  

 373 15.07 1.37 0.00  chrX_76767019_76769972     2004  2076 (878)    L1M4_orf2#LINE/L1      756   829 (79)  

  chrX_76767019_7   2004 ATTTAGAATATATAAAGAATTCTTACAAATCAACAATGAAAGCATAAAT- 2052
                           ii               i        v    i   i   iv i    -
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_76767019_7   2053 ACCCATTTTAAAAATGGGCAAAGG 2076
                              v  ?               
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1)  

 494 15.96 0.00 0.00  chrX_76767019_76769972     2368  2461 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_76767019_7   2368 AAGACTGGACAGAGGGTTTGAATAGAAGTTTCTCCAAGGAATATATACAA 2417
                           i v   i  i   i          vi         i   v        
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_76767019_7   2418 ACTACAAATAAGCACATGAAATGATGTTCAACATCATTACCCTT 2461
                          ivi v               v    i         ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3081 26.03 0.54 2.48  chrX_76782068_76784724     1239  2164 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_76782068_7   1239 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 1288
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76782068_7   1289 GGCCATACTGCCCAAAGTAATGTATACATTCAATGCTATCCCCATCAAGC 1338
                            v     v      v i  v  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76782068_7   1339 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAAAAGCT-ACTTTAAAT 1385
                          v   -   v    i  -i     -   ----- v     - iii    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG-----ACAAGCTGATCCTAAAA 144

  chrX_76782068_7   1386 TTCATATGGAACCAAAAAATACCCCACAGGGCCACGACAATCCTAAGCAA 1435
                                    viiv  iiv    viv vi    vi      i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_76782068_7   1436 ACAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACA 1485
                         iv         i      vv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_76782068_7   1486 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 1535
                          i          i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_76782068_7   1536 GAACAATGGAACAGAACCGAGGCCTCAGAAATAACACCACATATCTACAA 1585
                           v        i    ii   ivii         vv   i i  i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_76782068_7   1586 CCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGAGAAAGGACT 1635
                         i  vi    i  i     ivv  v   i v  vv      i     i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_76782068_7   1636 CCCTATTTAATAAATGGTGTTTGGAAAACTGGCTAGCCATATGCAGAAAA 1685
                         vi  v  i  i        i v   v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_76782068_7   1686 CTGAAGCTGGACTCCTTCCTTACACATTATATAAAAATTAACTCAAGATG 1735
                         v     i     i   v   i    vv    i              i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_76782068_7   1736 GATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAA 1785
                            i ?    i    ii     v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_76782068_7   1786 ACCTAGGC--AAACCACCATTCAGGACATAGGCATGGGCAAAGACTTCAT 1833
                           v    ?--   i ----   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC----TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_76782068_7   1834 GACTAAAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGG 1883
                         iiv  vi            vvii         vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_76782068_7   1884 ATCTAACTAAACTAAAGACCTTCTGCACAGCAAAAAAAAAATATATATAT 1933
                          ii v ii   v v  i v   i  ii vv    ii ----------i i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA----------CAC 680

  chrX_76782068_7   1934 ATATCTCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAACTTTTTTG 1983
                         -    -- vv i      v  i     i              vv v    
  L1M4_orf2#LINE/    681 -TATC--AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_76782068_7   1984 TGATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTT 2033
                         ii vii  vi      i  i  i  vi          v  i        i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_76782068_7   2034 AAACAAATTTACAAGAAAAAAGCAAACAACCCTAACAAAAAGTGGGCAAA 2083
                         vv    v iv i  v     ii    i     v vi?    i        
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_76782068_7   2084 GGATATGAACAGACATTTCTCAAAAGAAGACATTTATGTGGCCAACAAAC 2133
                             v    i           v        i  vi vi       i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_76782068_7   2134 ATATGAAAAAAAACTCATCATCACTGGTCAT 2164
                          i       i vi    v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.80 (28 / 10)  


1156 20.93 11.05 7.27  chrX_76852254_76854956     1001  1344 (1359)    L1M4_orf2#LINE/L1        1   357 (551)  

  chrX_76852254_7   1001 TAGAAGGGTATCCCATGCTGATGAATTAGAGGACTTAATGTTGTAAAAAT 1050
                          i   i i         i v   i   i  i        i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76852254_7   1051 GTCCATACTACTCAAAGGAATCTACAGATTCAATGCAATCCCTATCAAAA 1100
                          v v     v i    vvi              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_76852254_7   1101 TCCCAATGGCATTCTTTGCAGA----GAAAAACCCATCCTAAAATTTCCG 1146
                              iiv  v  i        ----  v  i iv           ivii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_76852254_7   1147 TGGGATCTCAAAGGATGCTGAAAAGCTAAAACAATCTCAAAAAAAAAAAA 1196
                            i viv   i   iv v   v   i          ii     i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_76852254_7   1197 AACAAAAACAAACAAAAAAAAACAGCAAAGCTGGGGGCCACAAATTTCCT 1246
                         -------------------------     i   i  v v  v i    i
  L1M4_orf2#LINE/    201 -------------------------CAAAGTTGGAGGACTCACACTTCCC 225

  chrX_76852254_7   1247 GATT----------------------AGTAAACAAGATGGTGTGGTACTG 1274
                         i   ----------------------     v     ii           
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_76852254_7   1275 ACTTAAAAATAGATATATGGACCAATGAAACAGAAT------------AA 1312
                         i v   ii     i    i  i     i  i     ------------  
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_76852254_7   1313 TAAACCCTTGCATATATGGCCAAATAATTTTC 1344
                                v i   v     i   v i      
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTC 357

Transitions / transversions = 1.88 (47 / 25)
Gap_init rate = 0.01 (4 / 357), avg. gap size = 15.75 (63 / 4)  

2494 19.44 4.81 0.00  chrX_76852254_76854956     1671  2210 (493)    L1M4_orf2#LINE/L1      343   908 (0)  

  chrX_76852254_7   1671 GGCCAAATGATTTTTGACAAGGATTCCAAAACTACACAATGAG-AAAGGA 1719
                           i   v       i       i v    i  i iv     i -    i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_76852254_7   1720 CAGTTTCTTCAATAAATGGTGTTAGAAGTACTAGATATCCACATGTAAAA 1769
                         i   i i     i        i i i vv   i    ?       i    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_76852254_7   1770 GAATGAAGTTGGACCCTTATCTGACACCACATACAAAAATTAACTCAAAG 1819
                                         i  i  v      i                   i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_76852254_7   1820 CAGATTAAAAAACTAAACATAAGACATAAAACTATAAAACTCCTGGAAGA 1869
                         ii   i ? i v     ii     vv                i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_76852254_7   1870 AAACATAGACGAAAAGCTTCAGGACATTATATTTGGCAATTATTTCTTGG 1919
                                 i? v   v    iv   v  ivi  v      vi      i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_76852254_7   1920 CTATGACACCAAAAGCACAAGCAACAAAAGCAAAAAAAGGCAAGTGAGGC 1969
                         v                             v     v  ii  i vi i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_76852254_7   1970 TACATCAAACTTAAAAACTTATTCACGTAAAAAGAAACTATCAACCGAGT 2019
                          v       v          v vii v v   i  v        vvi   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_76852254_7   2020 GAAAAGACAACCTATGAAATGAGAGAAAATATTTGTAAGTCGTATATCTG 2069
                                     i iii    i             i  i  i        
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_76852254_7   2070 ATAATGGGTTAATATTCAGAATATAAAAGGGACTTCTA------------ 2107
                             v  ii vi   i         v  i i   ii  ------------
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_76852254_7   2108 AAAAA------------AATTCAAAAATGTGCAAAGGACTTGAATGGACA 2145
                              ------------    ?       v        i      i    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_76852254_7   2146 ATTCTCTAAAGAAAATATA-AATTGGCCATTAAGCATATGAAAAGATGCT 2194
                         v     i      i     -  v      v      i             
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_76852254_7   2195 CAACATCACTAATCAT 2210
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (65 / 36)
Gap_init rate = 0.01 (4 / 566), avg. gap size = 6.50 (26 / 4)  


 968 24.01 20.06 0.00  chrX_76856717_76858840      500   828 (1296)    L1M4_orf2#LINE/L1      268   662 (246)  

  chrX_76856717_7    500 TGTTATTGGTGAAAGAATAGACAAATAGACCAAAGGGATAGAATAGAGAG 549
                           v  i   iiv   i       v     i   v  i       v     
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_76856717_7    550 ACCAGAAATAGACCCACACAAATATAGTCAACTGATCTCTGACAAAGA-- 597
                         v         i     i   vv   i     i    i ii     i i--
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_76856717_7    598 ------------AACGAAAAAAAAAAAGACTCT-----AAA--------- 621
                         ------------  i iii   i  v  v  i -----   ---------
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_76856717_7    622 ----------------CAT-----AGA-----------------CCTTAC 633
                         ----------------   -----   -----------------   i  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_76856717_7    634 ACTTTTCACAAAAATTAATTCAAAATGGATCATAGATCTAAATTTAAAAC 683
                           iv vi           i             ?   i      v   i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_76856717_7    684 ACAAAGCTATAAAATCCCTAGAAGATAGCACAGGATAAAATCCAGATGAC 733
                         vi   i        ii i       v i  i   ?vv     ivvi    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_76856717_7    734 CTTGGGTTTGACAATGACTTCTTAGGTATAACACAAAAAGTATGATCCAT 783
                                 v i     ii       i   i    v     i ii v v i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_76856717_7    784 AAGAGAAAAAATTGATAAGTTGGATTTTATTAAAATGGAAAACTT 828
                           i         v     i     i  i  i     vi       
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

Transitions / transversions = 1.96 (51 / 26)
Gap_init rate = 0.01 (5 / 395), avg. gap size = 13.20 (66 / 5)  

 801 21.09 11.72 0.00  chrX_76856717_76858840     1390  1645 (479)    L1M4_orf2#LINE/L1      623   908 (0)  

  chrX_76856717_7   1390 AAAAAATAAA--AATAAAAT------AAAATGGAAAACTTGTGCTCTGCA 1431
                                 i --   vii i------     vi       v  iv  v  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_76856717_7   1432 AAAGAAATTGTTAAGGGAATGAAAACACAAGCCACAGAC--AGAGAAAAT 1479
                           i  v i i i   ii i      v    v       v--i        
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_76856717_7   1480 CTTTGCAAAACACATATTTGATAAAGAACTGGTATCCAAAATATA---AG 1526
                         v        v  i    i      i i   v       i      ---  
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_76856717_7   1527 AAATCTTCCCACTCAACAATAGGAAAACAAA-GACCTAATTTAAAAATGG 1575
                           v    v v      i    ii  i     -i   i    ?        
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_76856717_7   1576 ACAAAAAACTTG----GAAACCTCACCAAAGAAGATATACATATGGCAAA 1621
                         i    ii i   ----  v ii  v                v     v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_76856717_7   1622 TA-GC-----------TTCTCAGTATCATATGTCAT 1645
                           -  ----------- v    ii    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (33 / 20)
Gap_init rate = 0.03 (8 / 286), avg. gap size = 3.75 (30 / 8)  


 913 26.47 0.65 4.58  chrX_76870046_76872320.rev      592   897 (1378)    L1M4_orf2#LINE/L1        1   294 (614)  

  chrX_76870046_7    592 TGGAAACACATCCCATGCTCACGAATGAGTAGAACAAATATAGTGAAAAT 641
                               v i        i   i i  vi v   viv     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_76870046_7    642 GGCCAATATTTTGAAATAATTGCCAAAAGCAATCTACATATTCAATGCAA 691
                            -    i i-----------  v   vii       v      i    
  L1M4_orf2#LINE/     51 GGC-AATACTC-----------CCCAAATTGATCTACAGATTCAACGCAA 88

  chrX_76870046_7    692 TTTCCATCAAAATTCCATCATCATTCTTCACAGAATTTTTTAAAA-AACC 740
                          ii i        i   v vv v  i  ii     v  vvi  iv-i i 
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chrX_76870046_7    741 CTAAAATTCATATGGAACTAAAAAAAGAGCCCACA-TAGCCAAAGCAATA 789
                                          v iv  i-- ii    v -        i    v
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATC 186

  chrX_76870046_7    790 CCAAATAAAAAGAACAAATCTGGAGGCATCACATTACCTGACTTCAAACC 839
                         iii  v  i         vi      vv     i v  ii i      v 
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_76870046_7    840 ATACTACGAGGCTATAGTTACCAAAACAGCATGGCAATGGTATAAAAATA 889
                         v      i i    i   v i   i    ii   i v   i    ii   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_76870046_7    890 GGCATGTA 897
                          i   i  
  L1M4_orf2#LINE/    287 GACATATA 294

Transitions / transversions = 1.61 (50 / 31)
Gap_init rate = 0.02 (5 / 294), avg. gap size = 3.20 (16 / 5)  

1995 25.17 5.33 0.17  chrX_76870046_76872320.rev     1185  1784 (491)    L1M4_orf2#LINE/L1      278   908 (0)  

  chrX_76870046_7   1185 ATAAAAA-AGGCATGTAGGCCAATGGAACAGAATAGAGAGCCCAGAAATA 1233
                             ii -  i   i   ii        i     v     i         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_76870046_7   1234 AAGCCAAATGCTTATAGCCAACTTATTTTTGACAAAGCAAACAAAAACAT 1283
                           v   v iii    i i   i v     i     i vviv   i v   
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_76870046_7   1284 AAAGTGGGGAAAGGACACCCTATTCAACAAATGGTGCTGGGATAATTGGC 1333
                         vv i         i i vi  v                    i  i   v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_76870046_7   1334 AAGCCACATGCAGAAGAATGAAACTGGATCCTCATCTTTCATCTTATACA 1383
                         v ?         i         ii    i  ii i  iv  i v      
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_76870046_7   1384 AAAATCAACTCAAGATAGATCAAAAATTTAAATATAAGACCTGAAACCAT 1433
                              i       i  i     ? i ii     i     v  i    i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_76870046_7   1434 AAAAATTCTAGAAGATAACATCAGAAAAACTCTTCTAGACATTGGCTTAG 1483
                             v ii       v     vi ?iv  v     vv   v    v    
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_76870046_7   1484 ACAAATAATTCATGACCAAGAACTCAAAAGCAAATGTGACAAAAACAAAA 1533
                         i   vviv   v iivi v  vvi        v v ii      iv    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_76870046_7   1534 GTAAATAGATGGGACCT----AAAA-----AGCTTCTGCACAGCAAAACA 1574
                         i  i   i  v    i ----    ----- i   i  ii vv    iv 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_76870046_7   1575 AACAATCAGCAGAGTAAACAGACAACCCA--GAGTGGAAGAAAATATTCA 1622
                         v  v    iv i   i  v          --  i   i          ii
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_76870046_7   1623 CAAA----------------GGCCCAATATCTAGAATCTACAAGGAATTC 1656
                             ----------------  v ivi    i     v  i  i   i  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_76870046_7   1657 ----AAATCAGCAAGAAAAAAAACCAATAATCCCGTCAAAAAGTGGGCCA 1702
                         ----  v   ii  v     i - v     i  vi i?    i     v 
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_76870046_7   1703 AGGACATGAATAGAGAATTCCCAAAAGAAGATATACAAATGGCCAACAAA 1752
                             iv        v v   i v                       i  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_76870046_7   1753 CACATGAAAAAATGGTCAACATCACTAATTAT 1784
                                   i   v         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (89 / 58)
Gap_init rate = 0.01 (7 / 631), avg. gap size = 4.71 (33 / 7)  


3119 27.39 0.66 0.77  chrX_77138253_77143672.rev     4021  4929 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77138253_7   4021 TGGAAGAGCATTCCATGCTGATGGATAGGAAGAATCAATATCATGAAAAT 4070
                              iiii  i     i v      v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77138253_7   4071 GGCCATACTGTCCAAGGTAATTTAAGGATTCAGTGCCATCCCCATCAAGC 4120
                            v     vi    iv i  i  vi      ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77138253_7   4121 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4168
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_77138253_7   4169 TATGGAACCAAAAAAGACCCCACATTGTCAACTCAATCCTAAGCCAAAAG 4218
                                viiv  ii     viv  v i   vv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77138253_7   4219 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4268
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77138253_7   4269 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAAC 4318
                                 i   i    ii         i iv ii i   v       v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77138253_7   4319 AATGGAACAGAC---AGAGCCCTCAAAAATAATACCACACATCTACAACC 4365
                                i   v---    i  -- i      vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_77138253_7   4366 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4415
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_77138253_7   4416 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4465
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_77138253_7   4466 GAAACTGCATCCCTTCATTACACCTTATACAAAAATTAACTCGAGATGGA 4515
                            ii  v i    v v i     v                 i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_77138253_7   4516 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAATCCCTAGAAGAAAAC 4565
                          i ?    i       v   v       i      ii i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_77138253_7   4566 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 4614
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_77138253_7   4615 AAACACCAAAAGCAAAGGCAACACAAGACAAAATTGACAAATGGGATCTA 4664
                         vi            v i      v    v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_77138253_7   4665 ATTAAACTAAAGAGCTTCTGCACAGTGAAAGAAACTACCATCACAGTGAA 4714
                           i   v v  i i   i  ii vvii  i  v    i  vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_77138253_7   4715 CAGGCAACCTGCAGAATGGGAGAAAATTTTTACAATCTACCCATCTGGCA 4764
                         v  i     ii                v   i   vii ivi     ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_77138253_7   4765 AAGGGCTAATGTCAAGAATCTACAAAGAACTCAAACAAATTTGTGAGAAA 4814
                          i  i  vi i  v     v  i         vv    v ivi i v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_77138253_7   4815 AAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 4864
                           i --    i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    796 AAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_77138253_7   4865 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACAAGAAAAAATGCTC 4914
                              v        i  vi viii     i ii    v     i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_77138253_7   4915 ATCATCACTGGCCAT 4929
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2861 26.40 0.71 0.95  chrX_77207089_77213575.rev     5156  5996 (491)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_77207089_7   5156 ATCTACAGATTCAACAAAATTTCCATCAGTATACCGATGACATTCTTCAC 5205
                                        iv   ii i    iv  v  iiivi v  i  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_77207089_7   5206 AGAAACAGAAAAAACAATCCTAAAATGTTTATAGAAC--CAATAAAACTC 5253
                              iv  v  ivii          viv   i   v--   -iii  - 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA-GGGAC-C 167

  chrX_77207089_7   5254 CAGAATAGCCAATGCTATCCTAAGCAATAAGAACAAAACTGGAGGAATCA 5303
                                     vi v   i i iv  v         ii       v   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_77207089_7   5304 CATTACCTGACCTCAAATTATATTACAGAGCTACAGTTACCAAAACAACA 5353
                           i v  ii ii     viv  i    i         v i   i   iii
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_77207089_7   5354 TGGTACTGGCATTAAAACGGACACATAGACCAATGGAACAAAGTATAAAA 5403
                                     v ii ii    i     i        i i i vv i i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_77207089_7   5404 TCCAGAAACAAATCCACACAAATACAGTGAACTCATTGTTGACAAAGGTG 5453
                                 i   i   i   vv  ii  v  i v   v i     i    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_77207089_7   5454 CCAAGAATGTACACTGGGAAAAAGACACTCTCTTCAATAAATGGTGCTGG 5503
                               vii v  v    i   ii i v   i     i            
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_77207089_7   5504 GAAAACTGAATATCCATATGCAGAAGAATGAAACTAGACTCATATATCTC 5553
                           v     i   ?   i     i         ii i   i v  i--   
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC--CTC 465

  chrX_77207089_7   5554 TTGCCATATACAAAAATCAAATCAAAATGGATTAAATACCTAAATCTAAG 5603
                         vii              i  v           i ? v        v    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_77207089_7   5604 ACCTGAAACTATGAAACTACTGAAACAAAACACTGGAGAAATTCCAAGAG 5653
                          v  i       i     vi ii  v      iv  ? v  v  ivv v 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_77207089_7   5654 GCATCAATCTTGGCAAAGATTTCTTGAGTAATACCCCACAAGCACAGGCA 5703
                         i v iiivi v     v i      iii  vv  v   v       i   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_77207089_7   5704 ACCAAAGCAAAAATAGGCAAATGAGATCACATCAAG-TTAAAAAGCTCCT 5752
                           v    v        ii    vi  iiv      i-       -  ii 
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTT 664

  chrX_77207089_7   5753 GTACAGCAAATGGTACAACCAACAATGTGAAGAGACTACCCACAGAATAG 5802
                           i vv    v ii  v i   v  v     i    v           i 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_77207089_7   5803 GAGAAAATATTTGCAAACTACCCATCTGACAAGGGATTAATAACCAGACA 5852
                                          ii ivi      i      i vi  v     vv
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_77207089_7   5853 ATATAAGAAGCTCAAACAACTCTATAGGAAAACAATCTAATAATCTGATT 5902
                               ii i   vv       v   iv    vi - v     i ii   
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATT 813

  chrX_77207089_7   5903 TTAAAAAATAGGCAAAAGAGTTGAATAGACATT-ATCAAAAGAAGACACA 5951
                         ?--      i      i  v             -v  v        i i 
  L1M4_orf2#LINE/    814 W--AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_77207089_7   5952 AAAATGGAAAAT--GTATATGAAAAGGTGTTTGACATCACTGACCAT 5996
                         v      vv   -- i i        i  i ii      ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (135 / 83)
Gap_init rate = 0.01 (10 / 839), avg. gap size = 1.40 (14 / 10)  


3136 27.42 0.66 0.66  chrX_77214336_77220171.rev     4438  5345 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77214336_7   4438 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAAGATCGTAAAAAT 4487
                              ii i  i     i      i v      v i  v  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77214336_7   4488 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 4537
                            v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77214336_7   4538 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT--TCTTTAAAGTTC 4584
                          v   iivi i  i  ii     -   -- v  i  --  i -   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCT-AAAATTC 147

  chrX_77214336_7   4585 ATATGGAATCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAA 4634
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_77214336_7   4635 GAACAAAACTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 4684
                                ii      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_77214336_7   4685 CTACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAGATATAGAC 4734
                                  i   ii   ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_77214336_7   4735 CACTGGAACAGAAT--AGAACCCTCAGAAATAATGCCGCATATCTACAAC 4782
                           v     i     --   ii  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_77214336_7   4783 TATCCAATCTTTGACAAACTTGACAAAAACAAGAAATGGGGAAAGGATTC 4832
                         i viii  i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_77214336_7   4833 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGTAGAAAGC 4882
                         i  v  i  i              v      v  ?   v   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_77214336_7   4883 TGAAACTGGATCCCTTCCTTACACGTTATACAAAAATTAATTGAAGATGG 4932
                             ii    i    v   i    vv              i v  i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_77214336_7   4933 ATTAAAGACTTAAATGTTAGTCCTAAAACCATAAAATCCCTAGAAGAAAA 4982
                           i ?    i       v  vv       i      ii i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_77214336_7   4983 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAACGACTTCATGACT 5031
                          v    ?i- v i -   iv   v v  vv i     i ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_77214336_7   5032 AAAACACAAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5081
                          vi    v       vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_77214336_7   5082 AATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5131
                         v  iv  v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_77214336_7   5132 ACAGGCAACGTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5181
                          v  i    vi                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_77214336_7   5182 CAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAA 5231
                         v i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_77214336_7   5232 AAAAACAAACAACCCCATCAGAAAGTGGGCGAAGGATATGAACAGACACT 5281
                            i     i     v  i?i   i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_77214336_7   5282 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5331
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_77214336_7   5332 TCATCACTGGCCAT 5345
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


2663 27.28 2.51 0.80  chrX_77245740_77256394     3875  4750 (5905)    L1M4_orf2#LINE/L1        1   891 (17)  

  chrX_77245740_7   3875 TGGAAACACAACCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3924
                               v i v      i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77245740_7   3925 GACCATATTGCCAAGAGCATTCTACAAATTCAATGCAATCCCCATCAAAA 3974
                          i v   i v  v i viiv      i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77245740_7   3975 TACCA--TAATCATTCTTCACAGAATTAGAAAAAA-AATTCTAAAATTCA 4021
                          v   -- i-- v  i  ii     v v  v  iv-i  i          
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_77245740_7   4022 TAAGGAACTAAAAAAGACCCCTCGTAGCAAAAGGAAGACTAAGCAAAAAG 4071
                           v    v iv  ii     vvvi    v   iv  vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77245740_7   4072 AACAAATCTGGAGGCAC-CACACTACCTGATTTCAAACTATACTATAAGG 4120
                               vi      -  -      v  ii        viv     i  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_77245740_7   4121 CCATAGTCACGAAAACAACATGGTACTGGCATAAAAATACATGCGTAGAC 4170
                          i i   v iv  i   iii              ii   v iiii    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_77245740_7   4171 CACTGGAACAGAATAGAGAACCCAAAAATAAACCCAAA----TACAGCTA 4216
                           v     i     v    ii   i           v ----  ii ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_77245740_7   4217 ACTAATCTTCGACAAAGCAAACAAAAAACATAAAGTGGGGAAAGGACTAC 4266
                          i i  i        i -ivi v  i v   vv i         i ivii
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_77245740_7   4267 CTTTTCAACCAAATGGTGCTGGGATAATTGGCTAGCCATATGCAGGAGAA 4316
                                  -              i  i   v  ?   i     ii    
  L1M4_orf2#LINE/    397 CTTTTCAAC-AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_77245740_7   4317 TGAAACTGGATCCTCATTTCTCACCTTATACAAAAATCATCTCAAGATGG 4366
                             ii    i  ii ii  v    v           i v     i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_77245740_7   4367 ATTAAGGACTTAAACCTAAGACCTGAAACTATAACAATTCT-AGAAGATA 4415
                           i ?i   i    iv     v  i         -  i   -      v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAA 544

  chrX_77245740_7   4416 ACATTGGAA-AAATCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGAC 4464
                             v  ?i-     -   vv   v    v        v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_77245740_7   4465 CAAAAACCCAAAAACAAATGGAATAAAAACAAAGATAAATAGCTGTGACC 4514
                         i vi vv      i  v v v  i    iv   i   i   iv vv   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_77245740_7   4515 TAATTAAACTAAAGAGCTTTTGCACAGCAAAAGGAAGAGTGAGCAGAGTT 4564
                          v  i   v v  i i      ii vv    i iv vvi v iv i   v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_77245740_7   4565 AACAGACAACCCACAGAGTGGGAGAAAATCTTCATAATCTATACATCTGA 4614
                           v              i           v  iii  vii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_77245740_7   4615 CAAAGGAATAATAACCAGAATCTACAATTAACTCAAACGAATCAG----A 4660
                         i  i   v vi  v       v  i  vv     vv  i v   i---- 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_77245740_7   4661 AAAA---AAACAATCCCATCAAAAAGTGAGCTAAAGAC---AA-GGACAA 4703
                             ---   i  i  v  i?    i  i  v  i  i---  -i    v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_77245740_7   4704 TCCTCAAAAGAAGATATGCAAATGGCCAACCA-CGTATGAAAAAATGC 4750
                          i   v           i           iv - ii       i    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.02 (17 / 891), avg. gap size = 1.71 (29 / 17)  

3043 28.56 0.33 0.22  chrX_77245740_77256394     9256 10162 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77245740_7   9256 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATGAAGATCGTGAAAAT 9305
                              ii i  i     i      i v      v v  v  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77245740_7   9306 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATGAAGC 9355
                            v i   v     iv i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77245740_7   9356 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 9403
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_77245740_7   9404 TATGGAATCAAAAAGGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAT 9453
                                viiv  i   v  v v  v     iv     i i ivv i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77245740_7   9454 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 9503
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77245740_7   9504 TACAGTAACCAAAATAGCATGGTAGTGGTACCAAAACAGAGATATAGATC 9553
                                 i   i i  ii     v   i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77245740_7   9554 AATGGAA-AGAACAGAGCCCCCAGAAATAATGCCGCATATCTACAACTGT 9602
                                -    iv   vvi          vv  ii i  i  iiiiiiv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_77245740_7   9603 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 9652
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_77245740_7   9653 ATTTAATAAATGGTGCTGGTAAAACTGGCTAGCCATATGTAGAAAGCTGA 9702
                         v  i  i            v v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_77245740_7   9703 AACTTCATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 9752
                          ii vv i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_77245740_7   9753 AAAGGCTTAAACGTTAGACCTAAGACCATAAAAACCCTAGAAGAAAACCT 9802
                          ?  i i    i  v   v    i  i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_77245740_7   9803 AGGCATTAGCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 9852
                            ?i v iiv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_77245740_7   9853 CACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 9902
                            v       vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_77245740_7   9903 CAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 9952
                         v  v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_77245740_7   9953 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 10002
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_77245740_7  10003 GGCTAATATCCAGAATCTACAATGAACTCAAAGAAATTTACAAGAAAAAA 10052
                          i  vi          v  i  v      vv v  v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_77245740_7  10053 ACAAACAACCCCATCAAAAAGTGGGCGAAGTAAATGAACAGACACTTCTC 10102
                              i     v  i?    i     i   v vv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_77245740_7  10103 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 10152
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_77245740_7  10153 CACTGGCCAT 10162
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.32 (145 / 110)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.25 (5 / 4)  


3013 27.31 0.99 0.99  chrX_77266690_77269927     1838  2745 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77266690_7   1838 TGGAAAAACATTCCAAGCTCATGGATAGGAAGAATCAGTATTATGATAAT 1887
                               i i  i   v i        v      v i i    i v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77266690_7   1888 GGCCATACTGCC-AAAGTAATTTATAGATTCAATGCTATCCTCATCAAGC 1936
                            v     v  -   v i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77266690_7   1937 TACCATTGACTTTCTTCACAGAGTTAGAAAAAACT-ACTTTAAAGTTCAT 1985
                          v   vivi i  i  ii    iv v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_77266690_7   1986 ATGGAACCAACAAAGAGCCT-GTATAGCCAAGACAATCCTAAGCAAAAAG 2034
                               vii-   i ii  i- v        i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77266690_7   2035 AATAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2084
                           i    i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77266690_7   2085 TACAGTAACCAAAATGGCATGGTACTGGTACCAAAACAGATATATAGACC 2134
                                 i   i ii ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77266690_7   2135 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCATACATCTACAACC 2182
                                i    i--    i  --        vv        i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_77266690_7   2183 ATCTGATCTTTGACAGACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 2232
                          vi    i  i    iivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_77266690_7   2233 CTATTTAATAAATTTTGTTGGGAAAACTGGCTACCCATGTGTAGAAAAAT 2282
                           v  i  i    vv  i     v      v  ?   ii  i i  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_77266690_7   2283 GAAACTGGATCTCTTCCTTACAACTTATACAAAAATTAACTCAAGATGGA 2332
                            ii    i i  v   i   v v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_77266690_7   2333 TTAGTGACTTAAATGTAAGACCTAAAACCATAAAAACCCCAGAAGAAAAC 2382
                          i ?v   i           v       i      vi ii          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_77266690_7   2383 CTAGGCAGTA--CCATTCAGGGCATATACATGGGCAAAGACTTCATCATT 2430
                         v    ?-   --i -   iv i v vvivv i     v ii   v viv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_77266690_7   2431 AAAACATCTAAAGCAATAGCAACAAAAGCCAAAATTGACAAATGGGATCT 2480
                          vi   i v      vv           vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_77266690_7   2481 AATGACAATAAAGAACTTCTGTACAGTGAAAGAAACCATCATCAGCAGG- 2529
                         v  v v   v  i     i   i vvii  i  v  i    --  v i -
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--AGAAAGT 692

  chrX_77266690_7   2530 -AATAGGCAACATACATAATGGGAGAAATTTTTTGCAATCTATTCATCTG 2578
                         -  v  i    vi   v           v v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_77266690_7   2579 ACAAAGAGCTAATATCCAGCATCTACAAAGAACTTAAACAAATTTGCAAG 2628
                          i  i ii  vi       v  v  i        ivv    v ivii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_77266690_7   2629 AAAAAAATCAAACAACCCCATCAGAAAGTGGGCGAAGGATATGAACAGAC 2678
                              i -    i     v  i?i   i     i      v    i    
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_77266690_7   2679 ACTTCTCAAAACAAGACATTTATGCAGCCAACAGACACATGAAAAAATGC 2728
                          i     v   v    i  vi viii     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_77266690_7   2729 TCATTATCACTGGTCAT 2745
                            vi    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.38 (18 / 13)  


3164 25.76 0.87 1.75  chrX_77271986_77274809.rev     1418  2333 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77271986_7   1418 TGAACAGATATTCTATTTTCATTGATTCAAAAAAATAATATTGTTAAAAT 1467
                           i v      i i  v     v    vi  i vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77271986_7   1468 GTCTACATTACCAAAAGCAATCTACAGATTCAGTGCAATCCCTATCAAAA 1517
                          v v i i v  v   vii             ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77271986_7   1518 TACCAAAGACATTCTTCACAGACATAGAAAAAA-AATCCTGAAATTTATA 1566
                          v   ivvi v  i  ii    v  v  v  iv-i     i     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_77271986_7   1567 TAGAACCACAAAAGACTTAGAATAGCCAAAGTTATCCTAAGAAAAAATAA 1616
                          i   vii   ii   ii            iiv   i i i   i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_77271986_7   1617 CAAAACTGGAGGAACTACATTACCTGACTTCAAATTATACTGCAGAGCTA 1666
                             ii       vii   i v  ii i      viv    i  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_77271986_7   1667 TAGTCACCAAAACAGCATGGTATTAGCATAAAAACAGAGACACAGACCAA 1716
                         i   v i   i    ii     i i      ii i   v i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_77271986_7   1717 TAGAACAGAAAAGAGAACCCAGAAACAAATCCACTCACCTACAG-AAACT 1765
                          i   i    vv    ii       i   i   iv  ii  ii -v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_77271986_7   1766 CACTTTTTATGAAGGTGGCAAAAATATACACTGAGGAAAAGACAGTCTCT 1815
                         v i   iv ii i    v   i vi  v  v  i     ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_77271986_7   1816 TCAATAAATGGTTCTGGGAAAACTAGATATCCATATGCAGAAGAATGAAG 1865
                             i       v      v    i    ?   i     i          
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_77271986_7   1866 CTGGACTCCTATCTCTCACCATAC-TAAAAA--AAATCAAAATGGATTAA 1912
                         i     i    i   v       i-i     --  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_77271986_7   1913 AGACTTAAGTTTAAGACTTCAAACTATAAAACTGCTACAAGAAAACATTG 1962
                             i   i v     vi v             vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_77271986_7   1963 GGGGGACTCTCCATGACATCAGTCTGAGCAAAAATTTCTTGAGCAATACC 2012
                          ? vi v   i i    v ii vi ii    vii      -  vv  iv 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGAC 599

  chrX_77271986_7   2013 CCCACAAACACAGGCAACCAAAGCAAAAATGGGCAAATGCGA--TCA-CA 2059
                         v   v  i    i     v    v      i ii    vv  --   -  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_77271986_7   2060 ACAATTTAAAAAGCTTCTGAATAGCAAAGGATGCAATCAACAAACTGAAG 2109
                          -    --    i   i  viivv       ii v     v   v    i
  L1M4_orf2#LINE/    650 A-AATT--AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_77271986_7   2110 AGACAACCCACACAATGGGAGAAAATACTAGCAAACTACCCATCTGACAA 2159
                                     v              i v     ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_77271986_7   2160 GGGATTAAAGGGGATTAATAACCTGAATATCAAATTATTTCTTATCAACT 2209
                             i --------- i-  v  v      vv  vv vi     -     
  L1M4_orf2#LINE/    747 GGGACT---------TG-TATCCAGAATATATAAAGAACTCTTA-CAACT 785

  chrX_77271986_7   2210 CTATAGGAAATAATCTAATAATCTGATCAAAAAATGGGCAAAAGATCTGA 2259
                          v   iv   v iv v     i ii  i?             i   i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_77271986_7   2260 ATAAACATTTCTTCAAAAGAAAACATATAAATTGCAAACAGGTATATGAA 2309
                            i        i    -   i i   i    v  v  i i i i     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_77271986_7   2310 AAGGTGCTAAACATCATTGGTCAT 2333
                            i    v       ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (146 / 86)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


2556 29.13 1.55 1.00  chrX_77279540_77281972.rev     1040  1942 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77279540_7   1040 TGGATAAACATTCCACGTTCATGGATAGGTAGAATAAATAT-GTTAAAAG 1088
                             v i i  i   i          v  v   v v     -     i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77279540_7   1089 GGCCAAACGGCCAAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAG 1138
                            v v  vv  v   vii  i           i  v  i         i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77279540_7   1139 TACCAA-TGTCATTCTTCACAGAACTAAAAATAAGT--ATTCTAAAATTC 1185
                          v   i-  i -  i  ii     v vi --i   i--  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTC 147

  chrX_77279540_7   1186 ATACAGAACCAAAAAAGAGCCCAAATACCCAAGACTTTCCTAAGCAGAAA 1235
                            ii   viiv  ii  v  vi    v    i  vv  i i iv ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_77279540_7   1236 GAACGAAGCTTGAAGTA-TCACCTTATACAACTTTAAACTATTCTACAAT 1284
                             i   -   i  v -    vi viv   i  i   viv v      v
  L1M4_orf2#LINE/    198 GAACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_77279540_7   1285 GCTACAGTAACAAAAACAGCATGGTACTGGTACAAAAACAGACACATAGA 1334
                                   iv  i    ii         i i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_77279540_7   1335 CCAATGTGACAGAAGAGATAGCCCAGA--TAATGCCACACACCTGCTACC 1382
                         i     vi i    vv  v  i     --   vv   i   ii iivii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_77279540_7   1383 ATCTGATCTTTGACAAAATCTACAAAAATAAGCAATGGACAAAGGATTCC 1432
                          vi    i  i     iivivv   i vi vv      iv    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_77279540_7   1433 CTATTCAATAAATGGTGATGAGATAATTGATTAGCCATATGCAGAAGACT 1482
                           v     i        v  i  i  i  iv  ?   i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_77279540_7   1483 GAAACTGGACCCCTGTTTTATACCATATATAAAA-TTAACTCAAGATAGA 1531
                            ii         iii i i        i    -         i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_77279540_7   1532 TTAAAAACTTAAATCTAAAACCAAAAACTAGAAATACCCT-GGAAGATAA 1580
                          i ? i  i     v   i v v       v   -  i  -i     v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chrX_77279540_7   1581 CCTAGG---AAATACCATTTTTGACATAAGACCTAGCAAAGACTTTATGA 1627
                          v    ---    -- -  iv    v vi iiivi    v ii  iv ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_77279540_7   1628 AAAAGACACCAAAAGTATTTGCAACAAAAATGCACCTTGACAAATGGGAC 1677
                          v v           i ivv         iviv vv v  i    v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_77279540_7   1678 CTAATTAAACTAAAGAGCTTCTGCACAATAAAAGAAACTATCAACAGAAT 1727
                         i v  i   v v  i i   i  ii vvi   i  v        v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_77279540_7   1728 AAACAGACAAGCTAGAGAATGG-AGAAAATGTTCACATACTGTGCATCCA 1776
                         i  v      v i v       -       i  ii  v iii ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_77279540_7   1777 TTAAAGGACTAATATCCAGAATCTATCAAGAACTTTAACAAATTTACAAG 1826
                         v   i     vi          v   v       i v    v iv i  -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA- 791

  chrX_77279540_7   1827 TGAAAAG-CAAACAACATGATTAAAAAGTGAGCAAAGGACATGGAAAGAC 1875
                          i     -    i   vii   ?    i  i        iv  i v    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_77279540_7   1876 AGTTTTCAAAACAAGGTATTCATGCAGTCGATGAGCATATGAATAAATGC 1925
                          v  i  v   v   i   v  viii i i  i    i     v i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_77279540_7   1926 TCAACATCACTAATCAT 1942
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (157 / 103)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.35 (23 / 17)  


2281 26.72 2.91 6.03  chrX_77283954_77286162      789  1716 (493)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_77283954_7    789 ATTGCATGCTCATGGATAGGAAGAATCAATACTATTAAAATGCCCATACT 838
                           iv    i        v      v i    i i    i   v v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_77283954_7    839 GCCAAAAGCAATTTACAGATTCAATGATATTTCTATCAAACTACCAATGA 888
                         v  v   vii  i           i vv  ii        v v   iivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_77283954_7    889 CATTCTTCCTAGAACTAGAAAAAAACT-ATTCTAAAATTCATATGGAACC 937
                          v  i  ivi    v v  v  i--  -  i                 vi
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATATGGAAAT 157

  chrX_77283954_7    938 AAAAAAGAGCCCAAATATCCAAGGCAATCCTAAGCAACAAACCAAAAAAC 987
                         iv  ii  v  vi    v    ii     i i -----------------
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGA----------------- 190

  chrX_77283954_7    988 CAAAAAACCAAAAAACAAAAACAAAAACAAACAAAAAAAAGCAGCTGGGG 1037
                         -----------------    v  i      ------------ i   i 
  L1M4_orf2#LINE/    191 -----------------AAAAGAAGAACAAA------------GTTGGAG 211

  chrX_77283954_7   1038 GCATCACACTACCTGACTTCAAACTATACTATAGGGCTAGAGAAACTGAA 1087
                          vv       v  ii i      viv     i ii    v  v  iii i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_77283954_7   1088 ACAACAAGGTACTGGTACAAAAACAGACATGTAAACAAATCAAATAGA-- 1135
                            iiiv        i i  ii i      i  i iv   vi      --
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_77283954_7   1136 -------CCAGAAACAAGGCTGCGTATCTATAACCGTCTTATCTTCAACA 1178
                         -------       i  iv iiiii  i   iii ivi v  i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_77283954_7   1179 AAGCTGACAAAAGCAAGCAATGGGGAAAGAACTCG-CTATTCAATAAATG 1227
                          i v  v   i v  vv              - v -  v     i     
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTTTTCAACAAATG 410

  chrX_77283954_7   1228 GTGCTGGGATAACTGGCTAGTCATATGCAGAAGATTGAAGTTAGACTCCT 1277
                                  i      v  ?i  i     i    v       i   i   
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_77283954_7   1278 TCCTTGTGCCATACACAAAAATCAACACAAGATAAATTAAAGACTTAAAT 1327
                         v   iiii     i        i   v   i  ii  i ?    i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_77283954_7   1328 GTAAAACCTGAAAATATAAAAACCCTGGAAGAAAATCTAGGCAATAATAT 1377
                             i v  i   v       vi i i        iv    ?ivv   v 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_77283954_7   1378 T-GTGGAAATAGGAATGAGCAAAGGTTGCATGAAAAAGACACCAAAAGCA 1426
                          -   - vv v  iv ii    v    v v ii v v             
  L1M4_orf2#LINE/    561 TCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_77283954_7   1427 ATTCCAACAAAAGTAAAAATTGGCAAATGAGATCTAATTAAACTTAAGAG 1476
                         vvvv         v      v ii    vi  ii v  i   v    i i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_77283954_7   1477 CTTTGCTTCTGCACAGCAAAATAAACTATCAACAGATTAAACAGGCAACC 1526
                             -----  ii vv    iv v        v i v i  v  i     
  L1M4_orf2#LINE/    660 CTTT-----TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_77283954_7   1527 TACAGAAT-------AATATGTGCAAGCTATGCATCTGACAAATGTCTAA 1569
                         i       -------     v     iii  ii      i  iv v  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_77283954_7   1570 TATTCAGCATCTATAAGAAATTTAAACA-TTTAC-----AAGAGAAAAAC 1613
                            i   v  v     ii  i ivv   -i i v-----  i   v   i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_77283954_7   1614 AACCCCATTAAAAAGTGGTCAAAA-ACATGAACAGACAATTTTC-AAAAA 1661
                              v   ?    i   v    i- iv    i     v  i  -   i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_77283954_7   1662 AGACATATCGCGTGTCCAAAAAGCACATGAAAAAAACCTCAATATCACTG 1711
                            i   - ivi  v    v             i vv     i    ???
  L1M4_orf2#LINE/    855 AGATATA-CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_77283954_7   1712 ATTAT 1716
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.02 (16 / 899), avg. gap size = 5.19 (83 / 16)  


2527 27.00 3.49 1.35  chrX_77339501_77341505      624  1512 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77339501_7    624 TAGAAATACATTTTATGCTCCTGGAGGGGAAGAATCAATATTGTTAAAAT 673
                          i    v i  iii   i  v    vv      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77339501_7    674 GGCCATACTGCCCA------TTTACAGATTTAATGCTATTCCTATGAAAC 717
                            v     v    ------ i        i  i  v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77339501_7    718 TACCAACAGCACTTTTCACAGAA-TTAAGAAAATCACTTCTAAAATTCAT 766
                          v   i v  vi    ii     -  i v  iv v - i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_77339501_7    767 ATGGCACCAGAAAAGAGCCTGAACACCCAAAGCAAACT-AAGCAAAAAGA 815
                             v viiv  ii  v  v   i v     i   v  -i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_77339501_7    816 ACAAAGCCGGAGGCATCACACT-----ACTTTAAA--CTACAGTACAAAG 858
                               ii     vv       ----- i  i   --i   --       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAG 247

  chrX_77339501_7    859 CTAGAGTAACCAA-ACAGCATAATACAGGTACAAAAACAGACACATGGAC 907
                            v     i   -    ii ii   v  i i  ii i     i  i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_77339501_7    908 CAATGACACAGAATAGGGATTCCAGAAATAAATCTGCACACCTACAACCA 957
                              iv i     v i  v            i iii   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_77339501_7    958 TCTGATATTCAACAAAGTCAACAGTAACAAGCCATGGAGAAGTGACT--T 1005
                         vi    v   i    i viiv  iv v  vv v    i   i-  v -- 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGT 396

  chrX_77339501_7   1006 CCTATTCAAAAAAATGGTGCTGAGATAACTGGCTAGTGCCATATGCAGAA 1055
                          i -     v   -        i  i      v  ?--   i     i  
  L1M4_orf2#LINE/    397 CTT-TTCAACAAA-TGGTGCTGGGACAACTGGATAK--CCACATGCAAAA 442

  chrX_77339501_7   1056 GATTGAATCTGGACCCCATCCTTTCACCATCTACAAAAATAAACTCAAGA 1105
                           v    vi        vv   iv      v         v       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_77339501_7   1106 TGAATGAAAGACTTAAACATAAGACCTAAAAGTAAAGAAAGCCTACGAGA 1155
                           i  v ?    i    ii     v      v  v i  vv i  vi   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_77339501_7   1156 AAACTTAGG---AAATACCATTCTCGACATAGTACCTACCAAAGATTTCA 1202
                             v    ---    -- -   vi   v v viiiviv   v i    v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_77339501_7   1203 TGACGAAAACATCAAAAGCAATTGCAGCAAA-GCAAAAATTAACAATTGG 1251
                          iivv vi   i        vvv   i    - v      vi i  v v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_77339501_7   1252 GATCTAATTATACTAAAGAGCTTCCACACAGCAAAAGAAGCTATCAACAG 1301
                           ii v  i v v v  i i   iiiii vv    i  vi       v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_77339501_7   1302 AGTAAACAGACAACCTATAGAATGGGAGAAAATATTTGCAAACTATACAT 1351
                            i  v        i i                        ii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_77339501_7   1352 CCAACAAAGGTCTAATATCCAGAATCTATAAGAAACTT----AAATCAAC 1397
                          ii i  i  v  vi          v     ii    i----  v    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_77339501_7   1398 ATGCAAAAAAA-----AACCTGTTAAAAAAATGGGCAATGGACATGAACA 1442
                          -ii     i -----    iiv v?            v   iv    i 
  L1M4_orf2#LINE/    790 A-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_77339501_7   1443 GACACTTCTCAAAACAAGACATAGATGCAGCCAACAAACATACGAAAAAA 1492
                             i     v   v    i   v viii     i  i  i i     i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_77339501_7   1493 TGCTCAACATCACTAATCAG 1512
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.15 (43 / 20)  


3235 24.84 1.32 1.54  chrX_77350856_77361037.rev     2851  3760 (6422)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77350856_7   2851 TAGAAAGATATTTCGTTTTCATATTTTGGAATAATCAATATTTTTTAAAT 2900
                          i         ii i v     ivv      v v i      v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77350856_7   2901 GTCCATACTACCCAAAGCAGTCTATAGATTCAATGCAATTTCTATCAAAA 2950
                          v v     v      viii    i        i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77350856_7   2951 TATCAATGACATTCTTCACAGAAATAGAAAAAACAATGCTAAAATTTATA 3000
                          vi  iivi v  i  ii       v  v  ivii  v        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_77350856_7   3001 TGGAAACACAACAGACCCAGAATAGCCAAAGCTGTCCTAAGCAAAATAAG 3050
                               ii   vi                 i vi  i i --    v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chrX_77350856_7   3051 AA---AACTGGAGGAATCACATTACCTAACTTGAAATTATACTATTAAAC 3097
                           --- ii       v     i v  i  i  v   viv     iv  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77350856_7   3098 CATAGTAACCAAAACAGCATGGAACTGGCATAAAAACAGACAGGCAGACC 3147
                         i i     i   i    ii   v          ii i     vii   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77350856_7   3148 AACGGAACAGAATAGAGAACCCAGAAACACAATCACTCACCTATAGTGAA 3197
                           i    i     v    ii       i v vi  iv  ii   i  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_77350856_7   3198 CTCATTTTCAACAAAGTTGCCAAGAACATACACTGGGGAAAAGACACACT 3247
                         i v      i    i v        v   v  v        ii i vv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_77350856_7   3248 CTTCAACAAATGGTGCTGGTAAAAATAAATATCCATAGGCAGGAGAATAA 3297
                         i                  v v  v ii   ?   i v   ii     i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_77350856_7   3298 AATGTGACCCCCATCTCTTACCATATACAAAAATCAAATCAAAATGGATT 3347
                          i vv      i i   vi               i  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_77350856_7   3348 AAAGACTTAAATCTAAGGCCTCAAGCT-TGAAACTACTACAAGAAAACAT 3396
                          ?    i     v    iv  v  i  - i     vi  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_77350856_7   3397 TGGGG-AAATGCTCCAGGACATTGTTCTGGGCAAAAA------AAATATT 3439
                         v  ? -    -  i iv   v   vvi i     vii------ i    -
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT- 596

  chrX_77350856_7   3440 GAGTAATACCCTACAAGCACAGGCAACCAGAGCAAAAAATGGACAAATGG 3489
                         ----i i   -- v       i     v i  -       i  i    v 
  L1M4_orf2#LINE/    597 ----GACACC--AAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTG 639

  chrX_77350856_7   3490 GATACTATCAAG-TTAAAAATCTTCTACATAGCAAAGGAAACAATCAACA 3538
                           ivii     i-       -   i iiiivv       v  v     v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_77350856_7   3539 AAGTGAACAGAAAACCCACAGATTGGGAGAAAATATTTGCAAACTACCCA 3588
                                v   v          v                    ii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_77350856_7   3589 TATGACAAGAGATTTATAACCATAATATATAAGGAGTTCAAACAATTGTA 3638
                          v   i   i  i  i  v   v         i  ii  vv    i vv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_77350856_7   3639 TAGGAAAAGAAATCTAATAATTTAATCAAAAAATGGGCAAAAGATTTGAA 3688
                           iv    ii -- v     iii   i?             i        
  L1M4_orf2#LINE/    789 TAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_77350856_7   3689 AAGACATTTCTCGAAAGAAGACATACAAATGTTAAATAGGCATATGAAAA 3738
                         v           v        i         viv    i   i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_77350856_7   3739 GGCATTCAACATCATTTATCAT 3760
                          iiii         ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (136 / 86)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.17 (26 / 12)  

3139 26.78 1.56 0.67  chrX_77350856_77361037.rev     8792  9691 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77350856_7   8792 TAGAAGAAAATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAGT 8841
                          i   ii v  i     i        v      v i        v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77350856_7   8842 GGCCATACTGCCTGAGATAAT-------TTCAATGCCATCATCATCAAGC 8884
                            v     v  ii iv i  -------     i  v   vii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77350856_7   8885 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 8932
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_77350856_7   8933 ATATGGAACCAAAAAAGAGCCAGCATTGCCAAGACAATCCTAAGCCAAAA 8982
                                 viiv  ii  v    v  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_77350856_7   8983 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAGCTATACTATAAGG 9032
                                 i      vv       v  ii i     iviv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_77350856_7   9033 CTACAGTAACCAAAACAGCATGGTTCTGGTACCAAAACAGGTATACAGAC 9082
                                  i   i    ii    v    i iv ii i  ii   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_77350856_7   9083 CAATGGAACAGAA--GAGAGGCCTCAGAAGTAACACCACCCATCTACAAC 9130
                                 i    --     v  --    i   vv   iv   i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_77350856_7   9131 CATCTGATTTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 9180
                           vi       i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_77350856_7   9181 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 9230
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_77350856_7   9231 TGAAACTGGATCCCTTCCTTATACCTTATACAAAAAGTAATT-AAGATGG 9279
                             ii    i    v   i i   v          v   i -  i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_77350856_7   9280 ATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAA 9329
                           i ?    i           v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_77350856_7   9330 CTTAGGCA-ATACCATTCAGGACAAGGGATT-GGCAAAGCCTTCATGACT 9377
                          v    ?i- v i -   iv   vvv  i  -     v vi   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_77350856_7   9378 GAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 9427
                         ivi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_77350856_7   9428 AATTAAACTAAAGAGCTTCTGCACAGCAGAAGAAACTACCATCAGAGTGA 9477
                         v  i   v v  i i   i  ii vv  i i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_77350856_7   9478 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 9527
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_77350856_7   9528 AAAGGGCTAATATCCAGAATCTACAATGAACTTAAACAAATTTACAAGAA 9577
                           i  i  vi          v  i  v     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_77350856_7   9578 AAAAATAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 9627
                            i i   i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_77350856_7   9628 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 9677
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_77350856_7   9678 TCATCACTGGCCAT 9691
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2812 27.25 2.82 0.56  chrX_77372617_77374867      871  1758 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77372617_7    871 TGGAAAAATATTCGATGCTCATAGAGTGGAAGAATCAATATTGTTAAAAT 920
                               i    i v   i    i  v       v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77372617_7    921 GGCCATACTGCCCAAAGCCATTTATGGATTTAATGTTATCCCTATCAAAA 970
                            v     v      viv  i  ii    i  i iv             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77372617_7    971 TACCAA-TGTTATTTTTCACAG---TTAGAAAAATGAATTCTAAAAATTC 1016
                          v   i-  ii-     ii   ---  -  v  iivi  i      -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATT-GACAAGCTGATCCTAAAA-TTC 147

  chrX_77372617_7   1017 ATATGAAACCA-AAGAAAGCCTAATTTACCAAAGCAATTGTAAGCAAAAG 1065
                              i  vii-   ii v  vi v vi     i    iv i iv  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_77372617_7   1066 GAACAAAGCTTGAGTCATCACATTACTCAACGTCAAACCATACTATAAGA 1115
                                 i v   vvv     i v i   iv     v v     i  ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_77372617_7   1116 CTACAGTAACCAAAATAGCATGATACTGGTACAAAAACAGACACATACAC 1165
                                  i   i i  ii  i      i i  ii i     i   v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_77372617_7   1166 CAATGGAACACAATATAGAACCCAGAAATAA-CCTGCACACCTACAACCA 1214
                                 i v   vv   ii          -  iii   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_77372617_7   1215 TCTGATCTTTGACAAAATTGACAAAAATAAGCAATGGGGAAAGGACTCCC 1264
                         vi    i  i     iiv  v   i vi vv            i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_77372617_7   1265 TATTCAACAAATGGTGCTGGGATAACTGGCTAGCCATATGCAAAAGAATG 1314
                          v                    i      v  ?   i             
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_77372617_7   1315 ------GACCCTATACCTCTCACTATATACAAAAATTAACTGAAGATGAA 1358
                         ------     i-      v   i                 v  i   i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_77372617_7   1359 TTAAAGTTTTAAATGGAAAACCTCGAACCTTAAAATACT-AGAAGAAAAC 1407
                          i ?  vii      v  i v  vi   iv     iv  -          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_77372617_7   1408 CTAGGAAACACCCTTCTCAAGATTGATTTTGGCAAATAATTTAT-GGCTA 1456
                         v    ?ivv vi    vii vv   iv  v     - ii   v -i v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATA 595

  chrX_77372617_7   1457 AGTCCCTAAAATCAATTCCAACAAAAACAAAAATAAACAAGTAGAACCTA 1506
                         v v v i    v  vvvv        iv       i i  i v i  i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_77372617_7   1507 ATTTAACTAAAGAATTTCTGCAAAGCAAAAGAAATTACCAACAAAGTAAA 1556
                           iv  v v  i  i  i  iivvv    i  v i  i   v     i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_77372617_7   1557 TATACAGCTTACAGAATGGGAGAAAATATTTGCAAGCTGTACACCTGACA 1606
                         v v   i ii                         iiii  i i    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_77372617_7   1607 GAGGTCTAATATCCGGAATCTATAAGGAAC----ATAAATCAACAAGCAC 1652
                         ii  v  vi     i    v     i    ---- i  v    i  vv v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_77372617_7   1653 AA----AATAATCCAATTTAAAAATGGGGAAAGAACAGGAACAGACCCTT 1698
                           ----     i      ?         v    i ivv   i    vi  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_77372617_7   1699 CTTAAAAGAAGATGTACAAGCAACCAACAA--ACATAAAAA-ATACTCAA 1745
                           iv         i     iiii    i  --    i    -  i     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_77372617_7   1746 CATCACTAATCAC 1758
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (146 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


2972 25.48 2.69 0.90  chrX_77397668_77402644.rev     3596  4486 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_77397668_7   3596 GGAAAAACATTTCATGCTCGTGGATAAAAAGAATCAATATTGTTAAAATG 3645
                              i i  ii    i  i     vii    v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_77397668_7   3646 ACAATACTGCCCAAAGCAATTAACAGTTTCAATGCTATCCATATCAAATT 3695
                         i       v      vii  iv    v     i  v    v       v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_77397668_7   3696 CCCAGTGGCATTCTTCACA-AAATTAAGAAAAAAACATTTTAAAATTCAT 3744
                              iv  v  i  ii  -     --  v  ivvv  ii          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCAT 149

  chrX_77397668_7   3745 ATTGAAACAAAACAGAGCCCAAAAC--CCAAGGCAATCCTAGGCAAGAAG 3792
                           v    iiv  vi  -    i  i--    ii     i iiiv      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77397668_7   3793 AACAAAGCTGGAGGCATCAGA-TTACCAACTTCAAATTATACTACAAGGC 3841
                                i      vv   v -  v    i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77397668_7   3842 TACAGTGACCAAAAAAGGATGGTACTGGTACAAAAATAGACACATAGAAC 3891
                               i i   i v  vi         i i  ii       i     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77397668_7   3892 AATGGAGCAGAAAACAGAGCCCAGAAATAAAGCCACACACCTACAACTAT 3941
                               ii    vvv    i           v   i   ii  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_77397668_7   3942 CTGATCTTCAACAAAGTCGAGAAAAACAAGCAATGGGAAAAGGA--GTCC 3989
                         i    i   i    i vi vv  i v  vv       i    i --   -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chrX_77397668_7   3990 CTATTCAACAAATTGTGCTGGGATAACTGGCTACCCATATGCAGAAGAAT 4039
                         - v          v         i      v  ?   i     i      
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_77397668_7   4040 GAAACTGGATCCCTTCCTTAATCCATATACAAAAATCAATTCAATATGGA 4089
                            ii    i    v   i vv              i  i    v     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_77397668_7   4090 TTAAAGACTTAAACATAAGACCTAAAACTATAAAAGCCCTGAAAGATACC 4139
                          i ?    i    ii     v              vi i ii    v v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_77397668_7   4140 -TAGG---AAATACCATTCTGGACATAGGCCTGGCAAAAATTTCAT-GAT 4184
                         -    ---    -- v iv  iv v i  iiv     vii    v -   
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_77397668_7   4185 GAAGATGCCAAAAGTAATTGCAACAAAAAGAACAATAGACAAATGGGACC 4234
                         - v  ii       i vvv         ii  v      i    v    i
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_77397668_7   4235 TAATTAAACTAAAGAGCTCCTGCACAACAAAAGGAACTATCAACAGAGTA 4284
                          v  i   v v  i i  ii  ii vv    i iv        v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_77397668_7   4285 AACAGCCAGTCTACAGAATGGGAGAAAATAT--GCA---------TTTGA 4323
                           v  v  ii i                   --   --------- i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_77397668_7   4324 CAAAGGTCTAACATCCAGAATCTATGAGAAACTCAAATGAATGTACAAGC 4373
                         i  i  v  vii         v   i ii     vv ii v vv i  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_77397668_7   4374 AAAAAACAAACAACTTCATTAAAAGGTGGACAAATGACATGAGTAGACAC 4423
                             i     i   iiv   ?   ii   i    v  iv   i      i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_77397668_7   4424 TTC--AAAAGAAGACATACATATGACCAACAAGCATATTAAAAAATGCTC 4471
                            --v        i     v   i    i     i  v    i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_77397668_7   4472 AACATCACTAATCAT 4486
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (136 / 88)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 2.13 (32 / 15)  


 671 27.72 1.98 0.00  chrX_77403949_77408669        7   208 (4513)  C L1M4_orf2#LINE/L1   (702)   206     1  

C chrX_77403949_7    208 TGAAGAGACAAATTATGTTCATGGAGTAAATGATTAAACATAGTAAAGAT 159
                           i i   i vvii           v ii v  i v  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_77403949_7    158 ATCATTTTTCTGCAAATTAATCTATAGGCATAACACAAT----ATCAAAA 113
                         iv  v vi  iv      i     i  iivi   i    ----       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_77403949_7    112 TCTCAGCAAGGGTTTTTGTAGACAGAGAAAAGTTTATTCTAAAATTTATG 63
                           i    vivvv      i   v vv  v   i v  i        i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chrX_77403949_7     62 TGGAAAGGCATGAGACTTAGAATAGCTAAGACAATATTGAAAAAGAAAAA 13
                               v   v i   ii        i  i     v           i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chrX_77403949_7     12 TAAAGT 7
                         i     
  L1M4_orf2#LINE/    201 CAAAGT 206

Transitions / transversions = 1.33 (32 / 24)
Gap_init rate = 0.00 (1 / 206), avg. gap size = 4.00 (4 / 1)  

2949 27.42 2.58 0.56  chrX_77403949_77408669     3339  4228 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77403949_7   3339 TGGAAAAACATTTCACGTACATGGATAGGAAGAATCAATATCGTGAAAAT 3388
                               i i  ii  i  v       v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77403949_7   3389 GGTCATACTGTCCAAAGTAATTTATAGATTCAATGCTAACCCCATGAAGC 3438
                           iv     vi     v i  i  i        i  v v   i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77403949_7   3439 TACTATTGACTTTCTTCACAGAA-TTAAAAAAAATACTTTAAATTTCATA 3487
                          v i vivi i  i  ii     -  i v  ivvv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_77403949_7   3488 TGGAACCAAAAAATATCCCGCATAGCCAAGACAATCCTAAGCAAAAAGAA 3537
                              viiv  iiv i  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_77403949_7   3538 CAAAGCTGAAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 3587
                              i  i   vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_77403949_7   3588 CAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGATATATGGACCAA 3637
                               i   i    ii       v i iv ii i   i    i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_77403949_7   3638 TGGAACAGAA--GAGAGGCCTCAGAAACAACACCACACATCTACAACCAT 3685
                              i    --     v  --     i  vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_77403949_7   3686 CTGATCTTTGACAAATCTGGCAAAAACAAACAATGGGGAAAGGATTCCCT 3735
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_77403949_7   3736 ATTTAATAAAAGTTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 3785
                         v  i  i   v v  i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_77403949_7   3786 AACTGGACCCCT-TCTTATGCCATATACAAAAATTAACTTAAGATG-ATT 3833
                          ii         -i  i ii                   i  i   -  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_77403949_7   3834 AAAGACTTAAATGTA-GACCTAAAACCATAA-----------GAAAACCT 3871
                          ?    i        -  v       i    -----------      v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_77403949_7   3872 AGGCA-ATACCATTCAGGATATAGGCATGGGCAAAGACTTCATGACTAAA 3920
                            ?i- v i -   iv  iv v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_77403949_7   3921 ACACCAAAAGCAATGGCAACAAAGGCCAAAACTGACAAATGGGGTCTAAT 3970
                                     vvi        i vv    iv  i    v  iii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_77403949_7   3971 TAAACTAAAGAGTTTCTGAAGAGCAAAGGAAACTTTCATCAGAGTGAACA 4020
                         i   v v  i ii  i  vivvv       v   v   vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_77403949_7   4021 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTCCCCATCTGGCAAA 4070
                          i     i                 v       viivivi     ii  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_77403949_7   4071 GGGCTAATATCCAGAATCTACAAGGAACTTGTAAACAAGTTTACAAGAAA 4120
                           i  vi          v  i  i     iv  --   v iv i  v   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAA 795

  chrX_77403949_7   4121 AA-----ACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 4165
                           ----- i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_77403949_7   4166 CTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTCAT 4215
                            v        i  vi vi       i  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_77403949_7   4216 CATCACTGGTCAT 4228
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.55 (28 / 11)  


1963 25.18 12.95 1.44  chrX_77421696_77423410      516  1210 (505)    L1M4_orf2#LINE/L1      119   893 (15)  

  chrX_77421696_7    516 CAGAACTAGATGAAACT-ATTTTGAAATTCCTATGGAAACAAAAAAGAGT 564
                              v v  i-  i  -  ii i      v        iiv  ii  vi
  L1M4_orf2#LINE/    119 CAGAAATTGAC-AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_77421696_7    565 CTGAATAGCCAAGGCAGTCCTAAGCAAAAAGAACAAAGCTAGAGACATCA 614
                          v          ii  i  i i iv  i          i i   ivv   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_77421696_7    615 TGCTACCCAACTTCAAACTATACTACAGGGCTACAGTAATCAAAACAGCA 664
                         ii  v     i      viv       ii              i    ii
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_77421696_7    665 TAGCACTGGTACAAGGACAGACACATAGACCAATGGAA------------ 702
                          i i     i i     i     i     i        ------------
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_77421696_7    703 --CAGAAA-------------------------GATTTTC---------- 715
                         --      -------------------------       ----------
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_77421696_7    716 -------TATTTAAT-----------------------AAATGGTGCTGG 735
                         -------i   i   -----------------------            
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_77421696_7    736 GAGAACTGGCTAGCCATATGCAGAAGATTGAAACTGGACTCCTTCCTTAT 785
                           v      v  ?   i     i    v    ii     i   v   i i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_77421696_7    786 GCCACATACAAAAATCATCTCAAGGTAGATTAAAAACTTAAATATAAAAC 835
                         i   i          i v     ii i   i ? i  i     i   i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_77421696_7    836 CCAAAACTATAAAAATTCTAGAAGAAAACCTGGGC---AATGTTCAGGAC 882
                          i            v ii           v i  ?---   v   iv   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_77421696_7    883 ATAGGCACAGGCAAAAAAATTTATGATTAAAAATG---CCAAAAGCAATT 929
                         v v  vvi      vii--   v ---  i v   ---         vvv
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGG--TTTCT---TAGATATGACACCAAAAGCACAA 612

  chrX_77421696_7    930 TCAAGAAAAGCAAAAATTGACAAATGGAATCTAATTAAACTAAAGAGCTT 979
                         v   v     v      v  i    v i ii v  i   v v  i i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_77421696_7    980 CTGCACATCAAAAGAAACTATCAACAGAGTAAACATATAAGCTACAGAAT 1029
                         i  ii v     i  v        v i   i  v v i  v i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_77421696_7   1030 GGGAGAAAATTTTTGCAATTTCTCCATCTGACAAAGGTCTAATATCCACC 1079
                                   v       v iv vi      i  i  v  vi      vv
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_77421696_7   1080 -TCTGTAAGAAACTTAAACCATTTTACAAGAAAAAAAAAACCAAACAACT 1128
                         - v i   ii    ivv  v i ---   v  v     i  -   i   i
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACT---CAATAATAAAAAGAC-AAATAACC 808

  chrX_77421696_7   1129 CCATTAAAAAGTGGGCAAAGGATATAAACAGATACTTCTC-AAAGAAGAC 1177
                          v   ?    i            v i  i   i i     -        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_77421696_7   1178 AAGCATGCGGCTAACAA--ATATGAAAAAAAGCTC 1210
                          vi  vii   i  i  -- i       i v    
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.63 (106 / 65)
Gap_init rate = 0.02 (15 / 775), avg. gap size = 6.67 (100 / 15)  


3046 26.53 0.76 1.64  chrX_77430276_77435327.rev     3646  4561 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77430276_7   3646 TGGAAAAACATTCCATGCTCATGGATAGGAAAAATCAATATCGTGCAAAT 3695
                               i i  i     i        v    i v i     i  vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77430276_7   3696 GGACATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCTCATCAAGC 3745
                           vv     v      v i  i  i        i  v  i ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77430276_7   3746 TACCA-TTGACTTTATTCACAGAATTAGAAAAAAACT-ACTTTAAATTTT 3793
                          v   -i  v    -  ii     v v  v  i--  - iii    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_77430276_7   3794 ATATGAAACCATAAAAAGCCCATA-TAGCCAAGACAATCCTAAGCAAAAA 3842
                              i  viii  iiii    v -       i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_77430276_7   3843 GAACAAAGCTGGAGGCATCACGCTATGTGACCTCAAACTATACTACAAGG 3892
                                 i      vv    i  vivii ii     viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_77430276_7   3893 CTACAGTAACCAAAACAGCATGGTACTTTTTACCAAAACAGATATATAGA 3942
                                  i   i    ii       vvi- iv ii i   i       
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGACATATAGA 296

  chrX_77430276_7   3943 CCAATGGAACAGAA--GAGAGGCCTCAGAAATAACACCACACATCTTTAA 3990
                         i        i    --     v  --        vv   i    i v ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_77430276_7   3991 CCATCTGATCTTTGAGAAACCTGACAAAAATAAGCAATGGGAAAAGGATT 4040
                         i  vi    i  i  v  ivv  v   i vi vv       i    i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_77430276_7   4041 CTCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAA 4090
                         v   v  i  i              v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_77430276_7   4091 CTGAAACAGTACCCCTTCCTTATTATACCTTATACAAAAATTAACTCAAG 4140
                         v    iiv v      v   i i---   v                   i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCAC---ACCATATACAAAAATTAACTCAAA 491

  chrX_77430276_7   4141 ATGGATCAAAGATAGATTTAAATGTAAGATGTAAAATCATAAAAACCCTG 4190
                                 ?   i----i           vv     ii      vi i i
  L1M4_orf2#LINE/    492 ATGGATCAWAGAC----CTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_77430276_7   4191 GAAGAAAACTTAGGCA-ATACCATTCAGGACATGGGCATGGGCAAAGACT 4239
                                  v    ?i- v i -   iv   v v  vv i     v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_77430276_7   4240 TCATAACTAAAACACCAAAAGCAATTGCAACAAAAGCCAGAATTGACAAA 4289
                           v  iv  vi            vvv          vv i   v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_77430276_7   4290 TGGGATCTAATTGAACTAAGGAGCTTCTGCACAGCAAGAGGA-GCTATCA 4338
                          v   ii v  ii  v v ii i   i  ii vv   -    -i      
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACTATCA 685

  chrX_77430276_7   4339 TCAGAGTGAACAGACAACTTACAGAATGGGAGAAAATTTTTGCAATCTAT 4388
                         vv i      v       ii                 v       vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_77430276_7   4389 CCATCTGTCAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAAT 4438
                         vi     vi  i  i  vi          v  i  i     ivv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_77430276_7   4439 TTACAAGAAAAAAACAAGCAACCCCATCAAAAAGTGGGCAAAGGATATGA 4488
                         iv i  v     i    ii     v  i?    i            v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_77430276_7   4489 ACAGACACTTCTCAAAAGAAGATATTTATGCGGCCAACAAACATGTATAA 4538
                          i     i     v           vi vii      i  i  ii iv  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_77430276_7   4539 AAAAGCCCATCATCACTGGTCAT 4561
                          i v  i  v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.57 (22 / 14)  


3146 26.68 0.55 0.44  chrX_77452826_77456222     1998  2904 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77452826_7   1998 TGGAAAGACATTCCATGTTCATAGATTGGAGGAATCAATATTGTTAAAAT 2047
                                 i  i          i       i  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77452826_7   2048 GTTCATACTACCAAAAGAAATCTATATATTTAATGCAATCCCTATCAAAA 2097
                          viv     v  v   vvi     i v   i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77452826_7   2098 TACCAATGACATTCTTCACAGAAGTAGAAAAA--AATCCTAAAATTTATA 2145
                          v   iivi v  i  ii     i v  v  i--i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_77452826_7   2146 TGAAACCACAAAAGACCCAGAATAGCCAAAGGTATCCCAGGCAAAAAGAA 2195
                           i  vii   ii                 ivv   iiiiiv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_77452826_7   2196 TAAATCTGAAGGAGTTACATTACCTGACTTCAAATTATGCTACAGAGATG 2245
                         i   vi  i    v i   i v  ii i      viv i     i  v i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_77452826_7   2246 TAGTAACCAAAACAGCATGGTACTGGCATAAA-ACAGACACATAGGCCAA 2294
                         i     i   i    ii              i- i     i    ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_77452826_7   2295 TTGAAAAGACTAGAGAACCCAGAAACAAACCCACACACTTACAGTAAACT 2344
                          v   v   v v    ii       i       i   i   ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_77452826_7   2345 CATTTTCAATAAAGGTGCCAAGAATATACATTGGAGAAAAGATAGTCTCT 2394
                         v      i i  i          vi  v  v   i    ii       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_77452826_7   2395 ACAATAAATGGTGCTGGAA-AACTTGATATGTATGAGCAGAGGAATGAAA 2443
                         v   i            i -    v    ?vi iiv   i i       i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_77452826_7   2444 CCAGACCCCTATCTCTCACCAAATACAAAAATTAAATCAAAACCAATTAA 2493
                         iii        i   v     v             v      ivi  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_77452826_7   2494 AGACTTAGGAATCTAAGACATCAAACTATGAAAGTGCTACAAGAAAACTT 2543
                             i  --   v     vv v       i   v vi  v        v 
  L1M4_orf2#LINE/    501 AGACCTA--AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_77452826_7   2544 TGTGGAAAATCTCCAGGACATTGACCTCTGCAAAATTTTCTTGAGAAAT- 2592
                         v v? v      i iv   v   ivi vv    viv      -   v  -
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chrX_77452826_7   2593 ATTCCAAAAGCACAGACAGCCAATGCAAAAATGTACAAATGGGATCACAT 2642
                          iv           ii  i v  v v      iv i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_77452826_7   2643 CAAGGTAAAAAAGTATCTTCACAGCAAAGAAAACAATGAACACGGTAAAG 2692
                            ii v     v - i vii vv     i v  v  v  v vi  i  i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_77452826_7   2693 AGACAACCCACAGAACAGGATAAAATAGTATCAAACTACCTATCTGACAA 2742
                                        ii   v      v vv    ii iv       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_77452826_7   2743 GGGATTAATAACTAGAATATATAAGGAGATTAAGCAACTCTATAGGAGAA 2792
                             i vi  v i           i  iv ivvi      v   iv i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_77452826_7   2793 AATCTAATAATGTAATCAAAAGCTGGTCAAAGGATTTAAAGAGACATTTC 2842
                          iv v     ivi   i?   iv   v          i  v         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_77452826_7   2843 TCAAAAGACAACATACAAATGAAAAACAGGCATTTGAAAAGGTGCTCAAC 2892
                           v     vi i         ivv  i i   iv       i        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_77452826_7   2893 ATCATCAATCAT 2904
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


2901 26.01 1.31 2.50  chrX_77457017_77461241     2814  3732 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77457017_7   2814 TGGAAAGATATTTCATGGTCCTGGATTAGAAGAATCAATATTGTTATAAT 2863
                                    ii    v  v      i     v i          vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77457017_7   2864 GTCCATACTACACACAACAGTTTATACATTTAATTCAATTGCTATCAAAA 2913
                          v v     v v  v viii i  i v   i  iv    iv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77457017_7   2914 CACCAACGACATTCTTCACAGAATTAGAAAAAT--ATTCTAAAAACCACA 2961
                         iv   i vi v  i  ii     v v  v  ii--  i      ------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA------ 144

  chrX_77457017_7   2962 AAAGTTAAAATAAGAAATTAAAAAAACTTACATCGAACAACAAAAGTTCC 3011
                         ----  v v  i-     vv  iii  ii ----   i i v   -----
  L1M4_orf2#LINE/    145 ----TTCATATG-GAAATGCAAGGGACCCA----GAATAGCCAAA----- 180

  chrX_77457017_7   3012 AGAATAGTGAAAA-TAATACCAAA-CTGGAAGAATTACATTATTTTATTT 3059
                          v   vv      -v  v v    -i    i  v i   i viiiv    
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_77457017_7   3060 -AAAATTATACTACAGAGCTATAGTAAGCAAAATAGCATGATACTGGAAT 3108
                         -    i -       i     i     v   i i  ii  i      v  
  L1M4_orf2#LINE/    231 CAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_77457017_7   3109 AAAAACAGACACATAGACCAATGAAATAGAACAGGGAACTCAGAAAAAAA 3158
                           ii i     i     i     i       iv i  iii      v   
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_77457017_7   3159 TACATACATCTACAGTGAACTCATTTTCAACAAATGCTCCCAGAACATGC 3208
                         iv       i  ii  v  i v      i    iv iv  v   v   v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_77457017_7   3209 AATACAGCAAGGACAGTTTCTTCAATAAATGGTGCTGTGAAAACTGGATA 3258
                            ivi v   i i   i i     i           v  v         
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_77457017_7   3259 TCCATATGCAAAAGAATAAAAGTAGACTTCTATATCTTGCCACATACAAA 3308
                         ?   i            i  iv i   ii   iv  vii   i       
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_77457017_7   3309 AAGCAATTCAAAATGGATTACAGACTT-----TAAGACTTCAAACTATAA 3353
                           vi  i           i ?    i -----     vi v         
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_77457017_7   3354 AACTACTTAAAGAAAAACTTGGGAGAAACATTCCAAGATAATTGTCTGGG 3403
                             -    i ii     v i  ? v  vvi i iv  ivv v vi i  
  L1M4_orf2#LINE/    530 AACT-CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_77457017_7   3404 CAAAATTTTTTTGAGTAATACCCCACAAGCACAGGCAAAGAAAGCAAAAA 3453
                            viv   i  iii  vv  v   v       i    vi    v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_77457017_7   3454 TGGACAAATTTGATTCTATCAAG-TTAAAATGTTTCTGCATTGCAAAGGT 3502
                          i  i     v  i ii     i-      -ii  i  iii v      v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGA 677

  chrX_77457017_7   3503 AACAATCAGGAAATTGAAAAG-CAACCCACAGAATGGGAGAAAATGTTTG 3551
                         v  v    i    v       -                       i    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_77457017_7   3552 CAAATTATCCATCTGATGCAATATTAATAACCAGAATATGTAAGTAACTC 3601
                              i  vi       iviiv i vi  v         i   iv     
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_77457017_7   3602 AAATAACTCTATATGAAAAAATCTAATAATTCAACCAAAAAATGGGCAAA 3651
                         vv i     v   vv     iv v     ii   ii?             
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_77457017_7   3652 AGATTAGAATAGACATTTCTCAAAAGAAGACATACAAATAGCAAACAGGT 3701
                         i    v               v        i        i  v  i i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_77457017_7   3702 ATATGAAAAGATGCCCAACCTCATTCATTAT 3732
                          i            i    v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.50 (35 / 14)  


1139 26.35 0.00 0.00  chrX_77463888_77469469     1549  1882 (3700)  C L1M4_orf2#LINE/L1   (0)   908   575  

C chrX_77463888_7   1882 TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACACAAGAC 1833
                          i     v ii   v ivv  vi            vvi      v    v
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

C chrX_77463888_7   1832 AAAATTGACAAATGGGATCTAATTCAACTAAAGAGCTTCTGCATAGCAAA 1783
                              v  i    v   ii v  iv  v v  i i   i  iiivv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

C chrX_77463888_7   1782 AGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTT 1733
                         i  v    i  vv i      v  i     i   i             v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

C chrX_77463888_7   1732 TTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAA 1683
                               vii ivi      i  i  i  vi          v  i  v   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

C chrX_77463888_7   1682 CTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGC 1633
                            vv    v iv i  v     i     i     v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

C chrX_77463888_7   1632 GAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 1583
                         i     iv    i     i     v        i  vi viii     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

C chrX_77463888_7   1582 AACACATGAAAAAATGCTCATCATCACTGGCCAT 1549
                          i          i       v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (48 / 39)
Gap_init rate = 0.00 (0 / 334), avg. gap size = 0.00 (0 / 0)  

2709 26.09 5.29 0.92  chrX_77463888_77469469     4220  5089 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77463888_7   4220 TGGAAAAATATTTCATGCTCATGAATAGGAAGATTCAATATTGTGAAAAT 4269
                               i    ii    i     i  v      i i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77463888_7   4270 GGCCATACCACCCAAAGTAATTTATAGATTCAATG--GTACC-AT----- 4311
                            v    iv      v i  i  i        i --i v  -  -----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77463888_7   4312 TTCCA------TTCTTCACAGAA--TGAGAAGAAGCACTTTTAAAATTCA 4353
                          i   ------  i  ii     --   v   vv - - ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-A-TCCTAAAATTCA 148

  chrX_77463888_7   4354 TATGGAACTAAAAAGAGCCC-GAATAGCCAAGACAATTCTAGGAAAAAAG 4402
                                v iv  i ii   -          i     ii iii   i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77463888_7   4403 AATGAAGTTGGAGGAATCATGCT-----------------ACTACAGGGT 4435
                           ii           v   ii  -----------------      ii i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77463888_7   4436 GACAGTAACCAAAACAGCACGGTACTGGTACAAAAA-AGACACATAGACC 4484
                         v       i   i    iii        i i  ii -     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77463888_7   4485 AATGAAACAGAATAGAGAACTCAGAAATAAGACCGCACACCTACAACCAT 4534
                             i  i     v    iii         iv  ii   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_77463888_7   4535 CTGATCTTCAAAAAACCTTACAAAAACAGTCAATGGGGCAAGGATTCCCT 4584
                         i    i   i v  ivv vv   i v  v         v   i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_77463888_7   4585 ATTTAATAAATGGTGCTGTGAGAACTGGCTAACCATATGCAGAAAATTGA 4634
                         v  i  i           v  v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_77463888_7   4635 AACAAGACTCCTTCCTTACACCTTATACAAAAATTAACTCAGGATTGTTT 4684
                          iivi   i   v   i     v                  ii  v v i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_77463888_7   4685 AAAGACATAAATGCAAAACCCAAA--TATAAAAATGGTGGGGAAAAACCT 4732
                          ?    v      i  i v i   --       v vv i iii     v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_77463888_7   4733 AGGC--AAACCATTCATGACATAGGCACAGGCAAAGACTTCAT-GATGAA 4779
                            ?--   i -   i    v v  vvi      v ii   v -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chrX_77463888_7   4780 AATGCCGAAAGCAAAGGCAACAAAAGCAAACATCGACAAATGAGATCTAA 4829
                         i ii  i      v i          v   v  v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_77463888_7   4830 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTTAAC 4879
                          i   v v  i i   i  ii vv    i  v       vv i   v  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_77463888_7   4880 AGGCAACCTACAGAGTGGGAGAAAACTTTTGCAATCTATCCATCTGACAA 4929
                           i     i     i          iv       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_77463888_7   4930 AAGTCTAATAACCAGAATCTACAAGGAACTTAAACAATTTTACTTACAAA 4979
                         ii v  vi  v       v  i  i     ivv    i i- v v i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC-AATAATAAA 795

  chrX_77463888_7   4980 AAAACCCCAAACAACTCCATTAAAAAGTGGGCAAAGTACATAAACTGACA 5029
                           i  ---   i   i v   ?    i         v iv i  iv    
  L1M4_orf2#LINE/    796 AAGAC---AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_77463888_7   5030 CTTCTCAAAAGAAGAC-T-CATGTGGCCAATGAACAC--GAAAAAA--CT 5073
                         i     v        i- -  vi        i i   --     i --  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_77463888_7   5074 CAACATCACTGATCAT 5089
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (142 / 81)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.57 (54 / 21)  


3219 26.76 0.55 0.55  chrX_77471005_77476172     3768  4675 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77471005_7   3768 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3817
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77471005_7   3818 GGCCACACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3867
                            v i   v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77471005_7   3868 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3915
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_77471005_7   3916 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 3965
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77471005_7   3966 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4015
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77471005_7   4016 TACAGTAACCAAAACAACATGGTACTAGTACCAAAACAGAGATACAGATC 4065
                                 i   i   iii       i i iv ii i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77471005_7   4066 AATGGAAAAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 4113
                                v    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_77471005_7   4114 ATCTGATTTTTGACAAACCTGGCAAAAACAAGCAATGGGGAAAGGATTCC 4163
                          vi       i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_77471005_7   4164 CTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAACCT 4213
                           v  v  i              v      v  ?   i   v i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_77471005_7   4214 GAAACTGGATGCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4263
                            ii    iv   v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_77471005_7   4264 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4313
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_77471005_7   4314 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4362
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_77471005_7   4363 AAACACCAAAAGCAATGGCAGCAAAAGACAAAATTGACAAATGGGATCTA 4412
                         vi            vvi   i       v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_77471005_7   4413 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAG 4462
                           i   v v  i i   i  ii vv    i  v    i  vv i     i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_77471005_7   4463 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 4512
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_77471005_7   4513 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAGATTTACAAGAAA 4562
                          i  i  vi          v  i  v      vv   iv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_77471005_7   4563 AAAACAAACAACCCCATCAAAAAATGGGCGAAGGACATGAACAGACACTT 4612
                           i     i     v  i?          i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_77471005_7   4613 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 4662
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_77471005_7   4663 CATCACTGGCCAT 4675
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3353 21.64 2.26 4.74  chrX_77477810_77481263     2033  2961 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_77477810_7   2033 GGAAGATATCCTGTGTTCACAGGTTGAAAGGTTTAATACTTTTATGATTT 2082
                          i         ii      ii i   i   ii      i v   v   vv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_77477810_7   2083 CAGTACTACCCAAAGCAATCCATAGATTCAATGCAATCTCTATCAGAATC 2132
                           i    v      vii   i i        i      i      i    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_77477810_7   2133 CCAAAAACATTGTTTTTAGGA-TTAGCAAAATCCG-TCCTAAAATTCATA 2180
                            ivvi v  v   vi  i -  ii   i-- i -              
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chrX_77477810_7   2181 TGAATCTG-AAGGGACCACCAATAGTAAAAATACTCT------ACAAGAC 2223
                           i vv  -        vvv     iv    i v   ------ v    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_77477810_7   2224 CAAAGTTGCATGTTTCACACTTCCTGATTTCAAAACATACTACATAGCTA 2273
                                 v v vi          ii          v       v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_77477810_7   2274 TAGTAATGAAAACAGTATGGTA-TAGCATAAAGGCAGACATATAGCTCAA 2322
                         i      v  i     i     - i      i ii          v    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_77477810_7   2323 TGAAAAAGAATCGATA-TCTGAGATGTAAACCCTCACATATAAGGTCAAA 2371
                           i  v     i  v -  i-   vi       vi    v  v      v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC-AGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_77477810_7   2372 TGATTTTCTGGTTACGTATATATATGATGCTAAGGTGCTATTTATAAGGG 2421
                                 -----------------  i-----------------     
  L1M4_orf2#LINE/    350 TGATTTTC-----------------GAC-----------------AAGGG 365

  chrX_77477810_7   2422 TGCTAACTTTATTCAGTGGGTAAAGAACAGTCTTTTCAATATAGGACATT 2471
                            i  vvii     i    v      i           i v v iiii 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_77477810_7   2472 GGCAAAACTAAATATTCATATAGAAAAGAATGAAGTTG-ACCCTTACCTT 2520
                           v v    ii   ?i  i  iv               -    i     i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_77477810_7   2521 ATGCCATATACCAAAGTTAACTAAAAACGGATAAAAAACTGAAAGATAAT 2570
                          ii        v   i      v    i    v ? i  iv   vi   v
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_77477810_7   2571 AACTAAAACTATAACAATCTTATAAGAGAACATGGAGAAAAAGCTGGATG 2620
                          i            v v     v    i     i i?iv   v  vvi  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_77477810_7   2621 GTATTAGATTTGGCAATAATTTTGGGGGGATATGACATAAAAAATACA-G 2669
                         iiv  i i  v      ii   ivvi --        iv    ii   - 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAG--ATATGACACCAAAAGCACAAG 613

  chrX_77477810_7   2670 CAGCATAAGAAAAAATAGAT----TAAACCATATCAAAGTTAAAAAAACT 2715
                           i  v              ---- ii  ivi      i       --  
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA--CT 661

  chrX_77477810_7   2716 TTTTT--TGCAAGAAGGACATTATTAGCCGAGTGAAAAGGCAATCCACAA 2763
                            v -- v   --      i   i ivvi         i   i     i
  L1M4_orf2#LINE/    662 TTTGTGCTTCAA--AGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_77477810_7   2764 AATTGGAGAAAATATTTGCAAATCATATATCTGATAAGGGGTTAATATCC 2813
                            v                                    ii vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_77477810_7   2814 AGAATACAAAAAGAGCTTTTACAAGTCAA--ACACAAAAACAAACAACTT 2861
                               i v     i  i      v    -- i v   i     i   ii
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_77477810_7   2862 GATTTTTAAAATGGGAAAACAGCTTGAATAGACATATCTCAAAAGAAGAT 2911
                         i   ?v-        v   viii            v    v         
  L1M4_orf2#LINE/    810 AATTWA-AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_77477810_7   2912 GTACAAGCCACCAATAAACACATGAGAAGATGCTCAACATCACTAATCAT 2961
                         i     iivi       i       i                ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (120 / 77)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 3.42 (65 / 19)  


3124 27.17 0.55 0.66  chrX_77504739_77510337.rev     1462  2370 (3229)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77504739_7   1462 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAAGATCATGAAAAT 1511
                              ii i  i     i      i v      v i  v  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77504739_7   1512 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 1561
                            v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77504739_7   1562 TACCAATGACTTTCTTCACAGAATTGGAAAAAACCT--CTTTAAAGTTCA 1609
                          v   iivi i  i  ii     v v  v  i--  --iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_77504739_7   1610 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAACCCTAAGCCAAAAG 1659
                                viiv  ii  v  v v  v     iv   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77504739_7   1660 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATATTACAAGGC 1709
                                i      vv    i  v  ii i      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77504739_7   1710 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGATC 1759
                                 i   i    ii  i      i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77504739_7   1760 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCATATATCTACAACT 1807
                                i    i--    i  --        vv     i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_77504739_7   1808 ATCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAAGGATTCC 1857
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_77504739_7   1858 CTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1907
                           v  v  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_77504739_7   1908 GAAACTGGACACCTTCCTTACACCTTATACAAAAAGTAATTCAAGATGGA 1957
                            ii     v   v   i     v          v   i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_77504739_7   1958 TTAACAACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2007
                          i ?vi  i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_77504739_7   2008 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 2056
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_77504739_7   2057 AAACAACAAAAGCAAGGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2106
                         vi   v        vii          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_77504739_7   2107 ATTCAACTAAAGAGCTTCTGAACAGCAAAAGAAACTACCATCAGAGTGAA 2156
                           iv  v v  i i   i  vi vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_77504739_7   2157 CACGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 2206
                         v vi     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_77504739_7   2207 AAGGGCTAATATCCAGAATCTAAAATGAACTGAAGCAAATTTACAAGAAA 2256
                          i  i  vi          v  v  v     vvvi   v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_77504739_7   2257 AAAAACAAACAACCCAATCAAAAAGTGGGCAAAGGATATGAACAGACACT 2306
                           i -    i        i?    i            v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_77504739_7   2307 TCTCAGAAGAAGACATTTACACAGCCAAAAAACACATGAAAAAATGCTCA 2356
                             vi       i  vi v ii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_77504739_7   2357 TCATCACTGGCCAT 2370
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (139 / 104)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  

3466 20.42 6.11 1.73  chrX_77504739_77510337.rev     4247  5113 (486)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_77504739_7   4247 AAAGATACCCTGTGTTCATGAATC---AGATTTGATATTGTTAAGATGGC 4293
                                i  ii        i  i---   i  i                
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_77504739_7   4294 TATCCTCCCCAATTTGACCTACAGATTCAATGCAATTCTTACCAAAAATC 4343
                         v  v        v    i            i     i i  i     -  
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TC 102

  chrX_77504739_7   4344 CCAGATGGCCTTTGTACAGAAATTGACAATTTTGCCCTAAAATTCAAATG 4393
                             v  v i   v i             vi vii           v   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_77504739_7   4394 AAAATGCAAGAGACCCAGCACAACCAAAAAAAATATGAAAAAGAACAACA 4443
                         i         i       v i i      v  viv          v    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_77504739_7   4444 AAGTTAAAGCACTCACACATCTGAATTTCAAAAC--AGTATAAAGCTAGA 4491
                              ii  v        v  iv           -- v  i       v 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_77504739_7   4492 GTAATTATTACCATATGGTACTGGCATGAAGGTATACATATATACCAATG 4541
                              i vv  vi i            i i i  v       v i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_77504739_7   4542 GAACAGAACTGGGAGTCCAGAAATAAACACACACATTTATGATTAATTAA 4591
                            i    i  i                v  i         i i    i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_77504739_7   4592 TTTTTGACAAGGGGGCCAACAGAGAAAAAGAGTTTCAATAGAGGAA-AAG 4640
                             i        v     ----  vv -----      i i i  -  v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAA----GACCA-----TTCAATGGGGAAAGAAT 393

  chrX_77504739_7   4641 AGTTTATTTAACAAATGGTGTTATAACAAGTTAATATCCACATGCAAAAG 4690
                            i v  i           i ivi    v vi   ?             
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_77504739_7   4691 AATGAAATTGTACCCTTATTTTGCACTATATACAAAA-TGAACTTTAAAC 4739
                               i   v    i  ii ii   i          - v    iv   i
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_77504739_7   4740 GGATGAAAGAACTAAACAGAACAGCTAAAATTACAACACTCTTA-----A 4784
                             v ?   v     iiv  v        i  i  v       ----- 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_77504739_7   4785 AACATAAAAGAACATCTTCATGGCCTTCAATTTGTCAATGATTGCTTAAG 4834
                               ii? v v      i  i    vii  v v     i  v    ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_77504739_7   4835 TATGTCAACAAAAACACAATCAACAATG-----AATAGATAATTTGGACT 4879
                             v  v     i     v      vi-----         v       
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_77504739_7   4880 TCATCAAAATTAAAAA-TTTTGTACAGAAAATTACATCCTCAAAAAAGTG 4928
                                         -      i vvv   vv   iiv    i      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_77504739_7   4929 AAAATACAACACATAGAATATAATAAAATATATGCAAAACACTTAGCTCA 4978
                             v     v  i     ivi v       v      v  iv  v  v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_77504739_7   4979 CAAAGGACTTGTAT-----------------------------------A 4993
                         i  i          ----------------------------------- 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_77504739_7   4994 GAAAGACAAGCAATCCGATTTTAAAACAGTCAAAAAACAGTCTGAACAGA 5043
                         i        ii  i  i   ?v    ii v    ii --- i    i   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA---TTTGAATAGA 840

  chrX_77504739_7   5044 CATTTCTTCAAGGAACATATAAAAATGGCCAATATGCCCATGAGAAGATA 5093
                                i   i   v     v            v  v     i     i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_77504739_7   5094 CTCAACAAATTAGCCATCAA 5113
                                -- i ????????
  L1M4_orf2#LINE/    891 CTCAACA--TCAZZZZZZZZ 908

Transitions / transversions = 1.37 (100 / 73)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 5.23 (68 / 13)  


2927 23.79 2.80 0.51  chrX_77521638_77526194.rev      482  1267 (3290)    L1M4_orf2#LINE/L1      105   908 (0)  

  chrX_77521638_7    482 AGCTGTTTTT-----AAAAATTAGTAA-CTCATCCAAAAATCTATATAGA 525
                              ii   ----- i     iii  -  v    v     ii    i  
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_77521638_7    526 ATCTCAAGGGACCCTGAACAACCGAAAATATCTTGAAAAAGAAAAATGAA 575
                          viv          v   i i  i   vv              i  ii  
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_77521638_7    576 GTTAGAGGTCTCACACTTCTTGATTCCAAA-----TTATAAAACTACCAT 620
                            i    v          iii   i    -----i  i   i    vi 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_77521638_7    621 AATCAAAATAGCATGGTAGTGGCATAAAGTCATACATATAGCCCAATGTA 670
                               i i  ii     v        i vi v        vi     v 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_77521638_7    671 GTAGGATAGAAAGTCCAAAAAATAGACCTTCACATATATGATGAAATGAT 720
                         i   i  v  i      i   -  i   ivi    v    i v  v    
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGTCAATTGAT 353

  chrX_77521638_7    721 TTTTGACAAGGGTGTCAAGACCATTCAATAGAAAAAGGATGGTGTCTTCA 770
                            i          i              i ii    i  i  v i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_77521638_7    771 ACAAATAGTGCTGGGAAACACTGAAT--CCAAATGCAAAATAATGAAGTT 818
                               i         v -    i  --   v        v         
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACA-ACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_77521638_7    819 GGACCCTCACCTTACAACATACACAAAAAATAACTAAATTTGGATAAAAG 868
                               ii    i   v    i       v     v  vv     v ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_77521638_7    869 ACAAAGATTTAATATTTAAAATTATAAAAATCCTAGAAGAAAATATTAAG 918
                           vv i  v   v vi     i       v  i          i  vii?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_77521638_7    919 GAAAAGCCTCATGACATTGGATTTGGTAAGGATTTCTTGAATATTACACC 968
                          v   v i  i    v    i  v  i  v i      ii    v     
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_77521638_7    969 AAAAGTACAGGTACCAAAAGCAAAAATAGACAAACTGGACTACATTAAAA 1018
                              i   i i v      v         i   i      v   i    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_77521638_7   1019 CAAAAAGTTGCTGTATATCAAAAGAAACAATCAACAGAGTAAAAA----A 1064
                         iv    ii vi   iiv     i  v  v     v i   i    ---- 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_77521638_7   1065 CTTATGGAATGGGATGAAATATTTGTGCACCATATATTTGAATAAAGAGT 1114
                          ii ii        vi         iiv i       i   -   i iii
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA-TAAGGGAC 751

  chrX_77521638_7   1115 TAACATCCAGAAAA-ATTTAAAACGTTTACAACTCAACAACAAGAAATCA 1163
                          vii        v -  vv i   vi           i  i  i  iv  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_77521638_7   1164 AATCACTTGATTTTTTTAATAGGCAAAACATTTGAATATACATTTTTG-A 1212
                            v  iii   ?vvv-   i      iv         v      i v- 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_77521638_7   1213 AAGATTATATAATAATTGC-AACAAGCATATGAAAA--TGCTTAACATCA 1259
                             vv     vv   v  -  i     i       --    i       
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_77521638_7   1260 CTTATTAG 1267
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.59 (113 / 71)
Gap_init rate = 0.02 (13 / 804), avg. gap size = 2.00 (26 / 13)  

2635 27.14 2.22 1.45  chrX_77521638_77526194.rev     3168  4066 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_77521638_7   3168 GAAAAACATTTCATCCTCATGGATTGGAAGAATCAATACTGTTAAAATGG 3217
                             i i  ii   vi               v i    i      i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_77521638_7   3218 ACACACTGCCCAGAGCAATCTACAGATTCAAT-CTATTCCTATCAAGATA 3266
                         vv i   v    i vii              i- v  i        i  v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_77521638_7   3267 CCAAC-ATCAGTTTT-CAAATAACTACAAAAAGCT-ATTCTAAATTTCAC 3313
                            i -ii vv    -  i -  i i-- v     -  i     v    i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_77521638_7   3314 ATGGAACCAAAAAAAAGCCTAAATAGACAAAGCAATTTTAAGCAAAAAGA 3363
                               viiv  iii v  vi     v    i    i  i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_77521638_7   3364 ACAAAGTTGGAGACATTGCACTACCCAACTTCAAACTACACTATAAGGCT 3413
                                     ivv ii    v     i      vivi    i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_77521638_7   3414 ACAGTAAACAAGACAGCATGGTACTGGTACAAAAAAAGACATATAGACCA 3463
                                v        ii         i i  ii v           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_77521638_7   3464 ACGAAACATAATAGAGAACCCAGAAATAAAACCTCACACCTGTAGTCATT 3513
                          i i  i v   v    ii           v  vi   ii i i    v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_77521638_7   3514 TGATCTTGAACAAAGTCAACAAAAATAATCAATGGTGAAGGGACCCCTTA 3563
                             i  vi    i viiv   i vi v       v   i i ivvii v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_77521638_7   3564 TTCAATAAATTGTGATGGGATA-CTGGGCTAGCCACATGCAGAAGAATGA 3612
                              i    v   v     i -    i-  ?         i        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGA-TAKCCACATGCAAAAGAATGA 448

  chrX_77521638_7   3613 AAATGGACGCCTATATTTCATCTTATACAAAAATTAACTCAAGGTAGATT 3662
                          iv     v    iv iv  i v                   ii i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_77521638_7   3663 AAAGATTAAAATATAAGATTTCACACTACAGAAATCCTAGAATTAAACCT 3712
                          ?   iiv    i     vi v v    i i  v  i     vv    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_77521638_7   3713 AGGAA-ACACCATTCTGGACATAAGCTTTGGGAAATAATTTAT--GACTA 3759
                            ?i- v i v iv  iv v ii --  i  v   ii   v --  -  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGA-TA 595

  chrX_77521638_7   3760 AGTCCTCAAAAACATTTGCAACAAAAACAGAAATTGACTAGTGGGACCTA 3809
                         v v vi     i  ivv         iv i    v  iv i v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_77521638_7   3810 AGTAAACTAAACAGTTTCTTCACAGCAAAATAAGCTGTCAACAGAGTAAA 3859
                          vi   v v  v ii  i vii vv    iv vi  i    v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_77521638_7   3860 CAGACAACCTACAGAATGGGATAAAATATTCAGAAACTATGCATCCAACA 3909
                         v        i           v        iiv   ii  ii   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_77521638_7   3910 AAAGTCTAATATCCAGAATTTATAAGGAACTCA-AAAATTCAACAAGCAA 3958
                          ii v  vi          v     i      v- v  i    i  vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_77521638_7   3959 AA---AAACAACCCCATT-AAATATGGGCAAAAGACATGAACAGAAACTT 4004
                           ---   i     v   -   v         i  iv    i   v i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_77521638_7   4005 CTCAAAAAAAAA-----AAATGCTTGCAGCTAACAA--ACATGAAAAAAT 4047
                            v   i  i -----     ------  i  i  --         i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG------GCCAATAAGCACATGAAAAGAT 889

  chrX_77521638_7   4048 GCTCCACATCACTAATCAT 4066
                             v      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 1.83 (33 / 18)  


2649 28.73 1.10 1.54  chrX_77528117_77538020.rev     2877  3788 (6116)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77528117_7   2877 TGAAAACACTTTCCATGTTCATAGATGGGTAGAATCAACATTGTGAAAAT 2926
                           i   v iv i          i   v  v   v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77528117_7   2927 GATCATACTGCCAAAAGCAATCTACAAACTCAATGCAATTCCCATTAAAA 2976
                          iiv     v  v   vii       i i    i     i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77528117_7   2977 TATCACCATCATTTCTTCATAGAACTAGAAAAAACAATCTTAAAATTAAT 3026
                          vi  v vv v   i  -ii    v v  v  ivii   i       v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_77528117_7   3027 ATGGAACCAAAAAAGAGCCTGCATAGCCAAGGCAAGACTAAGCAAAAAGA 3076
                               viiv  ii  v  v v        ii   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_77528117_7   3077 ATAAATCTGGAAGTATCACAATACTCGACTTCAAACTATACTATAAGGCC 3126
                          i   vi    i vv     v v i i i      viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_77528117_7   3127 ATATTCATTTAAAAAAAGCATGGTACTTGCATAAAAATAGGCACATAGAC 3176
                          i v v  i--  i v  ii       v      ii    i  i     i
  L1M4_orf2#LINE/    250 ACAGTAATC--AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_77528117_7   3177 CAATGGAACCAAAGACAGAACCCAGAAATAAAGCCAAATACTTACAGCCA 3226
                                 ivi  vvv   ii           v   v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_77528117_7   3227 ACTGATGTTCGACAAAG----CAAATGAAACATATAGTGGGGAAAGGACA 3272
                          i    v        i ----   i--- v   vi i         i i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAG---ACCATTCAATGGGGAAAGAATA 394

  chrX_77528117_7   3273 CCCTTTTCAACAAATGGTGCTGAGATAATTGGCAAGCCCCATGTAGGAGA 3322
                         vi                    i  i  i   vv ?  v    i ii   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_77528117_7   3323 ATGAAACTGGATCCTCATCTCTAACCTTATACAAAAATCAACTCAGGATG 3372
                              ii    i  ii i   vv   v           i      ii   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_77528117_7   3373 GATCAAGGACTTATATCTAAGAACTGAAACTGTAAAAATTTTAGAAAATA 3422
                              ?i   i  v  v     i  i     i     v i      i v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_77528117_7   3423 ACATTGAAAAAAGCCTTCTAGATATTGACTTAGGCAAAAACAT------T 3466
                             v i?iv  ii    vv  iv   iv        viiiv ------ 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_77528117_7   3467 ATGACCAAGAACTCAAAAGCAAATGCAACAAAAACAAAAATAAGTAGCTG 3516
                              -----  -        v v         iv       ii  iv v
  L1M4_orf2#LINE/    595 ATGAC-----AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_77528117_7   3517 GGACTTAATTAAACTAAACAGCTTTTGCACAGGAAAAAAAAAATGTCAGC 3566
                               v  i   v v  v i      ii -vvv   ii v v i   iv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAG 687

  chrX_77528117_7   3567 AGAGTAAATAGACCACCCACAGAGTGTGAGAAAACCTTCACAATCTATAC 3616
                          i   i  v    v         i  v       iv  ii   vii   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_77528117_7   3617 ATGCAACAAAGGACTAATATGCAGAATCTTCAAGAAACTCAAACAAATTA 3666
                           vii i  i     vi   v      v vi  ii     vv    v i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_77528117_7   3667 GCAAGAAAAAAGCAAACAATCCCATCAAAATGCAGACTAAGGACATGAAT 3716
                         ii  v     ii    i  i  v  i?   viii i v     iv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_77528117_7   3717 AGACAATTCTCAAAAGAATATATACAAATAGCCAACGAATGTATGAAAAA 3766
                              v     v      v          i     ii iiii       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_77528117_7   3767 AATGCAAAACATCATTAATGAT 3788
                          -   vv       ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (153 / 105)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  

3025 28.41 0.55 0.55  chrX_77528117_77538020.rev     8506  9413 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77528117_7   8506 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 8555
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77528117_7   8556 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 8605
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77528117_7   8606 TATGAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTCC 8653
                          viv iivi    i  ii     -   -- v  i  - iii i  i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_77528117_7   8654 TATGGAACCAAAAAAGGGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 8703
                                viiv  ii iv  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77528117_7   8704 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTGCAAGGC 8753
                                i      vv    i  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77528117_7   8754 TACAGTAACCAAAAGAGCATGGCACTGGTACCAAAACAGAGACATAGATC 8803
                                 i   i v  ii   i     i iv ii i   v i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77528117_7   8804 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCGACATATCTACAATC 8851
                                i    i--    i  --        vv v i i  i  iii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_77528117_7   8852 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAACAATTCC 8901
                          vi    i  i     ivv  v   i v  vv           v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_77528117_7   8902 CTATTGAATAAATGGTGCTGGGAGAACTGGCTAGCCGTATGTAGAAAGCC 8951
                           v  v  i              v      v  ?  ii   i i  iivi
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_77528117_7   8952 GGAACTGGATCCCTTCCTTACACCTTATACAAAAACTAATTCGAGATGGA 9001
                          i ii    i    v   i     v          i   i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_77528117_7   9002 TTAAAGATTTACATATTAGACCTAAAACCATAAAAACCCTAAAAGAAAAC 9051
                          i ?   ii  v  i v   v       i      vi i  i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_77528117_7   9052 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 9100
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_77528117_7   9101 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 9150
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_77528117_7   9151 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 9200
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_77528117_7   9201 CACGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 9250
                         v vi     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_77528117_7   9251 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 9300
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_77528117_7   9301 AAAAAAAACAACCCCATGAAGAAGTGGGTGAAGGATATGAACGGACACTT 9350
                           i v   i     v  v? i  i    ii      v    ii    i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_77528117_7   9351 CTCAAAAGAAAACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 9400
                            v      i i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_77528117_7   9401 TATCACTGGCCAT 9413
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (152 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2714 29.27 0.89 0.22  chrX_77570756_77575052     2903  3804 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77570756_7   2903 TGGAAACACATTCCATGCTCATGGAGTGGTAGAATCAATATTGTGAATAT 2952
                               v i  i     i       v   v   v i        v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77570756_7   2953 TACCATAATGCCAAAAGCTATCTAAAAATTCAATGCAATTCCCACCAAAG 3002
                         vi v   v v  v   viv     v i      i     i  i i    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77570756_7   3003 TATCATCATCATTCTTCACAGAAATAGAGAAAACAATTCTAAAATTCATA 3052
                          vi  v vv v  i  ii       v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_77570756_7   3053 CAGAACTAAAAAAGAGTCCACACAGCCAAAGCAAGACTAAGCAAAAAGAA 3102
                         ii   v iv  ii  vi viv i       i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_77570756_7   3103 TAA-TCTGGAAGTATCATTTTACTCAACTTCAAACTATACTATAAGAACG 3151
                         i  -vi    i vv   ivi v i   i      viv     i  iivii
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_77570756_7   3152 TAGTCACCAAAACATCATAACACTGGTATGAAAATAGGCACATAGACCAA 3201
                         i   v i   i   vii iii     i  i ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_77570756_7   3202 TGAAACGGAATAGAGAAACCGTAAGCAAAGCCAAA----TACAGCCAACT 3247
                           i  ii    v    iv  iv  ii   v   v ----  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_77570756_7   3248 GATCTTTGACAAAGCAAACAAAAACATTAGGTGGGGAAAGGACACCATAT 3297
                            i  i     i vviv   i v    vii         i i viv v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_77570756_7   3298 TCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGAAGGATGAAA 3347
                                            i  i   vv ?       i i   i     i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_77570756_7   3348 CTGTATCCTCATCCCTCACCCTATATAAAAATCAACTCAAGATGAACCAA 3397
                         i  v i  ii i i v    v    i      i       i   i i  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_77570756_7   3398 AGACTTAAATCTAAGACGTGAAGCCATAAAAATTCTAGAAGATAACATCG 3447
                             i     v     vv i  i i      v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_77570756_7   3448 GCAAAACCCTTCTAGACAATGGCTTATCCAAAGACTTC--AGGACCAAGA 3495
                          ?iv  vi    vv   vv   v   vv   v ii   --  i--i v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA--TATGA 598

  chrX_77570756_7   3496 ACCCAAAAACAAATGCAACAAAAACAAAGATAAATAGATGAGACCTAATT 3545
                         vv      i  v v         iv   i   i   i  vi   i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_77570756_7   3546 AAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAACATAGTAAACAG 3595
                            v v    i   i  ii vv    i  v iv     v v   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_77570756_7   3596 ACAACCCACAGAATGGAAGAAAATCTTTGCAAACTATGCACCCAACGAAG 3645
                                         i       v        ii  ii i ii ii i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_77570756_7   3646 GACCAATATAAAGAATCTACAAGGAACTCAAGTAAATCAGCAGGAAAAA- 3694
                            ivi   vv     v  i  i      vvii  v   ii iv     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_77570756_7   3695 ACAAATAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTC 3744
                                 i  v  i?    i     v     iv          v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_77570756_7   3745 AAAAGAAGATACACAAATGGCCAACAAACATATGAAAAAATGCTCAACAT 3794
                         v          i            i  i  i       i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_77570756_7   3795 CACTAATGAT 3804
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (155 / 105)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.00 (10 / 5)  


2185 30.67 4.22 0.68  chrX_77601539_77606894.rev     3991  4867 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77601539_7   3991 TGGAGAAACATTCCATGTTCATGGAT-AGAAAAATAAATATTGTTAAAAT 4039
                             i i i  i              -i   i v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77601539_7   4040 AGCTATATTTCCCAAAGCAATTTACAGATTCAG-GCTATTATTTTTAAAT 4088
                         i  v   i i      vii  i          i-  v  ivi v i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77601539_7   4089 TACTGG-TGTTGTTTCTCACAGAATTATAAAAATCT-ATTCTAAAGTTCA 4136
                          v ii -  ii-   i ii     v - i v  v  -  i     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chrX_77601539_7   4137 TTTGGAACCAAAAAAGGGCCTGAATAGCCAAAGTAATCTTAAACAAAAAG 4186
                          v     viiv  ii iv  v           ii      i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77601539_7   4187 TACAAAGCCAGAGGAATTACACTACCCAACTTCAAACTATATTACAAATC 4236
                         v      iii     v i     v     i      viv  i      v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77601539_7   4237 TACAGTAGCCAA-ACATCATGATACCGGTACAAGAA----CAAAGAGACC 4281
                                ii   -   vii  i   i  i i   i ----  v v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77601539_7   4282 AAGGGAACAGAATAAAGAACACAGATATAAAGCCACACTCCTACACCCAT 4331
                           v    i     vi   iiv    v     v   i  vii  iivi  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_77601539_7   4332 GTGATCTTTGACAAAGTTGAGAACAACAAGTAATAGGAAAAGGAT----- 4376
                         v    i  i     i v  vv  v v  vvi   i  i    i  -----
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_77601539_7   4377 ----------TG-TGCTGGGATAACTGGTTAGCCATATTCAGCATATTGA 4415
                         ----------  -        i      v  ?   i  v  iv v v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_77601539_7   4416 AACTGGACCCCTTCCTTTTGCCGTATACAAAAATCAATTTGCATTGGATT 4465
                          ii         v   ivii  i           i  i iiv v     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_77601539_7   4466 AAAGACTTAAATGTAAGACCTAAAACTACAAAAA----AAAAGAAGGTCT 4511
                          ?    i           v         i    v---- i     iiiv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_77601539_7   4512 AGGA-CATACCCTTCTGAATATAGGCCTAGAAAAACTTTTCATGAGGAAG 4560
                            ?-i v i i iv   viv i  i-   iv  vvv    v iiiv v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chrX_77601539_7   4561 TCTCCAAAAGCAATTGAACCAAAAACAAAAATAAGCAAGTGGGATCTAGT 4610
                         v v         vvv v v     iv       iii  i v   ii vi 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_77601539_7   4611 TAAACTAAAGAGCTTCTGCACAGAACAAAAAATTATCAAAAAAATAAAGA 4660
                         i   v v  i i   i  ii vvv v ii v i      i   i i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_77601539_7   4661 AATAACCTATGGAATGGAAGAACATATTTGCAAACTATACATCTGTCAAA 4710
                         i i    i ii      i    v           ii   i     vi  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_77601539_7   4711 GGTCTAATATGCAAAATCCAGAAGGAATTT----AAATCAGCATGCAGAA 4756
                           v  vi   v  i   vi v  i   i i----  v   ii -ii i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAAAA 796

  chrX_77601539_7   4757 AAACAAACATCACTATTGAGAAATGGA-AAAGAACATTCCCA-GGAC-CT 4803
                          i     i v v v   ? i      i-    i --  ivv -i   -i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGA--TTTGAATAGACATT 844

  chrX_77601539_7   4804 TCTCCAAAAACAACGTACAAGTGGTCAACAAACATATTTTAAAATGGTCA 4853
                                 i vi ii     i   i   i  i  i  vvv  i   v   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_77601539_7   4854 GCATGACTAATGAT 4867
                         i   v ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (163 / 102)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.26 (43 / 19)  


2549 27.82 3.38 1.13  chrX_77619714_77625464.rev     4374  5261 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77619714_7   4374 TAGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGC-AATAA 4422
                          i    i i  i     i        v      v i       i-  v v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77619714_7   4423 AGCAATA---------------TATAGATTCAACGTTATTCCCATTAAGC 4457
                         i      ---------------  i          iv  i  i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77619714_7   4458 CACCA-CTGACATTCTGAATAGAATTAGAAAAAACT-ATTTTAAAATTTA 4505
                         iv   -   v v  i vi-i    v v  v  i-  -  ii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_77619714_7   4506 TATGGAACCA-AAAAGAGCTTGTATAGCCAGGACAATCCTAAGCAAAAAG 4554
                                vii-  ii  v iv v       ii      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77619714_7   4555 AGCAAAGCTGGAGGCATTACACTACCCAATATCAAACTATACTACAAGGC 4604
                          i     i      vv i     v      v     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77619714_7   4605 TGCAGTAACAAAAACAGCATAACACTGGTACAAAAACAGGCACATAGACC 4654
                          i      iv  i    ii iii     i i  ii i  i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77619714_7   4655 AATGGAACAGAATAGAGAATTCAGAAATAAGACCACATATCTAC--TCCA 4702
                                i     v    i i         iv   i i  i  i--  v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_77619714_7   4703 TCTGATCCTGGACAAACCTGACAAAAACTAGAAATGGGGAAAGGATTCCC 4752
                          -    ii v     ivv  v   i v vvvv           i  vvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_77619714_7   4753 TATTTAACAAATGGTACTGGAAGAACTGGCTAGCCATATGCAGAAAATTG 4802
                          v  i          i    i v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_77619714_7   4803 AAATTAGATCCCTTCCTTATACCTTATACAAAAATTAACTCAT--TTCAT 4850
                           i  i  i    v   i i   v                  v-- vv  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_77619714_7   4851 TAATGACTTAAATGTAAAACACAAAACTATAAAAACCCTAGAAGAAAATC 4900
                         i ?v   i         i vvi            vi i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_77619714_7   4901 TAAGTA-AAACCATTTAAAACATAGGCATGAGCAAATATTTTGT-GATAA 4948
                           i ?i-   i -  iivi  v v  vv ii    vvi   iv -    v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_77619714_7   4949 AATTGCCAAAGCAATTGCAACAAAAGCAACAATTGACAAATAGGATCTAA 4998
                         i ivv v      vvv          v  v   v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_77619714_7   4999 CTAAACTGAAGAGCTTCTGCTCAGCAAAAGAAACTATCATTAGAGTGAAC 5048
                         ii   v v  i i   i  iv vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_77619714_7   5049 AGACAACCTACAGATTGGGATAAAATTTTTGCAATCTATCCATCTGACTA 5098
                                 i     v     v     v       vii  vi      iv 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_77619714_7   5099 AGGTCTAATATCCAGAATCTACGAGGAACTTAAGCAAATTTACAGGAAAA 5148
                         i  v  vi          v  ii i     ivvi   v iv i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_77619714_7   5149 A---AAATAACCCCATTAAAATGTGGGCAAAGGACATGAACA--CATTTT 5193
                          ---         v   ?   vi           iv    i --     i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_77619714_7   5194 TCAAAAAAAAAAAAAGACATACATGCAACCAACAAATGTATGAAAAAAAG 5243
                           v   i  ------  i     viiii    i  iiii       i v 
  L1M4_orf2#LINE/    847 TCCAAAGAA------GATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_77619714_7   5244 CTCAACATCGCAGATGAG 5261
                                  i????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.50 (40 / 16)  


2165 26.65 1.79 1.92  chrX_77627940_77629659.rev      502  1229 (491)    L1M4_orf2#LINE/L1      182   908 (0)  

  chrX_77627940_7    502 CAATACTAAACAAAAAGAATAAATCTGGAGGCATCACATTACCCAACTTC 551
                             vi i  v  i     i   vi      vv     i v     i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_77627940_7    552 AAACTATACTACAAGGCTATAGTTACCAAAAGAGTAAGGTACTGGCATTA 601
                            viv        i    i   v i   i v   iv           v 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_77627940_7    602 AAAGAGTCATGTAGACCAATGGAACATAATATAGAACCAAGAAATAAAGC 651
                         ii v  v   i    i        i v   vv   ii v         v 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_77627940_7    652 CAGATACTTACAACCAACTGATCTTCAACAAAGCAATACATAAATAAATA 701
                           v i i   iiii   i    i   i    i --i i ---------i 
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGG--GTGC---------CA 370

  chrX_77627940_7    702 AATAAACCATAAACTGGAGAAAGAACACCCTATTCAACAAATGCTGCTGA 751
                          i---     vv v   i       i vi  v           v     i
  L1M4_orf2#LINE/    371 AG---ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_77627940_7    752 GATAATTGGCAAGCCACATTTAGAAGAATGATGCTGGATCCTCATCTCTC 801
                           i  i   vv ?      vi i        v i    i  ii i   v 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_77627940_7    802 ACCATATA-AAAAATCAACTCAAGATGGATCACAGACCTAAATATAAGAC 850
                                 -      i       i        ?          i     v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_77627940_7    851 CTGAAATTATAAAAATTCTACAAGATGATATCAGAAAAACTCTTCTAGAC 900
                           i   i       v ii  v    vi i  vi ?iv  v     vv   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_77627940_7    901 ATTGGCATAGGCAAAGAATTCATGACCAGGAGCCCAAAAGCAAATGTAAC 950
                         v    vv       v iv   v iivi v  vv         v v i   
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_77627940_7    951 AAAAACAAAAATAAATAGATGGGACTT-ATTTAACTAAAAAGCTTCTGCA 999
                             iv       i   i  v      -  iv  v v    i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_77627940_7   1000 CAGCAAAACAAATAATTAGCAGAGTTAACAGACAACCCACAGAGTGGGAG 1049
                          vv    iv v iv  i iv i   v  v              i      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_77627940_7   1050 AAAATCTTCATGAGCTATACATCCAACAAACAACTAATATTCAGAATCTA 1099
                              v  iiii iii   i   ii i  ivi   vi   i      v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_77627940_7   1100 CAAGGAATTCAAACAAATCATCAAGGAAAA---AAATAATTCCATCAAAA 1146
                         i  i   i  vv    v   vi  vi    ---      ii v  i?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_77627940_7   1147 AGTGGGCAAAGGACATGAATACACAATTGTC---AAAAGATATACACA-- 1191
                          i           iv      v   v  v  --- i          v --
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_77627940_7   1192 --CAACAAGGGTATAAAAAAA-ACTCAACATCACTAATTAT 1229
                         --   i   vii  i    i -i          ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (109 / 81)
Gap_init rate = 0.01 (9 / 727), avg. gap size = 3.00 (27 / 9)  


3138 24.19 1.29 3.66  chrX_77648469_77652555.rev     2668  3597 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77648469_7   2668 TGGGAAAATATTTCATGTTTATGGATTAAAAGAATCAATATTTTTTAAAT 2717
                            i  i    ii      i       ii    v i      v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77648469_7   2718 GTCCATACTACCCAAGGCAATCTACAGATTCAGTTCAATCCCTTTCAAAA 2767
                          v v     v     ivii             iiv        v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77648469_7   2768 TATCAATGACGATCTTCACAGAAATATTTAGAAAG--AATCCTACAATTT 2815
                          vi  iivi vv i  ii       --- iiv   --i      v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT---TGACAAGCTGATCCTAAAATTC 147

  chrX_77648469_7   2816 GTATGGAACCACAAAAGACCCAGAATAGCCAGTGTTATCCTATGGGAAAA 2865
                         i       vii   ii               iviiv   i i--------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-------- 189

  chrX_77648469_7   2866 AAAAAAGAAAAAAACAAAACAAAGCTGGAGGAATCATGTCACTTGACTTC 2915
                         -        i  -------     i       v   iiiiv iii i   
  L1M4_orf2#LINE/    190 -AAAAAGAAGAA-------CAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_77648469_7   2916 AAATTATACTACAGAACAATAGTAACCAAAACAACATGGTACTGGCATAA 2965
                            viv       i i v i     i   i   iii              
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_77648469_7   2966 AAACATACACATAGACCAATGGAACAGGATAGCAAATGCAGAAACAAATC 3015
                         ii i v   i     i        i  i  v vi i v      i   i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_77648469_7   3016 CACAC-CCTACAGTGAACTCATATTTTGACATACTTGCCAATAACATACA 3064
                           i  -ii  ii  v  i v  -   i    vivv      v v   v  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGAT-TTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_77648469_7   3065 CTGGGGAAAAAACAGTCTTTTCGATAAATGGTGCTGTGAAGACTGGATAT 3114
                         v        i  i         i i           v  vi        ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_77648469_7   3115 CTATATGCAAAAGAATGAAACTGGACTCCTATCTCTGATTACATAAAACC 3164
                          i i               ii     i    i   -----   -----  
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTC-----ACA-----CC 470

  chrX_77648469_7   3165 ATTAAATAAAAAATAA----AAATGGATTAAAGACTTAAACCTAAGACCT 3210
                           - v i     v   ----        i ?    i    iv     v  
  L1M4_orf2#LINE/    471 AT-ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_77648469_7   3211 CAAGCCATGAAACTACTACAAGAAAACATTGGGGGAATACCTAG-GACTT 3259
                         v  i i  i     vi  v          v  ? v  vv i v -   i 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_77648469_7   3260 TGGTCTTGGCAAAAATTTCTTGAGGAAT-ACCCCACAAGCACAGGCAACC 3308
                            vi v     vii      -  iv  -  v   v       i     v
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACA 618

  chrX_77648469_7   3309 AAAGCATAAACAGACAAATGTGATTACGTTAAGTTTATAAAGCTTGTGTA 3358
                             v v   i   i    vv  i v i i  iv   -   i   v   i
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA-AAAACTTTTGTG 667

  chrX_77648469_7   3359 CAGCACAG-ATACGATCAACAAAGTGAAGAGACAACCCACAAAATATGAG 3407
                          vv  v  - i  v     v        i            i   iv   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_77648469_7   3408 AAAATATTTACAACCTACCCATCTGCCAAAAGATTTTTAACAAGAATACA 3457
                                  i   vii ivi     vi  ii  i  v  v v      i 
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_77648469_7   3458 TAAGGAACCCAAACAACTCTATAGGAAAAA-ATATAATAATCCAATCAAA 3506
                            i    i vv       v   iv     - i -     i     i?  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACA-AATAACCCAATTWAA 816

  chrX_77648469_7   3507 GGATGGGCAAAG-ATTTGAATAGATATTTCTCAAAAGAAGACATACAAAT 3555
                         ii          -           i       v        i        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_77648469_7   3556 GGCAAACTGGCATATGAAAACGTGCTCAGCATCTTTGATTGA 3597
                            v  ivi   i       vi      i    v????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (136 / 85)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.56 (46 / 18)  


2696 26.09 1.85 3.48  chrX_77661577_77663513      525  1444 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_77661577_7    525 AAAACCATTCAGTATTCATGGATTGGAAGAATCAAT---GTCAAAATGGC 571
                            ivi  i vi i                v i   ---  i  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_77661577_7    572 CATTCTGCCCAAAGCAATCCACAGATTCAATGCTATTTCTATCAAACTAC 621
                         v  v  v      vii   i          i  v  ii        v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_77661577_7    622 AAATATCGTTTTTCACAGAA-TTGGAAAAAACTAGTC-TAAAATTCATAT 669
                         v iivv v     ii     -   -- v  i  ii  -            
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATAT 151

  chrX_77661577_7    670 GGAAGCAGAAAAGAGACTGGATAGCCAAAGCAACCTCATGCAAAATAA-- 717
                             iiiv  ii  vv v i         i   i  --  v    v  --
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT--TGAAAAAGAAGA 199

  chrX_77661577_7    718 ACAAGGCTGGAGGAATCACAGTCGCTGACTC--AAACTATACTATAAGGG 765
                             i i       v     v iv ii i i--     -     i  i v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_77661577_7    766 TAAAGTAATCAAAACAGCATGGTACTGGTACAAAAATGGACACATAGACC 815
                           v         i    ii         i i  ii  i    i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77661577_7    816 AAGGGAATAGAATAGAGAAAGAATAAGTAAAGCCACACACCTATATCCGT 865
                           v          v    ivvv v  i    v   i   ii   ivi iv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_77661577_7    866 CTGATATTTGACAAAGTTGACAAAAATAAGCTATGGAGAGAGAACTCCCT 915
                         i    v  i     i v  v   i vi vv v    i  i    ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_77661577_7    916 ATTAAATAAGTGGTTCTGGG-TAGCTGGCTAGCCGCATGTGAAAGAAAGA 964
                         v  v  i  i    v     -i i    v  ?  i    ii      v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_77661577_7    965 AACTGGACACTTACCTCTCACCGTATAAAAAAATTAACTCAGGATGGATT 1014
                          ii     v i      v    i    v             ii      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_77661577_7   1015 AAAGACTTAAATGTGAGA-CTCAAACTATAAAAATACTTGGAAGAAAATG 1063
                          ?    i       i   -  v           v -   i        ii
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACA 547

  chrX_77661577_7   1064 TAGGGAATACTATTCTCGACATCACCCTTGACAAATAATTTATTAC-TAA 1112
                             ?ivv v v   vi   v iivvi v i   - ii   v   v-  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATAT 596

  chrX_77661577_7   1113 GTTCTCAAAAGCAATTGCAATAAAAGCAAAAATTGACAAATGGGATCTAA 1162
                          vivi        vvv    i     v      v  i    v   -----
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA----- 641

  chrX_77661577_7   1163 CTAAACTAAGCTTCTGCACTGCAACTAACTAAACTAAGCTTTTGCACTGT 1212
                         ----------    --- i--   --  i    --- i      ii  vi
  L1M4_orf2#LINE/    642 ----------CTTC---AT--CAA--AATTAAA---AACTTTTGTGCTTC 671

  chrX_77661577_7   1213 AAATAAAAATATCAACAGCATGAGCAAACATCCTACAGAATGGGAGAAAA 1262
                            vi v v      v ivi   iv i   v  i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_77661577_7   1263 TATTGGCAAACTATGCATCTCACAAAGGTTTAATACGCAGAATCTATAAG 1312
                             v     ii  ii    v i  i  vi vi  iv      v     i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_77661577_7   1313 GAACTT----AATTCAACAAGCAAAAAGCAAATAATCCCATTAAAAACTT 1358
                              i----  i    i  vv    ii       i  v   ?    v v
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_77661577_7   1359 GGTAAAGTACATGAATAGACATTTTTCAAAAGAAGACGTACAAGCTATCA 1408
                           i    v iv             i  v        ii     iivii  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_77661577_7   1409 ACAAACTTATAAAAA-ATGCTCCACATCACTAATCAT 1444
                          i  i vi  i    -      v      ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.02 (20 / 905), avg. gap size = 2.45 (49 / 20)  


1362 25.03 19.87 2.25  chrX_77675258_77679418.rev     2916  3670 (491)    L1M4_orf2#LINE/L1       21   908 (0)  

  chrX_77675258_7   2916 ATGCATTGGAAGAATAAATATTGTTAAAATGCTTATATTTTCCAAAGCAA 2965
                            v         v v           i   viv   i ii     vii 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chrX_77675258_7   2966 TTTACACATTT----CAATCTCTATCAAAATTTCAACAATATTCTTTATA 3011
                          i    v   i----     i          ii  i viiv  i   ii 
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chrX_77675258_7   3012 GAAATAAAGAATAT-ATAC----ATTTTTATGGAAC--CAAAAAAACACC 3054
                              vi v  vv -  v ----   iv       v--   iii ---- 
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA----C 166

  chrX_77675258_7   3055 CCAGAATAGCCAAAGCTATTCTGAGCAAAAAGAACATAACAGAAGAGATC 3104
                                       i v  ii   iv  i       v iiv i  iiv  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_77675258_7   3105 ACATTATTAGACTT-AAAATTATACTACAGGGCTATAGTAACCAAAACAG 3153
                            i viivi i  -    i -       ii    i     i   i    
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_77675258_7   3154 CACAATACTGGCATA--------TTTAT---TTACTA----AGTATTTAA 3188
                         iiiii          --------iv   --- i v i----  v   v i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_77675258_7   3189 AAACTAAGAACTTACTCATGTA--------------------------AG 3212
                          iv i ii  ivv  i   ii --------------------------i 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_77675258_7   3213 TA--AACACCAC-------------------CTGTTCCCCAA-------- 3233
                          i--  v    i-------------------  v   vv   --------
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_77675258_7   3234 ----TAACTTG-TAG--AAATACAAA------------------------ 3252
                         ----i    v -  ?-- v  i    ------------------------
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_77675258_7   3253 ----CATATAAAAAAAGT--TTTAAAA--------AGACTGTCAATATT- 3287
                         ----      v     v --i i    --------    i- v   i v-
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC-TAAATGTAA 514

  chrX_77675258_7   3288 --TTTAA-----TAAAAC------AAGAAAACATTGGAAAAAACCCTCCA 3324
                         --vi   -----      ------          v  ?iv   i i  -i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC-G 563

  chrX_77675258_7   3325 GGACATTGGATTAGGTAAAGATTTCTTGAGTCAT-ACCCCACAAGCACGG 3373
                         v   v    i     i  v i      -  vi  -  v   v      ii
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAA 612

  chrX_77675258_7   3374 GCAACAAAAGCCAAAATTTACAGATACAATCA-----CATTAAG-TTAAA 3417
                                   vv     ----     -   ii-----   i  i-     
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAAT----AGATA-AATTGGACTTCATCAAAATTAAA 657

  chrX_77675258_7   3418 AAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAAGAGACAACCC- 3466
                           -   i  ii vv       v  v     v        i         -
  L1M4_orf2#LINE/    658 AA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_77675258_7   3467 CAGAACAGGAGAAAATATTTGAAAACTACTTATCTGACAAGAGATTAATA 3516
                              ii              v   ii iv       i   i  i vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_77675258_7   3517 ATCAGAATATACAAGAAACTCAAACAAATCTGTAGGAATAAAAAT-CTAA 3565
                         vi         i  ii     vv    v  --- iv        v- v  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTC---AATAATAAAAAGACAAA 803

  chrX_77675258_7   3566 TCATCCAATTTAAAAATGGGCCAAAGACCTGAATAGACATTTCTCAAAAG 3615
                          v i      ?          v  i  ii                v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_77675258_7   3616 AAGACATACAAATGGCAAGCAGGTATACGATAAGTTGCTCAACATCAGTC 3665
                             i           v ii i i i i  v   v            ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_77675258_7   3666 ATCAT 3670
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.58 (114 / 72)
Gap_init rate = 0.04 (34 / 888), avg. gap size = 4.91 (167 / 34)  


2842 26.03 1.74 3.25  chrX_77697546_77700601.rev     1643  2564 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77697546_7   1643 TGGAAAAACATTCCATACTCATGGATAAAAAGAATCAATATCATAAAAAT 1692
                               i i  i    ii        vii    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77697546_7   1693 GGCAATACTGCCCAAAGTAATTCATAGATTCAATGCCATCCCCATCAAGC 1742
                                  v      v i  ii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77697546_7   1743 TACCA-TTGACTTTATT-CAAAGAGTTAGGAAAAAAACT-ACTTTAAATT 1789
                          v   -i  v    v  -  i i -  i---- v  i  - iii    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA-TTG----ACAAGCTGATCCTAAAAT 145

  chrX_77697546_7   1790 TTATATGGAACCAAAAAAGCACCCACA-TAGCCAAGACAATCTTGAGCAA 1838
                          i        viiv  ii -     v -       i          ----
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGA---- 190

  chrX_77697546_7   1839 AAAAAAAAAACAAAAAAAACAAAAAAAACAAAGCTGGAGACATCACACTA 1888
                             i  i      ------------------ i     ivv       v
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAA------------------GTTGGAGGACTCACACTT 222

  chrX_77697546_7   1889 CCTGACTTCAAACTATACTACGATGCTACGGAAA-CAAAACAACATGGTA 1937
                           ii i      viv      i v     i v  -   i   iii     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_77697546_7   1938 CTGGTACCAAAACAGATATATAGACCAGTGGAATAGAACC-----CTCAG 1982
                             i iv ii i   i       i  i          ii-----ii   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_77697546_7   1983 AAATAACACCACACATCTACAACCATCTGATCTTTGACAAACTTGACAAA 2032
                               vv   i    i  iiii  vi    i  i     ivv  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_77697546_7   2033 AACAAGAAATGGGGAAAGGATTCCCTATTTAATATATGGTGTTTGGAAAA 2082
                          v  vvv           i  vvi  v  i  i v      i v   v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_77697546_7   2083 CTGGCTTGCCACATGCAGAAAACTAAGACTAGACCCTTTCCTTACACTTT 2132
                             v v?         i  i v i iii i     i v   i    iv 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_77697546_7   2133 ATACAAAAATTAACTCAAGATGGATTAAAGACTTAAGTATAAGGCTTAAA 2182
                                           i      i ?    i   i i    ivi    
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_77697546_7   2183 ACCATAAAAATCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAG 2231
                           i      v  i           v    ?i- v i -   iv   v v 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chrX_77697546_7   2232 ACATGGGCAAAGACTTCATGACTAAAACACGAAAAGCAATGGCAACAAAA 2281
                         ivv i     v ii   v iiv  vi    v       vvi         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_77697546_7   2282 GGCAAAATAGACAAATAGGATCTAATTAAACTAAAGAGCTTCTGCACAGC 2331
                          iv        i    v   ii v  i   v v  i i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_77697546_7   2332 CAAAGAAACTATCATTAGAGTGAAACAGCAACCTACAGAATGGGAGAAAA 2381
                         v  i  v       vv i       vii     i                
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_77697546_7   2382 TTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAG 2431
                          v       vii  vi      i  i  i  vi          v  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_77697546_7   2432 GAACTTGAACAAATTTACAAGAAAAA--CCAATCAC---ATCAAAAAGTG 2476
                              ivv    v iv i  v     -- v   v  ---  i?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_77697546_7   2477 GGTGAAGGATATGAACAGACACTTCTCAAAAGAAGACATGTATGCAGCCA 2526
                           ii      v    i     i     v        i  ii viii    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_77697546_7   2527 ACAAACATATGAAAAAAAAGCTCATCATCACTGGTCAT 2564
                          i  i  i       i v-     v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (147 / 89)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.88 (46 / 16)  


2549 28.54 3.06 0.23  chrX_77705714_77710682     3594  4476 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77705714_7   3594 TGGAAACACAGAACATGCTCATGGATGGTTAGAATCAATATTGTGAAAAT 3643
                               v i vvv    i        v vv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77705714_7   3644 AGCCACACTGCTAAAAGCAATGTACACATTCAATGCAATTCCCATCAAAA 3693
                         i  v i   v iv   vii  v    v      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77705714_7   3694 TACCCCCATCATTATTCATAGAACTAGAAAAAACAATCCCCAAATTGATA 3743
                          v  vv vv v  v  iii    v v  v  ivii    iv     v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_77705714_7   3744 TGATACCAAAAAAGAGTCTGCATAGTCAAA-CAAGACTAAGCAAAAA-AA 3791
                           iv viiv  ii  vi v v    i    -   vvi i iv  i  -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_77705714_7   3792 TTAAGCTGGAG---------------ATATCAAACTATATTATAAGACCA 3826
                         iv   i     ---------------  v     viv  i  i  ii i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_77705714_7   3827 TAGTTACCAAAAGAGCATGGTATTGGTATAAAT-TGGGCATATAGACCTA 3875
                         i   v i   i v  ii     i   i    iv- i i        i v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_77705714_7   3876 TGGAACAGAATAAATAGCCCAGAGATGAAGCCAAATAATTACAGCCAACT 3925
                              i     vi v  i     i  i  v   v i v   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_77705714_7   3926 GATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTAT 3975
                            i  i     i vviv   i v   vv i         i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_77705714_7   3976 TCAACAAATGGTGCTTGGATAATTGGCAAGCCACATGTAGGAGAATGAAA 4025
                                        v   i  i   vv ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_77705714_7   4026 CTGGATCCTCATCTCTCACCTTATGCAAAAATCAACTCAAGATGAATCAA 4075
                         i    i  ii i   v    v   i       i       i   i    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_77705714_7   4076 AGACTTAAATCTAAGACCTGAAACCATAAAAATTCTGGAAGATAACATTG 4125
                             i     v     v  i    i      v ii i     v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_77705714_7   4126 GCAAAGCCCTTCTAGACATTGGCTTAGGCAG-GACTTCATGACCAAGAAC 4174
                          ?iv ivi    vv   v    v       i- ii   v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_77705714_7   4175 CCAAATGCAAATGCAACAAAAACAAAGATAAATATATCGGATTT-----A 4219
                              v   v v         iv   i   i   v  i   i  ----- 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_77705714_7   4220 AACTAAAAAGCTTCCGCCCGGCAAAAGAAATAATCAGCAGAGTAAACAGA 4269
                           i      -   ii iv vv    i  v iv    iv i   i  v   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_77705714_7   4270 CAACCCACAGAAAAAGA-AAAATCTTCACAAACTATGCATCCAACAAAGG 4318
                                     vii  -     v  ii    ii  ii   ii i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_77705714_7   4319 TCTAATATCCAGAATAAACAAGGAACTCAAACAAATCAGCAAGAAAAAAA 4368
                         v  vi           v i  i      vv    v   ii  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_77705714_7   4369 ACAAACAATTCCATCAAAAAGTGGATTAAGGACATGAACAGAAAATTCTC 4418
                         -    i  ii v  i?    i   iiv     iv    i   v v     
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_77705714_7   4419 AAAAGAAGATATACAAATGGCCAACAA--ACGTGAAAAAATGCTCAACAT 4466
                         v                       i  --  i      i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_77705714_7   4467 CACTAATGAT 4476
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.34 (142 / 106)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.90 (29 / 10)  


2749 27.03 2.11 1.33  chrX_77738141_77740156      626  1524 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_77738141_7    626 GAAACACATTCAATGCTCACAGATAGAAAGAATCAATATTGTTAAAATAG 675
                             v i  i v   i   ii   v i    v i           i  i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_77738141_7    676 TCATACTACCCGAAGCAATTTATGGATTCAATGCTATTCCCATTAAACTA 725
                         iv     v   i  vii  i  ii       i  v  i  i  i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_77738141_7    726 CCATTGACATTCTTCACAAAACAAGAAA---AAAAACT-ATTTTAAAATT 771
                            vivi v  i  ii  ------    --- v  i  -  ii       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCA------GAAATTGACAAGCTGATCCTAAAATT 146

  chrX_77738141_7    772 GATATGGAATCAACAAAGAGTCT-GAATAGACAAGGCAACCCTAAGCAAA 820
                         v        vii-   i iii i-      v   ii   i i i iv  i
  L1M4_orf2#LINE/    147 CATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_77738141_7    821 AAGAACAAAGCTGGAGGCATGATGCTACCCAACTTCAACCTATACTACAG 870
                                   i      vv v ii  v     i     vviv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_77738141_7    871 GGCTACAGTAATCAAAACAGCATGGTACTGGTACAAGAATAGACATATAA 920
                         i              i    ii         i i   i           i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_77738141_7    921 ACCAATGGGACACAATGGATAACCCAGAAATAAGAGTGCACGCCTACAAC 970
                          i      i i v   v  v ii          ivviii  iii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_77738141_7    971 TATTTGATCTTTAACAAACTGAAAAAAAAACAAGCAATGGGGAAAGGA-A 1019
                         i v     i  ii    iv- vivv  i v  vv            i - 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_77738141_7   1020 TTCATATTCAATAAATGGTGCTGAAATAACTCACTAGCCATATCCAGAAG 1069
                         v  v -     i           ii i    viv  ?   i  v  i   
  L1M4_orf2#LINE/    395 GTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_77738141_7   1070 ATTGAAGCTGGACCCCTTCCTTACATCACACACAAAAATTAACTCAAGAT 1119
                          v     i         v   i   i  i i                i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_77738141_7   1120 GTATTCAAGACTTAAATGTAAAACCAAAAACTATAAAAATCCTGGAAGAC 1169
                          v  iv?    i         i v v            v  i i     v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_77738141_7   1170 AACACAGACATTACTATTCAGGATACATGAAC-AGACGAAGATTTCATAA 1218
                             i  i?i v v v   iv  i- v  iii-  i i v i    v  i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_77738141_7   1219 CAGA-GACACCAAAAGCAATTGCAACAAAAGAAAAAATTGATAAATGGAA 1267
                         - v -             vvv                 v       v i 
  L1M4_orf2#LINE/    593 -ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_77738141_7   1268 TCTAATTAAACTAAAGAGCTTCTGCACAGCCAAAGATGCTATCAACAGAG 1317
                         ii v  i   v v  i i   i  ii vv v  i  ii       v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_77738141_7   1318 TAAATAG----CCTACAGAATGGGAGAAAATATTTGCGAACTATGCATCC 1363
                          i  v  ----  i                       i  ii  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_77738141_7   1364 CACAAAAGTCTAATGTCCAGCATCTATAAGGAATT--TA-AAC-CAATTT 1409
                         v i  ii v  vi i     v  v     i   i --  -   -    v-
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA- 790

  chrX_77738141_7   1410 ACAAGAAAAAAAA-AACCCCATAATAAAGTAGGCAATGGACATGAACAGA 1458
                          i  i  i v   -     v  v?v   i i     v   iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_77738141_7   1459 CACTTTTCAAAAGAAGACATACATGAGGCCAACAATCACATGAAAA-AT- 1506
                           i  i  v        i     viv      i  v          -  -
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_77738141_7   1507 CTCAACATCCCTGATCAT 1524
                                  v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (150 / 89)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 1.55 (31 / 20)  


2274 27.27 4.34 0.14  chrX_77781493_77783221      500  1236 (493)    L1M4_orf2#LINE/L1      141   908 (0)  

  chrX_77781493_7    500 AAAATTCATATGCAACCAAAAAAGATCCCGCATC-CCAAAGCAAGACTAA 548
                                     v  viiv  ii  i  v v  v-     i   vvi i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_77781493_7    549 GCAA-ATGAACAAATCTGGAAGCATCATGTTACCGGACTTTATACTACAT 597
                         iv  - v       vi    i vv   iii v  vi i  i v vivi i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_77781493_7    598 TATAAAGCTAGTGTCACCAAAACAGCATGGTACTGATATAAAAAATAGGC 647
                           i       vv  v i   i    ii        ii    ii -   i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGAC 289

  chrX_77781493_7    648 ACATAGATCAATGGAACAGAATAGAGGGCCCAGAAATAGAGCCAAATTTT 697
                          i              i     v   i i         i v   v iv  
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_77781493_7    698 AATAGCCAACTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGTAAA 747
                         v  i i   i    i  i     i vviv   i v   vv i    v   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_77781493_7    748 AAACACTCTATTCAACAAATGGTGCTGGGATAATTAGCAAGCCACATGTA 797
                         i  i v   v                    i  i i vv ?       i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_77781493_7    798 ---GAATAAAACTAGATCCTCATCTCTTGTCTTATGTAAAAATTAACTTA 844
                         ---    i  ii i  i  ii i   viii v   ii           i 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_77781493_7    845 GGATGGATCAAAGACTTAAATCTAAGACTCAAAATAATAAAAATTCTACA 894
                         ii        ?    i     v     vii    iv      v ii  v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_77781493_7    895 TGATAACATCAGAAAAACTCTTCTAGACATTGGCTTAGGCAAAGACTTCA 944
                         v  v     vi ?iv  v     vv   v    v        v ii   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_77781493_7    945 TGACCAAGAACCCAAAAGCAAATGCAACAAAAGCAAAGATAAATAGGTAG 994
                          iivi v  vv         v v          v   i   i   ii v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_77781493_7    995 GACTTAATTGAACTAAAAAGCTTCTGCACAGCAAA--ATGCTAC------ 1036
                              v  ii  v v    i   i  ii vv    -- ii   i------
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_77781493_7   1037 -------ATACCACACGCAGATTGAGAGAAAATTTTTGCGTACTATGCCT 1079
                         ------- v  v  v i    v  i        v     iv ii  iiv 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_77781493_7   1080 CTGACAAAGGACTAATATCCAGAATCTATAAGGAACTC----AAATCAGC 1125
                             i  i     vi          v     i      ----  v   ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_77781493_7   1126 AAGAAAAA-----ACAACCCA-TCAAAAAGTGGGCTAAGGACATGAATAG 1169
                           v     ----- i      - i?    i     v     iv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_77781493_7   1170 ACAATTCTCAAAAGAAGATATACAAATGGCCAGCAA--ACATAAAAAAAT 1217
                            v     v                      ii  --    i    i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_77781493_7   1218 GCTCAACATCAATAATGAT 1236
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (114 / 83)
Gap_init rate = 0.01 (10 / 768), avg. gap size = 3.30 (33 / 10)  


3270 25.25 1.56 0.34  chrX_77791878_77796130.rev     2868  3762 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_77791878_7   2868 GAACAATAGCCAATGTTCATGGATTGGAAGAATCAATATTATCGAAATGT 2917
                            vi   v  v                   v i      i ii i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_77791878_7   2918 TCATACTACCCAAAGCAATCTGCAGATATAATGAAATGCCTATCAAAATA 2967
                         iv     v      vii    i     vi  i v   v           v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_77791878_7   2968 CCAATAATATTCTTCACAGAAATAGAAAAAA-AATCCTAACATTCATATG 3016
                            iiviiv  i  ii       v  v  iv-i       v         
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_77791878_7   3017 GGCCCACAAGAGACCCAGAATAGCCAAAGCTATCCTAAGCAAAAAGAACA 3066
                          ivvii    i                 i v   i i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_77791878_7   3067 CAATTGGAAGAATCACATTTCCTGACTTCAAAATAGCCTCCAGAGCTAAA 3116
                         v i     i  v     i    ii i       ivvv  v  i     v 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_77791878_7   3117 GTAACCAAG-CAGCATGATACCGGCATCAAGACAGAAACATAAACCAGTG 3165
                             i    -   ii  i   i     v i  i   v i   i i  i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_77791878_7   3166 GAACAGAATGAAAAACCCAGAAAGAAATCCACACACCTACAGTGAACTCA 3215
                            i     vi i ii       v   i   i   ii  ii  v  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_77791878_7   3216 GTTTCGACAAAGGTGCTAAAAA-ATATACTGGGGAAAAGGCAGCCACTTC 3264
                         v         i     i  i v-  vi v        iiii  i vi   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_77791878_7   3265 AATATATGGTGCTGGAAATACTGGATATCCATAGGCAAAAGAATAAAACT 3314
                           i v          i vv        ?   i v          i  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_77791878_7   3315 AGACCCC-ATCCCTAGCCATGTACAAAA-TCAAATCAAAATCGACTAAAG 3362
                         i      - i i vvi    i       - i  v       v  ii ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_77791878_7   3363 ACTTAAATATAATACCTCCAACTATGAATCTACTACAAGAAAACATTGGA 3412
                           i     i   v v  vv      i  v  vi  v          v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_77791878_7   3413 A-AAATCCCTCAGGACATTGGTCTGGGAAAAAATGTCTT-GA----ACAC 3456
                         i-     i-  iv   v    vi i  v  vii v    -  ----    
  L1M4_orf2#LINE/    553 GTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_77791878_7   3457 ---AAGCACAGGCAACCAAAGCAAAAATGGACAAATGGAATCACATCAAG 3503
                         ---       i     v    v      i  i    v i iiv      i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_77791878_7   3504 TTTAAAAGCTTCTTCACAGCAAAGGAAACAATAAATAATGTGAAGAAACA 3553
                         v      i   i vii vv       v  v  v  v  v     i i   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_77791878_7   3554 ACCCACAGAATGAGAGAAAATATTTGCAAACTATCCATCTGACAAGGGAT 3603
                                     i                 ii  vi      i      i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_77791878_7   3604 TAATACTCAGAATATATAAGAAGCTCAAACAACTCTATAGGAAAAAAAAT 3653
                          vi  ii            ii i   vv       v   iv     i --
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-- 799

  chrX_77791878_7   3654 CTAATAATCTGATCAAAAGACGGGCAAAATATTTGAATAGACATTTCTCA 3703
                          v     i ii  i?   i i       iv                   v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_77791878_7   3704 AAAGAAGACATACAAATGGCAAACAGGCATGTGAAAATGTGCTCAACATC 3753
                                 i           v  i i   ii      vi           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_77791878_7   3754 ATTGATCAT 3762
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.58 (136 / 86)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.55 (17 / 11)  


 262 19.05 0.00 0.00  chrX_77821243_77823185.rev      438   500 (1443)  C L1M4_orf2#LINE/L1   (0)   908   846  

C chrX_77821243_7    500 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 451
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chrX_77821243_7    450 CATCACTGGCCAT 438
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (7 / 5)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.00 (0 / 0)  

2818 28.54 0.58 0.94  chrX_77821243_77823185.rev      590  1444 (499)    L1M4_orf2#LINE/L1        1   852 (56)  

  chrX_77821243_7    590 TGGAAGAACATTCCATGCTCATGTGTAGGAAGAATCAATATCATGAAAAT 639
                              ii i  i     i     vi v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77821243_7    640 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 689
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77821243_7    690 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 737
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_77821243_7    738 TATGGGACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 787
                              i viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77821243_7    788 AACAAAGCCAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 837
                                iii    vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77821243_7    838 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 887
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77821243_7    888 AATGGAACAGAAC--AGGGCCCTCAGAAATAATGCGGCATATCTACAACC 935
                                i    i--  i i  --        vv vii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_77821243_7    936 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 985
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_77821243_7    986 CTATTTAATAAATGGTGCCGGGAAAACTGGCTAGCCGTATGTAGAAAGCT 1035
                           v  i  i         i    v      v  ?  ii   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_77821243_7   1036 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGA 1085
                            ii    i    v   i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_77821243_7   1086 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1135
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_77821243_7   1136 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1184
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_77821243_7   1185 AAACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGGATCTA 1234
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_77821243_7   1235 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1284
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_77821243_7   1285 AAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 1334
                            i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_77821243_7   1335 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1384
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_77821243_7   1385 AAAACAAACAACCTCATCAAAAAGTGGCCGAAAGATATGGGCAGTACGTG 1434
                           i     i    iv  i?    i   v i  i   v  iii  -  i -
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG-ACAT- 843

  chrX_77821243_7   1435 GTTCTTAAAA 1444
                         -    iv   
  L1M4_orf2#LINE/    844 -TTCTCCAAA 852

Transitions / transversions = 1.61 (148 / 92)
Gap_init rate = 0.01 (9 / 852), avg. gap size = 1.44 (13 / 9)  


2807 28.51 1.10 0.77  chrX_77835787_77840318.rev     3137  4041 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77835787_7   3137 TGGAAACACATCTCATGCTCATGGATGGGTAGATTAAATATTGTGAAAAT 3186
                               v i   i    i        v  v   i v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77835787_7   3187 GACTATACTGTCAAAAGCAATCAAAAAAGTCAGTGTGATTCCCATCAAAA 3236
                          i v     vi v   vii   v v i v   ii ii  i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77835787_7   3237 TACCA-CCGTCCTTC--ACAGAGCTAGGAAAAA-AATCCGAAAATTCATA 3282
                          v   - i i i  i--i    iv v iv  iv-i    v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_77835787_7   3283 TGGAACCAAAAAAGAGCCCGCATTGCCAAAGCAAGACCAAGCAAAATGAA 3332
                              viiv  ii  v  v v  v      i   vviii iv  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_77835787_7   3333 CAAATCTGGAGGCATCACATTACCTGATTTCAAACTATACTATAAGACCA 3382
                             vi      vv     i v  ii        viv     i  ii i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_77835787_7   3383 TAGTCACCAAAACAGCATGGTACTTGTATAAAAATAGGTGCATAGACCAA 3432
                         i   v i   i    ii       v i    ii    iiii     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_77835787_7   3433 TGGAACAGAATGGATAACCCAGAAATAAAGCCAAATTCTTACAGCCAAAT 3482
                              i     v  v ii           v   v ivi   ii i   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_77835787_7   3483 GATCTTCGACAAAGCAAACAAAAACGTAAAGTGGGGAAAATACATTATTT 3532
                            i        i vviv   i v i vv i        iv i v v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_77835787_7   3533 TCAACAAATTGTGCAGGGATAATTGGCAAGCCACATGTAGGTGAATGAAA 3582
                                  v    v    i  i   vv ?       i iiv       i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_77835787_7   3583 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGAATTAA 3632
                         i    i  ii i   v    v           i       i   i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_77835787_7   3633 GGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAAATAACATCA 3682
                         i   i     v     v  i    i      v ii     i v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_77835787_7   3683 GAAAAACCCTTCTAAACATTGGCTTATGCAAGGATTTCATGACCAAGAAC 3732
                          ?iv  vi    vvi  v    v   v    v i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_77835787_7   3733 CCAAAAGCAAATGCAATACAAACAAAAATAAATAGCTGGGATTTAATTAA 3782
                                  v v    i v  iv       i   iv v   i  v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_77835787_7   3783 ACTAAAGAGCTTTTGCATGGCAAAAGAAAC----AGCAGAGCAAACAGGC 3828
                          v v  i i      iiivv    i  v  ---- iv i  ii  v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_77835787_7   3829 AACCCAAAGAGTGGGAGAAAATCTTCACAATCTATACATCTGCCAAAG-A 3877
                               v   i           v  ii   vii   i     vi  i - 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_77835787_7   3878 CTAATATCCAGAATATATAACAAACTCAAACAAATTAGCAAGAAAAAAAA 3927
                           vi                vi     vv    v i ii  v     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA- 799

  chrX_77835787_7   3928 AACAAACAAACAATCCCATCAAAACATGGGCTAAGGACATGAACAAACAT 3977
                         ------    i  i  v  i?   v      v     iv    i i    
  L1M4_orf2#LINE/    800 ------CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_77835787_7   3978 CTCTTAAAATAAGATATACAAATGGCCAG-AAACATATGAAAAAATGCTC 4026
                         i   iv   v                  i-  i  i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_77835787_7   4027 ATTATCACTAAAGAT 4041
                          vi    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (147 / 107)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.43 (17 / 7)  


2510 27.58 2.31 2.53  chrX_77878376_77881127     1358  2267 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77878376_7   1358 TAGAGAGCTATAATCTGCTGATAGGTTAGAAGATACAATATTATTAACGT 1407
                          i  i  v   vviv  i v  i i  i     ivi      i    vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77878376_7   1408 GCCAATTCTCTCCACATTGACTTATATATTTAAAGTAATTCAGATAAAAA 1457
                          v    v   i   v     ii  i v   i  v i   i vv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77878376_7   1458 TTCCAGCAGGGTTTTTTTTTTTTCGTAAAAATGTATGAGCTGATTATAAA 1507
                          i     v -------ii     i i i    vv ii       iv    
  L1M4_orf2#LINE/    101 TCCCAGCTG-------CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_77878376_7   1508 TTTGATGTGGAAATGTAAAGGACATAGGAATAGGCAAAACAAATCTGAAT 1557
                         v  v  i        i  i    vi  -     v        vii    v
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAG-AATAGCCAAAACAATCTTGAAA 192

  chrX_77878376_7   1558 ATAAAAAACAAAGCTAGAGAATTAACGCTATCTGATTTCAAGATTTATTA 1607
                          vi  i       i i   i i v  i  vi ii       i i   i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_77878376_7   1608 TAAAGCTACAGCAATCAAAACAGTG--ATATTGATATAAAG--------- 1646
                         i          i      i      --i  i  ii    i ---------
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_77878376_7   1647 TAGACCAAAGGAACAGAATAGAGAATCCGGAAGTGGTCCCACACATATAT 1696
                             i   v    i     v    i   i   i iiv    i    v   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_77878376_7   1697 GAACAATAGATTTTCTACAAATGTGAAAAGACAACTTAGTAGAGAAAGAT 1746
                          iv    v       v    iv   vv     v i i i i i      v
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_77878376_7   1747 T-GCCTTTTCAACAAACAGCACTGAAACAACTGAATATCAAAACCTGCAA 1795
                          - i            ii ii   ii       i   ? v -- v     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA--CATGCAA 440

  chrX_77878376_7   1796 AAAA--GAACTTTTATCCATACATTGCATTATGTACAAAAATTACCTCAA 1843
                           i --   v  vv i  v   v ii  ii  i           v     
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_77878376_7   1844 AATGGGTCATAGAGCTAAATATAAAAACTAAAACTGTAAAAATTTCCAGA 1893
                              i   ?   v      i   i i        i     v i i-   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT-AGA 539

  chrX_77878376_7   1894 AGGAAATATAAAAGAATATCGTTGTGACTTAGGTTTAGAAAAAATGTTTC 1943
                           i   i   ii? v v   v i     i v  v    iv  vi-     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTC 588

  chrX_77878376_7   1944 TACATGGTCACATG-CATGGTGAAAAGCTAGATCTATGAAA-AATAAATT 1991
                          --- i -- i   -  iv---      vvi v v ii   -  v    v
  L1M4_orf2#LINE/    589 T---TAG--ATATGACACC---AAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_77878376_7   1992 GATAAATTGGATTGTATCAAAGTTAAAAACTTTGGTTTTCCCAAAGGTGC 2041
                                    i vi      i           v  vi i v  i iii 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_77878376_7   2042 TGTTAAGAGAATGAGAATACAAGCCAAAGGTTGGAATAGAAAATTTGCAA 2091
                          i i    i i   i  v    v   v  iv   i v i  v        
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_77878376_7   2092 AATAAATAGTTGGTAAAGGAATTAAATATACAATTTCTAAATAATTCTCA 2141
                          vi v   vi  i   i   v  iv  vi v   v v    v  i   i 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_77878376_7   2142 AATCTCAATAATTAGGAAACAAA----CTGGAATTAAAAACAAGAGGAAA 2187
                         v v         v ii i     ---- i--    ?    - v i v   
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCC--AATTWAAAA-ATGGGCAAA 827

  chrX_77878376_7   2188 ATATTTGAACAGACACATCATCAAATAAGAAACATAAATGGCAAATAAAT 2237
                         iv       i     iv  vi    v    v i i       v     ii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_77878376_7   2238 A-AGGAAATAATGTTTGATGTAACTAGTCGT 2267
                          - v    vi   i ii ii v ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.44 (44 / 18)  


3196 24.43 1.41 3.35  chrX_77906322_77908516      779  1703 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_77906322_7    779 GAAAAGGTATCCAATGTTTGTGGATGGAAAGACTTCATATT-TTGAAATG 827
                          i    i     v     ii     v i       v     -  i i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_77906322_7    828 TCCATACTATCCAAAGTGATCTACAGATTCAATGCTATCCCCATTATAGT 877
                         v v     vi     v                i  v     i  i v i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_77906322_7    878 CTCAATGGCATTTTTTAAAGCAAT-AATAAAAAAACCCTAAAATTTATAT 926
                          i  iiv  v      iv  v   -i i  ivvi i         i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_77906322_7    927 AGGAACAACAACAACAAAAAGACTGAGAATAGCCAAAGTGAACTAGCAAA 976
                         i i  ii-------   ii-   iv            iii v  v v   
  L1M4_orf2#LINE/    152 GGAAATG-------CAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_77906322_7    977 AAGAGAACAAAGCTGGAGTCTTCATATTTCCTCATTTCAAATTTTATTAC 1026
                          ii         i     vvi   i i    iv        vi   i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_77906322_7   1027 AAAGCTACAGTAATTACAAAACAATATTAGT-CTGACCTAAAGACAAATG 1075
                                       --   i   i i -i  -   i v   i  i i ii
  L1M4_orf2#LINE/    244 AAAGCTACAGTAAT--CAAGACAGTGT-GGTACTGGCATAAGGATAGACA 290

  chrX_77906322_7   1076 TATAGACCAATGGAACAGAAGAGAGAGCACAGAAATAAATCCACACATAT 1125
                               i        i    vv     iv          i   i    v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_77906322_7   1126 ATGGTTAATTGATCTTTGACAAGGGTGCCAAAAT-ATACAAAAGGGAAAG 1174
                              i       i  i              i i-  v   vi       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_77906322_7   1175 AGTAGTTTCTTCAATAAATGTTGATGGGAAAACTGGATATCCACATGCAA 1224
                          i    i i     i     v  v     v         ?          
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_77906322_7   1225 AAAAAAAAATGAAATTGAACTTTTCCTTTATACCATACACAACAATCAAC 1274
                           i  ----    i   i  iii v i i i      i    v   i   
  L1M4_orf2#LINE/    441 AAGAA----TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_77906322_7   1275 TCAAAAT-----AAAGACTTAC-CATAAAACTTGAAACTGTACAACTTCT 1318
                                ----- ?    i  v-ii   i vi i     i  v    ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_77906322_7   1319 AGAA-AAAACATAGGCAAAAATTCTCTTCATATTGATCTTAGCAATAATG 1367
                             -          ?iv    ii  v v iv   ivi vi     ii v
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_77906322_7   1368 TCTTGAATGTAACATAAACACCACAAAAAACAAAAGCAAAAATATATAAG 1417
                             ii  i i   iv  v v     iv        v       v    i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_77906322_7   1418 TGGGGCTACACCAAACTAAAAAGCTTTTACACAGCAAAAGAAATAATTTA 1467
                          v  i  v  i    v v    i     iii vv    i  v iv  iv 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_77906322_7   1468 CAGAGTGAAAAGGCAACTTACATAATTAGAGAAAATATTTTCCAATCATA 1517
                         v i         i    ii   v   vi            v v       
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_77906322_7   1518 TATCTATTAAGGAGTTCATTTCCAAAATTTATGA-GAAATCCTAAAACTC 1566
                              iv     iii ii v    i   v   i -   v  i  v     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_77906322_7   1567 AACAGCATACAGACACACATGCACACACACACACAACTCGATT-AAAGAT 1615
                           i --   v i v   v  --------------   i i   -   i  
  L1M4_orf2#LINE/    787 AATA--ATAAAAAGACAAAT--------------AACCCAATTWAAAAAT 820

  chrX_77906322_7   1616 AGGGAAATGATTTGAACAGACGTTTCTCCAAGGAAGTCATACAAATACTT 1665
                         i  v   v        i    i         i    vi        ivii
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_77906322_7   1666 AACAGATATATAAAAACATGCTCAACATCTAATTTTCA 1703
                           i iii i  i    v            v????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (144 / 79)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 2.75 (44 / 16)  


3049 28.34 0.55 0.44  chrX_77925778_77928222.rev     1049  1955 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77925778_7   1049 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1098
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77925778_7   1099 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1148
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77925778_7   1149 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1196
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_77925778_7   1197 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1246
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_77925778_7   1247 AACAGAGCTGGAGGCATCATGCTACCTGACTTCAAACTATAGTGCAAGGC 1296
                             i  i      vv   ii  v  ii i      viv  v i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_77925778_7   1297 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1346
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_77925778_7   1347 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 1394
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_77925778_7   1395 ATCTAATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1444
                          vi i  i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_77925778_7   1445 CTATTTAATAAATGGTGCTGGGAAAACTGCCTAGCCAGATGTAGAAAGCT 1494
                           v  i  i              v     vv  ?   v   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_77925778_7   1495 GAAACAGGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAGACGGA 1544
                            iiv   i    v   i     v    i         i    i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_77925778_7   1545 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAA-AAAAC 1593
                          i ?    i    ii v   v       i      vi i     -     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_77925778_7   1594 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1643
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_77925778_7   1644 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1693
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_77925778_7   1694 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1743
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_77925778_7   1744 AAGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 1793
                          ii     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_77925778_7   1794 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 1843
                         i  i  vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_77925778_7   1844 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 1893
                          i     i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_77925778_7   1894 TCAAAAGAAGACATCTATGCAGCCAAAAAACACATGAAAAAATGTTCACC 1943
                           v        i  vi viii     v  i          i   i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_77925778_7   1944 ATCTCTGACTAT 1955
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (152 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  

 513 17.76 1.87 1.87  chrX_77925778_77928222.rev     2282  2388 (57)  C L1M4_orf2#LINE/L1   (414)   494   388  

C chrX_77925778_7   2388 AAGAGTCACCTTATTCAATAAATGGTGCTGAG-CAAGCTGGCTAGCCATA 2340
                             i vii   -     i           i -   -    v  ?   i 
  L1M4_orf2#LINE/    388 AAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACA 435

C chrX_77925778_7   2339 TGTAGAAGAATGAAGCT-AACACCTATCTCTCATCATATACAAAAATTAA 2291
                           i i          i -i  v    i   v  i                
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

C chrX_77925778_7   2290 CACAGAATG 2282
                          v  i    
  L1M4_orf2#LINE/    486 CTCAAAATG 494

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.04 (4 / 107), avg. gap size = 1.00 (4 / 4)  


2773 27.04 1.20 2.18  chrX_77936594_77942434     4433  5349 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77936594_7   4433 TGTAAAAATATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4482
                           v   i    i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77936594_7   4483 GGCTATATTGCCCAAAGTAATTTGTAGATTCAATGCTATTCCCATTAAAC 4532
                            v   i v      v i  i ii        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77936594_7   4533 TACCATTGACATTTTTCACAGAAATAGAAAAAATATATTTTAAAATTCAT 4582
                          v   vivi v     ii       v  v  iv i-  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chrX_77936594_7   4583 ATGGAACCCAAAAAGAGCTAGTATAGCCAAGGCAGTCCTAAGCAAAAAGA 4632
                               vivv  ii  v i  v        ii  i  i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_77936594_7   4633 ACAAAGCTGGAAGCATCATGCTACCTGACTTCAAACTACACTACAATGCT 4682
                               i    i vv   ii  v  ii i      vivi       v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_77936594_7   4683 ACAGTAACAAAAACAGCATGGTACTAGCACAAAAACAGCCATGTAGACCA 4732
                                iv  i    ii       i   i  ii i  v   i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_77936594_7   4733 GTCGAACAGAATAGAGATCTCAGAAATAAGACTGCACATCTACAGCCATC 4782
                         i v   i     v    vii         iv iii    i  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_77936594_7   4783 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCTCTG 4832
                             i  i     ivv  v   i v  vv            i  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_77936594_7   4833 TTTAATAAATGGTGCTAGGAGAACTGGCTAGCTATATGCAGAAAATTAAA 4882
                           i  i          i   v      v  ? i i     i  i v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_77936594_7   4883 ATGGGACACTTTACTTACACCTTATACAAAAAGCAACTCAAGATGGATTA 4932
                         i v    v i vv  i     v          vi       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_77936594_7   4933 AAAACCTAAATGTAAAACCCAAAACTATAAGAACCCTC-GAAGAAAATCT 4981
                         ? i            i v i          -   i  i-        iv 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACAT 548

  chrX_77936594_7   4982 AGGCA-ATACCATTCAGGACATAGGCACGGGAAAATATTTCAT-GATGAA 5029
                            ?i- v i -   iv   v v  vvii  v  vvi    v -   ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_77936594_7   5030 ATCGCCAAAAGCAATTGCAACAAAAGCAAAAATGGAAACTAAGTAAACTA 5079
                          - i         vvv          v      i  -------    i -
  L1M4_orf2#LINE/    598 A-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGA-------TAAATT- 638

  chrX_77936594_7   5080 TAGAGCTTCTGCACAGGGAAAATAAATAA-----ATAAAT-AAATAA-AC 5122
                         -- ii    vv  -----   v    -  -----i ivv -   vi -  
  L1M4_orf2#LINE/    639 --GGACTTCATCA-----AAATTAAA-AACTTTTGTGCTTCAAAGGACAC 680

  chrX_77936594_7   5123 TATTATCAGTGTGAACAGGTCACCTACAGAGTGTGAGAAAATTTTTACAA 5172
                            i vv iv     v  iiv   i     i  v        v   i   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_77936594_7   5173 TCTGTCCATCTGACAAAGGTCTAGTATCCAAAATCTACAAAAAACTTAAA 5222
                         viii vi      i  i  v  v       i   v  i   i    ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_77936594_7   5223 CAAATTTGCAA-AAAAACCCAAACAACCCCATTAGAAAGTGGGCAAAGAA 5271
                            v ivii  -     vv    i     v   ?i   i         i 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_77936594_7   5272 CATGAACAGACACTTCTCAAAAGAAGACATTCATGTGCCCAAAAAACATA 5321
                         iv    i     i     v        i  v  vi  v    v  i  i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_77936594_7   5322 TGAAAAAAAGCTCAACATCTTGGATTAT 5349
                               i v          v????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.07 (31 / 15)  


2343 27.82 3.46 2.01  chrX_77954717_77959012.rev     2911  3805 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77954717_7   2911 TGAAAGAACATTTCATGCTCTTGGATAGGAAGAATCAATATTGTTAAAAT 2960
                           i  ii i  ii    i  v     v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77954717_7   2961 GGCCATACCGTCCAAAGCAATTTACAGATT--------TCCC-ACCAAAC 3001
                            v    ivi     vii  i        --------    - i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77954717_7   3002 TAT-ATATGACATTTTTTCACAGAATTAGAAAAAAACT-ATTCTAAAATT 3049
                          vi- vv  v --     ii     v v  v  i--  -  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT 146

  chrX_77954717_7   3050 TTTATGGA---GCAGAAAAGAGCCTGAACAGCCAAAGCAAATCTCAATAA 3096
                         iv      ---   -- ii  v  v   i       i   -   ii v  
  L1M4_orf2#LINE/    147 CATATGGAAATGCA--AGGGACCCAGAATAGCCAAAACAA-TCTTGAAAA 193

  chrX_77954717_7   3097 AAAGGAACAAAACTAAAGGCATCACACCACCTGCCTTTAAACTACACCAC 3146
                          i i       ii ii   vv      iv  iivi  i   vivi  i  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_77954717_7   3147 AAGGCTACAGTTACCAAAACAGCATGGTCCTGATATAAAAACAGACACAT 3196
                           i        v i   i    ii    v   ii    ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_77954717_7   3197 ATACCAATTTAACAAGTTAGCGAACCCAGAAATAAGGCCACACACACACA 3246
                          v i    vv  i iiv v v  ii          ----  v  i   iv
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAA----ACCCATACATT 339

  chrX_77954717_7   3247 TACAACCATCTTATCTTTGACAAAGTTGACATTAACATGCAATGGGGAAA 3296
                           iiii  vi v  i  i     i v  v  vv v   v           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_77954717_7   3297 GGACTGCCTATTCAATAAATGGTGCTAAGAGAACTGGTTATTTATACACA 3346
                          i iv i  v     i          ii  v      v  ?ii i ii  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_77954717_7   3347 GAAGATTTAAACTGGACCCCCTCCTTTTATCATATACAAAAGTCATCTCA 3396
                         i    v v  ii        iv   ivi i           i i v    
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_77954717_7   3397 AGATGAAT--------TAAATGTATAAGCTAAAACTATAAAAATCCTAGA 3438
                          i   i  --------        vi                v  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_77954717_7   3439 AGAAAAACTAGG---AAATAC-CAT--TCTTGAGAAAGTCCCTAACAAAT 3482
                               vv    ---    vi- i --i    i vv  ------i   vv
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG------GCAATG 583

  chrX_77954717_7   3483 GTTTCAT-GATGAAGACTCCAAAAGCAATTGCAACAACAACAAGCATTGG 3531
                              v -   - v   v         vvv       v iv  iv  v i
  L1M4_orf2#LINE/    584 GTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_77954717_7   3532 CAAATGGGAACTAGTTAATCTAAAGAGCTTCTGAACAGCAAAATAAGCCA 3581
                         i    v   vi vi i  vv v  i i   i  vi vv    iv vi i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_77954717_7   3582 TCAAACAAGCAAACAGAAAACCCACACAATAGGAGAAGATATTTGCAAAC 3631
                             iv   ii  v   v        v   i      i           i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_77954717_7   3632 TATGTATATGACAATAGTCTAATATCAAAAGTCGTTAAGGAACT-TAACA 3680
                         i  i   v   i  vi v  vi    v i i vvv   i     - v   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_77954717_7   3681 TATCAGCAAGCAAAAAACAAACAACCCAATT-AAAAGTTGGCAAAGTATA 3729
                         vv   ii  vv    i     i         -    i v       v  v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_77954717_7   3730 CAAACAGATAGTTCTCAAAAGAAGACTTATATGTGGAAAATAAGCATATG 3779
                         ii  i   i v     v        iv  i vi   vv        i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_77954717_7   3780 AAAAAGTGTTCAACATCACTAATCAT 3805
                             ii  i         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (141 / 107)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.58 (49 / 19)  


 608 22.38 4.90 0.00  chrX_77966007_77971943.rev     2854  2996 (2941)    L1M4_orf2#LINE/L1        3   152 (756)  

  chrX_77966007_7   2854 GAATGATATTCTATGTTTATGGATTGGATGAATCAATACTGTTAAAATGT 2903
                            v     i i     i          v  v i    i      i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_77966007_7   2904 CCATACTGCCCAAAGCAATGTACAGATTCAACGCAATCTCTGTCAAATTG 2953
                          v     v      vii  v                  i  i     v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_77966007_7   2954 ACAATGACATTCTTCACAGAAA-----AAA--AATCCTAAAATTTATATG 2996
                         v  iivi v  i  ii      -----  i--i           i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

Transitions / transversions = 1.46 (19 / 13)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 3.50 (7 / 2)  

2059 24.87 1.73 1.21  chrX_77966007_77971943.rev     2997  3575 (2362)    L1M4_orf2#LINE/L1      327   908 (0)  

  chrX_77966007_7   2997 AAACC---ACGTCTACAGTGAACTCATTTTTTACAAAGGTGCCAAGAACC 3043
                              ---  i i  ii  v  i v     iv    i          -- 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA--C 374

  chrX_77966007_7   3044 TATGC--TGGGAAAAGA---GTCTCTTCAGTAAGTGGTGCTGGGCAAACT 3088
                         i  v --    i     ---    i    ii  i          vv    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_77966007_7   3089 AGATATCAATATGCAGAAGAATGACACGAGATTCTTATCTCTCACCATAT 3138
                         i    ? v i     i        viivi  ii i  i   v        
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_77966007_7   3139 ACAAAAATCCAATCAAAATGGATTAAAGACTTAAATCTAACACCTCAAGC 3188
                                 iv v           i ?    i     v   v v  v  i 
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_77966007_7   3189 TCTAAAATTCCCATA-GAAAACATTGAGGTAACTGTACAGGAAATTGGAG 3237
                          v     i  ii v -        v i?    v v v iv  vv    iv
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_77966007_7   3238 TAGGCTGAGATTTCTTGAGTAATACTCCACAAGCACAAGCAACCAAAGGA 3287
                              viv i      iii  vv  v   v             v    --
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-- 622

  chrX_77966007_7   3288 AAAAAAAATGAAGAAATGGGGTCACATTAAGTTTAAAACCTTCTGCACAG 3337
                         --       ii v    v  iiiv   i  iv      v   i  ii vv
  L1M4_orf2#LINE/    623 --AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_77966007_7   3338 CAAAGAAAACAATCAACAAAGTGAAGATACAACACAGAGAATGGGAGAAG 3387
                              i v  v     v        i v     v  v            i
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_77966007_7   3388 ATATTTGCAAACTACTA-ATCTGACAAGGGATTGATAACCAGAATATATA 3436
                                    ii -  -      i      i vi  v            
  L1M4_orf2#LINE/    721 ATATTTGCAAATCA-TATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_77966007_7   3437 AGAAGCTCAAACAACTTTATAGGAAAAAATCTAATAATCTAATTAAGAAA 3486
                          ii i   vv      iv   iv     iv v     i i    ? i   
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_77966007_7   3487 TGAACAAAATATCTGAATAGGCACTTCTCAAAAGAGGACATAAAAATGGG 3536
                           ii    iv  i       i  i     v     i  i   v      v
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_77966007_7   3537 AAACAGGTATATGAATAGGTACTCAACATTATTAATCAT 3575
                         v  i i i i     v  i i        i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (80 / 60)
Gap_init rate = 0.01 (8 / 582), avg. gap size = 2.12 (17 / 8)  

3017 24.17 5.06 0.58  chrX_77966007_77971943.rev     4586  5454 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_77966007_7   4586 TGGAAATGCATCCCATAACAATCCACTAGAAAACT-AATATTGTTAAGAT 4634
                               vii       iviv  vv i i   i   -              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_77966007_7   4635 ATCAATGCTAGAAAAACTAATCTACATATTCAGTGCAAGCTGTATCAGAA 4684
                         iv    i  vvvv   i i       v     ii    v iv     i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_77966007_7   4685 TTTCAATAATGTATTTTGAAGAAACAGAAAAATCTATCTGAAAATTCATA 4734
                          ii  iiviiv v     v     iv  v  iiiv   iv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_77966007_7   4735 TGGGATTCTAAGAGACCGCAAATAAGAAAAAAACGTATAATGAAAGAGAA 4784
                            i v vi   i    vvi    ivv    v ---  vv     i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACA---ATCTTGAAAAAGAA 197

  chrX_77966007_7   4785 GTACAAAGTTTGAGGACTCAGTCTTCCTGATTTTAAAACTTACTACATAG 4834
                          v        v         vv     ii    i             v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_77966007_7   4835 CTACAGTAACTAAAACAGTGTAGTGTTGACCAAAATACATACATTCAGAC 4884
                                  ii  i       i  ii  i vv  iv i v    vi   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_77966007_7   4885 TAGTGAAATAGAATGAAGAGAACAGAAACAAACTCTCACATATATAGTCA 4934
                         i i  i        vi    vv      i    i vi    v   i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_77966007_7   4935 AATGATTTTTGATGAGGGTGCCAAGATCACACAATAAGGAAAGAACAGTC 4984
                          v       i  ii            i  iv    ii        i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_77966007_7   4985 TTTTCGATAAATGGTTTTGGCAAAACTGTATATGCAC-TACAAAATAATG 5033
                              i i       vi   v v     v   ?v   - i     v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_77966007_7   5034 AAGTAGGACCCTTACCTTACAG-------AAAGATTACCTCAGAATAAGT 5076
                             v      i     i   v-------   i    v    i   iii 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_77966007_7   5077 AAGACACCTAAGTGTCAGAGCTAAAAGCATAAAACTCTTAGA-GAAAGCA 5125
                         v ? v      i   v          vi              -    i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_77966007_7   5126 TAGGAATA------TGTA-------GTCAG--------TTCTTGGATATG 5154
                             ?i  ------i  i-------  i  --------     i      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_77966007_7   5155 ACACCAAA-TTACATATCAA-AATAGGAAAAATGGATAGATTGGACTTCA 5202
                                 -vi   - v   -  v  i      i    i           
  L1M4_orf2#LINE/    598 ACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_77966007_7   5203 TCAAAATTAATAATGTTTATGCATGAAACGACATAATCAGGGGAGTAAAA 5252
                                   v  iv   i   v v   v    iv    i ii   i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_77966007_7   5253 ATGA-AAC--ACAGAATGGGAGATGATATTTTTCAATTATATATATGATA 5299
                          -  -   --             vi      viv   i      v     
  L1M4_orf2#LINE/    697 A-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_77966007_7   5300 AAGGATTAATAATCACAATATATAAAGAACTACTATAAC------ACAAA 5343
                          i   i vi  vi  v               vi  i   ------ i   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_77966007_7   5344 ACAATAAA--ATTTGATTTAAGAGTGGGAAAAAGACTTCAATAAGCTTTT 5391
                          vi i   -- iiii   ?  i i    v   i  i  v    ii v   
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_77966007_7   5392 ATCCAAAGAAGACATACAAATAGGCAATAAGCACATAAAAAGACGTTTGC 5441
                         v           i        i v            i      i i iiv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_77966007_7   5442 AATCACTAATCAC 5454
                         v    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (121 / 85)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.06 (49 / 16)  


2310 29.00 1.04 0.39  chrX_77986499_77988285      526  1294 (493)    L1M4_orf2#LINE/L1      135   908 (0)  

  chrX_77986499_7    526 GATTCTAAAATGCATATGGAACCCAAAAATATCCTGCATACACAAAGCAA 575
                            i       v         vivv  iiv i  v v   vv    i   
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_77986499_7    576 GACTAAGCAAAAAGACCAAATTTGAAGGCATCACATTATCT-ATTTCAAA 624
                         vvi i iv  i    v    v   i   vv     i vi i-        
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_77986499_7    625 CTATACTCTAAGGCCATATTTCACCAAAACAACGTGATACTGGTATAAAA 674
                         viv    vi  i  i i -v v i   i   ii   i      i    ii
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACA-GTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_77986499_7    675 AAAGGAACATAGATCAATGGATCAAAATAGAGAATCCAGAAATAAACCCA 724
                          v  iv i             vi i   v    i                
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_77986499_7    725 CAAACTTATAGCCAACTGATCTTTGACAAAACAAACAAAAACATAAAGTG 774
                         i v i    i i   i    i  i     iivviv   i v   vv i  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_77986499_7    775 AAGAAAGGACAACCTTTT-ATCAAATGGTGCTGCGATAATTGGCTTGCCA 823
                         ii     i i ii     - v            v  i  i   v v?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_77986499_7    824 CATGTAGGAGAGTGAAACTAAATCCTCATATCTAATCTTATACAAAAATC 873
                             i ii   i    ii ii i  ii iv  vv i v           i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_77986499_7    874 AACTCACGATGGATTAAGGACTTAAATCTAAGACTTAAAACTGTAAAAAT 923
                               vi      i ?i   i     v     vi       i     v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_77986499_7    924 TCTAGAAGATAACATTGGGA-AAACCCTTGTAGACATTGGCTCAGGCAAG 972
                         ii       v     v  ?i-   i i i  -   v    v i      v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAAT 582

  chrX_77986499_7    973 GAATTCATGGCCAAGGAC-CCAAGAGCAAATGCTATAAAAACAAAGATAA 1021
                          iv   v i vi- v   -    i    v v  v i    iv   i   i
  L1M4_orf2#LINE/    583 GGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_77986499_7   1022 ATTACTTGGACTTAATTAAACTAAAGACCTTTTGCATGACAAAAGGAGCA 1071
                           v v        v  i   v v  i v      iiivv    i ivi v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_77986499_7   1072 GTCAGCAGAGTAAACAGACAACACATAGAGTGAGAGAAAATCTTCACAAT 1121
                         i   iv i   i  v       v  i   i  i        v  ii   v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_77986499_7   1122 CTGTACATATGATAAAGGGCTAATATCCAGAATCTGCAATGAACTCAAAC 1171
                         iii  i  v      i  i  vi          v ii  v      vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_77986499_7   1172 AAATCAGCCAGAAAATTACAAACAATCCCATCAAAAAGTGGGATAAGGAC 1221
                           v   iiv v    vv     i  i  v  i?    i    vv     i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_77986499_7   1222 ATGAACAGACAATTCTCAAAAGAAAGTATACTAATGCCCAACAAAC---- 1267
                         v    i     v     v      ii     v    v    i  i ----
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_77986499_7   1268 GAAAAAATGCTGAACATCACTAATGAT 1294
                              i     v       ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (126 / 93)
Gap_init rate = 0.01 (8 / 774), avg. gap size = 1.38 (11 / 8)  


2684 25.46 1.97 3.12  chrX_77997559_77999417.rev      505  1368 (491)    L1M4_orf2#LINE/L1       55   908 (0)  

  chrX_77997559_7    505 ATACTATCCAAAGCAATCTAAAGATTCAGTGCAAACCCTATGAAAACACC 554
                              vi     vii     v       ii    v      v    iv  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_77997559_7    555 AATGACATTCTTCACAGAAATAGAAAAAAAAATCCTAAAATTCATATGAA 604
                          iivi v  i  ii       v  v  ivvi                 i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_77997559_7    605 ACCCCCAAAGACCCCAAATAGTTAAAATAA-----AAAATTCTAGGCCCA 649
                          viv v ii     vi     ii    i  -----    ----  -----
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA----AG----- 195

  chrX_77997559_7    650 AAGAACAAAGCTAATGGCATTACACTCTTTGTTTTCACAATGTATTACAA 699
                                   i iiv  vv i     iiiiiv     v  iv  i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_77997559_7    700 AGCTATAATAATCAAAATAGCATGGCAGTGGTATAATAA-AGAAACACAG 748
                              i i       i i  ii   i v   i    vi -   v i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_77997559_7    749 ACTAATAAAACAAAATAGAGAACCCAGAAATAAATCCATGCATTTACAGT 798
                          ii   ii  i i   v    ii           i    i      ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_77997559_7    799 TAACCCAATTTTGACAAAGGTGCCAATAATATACACTGGGGAAAGAATAG 848
                         i  iiv v   i     i        v vi  v  v              
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_77997559_7    849 TCTCTTCAATGAATGTTACTAGGAAAACTGGATATCCACATGCAGAAGAA 898
                            i     ii    v i  i   v         ?         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_77997559_7    899 TGACACTAGACGCCTATCTCTTGCCATATACAAAAATAAAATCAAAATAG 948
                            vii i   v    i   vii              v  v       i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_77997559_7    949 ACTACAAACGTAAATCTAAGACCTGAAACTACAAGACTACTAGAAGAAAA 998
                          ii ? i  v     v     v  i      i  i   vi          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_77997559_7    999 CAGTGGGAAAACTCTCCAGGAAACTATCCAGGACAATGGTCAGAGCAAAG 1048
                           vv  ?iv  v   i iv  ------  vv -----   i  -    v 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGA------CCTTG-----GGTTAG-GCAATG 583

  chrX_77997559_7   1049 ATTTCTTGAGTAAAACCTAAAAAGCACAGGCAACCAAAGCAAACATGCAC 1098
                         i      iii  vi  viv         i     v    v   v  iv i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_77997559_7   1099 AAATGGGATAATATCAAGGTAAAAAGCTACTGCTCAGCAATGGAAACAAT 1148
                             v   ivvi     ii v    i  vi  iv vv   v   v  v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_77997559_7   1149 CAACCAAGTGAAGAGACAACACAGAGAATCAGAGAAAATATTTGCCAACT 1198
                            vv       i       v  v     vi              v  ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_77997559_7   1199 ACCCATCTAACAA--------TA---AAAATATATAAGAAGCTCAAACAA 1237
                          ivi    i i  --------  --- i         ii i   vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_77997559_7   1238 CTCAATAGGAGAAAAAAAACACAAATAATCAGATTTTTAAAATGGGCAAA 1287
                                ----- v     v        i vi   ?v-            
  L1M4_orf2#LINE/    784 CTCAATA-----ATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAA 827

  chrX_77997559_7   1288 AGACCTGAGTAGACATTTCTCGAAAGAAAACATACACATGGCAAGCAGGT 1337
                         i  ii   i            v      i i     v     v ii i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_77997559_7   1338 GTACGAAAAAATGTTCAACATCACTAATTGT 1368
                         ii i     i   i         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (131 / 85)
Gap_init rate = 0.01 (11 / 854), avg. gap size = 4.00 (44 / 11)  


3007 27.45 0.65 1.74  chrX_78035851_78040777.rev     3519  4436 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78035851_7   3519 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATAAATAT-G--AAAAT 3565
                              ii i  i     i        v      v v     - --  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78035851_7   3566 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3615
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78035851_7   3616 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3663
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_78035851_7   3664 TATGGAACCAAAAAAGAGCCTGCATGGCCAAGACAATCCTAAGCAAAAAA 3713
                                viiv  ii  v  v v  i     i      i i --------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-------- 190

  chrX_78035851_7   3714 AAAAAAAAAAAAAAAAAAAGTTGGAGGCATCACGCTACCTGACTTCAAGC 3763
                         -----    i  i  v           vv    i  v  ii i     iv
  L1M4_orf2#LINE/    191 -----AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_78035851_7   3764 TCTACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAAG 3813
                         ii        i          i   i    ii         i iv ii v
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_78035851_7   3814 AGATATATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACA 3863
                            i       i        i    iv   ivii         vv   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_78035851_7   3864 CATCTACTACCATCTGATCTTTGGCAAACCTGACAAAAACAAGAAATGTC 3913
                            i  ivii  vi    i  i i   ivv  v   i v  vvv    vv
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_78035851_7   3914 AAAAGGATTCCCTATTTAATAAATGAAGTTGGGAAAACTGGCTAGCCATA 3963
                         i    i  vvi  v  i  i     iv i     v      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_78035851_7   3964 TGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAGTTAA 4013
                           i i  iiv    ii    i    v   i     v         i    
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_78035851_7   4014 TTCAAGATAGATTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCC 4063
                         i    i  i   i ?    i     i v   v       i      vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_78035851_7   4064 TAGAAGAAAATCTAGGCA-ATACCATTCAGGACATAGGCATGCGCAAGCA 4112
                                   iv    ?i- v i -   iv   v v  vv iv    vvi
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_78035851_7   4113 TTTCATAGCTAAAACACCAAAAACAATGACAACAAAAGTCAAAGTTGACA 4162
                             v   v  vi         i  vvii         vv   i v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_78035851_7   4163 AATGAGATCTAATTAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTACC 4212
                            vi  ii v  i   v v  i i  ii  ii vv    i  v    i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_78035851_7   4213 ATCAGAGTGAACAGGCAACTTACAGAATGGGAGAAAATTTTTGCAATCTC 4262
                          vv i      v  i    ii                 v       viiv
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_78035851_7   4263 CCCATCTGACAAACGGCTAATATCCAGAATCTACAAAGAACTTAAACAAA 4312
                         ivi      i  iv i  vi          v  i        ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_78035851_7   4313 TTTACAAGAAAAAAACAAACAACCACATCAAAAAGTGGGCAAAGGATGTG 4362
                          iv i  v     i     i    vv  i?    i            v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_78035851_7   4363 AACAGACACTTCTTAATAGAAGACATTTATGCAGCCAACAGACACATGAA 4412
                           i     i    iv v      i  vi viii     i ii        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_78035851_7   4413 AAGATGCTCATCATCACTGGCCGT 4436
                                   v     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.75 (22 / 8)  


2169 29.79 1.53 2.19  chrX_78064520_78066810      888  1800 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_78064520_7    888 GGAAGAAACATTTCATCCTCATGGATTGAAAAAAATAAATATAATAGAAA 937
                             - i i  ii   vi          i  i vv   -   vi vi i 
  L1M4_orf2#LINE/      2 GGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAA-TATTGTTAAGA 49

  chrX_78064520_7    938 TGACTTCACTGCCCAAAAAAATCTATATATTCAACACATTCTCAATCAAA 987
                           i vvi   v      vvi     i v       i  v  i v      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_78064520_7    988 TTACCAATTACCATTTTTATTTTTCACAGGATTGGAAAAGTT----CTTA 1033
                         v v   ii i  -------     ii   i v v  v   i ----  v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-------TTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_78064520_7   1034 AGTTCATATAAAACCAAAAAAAAACTTTAATAGCCAAAACAATCCCAAGC 1083
                          i       ii  viiv  iii v ivv                iii iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_78064520_7   1084 AAAAAGAACAAATATGGAGACAGGACACTGCCTGACCTCAAATTATACTA 1133
                           i         vv     ivvvv     v  ii ii     viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_78064520_7   1134 CAATACTATAGTAACTAAAACAGCATAGTACTGGAAAAAAAAAACAGACA 1183
                            vi   i     ii  i    ii i       v v  ii --i     
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA--TAGACA 290

  chrX_78064520_7   1184 CATAGATGAATGGTACAGAATGAAGAATGCCTAAATAAAGCCATACGCCT 1233
                         i      v     v i     vi   i v vv       v      iii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_78064520_7   1234 ACAACCAAGTGATCCTTGACAAATTTCACACAAATAAGCAATAGGGAAAA 1283
                          iiii   v    ii i     ivv vv  vi vi vv    i      i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_78064520_7   1284 GACAGCCTATTCAGTAAATGGTGCTGAGAAAATT----AACCATATGCAG 1329
                         i i  i  v    ii           i  v  i ---- ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_78064520_7   1330 CAGAATTAAACCAGACCCCTATCTCTCACCATATTCAAAAAGTAACTCAA 1379
                         v     v  iiii        i   v        v      v        
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_78064520_7   1380 GATCAACTAAATGCTTAAATGTATGACCTGAAAATATAAAATT-TTATGA 1428
                         i  vi ii ? vi i        v  v  i   v       i -   vi 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_78064520_7   1429 GAATATCTAGGAAAAACACTTCTGGGCATTGATCTAGGCAAATAATTGGT 1478
                            v iv    ?iv  vv    vv i v   ivi       - ii  vv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chrX_78064520_7   1479 --GATAAAGACCCTACTAAAAGCAAATGCAACAACAAAGAAAAATAGACA 1526
                         --    v-   ---  i       v v       -  ii         i 
  L1M4_orf2#LINE/    590 TAGATAT-GAC---ACCAAAAGCACAAGCAACAA-AAGAAAAAATAGATA 634

  chrX_78064520_7   1527 AATTGAACTTAATTAAA-CTAAAAAGCTGCATAC--CAAAATAAATAGTC 1573
                              i    v  i   -i      vi vii i --    iv v ivi  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_78064520_7   1574 AACAGAGTAAAAGGACAACATACAGAATAGCAGAAAATGTATGCAAATTA 1623
                           v i   i   i      vi       i v       i v       i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_78064520_7   1624 TGCCCATGGCTAAAGACTAATATCCAAGATCTACAAGAAACGCAAACACC 1673
                          iiviv  iiv ii    vi      ii  v  i  ii   v vv   v 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_78064520_7   1674 TCAACAACAACAAAAAAAGAAAGCCCATTCAAAACTAGGAAAAGGACATG 1723
                             i  i  v  i v  iv  v  v   ?    v i  v      iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_78064520_7   1724 AACCGACTTTTTTTTTCAAAAGAAGACATACAAGCATCTGAGAAACACAT 1773
                           iv   v   i --- v        i      iiiv ii v  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCT---CCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_78064520_7   1774 GAAAAAATGCTTAACATTGCTAATCAT 1800
                              i     i     ii????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (156 / 112)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 2.27 (34 / 15)  


2715 26.17 1.57 2.57  chrX_78069318_78076010.rev     5296  6189 (504)    L1M4_orf2#LINE/L1        1   885 (23)  

  chrX_78069318_7   5296 TGGAAAAACACTCCAGGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5345
                               i i ii   v i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78069318_7   5346 GGCCATACTGCCCAAAGTAAGTTATAGATTCAATGCTATCCCCATCAAGC 5395
                            v     v      v i vi  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78069318_7   5396 TAACA-TTGACTTACTTCACAGAATTAGAAAAATCTACTTTAAATTTCAT 5444
                          vv  -i  v   -i  ii     v v  v  iiiv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_78069318_7   5445 ATGAAACCAAGAAAGAG-CCCACA-TAGCAAAGACAATCCTAAGCAAAAA 5492
                            i  -- v v   i -    v -    v  i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_78069318_7   5493 GAACAAAGCTGGAGGCATCACATTAGCTGATTTCAAACTACACTACAAGG 5542
                                 i      vv     i vv ii        vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_78069318_7   5543 CTACAGTAACCAAAACAGCAGGGTACTTGTACCAAAACAAATATATAAAC 5592
                                  i   i    iiv      v i iv ii i i i     i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_78069318_7   5593 CAATGGAACAGAACAGGGGCCTCAGAAATAACATCACTCATCTACAACCA 5642
                                 i    iv i ivii         vvi  iv   i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_78069318_7   5643 TCTGATCTTTGACAAATCTGGCAAAAACAAGCAATGGG-AAAGAAT--TC 5689
                         vi    i  i     ivv  v   i v  vv       -       --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_78069318_7   5690 CTTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 5739
                         i  -- i  i        i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_78069318_7   5740 GGAAACTGAACCCCTTCCTTACACCTTATACAAAAATTAACTCACGATGG 5789
                         v   ii  i      v   i     v                  vi    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_78069318_7   5790 ATTAAAGACTTAAATGTAAGACCGAAAACCATAAAAACCCTAGAAGTAAA 5839
                           i ?    i           v v     i      vi i      v   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_78069318_7   5840 CCTAGGCA-ATACCATTCAGAACATAGGCATGGGCAAAGACTTCATGACT 5888
                          v    ?i- v i -   ivi  v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_78069318_7   5889 ACAACATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5938
                          ii   i        vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_78069318_7   5939 AATTAAA-TTAAAGAGCTTCTGCAGCGAAAAAAAGAAACTATTATCAGAG 5987
                         v  i   -     i -   i  i-  vvv   i-  v     i vv i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGT-GCTTCAAAG-GACACTATCAAGAAAG 691

  chrX_78069318_7   5988 TGAACAGGTAACCTAGAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 6037
                             v  ii    i v               v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_78069318_7   6038 GACAAACGGCTAATATCCAGAATCTACAAAGAATTTAAACAAATTTACAA 6087
                           i  iv i  vi          v  i      i i--------      
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTC--------TTACAA 783

  chrX_78069318_7   6088 CAACAACAACAACAACAACAAA-AACCCA-TCAAAAACTGGGAGAAAAAT 6135
                          v-   i  i  v  -i     -      - i?    v    vi  ii  
  L1M4_orf2#LINE/    784 CT-CAATAATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_78069318_7   6136 ATGAACAGATACTTCTCAAAAAAAGACAGTTTTGCA----GCCAACAAGC 6181
                         v    i   i i     v   i    i ---- i  ----     i    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATA----TACAAATGGCCAATAAGC 877

  chrX_78069318_7   6182 ATATGAAA 6189
                          i      
  L1M4_orf2#LINE/    878 ACATGAAA 885

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.02 (21 / 885), avg. gap size = 1.76 (37 / 21)  


2335 27.62 6.64 0.82  chrX_78077386_78079804     1069  1926 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78077386_7   1069 TGTAAACACATCCCATGCTCATGAATGGGTGGAATCAATATTGTAAAAAT 1118
                           v   v i        i     i  v  vi  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78077386_7   1119 GACCATACTGCCAAAAGAAATCTACAAATTCAATGTGATCTCCATTAACA 1168
                          i v     v  v   vvi       i      i ii   i i  i  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78077386_7   1169 TAC-AACGATCATTCTTTCAGAATTAGAAAAAAACAATTCTAAAATCCAT 1217
                          v - i vii v  i  v     v v  v  iv-ii  i       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_78077386_7   1218 ATGGAACCAAGAAAGAACCTGCATAGTCAAAGCAAGACGAAGCAAAAAGA 1267
                               viivi ii  v  v v    i    i   vvivi iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_78077386_7   1268 ACAAATCTGCAGGCATCACACAACCTGATTTCAAACTTTACTATAAGGCC 1317
                              vi  v   vv      vv  ii        vi      i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_78077386_7   1318 ATAGTCACCAAAACAGCATCATACTGGTATAAAAATAGGCACATAGACAA 1367
                          i   v i   i    ii vi      i    ii    i  i     iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_78077386_7   1368 ATTGAACTACATAGAGAACCAAAAAATAAAACCAAATACTTACAGCCAAC 1417
                           v   iviv  v    ii v i       v   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_78077386_7   1418 TGATCTTTGACAAAG----CAA-AC-------------AAAAATA----- 1444
                             i  i     i ----   -  -------------  i    -----
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_78077386_7   1445 ------------TGC--------------AGCCACATGCAGAAGAATGAA 1468
                         ------------   -------------- ?         i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_78077386_7   1469 ACTGGATCCTCATCTTTTACCTTATACAAAAAGCAACTCAAGATGAATTA 1518
                         ii    i  ii i  ivi   v          vi       i   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_78077386_7   1519 AGGACTTAAATCTAAGACTTGAAACTATAAAAATTCTAGAAGTTAACAT- 1567
                         ?i   i     v     vi i           v ii      vv     -
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_78077386_7   1568 --TGTAAAACTCCTTTTAGACATTGGCTTTGGCAAGGATTTCACGACCAA 1615
                         --?     v  i v ---   v    v  v     v i    viiivi v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT---GACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_78077386_7   1616 GTAC-CCAAAAGCAAATGTAATAAAAAGCAAATATAAATAACTAGGACTT 1664
                          -  -         v v i  i    - v   v   i    v v      
  L1M4_orf2#LINE/    597 G-ACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTT 644

  chrX_78077386_7   1665 AATTAAA-TTAAAGAGCTTTTGCATGGCAAAAGGAACAGTTGGCAGAGTC 1713
                         v  i   -     i -      iiivv    i iv  vi iiiv i   v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_78077386_7   1714 AACAGACAACCTACAGAGCAGGAGATAATCTTCACAATCTATACATATGA 1763
                           v        i     iii     v   v  ii   vii   i  v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_78077386_7   1764 CAAAGGACTAATATCCACAATCTACAAAGAACTCAAACAAATCAGCAAGA 1813
                         i  i     vi      v   v  i         vv    v   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_78077386_7   1814 AAAAAACAAAAAATTCTATCCGAAAGTGGGCTAAAGACATGAATAGACAA 1863
                             i     v  ii v  i?i   i     v  i  iv          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_78077386_7   1864 TTCTCAAAAGAAGACATGCAAATGTCCAACAA--ACATGAAAAAATGCCC 1911
                              v        i  i      v    i  --         i    i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_78077386_7   1912 AGCATCACTAATGAT 1926
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.27 (64 / 15)  


1751 26.77 2.79 0.37  chrX_78082021_78086189      501  1038 (3131)    L1M4_orf2#LINE/L1      358   908 (0)  

  chrX_78082021_7    501 GACAAAATT--CAACACCCTTTAATA---AAAGAATGCTC---------A 536
                              iiv --   v   v  i   i---       iv  --------- 
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_78082021_7    537 ATGGTGTTGGGAAAATTGGCTAGCTACATGTAGAAAGCTGAAACTGGATC 586
                               i     v  i   v  ? i     i i  iiv    ii    i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_78082021_7    587 CCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTG 636
                            v   i     v              i    i      i ?    i i
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_78082021_7    637 CATGTCAAGCCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATA 685
                         v    v iiv       i      vi i           v    ?i- v 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_78082021_7    686 CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAA 735
                         i -   iv   v v  vv i     v ii   v ivv  vi         
  L1M4_orf2#LINE/    558 TC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_78082021_7    736 GCAATGGCAACAAAAGTCAAAATTGACAAATGGGATCTAATTCAACTAAA 785
                            vvi          vv     v  i    v   ii v  iv  v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_78082021_7    786 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAGAGGCAACCTA 835
                         i i   i  ii vv    i  v    i  vv i      i  i     i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_78082021_7    836 CAGAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAGGGCTAATA 885
                                         v  ii   vii ivi      i  i  i  vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_78082021_7    886 TCCAGAATCGACAATGAACTCAAACAAATTTACAAGAAAAAAAACAAACA 935
                                 vv i  v      vv    v iv i  v     i -    i 
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATA 805

  chrX_78082021_7    936 ACCACATCAAAAAGTGGTTGAAGGATATGAACAGACACTTCTCAAAAGAA 985
                            vv  i?    i   vii      v    i     i     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_78082021_7    986 GACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCGTCACTGGC 1035
                           i  vi viii     v  i          i       v i   ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_78082021_7   1036 CAT 1038
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.30 (79 / 61)
Gap_init rate = 0.01 (6 / 551), avg. gap size = 2.83 (17 / 6)  

2447 28.06 1.84 3.47  chrX_78082021_78086189     2767  3689 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78082021_7   2767 TGGAAAAACCATTTTATGTTTATGTCTTGGAAGAAACAATATTATTAAAA 2816
                               i i-  iii     i   vv        vvi      i    i 
  L1M4_orf2#LINE/      1 TGGAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_78082021_7   2817 TGCCCATACTACACAAAGCAATCTACAGACTAAAATCAATCCCTGTAAAT 2866
                           v v     v v    vii         i v  vv        i v  v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_78082021_7   2867 ATGCAAATGACATTCTTCACAGAAATAGAAAAAAATAATTTTAAAATGTA 2916
                           v v iivi v  i  ii       v  v  iv- i  ii      vi 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chrX_78082021_7   2917 TATGGAACCACAACAGACACAGAAGAGTCAAAGCTATTCTAAGTAAAATG 2966
                                vii   vi   v     v  i    i v  ii i iv  i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_78082021_7   2967 AACAAGACTGGAGAAATTACCTTATTTTCC---TTCATTA--TATTACAG 3011
                              iii     i v i  --- i  i  ---    vv --  i    i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCAC---ACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_78082021_7   3012 AGTTATAGTAACCAGAACATCATGGTACTGGCATAAAAAAAGATACATAG 3061
                           i  i     i  ii   vii              ii v   i i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_78082021_7   3062 ACCAATAGAACACAACAAAGAACTCAGAAACAATTCCACACACTTTCAGT 3111
                          i    i   i v  ivi   iii      i  vi   i   i  vii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_78082021_7   3112 GAATTTATTTTTGACAAAACGTTTCCAAAAACATATGCTATGGAAATA-C 3160
                         v    v     i     i-- v v    i v   viiv iv     v -i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAG--GGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_78082021_7   3161 AGGCTCTTCAATGAATATTGCTGGGAAAATTGGATATCCATATGCAGAAT 3210
                           v  i     ii   iv        v  i      ?   i     i  v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_78082021_7   3211 AGTGAAATTAGACCTCTATCTTATGCTGTATATAAAAATTAAATTAAATT 3260
                          i    i  i    i   i  i ii ii    i         v i   v 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_78082021_7   3261 GAATGAAAGATTTAAATCTAAGAAACCAAACTATGAAACTACTAAAAAAA 3310
                          i  v ?   ii     v     iviv       i     vi  i  i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_78082021_7   3311 GTTTGGATAAATTTTACAGGTCATTGGTCTCAGTACAACTTTCTGGAGCA 3360
                         ---------  i--- i   ?-i vii   iv  i--  i  --  ivi 
  L1M4_orf2#LINE/    544 ---------AAC---ATAGGN-GTAAATCTTCGTG--ACCTT--GGGTTA 576

  chrX_78082021_7   3361 GGATACAAT--TTTCTGGAGCATTACCGCAGGAGCACAGGCAACCAAAGC 3408
                           ---    --     viiii  v  vv  ii      i     v    v
  L1M4_orf2#LINE/    577 GG---CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_78082021_7   3409 AAAAATGGACAAATGGGATCAAATCAAG-TTAAAAAC----GTACTGCAA 3453
                               i  i    v   iivv     i-        ----  i  v   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_78082021_7   3454 AGCAAAGGAAGCAATCAACAAAGTGAAAAGACAACTCAGAGAATGAGAGA 3503
                           -----  vi v     v                i  v      i    
  L1M4_orf2#LINE/    674 AG-----GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_78082021_7   3504 AGATATTGGCAAAGTACCTATCTGAGAAGGGACTAAGAATGAGAATATAT 3553
                          i     v     vi iv       v        viv viv         
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_78082021_7   3554 AAG---CTCAAACAACTATGTAGAAATAAATCTAATAATCTGATCCAAAC 3600
                           i---   vv      vvi  iv  v  iv v     i ii  i?   v
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_78082021_7   3601 TTGGGCAAAAGACTTGAACAGACATTTCTCAAAAGGAGGCATGCAAATGA 3650
                         v        i  i     i           v    i  ii  i      i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_78082021_7   3651 CAAACAGTCATATAAAAATGTCTTCAAGA-CAATTGAATA 3689
                          v  i iv  i  i    vi vi    v -  ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (156 / 99)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.58 (49 / 19)  


1700 30.05 4.07 1.57  chrX_78086429_78088140      458  1219 (493)    L1M4_orf2#LINE/L1      128   908 (0)  

  chrX_78086429_7    458 ACAACCT-ACCCCAAAAT--AT-TAAAAAT-CAAAACATTCAAAA-AG-- 499
                             v  - i  i     --  - ii    -   iiv ii  i  -  --
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chrX_78086429_7    500 -AAGCAA----AAAGTAGGAAAACAGAGCTGGAGTCATCACATTGCTCAA 544
                         -  i   ----i  iv  i i    i  i     vvv     i v i   
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_78086429_7    545 TTTCCATCTATAATA-AAAGTGTACAGTAACCAAAACAGCATGGTACAGA 593
                             v vviv  v  -    i-        i   i    ii      v i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGC-TACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_78086429_7    594 CACAAAAGCAGACACACAGACCAACTGAACATGAGAGAGAGTCCAGAAAT 643
                           i  iiii     i i   i   iv   i vi vv              
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_78086429_7    644 AATGCTGCACACCTACACCTATCTGATCTTTAAAAAAATCATCAAAAACG 693
                           vv iii   ii  iivii vi    i  ii v  iiviii   i v i
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_78086429_7    694 GGAAATAGGGAAAGGACTTCCTATTCAATAAACGGTGCTGGAATAACTGG 743
                         vvv   i       i ivvi  v     i   i        i i      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_78086429_7    744 CTAATAAAATGCAGAAGATTGAAACTTGTCGTGTCCCTTACACTATTTA- 792
                         v  ?iv v     i    v    ii v v viv v   i    i  v  -
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_78086429_7    793 AAAAACC--CTCAAGATCAATTTAAGACTTAAATATAAAACCTAAAACTA 840
                              ii--     i  vi  iv?    i     i   i v         
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_78086429_7    841 TAAACAC-CATGGAAAATAACCTAA----AAAGTTTCAT---TCTGGATG 882
                             -  - v i   i v   v  i----   vi   i ---ii   i -
  L1M4_orf2#LINE/    527 TAAA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT- 574

  chrX_78086429_7    883 TATAAACAGGCAAAGATTTTACAAAAAAAGATGCCAAAAGC-CATTGCAA 931
                         ------i      v i   ivi i v v-  ii        -  v-    
  L1M4_orf2#LINE/    575 ------TAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCACAA-GCAA 616

  chrX_78086429_7    932 CAAAAACAAAAATTGACAAACGGGACCTAATTAAA-TTAAAGATCTTCTG 980
                              iv      v  i   iv    i v  i   -     i -   i  
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTG 665

  chrX_78086429_7    981 CACAGTAAAAGAAGCTATCAACGGAATAAATAGAAAACCTACACAATGGG 1030
                         ii vvi   i  vi       vii i i  v   v    i   v      
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_78086429_7   1031 GGAAGACATTCACAAACTATGCATCCAACAAAGGTCTAATACCCAGAATA 1080
                         i   i i   ii    ii  ii   ii i  i  v  vi  i        
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_78086429_7   1081 TGTAAGGAACT--TA-AATTTA-CAAGCAGAAAACAAACAACTGAGTTAA 1126
                          i   i     --  -  i i -i  vv i  i     i   iv i  ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_78086429_7   1127 AAAGTGGGCAAATAACATGAGCAGATACTTTTCAAGAGAAGACTTACATA 1176
                            i        vi iv   ii   i i  i  v i      iv    v 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_78086429_7   1177 CAGCCAATAAGTATATGAAACAATGCTCAACACCACTAATTCT 1219
                         ii         i i      vi          i  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (152 / 74)
Gap_init rate = 0.03 (24 / 781), avg. gap size = 1.79 (43 / 24)  


3179 27.53 0.44 0.44  chrX_78088487_78094868.rev     4984  5891 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78088487_7   4984 TGGAAGAACATTCCATACTCATGGATAGGAAGAATCAATATTGTGAAAAT 5033
                              ii i  i    ii        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78088487_7   5034 GGCCATACTTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5083
                            v     i     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78088487_7   5084 TACCAATGACTTTCTTCACATAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5131
                          v   iivi i  i  ii  v  -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_78088487_7   5132 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAACCCTAAGTCAAAA 5181
                                 viiv  ii  v  viv  v     i    i i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_78088487_7   5182 GAACAAACCTGGAGGCATCATGCTACCTGACTTCAAACTCTACTACAAAG 5231
                                vi      vv   ii  v  ii i      vii          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_78088487_7   5232 CTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATGGAC 5281
                                  i   i    iii        i iv ii i   v    i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_78088487_7   5282 CAATGGAACAGAACAGAGCTCTCAGAAATAATACCACACATCTACAACCA 5331
                                 i    iv   vvii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_78088487_7   5332 TCTGATCTTTGTCAAACCTGACAAAAACAAGAAATGGGGAAAGGATTGCC 5381
                         vi    i  i v   ivv  v   i v  vvv           i  v i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_78088487_7   5382 TATTTAATAAAAGGTGCTGAGAAAACTGGCTAGCCAGCTGTAGAAAGCTG 5431
                          v  i  i   v       i  v      v  ?   vv  i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_78088487_7   5432 AAACTGGATCCCTTCCTTACACCTTATACGAAAATTAATTCAAGATGGAT 5481
                           ii    i    v   i     v     i        i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_78088487_7   5482 TAAAGACTTACATGTCAAGCCTAAAACCATAAAAACCCTAGAAGAAAACC 5531
                         i ?    i  v    v iiv       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_78088487_7   5532 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5580
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_78088487_7   5581 AACACCAAAAGCAATGGCGACAAAAGCCAAAATTGACAAATGGGATCTAA 5630
                         i            vvi  i       vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_78088487_7   5631 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAG 5680
                          iv  v v  i i   i  ii vv    i  v    i  vv i      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_78088487_7   5681 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5730
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_78088487_7   5731 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5780
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_78088487_7   5781 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGATAAGAACAGACACTTC 5830
                          i     i     v  i?    i    ii      vv   i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_78088487_7   5831 TCAAAAGAAGACATTTATGTGTCCAACAGACACATGAAAA-ATGCTCATC 5879
                           v        i  vi vi  v    i ii          -       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_78088487_7   5880 ATCACTGGCCAT 5891
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2885 28.30 1.33 0.55  chrX_78100163_78102247.rev      694  1594 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78100163_7    694 TGAAAAAACATCTCATGCTCATTGATAGGAAGAATCAGTATCATTAAAAT 743
                           i   i i   i    i    v   v      v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78100163_7    744 GCTTATACTGCCAAAAGTAATTTACAGATTCAGTGCTACTCCTATCAAAC 793
                          viv     v  v   v i  i          ii  v ii         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78100163_7    794 TACAAATGACATTCTTCACAGAA--CAAGAAGAAAACTTTTTAAAAATTC 841
                          v v iivi v  i  ii     --ii v   vvi iii ---       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT---AAAATTC 147

  chrX_78100163_7    842 ATACAGAACAAAAAAAGAGCCTGAATGGCCAAGGCAATCCTCAGCAAAAA 891
                            ii   vviv  ii  v  v    i     ii     i v iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_78100163_7    892 GAACAAAGCTGGAGGCATAATGTTACCAGACTTCAAACTATACTACAAGG 941
                                 i      vv v iii v  vi i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_78100163_7    942 CTGCAGTAACCAAAACAGCATAGTACTTGTACAAA-ACAGGTACATAGAC 990
                           i      i   i    ii i     v i i  i- i  ii i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_78100163_7    991 CAATGGAACAGAATAGAGAGCCCAGAAA-AAGGCTGCTCATCTATGACCA 1039
                                 i     v     i       -  iv iiiv   i    ii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_78100163_7   1040 TTTGATCTTTGACAAAGCTGACAAAAATAAGCAATGGTGAAATGACTGCC 1089
                         v     i  i     i v  v   i vi vv      v    vi iv i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_78100163_7   1090 TATTCAATAAATGTTGCTGGGATAACTGGCTAGCTATATACAGAAGATTG 1139
                          v     i     v        i      v  ? i i  i  i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_78100163_7   1140 AAGCTGGACCTCTTTCTTACATCATACACACAAATAAATTTAAGATGCAT 1189
                            i      i  vi  i   i    i   v    v  i i  i   v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_78100163_7   1190 TAAAAACTTAAATGTAAAA-CTGAAAGTGTAAAATCCCTAAAAGACAACG 1238
                         i ? i  i         i -  i   v i     ii i  i    v   i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_78100163_7   1239 TAGTCAATATAATCCT-G-GACATAGGAACAGGCAAAGATTTTATGACAA 1286
                            v?i-  -    i - -   v v  ivi      v i   iv iivv 
  L1M4_orf2#LINE/    548 TAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_78100163_7   1287 AGACAACAAAAGCAATTGCAACAAAAGTATAAGTTGACAAGTAGGATCTA 1336
                         v    v        vvv          v v  i v  i  i v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_78100163_7   1337 ATTAAACTTAAGAGTTTCTGCACAGCTAAAGAAAGTATCAACAGTGTAAA 1386
                           i   v    i ii  i  ii vv v  i  v v      v iv  i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_78100163_7   1387 CAGACAACCTACAGAATGGGAAAAAATATATTCAAACTATGCATCTGACA 1436
                         v        i           i       v v    ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_78100163_7   1437 AAGGTCTAATATCCAGCATTTATAAGAAACT--TA-AATTTACTAG-AGG 1482
                          i  v  vi       v  v     ii    --  -  i i v  i- ii
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_78100163_7   1483 AAAACAAACAACTCAATT-AAAAGTGGGCAAAGGACGTAAACAGACACTT 1531
                           i     i   i     -    i           iv i  i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_78100163_7   1532 CTCAAAAGAAGACATGCATGTGGCCAACAAGCATATGATAAAAAGCTCAA 1581
                            v        i  i  vi       i     i    v  i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_78100163_7   1582 TATCACTGATCAC 1594
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (159 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.31 (17 / 13)  


2662 27.57 3.05 0.45  chrX_78106472_78108845      997  1881 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78106472_7    997 TGGAAACACATCCCACGCTCATAGATGGGTAGGATCAATATTGTGATAAT 1046
                               v i      i i    i   v  v  iv i        v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78106472_7   1047 GACCATACTGCCAAAAGCAATCTACAAATTCAGTGTGATTCCCATCAAAA 1096
                          i v     v  v   vii       i     ii ii  i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78106472_7   1097 TATCACCATCATTCTTCATA-AAATTAGAAAAAAAATCTTAAAAAATTCA 1145
                          vi  v vv v  i  iii -     iiv  ivvi   i     --    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA--TTCA 148

  chrX_78106472_7   1146 TATGGAACCAAAAAAGAGCTCATATCGCCAAAGCAAGACTAAGCAGAAAG 1195
                                viiv  ii  v iviv  v      i   vvi i iv ii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_78106472_7   1196 AACAAATCTGGAGGCATCACATTACCCAACTTCAAA-----CTATA---- 1236
                               vi      vv     i v     i      -----   i ----
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_78106472_7   1237 TGTAGTCACCAAAACAGCATGGTACTGGCATAAAAACAGGTGCATAGACC 1286
                          ii   v i   i    ii              ii i  iiii     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_78106472_7   1287 AATGGAACAGAATAGAAAACCAAGAAATAAAGCCAAA----TACAGCCAA 1332
                                i     v  i ii v         v   v ----  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_78106472_7   1333 ATGATCTTCAACAAAGCAAACAAAAACATAGAGTGGGTAAAGGACACCCT 1382
                         v    i   i    i vviv   i v   vv i    v    i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_78106472_7   1383 ATTAAACAAATGGTGCTGGTATAATTGGCAAGCGACATGTAGGAGAATGA 1432
                         v  v               v i  i   vv ? v     i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_78106472_7   1433 AACTGGATTCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATC 1482
                          ii    ii ii i   v    v           i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_78106472_7   1483 AAAGACATAAATCTAAGACCAGAAACCTTAAAAATTCTAGAAGATAACAT 1532
                          ?    v     v     v vi    iv     v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_78106472_7   1533 TGGA--AAATCCCTTCTAGACATTGGTTTATGCA--GACTTC------AT 1572
                         v  ?--     --   vv   v    v   v   -- ii   ------  
  L1M4_orf2#LINE/    549 AGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_78106472_7   1573 GAC-CCAAA-GCAAATGCAACAAAAACAAAGATAAATAGAGGGAACTTAA 1620
                            -     -   v v         iv   i   i   i vv i    v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_78106472_7   1621 TTAAACTAAAAAGCTTCTGCACAGAAAAGAA-ATAATCAGCATAGCAAAC 1669
                          i   v v    i   i  ii vvv    i - iv    iv v  ii  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_78106472_7   1670 CAACAACCCACAGACTGGGAGAAAATCTTTGCAATCTATACTTCCAGGAA 1719
                         vi            v           v       vii   iv  iiiv  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_78106472_7   1720 AGGACTAATATCCAGATTTTATAAGGAATTCAAACAAATCAGCAAGAGAA 1769
                         i     vi        v v     i   i  vv    v   ii  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_78106472_7   1770 AAACAAGAAATCTCATCAAAAATTGGGCTAAGTACATGAATAGACAATTC 1819
                          i    iv  i iv  i?    v     v   v iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_78106472_7   1820 TCAAAAGAAGATGCATAAAAGGCCAACAAACATATGAAAAAATAGTCAAC 1869
                           v         ii i   v      i  i  i       i  iv     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_78106472_7   1870 ATCACTAATTAT 1881
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (136 / 104)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


1228 26.94 5.90 7.01  chrX_78122717_78126861.rev       32   844 (3301)    L1M4_orf2#LINE/L1        1   804 (104)  

  chrX_78122717_7     32 TGGAAAAATAGTCCATATTCATTGATTAAAAGAATCAATATTGTTAAACT 81
                               i   vi    i     v    ii    v i           iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78122717_7     82 CTCCATACTATCCAAAACAATCCACATATTCAACACAATCCCTTTCCAAA 131
                         vv v     vi     vii   i   v       i        v  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78122717_7    132 CACCAATGACTTTCTTCACAGAAATAGAAAAAGCAATTCTAAGATTGACA 181
                         iv   iivi i  i  ii       v  v  ivii  i    i   v i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_78122717_7    182 TGAAACCAAAAAAGACACAAAATGTCCAAAGCTATCCTAAGATAAAAGAA 231
                           i  viiv  ii   v  i   iv     i v   i i ---       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAA 197

  chrX_78122717_7    232 GAACCAAACGGGAGGAATCATACTACTTGACTTCAAATTATACTACAGAG 281
                             v  iiv      v   i   v iii i      viv       i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_78122717_7    282 CTATAGTAACCCAAACAGCATGAAATTGGCATAAATACAGATAACATAGA 331
                            i     i v i    ii  iv i        iv i   i -i     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA-TATAGA 296

  chrX_78122717_7    332 CCAAGAGGACATAATAGAGAACCCAGAAACAAATCCACACACCTA----C 377
                         i   vi i i v   v    ii       i   i   i   ii  ---- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_78122717_7    378 AA------------AA---TGCCAAGAACATACACTGTGGAAAAGACAGT 412
                           ------------  ---        v   v  v  v     ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_78122717_7    413 CTCTTTAATAAATGTCACTGGAAAAACTGGATATTCATATTCAGAAGAAT 462
                           i  i  i     vii    i v         ?i  i  v  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_78122717_7    463 GAAGGTAGGCCCCTATCTCTCACTATACACAAAAGCAAAATAAAAATTAA 512
                             v i i      i   v   i   i      iiv  v v     vi 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_78122717_7    513 ATAAAATCCT---CCTGAGCAATTAATGAATCAATAAGGAAGT-TCAGAA 558
                         vi ? iv   ---iv i  - ii   --  - v    --  v - i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAG-AGCTAA--AA-CTATAA--AACTCTTAGAA 540

  chrX_78122717_7    559 GAAAATTTAG---TAATATCTTTAAAATAAATCAAAATGAAAACACAACA 605
                              iv   ---   -     ii--- i viiviii v ii---   --
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAA-ATCTTCG---TGACCTTGGGTTAGG---CAA-- 581

  chrX_78122717_7    606 TACCATAATTTATGGGATA---CATCAAATGTA---GCAATAAGAGGGAA 649
                         ----- ii   v vi    ---  i    v i ---    i  i  ii  
  L1M4_orf2#LINE/    582 -----TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_78122717_7    650 GTTTATAGCAACAAAT--GCCTACATCAAAAAAGTAGAA------GTATT 691
                         i---    -- i    -- v  v        --v  i  ------  ii 
  L1M4_orf2#LINE/    627 A---ATAG--ATAAATTGGACTTCATCAAAA--TTAAAAACTTTTGTGCT 669

  chrX_78122717_7    692 TCAAATAAAAAAACT--CAAGGAACTAAAAAAGCAGGAACAAACCAACCC 739
                              ---ii v   --    i  v i    i------    v   --- 
  L1M4_orf2#LINE/    670 TCAAA---GGACACTATCAAGAAAGTGAAAAG------ACAACCCA---C 707

  chrX_78122717_7    740 AAAATTTAGTAGAACAAAAGAAGTATTAAAGATCAAAGCATAAATA-AAT 788
                          i   -----i i v    ----    vi----    v    v  v-i  
  L1M4_orf2#LINE/    708 AGAAT-----GGGAGAAAA----TATTTG----CAAATCATATATCTGAT 744

  chrX_78122717_7    789 AAA--ACTAGAA--CAAAAAATATGAAAGACCAATGGAACTAAA-AGTAA 833
                           i--   v v --  i  v    i  ii  ivv iv    v  - i   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_78122717_7    834 ATAAGATCAAT 844
                          -    iv   
  L1M4_orf2#LINE/    795 A-AAGACAAAT 804

Transitions / transversions = 1.75 (138 / 79)
Gap_init rate = 0.04 (35 / 804), avg. gap size = 3.00 (105 / 35)  

 261 20.69 0.00 0.00  chrX_78122717_78126861.rev     2416  2473 (1672)    L1M4_orf2#LINE/L1        1    58 (850)  

  chrX_78122717_7   2416 TGGAAACATTTGTCATACTCTTGGAATGGAAGAATTACTATTGGTAAAAT 2465
                               v  v vi   ii  v    v       v   v     v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78122717_7   2466 GGCAATAC 2473
                                 
  L1M4_orf2#LINE/     51 GGCAATAC 58

Transitions / transversions = 0.50 (4 / 8)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.00 (0 / 0)  

2466 27.76 3.88 1.09  chrX_78122717_78126861.rev     2830  3654 (491)    L1M4_orf2#LINE/L1       61   908 (0)  

  chrX_78122717_7   2830 CCCAAAACAATCTACAGACTTAATGTAGTATCTGTCAGAATATAAATGAC 2879
                               vii         i i  i i i vi  i   i   viv iivi 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_78122717_7   2880 ATTCTTCACAGATATAGGGAAAAC--ATCCTAAAATTTGTATGAAACCAC 2927
                         v  i  ii    v  -v iv  i --           ii    i  vii 
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_78122717_7   2928 AGAAAATCCAAAATA-CCAAATAAAAATGCTGAGGAGAAACAGTACAAAG 2976
                          iiii i   i    -     -- v   vi   -- i  iv  v      
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAA--ACAATCTTGA--AAAAGAAGAACAAAG 205

  chrX_78122717_7   2977 CTGGAGACATCACAC--------------ACATTCTCCAAAGCCATAGTA 3012
                         i     ivv      --------------  v v  v      i i    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_78122717_7   3013 ACCAAAGCAGCATGGTACTGGCATAAAAACC--CACATAGACAAATGGAA 3060
                          i   ii   ii              ii iv--  i     iv       
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_78122717_7   3061 CAGAATAGAGGCCTTAGCAATAAATCCACACATTCATGGTCAACTCATTT 3110
                         i     v   iviii  v      i   i     i        i v    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_78122717_7   3111 TTGACAAAAATGCCAAGAACATATACTGAGGAAAGAACAGTCTCTTCAAT 3160
                          i     iii        v   vi v  i        i     i     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_78122717_7   3161 AAATGGTACTGGGAAAACTGAATAACCATGTGCAGAAGAATGA---TGAC 3207
                                i      v     i   ?   ii    i        ---  iv
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_78122717_7   3208 CCCCCATCTCCCACCAAATACAAACATCAAATCAAAA---AT-AAAGACT 3253
                             i i   v     v       v  i  v      ---  - ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_78122717_7   3254 TAAATTTGATACTTGAAAGTATAAAACTACAAGAAGAAAA-ATGTTTGGG 3302
                              v i v vi i   v         viv         -  i---  ?
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA---GGN 552

  chrX_78122717_7   3303 GACACTCTTGAGAACATTGGTCTGGGCAAAGATGTTTTGAGTAAGACCTC 3352
                          vv v    vivi  v    vi i     v i v i  iii  v   vi 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_78122717_7   3353 AAAAACATATGTGACAAA-GAAGAAACAGACAAA----ATTACACCAAAC 3397
                             i  i v ii     -   i   i   i   ---- i v  i    v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_78122717_7   3398 CTAAATGCTTCCACATGGCAAAGAAAGCCACTAACAAAATGAAGATACAA 3447
                         i    vi   iiiiiivv     i vi i ii  v   i    i v    
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_78122717_7   3448 CCTAAAGAATAGAAGAAAATATTTTCAAGCTATTCATTCAACAAAGGATT 3497
                           i v     i i           v   iii  vi  iii i  i   i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_78122717_7   3498 AATAACGAAAATATGTAAAGAATTCAAGCAACTCAATAGGAAAAAATTCT 3547
                         vi  v v i     i       i  vvi          iv     iv- v
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CA 801

  chrX_78122717_7   3548 AACAATCTGATTTAGAAATGGGCAAAATATCTTACTAGACATTTCTCAAA 3597
                           i  i ii   ? i           iv  i v v            v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_78122717_7   3598 AGGTGACATACAAATGGCAAACAAGCATATGAAAAGATACTCAATATTAC 3647
                           iv  i           v  i     i          i     i  i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_78122717_7   3648 CGATTAT 3654
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.92 (148 / 77)
Gap_init rate = 0.02 (15 / 848), avg. gap size = 2.73 (41 / 15)  


2930 27.26 1.43 1.21  chrX_78133151_78139085     4537  5442 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78133151_7   4537 TGAGAAAACATTTCATGCTCATGGATAGGAAGAATCAATATCATAAAAAT 4586
                           ii  i i  ii    i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78133151_7   4587 GGCCATACTGTCTAAAATAATTTATAGATTTGATACTATTCCCATCAAGC 4636
                            v     vi i   v i  i  i     ii ii v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78133151_7   4637 TACCATTGACTTTCTTTGCAGAA-TTAAAAAAAAAAAACT-ACTTTAATT 4684
                          v   vivi i  i         -  i v  i------  - iii   vv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG------CTGATCCTAAAA 144

  chrX_78133151_7   4685 CTCATATG-AAACCCAAAAAGAGCCCATA-TAGCCAAGACAATTCTAAGC 4732
                         i       -   iv   i-- ii    v -       i     ii i iv
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_78133151_7   4733 AAAAAGAACAAAGCTGGAGGCATCACACTGCCTGACTTCAAACTATACTA 4782
                           i          i      vv       v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_78133151_7   4783 CAAGGCTACAGTAATGAAAACAGCATGGTACCGGTACCAAAACAGATATA 4832
                            i           v  i    ii      i  i iv ii i   i   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_78133151_7   4833 TACGCCAATGGAACAGA-CAGAGACCTCAGAAATAACACCTCACATCTAC 4881
                           vii        i   -iv    vii         vv  vi    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_78133151_7   4882 AACCATCTGATCTTCAACAAACCTGACAAAAACAAACAATGGGGAAAGGA 4931
                         iii  vi    i   i    ivv  v   i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_78133151_7   4932 TTCCCTATTTAATAAATGGTGCTGGGAAACCTGGCTAACCATATGCAGAA 4981
                          vvi  v  i  i              v v    v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_78133151_7   4982 AACAGAAACTGGACCCCTTCCTTACATCTTATACAAAAATTAACTCAAGA 5031
                         i vv   ii         v   i   i v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_78133151_7   5032 TGGATTAAAGACTTAAATGTAAAACCCCAAACCTTAAAAACCCTGTAAGA 5081
                              i ?    i         i v iv    iv     vi i iv    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_78133151_7   5082 AACC-TAGGCA-ATACCATTGAGGACATAGGCATGGGCAAAGTCTTCATG 5129
                           v -    ?i- v i v i v iv v i  i- i     v vi   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTA 591

  chrX_78133151_7   5130 ATTACAACACCAAAA--ACAATTGCAACAAAAGCCAAAATTGACAAATGG 5177
                         iv  ii         --    --          vv     v  i    v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_78133151_7   5178 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAAGAG 5227
                           ii v  i   v v  i i   i  ii vv    i  v          i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_78133151_7   5228 AGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCTAT 5277
                               v  i     i                 v       vii iv   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_78133151_7   5278 CTGACAAAGGTCTGATATCCAGAAACTACAAAGACATTAAACAAAT---T 5324
                             i  i  v  vi         vv  i     vv ivv    v --- 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_78133151_7   5325 TACAAGAAAACAA-CGACCCCATCAAAAAGTGGAGGAAGGATGTGAACAG 5373
                         v i  i  i    -ii    v  i?    i   ivi      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_78133151_7   5374 ACACTTCTCAAAGGAAGACATTTGTGTGGCCAACAAACATATGAAAAAAA 5423
                            i     v  i     i  viivi       i  i  i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_78133151_7   5424 GCTCATCATCACTGGTCAT 5442
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (149 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.71 (24 / 14)  


2438 22.36 8.27 1.90  chrX_78188642_78190306      435  1172 (493)    L1M4_orf2#LINE/L1      124   908 (0)  

  chrX_78188642_7    435 ATTGA-AAACTG----TAAAATATCAT--GAAAATAATTATAGGTAAGTT 477
                              -  i   ----      -    -- i    -------- i   --
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAAT-TCATATGGAAAT--------GCAAG-- 162

  chrX_78188642_7    478 AAATAAAGAAAAGTCATCCATGATCTTGAAAATGAAGAATGAATTTGGAG 527
                         ii ivv    v  i  -vv ii          v      ii  v      
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCA-AAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_78188642_7    528 AAATCACAATTCCAGATTGCAAAACTTAATAGAAAGCAATAGCCATCAAG 577
                         i v     v    vi   v         v  v     v i  iv      
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_78188642_7    578 ACAATGTGTCACTCGCATAGGGATAGATATATTAGTCAATGGAATAGGTT 627
                            i    vi   v     i       i    vii            iv 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_78188642_7    628 TGAGAGTTTGGACATAA-CCCATACATCTATGG-CAA------------- 662
                                iii  v    -         i     -   -------------
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_78188642_7    663 ---------AGACAATTTACTGCAGAAA-AATAGCCCTTTTAAACAAATG 702
                         ---------    v   i v  vi    -     i -    v        
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-TTTTCAACAAATG 410

  chrX_78188642_7    703 GTGCTGGGAGAACTGGATGTCTACATGTAAAAGTATGAG----------- 741
                                  v        i? i     i     v    i-----------
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_78188642_7    742 ----------ATATAAACAAATGAAATAAAAATGGATCATAGACCTAAAT 781
                         ----------     v v    v  v v           ?          
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_78188642_7    782 GTAATAGGTAACA-TATAAAAATCTTAGCAGAAAGCATAGCAATATATT- 829
                             v  v   v -       v      v     i     v?i  v  i-
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_78188642_7    830 --ATGTTTTTGGTTTAGACAATATCTTCTTGGTTACAACAGAGGAAGGTA 877
                         --i  vii    v    i    ivi     i v  ii   vvii   -i 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG-CA 609

  chrX_78188642_7    878 TAAATGATAGAAGAGAACACTGACAAGTTGGACTTTATCAGAATGAAAAA 927
                         i  iii i i    i  v iv  i  i        i    i   v     
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_78188642_7    928 TCTTTATATTTCAAGGGGCACAATCAAGAAAATGAAAAGATAATTCATAC 977
                         ii   i ii     i  i   v         i        i  ii  i v
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_78188642_7    978 ACTGGGGGGACACATTTACAAATTATATATCTCCTACATGTCTTTTATCC 1027
                          v    i i v i    i     i        vv  viv v   v     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_78188642_7   1028 AGAATATATAAAGAACTCTTATAATTTAATAG-AAAAAGACAAGTAAATG 1076
                                              i  i i    i-          i   viv
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_78188642_7   1077 AAT-AAAAAGTTGGTAAAGAACATTAATAGACATTTCTGTAATGCAGATA 1125
                            -?    i v  i    i iv v             vi  v v     
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_78188642_7   1126 AACAAATAGCCAATACCCATATGAA--GATGCTCAGTATCATCACTAGC 1172
                         v      i       vv  i     --        ii    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (93 / 68)
Gap_init rate = 0.02 (19 / 785), avg. gap size = 3.95 (75 / 19)  


2903 25.18 3.39 0.85  chrX_78251549_78253369.rev      505  1330 (491)    L1M4_orf2#LINE/L1       62   908 (0)  

  chrX_78251549_7    505 CCAAAATGATCTACAGGTTCAATTCAATCTCTAAAAAAGCCCCAATGGCA 554
                              v          i     iv     i   vv   ii    iiv  v
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chrX_78251549_7    555 TTTTCTGCAGAAATAGAAAAATCTATGC-AAAATTTGTATGCAATCTG-G 602
                             i         v  v  iiiv  v -      ii    v  -v  -i
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA-ATGCA 160

  chrX_78251549_7    603 AGAGATTCA-AATAGCCACAACAGTCTTGATAAAGAAGAACAAATCTGGA 651
                           i  ii  -        v    i      v             vi    
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_78251549_7    652 AATCTCACACTTTCTGATTTAAAAAAAATATTACAAAATCACAGTACTCA 701
                         iiv         i ii    v    vv-  i      iii      v   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCA 259

  chrX_78251549_7    702 AAACAGTGTGGTACTGGGATGAAGACAGACAAATAGACCAATAGGCTATA 751
                          i               v  i i  i     v     i    i iv  v 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_78251549_7    752 TTAGAAACCTCAGGTATAAGCTCTCATGTATATGATCAAATAATTTTAGA 801
                         v v  i vii   iv    i i vi ii v    i    v i     v  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_78251549_7    802 CAAGGGTGGCAAGAACACTCAGTGGGAAAAGGACAG-CTCTTCAACAAAT 850
                                 v     v  i   i    i    i i  -  i          
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_78251549_7    851 GGCTTTAGAAAAACTGGATATCTACA--CACAAGAGTGAAGTTGAATCCT 898
                           ivi i i v         ? i   --  v    i        i i  i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_78251549_7    899 GATTTTATATAATATTAACATGTAAAAATAACCCTAAATCGATTAAAGAC 948
                         v ii i i iv    --   ---    v    i v    v   i ?    
  L1M4_orf2#LINE/    460 TACCTCACACCATAT--ACA---AAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_78251549_7    949 CAAAGCATAAAACCCAAAATAATAAAACTTTTAGAAGAAAAGCTAGGAGA 998
                          v  iii   i v i    iv        i           vv    ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_78251549_7    999 GAAGCTTTATGACATTAGATCTGGCAATGATTTCTT-GCCATGACATGGA 1047
                         i  v   ii    v  i i iv       i      - vi      ivi 
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_78251549_7   1048 AATTACAGACCACAAAAACAAAGATGGTCAAATGAGACTACATCAAAGCC 1097
                           vi   ii v      iv   i  i vi    vi    v       iii
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_78251549_7   1098 AAAAACTCCTCTGCATTGAAGGACACATTTAACAAAGTGAGAAGGCAAAC 1147
                                ii v   v ii        vv i  v       i   i   v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_78251549_7   1148 TATACAATG--ATAAAATATTTTAAAATCATATGTCTGATAAGGGGTTAG 1195
                         i i v    -- v         vv         i           ii v 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_78251549_7   1196 TATACAGAATATATCAAGAATTTCTACAATTCAACACCACCA---CAAA- 1241
                            v          v     i ii     i    i vi vv ---    -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_78251549_7   1242 -ACTTGATTTAAAAATAGGTATAAGACTTGAATAGGT------------- 1277
                         -  iii   ?      i  i v i  i        ii-------------
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_78251549_7   1278 -GATTTACATATTGCCAAAAAGCATATGAAAAGATGCTCAACATCACTAA 1326
                         -   v    v  v     v     i                     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_78251549_7   1327 TCAC 1330
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.55 (124 / 80)
Gap_init rate = 0.02 (14 / 847), avg. gap size = 2.50 (35 / 14)  


2518 26.14 1.45 7.26  chrX_78257707_78265963     3661  4624 (3633)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78257707_7   3661 TGAATAAACATTCCATGCTCCTTGATAGGAAGAATCAATATTGTGAAAAT 3710
                           i v i i  i     i  v v   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78257707_7   3711 GGCCACACTGCCTAAAGTAATTTATAGATTCAATGCTATCCCCATGAAGC 3760
                            v i   v  i   v i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78257707_7   3761 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 3809
                          v   vivi v  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_78257707_7   3810 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCACAAAGG 3859
                               viiv  ii  v  viv        i      i i iv vi   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_78257707_7   3860 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 3909
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_78257707_7   3910 ACAGTAACCAAAACAGAATGCTACTGGTACCAAAATAAACAGATATGTAG 3959
                                i   i    vi  v      i iv ii   i   ---- i   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA----TATAG 295

  chrX_78257707_7   3960 ACAAATGGAGCAGAACAGTGGCCTCAGAAATAACACCACACATCTATAAC 4009
                          iv      ii    iv v ivii         vv   i    i   iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_78257707_7   4010 CATCTGATCTTTGACAAACCTGACAAAAACAAGTAATGGAGAAAGGAT-T 4058
                           vi    i  i     ivv  v   i v  vvi     i     i  -v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_78257707_7   4059 TCTTATTTAATAACTGGTGTTGGGAAAACTGGTTAGCCATATGCAGAAAA 4108
                             -  i  i  v     i     v      v  ?   i     i  i 
  L1M4_orf2#LINE/    396 TCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_78257707_7   4109 CTGAAACTTGACCCCTGCCTTACATGTTATACAAAAATTAACTCAAGATA 4158
                         v    ii v       i   i   ivv                   i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_78257707_7   4159 GATTAAAGACTTAAACATAAAACTTAAAACCATAAAAACCCTAGAAGAAA 4208
                            i ?    i    ii   i vi      i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_78257707_7   4209 ACCTAGGCA-ATACCATCTAAGACATAGGCACGGGCAAAGTCTTCATGAC 4257
                           v    ?i- v i v  -iv   v v  vvii     v vi   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_78257707_7   4258 TAAAACACCAAAAAGCAATGACAACAAAAGTCAAAATTGACCAATGGGAT 4307
                           vi         -   vvii         vv     v  iv   v   i
  L1M4_orf2#LINE/    594 TATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_78257707_7   4308 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAAAAAAAAAAAAAAAAAA 4357
                         i v  i   v v  i i   i  ii vv    ii v -------------
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA------------- 679

  chrX_78257707_7   4358 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAC 4407
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    680 -------------------------------------------------C 680

  chrX_78257707_7   4408 TATCAG---AGTGAACAGGCAACTTACAGAATGGGAGAAAATTTTTGCAA 4454
                              i---      v  i    ii                 v       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_78257707_7   4455 TCTATCCATCTGACAAAGGGCTAATACCCAGAATCTACAAGGAATT--TA 4502
                         vii  vi      i  i  i  vi  i       v  i  i   i --  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_78257707_7   4503 -AAC---ATATTTACATGA--AACAACCCCTTCAAAAAGTGGGCAAAGGA 4546
                         -   ---   v v v v  --  i     vv i?    i           
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_78257707_7   4547 TATGAACAGATACTTTTCAAAAGAAGACATTTATGCAGCCAATAAACATA 4596
                          v    i   i i  i  v        i  vi viii        i  i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_78257707_7   4597 TGAAGAAATGCTCTTCATCACTGTTCAT 4624
                             i i      vv     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 6.00 (84 / 14)  

2722 26.32 4.46 0.69  chrX_78257707_78265963     6891  7764 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_78257707_7   6891 GAAAATATATTTCATGTTCATGGTTTGGAAAAATTGATGTTATTAAAATG 6940
                          i   v    ii           v      i v  i  i  i    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_78257707_7   6941 CCCATATTACCCAAAGCAATCTACGGATTCAATTCAAGACCCATCAAAAT 6990
                         v v   i v      vii      i       iv   vv  i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_78257707_7   6991 ACCAATAACATTCTTCACAAAAATGGA--AACTAAAAATCCTATAATTTC 7038
                         v   iivi v  i  ii  i    v  -- i  i ---     v    iv
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA---TCCTAAAATTCA 148

  chrX_78257707_7   7039 TATGGAACCACAAAAGACCCAGAATAGCCAAAGCTATCATAAGCAAAAAG 7088
                                vii   ii                 i v   v i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_78257707_7   7089 AACAAAATTAGAGGAATCACAATACCTGACTTCAGATTATACTGCAGAAC 7138
                               i  i     v     v v  ii i    i viv    i  i i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_78257707_7   7139 CATAGTAGCCTAAACAGCAAGGTACTGGCATAA----AAACACATAGACC 7184
                         i i    ii v i    iiv             ---- i   i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_78257707_7   7185 AATGGAATAGAATAGAGAACCCCAAAACAAATCTACACACATACAGTGAA 7234
                                      v    ii  vi   i   i i i   iv  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_78257707_7   7235 CTCATTTTTACCAAAGGTGCCAAGAACATACACTGGGGAATAGACAGTGT 7284
                         i v     iiv   i          v   v  v       vii i   v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_78257707_7   7285 CTTCAATAAATGGTGCTGGGTAAACTGGATATCCATATTCAGAAGAATGA 7334
                         i     i             vv         ?   i  v  i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_78257707_7   7335 AAGTAAACCCCTCTCTCTTGCCATA---AAAAATCAA----------ATC 7371
                          iv ii      vi   vii     ---      i  ----------   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_78257707_7   7372 ACAGA-------GGAAGATGTCAAACTAGGGAATTACTACAAGAAAACAA 7414
                          ?   ------- v    vv v      vii  i vi  v         v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_78257707_7   7415 TGGGGAAAATCTCCTGGATATTGGTCTGGGCAAAGAGTTTTGAGTAATGC 7464
                         v  ? v      i vv  iv    vi i     v iv  i v  vv   v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_78257707_7   7465 C-CCACAATTACAGGCAACAAAAGCAAAAATAGACAAATGAGA-TTCTTG 7512
                          -   v  vi   i          v         i    vi  -   v v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_78257707_7   7513 TAAGTTAAAAAGCTTCCAGACAGCAAGAAAAACACT--CAACAAAGT--A 7558
                         v  i       -   iiivi vv   -- ii     --   v     -- 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAA--AGGACACTATCAAGAAAGTGAA 695

  chrX_78257707_7   7559 GAGTCAACCAAAAGAATGATA-AAAACATTGACAAACTACCC-TCTGATG 7606
                         i  v     v v      iv -    i   vi    ii ivi-      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_78257707_7   7607 AGGCGTTAATAAGCAGACTATA---AGAGTTCAAACAACACTATAGAAAA 7653
                            vii vi  vv    v    ---   ii  vv     v v   iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_78257707_7   7654 AAATCTAATAATCCAACT--AAAATGGATAAAATATTTAAATAGACATTT 7701
                           iv v     i    i --       ii   iv    i           
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_78257707_7   7702 CTCAAAAGACGATATACTAATGGCAAACAGGCATATAAAAAGGTACTCAA 7751
                            v     v       v      v  i i   i  i     i i     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_78257707_7   7752 CATCATTGATCAT 7764
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (129 / 98)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 2.81 (45 / 16)  


3075 28.03 1.00 0.11  chrX_78267600_78273975.rev     4987  5885 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_78267600_7   4987 GGAAGAACATTCCATGCTCGTGGGCAGGAAGAATCAATATCGTGAAAATG 5036
                             ii i  i     i  i   iiv      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_78267600_7   5037 GCCATACTGCCCAAGGGAATTTATAGATTCAATGCCATCCCCATCAAGCT 5086
                           v     v     ivvi  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_78267600_7   5087 ACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCATA 5135
                         v   iivi i  i  ii     v v  v  i-  - iii    i      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chrX_78267600_7   5136 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5185
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_78267600_7   5186 CAAAGCTGGAGTCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5235
                              i     vvv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_78267600_7   5236 CAGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGAGATATAGATCAT 5285
                               i   i v  ii         i iv ii i   v          v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_78267600_7   5286 TGGAACAGAACGGAGCCCTCAGAAATAATGCCACATATCTACAACTATCT 5335
                              i    iv   vvii         vv   i i  i  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_78267600_7   5336 GATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 5385
                            i  i     ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_78267600_7   5386 TTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCTGAAA 5435
                          i  i     i        v      v  ?   i   i ii iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_78267600_7   5436 CTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGATTAA 5485
                         i    i    v   i   i v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_78267600_7   5486 AGACTTAAACATTAAACCTAAAACTATAAAAACCCTAGAAGAAAACCTAG 5535
                             i    ii v i v              vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_78267600_7   5536 GCATTACCATTCAGGGCATTGGCATGGGCAAGGACTTCATTTCTAAAACA 5585
                          ?i v viv   iv i v    vv i     v ii   v vvv  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_78267600_7   5586 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAATTAA 5635
                                  vvi          vv     v  i    vi  ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_78267600_7   5636 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 5685
                          v v  i i   i  ii vv    i  v    i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_78267600_7   5686 AACCTACAGAATGGGAGAAAATTTTCACAACCTACTCATCTGAAAAAGGG 5735
                             i                 v  ii   vii ivi      v  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_78267600_7   5736 CTAATATCCAGAATCTGCAATGAACTC--A-AAC---ATATTTACAAGA- 5778
                           vi          v ii  v      -- -   ---   v v v    -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_78267600_7   5779 AAA-AACCCCATCAAAAAGTGGGTGAAGGACATGAAGAGACACTTCTCAA 5827
                            -     v  i?    i    ii     iv    v     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_78267600_7   5828 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCA 5877
                                i  vi viii     v  i          i       v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_78267600_7   5878 CTGACCAT 5885
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 1.43 (10 / 7)  


3011 27.30 0.55 0.99  chrX_78276376_78281620.rev     3843  4754 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78276376_7   3843 TGGAAAAACATTCCATGGTCATGGATAGGAAGAATCAATATCATAAAAAT 3892
                               i i  i     v        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78276376_7   3893 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGGTATTCCCATCAAGC 3942
                            v     v      v i  i           i vv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78276376_7   3943 TACCATTGATTTTCTTCACAGAACTAGAAAAAAAAAGCT-ACTTTAAATT 3991
                          v   viviii  i  ii     v v  v  -----   - iii    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-----GCTGATCCTAAAAT 145

  chrX_78276376_7   3992 TCATATGGAATTAAAAAAGAACCTGTATAGCCAAGACAATCCTAAGCAA- 4040
                                   v iv  ii  v  v v        i      i i iv  -
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_78276376_7   4041 AAGAACAAAGCTGGAGGTATCATGCTACCTGACTTCCAACTATACTACAA 4090
                                   i      vv   ii  v  ii i   v  viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_78276376_7   4091 GGCTACAGTAACCAAAATAGCATGGTACAGGTACCAAAACAGATATATAG 4140
                         i          i   i i  ii      v  i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_78276376_7   4141 ACCAATGGAACAGAACAGTGGCCTCAGAAATAACTCCACACATCTACAAC 4190
                          i        i    iv v ivii         vi   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_78276376_7   4191 CATCTGATCTTTGACAAACTTGACAAAAACAAGTAATGGGGAAAGGATTC 4240
                           vi    i  i     ivv  v   i v  vvi           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_78276376_7   4241 CCTATTCAATAAACAGTTTTGGGAAAACTGCCTAGCCATATGCAGAAAAC 4290
                         i  v     i   ii  vi     v     vv  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_78276376_7   4291 TGAAACTGAACCCCTTCCCTACACCCTGTACAAAAATTAACTCAAGATAG 4340
                             ii  i      v  ii     v i                 i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_78276376_7   4341 ATTAAAGACTTAAATGTACGACCTAAAACCATAAAAATCCTACAAGAAAA 4390
                           i ?    i        v  v       i      v  i  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_78276376_7   4391 CCTAGGCG-ATACCATCCAGGACATAGGCATGGGCAAAGACTTCATGACT 4439
                          v    ? - v i - i iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_78276376_7   4440 AAAACACCAAGAGCAATGGCAACAAAATCCAAAATAGACAAATGGGATCT 4489
                          vi       i    vvi         vvv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_78276376_7   4490 AATTAA--CTAAAGAGCTACTGCACAGCAAAAGAAACTGTCTTCAGAATG 4537
                         v  i  --i    i -  vi  ii vv    i  v   i  vvv i i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_78276376_7   4538 AACAGGCAACCTAGAGAATGGGAGAAAATTTTTGCAATCTATACATCTGA 4587
                           v  i     i v               v       vii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_78276376_7   4588 CAAAAGGCTAATATCAAGAATCTACAAAGAACTTAAACAAATTTACAAGT 4637
                         i  ii i  vi    v     v  i        ivv    v iv i  - 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-T 792

  chrX_78276376_7   4638 AAAAAAACCAAACAACTCCATGAAAAATTGGGCAAAGGATATGAGCAGAC 4687
                              i  -   i   i v  v?    v            v   ii    
  L1M4_orf2#LINE/    793 AAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_78276376_7   4688 ACTTCTCAAAAGAAGACATTTATGGGGCCAAAAAACATATCAAAGAAAGC 4737
                          i     v        i  vi viv      v  i  i  v   ii v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_78276376_7   4738 TCCTCATCACTGGTCAT 4754
                           vv     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (140 / 105)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  

 390 22.95 5.74 0.00  chrX_78276376_78281620.rev     4780  4901 (344)    L1M4_orf2#LINE/L1      780   908 (0)  

  chrX_78276376_7   4780 ACAAATTTACAAGAAAAAAATAAA---CCCA-TCAAAAACTGGGTGAAGG 4825
                             v iv i  v     i i   ---    - i?    v    ii    
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_78276376_7   4826 ATATGAACAGACACTTCTC---AGAAGACATTTATGCGGCCAAGAAACAC 4872
                           v    i     i     ---      i  vi vii      v  i   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_78276376_7   4873 ATGAAAGAAAGCTCATCCTCACTGGTCAT 4901
                               ii v     v v   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (16 / 11)
Gap_init rate = 0.02 (3 / 129), avg. gap size = 2.33 (7 / 3)  


3016 27.27 1.33 0.67  chrX_78287880_78292145.rev     2874  3775 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78287880_7   2874 TGGAAAGATATTTCATGTTCATAGATTGGAAGAATGAACATTGTTAAAAT 2923
                                    ii         i          v v  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78287880_7   2924 GTCCATACTGTC-AAAGGAATCTTTAGATTCAATGAAATCCCTATCAAAA 2972
                          v v     vi -   vvi    vi        i v              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78287880_7   2973 CACCAACAACGTTCTTCACGGAAATAGA-AAAT--ATTATAAAATTTATA 3019
                         iv   i vi v  i  ii i     v  -  ii--  iv       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_78287880_7   3020 TGGAGCCACAAAAGACTCAGAATAGCCAAAGCTATCCTGAACGAAAAGAA 3069
                             ivii   ii   i             i v   i    vi i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_78287880_7   3070 CATAACTGGAGGAATCACACTCCCTGACTTCAAATTATATTACAAAGATA 3119
                           v ii       v       i  ii i      viv  i       v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_78287880_7   3120 TACTAACGAAAATAACATGGTACTGACATAAAAACAAACATAGGGATCAG 3169
                         i v   iv  i i iii        i     ii i i     vi     i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_78287880_7   3170 TGAAACAGAAAGGAGAATGCAGAAACAAATTCACACACCTACAGATAACT 3219
                           i  i    vv    i v      i   ii  i   ii  ii vi  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_78287880_7   3220 CATTTTTGACAAAGAGGTCAAGAAGATACACCTGGGAAAAGATATTCTCT 3269
                         v     i     i iv i     vv  v  viv      ii   v   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_78287880_7   3270 TCAGGAAATGGTGCTGGGAAAACTAGAAATCCAAATGCAGAAGAATCAAA 3319
                            iv              v    i  v ?   v     i      v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_78287880_7   3320 CTAGATTTCCCTCTTTTGCCATACACAAAAGTCAAATCAAAATGGATTAA 3369
                         i i  iii ivi  ivii     i      i i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_78287880_7   3370 AGAATTACAAT-TAAGACTTCTAACTATGAAACTACTATGAGAAAACATT 3418
                            vi  -   -     vi vv      i     vi  vi         v
  L1M4_orf2#LINE/    501 AGACCTA-AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_78287880_7   3419 GGGGAAACTCTCCAGGACATTGGTCTGGGCAAAATCCTCTTG--TGCAAT 3466
                           ? v  v   i iv   v    vi i     vivii    i-- iii i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_78287880_7   3467 ATTCCACAAGCACAAGCAATAAAAAAAAAATTGGACAAATGAGATCACAT 3516
                          --   v            i    i     v i  i    vi  iiv   
  L1M4_orf2#LINE/    600 A--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_78287880_7   3517 -AAAGTTAAAAAGCTTCTGCACAACAAAGGAAACAACCATCGAAATAAAG 3565
                         -   i       -   i  ii vv       v  v i  vvi  i i  i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_78287880_7   3566 GCATAACCCACAGAA----AGGAAATATCTTTGCAATCTACCAATCTGAC 3611
                         iv i           ----  i      --      vii ivv      i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATAT--TTGCAAATCATATATCTGAT 744

  chrX_78287880_7   3612 AAGGGATTAATAACTGGAATATATAAGGAGCTCAATCAACTCTATAAGAA 3661
                               i vi  v ii          i  i   vvv      v    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_78287880_7   3662 ACCATCTAATAATCCATTTACAAAATGGGCAAGATACCTAAATAGACATT 3711
                          vviv v     i   v  ?v           iiv ii i          
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_78287880_7   3712 TCCAAAAACAAGACATACAAATGGCAAACAGGCATATGAAAAGGTGCTCG 3761
                           ivv   v    i           v  i i   i        i     i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_78287880_7   3762 ACATCAATGAAAGT 3775
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (151 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


2748 27.87 1.37 1.37  chrX_78316205_78318075      500  1378 (493)    L1M4_orf2#LINE/L1       30   908 (0)  

  chrX_78316205_7    500 AAAAATCAGTACTGTTTAACTG-CACATACTACCTAAAACAGTCTATGGA 548
                           i v i i  i    v iv  -  -     v  i   viii    ii  
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCA-ATACTCCCCAAATTGATCTACAGA 78

  chrX_78316205_7    549 TTCAATGACATCCCCATGAAAATATCAATGACATTCTTCACAGAAATAGA 598
                              i vv     i  v     vi  iivi v  i  ii       v  
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chrX_78316205_7    599 GAAAACAATCCCAAAATTTATATGGAATCACAAAATACTCAGAATAACCA 648
                         v  ivii    i      i        vii   iiv  i       i   
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chrX_78316205_7    649 AAACTATCCTGGGCAAAAAGA-CAAAACTGAAAGAATCATATTACCTGAC 697
                             v   i  iiv  i    -    ii  i i  v   i i v  ii i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_78316205_7    698 TTGAAATTATACTCTAGAGCTACAGTAACTAAACCAGCATGGTACTAGCA 747
                           v   viv    vi i           ii  iv   ii       i   
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_78316205_7    748 TAAAAACAGACACG--AACTAATGAAACAAAATAGAGAAACCAGAAATAA 795
                            ii i     ii--i ii    i  i i   v    iv          
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_78316205_7    796 ATTTATACATCTACAGTGAACTCATTTTCAACAAAGGTGCCAAGAACATA 845
                          iii      i  ii  v  i v      i    i          v   -
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT- 377

  chrX_78316205_7    846 TTATACATTGGGAAAAGGCAGTCTC--CAATAAATTGTCCTGGGAAAACT 893
                          i ---  v      iiii     i--   i    v  v      v    
  L1M4_orf2#LINE/    378 TCA---ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_78316205_7    894 G-ATATTCATTTGTAGAAGAATGAATCTAAAACCCTATATTTCATCTTTT 942
                          -   ?i  iv  i i         vi ii v     iv iv  i v v 
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_78316205_7    943 GCAAAAATCGAATCAAAATTGGTTAAAGACTTAAATCTAAGACCTCAAAA 992
                         i       ii v       v i i ?    i     v     v  v   v
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_78316205_7    993 TGTGAAGCTACTAAAAAAAA---TTGAGGAAACTCTCCAGGTTATTAAAC 1039
                          i i  i  vi  i  i   --- v i? v  v   i iv viv  iiii
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_78316205_7   1040 TGGGCAAAGATTTCTTAAGTAATATTCTACAAGCACAAGCAAGAGAGGAA 1089
                          i     v i       ii  vv iv i v            v i i   
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_78316205_7   1090 ACAATGAACAAATGGCATCATATCAA--TTAAAAAGCTTCTGCCCAGAAA 1137
                          v   ii i    v v iivi     --       -   i  iv vvv  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chrX_78316205_7   1138 AGGAAACAATCAACAAAGTGAGGAGACAACCCCCAGAATGGGAGAAAATA 1187
                             v  v     v       ii         v                 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_78316205_7   1188 TTTGCGAACTATCCTTCTGACAAGAGACTAATAACTAGAATATATGACAT 1237
                              i  ii  viv     i   i    vi  v i         i viv
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_78316205_7   1238 GCTCAAACAACTCTATAGGAGAAAACCTAAACCTAATAATCTGATTAAAA 1287
                         i   vv       v   -- v    --- i  v-     i ii   ?   
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATA--ATAAAA---AGACA-AATAACCCAATTWAAA 817

  chrX_78316205_7   1288 AATGGGCAAAAGATTTGGATAGATATTTCTCAGAAAAAGACATACAAATG 1337
                                   i      i     i       vi  i    i         
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_78316205_7   1338 GCAAACAAATACATGACCAGGTGCTCAACATCATTGATCGT 1378
                           v  i  ii      vv  i            ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (154 / 87)
Gap_init rate = 0.02 (14 / 879), avg. gap size = 1.71 (24 / 14)  


2054 28.39 2.26 2.60  chrX_78361323_78367297     4591  5474 (501)    L1M4_orf2#LINE/L1        3   883 (25)  

  chrX_78361323_7   4591 GAAAAACATTTGTTGCTCATAAATTGGAAAAATAAGTATT-TTACAAATG 4639
                             i i  iivv  i    ii       i v v i    -   - i   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGATG 51

  chrX_78361323_7   4640 GCCATACTGCCCAAAGCAATTTAAAGATTCAATGATATTCCTATTACTAT 4689
                           v     v      vii  i  v        i vv  i     i vv  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_78361323_7   4690 TCCAA-TGTCATTCTT-CACACAATTAGCAAAGGGTATTCTTAAATTTAT 4737
                         i   i-  i v  i  -  v -    ii   ivv -  i  v     i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTG-ATCCTAAAATTCAT 149

  chrX_78361323_7   4738 ATGCAA-TCAAAAAGAGCCTGAATAGACAAAACAATTATAAGCTA-AAGT 4785
                            v  - vv  ii  v  v      v         iv i ivv -   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_78361323_7   4786 ATAAAGCTGGAGGCATTGAAATATCTGATTTCAAATGATACTATAAAGTC 4835
                          i    i      vv iiv v vi ii        vvv     i    ii
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_78361323_7   4836 ACAGTAACCAAAAGAACTTGGTACTAGCAAAAAAAAAAAAAAAAAAACCA 4885
                                i   i v iiv       i   v  ii v i v v v i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_78361323_7   4886 GATG-AATAGAA-----AACTGAGAAATAAACC-ATAAACCTAACACCAT 4928
                         -   -       ----- iiiv           -   v ii  vvii  v
  L1M4_orf2#LINE/    300 -ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_78361323_7   4929 CTGATCTTCAACAAAACCAACCAAAACAAG-CAATGAGGAAAAGACTCCC 4977
                         i    i   i    iivii-    i  v v-     i     ii ivvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_78361323_7   4978 TATTCAATAAATTGTGCTTGGATAAATCCAATAGCATAATATTAAGCCAT 5027
                          v     i    v     v   i  v ------ v   -------?   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACT------GGATA-------KCCAC 434

  chrX_78361323_7   5028 ATGCTTAATATTGAGCCTTAAGCCTTCCTTTTCCCCATATACAAAAATTA 5077
                             vv  v v   ivi vi v  i v i iv v                
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_78361323_7   5078 ACTGGAAATGGATTAAAGACTTAAATGTAACACCTAAAACTGTAGAAACT 5127
                            vi        i ?    i         v v        i  -     
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACT 533

  chrX_78361323_7   5128 CA-AGAAGAAAAGTTAGGAA-ATATCATTCTGGACGTGGGACCTGGCAAA 5175
                          v-         vv    ?i- v   -   vv   v v  iiiv     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chrX_78361323_7   5176 GATTTGAT-GATGAAGATGCCAAAAGTAATTGCAAAAAAAAAGCAAAAAT 5224
                          i   vv -   - v  ii       i vvv    v    i --      
  L1M4_orf2#LINE/    583 GGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGA--AAAAAT 629

  chrX_78361323_7   5225 TGACATGTAAGACCTAATTAAACTGGAGAGCATCTGTACAGCAAAAGAAA 5274
                         v  i vi vi   i v  i   v vi i i v i   i vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_78361323_7   5275 CTATCAACAGAGTAAACAGACAACCTACAGAATGGGAGAAGATATTCACA 5324
                                v i   i  v        i              i     ii  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_78361323_7   5325 AACTATGCATCTGACAAAAGCCTAATATCCAGAACCTATAGAGAAC---- 5370
                           ii  ii      i  ii v  vi         iv    i     ----
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_78361323_7   5371 ATAAATCAACAAGCTAAAAACAAATAACCCCACTAAAAAATAGGCAAAGT 5420
                          i  v    i  vvv   i           v i ?      i       v
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_78361323_7   5421 ACACAAACAGACACTTCTCAAAAGAAGACATACATGGGGCCAACAAACAT 5470
                          ivii  i     i     v        i     viv      i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_78361323_7   5471 ATAA 5474
                           i 
  L1M4_orf2#LINE/    880 ATGA 883

Transitions / transversions = 1.21 (135 / 112)
Gap_init rate = 0.03 (24 / 881), avg. gap size = 1.79 (43 / 24)  


2387 29.09 3.72 1.35  chrX_78373091_78377108     2639  3525 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78373091_7   2639 TGAAAAGATATTTCATCTTCATGGATAGGATAATTCAATACTTTAAAAAT 2688
                           i        ii   v         v   vi i i    i v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78373091_7   2689 GTCCATAATACCCAAAGCAATCAACAGATACAATACAATTCCCGTAAAAA 2738
                          v v   v v      vii   v      v   ii    i  ii v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78373091_7   2739 TACCAATGACCTTCCTAACAAAAATAGAATAAATAATGTAAAAATATATA 2788
                          v   iivi    ii vi  i    v  vv iv i  viv     vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_78373091_7   2789 TGGAGTAACAATG-ACACAGAATAGCCAAAGCTATCCTAGGCAAAAAGAA 2837
                             ivvi   v -  v             i v   i iiiv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_78373091_7   2838 CAAAACTGGAGGAATCATGGTAACTGACTCTAAATTATACTACAGAGCTA 2887
                             ii       v   iiv vv ii i ii   viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_78373091_7   2888 TCTATAGTAACCAAAACAGTATGGTACTGGCATGAGAAACAGACACATAT 2937
                         i----     i   i     i            i  i -i     i   v
  L1M4_orf2#LINE/    251 C----AGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAG 295

  chrX_78373091_7   2938 ACCAATTGAACAGAGGAAATAATCCAGAGATAAGTCCATACATCTACAGT 2987
                          i    v   i   ivvi v i      i    ii        i  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_78373091_7   2988 AAACTCATTTTTGACAAAGATGTCAAGAACATACATTGGAAAAGGGGAAG 3037
                         v  i v     i     i i  i     v   v  v   ii  i iiv  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_78373091_7   3038 CATCTCCAATAAATGGCGCTGGGGAACCTGGCAGTCCATATGCAGA-TAC 3086
                         iv i i   i      i      iv v    vvi?   i     i -v v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_78373091_7   3087 TTAAACTACACGCCTGTCTCTCCCCATATATCAAAATAAAATAAAAATGG 3136
                          v  ii iv  v   ii   v v       iv     v  v v       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_78373091_7   3137 ATTAAATACTTAAAT-------CTAAGACT-------TCTTCTATGAAA- 3171
                           i ? v  i     -------    i   -------    vv v    -
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_78373091_7   3172 --TAGATTGAGAAACTCTCCATGACATTGGACTGGGCAAATATTTCTTGA 3219
                         --   --- ? v  v   i i    v    ii i     vvi      ii
  L1M4_orf2#LINE/    546 CATAG---GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_78373091_7   3220 ACA--ATATCTTGTGAGAACTGACAACCAAAACAAAAATGGACAAGTGGA 3267
                          i -- i i --ivi  v  vii    v   iv      i  i  i v i
  L1M4_orf2#LINE/    593 ATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_78373091_7   3268 ATTACATTAAG-TTAAAAGTCCTCTGCACAGTAAAGAGACA------ACA 3310
                          i v   i  i-      i- i i  ii vvi    -    ------ v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAG-GACACTATCAAGA 688

  chrX_78373091_7   3311 AAGTGAAGAGACACCCCACAGGATGGGAGTAAATATTTGCAAAATATTCA 3360
                                i     v       i       v             vi  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_78373091_7   3361 TCTGACAAAGGATTAATAATTACATTATATAAGAAGCTCAAACAACTCTA 3410
                              i  i   i vi  vii v v       ii i   vv       v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_78373091_7   3411 CAGAAAAAATACAA----TCCAATTTTAAAATGAAGAAAAGATCTGAATA 3456
                         i iv     v    ----i      ?v      iiv   i   i      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_78373091_7   3457 GATATTTCTC-AAAAAATACATGCAAATATTAAATAGTTATATGCCAAGG 3505
                           i       -   i  v i  i     iviv    ivi i   vv   i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_78373091_7   3506 TGCTCAATATCATTGATCAT 3525
                                i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (152 / 102)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.81 (45 / 16)  


2785 25.11 3.96 1.47  chrX_78389573_78394836.rev     3890  4773 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_78389573_7   3890 GAAATATATTTTTATGTT-ATGGAATTGAAGAGGTAAAATTGCTAAAATG 3938
                             v    iii-     -     v v     vv   v    i   i   
  L1M4_orf2#LINE/      3 GAAAGATATCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_78389573_7   3939 TTCATACTACACAAAGCAATCAACAGATTCAAGTCAATCCCTATCAAAAT 3988
                         viv     v v    vii   v          vv                
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_78389573_7   3989 TCCAGTGGCCTTTTCCACAGAAATAGAATAAATT-ATCCAAAAATTTATA 4037
                         i    iv       iii       v  -i  ii -    v      i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATA 150

  chrX_78389573_7   4038 TGAAACCAGAAAAGACCCTG--TAAGCAAAGCAATTTTGAGTAAGTAGAA 4085
                           i  viiv  ii     v --  iv    i    i    iv   v    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_78389573_7   4086 CAAAGT--AAAGACAACAGACTTCTTGATTTCAA--TTATATTACGTATT 4131
                               --i i   v-  v     iii       --i -  i   iv vi
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACT-CACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_78389573_7   4132 TATAGTAATTAAAACAGTACTGGCACTGGCATAAA-ACAGACATGTAGAC 4180
                           i      i  i     i-   i          i- i      i    i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTG-TGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_78389573_7   4181 CAATAGAACAGAATGAAGAACCCTGAAATAAATCCTCACATATAAAGTCA 4230
                             i   i     vi   ii  v        i  vi    v  vi    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_78389573_7   4231 GCTAACTTTTGACAAGGATGCAAAGA--ATACAAGTGGGCAAAGAATGGT 4278
                         ii i i   i       i   v    --  v   -    v       i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGT 396

  chrX_78389573_7   4279 CACTTCAATAAATGGTGTTGGAAATACTGGTTATCTACATGAAAGCAGGT 4328
                          vi     i        i   i vv     v  ? i     v  iviii 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_78389573_7   4329 AAAATTTGACTCTTATCTT---CCCTATACACAAAATCAATGCATAATGA 4375
                         i  i  v   i i  i  i---  v      -     i  iv  v    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACA-AAAATTAACTCAAAATGG 495

  chrX_78389573_7   4376 ATTCGTGACCCAACAATAAG-GCATGAATCTGTAAAAGTCCTAGAAAAAA 4424
                           iv?v    i  vvi    -  - i  v  i     v  i     i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_78389573_7   4425 A---AAGTGGAAAAATTCCTAGAAAGTGATTTTGATAATAATTT-TCGTA 4470
                          --- i ? v   vv   v -  vvv  iv  v ii   ii   - iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_78389573_7   4471 TATGACATAAAAAGCAAAAGCAAGAGATGTAAAAATAAACAAGTGGGAAT 4520
                                iv       v      v i v v       i i  i v   v 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_78389573_7   4521 ACATCAAACTAAAAAGCTTCTGCAGAGCT---AAGAA-AC----AACAAA 4562
                         v       v v    i   i  i---   ---   i -  ----  v   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGT---GCTTCAAAGGACACTATCAAGAAA 690

  chrX_78389573_7   4563 ATAAAAAGGCAACCTATGGAATGGGAGAAAATATTTGCAAACCATGCATC 4612
                         i i     i     i ii                       i   ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_78389573_7   4613 TGATAAGGGGTTAATATCCAAAATATCCAAGAAACTCATACCGTGGAACA 4662
                                  ii vi      i     vi  ii     v   viivv  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_78389573_7   4663 GCTAAAGTACA-----CCCAATTTTAATAATGGGCAAAGGACCTAAGTAG 4707
                         iiv   iv   -----       ?v  -             ii i i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAG 839

  chrX_78389573_7   4708 ACATTCTTCCAAAGAAAACATACAAATGCCCAA---GTATATGAATAGTT 4754
                              ii         i i         v    --- i i     v  v 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_78389573_7   4755 GCTCAATATCACTAATAAC 4773
                               i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (134 / 84)
Gap_init rate = 0.03 (27 / 906), avg. gap size = 1.78 (48 / 27)  


2790 24.77 3.60 1.35  chrX_78405465_78410014     3170  4057 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78405465_7   3170 TGGAAACACATTACATGCTCATGGATGGGTAGAATGAATATTGTGGAAAT 3219
                               v i  iv    i        v  v   v v        vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78405465_7   3220 TACCATATGGCCAAAAGCAATCTACAGATTCAATGCAATTCACATCTAAG 3269
                         vi v   ivv  v   vii              i     i vi   v  i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78405465_7   3270 TACCATCATCATTCTTCACAGATCTTGAAATAAAC-AATTCTAAAATTTA 3318
                          v   v vv v  i  ii    vv    --i  i -i  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCA 148

  chrX_78405465_7   3319 TATGGA---GCCAAAAAAAGACCCTGCATAGACAAATCAAGACTAAGCAA 3365
                               ---  ----  ii     v v    v    v   vvi i iv  
  L1M4_orf2#LINE/    149 TATGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_78405465_7   3366 AAAGAACAAATCTGGGGGCATCAAATTATCCTACTTCAAACCATAACACA 3415
                         i         vi   i  vv   v i vi  v i      v v  vi   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_78405465_7   3416 AGGCTATAGTCAACAAAACAGCATGGTACTGGTATAAAAATAGGAAAGTA 3465
                          i    i   v v   i    ii         i    ii    iv vi  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_78405465_7   3466 GGCCAATAGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACT----G 3511
                          ii    i   i     v    ii           v   v i i ---- 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_78405465_7   3512 TCAACTGATATTTCACAAAGTATACAAAAAC-ATACAGTGGGGAAAGGAC 3560
                             i    v  iv    i -i i v  i  -  v  i         i i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_78405465_7   3561 C-CCTGTTCAACAAAAGGTGCTGGGGATAATTGGCAAGCCACATGTAGAA 3609
                         v-i  v         v         - i  i   vv ?       i i  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGG-ACAACTGGATAKCCACATGCAAAA 442

  chrX_78405465_7   3610 GAATGAAACTGGATTCTCACCTCTCACCTTATAGAAAAATCAACTCAAGA 3659
                                ii    ii ii     v    v    v      i       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_78405465_7   3660 TGGAACAAAGAC----ATG---------AAACTATAAAAATTCTGTAAGA 3696
                             v  ?    ----   ---------           v ii iv    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_78405465_7   3697 TAACATCAGAA-AAACTTTTA-GACATTGGCTTAGGCAGAGAGTTTAT-- 3742
                         v     vi ?i-   ii  ii-   v    v       - vi    v --
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTA 591

  chrX_78405465_7   3743 GAC-CAACAGCCCTAAAGCAAATGCAACAAAAGTAAAAATAAATAGATGG 3791
                           i-ii   --  v      v v          v       i   i  v 
  L1M4_orf2#LINE/    592 GATATGACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_78405465_7   3792 GACTGAATTAAACTAAAAAACTTCTGCACAGCAGAAGGA-ATAATCAGCA 3840
                             vv  i   v v        i  ii vv  -     - iv    iv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGA 688

  chrX_78405465_7   3841 GGGTTAACAGGTAACCCACAGAATGAGAGAAAATATTTGCAAATTATGCA 3890
                         ii  v  v  ii             i                  i  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_78405465_7   3891 TCCAACAAAGGACTAATATCCAGAATCTAAAAGGAGCTCAAACAAATGTA 3940
                           ii i  i     vi          v  v  i  i   vv    v vv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_78405465_7   3941 CAGGGAAAAAATAAATAAAT-AATT-AAAATTGGGTAAAGAACATGAATA 3988
                         i ivi    i i      vi-    -    v    i    i iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_78405465_7   3989 GACAATTCTGTAAAGAAGATATACAAATGGCCAACAAACATATGAAAA-A 4037
                             v    vi                       i  i  i       - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_78405465_7   4038 TGCTCAACATCAATAATTAT 4057
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (122 / 95)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.00 (44 / 22)  


2420 26.16 2.59 4.43  chrX_78441843_78447622     4363  5287 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78441843_7   4363 TGGAAAAACATTCCAGGCTCATAGATAGGAAGAATCAATATTGTGAAAAT 4412
                               i i  i   v i    i   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78441843_7   4413 GGATATACTGCCCAAAGATATTTATAGATTCTATGATATTCCTATTAAAC 4462
                           vv     v      vvv  i  i      v i vv  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78441843_7   4463 TACCA--TGAACATTCTTCACAGAAGTAGAAGAAACT-ATTTTAAAATTC 4509
                          v   --  -- v  i  ii     i v  v-  i  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTC 147

  chrX_78441843_7   4510 ATATGGGACCAGAAAAGAACCAGAATAGCCAAGAAAATCCCAAACTATTT 4559
                               i viiv  ii  v             i v    iii  ------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA------ 191

  chrX_78441843_7   4560 AGATTAGCTTAATCTAATCTAAAGATTAAAGAACAAAGCTGTAGATATCA 4609
                         --------------------     ----         i  v  ivv   
  L1M4_orf2#LINE/    192 --------------------AAAGA----AGAACAAAGTTGGAGGACTCA 217

  chrX_78441843_7   4610 ATCTAACTGTCTTCACACTATTCCACAAGGCTACAGAAACCAAAACAACA 4659
                         vv  vv iivi    v viv v i    i       v  i   i   iii
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_78441843_7   4660 TGGTACTGGTACAAGAACAGACACATAGACCAATGGAACAGAGTAGAGAA 4709
                                  i i   i i     i     i        i   i v    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_78441843_7   4710 CACAGAAGTAAGACCTCACACTTACAACCATATGATCTTTGACAAATCTG 4759
                         iv     i   iv  vi   i   iiii  vv    i  i     ivv  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_78441843_7   4760 AGAAAAA-A---AATGGGAAAAAGATTCCCTATTTAATAAATGATGCTGG 4805
                         vv  i v- ---      i   ii  vvi  v  i  i     i      
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_78441843_7   4806 GAGAGATGGGTAGCCATATGCAGAAAATTGAAACTAGACCCCTTCCTTAC 4855
                           v iv   i  ?   i     i  i v    ii i       v   i  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_78441843_7   4856 ACCTTAAATAAAAATTAACTCAAGATGGATTAATCACTTAAATGTAAAAC 4905
                            v  v i              i      i ?vv  i         i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_78441843_7   4906 CCAAAACTTTATAAACTCT-AGAAGAAAATGTAGGC---AATGCCATTCA 4951
                          i      v  -       -         ii    ?---   -- -   i
  L1M4_orf2#LINE/    518 CTAAAACTATA-AAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCG 563

  chrX_78441843_7   4952 GGACATAGG--TAGGGGCAAAGATCTTGTGAGGAAAATGCCAAAAGTAAT 4999
                         v   v v  --    --   v i i iv iiiv vi ii       i vv
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGG--CAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_78441843_7   5000 TGTGACAAAAGCAAAAATTGACTAATGGCATCTAATTAAACTAAAGAGCT 5049
                         v ii       v      v  iv   v v ii v  i   v v  i i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_78441843_7   5050 TCTGTAAAGCAAAAGAAAATATCATCAGAGGAGGAACAGACAACCTACAG 5099
                          i   ivvv    i  v v     --   iiiv   v        i    
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCA--AGAAAGTGAAAAGACAACCCACAG 709

  chrX_78441843_7   5100 AACGGGAGAAAATTTTTGCCATCCATCCATTTGACAAAGGTCTAATATCC 5149
                           i          v     v vi   vi  i   i  i  v  vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_78441843_7   5150 AGAGTCTACAAGGAACTTAAACAAATTTACAAGAAAAA---AAA-AAC-- 5193
                            i v  i  i     ivv    v iv i  v     ---   -   --
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_78441843_7   5194 -ATTAAAAAGCAGGCAAAGGAATTGAACAGAC-CTTCCCAAGAGAAGACA 5241
                         -   ?    iii         v     i    -i   i v i      i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_78441843_7   5242 TACATGCGGCCAAGAAGCA--TGAAAAAAT-CTTAACATCACTGATTAT 5287
                             vii      v     --      i  -  i       ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.95 (65 / 22)  


2450 24.29 12.82 0.86  chrX_78490069_78492233.rev      865  1675 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78490069_7    865 TGGAAAGATATCCTGTGTTCAAGCATTGGAAGAATTACTATTGTTAAAAT 914
                                      ii      v v         v   v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78490069_7    915 GCCTATATTACCCAAATCATTCAACAGATTCAATGCAATCCCTATAAAAA 964
                          v v   i v       iiv  v          i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78490069_7    965 TTCCAATAACATTTTTCATATAAATAGA-------ACCATAAAA------ 1001
                          i   iivi v     iii v    v  ------- i v     ------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_78490069_7   1002 -------------AACTCTAACTAGCCAAAGTAATCTTGAGTGAAAAGAA 1038
                         -------------i  i vi v        ii        ivi i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_78490069_7   1039 CAAAGCTGAAGGCATCACACTTTTTTATTTTAAATTATATTACAAAGCTA 1088
                              i  i   vv        iiiv    i   viv  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_78490069_7   1089 TGGTAATCAAAACAGTAGAGTCCTTGCATAAAAACCAAACATCTAAACCA 1138
                         ii        i     ivi  v  v      ii i- i    v  i i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGATCA 299

  chrX_78490069_7   1139 AAGGAA-AAAATAGAGAGCCCAGAAACAGACCTATTAATATACAATCAAC 1187
                          v    - i   v     i       i i   i  vv  v  iii    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_78490069_7   1188 TAATTTTTATCAAGAGAGCCAAGAAAATGCAATGGAGAAAG--T--TCTC 1233
                          i     iiv    i v       vv  v      i     -- --   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_78490069_7   1234 TGCAATAAATGGTACTGGGAAAACT----ATCCATATTCAGAAGAATAAA 1279
                          v   i       i      v    ---- ?   i  v  i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_78490069_7   1280 -TTAGACTCTTACTTCATAC-----ATAAAAATTAACTCAAAATAAATCA 1323
                         -  i   i i   i   i  ----- i                 ii    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_78490069_7   1324 --GACTGAAATGTAAAGCCTAAAACTGTAGAACTCTTAAAAGAATATGTA 1371
                         --   iv        iiv        i  i        i     v ii  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_78490069_7   1372 GGAATAAAGCTTCTTGACATTAGTCTTTGCAACAAATTTTTTTTGGATAT 1421
                           ?i    v    v    v  i vi vv    iii---   i  i     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG---TTTCTTAGATAT 596

  chrX_78490069_7   1422 GACTCCTGAAACACAAGCAACAAAACCAACAATAAACAAGT--------- 1462
                            v  vi  i              vv  v    i i  i ---------
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_78490069_7   1463 -CAAAACTAAAAAGCTTCTGCACAGTAAA----ATCAAGTCAACAAACTG 1507
                         -     i      -   i  ii vvi   ---- ii --    v   v  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA--TCAAGAAAGTG 693

  chrX_78490069_7   1508 AAAAGGTAACCTATAGAATAGAAAAAAAT----GCAAAT----------- 1542
                              ii    i i     i i i     ----      -----------
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_78490069_7   1543 --------------------------------TCATACAACTGAACAACC 1560
                         --------------------------------  v       v  i  iv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_78490069_7   1561 AAAAAACTCACAATCCAATTAAAAATCAGCCAAAGAACTCAAACAGACAT 1610
                             i  vv i  i      ?    vii v     i i ii  i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_78490069_7   1611 TTTTTCAAAGAAGACATACAAATGCCCAATGCAAATATGAAAATGTGCTC 1660
                           i i         i         v     iviv i       vi     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_78490069_7   1661 AACATCCCCAATCAT 1675
                               v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (124 / 70)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 6.53 (111 / 17)  


2640 25.79 4.30 1.58  chrX_78495791_78499211     2045  2928 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78495791_7   2045 TGAGAAAACATTCTGTGTTCATGGATTGGAAGAATCAATATCATAAAAAT 2094
                           ii  i i  i ii                  v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78495791_7   2095 AGCTATACTGTCCAAAGCAATTTACAGATTCAACAATAGCCTTATCAAAC 2144
                         i  v     vi     vii  i            ivv v  i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78495791_7   2145 TATCAA-TGTCATTCTTAACAGAGCTAAACAAA--AACTCTAATATTCAT 2191
                          vi  i-  i v  i  i-    iv vi    i--i ii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_78495791_7   2192 GTGGAAA---AAAGAGCACA-AATAGCCAAAGCAATCCTGAGCTTAAAAA 2237
                         i      ---  i ii v  -          i     i   ivvvi  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_78495791_7   2238 ACAAAGCTGGAGGTGTCACACTACCCAACTTCAAACTATACCATAAAGCT 2287
                               i      vv       v     i      viv   i i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_78495791_7   2288 ATAGTAACCAAAACAGCATTGTGCTACTA-CA-AAAAACAGACACATAGA 2335
                          i     i   i    ---    v    i-  -  ii i     i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAG---TGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_78495791_7   2336 CTAATAGAACAGAACAGAAATCTCAGAAATAAAGCTCCACACCTACAACT 2385
                         ii   i   i    iv  i vii          v ivi   ii  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_78495791_7   2386 ATCTGATCTTCAGCAAGGCTGACCAAAACAAG-CAACAGGGAAAGGACTC 2434
                          vi    i   ii     v  -    i  v v-   ii       i ivv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_78495791_7   2435 CCTATTCTATAAATGGTACTGGGATAACTGACTAGC--------AAAGAT 2476
                         i  v   v i       i      i     iv  ? --------     v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_78495791_7   2477 TAAAACTGAACCCTTACTTTTCACCATATATAAAAATTAACTCAAGAAGG 2526
                          i  ii  i    i   i iv         i              i v  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_78495791_7   2527 ATTAAAGATTTAAATTTAATACCTAAAACTATAAAAATCCTGGAAGTAAA 2576
                           i ?   ii     v   v v              v  i i    v   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_78495791_7   2577 CCTAGGAAGTACCCTTATTGACATCAGCCTTGACAAATAATTTTT--GAT 2624
                          v    ?ivv vi   vv    v ii vi v i   - ii   i --   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT 594

  chrX_78495791_7   2625 -CGAGTTCCCAAAAGCAATTTAA---ACAAAAACACAAATTGACAAGTGG 2670
                         -i  --iv         ---i  ---      iv v    v  i  i v 
  L1M4_orf2#LINE/    595 ATGA--CACCAAAAGCA---CAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_78495791_7   2671 GACATAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCAACAG 2720
                            v v  i   v v  i i   i  iiivv    i  v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_78495791_7   2721 AGTAAACAGACATCCTACACAATGAGAGAAAATATTCACAATCTATGCAT 2770
                            i  v     v  i   v    i           ii   vii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_78495791_7   2771 CTCACAATGGTCTAATATCCAGAATCTATAAAGAACT--TA------AAT 2812
                           v i  v  v  vi          v           --  ------   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_78495791_7   2813 AAGCAAGCAAGATCAAATAACCCAATT-AAAAATGGGCAAAGAACACGAA 2861
                           vv  --    -              -              i ivi   
  L1M4_orf2#LINE/    790 AATAAA--AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_78495791_7   2862 CAGATAATTCTCAAAAGAATACATACAAGTGGCCAACAAACA-----AAA 2906
                         i   i v     v      v i      i       i  i  -----   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_78495791_7   2907 AATGATCATCATCACTAATCAT 2928
                         i   v   v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (141 / 84)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.26 (52 / 23)  


 358 24.72 0.00 0.00  chrX_78504088_78506926.rev       61   149 (2690)  C L1M4_orf2#LINE/L1   (0)   908   820  

C chrX_78504088_7    149 TGATTAAAGGACATGAACAGACGCTTTTCAAAAGAACATATACAAACAGC 100
                           ivi      iv    i    ii  i  v      v         ii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

C chrX_78504088_7     99 CAACAAGCGTATGGAAAAAAGCTTGATATCACTCATCAT 61
                            i    ii   i   i v   ii i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.40 (17 / 5)
Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.00 (0 / 0)  

3113 25.09 3.99 0.46  chrX_78504088_78506926.rev     1472  2348 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78504088_7   1472 TAAAAGGATTTTCCATGTTCATGGATTGGAAGAATAAGTATTGTTAAAAT 1521
                          ii  i   v i                     v v i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78504088_7   1522 GTCCATCCTACCCAAAGCAATCTACACATTAAATGTAATCCCCACCAAAA 1571
                          v v  v  v      vii       v   v  i i      i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78504088_7   1572 TATGAATGACATTTTTCACAGATGTAAAAAAA---ATTCTAAATTTTTTA 1618
                          viv iivi v     ii    vi vi v  i---  i     v  iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_78504088_7   1619 TGGAACCACAGAAGACCCAGAATAGCCAAAGCTATTGTGAGCAAAAAGAA 1668
                              vii  iii                 i v  iv   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_78504088_7   1669 CAAAACTGGAGGAATCACACTACCTGACTTCATATTATACTACAGAGATA 1718
                             ii       v       v  ii i    v viv       i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_78504088_7   1719 TAGTAACCAAAATAACATGGAACTGGAATAAAAACAGGCACATGGATCAA 1768
                         i     i   i i iii   v     v    ii i  i  i  i      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_78504088_7   1769 TGAAACAGAATAGAGAACCCAGAGATAAATCTATTCATCTACAGTAAACT 1818
                           i  i     v    ii     i     i i  v   i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_78504088_7   1819 CACTTTTGACAAGG-TGCCAAGAACATACATTGGGGAAAAGACAGTCTGT 1867
                         v i   i       -        v   v  v        ii i     v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_78504088_7   1868 TCAATAAATGGTGCTGGGAAAACTGGATATCCATATACAAAAGAATAAAA 1917
                             i              v         ?   i  i         i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_78504088_7   1918 CTAGACCCC-ACTGTCTTTTCATATTCAAAACTAAAGTTAAAATGAATTA 1966
                         i i      -  i-  vivi     v     v v  v i      i  i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACC-TCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_78504088_7   1967 AAGACTTAAATCTAACACCTCAAACTATTAAAA----TAGATTAGGACAC 2012
                         ?    i     v   v v  v       -    ----    vv ii   i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chrX_78504088_7   2013 ---------TCTCCATGACAATGGACTGGACAAAGGTTTATTGAGTACTA 2053
                         ---------   i i    vv   ii i i   v     v  iii  iv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_78504088_7   2054 CCCCAG--GCGCAGGCAAGCTAAGCAAAAATGGACAAATGGGATCATATC 2101
                          v   i--  i  i    vvv   v      i  i    v   iivi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_78504088_7   2102 AAG-TTAAAAATCTTCTGCACAACAAAGGA-----------AAGTGAAGA 2139
                           i-       -   i  ii vv       -----------       i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_78504088_7   2140 GACAACCAGCAGAATGGGAGAAAATATTTGCAACT-ATCCATCTGAGAAG 2188
                                vi                        v -  vi      v   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_78504088_7   2189 AGA-TAATAACCAAAATATATAAGGAGCTCAAACAACTCTTTAGGAAAAA 2237
                         i  - vi  v   i         i  i   vv       vv  iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_78504088_7   2238 AATCAAATAATCTAATTTAAAA-TAGGGAAAAGATCTGAATAGACATGTC 2286
                         i -       i i    ?    - i  v   i   i           v  
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_78504088_7   2287 TCAAAAAGAGACATATAAATGGCAAAAAGGTATGTGAAAAAGTGCTCAAT 2336
                           v   ii   i   i       v  v i i ii      ii       i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_78504088_7   2337 GTTATTGATCAT 2348
                         i i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (135 / 82)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.60 (39 / 15)  


2057 26.94 9.89 2.03  chrX_78539936_78543833.rev     2569  3407 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_78539936_7   2569 AAAAACATTGCATGCCCGTGGATTGGAAGACTTAATCTTGTTAAAATGAC 2618
                            i i  iv    ii i                  v       i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_78539936_7   2619 CATACTGCCCAAAGCAGTATACAGATTTAACACTCTTCCTACCAAGCTTC 2668
                         v     v      viii v        i   i vv i    i   iv i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_78539936_7   2669 TAAG-GTCATTTTTGACAAAAA--AAAGAAC--ATTTTAAAATTAATAAG 2713
                         i iv- i v      -  i   --i vi i --  ii       v   v 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_78539936_7   2714 GAAACAAAAAGAGCCCA-AATGGCCAAAGCAATACTAGGCAAAAAAGAAC 2762
                             iiv  i ii    -   i      i    -  v iv   i      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAAC 201

  chrX_78539936_7   2763 AAAACCAGAGACATCACATTACTCAACCTCAAACTATACCGTAAGACCAC 2812
                            iiii   ivv     i v i   ii     viv   iii  ii i  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_78539936_7   2813 AGTAACCAAAACAGCATGGTACTTGTACAAAAA-AGAAACATAGACCAAT 2861
                              i   i    ii       v i i  ii -   v i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_78539936_7   2862 GGAACAAAATACAGACCCCAGGAATAAAGCTGCACACCTACAG------- 2904
                             i i   vv   vi    i      v iii   ii  ii -------
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_78539936_7   2905 --------CAAGG--------------CAATAAGAAGAGGACTACCTACC 2932
                         --------     --------------    ii i i  i -  ---ii 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TA---GTC 397

  chrX_78539936_7   2933 TATTCAATAAATAGTGCTGAGATAGCTGGCTAACCATATGAAGAAGAATA 2982
                          v     i    i      i  i i    v  ?   i   v i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_78539936_7   2983 AAACTGGATCACTACTTCTCACCATGTACAAAAATTAACTCAAGACAGAT 3032
                           ii    i v    i  v      i                 i ii   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_78539936_7   3033 TTAAGTCTTAAATGTAAGACCTAAAA--AT------CCTAGAAGAAAATC 3074
                         iv?  v i           v      --  ------ i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_78539936_7   3075 TAAG---AAATACCATTCTGGACATCAGCCTTGGCAAATAATTT------ 3115
                           i ---    -- -   vv   v ii vi v     - ii   ------
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA 593

  chrX_78539936_7   3116 -ATGACTAAGTACTCAAAAGCAATTGCAATAGAAATAAAAATTGACAAAT 3164
                         -     -----  -        vvv    i i  iv      v  i    
  L1M4_orf2#LINE/    594 TATGAC-----AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_78539936_7   3165 AAGACCCAATTATACTAAAGAACTTTTGCACAGCAAAAGAAACTATCAAC 3214
                         vi   iiv  i v v v  i        ii vv    i  v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_78539936_7   3215 AGAATACACAGACAACTTACAGAAAAGGATAAAATATTCACAAACTATGC 3264
                          i i iv v       ii      vi   v        ii    ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_78539936_7   3265 ATCCAACAAATATCAAATATCCAGAATCTATAAGAAAGTT----AATTTA 3310
                            ii i  iviv vvi          v     ii  v i----  i i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_78539936_7   3311 GCAAGCAATAAACAAATAACACCAATT--AAAGTGGGCAAA--------- 3349
                         ii  vv  v i         -      --   i        ---------
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAAC-CCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_78539936_7   3350 -------------AAGGAAAACATACAAGTGGCCAACAAACATACAAAAA 3386
                         -------------  i   i i      i       i  i  i ii    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_78539936_7   3387 -ATGCCCAACATTACTAATCAT 3407
                         -    i      i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (155 / 69)
Gap_init rate = 0.03 (25 / 905), avg. gap size = 4.00 (100 / 25)  


1834 26.54 1.65 0.21  chrX_78554994_78561678        1   486 (6199)    L1M4_orf2#LINE/L1       18   510 (398)  

  chrX_78554994_7      1 TTCATGGATTGGAAGAATCAATATTGTTAAAATGTTCATACTGCTCAAA- 49
                                         v i           i   viv     v i    -
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_78554994_7     50 ------ATAGATTCAGTGAAATCTCTATCAATGTACCAATGACATTCTTC 93
                         ------ i       ii v    i       vi v   iivi v  i  i
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_78554994_7     94 ACATAAATAGAAAAAAAAATCCAAAAATTTATATGGAACCACAAAAGACC 143
                         i  v    v  v  ivvi    v      i        vii   ii    
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_78554994_7    144 CAGAATAGCTAAAGCTATTTTAAGCAAAAATATTAAAACTGGATGAATCA 193
                                  i   i v  i  i iv  i  v vi   ii    v  v   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_78554994_7    194 CATTGCCTGACT-GAAAATTATACTACAGAGCTATAGTAATCAAAACAGC 242
                           i v  ii i -v    i -       i     i         i    i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_78554994_7    243 ATGATACTGGCATAAAAACAGACATATAGACCATTTGAACAGAATAGACA 292
                         i  i           ii i           i  v v   i     v  v 
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_78554994_7    293 ATCCAGAAACAAATCCATGCACCTACAGGGAGCTCATCTTCGAAAAATTC 342
                         i        i   i    i  ii  ii vv ii v  i     v  ivvi
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_78554994_7    343 TCCAAGAAAACACACTGAGGAAAAGAAAGTCTCTTTTGTAAACGGTGCTG 392
                         v      vv iv  v  i     ii v     i  ivii   i       
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_78554994_7    393 GGAAAACTGAATATCCAGATGCAGAAGAATGAAACTAGACCCATATCTGT 442
                            v     i   ?   v     i         ii i     v  i  vv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_78554994_7    443 CACCATATACAAAAATCAAATCAGAATGGTTTAAAGACTTAAAT 486
                                         i  v   i     v i ?    i     
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

Transitions / transversions = 1.65 (79 / 48)
Gap_init rate = 0.01 (3 / 493), avg. gap size = 3.00 (9 / 3)  

1212 26.92 1.10 3.30  chrX_78554994_78561678     4955  5318 (1367)    L1M4_orf2#LINE/L1        1   356 (552)  

  chrX_78554994_7   4955 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAA 5004
                              ii i  i     i        v      v i        v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78554994_7   5005 GGCCATACTGCCCAAGGTAATTTATAGATTCAATTCAATTCAATTCATCC 5054
                            v     v     iv i  i  i        iv    ---------  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT---------CC 91

  chrX_78554994_7   5055 CCATCAAGCTCT--GATGACTTTCTT-CATATAATTGGAAAAAACT-ACT 5100
                          i     iv  i-- v  v    i  -  v -     -- v  i  - ii
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATC 138

  chrX_78554994_7   5101 TTAAAGTTCATATGGAACCAAAAAAGAGCTGGCATTGCCAAGACAATCCT 5150
                         i    i           viiv  ii  v ii v  v     i      i 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chrX_78554994_7   5151 AAGCAAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTAT 5200
                         i iv  i          i      vv   ii  v  ii i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_78554994_7   5201 ACTACAAGGCTACAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGA 5250
                                i          i   i    ii       v i iv ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_78554994_7   5251 GATGTAGACCAGTGGAACAGAACAGAGCACTCAGAAATAATGCCACATAT 5300
                         v  i    i  i     i    iv   viii         vv   i i  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_78554994_7   5301 CTACAACCATCTGATCTT 5318
                         i  iiii  vi    i  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTT 356

Transitions / transversions = 2.06 (66 / 32)
Gap_init rate = 0.02 (6 / 356), avg. gap size = 2.67 (16 / 6)  

1842 25.53 1.58 1.76  chrX_78554994_78561678     5625  6192 (493)    L1M4_orf2#LINE/L1      342   908 (0)  

  chrX_78554994_7   5625 TGGCCAACTATCTGATCTTTAACAAACCTGACAAAAACAAGCAATGCGGA 5674
                            i   i ----   i  ii    ivv  v   i v  vv     v   
  L1M4_orf2#LINE/    342 TGGTCAATT----GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_78554994_7   5675 AAGGATTCCCCATTTGATAAATGGTGCTGGAAAAACTGGCTAGCCATATG 5724
                            i  vvi iv  ii i            i v      v  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_78554994_7   5725 TAGAAAGCTGAAACTGGATCCTTTCCTTACACCTTATACAAAAATTAATT 5774
                         i i  iiv    ii    i  i v   i     v              i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_78554994_7   5775 CAAGATGGATTAAAGACTTAAATATTAGACCTAAAACCATAAAAATCCTA 5824
                            i      i ?    i     i v   v       i      v  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_78554994_7   5825 GAAGAAAACCTAGGCA-ATACCATTCAGGAAATAGGCATGGGCAAAGACT 5873
                                  v    ?i- v i -   iv  vv v  vv i     v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_78554994_7   5874 TCATGACTAAAACATCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAA 5923
                           v iiv  vi   i        vvi          vv        i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_78554994_7   5924 TGGGATCCAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAT 5973
                          v   iiiv  i   v v  i i   i  ii vv    i  v    i  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_78554994_7   5974 CAGAGTAAACAGGCAACCTACAGAATGGGAGAAAATTTTTATAATCTACC 6023
                         v i   i  v  i     i                 v   ii  vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_78554994_7   6024 CATCTGACAAAGGGCTAATATACAGAATCCACAAAGAACT--TA-AATTT 6070
                         i      i  i  i  vi   v      vi i        --  -  i i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_78554994_7   6071 A-CAAGAAAAAAATCAAACAACCACATCAAAAAGTGGGCAAAGGTTATGA 6119
                          -i  v     i -    i    vv  i?    i          v v   
  L1M4_orf2#LINE/    787 AATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_78554994_7   6120 ACAGACACTTCTCAAAAGAAGACTTTTATGCA----GCCAAAAGACACAT 6165
                          i     i     v        ----   i  ----     v ii     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACAT 881

  chrX_78554994_7   6166 GAAAAAATGCTCATCATCACTGACCAT 6192
                              i       v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (83 / 58)
Gap_init rate = 0.02 (9 / 567), avg. gap size = 2.11 (19 / 9)  


2402 26.01 5.07 2.82  chrX_78626107_78632183.rev     4706  5593 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78626107_7   4706 TAGAAAAACATTCTATGCTCATAGATAAAAATATTCAAAATTGTTAAAAT 4755
                          i    i i  i i   i    i   vii  v i i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78626107_7   4756 GTCCTTACTGCCCAAGT--------AAGTT--------TTCCCATTAAAC 4789
                          v vv    v     i -------- ii  -------- i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78626107_7   4790 TATCA-CTGACATTCTTTGCAGAA-CTAAAAAATTTATTTTAAAATTAAT 4837
                          vi  -   v -  i         -i i v  ii v  ii       v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_78626107_7   4838 ATG-AAACCCAAAAAAGCACCCA-AATAGCCAAGACAATCCTAAGCAAAA 4885
                            -   iv   i--- v     -         i      i i iv  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG---GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_78626107_7   4886 AGAACAAAGCTGAATGCATCATGCTACTCAACATCAAATTATACTACAGG 4935
                                  i  i v vv   ii  v i   iv     viv       ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_78626107_7   4936 GCTACAGTAAACAAAAGAGCATGGTACCAGTACGAGAACAGACACATAGA 4985
                                   v   i v  ii      ii i ii  i i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_78626107_7   4986 CCAATGGAACAGAATAGAAAACTCAGAAATAAGAGTTTCCACCCCTACCT 5035
                         i        i     v  i iii         --------    v   --
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAA--------ACCCATAC-- 336

  chrX_78626107_7   5036 ATTT--------TTGACTTT-GACAAACCTGAAAAAAAAAACAAGCAATG 5076
                             --------    i   -     ivv  vv  i v---  vv     
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC---CATTCAATG 383

  chrX_78626107_7   5077 ATGAAAGGAC--TCCTAGTCAATAAAAGGTGCTGGGATAACTGACTAGCT 5124
                         iv     i i--  i -v    i   v          i     iv  ? i
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_78626107_7   5125 AGTTGCAGAAAACTGAAACTAGACCTGTTCTTTACACCATATACAAAAAT 5174
                          vv    i  i v    ii i    iv v i i                 
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_78626107_7   5175 TAACTTGAGATGGATTAAAGACTTAAATGTAAAACAGAAAACTATAAAAA 5224
                              ii i      i ?    i         i vvv            v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_78626107_7   5225 CCCTGGAAGACAAAC-TAGGCA-ATACCATTCAGGACATAGGTCCAGGAA 5272
                         i i i     -    -    ?i- v i -   iv   v v  vii   v 
  L1M4_orf2#LINE/    533 TCTTAGAAGA-AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chrX_78626107_7   5273 AAGATCTC----ATGTCCCAGATGCCAAAAGAAATTGCAACAAAAGCAAA 5318
                          v i i  ----  i ----  ii       v vvv          v   
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATAT----GACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_78626107_7   5319 AATTGACAAATAGAATCTAATTAAACTAAAGAGCTTCTGCATAGCAAAAG 5368
                            v  i    v i ii v  i   v v  i i   i  iiivv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_78626107_7   5369 AAACTATCAACAGAATAAATAGACAACCTACAGAATGGTAAAAAATATTT 5418
                          v        v i i i  v        i         v i         
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_78626107_7   5419 GCAAGTCATGCATCTGCCAAAGGTCTAATATCCAGCATATATAAGGAATT 5468
                             i    ii     vi  i  v  vi       v        i   i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_78626107_7   5469 GAAACAAATTTACAAGCAAAAAAA-----AAC---ATTAAAAAGTGAGCA 5510
                         vvv    v iv i  -i     i -----   ---   ?    i  i   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_78626107_7   5511 AAGGATATGAACAGACACTCCTCAAAAGAAGACATACATGCAGCTAACAA 5560
                               v    i     i i   v        i     viii  i  i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_78626107_7   5561 TCATATAAAAAAATTCTCCAAGTCACTGATCAT 5593
                         v  i  i    i  v   v vi   ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (141 / 86)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.92 (70 / 24)  


2710 27.77 2.10 1.66  chrX_78646063_78647702.rev      252  1155 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78646063_7    252 TGCAAAAACATTCCATGCTTATGGATTGGAAGAATCAATATTATAAAAAT 301
                           v   i i  i     i i             v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78646063_7    302 GGCTGCACTGCCCAAAGCAATTTACAGATTCAATGACATTCCTATCAAAC 351
                            vii   v      vii  i           i vv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78646063_7    352 TAACAACAACATTCTTCACAGAATTAGAAAAAAATGATTGTAAATTTTAT 401
                          vv  i vi v  i  ii     v v  v  iv-    iv    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_78646063_7    402 ATGGATCCAAA---AAAAGAGCTTGAATAGCTAAGGCAATACTAAGCAAA 448
                              ----  ---  ii  v iv       i  ii    vi i iv  i
  L1M4_orf2#LINE/    150 ATGGA----AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_78646063_7    449 AAGGACAGAGCTGGAGGCATCACATTACCTGATTTCAAACTATGCTACAA 498
                            i   i  i      vv     i v  ii        viv i      
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_78646063_7    499 GGTTACAGTAACTGAAACAGCATGGAACTGGTACAAAAACCAACACATAG 548
                         i i        iii i    ii   v     i i  ii ivi   i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_78646063_7    549 ACCAATGGAACAGAAC--AGAGTCCAGAAATAATGCCACACACATACAAC 596
                          i        i    i--               vv   i   iv  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_78646063_7    597 CTTCTAATCTTTGTCAAAGTCAACAAAAACAAGCAATGGGAAAAGGACTC 646
                          vvi i  i  i v   i viiv   i v  vv       i    i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_78646063_7    647 CCTATTCAATAAGTGGTGCTAGAATAATTGGTTAGCCATATGCAGAAGAT 696
                         i  v     i  i       i i i  i   v  ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_78646063_7    697 TGAAACTAAACTCCGTTCTTACACCATATACAAAAAATTAACTCACAATA 746
                             ii ii  i  vvi  i                -        v   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATG 494

  chrX_78646063_7    747 GATTGAAGACTTAACTATGAAACCTGAAACTATAACAACCCT-GGAAGAT 795
                            ii?    i   v i i i v  i         -   i  -i     v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAA 543

  chrX_78646063_7    796 AACCTAGG---AAAT-TCCAT---TTTGAATAAAACCAGGCAAATATTTC 838
                            v    ---    - i i ---i   ii -----i      vvi    
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGT-----TAGGCAATGGTTTC 588

  chrX_78646063_7    839 ATGACAAAGATGCCAAAGGTAATTGCATCAAAAACAAAAATTGATAAATA 888
                         v iivv v  ii     i i vvv   v     iv      v       v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_78646063_7    889 GGACCT-----AAACTAAAAAGCTTCTGCACAGCAAAATAAACTATCCAC 933
                             i -----   i      -   i  ii vv    iv v      v v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_78646063_7    934 AAAGTAAACAATCAGTCTACAGAATGGGAGAAAATATTTTTAAACTATGC 983
                              i  v iv  ii i                     vi   ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_78646063_7    984 ATCTGACAAAGGTCTAATATCCAGAATCTATAAGGAACTTAAACTAATTC 1033
                               i  i  v  vi          v     i     ivv  -  i  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC-AACTC 786

  chrX_78646063_7   1034 A-TAAGCAAAAAAAAAACCAAACTCATTAAAAAGTGGTCAAAGGACATAA 1082
                          -   -i     i v  vi  v iv   ?    i   v       iv i 
  L1M4_orf2#LINE/    787 AATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_78646063_7   1083 ATAGACACCATTCAAAAGAAGACATACATGTGAGCAACAAGCATATGAAA 1132
                                iivi  v        i     vi  iv   i     i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_78646063_7   1133 AAACGCTTAATGTCACTAATCAC 1155
                          i i   i  ii   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (158 / 90)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.12 (34 / 16)  


1226 28.89 3.78 2.44  chrX_78668111_78672960     3256  3705 (1145)    L1M4_orf2#LINE/L1        1   456 (452)  

  chrX_78668111_7   3256 TGAAAATTTATTCCATTTTCAT----TGGCAAGAGTAAACAATATTGTTA 3301
                           i   vv   i    v     ----   -    v ---i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGG-AAGACT---TAATATTGTTA 46

  chrX_78668111_7   3302 AAATGACCATACTACCCAAAGCAATTTACAGATTCA------TTTATATG 3345
                          i   i v     v      vii  i          ------ iiv   v
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_78668111_7   3346 AAACTACCAATGATATTTTTCACAGAATTAGTAAAAAAAAATAAT--TAA 3393
                            v v   iiviiv     ii     v v ---- v  iv i  --   
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAA 142

  chrX_78668111_7   3394 ATTTAATACAGAAACAAAAAGAGTTTA-AATAGCCAAGGCAATTTTAAGC 3442
                          v  v   ii    iiv  i iiiii -         ii    i  i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_78668111_7   3443 AAAATGAATGAAGCTGGAGGCATCATGTTACTCAACTTCAAACCATATTA 3492
                           i v   ii   i      vv   iii v i   i      v v  i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_78668111_7   3493 TGAGGCTACAGTAACCAAAACAGCATGGCAGTGGCACAAAAACAGACATG 3542
                         ii i          i   i    ii   i v     i  ii i      i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_78668111_7   3543 TAGACCAATGAAACAGAATACAGAGCACATAAATAATGCTGTAAACTTGC 3592
                             i     i  i     vv    iv  v      vv ii  v i  ii
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_78668111_7   3593 AACTACATGATCTTTGACAAAGTTGAGCAAAA--AAGCAATGGGGAAGTG 3640
                         iiii vv    i  i     i v  v-   i -- vv          i- 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAA-G 390

  chrX_78668111_7   3641 AAT--CCTTATCCAATAAATGATGCTGGGATAATTGGCTAGTGATATGCA 3688
                            --i   - i   i     i        i  i   v  ?iv i     
  L1M4_orf2#LINE/    391 AATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_78668111_7   3689 GAAGATTGAAAGTGGAC 3705
                         i    v    iv     
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGAC 456

Transitions / transversions = 1.87 (84 / 45)
Gap_init rate = 0.03 (12 / 456), avg. gap size = 2.33 (28 / 12)  

1899 26.75 3.73 0.47  chrX_78668111_78672960     3715  4357 (493)    L1M4_orf2#LINE/L1      245   908 (0)  

  chrX_78668111_7   3715 AGGCTATAGTAACCAAAATAGAATAATACTGGTACAAAAATAGACATCTA 3764
                          i    i     i   i i  vi ii      i i  ii        v  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_78668111_7   3765 AATAAATGAAACAGAATAGAGAACCCAGAAATAAAAGTCAAATACCTATA 3814
                         i  v    i  i     v    ii           v-i  v i ii   i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTTATG 343

  chrX_78668111_7   3815 ATCAACTGATCTTTGAAAAATTTGACAAAAGTA----ATGTGAAAAGGAC 3860
                         i    i    i  i  v  ivv  v   i vi ----   v i    i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_78668111_7   3861 ATCCTATTTAATAAATGGTTCTGAAAAAACTGGCTAGCCATATGCAGAAA 3910
                          vi  v  i  i       v   ii v      v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_78668111_7   3911 AATCAAAATGGGCCCCAATCTTTCACCATATACAAAAATTAACTCAAGGT 3960
                            v  iv   i    v i  iv                        ii 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_78668111_7   3961 CAATTAAAAACTTAAATGTGAGACCACAGACTTATAAAAATTCCAGATGA 4010
                         vi  i ? i  i       i   v vv i   -      v iii   v  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTTAGAAGA 542

  chrX_78668111_7   4011 AAATCTAGGAAAAACTTTTC-TGAGTGTTCGCCTAGGCAAAGAGGCTATG 4059
                            iv    ?iv  v i   -   vi-  v vi       v ivviiv i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTA 591

  chrX_78668111_7   4060 ATTAAGACCTCAAAAGCAAATGCAAGAAAAGTGAAAATAGATAAATGGGA 4109
                         iv  v   vi        v v    v     vi             v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_78668111_7   4110 CTT-------GTAAACAGCTTCTGTACAG-AAAGAAAATT-TCAACATTA 4150
                            -------i v  v i   i   i vv-    i v i -    v vvi
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_78668111_7   4151 TAAACTGACAACATACAGAATAGGAGAAAATATTTGCAAATTATGCCTTT 4200
                          i  vv      vi       i                   i  iiv i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_78668111_7   4201 GATAAAGAACGAATATCCAGAATCTACAAATAACTCAAACAATGTAATAA 4250
                              i i  vvi          v  i   v     vv    ivi     
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_78668111_7   4251 GAAAAAAA-----AAC---ATTAAAAAGTGAGCAAAGGACAGGAACAGAC 4292
                         v     i -----   ---   ?    i  i        ivv   i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_78668111_7   4293 ACTTCCCAAAATAAGACATAAAAGTGGCCAATAA--ACATGAAAAAATGC 4340
                          i   i v   v    i   v  i          --         i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_78668111_7   4341 TCCACATCACAAGCCAT 4357
                           v      ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (97 / 71)
Gap_init rate = 0.02 (11 / 664), avg. gap size = 2.45 (27 / 11)  


3167 28.08 0.44 0.44  chrX_78696685_78700963.rev     2884  3791 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78696685_7   2884 TAGAAAAATATTTCACGTTCATGGGTTGGCAGCATCAATATTGTTAAAAT 2933
                          i    i    ii  i        i    v  vv i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78696685_7   2934 GACCATACTACCCAAAGCAATCTACAGTTTCGATGCAATCCCTATCAAAA 2983
                          i v     v      vii        v   i i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78696685_7   2984 TGCCAATGGCGTTCTTCACAGAGATAGAATAAATAATCCCAAAATGTATA 3033
                          v   iiv  v  i  ii    i  v  vv iv i    i     vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_78696685_7   3034 TGGAACTGCAGAAGACCCAGAACAGCCAAAGCTATTCTAAGTCAAAAGAA 3083
                              v    iii         i       i v  ii i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_78696685_7   3084 CAAAACTGGAGTACTCACATTCCCTGAATCCCGATTTATACTCCAGAGCT 3133
                             ii     v       i i  ii v i vi vi -    v  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_78696685_7   3134 ATAATAACCAAAACAGGATAGTACTGACATAAAAACAGGCACATACAACA 3183
                          i i   i   i    vi i      i     ii i  i  i   v v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_78696685_7   3184 GTGGAACAGAATAGATAATCCAGAAATAAGTCTACACACCTACAGTGAAC 3233
                         i     i     v  v i           ii i i   ii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_78696685_7   3234 TAATTTTTGAGAAAGTTGCCAAGACCATTCATTGAGGAATGGACAATTGC 3283
                          i     i  v  i v               v  i    v i i i ivi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_78696685_7   3284 TTCCATAAATGGTGCTAGGAAAACTGAATATCCATATGCAGAAAAAGGAA 3333
                            v i          i   v     i   ?   i     i  i  v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_78696685_7   3334 ACTAGACCCCTATTTCTTGTCATATCCAACAAACAAATCAAAATAGATTA 3383
                         ii i        ii  viii     v   v  vi  v       i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_78696685_7   3384 AAGAC--AAACTTAAGACCCCAAAATATGAAACTACTAAAAGAAAACTTT 3431
                         ?    --   iv     v iv   v   i     vi  i        v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_78696685_7   3432 GAGAAGACACTCCAAGACAATGAACTGTGCACAGATTTCTTGAGTAGTAC 3481
                          i?ivi vv  i iv   vv  iii iv   vv i      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_78696685_7   3482 CCCATAAACACAGGCAACGAAGGCAAAAATGAACAACTGAGACTACATCA 3531
                         v   v  i    i     i  i v      ii i  v vi    v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_78696685_7   3532 AGTTCAAACTCTCCTGAACAGTGAATGAAGCAATCACAAAAGTAAAGAGA 3581
                          iv i   vv  ii  vi vvii  v  vi v    vi     i  i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_78696685_7   3582 CAACCCACAGAATGGAAGAAAAAATTTGCTAACTATCATCAGTCTGATA- 3630
                                        i      v      -  --     vvi       -
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGC-AA--ATCATATATCTGATAA 746

  chrX_78696685_7   3631 TGGATTAATAACCAGAATATATAAGGAATTCAAACAATGCAATGGGAAAA 3680
                         v   i vi  v             i   i  vv    iv    iiv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_78696685_7   3681 AATCTAATAATCTAATTAAAAAA-GGGCAAAATATCTGAATAGATGTTTC 3729
                          iv v     i i    ?     -       iv  i        ii    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_78696685_7   3730 TCCACAGAGGACATACAAATAGCAAGCAGGTGTCTGAAAAGGTGCTCAAC 3779
                             v   i  i        i  v ii i iiiv       i        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_78696685_7   3780 AGAATTATTAAT 3791
                          vv ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (156 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2212 25.57 3.03 5.20  chrX_78707120_78710799.rev      529  1451 (2229)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_78707120_7    529 AGATGTACCATGT------ATTAGAAGACTAAATATTGTTAAGTT--CA- 569
                             i v      ------   i       v            v --  -
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_78707120_7    570 TACTCTCCAATTTGATCTATATATCCAAGACAATCCTAATCCTAAAAATA 619
                              i    v        i v  i   vi      iv   ---     -
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC---AAAAT- 101

  chrX_78707120_7    620 GCATGCTAATCCCTAGTATGC-TCTTTTGTGAATATCAACAAATGTATTC 668
                         -----------  i  i-   - i     iii v  ii    iivv  i 
  L1M4_orf2#LINE/    102 -----------CCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chrX_78707120_7    669 TTAAATTTATATAGAAAGGCAAAGCAGCCAGAATCATCAACAAAACACTG 718
                          v     i    i    v    i v v       vii   v v  ivi  
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_78707120_7    719 AAAAATAG---CAAAGTTGGAACACTGACATGATCCAACTCTAAGACTTC 765
                              v i---          iv   v   ivvi    i ii  i    v
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_78707120_7    766 ATAAAAAGCTACAGTGATCCAGACAGTATGGTACTG--ATAAAAATAACA 813
                         v  v           i   v       i        --    ii   ---
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA--- 286

  chrX_78707120_7    814 GACACTTTTATGTATGGAACTGAATGGAGAGGCCAGAAATAGATGATAGT 863
                             iv vv  vv      iv    v     v         i iv----i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC----C 332

  chrX_78707120_7    864 ATGAAAACAGATGAAAATAGTCAACTGATCTCTGACAAAAAAAAAAAACA 913
                           ----   vv ----  i     i    i ii     iiivi----- v
  L1M4_orf2#LINE/    333 AT----ACATTT----ATGGTCAATTGATTTTCGACAAGGGTG-----CC 369

  chrX_78707120_7    914 AAGGCAATTCAATGAAGAAAAAATGTTATTCTTTCCAACAAATACTGCTA 963
                            i v        ii    i   --- v     i        iv    i
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAAT---AGTCTTTTCAACAAATGGTGCTG 416

  chrX_78707120_7    964 AAA--ATTTAATGTCAATTTGCAAAA-AGTTAATCTAGACAATGATGTTA 1010
                         ii -- i vi  i? v iv       - i v  vi i   vviv iv i 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_78707120_7   1011 CACCTTTAACAAATATTAACTAAAAATGGTTCACAGACTTAAACAGAAAA 1060
                             v vv     v       v       v   ?    i    iiv  i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_78707120_7   1061 --CAAAATGAATACTAAACCTTCTACGAAATAATATAGGAGAAAATCTCA 1108
                         --i    i---  -    v  ii  vi i v  i     ? v      iv
  L1M4_orf2#LINE/    517 GCTAAAAC---TA-TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_78707120_7   1109 ATGATCTTGGATTTGGCAATGAGTTTTTAGAAGCAACACTTAAAGCATAA 1158
                         i   i     i  v       iv  i     viii    iv      i  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_78707120_7   1159 TTCATGAAAGAAAAATGTGACA--TTTGACTTTATTAAATAAAAAAAACT 1206
                         viv ii         vvv  i --  v     i  i   - vv       
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA-ATTAAAAACT 661

  chrX_78707120_7   1207 TGTCCTCTGTGAAATAAATTATTAAGAGAATGAAAAGGCAAGCCACAGAC 1256
                          v viv  vii  iv v i   i    i i       i   v       v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_78707120_7   1257 TCATAGAAAATATTAGCAAA-CATATATCTGATAAAAGACTTATATACAA 1305
                          viv          v     -              ii     i   v  i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_78707120_7   1306 AATATACAAAAATCTCCTAAAAC--AACAATAAGAA-ACAGCCATGTCTT 1352
                               i   i v   i  v   --  i     i  -   i--  iv ii
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA--ATAACCC 809

  chrX_78707120_7   1353 TTTTAAAAAAGATAGGCAAAAATTTTAAATAGATACCTCACCAAAGAAAA 1402
                         vv  ?     -- i      iiv   i      i ii  v        i 
  L1M4_orf2#LINE/    810 AATTWAAAAA--TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_78707120_7   1403 TATACAAATG-CAAATAAGCATGTGTAAAGGTGCT-ACTACCATATATAA 1450
                                   - v        ii  v    i    - vi i  ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_78707120_7   1451 T 1451
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.37 (134 / 98)
Gap_init rate = 0.03 (29 / 903), avg. gap size = 2.62 (76 / 29)  

2431 27.81 2.78 2.11  chrX_78707120_78710799.rev     2291  3189 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_78707120_7   2291 AAAAAT-TTCCATGCTCATTGACTG-AAGAATCAATATTGTTAAAATGGC 2338
                            i  - i     i    v  i  -    v i           i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_78707120_7   2339 CATACTCCCCAAAGGAATCCATAGATTCAATGCTATTCTCACCAAAATAC 2388
                         v            vvi   i i        i  v  i ii i      v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_78707120_7   2389 CAACATTATTGCCCACAGAATTAGAAAAAT--AAAAACT-ATTCTAAACT 2435
                           i -----    iviv---  iv i    -- v  i  -  i     v 
  L1M4_orf2#LINE/    104 CAGC-----TGCCTTTT---TTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_78707120_7   2436 TCACATGAAACCAAAAAGAGCCCA-AATTGCTGAAGCAATTGTAAGCAAA 2484
                            i   i  viiv  i ii    -   v  ii  i    iv i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_78707120_7   2485 AAGAACAAGGCTGAAGGCATTACATTCCCCAACTTCAAACTATACTACAA 2534
                                 i i  i   vv i   i i     i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_78707120_7   2535 GGCTGCAATAAGAAAAACAACATGGGACTTGTATAAAAACAGACACCAAG 2584
                         i   i  i   vv  i   iii   v   v i    ii i     ivv  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_78707120_7   2585 GCCAATGGAACAGAATAGAGAACCCAGACAGAAAGCTACACACCTACAAC 2634
                         ii        i     v    ii     v v   v i i   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_78707120_7   2635 CAACTGATCTTCAACAAAG-TGAAAAAAAAAAAAAAGCAATGAGGAAAAG 2683
                            i    i   i    i -  vv  i vv v----v     i     ii
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCAT----TCAATGGGGAAAGA 391

  chrX_78707120_7   2684 ACTTTCTATAAAATAAATGGTGCTGGGATAACCGGCTATCTATATGCAGA 2733
                          ivv   v vv  i              i   i  v  ? i i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_78707120_7   2734 AGGATGAAACTGGACCCTTACCTGTCACCATATAAAAATAATTAACTCAC 2783
                           i     ii       i     vv         v   -          v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAA-AATTAACTCAA 490

  chrX_78707120_7   2784 GATGAATTAAAGGA--AAATCTAAGACCTAAAACAATAGAAATTCTAGAA 2831
                         i   i  i ?  iv--    v     v       v   i  v ii     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_78707120_7   2832 GGAAGCCTAGG---AAATACCCTTCTGAACATCAATGTTGGTGAATAATT 2878
                          i  i v    ---    ---    vvi  v iii-   i vv   ii  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT---CTTCGTGACCTTGG-GTTAGGCAATGGTT 586

  chrX_78707120_7   2879 TAT--GACTAAGTCCTCAAAAGC-CATTGAAACAAAAACGAAGCTTGACA 2925
                          v --  -  v v vi       -  v- v       ivi  iv v  i 
  L1M4_orf2#LINE/    587 TCTTAGA-TATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATA 634

  chrX_78707120_7   2926 AATGAAACCTAAGTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACTAC- 2974
                            vii  i v vi   v v    i   i  ii vv    i  v    i-
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_78707120_7   2975 ---AGAGTAAACAGACAACCTACAGCATGGGAGAAAATATTCACAAACTG 3021
                         --- i   i  v        i    v               ii    iii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_78707120_7   3022 TGCTCTTGACAAAGTTCTAATATCCAGAATCTGTAAGAAATTTAAACAAA 3071
                          iivii   i  i vv  vi          v i   ii  i ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_78707120_7   3072 TCAACGAGCAAAAAACAA----TCCTATTAAAAACTGGGCAAAAGATATC 3117
                             ii vv    i    ----i  v   ?    v        i   v v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_78707120_7   3118 AACAGGCACTTCTCAAAAGAAGACATATAAGTGGCCAATAAGCG--TGAA 3165
                           i  i  i     v        i   i  i            i--    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_78707120_7   3166 AGAATTCTAAATATCACGAATCAC 3189
                          ii  v  v  i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (153 / 94)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 2.10 (44 / 21)  


2689 27.67 1.32 1.21  chrX_78721104_78724149.rev     1649  2555 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78721104_7   1649 TGGAAACACATCCCATACACATGGATGGGTAGAATCAATATTGTGAAAAT 1698
                               v i       iiv       v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78721104_7   1699 GACTATACTGCCAAAAGCTATCTACAAATTCAATGCAATTCCCATCAAGA 1748
                          i v     v  v   viv       i      i     i  i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78721104_7   1749 TACCA-CCATCATTTTTCAAGAAACTAAAAAA---ATTATAATATTCATA 1794
                          v   - iii v     vv     i i v  i---  iv   v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_78721104_7   1795 TAGAACCAAAAAAGTGCCCCACAG-AGCCAAAGCAAAACTAAGCAAATAG 1843
                          i   -- viv   v v    v i-       i   vvi i iv  iv  
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_78721104_7   1844 AACAAATGTGGAGGCATTACGTTGACAGACTTCAAACTATTCTATAAGAC 1893
                               vv      vv i  ii vv vi i      viv v   i  ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_78721104_7   1894 CATGGTCACTGAAACAGCATGTTACTGATATAAAAACAGGTGTATAGACT 1943
                         i ii  v iii i    ii  v     ii    ii i  iii      ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_78721104_7   1944 AATGGAACAGAATTAATATCCCAGAAATAAAGCCAAATACTTACAGTCAA 1993
                                i      i v vi           v   v i i   ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_78721104_7   1994 CTGATATTCGACAAAGCAAGCAAAAACACAAAGTGGGAAAAGGACACCCT 2043
                         i    v        i vviv   i v  ivv i    i    i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_78721104_7   2044 ATTCAACAAATCATGCTGTAATAATTGTCAAGCCACAAGTAGACAAATGA 2093
                         v          vi     vi i  i  vvv ?     v i i vi     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_78721104_7   2094 ATCTGGATCCTCATCTCTCACCATATACAAAAATCTACTCAAGATGGATC 2143
                          vi    i  ii i   v                iv      i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_78721104_7   2144 AAAGACTTAAATCTAAGACCTGAAACCATAAAAGTTTTAGTAGATAATAT 2193
                          ?    i     v     v  i    i      v i    v   v  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_78721104_7   2194 TGGAA-AAACCTTTCTAGACATTGGCTTAGGCCAAGGCTTCATGACCAGG 2242
                         v  ?i-   i   iv -   v    v      v v  i   v iivi v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_78721104_7   2243 AACCCAAAAGCAAACACAAGAAAAACAAATATAAATAGATGGGACTTAAT 2292
                          vv         v vi   v    iv   v   i   i  v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_78721104_7   2293 TAAACTAAAAAGCTTCTGCAC--AGAAGAAAA--AGTAAGCAGAGTAATC 2338
                         i   v v    i   i  ii --vi   i v -- vi   - i   i vv
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAA 696

  chrX_78721104_7   2339 AGACAACCCACAGAGTGGGAGAAAATCTTCGCAATCTATATATCTGACAA 2388
                                       i           v  i    vii          i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_78721104_7   2389 AGTACTAATATCCGGAATCTACAAGGAACTCAAATAGATAAGCAAGAAAA 2438
                         i v   vi     i    v  i  i      vv i iv v ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_78721104_7   2439 ACAAACAAACAAACAATCCCATCAAAACGTGGGCTAAGGACATGAATATA 2488
                          ------i     i  i  v  i?   vi     v     iv      v 
  L1M4_orf2#LINE/    797 A------GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_78721104_7   2489 CAAGTCTCAAAAGAAGATATACAAATGACCTACAA--ACATGAAAAAAAT 2536
                           vv    v                  i  v i  --         i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-T 889

  chrX_78721104_7   2537 GTTCAACATCACTAATGAT 2555
                          i         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (136 / 111)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


1324 28.11 23.11 0.68  chrX_78726228_78730062     2603  3342 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_78726228_7   2603 GAAAAACATTTGATGCTCATGGATTTGAAGAATCAATATCAGAAAAATCG 2652
                             i i  iiv   i         v     v i     iivv  i  v 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_78726228_7   2653 CCATACTGCCCAGAGCAACTTACAAATTCGGTGACATTTCTATAGAACTA 2702
                          v     v    i vii ii    i    iii vv  ii    vi  v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_78726228_7   2703 CCAA-TGCCATTTTTAGAGACTTAGAGAAACACTATTTTAAACTTTATAT 2751
                            i-    v     iv   vv v  v  i -iv  ii    v  i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATAT 151

  chrX_78726228_7   2752 GTGATAAGAAAGAG-CCCA-AATAGCCAAAGCAATCTTAAGAAAAAGGAA 2799
                          -  v v v   i -    -          i       i i   i i   
  L1M4_orf2#LINE/    152 G-GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_78726228_7   2800 CAAAGCTAAAGACATCACAATACCC---TTCAAACTATACTATAAAGCCA 2846
                              i ii  ivv     v v   ---      viv     i     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_78726228_7   2847 TAGTAACAAAAACAGC-TGATTATTGATACAAA-ACAGCCACATAGACCA 2894
                         i     iv  i    i-  i - i  ii i  i- i  v  i     i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGT-ACTGGCATAAGGATAGACATATAGATCA 299

  chrX_78726228_7   2895 ATGAAACAAAATAGAAAACTCAGAAATAAAGCCACACATCTACAAACATC 2944
                            i  i i   v  i iii          v   i    i  iiiv  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_78726228_7   2945 TGGTCTTCTAGAAGGCTCACAAAACCAACAAATGGGGAAAGAATTATATA 2994
                           i i   v v    v vv   i    viv              vi v v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_78726228_7   2995 ATTAATAGATGGTGTTGGGATACCTGGCTAGCCACATGGAAAGTATTGAA 3044
                         v i  i i      i     i v    v  ?       v   iv v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_78726228_7   3045 TCTGGAGTGTAACCTTCCAACATATATAAAAATTTACTCA---------- 3084
                         vi    viviv    iv  v      i       v     ----------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_78726228_7   3085 -------------------------TAT---------------------- 3087
                         -------------------------   ----------------------
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_78726228_7   3088 GGAG-----CTT-----------------------TTTC---------AC 3100
                           ? -----   -----------------------    ---------  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_78726228_7   3101 AGTAAAAG--------------------------AAACTG-------TCA 3117
                          vi     --------------------------   i  -------   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_78726228_7   3118 A--------------------TAGAGAAAACT----------------GA 3131
                          --------------------i i  i v   ----------------  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_78726228_7   3132 TAATGTAAAGAATGGGATAAAATATTCACGAACTATACATCTGACAAACG 3181
                         i  ivi v         v        ii i  ii   i      i  iv 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_78726228_7   3182 CCTAATATCTAGAATCTATGGGAAACTAAAACAAATCGTCAAGCAAAAAA 3231
                         v  vi    i     v   iiii    vvv    v  ivi  -i     i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAG 798

  chrX_78726228_7   3232 ACAAATAACACCATTAAAAAGGTGGGCAAAGAACATGAGCAGACACTTCT 3281
                                  v v   ?    i-         i iv   ii     i    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_78726228_7   3282 CAAAAGAAGACATACAAGTGATCAACAAACATATACAAAAATGCTCATCA 3331
                          v        i      i  ii   i  i  i  iv   i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_78726228_7   3332 CCACTATTCGC 3342
                         i  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.56 (125 / 80)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 8.80 (176 / 20)  


2075 28.92 1.46 4.04  chrX_78745440_78747614.rev      785  1676 (499)    L1M4_orf2#LINE/L1        1   869 (39)  

  chrX_78745440_7    785 TGAAAAGATATTTCATATTTATAAATTGGAAGAATAAATATTGTTAAAAT 834
                           i        ii   i  i  ii         v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78745440_7    835 GTCCATACTGCACAAAGTAATCTAGAAATTCAATGATGTTCCTATCAAAA 884
                          v v     v v    v i     v i      i vvi i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78745440_7    885 TACAAATGACATTCTTCACAGAAACTAAAAAAAAAATCCAAAAAATTATA 934
                          v v iivi v  i  ii      i i v  ivvi    v    v i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_78745440_7    935 TGGAACCACAAAAGACCTAGAATAGTCAAAGCTATCACGAGAAAAATTTA 984
                              vii   ii    i       i    i v   vi  i   i vvv 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_78745440_7    985 CAAAACTCGAGAAATTATACTACATAACTTTCAATTATACTACAGAAATA 1034
                             ii v   i v i i   v vi  i  iv  viv       i iv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_78745440_7   1035 TAGTAACGAAATTGGCATGGTACTGGCATAAAAAACAGACAAATAGTCCA 1084
                         i     iv  ivii ii              ii -i     v    vi  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCA 299

  chrX_78745440_7   1085 ATGAAACAGAATAGAGAACCCAGAAAGTAATCCACACACCTACAGGGGAC 1134
                            i  i     v    ii       vv  i   i   ii  ii vvi i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_78745440_7   1135 TCATTTTCAACAAAGATGTCAAGAACATGCATTGAGGAAATA-TATCTAT 1183
                          v      i    i i  i     v   v  v  i     v -  -----
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA----- 394

  chrX_78745440_7   1184 GTCTATATGGATATATCTTATATATATGTATATAAAGAGATCTATTTATC 1233
                             ----------- i i - i v   -i iivii  v v  iv-----
  L1M4_orf2#LINE/    395 GTCT-----------TTTCA-ACAAATG-GTGCTGGGACAACTGG----- 426

  chrX_78745440_7   1234 TATCTATATCTATAGCTATGCAGAAGAATGAAATTAGAACTCTCTCTGCA 1283
                         -----   ? i i ----    i         i  i  v i  vi  -  
  L1M4_orf2#LINE/    427 -----ATAKCCACA----TGCAAAAGAATGAAGTTGGACCCCTACCT-CA 466

  chrX_78745440_7   1284 TAA-ATATACACAAAGAAA---AAAATG-ATTAAGGACTTAAATCTAGAA 1328
                         i v-       v   vv  ---      -  i ?i   i     v  ii 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_78745440_7   1329 TATCAAACTATAAAATTTCTGAAAGAAAACATTGGTGAAACTCTCCAAAA 1378
                         vv v           i ii ii          v  ? v  v   i ivi 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_78745440_7   1379 CATTGGAGTGGGCAAATATTTCTTGAAGAATACCCCACAAGCATAGGCAA 1428
                          v    iv i     vvi      ii v vv  v   v     i i    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_78745440_7   1429 CCAAAGCAAAAATGAACAAATGAGATCACAT-GAAGTTAAAAAGCTTCTG 1477
                          v    v      ii i    vi  iiv   -i  i       -   i  
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTG 665

  chrX_78745440_7   1478 TAAAGCAAGGAAAACAATAAACAAAATGAAAAGAAAACTCAGAGTATGGG 1527
                          ivvv   i i v  v  v  v   i        v   i  v  v     
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_78745440_7   1528 AGAAAATATTTGCTAACTACTGATTTAATAAGGTATTAATAACCAGTATG 1577
                                      v  ii ivv  i i      v i vi  v    v  i
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_78745440_7   1578 TATAAGGAGCTGAAACAACTTCATAG-AAAAACTCTAATAATCTGAT--- 1623
                              i  i  vvv      iv   i-     vv v     i ii  ---
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_78745440_7   1624 --ATTCAGCAAAAAATCTGAATAAACATTTCTTTAAAAAAAGACATTTAA 1671
                         -- v vi     ii  i      i        ii   i  -  i  vi  
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-GATATACAA 864

  chrX_78745440_7   1672 ATGGC 1676
                              
  L1M4_orf2#LINE/    865 ATGGC 869

Transitions / transversions = 1.41 (149 / 106)
Gap_init rate = 0.02 (17 / 869), avg. gap size = 2.88 (49 / 17)  


3226 26.70 1.22 0.22  chrX_78752910_78759881.rev     5583  6481 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78752910_7   5583 TGCAGAAACATTCCATGCTTATGGATAGGAAGAATCAATATCGTGAAAAC 5632
                           v i i i  i     i i      v      v i     i  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78752910_7   5633 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5682
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78752910_7   5683 TACCATGGATTTTCTTCACAGAATTAGAAAAAACTACTTTAAATTTCATA 5732
                          v   vvviii  i  ii     v v  v  iviv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_78752910_7   5733 TGGAACAAAAAAGAGACC--GTATAGACATGACAATCCTAATCAAAAAGA 5780
                              - viv   i    -- v    v  vi      i i vv  i    
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_78752910_7   5781 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5830
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_78752910_7   5831 ACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGATATATAGACCA 5880
                                i   i   iii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_78752910_7   5881 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAGCCATC 5930
                               i    iv   ivii         vv   i    i  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_78752910_7   5931 TGATCTTTGACAAACCTGACCAAAACAA-GCAATGGGGAAAGGATTCCCT 5979
                             i  i     ivv  -    i  v -v            i  vvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_78752910_7   5980 GTTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 6029
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_78752910_7   6030 AATTGGACCCCTTCCTTACACTTTATACAAAAATTAACTCCAGATGGATT 6079
                          i          v   i    iv                 v i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_78752910_7   6080 AAAGACTTATATGTAAGACCTAAAACAATAAAAGCCTTAGAAGAAAACCC 6129
                          ?    i  v        v       v      vi             vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_78752910_7   6130 AGGCATTACCATTCAGGACATAGGCATGGGCACAGTCTTCATGACTAAAA 6179
                            ?i v viv   iv   v v  vv i    vv vi   v iiv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_78752910_7   6180 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCAGACCTAATT 6229
                                    vvi          vv     v  i    ii   i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_78752910_7   6230 AAACTAAAGAGCTTCTGCTCAGCAAAACAAACTATCATCAGAGTGAACAG 6279
                            v v  i i   i  iv vv    iv v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_78752910_7   6280 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGATGAAG 6329
                         i     i                 v       vii  vi       i i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_78752910_7   6330 GGCTAATATCCAAAATCTGCAAAGAACTTCAACAAATTTACAAGAAAAAA 6379
                          i  vi      i   v ii        iiv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_78752910_7   6380 ATGCATAA--------AAAAGTGGGTGAAGGATATGAACAGACAATTCTC 6421
                          iiv    --------    i    ii      v    i     v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_78752910_7   6422 AAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCATCAT 6471
                         v        i  vi viii     i  i  i       i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_78752910_7   6472 CACTGGTCAT 6481
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.32 (135 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.60 (13 / 5)  


3121 24.04 2.21 2.32  chrX_78793997_78798259     2864  3770 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_78793997_7   2864 GAAAAATATTCTATCTTCATGGATTGGAAGAATCAATATTATTAAAATGT 2913
                             i    i i  v                v i      i    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_78793997_7   2914 CCATACTATCCAAAGCAATCTATAGATTCAATGCAATCCCGATTAAAATA 2963
                          v     vi     vii     i        i        v  i     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_78793997_7   2964 CCAGGCACATTCTTCACAGAAATAGAAAAG--GACATTTCTAAAATTTAA 3011
                             vii v  i  ii       v  v   --  --- i        i v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA---TCCTAAAATTCAT 149

  chrX_78793997_7   3012 ATGGAATTACAAAAGACCCAGAATAGTCAAAGCTATCCTAAGGGGGAA-A 3060
                               v i   ii            i    i v   i i iiii   - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_78793997_7   3061 ATAAAGCTGAAGGAATTACATTACCTGACATCAAA--TTATTCTACTGAG 3108
                          i    i  i    v i   i v  ii iv     --   --    vi  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAG 247

  chrX_78793997_7   3109 CGATAGTAACTAAAA-AGCATGGTACTGGCATAAAAAGAGACAAATAGAC 3157
                          v i     ii  i -  ii              ii v     v     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_78793997_7   3158 CAATGGAAAAGAATAGAGAA-CCATGAAACAAATCCACACACCTACAGTG 3206
                                 v     v    i-   -    i   i   i   ii  ii  v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATGGTC 346

  chrX_78793997_7   3207 AATTCATTTTTGAGAAAAGTGTAAAGAACATACACTGGGGAAAATATAGT 3256
                             v     i  v  ii   iv    v   v  v        iv     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_78793997_7   3257 CTCTTTGATAAATGGTGCCAGGAAAACTGAATATTTGTATGCAGAAGAAT 3306
                           i  ii i         ii   v     i   ?iiii     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_78793997_7   3307 AAAGCTAGATGTTTGTCTCTCACCATATACAAAAATCAAATCAAAATGAA 3356
                         i   i i  ivii ii   v                i  v        i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_78793997_7   3357 TTAAAGACTTAAATGCAAGACCACAAACTATGAAACTACTACAAGAATAC 3406
                          i ?    i      i    v vv       i     vi  v     v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_78793997_7   3407 TTTGGAGAAACTCTTTCGGATGTTAGTTTGGGCAAAATATGTTTGAAAAA 3456
                         v v  ? v  v    ivv  iv  i v  i     -- i-    vvv i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA--TG-GTTTCTTAGA 593

  chrX_78793997_7   3457 TAT--C-CCACGACCACAGGCAATGAAAGCAAAAATGAACAAATTGAATT 3503
                            -- -   vi v    i    ii    v      ii i      i i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_78793997_7   3504 ACA--AAAGTTAAAAAGTTTCTGCACAGCAACAGATACAATTTAAAAAGT 3551
                         v  --   i       v   -  ii vv   vi  i  v  iv i     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_78793997_7   3552 GAAAAGACAACCTAAATAATGGGAGAAAATATTTGCAAACTAGTCATCTC 3601
                                     i v v                      ii vvi    v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_78793997_7   3602 ACAAGGGA-TTGATTAATAACCAGAATATATGAGGAGCTCAAACAACTC- 3649
                          i      -   -----  v           i i  i   vv       -
  L1M4_orf2#LINE/    743 ATAAGGGACTTG-----TATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_78793997_7   3650 -TAA-AAAAAATCTAACAGTCTGATTTTTTTAGAAAAGTGAGCAGAAGAT 3697
                         -   -     iv v  i ii ii   ?------    i  i   i i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTW------AAAAATGGGCAAAGGAT 831

  chrX_78793997_7   3698 TAAAATAGATATTTCTCAAAAGAA-ATA---AAATGGTGCACAAGCAGTT 3743
                          vi      i       v      -   ---      ivv i     vv 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_78793997_7   3744 GAAAAGGTGCTCAGTATCACTGATCAT 3770
                               i      ii    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (135 / 79)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 1.95 (41 / 21)  


2318 29.28 1.86 2.30  chrX_78818914_78822221.rev     1906  2817 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78818914_7   1906 TGAAAAGAACATTCCATTCTCATAGATAGGAAGAATCAATATTGTTAAAA 1955
                           i     -i  i    vi    i   v      v i           i 
  L1M4_orf2#LINE/      1 TGGAAAGA-TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_78818914_7   1956 TGGCCATACTGTCCAATGCAATTCACAGATTCAATGCCGTTCCTATCAAA 2005
                             v     vi    vvii  ii          i  vi i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_78818914_7   2006 TTATCAATTACATTATTTGCATAATTAGAAAAAAACT-ATTCTAAAATTC 2054
                         v vi  ii i v  v      v  v v  v  i--  -  i         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_78818914_7   2055 ATATGGAACCAAAAAGAAGCCTGGATAGGCTAGGCAATTTTAAATAAAAA 2104
                                 viiv  i i v  v i    v v ii    i  i  v  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_78818914_7   2105 GACTGAAGCTGGATACATCACACTACCTAACTTCAAATCTATACTTCAAA 2154
                           vii   i    vivv       v  i  i      v  -    v    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chrX_78818914_7   2155 TATTATGAGGCTATAGTAACCAA-ACAGCATGACACTGGTACAAAAGCTA 2203
                         ---------    i     i   -    ii  ii     i i  iiiivi
  L1M4_orf2#LINE/    247 ---------GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_78818914_7   2204 ACATACAGAACAATAGAAAAGGCAA--GAGAACTCAGAAATAAAGCCGCA 2251
                              i   v    i   v  --  --    iii          v  ii 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAG--AATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_78818914_7   2252 CAACTACAACCATCTGATCTATGAAAAAGTTGACAAAAATATTCAATATA 2301
                           vi  iiii  vi    i vi  v  i v  v   i vi       ivi
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_78818914_7   2302 GGAAAACTTCTCTATTCAGTATGTGGTGCTGTGATAACTGACTAGCTAGA 2351
                          i  i v vv   v    ii vi        v  i     iv  ? i v 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_78818914_7   2352 TGCAGAACAATTAAACTGGACCATTTTGTTTTACCATATACAAAAATCAA 2401
                             i  v   v  ii      vi viv ivi               i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_78818914_7   2402 CTCAAGATGGATAGAAAACTTAAATGTAAAACCTAAACCTATAAAAACCC 2451
                              i      vi? i  i         i v     v        vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_78818914_7   2452 TAGAAAGAAATTTATTAATAAAAATTTCATTCTGAACATAAGCTCTGAAA 2501
                              ii   iv  vv?i    ----  v iv   v v ii i v- iv 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAA----TCTTCGTGACCTTGGGTTA-GGCA 580

  chrX_78818914_7   2502 AAGATTTCAT-GATGAAAATGCTAAAAGCAATTGCAACGAAAACATACAT 2550
                          v i    v -   - vi ii i       vvv     i   iv v v  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_78818914_7   2551 TGACAAGTGGGACCTAATTAAACTGAAAACCTTCTGCACAGCAAAAGAAA 2600
                         v  i  i v    i v  i   v v    v   i  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_78818914_7   2601 CTACCAACATAGTTAACAGACAACCTACAGAATGTGACAAAATATTTGCA 2650
                            i   v v   v  v        i        v  v            
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_78818914_7   2651 AACTATGGATCTGACAAAGGTCCAGTGTTCAAAAC-CATAAGGAAAGTAA 2699
                           ii  iv      i  i  v iv  i i  i  i-i    i   vvivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_78818914_7   2700 ACAAATTTGCAATAAAAA--------ACTTA--TTAAAAATGGACAAAGT 2739
                             v ivii        --------  ii -- ?        i     v
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_78818914_7   2740 ACATGAACAGAGACTTCTCTAATAAAAGCATACATACAGCCAACAAAAAT 2789
                          iv    i   v i     i  vi  iii     v ii     i  iv i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_78818914_7   2790 CTTAAAA-ATGCTCAGCGTCACTAATTAA 2817
                         v v    -       i i   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (153 / 110)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.38 (38 / 16)  


1826 28.84 3.79 3.56  chrX_78827490_78836841.rev     2397  3294 (6058)    L1M4_orf2#LINE/L1        9   908 (0)  

  chrX_78827490_7   2397 TATTTCATGTTCATGAATAGAAAGAATCAATATTGCTAAAATGGT--CAC 2444
                            ii          i  v i    v i       i   i    i--i  
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chrX_78827490_7   2445 TCAGCCCAAAGCAATTTACAGATTCAAATCAAAGACATTGTCTTTCTTAT 2494
                           --      vii  i           vv   ----------- i i   
  L1M4_orf2#LINE/     59 TC--CCCAAATTGATCTACAGATTCAACGCAA-----------TCCCTAT 95

  chrX_78827490_7   2495 CAAACTACAAATGACATTTTTTACAGTTAGAAAAAAAAAAACT-ATTCTA 2543
                             v v v iivi v      i   ----   vvi v  i  -  i   
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAG----AAATTGACAAGCTGATCCTA 141

  chrX_78827490_7   2544 AAATTT-TATAGAACAGAAAAAGAGCCTAAGTAGCCAAAGTAATTCTAAG 2592
                              i-   i   vv v  ii  v  vi i        ii   ii i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_78827490_7   2593 CAAACAGAATAAAACTTGAGACTTCACACT----AACTTCAATCTATACT 2638
                         v  iv    i   ii v   ivi       ----  i     vviv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_78827490_7   2639 GCAAGTCCACAGGAAATAAAACAGTATGCTACTGGTACAAAAAACAGAAA 2688
                         i   iv i    v  vi  i     i  v      i i  ii -i   v 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACA 290

  chrX_78827490_7   2689 TATAGACCAAAGGAACAG--CTTAGAGTAACATGAAATAAAGTCACACAC 2736
                               i   v    i  --i v     v-  -        vi  i   i
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTC-CA-GAAATAAACCCATACAT 338

  chrX_78827490_7   2737 CTACAATCATCTGAGCTTTGACAAAGATGACAAAAATAAGCAACGAGAAA 2786
                         i  iii   vi   vi  i     i i  v   i vi vv   i i i  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_78827490_7   2787 AAAAC--TCCATATTTAATAAATGGTGCTGGGATAACTGACTAGCCAGAT 2834
                          i  i--  -- v  i  i              i     iv  ?   v  
  L1M4_orf2#LINE/    389 AGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_78827490_7   2835 GCAGA-TATTAAAACTGGAC---TATTTCATTTCATCATATACAAAAATC 2880
                            i -v v i  ii     ---  ii   ---  i             i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCA---CACCATATACAAAAATT 483

  chrX_78827490_7   2881 ATCTCCAGATGAATTGAAGACTTAAATATAAAACCTAAATCTATAAAAAC 2930
                          v   v i   i  ii?    i     i   i v     v        vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_78827490_7   2931 ATTGGAAGAAAACCTAGGATATTATTATTC-TGTACATAGGCCCTGGCAA 2979
                         v  i         v    ?-i v v v   -  -  v v  viiv     
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGN-GTAAATCTTCGTG-ACCTTGGGTTAGGCAA 581

  chrX_78827490_7   2980 AGGTTTTGT-GACA-AACACTCCAAAAGCA--ATCA-CAAAAAAAGTAAT 3024
                         v     iv -  i -i    --        -- v  -     i  iv   
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACAC--CAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_78827490_7   3025 TAGCAAGAGGGAACTAATTACATTCAAGAGATTCTGCACAGGAAAAAAAA 3074
                         viii  ivv   vi v  i v v i  i iv  i  ii vvv   ii v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_78827490_7   3075 CTATCAACAGAGTAGATAGACTATCT-CAAAATGAGTGAAAGTATTTGCA 3123
                                v i   ii v    v i i-  i    i v    i        
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_78827490_7   3124 AACTAGGCATTGGACAAAGG-------TCTA-AATCTAAAAGAAACTTAA 3165
                           ii vii  iv  i  i  -------  i -   v  v  ii    ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_78827490_7   3166 ATAAACAAGCAAAAAAAAAATAATAATAAGCCCATTAAGAAATGGGAAAA 3215
                          i  viv ii  v     i i  --    v  v   ? i       v   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAA--ATAACCCAATTWAAAAATGGGCAAA 827

  chrX_78827490_7   3216 TGACATGAAAAGCTACTTCTTTAAAGATGACTTAGATGTGGCCAACAAGG 3265
                         v  iv    v  vi i    ii     v  iv  v vi       i   v
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_78827490_7   3266 A---AAAAAAACAGCTGAACATCACTAATCAC 3294
                          ---i    i i-   v       ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (154 / 101)
Gap_init rate = 0.03 (30 / 900), avg. gap size = 2.20 (66 / 30)  

3247 27.20 0.44 0.44  chrX_78827490_78836841.rev     7954  8861 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78827490_7   7954 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 8003
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78827490_7   8004 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATTCCCATCAAGC 8053
                            v     v     iv i  i           i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78827490_7   8054 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 8101
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_78827490_7   8102 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 8151
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_78827490_7   8152 AACAAAGCTGGAGGTATCACACTACCTGACTTCAAACTATACTACAAGGC 8201
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_78827490_7   8202 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 8251
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_78827490_7   8252 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 8299
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_78827490_7   8300 ATCCGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 8349
                          vii   i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_78827490_7   8350 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 8399
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_78827490_7   8400 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 8449
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_78827490_7   8450 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 8499
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_78827490_7   8500 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 8549
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_78827490_7   8550 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 8599
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_78827490_7   8600 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 8649
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_78827490_7   8650 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 8699
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_78827490_7   8700 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 8749
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_78827490_7   8750 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 8799
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_78827490_7   8800 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 8849
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_78827490_7   8850 ATCACTGGCCAT 8861
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2932 26.12 4.01 0.34  chrX_78861162_78865684.rev     3185  4057 (466)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_78861162_7   3185 AAAAACATTCCATATTCATTGATTGGAAGAATCAATATTGTTAAAATGTC 3234
                            i i  i    i     v          v i           i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_78861162_7   3235 TGTACTACCCAAAGCAATCTACAGATTCAATGTTATCTCTATCAAAATAC 3284
                         vi    v      vii              i iv   i          v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_78861162_7   3285 GAATGACATTCTTCACAGAAATAGAAAAAAACAATCCTAAAATCTATGTG 3334
                         v iivi v  i  ii       v  v  iv-ii          ii  i  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATG 152

  chrX_78861162_7   3335 GAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAGTAAAAATAACA 3384
                            vii   ii                 i v   i i iv  i  v    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_78861162_7   3385 --------GAAATCACATTACCTGACTTCAAATTACACTACAGAGCTATG 3426
                         -------- i v     i v  ii i      vivi      i     ii
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_78861162_7   3427 GTAATAAAAACAGCATGTTACTGGCATAAAAACAGACACATAGACCAATA 3476
                              v  i    ii  v           ii i     i     i    i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_78861162_7   3477 GGATAGAATAGATAATACAGAAACAAATCCACACA-----G---AACTCA 3518
                          i       v  v i v      i   i   i   ----- ---  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_78861162_7   3519 TTTTTGACAAAGGTGCCAGGAATCTACACTAGGGAAA----AGGCTCTTC 3564
                             i     i       i  viv v  v i      ----  v  i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_78861162_7   3565 AATAAATGCTGCCTGGAAAACTGGATAT-----TG-------ATGAAATT 3602
                           i     v   iv   v         ?-----  -------     i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_78861162_7   3603 AGACCTCTATCCCTCATCACATGCAAAAATCAAATCAAAATTCATTGAAG 3652
                         i    i   i i v  i  i  i       i  v       vv  ii?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_78861162_7   3653 ACCTAAATCTAAGACATCGAGTTTTAAAACTACTACAAGAAAGCATTGAG 3702
                                 v     vv vi ii v       vi  v      i   v i?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_78861162_7   3703 AAAAATCTCTTG-GACATTGGTCTGGGCAAAAAATTCTTGAGCAACACCC 3751
                         iv      - i -   v    vi i     viiv     iiii vv  v 
  L1M4_orf2#LINE/    553 GTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_78861162_7   3752 CACAAGCAAAATCAGCCAAAACAAAAATAGACAAATGGGATCACATCAAG 3801
                           v     v  v  i v   iv         i    v   iiv      i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_78861162_7   3802 -TTAAAAATCTTCTTCACAGCAAAAGATAAAATCAACAAAGTGAAGAGAC 3850
                         -       -   i vii vv    i  i vv     v        i    
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_78861162_7   3851 AACCCACAGAATGAGAGAAAATATTTGTAAACTACCCACCTGACAAGAGA 3900
                                      i             i   ii ivi i    i   i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_78861162_7   3901 TTAATATCCACAATATATAAGGAGTTCAAACAACTCTATAAGAAAAAATC 3950
                         i vi      v         i  ii  vv       v    v     iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_78861162_7   3951 TAATAATCTGATCAAAAAGTAGGCAAAAGATTTTCATAGATATTTTGCAA 4000
                         v     i ii  i?    i i      i     vv     i    iv v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_78861162_7   4001 AAGAAAACATACAAATAGCAAACAACCGTTTTGACAG-TGCTCGACATCA 4049
                              i i        i  v  i  v iiv vi v  -     i      
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_78861162_7   4050 TTCATTTT 4057
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.57 (137 / 87)
Gap_init rate = 0.01 (12 / 905), avg. gap size = 3.17 (38 / 12)  


2559 26.76 2.79 1.56  chrX_78874900_78879432.rev     3146  4042 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78874900_7   3146 TGGAAAATCATCTCATGATCATGGATAGAAAAAAAATATATCATTAAAAT 3195
                               ivi   i    v        v i  i vvvv    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78874900_7   3196 GGCCATAGTGCCCAACAAAATTTAAAGATTCAATGCA-TTCCTATCAAAC 3244
                            v   v v     vvvi  i  v        i   - i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78874900_7   3245 TACCAGTGGCATTCTTCACAGAACTAGAATAAAACT-ATTTTAAAATGTA 3293
                          v    iv  v  i  ii     v v  v--  i  -  ii      vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chrX_78874900_7   3294 TATCAGATTAAAAAAAAAAAC---AAATAGCCAAGGCAATCTTATACATA 3340
                            -i  --  viv  iii  ---i         ii       iv v vi
  L1M4_orf2#LINE/    149 TAT-GGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_78874900_7   3341 AAGAACAAAGCTGGAGG---CATCGTTACCAAACTTCAAACTATTCTACA 3387
                                   i      ---  - ii v  v  i      viv v     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACA 244

  chrX_78874900_7   3388 GGGCTACAGCAACCAAAAAAGCAAGATGCTGGTAGAAAAATGTGCACATA 3437
                         ii       i  i   i v  iiv i i    i v  ii  ivi  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_78874900_7   3438 GACCAAAGCAACATAATAGAGAACCCAGAAATAAGGCCACACATCTACAG 3487
                           i   v v  i v   v    ii          iv   i    i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_78874900_7   3488 CCATCTGATTTTTGACAAAGCTAACCCAAA--CAATCAATGGGGAAAAGA 3535
                         i  vi       i     i v i--    i--  v            -  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTG--CCAAGACCATTCAATGGGGAAA-GA 391

  chrX_78874900_7   3536 CT--TCTTATTCCCA------GCTGAGATAACTGGCTAGCCATACGCAGA 3577
                         v --    v ivv  ------    i  i      v  ?   i i   i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_78874900_7   3578 AGATTAAAGCTGGACCCCTTACTTACACCATACA-AAAAATCAACTTGAG 3626
                            v i   i         vv  i        i -      i    ii i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_78874900_7   3627 AAGGATTAAAGACTTAAATGTGAAACCCAAACCTATAAAAACCTTGGAAG 3676
                          v    i ?    i       i i v i   v        vi   i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_78874900_7   3677 ACGACCTAGACA-ATACCATCTTGGCCATAGAAATGATCAAATATTTCAT 3725
                          vi  v   i?i- v i v  v  i  v i iv- iiv   vvi    v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTT 590

  chrX_78874900_7   3726 -GACGCAGACACCAAAAGCAATCA--CAACAAAAGCAAAAATTGACAAAT 3772
                         -  iii-             --  --         v      v  i    
  L1M4_orf2#LINE/    591 AGATAT-GACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_78874900_7   3773 GAGATATAATTAAACTAAAGAGCTTCTGCACAGGAAAAGAAACTATCAAC 3822
                         vi  iv v  i   v v  i i   i  ii vvv   i  v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_78874900_7   3823 AGAATAAAAAGACAACCTACAGACTGGGAGAAAATATTTGCAAACTATGC 3872
                          i i i           i     v                    ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_78874900_7   3873 ATCTGACAAAGGTCTAGTATCCAGCATATATAAGGAACTTAAACAAATTT 3922
                               i  i  v  v        v        i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_78874900_7   3923 ACAAGAGAAAAACAAACAACTTCACTAAAAAGTGGGCACAGGACAT-AAC 3971
                          i  v i   i     i   iiv i ?    i      v    iv -  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_78874900_7   3972 AGATACTTCTCACAAAAAGACATACATGTAGCCAAGAAGCATATGAATAA 4021
                            i i     vv  i    i     vi i     v     i     -  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-AA 886

  chrX_78874900_7   4022 AAT-CTCAATATCACTTATCAT 4042
                         i  -     i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.70 (39 / 23)  


2813 21.10 5.79 0.00  chrX_78926489_78928862.rev      723  1447 (927)    L1M4_orf2#LINE/L1       13   779 (129)  

  chrX_78926489_7    723 CCATGTACCAGGAGTGGAAGACTTAATAGTGCTAAAATGACAACACTTCC 772
                               v vv   v              v  i   i   i   i   i  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_78926489_7    773 -AAATTGATCTGCAGATTCACCA-AATTCCTATCAAAGTCCCAGCAGCCA 820
                         -          i        v i-   i         i       v   v
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_78926489_7    821 TATTTGCAGAAATTGGCAGTCTGTTCCTAAAAGCCACATGGAAATGCATG 870
                          v             i  iv   v        vi  i           v 
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_78926489_7    871 AGACCCAGAATTGTCAAAAAAAAGTTGCAAATGAGAAATTAAG---GAGA 917
                         i          v i     v  vv   v   v  ii  iv   ---   i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_78926489_7    918 ---CAGACTTCTGAATT-CAAAATTTATTACAATA-TACAGTAAGTAAGA 962
                         ---  v     iv    -     i   i     vi-        vi    
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_78926489_7    963 CAGTATGACACTGGGATCTGGATAGACATA--GATCAAT----TAAAGTT 1006
                             i  ii     v  vv           --       ----  i i  
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_78926489_7   1007 GACAGTCAAGAAATAA-----TA-----ATGA-CAACTGATTTT-GACAA 1044
                           v    v        -----  -----   i-   i       -     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_78926489_7   1045 GCATTCTAAGACAATCAAACGGGAAAAGTACACTCTTTTCAACTAATAGT 1094
                          vi v i     v  iv  i   i    v i v          v   i  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_78926489_7   1095 CATGGGATAACTGAATATCTACATGTAAAATGACGAAGTTTAACCACTAC 1144
                         vv     i     i   ? i     i    vi i      vi   v    
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_78926489_7   1145 TTCACACCATACACAAAA--TA-TTCATAATGGGTCAGGTATCTAACTGT 1191
                         i          i      --  -i   v     i   ?iv i    v   
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_78926489_7   1192 AAGAGCTAGAACTATAAAATATGTAGAAGAAAATATAAGAGTAAAT---- 1237
                                 i          iviv          i   i ?      ----
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_78926489_7   1238 GTCACCTTGGAATAGGCAACGGTTTCTTTACTATGGAACTAAAAGCAAAA 1287
                           v       iv       i        viv    iv  i       v  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_78926489_7   1288 GCAACAATA-AAGAAACAGA-ATATT---TTTAATAAAAATATAAAACAT 1332
                                v -  i   i   - v   ---i  v  v     vv     v 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_78926489_7   1333 TTCTTCCTCAAAGGATACTATAATGAAAATGAAAAGACTATTCACTAAAT 1382
                           v v i        i     v v    i         v ii   vi   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_78926489_7   1383 GTGA-AAAATATTTGTAATTTATATATTTAATAAAAATCTTGTATACGAA 1431
                          v  -          i  v i      i i    iiiv       v ii 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_78926489_7   1432 ATATA-AAAGTACTGTT 1447
                              -    v   v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTT 779

Transitions / transversions = 1.11 (79 / 71)
Gap_init rate = 0.03 (20 / 767), avg. gap size = 2.10 (42 / 20)  

 411 19.57 5.07 3.62  chrX_78926489_78928862.rev     1746  1883 (491)    L1M4_orf2#LINE/L1      769   908 (0)  

  chrX_78926489_7   1746 AAAGTACTCCTAAAATTAAACAATTACAATACAAATGACGGTATT--AAA 1793
                             v    i  v  i v  i   v v  v      i  vvv   --   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_78926489_7   1794 ATGAGCAAAGGATTT---TTTCTCACACTTTTCTTTAAAGAAGATGTGCA 1840
                            i           --- ----- v  v     ii         i i  
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAAT-----AGACATTTCTCCAAAGAAGATATACA 863

  chrX_78926489_7   1841 AACAACTAAAAAGC-CATGAAA-GATGTTCAATATCAGTCATTAG 1883
                           iii i  v    -       -    i    i    ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.04 (5 / 140), avg. gap size = 2.40 (12 / 5)  


2345 24.90 1.53 9.29  chrX_78929935_78935362     3962  4941 (487)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_78929935_7   3962 AAGA-ATCCCACGCTCATGTATAGGAAGAATCAATATCATTATAATGGCT 4010
                             -      i i     v  v      v i     ii   vi     v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_78929935_7   4011 CTACTTCCCAAAGCAATTTGTAGATTCAATGCTATTCTTATCAAACTAGC 4060
                         v    i      vii  i ii        i  v  i i       v vv 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_78929935_7   4061 AAGGACATTCTTCACAGAGCCAAATAAAACTATTTTAAAATATATATAAG 4110
                          ivvi v  i  ii    i------------   --------------- 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAA------------ATT---------------G 127

  chrX_78929935_7   4111 ACCAAATAAAACT-ATTTTAAAATTTATATAAGACCAAATAAAACTATTT 4159
                           ------  i  -  ii       i    ii----    iv  ------
  L1M4_orf2#LINE/    128 AC------AAGCTGATCCTAAAATTCATATGG----AAATGCAA------ 161

  chrX_78929935_7   4160 TAAAATTTATATAAGACCAAAAAAGAGCCCAAGTACCCAAGGCATTCCTA 4209
                         ------------ii    v i  ----------  v    ii  v  i i
  L1M4_orf2#LINE/    162 ------------GGGACCCAGAA----------TAGCCAAAACAATCTTG 189

  chrX_78929935_7   4210 AGCAAAAAGAACAAACCTGGAGGCATCACACTACATGACTTCATGCTACA 4259
                          iv  i         vi      vv       v vii i    vivivi 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_78929935_7   4260 CTACAAGGCTACAGTAACCAAATCAGCATGGTACTGGAAAAAAAAAGGTG 4309
                               i          i   iv   ii         v v  --------
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA-------- 281

  chrX_78929935_7   4310 GGGGGGTGGGTGTATAGATCAATGGAACAGAATAGAAAGCCCAAAAATAA 4359
                         ---  i i iii               i     v  i  i   i      
  L1M4_orf2#LINE/    282 ---GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_78929935_7   4360 GGCCGCACATCTTTGACCATCTAGTCTTCAAAAAAGCTGAGGAAAACAAG 4409
                         iv  ii    i v  ii  vi ii i   i v  i v  vvi i v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_78929935_7   4410 TAATGGGGATAAAAC--TCCATATTCAATAAATGGTGCTGGGACAACTGG 4457
                         i        v i  i--  -- v     i                     
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_78929935_7   4458 ATAGCCATAAGCAAAAGATTGAAGCTGGACCCTTTCCTCACACCATACAC 4507
                            ?   i v        v     i       i v            i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_78929935_7   4508 AAAAATCAATTCAAGATGGATTCAAGACTTAAACGTAAAACCCAAAACCA 4557
                               i  i    i      iv?    i    i    i v i     i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_78929935_7   4558 TAAAACCCT-GGAAGACTACCTAGG--TAATATGATCCTGAACGTAGAAA 4604
                               i  -i     vv  v    --   -  vv  v   v v i i--
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGG-- 573

  chrX_78929935_7   4605 TCAGCAAATA-TTTCATGACAAAAGATACCAAAAGCAATCA--CAACCAA 4651
                          i  vv   i-    - v v v v  i          --  --    v  
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTC-TTAGATATGACACCAAAAGCA--CAAGCAACAAA 620

  chrX_78929935_7   4652 AGCAAATAT-GACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAG 4700
                           v   v  -  i    v   ii v  i   v v  i i   i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_78929935_7   4701 TAAAGGAAACTATCAACAGAGTAAACAGACAACCTACATAACAGAAAAAA 4750
                         i      v        v i   i  v        i   v  ii i i   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_78929935_7   4751 ATATTTGCAAACTATGCGTCTGGCAAAGGTCTAATATCCAGCGTCTCTAG 4800
                                    ii  iii    ii  i  v  vi       vi v v  i
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_78929935_7   4801 GGAGCTTAAGCAAATTTACAAGAGAAAAACAAG---CCCA-TTAAAAAGT 4846
                         i  i  ivvi   v iv i  v i   i    i---    -  ?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_78929935_7   4847 GGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACATCCGTGCAACC 4896
                                   iv    i     i  i  v        i  v iviiii  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_78929935_7   4897 AACAAGTATATATATTTTTAAAAAAAGCTCAATATGACTGATCAT 4941
                           i   i i  i-------    i v      i  v ????????
  L1M4_orf2#LINE/    871 AATAAGCACATG-------AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (150 / 91)
Gap_init rate = 0.03 (23 / 904), avg. gap size = 4.61 (106 / 23)  


2310 27.78 2.33 2.56  chrX_78935385_78937230.rev      456  1355 (491)    L1M4_orf2#LINE/L1       11   908 (0)  

  chrX_78935385_7    456 TCCAATGT--ATAAATTCTAGGAAAACATCAAAATTC---AGATTATAGT 500
                            v    --  ii   ---    i  - i  v   v---    vii i 
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATT---GGAAGAC-TTAATATTGTTAAGATGGCAAT 56

  chrX_78935385_7    501 ACTACCCAAAGTGGGTTACATATTCAATGATGTTCCCATCATAATCCCAA 550
                            v      v  ivi    v      i vvi i  i    v       i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_78935385_7    551 TGGCAATTTACACAGAAACAGAAAAAATTA--CAAAAATTAATATGAAAC 598
                         iv  vv   vii      iv  v  iv v -- v      v     i  v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_78935385_7    599 TACCAAATACCTCAATTGGTCATGGTAATTCTCTCCAGAAAGAACAAAGT 648
                          i v iiv   ivi v i i  viii   ii vvvv ii           
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_78935385_7    649 TGGAGACATCCA-ACATCCTGCATTCAAATAATATTACAATCCTATAGTA 697
                              i- ii  -  v   iivv      vvv  i     vv   i    
  L1M4_orf2#LINE/    207 TGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_78935385_7    698 ATACAAACTGTATGGTACTGACATAAA-ACAGAAACATAAACCAATAGGA 746
                           vv i  v  i        i     i- i   v i   i i    i i 
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_78935385_7    747 CAGAATACACAGCCAAGAAATAAACCCATGCACATTTTATCAATTAATCT 796
                         i     vv v  i v              i  iv v vi      i  i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_78935385_7    797 GCAATAAAGACACAAAGAATACACAATGAGGAAAGAATAGTCTCTCCAA- 845
                         v i i  i iii v    vi iv     i              i i   -
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_78935385_7    846 AAATGGTGTTGGAAAAACTGGATATCTATATACAACAGAATAAAATTAGA 895
                                 i   i v         ? i i  i   v     i  i  i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_78935385_7    896 CATGTATCTCATACCCTACACAAAATTTAACT-AGAGTATATTAAAGACT 944
                          viv  i    i   v  i      v      - i i iv  i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_78935385_7    945 TAAACCTAAAGGTAGAAATTATTAAAACTC--ATAAAAATACATAGAAA- 991
                             iv   ii ivi   i   -       -- v  i  v      i?i-
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_78935385_7    992 AAATACTCATTGATGTTTGTCTTAG-CAATAATATTATGAATAGGATGCC 1040
                             vi  i -  i-i   vv    -    ii v iv ii   v  ii  
  L1M4_orf2#LINE/    555 AAATCTTCGT-GAC-CTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_78935385_7   1041 AAATGCACAGGCAA-AAAATAAATAATAAA-AAGTGGGATTACATCAGA- 1087
                            v     i    -    v   v    i -  i v   i v     i -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_78935385_7   1088 CTAAAAATATTTTGCACTACAAAGGAAACAATCAACAA--TGAAAAGGCA 1135
                         i      i-     ii  v       v  v     v  --       i  
  L1M4_orf2#LINE/    653 TTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_78935385_7   1136 GCCTGTGGAATAGAAGAAAATATTAGCAAACCATATATCAGATGAAGGGT 1185
                         i  iiii    i i          v     i        v   i i  ii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_78935385_7   1186 TAATATCCAAAGTATATAAGGA-TACATACCACTCAATGGCAAAAACCAA 1234
                          vi      i i       i  -iv v   v       ----------- 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-----------A 790

  chrX_78935385_7   1235 ACAAACAAACATCAAATAACTCAAGTAAAAAATGAGCAGTGGAGGAGAAC 1284
                          i   v i   ---      i   v ?       i   iv   vvv   i
  L1M4_orf2#LINE/    791 ATAAAAAGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_78935385_7   1285 AGGTATTCCTCCACAGAAGAGATAGTCATGGCCAACAGTTATATGAAAAG 1334
                           ii   i     v      v   vvv        i ivi i        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_78935385_7   1335 GCGCTCAACATCACTAACTAT 1355
                         ii           ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.03 (24 / 898), avg. gap size = 1.83 (44 / 24)  


1986 29.47 1.76 0.00  chrX_78958589_78960246      505  1186 (472)    L1M4_orf2#LINE/L1      215   908 (0)  

  chrX_78958589_7    505 TCACATTACCTAACTTTGAACTATACTATAAGGTCATAGTTATCAAAACT 554
                              i v  i  i  ii  viv     i  i ii i   v     i  v
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_78958589_7    555 GCATGGTACTGGTAAAAAAACAGGCATGTAGACCAATGGAAAAGAATAGA 604
                          ii         i v  ii i  i   i    i        v     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_78958589_7    605 AAACACAGAAATAAAGGCAAATACTTACAGCCAACTGATCTTCACCAATG 654
                         i iiv          vv  v i i   ii i   i    i   iv   v 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_78958589_7    655 AAAACAAAAACA---AAGTGGGAAAGGACACCCTATTCAACAGGTGGTGC 701
                         iviv   i v  ---  vv       i i vi  v       ii      
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_78958589_7    702 TGGGATAATTGGGAGGCCACATGTAGAAGAATGAAACTGAATTCTCATAT 751
                              i  i   ivi?       i i         ii  i ii ii iv 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_78958589_7    752 CTCACCTTATA-AAAAAC-AACTCAGGATGAATAAAATACTTAAATCTAA 799
                          v    v    -     i-      ii   i  v ? v  i     v   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_78958589_7    800 GAGATGAAAACATGAAAATTCTAGAAAATAACACTGGAAAAATTCTCCTG 849
                            v i   vi  i   v ii     i v    iv  ?iv  v   i vv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_78958589_7    850 GACATTGGCTTAGGCAAAGAATTTATGACTAAGTCCCCAAAAGCAAACAC 899
                            v    v        v iv  iv iiv  v v v         v vi 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_78958589_7    900 AACTAAAATAAAAACAAGCAAGTGTAATCTAATTAAACTGAAAAGCTTCT 949
                            v   iv     i iii  i vvi ii v  i   v v    i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_78958589_7    950 GCACAGCAAAAGAAATAATCAGTGGAGTACAAAGACAACCTGAAGAGTGG 999
                          ii vv    i  v iv    ivii   iv          iiv   i   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_78958589_7   1000 GAGAAAATTTTCACAATCTATGCATCCAACCAAGGACTAGTATCTAGAAT 1049
                                 v  ii   vii  ii   ii iv i     v     i     
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_78958589_7   1050 CTACAAGAAACTCAAACAAATCAGGAAGAAAAA-ATAAGTAATCTTAGT- 1097
                         v  i  ii     vv    v   iv  v     - i  i   i iv v -
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_78958589_7   1098 AAAAGTGGGCAAAGGACATGAATAGACATTTCTCAAAAGAAGATATACAA 1147
                             i           iv                v               
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_78958589_7   1148 ACAGCCAATAA-C-CATGAACACATGC---ACATTACTAATCAC 1186
                          ii        - -      v v    ---    i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (120 / 78)
Gap_init rate = 0.01 (8 / 694), avg. gap size = 1.50 (12 / 8)  


3279 26.90 0.55 0.44  chrX_78963888_78966442     1156  2062 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78963888_7   1156 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1205
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78963888_7   1206 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCTAGC 1255
                            v     v     iv i  i           i  v     i   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78963888_7   1256 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1303
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_78963888_7   1304 TATGGAACCAAAAAAGAGCCCGCATTGCTGAGCCAATCCTAAGCCAAAAG 1353
                                viiv  ii  v  v v  v  ii iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_78963888_7   1354 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1403
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_78963888_7   1404 TACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1453
                                 i   ii   ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_78963888_7   1454 AATAGAAAAGAAC--AGAGCCCTCAGAAATAATGCCGCATGTCTACAACT 1501
                            i   v    i--    i  --        vv  ii ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_78963888_7   1502 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1551
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_78963888_7   1552 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1601
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_78963888_7   1602 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1651
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_78963888_7   1652 TTAAAGACTTAAACGTTATACCTAAAACCATAAAAACCCTAGAAGAAAAC 1701
                          i ?    i    i  v v v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_78963888_7   1702 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1751
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_78963888_7   1752 AATACCAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGGATCTAA 1801
                         i i          vvi          v      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_78963888_7   1802 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAA 1851
                          i   v v  i i   i  ii vv    i  v    i  vv i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_78963888_7   1852 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACCCATCTGACAA 1901
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_78963888_7   1902 AGGGCTAGTATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1951
                         i  i  v           v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_78963888_7   1952 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 2001
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_78963888_7   2002 TCAAAAGAAGACATTTATGCAGCCAA-AAACACATGAAAAAATGCTCACC 2050
                           v        i  vi viii     -  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_78963888_7   2051 ATCACTGGCCAT 2062
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2686 27.73 1.66 1.33  chrX_78977137_78980471.rev     1940  2844 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78977137_7   1940 TGGAAACACAGCCCATGCTCATTGATCAGTAGAATCAATATTGTGAAAAT 1989
                               v i v      i    v   ii v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78977137_7   1990 GATCATACTGCCAAAAC-AATCTATAAATTGAATGCAATTCTCATCAAAA 2038
                          iiv     v  v   i-i     i i   v  i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78977137_7   2039 TACCAGCATCGTTCTTCACGGAGCTGGAAAAAAACAATTCTAAAATTCAT 2088
                          v     vv v  i  ii i  iv v  v  iv-ii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_78977137_7   2089 ATGGAACCAAAAAAGAGCCTGCATAACCAAAGTTAGACCAAG--TGAGAA 2136
                               viiv  ii  v  v v   i     i------   v--   i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAA------CAATCTTGAAAA 193

  chrX_78977137_7   2137 ACAACAGCAACCAATCTGGAGGCATCACATCATCAGGCTTCAAA-----C 2181
                          v  v i   -- i -      vv     iivi viii      ----- 
  L1M4_orf2#LINE/    194 AGAAGAACAA--AGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_78977137_7   2182 TATATGTCTATATTTACCAAAACAACATGGCACTGGTATAAAAACAGGCA 2231
                           i viv   i v v i   i   iii   i     i    ii i  i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_78977137_7   2232 TGTAGACCAATGGAAGAGAGTAGAGAACCCAGAAATATAGCCAAATGCCC 2281
                          i    i        v   i v    ii         v v   v iiiii
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_78977137_7   2282 ACAGCCAATTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAG 2331
                          ii i        i   i    i vviv   i v   vv i         
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_78977137_7   2332 GACATCCTATTCAACAAATGCTGCTGAGATTATTGGCAAGTCACATGTAG 2381
                         i i vi  v           v     i  iv i   vv ?i      i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_78977137_7   2382 AAGAATAAAACTGGATCTTCATCTCTCACCTTATGCCAAAATCAACCCAA 2431
                               i  ii    i iii i   v    v   i v     i   i   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_78977137_7   2432 G-TGGATCAAAGACATAAATCTAAGACCTAAAAACATAAAAATTCTACAA 2480
                         i-       ?    v     v     v      vi      v ii  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_78977137_7   2481 GATAACATCAGAAAAACCCTTCTAGACATTGAATTAGGCA--GAGTTCAT 2528
                           v     vi ?iv  vi    vv   v   ii       -- iv   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_78977137_7   2529 GACCAAG-CACCCAAAAGCAAATGCAACAAAAACAAAAATAAATAGATGG 2577
                         iivi v -    -       v v         iv       i   i  v 
  L1M4_orf2#LINE/    591 AGATATGACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_78977137_7   2578 GACTTCATTAAACTAAAAAACTTCTGCACACCCAAAGAAATAATCAGCAG 2627
                                 i   v v        i  ii vi v  i  v iv    iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_78977137_7   2628 AGTAAACAGACAACCCATGGAGTGGGAAAAAATATTTGAAACTC-TACAT 2676
                            i  v          ii  i     i          v  v  -  i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_78977137_7   2677 CTGACAAAGAACTAATATCCAGAATCTACAAAGAATTCAAACAAATCAGC 2726
                             i  i i   vi          v  i      i  vv    v   ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_78977137_7   2727 AAGAAAAAAATATAATAATTCCATCAAAAAGTAGGCTAAGGACATGAATG 2776
                           v     i i -     ii v  i?    i i   v     iv     i
  L1M4_orf2#LINE/    790 AATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_78977137_7   2777 GACAATTCTTAAAAGAAGATATACAAATGGTAAACAAACATTTAAAAA-- 2824
                             v    iv                   iv  i  i  iv i    --
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_78977137_7   2825 TGCTCAAAATTAATAAATGT 2844
                                v  i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.93 (27 / 14)  


3191 27.28 0.44 0.55  chrX_78987942_78994218     4876  5784 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_78987942_7   4876 TAGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4925
                          i   ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_78987942_7   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_78987942_7   4976 TACCAATGACTTTCTTCACAGAATTGGAAGAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     v v  v--  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chrX_78987942_7   5025 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_78987942_7   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_78987942_7   5125 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_78987942_7   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5222
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_78987942_7   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_78987942_7   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_78987942_7   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_78987942_7   5373 TTAAAGATTTAAACGTTAGACCTAAAACCATAACAACCCT-AGAAGAAAA 5421
                          i ?   ii    i  v   v       i    -   i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAA 545

  chrX_78987942_7   5422 CCTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCCA 5471
                          v    ?i v viv   iv   viv  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_78987942_7   5472 AAACACCAAAGGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5521
                         vi        i   vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_78987942_7   5522 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5571
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_78987942_7   5572 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGATA 5621
                         v  i     i   iv            v  i    vii ivi        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_78987942_7   5622 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5671
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_78987942_7   5672 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5721
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_78987942_7   5722 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATTCTCAT 5771
                            v        i  vi viii     v  i          i  v    v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_78987942_7   5772 CATCACTGGCCAT 5784
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


 465 29.30 0.00 2.55  chrX_79028377_79032961.rev     2872  3028 (1557)    L1M4_orf2#LINE/L1        1   153 (755)  

  chrX_79028377_7   2872 TAGAAATACATCCCATGCTTATTAATTGGAAGGATCAATATTGTCAAAAT 2921
                          i    v i        i i  vi        iv i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79028377_7   2922 GAGCATACTGACCAAAGCAATCCATAGAATCAATGCAATTCCTATCAAAA 2971
                          ivv     vv     vii   i i   v    i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79028377_7   2972 CACCAATATCATTTTTTATGGAATTCAAAAAAACATTTCAAAAATTCTAT 3021
                         iv   iivv v      iii   v ii v  iviiv i v       ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC--- 147

  chrX_79028377_7   3022 AATATGG 3028
                         -      
  L1M4_orf2#LINE/    148 -ATATGG 153

Transitions / transversions = 1.56 (28 / 18)
Gap_init rate = 0.01 (1 / 153), avg. gap size = 4.00 (4 / 1)  

2015 27.67 3.64 1.08  chrX_79028377_79032961.rev     3391  4131 (454)    L1M4_orf2#LINE/L1      149   908 (0)  

  chrX_79028377_7   3391 TATGAAACAAACAAAAAAGCCTGAATAGCCAAAGCAATCCTAAGCAAAAA 3440
                             i  - vi   iii v  v           i     i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_79028377_7   3441 GTACAAATCTGAAAGCATCACATGACCCAACTTCAAATTATACTACAAAG 3490
                          v     vi  i i vv     ivv     i      viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_79028377_7   3491 CTAGCATATCCAAAACAGCATTGTACTGGCATAAATGTAGATATATAGAC 3540
                            vvi  vi   i    ii v            ivi    i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_79028377_7   3541 CAATGTAATAGAAGAGACAACTCAGAAATAAAGCCAAATACTTACAACCA 3590
                              v       vv  v iii          v   v i i   iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_79028377_7   3591 ACTCATCTTTAACAAAGCAGACAAAAATATATATTGGAGAAAGGACATGC 3640
                          i v  i  ii    i vv v   i vi  vi v   i     i i vv 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_79028377_7   3641 TATTCAATAAATGGTGCTGGGAAAACTGGATAGCCACATGCAGAAGAATA 3690
                          v     i              v         ?         i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_79028377_7   3691 AGACTGAATTCCAATCCCTTACGGTCTACAAAAATCAACTCAAGATGAAT 3740
                          iii  i ii  v i i vi  vi v         i       i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_79028377_7   3741 GAAAGACTTAAATCTAAG-GCACAAAACAATAACAATTTTAGAAGAGAAA 3789
                         v ?    i     v    -  -i     v    v v i        -   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGA-AAA 545

  chrX_79028377_7   3790 C-TAGAAAAACACTTTTGT-ACGTTGGCCTAGGCAAATAATTTATAACTA 3837
                          -   i?iv v ii  i  -  v    vi       - ii   v ---  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT---TA 591

  chrX_79028377_7   3838 AAAAT----CCAAAAGCAAATGCAACAAAAAGAAAAATACATG----GCA 3879
                         i v  ----         v v         ii       v  i---- v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_79028377_7   3880 CCT------AATTAAAAATCTTCTGTACAGCAAAAGAAATAGTCGTCATA 3923
                          i ------         -   i   i vv    i  v ivi  ivv v 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_79028377_7   3924 GTAAACAGACAGCCCACAGAATGGAAGAAAATATTTGCAAACTATGCATC 3973
                           i  v     i            i                ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_79028377_7   3974 TGGCAAAGAACTAATGTCAGGAGTCTACAAGAAACCCAAACAA----ATA 4019
                           ii  i i   vi i  vi  i v  i  ii   i vv    ----   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_79028377_7   4020 AGCAAGAAAAAAATGATTCTATCAAACAGTGGGCAAATAACACAAATACA 4069
                          vv  i i v    i ii v  i?  v i        vi ivii    v 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_79028377_7   4070 CATTTCTCCAAAGAAGA-ATATCACTAATCATCAGGGAAATGCAAA---- 4114
                                          -   iv v iii  vi i v v   v   ----
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_79028377_7   4115 -TTAAAATCACAGTGAGA 4131
                         - i  v    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (120 / 81)
Gap_init rate = 0.02 (15 / 760), avg. gap size = 2.33 (35 / 15)  


2449 26.81 3.45 2.45  chrX_79054794_79057310     1126  2024 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79054794_7   1126 TGAAAAGATACCCCAAACTCATGGACTGGAAGAATTACCATCATTAAAGT 1175
                           i       i    vii       i       v   vi  ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79054794_7   1176 CACCATGCTACCCAAAGAAATCCACAGATTAAATGTAATCCTTATAAAAA 1225
                         vi v  i  v      vvi   i       v  i i     i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79054794_7   1226 TGCCAGT--CATTTTTCAGAAAAATAGAAAAAGAAATTCTAGAATTTGTA 1273
                          v    i-- v     iiv i    v  v  ivvi  i   i    ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_79054794_7   1274 TGGAACCAAGACAAAG--CCCA-AATAGCCAAAGCAATTCTCAGCAAAAA 1320
                              --- vi   i --    -          i    ii v iv  i  
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_79054794_7   1321 GAACAAAGTTGTAGACATCACATTATCTGACAACAAAATATATTAATTAC 1370
                                    v  ivv     i vi ii ivv     i---   -i   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC---TTA-CTAC 243

  chrX_79054794_7   1371 TAATCTATAGTAACCAAAACAGCATCATACTGGCATAAAAACAGATATAT 1420
                         v  v   i     i   i    ii vi           ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_79054794_7   1421 TGATCAATGGAACAGAGTAGAGGGCCTAGATACAAATCTATGCATTTACA 1470
                         v           i   i v   i i i   v i   i i  i      ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_79054794_7   1471 ACCAACTTATTTTTGACAGAGGTGTC--TCTCATTTAA----AAAGGGGG 1514
                         ii   i v     i    ii    i --vvi    i  ----i  i iiv
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_79054794_7   1515 AGTCTCTTGAATAAATGTTGCTTGCAGTACTGGATGGATATCCATATGCA 1564
                              i  v  i     v    v v vv       ---- ?   i     
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT----AKCCACATGCA 439

  chrX_79054794_7   1565 GAAGAAAAGAATGAAACTTGATCCGTATATCTCCCTACATA-AAACATCA 1613
                         -----          ii v  i  v  iv  v v i i   -   v  i 
  L1M4_orf2#LINE/    440 -----AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_79054794_7   1614 ATTAAAAA---AT-AAAAATATAAATATTAAGTCCTGAATCTATAAAACT 1659
                          i v    ---  - ? i iv     i -   vv  i  v          
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACT 533

  chrX_79054794_7   1660 AGTAGAAAAATACATTGGA-CAAATGCTTCAGGACATTGGTCTTGGCAAA 1708
                         vv     i  v    v  ?-i    -    iv   v    vi v     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_79054794_7   1709 GAGTTTTTG---------TCAAAAGAACAGTCAACTAGATTAAAAAAAAT 1749
                          iv  i  i---------i      v   iv    - i -- i       
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-AAA--AGAAAAAAT 629

  chrX_79054794_7   1750 AGACACATGGGACTACATCAAGGTAAAAAACATTTTGTATAGCAAATGAA 1799
                            i v  v     v      ii v      -      iivv    v  v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGAC 678

  chrX_79054794_7   1800 ACAATTAA---AGTGAAAAGACAACATACCAAATCAGAAAAAAATTTTGC 1846
                           v  i  ---              vi  vi   vi  i    vv     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_79054794_7   1847 AAACTTTCCATCTGACAAGGTATTAATAAGCAAAATCGATAAGAAATTCA 1896
                            iiv vi      i    v i vi  vv  i   vv    ii  i  v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_79054794_7   1897 AACAACTCAGTTGGAAAAA-ATATATAATTTAAT-AAAAAATAGGTAAAA 1944
                         v        i viv     - i v    iii   -?      i  i   i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_79054794_7   1945 TATCTAAATAATCATTTCTCTAAAGAAGACATACAAATGGCCAACAGGTA 1994
                         v  i i    iv        i        i              i i i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_79054794_7   1995 CATATAAAAATGTTCAACATCACTAATCAC 2024
                            iv   i   i         ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.30 (53 / 23)  


1852 27.88 5.41 2.08  chrX_79057565_79059285      500  1220 (501)    L1M4_orf2#LINE/L1      123   867 (41)  

  chrX_79057565_7    500 AATTAACACGTTGATTCTCAAATTTAT---GAAATGGCAAAGGATCTGAA 546
                             i   v i    i  v     i  ---      -   i   i iii 
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATG-CAAGGGACCCAGA 171

  chrX_79057565_7    547 ACAGCCAATATAATTCTT--AAAATAAGACCAAATTTGGAG-----ACAG 589
                          i      v i   -   --    v    v    v      -----   v
  L1M4_orf2#LINE/    172 ATAGCCAAAACAAT-CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_79057565_7    590 GTATCTGGTTTCAAAACTTACTAGAAAACTATGGTCATTAAGACAGCATG 639
                         v -i iii               v   i   ii  v  i       ii  
  L1M4_orf2#LINE/    221 TT-CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_79057565_7    640 GTGTTAGCATTAAGACAGATAAATAGAGCAATGGAATACAAT--AGAGTC 687
                           ii i    v i  i   i v     v          v   --      
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_79057565_7    688 TATTTCTAGACTCACA----TATAATCACTTAATTTTCCACAGAAGTGAC 733
                         i vvvv  i  i  i ----   ii   v  i      v   iii   v 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_79057565_7    734 AAGGTAATTCAGTGTGGAAAGCAGGGACTTTTCAA-----GGTGCTGGAA 778
                            iiv     i  v      v vi v        -----        i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_79057565_7    779 AAACCAGATATCCATATACAGAAATATTAACCTCAATTCCTACCTTATAT 828
                         v   ii    ?   i  i  i  iv  v  vi vi ii       i i i
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_79057565_7    829 CACAAAGAATAGTTGATTCAAGATGAACAATCAACTTAAACATAAAAGCT 878
                           i v v  v i  i i    i   i iv ?vi  i    ii   i    
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_79057565_7    879 AAGACTAACATGTTTCTAAAGAAAAACATAGA---ATATTTTTACAGC-- 923
                           i    vv vii ii  i ii         i--- v  i  iiiii --
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_79057565_7    924 ----TTAAGCAAAGATTTGTTTTAAGCAAATTACAC-AAAAGCACTA--A 966
                         ----   i    v i   v  ---  - v  v    -        v -- 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTT---AG-ATATGACACCAAAAGCACAAGCA 615

  chrX_79057565_7    967 ACATAAACAAAAA-AGATAAATGATACTTCATCAAAATTAAAACTATCTG 1015
                            v  iv     -        viv                  viv i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_79057565_7   1016 CTCATCAAAAAATAC-ATTACCTAACTGGTAACGCAAATTACAGACTTGG 1064
                         iv v     ii i  -  i vvv  v  iv  vi   vii     v v  
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_79057565_7   1065 AGATAATACTTGCAATTCACATATAGAACAAAGGACTC--AACCAGAATA 1112
                            v    i      v   i    vvi i  i     i-- v        
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_79057565_7   1113 TGTAAAAAAATAAAACCCTTCTATAATTAGACTATAAAAAGAAAAACAAA 1162
                          i    i  --------  ii  i  i vi iv         v   i  v
  L1M4_orf2#LINE/    766 TATAAAGAA--------CTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_79057565_7   1163 CTGATT--AAAATGAGCTAAACACTTGAATAGATACTTCACAGAAGAAAA 1210
                          ii   --      i  v  iv i         i i   v vi     i 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_79057565_7   1211 TATATGAGTG 1220
                             ii i  
  L1M4_orf2#LINE/    858 TATACAAATG 867

Transitions / transversions = 1.65 (124 / 75)
Gap_init rate = 0.03 (20 / 745), avg. gap size = 2.70 (54 / 20)  

 264 18.03 3.28 0.00  chrX_79057565_79059285     1361  1421 (300)    L1M4_orf2#LINE/L1      846   908 (0)  

  chrX_79057565_7   1361 CCCCAAAAAA--TATGTAAATGGATAATTAGCATGTGAGAAGATCCTCAA 1408
                          i     i  --   ii      vi   v    ii   i     v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_79057565_7   1409 CATCAAGAGTCAT 1421
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.02 (1 / 63), avg. gap size = 2.00 (2 / 1)  


2629 26.24 1.80 3.38  chrX_79070362_79072590.rev      851  1738 (491)    L1M4_orf2#LINE/L1       35   908 (0)  

  chrX_79070362_7    851 TCAATATTGTTAAAATGGCCATACTTCCCAAAGCAATCTACAGATTCAAT 900
                          i           i     v     i      vii              i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chrX_79070362_7    901 TCTATTCCTGTCAAACTATCTATGACATTCTTCACATAATTAGGGAAAAA 950
                         v v  i   i     v vi viivi v  i  ii  v  v v ----- v
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG-----AC 129

  chrX_79070362_7    951 AAACT-ATTTTAAAAGTCATATGGAACCAAAACAGGGCTTGAATGGCCAA 999
                           i  -  ii     v          viiv  vi iv iv    i     
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_79070362_7   1000 GGCAATTGAACAAAGACCATGAACAAAGAACAAAAGAACAAAGCTGGAGG 1049
                         ii    ----------- v    -      -----        i      
  L1M4_orf2#LINE/    180 AACAAT-----------CTTGAA-AAAGAA-----GAACAAAGTTGGAGG 212

  chrX_79070362_7   1050 CATCATGTTACCCAACTTCAACCTATAATACAAGGCTGTAGTAAACAAG- 1098
                         vv   iii v     i     vviv  v     i   ii     v    -
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_79070362_7   1099 CAGCATGGTATTGCTACAAAAACAGATACATAGACCAATGTGACAGAATA 1148
                            ii     i  vi i  ii i   i i     i     vi i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_79070362_7   1149 GAGAGCCCAGAAATAATGCCACACACTTAAAACCATCTGATCTTTGACAA 1198
                              i          vv   i   i   viii  vi    i  i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_79070362_7   1199 ---TGCCCACAAAAACAAGCAATGAGGGAAGAACTCCCTATTTAATAAAT 1245
                         ---    ---  i v  vv     i  i     ivvi  v  i  i    
  L1M4_orf2#LINE/    363 GGGTGCC---AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_79070362_7   1246 GGTGC-----CATATGGCTAGCCATATGCAGAAGATTGAAACTGGACACC 1290
                              -----  vv   v  ?   i     i    v    ii     v  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_79070362_7   1291 TTCCTTACACCATATGCAAAAATCAACTCAAGGTGAATTAAAGACTTAAA 1340
                          v   i         i       i       ii  i  i ?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_79070362_7   1341 TGTAGAAACTAAAACTATAAAAACCTGGGGAGATAACCTAAG---AAATA 1387
                             ii i              vi  vi i   v   v  i ---    -
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT- 558

  chrX_79070362_7   1388 CCATTCTGGATATAAGACCTGGCAAAGATTTCATTATGA-A-GATGCCAA 1435
                         - -   vv  iv vi iiiv     v i    -   -  - -  ii    
  L1M4_orf2#LINE/    559 -C-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTA-GATATGACACCAA 604

  chrX_79070362_7   1436 AAGCAATTGCAACAAAAACAAAACTTGACAAGTGGGACCTAATTAAACTA 1485
                              vvv         iv    v v  i  i v    i v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_79070362_7   1486 ACGAGCTTCTGTGCAACAAAAGTAAATATCAACAGAGTAAACAGATAACC 1535
                          vi i   i     vv    i vv v      v i   i  v   i    
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_79070362_7   1536 TACAGAATGGGAGAATATATTCACAAACTATGCATCTGACAAAGTTCTAA 1585
                         i              v     ii    ii  ii      i  i vv  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_79070362_7   1586 TATCCAGAATCTATAAGGAACTTAAGTGAATCAACAAAGAAAAGACAAAC 1635
                                   v     i     ivviii v    i  vi          i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_79070362_7   1636 CACACCATTAAAAAGTGGGCAAAGGACATGAACAACCACTTTTCAAAAGA 1685
                         v  v v   ?    i           iv    i iv  i  i  v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_79070362_7   1686 AGACATAAACGCAGTTAACAAACGTATAAAAA-ATGCTCAACATCACTAA 1734
                            i   v viii ii  i  i ii  i    -             ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_79070362_7   1735 TCAT 1738
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.02 (17 / 874), avg. gap size = 2.71 (46 / 17)  


2312 25.00 2.04 3.06  chrX_79103014_79104776.rev      489  1272 (491)    L1M4_orf2#LINE/L1      133   908 (0)  

  chrX_79103014_7    489 CTGTTCCCAACA---ATATGGAACCAAAAAAGAGCCTGCATAGCCAAATC 535
                            v   i  v ---        viiv  ii  v  v v         v 
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chrX_79103014_7    536 AAGATTAAGCAAAAAGAACAAATCTGGAGGCAACACATTACCCAACATCA 585
                           vv  i iv  i         vi      vvv    i v     iv   
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_79103014_7    586 AACTATACTACAAGGCTATATTTACCAAAAGAGCATCATATGATACTGGA 635
                           viv        i    i v v i   i v  ----- i  i      v
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAG-----TGTGGTACTGGC 277

  chrX_79103014_7    636 ATAAAAACAGGCATGTAGACCTATGGAAGAGAATAGAGAG--CAGAAAAT 683
                             ii i  i   i    i v      v     v     --      --
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA-- 325

  chrX_79103014_7    684 TAAAACCA-ATCCTTACAACCAACTCGTCTTTGACAAAGCAAACAAAAGC 732
                             v   - ivi   iiii   i vi i  i     i vviv   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_79103014_7    733 ATAAAGAGGGAAAAGACACCCTATAAGACACCCTATTCAACAAATGGTAC 782
                           vv iv   i     ------   i-----i  v             i 
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGA------ATAG-----TCTTTTCAACAAATGGTGC 414

  chrX_79103014_7    783 TGGGATAATTGGCAAGCCACATGTAGAAGAATGAAACTGGATCCTCATCT 832
                              i  i   vv ?       i i         ii    i  ii i  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_79103014_7    833 CTCACCTTATACATAAATCAACTCAAGATGGGTCAAAGACTTAAATCTAA 882
                          v    v      v    i       i    i   ?    i     v   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_79103014_7    883 GACCTCAAACCATAAAAATTCTAGAAGGTAACATTGGAAAAACCCTTCTA 932
                           v  v    i      v ii      iv     v  ?iv  vi    vv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_79103014_7    933 GACATTGGCTTAGGCAAAGACTTCAT-GACCCAGAAC-CCAAAAGCAAAG 980
                            v    v        v ii   v -  i-- vi  -         v i
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGACACCAAAAGCACAA 612

  chrX_79103014_7    981 GCAACAAAAACAAAGATAAATAAATAGATGGGAGTTAACTAAACTAAAAA 1030
                                  iv   i   i      ---   ivv i v v   i      
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAAT---TGGACTTCATCAAAATTAAAAA 659

  chrX_79103014_7   1031 GCTTCTGCACAACAACAGAAATAGTCAGCAGAGT----AGACAACCCACA 1076
                         -   i  ii vv   vi  v ivi   iv i   ----            
  L1M4_orf2#LINE/    660 -CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_79103014_7   1077 GAGTGGAAGAAAATCTTTATAAACTATGCATCCGACAAAGGACTAATATC 1126
                           i   i       v   ii   ii  ii   i  i  i     vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_79103014_7   1127 CAAAATATACAAGGAACTCAAAGAAATCAGCA-TGAAAAAA-AAATTATC 1174
                           i      i  i      vv v  v   ii - i    i -    v i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_79103014_7   1175 --ATCAAAAAGTGGGCTAAGGACATGAATAGAGAATTCTCAAAAGATGAT 1222
                         --  i?    i     v     iv        v v     v     v   
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_79103014_7   1223 ATACAAATGGCCAACAAGCATATGAAAAAGTGCTGAACATTATTAATTAT 1272
                                       i     i       ii    v     i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (109 / 83)
Gap_init rate = 0.02 (16 / 776), avg. gap size = 2.50 (40 / 16)  


 741 29.05 1.66 0.83  chrX_79121033_79128833.rev      253   493 (7308)    L1M4_orf2#LINE/L1       15   257 (651)  

  chrX_79121033_7    253 ATGCTCATGGATTGGAAGAATCCATATTGTTAAAGTGGCCATACCACCCA 302
                            i               v iv          ii    v    iv    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_79121033_7    303 AAGAAATCTACAGATTTAATGCTATTTCTATCAAGCTATAAA-TGTCATT 351
                           vvi           i  i  v  ii       iv viv i-  i -  
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TT 113

  chrX_79121033_7    352 TTTCACAGAACTAGAAAAAAT--TTCCAAAATTTATATGGAACCAGAAAG 399
                            ii     v v  v  iv -- i i      i        viiv  i 
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chrX_79121033_7    400 TAGCACAAACATCCAAAGCAATCCTAAGCAGAAAGAATAAAGCTGGAGAC 449
                         v v vvi  i v     i     i i iv ii     i    i     iv
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_79121033_7    450 ATCCCATTACCTGACTT-GAAACTATGCTATAAGACTACATTAAT 493
                         v  v  i v  ii i  -i     - i   i  ii     v    
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAAT 257

Transitions / transversions = 1.59 (43 / 27)
Gap_init rate = 0.02 (5 / 243), avg. gap size = 1.20 (6 / 5)  

3039 26.99 1.11 0.66  chrX_79121033_79128833.rev     4997  5900 (1901)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79121033_7   4997 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATC-TGAAAAT 5045
                              ii    i     i      i v      v i     i- v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79121033_7   5046 GGCCATACTGATCAAGGTAATTTATAGATTCAATGCCATCCCCATCTAGC 5095
                            v     vvi   iv i  i  i        i  v     i   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79121033_7   5096 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_79121033_7   5144 TATGGAATCAAAAAGAGCCC-GCATTGCCAAGACAATCCTAAGCCAAAAG 5192
                                viiv  i ii   - v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_79121033_7   5193 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5242
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_79121033_7   5243 TACAGTAACCAAAACAGCATGCTACTGGTACCAAAACAGAGATATAGACC 5292
                                 i   i    ii  v      i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_79121033_7   5293 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5340
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_79121033_7   5341 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAATGGATTCC 5390
                          vi    i  i     ivv  v   i v  vvv         v i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_79121033_7   5391 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5440
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_79121033_7   5441 GAAACTGGATCCCTTCCTTACACCTTATGCAAAAATCAATTCAAGATGGA 5490
                            ii    i    v   i     v   i       i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_79121033_7   5491 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5540
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_79121033_7   5541 CTAGG--TAATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACG 5588
                         v    --   - i -   iv   v v  vv i     v ii   v iivv
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_79121033_7   5589 AAAACACCTAAAGCAGTGGCAACAAAAGCCAAAACTGACAAATGGCATCT 5638
                          vi     v      vvi          vv    iv  i    v v ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_79121033_7   5639 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5688
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_79121033_7   5689 ACTGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5738
                          vv i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_79121033_7   5739 AAAGGGCTAATAACCAGAATCTACAAAGAACTCAAACAAATTCACAAGAA 5788
                           i  i  vi  v       v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_79121033_7   5789 AAAATCAAACAACCCCATCAAAACGTGAGCAAAGTATATGAACAGACACT 5838
                            iv    i     v  i?   vi  i      v  v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_79121033_7   5839 TTTCAAAAGAAGACATTTATGCAGGCAACAG--ACATGAAAAAATGCTCA 5886
                          i  v        i  vi viii v   i i--         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_79121033_7   5887 TCATCACTGGCCAT 5900
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  

1581 29.02 3.01 3.01  chrX_79121033_79128833.rev     6652  7316 (485)    L1M4_orf2#LINE/L1      244   908 (0)  

  chrX_79121033_7   6652 AAAGACTACTTTAAACAAAACA---TGATACTGGTACAAAAACAGACACA 6698
                             -    vv   v   i   ---  i      i i  ii i     i 
  L1M4_orf2#LINE/    244 AAAG-CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_79121033_7   6699 TAGACCAATGGAACAGAACAGACAACCCAGAAATAAAGCCACACACCTAC 6748
                             i        i    iv  v ii           v   i   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_79121033_7   6749 AGCCATCTGATCTTTGACAAAGTCAACAAAAAAAAAAAATGAGGAAAGGG 6798
                         i i  vi    i  i     i viiv   i vv vvv    i      ii
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_79121033_7   6799 CTCTCTATTCAATATATGGTTCTGGGGTAGCTGGCTAGTCATATGCAAAA 6848
                         ivv   v     i v     v     ii i    v  ?i  i        
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_79121033_7   6849 GAATGAAAATGGGCCCATACCTTTCACCGTATGCAAAAAATAACTCAAGA 6898
                                iv   i   v     iv    i   i      v        i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_79121033_7   6899 TAGATTAAAGATTTCAGTTTTAGAGTTA------TAAGATTCCTAGAAGA 6942
                          i   i ?   ii v i v v    i  ------   i i  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_79121033_7   6943 AAACCTGGAAAACACTATTTTGGATATCGGCCTTAAGACA--GATTTCAT 6990
                             v i i?ivv v v  ivv  iv i  vi --  i  -- i    v 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTT--AGGCAATGGTTTCTT 590

  chrX_79121033_7   6991 GACAAAGATACCAACAGCAATTGTGACAAAA-ACAAACTTGACATGTAGG 7039
                         iivv v  i     v    vvv ii      - v   v v  i vi v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_79121033_7   7040 ACCTAAT-AAAATCAAAAAGCTTCTTTATAGCAAAAAAAAAAAAAAAAAA 7088
                           i v  -     i     -   i v iivv    ii v ----------
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA---------- 679

  chrX_79121033_7   7089 GATTATCAGCAGAGTAAACAGATGGCCTAGAGAATGAAATAAAATATTTG 7138
                         --i     iv i   i  v   iii  i v      ii v          
  L1M4_orf2#LINE/    680 --CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_79121033_7   7139 CAAAG-GTACGTCCAACAAAGGTCCAATATCCAGAGTCTATAAGAAATTG 7187
                             v-i  ii  ii i  i  v ivi        i v     ii  i v
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_79121033_7   7188 TTTTAA---AATATACAAGCAAAAAACAAATAAACCCATTAAGAAGTGGA 7234
                           vi  ---    - i  ---   i        v  v   ? i  i   i
  L1M4_orf2#LINE/    778 TTACAACTCAATA-ATAA---AAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_79121033_7   7235 CAAAGAACATGAGCAGACACTTCTGAAAAGAAGACATGCAAGCATCTCAC 7284
                              i iv   ii     i    vv        i  i   iiiv iv i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_79121033_7   7285 AA--ACATGAAAA-ATGCTCAGTCTCACTAACCAT 7316
                           --         -       iiv   ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (117 / 72)
Gap_init rate = 0.02 (15 / 665), avg. gap size = 2.67 (40 / 15)  


2791 25.51 4.00 1.14  chrX_79129339_79132906.rev     2204  3077 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_79129339_7   2204 ATTCCATGCTCATGGATAGAAATAATCAATACTGTTAAAATAGTAATATT 2253
                           i     i        v i  v v i    i      i  i i    i 
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_79129339_7   2254 ACCCAAAACAATCTACAGATTCAATGCTATTCCTACCAAACTACCAATGA 2303
                         v      vii              i  v  i    i    v v   iivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_79129339_7   2304 CATTATTTGCAGAATTAGAAAAACT-ATATTAAAATTTGTATGGAAACAA 2352
                          v  v         v v  v  i  -  vi       ii        iiv
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_79129339_7   2353 AAGAGAGCTTGAATAACCAAG-CAATCCTAAGAAATAAGAACAAAGCTGA 2401
                            i  v iv     i    i-     i i i   v          i  i
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_79129339_7   2402 AGACATCATGTTACATAATTTTAAACTATATTGTAAGGCTACAGTAACCA 2451
                           ivv   iii v vi     i   viv  i ii  i          i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_79129339_7   2452 AAACAGTGTGGTACTGGTACAAAAACAAACTCATAGACCAATGGAACAAA 2501
                          i               i i  ii i i  vi     i        i i 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_79129339_7   2502 ATAGAGAGCCCAGAAATAATACCACACATCTACAACCATCTGATCTTTGA 2551
                           v     i          vv   i    i  iiii  vi    i  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_79129339_7   2552 CAAATCTGACAAAAACAAGCAATGAAGAAATGACTCTCTCTTTC--TAAA 2599
                            ivv  v   i v  vv     ii    vi ivv   -    --i   
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT-TTTCAACAAA 408

  chrX_79129339_7   2600 -GGTGCTGGCATAACTAGCTGGCCATATGCAGAAGACTGAAAGTGAAACC 2648
                         -        v i    i v i?   i     i    v    iv  i v  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_79129339_7   2649 CTTCCTTACACCACATGCAAAAATCAACTCAAGATTGATTAAAGGTTTAA 2698
                           v   i      i  i       i       i  v   i ?  iii   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_79129339_7   2699 ATGTAAAGCCTAAAACTATAATGCACTGA-AAGATAACCTAGG---AAAT 2744
                               iiv            vi v  v -    v   v    ---    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_79129339_7   2745 ATTCTAGAAATATGACCT-------GGCAAAGATTTCACTACGA-AT-AC 2785
                         v   -------i      -------     v i    -i  -  -  -  
  L1M4_orf2#LINE/    559 CTTC-------GTGACCTTGGGTTAGGCAATGGTTTC-TTA-GATATGAC 599

  chrX_79129339_7   2786 ACCAAAAA-ATTTGCAATAAAAACAAAAATTTATAAGTGAGACCTAATTA 2834
                                i- ivv    i    iv      vv    i vi   i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_79129339_7   2835 AAGT-----GCTTCTACATAGCAAAATAAACTATTAACAGGGTAAACAGA 2879
                           i -----i   i iiiivv    iv v     i  v ii  i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_79129339_7   2880 AAACCTACAAATTGGTAGAAAATACTTGCAAACTATACATCTGACAAAGG 2929
                         v    i   i v   v        i       ii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_79129339_7   2930 TCTCATATCCAGAGTCTATAAGAAATTT----AAATCAACAAGGAAAA-- 2973
                         v  ii        i v     ii  i i----  v    i  vi    --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_79129339_7   2974 CAAA-AA---AATTAAAAAGTGGGCAAAGGACATGAACAGGCACTATTCA 3019
                             -  ---    ?    i           iv    i  i  i vi  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_79129339_7   3020 AAAGAAGACAAAAATATGGCCAATAAGCATATGAAAA-ATGGTCAACATC 3068
                                 i v v v              i       -   v        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_79129339_7   3069 ACTAATCAT 3077
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.72 (139 / 81)
Gap_init rate = 0.02 (20 / 899), avg. gap size = 2.25 (45 / 20)  


2836 27.97 1.33 0.55  chrX_79187156_79190853.rev     2307  3207 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79187156_7   2307 TGGAAACCCCTTCCATGCTCATGGATAGGTAGAATCAATATTGTGAAAAT 2356
                               vviv i     i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79187156_7   2357 TACCATACTTCCCAGAGCAATCTACAGATTCAATGCAATTCTCATTGAAA 2406
                         vi v     i    i vii              i     i ii  ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79187156_7   2407 TACCATCATCATTCTTCAAATGACTAGATAAAGCAATTCTAAAATTCATA 2456
                          v   v vv v  i  iiv vi v v  i  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_79187156_7   2457 TAGAATAAAAAAGGTGCCCACA-TAGCCAAAGCAATACTAAGCAAAAAGA 2505
                          i   - viv    vi    v -        i    vi i iv  i    
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_79187156_7   2506 ACAAATCTGGAAGCATCAAATTACCTGACTTCAAATTATACTACAGGGCT 2555
                              vi    i vv   v i v  ii i      viv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_79187156_7   2556 ATAGTTAACCAAAACAGCATGGTAATGGTATAAAAATAGGCACATAGGCC 2605
                          i   -  i   i    ii     v   i    ii    i  i    ii 
  L1M4_orf2#LINE/    250 ACAGT-AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_79187156_7   2606 AATGGAACAGAATAGAAAACTCAGAAATAAAGCCAGATATTTACAGCCAA 2655
                                i     v  i iii          v   v i     ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_79187156_7   2656 CTGATCTTTGAAAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCT 2705
                         i    i  i  v  i vviv   i v   vv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_79187156_7   2706 ATTCAACAAATCATTCAGGGATAACTGGCAAGCCACTTGTGGAAGAATAA 2755
                         v          vi v v    i      vv ?    v  iii      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_79187156_7   2756 AACTGTATCCTCCTCTCTCACTTTACAAAAAAATCAATTCAAGATGGCTC 2805
                          ii  v i  iivi   v   iv  i v      i  i    i    v  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_79187156_7   2806 AAAGACTTAAATCTAAGACCTGAAACCATAAAAGTTATAGAAAATAACAT 2855
                          ?    i     v     v  i    i      v iv     i v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_79187156_7   2856 ---CATAAAAACTTTTCTAGACCTTGGCTTAGGCAAATAATTCATGACTA 2902
                         ---?i    --- i   vv        v        vviv   v iiv  
  L1M4_orf2#LINE/    549 AGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_79187156_7   2903 AGACTCTAAAAACGAATGCAATAAAAACACAAATAAATAAATGGAACCTA 2952
                         v   v i    i iv v    i    iv v     i      v i  i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_79187156_7   2953 ATTAAACTAAAAGGCTTCTTCACAGCAAAAGAAATAATCAGCAGAGGAAA 3002
                           i   v v   ii   i vii vv    i  v iv    iv i  vi  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_79187156_7   3003 CAGACAACCCACAGAGAGGGAGAAAATATTTACAAACTATGCATCCAACA 3052
                         v              iv              i    ii  ii   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_79187156_7   3053 AAAGACTAATATTCAGAATCTATAAGGAACTC----AAATCAACAAGAAA 3098
                          ii    vi   i      v     i      ----  v    i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_79187156_7   3099 AA---AAATAATCCCATCACAAAATGGGCAAAGGACATGAATAGACAGTT 3145
                           ---      i  v  i?v               iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_79187156_7   3146 GTC-AAACAAGATATACAAACAGCCAACAAATATATGAACAAATGCTAAA 3194
                         v  -   v            ii     i  ii i     v i     v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_79187156_7   3195 TATTACTAATTAC 3207
                         i  i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


3030 27.81 0.77 0.55  chrX_79213196_79219602.rev     5011  5916 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79213196_7   5011 TGGAAGAACATTC-ATGCTCATGGGTAGGAAGAATCTATATCGTGAAAAT 5059
                              ii i  i -   i      i v      v iv    i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79213196_7   5060 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5109
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79213196_7   5110 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5157
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_79213196_7   5158 TACGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5207
                           i    viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_79213196_7   5208 AACAAAGCCAGAGGCATCACAATACCTGACTTCAAACTATAGTACAAGGC 5257
                                iii    vv     v v  ii i      viv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_79213196_7   5258 TACAGTAACCAAAACGGCATGGTACTTGTACCAACACAGAGATATAGATC 5307
                                 i   i  i ii       v i iv iv i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_79213196_7   5308 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5355
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_79213196_7   5356 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5405
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_79213196_7   5406 CTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCT 5455
                           v  i  i              v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_79213196_7   5456 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5505
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_79213196_7   5506 TTAAAGATTTAAACGTTAGACCTAAAATCATAAAAACCCTT-GAAGAAAA 5554
                          i ?   ii    i  v   v      ii      - i   -        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_79213196_7   5555 CCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCTA 5604
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_79213196_7   5605 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5654
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_79213196_7   5655 ATTAAACTAAAGAGCTTCTGCACAGCAAAGAA-ACTACCATCAGAGTGAA 5703
                           i   v v  i i   i  ii vv     i -    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_79213196_7   5704 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATATGACA 5753
                         v  i     i   i             v  ii   vii ivi  v   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_79213196_7   5754 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAC 5803
                          i  i  vi          v  i  v      vv    v iv i  v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_79213196_7   5804 AAAACAAACAACGCTATCAAAAAGTGAGTGAAGGACATGAACAGACACTT 5853
                           i     i   v v  i?    i  i ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_79213196_7   5854 CTCAAAAGAAGATATTTATGCAGCCAAAAACCACATGAAAAAATGCTCAC 5903
                            v           vi viii     v  v          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_79213196_7   5904 CATCACTGGCCAT 5916
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2313 25.86 1.54 3.91  chrX_79235268_79237104.rev      504  1346 (491)    L1M4_orf2#LINE/L1       86   908 (0)  

  chrX_79235268_7    504 CAATTCCCACCAAAATACCAGAATCATTCTTCACAGAGCTACAAAAAAAA 553
                             i  i i      v    vvv v  i  ii    ------------ 
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA------------A 123

  chrX_79235268_7    554 AAAGAAAAAA-AATCCTAAAATTCACATGGGGCCAAAAAAAAGCCTTCAT 602
                          vv  v  iv-i             i    iiviiv  iii v  vvv  
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chrX_79235268_7    603 AGCCAAAGCAAGACTAAGCAAAAAGAACAAATATGGAGGCATCACAATAC 652
                                i   vvi i iv  i         vv      vv     v v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_79235268_7    653 CTGATTTCAAACTATATTATAAGGCCATAGTCACCAAGACAGCATGGTAC 702
                          ii        viv  i  i  i  i i   v i        ii      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_79235268_7    703 TGGTACGAAAATAGGCACATAGAGCAATGGAACAGAATAGAGAACCCAGA 752
                            i ii ii    i  i     v        i     v    ii     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_79235268_7    753 AATAAACCCAAATACTTACAGCCAACTGATCTTTGACAAAGCAAACAAAA 802
                                   v i i   ii i   i    i  i     i vviv   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_79235268_7    803 ACATAAAGTGGGGGAAAGGACAACCTTTTCAACAAATGGTGTGGGGATAA 852
                         v   vv i     -    i i ii                 iv    i  
  L1M4_orf2#LINE/    374 CCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_79235268_7    853 TTGGCAAGCCGTATGTAGGAGAATAAAACTGAATCCTCATGACTCACCTT 902
                         i   vv ?  ii   i ii     i  ii  i i  ii ivv v    v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_79235268_7    903 ATACAAAAATCAACTCATGATGAATCAAGTACTTAAATCTAAGTCCTGAA 952
                                   i      vi   i    ?iv  i     v    vv  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_79235268_7    953 ACTATAAAAGT-TTAGAAGATAACATCCGAA-AAATCCTTCTAGACATTG 1000
                                  v -        v     vv ?i-     -   vv   v   
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chrX_79235268_7   1001 GCTTAGGCAAAGATTTCATGACCAAGA-ACCGAAAAGCAAATGCAGCGAA 1049
                          v        v i    v iivi v  -   -       v v   i i  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACC-AAAAGCACAAGCAACAAA 620

  chrX_79235268_7   1050 AACAAAAACAAAAAAATAGGTGGGACTTAATTAAACTAAAGAGCTTTCTC 1099
                          iv     i i v    ---   -    v  i   v v  i i    ivi
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAAT---TGG-ACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_79235268_7   1100 ACGGCAAAAGGAATACT--CAGCAGAGTAAACAGACAACCCAAAGAGTGG 1147
                         i vv    i -- i   --  iv i   i  v          v   i   
  L1M4_orf2#LINE/    667 GCTTCAAAGG--ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_79235268_7   1148 -------TATCTTCACAATATATACATCTGACAAAGTACTAACATCCAGA 1190
                         -------   i v  -   -i   i      i  i v   vii       
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCA-AAT-CATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_79235268_7   1191 ATCTACAAGGAACTCAAAGAAACTAGCAAGAAAAACAAACAAACAAACAA 1240
                           v  i  i      vv v  -  --   v  -------i   v i    
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAA-CT--CAATAA-------TAAAAAGACAA 802

  chrX_79235268_7   1241 ACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTGAAAA 1290
                          i  i  v  i?    i     v     iv          v    vv   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_79235268_7   1291 GAAGATATACAAATAACCAACAAACATATGAAAGAATGCTCAATATCACT 1340
                                       ii    i  i  i      ii        i    ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_79235268_7   1341 AATGAT 1346
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.43 (126 / 88)
Gap_init rate = 0.02 (18 / 823), avg. gap size = 2.56 (46 / 18)  


2648 24.69 2.90 2.02  chrX_79253745_79255521.rev      499  1292 (485)    L1M4_orf2#LINE/L1      108   908 (0)  

  chrX_79253745_7    499 TACCATTTTTTACAGAAATAAAAAAATCCATCCTAAAATTTATATGAAAT 548
                          i  -      i       vi v  iiiv           i     i  v
  L1M4_orf2#LINE/    108 TGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_79253745_7    549 CTCATGGGATCCTGTGTGGCCCAAATGATGGTGAAAAA--AGAATA--GC 594
                         iv  v    i  v vi i   v   ii  vv       --    i -- i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_79253745_7    595 TGAAGGTATCATAATTCCTGCTTTCAAAACTTATTACAAAGCTACAGTAA 644
                           i   vv   i v    iiv            i                
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_79253745_7    645 TCAAAACAGTG--GTACTGGCATGAATACAGACATAAAGACCAACGGGAT 692
                             i      --          i iv i       v   i   i  i  
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_79253745_7    693 AGAATTGAGAGCCCAGAAATAGAGCCTTGTATATCTGGTTAAATATTTTT 742
                                    i         i v  v ii  v v    i  v iv    
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_79253745_7    743 TAACAAAGGTGTCATGAC-ATTAAATGAGAGAAGGACACTCTTTTCAATT 791
                         ii    i    i  v   -   v    i ii   i i v         iv
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_79253745_7    792 AATGGTTTTGGGAAAGCTGGATCTTCACATGCAAATAAATGATGTTGAAC 841
                               vi     v i      v?i          vi     v    i  
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_79253745_7    842 ATTTAAAGATAAGTAAAGTAAAGATATGCAAAACTTAACTCAAAGTAAAT 891
                         vii  vv-- ---i v vi ----   i     v          i ii  
  L1M4_orf2#LINE/    457 CCCTACC--T---CACACCA----TATACAAAAATTAACTCAAAATGGAT 497

  chrX_79253745_7    892 GAGAGACCTAAATATAAGGACTAAA-TTATAAATATTGTAGAAGCAGACA 940
                         v ?          i    ii     -i      vv iv      v i   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_79253745_7    941 --GGGGAAAAGCT-CATGACATTAGATTTGGCAATGTGTTCTTGAATATG 987
                         --  ? v   v  - i    v  i i  v       vv     ii     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_79253745_7    988 ACAC-AAAAATACTGACAATAACA-------T---TAAATTGGACCACAG 1026
                             -    ii  vii   i  v ------- ---          iv  v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_79253745_7   1027 AAAAATTAAAAACTTTCGTACATCAACAACCATAGTCAACTGATTAAAAA 1076
                         v               i  i v    viiv  ivi    vvi v i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_79253745_7   1077 TGCAACCTATGAAATTAAATGAAGTATTTTCAAATTAAATATCTGATAAG 1126
                         vi     i iii   vii vi  i     v     i v            
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_79253745_7   1127 AAATTAATGTTCAGAATATACAATGAACTCCTGCACCTCAACAACAAAAA 1176
                         ii i vi i i         i  v      i i  v     i  i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_79253745_7   1177 T-CAAACAACCAAATTTAAAAAATGGTCAAAAGACATGAATAACTGTTTT 1225
                         v-    i    v    ?     -   v    i  iv      ivii   i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_79253745_7   1226 TTTTTAAAAAAAGACATACAAATGGCCAAGAAGTACATGAAAAGATTCTT 1275
                          ii---   i    i              v   i            v  i
  L1M4_orf2#LINE/    847 TCC---AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_79253745_7   1276 AACTAATCATCAGGGAA 1292
                            --    ????????
  L1M4_orf2#LINE/    894 AAC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (116 / 76)
Gap_init rate = 0.02 (18 / 801), avg. gap size = 2.17 (39 / 18)  

1450 24.27 0.97 2.43  chrX_79253745_79255521.rev     1366  1777 (0)  C L1M4_orf2#LINE/L1   (362)   546   141  

C chrX_79253745_7   1777 AAATTTCATATGGAACAAAAAAAGAGCCCACA-TAGCCAAGACAATCCTA 1729
                            v           - viv  i ii    v -       i      i i
  L1M4_orf2#LINE/    141 AAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

C chrX_79253745_7   1728 AGCAAAAAAAAAAAAAAAGCTGGAGACATCATGCTACCTGAAA---CAAA 1682
                          ---    i  i  v    i     ivv   ii  v  i--  ---    
  L1M4_orf2#LINE/    190 A---AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC--AATTTCAAA 234

C chrX_79253745_7   1681 TTATACTACAAGGCTACAGTAACCAAAACAGCATGGCTGGCACTGGTACC 1632
                         viv        i          i   i    --  --   i     i iv
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAG--TG--TGGTACTGGCATA 280

C chrX_79253745_7   1631 AAAACAGATATATCAACCAAAGGAACAGAACAGAGGCCTCAGAAATAACA 1582
                          ii i   i    vi i   v    i    iv   ivii         vv
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

C chrX_79253745_7   1581 CCACACATCTACAACCATCTGGTCTTTGACAAACCTGACAAAAACAAGCA 1532
                            i    i  iiii  vi  i i  i     ivv  v   i v  vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

C chrX_79253745_7   1531 ATGGGGAAAGGGTTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAG 1482
                                   ii vvi  v  i  i        i     v      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

C chrX_79253745_7   1481 CCCTATGCAAAAAACTGAAAATGGACCCCTTCCTTACACCTTATACAAAA 1432
                           vi        i v    iv         v   i     v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

C chrX_79253745_7   1431 ATTAACTCAAGATGGATTAAAGATTTAAACGTAAGACCTAAAACCATAAA 1382
                                   i      i ?   ii    i      v       i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

C chrX_79253745_7   1381 AACCCTAGAAGAAAAC 1366
                          vi i           
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAAC 546

Transitions / transversions = 1.72 (62 / 36)
Gap_init rate = 0.02 (7 / 406), avg. gap size = 2.00 (14 / 7)  


 219 33.05 5.41 3.42  chrX_79255880_79259540.rev       52   402 (3259)  C L1M4_orf2#LINE/L1   (171)   737   380  

C chrX_79255880_7    402 AATGGAGTAATGATGGATTTCTTAAAAAACACATCTGG-ATA-CTGAATA 355
                              i v  vi  i vi  i i  v   iivvv    - i -   i   
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

C chrX_79255880_7    354 GCCATATGGAAGAAAGAGAAAATTGGATTTATCCTTTTTTAC----TATG 309
                         ?   i   v  i i - vi  i     ii---   vii i  ----   i
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGA-ATGAAGTTGGACC---CCTACCTCACACCATATA 475

C chrX_79255880_7    308 CAACAAGATAGATTTAAAATAAATCTGATATTTAAAATAATAAAAAATAA 259
                            -- i  vi i i     ii   v? v ii    - i-   i iv   
  L1M4_orf2#LINE/    476 CAA--AAATTAACTCAAAATGGATCAWAGACCTAAA-TG-TAAGAGCTAA 521

C chrX_79255880_7    258 AACCTATA----TTATAGAATAAAAACATGGATG-AATTCT--GTCACCC 216
                            -    ---- iv     -i       i i? -  v   --  v   i
  L1M4_orf2#LINE/    522 AAC-TATAAAACTCTTAGAA-GAAAACATAGGNGTAAATCTTCGTGACCT 569

C chrX_79255880_7    215 CCAAAGAGATAA-ACTTTTCTAGTTATTAT-TCAGAATAAAGAACTATGA 168
                         iviivv  ii  -iv   ii   v   v i-i  i  vv vi i v ii 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

C chrX_79255880_7    167 AGGCAAATATTAATATACTT-ATTACATTGAA-TTAAAAACAATATTTTA 120
                          i v   v  vi   v i v- i v   ii  -        -- v  v i
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC--TTTTGTG 667

C chrX_79255880_7    119 ATTTATAA-ATACTCTGAGCAATGTGAAAAAACAAATGACAGAATTTG-G 72
                         v  i v i- i   v v iv  v       i    viv       vv - 
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

C chrX_79255880_7     71 AAAATATTTACAATTTATAT 52
                                  i   v i    
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATAT 737

Transitions / transversions = 1.46 (67 / 46)
Gap_init rate = 0.06 (20 / 358), avg. gap size = 1.55 (31 / 20)  

1328 28.50 1.00 1.25  chrX_79255880_79259540.rev      850  1249 (2412)    L1M4_orf2#LINE/L1        3   401 (507)  

  chrX_79255880_7    850 GAAAGCTATACTGTCCTTATAAATTGGAAAATCTAATATTGCTCAAATGT 899
                              v   v ii vi i  ii       i ii        i v i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_79255880_7    900 CCATAATACTCAAAGCAATCTACAGATTCAATACAATCCTTATCAAACTT 949
                          v   v v i    vii              ii      i       v i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_79255880_7    950 CCAAAGAGCTTTGTCACAAAAATAGAAACAAACAATTTCTAAAATTTGTA 999
                            ivviv    v ii  i    v  --   i viv i        ii  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCATA 150

  chrX_79255880_7   1000 TGGAAATACTAAACACTT-GAATAGCCAAAGAAATCATGAATAACAAGAA 1048
                                i v iiv  ii-           iv    v    v  v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_79255880_7   1049 CAAAGCTAGGGGAACCACACTTCATGATTTGAAATTGTATTACAAAGCCA 1098
                              i i i   vi        vii    v   viv  i        i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_79255880_7   1099 AAGTAATCAGAATATGACGGTAATATCATAAAAACAGACACACAGACCGA 1148
                         v        ii i vvii    v iv     ii i     i i   i i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_79255880_7   1149 CAGAAGAAAATAGAGAGCCCAGGAATAAACTCACCCATATACAGTCAA-- 1196
                         ii   v i   v     i    i       i  iv   v  ii     --
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_79255880_7   1197 -ATTTTCTTGGACAAGGGCACTAAGAATACACTATGGGAAAAGGATAGCC 1245
                         -      ---        ii i    vi iv v     i    i    i 
  L1M4_orf2#LINE/    351 GATTTTC---GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_79255880_7   1246 TCTT 1249
                          i  
  L1M4_orf2#LINE/    398 TTTT 401

Transitions / transversions = 1.85 (74 / 40)
Gap_init rate = 0.01 (4 / 399), avg. gap size = 2.25 (9 / 4)  

1989 25.83 0.79 2.06  chrX_79255880_79259540.rev     2018  2648 (1013)  C L1M4_orf2#LINE/L1   (0)   908   286  

C chrX_79255880_7   2648 AGATTTATAGATGAATGGAACAGAACAGAGGCCTCAGAAATAATGCCATG 2599
                            iv       v       i    iv   ivii         vv    i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

C chrX_79255880_7   2598 CATCTACAATCATCTGAACTTTGACAAACCTGACAAAAACAAGCAATGGG 2549
                            i  iii   vi   vi  i     ivv  v   i v  vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

C chrX_79255880_7   2548 GAAAGGATTCCCTATTTAATAAATGGTGTTGGGAAAACTCACTAGCCATA 2499
                              i  vvi  v  i  i        i     v    viv  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

C chrX_79255880_7   2498 TGCACAGAGTTGAAACTGGATCCCTTCCTTACACGTTATACAAAAATTAA 2449
                             v iiiv    ii    i    v   i    vv              
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

C chrX_79255880_7   2448 CTCAAGATGGATTAAAGACTTAAACGTAAGACCTAAAATCATAAAAACCC 2399
                              i      i ?    i    i      v      ii      vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

C chrX_79255880_7   2398 TGGAGGAAAGCCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGA 2350
                          i  i    i v    ?i- v i -   iv   v v  vv i     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

C chrX_79255880_7   2349 CTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACA 2300
                         i   v iiv  vi            vvi          vv i   v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

C chrX_79255880_7   2299 ATTGGGATCTGATTAAA-TTAATAAGCTTCTGCACAGCAAAAGAAACTAT 2251
                          v v   ii v  i   -    -  i   i  ii vv    i  v     
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTAT 683

C chrX_79255880_7   2250 CATCAGACTGAACATGCAACCTACAGAATGGGAGAAAAATTTTGCAA--T 2203
                           vv i v    v vi     i                vv       --i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

C chrX_79255880_7   2202 ATATCCATATGACAAAGGACTAATATCCAGAATCTACAA-GAACTTAAAC 2154
                             --  v   i  i     vi          v  i  -     ivv  
  L1M4_orf2#LINE/    734 ATAT--ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

C chrX_79255880_7   2153 AAATTTACAAGAAACAAACAAACAAACAAACAACCCCACCAAAAAGTGGG 2104
                           v ---   v  -----i   v i     i     v ii?    i    
  L1M4_orf2#LINE/    782 AACT---CAATAA-----TAAAAAGACAAATAACCCAATTWAAAAATGGG 823

C chrX_79255880_7   2103 CAAAAGATATGAACAGACACTTTTCAAAAGAAGACATTTATGCAGCCAAC 2054
                             i   v    i     i  i  v        i  vi viii     i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

C chrX_79255880_7   2053 AAGCATATGAAAAAAAAGCTCATCATCACTGGTCAT 2018
                              i       i v-     v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (88 / 71)
Gap_init rate = 0.02 (10 / 623), avg. gap size = 1.80 (18 / 10)  

1397 26.00 4.78 5.54  chrX_79255880_79259540.rev     2649  3171 (490)    L1M4_orf2#LINE/L1      390   908 (0)  

  chrX_79255880_7   2649 GGATAGCCCCTTTTATAAAGGATGTTGGGAAAATTGGCTACCAACATGCA 2698
                          i    i ii  iv i   v i  i     v  i   v  ? v       
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_79255880_7   2699 AAAGAATTAAAATGAATCCTTATCTTACA---TATG-------------- 2731
                                v  iv  i i  i  i  i   ---   i--------------
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_79255880_7   2732 AGATGAGTTAAAGACTTAAATGTAAGACTTGAAACAATGAAAATTCT--A 2779
                          i   ii i ?    i           vi i    v  -    i   --i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAG 538

  chrX_79255880_7   2780 AAAAACACTTTGAGATAAGGCTTTTTTACATTAGTCTCCGCAATGGTTTT 2829
                           i  v  v v i?i   iv   iv v  v  i vi vv          i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_79255880_7   2830 TTGGATATAATAT-AAAAGCACAGGCAACACAAACAAAAATAAACAAATG 2878
                           i     i i i-         i      v  iv       i i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_79255880_7   2879 ACACTACATCAAAA----AAGTCTCTGCATTGCAAAATAAATAAATAGAT 2924
                         iv   v        ----  iii i  iii v    i-------------
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG------------- 675

  chrX_79255880_7   2925 AAATAAATAAATAAAACAACTATTTACAAAATGAAAAGGGAACATATGGA 2974
                         --------------i   -    iv v   i       iv   vi ii  
  L1M4_orf2#LINE/    676 --------------GACA-CTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_79255880_7   2975 GTGGGAGAAAATATTTGCAAACCATATATCTAAAAAGAGATTAACATCTA 3024
                         i                    i         i v   i  i vii   i 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_79255880_7   3025 AAATATATAAGGGACTCATAAAACTCAATAACCTATAAACAAATAACCTG 3074
                         i         i i    v  v          ivv v i          ii
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_79255880_7   3075 ATTACTAAATGGGCAAATTACCTAAAT-GACATTTTTCCATGAAAGACAT 3123
                            ?vv           vv ii i   -       i    vii    i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_79255880_7   3124 ACGAATGGACAACAGGTATATAAAACAAAACTCAACATCGCTAATAAT 3171
                           i     v   i i i i  i   vi vi         i????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (88 / 44)
Gap_init rate = 0.02 (9 / 519), avg. gap size = 6.00 (54 / 9)  


2324 27.59 2.78 1.78  chrX_79263656_79267554.rev     2510  3408 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79263656_7   2510 TGGAAATTCACCTCATACTCAGGTATTATAAGAATCAATATTATTAAAAT 2559
                               vvi i i   ii   v v   iv    v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79263656_7   2560 GACCATGCTACCCAAAGCAATCTACAGATTCAATACAATTCCTATCAAAT 2609
                          i v  i  v      vii              ii    i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79263656_7   2610 AACCAA-TGTCATTTTTCACAGAATTT------TTTTTTTAAAATAAAAT 2652
                         vv   i-  i -     ii     v  ------i vv ii----      
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCC----TAAAAT 145

  chrX_79263656_7   2653 TCATATAAAA---CAAAAAATCCTGAATAGCCAAAGCACTCCTAAAAAAT 2699
                               ii  ---   iii i  v           i  v  i i     v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_79263656_7   2700 GA---TAAATCTGGAGACCTCACATTGCCTGACTTCAAATTATATTACAA 2746
                         i ---i   vi     iv      i v  ii i      viv  i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_79263656_7   2747 GGCTATAGTAACTAAAAAAGTAGGGTACTGGTACAAAAATAGACACAAAG 2796
                         i    i     ii  i v   iv        i i  ii       i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_79263656_7   2797 ATCAAGGGAACAGAATAGAGAACCCAGAAATAAAACCACATGCCTACAAG 2846
                              v    i     v    ii           v   i iiii  iiiv
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_79263656_7   2847 AAACTGATTTTCAATAACATGGACAAAAGTAAACAATGGGAAAAGGACAC 2896
                         v  i        i i  vivv v   i vi vv       i    i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_79263656_7   2897 CTTATTAAATAAATTATCCTGTGAAAAATGGCTAGCCATATGCAAAATAA 2946
                         ii v  v  i    vi v   v  v  v   v  ?   i        v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_79263656_7   2947 --AAGT-GCACCCCTATCTCTCAGCATGTACAAAAATTAAATCAAGATGG 2993
                         --    - v       i   v  v   i            v    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_79263656_7   2994 ATTAAAGAGCTAAATATATAACATGAAGCTGTAAAAATCTTAGAA-AACA 3042
                           i ?   v      i  vi vv i  i  i     v        -  v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_79263656_7   3043 CTTAGAAA-AAACCTCTTCTGGACATCAGCCTAGGCAAAGAACTCAT-GA 3090
                          v   i?i-   --     vv   v ii vi       v ivi  v -  
  L1M4_orf2#LINE/    546 CATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_79263656_7   3091 TCAAGATCCCAAAAGCAATTGCAACAAGACCAAAAATAGACAAATGATAC 3140
                          - v  iv         vvv       i vv         i    viv  
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_79263656_7   3141 TTAATCAAA-TTAAAAAGCTTTGGCACAGCAAAAAAT-CAATAAATAAAT 3188
                           v      -       -    v ii vv    ii i- v  v  v   -
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA- 690

  chrX_79263656_7   3189 AACAAACAGAATCAATTATCTACAGAATAGGAGAAAATATTCACAAATTA 3238
                         -iii  v   --   i--- i       i            ii     i 
  L1M4_orf2#LINE/    691 -GTGAAAAGA--CAAC---CCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_79263656_7   3239 TGCCTCCGAGAAAGGATTAATACCTAAAATATGGAAAGAACTAAAATGAT 3288
                          iiv  i  v  i   i vi  i i i     iv        vvv ii i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_79263656_7   3289 TCAACAAGACAAAAATGGACAACCCCAT-AAAAACTGGGCAAACGACATG 3337
                             i  v v   i iii i     v  -?    v        v  iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_79263656_7   3338 AACATATATTTTTCAAAAAAAGAAACACAAGCAGACAGGAA--ACATAAA 3385
                           i v i    i  v   i    v i    iii v  iv  --    i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_79263656_7   3386 AA-ATGCTAAACATCACTAGTAAT 3408
                           -     v       ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.86 (41 / 22)  


3125 25.70 2.24 0.34  chrX_79334580_79341279     5317  6207 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79334580_7   5317 TGGAAAGACATTCCATGGTCATGGATAGGAAGAATCAATATCGTGAAAAT 5366
                                 i  i     v        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79334580_7   5367 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5416
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79334580_7   5417 TACCA-CTGACTTTCTTCACAGAATTGGAAAAAGCAACTTTAAATTTCAT 5465
                          v   -   v    i  -i     v v  v  ivii iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_79334580_7   5466 GTGGAACCAAAAAGGAGCCCACATAGCCAAGACAATCCTAAGCAAAAAGA 5515
                         i     viiv  i   v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_79334580_7   5516 ACAAAGCTGGAGGCATCACGCTACCTAACTTCAGACTATACTACAAGGCT 5565
                               i      vv    i  v  i  i    i viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_79334580_7   5566 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAATAGATATATAGACAA 5615
                                i   i    ii         i iv ii     i       iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_79334580_7   5616 ATGGAACAGAACAGAGGCCTCAGAAATAACATCACACATCTACAACCATC 5665
                               i    iv   ivii         vvi  i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_79334580_7   5666 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGTATTTCCTA 5715
                             i  i     ivv  v   i v  vv            v  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_79334580_7   5716 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCC-CTTGCAGAAAACTGAG 5764
                           i  i        i     v      v  ?  - v    i  i v   i
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_79334580_7   5765 ACTGGACCCCTTCCTTACAATTTATACAAAAATTAACTCAAGATGGATTA 5814
                         ii         v   i   viv                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_79334580_7   5815 AAGACTTAAATGTTAGACCTACAACCATAAAAACCCTAGAAGAAAACCTA 5864
                         ?    i       v   v   v   i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_79334580_7   5865 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 5913
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_79334580_7   5914 CACCAAAAGCAATGGCAACAAAAGCCAAAACAGACAAATGGGATCTAATT 5963
                                    vvi          vv    i   i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_79334580_7   5964 AAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATCATCCGAATCAACAG 6013
                            v v  i i   i  iv vv    i  v       vvvi i v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_79334580_7   6014 -CAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCACAACAAA 6062
                         -     i                 v       vii  vi   -ii i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC-TGATAAG 747

  chrX_79334580_7   6063 GGACTAATATCCAGAATCTACAAAAAACT--TA------AAT--TAAAAA 6102
                              vi          v  i   i    --  ------   --      
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_79334580_7   6103 ---AAAAAAC---ATCAAAAAGTAGGTGAAGGATATGAACAGACACTTCT 6146
                         ---   v   ---  i?    i i  ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_79334580_7   6147 CAAAAGAAGACATTTATGCAGCCAACAAACATATGACAAAAAGCTCATCA 6196
                          v        i  vi viii     i  i  i    v  i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_79334580_7   6197 TCACTGGTCAT 6207
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.34 (129 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


1692 26.10 1.59 1.99  chrX_79347688_79349749      499  1000 (1062)    L1M4_orf2#LINE/L1      114   613 (295)  

  chrX_79347688_7    499 TTTCCCAGAAATAGAAAAAAAAGACAATCTTCAAATTCATACAGAAATGC 548
                            iv       v  v  ---- vii   i v         ii       
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAA----GCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_79347688_7    549 AAAAGACTCTGGATAGTTAAAGCAATCATGAGCAAAATGTACCAAGCTGG 598
                           ii   i v i    ii   i     v   iv  i v v  v   i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_79347688_7    599 GGGCATTAATACAACTTAACTTTAAAATACACCACAAAGCTATAGTAACC 648
                         i  - i v i  vv ii  i  i    ivi  i         i     i 
  L1M4_orf2#LINE/    210 AGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_79347688_7    649 CAAACAACATGTTACTGGCCTAAAAACAAACACACAGACAAATAGAACAG 698
                         v i   iii  v       v   ii i i   i i   iv   i   i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_79347688_7    699 AAT--AGAATAACCAGAAATAAATCCACATGTTTACACCCAACATG-TAT 745
                            --   i --           i   i ii    iivi   i-  - v 
  L1M4_orf2#LINE/    309 AATTGAGAGT--CCAGAAATAAACCCATACATTTATGGTCAAT-TGATTT 355

  chrX_79347688_7    746 TTGACAAAGGCACCAAGAACATACACTGGGGAAAGAACAGTTTCTTCAAT 795
                          i     i  ii      v   v  v           i   i i     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_79347688_7    796 AAATGGTGCTGGGAAAACTAGACAACCATATGTAGAAGAATAAAAC-AGA 844
                                       v    i  i ?   i   i i      i  ii-i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_79347688_7    845 CCTCTGTCTCTTACCATATAGAAAACTCAACTCTAAATGGATTAAAGACA 894
                           i  ii   vi        v    v i     v        i ?    v
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_79347688_7    895 TAAATGTAAAAACCTTAAATTATGAAACTAATAAAATAAAACA--GGG-- 940
                                  i i - v   i   i     vv  i  v      --  ?--
  L1M4_orf2#LINE/    506 TAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_79347688_7    941 AAATGCTTCATAAAATTGGATCAGGCAAGGAGTTTTTGAATAAGATAACA 990
                             -    i i vv    i i      v iv  i  ii   v  i v  
  L1M4_orf2#LINE/    555 AAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_79347688_7    991 AAAGCACAGG 1000
                                 i 
  L1M4_orf2#LINE/    604 AAAGCACAAG 613

Transitions / transversions = 2.20 (88 / 40)
Gap_init rate = 0.02 (11 / 500), avg. gap size = 1.64 (18 / 11)  

 415 20.71 5.00 1.43  chrX_79347688_79349749     1353  1492 (570)    L1M4_orf2#LINE/L1      587   731 (177)  

  chrX_79347688_7   1353 TCTCAAAAACCAAACCAAAAAGCACAGGCAGCAAAAGTAAAAATAGATAA 1402
                            i i v iv v       -     i   i      v            
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_79347688_7   1403 ATTA-----CATCAAA-TTAAAAAGCTTCTGCACAGGAAAAAACAC-ATA 1445
                            i-----       -       -   i  ii vvv   ii    -  v
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chrX_79347688_7   1446 AATACAGTGGAGAAAGTACCTACAGAATGGGAGAAAGTAGTTGCAAA 1492
                           v v    i i i vv   i               i  v       
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.03 (5 / 145), avg. gap size = 1.80 (9 / 5)  

 412 14.29 3.90 0.00  chrX_79347688_79349749     1494  1570 (492)    L1M4_orf2#LINE/L1      829   908 (0)  

  chrX_79347688_7   1494 GACCTGAATAGACATTTTTCGAAAGA---CATACAAATGGCCAACAAGTA 1540
                           ii             i  v     ---i              i   i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_79347688_7   1541 TGTGAAAAAATGCTCAACATCGGTAATCAT 1570
                         ii      i            i????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 10.00 (10 / 1)
Gap_init rate = 0.01 (1 / 80), avg. gap size = 3.00 (3 / 1)  


3087 25.93 2.58 0.67  chrX_79362263_79366513.rev     2886  3776 (475)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79362263_7   2886 TGGGAAAATATTCCATGTTCATGGATTGGAAGAATAAATATTGTTAAAAT 2935
                            i  i    i                     v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79362263_7   2936 GTCCACACTACCCAAAACAGTATACAGATTCAGCACAATCCCTGTCAAAA 2985
                          v v i   v      viii v          i i        i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79362263_7   2986 TACCAATGACATTCTTTACAGAAATAGAAAAAACAAT------ATGTATG 3029
                          v   iivi v  i   i       v  v  ivii  ------  vi  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_79362263_7   3030 GGGAACCACAGAAGATCAAGAATAGCCAAAGCTATGTTAAACAAAAAGAA 3079
                         v    vii  iii  i v            i v  v  i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_79362263_7   3080 CAAAACTGGAAGAATTACATTACCTGACTTCAAATTATACTA--GAGGTA 3127
                             ii    i  v i   i v  ii i      viv     --i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_79362263_7   3128 TAGTAACCAAAACAGCATGGTACCAGTATAAAAACAGACACACAGACCAA 3177
                         i     i   i    ii      ii i    ii i     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_79362263_7   3178 TGGATCAGAATAGAGAACCCAGAAACATATCCACACATTT-TTGTCAAAC 3226
                             vi     v    ii       i v i   i      - v     -i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA-T 349

  chrX_79362263_7   3227 TTATTTTCCACAATGGTGCGAAGAATCTACACTGGAGAAAAGACAGTCTC 3276
                          v      v    v     v    viv v  v   i    ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_79362263_7   3277 TACGTTAAATGGTGCTGGGAAAACTGAATATTCATATCCAGAAGAATGAA 3326
                          v ivi              v     i   ?i  i  v  i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_79362263_7   3327 ACTAGACCTTTATCTTTTTCCATATACAAAAAATCAAATCAAAGTGGATT 3376
                         ii i    ii  i  iviv             - i  v     i     i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATC 498

  chrX_79362263_7   3377 AAGGACTTAAATCTAAGACCTCAAACTGTGTAACTATTACAATAAAACAT 3426
                          ?i   i     v     v  v     i iv    v   v  v       
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_79362263_7   3427 TTGGGTAAATCT--G-GACATTTATCTGGGCAAAAAATTCCTTGAGCAGT 3473
                         vv ?        -- -   v  vivi i     vii-  i   iiii vv
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATG 597

  chrX_79362263_7   3474 ACTGTACAAGTCCAGGCAACCAAAGCAGAAATGGACAAATGGGATCACAT 3523
                           vvi v   iv  i     v    v i    i  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_79362263_7   3524 CAAG-TTAAAAAGCTTCTGCACAGCAAAGGAAACAATCCACAAAGTAAGG 3572
                            i-       -   i  ii vv       v  v   v v     i ii
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_79362263_7   3573 AGACAACCTCCAGAAAGACAGAAAATATTTGCAAATTACTCATCTGACAA 3622
                                 iv     v iv                 i ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_79362263_7   3623 GGGATTAATAACCAGAATATATAAGAAGCTCAAACAACTCTATAGAAAAA 3672
                             i vi  v             ii i   vv       v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_79362263_7   3673 AAACTAATAATCCGATCACAATATGACCAAAAGATTTGAATAGACCTTTC 3722
                          i  v     i  i  i?v  v   iv    i             v    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_79362263_7   3723 TCAAAAGAAGACGTACACATGAC----AAACA------AAGGTGCTATAA 3762
                           v        ii    v   i ----  i  ------   i    v-- 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC--A 894

  chrX_79362263_7   3763 ACATCATTGGTTAT 3776
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (136 / 91)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.23 (29 / 13)  


3167 26.99 0.77 0.33  chrX_79380423_79386981     5163  6066 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79380423_7   5163 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5212
                              ii    i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79380423_7   5213 GGCCACACTACCCAAAGTAATTTATAGATTCAAGGGTATCCCCATCAAGC 5262
                            v i   v      v i  i  i        v vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79380423_7   5263 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5310
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_79380423_7   5311 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCCAAGCAAAAAG 5360
                                viiv  ii  v  v v  v     iv     iii iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_79380423_7   5361 AACAAAGTTGGAGGCATCACGCTACCTGACTTCAAACTATACTGCAAGGC 5410
                                       vv    i  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_79380423_7   5411 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATACACC 5460
                                 i   i    ii         i iv ii i   v     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_79380423_7   5461 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACACCCAT 5510
                                i    iv   ivii         vv   i    i  iivi  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_79380423_7   5511 CTGATCTTTGACAAACCAGACAAAAACAAGAAATGGGGAAAGGATTCTCT 5560
                         i    i  i     ivvv v   i v  vvv           i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_79380423_7   5561 ATTTAATAAATGGTGCTGGGAAAACTGGGTAGCCATATGTAGAAAGCTGA 5610
                         v  i  i              v      i  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_79380423_7   5611 AACTGGATCCCTTCCTTACACCTTATACAAA--TTAATTCAAGATGGATT 5658
                          ii    i    v   i     v        --    i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_79380423_7   5659 AAATACTTCAATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAACCT 5708
                          ? v  i v     v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_79380423_7   5709 AGGCATA--CCATTCAGGACATAGGCATGGGCAAGGAATTCATGACTAAA 5756
                            ?i  --i -   iv   v v  vv i     v iv   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_79380423_7   5757 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5806
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_79380423_7   5807 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAATG 5856
                         i   v v  i i   i  ii vv    i  v    i  vv i      vi
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_79380423_7   5857 GACAACTTACAGAATGGGAGAAAATTTTTGCCATCTACCCATCTGACAAA 5906
                               ii                 v     v vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_79380423_7   5907 GGGCTAATACCCAGAATCTACAAAGAACTTAAACAAATTTAAAAGAAAAA 5956
                           i  vi  i       v  i        ivv    v iv v  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_79380423_7   5957 ATGAAACAACCCCATCAAAAAGTGGGCAAAGGATATAAACAGACACTTTT 6006
                         ivv   i     v  i?    i            v i  i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_79380423_7   6007 CAAAAGAATACATTTATGCAGCCAA-AAACACATGAAAAAATGCTCATCA 6055
                          v      v i  vi viii     -  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_79380423_7   6056 TCACTGGCCAT 6066
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.35 (138 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 505 23.19 5.07 0.00  chrX_79408574_79415273.rev      357   494 (6206)    L1M4_orf2#LINE/L1      685   829 (79)  

  chrX_79408574_7    357 AAGATAATGAAAGAACAAGCCATAAACTGGGAGATAATATTTGCAAGTCA 406
                             v i     ii    v   i i v       v           i   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_79408574_7    407 CACATCTTACAAAGAACTTATAGCCAGAATATGCAAAGATATCTCAAAAC 456
                         i i    v i  i i    i  v         ii     vv   i v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_79408574_7    457 TTAAGAATAA---GACAAA----CCAATTAAAAAGTAAACAAGGG 494
                          i  v     ---      ----      ?    i iii   i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 2.10 (21 / 10)
Gap_init rate = 0.01 (2 / 145), avg. gap size = 3.50 (7 / 2)  

2768 27.15 2.46 1.01  chrX_79408574_79415273.rev     5315  6209 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79408574_7   5315 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5364
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79408574_7   5365 GGCCATACTGACCAAAGTAATTTACAGATTCAAGGGTATCCCCATCAAGC 5414
                            v     vv     v i  i           v vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79408574_7   5415 TACGATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5463
                          v v vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_79408574_7   5464 ATGGAAC--CAA-------AAAAGAGCCAAGACCATCTTAAGCAAAAAGA 5504
                               v--   ------- i  v      i  v     i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_79408574_7   5505 GCAACGCTATAGGCATCATGCTACCTGACTTCAAA--CTA-TACAAGGCT 5551
                         i   v i iv   vv   ii  v  ii i      --i  -     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_79408574_7   5552 ACAGTAACCAAAACAAAAACAGCATGATACTGGTGCCAAAACAGATATAT 5601
                                i   i   ------ ii  i      iiiv ii i   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACA------GTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_79408574_7   5602 AGACCAACAGAATAGAACAGAGGCCTCAGAAATAACACCACACATCTACA 5651
                            i   ii        iv   ivii         vv   i    i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_79408574_7   5652 ACCATGTTATCTTCAACAAATCTGAGAAAAACAAGCAATGGGGAAAGGAT 5701
                         ii  vv v  i   i    ivv  vv  i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_79408574_7   5702 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGCAGAAA 5751
                         vvi  v  i  i              v      v  ?         i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_79408574_7   5752 ACAGAAACCAGACCCCTTCCTTACACACTACACAAATATTAACTCAAGAT 5801
                          vv   iiii       v   i    vv  i     v          i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_79408574_7   5802 GTGTTAAAGACTTAAATGTAAAACCTGAAACTATAAAAACCATAGAAGAA 5851
                          vi i ?    i         i v  i           vi v        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_79408574_7   5852 AACCTAGGAG-ATACCATTCAGGACGTAGGCATGGGCAAAGACTTCATGA 5900
                            v    ? - v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_79408574_7   5901 CTAAAACACCTAAAGCAATTGCAACAAAAGCCAAAACTGACAAATGAGAT 5950
                         v  vi     v      vvv          vv    iv  i    vi  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_79408574_7   5951 CTAATTAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATCATCTGTGT 6000
                         i v  i   v v  i i   i  iv vv    i  v       vvviv  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_79408574_7   6001 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTG 6050
                            v  i     i                 v       vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_79408574_7   6051 ACAAACGTTTAACATCCAGAGTCTACAAGGAACTTAAACAAATTTACAGG 6100
                          i  iv vi vii       i v  i  i     ivv    v iv i iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_79408574_7   6101 AAAAAAACCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 6150
                              i  -   i     v  i?    i            v    i    
  L1M4_orf2#LINE/    793 AAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_79408574_7   6151 ATTTCTC-----AAGACATTTATGTGGCTAACAA--ACATAAAAAAA-GC 6192
                                -----    i  vi vi    i  i  --    i    i -  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_79408574_7   6193 TCATCATCACTGGTTAT 6209
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (133 / 106)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.38 (31 / 13)  


1421 23.86 2.54 0.51  chrX_79459312_79460985.rev        9   402 (1272)    L1M4_orf2#LINE/L1      427   828 (80)  

  chrX_79459312_7      9 ATATCCACATGCAAAAGAATTAAATTGGACTCTCATCTCACACAATATAT 58
                            ?                v  i      i ii i       v     i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_79459312_7     59 AAAA-TCAATTCAAAATGAACTAAAGACTTAAAAATGAGACTTGAAACTA 107
                             - i  i        i ii ?    i    vi i   vi i      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_79459312_7    108 TAAGACAACTAGTAGAAAAACACGGGAGAAAA-CTACATGACACTGTTCT 156
                            i  vvi   v      -  ii  ? v   -  v i    vi  vvi 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAA-CATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_79459312_7    157 GGGCAATGATCTTCTACATTTGATCCCCAAAGCTCAGGTAACAAAAGCAA 206
                         i       i i ii  v  v   iv  v     v  i i        v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_79459312_7    207 AAATAGACAAATGGGATTTCATCAAAATAAAAAGCTTCTGCACAACAAAG 256
                                i    v   i           v    i   i  ii vv     
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_79459312_7    257 GACACAATTAACAAAATGAAGAGACATCCTAGAGATTGGGAGAAAATATC 306
                              v  i  v   i    i     v  i v   v             i
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_79459312_7    307 TGCAAACAACACATATGAGAAGGGATTATTGTCCAAAATATATAAGGAAC 356
                               iv i i  v   v      i vv i    i         i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_79459312_7    357 T-TAACA-CT-----ATAGAATGA-AAACAATCTAATTTAAAAAATGAGT 398
                          - v   -  -----   i  v  -   i  i i    ?     -  i i
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGC 824

  chrX_79459312_7    399 AAGG 402
                           i 
  L1M4_orf2#LINE/    825 AAAG 828

Transitions / transversions = 1.65 (56 / 34)
Gap_init rate = 0.02 (8 / 402), avg. gap size = 1.50 (12 / 8)  

 258 25.00 6.48 3.70  chrX_79459312_79460985.rev      406   513 (1161)  C L1M4_orf2#LINE/L1   (684)   224   114 *

C chrX_79459312_7    513 TTTTGGGGTCAGAAA----CAAA---ATACTAAAATTTCTATGGAACCAT 471
                              ----      ----   i---  v        iv       viii
  L1M4_orf2#LINE/    114 TTTTG----CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

C chrX_79459312_7    470 GAAAGACCCTGAATAGCCAAAGAAAACCTGACCAAAAATAACAACGTTGC 421
                         i ii     v           iv  v i   vv  i  v     v    v
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

C chrX_79459312_7    420 ATGTATCATACTACC 406
                          v vv   i   v  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCC 224

Transitions / transversions = 0.80 (12 / 15)
Gap_init rate = 0.03 (3 / 111), avg. gap size = 3.67 (11 / 3)  

2066 26.42 2.77 2.34  chrX_79459312_79460985.rev      499  1183 (491)    L1M4_orf2#LINE/L1      221   908 (0)  

  chrX_79459312_7    499 TTTCTGACCCCAAAATGTACCACAAAGCTGTAGTAACCCAAACAGCAAGG 548
                           i ii iii     iv   i        ii     i v i    iiv  
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_79459312_7    549 CACTGGCATTATAAAAAAAAAAGACACATAGATCAATGGAACAGAACAGA 598
                         i        ------  ii v     i              i    iv  
  L1M4_orf2#LINE/    271 TACTGGCAT------AAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_79459312_7    599 AAATCCAGAAATTAATCCACATGTCCATAGCCAATTGATCTTTGACAAAG 648
                         i i         v  i   i ii ii  i i        i  i     i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_79459312_7    649 GTACCAAGAAAATTAATTGGTGAAAGGACACTCTCTTCAATAAATGGTAC 698
                           i      vv   v v   v     i i v   i     i       i 
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_79459312_7    699 TGGGAAAACTAGATATCCATATACACGAGGATGAAACTAGGCTACTGCTC 748
                              v    i    ?   i  i  vi  i     ii i i iv  i ii
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_79459312_7    749 CTTACCCTACATAAAAATCAACTCAAAATAGAAAAAAAAAACATAAATGT 798
                          vi   v  i i      i          i  vv ? i -- v       
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGA--CCTAAATGT 512

  chrX_79459312_7    799 AAGTCCTGAAATGATAAAACGACTGAAAGAAAACACAGGTG-AAATGTTT 847
                            vv  i   iv       vvi ii         i   ? -    v  i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_79459312_7    848 CAAAACATGAGTCTGGGAAAAGATTGTATAAATAAAGACCCCAAGA-TAC 896
                         vvi v v  i  - i  v  v i  viv  i   v-   v    i -i  
  L1M4_orf2#LINE/    563 GTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCAC 610

  chrX_79459312_7    897 AGGTAACAAAAGCAAATAAAAAACAAACAGGATTATATCAAA-CCAAAAA 945
                          i i        v   -  v i i   iv   i vi      -ii     
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_79459312_7    946 CTTCTGCACAGCAAAGGAAATGTTATATATAACAGAGTAGAAACACAATG 995
                            i  ii vv       v i----   -i  v i   ii   v    iv
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACAC----TAT-CAAGAAAGTGAAAAGACAACC 704

  chrX_79459312_7    996 TACAGAATAGTAGAAAATATTTGCAAGCTACTCATCTGACAGGGGATTAA 1045
                         i       i v               iii ivi      i i    i vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_79459312_7   1046 CATCCAGAATATATAATGAACTCAAATATCTCAACAGCAAA----CAAA- 1090
                         i               v      vv i v     i ii   ----    -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_79459312_7   1091 ----------AAAAATGGACAAATGATCTGAACAAACATTTTTG-ATAGA 1129
                         ----------        i    v   i    i i      i v- v   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_79459312_7   1130 AGGCAAACAAATGGCCAACAGATACTTGAAAAAATGTTCAACATCACTGA 1179
                           ii v            i iii  v      i   i         ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_79459312_7   1180 TCAA 1183
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.07 (120 / 58)
Gap_init rate = 0.02 (13 / 688), avg. gap size = 2.69 (35 / 13)  


3266 26.77 0.88 0.44  chrX_79466386_79472649     4868  5771 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79466386_7   4868 TGGAAGAACATTCCATGCTCATGGGTGGGAAGAATCAATATCATTAAAAT 4917
                              ii i  i     i      i v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79466386_7   4918 GGCCATACTGCCCAAGGTAACTTACAGATTCAATGCCATCCCCATCAAGC 4967
                            v     v     iv i ii           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79466386_7   4968 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5015
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_79466386_7   5016 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5065
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_79466386_7   5066 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5115
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_79466386_7   5116 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5165
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_79466386_7   5166 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACT 5213
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_79466386_7   5214 ATCTGATCTTTGACAAACCTGAGAAAAGCA----ATGGGGAAAGGATTCC 5259
                          vi    i  i     ivv  vv  i v  ----          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_79466386_7   5260 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5309
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_79466386_7   5310 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5359
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_79466386_7   5360 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5409
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_79466386_7   5410 CTAGGCATCACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5459
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_79466386_7   5460 AACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAA 5509
                         i            vvi      i   vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_79466386_7   5510 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5559
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_79466386_7   5560 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5609
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_79466386_7   5610 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5659
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_79466386_7   5660 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5709
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_79466386_7   5710 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5759
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_79466386_7   5760 ATCACTGGCCAT 5771
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (146 / 92)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2745 27.89 1.54 1.43  chrX_79523334_79530108     5376  6282 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79523334_7   5376 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5425
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79523334_7   5426 GGCCATACTGCCCAAAGTAATTTATAGATTCAAGGATATCCCCATCAAGC 5475
                            v     v      v i  i  i        v vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79523334_7   5476 TACCATTGACTTTCTTCACAGAATTATATAAAACT-ACTTTAAATTTCAT 5524
                          v   vivi i  i  ii     v vv i  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_79523334_7   5525 ATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAACAAAAAGA 5574
                               viiv  ii  v  viv        i      i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_79523334_7   5575 ACAAAGCTGGAAGCATCACGCTACCTGACTTCAAACTATACTACAG-GCT 5623
                               i    i vv    i  v  ii i      viv       i-   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_79523334_7   5624 ACAGTATCCAAACCAGCATGGTACTGGTACCAAAGCATA----TATATAC 5669
                               vi   iv   ii         i i--   v   ----    v i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGAT 297

  chrX_79523334_7   5670 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATTTACAACCA 5719
                                 i    iv   ivii         vv   i       iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_79523334_7   5720 CCTGATATTTGACAAACCTGAAAAAAAAAAAACAG-CAATAGAGAAAGGA 5768
                         vi    v  i     ivv  vv  i v-----  v-    i i     i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGAC-----CATTCAATGGGGAAAGAA 392

  chrX_79523334_7   5769 TTCCCTATTTAATAGATGTTTTTGGGACAACTGGACAGCCATATGCAGAA 5818
                          vvi  v  i  i i   v vi             i ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_79523334_7   5819 AACTGAAACTGGGCCCCTTTCTTACATGGTATATGAAAATTAACTCTAGA 5868
                         i v    ii   i     vi  i   ivi    ii           v i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_79523334_7   5869 TGGATTTAAGACTTAAACGTAAGACCTAAAACAATAAAAACCC-AAAAGA 5917
                              iv?    i    i      v       v      vi i- i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_79523334_7   5918 AAACCGAGGCA-ATATGCTTCAGGACAT--AGTCATAGGCAAAGACTTCG 5964
                             vv   ?i- v  -    iv   v --i  --       v ii   v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT-CTTCGTGACCTTGGGT--TAGGCAATGGTTTCT 589

  chrX_79523334_7   5965 TTACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACTAATGG 6014
                          viv  vi            vvi          vv     v  iv   v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_79523334_7   6015 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTATTGG 6064
                           ii v  i   v v  i i   i  ii vv    i  v     i vvii
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_79523334_7   6065 AATGAACAGGAAACCTACAGAATAGGAGAAACTTTTTGCAATCTATTCAT 6114
                          i    v  iv    i       i       v v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_79523334_7   6115 CTGACAAAGAGCTAATATCCAGAATCTGCAAAGAACTTAAACAAATTTCC 6164
                             i  i ii  vi          v ii        ivv    --i  v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CTCA 787

  chrX_79523334_7   6165 AAAAAAAAAAAAC---CCACTCCATCAAAAACTGGGTGAAGTATATGAAC 6211
                          v  v     i  ---iv  i v  i?    v    ii   v  v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_79523334_7   6212 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAA 6261
                              i     v        i  vi viii     i  i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_79523334_7   6262 AAGCTCATCATCACTGGTCAT 6282
                          v     v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (144 / 105)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.93 (27 / 14)  


3062 26.37 0.55 1.20  chrX_79551581_79553750.rev      786  1699 (471)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79551581_7    786 TGGAAAAACTTTCCATGCTCATGGATAGGAAGAGTCAATTTGGTGAAAAT 835
                               i iv i     i        v      v i   v v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79551581_7    836 GGCCATACTGCCCAAAGTAATTTATAGATTCAAGGGTATCCCCAGCAAAC 885
                            v     v      v i  i  i        v vv     i v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79551581_7    886 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAATTTC 933
                          v   vivi i  i  ii     -   --- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_79551581_7    934 ATATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAA 983
                                 viiv  ii  v  viv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_79551581_7    984 GAACAAAGCTGGAAGCATCACACTCCCTGACTTCAAACTATACTACAAGG 1033
                                 i    i vv       i  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_79551581_7   1034 CTACAGTAATTAAAACAGCATGATACTGGTGCCAAGACAGATATATAGAC 1083
                                   i  i    ii  i      iiiv i  i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_79551581_7   1084 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATGTACAACCC 1133
                                 i    iv   ivii         vv   i    v  iiii v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_79551581_7   1134 TCTGATCTTTGACAAACCTGACAAAAACAAGCAAAGGGGAAAGGATTCCC 1183
                         vi    i  i     ivv  v   i v  vv   v        i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_79551581_7   1184 TATTTAATAAATCTTGTAGGGGAAAACTGGCCAGCCATACACAGAAAGCT 1233
                          v  i  i    vv  i-v    v      vi ?   i ii  i  iiv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGC-TGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_79551581_7   1234 GAACCTGGATCCCTTCCTTACACCTCATACAAAAATTAACTCAAGATGGA 1283
                            vi    i    v   i     vi                  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_79551581_7   1284 TTAAAGACTTAAATATAAGATCTAAAACCATAAAAAATCCTAGAAGAAAA 1333
                          i ?    i     i     v       i      v-  i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chrX_79551581_7   1334 CTTAGGCA-ATACCATTTGGGACATAGGCATGGGCAAAGACTTCATGAAT 1382
                          v    ?i- v i -  i v   v v  vv i     v ii   v ii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_79551581_7   1383 AAAACACAAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATTGGATCT 1432
                          vi    v       vvv          vv     v  i        ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_79551581_7   1433 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAAAGTGA 1482
                         v  i   v v  i i   i  ii vv    i  v       vv       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_79551581_7   1483 ACAGGCAACCTACAGAATGGGAGAATCTTTTTGCAATCTATCCATCCGTC 1532
                          v  i     i              vv v       vii  vi   i vi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_79551581_7   1533 AAAGTACTTATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAA 1582
                           i v    i          v  i  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_79551581_7   1583 AAAAAACAAACAACCCCATCAAAAAGAGGGCAAAGGATATGAACAGACAC 1632
                            i -    i     v  i?    iv           v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_79551581_7   1633 TTCTCAAAAGAAGACATTTATGAA--GCCAACAAACATATGAAAAAATGC 1680
                              v        i  -- ii  --     i  i  i       i    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATAT--ACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_79551581_7   1681 AGGAAACAACAGATGCTGG 1699
                         --vv    v  ????????
  L1M4_orf2#LINE/    892 --TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (133 / 104)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


2166 27.01 0.86 0.72  chrX_79560945_79562625      493  1188 (493)    L1M4_orf2#LINE/L1      212   908 (0)  

  chrX_79560945_7    493 GACTTCTACATTAGCCTATTTCAAATTATACTACAAAGCTATAGTTACCA 542
                             i--   i vv  v        viv             i   v i  
  L1M4_orf2#LINE/    212 GACTC--ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_79560945_7    543 AAACAGCATGGTACTAGTATAAAAATGTGCATACAGACTAATGGAACAGT 592
                          i    ii       i i    ii  ivi    i   ii       i  v
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_79560945_7    593 ATAGAGAACCCAGAAATAAACCCAAATACTTAAAGCCAACTAATCTTCAA 642
                           v    ii               v i i   vi i   i i  i   i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_79560945_7    643 CAAAGCATAC-AACAACATACATTGGGGAAAGGACACCCTACTCAATAAA 691
                            i -i i -  v v   v  v         i i vi  vi    i   
  L1M4_orf2#LINE/    360 CAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_79560945_7    692 TGTTGCTGGGGAAGCTGGAAAGCCACATGTAGAAAAATGAAATTGGAGCC 741
                           v       iv i     v ?       i i  i      i     v  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_79560945_7    742 TCATCTCTCAGCTTATACATAAATCAACTTAAACTGGATCAAACACTTAA 791
                         ii i   v  v v      v    i    i   v       ? v  i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_79560945_7    792 ATCTAAGACCTGAAACCATGAAAATTCTGGACGATAACATCGAAA-AACC 840
                           v     v  i    i  i   v ii i  v  v     v i?i-  vi
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_79560945_7    841 CTTCTAGACATTGGGTTAGGCAAATAATTCATGACTAACACTCCAAAAGC 890
                             vv   v             vviv   v iiv  vv  v        
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_79560945_7    891 AAACGCAGTAAAACCAAAAATAAATAAATGAGGTTTAAT-AAAACTAAAA 939
                          v v   ii    vv       i      vi ii  v  -    i     
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_79560945_7    940 AGCTTCTTCACAACAAAAGAAATTATCAGCTGACTAAACAGACAACACAC 989
                          -   i vii vv    i  v i     ivvi v i  v       v   
  L1M4_orf2#LINE/    659 A-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_79560945_7    990 AGAGTGGGGAAAAAGTATTCACAAACTATGCCTCCAACAAAGGACTAATA 1039
                            i    ii    -    ii    ii  iiv  ii i  i     vi  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_79560945_7   1040 TCCAAAATATACAAAAAACTCAAACAAATCATCAAGGAAAAAACAAATAA 1089
                             i      i   i     vv    v   vi  vi    i        
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_79560945_7   1090 TCTCATTAAAAACTGTGCAAGTGACATGAGTAGAAAATTTTGATAAGAAG 1139
                         i iv   ?    v  v    iv  iv   i    v v  i vvv      
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_79560945_7   1140 ATATACGAACAGCCAACAA--ACATGAAAAAA-GCCCAACATCACTAATT 1186
                               i  ii     i  --         i -  i        ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_79560945_7   1187 AT 1188
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.39 (107 / 77)
Gap_init rate = 0.01 (9 / 697), avg. gap size = 1.22 (11 / 9)  


2397 29.69 2.12 0.78  chrX_79563561_79567763     2817  3712 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79563561_7   2817 TGGAAACAAATTCCATGCTCATGGATTGGAAGAATCAGTATCATAAAAAT 2866
                               v v  i     i               v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79563561_7   2867 CACA-CGGTGCCCAAATCGACCTGCAGATTTAATGAAATTCCCATCAAAA 2915
                         vi  -iiv v       i  i  i      i  i v   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79563561_7   2916 CAGTAACATCATTTCTCACAGAATTAGAAAAAACAATTTTAAAATTCATA 2965
                         ivvi i vv v   i ii     v v  v  ivii  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_79563561_7   2966 TGGAATCAAAAATAGCCTA-AATAGTCAAAGCAATACTAAGCAAAAAGGA 3014
                              viiv  ivii  i -     i    i    vi i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_79563561_7   3015 CAAATCTGAAGGCATCACGTTACCCAGCTTTAAGTCATACTACAAGGCTG 3064
                             vi  i   vv    ii v    ii  i  iv v        i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_79563561_7   3065 TAGTAGCCAAAACAGCATAATAATGGGATAAAAGTAGATACATAGACAAA 3114
                         i    ii   i    ii ii  v   v    iii    i i     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_79563561_7   3115 CGAGACAAAATAGAGAACTTAGTAATCAAGCCAAATACTTACAACCAGCT 3164
                         i ii i i   v    iiii  v   v  v   v i i   iiii  ---
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA--- 347

  chrX_79563561_7   3165 ATTT-TTTTTAACAAAGTATACAAAAAC-ATAAATTGGGGAAAGGGCACC 3212
                            v-    ii    i -i i v  i  -  vv v         iii vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_79563561_7   3213 CTATTCAATAAGTAGTGCTGGAAACATTGGATAGTCATATGTA---GAAT 3259
                           v     i  i i       i vv i      ?i  i   i ---    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_79563561_7   3260 AAAATTGGATCTCTATC----ACCATATACAAAAATTAACTCAAGATGGA 3305
                         i  i     i i   i ----                       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_79563561_7   3306 TGAAAGACTTAAATGTATGACCAGAAACTATAAAAATTCTGGAATAAAAC 3355
                          v ?    i        v  v vi           v ii i   v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_79563561_7   3356 CCAGTAGAAACTCTTATGGACATTGGCCTGGGCAAAGAAAATTAT--GAC 3403
                         vi  v? v  v    vvv   v    vi i     v iv--  v --  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT--TTCTTAGA- 593

  chrX_79563561_7   3404 TAAGACCCCAAAAGCAAATGCAACAAGAACAAAAATAAATAAACAGGACC 3453
                           v   v         v v       i iv       i     iv    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_79563561_7   3454 TAATTAAACCAAAAGGCTTGTGCACAACAACA-ACAAAATCATCAAAATA 3502
                          v  i   viv   ii   v  ii vv   vi-   vv    vv   i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_79563561_7   3503 AA----CAGCCCACAGAATAGAAGAAA-TATTTCCAAACTATGCATCTCA 3547
                           ----  i          i i     -     v    ii  ii    v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_79563561_7   3548 CAAAGTAGTAATATCCAGACCCTACAAGAAACACAAACAAATCAGCAAGA 3597
                         i  i v v vi        viv  i  ii   v vv    v   ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_79563561_7   3598 AAAAAGCAAATATTTCCATGAAAAAGTGGGCAAATGACATGAATAGACAC 3647
                             ii      vii v  v?    i        v  iv          i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_79563561_7   3648 TTCTCAAAACAAGATATGCAAATGGACAATGAATATATTTTAAAATGTTC 3697
                              v   v       i       v    i ii i  vvv  i   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_79563561_7   3698 AACATTTCTAATTAT 3712
                              iv????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (158 / 104)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.86 (26 / 14)  


2550 25.30 2.75 3.30  chrX_79567781_79570043      863  1771 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_79567781_7    863 AAAATACCCCATGGT-ATGGGTAGGAAGAATCAATACTGTTAAAATAACT 911
                           i   i      v -    i v      v i    i      i  ii v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_79567781_7    912 ATACTTCCTAAAGCAATGTATAGATTCAA-GCAACTCCTGTCAAATTACC 960
                              i  i   vii  v  i        -    ii   i     v v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_79567781_7    961 AAGGTAACTATTTT-CA-AAATTGGAAAAAAAAAGTTTCTAAAATACAAA 1008
                          - v iv  v    -  -      --- v  ivv v i       v  --
  L1M4_orf2#LINE/    105 A-GCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCA-- 148

  chrX_79567781_7   1009 AAAACATATGGAACTTAT-TAAAAG-CCCA-AATGGTTAAAGCAATCCTA 1055
                         ------       ---  -i  ii -    -   i ii   i     i i
  L1M4_orf2#LINE/    149 ------TATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_79567781_7   1056 ATCAAATAAGC-CAGAATGTG------TCACATTATTTTATTTCAAACTA 1098
                          -v   v   v-  i i -  ------     i viiiv        viv
  L1M4_orf2#LINE/    190 A-AAAAGAAGAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_79567781_7   1099 TACTACAAGGCTATAGTAACCAAAACAGCATGGAACTGGTGCACAAATAG 1148
                                 i    i     i   i    ii   v     iii vii    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_79567781_7   1149 ACACATAGATCAATGGAACAAAATAGACAACTCAGAAATAGAGCCACATA 1198
                            i              i i   v  v iii        i v   i i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_79567781_7   1199 GTTACAGCCAACTGATATTTGACAAAGTTGACAAAAATAAACAATGGAGA 1248
                         v   ii i   i    v  i     i v  v   i vi vv      i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_79567781_7   1249 AAGAACACCTTATTCAACAAATGGTGCTGGAAAACCTGGCTAGTCATATG 1298
                              i vii v                  i v v    v  ?i  i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_79567781_7   1299 CAGAAGGATGAAACTGGAACCCTATTTTTCAACATGTA-AAAAATTATCT 1347
                           i   i     ii    v     ii iv  v   i  -        v  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_79567781_7   1348 CAAGATAAATTAAAGACTTAAACGTAACACCTGAAAATGTAAAAATTCTA 1397
                            i  ii  i ?    i    i    v v  i   v i     v ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_79567781_7   1398 AAAGAAAAACTAGAAA-AAATCTCTTGTGGACATTGGCCTAGGCAAACAG 1446
                         i       vv   i?i-      - i   -  v    vi       -ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCT-TCGTG-ACCTTGGGTTAGGCAA-TGG 584

  chrX_79567781_7   1447 TTTAT--GACTGAGACCTCAAAAGCAAATGCAATGAAAATAAAAATCGAC 1494
                            v --  - iv   vi        v v    ii   iv      v  i
  L1M4_orf2#LINE/    585 TTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_79567781_7   1495 AAACGGAATTTAATTAAA-TTAAAGAGATTCCGCCCAGCAAAAGAAACAA 1543
                            iv i i  v  i   -     i v-  ii iv vv    i  v  v 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTA 682

  chrX_79567781_7   1544 TCAATAGAGTAGACAGACAGCTTACAGAATGGTGGAAAATATTTGCAAAC 1593
                             v i   ii v     i ii         vi               i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_79567781_7   1594 TACTCATCTGACAAAGGACTAATATCCAGACTCTATAAGGAAG----ATA 1639
                         i ivi      i  i     vi        v v     i   v---- i 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_79567781_7   1640 ATCTAATCAAATGAGAAGAAAACATCAAATAACACA-TTAAAAAGTCA-C 1687
                          iii   --   i i    ------        v  -  ?    i vi- 
  L1M4_orf2#LINE/    783 ACTCAAT--AATAAAAAGA------CAAATAACCCAATTWAAAAATGGGC 824

  chrX_79567781_7   1688 AAAGAACATGAACAGACATTTCTCAAAAGAAGCTATACAATAAACCAAAA 1737
                             i iv    i           v       v       vvii    v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_79567781_7   1738 ATCATTTGAAAAAATGCTCAACATCGCTAATCAT 1771
                          v  iv      i            i????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (141 / 85)
Gap_init rate = 0.03 (29 / 904), avg. gap size = 1.90 (55 / 29)  


2277 29.79 1.88 1.33  chrX_79604555_79609529     3583  4485 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79604555_7   3583 TGGGAAAACATTTCATGCTCAAGGATAGAAAGAATCAATGTTCTTACAAT 3632
                            i  i i  ii    i   v    v i    v i   i  v   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79604555_7   3633 GACCACACTGCCCAAAACAATTCACAGATTCAACACTATTCTCACCAAAC 3682
                          i v i   v      vii  ii           i v  i ii i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79604555_7   3683 TAAAAATGACATTCTTGACATAA-TTGAAAAA--AAATTAAAAATTCATA 3729
                          vvv iivi v  i  vi  v  -    v  i--i viiv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_79604555_7   3730 TGGAACAAAAAAAGAGCCAGAATAGCTAAAGAAATCCTGAGCAAAAAAAA 3779
                              vviv  ii  v          i   iv    i   iv  i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_79604555_7   3780 CAAAGCTGAAGGCACT-GCATTACCCGACTTCAAACTATACCAAAAGGTT 3828
                              i  i   -   -i  i v   i i      viv   i v  i i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_79604555_7   3829 ATAGCAACCTAAACAACATGACACTTGTACAAAAACAGATATATAGACAA 3878
                          i  i  i v i   iii  ii   v i i  ii i   i       iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_79604555_7   3879 ATGAAACATAATAGAAAGCCCAGAAATAAAGCCACACAGCTACAACCATC 3928
                            i  i v   v  i  i           v   i   vi  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_79604555_7   3929 TGATCTTCAATAAAATCAACAAAAACAATCAATGGGAAAAGGTCGCTCTA 3978
                             i   i i  iiviiv   i v  v        i    iviiv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_79604555_7   3979 TTCTATAAATTGTACCAGTATAACTGGCTAGCCATATGCAGAAGATGGTA 4028
                            v i    v  i ii v i      v  ?   i     i    vv v 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_79604555_7   4029 ATTTCAGCCCTTTCTTACATCATCTACAAAAGGTAACTCAAAATTAATTA 4078
                         i  vv v    vi  i   i   v       iv           vi  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_79604555_7   4079 AATACTTAAATGTAAAACCTAAAACTATAAACACTCCT-TCAGAAATTTT 4127
                         ? v  i         i v             -    i -vv     viv 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACAT 548

  chrX_79604555_7   4128 AGA---AAATACCATTCTGAATGTAGGCTCTGGCAATAATTTCAT-GATG 4173
                           i---    -- v iv   viv i  i v-      ii    v -   -
  L1M4_orf2#LINE/    549 AGGNGTAAAT--CTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGAT- 594

  chrX_79604555_7   4174 AAGATGCCAAAAGCAATTGCAACAAAAACAAAACTAAATTAGTGGAACCT 4223
                          v  ii         vvv         iv    v  i  v i v i  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_79604555_7   4224 AATTAAACTAAAGATCTTCTACCCAGCAAAAGAAACTATCCAAACAGTAA 4273
                         v  i   v v  i v   i iiv vv    i  v      v i v   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_79604555_7   4274 ACAGAAAACTCACAAAATGGAAGAAAATATTTGCAAACTATGTATCCAAC 4323
                          v   v   i    i     i                ii  i    ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_79604555_7   4324 AAAGGCCTAATATCCAGAATCTATAAGGAACT--TA-AATT----AACAA 4366
                           i  v  vi          v     i     --  -  i ----  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_79604555_7   4367 GCAGA-AAACAACTCCATTAAACAGTAGGCAAAAGACACAAACAGTCACT 4415
                         iv   -   i   i v   ?  v i i      i  ivii  i  v  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_79604555_7   4416 TCTCAAAAGAAGACACACATGTGACAAAGAAGAAGCATATGAAAAAAAAA 4465
                             v        i i   vi  i v  v   ---  i       i ---
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAG---CACATGAAAAGA--- 888

  chrX_79604555_7   4466 TACTCAGCAGTACTAATTGT 4485
                          i    i  vi ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (162 / 104)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.71 (29 / 17)  


2237 26.74 2.11 6.74  chrX_79627203_79631565.rev     2924  3873 (490)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_79627203_7   2924 GAAAAACATTACATGCTCATTGATAGGAAGAATCAATGTCATTAAAATGG 2973
                             i i  iv    i    v   v      v i   i ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_79627203_7   2974 CCATAGTGCCCAAAGCAATTTATAGATTCAGTGCTATTCCTATCAAACTA 3023
                          v   v v      vii  i  i       ii  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_79627203_7   3024 CGAA-TGAC------ACAGAATTTAAAAAAAAAACTG-TTTTAAAATTCA 3065
                          v i-  v ------i     v  i v  i----   - ii         
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATTCA 148

  chrX_79627203_7   3066 TACGAAACAAACAAAAAAAGATCTTGAATAGCCAAGGCAATTCTAAGCAA 3115
                           i i  - vi   ii---  i iv          ii    ii i iv  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGG---GACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_79627203_7   3116 AAAGAACAAAGCTGAACGCCTCACGTTACCTGAATTTTAAT-CATATTAC 3164
                         i          i  i v v     ii v  i-     i  v- v  i   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCC-AATTTCAAAACTTACTAC 243

  chrX_79627203_7   3165 AAGGCTATAGTAAAAACAAACAAAGAAAAAAAACCAACCAAACTGACAAC 3214
                           i    i     -------------------------------------
  L1M4_orf2#LINE/    244 AAAGCTACAGTAA------------------------------------- 256

  chrX_79627203_7   3215 AATAACAAAAAAATCCTCCAGAATGGTACTGGTACAAAAACAGACACACA 3264
                         -- --   i --------   vi         i i  ii i     i i 
  L1M4_orf2#LINE/    257 --T--CAAGA--------CAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_79627203_7   3265 GAACAATGGAACAGAATAGAGATCCTGGAAACAAGGTTACATGCCTACAA 3314
                           v        i     v    vi ii    i  ivii i iiii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_79627203_7   3315 CTATGTGATCTTCTACAAAGCTGCCAAAAAACAAGCAATGGGTGAAAAGA 3364
                         ii vv    i   v    i v      i v-  vv       -    ii 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGG-GAAAGAA 392

  chrX_79627203_7   3365 CTCCCTATTCAATAAATGATGCTGGGATAACTGGCTAGCCATATGCAGAA 3414
                         ivvi  v     i     i        i      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_79627203_7   3415 GATTGAAACTGGACCCTT-TCTTACATCAAATAAAACTGTAAACTCGAAA 3463
                           v    ii       i -i  i   i  v   v  vvi v     i   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_79627203_7   3464 TGGATTAAATACTTAAATTTAAAACCTAAAACTATGAACAACCTAGAAGA 3513
                              i ? v  i     v   i v          i  vvv i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_79627203_7   3514 CAACTT--GTGCAATACCATTCTGGACATAGGACCTGACAAAGATTTCAT 3561
                         v   v -- ? i  - i -   vv   v v  iiiv i   v i    - 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC-T 589

  chrX_79627203_7   3562 TACAAA-GATACCAAAAGCAATTGCAACAGAAACAAAAAATAGACAAATG 3610
                           v v -  i          vvv      -   v          i    v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAATT 638

  chrX_79627203_7   3611 GGATCTAATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTATTAACA 3660
                            ii v  i   v v  i ii  i  ii vv    i  v     i  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_79627203_7   3661 GAATAAACAAACAATTGAAATGATGGGACAAAATCTTTGCAAACTATACA 3710
                         i i i  v i    iiv v vi      v     v        ii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_79627203_7   3711 TCTGACGAAGGTCTAATATCTAGCATCTATAAGAAACTTAAACAAATTTA 3760
                              ii i  v  vi    i  v  v     ii    ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_79627203_7   3761 CAAGTAAAAAACAA----CCTCATTAAAAAGTGGGCAAAGTACATCCACA 3806
                         i  vv    i    ----  iv   ?    i         v iv vv i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_79627203_7   3807 GACACTTCTC---AAAAGACATACACACAACCAAGAAGCGTATGAAACAA 3853
                             i     --- i    i     v iii    v    ii      vi 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_79627203_7   3854 AGCTCAACATCGCTAATCAT 3873
                         v          i????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (152 / 98)
Gap_init rate = 0.02 (22 / 906), avg. gap size = 3.82 (84 / 22)  


2805 28.07 0.77 1.21  chrX_79642761_79647702.rev     3540  4451 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79642761_7   3540 TAGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3589
                          i    i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79642761_7   3590 GGGCATACTGATGAAAGCAATGTATAGATTCAATGCTATTCCCATAAAGC 3639
                           vv     vviv   vii  v  i        i  v  i  i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79642761_7   3640 TACCATTGACTTTCTTCACAAAACTAGAAAACACT-ACTTTAAGTTTCAT 3688
                          v   vivi i  i  ii  i  v v  v  -i  - iii   iv     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_79642761_7   3689 ATGGAACCAAAAAATAGCCCGTGTAGCCAAGACAATCCTAAGCAAAAAGG 3738
                               viiv  iiv v  v vi       i      i i iv  i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_79642761_7   3739 AAAAAGCTGGAGGCATCACACTACCCAACTTCAAGGTATACTACATGGCT 3788
                          v    i      vv       v     i     iiiv       vi   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_79642761_7   3789 ACAGTAATCAAAACAGCATGGTACTGGTACCAAAACGGGTATATAGAACA 3838
                                    i    ii         i iv ii ii ii       v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_79642761_7   3839 GTGGAACAGAACAGAGGCCTCAGAAATAACACCTCACATCTACAA-CAAT 3887
                         i     i    iv   ivii         vv  vi    i  iii-    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_79642761_7   3888 CTGATCTTCGAAAAACATGACAAAAACAAGCAATGAGAAAAGGATTCCCT 3937
                         -    i     v  ivi  v   i v  vv     i i    i  vvi  
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_79642761_7   3938 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACAGA 3987
                         v  i  i              v      v  ?   i   i i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_79642761_7   3988 AACTGGACCCCTTCCTTATCTTTACACCTTATACAAAAATTAACTCAAGA 4037
                          ii         v   i ------    v                   i 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCA------CACCATATACAAAAATTAACTCAAAA 492

  chrX_79642761_7   4038 TGGATTAAAGACATAAATGTAAAACCTAAAACCATAAAAACCCTAGAAGA 4087
                              i ?    v         i v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_79642761_7   4088 AAACCTAGGCA-ATACCATTCAGGACATACGTATGGGCAGAAACTATATG 4136
                             v    ?i- v i -   iv   v vv vv i    iviii viv i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_79642761_7   4137 ACTAAGACACCAAAAA-GCAACTGCAACAAAGGCCTAAACTGACAAATGG 4185
                         iv  v          i-i   --        i vvv   iv  i    v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_79642761_7   4186 GATCTAATTAAACTAAAGAGCTTCTGCTCAGCAAAAGAAATTATCATCAG 4235
                           ii v  i   v v  i i   i  iv vv    i  v i     vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_79642761_7   4236 AGTGAATAGGTAACCTAGAGAATGGGAGAAAATTTTTGCAATCTATCCAT 4285
                               v  ii    i v               v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_79642761_7   4286 CTGACAAAATTCTAACATCTAGAATCTACAAGGAACTTTAACAAATGTAC 4335
                             i  iivv  vii   i     v  i  i     i v    v vv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_79642761_7   4336 AAGAAAAA-ACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAG 4384
                           v     -     i     v  i?    i    ii      v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_79642761_7   4385 ACACTTCTCAAAAGAATACATATATGCAGCCAACAA--ACATGAAAAAAA 4432
                            i     v      v i   i viii     i  --         i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_79642761_7   4433 GCTCATCATCACTGGTCAT 4451
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (146 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


2950 27.37 0.87 1.85  chrX_79657876_79660745.rev     1463  2379 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79657876_7   1463 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1512
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79657876_7   1513 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1562
                           iv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79657876_7   1563 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1610
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_79657876_7   1611 TATGGAACCAAAAAAGAGCCCGCAAT-GCCAAGTCAATCCTAAGCCAAGA 1659
                                viiv  ii  -   iv   -     iv     i i ivv ii 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_79657876_7   1660 GAACAAAGCTGGAGGCATCACGCTACGTGACTTCAAACTATACTACAAGC 1709
                                 i      vv    i  v vii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_79657876_7   1710 CTACAGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGAGATATAGAC 1759
                                  i   i    ii     v   i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_79657876_7   1760 CAATGGAACAGAAC--AGAGCCCTCAGAAATACTACCACACATCTACAAC 1807
                                 i    i--    i  --       vvv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_79657876_7   1808 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGAAATGGAT-- 1855
                           vi    i  i     ivv  v   i v  vvv      i  v i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_79657876_7   1856 TCCTTATTTAATATTTAAATTAAATGGTGCCGGGAAAACTGGCTAGCCAT 1905
                           i  -- i  i ---------        i    v      v  ?   i
  L1M4_orf2#LINE/    396 TCTTT--TCAACA---------AATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_79657876_7   1906 ATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATGCAAAAATTA 1955
                            i i  iiv    ii    i    v   i     v   i         
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_79657876_7   1956 ATTCAAGATGGATTAAAGACTTACATGATATATCTAAAACCATAAAAACC 2005
                          i    i      i ?    i  v   vv v v       i      vi 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_79657876_7   2006 ATAGAAGAAAACCTAGGCA-ATACCATTCAGGGCATAGGCATGGGCAAGG 2054
                         v           v    ?i- v i -   iv i v v  vv i     v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chrX_79657876_7   2055 ACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAC 2104
                         ii   v ivv  vi            vvi          vv     v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_79657876_7   2105 AAATGGGCTCTAATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTTC 2154
                             v  vii v  i   v v  i ii  i  ii vv    i  v   vi
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_79657876_7   2155 TATCAGAGTGATCAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCT 2204
                         i vv i     vv  i     i                 v       vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_79657876_7   2205 ACTTATCTGACAAAGAGCTAATATCCAGAATCTACAAAGAACTCAAACAA 2254
                          iv       i  i ii  vi          v  i         vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_79657876_7   2255 ATTTACAAGAAAAAAACAAACAACCCCATCAACAAGTGGGTGAAGGATAT 2304
                         v iv i  v     i     i     v  i? v  i    ii      v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_79657876_7   2305 GGACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGA 2354
                          i i     i     v        i  vi viii     v ii       
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_79657876_7   2355 AAAAACGCTCATCATCACTGGCCAT 2379
                            i i     v     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.08 (25 / 12)  


2699 28.22 2.24 0.56  chrX_79679069_79684861.rev     4411  5303 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79679069_7   4411 TAGAAAAACATTCCATCCTCGTGAATAGAAAGA-------------AAAT 4447
                          i    i i  i    vi  i  i  v i    ------------- i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79679069_7   4448 GGCCATACTGCCAAAAGTAATTTATAGATTTGATGCTATTCTCATCAAAC 4497
                            v     v  v   v i  i  i     ii i  v  i ii      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79679069_7   4498 TGCCATTGACATTCATTGCAGAATCAGAAAAATACT-ACCTTAAAATGTA 4546
                          v   vivi v  iv        viv  v  i--  - i i      vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_79679069_7   4547 TATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCTTAAGCAAAAAG 4596
                                viiv  ii  v  viv        i        i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_79679069_7   4597 AACAAAGCTGGAGGCATTACGTTACCTGACTTCAAAGTATACTACAAGTC 4646
                                i      vv i  ii v  ii i      iiv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_79679069_7   4647 TACAGTAACCAAAACAGCATGGTAGTGGTACAAGAACAGACACATAGACC 4696
                                 i   i    ii     v   i i   i i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_79679069_7   4697 AATGGAACAGAATAAAGATCTCAGAAATAACACCTCACATCTACAACCAT 4746
                                i     vi   vii         vv  vi    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_79679069_7   4747 CTGATCTTCGACAAACCTGACAAAACAAG-CAATAGAGAAAGGATTCTCT 4795
                         i    i        ivv  v   i  v v-    i i     i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_79679069_7   4796 TTTTAATAAACCGTGCTGGAAAAACTGCCTAGCCATATGAAGAAAACTGA 4845
                            i  i   iv       i v     vv  ?   i   v i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_79679069_7   4846 AACTGGACCATTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATT 4895
                          ii      vi v   i     v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_79679069_7   4896 AAAGACTTACATGTGAAATCTCAAAATACAAAAACCCTAGAAAAAAATGT 4945
                          ?    i  v    i i v  v   v  i    vi i     i    ii 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_79679069_7   4946 AGGCA-ATATGATTCAGGAAATATGCATGAG-CAAAGATTTTAT-GATGA 4992
                            ?i- v  v-   iv  vv -  vi v  -   v i   iv -   iv
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_79679069_7   4993 AATCCCCAAAAGCAATTGCAAAAAAAGCTAAAATTGACAAATGGCATTTA 5042
                         i - v         vvv    v     vv     v  i    v v i  v
  L1M4_orf2#LINE/    597 GA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_79679069_7   5043 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCTTCAGAGTGAA 5092
                           i   v v  i i   i  ii vv    i  v      vvv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_79679069_7   5093 CAGACAACCTACAGAATGAGAGAAAATTTTTGCAATCTACCCATCTGACA 5142
                         v        i        i        v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_79679069_7   5143 AAAGTCTAATACCCAGACTTTACAAAGAACTTAAACAAATGTACAAGAAA 5192
                          ii v  vi  i     v v  i        ivv    v vv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_79679069_7   5193 AAAACAAATAACCTCATTAAAAAGTGGGCAAAGGACATGAACAGATGCTT 5242
                           i          iv   ?    i           iv    i   iii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_79679069_7   5243 TTCAAAAGAAGACACTTATGTAGCCAACAA--ACATGAAAAAAAGCTAAA 5290
                         i  v        i ivi vi i     i  --         i v   v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_79679069_7   5291 CATCCTGATTATT 5303
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (141 / 107)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.27 (25 / 11)  


2956 26.04 1.31 2.08  chrX_79699969_79705126     3752  4665 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_79699969_7   3752 GGAAACAAATCCAATGCTCATGGATGGGTAGAATAAATATTGTGAAAATG 3801
                              v v    v   i        v  v   v v        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_79699969_7   3802 ACCATACTGCCAAAAGCAATCTATAAATTCAATGCAATTCCCATCAAAAT 3851
                         i v     v  v   vii     i i      i     i  i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_79699969_7   3852 ACCACCATCATTCTTCACAGAACTAGAAAAAATTATCCTAAAATTTATAT 3901
                         v   v vv v  i  ii     v v  v  iv v           i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_79699969_7   3902 GGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGTCTAAGCTATAAAAAT 3951
                             viiv  ii  v  v v         i   vii i ivv v  i  i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_79699969_7   3952 AAATCTGGTGATATTGCATTACCTGACTTCAAATTATACTATAAGGCCAT 4001
                            vi   v ivv ii  i v  ii i      viv     i  i  i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_79699969_7   4002 AGTCACGAAAACAGCATGGTACTGGTATAAAAACAGGCATGTAGACCAAT 4051
                            v iv  i    ii         i    ii i  i   i    i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_79699969_7   4052 GGAACAGAATAGAGAACCCAGAAACAAAGCCAAATAGTTACAGCCGAT-G 4100
                             i     v    ii       i   v   v i v   ii i i  - 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_79699969_7   4101 ATCTTCAACAA---TGCAAATAAAAACATAAAGTGGGGAAAGGACATCCT 4147
                           i   i    ---   ---i  i v   vv i         i i vi  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGC---CAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_79699969_7   4148 ATTCAACAAATGGTGCTGAAATAATTGGCAAGCCACATGTAGGAGAATGA 4197
                         v                 ii i  i   vv ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_79699969_7   4198 AACTGGATCGTCATCTCTCACCTTATATAAAAGTCATCTCAAGATGAGTC 4247
                          ii    i vii i   v    v    i    i i v     i   ii  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_79699969_7   4248 A--GACTTAAATCTAAGACCTGAAACCATAAAGATTCTAGAAGATAACAT 4295
                          --   i     v     v  i    i     iv ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_79699969_7   4296 TGGAA-AAATACTTC-TGGTCATTGGCTTAGGCTAAGATTTCATTACCAG 4343
                         v  ?i-    -    -  ii -    v      v v i    -   vvvi
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACC-TTGGGTTAGGCAATGGTTTC-TTAGATA 595

  chrX_79699969_7   4344 GGAC-CCAAAAGCAAATGCAAAAAAAAAAAAAAAAAAAAAAAAAGATAAA 4392
                         v   -         v v    v    i      -------------  i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAA-------------TAGA 632

  chrX_79699969_7   4393 TAAATGGGACTTAATTAAACTAAAAAGCTTCTGCACGGCAAAAGAAATAA 4442
                              v      v  i   v v    i   i  ii vv    i  v iv 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_79699969_7   4443 TTGGCAGAATTAACAGAAAACCCACAGAGTGGGAGAAAATCTTCATAATC 4492
                          iiiv i i v  v   v          i           v  iii  vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_79699969_7   4493 TATACATCCAACAAAGGCCTAATATCCAGAATCTACAAAGAACCCAAACA 4542
                         i   i   ii i  i  v  vi          v  i       i vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_79699969_7   4543 A---AGCAAGAAAAGAACAAACAATCCCATCAAAAAGTGGGCTAAGGATA 4589
                          --- ii  v    ii     i  i  v  i?    i     v      v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_79699969_7   4590 TGAATAGACAATTCTCAAAATAAGATATACAAATGGCCAACAAGCATATG 4639
                                   v     v   v                   i     i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_79699969_7   4640 TAAAAATGCCAAACATCACTAAATAT 4665
                         v   i    iv       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 2.58 (31 / 12)  


3146 27.26 0.77 0.55  chrX_79711740_79718122     4985  5890 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79711740_7   4985 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5034
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79711740_7   5035 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGT 5084
                            v     v     iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79711740_7   5085 TACCAATGACTTTCTTCAAAGAACTGGAAAAAAGTACTTTAAAGTTCATA 5134
                          v   iivi i  i  iiv    v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_79711740_7   5135 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5184
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_79711740_7   5185 CAAAGAAGGAGGCATCATGCTACGTGACTTCAAACTATACTACAAGGCTA 5234
                              vv     vv   ii  v vii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_79711740_7   5235 CAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAG 5284
                               v   i    ii         i iv ii i   v       i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_79711740_7   5285 TGGAACAGAAC--AGAGCCCTCAGAAATAATGTGACATATCTACAACTAT 5332
                              i    i--    i  --        vviv i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_79711740_7   5333 CTGATCTTTGACAAACCTGACAAAACAAG-CAATGGGGAAAGGATTCCCT 5381
                         i    i  i     ivv  v   i  v v-            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_79711740_7   5382 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGG 5431
                         v  i  i              v      v  ?   i   i i  iiv  i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_79711740_7   5432 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5481
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_79711740_7   5482 AAAGACTTAAATGTTTGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5531
                          ?    i       vv  v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_79711740_7   5532 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5580
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_79711740_7   5581 ACACCAAAA---CAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5627
                                  ---   --           v     v  i    v   ii v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_79711740_7   5628 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5677
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_79711740_7   5678 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5727
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_79711740_7   5728 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5777
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_79711740_7   5778 AAAAAAAACAACCCCATCAACAAGTGGGCGAAGGATATGAGCAGACACTT 5827
                           i v   i     v  i? v  i     i      v   ii     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_79711740_7   5828 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGTTCAT 5877
                            v        i  vi viii     v ii          i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_79711740_7   5878 CATCACTGGCCAT 5890
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


4410 15.43 4.05 1.80  chrX_79722585_79726303.rev     2341  3228 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79722585_7   2341 TGGAAAGTCATTCCATGTTTATGGTTTGGAAGACATGATATTGTTAAGAT 2390
                                vi  i       i    v         v i             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79722585_7   2391 GGTGATGT--CCCACATTGACCTACAGATTCAACACAATCTCTAGCCAAA 2438
                           ii  ii--    v     i             i     i   v v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79722585_7   2439 TTCTAGCTGGCTGTTTTTGCAAAACCTG-CAG----------AAATTGAT 2477
                          i i     v  -        i  vi  -  i----------     v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_79722585_7   2478 ATGGAAATGCAAGGAACTCAGAATAGCCAAAACAATCCTGAAAA-GAAAA 2526
                                       i  i                   i      -   i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_79722585_7   2527 ACAGAGTTGGAAGAC--ACACTCCCCAAGTTCAATCCTTACTA-AAATCT 2573
                            i       i   --     i     v     vv       -   v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_79722585_7   2574 ACTATAAGGAGCACTATGTGGTACTGAAATAAAGATGGACATATAGATCA 2623
                           vi   vv iv  vi          iv    i   i             
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_79722585_7   2624 ATGGAACAAAACTGAGAATC-AGAAAATAGCCCATACATCTATGATTAAT 2672
                               i i  i     i  -     vv i         i    i i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_79722585_7   2673 TGATTTTTGACAGTGGCACT--GACAATTCAACGGGGGAAATGAATAGTC 2720
                                i    iv  ii i--   v      i    i  --        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA--GAATAGTC 397

  chrX_79722585_7   2721 CTTTCAACAAATTTTGTTGTGACAACTGGATAACCAGATGCAAAATAATA 2770
                         i           vv  i  v            ?   v        v   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_79722585_7   2771 ATAATAATAATAAGTTGGACCACTACATCACACCACATATAAAAATTAAC 2820
                          -----------         v    v        i   i          
  L1M4_orf2#LINE/    448 A-----------AGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_79722585_7   2821 TCAAAATAGATCAAAGACCTAAAGGTAAGAGCTAAAACTATAAAACGCTT 2870
                                i     ?         v                      v   
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_79722585_7   2871 TGAAGAAAACCCTGGTATAAATACTTGTTATCTTAGATTAGGCAATGGTT 2920
                         v         viv  ?i     vi i  v i   i i             
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_79722585_7   2921 TCTTAGGTGTGACACCTAAGACACAA-C--CAAAGGAAAAAA-ATATAAA 2966
                               i i       v  ii     - --    i       - v     
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_79722585_7   2967 TTGGACTCCATCAAAATTAACGACTTTTGTGCATCAAAGAACACTATCAG 3016
                                i            vi          v      i         i
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_79722585_7   3017 GAAAGTGAAAA-----CCCA-AAAATGGGAGAAAATGTTTGCAAATCATA 3060
                                    -----    - i             i             
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_79722585_7   3061 TATCTGATAAGGGTCTAGTTTCCAGAATATAGGTGAAGAACT--TAAATC 3108
                                      v  v  v           -- i       --  v v 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATA--TAAAGAACTCTTACAAC 784

  chrX_79722585_7   3109 TCAACCACAAAAAGA----TAACCCAATTTACAAATGGGCAAATAATTTG 3154
                             iv i       ----          ? v           vi     
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_79722585_7   3155 AATAAACATTTTTCCAAAGAATATAAGCAAATGGCCAATAGTTACATGAA 3204
                             i      i         v   vi             ivi       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_79722585_7   3205 AAGTTGCTTAGCATTATTAATCAT 3228
                            v    i i   i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (80 / 53)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.74 (52 / 19)  


2001 28.10 1.75 0.35  chrX_79813797_79817300.rev     1492  2064 (1440)    L1M4_orf2#LINE/L1        1   581 (327)  

  chrX_79813797_7   1492 TAGAAAAATAGCCTGTGCTCATGGACTGTAAAAAACAATATTGTTAAAAT 1541
                          i    i   v  ii  i       i  v  i vvi           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79813797_7   1542 GATCATACTGCTGAAAGCAACCTACAGATTCAGTGTAATCTCCATGAAAA 1591
                          iiv     v iv   vii i           ii i    i i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79813797_7   1592 TACCAA-TATCATTTTCACAGAAAT--AAAAAATAATCCTAAAATTCATA 1638
                          v   i- ii v    ii       -- v  iv i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_79813797_7   1639 TGGAACCAAAAAGAGTGCAGA-TAGCCACAGTAGTCCTGAGCAAAAAGAA 1687
                              viiv  i iiiv    -      v ii i  i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_79813797_7   1688 CAAAGCTGGAGACATCATGTTACCTGATGT--AAATTACATTGCAAGGTT 1735
                              i     ivv   iii v  ii  v --   i -i i i   i i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_79813797_7   1736 CTAGTAACCAAAACAGCATTGTACGGGTATAAAAATAGACAAACAGACCA 1785
                         vi     i   i    ii v    v  i    ii       v i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_79813797_7   1786 AAGGAACAGAATAGAAAACCCAGAAATAAATCTACATATTTATAGCCAAC 1835
                          v    i     v  i ii           i i i i      i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_79813797_7   1836 TGATCTTTGACAAAGCTGACAAGAACATGCATTGGGAAAAGGACACCCTC 1885
                             i  i     i v  v     v   v  v    i    i i vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_79813797_7   1886 TACTATAAACAGTGCTGGGATAAATGAATGTTCATATGCAGCAGAATAAA 1935
                          v v i   ii         i  v  i  i?i  i     iv     i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_79813797_7   1936 ACTGGACCCGTATCTCTAACCATATA-AAAAATCAACTCAAGATGAATTA 1984
                         ii       v  i   vv        -      i       i   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_79813797_7   1985 AAAACTTAAATGTAATACCCACAACTATAAAAATAATAGGGGAAAACA-- 2032
                         ? i  i         v v i v          v vv   ii       --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_79813797_7   2033 -GCAAAAACTCTTTTGGACATTGGTCTAGGCAA 2064
                         - ?iv   -    ivv   v    vi       
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA 581

Transitions / transversions = 2.04 (106 / 52)
Gap_init rate = 0.01 (8 / 581), avg. gap size = 1.50 (12 / 8)  

 890 20.75 3.14 6.92  chrX_79813797_79817300.rev     2389  2706 (798)    L1M4_orf2#LINE/L1      603   908 (0)  

  chrX_79813797_7   2389 AAAAGCACAGGCAACAATAACAAAAATAGACAAATGGGACTTACTGAAGT 2438
                                  i       v iv         i    v      - ----i 
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-C----AT 647

  chrX_79813797_7   2439 CCTAAAGTACTAAAAAGCTTATGCACAACAAAAGAAGC-ACCAGCAGAGT 2487
                          --   i --      -   v  ii vv    i  vi - i  iv i   
  L1M4_orf2#LINE/    648 C--AAAAT--TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_79813797_7   2488 GAAGAGACAATCTGTAGAATGTGTAGAATTGGAGAAAATAATTGCAAATT 2537
                            i      i iii      ---------          v        i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATG---------GGAGAAAATATTTGCAAATC 733

  chrX_79813797_7   2538 ATCCATCTGATAGGGGACTAATAACCAAAATATACAAGGAACTC----AA 2583
                           vi        i      vi  v   i      i  i      ----  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_79813797_7   2584 CTCAACAACAAAACTCAGA--AACAATCCCATTAACAAGTGGTTAAAG-A 2630
                              i  i    ---   --  i  i  v   ? v  i   vi    - 
  L1M4_orf2#LINE/    784 CTCAATAATAAAA---AGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_79813797_7   2631 CATAAATAGGTATTTTTCAAAAGAAGACGTGCAAATGGCCAACAGGTATA 2680
                         iv i     ii    i  v        ii i           i i i i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_79813797_7   2681 CAAAAAAATGATCGGC--CAGGCGTGGT 2706
                         ii    i   v  ii --  ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.61 (47 / 18)
Gap_init rate = 0.04 (12 / 306), avg. gap size = 2.67 (32 / 12)  


1852 21.90 6.21 3.97  chrX_79824645_79827071      745  1324 (1103)    L1M4_orf2#LINE/L1        1   593 (315)  

  chrX_79824645_7    745 TGGAGAGACATACTATACTATGTTCATGGATTGGAAAGTTTGACAGAGT- 793
                             i   -----   v i                 iii  i i vv  -
  L1M4_orf2#LINE/      1 TGGAAAGA-----TATCCCATGTTCATGGATTGGAAGACTTAATATTGTT 45

  chrX_79824645_7    794 AACATGTCAATTCTCCCCAAAT-GATTTACAGGTTTAACACAATTCCTTT 842
                           v   v    v          -   i     i  i   i    i   v 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_79824645_7    843 CAAAA----GGCT------TTTGTAGACATCAAGGAGCTTATTCTAAAAT 882
                              ----i   ------    i   v  ii vi    v  i       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_79824645_7    883 TCACAGGGAAA-------GACCCTAGAATATAGAAAACAATCTTTACAAA 925
                            i v     -------     -      vvv           v v   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCC-AGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_79824645_7    926 ----ACTAAAGTGAGAGGGAGTCTT-CTTCCCAATGTTAAGGCTTACTAC 970
                         ---- vi     vi    - v  vi-         v i  ii        
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_79824645_7    971 ATAGCTACAGAAATCAAAACAGCATGCTATTGGTGAGGAGATAAACACAC 1020
                          v        v      i    ii  v  i   iiviii    i   i i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_79824645_7   1021 AAATCAATGGAACAGAATAAAGGG-CCAAAAA--AATTTGCATAAATTTT 1067
                          i          i     vi  i -   i   --  ii--    v    v
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTA 341

  chrX_79824645_7   1068 C--TTAACTGATTTTTAACAAAGGTGC--AGCTCAATTTCAGTGGAGGAA 1113
                         i-- i  i       ii    i     --  vi  --    i   i i  
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA--TTCAATGGGGAAA 389

  chrX_79824645_7   1114 GAACAGCCTTTTCAACAAATGGTGCTGAAGCAATTTGACATACAGAAGTG 1163
                            i  i                    iii   i v  i ?v  v v ii
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_79824645_7   1164 AAAGAATAATGAACGTTG-ACCTAAACCTTACACC-T-TACAGAATTAAA 1210
                                ---   -    -   ivv    i     - -    i  v v  
  L1M4_orf2#LINE/    440 AAAGAAT---GAA-GTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_79824645_7   1211 CTCAAAATTAATCATAGAATTAAAT-TAAG-GCATTAAACTATCAAACGT 1258
                                 vi    ?   vi     -    -  - v       v    vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTC 534

  chrX_79824645_7   1259 TTAGAAAAAAAGACATGGGAGAAAATCTTCAGAATATGGGGCTAGGCAAA 1308
                               i    --   i  ? v        ivi iv v   i       v
  L1M4_orf2#LINE/    535 TTAGAAGAAAA--CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_79824645_7   1309 GAATTTTTTTTTTAGA 1324
                          i-----   i     
  L1M4_orf2#LINE/    583 GG-----TTTCTTAGA 593

Transitions / transversions = 1.64 (77 / 47)
Gap_init rate = 0.04 (26 / 593), avg. gap size = 2.27 (59 / 26)  

1160 26.07 3.72 0.00  chrX_79824645_79827071     1586  1934 (493)    L1M4_orf2#LINE/L1      547   908 (0)  

  chrX_79824645_7   1586 ACAGGTGTGAGCCACCGCG-CCCAGCCTTAGGCAAAGAATTCTTAAACTT 1634
                          i   ?  i ii vi  i -  iv vv        v iv      i iv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_79824645_7   1635 GACAACAAAAGCAAGATCCATAAAAGGGAAAATTGGTAAACAGGGTGTCA 1684
                             v        vi v v i     ii     v i    iv  iiv   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_79824645_7   1685 TCAAATTTTTTAAATTTCAGACTTTGAAAGCCCATGTGAAAAGAATGAAA 1734
                              v  vvv  v   iivi   ii  i v vv i v  i i i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_79824645_7   1735 AGACA-------GACTAGGAGAAAATATTTGCAGAGAATATATCTGACAA 1777
                              -------  v i                i vv          i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_79824645_7   1778 AAAACTGGTATCTAGAATACATGAAAAACTCTTAAAGTTCAACAATGAAA 1827
                         iii   v     i      i  i  i        v ii    i   i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_79824645_7   1828 TTAAAAATAATCTAATT-AAAAATGGGCAAAAG----GCATAGACACTTC 1872
                         vv v      i i    -             i ---- v       i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_79824645_7   1873 ACCAAAAAGGATATACATATGGTAAATAAGCATACAAAAAGATGTTCAAC 1922
                         v     i i        v    iv        i ii        i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_79824645_7   1923 ATTAGTAGCTGT 1934
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (54 / 36)
Gap_init rate = 0.01 (4 / 362), avg. gap size = 3.25 (13 / 4)  


2945 27.69 1.11 0.55  chrX_79884118_79889857.rev     4347  5249 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79884118_7   4347 TGGAAAAGCATTCCATGCTCATGGATAAGAAGAATCAATATAATGAAAAT 4396
                               iii  i     i        vi     v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79884118_7   4397 AGCCATAGTGCGCAATGTAATTTATAGATTCAATGCTATTCCCATCAACC 4446
                         i  v   v v v   vv i  i  i        i  v  i  i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79884118_7   4447 TACCATTGACTTTCTTCACAGAA-TTAAAAACAACT-ACTTTAAATTTCA 4494
                          v   vivi i  i  ii     -  i v  --i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chrX_79884118_7   4495 TATGGAACCAAAAAAGAGCCTGTAAAGCCAAGGCAATCCTAAGGAAAAAC 4544
                                viiv  ii  v  v v v      ii     i i ii  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_79884118_7   4545 AACAAAGCTGGAGGCATCCTGCTACGTGACTTCAAACTATACTACAAGTC 4594
                                i      vv  vii  v vii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_79884118_7   4595 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATACAGACC 4644
                                 i   i    ii         i iv ii i   i   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_79884118_7   4645 AATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAT 4694
                                i    iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_79884118_7   4695 CTGATCTTCCACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 4744
                         i    i   v    ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_79884118_7   4745 ATTCAGTAAATTGTGCTGGGAAAATTGGCTAGCCATATGCAGAAAACAGA 4794
                         v    ii    v         v  i   v  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_79884118_7   4795 ATCCAGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGGTT 4844
                          viii       v   i     v                   i    i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_79884118_7   4845 AAAGACTTAAATGTAAAACCCCAAACCATAAAAACCCTAGAAGAAAACCT 4894
                          ?    i         i v iv    i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_79884118_7   4895 AGGCAATACCCTTCAGGACATAGGCATGGGCAAAGACTTCATTACTGA-- 4942
                            ?ivv vi    iv   v v  vv i     v ii   -   --  --
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTA--GATA 595

  chrX_79884118_7   4943 -AACAACAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4991
                         -i   v        vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_79884118_7   4992 ATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5041
                           i   viv  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_79884118_7   5042 CAGACAACCTATAGAATGGGAGAAAATTTTTGCAAGCTACCCATCTGACA 5091
                         v        i i               v       iii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_79884118_7   5092 ATGGTCTAATATCCAGAATCTTCAAGGAACTTAAACAAATTTACAAGAAA 5141
                          v  v  vi          v vi  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_79884118_7   5142 AA---AAA-AACCCA-TCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5186
                           ---   -      - i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_79884118_7   5187 CTCAAAAGAAGACATTTAGGCAGCCAAGAAACATATGAAAAAAGGCTCAT 5236
                            v        i  vi iiii     v  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_79884118_7   5237 CATCACTGATCAT 5249
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (142 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2769 25.90 1.42 2.19  chrX_79896899_79901514     3209  4123 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79896899_7   3209 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCGATATTGTTAAAAC 3258
                               v i        i        v  v   v ii          i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79896899_7   3259 GACCATACTGCCAAAAGAAATCTATAAATTCAATGCAATCCCCATCAAAA 3308
                          i v     v  v   vvi     i i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79896899_7   3309 TACCATCATAATTCTTCATAGTACTAGAAAAAA-AATCCTAAAATGTATA 3357
                          v   v vvvv  i  iii  v v v  v  iv-i          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_79896899_7   3358 TGGAACCAGAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 3407
                              viiv  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_79896899_7   3408 CAAATCTGAAGACATCACATTAACCAAGTTCAAA--CTACGTTATGAGGC 3455
                             vi  i  ivv     i vv    v      --i   --  ii i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGC 248

  chrX_79896899_7   3456 TATAGTTACCTTGTAATGTAGTATGATAGTGGTATAAAAACCGGCATGCA 3505
                           i   v i ----  vii   i  i  v   i    ii iv i   ii 
  L1M4_orf2#LINE/    249 TACAGTAATC----AAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_79896899_7   3506 GACCAATAGAACAG---TGAA--TCCGAAAATAAAGCCAAATATTTACAG 3550
                           i    i   i  ---   i--   ii       v   v i     ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_79896899_7   3551 CCAACTGATCTTTGACAAAGCAAACAAAAC-GTAAAGTGGGGAAAAGATA 3599
                         i   i    i  i     i vviv   i  -i vv i        ii   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_79896899_7   3600 TCCTATTCAACAAATGGTGCTGGGATAACTGGCAAGCCACATGGAGAAGA 3649
                         vi  v                    i      vv ?       v i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_79896899_7   3650 ATGAAACTGTAGGCTCATCTCTCACCTTATACAAAAAACAAATCAAGATG 3699
                              ii  v vv ii i   v    v          vi  v    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_79896899_7   3700 GATCAAAGACTTAAATCTAAGACCTCAAACCATAAAAATTCTAGAAGATA 3749
                              ?    i     v     v  v    i      v ii       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_79896899_7   3750 ACATTGTAAAAATAA-TGCTAGT--CATTGGCCTAGGCAAAGAGTTCATG 3796
                             --- ii?i   - vi v  -- v    vi       v iv   v i
  L1M4_orf2#LINE/    545 ACAT---AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_79896899_7   3797 ACCAAAAACCCAAAAGCAAATGCAACAAAAACAAAAATAAATAGATAGGA 3846
                         ivi vi vv         v v         iv       i   i  v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_79896899_7   3847 CCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATAATTAGCAGAA 3896
                          i v  i   v v  i i   i  ii vv    i  v iv  i iv i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_79896899_7   3897 TAAACAGACAACCCACAGAGTGGGAGAAAATATTTGCAAACTATGCATCT 3946
                          i  v              i                    ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_79896899_7   3947 GACAAAGGACTAATACCCAGAATCTACAAGGAACTCAAACAAGTCAGTAA 3996
                           i  i     vi  i       v  i  i      vv    v   i   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_79896899_7   3997 AGAAAAAAAAAAAAAACCCTAATTAATTCCATAAAAAAGTTGGCTAAGGA 4046
                         -v     i v   v     -    ? ---------   i v   v     
  L1M4_orf2#LINE/    792 -TAAAAAGACAAATAACCC-AATTWA---------AAAATGGGCAAAGGA 830

  chrX_79896899_7   4047 CATGAATAGACAATTATCAAAAGAAGATATACAAGTGGCCAAAAAACATA 4096
                         iv          v  v  v               i       v  i  i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_79896899_7   4097 TAAAAA-ATGCTCAACATTACTAATTAT 4123
                          i    -           i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (131 / 102)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.36 (33 / 14)  


2389 25.37 3.21 6.00  chrX_79924321_79927219.rev     1475  2408 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79924321_7   1475 TGGAAATACATTTCATGCTCATGGATAAGAAGAATCAATATCGTGAAAAT 1524
                               v i  ii    i        vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79924321_7   1525 GGTAAGACTGCCCAAAGCAATTTATAGATTCAACGTTATTAATTGAATAG 1574
                           i  v   v      vii  i  i          i----   i------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC----AATC------ 90

  chrX_79924321_7   1575 TTCCATTAAACTACCATTGACATTCTTCACA-AAATTAGAAAAAAAACT- 1622
                         -i i  i   v v   vivi v  i  ii  -     i---- v  i  -
  L1M4_orf2#LINE/     91 -CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTG 135

  chrX_79924321_7   1623 ACTTTAAAATTCCTATTGAAC--CAAGAAAAGCCCA-AATAGTCAAGACG 1669
                          iii        v   v   v--    ii --    -     i   i  i
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACA 183

  chrX_79924321_7   1670 ATCCTAAGCAAAAAAAAAACAACAAAAAAAAACAAACAAACAAAAAAAAA 1719
                            i i --    i  i     ----------------------------
  L1M4_orf2#LINE/    184 ATCTTGA--AAAAGAAGAACAA---------------------------- 203

  chrX_79924321_7   1720 AAAGCTGAAGGAATCACACTACCTGACTT-AAAACTATACTACAAGGCTA 1768
                         --  i  i    v       v  ii i  -      -        i    
  L1M4_orf2#LINE/    204 --AGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTA 250

  chrX_79924321_7   1769 CAGTAACCAAAACAGCATGGTACTAGTACAGGAACAGACACATATACCAA 1818
                               i   i    ii       i i i i i i     i   v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_79924321_7   1819 TGGTAAAGAATAGAGAACTTAGAAATAATACCACACACCTACAACCATCT 1868
                            v v     v    iiii        vv   i   ii  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_79924321_7   1869 GATCCTTCACAAACCTTACATAAAAAAGCAATGGGGAAAGGAC--TCCTT 1916
                            ii iv    ivv vv  vi vv vv            i i--  i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_79924321_7   1917 ATTTAATAAATGATGCTGGAAGAACTGGCTAGCCATATGCAGAAAATTGA 1966
                         -- i  i     i      i v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    401 --TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_79924321_7   1967 AACTGGACCCCTTTCTTACACCTTATACAAAAATTAACTGAAGATAGATT 2016
                          ii         vi  i     v                v  i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_79924321_7   2017 AAAGACTTAAACGTAAAACGC-AAAACTATAAAAGCCCTAGAAGAAAATC 2065
                          ?    i    i    i -  -            vi i          iv
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_79924321_7   2066 TAGGC---AATGCCATTCAGGATATAGGCACGAGCAAAGATTTTAAAAGA 2112
                             ?---   -- -   iv  iv v  vviii    v i   ivv iiv
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_79924321_7   2113 AAAATGCCAGAAGCAATTGCAACAAGAGCAAAAATTGACAAATGGGATCT 2162
                          vi ii   i     vvv       i  v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_79924321_7   2163 AATTAAACTGAACATCTCTTGCACAGTAAAAGAAACTATCATCAGAGTCA 2212
                         v  i   v v  v v  i   ii vvi   i  v       vv i   v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_79924321_7   2213 ACAGACAACCTA-AAAATTGGAGAAAATGTTTGCAATCTATCCATCTGAC 2261
                          v        i - i   v         i       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_79924321_7   2262 AAAGGTCT---A--CAAAGAGCATAAACAAAT-TTACAA----------G 2295
                           i  v  --- --  i ivii     v  v -      ----------i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_79924321_7   2296 AAAGA-AAACAACCCCATTAAAAAGTGGGCAAAGGAAATGAATGGATGCT 2344
                              -   i     v   ?    i           vv     i  iii 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_79924321_7   2345 TCTCAAAAGCAGACATTTATGTGGCCAACAGGCATATGATAAAAAACTCA 2394
                             v    v   i  vi vi       i i   i    v  i vi    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_79924321_7   2395 ACATCACTGATCAT 2408
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (146 / 87)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.44 (86 / 25)  


1978 28.57 7.08 3.05  chrX_79930294_79932051.rev      448  1266 (491)    L1M4_orf2#LINE/L1       57   908 (0)  

  chrX_79930294_7    448 ACCTCCCAAAGTGCTGCATTTACAGGCGTGAGCCACCATGCCTGGCCAAG 497
                           ii      v  ----  i     iivii -- i v  v   iv v  i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTG----ATCTACAGATTCAA--CGCAATCCCTATCAAAA 100

  chrX_79930294_7    498 TTCTTAAACCACCAATGACATTCTTCATAGAAATAGAAAAAAACAATTTT 547
                          i i-- i ii  -------  i  iii      v  v  iv-ii  ii 
  L1M4_orf2#LINE/    101 TCCC--AGCTGCC-------TTTTTTGCAGAAATTGACAAGC-TGATCCT 140

  chrX_79930294_7    548 AA--TTTATATGGAACCAAAAAAGAGCCCAAATATCCAAGGCAATTCTAA 595
                           --  i        viiv  ii  v  vi    v    ii    ii i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_79930294_7    596 CCAAAAAGAACAAAGCTGGAGGTATCATGTTACCCAACTTTA-----TAC 640
                         vv  i          i      vv   iii v     i  i -----   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_79930294_7    641 TACAGGGTTACAGTAATCAAAACAGTATGGTACTGGTACAAGAACAGACA 690
                             ii i            i     i         i i   i i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_79930294_7    691 CATAGATGAATGGAACAGAGTAGAGAGCCCAGAAGTAATGACACACACCT 740
                         i      v       i   i v     i      i   vvv  i   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_79930294_7    741 ACAATTATCTTATCTTTGACAAAGCTAACAAGAACA------GGAAAAAC 784
                          iii i vi v  i  i     i v iv     v  ------  ii   -
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA- 389

  chrX_79930294_7    785 CAAGATAGAACTCCCTATTCAATAAATGATGCTGGGATAACAGTCTAGTC 834
                         --ii    -----i  v     i     i        i   v vv  ?i 
  L1M4_orf2#LINE/    390 --GAATAG-----TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_79930294_7    835 ATATGTAGATGATTGAAACTGGACCCCTTCCTT----------------- 867
                          i   i i v  v    ii         v   i-----------------
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_79930294_7    868 -------------------GACTTAAATATAAAACCCAAAACTGTGAAAA 898
                         -------------------   i     i   i v i      i i   v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_79930294_7    899 CCCTGGAAGACAACCTAGGCAATAACATGCTGGACATAGGAATGGGCAAA 948
                         i i i     v   v    ?ivv  iv v vv   v v  iv i     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_79930294_7    949 GATTTGGTAATGAGGATGCCAAAGGCAATTGCAACAAAAGCAAAAACTGA 998
                          i   vv  ivv v  ii     i   vvv          v     iv  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_79930294_7    999 CAAATGGGATCTAATTAAA-CTAAAGAGCTCTGCACAGCAAAAGAAACTA 1047
                         i    v   ii v  i   -i    i vi i  ii vv    i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_79930294_7   1048 TTAACAGAATAAAGAGACAACCTACAGAATGGAAGAAAATTTTTGCAAAT 1097
                          i  v i i i  i        i         i       v         
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_79930294_7   1098 -ATGCATCCAACAAAGGTCTAATACCCAGCATGTACAGGGAACTTAAACA 1146
                         -  ii   ii i  i  v  vi  i    v  i  i ii     ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_79930294_7   1147 A---AATTACAAGAAAAAAAA-AAC---ATTCAAAACTAAGCAAAGGACA 1189
                          ---   v i  i  i v   -   ---   ?    v ii        iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_79930294_7   1190 AGAATAGGCACTTTTCAAAAGAATACATACATGTGGCCAACAGGCAAATG 1239
                         v      i  i  i  v      v i     vi       i i   v   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_79930294_7   1240 AAAAAAAAGCTCAATATCACTGACAAT 1266
                             i v-      i    ????????
  L1M4_orf2#LINE/    883 AAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (148 / 83)
Gap_init rate = 0.02 (17 / 852), avg. gap size = 4.88 (83 / 17)  


3123 27.01 0.77 0.66  chrX_79949505_79955896.rev     4995  5901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79949505_7   4995 TGGAAGAACATTCCAGGCTCATGGATAGGAAGAATCAATATCATGAAAAA 5044
                              ii i  i   v i        v      v i     ii v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79949505_7   5045 GGCCATACTGCCCAAGATAATTTGTAGATTCAATGCCGTCCCCATCAAGC 5094
                            v     v     iv i  i ii        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79949505_7   5095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5142
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_79949505_7   5143 TATGGAATCAAAAAAGAGCCTGCATTTCCAAGACAATCATAAGCCAAAAG 5192
                                viiv  ii  v  v v  vv    i      v i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_79949505_7   5193 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5242
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_79949505_7   5243 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5292
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_79949505_7   5293 AATGGAACAGAGC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5340
                                i   ii--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_79949505_7   5341 ATCTGATCTTTGACAAACCTGTCAAAAACAAGAAATGGGGAAAGGATTCC 5390
                          vi    i  i     ivv  i   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_79949505_7   5391 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCT 5440
                           v  i  i              v      v  ?   i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_79949505_7   5441 GAAACTGGGTCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5490
                            ii   ii    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_79949505_7   5491 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGGAAAAAAA 5540
                          i ?    i       v   v       i      vi i   -  i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG-AAGAAAA 545

  chrX_79949505_7   5541 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 5589
                          v    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_79949505_7   5590 AAAACAACAGAAGCAATGGCAACAAAAGCCAAAATA-ACAAATGAGGTCT 5638
                          vi   v  i     vvi          vv      - i    vi iii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_79949505_7   5639 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5688
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_79949505_7   5689 ACAGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTACCCATCTGAC 5738
                          v  i     i       i         v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_79949505_7   5739 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATGTACAAGAA 5788
                           i  i  vi          v  i        ivv    v vv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_79949505_7   5789 AAA-ACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5837
                            -     i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_79949505_7   5838 TCTCAAAAGAAGACATTTATGCAGCCAACAGGCACATGAAAAACTGCTCA 5887
                             v        i  vi viii     i i           iv      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_79949505_7   5888 TCATCACTGGCCAT 5901
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3080 25.71 1.21 1.43  chrX_79966959_79974264     5904  6813 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79966959_7   5904 TGGAGAAACATTCCATGCTCATGGATAGGAATAATCAATATCGTGAAAAT 5953
                             i i i  i     i        v    v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79966959_7   5954 GGCCATACTGCCCAAAGTAATTTATACATTCAATGCTATCCCCATCAAGC 6003
                            v     v      v i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79966959_7   6004 CACCA-TTGAATTTCTT-CACAGATTTAGAAAAACT-ACTTTAAATTTCA 6050
                         iv   -i  vv   i  -  v i   --  v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_79966959_7   6051 TATGGAACTGAAAAAGAGCCCGTATATCCAAGTCAATCCTAAGCCAAAAG 6100
                                v  v  ii  v  v v   v    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_79966959_7   6101 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6150
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_79966959_7   6151 TACAGTAACCGAAACAGCATGATACTGGTACCAAAACAGACATATAGACC 6200
                                 i i i    ii  i      i iv ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_79966959_7   6201 AATGGAACAAAACAGAGGCCTCAGAAATAACACCACACACCTACAACCAT 6250
                                i i  iv   ivii         vv   i   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_79966959_7   6251 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAATGAT--TCT 6298
                         i    i  i     ivv  v   i v  vv           vi  --   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_79966959_7   6299 TT--AATAAATTATGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 6346
                           --  i    vi  i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_79966959_7   6347 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCCAGGTGGATT 6396
                          ii         v   i     v                 v ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_79966959_7   6397 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 6446
                          ?    i           v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_79966959_7   6447 AGGCA-ATACCATTCAGGACATAGGCATGGGCAGAGACTTTGTGACTAAA 6495
                            ?i- v i -   iv   v v  vv i    iv ii  iv iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_79966959_7   6496 ACACCAAAAGC-CATGGCAACAAAACCCGAAATTGACAAATGAGATCTAA 6544
                                    -  -i         vvvi    v  i    vi  ii v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_79966959_7   6545 TTACACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 6594
                          i v v v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_79966959_7   6595 AGGCAACCGACAGAATGGGAGAAAATTTTTGCAATCTGTTCATCTGACAA 6644
                           i     v                 v       viii vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_79966959_7   6645 AGGGCTAATATCCAGAATATGCAAGAAACTTAAACAAATTTACAAAAAAA 6694
                         i  i  vi            ii  ii    ivv    v ---   v  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATA 793

  chrX_79966959_7   6695 AAAAAAACCCCACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAAC 6744
                             i ------    i     v  i?    i            v    i
  L1M4_orf2#LINE/    794 AAAAGA------CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_79966959_7   6745 AGACGCTTCTCAAAAGAAGACATTTATGCAGCCAAAAA--ACATGAAAAA 6792
                             ii     v        i  vi viii     v  --         i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_79966959_7   6793 AAGCTCATCATCACTGATTAT 6813
                          v     v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


3455 24.31 1.44 0.89  chrX_79977008_79979859     1459  2359 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_79977008_7   1459 GAAGCATACTTTGTGCTCACAGCTCAGAATGA-TTATTATTGTTAAAATG 1507
                            iv   iiiii  i   ii v ii   -  -   v         i   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAA-GACTTAATATTGTTAAGATG 51

  chrX_79977008_7   1508 TCTATATTACCAAAAGTAATACACAGATTCAATGAAGTCCCTATCAAAAT 1557
                         v v   i v  v   v i  vi          i v i             
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_79977008_7   1558 CCCAGT--CATTCTTCACAAAAATTAAAAAAA-AATTCTAAAATTTGTAT 1604
                              i-- v  i  ii  i     i v  iv-i  i        ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_79977008_7   1605 AGAGCCATAAAAGACTCCAAATAGCCAAAACAATTCTGAGAAAGAAAAAC 1654
                         i  iviii  ii   i vi               ii   i      i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_79977008_7   1655 AAAGTTGGAGGCATCATACCTCCTAATTT--AAATTATACTGCAAACCTA 1702
                                    vv   i  i   i     --   i -    i    v   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTA 250

  chrX_79977008_7   1703 TAGCAATCAAAACAGTATGAAACTGGCATAAAAACAGACATATAGACTAG 1752
                         i  i      i     i  iv          ii i           ii i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_79977008_7   1753 TGGAACAGGACAGAGGGCCCAGAAATAAACCCAAACATATGTGGTCAACT 1802
                              i  i iv   i i               v    v i       i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_79977008_7   1803 AATTTTTCACAAGGGCATCGAGAGGACACAATAAGGAAAGGATCATCTCT 1852
                         i     iv       iii i   vv iv    ii      i  vi   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_79977008_7   1853 TCAATAAATGGTGCTGGGAAAACTGGATTTCCACATGCAAAAGTATAAAA 1902
                             i              v        v?             v  i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_79977008_7   1903 CTGCACCCTTATCTTGTGCCATACACAAAAATCAACTAAAAATAGATAAA 1952
                         i  v    i  i  iiii     i        i    v     i   v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_79977008_7   1953 AGACCTAAATATAAGATCAGAAACTGTAAAACTCCTAGAAGAAAACATAA 2002
                                   i     v vi     i        i              i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_79977008_7   2003 GAAAAAAGCTCCTGGACATTGGCCTTGACAACGATTT-TTGGATATTACA 2051
                          ?iv   v  i vv   v    vi v i   i i   -  i     v   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_79977008_7   2052 CCAAAAGCTCAGGCCATTAAGGCAAAAATA----AATGGGACTACATCAA 2097
                                 v  i  v iv  i v       ----   v     v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_79977008_7   2098 A-CTAAAAACTTTGTGCACAGCAAGGGAAACAATAAACAAAATGAAACAT 2146
                          -i          -  ii vv   i   v  v  v  v   i     viv
  L1M4_orf2#LINE/    651 AATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_79977008_7   2147 CAGTCTATTGATTGAGAAAAAAAATT-GCAAACCATTTATCTGATAAGGG 2195
                           ii i iv  v  i  i    v   -     i   v             
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_79977008_7   2196 TGTTACATAGCCAAAATTCATAAAGAACTCCAATAACTCAATGGTGGAAA 2245
                         vv  ii  --   i   vi           iv i        ii ii   
  L1M4_orf2#LINE/    750 ACTTGTAT--CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_79977008_7   2246 AACAAATAACTTAATTTTTTTAATGAACAAAAGATCTGAACAGATATTTC 2295
                         i         ii    ?vvv-    ii    i   i    i   i     
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_79977008_7   2296 TCCAAAGAAGACAGAAAAAATGGCCAACAGTTATATGAAAAAAGTGCTCA 2345
                                    i v v   -       i ivi i       i -      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAA-TGGCCAATAAGCACATGAAAAGA-TGCTCA 894

  chrX_79977008_7   2346 ATGTCATTAATCAT 2359
                          ii   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (144 / 71)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 1.40 (21 / 15)  


 843 30.32 1.08 0.00  chrX_79984716_79987433.rev        1   277 (2441)  C L1M4_orf2#LINE/L1   (628)   280     1  

C chrX_79984716_7    277 TGAAAACACATCTCATGCTCATGCATGGGTAGAATCCATATTGTGAAAAT 228
                           i   v i   i    i     v  v  v   v iv       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_79984716_7    227 GACCATACTGCCAAAAGCAATCTACGAATTCAATTCAATTCCCATCAAAA 178
                          i v     v  v   vii      ii      iv    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_79984716_7    177 TACCATCACCATTCTTCACAGAACTAGAAAAAAAAATCTTAAAATTTTTA 128
                          v   v vv v  i  ii     v v  v  ivvi   i       iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chrX_79984716_7    127 TGGAA-CAAAAAGAGCCCA-AATAGCCAAAGCAAGACTAAGCAA-AAGAA 81
                              -iiv  i ii    -          i   vvi i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chrX_79984716_7     80 CAAGTCTGGAGGGACCACATTATCTGACTTCAAACTATACCAAGAGGCTA 31
                            ivi      ivi    i vi ii i      viv   i vi i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chrX_79984716_7     30 TAGTCACTAAAACAGTATGGTACTGATATA 1
                         i   v ii  i     i        ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATA 280

Transitions / transversions = 1.47 (50 / 34)
Gap_init rate = 0.01 (3 / 280), avg. gap size = 1.00 (3 / 3)  

 662 19.84 0.00 0.00  chrX_79984716_79987433.rev      343   468 (2250)    L1M4_orf2#LINE/L1      421   546 (362)  

  chrX_79984716_7    343 AACTGGGTAGCCATATGCAGAAAACTGAAGCTGGACTCCTTTCTTACATG 392
                               i  ?   i     i  i v     i     i   vi  i   iv
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_79984716_7    393 TTACACAAAAATTAACTCAAGATGGATTAAAGACTTAAATGTAAAACCTA 442
                         v  i                i      i ?    i         i v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_79984716_7    443 AAACCATAAAAACCCTAGAAGAAAAC 468
                             i      vi i           
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAAC 546

Transitions / transversions = 2.83 (17 / 6)
Gap_init rate = 0.00 (0 / 126), avg. gap size = 0.00 (0 / 0)  

3035 26.46 0.78 0.56  chrX_79984716_79987433.rev     1336  2227 (491)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_79984716_7   1336 ATGTATGTGGATTGCAAGAATAAATATTGTTTAAATGGCCTTACTTTTCA 1385
                             vii       v    v v         v i     vv    iii  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_79984716_7   1386 AAGCAATATATAGATTCAATGCAATCCCTATCAAAATACCAATGACATTC 1435
                           vii  v  i        i                 v   iivi v  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_79984716_7   1436 TTCACAGAAATAGAAGAAAACT-ATTCTAAGATTTATATGAAACAACAAA 1484
                           ii       v  v--  i  -  i    i   i     i  vvi   i
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_79984716_7   1485 AGACCCAGAATAGCCTAAGCTATCCTGAGCAAAAAGAACATAACTGGAGA 1534
                         i              v  i v   i   iv  i       v ii     i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_79984716_7   1535 AATCATATTACCTAACTTTAAATCATACTACAGAGCTATAGTAACCAAAA 1584
                          v   i i v  i  i  i   v v       i     i     i   i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_79984716_7   1585 CAACATGGTACTTACATAAAAACAGACACATAGAGCAACGGAAAACAATA 1634
                           iii       vi     ii i     i     v   i    v v   v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_79984716_7   1635 GAGAACCCAGAAACAAATCTACACACCTAATGTGAACTCATTTTTGACAA 1684
                             ii       i   i i i   ii  vv  v  i v     i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_79984716_7   1685 AAGTGCTGAGAATACACATTGGGTAAAACACAATCTCTAAGATAAATGGT 1734
                         ii    ii   vi iv  v    v   iv i i   i vvi i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_79984716_7   1735 GCTGGAAAAACTGGATATCCATATGCAGAACAATAAAGCTAGACTCCTAT 1784
                              i v         ?   i     i  v   i   i i   i    i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_79984716_7   1785 ATATCAAAATATACAAAAGTCTAA-TGAAACTGGATTAGAGACTTAAACC 1833
                         v vv  vv          i -   - v   v     i ?    i    iv
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAAT-TAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_79984716_7   1834 TAGGACCTCAAAGTATGAAACTATTACAA-AAAACTTTGTGGAAGCTCTC 1882
                           i  v  v   v   i     v   v  -     v v v? v iv   i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_79984716_7   1883 AAGGAGATTGGACTGGGCAAAGATTTCTTGAGCAATATCCCACAAGCACA 1932
                         viv  vv    ii i     v i      iiii vv iv   v       
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_79984716_7   1933 ACCAATTGAAGCAAAAATAGACAAATGGGATCACATCAAG-TTAAAAAGC 1981
                          v   ivi   v         i    v   iiv      i-       - 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-C 660

  chrX_79984716_7   1982 TTCTGCACTGCAAAAAATACAACCAACAAAGTGAAAAGTAAATGTACAGA 2031
                           i  ii  v    ii i  v i   v           vv  ivi     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_79984716_7   2032 ATGGG-GAAAATATTTACAAGATAGCCATGTGACAAGGGAGTTATAACCA 2080
                              -          i   ivi vvi  v   i      v  i  v   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_79984716_7   2081 GAATATATAAAGAGCTCGAATAGCTCTAGAGGAAAAAGTCTAATAATCTG 2130
                                      i   vv i i   v v iv      v v     i ii
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_79984716_7   2131 AT-AAAAAATGGGCAAAA-ATTTGAATAGACATTTATCATAAGAAGACAT 2178
                           -?             i-                v  vv       i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_79984716_7   2179 ACATATTGGAAAACAGGTATATGAAAAGGTGCTCAGCATCATTGATTAT 2227
                            v  -  vv  i i i i        i      i     ????????
  L1M4_orf2#LINE/    861 ACAAAT-GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (133 / 99)
Gap_init rate = 0.01 (11 / 894), avg. gap size = 1.09 (12 / 11)  


3114 26.33 1.78 0.89  chrX_79997714_80004093     4988  5887 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_79997714_8   4988 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5037
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_79997714_8   5038 GGCCATACTGCCCAAGGTAATTTATAGCTTCAATGCCATGCCCATCAAGC 5087
                            v     v     iv i  i  i  v     i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_79997714_8   5088 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5135
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_79997714_8   5136 TATGGAACCAAAAAAGAGCCTGCATTGCCAAATCAATCCTAAGCCAAAAG 5185
                                viiv  ii  v  v v  v      v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_79997714_8   5186 AACAAAGCTGGACGCATCACACTTC---------AAACTATACTACAAGG 5226
                                i    v vv         ---------     -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_79997714_8   5227 CTACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGACATATAGAC 5276
                                  i   i    ii  i      i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_79997714_8   5277 CAATAGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5324
                             i   i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_79997714_8   5325 TATCTGATCTTTGACAAACCTGACAAAA--AGTAGAAATGTGGAAAGGAT 5372
                         i vi    i  i     ivv  v   i -- v v--    v      i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTC--AATGGGGAAAGAAT 393

  chrX_79997714_8   5373 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5422
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_79997714_8   5423 GCTGAATCTGGATCTCTTCCTTACACCTTCTACAAAAATTAATTCAAGAT 5472
                         iv    vi    i i  v   i     v v            i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_79997714_8   5473 GGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5522
                             i ?    i    i  v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_79997714_8   5523 AACCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 5571
                            v    ?i- v   -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_79997714_8   5572 CTAAAACACCAAAAGCAATGGCAACCAAAGCCCAAATTGACAAATGGGAT 5621
                         v  vi            vvi     v    vvv    v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_79997714_8   5622 CTAATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5671
                         i v  v   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_79997714_8   5672 GAACAGGCAACCTACAGAATGGGAGAAAGTTTTTGCAACCTACTCATCTG 5721
                            v  i     i               i v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_79997714_8   5722 ACAAAGGGCTAATACCCAGAATCTACAAAGAACTCAAACAAATTTACAAG 5771
                          i  i  i  vi  i       v  i         vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_79997714_8   5772 AAAAAAACAAACAACCATATCAAAAAGTGGGCGAAGGATATGAACAGACA 5821
                              i     i    vv  i?    i     i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_79997714_8   5822 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCT 5871
                         i     v        i  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_79997714_8   5872 CATCATCACTGGCCAT 5887
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.18 (24 / 11)  


1459 28.03 0.80 0.99  chrX_80020763_80025499.rev       12   514 (4223)    L1M4_orf2#LINE/L1      350   851 (57)  

  chrX_80020763_8     12 TGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGGAAAGGTTCCCCTA 61
                             i  i i   ivv  v   i v  vv            iv vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_80020763_8     62 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 111
                           i  i              v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_80020763_8    112 AATGGACCCTTTTCTTACACCTTATACAAAAATTAACTCAAGAGGGTTTA 161
                         iv       i vi  i     v                   i v  v i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_80020763_8    162 AAAACTTAAATGTAAGACCTAAAACCATAAAAACGCTAGAAGAAAACCTA 211
                         ? i  i           v       i      vivi           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_80020763_8    212 GACA-ATACCATTCAGGACATAGGCATGGGTAAAGTCTTCATGACTAAAA 260
                          i?i- v i -   iv   v v  vv i  i  v vi   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_80020763_8    261 CACCAAAAGCAATGGCAACAAAACACAAAATTGACTAATGGGATCTAATT 310
                                    vvi         v v     v  iv   v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_80020763_8    311 AAACTAAACAGCTGCTGCACAGCCAAAAAAAAACTATCACCAGAGTCACC 360
                            v v  v i  vi  ii vv --   ii v       vv i   v vv
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTC--AAAGGACACTATCAAGAAAGTGAAA 696

  chrX_80020763_8    361 AGGCAACCTACAGAATAGGAAAAACAT-TTTTCAATTTACCCATCTGACA 409
                           i     i       i   i   -  -   v   v i ivi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAA-ATATTTGCAAATCATATATCTGATA 745

  chrX_80020763_8    410 AAGGGCTAATATCTAGAATTTACAAGGAACTTAAACAAATTTACAAGAAA 459
                          i  i  vi    i     v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_80020763_8    460 AAAACAAACAACCCCATCAAAAAGTGTCCAAGGAATATGAACAGAGCAA- 508
                           i     i     v  i?    i  vv   i i  v    i   -  v-
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA-CATT 844

  chrX_80020763_8    509 -CTCCAA 514
                         -      
  L1M4_orf2#LINE/    845 TCTCCAA 851

Transitions / transversions = 1.01 (69 / 68)
Gap_init rate = 0.01 (7 / 502), avg. gap size = 1.29 (9 / 7)  

3146 27.64 0.44 0.44  chrX_80020763_80025499.rev     3339  4246 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80020763_8   3339 TGGAAGAACATTCCTTGCTCATGGGTAAGAAGAATCAATATCGTGAAAAT 3388
                              ii i  i  v  i      i vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80020763_8   3389 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3438
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80020763_8   3439 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3486
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_80020763_8   3487 TCTGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3536
                          v     viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80020763_8   3537 AACAAAGCTGCAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3586
                                i  v   vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80020763_8   3587 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3636
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80020763_8   3637 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCTCATATCTACAACT 3684
                                i    i--    i  --        vv  vi i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_80020763_8   3685 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAATGATTCC 3734
                          vi    i  i     ivv  vv  i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_80020763_8   3735 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3784
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80020763_8   3785 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3834
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80020763_8   3835 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3884
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_80020763_8   3885 CTAGGCATTACCATGCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 3934
                         v    ?i v viv v iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_80020763_8   3935 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 3984
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_80020763_8   3985 TTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4034
                          i   v v  i ii  i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_80020763_8   4035 AGGCAACCTATAAAATGGGAGAAAATTTTCGCAACCTACTCATCTCACAA 4084
                           i     i i i             v  i    vii ivi    v i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_80020763_8   4085 AAGACTAATATCCAGAATCTACAATGAACTCAAACAAATTTATAAGAAAA 4134
                         ii    vi          v  i  v      vv    v iv    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_80020763_8   4135 AAACAAAGAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 4184
                          i     v     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_80020763_8   4185 TCAAAAGAAAACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 4234
                           v      i i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_80020763_8   4235 ATCACTGGCCAT 4246
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (144 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3181 27.31 0.44 0.44  chrX_80038675_80044950.rev     4878  5785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80038675_8   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80038675_8   4928 GGCCATACTGCCGAAGGGAATTTATAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v  v  ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80038675_8   4978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_80038675_8   5026 TCTGGAACCAAAAAAGAGCCCGCATCGACAAGTCAATCCTAAGCCAAAAG 5075
                          v     viiv  ii  v  v v  v v   iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80038675_8   5076 AACAAAGCTGGAGGCATCACACAACCTGACTTCAAACTATACTACAAGGC 5125
                                i      vv      vv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80038675_8   5126 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80038675_8   5176 AATGGAACACAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5223
                                i v  i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_80038675_8   5224 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5273
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_80038675_8   5274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80038675_8   5324 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5373
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80038675_8   5374 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_80038675_8   5424 CTAGGCATTACCATTCAAGACATAGGCATGGGCAAGGACTTCATGTCTAA 5473
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_80038675_8   5474 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5523
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_80038675_8   5524 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5573
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_80038675_8   5574 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTGCTCATCTGACAA 5623
                           i     i   iv            v  i    viiiivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_80038675_8   5624 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5673
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_80038675_8   5674 AGACAAAGAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5723
                                v     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_80038675_8   5724 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5773
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_80038675_8   5774 ATCACTGGCCAT 5785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2643 28.46 1.10 1.32  chrX_80054793_80058841     2647  3556 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80054793_8   2647 TGAAAAGATATTTTATGCTCATGGACTGGAAGAATCAATATTGTTAAAAT 2696
                           i        iii   i       i       v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80054793_8   2697 GTCAAGACAACCAAAAGCAATCTACAGTGCCTTTGCAACCCCTATCAATA 2746
                          v   v  vv  v   vii        vvi vvi    i         v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80054793_8   2747 TACCAATTACATCTTC-ACAGAAATAGACAAAACAATTTTAAAATTTATA 2795
                          v   ii i v i  i-i       v     ivii  ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_80054793_8   2796 TT-AGATGACAAAAGAAACACAGTACCCAAAGCTATCCTGACCAA-AAGA 2843
                          v- i   -   ii  vv  v i  v     i v   i   vv  -    
  L1M4_orf2#LINE/    151 TGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_80054793_8   2844 TCAAAACTGGAGAAATCAGATTACCTGACTTCAAATTATACTACTGAGTT 2893
                         v    ii     i v   v i v  ii i      viv      vi  i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_80054793_8   2894 AGAGTAACCAAAAACAGCATGGTACTTGCATAAAAAGAGGCACATAGATA 2943
                          v     i   i -   ii       v      ii v  i  i      v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80054793_8   2944 AATGGGACAAAACAGAGATCCCAGAAACAAATCCATACACCTACAGTGGA 2993
                              i i i  iv    vi       i   i       ii  ii  vi 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_80054793_8   2994 TTCCATCTTTGACAAACGTGCTAGGAATAC-CAATTTGAGAAAGGATAGT 3042
                           v-  i  i     iv    i i  vi i-    v- i     i     
  L1M4_orf2#LINE/    349 TTG-ATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGT 396

  chrX_80054793_8   3043 CTCTTTAATAAATGGTACTGGGAAAACTAGATATCCCTACGCAGAAGAAT 3092
                           i  i  i       i      v    i    ?  vi i   i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80054793_8   3093 AAAACTTGACATATATCTTTTGCCATATACAAAAATAAGATAAAATTTGA 3142
                         i  ii v   viv  i  ivii              v iv v   v v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80054793_8   3143 TTATAAATTTAAGCCCAAGACCTCAGACTTTGAAACTACTACAGAAAAAC 3192
                          i ? i ii   iivi    v  v i   v i     vi  v ii     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_80054793_8   3193 TTTGGGA-AACTCTCCAGGACATTGATTTGGGCTAAAATTTCTTGAGTAA 3241
                         v v  ?i-  v   i iv   v   iv  i   v vii      iii  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_80054793_8   3242 TAC-CCAACAACCATGACAGGCAAACAAAGCAAAAATGGAAAAATGGGAT 3290
                         v  -    v i ----   i    vv    v      i  v    v   i
  L1M4_orf2#LINE/    597 GACACCAAAAGC----ACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_80054793_8   3291 CACAT-GAAGTTAAAAAGCTTCTGCACAGCAAAAAAAGCAATCAACAAAA 3339
                         iv   -i  i       -   i  ii vv    ii vi v     v   i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_80054793_8   3340 TGAAGAGACCACTCACAAAATAGGAAAAACTATTTTCAAACTACCCATCT 3389
                             i    v  i    i   i   i   v     v    ii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_80054793_8   3390 GACAAGGGATTAATAATCAGAATATAAAAGGAGCTCAAACATTTCAATTG 3439
                           i      i vi  vi         v  i  i   vv   vi     --
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-- 789

  chrX_80054793_8   3440 GAAAAAAAAATCTAATAAT---ATTAAAAAATGGGCCAAATATTTTAATG 3486
                         -  v     iv v     i---   ?          v  iv    v   i
  L1M4_orf2#LINE/    790 -AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_80054793_8   3487 GAAATTTCTCAACAGAGGACACACAAATTGCAAATTGATCCATAAAAAGG 3536
                           v       v v   i  i i      v  v   viiiv   i     i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_80054793_8   3537 TGCTCAACATCACTGATCAT 3556
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (151 / 104)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.47 (22 / 15)  


2595 28.65 1.33 0.88  chrX_80068010_80071373.rev     1970  2873 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80068010_8   1970 TAAAAACACATCCCATGCTCATGGATGGGTAGATTCAGTATTATAAAAGT 2019
                          ii   v i        i        v  v   i i i    i v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80068010_8   2020 GACCATACTGCCAAAAGCAATCTACAGATTCAATGCAATTCCCAACAAAG 2069
                          i v     v  v   vii              i     i  i v    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80068010_8   2070 TACCATCATCATTCTTCACAGAACTAGAAAAA--AATCCTAAAATTTATG 2117
                          v   v vv v  i  ii     v v  v  i--i           i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_80068010_8   2118 TGGAACCAGAAAAGATTCTGCATAGCCAAAGCACAAC--TAAACAAAAGG 2165
                              viiv  ii  ii v v         --    i-- i  v  i i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAA--ACAATCTTGAAAAAGAAG 198

  chrX_80068010_8   2166 AACCAATCTGGAGGCATCACATTACCTGACTTCAAACTATCCTACAA-TC 2214
                            v  vi      vv     i v  ii i      viv v      -v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80068010_8   2215 TACAGTTACCAAAACAGCATGGTACTGATATAAAAATAGGCATGTAGACC 2264
                               v i   i    ii        ii    ii    i   i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80068010_8   2265 AATGGAAAAGAATAGAGAACCCAGAAATAAACCCAGATAATTACAGCCAA 2314
                                v     v    ii               v i v   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_80068010_8   2315 CCGATCTTTGACA-TAGCATCAAAAACATAAAGTGAGGAAAGGAAACCCT 2363
                         ii   i  i    -vi iii   i v   vv i  i      i v vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_80068010_8   2364 ATTCAACAAATGGTGCTGGAATAATTGGCAAGCCACATGTAGAAGAATAA 2413
                         v                  i i  i   vv ?       i i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_80068010_8   2414 AACTGAAACCACATCTCTCATTTTATACAAAAATCAACTCAAGATGGATC 2463
                          ii  i v  vi i   v  iiv           i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_80068010_8   2464 AGGGACTTAAATCTAAGACCTGAAACCATGAAAAATTCTACAAGGAAACA 2513
                          ?i   i     v     v  i    i  -    v ii  v   i     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chrX_80068010_8   2514 TTGG--TAAAGTTCTCCTAGATGTTGGCTTATGTAAAGACTTCATGACCA 2561
                          v  --    --   i vv  iv    v   v i  v ii   v iivi 
  L1M4_orf2#LINE/    548 TAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_80068010_8   2562 AAAACCCAAAAGAAAATGCAACAAAAACAAAAATAAATACATGGTGCCCA 2611
                         vi vv       v v v         iv       i   v  v vi iiv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_80068010_8   2612 ATTTAACTACAAAGTTTCTGCACAGCAAAAGAAATAATTAGCAGAGTAAA 2661
                           iv  v vv   ii  i  ii vv    i  v iv  i iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_80068010_8   2662 CTCACAACACAGAGAATGCAAGCATATCTTCACAAACTGTGCATCAGACA 2711
                         vvv     v  v      vi  v v  v  ii    iii ii   v  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_80068010_8   2712 AAGGACTAATATCCAGAATCTACAAGGAACTCAAACAAATCAGTAAGAAA 2761
                          i     vi          v  i  i      vv    v   i   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_80068010_8   2762 AAAACC--CAGCCCCATCAAAAAGTGGAGAAAGGACACGGATAGACAATT 2809
                           i  v--i i   v  i?    i   iv      ivi i       v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_80068010_8   2810 CTCAAAAGAACATATACTACACATGATCAGGAA--ACATGACAAAATTAT 2857
                            v      v      --- v   ii  iv  --      v  i  vv 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATAC---AAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_80068010_8   2858 TAACATCACTAATTAT 2873
                         i       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (146 / 110)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


2522 27.02 3.10 2.55  chrX_80085184_80087397      819  1721 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80085184_8    819 TGGAAAAACATTCCATGCTCATGGATAGAAATAATTGATATTTTTTTAGT 868
                               i i  i     i        v i  v v  i     v  vvii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80085184_8    869 GGCCATG-TGTCCAAAGCAACTTACAAATTCAATGCTATTCTTATCAAAC 917
                            v  i- vi     vii ii    i      i  v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80085184_8    918 TGCCAATAACATTCTTTACAGAATTAGAAAAGAAATATATTTTTAAATT- 966
                          v   iivi v  i   i     v v  v   v-- i-  ii v     -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TG-ATCCTAAAATTC 147

  chrX_80085184_8    967 ATATGGAA-TGTAAAAAGAGCTCCA--ATATTCAAAGCAATCCTAAGGAA 1013
                                 -  i  --- i vi   --   vi    i     i i ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAA---GGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_80085184_8   1014 AAAGAAGAAAGCTAGAGAGATCACATTATCCAACTTCAAACAATACTACA 1063
                         i     v    i i   iiv     i vi    i      vvv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_80085184_8   1064 AGGCCACAGTAACCAAAGCAGCATGGTACTAGTACTTAA--ACAGACAGA 1111
                          i  i       i   ii   ii       i i --   -- i     v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATA 292

  chrX_80085184_8   1112 TA-ATCAAATGGAACAGAAT--AGAGTTCCCAGAAATAAATTTGCACATC 1158
                           -     -     i     --     --           iiiii    i
  L1M4_orf2#LINE/    293 TAGATCAA-TGGAATAGAATTGAGAGT--CCAGAAATAAACCCATACATT 339

  chrX_80085184_8   1159 TACAA-CAATCTGGCCTTTGACAAAGTCAACAAAAACAAGCAAGGAGAAA 1207
                           iii-    -  iii  i     i viiv   i v  vv   v i i  
  L1M4_orf2#LINE/    340 TATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_80085184_8   1208 AGGAATC-CCTATTCAGTAAATGATGCTGGGATAACTGGGTAGCCATATG 1256
                           -   v-i  v    ii     i        i      i  ?   i   
  L1M4_orf2#LINE/    389 AG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_80085184_8   1257 TAGAAGATGGAAACTGAACTCTTTCCTTATACCATATA-AAAAGTCAACT 1305
                         i i    vv   ii  i  i i v   i i        -    i i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_80085184_8   1306 CAAGATGGATTAAAGACTTAAAAGTAAAACCTAAAACTATAACAACCCT- 1354
                            i      i ?    i    v    i v            -   i  -
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTT 536

  chrX_80085184_8   1355 GGAAGGTAACCTACAAA-ATATCATTCTGGATATAGGCCCTAGCAAAGAT 1403
                         i    iv   v  vi?i- v   -   vv  iv v  viivi    v i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_80085184_8   1404 TT------TATGACAAAGATGCCAAAAGCAATTGCAAAGGAAGCAAAAAT 1447
                           ------       ------         vvv    vii   v      
  L1M4_orf2#LINE/    586 TTCTTAGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_80085184_8   1448 TGACAAATGAGACCTAATTAAACTAAAGGGCTTTTGAACAGCAAAAGAAA 1497
                         v  i    vi   i v  i   v v  iii      vi vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_80085184_8   1498 CTGTCAACAGAGTAAATAAACAACCTGCAGAATGGGAGAAAAT----GCA 1543
                           i    v i   i  v i      ii                ----   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_80085184_8   1544 AACTATGCATGTGAGAAAGGTCTAATACCTTGAATTTATTATTA-TTTTT 1592
                           ii  ii  v   v  i  v  vi  i iv    v   v vv -i i  
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_80085184_8   1593 AAGCAAATCAAGGA--AAAAAACAAACTTCTTTATTAAAAAGTGGGCAAA 1640
                          --   v    vi --    i     ivv iiv   ?    i        
  L1M4_orf2#LINE/    780 A--CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_80085184_8   1641 GGACATGACCAGACACTTTTCCAAAGAATGTATACATGTAGTCAAGAAGT 1690
                            iv   vi     i  i         vi      vi i i   v   i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_80085184_8   1691 ATATGAAAAAATATTTAACATTACTTATCAT 1721
                          i       i  ii i     i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (153 / 87)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 1.82 (51 / 28)  


3272 26.32 0.66 0.66  chrX_80087979_80094377     5000  5907 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80087979_8   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5049
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80087979_8   5050 GGCAATACTGCCCAAGGTAATTTCTAGATTCAATGCCATCCCCATCAAGC 5099
                                  v     iv i  i vi        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80087979_8   5100 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5147
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_80087979_8   5148 TATGGAACCAAAAAAGAGCCCGTATCGCCAAGTCAATCCTAAGCCAAAAG 5197
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80087979_8   5198 AACAAAGCTGGAGGCATCACGCTACCTGACTT-GAAACTGTACTACAAGG 5246
                                i      vv    i  v  ii i  -i     -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_80087979_8   5247 CTACTGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATATAGAT 5296
                             v    i   i    ii i       i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_80087979_8   5297 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAAC 5344
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_80087979_8   5345 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5394
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_80087979_8   5395 TCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAAC 5444
                            v  i  i              v      v  ?   i   i i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_80087979_8   5445 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATAG 5494
                             ii    i    v   i     v              i    i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_80087979_8   5495 ATTAAAGACTTACATGTCAGACCTAAAACCATAACAACCCT-AGAAGAAA 5543
                           i ?    i  v    v   v       i    -   i  -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAA 544

  chrX_80087979_8   5544 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5593
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_80087979_8   5594 AAAACACCAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGGATCT 5643
                          vi            vvi          v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_80087979_8   5644 AATCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAAAGTGA 5693
                         v      v v  i i   i  ii vv    i  v    i  vv       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_80087979_8   5694 ACAGGCAACCCATAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5743
                          v  i       i i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_80087979_8   5744 AAAGGGCTAATATCCAGAATCTACAATGAAGTCAAACAAATTTACAAGAA 5793
                           i  i  vi          v  i  v   v  vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_80087979_8   5794 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGTCATGAACAGACATT 5843
                            i     i     v  i?    i    ii    viv    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_80087979_8   5844 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5893
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_80087979_8   5894 TCATCGCTGGCCAT 5907
                         v    i????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1977 26.86 17.61 0.90  chrX_80098283_80102159     1429  2206 (1671)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80098283_8   1429 TGGGAAAAGATTCCATCCTTATAAATAGAAATAATTAATATTGTGAAAAT 1478
                            i  i v  i    vi i  ii  v i  v v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80098283_8   1479 GACCATGATGCCCAAAGTAATTTATAGATTCAAGGCTATTCCCATCAAAC 1528
                          i v  iv v      v i  i  i        v  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80098283_8   1529 TACTATTGACATTCTTCACAGAATTAGAAAAAACAAACTA--CTTAAAAA 1576
                          v i vivi v  i  ii     v v  -----   i  i-- i     -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-----CAAGCTGATCCTAAAA- 144

  chrX_80098283_8   1577 CTCATATGGAACCAGAAAAGAGCCTGTATAGCCAAGACAATCCTAAACCA 1626
                         i          viiv  ii  v  v v        i      i i  vv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_80098283_8   1627 AAAGAACAAAGCTGGGGGCATCACACTACCTGAGTTCAAACTACACTACA 1676
                         i          i   i  vv       v  ii v      vivi      
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_80098283_8   1677 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATT 1726
                          i          i   i    ii         i i  ii i     i  v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_80098283_8   1727 GACCAATGGAATAGAATAGAGATTTTAGAAATAAGAATGCACATCTACAG 1776
                           i              v    v ii        ivviii    i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_80098283_8   1777 CTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 1826
                         ii vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_80098283_8   1827 CCCTGTTTAATAAATGGTGCTGAAAAAACTAGCTAGCCATGTGCAGAAAA 1876
                         vi  v  i  i           ii v    i v  ?   ii    i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_80098283_8   1877 CTAAAACTGGACCCCTTCCTTAAACCTTATAGAAAATTTAAC--AAAA-- 1922
                         v i  ii         v   i v   v    v    v     --    --
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_80098283_8   1923 -------------------------------------------------- 1922
                         --------------------------------------------------
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_80098283_8   1923 -------------------------------------------------- 1922
                         --------------------------------------------------
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_80098283_8   1923 -----ACCAAAA----------------------TTGACAAATGGGATCT 1945
                         -----       ---------------------- v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_80098283_8   1946 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 1995
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_80098283_8   1996 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 2045
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_80098283_8   2046 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 2095
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_80098283_8   2096 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGTCATGAACAGACATT 2145
                            i     i     v  i?    i    ii    viv    i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_80098283_8   2146 TCTCAAAAGACATTTATGCA----GCCAAAAACCACATGAAAAAATGCTC 2191
                             v     - vv   i  ----     v  v          i      
  L1M4_orf2#LINE/    845 TCTCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_80098283_8   2192 ATCATCACTGGCCAT 2206
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (121 / 86)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 18.00 (144 / 8)  

1159 23.83 2.80 1.87  chrX_80098283_80102159     2957  3384 (493)    L1M4_orf2#LINE/L1      477   908 (0)  

  chrX_80098283_8   2957 AAAATTTAACTCAAGATATATTAAAGAC--AAATATAAAACCAAAAACCA 3004
                             v         i  iv  i ?    --    i   i v v     i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_80098283_8   3005 TAAAAGCCCTAGAAGAAAACCTAGG--TAATACCATTCAGGACATAGGCA 3052
                              vi i           v    --   - i -   iv   v v  vv
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGT 574

  chrX_80098283_8   3053 TGGGCGAATATTTTATGATGAAAT--CATCAAAAGCAATTGTAATAAAAG 3100
                          i   -   iv   v v -  v  --  i        vvv i  i     
  L1M4_orf2#LINE/    575 TAGGC-AATGGTTTCTTA-GATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_80098283_8   3101 CAAATATTGAAAAATGGGATTTAATTAATCTAAAGAGCTTCTGCTACAGT 3150
                         v   v  v  v    v   i  v  i  vv v  i i   i  - i -v 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGC-TT 670

  chrX_80098283_8   3151 CAAACAA-ACTATCATCAGAGTGAATAGGCAACGTAAAGAATGGGAGAAA 3199
                             vi -       vv i      v  i    vi v             
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_80098283_8   3200 AGGTTTGCAATCTATCCATCTGACAAAGGTCTAATATCCAAAATCTACAA 3249
                          vi       vii  vi      i  i  v  vi      i   v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_80098283_8   3250 GGAACTTAAACAAATTTACAAGAAAAAACCAAACAACTGCATTAAAAAAG 3299
                         i     ivv    v iv i  v     iv    i   ivv   ?     -
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA- 819

  chrX_80098283_8   3300 TGGGCAAAGGATGTGAACAGACAATTCTCAAAAGACGACATGC----GGC 3345
                                     v    i     v     v     v  i  i ----   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_80098283_8   3346 CAACAAACATGTGAAAATGA-GCTCAACATCACTAATTAT 3384
                            i  i  ii      -  -           ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.92 (48 / 52)
Gap_init rate = 0.03 (14 / 432), avg. gap size = 1.43 (20 / 14)  


1241 26.16 1.39 4.40  chrX_80104193_80106774.rev      844  1275 (1307)    L1M4_orf2#LINE/L1        1   419 (489)  

  chrX_80104193_8    844 TAGAAATACATCCCATGCTCATGGATTAGCAGAATTAATATTGTAAAAAT 893
                          i    v i        i         i v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80104193_8    894 GGCCATACTACCCAAAGAAATCTACAGATTCAAAGCAATTCTTACAAAAA 943
                            v     v      vvi              v     i i  iv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80104193_8    944 ----AACTGATGTAATTTTTCACAGAAATAGAAAAGA-AATCTTAAAAAT 988
                         ---- i   vi----     ii       v  v   v-i   i     --
  L1M4_orf2#LINE/    101 TCCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-- 144

  chrX_80104193_8    989 TTTGTATAAAACCAAAAAAAAAAAAAAAAGAGCTTGAATAGCCAAAGCAA 1038
                           ii   ii  ---------- viv  ii  v iv           i   
  L1M4_orf2#LINE/    145 TTCATATGGAA----------ATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_80104193_8   1039 TTCTGAATAGAAAAAAATAAAGCTGGAGGCAC-CACACTGAGTGAATTCA 1087
                          ii    - i i  i  i    i      -  -      vvvii v    
  L1M4_orf2#LINE/    185 TCTTGAA-AAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCA 232

  chrX_80104193_8   1088 AAATATATGAAAAGGCTATAGTAACCAAAATAGTATGATATTGTTATTAA 1137
                            iv  iv v  i    i     i   i i   i  i  i  vi  -  
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AA 281

  chrX_80104193_8   1138 AAAAACACACATAAACCAACAGAACAGAATTGAGAACACAGAAATAAATC 1187
                         ii v v   i   i i   ii   i          iiv          i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_80104193_8   1188 GACATATTTACATCCAACTGATTTTTCACTAAGGTGCCAAAAGCATGCAT 1237
                         v i i     iivi   i       iv  v i        i v   v  v
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_80104193_8   1238 TGCGGAATCGACACACTCTTCAATAAAGAGTACTGAGA 1275
                           v    vvi i vv  i     i   vi  i   i  
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

Transitions / transversions = 1.69 (71 / 42)
Gap_init rate = 0.02 (9 / 419), avg. gap size = 2.78 (25 / 9)  

1404 24.75 3.62 1.81  chrX_80104193_80106774.rev     1598  2094 (488)    L1M4_orf2#LINE/L1      403   908 (0)  

  chrX_80104193_8   1598 AAAAAAGAGTACTGAGAAAAATGGATATTCATATGCAGGACAATGAAATT 1647
                           v   vi  i   i  v  v      ?i  i     ii v      i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_80104193_8   1648 AGACCCTTATCTCTCACCGTACACAAAAATCAACTCAAGATAGATTAAAA 1697
                         i     i  i   v    i  i        i       i  i   i ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_80104193_8   1698 AGCTTAAAAGTGAGACCCCAAAGTATACAACAACTAGAATAATACATAGG 1747
                          - i    v  i   v iv   v    v   vvi     v  v       
  L1M4_orf2#LINE/    503 A-CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_80104193_8   1748 A--AAATACTTCA-AACATTAGCCTAAAGAAAGATTTTATGGCTAAGATG 1794
                         ?--    -    i-i  v  i vi  iiv  v i   iv i v  v  ii
  L1M4_orf2#LINE/    552 NGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_80104193_8   1795 TCAAAAGCATAGGCAAC----TAAAACATAGA-GAATTGGAATTACATTA 1839
                         i        i i     ----v    v     -i       v  -   i 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATCA 649

  chrX_80104193_8   1840 AGCTAAAAAGCTTTTGCACAGCAAAGGA----ATCAATAGAGTAAAGAGA 1885
                          iv v    i      ii vv       ----     v i   i  i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_80104193_8   1886 AAAGCCACATAATAGGAGGGATTATTTGCAAACTCTCACATTCATCTGAC 1935
                         v  v     v   i    ii v          ---   i  --      i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAA---TCATAT--ATCTGAT 744

  chrX_80104193_8   1936 AATGGACTAATATCTAGAATATATAGGAAATTCAAACAACTCAA--GTAA 1983
                           v     vi    i          iii  i  vv         --i   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_80104193_8   1984 AAACACTAATAATCTCATTAAAAATTGGAAAAAATACATTAACATATATT 2033
                            v  v     i iv   ?    v   iv   iv iv v  i v i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_80104193_8   2034 TCTCAAAAGAAGAAATACTAATGGCCAACAA-C-TATGAAAAAAATGCTT 2081
                             v        v    v         i  - -i       i -    i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chrX_80104193_8   2082 AA--TTATGATTCAC 2094
                           -- i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (69 / 50)
Gap_init rate = 0.03 (15 / 506), avg. gap size = 1.80 (27 / 15)  


 739 27.90 1.81 3.26  chrX_80141229_80143986      852  1127 (1631)    L1M4_orf2#LINE/L1        1   272 (636)  

  chrX_80141229_8    852 TGGAAATACATCCCATGATCATTAATTGGAAGAATCAGTGTCATAAACAT 901
                               v i        v    vi         v i i ---------  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAAT---------AT 41

  chrX_80141229_8    902 TATGCAAATGACCATATTACCCAAAGCAATCTAGAGATTAAATGCATTTT 951
                          i vv i   i v   i v      vii     v     v  i   v ii
  L1M4_orf2#LINE/     42 TGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chrX_80141229_8    952 TTATCAAAATAGCAACAACATTTTTTATAGGATTAGAAAAAA-AATTCTA 1000
                         i         vv  i vi v      ii  i v v  v  iv-i  i   
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_80141229_8   1001 AAATCCATATGGAACCAAAAAAGAACCTTAATAGCCAAAGCAATTCTAAG 1050
                             i         viiv  ii  v  vv          i    ii i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_80141229_8   1051 CAA-ACTAATACATTTGGAGGCATCACATTACACAACTTCAAA--TTA-T 1096
                         v  - vv  i v v       vv     i v v   i      --   - 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_80141229_8   1097 ACAAGGCTGTAGTAATGGAAACAGCATGGTA 1127
                             i   ii      vi i    ii     
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

Transitions / transversions = 1.20 (42 / 35)
Gap_init rate = 0.02 (5 / 272), avg. gap size = 2.80 (14 / 5)  

1717 26.50 4.07 2.11  chrX_80141229_80143986     1649  2263 (495)    L1M4_orf2#LINE/L1      262   888 (20)  

  chrX_80141229_8   1649 ACGGTGTGGTA------TAAAAGTAGATACATAAGTTAATGGAACAGAAT 1692
                           i        ------   iii    i i   ii i       i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_80141229_8   1693 AGAGAACCCAGAAATGAAACCAAATATTTACAATCAATTAATCTATGAAC 1742
                         v    ii        i  v   v i     iii      i  i vi  - 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA-C 360

  chrX_80141229_8   1743 AAGCAT-TAAAAAACATAAATTGAGGAAAGGACATGCTATTGAATAAATG 1791
                            vi -iv  i v   vv v  i      i i vv  v  v  i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_80141229_8   1792 ATTCTGGGAAAATTGGATGGGCACATGTTTAAGAATAATACTGGATTTCT 1841
                         i v      v  i     i?v      ivv      i vii    iii  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_80141229_8   1842 --CTCTTACTGTATACAAAAATCAACTCAAGATGGAGTA-AG--CTAAAT 1886
                         --   vi  ii           i       i     vi -  --      
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_80141229_8   1887 CTAAGGTTTGAGATTATAAAAACTTTAGAAGAAAATGTATTTAAAAAAAA 1936
                         v    ivi i i i       vii           ii  -----ii?iv 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA-----GGNGTA 555

  chrX_80141229_8   1937 AACTCTTCTGGACATTGGCCTAGGCAAAGAATTTATGACTAAGACCCCAA 1986
                           -     vv   v    vi       v iv  iv iiv  v   v    
  L1M4_orf2#LINE/    556 AA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_80141229_8   1987 AAGCAAATGCAACA---GAAATAAATAAACAAATGGGACTTAATTAAACC 2033
                              v v      ---    -     i i    v      v  i   vi
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_80141229_8   2034 AAAAAAATT-----CTTCACAACAACA-----AAAAATCAGATTAAACAG 2073
                         v     v  -----     -  vi   -----  i  --  -- i  v  
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGAA--AG--TGAAAAG 698

  chrX_80141229_8   2074 ATAACCTATAGAACAAGATAAAATATTTTCAGATTATATATCTGACAAAG 2123
                          i    i i    iii  v         v  i  i          i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_80141229_8   2124 GACTAATATCCAGAATCTACAAGGAACCCAAACAAATCAGCAAGATAAAA 2173
                             vi          v  i  i    i vv    v   ii  v v   i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_80141229_8   2174 GCAAATAATCCTATTAAAAAGTGGCCAAAGGATATGAATAGACATTTCTC 2223
                         i       i  v   ?    i   v        v                
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_80141229_8   2224 AAAAGAAGATACATAGGCAGCTCCCACACATATGGACAGA 2263
                         v          i i iiii  ivvi vi  i   i v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.58 (98 / 62)
Gap_init rate = 0.02 (15 / 627), avg. gap size = 2.53 (38 / 15)  


2741 27.07 2.46 0.89  chrX_80145706_80156746     4342  5235 (5806)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80145706_8   4342 TGGAAAAATATTTCATGCTCATAGATAGGAG---TCAATATCATGAAAAT 4388
                               i    ii    i    i   v   i--- i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80145706_8   4389 GGCCATACTGCCCAAAGGAATTTATAGATTCAATGCTATCTCCATCAAGC 4438
                            v     v      vvi  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80145706_8   4439 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 4487
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_80145706_8   4488 ATGGAACCAAACAAGAGGCC--GCATATCCAAGATCAGCTTAAGAAAAAA 4535
                               -- vi    i i  -- v   v    i iv v   i -    i 
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGA 196

  chrX_80145706_8   4536 AGGACAAAGCTGGAGGCGTCACGCTACCAGACTTTA-----TACTACAAG 4580
                           i      i      vv    i  v  vi i  i -----        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_80145706_8   4581 GCTACAGTAACCAAAACCGCAGGGTACTGGAACCAAAACAGTTATATAGA 4630
                                   i   i  v iiv        v iv ii i  vi       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_80145706_8   4631 TCAATGGAACAGAACAGAGGCCTCAGAAATAACACTACACATCTACAACC 4680
                                  i    iv   ivii         vv i i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_80145706_8   4681 ATCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGAAAAGGATTCC 4730
                          vi    i  i     ivv  v   i vi vv       i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_80145706_8   4731 CTATTTAATAAATGGTGCTTGAA-AACTGGCTGGCCATATCCAGAAAATG 4779
                           v  i  i          v i -      v i?   i  v  i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80145706_8   4780 GAAACTGGACCCCTTCCTTACACCTTATACAAAAGTTAACTCAAGATGGA 4829
                            ii         v   i     v         i         i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80145706_8   4830 TTAAACACATAAATGTAAAACCAAAAACCATAAAAACCCTT-GAAGAAAA 4878
                          i ? v  v         i v v     i      - i   -        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_80145706_8   4879 CCTAGGCA-ATATCATTCAAG--CACAGGCATGGGGAAAGACTTCATGAC 4925
                          v    ?i- v   -   iv -- vii  i- i  v  v ii   v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGA 593

  chrX_80145706_8   4926 TAAAACACCAAAAGTAATTGGAACAAAAGTCAAAATTGACAAATGGGATC 4975
                           vi          i vvv v        vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_80145706_8   4976 TAAT-AAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 5024
                          v  -    i    i -   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_80145706_8   5025 GAACAGGCAACCTACAGAATGGGAGAAAAT-TTTGCAATCTACTCATCTG 5073
                            v  i     i                 -       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_80145706_8   5074 ACAAAGGTCTAACATCCAGAATCTATAAGGAACT--TA-AATTTACAAGA 5120
                          i  i  v  vii         v     i     --  -  i i vv iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_80145706_8   5121 AAAAAAACACACAACCCCATCCAAAT-TGGGCAAAGGATGTGAACAGACA 5169
                              i   v i     v  i?   v-            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_80145706_8   5170 CTTCTGAATAGAAGACATTTATGCAGCCAACAAATATATTTTAAAAAGCT 5219
                         i    vv v      i  vi viii     i  ii i  vvv  i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_80145706_8   5220 CATCATCACTGGTCAT 5235
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.50 (30 / 20)  

2964 26.67 1.90 0.56  chrX_80145706_80156746     9653 10548 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80145706_8   9653 TAGAAACATATCCCATGCTCATGAATGGGTAGAATCAATATTGTGAAAAT 9702
                          i    v          i     i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80145706_8   9703 GACCATCCTACCAAAAGCAATCTACAAATTCAACGCAATTCCCATCAAAA 9752
                          i v  v  v  v   vii       i            i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80145706_8   9753 TATCACCATCATTCTTCACAGAGCAGAAAAAACC-ATCCTAAAATTCATA 9801
                          vi  v vv v  i  ii    ivvvi v  i i-               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_80145706_8   9802 --GAAA-GCCAAAAAAGAGCCCACA-TAGCCAAAGCAAGACTAAGCAAAA 9847
                         --    -  ----  i ii    v -        i   vvi i iv  i 
  L1M4_orf2#LINE/    151 TGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_80145706_8   9848 AGAACAAATCTGGAGGCATCACATTATCTGATTTCAAGCTATACTATAAG 9897
                                 vi      vv     i vi ii       iviv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_80145706_8   9898 GCCATAGTCACCAA-ACAGCATGGTACTGGCATAAAAATAGGAACATAGA 9946
                           i i   v i   -    ii              ii    iv i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_80145706_8   9947 CCATTGGAACAGAATAGAGAACCCAGAAATAAACCCAAATCCTTACAGCC 9996
                         i  v     i     v    ii               v ivi   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_80145706_8   9997 AACTGATCTTTGTCATAGCAAACAAAAACATAAAGTGGGGAAAGGACACC 10046
                           i    i  i v  vi vviv   i v   vv i         i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_80145706_8  10047 CTATTCAACAAATGGTGCTGAGATAATCGGCAAGCCACATGTAGGAGAAT 10096
                           v                 i  i  ii  vv ?       i ii     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80145706_8  10097 GAAACTGGATCCTCACCTCTCTCTTTATACAAAAACAAACTTAAGATAGA 10146
                            ii    i  ii     v v iv          iv    i  i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80145706_8  10147 TCAAGGACTTAAATCTATGTCCTGAAACTATAATAATTCT-AGAAGATAA 10195
                            ?i   i     v  v vv  i         -  i   -      v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAA 545

  chrX_80145706_8  10196 CATTGGGAAAACCCTTCTAGACATTCGCTTAGGCAACAATTTCATGACCA 10245
                            v  ?iv  vi    vv   v  v v        iii    v iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_80145706_8  10246 AGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTA 10295
                         v  vv         v v    i    iv   i   i   iv v      v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_80145706_8  10296 ATTAAACTAAAGAGCTTTTGCACGTCAAAAGGAACAGTCAGCAGAGTAAA 10345
                           i   v v  i i      ii v     i iv  vi   iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_80145706_8  10346 CAGACAACCCATAGAGTGGGAGAAAATCTTCACAATCTATACATCTGATA 10395
                         v          i   i           v  ii   vii   i        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_80145706_8  10396 AATGACTAATATCCAGAATCTACAATGAACTCAAACAAATTAGCAAGGAA 10445
                          iv    vi          v  i  v      vv    v i ii  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_80145706_8  10446 AA--------ACCCA-CCAAAAAGTGGGTTAAGGACATGAATAGATAAT- 10485
                           --------     -ii?    i    iv     iv        i v -
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_80145706_8  10486 CTTAAAAGAAGATATACAAATGGCCAACAAACATATTAAAAAATTATCCA 10535
                           iv                       i  i  i  v    i  vv  v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_80145706_8  10536 CATTACTAATGAT 10548
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (135 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


2303 27.80 3.19 3.41  chrX_80161927_80167184.rev     3858  4767 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80161927_8   3858 TGGAAAAATATATCATGCTCATGGATAGAAAGAATCACTATCTTTAA-AT 3906
                               i    vi    i        v i    v i v   iv    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80161927_8   3907 GACCATATTGCCCAAAGCAATTTACATATCTAATGCTATTCCTATAAAAC 3956
                          i v   i v      vii  i    v  ii  i  v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80161927_8   3957 TAGTAATGGCATTCTTCATAGAATTAGAAAAAACT-ATTTTAAAATTTAT 4005
                          vvi iiv  v  i  iii    v v  v  i-  -  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_80161927_8   4006 ATGAAACTGAAAAAGAGCTCAAATAGTCAA-----TTCTAAGCAAAAAGA 4050
                            i  v  v  ii  v ivi     i   ----- ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_80161927_8   4051 ACAAAACTGTAGGCATCACATTACCCAACTTCAAGCTATACTACATGGCT 4100
                              ii  v   vv     i v     i     iviv       vi   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_80161927_8   4101 ACAGTAACCAA-ACAATCATAGTGCTGGTACCAAAACAGACACAAAGACA 4149
                                i   -   i -i i  i    i iv ii i     i v   iv
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGT-GTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80161927_8   4150 AATGGAACAGAATAGAGGACCCAGAAATAAAGCCACAAGCCTACAACCAT 4199
                                i     v   iii           v   i viii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_80161927_8   4200 CTGATCTTTGATAGTCATG--AAAAATGAGCAATGAGGAAAGGACACCCT 4247
                         i    i  i  i ivvi  --  i viivv     i      i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_80161927_8   4248 AGCCAGTAAATTATGCTGAGATAACTGGGTTGCCATATGCAAA-GATTGA 4296
                         vvi  ii    vi     i  i      i v?   i       -  v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_80161927_8   4297 AGTTAGACCTCATCTTTGCACCATATACAAAAATCAACTCAAGATGAATT 4346
                             i    i vv i ii                i       i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_80161927_8   4347 AAAGACTTCAATGTAAAACCTAAAACTATAAGAACCCAT-GAAGATAACC 4395
                          ?    i v       i v            -   i v -     v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACA 547

  chrX_80161927_8   4396 TAGG---AAATACT----ATTCTGGACATAGGCCCTGAAAAGATACCAT- 4437
                             ---    vi ---- iii   ii-     -----  v i vi v -
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGT-TAGGC-----AATGGTTTCTTA 591

  chrX_80161927_8   4438 GATAAAGATGTCAAA-GCAATTGCAACAAAAACAAAAATTGACAAACGGG 4486
                             v-  iii    -   vvv         iv      v  i   iv  
  L1M4_orf2#LINE/    592 GATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_80161927_8   4487 ATCTAATTAAACTAAATGGCTTCTGCACAGCAAAAGAAACTGTCAACAGA 4536
                          ii v  i   v v  vii   i  ii vv    i  v   i    --  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA--GA 688

  chrX_80161927_8   4537 CAGTAACCTACATAATGGGAGGGGAAAACATTACCTACATAACTGGAGAA 4586
                         v   i -----------------i  i   --   i   v  iv      
  L1M4_orf2#LINE/    689 AAGTGA-----------------AAAGACA--ACCCACAGAATGGGAGAA 719

  chrX_80161927_8   4587 AACATTTGTAAATTACACATCTGACAAAGGCCTAGT---CAGAATTTATA 4633
                           i     i    i i i      i  i  v  v  ---      v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_80161927_8   4634 AGAAACTT----AAATATACAAGCAAAAAACAAACACCCCA-TTAAAAAG 4678
                          ii    i----  v vv i  vv    i     i v    -  ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_80161927_8   4679 TTTACAAAGAATATGACCAGACACTTTTCAAAAGAAGACATACACATGGC 4728
                          vvi     i  v   vi     i  i  v        i     v     
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_80161927_8   4729 CACCAGGTATATGAAAAAACGCTGAACATCACTAATCAT 4767
                           vi i i i       i i   v       ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (156 / 94)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.61 (60 / 23)  


4093 16.32 6.25 1.27  chrX_80172533_80174771      883  1746 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_80172533_8    883 GGAAAGACATACTGTGTTCATGGATTGGAAGATTTAGTATTGTTAAAATG 932
                                i  v ii                  i   i         i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_80172533_8    933 GCAATATTCCCCAAGTGGATCTGCATATTAATTGCAACCCCAGTCAAAAC 982
                               i       i v     i  v   v vi    i   vi      i
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_80172533_8    983 ACCAACTGCTCCCTGCCTTGTTTTTGCAGAAATGGACAAGCTAATCCTAA 1032
                         v   i    -------   --            v        i       
  L1M4_orf2#LINE/    102 CCCAGCTGC-------CTT--TTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_80172533_8   1033 AATTTATGTGGAATTGCAAGAGACCTGAAGTAAT---------------- 1066
                             i  i     v      i    iii i  ii----------------
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_80172533_8   1067 -----GAGCAAAGTTGGAGAACTGACACTTCT-GATGTCAAA-CTTACTG 1109
                         -----  i           i   v       i-i  v     -      i
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_80172533_8   1110 TAATACTACAGTAATCAAAAT--TTTTGTACTGACA--AAGATTGACATG 1155
                         i  vi             i i-- v v      i  -- i   v     i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_80172533_8   1156 --GGTCAATGTTGCAAAATTCAGGGTCCAGAAATAAACCCATACATCTGT 1203
                         -- i      vvii i    v  i                      i i 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_80172533_8   1204 GGTTTATTGATTTT-GACACAGGTGCCAAGGCCATTGAATGGGGAAAGAA 1252
                            iv         -    vi         i     v             
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_80172533_8   1253 TAGTGTTTTTCAATAAATGATACTTGGGCAAATGGATAGCCAAATGTAAA 1302
                             -i       i     i i  v  i   v      ?   v   i   
  L1M4_orf2#LINE/    393 TAGT-CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_80172533_8   1303 TGAGTGAAAATTGATCCCTACTTCACTTCATATACAAAAATTAACACAAA 1352
                         v  i    iv v  i      i    vi                 v    
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_80172533_8   1353 ATGTACCAAAGACCTAAATGTATGAGAAAAAAGTATACAACTCTTAGAAG 1402
                            v i  ?             v   vv    v    v            
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_80172533_8   1403 AAAACATATGTGTACATCTTAGTAACCCAGGGTTTGACAAAA--TTCTTA 1450
                                 v ?   v     v  i   iv     v i   vi--      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_80172533_8   1451 GATATACCACCAAAAATATAAGCTATAAAAGAAAAAA---ATGAATTGA- 1496
                              iv        ii i    v i           ---  i     i-
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_80172533_8   1497 --TCATAAAAATTAAAAA--TTTGTGTATCAAAGGACACTATCAAGAAAA 1542
                         --    v           --      iv                     i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_80172533_8   1543 CGAAAA------CCACAGAATGGGAGAAAAATATT-GCAAATCATATATC 1585
                         i     ------                  -    -              
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATC 740

  chrX_80172533_8   1586 TGACAAGGGACTTGTATGTAAAAGATATACATA--TCTTAGAACTCAATG 1633
                            i             vi i  v     v v --     v        i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_80172533_8   1634 CTAAAGAGACAA----CCCAATTAAATAATGGA-AAATGATTTGCATAGA 1678
                         v    i      ----       ?  v     i-   v      v     
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_80172533_8   1679 CATTTCTCCAAAGAAGATATACAAATGACCAACCAGCACATCAGAAGATG 1728
                                                    i    iv       v i      
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_80172533_8   1729 CTCAACATCATTAGAGAA 1746
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (81 / 56)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 3.25 (65 / 20)  


3051 27.49 1.22 0.55  chrX_80204523_80216923     5117  6018 (6383)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80204523_8   5117 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5166
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80204523_8   5167 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5216
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80204523_8   5217 TACCATTGACTTTCTTCACTGAACTGGAAAAAATTACTTGAACTTTCATA 5266
                          v   vivi i  i  ii v   v v  v  iv v iiiv  vv      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_80204523_8   5267 TGGAACCAAAAAAGAACCTGCATAGCCAAGACAATCCTAAGCAAAAAGAA 5316
                              viiv  ii  v  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_80204523_8   5317 CAAAGCTGTGTGCATCACGTTACCTGACTTCAAA--CTACTACTAGGCAA 5364
                              i  viv vv    ii v  ii i      --i      v i  v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_80204523_8   5365 CAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 5414
                               iv  i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_80204523_8   5415 TGGAACAGAAC--AGAGTCCTCAGAAATAACACCACACACCTACAACCAT 5462
                              i    i--       --        vv   i   ii  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_80204523_8   5463 CTGATCTTTGACAAACATGACAAAAACAAGCAATTGGGAAAGGAT--TCT 5510
                         i    i  i     ivi  v   i v  vv    v       i  --   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_80204523_8   5511 TTATTTAATAAATGGTGTTGGGAGAACTGGCTAGCCATATGCAGAAAGCT 5560
                           -- i  i        i     v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80204523_8   5561 GAAACTGGATCCCTTCCTTACGCCTTATACAGAAATTAATTCAAGATGGA 5610
                            ii    i    v   i  i  v      i       i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80204523_8   5611 TTAAAGGCTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGATAAC 5660
                          i ?  i i           v       i      vi i       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_80204523_8   5661 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5709
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_80204523_8   5710 AATCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5759
                         viv           vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_80204523_8   5760 ATTAAAATAAAGAGGTTCTGCACAGCAAAAGAAGCTACCATTAGAGCGAA 5809
                           i     v  i iv  i  ii vv    i  vi   i  vv i  i   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_80204523_8   5810 CAGGCAGCCTACAGAATGGGAGAAAAATTTTGCAATCTACTCATCTGACA 5859
                         v  i  i  i                vv       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_80204523_8   5860 AAGGGCTAATATCTAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5909
                          i  i  vi    i     v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_80204523_8   5910 AAAA--AACAATCCCATCAAAAAATGGGCAAAGGATATGAACAGACACTT 5957
                           i --  i  i  v  i?                 v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_80204523_8   5958 CTCAAAAGACAAAATTTATGCAGCCAACAG--ACATGCAAAAATGCTTAT 6005
                            v     vi v  vi viii     i i--     v   i     i v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_80204523_8   6006 CATCACTGGTCAT 6018
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  

1586 27.27 0.93 0.93  chrX_80204523_80216923     8290  8718 (3683)  C L1M4_orf2#LINE/L1   (479)   429     1  

C chrX_80204523_8   8718 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 8669
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_80204523_8   8668 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 8619
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_80204523_8   8618 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 8571
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_80204523_8   8570 TATGGAACCAAAAAAGAGCCTACATCGCCAAGTCAATCCTAAGCCAAAAG 8521
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_80204523_8   8520 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 8471
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_80204523_8   8470 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGATC 8421
                                 i   i    ii         i i  ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_80204523_8   8420 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGTCGCATATCTACAACT 8373
                                i    i--    i  --        vvi ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chrX_80204523_8   8372 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 8323
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_80204523_8   8322 CTATTTAACAAATGGTGCTGGGAAAACTGGCTA 8290
                           v  i                 v      v  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

Transitions / transversions = 1.85 (76 / 41)
Gap_init rate = 0.01 (5 / 429), avg. gap size = 1.60 (8 / 5)  

1560 27.73 0.00 0.00  chrX_80204523_80216923     9060  9535 (2866)    L1M4_orf2#LINE/L1      433   908 (0)  

  chrX_80204523_8   9060 ATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAAT 9109
                          i   i i  iiv    ii    i    v   i     v           
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_80204523_8   9110 CAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAAACATAAAAA 9159
                         i  i    i      i ?    i    i  v   v      vi      v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_80204523_8   9160 CCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAG 9209
                         i i           v    ?i v viv   iv   v v  vv i     v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_80204523_8   9210 GACTTCACGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTCA 9259
                          ii   viivv  vi            vvi          vv     vv 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_80204523_8   9260 CAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA 9309
                         i    v   ii v  i   v v  i i   i  ii vv    i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_80204523_8   9310 CCATCAGAGTGGACAGGCAAGCTACAAAATGGGAGAAAATTTTCACAACC 9359
                         i  vv i    i v  i   v i   i             v  ii   vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_80204523_8   9360 GACTCATCTGACAAAGGGCTAATATTCAGAATCTACAATGAACTCAAACA 9409
                         v ivi      i  i  i  vi   i      v  i  v      vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_80204523_8   9410 AATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTCGGCAAAGGATA 9459
                          v iv i  v     i     i     v  i?    i v          v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_80204523_8   9460 TGAACAGACACTTCTCAAAAGAGGACATTTATGCAGCCAAAAAACACATG 9509
                             i     i     v     i  i  vi viii     v  i      
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_80204523_8   9510 AAAAAATGCTCACCATCACTGGCCAT 9535
                             i       v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (71 / 58)
Gap_init rate = 0.00 (0 / 476), avg. gap size = 0.00 (0 / 0)  

3304 25.03 2.47 0.67  chrX_80204523_80216923    11018 11908 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_80204523_8  11018 GGAAAAATACCTCAT--------------AGAATCAATATTATTAAAATG 11053
                              i   i i   --------------   v i      i    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_80204523_8  11054 TCCACACTACCCTAAGCAATCTACAGACTTAATGCAACCCCTATCAAAAT 11103
                         v v i   v   v  vii         i i  i    i            
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_80204523_8  11104 ACCAATGGCATTCTTCACAGAAATAGAAAAA--AATTCTAAAATTTATAG 11151
                         v   iiv  v  i  ii       v  v  i--i  i        i   v
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_80204523_8  11152 GGAACCACAGAAGACCCAGGATAGCCGAAATTATCCTAAGCAAAAAGAAC 11201
                             vii  iii       i      i   iv   i i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_80204523_8  11202 AAAACTGGAGGAATCCTATTACCTCACTTTAAA--TT-CTACAGAGCTTT 11248
                            ii       v  vi i v  iv i  i   --  -     i    vi
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_80204523_8  11249 AGTAATCAAAACAACATGGTACTGGCATAAAAACAGACATATACACCAAA 11298
                                  i   iii              ii i         v i   v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_80204523_8  11299 GGAATAGAATAGAAAACTCAGAGTTAA-TCCATACATATACAGTGAACTC 11347
                                   v  i iii    iv   -i        v  ii  v  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_80204523_8  11348 ATTTTTAAGGTAGCTGCCAAGAATATACACTGGGGAAAAGACAGTCTCTT 11397
                              ii vivi v        vi  v  v        ii i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_80204523_8  11398 CAATATATGGTGCTGGGAAATCTGGATATCAGCATGCAGAATAATGAAAC 11447
                            i v            v v       ? vi      i  v      ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_80204523_8  11448 TTGACTCCTATCTCTTGCCATATACAAAAATCAAATCAAAATGGATTAAA 11497
                          v   i    i   vii              i  v           i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_80204523_8  11498 GACTTAAATCTGACCCTTCAAGCTGTGAAACTAATACAAAGAAACACTGG 11547
                            i     v i vvvi v  i  i i     vv  v  ii     iv  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_80204523_8  11548 AGAAACTCCCCACGACAACAGACCAGGCAAAAATTTCTTGAGCATTATCT 11597
                         ? v  v  ii ii   vvii iii      vii      iiii  v iv-
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA- 600

  chrX_80204523_8  11598 CCCACAAGCACAGGCAACCAAAACAAACGTGGACAAATGGGATCACATCA 11647
                         -   v       i     v   iv   vi i  i    v   iiv     
  L1M4_orf2#LINE/    601 -CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_80204523_8  11648 AG-TTAAAAAGCTTTTGCACAGCAAAAGAAACAATCAACAAAGTAAACAG 11696
                          i-       -      ii vv    i  v  v     v     i  v  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_80204523_8  11697 ATAACCCACAGAATTGGAGAAAATATTTGCAAACTACCCATCTGACAAGG 11746
                          i            v                  ii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_80204523_8  11747 GATTCATAACCAGAATATATAAGGAGCTCAGACAACTCTATAGGAAAAAA 11796
                           i ii  v             i  i   vv       v   iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_80204523_8  11797 AAGTATAATAATCCAATT-AAAAATGAGCAAAAGATTAGAATAGACATTT 11845
                          --i -     i      -       i     i    v            
  L1M4_orf2#LINE/    799 A--CA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_80204523_8  11846 CTCAAAAGGAGACGTACAAATGGCAAACAGGCATATGAAAAGGTGCTCAA 11895
                            v    i   ii          v  i i   i        i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_80204523_8  11896 CATCATTGATTAT 11908
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (141 / 79)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 2.55 (28 / 11)  


1236 27.62 13.15 1.33  chrX_80254979_80256653      507  1183 (492)    L1M4_orf2#LINE/L1      152   908 (0)  

  chrX_80254979_8    507 GGAAATATAAAGGGCAATGAATAGTCAGGACA--CTTCATGAAGAAGACC 554
                               ii  i  i vvv      i  ii   --   v vi       v 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_80254979_8    555 AAAGTAGGAGAATTTGCCATATTAC---ATTTCAAGA--TATT-TAAATT 598
                              v    i i ---  i i v ---       i --  i -i   vi
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACT---CACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80254979_8    599 TATAATAAGTAATATAGTGTGGTAATGGCACAAGGGTAGACAAATAGACA 648
                           i i   vi  v i         v     i    i      v     iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80254979_8    649 AATGAAACAGAATACAGACACCAGAAACAGACTCACGCATGTATAATCAT 698
                             i  i     vv   vv       i i  i  ii   v   ii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_80254979_8    699 TTGATTTTTGACAAAGATGGTATTGCAAAATAGTGGGAAAAGGGT-GTAG 747
                                 i     i i  vi vvi v vvi i    i    ii -  vv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_80254979_8    748 TTTCAATTATTGGTGCTAGAATAATTGGATAGCTATTTG-AAAAAAATTA 796
                               iv v       i i i  i      ? i iv  -    i   v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_80254979_8    797 AACTTGACATATATCTCAAACCTTACACACAAATCAATTCCAGGTGGAAT 846
                          ii v   viv  i    v   v  i   v    i  i  v ii    vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_80254979_8    847 GTAGATCTAAATGTAAAAAGCACCACAATAAAGCTTTTATAAATAAATGT 896
                         i?   i          i ivi vv  v     i  i   v  iv   ii 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_80254979_8    897 AAGA-TAACATTTTCACGTTCTCAGGGTCTGGAAA-GATTTCTTTAAAAA 944
                          i ?-   -  i   ii vi  i-    iv  v  - i      --- i 
  L1M4_orf2#LINE/    549 AGGNGTAA-ATCTTCGTGACCTT-GGGTTAGGCAATGGTTTCTT---AGA 593

  chrX_80254979_8    945 T-TCACAG-AAAAGCATTAACCATAAAGAAAAATATTTTATATAT--GAC 990
                          - v   v-       iv i v i   ii    v  vv-   v  --   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG-ATAAATTGGAC 642

  chrX_80254979_8    991 T-------AATTAAAAA------TGTTT-AAA------------------ 1008
                          -------         ------  i  -   ------------------
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_80254979_8   1009 -AAAAGGCTAGCCTCAGGAT---AAAAGTTACTTGCAA--CACATA---- 1048
                         -     i v v  v   i  --- i  iv  i      --  i   ----
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_80254979_8   1049 ----GGGAC--------AAAATGT------------TGCTATT-AGGAAT 1073
                         ----     -------- i   i ------------ i v i - iv   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_80254979_8   1074 AGA--GACAAAAAAAT--ATAGAAAAATAGA-AAAAGTTCTTAACAGATA 1118
                          i --      v  vi--  v?      i i-   i v i v  i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_80254979_8   1119 TTCCACAAAAGAAAATATATAAATGGC-AATAAATATATGAAAAGATGCA 1167
                           i v v      i     i       -     ii i            v
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_80254979_8   1168 CAACTTCTTAGTAATC 1183
                             v  v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (110 / 73)
Gap_init rate = 0.04 (30 / 757), avg. gap size = 3.27 (98 / 30)  


2308 28.41 2.77 2.00  chrX_80307210_80310362.rev     1762  2662 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80307210_8   1762 TGGAAAAACTTTATATGCTAATGATTTGGAAGA---AAAGTATTGTTAAA 1808
                               i iv ivi   i v   iv        ---  --         i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAA--TATTGTTAAG 48

  chrX_80307210_8   1809 ATGACCGCACTGCCTAAAGAAATCTACAGATTCAATGTTATTGCTATCAA 1858
                            i vii   v  i   vvi              i iv  iv       
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_80307210_8   1859 ACTACAAATAACATTCTTCGCAGAACTAGAAAAAAACT-ATGCTAAAATT 1907
                          v v v iivi v  i  i      v v  v  i--  -  v        
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT 146

  chrX_80307210_8   1908 CATACGAAACT--AAAATATTGCCCA-AATAGCCCTAGAAATCCTAAGCA 1954
                             i i  v --  iiv ---    -       vv iv    i i iv 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_80307210_8   1955 AAAACAACAAAGCCAGAAGCGTCGCATTATCTGACTTCAAACTGCACTAT 2004
                          i  v       iii  i vv  i  i vi ii i      vivi    i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_80307210_8   2005 AAGGCTACAATAATCAAACCAGCATGGTACTGGTACTAAAACAGACTCAC 2054
                           i      i       iv   ii         i iv ii i    vi i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_80307210_8   2055 TGACTAAGATAAAAAAAAAATAGAGAACCCAGAAATAAAGCTGCACACCT 2104
                         v  ii  -- ii  v i  v -    ii           v iii   ii 
  L1M4_orf2#LINE/    294 AGATCAA--TGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_80307210_8   2105 ACAGTCATCTGATCTTTGACAAAGTTGAGAAAAATAAACAATTGG-AAAG 2153
                          ii    vi    i  i     i v  vv  i vi vv    v  -    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_80307210_8   2154 AACTTCCTATTCAATAAATGTTTCTGGGATAACTGGCTACCCATATGCAG 2203
                           ivvi  v     i     v v      i      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_80307210_8   2204 AAGATTGAATCTGGGCCCCTTCCTTTCATGAAGTACAAAATTTAACTCAA 2253
                             v    vi   i     v   iv  iv vi       v         
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_80307210_8   2254 GGTGAATTAAATATTTAGATGTAAGACCTCAAACTATAAAGATCCTAGAA 2303
                         ii  i  i ? v ii  i        v  v          iv  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_80307210_8   2304 GAAATCCTAGG---AAACCATACTGGACATCTTCC-TTGAGAAAGAATTT 2349
                             v v    ---   i v vv  --- i   vv-  ii v  vii   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTG---ACCTTGGGTTAGGCAATGGTTT 587

  chrX_80307210_8   2350 ATGACTAAGTA----ATCAAAAGCAACTGCAA-AAAGCAAAAAATTAACA 2394
                         v ---  ii  ---- i        vvv    -   iv       vi i 
  L1M4_orf2#LINE/    588 CT---TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_80307210_8   2395 AGTGTGACGT------AATTAAAGAACTTCTGCACAGCAAAAGAAACTAC 2438
                          i vv   v ------       -     i  ii vv    i  v    i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_80307210_8   2439 TGCCAGAGTAAACAGGCCACCTATAGAAGGTGAGACAATATTCACAAACT 2488
                         iivv i   i  v  i v   i i    v v    v      ii    ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_80307210_8   2489 ACACATCTGACCAAGGTTTAATATCCAGAATCTATAAGGAACTTAAACAA 2538
                          i i      iv i  vi vi          v     i     ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_80307210_8   2539 ATTAACAAGCAAAAACA-AAATAACCCCATT-ACAAATGGGCAAAAGACA 2586
                         v i  i  -i     v -         v   - v           i  iv
  L1M4_orf2#LINE/    784 CTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_80307210_8   2587 TGAACGGACACTACTCAAAGGAAGATATACAAACGGCCAATACACATATA 2636
                             ii    i v   v  i             i        vi  i  i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_80307210_8   2637 AAACAATGCTCCACATTACTAATCAT 2662
                            vi      v    i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (147 / 107)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.05 (43 / 21)  


3155 25.38 0.88 1.75  chrX_80327092_80329521.rev     1026  1939 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_80327092_8   1026 GAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTTAAAATGG 1075
                             i i  i     i        v      v i     i     i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_80327092_8   1076 CCTCACTGCCAAAAGCAATTTATAGATTCAATGCTATCCCCATCAAGCTA 1125
                          vvi   v  v   vii  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_80327092_8   1126 CCA-CTGACTTTCTT-CAAAGAATTGGGAAAAACT-ACTTTAAACTTCAT 1172
                            -   v    i  -  i -     -- v  i  - iii    v     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_80327092_8   1173 ATGAAAC--CAAAAAACAGCCCGCATAGCCAAGACAGTCCTGGGCAAGAA 1220
                            i  v--   iii  --  v v        i   i  i  iiv     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_80327092_8   1221 GAACAAATCTGAAGGCATCACACTATCTGACTTCAAACTTTACTACAAGG 1270
                                vi  i   vv       vi ii i      vi         i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_80327092_8   1271 CTACAGTAACCAAAACAGAATGGTACTGGTACCAAGACAAATATATAGAC 1320
                                  i   i    vi         i iv i  i i i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_80327092_8   1321 CAATGGAACAGAAC--AGAGTCCTCAGAAATAACACCACACATCTACAAC 1368
                                 i    i--       --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_80327092_8   1369 CATCTGATCTTCGATAAATCTGACACACGCAAGCAATGAGGAAAAGATTC 1418
                           vi    i     i  ivv  v  vivv  vv     i     ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_80327092_8   1419 CCTATTGAATAAATAGTGTTGGGAAAACACTATTTTTGCTAGCCATATGC 1468
                         i  v  v  i    i   i     v   ------- v v  ?   i    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAAC-------TGGATAKCCACATGC 438

  chrX_80327092_8   1469 AAAAATCTGAAACTGTACCCCTTCCTTACACTGTATACAAAAATCAACTC 1518
                             ivv    ii  v      v   i    ii           i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_80327092_8   1519 AAGATGGATCAAAGACTTAAATGTAAGACCTAGGACCATAAAAATCCTAG 1568
                           i        ?    i           v   ii  i      v  i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_80327092_8   1569 AAGAAAACCTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTT 1617
                                 v i  ?i- v i -   iv   v v  vv i     v ii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_80327092_8   1618 CATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGATAAAT 1667
                          v ivv  vi            vvi          vv i   v       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_80327092_8   1668 GGGATCTAATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTATCATC 1717
                         v   ii v  i   v v  i i   i  ii vv    i  v       vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_80327092_8   1718 AGAGTGAACAGGCAACCTACAGAACGGGAGAAAATTTTTGCAATCTGTCC 1767
                          i      v  i     i      i          v       viii vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_80327092_8   1768 ATCTGATAAAGGACTAATACCCAGAATCTTCAAATAACTTAAACAAATTT 1817
                                  i     vi  i       v vi   v    ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_80327092_8   1818 ACAAGAAAAAAGCAAACAACTGCATCAAAAAAATGGGCAAAGGATATGAA 1867
                          i  v     ii    i   ivv  i?     -            v    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAA 836

  chrX_80327092_8   1868 CAGACACATCTCAAAAGAAGACATTTATGCAGCCAACAAACACATGAAAA 1917
                         i     iv    v        i  vi viii     i  i          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_80327092_8   1918 AATGTTCATCATCACTGGTCAT 1939
                         i   i   v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 1.85 (24 / 13)  


2661 28.62 0.55 0.99  chrX_80364689_80368960.rev     2884  3795 (477)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80364689_8   2884 TGGAAAAATATTCCATGCTCATGTATGGGAAGAATTAATATCATTTAAAT 2933
                               i    i     i     v  v      v       ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80364689_8   2934 GGCCATACTGCCCAAAGCTATCAATATATTCAATGCTATTCTTATCAAAC 2983
                            v     v      viv   v i v      i  v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80364689_8   2984 TACCAA-TGCCATTTTTCACAGAAGTATAGA-AAGC-AATTTCAAAATTC 3030
                          v   i-    -     ii     --  v  -    -i  iii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chrX_80364689_8   3031 ACATAGAACCAAAAAAAGAGCCTGAATAATCAAAGCAATCCTAAGCAAAA 3080
                          i  i   viiv  ii-  v  v     ii    i     i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_80364689_8   3081 AGAGCAAAGCCAGAAGCATCACACTTACCAACTT-GAAACTACACTACAA 3129
                            i     iii  i vv        v    i  -i     -i       
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chrX_80364689_8   3130 GGCTAAAGTAACCAAAGCAGCATAATACTGGTACAAAAACACATCCATGG 3179
                         i    v     i   ii   ii ii      i i  ii i v ivi  i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_80364689_8   3180 ACCAATGGAACAGGAGAGAGAACCAAGAAATACAGCTGCACACTTACAAC 3229
                          i        i  i vv    ii v       v v iii   i   iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_80364689_8   3230 CATCTGATATTTGACAAAGTTGACAATGACAAGT-AATGGGGAAAGGACT 3278
                           vi    v  i     i v  v   -   v v -           i iv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATA 394

  chrX_80364689_8   3279 TCCTATACAATAAACTGTGCTTTGATAACTGGATAACTATATGCAGAAGA 3328
                         vi  v v   i   iv     vv  i         ? i i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_80364689_8   3329 TTAAAATTGGACCCCTTTCTTTAACCACTTACAAAAATCAACTCAAGCTG 3378
                         v i  i          vi  ivv    iv         i       iv  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_80364689_8   3379 AATTAAAGATTTAAGCATAAGACCTCAACCTATAAAAACCCTAAATGAAC 3428
                         i  i ?   ii   iii     v  v  v        vi i  i v   v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_80364689_8   3429 ACCTAGGAAATACTTTTCTCAACATAGGCCTTGGCAAAGATTTTATGACT 3478
                           v    ?ivv v i   vii  v v  vi v     v i   iv iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_80364689_8   3479 AAGTCCCAAAAAGCAACTGTAACAAAAACAAAAATTGACAAATGAGACCT 3528
                          v v v v       vvv i       iv      v  i    vi   i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_80364689_8   3529 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACGATCAACAATGTAA 3578
                         v  i   v v  i i   i  ii vv    i  v  v     v  v  i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_80364689_8   3579 ACAGACTACATACAAAATGGGAGAAAATATTCGTAAACTATGCATCTGAC 3628
                          v    v  vi   i                i i   ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_80364689_8   3629 AAAGGTGTAATATCCAGAATCTATAAGGAACTGAAACAAATCAAGAAGCA 3678
                           i  vv vi          v     i     vvv    v    v  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_80364689_8   3679 AAAACCAAATAGCCCCATTTAAAAAATGGTGAAAGGACATGAGCAGACAC 3728
                            iv      i   v   ?     -   vv      iv   ii     i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACAT 843

  chrX_80364689_8   3729 TTCCCAAAAGAAGACTATTTAAAGGAGCTATTAAATATATGAAAACATTC 3778
                            i v        -   vi   v -  i v   ii i       v  v 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGA-TATACAAATG-GCCAATAAGCACATGAAAAGATGC 891

  chrX_80364689_8   3779 ACAACTCCACTTATCAT 3795
                         v    vi  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (144 / 113)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.08 (14 / 13)  


3046 25.90 0.87 1.64  chrX_80372286_80374977.rev     1287  2201 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80372286_8   1287 TGAAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 1336
                           i   v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80372286_8   1337 GACCATACTGCCAAAAGCAATCTACAAATTCATCACAATTCCCATCAAAA 1386
                          i v     v  v   vii       i     v i    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80372286_8   1387 TACCACCCTCATTCTTCACAGAA-TTAAAAAAAACACAATCCTACAATTC 1435
                          v   v iv v  i  ii     -  i v  i-- -ii      v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--C-TGATCCTAAAATTC 147

  chrX_80372286_8   1436 ATATGGAACCAAAGAAGAGCCTGTATAGCCAAAGAAAGACTAAGCAAAAA 1485
                                 viiv iii  v  v v         iv  vvi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_80372286_8   1486 GAACAAATCTGGAGGCATCACATTACCTGATTTCAAACTATACTATAGAG 1535
                                vi      vv     i v  ii        viv     i i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_80372286_8   1536 CCATAGTCACAAAAACAACATGGTACTGGTATAAAAATGGCCACATTGAC 1585
                          i i   v iv  i   iii         i    ii  i v  i  v  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_80372286_8   1586 CAATGGAACAGAAAAGAGAACCCAGAAATAAACCGAAATACTTACAGCCA 1635
                                 i    vv    ii             v v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_80372286_8   1636 ACTTATCTTTGACAAAGCAAACAAAAAGATAAAGTAGGGCAAGAACACCC 1685
                          i v  i  i     i vviv   i vv  vv i i   v     i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_80372286_8   1686 CTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATG 1735
                         i                     i  i   v  ?       i ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_80372286_8   1736 AAACTGGATCCTCATCTCTCATTTTATATAAAAAAAATCAACTCAAGATG 1785
                           ii    i  ii i   v  iiv    i     --- i       i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAA---TTAACTCAAAATG 494

  chrX_80372286_8   1786 GATCAAGGACTTAAATCTAAGACCAGAAACTATAAAAATTCTGGAAGATA 1835
                              ?i   i     v     v vi           v ii i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_80372286_8   1836 ACATTGGAAAAACCCTTCTAGAAATTGGCTTAGGCAAGGATTTCATGACC 1885
                             v  ?iv  vi    vv  vv    v        v i    v iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_80372286_8   1886 AAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAGATAAATACCTGGG 1935
                          v  vv         v v    i    iv   i          ---   -
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT---TGG- 640

  chrX_80372286_8   1936 ACTT------AACTAAAGAGCTTTTGTATGGCAAAAGGAAGAGTCAGTAG 1979
                             ------  i    i -       iivv    i iv vvi   iv i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_80372286_8   1980 AGTAAACAGACAACTCACAGAGTTG-AGAAAATCTTCACAATCTATACAT 2028
                            i  v       i      i v -       v  ii   vii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_80372286_8   2029 CTGAAAAATGACTAATATCCAGAATGCATAATTAACTCAAACAAATCAGA 2078
                             v  iv    vi          ii    vv     vv    v   --
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-- 787

  chrX_80372286_8   2079 AACAAACAAACAAACAAATGATTCCATCAAAAAGTGGGCTAAGGACATGA 2128
                         - i  -i   v i      i ii v  i?    i     v     iv   
  L1M4_orf2#LINE/    788 -ATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_80372286_8   2129 ATAGACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATAAAA 2178
                                v     v                       i  i  i  i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_80372286_8   2179 AAATGCTCAACATCACTAATGAT 2201
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (135 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


 408 22.61 0.00 0.00  chrX_80392056_80394233.rev      306   420 (1758)    L1M4_orf2#LINE/L1      794   908 (0)  

  chrX_80392056_8    306 AAAAACCAAACAACCCTATTAAAAGGTGGACAAAGGACATGAACAGAAAT 355
                             iv    i     v   ?   ii   i       iv    i   v  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_80392056_8    356 GTTTCAAAAGAAGACATACACATGGACAATAAGCATAAGATGGAAAGCTC 405
                         v i  v        i     v    v         i v  viii v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_80392056_8    406 CACATCACTAATCAG 420
                         v      ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.08 (13 / 12)
Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.00 (0 / 0)  

2613 28.19 1.55 0.78  chrX_80392056_80394233.rev      787  1687 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80392056_8    787 TGAAAAAACATTCCATGATCACGGACAGAAAGAATCAATATCTTGAAAAT 836
                           i   i i  i     v   i   iv i    v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80392056_8    837 GGCCATACTGCCCAAATT----TATAGGTTCAATGCTATTTCCATTAAAC 882
                            v     v        ----  i  i     i  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80392056_8    883 TATCATTGACACTCTTCACAGAA-TTAAAAAAAAAAAACTTTAAAATTCA 931
                          vi  vivi vi i  ii     -  i v  ivvi --iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chrX_80392056_8    932 TACAGAACTA-AAAAGAGCCTGTATAGCCAAGACAACACTAAGCAAAATG 980
                           ii   v i-  ii  v  v v        i    ivi i iv  i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80392056_8    981 AACAAAACTGGAGGAATCATGCTACCTGACTC--AAACTATACTACAAGG 1028
                               ii       v   ii  v  ii i i--     -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_80392056_8   1029 GTACAGTAACCAAAACAGTATGGTACTGGTACAAAAACCAGACACACAGA 1078
                         v        i   i     i         i i  ii i-     i i   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGA 296

  chrX_80392056_8   1079 CCAACGGAACAGAATAGAGATCCCAGAAACAAGACCGCACATCTAAAACC 1128
                         i   i    i     v    vi       i  iv  ii    i  viii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_80392056_8   1129 ATTTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 1178
                          v     i   i    ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_80392056_8   1179 CTATTTAATAAATGGTGCTGGGATAGCTGGCTAGCCATTTTTAGAAAATT 1228
                           v  i  i              i i    v  ?   iv vi i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80392056_8   1229 GAAACTGGACCCCTTCCTTAAACCTTAT-TAAAAAACACCTCAAGATGGA 1277
                            ii         v   i v   v   -i     vi v     i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80392056_8   1278 TTACAGACTTAAAAGTAAAACCCATAACTATACAAACCCT-AGAAGAAAT 1326
                          i ?    i    v    i v i v       -    i  -        v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAA 545

  chrX_80392056_8   1327 TCTAGGCA-ATACCATTCAAGACATAGGCACAGGCAAAGATTTCATGGCA 1375
                         iv    ?i- v i -   iv   v v  vvi      v i    v i vv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_80392056_8   1376 AAAACAACAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGA-TC 1424
                          vi   v        vvv          v      v  i    v   - i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_80392056_8   1425 GATTTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTG 1474
                         v  iv   i    i -   i  ii vv    iv v       vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_80392056_8   1475 AACAGACAATCTACAGAATGGGAGAAAATGTTTGCAATCTACCCATCTAA 1524
                           v      i i                 i       vii ivi    i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_80392056_8   1525 CAAAGGTCTAATATCCAGAATCCACAAGAAACTTAAACAAATTTACAAGA 1574
                         i  i  v  vi          vi i  ii    ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_80392056_8   1575 GAAAAAAAAGCGACC-AATT-AAAATTGAGCAAAGGACACGAACAGAACC 1622
                         i   i v  iii   -    -    v  i        ivi   i   vvi
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_80392056_8   1623 TTCTCAAAAGAAGACATATATGCAGCCAAAAAACATATGAAAAAAAGCTC 1672
                              v        i   i viii     v  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_80392056_8   1673 AACATCAGTGATCAT 1687
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (151 / 100)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.31 (21 / 16)  


3180 26.77 0.88 0.44  chrX_80401776_80408050.rev     4881  5784 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80401776_8   4881 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATGTCGTGAAAAT 4930
                              ii i  i     i        v      v i   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80401776_8   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80401776_8   4981 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 5025
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_80401776_8   5026 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATTCTCAGCCAAAAGAA 5075
                              viiv  ii  v  v v  v     iv    ii v ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_80401776_8   5076 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5125
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_80401776_8   5126 CAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGATCAA 5175
                               i   i    ii         i i  ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_80401776_8   5176 TGGAACACAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTAT 5223
                              i v  i--    i  --        vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_80401776_8   5224 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCTCT 5273
                         i    i  i     ivv  vv  i v  vv            i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_80401776_8   5274 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5323
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_80401776_8   5324 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5373
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_80401776_8   5374 AAAGACTTAAACGTTAGACCTAAAACCATAAAAAACCCTAGAAGAAAACC 5423
                          ?    i    i  v   v       i      v-i i           v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACA 547

  chrX_80401776_8   5424 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5473
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_80401776_8   5474 ACAACAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGGATCTAAT 5523
                            v        vvi          v      v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_80401776_8   5524 TAAACTAAAGAGCTTCTTCACAGCAAAAGAAACTA-CAATCAGAGAGAAC 5572
                         i   v v  i i   i vii vv    i  v    -   v- i  v   v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAA 696

  chrX_80401776_8   5573 AGGCAGCCTACAAAATGGGAGAAAATTTTCGCAACCTGCTCATCTGACAA 5622
                           i  i  i   i             v  i    viiiivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_80401776_8   5623 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 5672
                         i  i  vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_80401776_8   5673 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5722
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_80401776_8   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5772
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_80401776_8   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2676 26.78 1.51 3.46  chrX_80418772_80420432.rev      245  1170 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80418772_8    245 TGGAAAAACATTCCATGATCATAGGTAGGGAGAATTAATATTGTTAAAAT 294
                               i i  i     v    i i v  i   v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80418772_8    295 GGCCATAGTGCCCAAAGCAATTTACACATTCAATGCTATTCCTATGAAAC 344
                            v   v v      vii  i    v      i  v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80418772_8    345 TACCAAGTCAATGCTATTCCTATCAAACACAAATTTCATTACAGAATTAG 394
                          v   -------   i--   ------------   --  i     v v 
  L1M4_orf2#LINE/    101 TCCCA-------GCTG--CCT------------TTT--TTGCAGAAATTG 127

  chrX_80418772_8    395 AAAACTCTAATT-TAAAATTCATTTGGAACCAAAGAAGAGCCCGAATAGC 443
                          v  v-  i  i-          v     viiv iii  v  v       
  L1M4_orf2#LINE/    128 ACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chrX_80418772_8    444 CAAGGCAACCCTAAGCTAAAAGAACAAAGCTGGAGGCATCACATTATCTG 493
                            ii   i i i ivv i          i      vv     i vi ii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_80418772_8    494 ACTTCAAACTATACTA-AAAGTCTACAGTAACCAAAATAGCATGATATTG 542
                          i      viv     -    -         i   i i  ii  i  i  
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAG-CTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_80418772_8    543 GTACAAAAAAAAAAGACACATAGGCTAATGGAACAGAATAGAGACTCCAG 592
                          i i  ii v ---    i    iii       i     v    v     
  L1M4_orf2#LINE/    276 GCATAAGGATA---GACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_80418772_8    593 AAATAATGCCAGCCACCTACAACCATCTGATCTTCAACAAAATTGACAAA 642
                               vv   vv  ii  iiii  vi    i   i    iiv  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_80418772_8    643 AACAAGCAATGGGGAAAGGACTCCCTATTGAATAAATGGTGCTGGAACAA 692
                          v  vv            i ivvi  v  v  i            i    
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_80418772_8    693 CTGGCTACCCATCTGCAGAAGACTGAAACTGAAGCCCTTCCTTACACCAT 742
                             v  ?   iv    i    v    ii  i v    v   i       
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_80418772_8    743 ATACAAAAATTATCTCAAGATGGATTAAACACTTAAATGTAAAACCTAAA 792
                                     v     i      i ? v  i         i v     
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_80418772_8    793 ACTATAAGAATTCTGGGGGATAACCTGGGAA-ACACCATTCTGGACAAAG 841
                                i v ii i ii  v   v i  ?i- v i -   vv   vvv 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chrX_80418772_8    842 GACCTGGAAAAGATTTTATGACCAAGATGCCAAAAGCAATTGCAACAGAA 891
                          iiiv  v  v i   iv iivi v  ii         vvv      i  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_80418772_8    892 ACACAAATTGACAATTGGAACCTAAATAAACTAAAGAGCTTCTGCACAGC 941
                         iv v    v  i  v v i  i v vi   v v  i i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_80418772_8    942 AAAAGAAACTATCAACAGAGTAAACAGACAATCTATTAAATGGGAGAAAA 991
                            i  v        v i   i  v      i i ivi            
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_80418772_8    992 TATTAGCAAATTATGCACCCAACAAAGGTCTAATATCCAGAATCTATAAG 1041
                             v      i  ii i ii i  i  v  vi          v     i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_80418772_8   1042 GAACT--TA-AAGT-AACATGCATAAAAA---AAACAACCCTATCAAAAA 1084
                              --  -  v -  i ---       ---   i     v  i?    
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATA---ATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_80418772_8   1085 GCAGGCAAGGGAT----GCAGACATTTTTCAAAATAAGGTATAGACCCAG 1130
                         iii     i    ----ii        i  v   v   i    v vvii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_80418772_8   1131 CCAACACGCATATGACAAAATTTTCAGTATCACTAATTAT 1170
                             i v   i    v  i  vi   ii    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.71 (46 / 17)  


3223 20.57 2.44 1.03  chrX_80440555_80442271.rev      449  1226 (491)    L1M4_orf2#LINE/L1      120   908 (0)  

  chrX_80440555_8    449 AGAAATAGACATGGCTGTGTTCTAATAAAAATTTAT-T---AAT-TAAC- 492
                               v    -i    -i i    ----    i  - ---   -i  v-
  L1M4_orf2#LINE/    120 AGAAATTGACA-AGCTG-ATCCTAA----AATTCATATGGAAATGCAAGG 163

  chrX_80440555_8    493 -ACTGAAAAAAGTCAAAACAATCTTGGAAAAGAAGAA-AAAGTTAAAAGA 540
                         -  iv i  v  i             i          -      ii i  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_80440555_8    541 GTTATACTTTATGATTTTAAAAGGCTGCTACTAAACTAAAGCAATCAAGA 590
                         v i i    ivii    i    v-i i    v  i   v  i        
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAAC-TTACTACAAAGCTACAGTAATCAAGA 262

  chrX_80440555_8    591 CTGTATAGTACTGGCATAAAGAGAAACATATAGCTCAATGAAATGGAATT 640
                          v  i i            i  v i        v      i   i     
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_80440555_8    641 AAGAATATAAGAATAAAGCCTTCATATTTAGGGTACATTGATTTTCGCCA 690
                         i   i vi ii      v  v - i     v   vv           v  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCAT-ACATTTATGGTCAATTGATTTTCGACA 361

  chrX_80440555_8    691 AGGGTGTCAGGAGAATTTAATGGGGAAAGAATAGTCCTTTCAGCAAATAG 740
                               i  i  vv   i                  i     i     i 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_80440555_8    741 TACCCTAACAACTAGATATTCTCATGCAAAACAAGGAAGTTGGACTCCTA 790
                          i ivvi      i    ?i v         v  v          i    
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_80440555_8    791 CTTCATACCATAAACAAAAATTTACTCAAAATGAATCATAGACCTAAATA 840
                          i   i      v         v          i    ?          i
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_80440555_8    841 TAGGCACTAAAATGATAAAACACTCAGAAGAAAACATAAGTGCAAA-CTT 889
                           i vi      iv       v  i             i ? i   -   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_80440555_8    890 TGTTATATTGGATTTGGCAAAGCCTTGTTAGACATGACA----AAGCACA 935
                         i  v iv    i  v     v vi  v     i      ----       
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_80440555_8    936 AGTAACCAAAGAAAAAATATATACATTGAACTTCA---AAATTAAATAAT 982
                           i   v            v   v    i      ---        v v 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_80440555_8    983 TTTGTGTGTAAAAGAACATGATCAAGACAGTGAAAATATAATACATAGAA 1032
                               iv v    i   iv       v        v i  iv  i    
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_80440555_8   1033 TGGGAGAAAATATTTAGAAATTATATAACTGATAAAGGTATAGTATCCAG 1082
                                        iv    i     v       i  vv v        
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_80440555_8   1083 AATATGTGAAGAACTATTACTACTCAACCACAAAAAGGCAAAAAATTCAA 1132
                              i i       v    v      iv i      i    v  ii   
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_80440555_8   1133 TTTATAAGTAAGAAAAAAAGTT---TAGATATTTTTCTAGAAAAGATATA 1179
                           ? v  i ii v   ii v  ---    i    i  i i i        
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_80440555_8   1180 CAGAAGGCTAACAAACACATGAAAAAATGCTCCACATCATTAGTCAT 1226
                           i v   i  i  i          i      v      ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (94 / 62)
Gap_init rate = 0.02 (14 / 789), avg. gap size = 1.93 (27 / 14)  


1673 27.94 1.10 1.84  chrX_80444146_80447549.rev        1   544 (2860)    L1M4_orf2#LINE/L1       89   628 (280)  

  chrX_80444146_8      1 TTCCCATGAAGCTACCATTAACTTTCTTCACAGAATTAGAAAACACT-AC 49
                          i  i  v  iv v   vivi i  i  ii     v v  v  -i  - i
  L1M4_orf2#LINE/     89 TCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGAT 137

  chrX_80444146_8     50 TTTAAATTTCATATGGAACGACAAAAGAGCCCATATACCCAAGACAATCT 99
                         ii    v           vvi   ii  v  viv   v    i       
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chrX_80444146_8    100 TAGGCAAAAAGAACAAAGCTGGAGGCATCGTGCTACCTGACTTCAAACTA 149
                          iiiv  i          i      vv  iii  v  ii i      viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_80444146_8    150 TATTACAAAGCTACAGTAACCAAAACCGCATGGTACTCGTACCAAAACAG 199
                           i                i   i  v ii       v i iv ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_80444146_8    200 ATATATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAACATCACACA 249
                          i       i        i    iv   ivii         vvi  i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_80444146_8    250 TCTACAACCATCTGATCTTTGACAAACCTGATAAAAACAAGCAATGGAGA 299
                          i  iiii  vi    i  i     ivv  vi  i v  vv      i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_80444146_8    300 AAGGAT--TCTTTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATA 347
                            i  --     -- i  i        i     v      v  ?   i 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_80444146_8    348 TGCAGAAAACTGA--CTGGACCCCTTCCTTACACCTTATACAAAAATTAA 395
                             i  i v   --i         v   i     v              
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_80444146_8    396 CTAAAGATGGATTAAAGATTTAAACATAAGACTTAAAACCATAAAAATCC 445
                           v  i      i ?   ii    ii     vi      i      v  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_80444146_8    446 TAGAAGAAAACCCAGGCA-ATATCCTTCAGGACAAAGGCATGGGCAAAGA 494
                                    vi   ?i- v   -   iv   vvv  vv i     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_80444146_8    495 TTTCATGACTAAAACTCCTGGGAAACAGCTAAAGCAGAGTAAAGAGGAAA 544
                             v iiv  vi  v  ----   -   vv     - vv     ii   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACC----AAA-AGCACAAGCA-ACAAAAGAAAAAA 628

Transitions / transversions = 1.48 (89 / 60)
Gap_init rate = 0.02 (10 / 540), avg. gap size = 1.60 (16 / 10)  

2057 26.80 5.82 2.62  chrX_80444146_80447549.rev     2037  2913 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_80444146_8   2037 AAAAACATTCCATGATCATGGATAAGAAGTATCAGTATTACTAAAATTGT 2086
                            i i  i     v        vi    vv i i    ii   i  v i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_80444146_8   2087 CATACTGTCCAAAGCAATTTACACATTCAATGCTATCCCTCTCAAACTAC 2136
                         v     vi     vii  i    v      i  v      v     v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_80444146_8   2137 CAATGAAACTCTTCACAGAATTAGAAAAAAAAAACT-ACTTTAAAATTAA 2185
                           iivivvi i  ii     v v  v  i-----  - iii       v 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAATTCA 148

  chrX_80444146_8   2186 TATGAAACTAAAAAAGAACCTAAATAGTCAAAACAATCCCATACAAAAAG 2235
                             i  v iv  ii  v  vi     i          iiiv v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80444146_8   2236 AACAAATGTTG-AGGCATCACA-TTCTAAGACTTCAAACTATACTA-AAA 2282
                               -    -   vv     -   iv - i      viv     -   
  L1M4_orf2#LINE/    199 AACAAA-GTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAA 246

  chrX_80444146_8   2283 GTCTACAATAACCAAAACAGCATAGTAGTGGTGAAAAAAAAAAAAACAGA 2332
                          -     i   i   i    ii i   v   i------- v  ii i   
  L1M4_orf2#LINE/    247 G-CTACAGTAATCAAGACAGTGTGGTACTGGC-------ATAAGGATAGA 288

  chrX_80444146_8   2333 CACATATACCAATGGAACAGAAGAGAAAACCCAGAAATAAAACAGCACAC 2382
                           i   v i        i    vv  i ii           v vii   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_80444146_8   2383 CTACAACCATCTGGTCTTTGACAAAGTCAACAAAAACAAGCAATGAGGAA 2432
                         i  iiii  vi  i i  i     i viiv   i v  vv     i    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_80444146_8   2433 AGGAC--TTTTTAATTCAATAAATGGTGCTGAAATAACTGG-----CA-- 2473
                           i i-- i   ---    i           ii i      -----  --
  L1M4_orf2#LINE/    389 AGAATAGTCTTT---TCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_80444146_8   2474 -GCAGAAGATTGAAACTAGGTTCCT----TACTCCATATACAAAAATCAA 2518
                         -   i    v    ii i iii   ----i  v              i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_80444146_8   2519 CTCAAGATGGATTAAAGATTTAAATGTAAAACCTAAAAGTATAAAAACCC 2568
                              i      i ?   ii         i v      v       - i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTC 534

  chrX_80444146_8   2569 TT-GACAAAAACCTAGGAA-ACACCATTCTGGACATAGGGCCTGACAAAG 2616
                           -  vi     v    ?i- v i -   vv   v v   iiv i   v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATG 583

  chrX_80444146_8   2617 ATATCAT-GATGAAGATGGCAAAGGCAATTGCAACAAAA------ACAGA 2659
                         i v  v -   - v  iiv    i   vvv         ------ i   
  L1M4_orf2#LINE/    584 GTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_80444146_8   2660 -------GACCTAATTAAA-CTAAACA-------GC---AAAAGAAACTA 2691
                         -------   i v  i   -i    v -------  ---   i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_80444146_8   2692 TCAACAGAATAAGCAGACAACCTACCAAATGGG-GAAAAAATTTGCAAAC 2740
                             v i i i iv        i  vi      -     v         i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_80444146_8   2741 TATGCATCTGAGAAAGTTCTAATATCCAGAATCCATAAGGAACTTAAGCA 2790
                         i  ii      v  i vv  vi          vi    i     ivvi  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_80444146_8   2791 AATTAACAACAACAAAA--AATGCTACTCCACTAAAAAGTGGACTAAGAA 2838
                          v i  i  i  v  i --   i--  i v i ?    i   i v   i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATA--ACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_80444146_8   2839 CAT-AACAGACACTTC--AAAAGAAGACATACATGCCGCCAAGAAGCATA 2885
                         iv -  i     i   --v        i     viiv     v     i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_80444146_8   2886 TGAAAAAATGTTCGACATCACTAATCAT 2913
                               i   i  i      ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (145 / 87)
Gap_init rate = 0.03 (30 / 905), avg. gap size = 2.47 (74 / 30)  


2302 28.83 2.79 1.34  chrX_80496089_80498902.rev     1431  2325 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80496089_8   1431 TGGAAAAACATTCCATGCTCATGGAGAGGAAAAACCAATATTGGTAAAAT 1480
                               i i  i     i       vv    i vii       v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80496089_8   1481 GGCCATACTGTGCAAAACAATTTACAGATTTAATGCCTTTCCAATCAATC 1530
                            v     viv    vii  i        i  i  vv i  v     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80496089_8   1531 TACCAAGGTCATTTTTCACAGAATTAGAAAAA--AATTCTAAAATTTATT 1578
                          v   ivvv v     ii     v v  v  i--i  i        i  -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT- 149

  chrX_80496089_8   1579 ATGGAACCAAAAAAGAGTCTGAATCACCAAAGCAAACCTAAGTATTAAGA 1628
                               viiv  ii  vi v    vi     i   v i i iv vv    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_80496089_8   1629 ACAAAGCCAGAGGCATCACACTACCCGACTTCAAACTACACTACAAGTCT 1678
                               iii    vv       v   i i      vivi       iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_80496089_8   1679 ATAGCAACCCAAACAGCATAATACTGGTACAAAAACAGACACATAGACCA 1728
                          i  i  i v i    ii ii      i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_80496089_8   1729 GTGGAAGAGAATAGAGAACCCAGAAATGAAGCCACACACCTACAACCACA 1778
                         i     v     v    ii        i  v   i   ii  iiii  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_80496089_8   1779 TAATCTTCAACAAAGGTAACAATAAAAAACAATGGGGAGCAGACT-TTCT 1827
                          i  i   i    i   iv   v vv vv         i-   v -v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAATAGTCT 398

  chrX_80496089_8   1828 ATTCAATAAATGGTGCAGGTATATCTAGCTAGCCATATGCAGAAGATTGA 1877
                         v     i         v  v i v  i v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_80496089_8   1878 AGCTGGATCTCTTCCTTTCACCATATACAAAAATCAACTCAAGATGAATT 1927
                           i    i i  v   iv                i       i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_80496089_8   1928 AAAGATTTAAATTTAAGATCGTAAATATTA-AAAACCCT-AGAAGAAAAA 1975
                          ?   ii     v     v -    - i  -     i  -         v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGC-TAAA-ACTATAAAACTCTTAGAAGAAAAC 546

  chrX_80496089_8   1976 GTAGA---AAATACCGTTCTCTG-GACATTCGCCATAGCAAAGAAATTAT 2021
                         i   i---    ------  ii -   v  v vivvi    v ivv iv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT------CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_80496089_8   2022 GACTAAGTCCCTGAAA--ACAATTGCTACAAAAACAAAAATTAA--AATG 2067
                         iiv  v v v ii   --    --  v      iv      vi --   v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATT 638

  chrX_80496089_8   2068 GGAC---AT---AATTAAAGAGCTTTGCACAGCAAAAGAAACTATTAACT 2111
                             ---  ---       i vi    ii vv    i  v     i  vv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_80496089_8   2112 GAGTAAGCAGACAACGTACAGAATGGGAGAAAATGTTCACAAACTATACA 2161
                         i   i iv       vi                 i  ii    ii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_80496089_8   2162 CCTGACAAAGATCTAATA----GAATCTACAAGAAACTTAAAGAATTCAA 2207
                         i    i  i iv  vi  ----    v  i  ii    ivv v  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_80496089_8   2208 AAAACAAAAATCAAATCACACCATTAAAAAATGAGCAGAAGACACGAACA 2257
                         v  vv    iv     v  v v   ?       i   i i  ivi   i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_80496089_8   2258 G-CACTTCTCAAAAGGTGACACACAAGGAGCCAACCAATACATAAAAA-A 2305
                          -  i     v    iv  i i    ivi     iv ii    i    - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_80496089_8   2306 CGCTTATCATTGCTAATCTC 2325
                         i   i v   ii????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (150 / 105)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.95 (37 / 19)  


2393 29.65 1.66 1.22  chrX_80502343_80505013.rev     1276  2179 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80502343_8   1276 TGGAAAAACTTTTCACATTCTTGGTTACAAAGAACAAATATCATTAAAAT 1325
                               i iv ii  ii   v   v vvi    viv     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80502343_8   1326 GGCCATACTACCCAAAGCAATCTACAGATTCAGTACTATACTTATCAAAC 1375
                            v     v      vii             iii v  v i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80502343_8   1376 TACCAATGATATTTTTTACAGGAGTAGAAAAAAAAACT-ACTCTAAAATG 1424
                          v   iiviiv      i   i i v  v  i----  - ii       v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chrX_80502343_8   1425 TATATAGAACCCCAAAAGGCCCTGAATAGCCAAAACAATCCTAAGCAACA 1474
                         i    i   viv   ii i   v                 i i iv  v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_80502343_8   1475 AGAGCAAAGCCAGAGGCATGACTTTACTTGACTTCAAACCATACTATAAG 1524
                            i     iii    vv v  vi v iii i      v v     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_80502343_8   1525 GCTACAGTAACCAAAACAACATGGTACAGTTACAAAAAAAAACACATACA 1574
                                   i   i   iii      v vi i  ii v i   i   v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_80502343_8   1575 GCAATGGAACAGATTAGAGAA-CCAGAAATAAAGCCATACAACTACTACC 1623
                         v        i   v v    i-           v       vi  ivii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_80502343_8   1624 ATCAGATATTTGTCAAAG---CAAAGAAAAATTTGCAATAGGGAAAAGAC 1670
                          viv   v  i v   i --- v    vv --  -    i      ii i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCA--TT-CAATGGGGAAAGAAT 393

  chrX_80502343_8   1671 CCCCTATTAAATAAATGATGCTGGGATTGCTGGCTACCCATATACAGAAG 1720
                         vvi  v  v  i     i        ivi    v  ?   i  i  i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_80502343_8   1721 ATTGAAACTAGACTCCTACATTGCACCATATACAAAAATTACCTCAAGAT 1770
                          v    ii i   i     v ii                  v     i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_80502343_8   1771 AGATTATAGATTTAAATGTAAGACCTCGAACTACAAATATCCTAGAATGA 1820
                         i   i ?   ii           v  vi     i   vv  i     vi 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_80502343_8   1821 AACTTTGAAA-ACACCATTCTGACCATTGACCATGGCAAATAATTTAC-- 1867
                            v v i?i- v i v iv     v v iii -     - ii   vi--
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTA-GGCAA-TGGTTTCTTA 591

  chrX_80502343_8   1868 GACTAAGTCCTCAAAATCAGTGGCAACAAAAACGAAAATTGACAAGTAAC 1917
                           -  v v vi     v  vvi         ivi     v  i  i viv
  L1M4_orf2#LINE/    592 GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_80502343_8   1918 AGCTGATTAAACTAAAGATCTTCCACACAGCAAAAGAAACTATCAGCAGA 1967
                          vi v  i   v v  i v   iiiii vv    i  v       iv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_80502343_8   1968 GTAAACATACAACCTACAGAATGGG-GAAAATATTCACAAACTATGAGTC 2016
                           i  v v      i          -         ii    ii  ivi  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_80502343_8   2017 CAACAAAGATCTAATATCCAGAATCAATAAGGAACTTAAATAATTCAGCA 2066
                         ii i  i iv  vi          vv    i     ivv i  i   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_80502343_8   2067 AGCAAAAGCACAAATAATCCCATTAAAAAGTGGGCAAAGGACATGAACAG 2116
                          vv     -        i  v   ?    i           iv    i  
  L1M4_orf2#LINE/    791 ATAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_80502343_8   2117 CCACTTCTC---AAAAGACATACAAGCAGCTAAAACACATATGAGCAAAT 2163
                         v  i     --- i    i      iii  i  v vi  i    iv i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_80502343_8   2164 GC---ACCTCATAATTAAT 2179
                           ---  v   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (157 / 107)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  


3033 26.45 1.79 0.45  chrX_80511080_80516783     4316  5211 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80511080_8   4316 TGGAAAAACATTCCATGCTCGTGGATAGGGAGAATCAATATCATGAAAAT 4365
                               i i  i     i  i     v  i   v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80511080_8   4366 GGCCATACCAGCCAAAGTAATTTATAGATTTAATGCTATCCCCATCAAGC 4415
                            v    ivv     v i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80511080_8   4416 TACCATTGACTTTCTTTGCAGAATTGGAAAATACT-ACTTTAAATTTCAT 4464
                          v   vivi i  i         v v  v  -i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_80511080_8   4465 ATGGAAC--CAAGAG-CCCACA-TAGCCACAACAATTCTAAGCAAAAAGA 4510
                               v--    i -    v -      v      ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_80511080_8   4511 ACAAAGCTGGAGGCATCTTGCTACCTGATTTCAAACTGTCCTACAAGGCT 4560
                               i      vv  vii  v  ii        viv v      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_80511080_8   4561 ACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGATGTATATACCA 4610
                                i   i    ii     i   i iv ii i   ii    v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_80511080_8   4611 ATGGAACATAAC--AGAGTCCTCAGAAATAACACCACACATATACAACCA 4658
                               i v  i--       --        vv   i    v  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_80511080_8   4659 TCTGATCTTTGACAAACCTGACAAAAAGAAGCAATGGGGAAAGAATTCCC 4708
                         vi    i  i     ivv  v   i vv vv               vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_80511080_8   4709 TATTTAATAAATGGTGTTGGGAAAACTGACTAGCCATATGCAGAAAACTG 4758
                          v  i  i        i     v     iv  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_80511080_8   4759 AAACTGGATCCCTTCCTTACACCTTATA-AAAAATTAACTCAAGATTGAT 4807
                           ii    i    v   i     v    -              i  v   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_80511080_8   4808 TAAAGACTTAAATGTAAGACCTAAAACCGTAAAAACCCTAGAAGAAAACC 4857
                         i ?    i           v       ii     vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_80511080_8   4858 TGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 4906
                          i  ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_80511080_8   4907 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATCGTATCTAA 4956
                         i            vvi          vv        i    i v ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_80511080_8   4957 TTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTGAAC 5006
                          i   v v  i i   i  ii vv    iv v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_80511080_8   5007 ACGCAACCTACAGAATGAGAGAAATTTTTTATAATCTGTCTATCTGACAA 5056
                          vi     i        i      v v   ii  viii v       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_80511080_8   5057 ATGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTATAAGAATA 5106
                         iv i  vi          v  i        ivv    v iv    v  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_80511080_8   5107 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTA 5152
                          i    ----   v  i?    i            v    i     i  v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_80511080_8   5153 TCAAAAGAAGACATTAATGTAGCCAACAA--ATATGAAAAAA-GCTCATA 5199
                           v        i  vv vi i     i  -- i       i -     vv
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_80511080_8   5200 ATCACTAGTCAT 5211
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (132 / 101)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


 317 28.91 6.64 1.90  chrX_80519955_80522159.rev       32   242 (1963)    L1M4_orf2#LINE/L1      688   908 (0)  

  chrX_80519955_8     32 AAAGTATCAAAAGGAAAGGCACAG---GGAAACAATATATTTACAA---- 74
                              i--     iv  vv     ---  i iv  -      i   ----
  L1M4_orf2#LINE/    688 AAAGTG--AAAAGACAACCCACAGAATGGGAGAAA-ATATTTGCAAATCA 734

  chrX_80519955_8     75 TATA----ATAAAGATATCATATTGAGAATATGTAAATAATTTGCACAAG 120
                             ----    i ivv ii   iv       i    v  i ivi    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_80519955_8    121 TAAATAGGAAAAAGATAGACACTGTAG--AAAATATAGGCAAGATATTTG 168
                          v    iv       i i i vivi i--?   v  i     iiv     
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_80519955_8    169 AACAGACACTTTACAAAAGACAATA-ATAATATAGCCATTAAGCCTATAA 217
                           i     i  iv v     vi   - i  -  i    v     vi  i 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAA-ATGGCCAATAAGCACATGA 883

  chrX_80519955_8    218 ATAAGTAGTCAACCTTATTAGGAAG 242
                          v ii iv     v i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (36 / 24)
Gap_init rate = 0.04 (8 / 221), avg. gap size = 2.25 (18 / 8)  

 510 29.30 0.64 0.00  chrX_80519955_80522159.rev      511   667 (1538)    L1M4_orf2#LINE/L1        1   158 (750)  

  chrX_80519955_8    511 TAGTAAAACATCCAATGCTCATGAA-TAAAAGAATCAATATTGTTAGAAT 559
                          i v  i i    v   i     i - ii    v i          ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80519955_8    560 GACTATATTGTCCAAAGCACTCTACAGATTCAATGCAATTCCTATCAAAT 609
                          i v   i vi     viiv             i     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80519955_8    610 TACCAACATCAATTTCCACAGAATTAGAAAACACAGTTCTAAAATTCATA 659
                          v   i vv vv   iii     v v  v  vviii i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_80519955_8    660 TTGGGATG 667
                          v ii   
  L1M4_orf2#LINE/    151 TGGAAATG 158

Transitions / transversions = 1.42 (27 / 19)
Gap_init rate = 0.01 (1 / 158), avg. gap size = 1.00 (1 / 1)  

2207 26.87 3.12 1.63  chrX_80519955_80522159.rev      978  1714 (491)    L1M4_orf2#LINE/L1      161   908 (0)  

  chrX_80519955_8    978 AAAGAGCCTGAATAGCTAAAGCGGTTCTAAGCAAAAATAACAAAGCTGGA 1027
                          ii  v  v       i   i ii ii i iv  i  v       i    
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_80519955_8   1028 GGCATCACATTACCTGACTTCAAACTATGCTACAAGACTATAGTAACCCA 1077
                           vv     i v  ii i      viv i      ii   i     i v 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_80519955_8   1078 AACAGCATG--ACCGGTACAAAAATGGACACACAGGTCAATGAAACAGA- 1124
                         i    ii  --  i  i i  ii  i    i i  i      i  i   -
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_80519955_8   1125 ----GAACCCAGTAATAAGGTCA--CATCAGTACAACCAAGTGATCTTTG 1168
                         ----  ii    v     ivi  --   i--  iiii   v    i  i 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAATTGATTTTCG 358

  chrX_80519955_8   1169 ACAAAG-TCCACAAAAATAGACAGTAAGGAAAGGACACCCTATTCAATAA 1217
                             i - v -   i vi vv  i ii      i i vi  v     i  
  L1M4_orf2#LINE/    359 ACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_80519955_8   1218 ATGATGCAGGGAAAACTGGCTAGCCATATTCAGAAGAATGAAACTGGACT 1267
                            i   v    v      v  ?   i  v  i         ii     i
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_80519955_8   1268 CCTGTCTTCCACCACATACCCAAACTAACTCAAGATGGATTAAAGACATA 1317
                            ii  iv     i    vv   i        i      i ?    v  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_80519955_8   1318 AATGGAAGAACTGAAACTATAAAAATCCTAGGAAAAAAAAAACCTAAGAA 1367
                             v    i  i           v  i   ----  i     v  i ?i
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAG----AAGAAAACATAGGNG 553

  chrX_80519955_8   1368 -AAATCTTCTGAACATTGGCCTAGGAAAATAATTAT---GATTAAGACCC 1413
                         -        vvi  v    vi    v  - ii  vi---   - v   v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT-ATGACAC 601

  chrX_80519955_8   1414 CAAAAGCAAATGCAATGAAAACAAAAATAGAAGAATAGGACTTAATTAAG 1463
                                 v v    ii   iv         vi   v      v  i  i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_80519955_8   1464 CTAAAGAGCTTCTGCACAGCAAAAGAAACAATTGACAGAGTAAACAGACA 1513
                         v v  i i   i  ii vv    i  v  v  ii v i   i  v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_80519955_8   1514 ACCTACAGAATGGAAAAAAATATTTGCAACTTATGCATCAAACAAAGGAA 1563
                            i         i i             v i  ii   vi i  i   v
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_80519955_8   1564 TAATATTTAGACTTTATAAGGAAAT--TATA--TCAACAAGAAAAGAACA 1609
                          vi   ii   v v     i   v --  i --    i  v    ii   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_80519955_8   1610 A-TATTCTCATTAAAAAGTGGGCAAAGGACAGGAACAGATATTTCTCAAC 1658
                          -  vi iv   ?    i           ivv   i   i       v v
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_80519955_8   1659 AGAAGACATATAAG----CAATCAGCATATATAAAAAAAATGGTCAACAT 1704
                               i   i  i----    v    i  i---    i   v       
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATG---AAAAGATGCTCAACAT 898

  chrX_80519955_8   1705 CACTTAGCAT 1714
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.85 (126 / 68)
Gap_init rate = 0.02 (16 / 748), avg. gap size = 2.19 (35 / 16)  


3015 25.52 0.99 1.10  chrX_80523461_80526192.rev     1333  2241 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80523461_8   1333 TGGAATGATATTTCATATTCAGGGATTAGAAAA-TTAACATTGTAAAAAT 1381
                              v     ii   i    v     i   i -    i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80523461_8   1382 GTTCACACTACCCAAGGCAATCTACAGATTCAATGGAAATCTTGGCAGGA 1431
                          viv i   v     ivii              i v  vi i iv  ii 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80523461_8   1432 TTCCAA-TGTCGTTTTTTACAGAATTTAAAAAAAAAAAAACTTAAATTTG 1480
                          i   i-  i -      i     v  i v  -ivvi vv  v     ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_80523461_8   1481 TATGGAACTACAA-AAACTCTGAATAGCCAAAACAATCTTTAGCAAAAAT 1529
                                v i   -ii  i v                   v iv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80523461_8   1530 AACAAAGCTGGAGGCATCACACTCACTAATTTCAAAACATATAATGAAGC 1579
                                i      vv       iv i           v  iv ii    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80523461_8   1580 GATTTTAATCAAGACAGCATGATTAATTACA-AAGAAAAGGACATATCAA 1628
                         v ivv            ii  i - v vi  -   i v -       vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGT-ACTGGCATAAGGATA-GACATATAGA 296

  chrX_80523461_8   1629 CTTTTGAAACAGAATTAGAAAG-CAGGAAATAAACCCACAAATTTATGTT 1677
                         iivv  i  i      -  i  - vi            i v       v 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_80523461_8   1678 CAATTGATTTTTGACAAATGTGTCAAGAACACACAATTAGGAAAAAGTA- 1726
                                    i     iv   i     v  iv    vi     i i  -
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_80523461_8   1727 --TTTTCAATGAATGGTGCTGAGGAAAACTGGGTATCCACATGAAGAATA 1774
                         --       ii          -   v      i  ?       v i  v 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_80523461_8   1775 ATGAAACTGATCCCTCTATCTCTCAACATAAACAAAAATAAACTCAAAAT 1824
                              ii  iv   -   i   v  v    v        v          
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_80523461_8   1825 GGATTA-AAACTTAAATCTAAGACCTGAACCTATGACACGACTAAAAGAA 1873
                             i - i  i     v     v  i  v    i v  vvi  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_80523461_8   1874 AACTTAGGAGGAATGCTTTATAAAAGTATACTGGGCAACAACTTTTTTTG 1923
                            v    ? v  vv   ii i vvv ivii i     iii-   i  v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAG 592

  chrX_80523461_8   1924 ATATGACCCCCAAAACACAGGCAATAAAAGCAAAAATTGGCAAATGGGAT 1973
                                v  v   i    i    i     v      v ii    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_80523461_8   1974 GCCATCAAACTAAAATAACTTCTGCACACCAAAAGAAACAATAAACAAAG 2023
                         vi       v v   -     i  ii vi    i  v  v  v  v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_80523461_8   2024 TAAAGAGGCAACCTACAGTGTGTGAAATAATTTCTGCAAACTATACATTT 2073
                          i  i  i     i    vi  v  i v   v i      ii   i  i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_80523461_8   2074 GATAAGGGAATAATATTCAAGATATATAAGGATCTCAAACAACGCAATAG 2123
                                  v vi   i  ii        i  v   vv     v     i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_80523461_8   2124 CAAGAAAACAAATAAATCAAATAAAAAATAGACTAAGGGCCTGAAAAGAC 2173
                         i  i  i        vi   v ?      i i v    iii    v    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_80523461_8   2174 AATTTGCAAAAGAAGACATATAAATGACCAATAAATATATGAAAAAAATG 2223
                          v  iv v        i   i     i       ii i       i -  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chrX_80523461_8   2224 CTCAGCATCACTAATCAT 2241
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (133 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.12 (19 / 17)  


3088 26.43 1.32 1.75  chrX_80531372_80537730.rev     4957  5868 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80531372_8   4957 TGGAAGAATATTCCATGCTCCTGGATAGGAAGAATCAATATCGTGAAAAT 5006
                              ii    i     i  v     v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80531372_8   5007 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5056
                            v     v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80531372_8   5057 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAATTTC 5104
                          v   iivi i  i  ii     -   --- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_80531372_8   5105 ATATGGAACCATAAAAGAGCCTGCATTGCCAAGGCAATCCTAAGCCAAAA 5154
                                 viii  ii  v  v v  v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_80531372_8   5155 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5204
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_80531372_8   5205 CTATAGTAACCAAAAATAACCAAAACAGCATAGTACTGGTACCAAAACAG 5254
                            i     i   i ----------   ii i       i iv ii i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGA----------CAGTGTGGTACTGGCATAAGGATAG 287

  chrX_80531372_8   5255 AGATATAGAACAATGGAACAGAAC--AGAGCCCTCAGAAATAGTGCCACA 5302
                          v       v        i    i--    i  --       ivv   i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATA 335

  chrX_80531372_8   5303 TATCTACAACCATCTGATCTTTGACAAACCTG--AAAAACAAGCAATGGG 5350
                         i  i  iiii  vi    i  i     ivv  --  i v  vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_80531372_8   5351 GAAAGAATTCCCTATTTAATAAATGGTGTTGGGAAAACTGACTAGCCATA 5400
                                 vvi  v  i  i        i     v     iv  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_80531372_8   5401 TGCAGAAAACCGAAACTGGATCCCTTTCTTACAACTTATACAAAAATTAA 5450
                             i  i vi   ii    i    vi  i   v v              
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_80531372_8   5451 TTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCC 5500
                         i    i      i ?    i       v   v       i      vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_80531372_8   5501 TAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGA 5549
                                    v    ?i- v i -   iv   v v  vv i     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_80531372_8   5550 CTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACA 5599
                         i   v iiv  vi            vvi          vv        i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_80531372_8   5600 AATGGCAACTAATTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACC 5649
                            v v vi v  i   v v  i i   i  iiivv    i  v    i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_80531372_8   5650 ATCAGAGTGAACAGGCAACCTACAGAGTGGGAGAAAGT-TTTCCAATCTA 5698
                          vv i      v  i     i     i         i -   v   vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_80531372_8   5699 CCCATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAA 5748
                         ivi      i  i  i  vi          v  i         vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_80531372_8   5749 TTTATAAGAAAAAGACAA----CCCCATCAAAAAGTGGCCAAAAGATATG 5794
                          iv    v          ----   v  i?    i   v    i   v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_80531372_8   5795 AACAGACACTTCTTAAAAGAAGACATTTATGCAACCAAAAGACACATGAA 5844
                           i     i    iv        i  vi viiii    v ii        
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_80531372_8   5845 AAAATGCTCATCATTACCAGTCAT 5868
                           i       v   i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.55 (28 / 11)  


 254 22.64 0.00 0.00  chrX_80541544_80545471     2210  2262 (1666)    L1M4_orf2#LINE/L1        1    53 (855)  

  chrX_80541544_8   2210 TGGAAAAATATTGCATGCTTATGGATAGGAAGAATCAGTACTATTAAAAT 2259
                               i    iv    i i      v      v i i  i i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80541544_8   2260 GGC 2262
                            
  L1M4_orf2#LINE/     51 GGC 53

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.00 (0 / 0)  

1829 28.64 3.70 4.04  chrX_80541544_80545471     2571  3436 (492)    L1M4_orf2#LINE/L1       46   908 (0)  

  chrX_80541544_8   2571 AAAATTACCATAGTGCCCAAAGCAACTTCCACATTCAATGCAATTGCTAT 2620
                           i  vi v   v v      vii ii v  v      i     iv    
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_80541544_8   2621 TAAACCACTAATGACATTCCTCACAGAACTAGAAAAAAAAAAGAGCT-AT 2669
                         i   viv i iivi v  ii ii     v v  v  --------   -  
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--------GCTGAT 137

  chrX_80541544_8   2670 ATTAACATTCACATAGGACCAAA---AAAAGAGTCTGAATAGTGAAGAAA 2716
                         vi   v     i  i ----   ---  ii  vi v      iv  i v 
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGG----AAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_80541544_8   2717 ATTTTAAGCAAAAAGAGCAAAGTTGAAGATATTATGCTACTATTATGCTA 2766
                           i  i iv  i    i        i  i---------   --i ii  v
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGG---------ACT--CACACTT 222

  chrX_80541544_8   2767 CTCCGCTTCA-----TGCTGTC---CTATGGTAACCCAAACAGCATGGTA 2808
                          i vii    ----- i  iiv---   ii    i v i    ii     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_80541544_8   2809 CTGGAAAAAAAAAAAAAAGGCACACAGACCAGTGGAAAATAATAGAGAGC 2858
                             v v  ii v i ----  i i   i  i     v v   v     i
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGA----CATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_80541544_8   2859 TGAAAAACAAGGCTGTAAACCTGCAACTATCTGCTCTTTCACAAAGCTGA 2908
                         iv i   i  iv ii  v ii iiiiii vi  v i  iv    i v  v
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_80541544_8   2909 CAGAAACCAG-CAATGGGGAAAGGAC--TCCCTAAACTATAAATGGTGCT 2955
                           - i    v-            i i--  ii vv -- i          
  L1M4_orf2#LINE/    369 CA-AGACCATTCAATGGGGAAAGAATAGTCTTTTCA--ACAAATGGTGCT 415

  chrX_80541544_8   2956 GGGATAACTGGCTAGCCATATACAGAAGATTGAAATGGTGCCACTTCCTC 3005
                             i      v  ?   i  i  i    v    i v vi  v  v    
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_80541544_8   3006 ACACCATATAAAAAAATTAACTTAAGATGGAGTAAATACTTAAATGTAAA 3055
                                   v           i  i     vi ? v  i         i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_80541544_8   3056 ACTTAACACTATAAAAACCT-AGACAATACCAT---------TCT--G-G 3092
                          vi   v         vi  -   vi v v   ---------   -- - 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_80541544_8   3093 ACATAAGAAAGAGCAAAGATTTTATGACAAAGACAACAAAAGCAATTGCA 3142
                           v vi ivvii    v i   iv iivv v    v        vvv   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_80541544_8   3143 ACAATAACAAAAATTGACAAATGGGATCTAATTAAA-TTAAAGAGCTTCT 3191
                             v iv      v  i    v   ii v  i   -     i -   i 
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTT 664

  chrX_80541544_8   3192 GGACAGCAAGAGAAACAATCAATAGAATAAACAGACAACCTACGTAATAT 3241
                          vi vv   ii  v  v     v i i i  v        i  iv   iv
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_80541544_8   3242 GAGAAAATATTTGCCAATTATGCATCTGACAAAGGTCTATTATCCAGCAT 3291
                                       v   i  ii      i  i  v  vv       v  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_80541544_8   3292 CTATAAGGAATGTAAGCAGATTTACTACAATAAAAA-AGAAAAAACCCTA 3340
                         v     i   ivivvi  - i i -- i        - v   v     v 
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACA-ACTCA--ATAATAAAAAGACAAATAACCCAA 811

  chrX_80541544_8   3341 TT--AAAATGGGCAAAGGATATGAACAGACAATTTTTTAAACAAGACACA 3388
                           --                v    i     v  i ii   v    i i 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_80541544_8   3389 CATGTGGCCAACATGCATACAAAAACAAAGCTCAACATCTCTGATCAT 3436
                           vi       i v   i ii    -i v          v????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (142 / 104)
Gap_init rate = 0.03 (24 / 863), avg. gap size = 2.79 (67 / 24)  


3067 26.42 1.44 0.67  chrX_80563997_80567926     2542  3442 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80563997_8   2542 TGGAAATATGTTCTATGTTCATGGATTTGAATGA-TTAATATTGTTAAAA 2590
                               v  i i i             v   -  -             i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAA-GACTTAATATTGTTAAGA 49

  chrX_80563997_8   2591 TGTCCATAATACTCAAAGCAATCTACAGATTCAGTGCAATCCCTATCAAA 2640
                           v v   v v i    vii             ii               
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_80563997_8   2641 ATTTCAAG-GATTTTTTTACAGAAATAGAAAAA-TAATTTTGACATTTAT 2688
                           ii  iv- vi      i       v  v  i- i  ii i v   i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_80563997_8   2689 GTGGAACCAGAAAAGAACCCA-AATAGCTAAAGCAATCTTGAGCAAAAAA 2737
                         i     vi- v  i i     -      i   i         i-   i  
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAA 197

  chrX_80563997_8   2738 GAACAAAGCTGAAGGTGTTACACTATGTGATTTGAAAATCTCCTACAGA- 2786
                                 i  i   vv i     vivii    v    ii v     i -
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_80563997_8   2787 TGATAGCAGTAAAAACAGCCTATTACTGGCATAAAAAACTGACACATTGA 2836
                         iv i  i i v  i    iv iv           ii -iv    i  v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGA 296

  chrX_80563997_8   2837 CCAAGGGAACAGAATAGAAAGTCCAGAAATAAATCCAAATATCTATGGTC 2886
                         i   v    i     v  i              i   v i  i       
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_80563997_8   2887 AATTGATTTTTGACAAAGATGTCAAGAACACACAATGGGGGAAACACAGT 2936
                                   i     i i  i     v  iv        i  iv i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_80563997_8   2937 CTTTTCAATAA--GATGTTGATAAAACTGCATATCCACATGCAGAAGAAA 2984
                                 i  -- i  i  iv v     v   ?         i     v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80563997_8   2985 AAGAAATTAGACCCTCATCTCACATCAGATG-AAAAATCAACTCGAAATA 3033
                         --   i  i     ii i      i  v  i-      i     i    i
  L1M4_orf2#LINE/    447 --GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_80563997_8   3034 AATTAAAGAGTTAAGTGTAAAACCTACAACTGTGAAACTACTAGAAGAAA 3083
                         i  i ?   vi   i     i v   v    i i     vi         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_80563997_8   3084 -CATAAAGGAAAACCTCCACAACATTGGTCTGGGCAATAATTT-TTATAT 3131
                         -    ii? v   i  i iii  v    vi i      ii   -   v  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_80563997_8   3132 ATGACACCAAAAGCACAAGCATTAGAAGCAAAAATAGACAAATGGAATTA 3181
                                              vi i   v         i    v i i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_80563997_8   3182 CATCACACTAAAAAGCATATACACAAAAAAGAAAACAATAAACAGAATGA 3231
                              v v v    i v v iii vvv    i v  v  v  v i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_80563997_8   3232 ATTGATAACCTATGAAATGGGAGAGAGTATTTCCAGGACATACATCTGAT 3281
                          vv  i    i iii         i i     v  iiv    i       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_80563997_8   3282 AATGGGTTAATATCCAAGATACAAAAGGAACTCAAGCAACTCAATATTAA 3331
                           v  ii vi      ii   i v  i      vvi          v   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_80563997_8   3332 GAAAATATATAATGCATTTCAA---TGGGTATAGGATCTGAACAAACATT 3378
                         i  i i v    iv  v  ?  ---    i v     i    i i     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_80563997_8   3379 TTTCAAAAACAGTCAAACAAATTCGTAACATTTATATTTTAAAATACTAA 3428
                          i  v   iv  vi v      vvvi  i vvi i  vvv  i  i  v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_80563997_8   3429 ATGTTACTAATCAT 3442
                          ii i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (146 / 88)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.27 (19 / 15)  


2336 28.09 1.41 2.93  chrX_80586037_80594617.rev     2564  3485 (5096)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80586037_8   2564 TGGAAAAATATTTCAAGCTCATTGATAGGAAAAATCAATGTTGTAAAAGT 2613
                               i    ii  v i    v   v    i v i   i    v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80586037_8   2614 GATCATACAGCCAAAAGCAATTTACAGATTCAATGCTTCTCCTATCAAAC 2663
                          iiv    vv  v   vii  i           i  vvii         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80586037_8   2664 TACCAATAATGTTGTTCACAGAATTAGAAAAA--AATTTCTAAAATTTAT 2711
                          v   iiviiv  v  ii     v v  v  i--i  i-        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-CTAAAATTCAT 149

  chrX_80586037_8   2712 -TTGAAACCCAAAAAGAGCCCA-AATAGCCAAAGCAATCCTAAGCAAATA 2759
                         - v    iv   i-- ii    -          i     i i iv  iv 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_80586037_8   2760 GAACAAAGCTGGAGGTATCACACTACCCAGCTTCAAACTATACTACAAGA 2809
                                 i      vv       v    ii      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_80586037_8   2810 ATACAGTAACTAAAACAGCTTACTACTGATA-AAAAACAGACACATAGAA 2858
                         v        ii  i    iv iv     ii -  ii i     i     v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_80586037_8   2859 TTATGGAACAGGTTAGAGAACTCAGAAATTAAGCCACACACCTATAACCA 2908
                         iv      i  iv v    iii       v  v   i   ii   iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_80586037_8   2909 TCTGATCTTTAACAAAGTTGAGAATAACAAGCAATGGGAAAATGAATC-C 2957
                         vi    i  ii    i v  vv  v v  vv       i   -    v-i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGT 396

  chrX_80586037_8   2958 CTATTCAATAAATGGTGATGGAATAACTGGCTAGCCATATACAAAAGATT 3007
                           v     i        v   i i      v  ?   i  i       v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80586037_8   3008 GAAACTGGACCCTTACATTTCATCATATACAAAA-TCAACTCAAGATGGA 3056
                            ii       i   v iv  i           - i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80586037_8   3057 TTAAAGACTTAAATGTAAAACCTAAAACTATAAAAACCCTAGAGGAAAAC 3106
                          i ?    i         i v              vi i    i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_80586037_8   3107 CTAAGAA-AGACCACTCTGGATATCAGCCCTGGCAAAGACCTCATGACAA 3155
                         v  i ?i- i i -i  vv  iv ii viiv     v iii  v iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_80586037_8   3156 AGACTACAAAAGCAATTGCAACAAAAACCAAAATTGAGAA----GACATA 3201
                         v   vv        vvv         ivv     v  v  ----   v v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_80586037_8   3202 ATTAAACTAAAGAGCTTCTGCAAAGCAAAAGAAATTATACACAGGGTAAA 3251
                           i   v v  i i   i  iivvv    i  v i   vv v ii  i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_80586037_8   3252 AAGACAACCTACAGAAGTTGAGAATATATTTGCAAGTTATACATCTGA-A 3300
                                  i      vvv     v          i i   i      - 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_80586037_8   3301 AAACATCTAATATCCAGATATCCAGAATCTATAAGTAACTTAAGCAAATC 3350
                          iiv ii i---------          v     iv    ivvi   v  
  L1M4_orf2#LINE/    746 AGGGACTTG---------TATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_80586037_8   3351 AACAAGCAAAAAAAAAAAAAAAGAAAGAAAAAAGAAAAATTACTAATGGG 3400
                           i  -i     i v   v  vvv  vv?    ------------     
  L1M4_orf2#LINE/    787 AATAA-TAAAAAGACAAATAACCCAATTWAAAA------------ATGGG 823

  chrX_80586037_8   3401 TCAAGGACATGAACAGACATTTCTCAAAAGAAGACATTCACGTAGCCAAC 3450
                         iv     iv    i           v        i  v  vi i     i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_80586037_8   3451 AAGCCTATAAAATAATATGCAACATCACTAATCAC 3485
                             vi  i   vi  iiv        ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (144 / 111)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.50 (40 / 16)  

1904 29.72 6.88 1.05  chrX_80586037_80594617.rev     7233  8090 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80586037_8   7233 TGAAAAAACATTCCACTGCTCATGCATTGGAAGAATCAATATCATTAAAA 7282
                           i   i i  i   -  i     v         v i     ii    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCA-TGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_80586037_8   7283 TGGCAA----------AGTAATCTACAGATTATATTCAATTCCTATCAAA 7322
                               ---------- v i           vv iv    i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_80586037_8   7323 CTACCAATGACAATTTTCACAGAATTAGAAAAAACT-ATTTGAAAATTCA 7371
                         v v   iivi vv    ii     v v  v  i-  -  iiv        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_80586037_8   7372 TATGGAA---CCAGA-----AGAAGAGCCCAAATAAT---AAGCAAAAAG 7410
                                --- v  i-----    v    v   i   ---i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80586037_8   7411 AAGAAAGCCAGAGGCATCACATAACCTGACTTGAAA-----CTAT---GC 7452
                           v    iii    vv     ivv  ii i  v   -----   i---  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80586037_8   7453 TATA-------AG-----GTGATACTGATATGAAAGCACACACAGAGATC 7490
                           i -------  -----   i     ii  i iiii v   i v     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80586037_8   7491 AATGGAACAAAAAAAAAACCTCAGGAATGAAGCTGCACATCTACAACCAT 7540
                                i i  vvi i vii   i   i  v iii    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_80586037_8   7541 CGGATCTTCAACAAGACCAACAAAAACAAGCAATGGGGAAAAAACTCCCT 7590
                         iv   i   i     iviiv   i v  vv           i  ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_80586037_8   7591 CATCAATAGATGTTGCTGGGATAACTGGCTAGCCATATGTGGAAGAATGA 7640
                         iv    i i   v        i      v  ?   i   iii        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_80586037_8   7641 AACTAGATGCCTGCCTTTCATCATGTACAAAATCAAACTCAAATTGAATT 7690
                          ii i  iv   i   iv  i   i       viv        v  i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_80586037_8   7691 AAAAATTTAAATGTAATACATCAAACCATAAAAATCCTAGAAGAAAACCT 7740
                          ? i ii         v vv v    i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_80586037_8   7741 AGA---AAATACCTTT-----CTCAATATAGGCAAATAATTTAT-GGCCA 7781
                           i---    --   i-----  iiivv       - ii   v -i vi 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATA 595

  chrX_80586037_8   7782 AGTTCCCAAAAGCAATTTCAATAAAAATAAAAAGTGAAGCAA---GACCT 7828
                         v viv         vvvv   i    i-     i ii vv  ---   i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTT 644

  chrX_80586037_8   7829 AATTAAACAAAAGAGCTTCTGCACAGCAAAAGAAACAATTAACAAAGTAA 7878
                         v  i   vvv  i i   i  ii vv    i  v  v  i  v     i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_80586037_8   7879 ACAGACAGGATACAGAACGGGAGAAAATAATCACAAACTATTACACACCT 7928
                          v     ivvi      i           v ii    ii  --- i i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT---ATATCT 741

  chrX_80586037_8   7929 AAAAAATGTCTAATATGTAGGATCTACAATAAACTGCAAGAATTCAACAA 7978
                         i v  iv v  vi   vi  i  v  i  vi    viv v  i    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_80586037_8   7979 AGAAAAATCAAATCACCCCATTAAACAATGAGCAGAGGACATGAA----C 8024
                         vi    iv     v    v   ?  v    i   i    iv    ---- 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_80586037_8   8025 ACTTTTCAAAAGAAGACACACATGTGGCCAACAAATATATGAAAA-ATGC 8073
                          i  i  v        i i   vi       i  ii i       -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_80586037_8   8074 TTATTATCACTAACCCT 8090
                          i vi    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (153 / 99)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.24 (68 / 21)  


1779 27.23 1.71 2.05  chrX_80613159_80618271.rev      677  1260 (3853)    L1M4_orf2#LINE/L1        1   582 (326)  

  chrX_80613159_8    677 TGGAAAGATATATTGTGTTCATGGATGGGAAAACTCAATATTATGAAAAT 726
                                    viii           v    i   i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80613159_8    727 GTTCATACTACCTAAAATGATATCCAGGTTCAATGCAATCCCTATCAATA 776
                          viv     v  i   v    v v   i     i              v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80613159_8    777 TTCCA-CTGATATTTTACACAGAAATAAAAAAAACAATTCTAAAATTTAC 825
                          i   -   viv    -ii       vi v  ivii  i        i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_80613159_8    826 ATGGAACCTCCAAACAACCCA-AATAGCCAAAGGAATACTGAG---GAAA 871
                               v- v   ivi     -          iv   vi   i---   i
  L1M4_orf2#LINE/    150 ATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80613159_8    872 AAAAAAGCTGAGTGAATTACACCATCTAGTATTAAATTACACTGCAAATC 921
                           v    i  iiv  v i    ivi i i v i   vivi   i    v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80613159_8    922 TATAGTAATAAATATAACACAGCCCTGGCATAAAAGCAGACTCATCAACT 971
                           i      v  v i iiiii iv         iiii    vi  vi ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80613159_8    972 AATGGAACAGAATAAAGAACCTATAAATAAAT--ATACACTTATATGGTA 1019
                                i     vi   ii i v       i--     i    --   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT--GGTC 346

  chrX_80613159_8   1020 AAGTAATTTTTCACAAGTTACTGTGTAACCTGTATGATACAATGGGGATA 1069
                           v i     iv     v----   ---  viv iv  v         v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGG----GTG---CCAAGACCATTCAATGGGGAAA 389

  chrX_80613159_8   1070 AAACTGTCTTTTCAATAAACGGTGTTGGGAAAACAGGATAATCATATGCA 1119
                         i  iv          i   i    i     v   v     ?i  i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_80613159_8   1120 AAATAACGAAATTGGACACATGTCTTACACCATATACAACATTCAACTCA 1169
                            v  i   i      v v ii  i             v v i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_80613159_8   1170 AAATGGACTAAAAATTTAAAC-TAAGACATGAAACCATAAAACTCCTAGT 1218
                                ii ? i ii    i-     vv i    i         i   v
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_80613159_8   1219 ACAAAACTCAAGGA-AAAGCTCCCTGACATTTGCCTTAA-CAAT 1260
                          v     vi i ?i-   v  i v    -i   vv   i-    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAAT 582

Transitions / transversions = 1.56 (95 / 61)
Gap_init rate = 0.02 (13 / 582), avg. gap size = 1.69 (22 / 13)  

 884 26.05 3.86 1.61  chrX_80613159_80618271.rev     1537  1847 (3266)    L1M4_orf2#LINE/L1      591   908 (0)  

  chrX_80613159_8   1537 AGAGAGAAAACCAAAAGCACATGCAGCAAAAGTAAAAACAGACG---TGG 1583
                            v vi v            v   i      v     i   ii---   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_80613159_8   1584 AA---ATCGAACTAAATACCTTCTGCACAGTCAAAAT-CA--ATCACCAA 1627
                          v---   i  v v  v v   i  ii -v     iv-  --    vv  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAA 689

  chrX_80613159_8   1628 AATGAAAAGGTATAGGATGTATTGA--GAAAAAAAATGTTTGTGAACTGT 1675
                          i       ii ---- ivi iv  -- ii i     i    ii  iii 
  L1M4_orf2#LINE/    690 AGTGAAAAGACA----ACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_80613159_8   1676 ATATTTGATAAGAGCTCAATATTCAAAATATATAAGGAATTCACACAACT 1725
                             i       i viivi   i  i         i   i  vi      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_80613159_8   1726 CCATAGCAAAAAATCAAATAATCTGATTAAACAATGGGCAAAGCATATAA 1775
                          v   ii     iv       i ii   ?  v           v  v i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_80613159_8   1776 ATAGACACTTTTCCAAAGAAGACATAAAAATGGCCGACGGTTGTATGAAA 1825
                                i  i           i   v        i iiiviii      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_80613159_8   1826 AGTTACTCAACAT-ATTAATCAT 1847
                           v i        - ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (53 / 27)
Gap_init rate = 0.03 (8 / 318), avg. gap size = 2.12 (17 / 8)  

1104 26.08 9.45 4.31  chrX_80613159_80618271.rev     3560  4046 (1067)    L1M4_orf2#LINE/L1      133   644 (264)  

  chrX_80613159_8   3560 CTGATTCTAAAATGTATACGTAAATGTAAAGGATAAAGAATAGCCAAAAC 3609
                              i       vi   i v     i  i   ivv              
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chrX_80613159_8   3610 AATTTTGAAAAAAAAGA-----------GAACTT----TACCTGATTCCA 3644
                            i        i    ----------- i   i---- v  ii   i  
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_80613159_8   3645 ACATTTATTATAAAGCTATAGTAATCAAGAAAATATAGTATTTGTATAAT 3694
                          v i   i  i       i           v i i i   i v i    v
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_80613159_8   3695 GGTAAACATATAGATGTAAGAGACA-AGCTCAAAATCCAGAAATAGACC- 3742
                          i  i          vv v ii i - ii v i i          i   -
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_80613159_8   3743 ACACATATAAGATCAACTTATTTTTGAGAAAGTTGCCAAACTTACTTAAT 3792
                          i    v  v i    i v     i  v  i v      ivii i i   
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_80613159_8   3793 ACAGCAGGAATAATCTTT-CAACAAGTCATGTTCCAACAACTTCATATTC 3841
                         ivi v i     i     -      i vi  i vvi      vv   ?i 
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_80613159_8   3842 AAATAGAAAAAAATTGAACCTTGACCCATTCCTC-CAAGTCTGCA-AAAA 3889
                          v  iv    i   -   vi v     v v    -  --- iii - v  
  L1M4_orf2#LINE/    433 ACATGCAAAAGAAT-GAAGTTGGACCCCTACCTCACA---CCATATACAA 478

  chrX_80613159_8   3890 AAATTACTTTGAAAATGGATCACAGATCTAA-TTTA-------------- 3924
                               vi i-           ?   i    - v  --------------
  L1M4_orf2#LINE/    479 AAATTAACTC-AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_80613159_8   3925 --------TAGAAGAAAATATAGAAA-AAATTGTTACAATTTTGGGGTAT 3965
                         --------          i    i?i-    iv iiii ii     v  v
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_80613159_8   3966 GTATTAGTCTGTTTTCACGATGCTGATAAAGACATACCTGAAACTGTGCA 4015
                          i v i  ---  i i -   ----  ---    --- ii   -- ii  
  L1M4_orf2#LINE/    578 GCAATGGT---TTCTTA-GAT----AT---GACA---CCAAAA--GCACA 611

  chrX_80613159_8   4016 ATTCACAAAAGAAAGAG--GTTTAATTGGACTT 4046
                          viv          i i-- v v          
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

Transitions / transversions = 1.88 (81 / 43)
Gap_init rate = 0.04 (20 / 512), avg. gap size = 3.35 (67 / 20)  

 504 23.31 11.49 0.68  chrX_80613159_80618271.rev     4329  4624 (489)    L1M4_orf2#LINE/L1      581   908 (0)  

  chrX_80613159_8   4329 ATAACTTCTTAGAGATATCAC--AAAACACAC-TAACAAAA---AAATT- 4371
                           iii        v  iv   --   i    v-i       ---   v -
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_80613159_8   4372 --TAAATTGAAATTCTTCAAAATGTATAACT---------CA---GTCAT 4407
                         --       i v   v       vv v    ---------  --- v  i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_80613159_8   4408 TATTAAGAAAATGAAAAGCCAAGGCAAACATTG--AAAAAATATTTACAA 4455
                            i      i       v   vv  v v v  -- i         i   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_80613159_8   4456 TTTATATATCTGACAAAGGAATTATATTCACAACATACGTAAGAA-TCTT 4504
                         v i          i  i   v  i   i  v  i   ii-     -    
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATA-AAGAACTCTT 779

  chrX_80613159_8   4505 ATAA---ACTAACAGAAAGATAATGCAACT---TTAAAAAGTAAACAAAT 4548
                          i  --- v   i i     i  -ii   i---  ?    i iii    v
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAA-ATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_80613159_8   4549 TTTTTT--TAAAAACTTCACAAAAGAAGAAATAAAAATT-CCAATAAGCC 4595
                         vv   v--  i v i   v v        v   v    v-         v
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_80613159_8   4596 CCCCAAAA-ATGCTCAACATAATTAATCAT 4624
                          viv    -           v ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (34 / 34)
Gap_init rate = 0.05 (15 / 328), avg. gap size = 2.40 (36 / 15)  


2302 26.46 3.53 3.42  chrX_80631570_80635766     2798  3704 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80631570_8   2798 TGGCAAATTATCCCCTGCTCATAGACTGAAATAATTAACATTGTTAAAAT 2847
                            v  iv      v  i    i  i  i  v v    i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80631570_8   2848 GACCATACCACACAAAGCAGTCTATAGCTTAAATGCAACCTCTATCAAAA 2897
                          i v    iv v    viii    i  v  v  i    i i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80631570_8   2898 TACTAATTTCATTTTTCACAGAAATAGTAAAAAC-AATCTTACAATTCAT 2946
                          v i ii v v     ii       v - v  i -i   i  v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chrX_80631570_8   2947 ATGGAACCAAAAAAAAAGCCTGAATGTAATCACGAATAAT---AGAAAAA 2993
                               viiv  iii v-  v    -- ii  -i  i   ---ii    i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC-CCAGAAT--AGCCA-AAACAATCTTGAAAAAG 195

  chrX_80631570_8   2994 AAGAGCAAAGCTGGAGGCATCACACTAGCTTCC---TTCAAAAAATACTA 3040
                             i     i      vv       --- i  ---       vv     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACT---TCCCAATTTCAAAACTTACTA 242

  chrX_80631570_8   3041 CAAAGC-ATCTTAACAAAAACTGAATGGTATTGATATAAAAACAGAAACA 3089
                               - ivv   iv  i  v vi     i  ii    ii i   v i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_80631570_8   3090 TAGACTAATAGAATAGA-----GAACTTGGAAATAAATGCATGTACTTAG 3134
                             ii   i       -----  iiiii        iv   ii i   v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_80631570_8   3135 AACAAAGTAATTCTTGACATTGGTGCCAAGAACATACACCAAGGAAAGGA 3184
                         iiiv  v i   i i    vv          v   v  viii      i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_80631570_8   3185 CACCCTCTTCAATAAATCAGGCTGGAGAAACTGGA-ATTCATATGCAGAA 3233
                         i vi  i     i    viv     iiv       - ?i  i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_80631570_8   3234 AAATGAAACAAGTATCCTACACTCAT--TATATACAAAAATGAACTGAAA 3281
                         i      iivi vvi     -    i--i            v    v   
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTAC-CTCACACCATATACAAAAATTAACTCAAA 491

  chrX_80631570_8   3282 AT---TTAAACACATGAAAT-TAAGATTCGAATCTATAAAACTGT-AGAA 3326
                           --- i ? v  v -    -     viii  v          v -    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCT-AAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_80631570_8   3327 GAAAACATTAG-GTAAATTCTTAAGGACATTGGTATAGTTA--GATTTCG 3373
                                 vi -      -   viv   v    vv   vi -- i    v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_80631570_8   3374 TGACTAAGAC-CTAAAATGTACAGGCAACAAAAACAAAAATGGGAAAATG 3422
                          iiv  v   - i    - i   i         iv      i iv    v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_80631570_8   3423 GTACTGTATTAAAGT-AAAAAAGATTGTGCATAGCAAAGAAAACAATCAA 3471
                          v   vi  i   i -     vvv      v --     i v  v     
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAA 686

  chrX_80631570_8   3472 CAGAATGAAGAAACAGCCTGCAGAGTAGGAGAAAATATTTCTAGGTAACT 3521
                         v i i    i i   i  ii    i i             ---- i  v 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT----GCAAAT 732

  chrX_80631570_8   3522 CATGTGACATTCTGGT------CTAATACCTAAGAATATACAAGGAAGTT 3565
                            i i----    i ------  vi  i i -       i  i   v i
  L1M4_orf2#LINE/    733 CATATA----TCTGATAAGGGACTTGTATCCA-GAATATATAAAGAACTC 777

  chrX_80631570_8   3566 AAACAATTCAATAGCAAAATAATACTAATAATATTGATCTCATTAGAAAG 3615
                         vv    i      ii    -- v  v     i------ iv   ?i   i
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAA--AGACAAATAAC------CCAATTWAAAAA 819

  chrX_80631570_8   3616 TGGGCAAAGGATATTAATAGATATTTCTCAAAATAACACATATAAATGGC 3665
                                     v v      i       v   v  v i   i       
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_80631570_8   3666 CAAGAGATATATGAAAAAGTATTCAATATCACTAATCAT 3704
                            v iii i       ii ii    i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.10 (63 / 30)  


2423 26.77 0.51 7.38  chrX_80640433_80645462     3563  4537 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80640433_8   3563 TGCAAAAGCATTCCATGTTCACGGATTGGAAGAGTAAGTACAATTAAAAT 3612
                           v   iii  i         i           v v i  ivi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80640433_8   3613 GTCCACATCACCTAAAGCAATGTACAGATTCAATACTAGTCCTATCAAAC 3662
                          v v i iiv  i   vii  v           ii v vi         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80640433_8   3663 TACCAA-TGTAATTCTTCACAGAACATGAAAAAACT-ATCCTACAATTAA 3710
                          v   i-  iv-  i  ii     -  vi v  i  -      v    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCA 148

  chrX_80640433_8   3711 TGTGGAAGTGAAAAAGAAGCAGAGTAGCCAAAACAATCGTAAGGAAAAAG 3760
                          i     i  v  ii  vv    i              v i ii  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80640433_8   3761 AATAAAGCCAAAGACATCCCACTTCAAAAGATATTATATTATGTCATATA 3810
                           i    iiii  ivv  v      ------------------i  ----
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTC------------------CCA---- 226

  chrX_80640433_8   3811 TATATGTATATATATAAATATATATTCAAGTTTTATTATACACGACTTCA 3860
                         ---------------------  -     ivi   i  ----------  
  L1M4_orf2#LINE/    227 ---------------------AT-TTCAAAACTTACTA----------CA 244

  chrX_80640433_8   3861 AACAATATTATAATGCTACAGTAACCAAAACAGCATAGTACTGGTACAGA 3910
                           ------------          i   i    ii i       i i ii
  L1M4_orf2#LINE/    245 AA------------GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_80640433_8   3911 AACACACATAGAAACCAATGGAACTTAATAGGATAATA-AGAAATAAAGC 3959
                         i i v     v i i        ivv   -v  v i v-         v 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAAT-TGAGAGTCCAGAAATAAACC 331

  chrX_80640433_8   3960 TGCACATCTACAACCATCTGATTTTCAACAAGTCTGATAAAAACAATTTA 4009
                         iii    i  iiii  vi        i     vv  vi  i v  v iv 
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_80640433_8   4010 TTGGGAAAGGACTCCCCATTTGATACATGGTGCTGGGATAACTGGCTAGC 4059
                          v       i ivvi iv  ii i v            i      v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_80640433_8   4060 CGTATGTAAAATAACGAAACTAGACCCCTACCTCTCCCCATATACAAAAA 4109
                          ii   i    v  i   ii i            v v             
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_80640433_8   4110 TTAAGTCAAGATGCATTAAATAATTAAATGTAAAATGTTAAAA-TATGAA 4158
                             v    i   v  i ? v vi         i - i     -   i  
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAA 530

  chrX_80640433_8   4159 AATCCTAGAAGGAAACATAGGAAATAGTATTCTGGACATCATCCTTGGGG 4208
                          v  i      i         ?ivv i v   vv   v iivv-  i  v
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGC 579

  chrX_80640433_8   4209 AATAATTTATT-GCTAAGTCCCCAAAAGCAATTGCAACAAAAACAAAAAT 4257
                            ii   v  - v  v v v         vvv         iv      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_80640433_8   4258 GGACAAATGGGACAAAATTAAGCTAAAAAGTTTCTGCACAGCAAAAGAAA 4307
                         i  i    v    vvv  i  iv v    ii  i  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_80640433_8   4308 CTATCAGTATAATAAACGGACAACCTACAGAGTGGGAAAAAATACTCACA 4357
                               iv v i i  vi       i     i     i      i ii  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_80640433_8   4358 AACTATGCACCTGATAAAGGTTTAATATCCAGAATCTTTAAGGAACTTAA 4407
                           ii  ii i       i  vi vi          v v   i     ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_80640433_8   4408 ACAATTCAACAAGCAAAAAGCAAATAACCTGATTAAAAAGCAAACAAAGG 4457
                             i    i  vv    ii         ii   ?    iiiii      
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_80640433_8   4458 ACACAAATAGACACTTCTCAAAAGAAGACATATAAGCAGCTAATGAAAAT 4507
                          ivii        i     v        i   i  iii  i   i iv i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_80640433_8   4508 GTTAAAACAATGCTCAACATTACAAGTTAT 4537
                         i v    -i           i ????????
  L1M4_orf2#LINE/    880 ATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (160 / 97)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.81 (77 / 16)  


2606 28.41 1.44 0.67  chrX_80672974_80675128.rev      764  1664 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80672974_8    764 TGAAAACACATCCCATGCTCATGGATGAGTAGAATCAATATTATAAAAGT 813
                           i   v i        i        vi v   v i      i v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80672974_8    814 GACAACGCTGCCAAAAACAGTATAGAAATTCAATGCAATTCTCATCAAAA 863
                          i   ii  v  v   viii v  v i      i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80672974_8    864 CACCATCATTATTATTCACAGAACTAGAAAAAGCAATTCTAAAATTCATT 913
                         iv   v vviv  v  ii     v v  v  ivii  i           v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_80672974_8    914 TGTAACCAAAAAAGAGCCCACATAGCCAAAGCAAAACTTAGCAAAT-TGA 962
                           v  viiv  ii  v  viv         i   -v   iiv   v-v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGA 199

  chrX_80672974_8    963 ACAAATCTGGAGGCATCACATTATTCCATTTCAAACTATACTGTAAGGGC 1012
                              vi      vv     i vii v        viv    ii  i vi
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_80672974_8   1013 ACAGTCACCAACACAGCATGGCGCTGGTATAGAAACAGGCATACAAAACA 1062
                              v i   v    ii   ii    i   iii i  i    i i v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_80672974_8   1063 ATGGATAAGAATAGAAAACCCAAAAATAAAGCCAAATATTTGCAGTTAAC 1112
                              vv     v  i ii   i       v   v i    iii  i  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_80672974_8   1113 TGATCTTCGACAAAG-CACATAAAAATATAAAGTGGTGATAAAACGCCCT 1161
                             i        i -ii -i  i vi  vv i   v  v i  iivi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_80672974_8   1162 ATTCAACAAATGGTGCTGAGATATTTGAA-AGCCACATGTA---GAATAA 1207
                         v                 i  i vi  i - ?       i ---    i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_80672974_8   1208 AACTGGATCCTCATCTCTCACCTTATACAAAAATCACCTCAAAATGGATC 1257
                          ii    i  ii i   v    v           i v             
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_80672974_8   1258 AAAGACTGAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACAT 1307
                          ?    iv    v     v  i    i      v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_80672974_8   1308 AGGAAGAACCCCTCTAGACATTGGCTTAGGCAAAGACTTCATGAGCAAGA 1357
                            ?iv  vi i  vv   v    v        v ii   v iiii v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_80672974_8   1358 ACCCAAAAGCAAATAGAACAAAAACAAAGATAAATAGATGTGAGTTAATT 1407
                         vv         v viv       iv   i   i   i  vv  v  v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_80672974_8   1408 ACACTAAAAAAGCTTCTGCATAGCAAAAAAAAC----AAAAATATTAGCA 1453
                          v v v     -   i  iiivv    ii v  ----  i  vi v iv 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_80672974_8   1454 GACAACCCACAGAGTGGGAAAAAA-ATCTTCACAATCTATACATCTGAGA 1502
                                      i     i    -  i v  -    -   i      v 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGATA 745

  chrX_80672974_8   1503 AAGGACTAATATTCAGAATCTACAGGGAACTCAAACATATCAGCAAGAAC 1552
                          i     vi   i      v  i ii      vv   vv   ii  v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_80672974_8   1553 AAAACAAACAATTCCATCAACAAGTGGGCTAAGGACATGAATAGACAATT 1602
                           i     i  ii v  i? v  i     v     iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_80672974_8   1603 CTCAAAGGAAGATATACAAATGGCCAAAAA--ATATGAAAATAATGTTCA 1650
                            v  i                    v  -- i       -i   i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCA 894

  chrX_80672974_8   1651 ACATCACTAATTAT 1664
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (144 / 108)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


2636 27.74 2.97 1.48  chrX_80701113_80709169.rev     6691  7566 (491)    L1M4_orf2#LINE/L1       20   908 (0)  

  chrX_80701113_8   6691 CATGGATAGGAAGAATTAATATCATTAGAATGGCCATACTGCAAAAAGCA 6740
                                v      v       ii   ii     v     v vv   vii
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chrX_80701113_8   6741 ATTTACAGATTGAATGATATTTCTATCAAACTACCAATGACATTTTTGAC 6790
                           i        v  i vv  ii        v v   iivi v     vi 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_80701113_8   6791 AGAACTGGAAAAAGT-ATTTTAAAATTTATATCAAACCAAAAATAGAGCC 6839
                             v v  v  iv -  ii       i    vi  viiv  i-i  v  
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG-GGACCC 168

  chrX_80701113_8   6840 TGACTAGCCAAGACAGTTATAAGCAAAAAGAACAAAACTGGAGGCATCAT 6889
                         v  v       i   i iv i iv  i         ii      vv   i
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chrX_80701113_8   6890 GTTACTTGACTT-AAAACTATACTGCAAGGCTCCAGTAACTAAAACAGCA 6938
                         ii v iii i  -      -    i   i   v      ii  i    ii
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_80701113_8   6939 TAGTACTGGTACAAAAACAAACACATAGAACAATGGAACAGAATAGAGAG 6988
                          i       i i  ii i i   i     v        i     v     
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_80701113_8   6989 CCCAGAAACAAAGCTGCATGCCTACAACCAGCTGATCTTTGACAAAGCTG 7038
                         i       i   v iii iiii  iiii  ii    i  i     i v  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_80701113_8   7039 ACAAAAACAAGCAATGGAGAAATGACT--CCTTATTCAATAAATGGTGTG 7086
                         v   i v  vv      i    -  v --i   -     i        iv
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAA-GAATAGTCTT-TTCAACAAATGGTGCT 415

  chrX_80701113_8   7087 GGGATAACTGGCTAGCCATATGTAGAAGATTGAAATTGGACCCCTTACCT 7136
                             i      v  ?   i   i i    v    i          -    
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT-ACCT 464

  chrX_80701113_8   7137 TTCACTGTATACAAAACTCAACTCCAGTTGGATTAAAGACTAAAATGTAA 7186
                         iv   ii         v i     v iv     i ?    iv        
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_80701113_8   7187 AACCCAAAACTACAAAAACACTGGAGGACAACCTAGGCA-ATACCATTCT 7235
                         i v i       i    vivi i  i  v   v    ?i- v i -   v
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCG 563

  chrX_80701113_8   7236 GGATATAGGAACTGGCAAAGATTTCATGACGGAAATG---CCAAAAGCAA 7282
                         v  iv v  iviv     v i    v i---  v   ---         v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTA---GATATGACACCAAAAGCAC 610

  chrX_80701113_8   7283 TTGGAACAAAGGCAAGAATTTACAAATGGGATCTAATTAAACTTAAGAGC 7332
                         vv v      i v  i   vv i    v   ii v  i   v    i i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_80701113_8   7333 TT-----CTACAAAGCAAGACATTATGAACAGAGTAAACAGACAACTTAA 7377
                           -----  v     ---    i   v  v i   i  v       ii v
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAG---GACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_80701113_8   7378 AGAATGGGTGAAAATATTTGTCACTTGTGCATCTGACAAAGGTCTAATAT 7427
                                 v           iv v ii ii      i  i  v  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_80701113_8   7428 ACAGCATCTATAAGAAGCTTAAACATACTTACCAA-AAAAA--------- 7467
                         v   v  v     ii i  ivv   -   i vi  -     ---------
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACA-ACTCAATAATAAAAAGACAAATAA 806

  chrX_80701113_8   7468 ---AATTAAAAAGTGGGCAAAGGGCATGAATAGACACTTTTCAAAATAAG 7514
                         ---    ?    i          iiv          i  i  v   v   
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_80701113_8   7515 ACATACGTGCAGCCAACAAGTGTATGAGAAAATGCTCAACATCACTGATC 7564
                          i    iviii     i   iii    i  i             ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_80701113_8   7565 AT 7566
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.02 (17 / 889), avg. gap size = 2.29 (39 / 17)  


1911 24.39 8.13 3.71  chrX_80783460_80785138      486  1186 (493)    L1M4_orf2#LINE/L1      177   908 (0)  

  chrX_80783460_8    486 CAAAATTTCAGTACTGAAAAAGAAGAATAAAGTTGGAGGACTGACACGAC 535
                              ---  i vi             i              v    vv 
  L1M4_orf2#LINE/    177 CAAAA---CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_80783460_8    536 CTCACTTCCAGATTTACTATAGAATGACAGTAATCAAGTGAGGTTAGTA- 584
                          iv i   v i i      i i iiv            vv  vv i   -
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_80783460_8    585 TGGCAAAAGAATAGACAAATAGAACAGTGGAACAGACTAGAGA-TCCCAT 633
                              v   i       v     v  i     i   v v    -   viv
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_80783460_8    634 AATAATACCTACATAAATATAATCAATATGGGGTCTATAGGGTCAATTCA 683
                              -   i i i ------------------ i   --        v 
  L1M4_orf2#LINE/    324 AATAA-ACCCATACA------------------TTTAT--GGTCAATTGA 352

  chrX_80783460_8    684 TTTTTGACAAAAGAGCAAAGTCAGTTTAATGTAGAAAGCATAGTCTTTTC 733
                             i     ii v  v   v vi  i    vi     v           
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_80783460_8    734 AACAAGTGACACTGGAATACCTGGACATCCACATGCAAAAAATT--ATCT 781
                              i  iii    i i v     i ?            i v -- vi 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_80783460_8    782 AGACACTAACCTTACACCTTTCACAAACATTAACTGAAAATGGATCACAA 831
                         i   v iv    i     v vi     v       v           ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_80783460_8    832 ACACTAA-CATAAAATTCAAAATGGTAAAAC----AGAAGTAA-CAAAGG 875
                           -    -ii   i vii    ivi      ----     v  -  v   
  L1M4_orf2#LINE/    503 AC-CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_80783460_8    876 AGAAAATCCAGGTGAT-TTGGATTTGGCAATGAGTTTTCAGGTACAAGAG 924
                         ? v     ivv    i-    i  v       iv  i i  i  ii v v
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_80783460_8    925 CATA--CACATGGACCATGAAAAATAAATTAATAAGTTTGATTTTTTTAA 972
                           v --    v v v  vi i   -    vi    i  v  i  iv i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAA 650

  chrX_80783460_8    973 A-TTAAAAGCTTTTGTTCTGTGAGAGACGTTTGTAAGATAATGGAAACAC 1021
                          -      i       v  vii ii   ii vvi    v i  i   v  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_80783460_8   1022 AAGTCACAGACTGGGAAAAAGTACTTGCAGA-CATGTAACTGATAA---- 1066
                           vi      v     i   i  i     i -   i  v       ----
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_80783460_8   1067 -------CCAAGTTATAT------------CAA--------------AAC 1083
                         -------   iiv     ------------   --------------i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_80783460_8   1084 AAA-----CAATGCAAAAGTGTGCAAAAGACCTGAACACACACCTCATCC 1128
                            -----    v?    i  v     i  ii    i v   ii  vi v
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_80783460_8   1129 AAGAATATATACAGATGGTAAATAATCATATGAAAGGATGCTCAGTATCA 1178
                              v       i    iv     v  i      i        ii    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_80783460_8   1179 TATGTCAT 1186
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.35 (96 / 71)
Gap_init rate = 0.03 (20 / 732), avg. gap size = 4.15 (83 / 20)  


 416 28.68 0.00 1.47  chrX_80802025_80810704      174   309 (8371)  C L1M4_orf2#LINE/L1   (510)   398   265  

C chrX_80802025_8    309 GTATGGTACTGGCCTATAAATAGACATCATATATTAATGGAATAGAGTCA 260
                           i          v  vii        -   v  i           i ii
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACAT-ATAGATCAATGGAATAGAATTG 313

C chrX_80802025_8    259 GGTCTTCCGAAATAAACTCATGCCGATAAAGATCATTTAGTCTTCCAGAA 210
                         i vv i v         i   i -iv v v i   v  ii i   v v  
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATAC-ATTTATGGTCAATTGATTTTCGACAA 362

C chrX_80802025_8    209 GGGGGCAAAGAATATACCGTTAGGAAATGATAGTCT 174
                            v  v    vi  v vi vi     vi       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

Transitions / transversions = 1.05 (20 / 19)
Gap_init rate = 0.01 (2 / 134), avg. gap size = 1.00 (2 / 2)  

1828 29.60 3.47 1.07  chrX_80802025_80810704      485  1234 (7446)  C L1M4_orf2#LINE/L1   (0)   908   141  

C chrX_80802025_8   1234 AAAAGTCAAATTGCACACCCAAAGGGCGCA-AATAGCCATAGTAATTCTA 1186
                             v   v  v v - iv   i  i v  -        v ii   ii i
  L1M4_orf2#LINE/    141 AAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

C chrX_80802025_8   1185 AGCAAAAAGAATGAAGCCAGAGGCATCACATTGCCTAAATTCAAACTAAA 1136
                          iv  i     ii   iii    vv     i v  i  v      vivv 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

C chrX_80802025_8   1135 CTACAACCCTATGGTAACCAAAAAAGCATGGTACTGGTACAAAAATAGAC 1086
                               vv   ii    i   i v  ii         i i  ii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

C chrX_80802025_8   1085 ATGTAGATCAGTGAAACAAAATAGGGAACCCAGAAATAAGGCCACACATC 1036
                           i       i  i  i i   v i  ii          iv   i    i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

C chrX_80802025_8   1035 CACAATCAATTGATCTTTGATAAAGTTGACAAAAG---TTAATGGTGAGT 989
                         i iii         i  i  i  i v  v   i v--- i     v  --
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-- 387

C chrX_80802025_8    988 AAAGGACACCGTAGTCAATAAATGGTGCTTGGAAAACTGGGTACGCAGAT 939
                         -   i i viv vv    i          v   v      i  ?v  v  
  L1M4_orf2#LINE/    388 -AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

C chrX_80802025_8    938 ACATAAGAATGAAACCCAATGCCTACTTCTCACGATAAACAAAAATTAAT 889
                         i  v         iiivi iv     i  v   v   v           i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

C chrX_80802025_8    888 TCAAGATGATTTAAATACTTAAATATAAGACCTCCTAGTATAAAAAATAC 839
                             i   iv i ? v  i     i     v  vvv v       v- vi
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCT 535

C chrX_80802025_8    838 TAAAAGAATGCGTAGGAA-AAACCTCTTCTGGACATTGGCCTCAGCAAAA 790
                           i     vi i    ?i-   --     vv   v    vi vi    vi
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATG 583

C chrX_80802025_8    789 AATT------TATGTCA--AAGATCTCAAA-AACAAATGCAACAA----- 754
                         iv  ------    v  --  i v v   i-      v v  v  -----
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

C chrX_80802025_8    753 AAATTG-ACTTAACTAAACTAAAGACCTTCTACACCATGAAAGAAAATAT 705
                               -    v ii   v v  i v   i iii ivii  i  v v   
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

C chrX_80802025_8    704 CAACAGAGTAAACAGAGAACCTACAGAATGGGAGAAAATTATCACAGAAT 655
                            v i   i  v   v    i                 vv ii  i vi
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

C chrX_80802025_8    654 ATGCATCTGAAAAAAGACTAATATCCAGGTTCTATAAGAAACTT----AA 609
                           ii      v  ii    vi       iv v     ii    i----  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

C chrX_80802025_8    608 GTAAATTAACAAGCAG-CAAACATCCTTAT-GAAAAGTGGACAAAATACA 561
                         v v   -  i  iv  -    i v  iv  -?    i   i    iv iv
  L1M4_orf2#LINE/    784 CTCAAT-AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

C chrX_80802025_8    560 TGAGCAGACACTTCTCAAAGGAAGACATACAGGCAGTCAAGAAATATATG 511
                            ii     i     v  i     i     iiii i   v  ii i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

C chrX_80802025_8    510 AAAACGTTCTCCACACCACTCTTCAT 485
                             vi v   v   i  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (128 / 90)
Gap_init rate = 0.02 (16 / 768), avg. gap size = 2.12 (34 / 16)  

1663 28.01 4.45 3.80  chrX_80802025_80810704     1995  2758 (5922)  C L1M4_orf2#LINE/L1   (0)   908   140  

C chrX_80802025_8   2758 TAAAATGCATATGG---TGCCAAAAAAAGCCTGACTAGCGGAAACATGTC 2712
                               v       ---   --  iii v  v  v    vi     -i  
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGC--AAGGGACCCAGAATAGCCAAAACA-ATC 186

C chrX_80802025_8   2711 T---AAGGAAAGAACCAAGGTGGAGAAATCATATTACCCAACTTCAACCT 2665
                          ---  iii      v   v     i v   i i v     i     vvi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

C chrX_80802025_8   2664 ATATTATATGGCTACAGTAGCCAAAACAGCATGGTCCTATTACAAAAACA 2615
                         v  i  i vi         ii   i    ii    v  ivi i  ii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

C chrX_80802025_8   2614 GACTCATAAAGAAACAGAAAAGAAAATAGAACCCAGAAGTTGAACTGCAT 2565
                            vi   i vv  ii   v    vvv   ii      i -i   i-   
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT-AAACC-CAT 334

C chrX_80802025_8   2564 AC--CTACTGCCGTTCAACCTGTGACAAAGTTTACAAAA--ATTAGCTAT 2519
                           --i  iv i iv ii ii vi     i v vv   i --   -- v  
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT--CAAT 382

C chrX_80802025_8   2518 AGGGGAAGGACTCTATATTCCATAAATGCTTGTGGGATAACTGGCTAGCC 2469
                         i   i   i ivv v v   v i     v vv     i      v  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

C chrX_80802025_8   2468 ATATGTAGATGAATAAAACTAGACTCTTACCATTTACCATATA-AAAAAT 2420
                          i   i i v    i  ii i   i i    vivi        -      
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

C chrX_80802025_8   2419 TAACTCAAGTTGAATCAAAGACTTAAATATGAGACCTCTTACTATAAAAA 2370
                                 iv  i    ?    i     i i   v  vvv         v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

C chrX_80802025_8   2369 TCTTAGAAAAAAACCTAGAA--AATGCTATTTTGGTCATCAGCCTTAGG- 2323
                                 i     v   i?--  ----  i  v  v ----    i  -
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAA----ATCTTCGTGA----CCTTGGGT 574

C chrX_80802025_8   2322 -AAAGAATG----------TATGACTAATTCCACAAAAGCAATTGCAAGA 2284
                         - iiv    ----------      -- i----        vvv    v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGAC--AC----CAAAAGCACAAGCAACA 618

C chrX_80802025_8   2283 AAAACAAAAATTGACAAGTGAGACCTAGTTAAA-CTAAAGAGCTTCTCTT 2235
                            iv      v  i  i vi   i vi i   -i    i ------   
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA------CTT 662

C chrX_80802025_8   2234 CTGCACAGCAAAAGAAACTATCAACAGAGAAAAAAAAT--CCTACAGAAT 2187
                         i  ii vv    i  v        v i  vi    i i--  i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

C chrX_80802025_8   2186 AGGAGAATGTATTCATAAGCTATGCATCTAACAAAACATTAATGTCCAGA 2137
                         i      vi    iii  iii  ii    i i  iiv i vi i      
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

C chrX_80802025_8   2136 ATCTATAAGAAACTT----AATTCTTAA-AGTAACAAC-CAAATAATTCC 2093
                           v     ii    i----  i  --  - i   v  v-       ii v
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTC--AATAATAAAAAGACAAATAACCCA 810

C chrX_80802025_8   2092 ATTAACAAATGGTAAAAGGAAATAAATAAACACTTATCAAAAGAAAACAT 2043
                            ? v      vv      vv i    i   i  v  v      i i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

C chrX_80802025_8   2042 ACAAGTGGCCAATAAACATCAGAAAACATGCTCCAGATCCCTAATCAT 1995
                             i          i  ivv     v      v v   v????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (126 / 84)
Gap_init rate = 0.03 (24 / 769), avg. gap size = 2.62 (63 / 24)  

3143 27.45 0.55 0.44  chrX_80802025_80810704     7281  8187 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80802025_8   7281 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCCTGAAAAT 7330
                              ii i  i     i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80802025_8   7331 GGCCACACTGACCAAGGTAATTTAGAGATTCAATGCCATCCCCATCAAGC 7380
                            v i   vv    iv i  i  v        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80802025_8   7381 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 7428
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_80802025_8   7429 TATGGAACTGAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 7478
                                v  v  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80802025_8   7479 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACATTACAAGGC 7528
                                i      vv    i  v  ii i      vivi i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80802025_8   7529 TACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGAGATATACACC 7578
                                 i   i    ii        vi iv ii i   v     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80802025_8   7579 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 7626
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_80802025_8   7627 CTCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 7676
                         vvi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_80802025_8   7677 CTATTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 7726
                           v     i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80802025_8   7727 GAAACTGGATCCTT-CCTTACACCTTATATAAAAATTAATTCAAGATGGA 7775
                            ii    i  i -   i     v    i         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80802025_8   7776 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 7825
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_80802025_8   7826 CTAGGCAATACCCTTCAAGACACAGGCATGTGCAAGGACTTCATGTCTAA 7875
                         v    ?ivv vi    iv   viv  vv iv    v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_80802025_8   7876 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 7925
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_80802025_8   7926 TGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 7975
                          v   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_80802025_8   7976 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 8025
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_80802025_8   8026 AGGGCTAACATCCAGAATCTACAATGAACTCAAACAAGTTTACAAGAAAA 8075
                         i  i  vii         v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_80802025_8   8076 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACTCTTC 8125
                          i     i     v  i?    i    ii      v    i    vi   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_80802025_8   8126 TCAAAAGAAGATGTTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 8175
                           v         i vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_80802025_8   8176 ATCACTGGCCAT 8187
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2446 27.04 3.24 1.79  chrX_80845544_80848216.rev     1288  2182 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80845544_8   1288 TGGAAA--CATTCAATGCTCATGAATTGGAAGAGTCAATATTATGAATAT 1335
                               --i  i v   i     i         v i      i v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80845544_8   1336 AACCATACTGCCCAAAGCAATTTACAGATTAAATGTAATTCCCATTAAAA 1385
                         ii v     v      vii  i        v  i i   i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80845544_8   1386 TACCAAC---ATTTTTCAC-GAATTAGAAAAAC-ATTCCTAAAAATTGTA 1430
                          v   i ---v     ii -   v v  v  i -iv        v ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_80845544_8   1431 TGGAATAAAATAAAAG-CTCA-AATAGCCAAAGAAATCTTAAGCAAAAAG 1478
                              -- vii  ii - i  -          iv      i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80845544_8   1479 AACAAATGTAGAGGCATCATA-TTACCAACTTCAAATTATACTATAAGAC 1527
                               vv i    vv   i -  v    i      viv     i  ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80845544_8   1528 TATAGTTACCAAAAGAGCATGGTACTGGTATAAACACTGGCACATGGTCC 1577
                           i   v i   i v  ii         i    iv iv i  i  i vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80845544_8   1578 AATAGAACAAAATAGAGAACACAGAAATAAAGCCAAATACATATAGCTAA 1627
                            i   i i   v    iiv          v   v i iv   i ii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_80845544_8   1628 CTGATCTTCGACAAAA-CATAAAAAATATAAATTGAGGAGCAGACACCCT 1676
                         i    i        ii-iiiv  i vi  vv v  i   ivii i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_80845544_8   1677 ATTTA-TAAATGGTCCTGGGAAAACTGGCAACCCACAGGTAAAATAATGA 1725
                         v  i -i       v      v      vv ?     v i    v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_80845544_8   1726 AAGTGGATCCCTATCTCTTACTGTATACAAAAATTAACTGAGAATGAATG 1775
                          iv    i     i   vi  ii                v i    i  v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_80845544_8   1776 AAAGGCTTAAATCAAAGACCTGAAACCATAAAAATTCTAGATGACAATGT 1825
                          ?  i i     vv    v  i    i      v ii    v  v  ii 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_80845544_8   1826 TAGAAAAACTCTTTTAGATACCCACCTTGGAA-AAGAAAT-----CATGA 1869
                         vi ?iv  v    i---i i---       iv- i v   ----- v ii
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTC---GTG---ACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_80845544_8   1870 GTAAGACTCCAAAAGCAAAAGCAACAAAAACAAAAATAATTAAATAGTAA 1919
                         i  v   v         v           iv       iv     v ---
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG--- 639

  chrX_80845544_8   1920 TAATTAAATAATTAAACTAAAAAGTTTCTGCACAT-AAAAGACA------ 1962
                         -i i --- v  i   v v    ii  i  ii v -   i    ------
  L1M4_orf2#LINE/    640 -GACT---TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_80845544_8   1963 ---GAGTAAACAGCCAACTCAAAGAATTCGAGAAAATATTTGCAAACTAT 2009
                         ---i   i  v  v    i  v     vv                 ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_80845544_8   2010 GCATCCCGAAAAAAGCCTAGTATCAAGAATCTACAGGGAACTGAAACAAA 2059
                         ii   i-  v  ii v  v     v     v  i ii     vvv    v
  L1M4_orf2#LINE/    736 ATATCT-GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_80845544_8   2060 TCAGTAAGAAAAAGA-AAATAATCCCATCAAAAAGTGGGCAAAGGACATG 2108
                            i   v       -      i  v  i?    i           iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_80845544_8   2109 AATAGACATTTCTCAAAAGAAGATATAGAAATGGCCAATAAACATGCAAA 2158
                                       v            v             i  iiii  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_80845544_8   2159 ATAATGCTCACTGTCACAAATAAT 2182
                          vi       vii   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.25 (45 / 20)  


3087 27.67 0.55 0.44  chrX_80853267_80858612     3947  4853 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80853267_8   3947 TGGAAGAACATTCCAGGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3996
                              ii i  i   v i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80853267_8   3997 GGCCATACTGCCCAAGGTAATTTAGAGATTCAATGCCATCCCCATCAAGC 4046
                            v     v     iv i  i  v        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80853267_8   4047 TACCAATGACTTTCTTCACAGAATTGGAGAAAACT-ACTTTAAAGTTCAT 4095
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_80853267_8   4096 ATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAAACCTAAGCCAAAAGA 4145
                               viiv  ii  v  viv  v     iv   v i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_80853267_8   4146 ACAAAGCTGCAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 4195
                               i  v   vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_80853267_8   4196 ACAGTAACCAAAACAGCATGGTGCTGGAACCAAAACAGACATATACACCA 4245
                                i   i    ii    i    v iv ii i         v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_80853267_8   4246 GTGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACGACTA 4293
                         i     i    i--    i  --        vv   i i  i  i iii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_80853267_8   4294 TCTGATATTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 4343
                         vi    v  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_80853267_8   4344 TATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4393
                          v  v  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_80853267_8   4394 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 4443
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_80853267_8   4444 TAAAGACTTACACGTTAGACCTAAAACTATAAAAACCCTAGAAGAAAACC 4493
                         i ?    i  v i  v   v              vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_80853267_8   4494 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4542
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_80853267_8   4543 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGGATCTAA 4592
                         i            vvi          vv     v  i   iv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_80853267_8   4593 TTCAGCTAAAGAGCTTCTGCACAGAAAAGAA-ACTACCATCAGAGTGAAC 4641
                          iv iv v  i i   i  ii vvv    i -    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_80853267_8   4642 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 4691
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_80853267_8   4692 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4741
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_80853267_8   4742 GAACAAGCAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 4791
                         ii    ii     v  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_80853267_8   4792 TCAAAAGAAGACATTTATGCAGCCAAAAGACACTTGAAAAAATGCTCATC 4841
                           v        i  vi viii     v ii   v      i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_80853267_8   4842 ATCACTGGCCAT 4853
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (142 / 105)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


2567 29.93 1.66 1.00  chrX_80860187_80862490.rev      912  1813 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80860187_8    912 TGGGAAAATATTTCATGCTTATGGATTGGAAGAACCAATATTGTAAAAGT 961
                            i  i    ii    i i             vii        v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80860187_8    962 GGTCATACTGTTTGCCCAAAGCAATTTACTGTTTCAATGCTATTTCAATC 1011
                           iv     v----      vii  i   v v     i  v  ii v   
  L1M4_orf2#LINE/     51 GGCAATACTC----CCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_80860187_8   1012 AAATCTCCAG-TGCCATTTTTTACAGAATTAGGAAAAATATATTCTAAAA 1060
                            vii    -    -      i     v v iv  iv i-  i      
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAA 144

  chrX_80860187_8   1061 TACATAAAGA---GCAAAAAAAGCCTGAATAATCAAAGCAATCCTAAGCA 1107
                          v    vi  ---    iii v-  v     ii    i     i i iv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_80860187_8   1108 AAAAAAATAAAGCCAGAGGAATAAAACTACCTGACTC--AAACTATACTA 1155
                          i  i  i    iii     v v v   v  ii i i--     -     
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTA 242

  chrX_80860187_8   1156 TAAAGACGTAGTAACCAAAACAGCTTGGT--TGGCACAAAAACAAAGACA 1203
                         i    viii     i   i    iv    --     i  ii i i v i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_80860187_8   1204 CAGCATAATGGAACACAATAGAAAACTCAGAAATAAATTTGTGCACCTAA 1253
                         i  vvi       i v   v  i iii          iiii i  ii  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_80860187_8   1254 AACCATCTGATCTTTGAGAAGGCTGACAAAAACAAGCAATGGGGAATGTA 1303
                         iii  vi    i  i  v    v  v   i v  vv          v v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_80860187_8   1304 CTCCCTATTCAATAATTAGTGCTGGGATAACTGGCTAGCCATGTGCAGCA 1353
                         ivvi  v     i  v i         i      v  ?   ii    iv 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_80860187_8   1354 GATTAAAGCTGGAGCCCTGTCTTTCACTATATATAAAAATTAACTCAAGA 1403
                           v i   i    v    ii  iv   i     i              i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_80860187_8   1404 TACATTAAAGATTTAAATGTAAGACCTCAAACTATAAGAATCCTGGAAGA 1453
                          iv  i ?   ii           v  v         i v  i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_80860187_8   1454 CAAAC-TAGAAAATACTGTTCTTGACATCAACCTTGGCAAAGAATTTTTG 1502
                         -    -   i?ivv v v   v    v iiivi v     v iv  i  i
  L1M4_orf2#LINE/    543 -AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_80860187_8   1503 GCTAAGTCTACAAAGGCA--ATTGAAAAAAACTAAAATAGGCAAGTGACA 1550
                          v  v v vv    i   -- vii v    ivv       ii  i viv 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_80860187_8   1551 CCTAATTAAACTAAAGAGCTTCTTTACAGAAAAAGAAACTATCAGCAGTG 1600
                          i v  i   v v  i i   i v i vvv   i  v       iv iv 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_80860187_8   1601 CAAACAGACAACCTACAGTATGGTAGAAGGTATTCACAAACTATGCATTG 1650
                         ii  v        i    v    v    ii    ii    ii  ii  iv
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_80860187_8   1651 GACAAAGGCCTAATACTCAGAATCTATAGGAAACTT----AAATCAATAA 1696
                           i  i  v  vi  ii      v    iii    i----  v       
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_80860187_8   1697 GTGAAAAACAAATAACTTCATTGAAAAATGGGAAAATCACTTGAACAGAC 1746
                         vvi   i         iiv   ?         v   vv i     i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_80860187_8   1747 ACTTCTCAAAAGAAGACACACAAGTGGCCAACGAACATATGAAAAAAAGG 1796
                          i     v        i i    i       ii i  i       i v v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_80860187_8   1797 TCAGTATCACTAATTAT 1813
                            ii    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (165 / 101)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


1953 30.04 2.40 1.20  chrX_80866147_80867880.rev      497  1245 (489)    L1M4_orf2#LINE/L1      151   908 (0)  

  chrX_80866147_8    497 TAGAAAACCACAAAAGGCCTAAGACAGTCAAAGTTATCCT-------AGG 539
                          i    --ii   ii i  i ii i  i    iiv   i ------- i 
  L1M4_orf2#LINE/    151 TGGAAA--TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80866147_8    540 AAAAAAACTGGAGAAATTACATTACCTGACTTCAAATTATAATACTGAGC 589
                           v   ii     i v i   i v  ii i      viv  v   vi   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80866147_8    590 TATATTAACTAAAATACCATGGTACTGGCATAAAAACAGGAATATA-ACC 638
                           i v   ii  i i vii              ii i  iv     - i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80866147_8    639 AACAGAACCAAATACAGAACAAAGAAACAAATCTACACATCTTCAATGAA 688
                           ii   ivi   vv   iivv     i   i i i    i viii v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_80866147_8    689 CTCATTTTTGGCAAAAAAGCCAAGAACATACATTGGGAAAAAGACAGCCT 738
                         i v     i i   iiiv       v   v  v    i   ii i  i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_80866147_8    739 CTTCAATAAATAGTGCTGGGAAAACTGGTTAGGCATACTG-AAAATAATA 787
                         i     i    i         v      v  ?v  i -  -    v   i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGAATG 447

  chrX_80866147_8    788 AAACTAGACTCCTATATCTTCCCACATGCAAACATCAA-TCAAAATAGTT 836
                           ii i   i    iv  viv   i  i    v  i  -       i v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_80866147_8    837 -----ACTTAAACATGAGACCTCAAACTATGAAGCTAATCAAAGAAAACA 881
                         -----  i    ii i   v  v       i  i  vv vi         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_80866147_8    882 CTGAAGAAACTTTTCAGGACAATGGACTGAGCAAGAATTTCTTGAGTAAT 931
                         iv i? v  v i   iv   vv   ii ii    vii      iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_80866147_8    932 ACCCCACAAATACAGACAACAAACACAAAAATGGACAAATGGAATCATAT 981
                           v   v  ii   ii       viv      i  i    v i iivi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_80866147_8    982 CAAG-TTAACACCCTTATACACAGCAAGGGAAACAATAAAAACAACATGA 1030
                            i-    v v i  - iii vv   i   v  v  v  i -  -i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGA-AA-GTGA 694

  chrX_80866147_8   1031 AGAGACAACACGCAGAATAAGATAAAATATTTGCAAGCTATCCATCTGAC 1080
                          i       v i      ii  v             iii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_80866147_8   1081 AAAGGATTAGTACTCATAATATGTAAAGGAGTTATACAACTCTACAGGAA 1130
                           i   i v   ii  v     i     i v iv        v i iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_80866147_8   1131 AAA-ATATCTAATAATCCAATT-AAAAATGGTCAAAAATTCTTAATAGAC 1178
                            - i ---     i      -        v    iiv i v       
  L1M4_orf2#LINE/    795 AAAGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_80866147_8   1179 ATTTCTCAAAAGAAGACATACAAATGACAAACATGCATATAAAAAGGTGT 1228
                                v        i         i v  i v   i  i     i  i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_80866147_8   1229 TGAACATGGTTGATTGT 1245
                          v     vi????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (147 / 76)
Gap_init rate = 0.02 (14 / 758), avg. gap size = 1.93 (27 / 14)  


 940 26.44 3.95 0.61  chrX_80887488_80890096      178   506 (2103)  C L1M4_orf2#LINE/L1   (0)   908   569  

C chrX_80887488_8    506 TTGAATAGGACAAAGATTTCAT-GATATAGACACCAAAAGCAATTGCACC 458
                            ii vi i   v i    v -     -             vvv   v 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAAC 617

C chrX_80887488_8    457 AAAAGCAAAAATTAACAG---GGATCTGGTTAAACTAAAGAGCTTCTGCA 411
                              v      vi i i---   ii vi i   v v  i i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

C chrX_80887488_8    410 CAGCAAATGGA-ACTATCAACAGACTAAACAGACAACTTACAGAATCGAA 362
                          vv    -   -        v i v i  v       ii       v i 
  L1M4_orf2#LINE/    668 CTTCAAA-GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

C chrX_80887488_8    361 GAAAAT-TTTTCAAATTGTGTATCTGACCAAGGTTTAATATTCAGCATCT 313
                               -   v     ii i       iv i  vi vi   i   v  v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

C chrX_80887488_8    312 ATGAGAAACTTAAACAAATTTACAATTAAAA-------AACCCCATTAAA 270
                           i ii    ivv    v iv i   v    -------     v   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

C chrX_80887488_8    269 ATGTGGACAAAGGTTATGAACAGACACTTCTTAAAAGAAGACATACATGA 220
                          vi   i      v v    i     i    iv        i     viv
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

C chrX_80887488_8    219 AGCCAACAATCATATGGAAAAAAGCTCAACATCACTGTTCAT 178
                         i     i  v  i   i   i v           ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (48 / 38)
Gap_init rate = 0.02 (7 / 340), avg. gap size = 2.14 (15 / 7)  

2620 28.09 1.33 0.97  chrX_80887488_80890096      897  1722 (887)    L1M4_orf2#LINE/L1        1   829 (79)  

  chrX_80887488_8    897 TGGAAAAACATTCCATGCCCATGAATAGGAAGAATCAATAACATGAAAAT 946
                               i i  i     ii    i  v      v i    vii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80887488_8    947 GGCCATACTACCCAAAGTAATTTACAGATTTAATGTTATCCCCATCAAGC 996
                            v     v      v i  i        i  i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80887488_8    997 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 1044
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_80887488_8   1045 TATAGAACCAAAAAAGAGCCCGCATAGCCAAGACAATCCTAAGCTAAAAG 1094
                            i   viiv  ii  v  v v        i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80887488_8   1095 AGCAAAGCCAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1144
                          i     iii    vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80887488_8   1145 TACAATAACCAAAACAGCATGGTACTGGTACCA----AAACAGATAGACC 1190
                             i   i   i    ii         i iv ---- i   v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80887488_8   1191 AATCAAACAGAA--GAGAAGCCTCAGAAATAATCCCACACATCTACAAAT 1238
                            vi  i    --    iv  --        v    i    i  iiivi
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_80887488_8   1239 ATATGATCTTTGAAAAACCTGAGAAAAACAAGCAATGGGGAAATGATTCC 1288
                          vv    i  i  v  ivv  vv  i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_80887488_8   1289 CTATTTAAGAAATGGTGCTGGGAAAACTGGCTAGCCACATGCAGAAAGCT 1338
                           v  i  v              v      v  ?         i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80887488_8   1339 GAAACTGGATCTCTTCCTTACACCTTAAACAAAAATTAACTCAAGACAGA 1388
                            ii    i i  v   i     v  v                i ii  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80887488_8   1389 TTAAAGACTTAAACGTAAGAACTAAAACCATAAAAACCCTAGAAGAAAAC 1438
                          i ?    i    i      i       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_80887488_8   1439 CTAAGCAATGCCATTCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 1488
                         v  i ?--- iv v  -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    547 ATAGGN---GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_80887488_8   1489 CTAAAATATCAAAAACAACGGCAACAAAAGCCAAAATAGACAAATGGGAT 1538
                         v  vi i i     i  vvi          vv        i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_80887488_8   1539 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCGGAGT 1588
                         i v  i   v v  i i   i  ii vv    i  v       vvii   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_80887488_8   1589 GAACAGGCAACCTACAGAATGGGAAAAAATTTCTGCAATCTATCCATCTG 1638
                            v  i     i           i     v i     vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_80887488_8   1639 ACAAAGGGCTAATATCCACAATCTACAAAGAACTTAAACAAATTTACAAG 1688
                          i  i  i  vi      v   v  i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_80887488_8   1689 AAAAA---AAACAACCCCATCAAAAAGTGGGTGAAGG 1722
                              ---   i     v  i?    i    ii    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.48 (136 / 92)
Gap_init rate = 0.01 (9 / 829), avg. gap size = 2.11 (19 / 9)  


3357 26.65 0.44 0.44  chrX_80902298_80908576     4879  5786 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80902298_8   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80902298_8   4929 GGCCATACTGTCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     vi    iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80902298_8   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_80902298_8   5027 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80902298_8   5077 AACAAAGCTGGAGGCCTCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      v        v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80902298_8   5127 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGATC 5176
                                 i   i    ii         i i  ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80902298_8   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_80902298_8   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_80902298_8   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_80902298_8   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_80902298_8   5375 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_80902298_8   5425 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_80902298_8   5475 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5524
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_80902298_8   5525 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5574
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_80902298_8   5575 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5624
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_80902298_8   5625 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_80902298_8   5675 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_80902298_8   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5774
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_80902298_8   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1701 27.30 3.22 0.92  chrX_80922243_80923847      467  1118 (487)    L1M4_orf2#LINE/L1      242   908 (0)  

  chrX_80922243_8    467 ACAAA-CTA-AATCATTATAA-AATATGAAAC-AGCAAAAACATA--CAC 510
                              -   - i v  i vi - i i  iv  -i   v  iv   --  i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_80922243_8    511 ATAGACCAACAGAACAGAATAGAGACCCCTGAAATAAAGCTGCACAACTA 560
                              i   ii   i     v    vi  v        v iii   vi  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_80922243_8    561 CAACCAACTAATGTTCTACAAAGTTTACAAAAATAAACAATAGGAAAAGA 610
                         iiii   i i  v   v    i v vv   i vi vv    i  i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_80922243_8    611 ATA-TCTTATTAAGTAAATGTTGCTAGAAAAACT----ATCTATATGGAG 655
                            -    v i  -i     v    i i v    ---- ? i i   v i
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAA-CAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_80922243_8    656 AAGAATAAAATTGGACCTTGACCTCTCACTATATATAAAAATTAACTCAA 705
                               i  i       iiv     v   i     i              
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_80922243_8    706 GATGGATTAAAGCCTTAAATATAAGACCTCCAGCTATAAAAATCCTAGAA 755
                         i      i ?  v i     i     v  vv i        v  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_80922243_8    756 GAAAACCTAAAAAACAGCCTTC-TAGTCATAGGCCTAAGCAAAAATTTTA 804
                               v  ii?ivv ii    - iii v i  i-  i    vii   iv
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCT 589

  chrX_80922243_8    805 TGGCAAAGATGCCAAAAGCAATTGCAACAAAA--AAAAATTGATAAGTGG 852
                          i vv v  ii         vvv         --      v     i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_80922243_8    853 GACCTAATTAAACTAAAGAGCTTCTATGCAGCAATATAAACTATCAGCAA 902
                            i v  i   v v  i i   i i   vv   viv v       iv  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_80922243_8    903 TTTAAAGAAACAACCTACAGAATGGCAGAAAATGTTTGGAAACTATCCAT 952
                         vv i  i i      i         v       i    v   ii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_80922243_8    953 CCAACAAAGGTATAATATCCAGACTCTATGAGGAAC----A-AACT-AAT 996
                          ii i  i  vv vi        v v   i i    ---- -    -   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_80922243_8    997 AATCAACAAGA-AAACAATCCCATAAAAAAGTGGGCAGAGGACATGAACA 1045
                            v  -    -   i  i  v  v?    i      i    iv    i 
  L1M4_orf2#LINE/    790 AATAAA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_80922243_8   1046 GACATTTTTCAAAAGAAGACATGCATAACAAGCCAACAAGGCATGTGAAA 1095
                                i  v        i  i  -  ii-     i   -  ii     
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACA-AATG-GCCAATAAG-CACATGAAA 885

  chrX_80922243_8   1096 AAATGTTCAATATGACTAATAAC 1118
                          i   i    i  v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (106 / 68)
Gap_init rate = 0.03 (19 / 667), avg. gap size = 1.42 (27 / 19)  


2586 27.37 1.88 1.66  chrX_80943724_80947973.rev     2874  3779 (471)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80943724_8   2874 TGGAAACACATCCCATACTCATGGATAGGTAGA---AACACTGTTGTACA 2920
                               v i       ii        v  v   ---  i i    i--- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA---A 47

  chrX_80943724_8   2921 TATGATCATACTACCAAAAGCAATTTATAAATTCAATGCAATTTCCATCA 2970
                         v   iiv     v  v   vii  i  i i      i     ii i    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_80943724_8   2971 AAATACCATCATTATTCTTCACAGAACTGGAAAAGACAATCCTAAAATTC 3020
                             v   v vviv  i  ii     v v  v   vii            
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_80943724_8   3021 ATATGGAATGAGAAAAGAGCCCACA-TAGCAAAAGTAAGGCCAAGCAAAA 3069
                                 -iv v  i ii    v -    v   ii  vviii iv  i 
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_80943724_8   3070 AGAATAAATCCAGAGGCGCCGCATTACCTGATTTCAAACTATACTATAAA 3119
                             i   viii    vvi i  i v  ii        viv     i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_80943724_8   3120 TTCATAGCCACCAAAGCAGCATGGTACTGGTAAAAAAGTAGGCATTTAGA 3169
                         vii i  iv i   ii   ii         i v  iii   i   v    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_80943724_8   3170 ACAATGGAACAAAACAGAGAACCCAGAAATAAAGCCAAATACTCACAGCC 3219
                         v        i i  iv    ii           v   v i i i ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_80943724_8   3220 AACTTATCTTCGACAAACTATACAAAAAC-AT--AACGTGGGGAAAAGAC 3266
                           i v  i        iv-i i v  i  -  --  --        ii i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGG-GTGCCAAGACCATTCAA--TGGGGAAAGAAT 393

  chrX_80943724_8   3267 ACCCTGTTCAACAAATGGTCCTGAGATAATTGCA-AGCCACATGTAGAAG 3315
                          vi  v             v   i  i  i  v - ?       i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_80943724_8   3316 AATAAAACTGGAATCTCATCTCTCACCACATACAAAAATAAACTCAAGAT 3365
                            i  ii    vi ii i   v     i          v       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_80943724_8   3366 GTATCAAAGACTTAAATCTGAGAGCTGAAACCACAAAATTCT-AGAAGAT 3414
                          v    ?    i     v i      i    i i    i   -      v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_80943724_8   3415 AACATTGGAAAAACCCTTC-TAGGCATGTCTTAGGCAAAGATTTCTTCAC 3463
                              v  ?iv  vi    - iiv v  vv        v i      viv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_80943724_8   3464 CAAGAACCCAAAAGCAAATGCAATAAGAACAAAGATAAATTTATGGGACT 3513
                         i v  vv         v v    i  i iv   i   i  vv  v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_80943724_8   3514 TAATTAAATTTATAA-CTTCTGCACAACAAAAGAAGTAATCAGCAGAGTA 3562
                          v  i   v   v  -   i  ii vv    i  viiv    iv i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_80943724_8   3563 AACAGACAACCCAAAAAGTAGGAGAAAATCTTCA-AAATCTATACTTCTG 3611
                           v          v i i i         v  ii-     -   iv    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTG 742

  chrX_80943724_8   3612 ACAAAGGGCTAATATC--GAATCTACAAAAACCTCAAACAAATCAGCAAG 3659
                          i  i  i  vi    --    v  i   i v   vv    v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_80943724_8   3660 AAAAAAGCAAATAATCCTATCATCAAAAAGTGGGCAAATGATATGAATAG 3709
                              ii       i  - --  i?    i        v   v       
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCC-A--ATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_80943724_8   3710 ACAATTCTCAGAAGAAGATATATAAACAACCAACAAACACATTTTTTAAA 3759
                            v     vi           i   iii    i  i     v----   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG----AAA 885

  chrX_80943724_8   3760 ---TGCTTAACAACACTAATTAT 3779
                         ---    i    v  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (149 / 95)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.68 (32 / 19)  


2708 27.93 2.12 0.67  chrX_80964320_80968445.rev     2741  3635 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_80964320_8   2741 TGAAAATACATATCATGCTCATGGATTGGAAGAATCAATATAATGAAAAT 2790
                           i   v i  vi    i               v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_80964320_8   2791 GACCATACTGCCCAAAGCAGTCTACAGATTCAAAGCAATTCCTATCAAAA 2840
                          i v     v      viii             v     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_80964320_8   2841 TAGTAAC-ATCATTTTTACAGAA-TTAAAGAAAGAATGATAAAATTCATA 2888
                          vvi i -ii v     i     -  i vi ivvi  vv           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_80964320_8   2889 TGGAACCAAAAAAAGAGCCC-TAATTGTCAAAGTAATCCTAAGCAAAAAG 2937
                              -- viv  i ii   -v   v i    ii    i i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_80964320_8   2938 AATAAATCTGAAGGCATCACATTACCTAACTTTAAATTACACTACAAGGT 2987
                           i   vi  i   vv     i v  i  i  i   vivi       i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_80964320_8   2988 TACAATAACCAAAACA-CAAGGTACTGATATAAAAGTAGATACAGAGACC 3036
                             i   i   i   -iiv       ii    iii    i i v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_80964320_8   3037 AATGGAACAGAATAGAGAAGCCAGAAACAAAGCCAAATACTTACAGTCAA 3086
                                i     v    iv       i   v   v i i   ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_80964320_8   3087 CTGATCTTTGGCAAAGCATACAGAAAC-ATAAATTGGGAAAAGAACACTC 3135
                         i    i  i i   i -i i vi i  -  vv v    i      i v  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_80964320_8   3136 TATTCAATAAATGGTGCTGGGGAAATTGTATAGCCACATGTGGAAGAATA 3185
                          v     i             iv  i  v   ?       iii      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_80964320_8   3186 AAACTGAATTCTTAGCTCTAACTATACACAAAAATTAACTTAAGATGGAT 3235
                           ii  i ii i  v   vv  i   i             i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_80964320_8   3236 TAAAGACTTAAATCTAAGACCTGAAGCCATAAAAATTCAAGAGCAAAACC 3285
                         i ?    i     v     v  i  i i      v iiv   iv     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_80964320_8   3286 TTGGAAAGACGTTTCTGGACATTGGCGTTTGCAAATAATTTAT--GACTA 3333
                          v  ?ivi vvi   vv   v    -   v vv   ii   v --  -  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGA-TA 595

  chrX_80964320_8   3334 AGACTCCAAAACCAAACACAATGAAAACAAAAAATAAATAA-TCGGACCT 3382
                         v   v      v  v vi   i-    v        i    - i    i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_80964320_8   3383 CATTAAAGTAAAAAGATTTTCTATGTCAAAATAAATAATCATCAGAGTAA 3432
                            i   i v    iv    v iiv     iv v iv    vv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_80964320_8   3433 ACAAACAACCTGTGGAATGGGAGAAAATATTTATAATGTATGCATCTGAC 3482
                          v i      iiii                  ii  vvi  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_80964320_8   3483 AAAAGACAAATATCCAGGATCTATATGAAGCTCAAACAAATTAGCAAGAA 3532
                           ii   vvi       i  v    vii i   vv    v i ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_80964320_8   3533 AAA-------AATCTTATCAAAAAGTGAGCAAAGGACATGAATAT---CT 3572
                            -------  i iv  i?    i  i        iv      v---i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_80964320_8   3573 TCTCAAAAGAAGATATACAAGTGACCAACAAACATATGAAGA-ATACTCA 3621
                             v               i  i    i  i  i     i -  i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_80964320_8   3622 ACATTACTAATCAT 3635
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (154 / 92)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


2158 26.52 5.64 4.18  chrX_80975495_80977462      590  1475 (493)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_80975495_8    590 ATTTTGTGTTTGTGGACTGGAATGTTCAATATTGTCAAAATG-C--TATT 636
                           iiii    ii    i     vii i        i  i   - --  i 
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_80975495_8    637 TTTAAAATACGAAATATAAATTGAATACAATTCTTTTAAAAATCTCAGCA 686
                         iiiv    -i  vv  i i   v  ii    i i v v      i    -
  L1M4_orf2#LINE/     60 CCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC- 107

  chrX_80975495_8    687 ATAAATTTTTTATGCA----TTGACCAACTGATTCTAAAATTTATACACA 732
                         - ivv      --   ----     v i     i        i   iiv 
  L1M4_orf2#LINE/    108 -TGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_80975495_8    733 AA-GAAAAAGACCTAAAATAGTCAATATAATCCTAAAAAAAA-------- 773
                           - v  ii    i i     i   v i    i i     i --------
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_80975495_8    774 -TTGGAGAGTTTACATTAGCTAATTTCAAGACTTACTATAAAGCCTACCA 822
                         -      iii i   i vv i        i        i     -   vi
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC-TACAG 253

  chrX_80975495_8    823 TAATGAAGACAAGATGGTATTGGTATAAGAATAAACACATTGATTAAAAG 872
                             v      ivi     i   i     i   i   i  v   i  vi 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_80975495_8    873 AACAGAGAAGACAGTCCAGAAATAGAGCCATCCACATATAGTCAACTGAT 922
                           i   ivv  v            i v    v  iv   i     i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_80975495_8    923 TTTGATAAAAAGGAT-CCAAGGCAATTTGATG----AAGAATATATATTT 967
                            --ii v    i -     i v   ii   ----       -i v   
  L1M4_orf2#LINE/    354 TTT--CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-GTCTTT 400

  chrX_80975495_8    968 TCAACAGAAGTTGCTGGCAAAATTGAATGCTTACATGCAATTTTAGAA-- 1015
                               i v v      v v  i  i  i?ii        v---    --
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA---AGAATG 447

  chrX_80975495_8   1016 AACTTAAACATAGATCTCACATCTTCAACA-ACAAAAAA-AATTTAAAAT 1063
                           v  ii  vivv i      i ---- i -       v-  i i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACC----ATATACAAAAATTAACTCAAAAT 493

  chrX_80975495_8   1064 -----ATACATCTAAATGTAGAATGAAAAAATATTTAAGTTCTAGAAGAA 1108
                         ----- ? v i         ii vvv    v   vv  v ii        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_80975495_8   1109 AGTA-AGATA-AAATCTGGGTGACCTTGGTTT-TGTGATGCATTTTTGAA 1155
                          ii -  i?i-      vv          v  -v ii   vv  i  ii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_80975495_8   1156 TATAATAACAAAAGTAGTCTTTGTTAAAGTTAACA---ATAAGTTGGACT 1202
                            i i v      i vvvviviiv    vv  v ---    i       
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_80975495_8   1203 TTACTAAAATTAACATTATTTATTATTAAGATTATTTTGCTCTGCCAAAG 1252
                          i ii        --------------- i i --    iv  v v  i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAA---------------AAACT--TTTGTGCTTCAAAGG 676

  chrX_80975495_8   1253 TCACTGTTAAGATAAAAAATAGACCAGCCACATATGGAAAGAAAATATTT 1302
                         v    i i    v ivi  v    v v     v vv ii           
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_80975495_8   1303 ATTTATAAATCATATAGCGGATAAAGGACTCGTGTCCAGAATATACAAAT 1352
                         ii----          v v     i     i  i           i   v
  L1M4_orf2#LINE/    727 GC----AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_80975495_8   1353 AATTCCTAAAACTCAACATTGAAAA---AAAAGGCCCAATTCAAAAATTA 1399
                           i  i  v       i v i    ---   vii       ?      vi
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_80975495_8   1400 GCAGAAGATCTAGATAGACATCTCACT----------TACAGCTGGCAAA 1439
                            i i   i ii        i  v i----------    iv    v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_80975495_8   1440 TAAGCATTTGAAAAGATGTCTAATGTCATTTGTCAT 1475
                               iv          iii  ii   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (145 / 86)
Gap_init rate = 0.03 (28 / 899), avg. gap size = 3.11 (87 / 28)  


3164 27.86 0.44 0.44  chrX_81001482_81007773     4892  5799 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81001482_8   4892 TGGAAGAACATTCTGTGCTCATGGGTAGGAAGAATCAATATCTTGAAAAT 4941
                              ii i  i ii  i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81001482_8   4942 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 4991
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81001482_8   4992 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5039
                          vi  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_81001482_8   5040 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5089
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_81001482_8   5090 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5139
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_81001482_8   5140 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5189
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_81001482_8   5190 AATGGTACAGAAC--AGAGCCCTCAGAAATAATGCCGTATATCTACAACT 5237
                              v i    i--    i  --        vv  i  i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_81001482_8   5238 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5287
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_81001482_8   5288 CTATTGAATAAATGGTGCTGGGAAACCTGGCTAGCCATATGTAGAAAGCT 5337
                           v  v  i              v v    v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_81001482_8   5338 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGACGGA 5387
                            ii    i    v   i     v              i    i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_81001482_8   5388 TTAAAGACTTAAATGTTAGTCCTAAAACCATAAAAACCCTAGAAGAAAAC 5437
                          i ?    i       v  vv       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_81001482_8   5438 CTAGGCAATAACATTCATGACATAGGCATGGGCAATGACTTCATTTCTAA 5487
                         v    ?ivv  iv   i    v v  vv i       ii   v vvv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_81001482_8   5488 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5537
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_81001482_8   5538 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAATGAAC 5587
                          i   v v  i i   i  ii vv    i  v    i  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_81001482_8   5588 AGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTACTCATCTGACAA 5637
                           i     i                 i       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_81001482_8   5638 AGGGCTCATATCCAGAATCTACAATGAACTCAAACACATTTACAAGAAAA 5687
                         i  i  ii          v  i  v      vv   vv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_81001482_8   5688 AAACAAAGAACCCCATCAACAAGTGGGCAACGGATATGAAAAGCCACTTC 5737
                          i     v     v  i? v  i       v    v    v  v  i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_81001482_8   5738 TCAGAAGAAGACATTTATGGAGCCAAAAGACACATGAGAAACTGCTCATT 5787
                           vi       i  vi vivi     v ii       i  iv      vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_81001482_8   5788 ATCACTGGCCAT 5799
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (145 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2901 26.80 0.80 0.69  chrX_81026174_81028040      502  1374 (493)    L1M4_orf2#LINE/L1       35   908 (0)  

  chrX_81026174_8    502 TCAATATCATGAAAATGGCCATACTTAGCAAAGCAATTCATAGATTCAAT 551
                          i     ii v  i     v     ivv    vii  ii i        i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chrX_81026174_8    552 GCTATCCCCATCAAGCTACCA-CTGACTTTCTTCACAGAATTAGAAACAT 600
                           v     i     iv v   -   v    i  -i     v v  v vii
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGC 133

  chrX_81026174_8    601 CTACTTTAAATTTCATATGGAAACAAAAAATAGCCCGTATAGCCAAGACA 650
                         iv iii    v            iiv  iiv v  v v        i   
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_81026174_8    651 ATCCTAAGCAAAACGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAA 700
                            i i iv  i v        i      vv    i  v  ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_81026174_8    701 ACTATACTACAAGGCTACAGTAACCAAAACAGCGTGATACTGGTACCAAA 750
                          viv        i          i   i    i   i      i iv ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_81026174_8    751 ACAAATATATAGACCAATGGAACAGAAC--AGAGTCCTCAGAAATAACGC 798
                          i i i       i        i    i--       --        vv 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACC 331

  chrX_81026174_8    799 CACAGATCTACAA-CAATCTGATCTTTGACAAATCTGACAAAAACTAGCA 847
                           i v  i  iii-    -    i  i     ivv  v   i v vvv  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_81026174_8    848 ATGGGGAAACGATTTTCTATTTAATAAATGGTGTTGGGAAAACTGGCTAG 897
                                  vi  vv   v  i  i        i     v      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_81026174_8    898 CCATATGCAGAAAACTGAAGCTGGACCACTTCCTAACACCTTATTCAAAA 947
                            i     i  i v     i      v  v   v     v   v     
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_81026174_8    948 ATTAACTCAAGATGCATTAAATACTTTAATGTAAGATGTAAAACTATAAA 997
                                   i   v  i ? v  i v         vv            
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_81026174_8    998 AACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGC 1046
                          vi i           v    ?i- v i -   iv   v v  vv i   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGC 579

  chrX_81026174_8   1047 AAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAAT 1096
                           v ii   v ivv  vi            vvi          vv     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_81026174_8   1097 TGACAAATGGGATCTAATTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAA 1145
                         v  i    v   ii v  i   -     i -   i  ii vv    i  v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chrX_81026174_8   1146 GCTATCATCAGAATGAACAGG-ATCCTAGAGAATGGGAGAAAATTTTTGC 1194
                         i      vv i i    v  i- v  i v               v     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_81026174_8   1195 AATCTATTCATTTGACAAAAGGCTAATGTCCAGAATCTACAGAGAACTTA 1244
                           vii  vi  i   i  ii i  vi i        v  i i      iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_81026174_8   1245 AACAAATTTACAAGAAAAAAACAAACAATCCCATCAAAAAGTGGACAAAG 1294
                         v    v iv i  v     i     i  i  v  i?    i   i     
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_81026174_8   1295 GATATAAACAGACACTTCTAGAAATAAGACATTTATGTGGCCAACAAACA 1344
                            v i  i     i    vv   v    i  vi vi       i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_81026174_8   1345 TATGAAAAACAGCTCATCATCACTGGTCAT 1374
                         i       ivv     v     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (127 / 103)
Gap_init rate = 0.01 (11 / 874), avg. gap size = 1.18 (13 / 11)  


2641 27.30 1.80 1.35  chrX_81066161_81071993.rev     4445  5334 (499)    L1M4_orf2#LINE/L1        1   894 (14)  

  chrX_81066161_8   4445 TGAAAACACATCCCATGCTCACGGATGGGTGGAATCACTGTTGTGAAATT 4494
                           i   v i        i   i    v  vi  v i v i    v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81066161_8   4495 GACCATACTGCTTAAAACAATCGACAGATTCAATGCAATTCCTATCAAAA 4544
                          i v     v ii   vii   v          i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81066161_8   4545 TATCATCATCATTATTCATGGAATTAGGAAAA--AATTATAAAATTCATA 4592
                          vi  v vv v  v  iiii   v v iv  i--i  iv           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_81066161_8   4593 TGCAACAAAAAAGAGCCCACAG-AGCCAAAGCAATCCTAAACAAAAAGAA 4641
                           v  vviv  i ii    v i-       i     i i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_81066161_8   4642 CAAATCTGGAGACATCATATTACCAAACTTCAAGGTATACTACAAGGCTA 4691
                             vi     ivv   i i v  v  i     iiiv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_81066161_8   4692 TAGTTACCAAAACGGCATGGTACTGGTACAAATAGAGTCATGTAGACCAA 4741
                         i   v i   i  i ii         i i  iv v  v   i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_81066161_8   4742 TGGAACAGAATACAGAACCCAGAAATAAAGCCAAATACTTACAGCCAACT 4791
                              i     vv   ii           v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_81066161_8   4792 GTTATTTGACAAAGTATACAAAAAC-ATGAAGTGGGGAAAGGACACCCTA 4840
                          v v  i     i -i i v  i  -  vv i         i i vi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_81066161_8   4841 TCCAACAAATGGTTCTGGGAAAACTGGTAAGCTACATGTAGAAAAAGGAA 4890
                          i           v      v      vv ? i     i i  i  v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_81066161_8   4891 ATTGGATTCTCATCTCTCACCTTATACAAAAATCAACTTAAGATAAATTA 4940
                         i     ii ii i   v    v           i    i  i  ii  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_81066161_8   4941 AAGTATTAAATCTCAGACCTAAAACCATATAAATTCT-AGAAGATAACAT 4989
                         ?  vvi     v v   v       i   -   i   -      v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACAT 548

  chrX_81066161_8   4990 AAGGAAAACTTTTCTAGACACTGGTTTAGGCAGAGAATTTATGACTAAGA 5039
                          i ?iv  v i   vv   vi   v       iv iv  iv iiv  v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_81066161_8   5040 ACTCAAAAGC-CAATTCAACAAAAACAAAAATAAATAAATTGGACCTAAA 5088
                         vvi       -   v-        iv       i           i v v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_81066161_8   5089 TAAACTAAAAGACTTCTGCACAGCAAAAGAAATAATCA-----GTAAACA 5133
                         i   v v   i    i  ii vv    i  v iv    -----  i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_81066161_8   5134 GACAACCTACAGAGTGAGAGAAAATATTTGCAAACTATGCATCTAAAGAA 5183
                                i     i  i                 ii  ii    i vi i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_81066161_8   5184 TAACTAATATCAAGAATATACAAGGAGCTCAAACAAAT-AATCAAGAAAA 5232
                         vi   vi    v        i  i  i   vv    v -   -  v    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-AATAAAA 796

  chrX_81066161_8   5233 AAGCAAATCCAATCAAAACCCA-TCAAAAAGTGGGCAAATAACATGAATA 5281
                          ii     --------      - i?    i        vi iv      
  L1M4_orf2#LINE/    797 AGACAAAT--------AACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_81066161_8   5282 GACAATTCTCAGAAGACCATATACAAACAACCAACAA--ACATAAAAAT- 5328
                             v     vi    vv         iii    i  --    i    v-
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_81066161_8   5329 TGCTCA 5334
                               
  L1M4_orf2#LINE/    889 TGCTCA 894

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.02 (15 / 894), avg. gap size = 1.87 (28 / 15)  


1930 28.69 3.04 0.80  chrX_81087423_81092476     3118  3741 (1313)    L1M4_orf2#LINE/L1        1   638 (270)  

  chrX_81087423_8   3118 TGAAAAGACATTCCATGCTCATGAATTAGAACAATTGATACCAT-AAAAT 3166
                           i     i  i     i     i   i   v v  i   iii -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81087423_8   3167 GGCCACACTTCCCAAAGCAATATACATGTTCAACGCAATTCCTATCAAAA 3216
                            v i   i      vii  v    vi           i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81087423_8   3217 TACT-GATGTCATTTTTCACAGAAATAAAAAAA--AATC-TAAAATATAT 3262
                          v i- v  i -     ii       vi v  i--i   -      vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_81087423_8   3263 ATGAAACAACAACAAAAAATTCATA-CAGCCAAGGCAATTCTGAGCCAAA 3311
                            i  -- ii-   iii ii  v -i      ii    ii   ivv i 
  L1M4_orf2#LINE/    150 ATGGAA--ATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_81087423_8   3312 AGCACAAAGATGGACATATCATGCTACCTGTCTTCAAAATGCATTACGAG 3361
                           v      v    vivv   ii  v  iivi       ivi i   i i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_81087423_8   3362 TCTAGGGTAACCAAAACATTATGGCACTGGCAAAAAACAAGACATATAGA 3411
                         v   vi    i   i   v i   i       v  iivv           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_81087423_8   3412 CCAGTGGAACAGAATGTAGAACCCAGAAATAAATTTATATATGTGCAGCT 3461
                         i  i     i     vv   ii           iii   i  v iii ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_81087423_8   3462 ATCTGATTTTTTACAAGG-CACCAAGAACATAAATTGGGAAAAGGGCACC 3510
                          vi       iv      -ii      v   vv v    i    iii vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_81087423_8   3511 CTCCTCAATAAATAATGGTGGGAAAATTAGATATCCATGTGCAAAAGAAT 3560
                           ii    i    ii  v     v  i i    ?   ii           
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_81087423_8   3561 AAAACTGGACCCCTATCTCTTACCATATACAAAAATCTACTTAATAAGGA 3610
                         i  ii          i   vi               iv   i  v v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_81087423_8   3611 GTAACAACTTAAATGTGACACCTGAAACTATAAAACTACCAAAACCAAAC 3660
                         vi ?vi  i       i v v  i             vii i  vv    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_81087423_8   3661 A-----------CTTCAGGACATTGGTCTAGGCAAATAGTT-CATGGCTA 3698
                          -----------    iv   v    vi       - i   - v i v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATA 595

  chrX_81087423_8   3699 AGAGCTCAAAGGTACAGGCAACATAAACAAAAATAGACTAATT 3741
                         v  vvi    i i   i      v  iv         iv    
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

Transitions / transversions = 1.85 (115 / 62)
Gap_init rate = 0.02 (12 / 638), avg. gap size = 2.00 (24 / 12)  

 748 25.27 0.71 3.20  chrX_81087423_81092476     4281  4561 (493)    L1M4_orf2#LINE/L1      635   908 (0)  

  chrX_81087423_8   4281 AATTGGATTATATTACAATAAAAAAGCTTCTACATAGCATAGCAAAATGT 4330
                                i vi  i v   v     -   i iiiivv  v  v v v i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chrX_81087423_8   4331 TAACAGAGTGAAGAGACAACCTGTTGAATGAGAGAAAATAGCTGTAAACT 4380
                         i  v i      i        iiiv     i         vi  i   ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_81087423_8   4381 ATTCATCTGACAAGTGAATAATATCAAGAATGTACATGGAATT-TAAAAA 4429
                           vi      i   v  v vi    v     i  i vi   i - v v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_81087423_8   4430 CTCAACAGTAAATAATGATCAAATAACACAATTTAAGAAGTGGTAAAT-A 4478
                              i i    -  -  -        v     ?  i  vv  i   v- 
  L1M4_orf2#LINE/    784 CTCAATAATAAA-AA-GA-CAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_81087423_8   4479 TGTAAATAGACATTTCTCAAAAGAAGACATACAAATGGCTAGCAGGTATA 4528
                          v i              v        i           i ii i i i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_81087423_8   4529 TATGAAAAAAAAAAGCTCTACATTACTAAGCAT 4561
                          i-----    i v    v    i ????????
  L1M4_orf2#LINE/    881 TG-----AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (42 / 28)
Gap_init rate = 0.03 (7 / 274), avg. gap size = 1.57 (11 / 7)  


 350 28.78 12.23 0.00  chrX_81098268_81100550      497   635 (1648)    L1M4_orf2#LINE/L1      174   329 (579)  

  chrX_81098268_8    497 AATCAAGGCAATCTTAAGCAAAAAGAACAAAGCTAGAAGCATCATGTTAC 546
                          ii   ii       i iv  i          i i  i vv   iii v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_81098268_8    547 CTGACCTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTA- 595
                          ii ii     viv        i          i   i    ii     -
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_81098268_8    596 -------------GACACACAGACAAATTGAACAGAATAAACA---CAGG 629
                         -------------    i i   iv   v   i     vi v ---   i
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_81098268_8    630 AACAAA 635
                           i   
  L1M4_orf2#LINE/    324 AATAAA 329

Transitions / transversions = 3.00 (30 / 10)
Gap_init rate = 0.01 (2 / 156), avg. gap size = 8.50 (17 / 2)  

 691 30.57 2.18 0.00  chrX_81098268_81100550      897  1125 (1158)    L1M4_orf2#LINE/L1      292   525 (383)  

  chrX_81098268_8    897 ATAAAAAAATAAAATAAAA----AAGTCAAGAAATAATGTTGCACACCCT 942
                            i vv   ii    i  ----i    v        vviiii   iiiv
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_81098268_8    943 TAACTATCTGAGATTTGATAAAGTTGACAAAAACAAGCAAAGGAGAAAGG 992
                          iiii vi   vv  i  i  i v  v   i v  vv   v  i     i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_81098268_8    993 ATCCCCTGTTCAATAAATGGTGCTGGGGTAACTGGCTAGCTATATGCAGA 1042
                           vvi  v     i             ii      v  ? i i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_81098268_8   1043 AGATTGAAGCTGGACCACTTCCTGGCACCATATACAGAAATCAACTCAAG 1092
                            v     i      v  v   vi           i    i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_81098268_8   1093 ATTAATAGAATACTTAA-TTTAAAACCTAAAATT 1125
                           vi  vi? v  i   - v   i v      i 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

Transitions / transversions = 1.43 (40 / 28)
Gap_init rate = 0.01 (2 / 234), avg. gap size = 2.50 (5 / 2)  

 995 26.09 2.81 1.53  chrX_81098268_81100550     1400  1790 (493)    L1M4_orf2#LINE/L1      513   908 (0)  

  chrX_81098268_8   1400 AAAACCTAAAATTATAAAAATACTGAAAGATAACCTAGGAG-ATACCATT 1448
                           i v      i       v vi ii    v   v    ? - v i -  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TT 561

  chrX_81098268_8   1449 CTAGACATAGAGCCAGGCAAAGATTTTAT-GATGAAGATGCCAAAAGCAA 1497
                          vv   v v i ii      v i   iv -   - v  ii         v
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCAC 610

  chrX_81098268_8   1498 TTGCAACAAAAACAAATATTGACAAATTGGACATAATGAAACTAAAGAGC 1547
                         vv         iv   v  v  i         v v  v   v v  i i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_81098268_8   1548 TTCTGCACAGCAAAAGAAACTACCCCCCTGA--GTAAACAGGCAACCTAC 1595
                           i  ii vv    i  v    i vv---  --  i  v  i     i  
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAA---GAAAGTGAAAAGACAACCCAC 707

  chrX_81098268_8   1596 AGAACTGGAAAAATCACTAGCAAACTATGCATCTGGCAAAGTTCTAATAT 1645
                             iv   i   vi i v     ii  ii     ii  i vv  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_81098268_8   1646 CCAGAATCTATAAGTAACTT----AAATTAACAATCAAAAT-CTAACAAC 1690
                                v     iv    i----  v i  i   v    v- v  i   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_81098268_8   1691 CCCATCAAAAAAGTGGGCAGAGGACATGAACAGGCACTTTTCAAAAAAAG 1740
                           v  i?     -      i    iv    i  i  i  i  v   i   
  L1M4_orf2#LINE/    808 CCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_81098268_8   1741 ACATACAAATTGCCAACAAGCATATAAAAA--TGCTCAACATCATTAATC 1788
                          i        v     i     i  i    --            ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_81098268_8   1789 AC 1790
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.17 (54 / 46)
Gap_init rate = 0.03 (10 / 396), avg. gap size = 1.70 (17 / 10)  


1596 27.91 6.33 4.29  chrX_81101200_81103888.rev     1321  2205 (484)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_81101200_8   1321 AAATATTTAATGTGCATACAAGAAAAGATTCAATACTGTCCAGATATCAA 1370
                          i    iiv    v   iv vvii    i i    i   iv    iv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_81101200_8   1371 TTTTTTCTATGTTGATCTATTCATTTAAAAACAATCTCAATTAGAATTCC 1420
                          vi ii i vi        ivv   i  vi-     i v  i i   i  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACG-CAATCCCTATCAAAATCCC 104

  chrX_81101200_8   1421 AGTAAGTTATTATATAAATACCAACAAACTAACTTTTAAGTTTATACAAA 1470
                           ivivi v  v ii i v iii    i  i iii v  i  i   iii 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_81101200_8   1471 AAGGAACAAATATACAGAATAGCTAATATAATCTTGAAGAACAAAGACAA 1520
                           v v - iiv iv         i  v i         i  v  ii    
  L1M4_orf2#LINE/    155 AATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_81101200_8   1521 ACCTGAAGGACTAAAACTATGTATTCTAAAGATTTATTATAAAAGTACAG 1570
                          vi  i      v v   vivi v i v  i i   i  i   iv     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_81101200_8   1571 TCACCAAT-CAGTGTGGTATTTGTGAAGAAAAAGACCAGTAAAAAATTGT 1619
                          v i   v-          i v iiv iii v    vvi  i vv v  v
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_81101200_8   1620 AACAAAAT-AAG----CAGAAGTATACTCAAACA------GTCAAGTAAT 1658
                           i i   -i  ----     i  v  i  v   ------     v i  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_81101200_8   1659 TTT-GATAAGAAT--CAAAAACAATAAACTGGAGAAAATATTTGTTTCTT 1705
                            -  i   ii --   i v  v v  -   i    i------------
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAG------------ 390

  chrX_81101200_8   1706 TTAAATAAACATCTGCCTTTATAACAAATGACATTGGAACAGTTGGATAT 1755
                         ---    ------- i    vi        iiii   i   ii      ?
  L1M4_orf2#LINE/    391 ---AATA-------GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_81101200_8   1756 GTAAA-GCAAAGAAAAAAAATCTGGATGCAGATGTTACACTCTGTATACA 1804
                         vi v -     ii  vi  i -    iv vv iv i    iv i  i v 
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGT-TGGACCCCTACCTCACACCATATACAAA 479

  chrX_81101200_8   1805 AATTAACTCAAAATGGATTATAGACCTAAATGTAAAATGGAAAACAATAA 1854
                                           i ?              i vvv     v    
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_81101200_8   1855 AAGATAACTCCTAG-------CAT----GTAACATCTCCATGCCTTTGGG 1893
                           -----   i   -------   ----    -    i i  v i     
  L1M4_orf2#LINE/    530 AA-----CTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGG 573

  chrX_81101200_8   1894 TTTGGTAATGATATTTTAAAT------CCA---GCACAA-----AAAAGA 1929
                           v  i    i v i   i  ------   ---      -----      
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_81101200_8   1930 AAAATTTATGAAAGAAATAATCTTCATTAAAAT-AAAAA--TGTCTGCTC 1976
                             ---  ii vi  v iiv      i     -     -- v v    i
  L1M4_orf2#LINE/    624 AAAA---ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_81101200_8   1977 TAA--GATAGTACCAAAAA--TAAGAAGATAAGCCACAGACTTGG-GAAT 2021
                         i  --  i v  i   i  -- i i    i  v       v v  -   v
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_81101200_8   2022 ACATTTGCACAAAACATTTAA--GATAAATGACT-GCATCTGAAATATAC 2068
                          i       --  v   v  v--     iv    - i   iii      i
  L1M4_orf2#LINE/    721 ATATTTGCA--AATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_81101200_8   2069 AAAAAAAATCTTAAAATTCAACAA-AATAAAACGAACAACCTGATT-AAA 2116
                            i  v-     v  i    i  -  v  i  i  i    ii   -   
  L1M4_orf2#LINE/    769 AAAGAAC-TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_81101200_8   2117 AATAGACAAAATATCTGGACAGACACTTCACCAAAAAAGATATACAAATA 2166
                            i i    iv  i  i i     i   v     i             i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_81101200_8   2167 AAAAACAAACATAT-AAAATATGCTGTATAT-ATTTTGTTA 2205
                         ivv  i  i  i  -    v     vv i  - ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (154 / 91)
Gap_init rate = 0.04 (34 / 903), avg. gap size = 2.76 (94 / 34)  


2427 29.09 2.10 2.21  chrX_81110134_81114254     2731  3634 (487)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_81110134_8   2731 AAACATCTCATGCTCATTAATATAAATAATTAATATTATTAAAATGGCCA 2780
                          i i   i    i    vi  vvi  v v        i    i     v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_81110134_8   2781 TACTGCTTTTAATGCCCAAAGCACTTTACAGATTCATTGCTATTCCTATA 2830
                             - --------      viiv i          vi  v  i     v
  L1M4_orf2#LINE/     56 TACT-C--------CCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_81110134_8   2831 AAGGTACCAATGACATTCTTCACAGAACTAGAAAAAACT-ACTTTAAAAT 2879
                           ii v   iivi v  i  ii     v v  v  i-  - iii      
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAAT 145

  chrX_81110134_8   2880 ATATATGGAAC--CAAAAAATTACCCTAATACCCAAGAAAAACCTAAGCA 2927
                         vi        v--   iii i--  vv    v    i v  v i i iv 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_81110134_8   2928 AAAAGAACAAATCTGAAAGCATTAAATTACCTGACTTCAAATTCTACTAC 2977
                          i         vi  i i vv i v i v  ii i      vii      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_81110134_8   2978 AAGTGTACGGTAACCAAAACAGCATGGCACTGGTACAAAAACAGGCACAT 3027
                           ivv   i    i   i    ii   i     i i  ii i  i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_81110134_8   3028 AGATCAGTGGAACAGAATAAAGAACTCAGAAATAAGGCAGTACATCTATG 3077
                               i     i     vi   iii         iv vi     i    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_81110134_8   3078 ACCATCTGATCTTTGAGAAAGCTGACAAAAATAAGCAACGGAAAAAGACT 3127
                         ii  vi    i  i  v  i v  v   i vi vv   i  ii     v 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_81110134_8   3128 C-CCTATTCAATAAATAGTGCTAGGATAACAGGCTAGCCACATGCAGAAG 3176
                         v-i  v     i    i     i   i   v  v  ?         i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_81110134_8   3177 TCTTAAACTGAACCCTTTCCTTACATCATACACAAAAATCTACTCAAAAT 3226
                         vv v  ii  i    i v   i   i    i        iv         
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_81110134_8   3227 GAATTA-AGTCTTAAATGTAAACCCTCAAATTATAAAAACCCTGGAAAAC 3275
                          i  i -  v i         ivv  v   i       vi i i   i v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_81110134_8   3276 AACCTAGGCA-ATACCTTCCTCGACATATGAATGGGCAAAGATTT----- 3319
                            v    ?i- v i    v -   v vv iv i     v i   -----
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_81110134_8   3320 -TGTGACA---AAAACACCAAATCAATCACAACAGAAGCAAAATTGACAA 3365
                         - i     ---   i   --  v   ---   v    --     v  i  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCAC--AAGCAA---CAAAAGAA--AAAATAGATAA 635

  chrX_81110134_8   3366 GTGGGATCTAATTAAACCAAAGAGCTTCTGCGCAGCAAAATAAACTATCA 3415
                         i v   ii v  i   viv  i i   i  i  vv    iv v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_81110134_8   3416 ACATAGTAAACAGACAACCTACATAATGTGAGAAAATATTTGCAAACTAT 3465
                          v v   i  v        i   v    v                 ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_81110134_8   3466 GCATCTGTCAAAGGTCTAATATTTAACATCGATGAGGAACTT----AATT 3511
                         ii     vi  i  v  vi   ii iv  vv  i i     i----  i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_81110134_8   3512 TTACAAGAGGAAAGCAAACAACCTCATTAGAAAGTGGGCAAAGGACATGA 3561
                         iv i  v ii  ii    i    iv   ?i   i           iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_81110134_8   3562 CCAGACATTTCTCAAAATAAGACTTCCAGACAGACAATAAGCGTATGAGT 3611
                         vi           v   v    iv v  i ii v        ii    iv
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_81110134_8   3612 AAACTCTCAATACCAATGATCAT 3634
                          i iv     i i  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (159 / 101)
Gap_init rate = 0.02 (16 / 903), avg. gap size = 2.44 (39 / 16)  


2665 27.95 2.45 1.34  chrX_81122194_81127596     4013  4910 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81122194_8   4013 TGGAAAAACATTCCATACTCATGGAAAAGAAAATAATTAATATCATTAAA 4062
                               i i  i    ii       vvi   i i--       ii    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC--TTAATATTGTTAAG 48

  chrX_81122194_8   4063 ATGGTCATACTGCCCAAAGCAATTTACAAATTCAATGCTATTTCTATTAA 4112
                             iv     v      vii  i    i      i  v  ii    i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_81122194_8   4113 ACTACCATTGAGATATTTCACAGAACTAGACAAACCAATTTTAAAATTCA 4162
                          v v   vivivv v   ii     v v     i ii  ii         
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_81122194_8   4163 CATGGAACCAAAAAAGAGTCCAAATAGCCAAGGCATTTCTAAGCAAATGG 4212
                         i      viiv  ii  vi vi         ii  v ii i iv  ivi 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_81122194_8   4213 ATCAAAGCTTGAGACAACATGCTGCCTGACTT-AAAACTACACTACAAGG 4261
                          v     i v   ivvv  ii  v  ii i  -      -i       i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_81122194_8   4262 CTACAGTAACCAAAACAGAATGGTACTGGCACAAAAACAGACACATAGAC 4311
                                  i   i    vi           i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_81122194_8   4312 CAATGGAACAAAATAGAGAGCCTAAAAATAAGGCCACACACTTGCAA-CA 4360
                                 i i   v     i i i      iv   i   i  iiii-  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_81122194_8   4361 ACCTGATCTCTGATAAAGCTGACAAAAACAAACAATGGGGATAAAGCTCC 4410
                          i-    i ii  i  i v  v   i v  vv         v i iivvi
  L1M4_orf2#LINE/    348 AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_81122194_8   4411 CTATTTAGTGAATGGTACTGGGATAACTAGCTAGCCACGTGCTGAAGATT 4460
                           v  i iii      i      i    i v  ?    i   vi    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_81122194_8   4461 AAAACTGGGCCCCTTTCTTACACCATATACAAAACTCAACTCAAAGTGGA 4510
                         i  ii   i     vi  i               v i        i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_81122194_8   4511 T-AAAGACTTAAATGTAA-ATCTCAAAACTATAAAAACACTGGAAGATAA 4558
                          - ?    i         - v  -            vivi i     v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_81122194_8   4559 CCTAGGCA-ATATCATTCTGGACATAGGAACTGGCAAAAATTTCAT-GAT 4606
                          v    ?i- v   -   vv   v v  iviv     vii    v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_81122194_8   4607 GTAGACACCAAAAGCAATTGCAACAAAAGGAAAAATGGACAAAT-GCAAT 4655
                         i -             vvv          i      i  i    - v v 
  L1M4_orf2#LINE/    595 AT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_81122194_8   4656 TTATTTGAACTAAAGAGGTTCTCTGCAAAACAAAAGAAATGATCAGAAGA 4705
                          i  ivi  i    i v-  i v   vv--    i  v iv    ii i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAAC-TTTTGTGCTT--CAAAGGACACTATCAAGAAA 690

  chrX_81122194_8   4706 GTAAACAGACAACCTATAGAATGGGAGAAAATACATGTAAACTATGCATC 4755
                           i  v        i i                iv  i   ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_81122194_8   4756 TGAGGAAGGTCTAATATGTAGCCTCTATAGGGAAGTTAAATAAATTTCAA 4805
                            vi i  v  vi   vi  vv v    ii   v ivv i  --i    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CTCAA 788

  chrX_81122194_8   4806 ----AAAAAAACA----------TTAAAAATTGGGCAAGGGAAATGAACA 4841
                         ----     i   ----------  ?    v       i   vv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_81122194_8   4842 GGCACATTTCAAAAGAAGACATACATGTGGCCAAGGAGCATATAAAAAAA 4891
                          i  iv i  v        i     vi       vi    i  i    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_81122194_8   4892 -GCTCAAAATCATGAAGCAG 4910
                         -      v    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (156 / 91)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.79 (34 / 19)  


2645 28.73 0.77 1.21  chrX_81154635_81162486.rev     2864  3775 (4077)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81154635_8   2864 TGGCAAAATATTTTATTTTCATTAATTGAAACAATCAATATTGTTAA-AT 2912
                            v  i    iii  v     vi    i  v v i           -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81154635_8   2913 GTTCATACTACCCCAAGCAATCCACAGATTCAATACAATCTGTATCAATA 2962
                          viv     v   v  vii   i          ii     iv      v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81154635_8   2963 TACTAATGGCATTCTTCACAGAAATGGGAAAAATACATATATAATTTATA 3012
                          v i iiv  v  i  ii       v iv  iv ivviv  v    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_81154635_8   3013 TGAAACTACAAAAGACCCAGAATTCACAAGGCTTTCCTAAGCAA-AAGAA 3061
                           i  v i   ii          vvv   ii vv  i i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_81154635_8   3062 CAAAACTGGAGGAATCAAATTATTTGACTTCAAATTATACTACAGAGCTG 3111
                             ii       v   v i viiii i      viv       i    i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_81154635_8   3112 TAGTAACCACAACAGCGGGGTACTGGTATCTCAATAGTCACATAGACCAA 3161
                         i     i  vi    i v        i  vvvi    v  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_81154635_8   3162 TCAAAAAGAATAGAGAACCCAGAAACAAATCCACACATTTACAGTGAACT 3211
                          vi  v     v    ii       i   i   i       ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_81154635_8   3212 CATATACAATAGATGTGTCAAAAACATATA-CAGGGAAAAAATAGTCTCT 3260
                         v  v v i i iiv   i   i v   vi -ii      i        i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_81154635_8   3261 TCAGTTAGTGGTGGTGAAAAAAATGGATATTTATATGCAGAAGAATGAAA 3310
                            iiv i     v  ii v  v      ?ii i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_81154635_8   3311 CTGCACCCATATCTCTTGCCATATGCAAAAATCAAATCGAAATTGGTTTG 3360
                         i  v    v  i   vii      i       i  v  i    v i iv?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_81154635_8   3361 AGACTTAAATGTAAGACATTTAAGTATGAAACTGCTACCCAAATGCTTTG 3410
                             i           vv vv  v   i     vi  vvvi  vi v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_81154635_8   3411 GGAAAAATCTTCAGGACATTAGTTTGTGCAAAAAATTTCTT-GACCTATA 3459
                          ?iv        iv   v  i v  iv    vii-      -  --   i
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGA--TATG 597

  chrX_81154635_8   3460 TCCCCCAG-GCACAGACAACCAAAGCAAAAATAGACAAATGAAATCAAAT 3508
                         v v  v i-     ii    v    v         i    vii iivv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_81154635_8   3509 CAAA-TTAAAAAGCTTCTGCACAACAAAGTAAATAATCAACAAAGTGAAT 3557
                             -       -   i  ii vv     v v iv     v        v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_81154635_8   3558 AGACAATTGACAGAGTGGGAGAAAATATTTGCAAATTACCCATTTGACAA 3607
                               iiv     i                     i ivi  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_81154635_8   3608 GGAATTAATAACCACAATGTATAAGGAGCTCGAACAACTCTATAGGAAAA 3657
                           i i vi  v   v   i     i  i   vv       v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_81154635_8   3658 A-ATAATCTAATAATCCCATTAAAAAAATAACCAAAAGATTTGAATAGAA 3706
                          - i  ----    i  v   ?     - iiv    i            v
  L1M4_orf2#LINE/    797 AGACAA----ATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGAC 841

  chrX_81154635_8   3707 ATTTCTGAAAACAAAGACATGCAACTGGCAAATAGATGATATAAAAAAGT 3756
                               vv   -i    i  i   v    v    iii- i  i    ii 
  L1M4_orf2#LINE/    842 ATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGC-ACATGAAAAGAT 889

  chrX_81154635_8   3757 GCTCGATATAATTGATAAT 3775
                             i i  v ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (148 / 110)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.29 (18 / 14)  

2190 26.31 4.35 3.12  chrX_81154635_81162486.rev     6465  7361 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81154635_8   6465 TGGGAAAATATTCAATGCTTATGTACTGGAAGAATTAATATTGTTAAAAT 6514
                            i  i    i v   i i   v i       v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81154635_8   6515 GACCATACTGCCCAAAGCAATCTATGAATTAAATTCAATCT-TATCAAAA 6563
                          i v     v      vii     iii   v  iv     i-        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81154635_8   6564 TACCAACATCATATTTTTACATAACTGGAAAAAA-AATCTTAATATTTAT 6612
                          v   i vv v -     i  v  v v  v  iv-i   i   v   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_81154635_8   6613 GTGGAACTAAAAATATGTCCCA--ATAGCCAAAGCAATACTTAGCAAA-A 6659
                         i     v iv  iv-- v    --         i    -   iiv   - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAAT-CTTGAAAAAGA 196

  chrX_81154635_8   6660 AGAATAAAGCTGAAGAAATGACATTACTTCACA----CCAAATTATACTA 6705
                             i    i  i  i v v   ---    v  ---- v   i -     
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACA---CTTCCCAATTTCAAAACT-TACTA 242

  chrX_81154635_8   6706 CAAGATTATAGTCATCAAAATATCATATTACTGGTATAAAAATATACACA 6755
                            iii  i   v     i i vii iv      i    ii   v   i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_81154635_8   6756 TAGATCAATGAAAGAGAGTATAGAATCCACATA-AAACTACATACAT--A 6802
                                   i  v   i vv   i    v v -    i-       -- 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC-CATACATTTA 341

  chrX_81154635_8   6803 CAGCAAATTGACTTCTGACAAAGTCAACAAAGACATACCCTCTGGAAAGA 6852
                         ii iv      i  ii     i viiv   iiv   v vv vv       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_81154635_8   6853 C--ACCTATTTAATAAATGACGCTGTAAATATTGTAGGGCCATATGCAGA 6900
                         v--ii  v  i  i     ii    vi vv i  v vi?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_81154635_8   6901 AAAATGAAATTGGACATCTATTTCTCACTATATACAAAAATCAACTCAAC 6950
                          i      i      vi   ii  v   i            i       v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_81154635_8   6951 ATGG---------TTAAATATAAAATCTGTAACCATATAAATTCT-AGAC 6990
                             ---------i     i   i v  iv   i   -   i   -   v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAA 540

  chrX_81154635_8   6991 GTAAACA--GAAATACCTCTTCTTGATGTTGCCCTAGGCAAATAATTTAT 7038
                          v     -- i?i  vv     v   iv   vvi       - ii   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chrX_81154635_8   7039 TAC-TATGATTCCAAA-GCAAAGACAAAAAGAGAAGCTAAAACAGA--AA 7084
                           v-     iv     -   v ii   v  i    ---    i   --  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAA---AAAATAGATAAA 636

  chrX_81154635_8   7085 TGGGACTTAATTAAACTAAAAAAAATTCTGCAC---AAAGAA-GTAATTA 7130
                          v      v  i   v v     v-  i  ii ---    i -iiv  i 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCA 685

  chrX_81154635_8   7131 AGAGAGTAAACAGGCAGTTCACAAAATGCAATAAATTATTTACAAATTAT 7180
                            i   i  v  i  iii    i    vi v   v     i     i  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_81154635_8   7181 GCATCCAA-----GACTAATATCCAGAATGTACAAGGATCTCAAAGAGTT 7225
                         ii   ii -----    vi          i  i  i  v   vv v ii 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_81154635_8   7226 AAACAAGAAAAACAAACAAATAAAACAAAATAATGCCATTAAAAATAGGC 7275
                         v  i  v     --i        vv   ----- ---- ?      i   
  L1M4_orf2#LINE/    786 CAATAATAAAAA--GACAAATAACCCAA-----T----TWAAAAATGGGC 824

  chrX_81154635_8   7276 AAAGGACATGAACAAATATTTTTTTCAAAAGATGACACACAAATGGCCAA 7325
                               iv    i i i    i -- v     v  i i            
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCT--CCAAAGAAGATATACAAATGGCCAA 872

  chrX_81154635_8   7326 TGCAGATATGAAAAAATGCCCAATATCACTAATGAT 7361
                          iviv i       i    i   i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 2.16 (67 / 31)  


2792 26.12 5.27 1.26  chrX_81172248_81174769.rev     1159  2031 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81172248_8   1159 TGGTAAAATATTCCATGTTTGTGAATTGGAAGAATTAATATTGTTAAAAT 1208
                            v  i    i       ii  i         v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81172248_8   1209 ATCCATAGTACCCAAAGCAATCTATTAATTCA-TGCAATCTCTGTCGATA 1257
                         iv v   v v      vii     ivi     -i      i  i  i v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81172248_8   1258 TAACAATGGCATTTTTCACAGGAA--AAAAATCTGA-----AAATTTATA 1300
                          vv  iiv  v     ii   i  --i v  v    -----     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_81172248_8   1301 TGAAACCATAATAAATCCAGAATAACCAGAGCTATCCTAAGCAAAAGAAA 1350
                           i  viii  vii i        i   i i v   i i --       i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chrX_81172248_8   1351 AAAAAAAT-GGAGGAATCGCATTACCTTACTTCAAATTATACTACAGAGC 1399
                           v   i -      v  i  i v  iv i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_81172248_8   1400 TATAATAATAAAAACAGCATGATGCTGGCATAAAAAAAGGCACATAGAAA 1449
                           i i    v  i    ii  i i         ii v  i  i     vv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_81172248_8   1450 AATGGAACAAATTTGAGAGCCCAGAAACAAATCCACAGACCT-----TAA 1494
                                i i v       i       i   i   i v ii -----i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_81172248_8   1495 CTCATTTTTTACAAAGGTGTCTAGATGCCTAGACTATGTAGTGGGGAAAA 1544
                         i v     iv    i    --------  v    i  vi i        i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTG--------CCAAGACCATTCAATGGGGAAAG 390

  chrX_81172248_8   1545 GACAGTCTCTTCAATAAATGATGCTGAGAAACCTGAATATCCACATGCAG 1594
                         i i     i     i     i     i  v v   i   ?         i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_81172248_8   1595 AAGAAAAAAACTAGACCCCTATCTCTCACCATATACAAAAATCAAATCAA 1644
                              vi  ii i        i   v                i  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_81172248_8   1645 AATAAATTAAAGACTTGAATCTAAGGTCTCAAACCATGAAACTACTGTAA 1694
                            ii  i ?    i i   v    iv  v    i  i     vi iv  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_81172248_8   1695 GAAAACCTTTGAGAAAATCTCCAGGTTCTTGAGCC--GTA-----TTCT- 1736
                               v vv ? v      i iv vi    i ii-- i -----    -
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_81172248_8   1737 -------GCA-----AGCACAGACAACCAACACAAAAATGGACAAATGGG 1774
                         -------i  -----      ii    v  viv      i  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_81172248_8   1775 ATCATATCAAG-TTAAAATGTTTCTGCAGAGCAAAATAAATCATCAACAA 1823
                          iivi     i-      -ii  i  iivvv    iv v ii     v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_81172248_8   1824 AGTGAAGAGACAACTCACAGAATGGAAATAAATATTTGCAAACTAAGCCT 1873
                               i       i          i iv             ii viiv 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_81172248_8   1874 TTGACAAGG-ATTAATAGTCATAATATAAAACAAGCTCAAATAACT--AT 1920
                         i   i    - i vi  vi  v      v  vi i   vv i    --  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_81172248_8   1921 AGGAAAAATTCTAATAATC--AT------ATGGACAAAAGATTTGAATAG 1962
                          iv     vv v     i --  ------    i    i           
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_81172248_8   1963 ACATTTCTCAAAATGAGACATACGAATGGCAAACAGGCATATAAAAAGGT 2012
                                  v   vi   i    i      v  i i   i  i     i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_81172248_8   2013 GCTCAAAATCATTGATCAT 2031
                               v    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (146 / 79)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.35 (57 / 17)  


2832 26.57 0.65 3.13  chrX_81198150_81200561      994  1919 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_81198150_8    994 AGATATTCAATGTTCATGGATTGGCAGAATCAATAATGTTAAAGTGTCCA 1043
                               i v               v   v i    v      ii  v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_81198150_8   1044 TACTACTCAAAGCAATTTACAGATTAAATGCAGTCTCTTTCAAAATACCA 1093
                             v i    vii  i        v  i   i  i  v       v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_81198150_8   1094 ATGACATTCTTTCCAGAAATAGAAAAA--AATATGAAAATTTATATAAAA 1141
                         iivi v  i   v       v  v  i--i  viv      i    ii  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_81198150_8   1142 CTGCAAAAGACCCAGAATAGCCAAAGACATTCTAAGTAAAAACAAACAAA 1191
                         v     ii                 -   v   --- i    vi  ----
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAA-ACAATCT---TGAAAAAGAA---- 197

  chrX_81198150_8   1192 CAAACAAACAAAACTAATGGTATCACATTGCCTGACTTCAAATTCAAATT 1241
                         -----i      ii iiv  vv     i v  ii i      ----- i 
  L1M4_orf2#LINE/    198 -----GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-----ACT 237

  chrX_81198150_8   1242 TGTGTGCTACAGAGCTATAGTAACCAAAATAGCATAGTACTGGCATAAAA 1291
                          i----     i     i     i   i i  ii i            ii
  L1M4_orf2#LINE/    238 TA----CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_81198150_8   1292 ACAGACAAATATACCAAGGGAACAGAATGGAGAACCAAGAAACAAATCCA 1341
                          i     v   v i   v    i     v    ii v     i   i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_81198150_8   1342 AACACCTATGGTGAACTTATTTTTTACAAAGTTGCCAAGAACATACACTG 1391
                         v   ii      v  i v     iv    i v        v   v  v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_81198150_8   1392 GGGAAAAGACAGTCTTTTTAGTAAATGGTGCTGGGAAAACTGGCTATCTA 1441
                               ii i        i ii              v      v  ? i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_81198150_8   1442 TATGCAGAAGAATAAAACTGGACCCCTATTACTCACTGTATACAAAAATT 1491
                         i     i      i  ii          iiv v   ii            
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_81198150_8   1492 AAGTTAAAATGCATTAATGACTTCAATCTAATATGTCAAGA-TATGAAAC 1540
                           v i      v  i ?v   i v   v   v - ii  i -   i    
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAAC 532

  chrX_81198150_8   1541 GTCTACAAAGAAAACATTGTTG-AAACTATCAAAACTTTAGTCTGGGTAA 1589
                         -   vvi          v v? -   iiv  ivi  i  i vi i  i  
  L1M4_orf2#LINE/    533 -TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_81198150_8   1590 AAAATTTTTTGA-GTAATACCTTGCAAACACAGGCAACCAAAGCATAAAT 1638
                         viiv  i  v  -i i i   --iv  i    i     v    v v    
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_81198150_8   1639 GAACAAATGAAATTACATCAAGTATAAAGGCTTCTACACAGAAAGGGAAT 1688
                         ii i    vii i v      ivv    ii   i iii vvv  i   vv
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_81198150_8   1689 CAATCAATCAAGTGAAGAGACAACCTATAGAAATAGAGAAAATATTTGCA 1738
                          v     vv       i        i i    vvi               
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_81198150_8   1739 AACTATGCATCTGGCATGAAATTAATAACCAAAGTATTTAAGAAGCTCAG 1788
                           ii  ii     ii v ii i vi  v   i i   v   ii i   vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_81198150_8   1789 ACAAGTCTGTAAGAAAAAAAAAACTAACAATATAATT-AAAAGTGGACAA 1837
                             v  ---  v  v     i  v  i  ivi    -    i   i   
  L1M4_orf2#LINE/    780 ACAACTC---AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_81198150_8   1838 AATATTTAAATATAAATTTCTGAAAAGAAGACACACAAATGGCAAACAGG 1887
                          iv    i    v v      vv        i i         v  i i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_81198150_8   1888 CATATGGAAAGCTTCTCGACATCATTAATTAT 1919
                           i   i    v v   i      ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.02 (14 / 903), avg. gap size = 2.50 (35 / 14)  


2130 21.69 7.05 2.47  chrX_81210817_81215373     2554  3120 (1437)    L1M4_orf2#LINE/L1        1   593 (315)  

  chrX_81210817_8   2554 TGGAAAGATATCCTGTGTTCATTGCTTGGAAAA-TTAATATTGTTAACAT 2602
                                      ii       v v      i -             v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81210817_8   2603 TTCCATACTTCCCATATTGATCTACAGATTCAGTGCAATCTCTATCAAAA 2652
                         vv v     i    v                 ii      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81210817_8   2653 ACTTCAATGGCATTTTATACAAAAGAAGTAAATAAG----TCCTAAAATT 2698
                         v i-  iiv  v    v i  ---   i vi i   ----          
  L1M4_orf2#LINE/    101 TCC-CAGCTGCCTTTTTTGCA---GAAATTGACAAGCTGATCCTAAAATT 146

  chrX_81210817_8   2699 TGTATGAAAACACAAAGGACCGCCAG--TAACCAAACCAACCCCGTGAAA 2746
                         ii    i   ii   i     --   --  i     v   i ii vi   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACC--CAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_81210817_8   2747 GAA---CAAAGTTAAATTCTTTACACTTCCTGATTTCAAAATGTATCACA 2793
                            ---       ii vvvi i        ii         iv  ii   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_81210817_8   2794 AAGCTATAGTAGTTAAAGGAGTATGGTACTGGCATAACGACAGACATCTA 2843
                               i    i i  iiv   i              v  i      v  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_81210817_8   2844 AATTGATAGAACAGAATAGAGAGTTTAGGAATAAACCCA--CATGTATTA 2891
                         i  ii  i   i     v      ii  i          --   v   --
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT-- 342

  chrX_81210817_8   2892 GGTCAACAGTTCTTTGTCAAGGACACCAAGAATACAAAATGGGGAAA-AA 2940
                               iv v i  i v     iii      vi ivv          -  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_81210817_8   2941 TAGTTTCTTCACCAAATGGTACTCAGAAGACTGGATATGCACATGCAAAA 2990
                             i i    v        i  vi  vi        ?v           
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_81210817_8   2991 GTATAAAATTAGACCCTTATCTTCCAAAATACACAACA------TCAA-- 3032
                          v  i  i  i     i  i  iv  vv   i    v ------    --
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_81210817_8   3033 ------------CTAAA-----GATCTAAAACTATAAAA-TCCTAGAAAA 3064
                         ------------     -----  v              -  i     i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_81210817_8   3065 AAAACAAAGCTTAAGAA-AAGGCTTTATGACATTGGATTTGGCAATGATT 3113
                            -  -----  i ?i-  iv   ii    v    i  v       i  
  L1M4_orf2#LINE/    543 AAA-CA-----TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_81210817_8   3114 TCTTAAA 3120
                              i 
  L1M4_orf2#LINE/    587 TCTTAGA 593

Transitions / transversions = 1.88 (79 / 42)
Gap_init rate = 0.03 (17 / 593), avg. gap size = 3.18 (54 / 17)  

 463 27.80 3.47 5.02  chrX_81210817_81215373     3416  3674 (883)    L1M4_orf2#LINE/L1      577   831 (77)  

  chrX_81210817_8   3416 GGCAATGATTTTTTTATTTTGACCCCAAAA-CAAATGCAACAAA-GCAAA 3463
                                i   i  viv v    v      -  v v        - v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_81210817_8   3464 TATAGAAAAAT-GGGTCTCA----AACTAAACATTTTCCGCACAGCAAAA 3508
                         v     v    -  iii   ----  i    v i   i- ii vv    i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT-GTGCTTCAAAG 675

  chrX_81210817_8   3509 TAAATAATGAACAA--CAAAAAGGCAATCTACAAAATAGACTAAAGTATT 3556
                         v v iv  v  v  --ii     i   i i   i   i ivv   i    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_81210817_8   3557 GACATATCATATATGTGATTAGAGGTTAATATCACAAATGTAGAATAAAC 3606
                         vi  v         v    v  i ii vi    vvi   i  v  vi   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_81210817_8   3607 TCCTACACCTCGATATCAAAACAAATTTTAAAAAAGCAAATATCATGATT 3656
                           i    v   i   ---------  ---     ii      v vii   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATA---------AT---AAAAAGACAAATAACCCAATT 813

  chrX_81210817_8   3657 AAAAAACAGGCAAACAAT 3674
                         ?     ii      vi  
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.22 (39 / 32)
Gap_init rate = 0.03 (8 / 255), avg. gap size = 2.75 (22 / 8)  


2096 28.07 1.94 2.67  chrX_81218357_81220171.rev      502  1324 (491)    L1M4_orf2#LINE/L1       92   908 (0)  

  chrX_81218357_8    502 CTATCAAACTACCAATATAATTTTTCACAGAAATATATAAAA-AATTCTA 550
                                 v v   iivvvv     ii       vv i  iv-i  i   
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_81218357_8    551 AAATTTATATGAAACCA-AAAAGATCCCAAATAACCAATTCAATCCTAAG 599
                              i     i  vii-  ii  i  vi    i    vv     i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_81218357_8    600 CAAAAAGAACAAAGCCAGAGGCATCAGATTACCTATCTTTGAACAATAAT 649
                         v  i          iii    vv   v i v  i vi  ii  vvv  v 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_81218357_8    650 ATAAGGCTAAGGTAATCATAACAGCATGGAACTGGTACAAAAATCAAACA 699
                          i  i    vi       vi    ii   v     i i  ii  - i   
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACA 290

  chrX_81218357_8    700 CATAGACCAATGGAGCAGAATAGAGAACAGAGAACTAAAGCTTCACACCT 749
                         i     i       ii     v    iivv    v    v ivi   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_81218357_8    750 ATCACCATCTGACCTTCAACAAATTCAACAAAAATAAGCAATGGGGGAAA 799
                           vii  vi   ii   i    ivviiv   i vi vv        -   
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAA 389

  chrX_81218357_8    800 GACT--CCTTATTTAATAAATGGTGTTGGGATAGCTGGCTAGCCCCATGC 847
                           v --i   -  i  i        i     i i    v  ?  v     
  L1M4_orf2#LINE/    390 GAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_81218357_8    848 AGAAGAA-AAAGCTGGACTCCTACCTTTCACTATATACAAAAATTAACTC 896
                          i     -i   i     i       iv   i                  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_81218357_8    897 AAGATGGATTAAATATTTAAGTGTATAGAAACTCAAACTATAGAAATCCT 946
                           i      i ? v ii   i    -   i-  v        i  v  i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTA-AGAG-CTAAAACTATAAAACTCTT 536

  chrX_81218357_8    947 AGAAGAAAACATGGGAAACACCATTTCCCACACTGGCCTTCAGGAAACAA 996
                                     i  ?ivv --  i i v----  i    --- iivi i
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAA--ATCTTCG----TGACCTT---GGGTTAG 577

  chrX_81218357_8    997 ACAAACAAACAAAAACTTATGAC-TGAGTTCCCAAAAGCAATTGCAACAA 1045
                         i   -----iiivvv    -  i-   --iv         vvv       
  L1M4_orf2#LINE/    578 GCAA-----TGGTTTCTTA-GATATGA--CACCAAAAGCACAAGCAACAA 619

  chrX_81218357_8   1046 AAAGAGAAATTTTCATCTGGGACCTAATTAAG-CTAAAGAGCTCTGCCCA 1094
                           ii i    vvvi vv v    i v  i  i-i    i vi i  iv v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_81218357_8   1095 GCAAAGGAAACTAACA-GAATAT--ACCGACAACCTCCAGAATGGGAGAA 1141
                         v       v    v  -   vi -- vv       iv             
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_81218357_8   1142 AATATTTACAAACTATGCATACAATAAAGATCTAATATCCAGAATCTATA 1191
                                i    ii  ii  vii    i iv  vi          v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_81218357_8   1192 AGGAACTT----AATTTAACAAGCATAAAACAAATAACTGCATTAAAAAG 1237
                          i     i----  i i  i  vv v  i         ivv   ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_81218357_8   1238 TGGGCAAAAGACATGACCAGACACTTCTCAAAAGAAGACAAACAAGCAGC 1287
                                 i  iv   vi     i     v        i v    iii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_81218357_8   1288 CAATA-GT-CATGAAAAAATGCTCAGCATCACTAATGAA 1324
                              - i-        i       i     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.03 (22 / 817), avg. gap size = 1.73 (38 / 22)  


1106 27.66 4.31 2.72  chrX_81239057_81241065.rev        5   445 (1564)    L1M4_orf2#LINE/L1      337   784 (124)  

  chrX_81239057_8      5 ATTTACAGACAACTGATTTTTGACAAAGGTGCTAAGAATATACATTGGTA 54
                              ii v   i       i     i     i    vi  v  v   -i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-G 385

  chrX_81239057_8     55 AAAAGGACACTCTCCTTAATAAATGGTGCTGGGAAAAGTGAATGTCAATA 104
                         i    i i v   ii i  i              v  v  i  i? v i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_81239057_8    105 TGTAGAAAAATAAAACTATTTCTCTATCTTTTACCATATACAAAAATCAA 154
                           i i  i   i  ii ivvi i   i  ivi               i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_81239057_8    155 CTCCAGGTGGATTAAATATTTTAATGTAAGGCCAAAAACTATAAAAATAT 204
                            v ii     i ? v ii v        iv v            v v 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_81239057_8    205 TA------AATGTAGGAAAAACACTTCAAGACATA----CAGAAAAAGAT 244
                           ------  ii    ?iv  vv    iv   v v----i  iv  v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_81239057_8    245 TT--TAGATTTTATGACTAAGACCTAAAGAGCACAGGCAACAAACCAAAA 292
                           --     ---     ----   --  i      i        vv    
  L1M4_orf2#LINE/    586 TTCTTAGAT---ATGAC----ACC--AAAAGCACAAGCAACAAAAGAAAA 626

  chrX_81239057_8    293 A-CAGACAAATGGTGCTATATTCAA-TTAAAAAGCCTGTGCATACCAAAG 340
                          -i   i    v vi  vi  iv  -       - i v  iiivi     
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAG 675

  chrX_81239057_8    341 GAAATAATCACCAGAATAAAGAGACAACAATTTGTATGAAAGTAAATATT 390
                           v iv    vv i i i  i       vvviv v   ii  v       
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_81239057_8    391 T-----TTATTCATCTGACTGAGGGACTAATATCCAGAATATACAAGGAA 435
                          ----- i  vi      - i       vi             i  i   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGA-TAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_81239057_8    436 CTCAAATAAC 445
                            vv i   
  L1M4_orf2#LINE/    775 CTCTTACAAC 784

Transitions / transversions = 1.48 (71 / 48)
Gap_init rate = 0.03 (12 / 448), avg. gap size = 2.58 (31 / 12)  

2038 29.04 2.93 4.55  chrX_81239057_81241065.rev      596  1518 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81239057_8    596 TGGAAAAACATTCCATGCTAATGAATGGTAATAATTATTATTGTTGAAAC 645
                               i i  i     i v   i  v v  v v   v       i i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81239057_8    646 GGCC-TACTGCCCAAGGCGATT-ATTTTCAGAGTCAATGCTATTCTTATC 693
                            v-    v     ----   -  i v    v    i  v  i i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA----ATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_81239057_8    694 AGACTGC-AATGACATTTTTCACAGTAATAGGAAAAATAAAACTATTTTA 742
                          i v v - iivi v     ii   v   v iv  iv i ----- ii  
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-----TCCTA 141

  chrX_81239057_8    743 AATTTAATATAGAACCA-AAGAAAAGCTGAATAGCCAAAGCAATCCTAAG 791
                           v  v    i   vii-   ii vv v           i     i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_81239057_8    792 TAA-AAGAACAAAGC-AAAAGACATCACCTTACCTGACTTCAAACTATAT 839
                         v  -          i-ii i   -    vi v  ii i      viv  i
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTAC 240

  chrX_81239057_8    840 TCTAAGGTTGAATTAACCAAAACAGTACAGCACTGGTACAAAAACAGACA 889
                          vi  i i iv v   i   i     iii i     i i  ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_81239057_8    890 TGACACATAGGCCAATGGAACAGAATAGAGAACTCAGAAATAAAGACACC 939
                          -----    ii        i     v    iii          vv  iv
  L1M4_orf2#LINE/    291 T-----ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_81239057_8    940 CACCTAGAGCCATCTGATTTTCAACAAAGTTGGCAAAAATAAGCAGTGAA 989
                           ii  vi i  vi        i    i v  v   i vi vv  i  ii
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_81239057_8    990 GAAAAGACTCCATATATTCAACAAATGGTCCTGGGATGGCTGGTTAGCCA 1039
                             ii i--vi v v             v      iii    v  ?   
  L1M4_orf2#LINE/    386 GAAAGAAT--AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_81239057_8   1040 TATGCAGGAGAAGGAAACATGACTGCTACCTTTCAGAATATGCAAAAGTT 1089
                         i     ii    v   iivv   iv      iv  vv    i     i  
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_81239057_8   1090 AACTCCAGATATATTAAAAATTTAAATGTAGGACTTGAAACTGTAAGAAT 1139
                              v i  iv  i ? i ii        i  vi i     i   i v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_81239057_8   1140 CCTAGAAGAAAACCTAGGAA-ACACCATTCTGAACATCAGACTTGGGAAA 1188
                          i           v    ?i- v i -   vvi  v ii i-  i  v  
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAA 581

  chrX_81239057_8   1189 AAA------AAATTATGACAGTCCTCAGAAGCAATTGCAACAAAAACAAA 1232
                         vii------ i  -      ----i  i     vvv         iv   
  L1M4_orf2#LINE/    582 TGGTTTCTTAGAT-ATGACA----CCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_81239057_8   1233 AATTGACAAATGAGACCT-AT----GTAAAGAGTTTCTACACAGCAAAAA 1277
                            v  i    vi   i -  ----i v  i ii  i iii v-------
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT------- 669

  chrX_81239057_8   1278 GAATCAAAACAAACACAAAAAACATCAACAGTGTAAAGAGAAAATCTAAA 1327
                         ---     i--i    ------i     v iv  i  i   v  i i v 
  L1M4_orf2#LINE/    670 ---TCAAAG--GACAC------TATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_81239057_8   1328 GAATGGGAGAAAATATTTGCAAAATATGCACCCAACAAATGTCTAATATT 1377
                                                vi  ii i ii i  iv v  vi   i
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_81239057_8   1378 CATAATCTATAAGAAACTTCAACAATTCAACAA-------GCAAACAACC 1420
                           v   v     ii    iiv    i    i  -------i    i    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_81239057_8   1421 CCACAAAAAAGTGGGCAAACGACATTAGCAAACACTCCTCAAATGAAGAC 1470
                          v iv?    i        v  iv v ii i   i i   v  v     i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_81239057_8   1471 ATACCATCCGCCAATGA--ACATGAAAAAATGATCAGCATCACTAATCAT 1518
                             v viv      i --         i   v   i     ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (167 / 97)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.88 (69 / 24)  


2344 26.53 1.65 2.71  chrX_81245771_81249599.rev      651  1498 (2331)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_81245771_8    651 ATTTATAGATTGAATCCGGTTCTCATCAAGCTACCA-CGGACTTTCTTCA 699
                           i  i     v  iv ii i ii     iv v   - v v    i  -i
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT-G 118

  chrX_81245771_8    700 CAGAACAAGAAAAAAT-ACTTTAAATTTCATACGGAACCAAAAAAGGG-C 747
                              vvv  v  iv - iii    v      i    -- viv     - 
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA--ATGCAAGGGAC 166

  chrX_81245771_8    748 CCATAG-AGCCAAGACAATCCCAAGCAAAAAGAACAAAGCTGGAGGCATC 796
                            v i-      i      iii iv  i          i      vv  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_81245771_8    797 ACGCTACCTGACTTCAAACTATACTACAAGGCTAAAGTAAGCAAAACAGC 846
                           i  v  ii i      viv        i    v     v   i    i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_81245771_8    847 ATGATACTGCTACCAAAACAGATATATAGACCAATGGAAAACAATAGAGG 896
                         i  i     vi iv ii i   i       i        v v   v   i
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_81245771_8    897 CCTCAGAAAAAAACAACACACATCTACAA-CAATCTGATCTTTGACAAAC 945
                         vii      v    v-  i    i  iii-    -    i  i     iv
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACC-CATACATTTATGGTCAAT-TGATTTTCGACAAGG 364

  chrX_81245771_8    946 CTGACACACACAAGCGATGGGGAAAGGATTCCCTATTTAATAAATGGGAA 995
                         v  v  vivv  vv i          i  vvi  v  i  i      viv
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_81245771_8    996 TTAAATATACTGTATACTGGCAAGCCATATACAGAAAACTGAAACTGGAC 1045
                          vii i -    v   -------?   i  i  i  i v    ii     
  L1M4_orf2#LINE/    415 TGGGACA-ACTGGATA-------KCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_81245771_8   1046 CCCTTCCTTACACCTTATGCAGAAATTAACTCAAGATGGATTAAAGACTT 1095
                             v   i     v   i  i            i      i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_81245771_8   1096 AAAAATAAAACCTAAAACCATAAATAC-CTTAGAAGAAAACCTAGG---A 1141
                            vi   i v       i     -  -             v    --- 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_81245771_8   1142 AATACCATTCAGAACAT--AGTCATGGGCAAAGACTTCATGACTAAAACA 1189
                            -- -   ivi  v --i  i --     v ii   v iiv  vi   
  L1M4_orf2#LINE/    556 AAT--C-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATATGACA 600

  chrX_81245771_8   1190 CCAAAGGCAATTGCAACAAAAGCCAAAATTGATAAATGGGATCTAATTAA 1239
                              i   vvv          vv     v       v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_81245771_8   1240 GCTAAAGAGCTTCTGTACAGCAAAAGAAACTATCATCAGAGTGAACAGGC 1289
                         iv v  i i   i   i vv    i  v       vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_81245771_8   1290 AAACTACAGAAAGAGAGAAAGT-TTTGCAATCTATCCATCTGACAAAGGT 1338
                           v i      v i      i -       vii  vi      i  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_81245771_8   1339 CTAATATCCAGAATCTACAAGGA--TTTTAAACAAATTTACAAGAAAAAA 1386
                           vi          v  i  i  -- i   --   v iv i  v     i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAAAAG 798

  chrX_81245771_8   1387 AACAAACAACTTCATCAAAAAGTGGGCAAAGGATATGAACAGGCAATTCT 1436
                          -    i   iiv  i?    i            v    i  i  v    
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_81245771_8   1437 CAAAAGAGGACATTTATGTGGCCAACAAACATATGAAAAAAAAACTCATC 1486
                          v     i  i  vi vi       i  i  i       i vi-    v 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG-CTCAAC 896

  chrX_81245771_8   1487 ATCATTGGTCAT 1498
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (130 / 92)
Gap_init rate = 0.03 (23 / 839), avg. gap size = 1.61 (37 / 23)  

2252 30.82 1.14 0.68  chrX_81245771_81249599.rev     2463  3338 (491)    L1M4_orf2#LINE/L1       29   908 (0)  

  chrX_81245771_8   2463 GAAGAATCAATGTTGTTAACATGACCATATTAACTAAAGCAATCTATCTA 2512
                              v i   i       v   i v   i vv i   vii     ivv 
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chrX_81245771_8   2513 CCTAAAACACATTCCTTATCAAATTACCAACATCGTTTCTCACAGAATTA 2562
                         iii  -- i  v   i       v v   i vv v   i ii     v v
  L1M4_orf2#LINE/     79 TTCAA--CGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

  chrX_81245771_8   2563 GAAAAAAAAATCCTAAAGTTTATATGGCC-TCCCAGAAAGCCCAAATAGC 2611
                           v  ivvi        i  i      vv- v v  ii v  vi      
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chrX_81245771_8   2612 CAAAGCAATTCTAAGCAAAATAAACAAATCTGAAGAAAGCACATTATCTG 2661
                             i    ii i iv  i vi      vi  i  i vv    i vi ii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_81245771_8   2662 ATTTTAAATTATACTTCAAGGATGTAATAACAAAAACAGCATGGTACTAG 2711
                             i   viv    v   i v ii i   iv  i    ii       i 
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_81245771_8   2712 TAAGAAAATAGA-GTGTTGATGAATGGAATAGTATACAGAACACAGAAAT 2760
                         i vi ii     -i i v   v          v  vv   iiv       
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_81245771_8   2761 ATACC-ACATATCTATGACCAACTAATGTTTGACAAAGTCAGCGAAAATA 2809
                          v   - i i  i    ii   i i  v  i     i viiv i i vi 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_81245771_8   2810 TACACCAGAGAAAGGACA--CTATTCAATAAGTGGTACTGGGAAAATTGG 2857
                          v  vii i     i i --  v     i  i    i      v  i   
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_81245771_8   2858 ATAGCCATATGAAAAAGAATAAATCTGGACTCACATCTATTCCCATATAC 2907
                            ?   i   v        i  vi     i vi i  vviv        
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_81245771_8   2908 AAAAATTTACTCAAGATGTACTA-AGACTTAAATATAAGGCTTGAAACTG 2956
                                v      i   v ii -    i     i    ivi i     i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_81245771_8   2957 TAAAATTCCTAGAAGAAAAGAAAAAAA-AAGTGCTTCTTGAAATTGACCT 3005
                              i  i          v v ii?i-  i -    v   vv   ivi 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTT 575

  chrX_81245771_8   3006 AAGCAAAGAATTTATGACTGAGTCTTCACAAGCAAATTCAATAAAACAAA 3055
                          i    v iv  iv iiv iv v vi  v     v vv   i    v   
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_81245771_8   3056 A--CAGACAAGTGAGACTTAATTAATGTAAATGGCTTCTGTGCAGCAAAA 3103
                          --i   i  i vi     v  i  vi v  vii   i     vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_81245771_8   3104 GAAATAATCAATGGAGGAAGCGGACAAACTGCAGAATGGGAAAAAATATT 3153
                           v iv     vii  vi ivi     v ii          i        
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_81245771_8   3154 TGCAAATCATGCAGCTGACAAAGGGGTATTATCTGGACTCTATAAGAAAA 3203
                                   ii v    i  i  iv vv    ii  v v     ii  v
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_81245771_8   3204 TCAAACAAGTCAACAAGAGATAAAATCAAATAACCATATTTAAAAAGAGA 3253
                           vv    v    i  v i -  i -         vv   ?     vi -
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAA-AAGA-CAAATAACCCAATTWAAAAATGG- 822

  chrX_81245771_8   3254 GTAAAGAATATAAACAGACACTTTTCAAAAGAAAGCATACAACTGGCCAC 3303
                          i    i  v i  i     i  i  v      iii      v      v
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_81245771_8   3304 TAAACACATGCAAA-ATACTCAACATTACTCATTAT 3338
                            i      v   -  i        i ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (156 / 111)
Gap_init rate = 0.01 (13 / 880), avg. gap size = 1.23 (16 / 13)  


 207 12.20 0.00 0.00  chrX_81259725_81263921.rev      463   503 (3694)  C L1M4_orf2#LINE/L1   (0)   908   868  

C chrX_81259725_8    503 GCCAAAAGACACATGAAAAAATGCTCATCATCACTGGCCAT 463
                              v ii          i       v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (3 / 2)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  

3114 27.35 0.35 0.35  chrX_81259725_81263921.rev     2847  3698 (499)    L1M4_orf2#LINE/L1        1   852 (56)  

  chrX_81259725_8   2847 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 2896
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81259725_8   2897 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTTATCAAGC 2946
                           iv     v     iv i  i  i        i  v    i      iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81259725_8   2947 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2994
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_81259725_8   2995 TATGGAACCAAAAAAGAGCCCGTATCTCCAAGTCAATCCTAAGCCAAAAG 3044
                                viiv  ii  v  v v  vv    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_81259725_8   3045 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3094
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_81259725_8   3095 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3144
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_81259725_8   3145 AATGGAACAGAACAGAGCCCCCAGAAATAATGCTGCATATCTACAACTAT 3194
                                i    iv   vvi          vv iii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_81259725_8   3195 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAAGATTCCCT 3244
                         i    i  i     ivv  vv  i v  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_81259725_8   3245 ATTTAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3294
                         v  i ii              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_81259725_8   3295 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3344
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_81259725_8   3345 AAAGACTTAAATGTTTGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3394
                          ?    i       vv  v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_81259725_8   3395 AGGCA-ATACCATTTAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 3443
                            ?i- v i -  iiv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_81259725_8   3444 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCAT 3493
                                     vvi          vv     v  i    v   ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_81259725_8   3494 TAAACTAAAGAGCTTCTGCACAGCAAAAGACACTACCATCAGAGTGAACA 3543
                         i   v v  i i   i  ii vv    i       i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_81259725_8   3544 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCCGACAAA 3593
                          i     i   i             v       vii ivi   i  i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_81259725_8   3594 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAGTTTACAAGAAAAA 3643
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_81259725_8   3644 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACCGACACTTCT 3693
                         i     i     v  i?    i            v    iv    i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_81259725_8   3694 CAAAA 3698
                          v   
  L1M4_orf2#LINE/    848 CCAAA 852

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.01 (5 / 852), avg. gap size = 1.20 (6 / 5)  


2416 28.68 2.55 1.99  chrX_81274981_81280168.rev     3824  4726 (462)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81274981_8   3824 TGGAAAAACATTCCATGCTCACGGATAGGAAGAATCAATATTATTAAAAT 3873
                               i i  i     i   i    v      v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81274981_8   3874 GGTCATACTGCCCAAAGCAATTTAGAGATTCAATGCTAGTCCTATTGAAC 3923
                           iv     v      vii  i  v        i  v vi     ---- 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT----C 96

  chrX_81274981_8   3924 AAA----CAATTAAATTTTTCACAGAACTAAACCAAAAAAAAGTTTCAAA 3969
                            ----  ii ivv     ii     v vi  ---  ivvii iii   
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC---AAGCTGATCCTAAA 143

  chrX_81274981_8   3970 ATTCATATGGGACAACAACAAACAGTGCTCGAATAGCCAAGGAAATAATA 4019
                                   i vvi   vii  ---- iv          iiv   vv i
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGAC----CCAGAATAGCCAAAACAATCTTG 189

  chrX_81274981_8   4020 AGCAAAATGAAAGAAGCTGAAAGTATCACATTACCTGACTTCAAATTATG 4069
                          iv  i v   vi   i  i i vv     i v  ii i      viv i
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_81274981_8   4070 CTGCAAGGCTACAGTAACCAAAACAGCACGGTACTAGCACAAATACAGAT 4119
                           i   i          i   i    iii      i   i  iv i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_81274981_8   4120 ACACGGGCCAATGGAACAGAATAGAGAGCCTCAAAATAGGGCCATACACC 4169
                          i ii ii        i     v     i ivi     iiv       ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_81274981_8   4170 TACAACCATCTGATCTTTCCCAAAGCTGACAAAAAAAAAGCAATGCGGAA 4219
                           iiii  vi    i  ivv   i v  v   i vv v-v     v    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAA 388

  chrX_81274981_8   4220 AGGGCTCCCTATTCAAGAAATGGTGTTGGAA-AACTGGTTAGCCATATGC 4268
                           iiivvi  v     v        i   i -      v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_81274981_8   4269 AGAATATTGAAACTGGACCCCTCCCTTACAGTGTATAGAAAAATTAATTA 4318
                          i  v v    ii         v   i   vii    v         i v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_81274981_8   4319 AAGATGGATTAAAGACTTAAATGTAAACCCCAACACTATAGAAACTCT-G 4367
                           i      i ?    i         ivv i  v      -       -i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTA 537

  chrX_81274981_8   4368 GAAGACAACCTAGGCA-ATATCTTTTGGGCATAGAAACAAGGAAAGATTT 4416
                              v   v    ?i- v     ivv i v v iivi i v  v i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_81274981_8   4417 CACGAA---GAAGCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAAT 4463
                          viii ---  vi         vvv          v      v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_81274981_8   4464 GGGATCTAATTAAACTAAAGAGCTTCTGCAGAGCAAAGAAAACTATCAAC 4513
                         v   ii v  i   v v  i i   i  iivvv     i v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_81274981_8   4514 AGAGTAAACAAACAACCTTCAGAATTGGAGAAAACATTTGCAAACTATGT 4563
                          i   i  v i      iv      v        i         ii  i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_81274981_8   4564 ATCTGACAAAGGTCTAATATCCAGCATCTATAAGGAACTT----AAATTA 4609
                               i  i  v  vi       v  v     i     i----  v i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_81274981_8   4610 GCAAGAAAAAAATAAACA------TTAAAAATTGAACAAAGGACAAGAAA 4653
                         ii  v     i i   i ------  ?    v  ii       ivv   v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_81274981_8   4654 AAAATCATTTT---AAAGAGGAGACACCCATGAAGCCAAGTATGTGGAAA 4700
                          i --     i---     i  v i  vv   --     -  v iiv vi
  L1M4_orf2#LINE/    838 AGA--CATTTCTCCAAAGAAGATATACAAATG--GCCAA-TAAGCACATG 882

  chrX_81274981_8   4701 AAAAGAAGCTCAACAACACTGATCAT 4726
                               v        v  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (151 / 104)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.56 (41 / 16)  


3193 25.77 1.22 0.77  chrX_81282112_81284067.rev      564  1467 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81282112_8    564 TGAAAATGTATCCTGTGTGTTTGTGTGTAGGACTAATTAATATTGTTAGC 613
                           i   vi     ii   -- ii  vi v   vv v            iv
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGT--TCATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_81282112_8    614 ATGCCCATACTACCCAAAGTTATCTACAGATTCAATGCAATTCTTATCAA 663
                            v v     v      v v              i     i i      
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_81282112_8    664 AATATAAAC-ACTATTTTTATCAGAAGTTGAAAAAACAATTTTAAAATTA 712
                            viv i -i iv     i-     i    v  ivii  ii       v
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_81282112_8    713 ATTTAAAACTACGAATGACCCTGAATAGCTAACGCAATCTGGAGCAATAA 762
                           v ii  v i i iv     v       i  vi      v  iv  v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_81282112_8    763 GAACAAAGCTAAAGATAACACCCTATCTGACTTAAAAATATACTACAAAG 812
                                 i ii  ivvv   v  vi ii i  v    iv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_81282112_8    813 CTATAGCAACCAAAGCAGCATAGTACTGGTATAAACAAAGACATCTAGAA 862
                            i  i  i   ii   ii i       i    iv v      v    v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_81282112_8    863 GAATGGAATAGAGTAGGAAGCCAACAAATAAATCCAGGCATTTACAGTCC 912
                         v           i v ii  i v v       i   vi      ii   v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_81282112_8    913 ATTGATTTTTAACAAATTTGCTATAAATACACAATGGAGAAAAGATAGTT 962
                                  ii    ivv   i vi vi iv      i    ii     i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_81282112_8    963 TCTGTAAGAAATAGTGCTGGGAAGAGTGGATATTCACATGCAGA-GAATC 1011
                          i vi  v    i         vi v      ?i        i -    v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_81282112_8   1012 AAATTAGGCCCCTATATCACACCATACA-AAAAATTAACTAAAAATGGTT 1060
                           i  i i      iv          i -           v       v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_81282112_8   1061 GAAAGACTTAGATGTAAGACCTGAAACTGTAAAACTATTAGAAGAAAACA 1110
                         v ?    i  i        v  i     i       v             
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_81282112_8   1111 TAGGA-TAAATGTTTCATGACATTGGAGTGGGCAATGATTATTTTAATAT 1159
                             ?-     -i   i    v    iv i       i  - i   i-  
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAG-AT 594

  chrX_81282112_8   1160 CTATCCCCGAAAGCACAGGCAA-AAAAGTAAAAATAGACAAATGGGATTA 1208
                         v iv v  i        i    -     v         i    v   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_81282112_8   1209 CATCAAACTGAAAATCTTCTGGACAGCTAGGGAAACAATAAACATAGC-A 1257
                                v v    v   i  vi vv v i   v  v  v  v v  i- 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_81282112_8   1258 AAGGA-AACCTACAAAATCAGAGAAGATATTTGCAAGTCATTGGTGTGAG 1306
                           i  -    i   i   vi     i          i    vvi v   v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_81282112_8   1307 AAGGGGTTAATATTCAGA-CATATAAGGAACTCCTACAACTCAATGGCAA 1355
                              ii vi   i    -i      i      i           iii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_81282112_8   1356 AAATGTAAA---CCTGATTAAACAATAAGGAAATAATCTGAATAGAAATT 1402
                            vii   ---  ii   ?  v   ii v   vi  i        v   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_81282112_8   1403 TCTCTAAAGAAGACATGCAAATGACCAGCAGGTATGTAAAAACATTGTTC 1452
                             i        i  i      i   ii i i ii i    v  - i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTC 893

  chrX_81282112_8   1453 AACATTGCTAAACAA 1467
                              ii????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.20 (18 / 15)  


2298 28.06 2.84 3.93  chrX_81286337_81288511.rev      771  1686 (489)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_81286337_8    771 GAAAAACATTTCATGCTCATGGATTAGAAGAATCAATGTAATGAAAATGG 820
                             i i  ii    i         i     v i   i vi v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_81286337_8    821 CCATACCATCCAAAGCAATGTACAAGTTCAACCCTATTTGTAACAAAATA 870
                          v    ivi     vii  v    ii      v v  iiv  v      v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_81286337_8    871 CAAA-TGTCATTCTT-CAAGAATTAGTAAAATAACAATTCTAAAATTTAT 918
                          v i-  i v  i  -  ii    iii  iv i --- i        i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA---TCCTAAAATTCAT 149

  chrX_81286337_8    919 ATGGTAACATAAAGGAGCTCAAGTAGCCAAAGCAATCCTAAGCAAAAAGA 968
                             v  iii  i   v ivi i        i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_81286337_8    969 ACAAAATCATAAGCATCGGACTCTTTTATTTCATACTATACTATAAGGCT 1018
                              i iiv i vv  iv   iiiiv      v viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_81286337_8   1019 ATAGTAACCAAAAGAGCATGGTTCTGGTACAAAAAGAGACAT-T-GAGTA 1066
                          i     i   i v  ii    v    i i  ii v      - -  vi 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_81286337_8   1067 ATGGAATAGAACTGAAAACTCAGAAATAAACCTACACACTTACAACCATC 1116
                                    i   i iii            i i   i   iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_81286337_8   1117 TGATCTTCAACAAGGCTGACAAAAACAAACAATGGGAAAAGGACTCCCTA 1166
                             i   i      v  v   i v  vv       i    i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_81286337_8   1167 TTCAA---ATGGTGCTCAGTTAACTGGCTAGCTATATGCAGCAGAATGAA 1213
                              ---        vi vi      v  ? i i     iv        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_81286337_8   1214 ACTAGACCCTTACC-------ATAAACAAAAATTAACTCAAA-TGTATTA 1255
                         ii i     i    -------   v                 -  v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_81286337_8   1256 AATATTTAGGTGTAACACCTGCAACCATAAGAATCTTAGAAGACAAAGTA 1305
                         ? v ii  ii     v v  iv   i    i v          v  vi  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_81286337_8   1306 GG---AAATACCTTTCTAAGCATTGGCCTTTGCAAATAATTAATT-TATA 1351
                           ---    --   iv i v -    vi vv    - ii  vv  -v   
  L1M4_orf2#LINE/    550 GGNGTAAAT--CTTCGTGACC-TTGGGTTAGGCAA-TGGTTTCTTAGATA 595

  chrX_81286337_8   1352 AGTCCCCCAAACCAATTGCAACAAAAACAAAAATTGACAAGGGGAACTTA 1401
                         v v v  v   v  vvv         iv      v  i  ivv i    v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_81286337_8   1402 ATTAAACTAATGAGTTTCCACATAGCAAGGGAAACTATATATTGAGTAAA 1451
                           i   v v vi ii  iiiiiivv   i   v     ------------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT------------ 683

  chrX_81286337_8   1452 CAGACAATCTAAAAAATAGGTGAGTAAATAGACAACCTAAAAAATAGGAG 1501
                         ---------i  i   -------  i  v        i v i   i    
  L1M4_orf2#LINE/    684 ---------CAAGAAA-------GTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_81286337_8   1502 AAAATACTCACAAACTGTGCATCTTACAGAGGTCTAATATCCAGAATATA 1551
                               i ii    iii ii    v i ii  v  vi             
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_81286337_8   1552 TATGGAATTTAAACAA----ATAAGCAAAACACAAATAACTCCATT-AAA 1596
                           vi   i ivv    ----    vv    v         i v   -   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_81286337_8   1597 AATACACAAAAGATATGAACAGACACTTCTCAAAAGATGACATGCAAGCA 1646
                            ivi    i   v    i     i     v     v  i  i   iii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_81286337_8   1647 GCCAACA--CACATGAAAAAAATGCTCATCATTTCTAATCAT 1686
                              i --          i -      v   iv????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (157 / 98)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 3.26 (62 / 19)  


1598 26.30 4.08 4.36  chrX_81311725_81313390.rev      465  1175 (491)    L1M4_orf2#LINE/L1      200   908 (0)  

  chrX_81311725_8    465 ATAAAGCCTGAAGTACCTATATAT---AAATTCAGAAA--AATATACAGC 509
                          i    i-  i  v  ii i iv ---  v    i  v-- v  i v   
  L1M4_orf2#LINE/    200 ACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_81311725_8    510 TACAATAGTAAAAA-AGCA--GCATTGGTAAAAGATTAGACACATAGGTC 556
                             i  i v  i -  ii-- i i   i v   iv      i    i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_81311725_8    557 AATGAATCAGAATAGAGAGCTCAGAAATAGGCCCACAAAAATATAGTCAG 606
                             i vi     v     ii        ii    i v vv   i    i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_81311725_8    607 CTGATTTTTTTTTACAAAGATGCAAAAGCAATTCAACAGAGAAAGAATAG 656
                         i       iv---    i i   v  ii v      ii i          
  L1M4_orf2#LINE/    349 TTGATTTTCG---ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_81311725_8    657 TCTT----ATAAACTTTGACGCCAA-ACAACTGGACTTTGATATACAAAA 701
                             ---- i   ---  ii  iii-         iv?iv i  i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAA---TGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_81311725_8    702 ATATAAACCTCGACACGTACCTCACACTTTATACAAAAAATGAC-CAAAA 750
                         iv  i  vi v   v v          iv          v i  -     
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_81311725_8    751 TGGATCATAGACC-GAATTTAAAATTTTAAAATATAAACCTTTTATAACA 799
                                ?     -i   v   i vi v   v      v  i   v  v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_81311725_8    800 AAA-ATAGAAAAAAATCGCCATGATTTAAAGCTCTGTAATGTTTATCC-- 846
                            -    i?iv     vi i   ii vii i vv i    v  -  i--
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTA 591

  chrX_81311725_8    847 -ATACAACACCAAAA-CATAATTCATTAAAGAAATC-TCG-TAAATTGGT 892
                         -   ii         -  i  viv iv       vv- v -        v
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_81311725_8    893 CTCCATCAAAATTAACATCTTTTGCTCTATGAAAAAATCCTATAAAAAGA 942
                           i            v v      iv  - v   ii iv    v  i i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAA 690

  chrX_81311725_8    943 ATAAAAGGACAAACCACAGACTATGATACAATATTTGTAAATTATATTTC 992
                         i i   i     v       v iv  v v        i    i    v  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_81311725_8    993 AAATTTATTTAAAGAGGAGTTAGA--AAGAATGCATAAATAACATTTGAA 1040
                         vi  -------   -   v  iv --v     ii     v   vi  -- 
  L1M4_orf2#LINE/    741 TGAT-------AAG-GGACTTGTATCCAGAATATATAAAGAACTCTT--A 780

  chrX_81311725_8   1041 TGCCTCAATAATTTTAAAAAGGCAA----TGCAAT-AACAACTGAGCGAA 1085
                         iiv         ---      i   ----iv    -? v  v  i  i  
  L1M4_orf2#LINE/    781 CAACTCAATAAT---AAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_81311725_8   1086 GTATTTGGACAATCCCCTCACCAAAGAATATATATGAGATAAATGGATGG 1135
                          v     i i iv vii  v        v     ii ---------    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAA---------ATGG 868

  chrX_81311725_8   1136 CAAATAAGCATATGGAAAGATGTTCAACGTTATTTATTAT 1175
                          v        i   i       i     i i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (109 / 74)
Gap_init rate = 0.04 (26 / 709), avg. gap size = 2.31 (60 / 26)  


2467 28.10 4.36 1.61  chrX_81315828_81319914.rev     2731  3602 (485)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_81315828_8   2731 CCATGTTCATGGATAGAAA----TAATATTGTTAAAATGGACATACTACT 2776
                                       v i  ----            i    vv     v i
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_81315828_8   2777 GAAAGTAATTTACAGATTTAATGCTCTTCCTATTAAA---CTAACTCTGA 2823
                         v   v i  i        i  i  vv i     i   --- i i  ---i
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT---G 109

  chrX_81315828_8   2824 TATTCTTTGCAAAATTAGAAAAAAGAGCT-ATTTAAAAATTCACATGGAA 2872
                         iv  i      i  v v  v  ----   -  iiv        i      
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAA----GCTGATCCTAAAATTCATATGGAA 155

  chrX_81315828_8   2873 CCAAAAAAAGCCTA-AATAGCCAAGGTAATTCTAAGCATAAAGAACAAAG 2921
                         viiv  iiii  i -         iii   ii i iv vi          
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_81315828_8   2922 CCGGAGGCATAACATCATCAAAATTCCAATTTGTAGTACAAGGCTGCATT 2971
                         ii     vv v   - v  vv    i   vviv  v     i   i  v 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACA-CTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_81315828_8   2972 AACCAATATAGCATGGCACTGGTACAAAAACAGACACATAGGCCAATAGA 3021
                           i   v i  ii   i     i i  ii i     i    ii    i  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_81315828_8   3022 GCAGAATAGAGAGGCCAGAAATAAAGCTGCACACCTACAACCA-TCAATC 3070
                         ii     v     v           v iii   ii  iiii  - ii  i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_81315828_8   3071 TTTGACAACGTTGACACAAGCAGTCAACGAGGAAAAGATTGCCTGTTCAA 3120
                           i     v v  v  vi v  v    i i     ii  v i  v     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_81315828_8   3121 TGAATGGTGCTGAGATAACTGGATAGCAATATGCAGAAGATTTACACTGG 3170
                         ii          i  i         ? v i     i    v v vii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_81315828_8   3171 ATTCCTTTCTTACACCATATACAGAAATCAACTCAAGATAGATTAAAGAC 3220
                          ii   vi  i            i    i       i  i   i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_81315828_8   3221 TTTAATATAAGACCTAAAACTATTAAAACCCT-GGAAGGTAACCTAGG-- 3267
                         i v   i     v          -     i  -i    iv   v    --
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_81315828_8   3268 -AAATACCATTCAAAACAT--AATCTGGCAAAGATTTTATAAAGGCAGTG 3314
                         -    -- -   ivi  v --ii iv     v i   iv  i viiiiii
  L1M4_orf2#LINE/    554 TAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_81315828_8   3315 CCATAAACAACAGCAACAAAAACAAAAATTGACAAGTGGGACCTAATTAT 3364
                            v  i  vv          iv      v  i  i v    i v  i v
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_81315828_8   3365 ACTAAATAGCTTCTGCACAGCAAAAGAAACTATCAATAGAGTAAA----C 3410
                          v v  v i   i  ii vv    i  v        v i   i  ---- 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_81315828_8   3411 AACCTAAAGAATGGAAGAAAATATTTGCAAACTATGCATTCAACAATGAT 3460
                             i v       i                ii  ii  iii i  v iv
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_81315828_8   3461 CTAATATTCATAATCTATAAGAAACTTAAACAAATTAACAAGGAAAAC-C 3509
                           vi   i  v   v     ii    ivv    v i  i  vi    v- 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_81315828_8   3510 ATAGAACTCCATTAAATAGTGGACAAAGGACATGAACAGACAT------- 3552
                          v v   i v   ?  v i   i       iv    i      -------
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_81315828_8   3553 ----------ACATGTAGCCAATAAGCACAAGAAAAAAAATACTCAATAT 3592
                         ----------   vi i             v     i -- i     i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGCTCAACAT 898

  chrX_81315828_8   3593 TGTTAACCAT 3602
                         ii????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.75 (154 / 88)
Gap_init rate = 0.02 (18 / 896), avg. gap size = 2.89 (52 / 18)  


2681 26.40 1.91 1.91  chrX_81331295_81333177.rev      503  1392 (491)    L1M4_orf2#LINE/L1       19   908 (0)  

  chrX_81331295_8    503 TCATGGATCGGAAGAATCAATATCTTGAAAATGGCCATACTGCCCAAAGT 552
                                 i      v i     iv v  i     v     v      v 
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chrX_81331295_8    553 ACATTT-TAGATTCCATGCTATTCCCATTAAAATGCCATTGACATTCTTC 601
                         i-  i -i      v i  v  i  i  i     v   vivi v  i  i
  L1M4_orf2#LINE/     69 G-ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_81331295_8    602 ACAGAA-TTAAAAAAAAAACT-ACGTTAAAATTCATATGAAACCAAAAAA 649
                         i     -  i v  i----  - ivi             i  -- viv  
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAG----CTGATCCTAAAATTCATATGGAA--ATGCAA 161

  chrX_81331295_8    650 AGAGCCCATG-TAACCAAGACAATCATAAGCAAAAAGAACAAAGCTGGAG 698
                         i ii    vi-  i    i      v i iv  i          i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_81331295_8    699 GCCTCACACTACCCAATTTCAAATTATACTATAAGGCTACAGTAACCAAA 748
                          v        v            viv     i  i          i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_81331295_8    749 ACACCATGGTACTGGTACAAGAACAGACACATAGACCAATGGAAAAGAAT 798
                            vii         i i   i i     i     i        v     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_81331295_8    799 AGAGTACTCAGAAATAAGACCATACACCTACAACTATCTGATCTTTGACA 848
                         v   viii         iv       ii  iiiii vi    i  i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_81331295_8    849 AACCTGACAAAAACAAGCAATGGGGAAA---TGGCTTCTTATTTAATAAA 895
                          ivv  v   i v  vv           --- i --    -  i  i   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAG--TCTT-TTCAACAAA 408

  chrX_81331295_8    896 TGGGGCTGGAAGAACAGGCTAGCCCTATGCAGAAAATTGAAAATGGAACT 945
                            v     i v   v  v  ?  vi     i  i v    iv    v i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_81331295_8    946 ATTTCTTACACCATATACAAAGATTAACCCAAGATGGATTAAAGACTTAA 995
                         v vi  i              i      i   i      i ?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_81331295_8    996 ATGTAAAACCCAAAACAATAAAA-TCCTAGACGAAAATTTAG-TGCAACA 1043
                               i v i     v      -  i    v     iv   -? i  - 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-A 557

  chrX_81331295_8   1044 CTATTCAGGACATAGGCATGGGCAAATATTT------TATGACGAAAAGC 1087
                         - v   iv   v v  vv i     vvi   ------      i----- 
  L1M4_orf2#LINE/    558 -TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA-----C 601

  chrX_81331295_8   1088 CAAAAGCAATTGCAATGAAAGCAAAAATTGTCAAATGGGATCTAATTAAA 1137
                                 vvv    ii    v      v vi    v   ii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_81331295_8   1138 CTAAAGAGCTTCTGCACATCAAAAGAAACTATTATCAGAATGAACAAACA 1187
                         v v  i i   i  ii v     i  v     i vv i i    v i   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_81331295_8   1188 ACCTACAGAATCAGAGAACATTTTTGCAA-TCTTTCCACTGACAAAGGTC 1236
                            i       vi     v  v       -  v vivv    i  i  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_81331295_8   1237 TAATATCCAGATTCTACAAATAACTTAAACAGATTTACAAGAAAAAAACA 1286
                          vi        v v  i   v    ivv   iv iv i  v     i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_81331295_8   1287 AACAACCCCATAAAAAAA-GGGCAAAGTACATGAACAGATGCTCCTCAAA 1335
                           i     v  v?     -        v iv    i   iii i   v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_81331295_8   1336 AGGCGACATTCATGCAGCCAACAAATATATGAAAACAAGCTTACCATCAT 1385
                           iv  i  v  viii     i  ii i       v v   i v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_81331295_8   1386 TGATCAT 1392
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.31 (131 / 100)
Gap_init rate = 0.02 (18 / 890), avg. gap size = 1.89 (34 / 18)  


2361 25.70 2.93 4.45  chrX_81344553_81346522      556  1477 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81344553_8    556 TGGAAATA-ATCCTTGTGTTTGTAGATTGGAATAATTGATGTCAGAATGT 604
                               v -    i-i    ii i        v v  i  i -----   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCC-ATGTTCATGGATTGGAAGACTTAATAT-----TGT 44

  chrX_81344553_8    605 CTATATGTCCATACTACACAGAGTGATATACAGATTCAACACCATGTCTA 654
                         iv v   v v     v v  i v    v            i v  vi   
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chrX_81344553_8    655 TGAAATTTACAA-TGACATTTTAACAGAAA--AACAGA--AATTCTAAAA 699
                          v   v iv  i-  v v    vi      --i   ii--i  i      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_81344553_8    700 TGAATGTAAAACCACAGAATTCCTAACATATCTTAAGGAA-CTTAAGAAT 748
                          vv  i ii  vii  iiivv  i iv   v iv  iv  -   i i  v
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_81344553_8    749 TAAAAATAAAGTTCTAGGCATCACACTTCCTGATTTTAAATTATATTATA 798
                         v  i  i      vv   vv          ii    i   viv  i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_81344553_8    799 AAGCTATATTATCAACAATTTAAACAAAAACTATGCTAGTTGCATAAAAA 848
                               ------  ii   iv i   i---- i  v  v v      ii 
  L1M4_orf2#LINE/    245 AAGCTA------CAGTAATCAAGACAG----TGTGGTACTGGCATAAGGA 284

  chrX_81344553_8    849 TAGGCATATAGACCAATGAAACAGGATTGAGAGGCCAGAAATAAACTCAA 898
                            i        i     i  i  i        v            i  v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_81344553_8    899 AAATAAATGCTCAGCTACTTTTC-ACAAGCCATGAGG--AAGACC---CA 942
                          v  vv   v   ii iv     -     ---- iv --      ---  
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAG----GGTGCCAAGACCATTCA 380

  chrX_81344553_8    943 ATAAAGAAATGTTAGTCTCTTAAATAAATGATGCTGACAAAACCGGATAT 992
                           iii    viv      i  v  i     i     iv v   i     ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_81344553_8    993 CCACATGCAAAAGAATGACACTGG-CTTGTATATTACACTATACATAAAA 1041
                                           vii   - iiv  iv i    i   i i    
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_81344553_8   1042 ATTAACTTAAAGTGGATTAAAGATGTAAACATAAAACCTTAAAGGATAAC 1091
                                i   i     i ?   iv    ii   i v  v   vv    v
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_81344553_8   1092 ACTCGTAAAAGAAAACACAGCGGGAAATCTTCTTGGTGTCAGCGTT-GGC 1140
                             v  i         i  v? v        v  iiv ii -   -   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGC 579

  chrX_81344553_8   1141 AATGATTTTTCACATACCACACCAAAAGTTCAGGGAACAAAAGTAAAAAT 1190
                             i   i i v   iv          iv  i v        v      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_81344553_8   1191 AAACAAGTGAAATTGCATCAAC-TTGAAAA-------GCTTCAGAA-ACA 1231
                          i i  i vii i v      v-  i    -------      i i-   
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_81344553_8   1232 CTATAACAAAAAATATGAAAAAAACAAAAGGCAGCCTATGCATTGGGAGA 1281
                             --   i   -i      i --------  i  i iiv v       
  L1M4_orf2#LINE/    680 CTAT--CAAGAAA-GTGAAAAGA--------CAACCCACAGAATGGGAGA 718

  chrX_81344553_8   1282 AAATATTTGCAG-TCATAGATATACTAATGTGTTAATATCCAAAATCAT- 1329
                                    i-     v  v iv   v vii vi      i   -  -
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT-ATA 767

  chrX_81344553_8   1330 TAACAAAATTATACGAATCAATGGGAAAATATAACAAATA-CACAAATTT 1378
                            vi  v iv   i v     iiv    - -i       - v   --  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAA-A-GACAAATAACCCAA--TT 813

  chrX_81344553_8   1379 TAAAACCAGACATAGGGTTTGAATAGGTATTTTTTTTCCAATGAAGACAC 1428
                         ?    vii i  v   i         ii    i ---    v     i i
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCT---CCAAAGAAGATAT 860

  chrX_81344553_8   1429 AAAAAATGGCCAAAAGATACATGGAAAGATGATGAACATCACTTACCAT 1477
                          v   -       v iii     i       v v       ????????
  L1M4_orf2#LINE/    861 ACAAA-TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 2.19 (68 / 31)  


 884 29.94 1.91 0.96  chrX_81359660_81365102     3803  4116 (1327)    L1M4_orf2#LINE/L1        1   317 (591)  

  chrX_81359660_8   3803 TAGAAAAACATTCCAAGCTCATGGACAAGAAAAATCCATGTTGTTAAAAT 3852
                          i    i i  i   v i       ivi   i v iv  i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81359660_8   3853 TACCATACTGCCAAAAGCAAT-TACAGACTCAATGCTATTCCTATGAATC 3901
                         vi v     v  v   vii  -      i    i  v  i     v  vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81359660_8   3902 TTCCAA-TGTCATTTTTCAAAGAATTAGAAAAAAAAATTCTAAAATTCAT 3950
                          i   i-  i v     vv ii    -  v  ivvi  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chrX_81359660_8   3951 ATGGAACCAAATAAGTG-CCCA-AATAGCCAAAGCAATCGTATGGAAATA 3998
                               -- vii   v -    -          i     v ivii  iv 
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_81359660_8   3999 GAATAAAGTCACAAGTATTATATTACCTGATATCAAACTGCACTATAAGG 4048
                            i     iiv i vv i i i v  ii  v     vivi    i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_81359660_8   4049 CTAGAGTAATTAAAATAGCATGGTATTAGTACAAAAACAGACACATAGAC 4098
                            v      i  i i  ii     i i i i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_81359660_8   4099 CAACGGAACAAAA--GAGAG 4116
                            i    i i  --     
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAG 317

Transitions / transversions = 1.94 (62 / 32)
Gap_init rate = 0.02 (7 / 317), avg. gap size = 1.29 (9 / 7)  

 926 28.63 17.25 0.59  chrX_81359660_81365102     4441  4950 (493)    L1M4_orf2#LINE/L1      314   908 (0)  

  chrX_81359660_8   4441 AGAACCTGGAAATAAAGCCATACATGTAAAACCACTTGATTTTTGACAAA 4490
                            ii ii        v        v  viii  v        i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_81359660_8   4491 GTTGACAATAACAAACAATAGAGAAAGGACTCACCATTAAATAAATGGTT 4540
                          v  v   v v  vv    i i     i ivvv iv  v  i       v
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_81359660_8   4541 CTTGGATAACTGATCAGTGATGTGCAGGAGATTGAAACTGGCACCCTTCC 4590
                           v   i     ivi ?iv ii    ii   v    ii   vv    v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_81359660_8   4591 TTTTACCATCTACATAAATTT-TTC----TGGAC-----ATC-------- 4622
                          ivi     v    v     v-i  ----    i----- i --------
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_81359660_8   4623 --AGC---------------CTTGGA----------GATGCA----TTTA 4641
                         --   ---------------   i  ---------- i? i ----  ii
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_81359660_8   4642 TGAC--TAGGT------------------------CCCCAAAAGCAATTG 4665
                             -- i   ------------------------ v         vvv 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_81359660_8   4666 CAACACAC-AGAAAATTGTCACAAATATGGATATAATTAAACTAAAGAGC 4714
                              v v- i     v -- i    -    iv v  i   v v  i i 
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAG--ATAAAT-TGGACTTCATCAAAATTAAAAAC 660

  chrX_81359660_8   4715 TTCTG------AAA----ACTATACACAAAGCAAACAGGAAGCCTACAGA 4754
                           i  ------   ----     vv v    ii  v  iv i  i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_81359660_8   4755 GTGGGATAAGTTATTTGCAAACTATGCATCTAACAAAAGCCTATTATCCA 4804
                         i     v  iv          ii  ii    i i  ii v  vv      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_81359660_8   4805 GAATTTGTAAGCTACTTAAACAAATCACCAAGCAAAAAACAAATAAATCA 4854
                             v i   ivv   ivv    v   vi  vv    i        vi  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_81359660_8   4855 GTTTAAAAATGGGCAAAGAACATTAAAAGACCATTCT--AAAAACGATAT 4902
                         i  ?              i iv v  v    vv    --   i v     
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_81359660_8   4903 TCATGTGGTCCACAAATATATGAAAAAATGCTCATCATCACAAATCCT 4950
                         v  vi   i v i  ii i       i       v     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (75 / 68)
Gap_init rate = 0.03 (15 / 595), avg. gap size = 6.07 (91 / 15)  


1781 27.14 4.22 5.67  chrX_81383095_81390214      500  1328 (5792)  C L1M4_orf2#LINE/L1   (43)   865    49  

C chrX_81383095_8   1328 ATGCCAATTCTTCTCAAATTGATTCATAGGTTTAATTAAATTCTCATCAA 1279
                            v    v  i i         ii i  i  i  ivv   i ii     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

C chrX_81383095_8   1278 AA--CTAACAAAGACTTTTGTAGACATAGACAAACT---TCTAACATTTA 1234
                           -- i i vivvvi     i   v  v     i  ---i    v   i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

C chrX_81383095_8   1233 TAAGAAAAGTTTTAGGCATT-AGGATAGTCAAAAACATTTTTAAAAAGAA 1185
                           v i   - viv   v ii-  i    i     vv  i  v        
  L1M4_orf2#LINE/    149 TATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chrX_81383095_8   1184 CAATATAGTCAGAAGAATCACTCCACTAGATAGTAAATCCTTCTATATAG 1135
                         v  i v   ii  i  v    v iv ivi  vvi   v i v   i v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chrX_81383095_8   1134 TTAGGCTAATTAAGATAGTGTGATATTGGTGGAGAAATAGTCACAAAAAT 1085
                         i  viv    i    i      i  i   iiv iii    v  i v i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chrX_81383095_8   1084 CAATGAAACAGAGATATCAATGGAACCGAGTAAAAAAGCCAGAAACAGAT 1035
                              i  i   -------  v  ---    -------       i i i
  L1M4_orf2#LINE/    298 CAATGGAATAGA-------ATTGA---GAGT-------CCAGAAATAAAC 330

C chrX_81383095_8   1034 TCATAGAA--ATACTCAACTGATTTGTGGCAAAGGT-TTAGAATCAACAC 988
                         i    v v--  iv    i      vi i   i   -ii ii i  vi- 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT-C 379

C chrX_81383095_8    987 AATGGAGAAAGTGTAGACTTTTCAACAAATGGGACTAGGGCAATTGGCCA 938
                              i     vi   v               vi  i  i   i   vi 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

C chrX_81383095_8    937 TCCATAGGCAAAACAAACAAACAAACAAAAAGTCATAAACTTTGACCTAA 888
                         ?   i v      v  ------------------- i  v  v    ivv
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAA-------------------TGAAGTTGGACCCCT 460

C chrX_81383095_8    887 GTCTCACATTTTTTACAAAAAATAACTTAAACTAGATCACA--CATGAAT 840
                         ii      iiv v        v     i   v i     ? -- v i   
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

C chrX_81383095_8    839 ATAA----TA---CTATAAAACTTATTTTGAAATAAATGAGATAAATTTA 797
                         i   ----  ---          i--  v   iv   i---   ii?v  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTC--TTAGAAGAAAAC---ATAGGNGTA 555

C chrX_81383095_8    796 AATTTTTAATG--CTTAGG--AG--AATAGTTTTTT-GACTTAATACCAA 754
                            i  ii-  --   i  --  --   i    i  -  iv i i     
  L1M4_orf2#LINE/    556 AATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

C chrX_81383095_8    753 AAGTAAAACCCTATTAATGAAA-----GTTATATTTTATCCCACAAAAAT 709
                            i v  v v- iv  v    ----- v  v   vv iii  iv     
  L1M4_orf2#LINE/    605 AAGCACAAGCA-ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

C chrX_81383095_8    708 TAAAAACATT-GTTCTGTAAAAGACTCTATGAAGAGGATGAAAAGACAAG 660
                                v  -  v  vi   i   v    v    iii           v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

C chrX_81383095_8    659 ATACAGACTGGGAGAAAATATTTGGAAATCACATATCCAACAAAGAA--T 612
                         vi     v                v      i     ii i  i i -- 
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

C chrX_81383095_8    611 GATTATCTAGAGTGTATAAA-AAGTCTCAAAACTCAACAGTTTAAA-ACA 564
                          --    i   i i      -  v   i v       i i vv   -   
  L1M4_orf2#LINE/    754 G--TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

C chrX_81383095_8    563 AACAATCCAATTACAAAATGAGCAAGAGTCATGAAGAGACATTTCACTTA 514
                           i  i      ?v      i    ii viv    v         v iv 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

C chrX_81383095_8    513 AGAGTGTGTACAAA 500
                            ivi i      
  L1M4_orf2#LINE/    852 AGAAGATATACAAA 865

Transitions / transversions = 1.48 (132 / 89)
Gap_init rate = 0.03 (28 / 817), avg. gap size = 2.93 (82 / 28)  

2642 27.12 6.29 0.58  chrX_81383095_81390214     1731  2589 (4531)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_81383095_8   2589 TGTAAAGATATTCCATGTTCATGGATTGGAAG------------------ 2558
                           v        i                    ------------------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_81383095_8   2557 -----------------CGATCTAAAGATTCAATGCAATCCCCATCAAAA 2525
                         -----------------i      v        i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_81383095_8   2524 TACAAATGATTTTCCTCACAGAAATAGAAAAGC-AATCCTAAAATTTATA 2476
                          v v iiviii  ii ii       v  v    -i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chrX_81383095_8   2475 TGGCACCACAACAGACCCAGAGTAGCCAAGGGTATCTTGAACAAAGAGAA 2426
                            v vii   vi        i       iivv        v  ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chrX_81383095_8   2425 CAAAATGGGCAAAATTACATTACCTGACTTCAAATTATACTACAAAGCTA 2376
                             i v  vii v i   i v  ii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chrX_81383095_8   2375 TAGGAAAAAAAAAAGCAGCACAGTACTGGCATAAAATACAGACGCATAGG 2326
                         i  v  vv  i ---   iiii            ii- i    ii    i
  L1M4_orf2#LINE/    251 CAGTAATCAAGA---CAGTGTGGTACTGGCATAAGG-ATAGACATATAGA 296

C chrX_81383095_8   2325 CCAGTTAAACAAAATAGACAGCCCAGAAATAAGTCCACACACCTAGAGTG 2276
                         i  i vi  i i   v  v  i          ii   i   ii  vi  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

C chrX_81383095_8   2275 AACTCATTTTCAAAAAAGGTGCCAAGAACACACACTGGGGAAAAGACAAT 2226
                           i v      i v  i          v  iv  v        ii i i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_81383095_8   2225 TTTTTCAATCAGTGGTTCTGGGAATATTGAATATCCACATGCAGGTTTAT 2176
                         i       iv i    v      vv i  i   ?         iivvv  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_81383095_8   2175 GAAATTAGACGATTATCCTTTGCCATACAGAAAAATCAAGTCGAAATGAA 2126
                            i  i   vvi  i iivii     i v      i  v  i     i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_81383095_8   2125 TTAAAGACTTAAATATAAGACGTCAAACTATGAAACTATTAAAAGAAAAC 2076
                          i ?    i     i     vv v       i     v   i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_81383095_8   2075 ATGGGACAAATTCTCTAAGAA-TTGGTCTTGGCAAAAATTTATTGAGTAA 2027
                           i  ?vv  v   iiiv  v-    vi v     vii   v  iii  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_81383095_8   2026 TACTCCACAAGCATAGGCAACCAAAAAAAAA---GATAACTGGAATCACA 1980
                         v  v   v     i i     v   i     ---     v v i iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_81383095_8   1979 T-GAAGTTAGAAAGCTTCTGCACAGCAAATGAAGCAATCAGCAAAGTGAA 1931
                          -i  i   i   -   i  ii vv    v  vi v    iv        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chrX_81383095_8   1930 GAAACAACCAACAGAACTGGAAAAAAAATT-GCAAACTACCTATCTGACA 1882
                         i i      v      iv   i    v   -     ii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chrX_81383095_8   1881 AGGGACTAATAACCAGAATGTATAAGCAGCTCAAACAAATCTATGGCAAT 1832
                                vi  v       i     iv i   vv    v  v  iii  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chrX_81383095_8   1831 AAATCTAATAATCCAATTCAAAA-TGAGTAAAATATCTGAATAGGTATTT 1783
                           iv v     i      ?    -  i i   iv  i       ii    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chrX_81383095_8   1782 CTCAAAAGAAGA----CAAACAG-------GCACATGAAAAGGTGATTAA 1744
                            v        ----    ii -------            i  v i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chrX_81383095_8   1743 AGTCACTGATCAT 1731
                         vi   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 4.92 (59 / 12)  

2788 27.99 1.11 0.66  chrX_81383095_81390214     5724  6627 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81383095_8   5724 TGGAAAAACATTCCATGCTCAAAGATAATAAGAATCAATATTGTGAAAAT 5773
                               i i  i     i   vi   viv    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81383095_8   5774 GGCCCTACCACCCAAAGTAATTTATAGATTCAATGTTATTCCCATCAAAC 5823
                            vv   iv      v i  i  i        i iv  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81383095_8   5824 TACCATTGATATTCTTCACAGA--TTTAGAATAAACT-ACTTTAAATTTC 5870
                          v   viviiv  i  ii    --  ---i i  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chrX_81383095_8   5871 ATATGGAACAAAAAAGAGCTCATA-TAGCCAAAACAATCCTAAGCAACAA 5919
                                 vviv  i ii i  v -              i i iv  v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_81383095_8   5920 GAACAAAGCTGGAGACATCACACTACCTGACTTCAAGCTATACTACAATG 5969
                                 i     ivv       v  ii i     iviv        v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_81383095_8   5970 CTACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGACATATAGAT 6019
                                  i   i    ii         i  v ii i            
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_81383095_8   6020 GAATGGAACAGAACAGAAACCTCAGAAATGACACCACACATCTACAACCA 6069
                         v       i    iv  i vii       i vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_81383095_8   6070 TATGATCTTCAACAAACCTGACAAAAACAAGAAATAGGGAAAGGATTTCC 6119
                         vv    i   i    ivv  v   i v  vvv   i       i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_81383095_8   6120 TATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGGAGAAAACTC 6169
                          v  i  i              v      v  ?   i   v i  i v v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_81383095_8   6170 AAACTGTACCCCTTCATTACAACTTATGCAAAAATTAACTCAAGATGGAT 6219
                           ii  v      v v i   v v   i               i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_81383095_8   6220 TAAAGACTTAAATTTAAAACCCAAAACCATAAAAACCCTAGAAGAATACC 6269
                         i ?    i     v   i v i     i      vi i        v  v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_81383095_8   6270 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACAAA 6318
                             ?i- v i -   iv   v v  vv i     v ii   v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_81383095_8   6319 AACACCAAAAGCAATTTCAACAAA-GCCAAAATTGACAAATGGGATCTAA 6367
                         i            vvvv       - vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_81383095_8   6368 CTGAACTAAAGAGCTTCTGCAAAGCAAAAGAAGCAATCATCAGAGTAAAC 6417
                         iii  v v  i i   i  iivvv    i  vi v    vv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_81383095_8   6418 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 6467
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_81383095_8   6468 AGGGCTAATATCCAGAATCTACAAGGA--TCTTAAATAAATTTACAAGAA 6515
                         i  i  vi          v  i  i  --     --i  v iv i  v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAA 794

  chrX_81383095_8   6516 AAAAA-AAACAACCCCATTAAAAAGTGGGCAAATAATATGAACAGATACT 6564
                            i -   i     v   ?    i        vi  v    i   i i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_81383095_8   6565 TCTCAAAAGAAGACATTTATGTGGCCAACAAACATATTAAAAAA-ACTCA 6613
                             v        i  vi vi       i  i  i  v    i -i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_81383095_8   6614 TCATCACTGATTAT 6627
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (142 / 107)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


2777 27.62 2.23 1.11  chrX_81413671_81416889     1829  2726 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81413671_8   1829 TGGAACGACATCCTATGCTCATTGATGGAAAGAATTAACATCATTAAAAT 1878
                              v  i    i   i    v   v i    v    i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81413671_8   1879 GACCATACTACCCAAAGCAATCTACACATTCCATGCAATCTCTATCAAAT 1928
                          i v     v      vii       v    v i      i        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81413671_8   1929 TACCAA-TGTCATTTTTTCACAGATATAACAAAAATGATCCTAAAATGTC 1977
                          v   i-  i v     v  v i  - i    iv-            viv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGC-TGATCCTAAAATTCA 148

  chrX_81413671_8   1978 TATGGAACAAAAGAAGAGCCTGAATACCCAAAGCAATCTTGAGCAAAAAT 2027
                                vviv iii  v  v     v     i         iv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_81413671_8   2028 AACAAAGCTGGAGGCATCATACTACCTGACTTCAAAATATATTACAAGTC 2077
                                i      vv   i   v  ii i       iv  i     iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_81413671_8   2078 TA-GGTAACAAAAACATCAAGGCATTGGTATGAACACAAAAACATAAACC 2126
                           -i    iv  i   viiv  i i   i  i iv i i v i   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_81413671_8   2127 AGTGGAACAGAAAACAGAATACAGATATAAATCCACATATTTCCAGACAG 2176
                          i     i    vvv   i v    v     i   i i    vii v  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_81413671_8   2177 TTGAATTTTGACAAAGACAACAAGAATATACATTGGGGAAAGGACACCCT 2226
                             v   i     i iiiv     vi  v  v         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_81413671_8   2227 GTACAATAAACAATGCTGAAAAAAGTGGATAACCATATGCAGAAAAATAA 2276
                         v v   i   iii     ii v  v      ?   i     i  i   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_81413671_8   2277 ACGTGGACCCTTTTCTTTTATTATATACAAAAAGTAATCCAAGATTGATT 2326
                          vv       i vi  ivi ii           v   ii   i  v   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_81413671_8   2327 AAAGACTTAAACATGAAACCTGAAACTATAAAACTACCAGAAGGAAACA- 2375
                          ?    i    ii i i v  i             vii     i     -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_81413671_8   2376 ----------CTTCAGGACATTGGTTTAGGCAAAGATTTTATGGCCATGA 2415
                         ----------    iv   v    v        v i   iv i vi    
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_81413671_8   2416 ACTCGAAAGCACAGGCAACAAAAACCAAAGTAGACTAATGGGACTCTATT 2465
                         vvi i        i         ivv   i    iv   v     ii  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_81413671_8   2466 AAACTAAAAAGCTTCTATACAAAT--AAAGTAAATAAACAACACAGTAAA 2513
                            v v    i   i i i --- --    v v iv v   v v   i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGC---TTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_81413671_8   2514 GAGACAACCTGTGAAATGATAGAAATT-TTTACAAACTATTCATCTGACA 2562
                         i        iiiii    iv     v -   i    ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_81413671_8   2563 TGGGACTAATATTCAGAATATATAAGGAACTCAAACAACTAAACAGTATG 2612
                         v      vi   i            i      vv      v  i i  --
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA-- 793

  chrX_81413671_8   2613 AAAAATAAATAAATAATCTCATTAAAATGTGAGTAAAACACATGAATAGA 2662
                             i--- i      i iv   ?   vi  i i   iv iv        
  L1M4_orf2#LINE/    794 AAAAG---ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_81413671_8   2663 CATTTAT---AAAAAGACATACAAACAGCCAACAGGTATATAAAAA-ATG 2708
                              v ---  i    i       ii     i i i i  i    -   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_81413671_8   2709 CTCAACATTACTAATCAC 2726
                                 i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (152 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.50 (30 / 12)  


2780 27.21 1.03 1.49  chrX_81449389_81455564     4810  5680 (496)    L1M4_orf2#LINE/L1        1   867 (41)  

  chrX_81449389_8   4810 TGGAAAAATATTTCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4859
                               i    ii    i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81449389_8   4860 GGCCATCCTGCCCAAAGTAATTTGTAGATTCAATGCTATCACCATCAAGC 4909
                            v  v  v      v i  i ii        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81449389_8   4910 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ATTTTTAATTTCAT 4958
                          v   vivi i  i  ii     v v  v  i-  -  ii v  v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_81449389_8   4959 ATGGA---GCCAAAAAAAGAGCTCGTGTAGCCAAGACAATTCTAAGCAAA 5005
                              ---  ----  ii  v iv vi       i     ii i iv  i
  L1M4_orf2#LINE/    150 ATGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_81449389_8   5006 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAA 5055
                                   i      vv   ii  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_81449389_8   5056 GGCTACAGTAACCAAAAGAGCATGGTACTGGTATCAAAACTGATATATAG 5105
                         i          i   i v  ii         i  v ii iv  i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_81449389_8   5106 ACCAATGGAATGGAACAGAG-GTCTCAGAAATAACACCACACATCTACCA 5154
                          i         i   iv   -   -         vv   i    i  ivi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGG 344

  chrX_81449389_8   5155 CCATCTGATCTTTGACAAACCTGACCAAAACAAG-CAATGGGGAAATGAT 5203
                         i  vi    i  i     ivv  -    i  v v-           vi  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_81449389_8   5204 TCCCTATTTAATAAATGGTGTTGGGGAAACTCGCTAGCTTTATGCTGAAA 5253
                         vvi  v  i  i        i    iv    v v  ? ivi    vi  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_81449389_8   5254 ACTGAAACTGGACCCCTTGCTTACATGTTATACAATAATTAACTCAAGAT 5303
                          v    ii         vv  i   ivv       v           i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_81449389_8   5304 GGATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAA 5353
                             i ?    i    ii     v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_81449389_8   5354 TACCTAGGCA-ATACCATTCAGTG--CATAGGCATGGGCAAAGACTTCAT 5400
                         v  v    ?i- v i -   -   -- v i  i- i     v ii   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTC-GTGACCTTGGGT-TAGGCAATGGTTTCTT 590

  chrX_81449389_8   5401 GACTAAAACACCAAAAGCAAGGGGAACAAAAGCCAAAATTGACAAATGGG 5450
                         iiv  vi            vii v        vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_81449389_8   5451 GTCTAATTAAACTAAAGAGCATCTGCACAGCAAAACAAACTATCATCAGA 5500
                         iii v  i   v v  i i v i  ii vv    iv v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_81449389_8   5501 GTGAACAGGCAACCTACAGAAAGGGAGAAAATTTTTGCAACCTATCCATC 5550
                              v  i     i      v          v       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_81449389_8   5551 TGACAAAGGTCTAATATCCAGAACCTAAAAGAAACTTAAACAAATTTACA 5600
                            i  i  v  vi         iv  v  ii    ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_81449389_8   5601 AGAAAACACACACACACACACACATCAAAAAGTGGGTGAAGGATATGAAC 5650
                          v    - v   v i -  v  -  i?    i    ii      v    i
  L1M4_orf2#LINE/    791 ATAAAA-AGACAAATA-ACCCA-ATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_81449389_8   5651 AGACACTTCTCAAAAGAAAACATTTGAATG 5680
                              i     v      i i  vii    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATG 867

Transitions / transversions = 1.33 (133 / 100)
Gap_init rate = 0.02 (16 / 867), avg. gap size = 1.38 (22 / 16)  


2554 26.84 5.65 1.50  chrX_81466554_81470749.rev     2838  3705 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_81466554_8   2838 AAAATATAGCATGCATTCATGAATTTGAAAAATTCATATTGTT-----GG 2882
                           i    vv    --      i   v   i v  v        -----  
  L1M4_orf2#LINE/      5 AAGATATCCCATG--TTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_81466554_8   2883 T-----------------------GATTCAATACAATCCCCATCAAAATA 2909
                         i-----------------------       ii       i        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_81466554_8   2910 CCAATGGCATTTTTCACAGAAATAAAAAA----ATACTGAAATTTGTTTA 2955
                            iiv  v     ii       vi v  ----  v  i     ii v i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_81466554_8   2956 GAACAACAAATGACT-----TAGTCAAAGCAATTTTGAGCAAAGAAAAAC 3000
                            vvi   iv   i-----   i    i    i    i-      i   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAAC 201

  chrX_81466554_8   3001 AAAGCTGGAGAAATTATGCAACCTAATTTCAAAATATACTACAAAGCTAC 3050
                             i     i v i ii vv  i          iv              
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_81466554_8   3051 AGGAACCAAAACAGCATGGTACTGGCATGA----AAACATAGAAATCAGT 3096
                           v  i   i    ii            i ---- i     v i    i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_81466554_8   3097 AACATAAAATAGAGAACCAATAAATAATTTTACACATTTACAGTCAATTG 3146
                         iiv   i   v    ii v v      viii i       ii        
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_81466554_8   3147 ACTTTTCATGAAGGTGCCAAGAATACACGATGGTGAAAGTACCATTCTCT 3196
                          i   iv ii i          vi iv i    v     - vi v   i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTTT 400

  chrX_81466554_8   3197 TCAATAAATGCTACTAGGAAAATTGTATATCCACAAACAGAAGAATAACA 3246
                             i     v i  i   v  i  v   ?     vi  i      i vi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_81466554_8   3247 TAAGACTCCTATCTTTCACCATATACGAAAATCTACTAAAAATAAAATAA 3296
                          vi   i    i  iv          i     iv   v     ii vi ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_81466554_8   3297 AGCCTTAAATGTAC-ACCCAAATCTATGAAACTACTAGCAGCAAACTT-G 3344
                           v i        v- v i   v    i     vi   v  v    v - 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_81466554_8   3345 GCA-AAATCTTTGGGATACATGATTTTTGTCTGAACAATGATTTTCTGGA 3393
                          ?i-       i -------   ii  v vi iii     i   ii i  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCG-------TGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_81466554_8   3394 TATAAACTCAAATGCATGGATAATAAAAGAAAAAAACAGACAAAACACAT 3443
                            i vvi    v   iiiii  i           -i   i   viiv i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGAC 642

  chrX_81466554_8   3444 TGCATCAAACTAAAAAGCTTCTTTAGCAAAAAGAAAA--ATCCATGGCGT 3491
                          v       v v    i   i v ivivv    i v --   v viiv  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_81466554_8   3492 GAAGAGAAAAGCTACAGAATGGGAGAAAATATTTGCAAACCATACATCTA 3541
                            i   v  v i                          i    i    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_81466554_8   3542 ATAAGGGGTTAATATTCAAAATATGTAAGAAACT--TA-AACTGCTGAGC 3588
                                ii vi   i  i     i   ii    --  -    vvvv ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_81466554_8   3589 AAGAAAACATATAACCCTGTTAATAAGTCCACAAAAGGCCTAAGTAGACA 3638
                           i  i   v       vi  ? v  i vvi    i iii i i      
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_81466554_8   3639 TTTCTCAAAATAAGATATACACATTGCCAACAGGTATATGAAAAAAATGG 3688
                               v   v          v  v     i i i i       i -  v
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chrX_81466554_8   3689 TCAACATCACTAATCAT 3705
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (144 / 85)
Gap_init rate = 0.02 (17 / 904), avg. gap size = 3.65 (62 / 17)  


2775 26.56 2.90 1.56  chrX_81480085_81484373     2907  3802 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81480085_8   2907 TGAGAATATATCCCATATTCATTGGCTGAAAAGCTTAATATGTATTTAAA 2956
                           ii  v         i     v ii  i  ii        - i  -  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-TGTT-AAG 48

  chrX_81480085_8   2957 ATGTCTATACTACTGAAAGTGATTTAAAGAGTCAATGCAATTGATATTAA 3006
                            v v     v iv   v    i  v   v    i     ivv   i  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_81480085_8   3007 AATCTCAATAGCACTTTTTACAGAAATATAAAAAC-AATTCTAAGATTCA 3055
                             i  iiv  vi     i       vv v  i -i  i    i     
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_81480085_8   3056 TATGGAAA-ACAAAAGACTACAAATAGTCAAATCAATCTTGAGAAAGAA- 3103
                                 -i   ii   ivvi     i    v         i      -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_81480085_8   3104 --CAAAGCTGGGAGAATTATACTTCCTGATT-CAAAATATATTAACAAGA 3150
                         --     i   ii  v i i      ii   -     iv  i  vv   v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_81480085_8   3151 TACAGTGATGAAAACAGTGTTGTACTGGCATAAAGAAAGACATATAGGCC 3200
                               i  v  i       v            i  v          ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_81480085_8   3201 AATGAATTAGAAATAAAGAGCCCAGAAATTAATTCAAGCATATGTGGTCA 3250
                             i v     v i -   i        v  ii  vi   v i      
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_81480085_8   3251 ACCAAGTTTTGTTAAGAATGTCAAGAATACACAGTGGAGGTGTGGGTAGT 3300
                          iii v   i vi   ii  i     vi iv  i   -  viv ii    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGT 396

  chrX_81480085_8   3301 CTCCTCAGCAA-TTATATTGGAAAATCTAGATATCCACATACAAAAAAAT 3349
                           ii   i   - vi ii   i v v  i    ?      i     i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_81480085_8   3350 TAAAACTGGACT--TATCTTACACGATACCCAAATAACAACTCAAAATAG 3397
                         -i  ii     i--  i  i    v   iv    v vi          i 
  L1M4_orf2#LINE/    447 -GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_81480085_8   3398 AATAAATACTTAAATATAAGACTGTGAAGTGAAAAAAATCCTAGAAGAAA 3447
                          vi ? v  i     i     vi- i  iiv v    v  i         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_81480085_8   3448 ---TAGTAAAAAATT---ATGACATTGGTTTGAG----GATTTCTTAGAT 3487
                         ---   v?iv    i---i    v    v  ii ---- i          
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_81480085_8   3488 ATGATACCAAAAAACATAAGCAACAAAA---ACAACACACAAGTGGGGCT 3534
                             i       i-  i           --- v  i v i  i v  i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_81480085_8   3535 ACATTAAATTTAAAAGCTTCTGCAC---AAAGATGAGAATAATCAGCAGA 3581
                         v   i   v      i   i  ii ---    --  v v  -   iv i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAG--GACACTA-TCAAGAAA 690

  chrX_81480085_8   3582 GTTAAAAGGCAGTCTACGGTATGGAAAAACATATTTGCAAACCATATATC 3631
                           v     i  ii i  i v    i i  v           i        
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_81480085_8   3632 TGATAAAGGGTTAAAGTCTAAGATATATAAAGAACTCCTACAATTTAGTA 3681
                               i  ii vivi  i ii               i     i i i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_81480085_8   3682 GTAAAATAAACCCAATAATATAACTTAAAA-TGAGCAAAGGATTTGAAAA 3730
                         i     - i  v-     ivi  i ?    -  i              v 
  L1M4_orf2#LINE/    791 ATAAAA-AGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_81480085_8   3731 AAAACATTTCTTTAAAGAAAATATAGAAGTGTTCTCCTGGTATATAGAAA 3780
                         i --       ii      i     v  i  vi vvivi i i  ii   
  L1M4_orf2#LINE/    839 GA--CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_81480085_8   3781 GATATTCATTGTTGCTAATCAT 3802
                            ii   vii ii????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (157 / 77)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.67 (40 / 24)  


2475 26.01 3.70 2.02  chrX_81495068_81501672     5221  6112 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_81495068_8   5221 GGAAAAACATTCCACGCTCATGAATAGGA-GAATTAATATTGTTAAAATG 5269
                              i i  i   i i     i  v   -  v             i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_81495068_8   5270 GCCATACTGCCCAAAGCAATTTACAGATTCAGTGCTATTCCTATCAAACT 5319
                           v     v      vii  i          ii  v  i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_81495068_8   5320 ACCAATGAGATTCTTCACA-AAATTAGAAAAAACT-ATTTTAAAATACAT 5367
                         v   iivivv  i  ii  -     i-- v  i  -  ii      v   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_81495068_8   5368 ATGGAGCCAAT--AAAGGGCCCA-AAGAGCCAAATAAATCTTAAACAAAA 5414
                              ---   --  i  i    -  v       vv      i  v  i 
  L1M4_orf2#LINE/    150 ATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_81495068_8   5415 AGAATAGAGCTGGAGCCATCACTCTATGTGACTTAAAATGATACTACAAG 5464
                             i i  i     vvv    v  vivii i  v   vvv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_81495068_8   5465 GCTACACTAACCAAAACAGTGTGGTACTGGTACAAAAACAAACATATAGA 5514
                               v   i   i               i i  ii i i         
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_81495068_8   5515 CCAATGCAA--GAGTTTAGGGAACTGAGAAATAAAGCCACACACTTAAAA 5562
                         i     v  --  i  -- i  iiiv         v   i   i   vii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATT--GAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_81495068_8   5563 CCATCTGATCTTCAAGAAAGCTGACAATAGTAAGCCATGGGGAAAGAGTC 5612
                         i  vi    i   i v  i v  v   v vi vv v           i v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_81495068_8   5613 -CCTATTCAATAAATTGTGCTGGGATAACTGGCTACCCATATGGAGAAGA 5661
                         -i  v     i    v         i      v  ?   i   v i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_81495068_8   5662 TTGAAACTGGACCCGCT-CATTTTACCATATACAAAAATAAATGCAAGAT 5710
                         v    ii       -  - v ivi               v  iv   i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_81495068_8   5711 GGATCAAATACTTAAATGTAAAACCTAAACCTATAAAAACTCT-ACAAGC 5759
                               ? v  i         i v     v        -    - v   v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGA 542

  chrX_81495068_8   5760 AAACCTAGGAAATACCATTCTGGTAATC--GGCTCTGGCAAACACTTCAT 5807
                             v    ?i-  v-  ii v  i i --  v iv     vvii   v 
  L1M4_orf2#LINE/    543 AAACATAGGNG-TAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_81495068_8   5808 GACAAAGATGCTGAAAGCAGTTGCAACTAACTCAAAAATTGACAAGTAAG 5857
                         iivv v  ii ii      vvv     v  vvv      v  i  i vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_81495068_8   5858 ACATAATTAAAG--AGAATCCTC---ACAGCAAAAGAAACTATCAACAGA 5902
                           v v  i   i-- i  v i i---i vv    i  v        --  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA--GA 688

  chrX_81495068_8   5903 TAGACTATAAACAGACAACCTACATAATGGGAGAAAATATTTGCAAACTA 5952
                         v  ---- i  v        i   v                      ii 
  L1M4_orf2#LINE/    689 AAG----TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_81495068_8   5953 TGCATTTGACTAAGATCTAATATCCATATTCTATAAGGAATTTAAACAAA 6002
                          ii  i   iv i iv  vi      v v v     i   i ivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_81495068_8   6003 TCAATAA-GCAAAGGTAAACAACCTCAATAATAAATGGGGGAAGAACATG 6051
                                -iv    ii   i    iv v ? v       vi   i iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_81495068_8   6052 AAGAGAACATT---CTAAA-AAGA---------AGCCAAAAAGTGTATGA 6088
                           v   -    --- i   -    ---------i     v   iii    
  L1M4_orf2#LINE/    835 AATAGA-CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_81495068_8   6089 AAAAATG-TCAATATCAGTAATCGT 6112
                            i   -    i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (126 / 102)
Gap_init rate = 0.03 (27 / 907), avg. gap size = 1.89 (51 / 27)  


 998 28.02 1.47 0.88  chrX_81529272_81533484.rev      136   474 (3739)    L1M4_orf2#LINE/L1      304   644 (264)  

  chrX_81529272_8    136 AACAGAATTGAGAACTCAGAAATAAGACCGCACATCTACA-TCCATCAGA 184
                           i          iii         iv  ii    i  ii-  v  i-  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT-GA 352

  chrX_81529272_8    185 TCTTTGAGACACCTGACAAAAACAAGCAATGGGAAAAGAATTCCCTATTG 234
                          i  i  v vivv  v   i v  vv       i       vvi  v  v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_81529272_8    235 AATAA-TGGTGCTGGGAGAACAGGCTAGCCACACGCGGAGAATTGAAACT 283
                           i  -           v   v  v  ?     i  ii ii v    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_81529272_8    284 GTGCCCCTTCTTTACACTTTATACAAAACTTAACTCTAGATGGATTAAAG 333
                          vi     v i i    iv         v       v i      i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_81529272_8    334 ACTTAAACGTGAAACCCAAAACAATAAAAACCCTAGAAGAAAATCTAGGC 383
                           i    i  i i v i     v      vi i          iv    ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_81529272_8    384 A-ATACCATTCAGGACATAGGCACAGGCAA-AGTTTCAT-GATGAAATCA 430
                         i- v i -   iv   v v  vvi      -i     v -   ivi -  
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA-CA 600

  chrX_81529272_8    431 CTAAAAGCAATTGCAACGAAAGCAAAAATTGCCAAATGGGATTT 474
                          i       vvv     i    v      v vi    v   i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

Transitions / transversions = 1.19 (50 / 42)
Gap_init rate = 0.02 (8 / 341), avg. gap size = 1.00 (8 / 8)  

2847 24.35 1.99 2.73  chrX_81529272_81533484.rev     2607  3411 (802)    L1M4_orf2#LINE/L1        9   807 (101)  

  chrX_81529272_8   2607 TATCTCATGTTCATGGATTGGAAGCATAAATAGAGTTAAAATGCCCATAC 2656
                             i                   vv v    vv     i   v v    
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chrX_81529272_8   2657 TATCCAAATCAATCTACAGATTCAATGTAATCCCTATCAAAATTTCAA-T 2705
                          vi      ii              i i               ii  i- 
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chrX_81529272_8   2706 GTCATTCTTCACAGAAACAAAAAAAATAGTTCTAATATTTGCAGGGAACC 2755
                          i -  i  ii      ivi v  iv ii i    v   iii v    vi
  L1M4_orf2#LINE/    109 GCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_81529272_8   2756 ACACAGACTTCA-AACAGCCAAAGCAATTTTGAGGAGAAAATAACAAAAC 2804
                         i  vi ivii  -  i       i    i    ii - i  v      ii
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA-AGAAGAACAAAGT 206

  chrX_81529272_8   2805 TGGAGATGTCACATTAACTGAGTTCAAAATCTATTA--AGGCTATAGCAA 2852
                              ivv     i vv ii v       ii  i  -- i    i  i  
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_81529272_8   2853 TCAAAACAGCATGATACTGGCATAAAAACAGATTCATTGACCAATGAAAC 2902
                             i    ii  i           ii i   ivi  v  i     i  i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_81529272_8   2903 AGGATAGAGAGCCCAAAAATAAATCCATGTATTTATGGTCAATTGATTTT 2952
                           i  v     i   i       i    ii                    
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_81529272_8   2953 TGACAAAGGTGCCAGGCAAATATAATAGACAAAAGATGGTCTTTTCAATA 3002
                         i     i       i vvv  vi   i iv   ii  i          i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_81529272_8   3003 AATGGTGTTGGGAAACCTTGATGTCCATAAGCAGAAGAATCACATTGGAC 3052
                                i     v v  v   i?   i v   i      v vi      
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_81529272_8   3053 CCTTATCTCACACCATATACAAAAAT---CTCAAAATGAATTAAAGACTT 3099
                           i  i                    ---         i  i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_81529272_8   3100 AAACATAAGACTGGAAGCTGTAAAAATTCTAGAATAAAACACAGGAA-AA 3148
                            ii     vivi  i  i     v ii     v      i   ?i-  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_81529272_8   3149 ATGTTCCATGACATTGGTCTGGGCAATGATTTATTGAATATAATCCCAAA 3198
                           v   -i    v    vi i       i   v  ii    i iv     
  L1M4_orf2#LINE/    557 ATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_81529272_8   3199 ACCACAGAAAACAAAAGCAAAAATTTTAAA--AATGAGATTACATTAAA- 3245
                          v    iiv        v      --- i --   vi  i v   i   -
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAAT---AGATAAATTGGACTTCATCAAAA 652

  chrX_81529272_8   3246 CTAAAA-----TGTGCTTGCATATCAAAAAAAGAAAACAACAACAATTAT 3290
                         i     -----       ------    i---  v vi v   v  ----
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTT------CAAAG---GACACTATCAAGAA---- 689

  chrX_81529272_8   3291 TAGAGTGAAGAGACAACCCAAAGTTTGGGAGAAAATATTTACAAATTATA 3340
                         ---      i          v  vv               i     i   
  L1M4_orf2#LINE/    690 ---AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_81529272_8   3341 AATTTGATAAGGGGCTAATATACAAAATATATAAGAAAATCAACCATCTC 3390
                         v  i         i  vi   v  i         ii  v  vvv  v   
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_81529272_8   3391 AATAACAGGACAAAAAGTAAC 3411
                              i ii vi v  i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAAC 807

Transitions / transversions = 1.88 (126 / 67)
Gap_init rate = 0.02 (15 / 799), avg. gap size = 2.53 (38 / 15)  

 291 19.40 1.49 0.00  chrX_81529272_81533484.rev     3656  3722 (491)    L1M4_orf2#LINE/L1      841   908 (0)  

  chrX_81529272_8   3656 CATTTTTA-AAAGAGTACATACAAATGGCCAGCAGATATATGAAAAAATG 3704
                              i v-     iv i             ii iii i       i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_81529272_8   3705 CTCATCATCACTGATCAT 3722
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1)  


2969 26.64 2.12 0.89  chrX_81533933_81538772.rev     3453  4349 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81533933_8   3453 TGGAAAAACATTCCATGCTCATAGATAGGAAGAATCAATATCGTGAAAAT 3502
                               i i  i     i    i   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81533933_8   3503 GGCCATAATGCCCAAAGTAATTTATAGATTCAATGCTTTCCCCATCAAGC 3552
                            v   v v      v i  i  i        i  vv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81533933_8   3553 TACCA-CTGGCTTTCTT-CACGGAATTGGAAAAAACTA--CTTAAAATTT 3598
                          v   -   v    i  -  - i     -- v  i  i-- i       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_81533933_8   3599 TATATGTAA-T-CAAAAAACAGCCCGCATAGCCAAGACAATCCTAAGCAA 3646
                         -     v  - -   iii  --  v v        i      i i iv  
  L1M4_orf2#LINE/    148 -ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_81533933_8   3647 AAAGAATAAAGTCGGAGACATCATGCTACCTGACTTCAAATTGTACTACA 3696
                         i     i     i    ivv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_81533933_8   3697 AGGCTATAGTAAACAAAACAGCATGGTACTGGTACCA----AAAC----- 3737
                          i    i     v   i    ii         i iv ---- i  -----
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_81533933_8   3738 --TTAATGGAACAGAA--GAGAGGCCTCAGAAATAACATCACACATTTAA 3783
                         -- i       i    --     v  --        vvi  i       v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chrX_81533933_8   3784 CGTTGTCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAACA 3833
                         v  iivi    i  i     ivv  v   i v  vv           iv 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_81533933_8   3834 TTCCCTATTTCTTAAATGGTGTTGGGAAAACTTGATAGCCATATGCAGAA 3883
                          vvi  v  ivvi        i     v    v    ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_81533933_8   3884 AGCTGAAAGTAGATCCCTTCCTTACATCTTATACAAAAATTAACTCAAGA 3933
                         iiv    iv i  i    v   i   i v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_81533933_8   3934 TGGATTGAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAGGA 3983
                              ii?    i           v       i      vi i    i  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_81533933_8   3984 AAACCTAGGCAATACTATTCAGGACATAAACATGGGCAGAGACTTCATGA 4033
                             v    ?ivv v v   iv   v viivv i    iv ii   v ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_81533933_8   4034 CTTAAACACCAAAATCAATGGCAACAAAAGCCAAAATAGACAAATGGGGT 4083
                         v vvi         v  vvi          vv        i    v  ii
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_81533933_8   4084 CTAATTAAACTAAAGAGCTTCTGCTCAGGAAAATAAACTATCATCAGAAT 4133
                         i v  i   v v  i i   i  iv vvv   iv v       vv i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_81533933_8   4134 GAGCAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTGTCCATCTG 4183
                           iv  i     i                 v       viii vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_81533933_8   4184 ACAAAAGGCTAATATCCAGAATCTAAAAAGAACTTAAACAAATTTACAAG 4233
                          i  ii i  vi          v  v        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_81533933_8   4234 AAAAAAGCAAACAACCCCATCAAAAAGTGGGCAAAGTATATGAACAGACA 4283
                              ii    i     v  i?    i         v  v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_81533933_8   4284 CTTCTCAAAAGAAGACATTTATGTGGCCCACAGCCATATGAAAAAACGCT 4333
                         i     v        i  vi vi     v i iv  i       i i   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_81533933_8   4334 CATCATCACTGGTCAT 4349
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (132 / 103)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.08 (27 / 13)  


2308 24.76 9.57 0.96  chrX_81548990_81552306     1989  2824 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81548990_8   1989 TGGAAACACATCCCATGATCATGGAAGAGTAGAATTAATATTGTGAAAAT 2038
                               v i        v       vvi v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81548990_8   2039 GACCACATTGCCCAAAGCAATCTACAAATTCAATGCAATTCCCGTTAAAA 2088
                          i v i i v      vii       i      i     i  ii i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81548990_8   2089 TACCACCATCATTCATCACAGAACTAGAGAAAACT-ATCCTAAAATTCAT 2137
                          v   v vv v  iv ii     v v  v  i-  -              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_81548990_8   2138 GTG-AAAT-CAA-------AAAAGAGCTCACACAGT---GAAA------- 2168
                         i  -    -   ------- i  v   iv v   i ---    -------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_81548990_8   2169 ------------------------------TCAAAACT-------AAGCA 2181
                         ------------------------------        -------    v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_81548990_8   2182 AAAAGAA--AAAAT---------CTGGTATCAAAATAGGCATAGAGACCA 2220
                          v iv  --  i i---------    i  v ii    i    v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_81548990_8   2221 ATGGAACAGAATAGAGAAGCCAGAAATAAAAGCCAAATACTTATAACCAA 2270
                               i     v    iv           v-   v i i    iii   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTTATGGTCAA 348

  chrX_81548990_8   2271 CTGATCTTCATTAAAGCAAACAAAAACACAAAATGGGGAAAGGACA--CT 2318
                         i    i   ivi  i vviv   i v  ivv           i i --  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_81548990_8   2319 CTACATCAAATGGTGCTGAGATAATTGGCAAGCCACATGTAGGAGAATGA 2368
                         i v  v            i  i  i   vv ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_81548990_8   2369 AACTGGATCTTCATCTCTCACCTTATACAAAAATCAACTCTAAATGAATC 2418
                          ii    i iii i   v    v           i     v     i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_81548990_8   2419 AAAGACTTAAATCTGAGGCCAAAAACCATCAAAATTCT-GGGCGATAACA 2467
                          ?    i     v i  iv v     i  -    i   -i iv  v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chrX_81548990_8   2468 TCGGAA-ACACCCTCCTAGACATTGGGTTAGGCAAAGACTTC------AT 2510
                          v  ?i- v i i  v -   v             v ii   ------  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_81548990_8   2511 GACTCAAAATACAAAGGCAAATGAAACAAAAAAAATGAATAGATGGAACT 2560
                            v v   vi  v i    v--   - i       ii   i  v i   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAAC--AAA-AGAAAAAATAGATAAATTGGACT 643

  chrX_81548990_8   2561 TAATTAATCTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTA 2610
                          v  i  vv v    i   i  ii vv    i  v iv    iv i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_81548990_8   2611 AACAGACAACCCACAAAGTGGGAGAAAATCTTTGCAGTCTCTACATCCAA 2660
                           v            i i           v      iviiv  i   ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_81548990_8   2661 CAAAGGACTAATATCCAGACTCTATAAGGAACTCTAACAAATCAGTAAGA 2710
                         i  i     vi        v v     i       v    v   i   v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_81548990_8   2711 AAAA-ACAAACAATCCCATCCAAAAAGTGGGTTAAGGACATGAATAGAGA 2759
                             -     i  i  v  i?     -    iv     iv        v 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chrX_81548990_8   2760 ATACTCAAAAGAAGATATACAAATGACCAACAAACATATAAAAA-ATACT 2808
                         v v   v                  i    i  i  i  i    -  i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_81548990_8   2809 CAACATCACTAATGAT 2824
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (116 / 87)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 4.00 (88 / 22)  


2709 26.08 2.10 1.77  chrX_81559118_81564075.rev     3563  4467 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81559118_8   3563 TGGAAAATCATTTTATGCTTATGAATGGGAAGAATCAATATTGTTAAAAT 3612
                               ivi  iii   i i   i  v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81559118_8   3613 GTTA-TATTGCCCAAAGAGATTTACAGATTTGGTGATATTTCTATCAAAC 3661
                          vi -  i v      vv   i        iiii vv  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81559118_8   3662 TACCAATGACATTATTCACAAAATTAGAAAAACTCTGTTTTAAAATTTAT 3711
                          v   iivi v  v  ii  i  v v  v  i  v-i ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chrX_81559118_8   3712 ATGGAACCAAAAAAGGG-CCCA-AATAGCCAATGCAATCCTAAGCAAAAA 3759
                               -- viv     -    -         vi     i i i-   i 
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGA 196

  chrX_81559118_8   3760 ACAACAAAACCAAAGGCATCACATTACCCAACTTCAAAGTATACTACAAA 3809
                          v      iiiii   vv     i v     i      iiv         
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_81559118_8   3810 GCTACACTAACCCAAAGAGCATGGTTCTGGTATGAAAACAGACATATAGA 3859
                               v   i v i v  ii    v    i  i ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_81559118_8   3860 ACAATGGAACAGAATAGAGAGCCCTGAAATAACTCTGCACAGTTAAAATC 3909
                         v        i     v     i  v       vi iii   v   vii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_81559118_8   3910 ATTTGATCTTTGACAAAGCTGATTAAAACAAGCAGTGAGGAAAGACTC-C 3958
                          v     i  i     i v  viv i v  vv  i  i       v v-i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_81559118_8   3959 CTGTGCAGTAAATGGTGCTAGAATAACTGGCTTCCCATATGCAGAAGATT 4008
                           v v  ii          i i i      v v?   i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_81559118_8   4009 TAAACTGTACCCCTTCATTTCACCATATACAAAAATCAACTCCAGATGCA 4058
                         v  ii  v      v v iv                i     v i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_81559118_8   4059 TTAAAGCCTTTACATTAAACGTAAAACCTAAAACTATCAATACCCT-GGA 4107
                          i ?  -----  -i    i    i v          v  -  i  -i  
  L1M4_orf2#LINE/    497 TCAWAG-----AC-CTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGA 539

  chrX_81559118_8   4108 AGATAACCTGGGAAATACTATTCAGGACATAGGTGCT-GGCAAAGATTTC 4156
                            v   v i  ?ivv v v   iv   v v  - i -     v i    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTC 588

  chrX_81559118_8   4157 AT-GATGAAGACAGCAAAA--ACAATTGCAAGGAAAGCAAAAGTTGATAA 4203
                         v -   - v    v     --    --    vi    v    i v     
  L1M4_orf2#LINE/    589 TTAGAT-ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAA 635

  chrX_81559118_8   4204 AGGGAACTTAATTAAACCAAAAAGCTTTTGCACAGCAATAGAAGCTATCA 4253
                          vv i    v  i   viv    i      ii vv   vi  vi      
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_81559118_8   4254 ACAGAATAAACAGACAACCTACAGAATGGGAGAAAATATTTGCAA-TC-T 4301
                          v i i i  v        i                         -  - 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_81559118_8   4302 ATACTT--CAAAGGTGTAATATCCAGAATCTGTAAGAAACTTAAACAA-- 4347
                            ii --i  i  vv vi          v i   ii    ivv    --
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_81559118_8   4348 --AT--TAAGAAGCAAAAACAACCCTATTAAAAATTAGGCAAAAAACATG 4393
                         --  --   i   - v   i     v   ?    v i      ii iv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_81559118_8   4394 AACAGAGACTTTTCAAAAGAAGATATACATGTGTCCAACAAGCCTATGAA 4443
                           i   v i  i  v              vi  v    i    vi     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_81559118_8   4444 AAAATGCTGAACACCACTAATTCA 4467
                           i     v    i  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (130 / 102)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.52 (35 / 23)  


1479 23.30 2.88 17.64  chrX_81605245_81608116     1337  2379 (493)    L1M4_orf2#LINE/L1       20   908 (0)  

  chrX_81605245_8   1337 CATGAATTAGAAGCCCCAAAAT-GTTGAAGATGTCAATTCACCCTAAATC 1385
                             i   i    v ii  v  -   -      v    v v   i    i
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTT-AAGATGGCAATACTCCCCAAATT 68

  chrX_81605245_8   1386 -ATCTGTAGGTTTAATGCAATTTCTATCAAAATCCCAGCATAATTTCCTT 1434
                         -    ii  i  i  i     ii                - ivi  ii  
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCTTTTTT 117

  chrX_81605245_8   1435 GTAGATATAGAAAA--TGTTTTTATAAAATTTTTATGGTAAGGCACAGAA 1482
                          i   v  v  v  --  v ii  --     iv     v  v   vi i 
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTA--AAATTCATATGGAAATGCAAGGGA 165

  chrX_81605245_8   1483 TCTAAAAGAGTTAAAACAATCTTAAAAAAGTA---TGAAGTGGAAGAAAT 1529
                         i i i  v  ii           i      v ---ii    v i  i v 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_81605245_8   1530 AATTCTTAGTACATAATCAAGTCAATATTGAGGCTTACTATATAGCTATA 1579
                         v iv   ---------i ----    v ii ii       i v     i 
  L1M4_orf2#LINE/    216 CACACTT---------CC----CAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_81605245_8   1580 TTGATCAAAACAATGAAGCATTGGTGGAGGAATAGACTCATAGATCAAGA 1629
                         v i     i   i  vi i i   iiv i i      vi         vi
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_81605245_8   1630 GAAAATAACAGAAGACATAGAAATAGACTCA---------GGTGAATATT 1670
                            v v  iv  iiiivi       i  i  ---------   v   ---
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT--- 349

  chrX_81605245_8   1671 ACTGATTTTTGACAAAGATG--AAGAAGCAATTAATGCAGAGGATAGCAT 1718
                         --       i     i i  --    v-  v i    ---i   v  v  
  L1M4_orf2#LINE/    350 --TGATTTTCGACAAGGGTGCCAAGAC-CATTCAATG---GGGAAAGAAT 393

  chrX_81605245_8   1719 AACCTATTCAACAAATGG-GCTAGAAAAATTGTATGTTTATAGGTAAACA 1767
                          ii  v            -   i i v  i  v  i?ii i v i   vi
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_81605245_8   1768 AACAAATCTAAGTCTAAGTCTCAACCTAAGTCTCATACCTAATACAAAAA 1817
                           ii  vi iiii ----------    --i    i   vv         
  L1M4_orf2#LINE/    444 AATGAAGTTGGACC----------CCTA--CCTCACACCATATACAAAAA 481

  chrX_81605245_8   1818 TTAGCTCAAAATGGGCATAGTCGTTCATGCCTGTAATCTCAGTGAGTTGG 1867
                            i          i---------   ?----------------------
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGA---------TCAW---------------------- 500

  chrX_81605245_8   1868 GAGGCAGAGGTGGGCAGATTGCTTGAACTCAGGAGTTCAAGACCAGCCTG 1917
                         ---------------------------------------     ------
  L1M4_orf2#LINE/    501 ---------------------------------------AGACC------ 505

  chrX_81605245_8   1918 GGCAAGGTGTCAAGTTCCTGTCTCTAAAACAATAAAGTGAGCTCAAAATG 1967
                         --------------------------------    ------------  
  L1M4_orf2#LINE/    506 --------------------------------TAAA------------TG 511

  chrX_81605245_8   1968 TATCACAGA-CTAAAATATAAAATATAGATGTATAAAGTTGTTAGAAGAA 2016
                           ----   -      i--------------      ii v         
  L1M4_orf2#LINE/    512 TA----AGAGCTAAAAC--------------TATAAAACTCTTAGAAGAA 543

  chrX_81605245_8   2017 AACACAAAAGAAAATCTTCAGAGTCTAGGGCTAGGTAAAGGATACTTGGG 2066
                             i ii? v        iviii  v   i    i  v  v v   i i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_81605245_8   2067 --------CAGAAATATTACCCATAAAAGAAAAAACA-ACAAATCATATT 2107
                         --------  i  ii iv v v i           i - i    iiv i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_81605245_8   2108 TCATCAAAATTATAAAATATTCTGCCTTTGAGAGACTTTGTTAAGAAAAC 2157
                                     v   v v  v   -  ii ii   vi i i      ii
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGT 692

  chrX_81605245_8   2158 AAAAGGGACAACTTGCTGTCTGGAAGAAAATATTTG-AAATCCACATAGC 2206
                         i   i -     iii v vv   i            -     - i   v 
  L1M4_orf2#LINE/    693 GAAAAG-ACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATC 740

  chrX_81605245_8   2207 CATCAAAAGACTAATGCCTAGAATATATGAAGATCTCTCAAAATGCAACA 2256
                         iivi  ii    vi ii i         i    v    i v  iv   i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_81605245_8   2257 TTAAAAGGGGAAAAAAGCCAATTGGATTAGAAAATGAAAAAATAACATGA 2306
                         v     i iv   v  v      -----?i      iiv   vi iv   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATT-----WAAAAATGGGCAAAGGATTTGA 835

  chrX_81605245_8   2307 AAAGACATTTCGCTGAGAAGGATATACAAATACCAAATAAGCACATTAAA 2356
                          v         v ii ii i           iv v           v   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_81605245_8   2357 AAGTGTTCAGCATCAATAGCCAT 2379
                          ii  i   i     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (158 / 81)
Gap_init rate = 0.03 (31 / 889), avg. gap size = 6.90 (214 / 31)  


3271 26.76 0.55 0.55  chrX_81608382_81614666.rev     4887  5794 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81608382_8   4887 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4936
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81608382_8   4937 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4986
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81608382_8   4987 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5034
                          v    ivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_81608382_8   5035 TATGGAACCAAAAAAGAGCCCGCATAGCCAAGTCAATCCTAAGCCAAAAG 5084
                                viiv  ii  v  v v        iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_81608382_8   5085 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5134
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_81608382_8   5135 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5184
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_81608382_8   5185 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATGTCTACAACT 5232
                                i    i--    i  --        vv   i ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_81608382_8   5233 ACCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5282
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_81608382_8   5283 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTT 5332
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_81608382_8   5333 GAAACTGGATCCCTTCCTTACACCTCATACAAAAATCAATTCAAGATGGA 5382
                            ii    i    v   i     vi          i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_81608382_8   5383 TTAAAGACTTAAATGTTAGA-CTTAAACCATAAAAACCCTAGAAGAAAAC 5431
                          i ?    i       v   -  v    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_81608382_8   5432 CTAGGCATTACCATTCAGGACATAGGCATGGGAAAGGACTTCATGTCTAA 5481
                         v    ?i v viv   iv   v v  vv i  v  v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_81608382_8   5482 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5531
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_81608382_8   5532 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5581
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_81608382_8   5582 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5631
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_81608382_8   5632 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5681
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_81608382_8   5682 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5731
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_81608382_8   5732 TCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAAAATGCTCGT 5781
                           v        i  vi viii     v  i-          i      iv
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCAA 895

  chrX_81608382_8   5782 CATCACTGGCCAT 5794
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2935 22.13 3.15 4.16  chrX_81625624_81628342.rev     1331  2220 (499)    L1M4_orf2#LINE/L1        1   881 (27)  

  chrX_81625624_8   1331 TGGGAATAGATTCCACGTTCATGTATCAAACTATTTAACATTATTTAGAT 1380
                            i  v v  i   i       v  iii vv i    i   i  v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81625624_8   1381 GCCAATACTCCCCAAATTAATCTACAAAGCCAAAAAAATCC-TATCAAAA 1429
                          v                i       i vi   viv     -        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81625624_8   1430 TAACATCTGGCTTCCTTGCAAAAAAAAGGGTAATATAATCCAAAAATTCT 1479
                          vv  v   v   ii     i   v--v ii  vv i    v       v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCA 148

  chrX_81625624_8   1480 TATGGAAAGGCAAATAACTCAGAATAGGCAAAACAAGTTTGAAAAATAAG 1529
                                 v    ivi  i        v        vi        v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_81625624_8   1530 TATAAAAGTTCA--GATGCAAACTTTCTGATTTCATAACAGATTA-TATA 1576
                         v i   -   vi--  iv  v    i ii      v   ---   -  i 
  L1M4_orf2#LINE/    199 AACAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAAC---TTACTACA 244

  chrX_81625624_8   1577 AAACTACATTAAGCAAGACAGTATGTTAATGATATCGAGACA-ATATATT 1625
                           i     v   v         i  v  v  ii  vii  i - i    -
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT- 293

  chrX_81625624_8   1626 AGATCAATGGAATAGAATTAAGAGTCCAGAAATAAAACCACAGATTTTTG 1675
                                            i                v   i v    v  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_81625624_8   1676 GTCAATTGATTTTCCACAAAGATGACAA-ACTATTCAACGGGAAAAGAAC 1724
                                       v    i i  v   -  i      i   i      i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_81625624_8   1725 GGTCTTTTCAAAAAATACTACTGATACAACTGTATATCCATGTGCAAAAT 1774
                         i          v    iv i   iv       v   ?   ii       -
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA- 442

  chrX_81625624_8   1775 AAATAAATAAGGTTGGAC-------TCACACTATACACAAAAACTAA--- 1814
                         ----i   i i       -------      i   i       i   ---
  L1M4_orf2#LINE/    443 ----GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_81625624_8   1815 --AGTGTATCAAAGATGTAAACGTAAAAGCTTTTTAGCTCTTTTTTTAAC 1862
                         -- i  v    ?   iv    i    i    ---- i----------   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCT----AA----------AAC 524

  chrX_81625624_8   1863 -ATAAAAATCTTAGAAGGGTATGTATGAACGAATCTTCCTTGACCTTTGA 1911
                         -      v         iiv ii  v ?iii       v -      v i
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACCTTGGG 573

  chrX_81625624_8   1912 TATAGGTAATTGTTTTTTAGGCATAATAGCAAAAAAACTTGTGACAAAAA 1961
                          -    i   v    i    ii  i i v     iv  vv ii      i
  L1M4_orf2#LINE/    574 T-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_81625624_8   1962 ACAAAATAAATATATTGGACTATATTAAAATTAAAAGCTTTT---CTTCT 2008
                          v      i   v        vi  i          i     ---    v
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_81625624_8   2009 --GAAAATTAT--GGCA--TAAACAAAACAGCCCTCAAGATGTAAGAAGA 2052
                         -- i v i   --i v -- i  -  i   i   v  ii   vi    i 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAA-AAGACAACCCACAGAATGGGAGAAAA 721

  chrX_81625624_8   2053 TATTTGCAAATCATAACTTTGATAATAGATACATGACATATATCCAGAGT 2102
                                        vv i      -- i-----   v i        i 
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAA--GG-----GACTTGTATCCAGAAT 764

  chrX_81625624_8   2103 AAAATTAGCAATGTTTACAACTCAACAATAAAAACCAAAATAACCCCATT 2152
                          v - v iv  ivi           i        vvv         v   
  L1M4_orf2#LINE/    765 ATA-TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_81625624_8   2153 AAAATATGGGCCAAGGATGTAAGTAGAACTCTTTCTAAAGAAGATACACA 2202
                         ?   v      v      v i i    vv i i  i          i   
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_81625624_8   2203 AATGGCTAATATATACAT 2220
                               i    vii    
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACAT 881

Transitions / transversions = 1.38 (112 / 81)
Gap_init rate = 0.03 (25 / 881), avg. gap size = 2.60 (65 / 25)  


2857 25.34 2.25 1.58  chrX_81628619_81630504.rev      508  1395 (491)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_81628619_8    508 ATGTTCATGGATTAAAAGGATTATTCTTGTTAAAATGTTGATACCACCCA 557
                                      ii   iv   v v       i   vii    iv    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_81628619_8    558 AAGCAATCCACAGATTCAATGCAATCCCTATCAAAATAACAATGACATTC 607
                           vii   i          i                 vv  iivi v  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_81628619_8    608 TTCACAGAAATAGA-A---TAATCCTAAAATTTATATGGAATT--AATAA 651
                           ii       v  - --- i           i        v --  vii
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_81628619_8    652 ACAACCAAAAAAGCCAAAGC----TTGTCTAAGAAAAAAAACACA--TGA 695
                           --   i  v       i ----   ---  i  i  i    v --  i
  L1M4_orf2#LINE/    165 AC--CCAGAATAGCCAAAACAATCTTG---AAAAAGAAGAACAAAGTTGG 209

  chrX_81628619_8    696 AGGAATCACATTACCTAACTTCAAATTATACTATGGAGCTATAGTAACCA 745
                             v     i v  i  i      viv     iii     i     i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_81628619_8    746 AAACAGCGTGTT-CTGGCATAACAACACACATACA--CCAGTGGAACAGA 792
                          i    i   v -         vi i v     i --i  i     i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_81628619_8    793 ATATACAACCCAGAAAAATAATCCACACACCTACAGTGAATTCATTGTCT 842
                           vv v ii       v -  i   i   ii  ii  v    v   v  v
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATA-AACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_81628619_8    843 ACAAAGGTGTCAAGAAAACATACTGGGGAAAAGACAGTTTCTTCATTCAA 892
                             i    i     vv ivi v        ii i   i i    viv  
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_81628619_8    893 TGGTGCTGGAAAAACTAAATATTCATATGCAGAAGAATGAAACTAGACCC 942
                                  i v    ii   ?i  i     i         ii i     
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_81628619_8    943 ACATCTTTCATGGCATACAAAAATCAAATCTAAATTAATTTTAGACTTAA 992
                         vi i  iv  ivii          i  v  v    vi  iv?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_81628619_8    993 ATCTCAGACCTCAAACCATAAAATTACTACAAGAAAACTTTCAGGA--AA 1040
                           v v   v  v    i      i vi  v        v --   ?--  
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT--AGGNGTAA 556

  chrX_81628619_8   1041 GTCTCTAGTACATTGGTCTGGGCAAAAATTTCTTTGGCAATACCCCACAA 1090
                         i   iiivv  v    vi i     vii      v ii vv  v   v  
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_81628619_8   1091 GCGCAGGCAACCAAACCAAAAATGGAAAAATGGAATCACATCAAC-TTAA 1139
                           i  i     v   vv      i  v    v i iiv      v-    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_81628619_8   1140 AAGGTTTCTGCACAACACAGGATACAATTAATAAAGAGAAGAGAAAACCC 1189
                           iv   -  ii vv  v    i  v  i  v    v   i   v     
  L1M4_orf2#LINE/    657 AAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_81628619_8   1190 ACAGAAAGGGAGAAAATATTTGCAAATTACCCATCTGACAAGGAAGGGAT 1239
                               v                    i ivi      i    ----  i
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG----GAC 751

  chrX_81628619_8   1240 TAATAACCAGAATATAATAAGGACCTCAAACAATTCTGTAGAAAAAATAT 1289
                          vi  v          -   i  v   vv    i  vi  iv     v i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATA-TAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_81628619_8   1290 AA-TAATCTGATC-AAACATGGGCAAAAGATTTGAATAGACCTTTCTTAA 1337
                           -   i ii  i-   v         i             v     iv 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_81628619_8   1338 AAGAAGACATAAGAATGGCAAACAGGCATTTGAAAAGATTCTAAACATCA 1387
                                i   vi      v  i i   iv         v  v       
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_81628619_8   1388 CTGATCAT 1395
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.36 (128 / 94)
Gap_init rate = 0.02 (18 / 894), avg. gap size = 1.89 (34 / 18)  


1475 27.41 16.62 1.40  chrX_81663654_81667046     2113  2900 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81663654_8   2113 TGAAAAAATAATCCATGCCCATGGATTGAATGTATCAACATTATTGAAAT 2162
                           i   i   vi     ii         i v vv i  i   i  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81663654_8   2163 ATTTATACTGTCCAAAGCAATCTACAGACTCAATGCAATTGCTATCAAAT 2212
                         iviv     vi     vii         i    i     iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81663654_8   2213 TCCCAG-TG---TTATTGTACAAAT-----------------AATT---- 2237
                               -  ---  v   i v    -----------------    ----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_81663654_8   2238 ----------AGGAA------------AAAACTATCC------------- 2252
                         ----------   i ------------     v   i-------------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_81663654_8   2253 CAAAATTA----ACATGTACCCCCC---TGCAAAA--------------- 2280
                             i  i----  viii  ii   --- v     ---------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_81663654_8   2281 -AGTAATTTGGATAG-----------CA-AA----AGCCATCCAAAGCAA 2313
                         -      ivi  i  -----------  -  ----  v   vi i v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_81663654_8   2314 AAGAA-AAAATCCAGAGGCATCACAT---TCCAAACACATACAACCAACT 2359
                         vi   - i   iv    v vvv v  ---i   v   iv  iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_81663654_8   2360 GATTTTTGACAAAATTGGCAGAAATAAACAGTGTGGAATGAA-ACCCTAT 2408
                               i     iiv  v  ii vi vv  i  v    v   - vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_81663654_8   2409 TCAGTAAGCAGTGCTGGGAAAACTGGCTAACTATAAGGAGAAGAATAAAA 2458
                            ii  iii         v      v  ? i i v v i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_81663654_8   2459 CTGGGTCCCTACCTCTCATTATATACAAAAATCAACTCAAGATGG--CAT 2506
                         i   ii         v  ii            i       i    --  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_81663654_8   2507 AAAACTTAAATTTAAGACCTCAAACAATAAAAATACTAGAAGAAAATCAA 2556
                          i - i     v     v  v    v      v vi          ivv 
  L1M4_orf2#LINE/    501 AGA-CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_81663654_8   2557 GG---ACACCCT----ATTCTGGAAAATTCCTTAGGCAAAGAATTTATGA 2599
                           --- v i i ---- iii   i-------        v i-   v v 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGG-------TTAGGCAATGG-TTTCTTA 591

  chrX_81663654_8   2600 G---TGAGCTCTCAAAAGCAAACACAACAAAAACAAAAATAAACACTTGG 2646
                          ---   - v -        v vi        iv       i i vv v 
  L1M4_orf2#LINE/    592 GATATGA-CAC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_81663654_8   2647 GATCCAATTAACCTAAAGAGCTTCTGAACAGCAAAAGAAACTATCTAAGG 2696
                           iiiv  i  vv v  i i   i  vi vv    i  v      v iii
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_81663654_8   2697 AGTAGATAGACAACCTACAAAATGGGAGAAAATATTTGCAAACTATGCTT 2746
                            ii v        i   i                      ii  iiv 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_81663654_8   2747 CTGACAAAGGACTAATAACCAAAATCTATAGGATACT---AAAA-TCAAC 2792
                             i  i     vi  v   i   v    iiiv   --- v  -    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_81663654_8   2793 GACAAAAAAA----------AACTAAAAAGTAAGCAAAGCACATGAACAG 2832
                         i i     i ----------  i ?    i ii      v iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_81663654_8   2833 GCATTTCTTGAAAGAAGACATACTAGCAGCCAATAAAGATATGAAAA-AT 2881
                         i       iv        i    v iii        iv i       -  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_81663654_8   2882 ACTCATCATCACTAATCAT 2900
                         i    v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (130 / 83)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 5.07 (142 / 28)  


2295 25.94 6.74 2.97  chrX_81686062_81688928     1500  2374 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81686062_8   1500 TGGAAAGATATTTTATGTTCATGAACAGGAAGAATTAATATTGTTAGAAT 1549
                                    iii         i iv      v            ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81686062_8   1550 GTCCATACTACCCTAAACAATCTACAGATTTAA-GCAAACCCTTATCAAA 1598
                          v v     v   v  vii           i  -    v    -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT-ATCAAA 99

  chrX_81686062_8   1599 ATACTAATGACATTCTTCATAAAAATTTTTAAACT---CCTAATGTTTAT 1645
                           v i iivi v  i  iii i     vvi  i  ---     vi  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_81686062_8   1646 ATAAAACCACAAATGTCCTACAATAGCCAAAGCCATTTTGGGCAAAAATA 1695
                           ii  vii   iv v  i v          i v  i   ---     v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG---AAAAAGA 196

  chrX_81686062_8   1696 AAATAAAATAAAATAACAAAAACTGGAGAAACCACATTACTGGACTTCAA 1745
                          i ---- i   i ---------     i vi    i v ivi i     
  L1M4_orf2#LINE/    197 AGA----ACAAAGT---------TGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_81686062_8   1746 ATTATACTACAGAACTCTAGTAACCAACATAGCATTGTACTGGAATAAAA 1795
                          viv       i i  vi     i   v i  ii v       v    ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_81686062_8   1796 ATAGACACATAGACCAATGGAACACAATACAGAATAGAGAACTCATAAAT 1845
                                i     i        i -------    v    iii  v    
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATA-------GAATTGAGAGTCCAGAAAT 326

  chrX_81686062_8   1846 AAGTCCACACATCTACCATAAAGTAATTTTCAAAAAAGGTGCCAAAGTCA 1895
                           ii   i    i  ivi v  v i      i v  i        iii  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_81686062_8   1896 TGCAATGGGAAAATGACAGTTTCTTCAATTAATGGTGCTGGGAAAACTGG 1945
                          v       i   vi i   i i     iv             v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_81686062_8   1946 ATATC-GTACGCAAAAGAGTGAAACTT-ACCAGTGACTCCCAACATACAC 1993
                            ? -ii i        i    ii v-   vv iv   v  v    i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_81686062_8   1994 AAAAAACAA-TCAAAATTAGTTA-ATACCTAAATCTAAGACCTCAGACTA 2041
                              vi  -       vii i - v        v     v  v i    
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_81686062_8   2042 TGAAATTACTAAAAGAAGACATTGG-GTAAACTCTCCAGAAAACTGGTCT 2090
                          i   i vi  i     i    v  -     -   i ivi vvi   vi 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTT 575

  chrX_81686062_8   2091 GGGCAAAGACTTATTCAATAATACCCCCAAAGCATAGGCAACCAAATAAA 2140
                         i     v ii  v  vi   vv  v  v      i i     v   v   
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_81686062_8   2141 ---TTGACAAATTAAATCACATCAAG-TTAAAAAGCTTCTGCACAGCAAT 2186
                         --- v  i     ii iiv      i-       -   i  ii vv   v
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAA 674

  chrX_81686062_8   2187 ATAAACAATCAAAGAAGTAAAGAGACGACCAA-AGAATGAGAGAAAA--- 2232
                         iv v  v     ii    i  i    i   v -      i       ---
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_81686062_8   2233 ------------------------GAC---------------ATAAGGAG 2243
                         ------------------------   ---------------    i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_81686062_8   2244 CTCAAACAACTCTATAG--AAAATTCTAACTATCCACTT-AAAAATGGAC 2290
                            vv       v   i--    vv v  iv i   v  -        i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_81686062_8   2291 AAAAGATATGAATTGATACTTCTCAGAAGAAGAAATACAAAAGACAAACA 2340
                            i   v     v  i i     vi       v       v i v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_81686062_8   2341 GAAATATAAAAAGGTGCTCAACATCATTGATCAT 2374
                         iiv i  i     i            ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (136 / 90)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.05 (85 / 21)  


2724 27.50 1.20 2.61  chrX_81691174_81693729     1151  2070 (486)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_81691174_8   1151 GGAAAAATAGTTCATGTTTATGGATTGAAAAAATCAATATTGTTAAACTG 1200
                              i   vii      i        i  i v i           iv  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_81691174_8   1201 TCCAAAATACTG---AAAACAATCTCCAGATTCAATGCA-TGCCTATCAA 1246
                         v ---      v---   vii    v         i   - v        
  L1M4_orf2#LINE/     52 GC---AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_81691174_8   1247 AACACCA-CGACATTCTTCACAGAATTAGAAAAAACAATCCTAAAGTTTA 1295
                           iv   - vi v  i  ii     v v  v  ivii        i  i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_81691174_8   1296 TATGGAACCAATAAACACCCAAAATAGCCATAGCTACCTTAAGCAAAAAG 1345
                                viivv iiv     i        v i v i   i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_81691174_8   1346 AACAAAACTAGAGGAATCATATTACCTAACTTTAAATTATACTACAGAGC 1395
                               ii i     v   i i v  i  i  i   viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_81691174_8   1396 TATAGTCATGAAAACAGCATGATTTTTTCTTCTTTTCTTTTTTTTTTAA- 1444
                           i   v  v  i    ii  i vi vv v ----------------  -
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCAT----------------AAG 282

  chrX_81691174_8   1445 ---AGACATGTAGAAAAAGAGAACAGGATAGAGAACTCAAAAACAAATTT 1491
                         ---      i    vv  vi   i  i  v    iii  i   i   iii
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_81691174_8   1492 ACTA-ACTTACAGTTAACTCATTTTTTGACAAAGGTGCCAAAAACATACA 1540
                          -  - i   ii  i  i v     i-     i        i v   v  
  L1M4_orf2#LINE/    333 A-TACATTTATGGTCAATTGATTTTC-GACAAGGGTGCCAAGACCATTCA 380

  chrX_81691174_8   1541 CTGGGGAAAAAACAGCCTCTTTAATCAATGGTGCTGGGGAAACTGAATAT 1590
                         v        i  i  i  i  i  iv            iv     i   ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_81691174_8   1591 CCATATGCAGCAGATTTAAGCTAGACCTTTATTTCATGCCATATATAAAA 1640
                            i     iv   v v   i i    ii  ii   ii       i    
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_81691174_8   1641 ATCGAATCAAAATCAATGAAAAACCTAAATCTAAGACATCAAATTGTGAA 1690
                           ii v       vi  v ? i        v     vv v   i i i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_81691174_8   1691 ACTACTACAAGAAAACATTGGAGAAACTCTCCAGGACATTGGACTGGGCA 1740
                            vi  v          v  ? v  v   i iv   v    ii i    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_81691174_8   1741 AAAGTTTCTTGAGCAATACCCCACAAGCACAGACAAACAAAGCAAAAATG 1790
                          vi       iiii vv  v   v       ii   vv    v      i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_81691174_8   1791 GACAAATTGGATTACATCAAC-TTAAAAAGTTCCTGAACAGTAAAGAAAA 1839
                           i        i v      v-       v  i-  vi vvi    i v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACA 679

  chrX_81691174_8   1840 AAATCAACAAAGTGAAGCAACAACCTACAGAACGGCAGAAAATATTTGCA 1889
                         vv     v        ivi      i      i  v              
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_81691174_8   1890 AACTCTCCATTTGACAAGGGATTAATAACCAGAATATATAAGAAGCTCAA 1939
                           iiv vi  i   i      i vi  v             ii i   vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_81691174_8   1940 AGAAGTCTATAGGAAATGAAATCTAATAATCAGATTTAAAAATGGGCAAA 1989
                          v  v  v   iv   --  iv v     i vi   ?             
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAA--AAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_81691174_8   1990 AGAAGTGAACACATATTTCTCAAAATAAGACTTACAAGCGACAAACAGTC 2039
                         i  vv    i v i       v   v    iv     ii i v  i iv 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_81691174_8   2040 ATGGGAAAAGGGGCTCTATACTATTTTTTCA 2070
                          iiv      iv    v i ii ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (146 / 103)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 2.92 (35 / 12)  


2991 27.16 2.24 0.34  chrX_81743873_81746001.rev      748  1638 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81743873_8    748 TGGAAGGATGTCTTGTGTTAATGGATTGGAATAATTAATAATGTTAAAAT 797
                              i   i  iii    v           v v      v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81743873_8    798 TGTTATGCTATCCAACAGAATCTATAGGTTTAATACAATCCTTATCAAAA 847
                         v iv  i  vi    vvvi     i  i  i  ii      i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81743873_8    848 TTTTAACGACAATTTTTACATACAGTAA--AACTG-CACTAAATTTAGTA 894
                          iii i vi vv     i  v v v i -- i   -iv     v  vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_81743873_8    895 TGGAATCACGAAAGACC-AAAACAGCTAGAGCAATCTTGAAGAGGAATAA 943
                              vii i ii    - i  i   i i i          i i   v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_81743873_8    944 CAATGTTGGAAGGATCACACTACTTGATTTCTAAATATAATATAAAGTTA 993
                            v      i iv       v iii     v   iv  v  i    i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_81743873_8    994 TAATAATCAGAACACAATGGTACTGGCATAAAAACAAGCATATAAACCAA 1043
                         i i      ii   vvi              ii i ii      i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_81743873_8   1044 TGGAACTGAATAAAGAGTGAAGAAATAAATCCACACAATTATCAACAACT 1093
                              iv    vi     vv         i   i   v    viv   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_81743873_8   1094 GATATTTGACAAAGTTACCAAGAACACACAATGGGGAAAAAAGTATCTCT 1143
                            v  i     i v i      v  iv           i  vvi   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_81743873_8   1144 TCAATAAATGGTGTTTGGCAAACTGAGTATCCACATACAGAAAAATGAAA 1193
                             i        i v  vv     ii  ?      i  i  i      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_81743873_8   1194 TTAGAATCTTATTTTATACCATTCACAAAAATTAACT------GTATCAA 1237
                           i  vi i  ii i i     vi             ------ v    ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_81743873_8   1238 AGGCTTAAGCATACAACTTAAAACTACAAAAACC-------AAAGTATAG 1280
                           i i   iii  vi vi        i    vi -------   ii    
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_81743873_8   1281 GGAGAAAGCTTATTGACATTTAACTGGGCAATTATTGTTTGAATATGACA 1330
                          ?iv   v   vv    v  viii i      vi  vi  ii        
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_81743873_8   1331 CCAAAAACACAGGCATCAAAAGCTAAAATAGACAAATGAGACTGCATCAA 1380
                               i    i   v      vv        i    vi    v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_81743873_8   1381 ACTAAAAAGCTTATGCACGGAAAAAAAGTCAATCAGCAGAGTGAAAAGA- 1429
                          v v    i   v  ii vvv   ii vv v    iv i          -
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_81743873_8   1430 AACCTACAGAATGGGATAATATGTTGTCAAACCATACATATGATAAGGGG 1479
                             i           v  v  i  vv    i    i  v         i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_81743873_8   1480 TTAATAT--AAAAAAAGTAAAGATCTCAGTCATCTCAAAAACAAGAAAAC 1527
                         i vi   -- i  v vi      v   vvv  v     v  i  i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_81743873_8   1528 AAATAACATGATTACAAAATAGGACAAGGACCTGAATAGACATTTCTCAA 1577
                                vii   ?v     i  vv     ii                v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_81743873_8   1578 AAGAAGAAGTACAAATGGCCAACAGGTATATAAAAAAAAAATGTTCAACA 1627
                                vi             i i i i  i    i ---  i      
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA---TGCTCAACA 897

  chrX_81743873_8   1628 TCCCTAATTAC 1638
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.88 (23 / 8)  


2838 26.35 1.76 1.65  chrX_81830795_81835123.rev     2932  3838 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81830795_8   2932 TGGAAACATGTCTCATGTTCATGGATGGGTAGTATGAATATTGTGAAAAT 2981
                               v  i  i             v  v  vv v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81830795_8   2982 GACAACACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCTATCAAAA 3031
                          i   i   v  v   vii       i      i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81830795_8   3032 TACCATCATCATTCTTGACAGAACTAGAAAAAACAATTATAAAATTCATC 3081
                          v   v vv v  i  vi     v v  v  ivii  iv          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_81830795_8   3082 TGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 3131
                              viiv  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_81830795_8   3132 CAAATCTGGAGACATCACATTACCTGATGT-GAAACTATACTATAAGGCC 3180
                             vi     ivv     i v  ii  v -i     -     i  i  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_81830795_8   3181 ATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACTA 3230
                          i   v i   i    ii         i    ii    i  i     ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_81830795_8   3231 ATGTAACAGA-----GAACTTAGAAATAAAGCCAAATACTTACAGGCAAC 3275
                            v  i   -----  iiii         v   v i i   ii v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_81830795_8   3276 TGGTCTTTGACACAGCAAACAAAAACATAAAGTGGAGAAAGGACACTGTA 3325
                           i i  i    vi vviv   i v   vv i   i     i i v v v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_81830795_8   3326 TTCAACACATTGTGCTGGGATAATTGGCAAGCCACATGCAGAAGAATGAA 3375
                                v  v         i  i   vv ?         i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_81830795_8   3376 ACTGGATCCTCATCACTCACCTTATTCAAAAATCATCTCAAGATACCTCA 3425
                         ii    i  ii i v v    v   v       i v     i  ivv   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_81830795_8   3426 AGGACTTAAATCTAAGACCTGAAACCACAAAAATTTTAGAAGATAACATC 3475
                         ?i   i     v     v  i    i i    v i        v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_81830795_8   3476 CG---AAATACCCTTCTAGACATTGGTTTAGGCAAAGACTTCATGACCAA 3522
                         v ---    ---    vv   v    v        v ii   v iivi v
  L1M4_orf2#LINE/    550 GGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_81830795_8   3523 AATCCCAAAAGCAAATGCAAAAAATAAAATAAATAAAATAAATAAATAGC 3572
                         i iv         ----   iv  i    v   --     i      ---
  L1M4_orf2#LINE/    597 GACACCAAAAGCA----CAAGCAACAAAAGAAA--AAATAGATAAAT--- 637

  chrX_81830795_8   3573 TGGAACTTAATTAAACT--AAATTTTCTTCACAGCAAAAGAAACAGTCAA 3620
                             -   v  i   v --   vi  i vii vv    i  v  vi    
  L1M4_orf2#LINE/    638 TGGA-CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_81830795_8   3621 CAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCATCACAATCTATA 3670
                         v i   i  v              i           vv ii   vii   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_81830795_8   3671 CATCTGACAAAAGAGTTATATCCAGAATCTACAAGGAACTCAAATAAATT 3720
                         i      i  ii  v  i          v  i  i      vv i  v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_81830795_8   3721 AGCAAGAAAAACATAAACAATCCCATCAAAAAAATGGACTAAGGACGTGA 3770
                          ii  v     v i   i  i  v  i?     -   i v     iv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGA 835

  chrX_81830795_8   3771 ATAGTCAAGTCTCAAAGGAAGATATAC-----GCCAACAAACATATGAAA 3815
                             v  vv    v  i          -----     i  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_81830795_8   3816 AAATGCTCAACATCACTAATGAT 3838
                          i             ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (131 / 105)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


2680 27.87 2.68 1.45  chrX_81848930_81855357     5039  5935 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81848930_8   5039 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCCATATAGTGAAAAT 5088
                              ii i  i     i        v      v iv    v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81848930_8   5089 GCCCATGCTGAACAACATAATTTACAGATTCAGTGCTATCCTCATCAAGC 5138
                          v v  i  vvv   vv i  i          ii  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81848930_8   5139 TACCACTGGCTTTCTTCACTGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5186
                          v   viv  i  i  ii v   -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_81848930_8   5187 AAATGGAACCAAAAAGGAGTCCACATAGCCAAGACACTCCTAAGCAAAAA 5236
                          v      viiv  i   vi viv        i   v  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_81848930_8   5237 GAACAAAGCTGGTGGCATCATGCTACCTGACTTCAAACTATATTACAAGG 5286
                                 i   v  vv   ii  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_81848930_8   5287 CTACAGTAACCAAAA--GCATGGTACTGGTACCAAAACAGATATATAGAC 5334
                                  i   i -- ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_81848930_8   5335 CAATGAAACAGAAC--AGAGCCCTCAGAAATAACACCATACATCTACAGC 5382
                              i  i    i--    i  --        vv        i  ii i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_81848930_8   5383 CATCTGATCTTT-ACAAACCTGACAAAAACAAGCAATGGGGAATAGATTC 5431
                           vi    i  i-    ivv  v   i v  vv          vii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_81848930_8   5432 CCTATTTAATTAATGGTGCTGAGAAAACTGGCTAGCCATATGTAGAAAGC 5481
                         i  v  i  iv          i  v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_81848930_8   5482 TGAAACGGGATCCGTTCCTTACAACTTATACAAAAATTAACTCAAGATGG 5531
                             iiv   i  v v   i   v v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_81848930_8   5532 ATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAGCCCTGGAAGAAAA 5581
                           i ?    i           v       i      vi i i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_81848930_8   5582 CTTAGGCA-ATACCATCCAGAACATAGGCATGGGCAAAGACTTCATAATT 5630
                          v    ?i- v i v  vv  v v i  i- i     v ii   v  iv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_81848930_8   5631 AAAACACCAAAAACAATGGCAACAAA-TCCAAAATTGACAAATGGGATCT 5679
                          vi         i  vvi        -vvv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_81848930_8   5680 AATTAAACTAAAGAGCTTCTGCATAGCAAA--ATATCATCAAATATCATC 5727
                         v  i   v v  i i   i  iiivv    -- i ii     i-------
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG------- 687

  chrX_81848930_8   5728 AGAGTGAACAAGCAACATACAGAATGGGAGAAAAT---------TTACCC 5768
                          i      v ii    vi                 --------- i ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_81848930_8   5769 ATCTGACAAAGTGCTAATAACCAGAATCTAGAAAGAACTTAAGGAAATTT 5818
                               i  i vi  vi  v       v  v        ivviv  v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_81848930_8   5819 ACAAGAAAAAAACAA----CCCCATTAAAAAGTGGGTGAAGGATATGAAC 5864
                          i  v     i    ----   v   ?    i    ii      v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_81848930_8   5865 AGACACTTCTCAACAGAAGACATTTATGTAGCCAACAGACACATGAAAAA 5914
                              i     v v      i  vi vi i     i ii          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_81848930_8   5915 ATGCTCATCATCACTGGTCAT 5935
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.64 (37 / 14)  


3085 28.46 0.44 0.66  chrX_81864192_81870593.rev     5002  5911 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81864192_8   5002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5051
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81864192_8   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81864192_8   5102 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5149
                          v   iivi i  i  iii    -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_81864192_8   5150 ATATGGAACCAAAAAAGAGCCCGCATAGCCAAGTCAATCCTAAGCCAAAA 5199
                                 viiv  ii  v  v v        iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_81864192_8   5200 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5249
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_81864192_8   5250 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAT 5299
                                  i   i    ii         i iv ii i   i        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_81864192_8   5300 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATGTCTACAAG 5347
                                 i    i--    i  --        vv iii ii i  iiiv
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_81864192_8   5348 TATCTGATCTTTGACTAACCTGAGAAAAACAAGCAATGGGGGAAGGATTC 5397
                         i vi    i  i   v ivv  vv  i v  vv        i   i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_81864192_8   5398 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5447
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_81864192_8   5448 CGAAAGTGGATCCCTTCTTTATACCTTATACAAAAATTAATTCAAGGTGG 5497
                         i   iv    i    v i i i   v              i    ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_81864192_8   5498 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGGAAT 5547
                           i ?    i       v   v       i      vi i      i  v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_81864192_8   5548 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5597
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_81864192_8   5598 AAACACAAAAAGCAATGGCAACAAAAGCCCAAATTGACAAATGGGATCTA 5647
                         vi    v       vvi          vvv    v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_81864192_8   5648 ATTAAGCTAAAGAGCTTCTGCACAGCAAAATAAACTACCATCAGAGTGAA 5697
                           i  iv v  i i   i  ii vv    iv v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_81864192_8   5698 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACCCATCTGACA 5747
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_81864192_8   5748 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5797
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_81864192_8   5798 AAAAACAAGCAACCCCATCAAAAAGTAGGTGAAGGACATGAACAGACACT 5847
                           i -   ii     v  i?    i i  ii     iv    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_81864192_8   5848 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACAGATGAAAAAATGCTCA 5897
                             v        i  vi viii     v  i  v       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_81864192_8   5898 CCATCACTGTCCAT 5911
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (155 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


2343 29.13 1.10 1.22  chrX_81872527_81874334      499  1315 (493)    L1M4_orf2#LINE/L1       93   908 (0)  

  chrX_81872527_8    499 TATCAAGCTACTATTGACTTTCTTCACATAATTAGAAAAATCT--TCTTT 546
                               iv v i vivi i  i  ii  v  v v  v  i-  --  i v
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTA 141

  chrX_81872527_8    547 AAATTTTATATGGAACCAGAAAAGAGCGCACATAGCCAAGACAATCCTAA 596
                              i-        viiv  ii  v vviv        i      i i 
  L1M4_orf2#LINE/    142 AAATTC-ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_81872527_8    597 GCAAAAAGAAGAAAACTGGAGTCATCATGCTACCTGACTTCAAACTATAC 646
                         iv  i     v   ii     vvv   ii  v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_81872527_8    647 TACAAGACTATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGA 696
                              ii   i     i   i    ii         i iv ii i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_81872527_8    697 TATAGACCAATGGAACAGAACAGAGACCTCAGAAATAACATCACACATCT 746
                               i        i    iv    vii         vvi  i    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_81872527_8    747 ACAACCATCTGGTCTTTGACTAACCTGGCAAAAAAAAAAAAAAAGCAATG 796
                          iiii  vi  i i  i   v ivv  v   i vv v-------v     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT-------TCAATG 383

  chrX_81872527_8    797 CAGAAAGGATTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCA 846
                         vi     i  vvi  v  i  i        i     v      v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_81872527_8    847 TATGCAGAAAACTGAAACTCAATCCCTTCCTTACACCTTATACAAAAATT 896
                         i     i  i v    ii vi i    v   i     v            
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_81872527_8    897 AACTCAAGGTGGATTAAAGACTTAAAGATAAGACCTAAAACCACAAAAAC 946
                                ii     i ?    i    vi     v       i i    vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_81872527_8    947 CCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAA 995
                          i           v    ?i- v i -   iv   v v  vv i     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chrX_81872527_8    996 GACTTCAT-GATTAAACAACAAAAGCAATGACAACAAAAGCCAAAATTGA 1044
                          ii   v -   vvi   v        vvii         vv     v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_81872527_8   1045 CAAATGGGATCTAGTTAAACCAAAGAGCTTCTGCACAACAAAAGGAGCTA 1094
                         i    v   ii vi i   viv  i i   i  ii vv    i ivi   
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_81872527_8   1095 TCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATC 1144
                            vv i      v  i     i                 v       vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_81872527_8   1145 TATCCAACTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACA 1194
                         i  vi v    i  i  i  vi          v  i  i     ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_81872527_8   1195 AATTTACAAGAAAAA-----ACAACCCCACCAAAAAGTGGGCAAAGGATA 1239
                          v iv i  v     ----- i     v ii?    i            v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_81872527_8   1240 TGAACAGACACTTCTAAAAAGAAGACATTCATGCACCCAACAAACATATG 1289
                             i     i    vv        i  v  viiiv    i  i  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_81872527_8   1290 AAAAAAAGCTCTTCTTCACTGGTCAT 1315
                             i v    vv v   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (134 / 100)
Gap_init rate = 0.01 (8 / 816), avg. gap size = 2.38 (19 / 8)  


3213 27.31 0.44 0.44  chrX_81917133_81920137     1605  2512 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81917133_8   1605 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1654
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81917133_8   1655 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1704
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81917133_8   1705 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1752
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_81917133_8   1753 TATGGAACCAAAAAAGAGCCCGCATAGCCAAGTCAATCCTAAGCCAAAAG 1802
                                viiv  ii  v  v v        iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_81917133_8   1803 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACGAGGC 1852
                                i      vv       v  ii i      viv      i i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_81917133_8   1853 TACAGTAACCAAAACAGCATGTTACTGGTACCAAAACAGAGATATAGATC 1902
                                 i   i    ii  v      i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_81917133_8   1903 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATACCTACAACT 1950
                                i    i--    i  --        vv iii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_81917133_8   1951 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2000
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_81917133_8   2001 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2050
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_81917133_8   2051 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATCAATTCAAGATGGA 2100
                            ii    i    v   i   i v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_81917133_8   2101 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2150
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_81917133_8   2151 CTAGGCATTACCATTCAGGACATAGGCATGGGAAAGGACTTCATGTCCAA 2200
                         v    ?i v viv   iv   v v  vv i  v  v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_81917133_8   2201 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 2250
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_81917133_8   2251 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2300
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_81917133_8   2301 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 2350
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_81917133_8   2351 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2400
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_81917133_8   2401 AAACAAACAACCACATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 2450
                          i     i    vv  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_81917133_8   2451 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 2500
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_81917133_8   2501 ATCACTGGCCAT 2512
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 394 32.57 0.57 2.86  chrX_81940852_81946642     3895  4069 (1722)    L1M4_orf2#LINE/L1        3   173 (735)  

  chrX_81940852_8   3895 GAAAAGCATTTCATTCTCATGAATTGGAAGAGTCAATATATTTTAAATGA 3944
                             iii  ii   vi     i         v i     vv  v i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_81940852_8   3945 CCATATTGCCCAAAGCATTTTACAGGTCCAGTATTATTCCTGTTAAAACT 3994
                          v   i v      viiv i     i i  iiiiv  i   i i    - 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-T 101

  chrX_81940852_8   3995 ACTAA-TGTAATTCTTCACAGAATTAGAAAAATATAATATTCTAAAATTT 4043
                         v i i-  iv-  i  ii     v v  v  ii- i  --i        i
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGAT--CCTAAAATTC 147

  chrX_81940852_8   4044 GTATGAAACTAAAAAGGACCCTAAAT 4069
                         i    i  v iv  i      vi   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAAT 173

Transitions / transversions = 2.17 (39 / 18)
Gap_init rate = 0.03 (5 / 171), avg. gap size = 1.20 (6 / 5)  

1450 27.59 4.44 0.93  chrX_81940852_81946642     4759  5298 (493)    L1M4_orf2#LINE/L1      350   908 (0)  

  chrX_81940852_8   4759 TGTTCTTTAACAAGGCTGAGAAAAATAAGCAATAGAGAAA----AGACTT 4804
                           v i  ii      v  vv  i vi vv    i i    ----  v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_81940852_8   4805 CATATTAAATAAACAGTGATAAGACAGCTGGCTAGCCATAGG-AAGAAAA 4853
                         ----  v  i   ii   v ii    i    v  ?   i v -  i i  
  L1M4_orf2#LINE/    400 ----TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_81940852_8   4854 TTAAAACGGTTTTCTAAATTTCACCATATAACAAAATTGAATCAATATGG 4903
                          v  ivi  viii   vv iv         vv      i v    v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_81940852_8   4904 A----AGATTTAAAAGTAGAATCTGAAATTATAAAAGTCCTAGAAGAAAA 4949
                          ----   ii    v   ii v  i   i       v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_81940852_8   4950 TCTAAGCAATACCCCTCTTGATGTTGGCCTTGGCAAAGAATTTATGGGTA 4999
                         iv  i ?ivv vi i  v   iv    vi v     v iv  iv i i  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_81940852_8   5000 AATCCCCAAAAGCAGTTGCAACGAAAACAAAAAAGTGGTAAACAGAACCT 5049
                         viv v         vvv     -    v      vv i    iv i  i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_81940852_8   5050 AATTAAACTAAAAGGCTTCTGCACAGCAAAAG----TATCAACAGAGTAA 5095
                         v  i   v v   ii   i  ii vv    i ----      v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_81940852_8   5096 ACAGG-AACCTAGAGAATGAGTGAAAATATTTACAAACTATGCATCTGAC 5144
                          v  i-    i v      i v          i    ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_81940852_8   5145 AATAGTCTAATATCCAGAATCCATAAAGAACTT----AAATCAACC-TGA 5189
                           vi v  vi          vi          i----  v    iv- i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_81940852_8   5190 AAATA---ATAACCCCATT--AAAATGGGCAAAAGGCATGAACAGACACT 5234
                            v ---       v   --            i iiv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_81940852_8   5235 TTTCAAAAGAAGATGTACACATGGCCAACAAGCATATGAGAAAATGCTCA 5284
                          i  v         i    v        i     i    i  i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_81940852_8   5285 ACATCACTAATCAC 5298
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (81 / 66)
Gap_init rate = 0.02 (11 / 559), avg. gap size = 2.64 (29 / 11)  


 263 31.98 1.16 4.07  chrX_81961724_81965337     2437  2608 (1006)    L1M4_orf2#LINE/L1       13   179 (729)  

  chrX_81961724_8   2437 CCATACTAACTGACAGGAAAAATCTATATTGTTAAAATGGCCATTCTGTC 2486
                             ii v iv  iv    i v iv          i     v  v  vi 
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_81961724_8   2487 AAACACAATTGACAGTTTCAGTGCTATTCCTATCAAACTACAAAAGACAT 2536
                         v  vvii  iv    v    ii  v  i         v v v ivvi v 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_81961724_8   2537 TTTTCAAAGAATTAGAAAAAACT-ATTCCAAAATCCATATTGAACCAAAA 2585
                             iiv    v v  v  i-  -  i i     i     v   viiv  
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_81961724_8   2586 AAAAAAAGTGCCCA-AATAGTCAA 2608
                         iii ------    -     i   
  L1M4_orf2#LINE/    162 GGGA------CCCAGAATAGCCAA 179

Transitions / transversions = 1.04 (28 / 27)
Gap_init rate = 0.02 (4 / 167), avg. gap size = 2.25 (9 / 4)  

1281 25.82 0.25 0.25  chrX_81961724_81965337     2727  3121 (493)    L1M4_orf2#LINE/L1      514   908 (0)  

  chrX_81961724_8   2727 AGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTC 2775
                            v       i      vi i           v    ?i- v i -   
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC 562

  chrX_81961724_8   2776 AGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATG 2825
                         iv   v v  vv i     v ii   v ivv  vi            vvi
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_81961724_8   2826 GCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTT 2875
                                   vv     v  i    v   ii v  i   v v  i i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_81961724_8   2876 CTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAAT 2925
                         i  ii vv    i  v    i  vv i      v  i     i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_81961724_8   2926 GGGAGAAAATTTTTGCAATCTACTCATATGACAAAGGGCTAATATCCAGA 2975
                                   v       vii ivi  v   i  i  i  vi        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_81961724_8   2976 ATCTACAAAAAACTCAAACAAATTTACAAGAAAAAAACAAAGAACCCCAT 3025
                           v  i   i     vv    v iv i  v     i     v     v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_81961724_8   3026 CAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTT 3075
                         i?    i     i     iv    i     i     v        i  vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_81961724_8   3076 ATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCAT 3121
                          viii     v  i          i       v     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.08 (52 / 48)
Gap_init rate = 0.01 (2 / 395), avg. gap size = 1.00 (2 / 2)  


 842 23.81 4.76 3.30  chrX_81967436_81969230        2   274 (1521)  C L1M4_orf2#LINE/L1   (556)   352    76  

C chrX_81967436_8    274 AGACATAAGGCGACTCCATATCAAAATCCCAGAAAATTATTTTTTGGTTA 225
                            ivi  v  i -   v              ----i iii    --  i
  L1M4_orf2#LINE/     76 AGATTCAACGCAA-TCCCTATCAAAATCCCAG----CTGCCTTTT--TTG 118

C chrX_81967436_8    224 T-GAAA-----AAACTGACTCTAAGGTTTATATGGAAAGGCAAAAGACCC 181
                         i-    -----  i    ii    ii  i         v    ii     
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

C chrX_81967436_8    180 AGAATACCCAACTTGATATTAAAAAAG--GAACAAATATG-ACTACTGAC 134
                               v    vvii  v  i      --       vv  - vv   v  
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

C chrX_81967436_8    133 ACTACCTAACTTCAAAACTTCCTATAAAGTTATAATAATCAAGACAGTG- 85
                            v  i  i          v   i    i  i i              -
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

C chrX_81967436_8     84 -ATATTCACAAATGACTAGACAAATAGACCAATGGAACATAATAGAGAGC 36
                         -i  i vi  v v iv      v     i        i v   v     i
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

C chrX_81967436_8     35 CTGGAAAAGGAC--ATACGTGAATACAGTCAGTTGA 2
                          ii    vii  --    i v--  ii    i    
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATT--TATGGTCAATTGA 352

Transitions / transversions = 1.71 (41 / 24)
Gap_init rate = 0.04 (10 / 277), avg. gap size = 2.20 (22 / 10)  

 355 28.43 0.00 0.00  chrX_81967436_81969230      337   438 (1357)  C L1M4_orf2#LINE/L1   (801)   107     6  

C chrX_81967436_8    438 AGATAGTACGTGTTCATAAACAGAAAGACTCAATATCTTAAAGATGTCCA 389
                              viv i       ii iv i      i     iv v      v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

C chrX_81967436_8    388 TTATTCCTAAATTTATCTCTAGATTCAATGCCATCCCATTCAAAATTTCA 339
                          vv i  i     v    vi        i  v     vv       ii  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

C chrX_81967436_8    338 AC 337
                         i 
  L1M4_orf2#LINE/    106 GC 107

Transitions / transversions = 1.07 (15 / 14)
Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.00 (0 / 0)  

2559 27.90 1.68 1.08  chrX_81967436_81969230      470  1304 (491)    L1M4_orf2#LINE/L1       69   908 (0)  

  chrX_81967436_8    470 GATATAAGGAT--AACGTAA--CATGTAAAGATCCTACCATTGACTTTCT 515
                            v  vi   --    i  -- v i v  i    i v --  v    i 
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC--TGCCTTTTT 116

  chrX_81967436_8    516 TCACAGAA-TTAGGAAAAACTA--CTTTAAATATCATATGGAACCAAAAA 562
                          -i     -  --  v  i  i-- i v    -          viiv  i
  L1M4_orf2#LINE/    117 T-GCAGAAATT--GACAAGCTGATCCTAAAAT-TCATATGGAAATGCAAG 162

  chrX_81967436_8    563 AGAGTCTGTAGAGCCAAGACAATCCTAAGCAAAAAGAACACAGCTGGAGG 612
                         i  vi v v v      i      i i iv  i       v  i      
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_81967436_8    613 CATCATGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACAAAAA 662
                         vv   ii  v  ii i      viv        i          iv  i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_81967436_8    663 CAGCATGGTACTTGTACCAAAACAGATATATAGACCAATGGAACAAAACA 712
                            ii       v i iv ii i   i       i        i i  iv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_81967436_8    713 GAGGCCTCAGAAATAACACCACATATTTAAAACCATCTGATCTTTGACAA 762
                            ivii         vv   i i     viii  vi    i  i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_81967436_8    763 ACCTGACAAAAAGAAGCAATGGGGAAAAGATTCCCTATTTAATAAATGGT 812
                         ivv  v   i vv vv           ii  vvi  v  i  i       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_81967436_8    813 GTTGGGAAAACTAGCTAGCCATATGCAGAAAATTGAAACCGGACCCCTTC 862
                          i     v    i v  ?   i     i  i v    iii        v 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_81967436_8    863 ATTACACCTTACACAAAAATCAACTCAAGATGGATCAAAGACTTAAACGT 912
                         v i     v  i        i       i        ?    i    i  
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_81967436_8    913 AAGACCTAGGACCATAAAAATCCCAGTAGAAAACCT---GGTCAATACCA 959
                             v   ii  i      v  ii  v       v ---?  v   -- -
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C- 559

  chrX_81967436_8    960 TTCAGGATGTAGGTATGGGCAAATACTTCATGTCGAAAACACCAAAAGCA 1009
                            iv  iv v  vv i     vvii   v ivvv vi            
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_81967436_8   1010 ATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAC 1059
                         vvi          vv     v  i    v   ii v  i   v v  i v
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_81967436_8   1060 CTTCTGCACAGCAAAAGAAACTATCATCAGAGCGAATAGGGAATCTACAG 1109
                            i  ii vv    i  v       vv i  i   v  iv  i i    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_81967436_8   1110 AATGGGAGAAAATTTTTGCAATCTCTCCATCTGACAAAGGGCTAATATCC 1159
                                      v       viiv vi      i  i  i  vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_81967436_8   1160 AGAATCTACAAAGAACTTACACAAATTTACAAGAAAAAAACAA----CCC 1205
                              v  i        ivi    v iv i  v     i    ----   
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_81967436_8   1206 CATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACA 1255
                         v  i?    i            v    i     i     v        i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_81967436_8   1256 TTTATGCAGCCAGCAGACATATAAAAAAATGTTCATCATTGCTGGTCAT 1304
                          vi viii    ii ii  i  i    i   i   v   ii????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (133 / 96)
Gap_init rate = 0.01 (12 / 840), avg. gap size = 1.92 (23 / 12)  


2643 24.62 3.06 3.72  chrX_81973178_81975654     1071  1984 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_81973178_8   1071 TGAAAAAAAATCTCATCTTCATAGATTGGCAGTCTTAATATT---AACAT 1117
                           i   i v   i   v     i      v  v         ---  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_81973178_8   1118 T-TAACATTACCCAAAGTGATCTACAGATTCAGTGCAATCCCTATCAAAA 1166
                         v-i  i i v      v               ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_81973178_8   1167 TTCCAAAAGGATTTCTTGCAGAGATACAAAAATACATTCTCAATTCTGTG 1216
                          i   ivv vv   i       i  vv v  iivv  i  v  v iii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_81973178_8   1217 TGGGATAT-CAATGAATCCCAAATAGCCGAAGCATTTTTTAAA-----GA 1260
                            i -  -   v i i  vi       i  i  v i  v   -----  
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_81973178_8   1261 ACAAAGTTTCAAACACTCACACTTTCTGATTCTAATAATTTA-TACAAAG 1309
                                 vv ii-          i ii   ii  -  i   -       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAA-AACTTACTACAAAG 247

  chrX_81973178_8   1310 ATGCAATAATGAAAAAAAGTGAGGTGCTGTCACAAAAACAAACAAATTGA 1359
                         v i  i    v  i v -   v   i   v  i  ii i i   v  v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACA-GTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_81973178_8   1360 CAAATGGGGTGCAATAGAGAGCACAGAAACAAACCCTTGTATATATGGTC 1409
                         iv     ii iv   v     iv      i      v ii  v       
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_81973178_8   1410 AAATGATCTTTGACAAGGATGCCAAGATAACTTAAAGGAGAGAGAACACT 1459
                           v    i  i       i        iv i i  v  i  i    i --
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA-- 394

  chrX_81973178_8   1460 CGAACACTCTCTTCAACAAATATTGTTAAAACA---GTATATTGTTATGC 1506
                         - -----   i          iv  i iii   --- v   ?ivvi    
  L1M4_orf2#LINE/    395 -G-----TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_81973178_8   1507 AAAA-ATTATAGTTG--TCTTTATTATACACCTTAAACATAGACTAACTA 1553
                             - v iv     --i ii  iivi     v  v   v i i     -
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT- 487

  chrX_81973178_8   1554 AACTAAAACAAAAGTTTTAAAGACCTAAATAAAAGATTTAAAGCTATAAA 1603
                         ---i    iii ---- i ?          iv    vi    i       
  L1M4_orf2#LINE/    488 ---CAAAATGGA----TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_81973178_8   1604 ATTTTTAGAAGAAAACACAGGGGAGAAGCTTCATGACATTGAATTTGACA 1653
                          i i             i   ? vi  v    i    v   ii  v i  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_81973178_8   1654 ATTATTTATTGCATAACAACACCTACAGGCCAATAGGACAGGCAACAAAA 1703
                           vi   v  iv   -ii     --------  v  v   i         
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATA-TGACACC--------AAAAGCACAAGCAACAAAA 621

  chrX_81973178_8   1704 TCAAAAGGAGTCAAGTTAGGACTACATCAAACTTAA----CTTTGTTCAT 1749
                         vv    iv  vi  i  -     v       v    ----i     v v 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATT-GGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_81973178_8   1750 CAAACTATACAAT--AAACAGTGAAAAGGCAACTTACTAATTGGGAGATA 1797
                             vv i  v  -- i v         i    ii  vi v       v 
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_81973178_8   1798 ATATTTGAAAATCATATATCAAATTAGAAATTAGTTTGCAGAATAGATAA 1847
                                v            vi  v  ii i v  v v       v    
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_81973178_8   1848 AAATCTCTTGCAACTCAACAACAAAA-TATAAATAACACAATTTAAAAAT 1896
                          i v     i        i  i    -v i       v     ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_81973178_8   1897 GAGCTGAGGACTGGTGAA--AATATTTCTC--AAAAAGTTATATACAACT 1942
                          i  vi    i --    --i i       --  i   --        v 
  L1M4_orf2#LINE/    821 GGGCAAAGGATT--TGAATAGACATTTCTCCAAAGAAG--ATATACAAAT 866

  chrX_81973178_8   1943 GACCAACACATATATGAAAATATGCTCTACATCACTAATAAC 1984
                          i    i vii i       v      v      ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (129 / 92)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.38 (62 / 26)  


2602 26.66 3.49 1.69  chrX_81979914_81983056.rev     1764  2652 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_81979914_8   1764 AAAAAAATCC-ATGCTTATGGAT----ACAATCAATATTGTTAAAATGGA 1808
                            i v    -   i i      ---- v v i           i    -
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG- 52

  chrX_81979914_8   1809 CAA-ACTGTCCCAAGCAATTTATAGATTCAATGGTATTCCTATCAAACTT 1857
                            -   vi  v  vii  i  i        i vv  i         v i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_81979914_8   1858 GCAGCAATATTTTCAACCGAATTAGAAAAAACT-ATTCTAAAATTCATAT 1906
                         v    viiv    ivi v   v v  v  i-  -  i             
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chrX_81979914_8   1907 AGA--TCCCACAAAAGTACCCA-AATAGCCATAGCAGTCCTAAGCAGAAA 1953
                         i  -- ---i   ii -     -        v i  i  i i iv ii  
  L1M4_orf2#LINE/    152 GGAAAT---GCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_81979914_8   1954 TGAA-AAAGCTGGAGACATCAGATTACCTAGCTTCACACTATACGACAAG 2002
                         -   -    i     ivv   v i v  i ii    v viv   v    i
  L1M4_orf2#LINE/    198 -GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_81979914_8   2003 GCTACAGAAAGCAAAATAGCATGGTACTTGTACTAAAACAGACACATAGA 2052
                                v  v   i i  ii       v i iv ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_81979914_8   2053 TCAATGAACTAAAAC----AGCCCAGGAATAAATTCACACACCTACAA-C 2097
                               i v  i  i----  i    i      ii  i   ii  iii- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_81979914_8   2098 ATCTGATCTTTGACAAAGTCAGTAAAAACAAGCAATGTGGAAAGGAC--T 2145
                          vi    i  i     i viivi  i v  vv     v      i i-- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_81979914_8   2146 ATATTCAATAAATGCTGCTGGGATAACTGGTTAGCCTTATGCAGAAGATT 2195
                         v v     i     v        i      v  ?  vi     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_81979914_8   2196 GAAACTAGACCCCTTTCATACACCTTATACAGAAATCAACTCAAGATGGA 2245
                            ii i       vi vi     v      i    i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_81979914_8   2246 TTAAAGACTTAAATGTAAAACTTGAAACTATAAAAATCCTGGAGGGTAAC 2295
                          i ?    i         i vi i           v  i i  i iv   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_81979914_8   2296 CTAGG---AAATATT----ATTCTGGACATAAGCTGTGACAGAGTTCATG 2338
                         v    ---    v  ---- iii   ii-  i  vi  -----   iv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATG-----GTTTCTT 590

  chrX_81979914_8   2339 ACAAA-GTCATCAAAAGCAATTACAACAGAA-ACAAAATTGACAAATAGG 2386
                          v v - v  i        vvvi     i  - v     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_81979914_8   2387 ACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAGCTATCAACAGA 2436
                           i v  i   v v  i i   i  ii vv    i  vi       v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_81979914_8   2437 GTAAACAGACAACTTACAGAATTGGAGAAAATATTTGCAAACTATGCATC 2486
                           i  v       ii       v                  ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_81979914_8   2487 TGACAAAGGTCTAATATCCAGAATCT-TAAAGGAATTTAAACAAATTAAC 2535
                            i  i  v  vi          v -     -  i ivv    v i  i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAG-AACTCTTACAACTCAAT 789

  chrX_81979914_8   2536 AAGTAAAA---CCAACAATCCCATTACAAAGTGGGCAAAGGACATGAACA 2582
                           -     --- v  i  i  v   ?v   i           iv    i 
  L1M4_orf2#LINE/    790 AA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_81979914_8   2583 CACACTTTTCAAAAGAAGATATACATGCAACCACCAAGCATATGAAAGAA 2632
                         v   i  i  v              viiii   vi     i      ii 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_81979914_8   2633 TGTTCAGCATTACTCATCAT 2652
                           i   i   i ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (146 / 88)
Gap_init rate = 0.03 (25 / 905), avg. gap size = 1.84 (46 / 25)  


1678 30.39 5.05 2.29  chrX_82002298_82004950.rev     1301  2172 (481)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_82002298_8   1301 CCATGCTAACTGATAGGAAAAATCTGTACTGTTAAAATGGCCATTCTGCC 1350
                              i v iv   v    i v ivi  i      i     v  v  v  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_82002298_8   1351 AAACACAATTGACAGTTCCAGTGCTATTTCTATCAAACTACCAAAGATAT 1400
                         v  vvii  iv    v i  ii  v  ii        v v   ivviiv 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_82002298_8   1401 TTTT--CAAATAATTGGAAAAAACT-ATTCTAAATTTCA-----AACTG- 1441
                             --  i -     -- v  i  -  i     v    -----  v  -
  L1M4_orf2#LINE/    113 TTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_82002298_8   1442 ----AACCAAAAAAAGTGCCTGAATCAATCCTATTCAAAATGA------- 1480
                         ----i   v i  v  --- ii  v     ---  v    v  -------
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAG---CCAAAACAATC---TTGAAAAAGAAGAACAA 203

  chrX_82002298_8   1481 -----------TCTTCCTACCTGAATTCAAACTATACTACAAGGCTATAG 1519
                         -----------  viv  v  ii v      viv        i    i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_82002298_8   1520 TAA-AAAAATAGCACAGTACCAGTAGAAAAACA--CACATAAACCAATGA 1566
                            -v  i i  iiii    ii i v  ii i --  i   i i     i
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_82002298_8   1567 AACAGAATGAAGAACCCAGAAAGAAACCC-TACTGTCTACAATCACCTG- 1614
                           i     vi   ii       v      -   -i i  iii   vi  -
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATAC-ATTTATGGTCAATTGA 352

  chrX_82002298_8   1615 TCTTTGACAAAGTTGACAAAATCAAGCAACAGGGAAAGGATTAAAAAT-- 1662
                          i  i     i v  v   i i  vv   ii       i  ---- i --
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT----AGTCT 398

  chrX_82002298_8   1663 --TCGGTAAATGGTGCTGGCATAACTGACTAATCATATGCAGAAGATTAA 1710
                         --  iii            v i     iv  ?i  i     i    v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_82002298_8   1711 AACTAGACCACTTCCTTTCCCCATATGAAAAAAAATCAACAGAATATAAA 1760
                          ii i    v  v   iv v      -- v      i   vv  v  ii 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATAT--ACAAAAATTAACTCAAAATGGA 496

  chrX_82002298_8   1761 TTAAAAACTTTAAAATATAAAACATAAAACTATAAAATCCCTTGACGATA 1810
                          i ? i  i --    i   i vv             ii i v  v  v 
  L1M4_orf2#LINE/    497 TCAWAGACCT--AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_82002298_8   1811 ACCTAGGAAATAACATTCTGGACATAGGACCTATCAAACACGTCATGACT 1860
                           v    ?ivv  iv   vv   v v  iiiviv   vviiv  v iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_82002298_8   1861 AAGGCTCTGAAAGCAGTTAACGACAAAACCAAAAATTAACAAGTGAGACC 1910
                          v i v ii      -iv i i      vv      vi i  i vi   i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_82002298_8   1911 TAATTAAA-TGAAAGAGATTCTGCACAGCAAAAGAAACTACCAACAGTGT 1959
                          v  i   - v   i v-  i  ii vv    i  v    i   v iv  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_82002298_8   1960 AAATGGAAAACCTATAGAATGAAAGAAAATATTTGCAAATGATGCATCCA 2009
                         i  vi  v    i i      ii                 v  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_82002298_8   2010 ACAAAGGTCAT-TATTCAGAATCTGTAAGGAATTTAAACAAATTAACAAG 2058
                          i  i  v v -   i      v i   i   i ivv    v i  i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_82002298_8   2059 CAAAA-ATAAACAACCACATTAAAAATTGGGCAAAGGTCATAAACAGACA 2107
                         v    - i   i    vv   ?    v          viv i  i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_82002298_8   2108 CTTCTCAAGAGAAGACATAAACATGGCCAAAAGGCATATGAAAAAATAAT 2157
                         i     v i      i   v v        v i   i       i  iv 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_82002298_8   2158 CC-CATTAATCATTTG 2172
                          v-   i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (151 / 110)
Gap_init rate = 0.03 (24 / 896), avg. gap size = 2.67 (64 / 24)  


2612 28.97 1.33 0.55  chrX_82009338_82011600      870  1770 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82009338_8    870 TGGAAAAACATTTCATCCTCATGGATAAGAAGAATCAATATCGTAAAAAT 919
                               i i  ii   vi        vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82009338_8    920 TGCCACACTGCCCAAAGTAATTTATAGATTTAATGTTATTCCCATCAAAC 969
                         v  v i   v      v i  i  i     i  i iv  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82009338_8    970 AACCATTGACATTCTTCACAGAAATAGAAAAAACT-ACTTTAAATTTCAT 1018
                         vv   vivi v  i  ii       v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_82009338_8   1019 ACGGAATCGAAGAAGACACTGTATAGCCAAGACAATCCTAAGCAAAAAGA 1068
                          i    vi v iii   v v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_82009338_8   1069 ACAAAGCTGGAGGCATCACATTAGCTGACTTTAAGCTACACTACAAGGCC 1118
                               i      vv     i vv ii i  i  ivivi       i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_82009338_8   1119 ACAGTAACTAAAACAGCATTATACCTATATCAAAACAGACATATAGACCA 1168
                                ii  i    ii vi   ivii  v ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_82009338_8   1169 ATGGAACAGATCAAAGACCTCAGAAATAACATCACACATCTA-AACCATC 1217
                               i   vivi   vii         vvi  i    i  -iii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_82009338_8   1218 TGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGGAAAAGATCTCCTA 1267
                             i  i i   ivv  v   i v  vv           ii  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_82009338_8   1268 TTCAATAAATGGTGCTTGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 1317
                              i          v   v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_82009338_8   1318 ACACAGACCTCTTCCTTACACCTTATACAAAAATCAACTCAAGAAGGAAT 1367
                         ii-ii    i  v   i     v           i       i v   vi
  L1M4_orf2#LINE/    450 GT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_82009338_8   1368 AAATACTTAAATGTAAAACCCGAAACCATAAAAACCCTAGAATAAAACTT 1417
                          ? v  i         i v ii    i      vi i     v     v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_82009338_8   1418 AGGCA-ATACCACTCA-GGCATAGGCATGGGCAAAGACTTCATGACGAAA 1465
                            ?i- v i -i  i- i v v  vv i     v ii   v iivv vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_82009338_8   1466 ATGCCAAAAGCAATTGTAAAAGAAGCCAAAAT-TACAAATGGGATCTAAC 1514
                          ii         vvv i  v i   vv     -v i    v   ii v i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_82009338_8   1515 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 1564
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_82009338_8   1565 GGCAACCTACAGAATGGGAGAAAATTTGTGCAATCTACCCATCTGATAAA 1614
                          i     i                 v v     vii ivi         i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_82009338_8   1615 GGTCTAATAGCCAGAATTGATAAGAAACGTAAACATATTTACAATAAAAA 1664
                           v  vi  v       vv    ii   vivv   vv iv i        
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_82009338_8   1665 ---AAA-AACCCCATCAAAAAGTGGGCAAAGGGTATGAACAGACACTTCT 1710
                         ---   -     v  i?    i          i v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_82009338_8   1711 CAAAAGAAGACATA--AATGCAGCCAACAAACATATGAAAAAA-GCTCAA 1757
                          v        i   --    --     i  i  i       i -      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_82009338_8   1758 CATCACTGAACAT 1770
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (151 / 106)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.31 (17 / 13)  


2593 28.48 0.76 2.80  chrX_82024803_82027045.rev      826  1752 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82024803_8    826 TAGAAACACATCTCATTCTCATAGATGGGTAGAATCAATATTGTGAAAAT 875
                          i    v i   i   vi    i   v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82024803_8    876 GACCATATTGCC-AAA---ATCAACAGATTCAATGTAATTGTCATCAAAA 921
                          i v   i v  -   ---   v          i i   ivii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82024803_8    922 TACCATCACCATTGTTCACAAAAGTAAACAACAACAACAACACAATTTTA 971
                          v   v vv v  v  ii  i  i vi    --------i -ii  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--------GC-TGATCCTA 141

  chrX_82024803_8    972 AAATTCATATAAAACCAAAAAAGAGCCCACATAGCAAATGCAAAACTAAG 1021
                                   ii  viiv  ii  v  viv     v  vi   vvi i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_82024803_8   1022 CAGAAAGACCAAACTTGGAGGCATCACATTACCCAACTTCAAACTATACT 1071
                         v ii    v    v       vv     i v     i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_82024803_8   1072 ACAAGGCTGTAGCTACCACAACAGCATGGTAGTGGTATAAAAATAGGCAT 1121
                             i   ii  iv i  vi    ii     v   i    ii    i   
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_82024803_8   1122 GTAGACTAATGGAAGAGAATAGAGAACCCCAGAAGTAAAGCCAAATTCTT 1171
                         i    ii       v     v    ii  -    i    v   v ivi  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCC-AGAAATAAACCCATACATTT 340

  chrX_82024803_8   1172 ACAGCCAACTGATCTTTGAAAAAGGAAACACAAATATAAAGTGGAAGAAG 1221
                          ii i   i    i  i  v  i  viv  vi vi  vv i   iii   
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_82024803_8   1222 GACATTCTATTCAACAAACCGTGCTGAGATAATTAGCAAGCTACATGTAA 1271
                         i i v   v         iv      i  i  i i vv ? i     i  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_82024803_8   1272 AAGAATAAAACTGGACCCTCATCTCTCACCTTATAAAAAAATCAACTCAA 1321
                               i  ii       ii i   v    v    v      i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_82024803_8   1322 GATAAATCATAGGCTTACATCTAAGACCTGGAATCATAAAAATTCTCAAA 1371
                         i  ii    ?  i i  v  v     v  ii  ii      v ii vi  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_82024803_8   1372 GATAATGTTGGAAAAACTCTTTTAGACACTGGCTTAGGCAAAGAGTTCAT 1421
                           v  ii v  ?iv  v    ivv   vi   v        v iv   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_82024803_8   1422 GACCAAGAACCCAAAAGCAAATGTAACAAAAACAAACAACAACAACAACA 1471
                         iivi v  vv         -------------   i      -  v  v 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCA-------------CAAGCAACAA-AAGAAAA 626

  chrX_82024803_8   1472 ACAAAATAGATGGGACCTAAGTAAG-CTAAAAACTCCTGCACAGCAAGAG 1520
                          vv i   i  v    i v vi  i-i        ii  ii vv   ii 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_82024803_8   1521 AAATAATCAGCAGAGTACACAGACACCCCACAGAATGGGA-AAAATATTT 1569
                          v iv    iv i   iv v     v              -         
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_82024803_8   1570 GCAAACTATGCATCTGTCATAGGACTAATATCTAGAATCTATGA-TAACT 1618
                              ii  ii     vi vi     vi    i     v   i -v    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_82024803_8   1619 CAAACAAATCAGCAAGAAGAAAAACCAAATAACTGAATCAAAAAATGGGC 1668
                          vv    v   ii  v  i  i --        iv   i?          
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGC 824

  chrX_82024803_8   1669 AGAGGACATGAATAGATAATTCTCAAAAGTAGATACACGAATGGTCAACA 1718
                          i    iv        i v     v    v     i  i     i   i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_82024803_8   1719 AATATGTGAAAAGATGCTCAACATCACTAATTTT 1752
                          ii ii                    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (154 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.00 (33 / 11)  


2377 29.79 1.77 1.22  chrX_82037418_82040525     1713  2615 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82037418_8   1713 TGAAAAAGCATTCTATGCTCATGGGTAGGAAAAATAAATATTGTTACAG- 1761
                           i   iii  i i   i      i v    i v v          -  -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGA 49

  chrX_82037418_8   1762 -GGTACATACTGTCAAAAGAAATCTATAGATTCCATGCTATTCCTATCAA 1810
                         -  i -     vi v   vvi     i      v i  v  i        
  L1M4_orf2#LINE/     50 TGGCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_82037418_8   1811 ATGACTAGTGATGTTCTTCACAGAATTAGAAAAAAGTATATCTTTAAAAA 1860
                          vvv i  iviiv  i  ii     v v  v  -- ivv   i --    
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCT--AAAA 144

  chrX_82037418_8   1861 TTCATATGGAA-TAAAAAAAGTTTGTGA-AACTAAGGTAATTCTAAGCAA 1908
                                    - iv  iiiiiiiivi - i i  iii   ii i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_82037418_8   1909 TAAGGGCAAATCTGGAGACATGATGCTACCTGACTTCAAACTATACTCTA 1958
                         v   ii    vi     ivv v ii  v  ii i      viv    vi 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_82037418_8   1959 ATGCTGCAGTAAACAAAACAGAATAGTCCTGGTACAAAAACAGACACATG 2008
                          v   i      v   i    vi i  v    i i  ii i     i  i
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_82037418_8   2009 GACCAATCAAAGAGGATAGAGAGTCCAGAAATAATGTCACACAGCTACAA 2058
                           i    vi  v  i  v                vvi  i   vi  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_82037418_8   2059 CCAACTGATCTTCAAAAAAGCTGACCAATGCAAG-CAATGGAGAAAGGAT 2107
                         i   i    i   i v  i v  -    vi v v-      i     i  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_82037418_8   2108 TCCCTATTTGATAAATGTTGCTGGAATAATTGGCTAGCCCTATTCTGAAG 2157
                         vvi  v  ii i     v      i i  i   v  ?  vi  v vi   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_82037418_8   2158 ATTGAAACTGGATCCCTTCCTTATACAATATACAATAATCAACTCAAGAT 2207
                          v    ii    i    v   i i  v        v   i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_82037418_8   2208 GGATTAAAGACATAAATGTAAAAGCTAAAACTATAAATAC-CATGGAAGA 2256
                             i ?    v         i               -  - v i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGA 542

  chrX_82037418_8   2257 TAATCTCAGAAATA--CCATTCTGGGCACAGGCTCTGGCAAAGGTTTTAT 2304
                         v  iv -  i?i  --i -   vv i viv  v iv     v     iv 
  L1M4_orf2#LINE/    543 AAACAT-AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_82037418_8   2305 A-ATA-GACAACAAAAGTAATTGTATAATAAACAAAAATGGACAAATGTG 2352
                          -   -    v      i vvv i vv v  iv      i  i    vv 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_82037418_8   2353 ACCTAATTAAACTAATGAGCTTCTGCACAACAAAAGACACTATCAACCAA 2402
                           i v  i   v v vi i   i  ii vv    i           vv  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_82037418_8   2403 GTAAATAGACAACGTAGAGAATGG-AGAAAATATTTGCAAACCAGGCATC 2451
                           i  v       vi v       -                i  vii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_82037418_8   2452 TGAAAAAGGGCTAATATCCAGAATCTATAAGGAATTTAAACAAATTTACA 2501
                            v  i  i  vi          v     i   i ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_82037418_8   2502 TGCAAAAAAACC--CAACCCCATTACAAAGTAGACACAGGACATAAGCAG 2549
                         -ii     i  v--i     v   ?v   i i i  v    iv i ii  
  L1M4_orf2#LINE/    791 -ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_82037418_8   2550 ACACTTTTCAAAAGAAGACATACATGCAGGCAACA-GCCTATAAAAAA-- 2596
                            i  i  v        i     viii v   i -  vi  i    i--
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_82037418_8   2597 GTTCAACATCAGTAATCAT 2615
                          i         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (157 / 108)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.29 (27 / 21)  


1944 28.35 9.13 1.42  chrX_82085485_82089628     2809  3651 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82085485_8   2809 TGGAAACATATTC--TGTTTATAGGTTTGAAGCATTGATACTGATGAAAT 2856
                               v    i --    i  i i  v    vv  i   i  v i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82085485_8   2857 ATTCATACTACCCAAAGCAATCTAAAGATTCAATGAAAATAAAAATCCTA 2906
                         iviv     v      vii     v        i v  - -----i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAA-T-----CCCTA 94

  chrX_82085485_8   2907 TCAAAACACCAATGACATTTTTCTCAGAAACAGACAAAA-AAGACTAAGA 2955
                               iv   iivi v     iv      iv     iv-i vv    i 
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_82085485_8   2956 TTTATATAGAAGAACAAAAGACCCAGAATAATCAAG-CTATTTTAAGCAA 3004
                           i    i   ivi   ii           ii   i- v  i  i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_82085485_8   3005 AAAGGACAAAACTAGAGAAATCATATTAATGGACTTCAAATTATGCTACA 3054
                         i   i     ii i   i v   i i vvivi i      viv i     
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_82085485_8   3055 GAGCTCTAGTAAACTGAATGACAA---GCTACTGGCATTAAAACAGACAC 3101
                         i    vi     v --  -    i--- v         v ii i     i
  L1M4_orf2#LINE/    245 AAGCTACAGTAATC--AA-GACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_82085485_8   3102 ATAAATCAGTGGAACAGAATAGAGAACCCAGAGATAAAGGCATACATCTA 3151
                            i    i     i     v    ii     i     vv       i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_82085485_8   3152 CAGTGAACTCACTGTTGACAAAGGTGCCAATAACATACATCAAGGAAAGA 3201
                         ii  v  i v i v i     i        v v   v  viii       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_82085485_8   3202 AT----------------------------------TA------------ 3205
                           ----------------------------------  ------------
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_82085485_8   3206 --------------CCCCTATCTCTCTACC---TAAAAAAATCAAATAAA 3238
                         --------------      i   v -   ---  v      i  v v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCAC-ACCATATACAAAAATTAACTCAA 490

  chrX_82085485_8   3239 AATGGCTTA-AGAATTAAATATAAGACCTCGAACTATGAAAGTACTGCAA 3287
                              v i -   vi     i     v  vi      i   v vi iv  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_82085485_8   3288 GAAAATATTGGGAAAACTCTCAAGGACATTGGAATGGGCAAAAATTTATT 3337
                              i  v  ?iv  v   iviv   v    iv i     vii   v  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_82085485_8   3338 GAGTAACACTCCATAAGCGAAGGCACCTAAAGCAAAAATGGACAGATGAG 3387
                         iii  vv  v   v    iv i   v v    v      i  i i  vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_82085485_8   3388 ATCACATCAAG-TTAAG--CTTCTGCACAGTAAAGGATACAATCAGCAAA 3434
                          iiv      i-    i--   i  ii vvi      i  v    iv   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_82085485_8   3435 GTGAAGAGACCACACACAGAGTGGGACAAAATACTTGTAACCTACCCATT 3484
                              i    v  v      i     v      i   i  vii ivi  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_82085485_8   3485 GGAAAAGGGTTTAATAACCAGAATATATAAGGAGCTCAAACAATCCTATA 3534
                         v  v     vi vi  v             i  i   vv    ii v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_82085485_8   3535 GGAAAAAATACAA-CAATCTGACATAAAAATTAGGCAAAAGATTTGACTA 3583
                         iv     i-    -i  i ii iv?      -i      i       v  
  L1M4_orf2#LINE/    791 ATAAAAAG-ACAAATAACCCAATTWAAAAAT-GGGCAAAGGATTTGAATA 838

  chrX_82085485_8   3584 GACATTTCTCAAAAAAAGACATAAAAACGTCAAACAG--ACATAAAAAGG 3631
                                   v   i    i   v   i v v  i i--    i     i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_82085485_8   3632 CACTGAACATCAATGATCAT 3651
                         ii  v       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 4.68 (89 / 19)  


2699 25.17 3.45 2.34  chrX_82104887_82107336.rev     1066  1963 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82104887_8   1066 TGGAAAAAAATTATTTCATGTTCACAGATTGAAAAAATAAATATGGTTGA 1115
                               i ---   ii        ii     i  i v v     v   i 
  L1M4_orf2#LINE/      1 TGGAAAGA---TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chrX_82104887_8   1116 AATGTTTATACTACTGAAAACAAGCTATAGATTTAATGCAAAACCCATCA 1165
                         i   viv     v iv   vii v   i     i  i    vv  i    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_82104887_8   1166 AAATACCAATGGCATTCTTCACAGTAATAGA------------AAAAT-- 1201
                             v   iiv  v  i  ii   v   v  ------------     --
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_82104887_8   1202 ATATGGAGCAACAAAAGACCCAGAATAACCAAATCTATTCTGAGAAAAAA 1251
                                ivvi   ii           i     v v  ii   -    i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGA 196

  chrX_82104887_8   1252 ATAGCTAAACTTGCAGAA-TCACATTACCTGACTTCAAATTATACTACAA 1300
                          v i -   v   v  i -     i v  ii i      viv        
  L1M4_orf2#LINE/    197 AGAAC-AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_82104887_8   1301 AGCTTTAGTAAACAAAATACCATGATACTGGCATAAAATCAGACACATGG 1350
                             vi     v   i i vii  i           iivi     i  i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_82104887_8   1351 GCCAATGATAAAGAATAGAGAATCCAGAAACAAATCCAAATCCATACATT 1400
                         ii     iv v     v    i        i   i   ------      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA------TACATT 339

  chrX_82104887_8   1401 TTCAGTGAAATCATTATTGACAGAGGTGCCAAAAACATACATTGGGGAAA 1450
                          vii  v  v v   v i    ii        i v   v  v        
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_82104887_8   1451 ACACAGTCTCTTCAAGAAATTGTTCTGGGAAAACTGGATGTCCATAGGCA 1500
                         iv i     i     v    v  v      v        i?   i v   
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_82104887_8   1501 GAAGAATAAAACTAGACTCCTATCTCTCACCATATACAAAAATCAAA-CA 1549
                         i      i  ii i   i    i   v                i  v-  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_82104887_8   1550 AAATGAATTAAATACTTATATCTAAGATTTGAAACTATGAAACTACTACA 1599
                              i  i ? v  i  v  v     vi i       i     vi  v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_82104887_8   1600 AGTAAACAT--TTGGAAATGCTCCAAGACTTTGGTCTGGGCAAAGATTTC 1647
                           v      --v? v    -  i iv   i    vi i     v i    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_82104887_8   1648 TTCATTAATACCCTGCAAGAACAGGAAACCTAAGCAAAAATGAACAAATG 1697
                           viv  vv  v iiv   v   i v   vv   v      ii i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_82104887_8   1698 GAATCACATCAAG-TTAAAAGCTTATGCACAGAAATGGATGCAATCAACA 1746
                          i iiv      i-      i   v  ii vvv  v   ii v     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_82104887_8   1747 AAGTGAAGAGACAACCCACAAATTGGGAGAAAATATTTGCAAACTACCCA 1796
                                i            i v                    ii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_82104887_8   1797 CCGGACAAAGGATAAGTAACCAGAAAATATAAAGAGC----ACAATGAAC 1842
                         i v  i  i   ivv   v      v         i ----    ---- 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA----C 784

  chrX_82104887_8   1843 TCTATATTAGAAAAAAAAATCTAATAATCTGATTAAACAATGGAAAAAAG 1892
                           v   v  i   i v    -----  i ii   ?  v     iv   i 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAAT-----AACCCAATTWAAAAATGGGCAAAGG 829

  chrX_82104887_8   1893 ACCTGAATAAACATTTCTCAAAAGAAGACACACAAATGG--AATA----C 1936
                          ii      i         v        i i        --    ---- 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_82104887_8   1937 AGGAAAAG-TGCTGAA-ATCCCTGATCAA 1963
                          v      -    v  -   v????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (125 / 97)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.89 (52 / 18)  


3283 26.65 0.66 0.66  chrX_82121011_82127290.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82121011_8   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4931
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82121011_8   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82121011_8   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_82121011_8   5030 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82121011_8   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_82121011_8   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_82121011_8   5180 AATGGAACAGAACAGAGCTCTCTGAAATAATGCCACATATCTACAACTAT 5229
                                i    iv   vvii v       vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_82121011_8   5230 CCGATCTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAAGGATTCCCT 5279
                         ii   i  i     ivv  vv  i v  vv   i        i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_82121011_8   5280 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5329
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_82121011_8   5330 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5379
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_82121011_8   5380 AAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5429
                          ?   ii    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_82121011_8   5430 AGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAA 5479
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_82121011_8   5480 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5529
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_82121011_8   5530 AAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5579
                            v i  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_82121011_8   5580 GCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5629
                         i     i   iv            v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_82121011_8   5630 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5679
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_82121011_8   5680 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5729
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_82121011_8   5730 AAAAGAAGACAATTATACA----GCCAAAAAACACATGAAGAAATGCTCA 5775
                         v        ----      ----     v  i        i i       
  L1M4_orf2#LINE/    849 CAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_82121011_8   5776 TCATCACTGGCCAT 5789
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.40 (12 / 5)  


 682 23.08 0.55 0.00  chrX_82158305_82161821     1532  1713 (1804)  C L1M4_orf2#LINE/L1   (0)   908   726  

C chrX_82158305_8   1713 TGCAACCTACTCATCTGACAAAGGGCTAATATCTAGAATCTACAATGAAC 1664
                              vii ivi      i  i  i  vi    i     v  i  v    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

C chrX_82158305_8   1663 TCAAACAAATTTACAAGAAAAAAGCAAACAACCCCATCAAAAAGTGGGCA 1614
                           vv    v iv i  v     ii    i     v  i?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

C chrX_82158305_8   1613 AAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAA 1564
                               v    i     i     v        i  vi viii     v  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

C chrX_82158305_8   1563 GCACATGAAAA-ATGCTCATCATCACTGGCCAT 1532
                                    -       v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (24 / 17)
Gap_init rate = 0.01 (1 / 183), avg. gap size = 1.00 (1 / 1)  

2302 27.96 2.54 2.21  chrX_82158305_82161821     2120  3024 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82158305_8   2120 TGGAAACACATAACATGCTCATGGATTGGAAGTATCATTATCATCAAAAT 2169
                               v i  vv    i              vv i v   ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82158305_8   2170 GGCCATAATGCCCAAAGCAATACACAGATTCAACTC--TCCCTATCCAAC 2217
                            v   v v      vii  vi           v --        v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82158305_8   2218 TACCAACTTTGTTTTT--CAGAGAATAAAAAA--AATA-TAAAATTCATA 2262
                          v   i  viv     --    i v i v  i--i  v-           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_82158305_8   2263 TGGAAACACAAAGGAGGCTGAATAGCCAAAATAATTCTGAGCAAAAAGAT 2312
                               ii   i   vv v            i   ii   iv  i    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_82158305_8   2313 CAAAGCTGGAGGCAACAAATAACCTGACTTCAAACAATACTATAAGGCTA 2362
                              i      vvv  v ivv  ii i      vvv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_82158305_8   2363 TAGTAACCGAAACATCATGGTACTGGTACAAAAATAGTCACGTAGAATAA 2412
                         i     i i i   vii         i i  ii    v  ii    vi  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_82158305_8   2413 GAGAATAGGATAGACAATACAGAAATAAAGCCACATACCTACAACAAACT 2462
                         vi      i  v  v i v          v   i i ii  iiiiv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_82158305_8   2463 GATATTTGAGAAAGTTGACAAAAGTAAGTACTGGGGAA-GACTA-----T 2506
                            v  i  v  i v  v   i vi vvi v       -  v  ----- 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_82158305_8   2507 TCAATAAAGGGTGCTGAGATTACTGGCTAGCCATATGCGTAAGAAAGAAA 2556
                             i   v       i  iv     v  ?   i    iv     v   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_82158305_8   2557 CTGAACCTCTATTTTTCCCCTATATAAAAAAATTAACTAAATATAAGTTA 2606
                         i  i   i   ii iv v  -     v           v  v  iii i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACC-ATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_82158305_8   2607 AAAACTTAAATCTAAGACCTAAAACTATAAAAATTCTAGAAGCAAACGTA 2656
                         ? i  i     v     v              v ii      v    i  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_82158305_8   2657 GCAA-ACACCATTATGAACATCAGCCTTGGCAAGGAATT------TATGA 2699
                          v?i- v i v ii   v - ii vi v     v iv  ------     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_82158305_8   2700 CAAAGTCCCCAAAAGCAATTGCAACAAAAATAAAAATTGAGAAGTGGGAC 2749
                           ------         vvv         iv      v  v  i v    
  L1M4_orf2#LINE/    599 CA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_82158305_8   2750 CTAATGAAACTAAAGAGTTTCTGCACAGGAAAAGAAACCACCAACAGAAT 2799
                         i v  v   v v  i ii  i  ii vvv   i  v  i i   v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_82158305_8   2800 AGAAAGATAACTTACAGAATGATAGAAAATATTCACAAACAACGCATCTG 2849
                         ii     i   ii        iv          ii    iv iii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_82158305_8   2850 ACAAATGTTTAATATCCAGAATCTATAAGGAAATTAAACTACTGAAAAAC 2899
                          i  iv vi vi          v     i   ------  -  v v  vi
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAA------CT-CTTACAACT 785

  chrX_82158305_8   2900 CAAAAGAAACAAACAGAAAAATAACCTCATGAAAACTTGGGCAAAAGACA 2949
                            v --- i   v   v        iv  v?   vv        i  iv
  L1M4_orf2#LINE/    786 CAATA---ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_82158305_8   2950 TAAACAAGCACTTTTCAATAGAAAACGTACAA---GCACATAAGAAACAT 2996
                          i  i ii  i  i  v v    i ii     ---  vv     v -   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA-CAT 881

  chrX_82158305_8   2997 GTAAAAAATGCTCAAGATCACTAAATCA 3024
                          -    i        v    ????????
  L1M4_orf2#LINE/    882 G-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (136 / 113)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.53 (43 / 17)  


2163 28.70 4.52 1.92  chrX_82191158_82195998     3464  4348 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82191158_8   3464 TGAAAAAACGTTCCATGCTCATAGATAGGAAGAATAAATATTGT-AAAAT 3512
                           i   i ii i     i    i   v      v v        -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82191158_8   3513 AGCCATATTGCGAAAAACAATTTACAGATTCAATGGTATTTCTATCAAAC 3562
                         i  v   i v vv   vii  i           i vv  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82191158_8   3563 TACCAATGATTTTTTTCACAGAAGT--ATAA-----TTTTAAATTTTATA 3605
                          v   iiviii     ii     i -- i  ----- ii    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_82191158_8   3606 -GAAACCACAAAATAGCTTGAATAACGAAGGCAACCCTAAGCAAGAGCAA 3654
                         - i  vii   iiv v iv     i v  ii   i i i iv    iv  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_82191158_8   3655 CAATGATGGAGGATTCACATTATCCAGCTTTATACAATAATACAAGGCTA 3704
                            v v       i     i vi   ii  i v vvv  v     i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_82191158_8   3705 CAGTAACCAAAGCAGCATGGTACTGG--TAACAAAAGCCACATAGACAAA 3752
                               i   ii   ii         --   vi v  v  i     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_82191158_8   3753 TGAAACAGAATAAAGAGCACAGAAGCAATGCTTCTTATCTTTGATAACCA 3802
                           i  i     vi    iv     ii  --vii v  iv   -  iii  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAA--ACCCATACATTT-ATGGTCA 347

  chrX_82191158_8   3803 TCTTATCTTTGACAAAGTCAATCAAAGCAAGCAATGGGAAAAGGACTCCC 3852
                         vi v  i  i     i viiviv i v  vv       i    i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_82191158_8   3853 CTTTCAATAAATG----------AATTGGCTAGCCGTATGCAGAAGATTG 3892
                         i      i     ----------  i   v  ?  ii     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_82191158_8   3893 AAACTGGGCCCCTTCCTTACATCACATGCAGAAATCAATTCAACATGGAT 3942
                           ii   i     v   i   i  i  i  i    i  i    v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_82191158_8   3943 TAAAGACTTAAATGTAAAACCCAAAATTATGGAAGCCCTGGAA-ATAACC 3991
                         i ?    i         i v i    i   ii  vi i i   - v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_82191158_8   3992 TAGG---AAATACCATTCAGAACATAGAACCTGAGAAAGATTTCATTATG 4038
                             ---    -- -   ivi  v v iiiiv iv  v i    -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTA-G 592

  chrX_82191158_8   4039 A-A-GACGTTAAAA--ACAATTGCAACAAAACAAAAATT-GACAAGTGAG 4083
                          - -   iii    --    --         v     v -  i  i vi 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_82191158_8   4084 GCTTAATTAAA-CTAAAGAGCTTGACACATCAAGATAAGCTATCAACA-- 4130
                         i   v  i   -i    i vi  viii v    iiv vi       v --
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_82191158_8   4131 GTGGATACAGAGAACCTACAGACAGAATGGGAGAAAATATTTGCAAACTA 4180
                            i - -   v    i     ----                     ii 
  L1M4_orf2#LINE/    691 GTGAA-A-AGACAACCCACAGA----ATGGGAGAAAATATTTGCAAATCA 734

  chrX_82191158_8   4181 TGCATCCAAAAAAGCTCTAATACCCAGAATCCATAAGAAAATTAAACATA 4230
                          ii   ii v  i vv  vi  i       vi    ii  v ivv   vv
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_82191158_8   4231 TCAATAAGAAAAA-------AACTCCATTAAAAAGTAGGCAAATGACACA 4273
                                v     -------   i v   ?    i i      v  ivii
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_82191158_8   4274 AATAGATACTTTACAAAAGAAGACATACACATGGACAACAAGCACATGAA 4323
                               i i  iv v        i     v    v   i           
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_82191158_8   4324 AAAAATGCACAACATCACTAATCAT 4348
                           i -   v        ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (159 / 92)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.19 (57 / 26)  


3099 20.68 3.85 4.18  chrX_82200282_82204818     3136  4044 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_82200282_8   3136 GAAAGACTTCTTGTGTTTATG-ATTTGAAGGTTTAATACTGTTAAGATAT 3184
                               iv  iii    i   -   v    ii      i         iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_82200282_8   3185 CAACACTACCTAGAATAATCTAGAAAATCAATGTAATCCTCATCAAAATC 3234
                            i   v  i i v i     v i v    i i     ii         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_82200282_8   3235 CCAA-TGTCATTTTGTGAAGAAATGTAAAAACCCATCCTAAAGTTCATAT 3283
                            i-  i -    v  v      vv v  i iv        i       
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_82200282_8   3284 GCAATCTAAAAGGACCTCGAGTAACCAAAACAGTCTTATAAAAGAA---C 3330
                          v  vivv  i     iv  i  i        i    iv       --- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_82200282_8   3331 AAAGTTTAATGACTCACCCTTCCAGATTTCAAAACTTATTTACAAAGGTA 3380
                               vi v       v     vi             i -      v  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT-ACAAAGCTA 250

  chrX_82200282_8   3381 GATATAGTACTCCAAACCATGTGTAACTGGCATAAGGACAGACATATAGA 3430
                         ----i    v  v i  vi    vv             i           
  L1M4_orf2#LINE/    251 ----CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_82200282_8   3431 AATAATGGAATAGAACTGAATGCCCAGAAA-AAGTCCTCACATATATGGT 3479
                         v-i            i   iv i       -  ii  vi    v      
  L1M4_orf2#LINE/    297 T-CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_82200282_8   3480 CAAATGACTTTTGACAAAAATGCCCAGTCCATTAAATTGGGAAATAAAAT 3529
                            v   i   i     iii    v  v     v   v      --i   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA--GAAT 393

  chrX_82200282_8   3530 AATAAT--AAAAAAACAGTGCTAGGGAAACTGGATA------TGCCAAAA 3571
                          i vv --v  v   ii     i  iv         ------   v   i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_82200282_8   3572 TATGAGTGATGGATTTTTAGTTTTTACCACATACAAAAATGAACTCAAAA 3621
                         v    i- v    iiii  vi ivi    i          v         
  L1M4_orf2#LINE/    444 AATGAA-GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_82200282_8   3622 TGAATTGAAAAACTCTAAAT-TA---GCTACTACTCAATATTGGATTCCT 3667
                           i  i- ? i  -      -  ---    vv   --   --ii i  i 
  L1M4_orf2#LINE/    493 TGGATC-AWAGAC-CTAAATGTAAGAGCTAAAACT--ATA--AAACTCTT 536

  chrX_82200282_8   3668 AGAAAACTTAAAGGAAAGCATAGAGGAAAATCTGCATTACATTGGTTTTG 3717
                             ---------    i     i? v      v i v  v    v  v 
  L1M4_orf2#LINE/    537 AGAA---------GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_82200282_8   3718 AGAGTGGTTTCCTTAATATAACAG-AAAAGCACAAGCTATAAAAGAAAAA 3766
                         iv i       i vi    i   v-            v i          
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_82200282_8   3767 AT---------GAATTTTCTTA----TAAAAA-TTTTGTGCATCAAAGAT 3802
                           --------- i i  iv i ----      -        v      iv
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_82200282_8   3803 CACAATAAAGGAAGTGAAAATACAATCTACAGAATGGGA-AAAATATTTG 3851
                            v  v   i         v    i i           -          
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_82200282_8   3852 CAAATCATATATCTGCTAAGGGATTAATATCTAGAATATATTGAGGACAA 3901
                                        v       i vi    i         vi  ---  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG---AA 774

  chrX_82200282_8   3902 CTCAACCACCACTACCATTCAATTAAAAGAAGACAAAACACCCAACAAAT 3951
                            --------i   v i     v v  i        vv      iv? -
  L1M4_orf2#LINE/    775 CTC--------TTACAACTCAATAATAAAAAGACAAATAACCCAATTWA- 815

  chrX_82200282_8   3952 AAAATGGACAAAAGACTTGAATAAATTTTTTTCCAAAGAAAATACACAAA 4001
                                i    i  i       i iv   i         i   i     
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_82200282_8   4002 TGGCCAATAAACCCATGAAACAAAT-CTCAACATCATTAGTCAT 4044
                                   i v       - i  -          ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAA-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (107 / 78)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 2.52 (73 / 29)  


 338 25.62 4.38 3.12  chrX_82218178_82221020.rev     1330  1489 (1354)    L1M4_orf2#LINE/L1        1   162 (746)  

  chrX_82218178_8   1330 TGGAAAGATAATCTGTATTCATGAATTGGAATAATTAATATTGATAAAAA 1379
                                   vi ii i      i       v v         v   i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_82218178_8   1380 TATTCATAATACACAAATTGATATACAGATTCAATAATATAGCTATCAAA 1429
                          iviv   v v v         v           iivv  vv        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_82218178_8   1430 ATAGCATTAACATTATCAGCAGAAATATTATTATAAACC-ATTCTA---- 1474
                           vv  vivi v  v iv        ---- v i  i i-  i   ----
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAAT----TGACAAGCTGATCCTAAAAT 145

  chrX_82218178_8   1475 TCATAAGGA--TACAAG 1489
                              v   -- i    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAG 162

Transitions / transversions = 0.78 (18 / 23)
Gap_init rate = 0.03 (5 / 162), avg. gap size = 2.40 (12 / 5)  

2103 27.91 2.71 0.78  chrX_82218178_82221020.rev     1579  2352 (491)    L1M4_orf2#LINE/L1      120   908 (0)  

  chrX_82218178_8   1579 AGAAGTTAAAAA----ATCTTAATATTTATA-GGAAACACAGAAGGAAAC 1623
                             i  i v  ----   i   v   i   -     ii  --   i - 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA--AGGGA-C 166

  chrX_82218178_8   1624 CTTTTATAGTCAAAGCAATCCTGAGCAAAAAGAACAAGGCTGGAATCATC 1673
                          ivvv    i    i     i   iv  i        i i    ivvv  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_82218178_8   1674 AAACTCCCTAACTTTAAAATATACTACAAAGTTCTAATAATAAAAAAAG- 1722
                          v   i  i  i  i    iv          i vi i    v  i v  -
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_82218178_8   1723 ---GTATCAGTATAAAAAAAGACACATAGATCAATGAAGCAGAGTATAGA 1769
                         ---   iii i    ii v     i           i ii   i vv   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_82218178_8   1770 ACCCAGATCTAAATGAATTTATTTACCACCAACTCATTTTTGTCAAAGGG 1819
                         ii     vv    ivv  vi     ivii   i v     i v   i  v
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_82218178_8   1820 CCCAAGAATATGCATTGGCGAAAGGGCAGTCTATTTA-TAAATGGTGGTG 1868
                         v      vi  v  v   v     iii     v  i -i        v  
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_82218178_8   1869 AAAAAAATGAATATCCATATACAGAAAAATAAAATTA-ACCCCTATCTTT 1917
                         ii v  v  i   ?   i  i  i  i   i  i  i-       i  iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_82218178_8   1918 CACCATATATAAAAATAAAATGAAAGTAGAATTAAAGAC--AGATGGAAA 1965
                                  i      v  v v   i i  - i ?    -- i   v  i
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGA-TCAWAGACCTAAATGTAAG 515

  chrX_82218178_8   1966 ATACAAAATTATGAAACTATTAGAA-AAAATAT-TAAGCAAATGCTATAG 2013
                          vvi    i   i     v      -    i  -vi? i    -  viiv
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGT 564

  chrX_82218178_8   2014 GACATTGATCTGGGCAAAGAGTTTTTGCTTAAGACTTCAAATGCACAGGC 2063
                            v   ivi i     v iv  i  ivv  v   vi    v     i  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_82218178_8   2064 AA----AGTAAAAATAGGCAAATGGGATTAGAGTAGGGGAAAAAGCCTCT 2109
                           ----  v        ii    v   i vv vi iiivv    i i i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_82218178_8   2110 ACACATCAAAGAA-ACAATCAACAGAGCAAAGAGACAATGTAAAAAATGA 2158
                         iii v      i -  v     v i  ii  i      ivi v i    i
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_82218178_8   2159 GAGAAACACATTTGTAAACCATCCATCAGATAAGAGATTAATATCCAGAA 2208
                               - i     i   i   vi   v      i  i vi         
  L1M4_orf2#LINE/    715 GAGAAA-ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_82218178_8   2209 AATATAGACAACTCAAACAACTAGATAGTAAAAATGCAAATAATCCAATT 2258
                         v     i v     vv      vi   i      vi       i      
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_82218178_8   2259 CCAAAATGGGAAAATAAAATGAATTGACATTTCTCAAAACAAGACATACA 2308
                         ?v        v   vi vv     v          v   v    i     
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_82218178_8   2309 AATGGCAAAGTGGTATATGAAAA-ATGCTCAACATCATTAATCAT 2352
                               v  vvi i i       -             ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (125 / 87)
Gap_init rate = 0.02 (16 / 789), avg. gap size = 1.69 (27 / 16)  


2054 30.55 2.45 1.56  chrX_82229835_82232478.rev     1257  2153 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_82229835_8   1257 AAATGTATTTCATGCTTCTGTATTTGGAGAATTAATATTGCTCAAGTATC 1306
                            vi   ii    i iv  v   v i   v         i v ii iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_82229835_8   1307 TATACCACCCCCAAA--AATCTATAGATTCAGCCAAATCCCTTTAAAAAT 1354
                         v    i--       --i     i       i vv       v v     
  L1M4_orf2#LINE/     54 AATACT--CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_82229835_8   1355 AACAATGACATTTTTCACAGAAACAGAAAAAAAAAAACCTAAAATTTAAA 1404
                         vv  iivi v     ii      iv  v  ivvi v-         i v 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCATA 150

  chrX_82229835_8   1405 TGGGCCCATAGCAATACTGAG---CAAAATAAATAAATAAATAAATAAAT 1451
                            iv--  -    ---- i ---  i    ivi   vv   vvvv   v
  L1M4_orf2#LINE/    151 TGGAA--AT-GCAA----GGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_82229835_8   1452 AAATAAATAAAGCCTGTGGCATCACATAAACTGTCTTTAAATTATACTAC 1501
                          i vi  i    iiv v  vv     ivvv iivi  i   viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_82229835_8   1502 ACAGCCATAGTAACAGAAACAGTACACTACTGACATAAAAA-AATCACAT 1550
                          v   i i     ivi i     iiiv     i     ii - iv  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_82229835_8   1551 AGATAAATAGAAGGGAATAGAGTACACAGAAAAAAATCCATGCATTGGCA 1600
                             v   i   vi    v   viiv      v   i    i    viii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_82229835_8   1601 GCCAGCTCGTTTTTGACAGTGATGCCAAAAACATATATTGGCGTAATGAC 1650
                          i  ii vi    i    iv i      i v   vi v   v v  vi i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_82229835_8   1651 AGTTTCTTCAATAAATGATGCTGGAAAAACTAAATATCTATATACAGAAG 1700
                            i i     i     i      i v    ii   ? i i  i  i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_82229835_8   1701 GATAAAACTTGACCCTTATCTCTCACTGTACAGAAAAATCAAATTAAAAT 1750
                         i  i  ii v     i  i   v   ii  i v      i  v i     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_82229835_8   1751 ATATTAAAGACATAAATATAAGCCCCAAAACGATGAGACTACTACAGGAA 1800
                         iv  i ?    v     i    vv i     v  i i   vi  v i   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_82229835_8   1801 AATATTAAGAAAAAATGCTTCAAGACATTGGTCTGTGCAAAGATTTTTCG 1850
                           i  - i ?iv    -    iv   v    vi iv    v i   i ii
  L1M4_orf2#LINE/    544 AACAT-AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_82229835_8   1851 AGTAAGACTTCAATAGTATAGGCCACCAAAGCAAACATAGACAAATGGGA 1900
                         ii  v   vi   v  i i i  v  v    v   v     i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_82229835_8   1901 TTATATCATGCTAAAACGCTTCTGCACAGCAAAGGCAACAACCAACAAAG 1950
                         i vi    viv v   vi   i  ii vv      vv  v i   v    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_82229835_8   1951 TGAAGATTAGACCTTCAGAGTGGGAGAAAATATTTGCAACT-ATCTATCT 1999
                             i vvvi   iv    i                   v -  v     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_82229835_8   2000 GAGAATGAATTAATAATGAGAATATATA------TTTTGCA-CTCAATAT 2042
                           v  v i i vi  viv          ------ i  i  -       v
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_82229835_8   2043 CAAAAA-----ATA-TCAAATT--AAAATGGAAAAAATTTTTGAGTAGTC 2084
                         i     -----   -i v    --       iv   ivv     i   v 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_82229835_8   2085 ATTTGTCAAGTGAAGACATACAAATGGCCATCAGGTATATGAAAGAAAAT 2134
                             v  v iv     i             vi i i i      -- i  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA--AGAT 889

  chrX_82229835_8   2135 ATTCAACAACACTAATTAC 2153
                         ii      v  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (151 / 120)
Gap_init rate = 0.02 (17 / 905), avg. gap size = 2.12 (36 / 17)  


 455 25.00 1.25 5.62  chrX_82286537_82292270.rev     4006  4165 (1569)    L1M4_orf2#LINE/L1        1   153 (755)  

  chrX_82286537_8   4006 TGGAAAAAACCTATCC-ATGCTCATTGATAGGGAGAACAAATATTGTTAA 4054
                               i ---     -   i    v   v  i   viv           
  L1M4_orf2#LINE/      1 TGGAAAGA---TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chrX_82286537_8   4055 AATGGTCATTCTGCCCAGAGCAAGTTATAGATTCAACGCTATTACTATCA 4104
                         i    iv  v  v    i vii vi  i           v  iv      
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_82286537_8   4105 AACTACCAATGAGAGTCTGCACAGAAATAGGAAAAAAAAAGCT-ATTTTA 4153
                           v v   iivivvv i vii       v ------ v     -  ii  
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTG------ACAAGCTGATCCTA 141

  chrX_82286537_8   4154 AAATTCATATGG 4165
                                     
  L1M4_orf2#LINE/    142 AAATTCATATGG 153

Transitions / transversions = 1.00 (20 / 20)
Gap_init rate = 0.03 (4 / 153), avg. gap size = 2.75 (11 / 4)  

2168 26.26 3.85 1.99  chrX_82286537_82292270.rev     4490  5243 (491)    L1M4_orf2#LINE/L1      141   908 (0)  

  chrX_82286537_8   4490 AAAATTCATGTGGA---GCCTAAAAAGAGCCTGAGTAGCAAAAGCAATCC 4536
                                  i    ---  ---  ii  v  v  i    v   i     i
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGC---AAGGGACCCAGAATAGCCAAAACAATCT 187

  chrX_82286537_8   4537 TAAGCATAGAGAACAAAGCTGGAGGCCTCACAGTACCTGACTTCAAG--- 4583
                          i iv vii         i      v      v v  ii i     i---
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_82286537_8   4584 -----CAAAGCTATGGTAAGCAAAACAGCATGGTACTAGTCCATAA--AC 4626
                         -----        ii    v   i    ii       i --     -- i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG--CATAAGGAT 285

  chrX_82286537_8   4627 AGACACATAGACCAATGGAACAGAATAGGGAGACGAAAAATATGACCACA 4676
                              i     i        i     v i   v v i     viv   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_82286537_8   4677 TACCTATAACCATTTGTCCTTCGACAAAGTCAACAAAAACAAGCAATAGG 4726
                         i ii   iii  v   vii        i viiv   i v  vv    i  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_82286537_8   4727 GAAAGGACGCCCTGTCCAATAAACTGTGCTGTGATAATTGGCTAGCCATA 4776
                              i iivi  v i   i   iv      v  i  i   v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_82286537_8   4777 TGCAGTACAGTGAAACCAGCCACCTTCCTTACATCATATACAAAAATCAG 4826
                             iv v i    iiii v v   v   i   i             i i
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_82286537_8   4827 C-AAAGATGGAGTAAAGACTTAAATTGAAACCCTGAAACTATAAAAACCC 4875
                          -v  i     vi ?    i     vv  ivv  i           - i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTC 534

  chrX_82286537_8   4876 TT-GAAGAAAACCTAGG---AAATACCATTCTGGACAGAGACCTTGG--- 4918
                           -         v    ---    -- -   ------ v        ---
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT--C-TTC------GTGACCTTGGGTT 575

  chrX_82286537_8   4919 ---CAAAGATTTATGACAAA-GACTCCAAAAGAAATTGCAACAAAACCAG 4964
                         ---   v i   v v v v -   v       v vvv         vv i
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_82286537_8   4965 AAATTAATAAGTATGACCTAATTAAACTAAAAAGCTTATGCACAGCAAAA 5014
                             vi    i vv   i v  i   v v    i   v  ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_82286537_8   5015 TAAATTATCAACAGAGAAAACAGGCAACCCACAGAACTGGAGAAAGTATT 5064
                         v v i      v i  vi  v  i            iv       i    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_82286537_8   5065 TGCAAACTATGCATCTGATATAAGTCTAATATCCAGAGTCTATAAGGAAC 5114
                               ii  ii        vii v  vi        i v     i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_82286537_8   5115 TTAAACAAATTAACAAGTAAAAAACAA----CTCCATTACAAAGTGTGCA 5160
                          ivv    v i  i  vv    i    ---- i v   ?v   i  v   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_82286537_8   5161 AAGGACATGAACAGACACTTTTCAAAAGAAGACATATACCTGACTAACAA 5210
                              iv    i     i  i  v        i   i vv  i i  i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_82286537_8   5211 GCATATGAAAAAATATGCAACATCACTAATCAC 5243
                            i       i  iiv        ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (112 / 83)
Gap_init rate = 0.02 (15 / 768), avg. gap size = 2.93 (44 / 15)  


2429 26.17 6.60 3.30  chrX_82294385_82302915     3694  4572 (3959)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82294385_8   3694 TGGAAACACATCCCATGCTTATGGATGGGTATAATCAATATTGTGAAAAT 3743
                               v i        i i      v  v v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82294385_8   3744 GTCCATACTGCCAAAAGCAATACACAAATCCGATACAATTCCCATCAAAA 3793
                          v v     v  v   vii  vi   i  i i ii    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82294385_8   3794 TAC-AACCATCATTCTTCAGAGAAGTAGAAAAAACAATTCTAAAATTTAT 3842
                          v - i iii -  i  iiv    i v  v  ivii  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_82294385_8   3843 ATGGCACCAAAAAAAAAAAAAAGCACGCATA-TCAGAGCAAGACTAACCA 3891
                             -----   viv  iii vv  - v   -i  i i   vvi i vv 
  L1M4_orf2#LINE/    150 ATGG-----AAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAA 193

  chrX_82294385_8   3892 AAAAGAACAAATCTGGAAGCATCACACTACGTGATTTCAAACTATACTAT 3941
                          i         vi    i vv       v vii        viv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_82294385_8   3942 AAGGCCATAGTCACCAAAACAGAGTGATACTGATATAAAAATAGGCACAT 3991
                           i  i i   v i   i    v   i     ii    ii    i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_82294385_8   3992 AGATCAATGGAACAGAATGGAGAACCCAGAAAAAAAAAAAAAGAACTCAA 4041
                                     i     v    ii       v   --------- i  v
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA---------CCCAT 334

  chrX_82294385_8   4042 ATACTTGCAGCCAACTGATCTTCAACAAAG-----AAAACACAAACAAAA 4086
                          i i  iii i   i    i   i    i -----  i  -  vv   --
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAA-- 381

  chrX_82294385_8   4087 GTGGGGGAAAGACACCCTTTTCAACAAATGGTGCTGGGATAATTGGCTAG 4136
                         -     i  ii i vi                       i  i   v  ?
  L1M4_orf2#LINE/    382 -TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_82294385_8   4137 CCACATGTAGGAGAATGAAACTGGATCCTCATCTCTCACATTATACAAAA 4186
                                i ii        ii    i  ii i   v   vv         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_82294385_8   4187 AGTAACTCGAGATGGATTAAGGACTTAAACCTAAGACCCAAA-------- 4228
                          v      i i      i ?i   i    iv     v i   --------
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_82294385_8   4229 --TTCTAGAAGATAACATTGGAAAAACCCTTCTAGACATTTGCTTAGGCA 4276
                         -- ii       v     v  ?iv  vi    vv   v  v v       
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_82294385_8   4277 AGGATTTC------ATGACAAAGAACTCAAAAGCATATACAATAAAAACA 4320
                          v i    ------      ------i        i vi   i    iv 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAACAAAAGAA 624

  chrX_82294385_8   4321 AAGATAAAGAACTGGGACCTGATTAAACTAAAGAGCTTT----------- 4359
                           i   i v  v v    i v  i   v v  i i    -----------
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_82294385_8   4360 -------------------AACAGACAACCCACATAGTGATAGAAAATCT 4390
                         -------------------  v            v i  iv       v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_82294385_8   4391 TCACAATCTATATATCTGACAAAGGACTAATATCCAGAATCTACAACAAA 4440
                          ii   vii          i  i     vi          v  i  vi  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_82294385_8   4441 CTCAAGCAAATCAATAAGAAAAA--TAATTTTAAATTTCATCAAAAAGTG 4488
                            vvi   v       v     --i  v ---  iiiv  i?    i  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAAT---AACCCAATTWAAAAATG 821

  chrX_82294385_8   4489 GGCTAAGGACATGAATAAACAATTATCAAAAGCAGATATAT---TGGACA 4535
                            v     iv      i   v  v  v    v       i---   v  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_82294385_8   4536 ATGAACATGTTAAAAAATGCTTAACGTCACTAATAAT 4572
                           i i  ii v    i     i   i   ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (138 / 88)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 5.44 (87 / 16)  

3025 26.53 1.90 0.67  chrX_82294385_82302915     7142  8038 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82294385_8   7142 TGAAAAGACATTCCATGTTCATGAATTGAAAGAGTCAATATTGTTACAAT 7191
                           i     i  i           i    i    v i          vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82294385_8   7192 CACCATACTACCCAAAGCAACCTACACATTCAATACAATCCCTATCAAAC 7241
                         vi v     v      vii i     v      ii              v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82294385_8   7242 TAGCAATGGCATTCTTTACAGAAATAGAAAAA--AACTCTAAAATTTATA 7289
                          vv  iiv  v  i   i       v  v  i--i ii        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_82294385_8   7290 TAGAGCCAGAAGAGACCAGGAATAGCAAAAACTAGCCT---ACAGAAATT 7336
                          i  iviiv   i    vi       v     v v i --- v    i--
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG-- 198

  chrX_82294385_8   7337 AACAAAACTTGAGGAATCACATTACCTGACTTCAAATTACACTGCAGAGC 7386
                               ii v     v     i v  ii i      vivi   i  i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_82294385_8   7387 TATAGTAACAAAAACAGCATGGTATTGGCATAAAAACAGATACATAGACC 7436
                           i     iv  i    ii     i        ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_82294385_8   7437 AAAGGAGCAGAATAGAGAATCCATAAGCAGATCCACACACCTACAGTAAA 7486
                           v   ii     v    i    v  ii i i   i   ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_82294385_8   7487 CTCATTTTCAACAAATTTACCAAGAACATACACTGGAGAAAAGAGAGTCT 7536
                         i v      i    ivv i      v   v  v   i    ii v     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_82294385_8   7537 CTTCAATACACGGTGCTGGGAAAACTGGATATTTATAGGCAAAATAATGA 7586
                         i     i v i          v         ?ii i v      v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_82294385_8   7587 AACTAGACCTCTATCTGTCACCA----CAAAAATCAAATCAAAATGGATT 7632
                          ii i    i   i  vv     ----       i  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_82294385_8   7633 AAAGAAGTAAATCTAAAA-C--AAAGTATGAAACTGCTATGAGACAACAT 7679
                          ?   vv     v   i - --   v   i     vi  vi   v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_82294385_8   7680 TGGGGAAAATCTCTAGGATACTGGTGTGGGCAAAAATTTCTTGAGAAATA 7729
                         v  ? v      iiiv  ivi   vv i     vii      -   v  i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chrX_82294385_8   7730 CCAT-AGAAGCACAGGCAACCAAAGCAAAAACGGACAACTGGGGTCACAT 7778
                         v  i- i       i     v    v     ii  i  v v  iiiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_82294385_8   7779 TAAG-TTAAAAAGCTTCTGCACAGCAAAGGATACAGTCATCAAAGTGAAG 7827
                         i  i-       -   i  ii vv       i  vi   vv        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_82294385_8   7828 AGATACCCCATAGAATGAAAGAAAATATTTTCAAACTATCCATCTGACAA 7877
                            i v    i      ii           v    ii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_82294385_8   7878 GGGATTAATAAACAGAATATATAAGGAGCTCAAAGAACTTTCTT-TGAAA 7926
                             i vi  vv            i  i   vv v    ivv v- i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_82294385_8   7927 AAATGTAATAATTTGATCAAAACATGGGCAAAAGATTTGAATAGAC-TTT 7975
                          i ii-     iiii  i?   v         i             -   
  L1M4_orf2#LINE/    797 AGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_82294385_8   7976 TTCAAAAGAATAAATACTAATAAC-AATGAGGTATATAAAAAAGTGCTCA 8024
                         i  v      v v    v   ii -   i  -i i  i    ii      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCA 894

  chrX_82294385_8   8025 ACATCATGGATCAC 8038
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (146 / 88)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.53 (23 / 15)  


1612 24.74 17.98 2.17  chrX_82315833_82317742      634  1417 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82315833_8    634 TAAAAATACATTACATGCTCTCAGATTGGAAGATTTAATATGGAATATCA 683
                          ii   v i  iv    i  vii          i       v -------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTG------- 43

  chrX_82315833_8    684 TGAAAATGACCGTACTGCCCAAAGAAATCTATAGATTCAGTGCAATTCCA 733
                          v  i   i vi    v      vvi     i       ii     i  v
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chrX_82315833_8    734 ATCAAAAGATTTACATCATTTCTTACAGAATTAGAAAAAATAATCCTGAA 783
                                vviivi vv v   i  i     v v  v  iv i     i  
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_82315833_8    784 ATCCATAGGAAACCGAAAAAGAGCCTGAATAGTTAAAGCAATCCT-AAGT 832
                           i    v i  vi v  ii  v  v      ii   i     i -  iv
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_82315833_8    833 ATAAGGAAAAAATCTGAAGAT------------ATTATA----TTACT-- 864
                          v   i v   i iv  i  i------------   vi ----     --
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_82315833_8    865 -----------------------------TTGGCA-AAG------CATA- 877
                         -----------------------------i     -   ------    -
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_82315833_8    878 ---------------------------AAAAAT---CCCATA-------- 889
                         --------------------------- i    ---      --------
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_82315833_8    890 ---AATTG-----TGA-AACGG-----AAACC------------------ 907
                         ---     -----i  -  v  ----- i   ------------------
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_82315833_8    908 ---CTATTCAATAAATGGTGCTAGGAAAACTGGATAGCCCCATGTAGAAG 954
                         ---  v     i          i   v         ?  v    i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_82315833_8    955 AATGAAATTGGATCTCTATCTCTCATCATTTACAAAAATGTAGTCAAGAT 1004
                               i     i i   i   v  i   v         vv v    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_82315833_8   1005 GGATCAAAGACGTAAATCCAAGTTGTGAAATCATAAAAATTACACAAGAA 1054
                               ?    v     vi   vvv i   ii      v ivi v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_82315833_8   1055 AGCCTAGAGAAAAAACACTTC-TG--CTCAATGTCCTAGGCAATG----- 1096
                          i v   - ?iv   i-    -  --  iii-  --         -----
  L1M4_orf2#LINE/    544 AACATAG-GNGTAAAT-CTTCGTGACCTTGG-GT--TAGGCAATGGTTTC 588

  chrX_82315833_8   1097 TTATGACCAAGACCCCAAAAGTGAATGCAACATAACCAAAAATAAATAAA 1146
                            -  i- v   v       iiv v      v  vv       i     
  L1M4_orf2#LINE/    589 TTA-GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_82315833_8   1147 TAAAACCTAATTAAACTAAAAAGCTTCTACACTGCAAAAGAAATAATCAT 1196
                          vii  i v  i   v v    i   i iii  v    i  v iv    v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_82315833_8   1197 CAAAGAAAACAGACAACACAAAGAATAGGAGAAAATATCTGCAAACTATG 1246
                         v    vi  v       v  v     i           i      ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_82315833_8   1247 CATCTGACAAAGGACTAATATTCAGAATTTATAAGGAGCTCTAAGAAATC 1296
                         i      i  i     vi   i      v     i  i    v v  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_82315833_8   1297 TGCAAGAAATAAAACCAAATATTCCCACTTAAAAACTGAGCAAGTTACAT 1346
                         vii  v   -  i  -     v-    v  ?    v  i    ivv iv 
  L1M4_orf2#LINE/    787 AATAATAAA-AAGAC-AAATAA-CCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_82315833_8   1347 GAATAGACATTTTTCAAAAGAAAATA----AATGGCCAAGAAACATATGA 1392
                                     i  v      i   ----         v  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_82315833_8   1393 AACAATGCTCAACATCACTAATCAT 1417
                           vi             ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (105 / 85)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 5.85 (158 / 27)  


2125 31.07 1.44 0.91  chrX_82321576_82327723     4494  5259 (889)    L1M4_orf2#LINE/L1        1   770 (138)  

  chrX_82321576_8   4494 TGGAGAAACAGTTCATGCTCATGGAT----AGAATCAATATCAGTGTAAT 4539
                             i i i vii    i        ----   v i     iiv ivi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82321576_8   4540 AGCCATACTGCCAAGAGCAACTTGTGGATTCAGTGCTATTCCTATTAAAC 4589
                         i  v     v  v i vii ii iii      ii  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82321576_8   4590 TACCAGTGACATTCTTCAAAGAACTGGAAAATACT-ATTCAGAAATTCAT 4638
                          v    ivi v  i  iiv    v v  v  -i  -  i vi        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_82321576_8   4639 GTGGAACCAAAAAAGAGCCCAAATAGCCATGGCAATCCTAAGCAAAATGA 4688
                         i     viiv  ii  v  vi        vii     i i iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_82321576_8   4689 ACAAAGCTGGAGGCATCATGCTACCTGTTTTCAAACTATATTACAGTATT 4738
                               i      vv   ii  v  iiv       viv  i    ivii 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_82321576_8   4739 ACAATAACCAAAACAGCATGGTACTGGTACAAAACCAAAACAGATAG-TC 4787
                            i   i   i    ii         i i  iivi i -  v    -  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA-CATATAGATC 298

  chrX_82321576_8   4788 AAATGGAACAGAATAGAGAGCCCAGACGTAAAGCCACACACCTACAACTA 4837
                           -     i     v     i     vi    v   i   ii  iiiii 
  L1M4_orf2#LINE/    299 AA-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_82321576_8   4838 TCTGACCTTTGACAAAGCTGCCAAAAACAAGCAATGGGGGAAATGAATCC 4887
                         vi   ii  i     i v      i v  vv        i  --    vv
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA--GAATAG 395

  chrX_82321576_8   4888 CTATTTCA-TAAATGGTGCTGGGATAACTGGCTAGCCATAGGTAGAAAAT 4936
                         iiv     -i              i      v  ?   i v i i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_82321576_8   4937 TGAAACTGGACTCCTTCCTTACACCATATACAAAAATAAACTCAAGATGA 4986
                             ii     i   v   i                 v       i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_82321576_8   4987 AGTAAAGATTTAATTGTAAAACCAAAGACTATGAAAATCCTGGACAACAA 5036
                          vi ?   ii   v     i v v  i     i   v  i i  vi v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_82321576_8   5037 CATAGGCA-ATACCATTTTAGACATAGGACCTGACAAAGATTTTATGACA 5085
                               ?i- v i v iv -   v v  iiiv i   v i   iv iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_82321576_8   5086 AAGATACCAAAAGCAATTGCATCAAAAACAAAAATTGACACG--AGATTT 5133
                          v  i          vvv   v     iv      v  i vi--i  i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_82321576_8   5134 AATTAAA-TTAAAGAGCTTCTGTGCAGAAAAATAAACTGTCAACAGAGCA 5182
                         v  i   -     i -   i     vvv   iv v   i    v i  ii
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_82321576_8   5183 AAAAGAAAACCTACAGATTAGGAGAAAATTTTTGCAAACTATTCCTCCAA 5232
                               v    i     v i         v        ii  viv  ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_82321576_8   5233 CTAAGGTCTAATATCCAGCGTCTGTAA 5259
                         iv i  v  vi       vi v i   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAA 770

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.02 (13 / 770), avg. gap size = 1.38 (18 / 13)  

 227 23.19 4.35 3.62  chrX_82321576_82327723     5532  5669 (479)    L1M4_orf2#LINE/L1      770   908 (0)  

  chrX_82321576_8   5532 AAGA-CTC---CATCTCAAAAAAAAAAAAAAAAAAAAAGGAA--AAATAG 5575
                             -   ---  v     v  v     i v   v  vvv  --?  ---
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA--- 816

  chrX_82321576_8   5576 AAGTAGGCAAAGAACATGAACAGACACTTTTCAAAAGAATACATTCATGT 5625
                           i i       i iv    i     i  i  v      v i  v  vi 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_82321576_8   5626 GCCCAACAAGCATATGAAAAAAAAAGATCAATGTCACTGATCAT 5669
                          v    i     i       i v-- v    ii   ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.94 (15 / 16)
Gap_init rate = 0.04 (5 / 139), avg. gap size = 2.20 (11 / 5)  

 277 21.31 3.28 0.00  chrX_82321576_82327723     5699  5759 (389)    L1M4_orf2#LINE/L1      426   488 (420)  

  chrX_82321576_8   5699 GATA--CATAGGTAGAAAATTGAAACTGGACTCCTTCTTTACACCATATA 5746
                             --  i v i i  i v    ii     i   v i i          
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_82321576_8   5747 CAAAAATAAACTC 5759
                                v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTC 488

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.02 (1 / 63), avg. gap size = 2.00 (2 / 1)  


 500 24.14 0.86 0.86  chrX_82328773_82330817      504   619 (1426)    L1M4_orf2#LINE/L1      184   299 (609)  

  chrX_82328773_8    504 ATCTTGAGCAGAAAGAACAAAACTGGATGAATCATATCACCTAACTT-AA 552
                                iv ii         ii    v  v   i iiv  i  i  -  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_82328773_8    553 AATTATACTATAGAGCTAGAGTAACCAAAACAGTATGGTACTGGCATAAA 602
                           i -     i i     v     i   i     i              i
  L1M4_orf2#LINE/    234 AACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_82328773_8    603 AACAGATGTATAGGCCA 619
                         i i   ii     ii  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCA 299

Transitions / transversions = 4.60 (23 / 5)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.00 (2 / 2)  

1932 27.01 1.42 2.05  chrX_82328773_82330817      920  1552 (493)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_82328773_8    920 AAAAACAGATGCCTAAACCAATAGAATAGAGTAGAGAACCCAGAAACAAA 969
                           ii i   iiiv  i i    i       i v    ii       i   
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_82328773_8    970 TTTATGAACCTACAGTTAATTCATGTCTATCGTGTCTAACAAGGTTGCCA 1019
                         iii  iv ii  ii  i    v  v ---   ------      v     
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTT---TCG------ACAAGGGTGCCA 370

  chrX_82328773_8   1020 AGAAAATATGTTGGGAAAAAGACAGTCTTTTCAATAGATGGTGCTGAAAA 1069
                            vv  viiv    i   ii i           i i         ii v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_82328773_8   1070 AAACTGCATATCCATATGCAGAAGAATAAAAGTAAAC---TAC-TCTTGC 1115
                           -   v   ?   i     i      i  iv ii  ---   -  vii 
  L1M4_orf2#LINE/    421 AA-CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_82328773_8   1116 CATATATAAAAATCAAATCAAAATGGATTAAAAACTTACATCTAATATCT 1165
                               i      i  v           i ? i  i  v  v   v v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_82328773_8   1166 CAAATTATGACACGAATAAAATAAAACATTGGGAAAAGTCTCCAGGTCAT 1215
                         v   i   i v  vvv  i  v       v  ?iv  i   i iv v v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_82328773_8   1216 TAGTCTGGGCAAACATTTCATGAACA--ATACCGCACAAATACAGGCAAC 1263
                          i vi i     vvi    v ii i -- i   -- v  ii   i     
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACC--AAAAGCACAAGCAAC 617

  chrX_82328773_8   1264 CAGAGCAAAAATTTACAAATGGGATTGCATCAAGTTAAAAAACTTCTGCA 1313
                         v i  v      vv i    v   i v      iv v        i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_82328773_8   1314 CAGCAAGATAAATGATGAACAAAGTGAAGAGAAAACCCACAGAATGGAAG 1363
                          vv   iiv v iv  v  v        i   v              i  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_82328773_8   1364 ATAATATCTGCAAACTACCTATCTGACAAGGGATTAATAACCAGAATATA 1413
                          v     i      ii iv       i      i vi  v          
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_82328773_8   1414 TAAGGAGCTCAAACACCTCTATATTGAAAAGATCTAATAATCTGATTTTA 1463
                            i  i   vv   v   v   v i      - v     i ii   ?v 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAA 816

  chrX_82328773_8   1464 AAATGTGCAAAAGATTTAAACACACATTTTTC---AAAAGACTTATAAGT 1510
                              v     i     i  i v      i  --- i    iv  i  i 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_82328773_8   1511 GGCAAACAGGCATATGAAAATGTGCTCAACATCACTAATCAT 1552
                            v  i i   i       vi            ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (100 / 67)
Gap_init rate = 0.01 (9 / 629), avg. gap size = 2.44 (22 / 9)  


3137 27.20 0.66 0.66  chrX_82346951_82353326     4976  5883 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82346951_8   4976 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5025
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82346951_8   5026 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATTCCCATCAAGC 5075
                            v     v     iv i  i  i        i iv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82346951_8   5076 TACCAA-TGTCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5122
                          v   i-  i    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_82346951_8   5123 ATATGGAACCAAAAAGGAGCCGGCATCACCAAGTCAATCTTAAGTCAAAA 5172
                                 viiv  i   v  i v  vi    iv       i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_82346951_8   5173 GAACAAAGCCGGAGGCATCACGTTACCTGACTTCAAACTATACTACAAGG 5222
                                 ii     vv    ii v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_82346951_8   5223 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATGGAC 5272
                                  i   i    ii         i iv ii i   v    i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_82346951_8   5273 CAATGGAACAGAAC--AGAACCCTCAGAAATAATAATACACATCTATCGC 5320
                                 i    i--   ii  --        vvvi i    i   v i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_82346951_8   5321 CATCTGATCTTTGACAAACCTGACAAAAAGAAGCAATGGAGAAAGGATTC 5370
                           vi    i  i     ivv  v   i vv vv      i     i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_82346951_8   5371 CCTATTTAATAAATGGTGCTTTGAAAACTGGCTAGCCATATGTAGAAAAC 5420
                         i  v  i  i          vv  v      v  ?   i   i i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_82346951_8   5421 TGAAACTGGATCACTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5470
                             ii    i v  v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_82346951_8   5471 ATCAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5520
                             ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_82346951_8   5521 CCTAGGCA-ATACCATTGAGGACATAGGCATGGGCAAGGACTTCATGTCC 5569
                          v    ?i- v i v i v iv v i  i- i     v ii   v ivvi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_82346951_8   5570 AAAACACAATAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5619
                          vi    v v     vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_82346951_8   5620 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5669
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_82346951_8   5670 ACAGGCAACCTATAGAGTGAGAGAAAATTTTTGCAACCTACTCATCTGAC 5719
                          v  i     i i   i  i        v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_82346951_8   5720 AAAGGGCTAATATCCAGAATCTACGATGTACTCAAACAAATTTACAAGAA 5769
                           i  i  vi          v  ii v v    vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_82346951_8   5770 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGGCACT 5819
                            i     i     v  i?    i     i     iv    i  i  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_82346951_8   5820 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5869
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_82346951_8   5870 CCATCATTGGCCAT 5883
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


 312 20.97 0.00 0.00  chrX_82430016_82434141.rev     1116  1177 (2949)    L1M4_orf2#LINE/L1        1    62 (846)  

  chrX_82430016_8   1116 TAGAAAGATGTCCTGTATTCATGTATTGTAAGAATCAATATTGTTAAAAT 1165
                          i       i   ii i      v    v    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82430016_8   1166 GTCCATACTCTC 1177
                          v v      i 
  L1M4_orf2#LINE/     51 GGCAATACTCCC 62

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.00 (0 / 0)  

2622 27.63 1.18 1.18  chrX_82430016_82434141.rev     1639  2485 (1641)    L1M4_orf2#LINE/L1       62   908 (0)  

  chrX_82430016_8   1639 CCAAGGTGATATACAGATGCAATACAACCCATGTCAAAATTCCAATGAAT 1688
                             iv    v       v   ii   i  v i       i   iivivi
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chrX_82430016_8   1689 TTTTTTACAGAAATAGAAAAAAAAGTTCTAAAATTTGTATGGAAACATAA 1738
                               i       v  v  ivvii i        ii        iii  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_82430016_8   1739 AAGGCCCAGAAAAGCCAAAACAATTCTAAGAAAGAA---CAAGGGTGGAG 1785
                         ii i       v            ii i i      ---   i v     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_82430016_8   1786 GCATCACACTTCTTTATTTCAATTCATACTACAAAGTTATAGTAATCAAA 1835
                          vv         iiv       vv v          i  i         i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_82430016_8   1836 ATAGTGTGGTGCTAGCATAAAAATGAACACATAGACCAATAGAACAGAAT 1885
                          i        i  i      ii  ii   i     i    i   i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_82430016_8   1886 AGAGAGCCAAGAAATAAACCTAAGCATATATTGTCAACTAGTTATTGACG 1935
                         v     i v           i vi   v   v     i ii  v i   i
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_82430016_8   1936 AGGGCAGCAAGAAGACACAGAAGGGAAAAGCTAATCTCTTCAGCAAACGA 1985
                             iiv     vv iv  ivi      iiv  i   i    i    i i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_82430016_8   1986 TGATGAAAAAACTGAATATCCACATGCAAAATAATAAAATTGCAGCTTTA 2035
                           v  ii v     i   ?            v   i  i   v v ii  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_82430016_8   2036 TCTTACACTATAACCAAAAATCAACT-AAAATGGGATTAAATAACTAAAC 2084
                         i  i    i   vv       i    -       -  i ? v v     i
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGG-ATCAWAGACCTAAAT 510

  chrX_82430016_8   2085 GTAAGACCTAAAACTGCAACACTTCTTGATTAAAACACAGCAAACAA--C 2132
                               v        ii  v   ii v  vv      i  -i?ii  -- 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG-GNGTAAATC 559

  chrX_82430016_8   2133 TTCTTGACATTGATCTCGACAATAAATTTTTGGACAGGACAGCAAAAATA 2182
                            v    v   ivi v i    iiv  i  i  i v    v     ii 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_82430016_8   2183 CAGGTA-CAAAAACAAAAATAAACAAGTATAAACTT-GTCAAACTAAAAA 2230
                           i i -     iv       i i  i - ii    -i     v v    
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAAT-TGGACTTCATCAAAATTAAAA 658

  chrX_82430016_8   2231 CAAACACTTCTGCCCAGTAAAGAAAACAATCAACAAATTAAGAAAGTAGC 2280
                         -----    i  iv vvi    i v  v     v   v i i  iii i 
  L1M4_orf2#LINE/    659 -----ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_82430016_8   2281 CTAAATAATGGGA-AAAATATTTGTGGACTATATAATTAGTAGGGGATTA 2329
                          i v v       -          iii ii     vi ii  i    i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_82430016_8   2330 ATTTCCGAAAGATAGAAGGAACTCACACAAATCAATAGCAAAAAAAAGGT 2379
                         i v   ii  v   v  i      vi    v      ii     i vi--
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA-- 801

  chrX_82430016_8   2380 AATAACCCAAAT-AAAAATAAACAAAGATCCAGACTATATATTTCTCCAA 2428
                                   v -      iii     iviiv  v  v i          
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_82430016_8   2429 AGAATACATAAAAATGGCTGACAGATAAATAAAAATATACTTAACATCAA 2478
                             v i   v       ii i iii v  i    v  i  i       ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_82430016_8   2479 TAATAAT 2485
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.89 (151 / 80)
Gap_init rate = 0.01 (12 / 847), avg. gap size = 1.67 (20 / 12)  

3213 22.25 4.93 1.03  chrX_82430016_82434141.rev     2756  3627 (499)  C L1M4_orf2#LINE/L1   (0)   908     3  

C chrX_82430016_8   3627 GAAGGTTATCCTATGTTCATGGAATAAAAGACTTAATACCATTAAGATGT 3578
                            i v     i           v ii           iii        v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

C chrX_82430016_8   3577 CGATACTACCCAAAACAATCTACAGATTTAAGGTAATTGATATCAAAATA 3528
                          i     v      vii           i  v i   ivv         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

C chrX_82430016_8   3527 CCAACGCTGTTTTTTT--CAAAAATAGAAAAATCTCCATCTTAAAATTCA 3480
                            --    ii     --  i    v  v  i-  v-   i         
  L1M4_orf2#LINE/    103 CCA--GCTGCCTTTTTTGCAGAAATTGACAAG-CTG-ATCCTAAAATTCA 148

C chrX_82430016_8   3479 CATGGAATCTCAAAGGAGTCTAAATAATCAAAGAAATATTGGA------G 3436
                         i      viv   i   vi vi    ii    iv   v   i ------ 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_82430016_8   3435 AACAAAACTGAAGTTCTCACACTTCCTGATATCCAAAGTTTTTACAAAAC 3386
                               ii  i  vv           ii  v  v   v  vi      i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_82430016_8   3385 TACAGTATGCAAGACATTGTGGTCCTAGTGTAAAGACAGACACATAGACC 3336
                                vv       v      v  i ii   i  i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_82430016_8   3335 AATGGAA-AGTAACAGATATCCCAGAAATGCATCTTTCCATATATGGTCA 3287
                                -  -  iv  v vi        iv i iv v   v        
  L1M4_orf2#LINE/    299 AATGGAATAG-AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

C chrX_82430016_8   3286 AATGATTTTTGACAAGGTTGCCGAGATCATTTAATGGGGAAAGGA----- 3242
                          v       i       v    i   i    i           i -----
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chrX_82430016_8   3241 -----GAC------TGTTGAGAAAACTGGATGTATAAATGCAAAAGAATA 3203
                         -----i  ------  i  i  v        i?vi v            i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chrX_82430016_8   3202 AAGTTCCATCCTTATCTTACA--ATATACAAAAATTAAGTCAAAA--AA- 3158
                              vv i  i  i  i   --               v      --i -
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

C chrX_82430016_8   3157 -AAAAACCTTAAACGTAAGAGCTAAAGCTATAAAACTC--AGATTTACGC 3111
                         - ? i    -   i            i           --   vvv vi 
  L1M4_orf2#LINE/    498 CAWAGACCT-AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_82430016_8   3110 AAAGGGGGAAAAATTTACATAAC--TGAATTTGGCAATGATTTCTCAGAT 3063
                          v   ? v   -- i v i i  --  ii  v       i     i    
  L1M4_orf2#LINE/    547 ATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

C chrX_82430016_8   3062 ATGACACCAAAAGCACAAGCAACAAGAGCAAAAAATAGCCAAACTGAAAT 3013
                                                  i  -         vi   i  i v 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACT 643

C chrX_82430016_8   3012 ACAACAAAATTAAAAAATTGTTTACATCAAAGGACACAATCAATACAGTG 2963
                         v  v            v  v v i v           v     v v    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

C chrX_82430016_8   2962 AAAAGGCCACCTACAAAATGAGAGACAATGTTTGAAAATCGTGTATCTGT 2913
                              i v   i   i    i    v   i    v     i i      v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

C chrX_82430016_8   2912 TAAGGGA-TAATACTCAGAACATATAGAATGCTCCTGCAATTCAAGAACA 2864
                                - vi  ii     i     i ivi   i i   i    v  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

C chrX_82430016_8   2863 ACAGCATAA-CAATCTATTTTAAAACTGGGCAATATATTTTAATCAATAT 2815
                          v iv i  -i  i i v  ?    v       viv    v   vi i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

C chrX_82430016_8   2814 ATATCTGAAGACAATATACAAATAACCA-----CA-ATGAAAAGATGCTC 2771
                         v v  ii    vi          ii   -----  -              
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

C chrX_82430016_8   2770 AACATTACTGATTTA 2756
                              i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (110 / 80)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 2.48 (52 / 21)  


2452 28.55 0.95 0.71  chrX_82448520_82450337      482  1325 (493)    L1M4_orf2#LINE/L1       63   908 (0)  

  chrX_82448520_8    482 CAAGTGGACTTAACAGATATTTACAGAAATTTCCATCAAAATACCATCAT 531
                            i v  ii  -     - iv  - v   ii i        v   v vv
  L1M4_orf2#LINE/     63 CAAATTGATCTA-CAGAT-TCAAC-GCAATCCCTATCAAAATCCCAGCTG 109

  chrX_82448520_8    532 CATTCTTCACAGAACTAAGAAAGACAATCCTAAGATTCATATGGAACCAA 581
                          v  i  ii     v viiv   vii       i            viiv
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_82448520_8    582 AGAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAGAAAGAACAAATCTGG 631
                          iii  v  v v         i   vvi i iv ii         vi   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_82448520_8    632 AGGCATCACATTACTTGACTT-AAAACTATACTATAAGGCCATAGTCACC 680
                            vv     i v iii i  -      -     i  i  i i   v i 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATC 258

  chrX_82448520_8    681 AAAACATCATGGTACTAGCATACAAATAGGCATACAGACCAATAGAACAG 730
                           i   vii       i     vii    i    i   i    i   i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_82448520_8    731 AATAGAGAATCTAGAAATGAACGCTAAAACTTATAGCCAAAGGATCTTTG 780
                            v    i  i      i   v vv v i    i i   vv   i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_82448520_8    781 ACAAAGCAAACAAAAACATAAAGTAGGGAGAGGACACCCTATTTAACACA 830
                             i vviv   i v   vv i i    i  i i vi  v  i    v 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_82448520_8    831 TGGTGCAGAGATAA-TGGCAAGCTACCTGTAGGAGAATAAATCTGGATCC 879
                               v i  i  -   vv ? i  v  i ii     i  vi    i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_82448520_8    880 TCATCTCTCACCTTATACAAAAATCAACTCAAGGTGGATTAAGAACTTAA 929
                         ii i   v    v           i       ii     i ?ii  i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_82448520_8    930 ATCTAGGACCTGAAAATATATAAATTCT-AGGAGATAACATCAAAA-AGC 977
                           v  i  v  i   v    -   i   -  i   v     vii?i- iv
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_82448520_8    978 CCTTCTAAATATTGGTTTAGGGAAAGATTTCATGAACAAGAACCCAAAAG 1027
                         i    vvi iv    v     v  v i    v ii i v  vv       
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_82448520_8   1028 CAAATGCAATAAAAAAAAAGATAAATAGGTGGGGCTTAATTAAACTAAAG 1077
                           v v    i    i    i   i   ii v  i   v  i   v v  i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_82448520_8   1078 ACCTTCTGCACAGTAAAAGGA-ACAGTCAGCAGAGAAAACAGACAACCCA 1126
                          v   i  ii -v v      -  vi   iv i  vi  v          
  L1M4_orf2#LINE/    658 AACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_82448520_8   1127 CAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGGACTAATA 1176
                             i           v  ii   vii   i      i  i     vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_82448520_8   1177 TCCAGAATCTACAAGGAACTCAAACAAATTAGCAAGGAAAAAA-AAAGAT 1225
                                 v  i  i      vv    v i ii  vi    i -   v v
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_82448520_8   1226 CCCA-TCAAAAAGTGGGCAAAGTAAATGAATAGACAGTTCTCAAAAGAAT 1274
                             - i?    i         v vv          v     v      v
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_82448520_8   1275 ATATCTAAATGCCCAACAAACATATTAAAA-ATGCTCAACACCACTAAAG 1323
                             vi     v    i  i  i  v    -          i  ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_82448520_8   1324 AT 1325
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.02 (14 / 846), avg. gap size = 1.00 (14 / 14)  


2840 26.33 1.48 1.36  chrX_82458140_82464758     3258  4138 (2481)    L1M4_orf2#LINE/L1        1   882 (26)  

  chrX_82458140_8   3258 TAGAAA-ATATCCCATGCTCACGGATTGGAAGAATCAATATTGTTAAAAT 3306
                          i    -          i   i           v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82458140_8   3307 GAGCATACTGTCCAAAGCAACCTGCAGATTCAAGGCAATCCCTATCAAAT 3356
                          ivv     vi     vii i  i         v               v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82458140_8   3357 TACCAATATCATTTTTAACAGAATTAGAAAAATACAATCCTAAAATTCAT 3406
                          v   iivv v     vi     v v  v  ii-ii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_82458140_8   3407 ATGGAACGGCACCAAAAA---AAAGTAGTCAAGGCAATTCTGGGTGAAAA 3453
                               vv   -- iii --- i i   i   ii    ii  iivi i  
  L1M4_orf2#LINE/    150 ATGGAAATGCA--AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_82458140_8   3454 GAACAAATCCGAAGGTATCACACTGCATGACTTCAAG--TTAAACTACAA 3501
                                vii i   vv       v vii i     i--   --      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAA 245

  chrX_82458140_8   3502 GGCTACAGTAATTAAAACAGCATGGTACTGGAGCATAA--ATAGACACAT 3549
                         i           i  i    ii         --     --       i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGG--CATAAGGATAGACATAT 293

  chrX_82458140_8   3550 AGATAAAGAGGACAAAACAGAGAACCCAGAAATAAAGCCACATACT-ACA 3598
                             v  vi i i i  iv    ii           v   i i i - ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_82458140_8   3599 ACCAACTGATCTTCAACAAAGTTGCCAAAAATACAAAATGGAGAAAGGAC 3648
                         ii   i    i   i    i v      i vi ivv     i     i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_82458140_8   3649 ACCTTATTCAATCAATGGTGCTGGGAAAATTGACTAGCTATGTGCAGAAG 3698
                          vii v     iv             v  i  iv  ? i ii    i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_82458140_8   3699 AATGAAACTGGACCCCAATCTCTCACCATATACAAAAATCAGCTCAAGAT 3748
                               ii        v i   v                i i     i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_82458140_8   3749 GGATTAAAGACTTAAACGAAAAACATGGAACTACAAAAATCCTGGAAGAA 3798
                             i ?    i    i v  i vv ii     i    v  i i      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_82458140_8   3799 AATATAGAGA-AAACTTTCCTGGACATTGGCCAAGTCAA--ACCACTTAT 3845
                           i    i?i-   ii   v  -  v    viv  v   --iiiv    -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTA- 591

  chrX_82458140_8   3846 GATGAAGAACTCAAAAGCAAATGTAACCAAAACAAAGATAGACAAATGTG 3895
                            - v  vvi        v v i   v   iv   i     i    vv 
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_82458140_8   3896 ACTTAATTAAACCAAAATGCTGTTACACAGCAAAATAAACAATCAACAGA 3945
                             v  i   viv   vi  v  iii vv    iv v  v     v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_82458140_8   3946 GTAAACAGACAACCTACAGAATGGGAGAAAATATTTGCAAATTATTTATG 3995
                           i  v        i                           i  v   v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_82458140_8   3996 TGACAAAGGACTAATATCCAGAATCTACAAGAAAATCAATAACAAGAAAA 4045
                            i  i     vi          v  i  ii  v  -- v    vvv  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCAA 788

  chrX_82458140_8   4046 -AACAAACAAACAAACATCTCCACTAAAAGTTGGGCAAAGAACATGAACA 4094
                         -  i   v i     i v i v i ?   iv         i iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_82458140_8   4095 GACATTTCTTAAAGGAAAAAATGCAAGTGACCAACAAATACTTG 4138
                                  iv  i   i v  i   i  i    i  ii  v  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

Transitions / transversions = 1.65 (142 / 86)
Gap_init rate = 0.02 (16 / 882), avg. gap size = 1.56 (25 / 16)  

2209 22.02 2.12 5.06  chrX_82458140_82464758     4921  5533 (1086)    L1M4_orf2#LINE/L1       46   640 (268)  

  chrX_82458140_8   4921 AATATGTCAATATTTCCCAAAACAATGTACAGATTCAATGTGATTCCTAT 4970
                           v   v     i i      vii  v           i ii  i     
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_82458140_8   4971 -AAGATCCTATTAAATTTTTTTGCAAAAATAGTAAAATCT-ATCCTAAAA 5018
                         -  i    i vivivi         i    v - v  v  -         
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAA 144

  chrX_82458140_8   5019 TTTGTATGGTATTTCAAAGGACTCAAAATTACCAAAATGGTCTTGAGTAA 5068
                           ii     v v v   i    i  i   vi      iii      iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_82458140_8   5069 AGAGAGCAAAATTGGAGTTCTCACATTTCCTGATTTCAAAACTTACTATA 5118
                         ii   i    i      vv      i    ii                i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_82458140_8   5119 TAACTATGGTAATCAA-ACTGTGTATTAATGACATAATGACAGACCTACA 5167
                         v i   ii        -  v    iv  v  i     v  i    v  i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_82458140_8   5168 ATCCACTGCAATAGAATTGAGAACCCAGAAATATATACTCACATATATTG 5217
                         ivi  v  v             ii         v iv vi    v   v 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_82458140_8   5218 TCAAATCATTTTTGACAAAGGTGCCAAGGCCATTCAAATGAGGGAAGGAA 5267
                             v v     i     i         i        -  i  i   i v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAAT 393

  chrX_82458140_8   5268 AATCTTTTCAGCAAATGGTGTTAAAAGTACTGAATATCCATTTTAATATT 5317
                          i        i         i iii vv    i   ?   ----------
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA---------- 433

  chrX_82458140_8   5318 CAGTTAAAAGTACTGAATATCTGAAAAGAATGAAGTTGGATCCTTAACTT 5367
                           -------- i ----------                 i  i  v  i
  L1M4_orf2#LINE/    434 CA--------TGC----------AAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_82458140_8   5368 ACACCACTTACAAAAAATTAACTCAAA-TGG-TCAAAGACCTAA-TGTAA 5414
                               iv        -          -   -   ?        -     
  L1M4_orf2#LINE/    466 ACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_82458140_8   5415 AAGCTAAAATTATACGCGTTTTAGAAAGAAATGTAGAGTAAAAACTTTAT 5464
                         i        i    vivv i      ii   ii   i?vv   v   ii 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_82458140_8   5465 CACATTGAATT-TTCAATGATTTCTCAGACATGACACCTAAAGCACAAAC 5513
                         v  v   ii  -vv     i     i   i        v         i 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_82458140_8   5514 AACAAAAG------TAAACAAACTGG 5533
                                 ------  i i   i   
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGG 640

Transitions / transversions = 1.69 (83 / 49)
Gap_init rate = 0.02 (14 / 595), avg. gap size = 3.14 (44 / 14)  

1003 20.86 5.30 0.99  chrX_82458140_82464758     5827  6128 (491)    L1M4_orf2#LINE/L1      594   908 (0)  

  chrX_82458140_8   5827 TATGTACACGTAAAATTAAAAAAAGTTTAAAAATAAAAAGTTTAATCGGA 5876
                             -    -i    vi v  iv iivv  i  v   v  v v   i   
  L1M4_orf2#LINE/    594 TATG-ACAC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_82458140_8   5877 ATACTTCAAAATTTAAAAACTTCTGTGC-------------ATCAAAAGA 5913
                         v v v      -          i     -------------     i i 
  L1M4_orf2#LINE/    642 CTTCATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_82458140_8   5914 GTAAAAAGGCAACCTATAGAATGTGAGAAAATATTTGTAAATAATACATT 5963
                           i     i     i i      v             i    v   i  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_82458140_8   5964 TT-TAATGGGTTT-TACCCAGAATATATAAAGAACTCCTCCAATTCAACA 6011
                          v-   v  ii  -  i                    i v   i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_82458140_8   6012 AGAAAAATGCAAACAACCAAATTTAAAAATGATCAAATGACT-GAGTAGA 6060
                          v     vi    i    v    ?       iv    v  i -  i    
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_82458140_8   6061 CATTTCTCCAAATAATATATGTACATGTTCAATAATCACATGAGGAGATG 6110
                                     v  v    ii v   vi      v       ii     
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_82458140_8   6111 CTCAAAATAACTAATCCT 6128
                              v  v ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.14 (33 / 29)
Gap_init rate = 0.02 (7 / 315), avg. gap size = 2.71 (19 / 7)  


3101 26.19 1.55 1.22  chrX_82467789_82474104     4919  5823 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82467789_8   4919 TGGAAGAACATTTCGTGTTCATGGATAGGAAGAATCAATATTGTGAAAAT 4968
                              ii i  ii i           v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82467789_8   4969 GGCCATACTGCCCAAGGTAATTTACAGGTTCAATGCCATGCCCATCAAGC 5018
                            v     v     iv i  i     i     i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82467789_8   5019 TACCAATGACTTTATTCACTGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5066
                          v   iivi i  v  ii v   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_82467789_8   5067 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5116
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82467789_8   5117 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5166
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_82467789_8   5167 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGACC 5216
                                 i   i    ii         i iv ii i   v  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_82467789_8   5217 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTATAACC 5264
                                i    i--    i  --        vv   i    i   iii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_82467789_8   5265 ATCTGATCTTTGACACACCTGACAAAAACAAAAAATGGGGAAAGCAT--T 5312
                          vi    i  i    vivv  v   i v  vvv           v  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_82467789_8   5313 CCTTATTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5362
                          i  --    i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_82467789_8   5363 CTGAAAATGGATCCCTTCCTTACACCTTATACAAAAATTA-TTCAAGATG 5411
                         v    iv    i    v   i     v             -i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_82467789_8   5412 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5461
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_82467789_8   5462 ACTTAGAC---AAT-TCCAT--TCAGGAGACAGGCATGCAAACGACTTCA 5505
                           v   i?---   - i i --i vv i vi     ----- i ii   v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-----ATGGTTTCT 589

  chrX_82467789_8   5506 TGTCTAAAACACTAAAAGCAATGGCAACAAAAGCCAAAATTGCCAAATGG 5555
                          ivv  vi    i       vvi          vv     v vi    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_82467789_8   5556 GATCTAATTAAACTAAAGAGGTTTTGCACAGCAAAAGAAACTACCATCAG 5605
                           ii v  i   v v  i iv     ii vv    i  v    i  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_82467789_8   5606 AGTGAAGAGGCAACCTACAGAATGGGAGAAAAATTTTACAATCTACCCAT 5655
                               i  i     i                vv   i   vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_82467789_8   5656 CTGACAGAGGGTTAATATCCAGAATCTACAAAGAACTTAAACAAATTTAC 5705
                             i ii  ii vi          v  i        ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_82467789_8   5706 AAGAAAAA-ACAAACAACCCCATCGAAACGTGGGCAAAGGATATGAACAG 5754
                           v     -     i     v  i?   vi            v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_82467789_8   5755 ACACTTCTCAAAAGAAGACATTTATTCAGCCAACAGACACATGAAAAAAT 5804
                            i     v        i  vi vvii     i ii          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_82467789_8   5805 GCTCATCATCACTGGCCAT 5823
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.92 (25 / 13)  


2023 25.80 1.61 10.44  chrX_82535839_82539405     2079  3074 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82535839_8   2079 TGGAAAAACATTACATGCTTATGAAGAGAAAGCATCAGTATCGTTAAAAA 2128
                               i i  iv    i i   i vv i   vv i i   i     i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_82535839_8   2129 TGGATATACTGCCAAAAGCAATTTACAAATTCAAAGCTATTTCTATCAAA 2178
                            vv     v  v   vii  i    i      v  v  ii        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_82535839_8   2179 CTATCAATGGTATTTCCTAAATCATTAGAAA---AAAAACTGTTTTTATG 2225
                         v vi  iiv iv   ii i------i     --- v  i   v ii  vi
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTG------CAGAAATTGACAAGCTGATCCTAAA 143

  chrX_82535839_8   2226 -TACACAGGGAACCAAAAAAAGAGCCTGAATAGCCAAATCAGTCCTAAGC 2274
                         - v  i v    viiv  ii-  v  v           v  i  i i iv
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_82535839_8   2275 AAAAAGAACAAA-CTGGAAGCATCACATTACCTAACTTCGAACTATATTA 2323
                           i         -i    i vv     i v  i  i   i  --------
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-------- 234

  chrX_82535839_8   2324 CATTACCTAACTTCAAACTATATTACAGGGGTATAGTAATCAAAACTGCA 2373
                         ---------    -------- i    ii v  i         i  v ii
  L1M4_orf2#LINE/    235 ---------ACTT--------ACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_82535839_8   2374 TGGTACTGGTACAAAAACAGACACATAGGCCAATGGAACGGAA--AATAG 2421
                                  i i  ii i     i    ii        ii   --i v  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_82535839_8   2422 TCCAGAAATAAAGCCAGACACCTACAACCATATGATCTTTGACAAAGTCA 2471
                                     v   v   ii  iiii  vv    i  i     i vii
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_82535839_8   2472 ATAAAATAAG-CAATGAGGAAAGAACTCCCTATTCAATAAATGGTGCTGG 2520
                         vi  i iv v-     i        ivvi  v     i            
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_82535839_8   2521 AATAACTGGCTAGCCATTTGCAGAAGATGGAAGGGAGTAGACCACTTACT 2570
                         i i      v  ?   iv    i    vv    v--- i    v  vv  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGT---TGGACCCCTACCT 464

  chrX_82535839_8   2571 TACATCATATAAAAATACCAACTCCAGATGGATTAAAGACTTAAATGTAA 2620
                         i   i      v   v ii     v i      i ?    i         
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_82535839_8   2621 AACCTACAACTATAAAAATCCTTGAAGAAAACCTAGG---AAATACAATT 2667
                         i v   v          v  i v         v    ---    - --  
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-C--TT 561

  chrX_82535839_8   2668 CTGGACATAAGCTCTGGAAAAGATTTCATGGAGAAAAAGCCAAAAGCAAT 2717
                          vv   v vi v iv  v  v i    v i  v vi vi         vv
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_82535839_8   2718 TACAATGAAAACAAAAATTGGCAAATGGGACCTGTTTAAACTAAAGAGAT 2767
                         vi   ii   iv      v ii    v    i vv i   v v  i iv 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_82535839_8   2768 TCTGTACAGCAAAAGAAACTATCAACAGAGTAAACAGATAAATTAGAGAA 2817
                          i   i vv    i  v        v i   i  v   i  vii v    
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_82535839_8   2818 TGTTTGGAAACCATGCATCTGACAAAGAAATAAGAAATAAGAAATCTGAA 2867
                           ---   ------------------------------------------
  L1M4_orf2#LINE/    712 TG---GGA------------------------------------------ 716

  chrX_82535839_8   2868 TAAAGAAATCTGAATAAGAAAATGTTTGGAAACCATGCATCTGACAAAAG 2917
                         -----------------      i    v   i   ii      i  ii 
  L1M4_orf2#LINE/    717 -----------------GAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_82535839_8   2918 TCTAATATCCAGAATCTA-GAAGAAATTT---AAATTAACAAGTATAATA 2963
                         v  vi          v  -i     v i ---  v i  i  -  v  vi
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAG 798

  chrX_82535839_8   2964 ATAAACAATGCCGCTGAACAGTGGGCAATGGACTTGAACAGATAATCTTC 3013
                          i   i  iv vii ?  v i       v   i     i   i v ii  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_82535839_8   3014 AAAAGAAGACATACAG-TGGTCAATAAGCATACGAACAAAAATGCTCAAA 3062
                         v        i     i-   i         i i   --  i        v
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAA--AAGATGCTCAAC 896

  chrX_82535839_8   3063 ATCACTAATCAT 3074
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (149 / 105)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 5.71 (120 / 21)  


3235 26.99 0.88 0.44  chrX_82603050_82609323     4878  5781 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82603050_8   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82603050_8   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82603050_8   4978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_82603050_8   5026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82603050_8   5076 AACAAAGCCGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5125
                                ii     vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_82603050_8   5126 TACAGTAACCAAAACAGCATGGGACTGGTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii   v     i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_82603050_8   5176 AATGGAACAGAAC--AGAGTCCTCAGAAATAATGCCGCATATCTACAACT 5223
                                i    i--       --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_82603050_8   5224 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5273
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_82603050_8   5274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAACCATATGTAGAAAGCT 5323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_82603050_8   5324 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5373
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_82603050_8   5374 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_82603050_8   5424 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5473
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_82603050_8   5474 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5523
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_82603050_8   5524 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5573
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_82603050_8   5574 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5623
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_82603050_8   5624 AGGGCTAATATCCAGAATCTATAATGAACTCAAACAAATTTACAAGAAAA 5673
                         i  i  vi          v     v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_82603050_8   5674 AAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5719
                          i    ----   v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_82603050_8   5720 TCAAAAGAAGACATTTATGCAGCTAAAAAACACATGAAGAAATGCTCATC 5769
                           v        i  vi viii  i  v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_82603050_8   5770 ATCACTGGCCAT 5781
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


 203 29.63 0.00 0.00  chrX_82623165_82628902.rev        3    83 (5655)    L1M4_orf2#LINE/L1      560   640 (268)  

  chrX_82623165_8      3 TTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAACACCAAAAGCA 52
                            iv   v v  vv i     v ii   v ivvi vi            
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_82623165_8     53 ATGGCAACAAAAGACAAAATTGACAAATGGG 83
                         vvi           v     v  i    v  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGG 640

Transitions / transversions = 0.60 (9 / 15)
Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.00 (0 / 0)  

2766 26.16 1.77 1.55  chrX_82623165_82628902.rev     4342  5247 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82623165_8   4342 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATGGTAAAAAT 4391
                               i i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82623165_8   4392 GGCCATACCTCCCAAAGTAATTTACAGATTCAATGCCATTCCCATCAAAC 4441
                            v    ii      v i  i           i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82623165_8   4442 TATCA-CTGACATTCTTCACA-AAATTAGAGA-AAACT-ACTTTAAATTT 4487
                          vi  -   v -  i  ii  -     ---  -  i  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATT 146

  chrX_82623165_8   4488 TATATGGAATCAAAAAAGAGCCCACATACCCAAGACAATCCTAAGCAAAA 4537
                         i        viiv  ii  v  viv   v    i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_82623165_8   4538 ATAACAAAGCTGAAGGCATCGTGCTTCCTGACTTCAAACTATACTACAAG 4587
                          v       i  i   vv  iii     ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_82623165_8   4588 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACAGATAGA 4637
                                   i   i    ii         i iv ii i     v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_82623165_8   4638 TGAATGAAACAGAATAAAGACCTAAGAAAGAACAGCACACATCTACAACC 4687
                          v    i  i     vi   viiv     v  vvv  i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_82623165_8   4688 ATCTGATCTTCGACAAACCTGACAAAAACCAG-CAATGGGGAAAAGATTT 4736
                          vi    i        ivv  v   i -   v-           ii  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAG 395

  chrX_82623165_8   4737 CCTACTTAATAAATGGTACTGGGAAAACTGACTAGCCATACGCAGAACAC 4786
                         i  vi i  i       i      v     iv  ?   i i   i  v v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_82623165_8   4787 TGAAACTG-ACCCCTTCCTTAGAACTTATACAAAAAATAACTCAAGATGG 4835
                             ii  -      v   i v v v          v        i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_82623165_8   4836 ATTAAAGAGTTAAATGTAAAACCCAAATCCATAAAAACCCTAGAAGAAAA 4885
                           i ?   vi         i v i   v i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_82623165_8   4886 CCTAGGCA-ATACCATTCAAGACATAGGCCTGGGCAAAGATTTCCTGACA 4934
                          v    ?i- v i -   iv   v v  vi i     v i    i --- 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT---A 591

  chrX_82623165_8   4935 AAAATG---CCAAAA--ACAATTGCAACAAAAGACAAAATTGACAAATGA 4979
                         i v   ---      --    --           v     v  i    vi
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_82623165_8   4980 AATCTAATTAAACTAAAGAGCTTCTACACAACAAAAGAAATTATCATCAG 5029
                         i ii v  i   v v  i i   i iii vv    i  v i     vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_82623165_8   5030 AGTGAACAGAAAACCTATAGATTGGGAGAAAATTTTTGCAA-TCTTCCCA 5078
                               v   v    i i   v           v       -  v vi- 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-A 738

  chrX_82623165_8   5079 TCTGACAAGG-ACTAATATCCAGAATCTACAAGAAACTTAAACAAATTTA 5127
                              i    -   vi          v  i  ii    ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_82623165_8   5128 CAAGAAAAAAA--AACAGCCCAATCAAAAAGTGAGGAAAGGATATAAACA 5175
                         i  v     i --  i i      i?    i  i v       v i  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_82623165_8   5176 GACACTTCTCAAAAGAAGACATTTATGTGGCCAAAACAAACCTAAGAAAG 5225
                             i     v        i  vi vi       --i  i vi v    i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAA--TAAGCACATGAAAA 886

  chrX_82623165_8   5226 AAAGCTCAACATCACTGATCAT 5247
                         i v           ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.50 (30 / 20)  


 391 24.49 1.02 1.02  chrX_82645704_82651376     3456  3553 (2120)    L1M4_orf2#LINE/L1        2    99 (809)  

  chrX_82645704_8   3456 GAAAAAAAATTCCATGCTTATGTTTAGGAAGAACCTGATATTGTTAAAAT 3505
                          i   i v  i     i i   vv v     -  i i          i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGAT 50

  chrX_82645704_8   3506 GGTCATACTGACCAAG-CAATTTACAGATTCAATGCTATTTCTATCAAA 3553
                           iv     vv    i-ii  i           i  v  ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.02 (2 / 98), avg. gap size = 1.00 (2 / 2)  

2365 26.28 3.59 1.41  chrX_82645704_82651376     4407  5186 (487)    L1M4_orf2#LINE/L1      112   908 (0)  

  chrX_82645704_8   4407 TTCTTTCCAGAACTAGAAAAAATATTCATATTTAAAAATTCATTTGGAAC 4456
                           i   v     v v  v  iv iv  v  -----        v     v
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTA-----AAATTCATATGGAAA 156

  chrX_82645704_8   4457 CAAAAAGGATGCCTGAATAGTGAAGGAAATCCTAAGCAAAAAGAACAAAG 4506
                         iiv  i   i-  v      iv  iiv    i i iv  i          
  L1M4_orf2#LINE/    157 TGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_82645704_8   4507 CTTGAGAA-TCACATTACTTGACTTCAAACTATACTACACTGCTACAATG 4555
                         i v   i -     i v iii i      viv       vv      i i
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_82645704_8   4556 ACCAAAACAACATGGTCCTGGTACAAAAATAGATATAGAGACCAATGGAA 4605
                          i   i   iii    v    i i  ii     i   v   i        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_82645704_8   4606 GATAATAGAGAGTCTAAAAATAAGGCTGCACACCTACAACCATCTGATTT 4655
                         v v   v       i i      iv iii   ii  iiii  vi      
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_82645704_8   4656 TTGACAAACTTGACAAAAACAAGCAATGGGGAAAGGGTA----------- 4694
                          i     ivv  v   i v  vv            ii  -----------
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_82645704_8   4695 -AGTGGCGCTGGAATAACTGACTAGCCATATGCAGAAAATTAAAACAGGA 4743
                         - i   i     i i     iv  ?   i     i  i v i  iiv   
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_82645704_8   4744 CCCCTTCTTTACACCATATAGAAAAATTAACTCAAGATGGATTAAAGACT 4793
                              v i i          v              i      i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_82645704_8   4794 TAAATGTAAAACCCAAAACTATAAAAACCTTATAAGAAAACCTAGG---A 4840
                                  i v i            vi    v        v    --- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_82645704_8   4841 AATAGCATTCTCGACCTAGGAGGTGGAAAATA-TTTCATGG----GACGT 4885
                            -- -   vi     v  - v i iv   i-    v i ----   ii
  L1M4_orf2#LINE/    556 AAT--C-TTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_82645704_8   4886 CAAAAGCAATTGCAAACAAAGGAAAAATTGACAAATGAGATCTAATTAAA 4935
                                 vvv    vv    i      v  i    vi  ii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_82645704_8   4936 CTAAAGAGCTTCAGCACAGTACAATAAACTATTAATAGAGTAAAAAGGCC 4985
                         v v  i i   iv ii vvi v iv v     i  v i   i     i v
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_82645704_8   4986 ACCTACAGAATGGGATAAAATATTTGCAAACTATTTATCTCACAAAGGTA 5035
                            i           v              ii  v     v i  i  vv
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_82645704_8   5036 TAATATCCAGCATCTCTAAGGAACT---A-AACT-GATG-TAAAAGCAAA 5079
                          vi       v  v v   i     --- -    -i  i-     i-i v
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA-GAC 800

  chrX_82645704_8   5080 AAACAACCCAATTGAAAAGTGGGCAAAGGACATGAACAGACAGTTTTCAA 5129
                            i         ?    i           iv    i     v  i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_82645704_8   5130 AAGAAGATGTACATGAGACCAACAAGTAAATGAGAAAA-GCTCAATATTA 5178
                                 i    viv i    i   i v    i  i -      i  i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_82645704_8   5179 CTAATCAC 5186
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.49 (121 / 81)
Gap_init rate = 0.02 (16 / 797), avg. gap size = 2.44 (39 / 16)  


2438 27.77 1.79 1.46  chrX_82694524_82697506.rev     1600  2492 (491)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_82694524_8   1600 CCATCCTCATGGATAGTAAGAATTAATATTGTTAAAATTGCCATACTGCC 1649
                             vi        v v    v             i  v  v     v  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_82694524_8   1650 CAAAGAAATTTACAGATTCAATGCTATTCCTATCAAACTCCCAATGACTT 1699
                             vvi  i           i  v  i         v     iivi i 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_82694524_8   1700 TCTTCACAGAATTAGAGAAAATTATGCTAAAATTCATACAGGACCCAAAA 1749
                          i  ii     v v  v  iv v  v            ii i vivv  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_82694524_8   1750 AGAGCTTGAAGAGCCAAAGCATTCCTAAGAAAAAAAAACAAACCTAAAAC 1799
                         i  v iv   v       i  v  i i i   i  i      vi ii iv
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_82694524_8   1800 ATT-ACATTACCTGACTTCAAACCATGTTACAAGGCTACAGTAACTAAAA 1848
                          i -   i v  ii i      v v ii     i          ii  i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_82694524_8   1849 TAGCATGATACTCATACATAAACAAACACATAAACCAATGGAACAAAA-- 1896
                         i  ii  i    vii i vii i i   i   i i        i i  --
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_82694524_8   1897 --AAGGCCAGAAATAAAGCCACACAACTGCAA-CAATCTGATATTCAACA 1943
                         --i  v           v   i   vi iiii-    -    v   i   
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT-TGATTTTCGACA 361

  chrX_82694524_8   1944 AAGTCAACAATAACAAGCAATGGATAAAGGATTCCCTATTCAATAAACGA 1993
                          i viiv   v v  vv      iv    i  vvi  v     i   i i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_82694524_8   1994 TGCTGGGATAACTGGCTAGCCATATGCAGAAGATTGAAACAGGACTACTT 2043
                                 i      v  ?   i     i    v    iiv    iv  v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_82694524_8   2044 TCTTACACCATTTA-AAAAATTAACTAAAGATATATGAAAGACTTTAATG 2092
                         i  i       v  -           v  i  iv  v ?    i v    
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_82694524_8   2093 TAAAATCTAAAATTACAAAAACCCTT-GAAGAAAACCT-GTGGTATACTA 2140
                            i v      i  i    - i   -         v - v?   - v v
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTA-AATC 559

  chrX_82694524_8   2141 TTCTGGACATAGGACCTGGCAAAGATTTCAT-GATGAAGATGCTAAAA-- 2187
                            vv   v v  iiiv     v i    v -   - v  ii i    --
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGC 608

  chrX_82694524_8   2188 ACAATTGCAA----AAAAAAAATTGACAAATAGGACATAATTAAACTAAA 2233
                             --    ---- i       v  i    v    v v  i   v v  
  L1M4_orf2#LINE/    609 ACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_82694524_8   2234 CAGCTTCTGCACAGCAAAAAAAAAAAGTCATCAACAAAGTAAACAGACAA 2283
                         v i   i  ii vv    ii v ----ii     v     i  v      
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACA----CTATCAAGAAAGTGAAAAGACAA 702

  chrX_82694524_8   2284 CATACAGAATGGGAGAAAATACTTGCATAATATTCCTCTGACAAAAGTCT 2333
                          vi                  i     v vi  viv     i  ii v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_82694524_8   2334 AATATGCAGAATCTATAAGGAACTTAAACAGATTAGCAAGCAAAAACCAT 2383
                         vi   v      v     i     ivv   iv i ii  vv    iv  v
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_82694524_8   2384 GCAACCCCATTAAAAAGAGGACAAAGGAAATTAACAAACACTTCCCAAAA 2433
                         ii     v   ?    iv  i       vv v  i i   i   i v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_82694524_8   2434 GAAGACACACACACACAGCCAACAAGCATGTGAAAAAAATGCCCAACATC 2483
                              i i   - - ii     i     ii      i -   i       
  L1M4_orf2#LINE/    853 GAAGATATACA-A-ATGGCCAATAAGCACATGAAAAGA-TGCTCAACATC 899

  chrX_82694524_8   2484 ACTAATTAC 2492
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.02 (18 / 896), avg. gap size = 1.61 (29 / 18)  


3546 20.39 4.30 1.47  chrX_82702158_82705740.rev     2210  3092 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82702158_8   2210 TGGGAAAACATCCTGTGTTTATGAGTTGAAAGACTAATTACTATTTAAA- 2258
                            i  i i    ii    i   ii   i      v v  i i  v i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82702158_8   2259 ----ATAATTCTCAACTATATGATCTACAAAATCAAGGCAATTCTTAAAC 2304
                         ----   v i i   --  -         i v    v     i i  vvv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAA--AT-TGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_82702158_8   2305 AAATTCCAGCTCACCGTTTTCATAGAAATTTACGAACTGATTCTAAAATT 2354
                             i      -i  v    iii       v  i i     i        
  L1M4_orf2#LINE/     98 AAATCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_82702158_8   2355 CGTATGTAAGTTCAAGGGACCCAGAAAAGCCAAAACAATTCTGAGTAATA 2404
                          i    v  i v              v            ii   iv  v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_82702158_8   2405 AGAACAAATTTGGAGGACTCACATTTCCAGATTTTAAAACTTAGTACAAA 2454
                                 v              i    vi    i        v      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_82702158_8   2455 -TAACAGTAGTCAAGACAGTGTGGTGTTGGCATAAGGAAAAACATA--GA 2501
                         -iv      i               ii           v i     --  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_82702158_8   2502 TGAATGGAAAAACATAGATCAAAGTCCAGAAGTAAGTTGTCACATTTACA 2551
                          v       v iv  v  ---i         i   iiivvi       ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGA---GAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_82702158_8   2552 GTCACTTAATTTTCAACAAGTGTATCACGATAATTTAATGGAGGAAGAAT 2601
                             v  i      i     v  ii  v  iv   i     i i      
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_82702158_8   2602 AGTTTATTCAACAAATAGCTCTATGATAACTAG-TATACATATGCAAAAA 2650
                            i v          i iv  iv  i    i -  ?v  i        i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_82702158_8   2651 AA----ATTAAACTCTTACCACATATCATATTTTAAAAATTAGCTCAAAA 2696
                           ----i  ii  i i    v  i i     vi-        i       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAAA 492

  chrX_82702158_8   2697 TTGAGTACAGACCAAAAGGTAAGAGCTAAAACTATAAAATTCTTCGGATA 2746
                          v  vi ?     v   v                     i    v i v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_82702158_8   2747 AAA-AT---GGCAAATTATTTGTGGCATTGGATTATGCCATGGTTTCTTA 2792
                            -  ---? i    i-  i   i v    i   v  v           
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_82702158_8   2793 GATATGACAGCAACAGTTCAAGCAACAAAAGAAGA--T-GATAAATAGGA 2839
                                  v   v  iv               i -- -       v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_82702158_8   2840 CTGTGT-AAACTTTAAA---TATGTGTTTATTAAATAGACCTTAGGATGA 2885
                           vii -   v  v   --- v    i  --i   -i   vi  vv v  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTT--CAAA-GGACACTATCAAGA 688

  chrX_82702158_8   2886 AAGTGAAAAGACAAACCTCAGTGTGGAAGAAAATATTTGCAAATCACATA 2935
                                       v  v   vi   i                   i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_82702158_8   2936 TCTGATAAGGGTCTAGTATACAGAATATGTAA----------CAAGCTAA 2975
                                    v  v    v        i   ----------   -  v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCA 787

  chrX_82702158_8   2976 ACAATAAAAAGACAAATCATATAACTTAAAAATG----AAGGGTCAGAAT 3021
                          i               v ivi  i ?       ----    i iv    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_82702158_8   3022 AAACATTTTTTCAAATAAAATGTACAAATGGTCAATAGGCACATGTAAAA 3071
                          i      i i    v  i  i         i     i       v   i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_82702158_8   3072 ATGCTCAACATCAGTAGTCAT 3092
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (106 / 70)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.32 (51 / 22)  


3166 27.64 0.22 0.22  chrX_82710971_82717401.rev     5032  5939 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82710971_8   5032 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5081
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82710971_8   5082 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCACCATCAAGC 5131
                            v     v     iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82710971_8   5132 TACCAATGACTTTATTCAAAGAATTTGAAAAAACT-ACTTTCAAGTTCAT 5180
                          v   iivi i  v  iiv    v    v  i-  - iii v  i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_82710971_8   5181 ATGGAACCACAAAAGAGCCAGCATTCCCAAGTCAATCCTAAGCCAAAAGA 5230
                               vii   ii  v    v  vv    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_82710971_8   5231 ACAAAGCTGGAGGCATCAAGCCACCTGACTTCAAAAAATACTACAAGGCT 5280
                               i      vv   vi iv  ii i       vv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_82710971_8   5281 ACAGTAACCAAAACAGCATGGGACTGGTACCAAAACAGAGTTATAGAACA 5330
                                i   i    ii   v     i iv ii i   vv      v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_82710971_8   5331 ATGGAATAGAATGGAGCCCTCAGAAATAATGCCACACATCTACAACTATC 5380
                                     v   vvii         vv   i    i  iiiii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_82710971_8   5381 TGATCTTTGACCAACCTGACAAAAACAAGCAAGGGGGAAAGGATTCCCTA 5430
                             i  i   v ivv  v   i v  vv   v        i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_82710971_8   5431 TTTAATAAACGGTGCTGGGAAAACTGGCTAACCATATGTAGAAAGCTGAA 5480
                           i  i   i          v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_82710971_8   5481 ACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTA 5530
                         ii    i    v   i     v           i  i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_82710971_8   5531 AAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5580
                         ?    i    i  v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_82710971_8   5581 GGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAT 5629
                           ?i- v i -   iv   v v  vv i     v ii   v ivv  viv
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_82710971_8   5630 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5679
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_82710971_8   5680 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCGGAGTGAACAG 5729
                            v v  i i   i  ii vv    i  v    i  vvii      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_82710971_8   5730 GCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAG 5779
                         i  i  i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_82710971_8   5780 GGTTAATATCCAGAATCTACAATGAAGTCAAACAAATTTACAAGAAGAAA 5829
                          ii vi          v  i  v   v  vv    v iv i  v  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_82710971_8   5830 ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATAGACACTTCTC 5879
                              i     v  i?    i            v          i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_82710971_8   5880 AAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCGT 5929
                         v        i  vi viii     v ii          i       v i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_82710971_8   5930 CACTGGCCAT 5939
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.31 (140 / 107)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.00 (4 / 4)  


2002 27.07 10.30 1.56  chrX_82722143_82727802.rev     4337  5171 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82722143_8   4337 TGGAAAAACGTAACATGTTCATGTATAGGAAGAATCAATATCCTTCAAAT 4386
                               i ii vv          v  v      v i     iv  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82722143_8   4387 GGCCATACTGCCCAAAGCAAATTATAGATTAAATACTATTCCTATGAAAC 4436
                            v     v      vii vi  i     v  ii v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82722143_8   4437 AACCATTGACTTTTTTCACAGAACTAGAAAAAAAACAATTTTAAAATTCA 4486
                         vv   vivi i     ii     v v  v  iv--ii  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chrX_82722143_8   4487 TATAGAACTAAAAAATAACCCA-AATAGCCAAGGCAATCATAAACAAAAA 4535
                            i   v iv  ii-i     -         ii     v i  v  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_82722143_8   4536 GAACAATGCCAGAGGAATCACACTACCCAATTTTAAACTATTCTACAGGT 4585
                               v iii     v       v        i   viv v     iiv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_82722143_8   4586 CTACACTAACCAAAACAGCATGGTGCTGGTACAAAAACAGAAACATAGAC 4635
                              v   i   i    ii    i    i i  ii i   v i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_82722143_8   4636 TAATGGAACAGAATAGAGAGCCAAGAAATAAGGCCACACGTCTTCAACTA 4685
                         i       i     v     i v        iv   i  i i viiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_82722143_8   4686 TCTGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGG--------GTC 4727
                         vi    i  i i   ivv  v   i v  vv        --------   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_82722143_8   4728 TATTCAATAAATGGTGCTATGATAACTAGCTAGCTATATGCAGAAGA--- 4774
                          v     i          iv  i    i v  ? i i     i    ---
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_82722143_8   4775 -------------------------------------------------- 4774
                         --------------------------------------------------
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_82722143_8   4775 ------------TATAAAACCCAAAACTATAAAATCCCTAGAAGACCAAC 4812
                         ------------ i   i v i            ii i       v-   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA-AAC 546

  chrX_82722143_8   4813 -TAGGCA-ATACCATTCTGGACATAGAAACAGGCAAAGATTTAATGACAA 4860
                         -    ?i- v i -   vv   v v iivi      v i   vv iivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_82722143_8   4861 AGACACTAAAAGC-CATTGCAATGAAAGCAAAAATTGACAAATGTGAACT 4909
                         v     i      -  v-    ii    v      v  i    -  i   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAAT-TGGACT 643

  chrX_82722143_8   4910 -AATTAAACAAAAGAATTTCTGCATAGCAAAGGAAACTATCAACAGAGTG 4958
                         -v  i   vvv  i  i  i  iiivv       v        v i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_82722143_8   4959 AACAGACAGCCTACAGAATGGGAGAAAATGTTTGCAAAGTATGCATCTGA 5008
                           v     i  i                 i        vi  ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_82722143_8   5009 CAAAGGTCTAGTATCCATCATCTATAAGGAACGTAAACCAATTTACAAAA 5058
                         i  i  v  v       vv  v     i    vivv  -  i --   v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC-AACT--CAATA 790

  chrX_82722143_8   5059 CATAAATAAATAAATAAAACCCCATTAAAAAGTGAGCAA-GGAT----AT 5103
                         -     v i i      --   v   ?    i  i    -    ----  
  L1M4_orf2#LINE/    791 -ATAAAAAGACAAATAA--CCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_82722143_8   5104 AGACAGTTTGCAAAACAAGACATATGTGCATCCAACAAGCATA--AAAAA 5151
                              v  iv v   v    i   iiviiiv    i     i --    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_82722143_8   5152 A-GCTCAACATGACTGATCAT 5171
                          -         v ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (128 / 95)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.71 (99 / 21)  


1984 26.48 0.18 0.18  chrX_82729391_82738299     5772  6330 (2579)  C L1M4_orf2#LINE/L1   (0)   908   350  

C chrX_82729391_8   6330 TGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTA 6281
                             i  i     ivv  vv  i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

C chrX_82729391_8   6280 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTGAA 6231
                           i  i              v      v  ?   i   v i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

C chrX_82729391_8   6230 ACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTA 6181
                         ii    i    v   i     v           i  i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

C chrX_82729391_8   6180 AAGACTTAAACGTTAGACCCAAAACCATAAAAACCCTAGAAGAAAACCTA 6131
                         ?    i    i  v   v i     i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

C chrX_82729391_8   6130 GGCA-ATACCATTCAGGAAATAGGCATGGGCAAGGACTTCATGTCTAAAT 6082
                           ?i- v i -   iv  vv v  vv i     v ii   v ivv  viv
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

C chrX_82729391_8   6081 CACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 6032
                                    vvi           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

C chrX_82729391_8   6031 AAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGCGAACAG 5982
                            v v  i i   i   i vv    i  v    i  vv i  i   v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

C chrX_82729391_8   5981 GCAACTTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAG 5932
                         i    ii   i             v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

C chrX_82729391_8   5931 GGCTAATATCTAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5882
                          i  vi    i     v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

C chrX_82729391_8   5881 ACGAACAACCCCATCAAAAAGTGGGCAAAGGACATGGACAGACACTTCTC 5832
                           i  i     v  i?    i           iv  i i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

C chrX_82729391_8   5831 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 5782
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

C chrX_82729391_8   5781 CACTGCCCAT 5772
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.22 (79 / 65)
Gap_init rate = 0.00 (2 / 559), avg. gap size = 1.00 (2 / 2)  

1487 30.65 0.98 0.98  chrX_82729391_82738299     7198  7706 (1203)    L1M4_orf2#LINE/L1        1   509 (399)  

  chrX_82729391_8   7198 TGGAAAAACAATCCATACCCATGGATTGGAATAATCAATATTGTAAAAAC 7247
                               i i vi    iii            v v i        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82729391_8   7248 GGCCATACATCCCAAAACAATTTACAAGTTCAATGCTATTTCTATAAAAC 7297
                            v    vi      vii  i    ii     i  v  ii    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82729391_8   7298 TACCAA-TGTCATTTTT-CACATGATTGGAAAAAACT-ATTCTAAAATTC 7344
                          v   i-  i v     -  v -i    -- v  i  -  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_82729391_8   7345 ATATCAAACCAACAAATAACCCA-AATAAGAAAGGCAATCCTAAGCAAAA 7393
                             vi  vii-   ivi     -    ivv  ii     i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_82729391_8   7394 GGAACAAAGCTCGTGGCCCCA-ATATACCTGTCTTCAAACTATAATATAA 7442
                         i        i v v  v i  - iv v  vi i iv     -  v  i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chrX_82729391_8   7443 GGTTATTGTAATCAAAACAGCATGGCACTGATAGAAATCTAGACATGTAG 7492
                         i i  iv        i    ii   i    ii v  ivv       i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_82729391_8   7493 ACCAGTGAAACAGATTAGAGAACCCAGAAGTAAAGCTGAACACTCACAAC 7542
                          i  i  i  i   v v    ii      i    v iiv   i i iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_82729391_8   7543 TATCCGATTTTTGACAAAGCTGGCAATAACGAGCAATGGAGAGAGAACTC 7592
                         i vii      i     i v  v   v v ivv      i  i    ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_82729391_8   7593 CCTATTCAGTAAATGGTGCTGGGATAATTGGCTAGGAATATGCAGGAGAC 7642
                         i  v    ii              i  i   v  ?vv i     ii   v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_82729391_8   7643 TGAAACTGGACACCTGTTTTTCAAAATATACAAAAATCAACTCAAGAGCA 7692
                             ii     v   iii iv  vv            i       i vvi
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_82729391_8   7693 ATTAAAGACTTGAA 7706
                           i ?    i i  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAA 509

Transitions / transversions = 1.75 (98 / 56)
Gap_init rate = 0.02 (9 / 509), avg. gap size = 1.11 (10 / 9)  

1000 25.42 4.28 4.51  chrX_82729391_82738299     8002  8422 (487)    L1M4_orf2#LINE/L1      489   908 (0)  

  chrX_82729391_8   8002 AAGATAGATTAAAGAATTAAATGTAAAACCTGGAAGTATTAAATCCCTAG 8051
                           i  i   i ?   vi         i v  ii  v   v   ii i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_82729391_8   8052 AAGAAAACTTAAGA-CATACCATTCTGGACATAAGTCTTGGCAAAGATTT 8100
                                 v  i ?-i v i -   vv   v vi vi v     v i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_82729391_8   8101 C------ATGACAAAGTCTCCAAAAGCAATTGCAAAATAATAATAATAAT 8144
                          ------      ------         ----   i----i  i  v iv
  L1M4_orf2#LINE/    588 CTTAGATATGACA------CCAAAAGCA----CAAG----CAACAAAAGA 623

  chrX_82729391_8   8145 AAAACTAGATAAATGAGAGCTAATTAAA-CTAAAGAGCCTTCTGCATGGC 8193
                             v         vi  vi v  i   -i    i --   i  iiivv 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTC 671

  chrX_82729391_8   8194 AAAACATACTATCAAGAGAGTAAGCCGACAACCTACAGAATGGGAATAAA 8243
                            iv i          i   i ivv       i           iv   
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_82729391_8   8244 TATTTGCAAACTATGCATCTAACAAAGGTTTAATATTCAGAATCTATTTA 8293
                                   ii  ii    i i  i  vi vi   i      v   v- 
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA-A 770

  chrX_82729391_8   8294 AAAATT-----AAATAAACAAGTGAAAAATAAACAACCCCATTAAAAAGT 8338
                          i  i -----  v v  i  vvi   i i   i     v   ?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_82729391_8   8339 GGGCAAAA-ACATGAACAGATGCTTCTTAAAAGAAGATATACTATGTGGC 8387
                                i- iv    i   iii    iv             v -i    
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA-ATGGC 869

  chrX_82729391_8   8388 CAA----CATATGAAAAAATACTCAAAATTACTAATCAT 8422
                            ----  i       i  i     v  i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (66 / 38)
Gap_init rate = 0.03 (13 / 420), avg. gap size = 2.85 (37 / 13)  


3064 26.47 1.33 0.78  chrX_82744330_82751011.rev     5289  6191 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82744330_8   5289 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGG-AAAAT 5337
                               i i  i     i        v      v i     i v-  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82744330_8   5338 G----TACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 5383
                          ----    v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82744330_8   5384 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5432
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_82744330_8   5433 ACGGAATCAAAATAGAATCTGTATATCCAAGACAATCCTAAGCAAAAA-A 5481
                          i    viiv  vi  vi v v   v    i      i i iv  i  - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_82744330_8   5482 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAATTATACTACAAGGCT 5531
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_82744330_8   5532 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAGCAGGTATGTAGACCA 5581
                                i   i    ii         i iv iiii  ii  i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_82744330_8   5582 ATGGAACAGAACAGAGACCTCAGAAATAACGCCACACATCTACAACCATC 5631
                               i    iv    vii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_82744330_8   5632 TGATCTTCAATAAAGCTGACAAAAACAAGCAATGGGGTAAGGATTCCCTA 5681
                             i   i i  i v  v   i v  vv        v   i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_82744330_8   5682 TTTAATAAATGGTGTTGGGGAAACTGGCTAGCCATATGCAGAAAACTGAA 5731
                           i  i        i    iv      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_82744330_8   5732 ACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 5781
                         ii         v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_82744330_8   5782 AAGACTTAAACTTGAGACCTAAAACCATAAAAAAATCCTAGAAGAAAACC 5831
                         ?    i    iv i   v       i      v--  i           v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAAC--TCTTAGAAGAAAACA 547

  chrX_82744330_8   5832 TAGGCA-ATACCATTCTGGATACAGGCATGGGAAAAGTCTTCATGACTAA 5880
                             ?i- v i -   vv  iviv  vv i  v  v vi   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_82744330_8   5881 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGATAAATGGGATCTAA 5930
                         i            vvi          vv             v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_82744330_8   5931 TTAAACTAAAGTGCTTCTGCACAACATAAGAAACTATCATCAGACTGAAC 5980
                          i   v v  ivi   i  ii vv  v i  v       vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_82744330_8   5981 AGGCATCCTATAGAATGGGAGAAAATTTTTGCAATCTATCCACCTGACAA 6030
                           i  v  i i               v       vii  vi i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_82744330_8   6031 AGGGCTAATATTCAGAAACTACAAAGAACT-TAACAAATTTACAAGAAAA 6079
                         i  i  vi   i     vv  i        - v    v ---   v  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATA 793

  chrX_82744330_8   6080 AAAAAACAAACAACCCCATCAAAAAGTGGGAAAAGGATATGAACAGACAC 6129
                             i     i     v  i?    i    v       v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_82744330_8   6130 TTCTCAAAAGA-GATTTATG--TGGCCAACAAACATATGAAAAAAAGCTC 6176
                              v     -   v  ii--       i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_82744330_8   6177 ATCATCACTGGTCAT 6191
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


2362 25.72 1.29 0.43  chrX_82759387_82761078.rev      506  1201 (491)    L1M4_orf2#LINE/L1      207   908 (0)  

  chrX_82759387_8    506 TGGAGGTATCACATTACCCGACTTCAAACTATACTGTTAAGTCTATAGTT 555
                               vv     i v   i i      viv    iiv   -   i   v
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG-CTACAGTA 255

  chrX_82759387_8    556 ACCAAAACAGCATGGTACTGGTATAAAAATAGACATGTAGACCAATGAAA 605
                          i   i    ii         i    ii        i    i     i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_82759387_8    606 AAGAATAGGGAACCAAGAAATAAAGCCAAATACTTATAGCCAACTGACCT 655
                         v     v i  ii v         v   v i i    i i   i   ii 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_82759387_8    656 TTGACAAAGCAAACAGAAACATAAATTGGGGAAAGGACACCCCATTCAAC 705
                          i     i vviv  ii v   vv v         i i vi iv      
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_82759387_8    706 AAATGGTACTGGGATAATTGGCAAGCCACGTGTAGGAGAATGAAGCTGGA 755
                                i      i  i   vv ?    i  i ii         i    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_82759387_8    756 TCCTCATCTCTCACCTTTCACAAAAATCAACTCAAGATGGATCAAAGACT 805
                         i  ii i   v    v vi        i       i        ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_82759387_8    806 TAAATCTAAGA-CGAGAAACCATAAAAATTCTAAAAGATAACATCCGCAA 854
                              v     - v -    i      v ii  i    v     vv ?iv
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_82759387_8    855 AACTCTTC-TAATATTGGCTTAGGCAA-AGTTTTTGTGACCAAAAGCCAA 902
                           v     - i iv    v        -i    i vv  ivvi vi    
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_82759387_8    903 AAGTAAATGCAACAAAAACAAAAATAAGTAGATGGGACCTAATTAAACTA 952
                            i v v         iv       ii  i  v    i v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_82759387_8    953 AAAAGCTTCTGCACAGGTAAAGAAATAATCAGCAGAGTAAACAAACAATG 1002
                             i   i  ii vvvv  i  v iv    iv i   i  v i    iv
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_82759387_8   1003 CACAGAATTGGAGAAAATATTCAAGAACTAAGCATCTGACAAAGGACAAA 1052
                                 v            iivi  ii vii      i  i    vvi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_82759387_8   1053 TGTCTAGAACCCACAAGGAACTCAAACAAATCAACAAGAAAAAG-CAA-T 1100
                          i  i    ivi i  i      vv    v    i  v      -   - 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_82759387_8   1101 --CCCA--TCAAAAATAGGGCAAAGGACATGAATACACAATTCTCAAAAG 1146
                         --    -- ?      -          iv      v   v     v    
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAAT-GGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_82759387_8   1147 AAGATATACAAATGGCCAACAATCATATGAAAAAATGCTCAACATCACTA 1196
                                            i  v  i       i             ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_82759387_8   1197 CCTAT 1201
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.43 (103 / 72)
Gap_init rate = 0.01 (10 / 702), avg. gap size = 1.20 (12 / 10)  


2197 26.94 2.91 5.06  chrX_82761147_82764617.rev     2053  2980 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82761147_8   2053 TGGAAAACCATCTCATGTTCATGGAGAGAAAGAATCA-TATTGTCAAAAT 2101
                               ivi   i            vv i    v i -      i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82761147_8   2102 GGCCGTATTGCCCAAAGCAATTTACAGATTCAAT---ATTTCTATCAAAC 2148
                            vi  i v      vii  i           i---  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82761147_8   2149 CCCCAAAGACATTTTTCACAGAATTAGAAGAAAAC--ATTTTAAAGTTCA 2196
                         i    ivvi v     ii     v v  v--  i --  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chrX_82761147_8   2197 TATGAAACCATAAAAAAGCTTGAATAGCCAAGGCAATACTAAGCAGAAAG 2246
                             i  viii  iii v iv          ii    vi i iv ii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82761147_8   2247 ACTACAGCTGGAGGCATCTCATTACTCAACTT-AAAACTATACTACGAGG 2295
                          vi v  i      vv  v  i v i   i  -      -      i i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_82761147_8   2296 CTAGAGTAATGAAAACAGCATGGTACTGGTAGATAAACAGATACATAGAC 2345
                            v      v  i    ii         i v vii i   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_82761147_8   2346 AAGTGGAAAAAAAATAAAGACCCTCGAAGTAAGACCACACAACTACAAGC 2395
                         v i     v i  v i -  vi iv   i   iv   i   vi  iiiv 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_82761147_8   2396 ATTTGGATCTTGCACAAAATTTACAAAAACAAACAATGGGGAAAGACT-T 2444
                          v   -  i  vv    iiv vv   i v  vv             v -v
  L1M4_orf2#LINE/    347 AATTG-ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_82761147_8   2445 TCTATTTAATAAATTGTGCTGGGATAACTGACTAGGCCATATGCAGAAGA 2494
                            v  i  i    v         i     iv  ?-   i     i    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAK-CCACATGCAAAAGA 444

  chrX_82761147_8   2495 CTGAACCTGCCCTCCTTTCTTA-ATCATATACAAAAATTAAC--AAGATG 2541
                         v    vi  vv i   vi  i - i                 --  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_82761147_8   2542 GATTAAAGACTTAAATCTAAAA-TGAAAATGTATAAAAAAAAAAACCCTG 2590
                            i ?    i     v   i -iv    i-       v------i i i
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAAC-TATAAAAC------TCTTA 537

  chrX_82761147_8   2591 GAAGATAACCAAGGAA-ACACCATTCTGGATATAGGGCCTGGCAACCATT 2639
                              v   vv   ?i- v i -   vv  iv v   iiv     ivi  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_82761147_8   2640 TC------ATGACA---AAAACATCAAAAACAATTTCAAACAAAATTAAC 2680
                           ------      ---   i  iv iv     ---v i v     vi i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAA---AAGAAAAAATAGAT 633

  chrX_82761147_8   2681 AAATGGGACCTCATTACA-CTAAATATATTCTGTAAAGCAAAGAAAACTC 2729
                             v    i    i v -i    v i-  i   ivvv     i v   v
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTA 682

  chrX_82761147_8   2730 TCAACAAAGGCAACAGACAATTTACAGAATGGGAGGAAATACTTGCAAAG 2779
                             v    vv  v      iii            i     i       v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_82761147_8   2780 TATGCATCCAACAAAGTCTAACTT----CCAGGGTCTATAAGAAATTTAA 2825
                         i  ii   ii i  i ---i    ----    ii v     ii  i i--
  L1M4_orf2#LINE/    733 CATATATCTGATAAGG---GACTTGTATCCAGAATATATAAAGAACTC-- 777

  chrX_82761147_8   2826 ATTTACAAGCAAAAAAAAAAAAAAGAAAAAGAAAAAAGAAAAAGAAAAAC 2875
                         --      viv  v  ---------------------v       v   i
  L1M4_orf2#LINE/    778 --TTACAACTCAATAA---------------------TAAAAAGACAAAT 804

  chrX_82761147_8   2876 AACTTCGTCAAAAAGTGGGCAAAGTATATGAACAGACACTTCTCAAAAAA 2925
                            iivi i?    i         v  v    i     i     v   i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_82761147_8   2926 AGACATTCATGCAGCCAAAAAGCATATGAAAAGAATGCTCAACATCACTA 2975
                            i  v  viii     v     i         -            ???
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZ 903

  chrX_82761147_8   2976 ATCAT 2980
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.74 (74 / 27)  


1775 27.59 1.17 0.98  chrX_82764736_82769510.rev     2991  3501 (1274)    L1M4_orf2#LINE/L1        1   512 (396)  

  chrX_82764736_8   2991 TGGAAACACATCTCATGCTCATGAATTGGAAGACTCAATATTGTGAAAAT 3040
                               v i   i    i     i           i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82764736_8   3041 GACCATACTTCCCAAAACAATCTATGGATTCAATATAATCCCCATCAAAA 3090
                          i v     i      vii     ii       iii      i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82764736_8   3091 TATCAA-TGTCACTTTTCACAGAATTTAAAAAAGAAAATTCTAAAATTCA 3139
                          vi  i-  i -i    ii     v  i v  - vvi  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_82764736_8   3140 AATGGAACCAAAAACAGCACA-AATAGCCAAAGTAATTCTAAGCAAAAAG 3188
                         v      viiv  ivii v  -          ii   ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82764736_8   3189 AACAAATCTGGAAGCATCACATTATTGAACTT-GAAACTATAATACAAGG 3237
                               vi    i vv     i viiv  i  -i     -  v     i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_82764736_8   3238 CTATAGTTACCAAAACGGCATGGAGCTGGTATAAAAGCAGGCACATAGAC 3287
                            i   v i   i  i ii   vi    i    iiii  i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_82764736_8   3288 TAATGGAACATAATAAAAAGCCTAGAAATAAAATGAAATATGTACAGCCA 3337
                         i       i v   vi i  i i         viv v i  v  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_82764736_8   3338 ACTAATTTTTGACAAAACATG--AAAAACATAAATTAAGGAATGGACA-T 3384
                          i i     i     ii-i  --  i v   vv v ii    v i i - 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_82764736_8   3385 CATATTCAATAAATGGTGCTGGGAAAACTGGCAAGCCACATGTGGAAGAA 3434
                          v -     i              v      vv ?       iii     
  L1M4_orf2#LINE/    397 CTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_82764736_8   3435 TGAAACTGGATCCTTATCTCTCATCATATATAAAAATCAACTCAAGATGG 3484
                             ii    i  i  i   v  i      i      i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_82764736_8   3485 TTTGAAGACTTAAATAT 3501
                         v ii?    i     i 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGT 512

Transitions / transversions = 2.48 (99 / 40)
Gap_init rate = 0.02 (10 / 512), avg. gap size = 1.10 (11 / 10)  

1107 28.06 0.26 0.51  chrX_82764736_82769510.rev     3893  4284 (491)    L1M4_orf2#LINE/L1      518   908 (0)  

  chrX_82764736_8   3893 CTGAGACCCTAAAATTTCTAGAAGACAACTTTGGAAAAACTCTTCTAGAC 3942
                           i i  iv     i ii       v   v v  ?iv  v     vv   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_82764736_8   3943 ATTGGCTTAGGCAAATAATTTA-TAACTGTGACCCCAAAAGCAAATGCAA 3991
                         v    v        - ii   v-  iv i    v         v v    
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_82764736_8   3992 CAAAAACAAAAATAAACAAATGAGACCCAAATAAACAGAAAAGCATCTGC 4041
                              iv       i i    vi   iiv vi   vvv    i v i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_82764736_8   4042 AAGTCAAAATAAATAAGCAACAGAAGAAAAGGACAACCTACGGAGCAGGA 4091
                         ivv     iv v iv v   v i ivi   i       i  i  iii   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_82764736_8   4092 GAAAATATTTGCAAACTACACATTCGACAACAAACTAATATCCAGAATCT 4141
                                        ii i i  ii  i  vii   vi          v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_82764736_8   4142 ATAAGGATCTCAAGCAAATGACAAAGAAAAAAATCAAATAATCCCATTAA 4191
                             i  v   vvi   v v vv  v     i -       i  v   ? 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWA 815

  chrX_82764736_8   4192 AAAGTGGACAGAGAACACGAATAGACATTTCTTAAAAGAAAATATACAAA 4241
                            i   i  i  i ivi              iv      i         
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_82764736_8   4242 TGGCAAACAAATATATGAAGAAATGCTCAACATTATTAATCAT 4284
                             v  i  ii i     i i           i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (62 / 46)
Gap_init rate = 0.01 (3 / 391), avg. gap size = 1.00 (3 / 3)  


2101 26.25 1.94 9.40  chrX_82779993_82783794.rev      694  1672 (2130)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_82779993_8    694 GAAAGATATTCCATGTTCATGGGTCAGAA---TCAATATTATAAAAATAA 740
                                  i            i ii   --- i      i v  i  ii
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_82779993_8    741 TCATACTACACAAGC-AATCTACAGACTGAATGCCATCACTTTCAAAAAT 789
                         iv     v v   ii-i         i v  i  v   v  v      - 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-T 101

  chrX_82779993_8    790 ATGAAAGAAATTACTTACAGTAATAGGAAAAG--AATCCTAAGATTTATG 837
                         viv ivvivv  vi  i   v   -v  v   --i       i   i  i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATA 150

  chrX_82779993_8    838 TGAAACCACCAAAAACCCCAAATAGCAAATGAAATCTAGGGAAAAAACAA 887
                           i  vii v iii    vi      v  viv     v ---     v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG---AAAAAGAA 197

  chrX_82779993_8    888 AAATAAACCTGAACA--TCAGATTACCTGACTTCAAAATATATTACAAAG 935
                         i  i   vi  i vi--   v i v  ii i       iv  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_82779993_8    936 CTATTGTAGTATGTATGCTATAGCTATATACAAAGTATAGTAATCAAAAC 985
                            i----------------------------------         i  
  L1M4_orf2#LINE/    248 CTAC----------------------------------AGTAATCAAGAC 263

  chrX_82779993_8    986 AGCATGGCATTGATATAAATACAGACACATAGACCAATATAACAGAATAA 1035
                           ii   i i  ii    iv i     i     i    iv  i     vi
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_82779993_8   1036 AATACGCAGAAATAAATCCACATATTTACAGCCCAACTGATTTTTGACAA 1085
                          iviiv          i   i i     ii i -  i       i     
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTC-AATTGATTTTCGACAA 362

  chrX_82779993_8   1086 AACTGCCAAAAATATACATCGGAAATAGGACATCCTTTTCAATTAGTGGT 1135
                         iiv      i vi  v  vi  ii v  i i vi        iv i    
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_82779993_8   1136 TCTGAGAAAACTACCCATTTACATGCAGAAAAGGTAAACTAGACCCTTTT 1185
                         v   i  v    ivvi ?ii       i  i ivv  ii i     i vi
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_82779993_8   1186 TTT-CATCCTATACAGAAATCAACACAAAATGAATTA-AAACTTAAATCT 1233
                         i i-  i v      i    i   v       i  i - i  i     v 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_82779993_8   1234 AAGGCTTGAACCTCTAAAACTACTGAAAGAAAA--TAGGGG-AAACCCTC 1280
                            ivi i  v  v       vi ii       --    ? -   i i  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_82779993_8   1281 AGGACATTGGTCTAGACAAAGATTTTGTGACTGAGTCTTCCAAAGCACAG 1330
                         iv   v    vi   i   v i   iv iiv iv v vi v        i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_82779993_8   1331 GCAA----ACAAAAAATAGACAAATGTGATTACATTAAACTAAAAATCTT 1376
                             ---- v          i    vv  i v   i   v v    v   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_82779993_8   1377 CTA-GTTTTAGAAGAAATTAGAACAGAGTAAAACAATTAACAGAGT-AAA 1424
                         i i- i  i i i  v i  ---------------- i  v i   -   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTA----------------TCAAGAAAGTGAAA 696

  chrX_82779993_8   1425 AGACAAACTACATAATGGGGGAAAATATTTACAACTTACTCTTCTAACAA 1474
                               v i   v      i          i   v i iviv   i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_82779993_8   1475 TGGACCAATATCTAGAATATACAAGGAACTCACACAACTCAACAGCAAAT 1524
                         v    ivi    i        i  i      vi         i ------
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA------ 790

  chrX_82779993_8   1525 AAATAAATAAATAAATAAATAAATAATTATGTAATAAATAAAATAATTCC 1574
                         ----------     v i i      ii---------------i    --
  L1M4_orf2#LINE/    791 ----------ATAAAAAGACAAATAACC---------------CAATT-- 813

  chrX_82779993_8   1575 CATTAAAAGTGTGCAAAATATTTGAATAGACATTTCTCAAAAGAAAACAT 1624
                         ---?    i  v     iv                   v      i i  
  L1M4_orf2#LINE/    814 ---WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_82779993_8   1625 ACAAATGGCCAACAGGTATATTGAAAAATACTCAACATAATTTATTAT 1672
                                     i i i i  vi   i  i        v ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (164 / 90)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 5.55 (111 / 20)  

2230 26.25 1.47 0.88  chrX_82779993_82783794.rev     2620  3301 (501)  C L1M4_orf2#LINE/L1   (0)   908   223  

C chrX_82779993_8   3301 CCCGACTTCAAACTATACTACAAGGCTAAAGTAACCAAAACATCAGAGTA 3252
                            i i      viv        i    v     i   i   viivi   
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

C chrX_82779993_8   3251 CTGGTACGAAAACAGACACATAGACCAATGGAAAAGAACAGAGATCTCAG 3202
                             i ii ii i     i     i        v    iv    vii   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

C chrX_82779993_8   3201 AAATAAGACCATACATCTACAACCATCTGATCTTTGACAAACCTGACAAA 3152
                               iv        i  iiii  vi    i  i     ivv  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

C chrX_82779993_8   3151 AACAAGTAATGGGGAAATTATTCCCTATTTAATAAATGGTGCTGGGAGAA 3102
                          v  vvi          vv  vvi  v  i  i              v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

C chrX_82779993_8   3101 CCGGCTAGCCATA-GTTAGAAAATGGAAACTTGACCCCTTCCTTACGCCT 3053
                          i  v  ?   i - iv i i    -  ii v       v   i  i  v
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATG-AAGTTGGACCCCTACCTCACACCA 471

C chrX_82779993_8   3052 TATACAAAAATTAACTAAAGATGGATTAAAGACTTAAATGTAAAACCCAA 3003
                                         v  i      i ?    i         i v i  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

C chrX_82779993_8   3002 AACTATAAAAACCATAGAAGAAAATCTAGGCA-ATACCATTCACAACATA 2954
                                   vi v          iv    ?i- v i -   iii  v v
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTT 570

C chrX_82779993_8   2953 GGCATGGGCAAAGATTTTAT---CATGAAAACATCAAAAGCAATTGCAAC 2907
                           vv i     v i   iv ---i    ---  i        vvv     
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGA---CACCAAAAGCACAAGCAAC 617

C chrX_82779993_8   2906 AAAAGCAAAAATTGAAAAGTGGGACCTAATTAAACTAACCAGCTTCTGCA 2857
                              v      v  v  i v    i v  i   v v vv i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

C chrX_82779993_8   2856 CAGTGAAAGATACTATAATCAGAGTGAACAGAAAACCTACAAAATGAGGT 2807
                          vvii  i  i     v vv i      v   v    i   i    i iv
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

C chrX_82779993_8   2806 AAACATTTTTGCAATCTATTTATCTGACAAAGGTCTAATATCCAGAATCT 2757
                            -  v       vii  v       i  i  v  vi          v 
  L1M4_orf2#LINE/    718 AAA-ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

C chrX_82779993_8   2756 ACAAGGAACTTAAACAACTTTACAAGAAAAAGA-AAA---CCCA-TTAAA 2712
                          i  i     ivv      iv i  v       -   ---    -  ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

C chrX_82779993_8   2711 AAACAGGCAAAAGACATGAACAGACATTTCTCAAAAGATGACATTTATGT 2662
                            ii      i  iv    i           v     v  i  vi vi 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

C chrX_82779993_8   2661 GGCCAGCAAACATATGAAAAAATGCTCAATATCACTGATTAT 2620
                              ii  i  i       i        i    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (101 / 74)
Gap_init rate = 0.01 (10 / 686), avg. gap size = 1.60 (16 / 10)  


2893 27.86 1.44 0.67  chrX_82801340_82805593     2861  3761 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82801340_8   2861 TGAAAAGATATTTCATGTTCATGAAGTGGAAATAAATCAGTATTGTTAAA 2910
                           i        ii          i v     i-- v i i         i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAG--ACTTAATATTGTTAAG 48

  chrX_82801340_8   2911 ATGTCCGTGATACCCAAAGAAATGTATAAATTCAATGCAATCCCTATCAA 2960
                            v vi iv v      vvi  v  i i      i              
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_82801340_8   2961 TATACCAATGACATTCTTCACAGAAATAGAGAAA---ATTCTAAA-TTTA 3006
                         v  v   iivi v  i  ii       v  v  i---  i     -  i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_82801340_8   3007 CATGGAACCACAAAAGAG--AAACTAGACAAAGCTATCCTAAGCAAAAAG 3054
                         i      vii   ii  v-- i v   v    i v   i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82801340_8   3055 AACAAAATTGGAGGAATTACATTGCCTGACTTCAAATTATACTATGAAGG 3104
                               i        v i   i v  ii i      viv     ii   v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_82801340_8   3105 TATAGTAACCAAAACAGCAAGGTACTGGCATGGAAACAGACACACATACA 3154
                           i     i   i    iiv           iiii i     i i v iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_82801340_8   3155 AATGGATCAGAATAGAAAACACAGAAATAAATCCACACACCTGCAGAAAA 3204
                               vi     v  i iiv          i   i   ii iii vv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_82801340_8   3205 CCTATTTGTGACAAAAGTTCTAAGAAAGTACCCTGGGGAAAAGACAGTCT 3254
                         iiv    vi     ii  v i    vvi v vv        ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_82801340_8   3255 CTTCAAGAAATGGTGCTGAAAAAGCTGGATATCCATATGCTTAAGAATAA 3304
                         i     v           ii v i       ?   i    vv      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_82801340_8   3305 AACTAGACCCCTATCTCTCACCATATACAAAAATCAAATCAAAATTAATT 3354
                          ii i        i   v                i  v       vi  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_82801340_8   3355 AAAAACTGAAATCCAAGATTTCAAACCCTAAAACTGCTACAAGGAAACTT 3404
                          ? i  iv    vi    vi v    iv       vi  v   i    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_82801340_8   3405 TGGGGAAAACCTCAAGGACATTGATCTGGGCAAAAATTTATTGAGCAATA 3454
                         v  ? v   i  iviv   v   ivi i     vii   v  -  --   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AG--ATA 595

  chrX_82801340_8   3455 TCTCAC---AAGCACAGGCAACCAAAGCAAAAATGGAAAAATGGGATCAC 3501
                          vv   ---       i     v    v      i  v    v   iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_82801340_8   3502 ATCAAG-TTAAAAACCTTCTGCATACCAAAGAATACAATCAACAATTTGA 3550
                              i-        i  -  iiivi     i i  v     v  vv   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_82801340_8   3551 AGCTGCAACCTACAAAACGGGAGAGAATATTTTCAAACTACCCATCTGAC 3600
                          ivvi     i   i  i      i       v    ii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_82801340_8   3601 AAGGGATTAATAACAAAGATATATAAAGTGCTTACACAAATCTACAGAAA 3650
                               i vi  v v ii          vi  ivi    v  v i iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_82801340_8   3651 AAAATCTAATAATCCTATCAAAAGAGGGTTAAAAAATTTGAATAGACATT 3700
                            iv v     i  v  i?   i v  vi   ii               
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_82801340_8   3701 TCTCAAAAGGAGGTATACAAATGGCAGACAA---TATGAAAAGGTGCTCA 3747
                             v    i  i            vi i  ---i        i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_82801340_8   3748 ACACCACTGATCAT 3761
                            i  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (151 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


3094 27.97 0.55 0.55  chrX_82811154_82817552     4999  5906 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82811154_8   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5048
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82811154_8   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82811154_8   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCC 5146
                          v   iivi i  i  ii     -   -- v  i  - iii v  i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_82811154_8   5147 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCCATCCTAAGCCAAAAG 5196
                                viiv  ii  v  viv  v     iv v   i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82811154_8   5197 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5246
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_82811154_8   5247 TGCAGTAAACAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5296
                          i      v   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_82811154_8   5297 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 5344
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_82811154_8   5345 ATCTGATCTTTGACAAACCTGAGAAAAACACGCAATGGGGAAAGGATTCC 5394
                          vi    i  i     ivv  vv  i v  iv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_82811154_8   5395 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAACCT 5444
                           v  i  i              v      v  ?   i   i i  ivv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_82811154_8   5445 GAAACTGGATCCCTTCCTTACACCTTATACATAAATTAATTCAAGATGGA 5494
                            ii    i    v   i     v      v       i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_82811154_8   5495 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5544
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_82811154_8   5545 CTAGGCATCACTATTCAGGACATAGGCATGGACAAGGACTTCATGTCTAA 5594
                         v    ?i v v v   iv   v v  vv i i   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_82811154_8   5595 AACACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5644
                         i         i  vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_82811154_8   5645 TTTAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5694
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_82811154_8   5695 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTA-ATCTGACA 5743
                           i     i                 v  i    vii -  -      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGATA 745

  chrX_82811154_8   5744 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACACATTTACAAGAAA 5793
                          i  i  vi          v  i  v      iv   vv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_82811154_8   5794 AAAACAAACAACCCCATCAAAAAGGGGATGAAGGACATGAACAGACACTT 5843
                           i     i     v  i?    iv  iii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_82811154_8   5844 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCGCAC 5893
                            v        i  vi viii     v ii          i    v  v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_82811154_8   5894 CATCACTGGCTAT 5906
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (148 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2194 26.47 6.22 3.51  chrX_82844061_82847207     1771  2654 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82844061_8   1771 TGGAAAAATATTTCATGTTTATGGATAGAAAGCCTCAATAGTGTCAAGAT 1820
                               i    ii      i      v i   v  i    v   i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82844061_8   1821 GTCAGTTCTTCCAAAGTTGATCTACAAATTTAACACACCTTTTATGTAAA 1870
                          v  i v  i  v  i          i   i   i  viiii   vv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82844061_8   1871 CCACAGCAAGTTATTTTTTGAATGTCAACAAATGGATTCAACGGTTTATG 1920
                         i v    vivi v    viii vi ii    iiv   i v vii  i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_82844061_8   1921 TGTGGAAA--CAAAAGACCCAGAATAACCTACACAATATTAAAGGAGAAG 1968
                           --    --   ii           i  v v     v  i  ii     
  L1M4_orf2#LINE/    151 TG--GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82844061_8   1969 AACAAATTTGGATAAATAACACTGCCTGACTTCAAAACTGACTATAAAGC 2018
                               v     vi v v     v  ii i         v    i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_82844061_8   2019 TACAGTAATCAAGAAAGTGAGATATTGGCA-AAGAATAGCCAGATAGATT 2067
                                       v    v i  i     -   i    v  v      i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_82844061_8   2068 AATGGAACAGAATAGAGAGCTCATAAAGAGACATAATCTATTTAACATTG 2117
                                i     v     ii  v   v -----  i i  ---     -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATA-----AACCCAT---ACATT- 339

  chrX_82844061_8   2118 TTATAAACATAGTCAACCGATGTGTAAGAAAGA-ATAAAAACAGTACAAT 2166
                         -------i  i     ii   v vii v  i i-iiv  i  vi v    
  L1M4_orf2#LINE/    340 -------TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_82844061_8   2167 GGAGAAAAGATGGCATTTTCAATAAATGGTGCTGTAACAACAAGACATCC 2216
                           i    ii  i iv       i           vi     vi  i ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_82844061_8   2217 ACATAGTTAAAAAA--AACTCTAGACACAGACCTACAGACCTTATATGTT 2264
                             - iv   i  --  v - i   v vv    -  v   --    ---
  L1M4_orf2#LINE/    433 ACAT-GCAAAAGAATGAAGT-TGGACCCCTACCT-CACACC--ATAT--- 474

  chrX_82844061_8   2265 TTACAAAAATTAACTAAAAATTGAT----AACCAATTAATATAAAAA-TA 2309
                         --             v     v   ----i   v --   i   i i-  
  L1M4_orf2#LINE/    475 --ACAAAAATTAACTCAAAATGGATCAWAGACCTA--AATGTAAGAGCTA 520

  chrX_82844061_8   2310 AATCTATAAAA-TCTTAAGAAAATAATGTAGAAGAAGGTCTAAATGTCCT 2358
                           v        -     -   i v  ii   i? v ii   vvi  v   
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTA-GAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_82844061_8   2359 TGATTTGGTGAAGAATTTATT-GATACAATAGCAAAGGCACAATCTGTAG 2407
                           iv  i vv  vii   v  -    ii i v    i      v vii i
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_82844061_8   2408 AAGAAAGAATTGATAATCTGAACTTTAT-------------------GC- 2437
                               i   v     vi  i    i  -------------------  -
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_82844061_8   2438 ---------------AAGAGAATAAAATGACAAGCCACAGACTGGGACAA 2472
                         ---------------    i i i   v     v       v     v  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_82844061_8   2473 AACAATTGCAAA--AGACAT---ATAAAGAACTGTTATCTGAAATACACA 2517
                           i v       -- v i  ---    i i   vv    iii    i i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_82844061_8   2518 GA-AACACTTAAAGCACAAAAATAAGAAAACATATAACCTAACTTAAAAG 2566
                         i -   v    v i v   v     i  i   v      i  i ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_82844061_8   2567 TGAGCCAGGAACCTTAACAGACACCTTACTAAAGAAAATATACAG-TAAA 2615
                           i  v i i ii v  i     ii iv i      i       i- iiv
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_82844061_8   2616 AAATAAACATATACAAATGTGTTCCACATTATGTGTCAT 2654
                         v     i  i  iv   vi  i  v    i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (142 / 89)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.44 (86 / 25)  


2560 26.68 3.48 1.91  chrX_82850876_82855103     2844  3735 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_82850876_8   2844 GAAACATAGTCCATGCTCATAG-TTGAAAAAAAATGTATATTGTTAAAAT 2892
                             v   vi     i    i -   i  i v-- vv          i  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGAC--TTAATATTGTTAAGAT 50

  chrX_82850876_8   2893 GTCATTTAAAACTC---AAGGCAATTTATAGACTTGATGCAATCCTTATC 2939
                          v  v ----    ---  ivii  i  i   i ii i       i    
  L1M4_orf2#LINE/     51 GGCAAT----ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_82850876_8   2940 AAAGGATAAATGACATTCTTTAAAGATATAGAAAAA--AATTACAAAATT 2987
                            ivviv iivi v  i   iv   v  v  v  i--i  ivi      
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_82850876_8   2988 TACATGGAACCACAAAAGACTTTGAACAGACTAAACAATCCTGAGCAAAA 3037
                         i i      vii   ii   iiv   i  v v        i   iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_82850876_8   3038 ATAACAAAGCTGGAGGCATTATACTATCTGGCTTCAAAACATACCACAAA 3087
                          v       i      vv i i   vi iiii        v   i     
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_82850876_8   3088 TCTATAGTAATCAACTCAGCATGGTACTGGCATAAAATCAGACTCATTGA 3137
                         v   i         vv   ii              iivi    vi  v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_82850876_8   3138 CCAACGAAACAAAGCAGCAAACCAAGACAAAAATCCATGCATTTACAGCC 3187
                         i   i i  i i iiv vi ii v   v v   i    i      ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_82850876_8   3188 AACTCACTTTTTTTTCAAAGCATG--AAGAACATACAATGGGGAAAGGAC 3235
                           i v --    ivv   i -i  --    v   v            i i
  L1M4_orf2#LINE/    347 AATTGA--TTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_82850876_8   3236 AATGTCGTT---ATAAATGGTGCTGAGAAAACATGATAACCATATGCA-- 3280
                          --   v  --- i           i  v   vv    ?   i     --
  L1M4_orf2#LINE/    394 A--GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_82850876_8   3281 -GAAT-AAGATAGAAACCTATCTCTCATCACTTACAAAAAAATTAAATAA 3328
                         -    -   v i  vv    i   v  i  iv        --    v v 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCA 489

  chrX_82850876_8   3329 AAATGAATTAAAGACTTAAATGTAACACCTCAAACTATGAAACTACTAAA 3378
                              i  i ?    i         v v  v       i     vi  i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_82850876_8   3379 AGAAA-CATTGGCA-AAATGTTCCTGGACATTGGTGCAGGCAAATATATT 3426
                              -   v  ?i-    v   v  -  v    vvi      --- iv 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAA---TGGT 585

  chrX_82850876_8   3427 TTTGTGTGTAAAACCTCAAAAGTACAGGCAATCAAAGTAAAAATATGTAT 3476
                           iv ivi  vi  vi      i   i    iv    v       vi  v
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_82850876_8   3477 A--GGATTACATCAGGCTAAAGAGCTTCTGCACAGCAAAGGAAACAATCA 3524
                          --   i v     iiv v  i i   i  ii vv       v  v    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_82850876_8   3525 ACAAAGTGAAGAGACAATCCACAGAATGGGAGAAAATATTTGCAATCTAT 3574
                          v        i      i                           vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_82850876_8   3575 TAATATGACAAGGGATTAATACTCAAAATATAGAAGGAACTCAAACCACT 3624
                         vv  v   i      i vi  ii  i      v  i      vv  v   
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_82850876_8   3625 CAGTAGCAAAAA---------TCTGATTTTAAAATGGG-AAAATATCTAA 3664
                           i  ii     ---------i ii   ?v        -   iv  i i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_82850876_8   3665 ATAGACATTTCTTAAAAGATGACATACAAATGACTATCAGGTATATAAAA 3714
                                     iv     v  i         i i vi i i i  i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_82850876_8   3715 A--TGCTCAACATCACTAACATT 3735
                          --            ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 2.29 (48 / 21)  


2675 26.92 1.65 2.20  chrX_82866921_82870737.rev     2417  3326 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_82866921_8   2417 AAAAATATCCCATGCTAATGGATTTGAAGAATCAATATCATTAAAATGGC 2466
                            i          i v       v     v i     ii    i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_82866921_8   2467 CATACTGCTTAAAGCAACTTACAGATTCAATGCTATTCCTATTAAACTAC 2516
                         v     v ii   vii ii           i  v  i     i   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_82866921_8   2517 CAA-TGTCATTTTTCACAGAATTAGATAATACT-ATTCTAAAATTCA-AC 2563
                           i-  i -     ii     v v  i  -i  -  i          - i
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATAT 151

  chrX_82866921_8   2564 TGAAACCTAAAAAGAACACA-AATAGCCAAAGAAATTCTAAGAAAAAAGA 2612
                         v    -- iv  i i  v  -          iv   ii i i   i    
  L1M4_orf2#LINE/    152 GGAAA--TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_82866921_8   2613 ACAAAGCCAGAGGCATCACACTACTACACTTCAAACTATACTATAATGTT 2662
                               iii    vv       v ivv i      viv     i  v i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_82866921_8   2663 ATAGTAAAAGAAACAGCAAGATACTAGTACAAAGTCAGATACAGAGACCA 2712
                          i     vvi i    iiv i    i i i  i vi   i i v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_82866921_8   2713 ATGGAACTGAATAGAAAAGTCACAAATAAAGCCACATAATTACAACCATC 2762
                               iv    v  i ivi  v       v   i i v   iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_82866921_8   2763 TGATCTTTCACAAGGGTGACAAAAGAAAAGCAATGGGGAAACAACCCTCT 2812
                             i  iv         v   i vv v-v           v  ivv   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGTCT 398

  chrX_82866921_8   2813 TTTCAATAAATGGTGCTGAGATAACCAGATAGTCATATGTACAATAATGT 2862
                               i           i  i   ii    ?i  i   i v  v    v
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_82866921_8   2863 AACTGGACACCTACGTTTCACCATATACAAAAATTAATTCAGGTTGGATT 2912
                          ii     v     v iv                   i   iiv     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_82866921_8   2913 AAATATTGAAATGTAAAAACTCAAATTATAAAAC-CATAGAAGACTACCT 2961
                          ? v iiv        i i  v   i        - v       vv  v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_82866921_8   2962 AGGCA-ATATCCTTTTCAACATTGACCTTG--TCAA--AAGAGATTTTT- 3005
                            ?i- v   ---   i----        -- i i--  vi v  i  -
  L1M4_orf2#LINE/    549 AGGNGTAAATC---TTCG----TGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_82866921_8   3006 GCTAAGTCCCCCAAAGCAATTGCAACAAAAACAGAAATTGACAAGTGAGA 3055
                          v  v v v  v      vvv         iv i    v  i  i vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_82866921_8   3056 CCTAATTAAAATAAAGAGTTTTT---CCTCAGGGGGGGGAAAAAAACTAT 3102
                          i v  i     v  i ii    --- i   --------  ii v     
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCA--------AAGGACACTAT 683

  chrX_82866921_8   3103 CAAGAGAGGAAACAGACAAACTACAGAATGGGAGAAAATATCTACAGACT 3152
                              i  vi  v      v i                   i i  i ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_82866921_8   3153 ATGCATCGAATAAATGTTTAATATTCAGAATATGTAGTAAACTTAAACAA 3202
                           ii   vi    iv vi vi   i        i  ivi    ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_82866921_8   3203 GTCAACAAGCAAAATACAATTAACCCCTTTAAAAAATGGGCAAAAAATAT 3252
                         v    i  vv    v    v      vv  ?             ii  v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_82866921_8   3253 GAACGGATACTTCTCAAAAGAATACATATAAGCAGTCAACAAACATATGA 3302
                            ii  i i     v      v i   i  iii i   i  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_82866921_8   3303 AAAAATAC-CATCATCACTAGACAT 3326
                            i  i -  v     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.02 (18 / 905), avg. gap size = 1.94 (35 / 18)  


2349 29.22 2.09 2.32  chrX_82882101_82886447     2948  3854 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_82882101_8   2948 AAAAACATTTCATGCTCATGGATAGGAAGAAGCAATACCATTAAATTGGC 2997
                            i i  ii    i        v      vvi    iii    iv    
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_82882101_8   2998 CATATTGTCCAAAGAAATTTGTAGATTTGACCCTATTCCAATTAAACTAC 3047
                         v   i vi     vvi  i ii     ii  v v  i  v  i   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_82882101_8   3048 CAATGACATTTTTTAGAGAACTAGAAAAAGCT-ACTTTACAATTATTTAG 3096
                           iivi v      iv    v v  v  -   - iii  -  --   i -
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTA-AA--ATTCA- 148

  chrX_82882101_8   3097 TATGAAACTAAAATGGAGCATGAATAGCCAAGAAAATTCTAAACAAAAAG 3146
                             i  v iv  v   v vv          i v   ii i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82882101_8   3147 AACAAGGCTGAAGGCATCACCCTACCTGACTTCAGACTATGTTACACGAT 3196
                              i i  i   vv    v  v  ii i    i viv ii    viii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_82882101_8   3197 TACAGTAACCAAAAAGACATGGTACTGGTACAAAAACAGACACATCGACA 3246
                                 i   i viiii         i i  ii i     i  v  i-
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT- 297

  chrX_82882101_8   3247 CAA-GGAACTGAATAGAGA-TCACAGAAATAAGGATGCACACTTACAACT 3294
                            -    iv    v    -  -         ivviii   i   iiiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTC 346

  chrX_82882101_8   3295 TTCTGATCTTCAACAAAGCTGGCAAATATAAGCAATAAAGAAAAGACTTT 3344
                         vvi    i   i    i v  v   ivvi vv    iii    ii ivv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_82882101_8   3345 CTATTCAATAAATGGTGCTGGAATAACTGGCTACCCATATGCAGAAGA-T 3393
                           v     i            i i      v  ?   i     i    - 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_82882101_8   3394 GAAACTGGACCCCTTTCTTACACCATATACAAAAGCCAATTCAAGGTGGA 3443
                            ii         vi  i               iii  i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_82882101_8   3444 TTAAAGATTTAAATGTAAAACCCAAAACTATAAAACCCT-GTAAGACAAC 3492
                          i ?   ii         i v i             i  -iv    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_82882101_8   3493 CTAGGCA-ATATCCTTATGGTCGCGGGAATGAAAAAATA-TTCCATGACA 3540
                         v    ?i- v   i ii  ii vi   -- v iiv   i-  i v iivv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGAT 594

  chrX_82882101_8   3541 AAGATGCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCT 3590
                          v  ii         vvv          v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_82882101_8   3591 AATTAAA-CTGAAGACATTCTGCACAGCAAAGGAAAGTAGCAACAGAGTG 3639
                         v  i   -i i  i  -  i  ii vv       v v  v   v i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_82882101_8   3640 AACAGACAATCTACTACAGAATAGGAGAAAATTTTTGCAAACTATGCATC 3689
                           v      i i  ---     i         v        ii  ii   
  L1M4_orf2#LINE/    694 AAAAGACAACCCAC---AGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_82882101_8   3690 TGACAATGGTCTAAAAGCCAACATCTATAGGGAACGTAAACAAATTTACA 3739
                            i  v  v  viv v   iv  v    ii    vivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_82882101_8   3740 AGAAAAA-------AACCCA-TTAAAGAGTGGATAAAGAACATGAACAAA 3781
                          v     -------      -  ?  i i   ii    i iv    i i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_82882101_8   3782 CACTTTTCAAAAAAAAAAAAAAAGACATGCATGTGGCCTATA-GCATAT- 3829
                           i  i  v   i  --------  i  i  vi     v   -   i  -
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAA--------GATATACAAATGGCCAATAAGCACATG 882

  chrX_82882101_8   3830 -AAAGAAGCACAACATCACTAGTCAT 3854
                         -     v  v        ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (162 / 99)
Gap_init rate = 0.02 (22 / 905), avg. gap size = 1.82 (40 / 22)  


3366 26.43 0.44 0.44  chrX_82900514_82904983     3070  3977 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82900514_8   3070 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3119
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82900514_8   3120 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3169
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82900514_8   3170 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3217
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_82900514_8   3218 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 3267
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82900514_8   3268 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3317
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_82900514_8   3318 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGATC 3367
                                 i   i    ii         i  v ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_82900514_8   3368 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 3415
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_82900514_8   3416 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 3465
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_82900514_8   3466 CTATTTAATAAATGGTGCTGGGAAAATTGGCCAGCCATATGTAGAAAGCT 3515
                           v  i  i              v  i   vi ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_82900514_8   3516 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 3565
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_82900514_8   3566 TTAAAGACTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 3615
                          i ?    i    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_82900514_8   3616 CTAGGCATTACCATTCAGGACATAGGCTTGGGCAAGGACTTCATGTCTAA 3665
                         v    ?i v viv   iv   v v  v  i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_82900514_8   3666 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3715
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_82900514_8   3716 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3765
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_82900514_8   3766 AGGCAACCCACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 3815
                           i         i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_82900514_8   3816 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 3865
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_82900514_8   3866 AAACAAACGACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 3915
                          i     ii    v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_82900514_8   3916 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATT 3965
                           v        i  vi viii     v  i          i       vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_82900514_8   3966 ATCACTGGCCAT 3977
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2874 27.20 2.79 1.56  chrX_82951874_82953956.rev      702  1598 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82951874_8    702 TGGAGAAACTTTTCATATTCATGAATAAGAAGAATCAATATTGTTAAAAT 751
                             i i iv ii   i      i  vi     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82951874_8    752 GTCCGTACTGCCCAAAGCCATTTACAGATTCAATGCTATTCCTATGAAAG 801
                          v vi    v      viv  i           i  v  i     v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82951874_8    802 TACCAATTACATTCTTCATAGAA-TTAAAAAAAAACT-ATTTTAAAATTC 849
                          v   ii i v  i  iii    -  i v  i---  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_82951874_8    850 ATGTGGAAC--CAAAAAACAGCTCAAATAGCCAAGGGAATCCTAAACAAA 897
                           i     v--   iii  -- ivi         iiv    i i  v  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_82951874_8    898 AAGAACAAATCTGGAGGCATCATATTACCTGACTTCAAACTATCATGCAA 947
                                  vi      vv   i i v  ii i      viv vv i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_82951874_8    948 GGCTA-AGTAACCAAAACAGCATGGTACTGGTATAAAAACAGAAGCATAG 996
                         i    -     i   i    ii         i    ii i   vii    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_82951874_8    997 ACCAATG-AACAGAACTGAGAGTCCAGAAATAATCCTACACACCTACAAT 1045
                          i     -  i    i                 v  i i   ii  iii 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_82951874_8   1046 CATCTGATCTTTGTCAAAGTTGATGAGAACAAGCAATGGGAAAAGGACTC 1095
                           vi    i  i v   i v  vii   v  vv       i    i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_82951874_8   1096 CCTATTCAATAAATGGTTCTCAGATAACTGGCTAGCCACATGCAGAAGAT 1145
                         i  v     i       v  vi  i      v  ?         i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_82951874_8   1146 TGAAACTGAACTCCTTCCT-ACACCATATACAAAAATCAACTCAAGATGT 1194
                             ii  i  i   v   -                 i       i   v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_82951874_8   1195 ATTAAAGATTTACATGTAAAATGTAAAAGTACAAAATTTCTGAAAGATAA 1244
                           i ?   ii  v      i vv     v  i    i ii ii    v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_82951874_8   1245 CCTAG---CAAAT----GCAATTTTGAATATAGGAACTGTCAAAGATTTC 1287
                          v   ---i    ---- ii ii   ii -    ------   v i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGT-TAGG------CAATGGTTTC 588

  chrX_82951874_8   1288 ACCGATGAAGATATCAAAAGCAATTGCAACAAAAACAGAAATTGACAGAT 1337
                         viv   - v  i i        vvv         iv i    v  i i  
  L1M4_orf2#LINE/    589 TTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_82951874_8   1338 ATGACCT------AATTAAGGAGATTTTGCACAGCAAAAGACACTGTCAA 1381
                         vv   i ------      ii v-     ii vv    i      i    
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_82951874_8   1382 CAGAGTAAA----CAACCTACAGAACAGGAAAAAGTATTTGCAAACTATG 1427
                         v i   i  ----     i      ii   i   i          ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_82951874_8   1428 CATCCAACAAAAGTCCAACATCCAGAATCTATAAGGAACTTAAACAAATT 1477
                         i   ii i  ii v ivii         v     i     ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_82951874_8   1478 TACGAGCAAAA-ACAAACAGCCCCATTAAAAAGTGGGCAAAAGACTTGAG 1526
                         v ii vv    -     i i   v   ?    i        i  i    i
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_82951874_8   1527 CAGACATTTCTTTAAAGAAGACATACATGCAGCTGACAAAAATATGAATA 1576
                         i          ii        i     viii  ii i  iv i     v 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_82951874_8   1577 AATGCTCAATAGCACTAATCAT 1598
                         i        i v  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (163 / 78)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.29 (39 / 17)  


2669 28.65 1.11 0.66  chrX_82993194_82995336      747  1650 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82993194_8    747 TGGAAAAACATTACATACTCATGGATAAGAAGAATCAATATTGTTAAAAT 796
                               i i  iv   ii        vi     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82993194_8    797 TGCCATACTGCTCAAAGTGTTTTAATAGATTCAATGCTATTCCCATTAAA 846
                         v  v     v i    v  v i  -i        i  v  i  i  i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTA-CAGATTCAACGCAATCCCTATCAAA 99

  chrX_82993194_8    847 CCACCATTGACACTATTCACAGAACTAGAAGAAGCT-ATTTTAAAATTCA 895
                         viv   vivi vi v  ii     v v  v-     -  ii         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCA 148

  chrX_82993194_8    896 TATGAAACCAAAAAAGAGTCCGAATATCCTAAGCAATCCTAAGCAAAAAG 945
                             i  viiv  ii  vi v     v  v  i     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_82993194_8    946 TACCAAGCTGGAGGCATCACGGTACCTAACTTCAAACTATACTGCAGGGC 995
                         v  v   i      vv    iv v  i  i      viv    i  ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_82993194_8    996 TACAGTAACGAAAATAGCATGGTACTGGCACAAAAGCAGACACCTAGACC 1045
                                 iv  i i  ii           i  iiii     iv    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_82993194_8   1046 AATGGAACAAAACAGAGAACCCAGAAATAAAGCCACGCAGCTATAACTAT 1095
                                i i  iv    ii           v   ii  vi   iiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_82993194_8   1096 ATGATCTTTGACAAACCTGACAAAAGCAAACAATGGGGAATATATTCCCT 1145
                         v    i  i     ivv  v   i v  vv          viv  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_82993194_8   1146 ATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATACAGAAGA-TAG 1194
                         v     i              i      v  ?   i  i  i    - ii
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_82993194_8   1195 AACTGGAGACCTTCCTTACACCATATACAAAAATTAACTCAAGATAGATT 1244
                          ii    vv   v   i                         i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_82993194_8   1245 AAATACATAAATATGAAATCCAAATTTATGAAAACTCT-GGATGACAACC 1293
                          ? v  v     i i i v i   vi   -        -i  v  v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chrX_82993194_8   1294 GAGGCA-ATATCATTCTAGACATAGAAATAAGCAAAGATTTCAT-GATGA 1341
                         v   ?i- v   -   vv   v v iiv  i    v i    v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_82993194_8   1342 AGATGCCAAAAGCAATTACAAGAAAAGCAACAATTGACAAATGGAATATA 1391
                         v  ii         vvvi   v     v  v   v  i    v i iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_82993194_8   1392 AT-AAAACTAAAGAGCTTCTGCATAGCAAAGGAAACTGTCAACAGAGTGA 1440
                           -    i    i -   i  iiivv       v   i    v i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_82993194_8   1441 CCAAGCAACCTATAGAATCAGATAAAATTTTTGCAAACTATTCATCTGGC 1490
                         vv ii     i i     vi  v     v        ii  vi     ii
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_82993194_8   1491 AAAGGTCTCATATCCAGCATCTATAAGGAACATAAGCAAGTTTACAAGAA 1540
                           i  v  ii       v  v     i    vivvi   v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_82993194_8   1541 AAAAA--AATAACC--ATAAAAAAGTGGGCAAAGGACATAAACAGACACA 1586
                            i --       --  v?    i           iv i  i     iv
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_82993194_8   1587 TTTCAGAAGAAGACACACATGCAGCCAACAATCATATAAGAGAAAGCTCA 1636
                          i  vi       i i   viii     i  v  i  i i ii v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_82993194_8   1637 ACATCATCGATCAT 1650
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (147 / 108)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.14 (16 / 14)  


2071 24.55 1.82 10.10  chrX_82996252_83004756.rev     3982  4971 (3534)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82996252_8   3982 TAGAAAAACATTCTATGCTCATGAAT-AGATAAATTAATTTTGATAAAAT 4030
                          i    i i  i i   i     i  -i  vi v     v   v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82996252_8   4031 GGCCATATAGCCCAAACCAATTTACAGATCCAATGCTATTGCTATTAAAC 4080
                            v   ivv      iii  i       i   i  v  iv    i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82996252_8   4081 TATTAATGACATTATTTGCAGAATTAGAAAAGAAAAACT-ATTATAAAAT 4129
                          vii iivi v  v         v v  v   -----  -  iv      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAAT 145

  chrX_82996252_8   4130 GCATATGGTACCAAA-AAAAAAGACCACAAATAGGCAAGGCAATCCTAGG 4178
                         v       ----   -iv  ii    vvi     v   ii     i iii
  L1M4_orf2#LINE/    146 TCATATGG----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_82996252_8   4179 CAAAAAGAATTAA-TTAGAAGACATCATGCTATCTGACTTCAAACTATAC 4227
                         v  i     iv  -  i  i   -   ii  vi ii i      viv   
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTAC 240

  chrX_82996252_8   4228 TACAGGGCTGCCCTAACAACAACAAAAAACCAGCCTGGTATTGGTACAAA 4277
                             ii   ------   ii  iv  i --   iv     i   i i  i
  L1M4_orf2#LINE/    241 TACAAAGCT------ACAGTAATCAAGA--CAGTGTGGTACTGGCATAAG 282

  chrX_82996252_8   4278 AACAGATACATAGACCTATGGAACAGAAT-----GTCCAGAAATAAGGCC 4322
                         i i   i i     i v      i     -----            iv  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_82996252_8   4323 ACACACATACAACCATCTGAACTTCAATAAAGCTGACAAAAAAAAAATCA 4372
                          i   iv  iiii  vi   vi   i i  i v  v   i vv v--   
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT--TCA 380

  chrX_82996252_8   4373 GTGGGGAAAAGAC--TCTTTACTCAATAAATGGTTCTGAGATAACTGCCT 4420
                         i        ii i--     --    i       v   i  i     vv 
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_82996252_8   4421 AGCCATATGCAAAAGATTGAAACTGGACCCCTTTATTACACCATGAAATA 4470
                          ?   i          v    ii         viv i       ---   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT---ATA 475

  chrX_82996252_8   4471 CACAAATCAACTCACAATAAATTAAAGACTTACATGTACAACCCAAAGCT 4520
                           v    i      v   ii  i ?    i  v     vi v i   i  
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_82996252_8   4521 ATAAAAACACCAGAAGACAACCTAGGCAGTA--TCATTATGAACATAAGA 4568
                               vivii      v   v    ?-   --  v ii   v v ii -
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGN-GTAAATCTTCGTGACCTTGGG- 573

  chrX_82996252_8   4569 ACT-GGCAAAGATTTCAT-GATGAAGACACCAAAAGCAATTGCAACAAAA 4616
                         -i -     v i    v -   - v             vvv         
  L1M4_orf2#LINE/    574 -TTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_82996252_8   4617 GAAAAAATGACAGATGTGATCTAATTAAACTTAAGAGCTTCTATACAGCA 4666
                                 ---    i------    ii    -------------  v  
  L1M4_orf2#LINE/    622 GAAAAAAT---AGATA------AATTGGACTT-------------CATCA 649

  chrX_82996252_8   4667 AAAGAAACTATTAACAGAGTGATGTGATCTAATTAAACTTAAGAGCTTCT 4716
                            -------    --------------------      vv v     -
  L1M4_orf2#LINE/    650 AAA-------TTAA--------------------AAACTTTTGTGCTTC- 671

  chrX_82996252_8   4717 ACATAGCAAAAGAAACTATTAACAGAGTAAACAGACA-CCTACACAATGG 4765
                         -------   i  v     i  v i   i  v     -  i   v     
  L1M4_orf2#LINE/    672 -------AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_82996252_8   4766 GAGAATCTATTTGCAAACTGTGCATCTGATAAAAGACTGTTATCCAGCAT 4815
                              vv          iii ii         ii    vv       v  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_82996252_8   4816 CTATAGGGAACTTAAATTTACAAAAAAAAAAAAAAAAAAAAAAAAAAGAC 4865
                         v    ii     i----      vvv  v  v     ----------   
  L1M4_orf2#LINE/    765 ATATAAAGAACTC----TTACAACTCAATAATAAAAA----------GAC 800

  chrX_82996252_8   4866 AAGCTACCCCATTAAAAGGTGAAGAAAAAACATGAACAGTAAATTTTCAA 4915
                           iiv    v   ?   ii  iiv   ii iv    i  vv v  i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_82996252_8   4916 AGGAAGACATGCTTGTGGCCAGCAAGCATATAAAAAA--GATCAATATTA 4963
                          i     i  i vvi      ii     i  i    i-- v    i  i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_82996252_8   4964 CTAATCAT 4971
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 3.93 (118 / 30)  

2244 29.12 2.91 1.23  chrX_82996252_83004756.rev     7122  8014 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_82996252_8   7122 TGGAAA-ACATTCAATGCTCATGGATAGGAGGAATCAACATTGTTAAAAT 7170
                               - i  i v   i        v   i  v i  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_82996252_8   7171 GCCTATATTTCCCAAAGCAACTTACAGATTCAATAGTATTATTAGTAAAC 7220
                          v v   i i      vii ii           iivv  ivi  vi   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_82996252_8   7221 TGCCAAGGTAA-TTATTTACAGAATGGGGAAAAATTATTCTACAATTCAT 7269
                          v   - v iv-  v   i     vvv iv  iv v  i   v       
  L1M4_orf2#LINE/    101 TCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_82996252_8   7270 ATG--AATTCAAAAAAGAGCCCA-AATAGCCAAAGAAATCCCAAGCAAAA 7316
                            --   v   iii ---    -          iv    iii iv  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_82996252_8   7317 AGAACAAAGGCAGAGGCTTTACACTGCCTGACTTCAAA--CAAGTAGAAG 7364
                                  vii    vi i     v  ii i      --iv v  v  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_82996252_8   7365 GCTGCAGTAACCAA-ACAGCATGGTACTGGTACAAAAACAGACACATAGG 7413
                            i      i   -    ii         i i  ii i     i    i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_82996252_8   7414 CCAATCGATCAGAATAGAGAGCATGTAAACAAAGCTGCACACCTACAACC 7463
                         i    v  vi     v     iviiv   i   v iii   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_82996252_8   7464 ATGTGATCTGTTAGTAAGC-TGACAAAAAGAAGCAATAAGGAAGGAA-AC 7511
                          vv    i - iiii   v-  v   i vv vv    ii    i   - v
  L1M4_orf2#LINE/    347 AATTGATTT-TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_82996252_8   7512 CCTATTCAGTCAATGGTGCTGAAATAACTAGCTAGCCATAAGCAGAAGAT 7561
                         i  v    iiv          ii i    i v  ?   i v   i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_82996252_8   7562 CGAAACTGAATCCCTTCCTTTCACTATAAAGAAAAA--AACTCAAAATTG 7609
                         i   ii  i i    v   iv   i   v v     --          v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_82996252_8   7610 ATGAAAGACCTAAATGTAAGATCTAAAATTTTGAAAACCCTACAAGAAAA 7659
                           v ?                v      i v i   vi i  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_82996252_8   7660 CCTAGGAA-ATATCATTGTGAACATAGGCCTTGGTAAAGATTCCAT-GAT 7707
                          v    ?i- v   v i    v v i  i- v  i  v i  i v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_82996252_8   7708 CAATT-CACCAAAAGCAATTCCAACAGAAAGGAACATTTACAAGAGGGAT 7756
                         --  v-           vvvv     i  iii  v  vv i  ivv   i
  L1M4_orf2#LINE/    595 --ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_82996252_8   7757 CTAATTAAACCAAAGAAGTTCTGCACAAAAGAAGAAATTATTAGCAAAGT 7806
                         i v  i   viv  i  v  i  ii vvv i i  v i   i iv     
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_82996252_8   7807 ACACAGACAACCTTCAGAATAAAATAAAATATTTGCAAACCATGCATCTT 7856
                         iv v        iv      iii v              i   ii    v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_82996252_8   7857 ACAAAGC-CTAATGTCCAGAATTTACAAGGAACTTTAACAAAACTTCAA- 7904
                          i  i v-  vi i        v  i  i     i v    ---i    -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA---CTCAAT 789

  chrX_82996252_8   7905 -GCAAAAA-ACAACTG---CA--TTAAAAATGAGCAAAGGATATGAACAG 7947
                         -ii     -    v i---  -- ?       i         v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_82996252_8   7948 ATAATTCTCAAAGGAAGACTTACACA--GTCAACAAGTATATGAAAAAAT 7995
                          i v     v  i     iv    v -- i   i   i i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_82996252_8   7996 GTACAACATCACTAATCGT 8014
                          iv        ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (152 / 104)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.54 (37 / 24)  


2409 28.85 1.15 1.49  chrX_83010305_83013827     2161  3030 (493)    L1M4_orf2#LINE/L1       42   908 (0)  

  chrX_83010305_8   2161 TGTGAAAATTACCATACTGCCAAAAGCAATTTACAAACTCGATGCAATTC 2210
                            v  i  vi v     v  v   vii  i    i i  i i     i 
  L1M4_orf2#LINE/     42 TGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chrX_83010305_8   2211 C-ACCAAAATACCAGCATCATTCTTCACAGAACTAGAAAAAA-AATTCTA 2258
                          - i      v     vv v  i  ii     v v  v  iv-i  i   
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_83010305_8   2259 AAATTAATATGGAACCAAAAAAGAGCTCACATAGCCAAAACAAGACTAAA 2308
                              v        viiv  ii  v iviv             vvi i  
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_83010305_8   2309 CAAAAAGAACAAATCTGGAAGCATTACATTACCTGACTT-AAAACTATAT 2357
                         v  i         vi    i vv i   i v  ii i  -      -  i
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TAC 240

  chrX_83010305_8   2358 TATAGGGCCACAGTCACAAAAACATCATGGTACTGGTATAAAAATAGGCA 2407
                           i ii  i     v iv  i   vii         i    ii    i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_83010305_8   2408 CATAGACCAATGGAACACAATAGAGAACACAGTAGTAAACCCAAATACTT 2457
                         i     i        i v   v    iiv   v i        v i i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_83010305_8   2458 ACAGCTGACTGATCTTCAGCAAAGCAAACAAAAACATAAAGTGGAGAAAG 2507
                          ii iii i    i   ii   i vviv   i v   vv i   i     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_83010305_8   2508 GACACTCTATTCAACAAATGGTGCTGAGATAATTGGCAAACCACATGTAC 2557
                         i i v   v                 i  i  i   vv ?       i v
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_83010305_8   2558 G-GAATAAAACTGGATCATTATCTCTCACCTTATGCAAAAATCAACTCAA 2606
                         i-    i  ii    i vi  i   v    v   i       i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_83010305_8   2607 GATTAATCAAGGACTTAAATCTAATA-CTGGAACTATAAAAATTCCAGAA 2655
                         i  vi    ?i   i     v   v -  ii          -i  i----
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCT---- 535

  chrX_83010305_8   2656 GACTAGAAGATAACATTGTAAAAAGCCTTCTAGACATTGGCTTAGGCCAA 2705
                         ---       v     v v?iv  ii    vv   v    v      v v
  L1M4_orf2#LINE/    536 ---TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_83010305_8   2706 GACTTTAT-GATCAAGAACCCAAAAGCAAATGCAACAAAACCAAAGATGA 2754
                          ii  iv -   - v  vv         v v         vv   i  ii
  L1M4_orf2#LINE/    583 GGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_83010305_8   2755 ATATGTGGAACTTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGCAGAA 2804
                            vi v i    v  i   v v  i i   i  ii vv    i --- v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG---AC 678

  chrX_83010305_8   2805 ACAGTCAGCAGAGTAAATTGACAAAACAAAGAGTGGAAGAAAATCTTTAC 2854
                           vi   iv i   i  vv     vv  v   i   i       v   i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_83010305_8   2855 AATCTATCCATTTGACAAATGACTAATATTTAGAATCTACGAAAAATTCA 2904
                           vii  vi  i   i  iv    vi   ii     v  ii  i  i  v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_83010305_8   2905 AACAAATTAGCAGAAAAAAAACAA----TTCTATCAAAAAGTGGGCTAAG 2950
                         v    v i ii iv     i    ----ii v  i?    i     v   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_83010305_8   2951 GACATGAATAAACAATTCACTACAGAAGATATACAAATGGCCATCAAACA 3000
                           iv      i   v   v i v                    vi  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_83010305_8   3001 TATGAAAAGGTGCTCAACATCACTAATGAT 3030
                         i        i            ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (145 / 102)
Gap_init rate = 0.01 (12 / 867), avg. gap size = 1.92 (23 / 12)  


2873 27.31 1.10 1.10  chrX_83016331_83022414     2966  3873 (2211)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83016331_8   2966 TGGAAAAACATTCCATGCTCATGGATAGCAAGAATCAATATTATGAAAAT 3015
                               i i  i     i        v v    v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83016331_8   3016 GGCCATATTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 3065
                            v   i v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83016331_8   3066 TACCA-TTGACTTTATTCACAGAACTAGAGAAAACTACTTC-ACATTTCA 3113
                          v   -i  v    -  ii     v v  v  i-  iv i - v v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_83016331_8   3114 TATGGAACCAAAAAGGAGCT-GTATAGCCAAGACAATCTGAAGCAAAAAG 3162
                                viiv  i   v i- v        i       vi iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_83016331_8   3163 GACAAAGCTGGAGGCATCACACTACCTGACTTCAAATTATACTACAAGGC 3212
                         i      i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_83016331_8   3213 AATAGTAACAAAAGTAGCATGTTACTGGTACAAA-ACAGATATATAGACC 3261
                         v i     iv  iii  ii  v      i i  i- i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_83016331_8   3262 AATGGAACAGAATAGAG-GCCACAGAAATAACACCACACATCCACAACCA 3310
                                i     v   - i -         vv   i    ii iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chrX_83016331_8   3311 TCTGATATTTGAGAAACATGACAAAAACAAGCAACAGGGACAGGAT--TC 3358
                         vi    v  i  v  ivi  v   i v  vv   ii    v  i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_83016331_8   3359 CCTAATTAGTAAATGGTGCCTTGAAAACTGGCTAGCCATATGCAGAAAAC 3408
                         ii -- i ii         ivv  v      v  ?   i     i  i v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_83016331_8   3409 TGAATCTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGG 3458
                             vi         v   i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_83016331_8   3459 ATTAAAGACCTAAACATAAAACCAAAAACCATAAAAACGCTAATAGAAAA 3508
                           i ?         ii   i v v     i      vivi  iv      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_83016331_8   3509 CCTAGGCA-ATACCATTCAAGACATAGGCATGGGCAATGACTTTATAACT 3557
                          v    ?i- v i -   iv   v v  vv i       ii  iv  iv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_83016331_8   3558 AAAACACCGAAAGCAATTGCAACAGAAGCCAAAATTGACAAATGGGATCT 3607
                          vi     i      vvv      i   vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_83016331_8   3608 AATCAAACTGAAGAGTTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 3657
                         v      v v  i ii  i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_83016331_8   3658 ACAGGCAACCTACAGAATGGAAGAAAATTTTCACAATCTGTCCAGCTGAC 3707
                          v  i     i         i       v  ii   viii vi v    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_83016331_8   3708 AAAGGTCTAATATCCACAATCTACAAGGAACT--TAACCAAATTTACAAG 3755
                           i  v  vi      v   v  i  i     --  --   v iv i  v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAAT 792

  chrX_83016331_8   3756 AAAATAAAACAAGCAACCCTGTCAAAAAGTTGGCGAAGGATATGAACAGA 3805
                             -- i    ii     vi i?    i v   i      v    i   
  L1M4_orf2#LINE/    793 AAAA--AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_83016331_8   3806 CACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAG 3855
                           i     v        i  vi viii     i  i  i       i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_83016331_8   3856 TTCATCATCACTGGTCAT 3873
                         i   v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.33 (20 / 15)  

2718 26.22 2.21 1.77  chrX_83016331_83022414     4688  5591 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83016331_8   4688 TGGAAACACATCCCATGCTCATAGATGGGTAGAATCAATATTCTGAAAAT 4737
                               v i        i    i   v  v   v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83016331_8   4738 GTCCGCACTCCCAAAATCAATCTACAAATTCAATGCAATTTCCATCAAAG 4787
                          v vii      v    ii       i      i     ii i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83016331_8   4788 CACTATCATCATTCTTCACAGCACTAGAAAAAAAAATTCTAAAATTCAAA 4837
                         iv i v vv v  i  ii   v v v  v  ivvi  i          v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_83016331_8   4838 TGGAACAAATA-AAGAGCCTCC--ATATTTAAAGCAATTCTAAGCTAAAA 4884
                              ---  i-   i v i v--   vii   i    ii i iv-  i 
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGA 196

  chrX_83016331_8   4885 AAAACAAATCTACAGGTATCACATAACTCAACTTCAAACTGTACTGCAAG 4934
                          i      vi iv   vv     ivv i   i      viv    i   i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_83016331_8   4935 GCTATAGTTACCAAGAGAGCATGGTACTAGTATAGAAATAAGCATATAAG 4984
                             i   v i     v  ii       i i   iii   ii      ii
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_83016331_8   4985 CCAATGGAACAGAATAGAGAAGAGAAACAAAAAATAAAACCAAATACTTA 5034
                         i        i     v    iv----- v i       v   v i i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGT-----CCAGAAATAAACCCATACATTTA 341

  chrX_83016331_8   5035 CAGCCAACTGACCTTCGACAAAGCAAACAAAAACATAAAGTGGAGAAAGG 5084
                         ii i   i   ii        i vviv   i v   vv i   i     i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_83016331_8   5085 ACATCCTATACAATAAATGGTGCTGGGAAAATTGGCAAGCCAAATGTAGA 5134
                          i vi  v v   i              v  i   vv ?   v   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_83016331_8   5135 AGAATGAAGCTGGATACTGATCTCTCACCTTATACAAAAATCAACTCAAG 5184
                                  i    iv iv i   v    v           i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_83016331_8   5185 ATGGATCAAATAATTAAATCTAAGACATAAAACCATAAAAATTCTATAAG 5234
                                 ? v vi     v     vv      i      v ii  v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_83016331_8   5235 TTAACATTGAAAAAAACTCTTCTAGACATCGGCTTAGGCAAAGAGTT--- 5281
                         vv     v i?iv   -     vv   v i  v        v iv  ---
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_83016331_8   5282 ---TATGACAAAAACCCCAAAGCAAATGCAACAAAA-ACAAAACAGATG- 5326
                         ---       -----  v      v v         - v    i    i-
  L1M4_orf2#LINE/    591 AGATATGACA-----CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_83016331_8   5327 ---GGACCTAATTAAACTAAAAAGCTTCAGCACAGCAAAATAAATAATCA 5373
                         ---    i v  i   v v    i   iv ii vv    iv v iv    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_83016331_8   5374 GCAGAGTAAACAGACAACCCACAGAGTGGGGAAAAATCTTTGCAAACTAT 5423
                         iv i   i  v              i    ii     v        ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_83016331_8   5424 GAATTCTACAAAGGACTAATAATACAGAATCTATGCAGAACTCAAGCAAA 5473
                         iv  iiv i  i     vi  - v      v   iv       vvi   v
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTA-TCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_83016331_8   5474 TCAGCAAGAAAAA---AAAT--CCCA-TCAAAAAGTGGGCAAAGGACATG 5517
                            ii  v     ---    --    - i?    i           iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_83016331_8   5518 AATAGACATTTCTCCAAAGCAGATATACAAATGGCCGACAAACATATGAA 5567
                                            v                i i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_83016331_8   5568 TAAATGCTCAACATCACTAATTAT 5591
                         v i             ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (130 / 103)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.57 (36 / 14)  


2422 29.42 1.66 1.55  chrX_83030132_83034875     3348  4251 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_83030132_8   3348 AAAAAAATCT-ATGCTCTTAGATAGAAAGAATCAATATTGTGAAAATGGC 3396
                            i v   i-   i  v i   v i    v i        v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_83030132_8   3397 CATAGTGCCCAAAGTAATTTATAGATTCAATGCTTTCTCCATTAAACCAC 3446
                         v   v v      v i  i  i        i  vv  i i  i   viv 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_83030132_8   3447 CATTGACATTCTTCACAGAATTAGAAAAAATTATTCTAATATTCATATGT 3496
                           vivi v  i  ii     v v  v  iv v  i    v         v
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_83030132_8   3497 AAC--CAAAAATATGCCCA-AATAGCCAAGACAATCTTAAGCAAAAAGAA 3543
                           v--   iii---i    -         i        i iv  i     
  L1M4_orf2#LINE/    154 AAATGCAAGGG---ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_83030132_8   3544 CAAAGCTGGAAACATCATGCTACCAGACTTCAAACTATACTACAAGTCTA 3593
                              i    iivv   ii  v  vi i      viv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_83030132_8   3594 CA-TAACCAAAATAGCATAGGACAGGTACAAAAACAGACACATAGACCAA 3642
                           -   i   i i  ii i v  v  i i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_83030132_8   3643 TGGAACAAAATAGGGAACTCAGAAATAAGACCACACACCTACAATTATAT 3692
                              i i   v i  iii         iv   i   ii  iii i vv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_83030132_8   3693 GATCTTTGACAAACCCAACAGAAACAATGAATGAGGAAAGTATTTTCTAT 3742
                            i  i     ivviiv  ii v  v v    i      v  vv   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_83030132_8   3743 TTAATAAATTGTGCTGGAAAAACTGGTTAGCCATATGCAGAAAATTGAAA 3792
                          i  i    v       i v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_83030132_8   3793 CTGGACTCCTTTCTTACACCGTATACAATAATTAACTTAAGATGGAGTAA 3842
                         i     i   vi  i     i       v        i  i     vi ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_83030132_8   3843 AGACTTAAATGTATAATGCCAAATTTAAAAAAAACCCTAGAAGAAAATCT 3892
                             i        vi -  i   vi  v    v-i i          iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA-GCTAAAACTATAAAAC-TCTTAGAAGAAAACAT 548

  chrX_83030132_8   3893 AGGCAATATTTTTCAGGACATAGGCATGGGCAAAGATTTCATAATGAAAA 3942
                            ?ivv v i   iv   v v  vv i     v i    v  ivv vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_83030132_8   3943 TGCCAAATGCAATTACAACAAAAGCTGAAATTGACAAATGGGATCTAATT 3992
                         ii     v   vvvi         vvi    v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_83030132_8   3993 GAACTAATGAGCTGCTTCATGGCAAAACAAACAAAAAAC-CTATCATCAG 4041
                         i  v v vi i  --  ii  viv-------    ii  -      vv i
  L1M4_orf2#LINE/    649 AAAATTAAAAACT--TTTGTGCTT-------CAAAGGACACTATCAAGAA 689

  chrX_83030132_8   4042 AGTGAACAGGCAACCTACATAATGGGAGAAAATTGTAGCAATCTATTTGT 4091
                               v  i     i   v             vv v    vii  v i 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_83030132_8   4092 CTGACAAAGGTCTAATATCCAGAGTCTACAAGGAACT--TAATATACAA- 4138
                             i  i  v  vi        i v  i  i     --  vv iv   -
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_83030132_8   4139 AACAAAAC--CAAAT----CTATTAAAAAGTGGGCAAGGGACATGAACGA 4182
                           i    v--     ---- v   ?    i       i   iv    iii
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_83030132_8   4183 ACACTTCTCAAAAAAAGACATTGATGTTGTTAACAAACATATAAAAAAAA 4232
                            i     v   i    i  vv vi v ii  i  i  i  i    i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_83030132_8   4233 GCTCAATATCACTGATCAT 4251
                               i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (151 / 111)
Gap_init rate = 0.02 (14 / 905), avg. gap size = 2.07 (29 / 14)  


3140 26.93 0.99 0.77  chrX_83046693_83051600     3510  4415 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83046693_8   3510 TGGAAAAATATTCCATGTTCATGGATAGGAAGAATCAATATTGTAAAAAT 3559
                               i    i              v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83046693_8   3560 GGCAATACTGCCCAAAGTAATTTATAGATTCAATGTTATTCCCATCAAGC 3609
                                  v      v i  i  i        i iv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83046693_8   3610 TACCAGTGACTTTCTTTGCAGAATTAGAAAAATCTACTTTACATTTCATA 3659
                          v    ivi i  i         v v  v  iiiv iii  v v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_83046693_8   3660 TGGAACCAAAAAGAGCCCATA-TAGCCAAGACAGTCCCAAGCAAAGAGAA 3708
                              viiv  i ii    v -       i   i  iii iv  ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_83046693_8   3709 CAAAGCTGGAGACCTCATGCTACTTGACTTCAAACTATGCTACAAGCCTA 3758
                              i     iv    ii  v iii i      viv i      iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_83046693_8   3759 CAGTAACAAAAACAGCATAGTACTGGTACCAAAACAGATATACAGACTAA 3808
                               iv  i    ii i       i iv ii i   i   i   ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_83046693_8   3809 TGGAACAGAACAGAG-GTCTCAGAAATAACACCACACATCTACAACCATC 3857
                              i    iv   -   -         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_83046693_8   3858 TGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGGAAG--TAGCCCC 3905
                             i  i     ivv  v   i v  vv        i   --   i --
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-- 397

  chrX_83046693_8   3906 TATTTAATAAATGGTGTTGGGAAAATTGGCTAGCCATATGCAGAAAACCG 3955
                          v  i  i        i     v  i   v  ?   i     i  i vi 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_83046693_8   3956 GAACTGGACAACTTCCTTACACTTTATACAAAAATTAACTCAAGATGAAT 4005
                         i ii     vv  v   i    iv                   i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_83046693_8   4006 TAAAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAA-A 4054
                         i ?    i    i      v       i      vi i          - 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_83046693_8   4055 T-GAGGCAATACCATTCAGGACATAGGCATGAGCAAAGATGTCATGACTA 4103
                          - i? i  - i -   iv   v v  vv ii    v i v  v iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_83046693_8   4104 AAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAGTGGGATCTA 4153
                         vi            vvii         vv     v  i  i v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_83046693_8   4154 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAAAGTGAA 4203
                           i   v v  i i   i  ii vv    i  v       vv        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_83046693_8   4204 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 4253
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_83046693_8   4254 AACGGCTAATATCCAGAATCTACAA-GAAC-CTTAAACAAATTTACAAGA 4301
                          iv i  vi          v  i  -    -    --   v iv i  v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATA 793

  chrX_83046693_8   4302 AAAA-ACAAACAACTCCATGAAAAAGTGGATGAAGGATATGAACAGACAC 4350
                             -     i   i v  v?    i   iii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_83046693_8   4351 TTCTCAAAGGAAGGCATTTATGTGGCCAACAAATGTATGAAAAATAGCTC 4400
                              v  i    ii  vi vi       i  iiii       ivv    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_83046693_8   4401 ATCATCACTGGTGAT 4415
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (151 / 89)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.23 (16 / 13)  


1859 24.21 2.43 10.44  chrX_83098462_83100463.rev      525  1511 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83098462_8    525 TGAAAAAACATTAAATGCTCATGGATTGGAAGAATCAATACTTCTGAAAT 574
                           i   i i  ivv   i               v i    i vi i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83098462_8    575 ATCCATACTGCCCAAAGTATTCTACAGATTCAATGCAATTCCTATCAAAC 624
                         iv v     v      v iv             i     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83098462_8    625 TACCATGTGATTTTTCT-CA-AAATT-ATAAAATGATTCTAAAATTTATA 671
                          v   vv  vi    i -  -     - i  iv    i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_83098462_8    672 TGGAACCAAAAAAGAGCCTGAAGAGCCAAAGAAAATCCTAAGCCAAAAGA 721
                              viiv  ii  v  v   v       - v    i i ivv i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGA 199

  chrX_83098462_8    722 ACAAAGCTGGAGGCATCACATTAGCTGAATTCAAATTATAGTACAAGGCT 771
                               i      vv     i vv ii v      viv  v     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_83098462_8    772 ACA-TAATCACTAAAACATTATGGTACTGGTATAAAAGTGGACACATAGA 820
                            -      --- i   v i         i    iii i    i     
  L1M4_orf2#LINE/    250 ACAGTAATCA---AGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_83098462_8    821 CCCATGGAACAGAATAGAGAACCCAGAAATAAAGCTACATGCTTACAACC 870
                         i v      i     v    ii           v i i iii   iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_83098462_8    871 AACTGACATTTGATGAAGTAAAGAAAAATATACACTGGGGAAATGATATC 920
                           i   iv  i  ii i vvivv  i vi  v  v        vi   vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_83098462_8    921 CTATTCAGTTAATGGTGATGGAAAAATT--------------AAAATAAT 956
                           v    iiv       v   i v  i --------------    v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_83098462_8    957 AAAACTGGACCCCTATCGCTCACCATATA-AAAAACTAACTAAACATTTA 1005
                         i  ii          i v v         -     i     v  v  vv 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_83098462_8   1006 TTAAATACTTAAATGTATGACCTGAAACTATAAATATACTAGAAGAAAAT 1055
                          i ? v  i        v  v  i          vv vi          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_83098462_8   1056 CTTGGAAAAACTCTTCTGAACATTGGCCTATGCAAATAATTTATGACCAA 1105
                         v v  ?iv  v     vvi  v    vi  v    - ii   v v ----
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA---- 591

  chrX_83098462_8   1106 AAGGGAAATTTATGTCCTCAAAAGGAAATGCAATGAAACCAAAAAATAGA 1155
                         ----  ----    v vi      v v v    ii   v-          
  L1M4_orf2#LINE/    592 ----GA----TATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGA 632

  chrX_83098462_8   1156 CTAATAATGGGACTTAATTAAACT--AAAACTTTCTGCACAGAAAAAGAA 1203
                         -   --  v      v  i   v --        -  ii vvv   i  -
  L1M4_orf2#LINE/    633 -TAA--ATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGA- 677

  chrX_83098462_8   1204 GTAAGCAAATAATTTATGACTAAGTCCTTAAAATGAAATGCAACAAAACA 1253
                         -----  ------i   ---i   -----   i     ------------
  L1M4_orf2#LINE/    678 -----CA------CTAT---CAAG-----AAAGTGAAA------------ 696

  chrX_83098462_8   1254 AAAAATAGACAAATAAGACTTAAACTACAAATCTTCTACACTGCACAAGA 1303
                         ------      ------ ----- i   i ------------- iii  
  L1M4_orf2#LINE/    697 ------AGACAA------C-----CCACAGA-------------ATGGGA 716

  chrX_83098462_8   1304 AATAATATCTTACACAATGAAAAAAATTGCAAACAATTCATC-AACGAAG 1352
                         i v     ------------------       iv  vi   -i ii i 
  L1M4_orf2#LINE/    717 GAAAATAT------------------TTGCAAATCATATATCTGATAAGG 748

  chrX_83098462_8   1353 GGCTAATCTCCAGAATCAACAAGGAACAAAAACAAAGCAACAAGCAAATG 1402
                          i  vi v        vv i  i    vvvv    vv   i  vv   v 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_83098462_8   1403 AGCAAATATTTTA-TTACAAAGTGGGCCAAAGACACAAACAGACATTTTT 1451
                          -      viii -  ?v   i     v  i  ivii  i        i 
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_83098462_8   1452 CAAAAGAACAAATACAACTGGCCAACAAACATATAAAAA-ATGCTCAGCA 1500
                          v      v v      v       i  i  i  i    -       i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_83098462_8   1501 TCACTAATCAT 1511
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.17 (127 / 109)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 4.38 (127 / 29)  


 247 26.98 0.00 0.00  chrX_83109724_83111414.rev        1    63 (1628)    L1M4_orf2#LINE/L1      383   445 (463)  

  chrX_83109724_8      1 GGGGGCATGATAGCCTTTTCAACAAATGGAGCCAGAACAACTAGACACGT 50
                             iv vi    i               v  ii i      i  i ?vi
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_83109724_8     51 ATAGGCAAAACAA 63
                          i v      v  
  L1M4_orf2#LINE/    433 ACATGCAAAAGAA 445

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.00 (0 / 0)  

 603 27.62 4.60 5.37  chrX_83109724_83111414.rev      109   499 (1192)    L1M4_orf2#LINE/L1      439   826 (82)  

  chrX_83109724_8    109 AAAAAAATAAAAA-GAACCTCCACCTACATCTCACACATTATACAAAA-T 156
                             i   i  iv- i   ----     --       vv         - 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACC----CCTAC--CTCACACCATATACAAAAAT 482

  chrX_83109724_8    157 TAAATCAAAATTCATAGTAGATTTAAATA-AAAATATACAAATATAAAAC 205
                            v       vv  vi?   ii     i-  i vv  v  v        
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_83109724_8    206 TTTTTGAAACAAA--TAGA---AAATTTTTAGAATCTAAGACTAAGTAAA 250
                          i  v   iv   --   i---    i  iivi i  vi ii  i i  v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_83109724_8    251 GGTTTCTTAGTCTTTTCACCAAAAGCATTGTCCTTAGGAGAAATAAATAT 300
                                   viv vv           iviv vvi ii     -     v
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAG 631

  chrX_83109724_8    301 ACATAAATTGAACTTCATCAAAATAAAAAATAAAACTTTAGT-CTACAAA 349
                          --       i             v     -----    v  -  v    
  L1M4_orf2#LINE/    632 A--TAAATTGGACTTCATCAAAATTAAAAA-----CTTTTGTGCTTCAAA 674

  chrX_83109724_8    350 AGACCCTGATAATAGGATGAAATGACAAGCTATATTTTGGGAACTAATAT 399
                         i   v  ivi  v iii     v     v i i vvv     ivv     
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_83109724_8    400 TTTGCAAACCTCATGTTTCACAAAAGGTCTATTAAGTAGAATATGTTTTC 449
                           -     i vi  i i v i  ii iii i - vvi       i ----
  L1M4_orf2#LINE/    725 TT-GCAAATCATATATCTGATAAGGGACTTGT-ATCCAGAATATAT---- 768

  chrX_83109724_8    450 TAAAAATCTCTAAAAACTTAACCA---------AAACAATCTAATAAAAG 490
                         -   i v    v v    i  iv ---------   i  i i   v?  i
  L1M4_orf2#LINE/    769 -AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_83109724_8    491 GATGGGCAA 499
                         i        
  L1M4_orf2#LINE/    818 AATGGGCAA 826

Transitions / transversions = 1.26 (59 / 47)
Gap_init rate = 0.04 (15 / 388), avg. gap size = 2.60 (39 / 15)  

2384 26.56 0.44 0.44  chrX_83109724_83111414.rev      503  1191 (500)    L1M4_orf2#LINE/L1      172   860 (48)  

  chrX_83109724_8    503 ATTGCCAAGTCAATCCTAAGTCAACAGAACAAAGCTAGAGGCATCACACT 552
                           v     iv     i i ivv iv         i i    vv       
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_83109724_8    553 ACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGAATGGA 602
                         v  ii i      viv        i          i   i    vi   v
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_83109724_8    603 ACTAGTAACAAAACCGAGATATAGACCAATAGAACAGAAC--AGAGCCCT 650
                            i i vv ii iv  v       i    i   i    i--    i  -
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC- 320

  chrX_83109724_8    651 CAGAAATAATACCACACATCTACAACCATCTGATCTTTGACAAACCTGAC 700
                         -        vv   i    i  iiii  vi    i  i     ivv  v 
  L1M4_orf2#LINE/    321 -AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_83109724_8    701 AAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGA 750
                           i v  vvv           i  vvi  v  i  i              
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_83109724_8    751 AAACTGGCTAGCCATATGTAGAAAGCTGAAGCTGGATCCCTTCCTTACAC 800
                         v      v  ?   i   i i  iiv     i    i    v   i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_83109724_8    801 CTTATAAAAAAATTAATTCAAGATGAATTAAAGACTTAAATGTTAGACCT 850
                          v    v         i    i   i  i ?    i       v   v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_83109724_8    851 AAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACA 899
                              i      vi i           v    ?i- v i -   iv   v
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACC 568

  chrX_83109724_8    900 TAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACA 949
                          v  vv i     v ii   v ivv  vi            vvi      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_83109724_8    950 AAAGCCAAAATAGACAAATGGGATCTAACTAAACTAAAGAGCTTCTGCAC 999
                             vv        i    v   ii v ii   v v  i i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_83109724_8   1000 AGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGA 1049
                         vv    i  v    i  vv i      v  i     i             
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_83109724_8   1050 AAATTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTAC 1099
                             v       vii ivi      i  i  i  vi          v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_83109724_8   1100 AATGAACTCAAACAAATTTACAAGAAAAAAACAAACAAACCCATCAAAAA 1149
                           v      vv    v iv i  v     i     i  v  v  i?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_83109724_8   1150 GTGGGCGAAGGATATAAACAGACACTTCTCAAAAGAAGACAT 1191
                         i     i      v i  i     i     v        i  
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.27 (100 / 79)
Gap_init rate = 0.01 (4 / 689), avg. gap size = 1.50 (6 / 4)  


2558 27.63 2.80 1.23  chrX_83144626_83147693.rev     1684  2577 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83144626_8   1684 TGGAAAAACGTCCCATGCTCATTGTTAGGAAGAATCGATATCATGAAAGT 1733
                               i ii       i    v v v      v ii    ii v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83144626_8   1734 GGCCATACTGACCAAAGCAATTTATAGATTAAAGGGTATTCCCACTAAAC 1783
                            v     vv     vii  i  i     v  v vv  i  i ii   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83144626_8   1784 TACCATTGACATTCTTCACAGAATTAGAAGAAACT-ATTTTAAAATTTAT 1832
                          v   vivi v  i  ii     v v  v-  i  -  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_83144626_8   1833 ATAGAACCAAAAAATAGCCCAAATATCTAAGACAATCCTAAGCAAAAAGT 1882
                           i   viiv  iiv v  vi    v i  i      i i iv  i   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_83144626_8   1883 ACAAAGCTGGAGGCATCACACTACTTGACTTCAAACTATACTACAAGGCT 1932
                               i      vv       v iii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_83144626_8   1933 ACAGTAACCAAAACAGCTTGATACTTGTACGAAAACAGACACATAGACCA 1982
                                i   i    iv  i    v i ii ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_83144626_8   1983 ATGGAACAGAATAGAAACTC-AGAAATAAGACTACACATCTACAACCATC 2031
                               i     v  i v  -        iv i i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_83144626_8   2032 TGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT--TCCT 2079
                             i  i     ivv  vv  i v  vv            i  --  i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_83144626_8   2080 TATTTAATAAAGGGTGCTGGGG-AACTGGCTAGCCATATGCAGAAAATTG 2128
                          -- i  i   v         i-      v  ?   i     i  i v  
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_83144626_8   2129 AAACTGGACCCCTTCCATACACCTTATACAAAAATTAACTCTAGATGGAT 2178
                           ii         v  vi     v                 v i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_83144626_8   2179 TAAAGACTTAAATGTTAAACCCAAAACTATAAACACCCT-AGAAGAAAAT 2227
                         i ?    i       v i v i           -  i  -         i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chrX_83144626_8   2228 CTAGGCA-ATACCATTCAGGACATAGAAACAGGCAAAGATTTCAATGACA 2276
                         v    ?i- v i -   iv   v v iivi      v i    -- --i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC--T--TA 591

  chrX_83144626_8   2277 AAAATGACA---AAAGCAGTTGCAACAAAAGCAAACAATTGACAAATGGG 2323
                         i v      ---      vvv          v   -   v  i    v  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGG 640

  chrX_83144626_8   2324 ATCTAATTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACTATCATCAGA 2373
                          ii v  i   v v  i i   i vii vv    i  v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_83144626_8   2374 GTGAACAGAGAGACTACAGAGTGGGAGAAAA-ATTTTTCAATCTATCCAT 2422
                              v   v iv i     i          -    viv    -  vi  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATAT 739

  chrX_83144626_8   2423 CTGACAAAGGTCTAGTATTTACAATCTGCAAGGAACTTAAACAAAT---T 2469
                             i  i  v  v    ii v   v ii  i     ivv    v --- 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_83144626_8   2470 TACAAGAAAACA----------TTCAAAAGTTGTCAAAGGAGAAGAACAG 2509
                         v i  i  i   ----------  ?    i v v       vvv   i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_83144626_8   2510 ACACTTCTCAAAAGAAGACATTTATGTAGCCAG-AAATATAGGTAAAAAA 2558
                            i     v        i  vi vi i    i-  ii i v v   i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_83144626_8   2559 GCTCAACATCACTGATCAC 2577
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (139 / 104)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.89 (36 / 19)  


 285 24.14 0.00 0.00  chrX_83171799_83177018     3500  3557 (1663)    L1M4_orf2#LINE/L1        1    58 (850)  

  chrX_83171799_8   3500 TGGAGAAACATCTCATGCTCATGAATTGAAAGAATCAATATCATTAAAAT 3549
                             i i i   i    i     i    i    v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83171799_8   3550 GACCATAC 3557
                          i v    
  L1M4_orf2#LINE/     51 GGCAATAC 58

Transitions / transversions = 6.00 (12 / 2)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.00 (0 / 0)  

2558 26.77 2.24 1.53  chrX_83171799_83177018     3880  4727 (493)    L1M4_orf2#LINE/L1       55   908 (0)  

  chrX_83171799_8   3880 ATACTGACCAAAGCAATATCCACATTCAATACAATTCCTATCAAACTATG 3929
                              vv     vii  v v  v      ii    i         v viv
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_83171799_8   3930 AA-TGCCATCCTT-CAGAGAATTAGAAATAAC-AATCCTAATGTTTACAC 3976
                          i-    v ii  -    -    -  v - i -i       vi  i i i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGA-AATT-GACA-AGCTGATCCTAAAATTCATAT 151

  chrX_83171799_8   3977 AGAAC--CAAAAAACAGCCTAAATAGCCAAAGCAACCCTAAGTAAAATTA 4024
                         i   v--   iii  --  vi          i   i i i iv  i vv 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_83171799_8   4025 ACAAAGCCAGACGCATCACATTTCCTAATTTCAAATTATACTACAAGGCT 4074
                               iii  v vv     i    i         viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_83171799_8   4075 ATAGTAACTAAAACAGCAGAGTACTTGTACAAAAATAGACACATAGATCA 4124
                          i     ii  i    iivi     v i i  ii       i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_83171799_8   4125 ATGGAACAAAACAGAGAACCCAGAAATAAAGCTGCATACCTATAGCCATC 4174
                               i i  iv    ii           v iii i ii   i i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_83171799_8   4175 TGATTTTCTACAAAATCTACAACAATAAACAATGAGGAGAGAACACTCTA 4224
                                 v    iivivv   v vi vv     i   i    i v   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_83171799_8   4225 TTCAACACATGGTATTGGGAAAATTGCCTAGCCACATGAAGAAGAATAAA 4274
                                v     ii     v  i  vv  ?       v i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_83171799_8   4275 ACTGGACCCCTATCTCTCACTGTTTACAATAATTAACACAAGATTGTTTG 4324
                         ii          i   v   ii v     v       v   i  v v ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_83171799_8   4325 AAGACTTAAACATAAGATGTGAAACTACAAAGGTCCTAGAAGAAAACCTA 4374
                         ?    i    ii     vv i      i   iv  i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_83171799_8   4375 GGCAAAACTCTTCTGGACATTGATCTATACAAAGAATTTATGACTAAGAT 4424
                           ?iv  v     vv   v   ivi  vi   v iv  iv iiv  v  i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_83171799_8   4425 CCCAAAAGCAAATGCAACAAAAACAAAAGTAGACAAATTGGACTT----- 4469
                         v         v v         iv    i    i           -----
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_83171799_8   4470 -AATTAA----TTTCCTGCACAGCCAAATAA-ATAATCAATAGAGTAAAA 4513
                         -      ----   iv   ---vi    vi - iv     v i   i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGC---TTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_83171799_8   4514 AGATGACCTACAGAATGGGATAAAATATTTGCAAACTATGCCTCTGACAA 4563
                            ii   i           v              ii  iiv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_83171799_8   4564 AAGACTAATATCGAGA-TCTGCAAGGTACTCAAACAACTCAACAGGTAAA 4612
                         ii    vi    v   - v ii  i v    vv         i ----- 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-----A 791

  chrX_83171799_8   4613 CAAACAAACAAACAAACCTATTAAAAGGTGGGCAAAGGATATGAACACGC 4662
                         i   v i     i  v  v   ?   ii            v    i vi 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_83171799_8   4663 ATTTTACAAAAGAAGACATACAAGCAGCCAACAA--ACATGGAAAAATGC 4710
                             iv v        i      iii     i  --     i   i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_83171799_8   4711 TCAATATCACTAATCAT 4727
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.02 (15 / 854), avg. gap size = 2.13 (32 / 15)  


3169 24.78 2.01 0.67  chrX_83186657_83190909     2865  3760 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83186657_8   2865 TGGAAAGATATTCCAAGTTCATGAATTGAAAGAGTCAATATTGTTAAAAT 2914
                                    i   v       i    i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83186657_8   2915 TGTCCATACTACCCAAAGCAATCTACAGATTAAACACAATACCTTTCAAA 2964
                         v - v     v      vii           v   i    v   v     
  L1M4_orf2#LINE/     51 GG-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_83186657_8   2965 GT---AGAATGAGATTCTACACAGAAATAGAAAAAAAAGTCCTAAAATTT 3011
                         i ---  v-  vvv  i -ii       v  v  ivvii          i
  L1M4_orf2#LINE/    100 ATCCCAGC-TGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_83186657_8   3012 ATATGGATCCACAAAATACCCAGTATAGATAAAGCTACCT-ACACAAAAA 3060
                                vvii   iiv      v    vi   i v i  -iv v  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_83186657_8   3061 GAACAAAACTGGAGGAATCACATTATCTAACTTCAAATTATACTACAAAG 3110
                                ii       v     i vi i  i      viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_83186657_8   3111 CTATAGTAA-CA--------TGGTACTGTCATAAAAACAGAAACATAGAA 3151
                            i     -  --------        v     ii i   v i     v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_83186657_8   3152 CAG-GGAACAGAATAGAGAACCCAGAGATAAATCCATGTATCTACAGTAA 3200
                           i-    i     v    ii     i     i    ii  i  ii  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_83186657_8   3201 ATTCCTTTTTGACAAGG-TGCCAAGAACATACATTGGGTAAAGGACGGTG 3249
                            vv    i       -        v   v  v    v    i ii  v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_83186657_8   3250 TGTTCAATAAATGGTGCTAGGAAAACTGGATATGCATATACAGATGAATG 3299
                          v     i          i   v         ?v  i  i  i v     
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_83186657_8   3300 AAACTACATCTCTAGCTCTTGCTATATACAAAAATAAAAACAAAATGGAT 3349
                           ii iv i i   v   vii i            v  vv          
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_83186657_8   3350 TAAAAATTTACATCTGAGACCTTGAACAATAAAACTACTACAAGAAAACA 3399
                         i ? i ii  v  v i   v  vi   v        vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_83186657_8   3400 TTGGA-TAAACTTGCCAGCATATTGGACTGGGCAAAGATTTCTTAAGTAA 3448
                          v  ?-    ii v vv - iv    ii i     v i       ii  -
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATA- 595

  chrX_83186657_8   3449 TAGC-CCACAAGCACAGGTGATCAAAGCAAATATGGACAAACTGGATCAC 3497
                          ii -   v       i ii iv    v   v  i  i   i    iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_83186657_8   3498 ATCAAG-TTAAAAAGCTTCTGCACGGCAAAGGAAACAATCAATAACATGA 3546
                              i-       -   i  ii vv       v  v     v  vi   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_83186657_8   3547 AGAGACAATTCACAGAATAAGGGAAAATATTTGCAAACTGCCCATCTGAC 3596
                          i      ii        ii i               iiiivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_83186657_8   3597 AAGGGATTAGTAACAAGAATACATAAGGAGCTCAAACAACTCTACAGGAA 3646
                               i v   v v      i    i  i   vv       v i iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_83186657_8   3647 AAAGTCTAATAATCCAATTAAAAAATGAGCACAAGATCTGAATAAAAAAT 3696
                             v v     i      ?       i   v i   i      i v v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_83186657_8   3697 CCTCAAAAGAAAGCATACAAATGGCAAACAGGCATATGAAAAGGTGCTCA 3746
                         i   v      iii           v  i i   i        i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_83186657_8   3747 ACATCATTGATCAC 3760
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (128 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.60 (24 / 15)  


3235 22.27 3.71 1.80  chrX_83203983_83206088      725  1613 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_83203983_8    725 GAAAGATA--CCACGTTCATCAATTAAAAGACTCAATATTACTAAAATG- 771
                                 --   i      vi   ii      i      ii   i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_83203983_8    772 TAACTTA-TCTGCAAATTGACCTATACATTCAATAAAATTCCAACCAATA 820
                         i  --  -  iv        i   i v      iiv   i  v i   v 
  L1M4_orf2#LINE/     53 CAA--TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83203983_8    821 TCCCAGCAGGACATTTTTGTACAAAGTGAAAAGCCGATTTTAAAATTGAT 870
                                -v v v      i v   v   v    i   ii       v  
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_83203983_8    871 ATGGAAATGCAAAGGACCTAGAAGAGCCAAA----CTTTCAAAAAGAAAA 916
                                     i     i    v       ----ii  v        i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_83203983_8    917 GCAAAGCTCAAGGACTCGCACTGCCTCACTTCAAGACATATTATAAAGGT 966
                         i     i vi       i    v  iv i     i  v  i  i    v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_83203983_8    967 ACAGTAATTCAGACAGTGTGGTATTGTCATAAAGATAGACAAATGGATCA 1016
                                 iv             i  v     i        v  i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_83203983_8   1017 ATG-AACAGAACAGAGTATCCAGAAATAGGCCTTCATATATATGATCAAC 1065
                            -  i    iv   vi          ii  ivi i  v    i    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_83203983_8   1066 TGGTTTTCAAGAAAAATGT-AAGGTAATTCAGTGAAGAAAAGACAGACTT 1114
                           i     i v  iii  i-   iiv     i  ii    ii i  v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_83203983_8   1115 TTCCAATAATGATGCTATAACAACTGGCTATCTATGTG--AACAAATGAA 1162
                            v vv    i    ivi        v  ? i ii  --  vi      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_83203983_8   1163 AA-GGACTTCTGCACATACCTGTAACCATATACTAAAATGAACTCAAAAC 1211
                         iv-    ii  i - vi  -----         v     v         i
  L1M4_orf2#LINE/    450 GTTGGACCCCTAC-CTCAC-----ACCATATACAAAAATTAACTCAAAAT 493

  chrX_83203983_8   1212 GGATCCTAAATCTAGATGTAAAATGC--AAACTACAAAACCTCT----AG 1255
                              v? i i   i      i -  --      i     -   ----  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAAC-TCTTAGAAG 541

  chrX_83203983_8   1256 AAAACATAAGAGAAAATCTTT---AGCTGTGATTAGGCAGATA-TGCCTT 1301
                                 i ? v       i--- v  vv i       -  i- vi   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTT 590

  chrX_83203983_8   1302 ACAAAGGACACTAAAAACACAATTAATAAAGGGAAAAAATCCTATAAATC 1351
                          v v v     i    i     vi  i   i -       vv-      i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAG-ATAAATT 638

  chrX_83203983_8   1352 AGACTTCACCAAAATTAAGAACTTCTGCTTTTCAA--TACACTGTTAAGA 1399
                         i       i         i     i  ivi     --v     i i    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_83203983_8   1400 GAATGAAAAGACAAACTATAGACCAGAAGAAAATATTTCCAAATAACATA 1449
                         i i           v i i   vii i           v     v i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_83203983_8   1450 TATGATCAAGGACTTACATCCAAAATATATGAAGAACTCTCAAAACTCAA 1499
                          v    v i      ii     i       i         i v       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_83203983_8   1500 TAAGAAAA---CAAACAATCCAATAAAAAAAAACAGGCTAAAAATTTAAA 1546
                            v    ---    i  i     v?     --ii   v  ii    i  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAA 836

  chrX_83203983_8   1547 CAGACATTTTACCAA-GAGGATA----GATGGCAAATGAGCTCATGAAAA 1591
                         i        iv    -  i    ----i     v   i   v        
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_83203983_8   1592 GATGCTCAATGTCATTAGTCAT 1613
                                  ii   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (127 / 67)
Gap_init rate = 0.03 (26 / 906), avg. gap size = 1.88 (49 / 26)  


2757 25.32 7.70 1.75  chrX_83254447_83258080.rev     2287  3143 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83254447_8   2287 TGAAAAGACATCTCATGTTTACGAATTGCAAGAATTAATATTATTAAAAT 2336
                           i     i   i      i i i    v    v        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83254447_8   2337 AACCATACTATCCAAAGCAAGCTACAGATTGAATGTAATCCCTATCAAAA 2386
                         ii v     vi     vii v         v  i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83254447_8   2387 TACCAATGATATTCTTCACAGAAATAGAAAATAAAAACAATTCTAAAATT 2436
                          v   iiviiv  i  ii       v  v  ----ivii  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA----GCTGATCCTAAAATT 146

  chrX_83254447_8   2437 TATATGGAACCACTAAAGACCCCAAATAGCCAAAGCAATATTCAACAAGA 2486
                         i        vii v ii     vi          i    v  v  v    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_83254447_8   2487 A---CAAAGCTGGAGGCATCAGAAAACCTGACTTCAAATTATGCTGCAAA 2533
                          ---     i      vv   v vvv  ii i      viv i  i    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_83254447_8   2534 GCCATAGTAACCCAAACAGCATGGTATTGGTATAAAAACAAACA-GTAGA 2582
                           i i     i v i    ii     i   i    ii i i   -i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_83254447_8   2583 CCAATGGAACAGATCAGCAAGTGGAGAAATAAATTCATGTTTTTAAAATC 2632
                         i        i   viv vi   vv         ii   iiv    vii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_83254447_8   2633 AACTGATTTTTGACAAAGGTGCCAAGACCATTCATTTAAAAAAGGACACT 2682
                           i       i     i                 v viii    i i v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_83254447_8   2683 GTCTTCAAAAGAGGGTGCTGGAAATACTGTATATCCATGATCCATATACA 2732
                         v i     v i v        i vv    v   ?   i-------  i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC-------ATGCA 439

  chrX_83254447_8   2733 GAAGAATGAAACTAGATCCTTATCTCTCACTACATACAAAATTCAACTCA 2782
                         i         ii i  i  i  i   v   i i        v i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_83254447_8   2783 AAATGGATTAGAGACTTAAAAATAAGACCCAAAACTATACAGCTACTAGA 2832
                                 i ?    i    vi     v i         v i  vi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_83254447_8   2833 AAAAAAATGTAGAGGAAACACTTCATGACCTTGGTTAAGGCAAAGATTT- 2881
                          i    -ii   i? v  vv    i         v v      v i   -
  L1M4_orf2#LINE/    540 AGAAAA-CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_83254447_8   2882 TTAG----GGCA---AAGACTTAGATAACACAGG---------------- 2908
                             ---- i  ---  ii vi iii    v i ----------------
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_83254447_8   2909 ---------CAAAG------------------CAAAGGAAATAATCAACA 2931
                         ---------    i------------------       v iv     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_83254447_8   2932 GAGTGAAGAAACAAACTTTAGAATGAGAGAAAATATTTTCAAGGTATTTA 2981
                         i      i i    v ivi      i            v   ivi  v  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_83254447_8   2982 TCCAACAAGGAA--TGACTATTTGCAATATACAA-GAA--------ACTC 3020
                           ii i    i --  --   iiiv      i  -   --------    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTG--TATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_83254447_8   3021 AACAGCAAACCGACAAACAATCCCACTTAAAAATGGGCAAAGCATCTGAA 3070
                           i ii   vv      i  i  v i ?              v  i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_83254447_8   3071 CAGACATTTCTCAAAAGAAGACATGCAAATGGCCAACTGGTATATGAAAA 3120
                         i           v        i  i           ivi i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_83254447_8   3121 AAATGTTCAACATCACTAATCAT 3143
                         i -  i         ????????
  L1M4_orf2#LINE/    887 GA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (140 / 73)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 5.40 (81 / 15)  


1627 24.29 3.67 2.04  chrX_83259195_83261139      500   989 (956)    L1M4_orf2#LINE/L1      280   777 (131)  

  chrX_83259195_8    500 AAAGATAGACAAATAGGTCAATGGATTATAAT--ACA-TTCAGAAATAGG 546
                           i        v    i        v  v   -- v - i        ii
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_83259195_8    547 CCCAAATGTACATGGCCAACTGAGATTTTACAGAATTGGAAAGGTAATTC 596
                             v ii vi    i   i   vv  iv   iiiv  vv   iiv    
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_83259195_8    597 AGTGGAGAAAGAATAGATTTTTCAACAAAGGGTGCTGGAAAAATTTGGAT 646
                          i   i          vi           v        i v  i -    
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT-GGAT 428

  chrX_83259195_8    647 ATCCATGTGGAGGAAAATGAAGTTTGATCCATTGCTTGCAATATATACAA 696
                          ?   ii  v ii i         v  i  v vv  ii  vi        
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_83259195_8    697 AGAAAAACTCAAAATGGATTATAAACATAGGTACAAAACCTAAAATATAT 746
                          i vv              i ? i  v  ii ii  i v      i-   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC-TAT 527

  chrX_83259195_8    747 AACATTTCTAGAAAAAAATAAATGAGAAGAAAATTTTTGTGTTCCTTGGA 796
                           v i ii     i    i -- -  i? v    i  i   v-      i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACA--T-AGGNGTAAATCTTCGTGA-CCTTGGG 573

  chrX_83259195_8    797 T-GGGTAAAGATTTCTTAGATTTGGCACTAAAAGCATGATTCATACAAGC 845
                          -i  i  v i          v  i   i       ii viv i v   v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_83259195_8    846 AAAAAC--------TAGACTTCATCAAAATTCAAAATACCTTCT---CTT 884
                              i-------- i               v    ---   i ---   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAA---CTTTTGTGCTT 670

  chrX_83259195_8    885 ACAAA--ACACCATTAAGAGAATGATAAGATAGGCCATAGAA-AGAAAAA 931
                         -    --    i  i    i i   v    i iv   i    -i i i  
  L1M4_orf2#LINE/    671 -CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_83259195_8    932 AATATTTTCAAATCTTATATCTGAAAAGGATCTTGTATCCAGAATACATA 981
                                v      v         v    iv               i   
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_83259195_8    982 AGAAACTC 989
                          ii     
  L1M4_orf2#LINE/    770 AAGAACTC 777

Transitions / transversions = 1.76 (74 / 42)
Gap_init rate = 0.03 (14 / 498), avg. gap size = 2.00 (28 / 14)  

 359 22.54 5.63 0.70  chrX_83259195_83261139     1311  1452 (493)    L1M4_orf2#LINE/L1      760   908 (0)  

  chrX_83259195_8   1311 AGAAAATAAAAGGAACTC--AAAATTCAATAATTATGAGAAAAACAAC-- 1356
                             v   v  i      -- v  i        v vi   v   i   --
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_83259195_8   1357 --TTGTAAAATGTATAAATGATTTGA-CAAACACTCCACCAAAGAAGATG 1403
                         --  ?v      vii   v       -i i   i i v           i
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_83259195_8   1404 TACCAATGGG-AACAAACCATGTGAAAAAATGTTAAACACCATTAGCTAT 1452
                            v     v-  i  i - ii      i   i v    i  ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGC-ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (18 / 13)
Gap_init rate = 0.03 (5 / 149), avg. gap size = 1.80 (9 / 5)  


2644 29.29 0.90 1.23  chrX_83340589_83343332.rev     1363  2253 (491)    L1M4_orf2#LINE/L1       21   908 (0)  

  chrX_83340589_8   1363 ATAGATAGGAAGAATCAATATCATTAAAATGGCCACACTGCCCAAAGCAG 1412
                           i   v      v i     ii    i     v i   v      viii
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chrX_83340589_8   1413 TTTACAGATTTAATGCTATTCTTATCAAATTACCAATGACATTCTTCACA 1462
                          i        i  i  v  i i       v v   iivi v  i  ii  
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chrX_83340589_8   1463 GAACTAGAAAAAAGTACTTTAAAATGTATGTAGAATCAAAAAAGAACTCA 1512
                            v v  v  ivvv iii      vi  i i   viiv  ii  v ivi
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chrX_83340589_8   1513 AATATCCAAGGCAATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCATGT 1562
                             v    ii     i i iv  i          i      vv   iii
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_83340589_8   1563 TACTGAAATTCAAA--CTACTACAGGGCTATAGTAATCAAAACAGCATGG 1610
                          v iv  v      --i       ii    i         i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_83340589_8   1611 TACTGGTATGAAAACAGGCAAAAAGACCAATGGAGCAGAATAGAGAGCCC 1660
                               i  i ii i  i  v v   i       ii     v     i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_83340589_8   1661 AGAATTAAGGCCGCACACCTACAACCATTTAATCATCTACAAAGCTGACA 1710
                             v   iv  ii   ii  iiii  v  i  iv  v    i v  v  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_83340589_8   1711 AAAACAAGCAATGGGGAAAGGACTCCCTCTTCAATAAATGGAGATGGGAA 1760
                          i v  vv            i ivvi  i     i      v v     v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_83340589_8   1761 AACTGGCTAGCCATAAGCAGAAGATGAAAACTGGACTCCTTTCTTACACT 1810
                               v  ?   i v   i    vvi  ii     i   vi  i    i
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_83340589_8   1811 ATGTACAAATACAAACATCAACTCAAGATGGATTAAAGACTTAAATGGAA 1860
                           ------       v  i       i      i ?    i      v  
  L1M4_orf2#LINE/    471 AT------ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_83340589_8   1861 CACCTAAAACTATAAAAACCCTGGAAAACAACCTAGGT---AATACCACT 1907
                         v v              vi i i   i v   v    ?---   ----  
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT----CT 560

  chrX_83340589_8   1908 CTG-GACATAGGAAAGAGCAAAGATATCAT-GATGAAGAAGCCAGAAGAA 1955
                         ii -   v v  ivvii    v i v  v -   - v  vi   i   v 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCA 609

  chrX_83340589_8   1956 ATTGCAACAAAAGCAAAACTTGACAAATGGGATCTAGTTAAACCTAAGAA 2005
                         vvv          v    v v  i    v   ii vi i   vi   i  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_83340589_8   2006 CTTCTGCACAGCAAAAGAATCTATCAGCAGAATAAACAGACAACTTACAG 2055
                            i  ii vv    i  vv      iv i i i  v       ii    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_83340589_8   2056 AATGGGAGAAAATATTTGCAAACTATGCATCTGACAAAAGTCTGTTATCC 2105
                                               ii  ii      i  ii v  vv     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_83340589_8   2106 AGCACTTATAAGGAATTTAAACAAATTTACAGGGCAAA-ACAAACAACCC 2154
                           v iv     i   i ivv    v iv i iviv   -     i     
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_83340589_8   2155 CGTTAAAAAGTGGGCTAAGGACGTGAACAGACACTTTTTGAAGGAACACA 2204
                         vi  ?    i     v     iv    i     i  i iv  i   v i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_83340589_8   2205 AACATGCTGCCAACAAGCATATGAAGAAAAGCCCAATATCACTATTAGA 2253
                         v   viiv     i     i     i i v  i   i    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (154 / 103)
Gap_init rate = 0.01 (8 / 888), avg. gap size = 2.38 (19 / 8)  


2794 27.47 2.00 1.00  chrX_83345218_83348975.rev     2369  3267 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83345218_8   2369 TGGAAAAATATTCCATGCTCATGGATAGGAAGAATCAATGTTGTTAAAAT 2418
                               i    i     i        v      v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83345218_8   2419 GGACATACTGCCTAAATCAATTTACAGATTCAGTGCTACTCCTATAAAAG 2468
                           vv     v  i    ii  i          ii  v ii     v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83345218_8   2469 TATCAACATCATTTTTCACAGCA-TTATAAAAAAAGTT--TTCTAAAATT 2515
                          vi  i vv v     ii   v -  i---- v   i -- i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chrX_83345218_8   2516 CATATGGAATCAAAAAAGAGCCCAAATCACCAAAGCAATCCTAAGCAAAA 2565
                                  viiv  ii  v  vi   vi     i     i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_83345218_8   2566 TGAACAAAGCCAGATG-CTAACACTACCAAACTTTGGATTACACTACAAG 2614
                         v        iii  v -  v     v  v  i  iii vivi       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_83345218_8   2615 GTTACAGTATCCAAAATAAAATAGTACTATTACAAAAATAGACACATAGA 2664
                          i       vi   i i ivi i     ivi i  ii       i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_83345218_8   2665 CAAATGGAACAGGATAGAGAACACAGAAATAGAGCCACACACCTACATCC 2714
                         iv       i  i  v    iiv        i v   i   ii  iivi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_83345218_8   2715 ATCTGATCTCCAACAAAAA---CAAG------CAATGGGGAAAGGACTCC 2755
                          vi    i i i    iii---    ------            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_83345218_8   2756 CTATTAAATAAATGGTACTAGGATAACTGGCCAGCCATATGCAGGAGATT 2805
                           v  v  i       i  i   i      vi ?   i     ii   v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_83345218_8   2806 AAAACTGGACCCCCTAATTTTTACCATACACAAAAATTAACTCAAGATGG 2855
                         i  ii        -  vi ivi      i                i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_83345218_8   2856 ATTAAAGATATACATGGGAGACATAAAACTATAAAAATCGTAGAAGAAAA 2905
                           i ?   iv  v   vi   vv             v  v          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_83345218_8   2906 TCTAAAAA-ATATCATTCTGGGTATTGACCTGGGCAA--ATTATTTATGA 2952
                         iv  ii?i- v   -   vv iiv   ivi i     --i  vi   -  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GA 593

  chrX_83345218_8   2953 CTAAGTACAC-AAATGCAAGTGCAACAAAAACAAAACT-GACAAGTGGGA 3000
                         -  v -    -   v   viv         iv    v -  i  i v   
  L1M4_orf2#LINE/    594 -TATG-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_83345218_8   3001 CCTAATTAAACAAAACAGCTTCTGTACAGCAAAAGAAACTATCAACAGAG 3050
                          i v  i   vvv  v i   i   i vv    i  v        v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_83345218_8   3051 TAAACAGACAATAGGCAGAAAGGGAGAAAATATTTGCAAAGTATGCATCC 3100
                          i  v      ivvi     v                   vi  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_83345218_8   3101 AACAAAGGGCTAATATCCAGAATCTATAAGGAACTTAAACATATCAATAA 3150
                         i i  i  i  vi          v     i     ivv   vv       
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_83345218_8   3151 GGAAAAAGCAAACAACCTCATTAAAAAATAGGCAAAGACCATGAACAGAC 3200
                         vi    ii    i    iv   ?      i       iviv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_83345218_8   3201 ACTTCTCAAATGAAGACGTACATGTGGCCAACAAATATATGAAAAAATGC 3250
                          i     v  v     ii    vi       i  ii i       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_83345218_8   3251 TCAACACCACAATGAGG 3267
                               i  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (152 / 91)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.80 (27 / 15)  


3244 24.86 2.35 0.67  chrX_83349884_83354076.rev     2810  3702 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83349884_8   2810 TGGAAAAATGTCT-ATGTTCATGGATTGGAAAA-TCAATATTGTAAAAAT 2857
                               i  i  i-                 i - i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83349884_8   2858 GTCCATACTACCTAAAGACATCTACAGATTCAATGCAATCCTTGTCAAAA 2907
                          v v     v  i   vvv              i       i i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83349884_8   2908 TACCAATGGCATTCCTCACAGAAATAGAAGAAACT-ACTCTAAAATTTAT 2956
                          v   iiv  v  ii ii       v  v-  i  - ii        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_83349884_8   2957 ATGAA---GCCAAGAATTCCCCAGAATAGCCAAAGATATCCTGAGCAAAA 3003
                            i ---  v i i ---               ivv   i   iv  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_83349884_8   3004 AGAAGAAAACTGGAAGAATCACATTACCTGACTTCAAATTATATTACAGA 3053
                             v   ii    i  v     i v  ii i      viv  i    i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_83349884_8   3054 GTTATAGTTACTAAAACTGCATGGTACTGGCACGAAAAGAGACACATAGG 3103
                          i  i   v ii  i  v ii           ii ii v     i    i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_83349884_8   3104 CCAGTGGAAGAGAAGAGAGAACCCAGAAATAAGTCCACATACCTACAGTG 3153
                         i  i     v    vv    ii          ii   i i ii  ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_83349884_8   3154 AACTCATTTTTGACAAG--TGCCATGAGAATACACTGGAAAAAAGACAGT 3201
                           i v     i      --     v  vv  v  v   ii   ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_83349884_8   3202 CTGTTCAATAAATGGTGCTGGAAAAAACTGGATATCCATATGCAAAAGAA 3251
                           v     i            i v  -       ?   i           
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAA 445

  chrX_83349884_8   3252 TGAAATTTGACCCCTATCTTTCACTATACACAAAAATCAAATCAAAATGG 3301
                             i  v        i  iv   i   i        i  v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_83349884_8   3302 ATTAAAAACATATATATAGGACCTCAAAATATAAAACTACTATAAGAAAA 3351
                           i ? i  v  v  i  i  v  v   v         vi  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_83349884_8   3352 CTT-GGGGAAAATCTCCAGGACAT-GGTCTAGGCATAGATTTCTTAAGCA 3399
                          v -  ? v      i iv   v -  vi      vv i       iii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_83349884_8   3400 ATACTCCACAAGTGCAGGCAGCCAAAGCAAATCTGGACAAATGGGATCAC 3449
                         vv  v   v   ii  i   i v    v   vv i  i    v   iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_83349884_8   3450 CTCAAG-TCAAAAAGCTTCTCCACTGCAAAGGATACAGTTAACAAGTTGA 3498
                         v    i- i     -   i vii  v       i  vi i  v  iv   
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_83349884_8   3499 AGAGACAACCCACAGAATGAGAGAAAATATATGCAGAC--TACCCCCGAC 3546
                          i                 i          v    i i--  ivi i  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_83349884_8   3547 AAAG-ATTAATCACTAGAATATATAAGGAGTACAAACAACTCCACAGGAA 3595
                           i - i vi vv i           i  iiv vv       v i iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_83349884_8   3596 AAAT-CTAATAATCTGATCAAAAAATGGGCAAAAGGTTTGAATAGATATT 3644
                            v- v     i ii  i?             i i          i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_83349884_8   3645 TCTC-----AAGACATACAAATGGCAAACAGGCATAT-AAAAGGTGCTCA 3688
                             -----    i           v  i i   i  -     i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_83349884_8   3689 ACATCATTGATTAT 3702
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (136 / 82)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.59 (27 / 17)  


3415 24.86 1.33 0.99  chrX_83373198_83377401     2807  3711 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83373198_8   2807 TGGAATATTATTCCATGTTCCTGTATTGGAAAAATCAAGATTGTTAAAAT 2856
                              viv   i        v  v       i v i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83373198_8   2857 GTCCATACTCCCCAAAGCAACCTACAGATTGAATGCAATTCCTATCAAAA 2906
                          v v            vii i         v  i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83373198_8   2907 TACCAATGGCATTCTTCACAGAAATATGAAAAAC-AATTCTAAAATGTAT 2955
                          v   iiv  v  i  ii       -   v  i -i  i       vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_83373198_8   2956 ATACTACCACAAAAGACCTAGACTAGCCAAAGCTATCCTAAGCAGAAAGA 3005
                           ivv vii   ii    i   v        i v   i i iv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_83373198_8   3006 GCAAAACTGGAGAAATCACATTATCTGACTTCAAATTATACTACAGAGCA 3055
                         i    ii     i v     i vi ii i      viv       i   v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_83373198_8   3056 ATAGTTAACGAAACAGTATGGTACTGGCATAAAAACAGACCCATAGACCA 3105
                          i   v v i i     i              ii i    vi     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_83373198_8   3106 GTGTAACAGAATAGAACAGAACCCAGAAGCAAATCCGCATACCTGCAGTG 3155
                         i  v  i     v  ---  ii      ii   i  ii i ii iii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGA---GAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_83373198_8   3156 AACTCATTTTTGACAAAGGTGCCGAGAGCATATGCTGGGGAGAGGACAGT 3205
                           i v     i     i      i   v   viiv      i  i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_83373198_8   3206 CTCTTCAATAAATGGTGCTAGCTAGGAAAACTGGATATCCATATGCAGAA 3255
                           i     i          i ----  v         ?   i     i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGG----GACAACTGGATAKCCACATGCAAAA 442

  chrX_83373198_8   3256 GAATGAAACTAGGCCCCTATCTCTTGCCATATACAAAAAGTAAAGAAAAG 3305
                                ii i i      i   vii             v   vvv   i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_83373198_8   3306 TGGACTAAAGACTTAAATCTAAGACATGAAACTA-----CTCT---AAGA 3347
                             ii ?    i     v     vv i      -----    ---    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_83373198_8   3348 AAACAATGGGGAAAATCTTCAGGAAATTTGTCTGAGCAAAGATTTATTGA 3397
                              vv  ? v        iv  vv  v vi ii    v i   v  ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_83373198_8   3398 ATGAGACCCCAAACACAGAGGCAACCAAAGCAAAACTGGACAAATGGGAT 3447
                           iv   v     vi  v i     v    v    v i  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_83373198_8   3448 CACATCAAG-TTAAAAAGCTTCTGCGCAGCAAAGGATAAAATCAACAAAA 3496
                         iv      i-       -   i  i  vv       i vv     v   i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_83373198_8   3497 TGAAGAGAACACCCTCAGAATGGGAGAAGATATTTGCAAAGTACCCATCT 3546
                             i   vv    v             i           vi ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_83373198_8   3547 GAGAAGAGATTAATCACCAGAAAATATAAGGAGCTCAAACAACTCTATAG 3596
                           v   i  i vi vv      v      i  i   vv       v   i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_83373198_8   3597 -AAAAAATCTAATAATCTGATT-AAAAATGGGCAAAAGATTTTAATAGAC 3644
                         -     iv v     i ii   -             i     v       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_83373198_8   3645 ATTTCTCAAAGGAAGACATACAAGTGAAAAACAAGCATATGAAAAGATGC 3694
                                v  i     i      i  ivv  i     i            
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_83373198_8   3695 TCAATATCATTGATCAT 3711
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (134 / 88)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


3039 25.86 2.11 1.33  chrX_83439435_83443759     2932  3832 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83439435_8   2932 TGGAGAAGCATTCCATGTTCATCGACGGAAATAATCAATAATGTTAAAAT 2981
                             i iii  i          v  iv i  v v i    v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83439435_8   2982 TTCCATAGTCACCAAAGCAATCTACAGATTCAGTACAATCACTATCTAAA 3031
                         vv v   v  v     vii             iii     v     v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83439435_8   3032 TACCAGGGACATTCTCCACAGAGAA-AATAA-CT-ATCATAACATTTATA 3078
                          v    vvi v  i iii    i v-i i  -  -   v   v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_83439435_8   3079 CAGACCCACAAAG-ACCCAGAATAGCCAAAGCTATTCTAGGCAAAAATAA 3127
                         ii  vvii   i -                i v  ii iiiv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_83439435_8   3128 CAAAACTGGAGGAATTACATCATCTGCCTTCAAATTATACTACAGAGCTA 3177
                             ii       v i   iivi iivi      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_83439435_8   3178 TAGTAACCAAAACAGCATGAT-CTGGCATAAGAAATAGACATGTAGAGCA 3226
                         i     i   i    ii  i -          i -       i    v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCA 299

  chrX_83439435_8   3227 ATGGAATAAAATAGATAACCCAGAAACAAATCCAATCCACACACCTGCAG 3276
                                 i   v  v ii       i   i   -----i   ii iii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-----TACATTTATGG 344

  chrX_83439435_8   3277 TAAACTCATTCCC-ATAAAGGTGCCAAAAACATACACTGGGGAAAAAGAC 3325
                          v  i v   ii - i  i        i v   v  v        i - i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-AT 393

  chrX_83439435_8   3326 AGTTTCTTCAATAAATGGTGCTGGGAAAACTGGATATTCATATGCAGAAG 3375
                            i i     i              v         ?i  i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_83439435_8   3376 AATAAAACTAGACTCCTATCTTTTGCCATATACAAAAATCAAAACAAAAT 3425
                            i  ii i   i    i  ivii              i  vv      
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_83439435_8   3426 GGCCTTAAACATTTAG-TCTATAACCTCAGACTATTAAACTACTACAGGA 3474
                           v- i ? v ii  i- v  vi v  v i     v     vi  v i  
  L1M4_orf2#LINE/    494 GGA-TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_83439435_8   3475 AAACACTGGAAACAACCTTTAGGACATTGGGCTGGGCAAAAATTTCTTGC 3524
                              iv  ?ivv  i   iiv   v     i i     vii      iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_83439435_8   3525 ATA--ATACCACACGAGCACAGACAATCAAAGCAAAAAAATGAACAACTG 3572
                            -- i    v --      ii   iv    --       ii i  v v
  L1M4_orf2#LINE/    593 ATATGACACCAAA--AGCACAAGCAACAAAAG--AAAAAATAGATAAATT 638

  chrX_83439435_8   3573 GGATCATGTCAAGCTAAAAATCTTCTGCACGACAAAGAAAAC----AACA 3618
                            iivii    iv v    v   i  ii vv     i v  ----  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_83439435_8   3619 AAATGAAAAGACAACCCATAGAA--GGAGCAAATATTTGCAAATTGCCCA 3666
                           i               i    --    v              iiivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_83439435_8   3667 TCTGACAAGGGATTAATAACCAGAACATATAAGGAGCTCAAGCAACTTTA 3716
                              i      i vi  v      i      i  i   vvi     iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_83439435_8   3717 TAGAAAAAAATCTAATAATCCAATT-AAAAATGGGCAAAAGATTTGAATA 3765
                           iv     iv v     i      -             i          
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_83439435_8   3766 GATATTTTTC---AGAAGACATACAAATGGCAAACAGACATATGAAAAGG 3812
                           i    i  ---      i           v  i ii  i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_83439435_8   3813 TGCTCAACATCACTGATCCT 3832
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (149 / 81)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.72 (31 / 18)  


2259 28.62 4.30 1.58  chrX_83444953_83450294.rev     3971  4854 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83444953_8   3971 TGGAAAAA-ATTCCATGCTCATGAATTGGAAAAATCAATATCATTAAAAT 4019
                               i -  i     i     i       i v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83444953_8   4020 GGCCACATCACCCAAAGCAATTAACAG--TCAGTGCTATTCCTGTGAAAC 4067
                            v i iiv      vii  iv    --   ii  v  i   i v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83444953_8   4068 TCTGAACATCATTCTTCAAAGAATGAGAAAAAAAAATTCTAACTTTCACA 4117
                           iv i vv v  i  iiv    vvv  v  ivvi  i    vv    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_83444953_8   4118 TGGAACCAAAACAAGCCTA-AATAGCCAAGGGCAAATCT--AAGAAAAAG 4164
                              viiv  viii  i -         ii-   -   --  i  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAA-TCTTGAAAAAGAAG 198

  chrX_83444953_8   4165 AACAAAGCTGGAGACATTATACTACGTGACTTCAGACAATACTGTAAGGC 4214
                                i     ivv i i   v vii i    i vvv    ii  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_83444953_8   4215 TACAGGAACCAAAACAACAAAGTACTGGTACAAAAACAGACACACAGACC 4264
                              v  i   i   iiivi       i i  ii i     i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_83444953_8   4265 AATGAAATAGAATAGAAAACTCAGAAATAAAGCCACACACTTATAAGCAC 4314
                             i        v  i iii          v   i   i    iiv  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_83444953_8   4315 TTGATCTTTAACAAGA---CCAAGAAAAACAGAAAATAGGAAAAGTACTC 4361
                              i  ii     i---      v---  vvv   i  i    v ivv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAAAGAATAG 395

  chrX_83444953_8   4362 CCTATTCAATAAATGGTGTTGAGGTAACTGGCTAGTCATTTGCAAAATAA 4411
                         i  v     i        i  i ii      v  ?i  iv       v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_83444953_8   4412 TGAAATTAGACCCTTATCTTTCACCATATATAAAAATTAACTCAAGATGT 4461
                             i  i     i  i  iv         i              i   v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_83444953_8   4462 ATTAAAGATTTAAATATAAGACTGAAAACTACAAAAATCTTACAGGAAAA 4511
                           i ?   ii     i     viv       i    v     v i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_83444953_8   4512 CTTAGG---AAATACCCTTCTCCACATTAGCTTTGGTGAGGAATTTTTGG 4558
                          v    ---    ---    viv  v  i v  v  ii v iv  i  i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_83444953_8   4559 CTAAGTTCCCAAAAGCAATTACAGAAAAAAAAAAAAAAACTTGACAAGTG 4608
                         v  v viv         ----  iiv  v    i     v v  i  i v
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCA----CAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_83444953_8   4609 GGACCTAATTAAACTAAATAGATTCTACACAGTGAAGTTAACTATCAACA 4658
                             i v  i   v v  v iv  i iii vvii   vvv        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_83444953_8   4659 GAATAAACAGACAACCCACAGAATGGGAAAAAAATATTCACAAACTGTGC 4708
                         i i i  v                    i    -    ii    iii ii
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATAT 737

  chrX_83444953_8   4709 ATACT-ACAAAGGCCTGATATCTAGAATCTA--AAAAACTTAAACAAATC 4755
                           -  - i  i  v  vi    i     v  --  i    ivv    v  
  L1M4_orf2#LINE/    738 AT-CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_83444953_8   4756 AACAA-AAAACAAC------CCCAAT-ACAAAATGGGCAAAG-ACACGAA 4796
                           i  -    vi  ------      -?v             - ivi   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_83444953_8   4797 --------------AAGGAGGCATATAAGCAGCCAACAAAAACATGAAAA 4832
                         --------------   i  ii   i  iii     i  iv         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_83444953_8   4833 AATGCTCATCAATAATCATCAG 4854
                         i       v  vi ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (155 / 95)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.60 (52 / 20)  


2931 26.86 4.46 0.69  chrX_83452354_83456667.rev     2951  3825 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83452354_8   2951 TGAAAAGACACCCCATGCACACATATTGAAATCATTTAG-ATCATTAAAA 2999
                           i     i i      iv  iiv    i  v- i   i-  ii    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGA 49

  chrX_83452354_8   3000 TTATTATACTGCCCAAAGCAATCAACAAATTCAATGCAATCCCTACCACG 3049
                          viiv     v      vii   v   i      i          i  vi
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_83452354_8   3050 ATACCAGAGTCATTTTTCACATAATTAGAAAAAATGAATCCTAAAATTTG 3099
                           v    vvv v     ii  v  v v  v  iv   -          ii
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCA 148

  chrX_83452354_8   3100 CATGGAA---CAAATGGGGAGCCCAAATAGCGAAAGCAATCCTGGGAAAA 3146
                         i      ---   ---    v  vi      v   i     i  ii   i
  L1M4_orf2#LINE/    149 TATGGAAATGCAA---GGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_83452354_8   3147 AAGAACCAAGCTGGAGGTAC-CGCACTACCTAACTTCAAAATATATTACA 3195
                               v   i      -  - i    v  i  i       iv  i    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_83452354_8   3196 AGGCTGTAGTGACCAA-AGAGTATGGTATTGATATAGAAACAGGCGCATA 3244
                          i   ii   i i   - v   i     i  ii   iii i  i ii   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_83452354_8   3245 GGACAATGGGACATAAAAGAGGACCCAGAGATCAATATGCATATTTAAAG 3294
                          iv      i i v  vv   iii     i  v  iviii i     vi 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_83452354_8   3295 TCAACTGATTTTCAATATAGGTGCTAAGTACATACATTTGGGAAATGATA 3344
                             i        i i vi     i   vv   v  v v      vi   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_83452354_8   3345 GTCTCTTTAATAAATGGTGCTTGGAAAATCAAATATTCGTATGCAAAAGA 3394
                             i  i  i          v   v  iiii   ?i ii          
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_83452354_8   3395 ATGAAAGTGAACCCTTATTTCTCACCATATACAAA--------------- 3429
                              iv  i    i  ii  v             ---------------
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_83452354_8   3430 -------GGCTTAAATGTGAGATTCAAATCTATAATACTACTGGAAGGAA 3472
                         ------- i i       i   vii   v      v   vi i    i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_83452354_8   3473 ACCTAGAGAAAAATCTTCATGACCTTAGTCTAGGCAAAGATTTTATGCTT 3522
                           v   i?iv        i       i vi       v i   iv ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_83452354_8   3523 AAGAACTCAAAGGCACAGACAACAAAACACAAA-TAGACAAGTGAAATTA 3571
                          v  vvi    i     ii        v v   -    i  i vii i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_83452354_8   3572 TA-CTAAACTAAAAACTTCTGTACAACAAAGGAAGCAATCAAGAGAATGA 3620
                         i - v   i         i   i vv       vi v       i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_83452354_8   3621 AGTCACAACCTGTTGAATGGAAGAAAATATTTGCAAACTATTCATTTGAT 3670
                          ivv      iiiv      i                ii  vi  i    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_83452354_8   3671 AAGGGACTAATATCCAGAATATACAAGGGACTCTAATAACTCAATAGCTA 3720
                                 vi             i  i i     v i         iiv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_83452354_8   3721 AAAAACAA----TCCTATTAAAAATTGGGCAAATAATCT----AGGCATT 3762
                            i    ----i  v   ?    v        vi  i ----  i    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_83452354_8   3763 TCTC-AAAAAAGACATAAATATGACTGACAGGTATATGAAAAAATGCTCA 3811
                             -   i    i   v v   i ii i i i i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_83452354_8   3812 ACATTCCTAACTAA 3825
                             iv????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (152 / 80)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.21 (45 / 14)  


2839 25.96 1.54 1.65  chrX_83458789_83463121     2932  3840 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83458789_8   2932 TGGAAA-ACATTCTATCCTCATGGATAGGAATAATCAATATTGTGAAAAT 2980
                               - i  i i  vi        v    v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83458789_8   2981 GACCATTCTACCCAAAGTAATTTATAGATACAATGCTATTCCCATCAACC 3030
                          i v  v  v      v i  i  i    v   i  v  i  i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83458789_8   3031 TACCATTGACATTCTTCACAGAAATAGAAAAACT-ACTTTAAATTCCATA 3079
                          v   vivi v  i  ii       v  v  i  - iii    v i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_83458789_8   3080 TGGACCCAAAAAAGAGCTCGTACAGCCAAGAAAATCCTAAGCAAAAAGAA 3129
                             vviiv  ii  v iv v i      i v    i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_83458789_8   3130 CAAAGCTGGAGTCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 3179
                              i     vvv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_83458789_8   3180 CAGTAGCCAAAACAGCACAGTACTAGTACCAAAAGAGACATATAGATCAA 3229
                              ii   i    iiii     i i iv ii v               
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_83458789_8   3230 TGGAACAGAACAGAGACCTCAAAAATAACACCACACATGTACATCCATCT 3279
                              i    iv    vii  i      vv   i    v  iivi  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_83458789_8   3280 GATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTGT 3329
                            i        ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_83458789_8   3330 TTAATAAATGGTGCTGGGATAACTGGCCAGCCATATGCAGAAAACTGAAA 3379
                          i  i              i      vi ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_83458789_8   3380 CTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATATATTAA 3429
                         i    i    v   i     v                   i  iv  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_83458789_8   3430 AGACTTTAATGTAAAACCCAAAACCATAAAAACTCT-AGATGAAAACCTA 3478
                             i v       i v i     i      -    -   v      v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATA 549

  chrX_83458789_8   3479 G---TCAATGCCATTCAAGATATAGGCATGGGAAATGCCTTCAT-GATAA 3524
                          --- v   -- -   iv  iv v  vv i  v    vi   v -    v
  L1M4_orf2#LINE/    550 GGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_83458789_8   3525 AAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGAGATCTA 3574
                         i -           vvv          vv     v  i    vi  ii v
  L1M4_orf2#LINE/    597 GA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_83458789_8   3575 ATTAAACTAAAGAGTTTCTGCACAGCAAAATAAGTTATCATCAGAGTGAA 3624
                           i   v v  i ii  i  ii vv    iv vii     vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_83458789_8   3625 CAGGCAACCTACAGAATGGGAGAACTTTTTTCCAA--TATATCCATCGGA 3672
                         v  i     i              vv v   v   --i    --   v  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chrX_83458789_8   3673 CAAAGGTCTAAATATCCAGAATAATCTACAAGGAACT--TAATCAAATTT 3720
                         i  i  v  vi-           ---  i  i     --  --   v iv
  L1M4_orf2#LINE/    744 TAAGGGACTTG-TATCCAGAATA---TATAAAGAACTCTTA--CAACTCA 787

  chrX_83458789_8   3721 ACAAGAAAATTAAA-AAATAACCCCATCAAAAAGTGGGCAAAGGATATGA 3769
                          i  v    -- i -         v  i?    i            v   
  L1M4_orf2#LINE/    788 ATAATAAAA--AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_83458789_8   3770 ACAAACACTTCTCAAAAGAAGACATTTATGTGGCCAAGAA--ACATGAAA 3817
                          i i   i     v        i  vi vi       v  --        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_83458789_8   3818 AAAAGCTCAGCATCACTGATCAT 3840
                          i v     i     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (128 / 105)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.61 (29 / 18)  


 590 22.44 0.00 0.00  chrX_83468448_83470643.rev      350   505 (1691)  C L1M4_orf2#LINE/L1   (0)   908   753  

C chrX_83468448_8    505 TATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAGAAACAA 456
                          i          v  i  v      vv    v iv i  v   i i    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

C chrX_83468448_8    455 ACAACCCCATCAAAAAGTGAGCGAAGGATATGAACAGACACTTCTCAAAA 406
                          i     v  i?    i  i  i      v    i     i     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

C chrX_83468448_8    405 GAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCACT 356
                              i  vi viii     v  i          i       v     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

C chrX_83468448_8    355 GGCCAT 350
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.43 (20 / 14)
Gap_init rate = 0.00 (0 / 156), avg. gap size = 0.00 (0 / 0)  

2302 28.80 1.73 3.78  chrX_83468448_83470643.rev      780  1706 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83468448_8    780 TAGAAAAATCTTCCACTCTCATGGATAGGGAGACCCAATATCATTAAAAG 829
                          i    i  v i   ivi        v  i    ii     ii    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83468448_8    830 GGGTATGATGTTTAAATAAATTCACAGACTGAATGCTATTCTGATCAAAC 879
                           vv  iv viii    vi  ii     i v  i  v  i iv      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83468448_8    880 TACCAATGGCATTCATCACAGAATTAGAAAAACT-ATTTAAAAATT-ATA 927
                          v   iiv  v  iv ii     v v  v  i  -  iiv      -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_83468448_8    928 TGGAACCAAAATAGAGGCTGAATAACCAAAGGAATTGTAAGCAAAAAAAA 977
                              viiv  vi  vv v     i     iv   iv i ----------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---------- 190

  chrX_83468448_8    978 AAAAAAAAAAAAAAACAAAGCTGGAGGCATCACTTTATGCAACTTCAAAA 1027
                         -----    i  i       i      vv    vi viv   i       
  L1M4_orf2#LINE/    191 -----AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_83468448_8   1028 TATACTACCAGGCTATAGTTACCAAAAACAGCATGCTATTGGTACAAAAA 1077
                         iv      v i    i   v i   i -   ii  v  i   i i  ii 
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGA 284

  chrX_83468448_8   1078 TAGACATATAAACAAATAGAACAGAATAAAAATCCCAGAAATAAAGCTGC 1127
                                   i iv   i   i     vi i vi           v iii
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_83468448_8   1128 ATACCTACAGCCATCTGATCTTCGACAAAGTCAATAGTCAACAAAAACAA 1177
                          i ii  ii i  vi    i        i ------  -iv   i v  v
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGG------GT-GCCAAGACCAT 377

  chrX_83468448_8   1178 GCAATGGAGAGAGGACTCTCTATTTAATAAATGCTACTGGGAAACCTGGT 1227
                         v      i  i  i ivv   v  i  i     v i      v v    v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_83468448_8   1228 TAGCCATATGTGGAACACTGAAACTGGACTCCTTCCTTACACCACACA-A 1276
                           ?   i   iii  v v    ii     i   v   i      i i - 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_83468448_8   1277 AAAATCAACTAAAGATACATTAAAGACTGAAATTTAAAACCTAAAACTAT 1326
                              i    v  i  iv  i ?    iv    v   i v          
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_83468448_8   1327 AAAAACCCTGGAAGATATCCTATGAAGTG--TCATTCTGGATGTAGAGCC 1374
                             vi i i     v v v  - i?  i--  -   vv  iv v i ii
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATA-GGNGTAAATC-TTCGTGACCTTGGGTT 575

  chrX_83468448_8   1375 AGGTAATGATTTC------ATGACAAAAAGGCCAAA-GCAATAGTAACAA 1417
                            i    i    ------      ------     -   vv  i     
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAACAA 619

  chrX_83468448_8   1418 AAACAAAAAATTGATAAATGGGACCTAATTAAACTAAAGAGCTTCTGCAC 1467
                           i-       v       v    i v  i   v v  i i   i  ii 
  L1M4_orf2#LINE/    620 AAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_83468448_8   1468 TGCAAAAGTAACTATCAACAGTGTAAACAGGGAGTCTACACAATCGGGGA 1517
                          v    i vv        v iv  i  v  iv ii i   v   v  i  
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_83468448_8   1518 AGATATTTTCAAACTATGCATCTGACAAACATCTAATGTCCAGATTCTCT 1567
                          i      v    ii  ii      i  iviv  vi i      v v v 
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_83468448_8   1568 AAGGG-CTTT---AAATTAAGAAGCAAAACACAAAACAATCCCATTAAAA 1613
                           i i-  i ---  v i  v  vv    v     -i  i  v   ?   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAA-TAACCCAATTWAAA 817

  chrX_83468448_8   1614 AGTGGGCAAAGGACATGAAACAGACACTTTTCAAAAGAATACAGACACGC 1663
                          i           iv    -i     i  i  v      v i v   vii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAA-TAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_83468448_8   1664 GGCCAACAATCATAGGAAAAAAATGCTCAGTATCTCTAATCAT 1706
                               i  v  i v     i -      ii   v????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (156 / 107)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.68 (51 / 19)  


2677 27.24 2.21 1.99  chrX_83482218_83486879     3267  4169 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_83482218_8   3267 AAAAATACTCCATGTTCATGGA----AAGAATCAATATTGTTAATGTGTA 3312
                            i   ii             ----    v i           vi  vv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_83482218_8   3313 CATAATCCCCAAAGCAAT--AAAGATTCAATGCGATCCCATTCAAAATAC 3360
                         v   v        vii  -- v        i  i     vv       v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_83482218_8   3361 CAATGACATTCCTCACAGAAATTTAAAAAAAAAAATCTAAAATTTGCAAG 3410
                           iivi v  ii ii        -i v  ivvi vi        iii v 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCATATG 152

  chrX_83482218_8   3411 GAACCACAAAAGACCCAGAACAGCCAAATTTATCCTAAGCAAAGAGATTA 3460
                            vii   ii         i       viv   i i iv  ii   vi 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_83482218_8   3461 AAAATGGAGGAATCACATTACCTGACTTCAAATTATACTACAGTGCTATA 3510
                           iv       v     i v  ii i      viv       iv    i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_83482218_8   3511 GTGACTAAAAGAGCATGTTACTGGCATAAGAACAGACACATAAATCAATG 3560
                           i ii  i v  ii  v            i i     i   i       
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_83482218_8   3561 AAACAGAATAGAGAACTCAGATCCAAATCAACACACCTACAGGGAACTCA 3610
                         i  i     v    iii    vvi   i v i   ii  ii vv  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_83482218_8   3611 TTTTTGACAAAGCTTCCAGGAACATACACTGGGAAAAAGACAATATCTTC 3660
                             i     i v v   i  v   v  v    i   ii i i v i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_83482218_8   3661 AATACATGGTGCTGGGAAAACCGGATATGCATATGCAGAAGAATGAAACC 3710
                           i v            v   i     ?v  i     i         iii
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_83482218_8   3711 AGACCCCTATCTCTCACCATAGACAAAAATCAAATCAA---GGATTGAAT 3757
                         i        i   v       v        i  v    ---    ii? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_83482218_8   3758 ACTTAAATTTAAGA-CTGCAAATTATGAAACTACTACTACTACAAAAAAA 3806
                           i     v     -  i-   i   i     vi  -------i  i   
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTA-------GAAGAAA 544

  chrX_83482218_8   3807 AAATTGGGAAAAATCTTCAGGAAATTTGTCTGGGCAAAAATTTCT-GGA- 3854
                          v  v  ?iv        iv  vv  v vi i     vii     -i  -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_83482218_8   3855 GCAATACC----GCACAAGGGGAGGAAACCAATGCAAAAATGGACAAATG 3900
                         iii i   ----       v------   v  v v      i  i    v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGC------AACAAAAGAAAAAATAGATAAATT 638

  chrX_83482218_8   3901 GAATCACATCAAG-TTAAAAACCTTCTGCACAGCAAAGGAAACAATCAAT 3949
                          i iiv      i-        i  -  ii vv       v  v     v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAG 687

  chrX_83482218_8   3950 ACAGTGAAGAGACCACTCAGAGAATGGGAGGAAATATTTGCAAACTACCC 3999
                          v      i    v  i  v          i             ii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_83482218_8   4000 ATCTGGCAAGATATCAATAACCAGAATATATAAGGAGCTCAGACAATTTT 4049
                              ii   iv iivi  v             i  i   vv    i iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_83482218_8   4050 ATAGAAAAAAAATCTAATAATCTGAACAAAAAAATGG-CAAAAGATTTGA 4098
                            iv     i - v     i i-  iv?        -    i       
  L1M4_orf2#LINE/    788 ATAATAAAAAGA-CAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_83482218_8   4099 GTCAGTGTTTCTCAAAAGAAGACATAAAAATGAC--AGAGATATATGAAA 4146
                         i viiii      v        i   v     i -- v iii i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_83482218_8   4147 ATGTGCTCGACATTACTAATCAT 4169
                          vi     i    i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (151 / 91)
Gap_init rate = 0.02 (17 / 905), avg. gap size = 2.24 (38 / 17)  


1444 27.19 0.00 0.00  chrX_83493606_83496889.rev        1   434 (2850)    L1M4_orf2#LINE/L1      475   908 (0)  

  chrX_83493606_8      1 ACAAAAATCAATTCAAGATGGATTAAAGATTTAAACGTTAGACCTAAAAC 50
                                 i  i    i      i ?   ii    i  v   v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_83493606_8     51 CATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCG 100
                         i      vi i           v    ?i v viv   iv   v v  vv
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_83493606_8    101 TGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAAAAGCC 150
                          i     v ii   v ivvi vi            vvi          vv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_83493606_8    151 AAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCATAGCAAA 200
                              v  i    v   ii v  i   v v  i i   i  iiivv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_83493606_8    201 AGAAACTACCATCAGAGTGAACAGGCAACCTACAACGTGGGAGAAAATTT 250
                         i  v    i  vv i      v  i     i   ivi           v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_83493606_8    251 TCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAA 300
                          i    vii ivi      i  i  i  vi          v  i  v   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_83493606_8    301 CTCCAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGC 350
                            iv    v iv i  v     i     i     v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_83493606_8    351 AAAGGACATGAACAGACATTTCTCAAAAGAAGACATTTATGCAGCCAAAA 400
                               iv    i           v        i  vi viii     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_83493606_8    401 AACACATGAAAAAATGGTCATGATCACTGGCCAT 434
                          i          i   v   vv    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (63 / 52)
Gap_init rate = 0.00 (0 / 434), avg. gap size = 0.00 (0 / 0)  

2350 26.87 3.29 3.74  chrX_83493606_83496889.rev     1903  2784 (500)    L1M4_orf2#LINE/L1        1   878 (30)  

  chrX_83493606_8   1903 TAGAAACACATTCCAAGCTCATGGACTGGAAGAATTAATATCATTAAAAT 1952
                          i    v i  i   v i       i       v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83493606_8   1953 GACTATACGGCCCACAGGAATCTACAGATTCAATAAAATATTTATCAAAG 2002
                          i v    vv    v vvi              iiv   vii       i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83493606_8   2003 TACCAATGAAATGTTTTATGGAAATAGAAAAAATAATCCTAAAATTTATA 2052
                          v   iivivv v    iii     v  v  iv i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_83493606_8   2053 TGGAAC--CAAGGAAGAGCCAGAATAGCCAAAGCAATACTGAGTAAAAAG 2100
                              v--     --  v              i    vi   iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_83493606_8   2101 AACAATGCAGGAGGCATCACACTACCAAACGTCAAAATATGCTACAAAGC 2150
                              v iv     vv       v  v  iv      iv i         
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_83493606_8   2151 TGTAGTCACCACAAAAGTATGGTTTTGATATAAAAACGAACACATAGAAC 2200
                          ii   v i  vi v   i    vi  ii    ii iii   i     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_83493606_8   2201 CATAAAACAGAGGAGAGAACATATAAATTAATTCACGTACTTACAGCCAG 2250
                         v  ii  i   ivv    iivi v    v  ii  iii i   ii i  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_83493606_8   2251 ATGATTTTTGACAAAGGTGCCAAGAGCACTCGCTGGGAGAAGAA-AGCCT 2299
                         v       i     i          v  i  iv    ii     -  i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_83493606_8   2300 TCT--ATAAATGGTGATGGAAAAACTGGATATTCACCAGCAGAAGAATGA 2347
                          i -- i        v   i v         ?i   vv   i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_83493606_8   2348 AATTAGACCTCC-TCTCACACAAAAAATAAAAATCAACTACAAATGGATC 2396
                          i  i    i i-i       v v v i      i    vv         
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_83493606_8   2397 AAATACCTAAATGAGAGACCTCAAGCTACAAAGCTACTAGAAAGAAACAT 2446
                          ? v         vi   v  v  i   i   i  vi     ii      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_83493606_8   2447 AGGTAGTGTG---CTTCAGGACATTTTCCCAACAAATAGAACAAACAGCA 2493
                            ?---  i---    iv   v  ------------------------i
  L1M4_orf2#LINE/    549 AGGN---GTAAATCTTCGTGACCTT------------------------G 571

  chrX_83493606_8   2494 GGTCAGGAAAACATTTTATCAATAAGACCTCAAAGGCACAGGCAACAAGA 2543
                            i   v  vvi   iv vi   v   vi    i     i       i 
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_83493606_8   2544 GAAAAAATA----AATCGGATTGTATCAAACT--AAAACGTCTCTGCATA 2587
                                  ----   i   i vi      v --     v i v   v -
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT- 670

  chrX_83493606_8   2588 GCAAAG--CA--AACAACAGAGTTAAAGGTCAACCTAAAGAATGGGA-AA 2632
                         -     --  -- v   v i   v   i v     i v         -  
  L1M4_orf2#LINE/    671 -CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_83493606_8   2633 AATATCTGTGAACTGCTCACCCAACAGCAGATTAAGATCCAGAATATTTT 2682
                              i  ii  iiiivi i ii i ivi  i viv           v v
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_83493606_8   2683 TAAAAACTGCAACATCTCAACAGAAAAAAAATCAAATT-TTTAA---AGA 2728
                         -  i    viv   v     i iv     i -     v-iii  --- i 
  L1M4_orf2#LINE/    770 -AAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAA 817

  chrX_83493606_8   2729 AATAAGTAA----CCTGAAAAGATATTTCTC-AAAGAAGACAAAAAAATG 2773
                            ii i  ----ii    v   i       -        i v v     
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_83493606_8   2774 GCCAACAGGTA 2784
                              i i i 
  L1M4_orf2#LINE/    868 GCCAATAAGCA 878

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.02 (20 / 878), avg. gap size = 3.10 (62 / 20)  


3274 25.70 1.12 0.34  chrX_83519639_83523582     2557  3451 (493)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_83519639_8   2557 GATAGTCCAAGCTCATGAATTAAAGGAATCAATATTTTTAAGGTGTCTAT 2606
                             vi   v i     i   ii i  v i      v     i  v v  
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_83519639_8   2607 ACTATGTAAAGCAATCTATAGATTCAATTCAATCCCCGTCAAAATACCAA 2656
                            vivi   vii     i        iv       ii       v   i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_83519639_8   2657 TGACATTCTTCACAGAAACAGAAAAA--AATCCTAAAATTTATCTGGAAC 2704
                         ivi v  i  ii      iv  v  i--i           i  v     v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_83519639_8   2705 CATAAAAGAACCAGAATATCCAAAGCTATCCAGAGCAAAAAGATCAAAGC 2754
                         iii  ii  v        v     i v   iv  iv  i    v     i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_83519639_8   2755 TGGAGGAATCACATTACCTGACTTCAAATTATACTACAAAGCTGTAGTAA 2804
                                v     i v  ii i      viv            ii     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_83519639_8   2805 CCAAAATAGCATGATACTGGCATAAGAACATACACATAGACAAATGAAAC 2854
                         i   i i  ii  i            i i v   i     iv    i  i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_83519639_8   2855 AGAATGGAGAACCCAGAAACAAATCCATACATCTACAGTGAACTCATGCT 2904
                              v    ii       i   i        i  ii  v  i v  vi 
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_83519639_8   2905 TGACAATATTGCCAAGAACATACGCTAGGAAAAGGACAGCCTTTTCAACA 2954
                         i     viv        v   v iv i  i    i i  i          
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_83519639_8   2955 AATGGTGCTAGGAAAACTGGACATCTATATGGAGAAGAATGAAACTAGAC 3004
                                  i   v       i ? i i   v i         ii i   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_83519639_8   3005 CCCCATCTCTCACTATATA-----ATTAAAAAAAAAAGTATTAAAAAC-- 3047
                            i i   v   i     -----     vvv    v v  i ? i  --
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_83519639_8   3048 AAATCTAAGACCAGAAACTATGAAATTACTAGAAGAAAACTTCGGCAAAA 3097
                             v     v vi       i   i vi           v v  ?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_83519639_8   3098 ATCTCCAGGACACTGCACTTGACAAAGATTTCTTGAGCAATACTCCACAA 3147
                             i iv   vi  vii v i   v i      iiii vv  v   v  
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_83519639_8   3148 GCACAGGAAACCAAAGCAAAAATGGACAAATGGGATCACATCAAG-TTAA 3196
                              i v   v    v      i  i    v   iiv      i-    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_83519639_8   3197 AAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAAGAGACAACAC 3246
                            -   i  ii vv       v  v     v        i       v 
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_83519639_8   3247 ACAGAATGGGAGAAAAATACCTACAAACTACCTGTCTGATAAGGGATTAA 3296
                                         -  ii i    ii iv i            i vi
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_83519639_8   3297 TAATCAGAATACATAAGGAGCTCAAACAACTCTATAAGAAAAAAATCTAA 3346
                           vi       i    i  i   vv       v    v     i - v  
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAA 803

  chrX_83519639_8   3347 CAATCTGATTAAGTAATGGGCAAAATATCTGAACAGACATTTCTCGAAAG 3396
                         i  i ii   ? iv          iv  i    i           v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_83519639_8   3397 AAGAAACACAAATTGCCAACAGGCATATGAAAAGGTTCTCCACATCATTA 3446
                             v i      v     i i   i        i v   v      ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_83519639_8   3447 ATCAT 3451
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.57 (138 / 88)
Gap_init rate = 0.01 (7 / 902), avg. gap size = 1.86 (13 / 7)  


3157 26.79 0.77 0.66  chrX_83616196_83622591     4997  5903 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83616196_8   4997 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5046
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83616196_8   5047 GGCCATACTGCCCAAGGTAATTTATGTATTCAGTGCCATCCCCATCAAGC 5096
                            v     v     iv i  i  iiv     ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83616196_8   5097 TACTATCCACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5144
                          v i v ii i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_83616196_8   5145 CATGGAACCAAAAAGGGCC-AGCATTGCCAAGACAATCCTAACCCAAAAG 5193
                         i      viiv  i  i  -  v  v     i      i i vvv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_83616196_8   5194 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5243
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_83616196_8   5244 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5293
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_83616196_8   5294 AACGGAACAGAGC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5341
                           i    i   ii--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_83616196_8   5342 ATCTGATCTTTGACACACCTGACAAAAACAGGAAATGGGGAAAGGATTCC 5391
                          vi    i  i    vivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_83616196_8   5392 CTATTGAATAGATCGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5441
                           v  v  i i  v         v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_83616196_8   5442 GAAACTGGATCCCTTCCTTACAACTTATACAAAAATTAATTCAAGATGGA 5491
                            ii    i    v   i   v v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_83616196_8   5492 TTAAAGACTTAAATGTTAGAACTAAAACCATAAAAACCCTAGAAGAAAAC 5541
                          i ?    i       v   i       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_83616196_8   5542 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5590
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_83616196_8   5591 AAACACCAAAAGCA-ATGCCAACAAAAGCCAAAATTGACAAATGGGATTT 5639
                         vi            - v  -        vv     v  i    v   i  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_83616196_8   5640 AATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5689
                         v  i   viv  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_83616196_8   5690 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGGC 5739
                          v  i     i                 v       vii ivi     ii
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_83616196_8   5740 AAAGGGCTAGTATCCAGAATCTACAAAGAACTCAAACAAATTTACAGGAA 5789
                           i  i  v           v  i         vv    v iv i iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_83616196_8   5790 CAAAACCAACAACCCCATCAAAAAGTGGGCAAAGGATATGAAGAGAAACT 5839
                         v  i  v  i     v  i?    i            v    v   v i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_83616196_8   5840 TCTCAAAAGAAGACATTTATGCATCCAACAGACACATGAAAAAATGCTCA 5889
                             v        i  vi viiiv    i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_83616196_8   5890 TCATCACTGGCCAT 5903
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2952 28.04 1.68 0.34  chrX_83632400_83638596     4810  5704 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_83632400_8   4810 GGAAGAACATTCTCTGCTCATGGATAGGAAAAATCAATATCATGAAAATG 4859
                             ii i  i iv  i        v    i v i     ii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_83632400_8   4860 ATCATACTGCCCAAAGTAATTGATAGATTCAATGCTATCTCCATCAAGCT 4909
                         iiv     v      v i  iv i        i  v   i i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_83632400_8   4910 ACCATTGACTTTCTTCATAGAATTAGAGAAAACT-ACTTTAAATTTCATA 4958
                         v   vivi i  i  iii    v v  v  i-  - iii    v      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chrX_83632400_8   4959 TGGAACCAAAAAAGAGGTGGTATAGCCAGGACAATCCTAAGCAAAAAGGA 5008
                              viiv  ii  vvii v       ii      i i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_83632400_8   5009 TAAAGCTAGAAGCATCATGCCACCTGACTTCAAACTATACTATAAGGCTA 5058
                         i    i i  i vv   ii iv  ii i      viv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_83632400_8   5059 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 5108
                               i   i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_83632400_8   5109 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5158
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_83632400_8   5159 GATCTTTGACAAACCTGACAAAAACAAGCAATAGGAAAAGGATTCCCTAT 5208
                            i  i     ivv  v   i v  vv    i  i    i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_83632400_8   5209 TTAATAAATGGTGTTGGGA-AA----------ACATGCAGAAAACTGAAA 5247
                          i  i        i     -  ----------       i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_83632400_8   5248 CTGGACCCTTTCCTCACACCTTATA-AAAAATTAATTCAAGATGGATTAA 5296
                         i       i v         v    -         i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_83632400_8   5297 AGACTTAAATGTAAGACCTAAAGCCATAACAATCCTAGAACAAAACCTAG 5346
                             i           v     i i    v v  i     v     v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_83632400_8   5347 GCA-ATACCATTCAGGACATAGGCAAGGGCAAAGTCTTCATGACTAAAAC 5395
                          ?i- v i -   iv   v v  vvvi     v vi   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_83632400_8   5396 CCCAAAAGC-CATGACAACAAAAGCCAACATTGACAAATGGGATCTAATT 5444
                         v        -  v -         vv  v  v  i    v   ii v  i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_83632400_8   5445 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAATAG 5494
                            v v  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_83632400_8   5495 GCAACCTACAGAATGGGAGAAAATTTTTGGAATCTATCCATCTGACAAAG 5544
                         i     i                 v    v  vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_83632400_8   5545 GACTAATATCCAGAATCTACAAAGAACTTAAACAAATTTGCAAGAAAAAA 5594
                             vi          v  i        ivv    v ivii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_83632400_8   5595 ACAAACAACCCCATCAAAAAATGGGTGAAGGATATGAACAGACACTTCTC 5644
                              i     v  i?         ii      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_83632400_8   5645 AAAAGAAGACACTTATGTGGCCAACAAACATATGAAAAAAAGCTCATTAT 5694
                         v        i ivi vi       i  i  i       i v     vi  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_83632400_8   5695 CACTGACATT 5704
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.56 (151 / 97)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 2.00 (18 / 9)  


2079 28.50 1.26 0.63  chrX_83639434_83643524.rev      480  1114 (2977)    L1M4_orf2#LINE/L1      119   757 (151)  

  chrX_83639434_8    480 CAGAAAT-GAAAAATAGAATTTAAAAATTGATATAAAAACATGACAGACC 528
                                -  v  iiv  vii     -  v    ii   iiii vi    
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAA-TTCATATGGAAATGCAAGGGACC 167

  chrX_83639434_8    529 CAGAAAAGCCAAAGTGATCTTTAGCAAAAGGAGCAAAACTTGAAACATCA 578
                              v       iii     v iv  i i  i    ii v  iivv   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_83639434_8    579 CACTTTTTGAGTTATAAATGTATTACAAATTTAAAGTAATTAAAACTGTC 628
                              iiii v  vv   iv  i      vi  v      i  i  v  v
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_83639434_8    629 TGATAACAGCATAAAGACAGACATACAAACCAATGAAACAGAACAGAAAG 678
                           i  vii      i  i       i i i     i  i    iv  i  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_83639434_8    679 CCCCCAAGTAAACCCAAGTGTATACAGTCGATTGATCTTCTATGAGGTTG 728
                         i  vv  i        viii v  ii   i      i   v ii   v  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_83639434_8    729 CCAAGAGTGCACAATTGGGAAAGGATGATCTCTTCAACAAATGGGACATG 778
                               viiiv    v       i  ii   i            vi vv 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_83639434_8    779 AACAACTGGTTATTCACAAGCAAAATAATGAAATTGGTCCATTATTGTAC 828
                         i        v  ?i    v      v      i    v  vi  iivi  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_83639434_8    829 ATTATGCACAAAAATCAACTCAAAATGGATTAAAAACCTAAATATA-GCC 877
                          ii  ii        i              i ? i        i  - vv
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_83639434_8    878 CTGAAACTGTAAAACTTCTAGGATAAAATGTAGGGAAAAGTCTTCTCAGC 927
                           i     i       ii   i v    ii    ?iv  i     viii 
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_83639434_8    928 ATTGATCTTGGCAACAATTT-TTGGTTATGACATTAAAAGCATATGCAAC 976
                         v   ivi v     iii   -  i v       ii       i v     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_83639434_8    977 AAAAACAAAAACAGACAAGTGGGATTACATCAAACTAAAAAGCTTTCACA 1026
                             iv     i   i  i v   i v       v v    i    iiii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_83639434_8   1027 GAGCAAAGGCAACATT--CAACAGAGTGAAAAGTTAAGCCACAGAATGTG 1074
                         vvv      --   i --   v i         vi  v          v 
  L1M4_orf2#LINE/    668 CTTCAAAGG--ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_83639434_8   1075 A-AAAATGTTT-TAAATCTATGTATCTCATA-GGCATTTGTAT 1114
                          -     i   -i     -  i     v   -  v i      
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATC-ATATATCTGATAAGGGACTTGTAT 757

Transitions / transversions = 1.83 (115 / 63)
Gap_init rate = 0.02 (10 / 639), avg. gap size = 1.20 (12 / 10)  

 647 19.23 0.00 1.28  chrX_83639434_83643524.rev     3445  3600 (491)    L1M4_orf2#LINE/L1      755   908 (0)  

  chrX_83639434_8   3445 TATCCAAAATATATAAGAAACTCCAAGAATTCAGTGTTTTAAAGACCCGA 3494
                               i         ii     iv v  i   i iv vv      --i 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC--AA 802

  chrX_83639434_8   3495 ATAACCCAATTTAAAAATGGACAAAGGACTAGAATAGACATTTTTAAAAA 3544
                                    ?        i       i v            i vv   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_83639434_8   3545 TAAGACATACAAATGGCCATCAGATATATTAAAAGTTGCTCAACATCATT 3594
                         v    i             vi iii i  v     v            ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_83639434_8   3595 AACCAT 3600
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.42 (17 / 12)
Gap_init rate = 0.01 (1 / 154), avg. gap size = 2.00 (2 / 1)  


2574 26.00 2.28 3.90  chrX_83652726_83658589     4449  5371 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83652726_8   4449 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4498
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83652726_8   4499 GGACATACTGCTCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4548
                           vv     v i    v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83652726_8   4549 TACCATTGACTTTCTTCACAGAATTAGAAAAAAAACT-ATTTTATAACTC 4597
                          v   vivi i  i  ii     v v  v  i---  -  ii  v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_83652726_8   4598 ATAT---AACCCAAAAAGAGCACATATAGCCAATACAATCCTAAGCAA-A 4643
                             ---  iv   iiiivv  v -        v      i i iv  - 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGA-ATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_83652726_8   4644 ACAACAAAGCTGTAGGCATCATGCTACCTAACTTCAAACTACACTACAAG 4693
                          v       i  v   vv   ii  v  i  i      vivi       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_83652726_8   4694 GCTACAGTAACCAAAACAGCATATGACTGGTACAAAAACTGACACATAAA 4743
                                   i   i    ii ivv     i i  ii iv    i   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_83652726_8   4744 CCAATGGAACAGAATTGAAAACTCAGAAATGGGACCACACATATAAAAAC 4793
                         i        i        i iii       iiiv   i    v  viiv 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_83652726_8   4794 ATTTGATCTTTGACAAACCTGACAAAAACAAGCAATGGTGAAATGATTTC 4843
                          v     i  i     ivv  v   i v  vv      v    vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_83652726_8   4844 CTATTTAATAAATGGTGCTGGGAGCACTGGCTAGAAATATGCAGAAAATT 4893
                           v  i  i              vv     v  ?vv i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_83652726_8   4894 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGG 4943
                            ii         v   i     v                   i    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_83652726_8   4944 TTGAAGAATTAAATGTAAAACCTAAAACTATAAAAACCCTAGAGGGAAAT 4993
                          ii?   vi         i v              vi i    i i   i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_83652726_8   4994 ATAGGC---AATGCCATTCAGGATATGGGCACAGGCAGAGATTT--TACG 5038
                              ?---   -- -   iv  iv v  vvi     iv i   --  - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-G 592

  chrX_83652726_8   5039 ACGAAAACGTCAAAAGCATCTGCAACAAAAGCAAAAAAT-GACAAATGAA 5087
                          i- vi  ii        ivv          -       -  i    vii
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGG 640

  chrX_83652726_8   5088 ATCT------AATTAAAGAGCTTCAGCACATCAAAAGAAACTACCATTGG 5131
                          ii ------       i -   iv ii v     i  v    i  ----
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA---- 685

  chrX_83652726_8   5132 ATGCAAACAGAAACTATCTTTAGATGCAAACAACCTAGAGAATGGGAAAA 5181
                         --------     v i----- i --- i      i v         i  
  L1M4_orf2#LINE/    686 --------AGAAAGTG-----AAA---AGACAACCCACAGAATGGGAGAA 719

  chrX_83652726_8   5182 AAT---TATAATCTATCTATCTGACAAAAGTCTAATATCCAGAACTTA-A 5227
                            --- ii  vii  v       i  ii v  vi         iv  - 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_83652726_8   5228 AGGAACTTAAAGAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAG 5277
                          i     ivv v  v iv i  v     i     i     v  i?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_83652726_8   5278 TGAGCAAAGGACATGAACAGACACTTTTCTGAAAAGAAGACATTTATGTG 5327
                           i        iv    i     i  i  i--        i  vi vi  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCC--AAAGAAGATATACAAATG 867

  chrX_83652726_8   5328 GCCAAGAAACATATGAAAAAAAAAAGCTCAACATCACTGATCAT 5371
                              v  i  i       i v---           ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGAT---GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (145 / 91)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.59 (57 / 22)  


 716 24.92 4.65 4.32  chrX_83662466_83668436.rev        5   305 (5666)    L1M4_orf2#LINE/L1      521   822 (86)  

  chrX_83662466_8      5 AAATTATAGAAATTCTAGAAGACAATGTAGA---AAATATCCTTCTTGAT 51
                            i    i  v ii       v  ii   i---    ---    v   i
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGAC 567

  chrX_83662466_8     52 ACTTGCCTT-GGCAAATAATTT-TTGGCTGAGTCCTCAAAAGTAATTGCA 99
                         -    vv  -     - ii   -  i v iv v vi      i vvv   
  L1M4_orf2#LINE/    568 -CTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_83662466_8    100 ACAAGAACGAAAATTGAGAAGTGGGACCTAATTATA-CTAAGGAGTTT-- 146
                             i ivi     v  v  i v    i v  i v -i   ii v   --
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_83662466_8    147 --CTTCACAGAAAGAGGA-ACTATCAAAAGAGAAAAGAGACCACCTATAG 193
                         --     ------i    -        i i  vi  i    v   i i  
  L1M4_orf2#LINE/    666 TGCTTCA------AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_83662466_8    194 AATGTGAAAAAATATTCACAAACTATTCATCTGACAAAGATCTAATATCC 243
                             v  i        ii    ii  vi      i  i iv  vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_83662466_8    244 AGAATCTATAAAGAACT--TAAAAATTTCCACAA-ACAAAAACAAATAAC 290
                              v           --  v  --i  v i  - v   i         
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAA--CTCAATAATAAAAAGACAAATAAC 807

  chrX_83662466_8    291 CCTATTAAAAAGTGG 305
                           v   ?    i   
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGG 822

Transitions / transversions = 1.47 (44 / 30)
Gap_init rate = 0.04 (13 / 302), avg. gap size = 2.08 (27 / 13)  

3257 27.20 0.44 0.44  chrX_83662466_83668436.rev     1342  2249 (3722)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83662466_8   1342 TGGAAGGACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1391
                              i  i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83662466_8   1392 GGTCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1441
                           iv     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83662466_8   1442 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1489
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_83662466_8   1490 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 1539
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_83662466_8   1540 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1589
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_83662466_8   1590 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1639
                           i     i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_83662466_8   1640 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 1687
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_83662466_8   1688 ATCTGATCTTTGACAAACCTGAGAATAACAAGCAATGGGGAAAGGATTCC 1737
                          vi    i  i     ivv  vv  v v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_83662466_8   1738 CTATCTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTT 1787
                           v ii  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_83662466_8   1788 GAAACTGGATCCTTTCCTTATACCTTACACAAAAATGAATTCAAGATGGA 1837
                            ii    i  i v   i i   v  i        v  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_83662466_8   1838 TTAAAGACTTAAACGTCAGACCTAAAACCATAAAAACCCTAGAAGAGCAC 1887
                          i ?    i    i  v   v       i      vi i       iv  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_83662466_8   1888 CTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1937
                         v    ?v v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_83662466_8   1938 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1987
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_83662466_8   1988 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2037
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_83662466_8   2038 AGGCAACCTACAAAATAGGAGAAAATTTTTGCAACCTACTCATCTGACAA 2087
                           i     i   i   i         v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_83662466_8   2088 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAGA 2137
                         i  i  vi          v  i  v      vv    v iv i  v  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_83662466_8   2138 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 2187
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_83662466_8   2188 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 2237
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_83662466_8   2238 ATCACTGGCCAT 2249
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

2634 27.23 3.39 0.79  chrX_83662466_83668436.rev     4596  5480 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83662466_8   4596 TGGAACAATATTCTATGTTTATGGGTTGGAAAAGTCAATATTGTTAA-AT 4644
                              vi    i i     i    i      i v i           -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83662466_8   4645 ATCCATACTACCCAAAGCAATCTAAAGATTCAATGCAATCTCTACAAAGA 4694
                         iv v     v      vii     v        i      i   iv  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83662466_8   4695 TACCAATGACGTTCTTTCACAGAAATAAAAAAAAAAATC-TAAAATTTAT 4743
                          v   iivi v  i   -i       vi v  ivvi   -       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_83662466_8   4744 ATGGAACAACAAAAGATCCAAAAACAGCCATAGTTATCCT---AAGCAAA 4790
                               vvi   ii  i   i  -i     v iiv   i ---  iv  i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAA-TAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_83662466_8   4791 AATAA------------CATATTACCTGACTTTACATTATACTATAGAGC 4828
                           i  ------------  i i v  ii i  i v viv     i i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_83662466_8   4829 TATAGTAACCAAAACAGCATGGTACTGACATAAAAACATACACATAGA-C 4877
                           i     i   i    ii        i     ii i v   i     - 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_83662466_8   4878 AATGAAACAGAATAGAGGATCCAGAAATAAATACACACACCTACAGTAAA 4927
                             i  i     v   ii            iv  i   ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_83662466_8   4928 TTTATTTTTGACAAAAGTTCTAAGAACATACACTAGGTAAAAGATAATTT 4977
                           v     i     ii  v i    v   v  v i  v   ii   i i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_83662466_8   4978 CTTCAATAAATGGTGGTGAAAAAAACTGGATATTCATATGAAGCAGAAAG 5027
                         i     i        v  ii v  -       ?i  i   v iv    v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATG 447

  chrX_83662466_8   5028 AATATTGACCCCTATCT-ATAGTCATATATAAAAGTCAAATCAAAGTCAA 5076
                           vv v        i  - i -i      i    i i  v     i vi 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACA-CCATATACAAAAATTAACTCAAAATGGA 496

  chrX_83662466_8   5077 TTAAATAATTAAATCTAACACCTCAAACTATGAAACTGCTATTAGACTAT 5126
                          i ? v vi     v   v v  v       i     vi  vv   vv i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_83662466_8   5127 TTTGG-GTAAACTCTCTAGGACATTGGTCTGGGTAAAAATTTCTTGAGTA 5175
                         v v  -     -   iiiv   v    vi i  i  vii      iii  
  L1M4_orf2#LINE/    547 ATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_83662466_8   5176 ATACCCCACAAGCACAGGCAA----AGTGAAAATGG-TCAACTGAAATCA 5220
                         vv  v   v       i    ----  vi     i - v  i  i v i-
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT- 644

  chrX_83662466_8   5221 CATCAAGGTAAAAAGATTCTGCACAGCAAAGGAAACAATAAAGA---T-A 5266
                               ii v    iv  i  ii vv       v  v  v    --- - 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_83662466_8   5267 AGAGACAACATACAGAATGGAAGAAGATATTTGCAAACTATCTATCTGAG 5316
                          i       vi         i    i           ii  v       v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_83662466_8   5317 AAGGGATTAATAAACAGAATGTATAAAAAGCTCAAACAACTGTATAGGAA 5366
                               i vi  vv      i      i i   vv      vv   iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_83662466_8   5367 AAA-ATGGAAAACTTTGATTATAAAATGGGCAAAAGACTTTAATAGATAT 5415
                            - iii v   ii-i   ?v            i  i  v      i  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCC-AATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_83662466_8   5416 TTCTCAAAAGAGGACATACAAATGGAAAACAGGCATATGTAATGGTGCTC 5465
                              v     i  i          vv  i i   i   v  v i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_83662466_8   5466 AGCATCATTGATCAT 5480
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.95 (37 / 19)  


1846 24.96 7.13 2.02  chrX_83681972_83683608.rev      502  1146 (491)    L1M4_orf2#LINE/L1      231   908 (0)  

  chrX_83681972_8    502 CAAAACATTTACTATAAATCCACAGTAGTCAAGAAGGTGTGGTATAAGTG 551
                               --      i   v i      i      vi        ivi ii
  L1M4_orf2#LINE/    231 CAAAAC--TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_83681972_8    552 AAAGAATAAACCAGTCTATCAATGGAACAGAATAGAAGGATCAGAA-TAC 600
                         v   i   i  vvi vv          i     v  ii vi     -  v
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_83681972_8    601 ACACACACA---A-AATCAATAAAAGTATTTTTGAAAAAAGAACAAAGAC 646
                           v  i   --- -ii     vi ----    i  v  ii vi v     
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGA----TTTTCGACAAGGGTGCCAAGAC 374

  chrX_83681972_8    647 AATTCAATGAAGAATTGATAGTCTTTTCAACAAATGGTGCTGGAACAACC 696
                         v        ii   vvi                          i     i
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_83681972_8    697 GGACATTCACATGCAAAA--ATTAATCTAGACCCTGACCTTAGGCCTTTC 744
                            i ?i           --  v  vi i     iv    i vi  v vi
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_83681972_8    745 ATAAAAGCTAACCTAAAATGGATCAGAGACCTAAATGTAAA--TCAAAAT 792
                          i    ii    ii           ?              i--ii    i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_83681972_8    793 TATAAAACCTTTAGAAGATAACA---GAGCAATATCTAGCTGACTTTGAG 839
                                 ii        v    --- ? i  -    vvv    i   i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGG 573

  chrX_83681972_8    840 TTTAATCATAAGTTTTTTAGTTACAACACCAAATACATAATCACTGAAAG 889
                           viiiv  i-    i    v  ii        vi  i  v  vii    
  L1M4_orf2#LINE/    574 TTAGGCAATG-GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_83681972_8    890 AAGAATT-GATAAATT----TTCCATGTATTAAAAT-AAAAACCTCTTTT 933
                           i  v -        ----   -----  i     -      i i v v
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTC-----ATCAAAATTAAAAACTTTTGTG 667

  chrX_83681972_8    934 CTGAGAAATATAATGTTAAGGTAATAAAAAGACAAGCCACAGACTGGGAG 983
                           vvi  iv i v i i   iv i i         v       v      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_83681972_8    984 AAAATATTTCCAAA--ACGCATCTGATA---------------------- 1009
                                  v    -- iii        ----------------------
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_83681972_8   1010 CAAAGAGCTCTCAAAATTCAACAATAAGAGAAGAAACAACCCAATTTTAA 1059
                         i     i    i v  i    i     i ii v   i         ?v  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_83681972_8   1060 AATGAACAAAATATTGGAGCAGATACCTCAGTAAA-ACCATAAATAAATG 1108
                             ii    iv   v  ii   i ii  vvi   - vv   v i     
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_83681972_8   1109 GCAAATAAACTTATGA---GATGCTCAATATTATACATAAT 1146
                           v     i vi    ---         i  i ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (99 / 58)
Gap_init rate = 0.03 (18 / 678), avg. gap size = 3.28 (59 / 18)  


2607 28.16 1.66 1.22  chrX_83685339_83689575.rev     2845  3746 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_83685339_8   2845 GAAAAGCATTACATGCTCATTGATGGGTAGAATCAATACTGTGAAAATGA 2894
                             iii  iv    i    v   v  v   v i    i   v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_83685339_8   2895 CCACACTGCCTGAAGCAATCTACAAATTCAACACTATTCCCATCAAAATA 2944
                          v i   v  ii  vii       i       i v  i  i        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_83685339_8   2945 CCA-TTATCATTCTTCACGGAACTAGAAAAAACAATTCTAAAATTCATAT 2993
                            -i ii -  i  ii i   v v  v  ivii  i             
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_83685339_8   2994 GGAACCAAAGAAAAGCCTGCATAGCGAAAGCAATATTAAGCAAAAAGAAT 3043
                             viiv iiii v  v v     v   i    v  i iv  i     i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_83685339_8   3044 AAATCTGGAGCCATCGCATTACCTAACTTCAAACCATACTGCAAGGCTAC 3093
                            vi     vvv  i  i v  i  i      v v    i   i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_83685339_8   3094 AGTTACCAAAGCAGCATGGTGCTGATATAAAAATAGGCCT-TAGACCAAT 3142
                            v i   ii   ii    i   ii    ii    i v -    i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_83685339_8   3143 GGAACTGAATAGAAAACACAGAAATAAAGCCAAA----TAGAGTCAACTG 3188
                             iv    v  i iiv          v   v ----  vi     i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_83685339_8   3189 ATCTTTAACAAGGCATACAAAAAC-ATAAAGTGGGGAAAGGACACCTTAT 3237
                           i  ii      -i i v  i  -  vv i         i i vii v 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_83685339_8   3238 TCAACAAATGGTGCTGAGATAATTGGCAAGCCACATAGAGTAGAATGAAA 3287
                                         i  i  i   vv ?      iv iv        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_83685339_8   3288 CTGGTTCCTTATCTCTCACCTTATATAAAAATCAACTCAAGGTGAATGGA 3337
                         i   vi  i  i   v    v    i      i       ii  i  vi?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_83685339_8   3338 AGTCTTAAATCTAAGACCCAAAACCATAAAAATTCTACAAGATAATATTG 3387
                           v i     v     v i     i      v ii  v    v  i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_83685339_8   3388 AAAAAACTCTTC-TGGCCATTGGCTTAC-CAAAGAATTCATGACCAAGTA 3435
                         i?iv  v     -  i  -    v   v-   v iv   v iivi v - 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATG-A 598

  chrX_83685339_8   3436 C-CCAAAAGCACATGCAACAAAAATAAAAATAAATAAATAGGACCTAATT 3484
                          -           v         iv       i      v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_83685339_8   3485 AAAATAAAAAGCTTCTGCATGGCAAAAGAAATAATCAGCAGAGTAAACAG 3534
                              v    i   i  iiivv    i  v iv    iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_83685339_8   3535 ACAACCTACTGAATGCATGAAAATATTAAAAAACCATGAATCCAACAAAG 3584
                               i  v     viv         viv   i   iv   ii i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_83685339_8   3585 GCCAAATATTTAGAATCTAAAAGGAACTCAAATCAGCTAGAAAACAACAA 3634
                          v vvi   ii     v  v  i      vv -  i  ------   i  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTA-CAACT------CAATAA 791

  chrX_83685339_8   3635 CAACAGCAAAAACAATCTCATC-GTAAATGGGTAAAAGACATGAATGGAT 3683
                         i  v iv v   i  i iv  i-iv       i   i  iv     i  i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_83685339_8   3684 AATTCTCAAAAGAAGATACGCAAATGGCAAACAAACA----AAAAAATGC 3729
                          v     v          ii        v  i  i  ----    i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_83685339_8   3730 TCAACATCACTGATTAT 3746
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (151 / 100)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 1.73 (26 / 15)  


2726 27.27 1.55 0.89  chrX_83696309_83701902     4200  5101 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83696309_8   4200 TGAAAACACACCTCATACTCATGAATAGGTAGAATCAATATTGTGAAAAT 4249
                           i   v i i i   ii     i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83696309_8   4250 GACCATACTGCCAAAAGCAATCTACAAATTCAACACAATCTCCATCAAAA 4299
                          i v     v  v   vii       i       i     i i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83696309_8   4300 TACCATCATCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTC 4349
                          v   v --iii -  i  ii     v v  v  ivii            
  L1M4_orf2#LINE/    101 TCCCAGC--TGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_83696309_8   4350 ATATGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAA 4399
                                 viiv  ii  v  v v         i   vvi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_83696309_8   4400 TAACAAATCTGTAGGCATCAGATCACCTGATTTCAAACTATACTACAAGG 4449
                         v      vi  v   vv   v iiv  ii        viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_83696309_8   4450 CTATAGTCACCAAAACATCATGGTACTGGTATAATAAAAGGCGCATAGAC 4499
                            i   v i   i   vii         i    vi v  i ii     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_83696309_8   4500 CAATTGAACAGAATAGAGAACACAGAAATAAAGCCAAATACTTACAGCCA 4549
                             v   i     v    iiv          v   v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_83696309_8   4550 ACTGATCTTTGACAAGGCAAACAAAAATATAAAATGAAATAAAAGACTA- 4598
                          i    i  i       vviv   i vi  vv    iii--     v  -
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAAGAATAG 395

  chrX_83696309_8   4599 -TTATTCAACAAATGGCGCTGGGATAATTGGCAAGCCACATGTAGAAGAA 4647
                         -i v            i       i  i   vv ?       i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_83696309_8   4648 TGAAACTGGATCCTGATCTCTCATCTATTATACAAAAATCAACTCAAAAT 4697
                             ii    i  iv i   v  i -  -          i          
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACC-AT-ATACAAAAATTAACTCAAAAT 493

  chrX_83696309_8   4698 GGATCAAAGACTTAAATACAAGACCTCAAAGCATAAAGATTCTGGAAGGC 4747
                               ?    i     ii    v  v   vi     iv ii i    iv
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_83696309_8   4748 AACATCAGAAAAACTCTTCTAGACATTGGCTTAGGCAAAGACTTCATGAC 4797
                              vi ?iv  v     vv   v    v        v ii   v iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_83696309_8   4798 CAAGAACCCGAAAACAAATGCAACGAAAACAAAGATAAATACAGGGGACT 4847
                         i v  vv  i   i  v v     i   iv   i   i   v vv     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_83696309_8   4848 T------AATTAAAAACCTTCTGCAACACAAAAGAAATAATTAGCGGAGT 4891
                          ------          i  -  iiviv    i  v iv  i ivii   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_83696309_8   4892 -AACAGACAACCCACATAGAGTGAGAAAATCTTCACAAACTACACATTTG 4940
                         -  v            v iv v        v  ii    ii i i  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_83696309_8   4941 ACAAAGAACTAATATCCAGAATCTACAAAGAACTCAAAGAAATCAGCAAG 4990
                          i  i i   vi          v  i         vv v  v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_83696309_8   4991 AAAAA---AAATAATGTCATCAAAAAGTGGGCAAAGGACATGAGTAGACA 5037
                              ---      iviv  i?    i           iv   i      
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_83696309_8   5038 ATTTTGAAAAGAAAATATACAAAGGGCCAACAA--ACATAAAAAAATGCT 5085
                         v  i vv      i         v      i  --    i    i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_83696309_8   5086 AAACATCACTAATTAT 5101
                         v       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (140 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


2970 26.51 2.46 0.89  chrX_83711585_83716110.rev     3142  4035 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83711585_8   3142 TGAAACAATATTCCATGTTCATAGATTGGTATAATCAACATTGTTAAAAT 3191
                           i  vi    i          i      v v v i  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83711585_8   3192 GTCTGTACTATGCACAGCATTCTACAGATTCAATAC-----CTATGAAAA 3236
                          v vi    viv  v viiv             ii -----    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83711585_8   3237 TACCAATATCATTCTTTACAGAAATAGAAAA---AACTCTAAAATTTACA 3283
                          v   iivv v  i   i       v  v  ---i ii        i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_83711585_8   3284 TGGAACCACGAAAGTCCCAGAATAGCTAAAGCTATACTAAGCAA-AAGAA 3332
                              vii i ii v           i   i v  vi i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_83711585_8   3333 CAAAATAGGAGTAATCACATTACCTGACTTCATATTATACTATGGCGCTA 3382
                             i v    v v     i v  ii i    v viv     iiiv    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_83711585_8   3383 TAGTAATCAAAATGGCATGGTACTGGCGTAAAAACAGACACATAGACCAA 3432
                         i         i ii ii          i   ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_83711585_8   3433 TAGAATAGAA------ACCCAGAAACAAATCCACACACCTACAGAGAACT 3476
                          i        ------ii       i   i   i   ii  ii vv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_83711585_8   3477 CATTTTCGACAAAGGTACCAAGAACATACACTGAGGAAGCTATAGTCTTT 3526
                         v           i   i      v   v  v  i    ivv         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_83711585_8   3527 TCAGTATATGGTGCTGAGAAACCTGGATATCCATATGCCAAAGAATAAAA 3576
                            ii v         i  v v       ?   i    v       i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_83711585_8   3577 CTAGACTCCTATCTTTTGCCATACACATAAATCAAATCAAAATGGATTAA 3626
                         i i   i    i  ivii     i   v    i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_83711585_8   3627 AGACTTAAATCTAAGACTTAATACTATAAAATTGCTAATAGGAAACATTG 3676
                             i     v     vi   v         i vi  iv  i      v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_83711585_8   3677 GGAAAACTCTCCAAAACATTGGTCTGGGCAA-AATTTCTCGAGTAATACT 3725
                          ?iv  v   i ivi  v    vi i     -ii     iiii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_83711585_8   3726 CCACAAGCATAGGCAAGCAAAGAAAAAAAAATGGACTAATGGTATCACAT 3775
                            v     i i    -    -- i       i  iv   v v iiv   
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAA-CAAA--AGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_83711585_8   3776 CAA-GTTAAAAAGCTTCTTCACAGCAAAAAATGCAATTAACAAAGAGAAG 3824
                            -i       -   i vii vv    ii ii v  i  v    v   i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_83711585_8   3825 AAACAACCCATAGAATGAAAGAAAAATATTTGCAAACTACCCATCAGACA 3874
                          i        i      ii      -          ii ivi   v  i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATA 745

  chrX_83711585_8   3875 AG--ACTTTAATAACCAGAATATATAAGGATCTCAAACAATTCTGTAAGA 3922
                           --    --i  v             i  v   vv    i  vi   v 
  L1M4_orf2#LINE/    746 AGGGACTT--GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_83711585_8   3923 AAATATCTAATAATCCAATCAAATCATGGGCTAAAGATTTGAATAGGCAT 3972
                            viv v     i     i?  vv      v  i           i   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_83711585_8   3973 TTCTTATAAGAAGACATATAAATG---AAAAAGTCATATGAAAAGCTACT 4019
                             ivv       i   i     ---  v   -  i        v i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCT 892

  chrX_83711585_8   4020 CAATGTCATTGATCAT 4035
                            ii   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (144 / 89)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


2500 28.70 4.21 0.80  chrX_83724823_83728375.rev      613  1490 (2063)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83724823_8    613 TAAAAAGATATCCTGTGCCCTTGAATAGAGATAAATATTATCGTTAAAAT 662
                          ii          ii  ii v  i  v ii v vv  v   i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83724823_8    663 GTACCAATGA--CCCAAAGTGATGTACAGACTCAATGCAATCTCTATCAA 710
                          v--    iv--      v    v      i    i      i       
  L1M4_orf2#LINE/     51 GG--CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_83724823_8    711 AATATCAATAACATTCATCAAAGAAATAGCAAAAAAC--ATTCTACAATT 758
                            vi  iivi v  iv iiv      v -- v  i --  i   v    
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_83724823_8    759 CATTTAGAACCACAAAATACTTTCAATAGCCAAAGCAAT--TAAGCAAAA 806
                            v i   vii   iiv  iivv          i    -- i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_83724823_8    807 ATTATGAAGCTATAAGCATAACACTACCTAACTTCAAAATATACTACAAA 856
                          vv ii   i iv i vv v     v  i  i       iv         
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_83724823_8    857 G------TAACCAAAGCAGCATGCCACAGGCATAAAGCCAAACACATGGA 900
                          ------   i   ii   ii  vi  v       i vi i   i  i  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_83724823_8    901 TAAACTGAACA---------------AAATAATTCCATGCATCTGCATCC 935
                          v  iv   i ---------------      vi    i   i iiivi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_83724823_8    936 AACTGATTCTCAGTAAAGATGCCAGAAGCACACACTGGGGAAAGGGCAGT 985
                           i     i  iii  i i     ii v  iv  v         iii   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_83724823_8    986 TTCTTCAGTAAATGGTGCTGGGAAAACTGAATATTCACACACACGAAAAT 1035
                         i i    ii              v     i   ?i    ii  vi i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_83724823_8   1036 GAAATTGGAACATTATCTTGAACGACAAACAAAAAGCAACCCCAAATGGA 1085
                            i     v vi  i  iiv  v i v       vi   i v       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_83724823_8   1086 TTAAAGACTTAAATGAAAGACCCAGAACTGTGAACTTAATAGAAGGAAAC 1135
                          i ?    i      v    v i i    i i  vi vv      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_83724823_8   1136 -TGAGGGCAAATGCTTCATGATGTTAGTGTGGTCAAGGATATTTTGGATA 1184
                         - ii ? i    -    i   iv  i vv i v   v i v i  i    
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_83724823_8   1185 AGATATCAAAAGCACAGGCAACAAAGGCAAACATGAGACAAATGGGATTA 1234
                         v  i i          i        i v   v  -   i    v   i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAATTGGACTT 644

  chrX_83724823_8   1235 CATCAAA-TTAAGAAACTAATCCACAGCAAAGGAAACAATGGAGAAA--- 1280
                                -    -     vv vii vv       v  v  vi     ---
  L1M4_orf2#LINE/    645 CATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_83724823_8   1281 -AGAGACAACCTACATAATGGGAGAAAATATTTGGAAGCTATACATCTGA 1329
                         - i        i   v                  v  iii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_83724823_8   1330 CAATATGTTAATATCCAGAATACACGAGGAACTCCAAGAACACAACAGCA 1379
                         i  vivii vi           i ii i      iv v   v   i ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_83724823_8   1380 AAAA-ACAAACAACCCTACT-AAAAATGGGCACAAATTCTGAA--GATGT 1425
                             -     i     v i -           v iiv i    --  ii 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_83724823_8   1426 TTTTCAAAGGAAGACATGCAAATGACCATCAGGTGCATGAAAACATGCTT 1475
                           i  v  i     i  i      i   vi i ii        v     i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_83724823_8   1476 TATGTCACTAATTAT 1490
                         v ii   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (159 / 90)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.75 (44 / 16)  

2575 21.97 5.26 1.89  chrX_83724823_83728375.rev     2321  3062 (491)    L1M4_orf2#LINE/L1      142   908 (0)  

  chrX_83724823_8   2321 AAACTCATAAGGAAATGTAAGAGGCTTGAAATAGTCTAAAACGATATTTA 2370
                            i     v       i   i i iiii     i -     i  v  v 
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCC-AAAACAATCTTGA 190

  chrX_83724823_8   2371 AAAATAACAAATTTGAAGGCCTCAGGGGACTCATACTCCATGGTTTAAAA 2420
                             v  v  ---ii   --- ii i       i   i viii   v   
  L1M4_orf2#LINE/    191 AAAAGAAGAA---CAAAG---TTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_83724823_8   2421 ATTTATTGCAAAGCTAGGATAATCAAGTCAGCATATCACTATAATAAGAA 2470
                          i   i i        vii        v   ii ivi   ivv     i 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_83724823_8   2471 AAGACAAATGGATCACTGGAA--GAATTGAGTGTCCAGAAGTAAACCCTT 2518
                         v     v  i     v     --        v        i       v 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_83724823_8   2519 TGAAAATATATCATTAATAGGTTTTCAACAAGGGTGCTCATACATTTCAA 2568
                         --- v  v   vi i   v i     i          iv v  vv     
  L1M4_orf2#LINE/    335 ---ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_83724823_8   2569 AAAGGAAATAAT-GTTTTTTCAGTAAATGGTGCTGGGACAATTA-ATATC 2616
                         vii     v   -  i      ii                 i i-   ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_83724823_8   2617 ATCATGCAAAAGCATAAATTTGAAAAATTGTCTCTCACTAT-TACAAAAA 2665
                         vv          v  i  v   i vvvi ii   v   i  -        
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_83724823_8   2666 TTAACTCAAAATAGATGGTAGAGTTAA-TGAAAGAGCTAAGACTATAAAT 2714
                                     i   vi?   vi   -  v         i        v
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_83724823_8   2715 TTCT-AGAAGAAAACATAGGCGTAAATATTTGC-----TGGGTTGGCC-- 2756
                         i   -               ?      v  i i-----      i v --
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_83724823_8   2757 TTCCTTCTTAAGTATAACACCAGAAAGACAAGTGATAACAGTAACAGGAG 2806
                          vvi      ii   i      i  iv     ii i  v  v  v iv  
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_83724823_8   2807 AAAAATTGGACTACATCAAA-TTAAAAA--TTTGTGTTTGAGAGCACAC- 2852
                          v          v       -       --      i  v i  v    -
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_83724823_8   2853 ATTAA-AAAGTGAAAAGACAACTCACATACTACAAGAAAAAATCTTTTCA 2901
                           i  -                i    v -- iii  i     v   v  
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGA--ATGGGAGAAAATATTTGCA 729

  chrX_83724823_8   2902 AATCATAT--CCAAAGTACGTAACTTGTATCCAAGATAGATAAAAGACTG 2949
                                 -- ii --  v vi           ii   v     ii   v
  L1M4_orf2#LINE/    730 AATCATATATCTGA--TAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_83724823_8   2950 CTATAACACAATAACCAAAAGACAAATAGCACAATTTAAAATTGTGCAGG 2999
                         i  i   v      iv            i v     ?    v  v   ii
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_83724823_8   3000 AGATT-GAATGGACAT-----------------ACAAATGGCAAATAAGC 3031
                         i    -    i     -----------------         v       
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_83724823_8   3032 ACATGAAAAGATGCTCAAAATTATTAATCAC 3062
                                           v  i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (93 / 66)
Gap_init rate = 0.03 (21 / 767), avg. gap size = 2.52 (53 / 21)  


3141 26.76 0.67 0.45  chrX_83731918_83736184     2878  3774 (493)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_83731918_8   2878 ATTCAATCTTTATGAATTAGAAAAATCAATATTGTTAAAATATCCATACT 2927
                           i v  v  i   i   i   i v i           i  iv v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_83731918_8   2928 ATCCATAGCAATCTACAGATTCAATTCAATTCATTTCAAAATACCAGTAA 2977
                         vi   v vii              iv    i v v       v    ivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_83731918_8   2978 CATTCTTTACAGAAATAGAAAAAA-AATCCTAAAATTTACACAGAACCAC 3026
                          v  i   i       v  v  iv-i           i i ii   vii 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_83731918_8   3027 AAAACACCCAGAATAGCTAACGCTAGATTAAGCAAGAAGAACAAAAACAG 3076
                           iiv            i  vi v vv  i iv            ivii 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_83731918_8   3077 AAGAATCACATTACCTGGCTTCAGATTACACCACAAAGCTATGGTAATCA 3126
                          i  v     i v  iiii    i vivi  i         ii       
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_83731918_8   3127 AAACAGCATAGTACTGTTGTAAAAACAGACACATAGACCAATGGAATGGA 3176
                          i    ii i      vii   ii i     i     i         i  
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_83731918_8   3177 ATATAAAACCCAGAAACAAATCCGCACATCTACAGATAGCTCGTTTTTGA 3226
                           vv i ii       i   i  ii    i  ii vi ii vi    i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_83731918_8   3227 CAAAGGTGCCAAGAACATACACTGGGAAAAAAGATAGTCTCTTCAATAAA 3276
                            i          v   v  v    i   i -       i     i   
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACAAA 408

  chrX_83731918_8   3277 TGGTTTCAGGAAAACTGGATATCCATATGTAGAAGAA--AAACTAGATTT 3324
                             viii   v         ?   i   i i     --  ii i  iii
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_83731918_8   3325 GTATCTCTCGCTATATACAAAAAATCAAATCAAAATGAATTGAAGACATA 3374
                         v  i   v i i           - i  v        i  ii?    v  
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTA 507

  chrX_83731918_8   3375 AATATAAGACCTCCAACTGTGAAACTATTACATGAAAACATTGGGGAAAA 3424
                            i     v  vv    i i     v   v v        v  ? v   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_83731918_8   3425 TTTCCAGGACATTGGTCTGGGCAAAAATTGCTTGAGTAATACCCCACAAG 3474
                          i i iv   v    vi i     vii  v   iii  vv  v   v   
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_83731918_8   3475 CACAAACAACCAAAACAAAAAAGGACAAATGGGATTACAATAAG-TTAAA 3523
                              i    v   iv     vi  i    v   i v  vi  i-     
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_83731918_8   3524 AACCTTCTTCACATCAAGAGAAACAATCAACGAAGTAAAGAGACTACCCA 3573
                            i  iv -i v    ii  v  v     vi    i  i    v     
  L1M4_orf2#LINE/    658 AACTTTTGT-GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_83731918_8   3574 CAAAATGGGAGAAAATATTTGCAAACTATCCATCTGGCAAGGGATTAATA 3623
                           i                      ii  vi     ii      i vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_83731918_8   3624 ACCAGAAAATATAAAGAGCTCAAACTATTCTATAGGAAAAAAATCTAATA 3673
                         v      v         i   vv  v i  v   iv     i - v    
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATA 805

  chrX_83731918_8   3674 ATCCTGT-AAAAAACGGGCAAAATATTTGAGTATACATTTCTC-AAAGAA 3721
                          i  vi -?     i       iv      i  v         -      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_83731918_8   3722 GACATACAAATGGCAAACAGTCATATTAAAAGGTGCTTAACATCACTGAT 3771
                           i           v  i iv  i  v     i    i       ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_83731918_8   3772 CAC 3774
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.68 (148 / 88)
Gap_init rate = 0.01 (9 / 899), avg. gap size = 1.11 (10 / 9)  


2407 29.83 2.12 0.67  chrX_83785830_83790945.rev     3731  4625 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83785830_8   3731 TGGCAAAACATTCCATGCTCATAAATAAGAAGAGTCAGTTTTGTTAAAAT 3780
                            v  i i  i     i    ii  vi     v i i v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83785830_8   3781 GCTGATACAGCTCAAAGTAATCTACAGATTCAATGCTATTCCAATCAAAC 3830
                          vii    vv i    v i              i  v  i  v      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83785830_8   3831 TATCAA-TGTCATTTTTTATAGAAA--AACAA-----TTTTAAAATTCAT 3872
                          vi  i-  i -      ii     --i    ----- ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_83785830_8   3873 GTGGAA--GCAATAAAGACCCA-AATAGCCAAAGCAATTCTAAGCAAAAG 3919
                         i     --    --ii      -          i    ii i iv  i i
  L1M4_orf2#LINE/    150 ATGGAAATGCAA--GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_83785830_8   3920 GAATGAAGCCAGAGGCATCACATTACCCAACTTCAAACTATACCATAAGG 3969
                            ii   iii    vv     i v     i      viv   i i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_83785830_8   3970 ATACAGTAAACAACACAGCAGGGTATCGGTACTAAAACAGACACATAGTC 4019
                         v        v   v    iiv    ii  i iv ii i     i    vi
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_83785830_8   4020 CAAAGGGGGAAAAA-AAGAACCCCAAAATAAAGCTGCACACCTACAGCTA 4068
                            v  iiv i  v-i   ii  vi       v iii   ii  ii ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_83785830_8   4069 TGTAATCTT-GGCAAAGTTGACGATAATAAATAATGGGGAAAGTACTCCC 4117
                         vv i  i  - i   i v  v i v vi vvi           v ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_83785830_8   4118 TATTCAATAAATATTGCTGGGATACCTGGCTAGCCATATGTAGAAGAATA 4167
                          v     i    iv        i v    v  ?   i   i i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_83785830_8   4168 AAACTAGACCCCTACATTTCACCGTATGCAAAAATTAACTAAACATGGAT 4217
                           ii i         v iv    i   i            v  v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_83785830_8   4218 TAAAAATTTAAATGTAACACCTCAACCAATAAGAATCCTAGAAGAAAACC 4267
                         i ? i ii         v v  v  v v    i v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_83785830_8   4268 TAGGAAACACCCTTCTGGAGATTGGTCTTGAAAAAGAATTTATTAC-TAA 4316
                             ?ivv vi    vv  vv    v-  iiiv  vii   v   v-  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATAT 596

  chrX_83785830_8   4317 GTCATCAAAAGCAATTGCAAGAAAATCAGAAATTGACAAGTGGGACCAAA 4366
                          v  i        vvv    v    vv i    v  i  i v    ivv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_83785830_8   4367 TTAAACTGAAGTGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTAAAA 4416
                          i   v v  ivi   i  ii vv    i  v        v i   i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_83785830_8   4417 A----ACCTACAGAATGGGATAAAATATTTCCAAACAATGCATTTGACAA 4462
                          ----   i           v         v    iv  ii  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_83785830_8   4463 AGATCTAATATCCAGAATGTAAAAGAAACTGAAACAATTATACAAGCAAA 4512
                         i iv  vi          i  v  ii    vvv    i vv i  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_83785830_8   4513 ACTCAAATAATCCCATT-AAAAATGGGTGAAAGAGATGAGCAGACACTTC 4561
                          vv       i  v   -         ii  i  vv   ii     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_83785830_8   4562 TCAAAAACAAGACTTAAGAGTAGTCAACAAAAATGAAAAAAAAATGCTTC 4611
                           v   i-    iv  vi i i i   i  iv i- vi    i     iv
  L1M4_orf2#LINE/    847 TCCAAAG-AAGATATACAAATGGCCAATAAGCAC-ATGAAAAGATGCTCA 894

  chrX_83785830_8   4612 ACATCAGTAATCAT 4625
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (154 / 110)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


2849 27.52 1.33 0.55  chrX_83846904_83849381.rev     1087  1987 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83846904_8   1087 TAGAAACACATCCCATGCTCATTAATTAGGAGAATCAATATTGTGCAAAA 1136
                          i    v i        i    vi   i i   v i        vv i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83846904_8   1137 GACCATAATGCACAAAGAAATCTACAGATTCAATGTAATTCCCATCAAAA 1186
                          i v   v v v    vvi              i i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83846904_8   1187 TACCAAC-ATTATTTTAACAGAATTAGGAAAAAAAAAACCCTAAAATTCA 1235
                          v   i -iiiv    vi     v v -- v  ivvi i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_83846904_8   1236 TATGGAACCAAAAAAGAGCCTGAATATTTAAAGCAATGCTAAACAAAAAG 1285
                                viiv  ii  v  v     vii   i    vi i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_83846904_8   1286 AACCAATCTGGAGACATCACATTGCCAGACTTCAAGTTATACTACAAGAC 1335
                            v  vi     ivv     i v  vi i     iviv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_83846904_8   1336 TATAATTACCAAAGCAGTATGGTACTGGTAAAAGG-TAGGCACATAATCC 1384
                           i i v i   ii    i         i v    -   i  i   ivi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_83846904_8   1385 AATGGAATAAAATAGAGGACCCAGAAATAAGCCAA-ATACTTAAAACCAA 1433
                                  i   v   iii          i  v - i i   viii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_83846904_8   1434 CTAATCTTCAACAAAGCATATGAAAAC-ATACATTGAGGATAGGAAAACC 1482
                         i i  i   i    i -i iiv  i  -  v  v  i   v  i v ii 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_83846904_8   1483 TGTTTAATAAATGGTGCTGAGAAAACTGGAGAGCCACATGTAGAAAAGCA 1532
                          v  i  i           i  v       v ?       i i  i iii
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_83846904_8   1533 AAACTGGATCCCTGTCTTTCACCATCAATAAAAATCAACTCAAGATGGAT 1582
                           ii    i    ii  iv      vv i      i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_83846904_8   1583 CAAAGACTTAAATCTAAGACCTGACACCATAAAAATTCTAAAAGAATACC 1632
                           ?    i     v     v  i v  i      v ii  i     v  v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_83846904_8   1633 TAGGAAAAACTCTTCTGAAAATTGGTCTAAGCAAAGAATTTATTAC-TAA 1681
                             ?iv  v     vvi vv    vi  i    v i-   v   v-  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATAT 596

  chrX_83846904_8   1682 GACCCCAAAAGCAAATGTTACCAAAACAAAAATAAATAAATGAGACCTAA 1731
                            v         v v iv  v   iv       i      vi   i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_83846904_8   1732 TTAAACTGAAAAGCTTCTGTACAGCCAAAGAAATAATCAACGGAATAAAC 1781
                          i   v v    i   i   i vv v  i  v iv     vii i i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_83846904_8   1782 CGACAACCCATAGAG-GGGAGAAAATATTCATAAACTATGCATTTGACAA 1830
                         v         i   i-             iii   ii  ii  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_83846904_8   1831 AGGACTAATATTCAGAATCTACAGGGAACTCAAACAAATCAGCAAGAAA- 1879
                         i     vi   i      v  i ii      vv    v   ii  v   -
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_83846904_8   1880 ---CAAACAATCCCATCCAAAAGTGGGCAAAGGATATAAATAGGCATTTC 1926
                         ---    i  i  v  i?    i            v i     i      
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_83846904_8   1927 TCAAAAGAAGATATACAAATGGCCAACAA--ACTTGAAAAAAATGCTCAA 1974
                           v                       i  --  v      i -       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

  chrX_83846904_8   1975 CGTCACTAATTAT 1987
                          i   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


2738 29.56 1.79 0.34  chrX_83853278_83857745     3083  3975 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_83853278_8   3083 GAAAACCATTCCAGGCTACTGTGTAGGAAATATCATTATCATTAAAATGG 3132
                             ivi  i   v i vv  vi v    ivv i v   ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_83853278_8   3133 CCATACTACCCAAAGCAATTTGTAGATTCTATGCTATTCCTATCAAACTA 3182
                          v     v      vii  i ii      v i  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_83853278_8   3183 CCAAGGACATTCTTCACAGAAATAGAATAAACT-ATTTTAAAACTCATAT 3231
                            ivvi v  i  ii       v  -i  i  -  ii     i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATAT 151

  chrX_83853278_8   3232 GAAACCAAAAAAGAGCCTGAATAGCCAAGGCATTCCTAAGCAAAAACAAC 3281
                          i  viiv  ii  v  v          ii  v  i i iv  i  v   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_83853278_8   3282 AAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTAC 3331
                             i      vv   ii  v  ii i      viv        i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_83853278_8   3332 AGTAACCCAAACAGTATGGTAC------AAAAATAAATGCATAGACCAAG 3375
                              i v i     i      ------  ii   i iii     i   v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_83853278_8   3376 GGAACAGAATAGTCAGCCCAGAAATAAGTCTGCACAGCTACAATTGTCTA 3425
                             i     v vv  i          ii iii   vi  iii iivi i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_83853278_8   3426 ATTTTCGACAAACCTGACAAGAACAAGCAGTGGGGAAAGGATTCCCTACT 3475
                                    ivv  v     v  vv  i         i  vvi  vi 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_83853278_8   3476 GAATAAATGGTACTGGGATAACTGGCTAGCCATATGCCGAAGATTGAAAC 3525
                         v  i       i      i      v  ?   i    vi    v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_83853278_8   3526 TGGACCCCTTTCTTGTACCATATACAAAAATCAATTCAAGATGGATTAAA 3575
                                  vi  iii               i  i    i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_83853278_8   3576 GACTTAATTGTAAAACCCAAAACCATGAAAACCCTGGAAGACAACCTAGG 3625
                            i   v     i v i     i  i   vi i i     v   v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_83853278_8   3626 CA-ATACCATTCTGGATATAGGAATGGGTCAAGATTTCATGGCAAAGAGG 3674
                         ?i- v i -   vv  iv v  iv i  iv v i    v i vv v  vi
  L1M4_orf2#LINE/    552 NGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_83853278_8   3675 CCAAAACCAATGACAACAAATGCAAAAATTGACAAATGGAACCTAATCAA 3724
                               v  vvii       v v      v  i    v i  i v     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_83853278_8   3725 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTAGACCAAC 3774
                          v v  i i   i  ii vv    i  v        v i   ii vvi  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_83853278_8   3775 AACCTACAAAATGGGAGAAAATGTTTGCAAATTATGCATTCAATGAAGGT 3824
                             i   i             i         i  ii  iii  i i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_83853278_8   3825 TCAATATCCAGCATCTATAAGGAACT--TA-AATTTACATGA--AGAAAA 3869
                         iivi       v  v     i     --  -  i i -  i -- i  i 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-ATAATAAAAAGA 799

  chrX_83853278_8   3870 CAAACAACCCTATTAGTATGTGGGTAAAGAACATGAACAGACACTTTACA 3919
                             i     v   ?iv vi    i    i iv    i     i  iv v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_83853278_8   3920 AAAGAAGACTTACATGTGTTTGA-AA--ACATGAAAAAAAGCTCAGCATC 3966
                                 iv    vi  viii -  --         i v     i    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_83853278_8   3967 ACTGATCAT 3975
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.57 (159 / 101)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.73 (19 / 11)  


 691 26.67 0.00 1.54  chrX_83861497_83863732.rev      502   696 (1540)    L1M4_orf2#LINE/L1       37   228 (680)  

  chrX_83861497_8    502 AATATTGTTAAAATGATGATACTACCCAAAGCGATCAACAGATTTAACAT 551
                                    i   iii     v      vi    v       i   ii
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chrX_83861497_8    552 AATTCCTATCAAAATACCAATCACATCCTTCACAGAAATAGAAAATACAA 601
                            i           v   iiii v ii  ii       v  v  vvii 
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chrX_83861497_8    602 GCCTAAAATTTGTATGGTATCATAAAAGACCCCAAAAAGCTAAAGCAATA 651
                         v         ii     v viii  ii     vi  v   i   i    v
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_83861497_8    652 ATGAGGAAAAAAAAGAACAAAGCTGGAGGCCTCTCACTACCTGAT 696
                         v   ---    i          i      v   v    v  ii  
  L1M4_orf2#LINE/    187 TTGA---AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

Transitions / transversions = 1.74 (33 / 19)
Gap_init rate = 0.01 (1 / 192), avg. gap size = 3.00 (3 / 1)  

2043 26.86 4.40 0.46  chrX_83861497_83863732.rev     1087  1745 (491)    L1M4_orf2#LINE/L1      224   908 (0)  

  chrX_83861497_8   1087 CTAATTTCCAATTATACTACAAATCTGCACCAACCAAAACAGCATGATAC 1136
                          i      v  viv         v  i  vi  i   i    ii  i   
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_83861497_8   1137 TGGCATAAAAACAGGCACAGTGACCAATGGAACAGAACAGAACACCCAGA 1186
                                 ii i  i  i vv  i        i    iv  ivii     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_83861497_8   1187 AATAAATTTATCCCCTTATAGCCAACTCGTTTTCAA-AAAGGTGCCAAGA 1235
                               iii  v vi    i i   i vi     i -  i          
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_83861497_8   1236 ACATACACATAGGAAAAGAGT-GTCTCT--AAAAAATCATGCTGGGAAAG 1282
                         v   v  -  i  i     i -    i --  v    vi        v i
  L1M4_orf2#LINE/    374 CCATTCA-ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_83861497_8   1283 CTGGATAACCATATGCAGAAGAAATAAACTATATCTTCATTTTTCACCAT 1332
                                ?   i     i     vv  ii iv i iii ii iv      
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_83861497_8   1333 ATA--AAAATCAACTCAAAAATGGATTAAAGACTTAAATGTAAGACCTGA 1380
                            --     i         -     i ?    i           v  i 
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAA-TGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_83861497_8   1381 AGCTATAAAATTACTAAGATAAAACATTGGAG-AAATACTACAGGACATT 1429
                          i        i vi  ii v       v  ? -    -  v iv   v  
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTT 570

  chrX_83861497_8   1430 GGTCTGGGCAAAGATTTTTTGGATAAGACCTTAGAAGCAGAGGCATCAAA 1479
                           vi i     v i   i  i    v   vii i     v i   v    
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_83861497_8   1480 GGCAAAATTAAACAAATGAGATTATATCAAGCTAAAAAGCTTTTGCACAG 1529
                         i v    v  i i    vi  i vi     iv v    i      ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_83861497_8   1530 CAATGGAAA-----AATAGAGTGGGGAGACAACTAGTAGAATAGAATAAA 1574
                            v   v -----  v i    iii       ivii     i i v   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_83861497_8   1575 -TATTTGCAAACTATTAATCTGATAA----TTAATACATAGAATACATGA 1619
                         -          ii  vv         ----i vi  ivi      i  i 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_83861497_8   1620 GGAACTCAAACAAC-----AGCAAAAATACAA----TCTGATTTAAAAAT 1660
                         i      vv     ----- ii     v    ----i ii   ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_83861497_8   1661 AACCATGATATCTGAATAGACATATCTCAAAAGAAGGCATTCAAATGGCC 1710
                         iiv  viiv  i           v    v       ii  v         
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_83861497_8   1711 AA---GTACATGAAACAATGTGCAAAATCACTAATCAT 1745
                           --- i        vi   iv   v    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (110 / 63)
Gap_init rate = 0.02 (14 / 685), avg. gap size = 2.29 (32 / 14)  


2787 27.51 2.00 0.89  chrX_83865187_83867124.rev      550  1447 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83865187_8    550 TGGAAAAGTGTACCATGACCATGGATAGAAAGAATCGATGTCATTAAAAT 599
                               ii i v     vi       v i    v ii  i ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83865187_8    600 GACTAAACTGCCCAAAGCAATTTACAGATTGAATGCTATTATTATCAAAA 649
                          i v v   v      vii  i        v  i  v  ivi        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83865187_8    650 TACCAATCACATTCTTCACAGAGCTAGAAAAAGCT-ATTTTAAAATTCAC 698
                          v   iiii v  i  ii    iv v  v  -   -  ii         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_83865187_8    699 ATGGAACCAAAAACGAGCCTGAATACCCAAGGCGATCCTAAGCAAAAAGA 748
                               viiv  iv  v  v     v    ii i   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_83865187_8    749 ACAAAGCTGGGGGCATCACACTACCTGACTT-GAAACTATAGTAGGGGGC 797
                               i   i  vv       v  ii i  -i     -  v  viii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_83865187_8    798 CACTGTAACCAAAATGGTATGGTACTGGTACAAGAACAAACATA--GACC 845
                         i  v    i   i ii  i         i i   i i i     --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_83865187_8    846 AATGGATCAGGATAGAGAGCCCAGAAGTAAGACTGCACATCTACAACCAT 895
                               vi  i  v     i      i   iv iii    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_83865187_8    896 CTGATCTTTGACAAAGCTGAAAAAAATGAGCAATAG--AAAGAAGACTCC 943
                         i    i  i     i v  vv  i viivv    i --      v v  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chrX_83865187_8    944 CTATTCAATAAATGGTGCTGGGATAAATGGCTGATCATATGCAGAAGGTT 993
                         - v     i              i  v   v i?i  i     i   iv 
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_83865187_8    994 GAAGCCGGAACCCTTCCATAAAACATATACAAAAATCAACTCAAAATGGA 1043
                             ii   v    v  vi v v             i             
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_83865187_8   1044 TTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGAAAAC 1093
                          i ?    i         i v i            vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_83865187_8   1094 CTAGGCA-ATACCATCCTGGACATAGGAATGGGCAAAGATTTCATGACAA 1142
                         v    ?i- v i v  v  -  v v  iv i     v i    v --- i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTT---AG 592

  chrX_83865187_8   1143 ATAT---ACCAAATTCATT-GCAACAAAAGTAAAATTA-ACAAGTGGGAT 1187
                             ---      vv  iv-          v    v  - i  i v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_83865187_8   1188 CTAATTAAACTTAAGAGCTTCTGCACAGTAAAGGAAACTATCAACAGAGT 1237
                         i v  i   v    i i   i  ii vvi      v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_83865187_8   1238 AAACAGACATCCTACAGAAAGGGAGAAAATATTTGCAGACTACGCATCTG 1287
                         i  v     v  i      v                 i ii iii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_83865187_8   1288 ACAAAGGTCTAATATCCATCATGTATAAGGAACTTAAACAAAT---TTAC 1334
                          i  i  v  vi      vv  i     i     ivv    v --- v i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_83865187_8   1335 AAAAGAAAAAAAAAC---ATTAAAAAGTGCACAAAGGACATTAACAGACT 1381
                             ii v   v   ---   ?    i  vi       iv v  i    v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_83865187_8   1382 CTTTTCAAAAGAAGATGTACATGCAACCAACAAGCATATGAAAAAAAGCT 1431
                         i  i  v         i    viiii    i     i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_83865187_8   1432 CAATATCAAGATGGAT 1447
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (150 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  

 956 27.21 0.00 0.34  chrX_83865187_83867124.rev     1449  1742 (196)    L1M4_orf2#LINE/L1      499   791 (117)  

  chrX_83865187_8   1449 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1498
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_83865187_8   1499 AGGCATTACCATTCAGGACCTAGGCATGGGCAAGGACTTCATGTCTAAAA 1548
                            ?i v viv   iv     v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_83865187_8   1549 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 1598
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_83865187_8   1599 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 1648
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_83865187_8   1649 ACAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 1698
                               i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_83865187_8   1699 GGCTAATATCCAGAATCTACAATGAACTCCAACAACTACAATGA 1742
                          i  vi          v  i  v      iv      -    i 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACT-CAATAA 791

Transitions / transversions = 1.05 (40 / 38)
Gap_init rate = 0.00 (1 / 293), avg. gap size = 1.00 (1 / 1)  


2751 27.11 1.04 1.16  chrX_83940229_83942483.rev      903  1765 (490)    L1M4_orf2#LINE/L1       47   908 (0)  

  chrX_83940229_8    903 AAATGGCCATACTGCCCAAAGGAAATTAAAGATTCAATGCTATTCCCATC 952
                          i     v     v      vvi vi  v        i  v  i  i   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_83940229_8    953 AAACTATCAATGACATTCTTCACAGAACTAGAAAAAACT-ATTTTAAAAT 1001
                            v vi  iivi v  i  ii     v v  v  i-  -  ii      
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAAT 145

  chrX_83940229_8   1002 TCATATGGAACCAAAAAGAGCCCA-AATAGCCAAGGCAATCGGAAGAAAA 1050
                                   viiv  i ii    -         ii     vvi -    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAA 194

  chrX_83940229_8   1051 GGAAAACAAAGCTGGAGGCATCATAGTACCTGACTTCAAACTATACTACA 1100
                          i i       i      vv   i v v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_83940229_8   1101 AGGCTACAGTAATGCAGACAGCATGGCACTAGCACAAAAGCAGGCACATA 1150
                          i           vv      ii   i   i   i  iiii  i  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_83940229_8   1151 GACCAACAGAACAGAATAGAGAGCCCAGAAATAAGGCTGCACACCTACAA 1200
                           i   ii   i     v     i          iv iii   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_83940229_8   1201 CCACCTAATCTTTGACAAGGCTGACAAAATCAAGCAATGAGGAAAAGACT 1250
                         i  vi i  i  i       v  v   i i  vv     i     ii iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_83940229_8   1251 CCCTATTGAATAAATGGTGCTGGGATCACTGGCTAACCATATGCAGAAGA 1300
                         vi  v  v  i              iv     v  ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_83940229_8   1301 ATGAAGTTGGACCCCTTCCTTACACCATACACAAAAATCAACTCAAGATG 1350
                                         v   i        i        i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_83940229_8   1351 GATGAAAGACTTAAGTGTAAAACCAAACACTTACATAAAAACCCTAAAAG 1400
                            v ?    i   i     i v v  v   ---      vi i  i   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACT---ATAAAACTCTTAGAAG 541

  chrX_83940229_8   1401 AAAACCTAGGCA-ATACCATCCTGGACATAGGAACAGGCAA--ATTATTC 1447
                              v    ?i- v i v  v  -  v v  ivi      --i  vi i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_83940229_8   1448 ATGACAAAGACAACAAAAGCAATCA--CAACAAAAGCAAAAATTGACAAG 1495
                          -  i v-    v        --  --         v      v  i  i
  L1M4_orf2#LINE/    591 A-GATAT-GACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_83940229_8   1496 TGGGATCTAATTAAAAGTAAGAGCTCTC-TAAAGCAAAGGAAACTGTCAA 1544
                          v   ii v  i    v   i i  i i- ivvv       v   i    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_83940229_8   1545 CAGAATAAACTGACAACCTATAGAATGAGAGAAGGTTTTTGCAAACAATG 1594
                         v i i i  vv       i i      i     ii v        iv  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_83940229_8   1595 CATCTGATAAAAGTCTAATTTCCAACATCTATAAGGAACTTATACAAATT 1644
                         i         ii v  vi v    iv  v     i     iv     v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_83940229_8   1645 TATAAGAAAAA-ACAAGCGACCCTATAAAAAAGTGGATGAAAGACATGAA 1693
                         v    v     -    iii    v  v?    i   iii  i  iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_83940229_8   1694 CAGAAACTTTTCTAAAGAAGACATTCAAGTGACCAACAAGCATTTGAGAA 1743
                         i   v i  i  i        i  v   i  i    i     iv   i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_83940229_8   1744 AAAACTCAGTATCCCTGATAAT 1765
                         i vi    ii   v????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (144 / 86)
Gap_init rate = 0.02 (14 / 862), avg. gap size = 1.36 (19 / 14)  


2497 26.45 3.35 2.01  chrX_83976646_83980520     2487  3382 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83976646_8   2487 TAGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATATCACTAA-AT 2535
                          i    i i  i     i               v i     iii   -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83976646_8   2536 GGCTATACTGCCCAAACCAATCTACAGATTTAACACTATTCATATAAAAC 2585
                            v     v      iii           i   i v  i v   v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_83976646_8   2586 TACCAGCATCATTTTTCACAGAATTGGACAAAAGTATTCTACCATTCACA 2635
                          v     vv v     ii     v v     ivvv  i   vv     i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_83976646_8   2636 TGGAACCAAAAAAGAGCCTGAATAGCCAAAGCAATTTTAAACAAAAAGAA 2685
                              viiv  ii  v  v           i    i  i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_83976646_8   2686 CAAAGCTGGAGACATTACATTACCGGACTTCAAACTATACTGCAAGGCTA 2735
                              i     ivv i   i v  vi i      viv    i   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_83976646_8   2736 CACATTAACCAAAACAACATG-TACCGGTACAAAAGCACACACATAGACC 2784
                           v--   i   i   iii  -   i  i i  iiii v   i     i 
  L1M4_orf2#LINE/    251 CAG--TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_83976646_8   2785 AAAGGAAGGGAATAGAGAACCCAAAAATAAAACTGCATACCTACAACCAC 2834
                           v    vi    v    ii   i       v iii i ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_83976646_8   2835 GTGTTCTTTGAAAAAGTTGAAAAAA--AATAGCAATAGAGGAAAGGAT-- 2880
                         v  v i  i  v  i v  vv  i -- v --    i -      i  --
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATT--CAATGG-GGAAAGAATAG 395

  chrX_83976646_8   2881 TCCTTATTCAATAAGTGGTGCTGGGATAGCTGTCTAGCCATATGCAGAAG 2930
                           i  --    i  i           i i   vv  ?   i     i   
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_83976646_8   2931 AATAAAACTAGACTCCTACCTTTCACCATATAAAAAAATTAACTGAAGAT 2980
                            i  ii i   i       iv         v           v  i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_83976646_8   2981 GAATTAGAGATTAAAATGTAAAACCTCAAACTGTAAGAATCCTAGAAGAA 3030
                          i  i ?   iiv        i v  v     i   i v  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_83976646_8   3031 AACCTAGAA-TAACCATTCTGGACATTGGCCTTAAGAAAAAAT------- 3072
                            v   i?-   viv   vv   v    v-   i v  vii -------
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAG 592

  chrX_83976646_8   3073 ATATGACTAAGTCTTCAAAAGTAATTGCAACCAAA-AAAAAATTGACAAG 3121
                                -- ----i      i vvv     v   -       v  i  i
  L1M4_orf2#LINE/    593 ATATGAC--A----CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_83976646_8   3122 TAGGACTTAGATAAACAAAAGAGCTTCCGCACAGAAAAAAAAAAAACTAT 3171
                          v      vivi   vvv  i i   ii ii vvv   ii v ---    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA---CTAT 683

  chrX_83976646_8   3172 CAACAAAGT--AAAGACAACC---AAAA---GAGAAAATATTTGTCAAAT 3213
                            v     --          --- i  ---             -     
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG-CAAAT 732

  chrX_83976646_8   3214 -ATGCATCTGCCAAAGGTCTAATTTGCAGAATCCTTGAGGAACTT----A 3258
                         -  ii     vi  i  v  vi v v      viv i i     i---- 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_83976646_8   3259 ATTGAATAAGCAAAAC-TGAATTACCCCATT-AAAAATGGGCAAAAAACA 3306
                          i v     vv    v-ii   v    v   -             ii iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_83976646_8   3307 TGAACAGACGTTTCTCAAAAGATGACATACAAGTATCCTACCAACATATG 3356
                             i    i      v     v  i      i iv  v iv i  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_83976646_8   3357 AAAAAATGCTCAATATCACTAATATT 3382
                             i        i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.09 (48 / 23)  


2901 27.44 2.11 1.22  chrX_83982174_83987784.rev     4221  5120 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_83982174_8   4221 TGGAAAAACATCCAATGCTTACGGATAGGAAGAATCAACAGCACTGAAAT 4270
                               i i    v   i i i    v      v i  i viii i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_83982174_8   4271 GGTTATACTGCCCAAAGCAATTTACAGATTCAATGCTATTTCTATCCAAC 4320
                           iv     v      vii  i           i  v  ii     v  -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chrX_83982174_8   4321 TATTATATCAATGACATTCTTCACAGAACTATT-ATGAACT-ATTTTAAA 4368
                         ----  vi  iivi v  i  ii     --   - ii i  -  ii    
  L1M4_orf2#LINE/    100 ----ATCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAA 143

  chrX_83982174_8   4369 ATTTATGTGAAACCAAAAAGTAGCTTGAATAGCCAAGGCAATTCTAAGCA 4418
                            i  i  i  viiv  i v v iv          ii    ii i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_83982174_8   4419 AAAAGAACAAAGCTGGAAGCATCACTTTACTCAACTTCAAACTATACTAC 4468
                          i          i    i vv    vi v i   i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_83982174_8   4469 GTGGCTACAGTAACCCAAACAGCATGGTAGTGGTACAAAAACAGGCACAT 4518
                         ivi          i v i    ii     v   i i  ii i  i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_83982174_8   4519 AGACCAATGAAATAAAACAGAAAGCCCAGAAATAAGACCACACATCTGTG 4568
                            i     i    i  iv  i  i          iv   i    i i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_83982174_8   4569 ACCATCTGATCTTCAACAAAGCTGACAAAACAA--CAATGGGGAAAAGAC 4616
                         ii  vi    i   i    i v  v   i  v --           ii i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_83982174_8   4617 TCCCTATTCAATAAACGGTCCTGGGATAACTGGTTAGCTATATGCAGAAG 4666
                         vvi  v     i   i   v      i      v  ? i i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_83982174_8   4667 GTACAAGTAGAACCCCTTCCTTAGACCATACACAAAAATTAACTCAAGAT 4716
                         ivvv    v i      v   i v      i                i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_83982174_8   4717 -----AAAGACTTAAATGTAAAATCTGAACCTATGAAATCCCCGGAAGAC 4761
                         ----- ?    i         i v  i  v    i   ii iii     v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_83982174_8   4762 AACCTA--CGCAATACCATTCTGAACT-AAGTAATGGGCAATGATTTCAT 4808
                            v  --? i  - i v iv   v  -ii  -- i       i    v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAA-ATCTTCGTGACCTTGGGT--TAGGCAATGGTTTCTT 590

  chrX_83982174_8   4809 -GATGAAGATGC-AAAAGCAATTGCAACAAAAGCAAAAATTGACAAGTTG 4856
                         -   - v  ii -       vvv          v      v  i  i   
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_83982174_8   4857 GATCTAATTAAACTAAAGAGCTTCTGCACAACAAAATAAACTATCAGCAG 4906
                           ii v  i   v v  i i   i  ii vv    iv v       iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_83982174_8   4907 ATTACACAGACAACTCACAGAATGGGAGAAAATTTTTGCAAACTATGCAT 4956
                          v iv v       i                  v        ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_83982174_8   4957 CTGACAAAGGTCTGATATCCAACCTCTATAAGGAACTTAAACAAATTTAT 5006
                             i  i  v  vi      ivv v     i     ivv    v iv  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_83982174_8   5007 AAGAAAAA-----ACAACCCCATAAAAAAGTAACCAAAGGATATGAATGG 5051
                           v     ----- i     v  v?    i iiv        v     i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_83982174_8   5052 ACACTTCTCAGAAGGAGACATATATGCAGCCAATAAGCATACGAAAAAAA 5101
                            i     vi   i   i   i viii           i i     i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_83982174_8   5102 GCTCAACATCACTGATCAT 5120
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (156 / 87)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


2958 25.65 0.87 2.71  chrX_84026761_84032835.rev     4661  5584 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_84026761_8   4661 GAAAAAACATTCCATCCTCATGGATAGAAAGAATTAATATCGTGAAAATG 4710
                          i   i i  i    vi        v i    v       i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_84026761_8   4711 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAACT 4760
                           v     v      v i  i  i        i  v  i  i      v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_84026761_8   4761 ACCATTGACATTCTTCACAGAAATAGAAAAAAACT-ATTTTAAATTTCAT 4809
                         v   vivi v  i  ii       v  v  i--  -  ii    v     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCAT 149

  chrX_84026761_8   4810 ATGGAA-T-CAAAGAAGACCCCGTATAGCCAAGATAATCCTAAGCAAAAA 4857
                               - -   i --     v v        i i    i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_84026761_8   4858 CAACAAAACTGGAGGCATCACGCTACCTGACTTCAAAAAATACTACAAGA 4907
                         v      ii      vv    i  v  ii i       vv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_84026761_8   4908 CTACAGTAACCAAAACATCATGATGCTGCTACTAAAACAGACATATAGAC 4957
                                  i   i   vii  i i   vi iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_84026761_8   4958 CAATGGAGCAGAGCAGAGACCTCAGAAATAGGATGACACATCTACAACCA 5007
                                ii   iiv    vii        iiviv i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_84026761_8   5008 TCTGATCTTTGACAAATCTAACGAAAACAAGGAATGGGGAAAGGATCTCC 5057
                         vi    i  i     ivv iv i i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_84026761_8   5058 TACTCAGTAAATGGTGTTGGAAAAACTGGCTAGCCATTTGCAGACAACTG 5107
                          vi   ii        i   i v      v  ?   iv    i vi v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_84026761_8   5108 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 5157
                           ii         v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_84026761_8   5158 TAAAGACCTAAATGTAAAA-CCAAAACCATAAAAACCCTAGAAGAAAACC 5206
                         i ?              i - i     i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_84026761_8   5207 TAGGCA-ATACCATTCAGGATATAGGCAT-GGCAAAGACTTCAT-GATGA 5253
                             ?i- v i -   iv  iv v  vv -     v ii   v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_84026761_8   5254 AAATGCCAAAAGCAATTGCAACAAAAACCAAAATTGACAAATGGGA-TCC 5302
                         vi ii         vvv         ivv     v  i    v   - i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_84026761_8   5303 AAATTAAACTAAAGAGCTTCTGCACAGAAACAAACAAACAAACAAACAAA 5352
                          -- i   v v  i i   i  ii vv-----------    -ii   --
  L1M4_orf2#LINE/    646 A--TCAAAATTAAAAACTTTTGTGCTT-----------CAAA-GGACA-- 679

  chrX_84026761_8   5353 AAACTATCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTT 5402
                         ---      vv i      v  i     i                 v   
  L1M4_orf2#LINE/    680 ---CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_84026761_8   5403 GCAATCTACCCACCTGACAAACGTCTAATATCCAGAATTTACAAGGAACT 5452
                             vii ivi i    i  iv v  vi          v  i  i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_84026761_8   5453 TAAACACATTTACAAGAAAAAGACAAACAACCCCATTTAAAAGTGGGCAA 5502
                         ivv   vv iv i  v           i     v   ?    i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_84026761_8   5503 AGGATATGACCAGACACTTCTCAAAAGAAGACATTTATGTGGCCAAGAAA 5552
                              v   vi     i     v        i  vi vi       v  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_84026761_8   5553 CATATGAAAAAAAGCTCAACATCACTGATCAT 5584
                           i       i v           ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 2.06 (33 / 16)  


2825 26.11 1.99 1.55  chrX_84071748_84076003.rev     2862  3765 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84071748_8   2862 TGGAATCATATCCCATGCTCATGGATGGGTACAATCAATATTGTGAAAAT 2911
                              vv          i        v  v v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84071748_8   2912 GACCATACTGCCAAAAGTGATCTACGGATTCAATACAATTCACATCAAAA 2961
                          i v     v  v   v        i       ii    i vi       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84071748_8   2962 TATCATCATCATTCTCCACAGAACTAGAAGAAAACAATCCTTAAATTCAT 3011
                          vi  v vv v  i iii     v v  v-  ivii     v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_84071748_8   3012 ATGGAACCAAAAAAGAGCCCACATAGCTGAAGTAATACTAAGCAAAAAGA 3061
                               viiv  ii  v  viv     ii  ii   vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_84071748_8   3062 ACAAATCTGAAGGCATCGTATTACCCAACTTCAAACTATACTACAAACTA 3111
                              vi  i   vv  ii i v     i      viv         ---
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA--- 246

  chrX_84071748_8   3112 GGCTACAGTTACCAAAACA---TGGTACTGGTATAAAAGTAGGCACGTAG 3158
                         -        v i   i   ---         i    iii   i  ii   
  L1M4_orf2#LINE/    247 -GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_84071748_8   3159 ACCAATGGAACACAGTAGAGAACCAAGAAATAAAGCCAAATACTTACAGC 3208
                          i        i v i v    ii v         v   v i i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_84071748_8   3209 CAATTGATCTTAGGCAAAGCAAATAAAAACAG--AGTGGGAAAAGCACAC 3256
                                 i  v i   i vvivi  i v  v-- i    i    --- -
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG---A- 391

  chrX_84071748_8   3257 ACACCCTGTTCAACAAATCATGTTGGAATAACTGGCAAGCCACATGTAGA 3306
                          i vi  v          vi  i   i i      vv ?       i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_84071748_8   3307 AGAATTAAACTGGATCCTTATCTCTCACCTTATACAAAAATCAACTCAAC 3356
                              v  ii    i  i  i   v    v           i       v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_84071748_8   3357 ATGGATCAAAGACTTAAATCTAAGACCTGAAACCATAAAAATTCCAGAAG 3406
                                 ?    i     v     v  i    i      v iii     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_84071748_8   3407 ATAACATCAGAAAAACTCTTCTAGACATTGGCTTAGGCAAAGAGTAGTTC 3456
                          v     vi ?iv  v     vv   v    v        v -  --   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GT--TTC 588

  chrX_84071748_8   3457 ATGACCAAGAACCCAAAAGCAAATTCAACAAAAACAAAAATAAATAGATG 3506
                         v iivi v  vv         v vv        iv       i   i  v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_84071748_8   3507 GGACTTAATTAAACTAAAAAGTTTCTACACAGCAAACAAAA-TAGCAGAG 3555
                               v  i   v v    ii  i iii vv    vi v -  v  -  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA-AG 687

  chrX_84071748_8   3556 AAA----ACAGACAACCAACAGAGTGGGAGAAAATACTCATAAACTATGC 3601
                            ---- v        v     i            i iii   ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_84071748_8   3602 ATCTGACAAAGGACTAATATCCAGTATCTACAAGGAACTCAAACAAATCA 3651
                               i  i     vi       v  v  i  i      vv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_84071748_8   3652 AGAA---AAGAACAAATAATTTGCATCAAAAAGTAGGTGAAGGTCATGAA 3698
                          v  ---  ii        iiii-  i?    i i  ii    viv    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_84071748_8   3699 TAGACAATTCTC-----AAAATATGCAAATGTCCAACAAACATATGAAAA 3743
                               v     -----  i    i      v    i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_84071748_8   3744 AATGCTTAACATCACTAATTAT 3765
                         i     i       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (133 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.29 (32 / 14)  


2674 25.51 2.27 4.11  chrX_84095861_84098344.rev     1069  1993 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84095861_8   1069 TGGGAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTTTTTAAAT 1118
                            i  i i  i     i        v      v i      v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84095861_8   1119 GGTCACACTGCCCAAAGCAATTTACAGATTCAA-GTTATTCCTATCAAAC 1167
                           iv i   v      vii  i           - iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84095861_8   1168 TACCAACGACATTTGTCACAGAAGTAGAAACAACT-ATTCTAAAATTAAT 1216
                          v   i vi v   v ii     i v  v - i  -  i        v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_84095861_8   1217 ATGGAATCAAAAACAAG---CCCA-AATAGCCAAAACTATTCTAAGTAAA 1262
                               ---- vi    ---    -            v  ii i iv  i
  L1M4_orf2#LINE/    150 ATGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_84095861_8   1263 AAGAACAAAGCTGGTGTCATCACACTTCCTGACTTCAAA--CTACAGTAC 1310
                                   i   v vvv          ii i      --i   --   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TAC 243

  chrX_84095861_8   1311 AAGGCTATAGTAACCAACACAGCATAGTACTGGTACAAAAACAGACACAT 1360
                           i    i     i   v    ii i       i i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_84095861_8   1361 AGACCAATGTAACAGGTTAGAGGTTAGAGAACCCAGGTCAGATGTTGGAG 1410
                            i     v  i  --------------  -------------   -  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAG--------------AA-------------TTG-AG 315

  chrX_84095861_8   1411 AACCCAGAAATAAAGCCACACAACTGTAACCATCTGATCTCTGACAAACT 1460
                          ii           v   i   vi i iii  vi    i ii     ivv
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_84095861_8   1461 CAACAAAAACAAGTAATGGGTAAAGAATTCCCTATTCAACAAGTGGTGCT 1510
                         iiv   i v  vvi      v       vvi  v        i       
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_84095861_8   1511 GGGATAACTGGTGGGCCCTATGCAGAAGATTAAAACTAAACTTCTGCCTT 1560
                             i      vvi?  vi     i    v i  ii ii  ii  i   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_84095861_8   1561 TCACCATACACGAAAATCAACTCAAGATGGATTAAAGACTTAAATGTAAA 1610
                         v       i  i     i       i      i ?    i         i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_84095861_8   1611 GCCTAAAAAAATAAAAACCCT-GAAGAAAAGCTAGA---AAATACCATTC 1656
                         iv      vv      vi i -        vv   i---    -- -   
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTC 562

  chrX_84095861_8   1657 TGGACATCAGCCCTGGCAAAGGTTTCCCAGCAAAGACACCAAAAGCAATT 1706
                         vv   v ii viiv     v      ii  vv v             vvv
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_84095861_8   1707 CCAACAAAAGCAAAAATTGACAAATGGAACCTAATTAAACTAAAGAACAT 1756
                         v         v      v  i    v i  i v  i   v v  i   v 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_84095861_8   1757 GTGCACAGCAAAAGAAACTATTAA--------ACAGATAACTTACTGAAT 1798
                         v  ii vv    i  v     i  -------- v   i   ii  v    
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_84095861_8   1799 ATGAGGAAATATTCACAAACTATGCATCTAA-AAAGGTCTCATATCCAGA 1847
                         iv   i       ii    ii  ii    i -  i  v  ii        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_84095861_8   1848 ATCTACGCAAAACTTAGACAATCGAACAAGCAGAAAACAATTTACCCCAT 1897
                           v  iiv i    ivv    iiv  i  vv i  i    v v    v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_84095861_8   1898 TAAAAAATGGGGAAAAGATCTGAACAGACACTTGACAAAAGATAACATAC 1947
                          ?         v   i   i    i     i  vv v     vi i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_84095861_8   1948 AAGTGGCCAACAAATACATGAAAATAAGCTCAACAGCACTAATTAT 1993
                           i       i  ii         v v        v  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.47 (59 / 17)  


2726 27.33 2.02 1.91  chrX_84119475_84127254.rev     3093  3981 (3799)    L1M4_orf2#LINE/L1        1   890 (18)  

  chrX_84119475_8   3093 TGGAAAAACTTTCCATGCTCATGGATAGGAAGAAACAATATCGTGAAAAT 3142
                               i iv i     i        v      vvi     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84119475_8   3143 GGCCATGTTGCCCAA--TGGAATTTAAAGATTCAATGCTATTCCCATTCA 3190
                            v  ii v     --  --  i  v        i  v  i  i  iv 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_84119475_8   3191 GTTATCATTGACATTCTTCACAGAATTAGAAAAAACT-ATTTTAAAATTC 3239
                         iv vi  vivi v  i  ii     v v  v  i-  -  ii        
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chrX_84119475_8   3240 ACATGGAACCAACAAAGAGCTCATA-TAGCCAGGACAACCCTAAGCAAAA 3288
                          i      vii-   i ii i  v -      ii    i i i i-   i
  L1M4_orf2#LINE/    148 ATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAG 195

  chrX_84119475_8   3289 AAGAACAAAGTTGGAGCCATCATGCTACCTGACTTCAAACTATACCACAA 3338
                                         vvv   ii  v  ii i      viv   i    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_84119475_8   3339 GGCTACAGTAGCCAAAACAGCAAGGTATTGGTACAAAAACGGGCACACAG 3388
                         i         ii   i    iiv    i   i i  ii ii i  i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_84119475_8   3389 ACCAATGGAGCAGAAT--AGAG-----AACTAAAACCGCACATCTACAAC 3431
                          i       ii     --    -----  v    v  ii    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_84119475_8   3432 CATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 3481
                           vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_84119475_8   3482 ACTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGGAAAA 3531
                         v  v  i  i              v      v  ?   i     ii i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_84119475_8   3532 CTGAAATTTGATCCCTTCCTTACACCTTATACAAAAAGTAACTCATGATG 3581
                         -    i  v  i    v   i     v          v       vi   
  L1M4_orf2#LINE/    446 -TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_84119475_8   3582 GATTAATGACTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGAAA 3631
                            i ?v   i         i v i            vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_84119475_8   3632 ATATAGGCA-ATACCATTCA-GACATAGGCATGGGCAAAGATTTTAT--- 3676
                          i     ?i- v i -   i-   v v  vv i     v i   iv ---
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_84119475_8   3677 CATGAAATCACCAAAACCAATCA--CAACAAAAGCAAAAATTGACAAATG 3724
                         i    ---        v  --  --         v      v  i    v
  L1M4_orf2#LINE/    594 TATGA---CACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_84119475_8   3725 AGATCTAATTAAACTAAAGAGCTTCTGCATAGCAAAAGGAACCATCATCA 3774
                         i  ii v  i   v v  i i   i  iiivv    i iv  i    vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_84119475_8   3775 GAGTGAACAGACAACGTACAGAATGGGAGAAAATTTTTGCAATCTATCCA 3824
                         i      v       vi                 v       vii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_84119475_8   3825 TCTGACAAAGGTCTAATATCCAGAATCTACAAGGAATTTAAGCAGATTTA 3874
                              i  i  v  vi          v  i  i   i ivvi  iv iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_84119475_8   3875 TAAGAAAAAAAACTAAGAACCCCATTTAAAAATAGGCAAAGGACATGAAC 3924
                            v     i - v  v     v   ?      i         iv    i
  L1M4_orf2#LINE/    789 TAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_84119475_8   3925 AAACACTTCTCAAAAGAAGACCTGCTCCTGAATGATTACTGGGTAAATAA 3974
                          i   i     v        iv i ----i    iii v ii i v  i 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATAC----AAATGGCCAATAAGCACATGA 883

  chrX_84119475_8   3975 TGAAATG 3981
                         vi i   
  L1M4_orf2#LINE/    884 AAAGATG 890

Transitions / transversions = 1.63 (148 / 91)
Gap_init rate = 0.02 (19 / 890), avg. gap size = 1.84 (35 / 19)  

3325 26.21 0.66 0.66  chrX_84119475_84127254.rev     5577  6484 (1296)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84119475_8   5577 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAGTCAATATCATGAAAAT 5626
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84119475_8   5627 GGCCATACTGCCCAAGGTAGTTTATAGATTCAATGCCATCCCCATCAAGC 5676
                            v     v     iv ii i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84119475_8   5677 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5724
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_84119475_8   5725 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5774
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_84119475_8   5775 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5824
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_84119475_8   5825 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5874
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_84119475_8   5875 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5922
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_84119475_8   5923 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5972
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_84119475_8   5973 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGC 6022
                         i  v  i  i              v      v  ?i  i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_84119475_8   6023 TGAAACTGGATCCCTTTCTTACACCTTATACAAAAATTAATTCAAGATGG 6072
                             ii    i    vi  i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_84119475_8   6073 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 6122
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_84119475_8   6123 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 6171
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_84119475_8   6172 CAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 6221
                         vvi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_84119475_8   6222 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAAAGTGA 6271
                         v  i   v v  i i   i  ii vv    i  v    i  vv       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_84119475_8   6272 ACAGGCAACCTACAGAATGGGAGAAAAT-TTTGTAACCTACTCATCTGAC 6320
                          v  i     i                 -    i  vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_84119475_8   6321 AAAGGGCTAATATCCAGACTCTACAATGAACTCAAACAAATTTACAAGAA 6370
                           i  i  vi        v v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_84119475_8   6371 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 6420
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_84119475_8   6421 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 6470
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_84119475_8   6471 TCATCACTGGCCAT 6484
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  

 287  8.77 3.51 0.00  chrX_84119475_84127254.rev     7233  7289 (491)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_84119475_8   7233 AAAGAAGACATACATGTGGCCAATAA--ACATGAAAAAAAGCTCAACATC 7280
                                 i     vi          --         i v          
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_84119475_8   7281 ACTGATCAT 7289
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.50 (3 / 2)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 2.00 (2 / 1)  


3183 27.18 0.77 0.44  chrX_84138495_84144171.rev     4282  5186 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84138495_8   4282 TGGAAGAACAGTCCATGATCATGGATAGGAACAATCAATATTGTGAAAAT 4331
                              ii i vi     v        v    v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84138495_8   4332 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4381
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84138495_8   4382 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 4429
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_84138495_8   4430 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 4479
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_84138495_8   4480 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 4529
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_84138495_8   4530 CTACACTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGAC 4579
                              v   i   i    ii         i iv ii i   v v     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_84138495_8   4580 CAATGGAACAGAACAGACACCTCAGAAGTAACACCACACATCTACAACCA 4629
                                 i    iv  v vii     i   vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_84138495_8   4630 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 4679
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_84138495_8   4680 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCTG 4729
                          v  i  i              v      v  ?i  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_84138495_8   4730 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 4779
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_84138495_8   4780 TAAAGACTTAAATGTTAGACTTAAAACCATAAAAACCCTAGAATAAAACT 4829
                         i ?    i       v   vi      i      vi i     v     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_84138495_8   4830 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 4878
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_84138495_8   4879 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4928
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_84138495_8   4929 TTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACTACCATCAGAGTGAAC 4978
                          i   v v  i i   i vii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_84138495_8   4979 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 5028
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_84138495_8   5029 AGGGTTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5078
                         i  ii vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_84138495_8   5079 AAACAA----CCCCATCAAAAAGTGGGTAAAGGATATGAACAGACACTTC 5124
                          i    ----   v  i?    i    i       v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_84138495_8   5125 TCAAAAGAAGACATTTATGCAGTCAACAGACACATGAAAAAATGCTCATC 5174
                           v        i  vi viii i   i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_84138495_8   5175 ATCACTGCAAAT 5186
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


4259 18.67 2.75 0.11  chrX_84158603_84163097     3130  4002 (493)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_84158603_8   3130 CCCTGTGTATGCATAGGAATAC--AACATCGGTAGGATGCCAATACTATT 3177
                           v   vi   v  v    v  --  i  i v  i    v       vii
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_84158603_8   3178 CAAAATGATCTACATATTTAATGCAGTCCCTATTAGAATTCCAACAGCCT 3227
                             v         v   i  i   i       i i   i   i v    
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_84158603_8   3228 TTTTCACAGAAATAGAAAAGCTGATCCTCACATTCATATGGAATTCCAAG 3277
                             ii       v  v           v v            v v    
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_84158603_8   3278 GGGCCCCAAATAGCCAAAACAATCTTGAAAACAAAGAATAATATTGGAGG 3327
                           i   vi                       vi     i  vi       
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_84158603_8   3328 ACTCACACTTCCTGACTTTGAAACTTATTAGAAAGCTACAGCAGTTAATA 3377
                                     ii i  ii       i  v          i i i  v 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_84158603_8   3378 CTGTAGGGTAGTGACAAAAGGACAGACATATAGACCAAGGGAACAGAATA 3427
                          v  iv    v  i  v     i           i   v    i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_84158603_8   3428 GAGACCTCAGAAACAAACCCTCACATATCTGACCCATTGAT-----ACAA 3472
                             vii      i      vi    v v  ii v      -----    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_84158603_8   3473 GGGTTCTATGACCATTCATGGGGAAAAGGACCGTCTTTTCAACAAACAGT 3522
                             v i v         vv   i    i iv              ii  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_84158603_8   3523 ACTAGGGAAACTGAATATCCATATGCAAAATAATGAAGTTGGACCCTTAA 3572
                         i  i  iv     i   ?   i        v               i  -
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA- 461

  chrX_84158603_8   3573 CTTCACATCATGTACAAAATGTAACTCAAAATAGATCAAATACCTCAACA 3622
                          i     i   i       vv           i     ? v    v  ii
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_84158603_8   3623 TAAGTGCTAAACCTATAAAACTCTTAGAAGAAA-CATGGG---AAATCTT 3668
                             v      v                     -   i  ---       
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_84158603_8   3669 CAAGACATTGAATTTGGCAATGATTTCTTGGATATAACACCAAAAGCACA 3718
                          iv   v   ii  v       i      i     i              
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_84158603_8   3719 AGTGACAAAAGAA----TGAATAAATTGGACTTTATCAAAAATAAAATCT 3764
                           ii         ---- ii             i       v     v  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_84158603_8   3765 TTTGTATGTGAAAGGGCAATATCAAGA--GTAAAAAGGCAACCCATGGAA 3812
                              iiv v     i  v        --  i     i       ii   
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_84158603_8   3813 TGGGAGAAAGTATTTGGAAAT-A-ACATCTGATAAGGGATTAATATCCAG 3860
                                  i      v    - - i             i vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_84158603_8   3861 ACTATATAAAGGACTCCTACAACTCAACAACAAAAAACCAA----CTCAA 3906
                          v         i    i          i  i     iv   ---- i   
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_84158603_8   3907 TTCCAAAATGTGTAAATATCATAAATAGACACTTCTC-AAAGAAGATATA 3955
                           ?v      v i   viviv i        i     -            
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_84158603_8   3956 CAATGGGTCAATAAGCACATGAAAAGGTGTTCAACATCACTAATCAT 4002
                            vv  i                  i  i         ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (95 / 65)
Gap_init rate = 0.01 (11 / 896), avg. gap size = 2.27 (25 / 11)  


3116 27.89 0.66 0.55  chrX_84189049_84193157.rev     2712  3618 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84189049_8   2712 TGGAAGAACATTCCATGCTCATGGATAGGAACAGTCAATATCATGAAAAT 2761
                              ii i  i     i        v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84189049_8   2762 GGCCATTCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2811
                            v  v  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84189049_8   2812 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2859
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_84189049_8   2860 TGTAGAACCAAAAAAGAGCCTGCATTGCCAAGAGAATCCTAAGCCAAAAG 2909
                          i i   viiv  ii  v  v v  v     i v    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_84189049_8   2910 AGCAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCTATACTACAAGGC 2959
                          i     i      vv    i  v  ii i     iviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84189049_8   2960 TACAGTAACCAAAACAGCATGGCACTGGTACCAAAATAGAGAGATAGACC 3009
                                 i   i    ii   i     i iv ii     v v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_84189049_8   3010 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACT 3057
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_84189049_8   3058 ATCTGATCTTTGACCAACCTGACAAAAATAAGAAATGGGGAAAGGATTCC 3107
                          vi    i  i   v ivv  v   i vi vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_84189049_8   3108 CTTTTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCT 3157
                              i  i              v      v  ?i  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_84189049_8   3158 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCGAGATGGA 3207
                            ii    i    v   i     v              i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_84189049_8   3208 TTAAGGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3257
                          i ?i   i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_84189049_8   3258 CTAGGCA-ATACCATTCA-GGCATAGGCATGGGCAAGGACTTCATGACTA 3305
                         v    ?i- v i -   i- i v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_84189049_8   3306 AAACCCCAAAAGCAATGGCAACAAAAGCCGAAATAGACAAATGGGATCTA 3355
                         vi  v         vvi          vvi       i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_84189049_8   3356 ATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3405
                           v   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_84189049_8   3406 CAGGCAATCTAAAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 3455
                         v  i   i i v               v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_84189049_8   3456 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 3505
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_84189049_8   3506 AAATCAAACAACCATATCAAAAAGTGGGTAAAGGATATGAACAGACACTT 3555
                           iv    i    vv  i?    i    i       v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_84189049_8   3556 TTCAAAAGAAGACACTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 3605
                         i  v        i ivi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_84189049_8   3606 CATCACTGGTCAT 3618
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (153 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3135 27.34 0.77 0.66  chrX_84207489_84213879     4992  5898 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84207489_8   4992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5041
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84207489_8   5042 GGCCATACTGCCCAAGGTAATTTATAGGTTCAATGCCATTCCCATCAACC 5091
                            v     v     iv i  i  i  i     i  v  i  i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84207489_8   5092 TACCAATGACTTTCTTCACCGAATTCAAAAAAACT-ACTTTAAAGTTCAT 5140
                          v   iivi i  i  ii v   v ii v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_84207489_8   5141 ATGGAACCAAAAAGGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5190
                               viiv  i   v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_84207489_8   5191 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5240
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_84207489_8   5241 ACAGTAACCAAAACAGCATGGTACCGGTACCAAAACAGAGATATAGACCA 5290
                                i   i    ii      i  i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_84207489_8   5291 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACCA 5338
                               i    i--    i  --        vv  ii i  i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_84207489_8   5339 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGAATTCCC 5388
                         vi    i  i     ivv  vv  i v  vv               vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_84207489_8   5389 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5438
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_84207489_8   5439 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG-AT 5487
                           ii    i    v   i     v           i  i    i   -  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_84207489_8   5488 TAAATACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5537
                         i ? v  i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_84207489_8   5538 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTC--AAGTAT 5584
                             ?i- v i -   iv   v v  vv i     v ii   -- ii   
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_84207489_8   5585 AAAACACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5634
                         i --        i  vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    597 GA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_84207489_8   5635 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5684
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_84207489_8   5685 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5734
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_84207489_8   5735 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5784
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_84207489_8   5785 AAAAACAAACAATCCCATCAAAATGTGGGCGAAGGATATGAACAGACACT 5834
                            i     i  i  v  i?   vi     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_84207489_8   5835 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATAAAAAAATGCTCA 5884
                             v        i  vi viii     v ii     i    i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_84207489_8   5885 CCATCACTGGCCAT 5898
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (150 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2209 27.84 2.17 1.92  chrX_84226417_84228188      497  1279 (493)    L1M4_orf2#LINE/L1      124   908 (0)  

  chrX_84226417_8    497 ATTGAAAAAATAATTCTAAAATTCTTATGAAACCAAAAAAGAGCCCTCAT 546
                              v  iv i  i         v    i  viiv  ii  v  vvv  
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chrX_84226417_8    547 AGCCAAAGCAAGACTAAACAAAAAGAACAAATCTAGAGGCATCACATTAC 596
                                i   vvi i  v  i         vi i    vv     i v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_84226417_8    597 CTGAGTTCAAACTGTACTACCAGCCTATAGTTACTAAAGCAGCATGGCAC 646
                          ii v      viv      v iv   i   v ii  ii   ii   i  
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_84226417_8    647 TGGTATAATAGTAAGCAAGTAGATCAATGGAACAGAATAGAAAACCAAAA 696
                            i    vii  ii  vi             i     v  i ii v i 
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_84226417_8    697 AATAAAGCCAAATACCTATAGCCAACGGATCTTCAACAAGACATACAAAA 746
                               v   v i ii   i i   iv   i   i     i-i i v  i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAG 372

  chrX_84226417_8    747 ACAA---AAAGTGGGGAAAGGACACCCTATGTAATAAATGGTGCTGGGAT 793
                           v ---  --         i i vi  v vi  i              i
  L1M4_orf2#LINE/    373 ACCATTCAA--TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_84226417_8    794 AATTGGCAAGCCACATGTAGAAAAATGAAACTGGATCCTTATCTCTCACC 843
                           i   vv ?       i i  i      ii    i  i  i   v    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_84226417_8    844 TTGTTAAAAAATCAACTCAAGATGGATCAAAGACTTAAATCTAAGACCCC 893
                         v i vv      i       i        ?    i     v     v iv
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_84226417_8    894 AAACCACAAAAATTCTAGAAGATAACACCAAAAAAGCTCTTCTGGACATT 943
                             i i    v ii       v    ivii?iv iv     vv   v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_84226417_8    944 GTCTTAGGCAAAGA---ATTA---ATGAC--CAATAGCACAAAGGTACCT 985
                          vv        v i---v   ---     --   v       i-------
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG------- 613

  chrX_84226417_8    986 GCAACAACAACAAAAGAGATAAATAGCTGGGACTTAATTAAACTAAAAAG 1035
                         ----      v i  i i   i   iv v      v  i   v v    i
  L1M4_orf2#LINE/    614 ----CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_84226417_8   1036 GGTCTGCACAGCAAGAGAAATAATCA-----GCAAACAGACAACCAACAG 1080
                         vv i  ii vv   ii  v iv    ----- ii  v        v    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_84226417_8   1081 AGTGGGATAAAATTTTCACAATCTGTGCATCCAACAAAGGACTAATATCC 1130
                          i     v     v  ii   viii ii   ii i  i     vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_84226417_8   1131 AGAATCTACAAGGAACTCAAACAAATCATCAAGAAAAAATTCAAATAATT 1180
                              v  i  i      vv    v   vi  v     iv-       ii
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACC 808

  chrX_84226417_8   1181 CCATC-ACAACTGAGCTAAGGACGTGAATAGACAGTTCTCAAAAGAAGAT 1229
                          v  i- v  v  i  v     iv          v     v         
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_84226417_8   1230 ATACAAATGGCCAATGAATATATTAAAAAATGCCCCAAATCACTAATTAT 1279
                                        i ii i  v    i    i v v    ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (124 / 91)
Gap_init rate = 0.01 (10 / 785), avg. gap size = 3.20 (32 / 10)  


3452 21.39 2.98 2.87  chrX_84290317_84292486      772  1678 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84290317_8    772 TAGAAAGGCATCCTATGTTCATGAGTTGGAAAACTTAATATTGTTAAAAT 821
                          i     ii    i         ii      i               i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84290317_8    822 GTTCATACTACCCAAAGAGATCTATGGATTCAATGCAATCCCTATCAAAA 871
                          viv     v      vv      ii       i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84290317_8    872 TCCCAATGACATTTTTTACACAAATAAAAAATACAATCCTAAA-TTCATA 920
                              iivi v      i  v    vi v  vvii        -      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_84290317_8    921 TGGAACCACAAAAAGAACCCAAAA-AGCCAAAGCAATCTTGAGAAACAA- 968
                              vii   i-- i     i  -       i         i   v  -
  L1M4_orf2#LINE/    151 TGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_84290317_8    969 --CAAAGCTGGAGGCATCACATTTCCTGATTTCAATATATATTACAAAGC 1016
                         --     i      vv     i    ii       v iv  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84290317_8   1017 TATAGTAATAAAAACAATATG-CACTGGCATAAAATCAGACATATAGACC 1065
                           i      v  i   i i  -i          iivi           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_84290317_8   1066 AATGGAACAGAATAGATA-TCGTAGAAATAAAACCATGCATATACAACCA 1114
                                i     v  v -  -i         v    i   v  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chrX_84290317_8   1115 ATTGATCTTCAATAAGGATGCCAAGAATACACAATGAGAACATGATAATC 1164
                               i   i i    i        vi iv     i i v vi   i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_84290317_8   1165 TCTTCAAGAAGAAGTGTTGGGAAAACTAGATATACACATGCAAAATAATG 1214
                          i     v  ivi   i     v    i    ?v           v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_84290317_8   1215 AAATTGGTCATTTCTTTATTTTATGTCATACACAAAAATCAACTATAAAT 1264
                           i    v ---- ii  ii i iii    i        i    vv    
  L1M4_orf2#LINE/    448 AAGTTGGAC----CCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_84290317_8   1265 GAATTAAATATTTAAACATAAGACCTAAAACTGTAAAATGCCTATGAGAA 1314
                          i  i ? v ii    ii     v        i     iv i  vi    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_84290317_8   1315 AA----G--------CTTTATGATATTTGTCTTGGCATTTATTTCTTGGA 1352
                           ---- --------   ii   iv  v vi v    v vi      i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_84290317_8   1353 TATGAGACAAAAAGCAGAAGCAACAACAAAAACCAAGATAGACAAGTGGG 1402
                              v  v       v         -  i  --  i     i  i v  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAA-AAGAA--AAAATAGATAAATTGG 640

  chrX_84290317_8   1403 ACTACATCAAACTAAAAAGCTTCTACACAGCAAAGGAAACAGTCCACAGA 1452
                            v       v v    i   i iii vv       v  vi  v v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_84290317_8   1453 GTGAAATGACAAACTATGGAATGAGAGAAAATATTTCTAAATC------- 1495
                               v     v i ii     i            vi     -------
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_84290317_8   1496 TGATAAGGGTTTAATATCCAAAATACATAACAAACTCTTACAAATAAAAA 1545
                                  vi vi      i    i    vi           v -----
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT----- 785

  chrX_84290317_8   1546 GCAAACAA-AACAAAGCAAAAGAACCAAATAACCCAATTAAAAAATAGGC 1594
                         -----   -  i   ----    --              ?      i   
  L1M4_orf2#LINE/    786 -----CAATAATAAA----AAGA--CAAATAACCCAATTWAAAAATGGGC 824

  chrX_84290317_8   1595 AAAAGAGTTGAATAGACATTTCTCCACAGAGGACATACATATGGCCAATA 1644
                            i  v                   v   i  i     v          
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_84290317_8   1645 AATATATGAAATGATGCTCAATATCCTTAGTTAT 1678
                          ii i      v         i   v????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (120 / 71)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.12 (53 / 17)  


2821 24.16 1.13 2.88  chrX_84295491_84299619     2840  3638 (491)    L1M4_orf2#LINE/L1      124   908 (0)  

  chrX_84295491_8   2840 ATTGCTACAAGCAGCAATCCTAAAATTTATACAGAACCACAAAAGATGCA 2889
                             --      v --           i   ii   vii   ii  iv  
  L1M4_orf2#LINE/    124 ATTG--ACAAGCTG--ATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_84295491_8   2890 GAATAGCTAAAGCCATCTTAAGCAAAAAGAACAAAACTGGAGGAATCACA 2939
                                i   i v     i iv  i         ii       v     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_84295491_8   2940 TTACCTGACTTCAAATTATACTACAGAGCTACAGTAAACAAAGCAGCATG 2989
                         i v  ii i      viv       i           v   ii   ii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_84295491_8   2990 GTCTTGGCATTAAAATAGACACATAAATTAATGGAACAGAATAGAGAACC 3039
                           vi      v ii       i   i  i       i     v    i--
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG-- 317

  chrX_84295491_8   3040 AATTCTGAATGAATATCCAGAAACAAATCCACACACCTACACTGAATTCA 3089
                         ---------------        i   i   i   ii  iiv v    v 
  L1M4_orf2#LINE/    318 ---------------TCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_84295491_8   3090 TTTTCAACAAAGGTGCCAAGAACATACACTGGAGTAAAGACAGTCTCTTC 3139
                              i    i          v   v  v   i v  ii i     i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_84295491_8   3140 AATAAATGGTGCTGGGAAAACTGGATTTGTATATGCAGA-GAATGAAACT 3188
                           i              v        v?vi i     i -       ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_84295491_8   3189 AGATCCCTATTCCTCACCATATACAAAAAGCAAATCCAAATAGATTAACT 3238
                         i  i     iii v               vi  v  v    i   i ?vv
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_84295491_8   3239 ACTCAAATATAAGACTTCAAGCTAATAAACTACTAATAGAAAACATTGGG 3288
                           ii    i     vi v  i   vv     vi  iv         v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_84295491_8   3289 GGAAACTCTCCAGTACATTTATCTGGGCAAAGATTTCTTAAGTAATACCC 3338
                          v   -   i ivv  v  vivi i     v i       ii  vv  v 
  L1M4_orf2#LINE/    553 GTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_84295491_8   3339 CAGAAGCACAGG--ACCAAAGAAAAAATGGACAAATAGGATCATATCAAG 3386
                           i       i --  v           i  i    v   iivi     i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_84295491_8   3387 -TTAAACAGCTTATGCACAGCAAAGGAAATAATCAACAAAGTGTACAGAC 3435
                         -     - i   v  ii vv       v iv     v      v v    
  L1M4_orf2#LINE/    652 ATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_84295491_8   3436 AATTCACAAAATGGGAGAATATATTTGCAAACTACCCATCTGACAAGGGA 3485
                           ii    i          v           ii ivi      i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_84295491_8   3486 TTAATAACCAGAATATATACAGAGCTC--A-AAC--AATAGGAAAAAATC 3530
                         i vi  v            v   i   -- -   --    iv     iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_84295491_8   3531 TAGTAATTCAATTTAAAAATGGGTCAAATATCTGAGTAGACATTTCTCAA 3580
                         v i   ii     ?         iv  iv  i   i            v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_84295491_8   3581 TAGAAGGCATACAAATTGCAAACAGGTGTATAAAAACATGCTCAACATAA 3630
                         v     ii        v  v  i i iii  i    v           v 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_84295491_8   3631 TTGATAAT 3638
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.59 (116 / 73)
Gap_init rate = 0.01 (11 / 785), avg. gap size = 2.91 (32 / 11)  


2019 24.11 10.81 3.68  chrX_84299886_84301864      653  1494 (485)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_84299886_8    653 GACATACTGTGTTCATGAAT-AGAAGAATCATTATAGTAATGATGTCAAT 701
                           i  v ii        i  -i     v i v   v  v v    v    
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_84299886_8    702 TCTCCCTCAAAGAGATCTATAGATT-AACACAATATCAACCAAAATCCCA 750
                         v     -    vv      i     -   i    vi v i          
  L1M4_orf2#LINE/     57 ACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_84299886_8    751 GCAGAAATTTGTATATA----GACATGCTAATATTCAAATTTACATGTAA 796
                           v vvv   v ii v ----    v   i  vi v     i i   v  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_84299886_8    797 AGACACAAGAACTAGAATAGCTCATTACA-TTTTGACAAA----AACAAA 841
                          vi  vii  v i        -  vv   - i    v   ----      
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGC-CAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_84299886_8    842 G----AGGAATCACACTACTTAATTTTAGAAGTTACTATAAAGCTAAAGT 887
                          ----    v       v ii     i i  v      i       v   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_84299886_8    888 AATCAAGTCAGAGCAGTGTTTGTAAAGGGATAGATACACAAGTCCACAAG 937
                                v   v ii  ii v i v i       i i i ii  ------
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC------ 298

  chrX_84299886_8    938 TCAATGGAACCTAAACAATAGGACAGATATGCACCTACATGAATATGGCC 987
                         --       ivv  vii v  vv    v  iv   i i iivv     i 
  L1M4_orf2#LINE/    299 --AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_84299886_8    988 ATTTGATATTTTTACAAAGATACACAGGCAATTCAGTGGAGAAAAGGTTG 1037
                          v     -   iv    i i i vv  i v     i   i    iii v 
  L1M4_orf2#LINE/    347 AATTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_84299886_8   1038 TCTTTTGAACAAATATTGCTGGAACCTTTGAA----------------AA 1071
                               v       iv      i  vvi  i ----------------  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_84299886_8   1072 TGAACCTTAACCTGAATTTCACACCTTATATAAAGACCAACTCAAAATAA 1121
                             vi vi   ivv ii       v    i   i ii          ii
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_84299886_8   1122 TTAATATATGTAAATGCAAAAACTAAAA-TGTTAAACTTTTAGGGGAAAA 1170
                         v v ? v iv      i  i i      - i v     i    ii     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_84299886_8   1171 ---------AAA--------ACCTTA----AAAC---------------- 1183
                         ---------   --------     i---- ii ----------------
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_84299886_8   1184 TGACACCAAAGCACAACACATGCAAGAAAA-AAAAAAT-GACAAATTTGA 1231
                                   ---- i    v    v    -       -  i     v  
  L1M4_orf2#LINE/    596 TGACACCAAA----AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_84299886_8   1232 CTTCATCAAATTTGAAAACATTTTTTCTGC--CCAAGG-CACTGTAAAGT 1278
                                   v  i     ---    v   -- v    -    i v   v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAAC---TTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_84299886_8   1279 GAATGAAAAGAC---CCA-GTAATGATGTACAGAAAATATTTTCAAATCA 1324
                         i i         ---   -iv    i- ---           v       
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGG-G---AGAAAATATTTGCAAATCA 734

  chrX_84299886_8   1325 CGTATCTGATAAAGGACTAGTATCCAGAAAATGTATTTTTTTTAA--ACT 1372
                         ii          i     v          v  i  --------  --   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATA--------AAGAACT 776

  chrX_84299886_8   1373 CTGAAAACTCAATAGTAAGGAAACAA-----CCACATTAAAAGATGGGCA 1417
                           v v         i   ii i    -----   -   ?   i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCA 825

  chrX_84299886_8   1418 AAGAACTTAAATGGACGCTTCATCAGAGAAGTTAC------GGCAAATAA 1461
                            i i  i   i   ii   vi  i     v  i------   v     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_84299886_8   1462 GGACACAAACAGGTGTTAATTATTAGCTATTAG 1494
                          v   ii  v  i  i v vi  i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (114 / 87)
Gap_init rate = 0.03 (31 / 902), avg. gap size = 3.94 (122 / 31)  


2590 26.54 2.91 1.23  chrX_84319312_84321969.rev     1275  2167 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84319312_8   1275 TGGAAAAACATTCCATGCTCAAGGATTGGAAGAATCAATATCATTAAAAT 1324
                               i i  i     i   v           v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84319312_8   1325 GGACATACTGCCCAAAGCAATCTACAGATTCAATGCTATTCCTATCAAAC 1374
                           vv     v      vii              i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84319312_8   1375 TACTAAC-GTCATTTTCACAGAA-TTGGAAAAAACT-ACACTAAAATTCA 1421
                          v i i - i v    ii     -   -- v  i  - iv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_84319312_8   1422 TAAGGAAC--CAAGAAA---GAAATAGCCAAAATAACCCTAAGCAAAAAG 1466
                           v    v--    ii ---ii           i  i i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_84319312_8   1467 AACAAAGCCAGAGACATCA-ATTATCCAACTT-GAAACTACACTACAAGG 1514
                                iii   ivv   - i vi    i  -i     -i       i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_84319312_8   1515 CTACAGTAA-CATAAACAGCATGTTACTAGTACAAAAACAAACACATAGA 1563
                                  -  - i    ii  v    i i i  ii i i   i     
  L1M4_orf2#LINE/    248 CTACAGTAATCA-AGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_84319312_8   1564 CCAAAGGAACAGAAAAGAGAACCCATAAACAAAGCCACATAACTACAACC 1613
                         i   v    i    vv    ii   v   i   v   i i vi  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_84319312_8   1614 ATCTAATCTTTGGCAAAATCAACAGAAGTAAGCAATGGGAAAGGACTC-C 1662
                          vi i  i  i i   iiviiv  ii vi vv       i  i  v v-i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_84319312_8   1663 CTATTCAATAAATGGTGCTGGGATAGCTGGGAAGCCATATCCAGAAGAAT 1712
                           v     i              i i    iv ?   i  v  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_84319312_8   1713 GAAACTGGACCCCTATGTTTCACCATA--CAAAATTTAGC-CAAGATGGA 1759
                            ii          iv iv       --     v   i -   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_84319312_8   1760 CCAAAG-TTTAAAGATAAAACCTCTAGAC-ATAAGAATCCTAGAAGAAAA 1807
                         i  ?  -ii    vi   i v  v- i  -    i v  i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAA 545

  chrX_84319312_8   1808 CCTAG---TAAACACTATTCTGGACATTGGCCTCGGGAAAGAATTTATGA 1854
                          v   ---    --- v   vv   v    vi v  v  v iv  iv ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_84319312_8   1855 CTAAGTCCCCAAAACCAATTGCAACAAAAGCAAAAATTGACAAGTCAGAA 1904
                         v  v v v      v  vvv          v      v  i  i ii  v
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_84319312_8   1905 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACGGAGT 1954
                         i v  i   v v  i i   i  ii vv    i  v        vii   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_84319312_8   1955 AAACAGACAACCTACAGAATGGGAGAAAAATATTCACAAACTATGCATCG 2004
                         i  v        i                -    ii    ii  ii   v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCT 741

  chrX_84319312_8   2005 GACAAAGGTATAATATCCAGAATCTACAAAGAACTT----AAATCAGCAA 2050
                           i  i  vv vi          v  i        i----  v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_84319312_8   2051 GCAGAAAACAAGTAACTCCAAT--AAAAACGGGGAAAAGGCATGAACAGA 2098
                         vv i  i    i    -     --     i   v   i iiv    i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAAC-CCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_84319312_8   2099 CACTTCTCAAAAGAAAACATACAAGTGGTCAACAAACATAGGAAAAAAAT 2148
                           i     v      i i      i   i   i  i  i v     i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-T 889

  chrX_84319312_8   2149 GTTCCACATCACTAATCAT 2167
                          i  v      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (149 / 86)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.54 (37 / 24)  


2989 26.74 1.10 0.77  chrX_84372579_84374977.rev     1004  1908 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84372579_8   1004 TGGAAAAACATTCCATTGTTATGGATAGGAAGAATCGATATCTTGAAAAT 1053
                               i i  i    vv i      v      v ii    iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84372579_8   1054 GGCCATACAGCTGAAAATAATTTATAGATTCAGTGCTAACCCCATCAAGC 1103
                            v    vv iv   v i  i  i       ii  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84372579_8   1104 TACCATTGACTTTCTTCACAGAATTAGAAAAAATA--CTTTAAATTACAT 1151
                          v   vivi i  i  ii     v v  v  iv i-- i v     -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT-CAT 149

  chrX_84372579_8   1152 ATGGAACCAAAAAAAGAGCCCATA-TATCCAAGACAATCCTAAGCCAAAA 1200
                               -- viv  i ii    v -  v    i      i i ivv i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_84372579_8   1201 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 1250
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_84372579_8   1251 CTTCAGTAACAAAAACAGCATGGTACCGGTACCAAAACAGAGAGATAGAC 1300
                           v      iv  i    ii      i  i iv ii i   v v     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_84372579_8   1301 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATTTACAACTA 1350
                                 i    iv   ivii         vv   i       iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_84372579_8   1351 TTGGATCTTTGACAAACCTTACAAAAACAAGCAATGGGGAAAAGATTCCC 1400
                         v v   i  i     ivv vv   i v  vv           ii  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_84372579_8   1401 TGTTTAATAAATAATGCTGGGAAAACTGGCTAGCCATATGCTGAAAACTG 1450
                          v  i  i    ii        v      v  ?   i    vi  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_84372579_8   1451 AAACTGGACCCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGAT 1500
                           ii         v   i    iv                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_84372579_8   1501 TAAAGACTTAAAGGTAAGACCTAAAACCATAAAAACTCT-AGAAGAAAAC 1549
                         i ?    i    v      v       i      -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chrX_84372579_8   1550 CTAGGCA-ATACCATTCAGGACATAGGCATGGGGAA-GACTTCATGACTA 1597
                         v    ?i- v i -   iv   v v  vv i  v  - ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_84372579_8   1598 AAACACCAAAAGCAATAGCAACAAAAGCAAAAATTGACAAATGGGATCTA 1647
                         vi            vv           v      v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_84372579_8   1648 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTATCAGAGTGAA 1697
                           i   v v  i i   i  ii vv    i  v     i vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_84372579_8   1698 CAGGCACCCTACAGAATGGGAGAAAATGTTTGCAATCTATCCATCTGACA 1747
                         v  i  v  i                 i       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_84372579_8   1748 AAGGGCTAATACCCAGAATCTACAAAGAATTTAAACAAATTTACAAGAAT 1797
                          i  i  vi  i       v  i      i ivv    v iv i  v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_84372579_8   1798 CAAACAAACAACCCCATCAAAAAGTGGCCAAAGGGTATGAACAGACATTT 1847
                         v i     i     v  i?    i   v      i v    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_84372579_8   1848 CTCAAAATAAGACATT--AATGCAGCCAACAA--ACATGAAAAAATGCTC 1893
                            v   v    i  v--    --     i  --         i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTC 893

  chrX_84372579_8   1894 ATCATCACTGGTCAT 1908
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (132 / 106)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


2443 23.02 4.03 2.16  chrX_84397210_84398876.rev      482  1176 (491)    L1M4_orf2#LINE/L1      201   908 (0)  

  chrX_84397210_8    482 CAAAATTGGGCAGAACTCA-ACT----GACTTCAAATTATACTGCAGAGC 526
                             i    --  i     -   ----i i      viv    i  i   
  L1M4_orf2#LINE/    201 CAAAGTTGG--AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84397210_8    527 TACAGTAACCTGGTAAAATAGCCTGGTAATGGCATAAA-ACAAACACATA 575
                                 i ----  i i  iv     v        i- i i   i   
  L1M4_orf2#LINE/    249 TACAGTAATC----AAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_84397210_8    576 GATGAATGGAATAGAATAGAGAACCCAGAAACAAATTCATGTATCTATAG 625
                            v             v    ii       i   ii   ii  i   i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_84397210_8    626 TGAACTCATTTTCAACCAAGGTGCTATGAACACGCATTGGGAAAAGGACA 675
                          v  i v      i  v i     i v  v  iv  v    i    i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_84397210_8    676 GTCTCTTCCACAAACTGTGCTGGGAAAACTGGGTATCCATACGCAAAGGA 725
                             i   v     iv         v      i  ?   i i     i  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_84397210_8    726 -TGAAATTAAACCTCTATCTCTCACCATATACAAGAATAAAATCAAAATG 774
                         -    i  ii   i   i   v            i   v  v        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_84397210_8    775 GACTAAAGACATAAATCTAATGCCTCAAACTATGAAACTACTACAAGAAA 824
                           ii ?    v     v   viv  v       i     vi  v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_84397210_8    825 ACATTGAGGAAGCTATTCAGGACATTGGACTGGGCAAAGATTTCTTGAGT 874
                             v i? v iv v   iv   v    ii i     v i      iii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_84397210_8    875 AATAAC-CCAGAAGCACAAACAACCGAAGCAAAAATGAACAAATGGGATT 923
                          - i  -   i        i    vi   v      ii i    v   i 
  L1M4_orf2#LINE/    595 A-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_84397210_8    924 ACATCAAG-TTAAAATCTTCTGTACAGCTTTTAA-----CT-T------- 959
                         v      i-      v   i   ---    iv  -----  - -------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGT---GCTTCAAAGGACACTATCAAGAAA 690

  chrX_84397210_8    960 GTGAAGAGACAACCCACAGAGTGAAAGAAAATATTTGCATACTGCCCATC 1009
                              i              i  ii              v iiiivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_84397210_8   1010 TGACAAGGAGGTAATAACCAGAATATATGAGGAGCTC--A-AAC--AATA 1054
                            i    iiv vi  v           i i  i   -- -   --    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_84397210_8   1055 GGAAAAAAATCTAATAATTTAATTTTTTAAAATGGGCCAAATATCTGAGT 1104
                         iv     i - v     iii    ?v--         v  iv  i   i 
  L1M4_orf2#LINE/    791 ATAAAAAGA-CAAATAACCCAATTWA--AAAATGGGCAAAGGATTTGAAT 837

  chrX_84397210_8   1105 AGAGATTTCTCAATAGAAGGTGTACAAATGGCAAACGGG-AGGTGTAAAA 1153
                            v       v v     i i          v  iii - vi  v   i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_84397210_8   1154 ATGTGCTCAACATCATTGATCAT 1176
                            --          ????????
  L1M4_orf2#LINE/    888 ATG--CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (101 / 55)
Gap_init rate = 0.03 (20 / 708), avg. gap size = 2.15 (43 / 20)  


3038 25.81 2.92 1.01  chrX_84421628_84427030.rev     4022  4912 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84421628_8   4022 TGGAGAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTTAAAAT 4071
                             i i i  i     i        v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84421628_8   4072 CACCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCTATTAAAC 4121
                         vi v     v      vii  i  i        i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84421628_8   4122 TACCAAGGATATTCTTCACAGAACTTGAAATAAAACT-ATTTTAAAATTC 4170
                          v   ivviiv  i  ii     v    v --- i  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA---AGCTGATCCTAAAATTC 147

  chrX_84421628_8   4171 ATATGGAACAAGAAAAAGAGGCCAAATAGCCAAGGCAATCATAAGCAAAA 4220
                                 - v v  ii  vv vi         ii     v i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_84421628_8   4221 AGAACAAAGCTGGAGACATCACGCTACCCAACTTCAAA--CTACTACAGG 4268
                                  i     ivv    i  v     i      --i       ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_84421628_8   4269 GCTACAGTAACCAAAACAGCATGGTACTGGTACAAGAACAGACACATAGA 4318
                                   i   i    ii         i i   i i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_84421628_8   4319 CCAAGGGAACAGAATAGAGAGCGCAGAAAAAAGGCCGCACACCTACAACT 4368
                         i   v    i     v     iv      v  iv  ii   ii  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_84421628_8   4369 ATCAGATCTTTGACCAAGCTGTCAAAAACAAGCAATGGGGAAAGGACTCC 4418
                          viv   i  i   v i v  i   i v  vv            i ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_84421628_8   4419 CTATTCAATAAATGGAGCTGGGATAACTGGCTAGCCATATGCAGAAGATT 4468
                           v     i      v       i      v  ?   i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_84421628_8   4469 GAAACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATTGA 4518
                            ii         v   i                 i       i  - -
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT-G- 494

  chrX_84421628_8   4519 CTGATTACAGTCTTAAATGTAAAACCCCAAACTCTAAAAACCCTGGAAGA 4568
                         --   i ?  v i         i v iv     v     vi i i     
  L1M4_orf2#LINE/    495 --GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_84421628_8   4569 CAACCTAAGC---AAT-------ACCATT---CTGGACA-TAG------A 4598
                         v   v  i ?---   -------   -  ---i i i  - i ------ 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTA 591

  chrX_84421628_8   4599 AACAAAATGTCAAAAGCAATCCCAACAAAAGCAAAATT-GACAAATAAAA 4647
                         i i vi iii        vvvv         v    v -  i    vii 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_84421628_8   4648 TCTAACTTAACTAAAGAGCTTCTGCACGTTAAAGGAAACTATCAACAGAG 4697
                         ii v iiv  v v  i i   i  ii v i      v        v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_84421628_8   4698 TGAAACGAAAACCTATAGAATGGGATAAAATATTTGTCAACTACACATTT 4747
                              v  v    i i         v          iv  ii i i  i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_84421628_8   4748 GACAAGT--CTAATATCCAGCATCTATAAGGAACTTGCACAAATTTACAA 4795
                           i   v--  vi       v  v     i     ivi    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_84421628_8   4796 GAGAAAAGCAAACAACCCGATTAAAAAGTAGGCAAAGGACATGAACAGAC 4845
                         v i   ii    i     i   ?    i i         iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_84421628_8   4846 ACTTCTCAAAAGAAGCCATACATGTAACCAACAAGCATATGAAAAGAAAC 4895
                          i     v       vi     vi ii    i     i         vi 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_84421628_8   4896 TCAATATCACTGATCAT 4912
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (144 / 82)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.50 (35 / 14)  


1100 25.20 2.02 7.86  chrX_84455843_84457879.rev      502   997 (1040)    L1M4_orf2#LINE/L1      215   681 (227)  

  chrX_84455843_8    502 TCAGACTATCTGATTTGAACATTTACTATAAAGCTATAGTAATCAAGACA 551
                            v   vi ii    v  v i      i       i             
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_84455843_8    552 ATGTTCTGTTGGAA-AAGCGTGTTCTATATCTATTGGATACAGAAAAATA 600
                         i   vv ii   v -   vi ----- v i-------   i   vv   i
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGAT-----AGAC-------ATATAGATCAATG 302

  chrX_84455843_8    601 AAATGGAATTGAGAACCCAGAAATAGGCACACACATACATAGTCAATTGG 650
                         i   i         ii         ii v  i    vi  i        i
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_84455843_8    651 AATTCAA-AAGTGGTGAAAAAGCAATTAAACGGAGAA-GAATGGAATTTT 698
                         vv   i -   -    vv  ii v   v  i  i   -    i vv    
  L1M4_orf2#LINE/    353 TTTTCGACAAG-GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_84455843_8    699 CTTCAAATATT-CTAGGGCAACTGTACTTCCACGTGCAAAAAAAAGAAAA 747
                          vv     iv -  i  i      v iv?    i       i  v   i-
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG- 450

  chrX_84455843_8    748 AAGAAAAAAAAAGAATCTTGACATGGACCTCTTACAAGTTACAGTAAATG 797
                         ----------------i v   vivv     vi  v vv    i-    v
  L1M4_orf2#LINE/    451 ----------------TTGGACCCCTACCTCACACCATATACAA-AAATT 483

  chrX_84455843_8    798 AATTCATCATTGATTATGGACCTACACATA-GAACTAAAAACTACAAAAT 846
                           i   vv  v   i ?i      v ii  -  i      -   i    i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAAC 532

  chrX_84455843_8    847 TAATTAGAAGAAAATATA-----AAATTCTTACAACATTGGGTTAGACAA 891
                          v-           i   -----    ii iiii  v         i   
  L1M4_orf2#LINE/    533 TC-TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_84455843_8    892 ATATTATATATACATATATGACACCAAAAGCACAATATATAAAAAAGAAA 941
                         vvi  --- v -i v                    vvv i    i i   
  L1M4_orf2#LINE/    582 TGGTT---TCT-TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_84455843_8    942 ATAAGAATAAATTGGTCTTTGTTAAAATTAAAATCTTCTGTACTTTGAAA 991
                            i--         v   ii i          v   i   i   ii  i
  L1M4_orf2#LINE/    628 ATAG--ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_84455843_8    992 GTCATT 997
                          v  i 
  L1M4_orf2#LINE/    676 GACACT 681

Transitions / transversions = 1.37 (71 / 52)
Gap_init rate = 0.03 (16 / 467), avg. gap size = 3.06 (49 / 16)  

 653 21.08 8.97 1.79  chrX_84455843_84457879.rev     1324  1546 (491)    L1M4_orf2#LINE/L1      670   908 (0)  

  chrX_84455843_8   1324 TCAAAAGTCATTGTTAAGAAAGTGAAAATACAAGCCA-ATGATGGGGGGA 1372
                              i v  i i i             v    v   - vi     i i 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_84455843_8   1373 AATATTTGCAAAATGTACATCTCATAAAAGAC--ATACCCAGAAAACATT 1420
                                     vii  i    v    ii   --i  i      v i  -
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT- 768

  chrX_84455843_8   1421 TTTAAAAAATCCTCAAGCCTCAACAATTAAAA---AAAGAA--------A 1459
                         ---   i  ii  i viv     i   v    ---   v  -------- 
  L1M4_orf2#LINE/    769 ---AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_84455843_8   1460 AAAA-----AAAGGATTTCAACAGATAGTTGTCCAAAGAAGAAAAATGGA 1504
                             -----         v  i   i v  v           v v iii 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_84455843_8   1505 TGGAAAGTAAGCATATGAAA-GATGCTCAGCATCATGATTCTT 1546
                            vv i      i      -        i     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (29 / 18)
Gap_init rate = 0.03 (7 / 239), avg. gap size = 3.43 (24 / 7)  


3201 25.92 1.34 0.34  chrX_84457909_84462547.rev     3254  4148 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_84457909_8   3254 AAAAAATTCTATGTTGATGAATTGTAAGAATCAATATTGTTAAAATGTCC 3303
                           i v  i i     v   i    v    v i           i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_84457909_8   3304 ATACTACCCAAAGCAATCTTCAGATTCAATGCAATTTTTGTCAAAATACC 3353
                              v      vii    v         i     iii i       v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_84457909_8   3354 AATGACATTCTTCACAGAAATAGACAAAG-AATCCTAAAATTTATATGGA 3402
                          iivi v  i  ii       v     iv-i           i       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_84457909_8   3403 ACCATGAAAGACCCAGGATAGCCTAAGCTATCCTAAGCAAAAAGAACAAA 3452
                          viiii ii       i      v  i v   i i iv  i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_84457909_8   3453 ACTGGAGGAATCACGTTACCTAATGT-AAAATTATATTACAGAGCTTTAA 3501
                         ii       v    ii v  i   v -    i -  i    i    vi i
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAG 253

  chrX_84457909_8   3502 TAACCAAAACAACATGATACTGGCATAAAAACAGGCACATAGACCAAAGG 3551
                            i   i   iii  i           ii i  i  i     i   v  
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_84457909_8   3552 AGCTGAATAGAGCAGCAAGAAACAAGTCCACACACCCACAGTGAACTTAC 3601
                          iiv    v   viv v     i  ii   i   iii ii  v  i v i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_84457909_8   3602 TTTCAACAAAGCTGCCAAGAACATACACTGGGGAAAAGACAGTCTCTTGA 3651
                             i    i v        v   v  v        ii i     i  v 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_84457909_8   3652 ATAAACAGTGCTGGGAAAACGGAATATCCACAGGCAAGA-AATAAA-CTA 3699
                          i   ii         v   v i   ?     v    i -   i  -i i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_84457909_8   3700 GACCACTATCTCTCACCATATAAAAAAATCCAATCAAAATTGATTAAAGA 3749
                             v   i   v         v      iv v       v   i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_84457909_8   3750 GTTAAGTCTAA-ACCTCAAACTATGAAACTACTATAAGAAAACATCGGAA 3798
                         vi   i v   - v  v       i     vi  v          v  ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_84457909_8   3799 AATGTCTCCAGGACATTGGTCTGGGCAAAAATGTCTTAGGCAATACCCCA 3848
                         v vi   i iv   v    vi i     vii v      ii vv  v   
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_84457909_8   3849 CAAGCACAGGCAACCAAAGCAAAAATGGACAAATGGGATCATATCAAG-T 3897
                         v       i     v    v      i  i    v   iivi     i- 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_84457909_8   3898 TAAAAAGCTTCTGCACAGCAAAGGGTACAATCAACAAAGTGAAGAAACAA 3947
                               -   i  ii vv      ii  v     v        i i    
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_84457909_8   3948 CCCAGAGAATGGAAGAAAACATTTTGAAACTATCCATCTGACAAGGAATT 3997
                             v       i      i    vv   ii  vi      i    i i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_84457909_8   3998 AATAATAAGAATATATAAGGAACTCAAACAACTCTATAGGAAAAAATGTA 4047
                         vi  viv           i      vv       v   iv     ivvv 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_84457909_8   4048 ATAATCCCATCAAAAAATGGGCCAAACATTCTGAGTAGACATTTCTCAAA 4097
                             i  v  i?          v  iv   -   i            v  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATT-TGAATAGACATTTCTCCAA 851

  chrX_84457909_8   4098 AGAAGGCATAAAAATTGCAAACAGGCATATG------TGCTCAACATCAC 4141
                              ii   v    v  v  i i   i   ------            ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_84457909_8   4142 TGATTAT 4148
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.51 (137 / 91)
Gap_init rate = 0.01 (10 / 904), avg. gap size = 1.50 (15 / 10)  


2916 27.45 1.21 1.10  chrX_84463415_84465657.rev      846  1752 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84463415_8    846 TGGAGAAACATTCCATGCTCATGAATAGGAAGAACCAGTATTGTGAAAAC 895
                             i i i  i     i     i  v      vii i      v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84463415_8    896 GGTCGTACTGTCCCAAGTAATTTATAGATTCAGTGCTAACCCCATCAAGC 945
                           ivi    vi  v  v i  i  i       ii  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84463415_8    946 TACCATTGACTTTCTTCACAGAAAAAAAAAAAAACT-ACTTTAAATTTCA 994
                          v   vivi i  i  ii      vvi v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_84463415_8    995 TATGAAATCAAAAAAGAGGCC----ATTTAACCAAGACAATCCTAAGCAA 1040
                             i  -- viv   i i  ----  -- i    i      i i iv  
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAAT--AGCCAAAACAATCTTGAAAAA 194

  chrX_84463415_8   1041 AAAGAACAAAGCTGGAGGGATCACACTACCTGACTTTAAGCAA--TACTA 1088
                         i          i      iv       v  ii i  i  --  --     
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA--AACTTACTA 242

  chrX_84463415_8   1089 CAAGGCTACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGATATG 1138
                            i          i   i    ii        vi iv ii i   i  i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_84463415_8   1139 -AGACCAATGCAACAGAACAGAGGCCTCAGAAATAACACCACACATCTAC 1187
                         -   i     v  i    iv   ivii         vv   i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_84463415_8   1188 AACCATTTGGTCTTTGACAAACCTGACAAAAACAAGCAACGGGGAAAGGA 1237
                         iii  v   i i  i     ivv  v   i v  vv   i        i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_84463415_8   1238 TTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGAAGAA 1287
                          vvi  v  i  i        i     v      v  ?   i   v i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_84463415_8   1288 AACTGAAACTGGACCCCTTCCTTATATCTTATA-AAAAATTAACTTAAGA 1336
                         i v    ii         v   i i i v    -           i  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_84463415_8   1337 TGGATTAAAGACTTAAACGTAAGACTTAAAACCATAAAAACCCTAGAAGA 1386
                              i ?    i    i      vi      i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_84463415_8   1387 AAACCTAGGCA-ATACCATTCAGGACATGGGCATGGAGAAAGTCTTCAT- 1434
                             v    ?i- v i -   iv   v v  vv i iv  v vi   v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_84463415_8   1435 GATGAAAACACCAAAAGCAATAGCAACAAAAGCAAAAATGGACAAATGGG 1484
                            - vi            vv           v      i  i    v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_84463415_8   1485 ATCTAATTGAACTAAAGAGCTTCTGCACAGCAAAAGAAAGTATCTTCAGA 1534
                          ii v  ii  v v  i i   i  ii vv    i  v v    vvv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_84463415_8   1535 ATGAACAGGCATCCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATC 1584
                         i    v  i  v  i                 v       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_84463415_8   1585 TGACAAAGGGCTAATACCCAGAATCTACAAAGAACTTAAACACATTTACA 1634
                            i  i  i  vi  i       v  i        ivv   vv iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_84463415_8   1635 AGAAAAAAACAAACAACTCCATGAAAAAGTGGGCAAAGGATATGCATAGA 1684
                          v     i     i   i v  v?    i            v  v     
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_84463415_8   1685 CACTTCTCAAAAAAAGACATTTATGCGGACAACAAGCATATGACAAAAAG 1734
                           i     v   i    i  vi vii  v   i     i    v  i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_84463415_8   1735 CTCAATATCACTGATCAT 1752
                              i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (149 / 96)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


3245 27.09 0.44 0.44  chrX_84480528_84489512.rev     4878  5785 (3200)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84480528_8   4878 TGGAAGAATATTGCATGCTCATTGGTAGGAAGAGTCAATATCGTGAAAAT 4927
                              ii    iv    i    v i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84480528_8   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84480528_8   4978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_84480528_8   5026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAACCAAAAG 5075
                                viiv  ii  v  v v  v     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_84480528_8   5076 AACAAAGCCGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5125
                                ii     vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84480528_8   5126 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii        vi iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_84480528_8   5176 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACTTATCTACAAGT 5223
                                i    i--    i  --        vv   ivi  i  iiivi
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_84480528_8   5224 ATCTGATCTTTGACAAACCTGACAAAAAGAAGCAATGGAGAAAGGATTCC 5273
                          vi    i  i     ivv  v   i vv vv      i     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_84480528_8   5274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_84480528_8   5324 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAGGATGGA 5373
                            ii    i    v   i     v           i  i   ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_84480528_8   5374 TTAAGGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?i   i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_84480528_8   5424 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5473
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_84480528_8   5474 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5523
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_84480528_8   5524 TTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5573
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_84480528_8   5574 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5623
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_84480528_8   5624 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5673
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_84480528_8   5674 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5723
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_84480528_8   5724 TCAAAAGAAGACATTTATGCAGCCACAAAACACATGAAAAAATGCTCACC 5773
                           v        i  vi viii    vv  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_84480528_8   5774 ATCACTGGCCAT 5785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (141 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

2754 24.07 5.51 3.37  chrX_84480528_84489512.rev     7617  8505 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84480528_8   7617 TGGAAAGATATCCTTTGTCCGTGGATTGGAAGAATTGTTATTGTTAAAAT 7666
                                      iv   i i            v  iv         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84480528_8   7667 ATTCATACTACTCAAAGTAATCTACAGATTCAAGGCAACACCTATCAAAA 7716
                         iviv     v i    v i              v    iv          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84480528_8   7717 TACCAA-TGTCTTTCTTCACAGATATACAACAAAC-AATCCTTAAAATCA 7764
                          v   i-  i    i  -i    v  -ii    i -i     v   v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chrX_84480528_8   7765 TATGGACCTACAAAAGACTCTGAATAGCCAAATCAATCTTAAGCAATAAG 7814
                               vv i   ii   i v           v       i iv  v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_84480528_8   7815 AA-AAAGCTGGAGGCATCATACTACTTGACTTCAAAATATACCACATTTC 7863
                           -    i      vv   i   v iii i       iv   i   vvv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84480528_8   7864 TCTGGTAACAAAAAAGGCATAGTACTGGCATAAAAATGGTCACATAAACC 7913
                          vii    iv  i vi ii i            ii  i v  i   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_84480528_8   7914 AA-GAAACAGAATTGAGAGCACAGAAGTAAA----TACATCTACAGCCAA 7958
                           - i  i           iv     i    ----     i  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_84480528_8   7959 GTAACTTTCCACAAAGGGGCCAAGAACACATACCA-GGGGAAAGAACGAG 8007
                         v i i    v    i  v       - -   v v -          iiiv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGA-C-CATTCAATGGGGAAAGAATAGT 396

  chrX_84480528_8   8008 CACTTCAATAACTGGGGCTGAAAGAAAACTGTATATCCTCACATAGAAGA 8057
                          vi     i  v   v    i--  v     v   ?  v  iii i    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGG--GACAACTGGATAKCCACATGCAAAAGA 444

  chrX_84480528_8   8058 ATGAGGTTAGACCCCTATCTTTTACCATATACAAAAATCAACTCAAAATG 8107
                             i   i        i  ivi               i           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_84480528_8   8108 GATTAAAAACTTAAAGGTAAGAACTAAA-CTATGTTGCTACTAGAA---- 8152
                            i ? i  i    v      i     -    ivvi  vi     ----
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_84480528_8   8153 -TATAGGGG-AAATGCTTCATGGCATTGTACTGAGCAA------------ 8188
                         -i     ? -    -    i  i v   vii ii    ------------
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_84480528_8   8189 ---------GAAGGTAAGAGCA-CAAAAGCAAAAATAGGCAAGTGGGATT 8228
                         ---------i  i i vi    -      v        ii  i v   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_84480528_8   8229 GCATTAAACTAGAAAACGTATGCACATCAAAAGAAAGGATCAACA--GTG 8276
                         v   i   v vi     v v  ii v     i  v vv     v --   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_84480528_8   8277 GA--GAAAATCTCCAGAATGGAGGAAAATAATTGCAAACTATACATCTGA 8324
                         i --  v  i iv        ii       v       ii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_84480528_8   8325 CAAGGGGTCAATATTCATAATATATAAGGAA----TGCAACTCAATAGCA 8370
                         i     iiivi   i  v         i   ---- i          ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_84480528_8   8371 AAAA---AAATACACACAAGAAATAAAAGATTGTTTTTAAAATGGGCAAA 8417
                             ---     -  v   ---------------  ?v            
  L1M4_orf2#LINE/    794 AAAAGACAAATA-ACCCAA---------------TTWAAAAATGGGCAAA 827

  chrX_84480528_8   8418 ATACCTTAATAGATATTTTTCAAAATAACACAAACATATGGCCACTGGGT 8467
                         iv ii v      i    i  v   v  v i v   v       v ii i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_84480528_8   8468 CTATAAAATAATGCTCAACTTTCCTAATCATCAGGTAA 8505
                         vi  i   vi         -------    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAAC-------ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (130 / 80)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.29 (79 / 24)  


 470 14.88 3.31 5.79  chrX_84526077_84534055.rev      329   449 (7530)  C L1M4_orf2#LINE/L1   (0)   908   791  

C chrX_84526077_8    449 ATGAAAAGTACAAATTCTAGTAATCCAAT-AAAAAATGAGCAAA---TCT 404
                           i     -      ------  i     -?       i     --- i 
  L1M4_orf2#LINE/    791 ATAAAAAG-ACAAAT------AACCCAATTWAAAAATGGGCAAAGGATTT 833

C chrX_84526077_8    403 GAATAGGCATTTCTCAAAGGAAGGCATAAAAGTGGCAAACAGGTATATGA 354
                               i        v  i    ii   v  i    v  i i i i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

C chrX_84526077_8    353 AAAGGTGCTCAACATCATTGATTAT 329
                             i            ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.67 (14 / 3)
Gap_init rate = 0.03 (4 / 118), avg. gap size = 2.75 (11 / 4)  

1343 27.75 0.27 0.00  chrX_84526077_84534055.rev     2182  2545 (5434)    L1M4_orf2#LINE/L1        4   368 (540)  

  chrX_84526077_8   2182 AAACATATTTTATGTTTATGGACT-GAAGACTTAATACTGTAAAAATGTT 2230
                            v    iii     i     i -            i   v  i   vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_84526077_8   2231 CTTACTACTCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAACAC 2280
                         vv    v i    vii              i                iv 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_84526077_8   2281 CAATGACATTCTTTACAGAAATAGAAAACACAATCTTAAAATGTATACAG 2330
                           iivi v  i   i       v  v  vvii   i      vi   ii 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_84526077_8   2331 AACCACAAAAGATTCAGAATAGCCAAAGCTATCCTAAGCAAAAAGAACAA 2380
                           vii   ii  ii             i v   i i iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_84526077_8   2381 AACTGGAGGAATCACATTACCTGACTTCAAATTATACTATGAAGCTATAG 2430
                          ii       v     i v  ii i      viv     ii      i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_84526077_8   2431 TAAACAAAATAGCATGGTCCTCACATAAAAACAGACACATAGACCAATGG 2480
                            v   i i  ii    v  vi     ii i     i     i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_84526077_8   2481 AACACAATAGAAAACCCAAAAATAAATCCACACATATACAGTAAACTCAT 2530
                           i v   v  i ii   i       i   i    v  ii  v  i v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_84526077_8   2531 TATTAAGAAAAGTGC 2545
                          v ii v  ii    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGC 368

Transitions / transversions = 2.16 (69 / 32)
Gap_init rate = 0.00 (1 / 365), avg. gap size = 1.00 (1 / 1)  

1779 25.14 4.76 0.95  chrX_84526077_84534055.rev     2903  3427 (4552)    L1M4_orf2#LINE/L1      364   908 (0)  

  chrX_84526077_8   2903 GGTGCCAAGAAAATACACTGGGGAAAGGACAGTCTCTTCAATAAATCGTA 2952
                                   vv  v  v         i i     i     i    v  i
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_84526077_8   2953 CTGGGAAAACTGGATATCCATATGCAGGAGAATGAAACTAGACCCCTATG 3002
                               v         ?   i     ii        ii i        iv
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_84526077_8   3003 TCTCAACTTATACAAAAACCAAATTGAAATGGATTAAAGACTTCAATCTA 3052
                           v  v v          ii  v ii        i ?    i v   v  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_84526077_8   3053 ATTCCTCTAACTATGAAACT-TTAAAACAGAACATTGGGGAAACTCTCCA 3101
                          vvv  vv      i     -   i  v i     v  ? v  v   i i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_84526077_8   3102 GGATGTTGGTCTGGGAAAAAATTTTTGAG---CAATACCCTAAGCACAGG 3148
                         v  iv    vi i  v  vii   i v  ---ii i   vv       i 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_84526077_8   3149 CAACCGAAGCAACAATGGACAAATGGGATCACATCAAT-TTAGTAAGCTC 3197
                             vi   v  v   i  i    v   iiv      v-   i-  i  i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA-AAACTT 662

  chrX_84526077_8   3198 CTGCACAGCAAAGAAATCAATCAACAAAGTGAAGAGTCAACTCACAGAAT 3247
                         i  ii vv     i vv v     v        i  v    i        
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_84526077_8   3248 GGGAGAAAATATTTGCAAAGTATGCATCTGAC--GAGATTAATAAGCAGA 3295
                                            vi  ii      i-- i  i vi  vv    
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_84526077_8   3296 ATATATAAGGAGCTCAAACATCTCTATAGT---------------CTAAT 3330
                                 i  i   vv   v   v   i --------------- i   
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_84526077_8   3331 ---AAAATGAGCCAAACACCTGAGTAGATTTTTCTCAAAAGAAGGCATAC 3377
                         ---      i  v  iv ii   i    iv      v       ii    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_84526077_8   3378 AAATGGCAAACAGGCATATGTAAGGGTGCTCAATGCAAATCATAACTACA 3427
                                v  i i   i   v  i i       i----    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAAC----ATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (72 / 57)
Gap_init rate = 0.01 (8 / 545), avg. gap size = 3.75 (30 / 8)  

2332 25.21 2.05 1.64  chrX_84526077_84534055.rev     4364  5093 (2886)  C L1M4_orf2#LINE/L1   (0)   908   176  

C chrX_84526077_8   5093 CCAAAA-AAT---GGAAAA--ATAACAAAACTGGAGAAATTACATTACCT 5050
                               -   --- i    -- v      ii     i v i   i v  i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

C chrX_84526077_8   5049 GACTTTGAATTATACTATAGAGTTACAATAACCAAAACAGCATAGAACTG 5000
                         i i  ii  viv     i i  i    i   i   i    ii i v    
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

C chrX_84526077_8   4999 GCATAAAAACAGAAACATAGACCAATGGAACAGAATAGAGAACCCACAAA 4950
                               ii i   v i     i        i     v    ii   v   
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

C chrX_84526077_8   4949 CAAATGCACACACCTATAGTGAATTCAATTTCGACTAAGGTGCCAATAAC 4900
                         i   iv  i   ii   i  v    v v       v i        v v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

C chrX_84526077_8   4899 ATGTACTGGGGAAAAGACAGTCTCTTCAATAAATAGTGCTGGTAAAACTG 4850
                           vi v        ii i     i     i    i       v v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

C chrX_84526077_8   4849 GATATCCATATGCAGAAGA--GA--CTAGACCCCATCCCTGGACAC---A 4807
                             ?   i     i    --  --i i      - v   v-    --- 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCC-TACCTC-ACACCATA 473

C chrX_84526077_8   4806 TACAAAAATCAAAACAAAAAGAATTAAAGCCTTAAATGGAAGATTTCAAA 4757
                                  i  vv     v i  i ?  v i      v    vi v   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

C chrX_84526077_8   4756 CTACAAAACTACTAAAAGAGAACTTTGG-GCAAACTCTCCAGGACATTGG 4708
                            i      vi  i    i   v v  - i   -   i iv   v    
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGG 572

C chrX_84526077_8   4707 ACTGGGCAAAGGTTTCATGAGTAATACTTCACAAGCACAGGCAACCAAAG 4658
                         ii i     v      v iii  vv  vi  v       i     v    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

C chrX_84526077_8   4657 CAAAAATGGACAAATGGGATCACATCAAG-TTAAATAGCATCTGCATAGC 4609
                         v      i  i    v   iiv      i-     - i v i  iiivv 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTC 671

C chrX_84526077_8   4608 AAAGGATACAATCAACAAAGTGGAGAAACAACTCACAGAATAGGAGAAAA 4559
                               i  v     v      i i i     i        i        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

C chrX_84526077_8   4558 TATTTGCAAACTACCCATCTGACAGGGAATTAATAGCGAGACTATAAAAG 4509
                                   ii ivi      i i  i i vi  v v   v    v  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

C chrX_84526077_8   4508 GAGCTCAAACAACTCTACAGGAAAAAAATCTAAAAATCCAATCAAAAAAT 4459
                           i   vv       v i iv     i - v  v  i     i?      
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAAT 820

C chrX_84526077_8   4458 GGGCCAAACATCTGAGGAGACATTTCCCAAAAGAAGCCATAAAATTTGCA 4409
                             v  iv  i   iv         i v       vi   v  v v  v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

C chrX_84526077_8   4408 AACAGGTATATGTAACAGGCAAATGTGCTCAACATCTTTGATTAG 4364
                           i i i i   v  ----- i   --         v????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAA-----AGATG--CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (109 / 72)
Gap_init rate = 0.02 (15 / 733), avg. gap size = 1.80 (27 / 15)  

 332 25.00 0.00 0.00  chrX_84526077_84534055.rev     5743  5830 (2149)  C L1M4_orf2#LINE/L1   (818)    90     3  

C chrX_84526077_8   5830 GAAACACATCCCATGCTCATGAATGTGTAGAATCAATATTGCAAAAATGA 5781
                             v i        i     i  vv v   v i       iv  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

C chrX_84526077_8   5780 CCATACTGCCAAAAGCAATCTACAAATTCTAAGCAATC 5743
                          v     v  v   vii       i    v v      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

Transitions / transversions = 0.83 (10 / 12)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.00 (0 / 0)  


2772 28.27 1.33 0.67  chrX_84544635_84550399.rev     4373  5274 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84544635_8   4373 TGGAAAAACATTCCATGCACATAGAAAGGAAGATTCAATATAGTTAGAAT 4422
                               i i  i     iv   i  vv      i i     v    ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84544635_8   4423 GGCTATACTGCCCAAAGCAATTCATAGATTCAATGCTATTGCCATCAAAC 4472
                            v     v      vii  ii i        i  v  iv i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84544635_8   4473 TTCCATTGACATTCTCCACAGAACTAGAAAAAACT-ATTTTAAAATTTAT 4521
                          i   vivi v  i iii     v v  v  i-  -  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_84544635_8   4522 ATGGAATCAAACAGAGCCCA-AACGTCCAAGGCAATCCTAAGTGAAAAGA 4570
                               viiv vi ii    -  iiv    ii     i i ivi i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_84544635_8   4571 TCAAAGCTGGAGGCATCACACT-ACTGACTTCAAAAAATACTACAGGGCT 4619
                         v     i      vv       -v ii i       vv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_84544635_8   4620 ACAGTAACCAAAACAACATGGTACCAGTAGAAGAACAGACACATAGACCA 4669
                                i   i   iii      ii i v   i i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_84544635_8   4670 ATGGGACAGAATTGAGAACCTAGAAATAAGAATGCACACCTACCACTATC 4719
                             i i          ii i        ivviii   ii  iviii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_84544635_8   4720 TGATCTTCATCAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCCCTA 4769
                             i   iv   ivv  v   i v  vv       i    i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_84544635_8   4770 GTCAATAAATGGTGCTGGGTTAACTGGCTAGCCATATGCATAAGATCGAA 4819
                         v    i             vi      v  ?   i     v    vi   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_84544635_8   4820 AATGGACTACTTCCTTACATTATGTAAAATAATTAACTCAAAATTAATTA 4869
                         iv     iv  v   i   ii  i  v  v              vi  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_84544635_8   4870 AAGACTTAAAATGTAAATCCCAAAACTATAAAAACCCTAGAAGACAGCCT 4919
                         ?    i    -     ivv i            vi i       v i v 
  L1M4_orf2#LINE/    500 WAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_84544635_8   4920 AGGCA-ATACCATTCAGGACATAGGCACAGGCAAAGATTTCAT-GATGAA 4967
                            ?i- v i -   iv   v v  vvi      v i    v -   - v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chrX_84544635_8   4968 GACACCAAAAGCAATTGCAACAAAAGCAAAAATTGGCAAATGGGATCTAG 5017
                                      vvv          v      v ii    v   ii vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_84544635_8   5018 TTAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTGAAA 5067
                          i  iv v  i i   i  ii vv    i  v        v i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_84544635_8   5068 AAACAAACTACAGAATTCAAGAAAATTTTTGTAAACTATGCATTCTACAA 5117
                          i    v i       vvi       v    i   ii  ii  iiv i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_84544635_8   5118 AGGTCTAATATCCAGCATCTATAAGGAACT--TA-AATTTA-TAAGAAAA 5163
                         i  v  vi       v  v     i     --  -  i i -   v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_84544635_8   5164 GAACACACAACTACA--TAAAAAGTGGATAAAGGACATGAACAGAGGCTT 5211
                         ii   v i   i-  -- ?    i   ii      iv    i   vii  
  L1M4_orf2#LINE/    797 AGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_84544635_8   5212 TTCAAAAGAAGACATACATGCAGCCAACAAGCATAGGAAAA-ATATCTCA 5260
                         i  v        i     viii     i     i v     -  i-    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG-CTCA 894

  chrX_84544635_8   5261 ACATCACTGATCAT 5274
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (155 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.12 (18 / 16)  


3253 26.98 0.44 0.44  chrX_84589864_84598715     4865  5772 (3080)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84589864_8   4865 TGGAAGAACATTCCTTGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4914
                              ii i  i  v  i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84589864_8   4915 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCAACAAGC 4964
                            v     v     iv i  i           i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84589864_8   4965 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5012
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_84589864_8   5013 TAGGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5062
                           v    viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_84589864_8   5063 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5112
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84589864_8   5113 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGATC 5162
                                 i   i    ii         i i  ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_84589864_8   5163 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACGTATCTACAACT 5210
                                i    i--    i  --        vv   iii  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_84589864_8   5211 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5260
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_84589864_8   5261 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5310
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_84589864_8   5311 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5360
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_84589864_8   5361 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5410
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_84589864_8   5411 CTAGGCATTACCATTCAGGACATAGGCTTGGGCAAGGACTTCATGTCTAA 5460
                         v    ?i v viv   iv   v v  v  i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_84589864_8   5461 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5510
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_84589864_8   5511 TTAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTACCATCAGAGTGAGC 5560
                          i   v v  i i  ii  ii vv    i  v    i  vv i     iv
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_84589864_8   5561 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5610
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_84589864_8   5611 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5660
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_84589864_8   5661 AAACATAAAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5710
                          i   v v     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_84589864_8   5711 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5760
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_84589864_8   5761 ATCACTGGCCAT 5772
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

3465 24.78 2.13 0.34  chrX_84589864_84598715     7468  8359 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84589864_8   7468 TGGAAAGACATCCCACATTCATGGATTGGAGGAGTCAATATTGTTAAAAT 7517
                                 i      ii             i  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84589864_8   7518 GTCCATACTATCCAAGC-AATCTACAAATTTGATGCAATCGCTATGAAAA 7566
                          v v     vi    ii-i       i   ii i      v    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84589864_8   7567 CATGAAGGATATTCTTCATAGAAAT--A-AAAC--ATCCTAAACTTCATA 7611
                         iviv ivviiv  i  iii      -- -  i --        v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_84589864_8   7612 TGGAACCACAAAAGACCCTGAATACCCACAGCAATCTTGAACAAAAAAAA 7661
                              vii   ii     v     v   v i          -   i  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chrX_84589864_8   7662 ACAAGAGTTG------TCACACTACATTACTTCAAAATATGCTACAAAGC 7705
                             -     ------       v viv i       iv i         
  L1M4_orf2#LINE/    200 ACAA-AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84589864_8   7706 TATAGTAACAAAAACAGCATGATACTGGCATAGGAACTGATACAGAGACC 7755
                           i     iv  i    ii  i          i i iv  i i v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_84589864_8   7756 ACTGGAGCAGAATAGAGAACTCAGAAATAAATCTACACATTTACAGCCAT 7805
                          v    ii     v    iii          i i i       ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_84589864_8   7806 CTGATTTTCCACAAAGGTGTCAAGAACACACATTGGGGAAAGAACAGTCT 7855
                         i        v    i    i     v  iv  v           i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_84589864_8   7856 CTTTAATAAATGCTGTTGGAACAACTGGATATCCACATGTAGGAGAATGA 7905
                         i  i  i     v  i   i           ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_84589864_8   7906 AACTAGACCCTTATCTTACCTCATGTACAAAAATGAACTCAAAATGGATT 7955
                          ii i     i  i  i  vi   i         v              i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_84589864_8   7956 AAATACTAAAATCTAAAAGCCAAAATTATAAAACTTCTAGAAGAAAATAT 8005
                          ? v  iv    v   i   i    i         ii          i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_84589864_8   8006 AGGAGAAAAACTATATGACATTAG-TCATGTTAATGATTTTTTGGATATA 8054
                            ? v   v  vii    v  i - i v i-    i   i  i     i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTAGATATG 597

  chrX_84589864_8   8055 ACACCGAAAGCACAGGAAATAAAAACAAAAATAAACACGTTAAACAACAT 8104
                              i        i v  i    iv       i i vi  ii  vv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_84589864_8   8105 CAAA-CTAAAAAGCTCTACAAGGCCAAGAAAGCAGTTAATAAAATAGAAA 8153
                             -i      vi i iiivvv v   i vi vi i  v   i ii   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_84589864_8   8154 GACAATCTATAGAATAGGAGAATATATTTGCTAACCATCCCTCTGATAAG 8203
                              i i i     i      v        v  i   viv         
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_84589864_8   8204 GAGTTAATATACGAATTATATAAAGAACTTAAAGAATTCACTAGCAAGAA 8253
                          iii vi   v ii v             ivv v  i   v  ii  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_84589864_8   8254 AACAA----TCCAGTTTTAAAATGGGCAAAGGACCTGAATAGATATTTCT 8299
                         i    ----i   i  ?v               ii        i      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_84589864_8   8300 CAAAAGAAGACATACAAATT-CCAAGAGGTATATGAAGAAATGCTGAACA 8348
                          v        i        v-    v i i i     i i     v    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_84589864_8   8349 TCACTGATCAT 8359
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.10 (147 / 70)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


2690 27.51 2.28 1.26  chrX_84606242_84608229.rev      616  1491 (497)    L1M4_orf2#LINE/L1        4   888 (20)  

  chrX_84606242_8    616 AAAAACATCTCATGCTTACAGATTGGATGCATCAATATCGTTAAAATGGC 665
                            i i   i    i i ii       v vv i     i     i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_84606242_8    666 A-TACTGCCCAAAGCAATTTACAGATTCAACAATATTCTTATCAAACTAA 714
                          -    v      vii  i            ivv  i i       v vv
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_84606242_8    715 CA-TTGCCACTCTTTAGAGAATTAGAAAAAAAAGTTCTAAAATTCATATA 763
                           -i    -i i   iv    v v  v  ivvii i             i
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_84606242_8    764 GAACCAAAAAAGAAACTGAAGAGCTAAAGAAATCCTAAGCAAGAAAGAAC 813
                            viiv  ii  vv v   v   i   iv    i i iv     -    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GAAC 201

  chrX_84606242_8    814 AAAGCCAGAGGCATCACACTACCTAACTTCAAATTATATTATAAGGCTAT 863
                             iii    vv       v  i  i      viv  i  i  i    i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_84606242_8    864 AGTAACCAAAACATCATGGTACTAGCACAAAACTAGGCACATAGACCAAT 913
                              i   i   vii       i   i  iiv   i  i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_84606242_8    914 GGAACAGAATAGTAAACTCAGAAATAAAGCCTCATACTTACAAACATCTG 963
                             i     v vi iii          v  vi i i   iiiv  vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_84606242_8    964 ATCTTTGACAAGGCCAACAAAAACAAGCAATGGGGAAAGGAT--TCTCAA 1011
                           i  i       viiv   i v  vv            i  --   i--
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-- 399

  chrX_84606242_8   1012 TTCAATAAATGGTGCTGGGATATAGCTGGATAGCCATATGCAGAAGATTG 1061
                              i              i --i       ?   i     i    v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACA--ACTGGATAKCCACATGCAAAAGAATG 447

  chrX_84606242_8   1062 AAACTGGACCCTTGCCTTTAAACATATATAAAAATTAAGTCAATGTGATT 1111
                           ii       i i   ivv v      i         v    vi  iv 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_84606242_8   1112 TGAAGACTTAAATGTAAGACCTCTAAGTATGAGAATCCTAGAAGTAAACC 1161
                         ii?    i           v  vv  v   i i v  i      v    v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_84606242_8   1162 TAGG---AACCCTTCTTGACATCAGCCTTAGTGATGAACTTTTGGCTAAG 1208
                             ---  vi    v    v ii vi vi ii   ivi i  i v  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_84606242_8   1209 TTCTTAAAAGCAATTGCAG--AAAACAAAACTTGACAAGTACGACCTAAT 1256
                         vivii       vvv   i--   iv    v v  i  i vv   i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_84606242_8   1257 TAAA-CTAAAGAGTTC----CTTCACAGAAAAAAAAACTATCAATAGAGT 1301
                         i   -i    i v  i----     -----  ii v        v i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCA-----AAGGACACTATCAAGAAAGT 692

  chrX_84606242_8   1302 AAATAGAAAACTCACTGAATGAAAGAAAATATTCACGAAC--TGCATCCT 1349
                         i  v   v   i   v     ii          ii i  i-- ii   iv
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_84606242_8   1350 ACAAAGGTCTAATATCCAGGATCTATAAGGAACTCCAACAAATCAATAGG 1399
                          i  i  v  vi       i  v     i      iv    v      iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_84606242_8   1400 CAAAA-ACAAATAACCCCATT-AAAAATGGGCAAAGGACATAAACAAACA 1447
                         v    -           v   -                iv i  i i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_84606242_8   1448 CTTTTCAAAAGAAGACATACATGTGGCCAACAA--ACATGAAAAGA 1491
                         i  i  v        i     vi       i  --           
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.02 (16 / 885), avg. gap size = 1.94 (31 / 16)  


3144 21.49 6.09 1.72  chrX_84612516_84616677.rev     2802  3671 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84612516_8   2802 TAGAAAGATATCTTTCCAT-TTCATTGAT----ACACTTAATATTGTCAA 2846
                          i          ---    -     v   ---- v            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATC---CCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chrX_84612516_8   2847 GATTTTGATACTACTCAAAGTGGTCTACATATTCATTGCAATCCCTAACA 2896
                            vvii     v i    v  i      v     vi          ---
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA--- 94

  chrX_84612516_8   2897 AAATCAAAATCCTTAAGATG---TTTTTGCATAAATTACAAAATTCATCC 2943
                         ---         i--  v  ---        v     ivv  ii v    
  L1M4_orf2#LINE/     95 ---TCAAAATCCC--AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chrX_84612516_8   2944 TAAAATTCGTATGGAATCTCAAAGAACCCTAAATGACCAAAACAATCTTG 2993
                                 i       viv   i i    vi   ii              
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_84612516_8   2994 ACAAAGAA---CAAAGTTGAAGGAAGCACATTTCCTAATTTCAGAAGTTA 3040
                          v      ---        i    vv    i    i       i  v   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_84612516_8   3041 CCAAAAAGCTATAGTAATCAAAAGAGTATGGTGCTCGCATAAATACCAAC 3090
                          i v       i         i v   i    i  v      iv ivi  
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_84612516_8   3091 ATATAGTCTAATGTAACCGAA--GAGAGTTTCCAGAAATAAATCTTCACA 3138
                               vii    v  iv   --      --           i ivi   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGT--CCAGAAATAAACCCATACA 337

  chrX_84612516_8   3139 TATATGATCAAATGAATTTTTACACAAGTGCAAACACCATTCAATGAGGA 3188
                          v    i    v   v   iv   vii    v  v           i   
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_84612516_8   3189 AA-ATCAGACTTTCT--CAAAAGGTCCTGGAAAAACTTGATATACACATG 3235
                           - vi  v    ii--    v   v    i v    v    ?v      
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_84612516_8   3236 CAAAAC--TAAAATT--------------------ATAAAAATATTAAGT 3263
                              v-- i  i  --------------------   v   v     v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_84612516_8   3264 CAAATTTAATCAAAAGACCTAAATGTAAGCTCTAAAACGATAGCCCTCTC 3313
                             v vi    ? -              vv       v   ivv    i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWA-GACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_84612516_8   3314 AGAAGGAG-CATAAATGAAAAGCTTCACAACTATGGATTTGGCAGTAATT 3362
                              i i-    ii? v   v    iii  iv   i  v    i ii  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_84612516_8   3363 TCTTGGATACAACAACAAAAATGTAGACAACAACATGAAAG-TG--TAAA 3409
                             i    ii   v     iiii ii      v vi   i- i--    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_84612516_8   3410 TTGGACTACATTAAAATTTAAAACTTCTGTGCATCAAAGGAAACAATCAA 3459
                                v   i      v       i     v        v  v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_84612516_8   3460 TAGGGTGAAAAAACCACCAAGATTGTGAGAGAAAATATTTCCAAATTATA 3509
                         v ii       i  v   v v vvi  i            v     i   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_84612516_8   3510 TATATGTTAAGAGGTTAATATCTAGAATATA--AAGAAGTTCTACAACTC 3557
                            v  v    i ii vi    i        --     v ii        
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_84612516_8   3558 AACAATAGAAA-----ACAGCCTAATTTCAAAAATGGACAAAGGACTT-- 3600
                           i    i   ----- i i  i    ?-        i       i  --
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGA 835

  chrX_84612516_8   3601 --AGGCATTTTTCCAGAGAAGATACAAAAATGGCTAACAAACACATGAGA 3648
                         --  i     i    i        i v       i  i  i       i 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_84612516_8   3649 AGATACTCAACATCACTAATCAT 3671
                             i          ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (105 / 78)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.24 (68 / 21)  


2767 26.77 1.09 2.29  chrX_84616809_84622634.rev     4417  5335 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84616809_8   4417 TGGAAAAACATTCCATCCTCATAGATACTG--ATTCTTCTTATCCATATC 4464
                               i i  i    vi    i   --  -- vv   ------------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT--TGGAAGACTT------------ 36

  chrX_84616809_8   4465 AATATCACAAAAATGGTCATAGTGCCCAAAGTAATTTATAAGTTCAATCC 4514
                              iiiv  i    iv   v v      v i  i  i ii     iv 
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chrX_84616809_8   4515 TATTCCAATCAAACTATCATTGACATTCTTCACAGAATTAGAAAAAAACT 4564
                         v  i  v      v vi  vivi v  i  ii     v v  v  i--  
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CT 134

  chrX_84616809_8   4565 -ACTTTAAATTTCATATGGAAACAAAAAAGAGCCTGTATAGCCAAGACAA 4613
                         - iii    v            iiv  ii  v  v v        i    
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_84616809_8   4614 TCCTAAGCAAAAAGAGCAAAGCTGGAGGCCTCATGCTACCTGACTTCAAA 4663
                           i i iv  i    i     i      v    ii  v  ii i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_84616809_8   4664 CTATACTACAAGGCTACAGTAACCAAAATAGCACATTACTAGTATCAAAA 4713
                         viv        i          i   i i  iiiiv    i i  v ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_84616809_8   4714 CAGACATATAGACTAATGGAACAGAACAGAGACCTCAGAAACAACATCAC 4763
                         i           ii       i    iv    vii      i  vvi  i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_84616809_8   4764 AAATCTACAACCATCTGATTTTCTACAAACCTGACAAAAACAAGCAATGG 4813
                          v  i  iiii  vi        v    ivv  v   i v  vv      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_84616809_8   4814 GGAAAGGATCTCCTATTCAGTAAATGGCACTGGGAAAACTGGTTAACCAT 4863
                               i  vvi  v    ii      ii      v      v  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_84616809_8   4864 ATGCAGAAAACTGAAATTGGACGCCTTCCTTACACCTTATACAAAAATTA 4913
                              i  i v    i      v   v   i     v             
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_84616809_8   4914 ACTAAAGATGGATTAAAGACTTAAATGTAAAACCCCCAAACCATAAAAAC 4963
                            v  i      i ?    i         i v iv-    i      vi
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACT 533

  chrX_84616809_8   4964 CCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAA 5012
                          i           v    ?i- v i -   iv   v v  vv i     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chrX_84616809_8   5013 GACTTCAT-GATAAAAATGCCAAAAGCAATTGGCA-CAAAAGCCAAAATT 5060
                          ii   v -    vi -ii         -ivi   -      vv     v
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGA-CACCAAAAGCA-CAAGCAACAAAAGAAAAAATA 630

  chrX_84616809_8   5061 GACAAATGAGACGTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAC 5110
                           i    vi   v v  i   v v  i i   i  ii vv    i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_84616809_8   5111 TATCATCAGGGTGAACAGGCAAGCTACAGAATGGGAGAAAATTTTTGCAA 5160
                              vv ii     v  i   v i                 v       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_84616809_8   5161 TCTACCCATCTGACAAAGGGCTAATATCCAGAATTCACAAGGAACT--TA 5208
                         vii ivi      i  i  i  vi          vi i  i     --  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_84616809_8   5209 -AACATATTTACAAAAAAA-ACAGAACCCCATAAAAAAAGGGGGCAAAGG 5256
                         -   vi v v i     i - v v     v  v?     v   -      
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG-CAAAGG 829

  chrX_84616809_8   5257 ATATGAACAGACACTTCTCAAAAGAAGACATTTTCACGGCCAACAAACAT 5306
                           v    i     i     v        i  vivv i      i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_84616809_8   5307 ATGAAAACAAGCTCAACATCACTGATCGT 5335
                                v v           ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.94 (31 / 16)  


3026 26.15 2.09 2.31  chrX_84625048_84629817.rev     3370  4279 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84625048_8   3370 TGGAAAAAGATTCCATGCTCATGAATAGGAAGAATCAATATCATGAAAAT 3419
                               i v  i     i     i  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84625048_8   3420 GGCCATACTGCCTAAAGTAATTTATAGATTCAATGCTAGCTCCGTCAAGC 3469
                            v     v  i   v i  i  i        i  v v i ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84625048_8   3470 TACCATTGACTTTCTTCACAGAATTAGAAAAA---ACTTTAAGTTTCATA 3516
                          v   vivi i  i  ii     v v  v  i--- iii   iv      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_84625048_8   3517 TGGAAACAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAAAA 3566
                               iiv  ii  v  v v        i      i i i---------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--------- 191

  chrX_84625048_8   3567 AAAAAAAAAACAAAAAAAAACAAAGCTGGAGGCATCATGCTACCTGACGT 3616
                         -----------   i  i       i      vv   ii  v  ii iv 
  L1M4_orf2#LINE/    192 -----------AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_84625048_8   3617 CAAACTGTACTACAAGGTTACAGTAACCAAAACAGCATGGTACTGGTACC 3666
                             viv        i i        i   i    ii         i iv
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_84625048_8   3667 AAAACAGAGATATAGACCAATGGAACAGAACAGAGACCTCAGAAATAATG 3716
                          ii i   v       i        i    iv    vii         vv
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_84625048_8   3717 CCACACATGTACAACCATCTGATCTTTGGCAAACCTGACAAAAACAAGAA 3766
                            i    v  iiii  vi    i  i i   ivv  v   i v  vvv 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_84625048_8   3767 ATGGGGAAAGGATGCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAG 3816
                                   i  ivi  v  i  i              v      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_84625048_8   3817 CCATATGCAGGAAACTGAAACTGGATGCCTTCCTTATACCTTATACAAAA 3866
                            i     ii i v    ii    iv   v   i i   v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_84625048_8   3867 ATTAACTCAAGATGGATTAAAGACTTAAACATAAGACCTAAAACCATAAA 3916
                                   i      i ?    i    ii     v       i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_84625048_8   3917 AACCCTAGAACAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGAC 3965
                          vi i     v     v    ?i- v i -   iv   v v  vv i i 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGC 579

  chrX_84625048_8   3966 GAGGACTTCATGACTAAAATACCAAAAGCAATGGCAACAAAAGCCAAAAT 4015
                         i v ii   v iiv  vi i          vvi          vv     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_84625048_8   4016 TGACAAAT-GTATCTAATTAAACTAAAGAACTTCTGCACAACAAAAGAAG 4064
                         v  i    - v ii v  i   v v  i     i  ii vv    i  vi
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_84625048_8   4065 CTATCATTAGAGTGAAAAGGCAACCTACAGAATGGGAGAAAATTTTTGCA 4114
                               vv i         i     i                 v      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_84625048_8   4115 ATCTATCCATCTGACAAAGGGCTAATATCCAGAATATAGAAATAACT--T 4162
                          vii  vi      i  i  i  vi             v   v    -- 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_84625048_8   4163 A-AATTTA----CAAAAAAA-----AACCCA-TCAATAAGTGGGCAAAGG 4201
                          -  i i ----i     i -----      - i? v  i          
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_84625048_8   4202 ATATGAACAGACACTTCTCAAAAGAAGACTT-TATGTGGCCAACAAACAT 4250
                           v    i     i     v        iv -i vi       i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_84625048_8   4251 ATGAGAAAAAGCTCATCATCACTGGTCAT 4279
                             i  i v     v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (143 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.64 (40 / 11)  


3203 28.38 0.11 0.22  chrX_84645703_84650201     3098  4006 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84645703_8   3098 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 3147
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84645703_8   3148 GGCCATACTGCCCAAGGTCATTTATAGATTCAATGCCATCCCCATCAAGC 3197
                            v     v     iv v  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84645703_8   3198 TACCAATGACTTTCTTCACCGAATTGGAAAAAATTACTTTAAAGTTCATA 3247
                          v   iivi i  i  ii v   v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_84645703_8   3248 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 3297
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_84645703_8   3298 CAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATACCACACGGCTA 3347
                              i      vv   ii  v  ii        viv   i   vi    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_84645703_8   3348 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 3397
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_84645703_8   3398 TAGAACAAAACAGAGCACTCAGAAATAATACCACACATCTACAACCACCT 3447
                          i   i i  iv   viii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_84645703_8   3448 GATCTTTGACAAACCTAACAAAAACAAGCAGTGGGGAAAGGATTACCTAT 3497
                            i  i     ivv iv   i v  vv  i         i  vii  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_84645703_8   3498 TTAGTAAATGGTGCTTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 3547
                          i ii          -    v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_84645703_8   3548 ACTGGATCCCTTCTTTACACCTTATACAAAAATTAATTCAAGATGGATTA 3597
                         ii    i    v i i     v              i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_84645703_8   3598 AAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 3647
                         ?    i       v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_84645703_8   3648 GGCA-ACACCATTCAGGACCTAGGCATGGGCAAGGACTTCATGTCTAAAA 3696
                           ?i- v i -   iv     v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_84645703_8   3697 CACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGTGATCTGATT 3746
                                    vvi      i   vv     v  i    vv  ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_84645703_8   3747 TAACTAAAGAGCTTCTGCACAGCAAAAGGAATTACCATCAGAGTGAACAG 3796
                         v  v v  i i   i  ii vv    i iv i  i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_84645703_8   3797 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAG 3846
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_84645703_8   3847 GGCTAATATCCAAAATCTACAATGAACTCAAACAAATTTACAAGAAGAAA 3896
                          i  vi      i   v  i  v      vv    v iv i  v  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_84645703_8   3897 ACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCTC 3946
                              i     v  i?    i    ii     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_84645703_8   3947 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 3996
                         v        i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_84645703_8   3997 CACTGGCCAT 4006
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.54 (154 / 100)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.00 (3 / 3)  


2738 28.33 1.68 0.11  chrX_84656224_84660794     3186  4078 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_84656224_8   3186 GAAAACACATCCCATGCTCATAAAAGGGTAGAATCAATATTGTGAAAATG 3235
                          i   v i        i    ii vv  v   v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_84656224_8   3236 GTCATACTGCCAAAACCAA-CTACAAATTTAATGTGATTCCCATCAAAAT 3284
                          iv     v  v   iii -     i   i  i ii  i  i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_84656224_8   3285 AGCATCTTCATTCTTCACAGAACTAGAAAAAA-AATCCTAAAATTCATGT 3333
                         vv  v  v v  i  ii     v v  v  iv-i              i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_84656224_8   3334 GGAACCCTAATAGAGCCCACGTAGCCAAGGCAATTCTAAGCAAAATGAAC 3383
                             vivi  vi  v  vivi       ii    ii i iv  i v    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_84656224_8   3384 AAATCTAGAGGCATCACATTACCAGACTTCAAACTATACTACAGGGCTAT 3433
                            vi i    vv     i v  vi i      viv       ii    i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_84656224_8   3434 TGTCACTAAAACAGCATGACACTG-CATAAAAATAAGCACATAGATCAAT 3482
                         v  v ii  i    ii  ii    -     ii   ii  i          
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_84656224_8   3483 GGAACAGAATACAGAACCCAGAAATAAAGCCAAATACTTAAACCTAACTG 3532
                             i     vv   ii           v   v i i   vivii  i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_84656224_8   3533 ATTGTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGAACACCCTATT 3582
                            v i     i vviv   i v   vv i           i vi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_84656224_8   3583 CAACAAATGGTGCTTGGATAATTGGCAAGCCACATGTGGAAGAATGAAAT 3632
                                       v   i  i   vv ?       iii         i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_84656224_8   3633 TAGTTCCTCATCTCTCACTTTATACAAAAAT-----CAAGATGCATCAAG 3677
                          i vi  ii i   v   iv           -----   i   v    ?i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_84656224_8   3678 GACTTAAATCTAAGACCTGGAACCATAAAAATTCCGGAAGACAACATCAG 3727
                            i     v     v  ii   i      v iiii     v     vi 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_84656224_8   3728 AAAAGCCCTTCTAGACAGTGGCTAAGGCAAAGACTTCATGACCAAAAACC 3777
                         ?iv ivi    vv   vv   v v      v ii   v iivi vi vv 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_84656224_8   3778 CAAAAGCAAATTCAACAAAAACAAAAATAAATAGATAGAACTTAGTTAAA 3827
                                 v vv        iv       i   i  v i    vi i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_84656224_8   3828 -CTAAAAACTTCTGTACAGCAAAAGAAATAATCAGCAGAATAAGCAGACA 3876
                         -i         i   i vv    i  v iv    iv i i i iv     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_84656224_8   3877 ACCCACAGAGTGGGAGAAAATCTTTGCAAACTATGCATCCAACAAAGGAG 3926
                                  i           v        ii  ii   ii i  i   v
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_84656224_8   3927 TAATATCCAGAATCTACAAGGAACTCAAACAAATTAGCAAGAAAAAAA-- 3974
                          vi          v  i  i      vv    v i ii  v     i --
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_84656224_8   3975 AAT--CCCA--TCAAATGTGGGATAAGGACATGAATAGACAATTCTCAAA 4020
                            --    -- ?   vi    vv     iv          v     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_84656224_8   4021 AGCAGTTATACAAATGACCACTAAACATATTTAAAAAATGCTCAACATCA 4070
                           v  v          i   v   i  i  v-    i             
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTCAACATCA 900

  chrX_84656224_8   4071 CTAATTAT 4078
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.35 (143 / 106)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 1.78 (16 / 9)  


2897 27.70 0.77 0.55  chrX_84673919_84680932.rev     3516  4421 (2593)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84673919_8   3516 TGGAAAAACATTCCATGCTCATGGATATGAAGAATCAATATAATGAAAAT 3565
                               i i  i     i        vv     v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84673919_8   3566 GGTCATACAGCCCAAATTAATTTATAGATTCAATGCTATTTCTATTAAAC 3615
                           iv    vv        i  i  i        i  v  ii    i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84673919_8   3616 TGCCATTGACATTCTTCACACAACTAGAAAAACT-ATTTTAAAATTTACA 3664
                          v   vivi v  i  ii  v  v v  v  i  -  ii       i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_84673919_8   3665 TGAAACCAAAAAAGAGCCCAAATATCCAAGGCAATCCTAAGTAAAAAGAA 3714
                           i  viiv  ii  v  vi    v    ii     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_84673919_8   3715 CAAAACTGGAAGCATCACTCTACCTGACTTCAAACTATACTACAGGGCCA 3764
                             ii    i vv    v  v  ii i      viv       ii  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_84673919_8   3765 CAGTAACCAAAACAACATGATACTGGTACAAGAACAGACACATAGACCAA 3814
                               i   i   iii  i      i i   i i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_84673919_8   3815 TGGAGCAGTATAGAGAAACCAAAAATAAGACCACACACCTACAAG-AATC 3863
                             ii  v  v    iv   i      iv   i   ii  iiiv-   -
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT- 349

  chrX_84673919_8   3864 TGATCTTCAACAAACGTTACAAAAACAAGCAATGGGGAAAACATTCCCTA 3913
                             i   i    iv  vv   i v  vv           iv  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_84673919_8   3914 TTCAATAAGTGGTGCTGGAATAACTGACTAGCCATGTGCAGAAGGTTGAA 3963
                              i  i         i i     iv  ?   ii    i   iv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_84673919_8   3964 CCTGGACCCCTTCCTTACACCATATACAAAAATTAACTCAAAATGTATTA 4013
                         vi         v   i                             v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_84673919_8   4014 ATGACTTAAATATAA-ATCCCAAACTATAAAAATTCT-GAAAACAATCTA 4061
                         ?v   i     i   - v iv           v ii -   i v  iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_84673919_8   4062 GACA-ATACCATTCAGGATGCAGGCACAGGCAATTATTTCAT-GATGAAG 4109
                          i?i- v i -   iv  iviv  vvi       vi    v -   - v 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chrX_84673919_8   4110 ATGCCAAAAGCAAATGCAACAAAAGCAAACATTGAAAAATGGAATATAGT 4159
                          ii         v v          v   v  v  v    v i iv vi 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_84673919_8   4160 TAAAGCTAACAAGCTTCTGCATGGCAAAAGAAACTCTCAACAGAGTAAAC 4209
                         i   ii   -  i   i  iiivv    i  v   v    v i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_84673919_8   4210 AGACAACCTACAGAATGGGAAAAAAGTTTTTCAAACTATGCATCTGAGAG 4259
                                 i           i    vv   v    ii  ii      v i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_84673919_8   4260 AGGTCTAATATCCATTATCGATAAGGGACT-TAACCACATTTACAAGAGA 4308
                         i  v  vi      vv  vv    i i   - v  v  - iv i  v i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAATAATAAA 795

  chrX_84673919_8   4309 AAAACAAACCACCCCTTTAAAAAGTGGGCAAATGATATGAACAGACACTT 4358
                           i     iv    vv  ?    i        v   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_84673919_8   4359 CTCAAAAGAAGACATACATGAGGCAAACAAGCATATGAAAAAAAGCTCAA 4408
                            v        i     viv   v  i     i       i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_84673919_8   4409 CATCACTCATCAT 4421
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.00 (12 / 12)  

2696 27.77 0.99 1.32  chrX_84673919_84680932.rev     5615  6525 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84673919_8   5615 TAGAAAAGCATTCCACGATCATGGATATGAAGAATCAATATCATTAAAAT 5664
                          i    iii  i   i v        vv     v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84673919_8   5665 AACAACATTGCCCAAAGCAAGCTACAGATTTAATGCTATTTTTATCAAAC 5714
                         ii   i i v      vii v         i  i  v  iii       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84673919_8   5715 CACCAAC-ATCATTTTCACAGAA-TCAGGAAAACCTGGTT-TATAATTCA 5761
                         iv   i -ii v    ii     - i--  v  v   i i-  v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_84673919_8   5762 TATGGAACCAAAAAAGAGCCTGAA-ATCCAAAGCAATTCCCAGCAAAAAG 5810
                                viiv  ii  v  v   - v     i    iiiv iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_84673919_8   5811 AACAAAGCCAGAGGCATCCCATTACATGACTTCAAACTATACTATAAGGC 5860
                                iii    vv  v  i v vii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84673919_8   5861 CACAGTAACCAACTCAGCATGATCCTGCTATAAAAACAGACAAATAGACC 5910
                         i       i   vv   ii  i v   vi    ii i     v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_84673919_8   5911 AATGAAACAGAATAGAGAACCCAGAAATAAAGCTGAACACCTATAGCCAC 5960
                             i  i     v    ii           v iiv   ii   i i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_84673919_8   5961 ATGATCGTAGACAAAGTTGGGAAAAAGTAAGCCATGGGGAAAGGACTCTC 6010
                         v    iv v     i v  vv  i v-i vv v          i ivv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTC 397

  chrX_84673919_8   6011 CATTTAATAAATGGTGCTGGGATAGCTAGCTAGTCATATGCAGAAGAATA 6060
                         iv  i  i              i i  i v  ?i  i     i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_84673919_8   6061 AAACTGGATCCTTATCTTTCACCATATACAAAAATTAACTCAATATGGAT 6110
                           ii    i  i  i  iv                        v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_84673919_8   6111 TAATGATTTAAATCTAAGACCTCAAACTATAACAATTCT-ATATGAAAAT 6159
                         i ?v  ii     v     v  v         -  i   - v v     i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAAC 546

  chrX_84673919_8   6160 CTAGGAG-ACACCGTTCTGGACATTGGCCTTGGGAAAGAATTTATAACTA 6208
                         v    ? - v i -   vv   v    vi v  v  v iv  iv  iv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_84673919_8   6209 -AATACTCAAAAGCAATTGCAAGAAAAACAAAAATTGGCAAGTGAGACCT 6257
                         -i i  -        vvv    v    iv      v ii  i vi   i 
  L1M4_orf2#LINE/    596 TGACAC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_84673919_8   6258 AATTAAACTAAAGAGCTTCT-CACCACAAAAGAAACAATCAACAGAATAA 6306
                         v  i   v v  i i   i -ii iv    i  v  v     v i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_84673919_8   6307 ACAGAAACAACCTACATAATGGGAGAAAATATATTTAAACTATGCATCTG 6356
                          v   --     i   v               v vi   ii  ii     
  L1M4_orf2#LINE/    695 AAAGA--CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_84673919_8   6357 ACAAAGGTCTAATATCCAGAATCTATAAGGAACTTAAACAATTCGACAAT 6406
                          i  i  v  vi          v     i     ivv    i  i i   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_84673919_8   6407 CAAAAAACCCCAATAACCCCATT-AAAAATGGGCAAAATACATGAATAGA 6455
                         v    i  v--        v   -             iv iv        
  L1M4_orf2#LINE/    793 AAAAAGACA--AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_84673919_8   6456 CACTTCTCTGAAGAACACACACAAGTGGCCAAAAACCACATGAAAACAAT 6505
                           i     ii     v i i    i       v  v          -i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GAT 889

  chrX_84673919_8   6506 GCTTTAACATTGCTAATCAT 6525
                            i-     ii????????
  L1M4_orf2#LINE/    890 GCTC-AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (148 / 102)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.17 (21 / 18)  


2815 28.84 0.33 0.33  chrX_84697584_84702588.rev     3614  4518 (487)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_84697584_8   3614 AAACACATCCCATGCTCATGGATGGGTAGAACTGGTATTGTGAAAATCAC 3663
                            v i        i        v  v   vi ii      v  i  vi 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_84697584_8   3664 CATACTGCCAAAAGCAATCTACAAATTCAGTGCAATTCCCATCAAAATAC 3713
                         v     v  v   vii       i     ii     i  i        v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_84697584_8   3714 CACCATCATTCTTCACAGAACTAGAAAACACAATCTCAAAATTAATATAA 3763
                           v vv v  i  ii     v v  v  vvii   ii      v    ii
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_84697584_8   3764 AACCAAAAAAAGAGCCAGCATAACCAAAGCAAGACTAAGTAAAAAGAACA 3813
                           viiv-  ii  v    v   i     i   vvi i iv  i       
  L1M4_orf2#LINE/    154 AAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_84697584_8   3814 AATCTGGAGGCATCCCATTACCAGACTTCAAACTATACTATAAGGTCATA 3863
                           vi      vv  v  i v  vi i      viv     i  i ii i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_84697584_8   3864 GTCACCAAAACAGCATGGTACAGGTATAAAAGT-GACATTTAGACCAATA 3912
                           v i   i    ii      v  i    iii -     v    i    i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_84697584_8   3913 GAACAGAATTGAGAACCCAGAAATAAAGCTAAATACTTAGAGTCAACTGA 3962
                            i          ii           v i v i i   vi     i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_84697584_8   3963 TCTTTGACAAAGCAAACAAAAATATAAAGTGGGGAAAGGACACCCTTTTT 4012
                          i  i     i vviv   i vi  vv i         i i vi     i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_84697584_8   4013 AACAAATGGTGCTGAGATACTTGGCGAGCCACATGTAGAAGAATGAAACT 4062
                                       i  i vi   vv ?       i i         ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_84697584_8   4063 GAATCCTCATGTCTCATCTTTTACAAAAATCAACTCAAGATGGATCAAAG 4112
                          i i  ii iv  v  i v v         i       i        ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_84697584_8   4113 AATTAAATCTAAAA-CCAAAACCATAAAAATTATAGAAGATAACATTGGA 4161
                          vi     v   i - i     i      v iv       v     v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_84697584_8   4162 AAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTTATGACCAAGAACCC 4211
                         iv  vi    vv   v    v        v ii  iv iivi v  vv  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_84697584_8   4212 AAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGACTTAATTAAAC 4261
                                v v         iv   i   i   i  v      v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_84697584_8   4262 TAAAAAGCTTCTGCACAGCAAAAGGAATAATCAGCAGAATAAACAGACAA 4311
                          v    i   i  ii vv    i iv iv    iv i i i  v      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_84697584_8   4312 CCCACAGAGTGGGAATAATTCTTCACACTCTTTACATCCAACAAAGGACT 4361
                                 i     iv  v v  ii  vviiv  i   ii i  i     
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_84697584_8   4362 AATATCCAGAATCTACAAGGAACTAAAAAAAATCAGCAAGAAAAAAAACT 4411
                         vi          v  i  i     vvv v  v   ii  v     i --i
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--C 800

  chrX_84697584_8   4412 TAACAATTCCATCAAAAAGTGAGCTAAGGGCATAAATAGACAATTCTCAA 4461
                         v  i  ii v  i?    i  i  v    iiv i        v     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_84697584_8   4462 AAGAAGATATACAAATGGCCACCAAACATGTGAAAAAATGCTCAA-ATTA 4510
                                              vi  i  ii      i        -  i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_84697584_8   4511 CTAATTAT 4518
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.38 (149 / 108)
Gap_init rate = 0.01 (5 / 905), avg. gap size = 1.20 (6 / 5)  


1386 25.36 3.09 3.30  chrX_84703948_84709397        7   491 (4959)  C L1M4_orf2#LINE/L1   (132)   776   293  

C chrX_84703948_8    491 TAGTTCAAAAGACTGAAATTCA-AGCTCAGAAAT-----TATTTTTTCAA 448
                            v    vi  v ii    v -  ii       -----i  viv  i v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

C chrX_84703948_8    447 AGATGA--GATTTTCAACAAGCCTGGCAAAAACAAACAATAGGGAAATAA 400
                         i vii --       i     vv  v   i v  vv    i      v  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

C chrX_84703948_8    399 TTTTCTATTTAATAAATGGTGCTGGGGGAACAGGCTAGCCATATGCAGAA 350
                          vv   v  i  i             iv   v  v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

C chrX_84703948_8    349 AATTGAAACTGGATCCCTTCTTATCACCTTATAAAAAAATTAACTTAAGA 300
                         i v    ii    i    v i vv    v    v           i  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

C chrX_84703948_8    299 TGGATTAAAGACTTAAATGTAAAATCCAAAACTATAAAAGTCTTAGAAGA 250
                              i ?    i         i v i            v          
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

C chrX_84703948_8    249 AAATCTAGGCA-ATACCATTCAGGACATAGGCACGGGCAAATATTTC--- 204
                            iv    ?i- v i -   iv   v v  vvii     vvi    ---
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

C chrX_84703948_8    203 ---ATGACAAAATTGCCAAAAGCAATTGCAACAAAAGAAAAAATTGACAA 157
                         ---      ------         vvv                 v  i  
  L1M4_orf2#LINE/    592 GATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

C chrX_84703948_8    156 ATGGGAATTAATTAAACTAAAGAGCTGAAAGAGCTGCTGCGCAACAAAAT 107
                           v   v  v  i   v v  ------   ---  vi  i  vv    iv
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAA------AAA---CTTTTGTGCTTCAAAGG 676

C chrX_84703948_8    106 AAACTATCATCAGGCTGAACAGACAACCTACAGAATGGGGTAAAATTTTT 57
                          v       vv iiv    v        i          iv     v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

C chrX_84703948_8     56 ACAATCTATTCATCTGACAAAGGTCTAATATCCAGAGTCTACAAGAAACT 7
                         i   vii  vi      i  i  v  vi        i v  i  ii    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 0.90 (57 / 63)
Gap_init rate = 0.02 (9 / 484), avg. gap size = 3.44 (31 / 9)  

2347 29.35 1.85 3.15  chrX_84703948_84709397     4038  4957 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84703948_8   4038 TGGATAAACATCCCATGCTCATGGATTGACATAATCAATATTGTTCAAAG 4087
                             v i i        i          iv v v i         v i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84703948_8   4088 GACCATACTGCCCAGAGCAATCTACAGATTTAACTC--TTTCTATCAAGC 4135
                          i v     v    i vii           i   v -- ii       iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84703948_8   4136 TATGAACATCATTTTTCACAGAACTAGAAAAAACT-ATTCTACAATTCAT 4184
                          viv i vv v     ii     v v  v  i-  -  i   v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_84703948_8   4185 ATGAAGGCATAAAAAATCACAAATAGCCAAAGTAATTGGCTAGAAAATTG 4234
                            i iiiii  iii i vvi          ii   --------------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-------------- 185

  chrX_84703948_8   4235 CTCTTTTGCTTAGAACAAAAAGAAGAAAGCTGTAGGCATCATATTATCTG 4284
                         --------   -   v  i     v    i  v   vv   i i vi ii
  L1M4_orf2#LINE/    186 --------CTT-GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_84703948_8   4285 AGTT-GAAACTATACTATAAGGATGCAGTAACCCAAACAGCATGGTACTG 4333
                          v  -i     -     i  i v i      i v i    ii        
  L1M4_orf2#LINE/    227 ATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_84703948_8   4334 GTACAAAAAGAGACACATAGATAAATGAAACAGAATAGAGAACCAAGAAA 4383
                          i i  ii v     i      v    i  i     v    ii v     
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_84703948_8   4384 TAAAACTGTATACCTACCATC---TAAACTTTGACAAAGTTGATAAAAAT 4430
                             v ii  i ii  ivi  --- i vi  i     i v  vi  i vi
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_84703948_8   4431 AAGCAA-GAGGAAACGACTCCCTATTCAATAAATGGCATAAGGATAGCTG 4479
                          vv   - i     vi ivvi  v     i      iiivi   i i   
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_84703948_8   4480 GAAAGCCATATGCAGAAGAATGAAACTAAACTCCTGTCTTTCACCAGACA 4529
                           v ?   i     i         ii ii  i   ii  iv     v i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_84703948_8   4530 CAATAATTAAC--AAGGTGTATTAAAGACTTAAGTTTAAGACCTCAAACT 4577
                            v       --  ii  v  i ?    i   i v     v  v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_84703948_8   4578 ATAAGATTTCCAGAAGCAAATTTAGGAGATGGTATTCCAGACTTTGGCCT 4627
                             i i iii     v   iv    ? vvii v   vv   i    v- 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-T 574

  chrX_84703948_8   4628 TGGGAAATAATTTATTAC-TAAATCTTCAAAAGCAATTGCAAGTGAAATA 4676
                          i  v   ii   v   v-  viv vi        vvv    vvi  iv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_84703948_8   4677 AAAATTGACAAAGGGGACCTAATCAAACTAAAGAGCTTCTGCATAGCAGA 4726
                              v  i   vv    i v      v v  i i   i  iiivv  i 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_84703948_8   4727 AGAAACTATTAACAGAGTATGAAGACAACCTACAGAATTGGGGACATTAT 4776
                         i  v     i  v i   ivi         i       v  i  v v   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_84703948_8   4777 --GCAGAATCTATGAATTCAACAAAGGTGTAATATCCAGAATTCATAAGG 4824
                         --   -    -  iv  iii i  i  vv vi          vi    i 
  L1M4_orf2#LINE/    725 TTGCA-AATC-ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_84703948_8   4825 AATTTAAACAATTGAGCATGCAAAGAACAAGCAACCTTAAT--GAAAATG 4872
                           i ivv    i v ii vvv   ii    ii    i-   --i      
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCC-AATTWAAAAATG 821

  chrX_84703948_8   4873 GGCAAAAGGCATGAATAGGCACTTCTCTAAAGAAGACATACAAGCAACCA 4922
                               i iiv       i  i     i        i      iiii   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_84703948_8   4923 ACAA--ACATAAAAAAATGCTCAACACCACTAGTCAT 4957
                          i  --    i    i          i  ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (165 / 102)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.56 (46 / 18)  


2820 25.88 3.43 2.99  chrX_84714027_84720319.rev     4899  5802 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84714027_8   4899 TGAAAAGATATTGTGTGTCCATGGATCAGAAGAATCAATATTTTCAAAAT 4948
                           i        ivii   i       ii     v i      v i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84714027_8   4949 GTTTATACTACCCAAAGCAATCTATAGGT-CAATTAAATCTTAATGAAAA 4997
                          viv     v      vii     i  i -   ivv    iiv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84714027_8   4998 TTCCAATTGCATGTTTTACAGAAATAGAAAA---------AAAATTC--- 5035
                          i   ii   v v    i       v  v  ---------       ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_84714027_8   5036 TAAAACCACAAAAGATTCCAAGTAGCTAAAGAAATCTTGAGCAAAAAAAG 5085
                          ii  vii   ii  ii vi i    i   iv        iv  i  i i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_84714027_8   5086 TAAAGCAGGTGGCATCATACTTGTTTATTTCAAATTATACTACAAAGCTA 5135
                         i    iv  v  vv   i    viiv        viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_84714027_8   5136 CAACAAT-AAAACAGTATGGTCCCAGCATAAAAACAAACACATAGACCAA 5184
                           ii   -  i     i    v ii      ii i i   i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_84714027_8   5185 TGGAACACAATAGGAAGTCCAGAAATACATCCATGCATATTCAGTCAACT 5234
                              i v   v ii            v i    i   v vii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_84714027_8   5235 AATCTTTGACAAAAGTGCTGAGAATATAAAATGAGGAAAGAGTAGTCTCT 5284
                         i  i  i     ii    ii   vi  vv    i       i      i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_84714027_8   5285 CCCATAAATGATGCTGGGAAAACTGAATATCCACATGCAAGAAAAATAAA 5334
                         i v i     i        v     i   ?          -  i   i  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA-AAGAATGAA 449

  chrX_84714027_8   5335 ATTGGATCATTTTCTTACTCCATACACAAAAATAAACT-AAAATGGATTA 5383
                         i     i vi vi  i  v     i        v    -         i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_84714027_8   5384 AAGACTTGAA-ATAA------------TAAAACTTCTAGAAAAAACCATA 5420
                         ?    i i  -i   ------------       ii     i   v    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_84714027_8   5421 GAGGAAAAATTCCCTAACATTCATCTTAACAATAATTTCTTGGATATGAC 5470
                          i? v   vi i v i  v  vivi vii    ii      i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_84714027_8   5471 AGCAAAAACACAGACAATAAAAGCAGAAATAAACAAGTGAAACTACTTCA 5520
                          v     i    ii   i     v i     i i  i vii   v v   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_84714027_8   5521 AACTACGAAGTTTCTGCACA-AAAATGAAACAATAAACAGAATAAAAAG- 5568
                           v vvi  ii  i  ii v-v   v  v  v  v  v i i i     -
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_84714027_8   5569 CAACCTATGGAAGAGGA-AAAATCTTTGCAAACTATTTATCTTATAAGAG 5617
                              i ii   vi   -     v        ii  v     v     i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_84714027_8   5618 GTTAATGCCCAAAATATATAAGCAACTCTTACAACTCAATAACAAAAAAA 5667
                         ii vi ii   i         iv                   i     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_84714027_8   5668 CAAACAAAGCAAAACAAAAACAAAAACAAAATAGCCGGATTTTATATGGG 5717
                             i  vv   vv?     --------------------------    
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAA--------------------------TGGG 823

  chrX_84714027_8   5718 CAAAGGCACTGAATAGACGTTATTCCAAAGCAGACATACAAATGGCCAAC 5767
                               vvi         i  vi       v   i              i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_84714027_8   5768 AGGTATATGAAAAGGTGCTGAACATCACTAACCAT 5802
                          i i i        i    v       ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (150 / 80)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 4.83 (58 / 12)  


 370 18.75 7.29 0.00  chrX_84729039_84732037.rev      183   278 (2721)    L1M4_orf2#LINE/L1      806   908 (0)  

  chrX_84729039_8    183 ACCCAGT-----AATGGGCGAAGGACATGAACA--CACTTCTCAAAAGAA 225
                              i -----       i     iv    i --  i     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_84729039_8    226 GACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGC 275
                           i  vi viii     v  i          i       v     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_84729039_8    276 CAT 278
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.02 (2 / 103), avg. gap size = 3.50 (7 / 2)  

 900 30.75 11.36 0.55  chrX_84729039_84732037.rev      989  1349 (1650)    L1M4_orf2#LINE/L1        3   402 (506)  

  chrX_84729039_8    989 GAGACATGTGTCACAATTATGGATCAGTAAGCTCAATAATGTTAAGATGT 1038
                           i v  i vi  iiv i      ii v ii  i    v          v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_84729039_8   1039 CAGTTTCCCCCAAATTGAGCAATAGGTTCAATGCAATACTAATAAAAATA 1088
                           i vii           v v i  i     i     v iv  v     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_84729039_8   1089 CCAGTAGCATTTTCCATGGAAAACTGACAAGCTAATTCTAAAATTTACAG 1138
                             iv  v    iiiii    -i         i  i        i i v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_84729039_8   1139 GGAACTGCAACGGATTTAGAATAGCCAAGA-ATTCTTGAAGAAAAAGAAC 1187
                             v     v   iii           i - v       i  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_84729039_8   1188 AAA---------------CTTCT----------------TATGGAGTTAC 1206
                            ---------------    i----------------  iii  i   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_84729039_8   1207 AGTAATTAAGAGAATGTGGTATTAGTGTGAAGATAAAC--------CAAT 1248
                               i    v i       i i ii i i    i  --------    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_84729039_8   1249 TGTACAGAAAAGACAATTCAAAAATATGTCTACACATATGTAGTGTCCTG 1298
                         v v i    vv  v i i  i     vii i i    v i i  vvvi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_84729039_8   1299 ATTTATAATATATCT-CTACTACAATTCAATAAAGTAAAAGATGACCATT 1347
                             vii i vivv - i vv  v       iii -   ii  iii v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTT 400

  chrX_84729039_8   1348 TC 1349
                           
  L1M4_orf2#LINE/    401 TC 402

Transitions / transversions = 1.92 (73 / 38)
Gap_init rate = 0.02 (7 / 400), avg. gap size = 6.14 (43 / 7)  

1088 26.50 8.76 1.50  chrX_84729039_84732037.rev     2041  2508 (491)    L1M4_orf2#LINE/L1      407   908 (0)  

  chrX_84729039_8   2041 AATGTTTTTGGATCAATTGTATATCCA--TG----GGGATGAAGTGAGCC 2084
                             v vi   iv   i  v   ?   --  ----i i       -----
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT----- 451

  chrX_84729039_8   2085 TTGACCCCATGCTTTACACTGAAC-CAAAAATTAATTCGAAATGGATAAT 2133
                          v      - i i i    iiv i-          i  i        v ?
  L1M4_orf2#LINE/    452 TGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_84729039_8   2134 AGACATAATTGTGAAAACAAAATATATAAAGCTTCTAGAGGAAACTTTAA 2183
                             v   v   i i i v   vv      i  ii    i    viv  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_84729039_8   2184 GAAAATATTTTCATGAACTTGAGGCAGGTAAAAATTTATTAAACATGATA 2233
                          ?iv v  i   i   v    i vi   i  vii   v   i i    i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_84729039_8   2234 G-AAAAGAATTAACCATAAGAGA-----CTGATA----------CATTAA 2267
                         v-     v iv i v i  i   -----iv    ----------   i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_84729039_8   2268 AATTAAGAACTTCTCTTCATCAAAAGAC--TATTATGAGAGTAAAACGGC 2315
                               i     i v v v     i   --   i v  i   i   v i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_84729039_8   2316 AACC-ACAGAATGG-AGGAAATACTTGTAATACATAACATCTAATAACAA 2363
                             -         -  i     i   i  vv    -i    i    vii
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATA-TATCTGATAAGGG 749

  chrX_84729039_8   2364 ACTCATATGCAGAATGTACAAATAATTACTACAAATGAATAAAGAAAATA 2413
                            ii   v      i  i   v  i vi     v v     vi    v 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_84729039_8   2414 C---CCACCCAATT-AAAAATTGGCAAAACATTT----AGACCATTCAC- 2454
                          ---iv        -      v      iv    ----    vv   v -
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_84729039_8   2455 -----AAATTTCTAAATGGCTAATAAGAATTTGAAAATGTTCTCAGTATC 2499
                         ----- i  v vi       i      v iv      vi v    ii   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_84729039_8   2500 ATTAATTAG 2508
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.33 (69 / 52)
Gap_init rate = 0.03 (16 / 502), avg. gap size = 3.00 (48 / 16)  


 365 31.71 0.00 2.44  chrX_84749721_84751757      500   622 (1415)    L1M4_orf2#LINE/L1      243   362 (546)  

  chrX_84749721_8    500 CAAGGCCACAGTAACCAAAAATGGCATTGTAGTGGTATAAAAAAATAGAT 549
                            i  i       i -  i ii ii v   v   i    ii --    i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATC-AAGACAGTGTGGTACTGGCATAAGGA--TAGAC 289

  chrX_84749721_8    550 ACGTCAAACAATGGAACAGAATAGGGAACCTGGATATAAAGCCACATACC 599
                          ii vi v        i     v i  ii ii  v     v   i i ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_84749721_8    600 TACAACCAACTGATCTTTGACAA 622
                           iiii   i    i  i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAA 362

Transitions / transversions = 4.57 (32 / 7)
Gap_init rate = 0.02 (2 / 120), avg. gap size = 1.50 (3 / 2)  

1817 24.45 2.19 0.40  chrX_84749721_84751757     1047  1549 (488)    L1M4_orf2#LINE/L1      397   908 (0)  

  chrX_84749721_8   1047 CTCTCCAATAAATGATGCTGTGAAAACTGGCTAGCCATATGCAAATGAAT 1096
                           i i   i     i     v  v      v  ?   i       v    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_84749721_8   1097 AAGACTGGATCCCAATCTCTCACCATATACAAAAATTGACTCAAGATGAA 1146
                         i iii    i   v i   v                 i      i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_84749721_8   1147 CTGAAGACTTAAATGTAAGACCTCAAACTATCAGAGTCTTAGAAGGAAAC 1196
                         iii?    i           v  v       v i v         i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_84749721_8   1197 CTAGGAAAAACTATTCTGGACTTTGGCCTAGGCAAAGAATTTATGACTAA 1246
                         v    ?iv  v v   vv   i    vi       v iv  iv iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_84749721_8   1247 GACTTCAAAAGCAAATGCAATAAAAGCATAAAATAGACAAATGGGACTT- 1295
                            vi        v v    i     v -        i    v      -
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAA-AAAATAGATAAATTGGACTTC 645

  chrX_84749721_8   1296 ----AAACTAATGAGCTTCTGCACAGCACTAGACACTATCAACAGAGTAA 1341
                         ----   i   -i i   i  ii vv  vvi           v i   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_84749721_8   1342 ACAGACAACCTAAAGAATGAGAGAAAATGTTTGCAAACTATGCATCAGAC 1391
                          v        i v      i        i        ii  ii   v  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_84749721_8   1392 AAAGTTATAATATCTAGAATCTATAAAGAACT----TAATTCAACAAGTA 1437
                           i vvv vi    i     v           ----i  i    i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_84749721_8   1438 CAAAACAAATAATGCCATT-AAAAATGGGCAACGGACATGAACAGACACT 1486
                         v  i        iv v   -            v   iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_84749721_8   1487 TCTTCAAAGAAGACATACATGCAGTCAATTAAGATATGAAAAAATGATCA 1536
                            i         i     viii i    v iv i       i   v   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_84749721_8   1537 G-ATAAAGAAAAAG 1549
                         i-  v ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (68 / 52)
Gap_init rate = 0.01 (6 / 512), avg. gap size = 2.17 (13 / 6)  


2980 27.22 0.66 0.99  chrX_84754581_84760362.rev     4381  5291 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84754581_8   4381 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAATATTGTGAAAGT 4430
                               i i  i    vi        v      v i        v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84754581_8   4431 GCCCATACTGCCCAAAGTTAGTTATAGATTCAATGCTATTCCAATAAAAC 4480
                          v v     v      v v vi  i        i  v  i  v  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84754581_8   4481 TACCTTTGACGGTTTTTACAGAATTAGAAAAAATTATTTTAAATTTCATA 4530
                          v  vvivi vv     i     v v  v  iv v  ii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_84754581_8   4531 TGGAA-T-CAAAGAAGACCCTGTATAGTCAAGATAATCCTAAGCAAAAAG 4578
                              - -   i --     v v    i   i i    i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_84754581_8   4579 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTGTACTACAAGGC 4628
                                i      vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84754581_8   4629 TGCAGTAACAAAAACAGCATGATACTGGTATCAAAGCAAATATATAAACC 4678
                          i      iv  i    ii  i      i  v iiii i i     i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_84754581_8   4679 AATGGAGCAGAACAGAGACCTCAGAAATAACACCACAAATCTATAACCAT 4728
                               ii    iv    vii         vv   i v  i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_84754581_8   4729 CAGATATTTGACAAACCTGGCAATAACAAGCAATTGGTAAAGGATCTCCT 4778
                         iv   v  i     ivv  v   v v  vv    v  v    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_84754581_8   4779 ATTCAGTAAACGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 4828
                         v    ii   i          v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_84754581_8   4829 AACTGGACCCCTTCCTTACACCTTATACAAAAAGTAACTCGAGATGGACT 4878
                          ii         v   i     v          v      i i     ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_84754581_8   4879 GAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAACCT 4928
                         i?    i         i v i     i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_84754581_8   4929 AGGCA-ATACCATTCAGGACCTAGGCATGGGCAAAGACTTTATGAAAAAA 4977
                            ?i- v i -   iv     v  vv i     v ii  iv ii v vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_84754581_8   4978 ATGCCAAAAGCA-ATGCCAACAAAAGCCAAAATTGACAAATGGGATCTAG 5026
                          ii         - v  -        vv     v  i    v   i----
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGAC---- 642

  chrX_84754581_8   5027 TTAACTAAAGTTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAG 5076
                           v ii   i     i -   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_84754581_8   5077 AGAACAGGCAACTTACAGAATGAGAGAAAATTTTTGCAATCTACCCATGT 5126
                         v   v  i    ii        i        v       vii ivi  v 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_84754581_8   5127 GACAAAGTTCTAATATTCAGAATTTGCAAGGAACTTAAACATATTTACAA 5176
                           i  i vv  vi   i      v ii  i     ivv   vv iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_84754581_8   5177 GAAAAAGGCAAACAACCCCATCACAAAGTGGGCAAAGGATATGAACAGAC 5226
                         v      i    i     v  i?v   i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_84754581_8   5227 ACTTTTCAAAAGAAGACATTTACGTGGCCAACAA--ACATGAAAAAAAGC 5274
                          i  i  v        i  vi vi       i  --         i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_84754581_8   5275 TCAACATCACTGATCAT 5291
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (135 / 109)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


 269 28.17 0.00 0.00  chrX_84774732_84779717.rev        1    71 (4915)  C L1M4_orf2#LINE/L1   (837)    71     1  

C chrX_84774732_8     71 TGAAAAAACATTCCATGCTCATGGATAGAAATAATTAGGATCATGAAAAT 22
                           i   i i  i     i        v i  v v   iv  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_84774732_8     21 GGCCATACTGCTCAAAGTAAT 1
                            v     v i    v i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT 71

Transitions / transversions = 1.50 (12 / 8)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.00 (0 / 0)  

3080 24.81 2.21 1.66  chrX_84774732_84779717.rev     3607  4509 (477)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84774732_8   3607 TGCAAAGCCATATCT--TGCTCATAAATTGAAA----TAACATTATTAAA 3650
                           v    --     i--  i    ii    i  ----   i   i    i
  L1M4_orf2#LINE/      1 TGGAAAG--ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_84774732_8   3651 ATAGCCATATTACCAAAAAGAGTGTACATGTTCAATGTTATCTCCATTAG 3700
                           i  v   i v  v   vvii v    vi     i iv   i i  i i
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_84774732_8   3701 TATTCTAAAAGCATTTTTAAGCAGAAATAGAACAAAC-AATATTACAATT 3749
                         v  i i ivv  v     v-        v  -   i -i  vi  v    
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTT-GCAGAAATTGA-CAAGCTGATCCTAAAATT 146

  chrX_84774732_8   3750 TGTATG--AATTCAAAAACGATCTCAAATAGCAAAAGCAATCTTGAGAAA 3797
                         ii    --   v   ii--  i ivi      v   i         i   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_84774732_8   3798 GAAGAATAAAGCTGGAGGTAACACACTTCCTAATTGTCAAATATATTACA 3847
                               i    i      vvv         i    viv   iv  i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_84774732_8   3848 AACCTACAGTAATTAAAACCATATGATACAGGCATAAAAACAGACATATA 3897
                           v          i  i  vi i  i   v       ii i         
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_84774732_8   3898 GACAAATGAAACAAGTTAAAGAGTCCAGAAATAAACCAACACATGTACAA 3947
                           iv    i  i iiv vi                  v i    v  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_84774732_8   3948 TCAACTAAAACTTGATAAGAGTGCCAAGATAACTGCACAATGGGCAAAGT 3997
                             i i vvi i  i   i         iv i ---       v    v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAAGA 391

  chrX_84774732_8   3998 ATAGTCTCTTGAACAAATAGTGCTGGGAAAATTGGATATCAACATGCAAA 4047
                                i  v       i         v  i      ? v         
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_84774732_8   4048 AGGATAAAAGTCAACCCTTATCACATACCATACATAAAAATCAACTGTAA 4097
                           i  i  iv vi    i  i v  i      i i      i    vv  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_84774732_8   4098 ATGGTTTAAAAACTTAAACTTGTAAC--CTGAAACTA--AAACTTTTACA 4143
                             v i ? i  i    --     v--  i      --     i   v 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAA--TGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_84774732_8   4144 AGAAAACG--GGGAAAAATCATCTTGACCTTGGTCTTAGCAGTGTTTTAT 4191
                                i--  ?iv     v  v         vi vi   i  v   -i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-C 588

  chrX_84774732_8   4192 TTGGATATGACATCAAAAGCACAAACAACAAAAACAAAAATAAACAAGTG 4241
                           i         i           i        iv       i i  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_84774732_8   4242 GGACAACAT--GAACTAAAA-CTTCTACACAGCAAAAGAAACAATAAACA 4288
                             vv   --i  i     -   i iii vv    i  v  v  v  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_84774732_8   4289 GAGTGAGAAGGTAACTAATGGAATGGGAGAAAATATTTGCAA--CATATA 4336
                         i     i   ii   iv ii                      --      
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_84774732_8   4337 TAACTGATGAGTGGTTAATATCTAACATATATATGGAGCTACTACAACTC 4386
                          --     i  v ii vi    i iv       vi  i  vi        
  L1M4_orf2#LINE/    739 T--CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_84774732_8   4387 AATAGCAAAAGAAAAAATAAACATGATTAAAAAGTGGGCAAAAGACTTGA 4436
                             ii    ii v      v -ii   ?    i        i  i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_84774732_8   4437 ACAGACATTTCTCCAAAGAAGAAACACAAATCACCAACAGATATATGAAA 4486
                          i                    v i      vi    i iii i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_84774732_8   4487 AGGTCCTGAATGGTATTGCCTAG 4509
                           i v  v  iivi ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (141 / 79)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.84 (35 / 19)  

1705 25.00 4.80 1.60  chrX_84774732_84779717.rev     4486  4985 (1)  C L1M4_orf2#LINE/L1   (338)   570    55 *

C chrX_84774732_8   4985 ATACTGCCCAAGGTCATTTATAGATTCAATGCCATCCCCATCAAGCTACC 4936
                              v     iv v  i  i        i  v     i     iv v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

C chrX_84774732_8   4935 AA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATAT 4889
                          i-       i  -i     -   -- v  i  - iii    i       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTCATAT 151

C chrX_84774732_8   4888 GGAACCAAAAAAAGAGCCC-GCATTGCCAAGAGAATCCTAAGCCAAAAGA 4840
                             -- viv  i ii   - v  v     i v    i i ivv i    
  L1M4_orf2#LINE/    152 GGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

C chrX_84774732_8   4839 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 4790
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

C chrX_84774732_8   4789 ACAGTAATCAAAACAGCATGGTACCAGTACAA---CAGAGATATAGACCA 4743
                                    i    ii      ii i i  ---i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

C chrX_84774732_8   4742 ATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACGTCTACAACCA 4695
                               i    i--    i  --        vv   i  i i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

C chrX_84774732_8   4694 ACTGATCTTTGACAAACCTGATAAAAACAAGAAATAGGGAAAGGATTCTC 4645
                          i    i  i     ivv  vi  i v  vvv   i       i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chrX_84774732_8   4644 TATTTAATAAATTGTGCTGGGAAAACTGGCTAGCCATATTTAGAAAGCTG 4595
                          v  i  i    v         v      v  ?   i  vi i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chrX_84774732_8   4594 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 4545
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

C chrX_84774732_8   4544 TAAAGACTTAAAC-------------CTAGAAAACCCT-AGAAAAAAACC 4509
                         i ?    i    i-------------   v     i  -    i     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

C chrX_84774732_8   4508 TAGGCA-ATACCATTCAGGACCTT 4486
                             ?i- v i -   iv      
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTT 570

Transitions / transversions = 1.84 (79 / 43)
Gap_init rate = 0.03 (14 / 516), avg. gap size = 2.29 (32 / 14)  


3253 26.65 0.44 0.44  chrX_84789930_84795336.rev     4009  4916 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84789930_8   4009 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4058
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84789930_8   4059 GGCCATACTGCCCAAGGTAATTTACAGACTCAAAGCCATCCCCATCAAGC 4108
                            v     v     iv i  i      i    v  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84789930_8   4109 TACCAG-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTATAGTTC 4155
                          v    -       i  -i     -   -- v  i  - iii  v i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_84789930_8   4156 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTACGCCAAAA 4205
                                 viiv  ii  v  v v  v     iv     i ivivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_84789930_8   4206 GAACAAAGCTGGAGGCATCACAGTACCTGACTTCAAACTATACTACAATG 4255
                                 i      vv     v v  ii i      viv        v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_84789930_8   4256 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGAT 4305
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_84789930_8   4306 CAATGGAACAGAACAGAGCTCTCAGAAGTAACGCCACATATCTACAACTA 4355
                                 i    iv   vvii     i   vv   i i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_84789930_8   4356 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 4405
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_84789930_8   4406 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4455
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_84789930_8   4456 AAACTGGATCCCTTCTTTACACCTTATACAAAAATCAATTCAAGATGGAT 4505
                           ii    i    v i i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_84789930_8   4506 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4555
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_84789930_8   4556 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4604
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_84789930_8   4605 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4654
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_84789930_8   4655 TTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTACCATCAGAGTGAAC 4704
                          i   v v  i i   i iii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_84789930_8   4705 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 4754
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_84789930_8   4755 GGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4804
                            i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_84789930_8   4805 AAACAAACAACCCCATCAAAAAGTGGATAAAGGATATGAACAGACACTTC 4854
                          i     i     v  i?    i   ii       v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_84789930_8   4855 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 4904
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_84789930_8   4905 ATCACTGACCAT 4916
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


2282 28.75 6.29 0.58  chrX_84800350_84806349     4649  5507 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84800350_8   4649 TGGAAAAATACTCCATGCTCATTGATAGAAAAAATCAATATTCTTAAAAT 4698
                               i   ii     i    v   v i  i v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84800350_8   4699 GGTCATACTTTCCAAAGCAATATACAGGTTCAATGCTGTACCTATCAAAC 4748
                           iv     ii     vii  v     i     i  vi v         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84800350_8   4749 TACCAATGATATTCTTTGCAGAACTACAGA-AAACTAA-CCTAAAATTCA 4796
                          v   iiviiv  i         -- iv  -  i  i -           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chrX_84800350_8   4797 TATGGAACCAACAAAGAGCCCA-AATATCCAAAGCAATCCTAAACAAAAA 4845
                                vii-   i ii    -    v     i     i i  v  i  
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_84800350_8   4846 TAACAAAGCTGGAGGCATTATGCTACCTGACTTCAAATTATACTGTGAAG 4895
                         v       i      vv i ii  v  ii i      viv    iii   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_84800350_8   4896 ATACAGCAACCAAAACAGCATGGTACTAGTACAAAAACAGAC-------- 4937
                         v     i  i   i    ii       i i i  ii i    --------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_84800350_8   4938 CAACGGAATG-----------------------CCGTA-ATCT--GATCA 4961
                            i     i-----------------------  i  -  i -- i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_84800350_8   4962 --------TTGACAAAATAGAAAAAACAAGT-AATGGGGAAAGGA-ATTC 5001
                         -------- i     iivv vv  i  v v -           i - v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_84800350_8   5002 CTATTTAATAATTGGTTCCAGGACAACTGGCTAGCTATATGTAGTAGATT 5051
                         i -  i  i  v    v ii          v  ? i i   i iv   v 
  L1M4_orf2#LINE/    398 TT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_84800350_8   5052 GAAACTGGATGCCTTTCTTACACCATATACAAAAATCAACTGAAGATTAA 5101
                            ii    iv   vi  i                 i    v  i  vi 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_84800350_8   5102 TTAAAGACTTAAATGTAAGACATTGAACTCTAAATGCCCTT-GAAGTAAA 5150
                          i ?    i           vv vi    v    -i i   -    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chrX_84800350_8   5151 CCTAGAAAATACTATTCTGGAAATAGTCCTTGGCAGAGATTTTATGACAA 5200
                          v   i?ivv v v   vv  vv v vvi v    iv i   iv iivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_84800350_8   5201 AGACTCCAGAAGCAATTGCAACAAAACCAGAAACTGACACATGGGACCCA 5250
                         v   v   i     vvv         vv i   iv  i v  v    iiv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_84800350_8   5251 ATTAAACT--AATAC----GCACAGCAAAAGAAACTATCAACAGAGTAAA 5294
                           i   v --  v  ---- ii vv    i  v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_84800350_8   5295 CAGACAACCTACATAATGGGAGAAAATTTTTGCCAACTATGCATCAGACA 5344
                         v        i   v             v     v  ii  ii   v  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_84800350_8   5345 AAGGTCTAATACTCAGAATCTATAAGGAATGTAAACAAATCTTCAAGAGA 5394
                          i  v  vi  ii      v     i   ivivv    v  vvi  v i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_84800350_8   5395 TAAACAAACAACACCATTAAAAAGTGGGCAAAAGACATGAACCGAAACTC 5444
                         v i     i   v v   ?    i        i  iv    iv  v i i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_84800350_8   5445 TTCAAAAGAAGACATATATGTGACTGACAAGCATATGAGAAAATGCTCAA 5494
                         i  v        i   i vi  i ii i     i    i  i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_84800350_8   5495 CATCACTAATCAT 5507
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.47 (59 / 17)  


3133 26.90 0.77 0.66  chrX_84808539_84819517.rev     4999  5905 (5074)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84808539_8   4999 TGGAAGAACCTTCCATGCTCATGGATAGGAAGAATCAATTTCATGAAAAC 5048
                              ii iv i     i        v      v i   v ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84808539_8   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84808539_8   5099 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  - ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_84808539_8   5147 TATGGAACCAAAAAAGAGCCCGCATCACCAAATCAATCCTAAGCCAAAAG 5196
                                viiv  ii  v  v v  vi     v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_84808539_8   5197 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAATGC 5246
                                i      vv   ii  v  ii i      viv        v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84808539_8   5247 TACAGTAACCAAACCAGCATGGTACTGGCACCAAAACAGAAATATAGATC 5296
                                 i   iv   ii           iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_84808539_8   5297 AATGGAACAGAAC--AGAGCCCTCAGAAATGACGACGCATA--TCTACAA 5342
                                i    i--    i  --      i --  v    -- i  iii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAA--ACCCATACATTTATGG 344

  chrX_84808539_8   5343 CTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5392
                         ii vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_84808539_8   5393 CCCTATTTAATAAATGGTGCTGGGAAAAGTGGCTAGCCATATGAAGAAAG 5442
                         vi  v  i  i              v  v   v  ?   i   v i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_84808539_8   5443 CTTAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5492
                         v v  ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_84808539_8   5493 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5542
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_84808539_8   5543 ACCTAGGTGTTACCATTCAGGACATAGGCATGGTCAAGGACTTCATGTCC 5592
                           v    ?  v viv   iv   v v  vv i v   v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_84808539_8   5593 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5642
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_84808539_8   5643 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5692
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_84808539_8   5693 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTGCTCATCTGAC 5742
                          v  i     i   i             v       viiiivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_84808539_8   5743 AAAGGGTTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5792
                           i  ii vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_84808539_8   5793 AAA-AGAAACAACCCCATCAAAAAGTAGGCAAAGGACTTGAACAGACACT 5841
                            - v   i     v  i?    i i         i     i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_84808539_8   5842 TCTCAAAAGAAGACATTTATGCAACCAAAAAACACATGAAAAAATGCTCA 5891
                             v        i  vi viiii    v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_84808539_8   5892 CCATCACTCGCCAT 5905
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (139 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  

 253 28.92 1.20 0.00  chrX_84808539_84819517.rev     8291  8373 (2606)    L1M4_orf2#LINE/L1        1    84 (824)  

  chrX_84808539_8   8291 TAGAAACACATCCCATGCTCATAAACGGGTAGAATCAATATTGTGAAAAT 8340
                          i    v i        i    ii iv  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84808539_8   8341 GACCATACGGCAAAAAGCAGTCTACAAATT-AAC 8373
                          i v    vv vv   viii      i   -   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

Transitions / transversions = 1.18 (13 / 11)
Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1)  

1937 25.80 6.03 0.34  chrX_84808539_84819517.rev     8376  8972 (2007)    L1M4_orf2#LINE/L1      278   908 (0)  

  chrX_84808539_8   8376 ATGAAAATAGGCATATAGACCAATGGTACAGAATAGAGAACCCAGAAATG 8425
                           i ii    i        i      v i     v    ii        i
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_84808539_8   8426 AACCCAAATACTTATAGCCAACTGGTCTTTGACAAAGCAAACAAAAACAT 8475
                               v i i    i i   i  i i  i     i vviv   i v   
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_84808539_8   8476 AAAGCAGGGAAAGGACACCCTTTTCAACAAATGGTGTTGGGATAATTGGC 8525
                         vv iii       i i vi                 i     i  i   v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_84808539_8   8526 TAGCCACACATAGAAGAATGAAACTGGATCATCATCTGTCACCTTATACA 8575
                           ?     iii i         ii    i vii i  vv    v      
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_84808539_8   8576 AACATCAACTCAAGATGTATTAAGGACTTAAATCTAATATTTGAAACTAT 8625
                           v  i       i   v  i ?i   i     v   v vi i       
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_84808539_8   8626 AAAAATTCTAGAAGATAACATGGGA--AAACACTTCTAGACACTGGCTTA 8673
                             v ii       v     i  ?--   i-    vv   vi   v   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTA 576

  chrX_84808539_8   8674 GGTTAGGATTTCATGACCAGGA-ACCGAAAAGCAAGTGCAATAAAC--AA 8720
                           iv v i    v iivi v  -   -       viv    i   v--  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACC-AAAAGCACAAGCAACAAAAGAAA 625

  chrX_84808539_8   8721 AGATAAATAGATGGAACTTAATTAATCTAATGAGCTTTT-CACAGCAAAA 8769
                          i   i   i  v i    v  i  vv v vi i     -ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_84808539_8   8770 GGAACAGTCAGCAGAGTAAACAGACAACCCATAGAGTGGGAGAAAATCTT 8819
                          iv  vi   iv i   i  v          i   i           v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_84808539_8   8820 CACAATCTCTACATCTGACAAAGGACTAATATCCAGAAGCTACAATGAAC 8869
                         ii   viiv  i      i  i     vi         vv  i  v    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_84808539_8   8870 -----------------------ACAAAT---CCA--CAAAAAATGGGCT 8891
                         -----------------------      ---   --i?          v
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_84808539_8   8892 AAAGACATGAATAGACAACTCTCAAAAGAAGATATA--AATGGCCAACAA 8939
                           i  iv          vi    v            --         i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_84808539_8   8940 ACATATGAAAAAATGCTCAACTTCATTAATAAT 8972
                         i  i       i         v   ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (92 / 58)
Gap_init rate = 0.02 (10 / 631), avg. gap size = 3.80 (38 / 10)  

2396 26.28 2.42 1.40  chrX_84808539_84819517.rev     9705 10488 (491)    L1M4_orf2#LINE/L1      117   908 (0)  

  chrX_84808539_8   9705 TACAGAATTAGAAAAAACT-ATTTTAAATTTCATATGGAA-T-CAAAGAA 9751
                          i     v v  v  i-  -  ii    v           - -   i i 
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_84808539_8   9752 AACCCCATATAGCCAAGACAATCCTAAGCAAAAA-AACAAACCTGGAGAC 9800
                         --   viv        i      i i iv  i  -      vi     iv
  L1M4_orf2#LINE/    166 --CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_84808539_8   9801 ATCACGCTACCTGACTTCAAACTATACTACAAGGCCACAGTAACCAAAAC 9850
                         v    i  v  ii i      viv        i  i       i   i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_84808539_8   9851 AGCATGGTACTGGTACCAAAACAGACATATAGACCAATAGAGCAGAACAG 9900
                           ii         i iv ii i           i    i  ii    iv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_84808539_8   9901 AGAGCTCAGAAATAACACCTCACATCTACAACCATCTGATCTTCTACAAA 9950
                             ii         vv  vi    i  iiii  vi    i   v    i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_84808539_8   9951 CCTAACAAAAACAAGCAATGGGGAAAGGATCTTTTATTCAGTAAATGGTG 10000
                         vv iv   i v  vv            i  vv i v    ii        
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_84808539_8  10001 CTGGGAATACTGGCTAGCCATATGCAGAAAACTGAAACTGGACCCCTTCC 10050
                               vv     v  ?   i     i  i v    ii         v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_84808539_8  10051 TTACACCTTATATAAAACTTAACTCAAGATAGATTAAAGACTTAAATGTA 10100
                          i     v    i    v         i  i   i ?    i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_84808539_8  10101 AAGCCCCAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTC 10149
                          iiv iv    i      vi i           v    ?i- v i -   
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC 562

  chrX_84808539_8  10150 AGGACATAGGGATGGGAAAAGACTTC------ATGACAAAAACTCCAAAA 10193
                         iv   v v   v i  v  v ii   ------      ------      
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA------CCAAAA 606

  chrX_84808539_8  10194 GC-CATTTCAACAAAAGCCAAAATTGACAAATGGAATCTAGTTAAACTAA 10242
                           -  vv-         vv     v  i    v i ii vi i   v v 
  L1M4_orf2#LINE/    607 GCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_84808539_8  10243 AGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTTGATAGGCAACAT 10292
                          i i   i  ii vv    i  v       vv i   vi v  i    vi
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_84808539_8  10293 ACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGTCTAAT 10342
                                          v       vii  vi      i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_84808539_8  10343 ATCCAGAATTTACAAGAAACTTAAACAAATTTACAG-AAAAAAACAAC-- 10389
                                  v  i  ii    ivv    v iv i i-     i    v--
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_84808539_8  10390 ACC--ATAAAAAAGTGAGTGAAGAGCATGAACAGACACTTCTCAAAAGAA 10437
                            --  v?    i  i ii   iiiv    i     i     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_84808539_8  10438 GACATTCATGCAGCCAACAA--ACATAAAAAAAAGCTCAACATCACTGAT 10485
                           i  v  viii     i  --    i    i v           ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_84808539_8  10486 CAT 10488
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.49 (121 / 81)
Gap_init rate = 0.02 (16 / 792), avg. gap size = 1.88 (30 / 16)  


3167 27.09 0.77 0.77  chrX_84828293_84834684.rev     4994  5901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84828293_8   4994 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5043
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84828293_8   5044 GGCCATACTGCCCAAGATAATTTATAGATTCAATACCATCCCCATCAAGC 5093
                            v     v     iv i  i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84828293_8   5094 TACCAATGACTTTCTTCACAGAATTGTAAAAAACT-ACTTTAAAGCTCAT 5142
                          v   iivi i  i  ii     v - i v  i  - iii    ii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_84828293_8   5143 ATGGAACCAAAAAAGAGCAAGCATTGCCAAGTCAATCTTAAGCCAAAAGA 5192
                               viiv  ii  v v  v  v     iv       i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_84828293_8   5193 ACAAGGCCAGAGGCATCACGCTACCTTACTTCAAACTATACTACAAGGCT 5242
                             i iii    vv    i  v  iv i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_84828293_8   5243 ACAGTAACCAAAACAGCATGATACTGGTACCAAAGCAGAGATATAGATCA 5292
                                i   i    ii  i      i iv iiii   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_84828293_8   5293 ATGGAACAGAAC--AGATCCCTCAGAAATAATGCTGGATATCTACCACTA 5340
                               i    i--   vi  --        vv iiv i  i  iviii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_84828293_8   5341 TCTGATCTTTGACAAACCTAACAAAAACAAGCAATGGGGAAAGGATTCCC 5390
                         vi    i  i     ivv iv   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_84828293_8   5391 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5440
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_84828293_8   5441 AAAATGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5490
                           iv    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_84828293_8   5491 TAAAGACTTAAATGTTAGACCGAAAATCATAAAATCCCTAGAAGAAAACC 5540
                         i ?    i       v   v v    ii      ii i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_84828293_8   5541 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5589
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_84828293_8   5590 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAT-GGGTTCTA 5638
                         i            vvi          vv     v  i    -  ii ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_84828293_8   5639 ATGAAACTAAGGAGCTTCTGCACAGTAAAAGAAACTACCATCAGAGTGAA 5688
                         vii   i   ii -   i  ii vvi   i  v    i  vv i      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_84828293_8   5689 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAA--TATACTCATCTGA 5736
                         v  i     i                 v       --i   i--      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chrX_84828293_8   5737 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATCTAGAAGA 5786
                         i  i  i  vi          v  i         vv    v  v v  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_84828293_8   5787 AAAAAACAAACAATCCCATCAAAAAGTGGTTGAAGGATATGAACAGACAC 5836
                             i     i  i  v  i?    i   vii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_84828293_8   5837 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 5886
                              v        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_84828293_8   5887 ATCATCACTGGCCAT 5901
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2158 28.69 6.09 1.76  chrX_84852663_84857844.rev     3869  4722 (460)    L1M4_orf2#LINE/L1        3   893 (15)  

  chrX_84852663_8   3869 GAAAATTATTCCATGCTCACGGATAGAAAGAATCAATATCATTAAAACGG 3918
                             iv   i     i   i    v i    v i     ii    i i  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_84852663_8   3919 CCACACTCCTTAAAGCAATTGACAGATTCAATGCTATTCCTATTAAACTA 3968
                          v i     ii   vii  iv          i  v  i     i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_84852663_8   3969 TCAATGACATTCTTCACAGAAGTAGAATAAAC--ACTTAAAAATCCACAT 4016
                         i  iivi v  i  ii     i v  -i  i -- iiiv     i  i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATAT 151

  chrX_84852663_8   4017 GAAACCAAAAAGGAACCTGAATATTTAAGGCAATCTTAAGCAAAAAGAAC 4066
                          i  viiv  i   v  v     vii  ii       i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_84852663_8   4067 AAAGCTAGAG---CCATTGTTATCCAACTTCAAACTATACTACAGGGCTA 4113
                             i i   ---i  ivv  -i    i      viv       ii    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_84852663_8   4114 CGGAAACAAAAACATCATGCCATTGCTACAAAAACAGGCACATAGACCAA 4163
                          i v  iv  i   vii  vi i  vi i  ii i  i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_84852663_8   4164 TGGAACAGAATACAGAGCGCAAAAATAAGGCTGCACACCTATAACCACGT 4213
                              i     vv    iv  i      iv iii   ii   iii  vv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_84852663_8   4214 GATCTTCGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGA----CTCA 4259
                            i        i v  v   i v  vv            i ----  i-
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT- 399

  chrX_84852663_8   4260 TTCACTAAATGGTGGTGGGATAACTGTCTAGCAATATGCAAAAGATTGAA 4309
                             vi        v     i     vv  ? v i          v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_84852663_8   4310 GCTGAACTCCTCTCTTACAGCATGTA-AAATATCAACTCAAGGTAGATTA 4358
                          i  i  i   vi  i   v   i  -   v  i       ii i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_84852663_8   4359 AACACTTAAATGTAACACCCAAAACTATAAAAGCTCT-GGAAAACAATCT 4407
                         ? v  i         v v i            -    -i   i v  iv 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chrX_84852663_8   4408 AGGCA-ATACCATTCTGGACATAAAAACAGGCAA--ATATTATATGACAA 4454
                            ?i- v i -   vv   v viiivi      --i v iv  -  i v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GATAT 596

  chrX_84852663_8   4455 AGACACCAAAACCAATAATAACAAAAGCAATAATTGACAAGTAGAATCTA 4504
                         -          v  vv ii        v  v   v  i  i v i ii v
  L1M4_orf2#LINE/    597 -GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_84852663_8   4505 ATTAAACTTAGGAGTTTCTGTGCAGCAAAGGA------------------ 4536
                           i   v   ii ii  i     vv       ------------------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_84852663_8   4537 -----AACCTACAGAATGGGAGAAAATTTTTTCAAATTATGCATTTGACA 4581
                         -----    i                 v   v     i  ii  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_84852663_8   4582 AAGGCTTAATATCTAGAACCTATAAAGAACTTCAACAAATTTACAAGAGA 4631
                          i  vi vi    i    iv           iiv    v iv i  v i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_84852663_8   4632 AAAACAA----CCCCATTAAAAAGTGAGGCA-------TGAACA--CAGC 4668
                           i    ----   v   ?    i  -    -------    i --  vi
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATG-GGCAAAGGATTTGAATAGACATT 844

  chrX_84852663_8   4669 TTTTAAAAGAAGGCATAGGTACATAATGA--AATGAAGGCAGAAATAAAG 4716
                          i iv       --   --    -    i--   i --   v viv    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAG--ATA--TACA-AATGGCCAATAA--GCACATGAAAAG 887

  chrX_84852663_8   4717 ATGTTC 4722
                            i  
  L1M4_orf2#LINE/    888 ATGCTC 893

Transitions / transversions = 1.74 (153 / 88)
Gap_init rate = 0.03 (24 / 891), avg. gap size = 2.79 (67 / 24)  


3137 26.81 0.33 0.55  chrX_84883386_84888491     3704  4613 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_84883386_8   3704 TGGAAACACATTCCGTGCTCATGGATCAGTAGAATCAATATTGTGAAAAT 3753
                               v i  i  i  i        ii v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_84883386_8   3754 GATCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTGTCATCAAAA 3803
                          iiv     v  v   vii       i      i     ivii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_84883386_8   3804 TATCACCATCATTCTTCACAGAACTAGAAAAACCAATCCTAAAAATCATA 3853
                          vi  v vv v  i  ii     v v  v  i ii         v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_84883386_8   3854 TGGAACCAAATAAGAG-CCCA-CATAGCCAAAGCAAGACTAAGTAAAAAG 3901
                              -- vii   i -    -v         i   vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_84883386_8   3902 AACAAATCTGGAGGTATCACATCACCTGATTTCAAACTATACTATAAGGC 3951
                               vi      vv     iiv  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_84883386_8   3952 CATAGTCACAAAAACAGCATGGTACTGATATAAAAATAGGCACATAGACC 4001
                         i i   v iv  i    ii        ii    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_84883386_8   4002 AATGGAACAGAATAAAGAACCTAGACATAAACCCATATACTTACAGCCAA 4051
                                i     vi   ii i   v           i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_84883386_8   4052 CTGATTTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAAGACACTCT 4101
                         i       i     i vviv   i v   vv i        ii i v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_84883386_8   4102 ATTCAACAAATGGTGCTGGGAAAAATTGGCTAGCCACATTTAGGAGAAAA 4151
                         v                    v  -i   v  ?      vi ii    vi
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATG 447

  chrX_84883386_8   4152 AAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGAT 4201
                           ii    i  ii i   v    v           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_84883386_8   4202 CAAGGACTTAAATCTAAGACCAGGACCTATAAAAACCCTAGAAGATAACA 4251
                           ?i   i     v     v vii v        vi i       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_84883386_8   4252 TCAGAA-AAACCCTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAG 4300
                          vi ?i-   i i  vv   v    v        v i    v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_84883386_8   4301 AACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTGAT 4350
                          vv         v v    i    iv   i   i   iv v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_84883386_8   4351 TAAACTAAAAAGCTTTCGCGTGGCAAAAGCAACAGTCAGCAGAGTAAACA 4400
                         i   v v    i    i i ivv    i vv  vi   iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_84883386_8   4401 GACAGCCCACAGAGTGAGGGAAAATCTTCACAATCTATACATCTGACAAA 4450
                             i        i  i i      v  ii   vii   i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_84883386_8   4451 AAAACTAATATCCACAACCTACAACTAACTCAAATAAATTAGCAAGAAAA 4500
                         ii -  vi      v  iv  i  vv     vv i  v i ii  v    
  L1M4_orf2#LINE/    748 GGA-CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_84883386_8   4501 AAAACAAACAATCCTATCAAACAGTGGGCTAAGGATATGAATAGACAATT 4550
                          i -    i  i  v  i?  v i     v      v          v  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_84883386_8   4551 CTCAAAAGAAAATACACAAATGGCCAACAAGCATATGAAAAAATGCTCAA 4600
                            v      i   i            i     i       i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_84883386_8   4601 CATCACTAATGAC 4613
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


2277 25.29 8.82 2.00  chrX_85034571_85036752      842  1691 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85034571_8    842 TAGAGAGACATACCATGTTCATAGATTGGAAGACTCAAAATAATAAAGAG 891
                          i  i   i  v          i            i  v  vi v    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85034571_8    892 GTCAATCCTCCC-AAA-----CTATAGTATTAAAGTAATTGTTATCAAAA 935
                          v    v     -   -----   i  vv i  v i   ivi        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85034571_8    936 TCTCAGCAAGATTTTTCTTTAGACATAGACAAGCTTATTTAAACATTTAT 985
                           i    v- vi    i vi   v  v        v  iiv  v   i  
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_85034571_8    986 ATGGAAAGGCACAAACTCTAGAATATCTAAAACAATCTTGACAAGGAAAA 1035
                                v   viiivi i      v i             v  i   i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_85034571_8   1036 ATAAATTGGGAGGA-----ATTTATCTGATAGTAAAGCCTATCACATAGC 1080
                          i   v v      ----- i  -i ii  vvi   i i  ii   v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAAGC 248

  chrX_85034571_8   1081 TTCAGTAATAAAGATAATGTGGTATTGGTGGAGGAAAAAACATATAGATC 1130
                          v       v    i i       i   iiv i i v i           
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_85034571_8   1131 ----GAACAGAATAAAGAACCTCAAAATAGACCCATCCAAGTACAATCAA 1176
                         ----   i     vi   ii ivi     i      v  vv  iii    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_85034571_8   1177 CTGATTTTTGACCAAGGTATAAAAGTAATTCAATGGAGGAAGAATAGCCT 1226
                         i       i   v i   iiv  iiiv         i i        i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_85034571_8   1227 TTTCAATAAATGGTGTTGAAGCAATTGGATATCC---------------- 1260
                               i        i  iii   i      ?  ----------------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_85034571_8   1261 --TTAGATCG------------------AAAAA------CAAAAAAGAAC 1284
                         --  i  i v------------------     ------     vi  v 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_85034571_8   1285 ACTGATCTAAACGTACAACATAAAACTATAA-----TTAAAAAAAAA--- 1326
                          ?v  i     i   vi vv           -----   i  i    ---
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_85034571_8   1327 -AGAGAAAATCT--AT-ACCTATAGGT-AGGCAAAAAGTTCTTAGACTTC 1371
                         -i ? v      --i -    - i   -      viiv        iv v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_85034571_8   1372 ACACCAAAATAATCAAAATAATCAAAATAATAATAATTGATAAATTAGAC 1421
                                  vv i--  ii  -     v  -  -   v        i   
  L1M4_orf2#LINE/    598 ACACCAAAAGCAC--AAGCAA-CAAAAGAA-AA-AATAGATAAATTGGAC 642

  chrX_85034571_8   1422 CTCATCAAGATTAAAAATATTTGCTCTGCAAAATATCCTATTTAAAGAGG 1471
                         i       i        iv    iv  v    iv iv    i--    ii
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC--AAGAAA 690

  chrX_85034571_8   1472 ATGAAAAGACAAGCTAGAGTCATGGG-GAAAATATTCTCCAACCACATAT 1520
                         i           v i v  -v     -         iv v  i  i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAG-AATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_85034571_8   1521 CTGACAAAGGACACATATTTAGAATGGATTTTTTTTAACTCTGAAAACTC 1570
                             i  i    vii   ii     iv  vvvv---      v v     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAG---AACTCTTACAACTC 786

  chrX_85034571_8   1571 AACAGTAAAAA-AC---TACTCCAATTTTAAAAACAAGCAAAAGACATGA 1616
                           i i      -  ---  vi      ?-     iii     i  iv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGA 835

  chrX_85034571_8   1617 ACAGACACTTCACCAAAAATGGTATATGGATGGCAAATAAGAGAACATGA 1666
                          i     i   v     i v i    iii     v      v--      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC--ACATGA 883

  chrX_85034571_8   1667 AAAAATATTCAAAATGAGCCATCAA 1691
                            i  ii    v  v ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (128 / 83)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.41 (92 / 27)  


3117 27.65 0.77 0.33  chrX_85063084_85069317     4838  5741 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85063084_8   4838 TGGAAGAACATTCCATTCGCATGGATAGGAATAATCAATATCATAAAAAT 4887
                              ii i  i    viv       v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85063084_8   4888 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4937
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85063084_8   4938 TACCAATGACTTTCTTCACAGAATTGGAAAAAAGTACTTTAAAGTTCATA 4987
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_85063084_8   4988 TGGAACCAAAAAAGAGCCCACTTTGCCAAGTCAATCCTAAGCCAAAAGAA 5037
                              viiv  ii  v  vivv v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_85063084_8   5038 CAAACCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5087
                             vi      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_85063084_8   5088 CAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGATATAAACCAA 5137
                               i   i    ii   i     i iv ii i   v     i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_85063084_8   5138 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTAT 5185
                              i    i--    i  --        vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_85063084_8   5186 CTGATCTTTGATAAACCTGACAAAAACAAGAAATGGGGAAAGCATTCCCT 5235
                         i    i  i  i  ivv  v   i v  vvv           v  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_85063084_8   5236 ATTTAATAAATGGTGCTGGGAAAACTGGATAGCCATATGGAGAAAGCTGA 5285
                         v  i  i              v         ?   i   v i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_85063084_8   5286 AACTGGATCCCTTCCTTACGCCTTATACAAAAATTAATTCAAGATGGATT 5335
                          ii    i    v   i  i  v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_85063084_8   5336 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAAAAGAAAACCT 5385
                          ?    i  v    v   v       i      vi i  i        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_85063084_8   5386 AGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5434
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_85063084_8   5435 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5484
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_85063084_8   5485 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5534
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_85063084_8   5535 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 5584
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_85063084_8   5585 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAGATTTACAAGAAAAA 5634
                           i  vi          v  i         vv   iv iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_85063084_8   5635 AACAA----CCCCATCAAAAAGTGGGCAAAGGATATTAGTAGACACTTCT 5680
                         i    ----   v  i?    i            v v i      i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_85063084_8   5681 CAAAAGAAGACATCTATGCAGCCAATAAATACATGAAAAAATGCTCATCA 5730
                          v        i  vi viii        ii         i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_85063084_8   5731 TCACTGGTCAT 5741
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.37 (142 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.00 (10 / 5)  


2708 27.61 1.66 1.00  chrX_85147924_85150889     1572  2473 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85147924_8   1572 TGGAAACACATCCCATGCTCATGAATGGGCAGAATCAATGCTGTGAAAAT 1621
                               v i        i     i  v  v   v i   ii   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85147924_8   1622 AACTATACTGCCAAAAGCAATCTATAAACTTAATGCAATTTCCATCAAAA 1671
                         ii v     v  v   vii     i i i i  i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85147924_8   1672 TACCATCATCATTCTTCACAGAACTAGAAAAA--AATCCTAAAATACGTA 1719
                          v   v vv v  i  ii     v v  v  i--i          v i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_85147924_8   1720 TGGAACCAAAAAAAGAGCCTGCATAGCCAAAGCAAGGCTAAGCACTGAGA 1769
                              viiv  ii-  v  v v         i   vvi i iv vvi   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_85147924_8   1770 ACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATGCTACAAAGCT 1819
                              vi      vv     i v  ii i      viv i          
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_85147924_8   1820 CTAGTCACCAAAA-AACATGGTATTGGTATAAAAATAGGCACATAGACCA 1868
                         vi   v i   i - iii     i   i    ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_85147924_8   1869 ATGGAACAGAACAGAGAATCCAGAAATAAAGCCAAATACTTACAGACAAC 1918
                               i    iv    i            v   v i i   ii v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_85147924_8   1919 TGATCTTTGACAAAGCAAACCAA-AGCATAAAGTGGGAAAAGGACTACCC 1967
                             i  i     i -ivi    - v   vv i    i    i ivii i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_85147924_8   1968 TTCCAACAAATGATGCTGGGATAATTGGCAAGCCACATGTAGGAGAATGA 2017
                           i         i        i  i   vv ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_85147924_8   2018 AACTGCAGGGTCATCTCTCACCTTAT-TAAAAACAACAACTCAAGATGTA 2066
                          ii  v vvvii i   v    v   -i     i--i       i   v 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAAT--TAACTCAAAATGGA 496

  chrX_85147924_8   2067 TTAAAGACTCAAATCTGCGACCTCAAACCATCTAAATTCT-AGAATATAA 2115
                          i ?    ii    v iv  v  v    i  v-   i   -    v v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAA 545

  chrX_85147924_8   2116 CATAGAAAAAACTCTTCTAGACATTCGTTTAGGCAGAGAGTTCATGACCA 2165
                              i?iv  v     vv   v  v v       iv iv   v iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_85147924_8   2166 AGAACCCAAAAGCAAATGCAACCAAAACAAAGATAAATAGATAAGACCTT 2215
                         v  vv         v v     v   iv   i   i   i  vi   i i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_85147924_8   2216 ATTAAA-TTAAAAAGCTTCTTCACAGCAAAAGAAATAATCAACAGAGTAA 2264
                           i   -       -   i vii vv    i  v iv     v i   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_85147924_8   2265 ACAGACAACCCACAGAGTGGGAGAAATTATTCACAAAGTATGCATCTGAC 2314
                          v              i         v    ii    vi  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_85147924_8   2315 AAAGGACTAATAATATCCAGAATCTACAAGGAAGTC----AAATGAGCAA 2360
                           i     -- i-          v  i  i   v  ----  v v ii  
  L1M4_orf2#LINE/    745 AAGGGACT--TG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_85147924_8   2361 GAAAAATA---ATAATCACATCAAAAAGTGGGCTGAGGACATGAATAGAC 2407
                         v     v ---    i vv  i?    i     vi    iv         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_85147924_8   2408 AATTCTCAAAAGAGGATATACAAATGGCCAACAAAGATATAAAAA-ATGC 2456
                          v     v     i                 i  iv i  i    -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_85147924_8   2457 TTAACATTACTAATGAT 2473
                          i     i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.50 (24 / 16)  


2891 27.35 2.47 0.67  chrX_85166829_85171647     3449  4340 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85166829_8   3449 TGGAAAAATAACCCATGTACATGGATTGGAAGAATGACTATTGTTAAAAT 3498
                               i   v       v              v v v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85166829_8   3499 GTCCATAGTATCAAAACCAATCTACATGTTCAATGCAATCCTTATCAATG 3548
                          v v   v vi v   iii       vi     i       i      vi
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85166829_8   3549 TATCAGTGACATTCTTCACAGAAATAGAAAAAC--AACTTTAAATTTATA 3596
                          vi   ivi v  i  ii       v  v  i -- v i v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_85166829_8   3597 TGGAACCACAAAATATCCAGAGCAGCCAAAGCTATCCAAATTAAAAAGAA 3646
                              vii   iiv i     ii       i v   i--- v        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT---TGAAAAAGAA 197

  chrX_85166829_8   3647 AAA--AACCTGGAGGAGTCACATTACCTGGCTGCAAATTACACTGCAGAG 3694
                         i  --  vi       v     i v  iiii v    vivi   i  i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_85166829_8   3695 CTATAGGAACTGAAACAGCATAGTACTGGCATAAA-ACAGACACATAGGC 3743
                            i  v  iii i    ii i            i- i     i    ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_85166829_8   3744 CAATGGAACAGAATAGAGAAGACAGAAAAAAATACACACAACTACAGTGA 3793
                                 i     v    ivv      v   iv  i   vi  ii  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_85166829_8   3794 ACTCATTTTTGACAAAATTGCTAAGAAGATCCACTGGGGGAAAAGACAGC 3843
                          i v     i     iiv   i    vv  i  v     i  i - i  i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGT 396

  chrX_85166829_8   3844 TTCTTCAATAAATGATACTAGAAAAACGGGATATTCATATTCAGAAAAAT 3893
                         i i     i     i i  i i v   v     ?i  i  v  i  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_85166829_8   3894 TAAACTGGACCCCTCTCTCTCACCTCATACAAAAGTCAAATTAAAGTGAA 3943
                         v  ii         vi   v    vi        i i  v i   i  i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_85166829_8   3944 TTAAAGACTTCCATCTAACACCTCAAACTATAAAAGTACTACAAGAAAAC 3993
                          i ?    i vv  v   v v  v           v vi  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_85166829_8   3994 TTTGGGGAAAATCTCCAATTCATTGATCTGGGCAAAAATATATTAAACAA 4043
                         v v  ? v      i ivvv v   ivi i     vii v v   i i v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_85166829_8   4044 TACCCCATAAGCACAGGCAACCAA-GCAGAAATGGACAAATGGAATCACA 4092
                         v  v   v       i     v  - v i    i  i    v i iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_85166829_8   4093 TCAGG-TTAAAAAGCTTCTGCACTGTAAAGGATACAATCAACAAAGTGAA 4141
                            ii-       -   i  ii  vi      i  v     v        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_85166829_8   4142 GAGAAAACTCATAGAATGGGA-AAAATATTTGCAAACTGCTCATCTGACA 4190
                         i   v   i  i         -              iiiivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_85166829_8   4191 AGGGATTAATAACCAGGATATATAGAGAGTTCAAAAAGCTCTGTAGGAAG 4240
                              i vi  v    i       i   ii  vv v i   vi  iv  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_85166829_8   4241 AAAATCTAGTAAGCTGAACAAAAATTGGGCAAAAGATTTGAATAGACCTT 4290
                           i - v i   v ii vi?    v        i             v  
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_85166829_8   4291 TCTCAAAAGAAGACATACAAATGGCCAA--------------GGTGCTCA 4326
                             v        i              -------------- i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_85166829_8   4327 AAACCAGTGATCAT 4340
                          v i  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.55 (28 / 11)  


3337 26.65 0.33 0.33  chrX_85174719_85180997.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85174719_8   4881 TAGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                          i   ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85174719_8   4931 GGCCGTACTGCCCAAGGTAATTTACAGATTCAATGTCATCCCCATAAAGC 4980
                            vi    v     iv i  i           i iv     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85174719_8   4981 TACCAA-TGCCTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCAT 5029
                          v   i-       i  -i     v v  v  iv v iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_85174719_8   5030 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTGAGCCAAAAGA 5079
                               viiv  ii  v  v v  v     iv     i   ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_85174719_8   5080 ACAAAGCCGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5129
                               ii     vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_85174719_8   5130 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5179
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_85174719_8   5180 ATGGAACAGAAC--AGAGCCCTGAGAAATAATGCTGCATATCTACAACTA 5227
                               i    i--    i  --        vv iii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_85174719_8   5228 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5277
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_85174719_8   5278 TATTTAATAAATGGTGCTGGGAAAACTGGCTGGCCGTATGTAGAAAGCTG 5327
                          v  i  i              v      v i?  ii   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_85174719_8   5328 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5377
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_85174719_8   5378 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5427
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_85174719_8   5428 TAGCCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5477
                            v?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_85174719_8   5478 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5527
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_85174719_8   5528 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5577
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_85174719_8   5578 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5627
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_85174719_8   5628 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5677
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_85174719_8   5678 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 5727
                         i     i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_85174719_8   5728 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCA 5777
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_85174719_8   5778 TCACTGGCCAT 5788
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


2804 26.18 1.30 2.25  chrX_85226230_85230190.rev     2627  3470 (491)    L1M4_orf2#LINE/L1       73   908 (0)  

  chrX_85226230_8   2627 TACAAAATCAACGTA--------CAAA-TATCAGTAGCATTTCTATATGC 2667
                             i v      i --------    - vi   iv  v   i ---   
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTT---TGC 119

  chrX_85226230_8   2668 CAACAGTGAACAATCTGAAAAAGAAAAAATTCTAAAACTTATATGGAACC 2717
                         vi v v   -   v    ----------- i      i i        vi
  L1M4_orf2#LINE/    120 AGAAATTGA-CAAGCTGA-----------TCCTAAAATTCATATGGAAAT 157

  chrX_85226230_8   2718 ACAAAAGACCCAGAATAACCAAATCTATTCTAACCAAAAA-AGCAAAACT 2766
                         i   ii           i     v v  ii i vv  i  - i    ii 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_85226230_8   2767 AGAAGAGTTTTATTACCTTACTTCAAATTATACTATAGAGCTATAAGGAA 2816
                         i  i  v ivi i v  iv i      viv     i i     i - v  
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA-GTAA 256

  chrX_85226230_8   2817 CCAAAACAGCATGTTACTGGCATAAAAACAGACATATACACCAATGGAAC 2866
                         i   i    ii  v           ii i         v i        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_85226230_8   2867 AGAATAGAGAACCCAGAAACAAATCCACAAACCTACAGTAAACTCATTTT 2916
                              v    ii       i   i   i v ii  ii  v  i v     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_85226230_8   2917 CAACAAAGGTGCCAAAAATATACCCTGGGGAAAAGACGATCTCTTCAATA 2966
                          i    i        i vi  v vv        ii iii   i     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_85226230_8   2967 AAGAGTGCTGGGAAAGGTGGAAATGTATATACAGAGGAATGAAACTAGAT 3016
                           vi         v iv    v ?vi i  i  i i       ii i  i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_85226230_8   3017 TCCTATGTCTCACCATATGCAAAAATCAAATCAAAATGGATTAAAGACTT 3066
                         i    iv  v        i       i  v           i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_85226230_8   3067 AAACCTAAGACTTTGAACTGTGAAACTGCTACAAGAAAACTTTGGGAAAG 3116
                            iv     vi vi    i i     vi  v        v v  ?iv i
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_85226230_8   3117 ATCTCCAGGATATTGGTCTGGGCAAAGATTTCTTGAGCAATACCCCACAA 3166
                             i iv  iv    vi i     v i      iiii vv  v   v  
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_85226230_8   3167 GTATAGGCAACCAAAGCAAAAATAGACAAATGGGATTGCATCCAG-TTAA 3215
                          i i i     v    v         i    v   i v    v i-    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_85226230_8   3216 AAAGCTTCTGCACAGCAAAGGATACATTTAACAAAGTGAAGAGACAACCC 3265
                            -   i  ii vv       i  vv i  v        i         
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_85226230_8   3266 ACAAAATAGAAGAAAATATTTGCAAACTACCCATGTGACAAGGTATTAAT 3315
                            i   i i                ii ivi  v   i    v i vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_85226230_8   3316 AATCAGAATATATAAGGAGCTCAAACAACTATATATGAAAAAAATCTAAT 3365
                          vi            i  i   vv      vv   vv     i - v   
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAAT 804

  chrX_85226230_8   3366 AATCCAATCAAAAAAATAAGAAAAAGATTTGAGAAGACATTTCTCAAAGG 3415
                           i     i?     - ii v   i       iv           v  i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_85226230_8   3416 AAGACATACCAATGGCAAACAGGCATATGAAAAGGTGCCCAACATCATTT 3465
                             i    v      v  i i   i        i   i        ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_85226230_8   3466 GTCAT 3470
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.68 (136 / 81)
Gap_init rate = 0.01 (11 / 836), avg. gap size = 2.73 (30 / 11)  


2594 26.09 4.01 2.79  chrX_85256572_85262345     4385  5281 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85256572_8   4385 TGGAAAAACATTTCGTGCTCATGGATAGGAAGAATTAATATCATTACAAT 4434
                               i i  ii i  i        v      v       ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85256572_8   4435 GGCCATACTGCTCAAAGCAATGTATAGATTCAGTGCTATTTCTCTTAAAC 4484
                            v     v i    vii  v  i       ii  v  ii  v i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85256572_8   4485 TACCAATGACATTTTTCACAAAACTAGAAAAAAACT-ATTTTAAAATTCA 4533
                          v   iivi v     ii  i  v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_85256572_8   4534 TATGCAACCAAAAATAGCCCA-AATAAGTAAGGCAATCCTAAGCAAGT-G 4581
                             v  viiv  ivii    -    ivi  ii     i i iv   v- 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_85256572_8   4582 AACAAAGCTGGAAGCATCATGGTACTTGACTTCAGACTATGCTACACGGC 4631
                                i    i vv   iiv v iii i    i viv i     vi  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_85256572_8   4632 AACAGTAACCAAAACAGCATGGTACTGGTATAAGAACAGACACATGGAAC 4681
                         v       i   i    ii         i     i i     i  i  v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_85256572_8   4682 AATGGAACAGGATAAAGAGCCCAGAATTATGGCTGCACACCTACAATGAT 4731
                                i  i  vi    i      v  viv iii   ii  iii v v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_85256572_8   4732 CTGATCCTTGACAAAGCTGACATAGACAAC-CAATAGGGAAAGGACTCCC 4780
                         i    ii i     i v  v  -    v i-    i       i ivvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_85256572_8   4781 TATTCAATAAATGATGCTGGAATAACTGGCTAG----------AAGACTG 4820
                          v     i     i      i i      v  ?----------    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_85256572_8   4821 AAGCTAGACCCCTTCCTTACACCATATACTAAAATCAACTCAAGATGGAT 4870
                            i i       v   i           v     i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_85256572_8   4871 TAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGAAAACC 4920
                         i ?    i         i v i            vi i i         v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_85256572_8   4921 TAG---TCAATACCATTCTAGACATAGGATCAGGCAAAGATTTTATGCCA 4967
                            --- v   -- -   vv   v v  i i      v i   iv --- 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT---A 591

  chrX_85256572_8   4968 AAGATG---CCAAAAGCAATTGCAACAGAAGCAAAAATTCACAAATAGAA 5014
                         i v   ---         vvv      i   v      vv i    v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_85256572_8   5015 CCTAATTAAG-TTAAAGA-----GCACAACAAAAAA-ACTATCAACAGAG 5057
                          i v  i  i-     i ----- ii vv    ii -        v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_85256572_8   5058 TAAACAGAGAACATACAGAATGGGAGAAAATTTTTGCAAACAATGTGTCT 5107
                          i  v   v   vi                 v        iv  i i   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_85256572_8   5108 GACAATTGTCTAATACACAGGGTCTACAAGGAACT-TTACAAGAAATTTA 5156
                           i  vv v  vi  iv   ii v  i  i     -      ----i i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA----CTCA 787

  chrX_85256572_8   5157 A-AAGATAAAAGA-AAACAACCCCATTGAAAAGTGGGTAAAGGACATGAA 5204
                          -  v -      -   i     v   ?    i    i      iv    
  L1M4_orf2#LINE/    788 ATAATA-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_85256572_8   5205 C------TTTTCCAAAAAAAAAAAAAAAAAGACATATATGAGGCCAACAA 5248
                         i------  i      i  -----------  i   i viv      i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAA-----------GATATACAAATGGCCAATAA 875

  chrX_85256572_8   5249 GCATATGAAAAAAAGCTCAAAATCAGTGATCAT 5281
                            i       i v      v    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (143 / 88)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.77 (61 / 22)  


2705 27.16 1.86 2.41  chrX_85306626_85311110     3080  3992 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85306626_8   3080 TGGAGAAACACACCATCCTCATGGATAGGTAGAATCAATATTGTTAAAAT 3129
                             i i i iv    vi        v  v   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85306626_8   3130 GGCGTTACTCCCCAAAGCAGTGTATAGATTCAATGCTATTCCTATCAATC 3179
                            iv           viii v  i        i  v  i        vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85306626_8   3180 TACTAA-TACCATTTTT-CATGGAATTAGAAAAAATTGTTCC-AGAATTC 3226
                          v i i- i  v     -  - i    i-- v  ii  v   - i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_85306626_8   3227 ATATGAAACCAAAAAAGAGCTCAAATAGCTGAAACAATCCTAAGTAAAAA 3276
                              i  viiv  ii  v ivi      ii        i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_85306626_8   3277 GTGTAGAGCCTGAGGAATCACCATACCCAACTTCAGACTATACTACAAGG 3326
                          vii i  iiv     v    vv v     i    i viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_85306626_8   3327 CTACAGTAACCAAAACAGCGTGGTACTTGTACAAAGACAGGCACACAGAA 3376
                                  i   i    i        v i i  i  i  i  i i   v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_85306626_8   3377 TGATAGAACGTAATAGGGAATCCAGAAATCAGATTGCTTTATTGCACACC 3426
                         ii  i   iiv   v i  i         - i ii----i  ---   ii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAAT-AAACC----CAT---ACATT 339

  chrX_85306626_8   3427 CATAACCATCTGATCTTTGACAAAGTCAACAACAAAAAAAGCAATGGGGA 3476
                         i  iii  vi    i  i     i viiv   --i vv vv         
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAA--GACCATTCAATGGGGA 387

  chrX_85306626_8   3477 AAGAACTCCCTATTCAATAAATAGTGTTGGGATAACTGACTAGTTATATT 3526
                              ivvi  v     i    i   i     i     iv  ?ii i  v
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_85306626_8   3527 CAGAAGGTTGAAACTGGACCCCTTCCTTACACCATACACAAAAATCAACA 3576
                           i   iv    ii         v   i        i        i   v
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_85306626_8   3577 CAAAATGGATTAAAAACTTATAGGTAAAACCTACAACTTAAAAAACCCT- 3625
                                   i ? i  i  v v    i v   v    - v     i  -
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTT 536

  chrX_85306626_8   3626 AGAAGAAAACCTAGGAC--ATTCTATTCTGTACATAGCCCTTGGCAGAGT 3673
                                   v    ?v-- v   - iv  -  v v vvi v    iv v
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCT-TCGTG-ACCTTGGGTTAGGCAATGG 584

  chrX_85306626_8   3674 TTTC------ATGACAAAGCCTTCAAAAGCAATTTCAACAAAC--AAAAA 3715
                             ------      ------i        vvvv       v--     
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_85306626_8   3716 CTGATAAGTGGGGCCTAATTTAACTAAGGAGCTTTTGCAAATCAAAAGAA 3765
                         iv     i v  i i v  iv  v v ii i      iivv     i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_85306626_8   3766 ACTATTAACAGAGTAAACAGACAGCCCACAGAATGAGAGAAAATATTTGT 3815
                              i  v i   i  v     i           i             i
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_85306626_8   3816 ATCTTATGCATGCAACAAATGTCTCATATCCAGAACCTATAAGGAAATTA 3865
                          vv i  ii  vii i  iv v  ii         iv     i   v iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_85306626_8   3866 AGCAAATGAACAAGAAAAAGA--AACA-CCCTATTGAAAAATGGGCAAAG 3912
                         vi   v v  i  v       --  i -   v   ?              
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_85306626_8   3913 GACATGAACAGATACTTCTCTATAGAATACATACACTTGGCCAACAAGCA 3962
                           iv    i   i i     i v    v i     vv       i     
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_85306626_8   3963 TATGAAAAAATGTTCAATATCACTGTTCAC 3992
                         i       i   i    i    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.05 (39 / 19)  


3268 26.84 0.44 0.55  chrX_85350821_85357073.rev     4854  5762 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85350821_8   4854 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4903
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85350821_8   4904 GGCCATACTGCCCAAGGTAATTTACAGATTCAATACCATCCCCATCAAGC 4953
                            v     v     iv i  i           ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85350821_8   4954 TACCAATGACTTTCTTCACAGAA-TTGGAAATAAACT-ACTTTAAAGTTC 5001
                          v   iivi i  i  ii     -   --- i  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_85350821_8   5002 ATGTGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5051
                           i     viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_85350821_8   5052 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5101
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_85350821_8   5102 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5151
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_85350821_8   5152 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAAC 5199
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_85350821_8   5200 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5249
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_85350821_8   5250 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGC 5299
                         i  v  i  i              v      v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_85350821_8   5300 TGAAACTGGATCCCTTCCTTACACCTGATACAAAAATCAATTCAAGATGT 5349
                             ii    i    v   i     vv          i  i    i   v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_85350821_8   5350 ATTAAAGACTTAAACGTCAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5399
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_85350821_8   5400 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTT 5449
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_85350821_8   5450 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5499
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_85350821_8   5500 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5549
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_85350821_8   5550 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5599
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_85350821_8   5600 AAGGGCTAATATCCAGAATCTACAATGAACTCAAAGAAATTTACAAGAAA 5649
                          i  i  vi          v  i  v      vv v  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_85350821_8   5650 AAAACAAACAACCCCATCAAAAATTGGGCAAAGGACATGAACAGACACTT 5699
                           i     i     v  i?    v           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_85350821_8   5700 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5749
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_85350821_8   5750 CATCACTGGCCAT 5762
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.80 (9 / 5)  


 224 16.67 16.67 0.00  chrX_85416430_85418321.rev      375   428 (1464)    L1M4_orf2#LINE/L1      685   747 (161)  

  chrX_85416430_8    375 AAGAAAGTAAAAAGACAGCTT---------GAAAAAATATTTTCAACTCA 415
                                 i        i ii---------  i         v   v   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_85416430_8    416 TATATCTGCCAAG 428
                                 vi   
  L1M4_orf2#LINE/    735 TATATCTGATAAG 747

Transitions / transversions = 2.00 (6 / 3)
Gap_init rate = 0.02 (1 / 63), avg. gap size = 9.00 (9 / 1)  

3145 24.22 2.00 2.11  chrX_85416430_85418321.rev      502  1401 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_85416430_8    502 ATTCCATGCTCATGGATAGGAAGAATCAATATTGTTTAAATGGCCATATT 551
                           i     i        v      v i         v i     v   i 
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_85416430_8    552 GTCCAAAGCAATTTACGGATTCAGTGCTATTCCTATCAAGCTATCAAGGA 601
                         vi     vii  i   i      ii  v  i        iv vi  ivvi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_85416430_8    602 TATTTTTCATAGAATTAGAAACAATTCTTCTAAAATTCGCATGGAACCCA 651
                         iv     iii    v v  v viv vv i         ii      ----
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA---- 155

  chrX_85416430_8    652 AAACAAG---CCCA-AATAGCCAAAGCAATCTTAAGCAAAAAGAGCAAAG 697
                          vi    ---    -          i       i iv  i    i     
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_85416430_8    698 CTGGAGGCATCACATTACCCAACTT-AAAACTATGCTACAAGGCTACAGT 746
                         i      vv     i v     i  -      - i      i        
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGT 254

  chrX_85416430_8    747 AATGAAAACAACATGGTACTGCTAAAAAAAACAGACACATAGACCAATAG 796
                            v  i   iii        vi v  ii -i     i     i    i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAATGG 303

  chrX_85416430_8    797 AACAGAATAGAGAACTCAGAAATAAGGCCACACATCTACAACCATCTGAT 846
                           i     v    iii         iv   i    i  iiii  vi    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_85416430_8    847 CTTCAACAAACCTAACAAAAACAAACAATGGGGAAAGGACTCCCTATTCA 896
                         i   i    ivv iv   i v  vv            i ivvi  v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_85416430_8    897 GTAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGATTGAAATTG 946
                         ii              i      v  ?   i     i    v    i   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_85416430_8    947 GACCCCTTTCTTTCACCATATACAAAAATCAACTCAAGATGGATTAAATA 996
                                vi  iv                i       i      i ? v 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_85416430_8    997 TTTAAATGTAAAACCTAAAATTATAAAAATCCTTGAAGACAACCTAGGAA 1046
                         ii         i v      i       v  i v     v   v    ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_85416430_8   1047 ATACTATTTTAGACATAGGCTCTGGCAAAGATTTCATA---ATGAACACA 1093
                         vv v v  ivv   v v  v iv     v i    v  ---    ---  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA---CA 600

  chrX_85416430_8   1094 CTGAAAGCAATTGCAAAAAAAGGAAATATTGACAAGTTGGAC-----CAA 1138
                          ii      vvv    v     i   v  v  i  i      -----   
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_85416430_8   1139 ATATTATATTAAAGAGCTTTTGCAAAGCAAAAAAC-CTATCAACAGAGTA 1187
                          ------      i -      iivvv    ii  -       v i   i
  L1M4_orf2#LINE/    651 A------ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_85416430_8   1188 AA----CAACCTACAGAATGGGAAAAAAAAATTGGCAAACTATGCATCTA 1233
                           ----     i           i    v -  v     ii  ii    i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATA-TTTGCAAATCATATATCTG 742

  chrX_85416430_8   1234 ACAAAGGTCTAATATTTAGAATCTATAAGGAACTTAAACAATTAAATAAG 1283
                          i  i  v  vi   ii     v     i     ivv    i v     v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_85416430_8   1284 CAAAAAAGAAACAACCCCATTAAAAAATGGACAAAGGGCATGAACAGACC 1333
                         v    i v   i     v   ?        i      iiv    i    v
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_85416430_8   1334 CTTCTCCAAAGAAGACCTTTACATGTGGCCAACAAGCATATGAAAAAATA 1383
                         i              -- v    vi       i     i       i  i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGA--TATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_85416430_8   1384 CTTAACATCACTAATCAC 1401
                           i       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (127 / 87)
Gap_init rate = 0.02 (15 / 899), avg. gap size = 2.47 (37 / 15)  


3272 26.84 0.44 0.55  chrX_85456787_85465091      492  1400 (6905)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_85456787_8   1400 TGGAAGACCATTCCATGCTCACGGGTAGGAAGAATCAATATCGTGAAAAT 1351
                              iivi  i     i   i  i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_85456787_8   1350 GGCCATACTGCCCAAGGTCATTTACAGATTCAATGCCATCCCCATCAAGC 1301
                            v     v     iv v  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_85456787_8   1300 TACCAATGACTTTCTTCACAGAA-TTGGAAATAAACT-ACTTTAAAGTTC 1253
                          v   iivi i  i  ii     -   --- i  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

C chrX_85456787_8   1252 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 1203
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chrX_85456787_8   1202 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 1153
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chrX_85456787_8   1152 CTACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGAC 1103
                                  i   i     i         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chrX_85456787_8   1102 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTGCAAC 1055
                                 i    i--    i  --        vv   i i  i iiiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

C chrX_85456787_8   1054 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAAGGATCC 1005
                         i vi    i  i     ivv  vv  i v  vv   i        i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

C chrX_85456787_8   1004 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 955
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

C chrX_85456787_8    954 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 905
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

C chrX_85456787_8    904 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 855
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

C chrX_85456787_8    854 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 805
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chrX_85456787_8    804 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 755
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chrX_85456787_8    754 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 705
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chrX_85456787_8    704 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 655
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chrX_85456787_8    654 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 605
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chrX_85456787_8    604 AAAACAAACAACCCCATCAAAAAGCGGGCGAAGGACATGAACAGACACTT 555
                           i     i     v  i?    ii    i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chrX_85456787_8    554 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATCCTCAT 505
                            v        i  vi viii     v  i          i  v    v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chrX_85456787_8    504 CATCACTGGCCAT 492
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.80 (9 / 5)  

2418 29.00 1.65 1.76  chrX_85456787_85465091     6906  7812 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_85456787_8   6906 GAGAAATATTCCATACTCATGGAATGGAAGTATCAGTGTCATTAAAAGGG 6955
                           i i    i    ii       v      vv i i i ii    i v  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_85456787_8   6956 TCATAGTGCCCAAGGAAATGTACAGATTCCATGCCATTCCTATCAAGCTA 7005
                         iv   v v     ivvi  v         v i  v  i        iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_85456787_8   7006 CCAACATCATTTTTCACACAATTAGAAAGATTTAGTCTACAATTCATATA 7055
                            i vv v     ii  v  v v  v iii v vi   v         i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_85456787_8   7056 GAACCAAATAAAAAGAGCCCA-AATAGTCAAAGCAATCCTGAGCAAAAAG 7104
                            ----  iv  i ii    -     i    i     i   iv  i   
  L1M4_orf2#LINE/    153 GAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_85456787_8   7105 AACAAAACCAGAGACATCATACAACCTGACTTTAAACTGTTCTTTAAGGC 7154
                               iiii   ivv   i  vv  ii i  i   viv v  vi  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_85456787_8   7155 TACAGTAACCAAAAAAAGCAATGT---ATTGTTACAAAAACAGCCATATT 7201
                                 i   i ----  i   --- i  vi i  ii i  v     v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGA----CAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_85456787_8   7202 GACAAATGGTATGGAACAGAAAACTAAGAAATAAATCCACACACCTACAA 7251
                           iv     v  i   iv  i iiiv         i   i   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_85456787_8   7252 CCATCTGATCTTTT-TAAGGCTGACAAAAATAAGCAAAGGGGAAAGGACT 7300
                         i  vi    i  iv-i    v  v   i vi vv   v        i iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_85456787_8   7301 TCCTATCCAATAAATGACACTGGGATAACTGGCTAGCCATATGTAGAAGG 7350
                         vi  v i   i     iii      i      v  ?   i   i i   i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_85456787_8   7351 ATGAAACTAGAGGCCTAAATTTTACCATATACAAAAATTAACTGAAGATG 7400
                              ii i  vv    vv ivi                    v  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_85456787_8   7401 GATCAAAGATTTAAATGTAATACCTCAAACTATTAAAAAATTCTAGAAGA 7450
                              ?   ii         v v  v       --    v ii       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTAT--AAAACTCTTAGAAGA 542

  chrX_85456787_8   7451 AGTCCTAGGAAATACAT-TTCTTAACATTGGCCTTGGCAAAAAA--CTTT 7497
                          iv v    ?i-  v  -   v i  v    vi v     viiv--   v
  L1M4_orf2#LINE/    543 AAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_85456787_8   7498 GACTAAGTCCTCAAAAGC-CATTGCAACACAAACAAAAATTGAGAAATGG 7546
                           -  v v vi       -  v-      v  iv      v  v    v 
  L1M4_orf2#LINE/    592 GA-TATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_85456787_8   7547 GACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATTTTCATCAG 7596
                            i v  i   v v  i i   i  ii vv    i  v i v   vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_85456787_8   7597 AGTAAACAGGCAAACTACAGAATGGGAGAAAGTATTCACAAACTATGCAT 7646
                            i  v  i   v i               i    ii    ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_85456787_8   7647 CTGTCAAAGGTCTAATATACAGAATCTATCAGGA--TCTTA--AGTCAAC 7692
                            vi  i  v  vi   v      v   v i  --     -- v    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_85456787_8   7693 AGACAAAAACCAAAAAACTTCATTAAAAAATGGACAAAGGACATGAACAG 7742
                          ivv    iv    v   iiv   ?        i       iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_85456787_8   7743 ACACTTCTC--AAGAAGAGTCATAAAATTGGACAATGAAAATATGAAAAA 7790
                            i     --       --i   v  v   v    i iv i       i
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGA--TATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_85456787_8   7791 ATCACTAATCATCAGAGAAGTG 7812
                           -i  v v     ????????
  L1M4_orf2#LINE/    888 AT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (147 / 112)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 1.82 (31 / 17)  


2871 23.33 2.19 7.60  chrX_85502905_85506452.rev     2098  3057 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85502905_8   2098 TGGAAGAATATTCTGCGATTATGGATTGGACTAATTAATATTGTAAAAAC 2147
                              ii    i iii v i          vv v          v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85502905_8   2148 GTCAATATT--------------ACAGATTCAATGCAATCTCTATTAAAA 2183
                          v     i --------------          i      i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85502905_8   2184 TATCAATGACATTTCTTATGGAAATAGATAAA--AATTCTAAAAATTATA 2231
                          vi  iivi v   i  iii     v  i  i--i  i      v i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_85502905_8   2232 TGGAACTACAAAAGACCCCAAATAGCCAAAGCAAGCTTGAGCAAAAAAAG 2281
                              v i   ii     vi          i   v     --    i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chrX_85502905_8   2282 AA--AAGCTGGAGGCATCACACTACCTGACTTCCAAATATATTACAAAGT 2329
                           --   i      vv       v  ii i   v   iv  i       i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_85502905_8   2330 TATAGTAACCAAAACAGCATGGTACTGGCATGAAAACAGACACATAGACC 2379
                           i     i   i    ii            i ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_85502905_8   2380 CATGGGACAGAAAAGATAGCCCAAAAATAAATCCATGCATGCCCAGACAT 2429
                         v    i i    vv  v  i   i       i    i   ----------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT---------- 338

  chrX_85502905_8   2430 AAATCCATGTGTTTACAACCTACTGATTCTTCACAAAGGTGGCAAGGACA 2479
                         ------------   iiii v i     i iv    i    v    iv  
  L1M4_orf2#LINE/    339 ------------TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_85502905_8   2480 CACGATGGAGAAATGACCGTCTCTTCCACAAATAGTGCTGAGAAAGCTGG 2529
                         iv i    i    vi iv    i   v      i      i  v i    
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_85502905_8   2530 ATATCCACTTGCAGAGGAATGAAGCTAGAAGTCCCTTATCTCTTGGCATA 2579
                            ?    v    i i        i i  ---   i  i   viiv    
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGA---CCCCTACCTCACACCATA 473

  chrX_85502905_8   2580 TACAAAAATCAACTGGAAATGGATGAAAGACATAAATGCAAAACCTGAAA 2629
                                  i    vi        v ?    v      i  i v  i   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_85502905_8   2630 TGAAAAAAACTCCCAGAAGAAAACTTGGGG--AGATGCTTCATGACACTG 2677
                         iv v    -   ii          v i  ?-- i  -    i    vi  
  L1M4_orf2#LINE/    524 CTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTG 571

  chrX_85502905_8   2678 ATCTAGGCAAAAAATTTTTGGATAAGACCCCAAAAGAATAAGCTACAAAA 2727
                         ivi       viiv  i  i    v   v       v i    v      
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_85502905_8   2728 GCAAAAAGAAACAAATGGGATTTCAACAAACTTAAAAGTTTCTGCACAGC 2777
                          v     v i i    v   i    v    v      ii  i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_85502905_8   2778 AAAAGAAACAATCACCACAATGAAAAGACAACCTACAAAATGAGAGAAAA 2827
                            i  v  v    vv v i             i   i    i       
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_85502905_8   2828 AATATTTACAACT-ACACATCTGACAAGGGGTTAATATCCAGATTGCGTA 2876
                         --     i   v - i i      i     ii vi        v iii  
  L1M4_orf2#LINE/    722 --TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_85502905_8   2877 AGAAACTCAAAAAAGACAATAGCAAAAAAAAAAAAAAACATACACACACA 2926
                          ii     vv v  vv     ii     i v   ------  --------
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAA------TA-------- 805

  chrX_85502905_8   2927 CACACACACACACACACACACACAAAATACTACTTAAAAATGAGCAAAAG 2976
                         -------------------  v   -------i ?       i     i 
  L1M4_orf2#LINE/    806 -------------------ACCCAA-------TTWAAAAATGGGCAAAGG 829

  chrX_85502905_8   2977 ACCTGAATAGACATTTCTCAAAAGAAGACACAAGAATGGCCAACAGGCAG 3026
                          ii                v        i i vi         i i   -
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA- 878

  chrX_85502905_8   3027 GTAAAAAAAAATGTTCTGCATCATTCACCAC 3057
                         -i vi    i   i  vi     ????????
  L1M4_orf2#LINE/    879 -CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (144 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 6.27 (94 / 15)  


3276 26.87 0.44 0.44  chrX_85507694_85510337.rev     1246  2153 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85507694_8   1246 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1295
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85507694_8   1296 GGCCATACTGCCCAAGGTCATTTACAGATTCAATGCCATCCCCATCAAGC 1345
                            v     v     iv v  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85507694_8   1346 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1393
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_85507694_8   1394 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1443
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_85507694_8   1444 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1493
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_85507694_8   1494 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1543
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_85507694_8   1544 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1591
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_85507694_8   1592 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1641
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_85507694_8   1642 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1691
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_85507694_8   1692 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1741
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_85507694_8   1742 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 1791
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_85507694_8   1792 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 1841
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_85507694_8   1842 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 1891
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_85507694_8   1892 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1941
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_85507694_8   1942 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCTTCTGACAA 1991
                           i     i   iv            v  i    vii iviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_85507694_8   1992 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2041
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_85507694_8   2042 AAACAAAAAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 2091
                          i     v     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_85507694_8   2092 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 2141
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_85507694_8   2142 ATCACTGGCCAT 2153
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1029 24.05 1.58 5.06  chrX_85534764_85539342.rev     2858  3173 (1406)    L1M4_orf2#LINE/L1        4   308 (600)  

  chrX_85534764_8   2858 AAAGATATTCC-TTTTCATGGATTGAAATAATCAATATTGTTCAAATGTT 2906
                                 i  - v           i  v v i         v i   --
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG-- 51

  chrX_85534764_8   2907 GTCCATACTACCCTAAGCAATCTACAGATTCAATGTA-TCCCTATCAAAA 2955
                          - v     v   v  vii              i i -            
  L1M4_orf2#LINE/     52 G-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85534764_8   2956 TACCAATATCAATTCTGTTGATATTCCTCAACAGAAATAGAATAAATAAT 3005
                          v   i--------   ii----  ii ii-       v  vv iv i  
  L1M4_orf2#LINE/    101 TCCCAG--------CTGCC----TTTTTTG-CAGAAATTGACAAGCTGAT 137

  chrX_85534764_8   3006 TCTAAAACTTATATGGTACCACAAAAGACCCAGAATAACCAAAACTATCC 3055
                         i      i i      v vii   ii           i       v   i
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chrX_85534764_8   3056 CGAGTAAAAACAACAAAATTGGAGGAATTACATTACCTGACTTCAAATTA 3105
                         i  iv  i  v      i        v i   i v  ii i      viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_85534764_8   3106 TACTACAGAGCTGTAGGAATCAAAACAGCATGGTACTGGTATAAACACAT 3155
                                i    ii  v      i    ii         i    iv i v
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_85534764_8   3156 -TACATAGGCCA--GGAGCAG 3173
                         -i i    ii  --   ii  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAG 308

Transitions / transversions = 2.04 (51 / 25)
Gap_init rate = 0.03 (9 / 305), avg. gap size = 2.33 (21 / 9)  

2137 23.60 2.57 1.12  chrX_85534764_85539342.rev     3466  4088 (491)    L1M4_orf2#LINE/L1      277   908 (0)  

  chrX_85534764_8   3466 CAAAAAAACAAACAGAACATAGATCAATAGAACAGAATGAATAACCCAGA 3515
                           v  ii i i   ---i          i   i     vi v ii     
  L1M4_orf2#LINE/    277 CATAAGGATAGACA---TATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_85534764_8   3516 AACAACTCCACACAC--ACAGTGAACTCATTTCCAACAAAGATGGCAAGA 3563
                           i  vi   i   i-- ii  v  i v    i i    i i  v     
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_85534764_8   3564 ACATATACTGGGAAAAAGGTAGT----TCAAATAATAGTGCTGGAAAAAC 3609
                         v   vi v    i   iii    ----    vv   i       i v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_85534764_8   3610 TGGATATCCATATGCAGAAAAATGAAACTAGACCCCTATCTCTTGCCATA 3659
                               ?   i     i  i      ii i        i   vii     
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_85534764_8   3660 TAGAAAAATCAAATCAAAATAGATTAAATACTTAAATCTAAGACCTCAAA 3709
                           v      i  v       i   i ? v  i     v     v  v   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_85534764_8   3710 CTATAAATCTACTACAAGAAAACATTGGGGAAACTCTTCTTCAGGACATT 3759
                                v  vi  v          v  ? v  v     v ---   v  
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT---GACCTT 570

  chrX_85534764_8   3760 GATCTGGGCAAAATTTTCTTA-ATA---CTCCACAAACACAGCCAACCAA 3805
                          ivi i     viv       -   --- v   v  i    iv    v  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_85534764_8   3806 AGTAAAAATTGATAAGTATGATCACATCAAG-TTAAAATGCTTATGCACA 3854
                           v      v     i vv  iiv      i-      -i   v  ii v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCT 669

  chrX_85534764_8   3855 GCAAAGGAAACAATCAACAAAG-----ACACAACCCACAAAATAGGAGAA 3899
                         v       v  v     v    ----- v          i   i      
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_85534764_8   3900 AATATTTGCAAACTACCCATCTGATAAGGGATTAATAACAAGAATATATA 3949
                                     ii ivi             i vi  v v          
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_85534764_8   3950 AGGAGCTCAAACAACTCTATATGAGAAAATCTAATAATCAGATTTTAAAA 3999
                          i  i   vv       v   vv i   iv v     i vi   ?v    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_85534764_8   4000 TGGGACAAATATTTGCATAGACATTTCTCAAAAGCAGATATACAAATGGC 4049
                             vv  iv     v             v    v               
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_85534764_8   4050 AAACAGGCATATGAAAAGGTGGTCAACATTATTCATCAT 4088
                         v  i i   i        i  v       i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (75 / 68)
Gap_init rate = 0.01 (9 / 632), avg. gap size = 2.56 (23 / 9)  


2834 27.74 0.72 0.72  chrX_85577984_85583149.rev     3460  4288 (878)    L1M4_orf2#LINE/L1        3   831 (77)  

  chrX_85577984_8   3460 GAAAAACATCCCATGCTCATGGATGGGAATAATCAATATCATTAAAATGG 3509
                             i i        i        v    v v i     ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_85577984_8   3510 CCATACTGCCCAAAGCAATTTACAGATTCAATACTATTCCTGTCAGACTA 3559
                          v     v      vii  i           ii v  i   i   i v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_85577984_8   3560 CCAATGGCATTCTTCATAGAACTAGAAAAACCTATTTTAAAATTTATCTG 3609
                            iiv  v  i  iii    v v  v  i iv  ii       i  v  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_85577984_8   3610 GAACCAAAAAAGAGCCCAAATAGCCAAGGCAATCATAAGCAAAAAGAACA 3659
                            viiv  ii  v  vi         ii     v i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_85577984_8   3660 AAGCTGGAGGCATCATGTTACCCAACTTCAAACTATACTACAAGGCTACA 3709
                            i      vv   iii v     i      viv        i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_85577984_8   3710 GTGACCAAAACAGCATTGTATTCATACAAAAACAGGCACACAGACCAATG 3759
                           i i   i    ii v   i vii i  ii i  i  i i   i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_85577984_8   3760 GAACAGTTTGGAGCACCCAGAAATAATGCTATGCATCTATGACCACCTGA 3809
                            i  vv v   vii          vv i  i   i    ii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_85577984_8   3810 TCTTCAACAAAGCAGACAAAAATAAGGAATAGGAAGAAAACTTTCTTATT 3859
                          i   i    i vv v   i vi vvv   i  i i i  ivv    -  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-TT 401

  chrX_85577984_8   3860 CAATAAATGGCACTTTGATAATTTGCTAGCCATATGCAGAAGAC--AAAC 3907
                            i      ii  vv  i  i v v  ?   i     i    v--  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_85577984_8   3908 TGGACCCCTTCCTTACACCATATACAGAAATCAACTCAAGATGGATTAAA 3957
                                  v   i            i    i       i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_85577984_8   3958 GACTTAAATGTAAAACCCAAAATTATAAAATCCCTTGAAGACAACCAAGG 4007
                            i         i v i    i       ii i v     v   vv   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_85577984_8   4008 CA-ATACCATCCTAGACATAGGAATGGGCAAAGATTTCAT-GACATAGAC 4055
                         ?i- v i v  v -   v v  iv i     v i    v -  i  -   
  L1M4_orf2#LINE/    552 NGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATAT-GAC 599

  chrX_85577984_8   4056 ACCAAAAGCAATCA--CGACAAAAGCAAAAATTGACAAGTGGGATCTAAT 4103
                                   --  -- i       v      v  i  i v   ii v  
  L1M4_orf2#LINE/    600 ACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_85577984_8   4104 TAAACTTAAGGGCTTATGCACAGCAAAAGAAACTATCAACAGAGTAAACA 4153
                         i   v    iii   v  ii vv    i  v        v i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_85577984_8   4154 GACAACCTACACGATGGAAAAAAAATATTTGCAAACTATGCATCTGACAA 4203
                                i   vi    i i    -          ii  ii      i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAA 746

  chrX_85577984_8   4204 AGGTCTAGTATCCAGCATCTATAAGAAACTTTAACAAATTTACCAGAGAA 4253
                         i  v  v        v  v     ii    i v    v iv iv v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_85577984_8   4254 AAACAAACAACCCCATTAAAAAGCGGGCAAAGGGT 4288
                          i     i     v   ?    ii         i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.63 (140 / 86)
Gap_init rate = 0.01 (9 / 829), avg. gap size = 1.33 (12 / 9)  

 350 24.47 0.00 0.00  chrX_85577984_85583149.rev     4582  4675 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_85577984_8   4582 AAAAGTGGGCAAAGGACACGAGCAGACACTTTCCAAAAGGAGACATACAC 4631
                             i           ivi  ii     i  ii v    i   i     v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_85577984_8   4632 GCAGCCAACAAGCATATGAAGAAAAGCTAAATATCACTGATCAT 4675
                         iii     i     i     i i v   v  i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.60 (18 / 5)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


2523 26.64 4.06 1.58  chrX_85648282_85650798.rev     1141  2026 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85648282_8   1141 TGGAAA-ATATTCCATGCTCATGGATTGGAAGAATTAATATCGTTAAAAT 1189
                               -    i     i               v       i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85648282_8   1190 GGCCATACTGCCAAAAGCAATCGACAGATTTAATGTTCTTCCTATAAAGC 1239
                            v     v  v   vii   v       i  i ivv i     v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85648282_8   1240 TACCAA-TGTCACTTTTTGCAGAATTAGAAAAATCTATTCTAAAATTCAT 1288
                          v   i-  i -i           v v  v  iiiv  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_85648282_8   1289 ATTGAACC-CAATAGGAGCCTGAATATACAAAGCAGTCCT---AAGGGGG 1334
                           v   vi-   -i   v  v     vv    i  i  i ---  i ii 
  L1M4_orf2#LINE/    150 ATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_85648282_8   1335 AAAAAAGCCAAAGGCATCATG-TTATCAGATTCAATCTATACTATAAGGC 1383
                           v    iiii   vv   ii-  vi  iv     vviv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_85648282_8   1384 TATGATGATTGAAACAGCATGGTACTGGCATAAAAACAG-CACAGAGACC 1432
                           iii i  ii i    ii              ii i  -  i v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_85648282_8   1433 AATGGAA-AGAATAGACTGCCTAGAAAAAAGGCTGCACCCCTACA---AT 1478
                                -     v  vv i i     v  ------    v    ---  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAA------ACCCATACATTTAT 342

  chrX_85648282_8   1479 GATC---TGACTTTCAACAAAGTCAACAAAAATAAACAACAGGAAAATGA 1525
                          i  ---   i    i    i viiv   i vi vv   ii  i   -  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GA 391

  chrX_85648282_8   1526 CTA-CCTATTTAATAAATGGTGCTGGGATAACTGTCTATCCATACTCAGA 1574
                         v  -i  v  i  i              i     vv  ?   i iv  i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_85648282_8   1575 AGAATGAAACTAGATCCCTACCTTTTACCATATACAAAACCTAACTCATG 1624
                                 ii i  i        ivi             vi       vi
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_85648282_8   1625 ATGAATTAAAGATTTAAATTTAAGACCTCAAACTATAAAAATCCTAGAAG 1674
                            i  i ?   ii     v     v  v           v  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_85648282_8   1675 AAAACCTAGGAAATACCATTCTGCATATCACC----ATT-GGCAAAGAAT 1719
                              v    ?i-  -- v   v i i--   ----i  -     v iv 
  L1M4_orf2#LINE/    542 AAAACATAGGNG-TA--AATCTTCGTG--ACCTTGGGTTAGGCAATGGTT 586

  chrX_85648282_8   1720 TTATGACTAAATCCTCAAAAGCAATTTCAAGAAAAACAAAAATTGACAAG 1769
                          iv iiv  viv vi        vvvv   v    iv      v  i  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_85648282_8   1770 TAGGACCTAATTAAA--TGAAAGCTTTTGCACAGCAAAACAAACTATAAA 1817
                          v    i v  i   -- i   i      ii vv    iv v     v  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_85648282_8   1818 GAAAGTAAACAGCCAATGCACAGAATAGAAGCAAATATTTGCAAACTATG 1867
                               i  v  v   iv        i i  v             ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_85648282_8   1868 CATTCAATAAAGGTTTAATATCCCTAATCTG-AAA-----CTTA-AA-TC 1909
                         i  iii    i  vi vi     vv   v i-   -----    -  -  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_85648282_8   1910 AATGAGAA-----TAAACAACCACATTTATAAATGGGCAAAGGACATAAA 1954
                            i v  -----i   i    vv   ? v              iv i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_85648282_8   1955 CAGACACTTTTCAAAGGAAGACATACAAGCAGCCAACAACCATTTGAACA 2004
                         i     i  i  v  i     i      iii     i  v  iv    v 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_85648282_8   2005 AATGCTTATCATTAATAAACAT 2026
                         i     i v   i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.00 (50 / 25)  


3179 19.29 12.58 1.95  chrX_85652112_85658925.rev      502  1320 (5494)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_85652112_8    502 GAAAGACATCCTGTGTTCATGATTTGGAAAAC--AATATTGTTAAGATGT 549
                               i    ii        iv      i  --               v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_85652112_8    550 CAGTGCTCACCACAGCAATTAACAGACTCAATGCAATTCGAATCAATATC 599
                           i i   v   v vii  iv     i    i     i vv     v   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_85652112_8    600 GCAATTGCCTTTTT-GCAGAACTAGGAAACCCAAACATATAATTCATATG 648
                         v  ii         -      v v iv  v ii v v  v          
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_85652112_8    649 GAATTGCAAGGGGCCCTGAATAGGCAAAACA-TCTTGGAAAAGAAAAACA 697
                            v        i   v      v       -     i       i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_85652112_8    698 GTGCTCAGGGACTCAAACTTCCCAATTTCAAAACTTACTACAAGACTGCA 747
                         iv i vii       v                           ii  i  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_85652112_8    748 TTAATCAAGGCAGTCTAGAACTTTTGTAAAGATAGACATGTAGATCAATG 797
                         v        i    v i v   vvii   i         i          
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_85652112_8    798 AAAGAGAAATGAAAATCCAATAATAGACCTATAAATATGTGGTTAATTGA 847
                         i  v    v   i i    iv    i   i   v  v i    i      
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_85652112_8    848 CTTTCAACAACATTGATAAGGACACTCAATGGGGAAAAAAAAACAGTTGC 897
                         i    i    viv  vi   iv  i            i  ---i   ivi
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA---TAGTCTT 399

  chrX_85652112_8    898 TTCAACAAGTGGTGCTAGGATAAC--------CACA-------------- 925
                                 i       i   i   --------    --------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_85652112_8    926 -------------------------------------------------- 925
                         --------------------------------------------------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_85652112_8    926 -----------------GCTAAAGCTATAAAACTTTTAGAAGAAATTATA 958
                         -----------------      i          i          vi   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_85652112_8    959 AGGGTACATCTTGGTGATTTTGGATGTGGCAATAGTTTCTTAGATATGGC 1008
                         i ?   v     v    ii    i vv      i              i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_85652112_8   1009 ACTGAGGGGACAAGCAACAAAAGGAAAAATAGATAAATTGGAATTCA-CA 1057
                           ii ii v              i                  v    -  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_85652112_8   1058 AAAATAAAACATTTTGTGCATCAGATGACA-TATCAAGAGAGTTAAAAAG 1106
                            v     vv        v   i v    -        i   -i     
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT-GAAAAG 698

  chrX_85652112_8   1107 ACAACGGACAGAACTCGAGAGAATATTTTAAAACTATGTATCTGATAA-- 1154
                              vv      ivv    i       vv   ii  i          --
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_85652112_8   1155 -ATCTATATCCAAAAACCGTGGAGAACCCTAATAACTTAA----AAAAAG 1199
                         - ii i      i  vvii ii     i  v i    i  ----      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_85652112_8   1200 ACAAAAAATTAAATAATTAAACCAATTAAGTAATAGACAAAGGATTTGAA 1249
                              ------------   v      ? iv   i i             
  L1M4_orf2#LINE/    799 ACAAA------------TAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_85652112_8   1250 TAGACATTTCTCCAAAGAACATGTACAAATGGCCAATAAGAACAAGAAAA 1299
                                            v  i                 v   v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_85652112_8   1300 -ATGCTCAACATCATTAGTCAT 1320
                         -             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (92 / 64)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 9.15 (119 / 13)  

2475 24.13 3.12 3.96  chrX_85652112_85658925.rev     5111  5943 (871)    L1M4_orf2#LINE/L1        5   830 (78)  

  chrX_85652112_8   5111 AAGCATATTCTACATTCATGGAT-GTAAGCAATTAATATAATTAAGATAT 5159
                            -    i i ii         - v   - v       vi       iv
  L1M4_orf2#LINE/      5 AAG-ATATCCCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGATGG 52

  chrX_85652112_8   5160 CAGTTCTACATAACTTGATGTATACATTCAACACAATCCCAATCAAAATC 5209
                           i v  v vi  v     v  i v       i       v         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_85652112_8   5210 CCAGAAAATTAGTTTGT-GAAATTGGTAAACTCATTCTAACGTTTATATG 5258
                             vvivi vv    i-       ii  i  v  i    vi  i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_85652112_8   5259 AAAATGCAAAAGATCTGGAATGGCCACCACAATACTGAAAGAAAAAAGCA 5308
                         i        ii  i ii    i    vv     vi     i i  i i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_85652112_8   5309 AAGTCAGAGGACTGATACCACCTTATTCCAAGACTTACTATAAATTTATA 5358
                             ii       v i  iv  iv   i   i        i   vi  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_85652112_8   5359 GTAATCAAGACAGTGTGGTAATAGTGGGTAACAGTGAAAGAATAAACAAA 5408
                                             v i -------  - --   i   i   v 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGG-------CA-T--AAGGATAGACATA 292

  chrX_85652112_8   5409 AACATCAATGAAACAGACTAGAGAGCCCAGAAATAGACCCACACAAATAT 5458
                         v v       i  i   v v     i         i     i   vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_85652112_8   5459 AGTCAACT-----TTGACAAAC-TGCAAAGGCAAGTCA-TGGAGAAATCA 5501
                         i     i ----- i     iv-   v   i v v   -   i    vv 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_85652112_8   5502 TAATCTTTTTAACAAATGAT---------ACTGGATATCCACATGCAAAA 5542
                           i      i        i ---------        ?            
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_85652112_8   5543 AGAAAAATGAATCTAGATACAGATCTTACACCATTTACAACAATTTAATT 5592
                         i----      vi i  iv vv i  i       v     v    -  i 
  L1M4_orf2#LINE/    443 G----AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AACT 487

  chrX_85652112_8   5593 AAGAATGGATTCTAGACCTGAATATAAAACACAAAATTATAAAACTCCTA 5642
                         v i       iv?      i   i   i vvi    i          i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_85652112_8   5643 GAAAATAACATAGGAAAAAATCT-AATATACCTTGGGTTTGATGAAGACT 5691
                            i v        ?iv      -vi i-          v iii v ii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTT 586

  chrX_85652112_8   5692 TTTTAGATATAACACCATAAGCACAATCGATAAAATAAAAAAAAATCATA 5741
                          i        i      v        v i i    v      v i--   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG--ATA 634

  chrX_85652112_8   5742 GTTTAGAACTTTAAAAATTTTGGAAATTTAGAACTTTTGCTCTGCCAAAA 5791
                         iv  i  -   i ------- vi     v i        iv  v ---  
  L1M4_orf2#LINE/    635 AATTGGA-CTTCA-------TCAAAATTAAAAACTTTTGTGCTTC---AA 673

  chrX_85652112_8   5792 AGGTTATTA-CAAGAA--TGGAAAGACAAGCCACAGGCCAGAAACGAAT- 5837
                            vi i  -      --  i        v      ivii i ivi   -
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_85652112_8   5838 CTTACAAAACACATATATGATATAGGGTTTAT-TCTAAAATATACAAAGA 5886
                         i  i    v  i    v     vi  ii  i -  i i      i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_85652112_8   5887 ATA--TATAACTCTCAACAATAAGAAAATAAACAATCAAATTAAAAATTT 5934
                          iv--  i     --  i     i  i i   i  i v    ?    v v
  L1M4_orf2#LINE/    774 ACTCTTACAACTC--AATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_85652112_8   5935 AGCCAAAGA 5943
                         i  v  i  
  L1M4_orf2#LINE/    822 GGCAAAGGA 830

Transitions / transversions = 1.63 (122 / 75)
Gap_init rate = 0.03 (25 / 826), avg. gap size = 2.36 (59 / 25)  

 330 20.65 2.17 0.00  chrX_85652112_85658925.rev     6233  6324 (490)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_85652112_8   6233 AAAAATAGCCAAAGAA-CTGAGTAGACACCTAATTAAAGAAGATACACAG 6281
                               i v     i -i   i      ii vvii          i   i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_85652112_8   6282 ATGACAAATAACCATATGAAAA-ATGCCCAACATCCTATGTTAT 6324
                            i v     v  i       -    i       v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.00 (2 / 2)  


2616 28.01 1.64 2.30  chrX_85677168_85679177.rev      606  1519 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85677168_8    606 TGGAAAAACATCTCGTGCTTGTAGCTAGAAAGAATCAACATCATTAAAAT 655
                               i i   i i  i ii i v v i    v i  i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85677168_8    656 GGCCATACTGCCCAAAGAAATTTACAGACTCAATGCTATTCCTATCAAAC 705
                            v     v      vvi  i      i    i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85677168_8    706 TACCAATGATACTATTCATAGAAGTAGAAAAAAAAAACT-ATTTTAGAAT 754
                          v   iiviivi v  iii    i v  v  i-----  -  ii  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAAT 145

  chrX_85677168_8    755 TCGTATGGAACAACAACAACAAAAAAAAGAGCCTAAATAGCCAAGGCAAT 804
                           i       vvi   ----------ii  v  vi         ii    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAA----------GGGACCCAGAATAGCCAAAACAAT 185

  chrX_85677168_8    805 CCTAAGCAAAAAGAACAAAGTTGTAGGTGTCATACTACTCAACTTCAGAC 854
                          i i iv  i             v   vv   i   v i   i    i v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_85677168_8    855 TATACTACAGGGCTACAATAACCAAAACAGCATGGTACTGGTACAAAAAA 904
                         iv       ii      i   i   i    ii         i i  ii -
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA- 284

  chrX_85677168_8    905 TAGACACACAAACCAATGGAATAGAATAAAGAGCCCAGAAATAATGACAT 954
                               i i i i              vi    i          vvv   
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_85677168_8    955 ACACCTTCAACCATTTGATCTTCAACAAAGCAGT-TTAAAAC-----AAT 998
                            ii viiii  v     i   i    i --  -ii  i  -----   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGG--GTGCCAAGACCATTCAAT 382

  chrX_85677168_8    999 GGGGAAAGAACTCCCTATTGAATGATTGGTGCTGCGATAACTGGCTAGCC 1048
                                   ivvi  v  v  ii v        v  i      v  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_85677168_8   1049 AAATGCAGAAGATCGAAATTGGACACCTTTCTCACACCATATACAGAAAT 1098
                          v     i    vi   i      v   vi               i    
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_85677168_8   1099 CAACTCCAAGGTCAGTTAAAGAATTAAATGTAAAACCAAAAACTATAAAA 1148
                         i     -  ii vii i ?   vi         i v v            
  L1M4_orf2#LINE/    483 TAACTC-AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_85677168_8   1149 ACCGAAGAGGACAACCTAGGCA-ATACCATTGTGGACATAGAAATAGGCA 1197
                         vi vv   i  v   v    ?i- v i v i   -  v v iiv      
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCA 580

  chrX_85677168_8   1198 AAGATTACATGACAAAGACACCAAAAGCGATTGCCACAAAAGCAAAACTT 1247
                          v i  v v iivv v            ivvv  v       v    v v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_85677168_8   1248 GACAAATGAAATGTAATTAAACTTAATATTTTCTACACAGTGAAAGAAAC 1297
                           i    vii iv v  i   v    v vi  i iii vvii  i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_85677168_8   1298 TACCAACAGAGTAAACAGGCATCCTATAGAATGAGAAAAAA-AT--ACAA 1344
                           i   v i   i  v  i  v  i i      i  i    -  --i   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_85677168_8   1345 ATTATACATCTGACAAAGTTTTAATATGTAGCATCTATAAGGAACTTAAA 1394
                           i   i      i  i vvi vi   vi  v  v     i     ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_85677168_8   1395 GAAATTTACAAGTAAAAAG-CAAGCAACCCCATTAAAAAGTGGGCAAAGG 1443
                         v  v iv i  -       -   ii     v   ?    i          
  L1M4_orf2#LINE/    781 CAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_85677168_8   1444 ACATGAGCAGACACTTC--AAAAGAAGACATACAT-CAGCCAAGAGGCAT 1490
                          iv   ii     i   --v        i     v-ii     v i   i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_85677168_8   1491 ATGAAAAAATGCTCAGTATCACTCATCAT 1519
                                i       ii    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (154 / 98)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.25 (36 / 16)  


 418 25.60 6.55 4.17  chrX_85693324_85700317      370   537 (6457)    L1M4_orf2#LINE/L1      339   510 (398)  

  chrX_85693324_8    370 TTATGTTGAATTCTAAGTTAAGAAGAGGATGTAGAAAGAATACACAATGG 419
                              v v    --i v  vv  vi   i  iv--    vi iv      
  L1M4_orf2#LINE/    339 TTATGGTCAATT--GATTTTCGACAAGGGTGCC--AAGACCATTCAATGG 384

  chrX_85693324_8    420 GGACAAGGTAGTCCCTCCAATACATGGTG---GGAAAACTTGGTATTCAC 466
                            v iii     ii i   i v      ---   v    v i  ?i   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_85693324_8    467 -TTCAGA-GAATGAAGTTGGACCTTT------CAGCAAACACAAAACTCA 508
                         - v  i -               ii ------  v  v i      v i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_85693324_8    509 ACTCACAATGAATTAAAGATAGCCTCAAT 537
                              v    i  i ?   ---   v   
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGA---CCTAAAT 510

Transitions / transversions = 1.16 (22 / 19)
Gap_init rate = 0.04 (7 / 172), avg. gap size = 2.57 (18 / 7)  

 474 23.81 0.00 0.00  chrX_85693324_85700317     2625  2729 (4265)    L1M4_orf2#LINE/L1        1   105 (803)  

  chrX_85693324_8   2625 TGAAAATATATACCATGCTCATGAATTAGAAGAATTAATGTAATCAAAAT 2674
                           i   v    v     i     i   i     v     i vi i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85693324_8   2675 GACAGTACTGCCCAAAGCAATCTACAGATTCCCTGCAATCTTTATCAAAA 2724
                          i  i    v      vii            vvi      ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85693324_8   2725 TATCA 2729
                          vi  
  L1M4_orf2#LINE/    101 TCCCA 105

Transitions / transversions = 1.78 (16 / 9)
Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.00 (0 / 0)  

 884 30.04 0.71 1.41  chrX_85693324_85700317     3718  4000 (2994)    L1M4_orf2#LINE/L1        1   281 (627)  

  chrX_85693324_8   3718 TGGAAAAACATCCCATACTCATGGATAGAAATAAATAATATTTTTAAAAT 3767
                               i i       ii        v i  v vv       v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85693324_8   3768 GGTCATACTTCCCAAAGCAATTGATAGATTCAGTGCTATTCCTATTAAAC 3817
                           iv     i      vii  iv i       ii  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85693324_8   3818 TATCAATGACATTCTTCACAAACCCAGAGAAAACTATTTTAAAATTCATA 3867
                          vi  iivi v  i  ii  i vviv  v  iviv  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_85693324_8   3868 TGGAGCCAAAATGAGCCCA-AATAGCCAAAGCAATTTTAAGTAAAAGGAA 3916
                             iviiv  v ii    -          i    i  i iv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_85693324_8   3917 CAAAGCTCGGGGGA-TCATGCTACCTGAGTTTAAACTGTATTACAGGGCT 3965
                              i -  i   -   ii  v  ii v  i   viv  i    ii   
  L1M4_orf2#LINE/    201 CAAAGTT-GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_85693324_8   3966 ACATTAACCAAAACAGCATGCTAGGCTGGGCACAA 4000
                            v   i   i    ii  v  --    -  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTA--CTGG-CATAA 281

Transitions / transversions = 1.93 (56 / 29)
Gap_init rate = 0.02 (5 / 281), avg. gap size = 1.20 (6 / 5)  

1929 26.29 1.48 1.62  chrX_85693324_85700317     4282  4958 (2036)    L1M4_orf2#LINE/L1      233   908 (0)  

  chrX_85693324_8   4282 AAACTAACAAACAAA---ACA--AAACAAAACCAGCATGCTTCTGGTATA 4326
                              v  v -    ---   --  v   i  -  ii  v v    i   
  L1M4_orf2#LINE/    233 AAACTTACTA-CAAAGCTACAGTAATCAAGAC-AGTGTGGTACTGGCATA 280

  chrX_85693324_8   4327 AAAACAGACACATAGACCAATGAAACTGAATAGAGAGCCCAGAAATAAGG 4376
                          ii i     i     i     i  iv    v     i          iv
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_85693324_8   4377 CCACACGACTACAACTACCTGATCTTTGACAACACTGACAAAAACAAGCA 4426
                            i  ivi  iiiii vi    i  i     viv  v   i v  vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_85693324_8   4427 ATGGGGAAAGAACTGCCTATTCAATAAATGATGCTGGGATAACTGGCAAG 4476
                                     iv i  v     i     i        i      vv ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_85693324_8   4477 CTGTATGCAGAAGATTGACACTGTACCCCATTCTTACATCATCCACAAAA 4526
                          iii     i    v   vii  v     vvi  i   i   vi      
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_85693324_8   4527 ATTAACTCAATATGGATTAAAGTTTTAAATGTAACACCCCAAACTATAAA 4576
                                   v      i ?  vii         v v iv          
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_85693324_8   4577 AACCCTAGAATACAACCTA--CGCAATACCATTCTGGACAAAGGAATGGG 4624
                          vi i     v v   v  --? i  - i -   vv   vvv  iv i  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGG 578

  chrX_85693324_8   4625 CAAAGATTTCATGACAAAGACACCAAAAGCAATTGCAACAAAAACAAAAA 4674
                            v i    v iivv v             vvv         iv     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_85693324_8   4675 TTGACAAATGAGATTTAATTAAA-CTAAGAGCTTCTGTACAGCAAAAGAG 4723
                          v  i    vi  i  v  i   -i   i i   i   i vv    i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_85693324_8   4724 AGTATCAACAGAGTAAACACATAACCTACAGAATGGGAGAAAATTTTTTC 4773
                          v      v i   i  v v i    i                 v   v 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_85693324_8   4774 AAAGTATACCTGTGACAAAGTTCAAATATCCAGCATCTATAATAAACTTA 4823
                            vi   iv v   i  i vv vvi       v  v     vi    iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_85693324_8   4824 AACAAATTTACAAAAAAAAAAAAAAAACTGAGTAACCCCATTAAAAAGTG 4873
                         v    v iv i  v     i v   -------      v   ?    i  
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAA-------TAACCCAATTWAAAAATG 821

  chrX_85693324_8   4874 GGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACACACA--TGCAAA 4921
                                  iv    i     i  i  v        i i   --  vvv 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_85693324_8   4922 AGAAGCATATGAAAAAAAGCTCAACATCACTGATTAT 4958
                          v     i       i v           ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.02 (88 / 86)
Gap_init rate = 0.01 (10 / 676), avg. gap size = 2.10 (21 / 10)  

2401 28.33 1.31 0.52  chrX_85693324_85700317     5736  6501 (493)    L1M4_orf2#LINE/L1      137   908 (0)  

  chrX_85693324_8   5736 TCCTAAAATTCACGTGGAACCAAAAAGGAGCCTGAATAGCCAAGGCAATC 5785
                                     ii     viiv  i   v  v          ii     
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_85693324_8   5786 CTAAGCAAAAAGAACAAGGGCAGAGGTATCACAAT-ACTGATCCCAAATT 5834
                         i i iv  i        i vii    vv     v -v ii  ii    vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_85693324_8   5835 ATACATCAGAGGTACACTAACGAAAACAATAAGAAACTGGTGTTAAAACA 5884
                         v   vv  i  v    v   iv  i   i iv iv     ii v ii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_85693324_8   5885 GACACAGAGATCAGTGGAACAGAATAGAGATCCCAGAAATAAAGCCATGT 5934
                             i v      i     i     v    vi           v    ii
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_85693324_8   5935 ACATACAGCCAACTGATGTTTAACAAAGTTGACAAAAACATACACTGGGG 5984
                          iv  ii i   i    v  ii    i v  v   i v   v  v     
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_85693324_8   5985 AACGGACAGCCACCCTCTTCAA----TGGTGCTGGGAACATTGGATTACC 6030
                           v i i  i ---- i     ----           vv i     v?  
  L1M4_orf2#LINE/    387 AAAGAATAGTC----TTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_85693324_8   6031 ATATGCCGAAGAATGAAACTGGATCCCTGTCTCTCACCATATGAAAAAAC 6080
                          i    vi         ii    i    ii   v        iv     i
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_85693324_8   6081 TAGCTCCAGATGGATTAACGAGTTAAATGTAACACCTGAAATTATAAAAA 6130
                           i   v i      i ?v  vi         v v  i   i       v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_85693324_8   6131 TATCCGAAGAAAACCCAGGAGAAACTCATCTGGACATTTGTCTAAGCAAT 6180
                          v iv         vi   ? v  v  v  vv   v  v vi  i     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_85693324_8   6181 TAATTCATGACTAAGTCCTCAAAAGCACAAACAACAAAAACAGAAATAGA 6230
                         viv   v iiv  v v vi           i        iv i       
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_85693324_8   6231 CAAATGGGAATT-----AAACTGAAAAATTTGGCACAGAAAAAGAAATAA 6275
                         i    v   v  -----   i i    v   v ii vvv   i  v iv 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_85693324_8   6276 TCTACAGAGTGAACAGACCACTGGCAGAGTGGGAGAAAATATTTGCAAAC 6325
                           v v i      v    v  ivi    i                    i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_85693324_8   6326 TCTGCATCCAACAGGGGATTGATAGTCATAATTTATAAGAAACTTAAACA 6375
                         iv ii   ii i i    i vi  vi  v   v     ii    ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_85693324_8   6376 ACTCAACAACAAATAAAAAAAAGACCCCATTAACAAGCAGGTAAAGGACA 6425
                               i  i   v i v   vi    v   ? v  iii  i      iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_85693324_8   6426 TGAATAGACACTTTTGAAAAGAAGACATACAAATGGCAAACAAGCATGTG 6475
                                   i  i vv        i           v  i     ii  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_85693324_8   6476 AAAAAATGCTTAATGTCACTATTCAT 6501
                             i     i  ii   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (120 / 93)
Gap_init rate = 0.01 (4 / 772), avg. gap size = 3.50 (14 / 4)  


2976 26.59 1.89 0.89  chrX_85701882_85706960     3701  4599 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85701882_8   3701 TGGAAAAACATTCCTTGCCCATGGATAGGAAGAATCAAC-TAATTAAAAT 3749
                               i i  i  v  ii       v      v i  i- vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85701882_8   3750 GGCTAGACTGCCCAAAGCAATGTACAAATTTAACACTATTCCTATCAAAC 3799
                            v v   v      vii  v    i   i   i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85701882_8   3800 TACCAACAACATTCTTCACAGAACTAGAAAAA--AAT----AAATTTATA 3843
                          v   i vi v  i  ii     v v  v  i--i  ----     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_85701882_8   3844 TGGAACCAAAAAAGAGCTGGAATAGCCAAGGAAATTCTAAGCAAAAAGAA 3893
                              viiv  ii  v ii          iiv   ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_85701882_8   3894 CAAAGCTGGAGAAATCACATTACCTGACTTCAAACTATACTACAAGGCTA 3943
                              i     i v     i v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_85701882_8   3944 CAATGACCAAAACAGTGTGGCACTGGTACAAAAACAGGTGCATAGACCAA 3993
                           i i i   i         i     i i  ii i  iiii     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_85701882_8   3994 TGGAACAAAATAGAGAGTGCAGAAATAA--CAGTGAATATCTATGACCAT 4041
                              i i   v      v         -- vi -- i  i    ii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCAT--ACATTTATGGTCAA 348

  chrX_85701882_8   4042 CTGATCTTTGACATAGCTGACAAAAACAAGCAATGGGGAAAAGACTCCCT 4091
                         i    i  i    vi v  v   i v  vv           ii ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_85701882_8   4092 ATTTCATAAATGGTGCTGGGATAACTGGGCTAGTCATATGGAGCAGATTG 4141
                         v  iv i              i      i-  ?i  i   v iv   v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGA-TAKCCACATGCAAAAGAATG 447

  chrX_85701882_8   4142 AAGCTGGACCCCTTCCTTAAAGCATATACAAAAATTAACTCAATATGGAT 4191
                            i         v   i v v                     v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_85701882_8   4192 TAATGACTTAAATGTATAACCAAAAACTATAAAAACCCTGGAAGACAACC 4241
                         i ?v   i        vi v v            vi i i     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_85701882_8   4242 TAGGCA-ATACCATCCTGGACCTAGGAATGGGCAAAGATTTCATGAGA-A 4289
                             ?i- v i v  v  -    v  iv i     v i    - v   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTC-TTAGATA 595

  chrX_85701882_8   4290 GGACACCAAAAGCA--AGCAGAACAAAAGCAAACATTAACAAATGAGATC 4337
                         v             --    --       v   v  vi i    vi  ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCA--ACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_85701882_8   4338 TAATTAAACTTCAAAGCTTCTGCACAGCAAAAGAACCTATCAACAGAGTA 4387
                          v  i   v  v   i   i  ii vv    i  vv       v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_85701882_8   4388 AACAGACAACTTACAGAATAGGAGAAAATATTTGCAAACTATGCATCTGA 4437
                           v       ii       i                  ii  ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_85701882_8   4438 CAAAATTCTAATATCCAGCATCTATAAGGGACTTAAACAAATTTACAAGA 4487
                         i  iivv  vi       v  v     i i   ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_85701882_8   4488 TAAAAACAA----CCCCTCTAAAAAGTGGGCAAAGGACATGAACAGACAC 4533
                         v   i    ----   vvi ?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_85701882_8   4534 TTTTCAAAAGAAGACCTACATGCAGCGAACAAGCATATGAAAAAACAACT 4583
                           i  v        iv    viii  v  i     i       i ii-  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG-CT 892

  chrX_85701882_8   4584 CTATATCACTGATCAT 4599
                          v i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.79 (25 / 14)  


2531 24.47 4.85 2.84  chrX_85762680_85766317     2292  3137 (501)    L1M4_orf2#LINE/L1        1   863 (45)  

  chrX_85762680_8   2292 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATATTGTCAAAAT 2341
                               i i  i     i               v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85762680_8   2342 GGCCATACCGCCCAAAGCCATCTACAGACTTATTACAATTTCTATCAAAC 2391
                            v    iv      viv         i i vii    ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85762680_8   2392 TACCAA-TGCCATTATTAACAAAAA------AACT-ATCATAAAATTCAT 2433
                          v   i-    v  v  i-  i   ------ i  -   v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_85762680_8   2434 ATGGAA--GAAAAAAATTGGCCTGAATAGCCAAAGCATTCCTAAACAAAA 2481
                               -- v  iii i---  v           i  v  i i  v  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_85762680_8   2482 TGAACAAAGCTGGAGAGCCATCACATTGCTGGATTTCTAATTATGCTACA 2531
                         v        i     ii --     i v ivi     v  viv i     
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGAC--TCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_85762680_8   2532 AGGATATAGTAACCAAAACCAAAACAGCATGGTACTTATATGAATATAGA 2581
                          i v  i     i   i  ------  ii       vii  i iv     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGAC------AGTGTGGTACTGGCATAAGGATAGA 288

  chrX_85762680_8   2582 CATATAGACCAATGAAACAGAATAGAGAACCCAGAAATAAAGCTA----- 2626
                                 i     i  i     v    ii           v i -----
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_85762680_8   2627 -------------ATTTTTGACAAAGCATCCAAAAGCAT-AAATTGGGGG 2662
                         -------------     i     i vvv    i v   -v   --    
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT--GGGG 386

  chrX_85762680_8   2663 AAAGGGAACCCTATTCAACAAATGGTGCTTGGAAAATTGGATAACCATGT 2712
                             iiv vi  v                v   v  i      ?   ii 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_85762680_8   2713 GTAGAAGAATGAAACTAGATCCTTGTCTTTCACCATATACAAAAATAAAC 2762
                          i i         ii i  i  i ii  iv                v   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_85762680_8   2763 TTGAGATGGATTAAAGACTTAAATCTAAGACCTCGATTAATAAAAATTCT 2812
                          ii i      i ?    i     v     v  vi viv      v ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_85762680_8   2813 AGAAGAAAACATAGAA--AAATCTCTTATAAACATTGACCTAAACAAAGA 2860
                                       i?--      - ii i v -   ivi  ii   v -
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCT-TCGTGACC-TTGGGTTAGGCAATG- 583

  chrX_85762680_8   2861 GCTTGT--GAT-TAAGACCGAAAAAGCAAATGTAATAAAA--ATAAATAA 2905
                          i  v --   - i v   --       v v i  i    -- v     i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_85762680_8   2906 ATAAATGGGGCCTAATTAAACCAAAAAAAACCTTCTGCACAGCAAAAGTA 2955
                               v  i i v  i   viv     ---   i  ii vv    i vv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAA---CTTTTGTGCTTCAAAGGAC 678

  chrX_85762680_8   2956 ATAATCTTCAGAGTAAACAGCCAACTCACAGAATGGCAGAAAATGTTTGC 3005
                          iv   vvv i   i  v  v    i          v       i     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_85762680_8   3006 AAACTCTGCATCTAACAAAGGACTAATATCCAGATTCTACAAAGAACTCA 3055
                            iiv ii    i i  i     vi        v v  i         v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_85762680_8   3056 AACAAATCAGCAAGGCAAAAACAA-TA--CCA--TCAAAAATGTGGGCAA 3100
                         v    v   ii  viv   i    -  --   -- ?       --     
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG--GGCAA 826

  chrX_85762680_8   3101 GTGACATTAGTAGACACTTATCAAAAGAAGATATACA 3137
                         iv  iv v i      i  v  v              
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.51 (122 / 81)
Gap_init rate = 0.03 (24 / 863), avg. gap size = 2.71 (65 / 24)  


2853 25.11 3.48 1.68  chrX_85767191_85771448     2876  3767 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85767191_8   2876 TGGAGAGATATCTTACGTTCATGGATAGGAAGACTCAATATGATTAGAAC 2925
                             i       ii i          v        i     vi   ii i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85767191_8   2926 AGCAATTCTTCCCAC-TTGATCTATAGATTCAATATATTCCCCATCAAAA 2974
                         i     v  i    v-        i        iii v    i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85767191_8   2975 TCCAAGGAAGTTGTTTTGTGGATACTCACATAGTGATTCCAACATTTATA 3024
                            v  vvivi v     ii  v i v   viv    i i  v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_85767191_8   3025 TGGAAA-GTAAAAGACCCACAATAGCCAGCAAAGTATTGAACAAGAA--- 3070
                               - i  ii      v        iv v i v     v     ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_85767191_8   3071 -AAAATGTAGTGGACTGACACTACCATACTTCATTATTTACTGTAAAGTT 3119
                         -   i - i v     v     v  vv i    vv i     ii    i 
  L1M4_orf2#LINE/    201 CAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_85767191_8   3120 ATAGTAATCATGGTAGTGTGATTTTGGCAAAAGAACTGACAAGTAGATTA 3169
                          i        v ii      i vi     v   i iv    vi     i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_85767191_8   3170 GTATTAATAGAACAGAATAGAGAGCCTAGAAATAGATCCACACAAATGTA 3219
                         ------  i   i     v     i i       i i   i   vv i i
  L1M4_orf2#LINE/    300 ------ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_85767191_8   3220 GTCAATTGGTATTTGATGGAAGAGCAAAGACAATTCAATAG--AAAGATC 3267
                                 i v  i  iiiii v  v     v       i --     --
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-- 391

  chrX_85767191_8   3268 ATAGCATTTTTCTACAAATTACAGTGGAACAATTGGGATATC-ACATGCA 3316
                             i-i     v      viiiv   i    i   -   ? -       
  L1M4_orf2#LINE/    392 ATAGT-CTTTTCAACAAATGGTGCTGGGACAACTGG-ATAKCCACATGCA 439

  chrX_85767191_8   3317 AA-GAATGAACCTAGACACAGACCATCTGCCCTTCACAAAAATTAACTCA 3365
                           -       vi i   v vv   vivii  v vi               
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_85767191_8   3366 AAA-GGATCATAGTCCTAAATGTAAATTGC-AAAACTCTGAATCTATTAG 3413
                            -      ?  v           iv-  -      v i  v  v    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAG 538

  chrX_85767191_8   3414 AAGATAACATCAGAGAAAAGCTAGGTGATCTTGGGTTTGACAATGTGGTT 3463
                             v     vi ? v   v  vv    i        v i     vvv i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_85767191_8   3464 TTAGATACAATATCAAAAGCATAAACCTTAAAATAAAC--TA-ATAAGTT 3510
                                ii i i        i  i vvi    v   v--  -    i  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_85767191_8   3511 GGATTTCATTAAACTTAAAAACCGTTCATG-----ACACACACTGTTAAG 3555
                            i     i   v        i-  ii  ----- viv     i i   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_85767191_8   3556 AGAATGAAAAAACAAACAACAGAGTAGGAAAAAGTCTTTGCACAACTCAT 3605
                          i i      i    v v     i i   i   i v      -  -    
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AA-TCAT 735

  chrX_85767191_8   3606 ATAT--GATAAAGGACCAATA-----GATATACAAAGAACTTTTA-ATCT 3647
                             --     i    ivi  -----i     i        i   - v  
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_85767191_8   3648 CAACAATAAGAA-ATAAGCAACCAAATTAAAAAGTGGACAAAAGTCGTAA 3696
                            i     i  - i  ii    v    ?    i   i    i viv i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_85767191_8   3697 ACAGACATCTCATTAATTAAGGCATA--GTTGGATAATAAGCATATGAAA 3744
                          i      i  vii  vv   ii   --iv   vi        i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_85767191_8   3745 ACATGTTGAATATAATATGTCAC 3767
                          v   i v  i  v ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (132 / 88)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 1.84 (46 / 25)  


2935 26.33 3.29 0.23  chrX_85778897_85781127.rev      860  1740 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85778897_8    860 TGGAAAAATATCCCTTGCTCTTGGATTAGAAAAAACTAACATTATTAAAA 909
                               i       v  i  v      i   i v-i   i   i    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chrX_85778897_8    910 TGACCATACTGTGCAAAGCAATCTACAGATTTAACGCAATCCATAAAAAA 959
                           i v     viv    vii           i          v  vv   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_85778897_8    960 ATTC-A------TTTTTCACAGAAATAGAAAATACT-ATCCTCAAAATCA 1001
                           i - ------     ii       v  v  -i  -     v   v   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_85778897_8   1002 TATGGAACTAAAAAAGAGCACAAATAACCAAATAAATACTAAGCAAAAAG 1051
                                v iv  ii  v vvi    i     vv   vi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_85778897_8   1052 AATAAGGCTGGAGGCATCTCATTACCTGACTTCAAATTATACTGTAAGGC 1101
                           i  i i      vv  v  i v  ii i      viv    ii  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_85778897_8   1102 TACAGTAACCAAAGCAGCATGGTACTGATATAAAAATAGACACATAGATC 1151
                                 i   ii   ii        ii    ii       i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_85778897_8   1152 AAGGGAACAAAACAGGGAACACAGAAATAAAGCCATGCACTCAGAGCCAG 1201
                           v    i i  iv i  iiv          v    i  i i vi i  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_85778897_8   1202 CTCTTTTGTGACAAAATCAACAGGAACATATACTGGGGAAATGACACCCT 1251
                         i vv   vi     iiviiv  i  v   vi v        vi i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_85778897_8   1252 TTTCAACAAATGGTGCTGGGAAACTTTGATTGCCATACACAGAAGAATGA 1301
                                              v vi v   v?   i ii  i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_85778897_8   1302 AATTGGACCCTTATCTTTCAGCATATTCAAAAATCAACTCAACATGGATT 1351
                          i        i  i  iv  v     v       i       v      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_85778897_8   1352 AAACCCTTAAATGCAAGACATGAAATTATAAAAATACTATAAAAATACCT 1401
                          ? vv i      i    vv i   i       v vi  v  i  v  v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_85778897_8   1402 AAGGAAAATTCTCCTGGACATTGGTCTAGGCAAAGTATTTATGAATAAGA 1451
                          i ?iv  v   i vv   v    vi       v vv  iv ii   v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_85778897_8   1452 TGTAAAAAGCACAGGCAGCAAAAACAAAAATAGACAAATGGGACTTAATT 1501
                         iiiv         i   i     iv         i    v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_85778897_8   1502 AAACTAAAAATCTTTTGCACAGCAAAAGAAATAATCAAGA--TTGAACAG 1549
                            v v    v      ii vv    i  v iv       --v    v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_85778897_8   1550 GCAACCTATAGAATGGGAGATAATATTTGCAAATAATGCATGTGACAGGG 1599
                         i     i i           v             v  ii  v   i i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_85778897_8   1600 GATTAGTAATCAGAATTTAGAAGGAACTCAAACAACTCAAAAAGAAAACT 1649
                           i v   vi      v  v  i      vv         v  v    vv
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_85778897_8   1650 CAAAATAATCCCAGTACAAAGTGGGCAAAGGACATGGATAAACAT----- 1694
                         vv      i  v v ?v   i           iv  i   i    -----
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_85778897_8   1695 ------------ACAAATGGCTAACAGGCACATGAAAA--TGCTCAACAT 1730
                         ------------         i  i i           --          
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_85778897_8   1731 CACTAATTAT 1740
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.19 (124 / 104)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.88 (31 / 8)  


2686 20.81 11.77 3.92  chrX_85807154_85812041.rev     3559  4399 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_85807154_8   3559 GGAAA-ATATCTTGTTTTCATGGTTCAAAATACTTAATACTGCTTAATAC 3607
                              -     iii v       v iii  v        i  -    ---
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTG-TTAA--- 47

  chrX_85807154_8   3608 TGCTGATATGGCAATACTCGGCAAATGTATCTACAGTTTCAATAGAATCC 3657
                         ----   --          vv     vv        v     iiv     
  L1M4_orf2#LINE/     48 ----GAT--GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

  chrX_85807154_8   3658 TTGTTGTAATTCCAGTTGATATCTTATCAGAAA--------CTGATCTAA 3699
                         i i iiv   i    i  viv i  vv      --------      iv 
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_85807154_8   3700 AAATTCTCATAGAAACACAAAGGATC--AAATAGACCCAAAGCAATTCTG 3747
                               vi  i    ii   i   i --i     --     i    ii  
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAG--CCAAAACAATCTTG 189

  chrX_85807154_8   3748 AATAA----AATAA---TAAAAGACTCATATGTCTTTATTTTAAAACTTA 3790
                           v  ----  i  --- ii i      i iv  iiv    i        
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_85807154_8   3791 TTATAAAGCTATAGTAATCAAGATAGTATGATATTGGCAAAAGAATAGAC 3840
                         i  i       i           i   i  i  i     v   i      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_85807154_8   3841 ACGCAGAT-AATTAAACATAATTGAGTGTCCAGAAATCAGTGCTTAATTT 3889
                          iii    -   vi  i v       v          v iiv v  vv  
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_85807154_8   3890 TACAGAGAAGTGATTTTTGATGAGGGTGCCTACTTAATTCAATGAGGAAA 3939
                           ii vv  v       i  ii        v vviv        i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_85807154_8   3940 ------TGTTTAAAACAAACAGTGCTAGGATGATTGAATGTTCAAATGCA 3983
                         ------ v   vv      ii     i   ii i  i  i?i  v     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_85807154_8   3984 AAATAATGAAGTTGGTCCCCTATCTAACAC-A---ACAAAAATTAACTCA 4029
                            v           v      i  v    - ---               
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_85807154_8   4030 AAGGGGAGTACAGATCTAAGTGTAAG----------------------GA 4057
                           iv   vi ?   i    i      ----------------------  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_85807154_8   4058 CGAA----------------------------------GCA-----TTCT 4068
                         v   ----------------------------------   -----    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_85807154_8   4069 TAGATACAACACCAAAAGCACATGTGTCAAAA-----AATAGATAAATTG 4113
                               ii              v iiv     -----             
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_85807154_8   4114 ATCTTTATGAAAATGAATAACCT--GTCCATCAAAGGATACTACGAAAAC 4161
                         iv   i  v     v  v   i --  v v        i    iv  i v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_85807154_8   4162 AGTAAAAAGATAACCCACAAAATGGGATAAAATATTTAGAAGTCACATGC 4211
                            i      i        i       v         iv  i   i  ii
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_85807154_8   4212 CTGATAAAGATATTGTATCCATAATATAAAAAGAACTCCTACAACTTAAA 4261
                                i ivv         v      v         i       i  -
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA- 788

  chrX_85807154_8   4262 AACAAATGATAAATTAAATAAAATAAATAATTAAAATGCCTAAT--AAAA 4309
                         ------ i     ------  i i      --------  i   --    
  L1M4_orf2#LINE/    789 ------TAATAAA------AAGACAAATAA--------CCCAATTWAAAA 818

  chrX_85807154_8   4310 ATTGACAAAGGACTTAAATAGATATTTGTCCAAAGAAGATGTATAAATAG 4359
                           v i       i  i      i    v            i  i    i 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_85807154_8   4360 CCAATAAACACAGGAAAAGATGCTCAAAATGATTATTCAT 4399
                                i    v              v  v ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (107 / 66)
Gap_init rate = 0.02 (22 / 907), avg. gap size = 6.00 (132 / 22)  

 285 26.32 5.26 0.88  chrX_85807154_85812041.rev     4767  4880 (8)    L1M4_orf2#LINE/L1      753   871 (37)  

  chrX_85807154_8   4767 TGTATCCATGCA---ATGAAATAATATTCTACCTTAAAAAATAAAAG-CA 4812
                                 - v ---  i  iv v v  vi v  i  v  vv     -  
  L1M4_orf2#LINE/    753 TGTATCCA-GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_85807154_8   4813 AACAACTTCATTAAAAAGTGGACGAAGGACATGAACAGAC--TTTTCAAA 4860
                           i   iiv   ?    i   i i     iv    i    --  i  v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_85807154_8   4861 AGAAGGCATACATATAGCCA 4880
                              ii     v  i    
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.03 (4 / 119), avg. gap size = 1.75 (7 / 4)  


1744 25.94 1.67 1.05  chrX_85815817_85818784.rev     1256  1733 (1235)    L1M4_orf2#LINE/L1        1   481 (427)  

  chrX_85815817_8   1256 TGAAAAGACATC--ATGTTCTCATGGATCAGAAGAATTAATATT---AAA 1300
                           i     i   --      --      ii     v        ---  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTC--ATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_85815817_8   1301 ATTACCATAATGCCCAAAGCAATCTACAGATTCAATGCAATCTCTATTGA 1350
                           vi v   v v      vii              i      i    ii 
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_85815817_8   1351 AATACCAATATCACTTTTCATGGAAGTAGAATAGC-AATTCTAAAATTCG 1399
                            v   iivv vi    iiii   i v  vv   -i  i         i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_85815817_8   1400 TATGGAATCAAAAAGAGCCCA-AATAGCCAAAGGATTCCTGAGCAAAAAG 1448
                                viiv  i ii    -          iv v  i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_85815817_8   1449 AATGAACATGGAGGCAC-CACACTATCTGACTTCAAAATATATTACAAGG 1497
                           ii  vv      -  -      vi ii i       iv  i     i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_85815817_8   1498 CTATAGTAGCCAAAACAGCATGGTATTTGGTATAAAAATTAGACACAAAG 1547
                            i    ii   i    ii     i -  i    ii  -     i v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACT-GGCATAAGGAT-AGACATATAG 295

  chrX_85815817_8   1548 ACCACTGGAACAGAATAGAGAATCCAAAAATAAATCCACCCATTTATAGC 1597
                          i  v     i     v    i    i       i   iv       i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_85815817_8   1598 CAACTGATTTTTCACAAAGGCACCAAGAATATACATTGGGGTAAGGACAT 1647
                            i       iv    i  ii      vi  v  v     v   i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_85815817_8   1648 CCTCTTCAATAAATGGTGCTGGGAAAATAGGATATCCTTATGAAGGAGAA 1697
                         i  i     i              v  iv     ?  vi   v ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_85815817_8   1698 AGGAACCAGGCCCAAATCTCTCACCATATAAAAAAA 1733
                         v i iiii i   vv i   v         v     
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

Transitions / transversions = 2.00 (82 / 41)
Gap_init rate = 0.02 (9 / 481), avg. gap size = 1.44 (13 / 9)  

1367 26.03 0.68 2.05  chrX_85815817_85818784.rev     2040  2477 (491)    L1M4_orf2#LINE/L1      477   908 (0)  

  chrX_85815817_8   2040 AAAAATTAGGTCAAGACGGATTAAAGCCTTTAATGTAAGACCTGAAACTA 2089
                                 iv    i i    i ?  v i v         v  i      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_85815817_8   2090 TAAAACTACTAGAAGAAAACATAGGGG-AAATGTTTCAGGTATGCTTTGA 2138
                                vi                ? -    -i   --  i-i i   i
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTC--GTG-ACCTTGG 572

  chrX_85815817_8   2139 TTTAGGCAACGATTTTATGGCTAAAACCTCTAAAGCACACATGATAAAAA 2188
                         v        i i   iv i v  vi  vi v        viii i    i
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_85815817_8   2189 ACAAAACTAGACAAATAGGACTCTACTAAACTAAAAGGCTTTTTGCACAG 2238
                          v    -    i    v     ii ii   v v   ii     - ii vv
  L1M4_orf2#LINE/    623 AAAAAA-TAGATAAATTGGACTTCATCAAAATTAAAAACTTTT-GTGCTT 670

  chrX_85815817_8   2239 CAAAGGAAACAATAAACAAAGTAAAGAGACAGCCTGTTGAATGGGAGAAA 2288
                                v  v  v  v     i  i     i  iiiv            
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_85815817_8   2289 ACACCTGCAAACTATTCATCCAGCAAGAGATTAATATCCAGAATATACAA 2338
                          i ii      ii  vi   iiii   i  i vi             i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_85815817_8   2339 GGAACTCAAATAAGTCCACAGTAAATAATAATAAATA--TCATGTTAAAA 2386
                         i      vv i  v  v i i    -  -i i     --i  vv ?    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAA-AA-GACAAATAACCCAATTWAAAA 818

  chrX_85815817_8   2387 GTGGGCAAAGTGCATGAGTAGACACTTCTCAAAGGAAGACGTAAAAATAG 2436
                         i         viiv   i      i     v  i     ii  v    i 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_85815817_8   2437 CCCACAGATATATGAAAAAAATGTTCAACATCACAAAGTAG 2477
                           v i iii i       i -  i         ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (75 / 36)
Gap_init rate = 0.02 (10 / 432), avg. gap size = 1.20 (12 / 10)  


2246 25.24 3.11 5.59  chrX_85825629_85827629.rev      580  1510 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85825629_8    580 TAGAAAAATATTCCATGCTCATGGATTGGAAGTATCAATATAGTTAAAAT 629
                          i    i    i     i              vv i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85825629_8    630 GACTACACTGCTCAAAGCAATTTACGGATTCAACACTGTGG-TATAAAAA 678
                          i v i   v i    vii  i   i        i vi vv-   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85825629_8    679 ---AAAATGCCATTTTTAACAGAA--TAAGAGA--AATGC----ATTCAT 717
                         ---v iv    v     i-     -- i v ii--i  v ----      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_85825629_8    718 TTGGAACCAAAAAAAGCCCA-AATAGACAAAGCATTCCTAAGCAAAAAAA 766
                         v     viiv  iiii    -     v    i  v  i i ---------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--------- 190

  chrX_85825629_8    767 AAAAAAAAAAAAAAAAAACCAAAAAACAACAACAAAAAAAACCAGAGGCA 816
                         --------    i  i   ------------------   iiii    vv
  L1M4_orf2#LINE/    191 --------AAAAGAAGAAC------------------AAAGTTGGAGGAC 214

  chrX_85825629_8    817 TCACATTACCTGACTTTAAACTATACTCTAAGGCTACACTAAGCAAAACA 866
                              i v  ii i  i   viv    vi  i      v   v   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_85825629_8    867 CCATGGTATTGGCACAAA-ATATACATATAGACCAATGGAACAGAATAGA 915
                         vii     i     i  i-   v         i        i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_85825629_8    916 TAACCCAGAAATAATGCTTCACGTCTCCAAACATCTGATCTTCAACAAAA 965
                         v ii          vv ivi  i i viiiv  vi    i   i    ii
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_85825629_8    966 TTGACAAAAGCAAGCAATAGGAAAA--ATACTCCCTATTCAATAAATGGT 1013
                         v  v   i v  vv    i  i   --   v  -- v     i       
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTC--TTTTCAACAAATGGT 412

  chrX_85825629_8   1014 GCTGGGGTAACTGGCTAGCCATATGTGGAAGAATGAAATTGGACCCCTAC 1063
                               ii      v  ?   i   iii         i            
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_85825629_8   1064 TTTTCACCATATATAAAAGTTAACACAATATGGATTAAAAATGTAAGTGT 1113
                         i iv         i    i     v   v      i ? i iv   i   
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_85825629_8   1114 TAAATCCTCAAAATATGAAAATCCTACAAGAAAACCCAGGAAATACTCTT 1163
                         v i v - v   v   i   v  i  v        vi   ?ivv v    
  L1M4_orf2#LINE/    513 AAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_85825629_8   1164 CCTAAACTAGGCTTCATTTGGCAAAAAATTTATGGCTAAGTTCCCCCAAA 1213
                          v i v  v  ----i  v     viiv  iv i v  v v- v  v   
  L1M4_orf2#LINE/    562 CGTGACCTTGG----GTTAGGCAATGGTTTCTTAGATATGA-CACCAAAA 606

  chrX_85825629_8   1214 GCAATTGCAACATAAACAAAAATTGACAAGTGGCACCTAATTAAA-TTAA 1262
                            vvv      v  iv      v  i  i v v  i v  i   -    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_85825629_8   1263 AGAACTTATGCCCAGCAAAATAAATTACCAATGGAGTAAACAGACAACCT 1312
                          -     v  iv vv    iv v i  i   vii   i  v        i
  L1M4_orf2#LINE/    657 A-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_85825629_8   1313 ACAGAAGGGGA-AAAATATTCACAAACCATGCATCTGACAAAGG------ 1355
                               v    -        ii    i   ii      i  i  ------
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_85825629_8   1356 -TCCACAAT-TACAAGGAACTTAAACAAATCAACAAGCCAAAAACAAACA 1403
                         -    v   -  i  i     ivv    v    i  --i     --i   
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAA--TAAAAA--GACA 801

  chrX_85825629_8   1404 AAAAAAATCCACTT-AAAAATGGGAAAAGGACATGAACAGACACTTCTCA 1452
                           v  --i   v  -         v      iv    i     i     v
  L1M4_orf2#LINE/    802 AATAA--CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_85825629_8   1453 AAAGAAGACATACAAGTATCCAACAA--ATATGAAAAAAATGCTCAACAT 1500
                                 i      i iv    i  -- i       i -          
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACAT 898

  chrX_85825629_8   1501 CACTTATCAT 1510
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.32 (132 / 100)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.12 (81 / 26)  


2330 25.55 2.58 2.84  chrX_85908959_85910725.rev      502  1276 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_85908959_8    502 ACCCTAAAATTCATATTAAACAAAAAAAAGAGCTCGAATGGCCCAAGCAA 551
                          i              vi  - viv  ii  v iv    i   v  i   
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_85908959_8    552 TTTTAAGAAA-AATAACAGAGCTGGAAGCATCACATTACTTGACTTCAAA 600
                          i  i i   -  v    i  i    i vv     i v iii i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_85908959_8    601 TTATACTACACGACTACAATAACCAAAACAGCATGGAAATGGCATAAAAA 650
                         viv       vii     i   i   i    ii   v v        ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_85908959_8    651 TAGACACATAGGT-AATGGAACAGAACAGAGAACCCAGAAAAGAAACCAG 699
                               i    i -       i    iv    ii       vi  v   v
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_85908959_8    700 AGATCTACAGCCAGTTGATTTTTGATGAAGTCAACAGAAACATATGTGGG 749
                          v  i  ii i  i        i  ii i viiv  ii v   viivv  
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_85908959_8    750 GGAAAGGACGCCCTTTTCAATAAACAGTGATGGAAAAATCGGATTGTCAT 799
                               i iivi        i   ii   v   i v  ii    v?i  i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_85908959_8    800 ATGCAGAAGAAAGAAACTGGACTCCGATCTCTCAACACATACAAACATTA 849
                              i     v   ii     i  v i   v  v  i       v    
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_85908959_8    850 ACTCAAGATGGATTAAAGATCTAAATGGAAGACCTGACACTATAAAAATC 899
                               i      i ?   i       v    v  i v         v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_85908959_8    900 CTAGAAGAAAACCTAGGG--AAATCTCTTATAGACATTGGACATTGGTCT 947
                         i           v    ?--      - ii --------   v    vi 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCT-TCGT--------GACCTTGGGTT 575

  chrX_85908959_8    948 AGGCAAATCGTT-CATGACTAAGACCTTAATAGCTCAAGCAAGTAAAATA 996
                               - v   - v iiv  v   vii  v   v       vv   iv 
  L1M4_orf2#LINE/    576 AGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_85908959_8    997 AAAATAGACAAATGGGATTTAATTAAAAAAAGAAACTTCTGCACAGCAAA 1046
                                 i    v   i  v  i    vv i      i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_85908959_8   1047 AGAAATAATCAAACAGTCAACAGAGTGAAAAAGAAAACCTGCACAATGGG 1096
                         i  v iv     i-------- i        -  v    ii  v      
  L1M4_orf2#LINE/    675 GGACACTATCAAG--------AAAGTGAAAA-GACAACCCACAGAATGGG 715

  chrX_85908959_8   1097 AGAAAATATTTTCAAACTACGCATCAGACAGAAGACTTATATCCAGAATT 1146
                                    v    ii iii   v  i iii     i          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_85908959_8   1147 TACAAGGAACTCAAACAAC--AACAACAAGGTAAACCAAATTACCAAATT 1194
                           i  i      vv     --  i  i  i--  iv     v   v    
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAA--AAGACAAATAACCCAATT 813

  chrX_85908959_8   1195 AAAAAGTTGGCAAAGGATATGAATAGAC--TTTTTCAAA-----TA---- 1233
                         ?    i v          v         --  i i    -----  ----
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_85908959_8   1234 -ATGGTCCACAGGCATATGAAAA-ATTATCAATATCAGTAATTAT 1276
                         -    i v i i   i       -  vv    i    ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (119 / 75)
Gap_init rate = 0.02 (16 / 773), avg. gap size = 2.62 (42 / 16)  


1880 20.68 5.06 4.43  chrX_85910845_85913613.rev       34   507 (2262)    L1M4_orf2#LINE/L1        5   481 (427)  

  chrX_85910845_8     34 AAGGTGTCTGATTTTT-TGGATCTGAAAACTTAAAGATGTTAAGATGGCA 82
                            i i  iv  v  i-     iv   i      viv             
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_85910845_8     83 ATACTTGCCAAATTAATCTATAGGTCCAAAATGATCTCTATCAAAATTTC 132
                              iv       i     i  i i   viii   i          ii 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_85910845_8    133 AATGCT-CTTTCTTTAAATAAATGGACACATTTATTCTAATACTCATATG 181
                          --   - i  i   iv v    v    vii v  i    v i       
  L1M4_orf2#LINE/    105 A--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_85910845_8    182 TCAAAGCAAGGTACTGCTGAATGTCCAAATATTAAATAGCCAAAACGATC 231
                         vv  v      v  ----------   i ------           i   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGAC----------CCAGA------ATAGCCAAAACAATC 186

  chrX_85910845_8    232 TTGAAAAAGAAGAATCAAGTTTGAGGATTCACATGTGC-AGTTCTGAAAA 280
                                       iv     v     i     iv v - i  - v    
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT-TCAAAA 235

  chrX_85910845_8    281 CTTATTGCAAAGTTACAGTAATCAAAACAATGTAGTACAGGCA------- 323
                             i i     i            i   i   i    v    -------
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_85910845_8    324 ------------CACTGAAATGGAATTAAAAGTCTAGAAATAAATTCATA 361
                         ------------  v  i   i     i i    i         ii    
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_85910845_8    362 TGCTT-TGGTTAACTGATTTT-GAAAGGGGTGCCAAAATCATTCAGTGGG 409
                         iii  -    i  i       -  v i         i i      i    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_85910845_8    410 TAAAATGTAGTGTTTACAACAAATGGTGCTGAGACAAACAGATATCCACA 459
                         v   ivi    v   v               i     vii    ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_85910845_8    460 CACAAAAGAATGAACTTGGACCCTCACTTCACACCACCCATAGAGAAA 507
                         ii            v        ii  i        i--   v i   
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT--ATACAAAAA 481

Transitions / transversions = 2.03 (65 / 32)
Gap_init rate = 0.02 (11 / 477), avg. gap size = 4.09 (45 / 11)  

2541 28.01 2.46 1.12  chrX_85910845_85913613.rev     1383  2278 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85910845_8   1383 TGGAAACACATCCCATGCTCATGGAT-GGTAGAATCAATACTGTGAAAAT 1431
                               v i        i        -  v   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85910845_8   1432 AATCATACTGCTCAAAGCAATCTACAGACTCGATGCAAGTCCCACCAAAA 1481
                         iiiv     v i    vii         i  i i    vi  i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85910845_8   1482 TAGCATCATCATTCTTCACAGAACTAGAAAAAACAATCCAACAATTCATA 1531
                          vv  v vv v  i  ii     v v  v  ivii    v v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_85910845_8   1532 TGGACCCAA-GAAAGAG-CCCACA-TATCCAAAACAAGACTAAGCAAAAA 1578
                             ---  - v   i -    v -  v         vvi i iv  i  
  L1M4_orf2#LINE/    151 TGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_85910845_8   1579 GAACACAACTGAAGGCATCACATTACCCAACTTCAAATTATACTACAAGG 1628
                              v ii  i   vv     i v     i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_85910845_8   1629 CTGTACTTACCAAAACAGCTTGGTACTCATATAAAAATAGACATGCAGCC 1678
                           ii v v i   i    iv       vii    ii        ii  vi
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_85910845_8   1679 CAATGGAACAGAATAGGGAACCCAGAAATAAAACTAAATACTTACAGCCA 1728
                                 i     v i  ii           v i v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_85910845_8   1729 ACTGATCTTCAACAAAGAAAACAAAAACATAAAGTGGGGGAGAAAACACC 1778
                          i    i   i    i iviv   i v   vv i     i - i  i vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA-AGAATAGT 396

  chrX_85910845_8   1779 CTATTCAGTAAATGGTTCTGGAAAAACTTGCAACCCACATGTAGAAGAAA 1828
                           v    ii       v    i v    v vv ?       i i     v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_85910845_8   1829 GAAACTAGATCCTCATCTCTCACTTTATACAAAAATAAAATCAAGATGGA 1878
                            ii i  i  ii i   v   iv           v  v    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_85910845_8   1879 TGAAAGACTTAAATCTAAATCCTTAAACCATAACAATTTTAGAAGATAAC 1928
                          v ?    i     v   ivv  v    i    v v i        v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_85910845_8   1929 ATCAGAAACACTCTTCTAGACATTGACTTAGGCGAAGAATTCATGACTAA 1978
                           vi ?ivv v     vv   v   iv      i v iv   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_85910845_8   1979 GAACCTAAAAGCAAATGCAAAATAAACAAACAAATAAATAAATAAATGGC 2028
                           vv i       v v    ------    vi  v     i      v v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAA------CAAAAGAAAAAATAGATAAATTGG 640

  chrX_85910845_8   2029 ATCTAATTAAAACAAAAGGCTTCTGCACAGCGAAAGAAATAATCAACAGA 2078
                          ii v  i    iv   ii   i  ii vv i  i  v iv     v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_85910845_8   2079 GTAAATGGATAGCCCACAGAGGGGGAGAAAATATTCACAAACTATCCATT 2128
                           i  vi  i i        iv             ii    ii  vi  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_85910845_8   2129 TGACAAAGGACTAATATCCAGAATCTACAAGGAGCTCGAACCAATCAGCA 2178
                            i  i     vi          v  i  i  i   vv  v v   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_85910845_8   2179 AGAAAAAAACAAATAATCCCACCAAAAAGTGGGCAAAG-----------A 2217
                          v     i        i  v ii?    i         ----------- 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_85910845_8   2218 CA-------AAAGAAGATATACAAACAGCCAACAAACATATAAAAAAAGG 2260
                           -------                ii     i  i  i  i    i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_85910845_8   2261 CTCAAAATCACTAATTAT 2278
                              v    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (141 / 106)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.56 (32 / 9)  


1922 21.58 1.52 9.88  chrX_85918436_85922096     1813  2470 (1191)    L1M4_orf2#LINE/L1        1   603 (305)  

  chrX_85918436_8   1813 TGGAAAAA-AGCACAAATTCACAG-TAGAAATACTTAATTTTGTTGAGAT 1860
                               i - v v  vi    ii - v i  v       v     i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85918436_8   1861 GTTAACACTACTCAAAC-AATTTCTAGATTCAACACAATCCCTATCAAAG 1909
                          vi  i   v i    i-i  i vi         i              i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85918436_8   1910 TTTCACCAATAGTTTTTTTGCAAATCTAGACAATCTAATTCTCCAATTTA 1959
                          ii  v -- ivi         i vv v     v  i  i  vv    i 
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_85918436_8   1960 TGTGTAATTACAAGGAGCCCCAAATAACCAAAACAAT------AAAGAAG 2003
                          i  v  v i     ii   vi    i          ------       
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_85918436_8   2004 AACAATGTTGCATGATTCCCTCATTTAAATTTCAAAACTTACTACAAAGT 2053
                              v    v v  i  v v v iiv                      i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_85918436_8   2054 TGTATTAATAAAAACAGTGTAGACCTGGCAAAATAATAGGCATATAGACC 2103
                          ii v    v  i       i vv      v  vi    i        i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_85918436_8   2104 AACAGAATATAACTGAAAGTCATGTAATAAATGTATGAATCTATGTCCAA 2153
                           ii     v  i   i    vv v      ivi  iv  i    vi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_85918436_8   2154 TTGACAATTTTTTTTTGTAGATATAGGGTCTCATTCTGTGGCCTTGGCTG 2203
                             -------    i --- i -     -----------   vv i ii
  L1M4_orf2#LINE/    349 TTGA-------TTTTCG---ACA-AGGGT-----------GCCAAGACCA 376

  chrX_85918436_8   2204 TGGTGCAGTAGTACAATCATAGGTCACCAAAGTCTCAAACTCCTAAGATC 2253
                          -- -  i i viv  vv    -  ------v i    ----------- 
  L1M4_orf2#LINE/    377 T--T-CAATGGGGAAAGAATAG-TC------TTTTCAA-----------C 405

  chrX_85918436_8   2254 AAGTGATCCACCTATCTCAGCCTTCTGAG-TAGCTGGGATTTCCACATGC 2302
                           i  i ------------  ----  i -i i    -  v?        
  L1M4_orf2#LINE/    406 AAATGGT------------GC----TGGGACAACTGG-ATAKCCACATGC 438

  chrX_85918436_8   2303 AAAGGAATGAAGTTGGACCCCTACCTCACACGATATACAAAAATTATCTC 2352
                            i                           v              v   
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_85918436_8   2353 AAAATGTATAATAAAGGCATAAACATAAGAGCTAAAATCATAAAATTCCT 2402
                               v  --i ?  i v    ii            ii      i  i 
  L1M4_orf2#LINE/    489 AAAATGGAT--CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_85918436_8   2403 GTAAGAAAACTTAGGAGTAAGATATTTATGACCTTAGATTTGGCAATGGA 2452
                         iv        v    ?    -  v  ii       i i  v        v
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_85918436_8   2453 TTTTTCAGCATGACACCA 2470
                           i  viii         
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCA 603

Transitions / transversions = 1.40 (81 / 58)
Gap_init rate = 0.03 (20 / 603), avg. gap size = 3.75 (75 / 20)  

1280 21.24 1.96 0.00  chrX_85918436_85922096     2863  3168 (493)    L1M4_orf2#LINE/L1      597   908 (0)  

  chrX_85918436_8   2863 GACAACAAAAGCATATA-AACAGGAGAAAA--TAGA--AATGTGACTTTA 2907
                             v        i vi-    ii      --    --   vv     i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_85918436_8   2908 TCAAAAGTAAGCACTTTTGTGTATAAAGGGACATTATCAAGAAGGTAAAA 2957
                               v   iv         iv v  i     i         i  i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_85918436_8   2958 AGACTGTTCACAGAATGAGAGAAAATATTTGCAAATCATATAGCTGATTA 3007
                             viii         i                        v     v 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_85918436_8   3008 TGGTTTAATATCCTGAATATACAGAGATCTGCTGCAATTCAACAACAAAA 3057
                         v  vi vi     v       i i   v  vi i   i    i  i    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_85918436_8   3058 -GACAAATGTTTCAGTTACAAAATGGGCAAAATACATAGATGGACATTTC 3106
                         -       ivii  i  ?v            iv iv ii  i        
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_85918436_8   3107 TTCCAAAAATATATACAAATGACTGATAGGAACATGAAATGATGCTCAAC 3156
                          i v  i  v           i ii   i v        v          
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_85918436_8   3157 ATCAGTCACTAA 3168
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (39 / 25)
Gap_init rate = 0.01 (4 / 312), avg. gap size = 1.50 (6 / 4)  


2708 27.68 3.53 0.11  chrX_85938984_85943264.rev     2913  3790 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_85938984_8   2913 TGGAAACACATCTCATGCTTATGGATGAGTAGAATTAATATTGTGAAGAT 2962
                               v i   i    i i      vi v   v          v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_85938984_8   2963 GACCACACTGTCAAAAGCAATCTACAAATTCAACACAATTCCCATCAAAA 3012
                          i v i   vi v   vii       i       i    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_85938984_8   3013 TACCA-CAATCATTCTACACAGAATTAGAAAAAACAATTCTAAAATTCAT 3061
                          v   - vii v  i -ii     v v  v  ivii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_85938984_8   3062 --GGAAGTAAAAAAGAGCCCACATAGACAAAGAAAAACTAAGCAAAAAGA 3109
                         --    i iv  ii  v  viv    v    iv  vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_85938984_8   3110 ACAAATCGGGAGGCATCACACTACCCGACCTCAAACTATACTATAAGGCC 3159
                              viv     vv       v   i ii     viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_85938984_8   3160 ATAGTCACCAAAACAGCATGGTACTGGTATAAG----------------- 3192
                          i   v i   i    ii         i     -----------------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_85938984_8   3193 -TGAAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAAC 3241
                         -  i  i     v    ii               v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_85938984_8   3242 TAATCTTCGACAAAACAAACAAAAACATAAAGTGGGGTAAGGACACCCAA 3291
                          i  i        iivviv   i v   vv i     v   i i vi vv
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_85938984_8   3292 TTCAACAAATGGTGCTGGAATAATTGGCTAGTAACATGTATGATAGTGAA 3341
                                           i i  i   v  ?iv     i vi v i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_85938984_8   3342 ATTGGATCCTCATCTCACACCTTATACAAAAATCAACACAAGATGGATTA 3391
                         i     i  ii i        v           i   v   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_85938984_8   3392 AGGACTTAAATCTAAGACCTGAAACTTTAAAAATTATAGAAGATAACATT 3441
                         ?i   i     v     v  i     v     v iv       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_85938984_8   3442 GGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAA 3491
                           ?iv  vi    vv   v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_85938984_8   3492 CCTAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATTA 3541
                         v i       v v    i    iv   i   i   iv v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_85938984_8   3542 AAATAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAACAGA 3591
                             v  i i      iiivv    i iv  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_85938984_8   3592 CAACCCACAGAGTGAGAGAAAATCACCACAATCTACGCATCTGACAAAGA 3641
                                    i  i        vviii   vii iii      i  i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_85938984_8   3642 ACTAATATCCAGAATCTACAATGAAGTCAAACAAATCAGCAAGAAAAA-- 3689
                            vi          v  i  v   v  vv    v   ii  v     --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_85938984_8   3690 -AAATG--CCA-TCAAAAAGTACGCTAAGGACATGAATAGACAATTCTC- 3734
                         -    i--   - i?    i iv  v     iv          v     -
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_85938984_8   3735 --AAAAGATATGCGAATAGCCAACAAACATATAAAAA-ATTCTCAACATC 3781
                         -- i       i i   i     i  i  i  i    -  v         
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_85938984_8   3782 ACTAATGAT 3790
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.56 (32 / 9)  


2454 27.09 0.38 3.04  chrX_85955414_85957199.rev      506  1295 (491)    L1M4_orf2#LINE/L1      140   908 (0)  

  chrX_85955414_8    506 TAAATTTCCTATGGAACCAAAAAAGAGCTCGTATAGCCAAGGCAATCCTA 555
                             v   v       viiv  ii  v iv v        ii     i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_85955414_8    556 AGCAAAAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACCATA 605
                          iv  i          i      vv   ii  v  ii i      v v  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_85955414_8    606 CTACAAGGCTACAGCAACCAAAACAGCATGGTACTGCTACCAAAACAGAT 655
                               i       i  i   i    ii        vi iv ii i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_85955414_8    656 ATATAAATTAATGGAACAGAA--GAGAGGCCTCAGAAATAACACCACACA 703
                              i  i       i    --     v  --        vv   i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACA 337

  chrX_85955414_8    704 TCTACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAA 753
                          i  iiii  vi    i  i     ivv  v   i v  vv       i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_85955414_8    754 AATGATTCTCAAATAAATGGAAAACACCATTTATTTAATAAATGGTGTCA 803
                           --------i    i------------- i v  i  i        iii
  L1M4_orf2#LINE/    388 AA--------GAATAG-------------TCTTTTCAACAAATGGTGCTG 416

  chrX_85955414_8    804 GGAAAACTGGCTAACCATATGCAGAAAACTGAAACTGGAACCCTTCCTTA 853
                            v      v  ?   i     i  i v    ii    v    v   i 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_85955414_8    854 CACCTTATACAAAAATTAACTCAAGATGAATTATAAACTTAAACATAAGA 903
                             v                   i   i  i ? i  i    ii     
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_85955414_8    904 CCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGG 952
                         v       i      vi i           v    ?i- v i -   iv 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTG 565

  chrX_85955414_8    953 ACATAGGCATGGGCAAATATTTCATGACTAAAACACCAAAAGCAATTGCA 1002
                           v v  vv i     vvi    v iiv  vi            vvv   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_85955414_8   1003 GCAAAAGCCCAGATTGACAAATGGAATCTAACTAAACTAAAGAGCTTCTG 1052
                         i      vvv i  v  i    v i ii v ii   v v  i i   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_85955414_8   1053 CACAGCAAAAGAAACTATCATCAGAGTGAACAGGCATCCTACAGAATGAG 1102
                         ii vv    i  v       vv i      v  i  v  i        i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_85955414_8   1103 AGAACATTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCTAGAATC 1152
                             v  v       vii  vi      i  i  i  vi    i     v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_85955414_8   1153 TACAAGGAATTTAAACAAATTTACAAGAAAAAATCAAACAACCCCATCAA 1202
                           i  i   i ivv    v iv i  v     iv    i     v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_85955414_8   1203 AAACTGAGTGAAGGATATAAATAGACACTTTTCAAAAGAAGACATTTATG 1252
                            v  i ii      v i        i  i  v        i  vi vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_85955414_8   1253 CAGCCAACAAACATATGAAAAAATGTTCACCATCACTGGTCAT 1295
                         ii     i  i  i       i   i   v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (127 / 83)
Gap_init rate = 0.01 (6 / 769), avg. gap size = 4.50 (27 / 6)  

 610 23.12 0.00 0.00  chrX_85955414_85957199.rev     1298  1457 (329)    L1M4_orf2#LINE/L1      749   908 (0)  

  chrX_85955414_8   1298 GGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAA 1347
                          i  vi          v  i        ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_85955414_8   1348 TCAAACAACCCCATCAAAAAATGGGCAAAGGATATGAACAGACACTTCTC 1397
                         v    i     v  i?                 v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_85955414_8   1398 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAACGTTCATCAT 1447
                         v        i  vi viii     i ii          i i i   v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_85955414_8   1448 CACTGGTCAT 1457
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.57 (22 / 14)
Gap_init rate = 0.00 (0 / 160), avg. gap size = 0.00 (0 / 0)  


2591 26.76 2.24 1.90  chrX_85992084_85996881.rev     3425  4317 (481)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_85992084_8   3425 CCATGTGCATGTATAGGAAGAATCAATATTGTTAAAATGGCCATATTGCC 3474
                               v    v  v      v i           i     v   i v  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_85992084_8   3475 CAAAGGAATTTACCAATTCAATGCTATTTCTATCAAACTTCTAAGGATAT 3524
                             vvi  i   vi      i  v  ii        v i i -- v ii
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA--GCTGC 110

  chrX_85992084_8   3525 -TTTTTCACAGAAGTAGAATAAACT-ATTCTAAAATTCATATGGAACCAA 3572
                         -     ii     i v  -i  i  -  i                 --- 
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATATGGAA---A 156

  chrX_85992084_8   3573 AGAAAAAAAGACCAAAGAGAG--AAAGTAATCCTAAACAAAAACGGCAAA 3620
                         v v  ii--    v ii v  --   ii    i i  v  i  vii    
  L1M4_orf2#LINE/    157 TGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_85992084_8   3621 GCCAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTATAGT 3670
                          iii    vv       v  ii i      viv        i    i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_85992084_8   3671 AACCAAAACAGCATGGTGATGGTACCAAAACAAACATACAGACCCATGGA 3720
                           i   i    ii    iv   i iv ii i i     i   i v     
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_85992084_8   3721 ACAGAATAGAGAGCACATAAATAAAGCCACAAATCTATAACTATCTGATC 3770
                          i     v     iv  v       v   i v  i   iiii vi    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_85992084_8   3771 TTCGATAAAGTCAACAAAGA--AAGCAATGGGGAAAGA-CA--CTATTCA 3815
                              i  i viiv   -  -- vv             -i --  v    
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_85992084_8   3816 ATATATAGTGCTGGGATAACTGGCTAGCAATATGCAGAAGATTGAAACTG 3865
                          i v  i         i      v  ? v i     i    v    ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_85992084_8   3866 AATCCCTGTCTTATACCATATACAAAACTCAACACAGGATGGATTAAAAA 3915
                         i i    ii  i i             v i   v  ii      i ? i 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_85992084_8   3916 A--AAATGTAAAACCTAAAACTATATAAACCCTT-GAAGAAAATCTTAAA 3962
                         v--        i v           -    i   -        - v  ii
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAA-CATAGG 551

  chrX_85992084_8   3963 AATACCATTCTGAACATCTACCCTGG------CAAAGACTTTAT-GATAA 4005
                         ?i  -- v   v-- i v-   i   ------   v ii  iv -    v
  L1M4_orf2#LINE/    552 NGTA--AATCTT--CGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_85992084_8   4006 AGTCTTCAAAATTGATTGCAACAAAGACGAAAATTAACAAATGGGACCTA 4055
                         - v vi     viivvv        iivi     vi i    v    i v
  L1M4_orf2#LINE/    597 -GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_85992084_8   4056 ATTAAATTTAAAAGCTTCTGCACAGCCAAATAAACTATCAGCAGAGTAAA 4105
                           i   v      i   i  ii vv v  iv v       iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_85992084_8   4106 CAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCTTCCAACA 4155
                         v        i                          ii  iiv  ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_85992084_8   4156 AATGTCTGATATCCAGAATCTATAAGGAACTTAAGCAAATCAACAAGCAA 4205
                          iv v  vi          v     i     ivvi   v    i  vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_85992084_8   4206 AAAATAAACAACCTCATTATAAATTGGGCAAAGGACATGAACAGACAATT 4255
                           i i   i    iv   ?v   v           iv    i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_85992084_8   4256 CTA-AAAGAAGACATAGACACAGCAAACAAACATATGAAAAAGTGTACTA 4304
                           v-        i   v v ii  v  i  i  i       ii  iv v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_85992084_8   4305 AATCAATAAGCAT 4317
                         v    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.02 (22 / 896), avg. gap size = 1.68 (37 / 22)  


 628 27.72 12.44 2.85  chrX_86013192_86015644      301   686 (1767)    L1M4_orf2#LINE/L1        1   423 (485)  

  chrX_86013192_8    301 TGGAGGAGTATAGCCTATTCATAGATTAGAAGACTATATATT-TTAATGA 349
                             iiii   vv v i     i    i       vv     -    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA-GA 49

  chrX_86013192_8    350 TGTCAGTTCTTCT-AAACTTCTTGGTC---ATATTCATC-CAATCCCCAT 394
                           v  i v  i i-   ----   i  --- v     v -       i  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAA----TTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_86013192_8    395 CAAAATTCTATTAGG--TTTTTGTGAAAATTAACAAGATAATTTTCAAAT 442
                               i i viv v--      iii     i     v i  ii v    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_86013192_8    443 CTATTTGGATAAAT---AGAGCACCAGAA--------ATAATAT---AAG 478
                         ii  v    --   ---  i vv      -------- i   v ---  i
  L1M4_orf2#LINE/    146 TCATATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_86013192_8    479 TGAAGGAT---------GAACCAACA------GGTATCAAGACTCATTAT 513
                         v    i i--------- i  iv   ------ii v    i   i i  i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_86013192_8    514 ATAGCTACAGTAAAGATGAGAGTGTGGGATTGAGGTGAAGATAGTCAAAT 563
                          v           vv v  v       v i  ivi i i     v  v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_86013192_8    564 AAATCATTTGAACAG--TCTAGAGTTGTGAAATAGACA-ACACATATCTG 610
                          i    v v   i  -- iv     ivv      i  v- i    v v  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_86013192_8    611 GACAGTTGATATATGTTAAAGATGGCTCTAAAGAGCATGCA-T----AAA 655
                          v  i     v vi vi  i i  v ----    v   v  - ----   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCC----AAGACCATTCAATGGGGAAA 389

  chrX_86013192_8    656 GGACCATATTTTAAATAAATA-TGTTG--ACAAC 686
                          i ivi v    v  i    i-  i  --     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

Transitions / transversions = 1.23 (59 / 48)
Gap_init rate = 0.05 (20 / 423), avg. gap size = 2.95 (59 / 20)  

 371 27.00 8.64 7.13  chrX_86013192_86015644     1520  1982 (471)    L1M4_orf2#LINE/L1      439   908 (0)  

  chrX_86013192_8   1520 AAAAACATGAATATTGGACTC-----TCACACAATACACAATAAAGCAAT 1564
                             iv     -i      i -----      v   i    -   vi  i
  L1M4_orf2#LINE/    439 AAAAGAATGAA-GTTGGACCCCTACCTCACACCATATACAA-AAATTAAC 486

  chrX_86013192_8   1565 CCTA---GGTTTA-----CTATATGTACATAGCAAAGTTAAAACAATGAA 1606
                         i v ---  v i -----   v     ------ i  i      v  i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTA------AGAGCTAAAACTATAAA 530

  chrX_86013192_8   1607 AATTCTAGTAGTAT-CATAGGAGAATATCTTTTTATTATCTTGAAGTAAA 1655
                          v ii   v  v v-      ? v v     iv i-- i    iiv  ii
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG--ACCTTGGGTTAGG 578

  chrX_86013192_8   1656 TAAATATTTTATAAACAAGACA--AAATAATGCTGACTATAAAAGAAA-- 1701
                         i  vvi   iv  i i v    --   - iii vii v i        --
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAA-AGCACAAGCAACAAAAGAAAAA 627

  chrX_86013192_8   1702 -CAGCTACTTTAGACCCCACTAG---TAAAAATGCATTGT---TCAACAA 1744
                         -i  v  vv  i   ii  ii i---      ivi-    ---    - i
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTT-TTGTGCTTCAA-AG 675

  chrX_86013192_8   1745 GA----GTTAAAAAA---AAAAGCTAAACTAAATTACAGAGTGGGAGGAG 1787
                           ----i i  i   ---     ----  -  vii     i      i i
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAG----AC-AACCCACAGAATGGGAGAAA 720

  chrX_86013192_8   1788 ATAGTTGTAAACAATGTAATGGA-AAAAAA--TATATCAAAAACATACAA 1834
                            v   i   iv  i  viv  -  iii -- i    v i  i   i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_86013192_8   1835 ACAATGACTGTAACTAAATAAGAAATAGACAAACAATCCAAATTAAAAAA 1884
                          v  ivvi ii    v     v   v       i  i    -  ?     
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA-TTWAAAAA 819

  chrX_86013192_8   1885 AATAATCAAAAAGCATCAGCAGGCA---CTCCACAAAAGTACATAGCTAA 1931
                         -- iiv    iiiiv v ii  i  ---     v i   - i   --i  
  L1M4_orf2#LINE/    820 --TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG-ATATA--CAA 864

  chrX_86013192_8   1932 ATGGATAATAA--ATATGAAAAGTATATGATTTCAACGGTTATCAGGAAT 1979
                             vi     -- i        ---   --i     ----    ?????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAG---ATG--CTCAAC----ATCAZZZZZ 905

  chrX_86013192_8   1980 ATG 1982
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.93 (81 / 42)
Gap_init rate = 0.06 (30 / 470), avg. gap size = 2.43 (73 / 30)  

 360 24.72 7.30 5.62  chrX_86013192_86015644     2276  2453 (0)  C L1M4_orf2#LINE/L1   (249)   659   479  

C chrX_86013192_8   2453 AGATCAACTCAAAATGAATTAAAGACTTAAATGTAAAACCCAAAGCTATA 2404
                          i  i           i  i ?    i         i v i   i     
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

C chrX_86013192_8   2403 AAAACCCTGGAAGACAGCCTAGGCA-ATACCATCCTGGACATAGGAACGG 2355
                            vi i i     v i v    ?i- v i v  v  -  v v  ivii 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAG 577

C chrX_86013192_8   2354 GCAAAGATTTC------ATGACA---AAGACACAAATAACAATTGCAAAA 2314
                             v i    ------      ---  ii     ii     --------
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA-------- 619

C chrX_86013192_8   2313 AAGCAAAAATTGACAAGTATGG---TGACTATAATTAACAA 2276
                            v      v  i  i -   --- v ii v      v  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAAT-TGGACTTCATCAAAATTAAAAA 659

Transitions / transversions = 1.62 (26 / 16)
Gap_init rate = 0.04 (7 / 181), avg. gap size = 3.29 (23 / 7)  


2794 25.08 3.15 1.01  chrX_86016958_86019136.rev      800  1688 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86016958_8    800 TGAAAAGGCATCCCATATTTATGGATTGGAAGAATTAATGTTGTTAAAAT 849
                           i    ii       i  i             v     i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86016958_8    850 GACCATAATACCCAAAGTGACCCACAAATTTAATGCAATGCCTATCAAAA 899
                          i v   v v      v   i i   i   i  i     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86016958_8    900 TACCAA-TGACATTCTTACAAGAAA-----AAGC-AACGATAAAATTTCC 942
                          v   i-  v v  i  i  -    -----    -i ivv       ivi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_86016958_8    943 ATAGAAC--CAAAAAAACCCGAA-AGCCAATGCCTATCT-GAGCAAATAG 988
                           i   v--   iii v  v   -      vi v-    -  iv  iv  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACA-ATCTTGAAAAAGAAG 198

  chrX_86016958_8    989 AACAAAGCTACAGGCAC-CACATTACCTAATTTCAAAATATTCTACAAAG 1037
                                i iv   -  -    i v  i          iv v        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_86016958_8   1038 CCATAGTAACCAA--CAACATGGTACTGTCATTAAAAATAGACACATACA 1085
                          i i     i   --  iii        v   -  ii       i   v 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGA 296

  chrX_86016958_8   1086 CCAATGAAAGATAATAGAAAACCCAGAAATAAATCCACATATTTGCAACC 1135
                         i     i  v v   v  i ii           i   i i    iiiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_86016958_8   1136 ATCTCATTTTCAACAAGGGCACCAAGAACCTACACTGAGAAAAGGACACT 1185
                          vi v      i       ii      v v v  v  i i    i i v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_86016958_8   1186 CTCTTTAATAAAAACTGCTGGAAAAACTAGATAGCCATATGCAAAAGATT 1235
                           i  i  i   viv      i v    i    ?   i          v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_86016958_8   1236 GAAACTGCACCCCTTTCTCTTAACATATACAAAAATGAACTCAAAATGGA 1285
                            ii  v      vi   vi v             v             
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_86016958_8   1286 TTAAAAACCTGAATGTAAGACCCAAGTCTGTGAGAGTACTAGAAGAAAAC 1335
                          i ? i    i         v i  iv  i i i v vi           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_86016958_8   1336 ATAGAGG-AAATGCTTCAAGACATTGG-TCAGGGCAAAGATTTTACAGAT 1383
                             i? -    -    iv   v    - i   -   v i   ivi    
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTAGAT 594

  chrX_86016958_8   1384 AAGACTTCAAAACCACAGGCAACAAATATAAAAATAGACAAATAGGATTA 1433
                          v   vi     v    i        viv         i    v   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_86016958_8   1434 TGT-GAGACTAAAAACCTTTGGCACAGCAAAGGAAAC----AACGGAGTG 1478
                         ii -i i i       i    -ii vv       v  ----  vii    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_86016958_8   1479 AGGAGACAACACAAAGAATGGGAGAAAATGTTTACAAACTCTTCATCTGA 1528
                          ii       v  v               i   i    iiv vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_86016958_8   1529 AATAAAATTAATATCCAGAATAC-CAAAGAA-TCTGG-AAC--AACAGTA 1573
                         v viii i vi           i-i      -   vi-   --  i i  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_86016958_8   1574 AAATAATAAA-AATCTGATTCTACAATGGGTATAAATGATCTAAATAGAA 1622
                            vi i   -  i ii   ?v v      i --  v   i i      v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCA--AAGGATTTGAATAGAC 841

  chrX_86016958_8   1623 ATTTATTAAAGGAAGATCTGAAAATGGCAAAGGAATAGTTGAAAA-ATGC 1671
                             v iv  i      v iv       v  vi ii vv      -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_86016958_8   1672 TCAGCATCACTAATCAC 1688
                            i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (135 / 84)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 1.42 (37 / 26)  


2418 27.90 3.46 2.12  chrX_86028377_86036550      919  1814 (6360)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86028377_8    919 TGGAAAAATATTGTATGCTCATGGATAGAAAGAATCAATATATTAATGTT 968
                               i    ivi   i        v i    v i     -----    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-----TGTT 45

  chrX_86028377_8    969 AAAATGGCCATACTGCTTAAAGCAATTTACATATTCAATGGCATATCTAT 1018
                           i     v     v ii   vii  i    v      i vv  vi    
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_86028377_8   1019 CAAAACTACCAATGACATTTTTTACTGAATTAGAAAAA--AACCTTCTAA 1066
                              - v   iivi v      i v   v v  v  i--i -- i    
  L1M4_orf2#LINE/     96 CAAAA-TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAA 142

  chrX_86028377_8   1067 AATTCATTTGGAACAAAGAAAAAAAAAAAAGCCTGAGCAGCCAAAGTAAT 1116
                                v     ------- viv  iii v  v  ii       ii   
  L1M4_orf2#LINE/    143 AATTCATATGGAA-------ATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_86028377_8   1117 CCTAAACAAAAATAAAACAAAGTGAAAGGTATCACATTACTCAACTTTAA 1166
                          i i  -   i - i        vii   vv     i v i   i  i  
  L1M4_orf2#LINE/    186 CTTGAA-AAAGA-AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_86028377_8   1167 ACTGTGCAACAAGACTACAGTAACCTAAACAACATGGTAGTGGTACAAAA 1216
                          viv i v    ii         i v i   iii     v   i i  ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_86028377_8   1217 ACAGACATATAGATCCTTGGAGCAGAAGAGAGAGCCCAGATATAATGCTA 1266
                          i             vv    ii    vv     i     v    vv i 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_86028377_8   1267 CACACCTGCATTCATCTGATCATCACCAAAGTCAACAAAAAGA--CAATG 1314
                         i   ii iiiv   vi    iv  iv   i viiv   i vv --     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_86028377_8   1315 GTAAAATGACA-----TTCAATAAATGGTGCTGGGATAACTGGCTAGCCA 1359
                          vi   vi i -----     i              i      v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_86028377_8   1360 TATGCAGAGGATTGTAACTGGACCTCCTCCATTTCACCAGATACAAAAAT 1409
                         i     i i  v  v ii      -   v v iv     v          
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACC-CCTACCTCACACCATATACAAAAAT 482

  chrX_86028377_8   1410 CAGCTTAGGG-GGATTAAATACTTAAATGTAAAACCTAAAACAATAAAAT 1458
                         i i  i iii-    i ? v  i         i v       v      i
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_86028377_8   1459 CAGTAGAAGAAAACATAGGCA-ATACCATTCTGGACATAGGCCCTGGCAA 1507
                         ivv                ?i- v i -   vv   v v  viiv     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA 581

  chrX_86028377_8   1508 AGATTTTAT-GACA-GGCACCAAAAGAATTTGCAATAAAAGCAGAAATTG 1555
                         v i   iv -  i - i         v ivv    i     v i    v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_86028377_8   1556 ACAAATGGGACCTAATTAAACTAAAGAACCTCTGAGCTGCAGATAAAACT 1605
                          i    v    i v  i   v v  i   i i  v   v  i vi v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_86028377_8   1606 ATCAACAGAGTAAATAAACAATGTACAGAATGGGAGAACATATTAGCAAA 1655
                              v i   i  v i    ivi              v     v     
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_86028377_8   1656 CTATGCATCTGACAAAGGTCTAATGTCCAGAATCCATAAATAACTTAAAC 1705
                         ii  ii      i  i  v  vi i        vi     v    ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_86028377_8   1706 AAATTAACAAGTAAAAAACAA----CTGCATTAAAAAGTGGGCAAAGACC 1751
                           v i  i  vv    i    ---- ivv   ?    i         ivi
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_86028377_8   1752 ATGAACTGACACTTCTC--------ATGT------GACCAACATCCATAT 1787
                         v    iv    i     --------  i ------ i    i vv  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_86028377_8   1788 GAAAAAAAGTTCAAAATCACTAATTAT 1814
                              i v i    v    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (141 / 105)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.78 (50 / 18)  

3233 26.60 0.77 0.55  chrX_86028377_86036550     6776  7681 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86028377_8   6776 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 6825
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86028377_8   6826 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 6875
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86028377_8   6876 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 6922
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_86028377_8   6923 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCGATCCCAAGCCAAAA 6972
                                 viiv  ii  v  v v  v     ii i   iii ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_86028377_8   6973 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 7022
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_86028377_8   7023 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGA--TATAGAT 7070
                                  i   i    ii         i iv ii i   --       
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_86028377_8   7071 CAATGGAACAGAAC--AGAGCCCTGAGAAATAATGCCGCATATCTACAAC 7118
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_86028377_8   7119 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 7168
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_86028377_8   7169 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 7218
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_86028377_8   7219 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGCTGG 7268
                             ii    i    v   i     v           i  i    iv   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_86028377_8   7269 ACTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAG 7318
                          ii ?    i    i  v   v       i      vi i         i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_86028377_8   7319 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 7368
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_86028377_8   7369 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 7418
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_86028377_8   7419 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 7468
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_86028377_8   7469 CAGACAACCTACAAAATGGGAGAAAATTTTCGCAATCTACTCATCTGACA 7518
                         v        i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_86028377_8   7519 AAGGGCTAATATACAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 7568
                          i  i  vi   v      v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_86028377_8   7569 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 7618
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_86028377_8   7619 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTTAT 7668
                            v        i  vi viii     v  i          i     i v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_86028377_8   7669 CATCACTGGCCAT 7681
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


2314 27.81 4.88 2.04  chrX_86072163_86077167     3632  4512 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_86072163_8   3632 GAAAGATGGCCCATGTTTATAGATTGGAATAATTATTAGTATTAA-ATAT 3680
                                iv        i  i        v v   v  v i    -  iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_86072163_8   3681 CTATACTTTCAAAAGCAATCTACAGATTTATTGCAATTATT-TCAAAATT 3729
                          v     ii v   vii           i vi     ivi -       i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_86072163_8   3730 CCAATGATGTTCTTCACAGAAATAGAAAAAACAATTGCC---AATTTACT 3776
                            iiviiv  i  ii       v  v  ivii  --  ---    i - 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT--CCTAAAATTCA-T 149

  chrX_86072163_8   3777 ATGGAACCAGAAATTATCCCACATAAAAACAGCAATCTTGAGCAGCAGCA 3826
                               viiv  ivv i  viv   ivv v i         iv iv iv 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_86072163_8   3827 ACAAAGCTGGAGGCATCACACCACCTGATTTCAAATTATACTACTAGGCT 3876
                               i      vv      iv  ii        viv      v i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_86072163_8   3877 ACGGAACACCAA-ACA-TGT--CCCTGGCATAGAAAAAAACAGATTTACC 3922
                           i v - i   -   -   --iv        iii v i   v  vv i 
  L1M4_orf2#LINE/    250 ACAGTA-ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_86072163_8   3923 AATGGAACAGAATTAA------------------ATTCACTCACAGTCAC 3954
                                i      i ------------------  v  i i ii    v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_86072163_8   3955 CTCACTTTCTACAAAAGTGCCAAGAACTTCCATTGAGGAAAGAACAATCT 4004
                         i v i    v    ii         v v i  v  i        i i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_86072163_8   4005 CTTTAATAAATGGTGCTTAGATAACTAGCTGTTCATATGCAGAAAAATGA 4054
                         i  i  i          vi  i    i v i?i  i     i  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_86072163_8   4055 AATTATATCCCCATTTTTCAACATATATATATATAGAAAAATTAATTCAA 4104
                          i  iv i   i ii iv  v      i --------        i    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACA--------AAAATTAACTCAA 490

  chrX_86072163_8   4105 AATGCATTAAATACTTAAATGTAAGACCTAAAACTTTAAATCCACTAAAA 4154
                             v  i ? v  i           v        v    v ivi  i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_86072163_8   4155 GAAACCTT-GGGGAAAATGTTATAGGACATTGGTCCGAGCAAAGATATTT 4203
                             v v -  ? v    v  -iiv   v    viiii    v i -  i
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGT-TTC 588

  chrX_86072163_8   4204 TTGGATAAGAATTTGAAATCATAGACAATAAAAGCAAAACGAGACAAATA 4253
                           i    v  vviii   v  i ii   i     v    vv   i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_86072163_8   4254 GGATTACATCGATCAAAGAAAACCA-----GCAACAACAAAACA---TCA 4295
                            i v    i --  vv    v v-----  vv   - ii   ---   
  L1M4_orf2#LINE/    639 GGACTTCATCAA--AATTAAAAACTTTTGTGCTTCAA-AGGACACTATCA 685

  chrX_86072163_8   4296 ATAAAG-----AGACAACCTACAGAATGGGAGGAAATACTTGCAAATGAT 4340
                          v    -----        i            i     i        v  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_86072163_8   4341 CTATCTCACAAGGGGTTAACACCCAGAATAGATATGAAACTCAAACAACT 4390
                         v     v i     ii vii i        v   vii     vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_86072163_8   4391 CAATAACAAGAG--CAAATAATCCCATTAATAAATAGGCAAAATCCTTTA 4438
                               i  i i--       i  v   ? v    i      ivvi  v 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_86072163_8   4439 ATAGATATTTCCTAAAAGACAACATATGAACAGCCAAGAGCTGTATGAAA 4488
                              i     iiv     vi i   ii  ii     v iviii      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_86072163_8   4489 AAAATGTTCAACATCACTAATCAT 4512
                          i -  i         ????????
  L1M4_orf2#LINE/    886 AGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 2.90 (61 / 21)  


1539 27.11 6.13 2.45  chrX_86092620_86094260.rev      501  1153 (488)    L1M4_orf2#LINE/L1      232   908 (0)  

  chrX_86092620_8    501 AAAACTATACTACAATTCTACCATAAAGAAAACAGCATGCTACTGGTACA 550
                               -        vv    vi   vv  i    ii  v      i i 
  L1M4_orf2#LINE/    232 AAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_86092620_8    551 AAAGTAGACACATAGACCAATGGAACAGATTAGAGAGCTCGGAAATAAAG 600
                          iii      i     i        i   v v     ii i        v
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_86092620_8    601 CTGCATAACTACAACTATCAA---ATCTTCAACAAAGTTGAAAATAAGCA 647
                          iii i vi  iii---    ---  i   i    i v  vv  -i v  
  L1M4_orf2#LINE/    331 CCATACATTTATGG---TCAATTGATTTTCGACAAGGGTGCCAA-GACCA 376

  chrX_86092620_8    648 TT---TGGAAAAGGACTA-CATATTTAATAAATGCTGCT----CAA---- 685
                           ---   ii  i  v  -iv v  i  i     v    ----   ----
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_86092620_8    686 -TAGCCATATGCAGAAAATTTATACTGCACTTC---CTTTCACCATGTAC 731
                         -  ?   i     i  i v v vii  v  ii ---  iv      i   
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_86092620_8    732 AAAAATCAACTAAAGATGAATGAAAGACTTAAGTCTAAAACCTAAAACTA 781
                               i    v  i   i  v ?    i   i v   i v         
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_86092620_8    782 TTATATAGAAACCCTAGCGGAAAACCTAGG---AAATACCATTCTGGACA 828
                          ----- i  vi i   vi      v    ---    -- v iv  iv v
  L1M4_orf2#LINE/    527 T-----AAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCT 569

  chrX_86092620_8    829 TAGGCCTTGGAAAATATATTTTTA----------CAAAGAC-----CAAA 863
                          i  --  i iv   ivv  i   ----------    ii -----   v
  L1M4_orf2#LINE/    570 TGGG--TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_86092620_8    864 AAAAAAAAAAATCAAATAG-TGGGACCTAATTAAACTATAAAGCTTCTGC 912
                             i       - i   i- v    i v  i   v vv   i   i  i
  L1M4_orf2#LINE/    618 AAAAGAAAAAAT-AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_86092620_8    913 ACAGCAAAATAAATTATCAACAGAGTTAACAGACAACCTACAGAGTGGGA 962
                         i vv    iv v i      v i   v  v        i     i     
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_86092620_8    963 GAAAAATACTTGCAACCTATGCATTCAACAAAGGTCTAATATCCAGAATC 1012
                              -  i      vii  ii  iii i  i  v  vi          v
  L1M4_orf2#LINE/    717 GAAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_86092620_8   1013 TGTAAGTAATTTATATAAATCAACAAGAAACAACCAACCCACCCCAGT-- 1060
                          i   iv  i iv  i  v    i  v   v iv   viv    v v --
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_86092620_8   1061 AAAATGGGCAAAGGATATTAACAGACACTTCTGAAAAGAAGAAACGCACA 1110
                                         v v  i     i    vv        v ii  v 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_86092620_8   1111 TGGCCAGCAAGCATATGAAAAAATACTCAACAGTATTAATCAT 1153
                               ii     i       i  i       vi ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (104 / 71)
Gap_init rate = 0.03 (19 / 677), avg. gap size = 2.95 (56 / 19)  


3468 22.30 3.64 0.34  chrX_86114914_86118726     2442  3320 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86114914_8   2442 TGCAAATGCATTCCTTGTTCATAGATTGGAAAACTTAATATTATTAAGAT 2491
                           v   vii  i  v       i        i          i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86114914_8   2492 GGCAATATTTTCTAAATTGATATTCAGATTCAATGAAACTCATATTAAAT 2541
                                i ii i        v v         i v  ii v   i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86114914_8   2542 GTCCATTTGTTATATTTTCAGAAATGGACAAACCAATTCTAAAATTCATA 2591
                         vi   vi  iiv v   v       v     i ii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_86114914_8   2592 TGAAATTTCAGGTAATGGCAAATCGTCACAACCAATCTTGAAAAAGAA-A 2640
                           i  v v  i vi ivvvi   v i  v   -               - 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AATCTTGAAAAAGAAGA 199

  chrX_86114914_8   2641 ACAAAAATAGA--AC---CACTTCACCAATTTCAAAACTTAGTACAAGGC 2685
                              iv i  --  ---      -                v     i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTC-CCAATTTCAAAACTTACTACAAAGC 248

  chrX_86114914_8   2686 AATGATAACCAACACAATGTGGTGCTGACATAAATACAGCCATGTAGATT 2735
                         v iii   i   v   i      i   i     iv i  v   i     i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_86114914_8   2736 AATGAGATTAAATTGAGAGTCTAGAAAGAAAACTATATATCTGTGGTCAA 2785
                             ii  vi           i     v   v i   i  i i       
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_86114914_8   2786 CTAGTTTTAAACAAAGGTGATAAAACAGTTCTAAGAGGAGA-AAT-GTTT 2833
                         i ii    vi    i    vi  i  vi   v v i   i -   -  i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_86114914_8   2834 TTTAAACAAATGATGTTTGGATA------TGTCTACATGCCAAAGAATAG 2877
                            v        i  i v   i ------ i? i      v       ii
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_86114914_8   2878 AATTACACCTTTACTTCATACCATATACAAATATTAGCTCAAAATTGATC 2927
                          i  iv   ii   i   i            v    i        v    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_86114914_8   2928 AGATACCTAAATATAAGAGCTAAAACTATAAAAGTCTTAGAACAAATAGT 2977
                          ? v        i                    v        v   vvi 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_86114914_8   2978 AGGAGTGAGTCTTTGTAACTTTATATTAGGCAATGATTTCTTAGATACAA 3027
                            ?  i i    i  i  i  ivi          i           ii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_86114914_8   3028 TACAAAAAGCACAAGAAACAAAACAAAACGTATATAAAT-GGTCCTTAT- 3075
                         i  v           v       v    vi  v      -  v i i  -
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_86114914_8   3076 AAAATTAAAAACTTCTTTGCCTCAATAGAGTCCATCAA-AAAGTGAAAAT 3124
                                       i v   i    vi  vv i     -          v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_86114914_8   3125 TCAGCCCACAGAATGGGGGAAGATTTTTGCAAATTATAGATTTGACAAGT 3174
                         v  i             i   i  v         i   v  i   i   v
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_86114914_8   3175 GACCTATATATGTTACATATTAC-AACTATTACAAC-----AATTAAAAG 3218
                            i i   viivv i    v v-    v       -----   v     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_86114914_8   3219 GGAAATGTCTAAATT-AAAAATGCAGAAAAAGACT-GAATAG----TTTT 3262
                         iv    iv iv    -       -i v   i  i -      ----  i 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATG-GGCAAAGGATTTGAATAGACATTTCT 847

  chrX_86114914_8   3263 TCAAAGAAGGTATACCAATGGC---TAAGTATATGAAAAGATGTTCAACA 3309
                         i        i     v      ---    i i           i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_86114914_8   3310 TCATTAGTCAT 3320
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (118 / 75)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.94 (35 / 18)  


1855 25.03 4.87 3.48  chrX_86119161_86120870      500  1218 (492)    L1M4_orf2#LINE/L1      180   908 (0)  

  chrX_86119161_8    500 AACAACTTTGATAAAGAAGAACAAAATTGGAGG-TTTAAATTATTTGACT 548
                              ii    v             i       -i i v i viiii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_86119161_8    549 TAAAAA---ACTAAAAATTTACATTAATCATGACAGTGTATTAATGACGC 595
                          v    ---    v   vi    v      v        iv  v  i ii
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_86119161_8    596 TAAGATAGATATATAGATCAATGGAGAAGAATAGATCATCTAGACTCAGA 645
                         v i      i               iv     v  vvi  i   vvi i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_86119161_8    646 GTCCACACAT--ATGATGATTTGGCTTTTGGCAAAGGTGTAACGAGGCAA 693
                         -i   i    --   i v v   ii   i i   i    i-- i  i v 
  L1M4_orf2#LINE/    330 -CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC--CAAGACCA 376

  chrX_86119161_8    694 GTCAGTGG----AGAAT--TCTTTTCAACAAATGGTGCTAGAAAAAATGA 737
                         v   i   ----     --                    i i v  v  i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_86119161_8    738 ATATTAATATGTGTAAAAATTAACTTTAAGCCATAATTCACACCATACAC 787
                            ?iv i   iiv  i   v  v  vi v  v  vi          i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_86119161_8    788 AAATATTAACTGAAAATGCATCATAGATTTAAACATTAAACCTAAAATTA 837
                            v       v      v    ?   ii    ii v i v      i  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_86119161_8    838 TAAAACTCCTAGAAGAAAACATAGGAGAAAGTCTT---GACCTTCAATTA 884
                                 i                ? v  i    ---      vii   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_86119161_8    885 GACAAATACTTTTTAGATACATCCAATCCCCAAAAGCATGATTTATAAAA 934
                          i   vvii  i       ii-v  ----         ii viv i    
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATG-ACA----CCAAAAGCACAAGCAACAAAA 621

  chrX_86119161_8    935 GTAAATCTAAATAAATTGGACTTCA-CAATAATTAAGAACCCTGGT-CTT 982
                          v   vv  i               -   -      i   ii v  -   
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAA-AATTAAAAACTTTTGTGCTT 670

  chrX_86119161_8    983 CAAAAAATAGCTAGT--GGATG-GAAAAGGCAAAGCAAATATTGGGAAAA 1029
                             ii i -   vi-- i v -      i   vv  v v v     i  
  L1M4_orf2#LINE/    671 CAAAGGACA-CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_86119161_8   1030 AATATTTTCATATCAT------GGTAG------TGTAT--AGAA-ATACA 1064
                                v  v     ------ i  i------     --    -   i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_86119161_8   1065 ATTAATTTTGTATATTAAACTGTTTGATAAACAACCAGTTTCGGGAATAT 1114
                          vv  i i -  i ----   vvv i     v iv  --------    -
  L1M4_orf2#LINE/    770 AAGAACTCT-TACA----ACTCAATAATAAAAAGACA--------AATA- 805

  chrX_86119161_8   1115 ATCAAAATAAGGGAAGGAGCAGAATATTTGAAAAGACAGTTCCCCGAAAA 1164
                          i v  v ? ii-  v i   i iv       v     v   i  i  i 
  L1M4_orf2#LINE/    806 ACCCAATTWAAA-AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_86119161_8   1165 AGATATACTGATAGCAAACAAGAATGTAAAGAGATGTGCAACATCGGTAA 1214
                                 vi  i  v  i   v ii i  i     iv       i????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_86119161_8   1215 CCAT 1218
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.41 (103 / 73)
Gap_init rate = 0.03 (25 / 729), avg. gap size = 2.40 (60 / 25)  


2739 28.24 2.33 1.77  chrX_86139214_86141241.rev      635  1537 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86139214_8    635 TGGAAAAATATTTTATGATCATGGATAAGAAAAATCAATATT-TTAGAAT 683
                               i    iii   v        vi   i v i      -   ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86139214_8    684 GGCTGCATTGAACAAAGAAATTTATAGATTCGATGCTACTCCTAGCAAAC 733
                            vii i vvv    vvi  i  i      i i  v ii    v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86139214_8    734 TACCAATGGCATTCTTCATTGGATTGGAAAAATTTATTTTAAAATTCATA 783
                          v   iiv  v  i  iiiv i v v  v  ii v  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_86139214_8    784 TGGAACCAAAAAGGAGCTTAAACAGCCAACACAATCCTAAGTAAAAAGAA 833
                              viiv  i   v ivi  i      v      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_86139214_8    834 CAAAGCTGGTGGGATCACATTATCTAATTTCAAACTATACTACAAGGCTA 883
                              i   v  iv     i vi i         viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_86139214_8    884 CATTGATGAAAACAGTACGGTACTGTTACAAAAACAGACACATAGAGTAA 933
                           v i  v  i     ii       vi i  ii i     i     vi  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_86139214_8    934 TGGAACAGAATAGAGAACCCAGAAGTGAGACCGCACACCTACAACTATCT 983
                              i     v    ii      i i iv  ii   ii  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_86139214_8    984 GATCTTTCACAAACCTGACAAAAACAAGAGATGGGAAAAGGATTCCCTAT 1033
                            i  iv    ivv  v   i v  vvvi     i    i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_86139214_8   1034 TCAATGAATGGTGCTGTGATAACTGGCTAG--ACATGCAGAAGATTGAAA 1081
                             ii          v  i      v  ?--       i    v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_86139214_8   1082 CTGGATCCCCTCCTTACACCATA---AAAAATTAAC-AAAGATAAATTAA 1127
                         i    i   iv   i        ---          -v  i  ii  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_86139214_8   1128 ATATTTAGATGTAAGGCCTCAAATTATAAGAAAGAATCTTAGAAGAAAAC 1177
                          v ii  i       iv  v   i     i v----              
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAAC----TCTTAGAAGAAAAC 546

  chrX_86139214_8   1178 A--GG---AAA-CGCCAT--TCTT---TTCAGAAATAATTTTATGACTA- 1215
                          --  ---   - vi i --i   ---  vi v   ii   iv iiv  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_86139214_8   1216 GACCTCAAAAGCAATTTTAACAAAAATGCTCATGGGCTTAATTTGACAAG 1265
                            vi        vvvvi       ---------- vvv  v v  i  i
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAA----------GAAAAAATAGATAAA 636

  chrX_86139214_8   1266 TTGGAGTTAATTAAACTGAAGAGCTTCTCCACAGCAAAAGAAACTGTTAA 1315
                              v  v  i   v v  i i   i vii vv    i  v   i i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_86139214_8   1316 CA--GTAAACAGACAACCTACAGAATGAGAGAAAGTATTTGCAAACTATG 1363
                         v --  i  v        i        i      i          ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_86139214_8   1364 TATCTGACAATAGTCTCATATCCAGAATCTTTAAGGAACTTAAACAACTC 1413
                                i  vi v  ii          v v   i     ivv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_86139214_8   1414 AGTAAGCAGAAAGCAAATAACCCCATTAAAAGGTGGGCAAAAGACATGAA 1463
                          i   vv i  ii          v   ?   ii        i  iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_86139214_8   1464 CAGACGCTTTTCAAAAGAAGACATATATGTGGCCAGCAAGCATATTAAAA 1513
                         i    ii  i  v        i   i vi      ii     i  --i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT--GAA 884

  chrX_86139214_8   1514 AAAATACTCAACATCACTAATCTT 1537
                           i  i          ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (157 / 95)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.64 (37 / 14)  


2788 26.78 1.32 1.87  chrX_86145703_86148866     1761  2671 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_86145703_8   1761 GAAAAACATTCCATGGTCATGGAAAGGAAGAATCAATATCCTTTAAATGG 1810
                             i i  i     v       vv      v i     iv  v i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_86145703_8   1811 CTAAAATGCCCAAAGAAATTTATAGATTCAATGCTATCCCTATTAAACTA 1860
                          v v v v      vvi  i  i        i  v        i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_86145703_8   1861 TCATTAACATTCTTCACAGAACTTGAGAAAACT-ATTTTAAAATTCACAT 1909
                         i  vivi v  i  ii     v    v  i-  -  ii         i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chrX_86145703_8   1910 GGAACCAAAAAGAGCCCA-AATAGTCAAGGAATTTTTAAGCAAAAAGAAC 1958
                             viiv  i ii    -     i   iiv v i  i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_86145703_8   1959 AAAGCTGGAGGCATCATGCTACCCAACTTCAAACGATACTACAAGGATAC 2008
                             i      vv   ii  v     i      vvv        i v   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_86145703_8   2009 AGTAACCAAAGCAGCATGGTACTGGTACAAAAACAGACACAAAGACCAAT 2058
                              i   ii   ii         i i  ii i     i v   i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_86145703_8   2059 GGAAGA-AATAGAGAATTTGCAGAAATAAGACCACACACCTACAACCATC 2107
                             v -   v    i i--         iv   i   ii  iiii  vi
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_86145703_8   2108 CAATCTTTGACAAACCTGACAAGACCAAGCAATGGGGAAAGGATTCCCTA 2157
                         ii  i  i     ivv  v        vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_86145703_8   2158 TTCAACAAATGGTGCTGAGAGAACTGGCTAACCATATGCAGAAAATTGAA 2207
                                          i  v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_86145703_8   2208 ACTGGACCCCCTTTTTACACCATATACAAAAAAAATTAACTCAAGATAGA 2257
                         ii        ivii i                ---         i  i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAA---TTAACTCAAAATGGA 496

  chrX_86145703_8   2258 TTAAAGACTTAAATGCTAAACCGAAATCTATAAAAACCCTAGAAGACAAC 2307
                          i ?    i      iv i v v   v        vi i       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_86145703_8   2308 CTAGGCAATAACATTTAGGACATAAGCATAGGCAAAGATTTCAT-GATGA 2356
                         v    ?ivv  iv  iiv   v vi vv       v i    v -   - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_86145703_8   2357 AGACACTAAAAGCAATTGCAACAAAAAGAAAAATTGACAAATGAAATCTA 2406
                         v     i       vvv         ii      v  i    vii ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_86145703_8   2407 ACTAAACTAAAGAGCTTGTGCGTAACAAAAGAAACTATTAACAGATTTAA 2456
                          ii   v v  i i   v  i ivv    i  v     i  v i v v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_86145703_8   2457 CAGGCAACCTATAAAATGGGAGAAAATTTTTGCAAAC--TTCATCCAACA 2504
                         v  i     i i i             v        i-- vi   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_86145703_8   2505 AAAATCTAATGTTCAACATCTATAAGGAGCTAAAATAAATTTACA--TGA 2552
                          iiiv  vi i i  iv  v     i  i  --------i     -- v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACT--------CTTACAACTCA 787

  chrX_86145703_8   2553 ACAATAAAAA-ACAAATTACCCCATT-AAAAATGGGTAAAGGACATAAAC 2600
                          i        -      v    v   -         i      iv i  i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_86145703_8   2601 AGGCACTTTTCAAAGGAAGACATA--ACTGCAGTCAACAATCATATGAAA 2648
                           i  i  i  v  i     i   -- v  -- i   i  v  i      
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAA 885

  chrX_86145703_8   2649 TAAAGCTCAACATTACTGATCAT 2671
                         vi v         i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 1.93 (29 / 15)  


2313 30.98 1.10 0.99  chrX_86154476_86159480.rev     3608  4514 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86154476_8   3608 TGGAAAAACATTCCATGCTTATGAATGGGAACAATCAATATCATTACAAT 3657
                               i i  i     i i   i  v    v v i     ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86154476_8   3658 GGCTATACTGCTCAAAGCAATTTACAGATTCAATGCAATTCTTATTAAAT 3707
                            v     v i    vii  i           i     i i   i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86154476_8   3708 GACCAAGGAAATTCTGTATATAACTAGAAAAATAACT-ATTTTAAAATTT 3756
                         vv   ivvivv  i v ii v  v v  v  i---  -  ii       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_86154476_8   3757 ACATACAACCAAAAATTATCAGAAATGGGCAAGGCAATTCTAAGCAAAAA 3806
                          i  iv  viiv  ivv i vii   i v   ii    ii i i-   i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGA 196

  chrX_86154476_8   3807 AAAGCAAGGCAGGAAGGAC-CATGCTGTCTGAGTTCAAATTATACT---- 3851
                          i i   i iv   -    -  ii  vi ii v      viv    ----
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGA-GGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_86154476_8   3852 -GTTACAGTAACAAAAACAACATGGTACTGGTACAAAAACAGACACATAG 3900
                         - i        iv  i   iii         i i  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_86154476_8   3901 ACCAATGGAACAAAATAAAGAGCCTAGAAATAAGGCCACACACCTACAAC 3950
                          i        i i   vi    i i        iv   i   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_86154476_8   3951 CATCTGAGTTTAGACAAATCTGACAAAAAAAAAAGCAATGAGGAAAGGAC 4000
                           vi   v   v     ivv  v   i vv v--v     i      i i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAAT 393

  chrX_86154476_8   4001 TCCCTAGTTATTAAATGCTGCTAGAATAACTGGCTAACCATATGCAGAAG 4050
                         vvi  vv i vi     v    i i i      v  ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_86154476_8   4051 ATTGAAACAGAACCCCTTTCTTACACCATATATCAAAATCAATTCCAGAT 4100
                          v    iiv i      vi  i          iv     i  i  v i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_86154476_8   4101 GGCCTAAAGACTTAAATGTAA-AGTGAAAAACTATAAAAAGCT-GGAAGA 4148
                           vii ?    i         -  iv    -        vv  -i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGA 542

  chrX_86154476_8   4149 AAAACCTAGGCAATAACATTCTGAATATAGAAACAGGCAACGATTTCATG 4198
                            - v    ?ivv  iv   vvi iv v iivi      i i    v i
  L1M4_orf2#LINE/    543 AAA-CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_86154476_8   4199 ACAAAGACACCAAAAGCAATTGCAGCAAAATTAATAATTGACAAATGAAA 4248
                         ivv v             vvv   i     vv  v   v  i    vii 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_86154476_8   4249 TTTGATTAAACTAAAGTGCTTCTGAACAGCAAAAGAAACTATCAACAGAG 4298
                         i  v  i   v v  ivi   i  vi vv    i  v        v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_86154476_8   4299 AGAAAAGACAACCTACACAATGGGA-AAAATATTTATAAACTATACATCT 4347
                         v            i   v       -         ii   ii   i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_86154476_8   4348 GACAAAGATCTAATATCCAGCATCTGTAAGGAACTTAAACAAATTTACAA 4397
                           i  i iv  vi       v  v i   i     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_86154476_8   4398 GATAAAAACAAACAACTCCATTAAAAAGAGGGCAAATGACATTAACAGAC 4447
                         v v   i     i   i v   ?    iv       v  iv v  i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_86154476_8   4448 ACTTTTAAAAAGCAGACATACAGGCATTCAACAAGCACACGAAAAATTGT 4497
                          i  i vv    v   i     iiiivi   i       i     iv  i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_86154476_8   4498 GCAATATCACTGATCAT 4514
                         v   i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (164 / 113)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


2152 27.73 3.01 0.68  chrX_86171217_86172933      505  1236 (481)    L1M4_orf2#LINE/L1      160   908 (0)  

  chrX_86171217_8    505 AAAGAGCCCA-AATAGCAAAGACAATCCAAAGCAAAAAGAACAAAGCTGG 553
                           i ii    -      v  i      ivi iv  i          i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_86171217_8    554 AGGCATCATGCTACCCAAATTCAAACTATACTACAAGGCTGCAGTAACCT 603
                            vv   ii  v     v      viv        i   i      i v
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_86171217_8    604 AAACAGCATGGTACTGATACAAAAACAGACATGCAGACCAATGGAACAGA 653
                          i    ii        ii i  ii i      ii   i        i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_86171217_8    654 AAGGAGAACTAAGGAATAATACTGCACATCTACAACCATCTGATCTTCGA 703
                          vv    iiiv  i     vv iii    i  iiii  vi    i     
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_86171217_8    704 CAAATATGACAAAAACAAGCAATGGGGAAAGGGTTCCCTATTTAATAAGT 753
                            ivi  v   i v  vv            ii vvi  v  i  i  i 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_86171217_8    754 GGTGCTGGGAGAACTGGCTAGCCATATGAAGAACACTGAAACTGGACCCC 803
                                   v      v  ?   i   v i  v v    ii        
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_86171217_8    804 TTCCTTACACCTTATACAAAAATTAACTCAAA-TGGGTGAAAGAGTTAAA 852
                          v   i     v                    -   i v ?   vi    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_86171217_8    853 TGTAAAACCCAAAACTATAAAAGCCCTAGAAGAAAATCTAGGCA-ATATC 901
                              i v i            vi i          iv    ?i- v   
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_86171217_8    902 ATTCAGGACATAATCG--TCGGCAAAGATTTCAT-GATCAAAATGCCAAA 948
                         -   iv   v -- v -- v     v i    v -   - vi ii     
  L1M4_orf2#LINE/    560 -TTCGTGACCT--TGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAA 605

  chrX_86171217_8    949 AGCACTTACAACAAAGTCAAAAATTGACAACTGGGATCTAAATAAACCAA 998
                              vvi       ivv      v  i  v v   ii v vi   viv 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_86171217_8    999 AGAGCTTCTGCACAGCAAAAGGAGCTATCATCAGAGCAAACAGATAACCT 1048
                          i i   i  ii vv    i ivi      vv i  ii  v   i    i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_86171217_8   1049 ATGGAATGGGAGAAAAACTTTGCAATCTATCCATCTGACCAAGGTCTAAT 1098
                          ii             vv       vii  vi      iv i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_86171217_8   1099 TTTCAGAATCTACAAGGAACTTAAACAAATTTAGAAGAAAAAAATCGAAC 1148
                         v i      v  i  i     ivv    v iv v  v     i - i  i
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAAT 804

  chrX_86171217_8   1149 AAC---ATT-AAAATTGGACACAGAACATAAAAAGACACTTCTCAAAAGA 1194
                            ---   -    v   i  v  i iv i  v     i     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_86171217_8   1195 AAACATTTATGTGGC------------AAAAAAAAGCTCAACATCATTGA 1232
                          i i  vi vi    ------------i    i v           ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_86171217_8   1233 TCAT 1236
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.38 (116 / 84)
Gap_init rate = 0.02 (12 / 749), avg. gap size = 2.25 (27 / 12)  


1301 23.06 2.94 6.50  chrX_86176955_86183235        1   477 (5804)    L1M4_orf2#LINE/L1      153   612 (296)  

  chrX_86176955_8      1 GAAAGGCAAAAGACCCAATAATAGCCAGCATATCTTTGAA---GGAGAAC 47
                             v    ii      i-        iv i vii     --- i     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAG-AATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_86176955_8     48 AAATTTGGAGGACTGAGACTACCTAAAATAAAGACTTACAATAAAGCAAC 97
                            v          v v   v  i  vv v  i      v i     v  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_86176955_8     98 AGTAATCA-GAGAGTGTGATATTGACAAAAGCATAGACA----GATCTTA 142
                                 -  v      i  i  i  v   v       ----    -- 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC--A 299

  chrX_86176955_8    143 TTGGAAACAAATAGTGAGGCTAGAAAGATATGCATACAAATATAATCAAT 192
                         v     vvi   v v   v i     v v iv      vv   ii     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_86176955_8    193 TTAGCTTTGACAAGGGAACAAAGACAATGCCATGGAGAAAATATAGTCTT 242
                          v vi  i        vi v     v  v v    i    iv        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_86176955_8    243 TTCAACAAATAATGTTAGAACAACTGGACATCCACATACAAAAATAATGA 292
                                   ii  i i i         i ?      i     i-     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AATGA 448

  chrX_86176955_8    293 AAGTAGAGGCAGACATTACACCTTTCATAAAAATTAACTAAAAGTAGTCT 342
                          iv i  vv vv  v i     v vi i           v   i i vii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_86176955_8    343 ACCGACCTAAATGTAAACATAAATCTCCCAGATGTAAACATAAATGCAAA 392
                          ?v             i------------  v --------------   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAG------------AGCT--------------AAA 522

  chrX_86176955_8    393 AC-ATAAATCTCTCAGAAGATAAAATAGGAAACAAATTTAAGTGACCTTG 441
                           -     v    i      v  v     ?i-i    i vv         
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTG 571

  chrX_86176955_8    442 ACTT---TAATGATTA--TATATATGATATCAAGGGCACAA 477
                         iv  ---i    i  v--  v      i i   ii      
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

Transitions / transversions = 0.98 (53 / 54)
Gap_init rate = 0.03 (12 / 460), avg. gap size = 3.75 (45 / 12)  

3194 26.98 0.66 0.66  chrX_86176955_86183235     4881  5788 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86176955_8   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4930
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86176955_8   4931 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGT 4980
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86176955_8   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_86176955_8   5029 TATGGAACCAAAAAAGAGCCCGCATCAGCAAGTGAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  viv   ivv    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_86176955_8   5079 AACAAAGCTGGAGGCAC-CACACTACCTGACTTCAAACTATACTACAAGG 5127
                                i      -  -      v  ii i      viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_86176955_8   5128 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5177
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_86176955_8   5178 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5225
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_86176955_8   5226 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5275
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_86176955_8   5276 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5325
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_86176955_8   5326 CGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5375
                         i   ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_86176955_8   5376 ATTAAAGACTTAAACGTTAGACTTAAAACCATAAAAACCCTAGAAGAAAA 5425
                           i ?    i    i  v   vi      i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_86176955_8   5426 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5475
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_86176955_8   5476 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGGATCTA 5525
                         vi            vvi          vv     v  i   iv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_86176955_8   5526 ATTAAA-TTAAAGAGCTTCTGCACAGCAAAAAAAACTACCATCAGAGTGA 5574
                           i   -     i -   i  ii vv    ii v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_86176955_8   5575 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5624
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_86176955_8   5625 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5674
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_86176955_8   5675 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5724
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_86176955_8   5725 TCTCAGAAGAAGACATTTATGCAGCCAAAAAACATATGAAAAAATGCTCA 5774
                             vi       i  vi viii     v  i  i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_86176955_8   5775 TCATCACTGGCCAT 5788
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


2860 27.21 2.24 0.56  chrX_86191381_86195434     2669  3561 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86191381_8   2669 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 2718
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86191381_8   2719 GGCCATACTGCCCAAAGTAAT--ATAGATTCAATGCTACTCCCATGAAGC 2766
                            v     v      v i  -- i        i  v ii  i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86191381_8   2767 TTCCCTTTACTTACTTCACAGAA--TGA-AAACAAAACTTTAAATTTCAT 2813
                          i  vvi i i vi  ii     --   -  i vi v i v     -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT-CAT 149

  chrX_86191381_8   2814 ATGGAACCAAAAAAGAGTCCTCATAGCCAAGACAATCCTAAGCAAAAAGA 2863
                               viiv  ii  vi vvv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_86191381_8   2864 ACAAAGCTGGAGGCATCATGCTGCCCGACTTCAAACTATACTACAAGGCT 2913
                               i      vv   ii  v   i i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_86191381_8   2914 AGAGTAATGAAAACATCATGGTACTGGTACCAAAACAGATATATAGACCA 2963
                          v      v  i   vii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_86191381_8   2964 AAGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 3013
                          v    i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_86191381_8   3014 TGATCTTTGACAAACTTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 3063
                             i  i     ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_86191381_8   3064 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCTATATGGAGAAAACTGAA 3113
                           i  i        i     v      v  ? i i   v i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_86191381_8   3114 ACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 3163
                         ii         v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_86191381_8   3164 AAGACTTTAACATAAAACCCAAAACCATAAAAACCCTAGAAGAAATCCTA 3213
                         ?    i v  ii   i v i     i      vi i         v v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_86191381_8   3214 GGC---AATGCCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 3260
                           ?---   -- -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    550 GGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_86191381_8   3261 AACACCAAAAGCAATAGCAACAAAACCCAAAATTGACAAATGGCATCTAA 3310
                         i            vv          vvv     v  i    v v ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_86191381_8   3311 TTAACCTAAAGAGCTTCTGCACAGCAAATGAAACTACCATCAGAGTGAAT 3360
                          i  vv v  i i   i  ii vv    v  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_86191381_8   3361 AGGTAGCCTACAGAATGGGAGAAAATTTTTGCAATCTATCCACCTGACAA 3410
                           ii i  i                 v       vii  vi i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_86191381_8   3411 AATACTAATATCCAGAATCTACAAGCAACTTAAACAAACTTA-TAAGAAA 3459
                         iiv   vi          v  i  iv    ivv    -  i -   v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAA 795

  chrX_86191381_8   3460 AAAA-----AAC---ATCAAAAAGTGGGCAAAAGGTATGAACAGACACTT 3501
                           i -----   ---  i?    i        i i v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_86191381_8   3502 TTCAAAAGAAGACATTTATGCAGCCAGCAA--ACATAAAAAGA-GCTCAT 3548
                         i  v        i  vi viii    ii  --    i      -     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_86191381_8   3549 CATCACTGGTCAT 3561
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (138 / 101)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.92 (25 / 13)  


2868 26.87 2.53 2.53  chrX_86196281_86200749     3069  3976 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86196281_8   3069 TGGAAAGGTATTCCACATTCACCGATTGGAAGAATCAATATTGTTAAAAT 3118
                                i   i   ii    iv          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86196281_8   3119 GTCTGTACTACCCAAAACATTCTACAGATTCAATGCAATTTTTACCAAAT 3168
                          v vi    v      viiv             i     iii  i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86196281_8   3169 TACCA-TGGCATTCTTCACAGAAACT---------ATTGTAAAATTAATA 3208
                          v   -iv  v  i  ii      i ---------  iv       v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_86196281_8   3209 TGGAATCACAAAAGACCCAGAGTAGCTGAAGCTATCCTGAGCAAAAAGAA 3258
                              vii   ii        i    ii  i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_86196281_8   3259 CAAAACTGGAGGAATCACATTACCTGACTTCAAATTATAATGCAGAGCTA 3308
                             ii       v     i v  ii i      viv  v i  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_86196281_8   3309 TAGTAGGCAAAATAGCATGGTGGTGGCATAAAAACAGACACATGAATCAA 3358
                         i    iv   i i  ii    iv        ii i     i  ii     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_86196281_8   3359 TGGAACAGAGCAGAGAACCCAGTAATAAAGTTATACATCTACATTCAACT 3408
                              i   iiv    ii    v      vii      i  iiv    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_86196281_8   3409 CATTTTCAACAAAAATGCCAAGAATGTACATTGGGGAAAGGATAGTCTCT 3458
                         v      i    iii        vii v  v         i       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_86196281_8   3459 TCAAAATATTGTGCTGGGAAAACTGAATATTCATAGGTGGAAAACTGAAT 3508
                             v v  v         v     i   ?i  -----------------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCA----------------- 433

  chrX_86196281_8   3509 ATTCATAGGCAGAAAAATGACACTAAATTCCTGTATCTCACCATATACAA 3558
                         ---   --   i  i     vii ii ii   iiv  v            
  L1M4_orf2#LINE/    434 ---CAT--GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_86196281_8   3559 ATATTAAATCAAAATGATTTAAAGACTTAAATCTAAGACCTCAAACTACG 3608
                          v     v        iv i ?    i     v     v  v      ii
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_86196281_8   3609 AAACTACTGAAAAAAAAT-TGGGA--AACTCTTTAAGAGATTAAATTGAA 3655
                              vi ii  i    i- i  ?--  v    iiv  vv  iii  iii
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_86196281_8   3656 CAATAATTTCTTGAAAAAAACACCCACAAGCACAGGCAACCAAAGCAAAA 3705
                             ii      ii v vi     v -       i     v    v    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAA-AAGCACAAGCAACAAAAGAAAAA 627

  chrX_86196281_8   3706 ATGTACAAATGGAAGCACATTAAGTTCAAAAGC------ACAGCAAAGGA 3749
                           iv i    v i viv   i  iv i    i ------i vv       
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_86196281_8   3750 CAAAGTGAACAAAGTGTAGAGACAACCCACAGAATGGGAGAAAATATCTT 3799
                           vvi v  v      v i                            i v
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_86196281_8   3800 CAAACTATCTTCCTGGCAAGGAATTAAAAACCAAAAAATATAAGGAGCTA 3849
                             ii  v vi   ii    i i viv v   i  v      i  i  v
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_86196281_8   3850 ACAAAACTC--TAGGAGTAAGTATAATAATCTGTTTTAAAAGTGGTAAAA 3897
                         vi v     --  iv iv   vvv     i iiv  ?    i   vv   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_86196281_8   3898 ATATCTGAGTAAACATTTCTCAACAGAAGACATACAAATGGCAAACAGGC 3947
                         iv  i   i  i         v v      i           v  i i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_86196281_8   3948 A--TGTAAATCTGCTCAGCATTATTGATCAT 3976
                          --  v   vv      i   i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (149 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 4.60 (46 / 10)  


 888 29.25 10.69 3.93  chrX_86202138_86203757.rev      494  1129 (491)    L1M4_orf2#LINE/L1      230   908 (0)  

  chrX_86202138_8    494 TCAGGATATAATATAAAGTTACAATAATTAAGA---------------AT 528
                            ii iv  v  i    i    i    i    ---------------  
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_86202138_8    529 ATGGATGTGCAATTAGACCAATAAAATGGAAT---------AGAAAC--- 566
                          v    ivi  vv    i    ii   i    ---------     i---
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_86202138_8    567 CTTAGATATTTTAAAAAT--ATTTATTTATGACATGCATGACCCTGAAG- 613
                          ii v i    -- vii --   v    vi    v vi  --  --   -
  L1M4_orf2#LINE/    330 CCCATACATTT--ATGGTCAATTGATTTTCGACAAGGGTG--CC--AAGA 373

  chrX_86202138_8    614 ---TTCAATGAAGAAAAAATATAATCTCCAATTAATATTATTGAGTCACT 660
                         ---       ii    i    vvv i i   iv   iv ii  i v  vi
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_86202138_8    661 TGGATATTAATATGCAAA----TAA---TGGATCCTGATTTC------TA 697
                               ?iv i       ---- i ---    i  iv ii  ------  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_86202138_8    698 TATGACA-TTATGCACAAAGTG-ATTATAGGTCACAATGTGAGGAATAAA 745
                           ii v -   -i v    i  -  i ?  ii vv     i  iiv    
  L1M4_orf2#LINE/    474 TACAAAAATTA-ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_86202138_8    746 AGGA-AGAATATCCAGGAGAAAACAT----TTATACCTTTATGAATTTAG 790
                          vv - i  iviii  i         ----v  v i   ii   vi  i 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_86202138_8    791 A--ATGTGAAAATATTTTAAAAATGGAACACAAAAAACACTA--AATGTA 836
                         i-- v ii vii v i   i v   --    v    i   v --  iiv 
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATG--ACACCAAAAGCACAAGCAACAAA 620

  chrX_86202138_8    837 AAGAAAAATATATGCATCTACATATTGAAACTAGACTTCATTAAAATTAA 886
                          ii       v  --------------   i i        i        
  L1M4_orf2#LINE/    621 AGAAAAAATAGAT--------------AAATTGGACTTCATCAAAATTAA 656

  chrX_86202138_8    887 AGA--TATATGTTTACCATTGGACATTA---AGAGAGTATAAAAACAAGT 931
                          i -- v i  i  --  vv     i  ---   i   iv   i    vi
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_86202138_8    932 TCTAGTGTGGGA---AATATTTTCAAGAAACATATCTGTAAAAGGACTC- 977
                         ivi  vi     ---       v   ivv i       vv  i     i-
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_86202138_8    978 -ATTCATAATACATAAAGAACTTCCACAAATCCATTAGTAAAAGATAGAC 1026
                         -  i  v    i          iii    v  v  v vv      i i i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_86202138_8   1027 AACTCAGT-GATAAATGAGTAAAACTCTGGAATAGTTAATTCTCAAAAGA 1075
                            i  i -? v     i i   ivvi v      vi v     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_86202138_8   1076 GGATGTTTACATGGCTAATGAATATATGTAAAGATGCTTAACATTATTGG 1125
                         i   i vi v     i   i ii i   v         i     i ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_86202138_8   1126 TCGT 1129
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.69 (115 / 68)
Gap_init rate = 0.04 (26 / 679), avg. gap size = 3.58 (93 / 26)  


2213 24.63 3.37 7.79  chrX_86212134_86215586.rev     2013  2962 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86212134_8   2013 TGGAAAAACATGTTGTGTTTGTGAATAGGAACAATCAATATTATTAAAAT 2062
                               i i  viii    ii  i  v    v v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86212134_8   2063 GGCCATACTATCCAAAACAATTTGCAGATTCAATGCTATCATTATCAAAT 2112
                            v     vi     vii  i i         i  v   vi       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86212134_8   2113 TACCAATGACATTTTTCACACAATTAGAAAAATATTATTTGAAAATTCAT 2162
                          v   iivi v     ii  v  v v  v  ii- v  iiv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_86212134_8   2163 ATGGAA--GCAAAAAAAGCCCA-AGTAGCCAAGGCAACCCTATACACACA 2209
                               --    iii --    - i       ii   i i iv v viv 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_86212134_8   2210 CACACACACATACACACACACACACACACACACACATCACAAAACTGGAG 2259
                         v ------------------------------------     ii     
  L1M4_orf2#LINE/    198 GA------------------------------------ACAAAGTTGGAG 211

  chrX_86212134_8   2260 GCATTATATTAACTGGGTTCAATCTATACTTCTATACTACAAGGCTATAG 2309
                          vv i i i vv iiiv     --- -    ----       i    i  
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAA---A-ACTT----ACTACAAAGCTACAG 253

  chrX_86212134_8   2310 TAACCAAAACAATCATTGTAATGGTATAAAACCAGACACAGACATATAGA 2359
                            i   i   i -i v   v   i    ii------ i           
  L1M4_orf2#LINE/    254 TAATCAAGACAGT-GTGGTACTGGCATAAGG------ATAGACATATAGA 296

  chrX_86212134_8   2360 CCAATGAAACAGAATAGAGAGCTCAGAAACAAAGCCTCTTACCTACAACC 2409
                         i     i  i     v     ii      i   v  vivi ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_86212134_8   2410 ATCTGATCTTCAACAAAATTAACAAAAAGAAGCAATGGGGAAAGGATTAT 2459
                          vi    i   i    iiv iv   i vv vv            i  vi 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_86212134_8   2460 TTATTTATTAAATGGTGCTGGAATAACTGGCTAGCCATATGCAGAAGATT 2509
                         i v  i vi            i i      v  ?   i     i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_86212134_8   2510 TAAACTGGATTCCTTATTTTCATCATATACAAAAATTAACTCAAGAGGAA 2559
                         v  ii    ii   vvi iv  i                     i v i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_86212134_8   2560 TTA-AAACTT---TG------------CTATGAAAACTCT-GGAAGATAA 2592
                          i - i  i ---  ------------    -        -i     v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chrX_86212134_8   2593 CCTGGG---AAATACCATTTTG-GACATAGAAGGT--AGCAAAGATTTCA 2636
                          v i  ---    ----i  i -   v v --   --i    v i    v
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT----CTTCGTGACCTTG--GGTTAGGCAATGGTTTCT 589

  chrX_86212134_8   2637 T-GATGAAGATACCAAAAATCAGTTAAAATAAGAACAAAAGAAAT-GACA 2684
                          -   - v  i       i-  v---  ii  v  v i  i    -  i 
  L1M4_orf2#LINE/    590 TAGAT-ATGACACCAAAAG-CAC---AAGCAACAAAAGAAAAAATAGATA 634

  chrX_86212134_8   2685 AAAAGGACCTAATTAAA--CAAAAGATCTTTTGCACAGCAAAAGAAACTA 2732
                           vv    i v  i   --i    i--      ii vv    i  v    
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTA 682

  chrX_86212134_8   2733 TCAATAGAGTAAACAGATAATCTACAGAATGGGAGAAAATATTTGCAAAG 2782
                             v i   i  v   i  i i                          v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_86212134_8   2783 TAAGCATCTGACAAAGGTCTAATATTCAGCATCTGTAAGGAACTTAAACA 2832
                         i vii      i  i  v  vi   i   v  v i   i     ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_86212134_8   2833 ACTTTACAAAAAGCAAACAAACAAACAATCCCATGAAAAACTGGGCAAAG 2882
                            ---   v  -i   v i     i  i  v  v?    v         
  L1M4_orf2#LINE/    783 ACT---CAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_86212134_8   2883 AACATGAACAAACACTTTTCAAAAGAAGACATA--AATGCAGCCAAAAAG 2930
                         i iv    i i   i  i  v        i   --    --     v   
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG--GCCAATAAG 876

  chrX_86212134_8   2931 CATAGGAAAAAATGCTCAACATCATCAATCAT 2962
                           i v     i             ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (145 / 87)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 3.42 (106 / 31)  


 990 20.48 3.61 6.93  chrX_86256174_86258395      500   831 (1391)    L1M4_orf2#LINE/L1       18   338 (570)  

  chrX_86256174_8    500 TTCACGTACTGGAAGACTTAATATTGTCAAGATGTCAGCACTACTCAAAA 549
                             i v i                  i      v  ii   v i    v
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_86256174_8    550 TGGTGTACAGATTCAATGCAAACTCTATTAATGTCCAATGACATTATTTT 599
                           i v           i    v i    i  vi   v - viiiiv    
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA-GCTGCCTTTTT 116

  chrX_86256174_8    600 TG-AGAAATAGA-AAACCCATTTTAAAATTTATATGGAATAT-CAAGGGA 646
                           -      v  -  i iv  ii       i        -  -       
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA-ATGCAAGGGA 165

  chrX_86256174_8    647 ACCTAAATGGGCAAAAAAAATT---AAATGACAAACAAAGTTGGAGGGTT 693
                         v  vi   i v     v  vi ---   v  vi              ii 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_86256174_8    694 CACACTTCCTAATTTCAAAACTCACTACTACTACTATGTTGCAATAATCA 743
                                  i            ------      v v i i  i      
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACT------TACTACAAAGCTACAGTAATCA 259

  chrX_86256174_8    744 A-----TGTAATACCGGCATTACAGTATTG-CATTGTACAGTCCAATACA 787
                          -----   ii   i     - -  v  v -   -----------   v 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCAT-A-AGGATAGACAT-----------ATAGA 296

  chrX_86256174_8    788 TGAATAAAATATAATAGAGAGCTAAGAAAAAAAAACTCATATAT 831
                          v   ii    v   v     iiv     v   -- i    i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACAT 338

Transitions / transversions = 1.34 (39 / 29)
Gap_init rate = 0.04 (13 / 321), avg. gap size = 2.69 (35 / 13)  

1770 22.01 8.73 0.76  chrX_86256174_86258395     1204  1730 (492)    L1M4_orf2#LINE/L1      340   908 (0)  

  chrX_86256174_8   1204 TATGGTCATATAATTTTC-ACGAGTATGTCA------TTCAAGGGGAAAA 1246
                                 vv i      -  i  vi  i  ------     v   i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_86256174_8   1247 GGGATAGTTTCTCCAACAAAT--TGCTATTTAAAAACTGGATTTATATAT 1294
                          i-     i i i        --    iv--i v        v?vi i  
  L1M4_orf2#LINE/    390 GA-ATAGTCTTTTCAACAAATGGTGCTGG--GACAACTGGATAKCCACAT 436

  chrX_86256174_8   1295 GCAATAGAATAAAATTTGACCCTTACCTCAGGTCACGTACAAAAGTTAAG 1344
                             v     i  i  v     i       vii  ii       i    v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_86256174_8   1345 TCAATATAAATCAAATGCTTAAACATT-GAACTAAAACTAAAGAACTTTT 1393
                             v  ii    ? vi i    ii v-  i         v i    i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_86256174_8   1394 AGAAGAGAGGTTAAGAG-AA--CATCATAACATTGGATTTAGCAAGGATT 1440
                               i ivv  i ? -  -- v  i i  v    i  vi    v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_86256174_8   1441 TCTTAG----GAAACTAG--------GTTACAATG------ATAGACAAA 1472
                               ----  v  i i-------- iv    vi------     i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_86256174_8   1473 ATGGACTTCATCAAAGTTAAAAA---TTGTGTATCAAACAGA-ACTATAA 1518
                         v              i       ---     iv     -i  -     v 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA-GGACACTATCA 685

  chrX_86256174_8   1519 ATAGAGTGAAAAGACAACCCAAAATATGGGAGAAAATATTTGCTAATCAT 1568
                          v i                 v iv                  v      
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_86256174_8   1569 ATATCTGATATAGGA-TTATATCTATAATATATAAAGAGCTCCTATAACT 1617
                                   vi   -  i    i v            i   i  i    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_86256174_8   1618 CAACAAGCAAAAC-CAAACAACTCAG-------ATAG--AACAGACTTGA 1657
                            i  vv    v-    i   i  i-------  i --  vi  i    
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_86256174_8   1658 ATAGACATTTCTACAAATAAGATATAGGAATCACTGATAAGCACATGAAA 1707
                                     v    v        vi   vi ii              
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_86256174_8   1708 AGGTTTTGAGCATCGGCAATCAG 1730
                           i vi v i    i????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (69 / 44)
Gap_init rate = 0.03 (18 / 569), avg. gap size = 2.78 (50 / 18)  


2339 27.52 2.17 3.79  chrX_86274818_86277109.rev      879  1801 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86274818_8    879 TGAAAAAATATTTCATGCTCATCAATTAGAGGAATCAATATTGTTAAAAT 928
                           i   i    ii    i    vi   i  i  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86274818_8    929 AGCCATACTGCCCAAAGCAATCTAGAAATGCAATGCTATTTCCATCAAAA 978
                         i  v     v      vii     v i  v   i  v  ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86274818_8    979 TAACAA-TGTAATTTTTTATATAATTAGAAAAAAAACT-ATTCTAAAATT 1026
                          vv  i-  iv-      ii v  v v  v  i---  -  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chrX_86274818_8   1027 TGTATGGAA-CACAAAAGACCCTGACTAATCAAAATAATTGTAAGCAAAA 1075
                         ii       -ii   ii     v  v  ii     i   iv i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_86274818_8   1076 AGAACAAAGGTGGAAATATCACATTACCTGACTTCAAACTATACTATCAT 1125
                                  v    iivv     i v  ii i      viv     iv v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_86274818_8   1126 GATATAGTAACTAAAACAGCATGGTACTGATACAAAAAAAAAGATGCATA 1175
                          v  i     ii  i    ii        ii i  ii v i v  --   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT--ATA 294

  chrX_86274818_8   1176 GACCAATAAAACAGAATAGAGATCCCCAAAATAAAATCATACAACTA-AG 1224
                           i    ii  i     v    vi  vi       vi      vi  -i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_86274818_8   1225 CCATCTGATTTTTGACAAAGTTGACTGAAAAAGCAATAGATAAAGGAATC 1274
                         i  vi       i     i v  v ---  i v  ---------------
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCC---AAGACCA--------------- 376

  chrX_86274818_8   1275 TGTGTACTCCAATGGGTAAAGGACCCTCTATTTATACAATAATGGTGCTG 1324
                         ------- i       v    i ivv   v  i -    --         
  L1M4_orf2#LINE/    377 -------TTCAATGGGGAAAGAATAGTCTTTTCA-ACAA--ATGGTGCTG 416

  chrX_86274818_8   1325 AGATAGTTGGTTAGCCATATGCGGAAGAATGAAAACTTGACCACTACCCT 1374
                         i  i ii   v  ?   i    ii         i-i v    v     ii
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAG-TTGGACCCCTACCTC 465

  chrX_86274818_8   1375 TCACCATACACAAAAATTAATT-AAAATTGATTAAAAATTTACCTATAAG 1423
                         v       i           i -     v   i ? i ii  vv i    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_86274818_8   1424 ACATCAGAATATAAGAATACTAGAAGAAAACTTAGG---AAACATT---G 1467
                          vv v i v     i v vi           v    ---   iv  --- 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_86274818_8   1468 GCTTTGAA--AGAGAATTATGACT-AAAT-TG-TA--AAAAGCAATTGCA 1510
                         i i   ii--  iv   vi vv  - i  -  -i --       vvv   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_86274818_8   1511 TCAGAAACAAAACTCAACAAGTGAGACCTAATTCAACTAAAGAGCTTCTG 1560
                         v  i  iv    v vi i  i vi   i v  iv  v v  i i   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_86274818_8   1561 CACAGCAAAATAAACTAGCAACAGCATAAACAGACAACCTACAGACTGGG 1610
                         ii vv    iv v    v   v ivi i  v        i     v    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_86274818_8   1611 AGAATATATTCACAAACTATATATTAGACAAAGGTCTAATATCCAGAATC 1660
                             v     ii    ii      iv  i  i  v  vi          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_86274818_8   1661 CATAAGAAACTTATATAATTCAGCAAGCAAAAAGCAAATAACCCAATTAA 1710
                         i    ii    iv  i  i   ii  vv    ii              ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_86274818_8   1711 ACAGCTGGCAAAAGACATGAACAGACACTACCCAAAATAATTTATACAAG 1760
                          v iiv      i  iv    i     i v i v   v  vv       i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_86274818_8   1761 TGGCCAATAA--ACATGAAAAACTGCTCCACATCAATGATCAT 1801
                                   --         iv     v      ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (150 / 101)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.62 (55 / 21)  


2594 26.21 2.30 2.96  chrX_86307455_86309603.rev      747  1658 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_86307455_8    747 GAAAAACACTTTGCACATTTATGGATAATAAGACTCAATTTTGTTAAAAT 796
                             i i -- iv  ii  i      viv      i   v       i  
  L1M4_orf2#LINE/      3 GAAAGATA--TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86307455_8    797 AGCCATACTGCCCGAAGTAATTTGCAAATTCAATGCTATTTCTATCAAAC 846
                         i  v     v   i  v i  i i  i      i  v  ii        -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chrX_86307455_8    847 TACCCCA--TGACATTCTTTGCAGAATTAGAAAAAAATGATTTTTAAAAT 894
                         - i    --  v -  i         v v  v  iv-    ii -     
  L1M4_orf2#LINE/    100 -ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGATCCT-AAAAT 145

  chrX_86307455_8    895 TCACGTGGA---GCCCAAAGAGAGCTTGAATTGCCAAAGCAATTCTGAAC 941
                            ii    ---  ---   i  v iv    v      i    ii    v
  L1M4_orf2#LINE/    146 TCATATGGAAATGC---AAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_86307455_8    942 AAAAGGAAAGGAGCTGGAGGTGTCGTGTTACCCAACATCAAACTATACTA 991
                           i i   vii  i      vv  iiii v     iv     viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_86307455_8    992 CAATGTTATTGCAAACAAAACAACATACATGGTATTTGGTTTAAAAA--G 1039
                            v i  iv i  v   i   iii ----    i -  iv   ii -- 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGT----GGTACT-GGCATAAGGATAG 287

  chrX_86307455_8   1040 ACACATAAACCAAGGGAACAGAATAGAGAGTCCAGAAATAATGCCACATA 1089
                            i   i i   v    i     v                vv   i i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_86307455_8   1090 CCTACAACCATCTGATAGTCAAAAAGGCTGACAAATAAAAAGCAATAGGA 1139
                         ii  iiii  vi    vv  i v    v  v   i- vv vv    i  i
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGG 386

  chrX_86307455_8   1140 AGAGGAAT-TTCTATTTTATAAATGGTGCTGGAATAACTGGCTAGCC-TA 1187
                          i  -   -v   v  iv i            i i      v  ?  -i 
  L1M4_orf2#LINE/    387 AAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_86307455_8   1188 TGCAGAAGATTGAAACTGGACTCCTTCCTTACACTATGTACAAAAATTAA 1237
                             i    v    ii     i   v   i    i  i            
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_86307455_8   1238 CCCAATTTGGATTGAAGATCTAAGTGTAAAACCTAAAACTATGAAGAAAC 1287
                          i   vv     ii?   i    i     i v          i  ---  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA---AC 532

  chrX_86307455_8   1288 T----GAAAAATAACCTAGGCA-ATACCATTCCGGACATAGGACCTGACA 1332
                          ----   i  -   v    ?i- v i -   vv   v v  iiiv i  
  L1M4_orf2#LINE/    533 TCTTAGAAGAA-AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chrX_86307455_8   1333 AACATTTTAT-GATGATCATTCCAAAAGCAATTGCAAAAACAACAAAAAT 1381
                          vvi   iv -   -  v iv         vvv    v  v iv      
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_86307455_8   1382 TGAAAAATGAAACTTAATTAAACTAGAGAGCTTCCACACAGCAAAATAAA 1431
                         v  v    vii    v  i   v vi i i   iiiii vv    iv v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_86307455_8   1432 CTATCAAGGGAGTAAACAGACAACCTAAAGAATGGGAGAATATACTTGTA 1481
                                 ii   i  v        i v            v   i   i 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_86307455_8   1482 AACTATGCATCTGACAAAGGTCTAATACCCAGAATACATAAGGAACTTAA 1531
                           ii  ii      i  i  v  vi  i        i    i     ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_86307455_8   1532 ACAATTCAACAAGCAAAA-----ACAGCCCCATTAAAAAGTGGGCAAAAC 1576
                             i    i  vv    ----- i i   v   ?    i        iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_86307455_8   1577 ATATGAACAGACACTACTCAAAACCAAAAAGATATACATATGGCAAATAA 1626
                           v    i     i v   ---- v  i          v     v     
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTC----CAAAGAAGATATACAAATGGCCAATAA 875

  chrX_86307455_8   1627 GCATATCAAAA-ATGCTCAACATCACTAATCAT 1658
                            i  v    -             ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 1.92 (48 / 25)  


2890 28.67 0.66 0.55  chrX_86315007_86320674     4269  5175 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86315007_8   4269 TGGGAAAACATTCCATGCTCATGGATAGGAATAATCAATATCATGAAAAT 4318
                            i  i i  i     i        v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86315007_8   4319 GGCCATACTGCCCAAAGTAATTTGTAGATTCAATGCTATCCCCATCAAGC 4368
                            v     v      v i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86315007_8   4369 TAC-AACTGACTGTCTTCACTGAATTAGAAAAAACT-ACTTTAAATTTCA 4416
                          v - i   v  - i  ii v   v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_86315007_8   4417 TATGGAACCAAAAAAGAGCATGCATTGCCAAGACAATCCTAAGCAAAGAG 4466
                                viiv  ii  v vv v  v     i      i i iv  ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_86315007_8   4467 AACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTACACTACAAGGC 4516
                                i     ivv   ii  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_86315007_8   4517 TACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4566
                            i    i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_86315007_8   4567 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACTTCTACAACCAT 4616
                                i    iv   ivii         vv   i  v i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_86315007_8   4617 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGTATTCCCT 4666
                         i    i  i     ivv  v   i v  vv            v  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_86315007_8   4667 ATTTAATAAACAGTGTTGGGAAAATAGGCTAGCCATATGCAGAAAACTGA 4716
                         v  i  i   ii   i     v  iv  v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_86315007_8   4717 AACTGGACCCCTTTCTTACACCTTATAGGTAAATTATCTCAAGATGGATT 4766
                          ii         vi  i     v    viv      v     i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_86315007_8   4767 ATAGACTTAAACTTCAGACCTAAAATCATAAAAACTGTAGAAGAAAGCCT 4816
                          ?    i    iv v   v      ii      viiv         i v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_86315007_8   4817 AGGC---AATGCCATTCAGGACCTAGGCATGGGCAAAAACTTCATGACTA 4863
                            ?---   -- -   iv     v  vv i     viii   v iiv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_86315007_8   4864 AAACATCAAAAGCAATTGCAACAAAGGCCAAAATTGACAAATGAGATCTA 4913
                         vi   i        vvv        i vv     v  i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_86315007_8   4914 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAAAGTGAA 4963
                           i   v v  i i   i  ii vv    i  v       vv        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_86315007_8   4964 CAG-TAACCTACAGAATGGGAGAAAAATTTTGCAATCTATCCATCTGACA 5012
                         v  -i    i                vv       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_86315007_8   5013 AAGGGCTAATATCTAGAATCTACAAAGAACTTAAACAAAGTTACAAGAAA 5062
                          i  i  vi    i     v  i        ivv    vviv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_86315007_8   5063 AAAACAAACAACCCCATCAAAAAGTGGGTGAATGATATAAACAGACACTT 5112
                           i     i     v  i?    i    ii  v   v i  i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_86315007_8   5113 ATCAAAAGAAGACATTTATGCAGCCAACAAACATACGAAAAAAAGCTCAT 5162
                         v  v        i  vi viii     i  i  i i     i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_86315007_8   5163 CATCACTGGTCAT 5175
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (149 / 107)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2099 25.18 3.86 1.43  chrX_86322932_86324625      505  1203 (491)    L1M4_orf2#LINE/L1      193   908 (0)  

  chrX_86322932_8    505 AAGCAAGAATAAAACTTTAGGAATCACATTACCCAACTTCAAATTATACT 554
                            -     i   ii vv    v     i v     i      viv    
  L1M4_orf2#LINE/    193 AAG-AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_86322932_8    555 ACAGAGCCATAGTAACAAAAACAGCGTGGAACTGGCATAAAAAACAGAAA 604
                            i   i i     iv  i    i    v          ii -i   v 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACA 290

  chrX_86322932_8    605 AATAGACCAATGCAGCAGAACAGAGAACCCGGAAACAAATCCACACACCT 654
                         v     i     v ii    iv    ii  i    i   i   i   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_86322932_8    655 ACAGTGAACTCATTTTTGACAAAGATACTAAGAACATATACTGGGGACAA 704
                          ii  v  i v     i     i i i i    v   vi v      v i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_86322932_8    705 GATAGTCTCTTCAATAAATGATGCTGGGTACA-CTGGCTATCCATATGCA 753
                         i       i     i     i       -   -    v  ?   i     
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGG-ACAACTGGATAKCCACATGCA 439

  chrX_86322932_8    754 TAATAATCAAACTAGAC------------------ACAAAAATAAAATCA 785
                         v  v   v  ii i   ------------------        v  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_86322932_8    786 AG-TAAACTAAAGATATAAATTTAAGAACTGCAACTATTAAACTACTACA 834
                          i- ii ii ?   iv     v     i  iv      v     vi  v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_86322932_8    835 AGAAAACTTCAGAAAAAATCTCCAACACATTGATGTGGGCAAAGATTTTT 884
                                v vi ?iv      i ivv  v   ivv i     v i   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_86322932_8    885 T---TTTAGCAATTCCCAACAAGCACATGCAACAAAAGCAAAAATGGACA 931
                          --- v ii  ----    -       v          v      i  i 
  L1M4_orf2#LINE/    590 TAGATATGACA----CCAA-AAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_86322932_8    932 AATGAGATCACATCAAG-TTAAATAGCTTATGCACAGAAAAGGATACAAT 980
                            vi  iiv      i-     - i   v  ii vvv      i  v  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_86322932_8    981 CAACAAAGTGGAGATATAACCCACAGAATGGGATAAAATATTTGAAAATT 1030
                            v      i i v i                v          v    i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_86322932_8   1031 ACCCATGTGGCAAAAGATTAGTAAACAGAATGTATAAGTAACTCAACCAA 1080
                          ivi  v  ii  ii  i v   vv      i     iv     vvv   
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_86322932_8   1081 TTCTA-AATGAAAAAGTCTAATGATTTCAT-GAAAAATGGTCAAAAGATT 1128
                         i  v -   -      v v   i iiiv  -?        v    i    
  L1M4_orf2#LINE/    784 CTCAATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_86322932_8   1129 TGAATAGACATTTCTCAAAAGAAGATATGCAAATAAA-AACAGGCATATG 1177
                                         v           i     iiv-  i i   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_86322932_8   1178 AAAACAGTCTCAACATAACTGATCAT 1203
                             v vv        v ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (99 / 73)
Gap_init rate = 0.02 (15 / 716), avg. gap size = 2.47 (37 / 15)  


 345 27.84 2.06 0.00  chrX_86355189_86358570.rev     1042  1138 (2244)    L1M4_orf2#LINE/L1        3   101 (807)  

  chrX_86355189_8   1042 GAAAG-TATTCTGTGTTCATGGACGAGGAAAATCAGTATCTTAAAAAAGT 1090
                              -   i ii          ivi i i v i i   iv v  i v v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_86355189_8   1091 TCATGCTATCCAAGT-GATCTATAGATTCAACGTAATACCTATCAGAAT 1138
                         iv  i  vi    i -      i          i   v       i   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

Transitions / transversions = 2.00 (18 / 9)
Gap_init rate = 0.02 (2 / 99), avg. gap size = 1.00 (2 / 2)  

 560 24.55 2.40 0.00  chrX_86355189_86358570.rev     1917  2083 (1299)  C L1M4_orf2#LINE/L1   (0)   908   738  

C chrX_86355189_8   2083 ATCTGACAAAGGGCTAATATCTAGAATCTACAATGAACTCAAACAAATTT 2034
                               i  i  i  vi    i     v  i  v      vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

C chrX_86355189_8   2033 ACAAGAAAAAAACA----GCCCCATCAAAAAGTGGGCAAAGGATATGAAC 1988
                          i  v     i   ----i   v  i?    i            v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

C chrX_86355189_8   1987 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACACAAAAAA 1938
                              i     v        i  vi viii     v ii    ii    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

C chrX_86355189_8   1937 ATGCTCATAATCACTGGCCAT 1917
                                vv    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (24 / 16)
Gap_init rate = 0.01 (1 / 171), avg. gap size = 4.00 (4 / 1)  

2421 25.69 2.88 2.63  chrX_86355189_86358570.rev     2094  2891 (491)    L1M4_orf2#LINE/L1      109   908 (0)  

  chrX_86355189_8   2094 GCATTTTTCAAAGAA-TAGAAAAGATCAATCTTAAAATTCATAGAGAACC 2142
                           v     iiv    - v  v   v -i   i           vi   vi
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCT-GATCCTAAAATTCATATGGAAAT 157

  chrX_86355189_8   2143 ACAAAAGACCTCAAAAT-GCCAAAACAATCTTGAAAAAAGAAAAC----T 2187
                         i   ii    -  i   -                    ii i   ---- 
  L1M4_orf2#LINE/    158 GCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_86355189_8   2188 TAGAGGCATCATGCTTTCTTATTTCAAACTATATTACAAAGCTATTTCAA 2237
                          i    vv   ii   i iv        viv  i          ivvi  
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_86355189_8   2238 TCAAAATAGTATGACACTGGCCTAAA-ACAGGCACCTAAATCAATGGAAC 2286
                             i i   i  ii      v   i- i  i  iv  i          i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_86355189_8   2287 AGATTTGA---------AATAAACTCGTGTGTACACAGTCAACTAATACT 2327
                            v    ---------       i i iii vi ii     i i  vi 
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_86355189_8   2328 -GACATGAATGCTAAGAATACATAATGGAGAAATGACTGTCTTTTCAATA 2376
                         -    v ii   i    vi ivi     i    vi iv          i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_86355189_8   2377 AATCATCTTTGGAAAATAAATGGTCTTTGGAATATGCACATGCAAAAGAC 2426
                            vi vi v   v  i----------    -  ?v             v
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAAC----------TGGA-TAKCCACATGCAAAAGAA 445

  chrX_86355189_8   2427 TGAGATTTAGTCCATATCTTACACCACTCACAAATACTAACTTGACATAG 2476
                            ii  viii  v  i  i      ivi     v i     ii v  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_86355189_8   2477 ATTCATGGCTTAAATTTAAGACCTGAAACTGTACAATTTCTAGAGGAAA- 2525
                           iv?v i i     v     v  i     i  v  i ii    i    -
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_86355189_8   2526 TATAAAGAAAAATCTCTTTGACATTGGTTTGTGTAATGATTTTTT-TATA 2574
                         i   ii?iv      iiv    v    v  iv i    i   i  -v   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_86355189_8   2575 TAACACCAAAAGCAAAAGCAAAAAAATAAGCAAAAGTAAATAAGTGGGCC 2624
                          i            v      v    --- v    i  i    i v  v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAA---GAAAAAATAGATAAATTGGAC 642

  chrX_86355189_8   2625 TACATCAAATTTAAAGCCTTCTGCAAATAAAAGGAAATAAGGAACAAAAT 2674
                          v       v     iv   i  iivv v      v iv v---   i v
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT---CAAGAA 689

  chrX_86355189_8   2675 AATAAACAAAATGAAAATATGAAGTGAGAGAAAATATTTGCCAACCATAT 2724
                          i i  -  i i-  vvi iii i  i              v  i     
  L1M4_orf2#LINE/    690 AGTGAA-AAGAC-AACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_86355189_8   2725 ATCTGATAATTGGTTAATATCCAAAATATATAAGAAACTCGTAAAACTAA 2774
                                  vv ii vi      i         ii     v  v    v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_86355189_8   2775 ATAGCAAAAA-ACAAA--ATCCAATTAAAAAATGAGCAAGGGCTCTGATT 2821
                            ii     -     -- i      ?       i    i  v i   v 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_86355189_8   2822 GGACATTTCTCCAAAGAAGATACACAAATGGTCAATGAGCATATAAAAA- 2870
                         i                     i        i    i    i  i    -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_86355189_8   2871 ATGCTAAACATCACTAATCAC 2891
                              v       ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (128 / 73)
Gap_init rate = 0.02 (19 / 800), avg. gap size = 2.32 (44 / 19)  


 464 28.47 0.00 1.46  chrX_86363109_86366703.rev     2083  2219 (1376)    L1M4_orf2#LINE/L1        1   135 (773)  

  chrX_86363109_8   2083 TGGAAAAACATTCCATCCTCATTGATAGGAAGAATCAATATCGTGAAAAT 2132
                               i i  i    vi    v   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86363109_8   2133 GGCCACACTGACCAAAGTAATTTATAGATTCAATGCTATTCCCATTAAAC 2182
                            v i   vv     v i  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86363109_8   2183 TACCATTGACATTCTTCACAGAATTAGAAATAAACTG 2219
                          v   vivi v  i  ii     v v  --i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTG 135

Transitions / transversions = 1.29 (22 / 17)
Gap_init rate = 0.01 (1 / 135), avg. gap size = 2.00 (2 / 1)  

2526 25.54 1.92 1.15  chrX_86363109_86366703.rev     2322  3104 (491)    L1M4_orf2#LINE/L1      120   908 (0)  

  chrX_86363109_8   2322 AGAAAT----AAACT-ATTTTAAATTTCATATGGAA-T-CAAAGAAGACC 2364
                               ----  i  -  ii    v           - -   i --    
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG--GACC 167

  chrX_86363109_8   2365 CCATATAGTCAAAACAATTCTAAACGAAAAGAACGAAGCTGGAGGCATCA 2414
                          viv    i         ii i  vi i      i   i      vv   
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_86363109_8   2415 CACTACCTGAATTCAAGCAA--TACTACAAAGCTACAGTAACCAAAACAG 2462
                             v  ii v     --  --                   i   i    
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAA--AACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_86363109_8   2463 CATGTTACTGGTACCAAAACAGACATACAGACCAATGGAGCAGAACAGGA 2512
                         ii  v      i iv ii i       i   i       ii    iv ii
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_86363109_8   2513 ACCTCAGAAATAACACCACACATCTACAACCATCTGATCTTCAACAAACT 2562
                          vii         vv   i    i  iiii  vi    i   i    ivv
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_86363109_8   2563 TGACAAAAACAAGCAGTAGGAAAAAGATATCCTATTCAGTAAATGTTGCT 2612
                           v   i v  vv  i i  i   ii   vi  v    ii     v    
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_86363109_8   2613 GGGGAAACTGGCTAGCCATATGCAGAAAACTGAAACTGGACCCCTTTCTT 2662
                            iv      v  ?   i     i  i v    ii         vi  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_86363109_8   2663 ACACCTTATACAATAATTAACTCAAGATGGATTAAAGACTTTAATGTAAA 2712
                              v       v           i      i ?    i v       i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_86363109_8   2713 ATCCAAAACCATAAAAACAATAGAAGAAAACCTAGGCAGTA--CCATTCA 2760
                          v i     i      vivv           v    ?-   --i -   i
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN-GTAAATC-TTCG 563

  chrX_86363109_8   2761 GTACATAGGCATGGGCAAAGACTTCATGACAAAAACGCCAAAAGCAGAAT 2810
                         vv  v v  vv i     v ii   v iivv vi  i         v  -
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA- 612

  chrX_86363109_8   2811 TGCAACAAAAGCCAAAATTGACAAATGGCATCTAATTAAACTAAAGAGCT 2860
                         -          vv     v  i    v v ii v  i   v v  i i  
  L1M4_orf2#LINE/    613 -GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_86363109_8   2861 TCTGCACAGCAAATGAAAACTATCATCACAGCGAACAGGCAACCTACAGA 2910
                          i  ii vv    - i v       vv v  i   v  i     i     
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_86363109_8   2911 ATGGGAGAAAACTTTTGCAATCTACCCATCTGACAAAGGTCTAATATCCA 2960
                                    iv       vii ivi      i  i  v  vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_86363109_8   2961 GAATTCAAAAGGAACTTAAACAAATTTACAAGAAAAA-ACAAA---CCCC 3006
                             vi v  i     ivv    v iv i  v     -     ---   v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_86363109_8   3007 ATCAAAAAGTGGGCAAAGAATATGAACAGACACTTCTCAAAAGAAGACAT 3056
                           i?    i         i  v    i     i     v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_86363109_8   3057 TTATGTGGCTAACAAACATATGAAAAAAAGCTCAACATCACTGATCAT 3104
                         vi vi    i  i  i  i       i v           ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (115 / 81)
Gap_init rate = 0.02 (14 / 789), avg. gap size = 1.71 (24 / 14)  


2037 26.72 4.36 5.34  chrX_86390677_86392589      505  1421 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86390677_8    505 TAGAAAAATATTTCATCCTCATGGATTTGGAAAAATCAATATTGTTAAAA 554
                          i    i    ii   vi         -    i v i           i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT-GGAAGACTTAATATTGTTAAGA 49

  chrX_86390677_8    555 TGACTATACTGCAAAAATCAATTTACATATTCAATGTTATTCCTATCAAA 604
                           i v     v vv    ii  i    v      i iv  i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_86390677_8    605 CTGCCAACATCATTTTTCCCTGAAAAAAATAAACT-ATTCTAAAATTCAT 653
                         v v   i vv v     iv v    vvi i  i  -  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_86390677_8    654 TGGGGCCTAAAAAAGAGCCTGAATAGCCAAGGAAATCCTAAGCAAAAGGA 703
                         vv  ivv iv  ii  v  v          iiv    i i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_86390677_8    704 GCAAATCTGGAAGCATCACACTACCTAACATCAAAGTATACTGCAAGACT 753
                         i    vi    i vv       v  i  iv     iiv    i   ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_86390677_8    754 ACAGTAACTAAAATAGCATGGTACTGGTGCAAAAGCAGAAACATTGACCA 803
                                ii  i i  ii         iii  iiii   v i  v  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_86390677_8    804 GTGGAACAGATTAGAGAGACCAGAAATAATGCTGCACAAC-ACAGCCATC 852
                         i     i   v v     v          vv iii   vi- ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_86390677_8    853 TGATATTCAAGAAACTGACAAAAAAAAAAAACAATGGGGAAAGGACTCCC 902
                             v   i v  i-- iiivv  i vv vv            i ivvi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAG--GGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_86390677_8    903 TATGTAATAAATGGTGCTGGGATA---------CCATATGCAGAAGATTG 943
                          v vi  i              i ---------   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_86390677_8    944 AAACTGAATGCTTTTCTTTAACGATACAAAAACATTAAC-CAATGATGGA 992
                           ii  i iv i vi  ivv  v   i v   v      -   -i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA-AATGGA 496

  chrX_86390677_8    993 TTAAATAC----ATTTAAAACCTAAAACTATAAAACTCT-AGAAAAAGTC 1037
                          i ? v  ----  v   i v                  -    i  iv 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_86390677_8   1038 CTAGA--------TTCTGGACATCAGCCCTGGCAAAGGCCTCATA---AT 1076
                         v   i--------   vv   v ii viiv     v  ii  v  ---  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_86390677_8   1077 GAAGTCTCCAAAAGAAATTGCAACAAAAATAAATATAGACAAATGGGACC 1126
                           --- v       v vvv         iv   v     i    v    i
  L1M4_orf2#LINE/    597 GA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_86390677_8   1127 TAATTAAA-CTAAAGACTTTCTCTGCAGCAAAAGAAACCAATCGACTAAA 1175
                          v  i   -i    i     - v   vv    i  v  i -  i vv  i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTA-TCAAGAAAG 691

  chrX_86390677_8   1176 TGAA----CAACCTACAGAATGTGAGAAAATAGTTGCAAATTATGCATCC 1221
                             ----     i        v         v        i  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_86390677_8   1222 AACAGAGGTCAAATATCCAGAATCTGTAAGTAACTTAAACAAATTGACAA 1271
                         i i ii  v vvi          v i   iv    ivv    v ii i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_86390677_8   1272 GATTTTCCCTAGCCCATGGATTACTAAAAGTGTGTTTTTAAAAACGAACA 1321
                         ------------------------     ------------ i  i  i 
  L1M4_orf2#LINE/    792 ------------------------TAAAA------------AGACAAATA 805

  chrX_86390677_8   1322 A---AATTATTAATAATGGGCAAAG--TTCATGAACAGACAATTCTTCAA 1366
                          ---    ?--  v           --  --    i     v    i   
  L1M4_orf2#LINE/    806 ACCCAATTW--AAAAATGGGCAAAGGATT--TGAATAGACATTTCTCCAA 851

  chrX_86390677_8   1367 ATAAGACTTACACATGACCAACAA--ACATGAGAAAATCCTCGACATCTC 1414
                          v    iv    v   i    i  --      i  i  v   i     v?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_86390677_8   1415 TAATCAT 1421
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.31 (138 / 105)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.87 (89 / 23)  


2228 24.06 9.20 2.12  chrX_86395194_86397247.rev      716  1563 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86395194_8    716 TAGAAAGACATCCCATGCTCATGAACCAGAAGAATTAATATTGTTAAAAT 765
                          i      i        i     i iii     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86395194_8    766 AACCATACTGTTAAAAGCTATCTAGAGATTCAATGCATTCCCTATCAAAA 815
                         ii v     viiv   viv     v        i   v            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86395194_8    816 TACCAA-TGTCATTTTTCACAGAAATAGAAAAAAGC-AATCCTAAAATTC 863
                          v   i-  i -     ii       v  v  --  -i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTC 147

  chrX_86395194_8    864 ACAGGGCACCA-AAAAAATGTACAAATAGCCAAAGCAATTCTGAGCAAAA 912
                          i v  v vii-  iii ivi -i          i    ii   iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_86395194_8    913 AGAACAAAGCTGGAAG---CATCACTATCAGACTTCAAAATATACTACAG 959
                                  i    i ---  -    vi vi i       iv       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_86395194_8    960 A--CACA------AAAACATTATGGCAT--GCATAAAAACAGACACGTAG 999
                          --i   ------  i   v i   i i--      ii i     ii   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_86395194_8   1000 ACCAAAAGAAGAGAAAAAAAAGTAAGCCAGAAAGAAATCCACATATTTAC 1049
                          i   vi   v    vvi i   ---       v   i   i i     i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGT---CCAGAAATAAACCCATACATTTAT 342

  chrX_86395194_8   1050 AGCCAACTGAGTTT-GACAAAGGCACCAAGAACATACACTGGGGAAACAA 1098
                         i i   i   v   -     i  ii      v   v  v        v  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_86395194_8   1099 CACCCTCTTCAATAAATGGTGCTTGGAAAA----A-----ACA-GCTTAA 1138
                         i vi  i     i          v   v  ---- -----   -  vv  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_86395194_8   1139 GATTGA--TTAAAGACTTACTTAA----ATATA----------------- 1165
                           v   --  ii vv i   i v ----     -----------------
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_86395194_8   1166 --------AGACCCAAA----AGACCCAAAAATATAAAACTACTGGAAGA 1203
                         --------     i   ----   v i    v         vi i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_86395194_8   1204 ACACATAGGG--AAACATTC-TG-TCTCGGA------AAAGCTTTTATGG 1243
                          v       ?--   iv   -  -i  i  i------  v v   iv i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_86395194_8   1244 CTAAAACCTTAAAAGCACAGGCAACAAAAACAAAATGAGATAAATGGGAC 1293
                         v  vi  vii         i         iv    vv        v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_86395194_8   1294 TATATTAAA-CTGAAAACATTCTGCACAGCAAAGGAAAC----AATGGAG 1338
                          vi  i   -i i     -  i  ii vv       v  ----  vii  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_86395194_8   1339 TGAAGAAACAACCT-TAGAATGGGAGAAAACATTTAAAAACTATTCATCC 1387
                             i i      i-i              i    iv   ii  vi   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_86395194_8   1388 AACAAGAGACTAATATCTAGAATATGCAAGTAACTCAAACAACAGTAACA 1437
                         i i   i    vi    i       ii  iv     vv     -- ----
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC--T---- 785

  chrX_86395194_8   1438 ACAACAACAAAAACACCAAATAATCCCATTAAAAAGTGGACAAAGGACAC 1487
                         -   i  i     v  -      i  v   ?    i   i       ivi
  L1M4_orf2#LINE/    786 -CAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_86395194_8   1488 AAATGGACATTTCTCAAAAGAATACATACAAATGGCTAAAATGTATACGG 1537
                         i   i          v      v i           i  v v i i i -
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG- 882

  chrX_86395194_8   1538 AAAAAATACTCAACATCACTAGCCAT 1563
                             i  i          ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (130 / 72)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 3.00 (96 / 32)  


3184 27.56 0.44 0.33  chrX_86406934_86409058.rev      728  1634 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86406934_8    728 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 777
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86406934_8    778 GGCCATACCGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 827
                            v    iv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86406934_8    828 TACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 876
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_86406934_8    877 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGA 926
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_86406934_8    927 GCAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGGCT 976
                         i     i      vv    v  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_86406934_8    977 ACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 1026
                                i   i i  ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_86406934_8   1027 ATGGAACCGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTA 1074
                               iv   i--    i  --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_86406934_8   1075 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 1124
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_86406934_8   1125 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 1174
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_86406934_8   1175 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 1224
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_86406934_8   1225 TAAAGACTTAAACATTAAACCTAAAACCATAAAAACCCTAGAAGAAAACC 1274
                         i ?    i    ii v i v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_86406934_8   1275 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTACA 1324
                             ?i v viv   iv   v v  vv i     v ii   v ivv  ii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_86406934_8   1325 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGCCCTAAT 1374
                                     vvi          vv     v  i    v  v i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_86406934_8   1375 TAAACTAAAGAGCCTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1424
                         i   v v  i i i i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_86406934_8   1425 GACAACCTACAAAATGGGAGAAAATTTTCGCAATCTACTCATCTGACAAA 1474
                                i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_86406934_8   1475 GGGCTAATATACAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 1524
                           i  vi   v      v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_86406934_8   1525 AACAAACAACCCCATCAAAATGTGGGTGAAGGACATGAACAGACACTTCT 1574
                         i     i     v  i?   vi    ii     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_86406934_8   1575 CAAAAGAAGACATTTATGCAGCCAA-AAACACATGAAAAAATGCTCACCA 1623
                          v        i  vi viii     -  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_86406934_8   1624 TCACTGGCCAT 1634
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


3108 25.46 0.87 2.49  chrX_86420473_86424931     3044  3966 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86420473_8   3044 TGAAAAGATATGTCATGTTAATGAATCGAAAGAATCAATATTGTTAAAAT 3093
                           i        vi      v   i  i i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86420473_8   3094 GTCCATACAACCCAAATCCATCTACAGAGTCAATGCAATTCCTATCAAAA 3143
                          v v    vv       iv         v    i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86420473_8   3144 AACCAATTACATTCTTCATAGAAATAGAAAAAA-AATCCTAAAATTTATA 3192
                         vv   ii i v  i  iii      v  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_86420473_8   3193 AGGAAACAGAAATGACCCAGAATAGCCAAGGCTATCCTAAGCAAAACAAA 3242
                         v     iiv  iv                ii v   i i --    v  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chrX_86420473_8   3243 CAAACAAACAAAAAAAACTGGAGGAATAATATTACCTGACTTCAAATTAT 3292
                         ------      i----i       v v i i v  ii i      viv 
  L1M4_orf2#LINE/    199 ------AACAAAG----TTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_86420473_8   3293 ACTAGAGGTCTATAGTAAGCAAAACAAAACAGCATGGTACTGGCGTGAAA 3342
                             v iiv   i     v   i   ----- ii          i i ii
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACA-----GTGTGGTACTGGCATAAGG 283

  chrX_86420473_8   3343 ACAGACACATAGTCCAATGGAACAGACTAGAGAACCCAGAAATAAATCCA 3392
                          i     i    vi        i   v v    ii           i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_86420473_8   3393 CACACCTACAATTAACTGATTTTTGACAATGGTTCCAAGAACATACACCA 3442
                         i   ii  iii i  i       i     v   v      v   v  vii
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_86420473_8   3443 GGGAAAAGACAGTTTCTTCAATAAATAATGCTGGGAAATCTGGATATTCA 3492
                               ii i   i i     i    ii        v v       ?i  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_86420473_8   3493 TATGCAAAAGAATGAAACTAGACCTCTATCTCTTGCCATACACAATAATA 3542
                         i               ii i    i   i   vii     i    v   v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_86420473_8   3543 AAATCAAAATCGATTAAATATTTACATCCAAAAGCTCAA-CCATTAAACT 3591
                           v       v   i ? v ii  v  vi  i    v  - i  v     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_86420473_8   3592 ACCATAAGAAAACACTGG-GTAAGATCTCTAGGACATTGGTCTGGTCAAA 3640
                         vii v         iv  -    -    iiiv   v    vi i v   v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_86420473_8   3641 TATTTCTTGAGCAATATCCCACAAGGAAAGGCAACCAAAGCAAAAATGGA 3690
                         vi      iiii vv iv   v   v v i     v    v      i  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_86420473_8   3691 AAAATGAGATCACATCAAATTGAAAAGCTTCTGCACACCAAAGACTATAA 3740
                         v    vi  iiv       v v    i   i  ii vi     ivi iv 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_86420473_8   3741 TCAACAAAGTGAAGTGAAAACCCACAGAATGGGAGAAAATATTTGCAAAC 3790
                             v        iv  v                               i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_86420473_8   3791 TACCCGTCTGATAAGAGATTAATAACCAGAATTTAAAATAAGTGGAA--- 3837
                         i ivii         i  i vi  v       v  ---   i--   ---
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATA---TAAA--GAACTC 777

  chrX_86420473_8   3838 --ACAATTCTATATGAAAAAATCTAAGAATCTGATTTGAAAAAGGTCAAA 3885
                         --    i  v   vv     iv v  v  i ii   ?i    v  v    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_86420473_8   3886 AGATTTGATTAGACCTTTCTCAAAAGAAGACATACAAATGGCAAACCAGC 3935
                         i       v     v      v        i           v  iv   
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_86420473_8   3936 ATGTGAAAAGGTGTGCAACATCATTGATCAT 3966
                          ii       i  iv        ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (138 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.82 (31 / 11)  


3331 21.07 1.25 1.62  chrX_86425817_86427607      497  1298 (493)    L1M4_orf2#LINE/L1      110   908 (0)  

  chrX_86425817_8    497 CCATTTTTGCAGATATTTGTAAGCTGATCTTAACTAAAGTTCATATGAAA 546
                           v          v   vii         ----     i        i  
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATC----CTAAAATTCATATGGAA 155

  chrX_86425817_8    547 ATGCAAGAGGCCCAGAAAGACCAAAACAGCCTTGAGAAATAAAAG---AG 593
                                i i       vii        ii     i   v  i i---  
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_86425817_8    594 CTGGAGGGCTCAAATGTCCCAATCTCAAAACTCACTGTAAATCTACAATA 643
                         i      i    v iv       i        i   ii   v     i  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_86425817_8    644 ACCAAGGTATTGTGATAATAGCATA-GAAAAGACTTACAGATCCATAGAA 692
                          i    ii v    i  v i     - i v    v  i     v  i   
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_86425817_8    693 TAGAATTTAGAATCCAAAAATAAGCCCTTACATTTATGGTCAGTTAGTTT 742
                                v   i    i      i   v              i  ii   
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_86425817_8    743 TCAAAAAGATTGCCAAGGGAATTCAGTGAAAAAAAAAAAAACAGTCTCTT 792
                           i v   iv       ivv     i  iii   i  ----i     i  
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA----TAGTCTTTT 401

  chrX_86425817_8    793 CAAGAAATGGTGCTCCAACAACTGGATATACACACAGTCGAAAAAAATGC 842
                            v          vvi           ?v    ii-- -    i    v
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATG--C-AAAAGAATGA 448

  chrX_86425817_8    843 CACTGGATCCTTACATGATACTATATA--AAAATTATCTCAAAATGAATC 890
                         vii    i  i   v v i  i     --       v         i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_86425817_8    891 AAATATCACAATTTAAGAGCTAAAACTATATAACTCTTATAAGAAAACA- 939
                          ? v i vv   v                 v        v         -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_86425817_8    940 -GGGATAAATCATCATGATGCTAGATTTGGCAATTATTTCTCAGATATTA 988
                         -  ?i      v  i   ivi i i  v      vi     i      v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_86425817_8    989 CACAAGAAACACAAGCAACAGAAGAATAAACAAATACATTGAACTTCA-A 1037
                            v i  i           i     v   i i   v    i      -v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_86425817_8   1038 AAAATTCAAAATGTTTGTGCATTAAAAGTATGCTATTTAGAAATGAAAAA 1087
                               v    iv       -  v    v ii    iv     vvi    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_86425817_8   1088 GTCAATTCAAATACTAGAAGAAAATGTTTCCAAATCATGTATCTGATGAG 1137
                          v   ii  v v v i i       i   v        i        i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_86425817_8   1138 GGTCTAGCATCCAAAATAAA-AAAAAACTATTGCAACTCAACAATAAACA 1186
                           v  v i     i    v -   i    v  i        i      v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_86425817_8   1187 AACAAATAACCCAACTAAAAAAATGGTTAAAGGATCTGAATAGACATTTT 1236
                         i             i ?     -   vi       i             i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_86425817_8   1237 CCCAATGAAGATATAGAAAAGACCAGTAAGGACATGAAAAGACATTTAAC 1286
                         i    v         v   v i   i    v           iii i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_86425817_8   1287 ATCATTTCCATC 1298
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (100 / 65)
Gap_init rate = 0.02 (12 / 799), avg. gap size = 1.92 (23 / 12)  


1788 23.98 4.94 10.26  chrX_86476967_86479736.rev      976  1784 (986)    L1M4_orf2#LINE/L1        1   766 (142)  

  chrX_86476967_8    976 TGAAAACATATTCCACACTCATGGATTGGAATAATCAGTGTCATAAAAAT 1025
                           i   v    i   iii             v v i i i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86476967_8   1026 GGCCATACTTCCCAAAGCAGTCTACAGATTCAATGTCATTCCTATCAAAA 1075
                            v     i      viii             i iv  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86476967_8   1076 TACCAA-TGTCATTTTTAACAGA--TTAGACAAAAACT-ATTCTAAAATT 1121
                          v   i-  i v     i-    --  -     i--  -  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATT-GACAAG--CTGATCCTAAAATT 146

  chrX_86476967_8   1122 CAT--GGAAAAGCAAATAAGAGCACC---AATAGCCAAAGCAATCCTAAG 1166
                            --     v    ---- i -   ---          i     i i -
  L1M4_orf2#LINE/    147 CATATGGAAATGCAA----GGG-ACCCAGAATAGCCAAAACAATCTTGA- 190

  chrX_86476967_8   1167 CAAAAAACAAAACAAAACAAACAAAAAAAACAAAAACAAAAACAAAACAA 1216
                         --------------------------------    v  i      ----
  L1M4_orf2#LINE/    191 --------------------------------AAAAGAAGAACAAA---- 204

  chrX_86476967_8   1217 AACAAAACAAAAAAAGCAGGAGGCATCACATTACCTGACTTCAAACCATA 1266
                         --------------- iv     vv     i v  ii i      v v  
  L1M4_orf2#LINE/    205 ---------------GTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_86476967_8   1267 CT-----GCTA--GTAACCAAAACAGAATGGTAATGGTACAACACTGTTT 1309
                           -----    --    i   i    vi     v   i i  --------
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA-------- 281

  chrX_86476967_8   1310 ACACAGTAAGCAGACACACAGACCCATGGAACAGAATAAACAGCCCAGAA 1359
                         -------iiii     i i   i v      i     vi v  i      
  L1M4_orf2#LINE/    282 -------GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_86476967_8   1360 ATAAGGCTGAACACCTACAACCATTTGATCTTTTGACAAGGCTGACAAAA 1409
                             iv iiv   ii  iiii  v     -   i       v  v   i 
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGAT-TTTCGACAAGGGTGCCAAGA 373

  chrX_86476967_8   1410 ACAAGCAATGGGGAAAGGACTCCCTGTTCAATAAATGGTGTTGGGATAAA 1459
                         v  vv            i ivvi  v     i        i     i  v
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_86476967_8   1460 TGGATAGCCATATGCAGAACA------TTGAACCTTT------CACCATA 1497
                               ?   i     i  v ------   i   ii ------       
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_86476967_8   1498 TACAAATATTTATTAACTAGAAATGGATCTAAGACTTAAGTATAAAACCT 1547
                               - ---       vi         v?    i   i i   i v  
  L1M4_orf2#LINE/    474 TACAAA-A---ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_86476967_8   1548 CAAACTATAAAAATCCTAAGAGACAATATAAGGAGCACTCTTCACAACAT 1597
                         v           v  i  ii   v  i   i ?ivv v     iii  v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_86476967_8   1598 CAGTCTTAGCAAATAATTTTT---GT------CTAAAAGCAATTGCAACA 1638
                         ii v-    vv   ii   i ---i ------ i       vvv      
  L1M4_orf2#LINE/    570 TGGG-TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_86476967_8   1639 AAAACAAAAGTGGACAATTGGGGACTAATTAAACTAAAAAGCTTCTGCAC 1688
                            iv    i i  i  v v  ivi v  i   v v    i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_86476967_8   1689 AGCCAAAGAAACTAATAACAGAGTAAATAAATAACCTACAGAATGAGAGG 1738
                         vv v  i  v    vi  v i   i  v i i    i        i   i
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_86476967_8   1739 ---TATTCACAAACTATGCATCTAACAAAGGCATAATATCGAGTGATAT 1784
                         ---    ii    ii  ii    i i  i  vv vi    v  -i    
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG-AATAT 766

Transitions / transversions = 1.77 (122 / 69)
Gap_init rate = 0.03 (25 / 766), avg. gap size = 4.92 (123 / 25)  

 692 17.58 3.03 1.21  chrX_86476967_86479736.rev     2115  2279 (491)    L1M4_orf2#LINE/L1      741   908 (0)  

  chrX_86476967_8   2115 TGAGAACAAACTAATACATCCGGAATCTATAGGGAACTT----AAATCAA 2160
                            v  vii   -- ii    i    v    ii     i----  v    
  L1M4_orf2#LINE/    741 TGATAAGGGACT--TGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_86476967_8   2161 TAAGCAAAAGACAAGTAACCCAGTTTAAAAATGGGCAAAGGACATAAACA 2210
                            vv         i       i  ?                iv i  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_86476967_8   2211 TACATTTCTCAAAAGAAGACATACAAGTGGCCAACAAACATATGAAAA-A 2259
                         v         v        i      i       i  i  i       - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_86476967_8   2260 TGCTAAACATCATTAATTAT 2279
                             v       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.02 (3 / 168), avg. gap size = 2.33 (7 / 3)  


2736 25.89 4.03 0.92  chrX_86497933_86502531.rev     3240  4108 (491)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_86497933_8   3240 CCATGTTCATAGATTGGAAGAATCAATAATGTCAAAATATCTGTACAACC 3289
                                   i          v i    v   i  i  iv vi   vv  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_86497933_8   3290 CAAAGCAATCTAAAAATTCAATGCAATACTTAACTCAAA-TACTAATGAC 3338
                             vii     v i      i     v i  --     - v i iivi 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTA--TCAAAATCCCAGCTGC 110

  chrX_86497933_8   3339 CTTATTCACAGAAAAAAGAAAAAAAAATCCTAAAATTTATATGGATCCAA 3388
                            v  ii      vv-  v  ivvi           i       vviiv
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_86497933_8   3389 AAAAGACCCAGAATCGCCAAAGGTACCTTAAGCATAAAGAACAAAACTGG 3438
                           ii          v      ivv i   i iv vi         ii   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_86497933_8   3439 AGGAATCACATTACCTATCTTCAAATTATACTACAGAGCTATAGTAACAA 3488
                             v     i v  i vi      viv       i     i     iv 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_86497933_8   3489 AAACAGCATGG-GCTGGCATAGAAACAGATACATAGACCAATGGAAGAGT 3537
                          i    ii   -i        iii i   i i     i        v  v
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_86497933_8   3538 ATAGAGAACCCAGAAACAAATCCACACAAAGCTATAACGAACACATTTTT 3587
                           v    ii       i   i   i   --vi   iiiv  ivv     i
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACA--TTTATGGTCAATTGATTTTC 357

  chrX_86497933_8   3588 GACAACGGTGTCAAGAAC------TGGGGAAAAGACTATCTCT-CAGTAA 3630
                              v    i     v ------        ii ivi   i -  ii  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_86497933_8   3631 ATGGTGCCAGAAAAACCAAATACCCATATGCAAAATAGTGAAACTAGACC 3680
                                ii i v   iii   ?   i        v i    ii i    
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_86497933_8   3681 TGTATCTCTCATCAAATACAAAAAACCAATTCAAAACAGATTAAAGACTT 3730
                         iv  i   v  i  v         -ii  i      ii   i ?    i 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCT 506

  chrX_86497933_8   3731 AAATCTAAGACCTCAAACTATGAAACTACTACAAGAAAACATCAGGGGAA 3780
                             v     v  v       i     vi  v          vi ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_86497933_8   3781 ACCTCCAGGACATTGTTCTGGCCCAAAATTTCTTTAAAAATT-CTTCACA 3829
                          i  i iv   v   vvi i v v vii      - i v  v- vi  v 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAA 605

  chrX_86497933_8   3830 AGCACAGACAGACAAA-GCAAAAATGGACAAATGGGATCACATCAAGATA 3878
                               ii  -     - v      i  i    v   iiv      i  v
  L1M4_orf2#LINE/    606 AGCACAAGCA-ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_86497933_8   3879 AAAAGCTTCTGCACAGCAAAGGATACAATCAACAAAGTGAAGAGACAACC 3928
                             i   i  ii vv       i  v     v        i        
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_86497933_8   3929 CACAGAATAGGAGAAAATATTTG---------------ACAAAGGATTAA 3963
                                 i              --------------- i  i   i vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_86497933_8   3964 TAACCAGAATTTA-AAGAAATTCTAACAAGTGTATA-TGAAAA---AAAT 4008
                           v       v  -  ii  i   v    v vv   - i    ---    
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_86497933_8   4009 ----TGATCAAAATATGGGCAAAATATTTAAATAGGCACTTCTTAAAAGA 4054
                         ----ii  i?   v         iv    i     i  i    iv     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_86497933_8   4055 AGACATACAAATGGCATACAGGCATATGAAAAGATGCTTATCATCATCAA 4104
                            i           vv i i   i             i v     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_86497933_8   4105 TCAT 4108
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.60 (136 / 85)
Gap_init rate = 0.02 (17 / 896), avg. gap size = 2.53 (43 / 17)  


3116 27.33 1.33 0.44  chrX_86504523_86510337.rev     4425  5324 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86504523_8   4425 TGGAAGAACATTCCATGTTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4474
                              ii i  i            i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86504523_8   4475 GGCCATACTGTCCAGGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4524
                            v     vi   iiv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86504523_8   4525 TACCAATGATCTTC---ACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 4570
                          v   iivii   i---i     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_86504523_8   4571 AGGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 4620
                          v    viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_86504523_8   4621 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGTCT 4670
                               i      vv    i  v  ii i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_86504523_8   4671 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 4720
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_86504523_8   4721 ATGGAACCGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTA 4768
                               iv   i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_86504523_8   4769 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 4818
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_86504523_8   4819 TATTTAATAAATGGTGCTTGGAAAACTGGCTAGCCATATATAGAAAGCTG 4868
                          v  i  i          v   v      v  ?   i  ii i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_86504523_8   4869 AAACTGGATCCCTTCTTT-CACGTTATACAAAAATTAATTCAAGATGGTT 4917
                           ii    i    v i i-   vv              i    i    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_86504523_8   4918 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACA 4967
                         i ?    i       v   v       i      vi i            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_86504523_8   4968 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5016
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_86504523_8   5017 AACACCAAAAGCAATGGCGACAAAAGCCAAAATTGACAAATGGGATCTAA 5066
                         i            vvi  i       vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_86504523_8   5067 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAT 5116
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_86504523_8   5117 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5166
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_86504523_8   5167 AGGGCTAATATCTAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5216
                         i  i  vi    i     v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_86504523_8   5217 AAACAA----CCCCATCAACAAGTGGGCGAAGGATATGAATAGACACTTC 5262
                          i    ----   v  i? v  i     i      v          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_86504523_8   5263 TCAAAAGAAGACATTTATGCAGCTAAAAAACACATGAAAAAATGCTCGTC 5312
                           v        i  vi viii  i  v  i          i      iv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_86504523_8   5313 ATCACTGGCCAT 5324
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


2555 29.65 1.55 1.22  chrX_86516097_86520943     3451  4354 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_86516097_8   3451 GAAAAAACATTCCGTGCTCATTGATAGAAAGAATCAACATTATTAAAATG 3500
                          i   i i  i  i  i    v   v i    v i  i   i    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_86516097_8   3501 GCCATGCTGCCCCAAGCC-ATCTATAGAATCAATGCTACTTCTATCAAAT 3549
                           v  i  -      iii-     i   v    i  v iii        v
  L1M4_orf2#LINE/     52 GCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86516097_8   3550 TACCAATGACATTCCTCACAGAACTAGACAAATCTATTTTAAAATTCATA 3599
                          v   iivi v  ii ii     v v     iiiv  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_86516097_8   3600 TGGAACCA-AAAAGAGCCTGAATAGCCAAGGCAATCCTAGGCAAAAAAAC 3648
                              vii-  ii  v  v          ii     i - iv   i  iv
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT-GAAAAAGAAGA 199

  chrX_86516097_8   3649 ACAAAGCTGAAGGAATCACACTACCACTACCCAACTTCAAACTTTACTAT 3698
                               i  i    v       ----- -     i      vi      i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACT-----T-CCCAATTTCAAAACTTACTAC 243

  chrX_86516097_8   3699 GGGACTACTGTAAACAAAGTAGCATGGTACTGCTACAAAAAAAGACACAT 3748
                         iiii    v    v   iii  ii        vi i  ii v     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_86516097_8   3749 AGACTAAAGGAACTGAATAGAGAGCCCAGAAATAAGACCACACAGCCACG 3798
                            ii  v    iv    v     i          iv   i   vii i 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_86516097_8   3799 ACCATCTGATCTTTAACAAAGCTGACAAAATTAGGCAATGAGGAAAGGA- 3847
                         ii  vi    i  ii    i v  v   i ii vv     i      i -
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_86516097_8   3848 -GTTCCTATTTAATAAATGGTGCTGGTATAACTGCCTAGCCATATGTGGA 3896
                         -  --  v  i  i            v i     vv  ?   i   iii 
  L1M4_orf2#LINE/    394 AGT--CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_86516097_8   3897 AGACTGAAACTGGACCCCTCTCTTATACTATATACAAAGATCAATTACAG 3946
                            v    ii         vi  i i  i         i  i  i vv i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_86516097_8   3947 ATGGATTCAAGACTTAAATGCAAAACCCAATACTATAAAAACCCTGGAAG 3996
                               iv?    i      i  i v i  v         vi i i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_86516097_8   3997 ACAACCTAGGCA-ATACCATTCTGTACATAGGAAAGGGCAAAATATTTAT 4045
                          v   v    ?i- v i v iv  -  v v  ivvi     vivv  iv 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_86516097_8   4046 GCGTAAGACACCAGTAGCAATTGTAACAGAAGCAAAAACTGACAAATAGG 4095
                         ivi  v       iv    vvv i    i   v     iv  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_86516097_8   4096 ATATAATTAAA-CAAAAGAGCTCTGCACAGGAAAATAAATAATCAGTAGA 4144
                          iv v  i   -iv   i vi i  ii vvv   iv v iv    iv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_86516097_8   4145 GTAAACAGGCAACCTCCAGAATGGGAGAAAATTTTCACAAAC--TGCATC 4192
                           i  v  i     iv                v  ii    i-- ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_86516097_8   4193 TGAGAAAGGCCTAATATCTAGTACATATAGGGAA---TTAAAAC-AAATT 4238
                            v  i  v  vi    i  v i     ii   ---   v   -v   v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_86516097_8   4239 TTCAAGAAA-AAATACTTCA-TTAAAAAGTGGGCAAAGGACATGAACAGA 4286
                         v v  i i -     vii  -  ?    i           iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_86516097_8   4287 CACTTTTCAAAAGAAAGCATACATACAGTCAAAAAGTATATGAAGAAAAG 4336
                           i  i  v      iii     v ii i   v   i i     i i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_86516097_8   4337 CTCCACATCATGGATTAA 4354
                            v      ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (166 / 98)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 1.56 (25 / 16)  


2613 27.43 1.55 1.11  chrX_86530009_86533651     2247  3150 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86530009_8   2247 TGGAAACACATCCCATGCTCATGGATAGGTAGAATCAGTATTGTGAAAAT 2296
                               v i        i        v  v   v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86530009_8   2297 GACTGTATTGCCAAAAGCAAATTACAGATTCAATATAATTCCCATAAAAA 2346
                          i vi  i v  v   vii vi           iii   i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86530009_8   2347 TACCATCATTATTCTTCACAGAAACGGAAAAA--AATTCTAAAATTTATA 2394
                          v   v vviv  i  ii      iv  v  i--i  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_86530009_8   2395 TGGAACATAAAAATAGCCCACG-TAGACAAAGCAATACTAAGCTAAAAGA 2443
                              -  iv  ivii    vi-   v    i    vi i ivv i    
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_86530009_8   2444 ACAAATTTGGAGGCATAACTTTACCTGACTTAAAACCATACTACAAGGCT 2493
                              v       vv v  vi v  ii i  v   v v        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_86530009_8   2494 ATATTTA-CAAAACAGCATGACACTGGTATAAAAATATTCACATAGACCA 2542
                          i v v -   i    ii  ii     i    ii   vv  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_86530009_8   2543 GTGTGGAACATAATAGAAAACCCAGAAATAATGCCAAATACTGACAGCCA 2592
                         i  --   i v   v  i ii          vv   v i i v ii i  
  L1M4_orf2#LINE/    300 ATG--GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_86530009_8   2593 ACTGATCTTTAACAAAGCAAACAAACGCATAAAATAGAGAAAGGACA-CC 2641
                          i    i  ii    i vviv   ivv   vv   i i     i i -i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_86530009_8   2642 TATTCAACAAATGGTGCTGGGGTTATTGGCAAGCCACATGTACAAGAATG 2691
                          v                   iiv i   vv ?       i v       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_86530009_8   2692 AAAAGATGGATCCTCATCTCTCACTGTATAGAAAAATCAACTCAAGAAGG 2741
                           -- v    i  ii i   v   ii    v      i       i v  
  L1M4_orf2#LINE/    448 AA--GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_86530009_8   2742 ATTAAAGACTTAAATCTAATACCAGAAACCATAAAAATTATAGAAGATAA 2791
                           i ?    i     v   v v vi    i      v iv       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_86530009_8   2792 CATCAGA--AAATCTCTTCTAGACATTGGCTTAGGAAAAGAATTCATGAC 2839
                            vi ?--      --  vv   v    v     v  v iv   v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_86530009_8   2840 CAAGAACCTGAAAGCAAATGCAACAAAAACAAAAATAAATGAATAGGACC 2889
                         i v  vv ii      v v         iv       i  i   v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_86530009_8   2890 TAATTAAACTAAAAAGCATCTGTACAGGCAAAAGAAATAATTGGTAGAGT 2939
                          v  i   v v    i v i   i -vv    i  v iv  iiiv i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGT 692

  chrX_86530009_8   2940 AAACAGAAAACCCACAGAGTGGGAGAAAATATTCACAAACTATGCATCCA 2989
                         i  v   v          i              ii    ii  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_86530009_8   2990 ACAAAGGACTAATATCTAGAACCTATAAAGAACTCAAACGAATCAGTAAT 3039
                          i  i     vi    i    iv            vv  i v   i    
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_86530009_8   3040 AAAA---CAAATCATCTCATT-AAAAGCGGTCAAAGGACACATGAATACA 3085
                             ---     v i iv   -    ii  v       iv--      v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT--TGAATAGA 840

  chrX_86530009_8   3086 CAATTCTCAAAAGAGGATATACAAATGGCTAACA--TACATAAAAA-ATG 3132
                           v     v     i              i  i --i    i    -   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_86530009_8   3133 CTCAACATCAGTAATTAT 3150
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (138 / 107)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.60 (24 / 15)  


2637 25.08 1.59 5.82  chrX_86609519_86613950     2995  3939 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_86609519_8   2995 AAAAACATCCCATGCTCACAGATGGGTAGAATAAATATTGCAAAAATGAC 3044
                            i i        i   ii   v  v   v v       iv  i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_86609519_8   3045 CATACTGCCAAAAGCAATCTACAAATTCAACACAATCCCCATGAAAATAC 3094
                         v     v  v   vii       i       i       i  v     v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_86609519_8   3095 TACCATCATTCTTTACAGAATTAGAGAAAACAATTCGAAAGTTCATAGGG 3144
                         i v vv v  i   i     v v  v  ivii  i v   i      v  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_86609519_8   3145 AACCAAAGAAGAGCCTGCATAGCCAAAGCAAGGCTAAGCATAGATAGATA 3194
                           viiv iii  v  v v         i   vvi i -------------
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------------- 190

  chrX_86609519_8   3195 GACAGATAGATAAATAGATAGGTAGATAGATAGATAGATAGATAGAAATA 3244
                         -----------   -----------------   -   --- i i iv i
  L1M4_orf2#LINE/    191 -----------AAA-----------------AGA-AGA---ACAAAGTTG 208

  chrX_86609519_8   3245 GAAATCTTGTGTCATCACACTACCTGATTTCAAACTATACTATAAGGCCA 3294
                           iiv  --------      v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    209 GAGGACT--------CACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_86609519_8   3295 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGACACATAGACCAA 3344
                         i   v i   i    ii         i    ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_86609519_8   3345 TGGAACAGAAGAGAGAACCCAGAAATAAATCAAAATATTTACAGCCAACT 3394
                              i    vv    ii           i v v i     ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_86609519_8   3395 GATCTTCCACAAAGCAAACAAAAACATAAAGTGGGGAAGGGACACCCTTT 3444
                            i   v    i vviv   i v   vv i       i i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_86609519_8   3445 TCAACAAATGTTGCTGGGATAATTGGCTAGCCACATGTTGGAGAATGAAA 3494
                                   v        i  i   v  ?       ivii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_86609519_8   3495 CTGAATCCTCATCTCTCATATTCTACAAAAATCAACTCAAGAGGGATTAA 3544
                         i  i i  ii i   v  ivv v         i       i v    i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_86609519_8   3545 GGACTTAAATCTAAGACTTGAAACTA-AAAATTCT-AGAAGTTAACATAG 3592
                         i   i     v     vi i      -    i   -     vv       
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_86609519_8   3593 GAAGAACTCTTCTAGACATTGGCTTAGGCATGGATTTCAT-GATCAAGAA 3641
                          ?iv  v     vv   v    v       vv i    v -   - v  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGAC 599

  chrX_86609519_8   3642 CTCAAAAGCAAATGCAATAAAA--ACAAATAGCT---TGGGACTT-ATTT 3685
                         vi        v v    i    -- v      v --- v      -  iv
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_86609519_8   3686 AATCTAAAGAGCTTTTGCATGGCAAAAAA-ACAGTCACCTGAGTAAACAG 3734
                           vi    i -      iiivv    ii -  vi   vvvi   i  v  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_86609519_8   3735 ACAATCCACAGAGTTGGAGAAAATCTTCACAATCTGTACATCTGGCAAAG 3784
                             i       i v         v  ii   viii  i     ii  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_86609519_8   3785 GACTAATATCCAGAATCTACAACAAGCTCAAACAAATCAGTAAGAAAAAA 3834
                             vi          v  i  vi i   vv    v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_86609519_8   3835 ACAA----TCCCATCAAAAAGTGGGCTAAGGACATGAATAGAGAATTCTC 3880
                             ----i  v  i?    i     v     iv        v v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_86609519_8   3881 AAAAGAAGATACACAAATGGCCAACAAACATATAAAAA-ATGATCAACAC 3929
                         v          i            i  i  i  i    -   v      i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_86609519_8   3930 CACTAATGAT 3939
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.31 (132 / 101)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 4.38 (70 / 16)  


3586 15.90 3.77 11.21  chrX_86628868_86630875      535  1515 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86628868_8    535 TGGAAAGATATCCTGTGTTCCTGGATTGGAAGACTTAATATTTTTTAAAT 584
                                      ii     v                     v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86628868_8    585 GGTAATACTCCCCAAAGCAATCTCCATATTCAATGCAATCGCTATCAAAA 634
                           i             vii    v  v      i      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86628868_8    635 TCCCTACAGCTTTTTTTCTTTTTCTTTTCTTTTTTTCTTTTTTTTTTTTT 684
                             ---    vii   ---------------------------------
  L1M4_orf2#LINE/    101 TCCC---AGCTGCCTTT--------------------------------- 114

  chrX_86628868_8    685 TTTTTTGCAGAAATAGAAACACTAATTGTAAACGTTAGATATAATAGCAA 734
                         ---           v  v vi  i  iv    vv i v  iv  vv    
  L1M4_orf2#LINE/    115 ---TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_86628868_8    735 GGGACCCTGCATAGTCAAAACAATCTTGAAAATGAAGAACAAAGTTCAAG 784
                                v v    i                 v             vi  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_86628868_8    785 GACTAATAGGTTCTGATTTCAAATCTTAGCATAAAGCTACAGTAATCAAA 834
                             v i vv i ii        v    --------     ---------
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTA--------CTACA--------- 244

  chrX_86628868_8    835 AATAAAGCTACAGTAATCAAATATGTATAGTACTTTCATAAGGATAAAAA 884
                         ----                i-----------------------------
  L1M4_orf2#LINE/    245 ----AAGCTACAGTAATCAAG----------------------------- 261

  chrX_86628868_8    885 GCTTACAGTAATCAAATATGTGTAGTACTTTCATAAGGATAGACATATAG 934
                         ----     ------------  i     vv                   
  L1M4_orf2#LINE/    262 ----ACAGT------------GTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_86628868_8    935 ACCAACAAAATAAAAAAGAAGCTTCAGAACTAAACCCCATACATCTATGG 984
                          i   iii    i  vv  iiv i     v       -      i     
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC-ATACATTTATGG 344

  chrX_86628868_8    985 TCAGTTGATTTTTGACAAGTGTGCTAAGACTATACAATGGGGTAAGAATA 1034
                            i        i      v    i     i  v        v       
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_86628868_8   1035 GTCTCTTCAGTAAATGCTGTTGGGAAAACTGGATTTCCACATGCACAAGA 1084
                             i    ii     v  i     v        v?         v    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_86628868_8   1085 ATGAAGTTGGATCCTTAGCTCAAAGCATATA-AGAAAT-AACTCAAAATG 1132
                                    i  i  v    v v      - i    -           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_86628868_8   1133 GATGAAAGACCTGAATATAAGAGCTAAAGCTATAAAACTC--------AA 1174
                            v ?      i   i           i           --------  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_86628868_8   1175 ACAT----------TTTCATTACTTTGGATTTCACA-----TTTTTAAAA 1209
                             ----------i   i v  i    i  vvi  -----  i   i -
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA- 593

  chrX_86628868_8   1210 ATATGACGCCAAA-GTACAAGAAACAAA-GAAAACATCAATTAATTGGAA 1257
                         -      i     - i     v      -     v  vi  v       v
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_86628868_8   1258 CTCATCAAAAT--AAATTTTTTATGCTTCAGAGGATACAATCAAGGGAAT 1305
                         i          --   vi    i       i    i  v      ii i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_86628868_8   1306 GAAAAAGATAACCTACAAAAGGGGGAAAAACATGTGCAAATCATGTACCT 1355
                              -  i    i   i  v   ii    i  v          i  i  
  L1M4_orf2#LINE/    693 GAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_86628868_8   1356 GATAGAGGGCTTGTGTCTGGAATATATAAAGAACATATACAACTAAACAA 1405
                             ii  i     i  ii               viv       v  i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_86628868_8   1406 CTAAGAGATGAATAATACAGTTCATAAATAGGCAAAGGATT--------C 1447
                         iv  i   ii     iv  i  ? v    i           -------- 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_86628868_8   1448 ATTTCTTCAACGAAGATATACAAATGAGCAACAAGCACATTTAAAAGATG 1497
                               i   v               iv   i        v-        
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATG 890

  chrX_86628868_8   1498 CTCAACATCATTAGTCAT 1515
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (89 / 64)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 7.74 (147 / 19)  


2195 25.11 5.95 6.94  chrX_86646400_86650716     2917  3824 (493)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_86646400_8   2917 ATTCCATGTTCATAGATTGAAAAAATCAATAATGTTAAAATGTCCATACT 2966
                           i          i     i  i v i    v      i   v v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_86646400_8   2967 ACCCAAAGCAATCTATAGATTCAATGCAGTCTCTATCAAAATACCAATTA 3016
                         v      vii     i        i   i  i          v   ii i
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_86646400_8   3017 CATTATTCACAGAAATAGAAAAACAAATTG-AAAATTAATGTGGAACCAC 3065
                          v  v  ii       v  v  i vi  iv-      v  i     vii 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_86646400_8   3066 TACAGACCCTGAATAGCCAAAGCTATACTAAGCAAAAAGAACAAAACTGG 3115
                         v vi     v           i v  vi i iv  i         ii   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_86646400_8   3116 AGGAATCACATTACCTGACTTCAAATTATACTGCAAAGCTATAGTAACCA 3165
                             v     i v  ii i      viv    i        i     i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_86646400_8   3166 AAACAGCATGTTACTGGTGTAAAAACAGACACATAGACCAATGAAATGGA 3215
                          i    ii  v      ii   ii i     i     i     i   i  
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_86646400_8   3216 ATAGAGAATGAGGTAACAAGTCCACACACCTACAGTGAACTCATTTTAGA 3265
                           v    i vvi v  i  ii   i   ii  ii  v  i v     v  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_86646400_8   3266 CAAAGATGCCACAAACACACACTGGGGAAAAGACAGTCTCCTAAGTAAGT 3315
                            i i     vi v  iv  v        ii i     ii v ii  i 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_86646400_8   3316 GGTGCTGGGAAACCTGGATATCTATGTTCAGGAGACTAAAACTAGACCCT 3365
                                   v v       ? i ii v  ii   v i  ii i     i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_86646400_8   3366 CATATCTCACCATATTAAAAAAAATCAAAGCAACATGGATTAAACATTTA 3415
                         i iv  v        -- v      i  vv   v      i ? v ii  
  L1M4_orf2#LINE/    460 TACCTCACACCATAT--ACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_86646400_8   3416 AATCTAAGACCTTAAACTATGAAACTACTACAAGAAAACATTGGGTAAAA 3465
                            v     v  v       i     vi  v          v  ?vv   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_86646400_8   3466 TCTCCAGGACATTGGTCTGAGCGAAAATTTCTTGAGCAATAT--CTCCAC 3513
                            i iv   v    vi ii  i vii      -  --    -- v   v
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AG--ATATGACACCAA 604

  chrX_86646400_8   3514 AAGCACAGGCAACCAAAAGAAGAAGAAGAAGGAGAAGGAGAAGGAGAAGG 3563
                                i     -       i  i------------------------v
  L1M4_orf2#LINE/    605 AAGCACAAGCAAC-AAAAGAAAAAA------------------------T 629

  chrX_86646400_8   3564 AGAGGAAGAGGAAG--AGGAAGAGGAGGAA-----GAGGAGGAAGAGGAA 3606
                            vi  vv   vv-- vv  i vv ii  ----- v vvvv  ------
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA------ 673

  chrX_86646400_8   3607 GAGGAAGAAAAATAAGATTATTTCAAGTTAAAAAGCTGCATAGCAAAGGA 3656
                         -    v---------- i   --    ----    -  ------   i  
  L1M4_orf2#LINE/    674 -AGGAC----------ACTAT--CAAG----AAAG-TG------AAAAGA 699

  chrX_86646400_8   3657 CACAACCCACAGAATGGGAGAGAATATTTGCAAACTACTCATTTGACAAG 3706
                           --                 i            ii ivi  i   i   
  L1M4_orf2#LINE/    700 CA--ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_86646400_8   3707 AGATT---------AATAAGTA--GAATTT-------------------- 3725
                         i  i ---------    vi  --   i i--------------------
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_86646400_8   3726 -----ATAATTTGATCAAAAAATGAGCAAAAGATTTGAAAAAAACATTTG 3770
                         -----    iiii  i?       i     i        v i -     v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA-CATTTC 846

  chrX_86646400_8   3771 TTAAAAAAAGACA-AGAAACAGTTA-------TATGAGAAGGTGCTCAAC 3812
                          iv   i    i - v   ii ii -------i    i   i        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_86646400_8   3813 ATCATTGATCAT 3824
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.02 (22 / 899), avg. gap size = 5.32 (117 / 22)  


3070 27.37 1.56 0.11  chrX_86665173_86667983.rev     1426  2320 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86665173_8   1426 TGGAAAGATATCCCATGTTAACAGATTGAAAGAATTAATTTTCTCAA-AT 1474
                                            v ii     i    v     v  v i  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86665173_8   1475 GGCCATACTACCCAATGCAATCTACAGATTTAATGCAATACCAATGAAAA 1524
                            v     v     vvii           i  i     v  v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86665173_8   1525 TACAAATGACATTCCTCACAGGAATACAAAAACAAATCCTAAAATTCATA 1574
                          v v iivi v  ii ii   i   vv v  i vi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_86665173_8   1575 TGGAACCACAAAATATCTTGAATAGCCAAAGGAATCCTGAGCGAAAAAAA 1624
                              vii   iiv i iv           iv    i   ivi i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_86665173_8   1625 TGAGGTTGGAGCCATCATGCTACCTAACTTCAAAGTATATTACAAGACTA 1674
                         ii i       vvv   ii  v  i  i      iiv  i     ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_86665173_8   1675 TAGTAATCAACAAAGTATGATATTGGTATTAAAACAGGCACAAGGAATAA 1724
                         i         v v   i  i  i   i  v ii i  i  i vi  vi  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_86665173_8   1725 CGGAACAGAACAAAGAGCCCAGAAATAAATTCACACATCTATAGTCAAGT 1774
                         i    i    ivi    i           ii  i    i   i     v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_86665173_8   1775 GGTTTTCAATAAAAGTTTCAACAACACACACTGGGAAAAA-----TTTCT 1819
                          i     i i  ii  vi   v v  iv  v    i   i----- i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_86665173_8   1820 TCAATAAATGGTGTTGGGAAAATTGGATATCCAGCTGCAGGAGAATGAGA 1869
                             i        i     v  i      ?   vv    ii       ii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_86665173_8   1870 CTAGAATCCTGCCTCTCACCATATACAAAAATCAACTCAAAATAGATTAA 1919
                         i i  vi   i    v                i          i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_86665173_8   1920 AAACATGCATATAACACTCAAAAGTATTAAAATACTAGAAGAGAACATAG 1969
                          i  v iv  i   v vii    v   v   v vi       i       
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_86665173_8   1970 -TGCAAATGCTCTGTGACATTGGGAGGGGCAAGGAGTGTTTAAATAAGAC 2018
                         -? i    -  ii     v     vvi     v iv vi   i   v   
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_86665173_8   2019 CTCAAAAGCACAGGCAACAAAAACAAAAAGAAACAAAATGAACTACATCA 2068
                         vi          i         iv     v i i   v  i   v     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_86665173_8   2069 AACTGAAAAGTTTTTTTATAGCAAAGGAAACAATTAACAAAATGAAAAGA 2118
                           v v    ii    v iivv       v  v  i  v   i        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_86665173_8   2119 TAATGTTCAAATTGTGAGAAAATATTTCCAAGCTATACAGCTGACAAGGG 2168
                         i  iviv  i v  v            v   iii   i v    i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_86665173_8   2169 GTTAATACCTAGAATATATAAAGAATTTAAACAACTCACCA-TAAAC--- 2214
                         ii vi  i i               i ivv        vi -    v---
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_86665173_8   2215 CAAATAACCTGATT-AAAAATGGTCAAAATACTTTAATAGTCATGTCACA 2263
                                  ii   -        v    iv i  v     v   v  v v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_86665173_8   2264 AAAATGGACATATAAATGGCCAACTGGTATATAAAAA--TGTTTAATATC 2311
                            ivi  i   i          ivi i i  i    --  i i  i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_86665173_8   2312 ACTAATTAT 2320
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


1993 24.95 3.28 8.86  chrX_86818915_86823711.rev     3393  4306 (491)    L1M4_orf2#LINE/L1       46   908 (0)  

  chrX_86818915_8   3393 AAAATGTAGCTATACTATCCAAAGCAATTTATGGGTTCAGTGCTGTTCTT 3442
                           i   --  v     vi     vii  i  ii i    ii  vi i i 
  L1M4_orf2#LINE/     46 AAGATG--GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chrX_86818915_8   3443 AACAAACTACCAA-TGCCATTTTTCACAGAATTAGAACAAACTAATC-TA 3490
                          v    v v   i-    -     ii     v v  -   i  i   -  
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGA-CAAGCTGATCCTA 141

  chrX_86818915_8   3491 AAATTCATATGGAACCA-AAAATAGTCTGAATAGTCAAAACAATCCTAAG 3539
                                       vii-  iiv vi v      i          i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_86818915_8   3540 CTAGAAGAACAGAGCTGGAAACATCACTTTACTCAACTTCAATCTGTATT 3589
                         vv         i  i    iivv    vi v i   i     vviv  i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_86818915_8   3590 AGGAGGTTACGGTATCCAAAACAGCATGATATTGGTACGAAAACAGACAC 3639
                          vi i i   i   vi   i    ii  i  i   i ii ii i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_86818915_8   3640 ATAGACCAAAGGAACAGGCTACAGA-CCCATAAATAAAGCCGCTCACCTA 3688
                              i   v    i  iv vv   -i   v       v  iiv  ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_86818915_8   3689 CAACCATCTGATCTTCAACA--GCTTCAACAATGACTAG-CAATAAGCAA 3735
                         iiii  vi    i   i   -- v v --   -   i v-    ii v  
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGC--CAA-GACCATTCAATGGGGAA 388

  chrX_86818915_8   3736 TGAATTCCCCATTCAATAAATGGTGTTGAGGTAACTAGCTAGCCATATGC 3785
                         v    vvi iv     i        i  i ii    i v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_86818915_8   3786 AGATAATTGAAATGGCACACAGACTAGAAAAGAACCTAGGAGTCATGATG 3835
                          ---------------------------      -----------   --
  L1M4_orf2#LINE/    439 A---------------------------AAAGAA-----------TGA-- 448

  chrX_86818915_8   3836 GCAGGAGTAGTCAGAGGAATTCTCCACTTATCCCTTCCTTTTACCATATA 3885
                         --------   ii  ---------------i    v   ivi        
  L1M4_orf2#LINE/    449 --------AGTTGGA---------------CCCCTACCTCACACCATATA 475

  chrX_86818915_8   3886 CAAAAATTAAACCAACGTGGATTAAATAGTTAAATCTAAAACCTAAAACT 3935
                                   vi   vi     i ? v vi     v   i v        
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_86818915_8   3936 ATAAAAACCCTAGAAGAAAACCTAGG---AAATACCATTCTGGAATAGGA 3982
                               vi i           v    ---    -- v iv  ivv v  i
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGG 573

  chrX_86818915_8   3983 CTTGGCAAAGATTTC------ATGACAAAGTATCCAAAAGCAATTGCAAC 4026
                         i v     v i    ------      ------         vvv     
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAAC 617

  chrX_86818915_8   4027 AAT-GCAAAAATAGACACATGGGACCTAACCATAAAAAAAAGCTTGTGTA 4075
                           v- v         i v  v    i v i  v  vv    i   v   i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_86818915_8   4076 CAGAAAAATAAACTATGAACAGGGTAAACAAACAACCTACAAAATGGGC- 4124
                          vvv   iv v     v  v ii  i  v i      i   i      v-
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_86818915_8   4125 AAAATATTTCCAAACTAGGCATCTGACAAAAG---TGTAATTTCCAGAAT 4171
                                  v    ii vii      i  ii ---    ---        
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA---TCCAGAAT 764

  chrX_86818915_8   4172 CTATAAGGAACTT----AAATCGACAAGCACAAAACGAACAACCCCATTG 4217
                         v     i     i----  v  i i  vv v  i  i  i     v   ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_86818915_8   4218 AAAAATGGCCAAAAAA----AATGAACATT-CTCCTCAAAAGACATACAT 4262
                                 v    ii ----   ii     -    vv i    i     v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_86818915_8   4263 GTGGCCAACAAGCATATGAGAAAATGCTCAACATCACTAATTAT 4306
                         i       i     i    i  i             ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (134 / 91)
Gap_init rate = 0.03 (26 / 863), avg. gap size = 4.27 (111 / 26)  


2960 27.16 1.33 0.67  chrX_86838765_86845456     5298  6199 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86838765_8   5298 TGGAAAGCCATTACATGATCATGGATAGGAAGAATCAATATCGTGAAAAT 5347
                                vi  iv    v        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86838765_8   5348 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATCCCTATCAGGC 5397
                            v     v      v i  i           i  v          iiv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86838765_8   5398 TACCA-TTGTCTTTCTTCACAGAATTAGAAAAGAACT-ACTTTAAATTTC 5445
                          v   -i  i    i  -i     v v  v   --  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_86838765_8   5446 ATATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAA 5495
                                 viiv  ii  v  viv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_86838765_8   5496 GAACAAAGCTGGAGGCATCATGCTCCCTGACTGCAAACTATACTACAAGG 5545
                                 i      vv   ii  i  ii i v    viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_86838765_8   5546 CTACAGTAACCAAAACAGAATGATACTGGTACTAAAACAGATATATAGAC 5595
                                  i   i    vi  i      i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_86838765_8   5596 CAGTGGAACAGAACAGATTACTCAGAAATAACACCACACATCTACAACCA 5645
                           i     i    iv  vviii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_86838765_8   5646 TCTGATCTTTGACAAACCTGACAAAAATAAGCAATGAGGAAAGAATTCCC 5695
                         vi    i  i     ivv  v   i vi vv     i         vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_86838765_8   5696 TATTTAATAAATGGTGTTGGGAGAACTGGCTAGCCATATGCAGAAC--TG 5743
                          v  i  i        i     v      v  ?   i     i  v--  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_86838765_8   5744 AAACTGGACCCCTTTGTTACACCTTATACAAAAATTAACTCAAGATGGAT 5793
                           ii         viv i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_86838765_8   5794 CAAAGACTTAAATGTAATACCTGAAACCATAAAAACCCTAGAAGAAAACC 5843
                           ?    i         v v  i    i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_86838765_8   5844 TAGGC---AATGCCATTCAGGATATAGACATGGGCAAAGACTTAATAACT 5890
                             ?---   -- -   iv  iv v ivv i     v ii  vv  iv 
  L1M4_orf2#LINE/    548 TAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_86838765_8   5891 AAAACACCAAA-GCAATAGCAACAAAAGCCAAAATTGACAAATGGGATAT 5939
                          vi        -   vv           vv     v  i    v   iv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_86838765_8   5940 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAGTGCCATCAGAGTGA 5989
                         v  i   v v  i i   i  ii vv    i  v v ii  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_86838765_8   5990 GCCGGCAACCTATAGAATCGGAGAAAAT-TTTGTAATCTATCCATCTGAC 6038
                         ivv i     i i     v         -    i  vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_86838765_8   6039 AAAGGGCTAACATTCAGAATCTACAAGGAACTTAAACAAATTCATGAGAA 6088
                           i  i  vii  i      v  i  i     ivv    v iv  i v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_86838765_8   6089 AAAAGCAAACGACCCCATCGAAAAG-GGGCAAATGATATGAACAGACACT 6137
                            ii    ii    v  i?    i-       v   v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_86838765_8   6138 TCTCAAAACAAGACATTTATGCGACAAACAAACATATAAAAAAA--CTCA 6185
                             v   v    i  vi vii i v  i  i  i  i    i --    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_86838765_8   6186 TAATCACTGGTCAT 6199
                         vv    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


1368 23.14 3.65 13.15  chrX_86860377_86862733.rev      563  1193 (1164)    L1M4_orf2#LINE/L1        2   572 (336)  

  chrX_86860377_8    563 GAAAAGATATATT-TGTTTCATGAATTGGAAA---TAATATTGCTAAAAT 608
                          i        vii-    -    i       i---        i   i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTT-CATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86860377_8    609 TTTCATACTATCCAAGT-AATCTAAAAATTCAAAGCAATCTCTATCAAAA 657
                         vviv     vi    i -i     v i      v      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86860377_8    658 TTTCAATGACATTTTCCACAGTAAT-AAAAAAC-AATCCTAATATTCTAA 705
                          ii  iivi v    iii   v   -i v  i -i       v    ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC--- 147

  chrX_86860377_8    706 TAGAAGAATAATCCAAAACTTTGAATGGAGCTACCAAAGACCCCAAATGG 755
                         -------   ---------------    iv i v ii     vi   i 
  L1M4_orf2#LINE/    148 -------ATA---------------TGGAAATGCAAGGGACCCAGAATAG 175

  chrX_86860377_8    756 CCAAAACAATCTTCAGTAGAAAAAAAAGAACAAAACACTAAACTAAAGGC 805
                                      -----      i         i---------------
  L1M4_orf2#LINE/    176 CCAAAACAATCTT-----GAAAAAGAAGAACAAAG--------------- 205

  chrX_86860377_8    806 ATCGTACTATGACAGTATTTAGAGATACTATCATATCTCTAAATAGAGAT 855
                         ------------------  i   i-   --  i ii  i----------
  L1M4_orf2#LINE/    206 ------------------TTGGAGG-ACT--CACACTTCC---------- 224

  chrX_86860377_8    856 ACTATCATATCTCTAAATCTACTAAAATGTTGTAGTAATCAAGA--ATAT 903
                         -----  -  i  v   ii     v  v i ii           --i i 
  L1M4_orf2#LINE/    225 -----CA-ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chrX_86860377_8    904 AATACTGACTTATAAATGAATACGTAGCCCAGTAGAACAGAAT------- 946
                         ii     i v  vii  ii i ii   vi  i i   i     -------
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_86860377_8    947 CCAGAAATAAACCCATGCCTTTATAATGAATAGGTTTTTGACAAAGATGC 996
                                         i v     ii v   v i    i     i i   
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_86860377_8    997 CAAGAATA---AAT----AATGAAGAGTCTTTTCAATAAATGCTGTTGGG 1039
                              vi ---   ----  v   v           i     v  i    
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chrX_86860377_8   1040 AAAACTGGATATTCATATGCAGAAAAAGGAAATTAGTTATTTATCTTACA 1089
                          v         ?i  i     i  i  v   i  i vivii  i  i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_86860377_8   1090 TCCTATATAAAAGTCAACTCAAAGTGAATAAAATACTTAAACAAAAGACC 1139
                         i v    i    i i        i  i  v ? v  i    iiv    v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_86860377_8   1140 TGGAACTGTAAAAACATTAGAATAAAATATTGTGGAATAGCTCCATGACA 1189
                          ii    i     viv      v    i  v v? v v v  i i    v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_86860377_8   1190 TTGG 1193
                             
  L1M4_orf2#LINE/    569 TTGG 572

Transitions / transversions = 2.11 (97 / 46)
Gap_init rate = 0.03 (18 / 571), avg. gap size = 5.89 (106 / 18)  

 548 21.76 3.82 10.88  chrX_86860377_86862733.rev     1532  1871 (486)    L1M4_orf2#LINE/L1      593   908 (0)  

  chrX_86860377_8   1532 ATATAATTCCCAAGACAAGGGAAATAAAAATAAAAATAAACAAATGGGAT 1581
                             i iv  v  ii  vii v  i    iv       i i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_86860377_8   1582 TACATCAAA-CTAAAAAC----GTTCTTCAGAACAAAGAAAATTATTAAC 1626
                          v       -i       ----  v     -----   i v i   i  v
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCA-----AAGGACACTATCAAG 687

  chrX_86860377_8   1627 AGAGTGAAGAGACAAGCTATGGATTGTGAAAAAAGAGTTTCAA-CCATAA 1675
                          i      i      v i ii  v  v  i    v v  v   -i    v
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_86860377_8   1676 ACCTAAGAAAGGGTTAATATCTAAAATACATAAGGAACGGAAACAACTCA 1725
                          i  i v  i  ii vi    i i    i    i    vvvv        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_86860377_8   1726 ATAGCAAAAAAAAATAAAATTAAATTAAAATTAAAAAACTAAGTAACTCT 1775
                            ----------      ---------------- i  -  i    i v
  L1M4_orf2#LINE/    788 ATA----------ATAAAA----------------AGAC-AAATAACCCA 810

  chrX_86860377_8   1776 ATTTTAAAATGCACAAAATATTTAAA----CATTTC--CAAAATAAAGAT 1819
                            ?v      vi    iv    i  ----      --    i--     
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG--AAGAT 858

  chrX_86860377_8   1820 ATACAAATGGCAAACATGTATATGGAATAAATAGCTCAA-ATGCACAGAG 1868
                                    v  i v i i   i  - i  -      -  -  ?????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAA-AGAT-GCTCAACAT-CAZZZZZ 905

  chrX_86860377_8   1869 ATA 1871
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.52 (44 / 29)
Gap_init rate = 0.04 (14 / 316), avg. gap size = 3.57 (50 / 14)  


3283 26.98 0.44 0.44  chrX_86882053_86888316     4864  5771 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86882053_8   4864 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4913
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86882053_8   4914 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4963
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86882053_8   4964 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5011
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_86882053_8   5012 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5061
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_86882053_8   5062 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5111
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_86882053_8   5112 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5161
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_86882053_8   5162 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5209
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_86882053_8   5210 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5259
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_86882053_8   5260 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5309
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_86882053_8   5310 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5359
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_86882053_8   5360 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5409
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_86882053_8   5410 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5459
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_86882053_8   5460 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5509
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_86882053_8   5510 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5559
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_86882053_8   5560 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5609
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_86882053_8   5610 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5659
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_86882053_8   5660 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5709
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_86882053_8   5710 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5759
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_86882053_8   5760 ATCACTGGCCAT 5771
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2577 27.08 4.21 1.14  chrX_86889342_86895319.rev     2829  3707 (2271)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_86889342_8   2829 GATAGACATCC-ATACTCATGGATCAGCAAAATTAATATTGTTAAAATGA 2877
                           v   i    -  ii        ii v i v             i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_86889342_8   2878 CCATAGTGCTCAAAGCAATTTGTGGATTAAGTGAAATCCCCATCAAAATA 2927
                          v   v v i    vii  i iii    v ii v      i        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_86889342_8   2928 CAAATT---TTTTTT-CAAAATAAGAAAAAGC-AATTATAAAATTCATAT 2972
                          v ii ---      -  i  - vvi v    -i  iv            
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_86889342_8   2973 G-AAACCCAAAAGAGGCCCA-AATATTCAAAGCAAACCTGAATAAAAAAG 3020
                          -   iv   ii  --    -    vi    i   v i    -   i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAA-AAAGAAG 198

  chrX_86889342_8   3021 AATAAAGCTAGAGGCATCACACTACCTGATTTTAAAATGTATTACAAGTC 3070
                           i    i i    vv       v  ii    i    iv  i     iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_86889342_8   3071 TTGAGTTTCCAAAACAACGTGGTATTGGCATAACAATAGACACA------ 3114
                          vv   vvi   i   ii      i        vi       i ------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_86889342_8   3115 ----GGACA------------CAGAAATATATCCATGTATTTATGGCCAA 3148
                         ---- i i ------------        v i    ii        i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_86889342_8   3149 ATGATTTTCAAGAAAGGCCCCAAGAACATGCATTGGGAAAAGGACATGCT 3198
                         v        i v  i  iv      v   v  v    i    i i vv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_86889342_8   3199 CTTCCATAAATGGTACTTGCAAAA-TAGATACCTATATGCAGAAAAATAA 3247
                         i   v i       i  v v v  - i    ? i i     i  i   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_86889342_8   3248 AACTGGATTTCTATCTCCCACCATATTGAAAAATCAACACAAGATGAATT 3297
                          ii    iii   i   v        vv      i   v   i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_86889342_8   3298 A-AGACTTCAATTTAAGACCAAACAATATAAAATTACTAGAAGAAAACAT 3346
                          -    i v   v     v v  v v       i vi             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_86889342_8   3347 AGAAGAAACATGTTAG-GGCATTAGTCTAGGCAAAGATTTTATGGCTAAG 3395
                           i? v  -  v  v - i v  i vi       v i   iv i v  v 
  L1M4_orf2#LINE/    549 AGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_86889342_8   3396 ACCTCAAAAACATAGGCAATAGAAACAAAAATAGACAAATGGGATGATAC 3445
                           vi     i  i i    i i  iv         i    v   ivvi i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_86889342_8   3446 TAAGCTAAAAAGCTTTTGTACAGCAAAGAAAACCATCAACAAA----ACA 3491
                         i  iv v    i       i vv     i v  i     v   ---- v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_86889342_8   3492 ATTAACCTCTTGAATGGGAGAAAATATTCAAAAACAATTTGTTCAAAAAG 3541
                         ivi    iviv                 iiv   iv  v i iii v   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_86889342_8   3542 AGACTAATATCTAGAATATACAAGAAACTCAAACAACGCAATGGTAAAAT 3591
                         i    vi    i        i  ii     vv     v    ii     v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_86889342_8   3592 AATAATAATAATAATCCTATTGAAAAGAAGGCAAAGGGCATTAATAGATA 3641
                         i i  -----    i  v   ?    ivi        iiv v      i 
  L1M4_orf2#LINE/    798 GACAA-----ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_86889342_8   3642 TTTTTCAAAATAAGGCATACAAATGGCCAACCGGTATATGAAAAAATGCT 3691
                            i  v   v   ii              ivi i i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_86889342_8   3692 TAATATTACTAAGCAT 3707
                         i  i  i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 2.76 (47 / 17)  

2978 26.43 1.40 0.81  chrX_86889342_86895319.rev     4645  5503 (475)  C L1M4_orf2#LINE/L1   (0)   908    45  

C chrX_86889342_8   5503 TGAGATGG---TATTTC----ATTGTAATTTATAGATTCAATGCCATCCT 5461
                          i      ---  i i ----    --  i  i        i  v    i
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCC 92

C chrX_86889342_8   5460 CATCAAGCTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-T 5413
                         i     iv v   iivi i  i  ii     -   -- v  i   v i- 
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCT 140

C chrX_86889342_8   5412 AAAGTTCATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAA 5363
                            i           viiv  ii  v  v v  v     iv     i i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

C chrX_86889342_8   5362 GCCAAAAGAACAAAGCTGCAGGCATCACCCTACCTGACTTCAAACTATAC 5313
                         ivv i          i  v   vv    v  v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

C chrX_86889342_8   5312 TACAAGGCTACAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGAGA 5263
                              i          i   i    ii       i i iv ii i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

C chrX_86889342_8   5262 TATAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACAT 5215
                               i        i    i--    i  --        vv   i    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACAT 338

C chrX_86889342_8   5214 CTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAA 5165
                         i  iiiii vi    i  i     ivv  vv  i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

C chrX_86889342_8   5164 AGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATGT 5115
                           i  vvi  v  i  i              v      v  ?   v   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

C chrX_86889342_8   5114 AGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTC 5065
                          i  iiv    ii    i    v   i     v              i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

C chrX_86889342_8   5064 AAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAG 5015
                           i      i ?    i       v   v       i      vi i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

C chrX_86889342_8   5014 AAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTT 4966
                                 v    ?i- v i -   iv   v v  vv i     v ii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

C chrX_86889342_8   4965 CATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAT 4916
                          v ivv  vi            vvi          vv     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

C chrX_86889342_8   4915 GGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATC 4866
                         v   ii v  i   v v  i i   i  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

C chrX_86889342_8   4865 AGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTC 4816
                          i      v  i     i                 v       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

C chrX_86889342_8   4815 ATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTT 4766
                               i  i  i  vi          v  i         vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

C chrX_86889342_8   4765 ACAAGAAAAAAATAAACAACCCCATCAACAAGTAGGCAAATGATATGAAC 4716
                          i  v     i i   i     v  i? v  i i      v   v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

C chrX_86889342_8   4715 AGACACTTCTCAAAAGAAGACATTTATGCAGCTAAAGGACACATGAAAAA 4666
                              i     v        i  vi viii  i  viii          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

C chrX_86889342_8   4665 ATGCTCATCATCACTGGCCAT 4645
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (131 / 92)
Gap_init rate = 0.01 (10 / 864), avg. gap size = 1.90 (19 / 10)  


2997 25.73 2.80 1.23  chrX_86940467_86945049.rev     3199  4092 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_86940467_8   3199 TGGAAAAAT--TCCATGTTCATGGTTTGGAAAAATAGATATTGTTAAAAT 3246
                               i  --i            v      i v vi          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_86940467_8   3247 GCCATTACTAACCAAAGCAATCTACAGATTCAATGTAATCCCTATCAAAA 3296
                          v  v    vv     vii              i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_86940467_8   3297 TACCAATGACATTCTTCAAAGAAATGGGGAAAAATATCCTAAAACTTATG 3346
                          v   iivi v  i  iiv      v iv  ivvv         i i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_86940467_8   3347 TGAAACTGCAAAAGACCCTAAATAGTCAAAGCTATTTTCAGTAAAAAGAA 3396
                           i  v     ii     vi     i    i v  i  v iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_86940467_8   3397 CAAAACTGGAGGCTGGAAAAATCTCATTACCTCATTTCAAATTTTATTAC 3446
                             ii      ------- v  v  i v  iv        vi   i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-------ACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_86940467_8   3447 AGAGCTATAGTAACCAAAACAGCATGGTACTGTCATGAAAGCAGACACAT 3496
                          i     i     i   i    ii        v   i iiii     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_86940467_8   3497 AGACCAATGGAACAAAATAGAGAAACCAAAAACGAACCCACACACCTATG 3546
                            i        i i   v    iv   i   ii      i   ii    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_86940467_8   3547 GTGAACTTGTTTTTGACAAAAGTACCAAGAATATATACTGGAGAAAAGAC 3596
                           v  i vi    i     ii  i      vi  vi v   i    ii i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_86940467_8   3597 AGCCTCTTCAATAAATGGTGCTGCGAAAACTGGATATCCACATGGAAAAG 3646
                           i  i     i           v  v         ?       v     
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_86940467_8   3647 AATTAAA--------CTATCTCTCACCATATACAAAAATTATATCAAAAT 3688
                            v  i--------   i   v                  vv       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_86940467_8   3689 GGATAAAAGACTTAAATCTAAGACATCAAACCATGAAACTACTACAAGAA 3738
                             v ?    i     v     vv v    i  i     vi  v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_86940467_8   3739 AACACTAGGGA-AAATATCCAGGATGTTGGTCTGGGTAAAATATTTTTGA 3787
                             -    ?i-    v i iv  iv    vi i  i  vi-i   i v 
  L1M4_orf2#LINE/    544 AACA-TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTA 591

  chrX_86940467_8   3788 GCAAT-ACTCCACAAGCACAGGCAACCAAAGCAAAAATTCACAATATCAA 3836
                          vv  -  v   v       i     v    v      vv i  vv vi 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_86940467_8   3837 CTT----AAAA---AAAGCTTCTGCACAGCAAAGGTTAACATCAACAAAG 3879
                            ----    ---   i   i  ii vv      vi vi     v    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_86940467_8   3880 TAAAGAGACCACCCACAGAATGGCAGGAAATATTTGCAAACTACTCATCT 3929
                          i  i    v             v  i             ii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_86940467_8   3930 TACGAAGGA--TGTATTGCTAGTGTATATAAGCAGTTCAAATAACTCTGT 3977
                         v ii i   --     -- i  vi       iv ii  vv i     vi 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTAT--CCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_86940467_8   3978 AAGAAA----TTAATACTCTGATCAAAAACTTAGCAAAATATTTTCACAG 4023
                           v   ----iv    vi ii  i?    v vi     iv    vv i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_86940467_8   4024 ACATTTTTGAAAACAAGACATGTAAATGGCAAACAGCTACATAAACTGAT 4073
                               i vv   v    i  ii       v  i ivi    i  vv   
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_86940467_8   4074 GCTCAACAACACTGATCAT 4092
                                 v  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (130 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.00 (36 / 12)  


1965 26.76 5.00 1.03  chrX_86978423_86980482      888  1567 (493)    L1M4_orf2#LINE/L1      202   908 (0)  

  chrX_86978423_8    888 AATGCTAGAGGCATCATGCTACCTGATGTCAAACTATACTACGGAGATAC 937
                           v i i    vv   ii  v  ii  v     viv      ii  v   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_86978423_8    938 AGTAAGCAAAACAGCATGGTACTGGTACAAAAACAGACACACACACCAAA 987
                              v   i    ii         i i  ii i     i i v i   v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_86978423_8    988 GGAATAGAATAGAGAAAACAGAAATAAGGTTGCATACATGCACGTATC-- 1035
                                   v    ivv         ivi--       vi i -i  --
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATG-GTCAA 348

  chrX_86978423_8   1036 -TGACCTTTGACAAAAA---CAAG------CAATGGCAGAAGGATTTTCT 1075
                         -   ii  i     iii---    ------      vii   i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_86978423_8   1076 ATTCAATAAATGATGTTAGGATATCTGAATATCCATATGCAGAGGATTGA 1125
                         v     i     i  i i   i v   i   ?   i     i i  v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_86978423_8   1126 AACTGGGCCCCTTACTTACACCATATACAGAAATTAA-----GATGGATT 1170
                          ii   i     vv  i            i       -----i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_86978423_8   1171 AAAGATTTAA-TGTAAAATCAAAAAGTATAAAAACCCTGAAAGATAACTT 1219
                          ?   ii   -     i v v    v       vi i ii    v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_86978423_8   1220 AGA---AAATACCATTCTGGACACAGGGATAGACAATGGTTTCATAATGA 1266
                           i---    -- -   vv   viv   v   i          v  ivv 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_86978423_8   1267 AGACATCAGAAGCAATCGCAACAAAAGGAAAAATTGACAAATGGGATCT- 1315
                         v    i  i     vvv          i      v  i    v   ii -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_86978423_8   1316 -----AATTAAAGAGCATCTGCACAGAAATGGAAGCTATCAACAGAGTGA 1360
                         -----       i - v i  ii vvv  v   vi       v i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_86978423_8   1361 ACAGACAATCTAGAAAATGAGAGAAAATTTTTGCAAACTAAAGATCTGAC 1410
                          v      i i v i    i        v        ii v v      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_86978423_8   1411 AAAGTTCTAATATACAGTATCTATAAGGAACT--TA-AATTTA-TAAGAA 1456
                           i vv  vi   v   v  v     i     --  -  i i -   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_86978423_8   1457 AAAAAT---CAACTCCATTAAACAGTAGGCAAAGGACAGGAACAGACACT 1503
                            i i---i   i v   ?  v i i         ivv   i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_86978423_8   1504 TTTCAAATGAAGACATACATGCAGCCAACAATTATATGAAGAAAAGCTCA 1553
                          i  v  v     i     viii     i  vi i     i i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_86978423_8   1554 GTATCACTCATCAT 1567
                         ii    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (107 / 72)
Gap_init rate = 0.02 (16 / 707), avg. gap size = 2.56 (41 / 16)  


2373 29.18 1.61 1.50  chrX_87014063_87021630     4239  5105 (2463)    L1M4_orf2#LINE/L1        1   868 (40)  

  chrX_87014063_8   4239 TAGAAAAACATTCCATGCTCATTAATTGGAAGAATCAATGTTGTTAAAAT 4288
                          i    i i  i     i    vi         v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87014063_8   4289 GACCATACTGCTCAAAATACTCTA--GATTTAACATAATTCCTATGAAAT 4336
                          i v     v i    v iv    --    i   ii   i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87014063_8   4337 TAGCAAC-ATCGTTTTCACAGAAGTAGATAAAAACAATTACAGAATACAT 4385
                          vv  i -ii v    ii     i v  i  iv-ii  ivi i   v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_87014063_8   4386 ATAAAACCAGAAAAGAGGTTGAATACACAAAACAATACTAAGCAAAAGCA 4435
                           ii  viiv  ii  vviv     vv         vi i iv  i iv 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_87014063_8   4436 ACAAAGTGAGAGGTTTCACATTACCTGACATCAAATTATACTATAAGGCT 4485
                                vi    vi     i v  ii iv     viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_87014063_8   4486 TCAATAGTCCGAACAGCACAATACTGGTGTAACAATAGACACACAGATCA 4535
                         v  i  i  vii    iiiii      ii   vi       i i      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_87014063_8   4536 ATAGAACAGAATAGAGAACCCAGAAATAAAACCACACACGTACAGCCGAT 4585
                           i   i     v    ii           v   i   iv  ii i i  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_87014063_8   4586 GCATCTTTGATAAAGTCAACAAAAATAAACCACTGGGAAAGGACACCCTA 4635
                         vv  i  i  i  i viiv   i vi vv v iv       i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_87014063_8   4636 TTCAGTAAATGGTGGTGAGGAAACTGGCTACCCATATGCAGAAGAATGAA 4685
                             ii        v  i iv      v  ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_87014063_8   4686 ACTAGACACCTACCTCTCACCATACACAAAAATTAACTCAAGATGGATTA 4735
                         ii i   v        v       i                i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_87014063_8   4736 AAGACTTAAATGTAAGAACTTAAACTA-AAAGTTCT-AGAAGAAAACCTA 4783
                         ?    i           i  v      -   ii   -          v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_87014063_8   4784 GGA--AAATCTCTTCTGGACATTGGCCTAGATAAAAAATT-TAAGACTAA 4830
                           ?--      --  vv   v    vi   ii  viiv  - v   -  v
  L1M4_orf2#LINE/    550 GGNGTAAATCT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TAT 596

  chrX_87014063_8   4831 ATTCTTGAAATCAAATGCAGCAAAAATAAATATAGACAAATAGTAATTAA 4880
                         iviviii   v  v v   i     iv   v     i    v v v  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_87014063_8   4881 TTAAAATAAAGAGCTTCTGCAAAGAAAAAGAAACTATCAACAGGGCAAAC 4930
                          i     v  i i   i  iivvvv   i  v        v ii ii  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_87014063_8   4931 AGATAACATGCAGGGTGACAGGATGAAAGAAAATATTTGTAAACTATACA 4980
                            i   vi--------    i   ii            i   ii   i 
  L1M4_orf2#LINE/    697 AGACAACCC--------ACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_87014063_8   4981 TCTAACAAAGAAATAATATCCA-AACCTATAAGGAACTTAAACAAATCAA 5029
                            i i  i i v vi      -  iv     i     ivv    v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_87014063_8   5030 CAA----GAGA-AAATAACCCCATTATAAAGTGGACAAAGGATACGAATA 5074
                         i  ----i   -         v   ?v   i   i        vi     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_87014063_8   5075 AACACACTTCAAAAGAAGATGTATGATATGG 5105
                         i   ivii  v         i  ii -    
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAA-ATGG 868

Transitions / transversions = 1.65 (155 / 94)
Gap_init rate = 0.02 (14 / 868), avg. gap size = 1.93 (27 / 14)  

 263 12.00 0.00 0.00  chrX_87014063_87021630     5492  5541 (2027)    L1M4_orf2#LINE/L1      859   908 (0)  

  chrX_87014063_8   5492 ATACAACTGGCCGACAAACATATGAAAAAATGCTCAACATCACTAATCAC 5541
                               v     i i  i  i       i             ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 5.00 (5 / 1)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.00 (0 / 0)  

2291 26.64 2.89 1.97  chrX_87014063_87021630     6314  7075 (493)    L1M4_orf2#LINE/L1      140   908 (0)  

  chrX_87014063_8   6314 TAGAACTCATACTTAACCACAAGAAACTGAGAATAACCAAGGAAATCTTG 6363
                           i  i     ivv  vii    ii  iv      i    iiv       
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_87014063_8   6364 GATGAAAAG--CAAAGCAGGAGGCATCACACTTTCTGATTTTAAAATATA 6411
                         i vi i   --     iv     vv        i ii    i    iv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_87014063_8   6412 TCACAAAGATATGGTAATCAAAAGACCATGATATTGGCATAAAGACAGAC 6461
                         ii      v  ii        i v vii  i  i        i  i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_87014063_8   6462 ACAAAGACCCATAGACCAACAGAACAGAATAGAGATCCCAGGAGTAAAGT 6511
                          i --------    i   ii   i     v    vi    i i    vi
  L1M4_orf2#LINE/    290 ATA--------TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_87014063_8   6512 CATTTATATATGGTTAATTTGTCTTCGACAAGGGTGCCAGGAATAAATAA 6561
                            vi  v      i    vi i                i  vi vvi  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_87014063_8   6562 GGGAGAAAAGATCATCTCTGTAACAAATATTGTTGGGAAAACTGAATATC 6611
                         v  i    ii  vi   i vi       iv  i     v     i   ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_87014063_8   6612 CACATACAAAATAAGGAAATT-------------ACACCATACACAAAA- 6647
                              i     v  v   i  -------------        i      -
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_87014063_8   6648 TCAATTAAAAAGATATGAAAGACAAAAAAGTAAGACCCCAACCTCTAAAT 6697
                          i  i v    viv  v ?    vv   v      v iv  v  v    -
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA- 530

  chrX_87014063_8   6698 ATTTTTTTAA---AATATAGGTGAGAAGCTTTATGACATAGGTATTGGCA 6744
                          i i  vv  ---  i     ? vi  v   ii    v v  vv v    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_87014063_8   6745 ATGATTCTTTA-ATACAAGACCAAAATCACAGATATCAAAAACAAAAATA 6793
                            i  ii   -   ii v       v    iii v     iv       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_87014063_8   6794 AACAAGTGGGACTACGTTAACCTAAAACGTTTCTGCACAGCAAAAAAAAA 6843
                         i i  i v     v i i  vv v   vii  i  ii vv    ii v -
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA- 679

  chrX_87014063_8   6844 ACCATCAACAAAGTGAAAA-ACAACCTATGGAGTGGGAGAAAATGTTTCC 6892
                         - i     v          -      i ii  i           i   v 
  L1M4_orf2#LINE/    680 -CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_87014063_8   6893 AAAAAATATATCTGAAAAGAAGTTAATCTCAAAAGTATATAAGGAACTCC 6942
                            vv          v   iiii vi v  v i i       i      i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_87014063_8   6943 TATGATGCAATAGTTCAAATAATAATAATAACTCAATTTAAAAATGAGTT 6992
                           ii iv     i vv   -i i  --     i     ?       i iv
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAA-GACAA--ATAACCCAATTWAAAAATGGGCA 825

  chrX_87014063_8   6993 AAGGAATTGAATAGACATTTCTCCAAAGAAGACCTAAAAATGGCCA-CGA 7041
                              v                          iv  v         -ii 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_87014063_8   7042 GCTATATGAAAACATGCTCAATGTTACTAATCAT 7075
                           - i       v        ii i ????????
  L1M4_orf2#LINE/    876 GC-ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (121 / 78)
Gap_init rate = 0.02 (13 / 769), avg. gap size = 2.85 (37 / 13)  

 343 13.89 1.39 1.39  chrX_87014063_87021630     7446  7517 (51)    L1M4_orf2#LINE/L1      837   908 (0)  

  chrX_87014063_8   7446 TAGACATTTCTCCAAAGAAGACCTAAAAATGGCCA-CGAGCTATATGAAA 7494
                                              iv  v         -ii   - i      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC-ACATGAAA 885

  chrX_87014063_8   7495 ACATGCTCAATGTTACTAATCAT 7517
                          v        ii i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2)  


2515 28.70 2.00 1.00  chrX_87023012_87027636     3234  4132 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87023012_8   3234 TGAAAACACATCTCATGCTGATGGATGGGAAGAATCAATAGTGTAAAAAT 3283
                           i   v i   i    i v      v      v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87023012_8   3284 GATCATACTTCTCAAAGCAATCAACTGATTGAATGCAATTTCCATTATGA 3333
                          iiv     i i    vii   v  v    v  i     ii i  i vi 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87023012_8   3334 TACCATCATAATTTTTCACAGAATTAGTAAAAAC-AATCCTAAAATTTAT 3382
                          v   v vvvv     ii     v v - v  i -i           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chrX_87023012_8   3383 ATAGTACCCAAAAAGAGCCTGAATAGCCAAACCAATTCTAAGCAAAAATA 3432
                           i v vivv  ii  v  v           v    ii i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_87023012_8   3433 ACAAATCTGGAGGCAC-CACATTATTGAATTTTGGGTTACACTACAAAGC 3481
                              vi      -  -    i viiv     iiiivivi          
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_87023012_8   3482 TATACTTACCAA-ACAGCATGCTACTGGTATAAATGTAGGCACATATAAA 3530
                           i v v i   -    ii  v      i    ivi   --       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG--ACATATAGA 296

  chrX_87023012_8   3531 --AATGGAACTGAATAGAGAACCCGGGAATAAAGGCAGATACGTATAGCC 3578
                         --       iv    v    ii  i i      vv  v i iv   i i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_87023012_8   3579 AACTGATCCTTGACAAAGCATACTGAAAC-ATAAATTGGAAAAAGGACAC 3627
                           i    ii i     i -i i ii i  -  vv v   ii    i i v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_87023012_8   3628 CCTATTCAGTAAATGGTGCTGGGAAAACTGCCAAACCACATGTAGAAGAA 3677
                         i  v    ii              v     vvv ?       i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_87023012_8   3678 GGAAACTGGGTTCCCATTTCTCACCTTATACAAAAATCAACTCAAGAATG 3727
                         v   ii   iii  i ii  v    v           i       -    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA-AATG 494

  chrX_87023012_8   3728 -ATCAAAGACTTAAATCTAAAGCCTGAAAACATAAAAATTCTAGAAGATA 3776
                         -    ?    i     v   iiv  i   vi      v ii       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_87023012_8   3777 ACATTGGAA-AAATCTCTTTTGGACACCAACCCAGGCACAGAATTCATGA 3825
                             v  ?i-      iiv --   viiiivii     vv iv   v ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT--GACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_87023012_8   3826 CTAAGACCCCAAAATCAAATGCCTCCAAAACAAAAATAAATAAATGGGAC 3875
                         v  v   v      v  v v  vv v   iv       i      v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_87023012_8   3876 CTAATTAAACTAAAAAGCTTCTGCACAACAAAAGAAATAATCAGTAGAGT 3925
                         i v  i   v v    i   i  ii vv    i  v iv    iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_87023012_8   3926 AAGCAAACAACCAACAGAATGGAAGAATATATTTTTAAGCCATGCATCTG 3975
                         i iv i      v         i    v      vi  ii   ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_87023012_8   3976 G--AAAGACCAGTATCCAGAAGCTATATGGAACTCAAACAAATCAGCAAG 4023
                         i-- ii   iv          vv    vi      vv    v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_87023012_8   4024 AAAAAAAATGAATAATTTCATCAAAAAGTGTGTAAAGGACATGAGTAGAT 4073
                              i -ii     iiiv  i?    i  v i      iv   i    i
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_87023012_8   4074 ATTTCTCAAAAGAAGATTTACAAATGTCCAAT--------GAAAAAATGC 4115
                                v         v        v     --------     i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_87023012_8   4116 TCAACATCATTAATCAT 4132
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (147 / 107)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.69 (27 / 16)  


2823 27.67 1.44 0.56  chrX_87038131_87042421     2899  3798 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87038131_8   2899 TGGAAACACATGCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2948
                               v i  v     i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87038131_8   2949 GACCATACTGTCCAACGCAATCTATAGATTCAATGCAATTCCTATCAAAA 2998
                          i v     vi    vvii     i        i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87038131_8   2999 TACCATCAGCATTCTTTACAGAAATAGAAAAA--AATTA-AAAATTCATA 3045
                          v   v v  v  i   i       v  v  i--i  iv-          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_87038131_8   3046 CAGAACCAAAAAAGAGCCTGCATTGCCAAAGCAACACTAAGCAAAAAGAA 3095
                         ii   viiv  ii  v  v v  v      i   ivi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_87038131_8   3096 CAAATCTTCAGGCATGACATTACCTGACTTCAAATTATACTACAATGCTA 3145
                             vi vv   vv v   i v  ii i      viv        v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_87038131_8   3146 TATTTA-CAAAACAGCATGATATTGGTATAAAAATAGGCACATAGACCAA 3194
                         i v v -   i    ii  i  i   i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_87038131_8   3195 TGGAACAGAATAGAGAACCCAGAAATAAAGCAAAATACTTACCGCCAACT 3244
                              i     v    ii           v v v i i   iv i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_87038131_8   3245 GACCTTTGACAAGGCATACAAAAACG--TAAATTAGGGGAAGGACACCCT 3292
                           ii  i       -i i v  i  v-- v   -i   i   i i vi  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCT 398

  chrX_87038131_8   3293 ATTCAATAAATAATGCTGGGAAAACTGGCAAGCCACATGTAGAAGAATAA 3342
                         v     i    ii        v      vv ?       i i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_87038131_8   3343 AACTGGATTCTCATCTCTCACCTTATACAAAAATCAATACAAGGTGGATC 3392
                          ii    ii ii i   v    v           i  iv   ii      
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_87038131_8   3393 CAATAATTAAATTTAGTACCTGATACCTTAAATATTCT-AGAAGATAACA 3441
                         v? v vi     v  iv v  i v  iv    - i   -      v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chrX_87038131_8   3442 TTGGAAAAACTCTTCTTGGCATTGGCTTAGGCAAAGATT-CATGGCTAAG 3490
                          v  ?iv  v     v  i v    v        v i  - v i v  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_87038131_8   3491 ACCCCAAAAGCAAATGCAACAAAAACAAAGATAGATAAATGGGACCTAAG 3540
                           v         v v         iv   i          v    i v v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_87038131_8   3541 TAAACTAAAATGCGTCTGCACAGTTAAATTAATA--ATTAGCAGAGTAAA 3588
                         i   v v   vi v i  ii --  v  vvi i --  i iv i   i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGC--TTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_87038131_8   3589 CAGTCATCTCATAGAGTGAAAAAAAAT--TCACAAACTATGCATCCAACA 3636
                         v  v  v i  i   i  ii i     -- ii    ii  ii   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_87038131_8   3637 AAAGACTAATATCCAGAATCTACAAGGAACTCAAGCAAC-CAGCAAGGAG 3685
                          ii    vi          v  i  i      vvi    -  ii  vi i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_87038131_8   3686 AAAACAAATAATCCTATCAAAAAGTGGATAGAGGACATGAAGAGACAATT 3735
                           i        i  v  i?    i   ii i    iv    v     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_87038131_8   3736 CTCCAAAGAAAATATACAAACAGCAGACAAACACATGAAAAAATGCTCAA 3785
                                   i         ii  vi i  i          i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_87038131_8   3786 CATCACGAATTAT 3798
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.38 (18 / 13)  


2354 28.43 3.40 1.81  chrX_87083823_87085869      664  1546 (501)    L1M4_orf2#LINE/L1        1   897 (11)  

  chrX_87083823_8    664 TGGAGAAATATTCTTTGTTAGTGGATTGAAAAACTCAATATT------AT 707
                             i i    i iv    vi       i  i   i      ------  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87083823_8    708 GGTGCTTTTTTTTAAACATAACATTTAGATTAAATGAAATTTCCACCAAA 757
                           iiv vi iiii   i- i iv vi     v  i v   ii i i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_87083823_8    758 ATATTAGCAAGCAATTTTGTAGATATCAATAAACATATCCTAAAGTTTAT 807
                           vii   viv vv     i   v  ii i  i vv        i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_87083823_8    808 ATAGAAAGGCAAAAGATCCAAAAATACCTAATATTAATAT-AATATAAAG 856
                           i    v    ii  i   i  -  v i  v i-   v -i v v i i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAA-TAGCCAAAAC-AATCTTGAAAAAGAA 197

  chrX_87083823_8    857 GAACAAAGTTGGAAGGTGGATACTACCTAACTTCAAGACTCACTATCAAA 906
                                      i iivv i   v  i  i     i   i    iv  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_87083823_8    907 CCACAATAATCAAGACAGTGTGGTATAAGTGAAAGAATAGATGAATAGAT 956
                          i   i                   ivi iiv   i     iiv      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_87083823_8    957 CAACTTAACAGAATAGGGAGCCCAGAAATAGACCTACACAAATACAGCCA 1006
                            ivv  i     v i   i         i   i i   vv  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_87083823_8   1007 ACTGATCTT-GTCAAAGAGGT-AAGACAATTCAATGGAGAAAGGATAGCG 1054
                          i    i  - v   i iv i-     v         i     i    iv
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_87083823_8   1055 TTTTTAATAAATGGTGCTGGAATAATTGGACATTCACATGCAAAAAAA-G 1103
                             i  i            i i  i    i ?i           i  - 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_87083823_8   1104 TACACAGACACAAACCTTATACTTTAAACAAAGAATTAACTTTAAATGGA 1153
                         v vvii   v vv    i i  iv  v     -        iv       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAA-AATTAACTCAAAATGGA 496

  chrX_87083823_8   1154 TTAT---------TGTAAGAGGAAACTCTATGAAATTGT-AAAAGATAAC 1193
                          i ?---------        vv  vv    i   i v - i    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_87083823_8   1194 ATAGGAGAAAAAAGCTAACTTACTTTGGGTTTGGTAGCCAATA-TATTTT 1242
                              ? v   --v  vvv v  i       v  ----    i- v i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGG----CAATGGTTTCTT 590

  chrX_87083823_8   1243 -GACA---CATCAAAAGTACAATTCATGATATAAAATAT-TATAAATTGA 1287
                         -  i ---  i      i    viv ii v v    v  -v        i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_87083823_8   1288 ATTTTATTAAAATTAAAATGTTTTCT-CTGTGAAATACAATTTTAAAAGA 1336
                          i  i  i          vv    v -  vii  iv   v v i  i i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_87083823_8   1337 AGGAATAGATAAGCTACAAACCAAGGGAAAATATCTAGAAATCACATATC 1386
                         iv   v   i  v i   i viii i        i iv      i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_87083823_8   1387 TGATAAAGGACTTGTATCAAAAATATATTTTTAAA--ACTCTTAAAATTG 1434
                               i           v i       ----   --       v  i v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATAT----AAAGAACTCTTACAACTC 786

  chrX_87083823_8   1435 GCCAATACGAAAACAAACAAATCATTTAAAGAATGAGCGAAAGATCCTAA 1484
                         ivi    vi  i     i  vi  v  ?  i    i  i  i   iiv  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_87083823_8   1485 CAGACACCTCATGAAAGAAGATGTGCAGATGGA-AATAAACTATTTGTAA 1533
                         i     ii  viv         i i  i    v-     i - iv  v  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC-ACATGAAA 885

  chrX_87083823_8   1534 AAATGACTCAGCA 1546
                          i   -    i  
  L1M4_orf2#LINE/    886 AGATG-CTCAACA 897

Transitions / transversions = 1.68 (155 / 92)
Gap_init rate = 0.03 (23 / 897), avg. gap size = 2.00 (46 / 23)  


2506 26.73 4.45 3.34  chrX_87102288_87106826     3149  4046 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87102288_8   3149 TGGAAAGACATCACATGCTCATGGGTCATAAGAATTAATATTGTTAACAT 3198
                                 i   v    i      i iiv    v             v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87102288_8   3199 GATCATACTACCCAAAGCAACCTGTAGATACAATGTAATCTCTATCAAAA 3248
                          iiv     v      vii i  ii    v   i i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87102288_8   3249 TACCAATGATGTTTGTCACAGAAATAAAAAA----ATCTCTAAAATTTAT 3294
                          v   iiviiv   v ii       vi v  ----   -        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-CTAAAATTCAT 149

  chrX_87102288_8   3295 ATAGAACCAAAAAAGAGCCTGAATATCAAAAGTGATGCTGAGTAAAAAGA 3344
                           i   viiv  ii  v  v     v v   iii  vi   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_87102288_8   3345 ACAAAGATGGAGGCATCACATTACCTAACTTCAAAATATACTTCAAGGCT 3394
                               v      vv     i v  i  i       iv    v   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_87102288_8   3395 ATAGTAACCAA-ACAGTATGGTATTGGTATAAAAACAGACACATAGACCA 3443
                          i     i   -     i     i   i    ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_87102288_8   3444 ATGAAACAGAATACAGAACCCCAAAATAAATTCAAATATTTATAGCCAGC 3493
                            i  i     vv   ii  vi       ii  v i      i i  ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_87102288_8   3494 TGAGTGTCTACAAAGGCAGAAAGAAAAAATATTGAAAAAAGGACATCCTC 3543
                            v v  v    i  iivv    vv vvi v  iii    i i vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_87102288_8   3544 CTCAATAAATGATGCAGGGAAAACTGGGTACCTATA-------------- 3579
                         i    i     i   v    v      i  ? i i --------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_87102288_8   3580 ----GATCC-TATCTCTCATTATATACAGA---TAACTCAACAGGAATGA 3621
                         ----  i  -  i   v  ii       i ---        v v i  v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_87102288_8   3622 AATACTTAAATATAAGGCCTGATACATTAAGAGTACTAGAGGAAAATACA 3671
                         ? v  i     i    iv  i v  vv   i v vi    i     i --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-- 547

  chrX_87102288_8   3672 CTAGAAACAG---TCCAGGACATTGGTTTAGGCAGAAATGTGATGGCTGA 3718
                         -   i?ii i--- i iv   v    v       ivii v vv i v iv
  L1M4_orf2#LINE/    548 -TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_87102288_8   3719 AACCTCAAAAGCACAGGCAAAAACCCCAAAGGTAAACATATTACGCTATT 3768
                         i  vi          i    ------    i v   v   ---- -----
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAA------CAAAAGAAAAAATA----G----- 631

  chrX_87102288_8   3769 TACATAGTGTAGTATAGAACTATATTAGACTTAAAAGCTTCTGCACAGCA 3818
                         ---   i------  v i   vi  i i v      i   i  ii vv  
  L1M4_orf2#LINE/    632 ---ATAA------ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_87102288_8   3819 AAACAAACAATCAACAGAGAGAAGAGACAACCTGATGAATGGGAGAATAT 3868
                           iv v  v     v i  v   i        iivv           v  
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_87102288_8   3869 ATTTTCTAACTATTTATCTGACAAGGGACTAATATCCAGAATATACAAA- 3917
                             v v  ii  v       i        vi             i   -
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_87102288_8   3918 --------TAACTTAACAGTAAGAAAGCCCAAATAATTCTATT-AAAAAT 3958
                         --------i    i  i i   i  ii --      ii v   -      
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGAC--AAATAACCCAATTWAAAAAT 820

  chrX_87102288_8   3959 GAACAAATGACATGGATAGACATTTCTCAAAAGAAGACATACAAATAGCA 4008
                          ii    v  iv  i             v        i        i  v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_87102288_8   4009 AACAGGTATGTGAAAAAATGCTCAACATCACTAATTAT 4046
                           i i i ii      i             ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.67 (70 / 15)  

 223 28.97 1.87 1.87  chrX_87102288_87106826     4433  4539 (0)    L1M4_orf2#LINE/L1      521   627 (281)  

  chrX_87102288_8   4433 AAACCCTAAAAATTCTAGAAGATAACATTAGAAAAACTTTTCCAGGCATT 4482
                             iv     v ii       v     vi ?iv  v i   vv i v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_87102288_8   4483 GGCTTAGGCAAATAATTCCT--GACTAAGACCCCAGAAACAAATGCAAGA 4530
                           v        - ii  i  --  -  v   v   i  i  v v    v 
  L1M4_orf2#LINE/    571 GGGTTAGGCAA-TGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACA 618

  chrX_87102288_8   4531 GAAACAAAA 4539
                         i  iv    
  L1M4_orf2#LINE/    619 AAAGAAAAA 627

Transitions / transversions = 0.88 (14 / 16)
Gap_init rate = 0.03 (3 / 107), avg. gap size = 1.33 (4 / 3)  


2532 22.11 5.27 4.11  chrX_87116415_87118163      479  1256 (493)    L1M4_orf2#LINE/L1      122   908 (0)  

  chrX_87116415_8    479 AAATTAACTATTGCACTAA-CTTAGAATTTATATGAAAATTCAGGGGACA 527
                              i  v ----i  i - i  i    i     i    v  i     v
  L1M4_orf2#LINE/    122 AAATTGACAA----GCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_87116415_8    528 CAGAATAGCCAAAATAATACTGAATATGAGTCACAAAGTTGGAATACTCA 577
                                       i   vi    v v  ivv           iv     
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_87116415_8    578 CATTTCCATATTTCAAAATGTACTACAAAGCTACAGTAATCAAAACAGTT 627
                           i    vv         iv                       i     v
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_87116415_8    628 TTGAGCTGGTATAATGATAGCCTTATGGACCAATGGAATAAAATTGAGAA 677
                          v vi    i    v     v v   i  i          i        i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_87116415_8    678 CCTAAAGGTAAATTATTATATTCATTATCAATTGATTTTTGGCAAGAGTA 727
                         i i i ii    iivv  i   i  vi            i i    i  i
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_87116415_8    728 CCAAAACCATTCAATAGGGCAAAGAAAAATGTCTTCCATGAATGTTGCTG 777
                             i          i   -      v i v i   v ii    v     
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_87116415_8    778 AGAAAACT--ATATTCACATTTTCAAAA-AGTAAATTTAGACCCTTAGC- 823
                         i  v    --   ?i     v--     - i i  v  i     i  v -
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATG--CAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_87116415_8    824 ----CTAGATACAAAA-TTAACTGAAAATATATCAAAACTCCATATTTAA 868
                         ---- i v        -      v     iv    ? ivi i v  v   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_87116415_8    869 GAACCAAAGAGATAAA-CTCTTA----------TAGGC--AAATCTTCAA 905
                           i i   ivv     -      ----------    ?--        iv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_87116415_8    906 AACCTTTGAACTGACAATAGTTTATTAAATATGACACCAAAAGCATAGGT 955
                         i     v iviv i    i    v   i                 i i i
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_87116415_8    956 AATAACA---AAAATAGATATATTGTACTCCATCAAAATTAGCAACTTTT 1002
                           i  v ---          v    v   i           iv       
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_87116415_8   1003 GTGCATTGAAAGATACTACTCAAAAGAGTAGAAAGATAACCCACATACTG 1052
                             v ii  i  i    -    i i   ii     i        v v  
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_87116415_8   1053 TGAAAAAATATTTACAAATGTTTGCAAAATATTTATAAATCAGATATCTG 1102
                         v  i         i     ---------------------  v       
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAAT---------------------CATATATCTG 742

  chrX_87116415_8   1103 ATAATTGTTTAATAATTAAATTATGTTTTAAA------TCACAAGTCAAC 1146
                             vv vi vi  vii i v   i ---   ------ i    v    i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATAT---AAAGAACTCTTACAACTCAAT 789

  chrX_87116415_8   1147 CACAAAAAGGCAAGCAACCTAATCAAAAAGTGCCCAAACGAGTTAAATAG 1196
                         v i      i   ii    i   i?    i  vv    v  v  i     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_87116415_8   1197 ACATTTCTATAAAGAA--TATGGAAGT-------AAGCACATGCAAAGTT 1237
                                 vi      --   iv  i -------         v    v 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_87116415_8   1238 ATTCAGCATCATTAATCAT 1256
                         ii   i     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (101 / 67)
Gap_init rate = 0.02 (18 / 787), avg. gap size = 4.06 (73 / 18)  


1831 27.40 7.38 2.46  chrX_87135454_87137512      726  1579 (480)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_87135454_8    726 CCATGTTCATAGATTGCAAGACTCAACTTGGTAAATATATCAATTCTCAA 775
                                   i     v      i  iv v  v  v  iv    v   vv
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_87135454_8    776 TAAATTGATAAACAGGGTTAACATAATGCTGCTGACAA---CCCAGGAAG 822
                         i        vv    iv i   ii   v --  iv   ---     vviv
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCC--CTATCAAAATCCCAGCTGC 110

  chrX_87135454_8    823 ATACTCTGTAGTTATGGATAAGATTACTTGGAAAGTCATATGGAGA-GAA 871
                         v vi i  i  vv  v  i   v v iiivi   v         i - v 
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_87135454_8    872 AAATACGCTAGGATTGATGAAATAATTTTGAAAAGGAAGAATAAAGTGGG 921
                          iiv  - i  i  v vii   i   i       i      i     v  
  L1M4_orf2#LINE/    161 AGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_87135454_8    922 AGGAGTCAGTCTGTCTAATTACAAAACTTACTACAAAACT-TATTA--TA 968
                             v   vv  vi i    v                i  -i v  --i 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_87135454_8    969 TAAC--TAT--TATTTTTAGAAGGGACAGACACATAGA---ATGGAACCA 1011
                         vi  -- i --  i vvi v    - i     i     ---      ivi
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGG-ATAGACATATAGATCAATGGAATAG 308

  chrX_87135454_8   1012 AACAGA-AG---AAAAATAGGACTACATGTATATGGCCATTTGATTTTTG 1057
                           iv  -  --- i     iiv i i ii v     i  v        i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_87135454_8   1058 CCATAGGCACAAATGTGATTCAATGGAGGAATGATAAACTTTTTAACAAA 1107
                         v  vi  ii v  viiv         i i  vi   iv     i      
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_87135454_8   1108 TGGTGATGAAACACGTGCATACCAATAGGCAAAA-ATTGACCTTAAACTA 1156
                              v  ii   vv  v   ? v i v      - v   vv  ii  iv
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_87135454_8   1157 A-ATCTCTCA--AT-TA-AAAACTTAACCCAGAATGCATCATTGACTTAA 1201
                         v- i   v  --  -  -    v     i  i    v    ?v   i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_87135454_8   1202 ATATAAAACTTCAAAATATAAAACTATTAGAAGTAAACACAGGATAAAAT 1251
                           i   i vi v   v         v       v     i   ?vv    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_87135454_8   1252 CTTTGGAATATAGGGCTAAGCAAAAAAGTAT-TTAAACATGACACCAGAA 1300
                            i vi iv v   i  i    vi--  v -   i i         i  
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATG--GTTTCTTAGATATGACACCAAAA 606

  chrX_87135454_8   1301 A---AAATGACGCATAATTTTTGGAAAT-GATAAATTGGACTTCATCACA 1346
                         i---  iii  iv vi -----ii    -                   v 
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGA-----AAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_87135454_8   1347 AGTTAAACCTTTTGGTCTGCAGACACCTCTATTAAGAGGAAGAAAAGACA 1396
                          v v   v      vv  v  i viv v    i    iiiv         
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_87135454_8   1397 AGCTACAGACTGGGAGAAAGTATTTGCAAAC----TATCT---------- 1432
                          v i     v         i          i----     ----------
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_87135454_8   1433 TTATATTTAAAACTTATAAATACCTCAAGGTACAGTATACATTCAACAAT 1482
                           i   ii i  iv      v v   ---v    ------ i    i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTC---TTACA------ACTCAATAAT 792

  chrX_87135454_8   1483 AAAAG---------------CTAGAAATGGACAAAAGACATGAA-AAACA 1516
                             i---------------i? i      i    i  iv    - i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_87135454_8   1517 TTTCACAGAAGAGTATTTACACATGGCACATAAGCG-ATGAAACACAT-- 1563
                             v vi    iv  v    v     vv      i-      - v  --
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATGC 891

  chrX_87135454_8   1564 -TAATATCATGAGTCGT 1579
                         -i  i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.13 (122 / 108)
Gap_init rate = 0.03 (31 / 896), avg. gap size = 2.71 (84 / 31)  


1054 25.34 0.00 0.00  chrX_87146895_87151406.rev      202   497 (4015)  C L1M4_orf2#LINE/L1   (0)   908   613  

C chrX_87146895_8    497 GCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAACTT 448
                                   vv     v  i    v   ii v  i   v v  i     
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

C chrX_87146895_8    447 TTGCACAGCAAAAGAAACCACCATCAGAGTGAACAGGCAACCTACAGAAT 398
                            ii vv    i  v  i i  vv i      v  i     i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

C chrX_87146895_8    397 GGGAGAAAATTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCTAGA 348
                                   v       vii ivi      i  i  i  vi    i   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

C chrX_87146895_8    347 ATCTACAATGAAAACCAACAAATTTACAAGAAAAAAACAAACAACCCCAT 298
                           v  i  v   vv iv    v iv i  v     i     i     v  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

C chrX_87146895_8    297 TAAAAAGTGGGTGAAGGATATGAACAGACACTTCTCAAAAGAAGACATTT 248
                          ?    i    ii      v    i     i     v        i  vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

C chrX_87146895_8    247 ATGCAGCCAAAAGACACATGAACAAATGCTCATCATCACTGGCCAT 202
                          viii     v ii        v i       v     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (41 / 33)
Gap_init rate = 0.00 (0 / 296), avg. gap size = 0.00 (0 / 0)  

2451 28.59 2.73 1.82  chrX_87146895_87151406.rev     3135  4012 (500)    L1M4_orf2#LINE/L1        1   886 (22)  

  chrX_87146895_8   3135 TGGAAAAACATTTTGTGCTCATGGATAGGAAGAATCAAAGTTCTTAAGAT 3184
                               i i  iiii  i        v      v i  vi  v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87146895_8   3185 GGCCACACTTCCCCAAACAATCTACAGATTCAATGATATTCCTATCAATC 3234
                            v i   i   v  vii              i vv  i        vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87146895_8   3235 TACCAATGACATTCTT--CAGAGAATTAGAAAAAAACAATTTTCAAATTC 3282
                          v   iivi v  i  --    -    i-- v  ivii  ii v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_87146895_8   3283 ATATGTAACCAAAAAAGAGCCCAAATAGCCAAGACAATCCTAAGGAAAAG 3332
                              v  viiv  ii  v  vi         i      i i ii  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_87146895_8   3333 GAACAAATCTGGAGGCATCACGTTACTCAACTTCAAACTACACTACCAGG 3382
                                vi      vv    ii v i   i      vivi     v i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_87146895_8   3383 TTACCATAACCAAAACAGCATGGTATTAGTACAAAAACAGACACATAGAC 3432
                         i   vi   i   i    ii     i i i i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_87146895_8   3433 AAACGGAATAGAATAGAGAGTCCCAAAATAATGCTGCACATCAACAACCA 3482
                         v  i          v        vi      vv iii    iv iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_87146895_8   3483 TCTGATCTTTGACAAACTTGACAAAAACAAGCAATGGGGAAAG------- 3525
                         vi    i  i     ivv  v   i v  vv            -------
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_87146895_8   3526 ----CAATAAATGGTGCTGGGATAGCCAGCAAGTCATATTCAGAAGATTG 3571
                         ----   i              i i ii vv ?i  i  v  i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_87146895_8   3572 AAACTGGATCCCTCCCTTACACCATATACAAAAATCAGCTCAAGACAGAT 3621
                           ii    i    v   i                 i i     i ii   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_87146895_8   3622 TAAAGACTTAAACATAAAACATAAAACTGTAGAAACTCT-AAAAGAAAAC 3670
                         i ?    i    ii   i vv       i  -       - i        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAAC 546

  chrX_87146895_8   3671 CTAGAAA-ATATCATTCTGGACATACAACCTGGCAAATATTTC------A 3713
                         v   i?i- v   -   vv   v vviiiiv     vvi    ------ 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_87146895_8   3714 TGACAAAAATGCCAAAAGCAATTGCAAAAAAAAAGTAACAAAATTTGATA 3763
                              ------         vvv    v    i -----    v v    
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGA-----AAAAATAGATA 634

  chrX_87146895_8   3764 AATGGGACCTAATTAAA-TTAAGAGATTCTGCACAGCAAAGGAAACCACC 3812
                            v    i v  i   -    i iv  i  ii vv       v  i i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_87146895_8   3813 AACAGAGTAAACAGACAACATATGAAATAGGAGAGAATATTTGCAAACTA 3862
                           v i   i  v       vi iii   i     i            ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_87146895_8   3863 TGGCTCTGACAAAGTG-TGGTATCTAGAAACTATAAGAAGCTGGAACAAA 3911
                          ivv     i  i vi- v     i    vv     ii i  vvv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_87146895_8   3912 TTAACAAGCAAAA-ACAAATGACCACATTACAAAGTGAGCAAAGCACATT 3960
                          i  i  vv    -      i   vv   ?v   i  i      v iv v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_87146895_8   3961 AGCAGGGACTTTTCAAAAGAAGACATACACACAGCCAACAAGAATATGAA 4010
                          ii  iv i  i  v        i     v ii     i   v i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_87146895_8   4011 AA 4012
                           
  L1M4_orf2#LINE/    885 AA 886

Transitions / transversions = 1.55 (150 / 97)
Gap_init rate = 0.02 (14 / 886), avg. gap size = 2.86 (40 / 14)  


2712 28.13 1.32 1.54  chrX_87181658_87184837     1779  2688 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87181658_8   1779 TGGAAAATTTTTCCATACTTACGGATAGCAAGAATCAATATTGTTAAAAT 1828
                               iv v i    ii i i    v v    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87181658_8   1829 GGCCACACTTCCAAAAGCAATCTACAGATTCAATGCTATTCCTATCGAAC 1878
                            v i   i  v   vii              i  v  i      i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87181658_8   1879 TAACAATGACATTCCTCACAGAATTAGGAAAACTAATT-TAGAATTCATA 1927
                          vv  iivi v  ii ii     v v iv  i  i  i-  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_87181658_8   1928 TGGAACCAAAAAAGAACCCAAATAGCCAAGGCAATCCTAAGCAAAATAAA 1977
                              viiv  ii  v  vi         ii     i i iv  i vi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_87181658_8   1978 CAAAGCTGGAGGCATCACGTTACCCAACTTCAAACTACACTACGAGGCAA 2027
                              i      vv    ii v     i      vivi     i i  v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_87181658_8   2028 CAGTAATTAAAAAAAAAAACATGATATTGGCACAAAAACAGGCACATAGA 2077
                                i  i v i----ii  i  i     i  ii i  i  i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAG----TGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_87181658_8   2078 CCAACGGAACAGAAAAGGGAGCCCAGAAATATTGCTGCATACCTAAAGTC 2127
                         i   i    i    vv i   i         vvv iii i ii  vi   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_87181658_8   2128 ATCTGATCTTTGACAAAGTCAACAAAAACAAGCAATGGGGATAAGAAT-- 2175
                          vi    i  i     i viiv   i v  vv         -      --
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATAG 395

  chrX_87181658_8   2176 CCTTATTCAATAAATGGTGCTGGGATAACTGGTTTATCACATACAGAAGA 2225
                         i   -     i              i      v v?i     i  i    
  L1M4_orf2#LINE/    396 TCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_87181658_8   2226 CTGAAACTGGAGCCCTTCCTTTCAGTATATACAAAAGTCAACTCAAGATC 2275
                         v    ii    v    v   iv  vi          i i       i  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_87181658_8   2276 TATTTAAGACTTAAATGTAAAACTTTAAACTATAGCAATTCT-AGAAGAA 2324
                         v  iv?    i         i vi v        i-  i   -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAA 543

  chrX_87181658_8   2325 AACCTAGAC---AATGCTATCTGGACATATAACCT-GGCAAATATTTCAT 2370
                            v   i?---   -  -  vv   v - iivi -     vvi    v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CT-TCGTGACCT-TGGGTTAGGCAATGGTTTCTT 590

  chrX_87181658_8   2371 GACAAAGACACCAAAAGCAGTTGTAAGAAAAGCAAAAATTGACAAATGGA 2420
                         iivv v             vvv i  v     v      v  i    v i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_87181658_8   2421 ATCTAGTTAAACTTAAGAGCTTCTGCCCATCAAAAGAAACTATCAACTGA 2470
                          ii vi i   v    i i   i  iv v     i  v        vvi 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_87181658_8   2471 GTAAACAGACAATCTACAGTATGGGAGAAACTATTTGCAAACTATGGATC 2520
                           i  v      i i    v          v          ii  iv   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_87181658_8   2521 TGACAAAGT-CTGATATTCAAACTCTATAAGGAACTTGAACAAATTAACT 2569
                            i  i v-  vi   i  i v v     i     ivv    v i  iv
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_87181658_8   2570 AGAAAAAAGCAAACAAGCCCATTAAAAAGATGAGTAAAGACAAT---AGT 2616
                          v     ii    i  v  v   ?    -   i i    i--  --- i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGG--ATTTGAAT 837

  chrX_87181658_8   2617 AGACACTTTTTAAAAGAAGACATATATGTGAACAGCAACTATATGAAAAA 2666
                              i  i iv        i   i vi  iv  ii  vi i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_87181658_8   2667 AGTGCTTAACATCTCTAATCAT 2688
                          -    i      v????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (153 / 99)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.53 (26 / 17)  


1762 30.87 2.85 2.20  chrX_87243026_87246073.rev     1329  2099 (949)    L1M4_orf2#LINE/L1        1   776 (132)  

  chrX_87243026_8   1329 TGGCAAAACATTTTATGCTCATGGATAGAAAGAATCAGTATTGTTAAAGT 1378
                            v  i i  iii   i        v i    v i i         ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87243026_8   1379 GGCCATACTATCCAAGCAG-TTTACATATTTGGCGCTACTTATATCAAAC 1427
                            v     vi    iiv - i    v   iii   v iiiv       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87243026_8   1428 TACTAATGATATTTTTCACAGAA-TTCA-AAACATATTCTAAAATTTATA 1475
                          v i iiviiv     ii     -  v -  i vv  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_87243026_8   1476 TGGGAC--CAAAAAACAGCCCCAATAACCAAAGCAATTCTAAGCAAAAAG 1523
                            i v--   iii  --  vv    i     i    ii i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_87243026_8   1524 AACAAAGCCAGAGTCATAACATTACCTGACT-CAAAACTATACTATGAGG 1572
                                iii   vvv v   i v  ii i -       -     ii i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_87243026_8   1573 CTAAAATAACCAAAACAGCATGGTACTA-TACAAAAACAGACACACAGAG 1621
                            v i   i   i    ii       i-i i  ii i     i i   v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_87243026_8   1622 CAACAGAACAATATAGAGAACACGGAAATAAAGCTTCACACTGACAACCA 1671
                            ii   i iv  v    iiv i        v ivi   i v iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_87243026_8   1672 TCTGGTCTTTGGTAAAG---CCAACAGCAAGAAGCAATGAAGAAAGGACT 1718
                         vi  i i  i ii  i ---    v v  vv---     ii     i iv
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAAGAATA 394

  chrX_87243026_8   1719 TTCTATTTAATATATGGTGTTGAGATAACTGACTAAAATTACA--CAACA 1766
                         v   v  i  i v      i  i  i     iv  ?--ii   --   v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK--CCACATGCAAAA 442

  chrX_87243026_8   1767 GATTGAAGCTGAGACCATTTGTTTCAC--CATATGCGAAACTCAACTCAA 1814
                           v     i  -    -ii iii    --     i i   v i       
  L1M4_orf2#LINE/    443 GAATGAAGTTG-GACC-CCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_87243026_8   1815 GATGGATTACAGACTTAAATGTACAACCTAAAACTATAAAAATCCTAAAA 1864
                         i      i ?    i        vi v              v  i  i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_87243026_8   1865 GAAAACTTAGG---AAATACAATTCTGAACATTGGTCCTGGCAAATATAT 1911
                               v    ---    - --   vvi  v    viiv     vvi v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT-C--TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_87243026_8   1912 CATGACAAAGACTCCAAAATCAATTGTAACAAAAACAAAAATTGACAATT 1961
                          v iivv v   v      v  vvv i       iv      v  i  v 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_87243026_8   1962 GAGATGAAGTTAACCAAAA----GAGCTTCTGCACAGTGAAATAAAATAT 2007
                         ----  i v  v i     ----i i   i  ii vvii  iv v v   
  L1M4_orf2#LINE/    638 ----TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_87243026_8   2008 CGGCAAAGTAAACAGGCATCCTAAAGAATGGGAAAAAA-ATTTGCAAGCT 2056
                          iiv     i  v  i  v  i v         i    -        iii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_87243026_8   2057 ATGCATCCCAAGATGGTCTAATATCCACAATCTATAAGTAACT 2099
                           ii   iv vi v  v  vi      v   v     iv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.65 (147 / 89)
Gap_init rate = 0.03 (21 / 776), avg. gap size = 1.86 (39 / 21)  

 338 16.67 7.02 6.14  chrX_87243026_87246073.rev     2444  2557 (491)    L1M4_orf2#LINE/L1      794   908 (0)  

  chrX_87243026_8   2444 AAAACATCAACAATCCA-TTAAAAAATGGACAGAGAAC----ATAAAC-- 2486
                             v iv  i  i   -  ?        i  i  i i----   i  --
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_87243026_8   2487 TTCTC-AAAGAAGACATACACATGGCCAACAGCAAACAAGCATATGAAGA 2535
                              -        i     v        i -------    i     i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATA-------AGCACATGAAAA 886

  chrX_87243026_8   2536 AAGGCTCCACATCAGTAATTAT 2557
                         i v    v      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.04 (5 / 115), avg. gap size = 3.00 (15 / 5)  


2962 27.09 0.88 0.99  chrX_87251009_87260233     3182  4089 (5136)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_87251009_8   3182 GGAAAGATATTCCATGTTCAAGGATTGTAAGAATCAATATTGTTAAAATG 3231
                                   i         v      v    v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_87251009_8   3232 TCTATACTACCCAGAGCAAGCTACAAATTCAAAGCAATTTCTATTAAAAT 3281
                         v v     v    i vii v     i      v     ii    i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_87251009_8   3282 ACCAGTGATATTCTTCACAGAAATAGAAAACACT-ACCCTAAAATTTACG 3330
                         v    iviiv  i  ii       v  v  -i  - i         i ii
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATA 150

  chrX_87251009_8   3331 TGGAAGAACAAAAGACCTAGAACAGCCAAAGCTCTCCTAAGCAAATTGAA 3380
                              ivi   ii    i    i       i vv  i i iv  ivv   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_87251009_8   3381 CAAAACTGGAGGAATCACATTACCTGACTTCACATGATACTACAGAGCTA 3430
                             ii       v     i v  ii i    v vvv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_87251009_8   3431 TAGTAAGCAAAACAGCATGGTACTGGCATAAAAAGAGAAACATAGAACCA 3480
                         i     v   i    ii              ii v   v i     v v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_87251009_8   3481 TAGAACAGAATAGAGAACCCAAAAGCAAATCCACACCCCTACAGTGAACT 3530
                          i   i     v    ii   i  ii   i   i  vii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_87251009_8   3531 CACTTTTGACAAAGGTGCCAAGAAAATACACTCGGGGAAAGAG-AGCCTC 3579
                         v i   i     i          vv  v  v -         i-  i  i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTT 399

  chrX_87251009_8   3580 TTCAATAAATGGTACTGGACAAACTGGATATTTATGTGCACAAGAATGAA 3629
                              i       i    ivv         ?ii ii    v         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_87251009_8   3630 ACTGGACTCCTATCTCACACTATATACAAAAATTAAATCAAATTGAATTA 3679
                         ii     i    i       i               v     v  i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_87251009_8   3680 AAGCATTAAACCTAATATTGAAAACTATGAAACTACTACAA--AAACTTT 3727
                         ?  vvi    iv   v viv        i     vi  v  --    v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_87251009_8   3728 TCTGAAAAGTCTCCAAAACATTAGTCTGGACAAAGATTTTTTGAGTAATA 3777
                         vv? v   -   i ivi  v  i vi i i   v i   i  iii  vv 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_87251009_8   3778 CCCTACAAGCTTAGGCAACAAAAGCAGCAATGGAAAAATAAGATCCCATC 3827
                          v i v    vi i          v iv   i  v    vi  iii    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_87251009_8   3828 AATTTAAAAAACTTCTGCACAGCCAAGCAAAGAATCAACAAAGTGAAGAG 3877
                           vv v        i  ii vv v   v v vv     v        i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_87251009_8   3878 ACAACCCACACAATAGAAGATAAAATATTCTCAACCTAACCATAT----G 3923
                                   v   i i   --       iv   ---- i     ---- 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGA--AAATATTTGCAA----ATCATATATCTG 742

  chrX_87251009_8   3924 ACAATAAATTAATATCTAGAATATATAAGAAGCTCAAACAACTTTATATG 3973
                          i  vii i vi    i           ii i   vv      iv   vv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_87251009_8   3974 AATTAATCTAATAATCTGGTTTAAAAATTTCCAGAACATTTGAATTGACA 4023
                           vv iv v     i iii  ?      vvv  i iv        v    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_87251009_8   4024 TTTCTTAAAAGAAGACATACAAAGGGCAAACAAACATATGAAATGGTGCA 4073
                              iv        i       v   v  i  i  i      v i   v
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_87251009_8   4074 TAACATCATCAATCAG 4089
                         i       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (138 / 104)
Gap_init rate = 0.01 (9 / 907), avg. gap size = 1.89 (17 / 9)  

2354 27.54 3.16 1.13  chrX_87251009_87260233     7847  8732 (493)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_87251009_8   7847 AACACATCTCATGCTTGTTAATTGAAATAATCAATATCATGAAAATGACT 7896
                           v i   i    i ii vi    i  v v i     ii v  i   i v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_87251009_8   7897 ATACTAAACAAAGCAATTTATAGATTCAATACACTTCCTATTAAAACACT 7946
                              vvv    vii  i  i        ii  v i     i    iv i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_87251009_8   7947 GACATCATTTTTCACAGAATTAGAAAAAAAAATTCCCCAAATTCTAATGG 7996
                         ii vv v     ii     v v  v  ivvi  -  iv      vv    
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCATATGG 153

  chrX_87251009_8   7997 AACCAAAAAAGGGCGTGAATAATGAAACCAATCTTAAGCAAAAA-AACAA 8045
                           viiv  ii iv vv     iiv   v       i iv  i  -     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_87251009_8   8046 ATTTGGAGGTATCACAAAACCTGATTTCAAATTACACTACAAGGCTACAG 8095
                          v       vv     vvv  ii        vivi       i       
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_87251009_8   8096 TTACAAAGCCAGCATTTTACTGGTATAAAAGGAGATGCATAGACCAATAA 8145
                          v iv   v   ii vv      i    iiiv   iii     i    ii
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_87251009_8   8146 AACAGAACAGAGAACCCATAAATAAACCCAAACACTCACTACCAACTGTT 8195
                           i    iv    ii   v           v   i i ivii   i  v 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_87251009_8   8196 CTTAGATACAGCATAGAAAAAC-ATAAATTGGGGAAATGACA-CCTTATT 8243
                         i  v  i -  vi ivv  i  -  vv v        vi i -i   v i
  L1M4_orf2#LINE/    354 TTTCGACA-AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_87251009_8   8244 ATACAAATGGTGCTGGGAAAACTGGATAGCCACATGTAGAAGAATGAAAA 8293
                          -                v         ?       i i         iv
  L1M4_orf2#LINE/    403 A-ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_87251009_8   8294 TGGATCATTATCTCTCACCTTATAAAATAATTACCTCAAGATTGATTAAA 8343
                             i vi  i   v    v    v  v     v     i  v   i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_87251009_8   8344 TACTTAAATATAAGAGGTGAAACTATATAAATTCT-AGAAGACAACTTTG 8392
                         v  i     i      v i        -   i   -      v   v v 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAG 550

  chrX_87251009_8   8393 GAAAAATTCTTTTAGACATCAGCCTAGGCATAGAATTTAT--GATGAAGA 8440
                          ?iv  v    ivv   v ii vi      - vii   v --   - v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAGAT-ATGA 598

  chrX_87251009_8   8441 CCCCAAAAGCAAATGCAACAAAAAACAAAAATGAATGAATGGTACCTAAT 8490
                          v         v v         i -      ii  i   v v  i v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCAT 647

  chrX_87251009_8   8491 TTAACTAAAAAGCTT--GTGCATAACAAAAGAAAA-ATCATCAGAGTAAA 8537
                         iv  v v    i   --    v --    i  v v-    vv i   i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAA 695

  chrX_87251009_8   8538 CAGACAACTCAAATAATGGGATAAAATATTTGCAAACTATGCATCTGACA 8587
                         v       i  v v       v              ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_87251009_8   8588 AAGGACTAATATCCGGAATCTACAAAAGACTC-------------AGAAA 8624
                          i     vi     i    v  i   ii    ------------- v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_87251009_8   8625 AA---AAATCAC---ATGAGGAGGTTGGCAAATGATATGAATAGACATTT 8668
                           ---    v  ---  v?ii ii v      v   v             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_87251009_8   8669 CTCAAAAAAAGATATATAAATGGGTAATGAATATATTAAAAAATTGCTCA 8718
                            v   i        i      vi   i ii i  v    i  -     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCA 894

  chrX_87251009_8   8719 ACATCACTAATCAT 8732
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (129 / 111)
Gap_init rate = 0.02 (19 / 904), avg. gap size = 2.00 (38 / 19)  


3338 25.99 0.55 0.55  chrX_87268532_87274812     4882  5789 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87268532_8   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87268532_8   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87268532_8   4982 TACCAA-TGCCTTTCTT-CACATAATTGGAAAAAACT-ACTTTAAAGTTC 5028
                          v   i-       i  -  v -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_87268532_8   5029 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTGAGCCAAAA 5078
                                 viiv  ii  v  viv  v     iv     i   ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_87268532_8   5079 GAACAAAGCTGGAGGCATCACACTACCTGTCTTCAAACTATACTACAAGG 5128
                                 i      vv       v  iivi      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_87268532_8   5129 CTACAGTAATCAAAACAGCTTGGTACTGGTACCAAAACAGAGATATAGAT 5178
                                      i    iv         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_87268532_8   5179 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5226
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_87268532_8   5227 TATCTGATCTTTGACAAACCTGAGAAAAACAGGCAATGGGGAAAGGATTC 5276
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_87268532_8   5277 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5326
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_87268532_8   5327 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5376
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_87268532_8   5377 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5426
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_87268532_8   5427 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5476
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_87268532_8   5477 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5526
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_87268532_8   5527 ATTAAACTAAATAGCTTCTGCGCAGCAAAAGAAACTACCATCAGAGTGAA 5576
                           i   v v  v i   i  i  vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_87268532_8   5577 TGGGCAACCTACAAAGTGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5626
                         vi i     i   i i           v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_87268532_8   5627 AAGGGCTAATATTCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5676
                          i  i  vi   i      v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_87268532_8   5677 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5726
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_87268532_8   5727 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5776
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_87268532_8   5777 CATCCCTGGCCAT 5789
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (134 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2564 28.05 2.44 1.77  chrX_87284627_87286846.rev      841  1742 (478)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87284627_8    841 TGGAAA-ACATTCCATGCTCATGAATTGGAAGAGTCAACACTGTTAACAT 889
                               - i  i     i     i         v i  i i      v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87284627_8    890 GACCATACTGCCTACCCTCAAA---ATCTACAGTTTCAACACCATTGCTA 936
                          i v     ------  i    ---        v      i v  iv   
  L1M4_orf2#LINE/     51 GGCAATACT------CCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chrX_87284627_8    937 TCAAACTATCAA-TGTCATTTTTCACAGAACTAGAAAAAACTG-TTCTAA 984
                              v vi  i-  i -     ii     v v  v  i-   - i    
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAA 142

  chrX_87284627_8    985 AATTTATATAAAACCAAAAAAGAGGCCAAAGAGCCATGGCAACACTAAGC 1034
                             i    ii  viiv  ii  vv vi  v     vii   ivi i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_87284627_8   1035 AAAAATAACAAAGTCAGATGCATCACATTACCCAACTTCAAACTATACTA 1084
                           i  v        ii  v vv     i v     i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_87284627_8   1085 TAAGGCTACAGTAACCAAAACAGCAAAGTAATGGTACAAAAACAGATACA 1134
                         i  i          i   i    iivi   v   i i  ii i   i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_87284627_8   1135 TAGAACCGATGGAATAGAATTAAGAACCCAGAAAGAAAGCTCTACACCAA 1184
                             -i i             i   ii       v   v iv    iiv 
  L1M4_orf2#LINE/    293 TAGA-TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_87284627_8   1185 CAACCATCTGATCTTTGACAAAGTCAACAAAAATAAGCAATGGAGAAAGG 1234
                         iiii  vi    i  i     i viiv   i vi vv      i     i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_87284627_8   1235 ACTTTCTATCCAATAAATGATGCCGAGATAGCTGGCTAGCCATATTCAAA 1284
                          ivv   v i   i     i   i i  i i    v  ?   i  v    
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_87284627_8   1285 ATAATAAAACAGGACCCCTACATTTTAC-ATATAAAAAAATTAACTCAAG 1333
                          v   i  iiv          v ivi  -     v              i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_87284627_8   1334 ATTGATTAAAGATTTAAATATAAGACCTAAAACTGTAAAAGTTCTAGAAG 1383
                           v   i ?   ii     i     v        i     v ii      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_87284627_8   1384 AAAAGCTGGGAAATACTAATCTGGACATCACCCT----TGGGAAAGAATT 1429
                             vv i  ?i-  --     v-- i v   i ---- i  v  vii  
  L1M4_orf2#LINE/    542 AAAACATAGGNG-TA--AATCTT--CGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_87284627_8   1430 TTTT-GCCAAGTCCTCAAAA--ACAATTGCAACAAAAACAAAAATTGACA 1476
                          i  - vi v v vi     --    --         iv      v  i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATA 634

  chrX_87284627_8   1477 A-TAAGAGCTAATTGAGCTAAAGAGTTTCAGCACAGCAAAAGAAATTATC 1525
                          - vi  vi v  ii iv v  i ii  iv ii vv    i  v i    
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_87284627_8   1526 AACAGAGTAAACAGATAACTTACAGAGTGAGAAAAAACATTTGCAAAGTA 1575
                           v i   i  v   i   ii     i  i  i    i         vi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_87284627_8   1576 TGCATCTAACAAAGTTCTAATATCCAGAATTTATAAGAAACTT----AAT 1621
                          ii    i i  i vv  vi          v     ii    i----  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_87284627_8   1622 TCAACAAGCTAAAAACAAATA-CCCAATCAAAAAGTGGGCAAAAGACATG 1670
                             i  vvv   i       -      i?    i        i  iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_87284627_8   1671 GA--GACACTTCTCAAAAGAAGACATATAAGTGGCCAGCAAATGTATGAA 1718
                         i --    i     v        i   i  i      ii  iiii     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_87284627_8   1719 AAATAGCTTCATATCACTAATCAT 1742
                           ivv   iv i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (161 / 88)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.90 (38 / 20)  


1256 26.92 2.31 1.54  chrX_87292638_87294581      113   502 (1442)    L1M4_orf2#LINE/L1        2   394 (514)  

  chrX_87292638_8    113 GGAAAGTTATTCTAA--TCATGGATTGGAATAATCAATATTGTTAAAATT 160
                               v   i i v--             v v i           i  v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_87292638_8    161 TCCATACTACTCAAAGCAATCTGCCGATTCAATGCAATCCCTATCAAAAT 210
                         v v     v i    vii    i v       i                 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_87292638_8    211 ACCAATGACATTCTTCACAGAAATATTAAAAAA---ATCTAAAATTTTAT 257
                         v   iivi v  i  ii       -- i v  i---   iv   v  i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCAT 149

  chrX_87292638_8    258 TTGGAACCACAAATGGCCCTGAATAGTCAAAG--ATCTCACCAATAAAAA 305
                         v     vii   iv i   v      i    i--    ii--  v  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG--AAAAAGAA 197

  chrX_87292638_8    306 GAGAAAACCTCAAGTAATCACATTACCTGACTGCAAG--TTATTCTTCAG 353
                           iv   vi vi  v v     i v  ii i v   i--   --  v  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAA 245

  chrX_87292638_8    354 AGCTATAGTAACCAAAACAGCAAAGTACTGGCATAAGAACAGACACATAG 403
                              i     i   i    iivi             i i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_87292638_8    404 ACCACTGGAACAGAATAGAGAATGCAGAAAATAATTCACACACCTACAGT 453
                          i  v     i     v    i v      vv  ii  i   ii  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_87292638_8    454 GAACCTATTTTTGCCAAAGGTGCCAAGAACACACACTGGGGAAAAGACA 502
                         v  iiv     i v   i          v  iv  v        ii i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

Transitions / transversions = 1.56 (64 / 41)
Gap_init rate = 0.02 (7 / 393), avg. gap size = 2.14 (15 / 7)  

2740 24.70 6.80 1.07  chrX_87292638_87294581      606  1443 (501)    L1M4_orf2#LINE/L1        3   888 (20)  

  chrX_87292638_8    606 GAAAGACATCCCATGCTTGTAGTTTGGAAGACATAATATTATAAAAATGC 655
                               i        i ii i v         v       i v  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_87292638_8    656 CCATGCTACCCAAAGCAATCTACAGATTCATTGCAATCCCTAACAAAATC 705
                          v  i  v      vii             vi          v       
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_87292638_8    706 CAAATTGTAGTTTTTGCAGAAATAGAAATAAG----TACTAAAATTTATT 751
                          v ii  ivv             v  --i   ---- v        i  v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCATA 150

  chrX_87292638_8    752 TGTAACAAACAAAG-ACCACTAATAACCTAATCAATTGTGAGAAAGAAGA 800
                           v  - vi   i -   vvv    i  v  v    iv   i        
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_87292638_8    801 ATAAAGCTAGTGACATCATACTTCCTGATTCCAAAATACATTACAAAGTT 850
                          i    i i v ivv   i      ii   i     ivi i       i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_87292638_8    851 ACAATAATCAAAACAGTATGATAATGGCATAAAGA-------------CA 887
                            i       i     i  i  v        i  -------------  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_87292638_8    888 ACAGAATAGAC-----AGCCTAGAAATAAATCCACACATATACAGTCAAT 932
                          ii       v-----  i i         i   i    v  ii      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_87292638_8    933 -GATCTTTGACAAGGTTACCAACAATACATAATGGGGCAAGAATATTCTC 981
                         -   i  i       v i    v vi ivi       v       v   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_87292638_8    982 TTTACCAAGAGTTATTGGGAAAGCTG-ATTTCCAAGTACAAAAGGATAAA 1030
                           i v   iv v ii     v i   -  v?   vi i      i  i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_87292638_8   1031 ATTG-ACCCTTATCTTTTACCATACACAAAAATCAACTCAAG-TCAATTA 1078
                         i   -    i  i  ivi      i        i       i- vi  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_87292638_8   1079 AAGACTTAAACATAAGACCTTAAACTCAAAAACACCCTGAAAAAAA--TA 1126
                         ?    i    ii     v  v     vv     v iiv   i    --  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_87292638_8   1127 GGGAAAAAGAGTTGTGACTTTAGTTTTGGCAATTATGTGTTGGATATGAC 1176
                           ?iv   vvv i     i  i v  v      vi v v  i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_87292638_8   1177 ACTAAAAGCATAGGCAACAAAA---------------TT----------- 1200
                           i       i i         ---------------  -----------
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_87292638_8   1201 AAACTAGAAACTTTC-TACATAGCAAGTGAAACAGTCAACAGAATGAAAA 1249
                            i  i       i- i v --   iv  v  vi    v i i      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_87292638_8   1250 TTCAACCTATGGAATGAAAGAAAATATTTGCAAATCATATATCTTCATAA 1299
                         vv     i ii     ii                          v-    
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG-ATAA 746

  chrX_87292638_8   1300 GGTGCTAATTTTCAAAATATCTAAGCAACTTCTACAGCTCAATAGAAAAA 1349
                           vi  vi v i  i     v   iv    ii    i       iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_87292638_8   1350 ATAAAACTAATAACC-AATTAAAAACTGGGCTAAAAACTCAAAGTGACAT 1398
                          ---i  v       -    ?    v     v  ii i ii  vv     
  L1M4_orf2#LINE/    797 A---GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_87292638_8   1399 TTCCCAAAAGAAGACATCCAAATGGCCAACAGATATATGAAAAAA 1443
                            i v        i  v           i iii i       i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.54 (123 / 80)
Gap_init rate = 0.02 (18 / 886), avg. gap size = 3.67 (66 / 18)  


3645 17.49 3.35 8.27  chrX_87307448_87310924.rev     2032  2986 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87307448_8   2032 TGGGAAAACATCTCTGGTTCGTGGATTGGAATATATAATATTGTTAAGAT 2081
                            i  i i   i vv    i          v iv               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87307448_8   2082 GGCAATACTTCCCAAATTGATCTACAGATTCAATAGAGTCCCTATCAGTA 2131
                                  i                       iiv i         iv 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87307448_8   2132 TCCAAACTGGCTTCTTGATAGATACTGAAAAAGTGACCCTAAAATTAATA 2181
                            v i   v   i  vii   v i   v  iv   i         v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_87307448_8   2182 CAGAAATATAAGTGACTTGGAATAGCCAAAGCAACCTTGAAAAAGAA--- 2228
                         ii     ii   v   iii           i   i            ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_87307448_8   2229 CAAAATGAGATAACTTGCATTTT---------AAACTTACTTCAAAGCAA 2269
                             i vi  vi   ii  i  i---------         v      v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_87307448_8   2270 CAATAATAAAGATAGTGTGATATTGGCCTAAAGATATATATACAGATCAA 2319
                           i    v    i      i  i    v   i    v i   i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_87307448_8   2320 CGGAACAAAATTAAGAGTCCAGAAACAAACTCTTGTTTCTATAATCAACT 2369
                         i    i i    i            i    i --------   --  ---
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCC--------ATA--CA--- 337

  chrX_87307448_8   2370 TCTTTTTTAAAAAATCTTTTTTGTGGTGAACTTCTTTTTGACAAGGATGG 2419
                         -------------------   i    v  i vv    i       i  v
  L1M4_orf2#LINE/    338 -------------------TTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_87307448_8   2420 CAAGGTCAATCAATCGGGAAATTCATTCTTTTCAACAAATTTTATTCTTT 2469
                             ii  v     v      ---------------i   --- v     
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAA---------------GAAT---AGTCTTT 400

  chrX_87307448_8   2470 TCAACAAATGGTGCTGGAACAAGTGGATATCCACATGCAAGAGAATAAAG 2519
                                          i    v      ?          i     i   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_87307448_8   2520 TTACATACATATTCCCTACTATCTACAAAAATCAGCT-GAAATAGATCAA 2568
                           iv iv v  iii vi  i  v         i i  -i    i     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_87307448_8   2569 AGCCCTACATGTAAGAGATACAACTATAAAACTTTTAGAAG------CAG 2612
                           v    v         v  v            i       ------i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_87307448_8   2613 AGACAAACTATTGTGACCTAAAATTTGGCAATGGTTTCTTAGATACAACA 2662
                         i?ii   iiv i       viii  v                   ii   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_87307448_8   2663 TCAAAA-CTCAAGCAAATAGAAAAAAAA-AGAGAAATTGCCCATCAATAA 2710
                         i     - v       vv i i      -   v      vv v   vi  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_87307448_8   2711 AATTAAAAACTTCTGTACTTCAAAGGACACTATCAAGGAAGTGAATACAC 2760
                                     i   i                    i       v v  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_87307448_8   2761 AACACACAGAATGGGAGAAAATATTTGCAAATTATATATATATATAAAAT 2810
                            v                            i      -----------
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT----------- 739

  chrX_87307448_8   2811 CATATATTATACATATATAATAAGGGACTTGCATCTAGAATATATAATGA 2860
                         ----------- ----- i            i   i           v  
  L1M4_orf2#LINE/    740 -----------C-----TGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_87307448_8   2861 ACA--TATAACTCAATAATAATAAGACAAA----CCAATTAAGAATCAGT 2904
                           v--  i             v        ----      ? i  vii v
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_87307448_8   2905 CATTAAG---CTGAGTAGACATTTGTCCAAAGAAGATATATAAATGGCAA 2951
                           --   ---i   i         v               i       v 
  L1M4_orf2#LINE/    824 CA--AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_87307448_8   2952 ACA--CACACAAAAAGATATTCAACATCATTAGTAAT 2986
                          i --    ii       ii         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (104 / 59)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 6.17 (111 / 18)  


2426 21.34 6.07 1.40  chrX_87321214_87324652.rev     1793  2434 (1005)    L1M4_orf2#LINE/L1       21   692 (216)  

  chrX_87321214_8   1793 ATAAATAAAAAAGCATTAATATTGTTAAGATATCAATACAGATATCAAGC 1842
                           ii  vii  ii -                iv      v--ivi   ii
  L1M4_orf2#LINE/     21 ATGGATTGGAAGAC-TTAATATTGTTAAGATGGCAATACT--CCCCAAAT 67

  chrX_87321214_8   1843 TAA-CTACAAATTCAATACAATTCCTATAAAAATTTCAGT---CTCTTTT 1888
                          i -     i      ii    i     v     ii   i---  i    
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_87321214_8   1889 GCTGAAATGGA-AAATTATATCTTCAAATTCATATGACATTATTAGAGAC 1937
                           v     v  -  ii i-   i v           iv v iiv  i   
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTG-ATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_87321214_8   1938 ACAGAGTAGCCAAAACTAT-TTAAAAAA----AAC----TTGGTGG--TC 1976
                         v    i          v  -  i     ----   ----    v  --  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_87321214_8   1977 ACAGTTTCTGATTTTAAAACTTACTACAGA--TATAGATTAGTTAAAATA 2024
                            v  i ii    i             i --  i  --  i i  i i 
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG--TAATCAAGACA 264

  chrX_87321214_8   2025 GTGTGGCACTGGCATAAACATAGACATGTAGGCCAATGGCATAAAACTGA 2074
                               i          iv        i   ii      v   i  i   
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_87321214_8   2075 GAGAATAGAAATAAACCCATACATTTACAGCCAATTTGTTTTTAACAAGG 2124
                            vvi                     ii i     vi    ii      
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_87321214_8   2125 -TGT---GACCTATTAAATGGAGAAAAAGCAGTTTCTTCAACAAATAGTG 2170
                         -  i---    -   v     i    i ii   i i          i   
  L1M4_orf2#LINE/    365 GTGCCAAGACC-ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_87321214_8   2171 CTAGGACAACTGGATATCCAGATTCAAAAGAATAAAAT-GGACCTCTACC 2219
                           i             ?   v  v         i  i -     i     
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_87321214_8   2220 TCATACCACATACAAAAGTTAAGTCAAAATGGATCAACAACCTAAACATA 2269
                            i    i        i    v             ?vi       ii  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_87321214_8   2270 AAAACTAAATCTGTAAAACTTGTAGAAAATAACATAGGTATACATCTTTT 2319
                          i i     v  i       iv     i v        ?i  v     iv
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_87321214_8   2320 TAATCTTGGATTTGGCAATTAATGTTTAGATATGACAC-AAAA----AAG 2364
                          i i     i  v      viv vi             -    ----   
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_87321214_8   2365 CTCAACAAA-GAAAAAATAGACATATTTATCTACAACAAAATT------T 2407
                          --      -           i v   viv  v  v       ------ 
  L1M4_orf2#LINE/    614 C--AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_87321214_8   2408 TTT----TCCATAAAATCGTATCAAAGAAGT 2434
                            ---- i  v ii ivv      ii    
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

Transitions / transversions = 2.19 (92 / 42)
Gap_init rate = 0.03 (22 / 672), avg. gap size = 2.18 (48 / 22)  

 803 17.76 5.61 0.93  chrX_87321214_87324652.rev     2735  2948 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_87321214_8   2735 AAGGAAGTACAAACATTACCTACATTATGGGAGAAAAATGTTTGCAAATC 2784
                            i    iv   v iv   i   vv           - i          
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATC 733

  chrX_87321214_8   2785 ATTTATGTAATAAGGGTATAATTTCAAGTACATATTAAAAA---TTACAA 2831
                           v   v i       vv vi v  v  v i    v  i  ---      
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_87321214_8   2832 TTCAATAACAGGAAGACAA----CCCAATT-AAAAATAAGTAAAGGAATT 2876
                         i       i ii       ----       -      ii i      v  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_87321214_8   2877 GAA----CATTTATCCAAAGAAGATATACAAAATGGCCAGTAAGCACATG 2922
                            ----     v                   -      i          
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACATG 882

  chrX_87321214_8   2923 AAAATTTCCTCAATATTATTAGTCAT 2948
                             vv v     i  i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (19 / 19)
Gap_init rate = 0.03 (6 / 224), avg. gap size = 2.33 (14 / 6)  


2847 25.17 1.55 1.32  chrX_87350263_87352213      553  1458 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87350263_8    553 TAGAAAAACATCCTATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 602
                          i    i i    i   i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87350263_8    603 GACCATACTGCCAAAAGCAATCTACAAATTCAATGTAATTCCCATCAAAA 652
                          i v     v  v   vii       i      i i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87350263_8    653 TACCA-CCATCATTCTTGACAGAACTAGAAAAAAACAATCCTAAAATTCA 701
                          v   - iii v  i   -     v v  v  iv-ii             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chrX_87350263_8    702 TATGGAACCAAAAAAGAACCCACATAGCCATAGCAAGACTATGCAAAA-- 749
                                viiv  ii  v  viv       v i   v-  -  v    --
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGA 196

  chrX_87350263_8    750 AGAACAAATCTGGAGGCATCACATTACCCAACTT-AAAACTATACTGTAA 798
                                 vi      vv     i v     i  -      -    ii  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chrX_87350263_8    799 AGCCACAGCCACCAAAACAGCATGGTACTAGTCTAAAATTGGGCAAATAG 848
                            i    iv i   i    ii       i iv   iiv i i  v    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_87350263_8    849 ACCAATGGAACACAATAGAGAATGCAGAAATAAACCCAAATACTTACCAC 898
                          i        i v   v    i v              v i i   ivii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_87350263_8    899 CAACTGATCTTTAACAAAGCAAACAAAAACATAAAAGTGGGGAAAGGACA 948
                            i    i  ii    i vviv   i v   vv  -         i i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATA 394

  chrX_87350263_8    949 CCCTATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAGA 998
                         vi  v                    i  i   vv ?       i ii   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_87350263_8    999 ATAAACCTGGATACTCATCTCTCACCTTATACAAAA-TAAACTCAAGATG 1047
                           i  vi    iv ii i   v    v         - v       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_87350263_8   1048 AATCAAGGAATTAAATCGAAGGCCTGAAACCATAAAAATTCTAGAAGATG 1097
                         i    ?i  vi     vv   iv  i    i      v ii       vi
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_87350263_8   1098 ATGTTGGAA-AACCCTTCTAGACATTGGCTTAGGCAAAGAATTCATGGCC 1146
                          ii v  ?i-  vi    vv   v    v        v iv   v i vi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_87350263_8   1147 AAGAACCCAAAAGGAAATGCAACAAAACAATCA-TAAACAGGTGGGACTT 1195
                          v  vv       v v v         v  vv -  i i ii v      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_87350263_8   1196 AATTAAA-TTAAAAAGTTTCTGTACAGCAAAATAAAAAATCAGCAGAGTA 1244
                         v  i   -       v   -   i vv    iv v vv    --   -- 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCA--AGA--A 689

  chrX_87350263_8   1245 AACAAACAAACAACCCACAGAGTGGGAGAACATCTTCACAATCTATACAT 1294
                          iii  v i            i        v  v  ii   vii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_87350263_8   1295 CTGATAAAGGGCT-GTCATACAGAATCTACAAGGAACTCAAACAAAT--- 1340
                                i  i  -  -  v      v  i  i      vv    v ---
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_87350263_8   1341 TAGCAAGAAGA-AAACAATCCCATCAAAAAATGGGCTAAGGACATGAATA 1389
                           ii  i    -   i  i  v  i?          v     iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_87350263_8   1390 GACAATTCTCAAAAGAAGATATACAAATGACCAACAGACATATAAAAA-A 1438
                             v     v                  i    i ii  i  i    - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_87350263_8   1439 TGCTCAATATCACTAATGAT 1458
                                i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (126 / 98)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.24 (26 / 21)  


1862 27.19 3.47 6.35  chrX_87364224_87366032.rev      484  1318 (491)    L1M4_orf2#LINE/L1       98   908 (0)  

  chrX_87364224_8    484 AAATTCTAACTGCAAGAATTGTTTT--AGATATAGGAAATCTTATTCCAA 531
                             i i i    -----i v    --   v  v iv  v  v  i i  
  L1M4_orf2#LINE/     98 AAATCCCAGCTGC-----CTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_87364224_8    532 AATTTATAAGGATAGGTACAGATTTTATAACAGCTAAAATAATTTTGACA 581
                             i   v   v v i vi iviii v  i   i    i   i    v 
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_87364224_8    582 AA----AATAAAGTGAGAAGAATCACCCTGTACAACACTAAGTCTTACCA 627
                           ----  i     vi  i  v    v  viv   ivii  iv     i 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_87364224_8    628 TAAGACTATAGCAACCAAAATTGTGTGGTATTGGTGGAAGGACACATACA 677
                         i  ii   i  i  i   i iv        i   iiv     i v i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_87364224_8    678 TAGATCAATGAAACAGAACT-------TAGAAATGGAGTCTAACAAATAT 720
                                   i  i    i -------i      ii vi vv   vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_87364224_8    721 GCTCAACGGATTTTTTGCACAATTGTAGAAGCAATTCAGTGGAGGAAGAA 770
                          v    iv      ivi  viiv  ivi ii v     i   i i     
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_87364224_8    771 AAGCCTTTTTGACAAATGGATCTGCAGCAATTGAATTTCCATAGGCCAGA 820
                         v  i     ii        vv   vii   i  i  v?   i v  ----
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC---- 438

  chrX_87364224_8    821 AGAGAAAAAAGGAAAAGAAAAACAAACCAAAATTCTACAACTTGAACCTC 870
                         ------------       --------ii  i  vv  vv  ---     
  L1M4_orf2#LINE/    439 ------------AAAAGAA--------TGAAGTTGGACCCCT---ACCTC 465

  chrX_87364224_8    871 ATACATTATGCAAAAATTAACTAAAATATATATCATGAACTTAAATGTAA 920
                          i  vv   i            v   -  iv    ?ii  i         
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAA-ATGGATCAWAGACCTAAATGTAA 514

  chrX_87364224_8    921 ACTATAAAACTGTAAAACTTT---AAGAAAATAATAGGAGAAAATCTTTG 967
                         ivvv       i       i ---       i -    ? v       i 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACA-TAGGNGTAAATCTTCG 563

  chrX_87364224_8    968 GGATCCAAGG------AACAACTTCTTAGACTTGACTCCAAAAGCATAAT 1011
                         v  i ivi  ------  iiii        iv    v         i  v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_87364224_8   1012 CTATCAAAGAAAAAATGGATAAATTGGACATAATCAAACAACAACAACAA 1061
                          v iv           i            v v      ------------
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA------------ 651

  chrX_87364224_8   1062 CAACAAAATACTTTTGCTCTGCGAATGGTCA-TGTGAAGAGAAAGAAAAG 1110
                         - vi    -       iv  v i  -  v  - i v    i iv      
  L1M4_orf2#LINE/    652 -ATTAAAA-ACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAAAG 698

  chrX_87364224_8   1111 AGAAGATCTAGACTGGAAGAAAGTAT--ACAAACCATATATTCACCAAAA 1158
                          v  vvivi   v   i     i   --i    i       iiivi  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_87364224_8   1159 GACTAGTGTTTAGAATGTATAAGGAACTTTCA-AACTCAACAGTTAAAAA 1207
                             v  i ii     i     i     i i -       i i v    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_87364224_8   1208 AAAAAT---CTAATTAGAAAACGGGCCAAAAAAAAATGTGAACAGACATT 1254
                          v    --- i    ?i    i    ----   ii  v    i       
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGC----AAAGGATTTGAATAGACATT 844

  chrX_87364224_8   1255 TTACGAAAGATCATATAAATACAGCAAATAAGCGTGAGAAGATATGTTAA 1304
                          iv v     vv     v v ii  v       iiiv   i v   i v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_87364224_8   1305 ACATCATTATTCAT 1318
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.02 (19 / 811), avg. gap size = 4.32 (82 / 19)  


2182 30.09 3.39 0.68  chrX_87369364_87371485.rev      748  1631 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87369364_8    748 TGGATAAACATTCCATGGTCATGAACAGAAAGAATTAATATAATTAAAAT 797
                             v i i  i     v     i iv i    v       vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87369364_8    798 GAACATATTGCCCAAAGCAAT------ACTC-------TTCTTGTCAAAC 834
                          ivv   i v      vii  ------ i  ------- i i i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87369364_8    835 TATCAATGACAATTTTCACAGAATCAGAAAAAAAG-TTATAAAATTCTTA 883
                          vi  iivi vv    ii     viv  v  ivv - iv        v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_87369364_8    884 TGCAACCAGAAAATATTCTGAATAGCAAAAGCAATCCTAAACAAAAAGTA 933
                           v  viiv  iiv ii v       v   i     i i  v  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_87369364_8    934 TAAAGCCAGAGGCATGACACTACCTGACGTCAAAATATACTGCAATGCTA 983
                         i    iii    vv v     v  ii iv      iv    i   v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_87369364_8    984 CAGTAATCAAAATACCGTGGTACTCATACAAAAACAGACACATAGACCAA 1033
                                   i i vi        vii i  ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_87369364_8   1034 TGAAACAGGTTTGAAAATCCAAAAGTAAAGCTGCACAACTACAACCATGT 1083
                           i  i  iv    i i    i  i    v iii   vi  iiii  vv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_87369364_8   1084 GATCTCTGATAATGTTGACAATAATAAGCAATGAG-AAAGGACCCCCTAT 1132
                            i ii  i  v v  v   v vi vv     i -    i ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_87369364_8   1133 TCAATAAATGGTGAATATATAACTGGTAAGCCATATGCAGTAAGTCGCAA 1182
                             i        vvviv i      vv ?   i     iv iivi v i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_87369364_8   1183 CTGGACCACTTCCTTTCACCATACACAAAA-TCAACTCAAAGTAGATCAA 1231
                         i      v  v   iv       i      - i        i i     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_87369364_8   1232 AGACTTGAATGTAAAACCTAAAACTACAAAAACTTTAGAAGAAAACATAG 1281
                             i i       i v         i    vii                
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_87369364_8   1282 A---AAATACCACTGTGGACGTTGGCCTTGGAAAGGATTTCAT-GATAAA 1327
                         i---    -- vii   -  v    vi v  v  v i    v -    v-
  L1M4_orf2#LINE/    551 GNGTAAAT--CTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATAT- 596

  chrX_87369364_8   1328 GACTCCAAAA--ACAATTGCTACAAAAACTAAAATTGGCAACTGGGATCA 1375
                            v      --    --  v      ivv     v ii  v v   iiv
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_87369364_8   1376 AATTAAACTGAAGAGCTTCTGTACAACAAAAAAC-TTACCAACAAGGTAA 1424
                         v  i   v v  i i   i   i vv    ii  -i  i   v  i  i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_87369364_8   1425 TCCAATAACCTACACAATGGGATAAAATATTTGCAATTTATTCATCTGAC 1474
                         vvvi i    i   v       v             v i  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_87369364_8   1475 AAAGGTCTAATATTCAAAAACTGTAAGGAACTTAAATAAC-----AAGCA 1519
                           i  v  vi   i  i  vv i   i     ivv i   -----  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_87369364_8   1520 AAAAACAAACAGCCGCATTAACAA--GGGCCAAAGACATTAAAAGACACT 1567
                            i     i i  vv   ? v  --    v  i  iv v  v     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_87369364_8   1568 TCTCAAAAGAAGACACACACATGGCCACCAAGCATATGAAAAACTGTTCA 1617
                             v        i i   v       vi     i       iv  i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_87369364_8   1618 ACAGCACTAATTAT 1631
                            v  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (147 / 116)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.40 (36 / 15)  


2918 25.61 1.77 1.55  chrX_87372979_87375393     1017  1922 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87372979_8   1017 TGGAAAAACACTACATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 1066
                               i i iiv    i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87372979_8   1067 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTCTTCTCACCAAAC 1116
                            v     v      v i  i  i        i  vv i ii i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87372979_8   1117 TACCC--TTGACTTTCTTTGCA-AAATTAGAAAAAACT-ACTTTAAATTT 1162
                          -   --i  v    -      -     i-- v  i  - iii    v  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTT-TTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_87372979_8   1163 CATATGGAACCAAGAAAAGAGCCCATA-TAGCCAAGACAATCCTAAGCAA 1211
                                  -- v v  i ii    v -       i      i i iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_87372979_8   1212 AAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACA 1261
                         i          i      vv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_87372979_8   1262 AGGCTACAGTAACCAA-ACGGCATGGTAGTGGTACCAAAACAGACATATC 1310
                          i          i   -  i ii     v   i iv ii i        v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_87372979_8   1311 GACCAATAGAACAGAACAGAGACCTCAGAAATAACACCACACACCTACAA 1360
                           i    i   i    iv    vii         vv   i   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_87372979_8   1361 CCATCTGATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAAAAGAT- 1409
                         i  vi    i        ivv  v   i v  vv           ii  -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_87372979_8   1410 TTCTTATGTAATAAATGGTGCTGGGAAAACTGGCTAACCATACCCAGAAA 1459
                         v    - vi  i              v      v  ?   i iv  i  i
  L1M4_orf2#LINE/    395 GTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_87372979_8   1460 ACTGAAACTGGACCTCTTCCTTACACT-TATACAAAAATTAACTCAACAT 1508
                          v    ii      i  v   i    i-                   v  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_87372979_8   1509 AGATGAAAGACTTAAATGTAAAGCCCCAAACCATAAAACTCT-AGAAGAA 1557
                         i   v ?    i         iiv iv    i          -       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_87372979_8   1558 AATCTAGGCAATAACATTCAGGACATAGGCATGGACAAAGA---CTTA-- 1602
                           iv    ?ivv  iv   iv   v v  vv i i   v i---    --
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_87372979_8   1603 -ATGACAAAAATACCAAAAACA-ATGTCAACAAAACCTAAAATTGACAAA 1650
                         -      ------      i  - v -        vvv     v  i   
  L1M4_orf2#LINE/    594 TATGACA------CCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAA 636

  chrX_87372979_8   1651 TGGGATCTAATTAAACTAAAGATCTTCTGCACAGCAAATGAAACTAGAAT 1700
                          v   ii v  i   v v  i v   i  ii vv    v  v    vv v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_87372979_8   1701 CAGAGTGAACAGGCAACCTATAGAATGGGAGAAAATTTTTACAATCTACC 1750
                         v i      v  i     i i               v   i   vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_87372979_8   1751 CATCTGACAAAGGACTAATAACCAGAATCTATAAGAAACTTAAACAAATT 1800
                         i      i  i     vi  v       v     ii    ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_87372979_8   1801 TACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAGGGATATGAA 1850
                         v i  v     i     i     v  i?    i       i    v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_87372979_8   1851 CAGACACTTCTCAGAAGAAGACATTTACGCTGCCAACAGACATATGAAAA 1900
                         i     i     vi       i  vi viiv     i ii  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_87372979_8   1901 AAAGCTCATCATCACTAATCAT 1922
                         i v     v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.67 (30 / 18)  


2695 26.15 1.28 4.38  chrX_87385236_87387805.rev     1144  2080 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87385236_8   1144 TGGAAACACATCCTATGTTCATGGATTGGAAGAATCAATATTGTGAAAAT 1193
                               v i    i                   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87385236_8   1194 AACCATACTGCCCAAGGCAATCTACAGATTCAATGCGATTCCCATTAAAA 1243
                         ii v     v     ivii              i  i  i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87385236_8   1244 CACCAACAACATTTTTC-CAATAATTCAAAAAACAATCACAAAATTCATA 1292
                         iv   i vi v     i-  iv    v v  ivii   vi          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_87385236_8   1293 TTAAACCAAAAAATAGTTTGAATACCTAAAGACTTATTCTTTAGCCATAG 1342
                          vi  viiv  iiv viiv     v i   -  -- v    -- ---- i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAA-AC--AATCTT--G----AA 191

  chrX_87385236_8   1343 CAAAAAGAACAAATCTGGAGGCATTGCATTACCAAACTTCAAGTTGTAAC 1392
                         v  i         vi      vv ii  i v  v  i     iviv  vi
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_87385236_8   1393 ACAAGGCAATAGTTATCAAGACAGCATGGTATTGATATAAAAGTAGGTAC 1442
                             i  v i   v          ii     i  ii    iii   ii i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_87385236_8   1443 ATAGACCAATGGAACAGAAT-----ATTCAGAAATAGTTCCAAATATGTA 1487
                              i        i     -----i i        ivi   v i  v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_87385236_8   1488 CAGCCAACTACGTAATCTTTGATAAAGCATACGAAAAC-ATATATTGGTG 1536
                         ii i   i i----  i  i  i  i -i i v  i  -  vi v   v 
  L1M4_orf2#LINE/    342 TGGTCAATTG----ATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGG 386

  chrX_87385236_8   1537 AAAGGACATCCTATTTAATAAATGTTGCTGGGAAAACTGACAAGCCACAT 1586
                             i i vi  v  i  i     v        v     ivv ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_87385236_8   1587 ATAGAAGAGTGAAACTGGATCCTCATCTCTCACCTTATGCAAAAATTAAC 1636
                         ii i    i    ii    i  ii i   v    v   i           
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_87385236_8   1637 TCAAGATGGATCGAAGACTTAAATGTAAGACCGGAAACCATAAGAATTCT 1686
                             i       i?    i           v vi    i    i v ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_87385236_8   1687 AGAAAATAACATTGGAAAAACTCTTCTGGACCTTGGCCTAGGCAAAGAAT 1736
                             i v     v  ?iv  v     vv        vi       v iv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_87385236_8   1737 TCATGACTAAAACCCCATTATCATGACTAAGATCCCAAAAGTAAATGCAA 1786
                           ---------------   ----  -  v  iv       i v v    
  L1M4_orf2#LINE/    587 TC---------------TTA----GA-TATGACACCAAAAGCACAAGCAA 616

  chrX_87385236_8   1787 CAAAAACAAAAATAAATAAACAAATGGGACC-CGCCTAAATTAAAAACCT 1835
                              iv       i     ---- v    i- ii v           i 
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAA----TTGGACTTCATCAAAATTAAAAACTT 662

  chrX_87385236_8   1836 TCTGCACAAGAAAAGAAATAATTAGCTGAGTAAATAGACAACCAATGGAA 1885
                          -  ii vvv   i  v iv  i ivvi   i  v        v ii   
  L1M4_orf2#LINE/    663 T-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_87385236_8   1886 TGGGAGGAAACATTTCCACACTATAAATCCATCAAAGGACTGGTATCCAG 1935
                               i   i    v  v ii   v   iivi  i     v        
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_87385236_8   1936 AATCTACAAAGAACTCCAACAAATCAGCAAGAAAAAATCTAAATAATTCC 1985
                            v  i         iv    v   ii  v     iv -      ii v
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCA 810

  chrX_87385236_8   1986 ATCAGAAAGTTGGCCAATCATATGAACG--TATTTCTCAAAAGAAGATAC 2033
                           i?i   i v   v  vv  v    ii--i       v          i
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_87385236_8   2034 ATAAATGGCCAACAG--ACATGAAATAAATGCTCAACATCGCTAATCAT 2080
                          i          i i--        - i            i????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAA-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.79 (53 / 19)  


2548 23.73 7.52 4.05  chrX_87416399_87419714     1960  2823 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_87416399_8   1960 ATGGTTATGTATCAGAAGAATTAATTTTGTTAAAATAACTATACTACCCA 2009
                            v i   v  ii     v     v       i  ii v     v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_87416399_8   2010 AAGTAATTTACAGATTCAATGCAATCTGTATCAAAATAGCAATGACATTT 2059
                           v i  i           i      iv         vv  iivi v   
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_87416399_8   2060 TTCACAGAAAAAAATACAAC-AATCCTGCAGTTTATATGGAACGACAAGA 2108
                           ii      vvi i - i -i     iv i  i        vvi    i
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chrX_87416399_8   2109 GACTCTCAATATCCAAAGCAATTT--AAACAAAAAATCTAATCCAGAGGC 2156
                            i vv    v     i    i --   v i  i v v  viii    -
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG- 212

  chrX_87416399_8   2157 AC-CATATTATCTTACTTCAAAATACACTTTAAAGTCCCAGTAATCAAAA 2205
                           -  i i vi iv i       ivi   vi    iiv          i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_87416399_8   2206 CAGTATGGTACTGG------GA------------------GAAAAG---- 2227
                             i         ------  ------------------   v  ----
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_87416399_8   2228 --GAGCCCAGAAATA--------TATTTATG--CAATTGATCTTTGACAA 2265
                         --   i         --------i       --        i  i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_87416399_8   2266 AGGTGCCAAGAATACACAA------AAGAG-AGTCTCTTCAATAAATAGT 2308
                         i          vi iv   ------    i-     i     i    i  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_87416399_8   2309 GTTGGAATAACTGAATATTCACATACAGAAGAATGAAATTAGACTCTCAT 2358
                          i   i i     i   ?i     i  i         i  i   i ii i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_87416399_8   2359 CTGACATCATATATTAAAGGCAGCTCAAAAATGTATTAAACACTTAAATA 2408
                           v   i      iv   ivi i       -  v  i ? v  i     i
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAA-TGGATCAWAGACCTAAATG 511

  chrX_87416399_8   2409 TAGGA--CAAGGAACTATAAAACTACTAGAAGAAAGCATAGGGAAAAAGT 2456
                           i  --i  --            vi         i      ?iv   vi
  L1M4_orf2#LINE/    512 TAAGAGCTAA--AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_87416399_8   2457 TCTGTGACATTGGTCTGGGCAATGATTTTTTGTAGGTGTTCCCAAAAGGT 2506
                          ii     v    vi i       i   i  iv vi  viv       vv
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_87416399_8   2507 CATGCAACAAAACTGAAAATAGACAAATGGAATTATATCCAACTACAAAG 2556
                           v         vvi        i    v i i vi   v  v vv   i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_87416399_8   2557 CTTCTACACAGCAGCAACAACAAACAAACAACAAACCAACAAATGAAAAA 2606
                            i iii vv  -------------  vi   -- i v   --    --
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCA-------------AAGGACA--CTATCAA--GAAA-- 690

  chrX_87416399_8   2607 ACAACAGAGTGAAGGGACAACCTACATAATGGGAGAAAATATTTGCAAAC 2656
                         --------     ii       i   v                      i
  L1M4_orf2#LINE/    691 --------GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_87416399_8   2657 CATATATCTGATAAAAAGGTTAATATCCAAAATA----GAAAATTTAAAC 2702
                                       iiiiv  i-      i    ----i i  i ivv  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTAC 781

  chrX_87416399_8   2703 AACTCGTTAGAAAAAAAACA------CTA--TTAAAAATGAGCGAATGAT 2744
                              iv  iv     i   ------ i -- ?       i  i  v   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_87416399_8   2745 CTTAATATACATTTCTGAAAAGAAGACATACAAATGGCCAATAAGTATAT 2794
                         i v    v        vv        i                  i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_87416399_8   2795 GAAAAAAAATGCTCAACACCACTATCAGA 2823
                              i --         i  ????????
  L1M4_orf2#LINE/    882 GAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (129 / 72)
Gap_init rate = 0.03 (24 / 894), avg. gap size = 4.17 (100 / 24)  


2529 19.39 2.77 6.20  chrX_87420059_87421736      433  1190 (488)    L1M4_orf2#LINE/L1      177   908 (0)  

  chrX_87420059_8    433 CAGAACAGAGATTTTAAAAAGTAGAGAGACAAAGATGGAATTTTAAAGCT 482
                           i    ---  i  i    --   iii      v    i----------
  L1M4_orf2#LINE/    177 CAAAACA---ATCTTGAAAA--AGAAGAACAAAGTTGGAG---------- 211

  chrX_87420059_8    483 GCCTGATTTTGAAACTTCCTGATTTTGAAACTTCCTAAAAAGTTACAGCA 532
                         ----  i i-- v      ii    ii      v   v    i     i 
  L1M4_orf2#LINE/    212 ----GACTC--ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_87420059_8    533 ATAAAAACAGTGTAGTAGTTGTAGTAGTTGCATAAAAATAGACGTATAA- 581
                           v  i       i   -i  --------      ii      i    i-
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTA-CTG--------GCATAAGGATAGACATATAGA 296

  chrX_87420059_8    582 -CAATAGATTATAATTGACAGTCCAAAAATAAACCCATACAACTATGGTC 630
                         -    i  v  v      v      i               vi       
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_87420059_8    631 AATTTATTTTCAACA--GCCCCCAAGGCAAATTAATGGGGAAA-AATATT 677
                             v      i   -- viv     i v v i          -    v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_87420059_8    678 TGTTTCAACCAATACTACTGAGACAACTGAAT---CACATTCAAAAGGAA 724
                         iv       v   iv i   i        i  ---     v      -  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AA 445

  chrX_87420059_8    725 TTA--TTAGGAATCCTAACCCACACTAGATATAAAAAT-AATTCAAAAAT 771
                          v --  -   vi    v i     i v   i      -  i      vv
  L1M4_orf2#LINE/    446 TGAAGTT-GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_87420059_8    772 CATCAAATATCTAGATGCATGACCTAAAATTATAGAACCCTTAGAATAAA 821
                         v    ? v i   i   i v  v      i    i   i       v   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_87420059_8    822 ACATAGGTGTAAATCTGTATAACTTTAGACTATACAATGGTTTCTTAGAT 871
                                ?        vii i  i  i ii  vi                
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_87420059_8    872 ATGGTACCTGAGGCACAAATGCACCCCCCTAAAA--TAGATAAGTTGGAA 919
                            ii   vi i      --   v vvvvv    --       i     v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_87420059_8    920 TGCATCAAAATTGAAAAGCTTATTTTTGCTTTGAAAGAGTCTACCAAGAA 969
                          v          i    -   --  v     ii  i  vv   i      
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTT--TTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_87420059_8    970 AGTTAAAAAGA-AACACACATAATGGATAAAATTATTTGCAAAATATATA 1018
                            -i      -   v    v     ivi   v          vi     
  L1M4_orf2#LINE/    690 AGT-GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_87420059_8   1019 TTTGGTCAGTGTCATAAGCACCTAGTGTTCAGAATATATAAGAAACT--T 1066
                          i  ---------     viv  v  i i            ii    -- 
  L1M4_orf2#LINE/    739 TCTG---------ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_87420059_8   1067 AAGACTCAATAATAAAAACACAAG----CCAATT-AAAAATGGGTAAAGT 1111
                          vi               v    i----      -         i    v
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_87420059_8   1112 ATCTGAATAGACATTTCTTTAAGGAAGATATACAAAAGACCAATAATCAC 1161
                           i               ii  i             v i       v   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_87420059_8   1162 TTGAAAAGGTGTTAAAAACTATTAGTCAA 1190
                         v       i  i v  v ii ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (85 / 60)
Gap_init rate = 0.03 (24 / 732), avg. gap size = 2.83 (68 / 24)  


2836 23.80 4.02 2.57  chrX_87446509_87451522     3627  4521 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87446509_8   3627 TGGAAAAACACACTATGCTCATAGTTTGGAAGAATCAATATTATTAAAAT 3676
                               i i iv i   i    i v        v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87446509_8   3677 GGCCATATTGCCCAAACCAATCTACAGATTCAATGCTATTCCTATTAAAT 3726
                            v   i v      iii              i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87446509_8   3727 GACCAATTTAATTTTTCACAGAATTAGAAAAGTT-ATTATAAAATTCATG 3775
                         vv   ii vvv     ii     v v  v   i -  iv          i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_87446509_8   3776 TGCAACCAAGAAAGAG-CCCA-AATAACCAAAGCAATCCTAAACAAAAAG 3823
                           v  -- v v   i -    -    i     i     i i  v  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_87446509_8   3824 AAGAAAGCCAGAGACATTGCATTACCCATCTTCAAAGTATACTACAAGGC 3873
                           v    iii   ivv ii  i v    vi      iiv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_87446509_8   3874 TA---------AAACAGCATGGTGCTGGTAGAAAAAACAAACACATAGAT 3914
                           --------- i    ii    i    i v  ii -i i   i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGAT 297

  chrX_87446509_8   3915 AAATGGAACAGAATAGAAGACCCAGAAATAAAGCCACACATCTACAACCA 3964
                         v       i     v  iiii           v   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_87446509_8   3965 TCTGATCTTTGTGAAA--TTTCATAAACAAACAAAAAAGCATTGGGGAAA 4012
                         vi    i  i vv  i-- vi  vi v  vv   --------        
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAA--------TGGGGAAA 389

  chrX_87446509_8   4013 GGACTCCCTATTTAATAAATGGTGCTGGGAAAATTGGCTAACCATTTGTA 4062
                          i ivvi  v  i  i              v  i   v  ?   iv  i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_87446509_8   4063 GAAGAATGAAGATGGACCCCCTATCTCTCATCATATACAAAAATTAACTT 4112
                         i          v        -  i   v  i                  i
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTC 488

  chrX_87446509_8   4113 AAAATAGATTAAAGACTTGAATGCAAGACCTCCAACAGGGGAAATCCTAG 4162
                              i   i ?    i i    i    v  vv   vivii  v  i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_87446509_8   4163 AAGAAAACCTAGGA-TATACTCTTCTTGATATTGGCCTAGGCAAAGAATT 4211
                                 v    ?-  - v     v   iv    vi       v iv  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_87446509_8   4212 ------TATGACTAAGTACGCAAAAG-A-AAGCATACAAAA--AAAAATG 4251
                         ------      -----  -      - -     -      --      i
  L1M4_orf2#LINE/    588 CTTAGATATGAC-----AC-CAAAAGCACAAGCA-ACAAAAGAAAAAATA 630

  chrX_87446509_8   4252 AACAATTGGGACCTAATTAAA-TTACAGAACTTTTGCACAGCAAAAGAAA 4300
                         i i  v v    i v  i   -   - i        ii vv    i  v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACA 679

  chrX_87446509_8   4301 CTATCAACAGAGTAAACAGATAACCTAAAGAATGGGAGAAAATATTTACA 4350
                                v i   i  v   i    i v                   i  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_87446509_8   4351 AACTATGCATCTGACAAAGGACTAATATGCAGAATCTATAAGGAACTT-- 4398
                           ii  ii      i  i     vi   v      v     i     i--
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_87446509_8   4399 -------AAAAAGCAAAAAACAAATAACCCTATTTAGAAGTGGGTAAAGG 4441
                         -------  v  vv    i           v   ? i  i    i     
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_87446509_8   4442 ACATGAACAGACACTTCTGAAAAGAAGAAATATAATTTTCCAACAAATAC 4491
                          iv    i     i    vv        v   i  v vv    i  ii  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_87446509_8   4492 ATGAACCAAAA-GCTAAACATCACTATCAGA 4521
                              --  i -   v       ????????
  L1M4_orf2#LINE/    880 ATGAA--AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (126 / 83)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.57 (59 / 23)  


1284 20.10 2.52 23.50  chrX_87552160_87556368.rev     2570  3718 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87552160_8   2570 TGAAAAGACATCCTATGTTCATGGGTTAGAAGAATTAATATTGTTAAAAT 2619
                           i     i    i          i  i     v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87552160_8   2620 GCCTTATACTACCAAAAGCAATTTACAGATTCAATGCAAATTCTATAAAA 2669
                          v v-     v  v   vii  i           i    vii    v   
  L1M4_orf2#LINE/     51 GGCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_87552160_8   2670 AACCTAA-TGTTTTTCAATAGGACTCATTTGTTTTTCACAAAAAT--ACA 2716
                          v  i i-  ii   ------------    -------  i    --   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTT------------TTTG-------CAGAAATTGACA 130

  chrX_87552160_8   2717 AAAAAAT---AATAATTCATGTGGAACCACAAGGGATGCTAAATAACCAA 2763
                          ivvi  ---  -       i     vii       iv vi    i    
  L1M4_orf2#LINE/    131 AGCTGATCCTAA-AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_87552160_8   2764 AACAGTTTTGAGAAAGAAGACCATAGATGAGGGTTTCCAACTTTCTGATT 2813
                             i i    i        v  v  v  ii  vi  vv    i ii   
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_87552160_8   2814 AAAAGATATATTACAAATCAGTAGGAATCAAGCCCGTATGATGTTGGCAT 2863
                         vv  i iv  i      v vii  v       v v  i  i ii      
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_87552160_8   2864 AAAGACAGACACTT-GATAATTGAAGTAAAACAAAGAGCTCCAAACTAAA 2912
                           i  i     iv -   v v  i i  i  ivi    ii vi  v    
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_87552160_8   2913 TCCATGGATATACTGTAAAACGATCTTTAACAAGGGTGCCAAAACTACAC 2962
                         i    iv  v  iv  v  vi   i  ii             i  i iv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_87552160_8   2963 GATGGTGAAATGATA-TCTCTTAAACCAATGGTGCTGGGATA-CCAGATA 3010
                         i    v    vi   -   i  v   v             i - ii    
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_87552160_8   3011 GCCACTTAAAAAAAAGTTGGACCAGCCGGGCACGGTGGCTCACGCCTGTA 3060
                         ?    v iv    i i ---------------------------------
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAAT--------------------------------- 446

  chrX_87552160_8   3061 ATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACCTGAGGTCAGGAG 3110
                         ---------------  i i  ---------  i -   i----------
  L1M4_orf2#LINE/    447 ---------------GAAGTTG---------GACC-CCTA---------- 461

  chrX_87552160_8   3111 TTCGAGACGAGCCTCAACATGGAGAAACCCCGTCTCTACTAAAAATACAA 3160
                         -----------     -  ----------  i -----------      
  L1M4_orf2#LINE/    462 -----------CCTCA-CA----------CCAT-----------ATACAA 478

  chrX_87552160_8   3161 AA-TTAGCCGGGCGTGGTGGTGCATGCCTGTAATCCCGGCTACTCGGGAG 3209
                           -   -----------------------------------    -----
  L1M4_orf2#LINE/    479 AAATTA-----------------------------------ACTC----- 488

  chrX_87552160_8   3210 GCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCGGTGAGC 3259
                         ----------- i   ----- i i v?i  ------------------ 
  L1M4_orf2#LINE/    489 -----------AAAAT-----GGATCAWAGA------------------C 504

  chrX_87552160_8   3260 CGAGATCATGCCATTGCACTCCAGCCTGGGCAACAAGAGC-AAAACTCCG 3308
                          v i  --------------------------ii      -      ---
  L1M4_orf2#LINE/    505 CTAAAT--------------------------GTAAGAGCTAAAACT--- 525

  chrX_87552160_8   3309 TCTCAAAAAAGAAAAAAAAAAAAAAGTTGGACCATTATTATAATCTCTGA 3358
                         --------- v    -----------------------------    v 
  L1M4_orf2#LINE/    526 ---------ATAAAA-----------------------------CTCTTA 537

  chrX_87552160_8   3359 AATAAAAGCATAGATAAAAATCTTTATAATACTGGCCTTGACAATGAATT 3408
                         i vi   i     i?iv       ii i ivi   vi v i     i-  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TT 586

  chrX_87552160_8   3409 TCTTGGATCTAACACAAAAAGTACAGGCA------GAAAAATTTTTTAAA 3452
                             i   v i    v     i   i   ------      v ---- i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT----AGA 632

  chrX_87552160_8   3453 -AAGTGGGACTATATCAAACCACAAAGCTCCATATAGCAT-AAAAAATA- 3499
                         -  i v     vi      vivv   i  ii- i -  v -   ii i -
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTT-TGT-GCTTCAAAGGACAC 680

  chrX_87552160_8   3500 -AGCAGCAGAGTGAAAAGGCAATGGACAGAATGGGAGATAATATTTGCAT 3548
                         - v  iv i         i   ivv             v          v
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_87552160_8   3549 ATGATGTATTTGATAAAAGATTAATATGCAAAGTATA-AAAG--CTCCTA 3595
                           v  i   i      ii  i vi   v  i i    -    --   i  
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_87552160_8   3596 AAAATCAATAGCAAAA-TCCAAATAATCCCATTTAAAA-TGAGCAAAGTA 3643
                         v  v      ii    -vv       i  v   ?    -  i      v 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_87552160_8   3644 CTTGGATAGCTATTTCTTCAAAAAGAACATGTAAATGACCAA---GTTTA 3690
                         i   i    vi      i    i ii i  ii     i    --- ivi 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_87552160_8   3691 TAAAAAGATGCTAAACATTACTAATTCC 3718
                          i          v     i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (145 / 82)
Gap_init rate = 0.04 (39 / 908), avg. gap size = 7.67 (299 / 39)  


1351 28.60 2.37 1.72  chrX_87580844_87584532     1867  2331 (1358)    L1M4_orf2#LINE/L1        1   468 (440)  

  chrX_87580844_8   1867 TGGAAAAACATTCCAAGTTCATGGAGAAGAAGAATCAATATCATGAAAAT 1916
                               i i  i   v         vvi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87580844_8   1917 AGCTACAATGTGAAAAGCAATTTTTAGATTCAATGCTATTGCTATTAAAA 1966
                         i  v i v vivv   vii  i vi        i  v  iv    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87580844_8   1967 TACCATTGAGATTCTTCACATAATGAGAAAAGCT-ATTTAAAAATTCATA 2015
                          v   vivivv  i  ii  v  vvv  v     -  iiv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_87580844_8   2016 TAAAACCAAGAAAGAGACT--GAATAGCCAAGGCAATCCCAAACAAGAAT 2063
                          ii  -- v v   i   i--          ii     iii  v     v
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_87580844_8   2064 AACAAACCTGGAGACATCACACTACCCAACTTCTAATTATACTATAGGGC 2113
                               vi     ivv       v     i   v  viv     i ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_87580844_8   2114 TACAGTAACCAAAACAGCATTGTACTCATACAAAAACTGACATATAGATC 2163
                                 i   i    ii v     vii i  ii iv            
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_87580844_8   2164 AATGGAACAGAATAGGAAACCCAGAAATAAGACTTCACACATACAACTAT 2213
                                i     v ii ii          ------  v      vi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAA------ACCCATACATTTAT 342

  chrX_87580844_8   2214 G------TGATCTTGGACAAACCTGACAAAAACAA-CAATGGAGAAAGGA 2256
                          ------    i  v     ivv  v   i v  v-      i     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_87580844_8   2257 CTCCCCATTCAATAAATGATGCTGGGATAACTGGCAAGCCGTATACAGAA 2306
                         ivvi iv     i     i        i      vv ?  ii  i  i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_87580844_8   2307 AATTGAAACTGAACCCCT-TCTCATA 2331
                         i v    ii  i      -i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACA 468

Transitions / transversions = 1.44 (78 / 54)
Gap_init rate = 0.01 (7 / 468), avg. gap size = 2.71 (19 / 7)  

 870 26.11 2.95 7.37  chrX_87580844_87584532     2722  3196 (493)    L1M4_orf2#LINE/L1      455   908 (0)  

  chrX_87580844_8   2722 ACACCTTCCGTACACCATATTAAAAAATTAAC-CAAGATGGAACAAAGAC 2770
                           v   v  vi         vv          -   i     v  ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_87580844_8   2771 TTAAATTTTCAACCCCAAACTACAAAAACCCTGTAAGACAATCTAGGCA- 2819
                         i     v vvi v iv      i    vi i iv    v  iv    ?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_87580844_8   2820 ATACCATTCAGGATGTAGGCACGGGAAAATATTTCATGACAAAGATGA-A 2868
                          v i -   iv  iv v  vvii  v  vvi    v --- i v    - 
  L1M4_orf2#LINE/    555 AAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT---AGATATGACA 600

  chrX_87580844_8   2869 --AAAAGCAATTGCAACAAGAGCAAAAATTGACAAATGATATCTAATTAA 2916
                         --       vvv       i  v      v  i    viv ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_87580844_8   2917 GCTGAAGAGCTTCTGCACAGTAAAAACAAAACAAAACAAAACAACAACAA 2966
                         iv v  i i   i  ii vvi   ii----------------------- 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGG-----------------------A 677

  chrX_87580844_8   2967 CAAAAAAACCATCAACAGAGTAGACAGACAACCTACACAATGGGAAAAAG 3016
                           ------ i     v i   ii v        i   v       i   i
  L1M4_orf2#LINE/    678 CA------CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_87580844_8   3017 TTTTTGCAAACCGTGCATCTGACAAAGGGCTGATATCCAGCATCTACAAG 3066
                          v        i i ii      i  i  i  vi       v  v  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_87580844_8   3067 GAAC----ATAAATAAATGAACAAGAAAAACAAA-AAC---ATTAAAAAG 3108
                             ---- i  v v   -  i  -   i     -   ---   ?    i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAAT-AATAA-AAAGACAAATAACCCAATTWAAAAA 819

  chrX_87580844_8   3109 TGGACAAAGAACATGAGTAGACACTTTCCAAAAGAAGACATACATGCAGC 3158
                            i     i iv   i      i  ii v        i     viii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_87580844_8   3159 CAACAATCATATTTAAAAA-GCTCAACATCATTGATCAT 3196
                            i  v  i  vv   i -           ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (68 / 53)
Gap_init rate = 0.03 (14 / 454), avg. gap size = 3.50 (49 / 14)  


1788 24.30 7.65 5.77  chrX_87604589_87606325      500  1244 (493)    L1M4_orf2#LINE/L1      150   908 (0)  

  chrX_87604589_8    500 ATGGGACCATATAAG--ATCCTGATTGTCCAAAGAAATCTTTAGAAAGAA 547
                             i --  ii   -- i  v  v iv     iv      v i      
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_87604589_8    548 ---CAAAGCTTAAGACAC-CATACTTTCTGATTTTAAAATGTATTACAGA 593
                         ---     i vi  i-  -  i    i ii    i    iv  i    i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_87604589_8    594 GCTACAGTGATTTAAACTGCACAATATTGGTATAAAAAAAACTTACAGTA 643
                                 i  iv i  v iiiii  i   i    ii v i---   -  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG---ACA-TA 292

  chrX_87604589_8    644 TAGTTGAA--AAATA-AATAGAAAGCCCAGAAATAAACCCATGAATACTG 690
                            v v  --i    -   v  i  i                -- i i -
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT--ACATT- 339

  chrX_87604589_8    691 TATACAGTTAACTGATCTTTAACAAGTTTGTCAATAATACTGAATAAAGA 740
                         --  ii  i  i    i  ii     vv  i   v vi i v   iii  
  L1M4_orf2#LINE/    340 --TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_87604589_8    741 AAGGACAATCTATTCAAGTAATGGTGCTGGAA---------ATCCACATG 781
                            i i i   v     vv           i --------- ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_87604589_8    782 CAAGAAGAATGAAATTGGACCCTTTTTCTTCACACCACACACACATACAC 831
                            -         i        i ---------   v     -    i  
  L1M4_orf2#LINE/    438 CAA-AAGAATGAAGTTGGACCCCT---------ACCTCACAC-CATATAC 476

  chrX_87604589_8    832 ACACCACACGTGCACACACACATCAAACTCAAAATAGATTAAAGTTTGAA 881
                          v ---------------- -  i  -        i   i ?  viiv  
  L1M4_orf2#LINE/    477 AAA----------------A-ATTAA-CTCAAAATGGATCAWAGACCTAA 508

  chrX_87604589_8    882 ATATAAGACCTGAGAATGTAAAACTCCTAGG-GACAAC----GTGT---- 922
                           i     v  i i v i        i   i-  v   ---- ?  ----
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_87604589_8    923 ---TATGACATTGGTCTTGACACTAATTTCTTGGATATGCAATCAAAAGC 969
                         ---ii    v    vi v i  v ii      i      vv i       
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_87604589_8    970 ACAAGAAACAA--GCAGAAGTAGACAAGT-GTACATACATCCATCTAAAA 1016
                              v     -- v i  i    i  i - v  v -    v vv v   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATCAAAATTAAA 657

  chrX_87604589_8   1017 GGCTTCTGCACAACAAAAGAAACAATTGACTGAATGAAAAGGCAACCTA- 1065
                         ii   i  ii vv    i  v  v  ii vvi i       i     i -
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_87604589_8   1066 --------------TATTTGCAAATCATATATCTGATAAGTGGA-TAATA 1100
                         --------------                          -   - vi  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG-GGACTTGTA 756

  chrX_87604589_8   1101 TGTAATGTATATAAGGAACTCCTAAAAGTCAATAACAAAAA------TAT 1144
                          vi ivi       i      i  v  v       i     ------  v
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_87604589_8   1145 TTTGATTAAGAAATAGATCAAAGACTT-AATAGGCACCTTGCCAAAAAAG 1193
                         iiii   ? i    i iiv  i  i  -     i  ii iv     i   
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_87604589_8   1194 ATATACAGATGAA-AATCAGCATATAAAAAGATGCTCCACATTATATGTC 1242
                                i   iv-   v    i  i           v    i ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_87604589_8   1243 AT 1244
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.00 (118 / 59)
Gap_init rate = 0.04 (30 / 759), avg. gap size = 3.33 (100 / 30)  


1122 24.91 0.75 1.13  chrX_87607780_87609405.rev        1   265 (1361)  C L1M4_orf2#LINE/L1   (412)   496   233  

C chrX_87607780_8    265 AAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACAA 216
                              -        i          i   i    ii         i i  
  L1M4_orf2#LINE/    233 AAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

C chrX_87607780_8    215 AAACAGATATACAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAAT 168
                         ii i   i   i   i        i    i--    i  --        v
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAA 329

C chrX_87607780_8    167 GCTGCATATCTACAACTATTTGATCTTTGATAAACCTGACAAAAACAAGC 118
                         v iii i  i  iiiii v     i  i  i  ivv  v   i v  vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

C chrX_87607780_8    117 AATGGGGAAAGGATTCCCTATTTAATAAATGGCACTGGGAAAACTGGCTA 68
                                    i  vvi  v  i  i      ii      v      v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

C chrX_87607780_8     67 GCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAA 18
                         ?   i   i i  iiv    ii    i    v   i     v        
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

C chrX_87607780_8     17 AATTAATTCAAGATGGA 1
                               i    i     
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGA 496

Transitions / transversions = 2.82 (48 / 17)
Gap_init rate = 0.01 (3 / 264), avg. gap size = 1.67 (5 / 3)  

 291 25.42 5.93 1.69  chrX_87607780_87609405.rev      269   386 (1240)    L1M4_orf2#LINE/L1      149   271 (637)  

  chrX_87607780_8    269 TATAAAAA-GCAAAACAGTTACAATTTACTAAAATTAT-TTGAAAAATGA 316
                            ii   -    iiv vii v   v-i i    iv  -        vi 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATA-GCCAAAACAATCTTGAAAAAGAA 197

  chrX_87607780_8    317 ---CAAAGTTGAAGAACTTACTTTGCCTAATTTCAAAATTTATT-TAAAG 362
                         ---        i  i   i  vi v  i          i   i -i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_87607780_8    363 GTACAATAATCACC-CATGTGTGGT 386
                         v    i      vv-  -       
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACA-GTGTGGT 271

Transitions / transversions = 1.73 (19 / 11)
Gap_init rate = 0.06 (7 / 123), avg. gap size = 1.29 (9 / 7)  

1212 27.59 5.69 3.80  chrX_87607780_87609405.rev      451  1135 (491)    L1M4_orf2#LINE/L1      211   908 (0)  

  chrX_87607780_8    451 GGACTC---CTTCTC-----TAAAAGTAAAAATAAAAATGCAATATCCCA 492
                               ---    i -----i    v v vv i   iv i  i  vi v 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_87607780_8    493 TA---TGTCATTTTAGTAGAAGGATAAATACATAAATAAATGGAA-AGA- 537
                         v ---   vi vi i i v       i i i   i  v       -   -
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_87607780_8    538 --GATAGTCTAGAAATAGATCTACTCATATATTATTAATTAATTTTAAAT 585
                         --  v    i       i i i iv   v   vi i    i     vi i
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_87607780_8    586 AAATGTATCTGGGT-ACTTAAAAGGGAAATAGAATA-TGTTTTCAAAAAA 633
                           iv  ii vi ii- i i  vi      --     - v       v   
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAA--GAATAGTCTTTTCAACAAA 408

  chrX_87607780_8    634 TGGTGTTACATCAACTTGATAGCCACATGGAAAAAAA--AACATAAACTT 681
                              i iviv     v    ?       v    i  --  vv ii  ii
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_87607780_8    682 -TACATCAACACCATTCCCAAAAAT-AATTTGAGATATGTC-TGTACCTA 728
                         -   v   -      viv       -  i ii i  ivi  -?iv     
  L1M4_orf2#LINE/    459 CTACCTCA-CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_87607780_8    729 AATTTAAAACTTAAAACTATGTAAACTGT-GGAAGAAAACATAAGAAAAA 777
                            v   i vi         i-     v -i            i ?iv  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_87607780_8    778 AGAAGATTTTC-T-ATCTTAGGATAGGCAACTATTTCTTTTCCACAACAC 825
                          ----- i   - - i   i  v       ivi      vvvi ii    
  L1M4_orf2#LINE/    557 A-----TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_87607780_8    826 AAACACACATGCACACAAACAAACATGAAACGTAAAAAAATTG-TAAGTT 874
                         v  v -------i     i   -  --   ---i       v -   i  
  L1M4_orf2#LINE/    602 CAAAA-------GCACAAGCAA-CA--AAA---GAAAAAATAGATAAATT 638

  chrX_87607780_8    875 AAACATCACCATAATTTCAAAGAATTTAAAA--TCAAAAGAAGAGA--AA 920
                         ii  v   i  v    --   i v   vivi--     i  vivv --  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATT--AAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_87607780_8    921 GATAATGAAAAGCCAAGGTGTTTAGACTGAAAGTAATTATTCACAACACT 970
                           v i       v   --ivivi   v  ii  v  v    ii   vv v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAA--CCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_87607780_8    971 TCTAGCCAATA-----TTTGTATCCAGAGTATATAAAGCACAATTACAAC 1015
                          v  v ii   -----i           i         v  vv       
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_87607780_8   1016 TAGGTAATAGCAAATGAAACAATCTAATTTAAAAATGGGCAATATATTTA 1065
                          vii     iv  ivv   i  i i    ?            viv    i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_87607780_8   1066 ATTAAACATGTTGCC---GAACAGACATGAATGGCAAATAAGCATATGAC 1112
                          v  i    v iv  ---   v v i ii      v        i    v
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_87607780_8   1113 AAGATGCTCA-CATTATTTGTCAT 1135
                                   -   i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (104 / 81)
Gap_init rate = 0.04 (30 / 698), avg. gap size = 2.17 (65 / 30)  


2513 27.44 2.33 1.67  chrX_87639344_87641889     1154  2053 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_87639344_8   1154 GAAAAATCCTTCCATAATCACAAACTGGAATAATTAATATCATTAAAATG 1203
                             i  v- i    iv   iii i     v v       ii    i   
  L1M4_orf2#LINE/      3 GAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_87639344_8   1204 GTCATTCTGCCTAAAGCAATCTAAAGACTTAATACTACTCCTGTCAAACT 1253
                          iv  v  v  i   vii     v   i i  ii v ii   i     v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_87639344_8   1254 ACCAACATCATTTTTCACAGAAGTAGATAAAAATATTCTAAAATTCATAT 1303
                         v   i vv v     ii     i v  i  ivvv  i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_87639344_8   1304 AGGACCAACG-AAGAG--CCTGAATAGCCAAATCAATCCTAAGCAAAAAG 1350
                         -   --  i -   i --  v           v     i i iv  i   
  L1M4_orf2#LINE/    152 -GGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_87639344_8   1351 AACCAAGCTGCAGACATCACGTTAACCAGCTTCAAACTCTATTATAAGGC 1400
                            v   i  v  ivv    ii vv   ii      vii  i  i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_87639344_8   1401 TATGGCAACCAAAACAGAATTGCACTGGTACAAAAACAGACATAGAGACC 1450
                           ii i  i   i    vi v i     i i  ii i       v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_87639344_8   1451 AATGGAACAGAATATAAAACCCAGAAATAAATGAAGCTGCACACATACAT 1500
                                i     vv i ii           ----- i-  i    vi  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAA-----CC-CATACATTTAT 342

  chrX_87639344_8   1501 A--CATCTCATCTTTGACAAAGTTGACACAAACAAGCAATGAGGAAAGGA 1548
                         i--  vi v  i  i     i v  v  vi v  vv     i      i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_87639344_8   1549 CTCG-CTGTTTAATAAATGGTGCTGGGATAACTGGCTAGCTATATGGAGA 1597
                         - v -  v  i  i              i      v  ? i i   v i 
  L1M4_orf2#LINE/    393 -TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_87639344_8   1598 AGAATACAACTGGCCCCCTACCTTTCTCCATATACAAAA-TTAACTCCAG 1646
                              iv ii   v         iv v            -       v i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_87639344_8   1647 ATGGATAAAATATTTAAATGAAAGACTTCAAAGTATAAAAGTCCTAGAAG 1696
                               v ? v ii      v    vi v   v       v  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_87639344_8   1697 AAACCTTGAAAATA--TCATTCTGAATATTGGCTTTGGCAAATAATTT-- 1742
                            v v iii?i  --  -   vvi iv    v  v     - ii   --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chrX_87639344_8   1743 TGACTAAGTCTTCAAAACCAAACACAACAAAAATAAAAATTGACCAGTGT 1792
                          iiv  v v vi     v  v vi        iv      v  iv i vv
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_87639344_8   1793 GATCTAATTAAA-CTACAGATATTTTGCACAGCCAAACAAACTATCAACA 1841
                           ii v  i   -i  v i i-     ii vv v  iv v        v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_87639344_8   1842 GAGTAAACAGACAACACACAGACTTAGAGAAATTATTTGCAAACCACACA 1891
                         i   i  v       v      v vi      v          i  i i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_87639344_8   1892 TCTGACAAAAGTCTAATATCCAGGAATCCCTATGGAACTT----AACTCA 1937
                              i  ii v  vi       -   viv  vi     i----      
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAG-AATATATAAAGAACTCTTACAACTCA 787

  chrX_87639344_8   1938 AAAATAAGAAAA--AATATCTCCATTGAAAAGTAGGCCAAAGGCATGAAC 1985
                          v     i  i --    v i v   ?    i i   v  i iiv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_87639344_8   1986 AGACATATCCCAAAAGAAGGCATACAAGTGGCCAACAA--ACATAAAAA- 2032
                               v  i v       ii      i       i  --    i    -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_87639344_8   2033 ATGCTCAACATCACTAGTCAT 2053
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.02 (22 / 906), avg. gap size = 1.64 (36 / 22)  


2069 26.58 3.11 5.41  chrX_87646594_87651674     3346  4214 (867)    L1M4_orf2#LINE/L1        1   849 (59)  

  chrX_87646594_8   3346 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATAAATATTGTTAAAAT 3395
                               i i  i     i        v      v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87646594_8   3396 GGACATACTGCCCAAAGCAATTTATAAATTAAATGTGATTCCTATCAAAC 3445
                           vv     v      vii  i  i i   v  i ii  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87646594_8   3446 TACTAATGACATTCTTCACA-AAATTAGTACAAACTT-TTCTAAAATTCA 3493
                          v i iivi v  i  ii  -     i--    i  v- i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_87646594_8   3494 T-TTGAAATAAAAATTG---CCAATATATCAAAAAAAAAAATCTTGAGCA 3539
                          - v     iv  i-- ---   iv   v v    v  ---      iv 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAA---TCTTGAAAA 193

  chrX_87646594_8   3540 AAAAGAGCAAAGCTGAAGGCATCACATTATTTAACTTCAAAATATACTAT 3589
                          i    i     i  i   vv     i viii  i       iv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_87646594_8   3590 GAGGCTACAGTAACCCAAAGAGCATGGTACTAGTACAAAAACAGACACAC 3639
                         i i          i v i v  ii       i i i  ii i     i i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_87646594_8   3640 AGACCAATTTAACAGACTAGAGATCCTAGAAATAAAACCGCACACTTAAA 3689
                            i    vv  i   v v    vi i         v  ii   i   vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_87646594_8   3690 ACTATCTGATTCCCCACAAAGTTGACCAAAATAAG-CAATTGGGGAAATA 3738
                         iii vi     ii v    i v  -    i iv v-    -       v 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAAT-GGGGAAAGA 391

  chrX_87646594_8   3739 CTC-TCTATTTGATAAATGTTGCTGAGGTAACTGGCTAGCAATATGCAGA 3787
                         v v-   v  ii i     v     i ii      v  ? v i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_87646594_8   3788 AGATTGAAACAGGGACCTTTCTTT-CACCATATACAAAAATCAATTCACG 3836
                            v    iiv  iv  i v i i-                i  i   vi
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_87646594_8   3837 ATGGATTAAAGACTTAAATATAAAACATAAAACTATAAAAATCTTTGATA 3886
                               i ?    i     i   i vv             v    v  vi
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_87646594_8   3887 AAAACTTAGGAAATACCATTCTGGTTATAGACCTTGG------CAAAGAC 3930
                              v    ?i-  -- v   -- ii -        ------   v ii
  L1M4_orf2#LINE/    542 AAAACATAGGNG-TA--AATCT--TCGT-GACCTTGGGTTAGGCAATGGT 585

  chrX_87646594_8   3931 TTTAT-GATGAAGATGCCAAAATCAACTGAAACAAAATAAAAATT-GACA 3978
                           iv -   - v  ii      v  vvv v       v     v -  i 
  L1M4_orf2#LINE/    586 TTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_87646594_8   3979 AATGGAACCTAATTAAACTACAGTGCTTCTGCACAGCAAAACAAACACAG 4028
                            v i  i v  i   v vv ivi   i  ii vv    i--i    --
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG--GACAC-- 680

  chrX_87646594_8   4029 CAAAACAAAGAAAGAAACAAAAAACTATCAATGGAGTAAACAGAAAAC-- 4076
                         -------------------------      vii   i  v   v   --
  L1M4_orf2#LINE/    681 -------------------------TATCAAGAAAGTGAAAAGACAACCC 705

  chrX_87646594_8   4077 ACAAAATCAGAGAAAATATTTGCAAACTATGCTTCTGACAAAGGTCTAAT 4126
                            i   vi                 ii  iiv     i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_87646594_8   4127 ATGCAGACTCTAGAAGAAACTT----AAATCAACAAGCAAAAAACAA--- 4169
                           v    v v  v  ii    i----  v    i  vv    i    ---
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_87646594_8   4170 -CTCTGTGAAAAAGTGGGCAAAAGACATGAACAGACACTGTTCTCC 4214
                         - i vi v?    i        i  iv    i     i --     
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT--TCTCC 849

Transitions / transversions = 1.47 (135 / 92)
Gap_init rate = 0.03 (26 / 849), avg. gap size = 2.85 (74 / 26)  

 377 17.57 0.00 0.00  chrX_87646594_87651674     4515  4588 (493)    L1M4_orf2#LINE/L1      835   908 (0)  

  chrX_87646594_8   4515 AACAGACACTTTTCAAAAGAAGACATACAGGCGGCCAATAAGCATATAAA 4564
                           i     i  i  v        i     iii            i  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_87646594_8   4565 AAAATGCTCAGTATCACTAATTAT 4588
                           i       ii    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 12.00 (12 / 1)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.00 (0 / 0)  


2466 28.54 3.26 1.24  chrX_87655013_87656922      528  1417 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87655013_8    528 TGAAAAAATATTTTATGTCCATAAATTGGAAGAATCAACATCACTAAAAT 577
                           i   i    iii    i   ii         v i  i  iii   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87655013_8    578 GGCCACACAGCCCTAAGGAATCTATAGATTCAACACAATTTCTGTCAAAC 627
                            v i  vv   v  vvi     i         i    ii  i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87655013_8    628 CGCCAA-TGTCATTTTTTACAGAA-TTAAAAAA--AATTCTTAAATCTGT 673
                         iv   i-  i -      i     -  i v  i--i  i  v    iii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_87655013_8    674 ATTAAAACAAAAGTCATCCTGAATAGCCAAGGCAATCCT--AGGAGGAAA 721
                           vi   iiv   vv i  v          ii     i -- ii  i i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_87655013_8    722 ACAAAGCTGAATGTGTCACATTACCTGACTTCAAGCTACACTACAAGACT 771
                               i  i v vv     i v  ii i     ivivi       ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_87655013_8    772 ATAGTAACCAAAAGATCATAGTACTTGTAAAAAAACAGACTCAGAGATGA 821
                          i     i   i v vii i     v i v  ii i    vi v    v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_87655013_8    822 GTGGAACAGAAGACAGAACACCAAAATAAAGCCACACACTTACAACCAGT 871
                         i     i    vvv   iiv vi       v   i   i   iiii  i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_87655013_8    872 TAACTAAGCTTTGACAAAGTTGGAAAAA----TAAATGGGGGAAGGAGAC 917
                          i i ----  i     i v  vv  i ---- v       i   i v v
  L1M4_orf2#LINE/    350 TGATT----TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_87655013_8    918 CCTATTTAATAAATGGAGCTGAGATATCTGACTAACCATATACAAAAGAA 967
                         i  v  i  i      v    i  i v   iv  ?   i  i        
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_87655013_8    968 TGAAACTGGACCACTATCTCATACCACATATAAAAGTTAACTCATAATGG 1017
                             ii      v   i    i    i   i    i        v     
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_87655013_8   1018 ATTA-ATATTTAAATGTAAAACCTCAAGCTATTGAAATCCTACAAGAAAA 1066
                           i - v ii         i v  v  i    vi  v  i  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_87655013_8   1067 CCTACGAA-AAGTTTTTGTGCACATTGGTCTAAGAAAAGAATTTCT--GA 1113
                          v  v ?i-  i i  i   -  v    vi  i v  v i-     --  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGG-TTTCTTAGA 593

  chrX_87655013_8   1114 CTAAGTTCTTAAAAGCAAACATGACAAAACCAAAAAATATACAAGTGGGA 1163
                         -  v vivii       v viii      v-        v i  i v   
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGA 641

  chrX_87655013_8   1164 C---AT---AATTAAACAGCTTCTGTATAGCAAAATAAACCATCCACACA 1207
                          ---  ---       - i   i   iivv    iv v  i   v v v 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_87655013_8   1208 GTAAATAGACAAGCTACAGAAAGTGAGAAAATATTTGCAAACTATGCATC 1257
                           i  v      v i      v v                 ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_87655013_8   1258 TAACAAAGGACTAATATCCAGAATCCATAAGGAAATTAAACAA---AACA 1304
                          i i  i     vi          vi    i   v ivv    ---  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_87655013_8   1305 ATGAGAAAAAAAAT---CTTATTAAAAAGTGGGCAAAAGTCATGGACAGA 1351
                           i i  i v    --- iv   ?    i        i viv  i i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_87655013_8   1352 CACTTCTCTAAAGA---CATACAAACAGCCAACGAACATATGAAAAAAAT 1398
                           i     i     ---i       ii     ii i  i       i - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-T 889

  chrX_87655013_8   1399 GCCCACTATTATTAATCAT 1417
                           i  vi  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (163 / 88)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.90 (40 / 21)  


1482 29.40 1.71 1.37  chrX_87671003_87672828      500  1084 (742)    L1M4_orf2#LINE/L1      243   829 (79)  

  chrX_87671003_8    500 CAAAGCTATAGCAACCAAGACACCATGATATTGGCATAAAAACAGACCCA 549
                                 i  i  i       vii  i  i        ii i    vi 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_87671003_8    550 CAGAGCAAAAGAAGAGAATAGAGAACACAGATATATACTACCC---CAGC 596
                         i   v   vi   v     v    iiv    v   - --    ---  vi
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATA-A--ACCCATACATT 339

  chrX_87671003_8    597 TGCAAAAAATCTCATCTTCGACACAGGTGCCAAGCACACACAATGGGAAA 646
                          iiiivv   - v  i       vi         vv  iv       i  
  L1M4_orf2#LINE/    340 TATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_87671003_8    647 AGGACAGTTGTTTCAATAAATG-TGTTGGAAAAATCGATTAACTA--TGC 693
                           i i   iv      i     -  i   i v  ii iv  ? i --   
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_87671003_8    694 CAAAAAA-AAAATTAGACTGCCATCTTTCACCACACACAAAAATAAAATA 742
                         v   i  -i  i  i   iv i i  iv     i i        v  v v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_87671003_8    743 AAAATAAATTAGAAACTATAATCTACTACCTGAAACTAGGAAACTACTAG 792
                              ii  i ? i  ivv   v  vv v  i      vi     vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_87671003_8    793 AAGAAAACATTGGGGAAACACTGTAGGAAATTGGTCTGGGCAA-ATTTTT 841
                                   v  ? v  vv  viiv  vv    vi i     -iv   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_87671003_8    842 TTGTGTGTAAGACCTGAAAGGCACAGGGTACCAAAGCAAAAATAGACAAA 891
                           ivi i i v   --   i     i vv  v    v         i   
  L1M4_orf2#LINE/    589 TTAGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_87671003_8    892 TAAGATTACCTCAAGCTAAAAAGCTTTCACGCAACAAATGAAACAATCAA 941
                          vi  i v v    iv v    i    iii  vv    v  v  v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_87671003_8    942 AAAAATGAA--GACAATCCACAGAATTGAAGAAAACAGTTGCAAACCATT 989
                         i   i    --     i         v i      i v       i   v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_87671003_8    990 GATCTGACAAAGGATTAATAACCAGAATATATAAGTGGCTTAAACAGTTC 1039
                         v      i  i   i vi  v             ivii  ivv   ii  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_87671003_8   1040 AAGAGCAAAATAATAATAATAATTCAATTAAAAGATAAGCAAAAG 1084
                           v ii    vi i  --    ii     ?   i  ii     i 
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAA--ATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.40 (98 / 70)
Gap_init rate = 0.02 (11 / 587), avg. gap size = 1.64 (18 / 11)  

 247 21.35 5.62 0.00  chrX_87671003_87672828     1323  1411 (415)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_87671003_8   1323 AAAAAAAAGCAAAAGATCTGAATAGACTTTTCTC---AGAAG-TACATAA 1368
                              vii     i   i         v      ---     -  i i  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_87671003_8   1369 ATGACAAACATGTGTATGAGAA-ATGCTAAAAATAACAAATCAT 1411
                            i v  i v iii    i  -     v  v  v ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.03 (3 / 94), avg. gap size = 1.67 (5 / 3)  


1510 28.91 5.53 0.47  chrX_87672919_87674524      484  1116 (490)    L1M4_orf2#LINE/L1      244   908 (0)  

  chrX_87672919_8    484 AAAGAAACAAAAATGTAAAAAGCATGGAATTGTAATAAA-ACACACATAT 532
                             vv   iv   vv i v  ii   v i  vv    i- i v      
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_87672919_8    533 G--TCAATGAAACAGAATTGAGAAACCAATTATAAATTCACATATTTATA 580
                         i--      i  i          iv   ivv     ii  i i      i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_87672919_8    581 GCTAACTGATTTTCAAAAAAGGAGTCAAGAACATACATTAGGAAAATGCC 630
                          ii  i        i v  i  v i     v   v  v i  i   vivi
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_87672919_8    631 ACTCTTTTCAGTAAATAGTTTTAGACAAACTGGATATCGACATGTAGAAG 680
                          v        ii    i  vi i ivv         ? v     i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_87672919_8    681 AATAAATCTAAATTTCCATCTTTTACCATATATAATAAACAACTCAAAAT 730
                            i  vi ii iii i i  ivi        i  v  vi          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_87672919_8    731 GCATTAAAAACTTAGATGTAAGA-CACAAATTATAAAA------GAATAA 773
                          v  i ? i  i  i        - vv   i       ------   v  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_87672919_8    774 AACATAGGGG-AAATGCCTTAGAACATTGTTCTAGGTACAGATTTTATGA 822
                                 ? -    - i iivi  v   vvi    i vv i   iv ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_87672919_8    823 GTAATACTTCAAAAGTGAAGGCATTAAGA---AAAATAGAGAAATGAGAT 869
                         i  vv  vi      iiv i   vi  i ---        v    vi  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_87672919_8    870 TATGTCAAACAAAAAAGCTCCTGAACAGCAAAGGAAACAATCAGCAGTGG 919
                          vii     vvv    i  ii  vi vv       v  v    iv iv v
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_87672919_8    920 AAAGAGACAACCTGAAGAATAGGAGAAAATATTTGCAAACTATTCAT-TC 968
                         i  i        iiv     i                  ii  vi  - v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_87672919_8    969 ACAAGGCGTTAATGTCCAGAATATATAAGGAACTCAAACAACTGAACAGA 1018
                          i    vii vi i              i      vv      v  i iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_87672919_8   1019 AAAAA---AAAT----CTATTACAAAATTTTGGCAAA---------TAGA 1052
                              ---    ---- v   ?v     v--      ---------    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATG--GGCAAAGGATTTGAATAGA 840

  chrX_87672919_8   1053 CATTTTTC-AAAGAATAAATACAAATGACCAA---GTACATAAAAAAATT 1098
                              i  -      v v         i    --- i    i    i  v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_87672919_8   1099 TTCAACACTGACTTTCAG 1116
                         i      iii????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (105 / 74)
Gap_init rate = 0.02 (14 / 665), avg. gap size = 2.71 (38 / 14)  


 338 32.26 5.38 2.69  chrX_87675985_87681063     3118  3303 (1776)    L1M4_orf2#LINE/L1        1   191 (717)  

  chrX_87675985_8   3118 TAAAAAGACACTTCATATTT-TGAAATTGAAGAATTCATATTGTTAAAAT 3166
                          ii     i iii   i  i-  i v v     v  v          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87675985_8   3167 TATAATTTTATTTAAAGCAATTTGCAGATCTAATGCAATCTCTATCAAAA 3216
                         vii   vi viii   vii  i i     ii  i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87675985_8   3217 TACTAATGACATTCTTCATAGAAATAGAAAAA---ATATTAAAATTTATG 3263
                          v i iivi v  i  iii      v  v  i---  vi       i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_87675985_8   3264 TGGTACCACAAAATAT-----ATAGTCCCACAAAAATAATCT-GAA 3303
                            v vii   iiv i-----    i -----    i     -   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCC-----AAAACAATCTTGAA 191

Transitions / transversions = 2.53 (43 / 17)
Gap_init rate = 0.03 (5 / 191), avg. gap size = 3.00 (15 / 5)  

2209 26.63 1.53 1.94  chrX_87675985_87681063     3483  4203 (876)    L1M4_orf2#LINE/L1      112   829 (79)  

  chrX_87675985_8   3483 TTCTTCACAGAAATAGACAAAA-AATCATAAAATTTATATGGGACCACAA 3531
                           i  ii       v     iv-i   v       i      i vii   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_87675985_8   3532 AAGACCCTGA-TAGCCAAAGCAATCATGAGCAAAAAGAACAAAGCTGGAG 3580
                         ii     v  -        i     v   iv  i          i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_87675985_8   3581 ACATCATGCTACCTGACTTCAAAACACACTTCAAAGCTATAATAACCAAA 3630
                         ivv   ii  v  ii i        vi   v        i i   i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_87675985_8   3631 TCAGCATAGTACTCACATAAAAACAGACACACAGACCAATAAAACTGAAT 3680
                         v   ii i     vi     ii i     i i   i    ii  iv    
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_87675985_8   3681 AAAGGACACACATATAAATCCACGTATTTACAGCCAACTCATTTTTGATA 3730
                         vi  iiiv  v v     i   iii     ii i   i v     i  i 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_87675985_8   3731 AACGTGCCACAAACATACAATAGTGAAAGAACAGGCTCTTCAATAAATGG 3780
                          iv      vi v   v    i v       i  v  i     i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_87675985_8   3781 TTCTGGGAAAATTGGATATTCATATGCAAAATA-TGAAACTAGATCCCTA 3829
                          v      v  i      ?i  i        v -    ii i  i     
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_87675985_8   3830 TCTCTCATCATACACAAAAATCAAATTAATATGGATTAATGACTTGCATG 3879
                         i   v  i    i        i  v i  v      i ?v   i iv   
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_87675985_8   3880 TAAGACCTGAAACTATGAAACTACTAGAAGGAAACATTAGGAAAACAATA 3929
                              v  i       i     vi      i      -   ?iv -   v
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AGGNGTA-AATC 559

  chrX_87675985_8   3930 T--AGGACATTGCTCTGGGCAA-AATTTTTTACTATAAGATTTCAAAACC 3976
                          --iv   v   vvi i     -ii   i   v-   v  ivi     v 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-ATATGACACCAAAAGC 608

  chrX_87675985_8   3977 TCAGGCAAGCAAAGCTAAAATAGACAAAGGGGATCACAT-AAAGCTAAAA 4025
                         v  i    vv    vv        i   vv   iiv   -   ii     
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_87675985_8   4026 AAGAAACT---GTACAACAAAAGAAATAATCAATAAAGTGAAAAGAGGAC 4072
                          -----  ---  i vv    i  v iv     v            vi  
  L1M4_orf2#LINE/    659 A-----CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_87675985_8   4073 CAAGAGAAGAGGAGAAAATATTTGCAAACTATTCATCTGACAACGGATTA 4122
                          v v    vi                  ii  vi      i  v   i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_87675985_8   4123 ATAATCAGAGCATATAAGGAGCTTAAACAACTCAACAGCAAAAATTAAAA 4172
                         i  vi    ii      i  i  ivv         i ii     ----i 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA----GA 799

  chrX_87675985_8   4173 CCCAAATAATTGGATT-AAAAATGAACAAAGG 4203
                          --      iivi   -       ii      
  L1M4_orf2#LINE/    800 C--AAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.70 (119 / 70)
Gap_init rate = 0.02 (14 / 718), avg. gap size = 1.79 (25 / 14)  

 456 13.11 6.56 3.28  chrX_87675985_87681063     4465  4586 (493)    L1M4_orf2#LINE/L1      783   908 (0)  

  chrX_87675985_8   4465 ACTCCATCTCAAAAAAAAAACAAAAAA--------AAAAACGGAACAAAG 4506
                             v  ---  v     i     v  --------     i  i-     
  L1M4_orf2#LINE/    783 ACTCAAT---AATAAAAAGACAAATAACCCAATTWAAAAATGGG-CAAAG 828

  chrX_87675985_8   4507 GATCTGAATATACATTTCTCAAAAGAAGACACACGAATAGCCAATAAGTA 4556
                            i      v         v        i i  i   i         i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_87675985_8   4557 CATGAAACAATGCTCAACATCAGTAATCAT 4586
                                vi             ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.02 (3 / 126), avg. gap size = 4.00 (12 / 3)  


2582 28.11 1.98 1.87  chrX_87686604_87691721     3719  4625 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87686604_8   3719 TGGAAAAACATTTCATGCTCATGGATAGAAAAAAATCAATATAGTGAAAA 3768
                               i i  ii    i        v i  i v- i     v  v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chrX_87686604_8   3769 TGGCCATACTGTCCAAAGAAATTTATAGATTCAATGCTATTCCCATTAAG 3818
                             v     vi     vvi  i  i        i  v  i  i  i  i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_87686604_8   3819 CTACCATTGACATTCTTCACAGAATTAGAAAAAAAACT-ATTTTAAAATT 3867
                         v v   vivi v  i  ii     v v  v  i---  -  ii       
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chrX_87686604_8   3868 CCCATGGAACCAAAAGAGAGCCCCAATAGCCAAGGTAGTTCTAAACAAAA 3917
                          vi      viiv   i  v  vv         iii i ii i  v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_87686604_8   3918 AGAACAAAACTGGAAGTATCACACTACCTGGCTTCAAACTATACTACAAG 3967
                                 ii    i vv       v  iiii      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_87686604_8   3968 GCTACAATAACTAAAACAGCATGGTACTGGTACAAGAACAGATGCATAGA 4017
                               i   ii  i    ii         i i   i i   iii     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_87686604_8   4018 CTAATAGAACAGAATAGAGAACTCAGGAATGAGACCACACCCCTACAACT 4067
                         ii   i   i     v    iii   i   i iv   i  vii  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_87686604_8   4068 ATCTATTTTTTGACAAACCTGAAAAAAAAAACAAGCAATGAGGACAGGAT 4117
                          vi iv    i     ivv  vv  i v---  vv     i   v  i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAAAGAAT 393

  chrX_87686604_8   4118 TCTCTATTTAATAAACAATGTTAAGAGAACTTGCCAGCCGTATGCAGAAA 4167
                         vv   v  i  i   iii  i ii  v    v vi ?  ii     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_87686604_8   4168 ATTGAAACTGGGCCCCTTCCTTACACCATATACAAAAATTAACTCAAGAT 4217
                          v    ii   i     v   i                         i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_87686604_8   4218 AGAGTAAAGAC--AAATGTAAAACCCAAAACTATAAAAACTCT-AGAAGA 4264
                         i  vi ?    --        i v i            -    -      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGA 542

  chrX_87686604_8   4265 AAATCTAGGCA-ATACCATTCAGGGCATAGGCAT-GGCAAAGATTT---- 4308
                            iv    ?i- v i -   iv i v v  vv -     v i   ----
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_87686604_8   4309 --TATGACAAAAATGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAA 4356
                         --       ------         vvv          vv     v  i  
  L1M4_orf2#LINE/    592 GATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_87686604_8   4357 GTGGGATCTAATTAAA-CAAAAGACTTTCTGCACAGCAAAAGAAACTATC 4405
                         i v   ii v  i   -iv   i     -  ii vv    i  v      
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATC 684

  chrX_87686604_8   4406 ATCTGAGTGAACAGACAACTGACAGAATGGAAGAAA-TATTTCACAATTG 4454
                          vvvi      v       iv         i     -     -i   v v
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATC 733

  chrX_87686604_8   4455 ATCCATCTGACAAAGGTCTATTATCCAGAGTCTACAAGAAACTTAAGCAA 4504
                           vi      i  i  v  vv        i v  i  ii    ivvi   
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_87686604_8   4505 ATTTACAAGCAAAAAACAA----CCCCATTAAAATATGAGCAAACGCCAT 4550
                         v iv i  vv    i    ----   v   ?   v   i     v viv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_87686604_8   4551 GAACAGACACTTCTCAAAAGAAGACACACATGAGGCCAACAAGAATATGG 4600
                            i     i     v        i i   viv      i   v i   i
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_87686604_8   4601 AAAAAAGGTCAACATCACTGATCAT 4625
                            i v v         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (150 / 101)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.06 (35 / 17)  


3259 25.66 1.00 0.55  chrX_87692988_87697237     2854  3757 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87692988_8   2854 TGAAAAGTTATTCCATATTCATGGATTGGAAGAATCAATATTGTTAAAAT 2903
                           i    v   i    i                v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87692988_8   2904 GTTCATACCAACCAAAGCAATATACAGATTCAATGCAATCCCTATAAAAA 2953
                          viv    ivv     vii  v           i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87692988_8   2954 TATCAATGATAGTTTTCACAGGAAAAGAAAAAA-AATCCTCAAATTTATA 3002
                          vi  iiviivv    ii   i  vv  v  iv-i     v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_87692988_8   3003 TGGAAACACAAAAAACACAGAAGAACAAAAACTATCCTAAGCAA-AAGAA 3051
                               ii   iii  v     v i v     v   i i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_87692988_8   3052 CAAAACTGAAGGAATCACATTACCTGACTTCAAATTATACTACAGAGTCA 3101
                             ii  i    v     i v  ii i      viv       i  ii 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_87692988_8   3102 TAGCAACCAAAACAACATAGTAATTGCATAAAAACAGACATATAGACCAA 3151
                         i  i  i   i   iii i   v v      ii i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_87692988_8   3152 TGGAACAGAATAGAGAACCCAGAAGCAAATCCACACACCTATGGTGAACT 3201
                              i     v    ii      ii   i   i   ii      v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_87692988_8   3202 CATTTTTGCCAAAGGTGCCAAGAACAAACACTGGGGAAAGA-CAGTCTCT 3250
                         v     i v   i          v  vv  v          -i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_87692988_8   3251 TCAATAAATAGTGCTGGGAAAACTGGATATCCATAAGCCTGAGAAAAAAC 3300
                             i    i         v         ?   i v  vvi    vi  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_87692988_8   3301 CTAGACCCCTATCTCTTGCCATATACAAAAATCAAATCAAAATGAATTAA 3350
                         i i        i   vii              i  v        i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_87692988_8   3351 AGACCTAAATCTAAGACTTCAAACTGTGAAACTACTAAAAGAAAACTTTG 3400
                                   v     vi v     i i     vi  i        v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_87692988_8   3401 GAGAAACTCTCCAAGCCATCTGAATGGGCAAAGACTTCTTGAGCAATGTG 3450
                          ? v  v   i iv v v iv iv i     v ii     -  --  i  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AG--ATATG 597

  chrX_87692988_8   3451 TCACGGA---CACAGGCAACCAAAGGAAAAATGGACAAATGGGATCACCT 3497
                         v   vi ---    i     v    i      i  i    v   iiv v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_87692988_8   3498 CAAG-TTAAAAAGCTTCTACACAGCAAAAGATACAATCAGCAAAGCAAAG 3546
                            i-       -   i iii vv    i  i  v    iv    ii  i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_87692988_8   3547 AGACAACACACAGAGTGGGAGAAAATATTTGCAAGCTGCCCATCTGACAA 3596
                                v      i                   iiiiivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_87692988_8   3597 GG-ATTAATGACCAGAATACATAAGGAGCTCAAATAATTCTATAG-AAAA 3644
                           - i vi iv        i    i  i   vv i  i  v   i-    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_87692988_8   3645 AATTATGCTAATCCAATAAAAAAATAGTTAAAAGATCTGAAGAGACATTT 3694
                          ivi -iv   i     v?      i vi   i   i    v        
  L1M4_orf2#LINE/    797 AGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_87692988_8   3695 CCTAAGAGAAGACATACAAATGGCCAATAGACATATGAAAATGTCCTCAA 3744
                          iiv i      i                ii  i       vi v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_87692988_8   3745 CATCACTGATCAT 3757
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (144 / 84)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


2304 27.24 4.60 2.80  chrX_87714925_87716947      639  1530 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87714925_8    639 TGGAGAGCTATGACATATTCATAAATAAAAAGACTCAACAATGCCGAAAT 688
                             i  v   vv   i     ii  vii      i  i v  iii i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87714925_8    689 GTTCTTATCGATAGATTCTATAGATTCAATGCAATTTGATTTACAGATTC 738
                          v------ i   --i  i------- ----   v     i         
  L1M4_orf2#LINE/     51 GG------CAATA--CTCC-------C----CAAATTGATCTACAGATTC 81

  chrX_87714925_8    739 AATACAATCCCAACCAAA-TGCCAACAAATTATCTTGCGGGTATCAGCTA 787
                           ii       v i    - v   i vivi v i    i iv  iii v 
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

  chrX_87714925_8    788 ATTGGTATTAA----C---TGGAAA------AGACCCAGAATTGTCAAGT 824
                         ii  i vi   ---- ---      ------i          v i   iv
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chrX_87714925_8    825 CAATAGTGAA---GAAGAACAAAATCAGACGACTAACACTACCTGACTTT 871
                             vv    ---          i ii  v    v     v  ii i  i
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_87714925_8    872 AAGACATATTATAAAGCTACAGTAATCAAGATGGCATGATATGGGTGAAA 921
                           i  v  i  i                   ii ii  i  iv  iiv  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_87714925_8    922 GAATAGACAAACATACCAATGGAGGAGAGTAGAGAACCCAGAAATAGATC 971
                          i       v i v i       iv   i v    ii         i i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_87714925_8    972 TGCATAAATATATA---AATTGATCTTGGACAAAGGAGCAAAAGCAATAC 1018
                         --    v  v   i---       i  v     i  v  v  ii v  v 
  L1M4_orf2#LINE/    332 --CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_87714925_8   1019 AATAGAGAAA--ATA--TTTTTAAACAAATTATGTGGAAACAGATTGACA 1064
                            i i    --   --i    v       vi  iv ii   iv v  i 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_87714925_8   1065 TCCATATGCAAAAAAATCAATCTAGACAC--AGTTAACTTC-TA---AAA 1108
                         ?   i        i   v  vi i   v -- vi v  vi -  ---   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_87714925_8   1109 AATTAACTCAAAAACGAATCATAGTCTTACATGCAAAGTGC-AAAACTAT 1157
                                      -i i    ?  v i  v   i  - v  -        
  L1M4_orf2#LINE/    480 AATTAACTCAAAA-TGGATCAWAGACCTAAATGTAA-GAGCTAAAACTAT 527

  chrX_87714925_8   1158 AAAACTCCTAGAACATAACACACACACAAAATCTAGGTGACCCTGG-TTA 1206
                                i     v v    i vi?ii   -   vv      i   -   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTA 576

  chrX_87714925_8   1207 TAGCAATGATTTTTTAGATGCAGTTCAAAATGCATGGCCCATGAAAGAAA 1256
                         -i      i   i      iiiiiv v   v   iiiv v ii       
  L1M4_orf2#LINE/    577 -GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_87714925_8   1257 TAGTTGATAAAGTGTGTTTTATTAAAAGTAAAAACCTCTGCTCTGTGAAA 1306
                         v i v      v  vii  i  i    v       i i  iv  vii  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_87714925_8   1307 GACAATATCAAGAGGATGAGAAGACAAGATACTAAATAGGAGAAAATATT 1356
                             v        iii   i       vvi  vi   i            
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_87714925_8   1357 TCCAAAAGACATAGCTGATAAAAAACT-G----CAAAATATACAAAGAAC 1401
                          v    vv i   v       iii   - ----  i      i       
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_87714925_8   1402 ACTTAAAATTAAATAGTAATAAATTAAAGAACTTGATT-AAAAATGGGTT 1450
                         v    v  i v    i   v  ivi   v   iii   -         iv
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_87714925_8   1451 AAAGGCCTGAACAAATACCTCACAAAAACAGATG---AGATGGTAAATAA 1497
                           i iii    i i i ii  v v   iv    i--- i    iv     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_87714925_8   1498 GCATATGAAATGGTGATCAACATCATACGTCAT 1530
                            i      v i  v         ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (152 / 88)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.54 (66 / 26)  


2794 23.86 4.11 3.33  chrX_87724774_87727209.rev     1045  1945 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87724774_8   1045 TGGAGAAACATCCTGAGTTAAGAAATTGAAACATTTAATATTATCAAGAT 1094
                             i i i    iiv   v vii    i  v i        i i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87724774_8   1095 GTCAATACTACCCAAAGAAATTTACAAATTCAATGCAATCAATATCAACA 1144
                          v       v      vvi  i    i      i      vv      v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87724774_8   1145 TACAAGCAATGA---TTTTGAAGACATGCAAAAATTCAATCCCAAA-TTT 1190
                          v v   --  v---     v   v  vv v  ii -i    i   -  i
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCT-GATCCTAAAATTC 147

  chrX_87724774_8   1191 ATATGGACTCTCAAGGGACCTCAACTAGCAAAAAAAAAAAAAAAAAAAAA 1240
                                vviv         ivi v    v    v  -------------
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA------------- 184

  chrX_87724774_8   1241 AAAAAAACCCTGGAAAATGAAGAAAAAAGTCAGAGGACTTACACTTCTTG 1290
                         --------i  v     v      v     ii       i       iii
  L1M4_orf2#LINE/    185 --------TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_87724774_8   1291 ATTTTACATCTTTTTACAATGTAACACTAAGCAAAGCATTGTG---CTGG 1337
                             i v v   vi     v iv   v   v   ii  v    ---    
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_87724774_8   1338 CATAAAGA--GGCATATATACCAATGTAATAAAATAAAAACTCCATAGAA 1385
                              i  -- i      v i     v    i   vi i v    v i v
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_87724774_8   1386 AAGCTTTTAAGTATATTGTCAAATGCTTTCCAACAAGTGTACCGAGATCT 1435
                           i iiv  vi v   v     v  v   i i     v  i  i   i v
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_87724774_8   1436 TTCAATGGGGAAG----AGTGTTTTCAAGCAGTGCTTTTTGTAAAACTGA 1481
                                     i----   v       vv i  v vi v v v     i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_87724774_8   1482 ATATCCACATGCAAAAGAAAAAATTTGGACCTTTACCCTATAACATATA- 1530
                            ?               vi  v       ii    ii i v      -
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_87724774_8   1531 -AAAATTAACTAAAAATAGGTCAAGGATCTAAATGTAATAGCTAAAATTA 1579
                         -          v     i i   ?i  i          v        i  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_87724774_8   1580 TAAAATGCTTAGAAAAAAATATAAGAGGACTGCTTCATGACATTAGATTT 1629
                              iv       i    i   i ? v vvv    i    v  i i  v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_87724774_8   1630 GGAAATACTTCCTTGGACAAGACAGCAAATGCTCAGTTAACCAAAGAAAA 1679
                           v   iv  i   i  i v    v    v  v  ivi   v        
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_87724774_8   1680 AAAAATGAATAAAT--GGTTTCTTACCAAGTTAAAAACATCACTGCATCA 1727
                           --- ii      -- ii   v - v  i        v ivv   v   
  L1M4_orf2#LINE/    627 AA---TAGATAAATTGGACTTCAT-CAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_87724774_8   1728 AAGAACACTATGAAAACAATGCAAAAGCAACCAA-AGAATGGGAGAAAAT 1776
                            i       v  i v i  v   ii     v -               
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_87724774_8   1777 ATTTGCAAATCATCTACCATG-TAA------------------ATATAAA 1807
                                      v  i -  -   ------------------       
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATC-TGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_87724774_8   1808 ATATCCCTACAACTCAACAACAACAAATCAAACAACTCAATTTAAAAATG 1857
                         iv ii i          i  i  v  iv    i   i     ?       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_87724774_8   1858 GGCTAAAGACTTGAATAGATTTTTTTCCCAAAGAAAGTATGCAAATTGCC 1907
                            v  i  i         iv   i   -      ii   i     v   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCC-AAAGAAGATATACAAATGGCC 870

  chrX_87724774_8   1908 AAGAAGCACATAGAAATATAATTATCATCACTAATCAT 1945
                           v        ii   v  iv i v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (111 / 100)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.94 (67 / 17)  


1740 28.57 3.95 3.40  chrX_87781318_87784067.rev      791  1525 (1225)    L1M4_orf2#LINE/L1        1   739 (169)  

  chrX_87781318_8    791 TGGAAAAACATTTCATGCTCATAGATTGGAAGAATAAATATCATTAAAAT 840
                               i i  ii    i    i          v v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87781318_8    841 GGCCATACCACCCAAAGCAATCTACAGATTCGACGCTATTCCGATCAAAC 890
                            v    iv      vii            i    v  i  v      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87781318_8    891 TACCAAA-GTCATTACTTTTCAATGAACTACAAAAACTAATTCCAAAATT 939
                          v   iv- i v  --   v  --   v vv v  i  i  i i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT--TTTGCA--GAAATTGACAAGCTGATCCTAAAATT 146

  chrX_87781318_8    940 TATATGGAA---CCAGTCACCT-GTATGGCCAAGGAAATAT-GAAGCAAA 984
                         i        --- v  vv   i- v  i     iiv   v -   --   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA--AAA 194

  chrX_87781318_8    985 AACAAACAAACAGAAAGCTGGAGTCATCACGTTACCTGACTTCAAACTAT 1034
                         i vi      ------ i     vvv    ii v  ii i      viv 
  L1M4_orf2#LINE/    195 GAAGAACAAA------GTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_87781318_8   1035 ATTATAAGGCTAGAGCAATAAAATGGTACTATTACATGTATGGTACTATT 1084
                          i  i  i    v  i   v  i----------   -  i       ivi
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAG----------ACA-GTGTGGTACTGGC 277

  chrX_87781318_8   1085 ACCAAAACAGACACTTAGATCAATGGAAAAAAATAGAGAACCCAGAAATA 1134
                          iv ii i     iv             v i   v    ii         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_87781318_8   1135 AAGCCAGAGACCTATAGCCATGTGATCTTCGACAAAGTCAACAACAATCA 1184
                           v   v v ii   i i  vv    i        i viiv   -i i  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACCA 376

  chrX_87781318_8   1185 G-CAACTGAAAAGGGGCTGCTTATTCAATAAGTGGTGCTAGGATGACTGG 1233
                         v-   iv ii  i iiiv ii v     i  i       i   ii     
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_87781318_8   1234 CTAGCCATATACACAA---TGAAACTGGATTTCTATCTTTCAACACATAC 1280
                         v  ?   i  i  v  ---    ii    iii   i  iv  v  i    
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_87781318_8   1281 AAAAATTAACTCAAGTTGGATTAATGAATTAA----------TCCAACTA 1320
                                       iv     i ?v  vi   ---------- vv     
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_87781318_8   1321 TGAG--TCCTACGAGAAAATAAAGAAA-AACTATTCTGGACATTGGCCTT 1367
                          i i--  i  vi      i v  i?i-  v v   vv   v    v-  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TT 575

  chrX_87781318_8   1368 AGAAAAGAATTTATAAG-TAAGTCCTCAAAAGCAATTGCAACAAAAACAA 1416
                           iv  vii   v v  -  v v vi        vvv         iv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_87781318_8   1417 ATATTCACAAGTAGAACCTAATTAAACTAAAGAGCTTCTGCACAGCTAAA 1466
                          v  vv i  i v i  i v  i   v v  i i   i  ii vv v  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_87781318_8   1467 GAAACAATCAAGAGAGTAAA----CAACCTACAGAATGG-AGAAATTATT 1511
                           v  v       i   i  ----     i         -     v    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_87781318_8   1512 CACAAACTATGTGT 1525
                         ii    ii  i i 
  L1M4_orf2#LINE/    726 TGCAAATCATATAT 739

Transitions / transversions = 1.35 (119 / 88)
Gap_init rate = 0.03 (20 / 739), avg. gap size = 2.70 (54 / 20)  

 602 20.92 0.65 0.00  chrX_87781318_87784067.rev     2107  2259 (491)    L1M4_orf2#LINE/L1      755   908 (0)  

  chrX_87781318_8   2107 TATCCAGTATCTATAAGAAACTTAAAGAATTCAATAAACAAAATACAAAT 2156
                                v  v     ii    ivv v  i       vv    v      
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_87781318_8   2157 AACCCCATTAGAAAGTGGGCAAAAGACATGAACAGGCACTT-TCAAAAGA 2205
                              v   ?i   i        i  iv    i  i  i  -  v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_87781318_8   2206 AGATACACAAGTGGCCAACAAACATAAGAAAAAATGTTCAGCATCACTAA 2255
                              i    i       i  i  i v     i   i   i     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_87781318_8   2256 TCAT 2259
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.58 (19 / 12)
Gap_init rate = 0.01 (1 / 154), avg. gap size = 1.00 (1 / 1)  


2434 26.14 2.61 3.70  chrX_87827743_87830848     1698  2615 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87827743_8   1698 TGAAAGGTTTTTCCATGATTATGGATTGGAAAAATTAATTTTGTCAAAAT 1747
                           i  i v v i     v i           i v     v    i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87827743_8   1748 GACTATACTACCCCAAAGCAATCTACAGATTTAATGTAATACTTATCAAA 1797
                          i v     -       vii           i  i i   v i       
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_87827743_8   1798 ATACCAATGACATTCT--ACATAA--TAAAAAGAAAATCCTAATATGCGT 1843
                           v   iivi v  i --i  v  -- i v   vvi       v  v i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_87827743_8   1844 GTGAAACTATGAAAGACCATGAATATCCAAG-CAACTCT-----AAGACC 1887
                         i  i  v iii ii    vv     v    i-   -   -----    vv
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAG 198

  chrX_87827743_8   1888 CCACCAAAACGTTAGTGGCATTATACTATCCGATTT-AATATTATTCTAC 1936
                         -- v    --   i v  vv i i   vi  i    -  v i - v    
  L1M4_orf2#LINE/    199 --AACAAA--GTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTAC 243

  chrX_87827743_8   1937 AAAGCTATAGTAACCAAAACTAGACAAAGCATTGTGTTGGCATAAAAAAT 1986
                                i     i   i  -------  ii v  ii        ii - 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGAC-------AGTGTGGTACTGGCATAAGGA-T 285

  chrX_87827743_8   1987 AGACACATAGACTAATGAAACAGAATAAAGAACTCAGAAATAAATCCACA 2036
                              i     ii    i  i     vi   iii          i   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_87827743_8   2037 C--TCA--GCCAACTCATTTTTGACAAAGTTGCCAGGAACACACATTGGG 2082
                          -- i -- i   i v     i     i v     i  v  iv  v    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_87827743_8   2083 AAAAAGACAATCTTTTAAATAAATGGTGCTGGAAGGCCTGGATATTCATA 2132
                         i   ii i i      v  i            i viv       ?i  i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_87827743_8   2133 TGTAGAAGAATAAAACTAGTTATCCATA--TTGTACC-TATGCAAAAAAT 2179
                           i i      i  ii i -- i  v  -- iii   -   i      v 
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGG--ACCCCTACCTCACACCATATACAAAAATT 483

  chrX_87827743_8   2180 CAATTAAAATGGATTAAAGCTGTAAATGTTAGACTTCAAGTTATGAAACT 2229
                         v v i         i ?  viv       v   vi v  ii   i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_87827743_8   2230 ACTAGAAGATAACATTCAGGA--AAAACTACAGGACAATGATCTGAATAA 2277
                         vi       v     --   ?--   v  v iv   vv  ivi iiii  
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACAT--AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_87827743_8   2278 CTATGATTTGAATAAGATCTCAAAAGCACAGGAAACTAAAGCAAAATATA 2327
                         ivi vvi  ii   v  ivi          i v   v    v    -   
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATA 630

  chrX_87827743_8   2328 GACAAATGGGATTACATTATGCTAAAGAGCTTCTGT--TTAGGACTGGAA 2375
                           i    v   i v   i viv v  i i   i   --  vii --   v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA--GGAC 678

  chrX_87827743_8   2376 ACAATTAACAAAGTGAAAAGATAACCAATAGAATGGTAGAAAATATTTAC 2425
                           v  i  v            i    v i       v           i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_87827743_8   2426 AAACTATCCATCCAACAAGGGAGTAATAACCAGAATATATAAGTAACTCA 2475
                            ii  vi   ii i      v vi  v             iv     v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_87827743_8   2476 AACAGGTCAATAGCAATAATAATTAAATAATAATAATAATCTCATTTAAA 2525
                         v   iv      ------    --   -i i  --    i -  v  ?  
  L1M4_orf2#LINE/    779 TACAACTCAATA------ATAA--AAA-GACAA--ATAACC-CAATTWAA 816

  chrX_87827743_8   2526 AAATGGATAGAATACCTGAATAGACATTTCTCAAAACAAGACTTATAAAT 2575
                               ii i iv ii                v   v    iv  i    
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_87827743_8   2576 AGCCA-CAAG-GTATAAAAAAATGCTCAACATGACTATTAAT 2615
                         i    -i   -ii  i    i           v ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (146 / 90)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.00 (58 / 29)  


2607 29.42 1.22 0.77  chrX_87838801_87841955.rev     1761  2664 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87838801_8   1761 TGGAAACATATCTCAAGCTCACTGATGGGTGGAATCAATATTGTGAAAAT 1810
                               v     i  v i   iv   v  vi  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87838801_8   1811 GACCATACTGTCAAAAGCAATCTACAAATTCAATGCAATTCCCATTAAAA 1860
                          i v     vi v   vii       i      i     i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87838801_8   1861 CACCA-CTGTCATTCCTCATAGAACTAGAAAAAGCAATTCTAAAATTCAT 1909
                         iv   -   i -  ii iii    v v  v  ivii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_87838801_8   1910 ATGGAACCAAAAAGAGCCCACA-TATCCAAAGTAAGACTAAGCAAAAAGA 1958
                               viiv  i ii    v -  v     ii  vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_87838801_8   1959 ACAAATCTAGAGGCATAACATTACCTGACTTTG-----TATTATAAGGCC 2003
                              vi i    vv v   i v  ii i  ii-----  i  i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_87838801_8   2004 ATAGTCACCAAAAAAACAACATGGTACTGATATCAAAA--GTCACATAGA 2051
                          i   v i   i ---  iii        ii  v ii -- v  i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGA---CAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_87838801_8   2052 CCAATAGAACAGAAGAGAGAACCCAGAAATAATCCCAAATGCTTACAGCC 2101
                         i    i   i    vv    ii          v    v iii   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_87838801_8   2102 AACTGATCTTGGACAAAACAAACAATAACATAAAGTGGGAAAAAGACACC 2151
                           i    i  v     iivviv   v v   vv i    i   ii i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_87838801_8   2152 ATAATCAACAACTACTGGTGGGATAATTGGCAAGCCACATGTAAAAGAAT 2201
                         v vv       v iv  v     i  i   vv ?       i        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_87838801_8   2202 GAAACCGGGTCCTTATCTCTCACCTTATACAAAA-TCAACTCAAGATGGA 2250
                            iii  ii  i  i   v    v         - i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_87838801_8   2251 TCAAGGCCTTAAATCTAAGACTTGAAACCATAAAAATTCTAGAAGTTATC 2300
                            ?i v i     v     vi i    i      v ii      vv v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_87838801_8   2301 ATCAGAAAAACTTTTCTAGACATTGGTTTAGGCAAAGCCTTCATGACCAA 2350
                           vi ?iv  v i   vv   v    v        v vi   v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_87838801_8   2351 GAATCTAAAAGCAAATGCAACAAAAAATATGATAAATAGGTGGGATTTAA 2400
                           vv i       v v         i v vi   i   ii v   i  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_87838801_8   2401 TTAAACTAAAAAGTTTCTGCACAGCAAAAGAAACAATCAGCAGAGTAAAC 2450
                          i   v v    ii  i  ii vv    i  v  v    iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_87838801_8   2451 AGACAACCCATAGAGTGGGAGAACATCTTCACAATCTATACATCTGACAA 2500
                                   i   i        v  v  ii   vii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_87838801_8   2501 AGAACTAATATTCAGAATCTACAAGGACCTCAAACAAATTAGCAAGAAAA 2550
                         i i   vi   i      v  i  i  v   vv    v i ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_87838801_8   2551 AAATAAACAATCCCCTAAAAAAAAAATGG-CTAAGGACATGAATAGACAA 2599
                          i i   i  i  ---  vv?        - v     iv          v
  L1M4_orf2#LINE/    797 AGACAAATAACCC---AATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_87838801_8   2600 CTCTCAAAAGAAGATATAAAAATGGCCAGCAAACCTATGAAAACATGTTC 2649
                         i    v            v         ii  i vi       v   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_87838801_8   2650 AACATCATAATGATC 2664
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (154 / 108)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


3284 26.98 0.33 0.33  chrX_87842812_87849208.rev     4999  5906 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87842812_8   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5048
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87842812_8   5049 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5098
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87842812_8   5099 TACCAATGACTTTCTTCACAGAATCAGAAAAAACT-ACTTTAAAGTTGAT 5147
                          v   iivi i  i  ii     viv  v  i-  - iii    i  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_87842812_8   5148 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGA 5197
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_87842812_8   5198 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGTCT 5247
                               i      vv    i  v  ii i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_87842812_8   5248 ACAGTAACCAAAACAGCATGGTACTGCTAGCAAAACAGAGATATAGATCA 5297
                                i   i    ii        vi vv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_87842812_8   5298 ATGGAACAGAAC--AGAGTCTTCAGAAATAAAGCCGCATATCTACAACTA 5345
                               i    i--      --          v  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTCA 347

  chrX_87842812_8   5346 TCTGATCTTTGACAAACCTGAGAAAAATAAGCAATGGGGAAAGGATTCCC 5395
                         vi    i  i     ivv  vv  i vi vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_87842812_8   5396 TATTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5445
                          v     i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_87842812_8   5446 AAACTGGATCCCTTCCTTACACCTCATACAAAAATTAATTCAAGATGGAT 5495
                           ii    i    v   i     vi             i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_87842812_8   5496 TAAAGACTTAAACGTTAGACCTAAAGCCATAAAAACCCTAGAAGAAAACC 5545
                         i ?    i    i  v   v     i i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_87842812_8   5546 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5595
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_87842812_8   5596 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5645
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_87842812_8   5646 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5695
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_87842812_8   5696 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5745
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_87842812_8   5746 GGGCTAATTTCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5795
                           i  vi v        v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_87842812_8   5796 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 5845
                         i     i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_87842812_8   5846 CAAAAGAAGACATTTATACAGCCAACAGACACATGAAAAAATGCTCATCA 5895
                          v        i  vi v ii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_87842812_8   5896 TCACTGGCCAT 5906
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


2967 27.06 1.10 1.21  chrX_87861056_87866717     4261  5169 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87861056_8   4261 TGGAAAAACATTTTATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4310
                               i i  iii   i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87861056_8   4311 GACCATACTGCCAAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 4360
                          i v     v  v   v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87861056_8   4361 TACCA-TTGACTTTCATCACAGAATTAGAAAAAAACT-ACTTTAAATTTC 4408
                          v   -i  v    i- ii     v v  v  i--  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_87861056_8   4409 ATATGGAATCAAAAAAAGAACCC-GTATAGCCAAGACAATCCTAAGCAAA 4457
                                 -- viv  i i    - v        i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_87861056_8   4458 AAGAGCAAACCTGGAGGCATCACTCTACCTGACTTTAAACTATACTACAA 4507
                             i    vi      vv    v  v  ii i  i   viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_87861056_8   4508 GGCTACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAG 4557
                         i      i   i   i    ii         i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_87861056_8   4558 ACCAATGGAACAGAACAGAGGCCTCAGATGTGTGACACCACACATCTATA 4607
                          i        i    iv   ivii    vi i-i  -   i    i   i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATA-AAC-CCATACATTTATG 343

  chrX_87861056_8   4608 ACCATCTTATCTTTGACAAACCTGACAAAAACAAGCAATGAGAAAAGGAT 4657
                         ii  vi v  i  i     ivv  v   i v  vv     i i    i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_87861056_8   4658 --TCCATATTTAATAAATGGTATTGGGAAAACTGGCTAGCCATATGCATA 4705
                         --  -- v  i  i       ii     v      v  ?   i     v 
  L1M4_orf2#LINE/    394 AGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_87861056_8   4706 AAACTGAAACTGGACCACTTCCTTACACCTTATACAAAAATTAACTCAAG 4755
                          i v    ii      v  v   i     v                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_87861056_8   4756 ATGGATAGAAGATTTAAACGTTAAGACCTAAAACCATGAAAACCCTAGAA 4805
                               vi?   ii    i  -    v       i  i   vi i     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_87861056_8   4806 AAAAACCTAGGCA-ATACCATTCAAAACTTAGGCATGGGCAAAGACTTCC 4854
                         i     v    ?i- v i -   ivi  i v  vv i     v ii   i
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_87861056_8   4855 TGACTAAAACACCAAAAGCAATTGCAACAAAAGCCAGCATTGACAAATGG 4904
                          iiv  vi            vvv          vv iv  v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_87861056_8   4905 GATCTAATTAAACTAAAGAGCCTCTGCACAGCAAAAGAAACTATCATCAG 4954
                           ii v  i   v v  i i i i  ii vv    i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_87861056_8   4955 AGTGAACAGGCAACCTACAGAATGGGAGAATATTTTTGCAATCTATCCAT 5004
                               v  i     i              v  v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_87861056_8   5005 CTGACAAAGGGCTAATATCCAGAATCTACAAGAAACTTAAACAAATTTAC 5054
                             i  i  i  vi          v  i  ii    ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_87861056_8   5055 AAGAAAAAAACAA----CCGCATCAAAAAGTGGACAAAGGATGTGAACAA 5100
                           v     i    ----  vv  i?    i   i        v    i i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_87861056_8   5101 ACACTTTTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAA 5150
                            i  i  v        i  vi vi       i  i  i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_87861056_8   5151 GCTAACCATCACTGGTCAT 5169
                            v v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


1297 25.45 1.68 14.80  chrX_87867364_87869471      500  1391 (717)    L1M4_orf2#LINE/L1       56   830 (78)  

  chrX_87867364_8    500 TACTACTCCAAGTAATCT---GATTCGATGAAATCCCTATCAAAATTACT 546
                             v i v  v i    ---     i i v               iv v
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_87867364_8    547 ATGACGTTCTTTACAGAAATAGAAAAAGCAATTATAAAATCCTTGTGGAA 596
                         iivi v  i   i       v  v  ivii  iv      i v i     
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_87867364_8    597 CCACTAAAGAACCGAAACAGCTAATG-AATTTTGAAAACAAAACAAAGCA 645
                         vii v ii  v  ii  i   i  vi-   i       --------  v 
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA--------AGAA 197

  chrX_87867364_8    646 AAACAAAACAAGAAGTATCACCCTTTCGGATTTCAAATTATGTTATAAAG 695
                         i      iivi  i vv    v   i vi        viv ii  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_87867364_8    696 CTTTAGTAACCAAAACA-TGTGGTACTGGCATAAAAACAGACACATAGAC 744
                           vi     i   i   -                ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_87867364_8    745 TGATGAAATAGAATAAAAAGCCCAGTAATAAACCCCTACAT--AACATCA 792
                         ii   i        vi i  i    v         v     -- vvi   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_87867364_8    793 ATTAATTTCCATAAAGTACGCCACAAATATACAGTGCAGAAAGAACAGTG 842
                            i    i ivv   vii    vi vi  v  i  vi       i   v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_87867364_8    843 TCTTCAATACATGCTGCTGGAAAAGATGCAATATTATTTACATGCAATAG 892
                          i     i v   v      i v iv  v ----  ?ii        v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGA----TAKCCACATGCAAAAG 443

  chrX_87867364_8    893 AGTAAAATTAGACCAGCAAACCACCATATCACACGTTTACATATGTAACA 942
                          i i  i  i    ------------------------------------
  L1M4_orf2#LINE/    444 AATGAAGTTGGACC------------------------------------ 457

  chrX_87867364_8    943 AACCTGCACATCCTGCACATGTACCCCAGAACTTAAAATAAAAATATTTT 992
                         -----------   --------   i  ----------------------
  L1M4_orf2#LINE/    458 -----------CCT--------ACCTCA---------------------- 466

  chrX_87867364_8    993 TTAAAAAAATAAAATTGCACCATTTTTCACCACACAGAAAAATCAACTTC 1042
                         ---------------------------     i i v      i    iv
  L1M4_orf2#LINE/    467 ---------------------------CACCATATACAAAAATTAACTCA 489

  chrX_87867364_8   1043 ACTTGAATTGAAGACTTAGTGGTAAGAACTGAAACCATAAAACACCTACC 1092
                          vv  i  ii?    i  ivv      i  i    i       -i  ---
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCT--- 535

  chrX_87867364_8   1093 AAAAAATAAAATAAAAAACAGGAAAAAAAAACTT---GAAATTGGTCTTG 1139
                         ------  i  v    v i   ?iv   v--   ---  vv    vi v 
  L1M4_orf2#LINE/    536 ------TAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTAG 577

  chrX_87867364_8   1140 ACAATTGTTTTTTGAAGATGGCACCACAAGCTCAGGCAAAAAAAGCAAAA 1189
                         i    v    i  ii v   i     v    v  i    v     -    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAA 626

  chrX_87867364_8   1190 AATAAACAAGGAGGATTGTATCAA--CTAAAATGATCTAGCACACTAAAG 1237
                             i i  ivv   i vi     --i     -iv i v ii vii    
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAG 675

  chrX_87867364_8   1238 CAAACAATGAACAAAATCAAAAGGCACTTTAAAGAATAGGAGAAAATACT 1287
                         v v  v  v  v   i v     i  viii v     i          i 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_87867364_8   1288 TGCAAATGATACATCTAATAAAAAGTTAATGTCAAATATATACAAGAAAA 1337
                                v   i    i    iiiii vi i  v iv     i  ii  v
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_87867364_8   1338 CCATAAAACTGAATATCAAACAAAGTGAATTAACACA-TT--AATTTGGG 1384
                         i v  v    v    vi   --   vv  v    v  -  --  vv    
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAA--AAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_87867364_8   1385 CAAAGAA 1391
                              i 
  L1M4_orf2#LINE/    824 CAAAGGA 830

Transitions / transversions = 1.41 (131 / 93)
Gap_init rate = 0.02 (19 / 775), avg. gap size = 7.74 (147 / 19)  

 434 17.39 11.30 0.00  chrX_87867364_87869471     1501  1615 (493)    L1M4_orf2#LINE/L1      781   908 (0)  

  chrX_87867364_8   1501 CAACTTAA-AATAAAA-GTCAAA-----------AAAAGTGGGCAAAGCA 1537
                              i  -       - v    -----------    i         v 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_87867364_8   1538 CCTGAATGGACATTTCTTCAACTAAAACATATAAATGGCCAATAGGTATA 1587
                         ii     i         i   vv  i i   i            i i i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_87867364_8   1588 TAAAAAGATGATGAATATCATTAATTAT 1615
                          i        v v  i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.02 (3 / 128), avg. gap size = 4.33 (13 / 3)  


2129 29.44 1.52 3.25  chrX_87872838_87874769.rev      518  1441 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87872838_8    518 TAGAAATACATTTCATACTCATGGATTAAAAGAATCAATATCATCAAAAT 567
                          i    v i  ii   ii         ii    v i     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87872838_8    568 GGCCACACTCCTCAAAGCAATTTTTATATTCAATGCTATTTCTATCAAAC 617
                            v i     i    vii  i vi v      i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87872838_8    618 TACCAA-TGCCAATTTTCACAGAA-TTGGTAACACT-ATTCTAAAAATAA 664
                          v   i-    v-    ii     -   ii  -i  -  i      v v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_87872838_8    665 TATGGAAACAAAAAAATAAGCCTGAATAGGCAAAGCAATCCTAAGCAAAA 714
                                 iiv  iii-- v  v      v    i     i i --    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGG--ACCCAGAATAGCCAAAACAATCTTGA--AAAA 194

  chrX_87872838_8    715 GCAACAAACAAAAAGTCCAAAGCTGGAGGCATCACATTATGGGACTTCAA 764
                          --------  i  ---     i      vv     i vivvi i     
  L1M4_orf2#LINE/    195 G--------AAGAA---CAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_87872838_8    765 ACTACACTACGAGGCTTCAGTAACCAAAACAGCACGGTACTGGTACAAAA 814
                          vivi     i i   v      i   i    iii        i i  ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_87872838_8    815 CAAGATTTGTAGACAAATGTAACAAAATAGAGAACCAAGAAATAAAAGC- 863
                         vv   iv i    iv    v  i i   v    ii v         vv -
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_87872838_8    864 ----TTCACAGCCACTACTATCTATTCTTTGACAAAGCTGAAAAAAAATA 909
                         ----  i ii i  -----  iv   -  i     i v  vv  i v-i 
  L1M4_orf2#LINE/    334 TACATTTATGGTCA-----ATTGATT-TTCGACAAGGGTGCCAAGAC-CA 376

  chrX_87872838_8    910 AGCACTGTGGAAAGGACTTCCTATTCAATAAATTATGCTGGCATAGTTAG 959
                         vv  v  v      i ivvi  v     i    vi      v i ii i 
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_87872838_8    960 CTATCCATAAACAGAAGAATAAAACGGTACACCTACCTTTCACGATATGC 1009
                         v  ?   i vi  i      i  iiv v  v       iv   v    i 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_87872838_8   1010 AAAAATTGTCTCAAGATGGATTAAAGTTTTAAATGTAAAGGATATCAAAC 1059
                                iv     i      i ?  vii         ii v  --    
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA--AAAC 524

  chrX_87872838_8   1060 TATAAAAATGCACAAAGAAAACTGCAGAAACACCACTCTG-GACATCAGC 1108
                                v vivvi        -ii  i?ii vvv  ii -   v ii -
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAAC-ATAGGNGTAAATCTTCGTGACCTTGG- 572

  chrX_87872838_8   1109 GTTGATAAAATGATT-CATGACTAAGTCTTGAGAAACAACTGCAACAAAA 1157
                            - viv    i  - v iiv  v v viv i  i  vvv         
  L1M4_orf2#LINE/    573 GTT-AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_87872838_8   1158 CAAAAAATGGAAAAGTGGGACCTAACTAAGCTAAAGAACTTCTGCACAGC 1207
                         v       i  v  i v    i v ii  iv v  i     i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_87872838_8   1208 AGCAGAAACCCCCAACAGGGTAAACAGGTAAGCTGCAGAATGGGAGAAGA 1257
                          ivi  v  ivi   v ii  i  v  ii  v ii             i 
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_87872838_8   1258 TATTCACAAATTACAGATA-GACAAACGTCTAATATCCAGAATGAATAAG 1306
                             ii     i i v  v-  i  iv v  vi          iv    i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_87872838_8   1307 GAATTTAAACAATTGAACAAGTAAAAAAACAAATAACTCCATT-AAAAGT 1355
                            i ivv    i v  i  -      i         i v   -    i 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_87872838_8   1356 GGGCAAAAAAAT-GAACAGACACTTTTCAAAATAAGACATACAAGTGGTT 1404
                                ii v -   i     i  i  v   v    i      i   ii
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_87872838_8   1405 AACAAACATTTGAAAA-ATGCTCAATATCACTATTCTT 1441
                           i  i  iv      -        i    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (165 / 104)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.83 (44 / 24)  


 297 25.44 4.39 0.00  chrX_87879193_87881013.rev      225   338 (1483)  C L1M4_orf2#LINE/L1   (0)   908   790  

C chrX_87879193_8    338 AAGAAAAAAAAAAA-AAC---ATCAAAAAGTGGGTGAAGAATATGAACAG 293
                           v     i v   -   ---  i?    i    ii   i  v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

C chrX_87879193_8    292 ACACTTCTCAAAATAAGACGTTTATGCAGCCAACAAACAGTTGAAAAAA- 244
                            i     v   v    ii vi viii     i  i  vv      i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

C chrX_87879193_8    243 GCTCATCATTACTGGTCAT 225
                              v   i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.67 (5 / 3)  

 567 27.44 0.00 0.00  chrX_87879193_87881013.rev      338   501 (1320)    L1M4_orf2#LINE/L1      633   796 (112)  

  chrX_87879193_8    338 TGAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA 387
                          i   v   ii v  i   v v  i i   i  ii vv    i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_87879193_8    388 TCATCAGAGTGAACAGGCAACCCACAGAATGGGTGAAAATTTTTGCAATC 437
                            vv i      v  i                v      v       vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_87879193_8    438 TATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACA 487
                         i  vi      i  i  i  vi          v  i  i     ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_87879193_8    488 AATTTACAAGAAAA 501
                          v iv i  v    
  L1M4_orf2#LINE/    783 ACTCAATAATAAAA 796

Transitions / transversions = 1.14 (24 / 21)
Gap_init rate = 0.00 (0 / 164), avg. gap size = 0.00 (0 / 0)  

2377 27.74 2.41 1.93  chrX_87879193_87881013.rev      502  1330 (491)    L1M4_orf2#LINE/L1       76   908 (0)  

  chrX_87879193_8    502 AAACTCAATGCTATTTCTATTAAACTACCAATGACATTCTTTGCAGAATT 551
                          i i    i  v  ii    i   v v   iivi v  i         v 
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chrX_87879193_8    552 AGAAAAAAACTAATTA-AAAATTCATATTGAAACAGAAAACAGTCAGAAT 600
                         v  v  i--  i  iv-           v    iiv  iiv vi      
  L1M4_orf2#LINE/    126 TGACAAG--CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chrX_87879193_8    601 AGCCAAGGCAATCCTAAACAAAAAGAGCAAACCTGGAGGCATAACATTAC 650
                               ii     i i  v  i    i    vi      vv v   i v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_87879193_8    651 CCAACTTCAAACTATACTACAAAGCTATGATAACCAAAACATTATGGTAG 700
                             i      viv             iii   i   i   v i     v
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_87879193_8    701 TGGTACAAAAACAGGCACATAGACCAATGCAACAGAAGAGAGAGCCCAGA 750
                            i i  ii i  i  i     i     v  i    vv     i     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_87879193_8    751 AATAAGCCTACATGCCTGTGACCATCTGATCTTCAGCAAAGCTGACAAAA 800
                              i  i i iiii i  ii  vi    i   ii   i v  v   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_87879193_8    801 ACAAGCAATGGGGAAAGGATTCCCTATTCAATAAATGGTGCTGGGATAAC 850
                         v  vv            i  vvi  v     i              i   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_87879193_8    851 TGGTTAGCCGTAGGCAGAAGATTGAAACTGGACCCCTTCCTTATACCATA 900
                            v  ?  ii v   i    v    ii         v   i i      
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_87879193_8    901 TA--AAAGTTAGCTAAAGAGAAATTAAAGACTTAAATGTAAAACCTAAAA 948
                           --   i   i  v  i vii  i ?    i         i v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_87879193_8    949 CTATAAAAAACT---AGGAAGACAGAAAGATAA-TCTAGGAAATACC--- 991
                                 vv  --- i   i   v ii?i   -   vv vi --  ---
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA--CCTTG 571

  chrX_87879193_8    992 -ATTCTGTATATAGACCCTTGCAAAAAAAATTATGAAAATGCCAAAGGCA 1040
                         -i  vv i -  i vii   ------- i  -    v ---     i   
  L1M4_orf2#LINE/    572 GGTTAGGCA-ATGGTTTCTT-------AGAT-ATGACA---CCAAAAGCA 609

  chrX_87879193_8   1041 ATTTTAACAAAAAGAAAAATTGACAAATGGGACCTAATTAAACCAAAGAA 1090
                         vvvvi       ii      v  i    v    i v  i   viv  i  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_87879193_8   1091 CATCTGCACAGCAAAATAAATTATAAACAGAGTAAACATATAGCTTACAG 1140
                          v i  ii vv    iv v i   v  v i   i  v v i i ii    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_87879193_8   1141 AATGGGAGAAAATACTTGCAAAC--TGCATCTGACAAAGTTCTAACATCC 1188
                                       i       i-- ii      i  i vv  vii    
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_87879193_8   1189 AGAACATATATGGAACTT----AAATTAAAAAGCAGAAAACACAAAACCC 1234
                             i     vi     i----  v i  v  vv i  i   v v     
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_87879193_8   1235 TATTAAAAAGTGGGCAAAGGACACAAACAGAC---TCTTCAAAACAAACC 1281
                         v   ?    i           ivii  i    ---   i    iv i iv
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_87879193_8   1282 TACACGTGGGCAAGAAGCATATGAAGAAATGCTCAACATTACTAATCAA 1330
                             vi   v   v     i     i i           i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (139 / 87)
Gap_init rate = 0.02 (14 / 833), avg. gap size = 2.57 (36 / 14)  


2335 28.54 2.31 2.63  chrX_87918243_87920432.rev      795  1705 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_87918243_8    795 TGGAAAAAT----CATGCTCATGGACAGGAAGAATTAATATTGTTAAAAT 840
                               i  ----    i       iv      v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_87918243_8    841 AGCCATATTGCCCAAAGCAATTTACAATTTAAATGCTATTCCTGTCAACC 890
                         i  v   i v      vii  i    iv  v  i  v  i   i    vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_87918243_8    891 TACCAATTGCATTTTTT-CACATAATTAAAAAATAAAGTACTCTAAAATT 939
                          v   ii   v      -  v -    i v  iivi ---ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGA---TCCTAAAATT 146

  chrX_87918243_8    940 TACACAGAACCAAAAAAGAGCCTGAATATCCAAGGCAATCCTATGCAAAA 989
                         i i ii   viiv  ii  v  v     v    ii     i iviv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_87918243_8    990 AGAACAAAGCTGGAGGCATCACGTCACTCGACTTCAAACTATATTAAAAT 1039
                                  i      vv    iiiv i i i      viv  i  v  v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_87918243_8   1040 ACTACAGTAAGCAAAACAGCATGGCACT--CATAAAAATACAGACACACA 1087
                         i         v   i    ii   i   --     ii   --    i i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA--GACATATA 294

  chrX_87918243_8   1088 GACAAATGGAACAGAATGCAGAGCTTAGAAATAATGCTGCACACTTACAA 1137
                           iv       i     vv    iii        vv iii   i   iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_87918243_8   1138 CCATCTGATCTTTGACAAAACTGACAAAATCAAGCAATGGCTAAAAGACT 1187
                         i  vi    i  i     iiv  v   i i  vv      vv   ii iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_87918243_8   1188 CTCTATTCAATAAATGGTGCTGGGATAACTGGTTAGTCATATATAGATAA 1237
                         v   v     i              i      v  ?i  i  ii i vi 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_87918243_8   1238 TTGAAACTGAAACTCTTAATACA-ACTGAGTTGTATTAAAACCAGCTCAA 1286
                         v    ii  i - i i  viv  -  ii--- i  iv    ii i     
  L1M4_orf2#LINE/    445 ATGAAGTTGGA-CCCCTACCTCACACCA---TATACAAAAATTAACTCAA 490

  chrX_87918243_8   1287 GATAGATTAAAGACTTCACTTTAAAATGTAAAACTATAAAAATCCTGAAA 1336
                         i  i   i ?    i v v v   i vv             v  i ii  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_87918243_8   1337 GCAAACCTAGG---AAATACCATTCTGGACATATGACCT-GGCAAAGATT 1382
                          v    v    ---    -- -   vv   v -  ivi -     v i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT--C-TTCGTGACCT-TGGGTTAGGCAATGGTT 586

  chrX_87918243_8   1383 TTATAACAAAGATGCCAAAAGTATTTGAAACAAG-AACAAAAAATAGACA 1431
                          iv  ivv v  ii       i -------    -       i --- v 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCA-------CAAGCAACAAAAGA---AAA 626

  chrX_87918243_8   1432 ATTAGACAAATGGGACCTAAACAAACTGAAGGGCTTTTGAACAGCAAAAG 1481
                          v    i    v    i v v    v v  iii      vi vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_87918243_8   1482 AAACTATCAACAGAGTAAAGAGACATCCTTCAGAG-GGGAGAAAATATTT 1530
                          v        v i   i  i     v  iv    i-              
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_87918243_8   1531 GCAAACTACGCATCTGGCAAAAGTTTAATATCCACAATCTATTAGAAACT 1580
                              ii iii     ii  ii vi vi      v   v   v ii    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_87918243_8   1581 CAAACAAAT---TTACAAGCGCACACACAAAC--ATTAAAAAGTGGGCAA 1625
                          vv    v --- v i  iviv   v i  v --   ?    i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_87918243_8   1626 AGTACATGAACAGACACTTCTCAAAAGAAGACACACATGCAGCCAAAAAG 1675
                           v iv    i     i     v        i i   viii     v   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_87918243_8   1676 CATA--AAAAAATGTTCAACGGCACTAATTAT 1705
                           i --    i   i     iv  ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (156 / 101)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.14 (45 / 21)  


 756 28.80 3.16 5.38  chrX_87936105_87938246.rev      502   817 (1325)    L1M4_orf2#LINE/L1      150   458 (450)  

  chrX_87936105_8    502 ATGGAACCAAAAAAGAGCCCGCATAGTCAAAGCAAGACTAAGCAAAAAGA 551
                               viiv  ii  v  v v    i    i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_87936105_8    552 ACAAATCTGGAGGAATCACATTACCTGATTTCAAACTATACTATAAGGCC 601
                              vi       v     i v  ii        viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_87936105_8    602 ATAGTCACTAAAACAGCATGGCATTGGTATAAAAATAGGAACATAGACCA 651
                          i   v ii  i    ii   i i   i    ii    iv i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_87936105_8    652 ATGCAACAGAATAGAGAACCCAGAAGTGAAGCCAAATGCTTACAGCCAAC 701
                            v  i     v    ii      i i  v   v iii   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_87936105_8    702 TGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGTGTAT--TAGTCTG 749
                             i   i    i vviv   i v   vv i    viv v--      -
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT- 398

  chrX_87936105_8    750 TTTTCA-----TGCTGCTGATAAAGAAACACCCAAGACTGGGCA---ATT 791
                         -     -----  v     i------i   ------     ii --- iv
  L1M4_orf2#LINE/    399 -TTTCAACAAATGGTGCTGG------GACA------ACTGGATAKCCACA 435

  chrX_87936105_8    792 TACAAAAGAAAGGTTTAATTGGACTC 817
                          i        v i--- i      i 
  L1M4_orf2#LINE/    436 TGCAAAAGAATGA---AGTTGGACCC 458

Transitions / transversions = 1.94 (60 / 31)
Gap_init rate = 0.02 (7 / 309), avg. gap size = 3.86 (27 / 7)  

1631 25.09 2.73 2.55  chrX_87936105_87938246.rev     1102  1651 (491)    L1M4_orf2#LINE/L1      358   908 (0)  

  chrX_87936105_8   1102 GACACAGAGT--CAA-ACCATTTAAGTGGGGAAAGGACACCCTATTCAAC 1148
                             -  i  --   -      i  -         i i vi  v      
  L1M4_orf2#LINE/    358 GACA-AGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_87936105_8   1149 AAATGGTGCTGGGATAATTGGCAACCAACATGTAGGAGAATTAAAGTGGA 1198
                                       i  i   vv ? v     i ii     v  iv    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_87936105_8   1199 TCCTCATCTCTCACCTTATACAAAA-TCAACTCAAGATGGATCAAGGACT 1247
                         i  ii i   v    v         - i       i        ?i   i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_87936105_8   1248 TAAGTATAAGACCTGAAACCATAAAAGTTCTAGAAGATAAAATTGGTAAA 1297
                            i i     v  i    i      v ii       v  v  v  ?iv 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_87936105_8   1298 ACCCCTCTACACATCAGCTTAGGCAAGGATTTAATGACCAAGAACCCCAA 1347
                          vi i  vvv  v ii v        v i   vv iivi v  vv  v  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_87936105_8   1348 AGCAAATCTAATAAAAACAAAGGTAAATAGGTGGGAC------AAAG--- 1388
                             v vvi  i    iv   ii  i   ii v    ------   i---
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_87936105_8   1389 --AGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAATAAACAGACAACCC 1436
                         -- i      ii vv    i iv  vi   iv i i i  v         
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_87936105_8   1437 ACAAAGTGGGAGAAAATCTTCACAATTTATACATATGACAAAAAAAAAAA 1486
                            i i           v  ii   v i   i  v   i  iii -----
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA----- 750

  chrX_87936105_8   1487 AAACCTAATATCCAGAATCTACAACGAAATCAAACAAATTAGCAAGAAAA 1536
                         ----  vi          v  i  v   v  vv    v i ii  v    
  L1M4_orf2#LINE/    751 ----CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_87936105_8   1537 AAACCAAACAATCCCATCAAAAAAATTAGCTAAGGATATGAATAGACAAT 1586
                          i  -   i  i  v  i?     - vi  v      v          v 
  L1M4_orf2#LINE/    797 AGAC-AAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATT 844

  chrX_87936105_8   1587 TCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAAATGCTC 1636
                             v                       i  i  i       i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chrX_87936105_8   1637 AACATCACTAATGAT 1651
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (77 / 57)
Gap_init rate = 0.02 (11 / 551), avg. gap size = 2.64 (29 / 11)  


1873 25.71 4.17 0.50  chrX_87951229_87952816.rev      502  1100 (488)    L1M4_orf2#LINE/L1      288   908 (0)  

  chrX_87951229_8    502 ATATGTGAACCTATGGAATATAATAAAGAGCCCAGAAATAACCCCTAACT 551
                          i  i ii i v        v   vi    i          v   vv  v
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_87951229_8    552 TTTCTAGTCAATGACTCTTTGACTAGAATTTCAAGACCATTCAA-AGTGA 600
                            v i      viv i  i   v  ii vi             -i v  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_87951229_8    601 AA--ATATTCTTTTCGGCAAGTTGTCCTAGGAAAACTGTATATACACACT 648
                           --   v       ii   i v  v  i   v     v   ?v    - 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-T 436

  chrX_87951229_8    649 G-AAAAGCA----ATTAGACCATTATCTTATATCATATATAAAAATTAAC 693
                          -     v ----i  i    vi  i  i i i      i          
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_87951229_8    694 TGAAAATGGATCA-AAAGCTAAACTTAAGATCTAAAATTATAAAACCCTT 742
                          v           - i v     iv     v      i        i   
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_87951229_8    743 AGAGGAAAATATGCAGGAAAATTTCTATAATATTGGATTTGATAATAATT 792
                            i     i  ivi? v    i iii i iv    i  v ii   ii  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_87951229_8    793 TCTTGGATATGACATCAAAAGCAGAGTCAAGAAAA--AAAAGTAGAATAA 840
                             i         i        v iv   v    --    i    vv  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_87951229_8    841 TTAGAATGCGTCAAAACTAAAAATTTTTATTCATCAAGTGACCCAATCAA 890
                           i  v v i      i      i    i v v    iv   v v     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_87951229_8    891 GTCAGTGAAAAGGTGACCCACAGAATGGGAGAACATATCATTAAATAAAA 940
                          vv         iii                  v    ivvi    v v 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_87951229_8    941 TATTGAATA--GAATATGAATATGCAGAATA----ACCAACTTGTACAAC 984
                            ivi   -- i iv  --   v       ---- vv    iv      
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTG--TATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_87951229_8    985 CCAACAACAAGAA--------ATCCAATATAAAAATAGGCATTGAACTTA 1026
                         i   i  i  i  -------- i     v?      i    vv i i  i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_87951229_8   1027 AAAAGACATTTATTCAAAGAAAATGAACTTATGCTCATTAATTGTATGAA 1076
                           v        v i       i  iv  vv   vi  v   viii     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_87951229_8   1077 ATGATGCTCGACAAAACTAATCAT 1100
                          v       i   vv ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (83 / 68)
Gap_init rate = 0.02 (11 / 621), avg. gap size = 2.55 (28 / 11)  


1956 26.80 8.58 3.48  chrX_87958270_87964237     4614  5475 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_87958270_8   4614 GAAAACT-TCCCATTCTCATGGATCAGAATAATTAATACCTTTAAAATGA 4662
                             iv -      vi        ii   v v      iiv    i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_87958270_8   4663 CCATACAACCCAAAGCCATTTACAGCTATAATGCAATGCCTATCAAGATG 4712
                          v    vv      viv  i     v vi  i     v        i  v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_87958270_8   4713 CCAA-TGCCATTTTTCACATTGTTAGAAA--AGCAATCT-ATTCTAAAAT 4758
                            i-    -     ii  ------    --ii   v  -  i       
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCA------GAAATTGACAAGCTGATCCTAAAAT 145

  chrX_87958270_8   4759 GTATATG-AGACAAAAAAGAGCGTGAAAAGCCAAAGCAATCCTATGTAAA 4807
                         vi     - i iiv  ii  v vv   v       i     i iviv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_87958270_8   4808 AATAACAAAGCTGGAAATATCACATTATTTGACTTTAAATTACACTTCAA 4857
                           v       i    iivv     i viiii i  i   vivi   v   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_87958270_8   4858 GGCTATAGTAA-CAAAACCAGCATTGTGCTTGTATAAAAATAGACACATA 4906
                         i    i     -   i  -  ii v  i  v i    ii       i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGAC-AGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_87958270_8   4907 GATTAATAGCGCAGAATAGAGAACCTAAAAATA----------TTTAAAA 4946
                            i   i vii     v    ii i i     ----------    vii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_87958270_8   4947 CCACCTGATCTTCTAAAAAACTGTCAAGCACATATGCTGGGGAAATGACA 4996
                         i  vi    i   v v  iiv  i    vv   viiv        vi i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_87958270_8   4997 CCCTTTTCAATAAATGATGCTTGAAAAATTGGACTGCCAAGTGTAGAATA 5046
                         vi        i     i    v i v  i    iv?   vi  i i  v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_87958270_8   5047 TTAAAACTG-----------------AT-TACAAAA-TAAATGTAAGAAG 5077
                         v i  ii  -----------------  -       - v  ivi  i v 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_87958270_8   5078 AATGAAAGACTTAAATATAAGAGCTGAAATTATAAAAATACTAAAAGAAA 5127
                         i  v ?    i     i        i   i       v vi  i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_87958270_8   5128 ACCTACCGAAAACTCTTCCAAACATTGGTCTAGA-AAGAATTTATGAG-T 5175
                           v  vv?iv  v     vvi  v    vi   i-  vii   v v  - 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_87958270_8   5176 AAGATCACAAAAGCACAAGCAACAAAAACGAAAATATATAAACTA----- 5220
                          v  ivv                    ivi      v     i i-----
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_87958270_8   5221 ----AAAAT------CTTCTGTGCAGCAAAATTAATA--ATCAACAGAGT 5258
                         ----     ------   i     vv    i--i i --     v i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAG--GACACTATCAAGAAAGT 692

  chrX_87958270_8   5259 GAACAGACAACCTGCAGAATTGGTTAATTTATTTGCAAACTATGCATCTG 5308
                            v        ii      v  vv  vv          ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_87958270_8   5309 ACGAGGGACTAATATTCAGAATTTACAAGAAACTTGTAAATTAACAACAA 5358
                          ii       vi   i      v  i  ii    i-----   ----   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTC-----TTA----CAA 783

  chrX_87958270_8   5359 CATTAACAACAACAACACAAAAAACTCCAAATAATCCCATGAAAAAGTGG 5408
                          - i  i  i  -------   i  ---      i  v  v?    i   
  L1M4_orf2#LINE/    784 C-TCAATAATAA-------AAAGAC---AAATAACCCAATTWAAAAATGG 822

  chrX_87958270_8   5409 GCAAAGGA-------------------AAAGAAAACACAAAAGTGGCCAA 5439
                                 -------------------      i i i v  i       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_87958270_8   5440 CAGGCATATGAAAAAATGTTCAACATCACCAAATGT 5475
                         i i   i       i   i         ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 4.16 (104 / 25)  


 224 25.73 7.60 11.11  chrX_88026769_88034495     2744  2914 (4813)    L1M4_orf2#LINE/L1        1   165 (743)  

  chrX_88026769_8   2744 TGGAGGAATATAGCAAATTCATG-------AGAC--AGTATTTCTACCAC 2784
                             iii    vv  vi      -------    -- i    vi  vv i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88026769_8   2785 AACAATTCTTATT---TTGAGTTATAGATTCAATGTAATATTAATTAAA- 2830
                         ii    v  ivii---    vi  i        i i   viiv  i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88026769_8   2831 TCCCACAAAGTTTGTATGTTTGTGTGAGCATACATTGAAAATCTGATTCT 2880
                              ---- i - iv v   ---  --  v v     v  v     i  
  L1M4_orf2#LINE/    101 TCCCA----GCT-GCCTTTTT---TG--CAGAAATTGACAAGCTGATCCT 140

  chrX_88026769_8   2881 AAAATCTATGTGAAAAAGAATAAAATGCAAGGAA 2914
                              ii  i  i   ---------       i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAA---------TGCAAGGGA 165

Transitions / transversions = 1.59 (27 / 17)
Gap_init rate = 0.05 (9 / 165), avg. gap size = 3.56 (32 / 9)  

 218 27.78 7.22 6.11  chrX_88026769_88034495     3685  3864 (3863)    L1M4_orf2#LINE/L1      264   445 (463)  

  chrX_88026769_8   3685 AGTGTTTTACTGGCAAAAGAA-AGAAAAAAAAAGACAAGGAAGGAGAAT- 3732
                              vv        v   i -   v v v i v-   v i iv     -
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGAT-CAATGGAATAGAATT 312

  chrX_88026769_8   3733 -AGAGTCCAGAATCAGATCCACAAATATATAGACATCTTAGTT---ACAA 3778
                         -           vi i i   i v  v   i v  vi v v  ---    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_88026769_8   3779 G-------AAATAATTCATGAAATTAAGTAAAGGATAGTTGATCTTATTA 3821
                          ------- i iv     ----  vii -    i     ----   v i 
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCA----ATGGGG-AAAGAATAGT----CTTTTCA 403

  chrX_88026769_8   3822 ATACATGGTGTCAAGTCAATTGGATGTTGATATTGTAAAATAA 3864
                          i v      iiii v   i     i?iv i  - i    v  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAA 445

Transitions / transversions = 1.13 (26 / 23)
Gap_init rate = 0.05 (9 / 182), avg. gap size = 2.67 (24 / 9)  

 319 29.01 13.27 3.09  chrX_88026769_88034495     6601  6924 (803)    L1M4_orf2#LINE/L1      468   824 (84)  

  chrX_88026769_8   6601 ATCATATGCAAAA-TTATTTTGAGATAGATAACTGGTTTACTTATGAAAG 6649
                          i     i     -   vi ii i  i   v ?v iii  vv i i i  
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_88026769_8   6650 ATAAAACAATATAACTTCTAGAA---AAT-TAAGAGAATATCTTTGCAAA 6695
                         v      v   v    ii     ---  i-  i ? v v     i ii v
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_88026769_8   6696 TGTAAAATATACA--GACTTCTTAAATA-GAGCCCAAAAGGCACTAACCA 6742
                         iv iiiv  vi  -- ii      i   -  vv       -   v i v 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG-CACAAGCAA 616

  chrX_88026769_8   6743 TTAAAAACATATTAAATA-----GATGTCATTAAACTTAA---TTTCTTT 6784
                         iv   i v v v  i   -----  iv    i   v    ---i  i v 
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_88026769_8   6785 ATATCAAAG-ATACCATCAA------------ACAGC----AGAGTGGGA 6817
                         iiv      - i  i     ------------   i ----   i     
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_88026769_8   6818 GAAGATATTTGTA--TTATATTTATGTGAGAAAAAA-TAGTAATAAGAAC 6864
                            i       i -- i    --  v   v  iii - v   viv    i
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATAT--ATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_88026769_8   6865 ATAT-------TTTTAAAATACAACAAATAAGTAAGACAAAGGCAATCCA 6907
                             ------- i   v  iv   i  -   i-        --i  i   
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAA-TAAA-AAGACAAA--TAACCCA 810

  chrX_88026769_8   6908 ATTTTTAAAAAATGAAC 6924
                            ?---       ii 
  L1M4_orf2#LINE/    811 ATTW---AAAAATGGGC 824

Transitions / transversions = 1.76 (58 / 33)
Gap_init rate = 0.05 (19 / 357), avg. gap size = 2.79 (53 / 19)  


2997 25.93 3.48 1.57  chrX_88079201_88081248      666  1556 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88079201_8    666 TAGAACAACATTTTCTGATTATGGATTGGAAGAATCAATATTGTTAAAAT 715
                          i   vi i  iiiv  v i             v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88079201_8    716 GTCCATACTACTGAAAGCAATCTG--GATTCAATGTGATCCCTATCAAAA 763
                          v v     v iv   vii    i--       i ii             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88079201_8    764 ---CAACAATGTCATTCTTCACAGAAATTAAAAAA--ACCCCTAAAATTT 808
                         ---  i --  i -  i  ii        i v  i--ivi         i
  L1M4_orf2#LINE/    101 TCCCAGC--TGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_88079201_8    809 GTATGGAATCACAAAAGACCCAGAATAGCCAAAGCTATTTTAAGCATAAA 858
                         i       vii   ii                 i v  i  i iv vi  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_88079201_8    859 GAACAAAACTGGAGGAATTATATTACCTGACTTCAAATTATACTACAGAG 908
                                ii       v i i i v  ii i      viv       i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_88079201_8    909 CTATAGTAACAAAAACAGTATGGTACTGGCATAAATACAGACACATAGAC 958
                            i     iv  i     i              iv i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_88079201_8    959 CAATAGAACAGAATAGAGAACACAGAAAAAATTTGGCACACCTACAGTGA 1008
                             i   i     v    iiv      v  viivii   ii  ii  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_88079201_8   1009 ACTCATTTTCAACAAAAGTGCCA-GAACATACATTGAAGAAAAGATG--- 1054
                          i v      i    ii      -  v   v  v  ii    ii  i---
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_88079201_8   1055 ----CAATAAATAGTGCTCAGAAAACTGTGTATCTATATGCAGAAGACTA 1100
                         ----   i    i     vi  v     vi  ? i i     i    v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_88079201_8   1101 AAACTTGATCCCCATCTCTCACCTCATACAAAAATCAAATCAGAATGGAT 1150
                           ii v  i   i i   v    vi          i  v   i       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_88079201_8   1151 TAAAGACTTAAATCTAAGATCTCAAACTATGCTACC------AGAAAACT 1194
                         i ?    i     v     v  v       ivv  i------       v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_88079201_8   1195 TTGGGGTAAATATCCAGGACTTTGGAGATTTTTTCTGGGCAAAAATTTAT 1244
                          v  ?      v i iv   i    i--------i i     vii   v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGG--------TTAGGCAATGGTTTCT 589

  chrX_88079201_8   1245 TGAGCAATACACCATAAGCAAAATGGGAACCAAAGCAAAAATGGACAAAT 1294
                          iiii vv      v     v  -- v   v    v      i  i    
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAAT 637

  chrX_88079201_8   1295 AG----------AAGTTAAAAAGCTTCTGCACAATAAAGCATACAATCAA 1334
                         v ----------  i       -   i  ii vvi    v i  v     
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_88079201_8   1335 CCAAGTGAAAAGACAGCCCACAAAATGAGAGAGAATATTTGCAAGCTACT 1384
                         vv             i      i    i    i           iii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_88079201_8   1385 CATCTGATAGGGCATTTATACCCAGAATATAAAATGATCTCAAACAACTC 1434
                         i        i  v i  i  i          v  v  v   vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_88079201_8   1435 TATAGGAAAAAATTCAATAACACAACTTAAAAATGTTCAAAAGATTTGAA 1484
                         v   iv     iviv      v   i ?       vv    i        
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_88079201_8   1485 TAGACTTTTCTCAAAAGAAGACACACAAATGACAAAGAGGCATATGGAAA 1534
                              v      v        i i       i v  v i   i   i   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_88079201_8   1535 AGTGTTCAATACCCCTGATCAT 1556
                         ii  i    i i v????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (144 / 83)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.75 (45 / 12)  


2035 26.38 5.30 5.08  chrX_88087846_88091312.rev     2090  2995 (472)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88087846_8   2090 TGGAAACATATTACATTCTCACGGATTGAAAGTATCTGTATTGTGAAAAT 2139
                               v    iv   vi   i      i   vv ivi      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88087846_8   2140 GACTATACTGCCCAAGC-AATCTACAGATTCAATGAAATTCTTCTCAAAA 2188
                          i v     v     ii-i              i v   i i v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88087846_8   2189 TACCAATGTTGTTTTTTTTCACAGAC-TTAGCAAAAAACAATCCTAAAAT 2237
                          v   -- i  ii      -i    v-  ii   iv--ii          
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTT-GCAGAAATTGACAAGC--TGATCCTAAAAT 145

  chrX_88087846_8   2238 TTGTATAGAAC--CAATAAATCACCTGAATAGCCAATGCAATCCTGATCC 2285
                          ii   i   v--   vii i -- v          vi     i   ---
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACC--CAGAATAGCCAAAACAATCTTGA--- 190

  chrX_88087846_8   2286 AAAA-----ATAAATCTGTAGGCATCACA--------TTACAAAATTGA- 2321
                             ----- i   vi  v   vv     --------  v     i v -
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_88087846_8   2322 ----AATTTATAGTAGCCAAAAAAGCATGCTAATTGTATAAAAATAGATA 2367
                         ----  vi  i    ii   i v  ii  v  v v i    ii     i 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_88087846_8   2368 CAAAGACCAATGGAGTAGAATAGAGAACCTTTAAATAAAGCCCA-ATGGC 2416
                         i v   i       i      v    ii ivv       -    - iivi
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATT 339

  chrX_88087846_8   2417 TACAA-CAACTAATCTTTGACAAAG---CCAAAAACAAAAAACAAAAAAA 2462
                           iii-   i i  i  i     i ---    i v  -------------
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA------------- 376

  chrX_88087846_8   2463 CAAAAAATGTACACTGGAGAAAGGGCACTTTGTTCAATAAATGGTG--GA 2510
                         --------- v  v   i     iii v i v     i        -- i
  L1M4_orf2#LINE/    377 ---------TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_88087846_8   2511 GAAAATTGGATGGCCACATACAGGAAAATGAAACTGGATCCCTATATCTC 2560
                           v  i     i?      i  ii i      ii    i     iv  v 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_88087846_8   2561 ACCACACACAAGGATTAAGTAAAGTTAGATTAAAGGCTTAAACC-----A 2605
                             i i    ii     v v  iv i   i ?  i i    iv-----i
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_88087846_8   2606 TTAAAATTATA---C------AAGAAAACCT-GGGATAAGCTCTTCTGGA 2645
                         i     i    --- ------        v -  ?i   i-     vv  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGA 566

  chrX_88087846_8   2646 CATTGGCCTATGCAAGGAATTTATTAC-TAAGATTTCAAAAGCAAATATA 2694
                          v    vi  v    v i-   v   v-  v  ivi        v vii 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_88087846_8   2695 AGTAAAACAAAAGTAAATAAATTGGACTTAATTAAACTAAAAAGCTTCTG 2744
                          vv   iv    i  i             v  i   v v    i   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_88087846_8   2745 CACAGCAAAAGAAATAATAAACAGAATAAACAGGCAACGTATAGAA-GGG 2793
                         ii vv    i  v iv  v  v i i i  v  i    vi i    -   
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_88087846_8   2794 AGAAAATATTTGCAAACTATACATCC-ACAAGAGGAAAACTAATATTCAG 2842
                                         ii   i   i- i   i ----   vi   i   
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGG----ACTTGTATCCAG 761

  chrX_88087846_8   2843 AATCTACAAGGAAGTTAAAAAAAT-AGGAAGAAAAAAACCAAATAATCCC 2891
                            v  i  i   v ivv v  v - iv  v     i  -      i  v
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCA 810

  chrX_88087846_8   2892 ATGAAAATGTGAGCAAATGACACGAAGGGACATTTTTCCAAAGAAGATAT 2941
                           v?   vi  i     v  ivi   vi       i              
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_88087846_8   2942 ACACATGGCCAACAAACACGCAAAAAAGAAACATATCTCAAAATAATGGG 2991
                            v        i  i   iii    i-----  i-     v  v ????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAG-----ATG-CTCAACATCAZZZZ 904

  chrX_88087846_8   2992 AGCC 2995
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.58 (144 / 91)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 3.03 (94 / 31)  


 588 28.32 4.05 0.58  chrX_88101907_88105829.rev     2206  2378 (1545)    L1M4_orf2#LINE/L1        1   179 (729)  

  chrX_88101907_8   2206 TAAAAAGATAGTTTATGTTCATGGATGGAAGGAATTAATATAGTTAAAGT 2255
                          ii       viii            v i i  v       v     ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88101907_8   2256 GTCCATACTACTCAAAGCAATCTATGAATTTACTGCAATCGCTATCAGAA 2305
                          v v     v i    vii     iii   i vi      v      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88101907_8   2306 TACCAATGACATTCTTCAGAGAATTTTTTAA-------CTATAAATTTAT 2348
                          v   iivi v  i  iiv    v  vvi  -------   -     i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA-AAATTCAT 149

  chrX_88101907_8   2349 ATGGAACCACAAAAGACCTAGAATAGCCAA 2378
                               vii   ii    i           
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAA 179

Transitions / transversions = 1.72 (31 / 18)
Gap_init rate = 0.01 (2 / 179), avg. gap size = 4.00 (8 / 2)  

2265 27.37 2.75 0.41  chrX_88101907_88105829.rev     2706  3432 (491)    L1M4_orf2#LINE/L1      165   908 (0)  

  chrX_88101907_8   2706 ACCTGGTCTAGCCAAAGCTATTCTAAGAAAAAGAAACAAAGCTGAAGGAA 2755
                            ii vv        i v  ii i i   i ii       i  i    v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_88101907_8   2756 TAACATTACCTGACTTCAAATTGTACTACTGAGCTATAGTAACCAAAACA 2805
                          v   i v  ii i      viv      vi     i     i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_88101907_8   2806 CCAAGGTACTGGC-T-----TAGACACATAGACCAATGGAACAGAATAGA 2849
                         viiv         - -----      i     i        i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_88101907_8   2850 GAACCCCAAAACAAACCCACACACTCACAGTGAACTCATTTTT------- 2892
                           ii  vi   i       i   i i ii  v  i v     i-------
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_88101907_8   2893 ---CCAAGAATGTGCACTGAGGAAAAGACAATCTCTTCAATAAATTGTAC 2939
                         ---      vii v  v  i     ii i i   i     i    v  i 
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_88101907_8   2940 TGTGAAAACTGGATTTTCATATGCAGAAGAATGAAAACTGG-CACTTATC 2988
                           v  v        v?i  i     i         i-i   - v i  i 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAG-TTGGACCCCTACC 463

  chrX_88101907_8   2989 TCTAACCACACACAATAATTACCTCAAAGTGGATTAAATATTTAAATCTA 3038
                           vv    i i    v     v      i     i ? v ii     v  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_88101907_8   3039 TGACCCGAACTAATAAACCCACTACAAGCAAACCTCAAGGAAACTTTCCA 3088
                         v  v ii  viv     v ivi  v   v    v vii? v  v i i i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_88101907_8   3089 AGTCATTGGTCTAGGCAACGATATTTTGAGTAACACCCCATAAGCAAAGA 3138
                         v v v    vi       i i v i  iii  vv  v   v     v ii
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_88101907_8   3139 CAACCAAAGCAAAAATAAATGAATAAGATTATATCTAG-TTAAAAAGCTT 3187
                             v    v       i  i   vi  i vi   v i-       -   
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTT 662

  chrX_88101907_8   3188 CTGCGCGGCAAAGGAAACAATCAACAAAGTGAAGAGACAACACAAAAAAT 3237
                         i  i  vv       v  v     v        i       v  v i   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_88101907_8   3238 GGGAGAAAATATTTGCAAACTACCAATGTGACAAGAGATTTATAACTGGA 3287
                                            ii ivv  v   i   i  i  i  v ii  
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_88101907_8   3288 ATATATAAAGAATTCAAACAACTCTATAG-AAAAATATCTAGTTACCTAA 3336
                                     i  vv       v   i-     v - v i v   i  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAA 811

  chrX_88101907_8   3337 TTAAAAAATAGGCAAAT-ATTTCAATAGATATTTCTCAAAATAAGATAAT 3385
                           ?      i      v-    v      i       v   v      vv
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_88101907_8   3386 TAATTGGTAAACAGACATATAAAAAGTTTCTCAACATTACTGATCAT 3432
                         i  v   iv  i ii  i  i     v v        i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (112 / 83)
Gap_init rate = 0.01 (10 / 744), avg. gap size = 2.30 (23 / 10)  


2223 27.47 2.61 4.02  chrX_88182650_88188079.rev     4019  4939 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88182650_8   4019 TGAAGGAACATTCCATGCTCACAGATAGAAAGAATT----TTGTTAAAAT 4064
                           i iii i  i     i   ii   v i    v  ----       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88182650_8   4065 GGCCATACTACCCAAAGCAATTTGTAGATTCAGTTTTATTCTCACTATAC 4114
                            v     v      vii  i ii       iiviv  i ii ii v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88182650_8   4115 TACCATGGAGATTCTTCACAGAACTAGAAAGCAAACT-ATTTTAAAATTC 4163
                          v   vvvivv  i  ii     v v  ---   i  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA---CAAGCTGATCCTAAAATTC 147

  chrX_88182650_8   4164 ACATG-AAACCCAAAAACAGCCCA-AATAGCTAAGGGAATCTTAAGCAAA 4211
                          i   -   iv   iii--i    -      i  iiv      i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGG--ACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_88182650_8   4212 AGGAAAAAAGCTGGAAGCATCACGCTACCCAACCTCAAA-CTAACTACAG 4260
                          i   v    i    i vv    i  v     ii     -  v      i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_88182650_8   4261 GGCTACAGTAACCA--------TGGTACTGGCACAAGAACAGAAACATAG 4302
                         i          i  --------           i   i i   v i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_88182650_8   4303 ACCAATGGAACAGAGTGGAGAA-CCAGAAATAAGACTGCACACCTACAA- 4350
                          i        i   i v    i-          iv iii   ii  iii-
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_88182650_8   4351 CAATCTGATCTTCAACAAAGCTGACAAAAACAAGCAAAGGGGAAAGAATT 4400
                             -    i   i    i v  v   i v  vv   v           v
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_88182650_8   4401 CTGTATTTAAAAAATAGTGCTGGAATAGCTACCTAGCCATATGCAGAAGA 4450
                         v v v  i  v    i       i i i  ivv  ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_88182650_8   4451 TTGAAACTGGACTCTTTCCTCACACCATATAAAAAAAT-AACTCAAGATA 4499
                         v    ii     i i v              v      -       i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_88182650_8   4500 AATTAAAGACTTAAACATAAAATCCAAAACTATAAAAGCCCTT-GAAGAT 4548
                         i  i ?    i    ii   i v i            - i   -     v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chrX_88182650_8   4549 GACCTAGGCA-ATACCATACAGGACATAGGTATGGGCAAAGATTTCAT-G 4596
                         i  v    ?i- v i v - iv   v v  vv i     v i    v - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_88182650_8   4597 ATGAAGACACCAAAAGCAATTGCAGAAAAAGCAAAATTTGATGAATGGGA 4646
                           - v             vvv   iv     v    v v   i   v   
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_88182650_8   4647 TCTAATTAAACTAAAGAGCTTCTACACAGCAAAAAAAAAAAAAAAAAAAA 4696
                         ii v  i   v v  i i   i iii vv    ii v vv vv  i   i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_88182650_8   4697 AAAAAAAAAAAAAACAGTCAACTAAATAATCAGACGATCTACAGAATGGG 4746
                         vi    --------------------------   i i i          
  L1M4_orf2#LINE/    692 TGAAAA--------------------------GACAACCCACAGAATGGG 715

  chrX_88182650_8   4747 ATAAAAGTTTGGCAAACTATGCATCTGACTAAGGTCTAATATCC-TAATT 4795
                          v    vv  v     ii  ii      iv i  v  vi     -v   v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_88182650_8   4796 TGTTATGGAACTTACACAAATGTACAAGAAAAAGA-AAACAACCTCATTT 4844
                          i v -i     ivi    v vv i  v       -   i    iv   ?
  L1M4_orf2#LINE/    766 TATAA-AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_88182650_8   4845 AAAAAGTGGACAAATGACATAAACAGAGACTTTTCAAAAGAAGACATACA 4894
                              -   i    v  iv i  i   v i  i  v        i     
  L1M4_orf2#LINE/    815 AAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_88182650_8   4895 CGTGGAAAACAATCATATGAAATAAAGCTCAGTATCACTAATCAT 4939
                         vi   vv  i  v  i      vi v     ii    ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.65 (61 / 23)  


 858 25.89 1.79 5.06  chrX_88190036_88193157.rev     1346  1681 (1441)    L1M4_orf2#LINE/L1        1   325 (583)  

  chrX_88190036_8   1346 TGGAAAAATATTT--TGTTTATAGATTGGAAGAATCAATATCATTGAAAT 1393
                               i    ii--    i  i          v i     ii  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88190036_8   1394 GTCCATACTACCCAAGACAATTTACAGATACAATGCAACCCCTATCAAAA 1443
                          v v     v     ivii  i       v   i    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88190036_8   1444 TACCAATAACATTCTTCACAGAAATAAAAAAA--AATTATAAAATTCATA 1491
                          v   iivi v  i  ii       vi v  i--i  iv           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_88190036_8   1492 TAGAACCAAGAAAGACCCAGAATAGCCAAAGCCATTCTAAGCAAAAAATG 1541
                          i   viivi ii                 i v  ii i --    i --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGA-- 196

  chrX_88190036_8   1542 ACATAAAATAAAATAAACTACAGGAATTACATTACCTGAGTTTATA--TT 1589
                         ---- i  i   i ---- iv    v i   i v  ii v  i v --  
  L1M4_orf2#LINE/    197 ----AGAACAAAGT----TGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_88190036_8   1590 AAACTACAGAGCTAAAGTAAACAAAACAACAGCATGGTTCTGGCATAAAA 1639
                          --     i     v     v   i   --- ii    v         ii
  L1M4_orf2#LINE/    239 A--CTACAAAGCTACAGTAATCAAGACA---GTGTGGTACTGGCATAAGG 283

  chrX_88190036_8   1640 TAAGACAAATAGACCAAAGGAAGAGAATAGACAACAAAGAAA 1681
                         vv     v     i   v    v     v  v iivv     
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

Transitions / transversions = 1.72 (55 / 32)
Gap_init rate = 0.02 (8 / 325), avg. gap size = 2.88 (23 / 8)  

2022 25.25 0.33 2.51  chrX_88190036_88193157.rev     2034  2631 (491)    L1M4_orf2#LINE/L1      324   908 (0)  

  chrX_88190036_8   2034 AATAAATCCATACACATGCAGTGAACCTATTTTCGACAAAGGTGCCAATA 2083
                               i       iv iii  v  iiv           i        v 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_88190036_8   2084 AAATACACTGAGGAAAAGACAGTCTTTTCAATAAATGGTGCTGGGAAAAC 2133
                         vv  v  v  i     ii i           i              v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_88190036_8   2134 TGGGTATCCATACACATAAGAATAAAACTAGACCTCAATCACTTTTCGTA 2183
                            i  ?   i ii  v      i  ii i    i v i v vivi i  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_88190036_8   2184 TACAAAAATCAAATCAAAATGGATTAAAGACTTAAACCTAAGACCTCGAT 2233
                                  i  v           i ?    i    iv     v  vi v
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_88190036_8   2234 CTATAAAACTACTGCAAGAAAACATTGGGGAAACTCTCAAAAGTC-TGGC 2282
                                   vi iv          v  ? v  v   ------  -  --
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT------TCGTG-- 565

  chrX_88190036_8   2283 AATACATCAGTCTGGGCAAAGATATCTTGAGCAATATCCCACAGGCACGG 2332
                         ---  v ii vi i     v i v    iiii vv iv   v i    ii
  L1M4_orf2#LINE/    566 ---ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_88190036_8   2333 GCAACCAAAGCAAAAAATGGAGAAATGGGATCACAT-GAAGTTAAAAAGC 2381
                              v    -       i  v    v   iiv   -i  i       - 
  L1M4_orf2#LINE/    613 GCAACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-C 660

  chrX_88190036_8   2382 TGCTGCACAGCAAAGGATATGATCAACAAATTGAAGAGGCAACCCACAGA 2431
                          vi  ii vv       i iv     v   v    i  i           
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_88190036_8   2432 ATGGGAGAAAATATTTACAAACTACCCATCTAACAAGGGATTAATAACAA 2481
                                         i    ii ivi    i i      i vi  v v 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_88190036_8   2482 TAATATATATGGCACCTTAATAACTCTATAGAGAAAAAATCGAGTAATCT 2531
                         v        vi v  ii v i     v   - v     iv i i   i i
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATA-ATAAAAAGACAAATAACCC 809

  chrX_88190036_8   2532 GATCCACAAATGGACAAAAAATCTGAATAGTCATTTCTCAAAGGAAGACA 2581
                         i  i? v      i    ii  i       v        v  i     i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_88190036_8   2582 TGCAAATGGAAAACAAGCATATGAAAAAAATGCTCAACATTATTAATCAC 2631
                          i       vv  i     i       i -          i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (89 / 58)
Gap_init rate = 0.01 (8 / 585), avg. gap size = 2.12 (17 / 8)  


 884 29.93 0.66 0.66  chrX_88219192_88225211.rev     4273  4576 (1444)    L1M4_orf2#LINE/L1        1   304 (604)  

  chrX_88219192_8   4273 TGAATAGACATCCTATTTTCATGGACTGGAAGAATTAATATTCTTAAAAG 4322
                           i v   i    i  v        i       v        v    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88219192_8   4323 GAACATTTTACACAAAGCAATATACAAATTCAATAAAATCCCCATTAAAA 4372
                          ivv  vi v v    vii  v    i      iiv      i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88219192_8   4373 TACCAGTAACATTCTTTACAGAAACAGATAAAATAATCTCCAAAATTCTT 4422
                          v    ivi v  i   i      iv  i  iv i   - i       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-CTAAAATTCAT 149

  chrX_88219192_8   4423 -TAGAACAAAAAATGAGCCCATA-TACCTGAAGCAATCTGGAGCAAAAAA 4470
                         - i   - viv  v ii    v -  v ii  i      v  iv  i  i
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_88219192_8   4471 AACAAAGCTGGAGGCAGCACACTAACTGACTTTAAACCATATTACAAGGT 4520
                                i      vvv      vv ii i  i   v v  i     i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_88219192_8   4521 TATAGTAACCAAAACGCCATGGTTTTGTTTTAAAAATAGACCCATAGACC 4570
                           i     i   i  ivii    vi  viv   ii      vi     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_88219192_8   4571 AATGGA 4576
                               
  L1M4_orf2#LINE/    299 AATGGA 304

Transitions / transversions = 1.39 (53 / 38)
Gap_init rate = 0.01 (4 / 304), avg. gap size = 1.00 (4 / 4)  

1935 27.18 1.88 0.00  chrX_88219192_88225211.rev     4945  5529 (491)    L1M4_orf2#LINE/L1      313   908 (0)  

  chrX_88219192_8   4945 GAGCATATAGAAATAAATCCACATATTTACAACTAACTGATCTTGAATAC 4994
                            vi vi         i   i i     iiiii  i    i  vi i v
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_88219192_8   4995 AGTCATCAATCACATACATTGGAGAAAGGCCACTATTTTCAATAAACAGT 5044
                         i viii   vvv   v  v   i     ivi v v       i   ii  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_88219192_8   5045 GCTTGGAAAACTGGATAATCAGATGCAGGAGAATAAATGTGAACCCCTAT 5094
                            v   v         ?i  v     ii     i  vv  i       i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_88219192_8   5095 CTCTCACCATATACAAAAATCAACTCAAAATGTATTAAAGACTTAAATAT 5144
                            v                i           v  i ?    i     i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_88219192_8   5145 AAGAAACAAAGTTAGAAAACTATT-GAAGAAAACATAGGGGGAACACTTC 5193
                             ivi   ii  v      v  -              ? v  vv    
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_88219192_8   5194 AGGACATAGGTCTGGGCAAATATTTTATGGATAAGACTTCAAAAGCATGA 5243
                         iv   v v  vi i     vvi   iv i    v   vi        ii 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_88219192_8   5244 GCAACAGAAACAAAAATAGACAAATCAAATATT-TCAAA-TTAAAAATCT 5291
                               i  iv         i    iii iv i-     -       ii 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_88219192_8   5292 TTA--CAGCAAGGGAAACAATCAACAGAATAAAGAGACTACCTGTAGAAT 5339
                           i-- vv   i   v  v     v i i i  i    v   iii     
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_88219192_8   5340 GATAGAAAGTATTTGCAAACTATTCTTCTGACAATG-ACTAATATCTCAA 5388
                          iv     i          ii  viv     i  v -   vi    ivi 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_88219192_8   5389 ATATACAAGAAGCTC--A-AAC--AATAGCAAAAAATCAAGTAATTTTAT 5433
                              i  ii i   -- -   --    ii     iv   i   iiiv  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_88219192_8   5434 TAAAAAAAGGGCAAAGGACCTGAATAGACATTACTCAAAGGAAGACATAC 5483
                          ?     v          ii            v   v  i     i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_88219192_8   5484 TAGTGACCAACAGCTATATGATATAATGCTCAACATCACTAATCAT 5529
                         v i  i    i ivi i    v vi             ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (97 / 58)
Gap_init rate = 0.01 (8 / 596), avg. gap size = 1.38 (11 / 8)  


2459 24.34 1.02 8.55  chrX_88228107_88232474     2894  3875 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88228107_8   2894 TGTAAACATAGCCCATGCTCATGGCTTGGTAGAATCAACATTGTGAAAAT 2943
                           v   v   v      i      v    v   v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88228107_8   2944 GACCATACTGCAAAAAGGAATCTACGAATTCAATCCTCATTGAATTAGTC 2993
                          i v     v vv   vvi      ii      ---------------- 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA----------------C 84

  chrX_88228107_8   2994 ATCAAAACACCATTGTGATTCTCCATCAAAACACCAATCCTCATTGAATT 3043
                         i-   --------------  i i       ------   i----- ii 
  L1M4_orf2#LINE/     85 G-CAA--------------TCCCTATCAAAA------TCCC-----AGCT 108

  chrX_88228107_8   3044 GGTCATCAAAACACCATTATGATTCTTCACAGAACTAGAAAAGACAGTGC 3093
                          ------------  -------  i  ii     v v  v   viii v 
  L1M4_orf2#LINE/    109 G------------CC-------TTTTTTGCAGAAATTGACAAGCTGATCC 139

  chrX_88228107_8   3094 TGAAATTCATATGGAACCAAAAAAGAGCCTGCATAGCCAAAGTGAGACTA 3143
                          i              viiv  ii  v  v v         iii vvi i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_88228107_8   3144 AGCAAAAAGAAGAAATCTGGAAGAATCACATTTCCCGACTTCAAACTATA 3193
                          iv  i     v   vi    i  v     i     i i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_88228107_8   3194 CTATTAAGGCTATAGTCACCAAAACAGCATGGTATTGGTATAAAAATACA 3243
                            i-  i    i   v i   i    ii     i   i    ii   v 
  L1M4_orf2#LINE/    240 CTAC-AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_88228107_8   3244 CATATAGATTAATGCAAAACAACAGAGAACCCAAATATAAAGCCAAATTC 3293
                                  i    v  v v  iv    ii   i v     v   v ivi
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_88228107_8   3294 TTACAGCCAAGTGAACTTTGACAAAGTGAACAAAAACATAAAGTGAAGAA 3343
                            ii i   v   vi  i     i vviv   i v   vv i  ii   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_88228107_8   3344 CGGACACCCTATTCAACAAATGGTGCTGGGATAATTGTCAAGCCACATGT 3393
                         v i i vi  v                    i  i  vvv ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_88228107_8   3394 AGAAGAATAAAACTGGATCCTCATCTCTCACC-TATTGAAAACTCAACTC 3442
                          i      i  ii    i  ii i   v    -   vv    v i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_88228107_8   3443 AAGATGGATCACAGATTTAAACCTAAGACCTGAAACCATAAATATTCT-A 3491
                           i        ?   ii    iv     v  i    i     - i   - 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTA 537

  chrX_88228107_8   3492 GAAGATGATAAAATTGGAAACACCCTTCTTGGCTTAGCAAAGATTAGGCA 3541
                              vi i v iv? v   i---    v  i i v ---- i       
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTG----GGTTAGGCA 580

  chrX_88228107_8   3542 AAGATTTCATGACCAAGAACAC-AAAAGCAAATGCAACAAAATGCAACAA 3590
                          v i    v iivi v  -   -       v v         ------i 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAA------GA 623

  chrX_88228107_8   3591 AAACATAGATACATAGATGGGACTTAATTAAA-TTAAAAAGCTTCTGTAC 3639
                            v       ----i  v      v  i   -       -   i   i 
  L1M4_orf2#LINE/    624 AAAAATAGATA----AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGC 668

  chrX_88228107_8   3640 AGCAAAAGAAATGATCAGCAGAGTAAACAGACAGCCCACAAAGTAAGAAA 3689
                         vv    i  v iv    iv i   i  v     i      i i ii  i 
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_88228107_8   3690 AAAATCTTTGCAAACTATGTATCTATTAAAGGGCTAATATCCAGAATGTA 3739
                            - v        ii  i     iv   i  i  vi          i  
  L1M4_orf2#LINE/    719 AAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_88228107_8   3740 CAAGGAACTCAAATAA-TCAAGAACAAAA---CAAATGATTCTATCAAAA 3785
                         i  i      vv i  -    v  i    ---     i ii v  i?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_88228107_8   3786 AGTGGGCTAAAACAT--GAGGAGAGAATTATCAAAAGAAGATGTACAAAT 3833
                          i     -   iv  --  iv   v v  v  v         i       
  L1M4_orf2#LINE/    818 AATGGGC-AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_88228107_8   3834 GGCCAACAAGCATATGGAAAAATGCTCAACATCACTAATTAT 3875
                               i     i   i   i             ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.92 (94 / 24)  


2703 24.91 6.93 0.47  chrX_88289379_88291571      850  1700 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_88289379_8    850 GATAAACATCCCATGTTTGTGTATCAAAA---TTGATATCATTAAAATTA 896
                           v i i          ii  v  iii  ---  i    ii    i  vi
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_88289379_8    897 CCATACTACCCAAAGCAATCTACAGATTCAATACAATCCATATCAAAATA 946
                          v     v      vii              ii      v         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_88289379_8    947 CTAAAATCATTTTTCACAGAAATGGAAAAA--AATCCTAAAACTTATATG 994
                          i ivvv v     ii       v  v  i--i         i i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_88289379_8    995 GGAAAACAAG----CCAGAATAGTCAAG-CAATCCTAAGCATAAAGAACA 1039
                          i  vi    ----         i   i-     i i iv vi       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_88289379_8   1040 AAATTGGAGGCATCACAGTACCTGACTTAAAAACAGATTACAAAAATATA 1089
                           i       vv     v v  ii i  v     vv i      iv  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_88289379_8   1090 ATAACCAAAAGAGCATGATATTGGTATAAAAATAGA--TACAGACCAATG 1137
                         i   i   i v  ii  i  i   i    ii     --  i   i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_88289379_8   1138 AAACAGAATAGACGACAGAGAAATAAATCCACATATTTACAGGCAACTGA 1187
                         i  i     v  viiivv         i   i i     ii v   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_88289379_8   1188 TCTTTGACAAAGCTGCCAAGAACATACACTGGGGAAGGAA-AACCTTCTT 1236
                          i  i     i v        v   v  v       i   - ii   -  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-TT 401

  chrX_88289379_8   1237 CCATAAATGGTGCTGGAAAAATTGGATAACCAGATACAGAAGAATGAAAC 1286
                          v i            i v  i      ?   v  i  i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_88289379_8   1287 TGGACCCC-ATCTCTCACCATATACAAAAGTAATCTCAAAATGGACTAAA 1335
                                 - i   v              i v v           ii ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_88289379_8   1336 GACTTAAATGTAAAAGTCAAAACTATAG------CAGTAGAAAACATAGG 1379
                            i         i  ii         i------i  v            
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_88289379_8   1380 GA-ATATGCTTCAGGAA-TTGGTCTAGGCAAAATTTTTATAACTAAGACC 1427
                         ?i- v  -    iv  v-    vi       viv   iv  iv  v   v
  L1M4_orf2#LINE/    552 NGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_88289379_8   1428 TCAAAAGAACAGGTAACAAAAATAAAAACA----AATGGGACTATATTAC 1473
                         i      v   i i       iv     i ----   v     vi  -- 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT--C 648

  chrX_88289379_8   1474 ACAA--AAAAGCTTTGGTTGAGCAGAATAAATTATCATCAGAATGAGGAG 1521
                          v  --    i    v  vvvv  i iv v i     vv i i   ii  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_88289379_8   1522 ACAACCTCTTAAGTAGGAGAAAATGTTTTCAAATTACTTATCCAACAAGG 1571
                               ivivi i i         i   v     i iv    ii i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_88289379_8   1572 GACT------CA-------------------ACAACTAAACAATAAAA-- 1594
                             ------  -------------------      v  i       --
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_88289379_8   1595 -CAAATGCATCAATT--AAAATGGCTATGTGTCACGCATAGACATTTCTC 1641
                         -     ivvi     --       vi viv vivi v             
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_88289379_8   1642 AAAGGAAGACATAAAAATGGCCAACAGGCATATGAAAA-ATGCTCAACAT 1690
                         v  i     i   v          i i   i       -           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_88289379_8   1691 CATTAATCAC 1700
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.58 (128 / 81)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 3.15 (63 / 20)  


 386 31.41 7.69 0.00  chrX_88305780_88308080.rev      615   770 (1531)    L1M4_orf2#LINE/L1        1   168 (740)  

  chrX_88305780_8    615 TGAAGAGATATTTCATATTTATGGATTAGAAAACTCAACATTGTTAAGAT 664
                           i i      ii   i  i       i   i   i  i           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88305780_8    665 GTGAATTTTTCCCAAATTGA----CAA---CAACATGA-----AACAAAA 702
                          vv   vi i          ----  i---    iii ----- v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88305780_8    703 TTTCAGGAAGATATTTTGTGGTTTTTGAAAAATTAATATTAAAGTTGTTA 752
                          ii   vvivv v     ii vvv    v  ii i  vi    i  vv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_88305780_8    753 CGAGATGGCAAAGGACTC 770
                         i ii vv    i    i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCC 168

Transitions / transversions = 1.72 (31 / 18)
Gap_init rate = 0.02 (3 / 168), avg. gap size = 4.00 (12 / 3)  

1739 24.76 4.98 4.58  chrX_88305780_88308080.rev     1072  1814 (487)    L1M4_orf2#LINE/L1      163   908 (0)  

  chrX_88305780_8   1072 GGACTCTTAATAGCCAACAAAATCCTGAAGAAAAAGAAAAAAAATTTGCA 1121
                             i vv         v v    i    i  i     v   i--   v 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG--TTGGA 210

  chrX_88305780_8   1122 GGTATGACA-TACCTAACTTCAGG-CACAGTATAAAGATACTGTAATTAA 1169
                           vv v   - v  i  i    ii- vi v  i    v   v     i  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_88305780_8   1170 GACATT-T--CATTGGTAAAAGAATAGGCATATAGATTAATGGGACATAA 1216
                             v - --i i   i v   i    i         i     i i v  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_88305780_8   1217 TAGAGAATTCAGAAATACACCCATAGAAATATAGTCAATGGGTCTTTGTC 1266
                          v    i i        v       v vv   i      v i i  i --
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG-- 358

  chrX_88305780_8   1267 AAAAAAAAAAAAAAAAAAACAAAGAAAAAACAAAGGAAATTTAATGGAGA 1316
                         ------------------    i ivi--- v   ivv   i     i  
  L1M4_orf2#LINE/    359 ------------------ACAAGGGTG---CCAAGACCATTCAATGGGGA 387

  chrX_88305780_8   1317 GAGAATAAT-TTGTCAACAAATGGTCCTGGAATAATTGGAAATACATTAT 1365
                         i      i -  v            v    i i  i    v ?v  i-  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC-AT 436

  chrX_88305780_8   1366 GTAAGAAAAAAAAAGTAATTTAGGCACAGTCTTTATGCCTTTCACAAAAA 1415
                          i  -  i  vi    ---- i i v vvv i i ii  v vi       
  L1M4_orf2#LINE/    437 GCAA-AAGAATGAAGT----TGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_88305780_8   1416 TTTACTCAAAATGAGTCA--GACCTAAAGGTAAAATGC-AAAACTATAAA 1462
                           v          ii   --        v    i -  -           
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAA 530

  chrX_88305780_8   1463 ACTGATAGAAGAAAACA--AGAGAAAATATAGATGGCCTTTGGTTTTG-G 1509
                            vv            --i ? v    v vvi  i    v    vv -i
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_88305780_8   1510 ATGATTTTTTTAGCTACAACACCAAAAGCAGAATTCATGAAAGAAAAATT 1559
                            i   i  -  v  ii            v  viv ii         v 
  L1M4_orf2#LINE/    581 ATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_88305780_8   1560 -GATAAACTGGACTTTATTAAAATTTAAAATATCTGCTGCAT-AACTTAT 1607
                         -      i       i  i      v    iv i  -   v -  vvv i
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGAC 678

  chrX_88305780_8   1608 GCTCTTCAGACATTGAAAGGAGAAGTTA---AATACTAGAAAA-----AC 1649
                         i  v iv   v v     i  v  vii ---   ivv      -----i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_88305780_8   1650 AA----TATATCTAATAAAGGACATGTGCCAAAAATATACAAAGAATTCT 1695
                           ----       i    i    v   ii v i      i      i   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_88305780_8   1696 TGTAACTGAACAATAAGAA-ACAAGCAACTCAATTAGTAAATAGGCAAAA 1744
                          ii    v  i     i  -    ii   i     ?iv    i      i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_88305780_8   1745 TACT-GTGCAAACATGCCATGAAAGAAGAT--------GGTAAATAAGCA 1785
                         v i - vii i    vi viv         --------  iv        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_88305780_8   1786 AGTGAAAAGATGTTCAA-GTCATATGTAAT 1814
                         vi          i    -i   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (102 / 79)
Gap_init rate = 0.04 (27 / 746), avg. gap size = 2.63 (71 / 27)  


2616 27.46 2.10 1.55  chrX_88310574_88312591.rev      625  1527 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88310574_8    625 TGGAAAAGGCTTCTATGTTCCTGGATTGGAAGAATTAATGCCATTAAAAT 674
                               iivv i i      v            v     iiii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88310574_8    675 GCCCATACTGTCCAAAGCAA-CTACAGATTCAACACTATTCCTATCAAAC 723
                          v v     vi     vii -             i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88310574_8    724 TACCAACATAATTTTTTTTTCACAGAA-TTGGTAAAAACT-ATTCTAAGA 771
                          v   i ---- vii     ii     -   -- v  i  -  i    i 
  L1M4_orf2#LINE/    101 TCCCAGC----TGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAA 144

  chrX_88310574_8    772 TTCACAGAGAAA--CAAAAAACAGCCCAGA-TAGCCAAAGCATTCATGTG 818
                             i vi    --   iii  ---     -        i  v  v  vi
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAA 191

  chrX_88310574_8    819 GAAAAAGATCAAAGCCAGAGGCATCACATCACCCAACTTCAAACTATACT 868
                         i  i    v     iii    vv     iiv     i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_88310574_8    869 ATAAGTCAACAGTAACCAAAATACCATGGTTCTGGTACAAAG-CAGACAC 917
                          i  iv v       i   i i vii    v    i i  i -i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_88310574_8    918 CTAGAACAATGGAAGATAATATATAACCCAGAAATAAAGCTTCACACCTA 967
                         v    v        v v   vv v ii           v ivi   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_88310574_8    968 CATTTATCTCATCTTCAGCA--GTCAATAAAAATAATCAATGAGGAAAGG 1015
                         iiv i vi v  i   ii  -- viivi  i vi v      i      i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_88310574_8   1016 AC--TCCTTGTTCAATAAATAGGGCTGGGATAGCTACA-AGGCATATGCA 1062
                          i--  i  --    i    i v       i i  iv - ?v  i     
  L1M4_orf2#LINE/    392 ATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_88310574_8   1063 AAAGAATTAAACTGGACTCCTACAATTCACCATATACAAAAATAAACTCA 1112
                                v  ii     i     vviv                v      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_88310574_8   1113 AGATGCATGAAAGATTTAAATGTAATACCTCAAAGTATAAGAATCCTAAA 1162
                          i   v  v ?   ii         v v  v   v     i v  i  i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_88310574_8   1163 GCAAAACCTAGGAA-ACACCATTCTGGATATCAGTCTTGGGAAAGAATTT 1211
                         iv     v    ?i- v i -   vv  iv ii vi v  v  v iv  i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_88310574_8   1212 ATGACTAAGTCCTCAAAAGCAAATGCAACAAAACCAAAAAATGGACAAGT 1261
                         v iiv  v v vi        v v         v-       i  i  i 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAAT 637

  chrX_88310574_8   1262 AGGACCT------AATTAAAGAGCTTACGCACAGCAAAAGAAACTATAAA 1305
                         v    i ------       i -   vi ii vv    i  v     v  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_88310574_8   1306 CAGAGTAAAGAGACAACCTACAGAATGGGAGAAAATATTTACAAACTATG 1355
                         v i   i  i        i                     i    ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_88310574_8   1356 CATCTGACAAAGGTCTAATATCCAAAGTCTATAAGTAACTTAAACAACTG 1405
                         i      i  i  v  vi      i i v     iv    ivv      v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_88310574_8   1406 AACAGGCAAAGAATAAATAACCCCATTAAAAAATGGACAAAAGACATAAA 1455
                           i ivv   ii i         v   ?        i    i  iv i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_88310574_8   1456 GAGAAACTTCTCAAAAGAAGACATACAAGTGGTCAACACACATATAAATG 1505
                         v   v i     v        i      i   i   i vi  i  i  vi
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_88310574_8   1506 AATGCTCAACATCACTAATCAT 1527
                         i             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.83 (33 / 18)  


2617 26.36 1.60 4.70  chrX_88325756_88328078.rev      898  1834 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88325756_8    898 TAGAAAGATATTCCATTTCCATAGACTGGCAGAATTAATATTGTTAAAAT 947
                          i         i    v i   i  i   v   v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88325756_8    948 ATGCA-TACTACCAAAAGCAATCTATGGATTCAATGCAATCCCCATAAAT 996
                         i-   -    v  v   vii     ii       i        i  v  v
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_88325756_8    997 ATCCCAATGACATTTTTTCCATA----GAGAAG--AATCCTAAAACTCAA 1040
                               iivi v      v  v ----  v   --i         i   v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_88325756_8   1041 ATGCAACCATAAAATCTGTAGA-TAGTCAAAACAATTTTGGGAAGGAA-- 1087
                            v  viii  iivvivi   -   i         i   ii  i   --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_88325756_8   1088 AGAAATCTGGAGGTATCACACTTTCTCATTTCAAAATATAGAACAAAGTT 1137
                          v   vi      vv        i iv         iv  vv      i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_88325756_8   1138 ACTATAGTTACCACTGTATGGTACTGGCATAAAAATAGACATATAGTCCA 1187
                           vi  i i vv  v  i              ii            vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_88325756_8   1188 ATGGAAGAGAATAGACAGCCAAGAAATAAACTCATGTAGATGCAGTTGCC 1237
                               v     v  v  i v          i   ii vv iii  iivi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_88325756_8   1238 TGACATTTCACAAGGGTGCCAAGGTTACCTAATCAGGAAAATATCACTCT 1287
                            iv  iv              iii iii   vi     iv  - v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT-AGTCT 398

  chrX_88325756_8   1288 ATTCAACAAATTCTGTTGAGAAAAT--AATATTTACATGCAGAAGAATGC 1335
                         v          vv  i  i  v  i--i   ?ii       i       v
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_88325756_8   1336 AATTGAATACTTTTTATTATACCATACACAAAAATTCACTCAAAATGAAT 1385
                          i   i iv i vii- i i      i         v          i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACC-TCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_88325756_8   1386 TAAAAATCTAAACAAAAAACCGGAAATTATAAAGCTACAGTTTTACAGAA 1435
                         i ? i i     iiv  i v vi   i      i  ----i  viv    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT----CTTAGAAGAA 543

  chrX_88325756_8   1436 AATATTGGGAAGAAAAACAGTTCATGACACTGGCCTTGGTAATAATTTTT 1485
                           i  v  ?-- v   v --   i    vi   vi v  i   ii   i 
  L1M4_orf2#LINE/    544 AACATAGGN--GTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_88325756_8   1486 TTGGATATTACACCAAAAGCTCAGACAATGAAAGCAAAGATAAACACATG 1535
                          -i     v           v  ii   ii    v   i   i i v  v
  L1M4_orf2#LINE/    590 T-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_88325756_8   1536 GGACTACATAAGAATAAGAAAGCTTCTGAATAGTAAAGAAAACGGTTAAC 1585
                              v   v i   v i   -   i  viivvi    i v  vi i  v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_88325756_8   1586 AGAATGAAAAGATAACCTAAGGAATGGGAGAAAATATTTGCAAACGATGT 1635
                          i i        i    i vi                       iv  i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_88325756_8   1636 ATC--ATAACAGGACA-ATACTTAAAATGCATAAGTAACTCCTTTAACTC 1682
                            --    -i    v-i  iii i   ii    iv     i vi     
  L1M4_orf2#LINE/    738 ATCTGATAA-GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_88325756_8   1683 AACAGCAAAAAAAAAAAAAAAAAGAACAAAACCAAATAAAACAATTTACT 1732
                           i ii     i -------------------       vv     ? v-
  L1M4_orf2#LINE/    787 AATAATAAAAAGA-------------------CAAATAACCCAATTWAA- 816

  chrX_88325756_8   1733 AGATAGACATCTAATAGATACCTTAATAGTTAGACATTTTTCCAAAGAAG 1782
                          i  i i  ---  -i   ---  i - --         i          
  L1M4_orf2#LINE/    817 AAATGGGCA---AA-GGAT---TTGA-A--TAGACATTTCTCCAAAGAAG 856

  chrX_88325756_8   1783 ACATACAGTTGACCAACAGATATATAAAAAAGTGCTCAATATTGTTGTTA 1832
                          i     iv  i    i iii i  i    ii       i  ii??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_88325756_8   1833 TT 1834
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.83 (157 / 86)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.46 (59 / 24)  


2445 29.88 2.01 0.78  chrX_88339292_88344286     3606  4502 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88339292_8   3606 TGAACGAACATGCTATGCCCATGGAT----AGAATCAATATGATTAAAAT 3651
                           i vii i  v i   ii       ----   v i     vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88339292_8   3652 GAATATACACCCCAAAGCATTCTACAGATTCAATACAATTCTTATGAAAA 3701
                          ivv    v       viiv             ii    i i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88339292_8   3702 TACCAACATCGTTTTTCACAGAGTTAGACAAAACAATTCTAAAATTCATA 3751
                          v   i vv v     ii    iv v     ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_88339292_8   3752 TGGAAA--CAAAGAAGAGCCCAAGATAGCCAAAGCAATCGTAAGCAATAA 3799
                               --   i i ---    ii         i     v i iv  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_88339292_8   3800 GAACAAAGTTGGAAACATCACATTGCCTGACTGCAAACTATGCTACAAGG 3849
                                      iivv     i v  ii i v    viv i      i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_88339292_8   3850 AGATAGTGACCCAAACAGCACTGCACAGGGACAAAAATAGACACATAAAT 3899
                         vv i   i i v i    iiiv i  v  v i  ii       i   i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_88339292_8   3900 CAATAGAATAGAAA-AAGAAACCAGAAATAAAGCCACATACCTACAACTA 3948
                             i        v-i   iv           v   i i ii  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_88339292_8   3949 ACTGATTCTTGACAAAGTAAACACAAGTAAACATTGGGGAAAGGACATCC 3998
                          i     i i     i vviv  vi vi vv  v         i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_88339292_8   3999 TATTCAATAAATGCTTCAGGAAGAACAGGCTAGCTAAATGTTGAATAATG 4048
                          v     i     v v v  i v   v  v  ? i v   ivi  v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_88339292_8   4049 CAACTGGACCATTATCTCCCACTGCATAGAAAAATTAACTCAAGATGGAG 4098
                         v ii      vi  i   v   iii   v              i     v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_88339292_8   4099 TAAAAGTTTACATTTTAGA-CTGGATTCTCAAAAAGTTCTGGAAGAAAAC 4147
                         i ? iiii  v  v v   -  ii v-  vv    v ii i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAAC 546

  chrX_88339292_8   4148 CTAGGAAAATGTCTTCTGGACATTGGCCTAGATAAAGAATTTATGGCTAA 4197
                         v    ?iv vi     vv   v    vi   ii  v iv  iv i v  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_88339292_8   4198 GGCATCAAAGGC-CAGTGCAACAAAAACAAAAATATACAAGTTAAA---- 4242
                          i  i    i  -  i-         iv       v i  i  ii ----
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_88339292_8   4243 ATTAAA--TAAAAGGGCTTCTGCACAACAAAAGACACTAACAACAGACTA 4290
                           i   --     i--   i  ii vv    i       v   v i v i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_88339292_8   4291 AATTGGTAACCTACAGCGTGGAAGAAAATATTTGCAAACTATGAGTCTGA 4340
                           vv ii    i    vi   i                ii  ivi     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_88339292_8   4341 TAAATGACTAATATTCATAATCTATAAGGAATTTAAACAAATCAACACTA 4390
                            iv    vi   i  v   v     i   i ivv    v    i v  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_88339292_8   4391 AGAA-ACCAATAACCTCATCAAATAGTGAGCAA-GGAGATGAACAGACAC 4438
                          i  -  v       iv  i?  v i  i    -   vv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_88339292_8   4439 TTCTC-AAAGAAGACATATAATGAGTCAACAAATATATGAAAAAAGACTC 4487
                              -        i   i  vvi i   i  ii i       i vi   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_88339292_8   4488 AATATTACAAATCAT 4502
                           i  i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (159 / 105)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.79 (25 / 14)  


3238 26.11 1.11 0.66  chrX_88353274_88359550     4881  5784 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88353274_8   4881 TGGAAGAACATTCCATGCTCATAG----GAAGAATCAATATCATGAAAAT 4926
                              ii i  i     i    i ----     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88353274_8   4927 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88353274_8   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_88353274_8   5025 TATGGAACCGAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCCAAAAG 5074
                                vi v  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_88353274_8   5075 AACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTGTACTACAAGGC 5124
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_88353274_8   5125 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5174
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_88353274_8   5175 AATGGAATAGAAC--AGAGTCCTCAGAAATAACGCCGCATATCTACAACT 5222
                                     i--       --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_88353274_8   5223 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_88353274_8   5273 CTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_88353274_8   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5372
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_88353274_8   5373 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_88353274_8   5423 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTCCATGTCTA 5471
                         v    ?i- v i -   iv   v v  vv i     v ii i v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_88353274_8   5472 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5521
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_88353274_8   5522 AT-AAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5570
                           -    i    i -   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_88353274_8   5571 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5620
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_88353274_8   5621 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5670
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_88353274_8   5671 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5720
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_88353274_8   5721 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5770
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_88353274_8   5771 CCATCACTGGCCAT 5784
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (141 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


1276 24.85 4.09 11.25  chrX_88381730_88386090     2891  3868 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88381730_8   2891 TGGAAAAACATCCCATGCTCATGGATACAAAGAATCATTATCTTTAAAAA 2940
                               i i        i        vvi    v i v   iv    i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_88381730_8   2941 TGGCCTTACTGCTCAAAGCAATTTATAGATTCAATGCTATTCCTATTAAA 2990
                             vv    v i    vii  i  i        i  v  i     i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_88381730_8   2991 TTACCAATGACATTCTTCACAGAACTAAACATAAAATCAACCTAAAAGCT 3040
                         v v   iivi v  i  ii     v vi   -- iv v v       -i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACA--AGCTGATCCTAAAA-TT 146

  chrX_88381730_8   3041 CATCAATTGTAGACCGAATAGAGAAAATGT--GGTACATATACACCATGA 3088
                            --------------  i  ---    i--  v  -------   --i
  L1M4_orf2#LINE/    147 CAT--------------ATGGA---AATGCAAGGGAC-------CCA--G 170

  chrX_88381730_8   3089 AATACTATGCAGCCATAAATAGAATGAGATCATGTCCTTTGCAGGAACAT 3138
                             -------    -   i -------   -------   - ii  v v
  L1M4_orf2#LINE/    171 AATA-------GCCA-AAACA-------ATC-------TTG-AAAAAGAA 197

  chrX_88381730_8   3139 GAATGGAGCTGGAGA--TCA---TTATCCATAGCAAA-CTAAC-ACAGGA 3181
                            iii  i     i--   ---  vi v  vv    -  v  -   iii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_88381730_8   3182 --ACAGAAAACCAAATACTGCATGTTCTCACTTATAAGTGGGAGCTAAAT 3229
                         --    v  v v i i v  ii-  v  vi --     ------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTG-GTACTGGC--ATAAG------------ 282

  chrX_88381730_8   3230 GATGAGAACACATAAA-CACATAGAGGGGAACAACAGACACTGGGTCCTA 3278
                            -   -  i   i -  -  i  ivi   ivi-   ------    --
  L1M4_orf2#LINE/    283 GAT-AGA-CATATAGATCA-ATGGAATAGAATTG-AGA------GTCC-- 320

  chrX_88381730_8   3279 TCAGAAGGTGAA-------GGTTGGGAGCAAAAAGTGGATTAGGAAAGAT 3321
                         --    i- i  -------iv  iv iv   ---- v    vvvi ----
  L1M4_orf2#LINE/    321 --AGAAA-TAAACCCATACATTTATGGTCAA----TTGATTTTCGA---- 359

  chrX_88381730_8   3322 ATCTCATGGGTACTAGGCTTAATACCTGGGTGATGAAATAATCTGTACAA 3371
                         ----  v    i i i vii v vvv    -  vii    i   v v   
  L1M4_orf2#LINE/    360 ----CAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTTTTCAA 404

  chrX_88381730_8   3372 CAAATCTCAATGGCATAAGTT--TACCTATAT----AAGAAATCTGCACA 3415
                              vviiv   v i  v v--  ? i i  ----     ---  v -i
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA---TGAA-G 450

  chrX_88381730_8   3416 TTTAACCGTGAACTTA----ATAGTTA-AAAAATTAACTCCAGATG-ATT 3459
                           vi   viv v  i ----   --  -            v i   -  i
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATA--TACAAAAATTAACTCAAAATGGATC 498

  chrX_88381730_8   3460 AAAGACTTAAATGTAAGACTTAAAACCATAAAAACCCTAGAAGAAAACCT 3509
                          ?    i           vi      i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_88381730_8   3510 AGGCAGTA--CCATTCAGGACATAGGCATAGGCAAAGACTTCATGACTAA 3557
                            ?-   --i -   iv   v v  vv       v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_88381730_8   3558 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3607
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_88381730_8   3608 TTAAACTAAACAGCTTCTGCACAGCAAAAGAAACGCTCATCAGGA---TG 3654
                          i   v v  v i   i  ii vv    i  -- i  -    i  ---  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGA--CACT-ATCAAGAAAGTG 693

  chrX_88381730_8   3655 AACATGCAACCTACAAAATGAGAGAAAATTTTTGTAATCTATCCATCTGA 3704
                           v vi     i   i    i        v    i  vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_88381730_8   3705 CAAAGGGCTAATATCCAAAATCTACAATGAACT--TA-AACTTA-CAAGA 3750
                         i  i  i  vi      i   v  i  v     --  -    i -i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_88381730_8   3751 AAAAAACAAACAACCCCATCAAAAAGTGGGAGAAAGCTATGAACAGACAC 3800
                             i     i     v  i?    i    vi  i v v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_88381730_8   3801 TTCTCAAAAGAAGACATTTATGCAGCCAACATACATATGAAAAAAAAAAG 3850
                              v        i  vi viii     i vi  i       i v--- 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT---G 890

  chrX_88381730_8   3851 CTCATCATCACTGGTCAT 3868
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (133 / 106)
Gap_init rate = 0.06 (51 / 908), avg. gap size = 2.94 (150 / 51)  


2751 24.92 3.28 4.04  chrX_88396016_88399116     1694  2608 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88396016_8   1694 TGGAAAGACATTTTGTGTTCATGGATTGAAACACATAATACTGTTAAAAT 1743
                                 i  iiii             i  v  v     i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88396016_8   1744 GCCCATACTGCCCAAAACAATCTACAGATACAATGCTATCCTTATGAAAA 1793
                          v v     v      vii          v   i  v    i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88396016_8   1794 TCTCAATGACATTTT--ATAAAAATAGAAAAA--AATCA-AAAGTTTATA 1838
                           i  iivi v    --ii i    v  v  i--i   v-   i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_88396016_8   1839 TGAAACCACAAGAGACCACAAAGAGCCAAAACAATCTTGA----GAAGAA 1884
                           i  vii    i    vvi  v                 ----      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_88396016_8   1885 CAAAGCTGGAGGTATCATACATTCTGATTTCAAATTATACTGCAGAGCTA 1934
                              i      vv   i  v i ii        viv    i  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_88396016_8   1935 CAGTAATCAAAACAGTATAGTACAGGTGTAAAAACAGACATATAGCCCAG 1984
                                   i     i i    v  ii   ii i          vi  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_88396016_8   1985 TGGAACAAAATGTAGAGCTCAGAAATAAATTCATGAATATATGACTAACT 2034
                              i i   vv    ii          ii   iv  v    iii  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_88396016_8   2035 GATCTTTAGCATAGTTTCCAAGAATACATAATGGGTAGAAGAGAATCTTG 2084
                            i  iii  vi v v      vi ivi      v i ii v i    v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_88396016_8   2085 TCTACAAATAGTATCAGGAAAACTGGACATCCATATG-AAAACAATGAAA 2133
                           v      i  iiii   v       i ?   i   -    v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_88396016_8   2134 TTGAATTCTTAC-----ACCATATACAAACATTTACACAAAATTGATTGA 2178
                            i ii i   -----            v   v  v      v   ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_88396016_8   2179 AGACTTAAATGTAAGACTTGA---CATAAATTTCTTAGAACA---CATAT 2222
                             i           vi i ---i     vi        v ---    v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_88396016_8   2223 GA--AAATAGCTTCTTGACATTGTCTT-TGTGATGTTTTCTTGAATATGA 2269
                          ?--    --    v    v   vv  -v ii   v      ii      
  L1M4_orf2#LINE/    551 GNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_88396016_8   2270 CACAAAAACCATAGGCAATGGAAGCAAAAGTAGTTG----GGATTGCATC 2315
                            v    v  i i    iii   v    i   v i----   i v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_88396016_8   2316 AAA-CTAAAAGCTTCTAGACAGGAAAAGAAATAATAAAAAGAATGAAAAG 2364
                            -i     i   i ivi vvv   i  v iv  v  i i i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_88396016_8   2365 GCAACCTACAGAATAGGAGAAAATGTTTGCAAACAGTATATATGACAAAG 2414
                         i     i       i         i        ivi     v   i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_88396016_8   2415 AGCTAATATGTGAAATATACAAATCATTCACGTGTGTATGTACTTTTTTC 2464
                         ii  vi   viii      i   ---------------- v   i  ---
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAA----------------GAACTCTT--- 779

  chrX_88396016_8   2465 AAAACAAATTAATAGCAATTCAATAGAAAAAATAAAAAATAAATATTAAA 2514
                         ---    v i    --------   -    i i   v  ivv -   ?  
  L1M4_orf2#LINE/    780 ---ACAACTCAATA--------ATA-AAAAGACAAATAACCCA-ATTWAA 816

  chrX_88396016_8   2515 AAGTAGACAAAAGCCTTGTATAGACATTTTTTTCCAAAAAA-ATATACAA 2563
                           i i i    i vi   v          i --     i  -        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCT--CCAAAGAAGATATACAA 864

  chrX_88396016_8   2564 ATGGCTAACAGAGATATAATAAAGAGGCTCCACAACACTACTCAT 2608
                              i  i iiv i  i -     v    v   v  ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGA-AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (143 / 81)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.19 (67 / 21)  


2538 25.57 3.93 4.70  chrX_88405899_88411359.rev     4056  4970 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88405899_8   4056 TGGAAAGTCATTTCATGCTCATGGATTGGAAGAATCAATATTATTAAAAT 4105
                                vi  ii    i               v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88405899_8   4106 GGCCATACTGTCCAAAGCAATTTACAGATTCAACGCTATTCTTATTGAAC 4155
                            v     vi     vii  i              v  i i   ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88405899_8   4156 TATCAAC-ATCATTTCTTCACAGATAGAAAAA--AATATATAAAACTCAT 4202
                          vi  i -ii v   i v  v i  v  v  i--i  vi-     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC-TAAAATTCAT 149

  chrX_88405899_8   4203 GTGGAACCA-AAAATAGCCTGTATAGCCAAAGCAATCCTAAGCAAATAAC 4251
                         i     vii-  iiv v  v v         i     i i iv  iv iv
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_88405899_8   4252 ACAAAGCTAGAGGCTTCACTCTACCTGACTTCGAACTACATTACAATGTT 4301
                               i i    vi    v  v  ii i   i  vivi i     v i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_88405899_8   4302 ACAGTTACCAAAACAGCATGGTACTGGTACAAAAGCAGACACATAGATCA 4351
                              v i   i    ii         i i  iiii     i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_88405899_8   4352 ATGGAACA-AATTATGTAACTCAGAAATAAAGCTGCACACCTACAACCAT 4400
                               i -    iv - iii          v iii   ii  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_88405899_8   4401 CTAATTTTTAACAAAGCTGACAAAAACAAGCAATGGGGATGATAACTCTC 4450
                         i i     ii    i v  v   i v  vv         -i v  ivv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATAGTC 397

  chrX_88405899_8   4451 CATTAATTAAATGGTG-----A----TGGATAATCATATGCAGAAGAATG 4491
                         iv  v vi        ----- ----      ?i  i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_88405899_8   4492 AAATTAGACCCTTTTTTT-CATCATATACAAAAATTAACTCAAGATAGAT 4540
                           i  i     i vii i-  i                     i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_88405899_8   4541 TAAAGATATAAATGTAAGACCTTTAACTATAAAAGTCCTAGAAGAAAATT 4590
                         i ?   iv           v  vv          v  i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_88405899_8   4591 TAGGA-TACACCCTT-----TTTGG--TA---AATAATTTAT-GGTCATG 4628
                             ?-  v i i i-----i    --  ---   ii   v -i vi   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_88405899_8   4629 TCCACAAAACCAATTAA--AACAAAAACAAAAATTGACAAAT--GACT-A 4673
                         v vv     v  --i  --       iv      v  i    --    -v
  L1M4_orf2#LINE/    598 ACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_88405899_8   4674 ATTAAAATGACTAATAAAAAATGACTAATTAAAGAGCTTTTGCACAGCAA 4723
                           i     ------      ----------------      ii vv   
  L1M4_orf2#LINE/    646 ATCAAAAT------TAAAAA----------------CTTTTGTGCTTCAA 673

  chrX_88405899_8   4724 AAAACAAAACAAAACAAAAAAACTAACAACAGAGAAAACAGACAACCTAC 4773
                          ii   ----------------   v   v i  vi  v        i  
  L1M4_orf2#LINE/    674 AGGACA----------------CTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_88405899_8   4774 AGAATGGTAGGAAATGTTTGCAAACTATGCATCTGACAAAGGTCTAATAT 4823
                                v  i    i        ii  ii      i  i  v  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_88405899_8   4824 CCAGAATCTATAAGGAACTTAAACAAATCAACAAGCAAAAACCAAGCAAC 4873
                                v     i     ivv    v    i  vv    iv   ii   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_88405899_8   4874 CCCATTAAAAAGTAGGCAAAAGACCTG----GATACTTCTCAAAGGAAGT 4919
                           v   ?    i i      i  ii  ----  i i     v  i    v
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_88405899_8   4920 CATATAAGTGGCCAGCAAATATTTGAAAAAATGCTCATCATCACTAATCA 4969
                         i   i  i      ii  ii iv      i       v     ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_88405899_8   4970 T 4970
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.84 (149 / 81)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.43 (79 / 23)  


3289 24.58 1.78 0.78  chrX_88431291_88433960     1279  2177 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88431291_8   1279 TGGAA---CATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 1325
                              ---i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88431291_8   1326 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 1375
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88431291_8   1376 TACCA-CTGACTTTCTT-CACGGAATTGGAAAAAAACT-ACTTTAAATTT 1422
                          v   -   v    i  -  - i     --- v  i  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG---ACAAGCTGATCCTAAAATT 146

  chrX_88431291_8   1423 CATATGGAACCAAAAAAGAGCACGCATAGCCAAGACAATCCTAAGCAAAA 1472
                                  viiv  ii  v vv v        i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_88431291_8   1473 ATAACAAAGCTGGAGG---CATGCTACCTGACTTCAAACTATACTACAAG 1519
                          v       i      ---  ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_88431291_8   1520 GCTACAGTAACCAAAACAGCATGGTACTGGTGCCAAAACAGATATATAAA 1569
                                   i   i    ii         iiiv ii i   i     i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_88431291_8   1570 GCAATGGAACAGAACAGA-AGCCTCAGAAATAACACCACACATCTACAAC 1618
                         v        i    iv  -  i -         vv   i    i  iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chrX_88431291_8   1619 CACTTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 1668
                           v     i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_88431291_8   1669 CCTATTTAATAAATGGTGTTGGGAAAACTGACTAGCCATATGTAGAAAGC 1718
                         i  v  i  i        i     v     iv  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_88431291_8   1719 TGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAACTCAAGATGG 1768
                             ii    i    v   i     v  i                i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_88431291_8   1769 ATTAAAGACTTAAATGTAAGATCTAAAGCCATAAAAACCCTAGAAGAAAA 1818
                           i ?    i           v     i i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_88431291_8   1819 CCTAGGCAGTA--CCATTCAGTACATAGGCATGGGCAAAGACTTCATGAC 1866
                          v    ?-   --i -   ivv  v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_88431291_8   1867 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATC 1916
                           vi            vvi          vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_88431291_8   1917 TAATTAAACTAAAGAACTTCTGCACAACAAAAGAAACTATCATCAGAGTG 1966
                          v  i   v v  i     i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_88431291_8   1967 AAGAGACAGCCTACACAATGGGAGAAAATTTTTGCAATCTATTTATCTGA 2016
                           i     i  i   v             v       vii  v       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_88431291_8   2017 CAAAGGGCTAATATCCAGAATCTACAAAGAAATTAAACAAATTTACAA-A 2065
                         i  i  i  vi          v  i      v ivv    v iv i  - 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_88431291_8   2066 AAAAAACAAACAATCCC-TCAAAAAGTGGGCAAAGGATATGAACAGACAC 2114
                             i     i  i  v- i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_88431291_8   2115 TTCTCAAAAGAAGACATTTATGCAGCCAACAG--ACATGAAAAAATGCTC 2162
                              v        i  vi viii     i i--         i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_88431291_8   2163 ATCATCACTGGTCAT 2177
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (131 / 86)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.53 (23 / 15)  


3011 23.07 2.07 3.26  chrX_88455522_88459773.rev     2843  3761 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88455522_8   2843 TGGAAACACATCCCACACTCATGAACGGATAGAATCAATATTGTTAAAAT 2892
                               v i      iii     i iv iv   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88455522_8   2893 GACCATACTGCAAAAAGTAATCTACAAATTCAATGCAATTCCCATCAAAA 2942
                          i v     v vv   v i       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88455522_8   2943 TACCACCAGCATTGTTCACAGAACTAGAAAAAACAATCCTAAAATTCATA 2992
                          v   v v  v  v  ii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_88455522_8   2993 TGGCATATGGACAAAAAAAAAAGCCTTAATAGCCACAGCAA----GACAA 3038
                            v -   --   iii vvv  ----        v i   ----  v  
  L1M4_orf2#LINE/    151 TGGAA-ATG--CAAGGGACCCAG----AATAGCCAAAACAATCTTGAAAA 193

  chrX_88455522_8   3039 AGCAATAATAACAGAACTGGAGGCATCACATTACCCAACTTCAAAAAATA 3088
                           ----  v    i ii      vv     i v     i       vv  
  L1M4_orf2#LINE/    194 AG----AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_88455522_8   3089 CTACAAGTCTATAGTTACCAAAACAACATGGTACTGGCATAAAACCAGGC 3138
                               iv   i   v i   i   iii              iivi  i 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_88455522_8   3139 ACATAGATCATTGGAACAGAATAAAGA-TCACAGAAATAAAGCCAAATAA 3187
                          i        v     i     vi   -  -          v   v i v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACAT 338

  chrX_88455522_8   3188 TTACAGCCAACTGATCTTTGACTAAGCAAACAAAAACATAAAGTGGGGAA 3237
                            ii i   i    i  i   v i vviv   i v   vv i       
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_88455522_8   3238 AGGACACCCTATTCAACAAATGGTGCTGGGATAATTGGCAAACCACACGT 3287
                           i i vi  v                    i  i   vv ?     i i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_88455522_8   3288 ACAAGAACAAAATTGGATCCTCATCTCTCACCTTTTACAAAAATCAACTC 3337
                          v     ii  i     i  ii i   v    v v         i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_88455522_8   3338 AAGATGGACCAAAGACTTAAATCAAATACCTAAAACCATAAAATTTCTAG 3387
                           i     i  ?    i     vv  v v       i      i ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_88455522_8   3388 AAGATAACATCAG---AAATCTTTTATAGACATTGGCTTAGGAAAAGAGT 3434
                             v     vi ---       i-i -   v    v     v  v -  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTC-GT-GACCTTGGGTTAGGCAATG-GT 585

  chrX_88455522_8   3435 TTAT--GACCAAGCACCCAGAAACAAATGCAACAAAAGCAAAGATAGATG 3482
                           v --  ivvii    - i  i  v v          v   i      i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_88455522_8   3483 ----GGACTT-----AAACTAAAAAGCTTCTGCATAGCAAAAGAAATAAT 3523
                         ----      -----   i      -   i  iiivv    i  v iv  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chrX_88455522_8   3524 CAGCAGAGTAAACAGACAACCCACAGAGTGGAAGAATATATTTGCAAACT 3573
                           iv i   i  v              i   i    v           ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_88455522_8   3574 ATGTATCTGACAAAGGACTAATATCCAGGATCTCTGAGGAACTCAAATAA 3623
                           i       i  i     vi       i  v v i i      vv i  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_88455522_8   3624 ATCAGCAAGAAAAAACAAAAAACAGAAAACAAATAATCCCATCAAAAGGT 3673
                         v   ii  v     i-------------        i  v  i?   ii 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAG-------------ACAAATAACCCAATTWAAAAAT 820

  chrX_88455522_8   3674 GGGCAAAGAACATGAATAGAGATTTCTCAAAAGAAGATATACAAATGGCC 3723
                                 i iv        v       v                     
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_88455522_8   3724 AACAAAAAAATGAAAAAATGCTCAACATCAGTAATGAT 3761
                           i  iv v       i             ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (120 / 89)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.88 (49 / 17)  


2581 25.25 3.62 2.12  chrX_88467475_88469266.rev      502  1301 (491)    L1M4_orf2#LINE/L1       97   908 (0)  

  chrX_88467475_8    502 AAAATCCCCAGCCAGTTATTTTGTGGATATTGACAAACTGATTCTAAATT 551
                                 -   iivi v     ii  v        i     i     v 
  L1M4_orf2#LINE/     97 AAAATCCC-AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_88467475_8    552 GTATGTGGAAAAGCAAAAGACCCAGAGGAGACAACGGTACA---CTGAAG 598
                         vi  i      v    ii        iv  v   v---   ---i    i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAA---ACAATCTTGAAA 192

  chrX_88467475_8    599 GAGAAGAA-AAAATAGGAGAACTTACATTAGCTGACTTCAGGACTAATAG 647
                         i       -   i v    i   i   i vv ii i    ii   v ivi
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_88467475_8    648 CTAAGTCAGAATAATCAAGACAGTGTAGTATTGGTAAAATGATAGACATA 697
                          v   ii v i               i   i   i v  v          
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_88467475_8    698 CAGGT---------AGAATAGAGAGCTCTGAAATAGATTCATACAAATAT 738
                         i  i ---------     v     ii v      i ii      vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_88467475_8    739 AGTCAACTGATCCGTGACAAAAATATGTGAATGTGCTTCAGTAGAGAAAG 788
                         i     i    iivi     iii -- iv  viivv    i i i     
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGT--GCCAAGACCATTCAATGGGGAAAG 390

  chrX_88467475_8    789 TATAGACTTTTAAA-AAGTAGTGTTGGAACAA----ACATTCACATGCAA 833
                         v    v     v  -  i i   i   i    ---- i ?i         
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_88467475_8    834 ACAAAAACAAAAACAAATCTAGACACAGATCTTACATCTTTCATAAAAAT 883
                          -------- i  ii  vi i   v vv i  i   i v vi i      
  L1M4_orf2#LINE/    441 A--------AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_88467475_8    884 TAACTTTAG-TGGACCATAAACCTAAATATA-GAAC-AAAACTATTACAC 930
                              iv i-    i  ? i        i  -  i -        v v  
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_88467475_8    931 TTTTAGAAGATAACATAGGAGAAAATCTAGGTGATCTTGGATTTGGCAAT 980
                          i        v        ? v      vv    i     i  v      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_88467475_8    981 GACTTCTTAGCTACAACACCAAAAGCAAAATCCATAAAATAAAAAATATA 1030
                          ii       v  ii            v  v v i    v        v 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_88467475_8   1031 TATAGTTGAGCTTTATTTAAATTAAAAACTTCTG--CTCTGAAAAATAC- 1077
                           - i   ii   i  iv             i  --  iii  ii i  -
  L1M4_orf2#LINE/    633 TA-AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_88467475_8   1078 ---AAGAGAATGAAAAGATAAGCCACAGAGTGGGAGAAAATCTTTTCAAA 1124
                         ---    i i        i  v       i           v   v    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_88467475_8   1125 GGACATACCTGATAAAGGACTGGTATTCA-AATGCACATAATAAACTATT 1173
                         vv i   i       i     v    i  -   -- i    vi    v  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAAT--ATATAAAGAACTCTT 779

  chrX_88467475_8   1174 TGAACTTAAAGATAAGAACACAAACGACCTAATTAACACATTAGCAAAAC 1223
                         vv    i  vi    i  v     ii   i    ? v v  vi     iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_88467475_8   1224 ATGTGG-CAGGCACCTGACCAAAGAAGACACATAAATGGCAAATAAGCCT 1272
                           v  i-i  i  ii vv          i i i       v       vi
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_88467475_8   1273 ATGAAAAGGTGTTCAGCAACATATGCTAT 1301
                                 i  i   i  v  ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (125 / 73)
Gap_init rate = 0.02 (18 / 812), avg. gap size = 2.56 (46 / 18)  


2322 28.00 3.09 2.98  chrX_88474555_88476559      606  1512 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88474555_8    606 TGGAAAAATAATATTACATGCTCATGAATAGGAAGCATCAATATTGCTTA 655
                               i   --- iv    i     i  v     vv i       i v 
  L1M4_orf2#LINE/      1 TGGAAAGATA---TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chrX_88474555_8    656 AATGGCCATACCACCGAAAGCAATTTACAGATCCAAAGTTATTCCTGTCC 705
                         i     v    iv  v   vii  i       i   v iv  i   i  v
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_88474555_8    706 AAGTACCAACATCATTCTTCACAGTATTGGAAAAATCTATGATAAACTTC 755
                           i v   i vv v  i  ii   v v v  v  iiiv  vv    v   
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_88474555_8    756 ATATGGAACCCCCGCCCCCCAAAAAAAGTGCA-AATAGCCAAAGCAGTCC 804
                                 vi---  -------  iiiiiv  -          i  i  i
  L1M4_orf2#LINE/    148 ATATGGAAAT---GC-------AAGGGACCCAGAATAGCCAAAACAATCT 187

  chrX_88474555_8    805 TAAGGAAAAAGAACAGA--CAGAAGAATCACACTACCAAACTGCAAACTA 852
                          i ii  i       i --ii  i  v       v  v  i v    viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_88474555_8    853 TGCTACAAGGCTACAATAACCGAAACATCATGATACTGATACAACATATA 902
                          i      i      i   i i i   vii  i     ii i  vi-   
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATA 286

  chrX_88474555_8    903 GACACATAGACCATTGGAACAGGTTACAGAACCCAGAAATGAAGCTATTC 952
                             i     i  v     i  iv vv   ii        i  v i  v 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_88474555_8    953 ATCTACCAACCACCTGATCTTCAGCAAATTTGGCAACAATACATGATGGG 1002
                           i  i-iii  vi    i   ii   ivv  v   v vi ivii     
  L1M4_orf2#LINE/    337 ATTTAT-GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_88474555_8   1003 CAAAAGGCTCCATAGTC-----AATAAATTGTGCTGGGATAACTGGCTAG 1047
                         -i    i----      -----  i    v         i      v  ?
  L1M4_orf2#LINE/    386 -GAAAGA----ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_88474555_8   1048 TCATATGCAGAAGACTGACTCTAAACCCTTTCCATTCACCATATGCAAAG 1097
                         i  i     i    v   vvi ii    i v  viv        i    i
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_88474555_8   1098 ATTAATTCAAGATGGGTTAAAAAACTTAAATGTAAGACCTAAAAC---AA 1144
                              i    i    i i ? i - i           v       ---  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGA-CCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_88474555_8   1145 AACCC--AGGAGAAAATCTAGG---AAATACCATTCTGAATATCAATTTT 1189
                            i --  i      iv    ---    -- -   vvi iv iiiv  v
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTA 576

  chrX_88474555_8   1190 GGCAAAGAAATTCT--GATTAAGTCCTCAAAAGCAATTACAACCAAAACA 1237
                              v iv-    --   - v v vi        vvvi    v   iv 
  L1M4_orf2#LINE/    577 GGCAATGGT-TTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_88474555_8   1238 AAATTTGACAAGTAGGACCT------AATTAAAGAGGTTTTGCCCAACAA 1281
                            v v  i  i v    i ------       i v-     iv vv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAA 673

  chrX_88474555_8   1282 AGGAGACTATCAACAGATTAAACAGACAACCTAAATAATGGGAGAAAATA 1331
                             v        v i v i  v        i v v              
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_88474555_8   1332 TTCATAAGCTATGCATCTAAGAAAGGTCTAATATCCAGAATCTATAAGAA 1381
                           iii  iii  ii    i v  i  v  vi          v     ii 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_88474555_8   1382 ACTTAAATAATTCAGGAACAAAAA-AGAAATATCTTTATT-AAAAATGGG 1429
                            ivv i  i   iv  i     - v     v iiv   -         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_88474555_8   1430 CAAAAGAC--AAACAGACGCTTCTCCAAAGAAGACATATATGTGGTCAAC 1477
                             i  i--i  i    ii              i   i vi   i   i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_88474555_8   1478 AAATTTATGAAATAATGTTCATCATCACTAATCAG 1512
                           iivi      vi   i   v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (153 / 99)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.29 (55 / 24)  


1465 28.94 0.80 1.00  chrX_88490736_88493107.rev        4   504 (1868)    L1M4_orf2#LINE/L1      169   668 (240)  

  chrX_88490736_8      4 AGAA-AAACAAAACAAACAAACAAACAAAAAACATTAAAGCTGGAAGCAT 52
                             - iv        v vviv   vi  i    ---   i    i vv 
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACA---AAGTTGGAGGACT 215

  chrX_88490736_8     53 TACATTACTGAACTTCAAACTATACTACAAGGCTACAGTAACCAAAATAG 102
                         i   i v iv  i      viv        i          i   i i  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_88490736_8    103 CGTGGAAGTGGTACAAAAACAGACACATAGATCAATGGAACAGAATAGAG 152
                         i    v v   i i  ii i     i              i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_88490736_8    153 AGCCCAGAAATAAAGCCACACGCCTACAACCATCTGTTCTTTGAAAATGT 202
                           i           v   i  iii  iiii  vi  v i  i  v  v v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_88490736_8    203 CAACAAAAAAAGGCAGTGGGAAAAGGCCTCCCTATTTAATAAATGGAGCT 252
                         iiv   i vv vv  i    i    ivivvi  v  i  i      v   
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_88490736_8    253 GGGATAGCTGGCTAGTCATATGCAGATGATTGAAAGTGAACCACTTTCTT 302
                             i i    v  ?i  i     i v  v    iv  i   v  vi  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_88490736_8    303 ACACCATATACAAAAATCAACTCAAGATT-ATTAAAGACATAAATGTAAA 351
                                          i       i  v-  i ?    v         i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_88490736_8    352 ACCTAAAATTATAAAAACCTTTGAAGAAAACCCAGGA--AAATCCATTCT 399
                          v      i       vi   v         vi   ?--     --   v
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC--TTCG 563

  chrX_88490736_8    400 AGACATAAGCCTTGACAAAGATTTTATGACAATGATGCCAAAAGCAATTG 449
                         v   v vi vi v i   v i   iv iivv    ii         vvv 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_88490736_8    450 CAACAGAAAGAAAAATTGACAAATGGGACCTAATTAAACTAAATAGCTTC 499
                              i  ii      v  i    v    i v  i   v v  v i   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_88490736_8    500 TGCAC 504
                           ii 
  L1M4_orf2#LINE/    664 TGTGC 668

Transitions / transversions = 1.29 (80 / 62)
Gap_init rate = 0.01 (5 / 500), avg. gap size = 1.80 (9 / 5)  

2424 28.01 3.46 2.12  chrX_88490736_88493107.rev      986  1881 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88490736_8    986 TGGAAAAACACTCCAAGCTCAGGGATAGGAAGAATCAATATTTTTAAAAT 1035
                               i i ii   v i   v    v      v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88490736_8   1036 GGCCACAAGAATGACCCGAGCAATTTACAGATTCAGTGCTACTCCTATCA 1085
                            ---  v v vv  vi vii  i          ii  v ii       
  L1M4_orf2#LINE/     51 GGC---AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_88490736_8   1086 AATTATTAA-TGCCATTCTTCACATAATCAGAAAAATCTTTTTTAAAATT 1134
                           v vii i-    -  i  ii  v  viv  v  iiivv ii       
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_88490736_8   1135 CACGTGGAA---CAAAA-ATATAACAAACATCCAAAGCAATCCTAAGCAA 1180
                           ii     ---   ii- ivi i--  i v     i     i i iv  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAG--AATAGCCAAAACAATCTTGAAAAA 194

  chrX_88490736_8   1181 AAAGAAAAAAGCTGGAAGCATCATAACATCCAACTTCACACTATAGTGCC 1230
                         i     v    i    i vv   i vivi    i    v viv  v i v
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_88490736_8   1231 AGGGTAAAATAACTAAAATAGCATGGTACTGGTACAGAGATGGGCACATA 1280
                          i v  v i   ii  i i  ii         i i ii   i i  i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_88490736_8   1281 GATCAATAGGAAAGGAT-GAAAGGCCACAAATAAAGCCACACACCTAAAA 1329
                                i i v  i  -  i  v   v       v   i   ii  vii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_88490736_8   1330 ACATCTGATCTTCGACAAAACTGACAAAAACAAGCAATTGGGAAAGAATC 1379
                         v  vi    i        iiv  v   i v  vv    v          v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_88490736_8   1380 -CCCATTCAATGAATGGTGCTGGGATAGCTGGCTTGCCATATGCAGAATG 1428
                         -i iv     ii             i i    v v?   i     i  vi
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_88490736_8   1429 TTGAAATGGGACTCCTTCCTTATACCCTATACAAAAATCAACTCAAGATA 1478
                         v    i v    i   v   i i   v           i       i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_88490736_8   1479 GCTTGAAGACTTAAATGTAAAACCTAAAGCTATAAAAACTATAGAGGAAG 1528
                          v ii?    i         i v     i        viiv    i   i
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_88490736_8   1529 ACCTATG---AAAT------GCCATTC--TTAGACATTGGCCCTTGCTCA 1567
                           v  v ---    ------ v v  v--    i  v   ---  v  i 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG---TTTCTTA 591

  chrX_88490736_8   1568 GAAATCATGATGCAGCCTCCAAAGGTAATTTCAACAAAAACAAAAAATTG 1617
                           ---i    --  ----     i i vvvv        i-       v 
  L1M4_orf2#LINE/    592 GA---TATGA--CA----CCAAAAGCACAAGCAACAAAAG-AAAAAATAG 631

  chrX_88490736_8   1618 ACAAATCGGACCTAATCAATCTAAAGAGCTTCTGCAAAACAAAAGAAACT 1667
                          i    i    i v     vv v  i i   i  iivvv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_88490736_8   1668 ATCAG---AGTAAACAGACAACCTACAATATGGGTGAAAATATTTGGAAA 1714
                             i---   i  v        i   iv     v           v   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_88490736_8   1715 CTGTGCATCCAGCAGAAGTCTAATATCCAGAATCTAGAAGGAACTC---- 1760
                         iii ii   iiii iii v  vi          v  v  i      ----
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_88490736_8   1761 AAGTCAACAAGCAAAA-----ATAATCCCATGTAAAAATGGGCAAAG-AC 1804
                           v    i  vv    -----    i  v  v?              - i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_88490736_8   1805 ATGAACAGACAATTTTCAAAAGAAGATACACACGTGGCTATCAAGCATAT 1854
                         v    i     v  i  v          i   vi    i vi     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_88490736_8   1855 GGAAAAATGTTCAATATCACAAATCAT 1881
                          i   i   i    i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.50 (50 / 20)  


 452 34.80 9.77 3.85  chrX_88510262_88511981.rev      495  1221 (499)    L1M4_orf2#LINE/L1      125   894 (14)  

  chrX_88510262_8    495 TTAACTGAAGTCAATCCTGAAATTTTAAATGGAAGTACAGTCAAGGAACC 544
                           i  --   iii     i     i- v      i i  --- i   v  
  L1M4_orf2#LINE/    125 TTGAC--AAGCTGATCCTAAAATTC-ATATGGAAATGCA---AGGGACCC 168

  chrX_88510262_8    545 AAAG--GCCAAAGAGCCAAGTGTAACCCAGAAGAAATAAGATATGAAAAT 592
                          i i--      i---   viv i vvv       vv   v i-  ii i
  L1M4_orf2#LINE/    169 AGAATAGCCAAAA---CAATCTTGAAAAAGAAGAACAAAGTTG-GAGGAC 214

  chrX_88510262_8    593 TTGC---TACAGCAGTGATTAAAATTTACTATCAAACAATTGCAATTAAC 639
                          ii --- v --  i v- i    i      iv  i v iv i   i  v
  L1M4_orf2#LINE/    215 TCACACTTCC--CAATT-TCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_88510262_8    640 ACTGCATGGTGTGAGTGCAAGGATTGA-----AAGCTAAT--AACACGTT 682
                           v ii    iivi iii      v  ----- iiii   --  i viv 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_88510262_8    683 AGAGAGTCAGGAAATACACCTGCAAAAATATGAACACCAGATATTGTATA 732
                         v       vi      v   iii v vv    iv  viv   v  vv i 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_88510262_8    733 GAGGTA-------------------AAAGTATAGACTAGTCAGTCAGTGG 763
                         ii   i-------------------    v    v  vv   iiv i   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_88510262_8    764 CCCTGAGATAAGTATTTATCCAGAAACTATAAAGCAAGCAAAATAGTGTA 813
                         iv   i  i  v ivv  ?   v --- ii   iv  -ii  i --  v 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACA---TGCAAAAGAA-TGAAGT--TGGA 455

  chrX_88510262_8    814 TCCGT----CATGACATATGCAAAAGTTAATTTCCAGTATATCAGAGACT 859
                         i  v ----  iiv     i     i    i ivv i iv    ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_88510262_8    860 TAAATATGAAAGGCAAATTTAAATAATTTTTTCAGGAATATAAATGGAGG 909
                              i i i  vi   vi  v v  i i  vv i   v i -- i i? 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA--TAGGNG 553

  chrX_88510262_8    910 TA--TTTTTCTGATATA----TAGATAAT----TTTTAAGAGAAATAACA 949
                           -- i  iv   iv v----   ii   ---- i   ---  v  i   
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA---GATATGACA 600

  chrX_88510262_8    950 TACTTAAGTAAAAGAAACTA--GTAAGTATTGATAAATTAATCTATTTTG 997
                         i- vv   i v   v   v -- v  iv  v        iiv  viv ii
  L1M4_orf2#LINE/    601 C-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_88510262_8    998 AA-TTGTGGACTTTTCATCATCAAAAGATGCCAT-----------AAAAA 1035
                           -  ivii      vvv v     i  ii i  -----------   i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_88510262_8   1036 TAATTTTCACTCTGAGAGCAGATCTTTGCAA--CATAAAAAACCAGTGTA 1083
                         i  iiiv  vvv  i   v i  v       --    v v-- iii ivi
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT--CTGATAAG 747

  chrX_88510262_8   1084 GGATTAATGTCCATAACATATTAAGAAATTCATATAAACCAA-AAT---- 1128
                            i vi i    v  i    v     -i  v  i  vi   -   ----
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATAATAAAA 796

  chrX_88510262_8   1129 -GTCAAACCACCCAATTAAACTGCAGGCAAAAGATGCAAACAAGTATTTT 1177
                         - v    iv        ?  vviii      i   vii  i iii    i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_88510262_8   1178 ATGGAAGAGAAAATCTGAATAGC-AATAA-CATAT--AAAGGTGATCA 1221
                         vivi    ii v  vii   i  -     -  i  --    i  v   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.04 (33 / 770), avg. gap size = 3.00 (99 / 33)  


3243 26.21 2.60 0.34  chrX_88553819_88556792.rev     1599  2483 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_88553819_8   1599 AAAAATCATCTATACTAATGAACTAAAAAACC-AATATTATTAAAAT--- 1644
                            i  vvi i  ii v   i i ii  i  i-      i    i  ---
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_88553819_8   1645 -ATACATATTACCAAAGCAATCTGCAGATTCAATGCAATGCCTATCAAAA 1693
                         -    --- iv     vii    i         i     v          
  L1M4_orf2#LINE/     54 AATAC---TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88553819_8   1694 TACCAATGACATTCTTCACAGAATTAGAAAAAATG---TTAAAATTTATG 1740
                          v   iivi v  i  ii     v v  v  iv  ---i       i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_88553819_8   1741 TGGAACCACAAAAGACCCAGTATAGCCAAAGCTGTCCTAAGCAAAAAGGA 1790
                              vii   ii       v         i vi  i i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_88553819_8   1791 CAAAACTGGAGGAATTACATTACCTGACTTCAAATGGTACTACAGAGCTA 1840
                             ii       v i   i v  ii i      vvv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_88553819_8   1841 TAGTAACCAAAACAACTTGGTACTGATATAAAAACAGACACATAGACCAA 1890
                         i     i   i   iiv        ii    ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_88553819_8   1891 TGGAACAGAATAGAGAACACAGAAACAAATTTATACACCCACAGTGAATT 1940
                              i     v    iiv      i   iii     iii ii  v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_88553819_8   1941 CATTTTTGACAAAGATGCCAAGAATATACATAGGGGAAAAGATAATCTCA 1990
                         v     i     i i        vi  v  vv       ii   i   iv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_88553819_8   1991 TCAATAAATGGTGCTGGGAAAACTGGATATTCATAGATAAAAGAATAAAA 2040
                             i              v         ?i  i vii        i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_88553819_8   2041 CTAGGCCCTTATTTTTCACTATATA--AAAATTAAATCAAAATAGATTAA 2088
                         i i i   i  ii iv   i     --        v       i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_88553819_8   2089 AGACTCTAATATAAGATCTCAAACTATGAAACTCCTGCAAGGAAATATTG 2138
                             iiv   i     v  v       i      i iv   i   i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_88553819_8   2139 CGGAAAGTCTCCCGGACATTGGTCTGGGCAAAGATTTCT--------ACA 2180
                         v? v  i   i vv   v    vi i     v i     --------   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_88553819_8   2181 -----AGCACAGGTAAGCAAACCAAACATGGACAAATGGAATCACATCAA 2225
                         -----      i i  vv   vv   v  i  i    v i iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_88553819_8   2226 ATTGAAAAGCTTCTGCACAGCAAAAAAAACAATTAACAAAGTGAAGAGAC 2275
                          v v    i   i  ii vv    ii v  v  i  v        i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_88553819_8   2276 AATCCACAGAATAGGAGAAAATATTTGCAAACTACCCATCTGACAAGGGA 2325
                           i         i                  ii ivi      i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_88553819_8   2326 TTAATAACCAGAATATATAAGGAACTCAAACAACTCTATAGGAAAAAATC 2375
                         i vi  v             i      vv       v   iv     iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_88553819_8   2376 TGATAAACTGATTTAAAAATAGGCAAAAGATTTTAATAGTCTTTTCTCAG 2425
                         vi    v ii   ?      i      i     v     v v      vi
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_88553819_8   2426 AGAAAGACATACAAATGGCAAACAGGCATATGAAAAGGTGTTCAACATTA 2475
                          ii    i           v  i i   i        i  i       i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_88553819_8   2476 CTGCACAT 2483
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.96 (151 / 77)
Gap_init rate = 0.01 (7 / 905), avg. gap size = 3.71 (26 / 7)  


2697 27.84 2.23 1.11  chrX_88580930_88585847.rev     3530  4427 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88580930_8   3530 TGGAAA-ACATTTCATGCTCATGGACAGGAAGACTCAATATTGTTGAAAT 3578
                               - i  ii    i       iv        i         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88580930_8   3579 AATCATACTGCCCAAAGCAATTTATGGATTCAATGCTATTCCTTATCAAA 3628
                         iiiv     v      vii  i  ii       i  v  i   -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT-ATCAAA 99

  chrX_88580930_8   3629 CTGCCAATGATATTCATTACAGAATTAGAAAACCTT-TTGTAAAATGTGT 3677
                         v v   iiviiv  iv  i     v v  v  v  v- iv      vii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_88580930_8   3678 ATGGAACCA-AAAAGAGCCAGAATAGCCAAAGTAATCCTAAGAAAAATGA 3726
                               vii-  ii  v              ii    i i i   i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_88580930_8   3727 AGAAAGTTGGAGAAATCACATTACCCAGCTTCAAACTATAATACAAGGCT 3776
                          v          i v     i v    ii      viv  v     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_88580930_8   3777 ACAGTAACCAGAACAGCATGGTACTTGTTGAAAAATAGGCACACAGACTA 3826
                                i  ii    ii       v ivv  ii    i  i i   ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_88580930_8   3827 ATTGAACAGAATAGAGAGCCTAGAAATAAAGCAGCGTATCTACAACCATC 3876
                           v   i     v     i i         v viiii  i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_88580930_8   3877 TGATCTTCAAAAAATTTGGCAAAAAAAAAAGCAACAGGGAAAACACTCCC 3926
                             i   i v  ivv  v   i vv v--v   ii      iv ivvi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAATAGTC 397

  chrX_88580930_8   3927 TATTTAATAAGTGGTGATGTAATAACTGGCTAGCCATAAGCAGAAGATTA 3976
                          v  i  i  i     v  vi i      v  ?   i v   i    v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_88580930_8   3977 AAACTGGACTAATTCCTTGTGTCATATACAAAAATCAACTCCAGATGAAT 4026
                           ii     ivv v   iiiii             i     v i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_88580930_8   4027 CAAAGACTTAAATGTAAAACCTAAAACTATAAAATCATTGGAATATAAGT 4076
                           ?    i         i v              iiv  i   v v  vv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_88580930_8   4077 TAGGCA-ATATCTTGTTCATAGGACCT-------GGCAAAGATTCATAAT 4118
                             ?i- v     --- i --     -------     v i  iv -- 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTT---CGT--GACCTTGGGTTAGGCAATGGTTTCT--T 590

  chrX_88580930_8   4119 AAAGATGGCA---AAAGCAATTGCATCAGAAACATAAATTGACAAGTGGG 4165
                          i v   i  ---      vvv   v  i  iv v    v  i  i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_88580930_8   4166 ACCTAATTAAA-TTAAGAGCCTCTATATTACAAAATAAACTATCAACACA 4214
                           i v  i   -    i i i i i ii v    iv v        v v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_88580930_8   4215 GTAAACAGACAACCTACCAAATGGGAGAAAATATTTGCAAACTATGTGTC 4264
                           i  v        i  vi                      ii  i i  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_88580930_8   4265 TGCTGATGGTCTAGTAGCCGGAATCTATAAGAAACTA--ACAAATTAACA 4312
                           v i v  v  v   v  i    v     ii    v--    v i  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_88580930_8   4313 AACAAAAAAGAAATAACCCCATT-AAAAATGAGCAAAGAACATTAACAGA 4361
                          vv    i v         v   -       i      i iv v  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_88580930_8   4362 CACTTTTC-AAAGAAAACTTACATGCAGCCAAAAAGCACATAAAAA-ATG 4409
                           i  i  -      i iv    viii     v        i    -   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_88580930_8   4410 CTCAAAATCACTATTTGT 4427
                              v    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  

 282 24.47 1.06 2.13  chrX_88580930_88585847.rev     4823  4916 (2)    L1M4_orf2#LINE/L1      489   581 (327)  

  chrX_88580930_8   4823 AGAATGAGTTTACAGACTTAAACATAAGACCTAAAACCATAAATATCCTA 4872
                          i    - v i ?    i    ii     v       i     vv  i  
  L1M4_orf2#LINE/    489 AAAATG-GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_88580930_8   4873 GAAGAAAACTTAGGC-TATACCATTCAGGACATAGGCATGGGCAA 4916
                                  v    ?-  v i -   iv   v v  vv i     
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA 581

Transitions / transversions = 0.91 (10 / 11)
Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.00 (3 / 3)  


2748 25.87 2.67 1.16  chrX_88669267_88671275      656  1517 (492)    L1M4_orf2#LINE/L1        1   875 (33)  

  chrX_88669267_8    656 TAAAAAGACAATCTATGTTCATGAATTGGAAGAACTGATACTGTCAATAT 705
                          ii     i vi i         i         vi i   i   i  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88669267_8    706 GACCATACTACCCAAAGGAAGCTACAGACAGAATGCAGTTTCTATCAGAA 755
                          i v     v      vvi v       ivv  i   i ii      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88669267_8    756 TACCCATTAACATTATT-CAAAGATAAAAAAA---ATCCAAAAATTTGTA 801
                          v  vii iv v  v  -  i i  vi v  i---    v      ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_88669267_8    802 TGGAACCACAAAATGACCACAAATAATCAAAGCAATCCTGAGAAA-AAGA 850
                              vii   ii-    vvi    ii    i     i   i   -    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_88669267_8    851 ACATCCT--GATG--TCACACCACCTGACATCAAAATATGCTACAAACTT 896
                            vvv --  v --      iv  ii iv      iv i       vi 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_88669267_8    897 ATAGTAACTAAAACTACATG-TACTGGTATAAAAACAGACACTTCAACCA 945
                          i     ii  i  viii  -      i    ii i     iv vi i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_88669267_8    946 ATGGAACAGAATAGAGAGCCCAGAAATAAATCTGTGCATTTACAGTTAAT 995
                               i     v     i           i ii i      ii  i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_88669267_8    996 TACTTTTCAACAAAGGAACCAGAAACATACATTGATAAAATAAAAGCCTG 1045
                          iv     i    i  vi   ii v   v  v  ivi   v  v  i  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_88669267_8   1046 TTCAATAAATGATGCTCAGAAAACTAGATATCCATATGCAGAAGAATAAA 1095
                              i     i    vi  v    i    ?   i     i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_88669267_8   1096 AATAAACCCTTACCTCTCACTATATGCAATAACTAGATTAAAATGATTTA 1145
                         iv ii    i      v   i    i   v  i  iv i      iv i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_88669267_8   1146 AAAACTCAAACGTAAGACCCAAAACTATAATTCTACTAGAAGAAAACATA 1195
                         ? i  ii   i      v i          vv  vi              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_88669267_8   1196 GG-GTAAATGTTTCAGGACATTTGTGTGGGCAAAGAGTTTATAGATAAGA 1244
                           -      -i   iv   v  v vv i     v iv  iv      v  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_88669267_8   1245 CTTCAAAAGCACAAACAACAAAAGCAAAAATAGACAAATAATAAGATATC 1294
                          vi           i         v         i    viv vvvi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_88669267_8   1295 AAA-CTAAAAACTT-----CTTCACAGGAAACAAAAATCACCAGAGTGAA 1338
                            -i         -----     v    v  v ---   vv i      
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTA---TCAAGAAAGTGAA 695

  chrX_88669267_8   1339 GGGATGATCTGCAGAATGGGAGAAAATATATGCAAACTATTCATCTGATA 1388
                         ii  ii i ii                  v      ii  vi        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_88669267_8   1389 AGGGATTAATATCCAGAATATACAAAGAACTC----AACTCC-CAACACC 1433
                              i vi             i         ----     v-i  i vv
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_88669267_8   1434 AAAACACAATAATC-AATTTACAAAATGGGAAAATTATCTGAATAGATAT 1482
                           i   -     i -    ? -        v   vv  i        i  
  L1M4_orf2#LINE/    796 AAGACA-AATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_88669267_8   1483 TCCACAAAAGAAGGCATACAAATGGCTTTAAATAA 1517
                          i v v       ii           i---     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCC---AATAA 875

Transitions / transversions = 1.59 (135 / 85)
Gap_init rate = 0.02 (18 / 875), avg. gap size = 1.83 (33 / 18)  


3019 26.71 0.66 0.44  chrX_88687693_88692267.rev     3179  4084 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88687693_8   3179 TAGAAACACATCCCATGCTCATGGATAGGTAGAATCAATATTGTGAAAAT 3228
                          i    v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88687693_8   3229 GACA-TACTGTCAAAAGCAATCAACAAATTAAATGTAATTCCCATCAAAA 3277
                          i  -    vi v   vii   v   i   v  i i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88687693_8   3278 TACCACCATCATTCTTCACAGAACTAGAAAAAA-AATTCTAAATTTT-TA 3325
                          v   v vv v  i  ii     v v  v  iv-i  i     v  i-  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_88687693_8   3326 TGGCACCCCCGAAAAAGAGCCATCATAACCAAAGCAAGACTGAGCAAAAA 3375
                            v viv ---  ii  v   vv   i     i   vvi   iv  i  
  L1M4_orf2#LINE/    151 TGGAAATGC---AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_88687693_8   3376 GAACAAATCTGGAGTCATGACATTACCCAACTTCAAACTATACTATAAGC 3425
                                vi     vvv v   i v     i      viv     i  iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_88687693_8   3426 CCATAGTCACCAAAACAGCATGGCACTGGTATAAAAATAGGCACATAGAC 3475
                          i i   v i   i    ii   i     i    ii    i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_88687693_8   3476 CAATGGAACGGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAGCCA 3525
                                 ii    v    ii           v   v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_88687693_8   3526 ACTGATTTTCAACAAAGCAAACAAAAACATAAAGTGGGAAAAGGACACCC 3575
                          i        i    i vviv   i v   vv i    i    i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_88687693_8   3576 TATTCAACAAATGGTGTTGGGATTATTGGCTAGCCACATGTAGAAGAATG 3625
                          v              i     iv i   v  ?       i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_88687693_8   3626 GAACTGGATCCTCATCTCTCATCTTTCACAAAAACCAACTCAAGATGCAT 3675
                         i ii    i  ii i   v  i v vi       ii       i   v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_88687693_8   3676 CAAAGACTTAAATCTAAGACCTGAAACCATAAAAATTATAGAAGATAACA 3725
                           ?    i     v     v  i    i      v iv       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_88687693_8   3726 TAGGAAAAAACCCTTCTAGATATTGGCTTAGGCAAAGACCTCATGACCAA 3775
                             ?iv   i -   vv  iv    v        v iii  v iivi v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_88687693_8   3776 GAACCCCAAAGCAAATGCAACAAAAACAAATATAAATAGATGACACCTAA 3825
                           vv  v      v v         iv   v   i   i  viv  i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_88687693_8   3826 TTAAACTAAAAAGCTTCTGTACAGCAAAAGAAACAATCAGCAGAGTAAAC 3875
                          i   v v    i   i   i vv    i  v  v    iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_88687693_8   3876 AGACAACCTACAGAGTGGGAGAAAAC-TTCTCAATCTATACATCTGACAA 3924
                                 i     i          i-  iv   vii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_88687693_8   3925 AGGGCTAATATCCAGAATCTACAAGGAAGTCAAACAAATCAGCAAGAAAA 3974
                         i  i  vi          v  i  i   v  vv    v   ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_88687693_8   3975 A--CAAACAGTCCCATCAAAAAACGAGCTAAGGACATGAATAGACAATTC 4022
                          --    i ii  v  i?     i i  v     iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_88687693_8   4023 TCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAAC 4072
                           v                       i  i  i       i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_88687693_8   4073 ATCACTAATGAT 4084
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2159 25.55 5.86 5.42  chrX_88701185_88706524     3947  4850 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88701185_8   3947 TGAAAAAACGTGATCCATAATCACGGATTGGAAGAGTCAGTATCATTAAA 3996
                           i   i ii --i    iv   i           v i i   ii    i
  L1M4_orf2#LINE/      1 TGGAAAGATAT--CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_88701185_8   3997 ATGGCCATGCT-------TTGAT--------TCAACACTATTCTTATCAA 4031
                              v  i  -------     --------     i v  i i      
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_88701185_8   4032 GATACCAACATCATTTTTTTACAGAACTAGAAAAAGACT-ATTCTAAAAT 4080
                         i  v   i vv -i      i     v v  v  i--  -  i       
  L1M4_orf2#LINE/     99 AATCCCAGCTGC-CTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAAT 145

  chrX_88701185_8   4081 TTATATGAAACCAAAAAATAGTCCAAATTGCCAAAGCACTTCTAAGCAAA 4130
                          i     i  viiv  iiv vi vi   v      i  v ii i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_88701185_8   4131 AAGAACGAAGCTGGAAGGATCACATTATTTGACTTCAAACTATACTACAA 4180
                               i   i    i iv     i viiii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_88701185_8   4181 GGCTACAGTAACCAAAGCAGCATAGTAGTGGTACAAAAACAGACACATAG 4230
                         i          i   ii   ii i   v   i i  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_88701185_8   4231 ACCAATGGAACAGAAGAGAGAATGCAGAAACTAAGACACGCATCTACAGC 4280
                          i        i    vv    i v      iv  vv  ii   i  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_88701185_8   4281 CATCTGATCTTCAACAAAGTTAATGAAAATC-TGCAATGAGGAAAGGAC- 4328
                           vi    i   i    i v ivi-  i i - v     i      i i-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCC-AAGACCATTCAATGGGGAAAGAATA 394

  chrX_88701185_8   4329 GTCCTATTCAAAACATGGTGCTGGGATAGCTGGCTAGCCATATGCAGAAA 4378
                            i -     v v            i i    v  ?   i     i  i
  L1M4_orf2#LINE/    395 GTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_88701185_8   4379 CGTAATTTCTTCATGTACAAAAATTAACTCATTTCTTCATGTACAAAATT 4428
                         ---   -------------i  i  iivi vi v i   i--  ------
  L1M4_orf2#LINE/    444 ---AAT-------------GAAGTTGGACCCCTACCTCAC--AC------ 469

  chrX_88701185_8   4429 TCTTCATGTACAAAAATTAACTCAAGATAAAT-----ACTTAAATGTAAG 4473
                         ----   i                 i  ii  -----  i          
  L1M4_orf2#LINE/    470 ----CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_88701185_8   4474 AGCTCAAGCTATAAGAATCCTAGAAGAAAATCTAGAAA-ACACCATTCTG 4522
                             v  i      i v  i          iv   i?i- v i -   vv
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGT 564

  chrX_88701185_8   4523 AATATTGGCCTTGGGAAATAATTTATGACTAAAT----CCTCAAAAGCAA 4568
                         i iv    v-  i  v   ii   v ---  i  ---- vi        v
  L1M4_orf2#LINE/    565 GACCTTGGG-TTAGGCAATGGTTTCT---TAGATATGACACCAAAAGCAC 610

  chrX_88701185_8   4569 TTGCAACAAAA----ATATTGACAAGTGTGACCTAATTAAGCTAATAAGA 4614
                         vv         ---- v  v  i  i vv   i v  i  iv --   i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT--TAAAA 658

  chrX_88701185_8   4615 ----TTGTGCACAAGCAAAGACGTTATCAATAGAGTAAACTGACA-CATA 4659
                         ----      viv --  i   ii      v i   i  vv    - vi 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCA--AAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_88701185_8   4660 CAGAATGGGAGAAAATATTCACAAACTATGCATCTGACAAAGGTCTGATA 4709
                                            ii    ii  ii      i  i  v  vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_88701185_8   4710 TCCAGAATGTA-ACAGGAATGTAAGCAATTGAACAAGCAAAAAGA--AAT 4756
                                 i  - v  i v v v -   i v  i  -i       --   
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTA-CAACTCAATAA-TAAAAAGACAAAT 804

  chrX_88701185_8   4757 --CCCA--TTAAAAATGGGCAAA---TTCCATGAACAAACACTTCTC--- 4796
                         --    -- ?             ---  ---    i i   i     ---
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATT---TGAATAGACATTTCTCCAA 851

  chrX_88701185_8   4797 AAAAGGCATAAAACTAGCCAAAAA--ATATAAAAA-ATGCTCATCACTAC 4843
                          i   ii   v  v i     v  -- i  i    -       v  ii ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_88701185_8   4844 TCATCAG 4850
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.00 (152 / 76)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 2.83 (102 / 36)  


3070 26.31 2.12 0.89  chrX_88722652_88726266.rev     2228  3124 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88722652_8   2228 TGGAAAGATATTCTACGTTCATAGGTCAGAGGATTCGATATTGTTAAAAA 2277
                                    i i i      i i ii  i  i ii          i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_88722652_8   2278 TGTTTACACTATCCAAAGCAATCTACAGATTTAATGCAATCCCTGTGAAA 2327
                           viv i   vi     vii           i  i         i v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_88722652_8   2328 ACACGAATGACATTCTTCACAATAATAGCAGAAATCCATCCTAAAATGTA 2377
                          iv v iivi v  i  ii  iv   v - v  iiiv          vi 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCA 148

  chrX_88722652_8   2378 TGTGAAA---CCAGAGAATACCCAGAGTAACCAAAACTATTCTAAGCAAA 2424
                          i  i  --- v  i  ---      i  i       v  ii i iv  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_88722652_8   2425 AAATATAAAACTAAAGAAATCACATTACCTGACTTGAAATTATACTACAG 2474
                           iv i   ii ii  i v     i v  ii i  v   viv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_88722652_8   2475 -GCTATAGTACCCAAAGAAGCATGGTATTTG-ATGATGAGAGACACATAC 2522
                         -    i    vi   iiv  ii     i v -  i v  v     i   v
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_88722652_8   2523 ATCAGTGGAATAGAATAGGGAACCCATAGATAAATCCACACATCTACAGT 2572
                             i           v i  ii   v i     i   i    i  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_88722652_8   2573 TAACTCATATTAAACAAAGGTGCCAAGAACATACATTGGGGAAAGGACAG 2622
                         i  i v  v  vi    i          v   v  v         i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_88722652_8   2623 TCTCTTCTATAAATGGTGCTGGGAAAAGTACACATTCATATGCAGAAGAA 2672
                            i   v i              v  v iv i ?i  i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_88722652_8   2673 TGAAACTAGACTCCTATCTCTCACCACATACAAACGTCAAGTCAAA-TGT 2721
                             ii i   i    i   v     i       vi i  v     -  v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_88722652_8   2722 ATTAAACACTTAAATCTAAGACCTGAAACTATGAAACTACTAAAAGAAG- 2770
                           i ? v  i     v     v  i       i     vi  i     i-
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_88722652_8   2771 CATTGTGGAAACTCTCCAGGACATTGGACTTGGCAAAGAATCCTTG---- 2816
                            v v? v  v   i iv   v    ii v     v iv i   i----
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_88722652_8   2817 -----CCACAAGCAAAGGCAACCAAAACAAAAATGGACAAATCGGATCAC 2861
                         -----   v     v i     v   iv      i  i    i   iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_88722652_8   2862 ATCAAG-TTACAAAGCTTCTGCACAGAAAAGGAAACTATCAACAAA-TGA 2909
                              i-   -   i   i  ii vvv      v        v   -   
  L1M4_orf2#LINE/    646 ATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_88722652_8   2910 AGAGACTGCCCAAAGAATGGGAGAAAATATTTGCAAACTACCCATCTGAC 2959
                          i    vi    v                        ii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_88722652_8   2960 AAGGGATTAATAACCAGAATATCTAAGAAGCTGAAACAACTTTATAG-AA 3008
                               i vi  v         v   ii i  vvv      iv   i-  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_88722652_8   3009 AAAAATGTAATAATCCAATTTAAAAAATGGGCAAAAGATCTGAAAAGACA 3058
                            i ii-     i      ?     -        i   i    v     
  L1M4_orf2#LINE/    795 AAAGACA-AATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chrX_88722652_8   3059 TTTCTCAAATGAAGACACATAAATGGCAAAAAGGCATATGAAAACGTTCT 3108
                               v  v     i i i       v  v i   i       vi v  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_88722652_8   3109 CAACATCATTCATCAT 3124
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (147 / 85)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.80 (27 / 15)  


2999 26.10 2.81 0.67  chrX_88736613_88741219     3226  4114 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88736613_8   3226 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 3275
                               i i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88736613_8   3276 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCTCATCAAGC 3325
                            v     v      v i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88736613_8   3326 TACCC--TTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTACATTT 3371
                          -   --i  v    i  -i     -   -- v  i  - i i  v v  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_88736613_8   3372 TATATGGAACCAAAAAGGAGCCCA--ATTGCCAAGACTATCCTAAGCAAA 3419
                         i        viiv  i   -    --  v     i  v   i i iv  i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_88736613_8   3420 AGGAGCAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATGCTACAA 3469
                          i  i     i      vv   ii  v  ii i      viv i      
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_88736613_8   3470 GGCTGCAGTAACCAAAACAACATGGTACTGGTACCATAACAGATATATAG 3519
                         i   i      i   i   iii         i iv vi i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_88736613_8   3520 ACCAATGGAACAGAACAGAG-GCCTCGAAATAACCCCACACATCTACAAC 3568
                          i        i    iv   - i iv       v    i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_88736613_8   3569 CATCTGATCTTTGACAAACCTGACAAAAGTA----ATGGGGAAAGGATTC 3614
                           vi    i  i     ivv  v   i vi ----          i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_88736613_8   3615 CCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCTTATGCAGAAAAC 3664
                         i  v  i  i        i     v      v  ?  vi     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_88736613_8   3665 TAAAACTGGACCCATTCCTTACACC-T-TACAGAAATTAACTCAAGATGG 3712
                          i  ii       v v   i     - -    i            i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_88736613_8   3713 ATTAAAGACTTAAATGTAAGACCTAAAACTATAAAAACCCTAGAAGAAAA 3762
                           i ?    i           v              vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_88736613_8   3763 CCTAGGCA-ATACCATTCAGGACATAGGCGTGGCCAA-GACTTCATAACT 3810
                          v    ?i- v i -   iv   v v  vv i v   - ii   v  iv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_88736613_8   3811 AAAACACCAAAAGCAATGGCAGCAAAAGCCAAAGTTGACAAATGAGATCT 3860
                          vi            vvi   i      vv   i v  i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_88736613_8   3861 AATTGAACTAAAGAGCTTCTGCACAGTAAAAGAAACTATTATCAGAGTGA 3910
                         v  ii  v v  i i   i  ii vvi   i  v     i vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_88736613_8   3911 GCAGGCAACGTACAGAATGGGAGAACATTTTTGCAATCTATCCATCTGAA 3960
                         iv  i    vi              v  v       vii  vi      v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_88736613_8   3961 AAAGGGCTAATATCCAGAATCTACAAATAACTTAAACAA----AT--TTA 4004
                           i  i  vi          v  i   v    ivv    ----  -- v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_88736613_8   4005 AAGGAAAAA-AA---AATCAAAAAGTGGGCAAAGGATATGAACAGACACT 4050
                           i  v   -  ---   i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_88736613_8   4051 TCTCAAAAGAAGACATTTATGCAGCTAACAAACATATCTAAAAAAGCTCA 4100
                             v        i  vi viii  i  i  i  i  vv   i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_88736613_8   4101 TCATCACTGATCAT 4114
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (138 / 90)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.63 (31 / 19)  


1467 27.10 2.34 5.46  chrX_88749365_88753936.rev     2858  3370 (1202)    L1M4_orf2#LINE/L1        1   497 (411)  

  chrX_88749365_8   2858 TGGAAAAATATTCCATGCTCATAGGTTAAAAGAATCAATA--GT-AAAAT 2904
                               i    i     i    i i  ii    v i    --  -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88749365_8   2905 GGCCATTCTGCCCAAAACAATTTACAGATTTAACACTACTCCTATCCAA- 2953
                            v  v  v      vii  i        i   i v ii      v  -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88749365_8   2954 ---CAACTAACACCATTTTTCTAGAATTAGCAAAAACAAACAAAACAAAC 3000
                         ---  i  i---  v     ---------   i   ivi    ivii --
  L1M4_orf2#LINE/    101 TCCCAGCTG---CCTTTTTT---------GCAGAAATTGACAAGCTGA-- 136

  chrX_88749365_8   3001 AAAAAAACCATTGTAAAATTTATATGGAA-T-CAAAAAAAGTCCCCCAAA 3048
                         ---------- iv       i        - -   iii ----   vi  
  L1M4_orf2#LINE/    137 ----------TCCTAAAATTCATATGGAAATGCAAGGGA----CCCAGAA 172

  chrX_88749365_8   3049 T--CCAAACCAATCCTAAGCATAAAGACTAAAGCTGAAGGAATCACACTA 3096
                          --     v     i i iv vi    vi    i  i    v       v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_88749365_8   3097 CCTGAATTCAAACTATGCTGTAAGTCTATAATAACCAA-ACAGCATGTTA 3145
                           ii v      viv i  ii  iv   i i   i   -    ii  v  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_88749365_8   3146 CTGGTACAAAAACAGACACATAAACCAATGGAACTGAATAGAAAACTCAG 3195
                             i i  ii i     i   i i        iv    v  i iii   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_88749365_8   3196 AAATAAGGCTGCACACTTACAACCATATGATCTTTGAAAAGGCCATCAAT 3245
                               iv iii   i   iiii  vv    i  i  v    viii   v
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_88749365_8   3246 AGCAAGCAATGGAGAAAGGATTTCCTATTCAATAAATGGTGCTGGGATAA 3295
                          v  vv      i     i  vvi  v     i              i  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_88749365_8   3296 CTGGCTGGCCATATGCGGAAGAATGAAACTAGACCATTGCATTTCACTGT 3345
                             v i?   i    ii         ii i    vi i v iv   ii 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_88749365_8   3346 GTACAAAAATTAACTCAAGATACAT 3370
                         i                 i  iv  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGAT 497

Transitions / transversions = 2.29 (96 / 42)
Gap_init rate = 0.02 (11 / 497), avg. gap size = 3.64 (40 / 11)  

 971 25.37 3.66 2.93  chrX_88749365_88753936.rev     3672  4081 (491)    L1M4_orf2#LINE/L1      496   908 (0)  

  chrX_88749365_8   3672 ATCTAATATTTAAATGTAAGACTTCAGAGTATAAAAATCTTAGAAGA--- 3718
                            v? v ii           vi v i v       v          ---
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_88749365_8   3719 CAT-GTAAAAAATACCCTTCTCAGCATCTGCCTTGGCAAATAATTT-TTG 3766
                            - v?iv    ---    viii v iv vi v     - ii   -  i
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA 591

  chrX_88749365_8   3767 GCTAAGTCCCCAACAGCAATTATACCCCCACCCAAAAATATAGACAAACT 3816
                          v  v v v    v    --i vi vv v vvv     -     i   i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAA-ATAGATAAATT 638

  chrX_88749365_8   3817 GGACCTAATTAAACTAAAAAAAGCTTCTGGACAGCAAAAGAAACTATCAA 3866
                             i v  i   v v     --   i  vi vv    i  v        
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_88749365_8   3867 GAGAGCAAACAGACAATCTACCAAATGGGAGAAAATACTTGCAAACTATG 3916
                           i  ii  v      i i  vi              i       ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_88749365_8   3917 TATAAGACAAAGGTCTGATATTCAGAATCTATAAGGAACTT----AATTC 3962
                            vv  i  i  v  vi   i      v     i     i----  i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_88749365_8   3963 AACAAGCAAAAACCAAATAACCCAATT-AAAAATGGTCAAAGTAAACGAG 4011
                           i  vv    iv              -        v     v vvi  i
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_88749365_8   4012 CAAACACTTCTC---AAAAGACAGAAAAGCAGCCAACAA--ACATGAAAA 4056
                         i i   i     --- i    i v v  iii     i  --         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_88749365_8   4057 ATATTTGCTCGACATCACTAATCAT 4081
                         i-  --    i      ????????
  L1M4_orf2#LINE/    887 G-AT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (54 / 48)
Gap_init rate = 0.03 (14 / 413), avg. gap size = 1.93 (27 / 14)  


2498 26.93 3.46 2.01  chrX_88785094_88789713.rev     3240  4134 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88785094_8   3240 TGGAGAGATATTACATGTTCATGGATGGAAAAACTCAATATTGTCAAGAT 3289
                             i      iv             v i  i   i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88785094_8   3290 GTCAGCTCTTTTCAACTTGATCTACAGAATGAAAGCAATCCTTATCAAAA 3339
                          v  iiv  iii   v            v v  v       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88785094_8   3340 TTGCAGAATGT-TATTTTGTGGATCTTCAAAAACTCATTCTAAAGTTTAT 3388
                          iv   v-  i- v     ii  vv  v v  i  v  i     i  i  
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_88785094_8   3389 AGGGAAAGTTAAAAGTCCCAGAAATGTCAACACAATATTGAAAC----GA 3434
                          v     vvi  ii v       vv i   v     v      v----  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_88785094_8   3435 ACAAAGTCTGAGGACGAACGCTATCAAACTTCAACATTTACTATGAAGTT 3484
                                iv      vv  i  vi v  i     v i      ii   i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_88785094_8   3485 TCTGCAATTAAGACAGTGGGGTATTGGCAAAATAATAGAAAAATTGATCA 3534
                         v v i   i         v    i     v  vi     v v  v     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_88785094_8   3535 ATGGAATGCAATAGAGAA-CCAGAAATAGACCCACATAATTATAGTCAAT 3583
                                iv   v    i-         i     i i v    i      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_88785094_8   3584 CAATATTTGGTGAAAGAGCAAAGGCAATACTCTAGAGCAAAGATAGTCTC 3633
                         ii  v  i iii ii v  v   i v  v vv i i v  ii       i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_88785094_8   3634 CTCAGTAAATG---CTAGGAAAGCAACTGGACATCACTATTCAAAAAAAA 3680
                         i   ii     ---  i   ---        i ? vvi  v     i  -
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGA---CAACTGGATAKCCACATGCAAAAGAA- 445

  chrX_88785094_8   3681 GTAAATTTAGATATAGACCTC-C-CTGTTCACAAAAATTAGCTCAAAATG 3728
                         - i  v  i  ivivv     - - ii vi          i         
  L1M4_orf2#LINE/    446 -TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_88785094_8   3729 GAACATAAACCTAAAAGTAAAATGAAAAAGTATATAACATTTAAAGGATA 3778
                           v  ? i       v    i vvv    v    v   vi   i i  v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_88785094_8   3779 ATATAGAAGAAAA----------CATGGGTATGGCAATGACTTTTTGGGC 3818
                          i    i? v   ---------- v     vv       ii  i  i ii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_88785094_8   3819 ATAATGACAGAGGCACAATCCATGAAGAAAAAAATGG-TAAGCTTAACCA 3867
                           i iiv  i i      v v ii  ii       i -   ii vi  iv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_88785094_8   3868 AATTAAAATTTAAACTTCCACTCTGTGC---AAA--ACACAAGGAAAAGG 3912
                         v  i      v   vi ---- i     ---   --    v vv  i ii
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACT----TTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_88785094_8   3913 ATGAAAAGACAAGCCAAAGAATGGAAGAAAGTATTTGTACAATATATTTC 3962
                         i           v   v       i     i      i v vi    v  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_88785094_8   3963 CAATAAATTACTGTTATTCA-AATATACAAAGAAAATCTT-CAGACTCAA 4010
                         ii    ivv   vv   i  -      i      v-    -  -      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAAC-TCTTACA-ACTCAA 788

  chrX_88785094_8   4011 CAACAGGAAAATGAACAACCAAATGTAGAAAGATGCCAAATCCATGAATA 4060
                         i  i ii  i ii  i    v   v? i   viv  v  ivviv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_88785094_8   4061 GACACCTAAACAACAATAAAAAAGATATACAGATGGCAAATAAGCACATG 4110
                             ii ------ vvi   i          i     v            
  L1M4_orf2#LINE/    839 GACATTT------CTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_88785094_8   4111 AAAAAATGCTCTGC--CATATGTAAT 4134
                             i      vi --  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (133 / 104)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.45 (49 / 20)  


2906 26.21 2.70 0.56  chrX_88808552_88812183.rev     2253  3141 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88808552_8   2253 TGGAAACACA-CCCAGGCTCACAGATGGATAGAATCAATATTGTCAAAAT 2301
                               v i -    v i   ii   v iv   v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88808552_8   2302 GACCATACTGCCAAAAGTAATCTACAAATTCAATGCAATTTCCATCAAAA 2351
                          i v     v  v   v i       i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88808552_8   2352 TAC-AACCATCATTCTTCACAGAACTAGAAAAAACAATTCTAAAATTCAT 2400
                          v - i iii -  i  ii     v v  v  ivii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_88808552_8   2401 ATGGAA-TGAAAACAGAACCCACA-TAGCCAAAAC-----TAAGCAAAAG 2443
                               -  v  i-- i     v -          ----- i iv  i i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_88808552_8   2444 GAACAAATCTGGAGGCATCACATTACCTGACTT-GAAACTATACTACAAG 2492
                                vi      vv     i v  ii i  -i     -        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chrX_88808552_8   2493 CCCATAGTCACTAAAACAGCATGGTACTGGCATGAAAATAGACACATAAA 2542
                         v i i   v ii  i    ii            i ii       i   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_88808552_8   2543 CCAATGGAACAGAATAGAAA-CCCAGAAATAAAGCTAAATGCTTACAGCC 2591
                         i        i     v  i -i           v i v iii   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_88808552_8   2592 AACTGATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACC 2641
                           i    i  i     i vviv   i v   vv i         i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_88808552_8   2642 CTATTCAACAAACGATGCTGGGATCATTGGCAAGCCACATTTAGGAGAAT 2691
                           v         i i        iv i   vv ?      vi ii     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_88808552_8   2692 GAAACTGGATCGTCATCTCTCATCTTATACAAAAATCAACTCAAGCTAGA 2741
                            ii    i vii i   v  i v           i       iv i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_88808552_8   2742 TCAAGGACTTAAATATAAAACCTGAAACCATAACAATTCG-AGAAGATAA 2790
                            ?i   i     i   i v  i    i    -  i  v-      v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAA 545

  chrX_88808552_8   2791 CATCAGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCATGAACA 2840
                            vi ?iv  vi    vv   v    v        v ii   v ii i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_88808552_8   2841 AGAAACCAAAAGCAAATGCAACAAAAACAAAGATAAATAGGTGAAACTTA 2890
                         v  v          v v         iv   i   i   ii vii    v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_88808552_8   2891 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGGAACATTCAGCAGAGTAAA 2940
                           i   v v  i i   i  ii vv    i iv  vv   iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_88808552_8   2941 CAGACAACCCACAGAGTGGAAGAAAATCTTCACAATCTGTACATCTGACA 2990
                         v              i   i       v  ii   viii  i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_88808552_8   2991 AAGGACTAATATCCAGAATCTACAAGGAATTCAAACAAATTAATAAGAAT 3040
                          i     vi          v  i  i   i  vv    v i     v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_88808552_8   3041 AA-ACAAGCAATCCCATCAAAAAGTG---AAA--------ATAGACAATT 3078
                           -    ii  i  v  i?    i  ---   --------       v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_88808552_8   3079 CTCAAAAAAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAA 3128
                            v   i                   i  i  i       i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_88808552_8   3129 CATCACTAATAAT 3141
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (147 / 82)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.93 (29 / 15)  


2747 26.72 3.16 0.79  chrX_88841654_88845871     2839  3725 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88841654_8   2839 TAGAAAAATATTACGTGTTCATGGATTGAAATAATCCATACTGTTAACAT 2888
                          i    i    iv i             i  v v iv   i      v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88841654_8   2889 GTCCATACAACCCCCCAAA---ATCTACAGGTTCATTGCAATCTGTATGA 2935
                          v v    ---i       ---        i    vi      iv   v 
  L1M4_orf2#LINE/     51 GGCAATAC---TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_88841654_8   2936 AAATACCAATGATATTCTTCACAAAAA-----AA----ATCTTAAAATTT 2976
                             v   iiviiv  i  ii  i   -----  ----   i       i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_88841654_8   2977 ATATGGAACTACAGATGACCCAAAATATCCACAGCTATCCTAAGCAAAAA 3026
                                 v i  iiv      i    v   v i v   i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_88841654_8   3027 GAACAAAATCAGAGGAATCACATTACCTGACTTCAAATTATACTACAGAG 3076
                                i ii     v     i v  ii i      viv       i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_88841654_8   3077 CTATAGTAACCAAAACAGCCTGAAACTGGCATAAAAACAGACACAGAGTC 3126
                            i     i   i    iv  iv          ii i     i v  vi
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_88841654_8   3127 TAATGGAACAGAATCAAGAA-CCAGAAACAAATACACACACCTACAGTAA 3175
                         i       i     ii   i-       i   iv  i   ii  ii  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_88841654_8   3176 ACTCATTTTAGAAAAAATTTTCAAGAACATACACTGGGGAAAGGACAGTT 3225
                          i v     v  v  iiv vi     v   v  v         i i   i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_88841654_8   3226 TCCTCAATAAACGGTTTTGGGAAAAGTGGATAATCATATGCAGAAGAATG 3275
                          ii    i   i   vi     v  v      ?i  i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_88841654_8   3276 AAACCAGACCCCCATTT--------ATACAAAAATCAAATAAAAGTGGAT 3317
                           iiii      i ii --------          i  v v   i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_88841654_8   3318 GAAAGACTTAAATCAAAAACCTCAAACTATAAAACCTACTACAAGAAAAC 3367
                         v ?    i     vv  i v  v            - vi  v        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAAC 546

  chrX_88841654_8   3368 ATTGGGAAAAATCTCCTGGACATTTTTTCTGGGCAAATACTTATTGAGCA 3417
                           v  ?iv      i vv   v  vvv - i     - iv  vi v  vv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAA-TGGTTTCTTAGAT 594

  chrX_88841654_8   3418 AT-ACCTCACAAGCACAGGCAACCAAAGCAGAAACAG-CAAATGAGATCA 3465
                           -  vi  v       i     v    v i   i  -i    vi  iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_88841654_8   3466 CATCAAC-TTAAG--CTTCTGCACAGCAAAGGATCCAAT-AAACAAGTGA 3511
                               v-    i--   i  ii vv       iv v  -  iv      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_88841654_8   3512 AGAGACAACTCACAGAATGGGAGAAAATATTTGCAAACTACCCATCTGTC 3561
                          i       i                           ii ivi     vi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_88841654_8   3562 ATGAGATTAAAAACTGAAATATATAGGAAGCTGAAACAACTCTATAAGAA 3611
                          v i  i viv v iii        iii i  vvv       v    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_88841654_8   3612 AAAGTCTAATAATCTGATC-AAAAATTGGCAAAAGATTTGAAGATACATT 3660
                             v v     i ii  i-      v      i        v v     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_88841654_8   3661 TCTCAAAAGAAAACATAACATTTGCAAAGCAGGCATATAAAAAGGTACTC 3710
                             v      i i   vv v v  v  -i i   i  i     i i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGATGCTC 893

  chrX_88841654_8   3711 AGCATCATTGATCAT 3725
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.19 (35 / 16)  


2324 28.41 3.19 3.30  chrX_88882030_88884925.rev     1499  2406 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_88882030_8   1499 GAAAAAACATTCCATGCTCATCAATTGGAAGAATCACTATCATCGAAATG 1548
                          i   i i  i     i    vi         v i v   ii ii i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_88882030_8   1549 GCCATACTGTTCAAAGGAACCTACAGATTTGATGCTATTCCTATCAAATT 1598
                           v     vii    vvi i         ii i  v  i         v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_88882030_8   1599 ACC-GATGTCATTTTTCATGGAGGTAGAAAACATTATTCTAAAATGTGTA 1647
                         v  - v  i -     iiii  ii v  v  vv v  i       vii  
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_88882030_8   1648 TGGAACAACCACAAAAAAAGAGCCCA-AGTAGCCAAAGCAATGCTAAGCA 1696
                              vvi -------  i ii    - i        i    vi i iv 
  L1M4_orf2#LINE/    151 TGGAAATGC-------AAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_88882030_8   1697 AAAAGA-----GT-----GAC-CACATTACCTAACTTTAAACTATACTAA 1735
                          i    -----  -----   -    i v  i  i  i   viv     v
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_88882030_8   1736 AATGCTGCAGTAAATAAAACAGCATAGTACAGATACAAAAACAGAAGCAT 1785
                           v   i      vi  i    ii i    v ii i  ii i   vii  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_88882030_8   1786 AGACCAATGGAACAAAAAAGAAAGCTCCCCCACCCCCTGCCAAAAAAAAA 1835
                            i        i i  vv  i  -   -------------- i   v  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAG-TCC--------------AGAAATAA 328

  chrX_88882030_8   1836 ATAGCTGTACATTTGCAGCTATCTGGTCTTCAACAAAGTTGATAACAATA 1885
                          i-- ii       iii ii vi  i i   i    i v  vi  v vi 
  L1M4_orf2#LINE/    329 AC--CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_88882030_8   1886 AGCAATGAGGAAATAAC--TCCTTATTAAATAAATGGAGCAGGGATAGCT 1933
                         vv     i     v  i--  i  -- v  i      v  v    i i  
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACT 424

  chrX_88882030_8   1934 GGCTAGCCCTATGCAAAAGAATGAAACTTGACCCCTACCTGTCACAATAT 1983
                           v  ?  vi               ii v           vv   v    
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_88882030_8   1984 ACAAAAATTAACTCAAGACAGATTAAAATCTTAAATGTAAGACTTCAAGC 2033
                                         i ii   i ? iv i           vi v  i 
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_88882030_8   2034 TATAAGAATCCTAGAAGAAAACTTAGGAAATAGCCTTCCCAAATTGGTTT 2083
                              i v  i           v    ?ivv ii    vii vi v vv 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_88882030_8   2084 TGGGAAATAATTC--TGGATGAAGTCCTCAAAAGCATTTGCAACAAAAAC 2131
                          i  v   ii  i-- i   - v v vi        ivv         iv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_88882030_8   2132 AACACTTGACAAGTGGAACCTAATTAAACTGGAGAGCTTCTGCACAGCAA 2181
                           v v v  i  i v i  i v  i   v vi i i   i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_88882030_8   2182 AATAAACTATCAACAGAGTAAAAAGACAACATGCAGAATAAGAGAAAATA 2231
                          iv v        v i   i          vii      ii         
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_88882030_8   2232 TTTGCAAACAATGCATCTGACAAATATCTATTATCTAGAAT-TGTTAAGG 2280
                                 iv  ii      i  iviv  vv    i     - i v   i
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_88882030_8   2281 AATCTAAACAATTGAAGAAGAAAAAAGCAAATAACCCCA-------ATGG 2323
                          v   v -   i v  v  v     ii          v -------    
  L1M4_orf2#LINE/    774 ACTCTTA-CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_88882030_8   2324 GCAAAGGACACGAA----CACTTTTCAAAAGAAGACACACAAGCAGCCAA 2369
                                 ivi   ----  i  i  v        i i    iii     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_88882030_8   2370 CATACATATGAGAAAAAGGCTAAACGTCGCTAGTTAT 2406
                         i vi  i    -   i v   v   i  i????????
  L1M4_orf2#LINE/    873 TAAGCACATGA-AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (157 / 98)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 3.11 (59 / 19)  


2556 24.95 2.99 6.18  chrX_88946730_88949753.rev     1596  2533 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88946730_8   1596 TGCAAAGATATTCCACATTCTTGAGTTGGAGGAATCAACATTGTTAGAAT 1645
                           v        i   ii   v  ii     i  v i  i       ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88946730_8   1646 GTCCATAATACCGAAAGCAATCTACAAATTCAATGAAATCTCTATTAAAA 1695
                          v v   v v  v   vii       i      i v    i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88946730_8   1696 TAACAATGACATTCCTCACAAAGATAGA--AGATAATCCTAAAATTTATA 1743
                          vv  iivi v  ii ii  i i  v  --  v i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_88946730_8   1744 TAAAACCACACACACACACACACACACACACACACACACACACACACACA 1793
                          ii  ------------------------------------ ii  - vi
  L1M4_orf2#LINE/    151 TGGAA------------------------------------ATGCA-AGG 163

  chrX_88946730_8   1794 CACACAAAATAGCTGGAGCTATCCTAAGCAAAAAGAACAAAACTG----- 1838
                         v  v  i      iii i v   i i iv  i         ii  -----
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_88946730_8   1839 -----ACTTC---------AAATTATACTACAGACCTATAGTAACCAAAA 1874
                         -----     ---------   i -       i v   i     i   i 
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGA 262

  chrX_88946730_8   1875 CAGCATGGTACTGTAATAACAACAGACACATAGACAAATGGAACAGCAGA 1924
                            ii        vv    vi i     i     iv       i  v vv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_88946730_8   1925 GAGAACCCAGAACAAAAACCACAGACATGCA--GTGAATTCATTTTATAC 1972
                             ii      - v     -  v    vi --  v    v     vv  
  L1M4_orf2#LINE/    313 GAGAGTCCAGAA-ATAAACC-CATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_88946730_8   1973 AACAGTGACAACAACATACACTGAGGAAA--AGAGTCTCTTCAATAAATG 2020
                           vi   v   v v   v  v  i     -- v     i     i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_88946730_8   2021 GTTCCGGGGTAAGTAGATATTCATCTGCAGAAGAGGGAAACTAGACCCCT 2070
                           v i   ii  v i    ?i  iv    i    iv   ii i       
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_88946730_8   2071 ATCTCTTGCCTTATACAAAAATCAAATCAATATGTATCAAAGACTTAAAT 2120
                          i   vii  v           i  v    v   v    ?    i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_88946730_8   2121 CAAAGACCTCAACCTGTGAAACTAC-AGCAAGAAAACATGAAGAG-AACT 2168
                         vv    v  v  v  i i     vi-  -          - i ? -  v 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAG-AAGAAAACAT-AGGNGTAAAT 558

  chrX_88946730_8   2169 CTCCAGGACATTGGTCTGGGTAAACATTTGTTGTGCAGTACTCCACAGGC 2218
                           i iv   v    vi i  i  vvi   v  ivii vv  v   v i  
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_88946730_8   2219 ATAGGCAACCAAAGCAAAAATGGACAAATAAGATTACATCAAG-TTAACA 2267
                          i i     v    v      i  i    vi  i v      i-    - 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA-A 657

  chrX_88946730_8   2268 AGCTTCTGCACAACAAAGCTGGAAATGATTAAGGAAACCATTAACAACAT 2317
                          i   i  ii vv     ---------------  v  i  i  v  vi 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAG---------------GACACTATCAAGAAAGT 692

  chrX_88946730_8   2318 GAAAAGGCAACCTACAAATTGGGAGAAAATATTTGCAAACTACACATCTA 2367
                               i     i   i v                    ii i i    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_88946730_8   2368 GGAAGGGATTAATAACCAGAATATATAGGGAGGTCAAACAGCTCTATAGG 2417
                         iv      i vi  v            ii  iv  vv   i   v   iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_88946730_8   2418 AAAAAATCTAATAATCTGACTGAAAAATGGGCAAAATATCTGAATAGGCA 2467
                              iv v     i ii i ?             iv  i       i  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_88946730_8   2468 TTTTTCAAAAGAAGAAATACAAATGGCAAACAGGCATATGAAAAGGTGCT 2517
                            i  v        v           v  i i   i        i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_88946730_8   2518 CAACGTCAATGATCAT 2533
                             i   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (136 / 94)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 5.06 (86 / 17)  


2757 26.70 1.08 2.92  chrX_88963890_88967356     2050  2974 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88963890_8   2050 TGGATAAACATTCCATGCTCATGGATAGGAAGAATCAATGTTGTTAAAGT 2099
                             v i i  i     i        v      v i   i       ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88963890_8   2100 GACTGAACTGCCCAAAGTATTTTCTGGATTTAATGCTACTCCCAATAAAC 2149
                          i viv   v      v iv i vii    i  i  v ii  i vi   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88963890_8   2150 TACCATTGATATTCTTCATAGAAATAGAAAAAACT-ATTTTAAAATTCAT 2198
                          v   viviiv  i  iii      v  v  i-  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_88963890_8   2199 CTGGGACAGAAAAAGAGCCCAAATAGCCAAGGCAAACATAAGCAA-AAGA 2247
                         v   i vv v  ii  v  vi         ii   v v i iv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_88963890_8   2248 ACAAAGCCAGAGGCAC-CATGATACCGAACTTCAAA-CTGCAGTACAAGG 2295
                               iii    -  -  iiv v  v  i      -  ----   ----
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACT----TAC---- 240

  chrX_88963890_8   2296 TTGTAGTTTGGTTACAAGGCTACAGTAACCAAAACAGCATGGAACTAGTA 2345
                         ------------     i          i   i    ii   v   i i 
  L1M4_orf2#LINE/    241 ------------TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_88963890_8   2346 CAGAAACAGACACATAGACCAATGGAACAAAATAGAGAACCCAAAAGTAA 2395
                         i iii i     i     i        i i   v    ii   i  i   
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_88963890_8   2396 AGCCACACACCTAAAACCATCTGATCTTTGACAAATCTGACAAAAATAAG 2445
                          v   i   ii  viii  vi    i  i     ivv  v   i vi vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_88963890_8   2446 CAATGGGGAAATGATTCTCTCCTCAGTAAATGGTGCTGGGATAACTGACT 2495
                                    vi  vv   ii   ii              i     iv 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_88963890_8   2496 AGTCATATGCAGAAGATAGAAACTGGACCTCTTCCTCACACCATATCCAA 2545
                          ?i  i     i    vv   ii      i  v             v   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_88963890_8   2546 AAATTAACTCACGATGGATTAAAGACTTAAATGTATAACCCAAAACTATA 2595
                                    vi      i ?    i        vi v i         
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_88963890_8   2596 AAAAACCTTGGAAGACAACCTAGACCATACTGTTCTGGACATAGAAATGG 2645
                            v-i   i     v   v   i?vvv v v   vv   v v iiv i 
  L1M4_orf2#LINE/    529 AAAC-TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_88963890_8   2646 GCAAGTATTTCGT-GATAAAGACACCAAAAGAAATTGCAATGAAAGCAAA 2694
                             vvi    v -    v-           v vvv    ii    v   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_88963890_8   2695 AATTGACAAATGAGA-TTCAATTAAACTAAAGAGCCTTCTGCATGGCAAA 2743
                            v  i    vi  -    viv   i    i --   i  iiivv    
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAA 674

  chrX_88963890_8   2744 AGAAGCTATCAAAAGAGTGAACAGAAAACCCACAGCATGGGAGACAATGT 2793
                         i  vi       i i      v   v         v        v   i 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_88963890_8   2794 TTGGAAACTATGCATCCAACAAAGGTCTAATATCCAGCATCAATAATGAA 2843
                            v   ii  ii   ii i  i  v  vi       v  vv    v   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_88963890_8   2844 CTTAAACAAATCAAAAAGTAAAAAAACAA----CCCCATTAAAAAGTGGG 2889
                           ivv    v    v  -      i    ----   v   ?    i    
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_88963890_8   2890 CAAAGGACATGAACAGCCACTTTTCGAAAGAAGACATACATGTGGCCAAC 2939
                                iv    i  v  i  i  v        i     vi       i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_88963890_8   2940 AATCATATATAAAAAAGCTCAACATCACTGATCAT 2974
                           v  i  iv   i v           ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (139 / 104)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.47 (37 / 15)  


2496 25.03 2.88 3.65  chrX_88968683_88970880      813  1715 (483)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_88968683_8    813 CCATGTTCATCAATAGGAAGACTCAATATTGTTAAGATGCCAAT-TTCTC 861
                                   vi  v        i               v    -i  i 
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_88968683_8    862 CAACATAAT-------TCTAATACAATACCAATCACAATCTCAGAAAGCT 904
                            vv i  ------- ii  ii    v  v    v    i   vviv  
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_88968683_8    905 GTTTTGTTGACATCAACAAATTAATTCTAAAGTTTATATGGAAAGGCAAA 954
                         v     iv  v  ii    ii i  i     i  i         v    i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_88968683_8    955 AGTGCCAGAATAGACAGCAAAAGACTGAAAAAGAAAAA--AAATCAGAGA 1002
                         i vv         v  iv v  vvi          i  --  i ii   i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_88968683_8   1003 ACTGATAATACACTACTTTAAGAAATATTATAATGATA-AGAAACAAAGA 1051
                            v i v v v v i  i  i vv  i  i  v v  -  v  iv    
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_88968683_8   1052 CAGTGTGGTATTGATTTAAAAAGTGAACAAATTGATCAATGAAACAGTAT 1101
                                   i  iiv   ii - ii   v  v        i  i  v  
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAAT 311

  chrX_88968683_8   1102 AGAAAGCCCAGAAATATACCTGAAAAACTATGGTCAACTGATCTTGGACA 1151
                         v  i  i         v   iiv v vi         i    i  v    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_88968683_8   1152 GTAAAAAGCAAAGACAATCCAATGGAGAAAGGATAACTTTTTCTACAAAT 1201
                         -- iiiv  v     v  i      i     i   iii     v      
  L1M4_orf2#LINE/    362 --AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_88968683_8   1202 GGTGTTGGAACAAGTAGACATT-ATATGCCAAAAAAATG--TCTAGACAC 1248
                             i   i    v i  i ?i- i    -    i    --vi i   --
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGC-AAAAGAATGAAGTTGGAC-- 456

  chrX_88968683_8   1249 AGTCCTTAGACCTTTCACACATACACATGCACACAC-ACCACTAAATGGA 1297
                         ---  i  --   --     ---  i  i  v v i- v v v       
  L1M4_orf2#LINE/    457 ---CCCTA--CCT--CACAC---CATATACAAAAATTAACTCAAAATGGA 496

  chrX_88968683_8   1298 TTATAGACCTAAATATGAAATAGAAAACTATAAAATGTTGTTTCAA-AAA 1346
                          i ?          i i i vvv            i-- v  vv  -   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC--TCTTAGAAGAAA 544

  chrX_88968683_8   1347 TCATAAGAGAAACTCTAGGTAACCTTGTGTTTTGTGGTTA--CGATGACT 1394
                         v    i ? v  v   vv  i      --------     -- i   ii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTG--------GGTTAGGCAATGGTT 586

  chrX_88968683_8   1395 TTTTAGATACAACACCAAAAATACTATCCATGGAAGAAAAAAT---TAAG 1441
                          i       ii         ii  v v v iii          ---   i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_88968683_8   1442 TTGCACATCATTACAATAAAAAACTTCTACTCTGTGAAAGATACTGTTAA 1491
                            v  v    i v   v        i iiv  vii  i  i   i i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_88968683_8   1492 AAGAATGAAAAGACAAGTCTATAGACATTTTA-AAAATATTTGCAAAGCA 1540
                         i i i           -i i i   -  vvv -              v  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAA-CCCACAGA-ATGGGAGAAAATATTTGCAAATCA 734

  chrX_88968683_8   1541 C-TATGTGATTAAAAATAAAACTTATATTCGAATTATACAAAGAACTCTT 1589
                         i-   v    -  iii----    i   i ii v    i           
  L1M4_orf2#LINE/    735 TATATCTGAT-AAGGG----ACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_88968683_8   1590 AAAAATCAATAATAAAAAAACAAACAACCCAATT-AAAAATAGGCAAAAC 1638
                          v  v             i     i         -      i      iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_88968683_8   1639 ATTCGAATAGATGCCTCATCAAAAAA--TATAGAGATGGCAAATAATCAT 1686
                            i       iiii  vi    i  --    v i     v     v  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_88968683_8   1687 ATGAAAAGATGTGCAGTTTCATATGTCAT 1715
                                    iv  iiv   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (134 / 89)
Gap_init rate = 0.03 (27 / 896), avg. gap size = 2.19 (59 / 27)  


3022 28.46 0.89 0.33  chrX_88992892_88999842.rev     5558  6460 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_88992892_8   5558 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAC 5607
                              ii i  i     i      i v      v i     i  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_88992892_8   5608 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5657
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_88992892_8   5658 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5705
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_88992892_8   5706 TATGGAACCAAAAAAGGGCCCGCACAGCCAAGACAATCT-GGGCAAGAAG 5754
                                viiv  ii iv  v v i      i       - iiv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_88992892_8   5755 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5804
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_88992892_8   5805 TACAGTAACCATAGCAGCAGGTTACTGGTACCAAAACAGATATATAGACC 5854
                                 i  vii   iiv v      i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_88992892_8   5855 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACATAGCTACAACCGT 5904
                                i    iv   ivii         vv   i i vi  iiii iv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_88992892_8   5905 CTGATCTTTGACAAACCTGACACACACAAGCAATGGGGAAAAGATTCCCT 5954
                         i    i  i     ivv  v  vivv  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_88992892_8   5955 ATTTAATAAATGGTGTTGGGAAAACTGCCTAGCCATATGCAAAAAACTAA 6004
                         v  i  i        i     v     vv  ?   i        i v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_88992892_8   6005 AACTGGACCCCTTCCTTACACCTTTTATAAAAATCAACTCAAGATAGATC 6054
                          ii         v   i     v v  i      i       i  i    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_88992892_8   6055 AAAGACTTAAACGTAAGACCTAGGACCATAAAAATCCTAGAACAAAACCT 6104
                          ?    i    i      v   ii  i      v  i     v     v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_88992892_8   6105 GGACA-ATACCATTCAGGACACAGGCACGGGCAAAGACTTCATGTCTGAA 6153
                         i i?i- v i -   iv   viv  vvii     v ii   v ivv ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_88992892_8   6154 ACACCAAAAGCATTGGCAACGAAAGCCAGAATAGACAAATGGCATCTAAT 6203
                                     ivi     i    vv i      i    v v ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_88992892_8   6204 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 6253
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_88992892_8   6254 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 6303
                          i     i                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_88992892_8   6304 GGGCTAATATCCAGAATCTACAAAGAACGTAAATAA---AATTACAAGAA 6350
                           i  vi          v  i       vivv i  ---   v i  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_88992892_8   6351 AA-AAACAACCCCATCAAAAAGCGGGTGAAGGATATGAACAGACACTTCT 6399
                         i -   i     v  i?    ii   ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_88992892_8   6400 CAAAAGAAGACACTTATGCAGCCAACAGACATATGAAAAAATGCTCATCA 6449
                          v        i ivi viii     i ii  i       i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_88992892_8   6450 TCACTGATCAT 6460
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.66 (158 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1807 22.83 4.89 12.44  chrX_89060387_89062566.rev      727  1707 (473)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_89060387_8    727 GGAAAGATATCTCATA--CACGGACAGAAAGACTCAATATTGTCAAGATG 774
                                    i   i--  i   iv i      i        i      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_89060387_8    775 GCTAT-TTTCCTAACTTGATTTCAAGATTCAACACAATCACAATAAAAAT 823
                           v  -i i  i  v     i vv         i     v v  v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_89060387_8    824 GAAAATTAGGTATTTTGTGAACATTCACAAAT--ATTCTAAAGTTTATAT 871
                         vvv ii ivv v     iii v   v    ii--  i     i  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_89060387_8    872 G-AAATGACAAAAGATATAGGATAGCTGACACAATTTTGAACAAGAA--- 917
                          -     -   ii  ivi  i     ii v     i     v     ---
  L1M4_orf2#LINE/    152 GGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_89060387_8    918 CAAAGTTGGATGACTGACACTATATAACTTCAATACTCGTTATAAAGCTA 967
                                   v    v     vivi  i     v   iii  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_89060387_8    968 CATTAAT-AAAATAGTGTGATACTAACA-----ATGGACAAGTAGATTCA 1011
                           v    -  i i      i    ii  -----  i    vi     -  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT-CA 299

  chrX_89060387_8   1012 ATAGAA-AGCACAGAGAGCCCCAAAATAGATCCATAC--TAATGTTATCA 1058
                           i   -  v iv     i  vi     i i      -- v   --i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG--GTCA 347

  chrX_89060387_8   1059 ATTGATTTTTGATAAAAGAGTGAAAGCAGTTCA-TGGGAAAAGGATATTC 1107
                                  i  i  ii v iv  ii vi    -    i    i   v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_89060387_8   1108 TTTTCAAGAAATGGTGCTGGAA-AACTGTACATACATGTTCAAAAATAAT 1156
                                v            i -     v i ?v  ii v     i-   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AAT 446

  chrX_89060387_8   1157 AATAATCTTACTTCTTTCACAAAAATTAACTAAAAATAAATGATACAACT 1206
                         i - i ivv  ii  -----------------------------------
  L1M4_orf2#LINE/    447 GA-AGTTGGACCCCT----------------------------------- 460

  chrX_89060387_8   1207 AAATGTAAAATGTATAATCTGTACACCCCAAACCCATGACACACAAATTA 1256
                         ------------------------   i  v   -  - i   v      
  L1M4_orf2#LINE/    461 ------------------------ACCTCACACC-AT-ATACAAAAATTA 484

  chrX_89060387_8   1257 -CTTATATAACAATCCTGCACATGTACCCCCAAACCTAAA-ATAAAAGTT 1304
                         -  i ------  --------   v i v?- i       -i   i  i 
  L1M4_orf2#LINE/    485 ACTCA------AA--------ATGGATCAW-AGACCTAAATGTAAGAGCT 519

  chrX_89060387_8   1305 AAAAAAAAAGTTGACATGACCACAAAACAAAAAACTAAAAACCCTCTTAG 1354
                             --------------- i i     ----------------      
  L1M4_orf2#LINE/    520 AAAA---------------CTATAAAAC----------------TCTTAG 538

  chrX_89060387_8   1355 CAAAACATGTAGGAGGAAACCTAAATGATCTTGGATTTGGTGATGACTTT 1404
                         v i  v ii    ? v   i  vvi   i     i  v  ii   ii  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_89060387_8   1405 TTACATATAAGACAAAAAGCCTGATCCAGGAAATAAAAGGTAGGTAAACT 1454
                            v    i v  v      vii v v vi   v    ii   i    i 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_89060387_8   1455 GGACTTAATTAAATGTAAATGCTTATTCTCTATCAAAA-ATACTGTTAAG 1503
                               v  i   vv    vi   -  v viv     i- i   i i   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTT-TTGTGCTTCAAAGGACACTATCAAG 687

  chrX_89060387_8   1504 AGAATGAGAAGAAAAGCCAC----TAAAGGAACATATTTGCAAAACACAT 1549
                          i i   i    v  v    ---- iiii   v           v  i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_89060387_8   1550 ---TGATAAATGACTGATACCTGAAATATGCAAAAAACACTTAGGTCTCA 1596
                         ---      iv    vi  i iii     ii   i   v    viv    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_89060387_8   1597 AGAAAAAAAAAACAA-TAA-------AAAAAAT---CTAAAAATATGAAT 1635
                          v  v     i    -   -------?      --- v  ii  v     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_89060387_8   1636 AGAAAGCTTCCCTAAGAAGGCATACAGATGGC--ATAATTGCATATGAGC 1683
                            v vi ii  v      ii     i     --    --   i    --
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA--GCACATGA-- 883

  chrX_89060387_8   1684 ATACAAAAAT-----ATATCATTAGAGAA 1707
                         ----   i  ----- i    ????????
  L1M4_orf2#LINE/    884 ----AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (139 / 81)
Gap_init rate = 0.04 (37 / 907), avg. gap size = 4.59 (170 / 37)  


2402 26.10 3.82 1.69  chrX_89063409_89068177.rev     3390  4278 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89063409_8   3390 TGAAAAAAAGTTCCATGTTCAAGGACTGGATGAATCAATATTGATAAAAT 3439
                           i   i vi i         v   i    v  v i       v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89063409_8   3440 GACCATACTGCCAAGAGCAATCTACAGAGTCA-TGCAATTTCTATCAAAT 3488
                          i v     v  v i vii         v   -i     ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89063409_8   3489 TACCA------TCATTCACAGA--TTAGAAAAAACT-ATTCTAAAACTCA 3529
                          v   ------ iv  ii    --  i-- v  i  -  i      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_89063409_8   3530 TATGGAACCAAAAAAGGAGCCCA-AATAGCCAAAGCAATCCTAAGCAAAG 3578
                                -- viv    ii    -          i     i i iv  ii
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_89063409_8   3579 TGAACAAAGCCAGAGATAC-CACATCACCCAAATTCATACTATTCTACAA 3627
                         v        iii   i-  -    iiv     v    v viv v      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_89063409_8   3628 GGTTATAGTAACCAGAAGAGCATGGTACAAG--TAAAAATCAGACACACA 3675
                         i i  i     i  ii v  ii      vi --   ii  -     i i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATA 294

  chrX_89063409_8   3676 TACCAACGGAACAGAATAGAGAACCCAGAAATAAAGCCACACAGCTACAT 3725
                         v i   i    i     v    ii           v   i   vi  iiv
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_89063409_8   3726 CTTATTGATGTTTGACAACGTCAACAAAGATAAACAATGGTGAAAGAACG 3775
                         iiv      v  i     v viiv   iivi vv      v       i-
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT- 393

  chrX_89063409_8   3776 TGCAAGCCATTCAATAAATGATGCTGGGAAAACTGGCTAGCCATATGCAA 3825
                         --- iv iv     i     i        v      v  ?   i      
  L1M4_orf2#LINE/    394 ---AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_89063409_8   3826 AAGAGTAGAACTGGACCCCTATCTCTCACTGTATACAAAAATCAACT-AA 3874
                             i ii ii          i   v   ii           i    -  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_89063409_8   3875 A---GATTAAAGACTTGAATATGAGA-CTTGAACTACAGAAGTCCTAGAA 3920
                          ---   i ?    i i   i i   -  vi     i i  v  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_89063409_8   3921 GAAACC-TAGGAAAAACTCTTCTGGACATTGGCCTAGGAAAATAATTTAT 3969
                             v -    ?iv  v     vv   v    vi    v  - ii   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chrX_89063409_8   3970 --GACTAAGACCTCAATAGCAAATGCAACAAAATAAAAATT-GACAAATG 4016
                         --  -  v   vi   v    v v         v     v -  i    v
  L1M4_orf2#LINE/    590 TAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_89063409_8   4017 GAACTT-----AAACTAAAGAGCTTCTTCACACCAAAATAAACTATCAAT 4061
                          i    -----   i    i -   i vii vi    iv v        v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_89063409_8   4062 AGAGTACACAGACAACCTACAGAATGAGAGAAAGTATTCACAAACGATAC 4111
                          i   iv v        i        i      i    ii    iv   i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_89063409_8   4112 ATCCTATAAAGGACTAAAATAAAGAATTTATAAGAAACTA--AAAAATCA 4159
                            iv    i     viv  vv     v     ii    v-- v  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_89063409_8   4160 ACAAAAAATAAAAAAAGAATTC--TTAAAAAGTGGGAAAAGGACATAAAA 4207
                          i  v   v i v   v  ii --  ?    i    v      iv i  v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_89063409_8   4208 TGACACTTCTCAAAAGAAAGCATACACA--GTCAAGAAATATAAGAAAAA 4255
                         v    i     v      iii     v -- i   v  ii i v     i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_89063409_8   4256 AAATGCTCAACATCACTAATCAT 4278
                          --            ????????
  L1M4_orf2#LINE/    888 A--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 1.88 (49 / 26)  


1813 26.52 1.82 0.20  chrX_89071851_89077066.rev     1569  2062 (3154)    L1M4_orf2#LINE/L1        3   504 (404)  

  chrX_89071851_8   1569 GAAAGATATCTTATGTTGATGTATTGGAAGAATTAATACTGTTATAATGG 1618
                                   ii     v   v         v      i     vi    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_89071851_8   1619 TCATACTACCCAAAGCAATATATAGGTTTAATGCAATCTACATCAATATA 1668
                         iv     v      vii  v  i  i  i  i      ivi     v  v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_89071851_8   1669 TAA------TTTTTCAAAGAACTAGAAAAA--AATCCTAAAAGTCATATG 1710
                         iv ------     iiv    v v  v  i--i         v       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_89071851_8   1711 TAACTACAAAAATCCCCAAATAGACACAGCAATGTTGTACAAAAAGAACA 1760
                         v  v i   iiiv   vi     v  v i    v   v v  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_89071851_8   1761 AAGCTATAGGTATCACACTACCTGATTTCAAATCCTACTAAAAATTTATA 1810
                            i iv   vv       v  ii        v i     v   vi  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_89071851_8   1811 GTAAATAAAGTAGCATGGTACTGGCATAAGAAACAGACATATAGACCAAT 1860
                             vi  iii  ii               i -i           i    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAAT 301

  chrX_89071851_8   1861 GGAACAGAATAGAAATTATAGAAGTAAATTTATGTATCTACAGTCAACTC 1910
                             i     v  i v vi    i    iii  ii  i  ii     i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_89071851_8   1911 ATTTTCAACAAAGTTTCCAAGAATATAGATTGGAGAAAAGATAATCTCTT 1960
                               i    i v v      vi  vv v   i    ii   i   i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_89071851_8   1961 CAATAAATAGTGCTGGAAAAACTGAATATTTATATGCAGAAGAATGAGAC 2010
                            i    i       i v     i   ?ii i     i        iii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_89071851_8   2011 TAGACCCCTACCTCTAATCATATATAAAAATAAATTCTAAGTG-ATTAAT 2059
                          i            vv i      i      v  i  v  i  -  i ?v
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_89071851_8   2060 GAC 2062
                            
  L1M4_orf2#LINE/    502 GAC 504

Transitions / transversions = 1.58 (79 / 50)
Gap_init rate = 0.01 (4 / 502), avg. gap size = 2.50 (10 / 4)  

1017 24.38 6.40 1.97  chrX_89071851_89077066.rev     4320  4725 (491)    L1M4_orf2#LINE/L1      485   908 (0)  

  chrX_89071851_8   4320 ACTCAAAGTCTAACCATATTTATGACTTAAATGTAACATTTAAAACTATA 4369
                                i v-i i  ? -----   i         v vi          
  L1M4_orf2#LINE/    485 ACTCAAAATG-GATCAWA-----GACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_89071851_8   4370 AAACTACTAGAAGAATCCATAGGAAAAAAATT--ATGGCATTGGACTAGG 4417
                              vi        vv      ?iv   vi --i  i v    ii    
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_89071851_8   4418 CAAAAATGTTTTAAATAAGAACTCAAAAGCAAAGGCAACAAAAGCAAAAT 4467
                            vii v i   i   v  vvi        v i          v    -
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA- 627

  chrX_89071851_8   4468 ATAGACAAATGTAATTACATCAAACTAAAAAGCTTTTGCATAGCAAAGG- 4516
                              i    vvi i v       v v    i      iiivv      -
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_89071851_8   4517 ---CAACAATAGAGTGAAGAGACAATATACAGAATAAGATATAAAATTTG 4563
                         ---i v   v i      i      ivi       ii  v v  v     
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_89071851_8   4564 CAAGCCATACATCTGACACAGGGTTAGTATCCAGAATATA---AGAAT-- 4608
                            ii    i      i vi  ii v              ---    i--
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_89071851_8   4609 ------CTGAACAGCAAAAAC-CAAATAAATGATTT--AAAATATGTAAA 4649
                         ------  v  i ii     v-       viv v  --     iv i   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_89071851_8   4650 AGATCTT--TAGACATTTC--CAAATAAACACACACAAATGGACCACA-- 4693
                         i   i v--          --    v  i- i i        v v i --
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAG 876

  chrX_89071851_8   4694 TACATGAAAAAATGCCCATCATCACTGATCAT 4725
                         i         i    i  v     ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (55 / 42)
Gap_init rate = 0.03 (13 / 424), avg. gap size = 2.62 (34 / 13)  


 859 26.63 5.89 6.71  chrX_89083354_89087801        1   492 (3955)    L1M4_orf2#LINE/L1      355   842 (66)  

  chrX_89083354_8      1 TTTGGAAAGAATAC-AAGAGCAATTAA---AGAAAAAATTGTTTTTTGAA 46
                           i iv   ii i -    v  v i  ---i    i   v  i    v  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_89083354_8     47 CAAATGGTACTGAAAGAATCAGACATCATTAAA-GAAAAAGATAAAATAT 95
                                 i   ii v  iii  i ? --i v - v      ------  
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKC--CACATGCAAAAGA------AT 446

  chrX_89083354_8     96 GGAAAAAATTTAAAAAATCAAAGATACAGACTTTACATCTTAC-CAAAAA 144
                          ----  i  -----------i  iv vv  i i   i v  i-      
  L1M4_orf2#LINE/    447 G----AAGTT-----------GGACCCCTACCTCACACCATATACAAAAA 481

  chrX_89083354_8    145 AAAATGCAAAATAGATAACACACCCAAATGTTAAATGTAAAAGTATAAAA 194
                         vv  iv      i   v ? v   i      v i vv     v       
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_89083354_8    195 TTTCTAGATGAAAATCTAGGAATAAATTTGTGTGATTTTGAGATTGTTGG 244
                         i ii    v     iv    ?i     i vi    ii   i -  i--  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG-TTA--GG 578

  chrX_89083354_8    245 TAAAA--TTCT---ATATGCAAGACCAAATGCACAATCCAT----GACAA 285
                         i  vi--    ---     -- v      v      v v i----  v  
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATG--ACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_89083354_8    286 GTTACTTTTATGAGTTGGACTTAAT-AAAATTATAACCTTTTTTCTCTCT 334
                         iv  v----  i i        v  -       v  v     v vii  -
  L1M4_orf2#LINE/    627 AATAG----ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC- 671

  chrX_89083354_8    335 GACAGTCACTATTAAGAGGATGAAAAGATAAGTCACAGACTTGAAAAAAC 384
                         i vi v      i    iii        i  vi      v v i i   v
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_89083354_8    385 TATCTGGAAATAGTGTTTCTAA-AAAAAACTTCTATCTGGGATATGCAAA 433
                            i  v    vi i v   i -  iii    v    ii i    ii   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_89083354_8    434 GAATACTTAAAACTTA----TAAAAAGA-----AACACATTTTAA---TG 471
                            iv    v    i ----        -----   v  v  ?  ---  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_89083354_8    472 GGCAAAAGATCTTGACAGACA 492
                               i   i vi i     
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACA 842

Transitions / transversions = 1.44 (75 / 52)
Gap_init rate = 0.04 (21 / 488), avg. gap size = 2.95 (62 / 21)  

2490 28.17 3.17 0.45  chrX_89083354_89087801     3073  3956 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89083354_8   3073 TGGGAAAACATTCCATGCTGATGGATAGGAAGAAACAATATTGTTAAAAT 3122
                            i  i i  i     i v      v      vvi           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89083354_8   3123 TGCCATACTACTCAAAGCAATGTAAAGATTTAATGCTCTTTTTATCAAAT 3172
                         v  v     v i    vii  v  v     i  i  vv iii       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89083354_8   3173 TACCAGTGACATTTTTCACAGGATTAGAAAAA--AAT--TAAAATTTATT 3218
                          v    ivi v     ii   i v v  v  i--i  --       i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89083354_8   3219 TAGAACCAAAACAGAGCCAGAATATGCAAACCAATTCTAAGCAATAAGAA 3268
                          i   viiv  vi  v        vv    v    ii i iv  v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_89083354_8   3269 CAAAGATGGAGGCATCTCACTACCTGATGTCAAAATATATTTCAAGGCTA 3318
                              v      vv  v    v  ii  v      iv  i v   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_89083354_8   3319 CAGTAACTAAAACA---TGGTACTGGTACAAAAAGAGACATATAGACCAA 3365
                               ii  i   ---         i i  ii v           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_89083354_8   3366 TGGAACAGG-TTGGAAAACCAGGAAATAAAGC---ACATCTACAACCATC 3411
                              i  i-   ii iv    -       v ---    i  iiii  vi
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAG-AAATAAACCCATACATTTATGGTCAAT 349

  chrX_89083354_8   3412 TCAACTTCAACAAAGCCAACAATAACAAGCAATGGGGAAAAGACTCCCTA 3461
                          v vi   i    i viiv   v v  vv           ii ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_89083354_8   3462 TTCAATGTATGGTGCTGAGATAACTGGCTAGCCATATACAGAAGATTGAA 3511
                              iiv         i  i      v  ?   i  i  i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_89083354_8   3512 ACTGGATGCCTACCTTTCACCATATACAAAAATCAACTCAAAGTGGATAA 3561
                         ii    iv       iv                i        i     v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_89083354_8   3562 AACACTTCAATGTTAAACATACAACTATAAAAATCAAAGAAGAAAGCCTA 3611
                         ? v  i v     v i vv  v          v  vv        i v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_89083354_8   3612 GGAA-ACATCATGCTGGACATAGGACCTAGCAAAGTCTTCAT-GATG-AA 3658
                           ?i- v   - v vv   v v  iiivi    v vi   v -   i-i 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_89083354_8   3659 AACTGTAAAAACAATTGCAACAAAACCAAAAATA---AAGTGGGATCTAA 3705
                         v  iiv  iv    --         vv       ---  i v   ii v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_89083354_8   3706 TTAAACTAAAAAACTTTTGCAAAGCAGAAGAGACTATTAG---AGTAAAT 3752
                          i   v v           iivvv  i i  v     i i---   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_89083354_8   3753 AGGCAACCCACATAATGGGAGAAAATATTTGCAAACTGTGAATCAAACAA 3802
                           i         v                      iii iv   vi i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_89083354_8   3803 AGGTCCAATAACCAGAATCTATAAGGAACT--TA------AACAAGGAAA 3844
                         i  v ivi  v       v     i     --  ------  i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_89083354_8   3845 AATCAAACAACCCCATTAAAAAATGGACAAAGTTTATGAACATACACTTC 3894
                          iv    i     v   ?        i     vv v    i v   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_89083354_8   3895 TCAAGATAAAGCATATATGTGCCCAACACACATATGGACACATGCTCGAC 3944
                           v i v  iii   i vi  v    i vi  i   i v v      i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_89083354_8   3945 ATCGCTAATCAG 3956
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (132 / 113)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.13 (32 / 15)  


2359 28.27 1.98 2.09  chrX_89128911_89134837.rev     4528  5436 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89128911_8   4528 TAGAAAAGCATTCCATGCTAATGCATGGAAAGAATCAGTATTGTCCAAGT 4577
                          i    iii  i     i v   v  v i    v i i      iv ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89128911_8   4578 GGCCACACTGCTCAAAGCAAATTACAGATTCAATGCTATTCCTATGAAAT 4627
                            v i   v i    vii vi           i  v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89128911_8   4628 TACCAATGAAATTATTTAT-GTAATTAGAATAAACT-ATTTGAAAATTCA 4675
                          v   iivivv  v   ii- v    i-- i  i  -  iiv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_89128911_8   4676 TATGGAATCAATGTA---GAGCCTGAATAGTCACAGCAATCCTAAGCAAA 4722
                                ---   i ---  v  v      i  v i     i i iv  i
  L1M4_orf2#LINE/    149 TATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_89128911_8   4723 AAGAACAAGCCTGGAGGCATCACATTACTCAACTTCAATCTATACCATAA 4772
                                 ivi      vv     i v i   i     vviv   i i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_89128911_8   4773 GGCTACAGTAACACACACAAAAAAATGGTATAGGTACACAAAAACCC-CA 4821
                         i          i---  vi v ivi     iv  --  i  ii ivv-  
  L1M4_orf2#LINE/    246 AGCTACAGTAAT---CAAGACAGTGTGGTACTGG--CATAAGGATAGACA 290

  chrX_89128911_8   4822 CATAGATCAATGGAACAGAATAGAAAACCCAGAAATAATGCTGCACACCT 4871
                         i              i     v  i ii          vv iii   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_89128911_8   4872 ACATCCATTTGATCTTTAACAAAA-TCCACAAAAAGAAACAATGGGGAAA 4920
                          iivi  v     i  ii    ii- v -   i vv vv           
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAA 389

  chrX_89128911_8   4921 AGACTCCCTATTCAATAAATGGTGCTGGGATAACTGACTAGCTACATGTA 4970
                         ii ivvi  v     i              i     iv  ? i     i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_89128911_8   4971 GAAGATTGAAAATGAACCCCTTCTTTATACCATATACAAAA-TCAACTCA 5019
                         i    v    iv  i      v i i i             - i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_89128911_8   5020 AGATTGATTAAAGACATAAATGTAAAA-CCAAAACCTCTAAAAAAACCCT 5068
                          i  v   i ?    v         i - i     ---  v    vi i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC---TATAAAACTCTT 536

  chrX_89128911_8   5069 AGAAGATAATCTAGA---AAATACCATTCTGTACATAGGACCCAGCAAAG 5115
                               v  iv   i---    -- v iv  -  v v  iiivi    v 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT--CTTCGTG-ACCTTGGGTTAGGCAATG 583

  chrX_89128911_8   5116 ACTTCATGACAAAGACTCCCAAAGCAATTGCAACAAAAACAAAAATTGAC 5165
                         ii   v iivv v   v  v      vvv         iv      v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_89128911_8   5166 AAATGGGACCTAATTAAACTAAAGAGCTTCCGCACAGCAAAAGAAACTAT 5215
                             v    i v  i   v v  i i   ii ii vv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_89128911_8   5216 CAACAGAGTAAACAAATAACCTTAATAATAGGA-AAAATATTTGTAAATT 5264
                            v i   i  v i i    ivv v   i   -          i    i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_89128911_8   5265 ATTCATCCAACAAAGGTCTAATATCCCGCATCTATAAGAAATT--TA-AA 5311
                           vi   ii i  i  v  vi     v v  v     ii  i --  -  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_89128911_8   5312 CTTACAAAAAGAAGAAAACCAACAACCCCATT-AAAATTGAGCAAAGGAC 5360
                           --   v  v  i  i  v  i     v   -    v  i        i
  L1M4_orf2#LINE/    784 CT--CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_89128911_8   5361 TTGAACAGACACTCTTTAAAAGAAGACATTCATGCAGTCAACAAGCTCAT 5410
                              i     i ii iv        i  v  viii i   i    v   
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_89128911_8   5411 GAGAA-ATGCTCAACCTCACTAATCAT 5436
                           i  -         v   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (151 / 104)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.68 (37 / 22)  


2781 27.21 1.66 1.22  chrX_89161883_89167687.rev     4411  5314 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89161883_8   4411 TGGAAAAACATTCCATCCTCATAGATAGCAAGAATCAATATAGTGAAAAT 4460
                               i i  i    vi    i   v v    v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89161883_8   4461 GGCCATATTGCCCAAAGTAATTTATAGATTCAACGTTAATCCC-ATCAAA 4509
                            v   i v      v i  i  i          i-      -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAAA 99

  chrX_89161883_8   4510 CTACCATTGATATTTTTCACATAATTAGAAAAAAACT-ACTTTAAAATTC 4558
                         v v   viviiv     ii  v  v v  v  i--  - iii        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_89161883_8   4559 ATAAGGAACCAAAAAAAGAGCCCACA-TAGCCAAGACAATCCTAAGCAAA 4607
                            v    -- viv  i ii    v -       i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_89161883_8   4608 AATAACAAAGCTGGAGGCATCACGTTACTTGGCTTCAAACTATACTACAA 4657
                           v       i      vv    ii v iiiii      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_89161883_8   4658 GGCTACAGTAACCAAAGCAGCATGGTACTTATACCAAAACAGACATATAG 4707
                         i          i   ii   ii       vii iv ii i          
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_89161883_8   4708 ACCAATGGAAGAGAATAGAGACTTCAGAAATAAGACCACACATCTCCAAC 4757
                          i        v     v    v i         iv   i    i viiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_89161883_8   4758 CATCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGAAGAGGATTC 4807
                           vi    i   i    ivv  v   i v  vv       i i  i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_89161883_8   4808 CCTATTTAATAAATGGTGCTGTGGA-AACAGTCTAGTCACATGCAGAAAA 4856
                         i  v  i  i           -   -   v vv  ?i        i  i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_89161883_8   4857 TTGAAACTGGATGCCTTCCTTACACCTTATACAAAAATTAACTCAAGATG 4906
                         v    ii    iv   v   i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_89161883_8   4907 AATTAAAGAATTGAATGTAAAACCCAAAATGATAACAACCCC-AGAAGAA 4955
                         i  i ?   vi i       i v i    iv    -   i i-       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAA 543

  chrX_89161883_8   4956 AACCTAGGCA-ATACCATCATGACATAGGCATGGGCAAAGATTTTAT-GA 5003
                            v    ?i- v i v  i    v v  vv i     v i   iv -  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_89161883_8   5004 TGAAATCACTAAAAGCAATTACAACAAA--------TTGACAAATGGGAT 5045
                          ivi -   i       vvvi       -------- v  i    v   i
  L1M4_orf2#LINE/    594 TATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_89161883_8   5046 CTAATTATACCAAAGCACTTCTGCATAGCAATAGAAACTATCATCAGAGT 5095
                         i v  i v viv  iv    i  iiivv   vi  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_89161883_8   5096 GAACAGGCACCCTATAGAATAGAAGAAAATTTTTGCAATCTACACATCTG 5145
                            v  i  v  i i     i i       v       vii i i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_89161883_8   5146 ACAAAGGTCTAATATCCAGAATTTACAAGGAACTTAAACAAATTTACAAG 5195
                          i  i  v  vi          v  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_89161883_8   5196 ACAAAAACAAATAACCCCATCAAAAAGTGGGCAAAGGATATGAATAGAAA 5245
                          v   i           v  i?    i            v        v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_89161883_8   5246 CTTCTCAGAAGAAGTTGTGCATTATGCAGCCAATAGTCGTATGAAAAAAA 5295
                         i     vi      v i i  v-   --       iv ii       i v
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAA-ATG--GCCAATAAGCACATGAAAAGAT 889

  chrX_89161883_8   5296 GCTCAATATCATTGATCAT 5314
                               i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.62 (26 / 16)  


1886 28.83 1.19 1.63  chrX_89177557_89179210      503  1175 (479)    L1M4_orf2#LINE/L1      239   908 (0)  

  chrX_89177557_8    503 ACTACAGGGCTACAGTAACCAAAACAGTGTGGCACTGGTATAAAAACAGA 552
                               ii          i   i         i     i    ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_89177557_8    553 CACATAGACTAATGGAACAGAATATAGAGCCCAGAAATAAGGCTGCCCAC 602
                           i     ii       i     vv    i          iv iiiv  i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_89177557_8    603 CTAAAATTATCTGATTTTTGACAAAG-TGACAAAAACAAGCAATGGAGAA 651
                         i  vii i vi       i     i -  v   i v  vv      i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_89177557_8    652 AAGACTCCCTCCTATTCAATAAATGGTGTTGGGATAACTGGCTAGCCACA 701
                          ii ivvi  i---     i        i     i      v  ?     
  L1M4_orf2#LINE/    389 AGAATAGTCTT---TTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_89177557_8    702 TGGAGAAGATTTAAACTGCACCCATTTTTTACTTCACATACAAAAATGAA 751
                           v i    v v  ii  v    v vii i  vi  i          v  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_89177557_8    752 CTCAAGGCAGAATAAAGATTTAAATGTGAAAACCAACACTATAAAAACCC 801
                              iiii  vi ?   ii       i i i i  v         vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_89177557_8    802 TGAAGGACAACCTAGAAAAATACCATCCTGGACCTAGAAACTGGCAAAGA 851
                          ii i  v   v   i?iv v i v  v  -    v iiviv     v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGG 584

  chrX_89177557_8    852 TTTCATGACAAAGATCCCAAAAGCA-ATGTTAGTAAAAGCAAAAATTTAC 900
                             v iivv v  iv         - v i- ii     v      vv i
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGAT 633

  chrX_89177557_8    901 AAATAGGATGT-ATTTAAATGTAAGAGCTTCACCATAGC--CAAAGAA-A 946
                             v   iv -  iv    -   i i   i--ii -  --     i - 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAAT-TAAAAACTTT--TGT-GCTTCAAAGGACA 679

  chrX_89177557_8    947 CTATCAACAGAGTACACAGACAACCTATGGAACAGGAGAAAATATTTGCA 996
                                v i   iv v        i ii   ii                
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_89177557_8    997 AACTATGCATTTGACAAAGGTCTAATATATAGTATCTATAAGGACCTTAA 1046
                           ii  ii  i   i  i  v  vi   vi  v  v     i  v  ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_89177557_8   1047 ACAAGTTTACAAGCAAAACACCAAGAGCCACATTAAAAAGGAGGCAAAGG 1096
                             v iv i  vv    v  v  v i  vv   ?    ivi        
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_89177557_8   1097 ACATGAGCA--CACTTTTCAAAAGAAGACATACATGTGGCCAACAAGCAT 1144
                          iv   ii --  i  i  v        i     vi       i     i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_89177557_8   1145 GTGAAAAAAAAATTCAATTATCACTGAGCAT 1175
                         i      i vi-i    i-    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATG-CTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (119 / 71)
Gap_init rate = 0.02 (14 / 670), avg. gap size = 1.36 (19 / 14)  


2446 26.82 3.30 0.83  chrX_89275312_89277028      498  1224 (493)    L1M4_orf2#LINE/L1      164   908 (0)  

  chrX_89275312_8    498 GACCC-TAATAGCTCCAGCAATCTTGGGCAAGAAGAATAAAGCTAGCGGC 546
                              -v      ivv i        iiv        i    i i v  v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_89275312_8    547 ATTATACTTCTTAATTTTAAATTATATTACAAAGCTATAGTGAGCCTAAC 596
                         v i i     ii     i   viv  i          i   i v vvi  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_89275312_8    597 AGCATAATTTTGACATAAAAAAACAGATACATAGACCAACAGAACATAAT 646
                           ii ii vi  i     ii --i   i i     i   ii   i v   
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGA--TAGACATATAGATCAATGGAATAGAAT 311

  chrX_89275312_8    647 AGAAGGACCAGAAATAAACCCACACATATACAGTCAACTAATCCTCAATG 696
                         v  ii v               i    v  ii     i i  ii  i ii
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_89275312_8    697 AAGGTGCCAAAAATACACAATGGAAAAAGGATAGAAGTTTCAGTAAGTGG 746
                          i        i vi iv      ii    i    vvv     ii  i   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_89275312_8    747 TGTTAAGAAAAT--GACATCCACATGCAGAACAATGAAATTGAATTATTA 794
                           i ii  v  i--  i ?         i  v      i   i iivi  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_89275312_8    795 TCTCACACCATACACAAAAATCAACTCAAAATAGATTATAGACTAAACTT 844
                         i           i        i          i   i ?    iv  v v
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_89275312_8    845 TAAGACCTGAAACTA--AATCTCCTAAAAGAAAACACAAGGGAAAAGTTT 892
                              v  i      --  v   i  i         i i ? v   vi  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_89275312_8    893 CATGACATTAATCCTGGCAATGATCTTTTGGATATCACACCAAAAGCAAA 942
                          i    v  iiviiv       i i i  i     v            v 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_89275312_8    943 GGCAACAAAAGCAAAAATAATCGAATGTGACTATAT----AT-------- 980
                         i          v       ivii   vv    vi  ----  --------
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_89275312_8    981 ---GCACAGGAAAGGAAACTGTTAACAAAATGAAAAGGCAACCTACAGAA 1027
                         --- ii vvv      v   i i  v   i       i     i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_89275312_8   1028 TAGAAGAAA-TATTTACAAATTATGTATCTGATAAGAGGTTAAAATTCAA 1076
                          i i     -     i     i  i           i ii viv  i  i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_89275312_8   1077 AACATGTAAGAAGCTGTTACGACTGAATAGCAAACAAGA--AATAACCTG 1124
                           i  i   ii i  v    i   v    ii   -    --       ii
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAAATAACCCA 810

  chrX_89275312_8   1125 ATTTTGAAAAATAACCATAGAATCTAAATAGATATTTCTCCAAGAAAGAC 1174
                            ?--      iiv  v  i  i i      i          ii    i
  L1M4_orf2#LINE/    811 ATTW--AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_89275312_8   1175 ATACAAATTGTCAACA-GTATCTGAAAAATTGATCAAACACCATTAATCA 1223
                                 v i   i - i iv      iv  v    -  i  ???????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA-CATCAZZZZZZZ 907

  chrX_89275312_8   1224 T 1224
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.35 (134 / 57)
Gap_init rate = 0.02 (12 / 745), avg. gap size = 2.50 (30 / 12)  


2667 26.70 1.40 3.66  chrX_89308513_89319759     3873  4801 (6446)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89308513_8   3873 TGGAAAAACATTCCATGCTTATGAATAGGAAGAATCAATATTGTAAAAAT 3922
                               i i  i     i i   i  v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89308513_8   3923 GAACATACGGCCCAAAGCGATGTATAAATTCAACAATATGCCTATCAAAC 3972
                          ivv    vv      vi   v  i i       ivv  v         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chrX_89308513_8   3973 GACTCA--TGACATTCTTCTCAGAACTAGAAAACACCATCTAAAAATTCA 4020
                         iv i  --  v -  i  iv     v v  v  vviv   iv        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_89308513_8   4021 TATAGAACTACAAAAAAGCCAGAATAGCCAAGGTAATCCTAAACAAACAA 4070
                            i   v i   iii v             iii    i i  -------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA------- 191

  chrX_89308513_8   4071 ACAAACAAAAAAAAAACCAAAAAACAAAAAACAAAGCTGGAGGCATCACG 4120
                         -------   i  i   ---------------    i      vv    i
  L1M4_orf2#LINE/    192 -------AAAGAAGAAC---------------AAAGTTGGAGGACTCACA 219

  chrX_89308513_8   4121 CTACCCAACTTCAAACTATACTACAGGGCTACAGTAACCCAAACAACATG 4170
                           v     i      viv       ii          i v i   iii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_89308513_8   4171 GGACTGGTACAAAAACAGAAACACAGACCAATGGAACAGAATAAAGAACC 4220
                          v     i i  ii i   v i i   i        i     vi   ii 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_89308513_8   4221 TGGAAATAATATTGCACACTTACAACTATGTGATCTTTGACAAACCTAAC 4270
                         ii       vviiii   i   iiiii vv    i  i     ivv iv 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_89308513_8   4271 AAAAACGAGCAATGGGAAAGGGATTCTGTATTCAATAAATGGTGCTGGGA 4320
                           i v ivv       i  i i  vv v v     i              
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_89308513_8   4321 TAACTGGCTAGCCATATGCAGAAGATTAAAACTGGACCCCTTCCTTACAC 4370
                         i      v  ?   i     i    v i  ii         v   i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_89308513_8   4371 CATATACAAAAATTAACTCAAAATGGATTAAATACTTAAATGAAAAACCC 4420
                                                     i ? v  i      v  i v i
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_89308513_8   4421 AAATCTATAAAAATCCTGGAAGATAACTTAGGCAGTA--CCATTCAAGAC 4468
                            v        v  i i     v   v    ?-   --i -   iv   
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGN-GTAAATC-TTCGTGAC 567

  chrX_89308513_8   4469 ATGGGCACAGGTAAAGATTTTACAACGAAGTCTTCAAAAGCAATTGCAAG 4518
                         v v  vvi   i  v i   ivi ivv v v vi        vvv    v
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_89308513_8   4519 AAAAGCAAAAATTGACAAATGGGATCTGATTAAACTAAAGAGCTTCTGCA 4568
                              v      v  i    v   ii v  i   v v  i i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_89308513_8   4569 CAGCAAAATAAACCATCAGCAGAGTAGGCAGACAACCTACAGAATGGTAG 4618
                          vv    iv v  i    iv i   iiiv        i         v  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_89308513_8   4619 AAAATTTTTGCAAACTATGCATCTCACAAAGGTCTAATATCCAGCATCTA 4668
                              v        ii  ii    v i  i  v  vi       v  v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_89308513_8   4669 TAAGGAAGTTAAACAAATT-----TACAAAGA-AAA--ACCTCATTAAAA 4710
                            i   v ivv    v i-----  v     -   --   iv   ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_89308513_8   4711 TAGTGGGCACAGTACATGAA-AGATACTTTGGAAAAGAAGACATACATGT 4759
                         - i      v  v iv    -   i i  ivvv        i     vi 
  L1M4_orf2#LINE/    818 -AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_89308513_8   4760 GGCCAGCAATCATATGAAAAAAAGCTCAACATCACTGATTAT 4801
                              ii  v  i       i v           ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (137 / 107)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.62 (47 / 13)  

2630 24.30 3.79 2.56  chrX_89308513_89319759     9858 10754 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89308513_8   9858 TGGAAACACTTCCCATGCTCATTGATTGGAAAAATCAATATTGTGAAAAT 9907
                               v iv       i    v        i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89308513_8   9908 GACCCTACTGCCCAAAGCCATCTAGAGATTCAATGCAATTC-TATCAAAA 9956
                          i vv    v      viv     v        i     i -        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89308513_8   9957 TACCAACATCATTTTTCATAGAACTAGAAAAAACAATAATCCTTAAAATT 10006
                          v   i vv v     iii    v v  v  i- -- i     -      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-C--TGATCCT-AAAATT 146

  chrX_89308513_8  10007 CATATGGGACCAAAAAAGAGCTCAAGTAACCAAAGCAAATCCTTAGCAAA 10056
                                i viiv  ii  v ivi i  i     i   -  i v iv  i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAG 195

  chrX_89308513_8  10057 AAGAACAAATACAGAGGCATCTCATTACCAAATTTCAAGTAA--TACTAC 10104
                                  vvii    vv  v  i v  v        --  --      
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA--AACTTACTAC 243

  chrX_89308513_8  10105 AAGGCTGTAGTTACCAAAACAGCATGGTACTGGTATAAAAGTAGACATAT 10154
                           i   ii   v i   i    ii         i    iii         
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_89308513_8  10155 AGACCAATGAACAAGAATCGATAACCCAGAAATAAAACTAAA----TACA 10200
                            i     i vv     i  v ii           v i v ----  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_89308513_8  10201 ACCAACTGATGTTCAACAAAGCATAC-AATAACAT--AATTTGGGGAAGA 10247
                         ii   i    v   i    i -i i -  v v   --   --      ii
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAAT--GGGGAAAG 390

  chrX_89308513_8  10248 GACACCCTATT-AATAAATGGTGCTGGGAAAACTGGCTAGCCACATGCAG 10296
                         i i vi  v  -  i              v      v  ?         i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_89308513_8  10297 AAGACTGAAACTGTATTCCTATCTCTCACCTTATAGAAAAATCAACTCAA 10346
                             v    ii  v ii    i   v    v    v      i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_89308513_8  10347 GATGGATTAAAGACTTAAATCCAACACCTAAAACCATACAAAATTTTAGA 10396
                         i      i ?    i     vi  v v       i   -   v i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGA 539

  chrX_89308513_8  10397 AAATAACAT---TGTAAAAACTCTTCTGGACAGTGCCCTAGAAAAATAAT 10443
                          i v     ---?     ---     vv   vv  vvi   iv  - ii 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAA-TGGT 585

  chrX_89308513_8  10444 TTATGTCTTAAA-----CCCCAAAAG-ACAATGCAACAGCAATAAAAACA 10487
                           ----    i ----- v       -    -      --  vi    v 
  L1M4_orf2#LINE/    586 TT----CTTAGATATGACACCAAAAGCACAA-GCAACA--AAAGAAAAAA 628

  chrX_89308513_8  10488 AAAATAAATGGGACCTGATTGAATTTAAAAGCTTCTGTGTGGCGAAACAA 10537
                         v i      v    i v  ii  v      i   i    ivv i  iv v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_89308513_8  10538 ATAATCA-----GCAAACAGACAA-----AAAGTGGGAGAAAATATTTTC 10577
                          iv    ----- ii  v      ----- i i               v 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_89308513_8  10578 AAAC--TGCATCCAGCAAAGGACTAGTATCTAAAATCTACAA-GAACTTA 10624
                            i-- ii   iiii  i     v     i i   v  i  -     iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_89308513_8  10625 AACAAGTCAGCAAGAAAAAGTCAA-TAATCCCATCAACAACTGGACAAAT 10673
                         v    v   ii  v      v   -   i  v  i? v  v   i    v
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_89308513_8  10674 GATATAAATAGGCATTTCTCAAAAGAAGATATGCAAATGACGAAAAAATG 10723
                            v i     i        v           i      i v  v  iii
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_89308513_8  10724 TATGAGAAAAATACTCAACATCACTAATCAC 10754
                         i    -   i  i          ????????
  L1M4_orf2#LINE/    879 CATGA-AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (124 / 90)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.04 (57 / 28)  


2146 28.26 2.07 3.37  chrX_89388764_89395050     1775  2694 (3593)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89388764_8   1775 TGGAAAAACATTCCATGCTCATGGATGGAAAAAATCAATATTTTTTAAAT 1824
                               i i  i     i        v i  i v i      v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89388764_8   1825 GGCCATACTACTCAAAGCAATTTATAGAGTCAATGCTATTCCTATTAAA- 1873
                            v     v i    vii  i  i   v    i  v  i     i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89388764_8   1874 TCACCATTAACATTCTTCACAGAAACAAAGAAAACT-ATTTTAAAATTCA 1922
                           -   vivi v  i  ii      ivi v  i-  -  ii         
  L1M4_orf2#LINE/    101 TC-CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_89388764_8   1923 TATAAAACCA-AAAAGAGCCTCAATGGCCAAGGCAACTGTAAGTAAAAAG 1971
                            ii  vii-  ii  v  vv   i     ii   iiv i ---     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAG 195

  chrX_89388764_8   1972 AAAAAAATAAAAAACCAAGCTGGAGGCATCACTGTACCTGACTT-GAAAC 2020
                           i  --------- v   i      vv    vv v  ii i  -i    
  L1M4_orf2#LINE/    196 AAGAA---------CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_89388764_8   2021 T-ACTATATAGGGCTACAGTAACCCAAACAA-ATGGGACTCGTACAAAAA 2068
                          -    i v  --         i v i   i-i   v   v i i  ii 
  L1M4_orf2#LINE/    237 TTACTACAAAG--CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_89388764_8   2069 CAGACAGATAGACCAATGGAACAGATTAGAGTACCTAGAAATAAGAAGAA 2118
                         i     v     i        i   v v   vii i        ----- 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA-----A 329

  chrX_89388764_8   2119 C--ATGAACCTACAACTAACTCATCATTGACAAACCAGACAAAAACAAGC 2166
                          --  iv ii  iiiii  i v  iv i     ivvv v   i v  vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_89388764_8   2167 AATGGGAAGAGCACTCCCTATGCAATAAATGGTGCTGGTATAACAGGCCA 2216
                               i i  v ivvi  v v   i            v i   v  vi 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_89388764_8   2217 GACATATGCAGGAGATTGAAACTGAAACCCTTCTTTACACCATACAAAAA 2266
                         ?v  i     ii   v    ii  i v    v i i        i v   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_89388764_8   2267 AATTACATCAAGATGAATTAAAGACTTAAATGTAAAACCCAAAATTATAA 2316
                              vv    i   i  i ?    i         i v i    i     
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_89388764_8   2317 AAACCCTGGAAGTCAACCTAGGCA-ATACCAGTTAG-GACATAGGCATGG 2364
                           vi i i    vv   v    ?i- v i --  v -   v v  vv i 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAG 577

  chrX_89388764_8   2365 GCAAAGATTTTAT-GATGAAGAAGTCAAAAACA-ATGTCAACAAAAGCAA 2412
                             v i   iv -   - v  vii     i  - v -         v  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAG-CAACAAAAGAAA 625

  chrX_89388764_8   2413 AAATGGACAAATTGGATCTAATTAAACTAAAGAGCCTATGCACAACATTA 2462
                             i  i        ii v  i   v v  i i i v  ii vv  -- 
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--A 673

  chrX_89388764_8   2463 AAAAAACTATCAACAAAGTAAACAGACACCCTACAGAATGGGAGAAATT- 2511
                          ii v        v     i  v     v  i               v -
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_89388764_8   2512 TTTGCAAACTATGCATCCAACGAAGGTCTGATATCCAGCATCTATAAGGA 2561
                                 ii  ii   ii ii i  v  vi       v  v     i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_89388764_8   2562 ACT-TAATGAATTTACAAGAAAAATACAAACAACCCTACAAAAAAGTGGG 2610
                            - v ii v iv i  v     v     i     v iv?    i    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_89388764_8   2611 CAAAAAAACATGAACAG-CACTTTTCAAAACAAGGCATATATGTTGACAC 2659
                             ii vi-    i  -  i  i  v   v   ii   i vi v --- 
  L1M4_orf2#LINE/    824 CAAAGGATT-TGAATAGACATTTCTCCAAAGAAGATATACAAATGG---C 869

  chrX_89388764_8   2660 CAATAATTTTTTAAAA----GCTCAACATCACTGATTAT 2694
                               viviv i   ----           ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (151 / 105)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 1.85 (50 / 27)  

2933 23.23 2.27 1.20  chrX_89388764_89395050     4533  5281 (1006)    L1M4_orf2#LINE/L1        1   757 (151)  

  chrX_89388764_8   4533 TGGAAAGTTATCCAGTATTCGTGAATTGCTATACCTAGTATTATTAAGAT 4582
                                v     vi i   i  i    vv v  i  i    i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89388764_8   4583 GCTTATACTGCCCAAAGCGATCTACAGATTTAACGCAATTGCTATCAACA 4632
                          viv     v      vi            i        iv       v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89388764_8   4633 TTCCAA--AATTTTTTTGCTTAAGTAGAAAAGTTTATACTCAAATTCATA 4680
                          i   i--ivi        vv  i v  v   i v  v  v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89388764_8   4681 TGGAATCACAAGGGACACAAAAAGGCAGAAAAAAAAAATCTATCTGATAG 4730
                              vii        v  i  vi  v----    v     ---   v i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCC----AAAACAATCT---TGAAAA 193

  chrX_89388764_8   4731 AGGAAACCAACGTCGTAGTACTCACACTTTCTTATGTCAAATTTTACTAA 4780
                           i i v   v  i v  v          i iv  v     vi      v
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_89388764_8   4781 AAGGTTACGGAAATCAAAATACCTTGATACTGGGATGAAGAGTGACAAAT 4830
                           i i   i v      i i viv  i      v  i i  vv    v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_89388764_8   4831 TGTTGAATTGAATAAAATAGGG-GCCCCCAAATGTGGTCTCACAT--GTG 4877
                         v v v   v     i   v i - i  vv    ivivi vi    --i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_89388764_8   4878 GTCAAATAATTTTCATCAAGGGTGCCAGTGCCATTCCTTGGTGAAA---T 4924
                              v i      iv           ivi      vv   v    --- 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_89388764_8   4925 AGTATTT--AACAAATTATATTGGGAAAGCTGAATATCCACATGCAAAAC 4972
                            v   --       vi ii     v i   i   ?            v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_89388764_8   4973 AATGAAGTTGGACCCTTATCTTACAGCCTACACAAAAATTAACTCAAA-T 5021
                                        i  i  i   v v  i                 - 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_89388764_8   5022 GAATAAAAGACCTAAATATGAGAACTATAACTATGAAACTTGTAGAAAGA 5071
                          i  v ?          i i   i   v      i     iv     ii 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_89388764_8   5072 GAAATAGGGGAAAAT-TTCCTTACCTTGCATTAGGCAATGTTTTCTTGGG 5120
                         i v     ? v    -   v v      vi          v      i i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_89388764_8   5121 TATGACACCAAGAGCACAGGCGGCAAAATTAAAAAAACAGATAGATTGGA 5170
                                    i      i  ii     --i      i     i      
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAA--GAAAAAATAGATAAATTGGA 641

  chrX_89388764_8   5171 CTATATCAAAACTAAAA---TCTGTGCCTCAAAAGACACAATCAGCAAAG 5217
                           vi       i     --- i     i     i     v    iv    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_89388764_8   5218 TAAAAATGTGAGCTGCACAATGGGA-AAAGTATTTGCAAGTCGTATATCT 5266
                          i    viii v ii  v       -   i         i  i       
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_89388764_8   5267 GATAAGGGG-TTGCAT 5281
                                 i-   i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTAT 757

Transitions / transversions = 1.22 (94 / 77)
Gap_init rate = 0.02 (13 / 757), avg. gap size = 2.00 (26 / 13)  

 608 16.55 11.03 0.69  chrX_89388764_89395050     5650  5794 (493)    L1M4_orf2#LINE/L1      749   908 (0)  

  chrX_89388764_8   5650 GATTCATATTCAGAACATATAAAGAACTCCTAAAACTCAATGACAAAAA- 5698
                           i ii   i     i             i  v        i i     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_89388764_8   5699 --AGACAACTTGATTAAAAAATGGGCCAAGGGTTTGAATACATATTTCTC 5746
                         -- i i   iii   ?          v    i        v i       
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_89388764_8   5747 CAAA------------ACGGCTAA-AAGCACCTGAAATAAATGCTCACCA 5783
                             ------------ i   i  -      v     - i       v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAA-AGATGCTCAACA 897

  chrX_89388764_8   5784 TCATGAATCAT 5794
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 3.60 (18 / 5)
Gap_init rate = 0.03 (4 / 160), avg. gap size = 4.25 (17 / 4)  


2709 26.53 2.34 1.23  chrX_89423961_89429302.rev     3955  4851 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_89423961_8   3955 GGGAAAACATTCCATGCTCATGGATAGAAAGAATCAATATCGTTAAAATG 4004
                           i  i i  i     i        v i    v i     i     i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_89423961_8   4005 GCCATACTACCCAAAGCAATTTACAGATTCAATGATACTCCCATTAAACT 4054
                           v     v      vii  i           i vv ii  i  i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_89423961_8   4055 ACTC--TTAACTTTCTT-CACCAAATTAGAAAAAATCT-ATTTTAAAATT 4100
                         - i --i iv    i  -  v-     -  v  i--  -  ii       
  L1M4_orf2#LINE/    102 -CCCAGCTGCCTTTTTTGCAG-AAATT-GACAAG--CTGATCCTAAAATT 146

  chrX_89423961_8   4101 CATATGGAA-TGAAAAAAAGAGCCTGAATAGCCAAGAAAATCCTAATAAA 4149
                                  -  v  ii--  v  v          i v    i i v   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_89423961_8   4150 -AAGGACAAAACTGGAAACATCACAGTACCTGACTTCAAAATATACTACA 4198
                         -   i     ii    iivv     v v  ii i       iv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_89423961_8   4199 GGGCTACAGTAACCAAAATATCATGGTACTGGTATAAAAACAGACACAAA 4248
                         ii          i   i i vii         i    ii i     i v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_89423961_8   4249 TGCCAATGGAACAGAATAGAGAACCCAGAAATACGAAC--ATGAGCCTGT 4296
                         vii        i     v    ii         --   --  iviii i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATA--AACCCATACATTTAT 342

  chrX_89423961_8   4297 AACTATCAGATCATTGACAAATCTGACAAAAACAAGCAATGAGGAAAGAA 4346
                         iiii viv   iv i     ivv  v   i v  vv     i        
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_89423961_8   4347 TTCCCTATTCAATAAATGCTGCTAGGATAACTGGCTAGCCATAAGCAGAA 4396
                          vvi  v     i     v    i   i      v  ?   i v   i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_89423961_8   4397 AATTGAAACTGGACCCTTTCCCTATACCTTACACAAAAATTAACTCAAGA 4446
                         i v    ii       i v  ii i   v  i                i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_89423961_8   4447 TGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAATA 4496
                              i ?    i         i v i            vi i i   v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_89423961_8   4497 AAACTTAGACA-ATACCATTCAGGATGTTGACATGGGCAAAGATTTCAT- 4544
                             v   i?i- v i -   iv  iv   ivv i     v i    v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_89423961_8   4545 GATGAAGATACCAAA-GCAATTGTAATATAAGCAAAAATTGACAAATGGG 4593
                            - v  i      -   vvv i  i v   v      v  i    v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_89423961_8   4594 ATCTAATTAAACTAAATAGCTTCTGCCCAGCAAAGGAAGCTATCAACACA 4643
                          ii v  i   v v  v i   i  iv vv       vi       v v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_89423961_8   4644 GTAAA----CAGTCTACAGAATAGGAGAAAATTTTTGAAAATTATGCATC 4689
                           i  ----  ii i       i         v    v    i  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_89423961_8   4690 TGATAAAGT-CTAATAGCCAATATCTATAAGGAACTTAAATAAATTTACA 4738
                               i v-  vi  v   iv  v     i     ivv i  v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_89423961_8   4739 AGAAAAA-ACTAACAACCTCATAAAAAAGTAGGCAAAGTACGTGAACAGA 4787
                          v     -  v  i    iv  v?    i i       v iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_89423961_8   4788 CACTTTTCAAAAGAAGACATACA----GCCAAGAATCATATAAAAAGAAG 4833
                           i  i  v        i     ----     v  v  i  i      v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_89423961_8   4834 CGCAATATCACTGATAAT 4851
                          v   i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 1.52 (32 / 21)  


2831 27.64 2.70 0.67  chrX_89467336_89470312.rev     1605  2494 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89467336_8   1605 TAAAAATACATTCCATGTTAATATATTGGAAGTATTAATACTGTCATAAT 1654
                          ii   v i  i       v  iv        vv      i   i vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89467336_8   1655 GTCCATACAAACCAAGGCAATCTACACACTCAATGCAATTTCTATCAGAA 1704
                          v v    vvv    ivii       v i    i     ii      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89467336_8   1705 TTCCAAAGGCATATTTTTCAAAAATAGAAAA--TAATTCTAAAATTCTAA 1752
                          i   ivv  v v    v  i    v  v  -- i  i         vv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89467336_8   1753 CAGAACCACAAAAT-CCCTGAATAGCTAAAGCAATCTTGAGCAAAAA--- 1798
                         ii   vii   iiv-   v       i   i         iv  i  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_89467336_8   1799 CAGAGCAGGAGATATCATGCTTTTTGACTTCATATTATATTACAATGCTG 1848
                           i  iv    ivv   ii   iiii i    v viv  i     v   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_89467336_8   1849 TAGTAAAGAAAACGATGTGGTACTGACATATAAACAGATATATAGATCAA 1898
                         i     vv  i  ii          i    vii i   i           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_89467336_8   1899 TAGAAGAAAAGAGAGAATGCTGAAATAAACCCACATATTTAGAACCAACT 1948
                          i   v i  vv    i v v            i i     viii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_89467336_8   1949 GTTCTCCCATCAGGGTGCTAAGAACACACGATGGAGAAAGGATAGTCTTT 1998
                          v i i v iv       i    v  iv i    i     i         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_89467336_8   1999 TTAGCAAACAGTGCTAGGAAAATTAGATATCCATACGCAAAACAATGAAA 2048
                          i i    ii     i   v  i i    ?   i i      v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_89467336_8   2049 CTGAGCCCCTATTACACAACATACATAAAAACAAACTCTAAGTAGATTAA 2098
                         i  ii      iiv    v    i i     iv     v  i i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_89467336_8   2099 AGACTTAAACATAAAACTTGAAACCATAAAAATCCTAGCAAAAAAAAACA 2148
                             i    ii   i vi i    i      v  i   ---  i      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG---AAGAAAACA 547

  chrX_89467336_8   2149 TGGAAAAAGCCCTTCCTGACATTTTTTTTTAGCAATAATATTTTGGATAT 2198
                          i i?iv ivi    v    -i  vvv  vi     ii v i  i     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_89467336_8   2199 TATACCAAAA-CACAGGCAACAAAAACACAAACAGACAAGTGGGATTATA 2247
                         v i       -    i         iv v   i   i  i v   i vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_89467336_8   2248 CCAAACTAAACAGCATCTTTGCAACAATGGAAACCATCAACAAAATGAAA 2297
                         i    v v  v i v i v   vv   v   v  i     v   i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_89467336_8   2298 AGGCAACTTACAGATTGAGAAAAAA-ATT-GCAAATTATATATCTGATAA 2345
                           i    ii     v  i  i    -   -      i             
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_89467336_8   2346 GGGATTAATATCCAAAATATGTAAAGCACACTTGCAATTCAATACCAAGA 2395
                             i vi      i     i     v  v   i   i      vi  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_89467336_8   2396 ATACAAATAATCCAATTAATAAATGAACTAA-------AAT--------C 2430
                          v        i      ? v     ii v  -------   -------- 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_89467336_8   2431 CACAAAACAGAAATTCACATGGCCAACATGTGTATGAAAAGGTGTTCATC 2480
                         iv    iv   v  v  v        i v iii        i  i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_89467336_8   2481 TAATCATCAGGGAA 2494
                         --    ????????
  L1M4_orf2#LINE/    897 --ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.73 (30 / 11)  

 269 20.43 2.15 4.30  chrX_89467336_89470312.rev     2578  2670 (307)    L1M4_orf2#LINE/L1      435   525 (383)  

  chrX_89467336_8   2578 ATGTGAAGAAAAGAAGCTCTTGTATAT-TATCTCACACCATACACAAAAA 2626
                            ii  ii  v    ---   v ivi-  i           i       
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAG---TTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_89467336_8   2627 TAAACTCAAAATACATGACAGGCATAAAGGTAA-AGCTTAAAACT 2670
                          v          iv  v ?  i v    v    -    -      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACT 525

Transitions / transversions = 1.25 (10 / 8)
Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.50 (6 / 4)  


2813 26.95 1.54 1.65  chrX_89470566_89474814.rev     2850  3758 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89470566_8   2850 TGGAAATATATTCTATGTCCATAGATTAGAATAATCAATATTGTTAAAAA 2899
                               v    i i    i   i    i   v v i           i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_89470566_8   2900 TGTCACTACTACCCAAAACAATCTACAGATTCAATGCAATCTCTATCAAA 2949
                           v  v    v      vii              i      i        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_89470566_8   2950 ACACCAAAATCATTCTGCACAGGTATATTTTTTAAAAAC----CCTAAAA 2995
                          iv   ivvv v  i vii   iv  ----- v v  i ----       
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAAT-----TGACAAGCTGATCCTAAAA 144

  chrX_89470566_8   2996 TTTATAGGAAACCAAAAAAGACCCAGAATAGACAAATCTATCCTAAGCCA 3045
                           i   v i  viiv  ii            v    v v   i i ivv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_89470566_8   3046 AAAGAACAAAACTGGAGAAATCACATTACTTGACTTCAAATAATACTACA 3095
                         i         ii     i v     i v iii i      vvv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_89470566_8   3096 GAGGTATAGTAACCAAAACGGCATGATACTTGTGTAAA-ACAGACATGCC 3144
                         i  v  i     i   i  i ii  i    v ii   i- i      iiv
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_89470566_8   3145 AAACAGTAGAACAGACTAGAGAACCCAGAAACAAATTCACACACCTATAG 3194
                         i v  i i   i   v v    ii       i   ii  i   ii   i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_89470566_8   3195 TTAACTCATTCTTGACAAAGATGCTGAGAACATACACTGGGGAAAGG-CA 3243
                          i  i v   i i     i i   ii   v   v  v         i-i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_89470566_8   3244 GTCTCTTCAATAAACGGTGCTGTGGA-AACTGGATATCCATATATAGACT 3292
                             i     i   i       -   -         ?   i  ii i vv
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCAAAAG 443

  chrX_89470566_8   3293 GATGATACTAGACCCCTATCTGTCACAGCATACAAAAATGAAATCAAAAG 3342
                         i    vii i        i  vv   vii          v  v      v
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_89470566_8   3343 ACATTAAAGACTTAAATCTAAAAGCTACCTCACACTATAAATCTACTACA 3392
                         iv  i ?    i     v   i     ---- v        v  vi  v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTA----AAACTATAAAACTCTTAGA 539

  chrX_89470566_8   3393 AGAAAACATTGGGAAATATATCCAGGACATCAGTCTGGGTGGAAATTTCT 3442
                                  v  ?iv v  v i iv   v ii vi i  iiivii     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_89470566_8   3443 TGAGCAATATCCCACAAGCACAGGCAACCAAAGCAAAAATGCACAACAAA 3492
                          iiii vv iv   v       i     v    v      i---i i   
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA---GATAAA 636

  chrX_89470566_8   3493 TAGGATCACCTCAAG-TTAAATACTTCTTCACAGCAAAGAAAAC----AA 3537
                          v   iiv v    i-     v    i vii vv     i v  ----  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_89470566_8   3538 CAAAGTGAAAAAA-ATCCCACAGAATGGGAGAAAATATTTGCAAACTACC 3586
                         v          i - v                             ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_89470566_8   3587 CATCTGATAAGTGACTAATAACCAGAAAATATAAGAAGCTCAAACAACTG 3636
                         i          v    vi  v      v      ii i   vv      v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_89470566_8   3637 TATAGGTAGAAACCTAATAACCAAATTAAAATAATGGGTTAAAGATTTGA 3686
                         v   ivv i  iv v       v    ?   -      iv  i       
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGA 835

  chrX_89470566_8   3687 ATATTTATT-CTCAAAAGAAGACATACAAATGGAAAGCAGGCATATGAAA 3735
                            vvi   -   v        i          vv ii i   i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_89470566_8   3736 AGGTTTTCAACATCACTGATCAT 3758
                           i vi         ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.07 (29 / 14)  


2826 27.42 2.01 0.78  chrX_89483323_89489473     4762  5658 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89483323_8   4762 TGAAAAAACATTCCATGTTCATGTACAGGAAGAATCAATATCCTGAAAAT 4811
                           i   i i  i           v iv      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89483323_8   4812 GGCCACACTGCCAAAAGTAATTTATAGATTCAATGCCATCCCCATCAAC- 4860
                            v i   v  v   v i  i  i        i  v     i     v-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89483323_8   4861 TACCA-TTGACTTTCTT-CACATAATTAGAAAAAACT-ACTTTAAATTTC 4907
                          v   -i  v    i  -  v -    i-- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_89483323_8   4908 ATATGGAACCAAAAAAGAGCCCATAA-AGCCAAGAGAATCCTAAGCAAAA 4956
                                 viiv  ii  -    v  -      i v    i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_89483323_8   4957 AGAACAAAGCTGGAGGCATCAGGATACCTGACTTCACATTATACTACAAG 5006
                                  i      vv   viv v  ii i    v viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_89483323_8   5007 TCTGCAGTAACCAAAACAGCATGGTACTGGTTCCAAATCAGATATATAGA 5056
                         v  i      i   i    ii         iviv iivi   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_89483323_8   5057 CCAATGGAACAGAACAGAGGCCTCAGAAATAATGCGACACATCTGCAACC 5106
                         i        i    iv   ivii         vv v i    i iiiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_89483323_8   5107 ATCTCATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT--T 5154
                          vi v  i  i     ivv  v   i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_89483323_8   5155 CCTTATTTAATAAATGGTTTTGGGAAAACTGGTTTTCCATATGCAGAAAA 5204
                          i  -- i  i       vi     v      v v?   i     i  i 
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_89483323_8   5205 CTGACACTGGACCCCTTTCTTACACCTTATATAAAAATTAACTCAAGATG 5254
                         v   vii         vi  i     v    i              i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_89483323_8   5255 GACTAAAGACTTAAATGTAAGACCTAAAA-------ACCCT-AGAAGAGA 5296
                           ii ?    i           v      -------  i  -      i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_89483323_8   5297 ACCTAGAA--ACACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAC 5344
                           v   i?-- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_89483323_8   5345 TAAAACCCCAAAGGAATG-GCAACAGAAGACAAAATGGACAAATGGGATC 5393
                           vi  v     i v ii-      i    v     i  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_89483323_8   5394 TAATTAATCTAAAGAGCTTCTGCAAAGCAAAAGAAACTATCACCAGAGTG 5443
                          v  i  vv v  i i   i  iivvv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_89483323_8   5444 AACAGGCAACCTGCAGAATGAGAGAAAATTTTTGCAATCTATCCATCTTA 5493
                           v  i     ii       i        v       vii  vi    v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_89483323_8   5494 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 5543
                         i  i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_89483323_8   5544 AAACAACAAACAACCCCATCAAAAAGTGAGTGAAGGATATGAACAGACAG 5593
                            vi     i     v  i?    i  i ii      v    i     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_89483323_8   5594 TTCTCAAAAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCTC 5643
                              v        i  vi vii      i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_89483323_8   5644 ATCATCACTGGTCAT 5658
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (141 / 101)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


1667 24.83 12.50 0.68  chrX_89523428_89525760.rev      684  1275 (1058)    L1M4_orf2#LINE/L1        3   664 (244)  

  chrX_89523428_8    684 GAAAAACATTATTGTGTTAATAGATTAGAAGATTTAATATTATTAAAATG 733
                             i i  i-iii    v  i    i     i        i    i   
  L1M4_orf2#LINE/      3 GAAAGATATC-CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_89523428_8    734 GCAAACACTGTCTAAGGTAAT-TATAGATTCTATTTGAAGCCTATTAAAA 782
                             -i   vi i  iv i  -  i      v ivii vv     i    
  L1M4_orf2#LINE/     52 GCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89523428_8    783 TTTTAATAGCATTTTT-GCACAAATTGACAAGATAGCCCTAAAATTCATA 831
                          iii iiv  v     -   v           v iii             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89523428_8    832 TAGAAATTTAAGGAACTCA-ACTAGTCCAAACCATTTTACATCAGAACAA 880
                          i     vi    i  i  - v   i v    v  i  iv vv    v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_89523428_8    881 CAAATTTGAAGTACTCACGTTTTC-AATATCAAAACTTACTTCAAAGATA 929
                             v   i  v      ii  i -   v            v     v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_89523428_8    930 CAGAAGTAAAGGCAGTGAGGTGCTGGGACAAGAACATGCATACATATAAA 979
                            v i v   i     v   i    v i   i i vi    i v  v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_89523428_8    980 TTGAATAAAATTGAGATTTCAGAAATAAATC--TAGATTGCTATAGTCAA 1027
                          v     i        v i          i --  v   --   i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAA 348

  chrX_89523428_8   1028 TTGATTTTTAAAAAGTGTGTAAACACAATTCGAT----------TACTAT 1067
                                 ii v   v   iv  v  v    i  ----------  v v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_89523428_8   1068 TTTGAACAATTGATG----------------------------------- 1082
                            v     v  i  -----------------------------------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_89523428_8   1083 --TTGGACTCTT---TCAG--CATATA-AAATTTTACCTCAAAATAGGTC 1124
                         --      i i ---   v--      -   vv   v        i i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_89523428_8   1125 AAAGCAAGAAATGTAAGAAATAAAACTATGAAAC------------ATGT 1162
                          ?  vvvv          iv         i    ------------ ii 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_89523428_8   1163 A--TGTAACCCTTTATGATCTTTCATTTGGCAAAATTTTCTTAGATACGA 1210
                          --?    vi   ii   i   vvi  v     viv           i  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_89523428_8   1211 TACTAAACATACAAATAATAAAACAATAAATAGATAACTTGAACTTCATT 1260
                         i  i   vii    ii  i    v  v          v   i       i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_89523428_8   1261 AAAAT-AAAGCCTTTT 1275
                              -   iv     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTT 664

Transitions / transversions = 1.30 (82 / 63)
Gap_init rate = 0.02 (16 / 662), avg. gap size = 4.88 (78 / 16)  

 880 15.04 4.14 8.27  chrX_89523428_89525760.rev     1579  1844 (489)    L1M4_orf2#LINE/L1      654   908 (0)  

  chrX_89523428_8   1579 TAAAGCCTTTTATGTTTCTAAGGATACTGTCAATAAAGTAAAAGAAACCC 1628
                             iv     i  i   v     i   i    v     i   - i  --
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA-AGAC-- 700

  chrX_89523428_8   1629 AAAACCCAAAAACAAAAACTAATCACAGAATGGGAGAAAATATTTGGAAA 1678
                         --      -----------------                     v   
  L1M4_orf2#LINE/    701 --AACCCA-----------------CAGAATGGGAGAAAATATTTGCAAA 731

  chrX_89523428_8   1679 TCATAGATCTGACAAGGAACCTGTATCCAGAATATATGAATACTTTTTA- 1727
                              v      i    i  i                i  v vi i   -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_89523428_8   1728 AA---AATAA--AAAAGAGAAATAACACAAT--AAAAGCAGACACATAAT 1770
                           ---     --      v       v    --    iii i  v vi  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_89523428_8   1771 TTAAAT-GACACTTTTCCAA-GAAGATATAAAAATGTCAAATAAACACAT 1818
                           i   -    i  i     -         v     v v     i     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_89523428_8   1819 GAAA-TATTCTCAACATTGTTAGTCAT 1844
                             -v  v        ii????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (24 / 16)
Gap_init rate = 0.04 (10 / 255), avg. gap size = 3.30 (33 / 10)  


2493 30.93 1.11 0.44  chrX_89569751_89575413     4269  5170 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89569751_8   4269 TGAAAACATATTTTGTTCTCATAGATGAGTAGAATCAATATTGTGAA-AT 4317
                           i   v    iiii vi    i   vi v   v i        v  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89569751_8   4318 GGCCATACTGCCAAAAACAATCTACACATTCAATTCAATTCCCATGAAAG 4367
                            v     v  v   vii       v      iv    i  i  v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89569751_8   4368 TACCAACATTATTCCTCACAGAGCTAGAAAAAACAATCCCAACATTCATA 4417
                          v   i vviv  ii ii    iv v  v  ivii    i  v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89569751_8   4418 TGGAACCAAAAAAGAGCCCACATAGGCAAAGCAAGACTAAGCAAAGAGAA 4467
                              viiv  ii  v  viv    v    i   vvi i iv  ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_89569751_8   4468 CAA-GTCCGAAGGCATCACATTACCTGACTTCAAACTATACTATGAAGCT 4516
                            -  iv  i i -     i v  ii i      viv     ii     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_89569751_8   4517 ATAGTCACCAAAACAGCATGGTACTGGTATAAAATTTGGCACA--GACCA 4564
                          i   v i   i    ii         i    iiv v i  i --  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_89569751_8   4565 ATGGAACAAAATAGAAAACCCAGAAATAAACTGAAATATTTACAGCCACC 4614
                               i i   v  i ii            iv v i     ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_89569751_8   4615 TGATCTTTGACAAAGCACACGAAAAC-AT-AAATCGGGGAAATGACACCT 4662
                             i  i     i -iii v  i  -  -v   -       vi i vii
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAAT-GGGGAAAGAATAGTC 397

  chrX_89569751_8   4663 TATTCAACAAATCTTGCTGGGATATTTGGCAAGCCACATGTAGGAGAATG 4712
                          v          vv        i vi   vv ?       i ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_89569751_8   4713 AAACCAGATTCTCATCTCTTACTTTACACAAAAGTCAACCCAAGATGGAT 4762
                           iiii  ii ii i   vi  iv  i      i i   i   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_89569751_8   4763 CAAGGATTTAAATCTAAGACCTAAATCTATAAAAATTCTAGAAGATAACA 4812
                           ?i  ii     v     v     v        v ii       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_89569751_8   4813 TCAGAAAAAACATTTTAGACATTGGCTTAGACAAAGAATTCATGACCAAG 4862
                          vi ?iv   iv  ivv   v    v    i   v iv   v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_89569751_8   4863 AATTCAAAAGAAAATGCAACATAAACAAAGATAACTAGGTTGGACTTCAC 4912
                          vvi      v v v      v  iv   i   iv  ii          i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_89569751_8   4913 TAAACTAAAGAGCTTCTGCACAGCAAAAGGAACTTCCAGCAGAGTAAA-- 4960
                         i   v v  i i   i  ii vv    i iv   vi  iv i   i  --
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_89569751_8   4961 --CAGCCCTCAGAGTGAGAGAAAATCTTCACAACCTATACATTCAACAAA 5008
                         --  i   v    i  i        v  ii   vii   i  iii i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_89569751_8   5009 AGACTAATATCCAGAATCTACAAGGAACTCAAACAAATTAGCAACAAAAA 5058
                         i    vi          v  i  i      vv    v i ii  i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_89569751_8   5059 ATCTAACAATCCCTTCAAAAAGTGGGTTAAACACATGCATAGACAATTCC 5108
                         iv v  i  i  vv i?    i    iv  iv iv  v       v   i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_89569751_8   5109 CAAAATAAAATATACTAAATGGCCAACAAGCATGTGATAAAATGCTCAAC 5158
                          v   v  i      -          i     ii   v  i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATAC-AAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_89569751_8   5159 ATCACTAATGAT 5170
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (169 / 106)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2512 25.29 2.88 5.98  chrX_89576158_89580406     2820  3756 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89576158_8   2820 TGGAGAGATATTCCCTGTTCACGAGTTGAAAGAATCAATCAATATTGTTA 2869
                             i      i  v      i ii   i    -- -- i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA--C--TTAATATTGTTA 46

  chrX_89576158_8   2870 AAATGTCCATACTC------------TATAGATTCAATGCAATCCCTACC 2907
                          i   v v      ------------  i        i          i 
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_89576158_8   2908 AAAATGCCAA-TGACTTTCTCGCAGAAATAGAGAAAAAAAAAAAACAATT 2956
                              v   i-  v    i i        v  v  iv--------ii  i
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--------TGATC 138

  chrX_89576158_8   2957 CTAAGATTTATATGGAACCACAAAACACCCAGAAGAACCAAAGGTTTCCT 3006
                             i   i        vii   iiv        v i     ivvv  i 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chrX_89576158_8   3007 GAGCTAAAAAAAAAAAAAAAA--AAAAGAATCACATTACTTGACTTGAAA 3054
                           ----    i  i  v   i--ii i  v     i v iii i  v   
  L1M4_orf2#LINE/    189 GA----AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_89576158_8   3055 TTATAATGCAAAGCTGTAGTAACCAAAATAGCAAAATAGTACTGGCAAAA 3104
                         viv  v i       ii     i   i i  ii--- i         v  
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTG---TGGTACTGGCATAA 281

  chrX_89576158_8   3105 AAAACAAAAACAAACAAAAACAAAAACAAAAACAAAACACATAGACCAAT 3154
                         ii v------------------------------ i   i     i    
  L1M4_orf2#LINE/    282 GGAT------------------------------AGACATATAGATCAAT 301

  chrX_89576158_8   3155 ACAATAGAACAGAGAACCCAGGAACAAATTCAAACACCTACAGTGAACTC 3204
                         iv       iv    ii    i  i   ii  v   ii  ii  v  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_89576158_8   3205 ATTTTCAAGAAAGATGCCAAGAC-ATACACTGGGGGAAAAGAGAGTATCT 3253
                               i v  i i         -  v  v     i  i - v   v i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTT 400

  chrX_89576158_8   3254 T-AATAAATGGCCCTGAAGAAACTGCATATCCACATGCAGAAGAATAAAA 3302
                          -  i      iv   iiiv     v   ?         i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_89576158_8   3303 CTAGACCTCTATATCTTTTTGATTTAACAAAAATTAAATCAAAATGGATT 3352
                         i i    i   iv  vivii-  v  -          v           i
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACC-ATATA-CAAAAATTAACTCAAAATGGATC 498

  chrX_89576158_8   3353 GAAAACGTAAATCGAAGACCTCAAACGATGAAGTTACTTCAGAAGAA--C 3400
                         i? i  v     vv    v  v    v  i  ii -   -       -- 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTT-AGAAGAAAAC 546

  chrX_89576158_8   3401 ATTGGGGAATATCTCCAGGACATTGATCTGAGCAA-ATTTTCTTGAGCAA 3449
                           v  ? v v    i iv   v   ivi ii    -iv      iiii v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_89576158_8   3450 TACTCCACAAACACAAACAA----AGCAAAAGTGAACAAATGGGATCACG 3495
                         v  v   v  i     i   ----  v    i ii i    v   iiv i
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_89576158_8   3496 TCAAG--TGAAAGGGCTTCTGCACAGCAAAGGATACAATCAACAAAATGA 3543
                             i-- i   i--   i  ii vv       i  v     v   i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_89576158_8   3544 AGAGACAACCAAGATAATAGGGGAAAATATTTGCAAATTACACATCTAAC 3593
                          i        v v v   i  i                i i i    i i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_89576158_8   3594 AAGGGATGAATAACCAGAATATATAAGAAACTCAAACAACTCTATAG-AA 3642
                               ivvi  v             ii     vv       v   i-  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_89576158_8   3643 AAAAACTAATAATGTGATCAAAAAGTGGGCAAAAGATTTAAATAGTTATT 3692
                            i  v     ivii  i?    i        i     i     vi   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_89576158_8   3693 TCTAAAAAGAAGACACACAAATGACAAGCAGGCATTTGAAAAGGTTCTCA 3742
                            vv        i i       i v ii i   iv       i v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_89576158_8   3743 ACATCATTGATCAT 3756
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (151 / 82)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.77 (83 / 22)  


2699 25.03 1.88 3.32  chrX_89604358_89608868     3123  4025 (486)    L1M4_orf2#LINE/L1       19   908 (0)  

  chrX_89604358_8   3123 TCATGGATAGAAAGACTCAGTATTGTCAACATGTCAGTTCTTCTCAATTT 3172
                                 v i      i i      i  v   v  i v  i i   v  
  L1M4_orf2#LINE/     19 TCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chrX_89604358_8   3173 GATCTAGAAATTAAATGCAATACCAATAAAAATCTCAGCAGCTCTTTTTG 3222
                               v i   v  i     v  v  v      i    v  ii      
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG 118

  chrX_89604358_8   3223 TGAATATTAACAAAATGTTTGCAAAGTTCATATGAAGAGGCAAAAGATCT 3272
                         iii v   i    iv  v ivi   i        i i v    ii  i i
  L1M4_orf2#LINE/    119 CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chrX_89604358_8   3273 AGAATAGCCAACACAATATTGAAGAAAAATAATAAAGTTGGAAGACTGAC 3322
                                    v     v     i  i  v  i         i    v  
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chrX_89604358_8   3323 ACTACCTGACTTAAAGACATACTATACAGCTACCATAAAAAAGAAAGTAT 3372
                            v  ii i  v  i  v     i v      vi   vv    v   i 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chrX_89604358_8   3373 GGTATTGACAAAATAATAGACAAAAAGATTTATAGAAAAGAGTAGAAAGC 3422
                             i  i  v  vi       v v    iv  i   v   i v  i  i
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_89604358_8   3423 CCAGAAGTATATCTACATAATATTTA--GTCAACCCATCTTTGGCAAAGT 3470
                               i  v i --    -i     --     iiv  i  i i   i v
  L1M4_orf2#LINE/    319 CCAGAAATAAACC--CATA-CATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_89604358_8   3471 GGCCAAGACAATACAACAGGGCAAAAATAGTCTTTTCAATAAATAAGTAA 3520
                         v        v  v   ii   v  i              i    ii----
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG---- 411

  chrX_89604358_8   3521 TGCTGAATTACCTGGACA-TTGGACATTCTTATGCAAAAGAAAAATATAT 3569
                              --------     -i    i ?i vi           vi -----
  L1M4_orf2#LINE/    412 TGCTG--------GGACAACTGGATAKCCACATGCAAAAGAATGA----- 448

  chrX_89604358_8   3570 AATCTAGACATTGACCTGACACCTT-TA-AAAAATTACCTTAAAATGGAT 3617
                          i - i   viiv    v     v -  -        v  i         
  L1M4_orf2#LINE/    449 AGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_89604358_8   3618 TACAGACCTAAATATAAAATGC-AAAACTATTAGAATTTTAGAAGATAAC 3666
                         i ?          i   i -  -        v i v i        v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_89604358_8   3667 ATGGGAGAAAACTTACTTGACCTTGGGT-ATGCTGATAGCTTATTACATA 3715
                           i  ? v   ii v v           - v  -i  i i  v   v   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTAGATA 595

  chrX_89604358_8   3716 CAACACAAGAGGCATGATTGAGGAAATAAATAAT---TAAAGGGAAGATT 3762
                         ii    v i i   ii vii vi   v   v   ---    vv --  i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG--GACT 643

  chrX_89604358_8   3763 TTTTTCAAATCAAAAAACTTCTCCTTTGCAAAAGACAATGTTAAGAAAAT 3812
                          iv iv    i     -   i vivi v    i    v i i      i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_89604358_8   3813 GAGAAAACAAGCCTCAGACAGAGA-AAAATATTTGCAAAAGACACATCTG 3861
                           i  i    v  v    vv i  -              vv i i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_89604358_8   3862 ATAAAGAAACGT-TATCTAATGTATACAAACAACCCTTGAAATTCAACAA 3910
                             i i - v -    i ivi    i   v   i   iv  i    i  
  L1M4_orf2#LINE/    743 ATAAGGGA-CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_89604358_8   3911 TAAGAAAACAA----CCCAATTAAAAAGTAAGACAAAGATCTGAACACAT 3956
                            i  i    ----       ?    i ii vv  i   i    i v i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_89604358_8   3957 ACCACAACAAAGAAAATATACAGTTGGTCAATAATCATATGAAA-GATGC 4005
                          iiv vv       i       iv   i      v  i      -     
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_89604358_8   4006 TCTACTATGTCATAAATGAA 4025
                           v  ---i   ????????
  L1M4_orf2#LINE/    892 TCAAC---ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (132 / 90)
Gap_init rate = 0.03 (23 / 890), avg. gap size = 2.04 (47 / 23)  


2598 27.70 3.86 0.79  chrX_89609734_89614553     3447  4327 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89609734_8   3447 TGAAAACACATTTCATGTTCATGGATGGGTAAAATCAACATTGTGAAAAT 3496
                           i   v i  ii             v  v i v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89609734_8   3497 GACCATACTGCCAAAAGCAATCTACAAATTCAGTGCAATTCCCATCAAAA 3546
                          i v     v  v   vii       i     ii     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89609734_8   3547 TACCACCATTG--TTCTGCACAGAACTAGAGAAAACAATCCTAAAATTCA 3594
                          v   v --  --  i vii     v v  v  ivii             
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_89609734_8   3595 TATTGATCCACAAAAGAGCCCACGTAGTCAAAGCAAGACTAAGCAAAGAG 3644
                            v  vvii   ii  v  vivi   i    i   vvi i iv  ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_89609734_8   3645 AACAAAACTGGAGGCATCACATTACCTGACTTCAAATTATACTGTAAGGA 3694
                               ii      vv     i v  ii i      viv    ii  i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_89609734_8   3695 TATAGTCACCAAAACAGCACAGTACTGGTATAAA---------------- 3728
                           i   v i   i    iiii       i    i----------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_89609734_8   3729 -----AACAGGATAGAGAACCCAGAAATAAAGCCAAATACTTACAGTTAA 3773
                         -----  i  i  v    ii           v   v i i   ii  i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_89609734_8   3774 CTAATCTTCAACAAAG---CAAATACAAACATGAAGTGGGGAAAGGACAT 3820
                         i i  i   i    i --- v  v  ---   vv i         i i v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAAAGAATAG 395

  chrX_89609734_8   3821 CCTATTCAACAA-TA-TACTGTGACAATTGGCAAGCCAAAAGTAGAAGAA 3868
                         i  v        - i- i   v     i   vv ?   v v i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_89609734_8   3869 TGAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACCCAAGATGA 3918
                             ii    i  ii i   v    v           i   i   i   i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_89609734_8   3919 ATCAAGGACTTAAATCTAAGACCTGAACCTGTAGAAATTCTCA-AAGATA 3967
                             ?i   i     v     v  i  v  i  -   i   i -    v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAA 544

  chrX_89609734_8   3968 AC-TATGGAAAAATTCTTCTAGACATTGGTTTAGGCAAAGATTTCATGAC 4016
                           -  v ?iv    -    vv   v    v        v i    v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_89609734_8   4017 CAAGAACCCAAAAGCAAGTGCAACAAAA-ACAAGATAAATAGATAGGACT 4065
                         i v  vv         viv         - v  i   i   i  v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_89609734_8   4066 TAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGTGTA 4115
                          v  i   v v    i   i  ii vv    i  v iv    iv iv  i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_89609734_8   4116 AACAGACAATTTACAGATTGGGAGAAAATCTTCACAAACCATGCATTTGA 4165
                           v      iii     v           v  ii    i   ii  i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_89609734_8   4166 CAAAGGACTAATATCCAGAATCTAAAAGGAACTCAATCAAATCAGCAA-- 4213
                         i  i     vi          v  v  i      vvv   v   ii  --
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_89609734_8   4214 AATAAACAAACAATCCTATCAAAAAGTGGGATAGGGATATGAACAGACAA 4263
                           v i     i  i  v  i?    i    vv i    v    i     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_89609734_8   4264 TTCTCAAGAGAAGATACGCAAATTCCCAACAAACATACAAAAA-ATACTC 4312
                              v i        ii     vv    i  i  i ii    -  i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_89609734_8   4313 AGCATCATTAATTAT 4327
                          i     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.93 (41 / 14)  


2127 25.89 3.95 2.34  chrX_89649916_89652040.rev      816  1626 (499)    L1M4_orf2#LINE/L1       70   893 (15)  

  chrX_89649916_8    816 ATCCATAGAGGCAACACAATCTCAATCAAAATCTTAGCAAATAATTTTAT 865
                            i i   vv    i     i v         ii   vivivv    ii
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_89649916_8    866 GAATGTTGAGAAATAGATCATAAAGTTTATATATGAAGGCAAAACACACA 915
                         ii vi    v  iiv    v    i  i    ivi  v    iiv  v  
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_89649916_8    916 ACCTGGCCAACACAATATTGAAAGACAAGA-CAAACTTGGAAAGCTGACA 964
                         ivv i     v     v      i v    -    v     iii  v   
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_89649916_8    965 CTACCTGACTTTGAGACTTAGTATAAAGCTAAAGCAATCAAGAAAGTATG 1014
                           v  ii i  ii i     v  i       v  i        v   i  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_89649916_8   1015 GTATTGGCAAAATATTATACAAATATAT-ACTGGAGTAGAAT--AGAGTC 1061
                            i     v  viv  v   v   v  - v    i      --      
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_89649916_8   1062 CAGAAATAGACCTTTACAAATATAGTCAACTGATTTTTGAGTAAGGAGAA 1111
                                 i   iv    vv   i     i       i  vv i  v vv
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_89649916_8   1112 AAGGCAAT---ATATGAATTAAGGAT--TTTTTCCAGCAAATAGTGCAGG 1156
                            i v  ---  iv i --   i  -- i   i  i     i    v  
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGA--AAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_89649916_8   1157 AACAACTGGATAACTTCATTCACAA-AATACA--TAAACAAAAAC---AA 1200
                         i           ? iv   v  v  -   iv -- ii  vvvv  --- v
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_89649916_8   1201 ACCAGACACGGAAGTTGTACTTTTCAAAAATTAATTTTAAAAATCCAGGT 1250
                             v i  ii  i  i-   i----     vi  i-- ? i i i ii 
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTA-ACTC----AAAATGGATC--AWAGACCTAAAT 510

  chrX_89649916_8   1251 -TAAAAATGC-AAAACTATAGAACTCCTATAAGATATCATAGAAA-AAAT 1297
                         -   i --  -         i     i  v    v v     i?i-    
  L1M4_orf2#LINE/    511 GTAAGA--GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_89649916_8   1298 GTCAGGTGACCTTGGATTTGGCAGTGACATTTTAGATACAAGAACAAAGG 1347
                         v iv -         i  v    i  iiv i       ii v v    i 
  L1M4_orf2#LINE/    559 CTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_89649916_8   1348 CATGATCTATTTAA-ATAAAATA-ATAAGCTGGTCTTCATTAAAACTTAA 1395
                           ii v v ivv  - v      -    ii   v      i    -    
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA-TTAA 656

  chrX_89649916_8   1396 AAACTTT-GCTCTTCAAAAGACACTGTCAAGACAGTGAGAAGACAAGCTA 1444
                                - iv       i      i      v     i       v i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_89649916_8   1445 CAGAATAGAAGAAGAAT-TTTGCAAAAGACATATAGAATAAAAGGACT-G 1492
                               i i    -   -        vv i    vvi    i-     - 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAA-AATATTTGCAAATCATATATCTGATAAG-GGACTTG 754

  chrX_89649916_8   1493 TAATCCAAAATATGACAAGAAC----ACAAAGTTTAACAATGTAAAAAAC 1538
                           -    i     ivv      ----    --i i  i   i-    i  
  L1M4_orf2#LINE/    755 TA-TCCAGAATATATAAAGAACTCTTACAA--CTCAATAATA-AAAAGAC 800

  chrX_89649916_8   1539 AAAGAACTCAA-----AAACGGGCTAGTGATCTAAACAGATACCTCATCA 1583
                            v   i   -----   i    v iv   i i  i   i ii  vi  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_89649916_8   1584 AAGAAGGTATACAAATGGCAAATAAGCTTATAAAAAGATGTTC 1626
                               i            v       vi  i        i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.44 (122 / 85)
Gap_init rate = 0.04 (30 / 824), avg. gap size = 1.70 (51 / 30)  


2884 25.33 1.20 2.93  chrX_89654437_89658860.rev     3014  3933 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_89654437_8   3014 AAAACATCCCA-GTCTCATGGATAAGAAAAATCAATATCATTTACATGAC 3062
                           i i      -  -        vi   i v i     ii  v v   i 
  L1M4_orf2#LINE/      5 AAGATATCCCATGT-TCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_89654437_8   3063 TATACTGCCCAAATCAATCTACAGATGCAACACAATTTCTATCAATTTAC 3112
                         v     v       ii          v    i    ii       vv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_89654437_8   3113 CAA-TGTTATTTTTTACAGAATTAGAAAAAAACT-ATTCTAAAATTCATA 3160
                           i-  ii-      i     v v  v  i--  -  i            
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chrX_89654437_8   3161 -GAAAACCAAAAATATCCTGAAGAGCCAAAGCAATCCTAAGTAAACAAGC 3209
                         - i   ivv  iiv i  v   v       i     i i ----------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---------- 190

  chrX_89654437_8   3210 AAAACAACAACAACAAAAAAACTGGAAGCATCTTGTTACCTGACTTCAAA 3259
                             v  v     ------ ii    i vv  viii v  ii i      
  L1M4_orf2#LINE/    191 AAAAGAAGAACAA------AGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_89654437_8   3260 CTATATTACAGTGCTATAGTAACCAAGGAAGCATGGTACTGGTATAAAAA 3309
                         viv  i    iv    i     i    iv  ii         i    ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_89654437_8   3310 TACACACATAGATCAATGGGATAGAATAAGGAACCCACAAATAAAGCCAC 3359
                           v   i            i       vii  ii   v       v   i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_89654437_8   3360 ATACATAAAAGAAACTGATCTTTGACAAAGTTGTCAAAAATAAACAATGG 3409
                          i iv  viivv  i    i  i     i v  i   i vi vv      
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_89654437_8   3410 GGAAAGGATATTCTATTCAATAAATGGTGCTAGGAAAACTGGGTAGGCAT 3459
                               i   v   v     i          i   v      i  ?v  i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_89654437_8   3460 ATGCAGAAGAATGAAACTGGACCACTAGCTCTCATTACGTACAAAAATTA 3509
                              i         ii      v   v   v  ii ii           
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_89654437_8   3510 ACTCAAAATGGATTAAAGACTTAAATGTAATACCTGAAAGTATAAAAATA 3559
                                      i ?    i         v v  i   v       v v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_89654437_8   3560 CTAAAAGAAAATCTAAGAAAAATTATTCTGGACACTGGCTTAGGCTAAGA 3609
                         i  i       iv  i ?iv  v v   vv   vi   v      -  vi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC-AATG 583

  chrX_89654437_8   3610 ATTTAT--GATTAAGACTTCAAAAGCAAATGCAATAAAAACAAAAAATAT 3657
                         i   v --   - v   vi        v v    i    i-        v
  L1M4_orf2#LINE/    584 GTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAG 631

  chrX_89654437_8   3658 GTCCAGTGGGACTT-----AAACTAAAGAGCTTCTGCACAGCAAAAGAAA 3702
                         i v- i v      -----   i    i -   i  ii vv    i  v 
  L1M4_orf2#LINE/    632 ATA-AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA 679

  chrX_89654437_8   3703 TGATCAGAAAAGTAAACGGTCAACCTACAAAATGACAGAAAGTGTTTTCT 3752
                         iv    ii     i  vi v     i   i    iv     i i   v v
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_89654437_8   3753 AACTCTGCATCTGACAAGGGACTAATATTCAGATTATATAAAGAACTTAA 3802
                           iiv ii      i        vi   i    v             ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_89654437_8   3803 GCAAATCAACAACAAAAAAACACAAATAAATCCATCAAAAAGTGGGCAAA 3852
                         i   v    i  i     i   --     vi v  i?    i        
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACA--AATAACCCAATTWAAAAATGGGCAAA 827

  chrX_89654437_8   3853 GAACCTAAACAGAGATTTCTCAAAAGAAGACATACACGTGGTCAATAAAC 3902
                          i ii i  i   v       v        i     vi   i      i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_89654437_8   3903 ATGTGTATAAGTGATCAACATCACTAATTAT 3933
                          ii  v v ii  v         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (137 / 92)
Gap_init rate = 0.02 (17 / 904), avg. gap size = 2.24 (38 / 17)  


1946 24.94 4.43 7.72  chrX_89675281_89678807.rev     2247  3036 (491)    L1M4_orf2#LINE/L1      145   908 (0)  

  chrX_89675281_8   2247 TCCACATGGAAATATGAAAACCATAAAACACCCAGAATA-TCCTAAGCAA 2295
                          i  i        iii iiiv vi i  i v   i  i -  i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_89675281_8   2296 AAAGAACAAAACAAGAGGAGTCACATTACCTGAGTTCAAATTATACTACA 2345
                         i         iivi     v     i v  ii v      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_89675281_8   2346 GAACTAAAGTAACCAAAACGACATGGTCCTGGCATAAAAACAGACGTATA 2395
                         i i   v     i   i  iiii    v         ii i    i    
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_89675281_8   2396 CTTCAGTAGAACAGAATAGAGAACCCAGAGATAA-TTCATACATCTACAG 2444
                         vv   i i   i     v    ii     i    -ii       i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_89675281_8   2445 TGAACTCAATTTTGACAAGTTTTCCAAGA--------TGAGAAAAGGATG 2486
                          v  i v v   i      vv v      --------  i i    i  i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_89675281_8   2487 ATATCTTCAATAAATGGTGCTATGAAAACTAGATATCCATATGCAAAAGA 2536
                         i v i     i          iv  v    i    ?   i          
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_89675281_8   2537 ATGAAACTAGATGCGTA----------TATACAAAAATCAAACCAAAATG 2576
                              ii i  iv v  ----------           i  vi       
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_89675281_8   2577 GATCAAAGACTTAACTCTAAGACCTCACACTACGTTACTAGTAGAAGAAA 2626
                              ?    i   v v     v  v v    iivv   vv         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_89675281_8   2627 ACATTGGGAAATATCTCCAGGACATTTATCTTGTTAACAATTTCTTGAGT 2676
                             v  ?iv v    i iv   v  vivi v vi  iii      iii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_89675281_8   2677 AATACAGCAGAAGCACAGGCACCCAAAGCAGAAATGGATAAAAATGCACA 2726
                          vv   v  i       i   v v    v i    i      --------
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA-------- 636

  chrX_89675281_8   2727 TGTACCCTAAAACTTAAAGTATAATAATAATAAAATAAAATAAAATAAAA 2776
                         ------- vii    ----i  ------------------i     ----
  L1M4_orf2#LINE/    637 -------TTGGACTT----CAT------------------CAAAAT---- 653

  chrX_89675281_8   2777 ATGGGATCACATCAAGTAAAAACCTTC-TGCATAGCAAAGGAAACAATCA 2825
                         ----------------       i  i-   v --       v  v    
  L1M4_orf2#LINE/    654 ----------------TAAAAACTTTTGTGCTT--CAAAGGACACTATCA 685

  chrX_89675281_8   2826 ACAAAGTGAAGAG--------------GGGTAGAAATATTTACAAACTAC 2861
                          v        i  --------------   vii        i    ii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_89675281_8   2862 CCATCTGACAAGGGATTTATAACCAGTACATGAAAGGAGCTAAAACAAAT 2911
                         vi      i      i  i  v    v i  iv  i  i  vvv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_89675281_8   2912 ATATAGTAAAAAATCTAATAATCCTATTTAAAAAATAGGCAAAAAGATAT 2961
                         vv   i      iv v     i  v   ?     - i      i-   v 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAG-GATTT 833

  chrX_89675281_8   2962 GAATAGACATTTCTTAAAAGAAGACACACAAATGGCAAACAGGCATATGA 3011
                                       iv        i i         v  i i   i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_89675281_8   3012 CAAGGTACTCCACATCACTGATCAT 3036
                         v   i i   v      ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (118 / 75)
Gap_init rate = 0.02 (13 / 764), avg. gap size = 7.38 (96 / 13)  


2644 28.57 1.33 0.78  chrX_89694851_89699779     3534  4436 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89694851_8   3534 TGGAAAAACATTCCATGCTCACAAATTAGAAAAATCAATATTATAAAAAT 3583
                               i i  i     i   iii   i   i v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89694851_8   3584 GGCCATATAGCCCAAAGAAATGTACAGATTTAATACTATTCCTATCAAAC 3633
                            v   ivv      vvi  v        i  ii v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89694851_8   3634 AACCAACATCATTTTTCACAGGATTAGA-AAACTAATC-TAAAATGAATA 3681
                         vv   i vv v     ii   i v v  -  i  i   -      vv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89694851_8   3682 TAAAGCCAAAAAAGAGCCCTAATATCCAAAACAATCCCAAGCAAAAAGTA 3731
                          ii iviiv  ii  v  vv    v           iii iv  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_89694851_8   3732 CAAAGCTGGAGGCATCACACTACCCATCTTCAAACTACACTAGAAAGCCA 3781
                              i      vv       v    vi      vivi    v     i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_89694851_8   3782 CAGTAACCAAAACAGCTTGGTACCGATACAAAAATGGACACATAGACCAA 3831
                               i   i    iv      i ii i  ii  i    i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_89694851_8   3832 TGGAAAAGAATAGAAAACTCAGAAATAAAGCTGAACACCTGCAGCCATCT 3881
                              v     v  i iii          v iiv   ii iii i  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_89694851_8   3882 GATCTTTAATGAGACTGAGCAAAAGAAG-CAATGGGGAACAGACATCCTA 3930
                            i  ii ii  iv  v-   i vv v-          vii i vi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_89694851_8   3931 TTCAATAAATGGTACTGGGATAAATGGCTAGCCATATACAGAAGATTGAA 3980
                              i       i      i  v   v  ?   i  i  i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_89694851_8   3981 ACTAGATCTCCATGTTTTACCATATACAAAAATTAACTCAAAATGG---- 4026
                         ii i  i i i iv ivi                            ----
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_89694851_8   4027 ----CTTAAATGAAAGGCCTCAAACTATAAAAATCCTGAAAAACAACCTA 4072
                         ---- i      v   iv  v           v  i ii  i v   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_89694851_8   4073 GGAAATACTCCTTTTCATATTTTCCTTGCCAAAGAATTTATGGCTGAGTC 4122
                           ?ivv v  i iv v iv  vvvi v v   v iv  iv i v iv v 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_89694851_8   4123 TTCAAAAGCAATTGCAACAAAAACAGAAATTTACAAAAGGGA-TACAGTT 4171
                         vi        vvv         iv i    vv i   vv   - v  - i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA-TC 648

  chrX_89694851_8   4172 AAACTGAAGAGCTTCTGAACAGCAAAAGAAACCATCAACAGAGTAAACAG 4221
                            v v  i i   i  vi vv    i  v  i     v i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_89694851_8   4222 ACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGTATCTAACAAAT 4271
                               i                          ii  i     i i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_89694851_8   4272 GTCTAATATCCAGAATCCATGAGAAACTCAAACAAATCAGAAAGCAAAAA 4321
                          v  vi          vi  i ii     vv    v   iv  vv    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_89694851_8   4322 ACAAATAACTCCACTTTGTTTTTAAATGGGCAAAAGACATGAAGAGACAT 4371
                                  -   v  ?iv----           i  iv    v      
  L1M4_orf2#LINE/    799 ACAAATAAC-CCAATTWAA----AAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_89694851_8   4372 TCCTCAAAAGAAGATATGCAAGTGGCCAACAAACAAATAAAAAAGTGCTC 4421
                          i   v           i   i       i  i  v  i    ii     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_89694851_8   4422 AACATCACTAATTAT 4436
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (145 / 110)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


2483 26.58 3.96 1.70  chrX_89717610_89721800.rev     2817  3700 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_89717610_8   2817 AAAACATCCCCTTTTCATGGATTGAAATAATTACTATCGTTAAAATAACC 2866
                           i i     v v           i  v v   v   i     i  ii v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_89717610_8   2867 ACACTACCCAAAGTTATCTACAGATTCCATGTAATCCCTAACAAAACATT 2916
                          i   v      v v            v i i        v     ivii
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_89717610_8   2917 CACAGGATTTTTCACAGAAATAGTAAAAAAAGACAATAAAAACATTTATG 2966
                         vi v vv     ii       v - v  ivv  ivv     ---  i  i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAA---TTCATA 150

  chrX_89717610_8   2967 TGGGACTAAAAACGATCTAAAATAGCCAAAGGAGTCTTCTGAAAA----G 3012
                            i v iv  iv  i i i          iv i    --     ---- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT--GAAAAAGAAG 198

  chrX_89717610_8   3013 AACAA-GCAAGAGGCATTACACTACCTGACCT-AAAATGTACTACAAA-- 3058
                              - ivi    vv i     v  ii ii -    iv         --
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_89717610_8   3059 CATAGTAATAAAAATAACATGGTACTGGCATAAAATCAGGCACATAGACT 3108
                         i i      v  i i iii              iivi  i  i     ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_89717610_8   3109 AATGGAAAAGGCTAAAGGACCCAGAAATAAATCTACATATATACAGCCCA 3158
                                v  iv vi  iii           i i i i  v  ii i v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_89717610_8   3159 ATG----TTAACAAAGTTTTCAAGAATACATATTGGGGAAATGACAGTAT 3204
                         v  ---- ii    i v vi     vi ivi v        vi i   v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_89717610_8   3205 CTTCAATAAATGGTGGTTGGAAAATTGCATATCCATGTACAAA-GAATAA 3253
                         i     i        v v   v  i  v   ?   ii i    -    i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_89717610_8   3254 AACTAAAGCCATATTCCCCACTATATACAAAGTTGAACTCAAAAGTAAAG 3303
                          ii ii v  v  iii v   i         iv v         - ii v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGAT 497

  chrX_89717610_8   3304 TAAACACCTAAATATAAGACCGGAAACTATAACACTTCCAAAAGAAAACA 3353
                         i ? v        i     v vi         v   iii i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_89717610_8   3354 --GGA--AAATCCTTCAGGACGTTGGCCTGGGCAAATATTTTATGGCTAG 3399
                         --  ?--     -   iv   v    vi i     vvi   iv i v  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_89717610_8   3400 GACCTCAAAAGCACAGGCAACAAAAGTAAAAATAGACAACTGGAATTGTA 3449
                            vi          i          v         i  v v i i vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_89717610_8   3450 TCAAAATTAAAAGTTTCTG-----CAAGGAAAGAAA--AACAATAAA-TG 3491
                                     ii  i  -----   --- i  v -- v   v   -  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAA---AGGACACTATCAAGAAAGTG 693

  chrX_89717610_8   3492 AAGAGACAATCAGCAGAATGGGAGAAAATATTTTCAAACTACTA-ATTTG 3540
                           i      i vi                    v    ii -  -  i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTG 742

  chrX_89717610_8   3541 ACAAGAGACTTACATGTAGAATATA-AAAGGA-TCT--CAACTCTACAGC 3586
                          i   i     ii  vi        -    i -   --      v i ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_89717610_8   3587 AGAAAAACAAATAACCTGATTAAAAA--GGACAGCAGAAGATCTGAACAG 3634
                          i   i          ii   ?    --  ---   i i   i    i  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGG---GCAAAGGATTTGAATAG 839

  chrX_89717610_8   3635 TAATTTCTCAAAAGAAGACATACAAACA-TTAAAAAGTATATCAAAA--T 3681
                         vv       v        i       ii-ii  v   i i  v    -- 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_89717610_8   3682 GTTCATTATTACTAATAAT 3700
                          i   vi  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (145 / 86)
Gap_init rate = 0.03 (26 / 904), avg. gap size = 1.92 (50 / 26)  


3145 25.11 3.39 0.68  chrX_89786681_89789935     1880  2763 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89786681_8   1880 TGCAAAGATTCCCTGTGTTTATGAATTGGAAGAGTTAATATTGTAAAAAT 1929
                           v      vi  ii    i   i         v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89786681_8   1930 ATACATACTACTCAAAATGACCTGCAGGTTTTTC-CAATCTGTATAAGAA 1978
                         ivvv     v i    v   i  i   i  ivv -     iv   v i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89786681_8   1979 ACTCAATT----TTTTTACATTAATAGAAAAAGCAATCTTAAAATTTATA 2024
                         v i  ii ----     i  vv   v  v  ivii   i       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89786681_8   2025 TGAGACTATAAAGGATT----GTACCCAAA----TCTT----AAGAGAAA 2062
                           ii v ii  i   ii----i  v     ----    ----    ii  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_89786681_8   2063 CAAAGACAAAGGACTCTAACATCCTAATTTTAACACACACTACAAAGCCA 2112
                              viii       vv  v   i     i  v  vi          i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_89786681_8   2113 CAGTAATCAAAATAGTATGATACTAGCGTAAA-ATAGACACTTAGACCAA 2161
                                   i i   i  i    i  i   i-       iv    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_89786681_8   2162 TAAAGCAGAATAGGAAGCCCAGAAATAACATCATGCATATATGGTCAACA 2211
                          ii ii     v ii  i          vvi   i   v         iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_89786681_8   2212 GAGCTTCAACATGGGTGCTAAGA--ATACAAAGTGGAGTAAGGGTAGTCT 2259
                           vi   i   v      i    --  v   --   i v   ii      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTCT 398

  chrX_89786681_8   2260 CTTCAACAAATGGTGATGAGAAAATTGCAAATTCACATGCAGAAGAATAA 2309
                         i              v  i  v  i  v v ?i        i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_89786681_8   2310 AATTGGGCTTTTATGTCACATAATTCACAAAAACCTACTCAAAATGAGTT 2359
                          i    i iii  iv     iv  vi       iiv          ii i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_89786681_8   2360 AAAGACTTAATTGTA-GAATGTAAACTGTAAAACTTCTAGAAAAAAA--T 2406
                          ?    i   v    -  iivv     i       ii     i    -- 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_89786681_8   2407 AGGAGAAAATCTTCATGACATTGATCTTGGCAATGATATATTGGATATAA 2456
                            ? v        i    v   ivi v       i v v  i     i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_89786681_8   2457 CACCAAAAGTACAGGTGAGAAAAGCAAAAATAGACCAGTGGGACCATATC 2506
                                  i   i ii v     v         iv i v    ivi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_89786681_8   2507 AAACTAAAACGCTTTTGCACAACAAAGGAAATAACCAACAGAATAAAAAG 2556
                            v v   vi      ii vv       v iv i   v i i i     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_89786681_8   2557 GCAACCTACAGTCTGTAGGAGAATATTTGCAAACCATATATCTGATAG-- 2604
                         i     i    vv  vii  i            i             i--
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_89786681_8   2605 --CTTAATATCCAAAATATATAAAAAACT---ACAACTCAATACCAAAAA 2649
                         --   i-      i          i    ---           vi     
  L1M4_orf2#LINE/    749 GACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_89786681_8   2650 AACCCCAAATAACCCAATTAATAAGTAATAAAATGATCTGAATAGATATT 2699
                         i  ---             ? v  i iivv   v   i        i   
  L1M4_orf2#LINE/    798 GAC---AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_89786681_8   2700 TGTTCAAAGAAGATGTCCAAATAGCCAAGAGGAATGTTAAAAGTTGCTCA 2749
                          v i          i v     i     v i v ii v     v      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_89786681_8   2750 ACATCCTAATCCCC 2763
                              v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (136 / 82)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.57 (36 / 14)  


2471 29.19 0.98 2.07  chrX_89798546_89804299     4345  5262 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89798546_8   4345 TGGAAAAACAGTCCATGCTCATAGATAGGAAGAATCAATATTGTGAAAAT 4394
                               i i vi     i    i   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89798546_8   4395 GGCTATACTGCCCAAGT-AATTTATAGATTCAAAGCTATTCTCATTAAAC 4443
                            v     v     i -i  i  i        v  v  i ii  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89798546_8   4444 TACCATTGACATTCTTCACAAAATTAGAAAAAAGTACTTTAAAGTTTATA 4493
                          v   vivi v  i  ii  i  v v  v  ivvv iii    i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89798546_8   4494 TTGAACCAAAAAGGAGTCCATGTA-AGTGAAGACAATCCTAAGCAAAAAG 4542
                          v   viiv  i   -i   - v -  iv  i      i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCA-GAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_89798546_8   4543 AATCAACCTAGAGACAC-CACGCTACTCAACTTCAAACTATACTACAAGG 4591
                           iv  vi i   i-  -   i  v i   i      viv        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_89798546_8   4592 CTACAGTAACCAAAACAGCATGGTACTTTTGCACCATGTACAGGTACAAA 4641
                                  i   i    ii       ---------------  i i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACT---------------GGCATAAG 282

  chrX_89798546_8   4642 AA-AGACACATAGACCAATGAAACAGAATACAGAACTCAGAAATAAGACC 4690
                         i -     i     i     i  i     vv   iii         iv  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_89798546_8   4691 ACACATCTACAACCT-CTGATCTTCGAGAAACCTGACAAAAACAAGCAAT 4739
                          i    i  iiii v-i    i     v  ivv  v   i v  vv    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_89798546_8   4740 GGGGAAAGGATTCCCTATTTAATAAATGGTGGTGGGAAAATTGGCTAGCC 4789
                                 i  vvi  v  i  i        v     v  i   v  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_89798546_8   4790 TTATGCAGAAAATAGAAACTGGACCCCTTCCTTATACCTTGTA-AAAAAT 4838
                         vi     i  i vv   ii         v   i i   v i  -      
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_89798546_8   4839 -AAATCAAGGTGGATTAAAGACTTATATGTAAAACCCAAAACTATAAAAA 4887
                         -  v    ii     i ?    i  v      i v i            v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_89798546_8   4888 CCCTAGACAAAAATCTAGGCAATAGCATTTAGGACATAGGTACAAGCAAA 4937
                         i i    vi    iv    ?ivv iiv  iiv   v v  vvi i    v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_89798546_8   4938 CATTTCACCAAAAAAACGTCAAAAGCAATTGCAACAAAAGCAAAAAATGG 4987
                         vi    vivi v vi  ii        vvv          -       i 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAG 631

  chrX_89798546_8   4988 -CAAATGGCATCTAATTAAACTAATGAGCTTCTACAGAGCAAAAGAAACT 5036
                         -i    v v ii v  i   v v vi i   i iiivvv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_89798546_8   5037 GCCATCAGAGTGAACAGACAACCTACAGAATGGGAGAAAGTTTTTGCAAT 5086
                         ii  vv i      v        i               i v       v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_89798546_8   5087 GTATCCATCTGACAAAGGTCTAATATCCACAATCTGCAAAGACCTTAAAC 5136
                         vi  vi      i  i  v  vi      v   v ii     v  ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_89798546_8   5137 AAATTTACAAGAAGAAAACAAGCAACCCCATTAAAAAGTGGGCAAAGAAC 5186
                           v iv i  v  i  i    ii     v   ?    i         i i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_89798546_8   5187 ACGAACAAACACTTCTCAAAAGAAGACATTTATGTAGCCAACAAACGTAT 5236
                         vi   i i   i     v        i  vi vi i     i  i ii  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_89798546_8   5237 CAAAAAA-GCTCAACATCTGTGATCAT 5262
                         v    i -          v????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (155 / 109)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  


2262 27.82 4.28 2.03  chrX_89809742_89813643     2522  3409 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89809742_8   2522 TAGAGAAACATTCCATCCTCGTAGATTG-AAGAATCAATATTATAAAAAA 2570
                          i  i i i  i    vi  i i     -    v i      i v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_89809742_8   2571 TTGTCATATGGACCAAAGCAATTTACAGATTCAATGTTATTCCTA-CAAA 2619
                          v iv   ivvv     vii  i           i iv  i    -    
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_89809742_8   2620 --CCTACCAATGTCCTTCTTTA-AGGAATTAGAGA-AAACTG-TTCTAAA 2664
                         --  i v --  -    i   i-  i    ---  -  i   - i     
  L1M4_orf2#LINE/    100 ATCCCAGC--TG-CCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAA 143

  chrX_89809742_8   2665 ATGCATATGAAA---CAAAAAATCCA-AATAGACAAAAGAATCCTAAGTG 2710
                           v      i  ---   iii i   -     v     v    i i ivi
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_89809742_8   2711 AAATGAACAAAGTCAGAGGCATCACATTACCCAACTTTAAGTATTT--TA 2758
                          i v         ii    vv     i v     i  i  i- i  --  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-ACTTACTA 242

  chrX_89809742_8   2759 TAAAACCACAGTAACGAAAACAGCTTGGTACTGGTATAAAAGCAGACACA 2808
                         i   i i       iv  i    iv         i    iiii     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_89809742_8   2809 TAGATGAATGGAAAAAAAAAAAGATAGAAACCTCAAAAATAAAGCTGCAC 2858
                              v       v i  ------ v  i vii  i       v iii  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAA------TTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_89809742_8   2859 ACTTACAACCATCTGATCTTTGACAAGGCCAACAAAGATAAGT-AATATG 2907
                          i   iiii  vi    i  i       viiv   -  iv v -   iv 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGG 385

  chrX_89809742_8   2908 GAAATAACTCCCCATTCAATAAATGGTGCTGGGATAACAGGTTAG----- 2952
                             v  ivvi iv     i              i   v  v  ?-----
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_89809742_8   2953 -----GAGATTGAAGCTCGACCCCTATTTT-TATCATATACAAAATTTAA 2996
                         -----i   v     i v        ii i-i i           v    
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_89809742_8   2997 CTCAATATGGAATAAAACTTTAAATGTAATACCTCCAAATACAAAAATCC 3046
                              v     vi ? ivii         v v  vv  v  i    v  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_89809742_8   3047 TTAAAGACAAAC-TAGGAAATACTCTT-GTCGACATCAGCCTTGGCAAAT 3094
                          vi    -    -    ?ivv v    -  -   v ii vi v     - 
  L1M4_orf2#LINE/    536 TAGAAGA-AAACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAA-T 582

  chrX_89809742_8   3095 AATTT-TTGGCTGT--CCCCAAAAGCAATTGCAACAAGAATAAAAATAGA 3141
                         ii   -  i v i -- v         vvv       i iv         
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_89809742_8   3142 C---TGGGACTTAATTAAACTAAACAGCTTCTGCATAGCAAAAGAAAC-- 3186
                         i--- v      v  i   v v  v i   i  iiivv    i  v  --
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_89809742_8   3187 --AACAGAGCAAACAGACAACCTACAGAATAAGAGAATATATTTATAAAC 3234
                         --  v i  ii  v        i       ii     v      ii   i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_89809742_8   3235 TATGCATTTTACAAAGGCCTCACATCCATAATCTGCAGAGAACTTAAACA 3284
                         i  ii  i v i  i  v  iii     v   v ii i      ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_89809742_8   3285 AATCAACAAGCAAAAACCAAATAACGACATTTAAAAATGGGCAAAAAACA 3334
                          v    i  vv    iv        vvv   ?             ii iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_89809742_8   3335 TGAGCAGACACTTTTCAATAGAAGACATGCAAGTGGCCAACAAATATATA 3384
                            ii     i  i  v v      i  i   i       i  ii i  i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_89809742_8   3385 AAAAAA-GTTCAGCATCACTAATCAT 3409
                             i - i   i     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (153 / 90)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 1.93 (56 / 29)  


2820 25.35 6.02 0.93  chrX_89814657_89817369     1357  2220 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89814657_8   1357 TGGAGAGATACTTCATGTTTTTGGATAGAAAGGCTCAATGTTGTCAAAAT 1406
                             i     iii      iv     v i   i  i   i    i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89814657_8   1407 GTCACTTATTCCCAACTTGAATTG-GGATTCAATACAATCCTAATCAAAA 1455
                          v  v vv i     v    vi i-i       ii      iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89814657_8   1456 TCTTAGCAAGTTATTTCGTGGGTATCAACAAACTTATTTTAAAGTGTATA 1505
                           ii   vivi v   i ii iv  ii    i  v  ii    i vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89814657_8   1506 TGATGAGGCAAAGGACTCAGTAATAGTTGACAAAATATTGAAGGAAAATA 1555
                           ivi v    i    i   -     iii v v   v     ii i  v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAG-AATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_89814657_8   1556 ACAAATTTGTAAGACTGACACTACCTCATTTCAAGACTCATTGTAAAGAT 1605
                              v   v i    v     v  iv       i   i i ii    v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_89814657_8   1606 ACAATAATCAAGACAATATGGTATTGGGCA-AAGAATAGAGAAATAGATC 1654
                            i           i i     i   -  -   i     v v       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGG-CATAAGGATAGACATATAGATC 298

  chrX_89814657_8   1655 AATGGCAAAGAAGATAAAGCCCAGAAATATATGCACATAAATATAGTCAA 1704
                              v v    vvv i  i         v iv  i i vv   i     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_89814657_8   1705 CTGAACTATGGCAAAGGAGCCAATGCAATACAATAGAGCAAGGGCTGTCT 1754
                         i   vi vi i   i  v     vi v  v    i i v   iiiv    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_89814657_8   1755 TT-CAACAAATGAGTCTGGAACAACTAGATAGCCACATG----------- 1792
                           -         ivv    i      i    ?       -----------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_89814657_8   1793 ----------------------------AAAAATTGAACTCAAAATGAAT 1814
                         ----------------------------       -           i  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATT-AACTCAAAATGGAT 497

  chrX_89814657_8   1815 CATAGACTCAAAAGTAAAATGC-AAAACTATGAAACTCCTAGAAGATAAC 1863
                           ?    ii   v    i -  -        i      i       v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_89814657_8   1864 ATAGAAG-AAACCTATTTGACCTTGGGTATGGTGATGACTTTTTATATAC 1912
                             i? -   i  viv           vv  ii   ii  i   v   i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_89814657_8   1913 AACACTAAAGGCACAATCCAAAAAAGAAAGAATTAGTAAACTCTTGGAAT 1962
                         i    i   i      v v v        i   vii    ---     v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA---TTGGACT 643

  chrX_89814657_8   1963 -CATTACAATTTAAAACTTCTGCTCTATGATAGACAATGTCAAGAGAATG 2011
                         -   i v    v       i  iv  vii vi    v i      i i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_89814657_8   2012 AGAAGTCAAACTACATACTGAGAGAAGATATTTGCAAATGACATATCTGA 2061
                          i   v   v i   v v  i     i            v i        
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_89814657_8   2062 TTAAGGACTGTTTTTCAAACTATGCAAAGAACTCTTAGAACTCAAAAATA 2111
                          v i     vv v i  i v   ii            v       v    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_89814657_8   2112 AGAAAAACAAACAACCTGATTGAAAAACAAGCT--GGACTT---T-GACA 2155
                          -   i     i    ii   ?     iii  v--   i  --- -    
  L1M4_orf2#LINE/    794 A-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_89814657_8   2156 GTTCACCAGATAACATATACAGATGGC-AACAAGCATATGAAATCATGTT 2204
                         v   v   i v  v       i     -  i     i      vv   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_89814657_8   2205 CCAAATCATATGACAT 2220
                          v v    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (128 / 87)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.53 (60 / 17)  


2477 20.14 5.25 0.85  chrX_89877488_89879068.rev      502  1092 (489)    L1M4_orf2#LINE/L1      292   908 (0)  

  chrX_89877488_8    502 ATAAACCAATAGGATAAAATAGAAAGCCCAGAAATAAACTTTTGCCTATA 551
                            i i    i i   i   v  i  i            iiv i v v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_89877488_8    552 TGGGCAAATGATTTTAGACAAAG---------TCATTGAATTGAGAAA-- 590
                            v   v       v     i ---------i    v   v i    --
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_89877488_8    591 ------------ACAAATGGTGATGGGAAAGCTGGATATCTACATGAAAA 628
                         ------------          v     v i       ? i     v   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_89877488_8    629 AGGATCATGTCTGATACTTACCTTATACCATATACAAAAATTAACTCAAA 678
                           i  v v  iv  iv i     i i                        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_89877488_8    679 ATTGATCAAATGCCTAAATGTAAGAGCTAAGGGCATAAGACTCTCAGGGA 728
                           v     ? vi                  iivi    i     i  iii
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_89877488_8    729 AAGACGTAAGGGAAAATCTTTGTAACATTGGATTTGGCAATAATTTCTGA 778
                           i  i  i ? v       i  i  v    i  v      ii     v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_89877488_8    779 AATATGATACCAAAAGCACAGGCGAAAGAAGAAACAATAGATAAATTGAA 828
                         i      i            i  i v i      v             i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_89877488_8    829 GTTTATTAAAATTAAATATATTTTTGCACT---AAAAATACTACCA-GAA 874
                         v  i  i         - - i     ii  ---  ii i    i  -   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAA-A-ACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_89877488_8    875 AGTAAAAATGCAACCTACATAATGGGA-AAAATATTTTCAAATCATATAT 923
                            i    vi     i   v       -         v            
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_89877488_8    924 CTGATAAAGAGTTAATATCCAGAATATACAAAGAACT---ACAACTCAGT 970
                                i iii vi             i        ---        i 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_89877488_8    971 AACAAGAAAATACAAAACAACTTGAGTAATAAATGGGCAAAAAAGTTGAA 1020
                           i  i  i i ---  i   iii v ? v           ii v     
  L1M4_orf2#LINE/    790 AATAAAAAGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_89877488_8   1021 TAGTCATTTCTCCAAAGAAGATATACAAGTGACCATTAAGTACAAGAAAA 1070
                            v                        i  i   v    i   v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_89877488_8   1071 AATGGTCAACATGACTAACAAA 1092
                         i   v       v ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (77 / 38)
Gap_init rate = 0.01 (9 / 617), avg. gap size = 4.00 (36 / 9)  


 997 27.13 0.95 0.95  chrX_89896875_89903265        7   323 (6068)    L1M4_orf2#LINE/L1      379   695 (213)  

  chrX_89896875_8      7 CAATGGGGAAA-AATTTTCTTTTTTAATAAATGGTGCTGGGAAAACTGGC 55
                                    -   vv      i-  i              v      v
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTC-AACAAATGGTGCTGGGACAACTGGA 427

  chrX_89896875_8     56 TAGCCATATGCAGAAAACTCAAACTGGACTCCTTCCTAACACCTTATAAA 105
                           ?   i     i  i v v  ii     i   v   v     v    v 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_89896875_8    106 GAAATTAAGTCAAGATGAATTAAATACTTAAATGTAAAACCTGAAACCAT 155
                         i       v    i   i  i ? v  i         i v  i    i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_89896875_8    156 AAACACCCTT-GAAAAAATTCTAGGCA-ATACCATTCAGGACCTAGGCAT 203
                            -  i   -   i   viv    ?i- v i -   iv     v  vv 
  L1M4_orf2#LINE/    528 AAA-ACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTT 575

  chrX_89896875_8    204 GGGCAAAGACTTCATGACTAAAACACCAAAAGCAAATGCACCCAAAGCCG 253
                         i     v ii   v iiv  vi            v v   v v    vvi
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_89896875_8    254 ACGTTGATGAATGGGATCAAATTAAAATAAAGAGCTTCTGCATAGCAAAA 303
                          vi v   i   v   iivv  i     v  i i   i  iiivv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_89896875_8    304 GAAACTATCATCAGAGTGAA 323
                           v       vv i      
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAA 695

Transitions / transversions = 1.02 (42 / 41)
Gap_init rate = 0.02 (6 / 317), avg. gap size = 1.00 (6 / 6)  

2953 27.31 0.99 0.99  chrX_89896875_89903265     4991  5898 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89896875_8   4991 TGGAAGAACATTCCATGCTCCTGGGCAGGAAGAATCAATATCATGAAAAT 5040
                              ii i  i     i  v   iiv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89896875_8   5041 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5090
                            v     v     iv i  i  i        i  v     i     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-- 98

  chrX_89896875_8   5091 AA--CCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 5136
                           --   iivi i  i  ii     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_89896875_8   5137 CATATGGAACCAAAAAAGAGCCTGCATTTCCAAGTCAATCCTAAGCCAAA 5186
                                  viiv  ii  v  v v  vv    iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_89896875_8   5187 AGAACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTAAACTACAAG 5236
                                  i      vv   vi  v  ii i      vivv       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_89896875_8   5237 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGTGATATAGA 5286
                                   i   i    ii         i iv ii i  vv       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_89896875_8   5287 CAAAGGGAACAGGAC--AGAGTCCTCAGAAATAATGCCACATATCTACAA 5334
                         iv  v    i  i i--       --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_89896875_8   5335 ATATCTGATCTTTGACAAACCTGACAGAAACAAGCAATGGGGAAAGGATT 5384
                         vi vi    i  i     ivv  v  ii v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_89896875_8   5385 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCAGATTTAGAAAG 5434
                         vi  v  i  i              v      v  ?   v  vi i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_89896875_8   5435 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5484
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_89896875_8   5485 GATTGAAGACTTACATGTTAGACCTAAAACCACAAAAATCCTAGAAGAAA 5534
                            ii?    i  v    v   v       i i    v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_89896875_8   5535 ACCTAGGCA-ATACCATTCAGGACATAGATATGGGCAACGACTTCATGTC 5583
                           v    ?i- v i -   iv   v v ivv i     i ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_89896875_8   5584 TAAAACACCAAAAGCGATGA-CAACAAAAGCCAAAATTGACAAATGGGAT 5632
                           vi           - ii -         vv     v  i    v   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_89896875_8   5633 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5682
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_89896875_8   5683 GAACAGGCAACCTACAAAATGGGAGAAAA-ATTTCGCAACCTACTCATCT 5731
                            v  i     i   i            -    -    vii ivi    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCT 741

  chrX_89896875_8   5732 GACAAAGGGCTAATATCCAGAATCTACAATGAACGCAAACAAATTTACAA 5781
                           i  i  i  vi          v  i  v    v vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_89896875_8   5782 GAAAAAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGAC 5831
                         v     i     i     v  i? v  i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_89896875_8   5832 ACTTCTCAAAAGAAGACATTTATGCAGACAAAAAACACATGAAAAAATGC 5881
                          i     v        i  vi viii v   v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_89896875_8   5882 TCATCATCACTGGCCAT 5898
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.38 (18 / 13)  


2560 26.98 3.16 0.68  chrX_89904190_89908425.rev     2860  3745 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89904190_8   2860 TGAAAACACTTCTCATGCTCATGAATGGGTAGAATCAATATTGTGAAAAT 2909
                           i   v iv  i    i     i  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89904190_8   2910 GACCATATGGCCAAAAGCAATCTACAGATTCAATGCAATTACCATCAAAG 2959
                          i v   ivv  v   vii              i     iv i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89904190_8   2960 TACCATCATCATTCTTCACAGAATTAGAAAAAA-AATCCTAAAATTTATA 3008
                          v   v vv v  i  ii     v v  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89904190_8   3009 CAGAACCAAAAAGAACCCACA-TAGCCTAGAAAGACT-AAGCAAAAAGAA 3056
                         ii   viiv  i i     v -     v i v iv  -i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_89904190_8   3057 CAAATCTGGAGGCATCATATTACTCAAATTCAAGCTATACTACAAGGATA 3106
                             vi      vv   i i v i   v     iviv        i v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_89904190_8   3107 TAGTTAACAAAACAGCATAGTCCTCGTATAAAAATAGGCATGTAGAGTGG 3156
                         i   v v   i    ii i  v  v i    ii    i   i    viii
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_89904190_8   3157 TTGAACAGAATAGAGAACCCAGATATAAAGCCAAATACTTACG-CCAACT 3205
                          v   i     v    ii     v     v   v i i   i -i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_89904190_8   3206 GATCATCAACAAAACAAACAAAAAC-TTAAAGTGGGGAAAGGACACCTTA 3254
                            iv  i    iivviv   i v -  v  -         i i vii v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTT 399

  chrX_89904190_8   3255 TTCAACAAATGGTTCTGGGATAATTAGCAAGCCACATGTAGAAGAATGAA 3304
                                      v      i  i i vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_89904190_8   3305 ACTGGATGCTTATCTC-CACCTTATACAAAAATCAAATCAAGATGGATCA 3353
                         ii    iv i  i   -    v           i  v    i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_89904190_8   3354 AAGACTTAAATCTAAGTCCTGAGGCTATAAAAATTCTGGAAGATAACATC 3403
                         ?    i     v    vv  i ii        v ii i     v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_89904190_8   3404 AGAAAAACTCTTCTAGACATTGTCTTAGGCAAAGAATTC------ATGAC 3447
                         i ?iv  v     vv   v   vv        v iv   ------     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_89904190_8   3448 --CAAGAACACAA-TAGCAAATGCAACAAAAACAAACAAATGAGATGTAA 3494
                         --   i i     -i i    --- iv     i i i    vi  iv v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAA---AGAAAAAATAGATAAATTGGACTTCA 646

  chrX_89904190_8   3495 TTAAA-CTAAAATCTTCTGCACAGCAAAAGAAATAATCAACAAAC----- 3538
                          i   -i     v   i  ii vv    i  v iv     v   v-----
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_89904190_8   3539 AGACAACCCACAGATTAGGTGAGAAAATATTCCCAAACTATGCATCCAAC 3588
                                       v i  --          iv    ii  ii   ii i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGG--AGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_89904190_8   3589 AAAGGACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGCAAGAA 3638
                           i     vi          v  i  v      vv    v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_89904190_8   3639 AAA----AATGATCTCATC-AAAAATAGGCAAAGG-TATGAATAAACAAT 3682
                            ----   i i iv  i-      i        - v      i   v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_89904190_8   3683 TTTCAAAAGAAGATATACAAATGGCCAACAAACATTTTAGAA-ATTCTCA 3731
                          i  v                       i  i  iv v i  -  v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_89904190_8   3732 ACATCATGAATTAT 3745
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (134 / 102)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.89 (34 / 18)  


2880 28.37 0.77 0.55  chrX_89926215_89935052     7440  8345 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89926215_8   7440 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATGAATATCATAAAAAT 7489
                               i i  i     i        v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89926215_8   7490 GGCCATACTTTCCAAAGTAATTTGTAGATTCAATGCTATTTCCATTAAAC 7539
                            v     ii     v i  i ii        i  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89926215_8   7540 TATCATTGACTTTCTTCACAGAATTAGAAAAACT-ACTTTAAAGTTCATA 7588
                          vi  vivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_89926215_8   7589 TGGAATCAAAAACAAG---CCCATA-TAGCCAAGACAATCCTAAACAATA 7634
                              ---- vi    ---    v -       i      i i  v  v 
  L1M4_orf2#LINE/    151 TGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_89926215_8   7635 ACAACAAAGGTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 7684
                          v       v      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_89926215_8   7685 CCTACAGTAACCAAAACAGCATGGTACTGGGACAAAAACAGACACATAGA 7734
                         v         i   i    ii         v i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_89926215_8   7735 CCAATGCAACAGAATAGAGAACTTATAAATAAGACCACACATCTACAACC 7784
                         i     v  i     v    iiii v      iv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_89926215_8   7785 ATCTGATCTTTGACAAACCTGACAAAAACAGGCAATGGGAAAATGACTCT 7834
                          vi    i  i     ivv  v   i v  vv       i   vi ivv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_89926215_8   7835 CTATTTAATAAATGATGCTAAGAAAACTGGCTATCCATATGCAGAAAATT 7884
                           v  i  i     i    ii  v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_89926215_8   7885 GAAACTGGACCCCTTCCTTACATCTTATACAAAAATTAAATCAAGATGGA 7934
                            ii         v   i   i v              v    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_89926215_8   7935 TTAAAGATTTAAATGTAAAACCCCAAACCATAAAAACCCTAGAAGAAAAT 7984
                          i ?   ii         i v iv    i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_89926215_8   7985 CTAGGCAATACTATTCAGGACATAGGCATGGGCAAATAGTTCATGGAAAA 8034
                         v    ?ivv v v   iv   v v  vv i     - i   iv vii v 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATA 595

  chrX_89926215_8   8035 AAAAATCACATGCAATTGCAACAAATTCAAAAATTGAGAAATGGGATCTA 8084
                         vi v i  v v   vvv        vvv      v  v    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_89926215_8   8085 ATTAAA-CTAAAGATTTTTGGACAGCAAAATAAACTATCATCACAATGAA 8133
                           i   -i    i i     vi vv    iv v       vv v i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_89926215_8   8134 CACACAGTCTATGGAATGGGAGAAAA-ATTTGCAATCTATCCATCTGACA 8182
                         v v   ii i ii             -        vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_89926215_8   8183 AATGTCTTATATCCAAAATCTACAAGGAAGTTAAACAAATGTACAAGTAA 8232
                          iv v   i      i   v  i  i   v ivv    v vv i  vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_89926215_8   8233 GAATCAAACAACCCCATTAAAAAGTGGGCAAAGAACATGAACAGACACTT 8282
                         i iv    i     v   ?    i         i iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_89926215_8   8283 CTCAAAAGAAGACACTTATCTAGCCAACAAATATATGAAAAAAAGCTCAA 8332
                            v        i ivi vv i     i  ii i       i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_89926215_8   8333 CATCACTGATCAT 8345
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (144 / 109)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


1709 27.43 2.66 7.29  chrX_89938873_89944136.rev     3489  4352 (912)    L1M4_orf2#LINE/L1        1   824 (84)  

  chrX_89938873_8   3489 TGAAAACACATTCCA-GTCTCATGTGAG-GAAAGAATCAATATTGTTAAA 3536
                           i   v i  i   -  -     -  v- i    v i           i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGT-TCATG-GATTGGAAGACTTAATATTGTTAAG 48

  chrX_89938873_8   3537 ATGACAATATTGCCCAAAGCGAT-TATAGTTTTAATGCTATTCCCATCAA 3585
                            i     i v      vi   -  i  v  i  i  v  i  i     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_89938873_8   3586 ACCACCAATGATGTTCTGCACAGAA-TTAGCAAAAATGCATTTTAAAAAT 3634
                          viv   iiviiv  i vii     -  ii   iv-  -  ii     v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TG-ATCCTAAAATT 146

  chrX_89938873_8   3635 TATATGGAA-CAAAAAAAAGCCTGAATAGCCAAGGCAATCCTAAGCAAAA 3683
                         i        -iiv  iii v  v          ii     i i ------
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------ 190

  chrX_89938873_8   3684 AACAAAACAAAAACAAACAAACAAACAAACAAAGCTGGAGACATTATCTT 3733
                         ---    v  i      ---------------- i     ivv i ivi 
  L1M4_orf2#LINE/    191 ---AAAAGAAGAACAAA----------------GTTGGAGGACTCACACT 221

  chrX_89938873_8   3734 ACTTGACTTCAAACTATATTAGAAGGCTACAATAAGCAAAAGAG------ 3777
                         v iii i      viv  i  v  i      i   v   i v  ------
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_89938873_8   3778 ACTAGTACCAAAATATACACATAGACAAATGGAGCAGAATAGAGAGCCTA 3827
                            i i iv ii   v   i     iv      ii     v     i i 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_89938873_8   3828 GAAATAATGCTGCACACCTACAATCATCTGATCTTTGACAACGTTCATCA 3877
                                vv iii   ii  iii   vi    i  i     v v -ii  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT-GCCA 370

  chrX_89938873_8   3878 A-AGCAAGCAATAGAGAAAGGACTCCCTATACAATAAATGGTCCTGGGAT 3926
                          - v  vv    i i     i ivvi  v v   i       v      i
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_89938873_8   3927 AACTGGCTAGCCATATGCAAAAGATTAAAAT--GACCCCTGTCTTACATT 3974
                               v  ?   i          v i  i --       ii  i   ii
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_89938873_8   3975 ACATATAAGAATAAATTCAAGATCGATTAAATACTTAAACATAAAACCTA 4024
                          i   i  i   v  i    i  v   i ? v  i    ii   i v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_89938873_8   4025 AAATGA-AAATCTCT-GGAAGATAACGTAAG---AAATACCATTCTGGAC 4069
                            iv -   v    -i     v   i  i ---    -- -   vv   
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGAC 567

  chrX_89938873_8   4070 ATAGGAACTGATAAAGATATTATGAAGAATT-TACCAAAAGCAATTGGAA 4118
                         v v  iviv ii  v i -  v v iiv  v-i          vvv v  
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGT-TTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_89938873_8   4119 CAAAAGCAAAAATTGACAAAGAGGACTTAACTCAA--TTAAAGAGCTTCT 4166
                               v      v  i   vv      v -    --     i -   i 
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCA-TCAAAATTAAAAA-CTTTT 664

  chrX_89938873_8   4167 GCACAGCAAAAGATACTATCAACAGCATAAACAAACAACCTATGCAATGG 4216
                          ii vv    i  i        v ivi i  v i      i iiv     
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_89938873_8   4217 GAAAAAATATTTTCAAATTATGCATCC-AGAAAACATCTAAATTCCAGAA 4265
                           i         v     i  ii   i- v  iiv ii iv  -      
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT-CCAGAA 763

  chrX_89938873_8   4266 TCCATAAGACACTTATACAAATTTATAAGCCAAAAAACAACAACAACAAC 4315
                          vi    iiv   iv     v ---------------------   i  i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACT---------------------CAATAAT 792

  chrX_89938873_8   4316 AAAAACAAAAAACAAATCACCCCATTAAAAAGTGGGC 4352
                              -----i      v    v   ?    i     
  L1M4_orf2#LINE/    793 AAAAA-----GACAAATAACCCAATTWAAAAATGGGC 824

Transitions / transversions = 1.63 (145 / 89)
Gap_init rate = 0.04 (29 / 824), avg. gap size = 2.97 (86 / 29)  

 371 18.64 5.08 1.69  chrX_89938873_89944136.rev     4656  4773 (491)    L1M4_orf2#LINE/L1      787   908 (0)  

  chrX_89938873_8   4656 AATAATAATAA-ATAAATAAA--AAATAAAAAGTGGGCAAAAGACATGAT 4702
                                 v  - i      v--  v ?    i        i  iv   v
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_89938873_8   4703 CAGACA---CTTCAAATGAAGACATATGTGTGGCCAACAAGCGTATGAAA 4749
                         i     ---  i    -     i   iivi       i    ii      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_89938873_8   4750 AAAATACTCAACATCACTAGTCAT 4773
                          i - i          ????????
  L1M4_orf2#LINE/    886 AGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.04 (5 / 122), avg. gap size = 1.60 (8 / 5)  


3123 25.00 1.78 0.89  chrX_89958394_89962606.rev     2823  3722 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_89958394_8   2823 TGCAAAGATATTCCATGTTCACGAATTGGAAGAATCAATATTGTTAAAAT 2872
                           v        i         i i         v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_89958394_8   2873 GTCCATACTGCACAAGGCAATCTACAGATTCAATGCAATCCCTATCAAAT 2922
                          v v     v v   ivii              i               v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_89958394_8   2923 TACCAATGATATTCTTCACAGAAACATAAACAA--TGAATCCTACAATTT 2970
                          v   iiviiv  i  ii      -- vi    --   -     v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA--TTGACAAGCTGA-TCCTAAAATTC 147

  chrX_89958394_8   2971 ATATGGA--TCCACAAGATTTATATTAGCCAAAAGTATCCTGAGCATAAA 3018
                                -- v  vii  iii v v         vv   i   iv vi  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_89958394_8   3019 GAACAAAACTGGAGGAATTGCATAACCTGACTTTAAATTGTACTATAGAG 3068
                                ii       v ii  ivv  ii i  i   viv     i i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_89958394_8   3069 CTATAGCAACGAAAATAGCATGGTATTTGCATAAAAAAAGAAACATAGGT 3118
                            i  i  iv  i i  ii     i v      ii v   v i    i 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_89958394_8   3119 CAATACAACATAATAGAGAACCGAGAAAGAAATCCATAGACCTAGAGTGA 3168
                             iv  i v   v    ii v     v   i     v ii  vi  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_89958394_8   3169 ACTAATTTTCCACAAATATGCCAAGGACATACACTGGAGAAATGACAGTC 3218
                          i i      v    ivi       iv   v  v   i    vi i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_89958394_8   3219 TCTTCTATAAATCGTGCTGGAA-AACGTGATATCCATATGCAGAAGAATA 3267
                          i   v i    v       i -   vv    ?   i     i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_89958394_8   3268 AAACTTGACCCCTATCTTGCAGCTTATACAAAAATAAAATCAAAATGCAT 3317
                           ii v        i  ii  v v           v  v        v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_89958394_8   3318 TAAATACTTAAATCTAAGACCTCAAACTATAAAACTAGTACAAGAAAACT 3367
                         i ? v  i     v     v  v             vv  v        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_89958394_8   3368 TTGGGGAAACTCTCTAGGACATTGGACTGGGCAAAAATTTCTTGAACAAT 3417
                          v  ? v  v   iiiv   v    ii i     vii      ii i vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_89958394_8   3418 ACCCCACAAGCACATGCAACCAACGCAAAAATTGATAAATGGGA--TCAA 3465
                           v   v       v     v  v v      v       v   --   -
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA- 646

  chrX_89958394_8   3466 GTCAAG-TTAAAAAGCTACTGCACAGCAAAGGAAGCAATCAACAAAATGA 3514
                         -    i-       -  vi  ii vv       vi v     v   i   
  L1M4_orf2#LINE/    647 -TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_89958394_8   3515 AGAGAAAACCCACAGAATGGGAAAAAGTATTTGCAAACTACTCATCTGAC 3564
                          i   v                i   i          ii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_89958394_8   3565 AAGAGA-TTA-----AAAATATAAAAGGAACATAAGCAACTC--TAGGAA 3606
                            i  -  i----- i      v  i    vivvi      --  iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_89958394_8   3607 AAAAATCTAATAATCTGACTTTTAAAATGGGCAAACAATTTGAATAGACA 3656
                            i - v     i ii -  ?v            vi             
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_89958394_8   3657 TTTCTCAAAAGAAGGAATACAAATGTGAAACAAGCATATGAAAAGGTGTT 3706
                               v       iv         vvv  i     i        i  i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_89958394_8   3707 CAACATTATTGATAAT 3722
                               i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (122 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.71 (24 / 14)  


1734 26.32 3.69 1.44  chrX_89974057_89975686.rev      502  1124 (506)    L1M4_orf2#LINE/L1      216   852 (56)  

  chrX_89974057_8    502 CACACTACCTTACTT-AAAATTATGCTACAAGGCTACAGTAACCAAAACA 550
                               v  iv i  -    i - i      i          i   i   
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACA 264

  chrX_89974057_8    551 ACATGGTACTGGTACAAGAAGACACATATAGGACAATAGAACAGAATAGA 600
                         iii         i i   i v v        iv    i   i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_89974057_8    601 GAGCCCAGAAATAATACCACACCCCTACAACTATCTGATCTTCAACAAAC 650
                            i          vv   i  vii  iiiii vi    i   i    iv
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_89974057_8    651 CTGACCAAAA------AA--AGGAAAATATTTTCTATTAAACAAATAGTG 692
                         v  -    i ------  --i     iv  vv   v  v       i   
  L1M4_orf2#LINE/    365 GTG-CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_89974057_8    693 CTGGGATAACTGGCTAGCCATATGGTGAAGATTGAAACTGGACCTCTTCC 742
                               i      v  ?   i   vvi    v    ii      i  v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_89974057_8    743 TTACACCATATGCAAAAATTAACTCAAA-TGGCTTAAAGACTTAAATGTA 791
                          i         i                -   v i ?    i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_89974057_8    792 AAACTCTAAACTATAAAAACCATGTAAGACAACCTAG---TCAATACCAT 838
                          i viiv           vi v iv    v   v   --- v   -- - 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-T 560

  chrX_89974057_8    839 TCAGGACATAGGCACAGGCAGGAATTTCAT-GATGAAGACACCAAAAGCA 887
                           iv   v v  vvi     ivii    v -   - v             
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCA 609

  chrX_89974057_8    888 ATTGCAACAAAAACAGAAATTTAAAAATTAGATCTAATTAAACTAAAGAG 937
                         vvv         iv i    vv v     i  ii v  i   v v  i i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_89974057_8    938 CTTCTGCACAGCAAATGAAAACTATCAACAGAGTAAA----CAGCATATA 983
                            i  ii vv    - i v        v i   i  ----  i vi i 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_89974057_8    984 GAATGAGATAATTATTTTTGCAAACTATGCATCCAACAAAGATCTAATAT 1033
                              i  v  v-  v        ii  ii   ii i  i iv  vi   
  L1M4_orf2#LINE/    709 GAATGGGAGAAA-ATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_89974057_8   1034 CCAGCATCTATGAGGACCTTAAACAAATTTACAAGAAAAAAAAAAAAAAC 1083
                             v  v   i i  v  ivv    v iv i  v     i v   v   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_89974057_8   1084 CCA--TAACAAAGTGGGCAAAGGAC--AAACAGACATTT-TCTAAA 1124
                            -- ? -   i           i--i  i        -  i   
  L1M4_orf2#LINE/    808 CCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

Transitions / transversions = 1.33 (92 / 69)
Gap_init rate = 0.03 (18 / 637), avg. gap size = 1.78 (32 / 18)  


2884 28.26 1.10 0.88  chrX_90044744_90050556     4415  5320 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90044744_9   4415 TAGAAAAACATTCCATGCTCATGGATGGGAAGAATCAATATCGTGAAAAT 4464
                          i    i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90044744_9   4465 GGCCATACTGCCCAAAGTAATTTATAAATTCTTTGCTATCCCCATCACGT 4514
                            v     v      v i  i  i i    vvi  v     i    viv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90044744_9   4515 TACCATTGGCTTTCTTCATAGAATTAGATAAAAACT-ACTTTAAATTTCA 4563
                          v   viv  i  i  iii    v v  i  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_90044744_9   4564 TATGGAACCAAAAAAAGAGCCCATA-TAGCCAAGACAATCCTAAGCCAAA 4612
                                -- viv  i ii    v -       i      i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_90044744_9   4613 AGAACAAAACTGGAGGCATCACACTACCTGACTTCAAACTATACTATAAG 4662
                                 ii      vv       v  ii i      viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_90044744_9   4663 GCTACCATAACCAAAACAGCATGGTACTGCTACCAAAACAGATATGTAGA 4712
                              vi   i   i    ii        vi iv ii i   i  i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_90044744_9   4713 GCAATGGAACAGAACAGAGGCCTCAGCAATAATGCCACACATCTACAACC 4762
                         v        i    iv   ivii   v     vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_90044744_9   4763 A-------TCTGACAAACCTGACAAAAACAAGCAATAGAGAAAGGATTCC 4805
                          ------- ii     ivv  v   i v  vv    i i     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_90044744_9   4806 CTATGTAATAAATGGTGTTAGGAAAACTGGCTAGCCATATACAGAAAACT 4855
                           v vi  i        i i   v      v  ?   i  i  i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_90044744_9   4856 AATACTGGACCCCTTCCTTACACCTTATACAAAAATAATTTACTCAAGAT 4905
                         i vii         v   i     v           v ---      i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTA---ACTCAAAAT 493

  chrX_90044744_9   4906 GTATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCTTAGAAGAA 4955
                          v  i ?    i           v       i      vi          
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_90044744_9   4956 AACCTAGGCA-ATACCATTCAGGACATAGGCATGCACAAAGATTTCATGA 5004
                            v    ?i- v i -   iv   v v  vv ivi   v i    v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_90044744_9   5005 CTAAAACACCAAAAGCAATGATAACAAATGCCAAAATTGACAAACGGGAT 5054
                         v  vi            vviii      v vv     v  i   iv   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_90044744_9   5055 CTAATTAAACTAAAGAGCTTCTGTGCAGCAAAAGAAACTGTCATCAGAGT 5104
                         i v  i   v v  i i   i     vv    i  v   i   vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_90044744_9   5105 GAACAGGCAACCTACAGAATGAGAGAAAATTTTTGCAATCTCTCCATCTG 5154
                            v  i     i        i        v       viiv vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_90044744_9   5155 ACAAAGGACTAATACCCAGAATCTACAAGGAAGTTAAACCAATTTACGAG 5204
                          i  i     vi  i       v  i  i   v ivv  v v iv ii v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_90044744_9   5205 AAAAAAACAAACAACCCCATCAAAAGGTGGGCAAAGTATACGAACAGACA 5254
                              i     i     v  i?   ii         v  vi   i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_90044744_9   5255 TTTCTCAAAAGAAGACGTTTATGCAGCCAAGAAACATATGAAAAAAAGCT 5304
                               v        ii vi viii     v  i  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_90044744_9   5305 CATCATCACTGGTCAT 5320
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (146 / 106)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.25 (18 / 8)  


2030 26.61 4.10 3.77  chrX_90050873_90053239.rev      975  1876 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_90050873_9    975 AAAGATATTTTTCATGTTCATGAATTAGAAGATGCAATATTGTTAAGATG 1024
                                 ii--          i   i     ivi               
  L1M4_orf2#LINE/      4 AAAGATATCC--CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_90050873_9   1025 TTCTTTTTTCTCAT-TTGCTATATGCACTTAACGATATTTCTATCATAAT 1073
                         vivv vi i i  v-   v v  iiv i i    vv  ii      v   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_90050873_9   1074 CCCAGCAAGATTTATT-CAGATATC-AGAAGCTGATTCTAAAATATATAT 1121
                               vivv   v  -    v  i- v        i       vi    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_90050873_9   1122 GGCAAAACAAAGGAACTACAATAGCTAAATCAACTCAGAAAAAGAAGAAA 1171
                           v  vi   i   v i v      i   v   iiiv            v
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_90050873_9   1172 AAAGCTAAAGGGCTCCCACTATCCAATTTCAGGACTTATTATAAAATTAT 1221
                             i ii   i   v    vi         ii     i  i   ii  i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_90050873_9   1222 AATAATTAAGACAGTGTGGTATTGGAAAAAAAGATAAACATACACATCAA 1271
                          i    i              i   v v  i-    i     i v     
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATATAGATCAA 300

  chrX_90050873_9   1272 CAGAATAGAATAGACAGTTGAGAAATAGGCTTATATGAATATCATTTATT 1321
                         ii         v  v   iv       ii ii   iivv   vi iv   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_90050873_9   1322 GCTTCTTTTTACAAAAAT-TCAATA--ATTTAAT----AAAGAAT--TTT 1362
                          v  --  iv    iii -i   v --   i   ----       -- i 
  L1M4_orf2#LINE/    351 GATT--TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_90050873_9   1363 TTTCAATAAATATTGCTGTATCAGTTGTAAATCCCTATGCAAAATAATAA 1412
                               i    iv     viv  ii  v v ?  vi        v   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_90050873_9   1413 ACCACAGCATATACCTGATACATTATCCAAAAATTAACT-GAAATAAGTA 1461
                          vivvii viv     v i  vv   v            -i    iii v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_90050873_9   1462 ATTTACCAAAATGTATAA--CAAAACTATAAAACATTTAAAAGCAAACAT 1509
                          ?vv   v       vi --i             vi   i   v      
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_90050873_9   1510 GAGGC---AATATACAAAATCTTTAGTTTAACAATAAGATTTAAAGATAA 1556
                         -   ?---   v v ivi i   vi   vii    i- v  ivv     v
  L1M4_orf2#LINE/    549 -AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTAGATAT 596

  chrX_90050873_9   1557 AATGC--AAAGCATGATCTACT---TTAAAAAT-GTTAAATTAGGCTTTG 1600
                         i ii --      ii v v  v---vv      - v      i i   ii
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_90050873_9   1601 TCAAGATTAGAATACTTT-GCTCTGTAAAAGACACTGTAAGGAGAATGAA 1649
                             i    i  -     - iv  vi   i      i v i  i i    
  L1M4_orf2#LINE/    647 TCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_90050873_9   1650 AAGGTAACACACACACTAAGAGAAAGTATTTGCAAATCAAATAACATATC 1699
                            ii   v    v v ii      i             -----i     
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-----TATATC 740

  chrX_90050873_9   1700 CAATAAAAT-CTTACATGCACAGTATATAAATAACTCTAAAAAGTCAACA 1748
                         ii    iiv-   ii  v  v i        v      v v  v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_90050873_9   1749 ATAAGGAAAAAAGCGACAAAATTAATA-AATTTTAATAAGTTTAATAAAT 1797
                             -----    --     --   iv-    ?v  -------   iiii
  L1M4_orf2#LINE/    791 ATAA-----AAAG--ACAAA--TAACCCAATTWAAA-------AATGGGC 824

  chrX_90050873_9   1798 TTTTTAAAAG-TCTAAAAAGACACTTCACCAAATTAGGTATGTGAA---- 1842
                         -----   i - i i  v     i   v     vv  i   iii  ----
  L1M4_orf2#LINE/    825 -----AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_90050873_9   1843 -----AGCATATGAAAAAATGCTCAACATCATTAGTTAT 1876
                         -----    i       i             ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.03 (30 / 905), avg. gap size = 2.37 (71 / 30)  


2873 22.01 5.70 2.17  chrX_90084785_90087083      930  1806 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90084785_9    930 TAGGAAGATATCTTGTGTTCATGGATTTAAAGACTTCATATTGTTAAGAT 979
                          i i        iii            vi       v             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90084785_9    980 GTTGCAGTACTACCCAAAGAAATGTAAGAATTAAATGAAATCCTTTTCAA 1029
                          --   i    v      vvi  v  vii   v  i v     i v    
  L1M4_orf2#LINE/     51 G--GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_90084785_9   1030 AATCCCAG-TAAAGATTTTGCAGAAATAGAAATGTACATCTTAAAATTAA 1078
                                 - ivvvv            v  v v ivv   i       v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_90084785_9   1079 TATGAAATTTCAAGGGATACCAAACAGCTAAAGCAATATTGAAAGAAAA- 1127
                             i  v v       iv vi  i   i   i    v      i i  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_90084785_9   1128 -------TTGGAGCTCTTATACTTTCTGATAGCAAA-TATATTACAAAAC 1169
                         -------      vv  i i    i ii  vv    -iv  i      i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_90084785_9   1170 TAAAGCAATCAAAACAGTCTGGGACTGGCATAAAGAAAGATATATAGATC 1219
                           v  i      i     v   v          i  v   i         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_90084785_9   1220 AATAGAATTGAACAGAGATTATAGAAAAAAATTGCATA-----ATGTTCT 1264
                            i    v   iv    v vi     v   ii-    -----   v  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACC-CATACATTTATGGTCA 347

  chrX_90084785_9   1265 TATGATTTTTGGCAGGGATGCCAAGACCCATTCAATGGGGAAAAAA--AT 1312
                         vv       i i  i  i          -              i  --i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACC-ATTCAATGGGGAAAGAATAGT 396

  chrX_90084785_9   1313 GTTTTCAACA---GATGTTGAGAAAACTGAGTATCTACATAAAAAAGAAT 1359
                         v         --- i  i  i  v     ii  ? i    iv        
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_90084785_9   1360 AATAAAGTAGGGCCCTTACTTTA-----TATTTAAAAA--AATTTAAAAA 1402
                         i ---   v  i   i   i i -----   vi     --  i i    v
  L1M4_orf2#LINE/    447 GA---AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_90084785_9   1403 GGTAAGAAAAACATATATTTAAACACTAAAACTATAAAACT-TTAGAAGA 1451
                           - vv ? i  v  v  v   ivi                -        
  L1M4_orf2#LINE/    494 GG-ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_90084785_9   1452 ACATATAAGGACATGATTT--GTGACATTGGATTTGGTAATGATATCTTG 1499
                          v i   i ?ii -i  i --     v    i  v  i    i v    i
  L1M4_orf2#LINE/    543 AAACATAGGNGTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_90084785_9   1500 AATGGCACATCAAAAGCATAGTAAACAAAAGGAAAAAAGGATGAATTAGG 1549
                         i  ivv   i        i ivv        i     vi   i    i i
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_90084785_9   1550 TTACATCAAAATTAAGT-TTTTTG-GCATCAAAGGGTACTATCAACAGAA 1597
                         i v            iv-i     -  v       ii        v i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_90084785_9   1598 GGAAAAGTCAATCCAGAGAATGGGAGAAAATATTTGCAAATTATATAT-- 1645
                         v      v   i   v                         i      --
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_90084785_9   1646 AACATG---TTAGTATCCAGAATATGTAAAGAACACCTAGAATTCAACAA 1692
                         i i v ---i v             i        v i  v  i    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_90084785_9   1693 CTTAAAAACAACAACAACAAAAAAAACAAATTATAAAATGGGTAAAAGGC 1742
                         --      -------i     v  vv   v ? -        i   i ii
  L1M4_orf2#LINE/    792 --TAAAAA-------GACAAATAACCCAATTWA-AAAATGGGCAAAGGAT 831

  chrX_90084785_9   1743 TTGAATAGACATT--------GAAGATA--CAAATGGCCAATAAGCACAT 1782
                                      --------       --                    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_90084785_9   1783 ---AACATGTTTGATATCACTAATTAT 1806
                         ---  v   i ii i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (109 / 80)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.65 (69 / 26)  


2005 26.25 1.34 0.57  chrX_90095179_90102245.rev     5318  5839 (1228)    L1M4_orf2#LINE/L1        1   526 (382)  

  chrX_90095179_9   5318 TGGAAAAACATTCCATATTCATGAATAGGAAGAATCAATATAGTGAAAAT 5367
                               i i  i    i      i  v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90095179_9   5368 GGCCGTACTGCACAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5417
                            vi    v v    v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90095179_9   5418 TACCA-TTGACTTTCTTCATTAGAAA-----AAACT-ACTTTAAATTTCA 5460
                          v   -i  v    i  v--i     -----  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG--CAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_90095179_9   5461 TATGGAACCCAAAAAAGACCTTGTATAGCCAAGACAATCCTGAGAAAAAA 5510
                                vi-iv  ii    iv v        i      i   i   i  
  L1M4_orf2#LINE/    149 TATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_90095179_9   5511 GAACAAAGCTGGAGGCATCATGCTACCTGAGTTCAAACTACACTACAAGG 5560
                                 i      vv   ii  v  ii v      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_90095179_9   5561 CTACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGATATGTAGAC 5610
                                  iv  i    ii         i iv ii i   i  i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_90095179_9   5611 CAACGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCA 5660
                            i    i    iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_90095179_9   5661 TCTCATGTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5710
                         vi v  v  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_90095179_9   5711 TATTTAATAAATGGTGTTGAGAAAACTGGCTAGCCATATGCAGAAAACCG 5760
                          v  i  i        i  i  v      v  ?   i     i  i vi 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_90095179_9   5761 AAACTGAACCCCTTTCTTACACCTTATACAAAAATTAACTCAAGATGGAT 5810
                           ii  i      vi  i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_90095179_9   5811 TAAAGACTTAAACATAAGACCTAAAACCA 5839
                         i ?    i    ii     v       i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTA 526

Transitions / transversions = 1.81 (87 / 48)
Gap_init rate = 0.01 (5 / 526), avg. gap size = 2.00 (10 / 5)  

1142 27.17 0.67 2.00  chrX_90095179_90102245.rev     6129  6577 (490)    L1M4_orf2#LINE/L1      466   908 (0)  

  chrX_90095179_9   6129 ACTCCATCT-CAAAAATAAAAACAAATTAATTAATTAATTTAAAAA-AAT 6176
                           v    v -       v  vv    v iiv v ?vi ii    vi-  v
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_90095179_9   6177 ACCTAAAACCATAAAAACTCT-AGAAGAAAACCTAGGCAATACTATTCAG 6225
                          v       i      -    -          v    ?ivv v v   iv
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_90095179_9   6226 GACATAGGCATGGGCAAAGACTTCATGACTAAAACACCAAAAGCAATGGC 6275
                            v v  vv i     v ii   v iiv  vi            vvi  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_90095179_9   6276 AACAAAAGCCAAAATTAACAAATGGGATCTAATTAAACTAAAGAGCTTCT 6325
                                 vv     vi i    v   ii v  i   v v  i i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_90095179_9   6326 GCACAGCAAAAGAAACTATCATCAGAGTGAACAGGCAACCTACAGAATGG 6375
                          ii vv    i  v       vv i      v  i     i         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_90095179_9   6376 GAGAATATTGTTGCAATCTATCCATCTGACAAAGGACTAATATCCAGAAT 6425
                              v  vv      vii  vi      i  i     vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_90095179_9   6426 CCACAAGGAACTTAAACAAATTTACAAAAAAAAAAAAAAAAAAAAGACAA 6475
                         vi i  i     i--------      vvv  v  v     i v i i  
  L1M4_orf2#LINE/    765 ATATAAAGAACTC--------TTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_90095179_9   6476 CTCTATCAAAAAGTGGGCAAAGGATATTAACAGACACTTCTTAAAAGAAG 6525
                          i v  i?    i            v v  i     i    iv       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_90095179_9   6526 ACATTTATGCGGCCAACAAGCATATGAAAAAAAGCTCATCATCTCTGGTC 6575
                          i  vi vii      i     i       i v     v    v??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_90095179_9   6576 AT 6577
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 0.89 (56 / 63)
Gap_init rate = 0.01 (5 / 443), avg. gap size = 2.40 (12 / 5)  


1891 27.19 2.63 4.19  chrX_90105084_90106890      480  1314 (493)    L1M4_orf2#LINE/L1       87   908 (0)  

  chrX_90105084_9    480 AACCCCAACTAATATAATTGCCAA-TGTCATTTTTCACAGAATTAGGGAA 528
                           i   v ii  ---   i-   i-  i -     ii     v v iv  
  L1M4_orf2#LINE/     87 AATCCCTATCAA---AATC-CCAGCTGCC-TTTTTTGCAGAAATTGACAA 131

  chrX_90105084_9    529 AATAACTCTAAAATTAATATGCAACCCCCAAAAAAGCTCA-AATAGCCAA 577
                         iv i ii        v     v  viv --  iiii i  -         
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGC--AAGGGACCCAGAATAGCCAA 179

  chrX_90105084_9    578 AGCAACCCAAAACAAAAAGAACAAAGCTGGAGG---CATCACTTCACATG 624
                          i   i ivi  v  i          i      ---  -      v  --
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA-CACTTCCCA-- 226

  chrX_90105084_9    625 ACTTTAAA--TT-CTTCAAGGCGATAGCAACCAAAACATTAGAGTACTGG 671
                          i  i   --  -  v   i  v i  i  i   i   v ivi       
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_90105084_9    672 TGCAAAAATAGACACACAGATAAGTGAAAAAGAAAAGAGGACCCAGAAAT 721
                         iii  ii       i i    v i  i  v    vv   iii        
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_90105084_9    722 GAAGGCTCACACAT--ACAACCAACTGATCTTTGACAAGGTTAAAAAAAA 769
                         i  -- i  i    -- iiii   i    i  i       v ivv  i v
  L1M4_orf2#LINE/    327 AAA--CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chrX_90105084_9    770 TAAACAATGGGGAAATGACACCCTATTCAATAAATGATGCTAGAAAAGCT 819
                         i vv           vi i vi  v     i     i    i i v i  
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_90105084_9    820 CACCAGCCATGTGCAGGAGACTGAAACTGGACCCTTACTTCTCAC----- 864
                         vivi ?   ii    ii   v    ii       i   i  v   -----
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_90105084_9    865 --GAAAACTAACTCAAGGTGGAT-AAAGACTTAAATGTAAGACCTGAAAC 911
                         --i    i        ii     - ?    i           v  i    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_90105084_9    912 TGTAAAAAATCATAGAAGAAAACCTAGAA--AAACCTTATATGGATATTG 959
                          i     v-  v           v   i?--   i   -ii  - iv   
  L1M4_orf2#LINE/    525 TATAAAAC-TCTTAGAAGAAAACATAGGNGTAAATCTT-CGTG-ACCTTG 571

  chrX_90105084_9    960 GCCTAGGCAAAGAATTTATGACTAACACATCAAATGCAATTGTATCCAAA 1009
                          vi       v iv  iv iiv  vv   i    v   vvv i v v   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_90105084_9   1010 ACAAAAATAGACAAATGGTACTTAATTAAACTAAAGAGCTTCTGCACAGC 1059
                         iv         i    v v    v  i   v v  i i   i  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_90105084_9   1060 AAAACAAAA-ATCAATAGATTAAACAGACAAGCTACAGAATACAAAAACA 1108
                            iv v v-     v i v i  v      v i       ivi i  - 
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA-A 720

  chrX_90105084_9   1109 ATATTTGCAAACTATGCATCCAGAAAAAGAATAATATTCAAAATCTATAA 1158
                                    ii  ii   iiiv  ii  v vi   i  i   v     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_90105084_9   1159 GGAACTTAAATAAATCAACTTGTAAAAA-ACAAATAACCACATTAAAAAG 1207
                         i     ivv i  v    - vi      -          vv   ?    i
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAA-TAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_90105084_9   1208 TGGGCAAAGAACATGAGAAGACACTTCTCCAAAGAAAACACACCTTCAAA 1257
                                  i iv   iv     i            i i i  -------
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC------- 862

  chrX_90105084_9   1258 GAAGAAACACATGTGGCCAACAAACGTATGAAAAAAATTTTCACCATCAC 1307
                         ----   ------       i  i ii       i - vi   v     ?
  L1M4_orf2#LINE/    863 ----AAA------TGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZ 901

  chrX_90105084_9   1308 TAATCAT 1314
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.72 (141 / 82)
Gap_init rate = 0.03 (26 / 822), avg. gap size = 2.19 (57 / 26)  


2550 28.06 2.12 1.00  chrX_90128198_90132968     3381  4278 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90128198_9   3381 TGGAAAAACATTCCATGCTCAAGGATTAAAAGAATCAATATTGTTAAAAT 3430
                               i i  i     i   v     ii    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90128198_9   3431 GGCCATACTGCCCAAAGAAATGTACAGATTCATTGCTATTCCTAGAAAAC 3480
                            v     v      vvi  v          vi  v  i    vv   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90128198_9   3481 TACCAA-TGTCATTTTACACAGAATTAGAAAAACATATACCATAATTTAT 3529
                          v   i-  i v    -ii     v v  v  i vv  v i v    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_90128198_9   3530 ATGGAATAAAAAAAGAGCCTGAATAATCATAGTAATCATAAGCAAAAGGA 3579
                               vviv  ii  v  v     ii  v ii    v i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_90128198_9   3580 ACAAAACCAGAGGCATCACGTTACCTGATTTTAAACTATACAAGAAGTCT 3629
                              iiii    vv    ii v  ii    i   viv   v v  iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_90128198_9   3630 ACAGTAACCAAAACAGCATGGTTCTGGTACAAAAACAAACACAAAGACCA 3679
                                i   i    ii    v    i i  ii i i   i v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_90128198_9   3680 AAGGAACAGAATAAAGAATACAGAGATAAAGCTGTACACTGACAACCATG 3729
                          v    i     vi   i v    i     v ii    i v iiii  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_90128198_9   3730 TGATCTTTGACAAAC---TCAAGAAAGTAAGGAATGGGGAAAAGGCTCCC 3776
                             i  i     iv---i     v--i vvv          iiiivvi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC--CATTCAATGGGGAAAGAATAGTC 397

  chrX_90128198_9   3777 TATTCAATAAATGTTTCTGGGATAACTGGATATTCATATACAGAAGAATA 3826
                          v     i     v v      i         ?i  i  i  i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_90128198_9   3827 AAATTAGAGCC-TACTTATCACCATATA-AAAAAT-AACTGAAGATGGTT 3873
                           i  i  v  -   i vv         -      -    v  i    v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_90128198_9   3874 TAAAGTCTTAAACGTAAGACCTAAAACTATAAAAA-CTTTGAAGGATACA 3922
                         i ?  v i    i      v              v-   v    i v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_90128198_9   3923 TAGG---AAATACCTTTCTCAATATCAGTCTTGGCAAATAATTTAT-GGA 3968
                             ---    ---i   vii iv ii vi v     - ii   v -i  
  L1M4_orf2#LINE/    548 TAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA 593

  chrX_90128198_9   3969 TAAGTCCTCAAAAGCAACTGTAACAAAA----AAATGTATAAGTGAGATG 4014
                           v v vi        vvv i       ----    iv    i vi  iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_90128198_9   4015 TAATTGAACTAAATAGCTTTTTCACAGCAAGAGGA-ACTATCAAAGAATT 4063
                          v  ii  v v  v i     vii vv   -    -        ii  v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACTATCAAGAAAGT 692

  chrX_90128198_9   4064 AAACAGGCAACCTATTGAATGGGAGAAAATATTAACAAACTATGCATCTA 4113
                         i  v  i     i iv                 vi    ii  ii    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_90128198_9   4114 ACAAAGGATCAATATCCAGAATCTGTAAGGAACTTAAACAAAAGAACAAG 4163
                          i  i   iivi          v i   i     ivv    vvv  i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_90128198_9   4164 CAGAAAACAACTAACCCCATTAAAAAGTGAGCAAAGGACGTAAATAGACA 4213
                         v i  i    v      v   ?    i  i        iv i        
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_90128198_9   4214 TTTCTCAAAAGAAGACATACAACCGATCGACA--CACATGAAGAAAATGC 4261
                               v        i      vi ii i i --        -  i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGATGC 891

  chrX_90128198_9   4262 TCATCATCACTAATCAT 4278
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (143 / 106)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.65 (28 / 17)  


2020 25.91 7.08 3.42  chrX_90133616_90135476      509  1384 (477)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90133616_9    509 TGGAGTGACATACCATCTCCTTGGATTGGAACACTCAACACAGTAAAAAT 558
                             iv  i  v    v i v          v   i  i iv  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90133616_9    559 GTTACTTCTCCCAAGTTTGAGCTATATACTGGACATCATTCCAAAGAAAA 608
                          vi v v     v iv    v   i v i vi  iiv  i  v vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90133616_9    609 TACCTGCAAAAATTTTTACAGATATAGACAAGCT-ATTTTTAAATTTATA 657
                          v  v  vivvv     i    v  v        -  ii v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_90133616_9    658 TGGAAA-------GACCCCAACAATTATTATAGC-AAAA-AAT-----AA 693
                               -------     vi --------     -    -   -----  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGA--------ATAGCCAAAACAATCTTGAAA 192

  chrX_90133616_9    694 AAAAAGATTAAATTTGTAGGAATAACATTACTTTGTTTTAAGACTTAATT 743
                           i    vi   v   v    v v   i v iivi   i  i     v v
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_90133616_9    744 TAGAGCTGCAGTATACAAGATGGTATGGTACTGAC-TAAGAGATAGGAAC 792
                         i i    i     vv     ii  i        i -    -     iv i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACAT 291

  chrX_90133616_9    793 ACAGATAAATGGA-CAGAAGAGATAGTCAAGAAAGAGATTGAAATAGGCT 841
                          i    v      -i    vv  v    v     v i iiv --  ----
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TA---- 335

  chrX_90133616_9    842 GACACTGATATGGCCAATATATTTTTGACAAAGGTGCAAAAGC------- 884
                         --  i --     i    vv     i     i     v  ii -------
  L1M4_orf2#LINE/    336 --CATT--TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_90133616_9    885 -------------------------AATGGTTTTGGGACA-CTGGATATT 908
                         -------------------------      vi       -       ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_90133616_9    909 CATATGCAAATAAGTTAGCTTTGAGGAAAACCTCATACCTTTTAAAAAAA 958
                           i       vi i v iv  v  vvvvv      i   v v  v     
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_90133616_9    959 TTAACAAAGAATGAGTCACAGATTTAAATGTAATATGTACAATTATAAAA 1008
                              vv i    ii   ?   ii         v vv  v  i       
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_90133616_9   1009 CTATTAGAAGAAAACACTGGAGAAAACCTTTGTGACCAAGAATTAGACAA 1058
                           v             iv  ? v   i   i      vv ii    i   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_90133616_9   1059 -GGTGTTCTTAGTCATGAAACCAAAAACACAATCAAGAAAAGTATAGAAT 1107
                         -   -       vi    v       i     v   v     v - i   
  L1M4_orf2#LINE/    582 TGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA-AAAAT 629

  chrX_90133616_9   1108 A-ATAAATTTGATTTTATCGAA-TTAAAAACAT--GAGTTTGGCAAAACA 1153
                          -       v  i  i   i  -        v -- v i  --    iv 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGA 677

  chrX_90133616_9   1154 CACCTCTAAGAGAA-AAATATATAGGTTGGAGACTTGAAGAAAATGTTTT 1202
                            ivii    i i-i  v v i iviiiv   v v i       i   v
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_90133616_9   1203 CAGAACATCACTTATGTGACAAAAGATTTGTATCCAGACTGTATCGATAA 1252
                           i ---   iv   v   i  ii  i           v i   vi v  
  L1M4_orf2#LINE/    728 CAAA---TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_90133616_9   1253 GTC--AAAACTCAACAGTAAGGAAGCAAATATCCCTATTTTAAAGTGGGC 1300
                         v  -- v       i i   ii ii      v   v   ?v   i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_90133616_9   1301 AAAATACTTG--TA--CACTTCACCAATGAAAACCTATAAATGGTGAATA 1346
                            iv i   --  --  i   v    v   i iv  i      iv    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_90133616_9   1347 AACATATGAAAAGACCATGCAGTAACATTATACATCTA 1384
                          i  i         ---   -vi     i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGA---TGC-TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.06 (115 / 108)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.29 (92 / 28)  


2874 26.94 1.55 0.89  chrX_90165280_90169864.rev     3193  4094 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90165280_9   3193 TAGAAACACATTTCATGCTCGTGGATGGGTAGAATCAATATTCTGCAAAT 3242
                          i    v i  ii    i  i     v  v   v i      v vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90165280_9   3243 GAACATACTGCCAAAAGAAATCTATAAATTCAATGTAATTCTCAGTAAAG 3292
                          ivv     v  v   vvi     i i      i i   i ii vi   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90165280_9   3293 TACCATCATCATTCTTCACAGGACTAGAAAAAACCATCCTAAAATTCATA 3342
                          v   v vv v  i  ii   i v v  v  iviv               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_90165280_9   3343 TGGAACCAAAAAAAAGAGCCCACA-TAGTCAAAACAATACTAAGCAAAAA 3391
                              --- viv  i ii    v -   i         vi i iv  i  
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_90165280_9   3392 TAACAAATCTGGAGGTATCACATTACCCAACTTCAAACTATACTACAAGG 3441
                         v      vi      vv     i v     i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_90165280_9   3442 CTATAATTGCCAAAACAGCATGGTACTGATATAAAAACCAGCATATAGAC 3491
                            i i vii   i    ii        ii    ii ivii        i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_90165280_9   3492 TAATGGAATAGAATAGAGAACACAGAAAGAAAACAATATACTTGTAGCCA 3541
                         i             v    iiv      v   v v   i i  i i i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_90165280_9   3542 ACTGAACTTTGACAAAGCAAACAAAATCATAAATTAGGCAAAGGACACCC 3591
                          i   vi  i     i vviv   i i   vv v i  v    i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_90165280_9   3592 TATTCAACAAATGGTGCCGGGATATTTGGCAAGCCACATGTAGGTGAAAG 3641
                          v               i    i vi   vv ?       i ----    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA----AAAG 443

  chrX_90165280_9   3642 AAAGAAACTGAATCCTTATTTCTCACTTTATACAAAATCCAACTCAAGAT 3691
                           v   ii  i i  i  ii  v   iv         vii       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_90165280_9   3692 GGATCAAAGACTGAAATGTAAGACCTGAAACCATAAAAATTTTACAAGAT 3741
                               ?    iv          v  i    i      v i   v    v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_90165280_9   3742 AAAACTGGAAAAACTCTTCTAGACATTGGCTTAGGCA-TAGTTCATGACC 3790
                           v iv  ?iv  v     vv   v    v       - i   iv v vv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_90165280_9   3791 TAGAAC-CCAAAAGCAAAAGTAACAAA--------TACATAAGTGGAACT 3831
                           vi  -         v   i      --------  v    i v i   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_90165280_9   3832 TAATTAAA-CTAAAAACTTCTGCACAGCAAAAGAAA-TAACGAGCAGAGT 3879
                          v  i   -i         i  ii vv    i  v -  v i  - i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGT 692

  chrX_90165280_9   3880 AAAATGACAACCCACAGAGTGGGAGAAAATATTTGCAAACTATGCATCCA 3929
                         i   v             i                    ii  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_90165280_9   3930 GCAAAGGACCAATATCCAGAATGTACAAGGAACTCAAACAAATCAACAAG 3979
                         ii  i    ivi          i  i  i      vv    v    i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_90165280_9   3980 AACAAAACAAATAATCTCATCAAAAAGTAGCCTAAGGGCATGAATAGACA 4029
                           v  i        i iv  i?    i i v v    iiv          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_90165280_9   4030 ATTCCCAAAAGAAGATATACAAGTGGCCAACAAACATATAAAAA-ATTCT 4078
                         v   i v               i       i  i  i  i    -  v  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_90165280_9   4079 CAACATCACTAATTAT 4094
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.20 (22 / 10)  


2217 27.91 6.00 1.27  chrX_90215491_90219317     2470  3336 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90215491_9   2470 TAGAAAAATATCCCGTGCTTATGGATT------------------AAAAT 2501
                          i    i       i  i i       ------------------  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90215491_9   2502 GGCTATATGGCCCAAAGCAATTTACAGATTCAACACTATTCCTATCAAAC 2551
                            v   ivv      vii  i            i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90215491_9   2552 TACAAAAGTCATTCATCACAGAA-TTAGGAAAAGCT-ATTCAAAAACTCG 2599
                          v v ivvv v  iv ii     -  --  v     -  i v    i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_90215491_9   2600 TATGGAACCAAAAAAAGAGCCTGAATAAACAAAGCAATCCTAAGCAA-AA 2648
                                viiv  ii-  v  v     iv    i     i i iv  -  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_90215491_9   2649 GAACGAAGCTAGAGGGATCATATTACCTGACTTCAAACCATAGTATATAA 2698
                             i   i i    iv   i i v  ii i      v v  v  i -- 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA--A 245

  chrX_90215491_9   2699 GGCTATAGTAGCCAAAATAGCCTGGTACTGGTATAAAAACAGAAACATAG 2748
                         i    i    ii   i i  iv         i    ii i   v i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_90215491_9   2749 ACAAATGGAACAGAATATAAAACCCAGACATAAAGCCTTACACACGCAAC 2798
                          iv       i     vv i ii     v     v  v    iviiiiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_90215491_9   2799 CATTTGATATTTGACAAG----CCAAGAAACACAAGCAATGGGAAAAGGA 2844
                           v     v  i      ----      -- -  vv       i    i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGA--C-CATTCAATGGGGAAAGAA 392

  chrX_90215491_9   2845 CTCCCTATTCAATAAATGGTGTTGTGACAAGTGGCTA------TACAGAA 2888
                         ivvi  v     i        i  v     v   v  ------ i  i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_90215491_9   2889 GAATGAAACTGAACCCTTACCTTTTACAATATACAAAAATTAACTCAGGT 2938
                                ii  i    i     ivi  v                   iiv
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_90215491_9   2939 AGGATTAAAGATTCAAATGAAAAATATCAAAATATAAAAAT--TCAAAAA 2986
                         v    i ?   iii     v  i vv v   v       v -- vi  i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_90215491_9   2987 AAACCTAGG---AAATGCCCTTCTCAATATCAGCCTCGGCAAAGAATTTT 3033
                             v    ---    ---    vii iv ii vi v     v iv  i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_90215491_9   3034 TGCCTATGTCTTCAAAAG---AAACTACAGCAAAAAATATTGACAAGTGG 3080
                          ivv    v vi      ---  i v   iv i    v  v  i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_90215491_9   3081 GACCTAATTAAGCTAAATAGCTTCTGCACAGCAAAATAAATTATCAACAA 3130
                            i v  i  iv v  v i   i  ii vv    iv v i      v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_90215491_9   3131 AGCAAACAGCCAACCTGCAGAATAGAAGAAAATATTCACAAACTATGCAT 3180
                           ii  v  v     ii      i i          ii    ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_90215491_9   3181 CTGACGAAAGACTAATATCAAGAATCTATACAAAATTTAAACAAATTAAC 3230
                             ii ii    vi    v     v    v i  i ivv    v i  i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_90215491_9   3231 AAGCAAAAAA-----AACACCATT---AAATGGGCAAAGGATATGAACAG 3272
                           vv    i -----   v v   ---               v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_90215491_9   3273 ACATTTCTC-AAAAAAGACATG--AACAGCCAACAAACATATAAAAA--T 3317
                                  -   i    i  i--  ii     i  i  i  i    -- 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_90215491_9   3318 GTTCCACATAACTGATCAT 3336
                          i  v    v ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.15 (63 / 20)  


 534 20.75 0.00 0.00  chrX_90230302_90234682.rev     1583  1688 (2693)    L1M4_orf2#LINE/L1        1   106 (802)  

  chrX_90230302_9   1583 TGGAAAGATATTCCATGTTCATGGATTGGAAGTATCAATATGTTTAAAAT 1632
                                    i                    vv i     vv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90230302_9   1633 GCCTACACTATCAAAAGCAATCTGCAGATTCAATGCAGTCTCTATTAAAA 1682
                          v v i   vi v   vii    i         i   i  i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90230302_9   1683 TACCAG 1688
                          v    
  L1M4_orf2#LINE/    101 TCCCAG 106

Transitions / transversions = 1.20 (12 / 10)
Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.00 (0 / 0)  

 252 26.16 1.27 14.35  chrX_90230302_90234682.rev     2015  2251 (2130)    L1M4_orf2#LINE/L1       99   304 (604)  

  chrX_90230302_9   2015 AATACCAATGACATTTTTCACAGAAACAGGGAAAAATATCCTAAAATTCA 2064
                            v   iivi v     ii      iv iv  ivvv             
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_90230302_9   2065 CA-AACAATGAAAAAAGACCCAGAAGAGCCAAAGGTATCCTGAGCAAAAA 2113
                         i -iiv    v  ii-         v       ivv   i   ---    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGA---AAAA 194

  chrX_90230302_9   2114 GGAAAAAAACAAAACAAACAAACAAACAAATAAAAAACAAACAGAGGAAT 2163
                          ---  i      ii--------------------------ii     v 
  L1M4_orf2#LINE/    195 G---AAGAACAAAGT--------------------------TGGAGGACT 215

  chrX_90230302_9   2164 CACGTAACTGAACTTCAAATTATACTACGGGG-TGTAGTAAACAA-ATGG 2211
                            iivv iv  i      viv      iii - ii     v   - ii 
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_90230302_9   2212 CATGGGACTGGAATAAAAAATACACACATAGATGAAGGGA 2251
                         ii   v     v    ii -  v   i      v  v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGA-TAGACATATAGATCAATGGA 304

Transitions / transversions = 1.48 (37 / 25)
Gap_init rate = 0.04 (8 / 206), avg. gap size = 4.62 (37 / 8)  

1841 28.27 1.13 0.81  chrX_90230302_90234682.rev     3272  3890 (491)    L1M4_orf2#LINE/L1      288   908 (0)  

  chrX_90230302_9   3272 ACACATAGATCTGTAGAAAAGAATAGAGAACCCATAAACAAATCCACAGA 3321
                            i       vi i   v     v    ii   v   i   i   i v 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_90230302_9   3322 CCTACAGTGAACTAATTTTTGACAAAGGCACTAAGAATATTCATTGGGGA 3371
                         ii  ii  v  i i     i     i  ii i    vi     v      
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_90230302_9   3372 GAAGACAATATTTTCAATACATGTTGCTGAGAAAACTGGGTATCCATATG 3421
                         i ii i i v       i v   v     i  v      i  ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_90230302_9   3422 CAGAAAAATAAAACTTGACCCCCATCTCTCACCTTA---AAAAATCAAAG 3468
                           i  i   i  ii v      i i   v    v  ---      i  vv
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_90230302_9   3469 GAAAATGTATTAAAGACATAAATCTAAGACCCCAAATTATGAAACTACTA 3518
                         v      v  i ?    v     v     v iv   i   i     vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_90230302_9   3519 AAATTATACACATTGGGAAAACTCTCCAAAACATTGATTTGGGCAAAAAT 3568
                         i  --iv v    v  ?iv  v   i ivi  v   iv  i     vii 
  L1M4_orf2#LINE/    538 GAA--GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_90230302_9   3569 GTCTTGAGCAATACCCCACAAGCACAGGCGAACAAAACAAA-TATGGTTA 3617
                         v    iiii vv  v   v       i  -       v   -v  i v  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATA 634

  chrX_90230302_9   3618 AATGAGATCACATCAA-GTTAAAATGCTTCTGCAGGGCAAAGGAAACCAT 3666
                            vi  iiv      -i      -i   i  iivvv       v  i  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_90230302_9   3667 TAACAGAGTGATGAAAAAACCCACAGAATGAGAGAAAACATCTGCAAACT 3716
                         i  v i     vi i v             i       i  i      ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_90230302_9   3717 ACACTTCTGACA--GGATTAATAACAAGAATATTTAAGGAGGTCAAAAAA 3764
                          i iv     i --   i vi  v v       v   i  iv  vv v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_90230302_9   3765 TTACATAGGAAGAGATCTAACAATCCAATATAAAAATGGGCAAAATATTT 3814
                         i vv   iv  i iiv v  i  i     v?             iv    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_90230302_9   3815 GGATATACATTTCTCAAAAGAAGACATCAAAATGGCAAACAGGCGTATGA 3864
                          i   v         v        i  vv       v  i i  ii    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_90230302_9   3865 AAAAGGTGCTTACCATCATTTATCAT 3890
                            - i    i v     ????????
  L1M4_orf2#LINE/    884 AAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (99 / 72)
Gap_init rate = 0.01 (8 / 621), avg. gap size = 1.50 (12 / 8)  


1615 27.95 4.21 2.95  chrX_90248795_90256503     3333  4044 (3665)    L1M4_orf2#LINE/L1       13   733 (175)  

  chrX_90248795_9   3333 CTATATTCATGGAA-GAAATACTCAATATAGTTAAGGTGTTGA-ACCCTC 3380
                          i  i        v- i  v   i     v      i  vii -  i i 
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_90248795_9   3381 CGAAATT-ATCTACAAATTTACTAAAATC----TCACAATTCTAGTGAAA 3425
                          -     -       i   i viiv    ----   v   i i  iv---
  L1M4_orf2#LINE/     63 C-AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT--- 108

  chrX_90248795_9   3426 GTTATTTTT--AGATATAGAGAAACTGATTTTAAAACTTAGATGGATAGG 3473
                          iiv     --   v  v  v  i     ii     i i v     v v 
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_90248795_9   3474 CAAAGGAACTAGAATAGAATTGGAAAGAAAAGCAATTTGGAAAAACTAGT 3523
                            i   v i       --ii-------   i    i v      vv  v
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAG--CC-------AAAACAATCTTGAAAAAGAAGA 199

  chrX_90248795_9   3524 AAAAAGTTGGAAGACTCATAGTACCTGATTT-AAGACATACCATTAAGGT 3572
                          v         i      i v v  ii    -  i  v   i iv   v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_90248795_9   3573 ACAGTAATCAAGATTGTGTTGT-TTTGTAAAAAGATAGAAATGTGGATCA 3621
                                      iv    v  -i v i v  i      v  i i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_90248795_9   3622 ATAAGACAGGACAGAGAGTCAAGTAATAGGCCCACAAAAATATACTCGAT 3671
                           iii i  i iv       v  v    ii    i v vv   iv  i  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_90248795_9   3672 TGGGTTT-GACAAAGATGCAAAGGCAGCTTGATAAAACAAGAGAATTCTT 3720
                           iv   -     i i   v   i vii ii  iiiiv    iv v    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_90248795_9   3721 TGAAAACAAT--TTCTAGAATAATTGGACATCCATATG---AAGAATATA 3765
                          vv  vv   -- v  i i i  i    i ?   i   ---      iv 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_90248795_9   3766 TTTAGACACATACCTTATACCTCATA--AAAAGTATCTAAAAATTGATTG 3813
                         v  i   v v     i i   vi   --    v  v  v     v   ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_90248795_9   3814 CAGACTTAAA-ATCA----TAAAACTGTAAAAGTCATAGGATAAAACATA 3858
                         ?    i    -i v ----       i     v  v   i v        
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_90248795_9   3859 GAGAATATATTCTTATA--CTTGAGATAGAAAAATAGTT-CTTAGATGTG 3905
                          - ?i  v  ii ii i--    i v   iv  - i   -       i  
  L1M4_orf2#LINE/    550 G-GNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATG 597

  chrX_90248795_9   3906 ACATAAACAAATACAATTTATAAAACTAAACAATGGATGATTTGGACCTC 3955
                            iv  -  ii    viv i    v-   v   i   i v      i  
  L1M4_orf2#LINE/    598 ACACCAA-AAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTC 645

  chrX_90248795_9   3956 ATCAAAATGTAAAAGTTTTTCT-CTGCAAAAGACATTGTTAAGAGAATTA 4004
                                 -     ii    v -  v    i    i i i    i i v 
  L1M4_orf2#LINE/    646 ATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_90248795_9   4005 CATGCACCATCCCAAGACTGAACCAGGAAGAACTTG--AATC 4044
                         v v -  v i  vv   v  ii--  i  iv i   --    
  L1M4_orf2#LINE/    695 AAAG-ACAACCCACAGAATGGG--AGAAAATATTTGCAAATC 733

Transitions / transversions = 1.42 (115 / 81)
Gap_init rate = 0.04 (28 / 721), avg. gap size = 1.82 (51 / 28)  

2869 26.66 1.99 1.55  chrX_90248795_90256503     5429  6332 (1377)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90248795_9   5429 TGAAAACGTATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5478
                           i   vi   i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90248795_9   5479 GGCCATGCTGCCCAAAGTAATTTATAGATTCAATGCTATTCC-ACTAAAT 5527
                            v  i  v      v i  i  i        i  v  i  - ii   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90248795_9   5528 TACCATTGACATTCTTCATAGAATTAGAAAAAAAAAAACT-ATTTTGAAA 5576
                          v   vivi v  i  iii    v v  v  i------  -  ii i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG------CTGATCCTAAAA 144

  chrX_90248795_9   5577 TGTATATGGAACCA-AAAAGAGCCTGAATAGCCAAGACAATCCTCAGCAA 5625
                          vi        vii-  ii  v  v          i      i v iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_90248795_9   5626 AAAGAACAAATCTGGAGGTATCACACTACCTGATTTCAAAATATACTACA 5675
                         i         vi      vv       v  ii         iv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_90248795_9   5676 GGGACACAGTAAGAAAAACAGCATGGTACTGGCACAAAAGCAAGCACACA 5725
                         ii vi       vv  i    ii           i  iiii i--   i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG--ACATA 292

  chrX_90248795_9   5726 TACACCAATGGAACAGAGTAGAGAACTCAGAAATAAGACCACACACCCAC 5775
                           v i        i   i v    iii         iv   i   iii i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_90248795_9   5776 ACTCATCTGATTTTCGATAAATATGAAAAAATCAAGAAATGGGGAAAGGA 5825
                         iv   vi          i  ivi  vv  i i  vvv           i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_90248795_9   5826 TTCCCTATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGCAGAA 5875
                          vvi  v  i  i     i        v      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_90248795_9   5876 AATTGAAACTGGACCCCTTCTTTACACTGTATTCAAAAATCAACTCAAGA 5925
                         i v    ii         v i i    ii   v       i       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_90248795_9   5926 TGGATTAAAGACTTAAATGTAAAACCCTAAACTATA---------GAAGA 5966
                              i ?    i         i v iv        ---------     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_90248795_9   5967 AAATGTAGGCA-ATACCATTCAGGACATAGGCACAGGCAAAGATTTCAT- 6014
                            ii    ?i- v i -   iv   v v  vvi      v i    v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_90248795_9   6015 GATGAAAACACCAAAAGCAATTGCAGCAAAAGCAAAAATTGACAAATGGG 6064
                            - vi            vvv   i      v      v  i    v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_90248795_9   6065 ATCTAGTTAAACTAAAGAGCTTCTGCAGAACAAAAGAAACTATCATCAGA 6114
                          ii vi i   v v  i i   i  iivvv    i  v       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_90248795_9   6115 GTGAACAGACAACCTACAGAAAGGGAGAAATTTTTTGCAATCTATCCATT 6164
                              v        i      v        v v       vii  vi  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_90248795_9   6165 TGACAAAAGTCTAACATTCAGAATCTACAAGGAACTTAAGCACATTTACT 6214
                            i  ii v  vii  i      v  i  i     ivvi  - i i v 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCAAT 789

  chrX_90248795_9   6215 AG-AGAAAAACAAAATTAAAACACATTAAAAAGTGGACACAGGACTTGAA 6263
                          i- i   i     --   vv  -   ?    i   i  v    i     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAA--TAACCCA-ATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_90248795_9   6264 CAGACACTTCTCAAAAGAAGACATTCATGTATCCAACAA---CATGAAAA 6310
                         i     i     v        i  v  vi iv    i  ---        
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_90248795_9   6311 AAAGCTCAACATCACTGATCAT 6332
                         i v           ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.13 (32 / 15)  

 430 27.40 4.11 1.83  chrX_90248795_90256503     7003  7221 (488)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_90248795_9   7003 AAGACAATGAAAAAAGCAAAGTACCGAATTAAAAAAAAATG---GAAAAT 7049
                             v i      i -   vvi  v    -iii i     i--- v    
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGA-CAACCCACAGAAT-GGGAGAAAATATTTGCAAAT 732

  chrX_90248795_9   7050 CACATAGCCTTCAAAAAACTT---TTCAGAATATTTTCAAAACTCT--CA 7094
                           i   v ivvi  iii    --- i        v vv i      --  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_90248795_9   7095 ATTCTCAGCAATAACAAAACCAGTGAGTCAATTTAAACATGGGCAAAATA 7144
                          --    ii     v  i  v i i vi     ?   v         iv 
  L1M4_orf2#LINE/    783 A--CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_90248795_9   7145 TATGAGCAGACGCTTAACCAAAAATAA-ATACACATGGCAAATAAATACA 7193
                          v   ii    ii  vv     i vi -     v     v     ii   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_90248795_9   7194 TAAAAAGATACACAATGGCATTAGATTA 7221
                          i       i v   iiv  ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (35 / 24)
Gap_init rate = 0.03 (7 / 224), avg. gap size = 1.86 (13 / 7)  


1983 28.10 3.76 3.65  chrX_90280780_90283169      994  1897 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_90280780_9    994 AAAGATATTTCCCTCATTCGTAAATTAGAAGGTGCAATATTGTTAACATG 1043
                                 --   vii   i ii   i    iivi           v   
  L1M4_orf2#LINE/      4 AAAGATAT--CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_90280780_9   1044 TCCATCCTTTCTCATTTGCTATATGCACTTAATGATATTCCTATCATAAT 1093
                         v v  v  ii iv v   v v  iiv i i  i vv  i       v   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_90280780_9   1094 CCCAGCAAGCTTTTATTCAGATATC-AGAAGCTGATTCTAAAATATATAT 1142
                               viv     v v    v  i- v        i       vi    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_90280780_9   1143 GGCAAAACAAAGAAACTACAATAGCTAAAACAATTCAGAAAAAGAAGAAA 1192
                           v  vi   i i v i v      i        iiv            v
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_90280780_9   1193 AAAGCTAAAGGGCTCCCACTGTCCAATTTCAGGACTTATTATAAAACTTT 1242
                             i ii   i   v    vi         ii     i  i   i  vi
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_90280780_9   1243 AATAATTAAAGC--TGTGGTATTGGAAAAAAAGATA-ACATATACATCAA 1289
                          i    i  ii --       i   v v  i-    -       v     
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATATAGATCAA 300

  chrX_90280780_9   1290 CAGAATAGAAGAGACAGCTGAGAAATAGGCCTATAAGAATACAGTTTATT 1339
                         ii        vv  v  iiv       ii  i   vivv  ii  iv   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_90280780_9   1340 GCTTCTTTTTACAGAGATTC----ACTAATTTAATAAAGAAAGGAT---T 1382
                          v  --  iv   ii i v ----  i -  i   iii     i  ---i
  L1M4_orf2#LINE/    351 GATT--TTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTC 397

  chrX_90280780_9   1383 TTTTCAACAAATATTGCAGTATCAACTGTAAATCCATATG-AAATTAATA 1431
                                     iv   v viv      v v ?   i   -   vv   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_90280780_9   1432 AACTACAGGCATATACCTGATACATTATCCAAAAATTAACTGAAAATATG 1481
                           v -ii i viv     v i  vv   v            v     ivi
  L1M4_orf2#LINE/    448 AAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_90280780_9   1482 TCATTTACCATAATGTATAA--CAAAACTATAAAACTTTTAAAAGGAAAC 1529
                            ?vv   vv      vi --i              i   i   i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_90280780_9   1530 AT--GAGACAATCTATATAATCTTTAGTTTAACAGTAAGA---CTTAACT 1574
                           -- ? vv     vii i i   vi   vii  i -- i---    iv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT--GGTTTCTTAGAT 594

  chrX_90280780_9   1575 AAAAAATACAAAGCGTGATCTACT---TTAAAAAT-GTTAAATTAGACTT 1620
                          vi v ivv     iii v v  v---vv      - v      i     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_90280780_9   1621 TATCAATATTAGAATACTTT-GTTCTGTAAAAGACACTGTAAGGAGAATG 1669
                         i     v    i  -     -  v  vi   i      i v i  i i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_90280780_9   1670 AAAAGGTAACACACACACTAAGAGAAAATATTTGCAAGTTAAAATCACAT 1719
                              ii   v    v v ii                ------    i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA------ATCATAT 737

  chrX_90280780_9   1720 CTCCAATAAAAT-CTTACATGTACAATATATAAATAACACTCAAAAGTCA 1768
                         v  ii    iiv-   ii  vi v          v   v  i v  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_90280780_9   1769 ACAATAAGGAAAAAAGCAACAAAATTAATAAATTTTAATAAATTTAATAA 1818
                          i     ii i v  ii   vv    ? v    v--iii   --------
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATG--GGCAAA-------- 827

  chrX_90280780_9   1819 TTTTTTAAGTCTAAAAAGACACTTCCCCAAAATAGATATGTGAA------ 1862
                         ------iii i i  v     i   i     iv      iii  ------
  L1M4_orf2#LINE/    828 ------GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_90280780_9   1863 ---ACCATGTGAAAAAAATACTCAACATCATTAATTAT 1897
                         --- v  ii      i - i          ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (145 / 105)
Gap_init rate = 0.03 (25 / 905), avg. gap size = 2.68 (67 / 25)  


1527 28.57 1.96 1.79  chrX_90299805_90304546.rev     2919  3478 (1264)    L1M4_orf2#LINE/L1        1   561 (347)  

  chrX_90299805_9   2919 TGGAAACACATCCCATGCCCCTGGAAGGGTAGAATCAATAGTGTGAAAAT 2968
                               v i        ii v    vv  v   v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90299805_9   2969 AAGCATACTGCCAAAAGCAATCTAAAAATTTAATGAAATTTCCATCAAAA 3018
                         iivv     v  v   vii     v i   i  i v   ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90299805_9   3019 CACCATCATCATTATTCACAGAACTAGAAAAA--AATACTAAAATTAATA 3066
                         iv   v vv v  v  ii     v v  v  i--i  v        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_90299805_9   3067 TGGAAACAAAAAAGAGTTCCCA---TATCCAAAGCAAGACTAAGCACACA 3113
                               iiv  ii  ---    ---  v     i   vvi i iv viv 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_90299805_9   3114 CACACAAAAAATCTGGAGGCATCGCATTACCCAACTTCAAACTACACTAT 3163
                         v -     i---i      vv  i  i v     i      vivi    i
  L1M4_orf2#LINE/    198 GA-ACAAAG---TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_90299805_9   3164 AAGGCTATAGTTACCAAAACAGCATGATACTGATATAAAAATAGGCACAT 3213
                           i    i   v i   i    ii  i     ii    ii    i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_90299805_9   3214 GAAT-GATATAACAGAATAGAGAACTCAGAAATAAAGCCAAATACTTACA 3262
                         ii  -i  iv  i     v    iii          v   v i i   ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_90299805_9   3263 GCCAACTGATCTTTGACAAAG-TACACAAAAACATAAAGTGGGGAAAGGA 3311
                          i   i    i  i     i - i -   i v   vv i         i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAA 392

  chrX_90299805_9   3312 CACCCTATTCAACACATAGTGCTGGAATAATTGCCAAGCCACATACAGAA 3361
                         i vi  v       v  i       i i  i  vvv ?      i  i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_90299805_9   3362 GAGTAAAACTAGATCCTCATCTTTCACTTTACACGAAAATCAACTCAAGA 3411
                           i i  ii i  i  ii i  iv   iv  i  i     i       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_90299805_9   3412 TGGATCAAAGACTTAAATCCAAGA-CTAGAAACCATATAAATTCT-AGAA 3459
                                ?    i     vi    -   -    i   -   i   -    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATA-AAACTCTTAGAA 540

  chrX_90299805_9   3460 GATAACATCTGA--AAATCTT 3478
                           v     vv ?--       
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTT 561

Transitions / transversions = 1.66 (98 / 59)
Gap_init rate = 0.02 (13 / 561), avg. gap size = 1.62 (21 / 13)  

 939 22.60 1.04 7.79  chrX_90299805_90304546.rev     3867  4251 (491)    L1M4_orf2#LINE/L1      550   908 (0)  

  chrX_90299805_9   3867 GGAAAAACTTTTCTAGACATTGGCTTAGGCA--GAGTTCATGACCAAGAA 3914
                           ?iv  v i   vv   v    v       -- iv   v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_90299805_9   3915 CCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGACTTAATTA 3964
                         v         v v         iv   i   i   i  v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_90299805_9   3965 AA-CTAAAAACTTCTGCATTGCAAAATAGATAATCAGTAGGATAAAAGGA 4013
                           -i         i  iii v    iv v iv    --------------
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA-------------- 685

  chrX_90299805_9   4014 TTAAAGAATAATCAGTAGGATAAATGGACAACCCACGGAATGGGAGAAAT 4063
                         ----    -----   --  -   --          i            v
  L1M4_orf2#LINE/    686 ----AGAA-----AGT--GA-AAA--GACAACCCACAGAATGGGAGAAAA 721

  chrX_90299805_9   4064 TATTCACAAAGCATGCCTCCAA-AAAGTACTAGTATCCAGAATCTATAAG 4112
                             ii    v   iiv  ii -  i v   v           v     i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_90299805_9   4113 GAACTCAAACAAATCAGCAAGAACCAAAAGAAATAATCCCATCAGAAAGT 4162
                               vv    v   ii  v  v-  i v      i  v  i?i   i 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAA-AAGACAAATAACCCAATTWAAAAAT 820

  chrX_90299805_9   4163 GGGCTAAAAACATGAATAAACAACTCTCAAAAGAAGATATATAAATGACC 4212
                             v  ii iv      i   vi    v            i     i  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_90299805_9   4213 AGCAAACATATGAAAAAAATGCTAAACATCACTAATGTT 4251
                          ii  i  i       i -    v       ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (46 / 39)
Gap_init rate = 0.03 (10 / 359), avg. gap size = 3.40 (34 / 10)  


2931 25.66 1.66 1.44  chrX_90355889_90362866      492  1395 (5583)  C L1M4_orf2#LINE/L1   (0)   908     3  

C chrX_90355889_9   1395 GAAAAAAATTCCATGCTCATGGATAAGAAGAATCAGTATAAGTGAAAATG 1346
                             i v  i     i        vi     v i i   v-  v  i   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-GTTAAGATG 51

C chrX_90355889_9   1345 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGCA 1296
                           v     v      v i  i  i        i  v     i     -- 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA--A 99

C chrX_90355889_9   1295 A---CAACTGACTTTCTTCACA-AAATTAAAAAAAAAAAAAACTAAGTTT 1250
                          ---  i   v    i  -i  -     i v  ivvi vv--    iv  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATC--CTAAAATT 146

C chrX_90355889_9   1249 CATTTGGAACCAAAAAGAGCCCATA-TAGCCAAGACAATCCTAAGCAAAA 1201
                            v     viiv  i ii    v -       i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

C chrX_90355889_9   1200 AGAACAAAACTGGAGGCATCATGCTACCTGACTTCAAACTGTACTACAAG 1151
                                 ii      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

C chrX_90355889_9   1150 GCTACAGTAACCAAAACAGCATGGTACTGGTGCCACAACAGATATATAGA 1101
                                   i   i    ii         iiiv vi i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chrX_90355889_9   1100 CCAATGGAACAGAACAGAGGCCTCAGAGATAATGCCACATATCTACAACC 1051
                         i        i    iv   ivii    i    vv   i i  i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

C chrX_90355889_9   1050 ATCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAATGATTCC 1001
                          vi    i  i     ivv  v   i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_90355889_9   1000 CTATGTAATAAGTGGTGTTGGAA-AACTGGCTAGCCATATGCAGAAAACT 952
                           v vi  i  i     i   i -      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_90355889_9    951 GAAACTGGACCCCTACCTTACACCTTATACAAAAATTCACTCAAGATGGA 902
                            ii             i     v            v      i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_90355889_9    901 TGAAAGACTTAAACGTAAGATCTAAAACCATAAAAACCCTAGAAGAAAAC 852
                          v ?    i    i      v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_90355889_9    851 CTCGG--TAATACCATTCAAGACAT--AGTCATGGGCAAAGACTTC--AG 808
                         v v  --   - i -   iv   v --i  i --     v ii   --  
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAG 592

C chrX_90355889_9    807 GACTAAAACACCGAAATCAATGGCAACAAAAGCCAAAATTGACAAATGGG 758
                         i--  vi     i   v  vvi          vv     v  i    v  
  L1M4_orf2#LINE/    593 A--TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

C chrX_90355889_9    757 ATCTAA-CTAAATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAG 709
                          ii v - v        i -   i  ii vv    i  v       vv i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

C chrX_90355889_9    708 AGTGAACAGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTATCCAC 659
                               v  i     i              v  v       vii  vi i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

C chrX_90355889_9    658 CTGACAAAGGGCTAATATCCAGAAGCTACAAGGAACTTAAACAAATCTAC 609
                             i  i  i  vi         vv  i  i     ivv    v  v i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

C chrX_90355889_9    608 AAGAAGAAAA-AAA-AATCCAATCAAAAAGTGGGCAAAGGATATGAACAG 561
                           v  i  i -   -  i     i?    i            v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

C chrX_90355889_9    560 ACAGTTCTCAAAAGAAGACATTTTTGCAGCCAACAAACATATGAAAAAAA 511
                            v     v        i  vivviii     i  i  i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

C chrX_90355889_9    510 ACCCATCACCACTGGTCTT 492
                         i i  v  i  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (137 / 92)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 1.47 (28 / 19)  

1797 24.50 9.77 0.50  chrX_90355889_90362866     5882  6485 (493)    L1M4_orf2#LINE/L1      249   908 (0)  

  chrX_90355889_9   5882 TACACCAAACGAAACAGCTTAGTAATGGCATAAAGAAAGACATATACACC 5931
                             vi  v i i    iv i   v        i  v         v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_90355889_9   5932 AATTGAATAAAACTGAGAGCTTAGAAATACACTTCTGTGTATATGG-AAA 5980
                            v     i  i      iii       v  iiv iii v     -v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_90355889_9   5981 TTG-TTTTCAACAAGTCTATCAAAAATATTCAAGCATGAAAATACCATTT 6029
                            -     i     vv ii   i vi      vviv    iv ivi i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_90355889_9   6030 TTTCAATAATTAGTATTGGGAAACCTACATATCCA-----AAAAAAGTGA 6074
                               i  v i  ii     v v  iv   ?   -----    i i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_90355889_9   6075 AGTTAAATTATTATTTTTTGCTAAGTACAAAAATTAATTCAAAAAGAATC 6124
                             ii iivi  ii ivii i vi            i      v i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_90355889_9   6125 AAAGTCCTAA-CATAGAAGCCAACATTCTAAAATATTT-GAAATAATCAT 6172
                          ?  v     -ii  ii   i  v i v     ivi  -   iv  v   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_90355889_9   6173 AGGGTAAAAGCTTCATGATATTGGATTTGGCAACA-TTTTTT-GACATAA 6220
                            ?vv   v    i   iv    i  v     ii-   i  -  i  i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_90355889_9   6221 CAC-AGAAACAAAGGCAACAATA-AAAGAATAGATAAGTTGGAATTCTTC 6268
                            - i  i  v i       v -   i         i     v   v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_90355889_9   6269 AAAATTAAAAACTTCTGTGC---------------------AATAAAAAT 6297
                                       i     --------------------- i i    v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_90355889_9   6298 ATGAT-------------GAAA---TTTGCAAATCATATATCTGATAATG 6331
                          ii i-------------    ---                       v 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_90355889_9   6332 TATTAACATCCAGACTATATAAAAA----TTACCCACTCAATGA-----A 6372
                         v i vii       v        i ----    v-       i ----- 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACA-ACTCAATAATAAAAA 797

  chrX_90355889_9   6373 AACATAACAACTAAATTAAAAAACTGTGCAAAGAACTTACATAGATATTT 6422
                         i   -  i   iv    ?     -  v      i i  iv     i    
  L1M4_orf2#LINE/    798 GACA-AATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTT 845

  chrX_90355889_9   6423 CTCTAAAGATAATATACAAATAGCCAATAAGCACACGAAAAGATGCTCAA 6472
                            i     vi          i             i              
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_90355889_9   6473 CATCATTAACCAT 6485
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (92 / 52)
Gap_init rate = 0.03 (17 / 660), avg. gap size = 3.65 (62 / 17)  


3008 26.34 2.12 0.78  chrX_90381856_90385611     2368  3263 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90381856_9   2368 TGGAAAAACATTCCATGCTCATGGATAGGAAGA---AAC---GTGAAAAT 2411
                               i i  i     i        v      ---  i---  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90381856_9   2412 GGCCATACTGCCCCAAAT-AATTTATAGATTCAAAGCCATCCCCATCAAG 2460
                            v     -        -i  i  i        v  v     i     i
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_90381856_9   2461 CTATGATTGACTTTCTTCTCAGAATTAGAAAAACT-ACTTTAAATTTCAT 2509
                         v viv vivi i  i  iv     v v  v  i  - iii    v     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_90381856_9   2510 ATGGAACCAAAAAAGAGTCCGTATAGCCAAGACAATCCTAAGCAAAAAGA 2559
                               viiv  ii  vi v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_90381856_9   2560 GCAAAGCTGGAGGCATCATGCTACCTGACTTCAAACC--ACATACAAGGC 2607
                         i     i      vv   ii  v  ii i      v --  -     i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC-TACAAAGC 248

  chrX_90381856_9   2608 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATGTAGACC 2657
                                 i   i    ii         i iv ii i   i  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_90381856_9   2658 AATGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACAACCAT 2707
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_90381856_9   2708 CTGATATTTGACAACCCTGACAAAAGCAAGCAATGGGGAAAGGATTTCCT 2757
                         i    v  i     vvv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_90381856_9   2758 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 2807
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_90381856_9   2808 AACTGGACCATTTCCTTACACCTTATAGAAAAATTAACTCAAGATGGATT 2857
                          ii      vi v   i     v    v              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_90381856_9   2858 AAAGACTTAAATGTAAGACCTAAAACCATAAAAAACCTAGAAGAAAACCT 2907
                          ?    i           v       i      vv i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_90381856_9   2908 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGGCTTCATAACTAAA 2956
                            ?i- v i -   iv   v v  vv i     v  i   v  iv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_90381856_9   2957 ACACTGAAAGAAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 3006
                             ii    v vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_90381856_9   3007 TAAACTAAAGCGCTTCTTCACAGCAAAAGACACTATCATCGTAGTGAACA 3056
                         i   v v  ivi   i vii vv    i          vviv      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_90381856_9   3057 GACAACCTACAGAATGGGACAAA-TGTTTTTCAATGTATCCATCCGACAA 3105
                                i           v   - i   viv   -i  vi   i  i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAAT-CATATATCTGATAA 746

  chrX_90381856_9   3106 AGGGCTAATATCCAGAAGCTACAAGGAACTTAAACAAATTTCCGAGAATA 3155
                         i  i  vi         vv  i  i     ivv    v --- i v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATA 793

  chrX_90381856_9   3156 AAA-------CAACCCCATCAAAAAGTGTGTGAAGGATATGAACAGACAG 3198
                            -------i     v  i?    i  v ii      v    i     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_90381856_9   3199 TTCTCAAAAGAAGACTTTTAGGTGGCCAACAAACATATGAAAAAAAGCTC 3248
                              v        iv vi ii       i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_90381856_9   3249 ATCATCACAGGTCAT 3263
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (131 / 101)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.00 (26 / 13)  


1956 20.70 3.20 17.78  chrX_90415648_90417267       65  1127 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90415648_9     65 TGGAGAGACA------GTCCATGAATAGAAAGACTCAATATTGTCAAGTT 108
                             i   i ------  i    i  v i      i        i   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90415648_9    109 GTCACTTCTTGCCAACTTTGTCTACAGATTCAACGCAATCTCAGACAAAT 158
                          v  v v  iv    v  vi                    i viv    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90415648_9    159 TATTAGGAAGTTATTTCACTTATTTTGTAGATATTGATAAATTGATTCTA 208
                          vii  ---------iii i v     i   v     i  ii    i   
  L1M4_orf2#LINE/    101 TCCCAG---------CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_90415648_9    209 AGGTTTGTGTGTAGAGGCAAATGATATAGAATAGCCAATAAAATACTGAA 258
                          ii  ii i  v i v    iv  ivi           v v   vi    
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_90415648_9    259 ---GAAGAACAAATTTGGAGTAGTGACACTAACTGACTTCAAGATTTACT 305
                         ---          v      v v v     vv ii i     i i     
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_90415648_9    306 ATAAAGCAACAATAATCAAGACAACGTGGTATTGGCAAAAGAATAAATGA 355
                          i     v   i           ii      i     v   i   i iiv
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_90415648_9    356 ACAAGTCAATGGAGCAGAATAGTTAGCCCACTAATAAACCTGAATACAGT 405
                          i ii        -------------------------------------
  L1M4_orf2#LINE/    292 ATAGATCAATGGA------------------------------------- 304

  chrX_90415648_9    406 CAACTAATATTTGACAAAGAAGGAAAAATAATAAAATAGACCAAAGATAA 455
                         -----------------------------------     ----------
  L1M4_orf2#LINE/    305 -----------------------------------ATAGA---------- 309

  chrX_90415648_9    456 TGTTTTAAACACATGGTGCTGGAATTATTGAACATCCACATGCAAATTAA 505
                         --------------------------     -------------------
  L1M4_orf2#LINE/    310 --------------------------ATTGA------------------- 314

  chrX_90415648_9    506 GTCAGTGTGGTATTGTTAAAAAAGAGACAGATTAATAAAACAGAATAGAG 555
                         -----------------------------------------------   
  L1M4_orf2#LINE/    315 -----------------------------------------------GAG 317

  chrX_90415648_9    556 CCCAGAAAGAAACCCACAGAA--ATTGTCAACTGATCTTTGACAAAGGAG 603
                         i       v       i v v--  v     i    i  i     i  v 
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_90415648_9    604 AAAAAGCAATGCAATAGAGAAAAGATAGTGTTTTCAATAAATCATGTTGG 653
                         vv  ii v  v    i i    ii     v       i    vi  i   
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_90415648_9    654 ATCAACTGGATATCCACATCCAAAAAAA--AA--TGAACACATAGACACT 699
                         iv          ?      v     i  --  --  i  v v  -- vii
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA--CCTC 465

  chrX_90415648_9    700 ACACCCTTCATAAAAATTAACTCAAAATCAATCACAGACCTAAATTTAAA 749
                              v vi i                 vi    ?          v   i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_90415648_9    750 ACATAAAATTATAAAATTCCCAGAAGACAGCATAGAAGAAAATCCAGATG 799
                          vv     i       i  ii      v i     i? v     ivvi  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_90415648_9    800 TCCTTGCATTTGCAAATA--TTTTTAGATATGA------AGGCATAATCT 841
                         v     vi  v vv   i--  i          ------ i   i  v v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_90415648_9    842 AT----GAAAAAACTGGTAAGTTGAACTTCATAAAAATTTAAAACTTCTG 887
                          i----       iv i   i   i       v      v       i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_90415648_9    888 CTCTGAAAAATATATCACCAAGAGAATGAGAAAACAAATCA--GACTGAG 935
                         iv  vv   iv i ii i     i i   i  i    vi  --  v  i 
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_90415648_9    936 AGAAAATATTTGCAAAAAAAAATATCTGATAAGGAGA--TGTCATCCAAA 983
                                         vv v -            -  --   -     i 
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATA-TATCTGATAAGG-GACTTGT-ATCCAGA 762

  chrX_90415648_9    984 ATATGCAAATAATACTTAAAAC--AACTATTTAAAGA-GAACAACTTGAT 1030
                             ii   v  iv    v   --  iv  vv     -i  i   iii  
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_90415648_9   1031 TTAAAAGATGGGCAAAATATCTGAACAGAGATCTCACTAAAATCGACATA 1080
                          ?    -         iv  i    i   v  i  v i   ivv  i   
  L1M4_orf2#LINE/    813 TWAAAA-ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_90415648_9   1081 CAGATGTCAAATTAGCATATGCCAAGATGTTCAACATTATATGTCAT 1127
                           i   v v   v    i   vv      i       i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (125 / 91)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 10.62 (223 / 21)  


2292 27.00 6.46 1.88  chrX_90429489_90432991.rev     2161  3012 (491)    L1M4_orf2#LINE/L1       18   908 (0)  

  chrX_90429489_9   2161 TTTGTAAATAAGAAGGCTCAATATTGTTAAGAATCTAGTTCTTCCTAACT 2210
                           ii ii  vi    i  i             vvvi i v  i  i  v 
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_90429489_9   2211 TGATCTATAGATTCAATGCATTCCCAATCAAAATCCCAGC---------- 2250
                                i        i   v    v              ----------
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_90429489_9   2251 ------------AAG-TG-TC----------TATGGAATGAGAAAATAAT 2276
                         ------------   -  -  ----------       vviv  iiv vi
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_90429489_9   2277 TAGAATAGCCAACCCAATAATGAA---GAAGAACAAAGTTGAAGTATTGA 2323
                         i           vv    vv    ---              i  v i --
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT-- 215

  chrX_90429489_9   2324 CCATACTT---AACTTGATGACAAACTGTAAAGCTTCGATAATTAAAACA 2370
                         -  i    ---  i  v vi  vv   ii      v ii    i  i   
  L1M4_orf2#LINE/    216 -CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_90429489_9   2371 ATGTCATATTGGAAAAATAGTAGATGAAGAGATTTAAAGGAACAGTATAA 2420
                         i   vi  i   v v  vii    iiv v    i-  v    i  v  vi
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATC-AATGGAATAGAATTG 313

  chrX_90429489_9   2421 GGAACTAAGGAAGCAGACACACAAATCTA--GTCCACTGATAATTCAACA 2468
                         i  iiiv  i  -i i  v  i v  i  --   v i    v-   i   
  L1M4_orf2#LINE/    314 AGAGTCCAGAAA-TAAACCCATACATTTATGGTCAATTGATT-TTCGACA 361

  chrX_90429489_9   2469 AAGGGGCAAAGGCAATTCAGCGGTAGAAATACAGTATTTTCCAGAAACA- 2517
                          i  v  v   i v     ii  vii  iv i   v     v v   ii-
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_90429489_9   2518 T-CTTGAAAAATTGGGCATCCACATGCCAAAAAATGAATCTAGACACCGA 2566
                          -  v i v  i   ii ?        v   i      vi i   v  v 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_90429489_9   2567 TTTTATATCTTTTACAAAAGTTAATTCAAAAAAGATTATAAATCTGAATG 2616
                         ii i i i v v       i    i      vi   i ? i i  i    
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_90429489_9   2617 TAAAATGC-AAAACTATAAAACTTCTAGTAGATTGCA-AGACA-AAACAT 2663
                            i -  -              ii   v   vvi  -  i?i-   iv 
  L1M4_orf2#LINE/    512 TAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_90429489_9   2664 AGGTGACCTTAAATTTGTTGATGACTTTTTAGATAAAATACCAAAAGCAT 2713
                         vv        iii  v vii   ii  i       vi i          i
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_90429489_9   2714 AGTTTTTGAAAGAAAAAATTGATAATTTGGACTTCATTAAAATTAAAAGC 2763
                          ivivvii           v     v           i          i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_90429489_9   2764 CTTTTTATCTGCTAAAGAAATTGTTGAGAGATTACAGAGATAATCCCCAG 2813
                         i   v i-  v v  i  v i i ii   i v iv i   i  i  v   
  L1M4_orf2#LINE/    661 TTTTGTG-CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_90429489_9   2814 ATTTGGAGAAAATGTCCGCAAAACACATAACTGGTAAATGACTTGTATCC 2863
                          v v         i ii     v  i   v   i   iv           
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_90429489_9   2864 AAAATATATGAAGAACTTTTAGAAACTCAACATCAACAACAACAACAAAA 2913
                          i       i       i   ------    -    i  i  v  -i v 
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTA------CAAC-TCAATAATAAAAA-GACA 801

  chrX_90429489_9   2914 AACAACCCAACTGAAAAATAGGCAAAAGATCTAATCAGAC-CCTCACCAA 2962
                           i       i ?      i      i   i i vi    -ii  v    
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_90429489_9   2963 AAA---TACACAGATGACAAATAAGCATATGAA----TGCTCAACATCAC 3005
                          i ---  i   i   i v        i     ----            ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_90429489_9   3006 TTGTCAT 3012
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.66 (141 / 85)
Gap_init rate = 0.03 (24 / 891), avg. gap size = 2.96 (71 / 24)  


3272 25.94 0.78 0.44  chrX_90446179_90450451     2880  3781 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_90446179_9   2880 AAGGATATTCCATGCTTACGGATTGGAAGAATCAATATTGCTAAAATTTC 2929
                           i     i     i i i           v i       i   i  vv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_90446179_9   2930 CCTACTACCCAAAGCAATCTATAGATTCAATGCAATTTCTATAAAAATAT 2979
                         vv    v      vii     i        i     ii    v     vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_90446179_9   2980 TAATGACATTCTTCACAAAAATAGAAAAACT-ATCCTAAAATTCATATGG 3028
                         i iivi v  i  ii  i    v  v  i  -                  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_90446179_9   3029 AACCACAAAAGACCCTGGATAGACAAAACTATCCTAAACAAAAAGAA--A 3076
                           vii   ii     v i    v      v   i i  v  i     -- 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_90446179_9   3077 AACTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAACTTTAG 3126
                          ii       v     i v  ii i      viv       i i  vi  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_90446179_9   3127 TAAACCAAATGGCATGGATCTGGCATAATAACAGACACAAAGACCAGTGG 3176
                            v v i ii ii   vv         vi i     i v   i  i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_90446179_9   3177 AACAGAACAGAGAACCCAGTAGTAAATCCATCCATCTACAGTAAACTCAT 3226
                           i    iv    ii    v i    i    v   i  ii  v  i v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_90446179_9   3227 TTTCAACAAAAGTTTCAAGAACATTCATTGGGAAAAGGACAGTCTCTTCA 3276
                             i    ii  vi     v      v    i    i i     i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_90446179_9   3277 ATAAGTGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAAACTA 3326
                          i  i           v         ?   i     i         ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_90446179_9   3327 GAACCCTATCTCTCACCATATACAAAAAATAAAATCTAAATGAATTTGAG 3376
                           v     i   v               v   -v  v     i  iv?  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAA-CTCAAAATGGATCAWAG 502

  chrX_90446179_9   3377 ACATAAACTTAAGACCTCAAATTATAAAACAACTAAAATAAAATATTAGG 3426
                           v    iv     v  v   i        vvi  i  v    i  vi ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_90446179_9   3427 GAAATTCTCCTGGACATTAGACTGGGCAAAGATTTCTGGAACAATAAC-C 3475
                          v  v   i vv   v  i ii i     v i     vii i-  i  - 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACAC 601

  chrX_90446179_9   3476 CACAGGCACAGGCAACCAAAGCAAAAATAGACAAATGAGGTCACCTC-AA 3524
                           v i     i     v    v         i    vi iiiv v  -  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_90446179_9   3525 GTTAAAGAGCTTCTGCACAGCAAATGAAACAATAAACAAAGTGAAGAGAC 3574
                         i     i -   i  ii vv    v  v  v  v  v        i    
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_90446179_9   3575 AACCCATAGAA--AGAGAAAATATTTGCAAACTACTCATATGACAAGGGA 3622
                               i    --i                 ii ivi  v   i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_90446179_9   3623 CTTATAACCAGAATATATAAGTAGGTGAAACGACTCTATAAGAAAAAAAT 3672
                            i  v             iv iv vvv  i    v    v     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA- 799

  chrX_90446179_9   3673 CTGATAATCTAATTAAAAAATAAATAGACGATCTGAATAGACATACTTCA 3722
                          vi    i i    ?      iiii i v   i           vii  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_90446179_9   3723 AAAGGAGACATATCAATGACAAACAGGTATATGAAAAGGTGCTCAACATC 3772
                             i   i   iv    i v  i i i i        i           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_90446179_9   3773 GTTGATCAT 3781
                         i????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.61 (142 / 88)
Gap_init rate = 0.01 (9 / 905), avg. gap size = 1.22 (11 / 9)  


2473 27.06 1.87 1.98  chrX_90464694_90468391     2307  3215 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90464694_9   2307 TGGAAA-ACATTCCATGCTCATGGATAGGAAGAATGAATATTGTTAAAAT 2355
                               - i  i     i        v      v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90464694_9   2356 GGACATACTGCTCAAAGCAAATTACAGA---AATGTTATTCCTTTCAAGC 2402
                           vv     v i    vii vi      ---  i iv  i   v    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90464694_9   2403 TACCAATGGCATGTTTAACAGAAGCGGAGAAATCTATTTTAAAATTTATA 2452
                          v   iiv  v v   vi     iiv  v  iiiv  ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_90464694_9   2453 TGGAA-TG-AATAGAGCCTGAATAGCCAAAGCAATCTTAAGCCAAAATAA 2500
                              -  -  vi  v  v           i       i ivv i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_90464694_9   2501 CAAACCAGAAGGCATCACATTACCTGACTT-AAAACTATACTACAAGGCT 2549
                             viv i   vv     i v  ii i  -      -        i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_90464694_9   2550 ACGCTAAGCAAAAAACCATGGTACTGGTACAAAAACAGACACTCAGAATA 2599
                           iv   v   i v vii         i i  ii i     ivi   vi 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_90464694_9   2600 ATGGAACAGG-TTAATGAACCCAGAAATAAAGCCACACACCTACAACCAC 2648
                               i  i-  i -  ii           v   i   ii  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGA-GAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_90464694_9   2649 CTAATCTTTGACAAAGTCTCCAAATGCAAGCAATGGGAAAAGGACTGCCT 2698
                         i i  i  i     i viv    ivv  vv       i    i iv i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_90464694_9   2699 ATAAAATAAATGGCACTGGCATATCTGGCTAGTCATATGCAGAAGACTGA 2748
                         v vv  i      ii    v i v    v  ?i  i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_90464694_9   2749 AACTAGACCCCTTCCTTTCCCTAACATTA-ATTCAAAAATCAACTCAAAA 2797
                          ii i       v   i------   ii -  v       i         
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTC------ACACCATATACAAAAATTAACTCAAAA 492

  chrX_90464694_9   2798 TGAATGAAAGAATTAAATGTAAAACCCAAACCTATACAAACCCT-AGAAG 2846
                           i  v ?   vi         i v i   v     -    i  -     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAG 541

  chrX_90464694_9   2847 AAATCGTAGG---AAATACCATTCTGGATATAGGCCTTGGCAAAGATTTC 2893
                            v i    ---    -- -   vv  iv v  vi v     v i    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_90464694_9   2894 ATCACAAA-GACTCCAAAAGCAATTGTAACAAAAACAAAAATTGATCAAT 2942
                         - i v v -   v         vvv i       iv      v   v   
  L1M4_orf2#LINE/    589 -TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_90464694_9   2943 CATTCCTAATTAAACTAAACAGTTTCTGCACTGCAAAATAAACTATCAAT 2992
                         iivv i v  i   v v  v ii  i  ii  v    iv v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_90464694_9   2993 AGAGTAATAAACAGACAAGCTAAAGAATAGGAGAAAATTTTTTCAAACCA 3042
                          i   i -   --     v i v     i         v   v    i  
  L1M4_orf2#LINE/    688 AAAGTGA-AAA--GACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_90464694_9   3043 TGCATCTGACAAAGGTCTACCATCTCAAATCTATAAGGAACCTAAACAAA 3092
                          ii      i  i  v  vvi   ivi   v     i    iivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_90464694_9   3093 TTAACAAGCAAAAAACAAA-AAAAAAGTTATTAAAAATGGGCAAATGACA 3141
                          i  i  vv    i     -  vvv i  ?--             v  iv
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATT 832

  chrX_90464694_9   3142 TGAACAGACACTTCTTAAAAGAAGACATACACGTGGTCCACAAGCATAT- 3190
                             i     i    iv        i     vi   i v i     i  -
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_90464694_9   3191 AAAAGAAG-TAAACATCACTGATTAT 3215
                               v - v       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (134 / 109)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.52 (35 / 23)  


2564 27.02 2.33 2.77  chrX_90470259_90474868     3215  4117 (493)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_90470259_9   3215 ATTCCATGCCCATGGATAGGAAGAATCAAGATCCCTAAAATGGCCATACT 3264
                           i     ii       v      v i  v  ivi   i     v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_90470259_9   3265 GCACAAAGCAATTTATAGACTCAATGCTATTCTTATCAAACTACTAATGA 3314
                         v v    vii  i  i   i    i  v  i i       v v i iivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_90470259_9   3315 TATTCTTCACAAAACTATAAAAAAA--GATTTTAAAATTCATTTGGAATA 3362
                         iv  i  ii  i  --  vi v  i--   ii          v     --
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCATATGGAA-- 155

  chrX_90470259_9   3363 ATAATAATAAAAAAAACAGCCTGAACAGCCAAGGCAATCCTAAGCAAAAA 3412
                         ------  iv  iii  --  v   i      ii     i i iv  i  
  L1M4_orf2#LINE/    156 ------ATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_90470259_9   3413 GAACAAAGTAGGAGACATCATGCTACCCGACTTCAAACTATACTACGGGG 3462
                                  v    ivv   ii  v   i i      viv      iii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_90470259_9   3463 CTACAGCAACTAAAACAGCATGGAACTGGTACAAAAACAGACACACAGAC 3512
                               i  ii  i    ii   v     i i  ii i     i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_90470259_9   3513 CAATGGAACAAAATAGAGAGCCCAGAAATAAGGCCACACACCTACCACTA 3562
                                 i i   v     i          iv   i   ii  iviii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_90470259_9   3563 TCTGATCTTCAACAAGGCTGACAAAAGCA----ATTGGGAAAGGACTCCC 3608
                         vi    i   i      v  v   i v  ----  v       i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_90470259_9   3609 TATTCAATAAATGGTGCTAGAATAATTAGCTAGCCGTATGCAGAAGATTG 3658
                          v     i          i i i  i i v  ?  ii     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_90470259_9   3659 AAAGTGGACCCTTTCCTTACATCATATACAAAAAGTAACTCAAGATGGAT 3708
                           iv       i v   i   i            v        i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_90470259_9   3709 TAATGACTTAAATGTAAAATCCAAAATTATTTTTAAAAAACCTGGTAGAC 3758
                         i ?v   i         i v i    i   ----    vv i i v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT----AAAACTCTTAGAAGAA 543

  chrX_90470259_9   3759 AACCTAGGCA-ATACCATTCTGGACACAGGAACTCA--CAAAGATTTAAT 3805
                            v    ?i- v i -   vv   viv  i-- i --   v i   vv 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGG--TTAGGCAATGGTTTCTT 590

  chrX_90470259_9   3806 -GATGAAGATGCCAAAAGCAACTGCAACAAAAGCAAAAAAT-TATAAATG 3853
                         -   - v  ii         vvv          -       -v      v
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATT 638

  chrX_90470259_9   3854 AGATCTAATTACACTAAAGAGCTCCTGCACAGCAAAAATAAACTATCA-- 3901
                         i  ii v  i v v v  i i  ii  ii vv    ii- v       --
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG-ACACTATCAAG 687

  chrX_90470259_9   3902 ---GTAAACAGACAACCTACAGAATTTGAGAAAATATTTGAAAACTATGC 3948
                         ---  i  v        i       vv             v   ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_90470259_9   3949 ATCTAACAAAGGTCTAATATCCAGTATCTATAAGGAACTTAAACAAATTT 3998
                             i i  i  v  vi       v  v     i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_90470259_9   3999 ACAAGAAAAAAACAA----CTCCATTAAAAAGTGGACAAAGGACATGAAC 4044
                          i  v     i    ---- i v   ?    i   i       iv    -
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA- 836

  chrX_90470259_9   4045 ATAAAC-TTTTTCAAAAGAAGACATACACGCAGCCAACAATCATATGAAA 4093
                         -  i  -   i  v        i     viii     i  v  i      
  L1M4_orf2#LINE/    837 -TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_90470259_9   4094 AAAAATCTCAATATCACTTATCAT 4117
                          i vi-     i    ????????
  L1M4_orf2#LINE/    886 AGATG-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (151 / 89)
Gap_init rate = 0.02 (20 / 899), avg. gap size = 2.30 (46 / 20)  


2689 22.22 7.73 2.29  chrX_90492669_90494488.rev      502  1329 (491)    L1M4_orf2#LINE/L1       36   908 (0)  

  chrX_90492669_9    502 TAATATTTTTTAAATCTCCATACTATCCAAACTGATC---------AATA 542
                                v  v i  vv v     vi     i     ---------  ii
  L1M4_orf2#LINE/     36 TAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACG 85

  chrX_90492669_9    543 TAATCCCTATCAAAAGCCCAATGGCATTTTTTTTTTACAGAAATAGAAAA 592
                         i              v    iiv  ----i      i       v  v  
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGC----CTTTTTTGCAGAAATTGACAA 131

  chrX_90492669_9    593 AACAA-CCTAAAATTCATTTGTAGTCACAAAAAAACCCTGAATAACCAAA 641
                         ivii -            v  v ivii   iii -   v     i     
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAA 180

  chrX_90492669_9    642 GCAATCT-GAGAACGAAGAAAAAAGCTGGAGACAC-CATTCTTCCTGATT 689
                         i      -  i  v      v    i     i-  -  iv     ii   
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATT 229

  chrX_90492669_9    690 TCAAAACATGTTACAAAGCTACAGTAATTACAACACTGTAGCACTGTCAT 739
                                v ii                 i vi   v   i i    v   
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_90492669_9    740 AAAAAACAGACATATAGGCCAATGAGGCAGAATAAAGAGCCCAGAAATAA 789
                           ii -i          ii     iiii     vi    i          
  L1M4_orf2#LINE/    280 AAGGA-TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_90492669_9    790 ACCCACACATGTACAGTTAAGTGGTCTTTGACAAAGGTGCCAAGAAAACA 839
                              i    v  ii  i  v  i i  i     i          vv iv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_90492669_9    840 CAATAAAGAAAGGATTGTCTCTTTCACAAATAGTGTTAAAA-ACTTGGAT 888
                             iii     i  v    i  iv      i   i iii - vi     
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_90492669_9    889 AT----ACGTAAAA--------TTGGATCCTTATCTTACACTGTACACAA 926
                          ?---- i i    --------     i  i  i  i    ii  i    
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_90492669_9    927 AAATCAACTCAAAAT-----ACAGACTTTCAACCT--GATCCGAAACTAT 969
                             i          ----- ?    i -v  iv --  v ii       
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCT-AAATGTAAGAGCTAAAACTAT 527

  chrX_90492669_9    970 AAAATT-TTAGAAGAAAACA---GGGTAAGAGCTTCTTGACATTAGTCTT 1015
                             i -             --- ?    - v    v    v  i vi v
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTA 576

  chrX_90492669_9   1016 ACCAATGACTTCTTGTATATGACACCAAAA-CACAAGCAAAAAAAAAAAA 1064
                         iv     ii     iv              -         v    i    
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_90492669_9   1065 AAAAGAATATAGAAAAA---GAGTACATCAAA-TTAAAAGGCTTCTGCAC 1110
                           -------    v   ---  v v       -      i-   i  ii 
  L1M4_orf2#LINE/    627 AA-------TAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGC 668

  chrX_90492669_9   1111 AGCAAAATAAACAATCAACA--GTGTAAAGGTAGCTTACAGAATGGGAGA 1158
                         vv    iv v  v     v --   v    ii i ii             
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_90492669_9   1159 AAATTTTTGTAAAACAAGTATTTGATAAGGGGCTATCGTCCCCAAA---T 1205
                             v    i   v  vi   i         i  --i  vi   i --- 
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACT--TGTATCCAGAATAT 766

  chrX_90492669_9   1206 AAAAGGAACTTTTACAACTTAATGGCAAAAA--CAAACAA--------AG 1245
                          v  i     i        i   iii     --    i  -------- i
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_90492669_9   1246 AAA----CAA----CTTGAATAGTCATCTCTCAAAAGAAGGAATATAAAT 1287
                            ----   ----i        v   i    v       iv   i    
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_90492669_9   1288 GGCTAATGGGTAAATGAAAAGATGCTCAACATCATAATCATC 1329
                            i   ii i v                     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (120 / 61)
Gap_init rate = 0.03 (29 / 873), avg. gap size = 2.86 (83 / 29)  


 729 26.71 13.95 6.86  chrX_90510318_90512174      521  1366 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_90510318_9    521 GAGAGAAGTACAATGTTCATAAATTA-AAGACATGA-ATTGT--AGAGGT 566
                           i   vi v v        ii   i-     v i -     --   v v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_90510318_9    567 CAA--CTATCAAAAATTGATTTATAGATTAAAT----TTCACATCAGTAA 610
                            --  vi v   -     i  i     v  i---- i vi    --- 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCA---A 98

  chrX_90510318_9    611 AATTTCCAACAATATTTCTTGTGTATAACTTGATAAGTTGACTCTAAAAT 660
                            i-   i -- iii i  v  i v  v    i   i   ii       
  L1M4_orf2#LINE/     99 AATC-CCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_90510318_9    661 TTATATGAAAATTCAAAGGGCCAAGTATAGTCAGAATAATGTTGCAAAAG 710
                          i     i    v   i  i  v  v    i  i  i   v   v     
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_90510318_9    711 AA---CATGATGGTATAAATAGCTCTGCCAAATATCAATAACCATATAAA 757
                           ---  vii v v vi v vi v  v  v   v    ----------  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA----------AA 235

  chrX_90510318_9    758 CTTATTATCCAAGATTATTATAAAGCTATAGTAGTTAATATGATGAGTTA 807
                             i  i-------------       i    i i  v iii  v v  
  L1M4_orf2#LINE/    236 CTTACTAC-------------AAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_90510318_9    808 AT--TATTGGGC---ACA-ATAGCTCAACAGAACAGAAAATAAAGCACGG 851
                         v --i  vi  v---   -    v    ii   i    vvv i  iv i 
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_90510318_9    852 AATGTTACTTTCACTCACTTATATATGGAAACTTGATTTATGAACAGAGG 901
                           -i v -----  i  ivi  v     vv v       vi  -  -   
  L1M4_orf2#LINE/    323 AA-ATAA-----ACCCATACATTTATGGTCAATTGATTTTCGA-CA-AGG 364

  chrX_90510318_9    902 CTGCAGTGATGA---AAAGATGTAATAACAAGACTTTTTAAAATTAAATA 948
                         v   viv  iv ---  v iv v  v  i - v     i  ---i    -
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATA-GTCTTTTCAA---CAAAT- 409

  chrX_90510318_9    949 AAGGGCAATAGAACAA-----TATTAAAGTGTAAAA-AATAA--TTGGA- 989
                         ---  iiv i i    -----  ?iv vi  i    -   i --     -
  L1M4_orf2#LINE/    410 ---GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_90510318_9    990 ---TACCATACACCACACACAAATATCAATTCCAGGTGTATTAAGCACCA 1036
                         ---    vi      i i     v  i  i  v ii  v  i ?iv   v
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_90510318_9   1037 ACATTTGTAAGAA--AAAACAACAAAGCCATTTAGA-GACAATGT---TG 1080
                          v  --      i--     v i   i i-i     -  v  ii ---? 
  L1M4_orf2#LINE/    507 AAAT--GTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNG 553

  chrX_90510318_9   1081 TAGATTTTTATGACAATA---TAG--AA-GGTTT---------------- 1108
                           i  i  ii    vv i---   --  -     ----------------
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_90510318_9   1109 -------------------GAAAAAT---TAAATTA-----CAT-----T 1126
                         -------------------i      ---      i-----   ----- 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_90510318_9   1127 TAAAAA-TTCTATTCATCAAAAAA-ATCATAAAGAACATTAACAAATAAG 1174
                               -  i i v v     ii - ii  v     vi v  v i i  v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_90510318_9   1175 CCACAGAGTGAGCATAGATATTTACTGTGCATATAACCAACAAG------ 1218
                                i  i viv i      i vivv      v ii i   ------
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_90510318_9   1219 --------AATATATAATAAACCTATATCGATTT--TAAAAAAAGAACAG 1258
                         --------         vi   iiv  - i i i--   v    ii   i
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATAAAAAGACAA 802

  chrX_90510318_9   1259 GTAACAATGCCAACTTCTAAAAATGGGCAATTGACTTGAAT-GAAA---C 1304
                         i    ----    i ?--            vv  i      -  v --- 
  L1M4_orf2#LINE/    803 ATAAC----CCAATTW--AAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_90510318_9   1305 TTCATAAGAAGAAAATCAAAATGGACAATAACCGTATGAAGAAGTGCTCG 1354
                          i  -       v - vv      v      v ii     i ii     i
  L1M4_orf2#LINE/    847 TCCA-AAGAAGATA-TACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_90510318_9   1355 AC--CATATTCAAG 1366
                           --  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (129 / 93)
Gap_init rate = 0.06 (51 / 906), avg. gap size = 3.45 (176 / 51)  


2406 29.28 3.52 0.45  chrX_90528603_90530621.rev      648  1528 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90528603_9    648 TGAAAAAGCATTCCATACTCGTGTATTTGAAGAGTGGATATTTAAAAAAT 697
                           i   iii  i    ii  i  v   v     v vi     vvv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90528603_9    698 GGCCAGAGTGCTTAAAGCAACTTACAGATTCAACATTATTCCAATCAAAC 747
                            v v v v ii   vii ii            iiv  i  v      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90528603_9    748 TACCAACATCGTGTTTCACAGAATGAGAAAAACCCATTCTAAATATAATA 797
                          v   i vv v v   ii     vvv  v  i iv  i     vv v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_90528603_9    798 TGGAACCAAAAAGAGCCCA-AATAGCCATAGTAATCCTGAGCAAAAAGCA 846
                              viiv  i ii    -        v ii    i   iv  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_90528603_9    847 CAAACCTGGAGACATCACACTACCCAACTTCAAACTATACTGTCAAGCCA 896
                             vi     ivv       v     i      viv    iiv    i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_90528603_9    897 CACTAACCAAAACAGCTTGGTACTGGAACAAATACAGACACATAGACCAA 946
                           v   i   i    iv         v i  iv i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_90528603_9    947 TGAGACAAAATAGAAAACTCAGAAATACAGCTGCACAAGTACAACCATCT 996
                           ii i i   v  i iii        v v iii   vv  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_90528603_9    997 GATTTTCATCAAGGCCAACAAAAATAAGCAATAGGGGAAAGGAC--TCCT 1044
                                iv     viiv   i vi vv    -        i i--  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTT 399

  chrX_90528603_9   1045 TATTAAACAAATAGTGCTAGGATAACTGGCTAGCCATATGCAGAAGA--- 1091
                          -- v       i     i   i      v  ?   i     i    ---
  L1M4_orf2#LINE/    400 T--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_90528603_9   1092 ---TTGAACCCTT-CCTTTCACCATATACAAAGATTAACTTAAA-CGGTT 1136
                         ---   i    i -   iv             i       i   -i  v 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_90528603_9   1137 TAAAGATTTAAATGTAAGACCTCAAAATATAAAAATCCTGGAAGACAACC 1186
                         i ?   ii           v  v   v       v  i i     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_90528603_9   1187 TAGGAAATACTCTTCTCAACATCATTCTTGGCAAATGATTT-TTGGCTAA 1235
                             ?ivv v     vii  v iivvi v     -  i   -  i v  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATAT 596

  chrX_90528603_9   1236 ATCCTTAAAAGCA--ATCA-CAACAGAAAAAATTGACAAGTGGGACCTAA 1282
                         iv vii       -- v  -   v         v  i  i v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_90528603_9   1283 TTAAA-CTAAAGA-------GC---AAAAGAGATGATCAACAGATCAAAC 1321
                          i   -i    i -------  ---   i  v iv     v i vii  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_90528603_9   1322 AGACAACCTGTGGAATAAAATAAGATATTCAAAAACTGTGTATCCAACAA 1371
                                 iiii    iii v  i     iiv   iii i    ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_90528603_9   1372 AGGCCTAATACCCAGGATCTATAAGGAACT--TA-AAC-CAACAAGCAAA 1417
                         i  v  vi  i    i  v     i     --  -   -   i  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_90528603_9   1418 AACCAAATAACCTCATT-AAAAATGGGTAAAGGACATGAACAAACACCTT 1466
                          iv         iv   -         i      iv    i i   ii i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_90528603_9   1467 TGGAAGGAAGACATACAAGCAGTCAATAAACATATGAAAAAATTCTCAGC 1516
                          vv  i     i      iii i      i  i       i  v    i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_90528603_9   1517 ATCACTAGTCAT 1528
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (154 / 101)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.94 (35 / 18)  


2128 29.14 2.63 2.29  chrX_90561950_90566822     3515  4389 (484)    L1M4_orf2#LINE/L1        1   878 (30)  

  chrX_90561950_9   3515 TGGAAAATAATTTGATGCACATGAATTGGAAGAATCAATATTACAGAAGT 3564
                               ivv  iiv   iv    i         v i      iivi ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90561950_9   3565 GGTCATACTGCCGCCCAAAGCAATTTTCAGATTCTATGCTATTCATATGA 3614
                           iv     -  --     vii  i v       v i  v  i v   v 
  L1M4_orf2#LINE/     51 GGCAATACT-CC--CCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_90561950_9   3615 AACTCTCAAA-GTCATTCTT-CAGAGAATTAGAAAACATATTCTAAA-TT 3661
                           v  i  iv- i v  i  -    -    iiv  i vv  i     -  
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATT 146

  chrX_90561950_9   3662 CACATGGAA---CAAAAAAAACCCCAG--TAGCCAAA-CAATCCTAAGCA 3705
                           i      ---   iii ---     --        -     i i iv 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_90561950_9   3706 AAAATAACAAAGCCAGAGACATCACACT-ACTAACTCCAAATTGTATTAT 3754
                          i  v       iii   ivv       -v i  i i    viv  i  i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_90561950_9   3755 GGGGTTACAGTAACCAAAACAGCAAGATACTGGGACAAAAAGAGACACAT 3804
                         iii i        i   i    iiv i      v i  ii v     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_90561950_9   3805 AGACCAATGGAACAGAATAGAACACTCAGAAGTAAAGCTTCACACTCACA 3854
                            i        i     v  iviii     i    v ivi   i i ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_90561950_9   3855 ATCACCTGATTTTCAACAAGA---CCAATAGAAACAGGCAATGGGAGTGG 3901
                         i   vi        i     i---    ---i v  vv       iivi 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAA---GACCATTCAATGGGGAAAG 390

  chrX_90561950_9   3902 ACTC-CCTATTCAATAAGTAAT-CTTGGATAACTGC-CAGCCACATGCAG 3948
                          v v-i  v     i  i ii -  v   i     v-i ?         i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_90561950_9   3949 AACAATACAATCAGAATCCTACTTTTTACCATATAGAAAAATTAACTCAG 3998
                           v   iv i ii  vi     i ivi        v             i
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_90561950_9   3999 GATGAAGTAAATATTTAAATGTAAAACCTCAAACTATCAAAATCCTAGAA 4048
                         i   i vi ? v ii         i v  v       v   v  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_90561950_9   4049 GAAAACCTAGGAAACACCCTTCCTGACATCAACTTTGGCAAATGATTT-T 4097
                               v    ?ivv vi    v    v iiiv  v     -  i   - 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chrX_90561950_9   4098 TGGCTAAGTCCCCAAAATCAACTTCGACAAAAACAAAAATAGACAAGTGG 4147
                          i v  v v v      v  vvvv i      iv         i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_90561950_9   4148 GACCTAATTTAA-TGAAAGAGCTTCTTCATAGCAAAAGAAATAATCAACT 4196
                            i v  iv  - v   i -   i viiivv    i  v iv     vv
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_90561950_9   4197 GAGTAAACAGGCAACCTAAAGAATGAGAGAAATTATTCACAATCTATGCA 4246
                         i   i  v  i     i v      i      v    ii   vii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_90561950_9   4247 TATGACAAAGGTTTAATATCCAGAGTTTATAAGAAACTTAAACAAATCAA 4296
                          v   i  i  vi vi        i v     ii    ivv    v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_90561950_9   4297 CAAGCAAAAAAAAAAAAAATAATAAGCTCATTTAAAAAATGGGCATAGTA 4346
                         i  v----     i v      ---- i  v  ?           v  v 
  L1M4_orf2#LINE/    789 TAAT----AAAAAGACAAATAA----CCCAATTWAAAAATGGGCAAAGGA 830

  chrX_90561950_9   4347 T----ATTAACACTTCTCAAAAGAAGACATAGAAGTGGTGAA-AAGCA 4389
                          ----  vi   i     v        i   v  i   iv  -     
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

Transitions / transversions = 1.44 (148 / 103)
Gap_init rate = 0.03 (24 / 878), avg. gap size = 1.79 (43 / 24)  

 899 26.28 1.71 0.68  chrX_90561950_90566822     4393  4685 (188)    L1M4_orf2#LINE/L1      613   908 (0)  

  chrX_90561950_9   4393 GCAACAAAAGCAAAAATTAACAAGTAGGATCTCATTAAACTAAAGAGCTT 4442
                                   v      vi i  i v   ii    i   v v  i i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_90561950_9   4443 CTGCAGAGCAAAGAAAACTATCAACAGAGTGAACAGACAATCTAGAGAAC 4492
                         i  iivvv     i v        v i      v      i i v    i
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_90561950_9   4493 GGAAGAAAATTTTTTCAAGCTATGCATCTGACAAGGGTCTAATATCCAGC 4542
                           i       v   v   iii  ii      i     v  vi       v
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_90561950_9   4543 ATCTTTAAGGAACTTAAGCAAATTTACAAGAAAAA-----ACAACCCCAA 4587
                           v v   i     ivvi   v iv i  v     ----- i     v v
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_90561950_9   4588 TAAAAAGTGAACAAAGGATATTAACAGAAACTTTTCAAAAGAAGATATAC 4637
                          ?    i  ii        v v  i   v i  i  v             
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_90561950_9   4638 ATGCAGCCAACAATCATATGAAAAAAAGAGCTCAACATTACTGATCAT 4685
                          viii     i  v  i       i --v         i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (43 / 33)
Gap_init rate = 0.01 (2 / 296), avg. gap size = 3.50 (7 / 2)  


1515 26.52 1.89 2.27  chrX_90568291_90571718        1   528 (2900)    L1M4_orf2#LINE/L1      278   803 (105)  

  chrX_90568291_9      1 ATAAAAATAGGCATGTAGACCAATGGAACAGAATAGAGAACTCAGAAATA 50
                             ii    i   i    i        i     v    iii        
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_90568291_9     51 AAGCCAAATACTTACAGCCAACTAACCTTCGCTAAAGCATACAAAAACAA 100
                           v   v i i   ii i   i i ii    vi  i -i i v  i  v 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCA 376

  chrX_90568291_9    101 A-AAATGAGTAAAGGACACCTTATTCAATAAATGGTGCTGGGAAAACTAG 149
                         v-v    i v    i i vii v     i              v    i 
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_90568291_9    150 CAAGCCACATGTAGAAGGATGAAACCAGATCCTCATCTCTCACTTTATAC 199
                         vv ?       i i   i     iiii  i  ii i   v   iv     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_90568291_9    200 AAAGATCAACTCAAGATGGATCAAAGACTTAAATCTAAGACTTGAAACCA 249
                            i  i       i        ?    i     v     vi i    i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_90568291_9    250 TAAAAATTCTAGAAGATAACATCAAAAAAACTCTTCTAGACATTGGCTTA 299
                              v ii       v     vii?iv  v     vv   v    v   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_90568291_9    300 GGCAAGGAATTCATGAGTAAGACCCCAAAAGCAAATACAACAAAAACAAA 349
                              v iv   v iii  v   v         v vi        iv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_90568291_9    350 AATAAATAGATGGTACCTAATTAAA-TTAAAAAGCTTCTGCACAGCAAA- 397
                             i   i  v v  i v  i   -       -   i  ii vv    -
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAG 675

  chrX_90568291_9    398 ------ATAAAGAATCAGCAAACAGACAACCTACAGAGTAGGAGAAAATA 441
                         ------  v     --  ii  v        i     i i          
  L1M4_orf2#LINE/    676 GACACTATCAAGAA--AGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_90568291_9    442 TTAGCTAACTATCCATTCAACAAAG-ACTAATATCTAGAATCTACAAGGA 490
                           v  v  ii  vi  iii i  i -   vi    i     v  i  i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_90568291_9    491 ACACAAACAAATCACAAAACACAATCAGAAATGACAAA 528
                           v vv    v   ------ i   - i   -      
  L1M4_orf2#LINE/    774 ACTCTTACAACTCA------ATAAT-AAAAA-GACAAA 803

Transitions / transversions = 1.69 (86 / 51)
Gap_init rate = 0.02 (10 / 526), avg. gap size = 2.20 (22 / 10)  

 202 24.49 0.00 0.00  chrX_90568291_90571718     1725  1773 (1655)    L1M4_orf2#LINE/L1        1    49 (859)  

  chrX_90568291_9   1725 TGAAAAAACATTCCATGCTCATGAATAGGAAGGATATATATTGTTAAAA 1773
                           i   i i  i     i     i  v     iv vv          i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.00 (0 / 0)  

2441 27.42 1.98 1.28  chrX_90568291_90571718     2081  2937 (491)    L1M4_orf2#LINE/L1       46   908 (0)  

  chrX_90568291_9   2081 AAAGTGGTCATGCTGCCCAAAGCAATTTACAGATCTAATATTATTCCTAT 2130
                           ii   iv  i  v      vii  i       ii  iiiv  i     
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_90568291_9   2131 CAAACTACTAACATTATATTTCACAGAACTAGAAAAACT-ATTCTAAAAT 2179
                             v v i i vviv v   ii     v v  v  i  -  i       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_90568291_9   2180 TC-TATGGAACCAAAAAGTAGCCCAAAGT-GTTAAAGCAATCCTAAGAAA 2227
                           -       viiv  i v -    i i - ii   i     i i -   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGA-AAA 193

  chrX_90568291_9   2228 AAAATAAAAATGCTGGAGACAGTACATTACCCAACTTCACACCATACTAT 2277
                          i  v  v  v i     ivvvi   i v     i    v v v     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_90568291_9   2278 AAGACTACGGTAGCAAAAATAACAAGGTAATGGTACAAAAACAGAAACAT 2327
                           ii    i   iiv  i i iiiv    v   i i  ii i   v i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_90568291_9   2328 ACATCAACAGAACAGGTAA--GAGAACTGAGAAATAAAGCTGCATACCTA 2375
                          v     ii   i  --  --    iiiv         v --     v v
  L1M4_orf2#LINE/    294 AGATCAATGGAATAG--AATTGAGAGTCCAGAAATAAACC--CATACATT 339

  chrX_90568291_9   2376 CATG--CATCTGATCTTTGACAAAACTGACAAAAATAAGCAATGGGAAAA 2423
                         i   --  vi    i  i     iiv  v   i vi vv       i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_90568291_9   2424 GGGTTTCCTATTCAATAAATGATGCTGGGACAACTGACCAGCAATATGCA 2473
                          ii vvi  v     i     i              ivi ? v i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_90568291_9   2474 GAAAATTAAAACTGGACCCCTTCCTTAGACCATATACAAAAAATCAACTC 2523
                         i  i v i  ii         v   i v              - i     
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTC 488

  chrX_90568291_9   2524 AAGATGGATTAAAGACTTAAATGTAAAACCTCAAACTATAAAAGCCT-AG 2572
                           i      i ?    i         i v  v           vi  -  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_90568291_9   2573 AAGAAAACCTAAGAAACACAACTCTG-GACATAGGCCCTGGCAAAGATTT 2621
                                 v  i ?i-i v v  ii -   v v  viiv     v i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_90568291_9   2622 CATGACAAATATG---CCAAAAGCAATTGCAACAAAAACAAAAATTGACA 2668
                          v --- i     ---         vvv         iv      v  i 
  L1M4_orf2#LINE/    588 CTT---AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_90568291_9   2669 AATGGGATCTAATTAAACAAAAGAGCTTCTGCACAGCAAAATAAACTATG 2718
                            v   ii v  i   vvv  i i   i  ii vv    iv v     v
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_90568291_9   2719 AACAGAGTAAACAGACAGCCTACAGAATGGGAGAAAATACTTGCAAACTA 2768
                           v i   i  v     i  i                  i       ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_90568291_9   2769 TTCATCTGACAAAGGTTTAATATCCAGAATCTATAAGGAAC-CT---AAA 2814
                          vi      i  i  vi vi          v     i    -  ---  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_90568291_9   2815 TGAACAAGCAAAAGACAAATAGGCCCATTAAAAAGTGGACAAAAGACATA 2864
                          v  i  vv            iv  v   ?    i   i    i  iv i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_90568291_9   2865 AATAGACACTTTTCAAAAGAAGACATAGATGCAGCCAGCAAGCACTTGAA 2914
                                 i  i  v        i   v viii    ii      v    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_90568291_9   2915 AA-ATGCTGAACATAACTAATCAT 2937
                           -     v     v ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.02 (18 / 863), avg. gap size = 1.56 (28 / 18)  


1933 25.44 0.88 0.44  chrX_90589927_90594686.rev     2886  3341 (1419)    L1M4_orf2#LINE/L1        1   458 (450)  

  chrX_90589927_9   2886 TGAAAAAATATTTTATGTTCATGGGTTGGAAGAATCAATATTGTTAAAAT 2935
                           i   i    iii          i        v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90589927_9   2936 GTCCTTATTTCCCAAAGCAATCTACAGATTAAATGAAATCCCTGTCAAAA 2985
                          v vv  i i      vii           v  i v       i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90589927_9   2986 TACCAATGACATTCTTTGCAGAAATAGAAAAAAAAAAACCGTGAAATGTA 3035
                          v   iivi v  i           v  v  --ivvi i v i    vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chrX_90589927_9   3036 TATGGAACCACCAAAGACCCAGAATAGTATATGCTATCCTGAGCAAAAGG 3085
                                vii v ii            ivv vi v   i   iv  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_90589927_9   3086 AACAAAACTGGACAACTCACATTGTCTGACTTCAAATTTTACTACAGAGC 3135
                               ii    vi       i vi ii i      vi        i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_90589927_9   3136 CATGGTAACCAAAACAGCATG---CTGGCAAAAAAGCAGACACATAGATC 3182
                         i ii    i   i    ii  ---      v  iiii     i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_90589927_9   3183 AATGGAACAGAATAGAGAATTCAGAAGCAAATTCGCACAGCTACAATGAA 3232
                                i     v    i i     ii   ii ii   vi  iii v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_90589927_9   3233 TTGATTTTTGACAAAGATGCCAAGAACATACACTGGGGAAAAAATTGTCT 3282
                                 i     i i        v   v  v        i   v    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_90589927_9   3283 CTTCAACAAATGATGCTGGGGAAACTTGATATCCATATG-AAAAGAATGA 3331
                         i           i       iv    v    ?   i   -          
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_90589927_9   3332 AACTAGACCC 3341
                          ii i     
  L1M4_orf2#LINE/    449 AGTTGGACCC 458

Transitions / transversions = 2.19 (79 / 36)
Gap_init rate = 0.01 (3 / 458), avg. gap size = 2.00 (6 / 3)  

1648 24.89 0.44 0.44  chrX_90589927_90594686.rev     3816  4269 (491)    L1M4_orf2#LINE/L1      455   908 (0)  

  chrX_90589927_9   3816 ACCCCTCTCTCTCCCCATATATAGAAATCAAATCAAAATGAATTAAAGGT 3865
                               vi   v v       i i    i  v        i  i ?  ii
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_90589927_9   3866 TTAAATCTAAAACCTCAAACCATGAAACTACTGCAAGGAAACATTGGGGA 3915
                         i     v   i v  v    i  i     vi iv   i      v  ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_90589927_9   3916 AACTCTTCAGGACATTGGTCTGGGCAAAAATTTCCTGAGCAGTACCCCAC 3965
                           v     iv   v    vi i     vii    i iiii vv  v   v
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_90589927_9   3966 AAGCACAGGCAACCAACGCAAAAATGAACAAATGGGATTACATTAA-GTT 4014
                                i     v  v v      ii i    v   i v   i  -i  
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_90589927_9   4015 AAACAGCTTCTTCGCAGCAAAATATACAATCAAGAAAGTGAACAGGCAAC 4064
                            - i   i vi  vv    iv i  v              v  i    
  L1M4_orf2#LINE/    655 AAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_90589927_9   4065 CCACAGAATGGGAGAAAACATTTGCAAACTACCCATCTGAGAAGAGATTA 4114
                                           i         ii ivi      v   i  i v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_90589927_9   4115 ATAACCAGAATATATAAGTAGCTCAAACAACTGTAGAGGGAAAAAA-ATA 4163
                         i  v             iv i   vv      vv v ivi    i - v 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_90589927_9   4164 TAATCTGATCAAAAAAGTGTACAAAATATTTGAATAGACATTTCTCAAAA 4213
                            i ii  i?     -  vi    iv                   v   
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_90589927_9   4214 GAAGACATACAAATTGCAAACAAGCATATGAAAAGGTGCTAAACATCATT 4263
                              i        v  v  i     i        i    v       ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_90589927_9   4264 GATCAT 4269
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.24 (61 / 49)
Gap_init rate = 0.01 (4 / 454), avg. gap size = 1.00 (4 / 4)  


2631 26.85 3.26 1.24  chrX_90600761_90605955     3813  4702 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90600761_9   3813 TGAAGAAACAGTCCATGCTCATGGAT----AGAATCAATATCATTAAAAT 3858
                           i i i i vi     i        ----   v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90600761_9   3859 GGACATACTGCCAAAAACAATGTATAGATTTAATGGTATACCTATTCAAC 3908
                           vv     v  v   vii  v  i     i  i vv  v     iv  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90600761_9   3909 TACCATGGACATTATTCACAGAGCT--AAAAATTTTTTTTTAAATTCATA 3956
                          v   vvvi v  v  ii    iv -- v  ii vv ii v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_90600761_9   3957 TGGAATCAATA-AAGAGGCT--GAATAGCCATGGCAATCCTAAGCAAAAG 4003
                              ---  i-   i i i--         vii     i i iv  i i
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_90600761_9   4004 G--CAAAGCTGAAGGCATCATGCTACCTGACTTCAAACTATACTACAGGG 4051
                          --     i  i   vv   ii  v  ii i      viv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_90600761_9   4052 CTACAGTAACCAAAACAGCACAGTACCAGTACAAAAGCAGACACATAGA- 4100
                                  i   i    iiii    ii i i  iiii     i     -
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_90600761_9   4101 CAATTGGAACAGAATAAAGTCTCCAGAAATAAGACCACACATCTATAGCT 4150
                             -    i     vi  vv           iv   i    i   i ii
  L1M4_orf2#LINE/    298 CAAT-GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_90600761_9   4151 ATCTGATCTCTGACAACCTGACCAAAAA-AGGCAATGGGGAAAAAATTCC 4199
                          vi    i ii     vvvvi    i v- vv           i   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_90600761_9   4200 CTCTTCAATAAGTGGTGCTGGCATAACTGGCTAGCCATATGCAGAAAATT 4249
                           i     i  i         v i      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_90600761_9   4250 ACAACGGGACCTCTTCCTTAGACCTTATACAAAAAATTAACTCAAGATGG 4299
                         iv iiv     i  v   i v   v          -         i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGG 495

  chrX_90600761_9   4300 ATTAAAGACTCAAATGTAAAACCCAAAACTATAAAAATCCTAGAAGACAA 4349
                           i ?    ii        i v i            v  i       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_90600761_9   4350 CCTTGG--TAATACCATTCAGGACACAGGCACAGGCAAATGTTTCCT-GA 4396
                          v v  --   - i -   iv   viv  vvi      vv     i -  
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_90600761_9   4397 TGAAGACCTCAAAAGCAATCCCAACGAAAGCAAAAATTGACAAATGGGAT 4446
                          - v   vi        vvvv    i    v      v  i    v   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_90600761_9   4447 CTACTTAA--CTAAAGAGCT--GCACAGCAAAAGAAACTATCATGA--GT 4490
                         i vv i  --i    i vi -- ii vv    i  v       v  --  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_90600761_9   4491 GAACAGACAACCTACACAATGGGAGAAAATTTTTGCAAACTGTGCATCCA 4540
                            v        i   v             v        iii ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_90600761_9   4541 ACAAAGGTCTAATATCCAGCATCTATAAGGAATTTAAACAAATTTACAAG 4590
                          i  i  v  vi       v  v     i   i ivv    v ---   v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAAT 789

  chrX_90600761_9   4591 AA-AAAAAAATGAACAACCCCATTAAAAAATGGGCAAAGGATATGAA--- 4636
                           -     i ii  i     v   ?                 v    ---
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_90600761_9   4637 -CACTTTTCAAAAGAAGACATACATGTGGTCAAGAATCATATAAAAAA-- 4683
                         -  i  i  v        i     vi   i   v  v  i  i    i--
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_90600761_9   4684 GCTCAACATCACTATAAAT 4702
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.82 (40 / 22)  


2389 24.80 7.22 1.86  chrX_90643333_90646378.rev     1698  2556 (490)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_90643333_9   1698 AAAATTATCTCATTCTCATGGATCAGAAGAATTAACACCATTATAATGAC 1747
                            iv    i   vi        ii     v    i iii   vi   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_90643333_9   1748 CCTACTGCCCAA--TGAAACATACAGATTTAATTTAATCACTATGAAAAT 1795
                         vv    v     --   --iv        i  ivi    v    v     
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGA--TCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_90643333_9   1796 ACCAA-TGCCATTCATCACATAATTAGAAAAA--AATTCTTAAAATGTAT 1842
                         v   i-    v  i- ii  v  v v  v  i--i  i  -     vi  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCT-AAAATTCAT 149

  chrX_90643333_9   1843 ATGGAA---CAAGTAAGAACCTGAATAGCCAAAGCAATCTTGAGCAGAAA 1889
                               ---    --i  v  v           i         iv ii  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_90643333_9   1890 GAAGAAAGCTGAAGGCATCACATCACCTGACTTCAGAATATACTACAAGG 1939
                            v    i  i   vv     iiv  ii i    i  iv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_90643333_9   1940 CTATAGTTACCAAAACAACATGGCATTGGTATGAAAATAGACACATAGAC 1989
                            i   v i   i   iii   i i   i  i ii       i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_90643333_9   1990 CAATGGAATAAAATAGATAACCCAGAAATAAATCCA-AC-----TGAT-- 2031
                                   i   v  v ii           i   -  -----  i --
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_90643333_9   2032 AT--ATTT---ACAAAGCCAACAAGAACTTACATTAAGGAAAAAATACCC 2076
                           --    ---    i viiv     v v v  v ii     i    vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_90643333_9   2077 TCTTTAATAACTAATGCTGAGAAAATTAGATAGCCACATGTAGAAGAA-- 2124
                          i  i  i  v ii     i  v  i i    ?       i i     --
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_90643333_9   2125 --ACTGGACTCTTATTTCTCACCATA---AAAAACTA-CTCTGAATGGAT 2168
                         --ii     i i  ii  v       ---     i  -   vi       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_90643333_9   2169 TACAGACTTAAATATAAGACCTGAAACTATCAAAATACTAGAAGAAAACC 2218
                         i ?    i     i     v  i       v   v vi           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_90643333_9   2219 CAGGAA-AAACTTTCCTGA-----------ACAAGGAGTTTGT--GACA- 2253
                         i   ?i-   ii   v   -----------i   v -    v --  i -
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTAGATAT 596

  chrX_90643333_9   2254 GACTCCAAA-GCATATGCAACAGAAAACAAAAATAGTAAAAGTGGGATAT 2302
                            v     -   i v      i  i -        - v  i v   iv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGA-AAAAATAG-ATAAATTGGACTT 644

  chrX_90643333_9   2303 AATTAAAGTAGAAAGC-----------AAATGATATAATCAACAGAGTGA 2341
                         v  i   i vi   i -----------   v  i iv     v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_90643333_9   2342 AGAGACAACCAGCTTGTTGAACAGGAGAAAATATTTGCAAACTAATTATT 2391
                          i        vi v----   ii                  ii vv   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACA----GAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_90643333_9   2392 T-ATAAGGAACTAATATCCAGAATATACAAGGAACCC----AAAT-GATA 2435
                          -      i   vi             i  i    i ----  v -i   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_90643333_9   2436 GGAAAATAACCCAAGTAATCCTATTAAAAACTGGGCAAAAAAACATGAAC 2485
                         iv    vi  --  i   i  v   ?    v        ii vi-    i
  L1M4_orf2#LINE/    791 ATAAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATT-TGAAT 837

  chrX_90643333_9   2486 AGACATTTCTCAAAAGAAGACACACAAACACGCAACAAGTTTATGAAAAA 2535
                                    v        i i     iivv   i   ivi       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_90643333_9   2536 ATGTTCAACATCCCTGATCAT 2556
                            i        v????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (135 / 74)
Gap_init rate = 0.03 (31 / 905), avg. gap size = 2.52 (78 / 31)  


2858 27.78 1.10 0.99  chrX_90648626_90652886     2862  3768 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90648626_9   2862 TGGAAGAACATTCCATGCTCATGTATAAGAAGAACCAATATGATGAAAAT 2911
                              ii i  i     i     v  vi     vii     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90648626_9   2912 GGCCATACTGCCCAAAGTAATTTATAGTTTCAATGTTATTCCCATTAAAC 2961
                            v     v      v i  i  i  v     i iv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90648626_9   2962 TGCCATTGGCATCCTTCGCAGAATTAGGAAAAATGATTTTAAAATTCATA 3011
                          v   viv  v ii  i      v v iv  iv    ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_90648626_9   3012 TGGAACCATA-AAGGAACTCATA-TAGGAAAGACAATCCTAAGCCAAAAG 3059
                              --  i-    i  i  v -   vv  i      i i ivv i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_90648626_9   3060 AACAAAGCTGGAGGCATCACACTACTAGACTTCAAACTATACTGCAGGGT 3109
                                i      vv       v ivi i      viv    i  ii i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_90648626_9   3110 TCCAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACC 3159
                          v      i   i    ii         i i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_90648626_9   3160 AAAGGAACAGAATAGAGAACTGAGAAATAAGACTGCACACCTACGACCAT 3209
                           v    i     v    iiiv        iv iii   ii  i ii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_90648626_9   3210 CTGATCTTTGGCAAATCTAACAAAAACAAGCAATGGAGAAA--ATATTCA 3257
                         i    i  i i   ivv iv   i v  vv      i    --   v  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chrX_90648626_9   3258 CTATTTAATAAATGTTGCTGGGAGAACTGGCTAGCCATATGCAGAAAATT 3307
                         - v  i  i     v        v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_90648626_9   3308 GAAACTGGACCCCTTCTTTACACCTTATATCAAAATTAACTCAAAGTGGA 3357
                            ii         v i i     v    iv              i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_90648626_9   3358 TTAAAGACTTAAATATAAAACCCAAAACTATAAAAACCTTGGGAAAAAAT 3407
                          i ?    i     i   i v i            vi   i i i    i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_90648626_9   3408 CTAGGCAGTA--CCATTTAGAACATAGGAACAGGCAAAGATTACATGACA 3455
                         v    ?-   --i -  iivi  v v  ivi      v i  v v iivv
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_90648626_9   3456 AAGTCACCACAAGC-CACTGCAATAAAAGCAAAACTCGACAAATGGGGTC 3504
                          v v     v    -  v-    i     v    v v  i    v  iii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_90648626_9   3505 TAATTAAA--TAAAGACCTTCTGCACAGCAAAATAAACTAATATCAGAGT 3552
                          v  i   --    i  i  -  ii vv    iv v    vi vv i   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_90648626_9   3553 GAACAAACAACCTACGGAGTTGAATAAAATTTTTGCAATCCGTCCATCTG 3602
                            v i      i  i  i v i v     v       vi i vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_90648626_9   3603 ACAAAGGTCTAATATCCAGAATCTATAAAGAATTTAAACAAATTTACAAA 3652
                          i  i  v  vi          v         i ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_90648626_9   3653 AAAATAATGAACAACCCCACTAAAAAGTGGGCAA-GTATCATGAAAAGAC 3701
                             vi ii  i     v i ?    i       - v  i-    v    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT-TGAATAGAC 841

  chrX_90648626_9   3702 ATTTCTCAAAAGAAGACATTCATGTGTCCAACAAACATATGAAAAAAAGC 3751
                                v        i  v  vi  v    i  i  i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_90648626_9   3752 TCAACATCACTGATGCT 3768
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.36 (19 / 14)  


3062 26.91 1.44 0.89  chrX_90679272_90683595.rev     2931  3833 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90679272_9   2931 TGGAAGAACATTCCATGCTCATGGGCAGGAAGAATCAATATCATGAAAAT 2980
                              ii i  i     i      iiv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90679272_9   2981 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3030
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90679272_9   3031 TACCAA-TGCCTTTCTTCACAGAA-TTGGTAAAAACT-ACTTTAAAGTTC 3077
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_90679272_9   3078 ATACAGAACCAAAAAAAGAGCCGGCATTGCCAAGTCAATCCTAAGCCAAA 3127
                            ii   viiv  ii-  v  i v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_90679272_9   3128 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 3177
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_90679272_9   3178 GCTACAGTGACCAAAACAGAATGGTACTGGTACCAAAACAGTCATATAGA 3227
                                 i i   i    vi         i iv ii i  v        
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_90679272_9   3228 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAA 3275
                         i        i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_90679272_9   3276 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATT 3325
                         ii vi    i  i     ivv  vv  i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_90679272_9   3326 CCCTATTTAATAATTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 3375
                         vi  v  i  i  v           v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_90679272_9   3376 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 3425
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_90679272_9   3426 GATTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 3475
                            i ?   ii       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_90679272_9   3476 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 3525
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_90679272_9   3526 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3575
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_90679272_9   3576 AACTAAACTAAACAGCTTCTGCACT-------GCACTGTTCATCAGAGTG 3618
                         v ii   v v  v i   i  ii  -------i    i -  vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT-CAAGAAAGTG 693

  chrX_90679272_9   3619 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCTATCTACTCATCTGA 3668
                           v  i     i                 v     v vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_90679272_9   3669 CTAAGGG-CTAATATCCAGAATCTACAATGAACTCAAACAAATTCACAAG 3717
                         -      -  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    744 -TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_90679272_9   3718 AAAAAAACACACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACA 3767
                              i   v i     v  i? v  i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_90679272_9   3768 CTTCTCAAAAGAAGACGTTTATGCAGCCAAAAGACCCATGATAAAATGCT 3817
                         i     v        ii vi viii     v ii v     v  i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_90679272_9   3818 CACCATCACTGGCCAT 3833
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


3109 27.97 0.44 0.44  chrX_90691158_90694145     1588  2495 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90691158_9   1588 TGGAAGAACTTTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1637
                              ii iv i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90691158_9   1638 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1687
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90691158_9   1688 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCT 1735
                          v   iivi i  i  ii     -   -- v  i  - iii    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_90691158_9   1736 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 1785
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_90691158_9   1786 AACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGGC 1835
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_90691158_9   1836 TACAGTGACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1885
                               i i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_90691158_9   1886 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACC 1933
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_90691158_9   1934 ATCCGATCTTTGACAAATCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1983
                          vii   i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_90691158_9   1984 CTATTTAGTTAATGGTTCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2033
                           v  i iiv      v      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_90691158_9   2034 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2083
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_90691158_9   2084 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2133
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_90691158_9   2134 TTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTAATGTCTAA 2183
                         v    ?i v viv   iv   v v  vv i     v ii  vv ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_90691158_9   2184 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATATAA 2233
                         i            vvi          vv     v  i    v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_90691158_9   2234 TTAAACTAAACAGCTTCTACACTGCAAAAGAAACTACCATCAGAGTGAAC 2283
                          i   v v  v i   i iii  v    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_90691158_9   2284 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 2333
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_90691158_9   2334 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2383
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_90691158_9   2384 AAACAAACAACCCCATCAAAAAGTGGGCGAAGTACATGAACAGACACTTC 2433
                          i     i     v  i?    i     i   v iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_90691158_9   2434 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 2483
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_90691158_9   2484 ATCACTGGCCAT 2495
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (147 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1084 28.52 2.25 6.00  chrX_90704632_90706622.rev      498  1030 (961)    L1M4_orf2#LINE/L1      291   803 (105)  

  chrX_90704632_9    498 TATTGACCAATAGAAGAGAATAAATAACACAGAAACAAATCCACATATCT 547
                            v  i    i   v     vi v iiv      i   i   i i  i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_90704632_9    548 ATAGTGAACTCACTTTCCACAAAGGTACCAAGAACATACACTGAGGAAAA 597
                           i  v  i v i    v    i   i      v   v  v  i     i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_90704632_9    598 CATAGTCTCTTTGATAAAAGTTACGGGGAAAACTGGATATTCTTATGTGC 647
                         v       i  ii i   v v i v    v         ?i --------
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC-------- 432

  chrX_90704632_9    648 GCACACACACACACACACACACACACACACAAAAGTAGAGCCTCTTTCTC 697
                         ----------------   ii  v viv ii  iv i  -  i  vi   
  L1M4_orf2#LINE/    433 ----------------ACATGCAAAAGAATGAAGTTGGA-CCCCTACCTC 465

  chrX_90704632_9    698 A-AC-ACATACAAAAATCAAATAAATATATATTAATGATTTAAATCTAAG 745
                          -  - i          i  v v  v  iv  i ?v  ii     v    
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_90704632_9    746 ATGTAAAACTATAAAATTGCTATTAAAAATTGT-----TAAACCTCTCTA 790
                          vv             i vi  vv i   vii -----    --   iii
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA--TCTTCG 563

  chrX_90704632_9    791 GGACATTAGTCTGGGCAAAAATTTCTTGAGTAATACCCCAGAGGCAGAGA 840
                         v   v  i vi i     vii      iii  vv  v   i i   v ii
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_90704632_9    841 CAATCAA-GCAAAAATGGATAAATGGGATCACTTCAAT-TTAAAAAGCTT 888
                            iv  - v      i       v   iiv v    v-       -   
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTT 662

  chrX_90704632_9    889 CTGTACAGCAAAGGAATCAATCAACAAAGTGAAGAGGCAGCCTATTGAAT 938
                         i   i vv       vv v     v        i  i  i  i iv    
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_90704632_9    939 AGGAGAAAATATTTCCAAACTACTCATCTGTATTAG---TCTGTTTTCAC 985
                         i             v    ii ivi     -  v  ---ii   v i  v
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTG-ATAAGGGACTTGTATCCAG 761

  chrX_90704632_9    986 AGGGCTATAAAGATACTACCTGAGACTGGGTAATTCATAAACAAA 1030
                          ivi-        -   - i ivi   vii    vv v i     
  L1M4_orf2#LINE/    762 AATA-TATAAAGA-ACT-CTTACAACTCAATAATAAAAAGACAAA 803

Transitions / transversions = 1.31 (85 / 65)
Gap_init rate = 0.03 (14 / 513), avg. gap size = 3.14 (44 / 14)  

 705 18.38 1.08 3.24  chrX_90704632_90706622.rev     1316  1500 (491)    L1M4_orf2#LINE/L1      728   908 (0)  

  chrX_90704632_9   1316 CACATCATATCACCATCTGTCAAGGAATTAATAACCAGAATATATAAGGA 1365
                           v       ----     vi    i i vi  v             i  
  L1M4_orf2#LINE/    728 CAAATCATAT----ATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_90704632_9   1366 TCTCAAGCAATTCTATGGAACAAAAAT-CTAACAATTCAATT-AAAAATG 1413
                         v   vvi   i  v  --  i     v- v  i  ii     -       
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAAT--AATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_90704632_9   1414 GGCAAAAGATTGGAATAGACATTTGTCAGAAGAAGACATACAAGTGGCAA 1463
                               i    v            v  vi       i      i    v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_90704632_9   1464 ACAGGCATAAGAAAAGGTGCTCAACATCATTGATCAT 1500
                          i i   i v      i            ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (19 / 15)
Gap_init rate = 0.02 (4 / 181), avg. gap size = 2.00 (8 / 4)  


2465 29.52 2.69 0.79  chrX_90747118_90752743     4245  5135 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90747118_9   4245 TGAAAAAAAATTCTATGCCCATGGATTGAAAGA----ACAATATTAAAAT 4290
                           i   i v  i i   ii         i    ---- i v i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90747118_9   4291 AACCATAGTGCCCAAAGCAATACATAGATTCAACTTTATTTCTATTAAAA 4340
                         ii v   v v      vii  vi i         viv  ii    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90747118_9   4341 CATTAAAGTCATTTTTCACACAACTAAGAAAAACT--TTCTAAAATTCAT 4388
                         ivii ivvv v     ii  v  v v-  v  i  -- i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chrX_90747118_9   4389 ATGGAATCAAATATCAG---TCCA-AGTAGCCAAAGTCATCCCAAGCAAA 4434
                               ----  iiv  ---i   - i        iiv   iii iv  i
  L1M4_orf2#LINE/    150 ATGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_90747118_9   4435 AAGGAAAAAGCTGGAGGCATAATATTACCAGACTTCAAATTATACTATAA 4484
                            i v    i      vv v i i v  vi i      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_90747118_9   4485 GGCTACAGTAAGCAAAACAGCATGATGCTGTTACAAAAACAGATACATAC 4534
                         i          v   i    ii  i i   vi i  ii i   i i   v
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_90747118_9   4535 ACTAAGGGAAGAGATTACAGGACCCAGAAATAAGGCCACACACCTACAGT 4584
                          ii  v    v   v vv  iii          iv   i   ii  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_90747118_9   4585 CACCTGATTTTTGACAAAGTTGACAAAAATGAGCAACAGGTAAACAACTC 4634
                           vi       i     i v  v   i viivv   ii  v   v  ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_90747118_9   4635 TCTATTCAAAAAATAGTGCTGGGCCAGCTGGCTAGCCACGTGCCGAGGAA 4684
                            v     v    i        v  i    v  ?    i   vi i   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_90747118_9   4685 TTAAAGTGGACCTCTACCTTTCACCATATACAAAAATTAACATAAGATGG 4734
                          v  iv      i      iv                    vi  i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_90747118_9   4735 ATTAAACATTTAAATGTAAGACCTCAAATGAGAGTAATCCTAGAAGAAGA 4784
                           i ? v ii           v  v   iv v iv v  i        i 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_90747118_9   4785 CCTAGGAA-ACACCATTCTGGACATCAGCCTTAGGAAAGAATTTAT-AAC 4832
                          v    ?i- v i -   vv   v ii v-     v  vii   v - iv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGA 593

  chrX_90747118_9   4833 TAAGTCCTCAAAAGAAATTGCAACAAAAACGAAAATTGATAAGTGGGATC 4882
                           v v vi      v vvv         ivi     v     i v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_90747118_9   4883 CAATTAAACCAAAAAGCTTCTACACTC--AAGGAAACTATCAACAGAGTA 4930
                         iv  i   viv    i   i iii  i--     v        v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_90747118_9   4931 AACAGACAATCTATAGAGTGTGAGAAAATATTGACAAACTATGCATCTGA 4980
                           v      i i i   i  v           vi    ii  ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_90747118_9   4981 CAAAAGTCTAATATCCAAAATCTGTAAG----TC-----ACTTAAGGAGC 5021
                         i  ii v  vi      i   v i   i----  -----   i  vi vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_90747118_9   5022 AAAAAACAAATAATCACATTAAAAATTGGGCAAAATGCATGAGCAGACAG 5071
                             i        i vv   ?    v        iviiv   ii     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_90747118_9   5072 TTCTCAAAAGAAGACATACTGATGGCTAAAAAGCATATGAAAAT-TGCTC 5120
                              v        i    vi     i  v     i       v-     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_90747118_9   5121 AACATAACCAATTAT 5135
                              v ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (150 / 109)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.21 (31 / 14)  


2790 19.04 2.51 11.52  chrX_90765598_90767464      499  1375 (492)    L1M4_orf2#LINE/L1      111   908 (0)  

  chrX_90765598_9    499 CTTTTTTGTAGATAT--ATAAAATGTTATTCTAAAATTCATATG-AAATA 545
                                 i   v  -- i  iv  --  i              -    i
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCATATGGAAATG 158

  chrX_90765598_9    546 TCAAAGGACCCCTG-TAGCCAAAACAA-CTTGGAAAA----AACCAAGTT 589
                         -   i      vvi-            -    i    ----   v     
  L1M4_orf2#LINE/    159 -CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_90765598_9    590 TAGTGGCTTCTTGCACTTCCTGATTTCAAAACTTACCACAAACCCATGGT 639
                         -i v  vi  --i       ii              i     v i ii  
  L1M4_orf2#LINE/    208 -GGAGGACTC--ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_90765598_9    640 AATCATAACAGTGTGGTAATGGTATAAAGACAGATACATAGGCCAGTAGA 689
                              vi           v   i    i  i   i i    ii  i i  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_90765598_9    690 ATAGAATAAAGAGCCCAGAAATAAACCCTCACATAAATGTCAGGAAACAC 739
                                vi    i              ----------------------
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCC---------------------- 332

  chrX_90765598_9    740 ACAACCTCGATTTTATTACACATTTTTCATTCATTACACACATATTAATA 789
                         ----------------- i      -------------------------
  L1M4_orf2#LINE/    333 -----------------ATACATTT------------------------- 340

  chrX_90765598_9    790 TTTATACATTACCTCACATTATCACAATGATTTTCTACAAGGATATCATG 839
                         -----------------  vi   - v        v      i ii  v 
  L1M4_orf2#LINE/    341 -----------------ATGGTCA-ATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_90765598_9    840 ACCATTTAATGGGGAAAGGACAATTTCTTTGACAAATGGTTTTGGGAAAA 889
                               i           i i i i i  ii         vi     v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_90765598_9    890 CTGGATATCCACAGAACACACGCAAAAA---GAAATTGGGCCCTTACCTT 936
                                ?     -------i      i---   i    i   i     i
  L1M4_orf2#LINE/    423 CTGGATAKCCACA-------TGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_90765598_9    937 ATACCATGTACAAAAATTAACTCCAAATTGATCAGAGACCTAAACATAAA 986
                          i     i               v    v     ?         ii   i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_90765598_9    987 AGTTAAAACTAGAAAACTCTTAGAAAAAAA---AAAAGAAAACTTTAATG 1033
                           i        v             i    --- ii? v   ii  vi  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_90765598_9   1034 ACCTTGAGTCTGGCAATGATTTCTTGTATAAAATACCAAAGG-ACAGGGA 1082
                               i  iv       i      iv   vi i      i -   i v 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_90765598_9   1083 ACAATGGAAAAACTAGTTAAGTTGGACTCCATCAAAATTAAAAAGTTTTT 1132
                             vi      v   v   i       i               -i    
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTT 664

  chrX_90765598_9   1133 ATATATTAAAGAATGCTGGCAAAAATGTGAAAAGGCAGTCTGTGGGATGG 1182
                         i iiv i    i ii  iv   i  v        i  ii iiii i    
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_90765598_9   1183 AA-AAAATACTTGCAAATTTAATATATGATAAGAGATTGATATCTACAAT 1231
                         i -      i        ivv    v       i  i vi    i v   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_90765598_9   1232 ACATAAAGAATTTCTGTAACTGGACAACAACAAAAA-ACAATCAACCCAA 1280
                          i        i ii ii    ---   i  i     -    vi       
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACT---CAATAATAAAAAGACAAATAACCCAA 811

  chrX_90765598_9   1281 TTAAGAATTGGACAAAGGACTCAAA----CATATCTCCAACATATATATA 1326
                           ? i  v   i       i ii  ----   v       viv v     
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_90765598_9   1327 TTCAAATGATTAATAAGCACATGAAAAGATTCTTACTATCCCTAGTCAC 1375
                         --      iii                   v  i vi   v????????
  L1M4_orf2#LINE/    862 --CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.54 (117 / 46)
Gap_init rate = 0.03 (22 / 798), avg. gap size = 5.59 (123 / 22)  


 479 26.03 2.05 0.68  chrX_90778482_90783145     3577  3722 (942)    L1M4_orf2#LINE/L1        3   150 (758)  

  chrX_90778482_9   3577 GAAACACATCCCATGCTCATGAATGGGTAGAATCAATATTGTGAAAATCA 3626
                             v i        i     i  v  v   v i        v  i  vi
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_90778482_9   3627 CCATACTGCCAAAAGCAATCTACAGATTCAATGTAATTCCCATCAAAGAA 3676
                          v     v  v   vii              i i   i  i      ivv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_90778482_9   3677 CCATC-GCCATTCTTCATAGAACAAGAAAAA--AATTCTAAAATTTATA 3722
                            v -   -  i  iii    vvv  v  i--i  i        i   
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

Transitions / transversions = 1.24 (21 / 17)
Gap_init rate = 0.02 (3 / 148), avg. gap size = 1.33 (4 / 3)  

1228 24.78 2.68 2.68  chrX_90778482_90783145     3724  4171 (493)    L1M4_orf2#LINE/L1      461   908 (0)  

  chrX_90778482_9   3724 ATCTCCCATCTTCTACAAAAATCAACCAAAGATGGATCAAAGACTTAAAT 3773
                          i   v  i v v         i   iv  i        ?    i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_90778482_9   3774 CTAAGATCTGAAATTATGAACATTCT-AGAAGATTACATTGA--TAAATC 3820
                         v     v  i   i   i  - i   -      vv    v i--      
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_90778482_9   3821 TA---GACTTTGGCTGAGGCAAAAACTTCATGACCAAAAACCCAAAAGCT 3867
                          v---   i    v v      viii   v iivi vi vv        v
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_90778482_9   3868 AATGCAGTAAAAACAAAAATAAGTAGATGGGACCTGATGAAACTAAAAAG 3917
                         v v   ii    iv       ii  i  v    i v  v   v v    i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_90778482_9   3918 CTTTTGCACAGCAAAAGAAATAATCAGCAGCAGAGTAAACAGACT-CCCA 3966
                               ii vv    i  v iv    --  - i   i  v    v-    
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCA--AG-AAAGTGAAAAGACAACCCA 706

  chrX_90778482_9   3967 CAGAAGGGGA-----TATTCACAAACTATGCATCCGACAAAGGACTAATA 4011
                              v    -----    ii    ii  ii   i  i  i     vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_90778482_9   4012 TCCAGAAAGTACAAGGAACTTAAACAAATCAGCAAGAAAAAAACAAACAA 4061
                                vi  i  i     ivv    v   ii  v     i     ---
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA--- 803

  chrX_90778482_9   4062 CAAGTAACCCCATCAAAAAGTGGGCAAATAACCTGAATAGACAATTCTCA 4111
                         ----      v  i?    i        vi ii          v     v
  L1M4_orf2#LINE/    804 ----TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_90778482_9   4112 AAAGAAGATATAAAAAATCCCCAATAAATATATTTAAAAATGTTCAACAT 4161
                                     v   - vv       ii i  vv   i   i       
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAA-TGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_90778482_9   4162 CACTAATTAT 4171
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.22 (60 / 49)
Gap_init rate = 0.02 (10 / 448), avg. gap size = 2.40 (24 / 10)  


2851 27.54 1.33 0.88  chrX_90789200_90795001.rev     4407  5310 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90789200_9   4407 TGAAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4456
                           i   i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90789200_9   4457 GGCCATACTGCCCAAAGTAATTTGTAGAGTCAGTGCTATTCCCATTAAAT 4506
                            v     v      v i  i ii   v   ii  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90789200_9   4507 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ATTTTAATATTAAT 4555
                          v   vivi v  i  ii     v v  v  i-  -  ii   v   v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_90789200_9   4556 ATGGCACAAA---AAAAGAGCTTGACTAGTCAAAAAAATCCTTAGCAAAA 4602
                             ---   ---  ii  v iv  v   i     v    i v iv  i 
  L1M4_orf2#LINE/    150 ATGG---AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_90789200_9   4603 ATATCAAAGCTGGAGCCCTCATGCTACCTAACTTCCAACTATACTACAAC 4652
                          v v     i     vv    ii  v  i  i   v  viv        v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_90789200_9   4653 ATTACGGTAATAAAAACAGCATGGTACTATTACAAAAACAGACACATGGA 4702
                         ii   i     v  i    ii       ivi i  ii i     i  i  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_90789200_9   4703 CCAATGGAACAGAATAGAGATCTCAGGAATAAAATCACACACCTACAACC 4752
                         i        i     v    vii   i      vi  i   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_90789200_9   4753 T-CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGAAAGG--TATT 4799
                         v-i    i  i     ivv  v   i v  vv       i  i --  v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_90789200_9   4800 CTTTATTTAATAAATGGTGCTGGGAAAACTGGCCAGCCATATGCAAAAAA 4849
                             -- i  i              v      vi ?   i        i 
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_90789200_9   4850 TTGAATCTAGTCCCCTTTTTTAAAGCTTATA-AAAAATTAATTCAAGATG 4898
                         v    vi i v     vii i v v v    -         i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_90789200_9   4899 GATTGAAGACTTAAATGTGAAACCCAAAACTATAAAAACTCT-GGAAGAA 4947
                            ii?    i       i i v i            -    -i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chrX_90789200_9   4948 CATCTAGACA-ATACCATTCAGAACATAGGCATGGGTAAAAATTTCATGA 4996
                         v iv   i?i- v i -   ivi  v v  vv i  i  vii    v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_90789200_9   4997 CAAAAACACCAAAAGCAATTGCAACAAAAGCAAAAACTGACAAATGGGAT 5046
                         vv vi            vvv          v     iv  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_90789200_9   5047 CTAATTAAACCAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGT 5096
                         i v  i   viv  i i   i  ii vv    iv v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_90789200_9   5097 GAACAGA-AACCTATAGAATGGGAGAAATTTTTTGCAATTTATCTGTCTA 5145
                            v   -    i i             v v       v i  v i   i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_90789200_9   5146 ACAAAGGTCTAATATCCAGCATCTACAAGAAATTTAAACAAATTTACAAG 5195
                          i  i  v  vi       v  v  i  ii  i ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_90789200_9   5196 AAAAAAACAAACAACCCCATTGAAAAGTGGGCAAAGGATATGAACAGACA 5245
                              i     i     v   ?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_90789200_9   5246 CTTCTCAAAAGAAGATATTCATGTGGCCAACAAACATATGAAAAAA-GCT 5294
                         i     v           v  vi       i  i  i       i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_90789200_9   5295 CAACATCACTGATTAT 5310
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.43 (20 / 14)  


3232 26.87 0.44 0.44  chrX_90813445_90819720     4876  5783 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90813445_9   4876 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                               i i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90813445_9   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCATGC 4975
                            v     v     iv i  i           i  v     i    viv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90813445_9   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_90813445_9   5024 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_90813445_9   5074 AACAAAGCTGGAGGCATCACACTACCAGACTTCAAACTATACTACAAGGC 5123
                                i      vv       v  vi i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_90813445_9   5124 TACAGTTTCCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5173
                               vvi   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_90813445_9   5174 AATGGAACAGAAC--AGTGCCCTCAGAAATAACGCCGCATATCTACGACT 5221
                                i    i--  v i  --        vv  ii i  i  i iii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_90813445_9   5222 ATCTGATCTTTGACAACCCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5271
                          vi    i  i     vvv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_90813445_9   5272 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5321
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_90813445_9   5322 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5371
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_90813445_9   5372 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5421
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_90813445_9   5422 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5471
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_90813445_9   5472 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5521
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_90813445_9   5522 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5571
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_90813445_9   5572 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5621
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_90813445_9   5622 AGGGCTAATCTCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5671
                         i  i  vi v        v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_90813445_9   5672 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5721
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_90813445_9   5722 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATTCTCATC 5771
                           v        i  vi viii     v  i          i  v    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_90813445_9   5772 TTCACTGGCCAT 5783
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (136 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3254 26.43 0.55 0.55  chrX_90881067_90887346.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90881067_9   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_90881067_9   4932 GGCCATACTGCCCAAGGTAACTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i ii           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_90881067_9   4982 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTATAAAGTTC 5028
                          v   i-       i  -i     -   -- v  i  - iiv    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_90881067_9   5029 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5078
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_90881067_9   5079 GAACAAAGCTGGAGGCATCACACTACCAGACTTCAAACTATACTACAAGG 5128
                                 i      vv       v  vi i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_90881067_9   5129 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5178
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_90881067_9   5179 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACGAC 5226
                                 i    i--    i  --        vv  ii i  i  i ii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_90881067_9   5227 TATCTGATCTTTGACAAACTTGAGAAAAACAAGCAATGGGGAAAGGATTC 5276
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_90881067_9   5277 CCTATCTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5326
                         i  v ii  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_90881067_9   5327 TGAAACTGGATCCCTTCCTTACACCTTATATAAAAATCAATTCAAGATGG 5376
                             ii    i    v   i     v    i      i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_90881067_9   5377 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACGCTAGAAGAAAG 5426
                           i ?    i    i  v   v       i      vivi         i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_90881067_9   5427 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5476
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_90881067_9   5477 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5526
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_90881067_9   5527 ATTAAACTAAAGTGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5576
                           i   v v  ivi   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_90881067_9   5577 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5626
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_90881067_9   5627 AAGGGCTAATATCCAGAATCTACGATGAACTCAAACAAATTTACAAGAAA 5676
                          i  i  vi          v  ii v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_90881067_9   5677 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5726
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_90881067_9   5727 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5776
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_90881067_9   5777 CATCACTGGCCAT 5789
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2629 26.22 2.88 2.43  chrX_90919864_90922993.rev     1736  2639 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_90919864_9   1736 TGGAAAAATATACCTTACCATGCTCATGGATAGGAAGAGTCAATATTGTC 1785
                               i    -  ----    i        v      v i        i
  L1M4_orf2#LINE/      1 TGGAAAGATAT-CC----CATGTTCATGGATTGGAAGACTTAATATTGTT 45

  chrX_90919864_9   1786 AAAATGTCCACACTGCCCAAAGTAATTTATAGAT-----GGTATTCCCAT 1830
                           i   v v i   v      v i  i  i    ----- vv  i  i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_90919864_9   1831 TAAACTACCATTGGCATTCTTCACATAATTAGAAA--AAAAAACT-ATTT 1877
                         i   v v   viv  v  i  ii  ------    --i v  i  -  ii
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCA------GAAATTGACAAGCTGATCC 139

  chrX_90919864_9   1878 TAAAATTCATATAGAATCAAAAAAGAGACT--ATATACTTAAGACAATTC 1925
                                     i   -- viv   i   i--iv   vii  i     ii
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chrX_90919864_9   1926 CAAGCGAAAACAACAAAGCTGGAGGCATCACACTACCTGACATCAAACTA 1975
                         ii ivi i  v       i      vv       v  ii iv     viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_90919864_9   1976 TACTACAAGGCTACAGTAACCAAAATAGCATGGTACTGCTACAAAAACAG 2025
                                 i          i   i i  ii        vi i  ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_90919864_9   2026 AAACATAGACAAATGCAACAGAATAGAGAACTCAGAAATAAGACTGCACA 2075
                          v i     iv    v  i     v    iii         iv iii   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_90919864_9   2076 CCTACAACCATCTGATCTTTGACAAACCTGAAAAAAAAAAAACAAGCAAT 2125
                         ii  iiii  vi    i  i     ivv  vv  i v-----  vv    
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-----CATTCAAT 382

  chrX_90919864_9   2126 GGGGAAAGGGTTCCTTTTTTAATAAATGGTGCTGGGAGAACTGGCTAGCC 2175
                                 ii vvii    i  i              v      v  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_90919864_9   2176 ATATGCAGAAAATTGAAATTGGACCCCTTCCTTACACCTTTTACCAAAAT 2225
                          i     i  i v    i          v   i     v v   v     
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_90919864_9   2226 TAACTCAAGATAGATGAATGAATTAAATGTAAAGCCCAAAACTATAAAAA 2275
                                 i  i   v ?v  vi         iiv i            v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_90919864_9   2276 CCCTAGAAGAAAATCTAGGCA-ATACCATTCAGGACATAGGCAAGGGCAA 2324
                         i i          iv    ?i- v i -   iv   v v  vvvi     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA 581

  chrX_90919864_9   2325 AGGCATCAT-GATGAAAATGTCAAATGCAACTGCAACAAAAGGAAAAATT 2373
                         v  iv  v -   - vi iii    v   vvv          i      v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_90919864_9   2374 GACAAATGGGATCT------AATTAAAGAGCTTCTGCACAACAAAAGAAA 2417
                           i    v   ii ------       i -   i  ii vv    i  v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA 679

  chrX_90919864_9   2418 CAATCATCAGAGTGAACAAACAACCTACAGAATGTGAGAAAATTTTTGCA 2467
                          v    vv i      v i      i        v        v      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_90919864_9   2468 ATCTATCCCTATGATAAAGGTCTCATATACAGAATCTATAAGGAACTTAA 2517
                          vii  viv v      i  v  ii   v      v     i     ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_90919864_9   2518 ACAAATTTACAAGAAAAAAA-----AAC---ATTAAAAAGTGGGCAAAGG 2559
                             v iv i  v     i -----   ---   ?    i          
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_90919864_9   2560 ACATGAACAGACAATTCTCAAAAGAAGATATACATGCGACCAGAAAACAT 2609
                          iv    i     v     v              vii i   iv  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_90919864_9   2610 ATGGAAAAAAAGCTCAACATCACTGATCAC 2639
                            -    i v           ????????
  L1M4_orf2#LINE/    880 ATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (134 / 99)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.67 (48 / 18)  


1142 27.39 3.50 0.00  chrX_91020692_91022683.rev      502   815 (1177)    L1M4_orf2#LINE/L1      200   524 (384)  

  chrX_91020692_9    502 ACAAAGCTTGGGGCATCACATTTTATGATTTCAAAGTATATTGCAAAACT 551
                               i v i  vv     i  ivii        iiv  i i    i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_91020692_9    552 ATAGTAAACAAAACAATATGGTGCTGGTATAAAAACAGACATATAAACTG 601
                          i     v   i   i i    i    i    ii i         i iii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_91020692_9    602 ATAGAACAGAATACAGAACCCAGAAATAAATCCACATGTATAGAGTCAAC 651
                           i   i     vv   ii           i   i ii v  vi     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_91020692_9    652 TAATCTTAGACGAGAGCACCAAGAACACACAATGGCAAAAGGATTGTCTC 701
                          i  i  v   i  i ii      v  iv      vi    i  v    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_91020692_9    702 TTCAACAAACTGTGTTGGGGAAACTGGATAGCAAGACCCTCAA-AATAAA 750
                                  iv   i    iv         ? v v iv vv  -   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_91020692_9    751 AGTGCACCCCTAC-----ACCACTTACAAAAATTAACTTGAAAT-----A 790
                         iv  v        -----    iv              ii    ----- 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_91020692_9    791 AAGACTTCAGTATAAGACCTGAAAC 815
                         ?    i v i i     v  i    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAAC 524

Transitions / transversions = 2.11 (57 / 27)
Gap_init rate = 0.01 (3 / 325), avg. gap size = 3.67 (11 / 3)  

1204 21.74 11.11 1.21  chrX_91020692_91022683.rev     1088  1501 (491)    L1M4_orf2#LINE/L1      454   908 (0)  

  chrX_91020692_9   1088 GACTCC-ATCTCAAACAACA-ACAACAACAAACAAACAAAGTGAA---AA 1132
                            i  - i    v  v i -    v  iv   v--    i  i ---? 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACT--CAAAATGGATCAWA 501

  chrX_91020692_9   1133 AACACAAA--------CTGACACCA-AAAACTCCTAGAAGAAAACATCAG 1173
                         i  vi   --------  i v  i -       i             vi 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_91020692_9   1174 GGAAAAGTTCCTTGACATTGGTTTTGGTAATGATTTTTTT--TATGACAC 1221
                         ? v   vi i v    v    v  v  i    i   i  v--        
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_91020692_9   1222 CAAAAGTACAA-CAACAAAAGCAAAAATAAACAAGTGGAATTGCATTAAA 1270
                               i    -         v       i i  i v i i v   i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_91020692_9   1271 CTAAAAAGCTTATACACAGCAAAGGAAACAAACAATAAAATGAAGAGGCA 1320
                         v v    i   v iii vv       v  v v   v   i    i  i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_91020692_9   1321 ACCTAAAGAATGAAAGAAAATGTTT-----------ATCTCGTAGGGGGT 1359
                            i v      ii       i   -----------    vi  i   ii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_91020692_9   1360 TAATATCTAAAATATATAAGAAAC----ACAACTCAAGAGTAAACAAAAA 1405
                          vi    i i         ii   ----         v i    --  i 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA--AAGA 799

  chrX_91020692_9   1406 CCAAATAATACAATTTAAAAATGGGTAAAAGA-----ATAGACATTTTCC 1450
                          -      iv     ?         i   i  -----          ii 
  L1M4_orf2#LINE/    800 C-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_91020692_9   1451 CAAAGAATATATACAAATGGCCAA---------GGAAAGGTGCTCAGCAT 1491
                                v                --------- i    i      i   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_91020692_9   1492 CACTAATCAT 1501
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.64 (54 / 33)
Gap_init rate = 0.03 (14 / 455), avg. gap size = 3.64 (51 / 14)  


2440 25.70 1.91 0.59  chrX_91032843_91034532.rev      519  1199 (491)    L1M4_orf2#LINE/L1      219   908 (0)  

  chrX_91032843_9    519 ACTTCCACAATGGTTGAACTATACTACAAGGCTACAGTAACCAAAACAGC 568
                               -    vvivi    -        i          i   i    i
  L1M4_orf2#LINE/    219 ACTTCC-CAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_91032843_9    569 ATGGTACTGGTAC-----------CATAGATCAATGGAACAGAAC--AGA 605
                         i         i i-----------i              i    i--   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_91032843_9    606 GCCCTCAGAAATAACGCCGCATATCTACAACCATCTGATCTTTGACAAAC 655
                          i  --        vv  ii i  i  iiii  vi    i  i     iv
  L1M4_orf2#LINE/    317 GTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_91032843_9    656 CTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGC 705
                         v  vv  i v  vv            i  vvi  v  i  i         
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_91032843_9    706 TGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCT 755
                              v      v  ?   i   i i  iiv    ii    i    v   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_91032843_9    756 TACACCTTATACAAAAATCAATTCAAGATGGATTAAAGACTTAAACGTTA 805
                         i     v           i  i    i      i ?    i    i  v 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_91032843_9    806 GACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAG 855
                           v       i      vi i           v    ?i v viv   iv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_91032843_9    856 GATGTAGGCATGGGCAAGGGCTTCATGTCCAAAACACCAAAAGCAATGGC 905
                           iv v  vv i     v  i   v ivvi vi            vvi  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_91032843_9    906 AACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCT 955
                                  v     v  i    v   ii v  i   v v  i i   i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_91032843_9    956 GCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGG 1005
                          ii vv    i  v    i  vv i      v  i     i   i     
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_91032843_9   1006 GAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAAT 1055
                                 v  i    vii ivi      i  i  i  vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_91032843_9   1056 CTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCA 1105
                         v  i  v      vv    v iv i  v     i     i     v  i?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_91032843_9   1106 AAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTAT 1155
                             i     i     iv    i     i     v        i  vi v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_91032843_9   1156 GCAGCCAAAAAACACATGAAAAAATGCTCATCTTCACTGGCCAT 1199
                         iii     v  i          i       v v   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (100 / 71)
Gap_init rate = 0.01 (5 / 690), avg. gap size = 3.40 (17 / 5)  


3234 22.65 1.71 5.34  chrX_91055543_91058173.rev     1205  2140 (491)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_91055543_9   1205 GATACCCCATGTGCTTAGATTGGAAGAATTTATAGTGTTACCATGTCTAT 1254
                             i       v v i          v  v   v     vv   v v  
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_91055543_9   1255 GATATCCAAAGCAATGTACAGATTTAATACAATTCCTATCAATATCCCAA 1304
                         iv vi     vii  v        i  ii    i        v      i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_91055543_9   1305 TAGCATTTTTCATGGAAATAGAACACAAAC-AACTCTAAAATTCATATGG 1353
                         iv  v     iiii     v  ---   i -i ii               
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGA---CAAGCTGATCCTAAAATTCATATGG 153

  chrX_91055543_9   1354 AACCACAAAAACCTCAGAATAGCTAAAAGACTCTTGAGGAAGAAGAACAA 1403
                           vii   iiiv i         i    v v      ii           
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_91055543_9   1404 AGCTGGAGGCATTACACTACTTGAGTCCAAA--CTACAGTACAAAGCTAT 1451
                           i      vv i     v iii v i    --i   --          i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGCTAC 251

  chrX_91055543_9   1452 AGTAATTAAAACAGTATGGTACTGGCATAAAGACAGACACATAGGCCAAT 1501
                               i  i     i              i  i     i    ii    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_91055543_9   1502 GGAACAGAAT--GGAGTCCATTAATAAACCCACACATAGACAGTTAAGTA 1549
                             i     --i       vv          i    vv ii  i  v i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_91055543_9   1550 ATCTTCAAGAAAGGTACCAAGAATGCACAATAGGGAAAGCATAGTCTCCT 1599
                           i   i v  i   i      viiiv    i       v       ii 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_91055543_9   1600 CAATAAGTGGCACTGGGAAAACTGGATATCCATATTCAAAAAGAAGAAAC 1649
                            i  i   ii      v         ?   i  v     ii v   ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_91055543_9   1650 ATAGACTCTTATCTTACATCACACACAAACATCAACTCAAAACTGATTA- 1698
                         - i   i i  i  i   i  i i     v  i         iv   i -
  L1M4_orf2#LINE/    452 -TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_91055543_9   1699 AGACTTAAATATAACTCATAAAACTGTAAAATTCCTAGAAGAAAACAGAG 1748
                             i     i   vvvv       i     i  i            v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_91055543_9   1749 G---AAAGCTCCTTGACATTTGTCTCAGCAGTGTTTTTTTTTTTGTTTGT 1795
                          ---   v  i v    v  v vi vi   i  ---------------  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATG---------------GT 585

  chrX_91055543_9   1796 TTTTTTGTTTTTTTTTTTTTAACGTGACACCAAAAGGATAGGCAACAAAT 1845
                           i  v -------------- ii            v i i        v
  L1M4_orf2#LINE/    586 TTCTTAG--------------ATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_91055543_9   1846 GCAAAGATAAACAATTGGAACTACATTAAACT--AAAACATTTCTGCATA 1893
                          v   i   i i  v v i   v   i   v --     v   v   v -
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT- 670

  chrX_91055543_9   1894 GCAAAGGAAACCACTAAA----TGAAAAGGCAACCTACAGAATAGGAGGA 1939
                         -       v  i ii  i----       i     i       i    i 
  L1M4_orf2#LINE/    671 -CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_91055543_9   1940 CATATTTACAAATCACATATCTGATAAGGGGTTAATATCTAAAATATACA 1989
                         v      i       i              ii vi    i i      i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_91055543_9   1990 ACTAACTCATACAACTAAATACTTTTGAAAGATTATAAAACACCGAATAA 2039
                          vv     v       v    -------------      viv i     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATA-------------ATAAAAAGACAAATAA 806

  chrX_91055543_9   2040 TCCAAT-GAACAATATGCAAAAGACTTGAATAGTCATTTTTCCAAAGACA 2088
                         i     -?  v   iv     i  i        v     i        vi
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_91055543_9   2089 AAAAAATGATGGCTAACAAGCACATGAAAATGTGTGCAACATCACTAATC 2138
                          v v vvi     i  i             vi  iv        ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_91055543_9   2139 AT 2140
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.62 (130 / 80)
Gap_init rate = 0.02 (15 / 902), avg. gap size = 4.40 (66 / 15)  


2670 25.23 1.68 1.29  chrX_91061973_91066869.rev     3181  3953 (944)    L1M4_orf2#LINE/L1        2   777 (131)  

  chrX_91061973_9   3181 GAAAAAAAATTCCATTTTCATGGATTGGAAGAATGAATGTTGTTAAAATG 3230
                          i   i v  i    v                v v   i       i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_91061973_9   3231 TCCATACTACCCTAAGCT-ATCTACACATTTAATGCAATCC-TATCAAAA 3278
                         v v     -   i  ii -       v   i  i       -        
  L1M4_orf2#LINE/     52 GCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91061973_9   3279 TACCAATGACATTCTTCACAGATTTAGAAAAAAAAATCCTAAAATTAATA 3328
                          v   iivi v  i  ii    vv v  v  ivvi           v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_91061973_9   3329 TGAAACCACAAAAGACCCAGAATAGCCAAAGCTATTCTAAGCGA-AAGAA 3377
                           i  vii   ii                 i v  ii i ivi -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_91061973_9   3378 CAAAACTTGAGGAATCACATAACATGTCC----TCAAATAATACTACAAA 3423
                             ii v     v     i---- vi  ----     vvv         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACAC----TTCCCAATTTCAAAACTTACTACAAA 246

  chrX_91061973_9   3424 GCTATAGTAACCAAAACAGC-TGGAACTTGCATGAAAACAGACACATAGA 3472
                             i     i   i    i-   v   v    i ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_91061973_9   3473 TCAATGGAACAGAATAGAGAACGCAGAAAGAAATCCACACCCCAAGAGTG 3522
                                  i     v    iiv      v   i   i  viiv vi  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_91061973_9   3523 AATTCATTTTTGACAAAGGTTCCAAGAACATATCATGGGGAAAGGCCAGT 3572
                             v     i     i   v      v   viv          ivi   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_91061973_9   3573 TTCTTCAATAAATGGTGCTGGGAAAACTGGATCCCTATATTCAGAAGAAT 3622
                         i i     i              v        v? i i  v  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_91061973_9   3623 GAAACTAAACCTCTATCTCTTGCCATATACCAAAATCAAATGAAAATGGA 3672
                            ii ii   i   i   vii        v     i  v v        
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_91061973_9   3673 TTAAAGACTTAACTCTAAGACCCCAAAGTCAAAGGCTATTACAAGAAAAC 3722
                          i ?    i   v v     v iv   v vv  ii  v   v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_91061973_9   3723 ACTGAAA-AAATCTCCAGGATATTGGTCTGGGCAAAGAATTCTTGAGCAA 3771
                          iv i?i-      i iv  iv    vi i     v iv     -  -- 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AG--A 593

  chrX_91061973_9   3772 TA-GACAATAAGAGCA--GGCAACCAAAGAAAAAAATGGACAAGTGGGAT 3818
                           -    vi  i    --i     v          - i  i  i v   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGAC 642

  chrX_91061973_9   3819 AACATCAAG-TTAAGAAGTTTCTGCACAACAAAAGATACAATAAAAAAAG 3867
                         vv      i-    i  v   -  ii vv    i  i  v  v  i    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_91061973_9   3868 TGAAGCAATAACTTACAGAATGGGAGAAAATATTTGCAAACTACCCATCT 3917
                             ivi i   ii                          ii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_91061973_9   3918 GACAAGAGATTAATAATCACAACATATAAAGAGCTC 3953
                           i   i  i vi  vi  v  i         i   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

Transitions / transversions = 1.46 (114 / 78)
Gap_init rate = 0.02 (15 / 776), avg. gap size = 1.53 (23 / 15)  

 650 17.73 0.00 0.71  chrX_91061973_91066869.rev     4266  4406 (491)    L1M4_orf2#LINE/L1      769   908 (0)  

  chrX_91061973_9   4266 AAAGAGCTCAAATAACTCTGTAGGAAGAAAATCTAATAATCCAATCAAAA 4315
                              i   vv i     vi  iv  i  i - v     i     i?   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAA 817

  chrX_91061973_9   4316 AATGAGCAAAAGATTTGAATAGACATTTCTCAAAACAAGACATACAAATG 4365
                             i     i                    v   v    i         
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_91061973_9   4366 GCAAACAGGCATATGAGAAGGTGCTCAACATCACTGATATC 4406
                           v  i i   i    i   i            ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.01 (1 / 140), avg. gap size = 1.00 (1 / 1)  


 361 16.67 1.19 1.19  chrX_91121725_91124177.rev      420   503 (1950)  C L1M4_orf2#LINE/L1   (0)   908   825  

C chrX_91121725_9    503 AAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACA 454
                                v    i     i     v        i  vi viii     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

C chrX_91121725_9    453 AGCATATGAAGAAGA-GCTCATCATCACTGGTCAT 420
                             i     -    -     v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.00 (2 / 2)  

2314 26.29 5.03 3.47  chrX_91121725_91124177.rev     1069  1962 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91121725_9   1069 TGCAAAAACATTCCATGCTCATGGATAAGAAGGATCAATATTGTTAA-AT 1117
                           v   i i  i     i        vi    iv i           -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91121725_9   1118 GGCCATACTGCCCAAAGCAATTTACAGATTCAGTGCTATTATTATCAAAC 1167
                            v     v      vii  i          ii  v  ivi       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91121725_9   1168 TACCAATGACATTCTT--CAGCAAATTAGAAAATGCT-ATCTTTAAATTT 1214
                          v   iivi v  i  --   -     -  v  -   -   i v     i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG-AAATT-GACAA-GCTGATCCTAAAATTC 147

  chrX_91121725_9   1215 ATATGAAACTAAAAAACAAACAAACAAACAAAAAAATCAACCCA-AATAG 1263
                              i  v i-----------------   iii -----    -     
  L1M4_orf2#LINE/    148 ATATGGAAATG-----------------CAAGGGA-----CCCAGAATAG 175

  chrX_91121725_9   1264 CCAAGGCAATCCTAAGTAAAAAGAACAAAGTTGGAGGCATCACATTACTC 1313
                             ii     i i iv  i                 vv     i v i 
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_91121725_9   1314 AACCTCAAACTATACTATATGGCTACAGTAACTAAAACATCATGGTACTG 1363
                           ii     viv     i vi          ii  i   vii        
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_91121725_9   1364 GCATCAAAAAAGACTCACTGACCAATGGAACAGAAGACAGAGCCCCCAAA 1413
                             v ii v    vi iv  i        i    vvv    i  vv   
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_91121725_9   1414 TAACGCAACACACCTACAATAACTTGATCTTCCAGAAAT-TGACAAAAAC 1462
                            vv v i   ii  iii v v     i   v v  iv-  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_91121725_9   1463 AAGCAATGGAGAAAGGACTCCCTATTCAATAAATGGTGCCGGAAC----- 1507
                          vv      i     i ivvi  v     i         i  i  -----
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_91121725_9   1508 --------------------------TGGACCCATTCCTCTCACCATACA 1531
                         --------------------------       v v    v       i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_91121725_9   1532 TAAAAATCTACTTAAGATGAATTAAAGACTTAAATGTAACACCTAACA-T 1580
                         i      iv   i  i   i  i ?    i         v v    v - 
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_91121725_9   1581 ATGAAAACTCT-GGAAGACAATTGAGGCAATACAATTCTGC---ACATAG 1626
                           -        -i     v  ivv   ?i---i  v   v ---  v v 
  L1M4_orf2#LINE/    526 AT-AAAACTCTTAGAAGAAAACATAGGNG---TAAATCTTCGTGACCTTG 571

  chrX_91121725_9   1627 GCTCTGGCAAAGATTTTATTACA-ATT-CGCCAACAGGAAATGAAATAAA 1674
                          v iv     v i   i-   v -  v- i    v  v v v v  i   
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTC-TTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_91121725_9   1675 -TCAAAAGTTGACACATGAGAACTAATTAAACTCAAGAACTCCTACACAG 1723
                         -vv    i v  i v  vi  vi v  i   v i  i    ii iii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_91121725_9   1724 CAAAAAGAAACTATCAACAGAGTAAACAGACAACCTACAGTATGGGAGAA 1773
                             i-  v        v i   i  v        i    v         
  L1M4_orf2#LINE/    671 CAAAG-GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_91121725_9   1774 AATATTTTCAAAGTATGCATCTGACAAAGGTCTTATATCCAGAATCTACA 1823
                                v    vi  ii      i  i  v   i          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_91121725_9   1824 AAGTACTTAAACAAATTAATGAGCAAAAATCAAACAATCCCATTAAAAAG 1873
                            v   ivv    v i   i vv    iv    i  i  v   ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_91121725_9   1874 TAGGCAAAGGACATGAACATATACTTTGCAAAAGTGTACATACATGTGGC 1923
                          i         iv    i v i i  iv v    viv i     vi    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_91121725_9   1924 CAACAAGCATATGAAAAAATGTTCAGTATCACTAATTAT 1962
                            i     i       i   i   ii    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (128 / 104)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.62 (76 / 21)  


2933 26.61 2.82 0.90  chrX_91126255_91131138.rev     3507  4393 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_91126255_9   3507 AAGATATTCCATGCTCATCAATCACAAGAGCCAATATTGTTAAAATGTCC 3556
                                i     i    vi  iiv    vii           i   v v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_91126255_9   3557 ATGCTACCCAAAGGAATTTACAGATTCAATGCAA----------AATACC 3596
                           i  v      vvi  i           i    ----------   v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_91126255_9   3597 AATGACATTTTTCACACAAATGGAAAAAAAAATAATTCTAAAAGGTATAT 3646
                          iivi v     ii  v    v  v  ---iv i  i      vvi    
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAA---GCTGATCCTAAAATTCATAT 151

  chrX_91126255_9   3647 GGAATCACAAGTGACTCATAATAGCCAAACCCATCCTGATCACAAGGAAC 3696
                             vii    v   i  v          v v   i   vv vi i    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_91126255_9   3697 AACACTACAGGAATCATATTACTTGACTTCAAATTATACTATGAAGCTAT 3746
                           vii iv    v   i i v iii i      viv     ii      i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_91126255_9   3747 AATAACCAAAACAGCATGGTACCAGCATAAAAA--GACACACAGATCAAT 3794
                          i   i   i    ii      ii      ii --    i i        
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_91126255_9   3795 GGAACAGCACAGACAACTCAGAAACAAATCCATACACCTGCAGTGAATTC 3844
                             i  v iv  v iii      i   i       ii iii  v    v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_91126255_9   3845 ATTTTTGACAAAGGTACCAAGAACATACACTAGAGAAAAGTCAGTTTCTT 3894
                              i     i   i      v   v  v i i    iivi   i i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_91126255_9   3895 CAATGGATGATGCTGGAAAAACTGGATATTCGTAGTCAGAAGAATGAAAC 3944
                            iii   i      i v         ?i ii vv  i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_91126255_9   3945 TTGATCTCTGTCTCTCACCTTACAAAAATATCAAATCAAAATCAATAAAA 3994
                          v  i i  ii   v    v  i v   v  i  v       vi  -v ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT-CAW 500

  chrX_91126255_9   3995 AGACTTAAAT-------CTAAGACTATGAAAGTACTACAAGAAAACTTTG 4037
                             i     -------    i     i   v vi  v        v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_91126255_9   4038 GAGAAACTCTCTAAGACATTGTTTTGGGCAAAAATTTCTTCAGTCATATC 4087
                          ? v  v   iiiv   v   vv  i     vii      -  vi  iv 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGAC 599

  chrX_91126255_9   4088 -CCAGAAGCACAGGCAACCAAAGCAAAA-TGGACAAATGGAATCACATCA 4135
                         -   i       i     v    v    - i  i    v i iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_91126255_9   4136 A-GTTAAAAAGCTTCTGCACAGCAAAATATATTATCAACTAAGTGAGGAG 4184
                          -i       -   i  ii vv    iv i i      vv      ii  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_91126255_9   4185 ACAGCCCAGAGAAAGGGAGAAACTATTTGGAAACTATCCATCTGACAAGA 4234
                            i    v    v        v      v   ii  vi      i   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_91126255_9   4235 GATTCATAATCAGAATATATAAGGAGCTCAAACAACTCTAGAGGAAAAAA 4284
                           i ii  vi            i  i   vv       v v iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_91126255_9   4285 AATCTAACAATCCAATT-AAAAATGGGCAAAAGATTTGAATAGACATTTC 4333
                          -- v  i  i      -             i                  
  L1M4_orf2#LINE/    799 A--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_91126255_9   4334 TGAATAGAAAACATG-AAATGGCAAACAGGCATATAAAAAG-TGCTCAAC 4381
                          vv v    i i  i-       v  i i   i  i     -        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_91126255_9   4382 ATCATTGATCCT 4393
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.02 (14 / 904), avg. gap size = 2.36 (33 / 14)  


3265 26.65 0.55 0.55  chrX_91275706_91282104     4999  5906 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91275706_9   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5048
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91275706_9   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATAAAGC 5098
                            v     v     iv i  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91275706_9   5099 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5145
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_91275706_9   5146 ATATGGAACCAAAAAAGAGCACGCATCGCCAAGTCAATCCTAAGCCAAAA 5195
                                 viiv  ii  v vv v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_91275706_9   5196 GAATAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGA 5245
                            i    i      vv   ii  v  ii i      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_91275706_9   5246 CTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGAT 5295
                                  i   i    ii         i i  ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_91275706_9   5296 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5343
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_91275706_9   5344 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5393
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_91275706_9   5394 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAAGC 5443
                         i  v  i  i              v      v  ?   i i i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_91275706_9   5444 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5493
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_91275706_9   5494 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5543
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_91275706_9   5544 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5593
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_91275706_9   5594 GAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5643
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_91275706_9   5644 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5693
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_91275706_9   5694 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCCACCTACTCATCTGACA 5743
                         v  i     i   i             v  i  v vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_91275706_9   5744 AAGGGCTAATATCTAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5793
                          i  i  vi    i     v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_91275706_9   5794 GAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5843
                         i i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_91275706_9   5844 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5893
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_91275706_9   5894 CATCACTGGCCAT 5906
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1678 28.95 4.97 3.57  chrX_91303509_91305278.rev      502  1285 (485)    L1M4_orf2#LINE/L1      114   908 (0)  

  chrX_91303509_9    502 TTTTGGAGGTATAAATAAGCT-ATTCTAAAATT-ATATGGAAAGGCACAT 549
                              v  iv  vi i     -  i        -         v   viv
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chrX_91303509_9    550 GACCTAGAATAATTAAAACAATTCTGAAAAAGAA---TAAAATGGAAGGA 596
                             i      iii        ii          ---i   i v i    
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_91303509_9    597 ATCACTCTACCTTACATTAAGGCCTATTAAATAGCTACAATAATCAAGAC 646
                         v    v  v  iv iv i  ii i  i  v v       i          
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_91303509_9    647 AGTGAGGTACTGACAAGGGAATAGAAACATAGATAACTGGAACAAAGTAG 696
                             v       i  vii i     v i      v v     i i i v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_91303509_9    697 ACCACCCAGAAATAAATTCTCACAAATGTCTGATC----GATTTTTGAAA 742
                          vvii           -- i  i v  v v  i  ----      i  v 
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAA--CCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_91303509_9    743 AGGGCGCAAAAGTGATTCAATGAAGGAAGGGTATCCTTTTCTATAAGTGT 792
                             i  v  iiiv        ii i   ii  vi      v i  i  v
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_91303509_9    793 TTCTCATGCAATTGGATATTTATAAATAAAATAATGTACCTTGATTTAAA 842
                          v  vivi   i      ?ii i vii    v    v vi v  iiivv 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_91303509_9    843 CTTCATACTTTACACAAAAATTAATTTAAAATTTAATTCAAAAATTAATT 892
                          i   i  iv  i           i i     ---------ii  -----
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAAT---------GGAT----- 497

  chrX_91303509_9    893 CAAAATTAACTCAAATGTAAGGTGTAAAATTATAAAACGTCTACAAAAAT 942
                           ? i---  ii         ivv     i        vii  v  i  v
  L1M4_orf2#LINE/    498 CAWAG---ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_91303509_9    943 ATTT---TTTAAAATTTCAGAATTTAAGGTTAGGCAAAGTGCTTTTGTAC 989
                          iv ---?v    vi   ivi ii vi          v vvi i  iv i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_91303509_9    990 TTGACACCTAAAGTGAAATGCT-TACAAGGTGAAATTGCTTAATTAGATT 1038
                         v       v    iiv  -  v-i v   ivi    v v v    i  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_91303509_9   1039 TCATTAGAAATGAAA--TCTTATGATTTACAAGATTCT---------GTG 1077
                             i i  v i   -- i  i  v  i v i  iv  ---------   
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_91303509_9   1078 AGAAGAT-----------TGGCAGAAAATATTTGCAATTCACATATCTGA 1116
                          i    i-----------   v               v   i        
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_91303509_9   1117 AAAAAGGAATAATATCTACACTAC-TAATGAACTTTAAAAATTCAATAGT 1165
                         v  i-   v vi    i v v  i-   v     i v v  i      i 
  L1M4_orf2#LINE/    744 TAAG-GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_91303509_9   1166 AAAAAAA-AGAGAGCAGTTCAGTCAGAACACGGACAAA--ACTATCAACT 1212
                              i - i v i ---i  i i?i  v i  i    -- i - v  iv
  L1M4_orf2#LINE/    793 AAAAAGACAAATAAC---CCAATTWAAAAATGGGCAAAGGATT-TGAATA 838

  chrX_91303509_9   1213 GCTATTTCAACAAAGAGTAAATCCGAATGTCAAACATGCACAAGAAAAGA 1262
                          vi     vv      iv v  v i    v v  i v     v       
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_91303509_9   1263 TGTTCAGCAGAGTTAGCCATCAG 1285
                           i   i  --- i ????????
  L1M4_orf2#LINE/    889 TGCTCAACA---TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (130 / 93)
Gap_init rate = 0.03 (21 / 795), avg. gap size = 3.19 (67 / 21)  


3813 21.33 3.16 0.68  chrX_91366596_91370539     2566  3451 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91366596_9   2566 TGGAAAGATATACTGTGTTTATGAACTGAGTGACTTAGTGTTATTAAGAA 2615
                                    v ii    i   i i  iiv      i i  i      v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91366596_9   2616 GTCAATACCCCCCAAAGCTG-TCTACATATTCAGTGCAACCCCTATCAA- 2663
                          v      i       -i  -      v     ii    i         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_91366596_9   2664 -TCCCAATAATACTTTTTGCAAAACTAGAAAAATACATCCTAAGAATGAT 2712
                         -     iiviivi        i  v v  v  iivv       i v v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_91366596_9   2713 ATGGAATCTCAAGGGACCTTGAATAGCTAATACAGTCTTAAAAAAGAA-- 2760
                               viv         iv       i  v   i    i        --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_91366596_9   2761 -CGAAGTGGGAGGCCTAACACTTTCTGATTTCATAACTTACTACAAAGCC 2809
                         - i    v     v  v      i ii      v               i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_91366596_9   2810 ATAGTGATCAAAACAGTGTGGGTGCTGGTATGAATACAGGTATATAGACC 2859
                          i   i     i         - i    i  i iv i  ii       i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGG-TACTGGCATAAGGATAGACATATAGATC 298

  chrX_91366596_9   2860 GATGGAATAGAATAGAAATCCCAGTAATAAACTATCATGTAT--ATGGTT 2907
                         i            v  i vi    v       i--   ii  --     i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTC 346

  chrX_91366596_9   2908 AAATGATTTTCGCCAAGAGTACCAAGACTTTTGAATAGGGAAAAGACAGT 2957
                           v         v    i  i       iv  v   i      ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_91366596_9   2958 CTATTTAACAAGTGGTGTTAGAA-ATCTGGATATGCACATGCAAAATAAT 3006
                           v  i     i     i i i - v       ?v           v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_91366596_9   3007 GAAGTGAGACTCTTACCTTATGCCATATACAAAAATTAATTCAAAATGAA 3056
                              vi   i i     i ii                 i        i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_91366596_9   3057 TCAATGACCTTAACCATAAGGGGTAATA-TATAAAAATGTTAGAAGAAAA 3105
                            ?v     -  vii    i v   v -       v v           
  L1M4_orf2#LINE/    497 TCAWAGACCT-AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_91366596_9   3106 CATAGGGGAAAAGCTTCATTACATTAGATTTGATAATGATTTCTTGGATA 3155
                               ? v   v    i v  v  i i  v ii    i      i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_91366596_9   3156 TGGAATCAAAAGCACAGGTAACAAAA------ATA-ATACATTAAA---- 3194
                           iv i          i i       ------   -   v   ii ----
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_91366596_9   3195 ATTAAA--CAAACACTTTTGTGCATCAAAGGACACTGTCGACAGGGTGAA 3242
                           i   --i   v          v            i  i v ii     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_91366596_9   3243 AAAGCAACCCACAGAATTAGAGAAAGTATTTGCAAACCATATATCTCATA 3292
                           ii             vi      i          i         v   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_91366596_9   3293 AGGAGTTGATATCCAGAATAGCTAAAGTATTCCTACAAC--AACAACAAC 3340
                            iii vi           vv     v i  i      --  i  i  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_91366596_9   3341 AAAACTAAACACTCAGATTAAGAAATGGACAAAGGACTTGAATA---AGT 3387
                           i  v  vv  i  -   ? i      i       i       --- v 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_91366596_9   3388 TCTCCAAAGATAATATATAAATTGCTAATAAGCATATTAAGAGATATTCA 3437
                                   vi     i    v  i        i  v  i    ii   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_91366596_9   3438 ATATCACTAATTAT 3451
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (120 / 65)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


3321 21.31 1.61 3.88  chrX_91423026_91425807.rev     1365  2293 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91423026_9   1365 TAGAAAGCTATTCTATGTTCATGGATTAGAATACTTAATATTGT--ACAT 1412
                          i     v   i i             i   v            -- v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91423026_9   1413 GGTTCAACACTTCCCAAAGAGATCTACATATTTAGTGTAATATCTATCAA 1462
                           --   i   i      vv        v   i ii i   vi       
  L1M4_orf2#LINE/     51 GG--CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_91423026_9   1463 AATCTAAAAGGTGTTTTTTAGAGAAATGGAAAAATCCATCCAAAAAA-CA 1511
                             iv ivv iv      iv      v  v  iiiv    v    v-  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_91423026_9   1512 TATGGAATTTCAAGAGACCTGCAATAGTGAAAACAATCTTGAAAA-GAAG 1560
                                v v    i    iiv     iv                -    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_91423026_9   1561 AATAAAGTAAAAAGTCTCACATTTAAGTTACTTGTAAA-CTTACTACAAA 1609
                           i     vii i v      i  v--ii v  vi   -           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTC--CCAATTTCAAAACTTACTACAAA 246

  chrX_91423026_9   1610 TCTACAATAATCAAAATGGTATGGTACTAGAATAAAGACAGATAAATAGA 1659
                         v     i       i ii  i       i v    i  i   i v     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_91423026_9   1660 CCAAAAAAAATAGATTAGAGAACCTAAAATTAAAGGTTCACATGATAGGG 1709
                         i   vii  -    v v    ii i i  v    vvivi    v-  v  
  L1M4_orf2#LINE/    297 TCAATGGAA-TAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGG 344

  chrX_91423026_9   1710 AACCTAAAAACAAAGGCTCAAATGATTTTTATCAAGAATGCCAAAACCAT 1759
                         -----------------    v       iiv    ii      i     
  L1M4_orf2#LINE/    345 -----------------TCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_91423026_9   1760 TTAATCAGAAAAGAACAGTCTTTTCAACCAATGATATTGGAA-ACCTTGA 1808
                          i   vi i      i            v    i ii   i - v  v  
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_91423026_9   1809 TACTCACATGCAAATGAATGAAGGTGGACCCTTTCCTTACAACACATACA 1858
                           ?i          v        v       i v   i   v  i     
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_91423026_9   1859 GAAA--AACTCAAAATG---CAATAACATAAATGTAGGACCTAAAACTAT 1903
                         i   --           ---  ?vi  v        i  v          
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_91423026_9   1904 AAAATTATTAGAAGAAAACAGAGAGAAAAAACTTCATGACATTGGGTTTG 1953
                             i v             v  i?iv   v    i    v       v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_91423026_9   1954 GCAATGAGTTCTTAGAAATAACGACAAAAATATA-GAAATAAAAGAAAAA 2002
                               iv        v  i  iv     ii i - v  i          
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_91423026_9   2003 ATAGATACATTTGACTACA-CAAAATTTAAAACTTTCATGAGTCAAAAAA 2051
                                v   v    v  -       v        ii  vv     ii 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_91423026_9   2052 CACAATCATCAGAATGAAAATGCAACCTACAGGGTGGAA-AAAATATTTT 2100
                            v    vv i i      vi     i    ii   i -         v
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_91423026_9   2101 CAAACCCTACATCTGGTATATGGTTAATATCCAAAACATCTAAAGAACTC 2150
                             i v  i     i  viv ii vi      i  i  v          
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_91423026_9   2151 ATACAACTCAACATCAAAAATAATAAATAAGTAAATAAATAACTCCTTTA 2200
                         v          ---------       -   --- i       i vv  ?
  L1M4_orf2#LINE/    778 TTACAACTCAA---------TAATAAA-AAG---ACAAATAACCCAATTW 814

  chrX_91423026_9   2201 AAAAATGGGCAAAGGACTTGAATAGCCATTT-TCCAAGGAAGATGAACAT 2249
                                         i        v     -     i      iv   v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_91423026_9   2250 ATGACCAGTATGCACACGAAAAGATACTCAGCATAACTAATAAT 2293
                            i   i  v     i        i    i   v ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (109 / 85)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.68 (51 / 19)  


2447 26.97 1.92 5.12  chrX_91503901_91507053.rev     1732  2669 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91503901_9   1732 TGGAAAAACGTTTCATGCTCATGGATTGGAAGACTTAATAC-ATTAATAT 1780
                               i ii ii    i                      i-i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91503901_9   1781 GGCCATACTGCCCAAAGCAATTTACAGATTCAACACTATTTCTGTCAAAG 1830
                            v     v      vii  i            i v  ii  i     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91503901_9   1831 TACCAACATCATTTTTTACAGAACTAGAAAAAAAAACT-ATTCTAAAATT 1879
                          v   i vv v      i     v v  v  i----  -  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chrX_91503901_9   1880 CATATGG---TACAAAAAAGAGCCTGAATAGCAAAAGCTATGTTAAGCTA 1926
                                --- i   ii--  v  v       v   i v  v  i --- 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGA---A 191

  chrX_91503901_9   1927 AAAGAAAAATA---CTGGAGGCATCACATTATCTGACTTTAAATTACACT 1973
                               i  i ---i      vv     i vi ii i  i   vivi   
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_91503901_9   1974 ATGAGGCTACAATAAAAAAAATAGCATGATACTAGTACAAAAACAGTCAT 2023
                          ii i      i   vv  i i  ii  i    i i i  ii i  v   
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_91503901_9   2024 GTAGACTAATGAAACAGGATAGAGAACCCAGAAATAAAGCTGCACACCTA 2073
                         i    ii    i  i  i  v    ii           v iii   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_91503901_9   2074 CATGAAACCATCTTATCTTCAACAAAGTCAACAAAATTAAGCAATAGGGA 2123
                         --  i--i  vi v  i   i    i viiv   i ii vv    i    
  L1M4_orf2#LINE/    342 --TGG--TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_91503901_9   2124 AAGGACTCCCTATGTTATAAATGATGCTGAGATAGCTGGCTAGCCACATG 2173
                            i ivvi  v viv i     i     i  i i    v  ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_91503901_9   2174 CAGAAGAATAATGGTAGATCCATACCTTTTACCACATACAAAAATTAACT 2223
                           i      i v v i  i  v     ivi    i               
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_91503901_9   2224 CAAGATAAGTTGAAGGTTTAAATGTAAAACCTCTAACTATAAGAATCCTA 2273
                            i  iii ii?  iii         i v  vv        i v  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_91503901_9   2274 GAAGAAAACCTAGAAA-ACACCATTCTGGAAATTGGCCTTGGGATA---- 2318
                                  v   i?i- v i -   -- ----  i       v  ----
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTC--G----TGACCTTGGGTTAGGCA 580

  chrX_91503901_9   2319 -TAATTTAT-GGCTGCATTCTCAAAAGTGATTA-CATCAAAAACAAAAAT 2365
                         - ii   v -i v iiivivi      i- iv -  v     iv      
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGC-ACAAGCAACAAAAGAAAAAAT 629

  chrX_91503901_9   2366 TCACAAGTGGGAACTGATTAAACTAAAGATCTTCTGCACAACAAAAGAAA 2415
                         vv i  i v   vi v  i   v v  i v   i  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_91503901_9   2416 CTATCAGCAGAGGAAAAACAAAAACTCCAGCATAGGAGAAAATATTTGCA 2465
                               iv i  vi    v v  v iv   v  i                
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_91503901_9   2466 AACTATGCATCTCACAGAGGACTAATATCAAGAATCTATCAGAGGACTAA 2515
                           ii  ii    v i ii     vi    v     v   - i  i   vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATAT-AAAGAACTCT 778

  chrX_91503901_9   2516 TATCAAGAATCTATAAGAAAGTCAAACAAATCAACAAGCAAAAACCTAAT 2565
                           -   v--  v    v   i-- i      -----------    i   
  L1M4_orf2#LINE/    779 TA-CAAC--TCAATAATAAAA--AGACAAAT-----------AACCCAAT 812

  chrX_91503901_9   2566 AACAACCCCATTAAAAATAGACAATGGACATGAACATACACTTCTCTTAA 2615
                         ---------- ?      i i   v   iv    i v   i     iv  
  L1M4_orf2#LINE/    813 ----------TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_91503901_9   2616 GAAGACATACAGGTAGCCAACAA--ACATGAACAAATGCTCCATATCACT 2663
                              i     ii i     i  --       v i      v i    ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_91503901_9   2664 AATCAT 2669
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.77 (159 / 90)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.75 (66 / 24)  


2993 26.12 2.59 0.47  chrX_91521663_91523580      565  1414 (504)    L1M4_orf2#LINE/L1        3   870 (38)  

  chrX_91521663_9    565 GAAAGACATTTCATATTCATAGATTTGAAAAATCTATATTGTTACAAAGT 614
                               i  ii   i     i    v   i v iv         vi v v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_91521663_9    615 CCATACTACCCAAAGCCATCTACA-----------ATTCCTATCAAAACA 653
                          v     v      viv       -----------  i          iv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_91521663_9    654 CCGATGACATTCTTCAGAGAAATGGAAAAAATAATCCTAAAATTTATATG 703
                           iiivi v  i  iiv      v  v  iv i           i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_91521663_9    704 GAACCACAAAAGACCCAGAATAACCAAAGCTATGCTAAGCAAAAATAACT 753
                            vii   ii           i     i v  vi i iv  i  v   v
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_91521663_9    754 ACACTGGGGGAATCATAGTACCTGACTTCAAATTATACTACAGAGCCATA 803
                          vii   i   v   i v v  ii i      viv       i   i i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_91521663_9    804 GTAACCAAAACAGCATGGTACTGGCATAAAAATAGACACATATACCAGGG 853
                             i   i    ii              ii       i   v i  iv 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_91521663_9    854 GAACAGAATAGAGAACCCACAAACAAATTCACATACCTACAGTGAACTCA 903
                            i     v    ii   v   i   ii  i i ii  ii  v  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_91521663_9    904 TTTTTGACAAAGGCGCCAGGAATATAAACTGAGGAAAAGAGAGTCTCTTC 953
                             i     i  i    i  vi  vv v  i     ii v     i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_91521663_9    954 ATTAAATGGTTCTGGGAAAACTGGATATCCATATGCAGAAGAATTAAACT 1003
                          vi       v      v         ?   i     i      v  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_91521663_9   1004 TGACCCGTATCTCTTGCTATATACAAAAATCAAATCCAAGTGGATTAAAC 1053
                         v     v  i   vii i            i  v  v  i     i ? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_91521663_9   1054 ACTTAAATCTAAGACCTTAAACTATGAAACTACTACAAGAAAACATTGGA 1103
                           i     v     v  v       i     vi  v          v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_91521663_9   1104 GAAACTATCCAGGACATTGGTCTTGGCAAAGACTTATT-GACCAATGCC- 1151
                          v  v v i iv   v    vi v     v ii  v  -  i--   v -
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGACA 600

  chrX_91521663_9   1152 CCAGAGGCACAAGCAATCAAACCAAAAAATGGACAAATGGGATCACAGCA 1201
                            i i          -    vv       i  i    v   iiv  v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAA-CAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_91521663_9   1202 AG-TTAAAAAGTTTCTGCACAGCAAAGGAAACAATCAACAAAGTGATGAG 1250
                          i-       v   -  ii vv       v  v     v       vi  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_91521663_9   1251 ACAACCCACAGAAGGGGGGGAAATATTTGTAAACTACTCATCTGGCAAGG 1300
                                      v   i i         i   ii ivi     ii    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_91521663_9   1301 AATTAATAACCAGAATATATGAGGAGCTCAAACAACTCAATAGGAAAAA- 1349
                         i i vi  v           i i  i   vv           iv     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_91521663_9   1350 --AGGTGA-----TTAATAAATAGACAAGAGATTGTAATAGACATTTCTC 1392
                         -- ii i -----  ? v    i i   ii    vv              
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_91521663_9   1393 AAAATAATATATACAAATGGCC 1414
                         v   v  v              
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCC 870

Transitions / transversions = 1.40 (127 / 91)
Gap_init rate = 0.01 (9 / 868), avg. gap size = 2.89 (26 / 9)  


2403 26.96 2.93 4.24  chrX_91532504_91534746.rev      833  1752 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91532504_9    833 TGGAAAAACATTTTATGCTCATGGATAGAAATAATCAATATCATTAAAAT 882
                               i i  iii   i        v i  v v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91532504_9    883 GGTCATCCTGCCTAAAACAATGTATACATTCAATGCTATTCCTATTAAAT 932
                           iv  v  v  i   vii  v  i v      i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91532504_9    933 TATCAATGACATTCTTTACAGAAATAAATTTTTAAAAAAAT-ATTTAAAA 981
                          vi  iivi v  i   i       ------- i v  iv -  iiv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-------TGACAAGCTGATCCTAAA 143

  chrX_91532504_9    982 ATTTATATGGTACCAAAAATAGCCC-TAATAGCCAAGGTAATCCTAAACA 1030
                            i      v viiv  ivii   -v         iii    i i  v 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_91532504_9   1031 AAATGAACAAAGGCAGAGGTAC-CATGCTACCTGACTTCAAACTATACTA 1079
                          i v        vii    -  -  ii  v  ii i      ----   -
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAA----ACT- 237

  chrX_91532504_9   1080 TACTACAGGATTATAGTAACCAGAATGGCATGGCACTGGTACAGGAACAG 1129
                                iiii  i     i  ii ii ii   i     i i i i i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_91532504_9   1130 ACACATAGGCAAATGGAATAGAACAGAGAACCCAGAAATAAGACCACACA 1179
                            i    iiv            iv    ii          iv   i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_91532504_9   1180 CCTACAACTCTCTGATTTTTGACAAACCTGACCAAAAAAAAAAAAAAAAA 1229
                         ii  iiiiivvi       i     ivv  -    i vv vvv  -----
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAA----- 381

  chrX_91532504_9   1230 AAAAGCTCTGAAGAAAGGATTTTCTATTCAATAAATGGTGTTGACATAAC 1279
                         --------  ii     i  vv   v     i        i  iv i   
  L1M4_orf2#LINE/    382 --------TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_91532504_9   1280 TGG-----CATATGCAGAAGATTGAAACTGGACCCCTTCCTTACACTATA 1324
                            -----  i     i    v    ii         v   i    i   
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_91532504_9   1325 TACAAAAATAAACTCAAGATGGATTAAAGACTTAAACATAAAACCCAAAA 1374
                                  v       i      i ?    i    ii   i v i    
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_91532504_9   1375 CTATAAAATTCCTGGAAGATAACCTAGGCAGTA--TCATTCCGGATACAG 1422
                                 i  i i     v   v    ?-   --  -   vv  iviv 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGN-GTAAATC-TTCGTGACCTTG 571

  chrX_91532504_9   1423 GCGCT-GGCAAAAGTTTCATAAAAAAAATTCCAAAAGCAATTGCAACAGA 1471
                          - i -     vi     v  i v vi iv         vvv      i 
  L1M4_orf2#LINE/    572 G-GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_91532504_9   1472 AGCAAAAACTGACGAATGAGATCTAAGTAAA--TGAAACGGCT-----GC 1514
                           v     iv  ii   vi  ii v vi   -- i   --i  -----  
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA--ACTTTTGTGC 668

  chrX_91532504_9   1515 TTCATAGCAAAAATAAACTATCAACAGAGTAAA----CAATCTATGGAAT 1560
                             ----  ii i --       v i   i  ----   i i ii    
  L1M4_orf2#LINE/    669 TTCA----AAGGACA--CTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_91532504_9   1561 GACAGAAAATTTTTGCAAACTCTGTATCTGACAAAGGTCTAATATCCAGC 1610
                          iv       v        iiv i       i  i  v  vi       v
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_91532504_9   1611 ATCTATAATGAACTTAAAAAA---AATTACAAAGAAAAAAAACAACTCCA 1657
                           v     v     ivv v  ---   v i   -  i v   i   i v 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAAATAACCCAA 811

  chrX_91532504_9   1658 TTAAAAAGTGA-CAAAATACATGAGCAGACACTTTTCAAAAGAAGACATA 1706
                           ?    i  i-    iv iv   ii     i  i  v        i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_91532504_9   1707 CATGTGGTCAACAATCATATGAAAAGA-GCTCAACAACATTGATTGT 1752
                           vi   i   i  v  i         -        v  ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (159 / 86)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.64 (66 / 25)  


2096 25.35 0.76 8.63  chrX_91565525_91569092.rev     2151  3077 (491)    L1M4_orf2#LINE/L1       55   908 (0)  

  chrX_91565525_9   2151 ATAGTGCCCAAAGCAATTTACACATTCAATGCTATTCCAATCAAACAACT 2200
                            v v      vii  i    v      i  v  i  v      vvv i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_91565525_9   2201 AATGACATATTTCACAGAATTAGAAAACAAAAAACTGCTC-TAAAACTTA 2249
                          iivi v v   ii     v v  ---   i---   v  -     i i 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGA---CAAG---CTGATCCTAAAATTCA 148

  chrX_91565525_9   2250 TGTGGAATCAAAAAAGAGTCTAAATGACTAAAGCAATCCTAGGCAAAAAT 2299
                          i     viiv  ii  vi vi   ii i   i     i iiiv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_91565525_9   2300 AACAAAGCTGGAGGCATCACATTATCCAACTTCAAACTACACTACAAGGA 2349
                                i      vv     i vi    i      vivi       i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_91565525_9   2350 TATAATAATCAAAACAGCATAGTACTGATACAAAAACAGACACAGAGACT 2399
                           i i       i    ii i      ii i  ii i     i v   ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_91565525_9   2400 AATGGAAAAGAATAAAGAGCCCAGAAATAAAGCCACACACTTACAGCCAT 2449
                                v     vi    i           v   i   i   ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_91565525_9   2450 CTGATCTTCAACAAAGTTGACAAAAACAAGCAATGAGGAAAGACTC-CCT 2498
                         i    i   i    i v  v   i v  vv     i       v v-i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_91565525_9   2499 ATTCAATAGAAGGTGTTGAGATAATTGGATAGCCATATCCAGAAGATTGA 2548
                         v     i i v    i  i  i  i      ?   i  v  i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_91565525_9   2549 AACAGGACCCCTTCCTTATACCATACACAAAAATTAACCCAAGTTGAGTT 2598
                          iiv        v   i i      i            i   iv  ii i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_91565525_9   2599 AAATGCTTAAATGTAAAACCTAAAACTACAAAAGCTCT-GGAAGATAACC 2647
                          ? vi i         i v         i    -    -i     v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chrX_91565525_9   2648 TAAG---AAATACCACTCAGGACGTAGGCCCTGGCAAAAATTTAAT-GAT 2693
                           i ---    - i--  iv   v v  viiv     vii   vv -   
  L1M4_orf2#LINE/    548 TAGGNGTAAAT-CT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_91565525_9   2694 GAAGACACCGAAAGAAATTGCCAAAAAAAAAAAAAAAAAGACAAGTGTGA 2743
                         - v      i    v vvv  --  v    i      v   i  i vv  
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGC--AACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_91565525_9   2744 CTTAATTAAACTAAAGTGCATCTGCACAGCAAAAAAAAACAAAAAAAAAA 2793
                            v  i   v v  ivi v i  ii vv    ii --------------
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-------------- 677

  chrX_91565525_9   2794 AAAAGAAAAAAGAAAAAAGAAAAAACAACTATCAACAAAATAAACAGACA 2843
                         -------------------------  -       v   i i  v     
  L1M4_orf2#LINE/    678 -------------------------CA-CTATCAAGAAAGTGAAAAGACA 701

  chrX_91565525_9   2844 ACATGCAGAATGGGAGAAAATTTATTCAAATGATACATCCAACAAAGGCC 2893
                           vii                v v v     v   i   ii i  i  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_91565525_9   2894 TAATATCCAGAATGTATAAGGAACTTAAACAAATTAACAAACAAAAAAAC 2943
                          vi          i     i     ivv    v i  i  -i     i  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAGAC 800

  chrX_91565525_9   2944 AACATACTAATTGAGCAAAAGCTGAAAGCATTCCCCATTCAAAAGTGGCC 2993
                           -   ----------------------- --   v   ?    i   v 
  L1M4_orf2#LINE/    801 AA-ATA-----------------------A--CCCAATTWAAAAATGGGC 824

  chrX_91565525_9   2994 AAAGAACATGAACAGATACTTTTCAAAATAAGTCATACACTTGGCCAACA 3043
                             i iv    i   i i  i  v   v   vi     vv       i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_91565525_9   3044 AGCATATGAAAAATTGCTCAACATTACTAATCAT 3077
                             i       iv          i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.02 (18 / 854), avg. gap size = 4.83 (87 / 18)  


3029 25.11 0.97 3.23  chrX_91657074_91660105     1612  2539 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_91657074_9   1612 GGTAAAATATTCCATGTTCATGAATTAGAAAAATTAATATTTTTTTAAAT 1661
                           v  i    i           i   i   i v        v  v- i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGAT 50

  chrX_91657074_9   1662 GTCCATATTACACAAAGCCA-CTACAGATTTAATGTAATCCCTATCAAAA 1710
                          v v   i v v    viv -         i  i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91657074_9   1711 TACCAATGGCATTCTTTATAGCAATAGAAAAAAGAATCCTAAAATTCATA 1760
                          v   iiv  v  i   ii  v   v  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_91657074_9   1761 TGGGACCACAAAAGACCCAGAATAGCCACAGTTATCTTAGGCAAAAAGAA 1810
                            i vii   ii               v iiv     iiiv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_91657074_9   1811 CAAAACCGGAGGAATTATATTACCTGCCTTCAAATTATGTTACAGAGCTA 1860
                             iii      v i i i v  iivi      viv ii    i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_91657074_9   1861 TAGTAACCAA-ACAGCATAAACCTGACATAAAAACAGACACATAGACCAA 1909
                         i     i   -    ii iivv   i     ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_91657074_9   1910 AGGAACAGAATCGAGAACCTACAAACAAATCCAAACACGTACAGTGAACT 1959
                         v    i     i    ii i v   i   i   v   iv  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_91657074_9   1960 CATTTTCTCCAAAAATGCTGAGAACATACACTGGGGAAAAGACAGTCTCT 2009
                         v      vv   iii   ii   v   v  v        ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_91657074_9   2010 TCAATAAATAGTGCTGGGAAAACTGGATATTCACATGCTGAAGAATGAGA 2059
                             i    i         v         ?i       vi        ii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_91657074_9   2060 CTAGATCCCTATCTCTCACCATATACAAAAATTAAATCTAAATGGATTAA 2109
                         i i  i     i   v                   v  v        i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_91657074_9   2110 AGACTTAAATCTAAGACCTCAAACTGTGAAACCATTAAAAGAAAACTATT 2159
                             i     v     v  v     i i    iv   i        -  -
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC-AT- 548

  chrX_91657074_9   2160 AAAAGGAAACATTTGAAAAATGCTCAACATCAATCCAGGCAAAGTTTTCT 2209
                          ii? v   iv  i -----  ----  v iiivii      v v     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCG-----TG----ACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_91657074_9   2210 GTAATA---CCCCACAAGAACAGGCAACGAAAGCAAAAATGTACAAATGG 2256
                         vvi   --- v   v   v   i     i    v      iv i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_91657074_9   2257 AATCATATCCAG-TTAAGAAGCTTCTGCACAGCAAATAAAACAATCAACA 2305
                         i iivi   v i-    i  -   i  ii vv    vi v  v     v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_91657074_9   2306 AAGTGAAGAGACAACCCACAGAATGGAAGAAAATATTTGCAAATTACCCC 2355
                                i                  i                 i iviv
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_91657074_9   2356 CCAGACAAGG---TTTTAACAAGCAGAACATTTAAGGAGCTCAGCTCAAA 2402
                         i v  i    ---  v  v ---     i  v   i  i   --- i --
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATC---CAGAATATATAAAGAACTC---TTA-- 780

  chrX_91657074_9   2403 CAACTGTATTAAAAAAAAGAAAAAAACACTAATAATTTAATCAAAAAATG 2452
                              -i v   v       ------  --     iii   i?       
  L1M4_orf2#LINE/    781 CAACT-CAATAATAAAAAGA------CA--AATAACCCAATTWAAAAATG 821

  chrX_91657074_9   2453 GACACAAAATGTGAATATACATTTCTCAAAAGATGACATGCAAATGGCAA 2502
                          i  v ii  v      v         v     v  i  i        v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_91657074_9   2503 GCAGGCATATGAAAGTGTGCACAATATCATTGATTAT 2539
                         ii i   i      ivi   v   i    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (142 / 87)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 2.29 (39 / 17)  


 401 15.97 18.49 2.52  chrX_91665996_91668576      976  1094 (1487)    L1M4_orf2#LINE/L1        1   138 (770)  

  chrX_91665996_9    976 TGAAAAGACATCCCATGTCCTTAATTTGTAAGAC--AATATTAT-AAGAT 1022
                           i     i         i v iiv   v     --      i -     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91665996_9   1023 G-CAATCCTTCACAAATTGATCTTCAGATTCGACACAAT-----TCAA-- 1064
                          -    v  i v           v       i  i    -----    --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91665996_9   1065 ----------CTTGAATTTTGCAGAAAT-AAGACGCTAATC 1094
                         ----------   ---            -i v v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT---TTTTGCAGAAATTGACAAGCTGATC 138

Transitions / transversions = 1.38 (11 / 8)
Gap_init rate = 0.05 (7 / 138), avg. gap size = 3.57 (25 / 7)  

2055 23.38 15.29 1.03  chrX_91665996_91668576     1409  2088 (493)    L1M4_orf2#LINE/L1      132   908 (0)  

  chrX_91665996_9   1409 GCTAATGCTAAAACC---ACGGGAATTTAAGAGAACTAGATTAGCCAAAA 1455
                            i  v      ii--- i  i   vi   i  v i   v         
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chrX_91665996_9   1456 TAATTGTGAAAAATAAGAACAAAGTTGGATAACTAAGCCTTTTCCATTTT 1505
                         i   iv       v               vi   v vv   ii v    i
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_91665996_9   1506 AAAAC----------GTTCC-----TCAAACCAATA--------GCA--- 1529
                              ---------- i v -----    iv  i i--------   ---
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_91665996_9   1530 --------------ATCAATGGA--------------------------- 1538
                         --------------         ---------------------------
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_91665996_9   1539 --------------CAATTGATTTTCA--------GCCAATTAA--AGTC 1564
                         --------------            i--------     --i -- v  
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA--GACCATTC 379

  chrX_91665996_9   1565 AATAAATAATAAATAGTCTTTCCA-CAAGTGGCATTGGGATTGCTGGATA 1613
                            iiiv  vi          i  -   i   iii     ivi       
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_91665996_9   1614 TCCACATGCAAAAGGATAATTTTTAGATACCTTCCTTACAAAATGCATAG 1663
                         ?             i  i vv  -i  iv   v   i   vv  ii i i
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTT-GGACCCCTACCTCACACCATATACAA 478

  chrX_91665996_9   1664 AAATAACCACTCCAAATGGATCATTGACCTTAATATGAGAACAGAAGCTA 1713
                             v --    v          ?v     v   i i   i vi  i   
  L1M4_orf2#LINE/    479 AAATTA--ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_91665996_9   1714 TAAAACTATTAGAA---ATCACAGGAGCAAACCTTTATGACTTTGCATTA 1760
                                v      --- v  i   ? i   i   ii    i   vi   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_91665996_9   1761 AGCAAAGTTTTCTTAGATCTGACACTAAAAGTACAAGCAACAACAAAAAA 1810
                         i    v v          v      i     i           v i    
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_91665996_9   1811 A-----TACATTATACCTCATCAAC-TTCAAAACTTTTGTACGTCAAAGG 1854
                          -----  v   iv  i       v-  v           i v       
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_91665996_9   1855 ATATCATCGAGAAAGTGAAAAGACAAACCACAGAATGTGAGAAAATATTT 1904
                          i ii   i                 v          v            
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_91665996_9   1905 GTAAATTGTATATCTTATAAGAGTCTTATATTTAGACCATAAAAAGAACT 1954
                          i    ii       v     i v   i   ii   vi   v        
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_91665996_9   1955 TGTAAAATCCAACAATAGTAATGCAAAAGATATAATTTTTAAATGGGTAA 2004
                         iv  v  ii   i    iv  vi    vi ivi    ?vv       i  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_91665996_9   2005 AAAATACAAATAGACATATTTTTCCAAAGAATATAAACAAATTACTAGTA 2054
                          ii  vii         --  i         v   v      vi i i  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACAT--TTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_91665996_9   2055 AGTATATCAAAAAATATTTAACTTCATTAGCAGT 2088
                           i i  v    i  ii i   v   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (95 / 60)
Gap_init rate = 0.02 (16 / 777), avg. gap size = 6.94 (111 / 16)  


2756 27.45 1.87 1.76  chrX_91670992_91675526.rev     3137  4043 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91670992_9   3137 TGAAAAAGCATCCTATGCTCATGGATTAGAAGAATAAATATA---AAAAT 3183
                           i   iii    i   i         i     v v     v---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91670992_9   3184 GGCCATACTATCCAAAGCAAAATACAGATTCAACACTCTTCCTATCAAAC 3233
                            v     vi     vii vv            i vv i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91670992_9   3234 TACCAAA-GTCGTTTTTCCAGAATTTGAAAAAAAAAAAACTG-TTCTAAA 3281
                          v   iv- i v     v     v    v  i-------   - i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-------CTGATCCTAAA 143

  chrX_91670992_9   3282 ATTTATATGGAACCACAAAATAAGCCA-AATAGCCAAAATAATCCTAAGC 3330
                            i        vii   ii-i v   -           i    i i iv
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_91670992_9   3331 AAAAAGAACAAAGCTGGAGGCATCACATTATCTGACTTCAGACTGTACTA 3380
                           i          i      vv     i vi ii i    i viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_91670992_9   3381 TAAGGCTACAGTAATAAAAAGAGCACAGGACTGATGCAAAAGCAAACACA 3430
                         i  i           v  i v  iiii v    iiii  iiii i   i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_91670992_9   3431 TAGACCAATGGAACAGAAATAGAGAACCCAGAAATAAAGTTGCACACCTA 3480
                             i        i    v -    ii           viiii   ii  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_91670992_9   3481 CAGCCATCTAATATTTGACAAAGTTGACAAAATTAAGCAGTGGGGAAAAG 3530
                         ii i  vi i  v  i     i v  v   i ii vv  i        ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_91670992_9   3531 ACTTTCTATTCAATAAATTGTGCTGGGACAGTTGACTAGCCACATGTAGA 3580
                          ivv   v     i    v           ii  iv  ?       i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_91670992_9   3581 AGAATGAAACTGGACCCCTACCTATCACCATATACAAAAATTAACCTAAG 3630
                                 ii             vv                    ii  i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_91670992_9   3631 ATGAATTAAAGATTTAAATGTGAGACCAATAACTGTAAGAATTCTAGAAG 3680
                            i  i ?   ii       i   v v v    i   i v ii      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_91670992_9   3681 GAACCATACGAA-ACACCATTCTGGACATTAGCCTTGGCAAAGAATT--- 3726
                         i  v    v ?i- v i -   vv   v  i vi v     v iv  ---
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_91670992_9   3727 ---TATGACTAAATCCTTAAAAGCAATTGCAACAAAAACAAAAATTGACA 3773
                         ---      --- i ---       vvv         iv      v  i 
  L1M4_orf2#LINE/    591 AGATATGAC---ACC---AAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_91670992_9   3774 AATGGGACCTAATTAAACTAAAGAGCTTCTGCAAAGCAAAATAAGCTATC 3823
                            v    i v  i   v v  i i   i  iivvv    iv vi     
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_91670992_9   3824 AACCAGGTGAACAGACAACCTATAGAATGGGAGAAAATGTTCCCAAAGTA 3873
                           vv i     v        i i               i  iv    vi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_91670992_9   3874 TACATTCAGCAAAGGTCTACTATCTAGACTGTA--GAGAACATAAACAAA 3921
                           i  iiiii  i  v  vv    i   v i  --i     vivv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_91670992_9   3922 -CAACAAGCAAAAAACAAAAGCCTCCATTCAAAAGTGGGCAAAAAATATA 3970
                         -   i  vv    i     viv i v   ?    i        ii  v i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_91670992_9   3971 AACAGACACTTCTCAAAAGAAGACATACAAGGGGCCAACAAACATATAAA 4020
                           i     i     v        i      iv      i  i  i  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_91670992_9   4021 AAAA-ATTCCTCATCATTCTTCAC 4043
                           i -ii  vv     ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


1126 20.16 1.60 23.48  chrX_91709111_91710975      502  1374 (491)    L1M4_orf2#LINE/L1      227   908 (0)  

  chrX_91709111_9    502 ACTTTAAAATATTCTACACAAAGCTGAAGTAACTAAAAACAGCATAGTAC 551
                          i  i    iv v     --     iv     - v  i    ii i    
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACA--AAGCTACAGTAA-TCAAGACAGTGTGGTAC 273

  chrX_91709111_9    552 TGATATAAAAAGAGACAAATACACCAGTGGAACAGAATAGAGAATCTAGA 601
                           ii    ii v     v   v i  i     i     v    i  i   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_91709111_9    602 AATAAATCCATGTGTTGACAGCCAACTGACTTTTGACAATGGCACCAAGA 651
                               i    iii  v ii i   i   i   i     v  ii      
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_91709111_9    652 ACATACATTATGGAAAGGACAATCTTTTTAATAAATGGTGCTAGGAAAAC 701
                         v   v  v iv      i i i      i  i          i   v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_91709111_9    702 AAGAAATCCATACTCAGAAGAATGAAACTAGACTCCTGTCTCTCACCTCA 751
                         vi  v ?   i iv  i         ii i   i   ii   v    vi 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_91709111_9    752 TACAAAATCGACTCAAAATGGATTAAAAAGCTGGGTGCAGTAGCATAAGC 801
                                --------------     ------------------------
  L1M4_orf2#LINE/    474 TACAAAA--------------ATTAA------------------------ 485

  chrX_91709111_9    802 TTGTAGTCCCAGCTACTCAAGAGATTGAAGCAGGAGAATCACTTGAGCCT 851
                         ---------------     ------------------------------
  L1M4_orf2#LINE/    486 ---------------CTCAA------------------------------ 490

  chrX_91709111_9    852 AGAAGCTTGAAGCTGTAGTGCTCTATGATTGTACTTGTGGCTGGCTAGTC 901
                         --------------------------------------------------
  L1M4_orf2#LINE/    491 -------------------------------------------------- 490

  chrX_91709111_9    902 ACTGCACTGAATTCTGAACAACAGAGTGTGACCCCATCTCTCATCTCTAA 951
                         --------------------------------------------------
  L1M4_orf2#LINE/    491 -------------------------------------------------- 490

  chrX_91709111_9    952 AAATATTTAAAAAATGGATTAAAGACTTAACATG--AGAATCAAAACTAT 999
                         ------------       i ?    i   -   --   iii        
  L1M4_orf2#LINE/    491 ------------AATGGATCAWAGACCTAA-ATGTAAGAGCTAAAACTAT 527

  chrX_91709111_9   1000 AAAACAACTAGGAGGATACATAGGTA-AAATGCTTTAGGACACTGGTCTG 1048
                              vvi   i  i v       ?i-    -   iiv   vi   vi -
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTT- 575

  chrX_91709111_9   1049 GAAAAAAAAAATGTCCGA-ATAAGACCTCAGAAGTACAAGCAACAAAAGG 1097
                         -- iiv  vii v  iv -   v   vi  i   i              i
  L1M4_orf2#LINE/    576 --AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_91709111_9   1098 GAAAACTGACAAATGGGGTTACATCAAACTAAAACACTTCTGCACAGCAA 1147
                         i    iv  i    v  ii v       v v   v    i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_91709111_9   1148 AGGAAACAATCCACAGAGTGAAGGCAAAACCTGAAGAATAGAAAAAATAT 1197
                             v  v   v v i      iiv v    iiv     i i i   -  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA-AT 722

  chrX_91709111_9   1198 ATTTGCAAAATATTTATCTGACAAGAGATTAATATTCAGGATATA----- 1242
                                  vi  v       i   i  i vi   i   i     -----
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_91709111_9   1243 AAC----AGAAATCAACAGCAAAAAATACAAATAATTCAATTATGAAATA 1288
                            ---- v  v    i ii     i-        ii     ?vi    i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAG-ACAAATAACCCAATTWAAAAATG 821

  chrX_91709111_9   1289 CACAAATAATC-GAATAGACATTTCTCAAATGGAGACATACAAATGACCA 1337
                         vi    vi  i-               v  v i   i         i   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_91709111_9   1338 ATAAGTATATTAAAGAATGTGCAACATTCTTAATTAT 1374
                              i i  v   ii   iv      iv????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (112 / 60)
Gap_init rate = 0.02 (16 / 682), avg. gap size = 13.69 (219 / 16)  


2509 30.35 1.55 1.32  chrX_91732596_91734646      651  1556 (495)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91732596_9    651 TGGAAAAACATTCTATGCTCATGGATTGGAAAATACAACATTAATAAAAT 700
                               i i  i i   i             i ivi  i   iv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91732596_9    701 GGTCATACTGCCCAAAGCAATTTACAGATTCAGTGTTATTCCTACCAAAC 750
                           iv     v      vii  i          ii iv  i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91732596_9    751 TACTTATGATATTTATCACAGAATTAGAAAAAAAAGTATTTTAATATTTA 800
                          v iviiviiv   v ii     v v  v  ivvi--  ii   v   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCA 148

  chrX_91732596_9    801 TGTGAAACCAAAAAGAACCT-GAATAGCCAAGGCAATCCTAAGCAGAAAA 849
                          i  i  viiv  i i   i-          ii     i i iv ii  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_91732596_9    850 GACAAAGCCAGAGGTATCACATTACCTGACATCAAAATACAGCACAGGGC 899
                         i      iii    vv     i v  ii iv      ivi vi   ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_91732596_9    900 TGCAGTAACCAAAACAGCGTGGTACTGGTACAAAAACAGACACAGAAACC 949
                          i      i   i    i          i i  ii i     i v i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_91732596_9    950 AATGGAACAGAATATAGACCCCAGAAATAAAGCCACACACCTACAACCAT 999
                                i     vv   vi           v   i   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_91732596_9   1000 CTGATTTTTAACAAAGTTGAGAAAAACAAGCAACGGTAAAAGGA----CT 1045
                         i       ii    i v  vv  i v  vv   i  vi    i ----  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_91732596_9   1046 TCAATATTCAATAAATGGTGCTGGGATAACTGGCTAACCATGTGCAAAAA 1095
                          -----     i              i      v  ?   ii       i
  L1M4_orf2#LINE/    399 T-----TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_91732596_9   1096 ATTGAAATTGGATAAATTCCTGATGCCATATACTAAAGTCAACTCAAGAT 1145
                          v    i     ivvv v   v ii        v   i i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_91732596_9   1146 GGATTAAAAACTTAAATGGAAAACCTAAAACTATAAAAACCCTGAAAAAT 1195
                             i ? i  i      v  i v              vi i ii  i v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_91732596_9   1196 AACCTGGG---AAATACCATTATGGATATAGGATCTGACAAAAATTTTAT 1242
                            v i  ---    -- v ii  - iv v  i iv i   vii   iv 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT--CTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_91732596_9   1243 -GATAAAGATGCCAAAAGCAATTGTAACAAAAACAAAAGTTAACAAATGG 1291
                         -    v-  ii         vvv i       iv    i vi i    v 
  L1M4_orf2#LINE/    591 AGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_91732596_9   1292 GACCTAATTAAACTAGAGAGCTTCTGCACAACAAAATAAACTATCAACAG 1341
                            i v  i   v vi i i   i  ii vv    iv v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_91732596_9   1342 AATAAACAGACAGTCTACATAATGGGAGAAAATATTTGCAAACTATGCAT 1391
                          i i  v     ii i   v                      ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_91732596_9   1392 GTGACAAAGGTCTAATATCTAGAATCTATAAGAAACTTAAACAAATTTAA 1441
                         v   i  i  v  vi    i     v     ii    ivv    -i i  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAA 788

  chrX_91732596_9   1442 AAGCAAAAA-ACAAACAGCTCCATTAAAAAGTGGACAAAGAACACAAACA 1490
                         v ii     -     i i i v   ?    i   i     i ivii  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_91732596_9   1491 GCCCCTTTTT---AAAAGACATACACACAACTAACAAGTATATAAAAAAA 1537
                          v vi  i i--- i    i     v iii i  i   i i  i    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_91732596_9   1538 GGTT-GACATCACCGATTAT 1556
                         v i -i      ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (183 / 89)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.00 (26 / 13)  


3216 26.99 0.88 0.44  chrX_91776588_91782566     4583  5486 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91776588_9   4583 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4632
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91776588_9   4633 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4682
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91776588_9   4683 TATCAATGACTGTCTTCACACAACTGGAGAAAACT-ACTTTAAAGTTTGT 4731
                          vi  iivi iv i  ii  v  v v  v  i-  - iii    i  ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_91776588_9   4732 ATGGAACCAAAAAAGAGCCTGCATCGCCAAGACAATCCTAAGCAAAAAGA 4781
                               viiv  ii  v  v v  v     i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_91776588_9   4782 ACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATAGTACAAGGCT 4831
                               i      vv     i v  ii i      viv  v     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_91776588_9   4832 ACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGAGATAGACCA 4881
                                i   i    ii     i   i iv ii i   v v     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_91776588_9   4882 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 4931
                               i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_91776588_9   4932 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAAGACTCCCTA 4981
                             i  i     ivv  v   i v  vvv          ii ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_91776588_9   4982 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCTGAA 5031
                           i  i              v      v  ?   i     i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_91776588_9   5032 ACTGTATCCCTTCCTTACACCTTATACAAAACTTAATTCAAGATGTATTA 5081
                         ii  v i    v   i     v         v    i    i   v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_91776588_9   5082 AAGACTAAAATTTTAGACCTAAAACCATAAAAGCCTTAGAAGAAAACCTA 5131
                         ?    iv    v v   v       i      vi             v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_91776588_9   5132 G---CAAATACCATTCAGGACATAGACATGGGCAAGGGCTTCATGAATAA 5178
                          ---i    -- -   iv   v v ivv i     v  i   v ii   v
  L1M4_orf2#LINE/    550 GGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_91776588_9   5179 AACACCAAAAACAATGGCAACAAAAGCCAAAATAGATAAATGGGGTCTAA 5228
                         i         i  vvi          vv             v  iii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_91776588_9   5229 TTAAACTAAAGAGCTTCTGCACTGCAAAAGAAACTACCATCAGAGTGAAC 5278
                          i   v v  i i   i  ii  v    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_91776588_9   5279 AGGCAACCTACAGAATGGGAGAAAATGTTGGCAATCTACCCATCTAACAA 5328
                           i     i                 i  v    vii ivi    i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_91776588_9   5329 AGGGCTAATCTCCAGAATCTACAAAGAACTTAAACAAATTTATAAGAAAA 5378
                         i  i  vi v        v  i        ivv    v iv    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_91776588_9   5379 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACATTTC 5424
                          i    ----   v  i?    i            v    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_91776588_9   5425 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5474
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_91776588_9   5475 ATCACTGGTCAT 5486
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


 242 28.99 0.00 1.45  chrX_91794809_91796541      230   298 (1435)    L1M4_orf2#LINE/L1       22    89 (819)  

  chrX_91794809_9    230 TAAATGAAAAGACATCTGTGTTGTTAAGAGGACAATAGTCCCCAAAGCGA 279
                          ii  vii     - ivi i         v i     v        vi  
  L1M4_orf2#LINE/     22 TGGATTGGAAGAC-TTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chrX_91794809_9    280 CATACAGGTTCAATATAAT 298
                         iv     i     iii   
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAAT 89

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1)  

2889 20.11 5.67 1.35  chrX_91794809_91796541      500  1240 (493)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_91794809_9    500 ATTCTAAAATTCACATGGATTTTCACGATACCCTGAATAGCAAAAAGTAA 549
                           i          i     vv v  v iv    v       v    -i  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAA 184

  chrX_91794809_9    550 TCTCAAAAAGAAACACAAGAAACAAAGT-GGAGGACTCACATGTCCTGAT 598
                            ii    ii  ------i        -            iv   ii  
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAA------GAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_91794809_9    599 TTCAAAACTTACTATAG---TACA-----CAAAACATAGTATGGTTCTCA 640
                                       i i---    -----   i   --  i    v  vi
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACA--GTGTGGTACTGG 276

  chrX_91794809_9    641 CATAGGGATATACATAAAGGCCAAGAGAATAGAAATGAGAGCTCGGAAGT 690
                             i     v     v  ii   vi        v      ii i   i 
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_91794809_9    691 AAACCTTCGCATATATCACTAATTGATTTATAACAAAG-TGCCAAGGCTA 739
                              ivii   v   viii         vii    i -       i i 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_91794809_9    740 TTCAATGTGGAATGAA-AGT-TGTTCAACAAATGGAGCTGATAAAACTGG 787
                                v    v   -   - v            v    iv v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_91794809_9    788 ATATGCAAATGTATT-GAATGATGTGAAATCCTTACTTTACAGCGTATCT 836
                            ?v  v   i vv-      v  vii i  i   i i   v i   vi
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_91794809_9    837 GAAAAT-AGCTCAAAATGAATGAAAGACCTAAATTGAAGAGGTGAGACTC 885
                         i     - i         i  v ?          vv     v i i   v
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_91794809_9    886 CAAAATTCTTAGTAGAAATCATAGGAACAAATTTTCATGACCCTTTATTT 935
                         i    i      v     v      ?ii    i   i     i vvi  v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_91794809_9    936 GGCAATAGTTACTTAAATATCATACCAAAACTACAATTAA---GAGAAAA 982
                               i   v    i    v i       vi    vi  ---i      
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_91794809_9    983 AAAAGGTAAATTCGACTTCATAAAAATTAA---CTTTTGTATATCAAAGG 1029
                           v  i      v        v        ---       iiv       
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_91794809_9   1030 ACACTATCAAGAGAATGAAAACACAACCCACAGAATTGAAGAATATATTT 1079
                                     i i      v              v i    v      
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_91794809_9   1080 GCAGAT-A-ATATCT--TAAG--ATTTAACATCTAGAATGTATAAAGAAC 1123
                            i  - -      --    -- i  i-i   i     i          
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAAC 775

  chrX_91794809_9   1124 TCTTACAA----------AAAGG-----TAACTCAATT-AAAAATGGTCA 1157
                                 ----------   i -----    i     -        v  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_91794809_9   1158 AAGTACTTCAACAGACATTGTTCCACAGAAGATATATAAATGGCTAATAA 1207
                            v i  v  i       vi    v          i       i     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_91794809_9   1208 GCATATGAAAATATTCTTAACATCATTAGTCTT 1240
                            i       v  v  i       ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (86 / 60)
Gap_init rate = 0.03 (21 / 773), avg. gap size = 2.48 (52 / 21)  


 401 32.82 0.00 0.00  chrX_91806435_91810869.rev     2878  3008 (1427)    L1M4_orf2#LINE/L1        1   131 (777)  

  chrX_91806435_9   2878 TGGAAATACATTCCATGCTCATGAGTAGGAAAAATCAATATCATTAAAAT 2927
                               v i  i     i     ii v    i v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91806435_9   2928 GTCCATACTGCCCAAAGCAGTTTATAGATTCAGTTGTATTTCTATCAAAC 2977
                          v v     v      viii i  i       iivvv  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91806435_9   2978 TACTAATGACATTCTTCACAGAACTAGAAAA 3008
                          v i iivi v  i  ii     v v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

Transitions / transversions = 1.53 (26 / 17)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.00 (0 / 0)  

2500 27.35 1.03 0.52  chrX_91806435_91810869.rev     3172  3946 (489)    L1M4_orf2#LINE/L1      130   908 (0)  

  chrX_91806435_9   3172 AAATTG-TTTTAAAATTAATATGAAACCAAAAAAGAGCCTGATTAGCCAA 3220
                           ii  - ii       v     i  viiv  ii  v  v  v       
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_91806435_9   3221 GGTAATCCTAAGCAGAAAGAGCAAAGCTGGAGGCCTCATAGTACCTGTCT 3270
                         iii    i i iv ii    i     i      v    i v v  iivi 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_91806435_9   3271 TTAAACTCTACTGCATGGCTACAATAACCAAAACAACATGGTACTTGTAC 3320
                          i   vii    i  vi      i   i   i   iii       v i i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_91806435_9   3321 AAAATCAGGCACATAGACCAATGGAATAGAATTGAGAACCCAGAAATAAG 3370
                           iivi  i  i     i                   ii          i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_91806435_9   3371 GTCACACACGTACAATCATCTGATCTTTGACAAAGCTAACAAAAACAAAC 3420
                         vi  i   iv  iii   vi    i  i     i v iv   i v  vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_91806435_9   3421 AATGGGGAAAGGACTTTCTATTCAATAAATGGTGGTGGGATAACTGGCTA 3470
                                    i ivv   v     i        v     i      v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_91806435_9   3471 GCCATTTGCAGAATATCGAAACTTGACCCCTTCCTTATAACATATACAAA 3520
                         ?   iv    i  v vi   ii v       v   i i v          
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_91806435_9   3521 AATTAACTAAAGATAAATGAAAGACATAAATATAAAAGCAAAAGCTATAA 3570
                                 v  i  ii  v ?    v     i   i   v   i      
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_91806435_9   3571 AAACCCTGGAAGACAAGCTAGGCAACACCAATCTA---GACAAAGAAATT 3617
                           vi i i     v  vv    ?i-i --     v---   vvv iiv v
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNG-TA--AATCTTCGTGACCTTGGGTTA 576

  chrX_91806435_9   3618 GGCAAATGTTTTAT-GATGAAGAACCCAAAAGCAATTGCAACAAAAGTAA 3666
                              vv    iv -   - v  vv         vvv          v  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_91806435_9   3667 AAAT-GACAAATAGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAA 3715
                             -  i    v   ii v  i   v v  i i   i  ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_91806435_9   3716 GAAACTATCAACAGAAT-AACAGACAACTTACAGAATGGGAGAAAATACT 3764
                           v        v i i -  v       ii                  i 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_91806435_9   3765 TGCAAATTATGCATTTGAAAAAGGTCCAATAGCCAGCATGTATAGAGAAC 3814
                                i  ii  i   v  i  v ivi  v    v  i    i     
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_91806435_9   3815 TTACACAAATTTACAAGAAAAAAATTATCAACCCCATTAAAAAGTGGGCA 3864
                          ivi    v iv i  v     i iv vi     v   ?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_91806435_9   3865 AAGTATATGAACAGACACTTTTCAAAAGAAGACATACATGTGGCCAACAA 3914
                            v  v    i     i  i  v        i     vi       i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_91806435_9   3915 TCATAGGAAAAAA-GCTCAACATAACTGAGCAT 3946
                         v  i v     i -         v ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (122 / 86)
Gap_init rate = 0.01 (9 / 779), avg. gap size = 1.33 (12 / 9)  


2448 30.45 2.70 0.67  chrX_91835083_91840426     3962  4851 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91835083_9   3962 TGGAAAAACATTCCATTCTCATGTATAGAAAAAATCAGTATCATTAAAAT 4011
                               i i  i    vi     v  v i  i v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91835083_9   4012 GTTCATACAGCCCAAAGCAATTTATAGGTTTAATTTTATTCCTATTAAAC 4061
                          viv    vv      vii  i  i  i  i  iviv  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91835083_9   4062 TGTCAATGAAATTTTTCACAGAACTAGAAAAAATGATTTTAAAATTTATA 4111
                          vi  iivivv     ii     v v  v  iv    ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_91835083_9   4112 TGAAAC--CAGGAAACATTCTGAGTAGCCGAGGAAATCCTAAACAAAAAG 4159
                           i  v--  i ii  --i v  i     i iiv    i i  v  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_91835083_9   4160 AACAAAGCTGAAGGCATCACACTACTTGACTTCAAACTGTACTACAGGGC 4209
                                i  i   vv       v iii i      viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_91835083_9   4210 TACAACAACCAAAATAGCATGGGATGGGTACGAAAACAGACATAGAG--C 4257
                             ii  i   i i  ii   v iv  i ii ii i       v  -- 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_91835083_9   4258 AATGGGACAGAATAGAGAGCCCAAACTTAAGGCCACACATCTACAACTAT 4307
                              i i     v     i   i vv   iv   i    i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_91835083_9   4308 CTCATCTTCTAGAAAGCTCACGAAACCAAGCAATGGGTAAAACACTCCCT 4357
                         i v  i   v v  i v vv i i    vv       v   iv ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_91835083_9   4358 ATTCAATAATTGGTGCTGGAATAACTAGCTAGTTATATGCGGAAGAGTGA 4407
                         v     i  v         i i    i v  ?ii i    ii    i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_91835083_9   4408 AACTGGATCCCATTCTTACGCTATATACAAAAATTAACTAAAGATGGATT 4457
                          ii    i   vvi  i  i i                 v  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_91835083_9   4458 GAAGACTTAAATGTAAAACTTAAAACTATAACAACCCT-GGAAGACAACC 4506
                         i?    i         i vi           -   i  -i     v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACA 547

  chrX_91835083_9   4507 TAAGCA-ATACCATTCTGGATACAGAAATGGGCAAAGATTTTAT-GATAA 4554
                           i ?i- v i -   vv  iviv iiv i     v i   iv -    -
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA- 595

  chrX_91835083_9   4555 CGATGTCAAAAGCAATTGCAACAAAAGCAAAAACTGACAAATGGGATCTA 4604
                         i  iii        vvv          v     iv  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_91835083_9   4605 ATTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTATCCACAGAGTAAA 4654
                           i   v v  i i   i  ii vv v  i  v      v v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_91835083_9   4655 CAGACATCCTACAGAATGGGACAAAATTATTT-CAAACTATGCATCTGAC 4703
                         v     v  i           v     -    -    ii  ii      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAAT-ATTTGCAAATCATATATCTGAT 744

  chrX_91835083_9   4704 A-----------TTCAGCATCTATAAGAAACAA--ACAAATTTACAATAG 4740
                          ----------- i   v  v     ii   vv--    v iv i    i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_91835083_9   4741 AAAAACAAACAATGCCATTAAAAACTGGTCAAAGGACATGAAGAAACACT 4790
                            i     i  iv v   ?    v   v       iv    v i   i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_91835083_9   4791 TTTCAAAACAAGACAAACATGTTGCCAACAAGCATGTGAAACAAAGCTCA 4840
                          i  v   v    i v   vi v     i     ii     vi v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_91835083_9   4841 ---TCACTGATTAT 4851
                         ---   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (164 / 103)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


2388 26.80 2.29 3.38  chrX_91841232_91843731     1135  2052 (448)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91841232_9   1135 TGGAAACACATCCCATGTCCATGAATTGGTAGAATCAATATTGTGAAAAT 1184
                               v i         i    i     v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91841232_9   1185 TACCATACTGCCAAAAGCAATATACAAATTCAATGCAATTCCCATCAAAA 1234
                         vi v     v  v   vii  v    i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91841232_9   1235 TGCCATCATCATTCTTTACAGAACTAGAAAAAACAATCTTAAAATTCATA 1284
                          v   v vv v  i   i     v v  v  ivii   i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_91841232_9   1285 TGGAACCAAAATGTGCCCACT-TAGCCAAAGCAAGACTAGGCAAAAAGGA 1333
                              viiv  v vi    vv-        i   vvi iiiv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_91841232_9   1334 CAAATCTGGAGGCATCACA-TTCCAGATGTCAAATTATACTACAAAGCTG 1382
                             vi      vv     -    vi  v     viv            i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_91841232_9   1383 TAGTTATCAAAACAGCATGGTACTGGTATAAAAATAAGCACTTAGACAAA 1432
                         i   v     i    ii         i    ii   ii  iv    iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_91841232_9   1433 GGAAACAGAATAGAGAACCCAGAAATAAAGCCCA-ATATTTACAGCCAAC 1481
                         v i  i     v    ii           -    - i     ii i   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATGGTCAAT 349

  chrX_91841232_9   1482 TGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGAGAAGGACACCCTA 1531
                             i   i    i vviv   i v   vv i    ii   i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_91841232_9   1532 TTAAACAAATGGTGCTCAGATAA-TACACAAGTCACATTTAGAAGAATGA 1580
                           v             vi  i  - iv i -?i     vi i        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATA-KCCACATGCAAAAGAATGA 448

  chrX_91841232_9   1581 AATTGGATCCTCATCCCTCACAT--TATACAAAAATCAACTCATGATGGA 1628
                          i     i  ii --       i--           i      vi     
  L1M4_orf2#LINE/    449 AGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_91841232_9   1629 TCAAAGACTTAAATCTAAGACCTGAAACCACAAAAATTCTAGAAGATAAC 1678
                            ?    i     v     v  i    i i    v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_91841232_9   1679 ATCAGAAAAGCGCTTCTAGACATGGACTTAGGCAAAGAGTTCATTACCAA 1728
                           vi ?iv ivv    vv   v v iv        v iv   v vivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_91841232_9   1729 GA-ACCAAAAAGAAATGCAATAGAAACAAAGATAAATAGATGAGACTT-- 1775
                           -       iv v v    i i  iv   i   i   i  vi     --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_91841232_9   1776 ----AATTAAAAAGCTTCCTCACAGCAAAAAAAAAAAAATAATAATAATA 1821
                         ----         -   iivii vv    ii -------------i v  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA-------------CACTA 682

  chrX_91841232_9   1822 ATCAGCAGGATTAACAGACAACCCAAAGAGTGGGAGAAAATGTATTCAAA 1871
                         -   iv iii v  v          v   i           i v v    
  L1M4_orf2#LINE/    683 -TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_91841232_9   1872 CTCTGTATGCAACAAAGAACTAGTATCCAGAATCTAGAAGGAACTCAAAC 1921
                         iiv i   vii i  i i   v           v  v  i      vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_91841232_9   1922 AAATCAACAAGACAAAAACCAAATAATCCCGTC-AAAAGTGGGCA----- 1965
                           v    i  v v   i  -      i  vi i-    i      -----
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_91841232_9   1966 --TGAATAGACAGTTCTCAAAATGTAATGAAGACATGGAATCAACCTAAA 2013
                         --          v     v   ------     i  iv  viii  --  
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAA------GAAGATATACAAATGGCC--AA 872

  chrX_91841232_9   2014 TGCTCATCAATGATAGAATGGATCAAGAGCATGGGGGTA 2052
                          ivv  i--    v ii   v-    v v  ????????
  L1M4_orf2#LINE/    873 TAAGCAC--ATGAAAAGATGC-TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (135 / 108)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.60 (52 / 20)  


1192 23.13 1.36 2.04  chrX_91856828_91863705     3172  3465 (3413)    L1M4_orf2#LINE/L1        4   295 (613)  

  chrX_91856828_9   3172 AAAAAAATTCTATGTTCCTGAATTAAAAGAATTAATACTGTTAAAATGTC 3221
                            i v  i i      v  i   ii    v      i      i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_91856828_9   3222 CATACTACCCAAAAGCAATCTACAGATTCAAGGCAATCCCTATTGAAATC 3271
                         v     v      -vii              v           ii     
  L1M4_orf2#LINE/     54 AATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_91856828_9   3272 CCAATGACCTTTTTCACAAAAATATTTTTAAAAA----ATTCTAACATTT 3317
                            iivi       ii  i    ----- i v  ----  i    v   i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAAT-----TGACAAGCTGATCCTAAAATTC 147

  chrX_91856828_9   3318 ATATAGAGCCACAAAAGACCCAGAATAGCCAAAACAATCCTGAATAAAAG 3367
                             i  ivii   ii                       i    v  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_91856828_9   3368 GAACAAAACTGGAGGAATCAAATTACCTATTTTTAAATTATACTACACAG 3417
                                ii       v   v i v  i v   i   viv       v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_91856828_9   3418 CTATAGCAACCAAAGCAGCATGGTACTTGCATAAAAACAGACACATAG 3465
                            i  i  i   ii   ii       v      ii i     i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 2.24 (47 / 21)
Gap_init rate = 0.01 (3 / 292), avg. gap size = 3.33 (10 / 3)  

2026 23.33 0.59 7.13  chrX_91856828_91863705     3734  4406 (2472)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_91856828_9   3734 AAAGGCAGACACATAGAAGAGTGAAATATAATAGAGAACACAGAAACAA- 3782
                           i ii     i     vv i  i    v   v    iiv      i  -
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_91856828_9   3783 TCCACACATCTACAGTGAACTAATTTTCAACAAAAGTGCCAAGAATATAC 3832
                         i   i    i  ii  v  i i      i    ii         vi  v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_91856828_9   3833 ACTGGGGAAAAGATAGTCTTTTACATCAGTGGTGCTGGGAAAACTAGATG 3882
                          v        ii          vv iv i           v    i   i
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_91856828_9   3883 TCCACATACATAAGAATAAAACTAGAACACTGTCTCTCACCATATACAAA 3932
                         ?      i  v      i  ii i  v v  ii   v             
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_91856828_9   3933 AATCAAATCAAAACGGATTAAAGACTTAAATCTAAGATCTCAAACTATGT 3982
                            i  v      i    i ?    i     v     v  v       iv
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_91856828_9   3983 AACTACCAAAAGAAAACTTTGGGAAAAATTTCCAAGACATTGG-TCAGGG 4031
                             vii i        v v  ?iv    i i iv   v    - i   -
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG- 578

  chrX_91856828_9   4032 CAAGTATTTCTTGAGCAATACTCCACATGTACAGGTAACCAAAGCAAACA 4081
                            vvi      iiii vv  v   v v i   i i   v    v   v 
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_91856828_9   4082 TGGACAAATGGCATCACATCAAG-TTAAAAAGCCTCTGCACAGCAAAGGA 4130
                          i  i    v v iiv      i-       - i i  ii vv       
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

  chrX_91856828_9   4131 CACAGTCATGAAAA-GAAGAGACAACCCACAGAGTGTGAGAAAATATTTG 4179
                            vi   v    i-   i              i  v             
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_91856828_9   4180 CAAATTACTCATCTGACAAGGGATAAATAACCAAAATATATAAGAAGTTC 4229
                              i ivi      i      ivvi  v   i         ii ii  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_91856828_9   4230 AAAGAACTCTACAGGAAAAAAAAAAAAAATATATATATATATATATATGT 4279
                         vv v     -------  v  v     i i -------------------
  L1M4_orf2#LINE/    778 TTACAACTC-------AATAATAAAAAGACA------------------- 801

  chrX_91856828_9   4280 ATATATATATATATATAAATAATAGTTCTACTAAAAACTGGGCAAAGGAT 4329
                         --------------------    iii v i ?    v            
  L1M4_orf2#LINE/    802 --------------------AATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_91856828_9   4330 ATGAATAGATATTTCTCAAAAGAAAACATACAAATGACAAATAAGCATAG 4379
                         v        i       v      i i         i v        i v
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_91856828_9   4380 GAAAGGGTGCCCAACATCAGTGATTAT 4406
                             i i   i        ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (92 / 61)
Gap_init rate = 0.01 (8 / 629), avg. gap size = 6.50 (52 / 8)  

 878 26.63 9.48 6.21  chrX_91856828_91863705     5396  6007 (871)    L1M4_orf2#LINE/L1      198   829 (79)  

  chrX_91856828_9   5396 GAACAATGCTGGAGGTATTGCACTGCCTGATATCAAACTGTACTACAAAG 5445
                               v i      vv ii    v  ii  v     viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_91856828_9   5446 TTGTCATACCCAAAACAGC-----AC-GTCATACAAACCAGACACA--GA 5487
                         i iivi  vi   i    i-----  - v    vii i-     i --  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGA 296

  chrX_91856828_9   5488 ACAATGGAACAGAATAGATAACACATAAATAA-TCCATGAACTTACAGCC 5536
                         v        i     v  v iiv  v      -i    iv i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_91856828_9   5537 AACTCATTTTCAGCA-TTGCACCAAGAACATACATTGGAGAAAGAACAGC 5585
                           i v      ii  -vv ii      v   v  v   i       i  i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_91856828_9   5586 CTTTTTAATAAAATGATGCTGGGAAAACTGAATATCT-CTTTCAAAAGAA 5634
                              i  i   -  i        v     i   ? i- v v        
  L1M4_orf2#LINE/    397 CTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_91856828_9   5635 TAAAACTAGATCCCCATCTTTTG--ATATGTAAAACTAGTAAACTCAAAA 5682
                          i  ii i  i   i i  ivii--    ii    ---i v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAA---ATTAACTCAAAA 492

  chrX_91856828_9   5683 TGGACTAAAGACTTAAATGCTAGGCATAAAAATTCGAAACTAATATTTTT 5732
                             ii ?    i      -------   i ii -i      --------
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATG-------TAAGAGCT-AAAACTA-------- 526

  chrX_91856828_9   5733 AGGGTAAAA-TCTCAAAAGAACAGAAAACAAAAGCAAAAATAGACAATTG 5781
                         ----     -   i i     -----    v i ?i----  ---   iv
  L1M4_orf2#LINE/    527 ----TAAAACTCTTAGAAGAA-----AACATAGGNG----TA---AATCT 560

  chrX_91856828_9   5782 TAATGACCTCAAAATAA--AAAGCTTTC---------ACACAGAAAAACA 5820
                          vi      iiiiv  i--  v v    ---------    v-    i  
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC-AAAAGCA 609

  chrX_91856828_9   5821 CA-----CACATGTAAACACACACACAC---ACA-CA-CACAACAAAAAA 5860
                           -----  v v v   v i v i v i---  v-  -  v  iv     
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_91856828_9   5861 C-----------AAAAAACA--ATTAACATGGTGAAGAGATTACCTGCAA 5897
                          -----------   ii   --  i  v vi     i   iv   ii  i
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_91856828_9   5898 AATTGGATTACATGTTAACAAACTATATA----ACAAGATATTAATAACC 5943
                            v   vv v  i  vi    ii     ---- i   iv i vi  v  
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_91856828_9   5944 AGAATATATAAGGTACTC--A-AACTCAATAGCAAAAATA---ATAATCC 5987
                                    i v    -- -         ii     v ---    i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_91856828_9   5988 CTTTAAAAAGTAAACAAAGG 6007
                         vv  ?    i iii      
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.69 (100 / 59)
Gap_init rate = 0.05 (30 / 632), avg. gap size = 3.20 (96 / 30)  

 282 17.58 6.59 3.30  chrX_91856828_91863705     6298  6388 (490)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_91856828_9   6298 AAAAGTAAACAAAATAGATT--AATACATATTTCTC-AAAAAAGACATGC 6344
                             i iii    i--    --    v i       -   i    i  i 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAG--GATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_91856828_9   6345 AAATGGC---TAAGCTGTATGAAAAAATACTCAACACTAATCATCAG 6388
                                ---     -ii       i  i       ii ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGC-ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 15.00 (15 / 1)
Gap_init rate = 0.05 (5 / 94), avg. gap size = 1.80 (9 / 5)  


3479 19.92 2.42 6.74  chrX_91875331_91877573      802  1750 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91875331_9    802 TGGAAAGACATTTCATGTTTATGGATTAGAAGACTTACTTTTGTTAAAAC 851
                                 i  ii      i       i         v v       i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91875331_9    852 GGCAATGCTAACTTCAAGC-AATCTATAGACTCAATGCAATC---ATAAA 897
                               i  -- ii   ii-i     i   i    i      ---  v  
  L1M4_orf2#LINE/     51 GGCAATACT--CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_91875331_9    898 AAGTCTAAGAGCCTTTCT-GCAGAAATGGAAAACACAATTCTTGAATTCA 946
                           vi i ivv      i -        v  v  vvii  i  vi      
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_91875331_9    947 TATGAAATTGCAAAGAGCCTTGAATA-TTAAAACAAACACTCACAAAGTA 995
                             i  v     i ii  iv     -ii       ----  vii  iv 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA----TCTTGAAAAA 194

  chrX_91875331_9    996 GAGGAACGAAGTTGAAGGACTATTATTTTCACATTTTATAACTTACTACA 1045
                           i    i      i      vvi i  i vv    i v           
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_91875331_9   1046 AAACTACAGTAATTAA-ACAGTATGGTCCTAGCATAAGAACAGACATATG 1094
                           i          i  -     i    v  i       i i        i
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_91875331_9   1095 CACTGATGGAACAGGATTGAGAGTCCAGGAATAATCACATGTATGTATGG 1144
                         v iii      i  i             i     v v   ii  v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_91875331_9   1145 TCAATTGATTTTCAACAAGGATGCCAAGATCATTCAATAGGTAAAGAATA 1194
                                      i      i        i        i  v        
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_91875331_9   1195 GTTTCCTCCAAAAAATGGTGCTGTGACAAATTGATATTCACATACAAAAT 1244
                           i ii  -  v           v     v v    ?i     i     v
  L1M4_orf2#LINE/    395 GTCTTTTC-AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_91875331_9   1245 AATAAAGTTGCAGCTTTATACAAAATTATACAAAAATATACAAATTATGT 1294
                            i      v v ii  i- ---- i i  -------------------
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTAC-C----TCACAC------------------- 469

  chrX_91875331_9   1295 ATATATACATATACAAAAATGTACTTAAAATTGTATCAAAGACTTAATGA 1344
                         -------             vv   i     v -    ?    i   vvi
  L1M4_orf2#LINE/    470 -------CATATACAAAAATTAACTCAAAATGG-ATCAWAGACCTAAATG 511

  chrX_91875331_9   1345 TAAGAGCTAAA-CTCTAAAGCTCTTAGGAAAAAA---AGGGTTTTCCTGA 1390
                                    -  v    i       i i    ---   ?v v----i 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA----AA 557

  chrX_91875331_9   1391 CCTTCATGACCTTGGATTTGGCAACGGATTCTGAGATCTGACATCAAGAG 1440
                         i    i         i  v     i  v    v    v     i   i  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_91875331_9   1441 TACAACCAACAAAAGAAAAAATAGATAAATTGGAGTTTGTTAAAATTAAA 1490
                         i    v                            v  ii i         
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_91875331_9   1491 ACGTTTTTCATGTTAAAGGACATTATCCAGGAAGAGAAA-GACAACTTAC 1539
                          vv    viiiv i        i    v  i   v    -      ii  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_91875331_9   1540 GGAATGGGAGAAAATATTTGCAAATCACATATCTGATAAGAATCTAGTAT 1589
                         i                          i            iiv  v    
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_91875331_9   1590 CCAGATTTTATAAAGAACGCCTTCTACTCAATAACAAAATGAAAAACACT 1639
                              v v          v i v v         i    v  v   i --
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA-- 805

  chrX_91875331_9   1640 CCCATTCAACTCTTAGAAGTCTTTAACAACAACAACAACATGGACTTGAA 1689
                         --- ii   ------------  ?  v  iii--i   - -   i     
  L1M4_orf2#LINE/    806 ---ACCCAA------------TTWAAAAATGG--GCAA-A-GGATTTGAA 836

  chrX_91875331_9   1690 TTGATGTTCCTCTAGAGA---TGTGCAAATGAC--------ACTTGAAAA 1728
                          v  ii  i   i i   --- i i      i --------  v      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_91875331_9   1729 GATGCTAAACATTATTAGTCAT 1750
                               v     i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (119 / 66)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.78 (87 / 23)  


2598 26.51 2.75 2.86  chrX_91993713_91995663      550  1458 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_91993713_9    550 TGGAAAAATATTTTATGCTCATGGATAAGAAAAATCAATATCATTACAAT 599
                               i    iii   i        vi   i v i     ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_91993713_9    600 GGCCATA-TCGCCAAAGGAATGTACAGATTGAACACTATTTTTATCAAAC 648
                            v   -  v     vvi  v        v   i v  iii       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_91993713_9    649 TACCAA-TGTCATTTTTCATAGAACTAGAATTAGGAAAAAAACT-ATTCT 696
                          v   i-  i -     iii    -----   i---- v  i  -  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA-----ATTG----ACAAGCTGATCCT 140

  chrX_91993713_9    697 AAAATTTATATGAAACCAAAAAAGAGCCTGTATAGCCAAAGGAATCCTGA 746
                               i     i  viiv  ii  v  v v         iv    i   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_91993713_9    747 GCAAAAAAAACAAAGCCAGAGACATCACATTACCAGACTTTACATTACCA 796
                         iv  i  i       iii   ivv     i v  vi i  i ------- 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA-------A 233

  chrX_91993713_9    797 AACTATACTATAAGGTTACAGTAAATAAAACAGCATGCTATTGCTACAAA 846
                             -     i  i i        vi  i    ii  v  i  vi i  i
  L1M4_orf2#LINE/    234 AACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_91993713_9    847 AACAGATACATAGACCAATG--ACAGAATAGAGAACCTAGAAATAAAGCT 894
                         i i   i i     i     -- i     v    ii i         v i
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_91993713_9    895 GCACACCTACAACCATCTGATGTTTGACAAAG-TCCACAAGAATA---AA 940
                         ii   ii  iiii  vi    v  i     i - v -     vi ---  
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAA 381

  chrX_91993713_9    941 TGATGAATAAGGACTCCCTATTCAATAAATTGTGCTGGTATAACTAGCTA 990
                           iv   --  i ivvi  v     i    v       v i    i v  
  L1M4_orf2#LINE/    382 TGGGGAA--AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_91993713_9    991 GCCATATGCAGAAGAATGAGACTCAACCCCTTCCTTATACCATATACAAA 1040
                         ?   i     i        iii vi      v   i i            
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_91993713_9   1041 AAATAACTCAAGATGGATTAAATATTTAAATGTAAGAACTGAAACTGTAA 1090
                           v        i      i ? v ii           i  i     i   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_91993713_9   1091 GAATCCTCAAAGAAAGCTTAGGAA-ACACCATTCTGGACCAGCCTGGG-- 1137
                         i v  i vi      i v    ?i- v i -   vv    ---i    --
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACC---TTGGGTT 575

  chrX_91993713_9   1138 --GAAATAATTTATTAT-TAAGTTCTGTAAAGTATTTGCAACCAAAACAA 1184
                         -- v   ii   v   v-  v vivivv    i ivv     -    v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-AAAAGAA 624

  chrX_91993713_9   1185 ACAAT-GACAAATGAAACGTAATTAAACTAAACAGCTTCTGCACAGCAAA 1233
                          v   -  i    vii  v v  i   v v  v i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_91993713_9   1234 AGAAACTACCAACAGAGTAAACAGACAACCTACAGAATGGGAGAAAATAT 1283
                         i  v    i   v i   i  v        i                   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_91993713_9   1284 TTAAAAACTATGTATCTGACAATGGTCTAATGTCTAGAATTTATAAGGAA 1333
                           iv   ii  i       i  v  v  vi i  i     v     i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_91993713_9   1334 CTTATACAATTGAACAAGCAAAAGACAAAAAAT---AT----AACTGGGG 1376
                           iv     i v  i  vv          v  i---  ----  v    v
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_91993713_9   1377 AAATGACACGAACAGACATTTCTCAAAATAAGACATACGAGCAGCCAACA 1426
                            v  ivi   i           v   v    i    i iii     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_91993713_9   1427 G--ACATGAAAAAATGCTCAATATCAATAATTAT 1458
                         i--         i        i    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (149 / 89)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.22 (51 / 23)  


2695 24.19 1.16 5.68  chrX_92004623_92008769.rev     2706  3656 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92004623_9   2706 TGAAAAAATATTCCATTTTCCTGGATTGGAAGCATCAATTTTATTAAAAT 2755
                           i   i    i    v   v           vv i   v  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92004623_9   2756 GTCCATGCTATCCAAAAACATCTACAGATTTAAAGCAACCCCTATCAAAA 2805
                          v v  i  vi     vvv           i  v    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92004623_9   2806 TACCAAATACATTCTTCA-AGAAAAAGAAAACACCATCCTAAAATTTATA 2854
                          v   iv i v  i  ii-     vv  v  vviv           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_92004623_9   2855 TGCAGTCACAAAATATTCAGAATAGTCACAGCTAAGTAAGTAAAAAACAA 2904
                           v ivii   iiv ii        i  v i v vv --- i     v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT---TGAAAAAGAA 197

  chrX_92004623_9   2905 CATCAACAACAAACTAGAGGAATCAAATTGCCTGATTTCAAATTATACTA 2954
                         v ---    -- ii i     v   v i v  ii        viv     
  L1M4_orf2#LINE/    198 GA---ACAA--AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_92004623_9   2955 CAGAGCTTATAGTAACCAAAACATAATGGTACTGGCATAAAAACAGACAC 3004
                           i    - i     i   i   vvi              ii i     i
  L1M4_orf2#LINE/    243 CAAAGCT-ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_92004623_9   3005 ATAGATCAATGGAACAGAATAGATAACCCAGAAACAAATCTACAAACCTG 3054
                                       i     v  v ii       i   i i i v ii i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_92004623_9   3055 CAGTAAACTAATTTTTTACAAAGGTGCCAAGACCATGTGCTGGAGAAAAG 3104
                         ii  v  i i     iv    i              viiv   i    ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_92004623_9   3105 ATACTCTCTTCAATAAATG-TGCTGGGAAAATTGGACATCCATATGGAGA 3153
                            v   i     i     -        v  i    i ?   i   v i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_92004623_9   3154 AGAAGGAAACTTGAACCCC-ATCTCTCATGGTATACAAAAATAAAATTAA 3202
                             v   i-   i     - i   v  ivi           v  v i  
  L1M4_orf2#LINE/    442 AGAATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_92004623_9   3203 AATAGATTAAATACTT-----TAAGATCTCAAACTTTGAAACTACTACAA 3247
                            i   i ? v  i -----     v  v     v i     vi  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_92004623_9   3248 GAAAACTTTGGAAAAATTCTCCAACACATTAGTCTGTGCAAAGATTTACT 3297
                               v v  ?iv  v   i ivv  v  i vi iv    v i   vi 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_92004623_9   3298 GAGTAATACACCACAAACACCAGCAACCAAAGCAAGTGTAGACAAATTGG 3347
                         iii  vv      v  i   v      v    v  ivi    i       
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_92004623_9   3348 ATGACATCAAG-TTAAAAAGCTCCTGCATAGCAAAGGAAATAATCAACAA 3396
                          ivv      i-       -  ii  iiivv       v iv     v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_92004623_9   3397 AGTGAAGAGACAACCCATAGAAAGGGAAAAAATATTTGCAAACTCCCCAA 3446
                               i          i    v    i              --------
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-------- 731

  chrX_92004623_9   3447 CTGGCAATGGATTCATAACCAGTATATATATATACTGGTTTTATACTGTA 3496
                         ------------     -------   v i-   vv  ------   ---
  L1M4_orf2#LINE/    732 ------------TCATA-------TATCTG-ATAAGGG------ACT--- 752

  chrX_92004623_9   3497 TATATACATACATATATATAAAAGGAACTCAAACAGCTTTATGG-GAAAA 3545
                          i   v  v ---         --      vv   i  iv  ii-i    
  L1M4_orf2#LINE/    753 TGTATCCAGA---ATATATAAA--GAACTCTTACAACTCAATAATAAAAA 797

  chrX_92004623_9   3546 TATATAATAATTCAATC-AAAAATGAGTAAAAGATTTAAATAGACATTTC 3594
                         v i -     ii    i-       i i   i     i            
  L1M4_orf2#LINE/    798 GACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_92004623_9   3595 TCAGAAGAAGACATACAAATGGCATGCAGGCATATGAAAACGTGCTCACC 3644
                           vi       i           vvii i   i       vi      v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_92004623_9   3645 ATCACTGATCAT 3656
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (129 / 98)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.10 (65 / 21)  


3439 20.14 5.38 1.49  chrX_92030321_92034465.rev     2781  3654 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92030321_9   2781 TGAAGAGACCTTTTGTGTTCATGGGTTGTCAGATTTAATATTGTGAAGAT 2830
                           i i   iv iiii         i   vv   i          v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92030321_9   2831 GTCAATAC-CACCAAAGAGATGTACAGATTCAATGCAAACCCAATCAAAA 2879
                          v      - v     vv   v           i    v   v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92030321_9   2880 ATCCAAATGACATTCTACGGCAAAATTAGAAAAATCTACCCCAAAATTCA 2929
                         vi   iv  v v  i --v   i  v v  v  iiiv i  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT--TGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_92030321_9   2930 TGTGGAATTTCAAAGGACTCTGAATAGCCAAGA-AATCATTTTAAAGAGA 2978
                          i     v v   i    i v          i -    --  v   i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC--TTGAAAAAGA 196

  chrX_92030321_9   2979 -GAG-AGATTTGGAGGTGCCACACTTCCTGATTTCAAAACTTATTACAAA 3026
                         -  i- i v       vvi         ii             i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_92030321_9   3027 GCTATGGTAATGAAAATAGTGTCATACTATCCTAAAGACAGACACATAAA 3076
                             ii     v  i i     vi    iv v   i  i     i   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_92030321_9   3077 T-----GCATAGAATAGAGAGCCCAGAAATAAATCTTCACATTCATAGTC 3121
                          ----- v       v     i           i ivi     i  i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_92030321_9   3122 AAATGATTTTTGGCAAGATT-CCAAGACAATTTAGTAAGAAATGAATAGT 3170
                           v       i i    iv -       v   i i ii i  v       
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_92030321_9   3171 CTTTTCAATAAGTGGCCCTGGGGAAATTGGATATAAATATGCAAAAAAAA 3220
                                 i  i   iv     iv  i      ?vv i        i  -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA- 445

  chrX_92030321_9   3221 TGAAGTCGGAT---TAATTAATTACTATGTA-AAGAATTAATTCAAAGTG 3266
                               i   i---  vi v i-  i  i  -  i      i     i  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCAC-ACCATATACAAAAATTAACTCAAAATG 494

  chrX_92030321_9   3267 GATCAAAGTCCTAAAAATAAGAGCTAGAAGTAGTAAACTCTTAGATAGAA 3316
                              ?  v      vi         i  v  vv           vii  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_92030321_9   3317 ATATATGAGAATATTTTCATTACATTGGATTAGGCAA-GATTTCTTGAAT 3365
                          i   v ? v v  i   i v  v    i        - i      ii  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_92030321_9   3366 ATGACACCAAA--TAGAGACAATAAAAGAAAAAAATAGATGAAATGGACT 3413
                                    --i v ii   i           -     i  v      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACT 643

  chrX_92030321_9   3414 TCACCAAAATTTAAAAACTGTTATACACCCAAGGACACTGACATAAGTGT 3463
                            i       -       v  i i vi v         iv  vi iv  
  L1M4_orf2#LINE/    644 TCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_92030321_9   3464 GAAAAG---------------GGAGAATATATTTGCAAATCATATATCTG 3498
                               ---------------      v                      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_92030321_9   3499 ATAAGGGA----TAT---GAGTATATAAAAACCTCACCTCTACAACTGAA 3541
                                 ----   ---  i        i v   ----i       v  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTC----TTACAACTCAA 788

  chrX_92030321_9   3542 CTAC-----GACAAA-AAC--AATTGAAAAAATGGGCAAAGCATTCGAAT 3583
                         iv i-----      -   --    -?              v   i    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAAT 837

  chrX_92030321_9   3584 AGACATTTCTCCAAAGTAGATATACAAATGGCCAATGAGCACATGAAAAG 3633
                                         v                   i             
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_92030321_9   3634 ATACCCGACATCACTAATCAT 3654
                           i i i      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (103 / 69)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.50 (60 / 24)  


 490 35.50 1.73 0.43  chrX_92062979_92071844.rev     6691  6921 (1945)    L1M4_orf2#LINE/L1        1   234 (674)  

  chrX_92062979_9   6691 TAGAAAACCCTTTTATGTTTGTGAAT--GAAGAATTCGTGTCATTAATAT 6738
                          i    iviv iii     ii  i  --     v  vi i ii    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92062979_9   6739 GGCCACACGGTCAAAAACAATTTACAGGTTCAATGCTACAGCTGTCAAAC 6788
                            v i  vvi v   vii  i     i     i  v ivv  i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92062979_9   6789 TACCAGTGACATTCTTCAAAGAACTAGAAAAAGCT-ATTTTAAAATTTTT 6837
                          v    ivi v  i  iiv    v v  v  -   -  ii       iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_92062979_9   6838 ATGAAACTAAAACTAGCCCA-AATAGACAAGGCAATCCAAAGGAAAGAGA 6886
                            i  v iv  vvii    -     v   ii     ivi ii  ii   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_92062979_9   6887 ACAAAGCAAGAAGTGTCATGCTACCTGACTTCAAA 6921
                               ivi  i vv   ii  v  ii i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

Transitions / transversions = 1.56 (50 / 32)
Gap_init rate = 0.02 (4 / 234), avg. gap size = 1.25 (5 / 4)  

1855 25.74 2.94 4.71  chrX_92062979_92071844.rev     7688  8367 (499)    L1M4_orf2#LINE/L1      214   881 (27)  

  chrX_92062979_9   7688 CTCCCTCCTGTCCATATCAAAACTATACTACAGGGTTACAGTAATCAAAA 7737
                            v v i vi v  v        -       ii i            i 
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGA 262

  chrX_92062979_9   7738 TCAACACGGTACTGGTGCAAAAAAAAAAAAGGACACATGGACCAATAGAA 7787
                         -  iiii        iii  ii v ------    i  i  i    i   
  L1M4_orf2#LINE/    263 -CAGTGTGGTACTGGCATAAGGATA------GACATATAGATCAATGGAA 305

  chrX_92062979_9   7788 CAGAATAGATAGCCCAGAAATAAGGCCACATACTTACAACCGTATAATTT 7837
                         i     v  v  i          iv   i i i   iiii ivv i    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_92062979_9   7838 TTGACAAAACCGACAAAAAACAAGCAGTAGGGAAAGGAC--TCTTCATTC 7885
                          i     iivi v   i v-  vv  i i       i i--    --   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCTT--TTC 402

  chrX_92062979_9   7886 AGTAAATGGTGCTGGGATAACTGGCTAACCATATGCAGAGAATTGAAACT 7935
                          ii              i      v  ?   i     i ii v    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_92062979_9   7936 GGACCCTTTCTTTACACCATATACAAAA-TCAATTTGAGATGGATTAAAC 7984
                               i v i i               - i  i ii i      i ? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_92062979_9   7985 ACTTAAATGTAAAACCCATAACTATAAAAACTCT-GGACAACAACCTAGG 8033
                           i         i v i v          -    -i  vi v   v    
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGG 551

  chrX_92062979_9   8034 TGGTAACATAC-TGAACATAAGAACT-GGAAAAGATTT------TATGAC 8075
                         ? vv  iv v -   v v ii --i -  v  v i   ------      
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_92062979_9   8076 AAAGTAGCCAAAAGTAATTGCAACAAAA-ATAAAATTGACAACTGGGATC 8124
                          ------       i vvv         - v     v  i  v v   ii
  L1M4_orf2#LINE/    600 A------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_92062979_9   8125 TAATTAATCTGCAGAGCTTCTGCACAACAAAAGAAACTATCAACAGGGTA 8174
                          v  i  vv vv i i   i  ii vv    i  v        v ii  i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_92062979_9   8175 AACAGACAATATATAGAATGGGA--AAACATTTGCAAGCTAAAAATTTGT 8222
                           v      ivi i         --   i        iii ---------
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA--------- 734

  chrX_92062979_9   8223 TGGATATCTGACAAAGGTCTGATATCCAACATCTATAAGGAAATTACACA 8272
                          --        i  i  v  vi      iv  v     i   v ivi   
  L1M4_orf2#LINE/    735 T--ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_92062979_9   8273 AATTTACAAGTGAAAA--CAAAT--CCCA-TTAAAAAGTGGGCAAAGAAC 8317
                          v iv i  - i    --     --    -  ?    i         i i
  L1M4_orf2#LINE/    783 ACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_92062979_9   8318 ATAGATAGACACTTTTCCAAAGAAGACATACATGTGGCCAACAAGCATAT 8367
                         v ii       i  i           i     vi       i     i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 1.80 (110 / 61)
Gap_init rate = 0.03 (22 / 668), avg. gap size = 2.36 (52 / 22)  


1543 27.97 4.34 1.77  chrX_92089282_92090895      500  1121 (493)    L1M4_orf2#LINE/L1      271   908 (0)  

  chrX_92089282_9    500 TATTAATATAAAAACAGACACATAGATTAATGGAAAAGAGTAGTAAACTC 549
                           i iii    ii i     i      i       v   i v vi iii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_92089282_9    550 AGAAGTAAAACCACACACTTACAATTATCTGATCATCAACAAGGCTGACA 599
                             i    v   i   i   iii i vi    iv  i      v  v  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_92089282_9    600 AAACCAAGCAATGGGAAAAGCACTACCTATTCAATATATAGTGCTGGGAT 649
                          i    vv       i    v ivii  v     i v  i         i
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_92089282_9    650 AACTGGCTAGTTATAAATGCAGAAGAATGAAACTGTACTCTTGCCTTTCA 699
                               v  ?ii i --    i         ii  v  i i i   iv  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACA--TGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_92089282_9    700 TCATATACAAAAATTACTCCAAGATGAATTAA----TTAAATTTAAGATA 745
                         i               vii   i   i  i ?----i     v     vv
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_92089282_9    746 TCAGTCTATAAAAAACTTAGAAGAAAACCTAGG---AAATATCCTTCTCA 792
                          v iv        vv             v    ---    ---    vii
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTG 565

  chrX_92089282_9    793 ACACGGGCCTTGGCAAATAATTT-TTGGCTGAGTTCTCAAAAGCAATTGC 841
                           viv  vi v     - ii   -  i v iv vivi        vvv  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_92089282_9    842 AAATATATGCCAAAAGTTGGCAA-CTGG--TACAT---AATTAAAATCTT 885
                           -i v v v-    i v ii  -i   -- v   ---        v   
  L1M4_orf2#LINE/    615 AA-CAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_92089282_9    886 CCGCACAGCAAAAGAAACTATTAATAGAGTAAACAGACTACCTACACAAT 935
                         ii ii vv    i  v     i  v i   i  v    v   i   v   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_92089282_9    936 GGGAGAAAATATTTGCAAACTACACATCTGA-AAAGGTTTAATATCCAGA 984
                                            ii i i      -  i  vi vi        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_92089282_9    985 AACTACAAGGAAATTAAGCAATTCAATAGTTTAAAAAACAAATAAAAACA 1034
                          vv  i  i   v ivvi   i      i v-    i        vvvv 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATA-AAAAGACAAATAACCCAA 811

  chrX_92089282_9   1035 TTAAGAAATGGGCAAA--ATATAATCATAGACA----------AAAGACA 1072
                           ? i           --  v i --       ----------i    i 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGA--ATAGACATTTCTCCAAAGAAGATA 859

  chrX_92089282_9   1073 TACATGCAGTCAAAAATTACATATAAAAATACTAATCATTAGAGAAATG 1121
                             viii i   v  vi    iv   i  i  v v   i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (101 / 70)
Gap_init rate = 0.03 (16 / 638), avg. gap size = 2.38 (38 / 16)  


1778 30.16 3.00 1.70  chrX_92111533_92114659.rev     1139  1904 (1223)    L1M4_orf2#LINE/L1        1   776 (132)  

  chrX_92111533_9   1139 TGGAGATATATTCCATGTTTATAGATAGAAAGCCTCAATGTTTTTAATAT 1188
                             i v    i       i  i   v i   v  i   i  v    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92111533_9   1189 GCTAGAGCTTTTTAACTTGATCTATCTATATATACAAC-CAATCCCAATC 1237
                          vi ivi  iiii  v        i---- v  v    -       v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTAC----AGATTCAACGCAATCCCTATC 96

  chrX_92111533_9   1238 AAAATCCCAGCAAG---TAGTGTGAATAGTGAAAAATTGATTCTAATGCT 1284
                                    viv--- vv  iii v v   v  ii    i    vii 
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_92111533_9   1285 TATATGAAGAGGTAAAGAACTCATGATTGCCGATTCAATATT---AAAGA 1331
                         i     i i v i  i i  i  vi  v   i vv    v  ---     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_92111533_9   1332 AGAACAAATATGGAGTACTGATAGTACCTGACTTCAAGACTTACTGTAAA 1381
                                 vv     v   v i v v  ii i     i       ii   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_92111533_9   1382 GCTAAAGTAATAATGACAGTTTTCTATTTGTG-AAAGA---ACAAATGGA 1427
                             v      v v      v vv  i v ii-  i  ---   v  i  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_92111533_9   1428 TCAGTGTAACTATATACAGAGACCAGAAATAAACCCACATAAT-GTAGTT 1476
                            i  v  iviv  vv    v               i i v -i i  i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_92111533_9   1477 CATTAATCTTTGACCAAAGGAGCAAAGGCAATAAAATTGAGCAAACATAG 1526
                         v   i  i  i   -  i  v  v   i v  vv   v i v  iv    
  L1M4_orf2#LINE/    347 AATTGATTTTCGAC-AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_92111533_9   1527 TATTTTCAACAAATG-TGTTGGAATATATGGACATATCTATTAAAATAAA 1575
                          v             -  i   i i vv    --  ? i i-- vii   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGA--TAKCCAC--ATGCAAA 441

  chrX_92111533_9   1576 AGAATG---TTGACACAGAACTTAATATCTTTCAAGAAAATTAACTGAAA 1622
                               ---   ivv vvv  i v i i v vi vi          v   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_92111533_9   1623 ACAAATCATGGACATCAAAATAAAACACAAAACTATAAAACTTCTAGAAG 1672
                          iii    ?i   v v  vi   i vvi              ii      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_92111533_9   1673 ATAACAGAAAAGAGAAACCAGATTATTTTGAGTATGGTGATAATTTTT-- 1720
                          v    v ii? vi  v ivvi v ii   i  vv  ii  ii   i --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_92111533_9   1721 ---ACAAGACTAAAGGCATGATTTATGAAATAAATAATCGATAAGCTGGA 1767
                         --- ii v  i   i   ii viv ii   v   v   v     ii    
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_92111533_9   1768 CTTCATTGAAATTACAAACTTCTGCTCTTAAAAAAGTCACTTTTGAGAAA 1817
                               ii      v      i  iv   v   i- v    v ii     
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAA 690

  chrX_92111533_9   1818 ATGAGAAGGCAAGCCA-AAACTGGAAAAAAGTATTTGCAAAAGACACATT 1866
                         i   i   i   v   - i v   i i   i          vv i i  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_92111533_9   1867 TTATAAATGACTATTATCTA-AATATATATTTAAAAACT 1904
                          v    iv    vv    i -        ---  i    
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATA---AAGAACT 776

Transitions / transversions = 1.24 (126 / 102)
Gap_init rate = 0.02 (17 / 776), avg. gap size = 2.12 (36 / 17)  

 482 20.69 0.00 6.21  chrX_92111533_92114659.rev     2492  2636 (491)    L1M4_orf2#LINE/L1      773   908 (0)  

  chrX_92111533_9   2492 AACACTTATAAAACTCAATAGTAATATATGGAGCAACTCAATTTTTAAAA 2541
                            v    i  --       i   v vivvi ii   i     ?--    
  L1M4_orf2#LINE/    773 AACTCTTACAA--CTCAATAATAAAAAGACAAATAACCCAATTW--AAAA 818

  chrX_92111533_9   2542 ATGAGCAAAAGACTTGAACAGATACTTTATCAAAGTATATATGCAGATGG 2591
                            i     i  i     i   i i  ivi     v v    i  i    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_92111533_9   2592 CAAGTAAGCACATGAAAATATTATATGCTCAGCATCATATTTTTG 2636
                          v i              v  -----     i     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGAT-----GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.02 (3 / 136), avg. gap size = 3.00 (9 / 3)  


3181 26.29 0.77 0.88  chrX_92120883_92127227     4944  5852 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92120883_9   4944 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4993
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92120883_9   4994 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5043
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92120883_9   5044 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5090
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_92120883_9   5091 ATATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAA 5140
                                 viiv  ii  v  viv  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_92120883_9   5141 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5190
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_92120883_9   5191 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5240
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_92120883_9   5241 CAATGAAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5288
                              i  i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_92120883_9   5289 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5338
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_92120883_9   5339 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAGC 5388
                         i  v  i  i              v      v  ?   i   iii  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_92120883_9   5389 TGAAACTGGATCCCTTCCTTAAACCTTATACAAAAATTAACTCAAGATGG 5438
                             ii    i    v   i v   v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_92120883_9   5439 ATTAAAGACTTAAATATTAGACCTAAAACCATATAAAACCCT-AGAAGAA 5487
                           i ?    i     i v   v       --        i  -       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAAC--TATAAAACTCTTAGAAGAA 543

  chrX_92120883_9   5488 ATCCTAGGCA-ATACCATTCAGGACATAGACATGGGCAAGAACTTCATGT 5536
                          v v    ?i- v i -   iv   v v ivv i     viii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_92120883_9   5537 CTAAAACACCAAAAGCAATGGCAACTAAAGCCAAAATTGACATATGGCAT 5586
                         v  vi            vvi     v    vv     v  i v  v v i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_92120883_9   5587 CTCATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5636
                         i    i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_92120883_9   5637 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTG 5686
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_92120883_9   5687 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 5736
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_92120883_9   5737 AAAAAAACAACCAACCCCATCAAAAAGTGGGCAAAGGAGATGAACAGACA 5786
                              i    vi     v  i?    i           vv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_92120883_9   5787 CTTCTCAAAAGAAGACATTTATGCAGACAAAAAACACATGAAAAAATGCT 5836
                         i     v        i  vi viii v   v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_92120883_9   5837 CATCATCATTGGCCAT 5852
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2957 25.99 0.99 0.99  chrX_92134523_92138788     2868  3775 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92134523_9   2868 TGGAAAAATATTTTATGTTGATAGATTGGAAGAATCAATATTGTTAACAT 2917
                               i    iii     v  i          v i           v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92134523_9   2918 GTCCATACTACTCAAAGCGATCCTAAAGATTCAATGCAATCCCTAACAAA 2967
                          v v     v i    vi    -  v        i          v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATC-TACAGATTCAACGCAATCCCTATCAAA 99

  chrX_92134523_9   2968 GTACCAATGGTATTTTTCACAGAAACAGAAAAAAAAAAATCCTAAAATTT 3017
                         i v   iiv iv     ii      iv  v  ivvi --          i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTC 147

  chrX_92134523_9   3018 ATATGAAACCACAAAA-ACCCAGAATAGCCAAG-CTCTCCTGAGCAAAAG 3065
                              i  vii   ii-               i- vv  i   iv  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_92134523_9   3066 GAAAAAAACTGAAAAAAATCACATTACCTAACTTCATATTATACTTCAGA 3115
                            v   ii  i ii v-     i v  i  i    v viv    v  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_92134523_9   3116 TCTATA-TAACCAAAACAGCATGGTAGTGGCATAAAAACAGATACATAGA 3164
                         v   i -   i   i    ii     v        ii i   i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_92134523_9   3165 CTAGTGGTACAGAATGGAGAACCCAGAAGGAAATTCACACACTTACAGTA 3214
                         ii i   v i     v    ii      iv   ii  i   i   ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_92134523_9   3215 AACCCACTTTCAAGAAATTTGCCAAGAACATACACTGGGGAATAGACAGT 3264
                           iiv i    i v  ivv        v   v  v       vii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_92134523_9   3265 CTTTTCAATTAATGGTTCTGGGAAAACTGGATCTCCATATAGAGAAGAAT 3314
                                 iv      v      v        v?   i  iv i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_92134523_9   3315 GAAACTACACCCCTGTCTCTCTTCATATATAGAAATCAAATCAAAATGGA 3364
                            ii iv      ii   v vi      i i    i  v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_92134523_9   3365 TTAAAAACTAAAATCTGAGA-CTGCAAACTATAAAACTACTACAAGAAAA 3413
                          i ? i  iv    v i   -  i-             vi  v       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAA 545

  chrX_92134523_9   3414 CATTGGGGAAAAATCTCCAAGACATTGGTCTCGGCAA-GGTTTCTTGAGC 3462
                            v  ? v   -   i iv   v    vi v     -        iiii
  L1M4_orf2#LINE/    546 CATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_92134523_9   3463 AATACCCCACAAGCACAGGCAACCAACCAAAAA-TGAAAAAATGGGATCA 3511
                          vv  v   v       i     v  vv     - ii v    v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_92134523_9   3512 CATTAAGGTTAAAACTTTATGTACAACAAAGTAAACAATCAACATGTTAA 3561
                            i  ii      vi  v   i vv     v v  v     v viv i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_92134523_9   3562 AGAGACAACCAACAGAATGGGAGAAAATATTTG-AAACC-TACCAATCTG 3609
                          i        v                      -   i -  i--     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTG 742

  chrX_92134523_9   3610 ACAAAGGATTAATAAATGTAATATATGAAAAGCTCAAACAACCCTATAGA 3659
                          i  i   i vi  vviiv       i  i i   vv     i v   iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_92134523_9   3660 AATAAATCTAATAATATGATTTTTAAAATGAGCAAAATATTTGAATACAC 3709
                           v  iv v     ivii   ?v-      i     iv         v  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_92134523_9   3710 ATTTCTC-AAAGAAGACATAGAAATGGCAAATAAGCATATTAAAAGTTGG 3758
                                -        i   v       v        i  v     v  v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_92134523_9   3759 TCAACATAATTGATCAT 3775
                                v ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (130 / 102)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.12 (18 / 16)  


3078 27.68 1.34 0.33  chrX_92144925_92147700.rev     1390  2285 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_92144925_9   1390 AAAAATATTCTATGTTCATGGATTGGGAAAATCACTATTGGTAAAATGTC 1439
                            i    i i               i i v i v     v   i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_92144925_9   1440 CATACTATCCAAAGCAATCTGCAGATTTAATGCAATCCCTATTAAAATAT 1489
                         v     vi     vii    i      i  i           i     vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_92144925_9   1490 CAATGACATTCTTCATGGAAATCGAAAAAAAAATCATGCAATTTATATGG 1539
                           iivi v  i  iiii     i  v  ivvi   v iv    i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_92144925_9   1540 AAACATCAAATG-CCTGGAATAGCCAAAGCTACCCTGAACAAAATGAACA 1588
                            ii-   iv -  ii           i v i i    v  i v     
  L1M4_orf2#LINE/    154 AAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_92144925_9   1589 AAACTGGAAGA-TCACCTTACCTGACTTCAAATTATGCTACAGAGCTATA 1637
                           ii    i  -    vi v  ii i      viv i     i     i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_92144925_9   1638 GTAACCAAAAGAGCATGATACTAGCATAAAAGCAGACACATCGATGAATG 1687
                             i   i v  ii  i    i      iiii     i  v   v    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_92144925_9   1688 GAAAACTATAGAGAACCCAGAAACAAATCCACATACCTACAATCAACTAA 1737
                            v vv  v    ii       i   i   i i ii  iii    i i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_92144925_9   1738 TTTTTTACAAAGATGCCAAGAACACATGCTGGGGAAA-AACAGTTTCTTC 1786
                             iv    i i        v  iviiv        -  i   i i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_92144925_9   1787 AATAAATGTTACAGGGAAAACTAGTTATCTGTATTCAAAAGAATTAAACT 1836
                           i     v i v    v    i v  ? iii  v         v  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_92144925_9   1837 AGACCCCTATCTCTTACCATATATAAAAATCAAATCAAAATAGATTAAGG 1886
                         i        i   vi        i      i  v       i   i ?i 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_92144925_9   1887 GCTTAAATTTAAGACCTCAAATCATAAAACTACTACAAGAAAACATTGGG 1936
                         i i     v     v  v   ii        vi  v          v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_92144925_9   1937 AAAAATCTTCACGACATTGGTCTGGGCAAAAATTTGTTGAGTAATATGC- 1985
                         iv        ii   v    vi i     vii   v  iii  vv ii -
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_92144925_9   1986 --AAGTGCAGGTAATCAAAGCAAAGATTGACAGATGTGATCACATTAAG- 2032
                         --   ii  i i  iv    v   i  v  i i  vv  iiv   i  i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_92144925_9   2033 TTAAAAAGCTTCTGCAGAGCAAAATATACAATCAACAAAGTGAAGAGACA 2082
                                -   i  iivvv    iv i  v     v        i     
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_92144925_9   2083 -TTCACAAAATGGGATAAAATATTTGCAAGCTACCCATCTGACCAGGAAT 2131
                         -ii    i       v             iii ivi      iv   i i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_92144925_9   2132 TAATAACCATAATATTTAAGGAGCTCAAGCAACTCTATAGGTAAAAATCC 2181
                          vi  v   v     v   i  i   vvi      v   ivv    iv v
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_92144925_9   2182 AATAATCTGATCAAACAAAAGGGCAAAA-ATTTGAATAGACATTTC---A 2227
                              i ii  i?  -   v       i-                 --- 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_92144925_9   2228 TAAAAGATATACAAATGACAAATAGACATATGAAAAGGTGCTCAACATCA 2277
                         v i              i v    ii  i        i            
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_92144925_9   2278 TTAATTAT 2285
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.90 (160 / 84)
Gap_init rate = 0.01 (11 / 905), avg. gap size = 1.36 (15 / 11)  


2272 29.86 2.22 1.66  chrX_92165172_92169528.rev     2972  3872 (485)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_92165172_9   2972 GAAAAACTTTTCATGTTGATGGATTAGAAGAATCAATATCATTAAAATGG 3021
                             i iv ii      v       i     v i     ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_92165172_9   3022 CCATACACCCCAAAGCAATGTACAGATTCAGTACTATTCTTACCATATTA 3071
                          v    v       vii  v          iii v  i i  i  v v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_92165172_9   3072 CCAAAGATATTTTACACAGAATTAGCCAAAAAAAAAAACATTTCTAAAAC 3121
                            ivviiv    vii     v v v   ivvi ------- i      i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-------TCCTAAAAT 145

  chrX_92165172_9   3122 TTATATAAAAC--CAAAAGAGCACAAATAACCAAAGAAATCC-AAACAAA 3168
                          i    ii  v--   ii  v vvi    i     iv    i-i  v  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_92165172_9   3169 AAGGACAAAGCTAGAGGCCTCACATTACCCAACTTCAAATTATACTACAA 3218
                            i      i i    v      i v     i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_92165172_9   3219 GGCTATAATAACCAAAACAGCATGGTACCAATACAAAAACAGACACATAG 3268
                         i    i i   i   i    ii      iiii i  ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_92165172_9   3269 ACCAATGGAACAGAATAGACAACTTGAAAATAAAACTAAACACCTACAGC 3318
                          i        i     v  v iiiiii       v i v   ii  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_92165172_9   3319 CATCTGCTCCAAGACAAAG---TCTAAACAAATAAACAATGGTGAAAAAA 3365
                           vi  v iivv     i ---i v i  v v ---      v    i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATT---CAATGGGGAAAGAA 392

  chrX_92165172_9   3366 CTCTCTATTCAGTAAATAGTGTGGGAGTAACTGGTTATCCATATGCAGAA 3415
                         ivv   v    ii    i   iv  iii      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_92165172_9   3416 GAATGAAACTGGACCACTACCTTTCACCATATATAAAAATTAAATCAAGA 3465
                                ii      v      iv         i         v    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_92165172_9   3466 TGGAGTAAAGATTGACATGTAAGACCTCAAAGTGTAAAAATTCTACAAGA 3515
                             vi ?   iiv v        v  v   v i     v ii  v    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_92165172_9   3516 AACTCTA--AATAATACCATTCTCAATATCGACCTTGGCAAAGAATTTAT 3563
                           viv  --?i   - i -   vii iv i ivi v     v iv  iv 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_92165172_9   3564 GGCTATGCCCTCAAAA--ACAATTGCAACAAAAACAAAATTGAATG---T 3608
                         i v    v vi     --    --         iv    v ii  i--- 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATT 638

  chrX_92165172_9   3609 GTGACCTAATTAAACTAAAGAGATTCTGAAGAGCAAGAGAAACTATCAAG 3658
                          -   i v  i   v v  i iv  i  vivvv   ii  v         
  L1M4_orf2#LINE/    639 G-GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_92165172_9   3659 GTCATAAATAGACAACCTACAAAATGGGAGAAAATATTCAAAAAGTATCC 3708
                         ivvi i  v        i   i                iiv   vi  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_92165172_9   3709 ATCTCAAAAAGGTCTAATATCCCAAATCTATTAGAAACTT----AATCCA 3754
                             v v  i  v  vi     vi   v   v ii    i----  ii  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_92165172_9   3755 AGAAGCAAAAAGCAAATGACCCA-CTAGAAAGTGGGCAAAGGACAGGAAA 3803
                          v  vv    ii     i     -i ?i   i           ivv   v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_92165172_9   3804 AAACCCTTCTCAAAAGAAGACATACAAGCAGCCAACAA--ACATGGAAAA 3851
                          i  vi     v        i      iii     i  --     i   i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_92165172_9   3852 ATTCTCATTGTCACTAATCAT 3872
                           v    vii   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (161 / 104)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 2.33 (35 / 15)  


1825 27.00 6.51 3.53  chrX_92177842_92180013      500  1236 (936)    L1M4_orf2#LINE/L1       73   831 (77)  

  chrX_92177842_9    500 TATAATTTGAAGGCTATTCCTATCAAACTACCAA-TGTCATTTCTTGACA 548
                           i iv  v  v  v  i         v v   i-  i -   i   -  
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTG-CA 120

  chrX_92177842_9    549 GAA-TTGAAAAAAAAACGTCTCTAAATTTCATGTGGAATCAAAAAAAAAG 597
                            -    v  ivvi --  -     v     i     --- viv  ii 
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGA--TC-CTAAAATTCATATGGAA---ATGCAAGGG 164

  chrX_92177842_9    598 AACCTGGATAGCTAAAGCAATCCTAAGCAAAAAGGACAAAGCTGGAGGCC 647
                          v  v i     i   i     i i iv  i   i      i      v 
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_92177842_9    648 TCACATTACTTAACTTCAAACTGTACTATAAGTCTACAGTAACCAAAAGA 697
                              i v ii  i      viv     i  iv         i   i v 
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_92177842_9    698 GCATGGTACTGGTACAAAAACAGACACATAGGCCAGTGGATCATAATAAA 747
                          ii         i i  ii i     i    ii  i    vi v   vi 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_92177842_9    748 CAACCCAGAAATAAAGCTGTATGCCTACAGCCATTTGATCTTTGACAAAG 797
                         v ii           v ii  iiii  ii i  v     i  i     i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_92177842_9    798 TTGACAAAATAAG-CAATGGATAAAGGA----CTCCAAATTCAATAGATG 842
                         v  v   i iv v-      iv    i ----  i----     i i   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT----TTCAACAAATG 410

  chrX_92177842_9    843 GTGCTAAGATAGCTGGCTAGCCATATGCAGAAGACCAAAACTGGACCTCT 892
                              ii  i i    v  ?   i     i    vii  ii      i  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_92177842_9    893 TCCTTACACATTATACAAAAATCAGCTCAAGGTGGATTAAATACTTAAAT 942
                         v   i    vv           i i     ii     i ? v  i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_92177842_9    943 ATAAAACCCAAAACTATAAAAACCCTGGAATACAACCTAGTCAATACCAT 992
                         i   i v i            vi i i   v v   v   v?i-  -- v
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG-TA--AA 557

  chrX_92177842_9    993 TCTAC---ACATAGGAGTGGGCAAAGATTTC------ATGACAAAGAGGC 1033
                            v ---  v v  iv i     v i    ------      ------ 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA------C 601

  chrX_92177842_9   1034 CAAAAGCAATTGCAACAAATGGAAAAAAAAAATTAACCAATGGGATCTAA 1083
                                 vvv        ----- i       vi iv   v   ii v 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAA-----AGAAAAAATAGATAAATTGGACTTCA 646

  chrX_92177842_9   1084 TTAAACTAAAGAACTTCTGCACAGCAAA--ACACCAT------------- 1118
                          i   v v  i     i  ii vv    --    i  -------------
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_92177842_9   1119 -----ACCAACAGAGTAA-ACAAACTATT-GCA---------TTTAACAA 1152
                         -----   v     i ii- v   v    -   --------- i i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_92177842_9   1153 AGGTCTAATATTCAGAATCTATAAGGAACTTAAACAATTTAAAAAGCAAA 1202
                         i  v  vi   i      v     i     ivv    i i  v  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_92177842_9   1203 TAACTAATAATTCCATTTAAAA-TGGGCAAAGCAT 1236
                         vi  v     ii v   ?    -         v  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.57 (119 / 76)
Gap_init rate = 0.03 (22 / 759), avg. gap size = 3.36 (74 / 22)  

 342 22.58 1.08 0.00  chrX_92177842_92180013     1587  1679 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_92177842_9   1587 AAAAATGGCAAAAAAACATGAACAGACATTTCTCAAAAGAAGACATGTGA 1636
                                 vv   ii iv    i           v        i  iii 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_92177842_9   1637 GTGTCCGATAAACATACGAAAA-ATGCTCTTTATCACTAATCAT 1679
                         i  v  i    i  i i     -      vvi    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


1907 20.73 5.09 2.18  chrX_92190595_92192588.rev        1   550 (1444)    L1M4_orf2#LINE/L1      239   804 (104)  

  chrX_92190595_9      1 ACTATAAA-CTAGACTGATCAAGACAATGTGGGAAAGGCATAAGCATAAT 49
                             i   -   v v i         i     v vv        v   iv
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_92190595_9     50 CATATAAATCAAC----------TGAAATTCTAAAAATATATCCTCATGT 89
                               i     i----------   i v  i i     v i  vi ii 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_92190595_9     90 TTCTGTTCAGTTGATTTTCAACAAGGGTGCCAAGACAATTAAATGGGGGG 139
                           v  v   i         i                v   v       ii
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_92190595_9    140 AGATTAATAGTCTT--CAACAGATGGTGCTGCACCAGCTGAATTTCAACA 187
                            ---        --     i         viv  i   i  v? v   
  L1M4_orf2#LINE/    389 AGA---ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_92190595_9    188 TAACAAAAGATTGAAATTGAAACCATCCCTGACTTTATATACAAAAATCA 237
                          i-       v    i   i v  v v   v  vii            i 
  L1M4_orf2#LINE/    436 TG-CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_92190595_9    238 AT--AATGAATGGATCAAAAACCTACTTGGAAAAAATAAAATTTTAAAAA 285
                          i--  --         ? i     vv  v  i iv     i v     v
  L1M4_orf2#LINE/    485 ACTCAA--AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_92190595_9    286 TCTTGGGCAAAAACATAATAGTAAATCTTTGCAGCCTTAGGTAAGTCAAA 335
                             i ivi        iv?         i iii    i   v  v   v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_92190595_9    336 GCCTTCTTAG-TCTGCCATCAAAAGCACAAGAAAAAAAAGAGAGAAAAAA 384
                          vi       - v  v  i            v  v      -----    
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-----AAAA 627

  chrX_92190595_9    385 ATAGATAAATTGGACTATAAAAAAATTTAAAA-TTTTATGCTGCAAATGA 433
                                         vi vv      v    -    i    v    v  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_92190595_9    434 TAATATCA-----GTGAAAAGATAACCAACAGAATGGGAGAAAAATATGT 478
                         i v     -----         i    v                -   v 
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTT 726

  chrX_92190595_9    479 ATAAATCATATATCTTATAATGAAATAGTATCCAGAATACATAAAAA--- 525
                         ii             v    v i v v            i     i ---
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_92190595_9    526 --TAGAAATAAATT-TAACAAAACAAAT 550
                         --  v  v v   v-   v  i      
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAAT 804

Transitions / transversions = 0.91 (53 / 58)
Gap_init rate = 0.02 (14 / 566), avg. gap size = 2.86 (40 / 14)  

3200 24.21 2.48 0.45  chrX_92190595_92192588.rev      616  1503 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_92190595_9    616 GAAAGATATTCCTGTGTTTAATGG-TTAAAATAACTAATACTGCTAAAAT 664
                                  i  -i    i -   -  ii  v vi     i  i   i  
  L1M4_orf2#LINE/      3 GAAAGATATCCC-ATGTTCA-TGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92190595_9    665 GACAATACTCTGAAAATT-ATCTGCAAATTATATAAAAGCTCTAGTAACA 713
                          i        ivv     -    i  i   vv iiv  v i   vi  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92190595_9    714 CCTTAGCTATTTTATACACAAAAATTGAAAAGCTCATTCTAACATTTACA 763
                         i ii    iii  v vii  i       v     v  i    v   i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_92190595_9    764 TAAAGACACAAGGGTCTGAGAGTAGCCCCCAACATTTTTTTTTAA--AGA 811
                          ii i ii      v iv   i     vv-    v i  vvvv  --   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAA-AACAATCTTGAAAAAGAAGA 199

  chrX_92190595_9    812 ACATATTTGGAGGACTTACACTTC--AATTTTAAGATATACTGCAATGCT 859
                            v v          i       --     i  i iv    i   v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_92190595_9    860 GCAATAATCAAGCCATAATGGTATTGGCATAGTGATAAACATAGAGATCA 909
                         i  i        v  vvi     i       iv    i     v      
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_92190595_9    910 TTCAAGCAGAATGGACAGTCCGTAAGTAAAAC-ATCATATCAATTGTCAA 958
                         v vi ii     v  v     iv  i    v -  - i  iv  v     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGGTCAA 348

  chrX_92190595_9    959 TTGATTTTTCACAAGTGT-TCAAGATAGTCTAATGGCAAAA-AGTGCTAT 1006
                                 iv     v  -i     ivi ii     vi   - i iv v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_92190595_9   1007 TTTCAAAAAATGGCATTGGGATAACTAGCTACTCACTTGCAAAAGAATGA 1056
                               v      iii     i    i v  ?i   v             
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_92190595_9   1057 TATTGGACC--TACCTCACACCATACATGAAAATAAACTCACAATGGATC 1104
                         vi       --              i ii     v      v        
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_92190595_9   1105 ATAGATCTAATTCTAAGAGCTAAACTTATCAAACTTTTAGAAGAAAACAT 1154
                          ?   i    v v           vi   v     i              
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_92190595_9   1155 AGGAGTAAATCTTCATTAATTTGA-TTAGGCTATGCTTTCTTACATA-GA 1202
                            ?          i v vi   i-      v   v       v   -  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_92190595_9   1203 AACCTAACATGTAAGTGACGAAACAAACA-----TCACTTTTATATCATC 1247
                         v   v  viiii   ii  i   v   v ----- v v  vv iv     
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_92190595_9   1248 AAAATTAAAA-CACTCATGCTTTAATGGTCATCAT-AAGAAAGTGAAAA- 1294
                                   - vi ii     i  v  v  ii  -             -
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_92190595_9   1295 ATAACCAAGAGACTGTAAGATAATGTTGACAAATTTTATATTTGACAAGT 1344
                          i    v v   v  vi   v   i  vi     iv     i   i   v
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_92190595_9   1345 AACTTGTACTGAGGATATATAAA-ATCTCTTATAACCCAATAACAAAGAG 1393
                         i       iiv  i         - v      i   i      i   i  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_92190595_9   1394 ATAAATAACCCAATTGAAACATGGGGAAAGGATTTGCATAGACCCCTAAC 1443
                          i             ?   v     v          v      vii vv 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_92190595_9   1444 CAAAGAAGTCGAACAAATGGCAAATAAGCACATGAAAAGATGTGCAACAC 1493
                                 viiv         v                    iv     i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_92190595_9   1494 CATATGTTAG 1503
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.22 (116 / 95)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 1.37 (26 / 19)  


3074 25.58 1.55 1.00  chrX_92193389_92197572     2789  3691 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92193389_9   2789 TGGAAGAACATTCCATGCTCATGGATAGAAAGAATCAATATCGTGAAAAT 2838
                              ii i  i     i        v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92193389_9   2839 GGCCATACTGCCCAAAGTAATTTATAGATTAAATGCTATCCCCATCAAGC 2888
                            v     v      v i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92193389_9   2889 TACCA-CTGACTTTCTTCACAGAATTGGAAAAATCTACTTTAAATTTCAT 2937
                          v   -   v    i  -i     v v  v  iiiv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_92193389_9   2938 ATGGAACCAAAAAAGAGCCTGCATAGCCAAGACACTCCTAAGCAAAAAGA 2987
                               viiv  ii  v  v v        i   v  i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_92193389_9   2988 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 3037
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_92193389_9   3038 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCC 3087
                                i   i    ii         i iv ii i   i       i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_92193389_9   3088 ATGGAACAAAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 3137
                               i i  iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_92193389_9   3138 TGATCTTCAACAAACCTGATGAAAACAAGCAATGGAGAAAGGATCTCCTA 3187
                             i   i    ivv  vii i v  vv      i     i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_92193389_9   3188 TTCAATAAATGATGCTGGGAAAACTGTCTAGCCACATGCAGAAAACTGAA 3237
                              i     i        v     vv  ?         i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_92193389_9   3238 ACTGGACCCTTTCCTAATACCTTATACAAAGATTCACTCGAGATGGATTA 3287
                         ii       i v   v i   v        i   v    i i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_92193389_9   3288 AAGACTTAAATGTAAAAACAAAAACCATAAAAACCCTT-GAAGAAAACCT 3336
                         ?    i         i i v     i      - i   -         v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chrX_92193389_9   3337 AGGCA-ATATCATTCAAGACAT--AGTTATGGGCAAAGGCTTTAT-GATG 3382
                            ?i- v   -   iv   v --i    --     v  i  iv -   -
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGAT- 594

  chrX_92193389_9   3383 AAAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATTT 3432
                          vi            vvv          vv     v  i    v   i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_92193389_9   3433 AATTAAA-TTAAGAGCTTCTGCACAGCAAAAGAAACTATCACCAGAGTGA 3481
                         v  i   -    i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_92193389_9   3482 ACAG-CAACCTACAGAATGGGAGAAAATTTTGGCAATCTACCCATC-AAC 3529
                          v  -     i                 v  v    vii ivi   -i i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_92193389_9   3530 AAAGGTCTAATATTCATTATTTACAAGGA--CCTTA-AACACATTTACAA 3576
                           i  v  vi   i  vv  v  i  i  --i    -   v  --- i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA---ATAA 791

  chrX_92193389_9   3577 GAAAAAACCAAACAGCCCCATCAAAAAGTGGGCAAAAGATATGAATAGAC 3626
                         v     iv    i i   v  i?    i        i   v         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_92193389_9   3627 ACTTCTCAAAAGAAGACATTTATGCAGCCAACAA--ACGTGAAAAAAAGC 3674
                          i     v        i  vi viii     i  --  i      i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_92193389_9   3675 TCAACATCACTGATCAT 3691
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (135 / 92)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.35 (23 / 17)  


1681 31.59 4.30 0.81  chrX_92219338_92221070.rev      501  1244 (489)    L1M4_orf2#LINE/L1      139   908 (0)  

  chrX_92219338_9    501 CTAAGACTCATGTGGAACCAAAAAGAAGTCCAAATAGCCAGAGCAATCTT 550
                             i i    i     viiv  i i vi vi        i i       
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chrX_92219338_9    551 AAGCAAAAAGTACAAAGCTGGAGGCATCACATCACCCATCTTCAAACTGT 600
                         i iv  i   v      i      vv     iiv    vi      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_92219338_9    601 ACAATAACTCTGTAGTATCTAAAACCGCACAGTACTGGTACAAAAATAGG 650
                           v i  vv  ii    vii  i  v iiii       i i  ii    i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_92219338_9    651 TACATAAACCAATAGAACAGAATAAAAAACTCAAAGATAAAGATGCACAA 700
                         i i   i i    i   i     vi i iii  i i     vviii   v
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_92219338_9    701 CTACAACCATCTTATCTTTGAAAAAGTTGACAAAAATAAGCAATAGGAAA 750
                         i  iiii  vi v  i  i  v  i v  v   i vi vv    i  i  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_92219338_9    751 AGGACTCCCTATTTGATAAATGGTGCTGGGATAGCTGGCTAGCCATGGGC 800
                           i ivvi  v  ii i              i i    v  ?   iiv  
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_92219338_9    801 AGAAGAATGAAACTAGACCCCTGCCTTTCGCTGTATA-AAAAA--AGCT- 846
                          i         ii i       i   iv i ii    -     -- i  -
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_92219338_9    847 AATATGGAT-AAAGATTTAA-TACAATACATCAAACTCTAAGAATCCCAG 894
                           v      - ?   ii   - ii  v vv v     v   i v  ii  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_92219338_9    895 AAGAAAACCTAGGAA-ACACCATTCCGGACATTGACCTTGGGAAAGAATT 943
                                 v    ?i- v i -   vv   v   iv-  i  v  vii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTT 586

  chrX_92219338_9    944 TAT--GATTATGTC-TCAAAAGCAATTGCAACAGAAACAAAAATTGACAA 990
                          v --   -   v -i        vvv      i  iv      v  i  
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_92219338_9    991 GTAGGAGCTGATTAAAG-----AGCTTCTACCAAGCAAAATAAACTGTGA 1035
                         i v   vi v  i   i----- i   i iivvvv    iv v   i v 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_92219338_9   1036 CTAGAGTAAA----TAATCTACAGAATGGGAGAAAGTATTTGCAAACTAT 1081
                         vv i   i  ----i  i i               i          ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_92219338_9   1082 GCACTCAGCAAAGGCCTAATACCTACAGTCTATAAGGAACT--TA----- 1124
                         ii iiiiii  i  v  vi  i i v i v     i     --  -----
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_92219338_9   1125 -AACAAGCAAAAAACAAATAACCTTATTGAAAAATGGAAAAAGGAC---A 1170
                         -  i  vv    i          iv   ?        iv      i--- 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_92219338_9   1171 ATCCCAAACACTTGTCAAAAGAAGATATTAGAGTGATCAACGAACATATA 1220
                           --- i   i  v  v           vvi i  ii   ii i  i  i
  L1M4_orf2#LINE/    836 AT---AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_92219338_9   1221 AAAA--TGCTCATCATAATGAATAAT 1244
                             --      v   v ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (148 / 83)
Gap_init rate = 0.02 (18 / 770), avg. gap size = 2.11 (38 / 18)  

 701 24.63 2.46 1.97  chrX_92219338_92221070.rev     1319  1521 (212)  C L1M4_orf2#LINE/L1   (704)   204     1  

C chrX_92219338_9   1521 TGGAAAAACATCCCAGGCTAATGGATCTGAAGAATTAATATTATTAAAGT 1472
                               i i      v i v      iv     v        i    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_92219338_9   1471 GACCATACTGTCCAAGC--ATCATACAGAATCAATGCAACCTCTATCAAA 1424
                          i v     vi    ii--   -      v    i    i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATC-TACAGATTCAACGCAATCCCTATCAAA 99

C chrX_92219338_9   1423 ATACCAA-TGTCATTTTTCATAGAAATAGA--AGTAACAATCCTAAAATT 1377
                           v   i-  i -     iii      v  --  i--ii           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATT 146

C chrX_92219338_9   1376 TGTATGGAACCAAAAAAGAGCCCAAGTAACCAAAGCAATCCTGAGAAAAA 1327
                         ii       viiv  ii  v  vi i  i     i     i   i   i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

C chrX_92219338_9   1326 ATAAGAAA 1319
                          v  v   
  L1M4_orf2#LINE/    197 AGAACAAA 204

Transitions / transversions = 2.33 (35 / 15)
Gap_init rate = 0.03 (6 / 204), avg. gap size = 1.50 (9 / 6)  


2813 28.57 1.11 0.55  chrX_92230193_92234308     2724  3626 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92230193_9   2724 TGAAAAGATATTACATGTTCAGGGATTGGAACAATCAGTATTGTTAAAAT 2773
                           i        iv        v         v v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92230193_9   2774 GTCCATACAACCCGAATCAATCTACAGATTCAGTGCAATCCCTATCAAAA 2823
                          v v    vv   i   ii             ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92230193_9   2824 TACCAATGACATTTTTCACAGAAATAGAACAAAC-AATCCTAAAACTTAT 2872
                          v   iivi v     ii       v  -   i -i         i i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_92230193_9   2873 GTGGAACAACAAAA-ACCCAGAATATTCAAAGCTATCCTAAGCCAAAGGA 2921
                         i     vvi   ii-          vi    i v   i i ivv i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_92230193_9   2922 ACAAAACTAGAGAAATCATGTCACCTGATTTTATATTATACCTCAGAGTT 2971
                              ii i   i v   iiiiv  ii    i v viv   iv  i  i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_92230193_9   2972 ATAGTAACCAAACCAGCATAGTTCTGGCATAAAAACAGACACAAAGACCA 3021
                          i     i   iv   ii i  v         ii i     i v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_92230193_9   3022 ATAAAATAGAA------ATCCAAAAGAAAAATTTCCACATACCTACAGTG 3065
                           ii       ------i    i  iv   ---i   i i ii  ii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAA---CCCATACATTTATGGTC 346

  chrX_92230193_9   3066 AACTCATAGTTCACAAAGTTGTCAAGAACCTACACTGGGGAACAGACAGC 3115
                           i v  vv iv    i v  i     v v v  v       vii i  i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_92230193_9   3116 CTATTCACTAAAGGGTACTGGGCAAACTGGGTATCCTTTTGCAGAGGAAT 3165
                           v    vi   v   i     vv      i  ?  viv    i i    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_92230193_9   3166 GAAACTAGACCCATATCTCTCACCATATACAAAAATCAAATACAAATGAA 3215
                            ii i     v  i   v                i  v vv     i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_92230193_9   3216 TGAAAACCTTCAACTCAAGATCTCTGACTATGAAACTACTACAAGAAAAG 3265
                          v ? iv i v  ivi    v  vvi     i     vi  v       v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_92230193_9   3266 TTTGGAGAAAATCACCAGGACATTTGATTGGGCAAGCATTTCTTGAGCAA 3315
                         v v  ? v     vi iv   v  v i  i     vvi      iiii v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_92230193_9   3316 TCCCCCACAAGTACAGGCAACCAAAGCAAACATGGATGAATGCAATCACA 3365
                         vv v   v   i   i     v    v   v  i   i   vvi iiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_92230193_9   3366 ACAAG-TTAAAAAGCTTCTGTGTAGCAAAAGAGATGATCAAGAAATTGAA 3414
                         v   i-       -   i    ivv    i  v iv         v    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_92230193_9   3415 GACACATCTCCAAAAATAACAGATAATATTTGCAAACTACTCACCTGACA 3464
                         i v   v i vv i   iiv   v            ii ivi i    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_92230193_9   3465 CGGGACTAATAACTAGAATATATAAGCAACTCAAACAAATCTATAGAAAA 3514
                         v      vi  v i           iv     vv    v  v   iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_92230193_9   3515 AAATCTAATAAGCTGATCAAAAATTGGACAAAAGATTTGAATAGACATTT 3564
                           iv v     v ii  i?    v   i    i                 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_92230193_9   3565 TTCAAAAGAAGATATA-AAATGCCCTACAGGCATATGAAAAGTTGCTCAA 3613
                         i  v            -     v  v i i   i        v       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_92230193_9   3614 CACTATTGATCAT 3626
                           ii ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (143 / 111)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


3051 25.36 0.99 1.32  chrX_92254243_92259184     3539  4449 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92254243_9   3539 TGGAAACACATCCCATGCTCATGTATGGGTAGAGTCAATATTGTGAAAAT 3588
                               v i        i     v  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92254243_9   3589 GACCATACTGCCAAAAGCAACCTACAAATTCTATGCAATTCTCATCAAAA 3638
                          i v     v  v   vii i     i    v i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92254243_9   3639 TGCCA-CCGTCATTCCTCACAGAACTAGAAAAAAAACTTCTAAAATTCAT 3687
                          v   - i i -  ii ii     v v  v  ivviv i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_92254243_9   3688 ATGGAACGAAAATAGAGCCCACATAGGCAAAGCAATAGTAAGCAAAAAGA 3737
                               vviv  vi  v  viv    v    i    vv i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_92254243_9   3738 ACAAATCTGGAGGCATCACATTACCCAACTTCAAACTATACTTTAAGGCC 3787
                              vi      vv     i v     i      viv    vi  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_92254243_9   3788 ATAGTCACCAAAACAGCATGGTACTGGTATGAAAAATAGGCACATAGAAG 3837
                          i   v i   i    ii         i  -  ii    i  i     vv
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATC 298

  chrX_92254243_9   3838 AATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTAGAGCCAA 3887
                                i     v    ii           v   v i i   vi i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_92254243_9   3888 CTGATCTTCAACAAAGCAAACAAAAGCATAAAGTGGGGGAAAAGACACCC 3937
                         i    i   i    i vviv   i v   vv i     i  i - i vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTC 397

  chrX_92254243_9   3938 TATTCAACAAATGGTGCTGGGAAAATTTGCCTAGCCAGCCACATGTAGAA 3987
                          v                    v  -----  i vi ?       i i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAA-----CTGGATAKCCACATGCAAAA 442

  chrX_92254243_9   3988 GAATGAAACTGGATCCTCATCTCTCACCTTACACAAAAATCAACTCAAAA 4037
                                ii    i  ii i   v    v  i        i         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_92254243_9   4038 TGGATCAAATACCTAAATTTAAGACTTGAAACCATAAACATCCTAGAAGA 4087
                                ? v        v     vi i    i     vv  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_92254243_9   4088 TAACATCAGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTC---- 4133
                         v     vi ?iv  vi    vv   v    v        v ii   ----
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_92254243_9   4134 --ATGAC-CCAAAAGCAAATGCAACAGAAACAAAGACAAATA-GTGGGAC 4179
                         --     -         v v      i  iv   i i i   -i v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_92254243_9   4180 TTAATTAAAGTAAAAAGCTTCTGCACAGCAAAAGAAATAAGCAGCAGAGT 4229
                           v  i   i v    i   i  ii vv    i  v iv v  iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_92254243_9   4230 TAACAGACAACCCACAGAGCGGGAGAAAATCTTTACATTCTATACATCTG 4279
                         v  v              ii          v   i  vvii   i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_92254243_9   4280 ACAAAGTACTAATATACAGAATCTACAAAGAACTCAAATCAGCATGAAAA 4329
                          i  i v   vi   v      v  i         --- i vv ivv  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTC---TTACAACTCAAT 789

  chrX_92254243_9   4330 AACAAAACAAACAAACAAGCCCATTAAAAAGTGGGCTAAGGATATGAACA 4379
                           i    - i     i  v  v   ?    i     v      v    i 
  L1M4_orf2#LINE/    790 AATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_92254243_9   4380 AACAATTCTCAAAAGAATATATACAAATGGCAAACAAGCACATGGAAAAA 4429
                         i   v     v      v             v  i         i   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_92254243_9   4430 TGTTCCACATCACTAATTAT 4449
                           i  v      ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (123 / 104)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


2446 26.73 7.78 1.82  chrX_92267297_92270345     1710  2532 (517)    L1M4_orf2#LINE/L1        1   872 (36)  

  chrX_92267297_9   1710 TGAAAAGATATCT-AGGCTCATTAATTGGAAGAATTA-TATTGTTAAAGT 1757
                           i         i- v i    vi         v   -         ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92267297_9   1758 TTCCATACTACTCGAAGTGACCAACAGATTGAATACCATAA-TATCAAAA 1806
                         vv v     v i i  v   i v       v  ii v  vv-        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92267297_9   1807 TACCTATTATATTCTTCATAGAAGTATGAAAATCAGTGATT---ACATTT 1853
                          v  vii iiv  i  iii    i -   v  v --    i--- v   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGC--TGATCCTAAAATTC 147

  chrX_92267297_9   1854 GTATAGAATCACAAAAATACCAGAAGTAGTCAAAGCAATCTTGAGCAAAA 1903
                         i   i   vii   iiivv      -   i    i         iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAA-TAGCCAAAACAATCTTGAAAAAGA 196

  chrX_92267297_9   1904 ATAATGAAGTTGAAAGCATCAAACTAGCTGACATCAAAATATGCTGCATA 1953
                          v  ii      i i vv   v   vv ii iv      iv i  i  v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_92267297_9   1954 GCTGCAGTAATAAAAACAGTATGGTACTGATATAAAAAAAAAAGAGAGGC 2003
                            i       v  i     i        ii    i-------  v  i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-------GATAGAC 289

  chrX_92267297_9   2004 ATACG--CTATTGGAATAGAAAATAGAGCCCAGAAATAAATCCACACA-- 2049
                            ii--ii v          vvv    i           i   i   --
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_92267297_9   2050 -----------------------------------------ATGGGAAAT 2058
                         -----------------------------------------     i  v
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_92267297_9   2059 GAATGTTCTCTTTAA---ATGGTGCTGGG-TAACTGGATATCCACATGCA 2104
                             iv   i  i  ---           -i         ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_92267297_9   2105 GAACAATAAAACTAGGCCCTTATCTCATACTGTATACAAAAATTAACTCA 2154
                         i  v   i  ii i i   i  i    i  ii                  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_92267297_9   2155 AAATAAGTTAAATAACTTAAATGTAAGACCTCAAACTTTGAAACTCCTGG 2204
                             iii i ? -i  i           v  v     v i      i i 
  L1M4_orf2#LINE/    490 AAATGGATCAWA-GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_92267297_9   2205 AAGGAAACATAGGGGAAAAGCTGCATGACATTGGTCTGAGCAATGATTTT 2254
                            i         ? v   v  v i    v    vi ii      i   i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_92267297_9   2255 TTTTATATGACCCTGAAAGCACAGACAAAAAAAGTAAAAAGAGAAAAATG 2304
                           vv       v ii        ii   v     v     v   v    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_92267297_9   2305 ATATTACATTACACTAACAAGCTTCCACAGAGCC----AGGAAATCAATA 2350
                         iv i v   i v v v v  i   ii--- v  i----    v ii vi 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTT---GTGCTTCAAAGGACACTATCA 685

  chrX_92267297_9   2351 ACAGAATAAAGAAACAACTTACACAATGGGAGAAAATAGTTGTATCCTGT 2400
                          v i i i  i i     ii   v              v   i vviii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_92267297_9   2401 ACACCTGATAAGGGGTTAATATCCAAATTACCTGAGTAACTC----AACT 2446
                          i i          ii vi      i v  iv i iv     ----    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_92267297_9   2447 CAATACCAATAAAATAAGTA-TCCAATTTTAAAATGGGCCGAGAACCTGA 2495
                              vi  v  i i  i  -i      ?v         vi  i ii   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_92267297_9   2496 ACAGACATTTTTCAAAAGAAGATATACGAATGGTCAA 2532
                          i        i  v             i     i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

Transitions / transversions = 1.70 (136 / 80)
Gap_init rate = 0.02 (17 / 872), avg. gap size = 4.65 (79 / 17)  


 869 27.50 0.71 2.50  chrX_92300606_92305657     2873  3152 (1900)    L1M4_orf2#LINE/L1        1   275 (633)  

  chrX_92300606_9   2873 TGGAAACACAGCCCAAGCTCATAGATGGGAAGAATCAATATTGTGAAAGT 2922
                               v i v    v i    i   v      v i        v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92300606_9   2923 GACTATACTGCCCAAAGCAATCTATAGATTCAACGCAATTTTTTTTTTCA 2972
                          i v     v      vii     i              iii v ---  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT---CA 97

  chrX_92300606_9   2973 AAATAGCAGCATTTTTTTTGTGTGTGGAACTAGAGAAAACAATCCTAAAA 3022
                             vv    vvii     ---  ii   v v  v  ivii         
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTT---TGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_92300606_9   3023 TTCATATGGAACCAAAAAGAGCCC-GATTACCCAAAGCAATACTCATCAA 3071
                                    viiv  i ii   -  v  v     i    vi v vv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_92300606_9   3072 AAGGAACAAAGCTGGAGGCATCACATCACTAGACTT-AATATTACACTAC 3120
                         i i        i      vv     iiv ivi i  -  v i -i     
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTAC 243

  chrX_92300606_9   3121 AAGGTTATAGTTACAAATACAGCATGGTACTG 3152
                           i i  i   v iv  v    ii        
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

Transitions / transversions = 1.26 (43 / 34)
Gap_init rate = 0.02 (5 / 275), avg. gap size = 1.80 (9 / 5)  

1566 27.80 2.84 1.90  chrX_92300606_92305657     3930  4562 (490)    L1M4_orf2#LINE/L1      270   908 (0)  

  chrX_92300606_9   3930 GTGCTGGTATAAAGAATAGGCACTTAGACGAAGGGAACAGAATGGAGAAC 3979
                           i    i    i  -   i  iv    iv  v    i     v    ii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_92300606_9   3980 GCAGAAATAAAGCAAAATACCTACAGACAACTGATCTTTGGCAAAGCATA 4029
                         v          v v v i ii  ii v   i    i  i i   i -i i
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTG 367

  chrX_92300606_9   4030 CAAAAAC-ATAAATTAGGGAAAAGATACCCTGTTCAATAAATGGTACTGG 4078
                          v  i  -  vv v i      ii   vi  v     i       i    
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_92300606_9   4079 AAAGACTGACAAGCCACATGTGGAAGAATGATACTGGGTCCCCCATCTAT 4128
                         i vi    ivv ?       iii        vii   i-    i i  vv
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA-CCCCTACCTCA 466

  chrX_92300606_9   4129 CACCTTTTACAAAAATCAACTCAAGATGAGTCAAAGATTTAAAT------ 4172
                             v v         i       i   ii   ?   ii     ------
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_92300606_9   4173 -CTGAAACCATAAAAATTCTAGAAGG---TGTTGGGAAAACTCTTC-TGA 4217
                         -  i    i      v ii      i---ii v  ?iv  v     -   
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_92300606_9   4218 ACATGGGCTTCATCAAAGAATCCATGAATAAGACTCCAAAAGCAAATGCA 4267
                         v v    -  viv   v iv i v ii   v   v         v v   
  L1M4_orf2#LINE/    567 CCTTGGG-TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_92300606_9   4268 G--GAACAAAAAACAAACAAATGTAAACT-AATTAAACTAAAAAGCTTCT 4314
                         i--i  v      i i i    - ii   -v  i   v v    i   i 
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAAT-TGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_92300606_9   4315 GCACAGCAAAAGGAATAATCAACATATTATACAGACAACCCACAGAATAG 4364
                          ii vv    i iv iv     v v v iv v                i 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_92300606_9   4365 GAGACAATATTTGCAAACTATGCAACTAACAAAAGACTAATATCCAGTAT 4414
                             v            ii  ii v  i i  ii    vi       v  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_92300606_9   4415 CAACAAGGAACTCAAATTAGCAAG--AAAAAAAAAACCAAAACAAATAAT 4462
                         vv i  i      ---   -   v--  v  v    --- i        i
  L1M4_orf2#LINE/    765 ATATAAAGAACTC---TTA-CAACTCAATAATAAAA---AGACAAATAAC 807

  chrX_92300606_9   4463 TACATCAAAAAGTGAGCAAATGACATGAATAGACATTTCTCAAAAGAAAA 4512
                         ivv  i?    i  i     v  iv                v      i 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_92300606_9   4513 TATGCAAACAGACAA-AAAAATTTGAAAAAAGGCTTAACAGTACATCAGG 4561
                            i    ii v   -  iv iv      i v   i    vi ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_92300606_9   4562 G 4562
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.46 (102 / 70)
Gap_init rate = 0.03 (16 / 639), avg. gap size = 1.88 (30 / 16)  


2038 27.45 1.16 0.83  chrX_92357315_92363110     2137  2737 (3059)    L1M4_orf2#LINE/L1        1   603 (305)  

  chrX_92357315_9   2137 TAGAGAAATATTCCATGTTCATGGATTGAAAGAATCAATATTGTTAAAAT 2186
                          i  i i    i                i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92357315_9   2187 GTCCATACCAACCACAGCTATCTACAGATTTAATGTAATCCCTATCAGAA 2236
                          v v    ivv   v viv           i  i i           i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92357315_9   2237 TACCAATAACATTATTCACAGAAATAGAAAAACAAATCCTAAAATTTATA 2286
                          v   iivi v  v  ii       v  v  i vi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_92357315_9   2287 TGGAACCACAAAAGACCCAGAACAGCCAA--CAATATAACAAGCAAAAAG 2334
                              vii   ii         i      --    v viv  --  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA--AAGAAG 198

  chrX_92357315_9   2335 AACAAAACTGGAGAAA-CACATTAACTGACTTCAAATTATACTGCAGAGC 2383
                               ii     i v-    i vv ii i      viv    i  i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_92357315_9   2384 TATGCTAACCAAAGCAGCATGCTACAGGAATAAAAAGAGACATGTAGACC 2433
                           iiv   i   ii   ii  v   v  v    ii v      i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_92357315_9   2434 AATAGAACAGAATAGAAAACCCAGAAACACATCCACACACCCACTGTGAA 2483
                            i   i     v  i ii       i v i   i   iii iv  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_92357315_9   2484 CTCACTTACAATAATAGTGCCAAGAACATAGACTGGTGAAAAGACAGTCT 2533
                         i v i  v i i  vi         v   vv v   v    ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_92357315_9   2534 CTTCAATAAATGGTGCTGGGAAAACCAGATATGCATATACAGAAGAATTA 2583
                         i     i              v   ii    ?v  i  i  i      v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_92357315_9   2584 AACTAGACTCGCATCTCTCACCATATATGGAAATT---TAAAAATGCAGA 2630
                          ii i   i vi i   v         iii     --- v      --  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG--GA 496

  chrX_92357315_9   2631 TTAAAGACTTGAATCTAAAGCCTCAAACTATGAAACTAATACAAGAAAAT 2680
                          i ?    i i   v   iiv  v       i     vv  v       i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_92357315_9   2681 ATTGTGGATAATCTTCAGAATATTGGTCTGGGCAAAAATTTCTTGAGCCA 2730
                           v v? vv       ivi iv    vi i     vii      -  vi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATA 595

  chrX_92357315_9   2731 T-ACACCA 2737
                          -      
  L1M4_orf2#LINE/    596 TGACACCA 603

Transitions / transversions = 1.61 (100 / 62)
Gap_init rate = 0.01 (7 / 603), avg. gap size = 1.71 (12 / 7)  

 921 24.67 5.00 1.33  chrX_92357315_92363110     5004  5303 (493)    L1M4_orf2#LINE/L1      598   908 (0)  

  chrX_92357315_9   5004 ACACCATAAGCCTAGGTGATCAAAGAATAAGTGAACAAATGGGATCACAT 5053
                               v    vi i ii iv      v  i ii i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_92357315_9   5054 CAAGATAAAAAGCCTCTGCACAGCCAAA-------ATAAAATAATGTGAA 5096
                            i  v    i i i  ii -vi    -------  v  iv  -     
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAA-GTGAA 695

  chrX_92357315_9   5097 GTGATAACCTACAGAATGCGAGAAAATATTTTCAAATTACTCATCTGACA 5146
                         iv  i    i        v            v     i ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_92357315_9   5147 AGGGATTAATAACCAAAATATACAAGGAGCTCA-ACAACCCTATAGGGAA 5195
                              i vi  v   i      i  i  i   v-     i v   ivi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_92357315_9   5196 AAATCTGTAACAATCTGATCAATAAATGGGCAAAATATTTGAATAGACAT 5245
                           iv v--  i  i ii  i? v           iv              
  L1M4_orf2#LINE/    796 AAGACA--AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_92357315_9   5246 TTCTCAAAAGAA-------AACTGGCAAATAGTCATATGAAAATGTGCTC 5288
                              v      -------  v    v    iv  i       vi     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_92357315_9   5289 AACATCACTGATCAT 5303
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (45 / 28)
Gap_init rate = 0.02 (6 / 311), avg. gap size = 3.17 (19 / 6)  


3582 20.19 2.09 1.97  chrX_92383986_92385839      500  1361 (493)    L1M4_orf2#LINE/L1       46   908 (0)  

  chrX_92383986_9    500 AAAATGATAATACTACCCAAAGCAACCTGCAGATTTAATGCAATCTCTAT 549
                           i   ii      v      vii i  i      i  i      i    
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_92383986_9    550 CAAAATCCCAG-TGTCATTTTTGCAGAAATAGAAAA----ATATTGAAAA 594
                                    -  i v             v  v  ----  vi -    
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAA 144

  chrX_92383986_9    595 TGCAT-TTGAAATACCAAGAGACCCCAAGTAGCCAAAACAATCTTGAATG 643
                          v   - v     i -   i     vi i                   vi
  L1M4_orf2#LINE/    145 TTCATATGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_92383986_9    644 AGGCATCCAAATTTGGAGGACTTGTCCATGTCCTGATTGTGAAACATACT 693
                           ivivv    v          ii--  iv   ii   vii    v    
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCA--CACTTCCCAATTTCAAAACTTACT 241

  chrX_92383986_9    694 AAATAGCTGCAGTGGTTTAAATAGTGCAGTACTGGCATAAGAGCAGACAT 743
                          v v    i    ii iv i i    ii             iii      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_92383986_9    744 ATAAACCAATGGAATATAAAATATTTTTTATTCCCCAAATAAATCCTTAC 793
                            i i          v  -----  vvv v   vv       i  v   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAA-----TTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_92383986_9    794 AT--ATGAGGCAATTGATTTTTGACAAAGGTGCCGAAAACATTCAATAGA 841
                           --   - v           i     i      i i v        i i
  L1M4_orf2#LINE/    337 ATTTATG-GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_92383986_9    842 GAAAGAAGTATCATTTCAACAAATGGAAGTAGGAAAACTGGATATCCACG 891
                                vvi  v             viv i   v         ?    i
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_92383986_9    892 TTCAAAACAATGAAGGTGGACCCATACCTTACATCATATATTAATATGAA 941
                          v     v       v       v     i   i      i-  ----  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC-AA----AA 480

  chrX_92383986_9    942 ATTTACTTCAACATGCATCAAAGACCTAAACATAAGAGCTAAAACTATAA 991
                            v   -   v   v    ?         ii                  
  L1M4_orf2#LINE/    481 ATTAACT-CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_92383986_9    992 AACTCTTAGAAGAAATCATAGAAGAAAATTTTCATGACACTGGATTTGGT 1041
                                        v     i? v    i   i    vi   i  v  i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_92383986_9   1042 GATGAGTTTT--GATGTTAACATCAAAAATAGAAACAACAAATTAAAAAA 1089
                         i   iv  i --   i -i   i     ii v  i       vv      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_92383986_9   1090 TAGATGAATTGGACTTCATTAAAACTAAAGGCTTTTGTGCAACAAAGGAT 1139
                              i             i    i    ii         vv       i
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_92383986_9   1140 GCTATTGAAATAGTGAAAAGACAACCCACATAATGGCATTAA-TATGGGC 1188
                         i    ii i v                   v     v vv  -   vv  
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_92383986_9   1189 AAATCAAATATCTGATAAAGGCTTTATATTAAGAATATATAATTAATTCC 1238
                               v           i  vi  i   iv           vv  i  i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_92383986_9   1239 TACAACTCCACAGTAAAAAT-CAAA------AATTCAAAAATATGAAAAG 1281
                                 v i i      v-    ------    ?      iv v    
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_92383986_9   1282 TACTTGAGTAGGCATTTATCCAAAGAAGATATGCAAATGACCAGTTAGCA 1331
                         v i    i   i     v              i      i   i v    
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_92383986_9   1332 CATGAAATGGTGCTCAACATTATATCATTA 1361
                                v i          i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (97 / 73)
Gap_init rate = 0.02 (17 / 863), avg. gap size = 2.06 (35 / 17)  


2693 27.11 2.92 1.01  chrX_92419110_92421374      884  1772 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_92419110_9    884 GAAAAAT---CTATGCTCATGGATTGGAGGAATAAATGTTGTCAAAATGG 930
                             i  --- i   i            i  v v   i    i  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_92419110_9    931 CCATATTGCTCAAAATAATCTACAGATTCAATGCTATTCCTATCAAACTA 980
                          v   i v i    v i              i  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_92419110_9    981 CACA--TGTATTTTTTTACACAATTAGAAAAATACTG-TTCTAAAATTCA 1027
                          -  --  i-i      i  v  v v  v  i--   - i          
  L1M4_orf2#LINE/    103 C-CAGCTGC-CTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_92419110_9   1028 TATGCAACTAAAAAGGAGACTGAATAGCCAAAACAATCTTAACCAAAAAG 1077
                             v  v iv  i   vv v                   i vv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_92419110_9   1078 AACAAAGCCAGAGGCTTCACATTACCCCCCTTCAAACTACACCATAAGTC 1127
                                iii    vi     i v   vvi      vivi  i i  iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_92419110_9   1128 TAC-----CCCAAACAGCATGATACTGGTA-AAAAACAGACATACAGACC 1171
                            -----i v i    ii  i      i -  ii i       i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_92419110_9   1172 ACAGGAACAGAATAGATAACCCAGAAATAAAGCTGCACACCTATAGCCAT 1221
                          vv    i     v  v ii           v iii   ii   i i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_92419110_9   1222 CTGAACTTTGACAAAGTCGATAAAAATAAGCAATACAGAAAGCACTCCCT 1271
                         i   vi  i     i vi vi  i vi vv    ivi     v ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_92419110_9   1272 ATTCAATAAAAGGTATTGGGGTAGCTGGTTAGCCAGATGCAGAAGAATGA 1321
                         v     i   v   ii    ii i    v  ?   v     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_92419110_9   1322 AACTGGACC---ATTTT-TACCATATACAAAAACTAACTCAAGATAGATT 1367
                          ii      --- ii i-i              i        i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_92419110_9   1368 AAAGATTTAAATGTAAGACCTCAGAATATAAGAATTCTAGAAGAAAATCT 1417
                          ?   ii           v  v i v     i v ii          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_92419110_9   1418 AGGAAATAACATTCTAGACATTGGCCTTAGGAAAAAAATTAT--GACTAA 1465
                            ?ivv  iv   vv   v    v-     v  viiv  v --  -  v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGA-TAT 596

  chrX_92419110_9   1466 GTTCTCAAAAGCAACTGCAACCAAAACAAAAATTGACAAGTGATACTTAA 1515
                          vivi        vvv     v   iv      v  i  i viv    v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_92419110_9   1516 TTAAACTAAAGCGCTTTTGCACAGCAAAAGAAACTATCAAAAGAGTAAA- 1564
                          i   v v  ivi      ii vv    i  v        i i   i  -
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_92419110_9   1565 ---CAGCCTACACAAGGGGGGAAAATATTTGCAATCTATGCATCTGTCAA 1611
                         ---  i  i   v  v   i              vii  ii     vi  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_92419110_9   1612 AGGTCTAATATCCAGAATCTATAAGGAAGT-TAAAGATTCAACAAGCAAA 1660
                         i  v  vi          v     i   v - v vi i    i  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_92419110_9   1661 AAGCAAATAATAATTCCATTCAAAAGTGGGCAAAAGACATGAACAGACAC 1710
                          ii       i---i v   ?    i        i  iv    i     i
  L1M4_orf2#LINE/    797 AGACAAATAAC---CCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_92419110_9   1711 TTCTCAAAGGAAGACATTCAAGCAGTCAGCAA--ACATGAAAA-ATGCTC 1757
                              v  i     i  v   iii i  ii  --         -      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_92419110_9   1758 AACATCACTATCAGA 1772
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 1.94 (35 / 18)  


 856 19.74 3.00 2.58  chrX_92427328_92432337.rev     3246  3478 (1532)    L1M4_orf2#LINE/L1       31   264 (644)  

  chrX_92427328_9   3246 AGACTTAATATTGCTAAAATGTCCAAATAA---CCAAAGCAATCTACAGA 3292
                                      i   i   v --    v---     vii         
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGC--AATACTCCCCAAATTGATCTACAGA 78

  chrX_92427328_9   3293 TTCAATGTCATCCCTATCAAAATCCCAAA-GCCATTTTTTTACAGAAATA 3341
                              i iv                  iv-   --      i       -
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCC--TTTTTTGCAGAAAT- 125

  chrX_92427328_9   3342 TGA-AAACCAATTCTAAAATTCTTATAGAACCACAAAGGACCCCAAATAC 3390
                            -  i ii  i         v   i   vii   i      vi    v
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chrX_92427328_9   3391 CCTAAATAATCTTGAAAAAAAAAGAACAAAAATGAAAGCATCACACT--C 3438
                           v   i            i  -       iv  i i vv       -- 
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAA-GAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_92427328_9   3439 TGATTTCAAAATATATTAAAAAGCTACCACAATTAAGATA 3478
                         ii         iv  i  v        vii   i    i 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

Transitions / transversions = 1.88 (30 / 16)
Gap_init rate = 0.03 (8 / 234), avg. gap size = 1.62 (13 / 8)  

2022 26.17 4.36 0.30  chrX_92427328_92432337.rev     3860  4524 (486)    L1M4_orf2#LINE/L1      217   908 (0)  

  chrX_92427328_9   3860 ACACATCTACTATTTTAAAAATTAAGAAAAAG-----GAAAACAAACCAC 3904
                             v  i- v    i    v   vv v    ----- v  v   iv  v
  L1M4_orf2#LINE/    217 ACACTTCC-CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_92427328_9   3905 TATGGTACTGACA-AAAGACAGACATATAAACCAATCGAACATAATAGGG 3953
                          i        i  -  i  i         i i    v   i v   v i 
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_92427328_9   3954 TGTCCTGAAATTAATTCACCCACGTATGGCCAAACAATCACTGACT-GAA 4002
                         v    v     v  ii  iv  iv     i   vii  ivii   v- ii
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_92427328_9   4003 TGCCAAGCGTATAAAATGGAGCAATAATACTGTCTTTAACAAATGGTATT 4052
                                vvi  vv     i v  v    v v i  i          ii 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_92427328_9   4053 GGAAAGACTAGATATCCAAATGCATAAGAATAAAATTAGACTCTAATTTC 4102
                           i vi   i    ?   v     v      i  i  i   i iv ii  
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_92427328_9   4103 ACATCATATATAAAAATAAACTCAAAATGGATTAAAGATTTAAATGCA-- 4150
                            i      i      v              i ?   ii      i --
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_92427328_9   4151 -GCTGGAACCCATAAAACTACTAAAAGGAAACATAGGAAAAAAGCTTCTC 4199
                         -   ii   i-        vi  i   i         ?iv   v    vi
  L1M4_orf2#LINE/    516 AGCTAAAACT-ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_92427328_9   4200 GACATTGGAATGGACAATGATTTCATCAATATGACCTCAGAA-CACAGGC 4248
                            v    iv i i     i    v vi       vi  i  -    i  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_92427328_9   4249 AACAAAAGCAAGAATACATGAGTTGGACTACATCAAATTAAAAAATGTCT 4298
                                 v  i    v  i i       v       v v     iv i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_92427328_9   4299 GCATAGCAAAGAGAAAAATCAATACAGTAAAAAAGCAGCATACAGAATGG 4348
                          iiivv     iiv vv     v v   i    ii  i vi         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_92427328_9   4349 GAAAAAATAATTGCTAACCATAAATTTGATGAG---TTCATTCCCCAAAT 4395
                           i      v    v  i    v  i    i  ---i ii vi  vi   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_92427328_9   4396 AAATAAGTAACCCCTCAAACTCAATAGCAAAAAGA-AAA-AATT-AATTT 4442
                          v    iv   i i vv         ii       -   -  ii-    ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_92427328_9   4443 TAAAATGGGC--------TG--TAGAGATTTCTCTATAGAAGACATACAA 4482
                         v         --------  --    v       i v      i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_92427328_9   4483 ATGGCCAACAG--ACATGAAAAAATGCTGAAAGTCGCTAATCAT 4524
                                 i i--         i     v  vi  i????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (99 / 71)
Gap_init rate = 0.02 (14 / 692), avg. gap size = 2.21 (31 / 14)  


2828 25.11 2.77 2.32  chrX_92501214_92505065     2456  3359 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92501214_9   2456 TGGACAAACAGCCCATGTTCATGGATTGGAAGAATTGATATCATTAAAGT 2505
                             v i i v                      v  i    ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92501214_9   2506 GGCCATGTTGCCCAAAGCACTCTACAGATTCAATGTAATCCCTATCAAAA 2555
                            v  ii v      viiv             i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92501214_9   2556 TACCAAG-GCATTCTTT-CACATAATTAAAAACAAAC-AATTCTAAAATT 2602
                          v   iv-  v  i   -  v -    i ---   i -i  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGA---CAAGCTGATCCTAAAATT 146

  chrX_92501214_9   2603 TACATAGAACCAAAAAAGGG-CACA-AACAGACAAGGCAATCCTGAGCAA 2650
                         i i  i   -- viv     - v  -  i  v   ii     i   iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_92501214_9   2651 TAAGA-CAAAAGTGGAGG---CACCATTTTATCTGACTTCAAAATATATT 2696
                         v    -    iv      ---   - i  i-- ii i       iv  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCAC-ACTTC--CCAATTTCAAAACTTACT 241

  chrX_92501214_9   2697 ACAAAGCTAGAGTAACCAGAACAGCATAGTATTGATATGAAAAATAGACA 2746
                                  v     i  ii    ii i   i  ii  -  ii       
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACA 290

  chrX_92501214_9   2747 TATAGGCTAATGTAACAGGATAGAGAGCCCAGAAATGAAACCACATGTTT 2796
                              iii    v  i  i  v     i        i  v   i ii   
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_92501214_9   2797 ACAGTCAACTGATCTTCAACAAAGGGGACAATA--ATTCACACTGGATAA 2844
                          ii     i    i   i    i  v v   v --     - -   iv  
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA-A-TGGGGAA 388

  chrX_92501214_9   2845 GGAA-ACCCTCTTCAATAAATGGTGTGGGGAAAATTGGATAGACACATGT 2893
                         i   - vi  i     i        iv    v  i      ?v      i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_92501214_9   2894 GAAAGAATGAAACTGGACCTCTACCTTTCACAATATACAAAAATTAACTC 2943
                         i          ii      i      iv   v                  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_92501214_9   2944 AAAATGAATTAAAGACTTAACTGTAAGACCTGAAACTATAAAAATACTAG 2993
                               i  i ?    i   v       v  i           v vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_92501214_9   2994 AAGAAATCCCAAGGAAAACTCTTCTGGACATCGGTCTAGGGAGATAGTTT 3043
                               v vi i ?iv  v     vv   v i  vi    v -  i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTTT 587

  chrX_92501214_9   3044 AT--GACTAAGACCTCAAAAGCACACACACACACACACACAAAAATC--C 3089
                         v --  -  v   vi          vi  ---   v viv      v--i
  L1M4_orf2#LINE/    588 CTTAGA-TATGACACCAAAAGCACAAGCA---ACAAAAGAAAAAATAGAT 633

  chrX_92501214_9   3090 AAATGAGACTT------AACTATAAAGCTTCTGCATAGCAAAATAAATAA 3133
                             vi     ------  i  -   i   i  iiivv    iv v iv 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_92501214_9   3134 ATCAACAGGGTGAAGAAGTAGGT-GTTGAGTGGAAAGAAACACTTGCAAA 3182
                         -    v ii     i iii ivi-iiv  i   i ii   i i       
  L1M4_orf2#LINE/    683 -TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_92501214_9   3183 C--TGGCTCTGACAAATGACTAATATCCAGAATCGACAAGAAACTCAAAC 3230
                         i-- ivv     i  iv    vi          vv i  ii     vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_92501214_9   3231 AACCCAACAAGAAAAAAGTAAGTAACTCTGTTAAAAAGTGGGCAAAGAAC 3280
                            i   i  v     iii  i    i vi  ?    i         i i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_92501214_9   3281 ATGAAGAAATACTTCCCCAAAGAAGACATACAAGTGGCCAACAAACATAT 3330
                         v    v i i i   i          i      i       i  i  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_92501214_9   3331 TTAAAAAAATGGTAAACATCACTAATAAT 3359
                         --i    i   v v       ????????
  L1M4_orf2#LINE/    882 --GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (146 / 77)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 1.64 (46 / 28)  


2584 26.70 3.02 1.56  chrX_92509881_92513937.rev     2672  3566 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92509881_9   2672 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATCACTATAATTTAAAT 2721
                               i i  i     i               v i v   vi  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92509881_9   2722 GACCATATGGCCTGAAGCACTCAAC-GATTAAATACTATTCCTATCAAAT 2770
                          i v   ivv  ii  viiv  v  -    v  ii v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92509881_9   2771 TACCAA-TGCCATTTTTTACAGGATTAGAAAAAAAAACT-ATTTTAAAAT 2818
                          v   i-    -      i   i v v  v  i----  -  ii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG----CTGATCCTAAAAT 145

  chrX_92509881_9   2819 TTATATG-AAATGAAACAAGACCCCTGATATCTAAAGCAATCCT---AAG 2864
                          i     -     v  -ii     vvi   v i   i     i ---  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_92509881_9   2865 TAAAAATAAAGCTGGAGACATCACATTACCTAACTTGAAATTATACTACA 2914
                         v  i  i    i     ivv     i v  i  i  v   viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_92509881_9   2915 AAGTTACAGTAACCAAAACAGCATGATATTGGTACAAAAATAGACATATA 2964
                            i        i   i    ii  i  i   i i  ii           
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_92509881_9   2965 GACCAAGGAAATGGAATAGAAAACTCATAAATACAGCCACACACCTACAA 3014
                           i   v i   i    v  i iii  v     v v   i   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_92509881_9   3015 CCAAATGATCTTTTATAAAGTTGACAAATATAAGCAATGGGTAAAGGA-A 3063
                         i   v    i  iv i  i v  v   ivvi vv       v    i - 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_92509881_9   3064 CCCATGTTCAATAAATGATGCTGGGAAAACTGGCTAACCATGGGCAAAAT 3113
                         vi - v     i     i        v      v  ?   iiv      v
  L1M4_orf2#LINE/    395 GTC-TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_92509881_9   3114 AATGAAACTGGAACCCTTCCTATCTCCATATAAAAAAGTTAACTCAAGCT 3163
                               ii    v    v   vv v       v    i         iv 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_92509881_9   3164 GGATTAACAACTTAAATGTAAGTTCTCAAACTATAAAATTCCTAAAAGAA 3213
                             i ?vi  i          vv  v           i  i  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_92509881_9   3214 AACTTAGA---AAATACCCTTCAGGACATAGACTTTGGCAAATCATTTAT 3260
                            v   i---    ---    iv   v v iv  v     - vi   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chrX_92509881_9   3261 --GACTAAGTCCTCAAAAGAAATTGCAACAAAA-----AATTGATAAATG 3303
                         --  -  v v vi      v vvv         -----   v       v
  L1M4_orf2#LINE/    590 TAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_92509881_9   3304 GGACCAAAT-AAAATAAAGAGCTTCTGCACAGCAAAAGATATTATCAATA 3352
                             ivv  -     v  i i   i  ii vv    i  i i      v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_92509881_9   3353 GAGTAACAAAGA--GTGTGCAGAATGGTAAAAAATATTTACAAGGTATGC 3400
                         i   i -     --iivii        v i         i   ivi  ii
  L1M4_orf2#LINE/    689 AAGTGA-AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_92509881_9   3401 ATCTAGCAAAGAACTCATATCCAGAATCTATAAGGAACTTAAATAAATCA 3450
                             iii  i i   ii          v     i     ivv i  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_92509881_9   3451 ACAA------GAAAAACAACCCCATATAAAAATCTGGCAAACAACATAAG 3494
                          i  ------  v   i     v  v?      v-      vi iv i i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATG-GGCAAAGGATTTGAA 836

  chrX_92509881_9   3495 CAGTCACTTCTCAGAAGAAGATATACAAACATCCAATAAACATATGAAGA 3544
                         i  v  i     vi               iiv       i  i     i 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_92509881_9   3545 AATGCTTAATATCACTAATCAT 3566
                         i     i  i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.95 (41 / 21)  


2420 26.64 2.89 2.44  chrX_92530652_92535606     3562  4462 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_92530652_9   3562 AAAAATAATTTCCAGGTTCATGGATTGAAAAAATTA---TCATTAAAATA 3608
                            i   -- i   v            i  i v   --- ii    i  i
  L1M4_orf2#LINE/      4 AAAGATA--TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_92530652_9   3609 ACCATACTACCAAAAGCATTCTACAGATTCAGTGCTATCCCTGTCAAATT 3658
                         i v     v  v   viiv            ii  v      i     v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_92530652_9   3659 ACCAAGATCATTTTTCACAGAATTAGAAAAAAAAAAGTATTTTAAAAGTC 3708
                         v   ivvv v     ii     v v  v  ivvi ---- ii     v  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA----TCCTAAAATTC 147

  chrX_92530652_9   3709 ATGGGGAACCGAAACAGATTCTAAATAGCCAAAGCATTTCTAAGCAAAAA 3758
                           iv    vi v  vi  ii vi          i  v ii i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_92530652_9   3759 GAACAACACCAGCAGCATCTCATTACCCAACTTCAAACTATACTGCAAGG 3808
                               viiii vi vv  v  i v     i      viv    i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_92530652_9   3809 CTACAGTAACCAAAATAGCATGGCACTGGTACACAAACAGACA-ATACAC 3857
                                  i   i i  ii   i     i i vii i     -   v i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_92530652_9   3858 CAAGAAAACAGAATAGAAAACTCAGAAATAAAGCCA--CATCTATAACCA 3905
                            vii  i     v  i iii          v   --   i   iii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_92530652_9   3906 ACAGATATTTGACAAAGTTGACAAA--CATAAGCAATGGTAAAGAAAT-T 3952
                          iv   v  i     i v  v   i--   --v      vi  ii   -v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAATAG 395

  chrX_92530652_9   3953 TCTGTTCAATAAATGGTGCTGGGAAAACTGGCTAACCATATGCAGAAGGA 4002
                            v     i              v      v  ?   i     i   i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_92530652_9   4003 TAAAACTGGAACCCTACCTATCACCATATACAAAAATTAACTCAACATAG 4052
                          i  ii    v        vv                        v  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_92530652_9   4053 ACTAA-----TAAATTTAAGACCTCACACAATAAAAATCCTAGAAAAGAA 4097
                          ii ?-----     v     v  v v  v      v  i     --   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA--GAA 543

  chrX_92530652_9   4098 AACCTAG---CAAATACCCTTTTGGACATTGACCTTGGCAAAGAAATTAT 4144
                            v   ---i    ---   ivv   v   ivi v     v iv-  v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGT-TTCT 589

  chrX_92530652_9   4145 TATGACTATGACCTCAAAAGCAATTGCAATGAAAACAAAAATTGACAAGT 4194
                           -  -      vi        vvv    ii   iv      v  i  i 
  L1M4_orf2#LINE/    590 TA-GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_92530652_9   4195 GGGACTT-AT-----TTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAA 4238
                         v      -  -----     i -   i  ii vv    i  v        
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_92530652_9   4239 CAGAGTAAAAAAAAAAACCTACAGAGTGGTAGGAAATATTCACAAAGTAT 4288
                         v i   i    i v  -  i     i   v  i       ii    vi  
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAA-CCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_92530652_9   4289 GTATCCAACAAAGGACTAATATTCCAAATCTATAAGGAACTTAAATAAAT 4338
                         i    ii i  i     vi   i vi   v     i     ivv i  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_92530652_9   4339 AAACAAGAACAAAACCAA--ACCCA-TAAAAAGGTTGTCAAAGAAAATGA 4385
                         v  i  v  v  i  v  --     - v?   ii v v     i vv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_92530652_9   4386 GCAGACACTTCTCCAAATAAGACATACAAGCAGCCAACAAATATATGGGA 4435
                         ii     i         v    i      iii     i  ii i   ---
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG--- 882

  chrX_92530652_9   4436 AAAAAGATGCCTAACATCACCAATCAT 4462
                         -         ii       ????????
  L1M4_orf2#LINE/    883 -AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.02 (22 / 905), avg. gap size = 2.18 (48 / 22)  


2814 28.09 0.66 1.42  chrX_92554865_92564013     4923  5837 (3312)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92554865_9   4923 TGGAGAAACATTCCATGCTCATTGATAGGAAAAATCAATATTATGAAAAT 4972
                             i i i  i     i    v   v    i v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92554865_9   4973 GGCCACACTGCCCAAAATAATTTATAGATTCAATGCTATTCCCATTAAAC 5022
                            v i   v      v i  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92554865_9   5023 TACCATTGACATTCTTTGCAGAA-TTAAAAAAAAAAAAACGATTTTAAAT 5071
                          v   vivi v  i         -  i v  iv------i   ii    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC------TGATCCTAAAA 144

  chrX_92554865_9   5072 CTCATATGGATCCAAAAAAAAGCTTGTATACCCAACACAATTCTAAGCAA 5121
                         i         vviiv  iii v iv v   v    v     ii i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_92554865_9   5122 AAAGAAAAAAGCTGGTGGCATCATGCTATCCAACTTCAAACTATACTACA 5171
                         i     v    i   v  vv   ii  vi    i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_92554865_9   5172 ATGCTACAGTAACCAAAACATCGTGGTACTGGTACAAACACTGATACCTA 5221
                          v          i   i   vi          i i  iv iv  i iv  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_92554865_9   5222 AACCAATGGAACAGAATAGAGACCTCAGAAATCAGACTGCACATCTACAA 5271
                         i i        i     v    vii       v iv iii    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_92554865_9   5272 CCATCTGATCTTGAACAAACCTGACAAAAACAAGCAATGGGGAAAGCATT 5321
                         i  vi    i  vi    ivv  v   i v  vv            v  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_92554865_9   5322 CTCTATTTAATAAATGGTGTGCTAAGATAACTGGCTAGAAATAGGCAGAA 5371
                         v   v  i  i        --  ii  i      v  ?vv i v   i  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTG--CTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_92554865_9   5372 AATTAAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 5421
                         i v i  ii         v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_92554865_9   5422 TGGATTAAAAACCTAAATACAAAATTCCAAACTATAAAAATCCTAGAAGA 5471
                              i ? i        ii  i viiv           v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_92554865_9   5472 AAATCTAAGCA-ATACCGTTCAGGACATAGGCATGGGCAAAGATTTCATA 5520
                            iv  i ?i- v i -   iv   v v  vv i     v i    v  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_92554865_9   5521 ---ATGAAATCATCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATG 5567
                         ---    ---  i        vvv          v      v  i    v
  L1M4_orf2#LINE/    592 GATATGA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_92554865_9   5568 GGAACTAGTTAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCA 5617
                            vi vi i  iv v  i i   i  ii vv    i  v       vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_92554865_9   5618 GAGTGGACAGGCCACCTACAGAATGGGAGAAAATGTTTGCAATCTACCCA 5667
                         i    i v  i v   i                 i       vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_92554865_9   5668 TCTGACAAGGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTA 5717
                              i     v  vi          v  i  i     ivv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_92554865_9   5718 TAAGAAAAAAA-AGACAACCCCATTAAAAAGTCAGTAAAATACATGAACA 5766
                            v     i - i i     v   ?    i vi i   iv iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_92554865_9   5767 GACAATTTTCAAAAGAAGACATTCACGCAGCCAACAAACATATGAAAAAA 5816
                             v  i  v        i  v  viii     i  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_92554865_9   5817 AAGCTCAACATCACTGATCAT 5837
                         v-           ????????
  L1M4_orf2#LINE/    889 T-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (145 / 108)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  

2614 28.34 3.75 0.59  chrX_92554865_92564013     7795  8648 (501)    L1M4_orf2#LINE/L1        4   884 (24)  

  chrX_92554865_9   7795 AAAAAAATTCCATGCTCATGGATAAGAAGAATCAATATTATTAAAATGGC 7844
                            i v  i     i        vi     v i      i    i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_92554865_9   7845 CATACTGTCCCAAAC-AATTTACAGATTCAATGGTATTTCTATCAAACTA 7893
                         v     -i      i-i  i           i vv  ii        v v
  L1M4_orf2#LINE/     54 AATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_92554865_9   7894 CAAATGACATTCTTCACAGAACTAGAAAAAGAAATTATTTTAAAATTCAT 7943
                          v iivi v  i  ii     v v  v  iv--- v  ii          
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGC---TGATCCTAAAATTCAT 149

  chrX_92554865_9   7944 ATGGAACCAAAAAAGAGCCTGAATAGCTAAGACAATCTTAAGCAAAAAGA 7993
                               viiv  ii  v  v       i  i        i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_92554865_9   7994 ACAAAGCTGGAGACTTCACGTTACCCAATTTCAAACTATACTACACAGCT 8043
                               i     ivi    ii v            viv       v    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_92554865_9   8044 TCAGTAACCAAAAGAGCATGGTACTTGTACAAAAACAGACACATAGACCA 8093
                         v      i   i v  ii       v i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_92554865_9   8094 GTGAAACAAAAT----AGCCCAGAAATACGGCTGCGCACCTACAACCATC 8139
                         i  i  i i   ----  i         viv iiii  ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_92554865_9   8140 TGATCATCAACAAAGCTGACAAAAATGAGCAACGGGGAAGGACTC-CCTA 8188
                             iv  i    i v  v   i viivv   i      i  v v-i  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_92554865_9   8189 TTCAATAAATGGTGCTCGGATAACCGGTTAGCCAAATGCAGAATATTGAA 8238
                              i          v   i   i  v  ?   v     i  v v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_92554865_9   8239 ACTGGACCCCTTTCTTACATCATATATGAAAATCAACTAAAGATAGATTA 8288
                         ii         vi  i   i      ii     i    v  i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_92554865_9   8289 AAGACTTAAATGTAAAACCCCAAACTGTGAAAATCCTGGAAGACAATCTA 8338
                         ?    i         i v iv     i i   v  i i     v  iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_92554865_9   8339 GGCA-ATACCATTCTGGACATAAGAATGGGCAAAGATTTCATGACAAAGA 8387
                           ?i- v i -   vv   v vi iv i     v i    v iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_92554865_9   8388 CGTCAAAAGCAATTGCAGCATAAGCAAAAAT-GACAAATGGCATCTAATT 8436
                          ii        vvv   i  v   v      -  i    v v ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_92554865_9   8437 ATACTAAAGAACTTCTGCACAGCAAAAGAAAGTATCAACAGAGTAAACAG 8486
                          v v v  i     i  ii vv    i  v v      v i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_92554865_9   8487 ACAACCTTTGGAATGGGAGAAAATATTTGCAAACTATACATCTGACAAAG 8536
                               ivii                       ii   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_92554865_9   8537 GTCTAAGATCTAGCATGTATAATGAACT---------------TAAA--- 8568
                          v  viv   i  v  i     v     ---------------    ---
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_92554865_9   8569 -CAAAT----TTATTAAAAAA-AGGAAAAGGGCATGAACAGGCACATCTC 8612
                         -     ----iv   ?     -i  v     iiv    i  i  iv    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_92554865_9   8613 AAAATAAGGCATACACATAGCCAACAAGCATATTAA 8648
                         v   v   ii     v  i     i     i  v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (12 / 881), avg. gap size = 3.08 (37 / 12)  


1738 22.37 4.81 15.70  chrX_92568180_92571494     1804  2822 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92568180_9   1804 TAAAGAGGCATACTATATTCATCGATTGGAAGACTCAACACCATT----- 1848
                          ii i  ii  v i  i     v            i  i iii  -----
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92568180_9   1849 GTCAATTCTCCCAAAATTGACCAATAGGATTTTAATGTAATCCCTTTCCA 1898
                          v    v     v       i v i  i--  i  i i       v  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGA--TTCAACGCAATCCCTATCAA 98

  chrX_92568180_9   1899 AATCCCAGCAAGGA---TTTTGTAGATATAAACAAGGTTGTTCTTAAATT 1945
                                  --v v---     i   v  vi     v vi i  v     
  L1M4_orf2#LINE/     99 AATCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_92568180_9   1946 TATATAAAAATTCACAGGCCCTAGAATAGCTAAAACAGTATTAAAAAAGA 1995
                         i    ii    v  vi  v  i        i      i v  i       
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_92568180_9   1996 AGAATCAAGTGGGA-----------------TATTAAGGCCCATTATATA 2028
                             iv    v   ----------------- v i  ii ii i  i v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_92568180_9   2029 TCAATAGTATTAAAAACAGTGTGATATTGGCAGAGAAATTGACACATAGA 2078
                         v v i    v v  i        i  i     v iii  v    i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_92568180_9   2079 TTGACCGAATGGAATAGAGGACCCAGAAATAGACCCACACAAATATGCCC 2128
                          ii iv    i    v   iii         i     i   vv    vi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_92568180_9   2129 AACTGATTTTTGAAAAAGAGACAAAAAGAAATTTAACGGAGGAAAGATAC 2178
                           i       i  v  i ivi v  i vv -  i  i  -       - i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGG-GGAAAGA-AT 393

  chrX_92568180_9   2179 AGCCTTTTCAACAAATGTTTCTGGAGTAATTGGACAAGAAAAAGAAGAAT 2228
                           i              v v    iii  i    i ?vv v ------- 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA-------T 436

  chrX_92568180_9   2229 GAAAAAAGAGGAGGAAGGAAGAGGCAGGTGAAGGAGTAAATAGAGAGGAC 2278
                          v    --------------------------------------------
  L1M4_orf2#LINE/    437 GCAAAA-------------------------------------------- 442

  chrX_92568180_9   2279 AAGGTGAATGGAGTAGGAAGAGAAAGGAGAATCAGAGGGGAGTAATAGGA 2328
                         -----     i   v   --------------------------------
  L1M4_orf2#LINE/    443 -----GAATGAAGTTGGA-------------------------------- 455

  chrX_92568180_9   2329 GGAACAAGGAGGAGGAAGGAGAAGGGAGAAGAAGGAGCAGAAGAAGATTC 2378
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    456 -------------------------------------------------C 456

  chrX_92568180_9   2379 CCCTAAACCTCATATCTTATTTAGAAAGGAACAAATTAACTTAAAATAGA 2428
                              --     i i v   -- v   ------        i     i  
  L1M4_orf2#LINE/    457 CCCTA--CCTCACACCATAT--ACAAA------AATTAACTCAAAATGGA 496

  chrX_92568180_9   2429 TCACGAGCTTAAATATAA-AGCATAAAACTATAAAACATTTAGGAAATAA 2477
                            ?iii i     i   -   -              vi    i i v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_92568180_9   2478 -ATAGGAG-AAACTGTCATTATTTACAATTAGTCAAAGAGTTCTTATGC- 2524
                         -     ? -   iiv  i v ii vvii    v   v iv      vii-
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_92568180_9   2525 TGACACCAAAAACAAAAACAATATTCATAAAAAAATTA--TAAACCTGAC 2572
                                    i  v  i   i --- v i     v  --    iiv   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACA---AAAGAAAAAATAGATAAATTGGAC 642

  chrX_92568180_9   2573 TTTA-----ACTTAAAACTCTCGCTGTGTGAAAGATC-CTCTTTATAGAA 2616
                           i ----- i v      i i -  iv v    iv -  v iv v i i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_92568180_9   2617 TGCAAAGACACTGTACAGAGTGGGAGAAA-CAT--GCA-----CATATCC 2658
                           v       vivi     i         -i  --   -----i     i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_92568180_9   2659 AACAACAGGATTTGTATCTAGAATATATAAATAACTTAAAAAATTCAACA 2708
                         i i  -i   i       i            v    ivv v  i    i 
  L1M4_orf2#LINE/    742 GATAA-GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_92568180_9   2709 GTAAGAAAACAA----TGTAATTTGAAAACGGGCTAAAGACATGCATAGA 2754
                         i   i  i    ----ivi    ?i    i    v  i  iv  v     
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_92568180_9   2755 CAGTTCACCAAAGAGGATATACGGATGGCAAATAAACACAGAACAAGATG 2804
                           v   v       i       ii     v     i    vi v      
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_92568180_9   2805 TTCAACGTCAACAGCCAT 2822
                         i     i   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (139 / 85)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 7.21 (209 / 29)  


 975 24.83 0.68 8.50  chrX_92606811_92609142      508   801 (1531)    L1M4_orf2#LINE/L1      242   512 (396)  

  chrX_92606811_9    508 ACAGGGCTAGAGTAACCAAAACAGCATGGTACTGGTTAAAAAAAAAAAAA 557
                            ii    v     i   i    ii         i--------------
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC-------------- 277

  chrX_92606811_9    558 AAAGAAAAGAAAAAAACAGACACACAGAACAATGGAATGGAATGGAGAGC 607
                         --------- v  ii i     i i   v         i    v     i
  L1M4_orf2#LINE/    278 ---------ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_92606811_9    608 CCAGAAATAAGGCCACACACCTATAACCATCTGCTCTTCAGCAAAGTTGA 657
                                   iv   i   ii   iii  vi  v i   ii   i v  v
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_92606811_9    658 CAAAAACAAGCAATGGGGAAAGGA--ATCCCCATTCAATAAATTGTGCTT 705
                            i v  vv            i --i  ii--     i    v     v
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTT--TTCAACAAATGGTGCTG 416

  chrX_92606811_9    706 GGATAACTGGCTAGCCATATGCAGAAGACTGAAACTGGACCTTTTCTTTT 755
                            i      v  ?   i     i    v    ii      ii v i iv
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_92606811_9    756 TATCATATATAAAAATCAATCCAAGATTAATTAAAGATTTAAATGT 801
                         i i      i      i  ii   i  vi  i ?   ii       
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

Transitions / transversions = 2.74 (52 / 19)
Gap_init rate = 0.01 (3 / 271), avg. gap size = 9.00 (27 / 3)  

1103 25.93 3.74 1.98  chrX_92606811_92609142     1385  1839 (493)    L1M4_orf2#LINE/L1      446   908 (0)  

  chrX_92606811_9   1385 TGAAACTGTACCCCTTCCTTTCACCATATAAAAAAATCAACTCCAGATTG 1434
                             ii  v      v   iv         v      i     v i  v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_92606811_9   1435 ATTAAATATTTAAATGTAAAACCTAAAAATATAAAAAAAACCTAGAAGAA 1484
                           i ? v ii         i v      v       vv-- i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT--CTTAGAAGAA 543

  chrX_92606811_9   1485 AACCTAGG---AAATATGGTTCTGGACATAGGCCTTGGCAAAGATTTCAT 1531
                            v    ---    v ---  vv   v v  vi v     v i    v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCT---TCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_92606811_9   1532 -GATGAAGACTCCAAAAGCAATTGCAAGAAAAACAAAAATTGACAAGTGG 1580
                         -   - v   v         vvv    v    iv      v  i  i v 
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_92606811_9   1581 GACCTAATTTAACTAAAGAGCTTCTGCACAGCAAAAGAAAATATCAACAG 1630
                            i v  iv  v v  i i   i  ii vv    i  v v      v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_92606811_9   1631 AGTAAT----CAAATTACAGAATGGGATAAAATATTTGCAAGCTATGCAT 1676
                            i v----   vii           v             iii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_92606811_9   1677 CTGACAAAGCTCTAATGTTCAGGATCTATTAGAAA----TGTAA---AAT 1719
                             i  i vv  vi i i   i  v   v ii  ---- ii  ---   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_92606811_9   1720 AACCAGCAAAGTACAAGTAATCCCACT-AAAAATCG-CAAATGACATGAA 1767
                           iv --    -    i   i  v i -      v -    v  iv    
  L1M4_orf2#LINE/    790 AATAA--AAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_92606811_9   1768 CAGACACTTCTGAAATGAAGACATACACATGAACAACAAACATGAGAAAG 1817
                         i     i    vv  v     i     v   iv   i  i  iiv    i
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_92606811_9   1818 AATACTCAATATCACTAATAAT 1839
                         i  i     i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.02 (59 / 58)
Gap_init rate = 0.03 (12 / 463), avg. gap size = 2.17 (26 / 12)  


2650 28.14 1.39 0.38  chrX_92629775_92631567.rev      514  1302 (491)    L1M4_orf2#LINE/L1      112   908 (0)  

  chrX_92629775_9    514 TTCTTCACA-AAATTAGAAAACACAATTCTAAAATTTATATGGAAC--CA 560
                           i  ii  -     iiv  i -ii  i        i        v--  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATGGAAATGCA 160

  chrX_92629775_9    561 AAAAACAGCCCGCATAGCCAAAGCAATACTAAGCAAAAAGAACAAATCTG 610
                          iii  --  v v         i    vi i iv  i         vi  
  L1M4_orf2#LINE/    161 AGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_92629775_9    611 GAGGCATCACACTACCTGATTTCAAGCTATACCATAAGGCCATAGTCACC 660
                             vv       v  ii       iviv   i i  i  i i   v i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_92629775_9    661 AAAACAGCATGGTGCTGGTACAAAAATAAGCACATAGACCAATGGAATAG 710
                           i    ii    i    i i  ii   ii  i     i           
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_92629775_9    711 AATAGAGAACCCGGGAATAAACCCA-ATACTTACAGCTAACTGATCTTTG 759
                            v    ii  i i          - i i   ii ii  i    i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_92629775_9    760 ACAAAGCAAACAAAACCATAAAGTGAGGTAAGGACACCCTTTCCAACAAA 809
                             i vviv   i     vv i  i  v   i i vi    i       
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_92629775_9    810 TGGTGCTGGGATACTTGGCTAGCCACATGCAGGAAAATGAAACTGGATTT 859
                                    i vi   v  ?         ii i      ii    iii
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_92629775_9    860 TCATCTCTCACCTTATATAAAAATCAACTCAAGATAAATTAAGGACTTAA 909
                         ii i   v    v    i      i       i  ii  i ?i   i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_92629775_9    910 ------GACCTGAAACTATAAAAATTCTAAAAGATAACCTTAGAAAAACT 953
                         ------  v  i           v ii  i    v   v vi ?iv  v 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_92629775_9    954 GTTCCAGACATTGGCCTCGGCAAGGATTTTATGACCAAGAACCCAAAAGC 1003
                         v   vv   v    vi v     v i   iv iivi v  vv        
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_92629775_9   1004 ATATGCAATAAAAACAAACACAAATAGCTGGGACATAATTAAACTAAAGA 1053
                          i v    i    iv   v i i   iv v    v v  i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_92629775_9   1054 GCCTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAACAGACAACCCACA 1103
                         i i    iiivv    i iv  vi   iv i   i  v            
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_92629775_9   1104 GAGCGGGAGAAAATCTTCACAATCTATATATCTGACAAAGGACTGATATC 1153
                           ii          v  ii   vii          i  i     vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_92629775_9   1154 CAGCATCTACAACAAACTCAAACAAATCAGTAAGGAAAA-ACAATCATTC 1202
                            v  v  i  vi     vv    v   i   vi    -    vi vi 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_92629775_9   1203 CCATCAAAAAGTGCTCTAAGGACATGGATAGACAATTCTCAAAAGAAGAT 1252
                          v  i?    i  vv v     iv  i       v     v         
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_92629775_9   1253 ATACAAATGGCTGACAAACATATGAAAAAATGCTCAACATCACTAGTGAT 1302
                                    ii i  i  i       i             ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (140 / 78)
Gap_init rate = 0.01 (7 / 797), avg. gap size = 2.00 (14 / 7)  


1688 25.03 5.95 9.15  chrX_92660512_92662517      599  1505 (501)    L1M4_orf2#LINE/L1        4   881 (27)  

  chrX_92660512_9    599 AAAAATACCTTAAAATTGTTCATATGTTGGAACATTCAATGTTTTCCAGA 648
                            i   i ii ----       ivi      v i i   i  v iv   
  L1M4_orf2#LINE/      4 AAAGATATCCCA----TGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_92660512_9    649 TG-TAA-GTTCCCTAAAAATGATCTGTAATTGCAATGCGATTCTGATAAA 696
                           -i  -ii    i   v-      ii iv v   i  i  i iv  v  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_92660512_9    697 ATTGTCAGAAAAAATATTTATAGAAATCAACAAGCTTATTCTAAAATTGA 746
                          v vi   vvivvv v   ii      ii       v  i        v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_92660512_9    747 CATTGAATAGCAAAGGAATTAGAATAGCCAAAA-------AAAAAATTGA 789
                         i  v   vv    i   vii             -------i     --  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA--GA 196

  chrX_92660512_9    790 AATTCATTAAGTTGGAAATCTTTAACTGTCTTATTTCGAGACT-ACCATA 838
                          ivv  --        iiv  ivv   vi iv     i i   -  i i 
  L1M4_orf2#LINE/    197 AGAACA--AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_92660512_9    839 AA-CTAAAGTAATCAAGATAGCATGGTGTTGATGAAAGGAAAAATATATA 887
                           -   v           i  ii    ii  iiiv     v i i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_92660512_9    888 GATTAATGGAGCATAATAAAGATTCCAGAAATAGATTCACAGATAAATAT 937
                            i      ii v   vi   v          i ii  i v  vv  iv
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_92660512_9    938 CCAATTAATTTTTGACCAAGGTGC-------------------------- 961
                         i     i     i   v i     --------------------------
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_92660512_9    962 --------AACAAATAGTGTTTGAATTATTGGAAAGCCATATCCCAAACA 1003
                         --------       i   i v i iv i    v ?   i  v v   v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_92660512_9   1004 ATGACCCTTGATTCATACATCCCACTACATACAAAATTTAAGTCTAAATA 1053
                             vvi v  ii v   v  v   i i        v    v  v    i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_92660512_9   1054 GACAACAAACCTAAATATAAAACCTAAA-TTATAAAACATTTAGCTGAAA 1102
                           iv ? i        i   i v     -i        vi    vv    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_92660512_9   1103 ATATAAGGGAAATTCTTCATGATCTCGAGTTAGGCAAAGATTTCTTAGAT 1152
                          i   i ? v  v     i   i  i i         v i          
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_92660512_9   1153 ATGACACCAAAAGCAAAATCTATAAAAGTAA---TGGATACACTGGATTT 1199
                                        v  v v i     v  --- i    v i    i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_92660512_9   1200 CATCAATATTTGAA-CTTTTTTCCTGTATCGAGGTAAAAATAATAAATAA 1248
                               v   vi  -     v v  vi -------  ii i v  -----
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCA-------AAGGACACTA----- 682

  chrX_92660512_9   1249 ATAAATAAATAAACAAACAGAAAAACAAATAAGT-AAAAGATTTTAAAAC 1297
                         --------- ---------------   iv    -      i-----   
  L1M4_orf2#LINE/    683 ---------T---------------CAAGAAAGTGAAAAGAC-----AAC 703

  chrX_92660512_9   1298 TTCCACTCTTTGAAACAGAATGAAAAGATAATACAGACTAAGATAGCAAA 1347
                         --    ----------      ii -  v    i--------- v     
  L1M4_orf2#LINE/    704 --CCAC----------AGAATGGGA-GAAAATAT---------TTGCAAA 731

  chrX_92660512_9   1348 TTTGAAGAACGCATAACTGATAAATGACTGATACCTAAAATAGATAAAGG 1397
                          -------- ii   v       iv    vi  i i i    v      i
  L1M4_orf2#LINE/    732 T--------CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_92660512_9   1398 AATTTAAAAATTAAAAAAAGTATAAAATATAAAGG---TGAATGAAAAGT 1444
                          v i v v  i v  v  --  -    v i   vi---ii v ?    i 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAA--TA-AAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_92660512_9   1445 GGGCAAAATATTTGAACAGATACTTCAGCAAAGAAGATAAATAAACATCA 1494
                                iv       i   i i   vv           v i   iiv v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_92660512_9   1495 AATAAGCACAT 1505
                                    
  L1M4_orf2#LINE/    871 AATAAGCACAT 881

Transitions / transversions = 1.32 (127 / 96)
Gap_init rate = 0.03 (26 / 878), avg. gap size = 5.27 (137 / 26)  


3217 26.54 0.66 0.66  chrX_92691158_92694376     1819  2726 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92691158_9   1819 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1868
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92691158_9   1869 GGCCATACTGCTCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1918
                            v     v i   iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92691158_9   1919 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 1965
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_92691158_9   1966 ATATGGAACCAAAAATGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 2015
                                 viiv  iv  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_92691158_9   2016 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 2065
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_92691158_9   2066 CTACAGTAACCAAAACAGTATGGTACTGGTACCAAAACAGAGATATAGAT 2115
                                  i   i     i         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_92691158_9   2116 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 2163
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_92691158_9   2164 TATCTGATCCTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 2213
                         i vi    ii i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_92691158_9   2214 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2263
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_92691158_9   2264 TGAAACTGGATCCGTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 2313
                             ii    i  v v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_92691158_9   2314 ATTAAAGTCTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2363
                           i ?  v i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_92691158_9   2364 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 2413
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_92691158_9   2414 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2463
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_92691158_9   2464 ATTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGAA 2513
                           i   v v  i i   i  ii vv v  i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_92691158_9   2514 TAGGCAACCTACAGAATGGGAGGAAATTTTCACAACCTACTCATCTGACA 2563
                         v  i     i            i    v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_92691158_9   2564 AAGGGCTAATATCCAGAATCTACAATGAACTCA-ACAAAATTTACAAGAA 2612
                          i  i  vi          v  i  v      v-    v- iv i  v  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAATAATAA 794

  chrX_92691158_9   2613 GAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 2662
                         i  i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_92691158_9   2663 CCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 2712
                         i   v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_92691158_9   2713 CCATCACTGGCCAT 2726
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1249 16.72 3.95 9.12  chrX_92700879_92702971        3   331 (1762)    L1M4_orf2#LINE/L1       18   329 (579)  

  chrX_92700879_9      3 TTTATGGAATAGACAAATTAGTATTGTTAATATGGCAATACTCCCCATAT 52
                           i     v i  vi v   i         v                v  
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_92700879_9     53 TGATATGGAAAGTCAATGAAATTCCTGTCAAATTTCCAGGTTGCTTTTTG 102
                             v iv i v    i v   i   i     v i    --------i  
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG--------CTG 109

  chrX_92700879_9    103 CTCTTTTTTTTTTTTTTTTTTTTTTAACAGAAATTGACATGCAGATCCTA 152
                          -       -----------------i            v  v       
  L1M4_orf2#LINE/    110 C-CTTTTTT-----------------GCAGAAATTGACAAGCTGATCCTA 141

  chrX_92700879_9    153 AAATTCACAGTGAAATTAAAGAAAACCAGAATAGCCAACATAA------- 195
                                i vv     vv   ii v             v i  -------
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_92700879_9    196 ------GAACGAAAGTTGGAGCACTCACAAGTTATTACTTCAAAACTTAC 239
                         ------    -          v       vv iviv i            
  L1M4_orf2#LINE/    192 AAAGAAGAAC-AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_92700879_9    240 TACAAAGCTACAGTAATCAAAACTGTGTGGTACTAGCATGAAGAAGGACA 289
                                             i  v          i    i i  vi    
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_92700879_9    290 TATGAATCAATGGAAGGAAATTGAGAGTCTAGTCTAAATAAA 331
                            ii          vii           i  ---       
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAG---AAATAAA 329

Transitions / transversions = 1.12 (29 / 26)
Gap_init rate = 0.02 (6 / 312), avg. gap size = 7.17 (43 / 6)  

2905 24.95 1.51 3.46  chrX_92700879_92702971      675  1600 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92700879_9    675 TGGGAAGATATACAATGCTCCTGGATTGAAAGTATCAACATGGTTAAAAT 724
                            i       v v   i  v       i   vv i  i  v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92700879_9    725 GTCAATAATACCCAAAGCAATTTACAGTTTCAAAGCAATCCCTATCAAAA 774
                          v     v v      vii  i     v     v                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92700879_9    775 TACCAACAG---TTTTCACAGAAATAGAAAAAAAAATCCTAAAACTTTTA 821
                          v   i v ---    ii       v  v  ivvi         i iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_92700879_9    822 TGGAACTACAAAATA-----AATAGCCAAAGCTATGCTATGCACAA--AG 864
                              v i   iiv -----          i v  -  -  v v  --  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT-TGAAAAAGAAG 198

  chrX_92700879_9    865 AACAAAAGTGGAGGAATTATATTACCTGACTTCAAATTATACTACAGAGC 914
                               iv       v i i i v  ii i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_92700879_9    915 TGTAGTAATCAAAATATCATGGTACTGACATGAAAACAGACACATAGACC 964
                          ii         i i vii        i   i ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_92700879_9    965 AATGAAACAGAATAGAAAACCCAGAAATAAATCCACACACCTACAGTAAA 1014
                             i  i     v  i ii           i   i   ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_92700879_9   1015 CTCATTTTTGACAAAGATGCCAAGAACATACACTGGGGATAAGATGGTCT 1064
                         i v     i     i i        v   v  v      v ii  i    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_92700879_9   1065 CTTAAATAAATGATGCTGGGAAAAGTGAATATCCCTATGCAGAAGAAAGA 1114
                         i  v  i     i        v  v  i   ?  vi     i     v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_92700879_9   1115 AACTAGATCCC-ACCTATCACCATATACAAAAGTAAAATAAAGATAGATT 1163
                          ii i  i   -    vv              i v  v v  i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_92700879_9   1164 AAAAACTTAAATCTAAGACATCAAACTACAAAATTACTAGACAAAAACAT 1213
                          ? i  i     v     vv v      i    i vi    vi       
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_92700879_9   1214 TAGGGAAAATTCCTAGGACATTGGTCTAGGCAGAAATTTCTTGAGCTTTA 1263
                         vi ? v    iiiiiv   v    vi      ivii      iiiiv v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_92700879_9   1264 CCCCACAAGCGCAGGCAACTATAATAAAAATAGACAAATGGGATCACATC 1313
                          v   v    i  i     v v iv         i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_92700879_9   1314 AAG-TTAAAAAGCTTCTGCACAGCAAAGAATACAATCAACAAAATGAAGA 1362
                           i-       -   i  ii vv     i i  v     v   i    i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_92700879_9   1363 GATAACAAGAGTAAATAACAAAATGAAGAGATAACAAGAGTAAAAAAAAA 1412
                           i   ---------iv   i    i-    -------------   v v
  L1M4_orf2#LINE/    698 GACAAC---------CCACAGAATGG-GAGA-------------AAATAT 724

  chrX_92700879_9   1413 TGGAAAACTACCCATCTGGCAAGAGATTAATAACCAAAATATATATTAAT 1462
                          v v   ii ivi     ii   i  i vi  v   i        -----
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA----- 769

  chrX_92700879_9   1463 AAGAAGCTCAAGCAACTCTGTAGAAAACAGTCTAATAATCCAAT-AAAAA 1511
                              -   vvi      vi  iv   v  v v     i     -?    
  L1M4_orf2#LINE/    770 AAGAA-CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_92700879_9   1512 ATGAGCAAAAGGTTTTAATGGACATTTCTCAAAAAAAGACATACAAATGG 1561
                            i     i i   v   i          v   i    i          
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_92700879_9   1562 C-AACAGGCATATAAAAAGGTGCTCAACATTACTGATTAT 1600
                          -  i i   i  i     i          i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (138 / 89)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.07 (46 / 15)  


2897 25.87 1.85 1.62  chrX_92707681_92710122     1084  1949 (493)    L1M4_orf2#LINE/L1        1   868 (40)  

  chrX_92707681_9   1084 TGAAAAGATATTCCAAGTTCATGGGTTGGAAGAATCAATATTGTTAAAAT 1133
                           i        i   v        i        v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92707681_9   1134 GTCCATACTACCTAAAGGAATCTACAAATTTAATGCAATCTCTATCAAAA 1183
                          v v     v  i   vvi       i   i  i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92707681_9   1184 CACCAAAGACATTTTTCACAAAAGTAGAAAAACAGA-CCTAAAATTAACA 1232
                         iv   ivvi v     ii  i  i v  v  i v  -         v i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_92707681_9   1233 CAGAACCACAAAAGACCCAGGATAGTCATAGTCATAGCTATCCTGATA-- 1280
                         ii   vii   ii       i    i  v --- i ---   i   v --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAA---ACA---ATCTTGAAAAA 194

  chrX_92707681_9   1281 GAAGAAAAAAACTGGAGGAATTGCATTACACTATTTCAAATTGTACTACA 1330
                               v   ii       v ii  i v v v        viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_92707681_9   1331 GAGCTATAGTAACCAAAATGGTATGGTGCCAGCATGAAAACAGACACATA 1380
                         i     i     i   i ii  i    i ii    i ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_92707681_9   1381 GACCAATGCAAAAGAATAGAGAACCCAAAAACAAATCCACACATCTGCAG 1430
                           i     v  v     v    ii   i   i   i   i    i iii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_92707681_9   1431 TGAACTCATTTTTGACAAAGATGCCAAGAAGACATATTGAGGAAAAAAAA 1480
                          v  i v     i     i i        vv ivi v  i     i  --
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-- 392

  chrX_92707681_9   1481 AAACAGTGTCTTCAATAAATGGTGCTGGAAAAAATGGATATTCATATGCA 1530
                         ---i   v i     i            i v  v      ?i  i     
  L1M4_orf2#LINE/    393 ---TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_92707681_9   1531 GAAAAATGAAACTAGACCCCTATCTATCACTACACACAAAAATCAAACCA 1580
                         i  i      ii i        i  vv   i i i        i  vi  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_92707681_9   1581 ATATGAACTAAAGACTTAAATACAAGGCCTCAAAATATGAAACTACTGAA 1630
                          v   i ii ?    i     ii   iv  v   v   i     vi ii 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_92707681_9   1631 AGAAAACATTGGGA-AACTCTCCAGGTCATTGGAATGGGCAAATATTTTT 1679
                                  v  ?i-  v   i iv v v    iv i     vvi   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_92707681_9   1680 TGAGTAATACAGCACAA--ACAAGCAATTGAAGCAAAAATGGACAAATGG 1727
                          iii  vv   v  v  --        ivi   v      i  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_92707681_9   1728 TATCACAT-AAAGTTAAAAAGCTCCTGCACAGCAAAGAAAAC----AACA 1772
                         v iiv   -   i       -  ii  ii vv     i v  ----  v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_92707681_9   1773 AAGTGAAGAGACAACCAAGAGAATGGGTGAAAATATCTGCAAATGATCCA 1822
                                i        v v        v        i       v  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_92707681_9   1823 TCTGACAAGGAATTAATATCAAGAATATATGAAGAACTC----AACACTA 1868
                              i    i i vi    v         i        ----   v v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_92707681_9   1869 TAGAGAAAAAACTAATAATCTAATTTTTAAAATGG-CAAAAGATCTGAGA 1917
                           ivi    i  v     i i    ?v-       -    i   i   iv
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAAT 837

  chrX_92707681_9   1918 AGACATTTCTTAAAAGAAGACATATGATATGG 1949
                                   iv        i   ii -    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAA-ATGG 868

Transitions / transversions = 1.75 (140 / 80)
Gap_init rate = 0.02 (14 / 868), avg. gap size = 2.14 (30 / 14)  


2953 28.24 0.89 0.33  chrX_92723294_92727507     2819  3721 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92723294_9   2819 TGGAAAAACATTCGATGCTAATGCATAGGAAGAATCAATATCATGAAAAT 2868
                               i i  i v   i v   v  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92723294_9   2869 GGCCATGCTGCCCAAACTAATTTATAGATTCAATGCTATTCCCATCAAGA 2918
                            v  i  v      i i  i  i        i  v  i  i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92723294_9   2919 TACCATTGACTTTCTTCATAGAATTAGAAAAATCTACTTTAAATTTCATA 2968
                          v   vivi i  i  iii    v v  v  iiiv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_92723294_9   2969 TGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGAA 3018
                              viiv  ii  v  v v        i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_92723294_9   3019 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATTCTGCAAGGCTA 3068
                              i      vv    i  v  ii i      viv v  i   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_92723294_9   3069 CAGTAACCAAAAGAGCTTGGTACTGGTACCTACACAGATATATAGACCAA 3118
                               i   i v  iv         i ivviv i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_92723294_9   3119 TGGAACAGAATAGAGGCTTCAGAAATAATGCCACACATCTAAAACCACGT 3168
                              i     v   iv i         vv   i    i  viii  vv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_92723294_9   3169 GATCTTTGACAAGCTTGACAAAAAACAAGCAATGGGGAAAGGATTCCCTA 3218
                            i  i      vv  v   i v-  vv            i  vvi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCTT 399

  chrX_92723294_9   3219 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATACAGAAAACTGTA 3268
                           i  i        i     v      v  ?   i  i  i  i v  v 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_92723294_9   3269 ACTGGACCCCTTCCTTACACTTTATACAAAAATGAATTCAAGATAGATTA 3318
                         ii         v   i    iv           v  i    i  i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_92723294_9   3319 AAGACTTAAACATAAGACTTAAACCT-TAAAAACCCTATAAGAACACCTA 3367
                         ?    i    ii     vi    v  -     vi i  v     v  v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_92723294_9   3368 GGCA-ATATCATTCAGGACCTAGGCATGGACAAAGACTTTATGACTAAAA 3416
                           ?i- v   -   iv     v  vv i i   v ii  iv iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_92723294_9   3417 CACCAAAAGCAATGGCAACAAAAGCCAAAACAGACAAATGGGATCTAATC 3466
                                    vvi          vv    i   i    v   ii v   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_92723294_9   3467 AAGCTAAAGAGTTTCTGTATAGCAAAAGAAACTGTCATCAGCGGGAACAA 3516
                           iv v  i ii  i   iivv    i  v   i   vv iv v   v i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_92723294_9   3517 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAG 3566
                         i     i                 v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_92723294_9   3567 GGCTAATATCCAGAATCTACAAAGAACTTAAACAA---AATTACAAGAAA 3613
                          i  vi          v  i        ivv    ---   v i  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_92723294_9   3614 AAAAA-AACCT--TCAAAAAGTGGGCAAAGTATATGAACAGACACTTATC 3660
                          v   -    i-- i?    i         v  v    i     i  v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_92723294_9   3661 AAAATAAGACATTTATGCGGCCAAAAAACATATGAAAAAAAAGGGCATCA 3710
                         v   v    i  vi vii      v  i  i       i v- vv  v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACA 897

  chrX_92723294_9   3711 TCACTGGTCAT 3721
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.30 (142 / 109)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1437 19.46 4.01 16.60  chrX_92738767_92740457.rev      502  1200 (491)    L1M4_orf2#LINE/L1      298   908 (0)  

  chrX_92738767_9    502 CAAAGGAACAGATTAGAGCTTCCA-ACATAGACCCACACATACAAGGACA 550
                            v    i   v v   vv    - v   i     i    vi v  v  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_92738767_9    551 GCTAATTTT-GACAAATGTGCAAAGGCAAATCAGTGGTGAAAAGACAGTC 599
                         ii i     -     iv    v   i v v   i   v    ii i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_92738767_9    600 TATTCAACAAATAGTGCTGGAACAACTGCATATCTATAT-CAAAAGAAAT 648
                          v          i       i       v   ? i i  -        - 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-T 446

  chrX_92738767_9    649 AAACCTTCAATCCATACCTTGTACTTTTTGCAAAAAT-----------GT 687
                         i  v-  vi i  v     iii  iv v i       ----------- v
  L1M4_orf2#LINE/    447 GAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_92738767_9    688 ATCA--GACCTAAATGCAAAACCTAAAAGTATAAAACT--TAAAAAAAA- 732
                             --          i  i v      v         --  i  i   -
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_92738767_9    733 --TGGAAGAAAATAATTGTGACTTTGGGTTAAGCAAAGATTTCTAAGAGA 780
                         -- i i? v    vv i     i        i    v i     v   v 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_92738767_9    781 TGACACACAAAGTATGCTCCATAGAAGAAAAACAAGATAAACTGGACTTC 830
                               vv    i iivv v i i        vv       i        
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_92738767_9    831 ATCGAAATTGCAAACTTCTTATCCCAATTACCCTGATTTGACCATTACAC 880
                            i     iv      i -------------------------------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTT------------------------------- 664

  chrX_92738767_9    881 ATTGTATTCATGTATTGAAATCACATGTGCCCCCAAAATATGATGTATCA 930
                         --------------------------    --------------------
  L1M4_orf2#LINE/    665 --------------------------GTGC-------------------- 668

  chrX_92738767_9    931 ATATAAAAATTACTAACATTTCCTCTTTAAAAACAGTAAAAGGCACCCTT 980
                         -------------------   ---------------   i i   iv i
  L1M4_orf2#LINE/    669 -------------------TTC---------------AAAGGACACTATC 684

  chrX_92738767_9    981 AAGAGAATGCAAAGAAAATATGCAGTCTGAGAGAAAATATTTGCAGAAGC 1030
                             i i  v     v  ivii   vv  i               -  v 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC 733

  chrX_92738767_9   1031 -TATAACTGATAAAGAACTTGCATCCAGAGTATATAAAGAACTATCAAAA 1079
                         -    v       i i     i       i             v i v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_92738767_9   1080 CTTAATGATAAAACAACAA----TCCTATTTTTTTAAATGGACAAA--AT 1123
                           i   i      vi    ----i  v   ?vv--      i    --  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAA--AAATGGGCAAAGGAT 831

  chrX_92738767_9   1124 ACAAATGGTCACTTCACCAAAAAAGATATGTGGATGGCAAATCAGCACAT 1173
                         vii   i v  i   v     i       iiii     v   v       
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_92738767_9   1174 GAAAAGGTATTCAACATCATTAGTCAT 1200
                               i ii         ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (76 / 57)
Gap_init rate = 0.03 (17 / 611), avg. gap size = 8.47 (144 / 17)  


2255 23.31 2.73 0.48  chrX_92744410_92746023.rev      502  1123 (491)    L1M4_orf2#LINE/L1      273   908 (0)  

  chrX_92744410_9    502 CTGGCATAAAAAGAGGCACGTAGTTCAATAGAACAGAACAGAAAATCAAA 551
                                  ii v  i  ii   v     i   i    iv  i i  v i
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_92744410_9    552 ACATTAATCCACATATCTACAGCCAACTGATTTTTGACAAAGGCTCCAAG 601
                          v  v  i   i i  i  ii i   i       i     i  iv     
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_92744410_9    602 AACACTCA-TTGGGAAAGGGCAGACTCTTCAATAAATAGTGCTGGGAAAA 650
                          v  i   - v       iii  v  i     i    i         v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_92744410_9    651 TTGGATAACCATAGGCAGAAAACTGAAACTAGACTCCCCCACCTCTCTGC 700
                         i      ?   i v   i  i v    ii i   --   i     v vv 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGAC--CCCTACCTCACACC 470

  chrX_92744410_9    701 CTATACAACAATACACTCAAAATGGATCA--GACTTACATGTAAGACACA 748
                         v       v   vv               --   i  v        vvi 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_92744410_9    749 AGACTATAAATCTATTAGAAGAAAACATAG-AGTAAATGCTTCAGGACAC 797
                          i        v  v                -?      -    iv   vi
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCT 569

  chrX_92744410_9    798 TGGTTTGGGAAAAGGCTTTATGAATAAGACCTCAAAAACACAGGCAACAA 847
                            v  i  v  v  i  iv ii   v   vi     i    i       
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_92744410_9    848 AAGCAAAAGTAAACAAATGGGACTATATCAAACTAAACAGCTTATGCACA 897
                            v    i  i i    v     vi      v v  v i   v  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_92744410_9    898 GCAAAGGAAACAATCAACAATGTGAAAAGTCTACCTAGAGAATGGGAGAA 947
                         v       v  v     v  v        v v   i v            
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_92744410_9    948 AATATTTGCAAAGTATTCATACAACAGGGAATTAATATCCAGAATATACA 997
                                     vi  vi  vii i i  i i vi             i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_92744410_9    998 AAGAACTC----AA---AACAGCCAAAA---AAA-AACCCATTTCAAAAA 1036
                                 ----  ---  i iiv    ---   -      v  ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_92744410_9   1037 TTGGCAAATTAGCTGAATAGACATTTC--AAAAGAAGACATGCAAACGGC 1084
                          v      vv vi              --v        i  i    i   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_92744410_9   1085 CAACAAATATATGAAAACATATTCAACATCATTAATCAT 1123
                            i  ii i       v  ii         ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (81 / 61)
Gap_init rate = 0.02 (10 / 636), avg. gap size = 2.00 (20 / 10)  


2976 19.15 7.73 6.05  chrX_92751612_92753509.rev      563  1455 (443)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92751612_9    563 TGAAGAGACATTTCATACTCTTGGGTTGGAAGGATCAACACTGTCAACAT 612
                           i i   i  ii   ii  v   i       iv i  i i   i  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92751612_9    613 GGCAATTCTCCCTAGTTTGAATAATAGATTAAATCCAACCCCTATAAAAA 662
                               v     i iv    viv i     v  iv   i      v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92751612_9    663 TACCAGCTGGCTTCTTCACAGAAATTGACAAGTTGATCTAAAACTGACAC 712
                          v       v   i  ii              i     -----  -----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-----CT----- 140

  chrX_92751612_9    713 ATTGATTGGAAGATTCGTATAAGAGTACAAGGGATCCAGAATAGCTGAAA 762
                         ---------  i    i   iii i i       i          ii   
  L1M4_orf2#LINE/    141 ---------AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chrX_92751612_9    763 CAATCTTGAAAACGTAGAGTAAAATTGGATGACTCATACTTTCTGATTTC 812
                                     v v   ii   i     v      i    i ii     
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_92751612_9    813 AAAACTTACTATAAAGCCACAGT---TAAGACAATGTGGTGTTGACATA- 858
                                    i     i     ---i      i      ii  i    -
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_92751612_9    859 ---TA---ATATAAATAAGTGGAGCAGAATTGACAGTTTAAAAACAAATG 902
                         ---  ---     i  v i    ii        v   ii i   i   iv
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_92751612_9    903 CATACATTTATGGTCAATTGATTTTTTACAAAAGGACAAAGACATTTCAG 952
                                                  iv    ii vi v     vv    i
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_92751612_9    953 TGGTGAAAACGATAGTCTTTTCAACAAATGG-------ACATTTGTGTAT 995
                            v    i-i                    -------   vi  vi  ?
  L1M4_orf2#LINE/    382 TGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_92751612_9    996 CCATCTTTTTTGAAAAGAAAGAAATTAGAC----ACTTCACACCATATAT 1041
                            iv vi----       v   i  i   ----  i            i
  L1M4_orf2#LINE/    431 CCACATGC----AAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_92751612_9   1042 AAAAAGTTAACTCAAAATAGATCACAGACCTAAATGTAAGATCTAAAGGT 1091
                              -            i     ?                ---------
  L1M4_orf2#LINE/    477 AAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGA--------- 516

  chrX_92751612_9   1092 AAGAGCTAAAATTATAAAATTCT-AGAAGAGAATATAGGAGAATATTTTG 1140
                         ----       i       i   -      i  i     ? v v  i  v
  L1M4_orf2#LINE/    517 ----GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_92751612_9   1141 ATGAGTTGGGGTTGGGCAAAGAGTTCTTAGGTAAAATATTGAAAGCATGT 1190
                         i   vi v     i     v iv       i  vi i iii      ---
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA--- 609

  chrX_92751612_9   1191 TTCAA---AGAAGAGAAAAATTA--TAAATTGGACTTCATCAA------- 1228
                         --   --- v  i       v  --                  -------
  L1M4_orf2#LINE/    610 --CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_92751612_9   1229 --CTTGTGTTACTCAAAAGTCATCATTAA---------AAGA------AC 1261
                         --   v   vvi     i v  ii  i  ---------    ------  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_92751612_9   1262 A---TAAGAGAAAATATT-GCAAATCATATATCTGATCA--------TAT 1299
                          --- ii           -                  v --------   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_92751612_9   1300 CCAGAATATTTGAAAAACTCTTACAAGTCAATAATTTTTAAGACCAA-AA 1348
                                  v i  i           v        vvv-     v  -  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAAATAA 806

  chrX_92751612_9   1349 ---AATT-AAAAATTGGCAAATAACTTGAATAAATATTTCTTCAAAGAAA 1394
                         ---    -      v      vi i       i i      i       i
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_92751612_9   1395 ACACATTAGGGAAATG-CAAATCAGAAGTCCAACAAGAAACTACTACACA 1443
                          i i i-----     - v   ---   iv  vv  i i - i  vv   
  L1M4_orf2#LINE/    857 ATATAC-----AAATGGCCAAT---AAGCACATGAAAAGA-TGCTCAACA 897

  chrX_92751612_9   1444 TACACTAGAATG 1455
                          -  ????????
  L1M4_orf2#LINE/    898 T-CAZZZZZZZZ 908

Transitions / transversions = 1.90 (110 / 58)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 4.10 (123 / 30)  


2692 27.07 2.43 2.10  chrX_92795194_92799454.rev     2867  3771 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92795194_9   2867 TAGAAAAATATTTCATGCTCACTGGTAGGAAGAATCAATATTGTTTAAAT 2916
                          i    i    ii    i   iv i v      v i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92795194_9   2917 GGCCGTTCTGTCCAAGA-AATTTACACATTCAGTGCTATTCCTATTAAAC 2965
                            vi v  vi    iv-i  i    v     ii  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92795194_9   2966 TACCAA-TGCCATTTTTCTCCAAATTACAAAAAAAAACT-ATTTTAAAAT 3013
                          v   i-    v     vivv     i----- v  i  -  ii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-----ACAAGCTGATCCTAAAAT 145

  chrX_92795194_9   3014 TCATATGAAACCTAAAGATAGCCCAAATGACCAAAGTAATCCTAAGCAAA 3063
                                i  vivv   iv v  vi   ii     ii    i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_92795194_9   3064 AAGAATAAAGCCAGAAGCATCATACT----GACTTCAAACTGTACTACAA 3109
                              i    iii  i vv   i   ----i i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_92795194_9   3110 GGCTGCAATAACAAAAACAGCATGGCACTGGTATGAAAACAGACATATAG 3159
                         i   i  i   iv  i    ii   i     i  i ii i          
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_92795194_9   3160 ATCAATTATACAGGTTAGAGAACTCATAAATAAAGCCATACACCTACAAC 3209
                               viv i  iv v    iii  v       v       ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_92795194_9   3210 CATGTAATCTTTGACGAAGTCGATAATAACAAGCA-TTGGGAAAGGATTT 3258
                           vv i  i  i   i i vi vi  v v  vv  - v       i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_92795194_9   3259 ACTATTCAATAAAAGGTGCTGAGATAACTGGATAACTGGCTAGTCATATG 3308
                         v  v     i   v       i  i         ? --------  i   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC--------CACATG 437

  chrX_92795194_9   3309 CAGAAAATTGAAACTTGATCCCTTCCTTTCACCATATACAAAAATCAACT 3358
                           i  i v    ii v  i    v   iv                i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_92795194_9   3359 AAAGGTAGATTAAAGACCTAAATGTAATACCTAAAACTGTAAAATCCCTA 3408
                         v  ii i   i ?              v v        i     ii i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_92795194_9   3409 GAAGAAAACTTAGGAAATACTATTCTGGACATAGGGTTTGTCAAAGATTT 3458
                                  v    ?ivv v v   vv   v v     v v   v i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_92795194_9   3459 ----AATGATGAAGTCTCCAAAAGCAATTGCAGTAAAACAAAAAATAGAT 3504
                         ----i  -    --- v         vvv   ii    v           
  L1M4_orf2#LINE/    588 CTTAGAT-ATGA---CACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_92795194_9   3505 AAGTGGTTCCTACTTAAACTAAAGAGCTTCCGCATAGCAAAAGAAACTAT 3554
                           i v vv i vv i   v v  i i   ii iiivv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_92795194_9   3555 CAACAGAGTAAACAGACAACCCACAGAATGGGAGAAAATAT----AAACT 3600
                            v i   i  v                            ----   ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_92795194_9   3601 ATGCATTAGGCAAAATCCTAATATCCAGAATCTGTAAGAAACTT----AA 3646
                           ii  iv ii  iivv  vi          v i   ii    i----  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_92795194_9   3647 ATCAACAACCAAAAAACAAATGACTGCATT-AAAAATGGACGAAGGACAT 3695
                         v    i  iv    i      i  ivv   -        i i     iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_92795194_9   3696 TAACAGACACCTCTCAAAAGAAGGCATATACACCTGGCCAACAAGCATAT 3745
                         v  i     ii    v       --       vv       i     i  
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAG--ATATACAAATGGCCAATAAGCACAT 881

  chrX_92795194_9   3746 GAAAAAATGCTCAACAT-AGCTAATCA 3771
                              i           - ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.73 (41 / 15)  


1927 28.39 2.68 0.32  chrX_92898818_92900821.rev      501  1134 (870)    L1M4_orf2#LINE/L1      181   829 (79)  

  chrX_92898818_9    501 ACAATCCTAAACAAGAAAAGCAAATCTGGAGGCATCACATTACTGGACTT 550
                               i i  v     i i    vi      vv     i v ivi i  
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_92898818_9    551 GAAATTATACTACAAGACTATAGTTACCAAAATAGCATGGTACTTTCATA 600
                         v   viv        ii   i   v i   i i  ii       vv    
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_92898818_9    601 AAAGTAGGCACATAGTCTAATGGAACAGAATAGAAAACCCAGAAACAAAG 650
                          iii   i  i    vii       i     v  i ii       i   v
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_92898818_9    651 CCAGATATGTACAGCAAACTGGCCTCCAACAACGCATACAGAAACG--TA 698
                            v i  v  ii iv  i  iii i i    v -i i vi i  v-- v
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTC 379

  chrX_92898818_9    699 AATTGGGGAATGGACACTCTATTTATTAAATGA-------AAAACTGGCA 741
                            -      v i i v   v  i vi     i------- v      vv
  L1M4_orf2#LINE/    380 AAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_92898818_9    742 AGCCACATGTGGAAGAATGAA-CTGGATCCCTATCTCTCACCTTATACAA 790
                          ?       iii         -i    i     i   v    v       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_92898818_9    791 AAATAAGCTCAAGATGGATCAAAGACTTAAATATAAGACCTGAAACCATA 840
                             v i     i        ?    i     i     v  i    i   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_92898818_9    841 AAAATTCTAGAAGTCAACGTGGGAAAAACTTTTCTAGATATTGACATAGG 890
                            v ii      vv   i i  ?iv  v i   vv  iv   ivv    
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_92898818_9    891 CAAATAATTCATGGTTAAGACCCCAAAGGCAAATGCAACAAAAACAAAAA 940
                            vviv   v i v  v   v     i   v v         iv     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_92898818_9    941 TGAATAAATAGGAGCTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAA 990
                          ii      v   vi v  i   v v    i   i  ii vv    i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_92898818_9    991 ATAATCAG---AGT----AGACAACCCATAGAATGGGATAAAATATTTGC 1033
                          iv    i---   ----          i         v           
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_92898818_9   1034 AAACTATGCATCTGGCAAAGGCCTAGTATCTGGAATCTATGAGGAAATCA 1083
                            ii  ii     ii  i  v  v     ii    v   i i   v  v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_92898818_9   1084 GACAAATCAACAAGAAATAAAGCAATAATCCTATTAAAATGTGGGCAAAG 1133
                         v    v    i  v   v i vv     i  v   ?   vi         
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_92898818_9   1134 G 1134
                          
  L1M4_orf2#LINE/    829 G 829

Transitions / transversions = 1.32 (100 / 76)
Gap_init rate = 0.01 (7 / 649), avg. gap size = 2.71 (19 / 7)  

 328 16.48 4.40 1.10  chrX_92898818_92900821.rev     1425  1515 (489)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_92898818_9   1425 AAAAAGGTGCAAGGGACATGAATAGACATTTCT--AAAAACATATATGCA 1472
                              v v    i   iv               --   i - v    i  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA-AGATATACA 863

  chrX_92898818_9   1473 AATGGCCAACAA--ACATGAAAAAGTTCTCAGTATAACTAATAAT 1515
                                  i  --         ii v    ii  v ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.03 (3 / 94), avg. gap size = 1.67 (5 / 3)  


2497 28.65 0.65 2.49  chrX_92901750_92903773.rev      609  1533 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92901750_9    609 TGGAAAAGTATTCCATGCTTATATGCTTATAGATTGGAAGAATCAATATC 658
                               ii   i     i i  i--------          v i     i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATG--------GATTGGAAGACTTAATATT 42

  chrX_92901750_9    659 ATAAAAATGGCCATACTGCCCAAAGCAATTTACAGATTTAATGCTATTCT 708
                         i v  i     v     v      vii  i        i  i  v  i i
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chrX_92901750_9    709 TATCACACTTCTAATGGCATTCTTCAGAGAATTAGAAAAAAAAATATTCT 758
                              v v i i iiv  v  i  iiv    v v  v  ivvi  --i  
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT--CCT 140

  chrX_92901750_9    759 AAAGTTTATATGGAATCAAAAAATAGCCTAAATAGCAAAAGCAATTAGAA 808
                            i  i        viiv  iiv v  vi      v   i    i----
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC---- 186

  chrX_92901750_9    809 CTAAGCAAAAAGAACAAAGCCAAAGACATCACAGAAACCTGATTTCAAAC 858
                         i i iv  i          iiii  ivv     vvv-  ii        v
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAA 235

  chrX_92901750_9    859 TATGCTATAAAGCCACAATAACCAAAACAGCTTGGTACTGGTATAAGAAA 908
                         iv i   i     i   i   i   i    iv         i     i v
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_92901750_9    909 AGGCACATAGACCAATGGAACAGAAT-AAAAACTCGGAAATAAAGCCAGA 957
                           i  i     i        i     -i i iii i        v   v 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_92901750_9    958 CACCTACAACCACCTGATCTTCGGTAAGTCTGACCAAAACAAG-CAATGA 1006
                           ii  iiii  vi    i    ii   vv  -    i  v v-     i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGG 384

  chrX_92901750_9   1007 GGAAAGGACTCCCTATTAAATAAATAATGCTGTGATAACTGGCTAGCCAT 1056
                               i ivvi  v  v  i    ii     v  i      v  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_92901750_9   1057 ATGCAGAAGATTTAAGCTTTACCCC-ATCTTTCACTACATACAAAACATT 1105
                              i    v v   i vv     - i  iv   i i        -   
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATT 483

  chrX_92901750_9   1106 AACTCAAAACACATTAAAGATTTAAATATAAGGCCTCAAAGTATACAGAT 1155
                                  iiv  i ?   ii     i    iv  v   v    - i i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAAC 532

  chrX_92901750_9   1156 TCACA-AAGACAACCTAGGAAATACTGTTCCTGACATAGATCTTGGCAAA 1204
                           vi -    v   v    ?ivv v v   v    v v ivi v     -
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA- 581

  chrX_92901750_9   1205 TAATTTAT-GGCTACATTCCCAAAAGCGATTGCATCAAAAGCAAAAATAG 1253
                          ii   v -i v  iiviv        ivvv   v      v        
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_92901750_9   1254 ACAAATGGAATGTAATTAAACTAAAGAGCTTCTGCAGATAAAACAAAACA 1303
                          i    v i iv v  i   v v  i i   i  iivv v   vi v  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_92901750_9   1304 AAACAAAAACCGAGCAAACAGACA-TTCACAGAATGGGAGAAAGTATTTG 1352
                          v-   i  ---  ii  v     -ii                i      
  L1M4_orf2#LINE/    682 AT-CAAGAA---AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_92901750_9   1353 CAAACTATGCATCAGACAAAGGCATAATATCCAGAATCTATAGTAAAGTT 1402
                             ii  ii   v  i  i  vv vi          v    ivi  v i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_92901750_9   1403 AAACAAATCAACATGCAAAAACCAAATAACCCCACTTAAAAATGGGCAAA 1452
                         vv    v    i vvv    iv          v i ?             
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_92901750_9   1453 GGACATGAACAAACACTTCTCAGAAGAAGACATACAAGTGACAAACAAAC 1502
                            iv    i i   i     vi       i      i  i v  i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_92901750_9   1503 ATATGAAAATATGCTCAGCATCACTAATTAT 1533
                          i       v       i     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (154 / 107)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.81 (29 / 16)  


2997 26.80 0.64 3.32  chrX_92944580_92948799.rev     2797  3729 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92944580_9   2797 TAGAAGAACATTCCATGCTCACAGGTAGGAAGAATCAATATCATCAAAAT 2846
                          i   ii i  i     i   ii i v      v i     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92944580_9   2847 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2896
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92944580_9   2897 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2944
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_92944580_9   2945 TACAGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 2994
                           ii   viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_92944580_9   2995 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3044
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_92944580_9   3045 TACAGTAACCAAAACAGCATCGTACTGGTACCAAAACAGAGACATAGATC 3094
                                 i   i    ii v       i iv ii i   v i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_92944580_9   3095 AACGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 3142
                           i    i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_92944580_9   3143 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCT 3192
                          vi    i  i     ivv  v   i v  vv            i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_92944580_9   3193 CTATTTAATAAATGGTGTTGTGATAGTGAATAAATGATGGAATGAATGAA 3242
                           v  i  i        i  v  i -------------------------
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACA------------------------- 421

  chrX_92944580_9   3243 AACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACC 3292
                         -     v  ?   i   i i  iiv    ii    i    v   i     
  L1M4_orf2#LINE/    422 -ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_92944580_9   3293 TTATACAACAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGACCTA 3342
                         v       v      i    i      i ?    i       v   v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_92944580_9   3343 AAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCA-GGCAT 3390
                             i      vi i           v    ?i- v i -   i- i v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT 569

  chrX_92944580_9   3391 AGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAA 3440
                         v  vv i     v ii   v ivv  vi            vvi       
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_92944580_9   3441 AAGCCAAAATTGTCAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACA 3490
                            vv     v vi    v   ii v  i   v v  i i   i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_92944580_9   3491 GCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAA 3540
                         v    i  v    i  vv i      v  i     i              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_92944580_9   3541 AATTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACA 3590
                            v       vii ivi      i  i  i  vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_92944580_9   3591 ATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAACAAG 3640
                          v      vv    v iv i  v     i     i     v  i? v  i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_92944580_9   3641 TGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGC 3690
                                     v    i     i     v        i  vi viii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_92944580_9   3691 CAACAGACACACGAAAAACTGCTCATCATCACTGGCCAT 3729
                            i ii    i     iv      v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (152 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 4.11 (37 / 9)  


2716 27.75 2.00 1.22  chrX_92975252_92977519      875  1775 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_92975252_9    875 TGGAAAAATATTCCCTGTTCGTGGATTGGAATAATCAATATCATTAAAAT 924
                               i    i  v     i          v v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_92975252_9    925 TGCCTTACTGCTCAAAGAAATTTATAGACTCAACCCTATATCTATCAAAC 974
                         v  vv    v i    vvi  i  i   i     v v  vi        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_92975252_9    975 TATCAA-TGCCATTCTTCACAGAATTAGAAAAAAAAAGCT-ATTGTAAAA 1022
                          vi  i-    -  i  ii     v v  v  -----   -  iv     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-----GCTGATCCTAAAA 144

  chrX_92975252_9   1023 TTCACATGAATCCAA--CAAAAAACCTCAAATAGCCAAAGCAATCCCAAG 1070
                             i   i ---  --   iii   ivi          i     iii i
  L1M4_orf2#LINE/    145 TTCATATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_92975252_9   1071 CAAAAAGAGCAAAAGTGGAGGCATCACACTTCCTGACTTCAGACTATACT 1120
                         v  i    i    iv      vv          ii i    i viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_92975252_9   1121 A--AGGCTATAATAACCAAAACAGCATGATACTGGTACAAAACCAGACAT 1168
                          -- i    i i   i   i    ii  i      i i  iivi      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_92975252_9   1169 GTAGACCAATAGAACATAATAGAAAACTCAGAAATAAAGCCACACACTTA 1218
                         i    i    i   i v   v  i iii          v   i   i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_92975252_9   1219 ACAATCATCTGATCTTCAACAAGGCTGACAAAAAGAAGCAACAAGGAA-G 1267
                         -iii   vi    i   i      v  v   i vv vv   iii    - 
  L1M4_orf2#LINE/    342 -TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_92975252_9   1268 AACTTTGTATTCAATAAATGGTGCTGAGCTAACTGGCTAGTCATAGGCAG 1317
                           ivv v v     i           i vi      v  ?i  i v   i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_92975252_9   1318 AAGAATGAAACTGGACCCTT------TACCATATACAAAAAGTAACTCAA 1361
                                  ii       i ------i              v        
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_92975252_9   1362 GATGAAATATAGATTTAAATGTAAAACATCAAACTATAAAAACCTTAGAA 1411
                         i   i vi ?   ii         i vv v           vi       
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_92975252_9   1412 GGAAACATAAGAAATAATCTTCTCAACATCAGCTTTGACAAAGAATTTTT 1461
                          i       i ?ivv       vii  v ii v  v i   v iv  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_92975252_9   1462 GCCTAAGTCCCCAAAAGCAATTGCAGCAAAAACACAGTTTAACAAGTGAG 1511
                         ivv  v v v         vvv   i     iv v iv vi i  i vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_92975252_9   1512 ACCT-----AAATAAAAAGGTTCTGCACAGAAAAAAAAAAAAGTCCACAG 1556
                           i -----    v    iv  i  ii vvv   ii v vv -  v v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAA 689

  chrX_92975252_9   1557 AGTAAACAGACAGCCTACAGAATGGGAGAAAATATTTGCAACCTATGCAT 1606
                            i  v     i  i                         vii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_92975252_9   1607 CTAACAAAGGTCTAATATGAAGATTCTGTAAGAAACTGAAAGAAATCAAC 1656
                           i i  i  v  vi   vv   v v i   ii    vvv v  v    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_92975252_9   1657 AAGAGAAAAACAAATAACCCAATTAAAAAATGAGCAAAGGACATGAACAG 1706
                           v i   i               ?       i        iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_92975252_9   1707 ACATTTTTCAAAAGAAGACATACAAGCCGCCAACAAACATATGAAACAGT 1756
                               i  v        i      iiv     i  i  i      vii 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_92975252_9   1757 TCGCAGCATCACTAATCAT 1775
                         v v  i     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  


1064 22.15 16.31 1.85  chrX_92978924_92980975      475   799 (1253)    L1M4_orf2#LINE/L1       85   456 (452)  

  chrX_92978924_9    475 GCAATCTCAATCAAAATCCCAG--------------GAAATT-------- 502
                               i v             --------------      --------
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chrX_92978924_9    503 ----CTGAAGTTTAAATGGAGAGGCAGAAGACCCATAATAGCCAACACAA 548
                         ----  i  i  i v     i v   iii      v         v    
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_92978924_9    549 TATTGAAGGACAGCACAACAAAGTTGGTGGACTGACATTATCTGACGTCA 598
                          v     -- v  v v           v     v   i vi ii iv   
  L1M4_orf2#LINE/    185 TCTTGAA--AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_92978924_9    599 AGACATACTGTAAAGCTATAGTAATTAAAACAGTGTAGTATTAGTAAAAG 648
                          i  v    ii       i      i  i       i   i i i v   
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_92978924_9    649 AACAGAC-T-TAGATCAATGGACCAGAATAGAGAGCCCAGAAACTGACC- 695
                         i i    - -            vi     v     i       ivi   -
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_92978924_9    696 --------------------TCTTTGACAAAGG----AAGAAACGCAATA 721
                         -------------------- i  i     i  ----    ---- v  v
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA----CCATT 378

  chrX_92978924_9    722 CAATGGAGAAAATATAGTCTTTCCAAAAAATCATGCTGGAACAACTGGAA 771
                               i    iv         i   v    vi      i         v
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_92978924_9    772 ATTTACATGTAAAATAGTGGATCTAAAC 799
                          ?ii     i    v i  i vi ii  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGAC 456

Transitions / transversions = 1.73 (45 / 26)
Gap_init rate = 0.02 (8 / 372), avg. gap size = 7.38 (59 / 8)  

1362 20.82 4.81 2.52  chrX_92978924_92980975     1123  1559 (493)    L1M4_orf2#LINE/L1      462   908 (0)  

  chrX_92978924_9   1123 CCTAACATCCTTTACAAAA-TTGACTCAAAATGGATCACAGACCTAA-CG 1170
                            v   i v v       -  i               ?        -i 
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_92978924_9   1171 TAAAACAGAAAACTACAAAAATCCTAGAAGATAACATATGAGAAATATCT 1220
                            i vvv       i    v  i       v      v ? v  -    
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCT 560

  chrX_92978924_9   1221 ACCTGACCTTGGATATGGCAATGACTT--TAGATATATCACCAAAGACAG 1268
                         v v         i vv       ii  --       iv       ii  v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_92978924_9   1269 AACCCATGAAAGAAAAAAAATCATCAACTAGACTTTATTAAAATTAAACA 1318
                           v v ii          v v-  v  i i     i  i         v 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAG-ATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_92978924_9   1319 TCCAGTTTTGTG------AAGACACTGTCAACAGTTTAAAAAGGCAAGTC 1362
                         i----       ------ i      i    v ivv i     i   vi 
  L1M4_orf2#LINE/    660 C----TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_92978924_9   1363 AAAGAATGGGAGAAAGCATTTGCAAAAGATATAACTGAATAAAGGATTGT 1412
                          v             ii         vv     v    -   i   i vv
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA-TAAGGGACTTG 754

  chrX_92978924_9   1413 TATCCAAAGTATAAGAAGATCTCTTAAAAATCTCAACAATAAAAAAACCA 1462
                               i i    vi    v      v  --     i        i  - 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAA--CTCAATAATAAAAAGAC-A 801

  chrX_92978924_9   1463 AACAAACTGATTTAAAAATGTGCCAAATTATT--AACAGACACTTCACCA 1510
                           i  v ii   ?       v  -   vv   --  i     i   v   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGC-AAAGGATTTGAATAGACATTTCTCCA 850

  chrX_92978924_9   1511 A-GAAGAT--------GACAAATAAGCATACAAATAGATGTTTTACATCA 1551
                          -      -------- i v        i ii  v     i iv      
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_92978924_9   1552 TATGTCAT 1559
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.05 (45 / 43)
Gap_init rate = 0.03 (14 / 447), avg. gap size = 2.29 (32 / 14)  


2538 23.77 1.43 0.79  chrX_92995311_92996933.rev      502  1132 (491)    L1M4_orf2#LINE/L1      274   908 (0)  

  chrX_92995311_9    502 TGACATAAAACCAGACACATAGACTAATGGAACAGAATAGAGAATACAGA 551
                           i     iivi     i     ii       i     v    i v    
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_92995311_9    552 AATAAATCCACACATTTACAGTCAACTCATTTTTGACAAAGGTGCCAACA 601
                               i   i       ii     i v     i     i        v 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_92995311_9    602 ATGTACATTGAGGAAAGGACAGCTTCCTCAATAAATGGTGCTGGGAAAAC 651
                         vii v  v  i      i i  ii ii    i              v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_92995311_9    652 TGGTTATCCATATGCAGAAGAAAAAAATTAGACCCCTATCTCTCACCATA 701
                            v  ?   i     i     vi  i  i        i   v       
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_92995311_9    702 TACAAACATCAACTGAAAATGGGATTAAAGACTTAAATGTAGCAATGAAA 751
                               v  i    v       -  i ?    i        iv iiv   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGG-ATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_92995311_9    752 ACTGTAAAACT---AGAAGAAAATATTGGAG-AAATCCTTCAGGACATTG 797
                            i       ---         i  v  ? -     -   iv   v   
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chrX_92995311_9    798 GTCTCAGCAA-AGTTTTATGGTCATGACCTTAAAAGCACAGGCAACAAAA 846
                          vi vi    -i    iv i vi     vii         i         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_92995311_9    847 GCAAAAATAGACAA----GATTACATTGAGCTAAAAGGCTTCCACACAAA 892
                          v         i  ----  i v   ii iv v   ii   iiiii v-v
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT-T 670

  chrX_92995311_9    893 CAAAGGAAACAATAAACAGAGTGAAAAGACAACCTGCAGAATATCAGAAA 942
                                v  v  v  v i               ii      ivv     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_92995311_9    943 ATATTTGCAAACTATCCATCTGACAAGGGATTAATAGTCAGAATGTGTAA 992
                                    ii  vi      i      i vi  vi      i i   
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_92995311_9    993 GGAACTCAAACAACTCAATAGTAATAAAAGGCAATTAATTTGATTTAAAT 1042
                         i      vv           i   --    i   v   iiii   ?   v
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAA--AAAGACAAATAACCCAATTWAAAA 818

  chrX_92995311_9   1043 ATGGACAAAAAATCTAAACAGGCATTTTTCAAAAGGAGACATGCAAATGA 1092
                             i    ii  i i  i  i     i  v    i   i  i      i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_92995311_9   1093 CCAACGGGTATATGAAACAATGCTTAACATCACTAATCAT 1132
                             iii i i      vi     i       ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.24 (101 / 45)
Gap_init rate = 0.01 (8 / 635), avg. gap size = 1.75 (14 / 8)  


 261 18.75 12.50 0.00  chrX_93000386_93006795        2    97 (6313)    L1M4_orf2#LINE/L1      781   888 (20)  

  chrX_93000386_9      2 CATCTCAAAAA-AAAAAAAAAAA-----------AAAAGTGGCCAAAGGA 39
                           v     v  -     i v   -----------    i   v       
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_93000386_9     40 AATGAAAAGACACTTTTCGAAAGAAGACATACATGCGGCCAATAAGCACA 89
                         vv    v     i  i  v        i     vii              
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_93000386_9     90 TAAAAAAA 97
                          i    i 
  L1M4_orf2#LINE/    881 TGAAAAGA 888

Transitions / transversions = 1.00 (9 / 9)
Gap_init rate = 0.02 (2 / 108), avg. gap size = 6.00 (12 / 2)  

3283 26.18 0.55 0.66  chrX_93000386_93006795     5009  5917 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93000386_9   5009 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5058
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93000386_9   5059 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93000386_9   5109 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5155
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_93000386_9   5156 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCGAAA 5205
                                 viiv  ii  v  viv  v     iv     i i ivvii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_93000386_9   5206 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5255
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_93000386_9   5256 CTACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5305
                             i    i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_93000386_9   5306 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAAC 5353
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_93000386_9   5354 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5403
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_93000386_9   5404 TCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5453
                            v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_93000386_9   5454 TGAAACTGGATCCCTTCCTTACACCTTATACAAAACTCAATTCAAGATGG 5503
                             ii    i    v   i     v         v i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_93000386_9   5504 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTACAAGAAAA 5553
                           i ?    i       v   v       i      vi i  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_93000386_9   5554 CCTAGGCATTACCATTGAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5603
                          v    ?i v viv  viv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_93000386_9   5604 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAATGGGATCT 5653
                         vi            vvi          vv     v  i   - v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA-TTGGACTT 644

  chrX_93000386_9   5654 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGACACTACCATCAGAGTGA 5703
                         v  i   v v  i i   i  ii vv    i       i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_93000386_9   5704 ACAGGCAAGCTACGAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5753
                          v  i   v i  ii             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_93000386_9   5754 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5803
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_93000386_9   5804 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5853
                            i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_93000386_9   5854 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5903
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_93000386_9   5904 TCATCACTGGCCAT 5917
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1224 28.16 6.94 1.63  chrX_93011903_93015183.rev     1586  2075 (1206)    L1M4_orf2#LINE/L1        1   516 (392)  

  chrX_93011903_9   1586 TAGAAAAACTTTCCATCCTCATGGATTGGAAGAATCAAAATCATCAAAAT 1635
                          i    i iv i    vi               v i  v  ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93011903_9   1636 GTCAATACTGCCCAAAGCAATCCACAGATTAAATACTATCTTAATCAAAT 1685
                          v       v      vii   i       v  ii v   iiv      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93011903_9   1686 TACCAAGGTTG--TTTTTTACAGAATTAGAAAAAACT--TCTCTAAAATT 1731
                          v   -- i  --      i     v v  v  i-  --  -        
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAG-CTGATC-CTAAAATT 146

  chrX_93011903_9   1732 AATATGGAA---CAAGAAAAAAAAAATAGGCAAAGCAAGCCTAAGCAAAC 1778
                         v        ---    ii vvv i     v    i   v i i iv  iv
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_93011903_9   1779 A-AACAAAGCTGAA-----TACA--------TTGCAATACCTAACATAAA 1814
                          -       i  i -----i   --------  v   v  i  vi i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_93011903_9   1815 ACTATACCATGTGGCCA---CAGCATGATAATAGTACAAAAATGGA-ACA 1860
                         i   i ----  iii  ---   ii  i  v i i i  ii  i  - i 
  L1M4_orf2#LINE/    247 GCTACA----GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_93011903_9   1861 CAAACCAATGGAACATAATAGAGAGCCCAGGAATAAATCTCCACACCTAC 1910
                         i i i        i v   v     i    i      i ivi   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_93011903_9   1911 AACCAACTGATATTCAACAAGGCAACAAAAAT-----AATGAGGGAATGA 1955
                         iii   i    v   i      vvi v  i i-----    i  i  vi 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_93011903_9   1956 CTCCCTATTCAGTTAATTGTTTTGTGAAAACAGGCTTCCTATATGTAGAA 2005
                         ivvi  v    iiv   v  vi  v  v   v  v v? i i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_93011903_9   2006 GAATGAAACTGGAC----ACTTCTCACCACATACAAAAATTAACTAAAAA 2051
                                ii     ----  i  v     i               v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_93011903_9   2052 TGGATTAAAGACTTAAATGGAAGA 2075
                              i ?    i      v    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGA 516

Transitions / transversions = 1.78 (87 / 49)
Gap_init rate = 0.03 (14 / 516), avg. gap size = 3.00 (42 / 14)  

 839 26.81 4.62 2.64  chrX_93011903_93015183.rev     2336  2790 (491)    L1M4_orf2#LINE/L1      445   908 (0)  

  chrX_93011903_9   2336 ATGGAGTAAGACTGC-ATCTCAAAAAAAATAAATAAATAATAAC--AAAA 2382
                            i   vi   iv - i    v vv v   v v    --    --    
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT--TAACTCAAAA 492

  chrX_93011903_9   2383 TAACAACAACAAACACTTAAATGGAAAACCTCAAACTATAAAAATCCTAG 2432
                          ii---- v  ? v  i      v  i v  v           v  i   
  L1M4_orf2#LINE/    493 TGG----ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_93011903_9   2433 AAGAAAACC---AAATAAATACTCTTCTGAATATTGGACTACACAAAAAA 2479
                                 v---i?i     ---    vvi iv    ii  vi   viiv
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_93011903_9   2480 TCAATGACTAAGTCTTCAAAAGCAATTACAACAAAAAACAAAAATTGACA 2529
                          ivv iiv  v v vi        vvvi        i -      v  i 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATA 634

  chrX_93011903_9   2530 A-TTGGTACTTAATTGAACTAAAGAGTTTCTGCACTGCAAAAGAAACTAT 2578
                          -    -    v  ii  v v  i ii  i  ii  v    i  v     
  L1M4_orf2#LINE/    635 AATTGG-ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_93011903_9   2579 CAACAGCTTAAACAGACAATCTATAAAATGGAAAAATATATTTGCATACT 2628
                            v ivv i  v      i i i i     i i  v         v ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_93011903_9   2629 ATGCATTTGATAAAGGACTAATATCCAGA-----TACTGAA-----ACAA 2668
                           ii  i      i     vi        -----  vv   -----    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_93011903_9   2669 ATCAACAAGAAAAAC-CAAATAACCATACTAAAAAGTGGACAAATG-TAT 2716
                         v    i  v     v-         vv i ?    i   i    v - v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_93011903_9   2717 GAACAGACACTTCTCAAAAGAAGACATTCAAGCAGTGAACAA--ACATGA 2764
                            i     i     v        i  v   iii iv  i  --      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_93011903_9   2765 AAAAATTCTTCAACATTACTAATCAT 2790
                            i  v  -      i ????????
  L1M4_orf2#LINE/    884 AAAGATGCT-CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (63 / 56)
Gap_init rate = 0.03 (15 / 464), avg. gap size = 2.20 (33 / 15)  

 372 20.62 1.03 2.06  chrX_93011903_93015183.rev     3142  3238 (43)    L1M4_orf2#LINE/L1      136   231 (677)  

  chrX_93011903_9   3142 ATTCTCAAATTCATATGGAACCAGAAAAAGCACCT-GAATAGCCAAACCA 3190
                           i  v              -- viv  i v   i-           v  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_93011903_9   3191 ATCCTAAAAGAAAACAACAAAGCTGGAGGCATCACATTACCCAATGTC 3238
                            i i   i i  v       i      vv     i v      v  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

Transitions / transversions = 1.00 (10 / 10)
Gap_init rate = 0.02 (2 / 96), avg. gap size = 1.50 (3 / 2)  


2494 27.37 2.91 1.45  chrX_93057884_93062657.rev     3389  4283 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93057884_9   3389 TAGAAA-ACGTTTCATGCTCACTAATACGAAGAATCAATATCATTAAAAT 3437
                          i    - ii ii    i   ivi  vv     v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93057884_9   3438 GGCCATACTGTCGAAAGCAATTTATAGATCCAATGCTATGCCTATTAAA- 3486
                            v     vi v   vii  i  i    i   i  v  v     i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93057884_9   3487 CCATAATTGACATTCTTCACAGTACTAGAAAAAGACAATTTTAAAATTCA 3536
                         i vi ii  v -  i  ii   v v v  v  - vii  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_93057884_9   3537 TATGGAA-TAAAAAAGAGCCAGAATAGCCAAAGTAATCATAATTAAAAAG 3585
                                - iv  ii  v              ii    v i vv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_93057884_9   3586 AACACATCTGGAAGAATCACACTACCCAACTTCAAACTATACTACAGAAC 3635
                             v vi    i  v       v     i      viv       i i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_93057884_9   3636 TACAGTAAACAAAACCAAAT-TGGTAGTGGTACAAAAACAAACACATAGA 3684
                                 v   i  -- i -     v   i i  ii i i   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGAC--AGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_93057884_9   3685 CCAATGGAACAGAATAGAGAACCCAGAAATAAGGCTGCACACCAATCACT 3734
                         i        i     v    ii          iv iii   iiv  viii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_93057884_9   3735 ATCTGATCTTTGACAAACCTAATGAAAGCAAGCAATTGGGAAAGGAT-TT 3783
                          vi    i  i     ivv ivii i v  vv    v       i  -v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_93057884_9   3784 CATTTTCAGTAG--GGTGCTGAGAAAACTAGCTAGCAATATGCAGAAGAT 3831
                          -      ii i--       i  v    i v  ? v i     i    v
  L1M4_orf2#LINE/    397 C-TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_93057884_9   3832 TAAAATTAGACCCCTTCCTTGCACTATATACAAAAATTAACTCAAGATTG 3881
                          i  i  i       v   ii   i                    i  v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_93057884_9   3882 ATTAAAGACTTAAGTGTAAAACCCCAAACTATAAAAACCCTGGAAGACAA 3931
                           i ?    i   i     i v iv           vi i i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_93057884_9   3932 CCTAGGCAATACAAT--TCAGGACATAGACACAAG-AATAGGTTTTATAA 3978
                          v    ?i-  -   --  iv   v v ivvi i -   -     iv  i
  L1M4_orf2#LINE/    546 CATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAAT-GGTTTCTTAG 592

  chrX_93057884_9   3979 TAAAGATGCCAAAA--ACAATTGCAACAAAAGCAAAAATTGACATATGTA 4026
                         vv v  ii      --    --          v      v  i v  vvi
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_93057884_9   4027 ATTTAATTAAGCTAAAAAGCTTCTGCACAGTGAAAGAAACTCCTAACAGA 4076
                          i  v  i  iv v    i   i  ii vvii  i  v   vii  v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_93057884_9   4077 GTAAACAGACAAACTACAAAATGAGAGAAACT-TTTGCAATCTATGCATT 4125
                           i  v      v i   i    i      v -       vii  ii  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_93057884_9   4126 CAACAGAGGTCTAGTATCCAGCATCTATAATGAACT--TAACCAATTCAC 4173
                         ii i ii  v  v        v  v     v     --  --   i   v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAA 788

  chrX_93057884_9   4174 AAAAAATAAAAATAAAAAAT--------AAAGTGGGCAAAGGATATGAAC 4215
                         v  v  -   i i   v  i--------   i            v    i
  L1M4_orf2#LINE/    789 TAATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_93057884_9   4216 AGACACTTC--AAAAGAAGACATACATGCAGCCAACAAGCATATGAAAAA 4263
                              i   --v        i     viii     i     i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_93057884_9   4264 A-GCTCAACAGCACTGATCAT 4283
                          -        v  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.62 (39 / 24)  


2767 24.57 2.96 2.47  chrX_93097335_93099136.rev      502  1311 (491)    L1M4_orf2#LINE/L1       95   908 (0)  

  chrX_93097335_9    502 TCAGGATTCCAATGTTGC--TTTTTAAAGAAATAGAAAAAAAAAATCTAA 549
                            ii  i   -- i   --     iv      v  v  ivvi vi    
  L1M4_orf2#LINE/     95 TCAAAATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_93097335_9    550 AGATTTATGTGGAACCAGAAAAACTCCA-AATAGCCAAAGCAATCTTGAG 598
                          -   i  i     viiv  iiivi   -          i         i
  L1M4_orf2#LINE/    143 A-ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_93097335_9    599 AAAGAGGAACAAAGCTGGAGGCATCACATGTCCTCATCTCAAAATCT--T 646
                              i        i      vv     iv   iv  i      ii -- 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_93097335_9    647 ACAATGCTATTGTTATTAAAATAGTATGGTACTGGCCAAGAAACAGATGT 696
                             v    iv  v  i  i i   i          vv iii i   ii 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_93097335_9    697 ATAGACCAATGGAACAGAATAGAGAATCCAGAATTAAACTCTCATATATA 746
                              i        i     v    i       v     i vi i  v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_93097335_9    747 TGGTCAACTGATATTCAATGAGAGTACCAAGAATCGAGAATACACAATAT 796
                                i    v   i ii  i  i      -i ------ iv    iv
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGA-CC------ATTCAATGG 384

  chrX_93097335_9    797 AGAAAGGATATTCTCTTCAACAAATGTTGTTGGGAAAGCTGAATATTCAC 846
                         i     i   v   i           v  i     v i   i   ?i   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_93097335_9    847 ATGGCAAAAAAAGAAAAAATTAAATCTGACCCCTATCTTATATCATACAT 896
                            -     i  ------- v  i iv        i  i i i    i i
  L1M4_orf2#LINE/    435 ATG-CAAAAGAA-------TGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_93097335_9    897 AAAAAAACAACTCAAAATAGATTAAAGACTTAAAC--AAGAACTGGAACT 944
                              v-i          i   i ?    i    i--    i  ii    
  L1M4_orf2#LINE/    477 AAAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_93097335_9    945 ATGTAACTCCTAGCAGAAAATGTCAGTGAAAACTATTATGACATTGGGCT 994
                           iv     i   v      ii vi ? v   iiv ii    v     i 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_93097335_9    995 TAACAATGTTTTCTTGGATATGACACAAAAAGCACAATCAACAAAAGCAA 1044
                         vii     v      i          v          v         v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_93097335_9   1045 AATTAGACAATTTGGATTATATCAAACTAAACAGTTTCAGCACTGCAAAA 1094
                           v    i  v     i vi      v v  v ii  iv ii  v    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_93097335_9   1095 GAAAC----AACAGATTGAAATGGCAATCTAAGAAATGTGAGAAAATATT 1140
                           v  ----  v i v     v i   i i vii    v           
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_93097335_9   1141 TGTAAACCCTACAACTGATAAAGGGTTAATATCCACAATACACAAGAAAC 1190
                           i   i v  i v       i  ii vi      v    i i  ii   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_93097335_9   1191 CACTACAACTCAAGGGTAAATAAACAAATAATTCAATTAGAAAAATGGGT 1240
                         ivi          vii    v i        ii     ?-         i
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGC 824

  chrX_93097335_9   1241 AA-GGACTTCAA------------CAAAGAAGACATACAAATGGCAAACA 1277
                           -   i  v  ------------         i           v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_93097335_9   1278 AGTATATGAAAACATGCTCAATTTCATTAATCAT 1311
                           i i       v        iv   ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (128 / 67)
Gap_init rate = 0.02 (15 / 814), avg. gap size = 2.93 (44 / 15)  


1953 25.67 2.83 1.00  chrX_93138554_93140145      500  1099 (493)    L1M4_orf2#LINE/L1      298   908 (0)  

  chrX_93138554_9    500 CAACAGAACAGAATAAATAACCCAGAAATAAATCCACACAGTTACACCCA 549
                            ii   i     vi v ii           i   i   v   iivi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_93138554_9    550 ACTCATTTTCAACAAAGGTGCTAAGAGCACACACTGGGGAAAGA-CAGTC 598
                          i v      i    i     i    v  iv  v          -i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_93138554_9    599 TCTTTAATAAATGATGATGGGGAAACTGGATATCCACACACAGAAGAATG 648
                          i  i  i     i  v    iv         ?     ii  i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_93138554_9    649 AAACTAGGTCCCCATCCTTTACCATAGACAAAGATCAACTCATAATGGAT 698
                           ii i ii   i i iivi      v     i  i      v       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_93138554_9    699 TAAAGACTTAAGTGTAAGACCTGAAACTATGAAAGTATTAAAAGAAAACA 748
                         i ?    i   i       v  i       i   v v   i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_93138554_9    749 CTGGGG-AAATGTAACAGAACATTACTCTGGGCAAAGATTTGTTGAGTAG 797
                         iv  ? -    v -v ivi  v  ivvi i     v i   v  iii  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_93138554_9    798 TACCTCAAAAGCTCAGGCAATAAAAGCAAAAATGAACACATGAGAGAGAT 847
                         v  vi       v  i    i     v      ii i v  vi  ----i
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA----C 642

  chrX_93138554_9    848 TACATCAAGCTAAAAAGCTTTTGCACAGCAAAGGAAGC-ATCCACAAAAT 896
                          v      iv v    i      ii vv       vi -   v v   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_93138554_9    897 TAAGGGACAA---ACAACATGGGAGAAAATATGTGAAAACTACCCATCTG 943
                         v  ii     ---   iv              v  v   ii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_93138554_9    944 AGAAGGGAC-AAAAACCAGGATATGTAAGGAACTC---------AATAAC 983
                          v       -viv v    i    i   i      ---------     i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_93138554_9    984 AAAAACACAA-TAATCCAATTTTAAAATGGGAAAATGAATAGAATAGAGA 1032
                              v    -   i      ?v        v   v  v v       v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_93138554_9   1033 TTTCTCCAAAGAAGACATACAAATGAACAACAGATCTATTTAAAAAATGC 1082
                                        i         iv   i iiivi - v    i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA-TGAAAAGATGC 891

  chrX_93138554_9   1083 TGAGCATTACTAATCAT 1099
                          v i   i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (90 / 60)
Gap_init rate = 0.02 (10 / 611), avg. gap size = 2.30 (23 / 10)  


 311 20.48 1.20 0.00  chrX_93209613_93213058        5    87 (3359)  C L1M4_orf2#LINE/L1   (45)   863   780  

C chrX_93209613_9     87 ACAAATTTACAAGAAAAA-ACAAATGACCCTATTAAAAAGTGGTCAAAGG 39
                             v iv i  v     -      i    v   ?    i   v      
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

C chrX_93209613_9     38 ACATGAACAGACACTTCTCAAAAGAAGACATTCA 5
                          iv    i     i     v        i  v  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.00 (8 / 8)
Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1)  

3179 27.53 0.33 0.33  chrX_93209613_93213058     2046  2953 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93209613_9   2046 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 2095
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93209613_9   2096 GGCCATACTGCCCATGGAAATTTATAGATTCAATGCCATCCCCATGAAGC 2145
                            v     v    vivvi  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93209613_9   2146 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2193
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_93209613_9   2194 TATGGAACCCAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGTAAAAAG 2243
                                vivv  ii  v  v v  v     iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_93209613_9   2244 AATAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGGC 2293
                           i    i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_93209613_9   2294 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 2343
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_93209613_9   2344 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 2393
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_93209613_9   2394 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGAGGAAAGGATTCCCT 2443
                         i    i  i     ivv  v   i v  vvv    i      i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_93209613_9   2444 ATCTAATTAATGGTGCTGGGAAAACTGGCTACTCATATGTAGAAAGCTCA 2493
                         v ii  iv             v      v  ?i  i   i i  iiv v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_93209613_9   2494 AACTGGATCCCTTCCTTACACCTTATACAACAATTGATTCAAGATGGATT 2543
                          ii    i    v   i     v       v    i i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_93209613_9   2544 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 2593
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_93209613_9   2594 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGAACTTCATGACTAAA 2642
                            ?i- v i -   iv   v v  vv i     viii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_93209613_9   2643 ACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAAT 2692
                                     vvi          vv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_93209613_9   2693 TGAACTAAAGAGCTTCTGCACAGCAAAAGAAACTTCCATCAGAGTCAACA 2742
                         ii  v v  i i   i  ii vv    i  v   vi  vv i   v  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_93209613_9   2743 GGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACAAA 2792
                          i     i                 v   i   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_93209613_9   2793 GGGCTAATATCCAGAATCTACAAAGAACTTAAGCAAATTTACAAGAAAAA 2842
                           i  vi          v  i        ivvi   v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_93209613_9   2843 AACAAACAACCCCATCAAAAAGTGGGCAAAGGAGATGAACAGACACTTCT 2892
                         i     i     v  i?    i           vv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_93209613_9   2893 CAAAAGAAGACATTTATACAGCCAACAGACACATGAAAAAATGCTCATCA 2942
                          v        i  vi v ii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_93209613_9   2943 TCACTGGTCAT 2953
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (145 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


2810 26.06 1.37 1.49  chrX_93216425_93218724.rev      926  1800 (500)    L1M4_orf2#LINE/L1        1   874 (34)  

  chrX_93216425_9    926 TGATAAGATATCCTATGCTTGTGTGTTAGAAGAATTAATATTGTAAAATT 975
                           iv         i   i ii  vi  i     v          v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93216425_9    976 GGCTATACTACCCAAGGTAATCTACAGATTCAATGCAATCTCTTTTAAAA 1025
                            v     v     iv i              i      i  v i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93216425_9   1026 TACCAATGACATTCTTCACAGAAATAGAAAATGC-AATTGTAAAATTAAT 1074
                          v   iivi v  i  ii       v  v  -  -i  iv       v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_93216425_9   1075 ATGGAACCAAAGAAGACCCCAGATAGCCAAAGAAGTATTGAGTAAAGAA- 1123
                               viiv iii     vii         iv i v    i-      -
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAG 198

  chrX_93216425_9   1124 AACAAAGCTGAAGACATCACTCTACCTGATTTCCAATTATACAACAAAGC 1173
                                i  i  ivv    v  v  ii     v  viv   v       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_93216425_9   1174 TACAGTAACCAAAAGAG-ATGGCATTGTGTCTGGCA-AAAAACAAACTTA 1221
                                 i   i v  -i   i ------      -  ii i i  v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTA------CTGGCATAAGGATAGACATA 292

  chrX_93216425_9   1222 CAGAACAACAGAACAGAATAAATAACCCAGAAGTAAATCCACACACTTAC 1271
                         i   v   ii   i     vi v ii      i    i   i   i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_93216425_9   1272 ACCCAACTCATTTTCAACAAAGGTGCTAAGAACATACATTGGGGAAAGA- 1320
                         ivi   i v      i    i     i    v   v  v          -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_93216425_9   1321 CAGTCTCTTTAATAAATGGTGATGGGAAAACTGGATATCTGCACATG--G 1368
                         i     i  i  i        v     v         ? --      --i
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC--CACATGCAA 440

  chrX_93216425_9   1369 AAGAATGAAACTAGGTCCCCATCCTTTACCATAGACAAAGATCAACTCAA 1418
                                  ii i ii   i i iivi      v     i  i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_93216425_9   1419 AATGGATTAAAGACTTAAATGTAAGACCTGAAACTATGAAAGTATTAAAA 1468
                                i ?    i           v  i       i   v v   i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_93216425_9   1469 GAAAACATTGGGG-AAATGTAACAGAACCTTACTCTCATCAAAGATTTGT 1517
                                 v  ? -    v v- ivi     ivvi viv   v i   v 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_93216425_9   1518 TGGGTAATACCTCAAAGGCCCAGGCAATAGAAGCAAAAATGAACACGAGA 1567
                          i i  vv  vi    i  v  i    i i   v      ii i -- iv
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA--AAT 637

  chrX_93216425_9   1568 CAGATTACATCAAGCTAAAAAGCTTTTGCACAGCACAGGAGAC-ATCAAC 1616
                         ii  i v      iv v    i      ii vv  v    v  -     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_93216425_9   1617 AAAGTGAAGCCACAGACAACAACATGGGAGAAAGTATTTGAAAACTATCC 1666
                                 ivv   iv v   iv          i      v   ii  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_93216425_9   1667 ATCTGA-AAAGGATAAAAATC-AGAATATATAAGGAACTCAAACAACTCA 1714
                               -  i   ivviv   -           i      vv        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_93216425_9   1715 ATAACAAAAACATGA-TAATCCCATTTTATAATGCACAAATGAATAGAAT 1763
                             i     v ii -   i  v   ?v v    vi    v  v v    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_93216425_9   1764 AGAAATTTATCCAAAGACGGCATACAAATAAACAACA 1800
                            v    v        v ii        iiv   i 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.38 (130 / 94)
Gap_init rate = 0.02 (17 / 874), avg. gap size = 1.47 (25 / 17)  


2555 26.58 1.50 4.18  chrX_93319427_93324903     4052  4984 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93319427_9   4052 TGGAAACACATCTCATGCTCACGGATGGCTAGCATCAATATTGTGAAAAT 4101
                               v i   i    i   i    v vv  vv i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93319427_9   4102 AACCATACTGCCAAAAACAATCTACAAATTTAATGCTATTACCATCAAAA 4151
                         ii v     v  v   vii       i   i  i  v  iv i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93319427_9   4152 TAT--GATAATCATTTTTTAAACAACTAGAAAAAC-AATTCTAAAATACA 4198
                          vi-- v i-- v      iv v  v v  v  i -i  i       v  
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_93319427_9   4199 TATGGAACCAAAAAATAGCCTGTATAGCCAAAGCAAGACTAAGCAAAAAG 4248
                                viiv  iiv v  v v         i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_93319427_9   4249 AACTATTTTGGAGGCATCACATTACTCAACTTCAAACTATACTGTAAGGC 4298
                            v vv       vv     i v i   i      viv    ii  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_93319427_9   4299 CATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACC 4348
                         i i   v i   i    ii         i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_93319427_9   4349 AATGGAACAGAACAGATAACCCAAGAATAAAGACAGATTCTTACAGCCCA 4398
                                i    iv  v ii   ii      vv  v ivi   ii i v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_93319427_9   4399 CTGATTTTTCACAAAGCAAGCAAAAACATAAAGTGGGGAAAGGACACCCT 4448
                         i       iv    i vviv   i v   vv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_93319427_9   4449 ATTCAGCAAATGGTGCTGGAATGATTGGCAGGCCACATGTAGAAGAATGA 4498
                         v    i             i ii i   vvi?       i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_93319427_9   4499 AACTGGATCCTCATCTCTCACTATATACAAAATACAACTCAAGATGTATC 4548
                          ii    i  ii i   v   i          vvi       i   v   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_93319427_9   4549 AAAGACTTAAATCTAAGACCTGAAACAATAAACACTGT-AGAATATAACA 4597
                          ?    i     v     v  i    v     -   v -    v v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chrX_93319427_9   4598 -------AACTTTTCCAGACATTGATTTAGCCAAAGACTTGATGACCAAG 4640
                         -------  v i   vv   v   iv    v   v ii  vv iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_93319427_9   4641 AACCCAAAAGCAAATGCAACAAAACAAAGA-TAAGTAGATGAGACTTAAT 4689
                          vv         v v         v   i -  ii  i  vi     v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_93319427_9   4690 TAAACCAAAAAACTTCTGCACAGCAAAAGAAATAATCAGAAGAATAAACA 4739
                         i   viv        i  ii vv    i  v iv    ii i i i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_93319427_9   4740 GATAACCAACAGAGTGGAAGAAAGTATTTGCAAACTGTGCATCCTATGAA 4789
                           i    v     i   i     i          iii ii   iv  i i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_93319427_9   4790 GAACTAATATCTAGAATCTATAAGAAACTCAAACAAATGAGCAAAGAAAC 4839
                          i   vi    i     v     ii     vv    ------------- 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAA-------------C 784

  chrX_93319427_9   4840 TCAAACAAATGAGCAAAGTAATAATAATAATAATAGTAATGATAATCTCA 4889
                             --------------      v  -i i  --------    i iv 
  L1M4_orf2#LINE/    785 TCAA--------------TAATAAAAA-GACAA--------ATAACCCAA 811

  chrX_93319427_9   4890 TCAAAACATGGGCAAAGGACATGAATAGACAATTCTCAAAAGAAGATATA 4939
                          i?   v            iv          v     v            
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_93319427_9   4940 CAAATGGCCCAAAA--ATATGAAAAAATACTCAACATCACTAATTAT 4984
                                  v v  -- i       i  i          ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (138 / 107)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 4.42 (53 / 12)  


1875 27.60 9.68 2.63  chrX_93327523_93329706      854  1690 (494)    L1M4_orf2#LINE/L1        1   896 (12)  

  chrX_93327523_9    854 TGAAAAAATATTCCATGTGCTGGTGGATAGGAAGAATAAATATTGTTAAA 903
                           i   i    i      v --i     v      v v           i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTC--ATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_93327523_9    904 A-GGCCATGCTATACAAAGCAATTTACAGATTCAATTCTATTCCTATCAA 952
                          -   v  i  viv    vii  i           iv v  i        
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_93327523_9    953 C-TACCAATAACATTTTTTATAGAATTTAAAAA----ATTCTAAAATGTA 997
                         v- v   iivi v      ii    v  i v  ----  i       vi 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_93327523_9    998 TATGGAACAACAAGAGAAGCCATAATAGCCAAACTAATTCTTAGCCAAAA 1047
                                vvi    i  v-   v          vi   ii v ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_93327523_9   1048 GAACAAAGCTGGAGGCAACACATTACCAGAATTCAAACTGTACTACAAAA 1097
                                 i      vvv    i v  vi v      viv         i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_93327523_9   1098 CTACAGTAACCAAAATGGCATGGTAC------------ACACATATAG-- 1133
                                  i   i ii ii      ------------ v        --
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_93327523_9   1134 ---------------------------------CCAT---TTTAT----- 1142
                         ---------------------------------    ---     -----
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_93327523_9   1143 ------CTTTGATAAAGTCAACAAAAACAAGCAATGAAAAAAAACTC-CC 1185
                         ------i  i  i  i viiv   i v  vv     iii   i v v-i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_93327523_9   1186 TATATAATAAATGGTTCTAGGATAACTGGTTAGTTACATGAAGAAGATTG 1235
                          v vi  i       v  i   i      v  ?ii     v i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_93327523_9   1236 AAACTGGACCCCTTCCTTATACCATATACTAAA-----CTCAAAATAGAT 1280
                           ii         v   i i         v   -----        i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_93327523_9   1281 TAAAGACTTAAATGTAAAGCCTAAAGCTATAAAAATTTTTGAAAAAATCC 1330
                         i ?    i         iiv     i        v i  v   i   v v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_93327523_9   1331 TGGAAAATAGTATTCTAAACATAGACCCTGGCAAAACTTTTATAATGAAG 1380
                          i i?ivv i v   vvi  v v iviiv     viv   iv  ivv v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_93327523_9   1381 AAACCAAAATTAATTGCAACAGAAACAAAAATTGACAAATGGCATCTAAT 1430
                          v       vi vvv      i  iv      v  i    v v ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_93327523_9   1431 TAAACTAAAGAGCTTCTGCACAGGAAAAAAAAAACAAACAAACTATTGAC 1480
                         i   v v  i i   i  ii vvv   ii --------  --    ii v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGA--------CA--CTATCAAG 687

  chrX_93327523_9   1481 AGAGTAAATAGACAACCCAAAGAATAAGAGAATATATTTGCAAACTATGC 1530
                          i   i  v          v     ii     v           ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_93327523_9   1531 ATCTGACAGAGGTCTAACATCCAGAATCTATAA-GAA-----ACAAATTA 1574
                               i ii  v  vii         v     -   -----    v i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_93327523_9   1575 ATAAGCAAAAAACAAACAACTCCATTAAAAAGTGGGCAAAGGACATAAAC 1624
                             vv    i     i   i v   ?    i           i- ----
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-T---- 832

  chrX_93327523_9   1625 ACATAAACAGACACTTTTCAAAATACAAATATATG--TGGCCAAAAAGCA 1672
                         --- i  i     i  i  v   v - i     ii--       v     
  L1M4_orf2#LINE/    833 ---TGAATAGACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCA 878

  chrX_93327523_9   1673 TATAAAGAAATTCACAGC 1690
                         i  i  i i  v v  i 
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAAC 896

Transitions / transversions = 1.27 (127 / 100)
Gap_init rate = 0.02 (19 / 896), avg. gap size = 5.42 (103 / 19)  


2554 27.18 0.64 4.25  chrX_93341116_93345301.rev     2753  3694 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93341116_9   2753 TGGAAACACATCCCATGCTCATGGATGGGTAGAAACAATATTGTGAAAAT 2802
                               v i        i        v  v   vvi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93341116_9   2803 GACCATACTGCTAAAAGCAATCTACAAATTCCATGCAATTCCCATCAAAA 2852
                          i v     v iv   vii       i    v i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93341116_9   2853 CACCA-CCATCATTTTTAAAAGAACTATAAAAAAAAATCCTAAAATTCAC 2901
                         iv   - iii v     iv ii  i i- v  ivvi             i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chrX_93341116_9   2902 ATGGAACCAAAAAAGTAGCCTGCATATCCAAAGCAAGACTAAGCGAAAAA 2951
                               viiv  ii - v  v v   v     i   v-  ---i      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAAT-CT---TGAAAAA 194

  chrX_93341116_9   2952 AAAAAAAAAAGGAAGAAAGAAAGAAAGAAAAAATCTGGAGGCATTATATT 3001
                         i  i  v    -----------------------i      vv i i i 
  L1M4_orf2#LINE/    195 GAAGAACAAAG-----------------------TTGGAGGACTCACACT 221

  chrX_93341116_9   3002 ACCTGACTTCAGACTTTACTATAAGGCTATTGTCACCAAAACAGCATGGT 3051
                         v  ii i    i vi      i  i    iv  v i   i    ii    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_93341116_9   3052 ACTGGTATAAAAACAGGCACATCAACCAGTGGAACACAATAGAGATCTCT 3101
                              i    ii i  i  i  vi i  i     i v   v    vii v
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_93341116_9   3102 GAAATAAACCCAAATACTCACAGCTAACATCTATTT--GACAAAGCCAAC 3149
                                     v i i i ii ii  -- iv    --     i viiv 
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAA--TTGATTTTCGACAAGGGTGCC 369

  chrX_93341116_9   3150 AAAAACATGAAGTGGGAAAAGGACAACCTATTCAACAAATGGTGCAGGGA 3199
                           i v   vv i    i    i i ii  v               v    
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_93341116_9   3200 TAATTGGCAT-GCTACATGTAGAAGAATAAAATTGAATCCTCATCTATCA 3248
                         i  i   -  -? i     i i      i  i   i i  ii i  vv  
  L1M4_orf2#LINE/    420 CAACTGG-ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_93341116_9   3249 TCCTATACAAAATTCAACTCAAGATGGATAAAAGACCTAAATCTAAGACC 3298
                         i v         v i       i      v ?          v     v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_93341116_9   3299 TGAAATCATAAATATTCT-ACAAGATAACTTTGAGAATAC-CCTTCTCGA 3346
                          i   ii     - i   - v    v   v v - ?i  v-i    vi  
  L1M4_orf2#LINE/    519 TAAAACTATAAA-ACTCTTAGAAGAAAACATAG-GNGTAAATCTTCGTGA 566

  chrX_93341116_9   3347 CATCGGTTTAGGCAAAGACTTCATGACCAAGATCCCAAAAGCAAATGCAA 3396
                          v i  v        v ii   v iivi v  iv         v v    
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_93341116_9   3397 CAAAAACAAAGATAAATAGATAAGACTTCATTAAACTAAAAAGTTTCTGC 3446
                              iv   i   i   i  vi        i   v v    ii  i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_93341116_9   3447 ACAGCAAAAGAAATAATCCACAGTGTAGTGTAAACAGACAACTCACAGAG 3496
                         i vv    i  v iv   v v i---    -   -       i      i
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAA---AGTG-AAA-AGACAACCCACAGAA 711

  chrX_93341116_9   3497 TGGAAGAAAATCTTCACAATCTGTACATCCTACAAAAAACTAATATCCAG 3546
                            i       v  ii   viii  i   iv i  iii   vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_93341116_9   3547 AATCTACAAAAAGATCAAATGAATCAGCAAGACAGAAACAAAGAATCCCA 3596
                            v  i   i iv  vv ii v   ii  v v i i     v  i  v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_93341116_9   3597 TCAAAATGTGGGCTACAGACATGAATAGACAATTCTCAAAAGAAGATAAT 3646
                          i?   vi     v vi  iv          v     v          - 
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA-T 860

  chrX_93341116_9   3647 ACAAATGGCCAACAAGTATATGGAAAAATGCTCAAGATCACTAATGAT 3694
                                     i   i i   i   i        v    ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (155 / 97)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.56 (46 / 18)  


2423 25.03 1.91 5.62  chrX_93358068_93362394.rev     2894  3836 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93358068_9   2894 TGGAAACAATTACCATGCTCATGGATGGGTAGAATTAATATTGTAAAAAT 2943
                               v vv v     i        v  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93358068_9   2944 GAACATACTGCCAAAAGCAATCTACAAATTCAATGCAATTTCCATCAAAA 2993
                          ivv     v  v   vii       i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93358068_9   2994 TACTACCATCACTTTTCACACAACTAGAAAAAACAATCCTAAAATTCATG 3043
                          v i v vv vi    ii  v  v v  v  ivii              i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_93358068_9   3044 TGGAACCAAAAGAGAGACTGCATAGCCAAAGCAGGACTAAGCAAAAAGCA 3093
                              viiv   i  vv v v         i  ivvi i iv  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_93358068_9   3094 CAAATCTGGAGGCATGACATTACCCAACCTCTAACTATACTGTAAGTATA 3143
                             vi      vv v   i v     ii  v  ----------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA---------------- 234

  chrX_93358068_9   3144 GCTTATACTTTACTTATACTTAAAACTTATACTATAAGTATAGCTCACCA 3193
                         ------    -   ---  --   i  ---  ----    ------ i  
  L1M4_orf2#LINE/    235 ------ACTT-ACT---AC--AAAGCT---AC----AGTA------ATCA 259

  chrX_93358068_9   3194 AAACAGCATGGTACTGGTGTAAAAATAGGCACATAGATCAATAGAATATA 3243
                          i    ii         ii   ii    i  i          i     v 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_93358068_9   3244 ATAGAGAACCTACAAATAAAGCCAAATACTTACAGCCAACTGATGTTTGA 3293
                           v    ii i v       v   v i i   ii i   i    v  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_93358068_9   3294 CAAAGCAAACAAAAACATAAAGTGGAGAAAGGACACCTTATTCAACAAAT 3343
                            i vviv   i v   vv i   i     i i vii v          
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_93358068_9   3344 TGTGCTAGGATAAATGG-TAGGCCACATGTAGAAGAATGAAATCGGATCC 3392
                         v     i   i  v   -  ?-       i i         i i   i  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAK-CCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_93358068_9   3393 TCA--TTATCACCTTATACAAAACTCAACTCAAGATGCATCAAGGACTTC 3440
                         ii -- i -    v         v i       i   v    ?i   i v
  L1M4_orf2#LINE/    459 CTACCTCA-CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_93358068_9   3441 AATCTAAGACCTGAAACTATAAAAGCTCT-AGAAGATAACATCAGAAAAA 3489
                            v     v  i           -    -      v     vi ?iv  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_93358068_9   3490 CCCTTCTAAACATTGGTTTAGGCAAAGACTT------TATGACCAAGAAC 3533
                         vi    vvi  v    v        v ii  ------      -----  
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC-----AC 601

  chrX_93358068_9   3534 CCAAAATAAAATTCAACAAAAACAAAAATAAATAGATGAGACTTAATTAA 3583
                          v   ii v  v-        iv       i   i  vi     v  i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_93358068_9   3584 A-CTAAAAATATTCTGCACAGCAAAATAAACAATCAGCCGAGTAAATAAG 3632
                          -i      i-  i  ii vv    iv v  v    ivvi   i  -   
  L1M4_orf2#LINE/    651 AATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA-AAG 698

  chrX_93358068_9   3633 ACAACCCCACAGAGTGGGAGAAAATCTTCCCAGTCTGTACATACGACAAA 3682
                                -     i           v  iv  iviii  i  vi  i  i
  L1M4_orf2#LINE/    699 ACAACCC-ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_93358068_9   3683 AGACTAATGTCCAGAATCTGCAAGGAGCTCAAACAAATTAGCAAGAAAAA 3732
                         i    vi i        v ii  i  i   vv    v i ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_93358068_9   3733 AACAA----TCCCATCAAAAGGAGGGCTAAGGACATGAATAAGCAATTTT 3778
                         i    ----i  v  i?   iiv    v     iv      ii  v  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_93358068_9   3779 CAAAAGAAG-TATACAAATGTCCAATGA--ACATGAAAAAATGCTTAATA 3825
                          v       -          v     i --         i     i  i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_93358068_9   3826 TCAATAATGAT 3836
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.32 (132 / 100)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.09 (71 / 23)  


2208 27.33 0.30 1.03  chrX_93433164_93434802      472  1148 (491)    L1M4_orf2#LINE/L1      237   908 (0)  

  chrX_93433164_9    472 TCACTACATAATGATAAAGGGGTCAATTCATCATGGTATTGGCATAAAAA 521
                          i      -  - v  v  vii    vv  vii     i        ii 
  L1M4_orf2#LINE/    237 TTACTACA-AA-GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_93433164_9    522 CAAACACATTGACCAATGGAACAAAACAGAGAAACCAGAATCAAATTCAC 571
                         i i   i  v  i        i i  iv    iv      vi   ii  i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_93433164_9    572 ACACCTATAGTAAACTAATTTTCAACAAAAGGTGCCAAGAACATACAAGA 621
                            ii   i  v  i i      i    i-          v   v   vi
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAG-GGTGCCAAGACCATTCAATG 383

  chrX_93433164_9    622 GAGAAAAGACAGTCTCTTTAATAAATGGCGCTGGCAAAACTGGATATTCA 671
                          i    ii i     i  i  i      i     v v         ?i  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_93433164_9    672 TATGCAGAAGAATGAAACTTGACCCTTACCTCTTGCCATATATATAAATC 721
                         i     i         ii v     i      vii       i v    i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_93433164_9    722 AAATCAAAATGGATTAAAGACATAAATATAAGACCTCAAACCATGAAACA 771
                           v           i ?    v     i     v  v    i  i    v
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_93433164_9    772 ACTACAAGAAAACACTGGGGAAACTCTCCAAGACATTGGTCTGGGCAAAA 821
                         vi  v         iv  ? v  v   i iv   v    vi i     vi
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_93433164_9    822 ATTTCTTGAGTAACACCCCACAGGCACAGGCAATCAAAGCAAAAAATTTA 871
                         i      iii  vv  v   v i     i    iv    -       -- 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAAT--A 630

  chrX_93433164_9    872 AAAAAATGGAATCACATCATG-TTAAGAAGCTTCTGCACAGTGAAGGAAA 920
                         i v    v i iiv     vi-    i  -   i  ii vvii     v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA 679

  chrX_93433164_9    921 CAATCAACAAAGTCAGGAGAAAATCCACAGAATGGGATAAAATATTTACA 970
                          v     v     v ii   v  i             v         i  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_93433164_9    971 AACTACCCATCTGACAATGTATCAATCACCAGAATTTATAAGGGGCTTAA 1020
                           ii ivi      i  v v iivi vv       v     i ii  ivv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_93433164_9   1021 ACAATGCTATAGAAAGAAATCTAATAATTTGATCAAAATATGGGCAAAAG 1070
                             iv v   iv  i  iv v     iiii  i?   v         i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_93433164_9   1071 ATT-GAATGGGCGTTTCTCAAAAGAAGACATAGAAATAGCAAGCAGGCAT 1119
                            -    i i i      v        i   v    i  v ii i   i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_93433164_9   1120 ATGAAAAGGTACTCAACATAATTGATCAT 1148
                                 i i        v ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (112 / 69)
Gap_init rate = 0.01 (8 / 672), avg. gap size = 1.12 (9 / 8)  


2251 27.44 4.15 1.74  chrX_93455125_93459085.rev     2177  2923 (1038)    L1M4_orf2#LINE/L1       10   774 (134)  

  chrX_93455125_9   2177 ATTCCATATACATGGATTAGAATAATCAATATTGTTTAAATGTCTGTACT 2226
                           i    i v        i   v v i         v i   v vi    
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_93455125_9   2227 ACTCAAAGTAATATACAGATTCAGCACAATTCCTATGAAAACACCAGTAA 2276
                         v i    v i  v          i i    i     v    iv    ivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_93455125_9   2277 CATTCTTCACAGAAATGGGAGGAAAAAATAAT---AAAATTTATATGCAA 2323
                          v  i  ii       v ---- v  iv i  ---      i     v  
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_93455125_9   2324 TTACAAAAGACCCAGAATAGCCAAAGACA-TACTGAGCAAAAGGAACAAA 2372
                         v i   ii                 -   - vi   iv  i i       
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGAACAAA 204

  chrX_93455125_9   2373 ACAGGAGGAATTATATTAGCTGACTTCA-------CTACAGAGCTATAGT 2415
                         iiv      v i i i vv ii i    -------     i     i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_93455125_9   2416 AACTAAAATGTCATGGTACTTGCATAAAAGCAGACACATAACCGAATGGA 2465
                           ii  i iivii       v      iiii     i   iviv      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_93455125_9   2466 ACAGGATAAAGAACCCAGAAACAAATTCACACACCTACACTGAACTCATT 2515
                          i  i  vi   ii       i   ii  i   ii  iiv v  i v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_93455125_9   2516 TTTAACAAAGTTGCCAGGAAGATACTTGGGAGAAAGGACAGTCTCTTCAG 2565
                           ii    i v     i  vv  v vvv  i     i i     i    i
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_93455125_9   2566 TAAACGGTGCTGGTAATACTAGATATCCATATGCAGAAGAATAAAACTGG 2615
                         i   i        v vv   i    ?   i     i      i  ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_93455125_9   2616 ACCCCTATCTCTCAAAGTATACAAAAATCAAATACAAATGGATTGAAGAC 2665
                                i   v  vvi           i  v vv        ii?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_93455125_9   2666 TTAAATCTAAGACATTAAACTATAAAATTACTATAATACAAGGAAACATT 2715
                         i     v     vv v           i -  ----  v   i      v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACT-CT----TAGAAGAAAACATA 549

  chrX_93455125_9   2716 GAGAAAGCTCTCTGGGATATTGGTCTTGAGCAATAGC------------- 2752
                          i?iv iv   ii v  iv    v-  ii     i i-------------
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGA 598

  chrX_93455125_9   2753 --CTACAAGTACAGGAAACCAAAGCAATAATGGACAAATGGGATCACATC 2800
                         -- i v   i   i v   v    v  v   i  i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_93455125_9   2801 AAG-TTAAAAGCTTCTCCATGGCAAAGAA-ACAACCAATAAAGTGAAAAG 2848
                           i-      i   i viiivv     i -  v i   v           
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_93455125_9   2849 ACAACCCTCAGAATAGGAGAAAATATTTGGAAACCACCCATCTGTATTAG 2898
                                v      i              v   i  ivi     -  v  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG-ATAAG 747

  chrX_93455125_9   2899 G---TCATTCTCAAATTGCTATAAAGAA 2923
                          --- ii vii  i v i-         
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATA-TATAAAGAA 774

Transitions / transversions = 1.62 (125 / 77)
Gap_init rate = 0.02 (14 / 765), avg. gap size = 3.14 (44 / 14)  

 634 23.00 2.00 3.50  chrX_93455125_93459085.rev     3271  3470 (491)    L1M4_orf2#LINE/L1      712   908 (0)  

  chrX_93455125_9   3271 TGGGCACAAATATC--CAAACTATATCACCATCTGATAAGGAATTAATAA 3318
                             viv      i--    ii    ----           i i vi  v
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATAT----ATCTGATAAGGGACTTGTAT 757

  chrX_93455125_9   3319 CCGGAATATATAAGAAACTCA-ACAATTTTATAG-AAAAAGAAATCTAAT 3366
                           i          ii     v-    i iv   i-       v ---   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA---AAT 804

  chrX_93455125_9   3367 GATCTAGTTACAGCACAGGCAAAAGACCTGAATAGACATTTCCAGAAAGA 3416
                         i i i i  ?v iv ii      i  ii              ivv     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_93455125_9   3417 AGACATAAAAATGTCAAGCAGGCATATGAAAAGGTGCTTAACATCATTTA 3466
                            i   v     v v ii i   i        i    i       ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_93455125_9   3467 TCAT 3470
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.21 (31 / 14)
Gap_init rate = 0.03 (5 / 197), avg. gap size = 2.20 (11 / 5)  


3032 25.53 2.12 0.89  chrX_93525843_93528120      902  1798 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93525843_9    902 TGGAAAAACATTACATGCTCATGCATAGGAAGAATCAATATCATTAAAAT 951
                               i i  iv    i     v  v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93525843_9    952 AGCTATACTGCCTGAAGCAATTTACAGATTCAATGGTTTTCATATCAAAC 1001
                         i  v     v  ii  vii  i           i vvv i v       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93525843_9   1002 TACCAACAACATTCTTTACAGAACTAGAAAAAACT-ATTTTAAAATTTAT 1050
                          v   i vi v  i   i     v v  v  i-  -  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_93525843_9   1051 ATGAAAC--CAAAAGATCCCAAATAGCAAAGGCAATACTAAGCAAAAAGA 1098
                            i  v--   ii  i  vi      v  ii    vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_93525843_9   1099 ACAAAGCTGGAGATATCACATTACCCAACTTCAAACTACACTACAGGGCT 1148
                               i     ivv     i v     i      vivi      ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_93525843_9   1149 ACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAAACATAGACCA 1198
                                i   i    ii         i i  ii i   v i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_93525843_9   1199 ATGGAACAGAATAGACAGCCCAGAAATAAGGCCACACACCTATATCCATC 1248
                               i     v  v  i          iv   i   ii   ivi  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_93525843_9   1249 TGATGTTTGACAAAGCTGACAAAAACAAGCAATGGAGAAAAGACTCCCTA 1298
                             v  i     i v  v   i v  vv      i    ii ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_93525843_9   1299 TTCGATAAATGGTGCTGGGAGAACTGGCTAGCCATATGCAAAAGATTGAA 1348
                            i i              v      v  ?   i          v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_93525843_9   1349 GCTGGACCCTTTCCTTACACCATATACAAAAATTAGCTCAAGATGGATTA 1398
                          i       i v   i                   i     i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_93525843_9   1399 AAGACTTGAATGTAAAACACAAAACTATAAAAACCCTGGAAGACAACCTA 1448
                         ?    i i       i vvi            vi i i     v   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_93525843_9   1449 GGT-TATACCATCCTGGACATAGAAACAGGCAAAGGTTTCATGACAAAAA 1497
                           ?-  v i v  v  -  v v iivi      v      - v v v vi
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTC-TTAGATATG 597

  chrX_93525843_9   1498 ACACCAAAAGCAATCA--CAACAAATGCAAAATTTCATAAGTGGGATCTA 1545
                                     --  --       v v    v vv    i v   ii v
  L1M4_orf2#LINE/    598 ACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_93525843_9   1546 ATTAAACTTAAGAGTTTCTGCACAGCAAAAGGAACTATCAAGAGAGTGAA 1595
                           i   v    i ii  i  ii vv    i iv          i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_93525843_9   1596 CAGATAACCTACAGAAAGGGAGAAAATAT--GCA---------TCTGACA 1634
                         v   i    i      v            --   ---------     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_93525843_9   1635 CAGGTCTAATATCCAGCATCTATAAGGAACTTAAACGAATTTAA-AAGAG 1683
                         vi  v  vi       v  v     i     ivv  -  i i  -  v i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTAC-AACTCAATAATAA 794

  chrX_93525843_9   1684 AAGAACAAACCACCCCATTAAAAAGTAGGCAAATGACATGAACAGATAAC 1733
                           ii     iv    v   ?    i i      v  iv    i   i -i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA-T 843

  chrX_93525843_9   1734 TTGTCAAAAGAATATATACATGTGGCCA-TGAGTATATGAAAAAAAAGCT 1782
                           v  v      v       vi      - i  i i       i v-   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCT 892

  chrX_93525843_9   1783 CCAGATTACTCATAAT 1798
                          v v  i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (130 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.80 (27 / 15)  


2647 28.32 0.99 1.32  chrX_93541926_93546589.rev     3263  4173 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93541926_9   3263 TGGAAAAACATTCCATCCTCATGAATAGGAAGAATCAATACAATGAAAAT 3312
                               i i  i    vi     i  v      v i    ivi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93541926_9   3313 GGCCA-ACTGCCTAAAGTAATTTATAGATTCAATGCTATTCCCATAAAAA 3361
                            v -   v  i   v i  i  i        i  v  i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93541926_9   3362 TACCATTGACATTGTTCACAGAACTAGACATAACT-ACTTTAAATTTCAT 3410
                          v   vivi v  v  ii     v v    - i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_93541926_9   3411 GTGGAAC--CAAAGAAGAGCCCATA-TAGCCAAGATAGATAATCTTAAAC 3457
                         i     v--   i i ---    v -       i i ----     i  v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACA----ATCTTGAAA 192

  chrX_93541926_9   3458 AAGAAGAACAAAGCTGGATGCATCATGCTACCTGACTTCAAACTATACCA 3507
                                      i    v vv   ii  v  ii i      viv   i 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_93541926_9   3508 CAAGGCTTCAGTAACCAAAACAGCATGGTACTGGTACCAGAACAGACATA 3557
                            i   v      i   i    ii         i iv  i i       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_93541926_9   3558 TAGACCAATGGAACAGAACAGGGACCTCAGAAACAACACCACACACCTA- 3606
                             i        i    iv i  vii      i  vv   i   ii  -
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_93541926_9   3607 AACCATTTAATCTTCAACAAATCTGACAAAAACAAGCAATGGGAAAAGGA 3656
                         iii  v  i  i   i    ivv  v   i v  vv       i    i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_93541926_9   3657 TCTCCTATTTAATAAATGGTAGTGGTAAAACAGGCTAGCCATATGCAGAA 3706
                          vvi  v  i  i       iv   v v   v  v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_93541926_9   3707 AACTGAAACTGGAACCCTTCTTTATACCTTATATAAAAATTAACTCAAGA 3756
                         i v    ii    v    v i i i   v    i              i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_93541926_9   3757 TCTATTGAAGACTTAAATGTAAAACCCAAACCCATAAAAACCCTAGAGGA 3806
                          vv  ii?    i         i v i   v i      vi i    i  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_93541926_9   3807 AAACCCAGACA-ATACCATTCAGCACATAGGTATGGGAAAAGACTTCATG 3855
                             vi  i?i- v i -   ivv  v v  vv i  v  v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_93541926_9   3856 ACAAAAATACCAAAAGCAATTGAAGCAAAAGCCAAAATTGACAAATGGGA 3905
                         ivv vi i          vvv v i      vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_93541926_9   3906 TCTAATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCAGAG 3955
                         ii v  i   v v  i     i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_93541926_9   3956 T--ACAGGCAACCTACAGAATGGGAGAAAATTTTTCCAATCTACCCGTCT 4003
                          -- v  i     i                 v   v   vii ivii   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_93541926_9   4004 GACAAAGGTCTAATATCCAAAATCTACAAGGAACTTAAACAAATTTACAA 4053
                           i  i  v  vi      i   v  i  i     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_93541926_9   4054 GAAAGAAACATGCAACCCCATGAAAAAGTGGGCAAAGGATATAAACAGAC 4103
                         v   i i   vii     v  v?    i            v i  i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_93541926_9   4104 ACATCTCAAAATAAGACATTTATGTGGCCAAGAAACATATGAAAAATAAA 4153
                          iv    v   v    i  vi vi       v  i  i       i--- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG---A 888

  chrX_93541926_9   4154 AGCTCAACATCACTGATCAT 4173
                         v           ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (143 / 111)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


1631 31.30 2.32 1.74  chrX_93566526_93568207      501  1190 (492)    L1M4_orf2#LINE/L1      215   908 (0)  

  chrX_93566526_9    501 TCACATTATCTGACTTCACACTATATTATAAGGTTATAAT--TTAAAAAA 548
                              i vi ii i    v viv  i  i  i i  i i -- i  i --
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA-- 262

  chrX_93566526_9    549 TTAGCACGATACTGGCACAAAAACAGACACATAAACCAATGAAACATAAG 598
                         -i  iii i        i  ii i     i   i i     i  i v  v
  L1M4_orf2#LINE/    263 -CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_93566526_9    599 AGAGAACCCAGG--TAAAGTTGCACACCTACAGCCATCTGATCTTCAAGA 646
                         v    ii    i--    viiii   ii  ii i  vi    i   i v 
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_93566526_9    647 AAGTTAAGAAAAATATGCAATGGGGAAAGGACTCCCTATTCAACAAAGGG 696
                          i v ivv  i vi  v            i ivvi  v         v  
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_93566526_9    697 GGCTTGGGTAACTGGTTAGCCATATGCAGAAGAATAACACTAGACCCCTG 746
                         v   v  ii      v  ?   i     i      i vii i       i
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_93566526_9    747 CATTTCAGCACATACAAAAATTAACTCAAGATCGATGAAGGATTCAAATG 796
                          v iv  v  i                  i  v   v ?i  iii     
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_93566526_9    797 TAAGTTCTCAAGCTATAACGATCCTGGAAGAAAACCTGGTTTCCTAGTTT 846
                             vv  v  i      viv  i i         v i ------- ?v 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG-------GNGT 554

  chrX_93566526_9    847 CCATTTT-GT-ACACTGGTCCTGGCAA--ATAACTTAGGACTAATTTCTC 892
                         vv  i  -  -  vi   viiv     --i vv     ivv i i--vi 
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC--ACC 602

  chrX_93566526_9    893 AAAAGCAATTGCAGCAAAAACAAAAATGAACAAGTGGAATCTAATTAAAC 942
                                vvv   i     iv      ii i  i v i ii v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_93566526_9    943 TAAGGGGCTTCTGCACAGCAAAATAAACTAACAACAGAGTAAAAATACAA 992
                          v iiii   i  ii vv    iv v    v   v i   i    v    
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_93566526_9    993 CCTACAGAAGAGGAGAAAATATTCACAAAATACTCATCAGA-AAAAATCT 1041
                           i      vi            ii    vi ivi   v  -  iiiv  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_93566526_9   1042 ATTATTCAGAATCTATAATGAACTTAAACAATTTAACA-TGCAAA---AA 1087
                         vv   i      v     v     ivv    i i  i - iv   ---  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_93566526_9   1088 ACAGCCCCATTAAAAA--GGACAAAGGATATGAACTGCCACCTTTCAAAA 1135
                          i i   v   ?    --  i        v    iv v  ii i  v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_93566526_9   1136 GAAGACATAAAAGCAGCTAACAAAGATTTGAAAA-ATGCTCAACATCCCT 1184
                              i   v  iii  i  i  iv iv      -            v??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_93566526_9   1185 AATTAT 1190
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.62 (131 / 81)
Gap_init rate = 0.02 (13 / 694), avg. gap size = 2.15 (28 / 13)  


1873 28.57 6.78 3.03  chrX_93586024_93587951      602  1427 (500)    L1M4_orf2#LINE/L1        1   857 (51)  

  chrX_93586024_9    602 TAGAAAGACATTCCATGCTCATGGATTGGACTAATTAACATTGTTAAAAT 651
                          i      i  i     i            vv v    i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93586024_9    652 AACTATACTACTCAAAGCAATCTACAGATTCAATGCAATGCCTATCAAAA 701
                         ii v     v i    vii              i     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93586024_9    702 TACCAA-TGCCATTTTTTCACAGAAATAGAAAAA--GAAGGTAGAAAATT 748
                          v   i-    --     ii       v  v  i--  vvv  --     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTA--AAATT 146

  chrX_93586024_9    749 TATATGGAACCTG-AACAGACCCTAAATAGCCAAAGCTATCTTAAGCAAA 797
                         i        v-  -  vi     vi          i v     i iv  i
  L1M4_orf2#LINE/    147 CATATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_93586024_9    798 ATAAACAGAACTGGAGGCATCACACTACCTGACTTGAACATATGTCACAA 847
                          vi    i ii      vv       v  ii i  v  v iv iii    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_93586024_9    848 AGTCGCAGCAA-CAAAACAACGCATAGAAAACAACATTATAAAACAACAC 896
                           iii   i  -   i   ii i--- iv viii   v vi v -i   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGT---GGTACTGGCATAAGGATA-GACAT 291

  chrX_93586024_9    897 ATAGAAAAATAGGACATAATAATGAACACAGAAATAAATTAATGCACTTA 946
                              vv   i i i v   viv  iiv          iiv  i  i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_93586024_9    947 CAATGAACTCATCTTTTGTAAAGGTGCAAAGAACGTACATGGAAGGAAGG 996
                         iii v  i v  i  ivii  i     v    v i v  vv ii i   i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_93586024_9    997 ACAGTGT-----ATGTATGGTTCTGTGAAAATGAAATATTTGTATGCAGA 1041
                          i   v ----- iiv     v   v  v  ivii   ?iiii     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_93586024_9   1042 AGAATGAAACTAGATACCCATATTTCACTACATACAAAGATCAACTCAAA 1091
                                 ii i  iv  i iv iv   i i       i  i        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_93586024_9   1092 ATTAATTAAAGACTTAAACATAAAA-CCAAAA---TAAA----------- 1126
                           vi  i ?    i    ii   i - i    ---    -----------
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_93586024_9   1127 ------------TAA------------TTGGCCTAGGCAAAGATTTTATG 1152
                         ------------   ------------    vi       v i   iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_93586024_9   1153 ACTAAGAACTCAAAGGCACAGGCATTAAAA----AAATAGAAAAATCAGA 1198
                         iv  v  vvi    i     i   vi    ----       v    ii  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_93586024_9   1199 CTATATTAAACTAAAAAGTTTCTGTATGGCAAAGGAAAATATCAACAGGA 1248
                           vi  i   v v    ii  i   iivv       v v      v iii
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_93586024_9   1249 TGAAGAGAAAACCTATTAAATGGTAGAATACATTTTTAAAATTTTA-ATC 1297
                             i   v    i ivi     v    v i    vi   - iv  -   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATC 740

  chrX_93586024_9   1298 TGACAAGGGATTAATATCCAGAATATACCAAAAATTTAAACAGCTTAACA 1347
                            i      i vi             iv  i  i ivv   i  i  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_93586024_9   1348 GTAAAACAAAATGAAACAAA--ACCAAGAATTCTCATTAAGAAGCGGGCA 1395
                         i     ------- i     --   v --------   ? i  ii     
  L1M4_orf2#LINE/    791 ATAAAA-------AGACAAATAACCCA--------ATTWAAAAATGGGCA 825

  chrX_93586024_9   1396 AAGTATCTAAATAGACAGTTCTCAAAAGAAGA 1427
                            v  i i        v     v        
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

Transitions / transversions = 1.71 (147 / 86)
Gap_init rate = 0.02 (20 / 857), avg. gap size = 4.05 (81 / 20)  


2585 24.89 1.72 4.36  chrX_93622076_93626208.rev     2763  3634 (499)    L1M4_orf2#LINE/L1       15   863 (45)  

  chrX_93622076_9   2763 ATGTTCATGGATTTAAAGAATCAATATTGTTAAAATTTCCATACTATCCA 2812
                                      vi    v i           i  vv v     vi   
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_93622076_9   2813 AAATA--CTACAGATTTGAGGCAATCCCTAACAAAATACCAATGACACTC 2860
                           v i--         ii v          v      v   iivi vi i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_93622076_9   2861 TTCACAGAAATCTAAAACAAACAAAAAACTAATCCTAACATTTATATGGA 2910
                           ii       i---i    i ------- i       v   i       
  L1M4_orf2#LINE/    115 TTTGCAGAAATT---GACAAGC-------TGATCCTAAAATTCATATGGA 154

  chrX_93622076_9   2911 ACCACACACACAAAAAAAACAAAAATATCCAAAGCCATTCTGAGAAAAAA 2960
                          ------ ii   iii vv  i  -  v     i v  ii   --    i
  L1M4_orf2#LINE/    155 A------ATGCAAGGGACCCAGAA-TAGCCAAAACAATCTTGA--AAAAG 195

  chrX_93622076_9   2961 AATAACAAAACTGGAAGAATCACATTACCTTATTTGAAATTTCACTACAG 3010
                           v      ii    i  v     i v  iv    v   vi i      i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_93622076_9   3011 GGCTCTGGTAACCAAAAGAACACGGTACTGGCATAAAACAAGACACATAG 3060
                         i   vii    i   i v iiii             iivv     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_93622076_9   3061 ACAAATGGAATGGAATAAAGAAGCCAGAAATAAATTTATACATCTATGGT 3110
                          iv        i    vi   iv           iii      i      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_93622076_9   3111 GAACTGATTTTTGACAAAGTTACCAAGAGTATACACTGGAGAAAGGATAG 3160
                         v  i       i     i v i      vi  v  v   i     i    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_93622076_9   3161 TCTCTTCAATAAATGGTGCTGGAAAAACTGGATATC-ATATGCAGAAGAA 3209
                            i     i            i v         ? - i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_93622076_9   3210 TGAAACTAGACACATATCTCTTGCCACATACAAAAAATCAAATCAAAATG 3259
                             ii i   v v  i   vii   i         - i  v        
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATG 494

  chrX_93622076_9   3260 GGTTAAAGCCTTGAACCTAGGAGATGAAACCATGAAAGTACTAAAAGAAA 3309
                          i i ?  v i i  iv  i   v i    i  i   v vi  i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_93622076_9   3310 ACATAGGGAAACATCTCTCG-GACATTGGTCTGGAGAAATATTTCTTGAG 3358
                                ?iv v    -   -   v    vi i iv  vvi      iii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_93622076_9   3359 TA--ATACCTACAAAGCATAGACAACCAAAGCAAAAAACGGGATCACATT 3406
                           -- i   - -      i ii    v    -      ii -  v -   
  L1M4_orf2#LINE/    594 TATGACACC-A-AAAGCACAAGCAACAAAAG-AAAAAATAG-ATAA-ATT 638

  chrX_93622076_9   3407 --ATGTTAAAAAAACAAAACAAACAAACAAAGACTTCTGCACA-AAAAGG 3453
                         -- iv i v-----     i-------i   i    i  ii v-v     
  L1M4_orf2#LINE/    639 GGACTTCAT-----CAAAAT-------TAAAAACTTTTGTGCTTCAAAGG 676

  chrX_93622076_9   3454 AAACAATCAACAAAGTTAAGAAACAACCCACGGGGTG--AGAAAATATGT 3501
                          v  v     v     v  i i         i ii  --         v 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_93622076_9   3502 TCAAACTACCCATCTGAGTAGGGATTAATAATCAGAATATATAAGCAGCT 3551
                         v    ii ivi      vv     i vi  vi            iv i  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_93622076_9   3552 CGAACTACCTAATAAGAAAAAAACAAA----CCAATGAAAAATTCGGTAA 3597
                          vv  v  ii     v     i     ----     v?    v v  i  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_93622076_9   3598 AATATTGTAACAGGTATTTCTCAAAAGAAGATATACA 3634
                          iv   vv  i  ii       v              
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.63 (132 / 81)
Gap_init rate = 0.03 (22 / 849), avg. gap size = 2.41 (53 / 22)  


 263 25.64 8.97 2.56  chrX_93641791_93646197      878  1033 (3374)    L1M4_orf2#LINE/L1      743   908 (0)  

  chrX_93641791_9    878 ATAAAGGTCAAATATATAGCACCTATAAAAAGCT--TAATCAAATTTACA 925
                             i  v vvi   vi  v iv      i i  --  --   v iv i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATA 790

  chrX_93641791_9    926 AGAAAAA---AAACAACCC--CTTAAA-----GCACAGGACATGAACA-- 963
                          v     ---   i     --i ?   -----   v    iv    i --
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_93641791_9    964 CACTTTTCAAAAGGAGACATACATGTGGACAGCAGTCATATACGAAAAAA 1013
                           i  i  v    i   i     vi   v  ii iv  i  --     i 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT--GAAAAGA 888

  chrX_93641791_9   1014 AGCTTAACATCACTGATAGT 1033
                         v   i       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (23 / 16)
Gap_init rate = 0.04 (7 / 166), avg. gap size = 2.57 (18 / 7)  

2931 26.69 2.93 0.68  chrX_93641791_93646197     3027  3914 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93641791_9   3027 TAGAAAGATATTCCATGTTCATGGATAAGAAGAATCAATATTGCTATAAT 3076
                          i         i              vi     v i       i  vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93641791_9   3077 GTTCATACTACCCAAAGACATTTACAGATTCAATGCAATCCCTATCAAAA 3126
                          viv     v      vvv  i           i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93641791_9   3127 TACCAATGACACTTC--ACAGAAATTTAAAAA--AATTCTAAAATTTATA 3172
                          v   iivi vi  i--i        v v  i--i  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_93641791_9   3173 TGGAGCAACAAAAGACTCAGAGTGAACAAAGATATTCTAAGTAAAAAGAA 3222
                             ivvi   ii   i    i iiv    ivv  ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_93641791_9   3223 CAAAACTGGAGGAATCACATTACCTGCCTTTAAATTATACTACTGAGCTA 3272
                             ii       v     i v  iivi  i   viv      vi     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_93641791_9   3273 TAGTAATTAAAATGATGTGCTACTG---CAAAAAAAAATGCATAGTTCAG 3319
                         i      i  i iii    v     ---i  ii v i iii    v   i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_93641791_9   3320 TGGAACAGTA--GAGAGTCTCAAGAGACAAATCCATACGTCTTCAGTGAA 3367
                              i  v --       i--   i i   i      i i vii  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_93641791_9   3368 CTCATTCTTAA-AAAAATGCCACGAATATACATTAGGGA-----CAGTCT 3411
                         i v   i ii -  iii     v  vi  v  v i    -----i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_93641791_9   3412 TTTCAATAAATGGTGCTGGGAAAACTGAATATC-ATATCCAAGAGAA--- 3457
                               i              v     i   ? - i  v   i    ---
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_93641791_9   3458 -ACTAGACTCCTATCTCTTGTCCTATGCAAAAATCAAATAATAGTAGATT 3506
                         -ii i   i    i   viii v   i       i  v v v i i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_93641791_9   3507 AAACACTTAAATCTAAGACCTAAAACTATGAAGCTACTAAAAGAAAACAT 3556
                          ? v  i     v     v          i  i  vi  i          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_93641791_9   3557 TGTGGAAACTCTCCAGAACATTGGCCCGGGCAAAAATTTCTTGAGCAATA 3606
                         v v? v  v   i ivi  v    viii     vii      -  vv  i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chrX_93641791_9   3607 AC-TCATAAGCACAGGCAACCAAAGCAAAAACGGACAAATGGGATTACAG 3655
                           -i  v       i     v    v     ii  i    v   i v  v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_93641791_9   3656 CAACTTGAAAAGCTTCTGCACAGCAAAGAAAACACTCAACA--GTGACA- 3702
                            vv v    i   i  ii vv     i v  vv    v --    v -
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_93641791_9   3703 --CAACCCACAGAATGAGAGATTATATTTGCAAACTACCCTTCTGACAAG 3750
                         --              i    vv           ii iviv     i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_93641791_9   3751 GGATTAATAACCAGAATATATAAGGGACTCAAACAACTCTACAGGAAAAA 3800
                            i vi  v             i i    vv       v i iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_93641791_9   3801 ATATATAATAATTTGATCTAAATATGGACAAAATATTTGAATAGACATTT 3850
                         i- i -     iiii  i?   v    i    iv                
  L1M4_orf2#LINE/    798 G-ACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_93641791_9   3851 CTCAAATGAAGACATACAAATGGCAAACAAAGCATATGAAAAGGTGGTCA 3900
                            v  v     i           v  i  -   i        i  v   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAA-GCACATGAAAAGATGCTCA 894

  chrX_93641791_9   3901 ATATCACTTATCAT 3914
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.00 (32 / 16)  


2031 27.07 1.81 3.11  chrX_93655157_93656919      499  1270 (493)    L1M4_orf2#LINE/L1      147   908 (0)  

  chrX_93655157_9    499 CATATGAAAAAGGCATAGGCCCTAGAATAGGAAAAAGAATCTTAAAACAT 548
                               i   -v   vi  v  i       vv    v      i   v v
  L1M4_orf2#LINE/    147 CATATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_93655157_9    549 ATGGATTAAGTAGGAGGAATCACTCTATCTGATATTGAATCTTACTATAT 598
                          v i iv    v      v    v  vi ii  v ii  v       i v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_93655157_9    599 AGCTATACTATTCAAGACAATGCAATATTGTTAGACGAATAGACACATAG 648
                              i v  v        i  iii  i  vi v v i       i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_93655157_9    649 ATCAATGGGAAAAAAAAGAGAAACCAAATACAGATTCACACAAATGTGCT 698
                                 i v i  vv    iv   i v i i ii  i   vv i  v 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_93655157_9    699 AGACTGATTTTTGACAAAGATGAAAAAGCAATTAAACAGGAAAATAGATA 748
                         vi i       i     i i  vv  ii v   v  ii  i   v -   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATA 394

  chrX_93655157_9    749 CCCTTTTAAATAAATGATATTGAAGCAACTGGGTA--CATATTAACCAGA 796
                         vi     v  i     i ii  iii       i  --  i  --i --- 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT--GC---A 439

  chrX_93655157_9    797 AAAAAAGGTAAACTTTGACATCATTCTCACGTCTTATACAAGACTTAACC 846
                            i  -- i  v  v   vi vvi     ii v       i v     i
  L1M4_orf2#LINE/    440 AAAGAA--TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_93655157_9    847 CAAAGTGGATTATAAACTTAACTATAAGATATAAAACTATACAACCCTTA 896
                             i     i ? i  i   v i     vv          v   i    
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_93655157_9    897 GGAAAAAAAAACATAGAGGAAAATTATTAAGATCTAGGGCTAGGCAAGTG 946
                          ---  i         i? v    iv iiv  i  v   i       -  
  L1M4_orf2#LINE/    538 G---AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TG 583

  chrX_93655157_9    947 GTT-CGTAGACTCGACACCAAAAACATGACCCATAAAATGAAAAAAATTG 995
                            - v    ivi          i  ii v v i    --i       v 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA--GAAAAAATAG 631

  chrX_93655157_9    996 ATAAATTGGAA---ATCAAAATTGAAAATATTTGCTGTGTGAAAGTCC-C 1041
                                   v---         i    iv    -  iv v    vv - 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGGACAC 680

  chrX_93655157_9   1042 CATAAAGAGGATGAAAATACAAGCTAT-GAA-GAGACAAAATACTTGCAA 1089
                         i  v    iii      v    v i i-   - i  v      i      
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_93655157_9   1090 CCTGAATATCTGATAAGAAACTTATATCTAGAGTATATAAAGACATCTTT 1139
                         viiiv            ii    i    i   i          vv    -
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT- 779

  chrX_93655157_9   1140 GTAAAAACATAGTAAATATAAGCAAATAAAGCAATCCAATT--AAAATGG 1187
                         --- v   vi i   ---   iv i i   -i  i      --       
  L1M4_orf2#LINE/    780 ---ACAACTCAATAA---TAAAAAGACAAA-TAACCCAATTWAAAAATGG 822

  chrX_93655157_9   1188 GCAAAGTGTTTGATGGGACATCTCACTGAAAAAAAGACATGGAAGCCTAA 1237
                               vi     vvi     i  v ii  i  i v i iii v v i  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_93655157_9   1238 TAAGTA---GGAGTAATTTTCAACATCATTAGCCAT 1270
                             i --- i ivi  vi         ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (123 / 84)
Gap_init rate = 0.03 (20 / 762), avg. gap size = 1.90 (38 / 20)  


2846 27.99 1.22 1.00  chrX_93668316_93672552.rev     2843  3746 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_93668316_9   2843 GAAAAATATTTCATGTCCATTCATTAGAAAAATTAATATTGTTAAAATGT 2892
                             i    ii     i   vv   i   i v             i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_93668316_9   2893 TAGTATGGCCCA---TGGCTATCTAC-GATTCAATTCAATTCCTGTTAAA 2938
                         i i  ivv    ---  ---      -       iv    i   i i   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTG---ATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_93668316_9   2939 ATACCTATTATATGCTTCACAGAAATAGAAAAAAAAAATCTAAAATTCAT 2988
                           v  vii iiv vi  ii       v  v  ivvi vi           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_93668316_9   2989 AAAGAACCACAAAACACTGAGAACAGACAATGTTATCCTAAGGAAAAATA 3038
                          vi   vii   iiv  iv    i  v   viiv   i i ii  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_93668316_9   3039 ACACAACTGGAGGAATTATATTGCCTTACTT-AAAATTATACTGTGGAAC 3087
                            v ii       v i i i v  iv i  -    i -    iiii i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_93668316_9   3088 CATACTAAGCAAAACAGCATGCTATTGTCATAAAAAAAACCAGAAACATA 3137
                         i i v   v   i    ii  v  i  v     ii ----i   v i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA----TAGACATATA 294

  chrX_93668316_9   3138 GACCAATGTAACTGAATAGAGAACCCACAAATAAATCCATACACCTACAG 3187
                           i     v  iv    v    ii   v       i       ii  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_93668316_9   3188 TGCACTTG-TTTTTGACAAAAGTGCCAAGAACATACACTGGGAAAAGA-C 3235
                          -  v   -    i     ii         v   v  v    i     -i
  L1M4_orf2#LINE/    345 T-CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_93668316_9   3236 AGTCTCTTTAATAAATAGTGTTGGGAAAATTGGATATCCATATGCAGAAG 3285
                              i  i  i    i   i     v  i      ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_93668316_9   3286 ACTGAAACTCAACCCCTATCTATCTCCATATAGAAAAATCAAATCAAAAT 3335
                          v    ii vi       i  vv v       v      i  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_93668316_9   3336 GGATTAAATATTTAAATCTA-GACCCCAAACAATGAAACCACTACAATAA 3384
                             i ? v ii     v  -  v iv    v  i    ivi  v  v  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_93668316_9   3385 AACATGAGGGAAAATCTCCAAGACACTGGTATGGGCAAAAATTTATTGAG 3434
                              ii ? v      i iv   vi   vv i     vii   v  iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_93668316_9   3435 CAATACCCCATAAATACAGGCAACCAAACAAAAA-TAGACAACTGGTATC 3483
                         i vv  v   v  ii   i     v   v     -    i  v v v ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_93668316_9   3484 ACAT-GAAGTGAAAAGCTTCCACATAGTAAAGGATACAATCAACAAAGTG 3532
                         v   -i  i v    i   iiiiiivvi      i  v     v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_93668316_9   3533 AGGAGACAATCCACAGATTGGGAGACAATATTGATAAACTACCCATCTAA 3582
                          ii      i       v       v      vii   ii ivi    i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_93668316_9   3583 TAAGGAATAAGTATCCAGAATATATAAGGAGCTCCAACAGCTCTATAGGA 3632
                              i ivv                 i  i   iv   i   v   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_93668316_9   3633 AAAAATCTAATAATGTGATC-AAATATGGGCAAAATATTTGAATGGACAT 3681
                             iv v     ivii  i-   v         iv        i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_93668316_9   3682 TTCTCAAAAGAAGACATACAAATGACAAACAGACATATGAAAAGGTGCTC 3731
                              v        i         i v  i ii  i        i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_93668316_9   3732 AACATCATTGATCAT 3746
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (155 / 95)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 1.54 (20 / 13)  


3269 21.50 3.81 2.13  chrX_93709093_93711319.rev      844  1736 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93709093_9    844 TGGAAAGACA-CCTATGTTTATAAATTG-AAG--TCAATATTGTTAAAAT 889
                                 i -  i     i  ii    -   -- i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93709093_9    890 ATCCATATGACCCAAAGTGATCTACAAGTTCAATATAATCTCTG-AAAAA 938
                         iv v   ivv      v         ii     iii    i  i-v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93709093_9    939 TCCCAGCAACCTTCTTATCAATGATAGAAGAACCCATTCTAAAATTTATA 988
                                vi    i  vv  ivi  v  vi i iv  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_93709093_9    989 GGTAAATTCAAGGGACGTCAAACAGCCCATAGAGTTGTACAAAAGAG--- 1035
                         v v    v        vivi  i    v v v i iv iv      i---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_93709093_9   1036 CAA----------CTCACATTTTCTGATTTCAAAACTTATTGCAAAGCTA 1075
                            ----------      i  i ii             i i        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_93709093_9   1076 CAGTAATCAAAGCAGCATGGTACTTTCATGAAGGCAGACATATGGATGAA 1125
                                   ii   ii       vv   i i ii        i   v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_93709093_9   1126 TGAAATAAAAGAGAAAGTTCAGAAATAAACCCTCACATATATGGTCAATT 1175
                           i    i  vv  i   i             vi    v           
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_93709093_9   1176 ACTTTTTGACAAGGGTTCCATGACCATCAAATGTGGAAAGAAGAATCTTT 1225
                         iv    i         v   v      iv    v        v i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_93709093_9   1226 TCAACCAACGGTGATGTGAAAACTGGATATCCACATGCAAAAGAATAAAG 1275
                              v  i    v  v  v         ?                i   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_93709093_9   1276 CTGGACCCTTACCTTAAAACATTTATAAAGATTAACTGAAATGTGGATTC 1325
                         i       i     i v v   v  i   i       v   -i     iv
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA-ATGGATCA 499

  chrX_93709093_9   1326 AAGACCTAAATATAAAAGATAAAATTGTAAAACTCTCTGTTAGAAAAAAG 1375
                         ?          i   i  v     i i         ----     i   i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT----TAGAAGAAAA 545

  chrX_93709093_9   1376 CATTCAAA-AAATGCTTCATGACACTGTATTTGGCTATGATTTCATCTAT 1424
                            vvi?i-    -    i    vi  vi  v   v   i    v vv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_93709093_9   1425 ATGAGACAAAAAGCACAGGCAAAAAAAGAAAGAA-AAATACTTTGGACTT 1473
                             v  v         i    v        i  - i   vv        
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_93709093_9   1474 CATTAAAAGTAAAAAAAAAATTATATA--TCACAGAGAC-CTA--AAAAC 1518
                            i    v      v----  v i i--   v  -   -   --  i -
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAAC----TTTTGTGCTTCAAAG-GACACTATCAAGA- 688

  chrX_93709093_9   1519 TGAGTAAAAATACAGCCCACAGAATGGAAGAAAATAATTTTACATTAAAT 1568
                         -i   i    v   i            i        v  vi v  i v  
  L1M4_orf2#LINE/    689 -AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_93709093_9   1569 ATATTGTAAAGGATTGATATCTAGAATATATCAAAAAACTTTTACAACTA 1618
                           v vi   i   i vi    i         -   i    i        -
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATAT-AAAGAACTCTTACAACT- 785

  chrX_93709093_9   1619 GACAAGAATAAAAA--------ACCCAATT-AATAATAGAGAAATAACTT 1659
                         --   v        --------        -  v   i iv   vi i  
  L1M4_orf2#LINE/    786 --CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_93709093_9   1660 GAATATCAACTTTTCTGCAAAGAAAATATACAAATGGATAATAAGCACAT 1709
                              --i  v     v       i            vi           
  L1M4_orf2#LINE/    834 GAATA--GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_93709093_9   1710 AAAAAGACACTTGTCATCACTAGCCAT 1736
                         i      ii  iiv     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (109 / 80)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.41 (53 / 22)  


2312 27.62 2.84 3.71  chrX_93730806_93733374.rev     1165  2080 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93730806_9   1165 TGAAAATATATTTCA-ATTTTTGGATTGGAAGAATCAATACTGTTAAAAT 1213
                           i   v    ii  -i  iv            v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93730806_9   1214 GTCCATACTACCAAAAGCAATTTACAGATTGAATTCAATTCTTATCAAAA 1263
                          v v     v  v   vii  i        v  iv    i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93730806_9   1264 TACCAATGACATTCTTTAAAGAAA--AAAAAA---ATTCTACAATTTTAT 1308
                          v   iivi v  i   iv     --i v  i---  i   v    i-  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC-AT 149

  chrX_93730806_9   1309 TTGCAACCACGGAAGACCCAGAGTAGACAAC-CTATCCTGAGGGTAAAAA 1357
                         v  v  vii iiii        i   v   v- v   i   ---------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--------- 190

  chrX_93730806_9   1358 AAAAAAAAAAAAAAAAAAAAAAAAAAGAATCAAATTACCTGACTCCAAAC 1407
                         -----    i  i  v   ivvii i  v   v i v  ii i i    v
  L1M4_orf2#LINE/    191 -----AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_93730806_9   1408 TATACTATAGCACTATAGTGAACAAAACAGGATGGTACTGGCATAAGTCC 1457
                         iv     i ivi   i   i v   i    vi               vvi
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_93730806_9   1458 AGACACATAGACCAAAGGAACAGAAT-AAGCATTTTACAAACAAATCCAT 1506
                              i     i   v    i     -i  - v ii v   i   i    
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAG-AGTCCAGAAATAAACCCAT 334

  chrX_93730806_9   1507 ATACCTACAGTGAACTCATTTTAAACAAAGGTGCCAAAAACATACACTGG 1556
                          i ii  ii  v  i v     vi    i        i v   v  v   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_93730806_9   1557 CAAAAAAAAAGTCTCTTCAATAAATCATCCAAGAAAAACTGTGCATCTTT 1606
                         vi   i  v     i     i    vi v vi i v     vii ? ivi
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_93730806_9   1607 ATGCAGAATAATGAAACTAGACATCTGTCTCACATCATATA--AAAATAA 1654
                              i  v      ii i   vi  ii      i      --     v 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_93730806_9   1655 AAGCAAAATGGATTAAATACTTAAATTTAAGACCTCAATCAATAAAACTC 1704
                          vv          i ? v  i     v     v  v  v v         
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_93730806_9   1705 CTAAAAGAAAACAT---TGCAAA-------AACTTTGA-TTGGGCAAACA 1743
                         i  i          ---? i   -------i  i   i-  i     vvi
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_93730806_9   1744 TTTCTTGAATTTAACCCCACAAGCACAGGCAGCCAAAACAAAAATGGACA 1793
                               ii  v i  v   v       i   i v   iv      i  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_93730806_9   1794 AACTGGATTGCATCAAG-TTAAAAAGCTTCTACACAGCAGAAAACAAAAA 1842
                           i    i v      i-       -   i iii vv  i ii   ----
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA---- 679

  chrX_93730806_9   1843 CAAAAACAAAAAACAATCAATGAAGTGAAG-GACAACC-ATTGAATGGGA 1890
                         ------------- v     vi       i-       - iv        
  L1M4_orf2#LINE/    680 -------------CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_93730806_9   1891 GAAAATATTTGCAAACTACCCATCTGAGTAAGAATTAATAACTGAAATAC 1940
                                        ii ivi      vv i i i vi  v iii    i
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_93730806_9   1941 ATAAAGAGTTCAAACAACTCTGTAGAAAAAAATCTAACTATATGATCTAA 1990
                                ii  vv       vi  iv     iv v  iv ivii  i?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_93730806_9   1991 AAATATGTTAAAGATTCAAATA--CATTTTTCAAAAGAAGACATACAAAT 2038
                             iv iv  i    ii    --     i  v        i        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_93730806_9   2039 GATGAACAGTCATATGAAAAGGTGCTGAACATAATTGAACAT 2080
                          iiv  i iv  i        i    v     v ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (153 / 96)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.33 (60 / 18)  


1993 27.14 3.19 5.05  chrX_93741840_93745123.rev     1876  2785 (499)    L1M4_orf2#LINE/L1        1   893 (15)  

  chrX_93741840_9   1876 TGGAAAGGCATTTCATGCTCATGGATTGGAAGAATCAGTATTGTTAAAAT 1925
                                ii  ii    i               v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93741840_9   1926 TGCCATACTCCTTAAAGCAATCTATAGAATAAATGCTATTCCTATCAGAC 1975
                         v  v       ii   vii     i   v v  i  v  i       i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93741840_9   1976 TACAAA-TGTCATTTTTTATAGAATTATAAAAAAACTCCTC-TAAAGTTC 2023
                          v v i-  i -      ii    --  vi v  i  vv  -    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chrX_93741840_9   2024 ATATGTAACCAAAAGAGACT--GAATAGTCAAAGCCATCCTATGGAAAAA 2071
                              v  viiv   i   i--      i    i v   i ---      
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT---GAAAAA 194

  chrX_93741840_9   2072 GAAGGA---AGCCAGAGGCATCACACTACTTGACTTCAAAGTATAATATA 2118
                             i ---  iii    vv       v iii i      iiv  v  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_93741840_9   2119 ---CTACAGTAACCAAAACAGCATGGTATTAGTACAAAATCAGACCAATA 2165
                         ---         i   i    ii     i i i i  iivi    vv   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_93741840_9   2166 CACCATTGAAACACAATAGAAAACCCAGAAATAAAGCCTCACACCTACAA 2215
                         v i  v  i  i v   v  i ii           v  vi   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_93741840_9   2216 CCATTGGATCATCAACAAAATCATCAAAAAAAAAAAAAAAAAAAAAAAAG 2265
                         i  v v   iv  i    iiviii   i vv vv----------------
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATT---------------- 378

  chrX_93741840_9   2266 AAAAAAAAACAAGGGGGAGATGACT--TTTTATTTAATAAATGGTGCTGT 2313
                         ---------   v     i -  v -- i  -  i  i           v
  L1M4_orf2#LINE/    379 ---------CAATGGGGAAA-GAATAGTCTT-TTCAACAAATGGTGCTGG 417

  chrX_93741840_9   2314 GATAACTGGCTATTTTTCTCACATAGACAGAAGAATAAA-CTGGAACCCT 2362
                           i      v  ?i-----     i--  i      i  -i    v    
  L1M4_orf2#LINE/    418 GACAACTGGATAKC-----CACATG--CAAAAGAATGAAGTTGGACCCCT 460

  chrX_93741840_9   2363 ACACTT-CATTATATATACAAATTAACTCAAGAAGGATTAAATAATTTAA 2411
                           -  i-  ii     i v            i v    i ? -i ii   
  L1M4_orf2#LINE/    461 AC-CTCACACCATATACAAAAATTAACTCAAAATGGATCAWA-GACCTAA 508

  chrX_93741840_9   2412 A----ACACCTCAAACACTAAAAATCCTAGAAGACAAGCCAGA---AAAT 2454
                          ---- v v  v    vv     v  i       v  vvi  i---    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_93741840_9   2455 ACCTTTTTGACATCAGCCTTGGTAATAAATAGTTGGCCAAGTCCCCAAAA 2504
                         --   iv    v ii vi v  i   iiv vv  i vi v v v      
  L1M4_orf2#LINE/    559 --CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_93741840_9   2505 GCAACTGTAACAGAAACAAAAACTAACAATTGGGACCTAAT-AAACTGAA 2553
                            vvv i    i  iv     ivi i  v v    i v  -   v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_93741840_9   2554 AAGCTTTCACACAACAAAAGAAACTATCAACAAAGTAAACAAACAACCTA 2603
                           i    iiii vv    i  v        v     i  v i      i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_93741840_9   2604 CACAATGGAAGAAAATGTTTGCAAACTCCT-CATTGGACAAAGATTTAAT 2652
                           v     i       i        -  v -i  iv  i  i ivi vi 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATAAGGGACTTGT 755

  chrX_93741840_9   2653 ATCCAGAATCTATAAGAAACT-TAGGAAATCAACAAACAAAAATTAAATA 2701
                                  v     ii    - viv  v    i  vv    ivi     
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_93741840_9   2702 AGGTCATT--AAAATGGAGAAAGTACATGGACTAGACAATTCTCAAAAGA 2749
                          vviv   --       iv    v iv  i -      v     v     
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAA-TAGACATTTCTCCAAAGA 854

  chrX_93741840_9   2750 AGACATACAAACGGCCAATTA--ACATAAAAA-ATGCTC 2785
                            i       i       v --    i    -      
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.03 (29 / 893), avg. gap size = 2.59 (75 / 29)  


1712 28.30 1.32 0.94  chrX_93772289_93776211     1901  2430 (1493)    L1M4_orf2#LINE/L1        2   533 (375)  

  chrX_93772289_9   1901 GAAAAAATATTTCATGTT-ATAGGTAGGAAGAATAAATATTGTTAAAATG 1949
                          i   i    ii      -  i i v      v v           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_93772289_9   1950 ACCATGCTGCTCAAAGCAATCTAGAG--TCAATGTTACTTCTATCAAACT 1997
                         i v  i  v i    vii     v  --    i iv iii        v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_93772289_9   1998 ACCAATGAAATTTTTCACAGATTTAGAGGAAACT-ATTCTAAAATTCATA 2046
                         v   iivivv     ii    vv v  v-  i  -  i            
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCATA 150

  chrX_93772289_9   2047 TGGAACCAATAAAGAGCCC-GAATAGACAAAGCAATCCTAAGCTAAAAGA 2095
                              vi-ii  i ii   -      v    i     i i ivv i    
  L1M4_orf2#LINE/    151 TGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_93772289_9   2096 ACAAAGCTGGAGGCATCACTTTACCTGACTTCAAACTACACTAGAAGGCT 2145
                               i      vv    vi v  ii i      vivi    v  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_93772289_9   2146 ATAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACTTAGACAA 2195
                          i     i   i    ii         i i  ii i     iv    iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_93772289_9   2196 ATGGAACAAAATAGAGAGCACAGAAATAAAGGGATACACCAACAACCATC 2245
                               i i   v     iv          vvv     iiv iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_93772289_9   2246 TGATCTTTG-TAAAAGTCAATAAGAATGAGCAATGAGAAAATGACTCA-C 2293
                             i  i -i  ii  -ivi    viivv     i i   -  v vi- 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAA-GAATAGTC 397

  chrX_93772289_9   2294 TATTCAATAAATGTTGCTGGGATAACTGGCTAGCCATATGTAGAAGATCA 2343
                          v     i     v        i      v  ?   i   i i    vii
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_93772289_9   2344 ATACTGGACCTCCTCCTTATACCATATACAAAAATCAACTCAAGATGGAT 2393
                          vii      i iv   i i               i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_93772289_9   2394 TAAACACTTAAATGTAAAACCCATAACTATTAAAACT 2430
                         i ? v  i         i v i v      -      
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACT 533

Transitions / transversions = 1.85 (96 / 52)
Gap_init rate = 0.02 (11 / 532), avg. gap size = 1.09 (12 / 11)  

 412 30.12 4.63 2.70  chrX_93772289_93776211     2732  2990 (933)    L1M4_orf2#LINE/L1      520   783 (125)  

  chrX_93772289_9   2732 AAAACAAAAAAAACCGTGGAAGATAACCGAGGAAATAACACT--GTAGAC 2779
                              v v    vi v i     v   vv   ?i-   vv  --  -   
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNG-TAAATCTTCGT-GAC 567

  chrX_93772289_9   2780 ATAAGACTGGACAAAAAATGTATTATGAG----GATGCCAAATGCAGCTG 2825
                         v vi ii i i   ----  vv  v v  ----  ii     v   vvv 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAA----TGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_93772289_9   2826 CAACAAAAACAAAAGT-GACAAATGGTATCTAGTTAAA-TTAAATAGCTT 2873
                                 iv    i -  i    v v ii vi i   -     - i   
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA-AACTT 662

  chrX_93772289_9   2874 CTTCACAGCAAAATAAACTATCAGCAGAGTAAA----TAATCTACACAAT 2919
                         i vii vv    iv v       iv i   i  ----i  i i   v   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_93772289_9   2920 AGGAGAACATATTTGCAAATTATTCCTCCAAGAAAGTTCTAATATCCAGA 2969
                         i      v            i  viv  ii v  i vv  vi        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_93772289_9   2970 ATCCATAAGGAACTTTAACAA 2990
                           vi    i     i v    
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAA 783

Transitions / transversions = 0.97 (38 / 39)
Gap_init rate = 0.03 (9 / 264), avg. gap size = 2.11 (19 / 9)  

 335 23.08 1.54 3.85  chrX_93772289_93776211     3301  3430 (493)    L1M4_orf2#LINE/L1      782   908 (0)  

  chrX_93772289_9   3301 AACTT--TAACAAGCAAAAACAAGTAACCATATTAAAAAGTAGGTAAAGG 3348
                             i--   i  --   i    i     vv   ?    i i  i     
  L1M4_orf2#LINE/    782 AACTCAATAATAA--AAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_93772289_9   3349 GCATGAACAGATACTTTTCAAAAAAAAAAAAAAATCATCTGGCCATCAAG 3398
                         iiv    i   i i  i  v   i  i v v ---  vv      vi   
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATA---CAAATGGCCAATAAG 876

  chrX_93772289_9   3399 CAAATGACAAAATGTTCAACATCACTAATCAT 3430
                           v    v  i   i         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (18 / 11)
Gap_init rate = 0.02 (3 / 127), avg. gap size = 2.33 (7 / 3)  


1658 28.87 0.35 5.11  chrX_93809485_93811728.rev      509  1076 (1168)    L1M4_orf2#LINE/L1        1   541 (367)  

  chrX_93809485_9    509 TAGAAAAACATTCCATGCTTACGAATAAGAAGAGTCAATATTGTTAAAGT 558
                          i    i i  i     i i i i  vi     v i           ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93809485_9    559 GTCCATACTGCCTAAAGCAGTTTATGATTTTAATGCTATTCCCATCAAAC 608
                          v v     v  i   viii i  iiiv  i  i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93809485_9    609 TATCAATGATATTCTTCACAGAAATAAAAAAAAAACT-ATTTTAAAGTTA 657
                          vi  iiviiv  i  ii       ---vi v  i  -  ii    i  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT---TGACAAGCTGATCCTAAAATTC 147

  chrX_93809485_9    658 ATATGGAACAACAACAAAATATCCCGAATAGCCAAGGCAATCCTAAGCAA 707
                                 -- i-i   iiv i  v          ii     i i iv  
  L1M4_orf2#LINE/    148 ATATGGAA--AT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_93809485_9    708 AAAGAACAAATCTGAAGAAATTTTTCTACCAAACCTCAAACTGTACTGCA 757
                         i         vi  i  i v iviv  v  v  ii     viv    i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_93809485_9    758 GGGCTGCAGTAACCAAAACAGCATGGTACTGGTAAAAAAAACAAACAAAC 807
                         ii   i      i   i    ii         i v  ii ----------
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA---------- 284

  chrX_93809485_9    808 AAACAAAAAAAAACGGACACATAGAACAAGGGAACAGAATAGAGAGCCCA 857
                         -------------ii    i     v   v    i     v     i   
  L1M4_orf2#LINE/    285 -------------TAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_93809485_9    858 TGAATAAGGTCACACACATACCACCATCTGATCTTTGATAAAGCTGACAA 907
                         vi     ivi  i   iv  ivii  vi    i  i  i  i v  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_93809485_9    908 AAACAAGCAATGCGGAAATATCTGTCTATTCAATAAATAGTGCTGAGTTA 957
                         i v  vv     v     v viv    v     i    i      i vi 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_93809485_9    958 ACTGGCTAGCCATATGCAGAAGACTGAAACTGGA-TGCTGCCTTATACCA 1006
                              v  ?   i     i    v    ii    -iv  i   i i    
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_93809485_9   1007 TAAACAAAAATCAACTCAAGATGAATTAAAGACTTAGATGTAAAAACCAA 1056
                           v        i       i   i  i ?    i  i      i i i  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_93809485_9   1057 AACTATAAAAACCCTAGAGG 1076
                                   vi i    i 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAG 541

Transitions / transversions = 2.18 (111 / 51)
Gap_init rate = 0.01 (6 / 541), avg. gap size = 5.17 (31 / 6)  

 632 23.25 4.14 6.37  chrX_93809485_93811728.rev     1451  1764 (480)    L1M4_orf2#LINE/L1      602   908 (0)  

  chrX_93809485_9   1451 CAAAAGCAATTGCAATAAAAGCAATAATTGAGAAATGGGATCTAATTAAA 1500
                                 vvv    i     v  v   v  v    v   ii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_93809485_9   1501 -TTAGAGAGCTTCTGCATAGTGCATAGCAAAAAAAAAAAAGCTATCAACA 1549
                         -   i i -   i  -----   v --    ii v -----       v 
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTG-----TGCTT--CAAAGGACA-----CTATCAAGA 688

  chrX_93809485_9   1550 GAGTAAACAGACAACCTACAGAATGAGAGAAAATTTTTTTAAAT-ATACC 1598
                         i   i  v        i        i        v   vi    -   iv
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_93809485_9   1599 TCTGACAAAGGTCTAATATCCAACATTTATAAGGAACTTAAATAAATTTA 1648
                              i  i  v  vi      iv  v     i     ivv i  v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_93809485_9   1649 GAAGAAAAA---AAATG-CCT--TTAAAAAGTGAACAAAGAACATGAACA 1692
                         v  v     ---    i-  i--  ?    i  ii     i iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_93809485_9   1693 GACACTTTTCAAAAGTGATTTTAATATATCCA----GTGAACAAGCATAA 1738
                             i  i  v    -------  v    v  ---- iv  i     i v
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAG-------AAGATATACAAATGGCCAATAAGCACAT 881

  chrX_93809485_9   1739 GAAAAAAAG-TCAATGTCATTGATCAT 1764
                              i v -    ii   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (39 / 33)
Gap_init rate = 0.04 (12 / 307), avg. gap size = 2.75 (33 / 12)  


2998 27.35 0.66 1.31  chrX_93824978_93829522.rev     3141  4054 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93824978_9   3141 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATTAATGTTGTGAAAAT 3190
                              ii i  i     i        v      v     i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93824978_9   3191 GGCCATACTGCCCAAGGAAATTAATAGATTCAATGCCATCCCCATCAAGC 3240
                            v     v     ivvi  iv i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93824978_9   3241 TATCAATGACTTTCTTCACAGAATTGGAAAAAAAGTACTTTAAAGTTCAT 3290
                          vi  iivi i  i  ii     v v  v  ivv - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chrX_93824978_9   3291 ATGGAACCAAAAAAAGAGCCCAAAAAAGATTTTGCAAGACAATCCTAAGC 3340
                               -- viv  i ii    i  v  v-----   i      i i iv
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGC-----CAAAACAATCTTGAAA 192

  chrX_93824978_9   3341 AAAAAGAACAAAGCTGGAAGCATCACGCTACCTGACTTCAAACTATACTA 3390
                           i          i    i vv    i  v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_93824978_9   3391 CAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATA 3440
                            i          i   i    ii         i iv ii i   v   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_93824978_9   3441 TAGACCAATGGAACTGAAC--AGAGCCCTCAGAAACAATGCCACACATCT 3488
                             i        iv   i--    i  --     i  vv   i    i 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTT 340

  chrX_93824978_9   3489 ACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGTGAAAG 3538
                          iiii  vi    i  i     ivv  v   i v  vv      v     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_93824978_9   3539 GGTTCCCTATTTAATAAAAGGTGCTTGGAAAACCGGCTAGCCATATGTAG 3588
                         ii vvi  v  i  i   v      v   v   i  v  ?   i   i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_93824978_9   3589 GAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAA 3638
                         i iiv    ii    i    v   i     v              i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_93824978_9   3639 TATGGATTAAAGACTTAAATGTTAGACCTAAAGCCATAAAAACCCTGGAA 3688
                         v      i ?    i       v   v     i i      vi i i   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_93824978_9   3689 GAAAACCTAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTC 3736
                               v    ?-   --i -   iv   v v  vv i     v ii   
  L1M4_orf2#LINE/    541 GAAAACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_93824978_9   3737 ATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATG 3786
                         v ivv  vi            vvi          vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_93824978_9   3787 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCA 3836
                            ii v  i   v v  i i   i  ii vv    i  v    i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_93824978_9   3837 GAGTGAACAGGCAACCTACAGAATGGGAAAAAATTTTTGTAATCTACCCA 3886
                         i      v  i     i           i     v    i  vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_93824978_9   3887 TCTGACAAAGAGCTAATATCCAGAATCTAAAAAGAACTTAAACAAATTA- 3935
                              i  i ii  vi          v  v        ivv    v i -
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_93824978_9   3936 CAAGAAAAAATCAAACAACCCCATC-AAAAGGGGGCAAAGGAGATGAACG 3984
                         i  v     iv    i     v  i-    iv          vv    ii
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_93824978_9   3985 AACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAA 4034
                         i   i     v        i  vi viii     i ii          i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_93824978_9   4035 TGCTCATTATCACTGGTCAT 4054
                               vi    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


2591 27.67 2.09 1.98  chrX_93857779_93862341.rev     3166  4072 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93857779_9   3166 TGTAAGGACATTTCATGTTTATGAATAGAATAAATTTATATTGTCAAAAT 3215
                           v  i  i  ii      i   i  v i vi v  v       i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93857779_9   3216 GACCGTACTACCCAAAGTAACCTATAGATTCAATTTCATTCC-ATTACAA 3264
                          i vi    v      v i i   i        iviv  i  -  i v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93857779_9   3265 TACCAATT----TCTTCACAGAAATAGAAAAAGCAATTATAAAATTTATA 3310
                          v   ii ---- i  ii       v  v  ivii  iv       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_93857779_9   3311 TGGAATCACAAAAGACCCCGGATGGCAAAAGCAATCCTGAGCAAGAAGAA 3360
                              vii   ii     v i  i  v   i     i   iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_93857779_9   3361 CATAACTGGAGGCATCACACTACCTGACTTTAAAACACACTGGAAAGCTA 3410
                           v ii      vv       v  ii i  i     vi   iv       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_93857779_9   3411 TTGTAACCCAAACAACATGGTACTGACATAAAAATATAATAACAGACACA 3460
                         iv    i v i   iii        i     ii   --------    i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA--------GACATA 292

  chrX_93857779_9   3461 AAGACCCATTGAATAGAAATAGATAACCCAGAAATCAATCCATGTATTTA 3510
                         v   i v  v        v -  v ii        v  i    ii     
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_93857779_9   3511 CACCCAACTGATTCTCGACACA--TCTCAAGAATATCCTTTGAGGAAAGG 3558
                         iivi   i     i      vi-- vi     vi  i vv  i      i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_93857779_9   3559 ACAGTCACTTTAATAATTGATGCTGATAAAACTGGATATTCATAGTCAGA 3608
                          i    vi  i  i  v  i     iv v         ?i  i vv  i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_93857779_9   3609 AGAATTAAACTAGAACCCTATGTCTTACCATATTCGATAATTAACTCAAA 3658
                              v  ii i  v     iv  vi       v i v            
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_93857779_9   3659 ATAGATGAAAAACTTAAAAGTAAGACCAGAAACTACGATAAAACTACTAA 3708
                           i   v ? i  i    v      v vi      ---       vi  i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA---TAAAACTCTTAG 538

  chrX_93857779_9   3709 AAGAAAACGTAGAGG-AAATGCTTCAGGAGTTTGGTTTGGGAAAATGTTT 3757
                                 i   i? -    -    iv  vi    v  i  v  vv    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_93857779_9   3758 TATAAATAAGACCTCAAAAACACACACAACAAAAACAAAAATAGACAAAT 3807
                         iv  i   v   vi     i    vi        iv         i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_93857779_9   3808 GGGATTAAAT-GAAACTAATGAATCTCTGCACCACAATGAAAACAATCCA 3856
                         v   i vv  -i   i   -i  ii i  ii iv   v i v  v   v 
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_93857779_9   3857 CAGAAGGGA---GACAACCTGTAGAATGGGAATAAAATATTCACAAACTA 3903
                         v -   v  ---       iii         i-        ii    ii 
  L1M4_orf2#LINE/    687 GA-AAGTGAAAAGACAACCCACAGAATGGGAG-AAAATATTTGCAAATCA 734

  chrX_93857779_9   3904 TTCATCTGATAAGGAA-TTATATCCAGAATATACAAGAATTTCAAACAAC 3952
                          vi           i -  i             i  ii vi  vv     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_93857779_9   3953 TCAACAG-AAAAATAATAATAATCTGATGAAAAAGTGAGCAAATAATGTC 4001
                             i i-     v vv     i ii  v?    i  i     vi  v v
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_93857779_9   4002 AATACATAT-----CAAATAAAGTCATACAAATAACCAACAGATATATTT 4046
                             v i  -----    v  ii -        ii    i iii i  vv
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGAT-ATACAAATGGCCAATAAGCACATGA 883

  chrX_93857779_9   4047 TCAAAATACTTAACATCACTTATCAT 4072
                         -v  i  i  i       ????????
  L1M4_orf2#LINE/    884 -AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (153 / 94)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.06 (37 / 18)  


2863 27.64 1.89 1.22  chrX_93900595_93907300.rev     5315  6215 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_93900595_9   5315 GGAAAAACATTCCATGCTCATGGATAGGAAGAATCAGTATCGTGAAAATG 5364
                              i i  i     i        v      v i i   i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_93900595_9   5365 ------CTGCCCAAAGTAATTCATAGATTCAATGCTATTCCCATCAAGCT 5408
                         ------  v      v i  ii i        i  v  i  i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_93900595_9   5409 ACCATTGACTTTCTCTGCAGAATTAGGAAAACCTACTTTAAATTTCATAT 5458
                         v   vivi i  i i       v v iv  i iv iii    v       
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_93900595_9   5459 TGAACCAAAAAGTAGCCTGTATAACCAAGACAATCCTAAGCAAAAAGAAC 5508
                         v   viiv  i v v  v v   i    i      i i ---       -
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAA- 197

  chrX_93900595_9   5509 AAAGGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAA-----CTAT 5553
                         ----        i      vv    i  v  ii i      -----   i
  L1M4_orf2#LINE/    198 ----GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_93900595_9   5554 A---CTACAGTAACCAAAACAGCGTGGTACTGGTACCAAAACAGATATAT 5600
                          ---         i   i    i          i iv ii i   i    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_93900595_9   5601 AGACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATTTACA 5650
                            i        i    iv   ivii         vv   i       ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_93900595_9   5651 ACCATCTGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGGATAGGAT 5700
                         ii  vi    i  i i   ivv  v   i v  vv         v  i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_93900595_9   5701 TCTGTATTTAATAAACAGTGTTGGGAAAACTGGCTAGCCATAGGCAGAAA 5750
                         vv v v  i  i   ii   i     v      v  ?   i v   i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_93900595_9   5751 ACTGAAACTGGACGCCTTCCTTACACCTGACACAAGAATCAACTCAAGAT 5800
                          v    ii     v   v   i     vv i    i   i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_93900595_9   5801 GGATTAAAAACTTAAATGTAAGACCTAAAACCATAAAAACCCTAAAAGAA 5850
                             i ? i  i           v       i      vi i  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_93900595_9   5851 AACCTAGGCAATATTGTTCAGGACATAGGCATGGGCAAAGACTTCATGAC 5900
                            v    ?ivv v v   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_93900595_9   5901 TAAAATGCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATTGGATC 5950
                           vi ii         vvi          vv     v  i        ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_93900595_9   5951 TAATTACACTAAAGAGCTTCTGCAACGCAAAAGAAACTACCATCAGAGTG 6000
                          v  i v v v  i i   i  iiviv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_93900595_9   6001 AAAAGGCCACCTACAGAAAGGGGGGAAATTTTTGCACTCTATCCATCTGA 6050
                              i v   i      v   i i    v      vvii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_93900595_9   6051 CAAAGGGTTAACATCCAGAATCTACAAGGAACATAAACAAATTTACAAGA 6100
                         i  i  ii vii         v  i  i    vivv    v ---   v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATA 790

  chrX_93900595_9   6101 A-AAAAAAACAAACAACCCCAACACAACGTGGGCAAAGGATATGAACAGA 6149
                          -     i     i     v vi?v  vi            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_93900595_9   6150 CACTTCTCAAAAGAAAACATTTATGTGGCCAACAA--ACATGAAAAACAG 6197
                           i     v      i i  vi vi       i  --         ivv 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_93900595_9   6198 CTCATCATCACTGGCCAT 6215
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 3.50 (28 / 8)  


2549 25.89 4.49 1.27  chrX_93918433_93921129     1336  2204 (493)    L1M4_orf2#LINE/L1       12   908 (0)  

  chrX_93918433_9   1336 CCAATGATCATGGATAGGTAGAAACAATATTGTGAAAATGACTATAGTGC 1385
                           v   v        v  v   vvi        v  i   i v   v v 
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chrX_93918433_9   1386 CAAAAGCAATCTACAGATTAAATGCAATTTTCATCAAAATACC-GCTATC 1434
                          v   vii           v  i     iiii        v  -   ii 
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chrX_93918433_9   1435 ATTTTTCACAGAACTAGAAAATGC-AATCCTAAAATTTATATGGAATAAA 1483
                         -     ii     v v  v  -  -i           i        - vi
  L1M4_orf2#LINE/    112 -TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATGGAA-ATG 158

  chrX_93918433_9   1484 GAAAAGAGCCTGCATAGGCAAAGCAAAACTT-----AGAAAAA-AAATCT 1527
                         v  ii  v  v v    v    i   v-   -----    i  -   vi 
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAACAAAGTT 207

  chrX_93918433_9   1528 GGAGGCATCACATCACCAGACTTCAAACTATACTATAAGGCTATAGCCAC 1577
                              vv     iiv  vi i      viv     i  i    i  iv i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_93918433_9   1578 CAGAACAATATGGTACTGGTGTAAAAATAAGCATACAGATCAATAAAACA 1627
                           ii   i i         ii   ii   ii    i        ii  i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_93918433_9   1628 GAAGAGATAACCCACAAATAAAGCCAAATACTTACAGACAACTGATCTTC 1677
                            vv  v ii   v       v   v i i   ii v   i    i   
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_93918433_9   1678 GACAA-----------------AACAGGAAAAGGACACCCTATTCAACAA 1710
                              -----------------  ii  i    i i vi  v        
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_93918433_9   1711 ATGGTGCTGGGATATTTGGCAAGCCACACACAGAAGAATTAAACTAGATT 1760
                                     i vi   vv ?     ii  i      v  ii i  ii
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_93918433_9   1761 CTCATCTATCACTTTATACAAAAATCAACTCAAGATGGACCAAAGATTTA 1810
                          ii i  vv   iv           i       i     i  ?   ii  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_93918433_9   1811 AATTTAAGACGTGAAACCATAACAATTCT-AGAAGACAATATCAGAAATA 1859
                            v     vv i    i    -  i   -      v  i  -  i?i  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACAT-AGGNGTA 555

  chrX_93918433_9   1860 C-TCTTCTAGACACTGCCTTAGGCAAAACTTTAT--GATCAAGGAC-CCA 1905
                         v-     vv   vi  vv        viv   v --   -- v   -   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGACACCA 603

  chrX_93918433_9   1906 GAAGCAAATGCAACAAAAACAAAGATATACAGATGGGACTTAATTAAACT 1955
                         i     v v         iv   i   v i i  v      v  i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_93918433_9   1956 AAAAAGCTTCTGCACAGCCAA--ACA--ATCAGCAGAGTAAACAGACAAC 2001
                         v    i   i  ii vv v  --   --    iv i   i  v       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_93918433_9   2002 CCATAGAGTGGGAGAAAATCCTCACAAACTATGCATCTGACAAAGGACCA 2051
                            i   i           vi ii    ii  ii      i  i    iv
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_93918433_9   2052 TTATCTAGAATCTACAAGAAACTC----AAATCAGCAAGAAAAATGCAAA 2097
                         v    i     v  i  ii     ----  v   ii  v     vi    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_93918433_9   2098 CAATCCCATCAAAAAAGTGGGCTATGGACATGAGTGGAAAAGTTTCAAAA 2147
                         i  i  v  i?     -     v v   iv   i i  v vv i  v   
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_93918433_9   2148 GAAGATATACAAATGGCCAA-AAACAGTATGAAAAAAATGCTCAACGTTA 2196
                                             -  i  -i       i -        i i 
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCA-CATGAAAAGA-TGCTCAACATCA 900

  chrX_93918433_9   2197 CTAATTAT 2204
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.46 (131 / 90)
Gap_init rate = 0.03 (23 / 897), avg. gap size = 2.17 (50 / 23)  


3296 27.09 0.33 0.33  chrX_93923020_93931142     4874  5781 (2342)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_93923020_9   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4923
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93923020_9   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 4973
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93923020_9   4974 TACCAATGACTTTCTTCACAGAATTGGAAAAAACGACTTTAAAGTTCATA 5023
                          v   iivi i  i  ii     v v  v  ivi  iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_93923020_9   5024 TGGAACCAAAAAAGAGCCCGTATCGCCAAGTCAATCCTGAGCCAAAAGAA 5073
                              viiv  ii  v  v v  v     iv     i   ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_93923020_9   5074 CAAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGGCTA 5123
                              i      vv   i   v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_93923020_9   5124 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5173
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_93923020_9   5174 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAGCTAT 5221
                              i    i--    i  --        vv  ii i  i  ii ii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_93923020_9   5222 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5271
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_93923020_9   5272 ATTTAATCAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5321
                         v  i  iv             v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_93923020_9   5322 AACTGTATCCCTTCCTTATACCTTATACAAAAATCAATTTGAGATAGATT 5371
                          ii  v i    v   i i   v           i  i ii i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_93923020_9   5372 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5421
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_93923020_9   5422 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5470
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_93923020_9   5471 ACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGGATCTAAT 5520
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_93923020_9   5521 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5570
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_93923020_9   5571 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5620
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_93923020_9   5621 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5670
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_93923020_9   5671 AACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCT 5720
                         i     i     v  i?    i     i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_93923020_9   5721 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCA 5770
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_93923020_9   5771 TCACTGGCCAT 5781
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  

2331 26.30 3.40 2.38  chrX_93923020_93931142     6751  7632 (491)    L1M4_orf2#LINE/L1       18   908 (0)  

  chrX_93923020_9   6751 TTCATGGATTAAAAGAATCAATACTGTTCACATGTCCATGCTACCCAGGC 6800
                                   ii    v i    i    v v   v v  i  v    iii
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_93923020_9   6801 -AATCTATAGATTCAATGCAATCCCAATCAAAATACCATTGATG--TTCT 6847
                         -i     i        i        v        v   -- v  --  i 
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA--GCTGCCTTTT 115

  chrX_93923020_9   6848 TTACATCAATAGAAAAA--AATTT--AAATTCATATG-AAATACAATAGG 6892
                           i  vv   v  v  i--i  ii--           -    i   -i  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA-GGG 164

  chrX_93923020_9   6893 ACCCAGAATAGCCAAG-TGATCCTGAATATAGAAAGAAGAAATTTGGAGA 6941
                                        i-ii   i    v -    -   v   v      i
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAA-AGAA-GAACAAAGTTGGAGG 212

  chrX_93923020_9   6942 AATCACATTACCTGACTTCAAATTATACTTCAGAGTTATATTAACCCAAA 6991
                          v     i v  ii i      viv    v  i  i  i v   i v i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_93923020_9   6992 TGTCAG---GGTATTGGCATAAA-ACAGTTATGTACACCACTGGAACTGC 7037
                         ---   ---    i        i- i  vi  i  v i  v     iv v
  L1M4_orf2#LINE/    263 ---CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_93923020_9   7038 ATAAAGAACCCATAAGTAAATTCATACATCTATAATAAACTCATTT-AAA 7086
                           vi   ii   v  i    ii       i   ii v  i v    -vi 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_93923020_9   7087 CAAAGCTGTCAAGAAACTACCTTG-GGGGAAAAAACATTCTT--CAATGA 7133
                            i v  i     -- i iiivi-       i  i v    --   ii 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGA--CCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_93923020_9   7134 ATGTTGCCAGGAAAATTGGGATATCTGTATGCAGAAGAATAAAACTAGAC 7183
                            v   ii   v  i   -   ? iii     i      i  ii i   
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGG-ATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_93923020_9   7184 CACTATCTCTCACCATATTCAAACAGCAAATCAAAATGGGTTAAAGACGT 7233
                          v   i   v        v    v vi  v         i i ?    v 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_93923020_9   7234 AAATATAAGACCTCAAACTTTGAAACTTCTGAAAGAAAAC-TGGACA-AA 7281
                             i     v  v     v i     ii ii        - i i?i-  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_93923020_9   7282 CTCTCTCA-GACATTCGTCTGGGGAAAAAAAAAAAATTATTGAGCAAT-A 7329
                         v   -  i-   v  v vi i  v  vii-------  vi v  vv  - 
  L1M4_orf2#LINE/    557 ATCT-TCGTGACCTTGGGTTAGGCAATGG-------TTTCTTAGATATGA 598

  chrX_93923020_9   7330 CCCCACAACCATAGGCAACCAAAACATAAATGGACAAATGGCATACTATC 7379
                          v   v  v  i i     v   iv v    i  i    v v ivii   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_93923020_9   7380 AAG-TTAAAA---TCCGCATACCAAAGGATACAATCAACAAGGTGAAAGG 7425
                           i-      --- ii iiivi       i  v     v  i      i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_93923020_9   7426 -CAACATACAAAATGGAATTAAAATATTTGCAAACTACATCTCTT-CAAA 7473
                         -    vi   i     i v-              ii i  v   v-i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAG-AAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_93923020_9   7474 TGATTAATAACCAGTATGTATAAGAAGCTCAAACAACTCATTA-TAAAAA 7522
                         v  i vi  v    v  i     ii i   vv        v  -      
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_93923020_9   7523 -ATAA-TAATAAAATTTAAAAATTGGGCCAAAAATTTGAATAGACATTTA 7570
                         - i  -   ivv    ?      -    v  ii                v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAAT-GGGCAAAGGATTTGAATAGACATTTC 846

  chrX_93923020_9   7571 TCTAAAGAGGACATACAAATGGCAAACAAGTATCGAAAAATTTGCTCAAA 7620
                           i     i  i           v  i   i ivvi    vv       v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_93923020_9   7621 ATGACTGATCAT 7632
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (136 / 92)
Gap_init rate = 0.04 (33 / 891), avg. gap size = 1.55 (51 / 33)  


2344 27.61 4.35 1.88  chrX_93943165_93947745.rev     3231  4081 (500)    L1M4_orf2#LINE/L1        1   872 (36)  

  chrX_93943165_9   3231 TGGCAAAACATCTGATGCTCATGAATTAGTATAATTAATACTGTAAACTT 3280
                            v  i i   iv   i     i   i v v v      i   v  vv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93943165_9   3281 GACCATACTTTCCAAAGCAATCTACCTATTCAA-----TTCTTATCAAAA 3325
                          i v     ii     vii      vv      ----- i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93943165_9   3326 TATTAATAAAAATTTTCAAAGAAATATTTTTAAAAAACT---TCAAAAAG 3372
                          vii iivivvv    iiv      ----- i v  i  ---i v    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-----TGACAAGCTGATCCTAAAAT 145

  chrX_93943165_9   3373 TCATGTGGAAGCACAAAATGCCCCAAATAGTAAGACCAATACTGACAAA- 3421
                             i     iii   iivi   vi     iv i v    vi   v   -
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_93943165_9   3422 AAGAACAAAGCTGGAGGTGTCAAAGTACCTGACTTTAAA-TTTACTGCAA 3470
                                   i      vv   v v v  ii i  i   -i     i   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_93943165_9   3471 AGCTATAGTAACAAAAACAACATGTTATTGGTATAAAAACAGACACATAG 3520
                              i     iv  i   iii  v  i   i    ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_93943165_9   3521 ACCAATAGAACAGAATAGAGGACACAGAAATAAATCCATG--TTTATAGC 3568
                          i    i   i     v   iiiv          i    i--     i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_93943165_9   3569 CAACTGATTTTTTTACAAAGGTGCTGAGGGCTTACAGTGGGCAAAATACA 3618
                            i       iv-    i     ii  iv v v  i    v   iv i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_93943165_9   3619 -TCATCTTTAACAAATGATTCTGGGAAAACTGGATATCCACA---AGGAG 3664
                         -  - i  i        i v      v         ?     --- ii  
  L1M4_orf2#LINE/    395 GTC-TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_93943165_9   3665 AATGAACCTAGACCCCTGTGTCTAACAACATACAAAAATCAACTCAAAAT 3714
                               vi i       iiv  vv  v i          i          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_93943165_9   3715 GCATTAAAGACTTAAG--------------CTTTGAAACTACCAGAAGAT 3750
                          v  i ?    i   i--------------  v i     vii      v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_93943165_9   3751 AATATAATGGTAATCCTTCAGGGCATTAACATGTGCAAAGATTTTATAAG 3800
                           i   iv?    vi    iv i v  iivv iv    v i   iv  ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_93943165_9   3801 TA--ACACTTCAAAATAACAGAAAACAAAACCAGAAATAGACAAATGGGA 3848
                           --    --     vv   iiv       vv i       i    v   
  L1M4_orf2#LINE/    594 TATGACAC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_93943165_9   3849 ATATATCAAACTAAAAATCTTCTGTATAGCAAAGAAAA--A--AAAAGAG 3894
                         v vi      v v    v   i   iivv     i v -- --  i i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_93943165_9   3895 TGAAGAGAAAACCTGGAGAATGAGAGAAAACATTTGTAAACCATCTATCT 3944
                             i   v    iiv      i       i     i   i   v     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_93943165_9   3945 AACAATAGACTAATAGCTAGAATATACAAAGAACTTAAACAACTCAACAG 3994
                         i i  vi    vi  v i        i        ivv         i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_93943165_9   3995 CAAACAATAATAATCATTGTCATCTGACT-AAAATTAGACAAAGGATCTG 4043
                         i   -  -i i  -----i v i ii i -    v i i        i  
  L1M4_orf2#LINE/    792 TAAA-AA-GACAA-----ATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_93943165_9   4044 AACAGATATTTCTCAAAAGAAGACATACAGATGGTCAA 4081
                           i   i       v        i     i    i   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

Transitions / transversions = 1.67 (145 / 87)
Gap_init rate = 0.02 (19 / 872), avg. gap size = 2.79 (53 / 19)  


2824 26.25 1.43 1.19  chrX_93957383_93962683.rev     3973  4810 (491)    L1M4_orf2#LINE/L1       69   908 (0)  

  chrX_93957383_9   3973 GAATTACAAAATCTTCAATGCCACCCCCATCAACCTACCAGTGACTTTCT 4022
                           vi    i ---     i  v i   i     vv v    ivi i  i 
  L1M4_orf2#LINE/     69 GATCTACAGA---TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_93957383_9   4023 TCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAA 4070
                          ii     -   -- v  i  - iii    i           -- viv  
  L1M4_orf2#LINE/    116 TTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAA--ATGCAA 161

  chrX_93957383_9   4071 GGGCCCCC--ATTGCCAAGACAATCCTAAGCCAAAAGAACAAAGCTGGAG 4118
                            v   v--  v     i      i i ivv i          i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_93957383_9   4119 GCATCACTCTACCTGACTTCAAAATATACTACAAGGCTATAGTAACCAAA 4168
                          vv    v  v  ii i       iv        i    i     i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_93957383_9   4169 ACAGCATGGTACTGGTACCAAAGCAGAAATATAGACCAATGGAACAGAAC 4218
                             ii         i iv iiii   v       i        i    i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_93957383_9   4219 --AGAGCCCTCAGAAATAATACCACACATCTACAACCATCTGATCTTCGA 4266
                         --    i  --        vv   i    i  iiii  vi    i     
  L1M4_orf2#LINE/    312 TGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_93957383_9   4267 CAAACCTGACAAAAACAAGAAATGGGGAAAAGATTCCCTATTTAATAAAT 4316
                            ivv  v   i v  vvv          ii  vvi  v  i  i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_93957383_9   4317 GGTGCTGGGAAAACTGTCTAGCCATATGTAGAAAGCTGAAACTGGATCCC 4366
                                   v     vv  ?   i   i i  iiv    ii    i   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_93957383_9   4367 TTCCTTACATCTTATACAAAAATTAATTCAAGATGGATTGAAGACTTAAA 4416
                          v   i   i v              i    i      ii?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_93957383_9   4417 TGTTAGATCTAAAACCATAAAAACCGTAGAAGAAAACCTAGGC-CATACC 4465
                            v   v       i      vi v           v    ?-i v i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_93957383_9   4466 ATTCAGGACATAGGCATGGGCAAGGATTTCATGTCTAAAACACCAAAAGC 4515
                         -   iv   v v  vv i     v i    v ivv  vi           
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_93957383_9   4516 AATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTCAAGA 4565
                          vvi          vv     v  i    v   ii v  i   v i  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_93957383_9   4566 GCTTCTGCACAACAAAAGAAACTACCATCAGCATGAACAGGCAACCTACA 4615
                         i   i  ii vv    i  v    i  vv ivi    v  i     i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_93957383_9   4616 GAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAGGGCTAATATC 4665
                                       v       vii ivi      i  i  i  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_93957383_9   4666 CAGAATCTACAATGAACTCAAACAGATTTATGAGAAAAAAACAA----CC 4711
                               v  i  v      vv   iv iv  i v     i    ----  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_93957383_9   4712 CCATCACAAAGTGGGTGAAGGATATGAAGAGACACTTCTC-AAAGAAGAC 4760
                          v  i?v   i    ii      v    v     i     -        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_93957383_9   4761 ATTTTTGCAGCCAACAGACACATGAAAAAATGCTCATCATCACTGGCCAT 4810
                           vivviii     i ii          i       v     ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (126 / 90)
Gap_init rate = 0.01 (12 / 840), avg. gap size = 1.83 (22 / 12)  


1818 27.49 1.08 0.90  chrX_93984698_93987735     1197  1749 (1289)    L1M4_orf2#LINE/L1        1   554 (354)  

  chrX_93984698_9   1197 TGGAAAGATGTCTCATGTTCATGGATTGAAACAATCAATATTGTTAATAT 1246
                                  i  i               i  v v i           v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_93984698_9   1247 GTCCATAGTTCACAGAGCAATCTATATATTTAATACAATCCTTATCAATA 1296
                          v v   v i v  i vii     i v   i  ii      i      v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_93984698_9   1297 TACCAATGACATTATTCAAAGAAATAAAAAAA--AATCCTAAAATTTATA 1344
                          v   iivi v  v  iiv      vi v  i--i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_93984698_9   1345 TGGAACCACCAAAGACCCAGAAGAGCCAAAGCTATGTAAAGCAAAAAGAA 1394
                              vii v ii         v       i v  v vi iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_93984698_9   1395 CAAAACTGGAGGAATCACATTACCTGGCT-CATAAATTATAATACAGAGC 1443
                             ii       v     i v  iiii -  -   i -  v    i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCA-AAACT-TACTACAAAGC 248

  chrX_93984698_9   1444 TA-AGTTAACCAAACTGATGTGGTGCTGGCATAAAAACTGAGAAATAGA- 1491
                           -   -  i   iviii      i         ii iv  v v     -
  L1M4_orf2#LINE/    249 TACAGT-AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_93984698_9   1492 -AATGTAGAACAAAATAAAGAACCCAGAAATAAACGTATAGATCTACAGT 1540
                         -    --   i i   vi   ii            vi   v  i  ii  
  L1M4_orf2#LINE/    298 CAATG--GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_93984698_9   1541 GGACTCATTTTCAAAAAAGTTTACAAGAATATGCATTGGAGAAAGGACAG 1590
                         vi i v      i v  i v vv     vi  v  v   i     i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_93984698_9   1591 TCTCTTCAATAAATGGTGCTGAGAAATCTGAATATGCATATGCAGAGGAA 1640
                            i     i           i  v v   i   ?v  i     i i   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_93984698_9   1641 TGAAACTTGACACCTATCTCTCATCTTATTAAAAAATCAAACCAAAATGA 1690
                             ii v   v    i   v  i v   vv      i  vi       i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_93984698_9   1691 GTTAAATGCTTAAATCTAAGACCTCAAATTATGAAAATGGTAAAATAAAA 1740
                         i i ? vi i     v     v  v   i   i   v vv  i  v    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_93984698_9   1741 TATTGGGGT 1749
                         i  v  ?  
  L1M4_orf2#LINE/    546 CATAGGNGT 554

Transitions / transversions = 1.40 (87 / 62)
Gap_init rate = 0.01 (8 / 554), avg. gap size = 1.38 (11 / 8)  

 660 29.18 2.12 3.98  chrX_93984698_93987735     2171  2547 (491)    L1M4_orf2#LINE/L1      539   908 (0)  

  chrX_93984698_9   2171 AAGAAAGAAT-TGTGAAAATTTTTAAAATCATTGGACTGGGCAAAGAATT 2219
                               iv  -v ? v    i  iivi i -    ii i     v iv  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTT 587

  chrX_93984698_9   2220 CTTGAGCAAAGAATACTTCACAGGCACATGCAACCAAACCCAAAATGGAC 2269
                            -  - v vi i  --  v i     v     v   vvv     i  i
  L1M4_orf2#LINE/    588 CTT-AG-ATATGACAC--CAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_93984698_9   2270 AAATGGGA--TCATGTCAAGTTAGAAAGCTTCTGAACAGCAAAAGA---- 2313
                             v   --    -iv  i   i   -   i  vi vv    i  ----
  L1M4_orf2#LINE/    634 AAATTGGACTTCAT-CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT 681

  chrX_93984698_9   2314 AGCAACCAAGTAAAGGGATGACTGAAAGAATAAAAGAAAATATTTGCAAA 2363
                          v   vv    i  ii  ii  iv v     iii                
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_93984698_9   2364 CTACTCATCTGACAAGAAATCAATAACTAGAATTTTTAATATATACAGTT 2413
                         ii ivi      i   ii iivi  v i     -------     v  vv
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAAT-------ATATAAAGAA 774

  chrX_93984698_9   2414 GTTTTCTAATAAAACATATAAAAATACAA-TAATCTTATTTAAATATTGA 2462
                         v i  vi  ivv  i -       v    -   i iv   ?   v  v i
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_93984698_9   2463 CAAAATATCTGAATAAGTATTTCTCAAAAGAAGACATACAAAGGAAAAAC 2512
                             iv  i      iii       v        i       v ivv  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_93984698_9   2513 AATTATATAAGAAAGTGTTCAACATAATTGATTAT 2547
                           vi i  i i  ii  i       v ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (63 / 45)
Gap_init rate = 0.03 (12 / 370), avg. gap size = 1.92 (23 / 12)  


2657 26.85 3.13 1.57  chrX_94003832_94009694     4477  5370 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94003832_9   4477 TGGAAAAACATTCCATCCTCATGGAATCAAAGAATCAATATTGGGAAAAT 4526
                               i i  i    vi       v vi    v i       vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94003832_9   4527 GGCCATACTGCCCAAAGTAACTTACAGATTCAGTGCTATTCCCATCAAAC 4576
                            v     v      v i ii          ii  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94003832_9   4577 TACCATTGACATTCTTTACAGAATTAGAAAAAAAAAAACTGCTT-TAATT 4625
                          v   vivi v  i   i     v v  v  i------   v i-   vv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG------CTGATCCTAAAA 144

  chrX_94003832_9   4626 TTCATGTGGAGCCAAAG-AAGAG-CCCATA-TAGCCAAGACAATTCTAAG 4672
                              i    ---  v -   i -    v -       i     ii i i
  L1M4_orf2#LINE/    145 TTCATATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_94003832_9   4673 CGAAAAGAGCAAAACTGGGGGCATCACGCTGTCTGACTTCAAACTATACT 4722
                         vi i    i    ii   i  vv    i  vi ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_94003832_9   4723 ACAAGACCACAGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGACAT 4772
                             ii i       i   i v  ii         i iv ii i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_94003832_9   4773 ATAGACCAATGGAACAGAACAGAGACCTCAGGAATAACACCACACATCTA 4822
                              i        i    iv    vii   i     vv   i    i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_94003832_9   4823 CAACCATCTGATCTTTGACAAACCTGATAAAAACAAGCAATGGCGAAAGG 4872
                         iiii  vi    i  i     ivv  vi  i v  vv      v     i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_94003832_9   4873 ATCTCCTATTCGATAAATGGTGCTGGGAAAACCAACTAGCCATATGCAGA 4922
                           vvi  v   i i              v   iiiv  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_94003832_9   4923 AAACTGAAACTGGACCCCTTTCTTACACCTTATACAAAAATTAACTCAAG 4972
                          i v    ii         vi  i     v                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_94003832_9   4973 ATGGATTAAATACTTAAATGTAAAACCCCAAACCATAAAAACCCTAGAAG 5022
                               i ? v  i         i v iv    i      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_94003832_9   5023 AAAACCTAGGCA-ATACCATTCAGGACATAGGCATGTT---CAAAGACTT 5068
                              v    ?i- v i -   iv   v v  ---   ---   v ii  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGG---GTTAGGCAATGGTTT 587

  chrX_94003832_9   5069 CATGACAAAAACACAAAAAGCAATTGCAACAAAAGCCAAAATTGACAAAT 5118
                          v iivv vi    v       vvv          vv     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_94003832_9   5119 GTAATCT------AATTAAACA-------GC---AAAAGAAACTATCATC 5152
                         vvi ii ------       v -------  ---   i  v       vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_94003832_9   5153 ACAGTAAACAGGCAACCTACAGAATGAGAAAAAAAAATTTGCAATCTACC 5202
                          v   i  v  i     i        i  i    v -       vii iv
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA-TTTGCAAATCATA 736

  chrX_94003832_9   5203 TATCTGACAAAGGTGTAATATCAAGAATCTCCAAGGAACTTAAACAAATT 5252
                                i  i  vv vi    v     v vi  i     ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_94003832_9   5253 TACAAGAGAAAAACAA----CCCCATCAAAAAGTGGACAGATGATATGAA 5298
                         v i  v i   i    ----   v  i?    i   i  i v   v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_94003832_9   5299 CAAACATTTCTCAAAAGAAGACATTTACATGGCCAACAAACATATGAAAA 5348
                         i i         v        i  vi v        i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_94003832_9   5349 AAAGGTCAACATCACTGATCAT 5370
                         i v v         ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (134 / 102)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.80 (42 / 15)  


1500 28.30 8.51 2.78  chrX_94033358_94038595.rev     3598  4173 (1065)    L1M4_orf2#LINE/L1        1   609 (299)  

  chrX_94033358_9   3598 TGGAAAAACATTCTATGCTCATGGATAGGAAGAATCAATGTCATTAAAAT 3647
                               i i  i i   i        v      v i   i ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94033358_9   3648 GGCCATACTGCCCAAATACATTTACAGATTCAATGCTATTCCTATTAAAC 3697
                            v     v       vv  i           i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94033358_9   3698 TACCAACAACATGCTTCACAGAACTATATAAAGAAAAACT-ATTTTAAAA 3746
                          v   i vi v vi  ii     --  - ---  v  i  -  ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--AT-T---GACAAGCTGATCCTAAAA 144

  chrX_94033358_9   3747 TTAATATGAAACCAAAAAAGAGCTCAAATAGCCAAGGCAGTCCTAAGCAA 3796
                           v     i  viiv  ii  v ivi         ii  i  i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_94033358_9   3797 AAAGAACAAGGCTGTAGACATCATGCTACCTGACTTCAAATTATACTACA 3846
                         i        i i  v  ivv   ii  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_94033358_9   3847 GGACTACAGTGAAAAACAACAAAAATCAGCATGATACTGGTACAAAAACA 3896
                         iii       ----  i--   i --   ii  i      i i  ii i 
  L1M4_orf2#LINE/    245 AAGCTACAGT----AAT--CAAGA--CAGTGTGGTACTGGCATAAGGATA 286

  chrX_94033358_9   3897 GACACATAGACCAATGGAATAGAATAGAGAGCCCAGAAACAAGTCCACAC 3946
                             i     i              v     i       i  ii   i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_94033358_9   3947 ACCTACAACCGTCTGATCTTTGAAGAAGCTG------------------- 3977
                          ii  iiii ivi    i  i  vi i v  -------------------
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_94033358_9   3978 AAAAAATA---------------------------ACTGACTAGCCATAT 4000
                            i    ---------------------------    iv  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_94033358_9   4001 GCAGAAGATGAAAACTAGACCCCTTCCTTACATCATATATAAAAATAAAC 4050
                            i    vvi  ii i       v   i   i      i      v   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_94033358_9   4051 TCAAGCTTGATTAAAAACTTAAATGTAAAACCCAAAACTATAAATACCCT 4100
                             iv v   i ? i  i         i v i           -  i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCT 535

  chrX_94033358_9   4101 -GGAAAACAATCTAAGC-CATAGCATTCTGGACACAGAAATGGGCAAAGG 4148
                         -i   i v  iv  i ?-i v v -   vv   viv iiv i     v  
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_94033358_9   4149 TTTCATGACCAAGATGTCAAAAGCA 4173
                             v iivi v  iii        
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCA 609

Transitions / transversions = 2.20 (110 / 50)
Gap_init rate = 0.02 (13 / 609), avg. gap size = 5.00 (65 / 13)  

 809 25.34 5.14 0.68  chrX_94033358_94038595.rev     4456  4747 (491)    L1M4_orf2#LINE/L1      604   908 (0)  

  chrX_94033358_9   4456 AAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATTTAGTTAAG-T 4504
                               vvv          v      v  i    v   i  vi i  i- 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_94033358_9   4505 TAAAGAGCTT-ATTCTCAGCAAAAGAAACTATCAGTAGAGTGATTAGACA 4553
                             i vi  -i v  i--    i  v       iv i     vv     
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_94033358_9   4554 ACCTAGAGAATGGAAGAAAGTATTTATAAACCATACAACTGACAAAAATC 4603
                            i v       i     i     ii   i    i v    i  iiiv 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_94033358_9   4604 TAATATCCAGCATCTATAAGGAACATAAACAAATTTACAAAAAAAA---- 4649
                          vi       v  v     i    vivv    v iv i  v     ----
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_94033358_9   4650 ---AATCCCATTAAAAAGTGGGCAAAGGAC----AT-GACACTTTTCAAT 4691
                         ---  i  v   ?    i           i----  -    i  i  v v
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_94033358_9   4692 GGAAGACACACATGTGAACAACAAGCACATGACAAAA-GCTCAGTATCAC 4740
                         i     i i   vi  iv   i          v  i -     ii    ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_94033358_9   4741 TGATCAT 4747
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.35 (42 / 31)
Gap_init rate = 0.02 (7 / 305), avg. gap size = 2.43 (17 / 7)  


2025 27.55 3.62 3.95  chrX_94045403_94047715      951  1861 (452)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94045403_9    951 TGAAAACACACCCCATGATCATGGGGTTGAAGAATCAATGTTGTGAAAAT 1000
                           i   v i i      v      iv v     v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94045403_9   1001 AGCCACACTGCCCAAAGCAATCTACAGATTCAATGCAATTACCATCAAAA 1050
                         i  v i   v      vii              i     iv i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94045403_9   1051 TACCAATATCATGTTTTATAGAA-TTAGGAGAAAC-AACCCTAAAGTTCA 1098
                          v   iivv v v    ii    -  --  v  i -i i      i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_94045403_9   1099 TATGGAAA---AAATGAGCCCAAATTGCCAAATTAATCCTAAGCAAAAAA 1145
                                 ---  iv  v  vi   v      vi    i i --------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-------- 190

  chrX_94045403_9   1146 AAAAAAAAAAAAGAAAAAAATCTGGAGGCATTACATTACCTGACTTCAAA 1195
                         -----    i     v   i -      vv i   i v  ii i      
  L1M4_orf2#LINE/    191 -----AAAAGAAGAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_94045403_9   1196 TAATATTACAAGACAATACTTATCAAAACTGCATAGTACTGATATAAAAG 1245
                         vvv  i     ii v i v v     i  v ii i      ii    iii
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_94045403_9   1246 TGGGCACATAGACCAATGGGATAGAATAAAGAATGGAGAAATAAAGCCGA 1295
                          i i  i     i      i       vi   i vv         v  iv
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_94045403_9   1296 ATATGTA----CAATCAACTT--GACAAAGCATACAGAAAC-AT-AAATT 1337
                          i  v  ----    ii i  --     i -i i vi i  -  -v   v
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATG 383

  chrX_94045403_9   1338 GGAAAATGTACACCCTATTTTAATAAATGATGATGGAGAAACTAGCAAGT 1387
                           i   - v i vi  -   i  i     i  v   iiv    i vv ?i
  L1M4_orf2#LINE/    384 GGGAAA-GAATAGTCT-TTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_94045403_9   1388 CACATGTAGAAGAATGAAACTGGATTCCTATCTCTTCCCATATATAAAA- 1436
                               i i         ii    ii    i   viv       i    -
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_94045403_9   1437 -TCATCCAACATGGATCAAAGACTTAAATATAAGACCTGAAACTATGAAA 1485
                         - v ii   v        ?    i     i     v  i       i   
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_94045403_9   1486 ATTCTGGAAGACAACATTGAA--AAGTCTCTACTAGATATTAGCCCAGGC 1533
                         v ii i     v     v i?--  i   iiii--  iv  i vii    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGT--GACCTTGGGTTAGGC 579

  chrX_94045403_9   1534 TAAGAATATACGACTAAGACCTCAAAAGGAAATGCAACAGAAACAAAAAT 1583
                         v v iv viviiiv  v   vi      v v v      i  iv      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_94045403_9   1584 AAATAAATGGGACTT-ATTTAAACTAAAAATCTTCTGAATAGCCAAAGAA 1632
                          i      v      -  iv   i      -   i  viivv v  i  v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chrX_94045403_9   1633 ATAATCA-----GCAAACAGACAACCCACAGAATGGGAAAAAGAATTTTG 1677
                          iv    ----- ii  v                    i   iv    - 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-G 727

  chrX_94045403_9   1678 TAAATGATGTGTCTGACCAAGGACTAGTATCCAGAATCTAAAAATAACTA 1727
                         i    v  i i     iv i     v           v  v   v    v
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_94045403_9   1728 AATCAAATCAGAAAGAAAAA-ACAAA-AACCAAAAAAATTGTCATCACAA 1775
                         vvv   v   iv  v     -     -    v  ---------- i?v  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAA----------TTWAAA 817

  chrX_94045403_9   1776 AGTGGGCAAAGGTCAAAAATAGATATTTAT-----GAAAAAATGCCCATC 1820
                          i          vivvi      i    v -----   i v  i vv  v
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_94045403_9   1821 ACTAATGGATCCA-GAAAA--TGCAAATTAAGACCACAATGAGA 1861
                         i i   iiiiv  -     --   --- i  v i  ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.56 (69 / 27)  


1387 27.17 7.96 0.94  chrX_94048586_94052811      611  1037 (3189)    L1M4_orf2#LINE/L1        4   460 (448)  

  chrX_94048586_9    611 AAAAATATTCCATGTTCATGGATTGGAAGAATTAGCATTGCTACAAAAAT 660
                            i    i                     v   ii    i  --- i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA---AGAT 50

  chrX_94048586_9    661 TTTA-TACAACTCAAAGCAATCTACAGATTTAATGGATTCTCTATCAAAA 709
                         vvi -   vv i    vii           i  i v v  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94048586_9    710 TACCAA-TGTCATTCTCCACAGAAACAGAGAAAACAATCCTATAACTTAT 758
                          v   i-  i -  i iii      iv  v  ivii      v  i i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_94048586_9    759 ATGGAACCACAAAAGGCCCAGAATACCCAAAGCTACAGTAAGCATAAAGG 808
                               vii   ii i         v     i v ivv i iv vi   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_94048586_9    809 CCAAAACTGGAGAAATCACATTACCTGACTTCAAATTATACTACAGAACT 858
                         v    ii     i v     i v  ii i      viv       i i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_94048586_9    859 ATAGTAACCAAAACAGCTTGGTACTTGCATAAATACAGACACATAGACCA 908
                          i     i   i    iv       v      iv i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_94048586_9    909 ATGAAATAGAATAGAGAACCCAGAAACAAATCCACATACCTA----CAGT 954
                            i        v    ii       i   i   i i ii  ----  i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_94048586_9    955 TAACTCT---------------------------GGGAAAAAACAATCTC 977
                          i i i ---------------------------      i  i i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_94048586_9    978 TTCAATAAATGTTGCTAGAAAAACTGGGTATCTATATACAGAATAATAAA 1027
                              i     v    i i v      i  ? i i  i  i  v   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_94048586_9   1028 -CTAGACCCTT 1037
                         -i i     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCT 460

Transitions / transversions = 2.59 (83 / 32)
Gap_init rate = 0.02 (7 / 457), avg. gap size = 5.43 (38 / 7)  

1156 26.01 1.43 1.43  chrX_94048586_94052811     3308  3726 (500)    L1M4_orf2#LINE/L1      455   873 (35)  

  chrX_94048586_9   3308 ACCCCTATCTCTCAAAATATATAGATCTAAAATAAAAATTGATGAAAGAC 3357
                                i   v  vv     i i vv v  v v     v   v ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_94048586_9   3358 TTAAATATAACACCTCAAACTATGAAACTACTACAAGAAAACATTGAGGA 3407
                         i     i   v v  v       i     vi  v          v i? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_94048586_9   3408 AAATCTCCAGGACCTTAGTCTGGGCAAAAATTTTTTGAACAGTAAC-CCA 3456
                               i iv      i vi i     vii   i  ii i - i  -   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGACACCA 603

  chrX_94048586_9   3457 CAAGCACAGGCAACCAAAACAAAAATAGAAAAATTGGATCACATCAAG-T 3505
                         v       i     v   iv         v        iiv      i- 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_94048586_9   3506 TAAAAAGCTTCTTCACAGCAAGGGATACAGTCAACAAAGTGAAGAGAAAA 3555
                               -   i vii vv   i   i  vi    v        i   v  
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_94048586_9   3556 TCCAGATAATGAGAGAAAATATTTACAAACTAACCATCTGACCAGGAATT 3605
                         i   v v    i            i    ii vvi      iv   i i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_94048586_9   3606 AATAACCAGAATGTATAAGAAGCTCAAAAAAACTC--TA-CAGAAACACA 3652
                         vi  v       i     ii i   vv v  -   --  -i i   v   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAAAAGACA 801

  chrX_94048586_9   3653 TCCAAAAATCTGATCAAACAGTGGGCAAAA-ATTACAATAGACTTTTCTC 3701
                         ---  v  i ii  i?  v i        i-   vv       v      
  L1M4_orf2#LINE/    802 ---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_94048586_9   3702 AAAAGAAGGAATAAAAATGGCAAAT 3726
                         v       iv   v       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAAT 873

Transitions / transversions = 1.08 (55 / 51)
Gap_init rate = 0.02 (9 / 419), avg. gap size = 1.33 (12 / 9)  


3175 21.39 9.98 0.84  chrX_94054293_94056292.rev      678  1509 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94054293_9    678 TGAAAAAATAGTCTCTATTTATAAATAGGAAGACTCAAT-TTGTTAAGAT 726
                           i   i   vi iv i  i  ii  v        i   -          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94054293_9    727 GTCAGTCCTTCCCAA------------------CACAGTC--TATCAG-- 754
                          v  i v  i     ------------------ i  i  --     i--
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94054293_9    755 -------------TTTTATA--------CAA--TGATTTTCAGAATTC-C 780
                         -------------    ii --------   --    ii - i     -i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAATTCAT 149

  chrX_94054293_9    781 A-------GCAAGACACTCCAAATAGCCAAAATAATATTGTGAAAGAAGA 823
                          -------     iv  i vi           i   v   vi        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_94054293_9    824 ATAAAGTTGGAAGCTTCACACTTCCTGATTTTACAACATATTACAAAGCT 873
                          i         i vi          ii    i v   v  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_94054293_9    874 ACATTAATCAAAATACTGTGGCACTGGCATAAGGACAGACATATGGACCA 923
                            v       i i v     i             i        i  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_94054293_9    924 GGGGTACAGAATAGAGAGCCCAGAAATACACCCTCACATATATGGTCAAA 973
                         iv  v i     v     i         v    vi    v         v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_94054293_9    974 TGTTGTTCAATGAGAGTGTCAAGATAATGCAATGAAGAAAGGATAATTTA 1023
                           v v   i ii  i   i     iv  v     ii     i   i i v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_94054293_9   1024 TTCAACAAATGGTGCTGGGGAAGCTGGATTTCCACATGCAAAAGAATGAA 1073
                                            iv i      v?                   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_94054293_9   1074 TTAGAACTCTTACTTTATACCATATATAAA---TAATTCAAAATGAACTG 1120
                         v v i  i i   i i i        i   ---   i        i iii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_94054293_9   1121 ACAATTTGAATTTAAGATTTAAAAGCATAAAACTCTTAGAAGACAAAAGA 1170
                         ?vi ii i   v     vi     vi                 --   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA--AAACA 547

  chrX_94054293_9   1171 CAGTGGAGAAGAAAACTTCATGACATTGGATT-GACAATGATTTCTTGGA 1219
                         i  ---- ?iv   v    i    v    i  - i     i      i  
  L1M4_orf2#LINE/    548 TAG----GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_94054293_9   1220 TGTGATCCCAAAAGCACAGGCAACAAGAGCAAAAATTGACAAATGGAACT 1269
                          i   iv           i       i  v      v  i    v i   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_94054293_9   1270 ACATCAAACTTAAAAACCTTTATACATTAAAAGAAACAATTGACGAAGT- 1318
                         v       v        i   i i v i   i  v  v  ii vi    -
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_94054293_9   1319 AAAAGGCAACCTATGAAATATAAGGAAATATTTGCAAATCATACTTCTGA 1368
                              i     i iii   ivi  i                  iv     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_94054293_9   1369 TAAGG-AGTAATATCTGGAATACATAAAAAAAACCTACAACTCAAGAACA 1417
                              - v vi    ii     i     i  vv i          v  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_94054293_9   1418 AAAA--CAAACAAGTCCATT-AAAAATGG-CAAAGAACTTAAATAGACAT 1463
                             --    i  vi v   -        -     i i  i         
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_94054293_9   1464 TTCTTCAAA--AGA-----------------AGCATATGAAAAGATGCTC 1494
                             i    --   -----------------    i              
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_94054293_9   1495 AACATTACACCATTA 1509
                              i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (118 / 57)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.50 (90 / 20)  


3056 26.23 1.34 1.23  chrX_94062804_94064682      493  1388 (491)    L1M4_orf2#LINE/L1       12   908 (0)  

  chrX_94062804_9    493 CCCATGCTCATGGATAGGTAAAAAC--AATATTGTGAAAATGACCATACT 540
                               i        v  --  i  --        v  i   i v     
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGG--AAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_94062804_9    541 GCCAAAAGCAAACTACAAATTCAATGCAATTTCCATTAAAA-CACAACTA 589
                         v  v   vii v     i      i     ii i  i    - v  i  i
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_94062804_9    590 TCATTCTTCACAGAAATAGAAAAAAAAATTCTAAAATTTATATGAAACCA 639
                         i -  i  ii       v  v  ivvi  i        i     i  vii
  L1M4_orf2#LINE/    110 CC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_94062804_9    640 AAAAAGAGTCTTCACAGCCAAAGCAAGACTAAACAAAAAGAACAAATCAA 689
                         v  ii  vi vvv i       i   vvi i  v  i         vivi
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_94062804_9    690 GAGGCATCACATTACCTGATTTCAAACTATACTATAAGGCCATAGTCACC 739
                             vv     i v  ii        viv     i  i  i i   v i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_94062804_9    740 AAAGCAGCATGGTACTGGCATAAAAGTAGGCACATAGACTAATGGAACAG 789
                           ii   ii              iii   i  i     ii       i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_94062804_9    790 AATAGAGAACCCAGAAATAAACGCTAATAC-TTAACAGCCAAATGATCTT 838
                            v    ii            v --    -  v ii i   v    i  
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCC--ATACATTTATGGTCAATTGATTTT 356

  chrX_94062804_9    839 TGACAAAGCAATCAAAAACATATAATGGGAAAAGA-CACCCTATTCAACA 887
                         i     i vvii   i v   vi      i     -i vi  v       
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_94062804_9    888 AATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAAACTGGAT 937
                                      i  i   v  ?       i ii        ii    i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_94062804_9    938 CCTCATCTCTCACCTTATACAAAAATCAACTCAAGATAGATCAAGGACTT 987
                           ii i   v    v           i       i  i     ?i   i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_94062804_9    988 AAATCTAAGACCTGAAACTATAAAAATTATAGAAGACAACATTGGAA-AA 1036
                             v     v  i           v iv       v     v  ?i-  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_94062804_9   1037 CCCTTCTAGACATTGGCATAGGCAAGGATTTC------ATGACAAAGAAC 1080
                         vi    vv   v    vv       v i    ------      ------
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA------ 600

  chrX_94062804_9   1081 CCAAAAGCAAATGAAATAAAAACAAAGATAAATAGCTGAGGCTTAATTAA 1130
                                  v v v  i    iv   i   i   iv vi i   v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_94062804_9   1131 ACTAAAGAGCTTTTGCACGGTAAAAGGAAGAGTCAGCGGAGTAAACAGAC 1180
                          v v  i i      ii vvi   i iv vvi   ivii   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_94062804_9   1181 AAACCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGGA 1230
                           v       i           v  ii   vii   i      i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_94062804_9   1231 CTAATATCCGGAATCTTCAACAAGCTCAAACAAATTAGCAAGAAATAAAC 1280
                           vi     i    v vi  vi i   vv    v i ii  v   v i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_94062804_9   1281 AAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCAA 1330
                            i  i  v  i?    i     v     iv          v     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_94062804_9   1331 AAGAGGATATACAAATGGCGAACAAACATATGAAAAATTGCTCAACATTG 1380
                             i              v  i  i  i       iv          ii
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_94062804_9   1381 CTAATGAT 1388
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.57 (141 / 90)
Gap_init rate = 0.01 (10 / 897), avg. gap size = 2.30 (23 / 10)  


2589 29.89 2.47 0.45  chrX_94067041_94071316.rev     2896  3785 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94067041_9   2896 TGAAGAGATAGTCCATGTTCCTGGAAAGGAAGACTCAATGTTGTCAAGAT 2945
                           i i     vi        v    vv        i   i    i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94067041_9   2946 GTCAGTTGTTCCCAACCCACGCTATAGATTCCATACAATCTCAATGAAAT 2995
                          v  i vv i     viiivv   i      v ii     i v  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94067041_9   2996 GTTCAGTAAATTATTTTGTGGATATTTACAAACTGCTTCTGCAATTTACA 3045
                         vii   ivivi v     ii  v   v    i   v i  iv    i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_94067041_9   3046 TGGAAATACAGAAGATCCAGGATAGAAAACACAATATTGAAGAAAAA--- 3092
                                i  iii  i    i    vv  v     v     i  i  ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_94067041_9   3093 -AAGGTCAGAGTACTGACCCTACTCAGCTTCAAGACTGAGTACAAAGCTA 3141
                         -  i  ii   v   v  v  v i  ii     i   v v          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_94067041_9   3142 CAGTAATTAAGATAGTGTGCTATTTGTAAAAGAATAGATACATAAATCAA 3191
                                i    i      v  i v i v   i     i i   i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_94067041_9   3192 TGGTACAGAATAAGGATTCCAGAAATAGAACTACATGAATATATCCAGCT 3241
                            v i     vii  v          i v i i iivv   ivi  ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_94067041_9   3242 GCTCTATAATAAAA-TATAAAGGGCAATTCAAATTTTAAAAAGATAGTTT 3290
                          v i vii i  ii- iiv   iv  -     - vvvi   ii     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCA-TTCAA-TGGGGAAAGAATAGTCT 398

  chrX_94067041_9   3291 TTTTAACAAATGGTGCTAGGACAACTGGACAATCACATGCAGAAAAATTA 3340
                            i             i           i ?i        i  i   v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_94067041_9   3341 GTCTAGACACAAATTTTACAGCCTTCATAAAAATTAACTCAAAATTAATT 3390
                         ivi i   v vv ii i   v v vi i                 vi  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_94067041_9   3391 ATAGTCTTAATT-------TTAAAACTACAAAATGCCTAGAAGATAATAT 3433
                          ?  v i   v -------i        i    iv i       v  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_94067041_9   3434 AAGAGAAAATCTAGATGACTTTGG-TTATAGCTATAAATTTTTAGATACA 3482
                          i ? v      vvi    i    -   -i  v  iiv  i       ii
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATATG 597

  chrX_94067041_9   3483 GTATCAAAGGCATGGTTGATAACA----AAATTAATAAGCTACACTTTAT 3528
                         ii i    i   iiivii i  v ----    vi    ii iv    i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_94067041_9   3529 TAAAATTAAAAG-TTTAGTCTCTGCAAAAGGCACTATCAGTAGATCAAAA 3577
                         i          i-   v  v-  v    i i        iv i vii   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTG-CTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_94067041_9   3578 AACCAAGGCACAGATTGTGAGAAA-TATTTGCAAAATACGTATCTGATAA 3626
                          iv   vv      v  v      -          vi ii          
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_94067041_9   3627 AGAGCTGTTACCTAAATTGTACAAGGACTACTAAAAGCTCAACAATAAGA 3676
                         i ii  vv  i i i v i  i  i  viv  v v i     i     i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_94067041_9   3677 AAATAAACAACCCAATT-AAAAATGTGTAAAAGATTTAAACAAAAAATCC 3725
                          i i   i         -       v i   i     i  i i v v i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_94067041_9   3726 TACA--GAAAATGTACAGATAAAAAGTAAGTATATGCACTTATGCTCAAC 3773
                          v  --   i  i    i  iivv i    i i   v vvv         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_94067041_9   3774 ATTATATGTCAT 3785
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (164 / 99)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.00 (26 / 13)  


2310 26.35 0.95 2.16  chrX_94098067_94099798.rev      502  1241 (491)    L1M4_orf2#LINE/L1      178   908 (0)  

  chrX_94098067_9    502 AAAGCGATCTTTTTTAAAAGAAAAAGAAAAAAGCTGGAAGCATCAAATTT 551
                            i i     -----i  i  i     v    i    i vv   v i  
  L1M4_orf2#LINE/    178 AAAACAATCTT-----GAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_94098067_9    552 TCTGATTTTAAAATGTGTTACAAGGCAACATTAGTTAAAACAGTATGGCG 601
                         i ii    i    iv ii     i  v   v  i i  i     i   ii
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_94098067_9    602 TTGGCATAAAGACAGACATATAGATGAACAAAACAGAATATAGAACCTGG 651
                         i        i  i            v  iii  i     vv   ii ii 
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_94098067_9    652 AAATAAACCCACACATACATGGTGAACTGAT---CAACATTATGGCTGCC 698
                                    i    vi     v  i    --- i   -- v  -    
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACA--AGGG-TGCC 369

  chrX_94098067_9    699 AAGAGTACATAGTGGGGAAATAATAGTTTCTTTAAAAAATGATGCTGAAA 748
                             vi ivi i        v      i i  i  v     i     ii 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_94098067_9    749 AAACTGAATATCTATATGCAAATAAATAAA--TAAATAAATATGGATGTT 796
                         v     i   ? i i       vi   i  -- ii ivvv  i-----i 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC-----CT 464

  chrX_94098067_9    797 TATACCATACA-AAAAATTAACTCAAACTGAATTAAAAACTTTAATATAA 845
                         i i      i -               v  i  i ? i  i v   i   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_94098067_9    846 GATCTGAAATGTTAACATTTCTAGAATAAAACACAGAGAAATATCATTAT 895
                           v  i   ivv   v i ii     v      i  i?iv v   v ii 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_94098067_9    896 GACATTGATCTTGGCAATGATTTATTGGATATGACACCAAAAGCATAGAC 945
                            v   ivi v       i   v  i                  i ii 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_94098067_9    946 AACAAAAATAAAAATAGATAAGTGGGACTACATCAAACTAAAAAGATTCT 995
                                iv            i v     v       v v    iv  i 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_94098067_9    996 TTACAGCAAAAGAAACAATCAGCCAAATCAAAATGCAATCTACA-AATAA 1044
                         v i vv    i  v  v    ivv  i v    vi   i i   -   ii
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_94098067_9   1045 AAGAAAGTATTTGTAAACCACATATCTGATTATGGATTAATTTTCAAAAT 1094
                         i     i      i   i  i         v v   i vi v i  i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_94098067_9   1095 ATATATAAGCCTATTACAATTCAATAGTAATAAAAACCTTATAACCCAAT 1144
                              v iiv  v      i      i   -   i  vv-          
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAA-AAAGACAA-ATAACCCAAT 812

  chrX_94098067_9   1145 TAAAATAGAGGCTAAAGATGTGAATAAACGCTTTTTCACAGAAGACATGA 1194
                          ?   v vi   v  i   v      i  ii  i i  v      i  iv
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_94098067_9   1195 AAATGGCCAAAAAGTATAGGAAAAAAATGCTCAGAATCACTAATAAT 1241
                                   v   i i v     i -      iv    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (122 / 69)
Gap_init rate = 0.02 (11 / 731), avg. gap size = 2.09 (23 / 11)  


2438 27.10 2.35 2.80  chrX_94140983_94144794     2427  3319 (493)    L1M4_orf2#LINE/L1       20   908 (0)  

  chrX_94140983_9   2427 CATGGTTAGGTAGAATCAATATTGTAAAAATAATCATTTTGCCAAAAGCA 2476
                              v v  v   v i        v  i  iiiv  vi v  v   vii
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chrX_94140983_9   2477 ATCTACAAATTCAATGCAATTCCCATAAAAATACCACCATCATTCTTCAC 2526
                                i      i     i  i  v     v   v vv v  i  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_94140983_9   2527 AGAACTAGAAAAAACAATCCTAAAATTTATATGGAACAAAAAAAAGAGCT 2576
                             v v  v  ivii           i        - viv  ii  v i
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAA-ATGCAAGGGACCC 168

  chrX_94140983_9   2577 TGCACAGCCAAAGCAAGACTTAGCAAA-AAGAACAAATCTGGAGGAATCA 2625
                         v v i       i   v-   iiv   -         vi       v   
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAAT-CTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_94140983_9   2626 CATTACCCGACTTCAAACTGTACAATAAGGCCATGTTCACCAAGATAGGG 2675
                           i v   i i      viv   v i  i  i iiv v i     i  v 
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_94140983_9   2676 TGGTACTCGTTTAGAAATAGGCACATAGACCAATGGAACAAAATAAAGAA 2725
                                v iv  iii    i  i     i        i i   vi   i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_94140983_9   2726 CCCAGAAATAAAGCCAAATACTTA--GTCAACTGATTTTCAACAAGTGGA 2773
                         i           v   v i i   --     i        i     -  -
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG-GG- 365

  chrX_94140983_9   2774 AAAATTAAAAAACAACAACAACAACAACAATATAAAGTGGGGAAACGACA 2823
                         ------------------iiv   -i  v  vi  --        vi i 
  L1M4_orf2#LINE/    366 ------------------TGCCAA-GACCATTCAA--TGGGGAAAGAATA 394

  chrX_94140983_9   2824 CCCTATTCTACAAATGGTGCTGGGATAATTGGCAAGACCCATGTAGAGGA 2873
                         vi  v   v                i  i   vv ?v v    i i i  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_94140983_9   2874 ATGAATCTGAAACCTCATCTTTCACCTTATATAAAAATCAACTTAAGATG 2923
                              vi  i v  ii i  iv    v    i      i    i  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_94140983_9   2924 GATCAAAGACTTAAATCTAAGACCTGAAACCATACAAATTATAGAAGATA 2973
                              ?    i     v     v  i    i   v  v iv       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_94140983_9   2974 GTATTGGAAAAACCCTTCTAGACATTGGCTTAGGTAAAGACGTAATGACC 3023
                         ii  v  ?iv  vi    vv   v    v     i  v iiv vv iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_94140983_9   3024 AAGACCCTAAAAGCAAATGCAACAAAAACAATGATAAATAGATGAGACTT 3073
                          v   v i       v v         iv  vi   i   i  vi     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_94140983_9   3074 AATTAAACTCAAAAGCTTCTA-ACAGCAGAAGAAATAATCA-----GCAA 3117
                         v  i   v i    i   i i-i vv  i i  v iv    ----- ii 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_94140983_9   3118 ACAGACAACCCACTAAGTGGAAGAAAATGTTTACAAGATACACTTTTGAC 3167
                          v           vi i   i       i   i   ivi i iv i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_94140983_9   3168 AAAGAACTAATATCCAAAATCTACAATGAACTCAAACAAATCAGCAA--- 3214
                           i i   vi      i   v  i  v      vv    v   ii  ---
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_94140983_9   3215 ---GA--AATGTCCCA-TCAAAAAATGGGCTAAGAACATGAATAGACAAT 3258
                         ---  --   iv    - i?          v   i iv          v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_94140983_9   3259 TCTCAAAAGAAAATACACAAATGACCAAAAAACA-ATAAAAA--TGCTCA 3305
                             v      i   i       i    v  i  -  i    --      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_94140983_9   3306 ACATCACTAATGAT 3319
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (135 / 103)
Gap_init rate = 0.02 (15 / 889), avg. gap size = 3.07 (46 / 15)  


 399 31.84 1.12 1.12  chrX_94152632_94155578        3   181 (2766)    L1M4_orf2#LINE/L1      487   665 (243)  

  chrX_94152632_9      3 TCAAAATGGATTAAAGACTTAAATCTAATACCTCAAACTGTAAAACTACT 52
                                    i ?    i     v   v v  v     i       vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_94152632_9     53 GCAATAAAACTTTGGAGAAAATCTATAGCACATTGGTCTGGGGTAAAAAT 102
                         iv  v     v v  ? v      viivv  v    vi -i  i  vii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT-AGGCAATGGT 585

  chrX_94152632_9    103 TTTTTGAGCAATACCTCACATGTACAAGCAACCAAAGCAAAGG-AAACAA 151
                           i  iiii vv  vi  v v i         v    v   ii- i i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_94152632_9    152 ATGAGATCACATCAA-GTTAGGAAGCTTCTG 181
                           vi  iiv      -i   ii  -   i  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTG 665

Transitions / transversions = 1.20 (30 / 25)
Gap_init rate = 0.02 (4 / 179), avg. gap size = 1.00 (4 / 4)  

 267 10.81 0.00 0.00  chrX_94152632_94155578     1152  1188 (1759)    L1M4_orf2#LINE/L1        1    37 (871)  

  chrX_94152632_9   1152 TGGAAAGACATTCCATGTTCATAGATTAGAAGACTTA 1188
                                 i  i          i    i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTA 37

Transitions / transversions = 1.00 (4 / 0)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.00 (0 / 0)  

2836 22.28 5.14 1.10  chrX_94152632_94155578     1638  2454 (493)    L1M4_orf2#LINE/L1       29   878 (30)  

  chrX_94152632_9   1638 GAAAACTTAATATTGTTAATATTTTTACACTTCGCAAAGAAATCTATAGA 1687
                            i               v  vviv i   i v    vvi     i   
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chrX_94152632_9   1688 TTCAAGGAAATCCACATCAAAATCTTAATGGTGCCTTCT--GCA-AAATA 1734
                              v v     vi         ii -- v      i --   -    v
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCA--GCTGCCTTTTTTGCAGAAATT 126

  chrX_94152632_9   1735 GTAAAATTTATC-TGAAATCTATTTAGGATTATAAGGGACTCAGATTAGT 1783
                          vv  ii v   - i    ii  v i i v ii       i    v   i
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chrX_94152632_9   1784 GAAAATAATTTTTAAAAAGAA---CAAAGTTGGAGTTCTGACACTCCCTC 1830
                         v    i   i  v        ---           vv  v     i  iv
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_94152632_9   1831 ATTTCAAAAATTACTGCAAAAGTACAGTAACCAAAACATTGTGGTAATGG 1880
                                  v     i    iv        i   i   v       v   
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_94152632_9   1881 CTTAAAGAAATACATATAG-TCAAATACTATAGAAGAGACAGTTCAGCAA 1929
                          v   i  v v        -    - ivv      vv  v   i   v  
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAA-TGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_94152632_9   1930 TTAACCCTTGTGTATATAACCAAATGATTTTTTACAAGAGTGGCAAGTCC 1979
                          v     v iii v   iii   v       iv     i   v    v  
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_94152632_9   1980 ATTCAATGGGGAA-GAA-AGTCTACTCAACAA-TGTTCTTGAGAAAAC-- 2024
                                      -   -     vi       -  v vi  i  v   --
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_94152632_9   2025 AATGTCCACTTGCAATAGAA--AAGT-GAACCCTTACCTTACACCATATA 2071
                         i  i?    v     v    --    - i    i     i          
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_94152632_9   2072 TAAAAAGTAATTCAAAATAAAT-----ACCTGAACATAAAAGCTAAAACT 2116
                         i     v   i       ii  -----    i  ii   i          
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_94152632_9   2117 CTAAAACTCTTAAAATTAAAACAAAAGGAAAACAAAATTGTTTATATCAT 2166
                         v           i  v-      v i ?iv  ----  i-  ii iv v 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAG-AAAACATAGGNGTAA----ATC-TTCGTGACCT 569

  chrX_94152632_9   2167 TGGCTTTTACAAGTACTTCTTGGATATTGTACCAAAAGCACAAGCAATT- 2215
                            v  vvi   vvii     i     vii                 iv-
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_94152632_9   2216 --TAAAAAATAGAAAAGTTTGACTTCTTCAAA--TCAAAACTTTTGTGCT 2261
                         --v          v  i  v      v     -- v              
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_94152632_9   2262 TCAAAGGACAGTATGAACAAAGTGAAAAGGCAATCCATGGAATGTGAGAA 2311
                                   v   v  v           i   i   ii     v     
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_94152632_9   2312 AATACTTTCAAATTATATATTGAATAAGTGATTAATATTCGGAATATACA 2361
                             i  v     i      ivi     v  i vi   i i       i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_94152632_9   2362 AATGACTGATACTACTT--T--TTAAAAGA------------TTCAAAAA 2395
                           vi   vv   v   i-- -- v      ------------  ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_94152632_9   2396 TCATCAAAGTTCTTAAATAGACATTTCTCCAAAGAACACATACAAATGGC 2445
                          viv     vvi  i                     v i           
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_94152632_9   2446 CCATAACCA 2454
                          v    v  
  L1M4_orf2#LINE/    870 CAATAAGCA 878

Transitions / transversions = 1.01 (90 / 89)
Gap_init rate = 0.03 (22 / 850), avg. gap size = 2.32 (51 / 22)  


2554 27.71 1.64 2.19  chrX_94174733_94180836.rev     4701  5613 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94174733_9   4701 TGGAAAAGAACATTCTATGCTCACAGATAGGAAGAATCAATATCATGGAA 4750
                               i-- i  i i   i   ii   v      v i     ii vi i
  L1M4_orf2#LINE/      1 TGGAAAG--ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chrX_94174733_9   4751 ATGACCACACTGCCCAAAACAATGTATAGATTCAATGCTATTCTCATCTT 4800
                            i v i   v      vii  v  i        i  v  i ii   vv
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_94174733_9   4801 ACTACCA-TTGACATTTTTCAAAAAATTGGAAAAAAATTATTTTAAAATT 4849
                          v v   -i  v v     vv i      -- v  iv v  ii       
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_94174733_9   4850 CATGTATAGCCAAAAAAGAGCCTGAATTGTCAAGGCAATCCTAAGAAAAA 4899
                            i iv iviiv  ii  v  v    v i   ii     i i i   i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_94174733_9   4900 CCAACAGAACTGGAGGCATCACCCTATCAGAATTCAAATTATATTATAGG 4949
                         vv    i ii      vv    v  vi vi v      viv  i  i ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_94174733_9   4950 GCAACAATAATTGAAACAGCATGGTACTGGTACAAAAACAGACATAGAGA 4999
                           v   i    ii i    ii         i i  ii i       v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_94174733_9   5000 CCAATGGGACAGAATAGAGAACCTAGAAATAAGATCACACACCTACAACC 5049
                         i      i i     v    ii i        ivi  i   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_94174733_9   5050 ATCTGACCTTTGACAAACTTGCCAAAAACAAGCAATGGGGAATAGATTCC 5099
                          vi   ii  i     ivv      i v  vv          vii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_94174733_9   5100 CTATTTAGTAAATAGTGCTGGGAGAACTGGCTAGCCAGATGCAGAAAACT 5149
                           v  i ii    i         v      v  ?   v     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_94174733_9   5150 AAAATTGGATCCCCTTCTTACACCATATACAAAAATAAACTCAAGACGGA 5199
                         i  i     i   ivi  i                 v       i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_94174733_9   5200 TTAAACACTTAAATGTAAAACCTGAAACAAATAAAACAAAAAACCCTAGA 5249
                          i ? v  i         i v  i    v -      ------i i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTA-TAAAAC------TCTTAGA 539

  chrX_94174733_9   5250 AGATAACCTAGGCA-ATATCATTCAGGACATAGGCATGAGCAAAGATTTC 5298
                            v   v    ?i- v   -   iv   v v  vv ii    v i    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_94174733_9   5299 AT-GACA-AACATGCTAAAAGAAATTGCAACAAAAGCCAAAATTGACAAC 5346
                         v -  i -i   -- i     v vvv          vv     v  i  v
  L1M4_orf2#LINE/    589 TTAGATATGACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_94174733_9   5347 TGGGATCT------AATTAAAGAGCTTCTGCACTGTAAAAGAAACTATAA 5390
                          v   ii ------       i -   i  ii  vi   i  v     v 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_94174733_9   5391 ACAGAGTAAACAGACAACCTAGAGAATGGGATAAAAATTTTGCAATATAT 5440
                          v i   i  v        i v         v    vv       vvi  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_94174733_9   5441 GCATCTGACAATGGTCTAAAATTCACCATTTATAAGGAACTTAAGCAAAT 5490
                         ii      i  v  v  viv  i  vv  v     i     ivvi   v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_94174733_9   5491 TTGCAAGAAAAAACAATCAAACAACCCTATTAAAAACTGGGCAAAGGATA 5540
                         ---   v  v   v iv    i     v   ?    v            v
  L1M4_orf2#LINE/    786 ---CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_94174733_9   5541 TGAACAGGCACTTCTCAAAAGAAGACATACA--TG--CAATGAACATACA 5586
                             i  i  i     v        i     --  --    i i  --  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA--CA 880

  chrX_94174733_9   5587 TTAAAA-ATGCTCAACATCACTGATCAT 5613
                          v    -             ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (142 / 107)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.06 (35 / 17)  


2923 28.06 1.45 0.33  chrX_94182588_94184618      641  1538 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94182588_9    641 TGAAAAGATACATTATGGTCATGGATTGGAAGAATCAGTACTGCTAACAT 690
                           i       ivii   v               v i i  i  i   v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94182588_9    691 ATTCATACTATCCAAAGCAATCTACAGATTCAGTGTAATCCCTATCAAAA 740
                         iviv     vi     vii             ii i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94182588_9    741 TATCAA-TGCCATTTTTCACAGAAATAAAAAAAATGGT---AAAATTTAT 786
                          vi  i-    -     ii       vi v  iv  i ---      i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_94182588_9    787 ATGGAATCGCAAAAGACCCAGAATAGCCAAAGATATCCTAAGTAAAAAGA 836
                               vi    ii                 ivv   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_94182588_9    837 ACAAGACTGGAGAAATTACATTACTTGAATTCAAATTATACCATAGAGAT 886
                             iii     i v i   i v iii v      viv   i i i  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_94182588_9    887 ATAGTAACCAAAACAGCATGATACTGGCATAAAAGCAGACATATAGATCT 936
                          i     i   i    ii  i           iiii             v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_94182588_9    937 AAGGAACAGAATGGAGA-TCCAGAAACAAATTCATGCACCTACAATGGAC 985
                          v    i     v    -        i   ii   i  ii  iii vi i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_94182588_9    986 TCATTTTCAACAAAAGTGCAAGGAGCACACCTTGGAGAAAAAACAGTCTC 1035
                          v      i    ii    v i  v  iv vv   i    i  i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_94182588_9   1036 TTTAATAAATGGTGCTGGGAAAACTGGCTCTTCATATGCAGATGAATAAA 1085
                           i  i              v      v v?i  i     i v    i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_94182588_9   1086 ACTAGACTGCTCTCTCATGCTCTAAACAAAAATCAAATCAAAATAAATTA 1135
                         ii i   iv  vi    ii iv  v        i  v       ii  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_94182588_9   1136 -AAACTGAAATTTAAGAGTTCAAGTTATAAAACTGCTACAAGTAAACATT 1184
                         - i  iv    v      i v  ii         vi  v   v      v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_94182588_9   1185 GAGAACACTCTCTAGAAAACT--GGTCTGGGAAAAATTATTGAGCTATAT 1232
                          i?ivv v   - v vi v  --   iv  v  vii  vi v  v   iv
  L1M4_orf2#LINE/    550 GGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_94182588_9   1233 C-CCACAAGTACAGGCAACCAAAGTAAAAATGGGCAAATGGAATCACATC 1281
                          -   v   i   i     v    v      i ii    v i iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_94182588_9   1282 AAG-TCAAAAAGTTTTTGCACAGCTAAAGAAACAATCAGCAATGTAAAGA 1330
                           i- i     -i     ii vv v  i  v  v    iv  v  i  i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_94182588_9   1331 GAAAATTCATGGAATGAAAGAAAATATTTGCAAACTACCCATCTGAAAAT 1380
                           v  ii  ii     ii                ii ivi      v  v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_94182588_9   1381 GGATTAATAACTAGAATATATTAGGAGCTCAAACAACTCTATAGGAATAA 1430
                            i vi  v i         v i  i   vv       v   iv  v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_94182588_9   1431 ATCTAAAAATGTGGTTGAAAAATGGGCAAAATATTTGAACAGACATTTCT 1480
                         iv v  v  iviii  ?             iv       i          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_94182588_9   1481 CAAAAGAA---ATACAACTGGTAAACAGGCATATGAAAACGTTATCAACA 1527
                          v      ---      v   iv  i i   i       vi vv      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_94182588_9   1528 TCATTGATCAT 1538
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.59 (153 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


2580 26.76 3.92 2.24  chrX_94188975_94190997      639  1531 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94188975_9    639 TAGAAAAACATCTTAGATTTATGTATTGAAAGACTTTGTATTGTTAAAAT 688
                          i    i i   ii vi  i   v    i       vi         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94188975_9    689 GTCTATGCTATTCAAAGCAATGTGCAGATTCAATGGAATCATTGTCAAAA 738
                          v v  i  vii    vii  v i         i v    vi i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94188975_9    739 TTCCAA--AGCATTTTTACAGAATTAGAAGAACAAATAGTCTTAAGATTC 786
                          i   i--iv v     i     v v  vi i --- ii  i   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC---TGATCCTAAAATTC 147

  chrX_94188975_9    787 ACATGGAATCATAAAAGACCCCAAATAGAAAAAGAAAAGTATTGAAAAA- 835
                          i      viii  ii     vi     vv   iv  -- v        -
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA--TCTTGAAAAAG 195

  chrX_94188975_9    836 ----ACAA-GCTGGAGGCATCACATTTTCTGATTTTACAATATATGACAA 880
                         ----    - i      vv     i  i ii    i v  iv  iv    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_94188975_9    881 AG------TAATTAAAACAGTATGGCACTGGCATAAAAATAAACACATAG 924
                           ------    i  i     i   i          ii   i   i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_94188975_9    925 ACCAGTGGAACATAATAGAAAATCCAGAGTAAGGAAACATGCACATTGA- 973
                          i  i     i v   v  i i      --- iv    viii     v -
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGA---AATAAACCCATACATTTAT 342

  chrX_94188975_9    974 -GTCAATTGATTTTTGACAAGCATGCCAAGGATACAGAATGACAAAACTA 1022
                         -             i      vi       ivi ivv    ivi   vv 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_94188975_9   1023 GAAACTTT--AACAAATGATGTTGGAACAATTG-ATGGGCACAAGTAAAA 1069
                         v iv    --        i  i   i    i  -  i?v    v i    
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_94188975_9   1070 AAAGAAAGAAAAACTAATTAGACGTTTTTCTCACACCACACACAGAAATC 1119
                         i  vi   ---------  i   vii vi         i i   i    i
  L1M4_orf2#LINE/    443 GAATGAAG---------TTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_94188975_9   1120 AATTCAAAATGTATTAAAGACTTTAA---AAAATATGAAAATATATAACT 1166
                           i        v  i ?    i v  ---  i vv i   v    v    
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_94188975_9   1167 CCTTGAAGGAAACGTAGGGA-AAATCTTCATTGATGCTGGTCTCAGCAAT 1215
                          i v    i    i    ?i-        i -  ivi   vi vi     
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAAT 582

  chrX_94188975_9   1216 TATTTATTGGATATGACACCAAAAGCACAAACAAAAAGAAGTAAAAATAG 1265
                         vi   v  i                     i   v  -   v        
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA-AAGAAAAAATAG 631

  chrX_94188975_9   1266 ATAAATAAGATTATATCAAACTACAATGCTTCTGCACAGCGATGGAAACA 1315
                               vi  i vi      v vv  vi   i  ii vv i v   v  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_94188975_9   1316 TTCAAACAAGTGAAAAAGCTGCCTACAGAACAGGAAAAACCTTTTTCAAG 1365
                         v    iv         ii vi  i      ii   i   viv   v   i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_94188975_9   1366 CCATAAATCTGATAAGAGCTTAATATCCAAATTATATAACTAATTCTTAC 1415
                         i    v          i vi vi      i v       vv  i      
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_94188975_9   1416 AAGTCAATAGCCAAAAAGA-AAA-----------AAAATTGGGAAAATGA 1453
                           v      ii-       -   -----------    v    v   v  
  L1M4_orf2#LINE/    782 AACTCAATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_94188975_9   1454 ATTTAATAAGGGTTCACCCAAAGAAGACATACAAATGGCTTACAGGTATA 1503
                         v  v    iivi  ivi          i           iv i i i i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_94188975_9   1504 CAAAAAGATTTTCAACATCTCTAGTCAT 1531
                         ii       vi        v????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.06 (55 / 18)  


 383 28.72 0.00 0.00  chrX_94218489_94224505     4324  4417 (1600)    L1M4_orf2#LINE/L1        1    94 (814)  

  chrX_94218489_9   4324 TGGAAAAACATCCCATGCTTATGGATAGGAGGAAGCAATATCATTAAAAT 4373
                               i i        i i      v   i  vvi     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94218489_9   4374 GGCCACACTGCCTAAAGCAATTTATAGATTTGCCACACTGCCTA 4417
                            v i   v  i   vii  i  i     iiv i  v v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

Transitions / transversions = 2.00 (18 / 9)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  

2283 27.20 2.97 1.90  chrX_94218489_94224505     4692  5533 (484)    L1M4_orf2#LINE/L1       58   908 (0)  

  chrX_94218489_9   4692 CTCCCAAAATGCTGGGAT-TACAGG---AATGCTATTTCTATCAATGTAC 4737
                              v    --  --  -     i---  i  v  ii       vi v 
  L1M4_orf2#LINE/     58 CTCCCCAAAT--TG--ATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_94218489_9   4738 CAATGACATTCTGCACAGGA--TGAGAAAAAAACT-ATTTAAAAATGCAT 4784
                           iivi v  i vii   i --   v  i----  -  iiv     v   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATTCAT 149

  chrX_94218489_9   4785 ATGGAAATGAAAAAGAGCCTGAATAGCTAAGGCAATCGTAAGCAAAAAGA 4834
                                  v  ii  v  v       i  ii     v i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_94218489_9   4835 ACAAATCTAGAGACATCACGTTACCTGACTTCATACTCTATTACAAGGCT 4884
                              vi i   ivv    ii v  ii i    v vii  i     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_94218489_9   4885 ACAGTAACCAAGACAGCATGGTATTGGTACAAAAACAGACACATAGACCA 4934
                                i        ii     i   i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_94218489_9   4935 ATAGAGTAGAATAGAGAGCCCAGAAATAATTCTGCACACCTATAATCATC 4984
                           i  i      v     i          vi iii   ii   ii   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_94218489_9   4985 TAATCTTTGATAAAGGTGACAAAAAACAAGCAAGGAGGAAATTATTCTCT 5034
                          i  i  i  i  i    v   i v-  vv   v i     vv  vv   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCT 398

  chrX_94218489_9   5035 ATTCAATAAATGGGCCTGGGTTAACTGGCTGGCCATATGCAGAAGATTGA 5084
                         v     i      vv     vi      v i?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_94218489_9   5085 CAATTG-ATGCCTTCTGTACACCACAGACAAAAATCAGCACAAGATAGAT 5133
                         - i   - iv   v ivi      i v        i i v   i  i   
  L1M4_orf2#LINE/    449 -AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_94218489_9   5134 TAAATACTTAAATTCAAAACCTAAAAATGTAAAAATCTTGAAAGAAAACC 5183
                         i ? v  i     vi  i v      v i     v    ii        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_94218489_9   5184 TAGGA-TATATTATTCTGGACATAGGAACAGACAAATATTTTATGGCAAA 5232
                             ?-  v  i-   vv   v v  ivi  i   vvi   iv i - v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-ATA 595

  chrX_94218489_9   5233 T-ACATCAAA--C-CAATTGCAACAATA-AAAACATTGACAAATGAGACA 5277
                          -   i    -- -   --       v -    v  v  i    vi   v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_94218489_9   5278 TAATTAAACTAAAGAGCTTTT-TACAGAAAAAAAACAACTATCAACTGAG 5326
                          v  i   v v  i i     - i vvv   ii -  -       vvi  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-CA-CTATCAAGAAAG 691

  chrX_94218489_9   5327 TAAAAAGACAACCTACATAATGGGAGAGAATTTGTGCAAACTATATATCC 5376
                          i           i   v         i   v v      ii       i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_94218489_9   5377 AACAAAAGTCTAATATTTAGCATTTATAAGGAATTTAAACAAATT--TAC 5424
                         i i  ii v  vi   ii  v  v     i   i ivv    v i--  v
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_94218489_9   5425 CAGAAA---AAATGATCCTATTAAAAAGTTGGCAAGGGATATGAACAGAC 5471
                         i i   ---    i i  v   ?    i v     i    v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_94218489_9   5472 ACTATTCGAAAGAAGACATACATGTGGCCAAAAATCTTATGAAAA----C 5517
                          i vi  v        i     vi       v  v vi       ---- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_94218489_9   5518 T-AACATCACTGATCAT 5533
                          -       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (132 / 93)
Gap_init rate = 0.03 (25 / 851), avg. gap size = 1.64 (41 / 25)  


2173 27.92 4.99 1.93  chrX_94246426_94250429.rev      561  1441 (2563)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94246426_9    561 TGGGGAGATATTCCATGTTCAAGAATAGGAAGTTGTAATATGGTTAAGAT 610
                            ii      i         v i  v     viv      v        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94246426_9    611 ATCAGTGCTTCCCAATTTGATCTCTAAATTTAATAAAATCTCAATGAAAT 660
                         iv  i i  i     v       vi i   i  iiv    i v  v   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chrX_94246426_9    661 GTCTAACAGTTAGCTATTCCTG------TTACTAAGTTTATGCTGAAGTT 704
                         i  i--   i iv  -  ii  ------  ivi   i v  v  i  i  
  L1M4_orf2#LINE/    100 ATCC--CAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_94246426_9    705 TATATGGAAAAGAATATACCCCAGAG-AGCTAACAATATATTT-----AA 748
                         i         v v viviv      i-   i  -  i -  i -----  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAA-AACA-ATCTTGAAAAA 194

  chrX_94246426_9    749 GAATATCTGATTTGGAATACTCCCACTACTCATTGTTAGAAATTATTATA 798
                            v v vi v     iv    v    v i  v v i i  v   i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_94246426_9    799 AACCTAAAACAGTCAAGACAGTATTGTGTTGGTG-AA--ATA-ACAGATA 844
                           v   v ii i          i v  ii   ii-  --   -   v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_94246426_9    845 G-----TGGAACAAAATGGAGAACCCAGAAATAAATTTAAACATATAGAG 889
                          -----     i i   v    ii           iii v    v  vi 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_94246426_9    890 TCAGCTGATTTTGGATAAATGAGAAAAGGCCATTCAATGAAGAAAGGATA 939
                            ii       v  i  iv v vv   i          ii     i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_94246426_9    940 GTCTTTTAAATAA-TGGTAATTAAACAACAAGAGATCCATATGCAAGAAA 988
                                v  i  -    iv vii     vi  v ?   i      i i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_94246426_9    989 ATGAATCTTGACACTGATTTAAAAACTTATGTGATAATTAACTTGAAATG 1038
                              vi v   v iv ii v v v v   iii v        ii     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_94246426_9   1039 AAACATATACCTAAATATAAAATGC-AACACTATAAATCTCAT----GAA 1083
                         i v  ? v        i   i -  -  v        v   v ----   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_94246426_9   1084 AATATGAGAGAAAGATCTAGGTGACTGGGGATTTGTCAATAAACTTTTAC 1133
                           i  ii ? v  -    vv     ivv  i  v v    iivi i   v
  L1M4_orf2#LINE/    544 AACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_94246426_9   1134 TTACAATACTGAAAGCACCCTTCATGAAA---AAAAT-GATAAATTAAAC 1179
                         v  ii i  ii       vvviv ii   ---     -        ii  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_94246426_9   1180 TTCATTATAAT-AAAAAATTCTGCTCTATGAAAGCCATTGT-AACAGAAT 1227
                              i v   -     v  i  iv  vii  i v  i i -  v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_94246426_9   1228 TAAAAGATGAGTCACCGA-TTGGAG------TT---AAA-CACATATCTG 1266
                         v      ii vi   v  - v    ------  ---   -  i       
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_94246426_9   1267 AAAAAAAAAAACAGAACCTTGTATTCAACATATACAAAGAACCCTTATAA 1316
                          v  iii ---------       i  iv     i       i    i  
  L1M4_orf2#LINE/    743 ATAAGGGA---------CTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_94246426_9   1317 CTCAACAAAAAGAAAACAAATAACCCAAATAAAAACTGTGTATAATAGCT 1366
                              i  v  i  i             v ?    v  v i v iv vi 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_94246426_9   1367 GAAAAGACACCACATCAAATAATATATACAGATGGGAAATAAGCATATGA 1416
                            v     iiv vi    v  v       i    vv        i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_94246426_9   1417 AAAGACACCAAACATCACATGTCAT 1441
                              ii iv       ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.35 (61 / 26)  

2908 27.86 0.69 0.46  chrX_94246426_94250429.rev     2641  3505 (499)    L1M4_orf2#LINE/L1        1   867 (41)  

  chrX_94246426_9   2641 TGAAAGGACATTTCATGTTTATGGATTAGAATAATCAATATTGTTAAAAT 2690
                           i  i  i  ii      i       i   v v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94246426_9   2691 GTTCATACTACACAAATCAATGTCTAAATTCAATGCAATCTCTATCGAAA 2740
                          viv     v v     ii  v vi i      i      i     i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94246426_9   2741 TACTAATCACATTCTTCACAGAAAGGGAAAAAATATTCTTACAATTTATA 2790
                          v i iiii v  i  ii      vv  v  iv iv  i  v    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_94246426_9   2791 CAAAGTAACAAAAGATCCAGAAGGCCCAAAACCATCCTGAGAAA-AAGAA 2839
                         iii ivvi   ii  i      viv       v   i   i   -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_94246426_9   2840 CAAAACTGGAGGAATCCCATTACTTGACTTCAAATTATACTGTAGAACTA 2889
                             ii       v  v  i v iii i      viv    ii i i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_94246426_9   2890 CAGTGACCAAAAAAATATGGTACTGTCATGAAAGCAGAAATACAGACCAA 2939
                             i i   i v i i        v   i iiii   v   i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_94246426_9   2940 TGAAACAGAATAAATAACACAGGAACAAATCTACACACTTACAGTAAACT 2989
                           i  i     vi v iiv   i  i   i i i   i   ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_94246426_9   2990 CCTTTTCAAGAAAGATGCCACTAACATACATTGGAGACAAGCCAGTCTAT 3039
                         vv     i v  i i     vv v   v  v   i  v iivi     v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_94246426_9   3040 CCAGTAAATGATGCTGGGAAAA-TGAATATCCATATGCAGAAGA-TTAAA 3087
                         i  ii     i        v  -  i   ?   i     i    - v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_94246426_9   3088 CTCGATCCCTGTCTCTCACTTTATACAAAAATCAAGTCAAAATGGATTA- 3136
                         i v  i    ii   v   iv           i  v           i -
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_94246426_9   3137 ATACTTAAGTCTAAGATCTCAAAATATGAAACTGCTACAAGAAAATATTG 3186
                          v  i   i v     v  v   v   i     vi  v       i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_94246426_9   3187 GGGGAAACTCTCCAAGACATTGGTCTGGG-AATAAATTTATTGAGCAATA 3235
                          ? v   -   i iv   v    vi i  -   ii-   v  iiii vv 
  L1M4_orf2#LINE/    551 GNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGA 598

  chrX_94246426_9   3236 CCCCAAAAGCACAGGCAACCAAACCAAAAATAGACAAATGGGATCATATC 3285
                          v           i     v   vv         i    v   iivi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_94246426_9   3286 AAGTTTAAAAGCTTCCTTACAGCAAAGGAAACAGTCAACAAAATGAAGAG 3335
                           iv      i   iiv i vv       v  vi    v   i    i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_94246426_9   3336 ACAACCCACAGAATAGGAGAAAGTATTTGCAAGTTACCCATCTGACAAGG 3385
                                       i       i         i i ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_94246426_9   3386 GATGAATAACCAGAATATATAAGGACCTCAAACAACTCTATAGGAAAAAA 3435
                           ivvi  v             i  v   vv       v   iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_94246426_9   3436 AATCTAATAATCCAAT-AAAAAATAGGCAAAATATTCAAATACACATTTC 3484
                          -- v     i     -?      i      iv   ii    v       
  L1M4_orf2#LINE/    799 A--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_94246426_9   3485 TCAAAAGAAGACACACAAATG 3505
                           v        i i       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATG 867

Transitions / transversions = 1.62 (147 / 91)
Gap_init rate = 0.01 (9 / 867), avg. gap size = 1.11 (10 / 9)  

 989 28.62 1.64 0.33  chrX_94246426_94250429.rev     3699  4002 (2)    L1M4_orf2#LINE/L1      344   651 (257)  

  chrX_94246426_9   3699 GCCAACAGACTTTC-ACAAAAATG---AGAACACACAGTTGAGGAAGAGA 3744
                          i   iv  i    -    iii  ---   v  iv  i v i i    - 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-A 392

  chrX_94246426_9   3745 CAGTCTCTTCAATAAATGGTGTTGGGAAAGCTGGATATCCTCATGCAGAA 3794
                         i     i     i        i     v i       ?  v      i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_94246426_9   3795 AAATAAAAAAGGGCCCTTATCTCTCCCCACATAGAAAAAACAACTCAAAA 3844
                         i   i  ivv  i   i  i   v v   i   v     vi         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_94246426_9   3845 TGGAAAAAGAACTTAAATCTAAGACTTGAAACTGTCAAACGATTAGAGAA 3894
                             vv ?ii  i     v     vi i     i v    vv     ii 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_94246426_9   3895 AGTCAT-TGAGAAAATCTTCTTGACATTAGTCTGGAAAAAGATTTTTTAG 3943
                          iv   -v ? v        v    v  i vi i iv  v i   i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_94246426_9   3944 ATATGGTCCTGAAAGCACAGACAATAAAAGGGAATATAAACAAATGGAAC 3993
                              iiv ii        ii   i     ii  v   i i    v i  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_94246426_9   3994 TGTATAAAA 4002
                          vi  v   
  L1M4_orf2#LINE/    643 TTCATCAAA 651

Transitions / transversions = 1.62 (52 / 32)
Gap_init rate = 0.01 (4 / 308), avg. gap size = 1.50 (6 / 4)  


2245 29.72 1.41 2.93  chrX_94252496_94257860.rev     3969  4890 (475)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94252496_9   3969 TGAAAAAACATTCCATGCTCATGGATAAGAAGAATCAATATCATTAAAAT 4018
                           i   i i  i     i        vi     v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94252496_9   4019 GGCCACACTGCCCAATGCAATTTATAGATTCAATGCTATTTCTATTGAAC 4068
                            v i   v     vvii  i  i        i  v  ii    ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94252496_9   4069 TACCAATAATATTCTTTACATACCTAAAAA--GAAAAG---ATTTCAAAA 4113
                          v   iiviiv  i   i  ------i   --  v   ---  iii    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA------GAAATTGACAAGCTGATCCTAAAA 144

  chrX_94252496_9   4114 TTTACCTCTAACCAAAACAGAGCCCAAATAGCCAATAAGATTCTAAGCAA 4163
                           i iv vv  viiv  vi  v  vi         v vi  ii i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_94252496_9   4164 AAAGCAAAAAGCTGGAAATACT-AGGCTACCGAACTTCAAACAATACTGC 4212
                         i   v v    i    ii-   - vi  v  v  i      vvv    i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_94252496_9   4213 AATACAACAGTAACCCAAACAGCAAGGTATTGGTACAAAAACAGTCACAT 4262
                           vi v       i v i    iiv    i   i i  ii i  v  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_94252496_9   4263 AGACCAGTGGAACAGAATAAAGAACCCAGAAATAATGCCACATACCTACA 4312
                            i  i     i     vi   ii          vv   i i ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_94252496_9   4313 GCTATCTAATCTTCAATAAAGCTGACAGAAAATAAGCAATGTGGAAAGAC 4362
                          ii vi i  i   i i  i v  v  - i vi vv     v       v
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAA 392

  chrX_94252496_9   4363 TC-CCTATTCAATAAATAGTGCTAAGATAACTGGCTAGGCATATGCAGAA 4411
                          v-i  v     i    i     ii  i      v  ?v  i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_94252496_9   4412 GATTGAAACTGGATTCTTTTCTTACACCGTTTACATAAATTAACTTAAGA 4461
                           v    ii    ii i vi  i     i v    v         i  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_94252496_9   4462 TGGATTAAAAACTTTAATGGAAAACCCAAAACTATAAAAACCCTGGAAGA 4511
                              i ? i  i v    v  i v i            vi i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_94252496_9   4512 CGACCTAGGCAATAACATTCTAGACATAGGCACAAGCAACAATTT--TAT 4559
                         vi  v    ?ivv  iv   vv   v v  vvi i    iii   --  v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_94252496_9   4560 ATTGAGGACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAACCAG 4609
                           -- v             vvv          v      v  i   iii 
  L1M4_orf2#LINE/    593 AT--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_94252496_9   4610 ATCTAATCAAACTAAAAAGCTACTGCGCAGTAAAATAAAAAAAAAAAAAA 4659
                          ii v      v v    i  vi  i  vvi   i-----------i v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG-----------GACA 679

  chrX_94252496_9   4660 CTATCAACAGGGTGAAAAGACAACCTACAGAATGAGAGAAAAATTTTGCA 4709
                                v ii              i        i       vv      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_94252496_9   4710 AACTATGCATCTGACAAAGGTCTAATATCCAATATCTATAAGAAACT--T 4757
                           ii  ii      i  i  v  vi      iv  v     ii    -- 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_94252496_9   4758 AACCAAATTTACAA-AAAATAATAAACAACCCTATTAAAAAGTGG-CAAA 4805
                          --   v iv i  -    vi i   i     v   ?    i   -    
  L1M4_orf2#LINE/    780 A--CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_94252496_9   4806 GGACACGAACCATCACTTTTCAATACAAAACATGCTTGCAGCCAACAAGC 4855
                            ivi   iviv  i  i  v v v  i i  i vviii     i    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_94252496_9   4856 ATATGAAAAAAAAAACCCTCAATATAACTGATCAT 4890
                          i       i vi----     i  v ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATG----CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (165 / 105)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  


2683 29.03 0.99 0.88  chrX_94259188_94264169.rev     3586  4491 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_94259188_9   3586 GGAAACACAACCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAATG 3635
                              v i v      i        v  v   v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_94259188_9   3636 ATCATATTGCCATAAGCAGTCTACAAATTCAATACAATCCCCATCAAAAT 3685
                         iiv   i v  vv  viii      i      ii       i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_94259188_9   3686 ACCACCATAATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCATAT 3735
                         v   v vvvv  i  ii     v v  v  ivii  i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_94259188_9   3736 GGAACCAAAAAAGAGCCCGCATAGCCAAAGCAAGACTAAGCAAAAAGAAC 3785
                             viiv  ii  v  v v         i   vvi i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_94259188_9   3786 AAATCTAGAGGCATCACACTGCCTGATTTCAAACTATACTATATGGTTAT 3835
                            vi i    vv       v  ii        viv     i vi i  i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_94259188_9   3836 AGTCACCACAATAGTGTGGTAGTGGTATAAAAAATAGGCACATAGACTAA 3885
                            v i  vi i         v   i    ii -   i  i     ii  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAA 300

  chrX_94259188_9   3886 TGGAACCCAACAGAGAAAGCAGAAATAAATCCTAACTTTTACAGCCAACT 3935
                              ivv  iv    ivv          i  vv  v    ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_94259188_9   3936 GATCTTTGACAACAAAAACAAAAAGATAAAGTGGAAAAAAGACACCCTTT 3985
                            i  i     viiviv   i vv  vv i   ii   ii i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_94259188_9   3986 TCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAAA 4035
                                            i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_94259188_9   4036 CTGGATCTCCATCTCTCACCTTATGCAAAAATCAATTCAAGATAAAATAA 4085
                         i    i i i i   v    v   i       i  i    i  ii vi ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_94259188_9   4086 GGACTTAAACCTAAGACCTATAACTATAAAAATTCTGGAAGAGAATATTG 4135
                         i   i    iv     v   v          v ii i     i  i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_94259188_9   4136 G---AAATACCCTTCCAGATATTGGCTTAGACAAGGAGTTCATGATTAAG 4182
                          ---    ---    vv  iv    v    i   v iv   v iiv  v 
  L1M4_orf2#LINE/    551 GNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_94259188_9   4183 AACCCCCAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTAAT 4232
                          vv  vv     v v    i    iv   i   i   iv v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_94259188_9   4233 TAAA-CTAATGAGACTT--GCACAGCAAAAGGAACAGTCAGCAGAGTAAA 4279
                         i   -i   -- i    -- ii vv    i iv  vi   iv i   i  
  L1M4_orf2#LINE/    648 CAAAATTAA--AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_94259188_9   4280 CAGACAACCCACAAAGTGGGAGAAAATCTTCACAATCTATACATCTGA-A 4328
                         v            i i           v  ii   vii   i      - 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_94259188_9   4329 AAAGATTAACATCTAGAATTTACAGTGAACTCA-AAAAATTAGTAAGAAA 4377
                          ii  i vii   i     v  i iv      v- v  v i i   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_94259188_9   4378 AAAACAAACAATCCCACAAAAAAGTGGATTAAGGATATGAACAGGCAATT 4427
                           i     i  i  v iv?    i   iiv      v    i  i  v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_94259188_9   4428 CTCAAAAGAAGATATGAAAATGGCCAA-AAATATGGAAAACAAAATATGC 4476
                            v           iv          -  ii iivi   -- i  iiv 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA--AGATGCTC 893

  chrX_94259188_9   4477 AACATCACTAATTAT 4491
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (153 / 107)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 1.70 (17 / 10)  


2650 27.33 3.26 1.12  chrX_94286860_94291733     3493  4381 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94286860_9   3493 TGCAAAAACATTCCATGCTCATGGACAGGAGGAATCAATATCGTGAAAAT 3542
                           v   i i  i     i       iv   i  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94286860_9   3543 GGACATACTGCCCAAAGTAACTTATACCTTCAATGCTATTCCCATCAAGC 3592
                           vv     v      v i ii  i vv     i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94286860_9   3593 TACCATTGACTTTCTTTGCAGAATTAGATAAGACT-ACTTTAAATTTCAT 3641
                          v   vivi i  i         v v  i   -  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_94286860_9   3642 ATGGAACCAAAAAAGAGCCCATATAGCCCAGATAATTTTAAGCAAAAAGA 3691
                               viiv  ii  v  viv      v i i   i  i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_94286860_9   3692 ACAAAGTTGGAGGCATCATGCTACCTGACTTCAAA-----CTATAAGGCT 3736
                                      vv   ii  v  ii i      -----   i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_94286860_9   3737 ACAGTAACCAAAA-AGCATGGTACT--CATACCAAAACATGTATATAGAC 3783
                                i   i -  ii       --    -- ii i vii       i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATATAGAT 297

  chrX_94286860_9   3784 CAATGGAA-AGCAACAGAGGCCTCAGAAAGAACACCACATGTCTACAACC 3832
                                 -  -  iv   ivii      v  vv   i ii i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAG-AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_94286860_9   3833 CTCTGATCTTCGACAAACCTGACAAAAGCAAGCAATGGGGAAAGGATACC 3882
                         vvi    i        ivv  v   i v  vv            i   vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_94286860_9   3883 CTATTTAAAAAATGGTGCTGGGAAATCTGGCTAGCCATATGCAGAAAAAA 3932
                           v  i  v              v v    v  ?   i     i  i  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_94286860_9   3933 GAAACTGGAACCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 3982
                            ii    v    v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_94286860_9   3983 TTAAAGGCTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGAAAGC 4032
                          i ?  i i         i v i            vi i i       i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_94286860_9   4033 CTAGGCA-ACACCATTAAGGGAATAGGCATGGGCAAAGACTTCAT-GACA 4080
                         v    ?i- v i v iiv ivvv i  i- i     v ii   v -  i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chrX_94286860_9   4081 AAACAGCAAA-GCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4129
                         vi   v    -   vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_94286860_9   4130 ATTAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATC------GTCA- 4172
                           i   v v  i i   i  iv vv    i  v      ------  v -
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_94286860_9   4173 --GGCAACCTACAGAATGGGAGAAAAT-TTTTCAATCTATTCATCTGACA 4219
                         -- i     i                 -   v   vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_94286860_9   4220 AGGT-CTAATATCCAGAATCCACAAGGAACTTAAAAAAATTTATAAGAAA 4268
                            v-  vi          vi i  i     ivv v  v iv    v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_94286860_9   4269 AA-ACAA-TGTC---ATCAAAAAGTGGGTGAAGAATATGAACAGATGCTT 4313
                           -    - iv ---  i?    i    ii   i  v    i   iii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_94286860_9   4314 CTCAAAAGAAGACATTTACGTGGCCAATAAACATGTAAAAAAAAAAAAAG 4363
                            v        i  vi vi          i  ii i    i v----- 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-----G 890

  chrX_94286860_9   4364 CTCATTATCACTGGTCAT 4381
                             vi    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.95 (39 / 20)  


2916 27.14 1.56 0.56  chrX_94302969_94307199     2840  3738 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94302969_9   2840 TGGAAGAGTATTCTATGTTCACTTATTGGCAGAATCAATAT-GTTAAAAT 2888
                              iii   i i       ivv     v   v i     -     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94302969_9   2889 ATCCATACTACCAAAAGCAATCCACAGATTCAATGCAGTCACTATGAAAA 2938
                         iv v     v  v   vii   i          i   i  v    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94302969_9   2939 TACCAATGACATTTCCCACAGAAATGGAAAAA-TAATCCTAATATTTATA 2987
                          v   iivi v   iiii       v  v  i- i       v   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_94302969_9   2988 TGAAATCACAAAAGACCCAGAATATCCAAAGTTATCCTAAGAAAAAATAA 3037
                           i  vii   ii           v     iiv   i i i   i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_94302969_9   3038 GAAAACCGAAAGAATCACATTACCTGATTTCAAATTATACTACAGATCTA 3087
                         v   iii i i  v     i v  ii        viv       i v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_94302969_9   3088 TCATAATCAAAACAGCATGGTACTGGCATAAAAACAGACACATACACCAA 3137
                         ivi       i    ii              ii i     i   v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_94302969_9   3138 TGAAACATAATAGAGAACCCAGAAACAAATCCATATACCTACTTTTTACG 3187
                           i  i v   v    ii       i   i     i ii  ivv iv iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_94302969_9   3188 CATTTTTCACCAATATGCCAT--TTATGC--TGGAGAAAAGACAATCTCT 3233
                         v     iv  v ivi     v--ii  v --   i    ii i i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_94302969_9   3234 TCAATAAATGGTGCTGGGAGAACTGGATATCCACATGCAGAAGAATGAAA 3283
                             i              v         ?         i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_94302969_9   3284 CAAGACTCCTATCTGTCACCATTTAGAAAAA--AAATTAAAGTGGATTAA 3331
                         ivi   i    i  vv      v  v     --  v i   i     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_94302969_9   3332 AGACTTAAATCTGAGACCTCAAAATATGAAACTACTACAAGGAACC-T-G 3379
                             i     v i   v  v   v   i     vi  v   i  v - - 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_94302969_9   3380 GTGAAAATCTCCAGGACATTAGTCTGGGAAGAAATTTCTTGAGCAATACC 3429
                          ? v      i iv   v  i vi i  v ivii      iiii vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_94302969_9   3430 CCACAAGCACAGGCAACCAAAACAAAAACAAACAAATGGAATAACATCAA 3479
                            v       i     v   iv     i i i    v i ivv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_94302969_9   3480 G-TTAAAAAGCCTTTGCACAGTAATGGAAACAATCAACAAAGTGACAAGA 3528
                         i-       - i    ii vvi  v   v  v     v       v    
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_94302969_9   3529 CAACTCACAGAGTGGAAGAAAGTATTTCCATACTACCCATCTTATAAGGG 3578
                             i      i   i     i     v  v ii ivi    v       
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_94302969_9   3579 ATTAATAATCAGAAGA-AGAAGAAGCTCAATTA--ACTCTATAGGAAAGA 3625
                          i vi  vi     v - v  ii i   --   --    v   iv   - 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCAATAATAAA-A 796

  chrX_94302969_9   3626 ATTCTAATAATCCAATCAAAAGATGGGCAAAATATCCAAATAGACATTTC 3675
                          vv v     i     i?   i         iv  iii            
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_94302969_9   3676 TGAAAATAACAACGTACAAACGGCAAAGAAGCATATGAAAAGATGCTCAA 3725
                          vv   v  -i ii      i   v  v     i                
  L1M4_orf2#LINE/    847 TCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_94302969_9   3726 CATCATGGAATAC 3738
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.36 (19 / 14)  


2798 26.03 1.40 3.35  chrX_94313382_94317681.rev     2884  3809 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94313382_9   2884 TAGAAACACATCCCATGCTCATGGGTGGGTAGAATCAATATTGTGAAAAT 2933
                          i    v i        i      i v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94313382_9   2934 GACCAGACTGCCGAAAGCAATCTACAAATTCAATGCCATACCCATCAAA- 2982
                          i v v   v  v   vii       i      i  v  v  i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94313382_9   2983 TTCCA-CTATCATTCTTCATGGAACTATAAAAAA--AATCATAAAATTCA 3029
                          i   -  ii -  i  iiii   v - i v  i--i   v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chrX_94313382_9   3030 TATAAACCAAAAAAAAAAAAAAAAAAAAAGAAAGTAAAAAGAGCCCACA- 3078
                            -------------------------- i  i iv  i ii    v -
  L1M4_orf2#LINE/    149 TAT--------------------------GGAAATGCAAGGGACCCAGAA 172

  chrX_94313382_9   3079 TAGCCAAAGCAAGACTAAGCAAAAAGAACAAATCTGGAGACATCACATTA 3128
                                 i   vvi i iv  i         vi     ivv     i v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_94313382_9   3129 CCTGATTTCAAACAATATTAGAAGGACATCATAACCAAAACAGCATGTTA 3178
                           ii        vvv  i  v  i vi ivi   i   i    ii  v  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_94313382_9   3179 CATGTATAAAAATAGGCACATAGACCAATGAAACAGAATAGAGAAACCAG 3228
                          vv i    ii    i  i     i     i  i     v    iv    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_94313382_9   3229 AAATAAATCTTAATACTTACAGCCAACTGGTTTCTGACAAAGCAAACAAA 3278
                                i ivv i i   ii i   i  i   ii     i vviv   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_94313382_9   3279 AACATAAAGTGGGGAAAGGGCACCCTATTTGACAAATGGTGCTGGGATAA 3328
                          v   vv i         iii vi  v  ii                i  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_94313382_9   3329 TTGACTAGCCACATGTAGGAGAATAAAACTGGATACTCATATCTCACCTT 3378
                         i  iv  ?       i ii     i  ii    iv ii iv  v    v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_94313382_9   3379 ATGCAAAAATGAACTCAAGATGGATCAAAGACTTAAATCTAAGACCTGAA 3428
                           i       v       i        ?    i     v     v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_94313382_9   3429 ACTA-ACAATTCT-AGAAGATAACATCGGAA-AAACCCTCCTAAACATTG 3475
                             - v  i   -      v     v  ?i-   i i  v i v -   
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC-TTG 571

  chrX_94313382_9   3476 GCTTAGGCAAGAATTTCATGACCAAGAACCCAAATGCAAATGCAATAAAA 3525
                          v        vii    v iivi v  vv     v   v v    i    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_94313382_9   3526 ACAAAGATAAATACCTGGAACTTAATTAAACTAACAAGCTTTTGCACAGC 3575
                         iv   i   i   vv v i    v  i   v v v  i      ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_94313382_9   3576 AAAGGA-ACAGTCAGCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAA 3624
                               -  vi   iv i   i  v              i          
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_94313382_9   3625 TCTTCACAATCTATACATCTGACTAAGAACTAATATCCAGAATCTACAAA 3674
                          v  ii   vii   i      iv i i   vi          v  i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_94313382_9   3675 GAACTC----AAATCAGCAAGAAAAAAACAAGCAATCCCATATCAAAAAG 3720
                               ----  v   ii  v     i    ii  -    -  i?    i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAA-CCCA-ATTWAAAAA 819

  chrX_94313382_9   3721 TGAGCTAAGGACATGAATAGACAACTCTCAAAAGAAGATACACAAATGGC 3770
                           i  v     iv          vi    v          i         
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_94313382_9   3771 CAACAAACATACGAAAAAATGCTCAACATCACTAATCAT 3809
                            i  i  i i     i             ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (145 / 92)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.93 (44 / 15)  


2499 27.15 3.24 1.79  chrX_94335759_94341102     3964  4858 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94335759_9   3964 TAGAAAAACATTCCTTGTTCATTAATAGAAAGAATCAATATCATTAAAAT 4013
                          i    i i  i  v       vi  v i    v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94335759_9   4014 GTCTGAACTGCACAAAGCAACTTACAGATTAAACGCTGTTCCTATTAAGT 4063
                          v viv   v v    vii ii        v     vi i     i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94335759_9   4064 T----ACTGACCTTCTTCACAGATA--GAAAAATT-ATTTTAAAATTCAT 4106
                          ----i   -    i  ii    v --  v  ii -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_94335759_9   4107 ATGGATCAA---AAACGACCCCACATTGTTAACGACA-TCCTAAGCAAAA 4152
                              --  ---  iv     viv  v ii  -i   -  i i iv  i 
  L1M4_orf2#LINE/    150 ATGGA--AATGCAAGGGACCCAGAATAGCCAA-AACAATCTTGAAAAAGA 196

  chrX_94335759_9   4153 AGAACAAAGCTAGAGGCATCACGCTGCCCTACTTCAAACTACACTAGAGT 4202
                                  i i    vv    i  v   v i      vivi    v iv
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_94335759_9   4203 GCTGCAGTAACCAAAACAGCATGCTACTGGCACAAAAACAGACTCATAGA 4252
                            i      i   i    ii  v        i  ii i    vi     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_94335759_9   4253 CCAATGGAACAGAATAGAGAACCGAGAAATAAGACCTCATAC--CTACAA 4300
                         i        i     v    ii v        -   -     --i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAA-ACC-CATACATTTATGG 344

  chrX_94335759_9   4301 CTATCTGATCATTGACAAATCTGACAAAAATATGCAGTGAAGAAAGGAT- 4349
                         ii vi    iv i     ivv  v   i vi  v  i  ii     i  -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_94335759_9   4350 -TCCTTATTCAATAAATGGTGCTGGGATAACTGGTTAGTTATATCCCCAA 4398
                         -  i  --    i              i      v  ?ii i  v vv  
  L1M4_orf2#LINE/    395 GTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_94335759_9   4399 AATGGAAACTTAGCCCTTTTCTTACAACATATACAGAAATTAACTCAAGA 4448
                         i vv   ii vii   i vi  i   v        i            i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_94335759_9   4449 TTGATTGAAAACTTAAATGTAA-AGCTCAAAACTATAAAAACCCTGGAAG 4497
                          v   ii? i  i         -    -            vi i i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAG 541

  chrX_94335759_9   4498 ATGACCTAGGC---AATACTATCCTGGGCATAGGAATAGGCAAAGATTTC 4544
                          vi  v    ?---   -  -  v  iv v i  v-       v i    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CT-TCGTGACCTTGGGT-TAGGCAATGGTTTC 588

  chrX_94335759_9   4545 AT-GATAAAGATGCCAAAAGCAATAATAACAAAAACAAAAATTGACAAAT 4593
                         v -    v-  ii         vv ii       iv      v  i    
  L1M4_orf2#LINE/    589 TTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_94335759_9   4594 GGAATCTAAT-GAAACTAAAAA--TCTGCACAGCAAAGGAAACTATCAAC 4640
                         v i ii v  -i   i      -- i  ii vv       v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_94335759_9   4641 AGAGTGAAAAGGCCAACCTACAGAATGGAAAAAAAT--TTGCAAACTGTA 4688
                          i         i -    i         i i     --       iii  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGAC-AACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_94335759_9   4689 CGTCTGACAAAGGTCTAATATCTACAATCTATAACAAATTCAAACAAATT 4738
                         ii     i  i  v  vi    i v   v     vi  i  vv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_94335759_9   4739 TACAAAAAAAACACCA----CCCCATTAAAAAGTGGGCAAAGGACATAAG 4784
                         v i  v     v  v ----   v   ?    i           iv i i
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_94335759_9   4785 CAGACGCTTTTCAATAGAAGACATACATATGGCCAACAATTATATAAAAA 4834
                         i    ii  i  v v      i     v        i  vi i  i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_94335759_9   4835 ATAACTCATGACACTGATCATAAG 4858
                         ivvi    --   iii????????
  L1M4_orf2#LINE/    887 GATGCTCA--ACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (150 / 89)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 1.67 (45 / 27)  


1805 21.52 4.43 1.69  chrX_94365757_94368699     1247  1720 (1223)    L1M4_orf2#LINE/L1        3   489 (419)  

  chrX_94365757_9   1247 GAAAAAGTTTTTATATTCATGGATTGAAAAAC--AATATT---AAGATGG 1291
                             i vv iii  i           i  i  --      ---       
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_94365757_9   1292 CAATAATACCCAATTAAATCTATAGATTCAATTCATTCTCTATCAAAATC 1341
                              v v     v vi     i        iv  v  i           
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_94365757_9   1342 CCAGTGGTAGTTTTATTTTACAGAAATAAAAACACTACTTCTAAAGTTAA 1391
                             i-- - ii  -    i       vi v vi  iv i     i  v 
  L1M4_orf2#LINE/    103 CCAGC--T-GCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_94365757_9   1392 TATAAAATTGCAAGAGACTTCAAATAGCCAAAACAACTTTGAGAAATAA- 1440
                            ii  v      i   iivi              ii    i   v  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_94365757_9   1441 AACAAAGTTGAAGGAC--ACCCTTCATGACTTCAAAACTTACTATAAAGC 1488
                                   i     --  v    vii i              i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_94365757_9   1489 TACAATAATTTTTAAAA--ATGTGATGTTGGGAGAAG-ATAGAAATATAG 1535
                             i    i---  i --i    i ii   v v   -     v      
  L1M4_orf2#LINE/    249 TACAGTAATC---AAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_94365757_9   1536 ATCACTGAAATAAAA------GTTCTAAAATACATCCTTAAATCTTTGGC 1579
                             v  i    i  ------  i vi     v i  v  v  i v   i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_94365757_9   1580 CTACTGATTTT-GACAAGGGTGCCAAGAC-ATTCAATAATAAAAGGA-AG 1626
                          v i       -                 -       iivi    i -  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_94365757_9   1627 TTCTCTTCTTTAAATGATACTAAGACAACTAGATAGCCACATG-AAAAGA 1675
                          -  i   vvi     i i  ii       i    ?       -      
  L1M4_orf2#LINE/    396 T-CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_94365757_9   1676 ATAAAGTTAGGCCATTTCCTCACGCCACATAAAAAAATTATCTCA 1720
                           i     i i  vi v      i   i   v        v    
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

Transitions / transversions = 1.89 (66 / 35)
Gap_init rate = 0.03 (16 / 487), avg. gap size = 1.81 (29 / 16)  

1396 22.14 2.10 0.93  chrX_94365757_94368699     2022  2450 (493)    L1M4_orf2#LINE/L1      475   908 (0)  

  chrX_94365757_9   2022 ACAAAAATTTATCTCAAAATGGATCAAAGAGCTAAATAAAACATCTAAAA 2071
                                -   v              ?   v      iv  v v      
  L1M4_orf2#LINE/    475 ACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_94365757_9   2072 ATACAAAACTCT-AAAAGAAAACTTGAGGGGAAAGCTTTATGACTTTGGA 2120
                         v  i        - i        v ii ? v   v   ii    i    i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_94365757_9   2121 TTTAGCAATGAATTCTCAGATACAAGA-AAAAAGGAAAAACAACAA--CA 2167
                           vi      iv    i     ii v -v     v v  i      --v 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_94365757_9   2168 AAAAATAGA-AAATTGGACATCATTAAAATTGATGTTTTGTGTGTATCAA 2216
                                  -         v    i      i vivi  v    iv    
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_94365757_9   2217 TAAATACTATAAAGAATGCCAAAAGAGAACACATAGAATGGGATAGATTG 2266
                         vii i     v     v iv      v   v  i         v i v i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_94365757_9   2267 TTGGTAAAATCATATTTCTGGTTTGGGCCTAATATCCAGAAGATATAAA- 2315
                           v i   -      v    i vv   v  vi         v       -
  L1M4_orf2#LINE/    724 TTTGCAAA-TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_94365757_9   2316 AACTCTTAAAACTCAATAAGAAAAATAGAGAAAACTCAATTTTTAAATGG 2365
                                 v          v     v v i v   i     ?vv      
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_94365757_9   2366 ATGAATAA-ATGGATAGACTTTTCTCCAA-GAAAACACACAAAAATGGCC 2413
                         iii  vi -v  i      v         -   i i i     --     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA--TGGCC 870

  chrX_94365757_9   2414 A-CAAGGACATAAAAAGATGTTCAAAATTATTAGTCAT 2450
                          -i   v    i        i    v  i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.92 (44 / 48)
Gap_init rate = 0.03 (11 / 434), avg. gap size = 1.18 (13 / 11)  


2626 25.67 5.25 1.87  chrX_94374814_94379018.rev     2849  3705 (500)    L1M4_orf2#LINE/L1        1   886 (22)  

  chrX_94374814_9   2849 TGGAAAATCATCCCATACTCATGGATTGAAAGA----ATACTGCTAAAAT 2894
                               ivi       ii          i    ----   i  i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94374814_9   2895 GATCATACTGCTCAAAACAATCTACAGATTCAACAAATTCCCTATCAAAT 2944
                          iiv     v i    vii               iv v           v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94374814_9   2945 TATCAATATCAACTTTTATAGAATTAGAAAAAAT--TTCTAACCCTTATA 2992
                          vi  iivv vvi    ii    v v  v  iv -- i    vvi i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_94374814_9   2993 TGGAACCAAAGAAAGATACC--AAATAGCCAAAGCAATCCCAAGCAAAAA 3040
                              --- v v   iv   --i          i     iii iv  i  
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_94374814_9   3041 GAACAAAGCCAGAGGTATCACATTAACTGACTCCAAAATGTACCATAAGA 3090
                                 iii    vv     i vv ii i i     iv   i i  ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_94374814_9   3091 CTGTGGTAACCAACATAGCATGGTAC----A-AAAAATAGACACATAGGT 3135
                           iii    i   v i  ii      ---- -  ii       i    i 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_94374814_9   3136 CACTGGAACAGAATAGAGAACCCAGAGTTAAAGCAATATACCTACAGCCA 3185
                           v     i     v    ii     iv    v v   i ii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_94374814_9   3186 ATTGATCTTTGACAAAATTGGCAAAAATATACAATGGGGAAAGGACACTC 3235
                               i  i     iiv  v   i vi  v            i i v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_94374814_9   3236 TATTTAATAAATGATGCTGGGAAAATTGTATAGCCATATGCAGAAGAATG 3285
                          v  i  i     i        v  i  v   ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_94374814_9   3286 AAACTGGACTCCTATCTCTCACCATAAACAAAAAATTAACTCAAAATGGA 3335
                           ii     i    i   v       v       -               
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGA 496

  chrX_94374814_9   3336 TTAAAGCCTTAAATGGATGACCTGAAATTATAAAAATCCTAGAAGAAAGC 3385
                          i ?  v i      v v  v  i   i       v  i         i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_94374814_9   3386 CTAAGAATATCTCTTCTGGACATTGGCCTAGGCAAATAAATTAT--GACT 3433
                         v  i ?i  vv     vv   v    vi       - iiv  v --  - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA-T 594

  chrX_94374814_9   3434 AAGACATCAAAAGCAAATGCAACAAAACAGACAAATGAGATGAAATTAAA 3483
                          v    i        v v         v i -    -    -     ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAA-AAAT-AGAT-AAATTGGA 641

  chrX_94374814_9   3484 AGGTTCTTCATAGCAAAATAAGAAACT----------------------- 3510
                         -----      --      v i     -----------------------
  L1M4_orf2#LINE/    642 -----CTTCAT--CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_94374814_9   3511 AACAGAGTAAACAGGCAATCTACAGAATGACAGGA--TATTTACAAACTA 3558
                           v i   i  v  i   i i        iv  i --     i    ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_94374814_9   3559 TGCGTTTGATCAGAAACTAATATCCAGAATCTAAAAGAAACCCAAAGAAC 3608
                          iii i    v  ii   vi          v  v  ii   i vv v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_94374814_9   3609 TTAACAAGAAAAAAA-----AACTCCATTAAAAAGTGGGCAAAGAACATA 3653
                          i  i  v     i -----   i v   ?    i         i iv i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_94374814_9   3654 AATATACATTGTTTAAAAGAAGACATACAAGTAGCCCATCAACATACGAA 3703
                             v     vi iv        i      i i   v  v i  i i   
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_94374814_9   3704 AA 3705
                           
  L1M4_orf2#LINE/    885 AA 886

Transitions / transversions = 1.70 (136 / 80)
Gap_init rate = 0.02 (18 / 886), avg. gap size = 3.39 (61 / 18)  


2522 29.55 0.65 1.64  chrX_94395780_94401413     4249  5165 (469)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94395780_9   4249 TGGAAACCCATCTAATGCTCATGGATGCATAGAATCAATATTGTGAAAAT 4298
                               vvi   iv   i        vviv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94395780_9   4299 AACCATACTGCCAAAAGGAATATAAACATTCAATGCAATTCTCATCAAAG 4348
                         ii v     v  v   vvi  v  v v      i     i ii      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94395780_9   4349 CACCATCATCATTCTTCACAGAAGTAGAAAAAACAATCTTAAAGTTCATA 4398
                         iv   v vv v  i  ii     i v  v  ivii   i    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_94395780_9   4399 TGAAACCAAGAAAGAG-CCCA-CATAGCGAGAGCAAGA-TAAGCAAAAAG 4445
                           i  -- v v   i -    -v     v i i   vv- i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_94395780_9   4446 AACAAATCTGGAGCCATCACTTTACCTGACTTCAAAATATACTACACGAC 4495
                               vi     vvv    vi v  ii i       iv       vii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_94395780_9   4496 TACAGTTACCAAAACAGCATGGTATTGGTATAAAAACAGGCATATAGACC 4545
                               v i   i    ii     i   i    ii i  i        i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_94395780_9   4546 AAAGGAACCAAATAGGGAGCCCAGAAATAAAGCCAAATACTTACAGCCTA 4595
                           v    ivi   v i   i           v   v i i   ii i v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_94395780_9   4596 CTGATCTTCAAAAAAGCAAGCAAAAACATTAAGTAGGGAAAGGACAGCCT 4645
                         i    i   i v  i vviv   i v    v i i       i i  i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_94395780_9   4646 ACTCAACAAATGGTGCTGGGATAATTGGGAAGCCACCTGTA---GAATAA 4692
                         vi                   i  i   iv ?    v  i ---    i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_94395780_9   4693 AACTGGGTCTTCATCCCTCAGCTTATAGAAAAATCAACTCAAGATGAATG 4742
                          ii   ii iii i i v  v v    v      i       i   i  v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_94395780_9   4743 AAGGACTTAAATCAAAGACCTGAAGCCATAAAAATTCTAGAAGATAACAT 4792
                          ?i   i     vv    v  i  i i      v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_94395780_9   4793 AGGAAAAACCCTTCTAGACATTGGCTTAGGTGAAGAATTCATGACCAAGA 4842
                            ?iv  vi    vv   v    v     ii v iv   v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_94395780_9   4843 GCTGCAAAGCACATGCAACCAAAACAAAGATAAAGACATGGGAACTAAGT 4892
                         vvivv        v     v   iv   i   i v v  v   vi v vi
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_94395780_9   4893 AAACTTAAAAGCTTCTGCACAGTAAAAGAAACAATCAGCAGAGTAAACAG 4942
                            v      i   i  ii vvi   i  v  v    iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_94395780_9   4943 ACAACACACAGAGTGGGAGAAAATCTTCACAAACTATGCGTCTGACAACA 4992
                              v      i           v  ii    ii  iii     i  vi
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_94395780_9   4993 GGCTAATATCCAGAATCCACAAGGGACCCAAACAAATCAGCAAGTAAAAA 5042
                          i  vi          vi i  i i  i vv    v   ii  vv    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_94395780_9   5043 ACAAAAAATCTCATCAAAAAAGTGGGCTAAGGATATGAATAGACAATTAT 5092
                              v  i iv  i?     -     v      v          v  v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_94395780_9   5093 CAGAAGAATGTATACAAATGGACAACAAACATATAAAACAAACATATAAA 5142
                          vi     vi           v   i  i  i  i   ------------
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA------------ 885

  chrX_94395780_9   5143 AAATGCTTACCGTTACTATCAGG 5165
                          i     i v i i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (151 / 116)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.00 (21 / 7)  

 281 29.21 0.00 0.00  chrX_94395780_94401413     5526  5614 (20)    L1M4_orf2#LINE/L1      688   776 (132)  

  chrX_94395780_9   5526 AAAGTACAGAGACAACCTACAAAGTGGTAGAATATTTTTGCAATCTATCC 5575
                              iv i        i   i i   v    v  v       vii  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_94395780_9   5576 ATCTGACAAATATCTAATAAACAGAATCTACAAGGAACT 5614
                               i  iviv  vi  vv      v  i  i     
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.17 (14 / 12)
Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.00 (0 / 0)  


3256 27.20 0.44 0.44  chrX_94431267_94437993      551  1458 (5269)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94431267_9    551 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 600
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94431267_9    601 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 650
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94431267_9    651 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 698
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_94431267_9    699 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 748
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_94431267_9    749 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 798
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_94431267_9    799 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGATC 848
                                 i   i    ii         i i  ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_94431267_9    849 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATGTCTACAACT 896
                                i    i--    i  --        vv iii ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_94431267_9    897 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 946
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_94431267_9    947 CTATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATCTAGAAAGCT 996
                           v  i  i       i      v      v  ?   i  vi i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_94431267_9    997 GAAATTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1046
                            i     i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_94431267_9   1047 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAACCTCTAGAAGAAAAC 1096
                          i ?    i    i  v   v       i       iii           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_94431267_9   1097 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1146
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_94431267_9   1147 AACACCAAAAGCAATGGCCACAAAAGACAAAATTGACAAATGGGATCTAA 1196
                         i            vvi  v        v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_94431267_9   1197 TGAAACTAAAGGGCTTCTGCACAGCAAAAGAAGCTACCATCAGAGTGAAC 1246
                          v   v v  iii   i  ii vv    i  vi   i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_94431267_9   1247 AGGCAACCTACAAAATGGGAGAAAATTTTCTCAACCTACTCATCTGACAA 1296
                           i     i   i             v  iv   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_94431267_9   1297 AGGGCTAATATCCAGAATCTACAATGAACTCAAACACATTTACAAGAAAA 1346
                         i  i  vi          v  i  v      vv   vv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_94431267_9   1347 AAACAAACAACCCCATCGAAAAGTGGGCGAAGGACATGAACAGACACTTC 1396
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_94431267_9   1397 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 1446
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_94431267_9   1447 ATCACTGGCCAT 1458
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

2887 25.80 1.99 1.44  chrX_94431267_94437993     5332  6234 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94431267_9   5332 TGGAAATGCTTCTCATGCTCATGAGTAGGAAGAATCAATATTGTAAAAAT 5381
                               viiv  i    i     ii v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94431267_9   5382 GACCATACTGTCCAAAGAAATCTACAGATTCAATGCAATTCCCATCAAAA 5431
                          i v     vi     vvi              i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94431267_9   5432 TACCAACATCATTTTTCATAGAATTAGAAAAAA-AATCCTCAAATTCATA 5480
                          v   i vv v     iii    v v  v  iv-i     v         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_94431267_9   5481 TGGAACCAAAAAAAGAGCCCA-AATAGTCAAAGCAACCCTAAGCCAGAAG 5529
                              -- viv  i ii    -     i    i   i i i ivv     
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_94431267_9   5530 AACAAATCTGGAGGCATAATATTACTGGACTTCAAAATTATACTACAAGG 5579
                               vi      vv v i i v ivi i       i -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_94431267_9   5580 CTGTAGTTACCAAAGCAGCATAATACTGTTATAGAAATAGACCAATAGAC 5629
                           ii   v i   ii   ii ii     vi   iii      vv     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_94431267_9   5630 CAATGGAACAGAATAGAGAACCCAGAAATAAAGACAAATACATACAACCA 5679
                                 i     v    ii           vv  v i iv  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_94431267_9   5680 ACTGATCTTTGACAAAGCATACCAA-AGCAT-AAATTGGGAAATGGACAC 5727
                          i    i  i     i -i i    - v   -v   v      - i i v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAA-GAATAG 395

  chrX_94431267_9   5728 CCTATTTAATAAATGGTGCTGGGAAAACTGGCAACTTACATGTA---GAA 5774
                         i  v  i  i              v      vv ?ii     i ---   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_94431267_9   5775 TAAAATTGGATCCCTATATCTCACTTTATATTAAAATCAACTCAAGATGG 5824
                          i  i     i     iv  v   iv    iv     i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_94431267_9   5825 ATCAAAGACTTAAATCTAAGGCCCGAGACTATAAAAACCCTATAATGTTC 5874
                             ?    i     v    iv ii i         vi i  v  -----
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA----- 540

  chrX_94431267_9   5875 GAAAA---------AACTCTTCTATTAA--TTGGCCCAGGCAAAGAATTC 5913
                              ---------  v     v-- i --    vii      v iv   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCG--TGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_94431267_9   5914 ATAATTGAGACCCCAAAAGCAAATGAAACAAAACCAAAAATAAATAAATG 5963
                         v  iv iv   v         v v v       vv       i      v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_94431267_9   5964 GGTCTTAATTAAACCAAAACGCTTCTGCACAGCAAAAGAAATAATCATCA 6013
                           v   v  i   viv   vi   i  ii vv    i  v iv    vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_94431267_9   6014 GAGTAAACAAACAACGCACAGAATAGGAGAAAATATTTGCAAATTATGCA 6063
                         i   i  v i     v        i                   i  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_94431267_9   6064 TTCCACCAAAGACTAGTATCCAGAATCTACAAGGAACACAAATGAATCAG 6113
                          iiv iv ii    v           v  i  i    v vv ii v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_94431267_9   6114 TAACAAAAGAAACAAATAATCCCATCAAAAAGTGGGCAAAAGACATGAAT 6163
                            i    - i        i  v  i?    i        i  iv     
  L1M4_orf2#LINE/    789 TAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_94431267_9   6164 AAACATTTTTCAAAAGAAGATGTACAAATGGCCAACAAACATATGTAAAA 6213
                          i      i  v         i             i  i  i   v   i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_94431267_9   6214 AGGCTCAACATCAGTAATCAT 6234
                          v           ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (136 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.21 (31 / 14)  


3057 24.97 2.76 2.43  chrX_94446122_94449745.rev     2229  3133 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94446122_9   2229 TGGAAAGATACTCCATGTTCATGAATTGGAAGAATCAATACTGTTAAAAT 2278
                                   ii           i         v i    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94446122_9   2279 GCCA-TACTACCCAAAGTAATCTACAGATTCAATGCAATCCCTATCAAAA 2327
                          v  -    v      v i              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94446122_9   2328 TACAAA-TGA-TATTCTGCAGAGAAATAGGAAAAACAATTCTAAAATTTA 2375
                          v v i-  v- v  i      --   v iv  ivii  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA--AATTGACAAGCTGATCCTAAAATTCA 148

  chrX_94446122_9   2376 TATGGAACTATAGAAGACCCCACTTAGCCAAGGC--TCTTATAAGCCAAA 2423
                                v ii iii     vivv       ii --    iv  i-- i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA--AGA 196

  chrX_94446122_9   2424 AAAACAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGA 2473
                          i      ii       v     i v  ii i      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_94446122_9   2474 GCTATAGTAACCAAAGCAGTCTGATATTGGCATAAAAGCAGACACATAGA 2523
                             i     i   ii    v  i  i        iiii     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_94446122_9   2524 CCAATGGAACAGAATGGAGGACTCAAAAACAAATTCATACACCTACAATG 2573
                         i        i     v   iiii  i   i   ii      ii  iii v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_94446122_9   2574 AATGCATTTTTGACAAAGGGGCCACTAACATACTCTGGGAAAAAGACAGT 2623
                            vv     i     i  v    vv v   v vv    i   ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_94446122_9   2624 CTTCCTAATAAATAGTGCTGGGAAAACTGGATATCCAGTTTTCTTCTGGA 2673
                            iii  i    i         v         ?   -------iv  --
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA-------CATG-- 437

  chrX_94446122_9   2674 TTTCCAGAATACTAAAACCAGACCACTATTTATTGCCATATACAAAATTC 2723
                         ----  i  v v i  iiii    v   ii vvii            v i
  L1M4_orf2#LINE/    438 ----CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_94446122_9   2724 GAATTAAA-TGGATTAAAGACTTAAATCTAAGACCCCAAACCATGAAACT 2772
                         i v i   -     i ?    i     v     v iv    i  i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_94446122_9   2773 ACTACCAGAAAACATTAGGGAAAATCTCCCAGGCATTGGTCTGGGCAAAA 2822
                         vi  vv         vi ? v      i vv i v    vi i     vi
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_94446122_9   2823 ATTTCTTAAGCAATTCTCTATAAGCACAGGCAACAAGAGTAAAAATGGAC 2872
                         i       iii vvv v i v       i       i  v      i  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_94446122_9   2873 AAATTG---------AAAAT------CTTCTGCTCAGCAAAAGATAAAAA 2907
                               ---------     ------   i  iv vv    i  i vv v
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_94446122_9   2908 CAAGAAAGGGAACACAGAACGCATACAATGGGAGAAAATATTTGCAAATT 2957
                                 v   v v v   v  i v                       i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_94446122_9   2958 ACCCAGCTGACAATAAATTAATAACCAGAATATAAAAGGAGCTCAAACAA 3007
                          ivi v    i  vii i vi  v          v  i  i   vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_94446122_9   3008 CTCTATAGGAATGAAAGGAATCAGATAATTCAAAT----AATGGGCAAGA 3053
                            v   ---  i   i  --  i    ii   v ----         ii
  L1M4_orf2#LINE/    784 CTCAATA---ATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_94446122_9   3054 GATTTGAATAGACATTTCTCAAAAGAAGACATACAAATGAGAAACAGGCA 3103
                                             v        i         ivv  i i   
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_94446122_9   3104 TATGAAAAGGTGTCCAACATCATGGATCAT 3133
                         i        i  ii        ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (138 / 85)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.36 (47 / 14)  


2694 26.55 1.31 2.50  chrX_94459636_94463649     2603  3521 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94459636_9   2603 TGGAAAAATATTCCATGCTCATGGATGTAAAAAAATCAATGTTGTTAAAA 2652
                               i    i     i        - ii  i v i   i       i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-TGGAAGACTTAATATTGTTAAGA 49

  chrX_94459636_9   2653 TGGCTATACTGCCTAAAGCAATTTACAGATTCAATGCTATTCCCATTAAA 2702
                             v     v  i   vii  i           i  v  i  i  i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_94459636_9   2703 CTACCAAGGACATTCTTCACAGAACTAGAAAAAAATATTCCAAAATTTAT 2752
                         v v   ivvi v  i  ii     v v  v  ivvv  i i      i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_94459636_9   2753 ATGAAATCAAAAAGGTGCCTGAATAACCAAGACAATTCTAAGCAAAAAGA 2802
                            i  viiv  i  vv  v     i    i     ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_94459636_9   2803 ACAAAGCTGGAGGCATCATGCTACCCAGCTTCAAACTATACTAGGCTATA 2852
                               i      vv   ii  v    ii      viv     ---i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA---CAAA 246

  chrX_94459636_9   2853 GCTTGAAGGATACGGTAACCAAAACAGCATAGTACTGGTACAACAACAGA 2902
                            --------  i    i   i    ii i       i i  vi i   
  L1M4_orf2#LINE/    247 GCT--------ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_94459636_9   2903 CACA--GACCAATGGAACCCAGAATGCAGAACCCAGAAATAAGGCTGCAC 2950
                           i --  i        i--     vv   ii          iv iii  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAAT--AGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_94459636_9   2951 ATCTACAACTATCTGATCTTCAAGAAACCTGACAAAAACAAGCAATGGGG 3000
                           i  iiiii vi    i   i v  ivv  v   i v  vv        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_94459636_9   3001 AAAGGAT-TTCTTATTCAATACCTGGTACTGGGATAACTGGATAGCCATA 3049
                             i  -v    -     i vv    i      i         ?   i 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_94459636_9   3050 TGCAAAACATTGAAACTGGAACCCTTACTTACACCATATA-AAAAATTAA 3098
                                v v    ii    v    vv  i          -         
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_94459636_9   3099 CTCAAGATGGGTTAAACACTTAAATGTAAAATTCAAACCTATAACAACCC 3148
                              i    i i ? v  i         i vii   v      -   i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTC 534

  chrX_94459636_9   3149 T-GGAAGAAAACTTAGGCAATACA-CTTCTGGACATAGGAAAGAGCAAAG 3196
                          -i         v    ?i-  v -    vv   v v  ivvii    v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_94459636_9   3197 ATTTCAC-GATGAAGATACCAAAAGCAATTGCAGCAAAAGCAAAAACTGA 3245
                         i    vi-   - v  i          vvv   i      v     iv  
  L1M4_orf2#LINE/    584 GTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_94459636_9   3246 CAAACTGGATCTAATTAAACTAAAAAGCTTCTCCACAGCTAAAGAAACTA 3295
                         i   i    ii v  i   v v    i   i vii vv v  i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_94459636_9   3296 TCAGCAGAATAAACAGAAAACCTACAGAATGGGAAAATTTGTTTGCAAGC 3345
                            iv i i i  v   v    i           i  vv i       ii
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_94459636_9   3346 GATGCATCTGACAAAGGTCTAATATCAAGCATCTATAAGGAACT--TA-A 3392
                         v  ii      i  i  v  vi    v  v  v     i     --  - 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_94459636_9   3393 ATCCAAATTTACAGAAAAAAACAAACAACCCTATAAAAAAGTGAGCAAAT 3442
                          ii   ---  - v     i     i     v  v?    i  i     v
  L1M4_orf2#LINE/    783 ACTCAA---TA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_94459636_9   3443 GACATGAACAGACATGTTTCAAAACAAGACATACATGAGACCAACAGTCA 3492
                           iv    i      v i  v   v    i     viv i    i iv  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_94459636_9   3493 TATTTTAAAAAT--TCAACATCACTGATCAT 3521
                         i  vv-   i  --         ????????
  L1M4_orf2#LINE/    879 CATGA-AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.75 (35 / 20)  


2452 27.78 1.49 2.64  chrX_94466382_94468231      488  1358 (492)    L1M4_orf2#LINE/L1       48   908 (0)  

  chrX_94466382_9    488 GATGG-AACATATCTCAAAATAAT--AAAGATTTAATGCAACTCCTATTA 534
                              -  i ivi i    v i  -- v     i  i    ii     i 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_94466382_9    535 AAATACCAATGATATTCTTCACAAAAATAGAAAAAGCAATCCTAAATTTT 584
                             v   iiviiv  i  ii  i    v  v  ivii        v  i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_94466382_9    585 CTGGAGAACCATAAAAGATTCAGTATAGGGAAAGCTAT-TTGAAGTAAAA 633
                         v ivi   viii  ii  ii   v    vv   i v  -     i-  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGA 196

  chrX_94466382_9    634 AGAACAAAACTGGAGAAATCACATTACCTGGCTTCACATTATACCACACA 683
                                 ii     i v     i v  iiii    v viv   i   v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_94466382_9    684 CTTATAGTCACCAAAACAGTAGGGTACTGGCACAAAAA-AGACACATAGA 732
                         vi  i   v i   i     iv          i  ii -     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_94466382_9    733 ACAATGGAACAGAATAAAGAACCCCAAAACAAATCCTCACACCTACATTG 782
                         v        i     vi   ii  vi   i   i  vi   ii  iiv v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_94466382_9    783 AACTCATTTTAGACAAAGGTATCAAGAACATCCATTGAGGGAAAAGACTA 832
                           i v     v     i   ii     v   i  v  i  --     v  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAAGAATA 394

  chrX_94466382_9    833 -TCTCTTCAATAAATGGTGCTGGGAAAACTAGTTATCTGGGAAAACTAGT 881
                         -   i     i              v    ---------   --------
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACT---------GGA-------- 427

  chrX_94466382_9    882 TATCTGTGTGCAGAAGAATGAAACTACACCCCTATCTCCTGTCACATACA 931
                           ? iiii    i         ii iv       i   viii  i     
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_94466382_9    932 AAAATAAAATAAAAATGAATTAAAGATGTAATTCTAACACATCAAACTCT 981
                              v  v v      i  i ?   iv   v v   v vv v     v 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_94466382_9    982 GAAACTACTACAAGAAAACATTGGGGAAACTCTCCAGGACATTGGAGTGT 1031
                         i     vi  v          v  ? v  v   i iv   v    iv iv
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_94466382_9   1032 GCAAAGATTTCTTGAGTAATGCC-CCACGAGTACAGGCAACCAACGCAAT 1080
                             v i      iii  -  v -   vi  i   i     v  v v  v
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_94466382_9   1081 GATGGAAAAAATGAA--TCACTTGAAGTTAAAAAGCTTCTGAACAACAAA 1128
                         i  i  v   v  i --   - ii  i       -   i  vi vv    
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCA-TCAAAATTAAAAA-CTTTTGTGCTTCAAA 674

  chrX_94466382_9   1129 GGAAACAATAAACAAAGTAAACAGACAACTCACAGAATGGAAGAAAATAT 1178
                            v  v  v  v     i  v       i          i         
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_94466382_9   1179 TTGCAAACTACCCACCTTACAAGGAATTAATAACCAGAACATATAGGAAG 1228
                                ii ivi i  v i    i i vi  v      i     iii i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_94466382_9   1229 CT---AAAACTCTGTAGGAAAAAG-CTAATAATCCATTTAATGAACGGGC 1274
                           --- v     vi  iv      - v     i   v  ? vi  i    
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_94466382_9   1275 AAAATATTTGAATAGACATTTCTGAAAATAAGGCATACTAATGGCAAACA 1324
                            iv                  vv   v   ii    v      v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_94466382_9   1325 GGTTTATAAAAAGGTCCTAAACATCGTTGATCAT 1358
                         i ivi  i     i v  v      i????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.02 (16 / 861), avg. gap size = 2.25 (36 / 16)  


2892 25.58 1.66 1.11  chrX_94511343_94513607.rev      873  1775 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94511343_9    873 TGGAAAAATAATCCATGTTAAAGAATTGGAATATTCAATATTGTTAAAGT 922
                               i   vi       v v i       v i i           ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94511343_9    923 GTCTATACTACCGAAATCCAACTGCAGATTCAATGCAGCCCCTGTCAGAG 972
                          v v     v  v    iv v  i         i   ii    i   i i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94511343_9    973 TACAAAAGACATTTTTTATAGAAATAGACAAAC-AATCCTAAAATTTATA 1021
                          v v ivvi v      ii      v     i -i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_94511343_9   1022 TGAAACCCCAAAAGAACCAGAATACCCAAAGCTATATCAAGCAAAAGAAG 1071
                           i  viv   ii  v        v     i v  v ii --        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chrX_94511343_9   1072 AG--AAGT-GGAGGAATCACATTACCCGACTTCAAATTATACCACAGAGC 1118
                          i--    -      v     i v   i i      viv   i   i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_94511343_9   1119 TATAGTAACCAAAAGAGCACGGTACCGGCTTAAAAACAGACACATAAGCC 1168
                           i     i   i v  iii     i   v   ii i     i   iii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_94511343_9   1169 AATGGAAGAGTGTAGAGAACCCAGGGAGAAATCCATAAATCTAAAGTGAA 1218
                                v  vi v    ii    ii v   i     v  i  vi  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_94511343_9   1219 CTCATTTTTTTTACCAAGTTGTCAAGAATATACA-CACGATAAGA-CAGT 1266
                         i v     iv--  v i v  i     vi  v  -iiv iv    -i   
  L1M4_orf2#LINE/    349 TTGATTTTCG--ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_94511343_9   1267 TGCTTCAATAAATGGTGCTGAGAAAACTGGATAGCCACATGCAGAGGAAT 1316
                         ivi     i           i  v         ?         i i    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_94511343_9   1317 TAAATTTGATCTTTAGCTCTCACCATATA--AAAATCAAATCAAAATGAA 1364
                         v  i  v  i ii  v   v         --     i  v        i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_94511343_9   1365 TTAAAGACATAAATCTAATA-CAACAAACTACAAAACTACTATAACAAAA 1413
                          i ?    v     v   v - v -      i      vi  v  v    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAA 545

  chrX_94511343_9   1414 CATTGGCAAAACTCTCCAGCACATTGGTGCAGGCAAAAATTTATTGAAAA 1463
                            v  ?iv  v   i ivv  v    vvi      vii   v  - i v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGAT 594

  chrX_94511343_9   1464 AT-ACCCTACAAGCACAAGCAACCAAAGCAAAAAGGGACGAATGGGATTA 1512
                           -  v i v             v    v     vi  ii   v   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_94511343_9   1513 CATCAAG-TTAAAAAGCTTCTGCACAGCAAAGGAAACAGTCATCAAAGT- 1560
                               i-       -   i  ii vv       v  vi   vv     -
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_94511343_9   1561 -AGAGACAACGCACAAAATGTGAGAAAATATTTGCAAACTACCCATCTGA 1609
                         - i       v    i    v                 ii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_94511343_9   1610 CAAGGCATGAATAACTATAAAGTATGAGGAACTCAAACAACTCTATAGGA 1659
                         i    v ivvi  v i v  vi   i i      vv       v   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_94511343_9   1660 GAAAAGCAAATAATCGAAG-AAAAAACTTGAGTAAAAGGTTTGAATAGAC 1708
                         i   ii       i v  v-?     --  i i   i i           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATAGAC 841

  chrX_94511343_9   1709 ATTTCTCAAAGGAAGACATACAAATGGCGAACAGG-ATATAAAAAAAATG 1757
                                v  i     i           v  i i - i  i    i -  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chrX_94511343_9   1758 CTCAACATCGAGGGTCAT 1775
                                  i????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (129 / 98)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.32 (25 / 19)  


1311 27.08 11.94 2.64  chrX_94526660_94528363.rev      499  1218 (486)    L1M4_orf2#LINE/L1      122   908 (0)  

  chrX_94526660_9    499 AATTTGATAACCTAATTTTGAA-TTTACATGAAAATACACAAGAACTGGA 547
                           v    i  v  i  ii i  -  i i   i    i  vii  v ii  
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chrX_94526660_9    548 ATAGTCAAAG-AACTTCAAAAAGAAAGAACAAATTTGAAGGAATAATAAT 596
                             i    i-  ii ii    ii         v   i    v v i v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_94526660_9    597 AATATCTGTTTTAAGGATTTATTACA----T----TAATCAAGCCTGCGT 638
                         -- vi vi   i  i- i   i    ---- ----        v v i  
  L1M4_orf2#LINE/    222 --TCCCAATTTCAAA-ACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chrX_94526660_9    639 GGTATTGTTGTAA---TAAAGCAAAAAGTGTGTTAGTGGAA-AACAT--- 681
                             i  vii   ---  i -  v v  ---i i i     - iv  ---
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGA-CATATAG---ATCAATGGAATAGAATTGA 314

  chrX_94526660_9    682 ---------AATAGACCTGCATATACCTTAAA---AACTGATTTTAGACA 719
                         ---------    i   --    i i-   vi---  i       v    
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACC--CATACAT-TTATGGTCAATTGATTTTCGACA 361

  chrX_94526660_9    720 AAGGCGAAAAGACAATTTACTG---AATAAATAGTGACTGTTTCAATAAA 766
                          i  i vv     v   i v  ---  vi      --  -      i   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT--CT-TTTCAACAAA 408

  chrX_94526660_9    767 TAGGGCTGGAACAATTTAGTATCTATATGCAAAGTAAGTGAACATCAATT 816
                          i v     i    i vii  ? i i       iv  -    vv vi ii
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACC 457

  chrX_94526660_9    817 TGTAACTCAAACCATAGGCCAAAATAGGCTCAAAATGGATCACAGATTAA 866
                         iv  v    v      vi v     vii              ?   iiv 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_94526660_9    867 AATTTGAAACCTAAAACTATAAAACTCACAGAA-AATTCACAGCAG-AAA 914
                            v i i v                 vi    -  vv  i  v? -   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_94526660_9    915 TCTTTGTGTCCTTGGATTATGCAA-ATTTTTTTAGATATGACACCCAAGT 963
                             i   v      i   v    -iv   i              v  iv
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_94526660_9    964 CATGATCTATTAAAAAGCAAAATA------TTGGACTTAA--AAATATTA 1005
                           ii v v i-    iiv      ------        v --   -    
  L1M4_orf2#LINE/    608 CACAAGCAAC-AAAAGAAAAAATAGATAAATTGGACTTCATCAAA-ATTA 655

  chrX_94526660_9   1006 AGAACTTCT---CTCTGAAAGATGCCTTCAAAGGAATGAAAGG-CAAGCC 1051
                          i     i ---  iii  i  ii iv    iii i     i -   v  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_94526660_9   1052 ACAAAGT---------------------ATATATTAGATAAAGTGTCTTA 1080
                            i i ---------------------      iv     i - v   i
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG-GACTTG 754

  chrX_94526660_9   1081 GTCCTAGAATATACAATGAACTTTAAGGACTCGATTGATGATAATGGGGA 1130
                         vvi i        i  v     i v vi    i  -i  i v  - ivi 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAAT-AATAAAAA-GACAA 802

  chrX_94526660_9   1131 AAAAC--AATGAAAAACTAA--AATAGATTTGAATGGATTCTTTATCAAA 1176
                          v   --   v?    v ii--  vi         i  ivi  ivi    
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_94526660_9   1177 GAAAATATA------ACC--------TATAAAAAGATGTTCAAAAGCATT 1212
                            i     ------i  --------i  i        i    v v  ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_94526660_9   1213 AGTTAT 1218
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.73 (121 / 70)
Gap_init rate = 0.04 (35 / 787), avg. gap size = 3.00 (105 / 35)  


3061 25.17 5.54 0.69  chrX_94537271_94540087     1459  2324 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94537271_9   1459 TGGAAAGATATCCCATGCTCACTTATTAGAATAATTAATGTTG---AAAT 1505
                                          i   ivv   i   v v     i   --- i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94537271_9   1506 ATTCATACTACTGAAAGTTATCTACAGATTCAATGCAGTCACTATCAAAA 1555
                         iviv     v iv   v v              i   i  v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94537271_9   1556 TTCCAA-TGTCATTTTTCACAGAAATAGAAAAAA-AATCTTAAAATGCAT 1603
                          i   i-  i -     ii       v  v  iv-i   i      v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_94537271_9   1604 AGGGAACCACAAAAGATCCTAAATAACTGAAGAAATTTTGAACAAGAA-- 1651
                          v    vii   ii  i  vi    i ii  iv   i     v     --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_94537271_9   1652 -CAAAGTTGGAGGCAC-CACATTTCCTGATTTCAAAATATGTTGCAAACT 1699
                         -            -  -    i    ii         iv ii i    vi
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_94537271_9   1700 TACAGTAATCCAAACAATATGACACTGGCATAAA-ACAGGCATATAGACC 1748
                                   v i   i i  ii          i- i  i        i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_94537271_9   1749 TTTGGAACAGAAAAGAGAGCCTAGAAATAAATC-ATGCATTTACAATAAG 1797
                         vv     i    vv     i i         i -  i      iii v i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_94537271_9   1798 TTGATCATCAAGAAGCATTCCAAGAACACATAATGGGGAAAGGATAATTT 1847
                              iv  i v   vi v      v  ivi           i   i i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_94537271_9   1848 CTTCAATAAATGATGTTGTGAAAACTGGATATCCACTTGCATAAAAATGA 1897
                         i     i     i  i  v  v         ?    v    v  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_94537271_9   1898 AATTAAGTGCTTATTTCATACCACATACAAAATCATCAACTCAAAATGGG 1947
                          i  iiiiv i  ii   i    i        --  i            i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAA--ATTAACTCAAAATGGA 496

  chrX_94537271_9   1948 TTAAAGACTTAAATGTAAGATCTGAAACTA--AAGCTACCAGAGAAAAAA 1995
                          i ?    i           v  i      --  i  vii   - i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA-AGAAAA 545

  chrX_94537271_9   1996 CACCGGGAAGCATTTTT-TGACTTTGGTCTGGGGAATAATTTTTTGG-TA 2043
                           iv  ?iviv  i  i-    i    vi i  v   ii   i  i -  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_94537271_9   2044 TGACCCTAAAAATCACAGGCAACAAATACGTAACTATACAAGTGGTATTG 2093
                             v i    i-    i        viviv  v  v i  i v v i v
  L1M4_orf2#LINE/    596 TGACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_94537271_9   2094 TATCAAAATGAAAAGCTTCTGCACAGCAGTGAAAACAACCACCAAAGTCA 2143
                         i        v    i   i  ii vv  iv i v  v i  vv     v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_94537271_9   2144 AATGGCAACCTACAGAATGGGAGAAAATATTTACAATCCATGTATCTGAG 2193
                           v i     i                     i   vi   i       v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_94537271_9   2194 AAGAG----------------------GAGCTT----AACACAATAGCAA 2217
                            i ----------------------  i  i----   v     ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_94537271_9   2218 AAATTCAAATAACCTGATTTTAAAATGGAC-------CTGAATAGATATT 2260
                            vv         ii   ?v       i -------i        i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_94537271_9   2261 TCTCCAAAGAAGACCTACAAATGGCTAACAGATATGTGAAAAAGTGGTCA 2310
                                      iv          i  i iii ii      ii  v   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_94537271_9   2311 GCATCACCAATCAT 2324
                         i     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (141 / 73)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.00 (54 / 18)  


3205 26.96 0.88 0.55  chrX_94586188_94590264     2682  3586 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94586188_9   2682 TGGAAAAATATTCTATGTTCGTGAATTGGAAGAATCAATATTGGTAAAAT 2731
                               i    i i      i  i         v i       v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94586188_9   2732 GTCCATACTACCTATAGAAATCTACTGACTCAATGCAATCCTTACCAAAA 2781
                          v v     v  i v vvi      v  i    i       i  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94586188_9   2782 TACCAATGAAATTCTTTACATAAATAGAAAAAACAATCCTAAAATATATT 2831
                          v   iivivv  i   i  v    v  v  ivii          vi  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_94586188_9   2832 TGGAACTACAAAAGACCCAGAATAGCCAAAGCTGTCCTAAGCAAAAAGAA 2881
                              v i   ii                 i vi  i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_94586188_9   2882 CAAAACTGAAGGAATCACATTACCTGACTTCAAATTATACTACAGCGCTA 2931
                             ii  i    v     i v  ii i      viv       iv    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_94586188_9   2932 TAGTTGCCAAAACAGCATGGTACGGGCACAA----AAACACATAGATGAA 2977
                         i   vii   i    ii      v    i  ---- i   i      v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_94586188_9   2978 TGGAACAGAATAAGGAACCCAGAAACAAATCCACACATGTACAGTGAATT 3027
                              i     vii  ii       i   i   i    v  ii  v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_94586188_9   3028 TGTTTCTGAGAAAGGTGCTAAGAACATACACTGGAAAAAAGATGGTCTCT 3077
                         vi   ii  v  i     i    v   v  v   ii   ii  i    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_94586188_9   3078 TCAATAAATGATGCTGGGAAAACTGGATGTTCATATGCAGAAGAATGAAA 3127
                             i     i        v        i?i  i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_94586188_9   3128 TTAGACCCCTATCTTTTGACATCTACAAACATTAAATTCAAATGGATTAA 3177
                           i        i  iviiv   v      v     v iv        i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_94586188_9   3178 GGACTTAAATCTAAGACCTCAAACTATGAAACTATTACAATAAAACATTG 3227
                         i   i     v     v  v       i     v   v  v       v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_94586188_9   3228 AGAAAAGTCTCCAGGCCATTGGTCTGCGCAAAAATTTCTT-GA-GCGATA 3275
                         i?iv  i   i iv v v    vi iv    vii      -  -ii  i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_94586188_9   3276 CCACAAACTCAGGCAACCAAAAAAAATTTAATGTGACAAAAGAGGTCACA 3325
                            v  i v  i     v   i    ---   i-  i   vvi iiiv  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAA---AATA-GATAAATTGGACTTCA 646

  chrX_94586188_9   3326 TAAAGTTTAAAAACTTAGGCACAACAAAGAATACAATCAAAGACATGAAG 3375
                          v  iv          vv ii vv     i i  v     ii vi    i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_94586188_9   3376 AAACAACCCACAGAATGGGAGAAAATATTTGCAAACTATCCAGCTGAAAA 3425
                          i                                 ii  vi v    v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_94586188_9   3426 GTAATTCATAATGAGATTATATAAGGAGTTCAAATAACT--GTAGGAAAA 3473
                          vi i ii  viv   v       i  ii  vv i    --i  iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_94586188_9   3474 ACATCTAATGATTTGATCAAAACATGGGCAAAATATTTGAATAGACTTTT 3523
                          v - v   i iiii  i?   v         iv            v   
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_94586188_9   3524 TTTAAAAGAAGACATACAAATGTCAAACAGGCATATGAAAATGTGCTCAA 3573
                         i iv        i         v v  i i   i       vi       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_94586188_9   3574 GATAATGGATCAT 3586
                         v  v ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2274 20.79 1.90 5.56  chrX_94602055_94604087      500  1129 (904)    L1M4_orf2#LINE/L1      216   822 (86)  

  chrX_94602055_9    500 CAAATTTCCAGATTTCAAGAGGTACTAAACAGCTGCAATATTTAAGAGAG 549
                           v i    vi       i vv     v v    i  i  v i    v  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_94602055_9    550 TGTGGTACTGGCATATTGATAGACATATAGATAAATAAAATAGAACCGAG 599
                                        vv               v   ii       ii   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_94602055_9    600 AGTCCAAAAATAATATTAATGTGTCTATCTACGATCAGCTGATCTGTCTA 649
                               i      - iiv  iii i   ---- i   ii    i -----
  L1M4_orf2#LINE/    316 AGTCCAGAAATAA-ACCCATACATTTAT----GGTCAATTGATTT----- 355

  chrX_94602055_9    650 TTATCAACAAAGTTGCTAAAACAATTTAATGGAGAAAATAGTGAAAACAG 699
                         ---  i    i v   i  i  v   i     i    i-------  i  
  L1M4_orf2#LINE/    356 ---TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-------AATAG 395

  chrX_94602055_9    700 TCTTTTCAACAAATGATGCTGGGGCCACTAGATACCAACGCGCAAAAGAA 749
                                        i       i v   i    ? v  ii         
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_94602055_9    750 TGAGCTTGAACCTTTTCTTTATGCCATCCATTAAAAATTAATTTAAAATG 799
                            iv   i   ii v i i ii    vi i-         i i      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAAATG 494

  chrX_94602055_9    800 TATCATACACCTAA-TGTGAAAGTTAAAACTATAAAACTCGTAGAAGAAA 848
                         v    ? v      -   i i  i                v         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_94602055_9    849 ACATAAAAGTAAATCTTCACAACTTTGGATTAGGTAATGGTTTATTAGAT 898
                              ii?          iii  i    i     i        v      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_94602055_9    899 ACAACACCAAAAGCACATACACACAAAA------AGAGATAAATTGAGCT 942
                          ii              vi  -      ------ v          ii  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCA-ACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_94602055_9    943 ACATAATAATTATTGATAAAAAGTTTAGCACTGAAAATTATTGATAACAT 992
                         v   v v     ------    v   v ii  vv   v----  i vi  
  L1M4_orf2#LINE/    644 TCATCAAAATTA------AAAACTTTTGTGCTTCAAAG----GACACTAT 683

  chrX_94602055_9    993 TAAGAAAGTGAAATGACAGCATACAAAATGACATGAAATATTTGCCAATC 1042
                         i            v    i vi   i    iv vi          v    
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_94602055_9   1043 ACATACCTGATAAGAAGCTAATATTCAG--TATATAAAGTATTCTTAGAA 1090
                          i   i        iii  vi   i   --         v i     v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_94602055_9   1091 CTCAAAAATAAAACTATAACAAATAGATTAA---AAAAATGG 1129
                              v       -- -i       ivii  ---        
  L1M4_orf2#LINE/    784 CTCAATAATAAAA--A-GACAAATAACCCAATTWAAAAATGG 822

Transitions / transversions = 1.91 (84 / 44)
Gap_init rate = 0.02 (14 / 607), avg. gap size = 3.36 (47 / 14)  

 392 19.83 1.72 0.00  chrX_94602055_94604087     1425  1540 (493)    L1M4_orf2#LINE/L1      791   908 (0)  

  chrX_94602055_9   1425 ACAAAAATTTAAAAAAT--AATTAAAAAATGGTCTAATGTTCTAAATATA 1472
                          i     vvi   v  i--    ?        v v  v v i i    v 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_94602055_9   1473 CATTTCTCTAAAAAAGATATATTAATAGCAAATAAGCACATGAAAATTTG 1522
                                 i   i        iv   i  v                vv  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_94602055_9   1523 CTTAACATCATTAGCCAT 1540
                           i       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.83 (10 / 12)
Gap_init rate = 0.01 (1 / 118), avg. gap size = 2.00 (2 / 1)  


3200 26.99 0.88 0.44  chrX_94605287_94611548.rev     4868  5771 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94605287_9   4868 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4917
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94605287_9   4918 GGCCATACTGCCCAAGATAATTTACAGATTCAATGCCATCCCCATCAAGC 4967
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94605287_9   4968 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 5015
                          v   iivi i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_94605287_9   5016 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTCAGCCAAAAG 5065
                                viiv  ii  v  v v  v     iv     i v ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_94605287_9   5066 AATAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5115
                           i    i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_94605287_9   5116 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5165
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_94605287_9   5166 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCCTATCTACAACT 5213
                                i    i--    i  --        vv  iivi  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_94605287_9   5214 ATCTGATCTTTGACAACCCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5263
                          vi    i  i     vvv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_94605287_9   5264 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5313
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_94605287_9   5314 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5363
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_94605287_9   5364 TTAAAGACTTAAAGGTTAGACCTAAAACCATAAAAACGCTAGAAGAAAGC 5413
                          i ?    i    v  v   v       i      vivi         i 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_94605287_9   5414 CTAGGCATTACCATTCAGGACATAGGCATGTGCAAGGACTTCATGTCTAA 5463
                         v    ?i v viv   iv   v v  vv iv    v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_94605287_9   5464 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5513
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_94605287_9   5514 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5563
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_94605287_9   5564 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5613
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_94605287_9   5614 AGGGCTAATATCCAGAATCTACAATGAATTCAAACAAATTTACAATAAAA 5663
                         i  i  vi          v  i  v   i  vv    v iv i       
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_94605287_9   5664 AAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTCC 5709
                          i    ----   v  i?    i     i      v    i     i i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_94605287_9   5710 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5759
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_94605287_9   5760 ATCACTGGCCAT 5771
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (139 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3015 26.79 3.29 0.57  chrX_94624291_94630581      492  1372 (4919)  C L1M4_orf2#LINE/L1   (0)   908     4  

C chrX_94624291_9   1372 AGAGACATTTCATGTTTATGATTAGGAAGACTCAATATTGTCAAGATGTC 1323
                          i   i  ii      i   iv v        i        i      v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

C chrX_94624291_9   1322 AGTTTTTCCCTACTTAATCTATAGATTCCATGCAATCTCAGTCAAAATTC 1273
                          i vi i   v v  i     i      v i      i vi       i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

C chrX_94624291_9   1272 CAGCAAGTTATTTTGTGAATATCAACAAAATGTTTCTAAAGTTAATATAT 1223
                             vivi v     iii v  ii    iv  v i     i  v    iv
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

C chrX_94624291_9   1222 AGAGAAAAAAGACCCAGAAGGGTCAACTCAATACTC----AAGAAAAACA 1177
                          i viv  ii         vi i   vv    -  i----     i    
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAACA 202

C chrX_94624291_9   1176 AAATCAAAGGACTGATACTACTCTACTTCAAGACTTACTATAAAGCTACA 1127
                           i iii      v i   v i v i     i        i         
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

C chrX_94624291_9   1126 GTAATCAAGACAGTGTGATAGTGTTAAAAGAATATACAAATAGACCAACA 1077
                                          i  v  vi v   i   v   v     i   ii
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

C chrX_94624291_9   1076 GAAAGGAATAAGGAACCAAGAAATAAACTCACATAAACATAATCAACTGA 1027
                            vi    vii  ii v          i  i i vvi  ii    i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

C chrX_94624291_9   1026 TCAT-GACAATGGAGCAAAGACTAT--GATGGAGCAAGAACAGCCTTTTC 980
                          iv -     v  v  v     i  --i    i v     i  i      
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

C chrX_94624291_9    979 AATAA-TGGTGCTGGAACAACTGGACATCCATGTACAAAAAAGTGAATCT 931
                           i  -         i         i ?   ii i     i i    vi 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

C chrX_94624291_9    930 AAACAAAGACATTACATCTTGCA-GAAAATTAACTTAAAATGAATTATAG 882
                         ii  vvvv  v i   i v ii -i          i      i  i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

C chrX_94624291_9    881 ACCTAAATGTAAAA-CACAGAGTATAAAACTCCTTGAATACAACATAGGA 833
                                     i - vv i v          i v   v v        ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

C chrX_94624291_9    832 GAAAATCCAGATGACCTTGTGT---GTAATGATGACTTTTTAGATTCCAC 786
                          v     ivvi        v  --- i    i ---  i      viv  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGT---TTCTTAGATATGAC 599

C chrX_94624291_9    785 ACTAAAGGCATTCTCCAT-------------GATAAGTCAGACTTCATTG 749
                           i   i   ivvv v i-------------     i ii        ii
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

C chrX_94624291_9    748 AAATTAAAAATTTCTTCTCTGTGAAAAGCACTGTCAAAATATTGAGAAGA 699
                                   i  i viv  vii  iii    i    i v v   i    
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

C chrX_94624291_9    698 CAGGGTATAGTCTTGGATAACATATTTGCAAAAGAAATATTTGATAAAGG 649
                           ivvi i  vv v   v  v           vv v    i      i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

C chrX_94624291_9    648 ACCT--ACCCAAAATATATGAAGAACTCCTAAAACTTAACAATAAGAAAA 601
                           i -- i   i       i        i  v    i  i     i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

C chrX_94624291_9    600 TGAACAACTGGGTTAAAAAATGAGCAAAAGTCTTGAATAGATACCTCATG 551
                         ii  i   ivii  ?       i     i vi         i ii  viv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

C chrX_94624291_9    550 AAAGAAGATATACAGATG-CCAAGTGAGCATATGAAATGATGCCCCACAT 502
                                       i   -    - i    i      v     i v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGATGCTCAACAT 898

C chrX_94624291_9    501 CATATGTCAT 492
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.76 (148 / 84)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 2.62 (34 / 13)  

3139 25.76 2.59 0.45  chrX_94624291_94630581     4910  5798 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94624291_9   4910 TGCAAAAATATTCCATGTTTATGGGTTGAAAGAGTCAACATTGTTAAAAT 4959
                           v   i    i       i    i   i    v i  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94624291_9   4960 GTCCATGCTCCCTGAAGCAATCTACAGATTCAATGCAATCCTTATCAAAA 5009
                          v v  i     ii  vii              i       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94624291_9   5010 TATCAATGACATACTTCACAGACTTTTTT--TTTAATCCTAAAATT-ATA 5056
                          vi  iivi v vi  ii    vv  vvi--vi i           -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_94624291_9   5057 TG-AAACACAAAAGACCCAGAATAGCCAAAGTTATCCTGAGCCAAAAGAA 5105
                           -   ii   ii                 iiv   i   ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_94624291_9   5106 CAAAACTGGAAGAATGACATTAGCTGACTTCAAATTGTATTACGCAGAAA 5155
                             ii    i  v v   i vv ii i      viv  i   iv  vv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_94624291_9   5156 TAGTAACAAAAACAGCCT---ATCAGCATAAAAACAGACACATATAACAA 5202
                         i     iv  i    iv --- iii      ii i     i   v v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_94624291_9   5203 TGAAACAAAATAGAGAACCCAGAAACAAATCCACACACCTACAATGAACT 5252
                           i  i i   v    ii       i   i   i   ii  iii v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_94624291_9   5253 CGTTTTTAACAAAGGTGCCAAGACCATACATTGGGGAAAAGCCAGTCTCT 5302
                         vi    ii    i              v  v        iivi     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_94624291_9   5303 TCTATAAATGATGCTGGAAAAACTGGATATCCATATGAAGAACAATAAAA 5352
                           v i     i      i v         ?   i   v i  v   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_94624291_9   5353 GTAGACCTCTATCTCTTACCATATACAAAAATCAAATCAAAATGGTTTAA 5402
                         v i    i   i   vi               i  v         v i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_94624291_9   5403 AGACTTAAATCTAAGACCTCAAACTATGAAACTACTGCAAGAAAACATAA 5452
                             i     v     v  v       i     vi iv           i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_94624291_9   5453 GGGAAAATCTCCAGGACATTGATATGGGCAA-AATTTTTTGGGTA--ATA 5499
                          ? v      i iv   v   ivv i     -ii   i  i i  -- i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_94624291_9   5500 CGCACAAGCACAGGCTACCAAAGCAAAAGTGGACAAATGGGATCGTATCA 5549
                          -  v       i  v  v    v    i i  i    v   iivi    
  L1M4_orf2#LINE/    601 C-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_94624291_9   5550 AA-TTAAAAAGCTTCTGCACAGAAAAGAAGACAATAAACCAAGTAAAGAG 5598
                           -       -   i  ii vvv    i v  v  v  vv    i  i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_94624291_9   5599 ACAACCCTCAGAATGAGAGAAAATCCTTGCAAACTACTCTTCTGAGAAGG 5648
                                v       i        vi       ii iviv     v    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_94624291_9   5649 AATT---------AATA-ACAAGAGGCTCAAAAAACTCTATAG-AAAAAG 5687
                         i i ---------    - i  iiii   vv v     v   i-      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_94624291_9   5688 AATCTAATTATCCAACT-AAAAATGGGCAAAATATCTGAATAGACATTTC 5736
                          -- v   v i    i -             iv  i              
  L1M4_orf2#LINE/    799 A--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_94624291_9   5737 TCTAAAGAAGACATAGAAATGGCAAACAGGAATATGAAAAGGTGCTCAAT 5786
                           i        i   v       v  i i v i        i       i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_94624291_9   5787 ATCATGGATAAT 5798
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (143 / 83)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.93 (27 / 14)  


1861 23.49 1.00 2.01  chrX_94639238_94641392.rev       10   507 (1648)  C L1M4_orf2#LINE/L1   (85)   823   331  

C chrX_94639238_9    507 CCATATAGTTGACAGTCAACTGATCTTTGACAAAGGAGCCAAGAACACAC 458
                              i v  - ii     i    i  i     i  v       v  iv 
  L1M4_orf2#LINE/    331 CCATACATTT-ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

C chrX_94639238_9    457 AATGGGAGAAAGA---GTCTTTTCTATAAATAGTTTTGGGACAACTGGAT 411
                               -      ---        v i    i  vi              
  L1M4_orf2#LINE/    380 AATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

C chrX_94639238_9    410 -GTGACCTGCAGAAAAATGAACTTGAACCATCATCTCACACCATATACAA 362
                         -?iv  v    i  i      v   i   vii i                
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

C chrX_94639238_9    361 ATATCAACTCAAAATGAATTAAAGACTTAAACATAAGACCAGAAAGTATA 312
                          v  i           i  i ?    i    ii     v vi   v    
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

C chrX_94639238_9    311 AAACTACTGGAAGAAAACATAGAAA-AAATTCTCTTTGCATTGCTCTGGG 263
                              vi i             i?i-    ii  v vi v   vvi i  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

C chrX_94639238_9    262 CAATGACTTTTTGGATATGCCACCAAAAGCACAGACAACAAAAGCAAAAA 213
                              ii  i  i      v             ii         v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

C chrX_94639238_9    212 TAGACAAAATAGATTGCATCAAACTAAAAAGCTTCTTTCTAGCAAAGGAA 163
                             i   v i  i v       v v    i   i v vivv       v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

C chrX_94639238_9    162 ACAGTCCACAGGGTGAAAAAACAACCTACATAATGGAAGAAAATATTAAC 113
                           vi  v v ii       i      i   v     i          vi 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

C chrX_94639238_9    112 AAACCACACAGGTGATAAGGAAATAATATTCAAAATGAATCCCCTATATG 63
                            i  i i vv        i v vi   i  i   i-------    vi
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATA-------TATAAA 771

C chrX_94639238_9     62 GCAACTCAAACAACTCAATAGCAAGAAAACAAATATTCCAATTAAAAACT 13
                          -     vv           ii  i  i       vi      ?    v 
  L1M4_orf2#LINE/    772 G-AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

C chrX_94639238_9     12 AGG 10
                         i  
  L1M4_orf2#LINE/    821 GGG 823

Transitions / transversions = 1.51 (68 / 45)
Gap_init rate = 0.01 (7 / 493), avg. gap size = 2.14 (15 / 7)  

2259 27.22 5.24 1.12  chrX_94639238_94641392.rev      864  1664 (491)    L1M4_orf2#LINE/L1       75   908 (0)  

  chrX_94639238_9    864 CAGATTTCACACA-TTTCTAACAAAATATTAGCATGTTTTTTTTGTAGAT 912
                               iv  i  - ii   v      vii   -  ii       i   v
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCTTTTTTGCAGAA 123

  chrX_94639238_9    913 ATTGACAAAGTAATCCTAAACTTTTCATGAGAATTCAAAGGCAGCAGGCT 962
                                 iv i        v  ivi   ii   v   i  vvv   iv 
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chrX_94639238_9    963 AGTAAAAA-GATTGTAAAAAAAATAAGAAAAAAGTTTGATCACTTACATT 1011
                           iv    -i  iv i     i --    v      v  vv   i   i 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGA--AGAACAAAGTTGGAGGACTCACACT 221

  chrX_94639238_9   1012 ATCCAATTTTAAGACTTACTATAAAGC-ACAATAATTAAAACAGTGTGGT 1060
                         vi       i  i        i     -   i    i  i          
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_94639238_9   1061 ATTGGTGAAATAATATACATA--AATCAGTAGAAGAGAACAAAGATCCCA 1108
                          i   iiv  vi   v     --i    i i   v    ivi   vi   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_94639238_9   1109 GAAATAGACTCGTACA---ATG---AACTGATTTTTGA--AAAGTGTTAA 1150
                               i  i i    ---   ---  i       i  -- ii   ii  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_94639238_9   1151 AA--ATTTAATAAAAAAAGA-TAGCCTTTTTACCAAATG-TGCTA--ACA 1194
                         i --   i   iiii     -   i     i v      -    i--   
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_94639238_9   1195 TTTTCTGATGACCATATG--AAAAAATT---CTATACCTATATCTCACAC 1239
                         vi v--   i?   i   --   i   v---i iv   iv  i       
  L1M4_orf2#LINE/    422 ACTG--GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_94639238_9   1240 TTTACATAAGAATTAACTCAAAATGGATCATTAACCCAATTGTCAAAATG 1289
                         iv  i i  i                    ?vi   i  v   v i iiv
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_94639238_9   1290 AAAAAGTCTAATACCTTTAGAAGAAATTATAAGACCAATTCTACGTGACC 1339
                             v- v   v  ii          vi   i ?vi  v   v       
  L1M4_orf2#LINE/    520 AAAAC-TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_94639238_9   1340 TTGTGTTTGACAATGAGCTTTTAGACATAATATCAAAAGCATGATCCCTG 1389
                            v   v i     ivi i     i  i i i        ii v vvii
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_94639238_9   1390 AAAAAAAACACA------TTAAACTTTATCAAACCTAAAATCTTTTGCTT 1433
                            i    v i ------  ii    i      vi     v      ivi
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_94639238_9   1434 TGCAAAATACATTGCTAAAAGAATGACAAGATAAG--ACAGATTAAGAGA 1481
                          v    iv   i iii  i i i   v    i  v--     v ii    
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_94639238_9   1482 AAATGTTTTCAAATCACATATCAGATATAAACAAAGTTTTATCCAGAATA 1531
                             i   v       i     v    --- vii v  v           
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATA---AGGGACTTGTATCCAGAATA 765

  chrX_94639238_9   1532 TACAAGGAACACTTAAAACTCAACAATTAGGGGA-AAA------AATAAA 1574
                           i  i    v    v       i   v iii  -   ------   v? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_94639238_9   1575 ATGATGGATAAAAAACCCAAACATACACTTCACTAAAGA---TACACTGA 1621
                          vi    ii   ii iiii  i v   i   v i     ---  i  vi 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_94639238_9   1622 TAGAAGATAAGCATATGAAAAGACACTCAACATCATGTGTTAT 1664
                          i vvi       i         ii          ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (141 / 73)
Gap_init rate = 0.03 (23 / 834), avg. gap size = 2.22 (51 / 23)  


3004 26.81 0.70 0.70  chrX_94661286_94665415      492  1345 (2785)  C L1M4_orf2#LINE/L1   (0)   908    55  

C chrX_94661286_9   1345 ATCCTCTCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACC 1296
                           v   i    iv i  i           i  v     i     iv v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

C chrX_94661286_9   1295 AATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATG 1248
                          iivi i  i  ii     -   -- v  i  - iii    i        
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATG 152

C chrX_94661286_9   1247 GAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAACA 1198
                            viiv  ii  v  v v  v     iv     i i ivv i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

C chrX_94661286_9   1197 AAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACA 1148
                            i      vv       v  ii i      viv        i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

C chrX_94661286_9   1147 GTAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGATCAATG 1098
                             i   i    ii        ii iv ii i   v             
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

C chrX_94661286_9   1097 GAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCT 1050
                            i    i--    i  --        vv  ii i  i  iiiii vi 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATT 350

C chrX_94661286_9   1049 GATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTAT 1000
                            i  i     ivv  vv  i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

C chrX_94661286_9    999 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 950
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

C chrX_94661286_9    949 CTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAA 900
                         i    i    v   i     v           i  i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

C chrX_94661286_9    899 AGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 850
                            ii    i  v i v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

C chrX_94661286_9    849 GCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAACA 800
                          ?i v viv   iv   v v  vv i     v ii   v ivvi vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

C chrX_94661286_9    799 CCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAA 750
                                  vvi           v     v  i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

C chrX_94661286_9    749 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 700
                          v v  i i   i  ii vv    i  v    i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

C chrX_94661286_9    699 AACCTACAACATGGGAGAAAATTTTCGCA--TCCTACTCATCTGACAAAG 652
                             i   iv            v  i   --  v  i--      i  i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGATAAGG 748

C chrX_94661286_9    651 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 602
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

C chrX_94661286_9    601 ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 552
                              i     v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

C chrX_94661286_9    551 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCAT 502
                         v        i  vi viii     v  i        i i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

C chrX_94661286_9    501 CACTGGCCAT 492
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.01 (7 / 854), avg. gap size = 1.71 (12 / 7)  

3211 25.81 0.43 1.95  chrX_94661286_94665415     2716  3637 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94661286_9   2716 TGGAAAAATCTTTCATGTTTGTGGATTGGAAGAATCAATATTGTTAAAAA 2765
                               i  v ii      ii            v i           i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_94661286_9   2766 TGTCCATACTACCCAAGGCAATCTGCAGATTCAATGCAATCCCTATCAAA 2815
                           v v     v     ivii    i         i               
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_94661286_9   2816 ATACTAATGACATTCTTTACAGAAATAGAAAAAATAATCCTAAAACTTAT 2865
                           v i iivi v  i   i       v  v  iv i         i i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_94661286_9   2866 ATGGTACTACAAAAGACACAGAAGAGCCAAAGCTATCCTAAGCAAAAAGA 2915
                             v v i   ii   v     v       i v   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_94661286_9   2916 ACTAACCTGGAGGAATCACATTACCTGACTTCAAATTATATTACAGAGAT 2965
                           v  vi       v     i v  ii i      viv  i    i  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_94661286_9   2966 ATAGTAACCAGAACAGCATAGTATTGGCATAAAAACAGACAATGAAACAG 3015
                          i     i  ii    ii i   i        ii i     - -------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA-T------- 291

  chrX_94661286_9   3016 AATAGAGAACCAATGAAACAGAATAGAGAACCCAGAAACAAATCCACACA 3065
                         -     ---i     i  i     v    ii       i   i   i   
  L1M4_orf2#LINE/    292 -ATAGA---TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_94661286_9   3066 CCTACAGTGAACTCATTTTTTTGACAAAGTTGCTAACAATATACACTGTG 3115
                         ii  ii  v  i v     i--     i v   i  v vi  v  v  v 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTC--GACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_94661286_9   3116 GAAAAGACAGTCTCTTCAATAAATGCTGCAAGAAAAACTGGATATCTATA 3165
                             ii i     i     i     v   vi i v         ? i i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_94661286_9   3166 TGCAGAAGAATGAAACTAAGCCCCCATCT-ATAGCCATATATGAAAATCA 3214
                             i         ii iii    i i  - i -       ii     i 
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACA-CCATATACAAAAATTA 484

  chrX_94661286_9   3215 AATAAAAATAGATTAAATACTTAAATCTAAGACCTCGCACCGTGAAACTA 3264
                          v v     i   i ? v  i     v     v  viv  ii i     v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_94661286_9   3265 CTACAATAAAACATTGTAGAAAAGCTCCAGGACATTGATCTGAGCAAAGA 3314
                         i  v  v       v v? v   v  i iv   v   ivi ii    v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_94661286_9   3315 TTTCTTGAGCAATATCCCACAAGCACTGCCAACCTAAGCAAAAATTGTAA 3364
                               iiii vv iv   v      viv    vv   v      v vv 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_94661286_9   3365 AATGGGATCACAT-GACATTAAAAATTCTTCTGCATAGCAAAGGATACAA 3413
                            v   iiv   -i v        i i  v   v --       i  v 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTA 682

  chrX_94661286_9   3414 TCATCGAAGTGAAGAGACAATCCACAGAATCGGAGAAAATATTTGCAAAC 3463
                            vvi       i      i         v                  i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_94661286_9   3464 TACTCATCTGAGAAAGAATTCATAACCAGAATATATAAAGAGGTCAAACA 3513
                         i ivi      v  i i i ii  v                iv  vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_94661286_9   3514 ACTCTACAG-AAAAAATTCAACAATCTGATTAAAAAATGGGCAAAATATC 3562
                             v i i-     iviv  i  i ii   ?             iv  i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_94661286_9   3563 TGAATAGACATTTCTTTAAAGATGACATA-AAACGGCAAACAGGCATATG 3611
                                        ii     v  i   -   i   v  i i   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_94661286_9   3612 AAAAGGTACTCAACATCATAGATCAT 3637
                              i i          ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (146 / 88)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.00 (22 / 11)  


2920 28.06 1.45 0.33  chrX_94674346_94681046.rev     5314  6211 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94674346_9   5314 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATTTCGTGAAAAT 5363
                               i i  i     i        v      v i   v i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94674346_9   5364 GGCCATAGTGCCCAAAGTAATTAATAGATTCAATGCTATCGCCATTAAGC 5413
                            v   v v      v i  iv i        i  v   v i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94674346_9   5414 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAC 5462
                          v   vivi i  i  ii     v v  v  i-  - iii    v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_94674346_9   5463 ATGGAACCAAAAAAGAGCCCATATAGCCAGA-CAATCCTAAGCAAAAAGA 5511
                               viiv  ii  v  viv       i -     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_94674346_9   5512 AGAAAGCTGGAGGCATCACGCTACCTGACTTCAAAATATACTACAAGGCT 5561
                          v    i      vv    i  v  ii i       iv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_94674346_9   5562 ACAGTCATCAAAACAGCATGGTACTGGTATCAAAACAGATATATAGACCA 5611
                              v     i    ii         i  v ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_94674346_9   5612 ATAGAATGGAACAGAGGCCTCAGAAATAACGCCACACATCTATAACCATC 5661
                           i    i   iv   ivii         vv   i    i   iii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_94674346_9   5662 TGATTTTTGACAAACCTAACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5711
                                i     ivv iv   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_94674346_9   5712 TTTAATAAATGGTATTGGGAAAACTGGCTAGCCATATGCAGGCAACTGAA 5761
                           i  i       ii     v      v  ?   i     iivi v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_94674346_9   5762 ACTGGACCCCTTCCTTACA---TGTATAAA--TTAACTTGAGATGGGTTA 5806
                         ii         v   i   --- i  i   --      ii i    i i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_94674346_9   5807 AAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5856
                         ?    i       v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_94674346_9   5857 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 5905
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_94674346_9   5906 CACCAAAAGCAATGGCAACAAAAGCCAAAATTCACAAATGGAATGTAATT 5955
                                    vvi          vv     vv i    v i iv v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_94674346_9   5956 AAACTAAAGAGCTTCTGCATAGGAAAAGAAACTATCATCAGAGTAAACAG 6005
                            v v  i i   i  iiivvv   i  v       vv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_94674346_9   6006 GCAACCTACATAATGGGAGAAAATTTTTGCCAACTATCCCTCTGACAAAA 6055
                         i     i   v             v     v  ii  viv     i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_94674346_9   6056 GGCTAATATCCAGAATCTACAAGGAACTTAGACACATTTACAAGAAAAAA 6105
                          i  vi          v  i  i     ivv   vv iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_94674346_9   6106 A-AAA-AACCC--TTCAAAAAGTGGGCAAAGAATACGAACAGATACTTCT 6151
                          -   -     --  ?     -         i  vi   i   i i    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_94674346_9   6152 CAAAAGAAAACATTTATGCAGCCAACGAACATATGAAAAAA-GCTCATCA 6200
                          v      i i  vi viii     ii i  i       i -     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_94674346_9   6201 TCGCTGGTTAT 6211
                           i????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


2077 25.08 1.18 8.29  chrX_94761247_94762847.rev      182  1110 (491)    L1M4_orf2#LINE/L1       46   908 (0)  

  chrX_94761247_9    182 AAAAGGACA-TACTGCCAAAAGTAATAGTAGACAGATTCAATGCAAATTC 230
                           i v i  -    v  v   v i  v-  --         i    vii 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATC-TA--CAGATTCAACGCAATCCC 92

  chrX_94761247_9    231 CATCAAAATGTTATCATCATTCTTCACAGAACTAGAAAAAACAATCCTAA 280
                         i        vii v vv v  i  ii     v v  v  ivii       
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_94761247_9    281 AATGCATATGGAACCAAAAAAGAGACC--ACATATCCAAA----TCCAGA 324
                            v         -- viv   i    --iv   v     ----  iv  
  L1M4_orf2#LINE/    143 AATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_94761247_9    325 CAAAGCAAAAAGTACAAATCTGGAGGTATCACATTACCAGACTTCAAATC 374
                         v    ----   v     vi      vv     i v  vi i      v 
  L1M4_orf2#LINE/    191 AAAAG----AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_94761247_9    375 ATACTACAAGGCCAAAATAGCATTTTGTTTACTTTGTCAAAGATCAGTTG 424
                         v        i  i v i  --  i---------------    -    --
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTA--ATC---------------AAGA-CAGT-- 266

  chrX_94761247_9    425 AATGCCAGTATTTAGCTTTATTTCTGGGTTCTCTATTCTGTTCCATTGGT 474
                         -i  ---   -------------    ----------------   vi v
  L1M4_orf2#LINE/    267 -GTG---GTA-------------CTGG----------------CATAAGG 283

  chrX_94761247_9    475 CTATTGCCTACTTTTATACCAGTATAAAACAGAACAGAATAGAGAACCCA 524
                         v  -- ---  v v  v i  i i-------   i     v    ii   
  L1M4_orf2#LINE/    284 ATA--G---ACATATAGATCAATG-------GAATAGAATTGAGAGTCCA 321

  chrX_94761247_9    525 GAAATAAAGTCAAATACTTACATTCAACTGATCTTCAACAAAGCAACCAA 574
                                 vi  v i i   iiv    i    i   i    i vvi    
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_94761247_9    575 AAACATAAAGTGGGGGAAAGGACACCCTATTCAACAAATGGTGCTGGGAT 624
                         i v   vv i     -    i i vi  v                    i
  L1M4_orf2#LINE/    372 GACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_94761247_9    625 AATTGGCAAGCCACATGTAGAAGAATGACACTGGATCCTCATCTCTCACC 674
                           i   vv ?       i i        vii    i  ii i   v    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_94761247_9    675 TTATACAAAAATAAATTCAATGTGGATCAAAGACTTAAATCTAAG-GCTC 723
                         v           v  i    vi       ?    i     v    -   -
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT- 519

  chrX_94761247_9    724 GAAACCATAAAAATTATAGAAGATAGCATCAGAA-AAACTGTTGTGGACA 772
                         i    i      v iv       v i   vi ?i-   iiv i   -  v
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACC 568

  chrX_94761247_9    773 TTGGCTTAGGAAAAGAATTCATGGCTAAGAACCCAAAAGCAAATGTTATG 822
                             v     v  v iv   v i v  v  vv         v v iv ii
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_94761247_9    823 AAAACAAAAATGAATAAATGGGACCTAATTAAA-TTAAAAGCTTCTGCAC 871
                            iv      ii      v    i v  i   -      i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_94761247_9    872 AGCAAAAGAAATAATTAACAGTGTTAGCAGACAACCCACAGAGTGGAAAA 921
                         vv    i  v iv  i  v iv  v iv              i   i i 
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_94761247_9    922 AAATGTTCACAAACTGTGCATCTAACCAATGACTAATATCCAGAATCTAC 971
                             i  ii    iii ii    i iv iv    vi          v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_94761247_9    972 AGGGAACTCAAGTAAG-CAACAAAGAAAAAGTTAATAATCCTATCAAAAA 1020
                          ii      vvii  v-   i  vi    iiiv     i  v  i?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_94761247_9   1021 GTGGACTCAGGACACGAATAGACAATTCTCAAAAGATGGTATACAAATGG 1070
                         i   i vv    ivi         v     v     v i           
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_94761247_9   1071 CCAACAAACATATGAAAAAAAGCTCAACATCACTAATTAT 1110
                             i  i  i       i v           ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (127 / 102)
Gap_init rate = 0.03 (24 / 863), avg. gap size = 3.67 (88 / 24)  


2319 25.49 3.66 1.83  chrX_94816727_94818491.rev      510  1274 (491)    L1M4_orf2#LINE/L1      130   908 (0)  

  chrX_94816727_9    510 AAACT-ATTTTAAAATTCATATGGAACCAAAAAAAGACCTTGCATAGCCA 558
                           i  -  ii                viiv  ii-    iv v       
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGG-GACCCAGAATAGCCA 178

  chrX_94816727_9    559 AGACAATCCTAAGCAA-AAGAACGAAGCTGGAGACATCACACTACCTGAC 607
                          i      i i iv  -      i   i     ivv       v  ii i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_94816727_9    608 TTCAAACTATACTACAAGGCCACAGTAACCAA-ACAGCATGGTACTGGTA 656
                               viv        i  i       i   -    ii         i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_94816727_9    657 CAAAAACAGGC--------CAGTGGAACAGAATAGAGTACTCAGTAATAA 698
                         i  ii i  i --------  i     i     v   viii   v     
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_94816727_9    699 AACCACACATCTACAGCCATCTGATCTTCAACAAA--TCCCACAAAAACA 746
                          v   i    i  ii i  vi    i   i    i-- v   -- i v  
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA--AGACCA 376

  chrX_94816727_9    747 AGCAATGGAGAAAGAATTCCCTGTTTAATGAATGGTGCTGGGAGAACTGG 796
                         vv      i        vvi  v  i  ii             v      
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_94816727_9    797 CTAGCCATATGCAGAAAATTGAAACTGCATCTCTTCCTTACACCTTATAC 846
                         v  ?   i     i  i v    ii  v i i  v   i     v     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_94816727_9    847 AAAAATTAACTCAAAATAGATTAAAGACTTAAATGTAAAACCCAAAACTA 896
                                          i   i ?    i         i v i       
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_94816727_9    897 TAAAAACCCTAGAAGAAAATCTAGGCA-ATACCATTGAGGACACAATCAT 945
                              vi i          iv    ?i- v i v i v ------ i v 
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG------ACCTT 570

  chrX_94816727_9    946 GGA-----CAAAGACTTCATG---ATGAAATTGCCAAAAGCAATCTCAAC 987
                           i-----   v ii   v i---    v ---         vvvv    
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACA---CCAAAAGCACAAGCAAC 617

  chrX_94816727_9    988 AAAAGCAAAAATTGACAAATGGGATCTAATTAAACTAAAGAGATTCTGCC 1037
                              v      v  i    v   ii v  i   v v  i iv  i  iv
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_94816727_9   1038 CAGCAAATGAAACTATCATCAAAGTGAACACAAAACCTACAGAATGGAAG 1087
                          vv    v  v       vv        v v v    i         i  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_94816727_9   1088 AAAATTTTTGCAATCTATCCACCTGACAAAGGGCTAATATCCAGAATCTA 1137
                              v       vii  vi i    i  i  i  vi          v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_94816727_9   1138 CAAGAAACTTAAGGAAATTTACAAGAAAAATATCCAGACAACCCCATTAA 1187
                         i  ii    ivviv  v iv i  v     v --  i i     v   ? 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWA 815

  chrX_94816727_9   1188 AAAGTGGGCAAAAGACATGAA----CACTTCTCAAAAGAAGACATACGTG 1233
                            i        i  iv    ----  i     v        i    ivi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_94816727_9   1234 CTGCCCACAA--ACATGAAAAACAGCTCAACACCACTGATCAT 1274
                         iv   v i  --         ivv        i  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (112 / 79)
Gap_init rate = 0.02 (15 / 779), avg. gap size = 2.80 (42 / 15)  


2757 27.11 3.87 0.80  chrX_94891237_94896289.rev     3685  4562 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_94891237_9   3685 AAAAACATCTCATGTTCATGGATAGGAAGACTCAATATCATTAAAATGGC 3734
                            i i   i             v        i     ii    i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_94891237_9   3735 CATGCTACCCAAAGTAATTT-----------------CCTATCAAACTAC 3767
                         v  i  v      v i  i -----------------         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_94891237_9   3768 CAATGACATTCTTCTCAGAACTAGAAAAACCTATTTTAAAATTCATATGG 3817
                           iivi v  i  iv     v v  v  i iv  ii              
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_94891237_9   3818 AACCAAAAAGAGCCCA-AATAGCCAAGGAAATTCTAAGCAAAAAAGAACA 3866
                           viiv  i ii    -         iiv   ii i i-   i       
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAACA 202

  chrX_94891237_9   3867 AAGCTGGAGGCGTCACTTTACCCAACTTCAAACGATACTACAGGGCCCCA 3916
                            i      vv    vi v     i      vvv       ii  iv  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_94891237_9   3917 GTAATCAAAACAGCATGGTACTGGTACATAAACAGGCACGTAGACCAATG 3966
                                 i    ii         i i vii i  i  ii    i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_94891237_9   3967 GAACAGAATAGAGTGCCCAGAAATAAGGCTGCACACCTTCAACCATCTGA 4016
                            i     v   v i          iv iii   ii viiii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_94891237_9   4017 TCTTCAACAAAGCTGACAAAAACTAGCAATGGGGAAAAGACTCCCTATTC 4066
                          i   i    i v  v   i v vvv           ii ivvi  v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_94891237_9   4067 AGTTAACTGGTGCTGTCATAACTGGCTAAGCCATAGGCAGAAGACTGAAG 4116
                          ii-  v        vv i      v  -?   i v   i    v     
  L1M4_orf2#LINE/    403 AAC-AAATGGTGCTGGGACAACTGGATA-KCCACATGCAAAAGAATGAAG 450

  chrX_94891237_9   4117 CTGGACTCCTTTCTTACACCATATACAAAAATCAACTCAAGATGGATTAG 4166
                         i     i   vi  i                 i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_94891237_9   4167 AGATTTAAATGTAA-AGCACATAACTATAAAAATCCTGGAAAACAACCTA 4215
                            ii         -   -i v          v  i i   i v   v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_94891237_9   4216 GGCA-ATAGCATGATGGACATAGGAACAGGCAAAGATTTCATGGCAAAGA 4264
                           ?i- v v v vi  -  v v  ivi      v i    v i vv v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_94891237_9   4265 AGCCAAAATCAGTCATG--GCAAAAGCAAAAATTGACA-------TCTAA 4305
                         vi      v  --  v --i      v      v  i -------ii v 
  L1M4_orf2#LINE/    599 CACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_94891237_9   4306 TTAACCTTAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTAAAC 4355
                          i  vv    i i   i  ii vv    i  v        v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_94891237_9   4356 AGATAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCCGACAC 4405
                            i    i                 v       vii  vi   i  i v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_94891237_9   4406 AGGTCTAATATCCAACATCTATGAGAAACTTAAACAAATTTACAAGAGAA 4455
                         i  v  vi      iv  v   i ii    ivv    v iv i  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_94891237_9   4456 AGACAAA---CCCA-TTAAAAAGTGGGCAGAGGACCTGAACAGACACTTT 4501
                                ---    -  ?    i      i    ii    i     i  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_94891237_9   4502 GCAAAAGAGGACATGTATACAGCCAACAATCATATGAAAAAA-GCTCAAC 4550
                         v v     i  i  ii v ii     i  v  i       i -       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_94891237_9   4551 CTCACTGATCAT 4562
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.02 (15 / 905), avg. gap size = 2.73 (41 / 15)  


2978 25.80 1.99 1.44  chrX_94928809_94934667     4464  5366 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94928809_9   4464 TGGAAAAACATTCCGTCATCATGGATAGGAAGAACCAATATCATGAAAAT 4513
                               i i  i  i vv        v      vii     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94928809_9   4514 GGCCATACTGCCCAAAATAATTTATAGATTCAATGCTATTCCTGTCAAAC 4563
                            v     v      v i  i  i        i  v  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_94928809_9   4564 TACCATTGACATTCTTCACAGAATTAGAAAAAAACT-ATTTTAAATTTCA 4612
                          v   vivi v  i  ii     v v  v  i--  -  ii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_94928809_9   4613 TATGGAA-T-CAAAGAAGACACCATATAGCCAAGACAATCCTAAGCAAAA 4660
                                - -   i --   v viv        i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_94928809_9   4661 AGAACAAAGCTGGAGGCATCATGCTACCTGACCTCAAACTATACTACAAG 4710
                                  i      vv   ii  v  ii ii     viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_94928809_9   4711 GCTACAATAACCATAACAGCATGGTACTGGTACCAGAACAAACATATACA 4760
                               i   i  vi    ii         i iv  i i i       v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_94928809_9   4761 CCAATGGAGGAGAACAGAGACCTCTGAAATAACACCACACATCTACAACC 4810
                         i       iv    iv    vii v       vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_94928809_9   4811 ATCTGATCTTCGACAAACCTGCCAAAAACAAGCAATGGGGAAAGGATCTC 4860
                          vi    i        ivv      i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_94928809_9   4861 CTATTCACTAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGGAAATT 4910
                           v    vi              v      v  ?   i     ii i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_94928809_9   4911 GAAACTGGACCCCTTCCTTACACCTTATGAGAAAATTAACTCGAGATGGA 4960
                            ii         v   i     v   ivi           i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_94928809_9   4961 TTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCAAGAAGAAAAC 5010
                          i ?    i         i v i     i      vi iv          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_94928809_9   5011 CTAGTCAATACCAATCT--GT-ACATAGGCACGGGCAAAGATTTC----- 5052
                         v   v?i-  --     --  -  v v  vvii     v i    -----
  L1M4_orf2#LINE/    547 ATAGGNG-TA--AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_94928809_9   5053 -ACGACAAAAATGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAAT 5101
                         - i    ------         vvv          vv     v  i    
  L1M4_orf2#LINE/    594 TATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_94928809_9   5102 GGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGGAACTATCATC 5151
                         v   ii v  i   v v  i i   i  ii vv    i iv       vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_94928809_9   5152 AGAGTGAACAGGCAACCTACGGAATGGTAGAAAATTTTTGCAATTGACCC 5201
                          i      v  i     i  i      v       v       v v ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_94928809_9   5202 ATCTGACAAAGGTCTAATGTCTAGAATTTACAAAGAACATAAACAAATTT 5251
                               i  i  v  vi i  i     v  i       vivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_94928809_9   5252 ACAAGAAAAAAACAA----CCCCATCAAAAAGTTGGCAAAGGATATGAAC 5297
                          i  v     i    ----   v  i?    i v          v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_94928809_9   5298 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAA 5347
                              i     v        i  vi viii     i  i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_94928809_9   5348 AAG-TCA-CATCACTGTTTGT 5366
                          v -   -     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (130 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.21 (31 / 14)  


2870 26.06 1.74 2.73  chrX_94997108_95001422.rev     2908  3824 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_94997108_9   2908 TGGAAACACATCCCATGCTCACGGATGGGTAGAATCAGTAGTGTGAAAAT 2957
                               v i        i   i    v  v   v i i  v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_94997108_9   2958 GACCATATTGCCAAAAGCAATCTGCATTGCCAAAAGCAATCTGCAAATTC 3007
                          i v   i v  -----   -----    ---------    i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCC-----CAA-----ATTG---------ATCTACAGATTC 81

  chrX_94997108_9   3008 AATGCAATTCTCATCAAAATACCA-CTATCATTCTTCACAGAACTAGAAA 3056
                           i     i ii        v   -  ii -  i  ii     v v  v 
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACA 130

  chrX_94997108_9   3057 AAAACAATCTTAAAATTCATATGGAACCAAAAAAGAGCCCACATAGCCAA 3106
                          iv-ii   i                viiv  ii  v  viv        
  L1M4_orf2#LINE/    131 AGC-TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_94997108_9   3107 AGCAGGACTAAGCAAAAAGAACAAATCTGGAGGCATCACATTAACCGACT 3156
                          i  ivvi i iv  i         vi      vv     i vv  i i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_94997108_9   3157 TCAAACTATACTATAAGGCCATAGTCACCAAAACAGCATGGCACTGGTAT 3206
                              viv     i  i  i i   v i   i    ii   i     i  
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_94997108_9   3207 AAAACTAAGCACAGAGACCAATGGAACGGAATAGAGAACCCAGAAACAAA 3256
                           iiv  ii  i v   i        ii    v    ii       i   
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_94997108_9   3257 GGCAAA-------GG--GA--GATTTTTGACAAAGCAAAGAAAAACATAA 3295
                         vv  v -------  --i --      i     i vvivv  i v   vv
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_94997108_9   3296 AGTGGGAAAAGGACACCCTATTCAACAAATGGTGCTGGGATAATTGGCAA 3345
                          i    i    i i vi  v                    i  i   vv 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_94997108_9   3346 GCCACTTGTAGAAGAATGAAACTGAATCCTCATCTTTCACCCTATACAAA 3395
                         ?    v  i i         ii  i i  ii i  iv    v        
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_94997108_9   3396 AATCAACTCAAGATGGATCAAAGACTTAAATCTAAGATCTGAAACCATAA 3445
                            i       i        ?    i     v     v  i    i    
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_94997108_9   3446 AAATTCTAGAAGATAGGATCGGAAAAACCCTTCTAGACATTGGCTTAGTT 3495
                           v ii       v iv  v  ?iv  vi    vv   v    v    vi
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_94997108_9   3496 AAAGACTTCAT-GACCAATAAC-CCAAAAGCAAATGCAACAAAAACAAAG 3543
                           v ii   v -  i--  i  -         v v         iv   i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGAT--ATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_94997108_9   3544 GTAAATAGATAAGATTTAAGTCAA--CTAGAAAGCTTCTGCACAGCAAAA 3591
                         i  i   i  vi  i  v -    --i  i   -   i  ii vv    i
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCA-TCAAAATTAAAAA-CTTTTGTGCTTCAAAG 675

  chrX_94997108_9   3592 GATATAATCAGCAGAGTTAACAGACAACCCATAGAGTGGGAGAAAATATT 3641
                           i iv    iv i   v  v          i   i              
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_94997108_9   3642 CACGACCTATACATCCGACAAAGGACTAACATCCAAAACCTACAAAGAAC 3691
                         ii i vii   i   i  i  i     vii     i  iv  i       
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_94997108_9   3692 TCAAACATATCAGCAAGAAAAAAACAAACAATCCCATCAAAAAGTGGGCT 3741
                           vv   vv   ii  v     i     i  i  v  i?    i     v
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_94997108_9   3742 AAGGATATGAATAGATGATTCTTAGAAGAAGATATACAAATAGCCAACAA 3791
                               v        iiv    ivi                i     i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_94997108_9   3792 GCATATGGAAAAATTCTCAACATCACTAATTAT 3824
                            i   i   i  v          ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (146 / 89)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.73 (41 / 15)  


3069 27.37 0.00 0.98  chrX_95042206_95046474.rev     2862  3778 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95042206_9   2862 TAAAAACACATCCCAAGCTCATGGATGCATAGAATCAATATTGTAAAAAT 2911
                          ii   v i      v i        vviv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95042206_9   2912 GACCATACTTCCAAAAGCAATCTACAAATTCAATGCAACTCCCATCAAAA 2961
                          i v     i  v   vii       i      i    ii  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95042206_9   2962 TGCCATCATCATTCTTCACAGAATTAGAAAAAACAATCCTAAAATTCATA 3011
                          v   v vv v  i  ii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_95042206_9   3012 TGGAACCAAAAACGATCCCACATAGCCAAAGCAAGACTAAGCAAGAAGAA 3061
                              viiv  iv  i  viv         i   vvi i iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_95042206_9   3062 CAAATATGGAGGCATCACATTAACTGACTTCAAACTATACTATAAGGGCA 3111
                             vv      vv     i vv ii i      viv     i  i vi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_95042206_9   3112 TAGTCACCAAAACAGCATGGCACTGGTATAAAAATAGGCACAGAGACCAG 3161
                         i   v i   i    ii   i     i    ii    i  i v   i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_95042206_9   3162 TGGAACAGAATAGAGAACCCAGAAACAAAGCCAAATAGTTACAGCTAACT 3211
                              i     v    ii       i   v   v i v   ii ii  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_95042206_9   3212 GATTTTTGACAAAGCAAAGAAAAACATAAGGTAGGAAAAGGATACCCTAT 3261
                               i     i vvivv  i v   vvii i  i    i   vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_95042206_9   3262 TCAACAAATGGCGCTGGAATATTTAATTGGCAAGCCACATGTAGAAGAAT 3311
                                    i     i i ---- i   vv ?       i i      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACA----ACTGGATAKCCACATGCAAAAGAAT 446

  chrX_95042206_9   3312 GAAATTGGATCCTCATCTCTCACCCTATTCAAAACTCAACTCAAGATGGA 3361
                            i     i  ii i   v    v   v     v i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_95042206_9   3362 TCAAAGACTTAAATCTAAGATCTGAAACCATAAAAATTCTAGGAGGTAGT 3411
                            ?    i     v     v  i    i      v ii   i  iv ii
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_95042206_9   3412 ATCAGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGACTTCATGACCAA 3461
                           vi ?iv  vi    vv   v    v        v ii   v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_95042206_9   3462 GAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATTGGAGTTTA 3511
                           vv         v v         iv   i   i   i      v  i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_95042206_9   3512 TTAAAATTAAAAAAAATACTTCTGTGCAGCAAAATAAATAATCAGCAGAG 3561
                          i           -----   i     vv    iv v iv    iv i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-----CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_95042206_9   3562 TTAACAGACAACCCACAGGGTTGGAGGAAGTTTTCACAATCTATACATCT 3611
                          v  v             ii v    i  i v  ii   vii   i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_95042206_9   3612 GACAAAGGACTAATATCCACAATCTACAAAGAACTCAAACAAATCAGCCA 3661
                           i  i     vi      v   v  i         vv    v   iiv 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_95042206_9   3662 GAACAAAACAAACAATTACATCAAAAAGTGGGCTAAGGACATGAATAGAA 3711
                         v  v  i     i  iivv  i?    i     v     iv        v
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_95042206_9   3712 AATTCTCAAAAGAAGATGCACAAATAGCCAAAAAGCATATGAAGAAATGC 3761
                          v     v         ii      i     v     i     i i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_95042206_9   3762 TCAACATCACTAATTAT 3778
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (141 / 106)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 4.50 (9 / 2)  


3338 26.54 0.44 0.44  chrX_95119208_95125486.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95119208_9   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95119208_9   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95119208_9   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_95119208_9   5029 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_95119208_9   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_95119208_9   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_95119208_9   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_95119208_9   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_95119208_9   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_95119208_9   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_95119208_9   5377 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_95119208_9   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_95119208_9   5477 AACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi         ivv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_95119208_9   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_95119208_9   5577 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_95119208_9   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_95119208_9   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_95119208_9   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5776
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_95119208_9   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3253 26.21 0.66 0.66  chrX_95137355_95143804     2355  3262 (3188)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95137355_9   2355 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2404
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95137355_9   2405 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2454
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95137355_9   2455 TACCAA-TGCTTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2501
                          v   i-   i   i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_95137355_9   2502 ATATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAA 2551
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_95137355_9   2552 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 2601
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_95137355_9   2602 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 2651
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_95137355_9   2652 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 2699
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_95137355_9   2700 CATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 2749
                           vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_95137355_9   2750 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2799
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_95137355_9   2800 TCAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 2849
                          v  ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_95137355_9   2850 ATTAAAGACTTAAACGTTCGACCTAAAACCATAAAAACCCTAGAAGAAAA 2899
                           i ?    i    i  vv  v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_95137355_9   2900 CCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 2948
                          v    ?i- v   -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_95137355_9   2949 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATCT 2998
                          vi            vvi          vv   i v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_95137355_9   2999 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3048
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_95137355_9   3049 ACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 3098
                          v  i     i   iv            v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_95137355_9   3099 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 3148
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_95137355_9   3149 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 3198
                            i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_95137355_9   3199 TCTCAAAAGAAGACATTTATGCAGCCAAAAATCACACGAAAAAATGCTCA 3248
                             v        i  vi viii     v  v    i     i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_95137355_9   3249 TCATCACTGGCCAT 3262
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  

3079 24.89 1.18 3.76  chrX_95137355_95143804     5026  5957 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95137355_9   5026 TGGAAAGATATTCCATGATCATTAATTGAAAGCAAAAATATAGTTAAAAT 5075
                                    i     v    vi    i   vvvv     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95137355_9   5076 GACAATACTACCCAAAGCAGTTTACAGATTAAATGAAATCCTTATCAATA 5125
                          i       v      viii i        v  i v     i      v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95137355_9   5126 TT--AATGACACTTTTCACAGAATTTCTTTTAAAACCAATTCCAAAATTT 5173
                          i-- iivi vi    ii     v  vvi---  i ii  i i      i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC---AAGCTGATCCTAAAATTC 147

  chrX_95137355_9   5174 ATGTGGGGCCACAAAAGATCTCCAAATAGACAAAGTCATCCTGAGCAAAA 5223
                           i   iivii   ii  i - vi     v    iiv   i   iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_95137355_9   5224 GGAACAGATCTGGAGGCATCACACGGC-----TTCAAGATATACTGCAAA 5268
                         i     i vi      vv      vv -----     i iv    i    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_95137355_9   5269 ATTATTTAAAACAAATCAGCATGGTACTGGCATAAAAACAGACACATGGG 5318
                         ii  ivvv  v   iv   ii              ii i     i  i i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_95137355_9   5319 CCACTGGAACAGAATAGAGAACCCAGATATAAATTCATGCTTTTACAGCT 5368
                         i  v     i     v    ii     v     ii   i v    ii ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_95137355_9   5369 AACTCATTTTTAACAAAGTTGCCAAGAACATACAATAAGTAAAGCACAGT 5418
                           i v     ii    i v        v   v    ii v    v i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_95137355_9   5419 CTCTTCAACAAATGGTGCTGGGAAAACTGAGTAACCATATACAGAAGAAT 5468
                           i                    v     ii  ?   i  i  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_95137355_9   5469 GATACTAGGCTCTTAACTCTCACCATATACAAACGTCAAATCAAAATGGA 5518
                           vii i i i i  v   v             vi i  v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_95137355_9   5519 TTACAGACTTAAACGTAAGACCTAAAACTATGAAACTATTCGACAAAAAG 5568
                          i ?    i    i      v          i     v  v  vi    v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_95137355_9   5569 ATTGGGG-AAATGCTTCAGGACATAGATCTATGCAAAGATTT---AGGGC 5614
                           v  ? -    -    iv   v v ivi  v    v i   ---  i--
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-- 593

  chrX_95137355_9   5615 TAAGATGTCAAATGCACAGGCAACAAAAGCAAAAATAGAACAGTGAGATT 5664
                           v  iii    v     i          v         vv i vi  i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_95137355_9   5665 ACATCAAGCTAAAGAGCTTCTGCACAGCAAAGGAAGCAATCAACAAAGTG 5714
                         v      iv v  i i   i  ii vv       vi v     v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_95137355_9   5715 AAAAGGCAACTCTCAGAATGGGAGAAAATAGTAACAAACTATTCATCTGA 5764
                              i    i v                 v vi    ii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_95137355_9   5765 AAAGTGATTAATATACAAAATATACAAGGACTTCAAACAACTCAACTGCA 5814
                         v   v  i vi   v  i      i  i  vi  vv         i----
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT---- 789

  chrX_95137355_9   5815 AAACAACAACAACAACAACAACAAAACACAAATAATCTAATCTAATTTTA 5864
                         ----------------  i  --   v        i i   ------ ? 
  L1M4_orf2#LINE/    790 ----------------AATAA--AAAGACAAATAACCCAAT------TWA 815

  chrX_95137355_9   5865 AAAATGGGCAAAAGAGCTGAATAGACATTTATCAAAAGAAGTTATACAAA 5914
                                     i  vi             v  v       v        
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_95137355_9   5915 TGGCCAACAGGTATATGAAAAAATGCTCAATATCACTAATTAT 5957
                                i i i i       i        i    ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (137 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 4.18 (46 / 11)  


2893 26.61 1.67 0.56  chrX_95149435_95154727     3903  4800 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95149435_9   3903 TGGAAATACAACCCAAGCCCATGGATTGGAAGAATTAATATCATGAAAAT 3952
                               v i v    v ii              v       ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95149435_9   3953 GACCATACTGTCCAAAGAAATCTACAAATTCAATGCAATGCCCATGAAAA 4002
                          i v     vi     vvi       i      i     v  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95149435_9   4003 TACCA-TTATCATTCTTCACGGAACTAGAAAACACAATCCTAAAATTCAT 4051
                          v   -i ii -  i  ii i   v v  v  vvii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_95149435_9   4052 ATGGAACCAAAAAAGAGTCCACATATTCAAAGCAATACAAAGCAAAAAGA 4101
                               viiv  ii  vi viv   vi    i    vivi iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_95149435_9   4102 ACAAATCTGGAGGCATCACATTACCTGACTTCAAATTATACTACAAGCCT 4151
                              vi      vv     i v  ii i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_95149435_9   4152 ATAGTTGCCAAAACAGCATGGTACTGGTATGAAAGTACATACATAGACCA 4201
                          i   vii   i    ii         i  i iii  v i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_95149435_9   4202 ATGGAACAAAATAGAGAACCCAGAAATAAAGCAAAATACTTACAGCCAAC 4251
                               i i   v    ii           v v v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_95149435_9   4252 TAATCTTTGACAAAGCAAACAAAAACA--CAAATTGAGAAAAGGACACCC 4299
                          i  i  i     i vviv   i v  --   --  i i    i i vi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTC 397

  chrX_95149435_9   4300 TATTCAATAAATGGTTCTGGAAAAATTCAA--GCTATATGTAAGAGAATG 4347
                          v     i       v    i v  i vi --? i i   i  i      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_95149435_9   4348 AAACTAGATCCCTGTCTCTCACCTAATACAAAAATAAACTCAAGATGGAT 4397
                           ii i  i    ii   v    vv          v       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_95149435_9   4398 CAAAGACTTAAATCTCAGACCCGAAACCACAAACATCCTAGAAAAAAAC- 4446
                           ?    i     v v   v ii    i i   vv  i     i     -
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_95149435_9   4447 TAGGAAAAGCTTTTCTGGACATTGGCCTATACAAAGAATTTATTAC-TAA 4495
                             ?iv iv i   vv   v    vi  vi   v i-   v   v-  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATAT 596

  chrX_95149435_9   4496 GACCCCAAAACCAAACATAACAAAA------ATAAATAAATAGGTCTTCA 4539
                            v      v  v vii       ------   i      v  v     
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_95149435_9   4540 TTAAACTAAAAAGCTTCTGCTCAGCAAAATA-ACTAATCATCAGAGTAAA 4588
                          i   v v    i   i  iv vv    iv -    -   vv i   i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAA 695

  chrX_95149435_9   4589 CAGACAACCCACAGAATGGGAGAAAATATTTGCAAGCTATGCATCTGACA 4638
                         v                                  iii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_95149435_9   4639 AAGGACAAGTATCCAGAATCTACAAGGAACTCAACTAAATCAGCAAGAAA 4688
                          i    vv           v  i  i      vvvi  v   ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_95149435_9   4689 TAAGCAAGTAATTCCATCAAAAAATGGGCGAATAACATGAATAGACATTT 4738
                         v ii   i   ii v  i?          i  vi iv             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_95149435_9   4739 ATCAAAAGAAGATATACAAATGGCCAACAAATATATGAAAA-ATGCTCAA 4787
                         v  v                       i  ii i       -        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_95149435_9   4788 CATCATTAATCAT 4800
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


4059 18.95 2.79 1.56  chrX_95202776_95205292     1130  2026 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95202776_9   1130 TAGAAAGACAACTCATGTTGATGGATTAGAAGATATAATATTG---AGAT 1176
                          i      i v i      v       i     iv        ---    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95202776_9   1177 GATGGTACTACCCAAAGTGATCCACAGAGTCAACATAATTCCTATTAAAA 1226
                          iiii    v      v     i     v     ii   i     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95202776_9   1227 TCCCAACAACACTTTTTTGAAGAAATAGAAAAACCAATACTAAAATTCAT 1276
                              i vi -        v      v  v  i ii  v           
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_95202776_9   1277 GTAGAATTTCAAGGGACCCTAAATAGCCAAAAGTATCCTGAAAAAGAA-- 1324
                         i i   v v          vi           vv   i          --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_95202776_9   1325 -CAA-GTTGGAAAGACTCTCAGTTCCATATTTTAAAACTTACTCCAAAGC 1372
                         -   -      i-     v  v    vv    i          v      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAG-GACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_95202776_9   1373 TGCCATAATCAAAATAGTGTGGTACTGTTATAAG-----ACATATAGACC 1417
                          i vi       i i            vi     -----         i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_95202776_9   1418 AATGGACTAGAATAGAGAACTCAAAAATAAACTCAAATATTCAT------ 1461
                               v      v    iii  i        i  v i   i  ------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_95202776_9   1462 -----CTTCAACAAAGGTGCCAAGATCACTCAATAGAGAAAGTACAGTCT 1506
                         -----i   i    i          i  i     i i     v i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_95202776_9   1507 TTTCACAAAATAGTACTGGGAAAATTGTATATTCACATGTGAAAGAATGA 1556
                              vv    i  i      v  i  v   ?i      ii         
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_95202776_9   1557 AGTTAAACCCTTATTTTACATTATATACAAATATTAACTCAAAATGGACC 1606
                             ii    i  ii i   ii         v                i 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_95202776_9   1607 AGAAATTCAATTTTAAGAGCTATAACTATAAAATCTTTAGAAGAAAACTT 1656
                          ? i iii  v v         v          iii            v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_95202776_9   1657 AGGGA-ACATTTTCATGACATTGGATCTGGCAATGATTTCTTGGACATGA 1705
                            ?i- v  i   i    v    i iv       i      i  i    
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_95202776_9   1706 CATCAAAAGCACGTGCAATAAAAGAAAAAAATTAATAAATTGGACTTTAT 1755
                           i         iv    i           - vi             i  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCAT 647

  chrX_95202776_9   1756 CAAAATTAAAGCCTTTTATTAATCAAAAGACACTGTCAAGAAAATGAAAA 1805
                                   iv     i vvv     i      i        i      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_95202776_9   1806 GACAACACACAGAATGGGAGAAACAACTAAAACAATCACATATCCTA-AA 1854
                               v                vv i viv -     i     iv -  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCA-AATCATATATCTGATAA 746

  chrX_95202776_9   1855 AATAATAATATCCAAAATACATGCTTTGTAAAAACTCCTACAACTCAACA 1904
                         iiv v vi      i    i  i------  i     i          i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATA------AAGAACTCTTACAACTCAATA 790

  chrX_95202776_9   1905 ACAACAACAAAAATGAACAACCCAATTCATAAATGGGCAAAACATTTGAA 1954
                          i  ----   i ii  i         ? v           iv       
  L1M4_orf2#LINE/    791 ATAA----AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_95202776_9   1955 TAGACATTTCTCCAAAGAAGATACACAAATGGCCAATAAGCACATAAAAA 2004
                                                i                     i    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_95202776_9   2005 GATACTCAACATTGTTAGTTAT 2026
                            i        ii????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (110 / 56)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.00 (39 / 13)  


2118 21.19 2.02 15.22  chrX_95205559_95207797      709  1746 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_95205559_9    709 ACATTCAGTGCTCATGAATAGGAAGAATCAATATTTTTAATATGGCCATA 758
                          i  i vi  i     i  v      v i      v    v     v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_95205559_9    759 CTGCCCAAAGCAATTTACAGATCCAATGCTATTCCTATTAAACTACCAAC 808
                           v      vii  i       i   i  v  i     i   v v   i 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_95205559_9    809 AACATTTTTCACAGAATTAGAAAAAAATTATTGTAAAATTAATATGGAAT 858
                         vi v     ii     v v  v  iv- v  iv       v        -
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATGGAA- 155

  chrX_95205559_9    859 CAAAAAAGAGACT--GCATAGCCAAAGCTACCC--AAAGCTAAAAGAACA 904
                         - viv   i   i-- v         i v i i--   i-- i       
  L1M4_orf2#LINE/    156 -ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA--AGAAGAACA 202

  chrX_95205559_9    905 AAGCTTCAGGCATCACA-TACCCAACTTCAAGCTATGCTACAAGGCCACA 953
                            i vv   vv     - v     i     iviv i      i  i   
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_95205559_9    954 GTAACCAAAACAGCATGGTACTGGCACAAAAACAGACATATAGACTAATG 1003
                             i   i    ii           i  ii i           ii    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_95205559_9   1004 CAAAAGAATAGAGAACTCAGAAATAAAGCTGCACACCTACTAACATTCAA 1053
                         v  v     v    iii          --------  i i--     i -
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAA--------CCCAT--ACATTTA- 341

  chrX_95205559_9   1054 TGCTCATGAATAGGAAGAATCAATATTGTTAAAATGGCCAATTTGACCAA 1103
                         ----------------------------------   i     -------
  L1M4_orf2#LINE/    342 ----------------------------------TGGTCAATT------- 350

  chrX_95205559_9   1104 TTTGATGAAATAAAACTGCACACTTACTACCACGTGATCTTCAACAAAGT 1153
                         -----------------------------------   i   i    i v
  L1M4_orf2#LINE/    351 -----------------------------------GATTTTCGACAAGGG 365

  chrX_95205559_9   1154 TGATGAAAACAAACGATGGTGAAAGGACTCCCTGTTCAATAAATGGTGCT 1203
                           vii i v  vv i    v     i ivvi  v     i          
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_95205559_9   1204 GGGATAACCAGCTACCCATATGCAGAACATTGAAACTGGACCCCTTCCTT 1253
                             i   ii v  ?   i     i  v v    ii         v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_95205559_9   1254 TCATCATATTCAAAAATCAACTCAAGATAGATTA-AGACTTAAAC-TAAA 1301
                         v  i     v       i       i  i   i -    i    i-   i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_95205559_9   1302 ACGTAAGACTATAAAAACTCT-AGAAGATAACCTAGG---AAATACCATT 1347
                          vv   i         -    -      v   v    ---    -- -  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAAT--C-TT 561

  chrX_95205559_9   1348 CTGGATATAGGCCCTGGCAATGATTTC------ATGACCAAGACTAAAAG 1391
                          vv  iv v  viiv       i    ------     ----  i     
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC----ACCAAAAG 607

  chrX_95205559_9   1392 CAATTACAACAAAAATAAAAATTGACAAGTAGGACCTAATTAAACTGAAG 1441
                           vvvi        iv      v  i  i v    i v  i   v v  i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_95205559_9   1442 AGCTTCTGCACAGCAAAAAAAAAAAAAAAAAAAAAAAAACCATCAAGAGA 1491
                          i   i  ii vv    ii v ----------------- i       i 
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACA-----------------CTATCAAGAAA 690

  chrX_95205559_9   1492 GTGAACAGACAACCTACAAAATGGGAGAAAATATTTGCAAGCTATGCATC 1541
                              v        i   i                     iii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_95205559_9   1542 CCACAAAGGTCTACTATCTAGAATCTATAAGGAACTT----AAATCAACA 1587
                         iv i  i  v  vv    i     v     i     i----  v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_95205559_9   1588 AGCAAAAAAAAAAAATAAAACAACTCCACATATATGGGGAACTTGAGGCT 1637
                          v--     i v      vv   i -------------------------
  L1M4_orf2#LINE/    791 AT--AAAAAGACAAATAACCCAATT------------------------- 813

  chrX_95205559_9   1638 CAGGCAAGGGTAAAAAAAAATGAGCAAGTGACAGGAACAGACACTTATCA 1687
                         --------------?       i    iv  ivv   i     i  v  v
  L1M4_orf2#LINE/    814 --------------WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_95205559_9   1688 AAAGAAGAAATACCTGTGGATAACAAGCATTTGAAAAAATGTTCAACATC 1737
                                 v    vvi   vi  i     iv      i   i        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_95205559_9   1738 ACTAATCAT 1746
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.37 (126 / 92)
Gap_init rate = 0.03 (23 / 901), avg. gap size = 7.78 (179 / 23)  


3554 22.08 2.87 2.65  chrX_95259471_95261918     1050  1955 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95259471_9   1050 TGGAAAGATATCTCATGTTTATGGATTAGAAAAAGTGATATTGTTAAATT 1099
                                     i      i       i   i vv i          iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95259471_9   1100 GTTCATACTACCCAAAGTGATATACAGATTTAATGCAATCTCTAACAAAA 1149
                          viv     v      v    v        i  i      i   v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95259471_9   1150 TTCTAATGGCATTTTTCACAGAAATAAAAAAATCAATCCTAAAATTCACC 1199
                          i i iiv  v     ii       vi v  iiii             iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_95259471_9   1200 TGGAAACACAAGG-ATCAAGAATAGCCATAGTAATCTTGGGAAAGAAGAA 1248
                               ii     - i v          v ii       ii         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_95259471_9   1249 CAAAGCTGGAGGCATCACATTTCCTGATTTCAAACTATCCTATAAATCTA 1298
                              i      vv     i    ii        viv v   i   v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_95259471_9   1299 CTATAGTAATGAAAACAGTATGGCACCAGCATAAAAACAGACACATAGAT 1348
                          ---      v  i     i   i  ii      ii i     i      
  L1M4_orf2#LINE/    251 C---AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_95259471_9   1349 AAAAGGAATACAAT--ACAGTCCCAAAATAAATCCATGAAT--ATGATCA 1394
                         v  v      v   -- v     vi       i    iv  --   i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_95259471_9   1395 ACTAATCTTTGACAAGGGCACCAAGAATATCCAATGGGGAAAAGGTAGTT 1444
                          i i  i  i        ii      vi  i           iii    i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_95259471_9   1445 ATTTCAATAAATGGTATTGGAAAAACTGGATATCCACATGCAAAAGGATG 1494
                         v      i       ii   i v         ?             i   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_95259471_9   1495 GAACTGGACCCTT--TTAACACTATACAAAAAAATCAACTCAAAATGGAT 1542
                         i ii       i --i v    i   i v      i              
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_95259471_9   1543 TA--GAC---------AGATTTAAA-TTATGAAACTCCTAGAAAAAAAAA 1580
                         i --   ---------   vi    -i   i      i     i    --
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-- 545

  chrX_95259471_9   1581 AACATAGAAGAAAAT-TCCTTGATGTTGGTTTTGGCAGTGATTTTTTGGA 1629
                         --     i? v    - i v   iv    v  v    i  i   i  i  
  L1M4_orf2#LINE/    546 --CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_95259471_9   1630 TATGACCTTAAATGCACAAGTAACAAAAGCAAAAATAAACACGTGGGACT 1679
                               vii   v       i        v       i i vi v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_95259471_9   1680 ACATTAAACTGAAAAGCTTCTG-----CACAGAAAACAATCAAGAATATT 1724
                         v   i   v v    i   i  -----  v  i v  v        vi v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_95259471_9   1725 AAAATGGAACCTACAGAATAAAAGAACATATTTTCAAACTATATATCTGA 1774
                             viv    i       iii    v      v    ii          
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_95259471_9   1775 TAAAGTGTTAACACCCAAAATGTATAAAGAACTCACACAACCCAA-AACA 1823
                            i vii vii i   i   i            vi     i   -  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_95259471_9   1824 GGAAAACAAAACAAAATGAAAACCTGGTTATAAAAAATGGGCAAAGGACC 1873
                         ii  i     ------ ---    iii  ?--                ii
  L1M4_orf2#LINE/    794 AAAAGACAAA------T---AACCCAATTW--AAAAATGGGCAAAGGATT 832

  chrX_95259471_9   1874 TGAACAAGCATTTTTCCAAAGAAACCATACAAATGGTCAGCACCTGCTGA 1923
                             i ii     i         ivi          i  ii v--  ---
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA--GC--- 877

  chrX_95259471_9   1924 AATGTGAAAAGATGCTCAATATCATTAGTCAT 1955
                         - ii               i    ????????
  L1M4_orf2#LINE/    878 -ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.18 (135 / 62)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.94 (50 / 17)  


3400 25.33 1.22 0.33  chrX_95265348_95269845     3106  4005 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95265348_9   3106 TGGAAAAA-ATTTCATGTTCATGGATTGGAAGACTCAATATTGTTAAAAT 3154
                               i -  ii                      i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95265348_9   3155 GTTCATACTC---AAAACAACATACAGATTCAATGCAAGCTCTATCAAAA 3201
                          viv      ---   vii iv           i    v i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95265348_9   3202 TACAAATGACAGTCTTCACAGAAACAAAAAAA--AATTATAAAATGTATA 3249
                          v v iivi vv i  ii      ivi v  i--i  iv      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_95265348_9   3250 TGAAACCACAGAAGACCCATAATAGCCAACACTATCCTAAGTAAAAAAAA 3299
                           i  vii  iii      v         v  v   i i iv  i  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_95265348_9   3300 CAAAACTGGAGAAATCAGATTACTTGACTTCAAATTATACTACAGAGCTA 3349
                             ii     i v   v i v iii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_95265348_9   3350 TAGCAACCAAAATAGCATGGTACTGGCATAAAAACAGACACATACACCAA 3399
                         i  i  i   i i  ii              ii i     i   v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_95265348_9   3400 AGGGACAGAACAGAGAACCTAGAAACAAATCCACATACTTACAGTGAACT 3449
                         v  i i    iv    ii i     i   i   i i i   ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_95265348_9   3450 TGTTTTCAACAAAGGGGCCAAGAATATACACTGGAGAAAGA-CAGTCTCT 3498
                         vi     i    i  v       vi  v  v   i      -i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_95265348_9   3499 TCAATAAATTTTGCTGTCAAAACTGGATATCCATATGCAGAAGAA-AAAA 3547
                             i    vv     vv v         ?   i     i     -i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_95265348_9   3548 CTAGACCATTATCTCTTGCCATATACAAAAATCAAATTAAAATGAATTAA 3597
                         i i    vi  i   vii              i  v i      i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_95265348_9   3598 AGACTTAAATGTAAGACCTCAAACTATGAAACTGCTACAAGAAAACATTG 3647
                             i           v  v       i     vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_95265348_9   3648 GGGAAAATCTTGAGGACATTGTTCTAGGCAAAGATTTATTGAGCCATAGT 3697
                          ? v       viv   v   vvi       v i   v  -  vi  iii
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGAC 599

  chrX_95265348_9   3698 GC-ACAAGC-CAGGCAACCAAAGCAAAAATGCACAAATGAGATCACATCA 3745
                         i - v    -  i     v    v      iv i    vi  iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_95265348_9   3746 GG-TGAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAAGAG 3794
                         ii- v     -   i  ii vv       v  v     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_95265348_9   3795 ACAACCCACAGAATGGGAGGAAATATTTGCAAACTACCCATCTGATGAGG 3844
                                            i             ii ivi       i   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_95265348_9   3845 GATTAATAACTAGAATATATAAGGAGTTCAGACAACTTTATGGGAAAAAA 3894
                           i vi  v i           i  ii  vv      iv  iiv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_95265348_9   3895 ATCTAATAATTCAATCAATAAATGAACAAAAGTTCTGAATAGACGTTTTT 3944
                          - v     ii    i? v     ii    i v i         i   i 
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_95265348_9   3945 CCAGAGAAGACATACAAATGGCAAACAGGCATATGAAAAGGTGCTCAACA 3994
                            i      i           v  i i   i        i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_95265348_9   3995 TCATTAATCAT 4005
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.87 (146 / 78)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


2887 28.13 1.22 0.66  chrX_95274859_95281567     5314  6216 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95274859_9   5314 TGGAAAAACATTCCATGCTCATGAATAGGAAGAATCAATATCGTGAAAAT 5363
                               i i  i     i     i  v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95274859_9   5364 GGCCATTCTGCCATAAGTAATTTGCAGGTTCAATGCTATCCTCATCAGGC 5413
                            v  v  v  vv  v i  i i   i     i  v    ii    iiv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95274859_9   5414 TACCA-TTGACTTTTTCACAAAATTAGAAAAATCTACTTTAAATATCATG 5462
                          v   -i  v      ii  i  v v  v  iiiv iii    vv    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_95274859_9   5463 TGAAAC--CAAAAAACAGCCCTTATAGCCAAGACAATCCTAAGCAAAAAG 5510
                           i  v--   iii  --  vvv        i      i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_95274859_9   5511 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAATTATACTATAGGGC 5560
                                i      vv    i  v  ii i      viv     i ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_95274859_9   5561 TACAGTAACAAAAACAGCATGCTACCAGCACCAAAGCAGATATATAGACC 5610
                                 iv  i    ii  v   ii   iv iiii   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_95274859_9   5611 AATGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACAACCAT 5660
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_95274859_9   5661 CTTATCTTTGAGAAACCTGACAAAAACAAGCAATGGGGAAAGGAT--TCC 5708
                         i v  i  i  v  ivv  v   i v  vv            i  --  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_95274859_9   5709 TTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACT 5758
                           -- i  i              v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_95274859_9   5759 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAGGATGGA 5808
                            ii         v   i     v                  ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_95274859_9   5809 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCAAGAAGAAAAC 5858
                          i ?    i           v       i      vi iv          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_95274859_9   5859 CTAGGCA-ATACCATTCAGTACATAGGCATGGGCAAGGACTTCATAAGTA 5907
                         v    ?i- v i -   ivv  v v  vv i     v ii   v  ii  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_95274859_9   5908 AAACAACAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCTA 5957
                         vi   v        vvi          vv    iv  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_95274859_9   5958 GTTAAACTAAAGAGCTTCTGCAAAGCAAAAGAAACTATCATCAGAGTAAC 6007
                         i i   v v  i i   i  iivvv    i  v       vv i   i v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_95274859_9   6008 CAGGCAACCTACAGAATGGGAAAAATTTTTTGCAATCTATCCATCTGACA 6057
                         v  i     i           i   v v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_95274859_9   6058 AAGGGCTGATATCCAGAATTGGCAAAGAACTTAAACAAATTTACAAGAAA 6107
                          i  i  vi          vvii        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_95274859_9   6108 AA-----ACAACCCCATCAAAAAGTGGGCAAAGAATATGAACAGACACTA 6152
                           ----- i     v  i?    i         i  v    i     i v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_95274859_9   6153 GTCAAAAGAAGACATTTATGCGGCCAACAAACATGGGGAAAAAAAGCTCA 6202
                         v  v        i  vi vii      i  i  iiv -    i v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTCA 894

  chrX_95274859_9   6203 TCATCACTGGTCAT 6216
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (146 / 104)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


2541 26.84 0.42 0.42  chrX_95315606_95320018.rev     3215  3922 (491)    L1M4_orf2#LINE/L1      201   908 (0)  

  chrX_95315606_9   3215 CAAAGCTGGAGGCGTCACACTACCTGACTTCAAACTACACTACAAGGCTA 3264
                              i      vv       v  ii i      vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_95315606_9   3265 TAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 3314
                         i     i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_95315606_9   3315 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACCAT 3362
                              i    i--    i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_95315606_9   3363 CTGATCTTTGACAAAACTGATAAAAACAAGAAATGGGGAAAGGATTCCCT 3412
                         i    i  i     iiv  vi  i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_95315606_9   3413 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTCA 3462
                         v  i  i              v      v  ?   i   i i  iiv v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_95315606_9   3463 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCATGATGGATT 3512
                          ii    i    v   i     v              i   vi      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_95315606_9   3513 AAAGATTTAAAAGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3562
                          ?   ii    v  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_95315606_9   3563 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 3611
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_95315606_9   3612 ACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTAAT 3661
                                     vvi     i    vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_95315606_9   3662 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAGA 3711
                         i   v v  i i   i  ii vv    i  v    i  vv i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_95315606_9   3712 GGCAACCTACAGAATGGGAGAAAATTTTTGCAGTCTACTCATCTGACAAA 3761
                          i     i                 v      ivii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_95315606_9   3762 GGGCTAATATCCAGAATCTACAAAGAACCTAAACAAATTTACAAGAAAAA 3811
                           i  vi          v  i       iivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_95315606_9   3812 AACAAACAATCCCATCAACAAGTGGGCAAAGGGTATGAACAGACACTTTT 3861
                         i     i  i  v  i? v  i          i v    i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_95315606_9   3862 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAATAAATGCTCATCA 3911
                          v        i  vi viii     i ii        v i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_95315606_9   3912 TCACTGGCCAT 3922
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (113 / 73)
Gap_init rate = 0.01 (4 / 708), avg. gap size = 1.50 (6 / 4)  


3026 27.64 1.44 0.67  chrX_95330036_95336415     4987  5887 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95330036_9   4987 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATTCCGTGAAAAT 5036
                              ii i  i     i      i v      v i   vii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95330036_9   5037 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5086
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95330036_9   5087 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5134
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_95330036_9   5135 TATGGAACCAAAAAAGAGCCTGCACCGCCAAGTCAATCCTAAGCCAAAAG 5184
                                viiv  ii  v  v v iv     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_95330036_9   5185 AACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTATACTACAAGGC 5234
                                i     ivv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_95330036_9   5235 TACAGTAACCAAAACAGCATGGTACTGGTGCCAAAACAGAGATATAGATC 5284
                                 i   i    ii         iiiv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_95330036_9   5285 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5332
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_95330036_9   5333 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT--T 5380
                          vi    i  i     ivv  v   i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_95330036_9   5381 CCTTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAG 5430
                          i  -- i  i              v      v  ?   i   v i  ii
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_95330036_9   5431 CTCAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5480
                         v v  ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_95330036_9   5481 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5530
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_95330036_9   5531 GCCTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCT 5580
                         i v    ?i v viv   iv   viv  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_95330036_9   5581 AAAACACCCAAAGCAATGGCAACAAA-GCCAAAATTGACAAATGGGATCT 5629
                          vi     v      vvi        - vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_95330036_9   5630 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGCATGA 5679
                         v  i   v v  i i   i  ii vv    i  v    i  vv ivi   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_95330036_9   5680 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5729
                          v  i     i   i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_95330036_9   5730 AAAGGGCTAATATCCAGAATCTACAGTGAACTTAAATAAATTTACAAGAA 5779
                           i  i  vi          v  i iv     ivv i  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_95330036_9   5780 AAAAACAA----CCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACT 5825
                            i    ----   v  i?    i    ii     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_95330036_9   5826 TCTCAAAAGAAGACATTTATGCAGCCAAAAA--ACATGAAAAAATGCTCA 5873
                             v        i  vi viii     v  --         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_95330036_9   5874 CCATCACTGGCCAT 5887
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (149 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


 515 31.84 0.00 0.00  chrX_95336423_95341170      269   447 (4301)    L1M4_orf2#LINE/L1        2   180 (728)  

  chrX_95336423_9    269 GAAAACACATCCCATGCTCACAAATGTAAAGAATCAATATTGTGCAAATG 318
                          i   v i        i   iii  vvi    v i        vv i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_95336423_9    319 ATGATACTGCCCAAAGCAATCTACAAATTCAATTCAATTTCTACCAAAAT 368
                         iii     v      vii       i      iv    ii   i      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_95336423_9    369 GCCAGCATAATTTTTCACAGAATTAGAAAAAATAATCTTAAAATGTGTGT 418
                         v     vvvv     ii     v v  v  iv i   i      vii i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_95336423_9    419 GGAACCAAAAATGAGCCTCCACAGCCAAA 447
                             viiv  iv  v  vvv i       
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAA 180

Transitions / transversions = 1.19 (31 / 26)
Gap_init rate = 0.00 (0 / 179), avg. gap size = 0.00 (0 / 0)  

2566 28.81 2.47 0.67  chrX_95336423_95341170     3364  4255 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95336423_9   3364 TGGAAAAACATCCTATGATCATGGATGGGTAGAATGAATATTGTGAAAAT 3413
                               i i    i   v        v  v   v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95336423_9   3414 GTCCATACTGCCAAAAGCAATCAACTGTTTCAATGCAATTCCCATGAAGA 3463
                          v v     v  v   vii   v  v v     i     i  i  v  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95336423_9   3464 CACCACCATCATTCTTCATAGAACTAGAAAAGACAATCCTAAAATTTATA 3513
                         iv   v vv v  i  iii    v v  v   vii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_95336423_9   3514 TGGAACCAAAAAAGAGCCCACATAGACAAAGCAAGACTAAGCAAAAA-AA 3562
                              viiv  ii  v  viv    v    i   vvi i iv  i  -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_95336423_9   3563 CAAATCTGAAGGCATGACATTACCAGACTTCAAACTATACTATAAGGTCA 3612
                             vi  i   vv v   i v  vi i      viv     i  i ii 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_95336423_9   3613 CAGTCACCAAAACAGCATGACACTGGTGTAAAAATAGGCTCATAGACGAA 3662
                             v i   i    ii  ii     ii   ii    i vi     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_95336423_9   3663 TGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACT----------- 3701
                              i     v    ii           v   v i i -----------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_95336423_9   3702 GATCTTCAATAAAGCAAACAAAAACCTAAAGTGGGGAAAGCACACCCTGT 3751
                            i   i i  i vviv   i v v vv i         v i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_95336423_9   3752 TCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGAAGAATGAAA 3801
                                            i  i   vv ?       i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_95336423_9   3802 CTGGATTCTTATCTCTCACCTTACATGGAAATCAACTCAAGGTAGATCAA 3851
                         i    ii i  i   v    v  i iii    i       ii i     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_95336423_9   3852 GGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGAAAACATTG 3901
                         i   i     v     v  i    i      v ii             v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_95336423_9   3902 GAAAAACCCTTCTGAACACTGGCTTCAGCAAAGACTTC------ATGAT- 3944
                          ?iv  vi    vvi  vi   v  vi    v ii   ------    i-
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_95336423_9   3945 -CAAGAACCCAAA-AGCAAATGAGACAAT-GATAAATAGGTGAGAAGTAA 3991
                         -   i i v   i- i    v  i v   -       ---  -  vv v 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT---TG-GACTTCA 646

  chrX_95336423_9   3992 TTAAACTAAAATGTTTCTGCACAGCAAAAGAAACAATCAGCAGAGTAAAC 4041
                          i   v v   vii  i  ii vv    i  v  v    iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_95336423_9   4042 AAACAGATGACAGAGTAGGAGAAAATCTTCACAATCTATACATTTGACAA 4091
                          i   iviv     i i         v  ii   vii   i  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_95336423_9   4092 AGGACAAATATCCAGAATCTACAAGTAACTCAAACAAATTAACAAGAACA 4141
                         i    vvi          v  i  iv     vv    v i  i  v  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_95336423_9   4142 AAACAAACAATTCCATCAAAAAAAATAGGCTAAGGACATGAATCGACAAT 4191
                          i     i  ii v  i?     -- i   v     iv     v    v 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATAGACATT 844

  chrX_95336423_9   4192 TCTCAAAACAAGATATACAAGTGGACAACAAATATATGATAAAATGCTCA 4241
                             v   v           i   v   i  ii i    v  i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_95336423_9   4242 ACATCACTAATTAT 4255
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (143 / 110)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.11 (28 / 9)  


1985 27.44 3.02 0.43  chrX_95341260_95342925      484  1179 (487)    L1M4_orf2#LINE/L1      171   884 (24)  

  chrX_95341260_9    484 AATAAATAAAA-AATTT---AAAAAAAAAAC----CTGTAGACATCACAT 525
                             ivi    -   i ---    i  i   ----i  v  ivv     i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_95341260_9    526 TACCAGACTTCAAATCATAGCACAAGTCCATATTTAACAAAATAGTAAGG 575
                          v  vi i      v v  vi    iv i i v v v   i i   iv  
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_95341260_9    576 TATTGGTATAAAAGTAGGCACATAGACCAATGGAACGGAATAGAGAATCC 625
                           i   i    iii   i  i     i        ii    v    i   
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_95341260_9    626 AGAAATAAAGCCAAATACTTAGAAGCAACTGATCTTTGACAAAGCATACA 675
                                  v   v i i   viiv   i    i  i     i -i i v
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCC 369

  chrX_95341260_9    676 AAAAT-ATAAATTGGGGAAACAACACCCTATTCAATAA-CAGTGCTGGGA 723
                           i i-  vv v        v  i vi  v     i  -ii         
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_95341260_9    724 AAACTATCAAGCCACATGTAGAAGAATGAAACTGGATCCTTATCCCTCAC 773
                         v    ivvv ?       i i         ii    i  i  i i v   
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_95341260_9    774 CTTATACAAAAATCAACTCAAGGTGAATAAAAGACTGAAACCTAAGACCT 823
                          v           i       ii  i  v ?    iv   iv     v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_95341260_9    824 AAAACCATAAACATTCT-AGAAGTAAACCTAGGAAAAACTCTTCTGGACA 872
                              i     - i   -     v    v    ?iv  v     vv   v
  L1M4_orf2#LINE/    520 AAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_95341260_9    873 TTGGACCAGGTAAATAATTCATAACTAAGATCCCAAAAGCAAAAGCAACA 922
                             iii   i  vviv   v  iv  v  iv         v        
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_95341260_9    923 AAAACAAAAATAAATAAATGAGAACTAATTAAACTAAAAAGCTTCTGCAC 972
                            iv       i      vi  vi v  i   v v    i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_95341260_9    973 AACAAAAGAAACAATCAGCAGAGAAAACAGAAAATCCACAGAATGGGAGA 1022
                         vv    i  v  v    iv i  vi  v   v  i               
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_95341260_9   1023 AAATATTTGCAAACTATTCATCCAACAAAGGACTAATATCCAGAACCTAC 1072
                                      ii  vi   ii i  i     vi         iv  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_95341260_9   1073 GAGGAAGTC----AAATCAGGAAGAAAAAAAACAAATAATTCCATTAAAA 1118
                         i i   v  ----  v   iv  v     i -       ii v   ?   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAA 817

  chrX_95341260_9   1119 AGTGGGCAAATTACATGAATAGATGTTTCTC---AAAATATATACAAATG 1165
                          i        vv iv        ii      --- i  v           
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_95341260_9   1166 T---ATGAGTACACAAA 1179
                         v---  i  i   ii  
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAA 884

Transitions / transversions = 1.40 (109 / 78)
Gap_init rate = 0.02 (12 / 714), avg. gap size = 2.00 (24 / 12)  


 461 28.48 1.21 1.82  chrX_95343389_95345959      334   498 (2073)    L1M4_orf2#LINE/L1      229   392 (516)  

  chrX_95343389_9    334 TTCAAGAACACATTAAAAAGATTATAC--ACCATGAACAACATGGTACTG 381
                              -   vi i  v    -i  i v-- i  v  -  iii        
  L1M4_orf2#LINE/    229 TTCAA-AACTTACTACAAAG-CTACAGTAATCAAGA-CAGTGTGGTACTG 275

  chrX_95343389_9    382 GTACAAAAACAGGCACATAGACCAATGGGACAGAAGAGAAAGCCCAGAAA 431
                          i i  ii i  i  i     i      i i    vv  i  i       
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_95343389_9    432 TAAGGCTGCACACCTAGGACCATCTGATCTTCAACAAGGCTGACAAAAAC 481
                            iv iii   ii  v ii  vi    i   i      v  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_95343389_9    482 AAGCAATGGGGAAAGGA 498
                          vv            i 
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAA 392

Transitions / transversions = 2.36 (33 / 14)
Gap_init rate = 0.02 (4 / 164), avg. gap size = 1.25 (5 / 4)  

3330 26.42 1.11 0.44  chrX_95343389_95345959     1178  2078 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_95343389_9   1178 GGAAATGTAACCCATGTTTGTGGATTTGAAGACTTAATATTATTAAAATG 1227
                              vi  v        ii      v              i    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_95343389_9   1228 TCCATAGTACTCAAACCAATATATAGATTTGACAGACTCTCTATCAAAAT 1277
                         v v   v v i    iii  v  i     ii  iv v  i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_95343389_9   1278 TCCCATAGCATTTTTCACAGAAAGAAAGAAAACAATTCTAATATTTGTAT 1327
                         i  viiv  v     ii      vvi v  ivii  i    v   ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_95343389_9   1328 GGAACAACAAAACATCCTGAATAGCCAAAGTAATCTTGAGAAAGAAAAAC 1377
                             vvi   iiv i  v           ii        i      i   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_95343389_9   1378 AAAGATAGATACATCATATTCTCTGATTTTAAACTACATTACAAAGCTAT 1427
                             v i  vivv   i i ii ii    i   vivi i          i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_95343389_9   1428 AATAATCAAAATAATATGGCACTGCCATAAAAACAGACACA--GACCAGT 1475
                          i       i i i i   i    v     ii i     i --  i  i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_95343389_9   1476 AGAACAGAATAGAGAGCTCAGAAATAAACCTAAGCATATGCAGTCAACTG 1525
                         i   i     v     ii            i vi   v iii     i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_95343389_9   1526 ATTTTCAACAAAGCCACCAAGAAGACACAATAGAGAAGGGATAGTCTCCT 1575
                               i    i vii      vv iv    i i   i i       ii 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_95343389_9   1576 CAACAAATGATGTTAGAAAAACTGGATATTCACGTGCAAAAGACTGAAAC 1625
                                  i  i i i v         ?i   i         v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_95343389_9   1626 TGGACACTTATTTTACAC-------AAAAAATAACTCCAAATGGATTAAA 1668
                              v i  ii i    -------     v      v        i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_95343389_9   1669 GACCTAATCATAAGACCTGAAACATTAAAAAAACTAGAAGAAAAAACAGA 1718
                                vii     v  i    vv     vvvi          v i  i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_95343389_9   1719 GGAAAAGCTTCTTGATGTTGGCCTTAGCAACGATTTTTTGGATGTGACAT 1768
                         ? v   v    v   iv    vi vi    i i   i  i   i     i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_95343389_9   1769 CAAAAGTTAAGGCAACAAAAGCAAAAATAAACAAGTGGGACTCGATCAAA 1818
                               ivv i          v       i i  i v     iv      
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_95343389_9   1819 TTAAAAAACTTCTGCACAGCAAAGGAAACAATCAATAAAATGAAAAGGCA 1868
                         v v        i  ii vv       v  v     v   i       i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_95343389_9   1869 GCCTACAGAATAGGATAAAATATTTGTGCAACATATATCCAATAAGAGG- 1917
                         i  i       i   v          iiv v        ii     i i-
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_95343389_9   1918 TAATATTGAAAATATATAAGGAACTCACACAACTAAATAGCAAAAAAAAA 1967
                          vi   iv i         i      vi      v    ii     i v 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_95343389_9   1968 AAAAAGAAACTTGTTTTAAAAATGGGCAAAGAAACTGAATAGACATTTTC 2017
                           v  ---- iiiv  ?              i vi             ii
  L1M4_orf2#LINE/    802 AATAA----CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_95343389_9   2018 CCAAAGAAGCCATACAAATGGACCATAGCTATATGATAAGGTGCCCAATA 2067
                                  vi          v v   ivi i    v   i   i   i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_95343389_9   2068 CCACTAATCAT 2078
                         i  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.82 (151 / 83)
Gap_init rate = 0.00 (4 / 907), avg. gap size = 3.50 (14 / 4)  


2680 21.70 4.26 7.98  chrX_95367199_95370823     2196  3135 (490)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_95367199_9   2196 AAAAAAAGTCTATATACATGAAAAGGAAGACTCAATATTTTTATCATGTC 2245
                            i v vi i  i v    i vv        i      v   vv   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_95367199_9   2246 AGTTCTTCCCAAACTTATCTAGAGATTCCACACAATCCCAATCAAATATC 2295
                          i v  i      i v     v      v  i       v      -   
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA-ATC 102

  chrX_95367199_9   2296 --------------TGTAGAAATTGACAAACTTATTCTAAAGTTTATATC 2331
                         --------------  i            i  v  i     i  i    v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_95367199_9   2332 AAAAGCCAAAATACCCAGGATGGCCAACACAATATTGAG---GGATAATA 2378
                         i   vv   iiv      i  i     v     v    i--- i v  i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_95367199_9   2379 AAGTTGAAGAACTGACACTACCTGACTTCAAGATTTACTTTAATTTACAA 2428
                               i  i   v     v  ii i     i i     -----------
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT----------- 241

  chrX_95367199_9   2429 GATTTACTTTACTTTACAAGATTTACTTTACAGTCTTCACTGTAGCTATA 2478
                         ---------------    ------------------------     i 
  L1M4_orf2#LINE/    242 ---------------ACAA------------------------AGCTACA 252

  chrX_95367199_9   2479 CAGGCAGAGTAGTAAACAGAGTATGGTACTGGCAAAAGAAGAGACAAATA 2528
                         --------   i v  v v   i           v   i v     v   
  L1M4_orf2#LINE/    253 --------GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_95367199_9   2529 GATCAACAGAAGAAAATATAAAGCCCAGAAACACAAATATAGAAAACCAC 2578
                               ii   v i   vv i  i       i ----------  v   i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATA----------AACCCAT 334

  chrX_95367199_9   2579 ACAACTATAGTCAACTGATCACTGACAAAGGAGCAAAAGCAATTCAATGA 2628
                            vi   i     i    ivii     i  v  v  ii v        i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_95367199_9   2629 AGA-------GTCTTTTCAACAAATGATGCTTGGACAATTGGACAGCC-T 2670
                         i  -------                i    v      i    i ?  -i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_95367199_9   2671 ATAATAACAAAATGACTCTAGACAGAGACTT-ATACCTTTCACAAAAATT 2719
                           i-i  v i     vvi i   vvvv  i - i   v vi         
  L1M4_orf2#LINE/    435 ATG-CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_95367199_9   2720 AACATAAAACAGGTC-TAGATCTGAATGTAAGATACAAAAGTATGAAAGT 2768
                            vi    ii i  -?   i  i         vvi    v   i   v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_95367199_9   2769 TCTAGAAGATAACATAGGCAGAAATCTAGGTGACCTTGGGTTTGGCAATG 2818
                         ii       v        ?iv      vv             v       
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_95367199_9   2819 ACTT-TTAAATATAATGCTAAAAGCAAAATCCATGAAAGAAAAATTTGAT 2867
                         ii  -   i    i ii i       v  v v ii         v v   
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_95367199_9   2868 AACTTGGATTTCATTAAAATTGAAAGCTCT-GCTCTGCAAAAGACACTGT 2916
                           v     i     i      i   i  i - iv  v    i      i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_95367199_9   2917 AAAGAGATTGAAACAACAAGCCACAGACTAGGAAAAAATATTTGCAAAGC 2966
                         v    i v     vi    v       v i   i              v 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_95367199_9   2967 ATAT--CTGATAAAGGACTGGTATCTAAAATACACAAATAACTATTAAAT 3014
                             --       i     v     i i    i i   v    v   v v
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_95367199_9   3015 CTCCATAAGAAAA---CAAACAACCAAATT-ACAAATGGACAAAAGATCT 3060
                            v    v    ---    i    v    - v      i    i   i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_95367199_9   3061 AAACAGACA-----CCAGATGAAAAAAGATTTATAGATTGCAAATAAGCA 3105
                         i  i     -----   -----  i     v  i i  v  v        
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCA-----AAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_95367199_9   3106 TACGAAAATATGTTCAACAACTAATATGAC 3135
                         i i     v   i      v v????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (113 / 88)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 6.05 (115 / 19)  


3307 25.58 1.33 0.78  chrX_95406764_95412535.rev     4379  5281 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95406764_9   4379 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4428
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95406764_9   4429 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCGTCCCCATCAAGC 4478
                            v     v     iv i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95406764_9   4479 TACCC--CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTT 4524
                          -   --   v    i  -i     -   -- v  i  - iii    i  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_95406764_9   4525 CATATGGAACCAAAAAAGAGCCCGCATTGCCAAGAGAATCCCAAGCCAAA 4574
                                  viiv  ii  v  v v  v     i v    iii ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_95406764_9   4575 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 4624
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_95406764_9   4625 GCTAAAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGATATAGA 4674
                             v     i   i    ii           iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_95406764_9   4675 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAA 4722
                         i        i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_95406764_9   4723 CCATCTGATCTTTGACAAAGCTGACAAAAACAAGAAATGGGGAAAGGATT 4772
                         i  vi    i  i     i v  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_95406764_9   4773 CCCCTTTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGTAGAAAG 4822
                         vi i   i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_95406764_9   4823 CCGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 4872
                         vi   ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_95406764_9   4873 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 4922
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_95406764_9   4923 ACCTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 4971
                           v i  ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_95406764_9   4972 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5021
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_95406764_9   5022 TAATTAAACTCAAGAGCTTCTGCACGGCAAAAGAAACTACCATCAGAGTG 5071
                          v  i   v i  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_95406764_9   5072 AACAGGCAATCTACAGAATGGGAAAAAATTTTTGCAATCTACTCATCTGA 5121
                           v  i   i i           i     v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_95406764_9   5122 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAATA 5171
                         i  i  i  vi          v  i         vv    v iv i    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_95406764_9   5172 AAAAAA-----AACCCCATCACAAAGTGGGCAAAGGATATGAACAGACAC 5216
                             i -----     v  i?v   i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_95406764_9   5217 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAATGCTC 5266
                              v        i  vi viii     i ii  i       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_95406764_9   5267 ATCATCACTGGCCAT 5281
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


4670 15.32 1.40 3.45  chrX_95539308_95541303      578  1504 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95539308_9    578 TGGAAAAATATCTT-TTTTTATGTATCAGAAGATCTAATATTGTTAAGAT 626
                               i     ii- v  i   v  ii     ii               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95539308_9    627 G-CAATATTCCCCAAATTAATTGACACATTCAACACAATCTCTATCAGAA 675
                          -     i          i  iv   v       i     i      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95539308_9    676 CTCCAGCTGGCTTATTTGTAGAAATTCACAAGATGATTCTAAAATTCATA 725
                         ii       v   v    i       v     v    i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_95539308_9    726 TGGAATTGCAAGAAACTCAGAATAGCCAAAACTATCTTGAAAAAGAACAA 775
                              v      ii  i               v              v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_95539308_9    776 --AAGTTGGAGGGCTCACAATTCCTGATTTTAAAACTTACTACAAAACGA 823
                         --          i      v    ii    i               i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_95539308_9    824 CAGTAATCAAAACAGTGTTGTACTGGCATAAGGAGAGACATAATAGATCA 873
                                   i       v               v       -       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGATCA 299

  chrX_95539308_9    874 CTGGAATGGAATTGAGAGTCCAGAAATACATCTATGTGTCTATAGTCAAC 923
                         v      i                    v i i  iii i   i     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_95539308_9    924 TGATTTTCAACAGGGGAGCCAAGACCATTTAATGGGGGAACA-TAGTCTA 972
                                 i   i   v            i       i  v -      v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_95539308_9    973 TTATACAGATTGTGCTAGGACAACTGGATATCCACATGCAAA-GAATAAA 1021
                           vv   i  v     i             ?           -    i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_95539308_9   1022 GTTGGACCCCTACCTCATACCATATTCAAAAATTAATTCAAAATGGATGA 1071
                                          i       v          i           v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_95539308_9   1072 TCAACCTAAAAATAAGAGCCAAAACCATAGAACTCTTAGAAGAAAACATA 1121
                         ?vi       vi       i     i   i                    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_95539308_9   1122 AAGGTAAATCTTGATGACCTAGGATTTGGCAGTGGATTCTTAGATATGAC 1171
                         ii?         vi      v  i  v    i   v              
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_95539308_9   1172 ACTCGAAGCATGAACAATGGATAAGAATGTTCAACAATGGATAAGAATGG 1221
                           ivi     i-----------   ------      -----     ---
  L1M4_orf2#LINE/    600 ACCAAAAGCAC-----------AAG------CAACAA-----AAGAA--- 624

  chrX_95539308_9   1222 AAAAAATGGATAAGTTAGACATCGTCAAAAATTTTTAAAATATTTTCTGC 1271
                         --     i     i  i   v  i      ----      vv    v   
  L1M4_orf2#LINE/    625 --AAAATAGATAAATTGGACTTCATCAAAA----TTAAAAACTTTTGTGC 668

  chrX_95539308_9   1272 ATGAAGGAACATTATCAAGAAAGTTAT--GATGACCTACAGAAGGGAAGA 1319
                         v v  i i   i            v v--  ii   i      v  i   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_95539308_9   1320 AAATATTTAAAAATCATGTATCTGAAAATGGCCTACTATCCAGACTATAT 1369
                                 iv       i       v  v  v  vv        v     
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_95539308_9   1370 ATAGAACTCTTACAACTCAACAACAAAGAGACATATAACCCAATTTAAAA 1419
                          v                  i  i   i     v           ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_95539308_9   1420 -TGAGCAAATCACTT----AGAGATTTCTCCAGAGAAAGTATATAAATGG 1464
                         -  i     vv i  ----   v         i    ii    i      
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_95539308_9   1465 CCAATAAGCACAGGAAAAGATATTTAACATCGTTAGATAC 1504
                                     v        ii i      i????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (84 / 54)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.21 (45 / 14)  


3317 26.18 0.44 0.55  chrX_95547388_95553464     4676  5584 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95547388_9   4676 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4725
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95547388_9   4726 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4775
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95547388_9   4776 TACCAAGGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 4825
                          v   ivvi i  i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_95547388_9   4826 TGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAGAA 4875
                              viiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_95547388_9   4876 CAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATACTACAAGGCTA 4925
                              i      vv   ii  v  ii        viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_95547388_9   4926 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 4975
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_95547388_9   4976 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATGTCTACAATTAT 5023
                              i    i--    i  --        vv   i ii i  iii i v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_95547388_9   5024 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGAGAAAGGATTCCCT 5073
                         i    i  i     ivv  v   i v  vvv     i     i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_95547388_9   5074 ATTTAATAAATGGTGCTCGGAAAACTGGCTAGCCATATGTAGAAGGCTGA 5123
                         v  i  i          v   v      v  ?   i   i i   iv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_95547388_9   5124 AAGTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGCATT 5173
                          iv    i    v   i     v     v        i    i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_95547388_9   5174 AAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5223
                          ?   ii       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_95547388_9   5224 AGA--TAATACCATTCAGGACCTAGGCATGGGCAAGGACTTCATGTCTAA 5271
                           i--   - i -   iv     v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_95547388_9   5272 AACACAAAAAGCAATAGCAACAAAAGCCAAAATTGAGAAATGGGATCTAA 5321
                         i    v       vv           vv     v  v    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_95547388_9   5322 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5371
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_95547388_9   5372 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5421
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_95547388_9   5422 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5471
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_95547388_9   5472 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5521
                          i -    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_95547388_9   5522 CTCAAAAGAAGACATTTATGTAGCCAAAAGACACATGAAAAAATGCTCAT 5571
                            v        i  vi vi i     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_95547388_9   5572 CATCACTGGCCAT 5584
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (134 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3036 24.58 2.16 0.84  chrX_95562721_95564533.rev      492  1325 (488)    L1M4_orf2#LINE/L1       64   908 (0)  

  chrX_95562721_9    492 AAATTGGCTCATATACAGATTCAATGGTATTCCTATCAAACTACCAA-TA 540
                               ----  v           i vv  i         v v   i- i
  L1M4_orf2#LINE/     64 AAATTG----ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_95562721_9    541 TCATTTTTACAGAATTAGAAAAAACTG-TTCTAAAATTCATATGGAACCA 589
                         i v     i     v v  v  i-   - i                 vii
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATG 158

  chrX_95562721_9    590 AAAAAGAGCACAAATAGCCAAAGCAGTCCTAAGCAAAAAGAACAAAGCTG 639
                         v  ii  v vvi          i  i  i i iv  i          i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_95562721_9    640 GAGCCATCACACTACCCAACTTCAAAA-----TACAAGGCTACAGTAACC 684
                            vvv       v     i       -----     i          i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_95562721_9    685 AAAACAACACGGTACTGGTATAAAAATAGACACA--GACCAGTGGAACAG 732
                           i   iiii        i    ii       i --  i  i     i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_95562721_9    733 AATAGAGAGCCCAGAAATAAAGCCACACACGTACAGCCATCTGATCTTTA 782
                            v     i           v   i   iv  ii i  vi    i  ii
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_95562721_9    783 ACAAAGTTGACAAAAATATGCAATGGAGAAAGGACACTCTATTCAATAAA 832
                             i v  v   i vi  v      i     i i v   v     i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_95562721_9    833 TAGTGCTGTGATAGCTGGCTAGCCTTATGCAGA-GAATGAAACTGTACTC 881
                          i      v  i i    v  ?  vi     i -       ii  v  i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_95562721_9    882 CTATCTTTCACCACATACAAAGATTAACTCAAGGTATATTAAAAATTTAA 931
                            i  iv     i       i          ii iv  i ? i ii   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_95562721_9    932 ATGTAAGACCTCAACCTATAAAAATCCTAGAAGAAAACATAGGA--ACAC 979
                                 v  v  v        v  i                ?-- v i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_95562721_9    980 CATTCTGGATATTGGCCTTGAGAAAGAATTTATCAC-TAAGTCTTCAAAA 1028
                          -   vv  iv    v-  ii v  vii   v i v-  v v vi     
  L1M4_orf2#LINE/    559 C-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_95562721_9   1029 GCAATTGCAACAAAACAAAAAATTGACAAGTGGGATCTAATTAAACTAAA 1078
                            vvv         v       v  i  i v   ii v  i   v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_95562721_9   1079 GAGCTTCTGTACAGCAAAAGAAACTATCAACAGTGTAAACAGACAACCCA 1128
                         i i   i   i vv    i  v        v iv  i  v          
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_95562721_9   1129 CAGAATGGGAGAAAATATTTGCCAACTATGCATCGAACAAAGGTCTCATA 1178
                                               v  ii  ii   vi i  i  v  ii  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_95562721_9   1179 CCCAGGATCTGTAAGGAACTT----AATTCAACAAGCGGAAAACTAATAA 1224
                         i    i  v i   i     i----  i    i  vvii  i  v     
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_95562721_9   1225 CCCCATTGAAAAATGGGCAAAGGACT-GAACAGACACCTCTCAATAGAAG 1273
                            v   ?                i -   i     ii    v v     
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_95562721_9   1274 ACATACAAGCGGCCAACAAACATATGAAAAAATGCTCCACAACGCTAATC 1323
                          i      ii      i  i  i       i      v   v i??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_95562721_9   1324 AT 1325
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.58 (123 / 78)
Gap_init rate = 0.02 (13 / 845), avg. gap size = 1.92 (25 / 13)  


4720 15.13 1.78 0.78  chrX_95588624_95590765      751  1649 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95588624_9    751 TGGAAAGATATC--ATATTTATATGATCAGAAGACTTAGTATAATAGAGA 798
                                     --  i  i  i-   ii         i   vi vi   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATG-GATTGGAAGACTTAATATTGTTAAGA 49

  chrX_95588624_9    799 TCTCAATATTCCCTAAATTGATCTATAGATTCCATTCAATCCCTATCAGA 848
                          vv     i    i           i      v iv            i 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_95588624_9    849 ATCTCATCTGGCTTTTTTTGCAGAAATTGACAAGCTGATACTAAAATTCA 898
                            i  v   - i                          v          
  L1M4_orf2#LINE/    100 ATCCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_95588624_9    899 TATAGAAATTCAAAGGACCCATAATAACATGAACAATCTTTAAAAA--AG 946
                            i     v   i       v    i vvi         v     --  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_95588624_9    947 AACAAAGTTTGAAGACTCACACTTTTCAGTTCCAAG-CTTACTACAAAGC 995
                                  v  i           ii  i  i   i-             
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_95588624_9    996 AATACTAATCAAGACAGTGTGGTAGTGGCATAAGGGTAGACATATATAGA 1045
                         v i v                   v          i          --  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA--GA 296

  chrX_95588624_9   1046 TCAATGAAATAGAATTGAGAGTTCAGGGAAAAAAACATATATCCATGGTC 1095
                               i               i   ii v   vv    i  ii      
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_95588624_9   1096 AATTGATTTTTGACAAGGGTATCA-GATCATTCAATAAGGAAAGAATAGT 1144
                                   i         ii  -  i        ii            
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_95588624_9   1145 CTCTTCAACAAATGGTGCTGGAACAACTTAATAGCCAAATGCATAAAGAA 1194
                           i                  i      vi   ?   v     -      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAA 445

  chrX_95588624_9   1195 TGAAGTTGAACCTCCTACATCACACCATATA-AAAAAC-AAGTCAAAACG 1242
                                 i   -     v            -     i-  v      i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACC-CCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_95588624_9   1243 GATCAATTATGTAAACATAAGTGCTATAACCATAACACTCTTACAAGAAA 1292
                              ?vv iv    ii    v    v   i    v       v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_95588624_9   1293 ACATAGGGATAAATCTTGATAACCTTGGATTTGGAAATGGATTCTTAGAT 1342
                                ?i        vi i       i  v  v     v         
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_95588624_9   1343 ATACTATCAAAAGCACAGACAACAAAACAAAAA-TATATAAATCGAACTT 1391
                           ivi i          ii        v     -  v      i i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_95588624_9   1392 CATAAAAATTAAACACTT--GTGCTTCGAAGTATACTATTAAGAAAGTGG 1439
                            v         v    --       i   v i     i         i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_95588624_9   1440 AAACACAACCCACAGAATGGAAGAAAGT----GCCAATCATATATCTGA- 1484
                            v                i     i ----  v              -
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_95588624_9   1485 AAGAGACTTGTATCTAGAACATATACATAACATTTACAACTCAATAATAA 1534
                            i          i    i     v v   vi                 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_95588624_9   1535 AAATGATAAATAACCCAAATAAAAAATGGACAAAGGATCTGAATAGACAC 1584
                            -  i           v ?        i        i          i
  L1M4_orf2#LINE/    795 AAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_95588624_9   1585 TTCTTCAAAGAAGATATACAAATATCCAATCAACACATGAATACATGCTT 1634
                             i                  iv     v i        v v     i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_95588624_9   1635 GACATTATTAGCCAT 1649
                         i    i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (81 / 51)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.44 (23 / 16)  


3205 26.02 1.10 0.99  chrX_95645705_95650996     3893  4799 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95645705_9   3893 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3942
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95645705_9   3943 GGCCATACTGCCCAAGGTAATTTACATATTCAATGCTATCCCCATCAAGC 3992
                            v     v     iv i  i    v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95645705_9   3993 TACCAATGACTCTCTCTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAG 4040
                          v   i---  vi  i i  -i     -   -- v  i  - iii    i
  L1M4_orf2#LINE/    101 TCCCAG---CTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAA 144

  chrX_95645705_9   4041 TTCATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCA 4090
                                    viiv  ii  v  v v  v     iv     i i ivv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_95645705_9   4091 AAAGAACAAAGCTGGAGGCATCACACT----GACTTCAAACTATACTACA 4136
                         i          i      vv       ----i i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_95645705_9   4137 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCATAACAGAGATATA 4186
                          i          i   i    ii         i iv vi i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_95645705_9   4187 GACCAATGGAACAGAAC--AGAACCCTCAGAAATAATGCTGCATATCTAC 4234
                           i        i    i--   ii  --        vv iii i  i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chrX_95645705_9   4235 AATTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGA 4284
                         ii i vi    i  i     ivv  v   i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_95645705_9   4285 TTCCCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 4334
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_95645705_9   4335 AGCTGAAAGTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 4384
                         iiv    iv    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_95645705_9   4385 TGGATTAAAGACTTAAATGTTATACCTAAAACCATAAAAACCCTAGAAGA 4434
                              i ?    i       v v v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_95645705_9   4435 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACCTCATG 4483
                             v    ?i- v i -   iv   v v  vv i     v iii  v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_95645705_9   4484 ACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACCAATGGGA 4533
                         iv  vi            vvi          vv     v  iv   v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_95645705_9   4534 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAG 4583
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv v  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_95645705_9   4584 TGAACAGATAATCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCT 4633
                             v   i  i i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_95645705_9   4634 GACAAAGGGCTAATATCCAGAATCTACAAGGAACTCAAACAAATTTACA- 4682
                           i  i  i  vi          v  i  i      vv    v iv i -
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_95645705_9   4683 TGAAAAAACAAACAACCCCATCAACAAGTGGACAAAGGATATGAACAGAC 4732
                          i    i     i     v  i? v  i   i        v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_95645705_9   4733 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGC 4782
                          i     v        i  vi viii     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_95645705_9   4783 TCATCATCACTGGCCAT 4799
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


3171 25.66 0.99 0.99  chrX_95658285_95664677     4993  5900 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95658285_9   4993 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5042
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95658285_9   5043 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5092
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95658285_9   5093 TACCAAGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5140
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_95658285_9   5141 TATGGAACCAAAAAAGGG-CCCACATT-GCCAAGACAATCCTAAGCCAAA 5188
                                -- viv     -    v v -     i      i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_95658285_9   5189 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5238
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_95658285_9   5239 TCTACAGTAACCAAAACAGCATGGTACTGGTACCATAACAGAGATATAGA 5288
                         v         i   i    ii         i iv vi i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_95658285_9   5289 CCAATGGAACAGAAC--AGAACCCTCAGAAGTAATACCACACATCTACAA 5336
                         i        i    i--   ii  --    i   vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_95658285_9   5337 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGCTAAAGGATT 5386
                         i  vi    i  i     ivv  v   i v  vvv     vv    i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_95658285_9   5387 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5436
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_95658285_9   5437 CTGAATCTGGATCCCTTCCTTACACCTTACACAAAAGTTAATTCAAGATG 5486
                         v    vi    i    v   i     v  i      i    i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_95658285_9   5487 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAGCTCT-AGAAGAA 5535
                            i ?    i       v   v       i      -    -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chrX_95658285_9   5536 AACCTAGGCA-ATACCATTCAGGACATAGGCATGAGCAAGGACTTCATGT 5584
                            v    ?i- v i -   iv   v v  vv ii    v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_95658285_9   5585 CTAAAGCACCAAAAGCAATGGCAACAAAACCCAAAATTGACCAATGGGAT 5634
                         v  vii           vvi         vvv     v  iv   v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_95658285_9   5635 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGT 5684
                         i v  i   v v  i i   i  ii vv    i  v    i  vv v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_95658285_9   5685 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTG 5734
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_95658285_9   5735 ACAAAGGGCTAATATCCAGAATCTACAAGGAACTCCAACAAACTTA-CAA 5783
                          i  i  i  vi          v  i  i      iv    -  i -i  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAA 791

  chrX_95658285_9   5784 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGAGATGAACAGAC 5833
                         v     i     i     v  i?    i           vv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_95658285_9   5834 ACTTCTCAAAAGAAGACATTTATACAGCCAACAGACACATGAAAAAATGC 5883
                          i     v        i  vi v ii     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_95658285_9   5884 TCATCATCACTGACCAT 5900
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.29 (18 / 14)  


1869 23.15 2.59 1.60  chrX_95691864_95693952      487   987 (1102)    L1M4_orf2#LINE/L1       98   603 (305)  

  chrX_95691864_9    487 AAACCCAAGCAAGTTATTTTGTGGGTATTGACTAACTGATTCTAAAGTTT 536
                            i  v   vivi v     ii iv      v i     i     i  i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_95691864_9    537 ATATAGAGAGGCAAAAGATCCAGAATAGCCAACACAATACTGATGGAGAA 586
                             i  i v    ii  i             v     vi   vii    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_95691864_9    587 GAACAAA-TAAGACGACTAATACTTC--------AAGACTTACTATAAGA 627
                                - vi  v    v i     --------  i        i  ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_95691864_9    628 CTACACAGTAATCAAGACAGTAATCAAGTATTGGAAGAAAAATAGACAGA 677
                              --              i- --i   i   v v  ii       v 
  L1M4_orf2#LINE/    248 CTACA--GTAATCAAGACAGTG-T--GGTACTGGCATAAGGATAGACATA 292

  chrX_95691864_9    678 TAGATCAGTAGAACAGACTAGAAAGACCAGAAATAGACCAACACAAATAT 727
                                i i   i   v v  i  v         i   v i   vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_95691864_9    728 ACTCAACTGAACTTTGACATAGGAGCAAAG--CAGTTAGGTGGGGAAAAG 775
                         iv    i   vi  i    vi  v  v   --  v i i-        ii
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGA 391

  chrX_95691864_9    776 ACAGTCTTTTCAACAA-TGGTACTGGAACAACTGAGTATCCACATAAAAA 824
                          i              -    i    i       ii  ?      iv   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_95691864_9    825 GAAAATGAATATTAACATAGACCTTACACTCTTCACAAAAATAAGTTCAA 874
                         - i      vv vi  vivv    i    iv vi        v ii    
  L1M4_orf2#LINE/    442 -AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_95691864_9    875 AATGGATCATAGACCTAAATGTAAAATGC-AAAACTATAAAATTCTGAGA 923
                                  ?              i -  -            i   v   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGA 539

  chrX_95691864_9    924 AGATAACATAGGAGAAAATCTAGATAATCTTGGGTTTGGCAATGACTTTT 973
                            v        ? v      vvi i i        v       ii  i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_95691864_9    974 AAGATACAACACCA 987
                         v     ii      
  L1M4_orf2#LINE/    590 TAGATATGACACCA 603

Transitions / transversions = 1.51 (68 / 45)
Gap_init rate = 0.02 (11 / 506), avg. gap size = 1.91 (21 / 11)  

1228 20.77 1.92 0.32  chrX_95691864_95693952     1284  1596 (493)    L1M4_orf2#LINE/L1      591   908 (0)  

  chrX_95691864_9   1284 AGATACAACACCAAAGACA-AAGCCCATGAAAGAAAGACTTGGTACATTG 1332
                              ii        ii  -    v- ii       i v v i  v    
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCA-ACAAAAGAAAAAATAGATAAATTG 639

  chrX_95691864_9   1333 AACTTCATTCAAAATAAAAACTTCTGCTCTGTAAAA-ACA--GTCAAAAG 1379
                         i       iv   v         i  iv  vi   i-   --i    i i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_95691864_9   1380 AATGAGAATACAAGCCACAGATTGGGAGAAAATATTTGCATAAGACATAT 1429
                          i   i  v    v       v                  v vv i    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_95691864_9   1430 CTGATAAAGGATTGTTATCCAAAATAAACAAAAGACTCTTAAAACTCAAC 1479
                                i   i vv      i    v i   ii       v       i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_95691864_9   1480 AGCAAGAAGTCTAACAACCTAATT-AAAAATGGGCAAAAGATCTGAACAG 1528
                          ii  i   v v  i    i    -             i   i    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_95691864_9   1529 ATGCCTCACCAAAGAAGATATACAGATGGCAAATAAGAATA-AAAAAGAT 1577
                          iiii  v                i     v      v i -i       
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_95691864_9   1578 GCTCAACATCATATGTAAT 1596
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (42 / 23)
Gap_init rate = 0.02 (6 / 318), avg. gap size = 1.17 (7 / 6)  


 567 27.45 0.65 0.65  chrX_95717318_95723356     4057  4209 (1830)    L1M4_orf2#LINE/L1        1   153 (755)  

  chrX_95717318_9   4057 TGGAAAATCATTCCATGCTCGTGGATAGGAAGAATCAATATCGTTAAAAT 4106
                               ivi  i     i  i     v      v i     i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95717318_9   4107 GGCCCTACTGCCCAAAGCAATTTATAGATTCAGTGCTATTCCTATTAAAC 4156
                            vv    v      vii  i  i       ii  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95717318_9   4157 TACCATCGAAATTATTCGTAGAACTCAA-AAATTATATTTTAAAATTCAT 4205
                          v   v vivv  v  i i    v ii -  ii i-  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chrX_95717318_9   4206 ATGG 4209
                             
  L1M4_orf2#LINE/    150 ATGG 153

Transitions / transversions = 1.62 (26 / 16)
Gap_init rate = 0.01 (2 / 153), avg. gap size = 1.00 (2 / 2)  

2440 26.73 0.71 0.57  chrX_95717318_95723356     4484  5190 (849)    L1M4_orf2#LINE/L1      140   847 (61)  

  chrX_95717318_9   4484 TAAAATTCATAAGGAACCCAAAAAGAGCCCAAATAGCCAAGGCAATCCTA 4533
                                    v    vivv  ii  v  vi         ii     i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_95717318_9   4534 AACAAATAGAGCAAAGCTGGAAGCATCATGCTACCTGACTTCAAACTATA 4583
                           v  iv   i     i    i vv   ii  v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_95717318_9   4584 CAACAGGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAC 4633
                          v   ii          i   i    ii         i i  ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_95717318_9   4634 ACATAAACCAATGGAACAGAATAGAGAACACAGAAATAAGGCCACACAAC 4683
                          i   i i        i     v    iiv         iv   i   vi
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_95717318_9   4684 TACAGCTATCTGATCTTTGACAAACTTGACGAAAACAAGCAATGGGGAAA 4733
                           ii ii vi    i  i     ivv  v i i v  vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_95717318_9   4734 GAAT--TCCTTATTTAATAAATGGTGCTGAGAGAACTGGCTAGCCATATG 4781
                             --  i  -- i  i           i  v      v  ?   i   
  L1M4_orf2#LINE/    390 GAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_95717318_9   4782 CAAAAGATTGAAACTGGATCCCTTCCTTAAACCATACACAAAAGTTAACT 4831
                                v    ii    i    v   i v      i      i      
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_95717318_9   4832 CAAGATGGATTAAAGACTTAAACGTAAAACCCAAAACTATAAAAGCCCTG 4881
                            i      i ?    i    i    i v i            vi i i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_95717318_9   4882 GAAAACAACCTAGGCA-ATACCATTCAGGACATGGGCACGGGCAAAGATT 4930
                            i v   v    ?i- v i -   iv   v v  vvii     v i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_95717318_9   4931 TCACGACAAAGACACCAAAAGCAATTGCAACAAAAGCAAAAATCGACAAA 4980
                           viiivv v             vvv          v      v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_95717318_9   4981 TGGAATCTAATTAAA-TTAAGGAGCTTCTGCATAGCAAAAGAAACTATCA 5029
                          v i ii v  i   -    ii -   i  iiivv    i  v       
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_95717318_9   5030 ACAGAGTAAAGAGACAAACTACAGAATGGGAGAAAATTTTTGCAAACTAT 5079
                          v i   i  i      v i                 v        ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_95717318_9   5080 GCAACTGACAAAGGTTTAATATCCAGCACCCATAAGGAACTTAAGCAAAT 5129
                         ii v    i  i  vi vi       v ivi    i     ivvi   v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_95717318_9   5130 TTACAAGAAAAAG-CAAACAAGCCCATTAAAAAGTGGGCAAAGGACATGA 5178
                         iv i  v      -    i  v  v   ?    i           iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_95717318_9   5179 ATAGACACTTTT 5190
                                i  i 
  L1M4_orf2#LINE/    836 ATAGACATTTCT 847

Transitions / transversions = 1.61 (114 / 71)
Gap_init rate = 0.01 (7 / 708), avg. gap size = 1.29 (9 / 7)  

 336 17.33 1.33 0.00  chrX_95717318_95723356     5478  5552 (487)    L1M4_orf2#LINE/L1      833   908 (0)  

  chrX_95717318_9   5478 TGAATAGACACTTTTCAAAAGAAGACATACATGCAGCCAACAATCATATG 5527
                                   i  i  v        i     viii     i  v  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_95717318_9   5528 AAAA-ATGCTCAATATAACTGATCTT 5552
                             -        i  v ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1)  


3048 24.10 1.44 1.92  chrX_95779674_95781499.rev      502  1335 (491)    L1M4_orf2#LINE/L1       79   908 (0)  

  chrX_95779674_9    502 TTTGATGCA-TCCCTATCAAAATACCAATGACATTCTTCACAGAAATT-- 548
                           ii i   -             v   iivi v  i  ii        --
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chrX_95779674_9    549 -----T--TTTTTAAATGGTAACTGTTATACAGAACCACAAAAGATACAG 591
                         ----- -- ii v    -------- i   ii   vii   ii  iv   
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAAT--------TCATATGGAAATGCAAGGGACCCAG 170

  chrX_95779674_9    592 AATAGCCAAAGCTATGCTGAGAAAAAAAGAACAAAACCGAAAGCATCAGA 641
                                   i v  vi   -    i         iii i i vv   v 
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGA-AAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_95779674_9    642 TTACCTGACTTCGAATTATACTATAGAGCTATAGTAACCAAAACAGCATG 691
                         i v  ii i   i  viv     i i     i     i   i    ii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_95779674_9    692 GTACTGGCATAAAAACAGACACAGAGACCAATGGAACGGAATAGAGAACA 741
                                     ii i     i v   i        ii    v    iiv
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_95779674_9    742 CAGAAATAAGTCCATAAATCTACAGTGAACTCATTTTCAACAAAGGTGCC 791
                                  ii     v  i  ii  v  i v      i    i      
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_95779674_9    792 AAGAACATACATCGGGTAAAGGACAGTTTCTTCAATAAATG-TAATGAGA 840
                             v   v  vi   v    i i   i i     i     - iv  i  
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_95779674_9    841 AAACTAGATCTCCATATGCAGAAGAAAGAAACTAGACCCCTGTGTCTCTC 890
                         v    i   v?   i     i     v   ii i       iiv  v v 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_95779674_9    891 CATATACAAAAATGAAATCAAAGTGGATTCAAGACTTAAATCTAAGACCT 940
                                      v  v     i     iv?    i     v     v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_95779674_9    941 CAAATTATGAAACTGTTACAAGAAAACATTGGGGAAGGTCCTCTAGGACA 990
                         v   i   i     v   v          v  ? v ii  i  -iv   v
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACC 568

  chrX_95779674_9    991 TTGGACCGGGCAAAGATTACTTGCATAATATTCCACAAGCACAGGCAACC 1040
                             iiii     v i  v   iv   vv iv   v       i     v
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_95779674_9   1041 AAACCAAAAATGGACACATAAGATCACATCAAA-TTAAAAAATCTTCTGC 1089
                            vv      i  i v  vi  iiv       -       --   i  i
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA--CTTTTGT 666

  chrX_95779674_9   1090 ACAGCAAAGGAAACAATCAACAAAGTGAAGAGATAACCCACAGTATAGGA 1139
                         i vv       v  v     v        i   i         v  i   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_95779674_9   1140 GAAAATATTTGCAAACTACCCATCTGACAAGGGATTAATAACCAGAATAT 1189
                                        ii ivi      i      i vi  v         
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_95779674_9   1190 ATAAGTAGCTCAAACAACTCTATATAGAGAAAAAAATCTAATAATCCAAT 1239
                             iv i   vv       v   --- v     i - v     i     
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATA---ATAAAAAGA-CAAATAACCCAAT 812

  chrX_95779674_9   1240 TTTAAAATGGACAAAAGATCTGAATAGACTTTTCTCAAAAGAAGACATAC 1289
                          ?v       i    i   i         v      v        i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_95779674_9   1290 AAATGGCAAACAGGTATATGAAAAGGTGCTTAACATCATTGATCAC 1335
                                v  i i i i        i    i       ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (122 / 75)
Gap_init rate = 0.01 (11 / 830), avg. gap size = 2.55 (28 / 11)  


3211 27.67 0.33 0.22  chrX_95870913_95874977.rev     2668  3574 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_95870913_9   2668 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 2717
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_95870913_9   2718 GGCCATACTGCCCAAGGTAATTTATAGATTCAAAGCCATCTCCATCAAGC 2767
                            v     v     iv i  i  i        v  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_95870913_9   2768 TACCAATGACTTTTTTCACAGAATTGGAAATACT-ACTTTAAAGTTCATA 2816
                          v   iivi i     ii     v v  v vi  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_95870913_9   2817 TGGAACCAAAAAAGAGCCCACATTGTCAAGACAATCCTAAGCCAAAAGAA 2866
                              viiv  ii  v  viv  v i   i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_95870913_9   2867 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 2916
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_95870913_9   2917 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAAACAGACCAG 2966
                               i   i    ii         i iv ii i   v v i   i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_95870913_9   2967 TGGAACAGAACAGA-AGCCTCAGAAATAACACCACACATCTGCAACCATC 3015
                              i    iv  -  i -         vv   i    i iiiii  vi
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_95870913_9   3016 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 3065
                             i  i     ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_95870913_9   3066 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 3115
                           i  i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_95870913_9   3116 ACTGGATTCCCCCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA 3165
                         ii    ii  iv   i     v              i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_95870913_9   3166 AAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 3215
                         ?    i    i  v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_95870913_9   3216 GGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACCTCATGACTAAAA 3264
                           ?i- v i -   iv   v v  vv i     v iii  v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_95870913_9   3265 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 3314
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_95870913_9   3315 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTCCCATCAGAGTGAACAG 3364
                            v v  i i   i  ii vv    i  v   vi  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_95870913_9   3365 GCAACCTACAGGATGGGAGAAAATTTTTGTAATCTACCCATCTGACAAAG 3414
                         i     i    i            v    i  vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_95870913_9   3415 GGTTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAA 3464
                          ii vi          v  i         vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_95870913_9   3465 ACAAACAACCCCATCAAAAAGTGGGTGAAAGATATGAACAGACACTTCTC 3514
                              i     v  i?    i    ii  i   v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_95870913_9   3515 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 3564
                         v        i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_95870913_9   3565 CACTGGTCAT 3574
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.57 (151 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


2955 26.13 3.05 0.34  chrX_96020024_96022884.rev     1487  2370 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_96020024_9   1487 TGGAAAGAGA--CAATGCTCATAGAATAAAGGAATTTACACTGTTAAAAC 1534
                                 v -- v   i    i  v ii i  v  v i i      i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_96020024_9   1535 GACCATACAACTCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 1584
                          i v    vv i    vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_96020024_9   1585 TACCATTAACATTTTTTCACAAAAAATAGGAAAAATAATCCTAAAATTCA 1634
                          v   vivi v      -i  i   v - iv  iv i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATT-GACAAGCTGATCCTAAAATTCA 148

  chrX_96020024_9   1635 TATGGAACCACACAAGAGCCTGAATAGCCAAAGCAATCCTGAGCAAAAAG 1684
                                vii  vii  v  v           i     i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_96020024_9   1685 ATCAAAGC---AGGAC----ATT----GACTTCAAAATATACTACAAGGC 1723
                          v     i---     ---- i ----i i       iv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_96020024_9   1724 TATAGTAGTCAAAACAGCATGGTACTAATGTAAAAAGAGATATATACACC 1773
                           i    i    i    ii       iiii   ii v   i     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_96020024_9   1774 AATGGAATAGAATAGAGAACCCAGAAGTAAATCCATATATTTACAGCTAA 1823
                                      v    ii      i    i     i     ii ii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_96020024_9   1824 CAGATTTGGCACAAATGTACCAAGAACATGCAATGGGGAAAGGACACCCT 1873
                         iv     vvv    iv  i      v   v            i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_96020024_9   1874 CTTCAATAAATGATGATAGGAAAACTGGACATCCATTTGCAAAAGAATTA 1923
                         i     i     i  v i   v       i ?   iv           v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_96020024_9   1924 AACCTGACCTATATCTCCCACAATATATAAAAATGGACTCAACATTGATT 1973
                          iiiv    iv  i   v   v     i      vi      v  v   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_96020024_9   1974 AAAGACTTAAGCATAAGACCTGAGACTATAAAACTACTAGAAGAAAACA- 2022
                          ?    i   iii     v  i i           vi            -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_96020024_9   2023 AGAC--AAATGCTCCAGGACACTAATATAGGCAAAGATTTTGTGGCTAAG 2070
                           i?--    -  i iv   vi iivv       v i   iv i v  v 
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_96020024_9   2071 ACCTGAAAAGCACAGGAAACAAAAACAAAAATGGGTAAGTGAGATTATAT 2120
                           viv         i v       iv      i i   i vi  i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_96020024_9   2121 TAAACTAAAACGCTTCCGCATAGAAAAGGGAACAATTAACAGAGTAAAGA 2170
                         i   v v   vi   ii iiivvv     iv  v  i  v i   i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_96020024_9   2171 GACAATCTGTTGAATGGGAAAAAATATCTGCAAAC----TATCCAACAAT 2216
                              i iiiv        i       i      i----    ii i  v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_96020024_9   2217 GGACTAATATCCAAAAAATACAAGAAACCC--A-AAC--AATAGCAACAA 2261
                              vi      i  v   i  ii   i -- -   --    ii  v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_96020024_9   2262 AACAAATAATCACATTAAAGAGTAGACAAATAATTTAAGTAGACATTTCT 2311
                         i        i vv   ?  i i i i    vi    i i           
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_96020024_9   2312 CAAAAGAAGACAAACAAATGGCCAAGA--TATATGAAAATGTGCTCAACA 2359
                          v        i v            v --i i       vi         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_96020024_9   2360 TCATTAATCAC 2370
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.77 (145 / 82)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


2590 28.21 2.20 1.50  chrX_96028806_96032613.rev     2093  2957 (851)    L1M4_orf2#LINE/L1        1   871 (37)  

  chrX_96028806_9   2093 TGGAAGAACATCTCATGCTCATAAATTGGATGAGTCAATATCATTAAAAA 2142
                              ii i   i    i    ii      v  v i     ii    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_96028806_9   2143 GGTCATACTGCCCAAAGCAATTTACAGATTCAATACTATTCCTACCAAAC 2192
                           iv     v      vii  i           ii v  i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_96028806_9   2193 TACCAA-TGTCATTTTTCACAGGCTTAGAAAA--AAAAAACT-ATTCTAA 2238
                          v   i-  i -     ii   -------   --i v  i  -  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAG-------AAATTGACAAGCTGATCCTAA 142

  chrX_96028806_9   2239 AATTCACATGGAATCAGAAAAGAGCCCAAATAGCCAAAGCAATCCTAAGC 2288
                               i      viiv  ii  v  vi          i     i i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_96028806_9   2289 GAAAAGCAGAAAGCCAGAGGCATCACATTACCTGCCTTCAAACTATATTA 2338
                         i i   v v    iii    vv     i v  iivi      viv  i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_96028806_9   2339 CAAGGCTACCGTAACCAAAACAGCATGGTACTGGTACAAAAATAGACACA 2388
                            i     v    i   i    ii         i i  ii       i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_96028806_9   2389 TAGACCAATGGAACAGACTAAGAGAACCAAGAAATAAAGCTGCACACCTA 2438
                             i        i   v v-    ii v         v iii   ii  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_96028806_9   2439 CAGCCATCTGAATTTTGACAAAGTCAAACAAAAATAAACAATGGAGAAAG 2488
                         ii i  vi   v   i     i viiv-   i vi vv      i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAG 390

  chrX_96028806_9   2489 GACTACCTATTCAATAAATGGCACTGTGATAGCTGGCTAGCCATATGCAG 2538
                         i ivii  v     i      ii   v  i i    v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_96028806_9   2539 AAGAACAAAACCGAAAGCCTCTCTTTTACCATACACAAAAAGT----CAA 2584
                              ii  iii i vv   vi  ivi      i       v ----   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_96028806_9   2585 AATGGATTAAAGAATTAAATGTAAGACCTCAAACTATGAAAATCCTATAA 2634
                                i ?   vi           v  v       i   v  i  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_96028806_9   2635 GAAAACCTAGGAA-ACACCATTCTGGACATCTGCCTTGGGAAATAACT-C 2682
                               v    ?i- v i -   vv   v -  vv  i  v   iii - 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCT-TGGGTTAGGCAATGGTTTC 588

  chrX_96028806_9   2683 ATGACTAAGTTCTCAAAAGCAACTGTAACAAAA------ATTGATGAATC 2726
                         v iiv  v vivi        vvv i       ------  v   i   i
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_96028806_9   2727 GAACTTAATTAAACTAAAGAGCTTCTGCACAACAAAATAAACTATTAACA 2776
                          i    v  i   v v  i i   i  ii vv    iv v     i  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_96028806_9   2777 GGATAAACAGACAACCTGCACAATGGAAGAAAATATTCACAAACTATGCA 2826
                         iii i  v        ii  v     i          ii    ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_96028806_9   2827 TCTGACAAAGGTCTAATACCCAGAATCTATAAGGAACTTAAAGAAATCAA 2876
                              i  i  v  vi  i       v     i     ivv v  v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_96028806_9   2877 CAACCAAAAAAACAAATAACCCCATTAAAAAGTGGGCAAAGAACATGAAC 2926
                         i  i-     i           v   ?    i         i iv    i
  L1M4_orf2#LINE/    789 TAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_96028806_9   2927 AGACACTTCTCAAAAGAAGACATATG---GGCCA 2957
                              i     v        i   ii---     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.79 (154 / 86)
Gap_init rate = 0.02 (15 / 871), avg. gap size = 2.13 (32 / 15)  


2855 27.40 2.24 0.67  chrX_96260572_96267212     5257  6150 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_96260572_9   5257 TGGGAAAACAGCCCATGCTCATGGATAGGAAGAATCAATATTGTCAAAAT 5306
                            i  i i v      i        v      v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_96260572_9   5307 GGCCATACTGCCCAAAGTAATGTATGGATTCAGTGCTATTCCCATCAAGC 5356
                            v     v      v i  v  ii      ii  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_96260572_9   5357 TACCATTGACTTTCTTCACAGAG-TTGGAAAAAAACT-ACTTTAAATTTC 5404
                          v   vivi i  i  ii    i-   --- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_96260572_9   5405 ATATGGAACCAAAAAAGATCCTGTATAGCCAAGACAATCCTGAGCAAAAA 5454
                                 viiv  ii  i  v v        i      i   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_96260572_9   5455 GAACAAAGCTGGAGGCATCACACTACCTGACTTTAAACTATACTACAAGG 5504
                                 i      vv       v  ii i  i   viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_96260572_9   5505 CTGTAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGACATATAGAC 5554
                           ii     i   i    ii       v i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_96260572_9   5555 CAATGGAGCAGAACAGAGACCTCACAGTGTAACCCCACACATCTAAAACC 5604
                                ii    iv    vii  v i-i   v    i    i  viii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAA-ATAAACCCATACATTTATGGTC 346

  chrX_96260572_9   5605 ATCTGATCTTCAACAAAACTGACAAAAAAAAAGCAATGGGGAAATGATTC 5654
                          vi    i   i    iiv  v   i vv v-v           vi  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAG 395

  chrX_96260572_9   5655 CCTATTTAATAAATGATGCTTGGAAAACTGGCTAGCCATATGCAGAAAAC 5704
                         i  v  i  i     i    v   v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_96260572_9   5705 AGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGT 5754
                         v   ii         v   i     v                   i   v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_96260572_9   5755 ATTAAAGACTTAAATGTAAATCCCAAAACCATAAAAACTGTAGAAGAAAA 5804
                           i ?    i         ivv i     i      viiv          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_96260572_9   5805 CCTAAGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCCTGACT 5853
                          v  i ?i- v i -   iv   v v  vv i     v ii   i iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_96260572_9   5854 AAACTGCCAAAAGCGATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5903
                          vivii        ivvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_96260572_9   5904 AATTAAA-CAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAGAGTGA 5952
                         v  i   -iv  i i   i  ii vv    i  v    v  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_96260572_9   5953 ATAGGCAACCTACAGAATGGAAGAATATTTTTGCATTCTACCCATCTGAC 6002
                          v  i     i         i    v  v      vvii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_96260572_9   6003 AAAGGTCTAATATCCAGAATCTACAAGGAACT--TA-AGC---ATATTTA 6046
                           i  v  vi          v  i  i     --  - i ---   v v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_96260572_9   6047 CAAGAAAAAAAA---AATCAAAAAGTAGGCAAAGGATATGAACAGACCTT 6093
                         v    v   v  ---   i?    i i          v    i    v  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_96260572_9   6094 TCTCAAAAGAA-ATGT------GGCCAACAGATACATGAAATAAAGCTCA 6136
                             v      -  i ------      i iii        vi v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_96260572_9   6137 TCATAACTGGTCAT 6150
                         v   v ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.86 (26 / 14)  


1382 20.10 1.58 26.33  chrX_96470049_96476758     5014  6217 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_96470049_9   5014 GAAGAATATTCCATGCTCATGGATAGGAAGA-TTAATATTGTGAAAATGG 5062
                            ii    i     i        v      -          v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_96470049_9   5063 CCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAACTA 5112
                          v     v     iv i  i  i       ii  v     i      v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_96470049_9   5113 CCAATGACTTCCTTCACAGAA-TTGGAAAAAACT-ATTTTACAGTTCACA 5160
                            iivi i ii  ii     -   -- v  i  -  ii  v i    i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATA 150

  chrX_96470049_9   5161 TGGAACCAAAAAAAGAGCCC-GCATTGTCAAGACAATCCTAAGCCAAAAG 5209
                              -- viv  i ii   - v  v i   i      i i ivv i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_96470049_9   5210 AACAAAGCTGGAGGCATCACACTACCTGACTTCAACCTATACTACAAGGC 5259
                                i      vv       v  ii i     vviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_96470049_9   5260 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGCCC 5309
                                 i   i    ii         i iv ii i   v v    vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_96470049_9   5310 AATAGAACATAACAGAGGCATCAGAAATAATACTACACATCTACAACCAT 5359
                            i   i v  iv   ivvi         vv i i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_96470049_9   5360 CTGATCTTTGACAAACCTGACAGTAACAAGAAATGGGGAAAGGATTCCCT 5409
                         i    i  i     ivv  v  iv v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_96470049_9   5410 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5459
                         v  i  i              v      v  ?   i   -----------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG----------- 437

  chrX_96470049_9   5460 AACTGTCCAGGCATGGTGGCTGACGCCTATAATCCCAGCACTTTTGGAGG 5509
                         --------------------------------------------------
  L1M4_orf2#LINE/    438 -------------------------------------------------- 437

  chrX_96470049_9   5510 CCAAGGCAGGTGGATCACGAGTTCAGGAGATCAAGACCATCCTGGCTAAC 5559
                         --------------------------------------------------
  L1M4_orf2#LINE/    438 -------------------------------------------------- 437

  chrX_96470049_9   5560 ATGGTGAAACCCTGTCTCTACTAAAAATATAAAAAATTAGCCGGGCATGG 5609
                         --------------------------------------------------
  L1M4_orf2#LINE/    438 -------------------------------------------------- 437

  chrX_96470049_9   5610 TGGTGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATG 5659
                         --------------------------------------------------
  L1M4_orf2#LINE/    438 -------------------------------------------------- 437

  chrX_96470049_9   5660 GTGTGAACCCAGGAGGCAGAGCTTCTTGCAGTGAGTGGGAGATCACGCCA 5709
                         --------------------------------------------------
  L1M4_orf2#LINE/    438 -------------------------------------------------- 437

  chrX_96470049_9   5710 CTGTACTCCAGCCTGGGCGACAGAGCAAGACTCTGTCTCAAAAAAAAAAA 5759
                         --------------------------------------     i  ----
  L1M4_orf2#LINE/    438 --------------------------------------CAAAAGAA---- 445

  chrX_96470049_9   5760 AAAAAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAA- 5808
                         ---------    ii    i    v   i     v              -
  L1M4_orf2#LINE/    446 ---------TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_96470049_9   5809 TCAAGATGGATTAAAGATTTAAGTGTTAGACATAAAGCCATAAAAACCCT 5858
                             i      i ?   ii   i   v   vv    i i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_96470049_9   5859 AGAAGAAAACCTAGGCA-ATACCATTCAGGACATGGGCATGGGCAAGGAT 5907
                                   v    ?i- v i -   iv   v v  vv i     v i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_96470049_9   5908 TTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGC---------CAA 5948
                            v iiv  vi            vvi          v---------i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_96470049_9   5949 ATGGGATCTAATTAAACTAAAGTGCTTCCGCACAGCAAAAGAAACCACCA 5998
                           v   ii v  i   v v  ivi   ii ii vv    i  v  i i  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_96470049_9   5999 TCAGAGTGAACAGGCAAGCTACAGAATGGGAGAAAATTTTCACAATCTAC 6048
                         vv i      v  i   v i                 v  ii   vii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_96470049_9   6049 CCATCTGACAAAGGGCTAACATCCAGAATCTACAAAGACCTTACACAAAT 6098
                         vi      i  i  i  vii         v  i     v  ivi    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_96470049_9   6099 TTACAAGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGA 6144
                         iv i  v     i    ----   v  i?    i            v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_96470049_9   6145 ACAAACAGTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAA 6194
                          i i   v     v        i  vi viii     v ii         
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_96470049_9   6195 AAATGCTCATCATCACTGGCCAT 6217
                          i       v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 25.85 (336 / 13)  


2983 23.22 3.43 1.52  chrX_96548510_96553387.rev     3163  3950 (928)    L1M4_orf2#LINE/L1        1   803 (105)  

  chrX_96548510_9   3163 TGAAAAGATATTC-----------AGTGAAAGACTTAATATTGTTAAAAT 3201
                           i        i ----------- v  i                  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_96548510_9   3202 GTCCATACTACTTAAGATAATCTATAGATTCAATGCAATCCCTTTAAATG 3251
                          v v     v ii  iv i     i        i         v v  vi
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_96548510_9   3252 TCCCAATGGCATTTTTCAGAGAAATAGAAAAACCCATCGTAAAATTCATA 3301
                              iiv  v     iiv      v  v  i iv   v           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_96548510_9   3302 ----ACTACAAAAGAGCATGAATAGCCAAAGAAATCTTGAGAAAGAAGAA 3347
                         ---- v i   ii  v vv           iv        i         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_96548510_9   3348 CATAGCTGGATTCGCCACACTTCCTTATTTTAAAATATATTACAAACCTT 3397
                           v  i    vvvvi         iv    i    iv  i      v  v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_96548510_9   3398 CAGCAATTTAAAAAATATGGGACTGACATAAAAACAGACATGTAGACCAA 3447
                            i   iv i v i i   v    i     ii i      i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_96548510_9   3448 GGAAACAGAATAGAGAGCCTAGAAATATATCCATGCATATATGGTCAACT 3497
                         v i  i     v     i i       v i    i   v         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_96548510_9   3498 GATCTTTGTATGGGGTGCCAAGAACACAGAATGAGAAAAGGAAAGTCTCT 3547
                            i  i vvvi           v  ivv    i i    i v     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_96548510_9   3548 TCAACAAATGGTAGTGGGAAAATTGGATATGGACATGCAAAAGAATGAAA 3597
                                     iv     v  i      ?vv                 i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_96548510_9   3598 TTGGACCTTCATCCCACATTATATATAAAAATCAACTAAAAATGGGTTAA 3647
                                iii i i    ii     i      i    v       i i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_96548510_9   3648 AGATTTAAACGTAAGACCTAAACCTACAAAACTCCTTGAAGAAAACAAAG 3697
                            ii    i      v     v   i       i v          v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_96548510_9   3698 GGGAAAAGCATCATGGTATTGGTCTGGGCAATGATTTCTTGGATATGACA 3747
                          ? v   v v  i  iiv    vi i       i      i         
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_96548510_9   3748 CCAAAAGCATAAGCAGCAAAAGCAAAAACACA---GTGAGATTACAT-AA 3793
                                  i     i      v     i v ---i vi  i v   -  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_96548510_9   3794 AACTAAAAAGCTTCTGTACAGCAAG---CA--ATCAAAA---TGAAAAGG 3835
                           i      -   i   i vv   i---  --     i ---       i
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_96548510_9   3836 CAATTTACAAAAATGAGAGAAAATATTTGCTAGCTGCATATCTGATAAAG 3885
                            iii   i  -  i              v iiiii           i 
  L1M4_orf2#LINE/    700 CAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_96548510_9   3886 GGCTAACTATGCAAAATGTGTCAAATACGTAAGGAACTCAAATAACTCAA 3935
                          i  vi-   v  i   -------   --   i      vv i       
  L1M4_orf2#LINE/    749 GACTTG-TATCCAGAAT-------ATA--TAAAGAACTCTTACAACTCAA 788

  chrX_96548510_9   3936 GATCAAAAAAACAAA 3950
                         v vi     i     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAA 803

Transitions / transversions = 1.57 (110 / 70)
Gap_init rate = 0.01 (12 / 803), avg. gap size = 3.25 (39 / 12)  

 529 10.79 1.44 8.63  chrX_96548510_96553387.rev     4249  4387 (491)    L1M4_orf2#LINE/L1      780   908 (0)  

  chrX_96548510_9   4249 ACAAAACAA-AATAAAAA-ACAAAAAAGCTCCCAAATAGCCAGTTTAAAA 4296
                             vv   -        -     v  ---     ---------  ?   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAA---CCCAA---------TTWAAA 817

  chrX_96548510_9   4297 AATAAGGAAAGGTTTTGAATAGACATTTCTCCAAAGTAGACATACAAATG 4346
                            ii v     v                       v   i         
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_96548510_9   4347 GCCAACAGGTATGTGAAAAGATGCTCAACATCACTAATCAA 4387
                              i i i ii                    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (8 / 6)
Gap_init rate = 0.03 (4 / 129), avg. gap size = 3.50 (14 / 4)  


3246 27.09 0.44 0.44  chrX_96570904_96577169.rev     4868  5775 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_96570904_9   4868 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCGTGAAAAT 4917
                              ii i  i     i      i v      v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_96570904_9   4918 GGCCATACTTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4967
                            v     i     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_96570904_9   4968 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5015
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_96570904_9   5016 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5065
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_96570904_9   5066 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5115
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_96570904_9   5116 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5165
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_96570904_9   5166 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5213
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_96570904_9   5214 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5263
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_96570904_9   5264 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5313
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_96570904_9   5314 GAAACTGCATCCCTTCCTTACACCTTAAACAAAAATTAATTCAAGATGGA 5363
                            ii  v i    v   i     v  v           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_96570904_9   5364 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5413
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_96570904_9   5414 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5463
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_96570904_9   5464 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5513
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_96570904_9   5514 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCTTCAGAGTGAAC 5563
                          i   v v  i i   i  ii vv    i  v  i i vvv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_96570904_9   5564 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAATCTACTCATCTGACAA 5613
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_96570904_9   5614 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5663
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_96570904_9   5664 AAACAAACAACACCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5713
                          i     i   v v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_96570904_9   5714 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5763
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_96570904_9   5764 ATCACTGGCCAT 5775
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3194 26.00 1.11 0.66  chrX_96639566_96645832.rev     4873  5776 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_96639566_9   4873 TGGAAGAACATTCCATGCTCATGGTTAGGAAGAATCAATATCGTGAAAAT 4922
                              ii i  i     i      v v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_96639566_9   4923 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4972
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_96639566_9   4973 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5019
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_96639566_9   5020 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGACAATCCTAAGCCAAAA 5069
                                 viiv  ii  v  v v  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_96639566_9   5070 GAACAAAGCTGGAGGCAACACACTACCTGACTTCAAACTATACTACAAGG 5119
                                 i      vvv      v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_96639566_9   5120 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5169
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_96639566_9   5170 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCCTATCTACAAC 5217
                                 i    i--    i  --        vv  iivi  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_96639566_9   5218 TATCTGATCTTTGACAAACCTGAGAAAAGCA----ATGGGGAAAGGATTC 5263
                         i vi    i  i     ivv  vv  i v  ----          i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_96639566_9   5264 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5313
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_96639566_9   5314 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5363
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_96639566_9   5364 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTACAAGAAAA 5413
                           i ?    i    i  v   v       i      vi i  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_96639566_9   5414 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5463
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_96639566_9   5464 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGCATCTA 5513
                         vi            vvi           v     v  i    v v ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_96639566_9   5514 ATTAAACTAAAGAGATTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5563
                           i   v v  i iv  i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_96639566_9   5564 CAGGCAACCTACAAAATGGGAGAAAA-ATTTCGCAACCTACTCATGTGAC 5612
                         v  i     i   i            -    -    vii ivi  v   i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGAT 744

  chrX_96639566_9   5613 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5662
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_96639566_9   5663 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5712
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_96639566_9   5713 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5762
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_96639566_9   5763 CCATCACTGGCCAT 5776
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (135 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


4256 15.48 2.44 6.15  chrX_96736463_96738600.rev      705  1647 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_96736463_9    705 TGAAAAGACATCTCGTGTTCATGAACTGGAAGATTTAAAATTGTTAAGAT 754
                           i     i   i i        i i       i    v           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_96736463_9    755 GGCAATACTCCCCAAAGTAATCTATAGATTCAGTGAATTCCCTATCAAAC 804
                                         v i     i       ii v v           v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_96736463_9    805 TTCCAAAGACCTTTTATTGCAGAAATGGAAAAGCCTATTCTAAAGTTCAT 854
                          i   ivvi      -          v  v    iv  i     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_96736463_9    855 ATGGAATTGCAAAGG-CCCTGAATAGCTAAAAAAAAAAAAAAAAAAAAAA 903
                               v     i  -   v       i    ------------------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAA------------------ 181

  chrX_96736463_9    904 AAAACCAACACAACCTCATAAAAGGAGAACACAGTGAGAAGACTCACACT 953
                         ----------   i  iiv     i      v   vi  i          
  L1M4_orf2#LINE/    182 ----------CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_96736463_9    954 TCCCAATTTCAAAAC--ACTGCAAACCTACAATAATCAGAACACCGTA-T 1000
                                        --   i    v     i      ii   vi  i- 
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_96736463_9   1001 GCTGGCATTAAGATAGATACATAGACAAATTGAATAGAATTGACAGTCCA 1050
                         i       v i      i i     iv   v            v      
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_96736463_9   1051 GCAATAAAATCATATATCTATGGGCAATTGATTTTCAACAAGGGGGCCAA 1100
                          v      vi    i  i     v            i       v     
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_96736463_9   1101 GGCCATTCAATGAGGAGAGAATAGTTTCTCTAATAAATGGCACTGGGACA 1150
                          i          i   i        i i ii  i      ii        
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_96736463_9   1151 ACTGGATATCCACATGCAAAAGAATGAAGTTGGACCTTTGTCTCACACCA 1200
                                 ?                           ii ii         
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_96736463_9   1201 TATATAAAAATTAACCCCAAATGGATCAACAAACCTAA-TA-AAGAACTA 1248
                             i          i v          ?- i      - i-    i   
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAW-AGACCTAAATGTAAGAGCTA 520

  chrX_96736463_9   1249 AAACTACAAAACTCTTAGAAGAATAACACAGGGGTTAATCTTCATGGCCT 1298
                               i                -    i   ?  v       i  i   
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAA-AACATAGGNGTAAATCTTCGTGACCT 569

  chrX_96736463_9   1299 CATTTTTGATAGTCGATTCCTAGATATGAAAATAAAAGTACAAAAAACAA 1348
                         iivv  v ii i v v   i         v vi     i    iv     
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_96736463_9   1349 ACAAAA-----GGTAAATTGGACTTCATCAAAATAAAAAG----TGTGCA 1389
                          vi   ----- i                     v    i----     v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_96736463_9   1390 TCAAAGAATATTATCCAGAAAGTAAAAAGATAACTTACAGAAAGGGATAA 1439
                               i i i    v       i      i   ii      v    v  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_96736463_9   1440 AATATTTGCAAATTATATATTTTCTA------TT--ACCCAGAATATATT 1481
                                      i      i vv  ------  -- i           -
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT- 768

  chrX_96736463_9   1482 TTTAAAAAACTCTTACAAAGTTCTCTTATAGAAAATATAAAGAACATCAA 1531
                         ---   i           ----   --------    --------  -  
  L1M4_orf2#LINE/    769 ---AAAGAACTCTTACAA----CTC--------AATA--------AT-AA 794

  chrX_96736463_9   1532 AAAGACAAAAAAATTCAATTAAAAAAATGAGCAAAGGATTTGAATAGACA 1581
                                  v  -ii     ?     -  i                    
  L1M4_orf2#LINE/    795 AAAGACAAATAA-CCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chrX_96736463_9   1582 TTTCTCTAAAGAAGATATTCAAATAACCAATAGGCATGTGAAAAGATGCT 1631
                               i           v     ii      i   ii            
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_96736463_9   1632 CAGCATTATTAATCAT 1647
                           i   i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.16 (97 / 45)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.05 (81 / 20)  


2618 25.69 1.70 0.92  chrX_96771087_96773574     1233  1995 (493)    L1M4_orf2#LINE/L1      140   908 (0)  

  chrX_96771087_9   1233 TAAATTTCACATGTAACCAAAAAAAGGGCCCA-AATAGCCAAAGCAATCA 1281
                             v    i   v  -- viv  i  i    -          i     v
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chrX_96771087_9   1282 TAAGTAAAAAGAACAAAGCTGGAGGCATCAATCACATTACCCAACTC--A 1329
                          i iv  i          i      ---- v     i v     i i-- 
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGG----ACTCACACTTCCCAATTTCAA 233

  chrX_96771087_9   1330 AACTATACTATAAGGCTACAGTAACCAAAAGAGCATGGTACTGGTACAAA 1379
                             -     i  i          i   i v  ii         i i  i
  L1M4_orf2#LINE/    234 AACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_96771087_9   1380 AACAGACACATAGACCAATGGAGCAGAATAGAGAGCCCAGAAATAAAGCC 1429
                         i i     i     i       ii     v     i           v  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_96771087_9   1430 ATGAACCTACAGTCATCTGCTCTTTGACAAATTGAAAAAAAAAAAGGAAT 1479
                           iv ii  ii    vi  v i  i     ivvvivv  i vv vvv   
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_96771087_9   1480 GGGGAAAGGACTCCCTATTCAATAAATGATGCTGGGATATCTGGTTAGCC 1529
                                 i ivvi  v     i     i        i v    v  ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_96771087_9   1530 ATATGCA---GAATAAAACTGAACCCCTACTTTTCACCATATACAAAAAT 1576
                          i     ---    i  ii  i        i iv                
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_96771087_9   1577 GATCTCAAGATGTATTACAGATTTAAATGTAAGACCTCAAACTATAAGAA 1626
                         v v     i   v  i ?   ii           v  v         i v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_96771087_9   1627 TCCTAGAAAAACACCTAGG---AAA----CACCACTCTGGACTTGATAAA 1669
                           i     i  v  v    ---   ---- iiv  ii   ii v ii  v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_96771087_9   1670 GAATTTATAACTAAGTCCTCAAAAGTAATTGCAACAAAACCAAAGATTGA 1719
                          iv  iv  iv  v v vi      i vvv         vv   i  v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_96771087_9   1720 CAAGTGGTACCTAATTAAACTAAAGATCCTCTACGTAGCAAAAGAAACTA 1769
                         i  i v v  i v  i   v v  i v i i ii ivv    i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_96771087_9   1770 TCAACAGAGTAAATAGACAACCTACAGAATAGGAGAAAATATTTGTAAAC 1819
                             v i   i  v        i       i              i   i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_96771087_9   1820 TATGCATCTGATGAGGGTCTAATATCTAGAATCTATAAGAAACTTGAACA 1869
                         i  ii       i    v  vi    i     v     ii    ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_96771087_9   1870 ATTCAAAAAGCAAAAAACAAATAACCCTATTAAAAAATGAGCAAAGGACA 1919
                          i    v  vv    i           v   ?       i        iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_96771087_9   1920 TGAACAGACACTTCTCAAGAGAAGGCATACAAGCAGCCAACAAACTAATG 1969
                             i     i     v i     ii      iii     i  i vv   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_96771087_9   1970 AAGAAATGCTCCACATCACTACTCAT 1995
                           i i      v      ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (115 / 78)
Gap_init rate = 0.01 (8 / 769), avg. gap size = 2.50 (20 / 8)  


2275 26.61 7.52 1.19  chrX_96845939_96847994      727  1564 (492)    L1M4_orf2#LINE/L1       18   908 (0)  

  chrX_96845939_9    727 TTCAAATATGGGTAAGTTCAATATTACTAAGATGCTAATTTTCCCCAAGT 776
                             viv  v  v iii i      ii       vi   vi       i 
  L1M4_orf2#LINE/     18 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 67

  chrX_96845939_9    777 TGATGTATAGATTCAACCCAATTCCAATCTAACTTTTAGCAAGATGC--- 823
                             v  i         v    i  v   v  v iii   ----   ---
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC----TGCCTT 113

  chrX_96845939_9    824 -TTTATACAAATTCATACAAGTTAATTCTAAAATTTATAAGAAAATACAA 872
                         -   ii v     v --    i i  i        i   v i    i   
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_96845939_9    873 TGG-CTTAAAAGGATCAAA-CAATTTTAAAAA----GAATAAAGTTGGGC 916
                         v  - ii i  viii    -    i  i    ----   i        iv
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_96845939_9    917 GACTTATGCCACCTGATTTCAGAACTTAT---AAAGCTACAGTAAAGAAG 963
                             i ii iv  ii      i      i---             vv   
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_96845939_9    964 ATAATATTGTTTTTGTGAATGGATTGACATGTATATTAGTA-AACAGAA- 1011
                          i i i v  vi v iiv v    v     i  v  i i i-  i    -
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_96845939_9   1012 --ACAGCCCAGAAATAGAGTCAGTCATATATAGCCTATTGATTTGTAACA 1059
                         -- v  i         i vi  vv   v   i i v        vii   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_96845939_9   1060 GAGGTGGCAAGGTAATTCAATGGTGGAAAGAAAAGTCATTTCAACAAACT 1109
                         ii    v    iiv         -        v    v          iv
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_96845939_9   1110 GTGCTGAAACAACTGCTTATCTGTATGGAAAAAACCCGAATATTTACTGC 1159
                               ii       vv  ? iii   v    i vi-   vv vv  iv 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT-GAAGTTGGACCCC 459

  chrX_96845939_9   1160 TACCTAAAACCATACTGAAAAAT---CT--AAACAAACCATACAATTAAA 1204
                              v v      ivv      ---  --   iii i  ? v vi    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_96845939_9   1205 TGTAAGAGTTAAAAGTATACAAATTCT-AGAAGAAAATGTAGAAG----- 1248
                                 i     v    -   i   -         ii   i? -----
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_96845939_9   1249 -------ACATCAGAGTAGGCAAAATTTTCTTAGAAA-------AGAAGC 1284
                         -------  v ii iv       viv         v ------- i    
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_96845939_9   1285 ATAAACCACACAA----AAACAGAGACCTTGGA--------AAATGTCAA 1322
                          i  i v   v  ----   i   v vv     --------    - v  
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT-TAAA 657

  chrX_96845939_9   1323 AAGCTTTACTCTTTGAAAGCTATCATTTAGAAA-TGAAAAGGTAAGCCAC 1371
                           vi   iiv   ii  i vi ii  iv     -       ii  v    
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_96845939_9   1372 AGAGTAGAAAACAATAATCACAAA--ACATGTCAGACAAATGGCTTTCAT 1419
                            i i i i v    v ii    -- i  i  v  i  iv i   vi  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_96845939_9   1420 CCAGAAAATATAAATAACTCTTATAACTCAATGATAAGAGGA--AAT--T 1465
                               v       v        i        i    i i  --   --i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_96845939_9   1466 TTAATATAAAA-TGAGAAAAATGTCTGAATAGACACTTCACAAAAGAATA 1514
                         ii   v?    -  i v   ivi i          i   v v      v 
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_96845939_9   1515 TATACCAGTGGCCCA-AAACACATAAAGAGATGCCCAACATCTTTAGTTA 1563
                              v i     v -  i     i  i      i       v???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_96845939_9   1564 T 1564
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.52 (132 / 87)
Gap_init rate = 0.03 (26 / 891), avg. gap size = 2.81 (73 / 26)  


3187 26.45 0.66 0.99  chrX_96859306_96865680.rev     4974  5884 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_96859306_9   4974 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5023
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_96859306_9   5024 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5073
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_96859306_9   5074 TACCAATAACTTTCTTTTCTTCACAGAATTGGAAAAAACT-ACTTTAAAA 5122
                          v   i---  vi     i v  v -     -- v  i  - iii     
  L1M4_orf2#LINE/    101 TCCCAG---CTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAA 144

  chrX_96859306_9   5123 TTCATATGGAACCAAAAAAGAGCCTGCATTGCCAAGAGAATCCTAAGCCA 5172
                                    viiv  ii  v  v v  v     i v    i i ivv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_96859306_9   5173 AAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACA 5222
                         i          i      vv       v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_96859306_9   5223 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 5272
                          i          i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_96859306_9   5273 GATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTAC 5320
                                    i    i--    i  --        vv  ii i  i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chrX_96859306_9   5321 AACTATCCGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGA 5370
                         iiii vii   i  i     ivv  vv  i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_96859306_9   5371 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 5420
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_96859306_9   5421 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 5470
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_96859306_9   5471 TGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGG 5520
                              i ?    i       v   v       i      vi i      i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_96859306_9   5521 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 5569
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_96859306_9   5570 ACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5619
                         iv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_96859306_9   5620 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5669
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_96859306_9   5670 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCT 5719
                             v  i     i                 v   i   vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_96859306_9   5720 GACAAAGGGCTAATATCCACAATCTACAAATAATTTAAACAAATTTACAA 5769
                           i  i  i  vi      v   v  i   v  i ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_96859306_9   5770 GAAAAAATAAAACAACCCCATCAAAAAGTGAGCAAAGGATATGAGCACAC 5819
                         v     ivv   i     v  i?    i  i         v   ii v  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_96859306_9   5820 ACTTCTCAAAAGAAGACATTTATGCAGCCAATAG--ACATGAAAAAATGG 5867
                          i     v        i  vi viii       i--         i   v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_96859306_9   5868 TCACCATCACTGGTCAT 5884
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2635 22.77 9.39 2.82  chrX_96948669_96951369.rev     1363  2214 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_96948669_9   1363 TGGAGAGAG---CCATAATCATGGATTGGAAAATTCAATGCTGTTAACGT 1409
                             i   v---    iv             i i i   ii      vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_96948669_9   1410 GTCAATTATCCCCAAATTAATCTGTAGATTCAACACAATCCTAATCCAAA 1459
                          v    vv          i    ii         i      iv   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_96948669_9   1460 TTCCAGCAGGGCTTTCTTAAGTAGAAATTGAAAAGTTGATTTTTAAATGT 1509
                          i     -v v    i  -- i         v   i    ii v    vi
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_96948669_9   1510 ATATGGAAATGCAAGTGACCTTAGAATTGCCAAAGCAATTTTTAAAAAGA 1559
                                        v    i-     v      i    i  v       
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCC-AGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_96948669_9   1560 AAAACAAAGCTGGAGAAAGTACAGTACCTGATTTCAAGGC--AGTATAAA 1607
                          i       i     i vvi   v v  ii       ii -- v  i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_96948669_9   1608 GCTTTAGTACTTGAG----TGTGGTA-TG----AATGA-AGACATATCAA 1647
                            vi    v ii  ----       -  ----  v  -        vi 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_96948669_9   1648 TCAAGGGAACAAAA--AAGAGTCCAGAAATAT-----TATATCCATAGTC 1690
                             v    i i  --i              v-----  i  ii  i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_96948669_9   1691 AAAATATTTTTCAACAACAATGTCAATGCAATTCAATGACGAGAGAA--- 1737
                           v- iv     i    vii  i   vi v        iv  i    ---
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_96948669_9   1738 -------AATGAATGTTG--------ATTG-------------------- 1752
                         -------  ii    v  -------- i  --------------------
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_96948669_9   1753 -------------TTACCTCATTCTGTATGCAAAAATTCACCCCAAATGG 1789
                         -------------i       iv ii   i        v  i v      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_96948669_9   1790 GTCATAGAT-TAAATATGAAAGATTAAAGCTATAAAACTTTTAGAGTAAG 1838
                         i   ?   i-     i i i  -i    i          i     iv  i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAG-CTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_96948669_9   1839 GTGAAGGAAGAAATCTTTATGACTTTGGGGTTGTCAA-AATTTTTTAGAC 1887
                         iiiv   ?iv       ii    i     v v v   -ii   i     i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_96948669_9   1888 AAATCACAGAAATCAATAAACA-TATAAGAAAAAATGATTAGATTAGAAT 1936
                          viv   vi   v  -i  i  -i v          iiv  i   i  v 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_96948669_9   1937 -CATTGAAATGAAAGACTTCTGCTCTTTAACGGACACTTTTAAGAAAGTA 1985
                         -   ii    v   i    i  iv   i  v       v i        i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_96948669_9   1986 AAAATACAAGCCACAGACTAAGAGGAAATATCCTACAGAGCTTACATCTG 2035
                             v    v       v ii   i      i- i  i v v  i     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATT-TGCAAATCATATATCTG 742

  chrX_96948669_9   2036 ACAAAGGACTTGTATCCAGATTATATAAAGTGCTATTACAATTCAATAAA 2085
                          i  i               v         vi  v      i       v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_96948669_9   2086 AAAAAGACTTCCCCACAAAAAAAAAAAAAAAAATGAAAAATGGAAAGAAT 2135
                                 -------------   v  vvv  v ?        iv i iv
  L1M4_orf2#LINE/    793 AAAAAGAC-------------AAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_96948669_9   2136 ATTTGAACAGAC---TCTTAACAAAAGAATATACAAATGGCCAATAAGCA 2182
                                i    ---   iv v i    -                     
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGA-TATACAAATGGCCAATAAGCA 878

  chrX_96948669_9   2183 CAGGAAGAGATGCTCAAGATATTAGTTATCAG 2214
                           v   i          --i  i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAA--CATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (118 / 73)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 4.00 (104 / 26)  


3092 24.68 1.73 3.46  chrX_96975610_96988099     5572  6495 (5995)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_96975610_9   5572 TGGAAAAACATTGCATG--CATGGATAGGAAGAATCAATATTGTGAAAAT 5619
                               i i  iv    --       v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_96975610_9   5620 GGCCATATTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5669
                            v   i v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_96975610_9   5670 TACCATTGACCTTCTTACCAGAAATGGAAAA---------AAATTTCATA 5710
                          v   vivi    i  vv       v  v  ---------   v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_96975610_9   5711 TGGAAACAAAAAAGAGCCCATATAGCCAAGACTGGAATAAACGAAGACTG 5760
                               iiv  ii  v  viv        i  ---   ------------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAAC---AAT------------ 185

  chrX_96975610_9   5761 GACTTGACTAAGCAAGAATAAGCAAAAAGAACAAAACTGGAGGCATCATG 5810
                         --     ------------  --  i         ii      vv   ii
  L1M4_orf2#LINE/    186 --CTTGA------------AA--AAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_96975610_9   5811 CTACCTGACTTCAAACTATACTATGAGTCTACAGTAACCAAAACAGCATG 5860
                           v  ii i      viv     ii iv         i   i    ii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_96975610_9   5861 GTATTGGTACAAAAACAGATATATAGACCAATGGAACAGAACAGAGGCCT 5910
                            i   i i  ii i   i       i        i    iv   ivii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_96975610_9   5911 CAGAAATAACACCACACATGTAAAACCATCTGATCTTTAACAAGCCTGAC 5960
                                  vv   i    v  viii  vi    i  ii     vv  v 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_96975610_9   5961 AAAAACAAGCAATGGGGAAAGAATTTCCTATTTAATAAATGGTGCTGGGA 6010
                           i v  vv               vvi  v  i  i              
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_96975610_9   6011 CAACTGGCTAGCCACAAGCAGAAAACTGAAACTGGACCCCTTCCTTACAT 6060
                                v  ?     v   i  i v    ii         v   i   i
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_96975610_9   6061 CTTATACAAAAATTAACTCAAGATAGATTAAGGACTTAAATGTAAGACCT 6110
                          v                   i  i   i ?i   i           v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_96975610_9   6111 AAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACA 6159
                              i      vi i           v    ?i- v i -   iv   v
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACC 568

  chrX_96975610_9   6160 TAGGTATGGGCAAAGACTTCATGACTAAAATACCAAAAGCAATGGCAACA 6209
                          v  vv i     v ii   v iiv  vi i          vvi      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_96975610_9   6210 AAAGCCAAAATTGACAAATGGGATCTAATCAAACTGAAGAGCTTCTGCAC 6259
                             vv     v  i    v   ii v      v v  i i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_96975610_9   6260 AGCAAAAGAAACTATCATCAGAGTGAACAGACAACCTTCAGAATGGGAGA 6309
                         vv    i  v       vv i      v        iv            
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_96975610_9   6310 AAAATTTTGCAATCTATCCATCTGTCAAAGGGCTAATATCCAGAATCTAC 6359
                            vv       vii  vi     vi  i  i  vi          v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_96975610_9   6360 AAAGAACTTAAACAGATTTACAAGAAAAAAACAA----CCCTATTAAAAA 6405
                                 ivv   iv iv i  v     i    ----   v   ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_96975610_9   6406 GTGGGCAAAGGATATGATCAGACACTTCTCAAAAGAAGACATTTATGCAG 6455
                         i            v   vi     i     v        i  vi viii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_96975610_9   6456 CCAACAGACGTATAAACAAAAGCTCATCATCACTGGTCAT 6495
                             i ii ii  i  v i v     v     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (126 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 5.33 (48 / 9)  

2973 27.83 1.11 0.67  chrX_96975610_96988099    11096 11997 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_96975610_9  11096 GAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAATGT 11145
                            ii    i     i        v      v i     ii v  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_96975610_9  11146 CCATACTGCCAAAAGTAATTTATAGATTCAATGCCAACCCCATCAAGCTA 11195
                          v     v  v   v i  i  i        i  v v   i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_96975610_9  11196 CCAATGACTTTCTTCACAGAA-TTGAAAAAAACT-ACTTTAAAGTTCATA 11243
                            iivi i  i  ii     -    v  i--  - iii    i      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chrX_96975610_9  11244 TGAAACCAAAAAAGAGCTCGCAAT-GCCAAGATAATCCTAACCAGAAGGA 11292
                           i  viiv  ii  - i iv   -     i i    i i vv ii i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_96975610_9  11293 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 11342
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_96975610_9  11343 ACAGTAACCAAAACAGCATGGTACTGGTTCCAAAACAGATATATAGCCCA 11392
                                i   i    ii         iviv ii i   i      vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_96975610_9  11393 AAAGAACAGAA--GAGAGGCCTCAGAAATAACACCACACATCTACAACCA 11440
                          vi   i    --     v  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_96975610_9  11441 TCTGATCTTTAACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCCC 11490
                         vi    i  ii    ivv  v   i vv vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_96975610_9  11491 CATTTAATAAATGGTGCCGGGAAAACTGGCTAGCCATATGTAGAAAGCCG 11540
                         iv  i  i         i    v      v  ?   i   i i  iivi 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_96975610_9  11541 AAACTGGATCCCTTCCTTACACTTCATACAAAAATTAACTCGAGGTGGAT 11590
                           ii    i    v   i    ivi                i ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_96975610_9  11591 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 11640
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_96975610_9  11641 TAGGCA-ATACCATTCAGGACATAAGCGTGGGCAAGGACTTCATGACTAA 11689
                             ?i- v i -   iv   v vi vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_96975610_9  11690 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 11739
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_96975610_9  11740 TTAAACTAAAGAGCTTCTACATGGCAAAAGAAACTACCATCGGAGTGAAC 11789
                          i   v v  i i   i iiiivv    i  v    i  vvii      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_96975610_9  11790 AGGCAACCTACAGAATGGGAGAAAATTTTCGCAATCTACCCATCTGACAA 11839
                           i     i                 v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_96975610_9  11840 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 11889
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_96975610_9  11890 A---AAAAAACCCA-TCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 11935
                          ---   v      - i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_96975610_9  11936 TCAAAAGGCGACATCTATGCAGCCAACAGACACATGAAAAAATGCTCATC 11985
                           v    iv  i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_96975610_9  11986 ATCACTGGTCAT 11997
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (153 / 94)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.45 (16 / 11)  


1997 26.72 3.24 3.10  chrX_97070237_97074771.rev      886  1626 (2909)    L1M4_orf2#LINE/L1       16   757 (151)  

  chrX_97070237_9    886 TGTTTATGGATCAGAACACTCAATAGGGTTAACGTGTCAGTTTTCCAAAA 935
                             i      ii   v   i    vv     vi  v  i vi   vv  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_97070237_9    936 ATTGATCTGCAGTTTCAATGTAATCTTAATTGAAATCCCAGCAGCCTTTT 985
                                 i   v     i i    iiv  ii          v       
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_97070237_9    986 TTATTAAACCAAAA---GAGAACCTAATTCTAAAATATATGTGGAAAAGC 1032
                           i------  i  ---  v  v  i  i       vi  i      v  
  L1M4_orf2#LINE/    116 TTG------CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_97070237_9   1033 AAATGACCCAAAACAGCCAAACCTATCTTGCAAAAAGGTAAGA-CAAAAT 1081
                           iv      i  i       v v      -      --    -    i 
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTG-AAAAAG--AAGAACAAAGT 206

  chrX_97070237_9   1082 TGGAAGACCGATGCTATCTGATATCAAGGCTTATTATAAATTTACAGCTA 1131
                             i   iv ii  vi ii  v    ii    i  i   vi     iv 
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_97070237_9   1132 TCAAGACAGCGTGGTAGTAGGTTAAATACAGACAGATCAATCAATGGAAG 1181
                                  i      v i vv   iv i     v  vi          v
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_97070237_9   1182 ATAATATAGA--CTATAT-TAGATCCATACTTGTACAGCCTATTGATATT 1228
                          v   vv   -- i v v-  i i      v v  ii i v      v  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_97070237_9   1229 TTACAAAGGCACCAAGACAATTCCATGGATAAAGGAAAGTTGTTTCAACA 1278
                         iv    i  ii       v    v    iv    i v   iv        
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_97070237_9   1279 AATGATGCTGGAATAACTGGA----CACATGTATGAAACAATGACACACA 1324
                             i      i i       ----      i --   v     viivvi
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCA--AAAGAATGAAGTTGG 454

  chrX_97070237_9   1325 GCTCCTACTTCATATCATACATATATATT--CT--AGATGAATCATAGAG 1370
                         i i     i   i i    i i v v   --  -- i   i    ?   v
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_97070237_9   1371 CTAAACATAAAAGTTAAA-TTATAAATCATCTAGGAATAAACATAGGAGA 1419
                              ii   i  i    -i      v vii   i iv         ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_97070237_9   1420 ATCTCTTCACAATGGTGTGGTAGAAAAATATTTTCTT-GACAGTAT-CCA 1467
                          vv     iii ivv  v v   iv  - iv      -  i vv i-   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCA 603

  chrX_97070237_9   1468 GAAATTGTTAACTAAAAAAGAAAAAAAAAAAGGATAAATTGGAATTGGAA 1517
                         i  ii-----  -  iv  v    i      ---  i  --i       v
  L1M4_orf2#LINE/    604 AAAGC-----AC-AAGCAACAAAAGAAAAAA---TAGAT--AAATTGGAC 642

  chrX_97070237_9   1518 TTCAAGAAAATCAGAGTCTTCTTTTCATTAAAAGATAACAATAAAAAA-T 1566
                             vv     i i iv   i v v v i   i  i vi vi  i   - 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_97070237_9   1567 GAATAGTCAAACTACAGATGGGGTGAATATAGTTGTAA--CACATAACTA 1614
                            v  v   v i     vv   v   v   v   i  --  i   v  i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_97070237_9   1615 ATAAAGG---TGTAT 1626
                             i  ---     
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTAT 757

Transitions / transversions = 1.28 (110 / 86)
Gap_init rate = 0.03 (22 / 742), avg. gap size = 2.14 (47 / 22)  

 549 21.33 2.67 0.67  chrX_97070237_97074771.rev     3895  4044 (491)    L1M4_orf2#LINE/L1      756   908 (0)  

  chrX_97070237_9   3895 ATCTAGTATATATAAAAGACACCTTCAACTTATTAA----AACACAGATA 3940
                            i  v         ii  v i v     i v   ----  v   i   
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_97070237_9   3941 AATCAAGCAATAAATGATCAAAATGCTTGAACAGACATTTCACAAAGGAA 3990
                          vi   vi? v     iv    ivii     i         v v  i   
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_97070237_9   3991 GATATACAAATGGTCAATAAGCACAATGAAAAAGTACTCAACGTCATTAG 4040
                                      i           -      ii i      i   ????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACA-TGAAAAGATGCTCAACATCAZZZZ 904

  chrX_97070237_9   4041 GTAA 4044
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.58 (19 / 12)
Gap_init rate = 0.01 (2 / 153), avg. gap size = 2.50 (5 / 2)  


 277 31.89 5.57 6.19  chrX_97104779_97111452.rev        5   327 (6347)    L1M4_orf2#LINE/L1      337   657 (251)  

  chrX_97104779_9      5 ATATATGGCCATTTAACAT--GGCAAGGTTGATATTTTAATCCTTTAAGA 52
                           v     i  v  i iv -- i     v  vi v---i i v  i  vi
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA---GACCATTCAATG 383

  chrX_97104779_9     53 AGGGATGGATTATCT-----ATAAATTTTACTGGCATAACTAGCTATCCA 97
                         i  i v i  vi   ----- i    vv i    v i    i v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_97104779_9     98 TATAAAAGAAAATAAATGTAATCCCCTCACGTAAAGCAAACAAAAACATT 147
                         i  iv  i i   i  vv iiv     vv vi v v  v i v   v   
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_97104779_9    148 AACAAGCTTCAAATGGATTAAAGGCTTGAATGT--GAAC-AAA----TAA 190
                            ---- iv        i ?  i i i     --  i -   ----   
  L1M4_orf2#LINE/    484 AAC----TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_97104779_9    191 AATTTATGTAAGACTATATAGGCGTCTACATATAAAATTGTGCACCAGAG 240
                           i iv iv    vv i     ?  -- v  v ---- i   -   vvi 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGT--AAATCT----TCGTG-ACCTTGG 572

  chrX_97104779_9    241 A--ACATAATCAGCTTCTTA-ACCTAA-ACTGGAAACTCAGGAGTTTTAA 286
                         i-- vii   -i i      - iv i -  iii  i v  --  ivvi  
  L1M4_orf2#LINE/    573 GTTAGGCAAT-GGTTTCTTAGATATGACACCAAAAGCACA--AGCAACAA 619

  chrX_97104779_9    287 AAGAAAATAAAGTAGACATATTAGACCACTTAAAAATTTAA 327
                                --- i    i v   i   iv v v      v  
  L1M4_orf2#LINE/    620 AAGAAAA---AATAGATAAATTGGACTTCATCAAAATTAAA 657

Transitions / transversions = 1.22 (55 / 45)
Gap_init rate = 0.05 (16 / 321), avg. gap size = 2.38 (38 / 16)  

2957 27.45 2.36 0.22  chrX_97104779_97111452.rev     5295  6183 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97104779_9   5295 TGGAAAAACACTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5344
                               i i ii     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97104779_9   5345 GACCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCTCCTCAAGC 5394
                          i v     v      v i  i  i        i  v  i iiv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97104779_9   5395 TACCA-TTGACTGTCTTCCCAGAATTAGAAAAAAATATTTTAAATTTCAT 5443
                          v   -i  v  - i  iv     v v  v  ivvv  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_97104779_9   5444 ATGGAA----------CCAAAAATAGCCAAGACAATCCCAAGCAAAAAGA 5483
                               ----------  v i         i      iii iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_97104779_9   5484 ACAAAGGTGGAGGCATCATGCTACCTGACTTCAAACTATACCTCAAGGCT 5533
                               v      vv   ii  v  ii i      viv   iv   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_97104779_9   5534 ACAGTAACCGAAACAGCACGGTACTGGTACCGAAACTGATATATAGACCA 5583
                                i i i    iii        i iviii iv  i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_97104779_9   5584 ACAGGACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 5633
                          ii i i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_97104779_9   5634 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5683
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_97104779_9   5684 TTTAATAAATGGTATTGGGAAAACTGGCTAGCCACATACTGAAAACTGAA 5733
                           i  i       ii     v      v  ?      i vi  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_97104779_9   5734 ACTGAACTCCTTCCTTTCACATTATACAAAAATTAACTCAAGATTGATTA 5783
                         ii  i  i   v   iv   vv                   i  v   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_97104779_9   5784 AAGACTTAAACATAAGACCTAAAAC-ATAAAAACCCTAGAAGAAAACCTA 5832
                         ?    i    ii     v       -      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_97104779_9   5833 GGCA-ATACCATTCAGGACATAGGCATGGCCAAAGACTTCATAGA----A 5877
                           ?i- v i -   iv   v v  vv i v   v ii   v    ---- 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_97104779_9   5878 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5927
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_97104779_9   5928 AAACTGAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAATGAACAG 5977
                            v v  i i   i  ii vv    i  v       vv i i    v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_97104779_9   5978 GCAACCTTCAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAG 6027
                         i     iv                v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_97104779_9   6028 GACTAATAGCCAGAATCTACAAAAAACTTAAGCAAATTTACAAGAAAAAA 6077
                             vi  v       v  i   i    ivvi   v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_97104779_9   6078 ACAA----CCCCTTCAAAATGTGGACAAAGGATATGAACAGATACTTTTC 6123
                             ----   vv i?   vi   i        v    i   i i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_97104779_9   6124 AAAAGAAGACATTTATGTGGCCAATAAACATATGAAAAAAAGCTCATCAT 6173
                         v        i  vi vi          i  i       i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_97104779_9   6174 CACGGGTCAT 6183
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.38 (139 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.88 (23 / 8)  


3432 24.67 0.88 0.88  chrX_97112664_97116938.rev     2877  3784 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97112664_9   2877 TGAAAATATATTCTATGTTCATGGATTGAAAGAATCTATATTGTTAAAAT 2926
                           i   v    i i              i    v iv          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97112664_9   2927 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATTTCTACCAAAA 2976
                          v v     v      vii              i     ii   i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97112664_9   2977 TAACAA-TGTCTTTCTTCACAGAAATAGAAAAAAACT-ATCCTAGAATTT 3024
                          vv  i-  i    i  -i       v  v  --i  -      i    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA--GCTGATCCTAAAATTC 147

  chrX_97112664_9   3025 AT-TGAAACCACAAAATATCCAGAATAGCCAAAGCTATCCTGACCAAAAA 3073
                           -  i  vii   iiv i              i v   i   vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_97112664_9   3074 GAACAAAACTGGAGGATTCACATTACCTGATTTCAAGTTTTACTATAGAG 3123
                                ii       i     i v  ii       ivi      i i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_97112664_9   3124 CTATAGTCACCAAAATAGCATGGTCCTGGCACAAAAACAGACACATGAAC 3173
                            i   v i   i i  ii    v      i  ii i     i  ii i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_97112664_9   3174 CAACGGAACACAAGAGAGAATCCAGAAATAAATTTACACACCTACAGTGA 3223
                            i    i v  vv    i            iii i   ii  ii  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_97112664_9   3224 ATTCATTTTCAACAGAGATGCCAAGAACATACACTAGGGAAAAGACGGTG 3273
                            v      i   ii i        v   v  v i      ii ii  v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_97112664_9   3274 TTTTCAATAAATTGTGCTGGGA-AACTGGATATCCATATCCAGAAGAATG 3322
                                i    v         -         ?   i  v  i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_97112664_9   3323 AAACTAGACCCCTTATCTCTAAACATCTACAAAAATGAAATTGAAATGGA 3372
                           ii i       - i   vv v   v         v  v ii       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_97112664_9   3373 TTGAAGACTTAAATCTAAGACTTCAAACTATAAAATTACTACAAGAAAAC 3422
                          ii?    i     v     vi v           i vi  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_97112664_9   3423 ATTCGGGAAACTCTATAGGATATTGGTCTGGGCAAAAAATTTCTTGAGTT 3472
                           vv ? v  v   viiv  iv    vi i     -vii      -  v 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTT-AGAT 594

  chrX_97112664_9   3473 AT-ACCCTACAAGCACAGCCAACCAAATCAAAAAGGGACAAATGTGATCA 3521
                           -  v i v       iv    v   vv     vi  i    vv  iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_97112664_9   3522 TATCAA-GTTAAACAGCTTCCACACAGCAAAGGATACAATCAATAAAGTG 3570
                         i     -i     - i   iiiii vv       i  v     v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_97112664_9   3571 AAGAGACAAGCCACAGAATGGCAGAAAGTATTTTCAAGCTATTCATCTGA 3620
                           i      v           v     i     v   iii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_97112664_9   3621 CAAGGGATTCATAATCAGAATATATAAGAAGCTCAAACAACTCCATAGGA 3670
                         i      i ii  vi            ii i   vv       v   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_97112664_9   3671 AAAAATCTAACAATCTGATTTTAAAATGGGCAAAAGATTTGAACAGACAT 3720
                             iv v  i  i ii   ?v            i        i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_97112664_9   3721 TTCTCAAAACAAAA-ACACAAAATGGCAAACAGGCATATCAAAAGGTGCT 3769
                              v   v  i - i     -    v  i i   i  v     i    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_97112664_9   3770 -AGCATCATTGATCAT 3784
                         - i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (138 / 82)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.07 (16 / 15)  


1724 25.81 11.28 2.16  chrX_97138712_97140350.rev      502  1148 (491)    L1M4_orf2#LINE/L1      203   908 (0)  

  chrX_97138712_9    502 AAGCTGGAGGCATCATGCTGCCCAACTTCAAAATATACTACAGGGCTACA 551
                            i      vv   ii  v     i       iv       ii      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_97138712_9    552 GTAACCAAAACAGCATGGTACTGATACAAAAACAGACACACAGACAAATA 601
                             i   i    ii        ii i  ii i     i --------  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA--------TA 294

  chrX_97138712_9    602 GACAAATAGAACAGAATAGAGAACCCCAAAAACAGACCACATAC--CTAC 649
                           iv   i   i     v    ii  - i   i i   -     --i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC-AGAAATAAACC-CATACATTTAT 342

  chrX_97138712_9    650 AACTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATAGGGAAAGGA 699
                         iiii vi    i  i     ivv  v   i v  vv    i       i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_97138712_9    700 TCCCTTATTCAATAAATAATGCTGGGATAACTGGCTAGTCATATGCAGAA 749
                          vvii v     i    ii        i      v  ?i  i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_97138712_9    750 AATTGTAACTGGACCCCTTTCTTATACCATATGCAAA------------- 786
                         i v  v ii         vi  i i       i    -------------
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_97138712_9    787 -------------------------------CTATAAAAACCCTGGAAGA 805
                         -------------------------------        vi i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_97138712_9    806 CAACCTAGGCA-ATACCATTCAGTACATAGGCATGGACAAAGATTTCAT- 853
                         v   v    ?i- v i -   ivv  v v  vv i i   v i    v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_97138712_9    854 GATAAAGACTCCAAAAGCAATTGCAGCAAAAGCAAAAATTGACAAATGAG 903
                             v-   v         vvv   i      v      v  i    vi 
  L1M4_orf2#LINE/    592 GATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_97138712_9    904 ACC------AAATTAAAGAGCTTCTGCACAGAAAAAGAAACTAGCAA--- 944
                           i------        i -   i  ii vvv   i  v    v   ---
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_97138712_9    945 ----------CAACCTACAGAATGGGAGAAAATTTTTGCAAACTATGCAT 984
                         ----------     i                 v        ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_97138712_9    985 CTGACAAAGGTCTAATATTCAGCATTTATAAGGAACTTAAACAAATTGAC 1034
                             i  i  v  vi   i   v  v     i     ivv    v ii i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_97138712_9   1035 AAGAAAAAAA------ACCCCACAAAAAAGTGGGCAAAGGACATGAACAT 1078
                           v     i ------    v iv?    i           iv    i v
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_97138712_9   1079 ACATTTTTTCAAAAGAAGACATACATGCGGCCAAAAAACATATGAAGAAT 1128
                               i i    -     i     vii      v  i  i     i iv
  L1M4_orf2#LINE/    840 ACATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_97138712_9   1129 AGTTCAACATCACTGATCAT 1148
                         v i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (102 / 62)
Gap_init rate = 0.02 (14 / 706), avg. gap size = 6.21 (87 / 14)  


1535 19.09 3.13 3.42  chrX_97183692_97190679     1938  2288 (4700)  C L1M4_orf2#LINE/L1   (558)   350     1  

C chrX_97183692_9   2288 TGAGAGGACATCTCCTGTTTATGGATTGCAGAACATAATATTGTTAAGAT 2239
                           ii i  i   i v    i        v ii  v               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_97183692_9   2238 GGAAATAATCCCAATATTGACCTATGGGTTCGATGCAATCCACATCAACA 2189
                           v    v    v v     i   ii i   i i       vi     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_97183692_9   2188 TTCCAGCTGACTTTTTTTTTTTTTTTTTGCAGAAATT---AAGCTGATCC 2142
                          i       v       -----------         ---          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-----------GCAGAAATTGACAAGCTGATCC 139

C chrX_97183692_9   2141 AAAAATTCATAGGGAAATGCAAAGAACCCAGAATAGTCAAAACAATCTTG 2092
                         v          v          i i           i             
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

C chrX_97183692_9   2091 T----GAAAAATCAAAGC----AGACTCACCGTTTGTGATTTCAAAAGTT 2050
                         v----   i  -     i----i       vv  ivii         v  
  L1M4_orf2#LINE/    190 AAAAAGAAGAA-CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

C chrX_97183692_9   2049 AATATAATGAAACAGTAATCAAGATTGTATGGTTTGGGCATAAGAGTAGA 2000
                          v  i  v vv             iv  i    viv        ii    
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

C chrX_97183692_9   1999 CATAAAGATCAATAGAATAAAATTGAGCATTCTAAAATAAACCGATATAT 1950
                             v        i     i       vi i vi         v   i  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

C chrX_97183692_9   1949 TTATGTTTAATT 1938
                              v i    
  L1M4_orf2#LINE/    339 TTATGGTCAATT 350

Transitions / transversions = 1.31 (38 / 29)
Gap_init rate = 0.01 (5 / 350), avg. gap size = 4.60 (23 / 5)  

2009 18.67 1.33 1.11  chrX_97183692_97190679     2647  3096 (3892)    L1M4_orf2#LINE/L1      352   802 (106)  

  chrX_97183692_9   2647 ATTTTCAACAAGGTTGCCAAAAA-ATTTAATGGGGTAAAGAATAGCCTTT 2695
                               i      v      i v-   i       -         i    
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTT 400

  chrX_97183692_9   2696 TCAACAAATGGTACTGGGACATCTGGATATTCACTTTTAAAATA-TGAAA 2744
                                     i        v       ?i   v vi    v -    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_97183692_9   2745 CTGGATTCCTATTTCACACCATATACAAAACTTAATTCAAAATAGATTAA 2794
                         i    ii    ii                 v    i       i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_97183692_9   2795 AAACCTAAATAAAAGAAGTGAAACAATAAGACTCTTAGAAGAAAACACAG 2844
                          i        iv    iv i    v    i                 i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_97183692_9   2845 CAGTAAAATCTTTGTGACCTTGGATTAGGCAATGGGATCTTAAATAT-AT 2893
                         v?     -    i          i           vv     i    - i
  L1M4_orf2#LINE/    551 GNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_97183692_9   2894 ATGTATAACACAAGCCTCAAAAGGGGTAAAAATAGATAAATGGGAATATA 2943
                          ivv v i       vv      i---              v   v vi 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGA---AAAAATAGATAAATTGGACTTCA 646

  chrX_97183692_9   2944 TCAAA-TTAAAATTGTTTGTGCTCCAAAGAATACTATCATGAAAGTTAAA 2992
                              -      viv        i     i i       v      v   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_97183692_9   2993 GGACAACTCACAGAACGAGAGAAAATATTTTTAACTCATATATCTGAAAA 3042
                         i      i       i i            vi  v            v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_97183692_9   3043 GCATATAGGACCCAGAATATATAAAGAATT-TAACA-TTAGACTATAAAA 3090
                          vivv v v i                 i - v   -i vi iv      
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_97183692_9   3091 AGACAA 3096
                               
  L1M4_orf2#LINE/    797 AGACAA 802

Transitions / transversions = 1.25 (45 / 36)
Gap_init rate = 0.02 (9 / 451), avg. gap size = 1.22 (11 / 9)  

3264 26.05 0.77 0.55  chrX_97183692_97190679     3858  4763 (2225)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_97183692_9   4763 TGGAAAAACATTCCATGCTCATGGAGAGGAAGAATCAATATTGTGAAAAT 4714
                               i i  i     i       vv      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_97183692_9   4713 GGCCATACTGCCCAAAGTAATTTATGGATCCAATGCCATCCCCATCAAGC 4664
                            v     v      v i  i  ii   i   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_97183692_9   4663 TACCA-TTGACTTTCTTGACAGAATTTAAAAAAAACT-ATTTTAAATTTC 4616
                          v   -i  v    i   -     v  i v  i--  -  ii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAG--CTGATCCTAAAATTC 147

C chrX_97183692_9   4615 ATATGGAACCACAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAG 4566
                                 vii   ii  v  viv        i      i i iv  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chrX_97183692_9   4565 GAACAAAGCTGGAGGCATAGTGCTACCTGACTTCAAACTATACTACAAGG 4516
                                 i      vv viii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chrX_97183692_9   4515 CTACAATAAGCAAAACAGAATGGTACTGGTACCAAAACAGTTATATAGAC 4466
                              i   v   i    vi         i iv ii i  vi       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chrX_97183692_9   4465 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCATACATCTACAACCA 4416
                                 i    iv   ivii         vv        i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

C chrX_97183692_9   4415 TCTGATCTTTGACAAGCCTGACAAAAACAAGCAATGGGGAAAGGATTTCC 4366
                         vi    i  i      vv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chrX_97183692_9   4365 TATTTAATAAATGGTTTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 4316
                          v  i  i       vi     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chrX_97183692_9   4315 AAACTGGACTCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGG-T 4267
                           ii     i   v   i     v                   i    - 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

C chrX_97183692_9   4266 TAAAGACTTAAATGTAAGACTTAAAACCATAAAAACCCTAGAAGAAAACC 4217
                         i ?    i           vi      i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

C chrX_97183692_9   4216 TAGGCA-ATACCATTTAGGACATAGGCATGGGCAAAGACTTCATAACAAA 4168
                             ?i- v i -  iiv   v v  vv i     v ii   v  ivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_97183692_9   4167 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACATATGGGATCTAA 4118
                         i            vvi          vv     v  i v  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_97183692_9   4117 TTAAACTAAAGAGCTTCCGCACAGCAAAAGAAACTATCATCAGAGTGAAC 4068
                          i   v v  i i   ii ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_97183692_9   4067 AGGCAACCTACAGAATGGGAGAAAAATCTTTGCAATCTATCCATCTGACA 4018
                           i     i                - v       vii  vi      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATA 745

C chrX_97183692_9   4017 AAGGGCTAATATCCAGAATCTACAAGGAATTTAAACAAATGTACAAGAAA 3968
                          i  i  vi          v  i  i   i ivv    v vv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chrX_97183692_9   3967 AA---AAACAACTACATCAAAAAGTGGGCAAAGAATATGAACAGACACTT 3921
                           ---   i   ivv  i?    i         i  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chrX_97183692_9   3920 CTCAAAAGAAGACATTTATGTGGCCATCAAACATATGAAAAAAAGCTCAT 3871
                            v        i  vi vi      vi  i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chrX_97183692_9   3870 CATCACTGGTCAT 3858
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (133 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  

 408 17.12 3.60 2.70  chrX_97183692_97190679     6390  6500 (488)    L1M4_orf2#LINE/L1      797   908 (0)  

  chrX_97183692_9   6390 AGACAACCAACCTTTTAATT-AAAAGTTGGCAAAGAATTTCAATTGACAT 6438
                               vi    i---    -    i v       i    v   v     
  L1M4_orf2#LINE/    797 AGACAAATAACCC---AATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_97183692_9   6439 TTCTTTAACAAA---ATAGAAATGACCAATAAGAACATGAAAACATGCTC 6485
                             ii  vi  ---   v     i        v         v      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_97183692_9   6486 AATCCCAAGAGTTAT 6500
                           ivi  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.03 (3 / 112), avg. gap size = 2.33 (7 / 3)  


2483 25.55 7.20 1.74  chrX_97292203_97295569     2014  2874 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97292203_9   2014 TGGAAAAACATTCCATGCTCATGGATAAGAAGAATCAATATTGCTAAAAT 2063
                               i i  i     i        vi     v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97292203_9   2064 GGCCATACTGCCCAAAGCAATTTATAGATTCAATGGTATTCCTATCAAAC 2113
                            v     v      vii  i  i        i vv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97292203_9   2114 TACCTGCAACATTTTTCACAGAACTAGAAAAAA-AATTCTAAAATTCACT 2162
                          v  v  vi v     ii     v v  v  iv-i  i          iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_97292203_9   2163 TGGAACCAAAAAAGAACCCAAAGAGCCAAAGCAATCCTAAGTGAAAAGAA 2212
                              viiv  ii  v  vi  v       i     i i ivi i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_97292203_9   2213 CAAATATGGAGGCCTCACACTAGCTGACTTAAAACTTTACTACAAGGTTA 2262
                             vv      v        vv ii i  v   vi         i i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_97292203_9   2263 CAGTAATTAAAACAGCATGGTATTGGTACAAA-ACAGACCCATAGACCAA 2311
                                i  i    ii     i   i i  i- i    vi     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_97292203_9   2312 TGAAACAGAATAGAGAACACAGAAATAAAGCCACACACCTACAACCATTT 2361
                           i  i     v    iiv          v   i   ii  iiii  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_97292203_9   2362 GATCTTCAACAAAG------------TT---------AACAATAA----- 2385
                            i   i    i ------------  ---------  v    i-----
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_97292203_9   2386 -----AAATGATGCTAGTATAACTGGCAAGTCATATGCAGAAGATCGAAA 2430
                         -----     i    i v i      vv ?i  i     i    vi   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_97292203_9   2431 CTGGACTCTTACCTTTCACCACATACAAAAATGAACTCAAGATGGATTAA 2480
                         i     i i     iv     i          v       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_97292203_9   2481 AGACTTAAATTCAATACCTGAAACTATAAAAACTATAAAAACCCTAGAAG 2530
                             i     vi  v v  i           -  -------- i      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA-CT--------CTTAGAAG 541

  chrX_97292203_9   2531 AAAACTTATG---AAATGCCACTT--TAACATCAGCCCTGGCAAAGACTT 2575
                              v  v ---    ----   -- i  v ii viiv     v ii  
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_97292203_9   2576 CAT-GATGAAGACACCAAAAGCAATTACAACAAAAACAAAAATCAACATA 2624
                          v -   - v             vvvi        iv      vi i v 
  L1M4_orf2#LINE/    588 CTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_97292203_9   2625 TAGGATCTAATTAAA-CTAAATACTTTTCTCACAACAAAAGAAACTTACA 2673
                          v   ii v  i   -i    v      v -i vv    i  v   vv  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGT-GCTTCAAAGGACACTATCA 685

  chrX_97292203_9   2674 ACAGACTAATCAGACAACCTATAGAATGGTAGAAAATATTCACAAACTAT 2723
                          v i v i vv        i i       v          ii    ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_97292203_9   2724 GTATCTGACAAAGGTCT---------AATA--------ACCC----AAAT 2752
                         i       i  i  v  ---------    --------  i ----  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_97292203_9   2753 CTATAATAAATATA-AAACAACCCCATTAAAAAGTGGGCAAAGAACATGA 2801
                          v        v v -   i     v   ?    i         i iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_97292203_9   2802 GCAGGCACTTTTCAAAAGAAGACACATATGCAGCCAACAATCATATGAAG 2851
                         ii  i  i  i  v        i i i viii     i  v  i     i
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_97292203_9   2852 AAAAGCTTGACATCATTGATCAT 2874
                          i v   ii      ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (133 / 84)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.28 (77 / 18)  


2913 28.25 1.22 0.22  chrX_97296255_97302940.rev     5297  6195 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97296255_9   5297 TGGAAAAACGTTCCATGCTCATGGATAGGAAGAATCAATAACATGAAAAT 5346
                               i ii i     i        v      v i    vii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97296255_9   5347 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5396
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97296255_9   5397 TACCATTGAGTTTCTTCACAGAATTAGAAAAAACT-ACTTTACATTTCAT 5445
                          v   vivivi  i  ii     v v  v  i-  - iii  v v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_97296255_9   5446 ATGGAACCAAAAACGAGCCCATATAGACAAAACAACCCTAAGCAAAAAGG 5495
                               viiv  iv  v  viv    v        i i i iv  i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_97296255_9   5496 ACAAAGCTGGAGACATCACACTGCCTGACTTCCAACTATACTACAAGTCT 5545
                               i     ivv       v  ii i   v  viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_97296255_9   5546 ACGGTAACCAAACCAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5595
                           i    i   iv   ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_97296255_9   5596 ATGGAACAGAACAGAGGCCTCAAAAATAATGCCACACATCTACAACCATC 5645
                               i    iv   ivii  i      vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_97296255_9   5646 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5695
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_97296255_9   5696 TTTAATAAATGGTTTTGGGAAAACTGGCTAGCCATATGAAGAAAACCAAA 5745
                           i  i       vi     v      v  ?   i   v i  i vii  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_97296255_9   5746 ACTGGACCCCTTCATTACACCTTATACAAACATTAACTCAAGATGGATTA 5795
                         ii         v v i     v        v          i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_97296255_9   5796 AAGACTTAGGTCTTATGTTTAAAACCATAAAAATCCTAGAAGAAAACCTA 5845
                         ?    i  ii v v vivi      i      v  i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_97296255_9   5846 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 5894
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_97296255_9   5895 CACAAAAAGCAATGGCAACAAAAGCCACAATACACAAATGGGATCTAATG 5944
                            v       vvi          vv v    v i    v   ii v  v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_97296255_9   5945 AAACTAAAGAGCTTCTGTACAGCAAAAGAAACTATCAGG---GTGAACAG 5991
                            v v  i i   i   i vv    i  v       i ---     v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_97296255_9   5992 ACAACCTACAGATTGGGAGAAAAATTTTGCAATCTATCCATCTGACAGAA 6041
                               i     v          vv       vii  vi      i iii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_97296255_9   6042 GGCTTATATCCAGAATCTATGAGAAACTTAAACAAATTTACAAGAAAAA- 6090
                          i   i          v   i ii    ivv    v iv i  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_97296255_9   6091 --AAACAACCCCATCAAAAAGTGGGCAAAGGATGTGAACAGACAGTTATC 6138
                         --   i     v  i?    i            v    i     v  v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_97296255_9   6139 AAAAGATGGCATTTATGTGGCCAACAAACATATGAAAAAAAGCTCA---T 6185
                         v     v ii  vi vi       i  i  i       i v     --- 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_97296255_9   6186 CACTGGTCAT 6195
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.25 (139 / 111)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2952 22.74 4.03 5.22  chrX_97316064_97320064     2590  3508 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97316064_9   2590 TGGAAAGATATCCCATTTTTATGAATTTTAAAAAACTTA-TATTGTTAAA 2638
                                         v  i   i   --ii  i     -         i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT--GGAAGACTTAATATTGTTAAG 48

  chrX_97316064_9   2639 ATGGCCATATTACC-AAAGAGAGCTACAGTTTTAGTGCAATCCCTATGAA 2687
                              v   i v  -   vv  v      v  i ii           v  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_97316064_9   2688 AATTCCAG-TGTCACTTCTTGTAGATATAGAAAAAGCAATCCTAAAGTTG 2736
                            i    -  i -i  i   i   v  v  v  ivii        i  v
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_97316064_9   2737 ATATTGAACCACAAAATACACAAATAAAGCTGGGGGTATCACACTATCTG 2786
                             v   vii   iiv  v  i - v   ii-------- v  v    -
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGA-ATAGCCA--------AAACAATCT- 187

  chrX_97316064_9   2787 ACTTCAAAATACACTACAAA-TTATCACGTGTACTC-CATAAATATTTGC 2834
                         --- v    viv vv     -  i---- v v    -  i-----  iv 
  L1M4_orf2#LINE/    188 ---TGAAAAAGAAGAACAAAGTTG----GAGGACTCACAC-----TTCCC 225

  chrX_97316064_9   2835 AATTATTATGTATACATAAATATAAGAATATATAATACAAAACTATACTG 2884
                             ------------------ v i  iv  i--      i   i v i
  L1M4_orf2#LINE/    226 AATT------------------TCAAAACTTAC--TACAAAGCTACAGTA 255

  chrX_97316064_9   2885 ACCAAAAGAGCATGGTGTGGGCATAAAAAAAGACACAAAGACTAAGGGAA 2934
                          i   i v  ii    iiv       ii v     i v   ii  v    
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_97316064_9   2935 CAGAATAGAGAGCCCAGAAATAAATTCACACATATACAGCCAACTGATTT 2984
                         i     v     i           ii  i    v  ii i   i      
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_97316064_9   2985 TTG-----------------------TGGAAAAAG-----TCTATTTAAT 3006
                          i -----------------------   ii    -----   v  i  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_97316064_9   3007 AAGTGGTTCTGGGAAAATTAAATATCCACACACAGAAGAATGAGACTAGA 3056
                           i    v      v  i ii   ?     ii  i        iii i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_97316064_9   3057 CACCTACCTCTCAGTATATACAAAAATCAACTCAACATAGATTAAAGACT 3106
                          v        v  vi            i       v  i   i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_97316064_9   3107 TAAATGTAAAACCTGAAACTATGAAACTACTAGAAGAAAA-ATAGGA-TA 3154
                                  i v  i       i     vi          -     ?-  
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_97316064_9   3155 AATACTTCATGATATTGGGCTGGGCAAGGATTTTTTAAATAAGACCTCAA 3204
                            -    i   iv     i i     v i   i   i   v   vi   
  L1M4_orf2#LINE/    556 AAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_97316064_9   3205 AAGCACAGGCAAAAAAAGCAAAAACAAACAAATGCTG--TTATATCGAAC 3252
                                i    v     v     i i i    --  --i vi   i  v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAAT--TGGACTTCATCAAAA 652

  chrX_97316064_9   3253 TAAAAAGCTTTTGCACAGTGAAAGAAACTATTAACAAGGTGAAAAGACAA 3302
                          v    i      ii vvii  i  v     i  v  i            
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_97316064_9   3303 CCTACACAATGGAAGAAAATATTTCCAAACTATACATCTGACAAAAGATT 3352
                           i   v     i           v    ii   i      i  ii  i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_97316064_9   3353 ACTATTCAGAATATATAAGGAACTTATACAATTCAACAGCAAGAAAACAA 3402
                         vv   i            i     iv     i    i ii  i  i    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_97316064_9   3403 ATAACCTAATTTAAAAATGGACAAAAGACCTTAATAGACATTTCTCAAAA 3452
                               i    ?        i    i  ii v              v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_97316064_9   3453 GAAGACATACAAATAGTCAACAGATATGTGAAAAAATGCTCAATATCACC 3502
                              i        i i   i iii ii      i        i    ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_97316064_9   3503 AATCAT 3508
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 2.06 (138 / 67)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.05 (85 / 21)  


3028 26.13 2.82 0.56  chrX_97327556_97332935     4000  4887 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97327556_9   4000 TGGAATGACATTCCATGCTCATGGACTGGGAAATATATTATTATTAAAAT 4049
                              v  i  i     i       i   i i iv  v    i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97327556_9   4050 GGTCATACTGCCCAAAGCAATCTACAGATTCAATGCAATCTCTATCAAAA 4099
                           iv     v      vii              i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97327556_9   4100 TATCAA-TGTCATTTCTCACA-AAATAAAAAAAAAAATCCTTAAATTTGT 4147
                          vi  i-  i -   i ii  -    vi v  ivvi     v     ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_97327556_9   4148 AAGGAACAGAGAAAGAGCTCA-AATAGCCAAAGCAATCTTGAACAAACAT 4196
                          v    - viv  i ii i  -          i          v  iv v
  L1M4_orf2#LINE/    150 ATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_97327556_9   4197 TGCAAAGCTGGAAACATCACATTAGTTGACTTCAAAATATATTACAAGGC 4246
                         vi     i    iivv     i vviii i       iv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_97327556_9   4247 TATAGTAAACAAAACAGCATGGTATGGGTAAATAAAAATAGATACATAGA 4296
                           i     v   i    ii     iv  i --   ii     i i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATAGA 296

  chrX_97327556_9   4297 CCAACGGAACAGAATAGAGAACCCAGGAATAAATCTATGTATTTAGAGTC 4346
                         i   i    i     v    ii    i      i i  ii     vi   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_97327556_9   4347 AACGGATATTTAACAAAGGTGGCAAAAACATACCATAGAAAAATGTCACC 4396
                           iv   v  ii    i    v   i v   v v  i ii   vivi vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_97327556_9   4397 CTCTTCAATAAATTGTACTGGGACAATTGGTTGTCCACATGCAGAATAAT 4446
                           i     i    v  i         i   v i?         i  v   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_97327556_9   4447 GAAACTTCACACCTATCTCTCATCGTATA-AAAAAC-AACACACAATAGA 4494
                            ii vv  v    i   v  i i    -     i-   v  v   i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_97327556_9   4495 TTAAAGACTTAAAGGTAAGACCCCAAATTATAAAACTACTGGAACAAAAC 4544
                          i ?    i    v      v iv   i         vi i   v     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_97327556_9   4545 A---GGGAAAATACTTCAGGACATTGATCTAGGCAAAGATTTGATGGCTA 4591
                          --- ? v    -    iv   v   ivi       v i   vv i v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_97327556_9   4592 AGACCTCAAAAGCACAGACAATAACA------ATAGACAAATGGGACTAT 4635
                         v   vi          ii   i  v ------     i    v     vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_97327556_9   4636 ATTAAACTAAAAAGCTTCTGCACAACAAAGGCAACAAGAAACAGAGTAAA 4685
                           i   v v    i   i  ii vv      vv  v vv  v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_97327556_9   4686 GAGACAACCTATTGAATGGGAGAAAACATTTGCAAACTGTACATTCAACA 4735
                         i        i iv             i         iii  i  iii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_97327556_9   4736 AGGGGCTAATATCCAGAATAGACAGGGAACTC----AAC--AGTA-TAAA 4778
                             i  vi           v i ii      ----   -- i  -    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_97327556_9   4779 AAAA-AAAT--CCCAAT-AAAAACTAAGCAAAGTACTTGAACAGACATTT 4824
                           i -    --      -?    v ii      v i     i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_97327556_9   4825 CTCTAAAGAAGACATACGGATGACCAAGAGGTATATGAAAAAATACTCTA 4874
                            i        i    ii   i    v i i i       i  i   v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_97327556_9   4875 CTTCACTTATCAT 4887
                          v   ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (146 / 82)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.76 (30 / 17)  


3165 27.28 0.44 0.55  chrX_97360987_97367255     4868  5776 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97360987_9   4868 TGGAAGAACATTCCACACTCATGCGTAGGAAGAATCAATATCGTGAAAAT 4917
                              ii i  i   iii     vi v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97360987_9   4918 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATTCCCATCAAGC 4967
                            v     v     iv i  i           i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97360987_9   4968 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5015
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_97360987_9   5016 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5065
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_97360987_9   5066 AAGAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5115
                           v    i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_97360987_9   5116 TACAGTAACCAAAACAGCATGGTACTGTTACCGAAACAGAGATATAGATC 5165
                                 i   i    ii        vi iviii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_97360987_9   5166 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5213
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_97360987_9   5214 ATCTGATCTTTGACAAACCTGACAAAAACAAGCATCGGGGAAAGGATTCC 5263
                          vi    i  i     ivv  v   i v  vv  vi        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_97360987_9   5264 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5313
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_97360987_9   5314 CAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGACGGA 5363
                         v  ii    i    v   i     v           i  i    i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_97360987_9   5364 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5413
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_97360987_9   5414 CTAGGCGTTACCATTCAAGACATAGGCATGGGCAAGGACTTCATGTCTAA 5463
                         v    ?  v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_97360987_9   5464 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGACCTAA 5513
                         i            vvi          vv     v  i    v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_97360987_9   5514 TTAAACTAAAGAGCCTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5563
                          i   v v  i i i i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_97360987_9   5564 AGACCACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCTATCTGACA 5613
                             v   i   i             v  i    vii - v       i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGATA 745

  chrX_97360987_9   5614 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5663
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_97360987_9   5664 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5713
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_97360987_9   5714 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5763
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_97360987_9   5764 CATCACTGGCCAT 5776
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2791 26.84 3.51 0.91  chrX_97382485_97385591     1732  2614 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_97382485_9   1732 GAAAAACATTCCATCCTGATTGATTGGAAAAATCAATGTCATTAAAATGG 1781
                             i i  i    vi v  v        i v i   i ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_97382485_9   1782 CCATACTGCCAAAAGCTATTTACAGAATTGATGGTATTCCAATTAAACTA 1831
                          v     v  v   viv  i      v ii i vv  i  v  i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_97382485_9   1832 CCAA-TGTCATTCTT-CAAATAATTAGAAACGACT-ACTGTAAAATTCAT 1878
                            i-  i v  i  -  i -    iiv  --i  - iiv          
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGA-AATTGACAA--GCTGATCCTAAAATTCAT 149

  chrX_97382485_9   1879 ATAGAACCAAAAAAGAGCCTGAATAGCCAAAGCAATCCTAAGCAAAAAGA 1928
                           i   viiv  ii  v  v           i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_97382485_9   1929 ACAAAGCTGGAGGCATCATACTACCCAACTTCAAACTATAGTGTAAGACT 1978
                               i      vv   i   v     i      viv  v ii  ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_97382485_9   1979 AGAGTAATCAAAACAGCATGGTACTAGTACAAAAACAGATACATAGACCA 2028
                          v         i    ii       i i i  ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_97382485_9   2029 ATGGAACAGGATAGAAAATCCAATAATAAAGCTTCACATCTACAGCCATT 2078
                               i  i  v  i i    iv      v ivi    i  ii i  v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_97382485_9   2079 TGATCTTCGACAAGGCAGACAAAAGCA----ATGGCAAAAGGACGCCCTG 2124
                             i          vv v   i v  ----    vi    i iivi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_97382485_9   2125 TTCCATATATGGTGCTGTGATAACTGGCTAGCCACATGCAGAAGAAAGAA 2174
                            v i v         v  i      v  ?         i     v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_97382485_9   2175 ATTGGACCACTCCTTTTCACCATATACAAAAATTAACTGTAGATGAATTA 2224
                         i       v  v i iv                     vv i   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_97382485_9   2225 TGAATTTAAATGTAAGGCCTCATACTCTAAAAATCCTAGAAGAAAACCTA 2274
                         ?ii ii          iv  v v   v     v  i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_97382485_9   2275 AG---AAATACCCTGTCTACATCAACCTGGGCAAAAAAATTTTGGCTA-- 2319
                         i ---    - iii  v-  v iiivi i     viivv i  i v  --
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_97382485_9   2320 --------AGTACCATTGCAACAAAATAAAAAATG------TGGGAATTA 2355
                         --------  i  v --         v       i------ v   v  v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_97382485_9   2356 ATTAAG-TTAAATAACTTTTGCACAGCAAAAGTAACTATCAACAGAGTGA 2404
                           i  i-     -        ii vv    i vv        v i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_97382485_9   2405 CCAGACAATCCATAGAATGGGAGAAAATATTCACAAACTATGCATCTCAC 2454
                         vv      i   i                  ii    ii  ii    v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_97382485_9   2455 AAAGGTCTAATATCCAGAATCTATAAGGAAATT----AAATTAACAAACA 2500
                           i  v  vi          v     i   v i----  v i  i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_97382485_9   2501 AAAAACAAACAACTCCATTAAAATGTCGGCAAAGGACATGAACAGACACT 2550
                            i     i   i v   ?   vi v         iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_97382485_9   2551 TCTCAAAAGAAGACATACAAGCAGCTGACAATCATTTGAAAAAATGCTCA 2600
                             v        i      iii  ii i  v  iv      i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_97382485_9   2601 ACATTACTAATTAT 2614
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 2.60 (39 / 15)  


2868 24.60 5.10 2.15  chrX_97400580_97405187.rev     3236  4117 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97400580_9   3236 TGAAAAGACATTCCATGTTAATGGATTGGAAAAATCGGCATGGTTAAAAT 3285
                           i     i  i       v           i v iiii  v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97400580_9   3286 GAAGATACTGCCCAAAGTAATCAACAGATTTAGTGCAGTCCCTACGAAAA 3335
                          ivi     v      v i   v       i ii   i      iv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97400580_9   3336 TACCAA-TGTCTTTCTTCACAGAATTAGAAAAATCAATCCTAAATATTAT 3384
                          v   i-  i    i  -i     v v  v  iiii        vv i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_97400580_9   3385 ATGAAA----------CCTAAGAAGAGC-ACAGCAATCCTGAGCAAAAGG 3423
                            i  ----------  i -   v   - v i     i   iv  i i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_97400580_9   3424 AACAAAGTTGGAGGCATCACACTACCTGACTTCAAAATATATTACAAGGC 3473
                                       vv       v  ii i       iv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_97400580_9   3474 TATAGAAACAAAAACAGCATGAAACTGTTATAA----AAACACA--GACC 3517
                           i  v  iv  i    ii  iv    vi    ---- i   i --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_97400580_9   3518 AATATAGAGAGAATAGAGAACCCGGAAATAAATCGATATATTTATAGCCA 3567
                            iv - v     v    ii  i        i v   i      i i  
  L1M4_orf2#LINE/    299 AATGGA-ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_97400580_9   3568 ACTGATTTTTGACAGAGATGGCAAGAATATATATTGGGGAAAGGACATGT 3617
                          i       i    ii i  v     vi  vi v         i i vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_97400580_9   3618 TCTTCAATAAATGGTGCTGGAAAAATTGGATATCTATATGCAGAAGAATG 3667
                          i     i            i v  i      ? i i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_97400580_9   3668 AAACTGGATTCCTGTCTCCCACTGTATACAAAAATCAACACACAATGGAT 3717
                           ii    ii   ii   v   ii           i   v  v       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_97400580_9   3718 GAAAGACTTAAACCTATGACCTGAAACTATTAATCTACTAGAAGAAAACA 3767
                         v ?    i    iv  v  v  i       v  v  vi            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_97400580_9   3768 TAGAGAAAACACTTCAGGACATTGGTCTGGGCAA---------AGA---- 3804
                            i?iv  vv    iv   v    vi i     ---------   ----
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_97400580_9   3805 -CCTCAAAAGCACAGACAACAAAAATAAAAATA----AATTGAACTATAT 3849
                         - vi          ii        iv       ----     i   vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_97400580_9   3850 -GAAACTAAAAACTTCTGCACAGCAAAG--CA--AACAACAGAGTGAAGA 3894
                         -i   i         i  ii vv     --  -- v   v i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_97400580_9   3895 GACAACCTGTTGTATGGAAGAAAGTATTTGCAATCTATTCTTCTGACAAG 3944
                                iiiv v    i     i         vii  viv     i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_97400580_9   3945 TGACCAATATCCAGAATATACAGGGAACTAAAACACTTCAACAGTAAAAT 3994
                         v   ivi             i ii     vvv   vi    i i     v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_97400580_9   3995 AATAA-TAATCATCATCCTTTCATTAAAATGTGGGAAAAGGCATC--AGT 4041
                         i i  -   i --  -------   ?   vi    v     -  i-- i 
  L1M4_orf2#LINE/    798 GACAAATAACC--CA-------ATTWAAAAATGGGCAAAGG-ATTTGAAT 837

  chrX_97400580_9   4042 CAACATTTCTCAAAAAAAAAAAAAGACATACAAATGGCCAACAGATATAT 4091
                         vi         v   i  ------  i              i iii i  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAA------GATATACAAATGGCCAATAAGCACAT 881

  chrX_97400580_9   4092 GAAGAAATGCTCAA-ATCATTCATCAT 4117
                            i i        -    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (138 / 75)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.05 (64 / 21)  


3306 26.87 0.44 0.44  chrX_97485721_97492000.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97485721_9   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4931
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97485721_9   4932 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97485721_9   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_97485721_9   5030 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_97485721_9   5080 AACAAAGATGGAGGCCTCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                v      v        v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_97485721_9   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_97485721_9   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5227
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_97485721_9   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_97485721_9   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_97485721_9   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_97485721_9   5378 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_97485721_9   5428 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_97485721_9   5478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5527
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_97485721_9   5528 TTAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_97485721_9   5578 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5627
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_97485721_9   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_97485721_9   5678 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_97485721_9   5728 TCAAAAGAAGACATTTATGCAGCCAACAGACCCATGAAAAAATGCTCATC 5777
                           v        i  vi viii     i ii v        i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_97485721_9   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2922 28.40 0.66 0.33  chrX_97502426_97506698     2876  3780 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97502426_9   2876 TGGAAATACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2925
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97502426_9   2926 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTTCCATCAAAA 2975
                          i v     v  v   vii       i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97502426_9   2976 TACCACCATTATTCTTCACAGAACTAGAAAAAAAAATCCTAAAATTCATA 3025
                          v   v vviv  i  ii     v v  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_97502426_9   3026 CAGAATCAAAAAGAGCCCA-CATAGCCAAAGCAAGACTAAGCAAAAAGAA 3074
                         ii   viiv  i ii    -v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_97502426_9   3075 CACATCTGGAGGCATCACA-TTCCTTACTTCAAACTATACTGTAAGGCCA 3123
                           v vi      vv     -    iv i      viv    ii  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_97502426_9   3124 TAGTCACCAAAACAGCATGGTACTGGTATATAAATAGGCATGTAGACAAA 3173
                         i   v i   i    ii         i   vii    i   i    iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_97502426_9   3174 TGGAACTGAATATAGAACCAAGAAATAAAGTCAAATACTTACAGCAAACT 3223
                              iv    vv   ii v         vi  v i i   ii iv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_97502426_9   3224 GATTTTTGACAAAGCAATAAAAAATATAAAGTAGGAAAAAGACACTCTAT 3273
                               i     i vviiv  i vi  vv i i  i   ii i v   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_97502426_9   3274 TTAACTAATGGTGATAGAATAATTGGCAACCCACATGTAGAAGAATAAAA 3323
                          i   v       v i i i  i   vv ?       i i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_97502426_9   3324 CTAGGTCCTCATCTCTTACCTGATACAAAAATCAACTCAAGATGGATCAA 3373
                         i i ii  ii i   vi   vv          i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_97502426_9   3374 AGACTTAAACATGAGACCTGAAACCATAAAAATTCTAGAAGATATCATTG 3423
                             i    ii i   v  i    i      v ii       v v   v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_97502426_9   3424 GCAAAAAACTCTTCTAGACATTAGCTTAGACA--GAGTTCGTGACCAAGA 3471
                          ?iv   --     vv   v  i v    i  -- iv   v iivi v  
  L1M4_orf2#LINE/    551 GNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_97502426_9   3472 ACCCAAAAGCAAATGTGACAAAAACAAAGATAAATAGATGGGACCTAATT 3521
                         vv         v v ii      iv   i   i   i  v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_97502426_9   3522 AAACTAAAAAGCTTCTGCATGGCAAAAGAAATAATCAGTGGAGTAACCAG 3571
                            v v    i   i  iiivv    i  v iv    ivii   i vv  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_97502426_9   3572 ACAACCCACAGAGTGGGAGAAAATATTCACAAACAATGCATCTGACAAAG 3621
                                     i              ii    iv  ii      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_97502426_9   3622 GACTAATATCCAGAATCCACAAGGAACTCAAACAAATCAGCAAGAATAAA 3671
                             vi          vi i  i      vv    v   ii  v  -   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AAA 797

  chrX_97502426_9   3672 AATAATTAATTCCATCAAAAAGTGGGTAAAGGACATGAATAGACAGTTCT 3721
                         i i  v   ii v  i?    i    i      iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_97502426_9   3722 CAAAAGAATATGTGCAAATGGCCAACAA--ACATGAAACAATTCTCAATA 3769
                          v      v  i i           i  --        vi  v     i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_97502426_9   3770 TCACTAATTAT 3780
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (151 / 102)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


4064 18.92 5.16 1.03  chrX_97520673_97522832.rev      798  1669 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97520673_9    798 TAAAAAGACATCCCCCACTTATGGATTAGATAAGTTAAGACTGTTAAGAA 847
                          ii     i     viii i       i  vi v    v i        v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97520673_9    848 ACTAATAGTCTCCAAATTAATCTGCAGATTCAATACAATCTCTATCAAAA 897
                         ivi    v  i       i    i         ii     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97520673_9    898 TTTCAGCTGCTTTCTTTGCAGAAACTGATAAAGTTATTTTAAAATTTATA 947
                          ii       i  i          i   i  iv v  ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_97520673_9    948 TGGAATGGAAAAGGACACAGAAGACCAAAAACAATCTTG----------- 986
                              vv v  i    v     v v v            -----------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_97520673_9    987 --------GAGAACTCATATGTCTTGATTTCAAAGCATACTACAAGGTTA 1028
                         --------   i     i iv  iii        i v        i i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_97520673_9   1029 TAGTAATCAAGACTGTGTGGGATCGGCATAAGGATAGACATGTAAATCAA 1078
                         i            v      v ii                 i  i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_97520673_9   1079 TGGAATAGAATTAGAAGTCCAGATATAAACCCCAATATTTAGGACTAATT 1128
                                     iii        v        vv i     v iii    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_97520673_9   1129 GATTTTCAACAAAAGTGTCAACACAATTTAATGGAAAAAGAATAGTATTT 1178
                                i    ii   i   v  v   i     ii          v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_97520673_9   1179 TCAACAAATGATGC-AGAACAACTGCATATCCATGTGCCAAAGTATTAAG 1227
                                   i   -i i       v   ?   ii   v    v  v   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_97520673_9   1228 GTGGACCCCTATTTCATACTTTATA-AAGAATTAATTCAAAGTGGATCAA 1276
                         v          ii   i  iv    -  i      i     i       ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_97520673_9   1277 AGACATTAGTGTGAGAGCTAAATCCATAAAATTCTTAGAAGAAAACATAC 1326
                             v v i   i         v i      i                 v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_97520673_9   1327 CTATGAATATTTATGACCTTGGATAAGGCAGTAATTTCTTA----TGACA 1372
                         v?i i   v  ii         i v     i ii       ----     
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_97520673_9   1373 CCAAAAGCACAAGCATCAAAGGAGAAAAATAGACAAATTGAACTTCATCA 1422
                                        v    i  -         i      i         
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCA 649

  chrX_97520673_9   1423 AAAAATGTTTTAGAACTTTTCTGC-------------ATCAAATAAGTGA 1459
                            -----  v i       v   -------------     iv      
  L1M4_orf2#LINE/    650 AAA-----TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_97520673_9   1460 GAGGACAATTCCTCA-AAAATGGGAGAAAATATTCACAAATCAAATACCT 1508
                         i i     --- i  - i                ii       v   i  
  L1M4_orf2#LINE/    695 AAAGACAA---CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_97520673_9   1509 GATAAGGTAATTGTATCCAGAATATAAAAA-----TTTGCAGCTCAATAA 1553
                                v v                v   -----i  i  i        
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_97520673_9   1554 CATAAAGCCAACTATGGCAGTTTTAAAATGGG-AAAGGAGCTGAATAGAC 1602
                         i v    v   v  vvv  i  ?v        -      vi         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_97520673_9   1603 ATTTCTCTAAATAAGATACACAAATGATCAGTAAGCACATGAAAAGATGC 1652
                                i   v      i       ii  i                   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_97520673_9   1653 TCAACATCATTAGTCAT 1669
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (104 / 57)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 4.91 (54 / 11)  


2712 28.29 2.23 1.11  chrX_97595998_97600719     3332  4229 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97595998_9   3332 TGGAAATACATTCCATGTTCATAGATTTGCAAAATCAATGTTGTTAAAAT 3381
                               v i  i          i    v v i v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97595998_9   3382 GTCCATTCTACCCAAAGCAATCTACAGATTCAATGCAGTCCCTATCAGAG 3431
                          v v  v  v      vii              i   i         i i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97595998_9   3432 TACAAACAGTATTCTTCACAGAATTAGAAAAAAACAATCCTAGAATTTAT 3481
                          v v i v iv  i  ii     v v  v  iv-ii      i    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_97595998_9   3482 ATGGAA-CACTGAAGACCCAGAATAGCCAAAGCTATCCCAAGCAAAAAGA 3530
                               -ii viii                 i v   iii iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_97595998_9   3531 AAAAAAATAGAGGAATTGCATGAGCTGACTTCAAATTATACTACAGAGAT 3580
                          v   iv i     v ii  ivvv ii i      viv       i  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_97595998_9   3581 ATAGTAA-AAAAACAAAAAACAAGGTACTGACATAAAAACAGATACATTC 3629
                          i     -v  i   i----iiv       i     ii i   i i  vv
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAG----TGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_97595998_9   3630 ATCAATGGAACAGAATAGAGAACTCAGAAACGAATCCACACACCTGCAGC 3679
                                   i     v    iii      ii  i   i   ii iii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_97595998_9   3680 AAACTCATGGTCCACAAATTTGCCAAGAACATACTCTTGGGAAAAGACAG 3729
                         v  i v  vv  v    ivv        v   v vv v      ii i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_97595998_9   3730 TATCTTCAAAGAGTGGTGGTGGGAAAACTAGGTATCCACATGCAGAAGAA 3779
                          v i     vi i     v     v    i i  ?         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_97595998_9   3780 TGATACTAGACCATTATCTCTTGCCTTGGGCAAAG-TCAAACCAAA-TAG 3827
                            vii i    vi  i   vii  v ivi    i- i  vi    - i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_97595998_9   3828 GTTAGATACTTAAATCTAAGACCTCAAATCATGAAACT-----------A 3866
                         i i ? v  i     v     v  v   ii  i     ----------- 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_97595998_9   3867 CAT-TGAGAAAACTCTCAAGACATTGATCTGGGCAAAAATTTCTTGAGCA 3915
                            -v ? v   iii  iv   v   ivi i     vii      -  vv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGAT 594

  chrX_97595998_9   3916 ATACCTCCACAAACACAGGAAACTAAAGCAAAAATGGACAAAT-GGATCA 3964
                           iv v   v  i    i v   v    v      i  i    -   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_97595998_9   3965 CGTCAAG-TTACGAAGCTTCTGCACAGCAAAGGATACAATCAACAAAGTG 4013
                          i    i-   -i  i   i  ii vv       i  v     v      
  L1M4_orf2#LINE/    645 CATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_97595998_9   4014 AAGAGACAACTCACAGAATGGGAGAAAATATTTGCAAACTACCCCTGTGT 4063
                           i       i                           ii iviv v  v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_97595998_9   4064 CAAGTGATTAATAACCATAATATATAAGGAACTTAAACTACTATATGGGA 4113
                         i   v  i vi  v   v         i     ivv  v   vv  iiv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_97595998_9   4114 AAAAAATCTCAAA--ATCTGATCAAAAGATGGGCAAAATGTTTGAATAGA 4161
                             i ---    -- i ii  i?   i         ivi          
  L1M4_orf2#LINE/    794 AAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_97595998_9   4162 CATTTCTCAAAAGAAGACGTACAAATGGCAACCATGTATATGGTAAGGTG 4211
                                 v        ii          v vi v i i   iv   i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_97595998_9   4212 CTCAACATCATTGATCAT 4229
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (151 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


3165 26.36 0.56 0.56  chrX_97621485_97627260.rev     4387  5285 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_97621485_9   4387 ATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAATGGCCATACT 4436
                           i     i        v      v i     ii v  i     v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_97621485_9   4437 GCCCAAGGTAATTTATAGTTTCAACGCCATCCCCATCAAGCTACCAA-TG 4485
                         v     iv i  i  i  v        v     i     iv v   i-  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_97621485_9   4486 CCTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCATATGGAACC 4534
                              i  -i     v v  v  i-  - iii    i           vi
  L1M4_orf2#LINE/    110 CCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAAT 157

  chrX_97621485_9   4535 AAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCT 4584
                         iv  ii  v  v v  v     iv     i i ivv i          i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_97621485_9   4585 GGAGGCATCACGCTACCTGACTTCAAACTATACTACGAGGCTACAGTAAC 4634
                              vv    i  v  ii i      viv      i i          i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_97621485_9   4635 CAAAACAGCATGGTACTAGTACCAAAACAGAGATATAGATCAATGGAACA 4684
                            i    ii       i i iv ii i   v                i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_97621485_9   4685 GAAC--AGAGCCCTCAGAAATAACGCCGCCTATCTACAACCATCTGATCT 4732
                            i--    i  --        vv  iivi  i  iiii  vi    i 
  L1M4_orf2#LINE/    308 GAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_97621485_9   4733 TTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAAC 4782
                          i     ivv  v   i v  vvv           i  vvi  v  i   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_97621485_9   4783 AAATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGA 4832
                              i        v      v  ?   i   i i  iiv    ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_97621485_9   4833 TCACTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACT 4882
                         i v  v   i     v              i    i      i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_97621485_9   4883 TACATGTTAGACCTAAAACCATAAAAACCATAGAAGATAACCTAGGCA-A 4931
                           v    v   v       i      vi v       v   v    ?i- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_97621485_9   4932 TACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAA 4981
                         v i -   iv   v v  vv i     v ii   v ivv  vi       
  L1M4_orf2#LINE/    556 AATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_97621485_9   4982 AAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTA 5031
                           i  vvi          vv     v  i    v   ii v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_97621485_9   5032 AAGAGCTTCTGCACAGCAAATGAAACTACCATCAGAGTGAACAGGCAACC 5081
                           i i   i  ii vv    v  v    i  vv i      v  i     
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_97621485_9   5082 TACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAA 5131
                         i   i             v  i    vii ivi      i  i  i  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_97621485_9   5132 TATCCAGAATCTACCAATAACTCAAACAAATTTACAAGAAAAAAACAAAC 5181
                                   v  iv  v     vv    v iv i  v     i     i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_97621485_9   5182 AACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGA 5231
                              v  i?    i            v    i     i     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_97621485_9   5232 AGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGG 5281
                            i  vi viii     v  i          i       v     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_97621485_9   5282 CCAT 5285
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.28 (131 / 102)
Gap_init rate = 0.01 (8 / 899), avg. gap size = 1.25 (10 / 8)  


 382 31.96 7.65 6.86  chrX_97627633_97630496.rev      972  1481 (1383)    L1M4_orf2#LINE/L1       31   544 (364)  

  chrX_97627633_9    972 AGAATCAATATTTTTGAG-T--CAATTCTCCCCAAGTTAATCTATGGATT 1018
                            v i      v  i  - --    v        i  i     ii    
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chrX_97627633_9   1019 TAATGCAAAAATTGAATCAACATCTTAAT-------------GAGATTTA 1055
                         i  i    vvvi --     v   ii ii-------------  i   v 
  L1M4_orf2#LINE/     81 CAACGCAATCCCT--ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chrX_97627633_9   1056 ---GGTGATTCTAAAGTTCATCTAGATGAT-CAAATG---CATACTAACT 1098
                         --- v    i     i     v i  -i  -   iv ---  v v  i i
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGA-AATGCAAGGGACCCAGAATAGCC 177

  chrX_97627633_9   1099 GTGA-AAT-TTGTAAAAAAAAAAAAAAATTATTACAGAGG---CACTCTT 1143
                         ivi -   -   v    i  i  v   i  i-----    ---   v   
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTG-----GAGGACTCACACTT 222

  chrX_97627633_9   1144 CTGCCAGTTTTCAAATCCATTCTAAAATTTTAGTGATTAAAATAATGTAA 1193
                          --   i   iv   iii i vi   ii vi   i  i  i i i   ii
  L1M4_orf2#LINE/    223 C--CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_97627633_9   1194 TATCAGTTCAAATCAAGACATGTATTTCTAAAGAAAACAATATATACTCC 1243
                           iii ivi  ivvv      i  vv  v vi   v v   vv v v   
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_97627633_9   1244 AGA--CAGGCCCATGTGTATATATGCATGTCTCTGTGTTTGTATTCTTAT 1291
                            --i ii     ii--  v    ---   -----iv   -   i ii-
  L1M4_orf2#LINE/    321 AGAAATAAACCCATAC--ATTTATG---GTC-----AATTG-ATTTTCG- 358

  chrX_97627633_9   1292 ACAAGA----TAAGGCAACATTTAAAATCACTGTTGAAAACATAGACAAT 1337
                              i----i   i --    i  ------  vv    iv    v vv 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGAC--CATTCAA------TGGGGAAAGAATAGTCTTT 400

  chrX_97627633_9   1338 TGAGTAAAGTGTGTTGACAAAATTAGAAATTTATTTATAAACCAGTAAAT 1387
                          v ii   vv   i  iv v  i i  v ?ii iv ii   vv i i  -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA- 449

  chrX_97627633_9   1388 GCGCATCACATCCCCACACCACATCATATATCAAAGTAAAATCTAGATGA 1437
                         ----i iiv i   i  vi    i      iv   i v  v  v i   i
  L1M4_orf2#LINE/    450 ----GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_97627633_9   1438 ATTGGTGATTAAAAAATTAAAAATAAAA---TAAAACTC--AGGAGGAA 1481
                           ii?v  iiv   vi v i iv     ---        --  i  i  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

Transitions / transversions = 1.60 (99 / 62)
Gap_init rate = 0.05 (25 / 514), avg. gap size = 2.96 (74 / 25)  

 237 27.79 5.16 7.74  chrX_97627633_97630496.rev     2025  2373 (491)    L1M4_orf2#LINE/L1      569   908 (0)  

  chrX_97627633_9   2025 TTGGGACAGGAAAGACCTTACTAAGAAA-GAAACAAAATCCAGAAGCCAT 2073
                              vi   v  vivi  -  v   v -  v  v   vv  v    v i
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTT-CTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_97627633_9   2074 ATAGGAAAAGATTAACAGATATAATTACATAAGAAGATAAAATATCTGTA 2123
                          v i     i  vi i i  vvi i v   v i  vvv    iv i   i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_97627633_9   2124 TTACAAAAGACACCATGAAAGAAATGCAAAATAATAGACACAAGAGAGAC 2173
                         i v    i     i  v  ii  i  ---------------  i   ---
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTG---------------AAAAGA--- 699

  chrX_97627633_9   2174 CAACCCAGGGGTCTGAGAGATATCATTTACAAA----------AGTAAAG 2213
                                vi i-v  i    v vi    i    ----------ii   i 
  L1M4_orf2#LINE/    700 CAACCCACAGA-ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_97627633_9   2214 TATTAGAATTCAAAATGTATAAAGAACT-TCACA-TTCATATTTTAAAAA 2261
                         v i v v  i  i   i           - i   -i   -  vv      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA-ATAATAAAAA 797

  chrX_97627633_9   2262 T-CAAATA-CCCAATT-AGAAATGTGACCAAAAGTATATATACTGACAAT 2308
                         v-      -       - i     - i v  iii v iv   --    v 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATG-GGCAAAGGATTTGAATA--GACATT 844

  chrX_97627633_9   2309 GC-ACAGAGTAGAAATGGCAAA-ATTCAATAACTAATTGAAAAAATTTAT 2356
                         v -v  i  v   v  i-    -ivi      vi vv      i  --ii
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATA-CAAATGGCCAATAAGCACATGAAAAGAT--GC 891

  chrX_97627633_9   2357 TCAACCTCACCAGTTGT 2373
                              v   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.06 (50 / 47)
Gap_init rate = 0.05 (18 / 340), avg. gap size = 2.50 (45 / 18)  


3035 27.16 1.33 0.67  chrX_97674676_97680371.rev     4304  5205 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97674676_9   4304 TGGAAAAACATTCCATACTCATGGATAGAAAGAATCAATATCACTAAAAC 4353
                               i i  i    ii        v i    v i     iii   i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97674676_9   4354 GGCCATACTGCCCAAAGCAATTTATACATTCAATGCTATTTCCATTAAAC 4403
                            v     v      vii  i  i v      i  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97674676_9   4404 TGTCATTGACATTCTTCACAGAACTAGGAAAAACT-ATTTCAAAATTCAT 4452
                          vi  vivi v  i  ii     v -v  v  i  -  iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_97674676_9   4453 ATGGAACCAAAAGAGAGCCCAAATAGCCAAGGCAATCCTAAGCAAGAAGA 4502
                               viiv   i  v  vi         ii     i i iv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_97674676_9   4503 ACAAAGCTGGAGACATCATGTTACCCAACTTTAAAACTATACTACAGGGC 4552
                               i     ivv   iii v     i  i      -       ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_97674676_9   4553 TACAGTAACCAAAAAACCATGGCACTGGTACAAAAACTGACACATAAACC 4602
                                 i   i v vii   i     i i  ii iv    i   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_97674676_9   4603 AATGGAACAGAATAAAAAACCCAGAAATAAAACTCCACACCTACAACTAT 4652
                                i     vi i ii           v ivi   ii  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_97674676_9   4653 CTGATTTTTTACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT--TCT 4700
                         i       iv    ivv  v   i v  vv            i  --   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_97674676_9   4701 CTAATCAATAAATGGTACTGGGATAACTGGCTAGCCATATACAGAAAATT 4750
                         i --    i       i      i      v  ?   i  i  i  i v 
  L1M4_orf2#LINE/    399 TT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_97674676_9   4751 GAAACTGGACCCCTTCCTTACAACATATACAAAAATTAATTCAAGATGGA 4800
                            ii         v   i   v                i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_97674676_9   4801 TTAAAGACTTAAATGTAAAACTCAAAACTATAAAAACCCTGGAAGACAAC 4850
                          i ?    i         i vii            vi i i     v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_97674676_9   4851 CTAGGCA-ATACCATTTAGGACATAGGCATGGGCAAATATTTCAT-GATG 4898
                         v    ?i- v i -  iiv   v v  vv i     vvi    v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chrX_97674676_9   4899 AAAATGTCAAAAGCAATTGCAACAAAAGAAAAAATTGACAAATGGCACCT 4948
                          vi iii        vvv                 v  i    v v  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_97674676_9   4949 AATTAAACTAAAGAGCTTCTACAAAGCAAAGGAGACTATCAACAGAGTAA 4998
                         v  i   v v  i i   i iiivvv       v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_97674676_9   4999 ACAGACAACCTACAGAATGCAAGAAAATTTTTGCAAACTATGCATGTGAC 5048
                          v        i        vi       v        ii  ii  v   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_97674676_9   5049 AAAGGTCTAACAGCCAGCCTCTGTAAGGAACTTGAACA---CATTTACAA 5095
                           i  v  vii v    vv v i   i     ivv   ---  v v i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_97674676_9   5096 GA-GAAAAACAACTCCATAAAAAAGTGGGCAAAGGACCTGAATAGACACT 5144
                         i -  v   i   i v  v?    i           ii          i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_97674676_9   5145 TTTC---AAAAGACATACATATGGCCAACAATCATATGGAAAAAAGCTTA 5191
                          i  --- i    i     v        i  v  i   i   i v   i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_97674676_9   5192 ACATCACTGATCAT 5205
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (152 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


3367 19.02 2.74 0.72  chrX_97700306_97703072      875  1568 (1199)    L1M4_orf2#LINE/L1        1   708 (200)  

  chrX_97700306_9    875 TGGAGAGACATTCTATATTCGTGGATTTGAAGATTTAATACTACTCAGAT 924
                             i   i  i i  i   i      v     i      i ii v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97700306_9    925 GACTATACTGCC-AAAGCAATCCACAAATTCAGTGCAATCCC-AGTAAAA 972
                          i v     v  -   vii   i   i     ii        - vi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97700306_9    973 TCCCAATTGCATTTTTTTTACAGAAATGAGAAAACCCATTCTAAAATTCA 1022
                              ii   --i      i       viiv  i iv  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_97700306_9   1023 TATGGAATTTGAAGAGACCCACCATAGTCAAAA-AATATTGGAAAAGAA- 1070
                                v vv   i      vv    i     -   v   i       -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_97700306_9   1071 --CAAAATTGGAGGACCCACACTTCCTGATTTCAAAACTTATTACAAAGC 1118
                         --    i         i         ii             i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_97700306_9   1119 TACAGTAATCAAAGTAGTGTCATACTGGCTTAAAAGTGTACATATATACC 1168
                                     iii     vi       v   iii iv       v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_97700306_9   1169 AATAGAATAGAATTGACAGTCCAGAAATAAACCCATATATCTATGGTCAA 1218
                            i            v                    i  i         
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_97700306_9   1219 TGTAATTTTT-ACAAGGAAGCCAAGACTATTCAATGAGGGAAAGAACAGT 1267
                          - i     i-      iv        i        -         i   
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGT 396

  chrX_97700306_9   1268 CTATTTAACAAATGGTGCTAGGGGAACTGAATATACACATGTAGAAGAAT 1317
                           v  i             i  iv     i   ?v      i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_97700306_9   1318 GAAGTTGGACCCTTACCTTACATCATACACAAAAATTAACT-AAAATG-- 1364
                                     i     i   i    i             -      --
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_97700306_9   1365 TCA--------ATTG-AAGAGCAAAAACTGTAAAGCTCTTAGAAGAAAAC 1405
                            -------- v  -      v      i    i               
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_97700306_9   1406 ACAGGGGAAAATATGTAGGCTCTTGGATTTGATAATGGCTTCTTAAATAC 1455
                          i   ? v    v viiv vi     i  v ii     i      i   i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_97700306_9   1456 AACACCAGAAATGCAGGCTAAAAAATTAAAAATGGACACATTTGACTTCA 1505
                         i      i  iii  i  v v    vv      i  i v   v       
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_97700306_9   1506 TCAAAATTAAAAACTTTTGTACCTGAAAGGACACTATCAAGAGACTGAAC 1555
                                             i i v                 i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_97700306_9   1556 AGCACTGTTCACA 1568
                           -  viii    
  L1M4_orf2#LINE/    697 AG-ACAACCCACA 708

Transitions / transversions = 2.10 (88 / 42)
Gap_init rate = 0.02 (13 / 708), avg. gap size = 1.85 (24 / 13)  

1209 13.90 0.90 0.45  chrX_97700306_97703072     2052  2274 (493)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_97700306_9   2052 AAGAGCGTGAACAG-CAACTTAGAGGATGGGAGAAAATACTAACAAATTA 2100
                             iv     v  -    ii v  i             i vi     i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_97700306_9   2101 TATATCTGA-GAGGGACTTAATATACACAATATATAAGAAACTCCTACAT 2149
                                  -i        -i   v  v         ii     i    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTT-GTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_97700306_9   2150 CTCAACAACAAAAAGACAAAAAACCCAATTAAGAAATGGGCAAAGGGCTT 2199
                              i  i           v         ? i             ii  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_97700306_9   2200 GAATAGACATTTCTCCAAAGAAGATACACAAATGGTCAATAGGCACATGA 2249
                                                   i        i     i        
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_97700306_9   2250 AAAAATGCTCAATATCATTAGTCGT 2274
                            i        i    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.75 (22 / 8)
Gap_init rate = 0.01 (3 / 224), avg. gap size = 1.00 (3 / 3)  


2546 23.29 4.12 5.74  chrX_97744809_97746757.rev      536  1458 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97744809_9    536 TGAAAAAAAATTCCATGTTCATGGATAGGAAGAAACAATATTGTTAAAAT 585
                           i   i v  i              v      vvi           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97744809_9    586 GGACTTACATCCCAAA-------GCAGATTCCATGCTATTTCTACCAAAT 628
                           vvv   vi      -------i       v i  v  ii   i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97744809_9    629 TACAAATGACATTCTTCACAGAACTAGAAAAAACT-ATTATAAAATTCAT 677
                          v v iivi v  i  ii     v v  v  i-  -  iv          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_97744809_9    678 ATTGAACCAAACAAAG--CCCA-AATAGCCAAGGCAATCCTAAGCAAAAA 724
                           v   -- vi   i --    -         ii     i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_97744809_9    725 GAACAAAGTTAGAAGCATCACATTACCCAATTTCAAACTATACTACAATG 774
                                   i  i vv     i v            viv        v 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_97744809_9    775 CTATATTAAGCAAAACAGCATGGTGCTGGTACAGAAACAGACACA--GAC 822
                            i v   v   i    ii    i    i i iii i     i --  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_97744809_9    823 GAGTGGAACAGAATAGAGAGCCTAGAAATGAAACCACACACCTACAA-CA 871
                         v i     i     v     i i      i  v   i   ii  iii-  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_97744809_9    872 ATCTCATCTTCAACAAAGTCAACAAG------CAATGGGAAAA------- 908
                           - v  i   i    i viiv    ------       i   -------
  L1M4_orf2#LINE/    348 AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_97744809_9    909 CTATTCAATAAATGATGCTGCAATAACTGGCTAGCCATATGCAGAAGAGA 958
                           v     i     i     vi i      v  ?   i     i    iv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_97744809_9    959 GAATCTGGACTCCTTCCTTACACCGTATATAAAAATCAACTCAAAATGTA 1008
                            vi     i   v   i     i    i      i           v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_97744809_9   1009 TTAAAGACTTAAATGTAA-ACCTATA--TATAAAACTTATAAAATGATAC 1055
                          i ?    i         - v   v --         iv  i  ------
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA------ 540

  chrX_97744809_9   1056 AGAATACTTATAAAACTATACATAAAACTATACAACCCTGGAAAATAACC 1105
                         -   v  --   ii?------i    v  viiii   i   i-------i
  L1M4_orf2#LINE/    541 -GAAAAC--ATAGGN------GTAAATCTTCGTGACCTTGGG-------T 574

  chrX_97744809_9   1106 TAGGAAATATCATTCTGGACATAGGACCTGGAAAATATTTCATGTTGAAG 1155
                             v   ivi-    -----   ----------    ----------- 
  L1M4_orf2#LINE/    575 TAGGCAATGGT-TTCT-----TAG----------ATAT-----------G 597

  chrX_97744809_9   1156 ATGCCAAAAGCAATTGCAACCAAAAAAAAGTTA-ACAAATGGGACCTAAT 1204
                          ii         vvv     v   i    iv  - i    v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_97744809_9   1205 TAAACTAAAGAGCTGCTGCACAGCAAAAGAAGCTATCAACAGAGTGAACA 1254
                         i   v v  i i  vi  ii vv    i  vi       v i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_97744809_9   1255 AACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCCAACAAA 1304
                         i      i                          ii  ii   ii i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_97744809_9   1305 GGTCTAATATCCAGCATCTATAAGGAACT--TA-AACTAACCAGCAAAAA 1351
                           v  vi       v  v     i     --  -    v vi ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_97744809_9   1352 -ACAAACAACCTCAT--AAAAATGGGCAAAGGACATGAACAGATATTTAT 1398
                         -     i    iv  --                iv    i   i    v 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_97744809_9   1399 CAAAAGAAGACATAAAGGTAGCCAACAAGCATACAAAAAAA-GCTCAATA 1447
                          v        i   v ii i     i     i ii    i -      i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_97744809_9   1448 TCAATAATCAT 1458
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.75 (135 / 77)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.37 (91 / 27)  


3004 28.45 0.55 0.44  chrX_97748890_97761211.rev     5275  6181 (6141)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97748890_9   5275 TGGAAAAACATTCCATGCCCATGAAGAGGGAGAATCAATATCATGAAAAG 5324
                               i i  i     ii    i vv  i   v i     ii v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97748890_9   5325 GGCCATACTGCCCAAAGTAATTTATAGATTTAATGCTATCCCCATTAAGC 5374
                            v     v      v i  i  i     i  i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97748890_9   5375 TGTCATTGACTTTCTTCACAGAATTGAAAAAACTA--CTTGAAATTTCAT 5422
                          vi  vivi i  i  ii     v vi v  i  i-- i i     -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT-CAT 149

  chrX_97748890_9   5423 ATGGAACCGAAAAAGAGCCCAGA-TAGCCAAGACAACCCTAAACAAAAAG 5471
                               vi v  ii  -      -       i    i i i  v  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_97748890_9   5472 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTGTACAACAAGGC 5521
                                i      vv   ii  v  ii i      viv   v    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_97748890_9   5522 TGCAGTAACCAAAACAGCATGGTACTGGTACAAAACCAGATATATGGACC 5571
                          i      i   i    ii         i i  iivi   i    i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_97748890_9   5572 AATGGTACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCAT 5621
                              v i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_97748890_9   5622 CTGATCTTTGACAAACCTGATGAAAACAAGCAATGGGGAAAGGATTCCCT 5671
                         i    i  i     ivv  vii i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_97748890_9   5672 ATTTAATAAATTGTGTTTGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5721
                         v  i  i    v   i v   v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_97748890_9   5722 AACTGGACCCCTTCCTTATACCTTATACAAAAAATTAACTCAAGATGGAC 5771
                          ii         v   i i   v          -         i     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGAT 497

  chrX_97748890_9   5772 TAAAGACTTACACATAAGACCTAAAACCATAAAAACCCTAGAAGGAAACC 5821
                         i ?    i  v ii     v       i      vi i      i    v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_97748890_9   5822 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5870
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_97748890_9   5871 AACAGCAAAAGCAATGGAAACAAAAGCCAAAATTGACAAATGAGATCTAA 5920
                         i   v        vvi v        vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_97748890_9   5921 TTAAACTAAAGAGTCTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 5970
                          i   v v  i iii i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_97748890_9   5971 AGGCAGCCTACAGAATGGGAGAAAAATTTTGCAATCTATCCATCTGACAA 6020
                           i  i  i                vv       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_97748890_9   6021 AGGGCTAATATCCAGAATCTACGAGGAACTAAAACAAATTTACAAGAAAG 6070
                         i  i  vi          v  ii i     vvv    v iv i  v   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_97748890_9   6071 AAACAAACAACCCCATCAAAAAATGGGTGAAGGATA-GAACAGAGACTTC 6119
                          i     i     v  i?         ii      v-   i   v i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_97748890_9   6120 TCAAAAGAAGACATTTATGCAGCCAACAAGCATATGAAAAAAAGCTCATC 6169
                           v        i  vi viii     i     i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_97748890_9   6170 ATCACTGGTCAT 6181
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (155 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  

3305 26.76 0.44 0.44  chrX_97748890_97761211.rev    10924 11831 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97748890_9  10924 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 10973
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97748890_9  10974 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 11023
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97748890_9  11024 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 11071
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_97748890_9  11072 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 11121
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_97748890_9  11122 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 11171
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_97748890_9  11172 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 11221
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_97748890_9  11222 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 11269
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_97748890_9  11270 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 11319
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_97748890_9  11320 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 11369
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_97748890_9  11370 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 11419
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_97748890_9  11420 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 11469
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_97748890_9  11470 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 11519
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_97748890_9  11520 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 11569
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_97748890_9  11570 TTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTACCATCAGAGTGAAC 11619
                          i   v v  i i   i  ii vv    iv v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_97748890_9  11620 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 11669
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_97748890_9  11670 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 11719
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_97748890_9  11720 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 11769
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_97748890_9  11770 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 11819
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_97748890_9  11820 ATCACTGGCCAT 11831
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3359 25.30 0.99 0.88  chrX_97806504_97811022.rev     3124  4028 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_97806504_9   3124 GACAGATATTTCATGTTCATGAATTAAAAGAATCAATATTGTTTAACTGT 3173
                           v      ii          i   ii    v i         v iv  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_97806504_9   3174 CCCTACTCCCCAAAGTAATTTACAGATTCAATGCAATCTCTATCAAAATA 3223
                          vv           v i  i           i      i          v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_97806504_9   3224 TCAATGACATTCTT--CAGACATAGAAAAAACAA-CCTAAAATTTATATG 3270
                         i  iivi v  i  --    v  v  v  ivii -         i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_97806504_9   3271 GAAACACAAAAGACCCAGAATAGCCAAAGCTATACTAAGCAAAAAGAACA 3320
                             ii   ii                 i v  vi i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_97806504_9   3321 AAACTAGAGCAATCACATTACCTGATTTCAAATTATACTACAGAGCAATG 3370
                           ii i   v v     i v  ii        viv       i   v ii
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_97806504_9   3371 GTAACTAAAACAGCATAGTACAGGCTCAAATAAAGGCACATAGACCAATG 3420
                             ii  i    ii i    v   vi  iv v  i  i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_97806504_9   3421 GAACAGAATAAAGAACTCACAAACAAATCCACACATTTACAGTGAATTAA 3470
                            i     vi   iii  v   i   i   i       ii  v    i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_97806504_9   3471 TTCTTCACAAATATGCCAAGAACATATGCTTGGGAAAAGACAATCTCTTC 3520
                           i iv    ivi        v   viiv v      ii i i   i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_97806504_9   3521 AGTAAATGGTGCTAGGAAAACTGGATATCCACAGGCAGAAGAATGAAACC 3570
                          ii          i   v         ?     v   i         iii
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_97806504_9   3571 AGATTCCTATCTCTTGTCATATACAAAAATAAAATCAAACTGGATTAGAA 3620
                         i  ii    i   viii             v  v     v     i ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_97806504_9   3621 GCTTAAATCTAAGACCTCAGACTATGAAACTACTATAAGAAAATATTAG- 3669
                         i i     v     v  v i     i     vi  v       i  vi -
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_97806504_9   3670 GTAAACTCTCCAGGACATTGGTCTGTGCAAAAATTTCTTGAGTAATACCC 3719
                              -   i iv   v    vi iv    vii      iii  vv  v 
  L1M4_orf2#LINE/    553 GTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_97806504_9   3720 CACAAGCACATTCAACCAAAGCAAAAATAAATAA----GATCACATCAA- 3764
                           v       vv    v    v       i    ----  iiv      -
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_97806504_9   3765 GTTAAAAATCTTCTGCACAGCAAAAGAAACTATCAACAAAGTGAAGAAAC 3814
                         i       -   i  ii vv    i  v        v        i i  
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_97806504_9   3815 AATCTACAGAATGAAAGAAAATATCTGCATACTACTCATCTGACAAGAGA 3864
                           i i        ii         i    v ii ivi      i   i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_97806504_9   3865 TTAGTAACCAGAATATATATATAAGGAGCTGAAACAACTCTATAGGAAAA 3914
                         i v   v            ---- i  i  vvv       v   iv    
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATA----AAGAACTCTTACAACTCAATAATAAAA 796

  chrX_97806504_9   3915 AAAATCTAGTAAGTCAATTTAAAAATAGGCCAAAGATTTGAACAGATATT 3964
                          i -- v i   vi     ?      i   v  i        i   i   
  L1M4_orf2#LINE/    797 AGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_97806504_9   3965 TTTCAAAAGAAGACATGCAAATGGCAAACAGGAATATGAAAAGGTGCTTA 4014
                          i  v        i  i        v  i i v i        i    i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_97806504_9   4015 ACATCATTGATCAT 4028
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (144 / 82)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 1.89 (17 / 9)  


1049 28.62 3.95 0.33  chrX_97822547_97824625      499   802 (1277)    L1M4_orf2#LINE/L1      193   507 (401)  

  chrX_97822547_9    499 AAAAAGAACAAAACTAGGGCA-TCGCACTACCCAACTTCAAATTATGCTA 547
                           i         ii i i v -  i    v     i      viv i   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_97822547_9    548 TAAGGTTACAATAACCAAAACAGCTTGTTACTAGTACAAAAACAGACACA 597
                         i  i i    i   i   i    iv  v    i i i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_97822547_9    598 TAGACCAATGGAAGAGTCT---GAACCCAGAAATAAGACCACACACCTAC 644
                             i        v  vv ---  ii          iv   i   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_97822547_9    645 AACCATGTGGTCCTCAACAAAG-TGT-------ATTGCAATGGGGAAAGA 686
                         iii  vv  i ii  i    i -  i-------   -             
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGA 391

  chrX_97822547_9    687 ACTTTCTAGGTAATAAATAGTGCCGGGATAACTGGCTAGCTATATGCAGA 736
                          ivv   vvvi  i    i    i    i      v  ? i i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_97822547_9    737 AGAATGCAATTGTAACCTCACCTTTCAACATATATGAACATTAATTCAAG 786
                               v i   v v  ii    iv  v      ii  v     i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_97822547_9    787 ATGGATTAAATATTTA 802
                               i ? v ii  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTA 507

Transitions / transversions = 2.40 (60 / 25)
Gap_init rate = 0.02 (5 / 315), avg. gap size = 2.60 (13 / 5)  

1086 27.45 2.21 1.72  chrX_97822547_97824625     1186  1593 (486)    L1M4_orf2#LINE/L1      499   908 (0)  

  chrX_97822547_9   1186 AAAGATTTAAATGTAAGGCCTCAAGCTATAAAAATGCTAGAAGAAACC-T 1234
                          ?   ii          iv  v  i        v vi         v - 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_97822547_9   1235 GGG---AAATACCCTTGTTGACATTGGTCTTGGCAGAGAATTTTTGGCTA 1281
                         i  ---    -- i i  -   v    vi v    iv iv  i  i v  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--CTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_97822547_9   1282 AGTCCCCAAAA--ACAATTGCAACAAAAACAAAAATTGACTAGTGGGATC 1329
                         v v v      --    --         iv      v  iv i v   ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_97822547_9   1330 TAAATAAACTAAAGAGCTTCTGCACAGCACAAAA-GCTATCACTAGAGTA 1378
                          v vi   v v  i i   i  ii vv  v ii -i      vv i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_97822547_9   1379 AACAGACCACTTACAAAATGGGAGAAAATATTCACAAATTATAAATTCGA 1428
                           v    v  ii   i                ii     i   v  ii  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_97822547_9   1429 CAGAGGTCTAATATTCAGAATCTGTAAGGACCTTAAACAAATCAACAAGA 1478
                         i ii  v  vi   i      v i   i  v  ivv    v    i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_97822547_9   1479 AACAAACAAATAATTCGATTTCAAAGTGGGCAAAGGACATGAACAGAGGC 1528
                           v i        ii i   ?v   i           iv    i   vii
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_97822547_9   1529 TTATCAAAAAAAAAGACATATAAGTGGCAAACAA--ACAGGAAAAAATAC 1576
                           v  v   i  --  i   i  i    v  i  --   v     i  i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAA--GATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_97822547_9   1577 TCCATATCACTAGTCAT 1593
                           v i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (63 / 47)
Gap_init rate = 0.02 (9 / 410), avg. gap size = 1.78 (16 / 9)  


2283 27.32 2.14 2.49  chrX_97851323_97853160      504  1345 (493)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_97851323_9    504 ATCTACAGTTTGAATGCTATTCCTATCAAACTATCAAT--CCAATTTTTC 551
                                 v  v  i  v  i         v vi  ii--  --     i
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC--TTTTTT 117

  chrX_97851323_9    552 ACAAAACTAGAAAAAACT-ATTACAAAATTCATAGGGAACTGAAAAAGAG 600
                         i  i  v v  v  i-  -  ivi          v    v  v  ii  v
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_97851323_9    601 CCTGAAAAACCAAAGCAATCCTAAGGAAAAATAAAAAAAGCCAGAGGCAT 650
                           v   v i     i     i i ii  i  -i  v    iii    vv 
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAA-GAACAAAGTTGGAGGACT 215

  chrX_97851323_9    651 CAAATTACACTACTTCAAACTATACCATAAGGCTACAGTAACCGAAACAG 700
                           v i v v v i      viv   i i  i          i i i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_97851323_9    701 CATGGTACTGGTTCAGAAACAGACACATAGACCAATAGAATAGAATAGAG 750
                         ii         ivi iii i     i     i    i         v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_97851323_9    751 AACCCAGAAATAAAGCCACACACCTACAACCACCTGATATTCAACAAAGT 800
                          ii           v   i   ii  iiii  vi    v   i    i v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_97851323_9    801 TGTCAAAAATAAACATTAGACAAAGGACAATCTCTTCAATGA-TGGTGCT 849
                           i   i vi vv  v i iv    i i i   i     ii -       
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_97851323_9    850 AGGGATAACTGACTAGCCATATGCAGTAGAATAAA-CTGGACCCCTACCT 898
                         -    i     iv  ?   i     iv     i  -i             
  L1M4_orf2#LINE/    416 -GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_97851323_9    899 TTCACCATATA--AAAATTAACTCAAGATAGATTAAAGATTTAAATGCAA 946
                         iv         --             i  i   i ?   ii      i  
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_97851323_9    947 TGCCTCAAACTATAAGAATCTTAGAAAAAAAAACGCAGAAA-ACACCATT 995
                         viv  v         i v        i    -- ii  i?i- v i -  
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATC-TT 561

  chrX_97851323_9    996 CTAGACATCAGTCTTGGGAAAGAATTTATGACTAAGTCCTCAAAAGCAGT 1045
                          vv   v ii vi v  v  v iv  iv iiv  v v vi        vv
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_97851323_9   1046 TGCAACAAAAATATTAATTGA-AAGTCGGACGT------AATTAAAGAGT 1088
                         v         iv vv   v  -  i i    v ------       i v 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_97851323_9   1089 ATCTGCACAGCAAAAGAAACCATTGCAGAA--TAAACAGACAATGGACAG 1136
                         - i  ii vv    i  v  i  ii-    -- i  v      ivv    
  L1M4_orf2#LINE/    662 -TTTGTGCTTCAAAGGACACTATCA-AGAAAGTGAAAAGACAACCCACAG 709

  chrX_97851323_9   1137 AATGGGAGAAAATACTCACAAACTATGCATCTAACAAACGTCTAATATTC 1186
                                       i ii    ii  ii    i i  iv v  vi   i 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_97851323_9   1187 AGAATCTAAAAGGAACTTAAACAACTGAAGAAGCAAAAAAAAAAAAAACC 1236
                              v  v  i     ivv      -------   v  v     i ---
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACT-------CAATAATAAAAAGA--- 799

  chrX_97851323_9   1237 CAAATAATTCTATT-AAAAATGGGCAAAAGACATGAACAGACGCTTCTCA 1285
                                ii v   -             i  iv    i    ii     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_97851323_9   1286 AAAGAGGACATATAAGTGGTCAACAGACATTTGAAAAAAATGCCCCACAT 1335
                              i  i   i  i   i   i ii  iv      i -   i v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACAT 898

  chrX_97851323_9   1336 CACTAATCAT 1345
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.67 (142 / 85)
Gap_init rate = 0.03 (21 / 839), avg. gap size = 1.86 (39 / 21)  


3097 23.99 2.91 1.79  chrX_97903239_97907436.rev     2816  3707 (491)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_97903239_9   2816 GGTATTCCAAGCTCATGGACTGGAAGAATCA-CATAACTAA-ATGGCACC 2863
                          i   i   v i       i       v i -i  vii   -      vi
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_97903239_9   2864 AATACCCAATGCAATTTAAAAACTCTATGCAATCCCTATTAAAATGACA- 2912
                          v v     vvii  i  v i i  v i           i     vv  -
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_97903239_9   2913 -----TTCTTCACAGGAATAGAAAAAC-AATTCTAAAATGTACATGGAAC 2956
                         -----  i  ii   i   v  v  i -i  i       vi i      v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_97903239_9   2957 CACAAAAGACTCA-AATAGCCAAAGCCATCCTGAGCAAAAAGTACAAAGC 3005
                         ii   ii   i  -          i v   i   iv  i   v      i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_97903239_9   3006 TAGAGGCATCACATTAACTAAATTCAAAATATACTACAAAGCTATAGGAA 3055
                          i    vv     i vv i  v       iv             i  v  
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_97903239_9   3056 -CAATATCAGCATGGTACTGGCATAAA-ACAGACACATAAACCAATGTAA 3103
                         -   v -   ii              i- i     i   i i     v  
  L1M4_orf2#LINE/    257 TCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_97903239_9   3104 CAGAATAGAGAATTTAGATATAAACCCATAAGTTTACAGCCAACCCATTT 3153
                         i     v    i ii   v           vi    ii i   iiv    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_97903239_9   3154 TCAACAAAGGTGCCAAGAACATATAATGGGAAAGGGACAGTGTCTTCAAT 3203
                           i    i          v   vi      i  i i i   v i     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_97903239_9   3204 AAATGGTGCTGGGAAAGCTGGATATCCATATGCATAAGAATGAAACTAGA 3253
                                       v i       ?   i     v         ii i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_97903239_9   3254 CCCCTATCTGCTGACATATA-AAAAATAAAATAAAAATGAATTACAGACT 3302
                               i  vviiv      -      v  v v      i  i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_97903239_9   3303 TAAATTTAAGACCTCAAACTTAAATTTAATACCTGAAACTACTATAAGAA 3352
                              v     v  v     --------   ----     vi  v     
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACT--------ATA----AAACTCTTAGAAGAA 543

  chrX_97903239_9   3353 AACACTGGGGAAACTCCCCAGGACATTGGTCTGGGCAAAGATATTTTTTG 3402
                             iv  ? v  v  ii iv   v    vi i     v i -  i  v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAG 592

  chrX_97903239_9   3403 GTAAGACCTCAAAAATGTAGGCAACAAAAGCAAAAATTGACAAATAGGAT 3452
                         i  v   vi     iiii i          v      v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_97903239_9   3453 TACATCAAGCTAATGAGCTT----GATACAAAGGAAATAATCAACAAAGT 3498
                          v      iv v vi i   ---- v v       v iv     v     
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_97903239_9   3499 GACAAGACAATCCACAGAATGAGAGAAA-TATTTGCTAACTATACATCTG 3547
                           v       i          i      -       v  ii   i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_97903239_9   3548 ATAAGGGATTAGTAACCAGAATATGTAAT--ATTCCCAAACAACTCAATA 3595
                                 i v   v         i   v-- i  ii --          
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATA 790

  chrX_97903239_9   3596 GCAAAAAAA-----GATTTGATTAAAAAATGGGCAAAACATCTGAATAAA 3640
                         ii     i -----i iiii   ?             iv  i      i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_97903239_9   3641 CATTTCTCAAAAAAAGACATATGAATTGTCAGCAAGTAT-TGAAAAAATC 3689
                                 v   i    i   ii   v i  ii   i i-      i  v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_97903239_9   3690 TTCAACATCACTAATCAT 3707
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (131 / 79)
Gap_init rate = 0.02 (18 / 902), avg. gap size = 2.33 (42 / 18)  


2591 27.90 1.97 2.63  chrX_97931388_97937240.rev     4449  5362 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97931388_9   4449 TGGAAGAACATTCCATGCTCGTGGATAGGAAGACTCAAT---GTTAAAAT 4495
                              ii i  i     i  i     v        i   ---     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97931388_9   4496 GGCTATACTACACATGGCAATTTACAGATTCAAT----TCTCTATCAAAC 4541
                            v     v v  vivii  i           i----  i        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97931388_9   4542 CACCAA-TGTCATTCTTCACAGAATTAGAAAAA--AAATTTAACATTTAT 4588
                         iv   i-  i -  i  ii     v v  v  i--i vii   v   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_97931388_9   4589 ATGGAAATCCCCCTCAAAAAAAAAAAAAAAGCAAGAATAGTCAAAGCAAT 4638
                                 v --------------  iii v v       i    i    
  L1M4_orf2#LINE/    150 ATGGAAATGC--------------AAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_97931388_9   4639 CCTAAGCAAAAAGAACAAAGCCAAAGACATCACACTATCTGACTTCAAGC 4688
                          i i iv  i          iiii  ivv       vi ii i     iv
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_97931388_9   4689 TATACTGCAAAGCTACAGTAACCAAAACAGCATGGTTCTGGTACAAAAAC 4738
                         iv    i              i   i    ii    v    i i  ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_97931388_9   4739 AGACACATAGACCGGTGGAACACAGTAAAGAGCCTAGGAATATACTTGCA 4788
                              i     i ii     i v i vi    i i  i    v  iiii 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_97931388_9   4789 CAATTACAACCATCTGATCTTCAACAAAGCTGAGAAAAACAATCAATAGG 4838
                           v   iiii  vi    i   i    i v  vv  i v  v     i  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_97931388_9   4839 CAAAGGACTGCATACTAAATAAATGGCGCTGGCATTACTGGCTAGCCATA 4888
                         v    i iv iv vi v  i      i     v iv     v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_97931388_9   4889 TGCATAAGATTGAAACTAGACCCTTTCCCTACATCATATATAAAAATCAA 4938
                             v    v    ii i     i v  ii   i      i      i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_97931388_9   4939 CTCAAGATGGATTAAAGACTTAAATGTAAAAACTCTAACTATGAAAATCA 4988
                              i      i ?    i         i i  vv      i   v  v
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_97931388_9   4989 TGAAAGATAACCTAGG---AAATGCCATTCTGAACATAGGCATTCTGGCA 5035
                          ii    v   v    ---    -- v iv   v v i  --- iv    
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGG---TTAGGCA 580

  chrX_97931388_9   5036 AAGATTTCATGTTGAAAAATG---CCAAAAGTGATTGCAACAGAAACAAA 5082
                          v i    ---  - i v   ---       iivvv      i  iv   
  L1M4_orf2#LINE/    581 ATGGTTTC---TT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_97931388_9   5083 AATTCAGAAATAGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAACAG 5132
                            vv v    v   ii v  i   v v  i i   i  ii vv   vi 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_97931388_9   5133 AAACTATCAACAGATTAACTAGACAATCTGAAGTATAGGAGATAATATT- 5181
                          v        v i v i vv      i iiv  v  i     v      -
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_97931388_9   5182 GCAGACTATGCATCCCATAAAGGTCTAATATCCAGAATCTATAAGAAACT 5231
                            i ii  ii   iv    i  v  vi          v     ii    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_97931388_9   5232 TAAATAAATTAACAAGCAAAAACCAAACAATGCCATTAAAAAGTGGGCAA 5281
                         ivv i  v i  i  vv    iv    i  iv v   ?    i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_97931388_9   5282 ATAACATGAACAGAAAATTCCCAAAAGAAGACATACACATGGCCAACAAG 5331
                          vi iv    i   v v   i v        i     v        i   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_97931388_9   5332 CATATGAAAAAATTC-CAACATCACTAATCAT 5362
                           i       i  v -        ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (154 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.00 (42 / 14)  


2727 27.97 1.66 0.89  chrX_97942112_97947816     4325  5225 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_97942112_9   4325 TGGAAAAACGTTCCATACTCATGAATAGGAAGAATCAATATTGAGAAAAT 4374
                               i ii i    ii     i  v      v i       vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_97942112_9   4375 GGCCACAGTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 4424
                            v i v v      v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_97942112_9   4425 CATCATTGACGTTCTTCACAGAATTAGAAAAAAAAATAATTTTAAT-TTC 4473
                         ivi  vivi v  i  ii     v v  v  iv--- i  ii   v-   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC---TGATCCTAAAATTC 147

  chrX_97942112_9   4474 ATATGGAACCAAAAAGGAGCCTGTATAGCCAACACAATCATAAGCAAAAA 4523
                                 viiv  i   v  v v        v      v i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_97942112_9   4524 AAA---AGCTGGAGGTATCATGCTACCTGACTTCAAACTATACTACAAGG 4570
                         i  ---  i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_97942112_9   4571 CTACAGTAACCAAAACTGCATGGTACTTGTACAAAAACAGACATATAGAC 4620
                                  i   i  v ii       v i i  ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_97942112_9   4621 CAATGGAACAAAACAGAGACCTCAGAAATAACACCACACAACTACAACCA 4670
                                 i i  iv    vii         vv   i   vi  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_97942112_9   4671 TCTGATTTTTGACAATC-TGACAAAAACAAGCAATGGGGAAAGAATTTCC 4719
                         vi       i     vv-  v   i v  vv               vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_97942112_9   4720 TATTCAATAAATGGTGCTGGAAAAACTGGCTAGCCATAGGCAGAAAACTG 4769
                          v     i            i v      v  ?   i v   i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_97942112_9   4770 AAACCAGACCCCTTCCTTACACCTTATACAAAAAATAACACAAGATGGAT 4819
                           iiii       v   i     v          v    v   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_97942112_9   4820 TAAAGACTTAAATGTAAAACCTCAAACCATAAAAATCCTAGAAGAAAACC 4869
                         i ?    i         i v  v    i      v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_97942112_9   4870 TAGGCA-ATACCATTGAGAACAAAGGCATGGGCAAAGACTTCAGGACAAA 4918
                             ?i- v i v i v  v vvi  i- i     v ii   v---i i 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCT---TAGA 593

  chrX_97942112_9   4919 AATGCCAC---AAGCAAGAGCAACAAAAGCCAAAATTGA-AAATGGGATC 4964
                         v   v   ---     vi           vv     v  -    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_97942112_9   4965 TAATTAAACTGAAGAGCTTCTGCATAGCAAAAGAAACTATTATAAGAGTG 5014
                          v  i   v v  i i   i  iiivv    i  v     i vi i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_97942112_9   5015 AACCGGTATCCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGA 5064
                           vv ii v  i                 v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_97942112_9   5065 CAAAGGTCTAATATCCAGAATTTACAAGGAACTGAAACAAATTTACAAGA 5114
                         i  i  v  vi          v  i  i     vvv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_97942112_9   5115 AAAA-----ATAACCCCATCAGAAAGTGGGTGAAGGATATGAACAGACAC 5159
                             -----       v  i?i   i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_97942112_9   5160 TTATCAAAAGAAGACATTTGTGCCACCAACAAACATATAAAAAAAAATCT 5209
                           v  v        i  viiviivi    i  i  i  i    i vi-  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG-CT 892

  chrX_97942112_9   5210 CGACAAAACTGATTAT 5225
                          i   vv ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (140 / 108)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


2230 26.65 7.40 3.99  chrX_98035100_98039353     2887  3764 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98035100_9   2887 TGGAGAGACAAACCATGTTCATTGATTGGAAGACTCAACATTGTAAAGAC 2936
                             i   i vv          v            i  i     v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98035100_9   2937 GTCCATTCTTCCCAAATTGATATAC-GAT--------ATCGCT--CAATA 2975
                          v v  v  i           v   -   --------   v  --   v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98035100_9   2976 TCCTAGTTAAGTTTTT-GTAGTTACAGATAAGATTATTCTAAAGCATATA 3024
                            i  i ivv     - i  vv iv  i   v v  i     iivi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_98035100_9   3025 TAGAAAAGCAAAGGAACTAGAATAGCTAATACAAATTTGAACAAGAAGAA 3074
                          i    v    i   v i        i  v    vi     v        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_98035100_9   3075 TAAAGTGAGAAGAATCAGTCTAGTCTATGTGATTTTAAGACTTCTTATAC 3124
                         i     vi  i  v   vv  --  i---ii    i  i    vi  i v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACT--TCC---CAATTTCAAAACTTACTACAA 245

  chrX_98035100_9   3125 AGCTATAATAATCCAGGTTGTGTGTAGTATTGATGGAGGAATAGACACAT 3174
                              i i     v  iiv     --   i  iiiv i i       i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTG--GTACTGGCATAAGGATAGACATAT 293

  chrX_98035100_9   3175 AGATCAATGGAACAACATAGAGATCCCAGAGATAGACCCATGCAGATATG 3224
                                     i iv  v    vi     i   i      i  vv    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_98035100_9   3225 CCCTATTGACTTTTTTTTTTTTTTTTACAAAAGTAGAAAAACATTTCAGT 3274
                         vi v     -----------    iv    ii  ivv  i  vv    i 
  L1M4_orf2#LINE/    344 GTCAATTGA-----------TTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_98035100_9   3275 GGAGAGAGAA-AGTTTTTTCAGCAAATTGTGCTGAAGCAATGGGACAGCC 3323
                           i  i    -   i      i     v      iii   iv   i ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_98035100_9   3324 ACAGGTACAAAAATGAACCTAGACCTATGTCTCACATATTATGGAAAATG 3373
                            v i v  i      vi i    iv ii      ivv   iv    vv
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_98035100_9   3374 TAACTTGAAAAAGATGATGAACGTTACTGTAAGTTTTTATAGCATAAAAT 3423
                              ii   vi   v ?ii  v v v      vvi v v vi      i
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_98035100_9   3424 TTTTGGAACTAAGTGTAGGAAAAAAGTCACTGGGATCTAGAACTAGGCAA 3473
                          i  i   vv  iii    ?iv   -  vii v  i  v iii       
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_98035100_9   3474 AG-------AGAT------CC--------------------------TCG 3484
                         v -------    ------  -------------------------- v 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_98035100_9   3485 ATAAACTGAATTTCGTGTAAATTAAAGG-TTTTGTG----AAAGGTC-TT 3528
                              i  i i   i vv        ii-       ----     v -i 
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_98035100_9   3529 AGTAATAAGATGAATAG-----TTACAGACTTAGAGAAAATATTTATAAA 3573
                          vi  v  ii    v  -----ii     v vi            ii   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_98035100_9   3574 CCACATCTCTGACCAATGACAAATTACTAATATTCAGAGTACATAAAG-- 3621
                         i  i  v     iv iv   ---  i----   i    i  i      --
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGAC---TTG----TATCCAGAATATATAAAGAA 774

  chrX_98035100_9   3622 CTCTTTCAACATTCAATGGTGAAAACAAAAAAATCAAATAATTCAATTAG 3671
                              v    --     ------  i     i -       ii     ?i
  L1M4_orf2#LINE/    775 CTCTTACAAC--TCAAT------AATAAAAAGA-CAAATAACCCAATTWA 815

  chrX_98035100_9   3672 AAAATGGGCAAAATACATGAGAAGATATTTTACTGAAGAGGATATACAGA 3721
                                     iv iv   iv   i    iv ii    i        i 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_98035100_9   3722 TGTCAAATAGATACATGAAAGGATATTAAACACTATCAGGCAT 3764
                           v v    iii        i   ii v    ii ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 4.35 (100 / 23)  


2591 23.88 13.06 0.12  chrX_98086489_98088582.rev      803  1606 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98086489_9    803 TGGAAAGCCATCCCGTGTTTATTAACTGAAAGATGCATTACTGTTAAAAT 852
                                vi     i    i  vi i  i    ivi v  i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98086489_9    853 GTTCACACTACTCAAAGCAATCTA-AGATTCAATA-AATTC-TGTTGAAA 899
                          viv i   v i    vii     -        ii-   i - i ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98086489_9    900 TTT--------TTTTTTGCAGAAATTAAAAAAATG----CAAAATTTATA 937
                          ii--------               i v  iv  ----i      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_98086489_9    938 TAGAACCACAAATAACCCAGCATAGCCAAAGTATTTTTGAGAAAGAAAAA 987
                          i   vii   ivi      v         ii v i    i      i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_98086489_9    988 CAAAG--------------------------------------------- 992
                              ---------------------------------------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_98086489_9    993 ----------------------CTGGCATAAAGACAGACATACAGCCCAG 1020
                         ----------------------         i  i       i  vi  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_98086489_9   1021 CAGAACTGA-TAGAGAACCCAGAGATAAAATCATTCACATACAGTCAAGT 1069
                         ii   iv  - v    ii     i     vi   v  iv  ii     v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_98086489_9   1070 GACCTTCAACAGGGGTGCCAAT-TTAAACAGTGTGGAAAGGATTGCCTCT 1118
                           ii   i   i         v-ii vv  i  v      i  v i  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_98086489_9   1119 TCTACAAATG---TTGAGAAAACTGGATATCCACCTGCAAAATA-TGAAA 1164
                           v       ---i  i  v         ?    v       v -    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_98086489_9   1165 TTGG-CCCATATCTTACAAGATACACAAAAATCAACCTAAAATTTATTAA 1213
                             -   v  i  i   vv   i        i   ii     vv  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_98086489_9   1214 AGACTTAAATGTAGGACCTGAAACTATAAA--TCC-ACAAGAAAGCATAG 1260
                             i        i  v  i          --  i- v      i     
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_98086489_9   1261 GGAGAAAGTTCCATGACATTGGTTTTGGAAAT---TTCTTGGATATTACA 1307
                          ?iv   vi i i    v    v  v  v   ---     i     v   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_98086489_9   1308 TAAAAAGCACAAGCAACAAAAGCAAAATTAGAAAAGTGGGACTACATCAA 1357
                         iv                    v    v    v  i v     v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_98086489_9   1358 A-TTAAAG-TTTCAGCACAGTAAAGGAAACAAGCCACAGACTGCAAAGAC 1405
                          -     i-i  iv ii vvi      v  v v v v i v  v      
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_98086489_9   1406 AGCCTACAGAATGAGAGAAAATATTTGCAAATAATATATCTGATGAAGG- 1454
                          i  i        i                  v           i i  -
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_98086489_9   1455 TTAATATC------ATATAATTAATTTCTACAACTCAATAGCAAACAAAC 1498
                         i vi    ------      vv  i ii            ii   v i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_98086489_9   1499 CAACTAACCTGATT-AAAAATGGGCAAGGGCCTCGAATAGATATTTCTCC 1547
                         v  -     ii   -            i  vi i       i        
  L1M4_orf2#LINE/    801 AAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_98086489_9   1548 AAATAAGACATGCAAATGACCAATAGGTATACGAAAAGATATTCAACAAC 1597
                            v    i  i      i      i i i i        ii      v 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_98086489_9   1598 CCTATGCAT 1606
                         v????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.70 (119 / 70)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 5.30 (106 / 20)  


3126 25.11 1.89 1.67  chrX_98104043_98108304.rev     2872  3771 (491)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_98104043_9   2872 GATATTCCACGTTGATGGATAGGAAGACTCAGTATTATCAAGATGTCAGT 2921
                              i   i   v      v        i i    i i      v  i 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_98104043_9   2922 TCTTCCCAACTTGATATATTGATTCAATTTGATCCCAATCAAAATTCCAG 2971
                         v  i     v     v  iv       ivii     v        i    
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_98104043_9   2972 CAAGTTATTTTGTGGATATCAGCAAACAAATTCTAAAGTTTACGTGGAG- 3020
                          vivi v     ii  v  iii   i vi  i     i  i ii    i-
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_98104043_9   3021 TGTCAAAATATCTGGAATAGCCAACACAATATTGAAAGGAAAGAACAAAG 3070
                           -   iiv i ii          v     v      iii          
  L1M4_orf2#LINE/    157 TG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_98104043_9   3071 T-AGAAGACTGACACCATCCAACTTCAAGACTTACTATAAA-CTACAGTG 3118
                          -i  i    v    ivi    i     i        i   -       i
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_98104043_9   3119 ATCAAGAAAGTGTGGTATTGGCAAAATAATAAACAATTAAACTAATGAAA 3168
                                v         i     v  vi   i   vv  i ii    i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_98104043_9   3169 TAGA-----GAGCCCAGAAATAGAACCACATAAATATAGTCAACCGATCT 3213
                             -----   i         i v   i i vv   i     ii   i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_98104043_9   3214 TTGACAAAGCAGCAAAGACAGTAAAATGGAGAAAAGATGATCTTTTCAAC 3263
                          i     i vv  v     vi vv     i    ii  ii          
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_98104043_9   3264 AAATGATGCTGGAACAATTGGAAATACACATGCCAAAGAAAAAAGTGAAT 3313
                              i      i    i    v ?v       v      vi    ----
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT---- 451

  chrX_98104043_9   3314 CTAGACACAGAACTTATACCCTTCACAAGAATTAATTCAAAATGGATCAT 3363
                         - i   v vv v  i i   v vi    i      i             ?
  L1M4_orf2#LINE/    452 -TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_98104043_9   3364 AGACCTAAATGCAAAATTCAAAACTGTAAAATTCCTACAAGGTAACATAA 3413
                                    i  i vii      i     i  i  v   iv      i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_98104043_9   3414 AATAAAATTTAGGCAACCACTGGT---ATAATGACTACTTTTTAGATGCA 3460
                         i?vv    i vv ii   viv   ---ii    ii --- i      iii
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT---TCTTAGATATG 597

  chrX_98104043_9   3461 ACACCAAAGGCAAGATCTGTGACAGAAATAATTGATAAACTAGACTTCAT 3510
                                 i   vi v viii v     v   v      i i        
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_98104043_9   3511 TAAAATGAAAAACTTCTCAGC--AAAAAAGCAATGTCAAAATAATGAGAA 3558
                         i     v        i vv  --v   iii  v i    i v i   i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_98104043_9   3559 GACAAGACACAAACTTGGAGAAAATATTTGTGGAAATCATAT--CTGATA 3606
                              vv    i v v              i--         --      
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGC--AAATCATATATCTGATA 745

  chrX_98104043_9   3607 AAAGATTGTTATTCAAAATATGCTAAGA-CTCTTAAAATTCAGCAGTAAG 3655
                          ii  i vv   i  i     iiv    -      v  i   ii i   i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_98104043_9   3656 AGCACAAAAAAACCCTGAATTTTAAAAATGGGTCAAAGACCTTAACATAC 3705
                          iv     v  -   --    ?-         iv  i  ii v  i v  
  L1M4_orf2#LINE/    796 AAGACAAATAA-CCC--AATTW-AAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_98104043_9   3706 ATCTCACAAAAGAAAATATACAGATAGCAAATA-GCATATGAAAGGATGT 3754
                           i  v v      i       i  i  v    -   i      i    i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_98104043_9   3755 TCAACATCATATGCCAT 3771
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (142 / 80)
Gap_init rate = 0.02 (16 / 902), avg. gap size = 2.00 (32 / 16)  


2606 28.01 3.15 1.01  chrX_98147173_98152887     4334  5222 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98147173_9   4334 TGGAAAAACATTCCGTGCTCATTGATTGGAAAAATCAATATCATGATAAT 4383
                               i i  i  i  i    v        i v i     ii v vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98147173_9   4384 GGCCATACTGCCCAAATCAAGTCATACATTCAATCACATTCCC-GTTAAA 4432
                            v     v       ii vii i v      - i  v    -i i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAA-CGCAATCCCTATCAAA 99

  chrX_98147173_9   4433 ATAACA-TTGACATTTCTTTACAGAGCTAGATAAAGAATATTTTAAAATT 4481
                           vv  -i  v --  i   i    iv v  i  - vvv  ii       
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC--TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATT 146

  chrX_98147173_9   4482 CACACAAAACTAAAAAGGAGCCTGAATAGCCAAGGCCATCCTAAACAAAG 4531
                           i iii  v iv  i   v  v          ii v   i i  v  ii
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_98147173_9   4532 AGAACAAAGCTGGAGGCATCATGCTACCCAACTTCAAACTATTCTACAGG 4581
                                  i      vv   ii  v     i      viv v     ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_98147173_9   4582 GCTACCATAACCAAAAGAGCATGGTACTGGTACAAAAACAGACATATAGA 4631
                              vi   i   i v  ii         i i  ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_98147173_9   4632 CCAATGCAACAGTATAGAGAACCCAGAAATAAGACAGCATAC--CTACAA 4679
                         i     v  i  v  v    ii          iv --     --i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGG 344

  chrX_98147173_9   4680 CTATCTGAACTTTGGCAAACCTGACAAAAACAAGCAACGGAGAAAGGATT 4729
                         ii vi   vi  i i   ivv  v   i v  vv   i  i     i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_98147173_9   4730 CCCTATTCAATAAATGATGCTGAGATTACTGGCTAGCCACATGCAGAAGA 4779
                         vi  v     i     i     i  iv     v  ?         i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_98147173_9   4780 TTGAAACTGGACATCTTCCTTCCACCATATACAAAAATTCACTCAAGATG 4829
                         v    ii     vi  v   iv                 v      i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_98147173_9   4830 GATTAAAGACTTAAATGTAAACCTCCAAACTATAAAAACCT-GGAAGACA 4878
                            i ?    i         ivviiv           vi  -i     v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_98147173_9   4879 ACCTAGGCA-ATACCACTCAGGACATAGGCATGAACAAACATTTTAT-GA 4926
                           v    ?i- v i -i  iv   v v  vv iii   vvi   iv -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_98147173_9   4927 TGAAGATGCCAAAAGGAGTAGCTATAAAAGCAAAAATTGACAAAGGGGAT 4976
                          - v  ii       v vv   v i     v      v  i   vv   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_98147173_9   4977 CTAATTAAACTAAAGAGTTTTTGCACAGCAAAAGAAACTATCAACAGAGT 5026
                         i v  i   v v  i ii     ii vv    i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_98147173_9   5027 AAACAGATAACCTAGAGAATAGAAGAAAATTTTTGCAAACTATGCATTCG 5076
                         i  v   i    i v     i i       v        ii  ii  ii 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_98147173_9   5077 GCAAAGGTCTAATATCCAGCATCTATAAGAAACTT----AA---AAT--T 5117
                         ii  i  v  vi       v  v     ii    i----  ---   -- 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_98147173_9   5118 ACAAAAACAACATAA--------AAAAGTAGGCAAAGG----GCATGAAC 5155
                          v   i    -    --------    i i        ---- v  ii  
  L1M4_orf2#LINE/    793 AAAAAGACAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_98147173_9   5156 ACTTTTCAGAAGAAAACATACATGTGGTCAACAACCATATGAGAAAAAGC 5205
                          i  i  vi     i i     vi   i   i  v  i    i  i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_98147173_9   5206 TCAACATCACCGATCAT 5222
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.06 (37 / 18)  


2982 23.43 1.81 5.32  chrX_98169012_98170999      557  1495 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_98169012_9    557 GAAAGAAGTCCTATGTAAATGAATTTGAAGAATTAAAATTATTAATACAT 606
                               vi   i    vv   i   v     v    v   i    v iiv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_98169012_9    607 TCATACTTCCCAAAGCAATCTACAGACTTAATGCAATCCCTGTGAATATT 656
                         iv     i      vii         i i  i         i v  v  i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_98169012_9    657 TCAA-TATAGTTTTTCCTAGAAGCAGAAAAAACAAACTTAAAATTTGTAT 705
                         i  i- iivv     v -    iiv  v  ivii v i       ii   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGC-AGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_98169012_9    706 GGAACCATAAAATACCCCAAATAGCCAAAGCAATCTTGAGCAAAAACAAC 755
                             viii  iiv    vi          i         iv  i  v   
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_98169012_9    756 AAAGCCAAAGGCATCACAGTACCTAATTTAAAAATATACTGCAAAGCTAT 805
                             iiii   vv     v v  i     v    iv    i        i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_98169012_9    806 AGTAATCAAAATAGCATGATTCTGGCATAAAAACAGACACATAGACCAAA 855
                                  i i  ii  i v         ii i     i     i   v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_98169012_9    856 GGAACAGAACAGA-AGTCTCAAAAATAAATCTATGCATTTATGGTCAATA 904
                             i    iv  -    -  i       i i  i              v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_98169012_9    905 GATTCTCAACAAAATCACCAATAACACACAATGGAGAAACAAAAATCTCT 954
                             i  i    iivii    v v  iv      i    v  v i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_98169012_9    955 TCAATAAATAGTGCTAGGAAAACTGGGTATACACATGCAGAAGAATTAAA 1004
                             i    i     i   v      i  ?v        i      v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_98169012_9   1005 TTAGAACCTCATCTCACACCACATACAAAAATCAACTTAAAATGGATTAA 1054
                           i  v  ii i         i          i    i         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_98169012_9   1055 TGAGTAAAATGTGA---------CTATAAAATTACTAGAAGAAAACGTCA 1095
                         v  viv      i ---------        i vi           --- 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC---A 547

  chrX_98169012_9   1096 TAG----AAAACTTCATGACATTGATCTGAGCAATGATTTTTTTTTTTTT 1141
                            ----   v    i    v   ivi ii      i   i  -------
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT------- 590

  chrX_98169012_9   1142 TTGGACATGACCCCAAAAGCATAGGCAACAAAAGCAAAACTAGACAAATG 1191
                         --i  i     v         i i          v    v    i    v
  L1M4_orf2#LINE/    591 --AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_98169012_9   1192 GGATTACATGAAACTTAAAAGCTTCTGTACAGCCAAGAA-ACTGGTTAAT 1240
                            i v   v   v      i   i   i vv v   i -   i- i  v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAG 687

  chrX_98169012_9   1241 ACAGTGAAGAGTCAACCCTTAGATTAGGAGAATATATTTGCAAAACATAC 1290
                          v      i  v      vi   v i      v           v    i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_98169012_9   1291 AATTGATAAGGGGCTAATGTCAAAAATATATAAGAAACACAAACAATTCA 1340
                          vi         i  vi i  v i         ii   v vv    i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_98169012_9   1341 ATAGTAATAAAACAAAAATGGGAAAGCACATAAAATAGACATTTCTTAAA 1390
                            i   v  i     v ---------  vi  ------------  ?  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATA---------ACCCAA------------TTWAA 816

  chrX_98169012_9   1391 AGAAGCCATAGGGAAAGTGGGCAAAAGGCATGAACATACACTT-TCAAAA 1439
                          i --------------        i iiv    i v   i  -  v   
  L1M4_orf2#LINE/    817 AAA--------------TGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_98169012_9   1440 GAAGACATACATGTGGCCAACAAACATGTGAAAAAATGTTCAACATCACT 1489
                              i     vi       i  i  ii      i   i         ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_98169012_9   1490 AATCAT 1495
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.68 (136 / 81)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 4.79 (67 / 14)  


2903 27.56 2.81 0.67  chrX_98214758_98219739     3601  4489 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98214758_9   3601 TGGAAAAACATTCTATGTACACAGTTAGGATGAATCAGTATTGTTAAAAT 3650
                               i i  i i    v  ii v v   v  v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98214758_9   3651 GGCCATATTGCCCAAAGCAATTTATAGATTCAATGCTATTCCTATCAAAA 3700
                            v   i v      vii  i  i        i  v  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98214758_9   3701 TATCAACATATTTTTTTCTCACAGGATTAGAAAAAACCACTCTAAAATTG 3750
                          vi  i - iii     i--i   i v v  v  iviv ii        v
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_98214758_9   3751 ATACAGAATTAAAAAGGAGCCCAAATAACCAAAGCAATCCTAAGCAA-AA 3799
                            ii   v iv  i   v  vi    i     i     i i iv  -  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_98214758_9   3800 GAACAAAGCCAGATACATCACATTACTCAACTTCAAACTAGACTATAAGG 3849
                                 iii  vivv     i v i   i      vivv    i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_98214758_9   3850 CTATGGTAACCAAAACAGCATGATACTGATACAAAAACAGTCACATAAAC 3899
                            ii    i   i    ii  i     ii i  ii i  v  i   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_98214758_9   3900 CAATGGAATGGATTAGATAACCCTGAAATAGATCCACACATCTACAGCCA 3949
                                  i  v v  v ii  v      i i   i    i  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_98214758_9   3950 TCTGATCTTTGACAAAATTGACAATAACAAACAATGGGAAAAGGATTCCC 3999
                         vi    i  i     iiv  v   v v  vv       i    i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_98214758_9   4000 TATTCAATAAATGGTGCTGAGATAACTGGCTAGCCATATGCAGATGATTG 4049
                          v     i           i  i      v  ?   i     i v  v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_98214758_9   4050 AAACTGGACTGCTTTCTTTCACCATATATAAAAATCAAGTCAAGATGGAT 4099
                           ii     iv  vi  iv         i      i  v    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_98214758_9   4100 TAAATACTGAAATGCAAGACCTGAAACTATAAAAATTCTAGAAGAAAACC 4149
                         i ? v  iv     i    v  i           v ii           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_98214758_9   4150 TAGGTA-----CTACC--ACTCTGGACATAGAGCAAATATTTCATGACAA 4192
                             ?i-----  v v--  ii   ii-   -    vvi    v iivv 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGT-TAG-GCAATGGTTTCTTAGATA 595

  chrX_98214758_9   4193 AGACTCCAAAAGCAATTGCAACAAAATCAAAAATTGACAATTGGGATCTA 4242
                         v   v         vvv         vv      v  i  v v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_98214758_9   4243 ATTAAA-TTAAAGAGCTTCTGCATAGCAAAATAAACCACCAAGAGAGTGA 4291
                           i   -     i -   i  iiivv    iv v  i i     i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_98214758_9   4292 ACAGACAACCTACAGAATGGGAGGAAATATTTCCATTTGGTGCATCCAAT 4341
                          v        i            i        v  vv vi ii   ii  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_98214758_9   4342 GAAAGTCTAATATCCAGAGTCTATAAGGAAC--------------AAGCA 4377
                         i ii v  vi        i v     i    --------------  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_98214758_9   4378 AAGAACAA-TAACCTCATTTAAAAATGGGCAAAGGACATGAACAGACACT 4426
                           ii    -     iv   ?                iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_98214758_9   4427 TCTCAAAAGGAGACATACATGTGGCCAACAAACATAAGGGAAG-TGCTCA 4475
                             v    i   i     vi       i  i  i v ii   -      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_98214758_9   4476 ACATCACTAATTAT 4489
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


2684 27.13 3.03 1.23  chrX_98235696_98238550     1471  2362 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98235696_9   1471 TGGAAAAACATTTCGTTTTCATGGATAGGAAGAATCAATATTGTAAAAAT 1520
                               i i  ii i v         v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98235696_9   1521 GACCATACTGTACAAAGCAATTTATAGATTCAATGCTATTTCTATTACAC 1570
                          i v     viv    vii  i  i        i  v  ii    i v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98235696_9   1571 TACCATTGAGATGC----TTCACAGAATTAGAACAAACT-ATTTTAAAAT 1615
                          v   ---- v   ----  ii     v v  -   i  -  ii      
  L1M4_orf2#LINE/    101 TCCCA----GCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAAT 145

  chrX_98235696_9   1616 TAA-ATGAAACCAAAAAGAGCCCA-AATAGGCGAGGCTATCTTAAGCTAG 1663
                          v -   i  viiv  i ii    -     v i ii v     i ivv  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_98235696_9   1664 AAGAACAAACCTGGAGGCATCATGCTACTCAACTTCAAACTGTACTACAT 1713
                                  vi      vv   ii  v i   i      viv       v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_98235696_9   1714 GGCTACAGTAATCAAAACAGCATGCTGCTGGTACAA----AGACACATAA 1759
                         i              i    ii  v i    i i  ----     i   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_98235696_9   1760 ATCAATGGAACAGAATAGAGAACCGAGAAATAATGCTGCACACCTACA-T 1808
                                   i     v    ii v        vv iii   ii  ii- 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_98235696_9   1809 CCCTCAGATCTTCAACAAAGTTGACAAAAACTAGCAATGGGGAAAGGATT 1858
                          vv i-   i   i    i v  v   i v vvv            i  v
  L1M4_orf2#LINE/    346 CAATT-GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_98235696_9   1859 CTCTATTCAATAGATGGTGCTGGGATTACCAGTTCGCTATATGCAGAAGA 1908
                         v   v     i i            iv  ii v v? i i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_98235696_9   1909 TTGAAACCAGAACCCCTTCCTTATACCATATACAAAAATTAACTCAAGAT 1958
                         v    iiii  -     v   i i                       i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGA-CCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_98235696_9   1959 AGATTAAAGACTTAAGTGTAAAACTCACAAATATAAAACCCT-GGAAGAT 2007
                         i   i ?    i   i     i vii v  v        i  -i     v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_98235696_9   2008 AACCTAGGCA-ATATC------ATTCCGGATATAGGAACAAAGATTTCAT 2050
                            v    ?i- v   ------ iiii  i -    --   v i    v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGG--CAATGGTTTCTT 590

  chrX_98235696_9   2051 GACAAAGATGCCAAAAGTAATTGCAACAAAAGCAAAAATTGACAAATGGA 2100
                         iivv v  ii       i vvv          v      v  i    v i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_98235696_9   2101 ATCTAATTAAA-CTAAAGAGCTCTACACAGCAAAGGAAACTATCAACAAA 2149
                          ii v  i   -i    i vi i iii vv       v        v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_98235696_9   2150 GTAAACAGAAAACCTACAGAATAGGAGAAAAATTTTGCACACTATGTATC 2199
                           i  v   v    i       i        vv      v ii  i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_98235696_9   2200 CAGCAAAGGTTTAATACTCAGCATCTATAAGGAACT-TAACAA---AATT 2245
                         iiii  i  vi vi  ii   v  v     i     - v    ---   v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_98235696_9   2246 -TACAAGGAAAAAAAGCCCA-TAAAAAAGTAGGCAAAGGACACAAACAGA 2293
                         -  v  i  v   v i    - v?    i i         ivii  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_98235696_9   2294 CACTTTTCAAAAGAAAACATACATTCGGCCAACAAATCATATGAAAAAAT 2343
                           i  i  v      i i     vvi      i  i-  i       i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGAT 889

  chrX_98235696_9   2344 GCTTAACATCACTGATCAT 2362
                            i       ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (146 / 92)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.81 (38 / 21)  


3637 24.11 1.00 0.11  chrX_98255690_98260187.rev     3110  4009 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98255690_9   3110 TGGAAA-ACAGCTCAAGTTCATGGATTGGAAGACTTAATATCATTAAAAT 3158
                               - i v i  v                         ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98255690_9   3159 GTCCATGCTACCAAAAACAATCTATAGATACTATGTATTCTCTATCAAAA 3208
                          v v  i  v  v   vii     i    v v i i v  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98255690_9   3209 TCTCAATGGCATTTTTAGCAAAAATAGAAAAAC-AATCGTAAAATGTATA 3257
                           i  iiv  v     v   i    v  v  i -i   v      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_98255690_9   3258 TGGAATCACAATTATTTTGGGATAACCAAAATTATCCTGAGAAAAAAGAG 3307
                              vii   vviviiii i   i      iv   i   i   i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_98255690_9   3308 TCAAGT-GGAGAAGTCACACTTCTGGAGTCTAAAACATATTATAGTGCTA 3356
                         iv    -    i v         ivi v ii     v  i  i iv    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_98255690_9   3357 AAATAAT-AAAACAGTATGGTACTGGCATAAAAGTAAACATAGAGACCAA 3405
                         v i    -  i     i              iii  i     v   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_98255690_9   3406 TGGAATAGAATAGAATGCCCAGAAATAAGCCCACCCATATACTGTCATAT 3455
                                    v  iv i          i    iv   v  iv    vv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_98255690_9   3456 GATCTTCAACCAGGGTGCAAAGACTACACAATAGGGAAAGGATATTCTCT 3505
                            i   i  v       v     i iv    i       i   v   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_98255690_9   3506 TCAACAAATGATATCAGGAAAACTGGATAACCATATGCAAAATAATGAAA 3555
                                   i iiii   v         ?   i        v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_98255690_9   3556 TTGGATTCTCATCTTACACCATAAACAAAGATCAACTTAAAATGGTTTA- 3604
                              ii ii i  i        v     i  i    i       v i -
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_98255690_9   3605 AAACTTAAACTTAAGACCCAAAACTATAAAACTCT-AGCAGGAAACATAG 3653
                          i  i    iv     v i                -  v  i        
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_98255690_9   3654 GGGAAAAACCTCATGACATTGGTCCAGGTAAAAATTTATTGGGTATGACA 3703
                          ? v   v i  i    v    vii   i  vii   v  i i       
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_98255690_9   3704 --AAAAGCACAGACAACAAAACCAAAAATAAACAAGTTGGACCACATCAA 3751
                         --         ii        vv       i i  i      iv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_98255690_9   3752 GCTAAAAAACATTATTTGCAGCGAAGGGAACAATCAACAGAGTGAAAGGA 3801
                         iv v      v  - v   vv i    iv  v     v i       i  
  L1M4_orf2#LINE/    651 AATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_98255690_9   3802 -AACTTATATAGTAGGAGAAAGTATTTGCAAACCACACATTTGAAAAGGG 3850
                         -   ii i v i i       i          i  i i  i   v     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_98255690_9   3851 TTTCATATCCGAAATATAGAAATAACACTTACAATTCAATAGCAGTAAAA 3900
                         vi ii     ii      v   v   v       i      ii iv  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_98255690_9   3901 CGAATAACCCAACTGAAAAATGGGCAAAGGACTTGATTAGACATTGCTTC 3950
                          i          i ?                i    v        v  i 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_98255690_9   3951 AAAGAAGACATACAAGTGACCAGCAGGTATATAAAAACATGCTCAACATA 4000
                                 i      i  i   ii i i i  i    v           v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_98255690_9   4001 ACTAATCAT 4009
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.78 (137 / 77)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


2972 24.24 7.06 0.59  chrX_98263371_98267607.rev     2897  3746 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_98263371_9   2897 AAAAGTATTCCATGCTCATGAATTGGAAGAATCAATATTGTTAAAATGTC 2946
                            ii   i     i     i         v i           i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_98263371_9   2947 CTTACTACCCAAAGCAGTCTACAGATTCGATGCAATTCCTATCAAAATAT 2996
                         vv    v      viii           i i     i           vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_98263371_9   2997 CAATGACATTCTTCATAGAAATAGAAAAAA-AATTCTAAAATTTATTTAG 3045
                           iivi v  i  iii      v  v  iv-i  i        i  v i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_98263371_9   3046 AATCAAAAAAGACTCAGAATAGCCAAAGTTATTTTAAGTAAAAAGAACAA 3095
                           viiv  ii   i             iiv  i  i iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_98263371_9   3096 AACTGGAGGAG----ACTGT---ATTTCAAA--TTA-TACATTGGAGCTA 3135
                          ii       v----   vi---        --   -    ---i     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA---AAGCTA 250

  chrX_98263371_9   3136 TAGTAACAAAAACAGCATGGTACTGGCATAAAAACAGACACATAGACCAA 3185
                         i     iv  i    ii              ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_98263371_9   3186 TGAAACAAAATAGAGAACTCAGAAACAAATCCACGCACTTA--------- 3226
                           i  i i   v    iii      i   i   ii  i   ---------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_98263371_9   3227 GA-----GACA------CAAAGAC-------------------AGTCTCT 3246
                           -----    ------ v     -------------------     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_98263371_9   3247 TCAATAAATGATGCTGGGAAAACTGAATATCCATATGCAAAAGAATGAAG 3296
                             i     i        v     i   ?   i                
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_98263371_9   3297 CCAGACCCCTATCTCTCACCATATACAAATATCAAATCAAAATAGATTAA 3346
                         iii        i   v             v  i  v       i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_98263371_9   3347 TGATTTAAATCTAAGACCTCAAACTATGAAACTACTACAAGAAAACCTTA 3396
                         v  ii     v     v  v       i     vi  v        v vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_98263371_9   3397 GGGAAAGTCTCCAGGACATTGGTCTGGGCGTATA-TATCTTGAACAATAT 3445
                          ? v  i   i iv   v    vi i   i-  i- v    ii i vv i
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAGATATGAC 599

  chrX_98263371_9   3446 CCTACATGCACAGGAAACCAAAGCAAAAATGGACAAATGGGATCACATCA 3495
                         v i v v     i v   v    v      i  i    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_98263371_9   3496 AG-TTAAAAAGCTTCTGCACAGCCAAAGATACAATCAATAAAGTGAAGAG 3544
                          i-       -   i  ii vv v  i  i  v     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_98263371_9   3545 ATAACCCAGAGTATAGAAGAAAATGTTTGCAAGCTATCTGTCTCATAAGA 3594
                          i      v  v  i i       i       iii  v i   v     i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_98263371_9   3595 GATTAATAATCAAAATATATAAGGAACTCAAACAACTCAATAAGAAAAT- 3643
                           i vi  vi  i         i      vv            v    v-
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_98263371_9   3644 ----ATAATCCAATATAAAAGTCGGCAATAAATCTGAAGAGACATTTCTC 3689
                         ----    i     v?    i v     vii  i    v           
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_98263371_9   3690 ---AAAAGACATACAAATGGCAAACAGATATGTGAAAAGGTGCTTAATAT 3736
                         --- i    i           v  i iii ii       i    i  i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_98263371_9   3737 CACTGATCAT 3746
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.93 (133 / 69)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 4.06 (65 / 16)  


1981 28.88 8.05 1.07  chrX_98287551_98289200      316  1160 (490)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_98287551_9    316 AAGACATTCTACTTTTGTATATAGGATGATTCAACATAGTAAAGATCCC- 364
                             i  i i iv  ii iv  v   v  i i  i  v  v     vv -
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_98287551_9    365 -TACTGTCCACAAATTGATCTATAGATTTAAGATAAGTTCTTTCAAAATT 413
                         -    --  v            i     i  vii  vii  v       i
  L1M4_orf2#LINE/     55 ATACT--CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_98287551_9    414 CCAGCAAGTTTTTTTGTACCTAGCAACCAGCTTATT-TACAATTTATAAG 462
                              vivi       i vvv vii  v    v  i-  v    i   v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_98287551_9    463 GAAA-ACACGGGATGTGGAATTACTAAAA-----------AAG------- 493
                             -i  v    ivii    vi i    -----------   -------
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_98287551_9    494 -------------CACAT------ATT--AAAATTTACTAAATAGATAGT 522
                         -------------    i------   --    i      v v  v  vv
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_98287551_9    523 GTAATCAAGACAGTATGATATTTGTGTAGAGATAGAGACATAGATCAAAA 572
                                       i  i  i v ii  ii      v i         vi
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_98287551_9    573 GAACAATATTGGGAACCTAGAAATTGACCTACATAAATAAGGTCAATGAA 622
                            i iv    i  ii i      vi   i i i vv  v       vi 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_98287551_9    623 TTTTTTACAAAAAAGCAAAAGTAATTTAATGAAGGAAAGATAGCCTTTTG 672
                             iv    iiiv  v  iiiv   i    ii i  ii    i     v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_98287551_9    673 AATGAAAAGTGCTGAAGCAATTGGAAATCCATAGGCAAAA-AGCAAACTT 721
                           ii  vi      iii   i    v ?   i v      - iii  v  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_98287551_9    722 TAACCTAAATCTCAGATCTAATATAAAAATTTACTTAAG-TGAATAATAG 770
                         vi   ivv i    v i vv   i       v   i  i-  i  v ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_98287551_9    771 AC--AAATGTAAAATAGAAGACTATAAAACTTTCAGAAACAAGACAT--- 815
                           --        i vvv  i           i i    i-  i    ---
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG-AAAACATAGG 551

  chrX_98287551_9    816 TGTAAACATTCTTTG-GAACTAGAGCTATGAGAAAAGTT-CTTAGATTTG 863
                         ?     ---    i -  v  v i i  - iv  vi   -       v  
  L1M4_orf2#LINE/    552 NGTAAA---TCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATATG 597

  chrX_98287551_9    864 ACACCAAAAGCATGATCCATAGGAGGAAAAAATGG-TAAATTCAAGCTAA 912
                                     ii v v i ii  -       i -      vi vi v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCA 646

  chrX_98287551_9    913 TCGAAATGAAAAACTT--GCTCTGTAAAGAAC-TTGTGAGGAGGTTCAAA 959
                           i    v        -- iv  vi    i  -i i v i  iiv v   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_98287551_9    960 ATATAAACTAGAAACTGGGAGAAAATATTTGCACACTACGTAGCGAACCA 1009
                          v i  v i v i v                  v ii ii  v vi iv 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_98287551_9   1010 AAGAGTAGTATATAGAATATAGAAAAGACTCTCCAAACTCAAGAATAAGA 1059
                         ii  v v    vi        v   ii     ivv       v     - 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-A 795

  chrX_98287551_9   1060 AAGA-----AATCCAGTTAGAAAGTGGGCATAAGAC----ACA---ATTT 1097
                             -----  i   i  ?i   i      v i  i---- i ---    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_98287551_9   1098 CACTAAAGAGGATATACAGACGTCAAATAAGCACATAGGAAGATGTTCAA 1147
                          v i     i        i i v v           iii      i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_98287551_9   1148 CACTGTTACCTGT 1160
                           iii????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.03 (25 / 904), avg. gap size = 3.08 (77 / 25)  


3077 27.32 1.11 0.66  chrX_98295277_98301656     4984  5887 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98295277_9   4984 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5033
                              ii i  i   i i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98295277_9   5034 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5083
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98295277_9   5084 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5131
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_98295277_9   5132 TATGGAACCAAAAAAAGAGCCCACATT-GCCAAGTCAATCCTAAGCCAAA 5180
                                -- viv  i ii    v v -     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_98295277_9   5181 AGAACAAAGCTGGAGTCATCATGCTACCTGACTTCAAACTATACTACAAG 5230
                                  i     vvv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_98295277_9   5231 GCTACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5280
                              i    i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_98295277_9   5281 CCAATGGAACAGTACAGAG-GTCTCAGAAATAATGCCGCGTATCTACAAA 5329
                         i        i  v iv   -   -         vv  iiii  i  iiiv
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chrX_98295277_9   5330 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5379
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_98295277_9   5380 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5429
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_98295277_9   5430 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5479
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_98295277_9   5480 ATTAAAGACTTACATGTTAGACCTAAAAACATAAAAACCCTAGAAGAAAA 5529
                           i ?    i  v    v   v      vi      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_98295277_9   5530 CCTAGGC--AAACCATTCAGGACATAGGCATGGGTAAGGACTTCATGTCT 5577
                          v    ?--   i -   iv   v v  vv i  i  v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_98295277_9   5578 CAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCA 5627
                         vvi            vvi          vv     v  i    v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_98295277_9   5628 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5677
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_98295277_9   5678 ACAAGCGACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5727
                          v ii i   i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_98295277_9   5728 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5777
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_98295277_9   5778 AAAAACGA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5823
                            i  i ----   v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_98295277_9   5824 TCTCAAAAGAAGACATTTATGCATCCAAAACACACATGAAAAAATGCTCA 5873
                             v        i  vi viiiv    v vi          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_98295277_9   5874 TCATCACTGGCCAT 5887
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2692 26.17 4.46 0.69  chrX_98307333_98310023     1355  2229 (462)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98307333_9   1355 TGGAAA-ACATCCCATGTTCATGAATCAGAG-----AATATCATTAAAAT 1398
                               - i              i  ii  i-----     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98307333_9   1399 TACCATGCTGTC-AAAGCAATCTACAGATTCAATGTAATCTCTATCAAAA 1447
                         vi v  i  vi -   vii              i i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98307333_9   1448 TTCCCG-TGTAATTTTTCACAGAAATAGGAAAAACAATCCTAAAATTCAT 1496
                          i  v -  iv-     ii       v iv  ivii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_98307333_9   1497 ATGGAACCAAAAAAGAGCCAGAATAACCAACACAATCCTAAGGAAGAAGA 1546
                               viiv  ii  v        i    v      i i ii       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_98307333_9   1547 AAAAAGCTGGAGGCATCTCATTACCTGAATTCAAATTATACTACAATGCT 1596
                          v    i      vv  v  i v  ii v      viv        v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_98307333_9   1597 TTAGTAACCAAAACAACATGTTACTGGTATAAACATAGACACATAGACCA 1646
                         vi     i   i   iii  v      i    iv       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_98307333_9   1647 ATAGAACAGAACAAAGAACCCAGACATAAAACCATGTATCCACAGCCAAC 1696
                           i   i    ivi   ii     v     v    ii  ii ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_98307333_9   1697 TGATTGTTTACAAAGTCAACAAAAATATACACTGGGATAAAGTCACTCTT 1746
                              v iv    i viiv   i vi  v  v    iv  iivi v    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_98307333_9   1747 TTAAA-ATATAGTGCTGGGAAAGTTAGAT-GCCATGTGCAGAAGAATGTA 1794
                           v  - v  i         v ii i   -?   ii    i       v 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_98307333_9   1795 ACTAGACCCATATCTCTCACCAAATACAAAAATCAACTAAAGCTGGATTA 1844
                         ii i     v  i   v     v          i    v  iv     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_98307333_9   1845 AAGACTTAAATGTAAGAACTGAAGCTATAAAAATACT-GAACAAAACCTA 1893
                         ?    i           i  i  i        v vi -   v     v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_98307333_9   1894 GGGA-AAATCCTTGTGGACATTGGGGTAGGCAAAGAATTTATGACTATGA 1942
                           ?i-     i i   -  v     v       v iv  iv iiv     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_98307333_9   1943 CCCCAAAAGCCTAAGAAATGAAAATAAAAATAGGCAAATAAGACTTAAAC 1992
                          v        vi   v  ii   iv        ii    vi     v v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_98307333_9   1993 ATACA--AAAAGCTTTTGAACACCAAAAGAAATAATCAACAGAATGAACA 2040
                          - v --    i      vi vi    i  v iv     v i i    v 
  L1M4_orf2#LINE/    649 A-AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_98307333_9   2041 GACAACCTG-AGAATGAGAGAAAATACTTGTAAGCTATGCATCCAACAGG 2089
                                ii-      i         i   i  iii  ii   ii i i 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_98307333_9   2090 AAACTGATATTCAGAATATGCAAAGAACT----------------AAAAA 2123
                         ii   vi   i        ii        ----------------     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_98307333_9   2124 ACTCAACAACTCCCATTAAAAAATGG--AAAAGACATGAATAAACATTTT 2171
                         iviv  i   -  v   ?        --   i  iv      i      i
  L1M4_orf2#LINE/    798 GACAAATAAC-CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_98307333_9   2172 TCTAAAGAAGACATACCAACATTACTAATCATCA---GAGAA-ATGC--A 2215
                           i        i    -  -  vi i   v v  ---  i  -    -- 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATAC-AA-ATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_98307333_9   2216 AAATAAAACCACAA 2229
                          v  v ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (144 / 81)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.14 (45 / 21)  


3105 27.39 0.22 0.33  chrX_98327740_98329522.rev      384  1292 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98327740_9    384 TGGGAACGCATCCCATGCTCATGGATGGGTAGAATTAATATTGTGAAAAT 433
                            i  vii        i        v  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98327740_9    434 GATCATTCTGCCAAAAGCAATCAACAAACTTATTGCAATTCCCATCAAAA 483
                          iiv  v  v  v   vii   v   i i i vi     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98327740_9    484 TACCACCATCATTCTTCACAGAAATAGAAAAAACAATTCTCAACTTCATA 533
                          v   v vv v  i  ii       v  v  ivii  i  v  v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_98327740_9    534 TGGAACCAAAAAGGAGCCTGCGTAGCCAAAACAAGACTAAGCAAAAAGAA 583
                              viiv  i   v  v vi            vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_98327740_9    584 CAAATTCTGGAGGCATCACATTACTTTATTTCAAACTATACTATAAGGCC 633
                             v -      vv     i v iiv        viv     i  i  i
  L1M4_orf2#LINE/    201 CAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_98327740_9    634 ATAGTCACCAAAACAACATGGTACAGGTATAAAAATAAGCACATAGACCA 683
                          i   v i   i   iii      v  i    ii   ii  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_98327740_9    684 ATGAAACAGAATAGAGAACCCAGAAATAAACTGAAATACTTACAGTCAAC 733
                            i  i     v    ii            iv v i i   ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_98327740_9    734 TGATCTTCAACAAAGGAAACAAAAACATAAAGTAGGGAAAGGACACCCTA 783
                             i   i    i  viv   i v   vv i i       i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_98327740_9    784 TTCAGCAAATGGTGCTGGGATGATTCGCTAGCCACATGTAGGAGTGTGAA 833
                             i               ii i v v  ?       i ii  vi    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_98327740_9    834 CGTGGATCCTCATCTCTTACCTTATAGAAAAATCAACACAAGATTGATTA 883
                         vv    i  ii i   vi   v    v      i   v   i  v   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_98327740_9    884 AGGACTTAAATCTGAGACCTGAAATTGTAAACATTCT-AGAAAATGACAT 932
                         ?i   i     v i   v  i   i i    - i   -    i vi    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACAT 548

  chrX_98327740_9    933 TGGAA-AACCCTTCTAGACATTGGCTTAGGCAATAATTTCATAACCAAGA 981
                         v  ?i-  vi    vv   v    v         ii    v  ivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_98327740_9    982 GCCCAAAAGCAAATGCAATAAAAACAATGATAAATTGATGGTAATTAATT 1031
                         vv         v v    i    iv  vi   i  vi  v v v  v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_98327740_9   1032 AAACCAAAAAACTTTTGCAAAGCAAAAGGAACAGTCAGCAGTGTAAACAG 1081
                            viv           iivvv    i iv  vi   iv iv  i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_98327740_9   1082 ACAACCCACAGAACGGGAGAAAATATTTGCAACCTATACATCTGACAAAG 1131
                                      i                  vii   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_98327740_9   1132 GACTAATATCCAGAATTTACAATGAACACAAACAAATCAACAAGAAAAAA 1181
                             vi          v  i  v    v vv    v    i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_98327740_9   1182 AACAAACAATTCCATCAAAAAGTGGGCTAAGGGCATGAATAGACAATTCT 1231
                          -    i  ii v  i?    i     v    iiv          v    
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_98327740_9   1232 CAAAAGAAGATATACAAATGGCCAACAGACATATGAAAAAATGCTCAGCA 1281
                          v                       i ii  i       i       i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_98327740_9   1282 TCACTAATAAT 1292
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.31 (139 / 106)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


2549 27.24 6.52 0.81  chrX_98337328_98341479     2802  3660 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98337328_9   2802 TAGAAAAATATTCCATGTTAACAAATTGGAAGAAACAACATTGTTAAAAT 2851
                          i    i    i       v iii         vvi  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98337328_9   2852 GTTCATACTACTCAAAGCAATCTACATATTCAGTGCACAATCCCTATCAA 2901
                          viv     v i    vii       v     ii   --           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA--ATCCCTATCAA 98

  chrX_98337328_9   2902 AATACCAATGACAATCTTCACAGAAATAGAGAAAACAATCTTAAAATGTT 2951
                            v   iivi vv i  ii       v  v  ivii   i      viv
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_98337328_9   2952 TATGGAACCACAAAAGACCCAGAATAGCCAAAGCTAATTTGGGCAAAAAG 3001
                                vii   ii                 i v vi   iiv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_98337328_9   3002 AAGAAAACTAGATGAATTACATTACCTGACACCAAATTATGCTACAGAGG 3051
                           v   ii i  v  v i   i v  ii ivi    viv i     i  v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_98337328_9   3052 GATAG----CAAAACAA------------------------ACATAAATG 3073
                         v i  ----   i   i------------------------ i   i  v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_98337328_9   3074 AACAGAACAGGATAGAGAACCCAGAAACAAATCCATACACCTACAGTGAA 3123
                           ii   i  i  v    ii       i   i       ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_98337328_9   3124 TGCATTTTTGACAAAGTTTCCAAAAACATACATTGG-------------T 3160
                          vv     i     i v v    i v   v  v   ------------- 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_98337328_9   3161 T-------------GCTGGGGAAACTGGATATCCATATACAGCAGAATGA 3197
                          -------------      iv         ?   i  i  iv       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_98337328_9   3198 AACTAAACACCTATCTGTTGCTATATACAAAAATCAAATAAAAATTGATT 3247
                          ii ii  v    i  vvii i            i  v v     v   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_98337328_9   3248 AAAGACTTAAATCTAATACCCCAAACTATAAAACTATTTTGTGAAAACAT 3297
                          ?    i     v   v v iv             v  vviv        
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_98337328_9   3298 TGGGGAAAGTCTCCAGGACATTAGTCTGGGCAAAACATTTTGAGCAAT-A 3346
                         v  ? v  i   i iv   v  i vi i     vivv  i v  vv  - 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_98337328_9   3347 CCCCACAAGCACAGGCAACCGAAGCAAAAATACACAAATGGGATCACATC 3396
                          v   v       i     vi   v       v i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_98337328_9   3397 AAG-TTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAGGCAAAGG 3445
                           i-       -   i  ii vv       v  v     v  i ii  ii
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_98337328_9   3446 GACAACCCACAGAATGGGAGAAAATGTATGCAAACCACCCATCTTACAAG 3495
                                                  i v      i  ivi    v i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_98337328_9   3496 GGATTAATAACCAGAATATACAAGGAGCTCAAGTAACTAACTCTTTAGGA 3545
                            i vi  v          i  i  i   --- v  -     vv  iv 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTC---TTAC-AACTCAATAATA 793

  chrX_98337328_9   3546 AAAAATCTAATAGTCTGATTAAAAAATGAGCAAAAGATTTGAATAGACAT 3595
                             iv v    ii ii   ?       i     i               
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_98337328_9   3596 GTTTCAGAAGAAGACATTCAAATAGCAAACTAGTATATAAAATGGTGCTC 3645
                         v i  vi       i  v     i  v  iv  i i  i   v i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_98337328_9   3646 AACATCGATTGTCAG 3660
                               i????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 6.30 (63 / 10)  


2281 29.27 4.56 1.14  chrX_98396438_98399482.rev     1677  2554 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98396438_9   1677 TAGAGAAATATTTCATGCTTGTTGATTGGTAGAATCACTATAATTATAAT 1726
                          i  i i    ii    i ii v      v   v i v   vi   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98396438_9   1727 GGCCATACTGCCCAAAGCAAGTTACGTATTGAAAGCTAATCCTATCAAAA 1776
                            v     v      vii vi   iv   v  v  v vi          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98396438_9   1777 TACCAACATCACTTTTCATAGACATAGGAAAAACGATTATTAAATTCATT 1826
                          v   i vv vi    iii   v  v iv  ivi   iv v        v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_98396438_9   1827 TGGAACCACAAAAGAACTCAAATAGCCAAAAGAATCCTGAGCAAACAGAA 1876
                              vii   ii  v ivi           v    i   iv  iv    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_98396438_9   1877 CAAATCCAGAAGCATCACATTGTCTGACTTCAAACAATACTGTAGGGCTA 1926
                             viii  i vv     i vi ii i      vvv    ii ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_98396438_9   1927 CAGTAATCAAAATAGCATGGTACTGGTATAATAATAAACACACAGACCAG 1976
                                   i i  ii         i    vi   i   i i   i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_98396438_9   1977 TGGAATAGATTAGAGAACCCAGAATTAAAATGGCATGCCTACAACGATC- 2025
                                  v v    ii      v    vi--   i v vi -i i  -
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTA-TGGTCA 347

  chrX_98396438_9   2026 --TGATCTTCAACAGAATCAACAAAAAAAG-CAATGGGGAAGGGAC--TC 2070
                         --    i   i   iiiviiv   i vv v-          i i i--  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_98396438_9   2071 TTTATTCAATAA------CTGG--CAA----AT---CATATGCAGAAGAA 2105
                            --    i  ------    --   ----  ---  i     i     
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_98396438_9   2106 TGAAACTGGACACCCTGTCTCTCATCATATATGAAAATCAACTCAAGATT 2155
                             ii     -    ii   v  i      ii     i       i  v
  L1M4_orf2#LINE/    446 TGAAGTTGGAC-CCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_98396438_9   2156 TATTAAATACTTAAATGTAAGATCCCAAACTATAAAAATCCTAGATAAAA 2205
                         v  i ? v  i           v iv           v  i    vi   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_98396438_9   2206 ACCTAGCAGATACCCTTCTCAACATAGGCTTTGGCACAGAATTTATGGTT 2255
                           v   v? vv vi    vii  v v  v  v    vv iv  iv i v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_98396438_9   2256 AAATCCTTAAAAGTAATTGCAACAAAAATAAACATTAACAA-TGGGACCT 2304
                          viv vii     i vvv         iv   v  vi i  - v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_98396438_9   2305 GATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTATCAACAGAGTAA 2354
                         v  i   v v  i ii  i  ii vv    i  v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_98396438_9   2355 ACAGACAAACCACAGACTGGGAGAAAATATTTGCACAATATGCATCTGAC 2404
                          v      v       v                  v vi  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_98396438_9   2405 AAAGGTCTAACATCCAGCATCTATATGGAACT---------------TAA 2439
                           i  v  vii      v  v    vi     ---------------   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_98396438_9   2440 ACAGATTTTTAAA-AACC--ATTAAAACGTAGACAAAAAACATGAACAAA 2486
                          v   i----   -    --   ?   vi i i    ii iv    i i 
  L1M4_orf2#LINE/    795 AAAGAC----AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_98396438_9   2487 CATTTTTCAAAAGAAGACTTACCTGTGGCCAGCATGTGTATGAAAAGAAG 2536
                              i  v        iv   vvi      ii v iii         v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_98396438_9   2537 CTTAATATCACAGATCAT 2554
                           i  i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (144 / 110)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.12 (50 / 16)  


2991 27.50 2.13 0.22  chrX_98402126_98406338.rev     2832  3722 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98402126_9   2832 TGGAAAACTATTCTAGATTCATGAACTGAAAACATCAATATTGT-AAAAC 2880
                               iv   i i vi      i i  i  ivv i        -  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98402126_9   2881 GTTGATGCTACCCAAAACAATCTACAGATTCAATGCAATCCCTATGAAAA 2930
                          vii  i  v      vii              i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98402126_9   2931 TACTAATGACATTCTTCACAGAAGTAGAAAAAACAATCCTACATTTTGTA 2980
                          v i iivi v  i  ii     i v  v  ivii      v v  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_98402126_9   2981 TGAAACCATAAATGACCCAGAATAACCAAAGCTATCCTGAGCAAAAAGAA 3030
                           i  viii  iv           i     i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_98402126_9   3031 CAAAACTGGAGGAATCACATTACCTGACTTCGTATTATACTA-ACAGCTG 3079
                             ii       v     i v  ii i   iv viv     - v    i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_98402126_9   3080 TAGTAAACAAAACAGCATGGTACTTGCATAAAAACAGACACATAGACCAG 3129
                         i     v   i    ii       v      ii i     i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_98402126_9   3130 TGAAACAGAATAGAGAGCCCAGAAGACAACCCACATATCTAGAGTGAACT 3179
                           i  i     v     i      ivv      i i  i  vi  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_98402126_9   3180 CGTTTTTAAAAAACTTGCCAAGAAGATACACTGGGGAAGT--CAGTCTCT 3227
                         vi    ii v  ivv        vv  v  v       iv--i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_98402126_9   3228 TCAATAAATGATACTGTGAAAAGTGGATATCTGTATGCAAAAAAATAAAA 3277
                             i     i i   v  v  v      ? iii        i   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_98402126_9   3278 CTAGACCCTTATCTTGCAACATGTACAAAAATCTACTCAAAATGGATAAA 3327
                         i i     i  i  ii  v   i         iv             v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_98402126_9   3328 AGACTTAAATCTAAGAACTCAAACTATGAAACTACTACCA-AAAATATTG 3376
                             i     v     i  v       i     vi  vv -    i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_98402126_9   3377 GGGGAACTCTCCAGGACATTGGCCTGGGCAAACATTTCTTGAGCAATATC 3426
                          ? v  v   i iv   v    vi i     vvi      iiii vv iv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_98402126_9   3427 CCATAAGCACAGGCAAGCAAAGCAAAAATGTACAAATGGGATCACATCAA 3476
                            v       i    vv    v      iv i    v   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_98402126_9   3477 G-TTAAGAACTTCTGCACAGCAAAGGATTCAGTCAACTTAGTGAAGAGAC 3525
                         i-    i     i  ii vv       iv vi    vvv      i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_98402126_9   3526 AACCTAAAGATTGGAAGAAAATATTTGCAAACTCCCCT-TTTGACACGGG 3574
                             i v   v   i                -  viv - i   i v   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATAAGGG 749

  chrX_98402126_9   3575 ATTAATAACGAGAACATGTAAGGAGCTCAAACAAGCC--TAACAGAAA-- 3620
                          i vi  v v    i  i   i  i   vv    vi --   i i   --
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_98402126_9   3621 ---ATAATCTA--TTAAAAATGGACAAAATATTTGAATTAGACACTTCTC 3665
                         ---    i i -- ?        i    iv        -     i     
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT-AGACATTTCTC 848

  chrX_98402126_9   3666 ---AAAAGACACACTAATGGGAAACAGGCGTATTAAAAGGTGCTCAACAT 3712
                         --- i    i i  v     vv  i i  ii  v     i          
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_98402126_9   3713 CACTGATCAT 3722
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


3029 26.92 1.11 0.44  chrX_98449900_98454145.rev     2859  3757 (489)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_98449900_9   2859 AAAAATATGCCATATTCATGGATTAGAAGAATCAATATTATTAAAATGTC 2908
                            i    v    i          i     v i      i    i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_98449900_9   2909 CATACTACCCAAAGCAATCTAGAGATTCAATGCAATACCTAT-AAAATGC 2957
                         v     v      vii     v        i     v     -     v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_98449900_9   2958 CAATGACATTCTTCACATAAACAGAATAAAAAATCCTAACATTATTATGG 3007
                           iivi v  i  ii  v   iv  vv ivvi       v   vv     
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_98449900_9   3008 AACTGCAAAAGAACCAGAATAGCCAAAGCTATCCTGAGCGAAAAGAACAA 3057
                           v     ii  v              i v   i   ivi i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_98449900_9   3058 AACTCGAAGAAGAACATTACTTGATTTTAAGTTATACCACAAAGCTATAG 3107
                          ii v  i  vvv   i v iii    i  iviv   i         i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_98449900_9   3108 TAACCAAAACAGCATGGTACTGGCATAAAAACAGACACATACATCAGTGA 3157
                            i   i    ii              ii i     i   v    i  i
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_98449900_9   3158 AACATGTTAGAGAACCAAGAGATCAACCCATACCTCTACAGTGAATTCAT 3207
                           i viv v    ii v   i  v         v i  ii  v    v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_98449900_9   3208 TTTTGACAAAGTTGACATGAACATACACTGGGAAAAGAACAGTCTCTTCA 3257
                            i     i v  v  v  v   v  v    i      i     i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_98449900_9   3258 ATAAATGGTGCTGGGATAAGGGGATATCCATATGCAGAAAAAGAAAAATA 3307
                          i              i  vv     ?   i     i  i  vi  iv i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_98449900_9   3308 GACCCCTATCTCTCACCATATTCAAAAATCAATTCCAAATGGATTCAAAA 3357
                                 i   v        v       i  i  v        iv? i 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_98449900_9   3358 CTTCAATCTAAAACCTCAAACTAAGAAACTTCTAAAAGAAAACATTGAGG 3407
                          i v   v   i v  v      vi     ii  i          v i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_98449900_9   3408 TAACTCAACCAGGACATTGGTCTAGGCAAAGATTTCTTGAGCAGTATTCC 3457
                            v  -vi iv   v    vi       v i      iiii vv iv  
  L1M4_orf2#LINE/    554 TAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_98449900_9   3458 ACAAGCACAGGTAATCAAACAAAAA-TGGACAAATGAAATTACATCAA-G 3505
                          v       i i  iv   v     - i  i    vii i v      -i
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_98449900_9   3506 TTAGAAAGCTTCTGCAAAGCAAATGAAACAATCGACAAAGTGAAGAGACA 3555
                            i   -   i  iivvv    v  v  v   i v        i     
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_98449900_9   3556 AACCACAAAATAAGAAA-----TTGGCAAACCACCCACCTGACAAGAGAT 3600
                          v     i   ii  i -----  v     i  ivi i    i   i  i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_98449900_9   3601 TAGGAGGCAGAATATATTAGGAACTCGAACAACTTTTTAGGAAAAAAAAT 3650
                          v v vv          v i      vv      ivv  iv     i -i
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-C 800

  chrX_98449900_9   3651 TAACAATCTGACTTGAAAAATGAACACAACATCTGAATAGACATGTCTCA 3700
                         v  i  i ii -  ?       ii  v iv  i           v    v
  L1M4_orf2#LINE/    801 AAATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_98449900_9   3701 AAAGAA--CACACAAATGGCAAACAGGTATATGAAATGGTGCTCAATATG 3748
                               --i i         v  i i i i      v i       i  v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_98449900_9   3749 ATTAATTAT 3757
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.01 (9 / 905), avg. gap size = 1.56 (14 / 9)  


3075 27.55 0.59 0.59  chrX_98463178_98465522      992  1844 (501)    L1M4_orf2#LINE/L1        1   853 (55)  

  chrX_98463178_9    992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1041
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98463178_9   1042 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTTGTCAAGT 1091
                            v     v     iv i  i  i        i  v    i i    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98463178_9   1092 TACCAATGACTTTTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1139
                          v   iivi i     ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_98463178_9   1140 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1189
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_98463178_9   1190 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1239
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_98463178_9   1240 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1289
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_98463178_9   1290 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 1337
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_98463178_9   1338 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1387
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_98463178_9   1388 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1437
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_98463178_9   1438 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGA 1487
                            ii    i    v   i     v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_98463178_9   1488 TTAAAGACTTAAACACTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1537
                          i ?    i    iiiv   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_98463178_9   1538 CTAGGCATTACCATTCAGGACTTAGGCATGGGCAAGGACTTCATGTCTAG 1587
                         v    ?i v viv   iv   i v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_98463178_9   1588 AACATCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCTAA 1637
                         i   i        vvi          vv i   v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_98463178_9   1638 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1687
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_98463178_9   1688 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTGCTA-ATCTGGCA 1736
                           i     i   i             v       viii-  -     ii 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGATA 745

  chrX_98463178_9   1737 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1786
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_98463178_9   1787 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGGACAGACACTT 1836
                           i     i     v  i?    i     i     iv  i i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_98463178_9   1837 CTCAAAAG 1844
                            v    
  L1M4_orf2#LINE/    846 CTCCAAAG 853

Transitions / transversions = 1.60 (142 / 89)
Gap_init rate = 0.01 (7 / 853), avg. gap size = 1.43 (10 / 7)  


1377 28.21 12.02 3.93  chrX_98503003_98505739     1405  2244 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98503003_9   1405 TGGAGAAACATCC-----TCGTGAATTGAAAGACTCAACATGGTAAAAAT 1449
                             i i i    -----  i  i    i      i  i  v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98503003_9   1450 GTGGAAGCCTCTCCAAATTAATCCATAGGTTTAATTATTAATAACTCCTA 1499
                          - v  vv   i       i   i i  i  i  i-----ii  ii    
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGATCTACAGATTCAAC-----GCAATCCCTA 94

  chrX_98503003_9   1500 TCAAAATACCAGAAAGGCTTTTTATG-----GCTTACAAGGCTTATTTTA 1544
                                v    v--v  i    v  -----ii v     -  v  ii  
  L1M4_orf2#LINE/     95 TCAAAATCCCAGC--TGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTA 141

  chrX_98503003_9   1545 AAAT------GGCAAGGCACAAGACCTAAAATAGCTTAAAAAA-CTTGAA 1587
                             ------  v  v   vii    i i      iv   v  -      
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_98503003_9   1588 AAAACAAAAATTAAGTGAGATAAATTACTCTACCTGATACTAATGATTTT 1637
                            i-  i  iv    vi  vi v i  v  v  ii  vii  viv  vi
  L1M4_orf2#LINE/    192 AAAG-AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_98503003_9   1638 TATGTAGTTAAAGTAACCAAGTCAGTGTGGCAGTAGTGGTA----GATAG 1683
                           iiv  i  v     i    v        ---  v   i ----     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGG---TACTGGCATAAGGATAG 287

  chrX_98503003_9   1684 GCACATAATTCAATAAAACAGAAAAGGTAACCCAGAAATACAAAACCATC 1733
                         i  i   iv     ii  i    vv iv ii         --  v    v
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA--AACCCATA 335

  chrX_98503003_9   1734 CTAATATGCCCAACTGA-----GA--GGAGTGCTAAAGCAATTCAATAGT 1776
                          vvv    vi   i   -----  --i i    i  ii v       i v
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_98503003_9   1777 AAAAGGATATCCTTTTCAACAATTAGTACTAGAGCAACGAAGCACCTAAG 1826
                         i    i   vi           v i  i  i ii    viiii ? i vi
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_98503003_9   1827 GGCAAACAACTACAACAATAACAAAAGCGATACC--AAACCA---ACAAA 1871
                         v     ----- v  ii - iivii v vv    -- v    ---     
  L1M4_orf2#LINE/    436 TGCAAA-----AGAATGA-AGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_98503003_9   1872 --------CAAAAT--ACCCTTTTCCTATAC-------CTCACAC----- 1899
                         --------      -- i v?vvv    v i-------  v v  -----
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_98503003_9   1900 --CTCATACAA--------------AAATTTACTTGA------------- 1920
                         --   v  v  --------------    i v v   -------------
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_98503003_9   1921 AATGGAT-CATGAACTTGACACCAAAAATATAATCCACAGGAAAAAAAAT 1969
                              v - v ii iv           ii i  v v   ii i       
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_98503003_9   1970 AACAGAACTAGGCCTCATCAA--TT-----TTTTTGAATTTTCTACAAAA 2012
                          ivvi  i i i i       --  -----i     ---- v  v    i
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTG----TGCTTCAAAG 675

  chrX_98503003_9   2013 GACCTTGTTAAGAATATGGAAAGACAAGCTACAGAATGGAAG-------- 2054
                            vi i i     vi  i        v i         i  --------
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_98503003_9   2055 TAGAAACCACATATCCTATAATGGAATAATATATTGAATACATGAAGAAC 2104
                          iv   i  i     iv    v   v vi   viv     i  i      
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_98503003_9   2105 TTTCAAAGCTAAACAGTAAAAAAACAAAACAAAACAAAATACAATT-ATA 2153
                          i i v i  v  i i      i     v--------  iv     - v 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAAT--------AACCCAATTWAAA 817

  chrX_98503003_9   2154 AATGGACAAAAGACATGAACAGACATTTCACTGTAGAGTATATACAGATG 2203
                              i    i  iv    i         v iiv   iv       i   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_98503003_9   2204 AAAAATAAGCACATGGGGAGATAATCAACTTCATTAGCCAT 2244
                         ivv            iii    iv     v   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 4.32 (134 / 31)  


2502 23.24 4.22 6.05  chrX_98525335_98527398.rev      649  1573 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98525335_9    649 TAGAAAGCTATCCCATGTTCATACACTGGAAGAATTAATATCTTTAAAAT 698
                          i     v              iv i       v       iv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98525335_9    699 ATCCATAGTATTTGAAGTGATTTACAGATTCAATAAAATTTCTATCAAAA 748
                         iv v   v viiii  v    i           iiv   ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98525335_9    749 TTCCAATGGAATTTTTCATGGTAAGAGAATAAAACAATCA-AAAATTCAT 797
                          i   iiv vv     iiii v  vv  -i  ivii   v-         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_98525335_9    798 GTGCAGGCCTAGAAGATTCAGAATAGCCAAAACAATCTTGAGAAAGAAGA 847
                         i  v iiivi iii  ii                       i        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_98525335_9    848 ACAAATTTGGAAACATCACATTTCCTGATTTCAGTTTATACTACAAAGCT 897
                              v     iivv     i    ii      ivviv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_98525335_9    898 ATAGTAATCAAAATAGTACGGTACTGTTATAAAAAACAGACACATAGACT 947
                          i         i i   ii       vi    ii -i     i     ii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATC 298

  chrX_98525335_9    948 AATAGAATAAAA-----GGCCCAGAAAAAAACCTATACATATATTGTCAA 992
                            i     i  -----i i       v     i      v   v     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_98525335_9    993 CTAATTTTCAACAAGGGTGCCAAGAAAATACAA----GA-------GTCT 1031
                         i i      i               vv  v   ----  -------    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_98525335_9   1032 CTTCAATAAATGATGTTTCAAAAACTGAATACCCACATAAAAAAGAATAA 1081
                         i     i     i  i vvi v     i   ?      iv        i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_98525335_9   1082 AATTTGACCCTTATATCACA-----TGCAAAAATCAATT-AAAATGGATT 1125
                          i  v     i  iv     ----- i       i  i -         i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_98525335_9   1126 AAAAAT-TAAATGTAAATTCAGAAACCATTAATCTGCTAGATTAAAGCTC 1174
                          ? i i-         ivv vi    i  v  v  vi    vv   i vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_98525335_9   1175 AGGAA-AAGTGCTACTTGACACTGCTCTTTAGAATGGTTTTTTTTTGAAT 1223
                            ?i-  i -  v v    vi  -----------    -------- i-
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTG-----------GGTT--------AG- 577

  chrX_98525335_9   1224 ACTGCTCTTTAGAATGGTTTTTTTTTAATGGTTTTTTTTGA-ATTAAAA- 1271
                         ---  -------        i  v--i  i--------   - ii    -
  L1M4_orf2#LINE/    578 ---GC-------AATGGTTTCTTA--GATA--------TGACACCAAAAG 607

  chrX_98525335_9   1272 CACAGTCAGTAAAAGCAAAAATAAACAAGTGGAACTACATCAAACTTAGT 1321
                             iv  ii     v       i i  i v i   v       v   iv
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_98525335_9   1322 AACCTATGCACAGCAAAGGAAACAATCAACAAAATGAAAAGGCGAGCTAC 1371
                            i v  ii vv       v  v     v   i       i i v i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_98525335_9   1372 TGATTGGGAGAAAATATTTGTAAACCATATATCTGATAAGGAACTCATAC 1421
                         v  v                i   i                i   ii  -
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA- 756

  chrX_98525335_9   1422 AATTCA--ATA-GTAAATA-----TACA--TAAATAAGTAAATAAGTACA 1461
                         -- i  --   -i    v -----    -- v     -    -   -   
  L1M4_orf2#LINE/    757 --TCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAA-AAG-ACA 801

  chrX_98525335_9   1462 TAAAAATAACCCAATTCAAACATGAACAAAGG-TCCCAA-AGACATAATT 1509
                         ----            ?   v   ii      - iiv  -      --- 
  L1M4_orf2#LINE/    802 ----AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT---T 844

  chrX_98525335_9   1510 TTTTCATAGAATACATACAAAGGGTTAACAGATATATGAAAAAATTCTTA 1559
                          i i  v    v i       v  ii  i iii i       i  v  i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_98525335_9   1560 GCTTCATAATCATT 1573
                         i v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (135 / 76)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 3.06 (95 / 31)  


2695 27.62 2.12 1.00  chrX_98539735_98541987      863  1760 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98539735_9    863 TGGTAAAAATGTTCCATACTCATGAATTGGAATAATTAATATTTTTAAGA 912
                            -   i  i i    ii     i       v v        v      
  L1M4_orf2#LINE/      1 TGG-AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_98539735_9    913 TGTCTGTATTTCCAAAAGCAAGCTA-AGATTCAATGCAATCCCTATGAAA 961
                           v vi  i i  v   vii v   -        i           v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_98539735_9    962 ATATCAATGACATTCTCCACAGAAATAGGGAACACAATTCTAAAATTCAT 1011
                           vi  iivi v  i iii       v iv  vvii  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_98539735_9   1012 ATGGAAATGTGAAAGACCCCATATAGCCAAAGCAATCTTAAACACAAAGA 1061
                                  ii ii     viv         i       i  v vi    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_98539735_9   1062 AAAAAGCTGGTGGCATCACATTACCTATTTTTAATGTATACTATAAAGCT 1111
                          v    i   v  vv     i v  i v   i  viiv     i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_98539735_9   1112 ATAGTAACCAAAACACCATGATAATGGCATAAAAACAGACATATAGACCA 1161
                          i     i   i   vii  i  v        ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_98539735_9   1162 ATGGAGGAGAAAATAGAAACCAGAAAAAAATCCACACACTTACAACTAAC 1211
                              iv    vvv   iv       v   i   i   i   iiiii  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_98539735_9   1212 TGATTTTTGACAAAGGGAACAAGAATACACACTGGAGATTTTTAAAAA-- 1259
                                i     i  viv     vi iv  v   i  -----  i  --
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-----AAGAATA 394

  chrX_98539735_9   1260 GTCACTACCAAAAAATGGTGCTAAAGAAAATGGATATCCATATGCATGAG 1309
                            vi -i   v          iiiiv  v      ?   i     vi  
  L1M4_orf2#LINE/    395 GTCTTT-TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_98539735_9   1310 AATGCAACTAGATCCCTAGGTCTCACCAGATACAAAAAACAACTGTAAAT 1359
                             v ii i  i     vv  v     v         vi    vv    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_98539735_9   1360 GGATCAAGGACTTATATGTGACACCTGAAACTCTGAA--TGTCAGACGAA 1407
                               ?i   i  v    i v v  i     v i  -- v i   v   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_98539735_9   1408 AACATAACAGAGACACTTAATCAAATTGAACTTGGTATAAAGGTTTA--A 1455
                               iv? vi vv   vi v vv   iii v  i -- v     v-- 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA--ATGGTTTCTTA 591

  chrX_98539735_9   1456 AATAAGACCCCAAA-GCACATACAACAAAAACGAAAGTAGTGCAATGGAA 1504
                         i   v   v     -     vi        ivi   i   vvv   v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_98539735_9   1505 TTACATCAAACTAAAAAGCTTCTACACAGCTAAGGAAACAATCAATACAG 1554
                         i v       v v    i   i iii vv v     v  v     v v  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_98539735_9   1555 TGAAGAGACAAACTTCAG--TGAGAAAAAGTATTGGCAGACTATGCATCT 1602
                             i      v iv   --  i  i   i    v   i ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_98539735_9   1603 GGCAAGGGGATAATATCCAAAATATATAAGGAGCCCAAACAACTCAATAG 1652
                          ii     iv vi      i         i  i i vv           i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_98539735_9   1653 GAAAAATATAA-T--CCCATTTTTAAAATGGGCAAAAGA---GCCTA--- 1693
                         v     v i  - --    v  ?v            i  --- vv  ---
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_98539735_9   1694 ATTCCTCTAATGATGATGTAAAAATGGCTAACATATATATTTAAAAATGT 1743
                            i   i  v  v   i  v       i  i vii i  vv   i   i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_98539735_9   1744 TCAACATCACTAATCGT 1760
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (136 / 108)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  


2505 26.16 4.28 2.82  chrX_98543580_98548689      492  1378 (3732)  C L1M4_orf2#LINE/L1   (0)   908     9  

C chrX_98543580_9   1378 TATTTCAGATGCATAAAT-GTAAGACTCAATATAATTAATATGTCACT-- 1332
                            ii  vi v   ii  - v      i     vi    v   v  v --
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

C chrX_98543580_9   1331 TCTCCA---TGATATATTGCTAAATTCAATGCAATCAAAATCAAAATCCC 1285
                           i   ---    v  i---- i      i      vvv           
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTAC----AGATTCAACGCAATCCCTATCAAAATCCC 104

C chrX_98543580_9   1284 AGCATG---TTTTTGTGCATATCAAAAACCTGATTCTAAAATGTGTATGG 1238
                            -  ---      iiv v  ii v  v     i       vii     
  L1M4_orf2#LINE/    105 AGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

C chrX_98543580_9   1237 AAAGGTAAAGAAATTAGAAGAGCCAAAACAATTTTGAAAAGGAG---CAG 1191
                            v i  i i vii    v            i       i  i---  i
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

C chrX_98543580_9   1190 AGTTAGAGGACTTGCA-TACCTGATTGCAAGTTTTTTCTCTAAAACTACA 1142
                             i       ii  - v  ii   v   ivi  v-  vi   i     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTACAAAGCTACA 252

C chrX_98543580_9   1141 ATAATCATGAAAATCTGCTATGGGCAAAAGGATAGAAATATGGAAGAGAC 1092
                         i      v  v i v  v  iv    v         v    -----   i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT-----AGAT 297

C chrX_98543580_9   1091 TAACAG--CAGCATAAAGCTTTCAGAAGTAGATTCACACAAATATAAACA 1044
                         i  ii --i  v  vi  vv i     i  i ii  i   vv   iiv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

C chrX_98543580_9   1043 AGTTACTTTTGATGAAAGCAATTGCAAAGAGAATTCAATGGAGAATGGTT 994
                          v v i   i  ii ii ----   v    vv         i   v iv 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGG----TGCCAAGACCATTCAATGGGGAAAGAAT 393

C chrX_98543580_9    993 AATCTTTTCGACAGGTGGTAGTGGGACCATTACTTGGATGTCCATACACA 944
                          i       i   ii    iv      v i ----    i?   i ii  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACT----GGATAKCCACATGCA 439

C chrX_98543580_9    943 AAATAATGAAGCTAAACACATGCCAGATACTATATTGTATATAAAACAT- 895
                            v       i ii  v v i  vv i  i    ----- i    -  -
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATAT-----ACAAAA-ATT 483

C chrX_98543580_9    894 -ATTCAAAATGTATCACAGACATAAATATAAAACATGAACTTACAAACTT 846
                         - i        v    ?    v     i   i vv i  vi  i   vi 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

C chrX_98543580_9    845 TCTAGAAGAAAACATGGGAGAAAATTTCCATGACCTTGTTTTAGCAAATA 796
                         ii             i  ? v    i i i        vv    vv   i
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

C chrX_98543580_9    795 ACTT-TTAGACATGACAGCAAAAGTTCAATTCAT----TACAAAACAGAC 751
                         ii  -     i      v      iv   viv i----v v    i   i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

C chrX_98543580_9    750 AAATTGAATTTCATCAAAATTAAAA--TTTTTTTCTGGAAAG-ACACTAT 704
                               i i                --    v v  vv    -       
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

C chrX_98543580_9    703 TAGAAGAATAAAAATCTAAAACACTGACTTGTAGAAG-TATTTGCAAATC 655
                         i ii i i i    vvi  vv   v  v v v    i-            
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

C chrX_98543580_9    654 TCATTTCTGAAAAAGAACTTGTATCCAGAATATGTGAACAACTCTTATAA 605
                         vi  v     v  i i                 i i  v        i  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

C chrX_98543580_9    604 CTCTACAA-GAAAGGA--AACAACCCAATTTGAAAAT---------ATTT 567
                            v i  -i   i  --  i         ?i     ---------    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

C chrX_98543580_9    566 AAATAGATGTTTTATCAAGGAAAGCATATGAGTGGCAAATAAATATAGGA 517
                         i      ii   ivi   i   iii   ii i    v     ii i v  
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

C chrX_98543580_9    516 AAATATGTTCAACATTATTAGTTAC 492
                            v   i       i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (138 / 90)
Gap_init rate = 0.03 (24 / 900), avg. gap size = 2.62 (63 / 24)  

3139 26.34 0.88 1.21  chrX_98543580_98548689     3707  4617 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98543580_9   3707 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3756
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98543580_9   3757 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3806
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98543580_9   3807 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 3853
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_98543580_9   3854 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 3903
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_98543580_9   3904 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 3953
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_98543580_9   3954 CTACAGTAACCAAAACAGCATGGTCCTGGTACCAAAACAGAGATATAGAT 4003
                                  i   i    ii    v    i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_98543580_9   4004 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACTGCATATCTACAAC 4051
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_98543580_9   4052 TATCTGATCTTTCACAAACCTGAGAAAAACAAGCAATGGGTGCTGTTTTT 4101
                         i vi    i  iv    ivv  vv  i v  vv       vivv -----
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG----- 390

  chrX_98543580_9   4102 AATAAATTT---AATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAG 4148
                             ivi  ---  i  i           v      v  ?   i   i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_98543580_9   4149 AAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAA 4198
                           iiv    ii    i    v   i     v           i  i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_98543580_9   4199 GATGGATTAAAGACTTAAAACGTTAGACCTAAAACCATAAAAACCCTAGA 4248
                         i      i ?    i    -i  v   v       i      vi i    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_98543580_9   4249 AGAAAACCTAGGCATTACCATTCAGGACCTAGGCATGGGCAAGGACTTCA 4298
                                v    ?i v viv   iv     v  vv i     v ii   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_98543580_9   4299 TGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAACATTGACAAATGG 4348
                          ivv  vi            vvi          vv  v  v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_98543580_9   4349 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAG 4398
                           ii v  i   v v  i i   i  ii vv    i  v    i  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_98543580_9   4399 AGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCAT 4448
                               v  i     i   i             v  i    vii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_98543580_9   4449 CTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAC 4498
                             i  i  i  vi          v  i  v      vv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_98543580_9   4499 AAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAG 4548
                           v     i     i     v  i?    i           iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_98543580_9   4549 ACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAAT 4598
                            i     v        i  vi viii     v  i          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_98543580_9   4599 GCTCACCATCACTGGCCAT 4617
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


1830 28.92 1.20 1.81  chrX_98554848_98556484.rev      487  1150 (487)    L1M4_orf2#LINE/L1      249   908 (0)  

  chrX_98554848_9    487 TACAGTAACCATTTCACCAAAGCAACATGGTATTACTATAAATACAGATA 536
                                 i  -------- ii  iii     i ivi    iv i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCA--------AGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_98554848_9    537 CATAAGTCAATGGAACAGAATAAATAACTCAGAAAGAAATCTACATATTT 586
                         i   ii         i     vi v iii      v   i i i i    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_98554848_9    587 ACCGCCAACTGATTTTTGACAAAAGTACCACAATCATACATTGAAGAAAA 636
                          iv i   i       i     ii  i   vi i   v  v  ii    i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_98554848_9    637 GACACCCTATTCAATAAATTATGCTGAAA-AAGTGTATGTCCATATGCAG 685
                         i i vi  v     i    vi     ii -  v  v  i?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_98554848_9    686 AAAAACGAAACTGGACTGCTATCTCTTACTATATGCAAACATCAACTCAA 735
                           i  i   ii     iv   i   vi  i    i    v  i       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_98554848_9    736 GATGGATTAAAAACTTAAATGTAAGACTTAAAACTATTAAACTAGTAAAA 785
                         i      i ? i  i           vi         v     vv  i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_98554848_9    786 GAAAACATAGGA--AAATCACTTTAGGAATTTTGTCAAGGCAAATATTTT 833
                                    ?--     --  iiv  vi  v viv      vvi   i
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_98554848_9    834 ATGGCTAACGAC-TGAAAAGCACAAGAAACAAAAGCGAAATTAAAAAAAT 882
                         v i v  -i   -iv           v        vi   v  i v    
  L1M4_orf2#LINE/    589 TTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_98554848_9    883 GGAAGTATATTAAACTAAAAAGCTTCTATACAGCCAAGGAAACAATCAAT 932
                         v i v vi  i   v v    i   i i i vv v     v  v     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_98554848_9    933 AAATTAAAGAGAAAATCTTTTGAAAGGGAGAAAATATTTATATACTATTG 982
                            v i  i   v  i iviv   v              ii v ii  vv
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_98554848_9    983 ATCTAACTAGTGACTAATATCCAGAATATGCAAGAATCTCAAATAACCCA 1032
                             i iv  v    vi            ii  ii v   vv i   i  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_98554848_9   1033 AAAGTTAATAAACTAATAATCCCATTAAAAAGTGAAGACAGTGCATAAAT 1082
                          v i v  v i  v     i  v   ?    i  iiv v  viiv i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_98554848_9   1083 CAAAATTTCTC----AAAAATATACAAATGGCCAACAAGTATATTGAAAA 1128
                         vi v       ----i  i                i   i i  -     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-GAAAA 886

  chrX_98554848_9   1129 AATGCTCAGCCTGACTAATCAA 1150
                         i       i v v ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (115 / 73)
Gap_init rate = 0.01 (8 / 660), avg. gap size = 2.50 (20 / 8)  


1843 27.26 4.22 1.20  chrX_98561279_98562931      497  1160 (493)    L1M4_orf2#LINE/L1      225   908 (0)  

  chrX_98561279_9    497 CAATTC--AAACTATACTATAAGGATACAGTAACCCAAACAGCATGGTAT 544
                              i--     -     i  i v        i v i    ii     i
  L1M4_orf2#LINE/    225 CAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_98561279_9    545 TGGTACAAAAACAGACACATAGACCAATTGAAAAGAATAGAGGGCCCAGA 594
                            i i  ii i     i     i    v   v     v   i i     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_98561279_9    595 AATAATTCCAGGCACCCACAACCCTCTAATCTTCAACAAAGTCTACAAAA 644
                              vi   vi  iii iiii vvi i  i   i    i vivv   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_98561279_9    645 ATAAGCAATGGGGGAATGACTAG-CTACTCAA-AAATAATGCTGGTATAA 692
                         vi vv        i  -  v   -  vi    -    ii      v i  
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_98561279_9    693 CTGGCTAGCCATATACAGAAGATTGAACCTAGACTCCTTCTTTACACCAT 742
                             v  ?   i  i  i    v    vi i   i   v i i       
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_98561279_9    743 ATTCAAAAATGAATTCAAGAT------------TAAATGTAAAACCTGAA 780
                           v       v  i    i  ------------         i v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_98561279_9    781 ACTATAAAAATCCTGGAAGATAACCTAGGAA-ATATCATTGTGGACATAG 829
                                  v  i i     v   v    ?i- v   v i   -  v v 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTG 571

  chrX_98561279_9    830 GCCTTGGTAAAAATTT--TACGATGAAGATGCCAAAAGCAATTGCAACAA 877
                          vi v  i  vii   --  -   - v  ii         vvv       
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTA-GAT-ATGACACCAAAAGCACAAGCAACAA 619

  chrX_98561279_9    878 AAACAAAACGCGACAAGTGTCAACT-------AATTAAAGAGCTTCTGCA 920
                           iv    vvv  i  i - vi   -------       i -   i  ii
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAAT-TGGACTTCATCAAAATTAAAAA-CTTTTGTG 667

  chrX_98561279_9    921 CAGCCAAAG--TAATGTCAACAGAGTAAATAGACAACCTACAGAATGGGA 968
                          -vi     --i v i    v i   i  v        i           
  L1M4_orf2#LINE/    668 C-TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_98561279_9    969 GAAAACATTTGCAAAGTATGCATCCAACAAAGGTCTAATATTCAGAAATT 1018
                              i         vi  ii   ii i  i  v  vi   i     vv 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_98561279_9   1019 TTCAGGAACTTAAGCAAATTTATAATTAAAAACCCAACAGCCCCATTAAA 1068
                         v v i     ivvi   v iv     v    iv v  i i   v   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_98561279_9   1069 AAGTAGACAAAGCGCATTAACAGACACTTTTCAAAAGAAGACATACATGC 1118
                           i i i     viiv v  i     i  i  v        i     vii
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_98561279_9   1119 AGCCCACAAGCATATGAAAAAATGCACAAAATCACTGATCAT 1160
                         i   v i     i       i    v   v    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (107 / 71)
Gap_init rate = 0.02 (16 / 684), avg. gap size = 2.25 (36 / 16)  


2787 28.30 1.44 0.78  chrX_98571406_98580778      492  1392 (7981)  C L1M4_orf2#LINE/L1   (0)   908     2  

C chrX_98571406_9   1392 GAAAAAAAATTCCATGTTCATGGATAGAAAGGCTCAATATTATGAAAATG 1343
                          i   i v  i              v i   i  i      i v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

C chrX_98571406_9   1342 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTTCCATCAGGCT 1293
                           v     v      v i  i  i        i  v  ii i    iiv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

C chrX_98571406_9   1292 ACC-GTTGGCTTTCTTCAAAAAATTAGAAAGAACC-ACTTTAAATTTCAT 1245
                         v  - i  v    i  vv i     iiv   -- i- iii    v     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCAT 149

C chrX_98571406_9   1244 ATGGAACCCAGGAAGAG-CCCATA-TAGCCAAG-CAATCCTAAGCAAAAA 1198
                               vi-- v   i -    v -       i-     i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAAT--GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chrX_98571406_9   1197 TAACAAAGCTGGAGGCATCATGCCACCTGGCTTCAAACTATACAACAAAG 1148
                         v       i      vv   ii iv  iiii      viv   v      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chrX_98571406_9   1147 CTACAGTAACCGAAACAGCACGGTATTGGTACCAAAACAGATATATAGAC 1098
                                  i i i    iii    i   i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chrX_98571406_9   1097 CGATGGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTGCAACCA 1048
                          i      i     v   ivii         vv   i    i iiiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

C chrX_98571406_9   1047 TCTGATCTTTGACAAACTTGACAAAAACAAGCAATAGGGAAAAGATTCCC 998
                         vi    i  i     ivv  v   i v  vv    i      ii  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chrX_98571406_9    997 TATTTAATAAATGGTGCTGGGAAAACTAGCTAGCCATATGCAGAAAACAG 948
                          v  i  i              v    i v  ?   i     i  i vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chrX_98571406_9    947 AAACTCCACCCTTTCCTTACACCTTATACAAAAATTAA-----GATGGAT 903
                           ii vv    i v   i     v              -----i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

C chrX_98571406_9    902 TGAACACTTAAATGTAAAACCCCAAACCATAAAAACCCTATTAGAAAACC 853
                         ii? v  i         i v iv    i      vi i  vv       v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

C chrX_98571406_9    852 TAGGCA-ATACCATTGAGGGCATATGAATGGGCAAAGACTTAATGACTAA 804
                             ?i- v i v i v iv v i- iv i     v ii  vv iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_98571406_9    803 AACACCAAATGCAATTGCAACAAAAGCCAAAATTGACAAACGGGATCTAA 754
                         i        v   vvv          vv     v  i   iv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_98571406_9    753 TTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTATCATCAAAGTGAAC 704
                          i   v v  i i   i  ii vv       v       vv        v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_98571406_9    703 AGTCAACCTTCAGAATGGGAGAAAATTTTTGTAATCTATCTATCTGACAA 654
                           v     iv                v    i  vii  v       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chrX_98571406_9    653 GGGTCTAATATCGAAAATCTATAAGGAATTTAAACAAATTTACAAGTAAA 604
                            v  vi    v i   v     i   i ivv    v iv i  -    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAA 795

C chrX_98571406_9    603 AA--CAAACAACCCCATCAAAAAGTGGGGGAAGGAATATGAACAGACACT 556
                           --    i     v  i?    i    vi     v -    i     i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT-TGAATAGACATT 844

C chrX_98571406_9    555 TCTCCAAAAAAGACATTTATGCAGCCCACAGACATATGAAAAAAAGCTCA 506
                                 i    i  vi viii   v i ii  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chrX_98571406_9    505 TCATCACTGATCAT 492
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (147 / 104)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 1.54 (20 / 13)  

1939 27.49 3.74 6.63  chrX_98571406_98580778     7946  8880 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98571406_9   7946 TGGAAA-ACATCC-ATGCACATGGATTAGAAGAATCAATATTATTAAAAT 7993
                               - i    -   iv        i     v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98571406_9   7994 GCCCATAATGCCAAAAGCAATCTATAGATTCAATGCAATTCCTATCAAGA 8043
                          v v   v v  v   vii     i        i     i        i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98571406_9   8044 ACCAACATCATTTTTCCTAGAACTAGAAATAACTATTCTAACATTCAAAT 8093
                         --------------   i  ------------  iiii ---------- 
  L1M4_orf2#LINE/    101 --------------TCCCAG------------CTGCCTT----------T 114

  chrX_98571406_9   8094 TTTAGAGTATTTCATAATTTGAATATTTTATATTTCATAATTAGAATATT 8143
                            iv  v v  v i  vi   --- ii  v v      -- i   ----
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGA---TCCTAAAATTCATA--TGGAA---- 155

  chrX_98571406_9   8144 TCATGATTAGAATATTCATAATTTGAATAGCCAAAGTAATTCTAAGCAAA 8193
                         --   --i iiiv ii  ------           ii   ii i iv  i
  L1M4_orf2#LINE/    156 --ATG--CAAGGGACCCA------GAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_98571406_9   8194 AAGAACAAAGCCAGAGATATCACATTACCTGACTTCGAACTATACACCAA 8243
                                   iii   ivv     i v  ii i   i  viv   vv   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_98571406_9   8244 GACTACAGTA-CCATAACAGCATGGTACTCATACAGAAACAGACACATAG 8292
                         ii        -i  vi    ii       vii i iii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_98571406_9   8293 AACAGAGGAACAGAATAGTAAACCCAGAAATAAAGCCACACAC----AAC 8338
                          v  iv    i     v vi ii           v   i   i----iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_98571406_9   8339 CATCTGATCTTCAACAAAGTCAATAAAAACAAGTAAATGAGAAAGGAT-- 8386
                           vi    i   i    i viivi  i v  vvi  vv i     i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_98571406_9   8387 TCCTGATCTGATAAATGCTGTTGATGTATCTAGCTAGCCATATGTAGATT 8436
                           i -- iii i     v  i  ivii v  i v  ?   i   i i vv
  L1M4_orf2#LINE/    396 TCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_98571406_9   8437 AATGAAACTGGACACCTACCTTCCGCCATATACAAAAATTAACTCAATGT 8486
                               ii     v       iv i                      vi 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_98571406_9   8487 GTATTAGATATATAAATGTAAGACCTCAAACTATGAAAATCCTAGAAGAA 8536
                          v  i ? v iv           v  v       i   v  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_98571406_9   8537 AACCTAGAAGAAAATTCTGGACATAA----GAGTTGGGAAAGAGTAT--- 8579
                            v   i? v    ii --- i i ---- i   i  v  vi  v ---
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTT---CGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_98571406_9   8580 ---TAAGACCTCAAAAGCAATTGCAATAAAAACAAAAATTCACAAGTGGA 8626
                         ---  v   vi        vvv    i    iv      vv i  i v i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_98571406_9   8627 AACTAATTATACTAAAGAGATTTTGCACAGCAAA--ATA--ATCAACAGA 8672
                          vi v  i v v v  i iv     ii vv    -- i --     v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_98571406_9   8673 TTAAATAGACAACATACAGAATGGGGGAAAGTATTCA-AAACTATACATA 8721
                         v i  v       vi          i    i    ii-   ii   i  v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_98571406_9   8722 TGGCAATGGTCTACTATCCAGAATCTATAAGGAACTT----AATTTGATA 8767
                           ii  v  v  vv          v     i     i----  i ii   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_98571406_9   8768 AGCAAAAAACAA----CCCCATTAAAAAGTGGGAAAAGGAAACCAAGAGA 8813
                          vv    i    ----   v   ?    i    v      vviv  v   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_98571406_9   8814 CGTGTCGCAAAAGAAAACTTG--AGTGGCCAATAAACATATGAACAAATT 8861
                          i v  v v      i iv i-- i          i  i     v i  -
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT- 889

  chrX_98571406_9   8862 GC-CAATTGTCAATTATTAA 8880
                           -   i-i   ????????
  L1M4_orf2#LINE/    890 GCTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (154 / 99)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.73 (97 / 26)  


2487 28.68 2.46 1.12  chrX_98583045_98588535     4105  5000 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98583045_9   4105 TGGAAATATATACCATTCTCACAGATTGGAAGAAGCAATATTGTGAAAAT 4154
                               v    v    vi   ii          vvi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98583045_9   4155 GACCATACTGCCCAAAGCTATTTACAGATTTGATAAAATTCCTATCAAAA 4204
                          i v     v      viv  i        ii iiv   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98583045_9   4205 CACTAACATCATTTTTCACAAAATTAGAGAAAACAATCCTAAAATTCATA 4254
                         iv i i vv v     ii  i  v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_98583045_9   4255 TGGAACAAAAAAAAAACCATA-TAGCCAAAGCAATCCTAAGTAAAAAGAA 4303
                              vviv  iii v   v -        i     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_98583045_9   4304 TAAATCTGGAGGCATCAAATTACCTGACT-CAAATTATACTATAAGGCTA 4352
                         i   vi      vv   v i v  ii i -    viv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_98583045_9   4353 TGGGAACTAAACCAGTATGCTACTAGCATAAAAGTAGATACATAAACCAA 4402
                         ii v  ii  iv    i  v    i      iii    i i   i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_98583045_9   4403 TGGAACAGAAT--AGAGTACGGACAAATAAAGCCAAATACTTACAACCAT 4450
                              i     --     v i  --      v   v i i   iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGA--AATAAACCCATACATTTATGGTCAA 348

  chrX_98583045_9   4451 CTGATCTTCAACAAAGCATGC--AGACACATGAACTCGGGAAAGGACACC 4498
                         i    i   i    i -i   --    -   vv v v       i i vi
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGAC-CATTCAATGGGGAAAGAATAGT 396

  chrX_98583045_9   4499 CGATTTAATAAATGGTGCTGGGGAAAATAGATAGCCATGTGTAGAAAAAC 4548
                          vv  i  i             iv  v i    ?   ii  i i  i  i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_98583045_9   4549 GAAGTTAGATACCTATTGCTCATCTCATATAACAATCAACTCAAGTTGGA 4598
                               i  iv    iiv v  i vi   i  v   i       iv    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_98583045_9   4599 TTAAAGACTTAAGTCTAAGAACTGAAATCATAAAGGTTCTGGAAGAAAAC 4648
                          i ?    i   i v     i  i   ii     iv ii i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_98583045_9   4649 CTAGGAAAAACTCTTCTGGACAATGACGTAGGCAAATAATTTAT--GACT 4696
                         v    ?iv  v     vv   vv  ivv       - ii   v --  - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGA-T 594

  chrX_98583045_9   4697 AAGACCTCAAAACCAAATGAGACAAAAAACCCATAAATTAATAAATGAAG 4746
                          v   vi     v  v v vi      i --- v    vi      viii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGA---AAAAATAGATAAATTGGA 641

  chrX_98583045_9   4747 CTT-----AAACCAAAAAGCTTTTGCACAGTAAAAGAAATAATCATCAGA 4791
                            -----   ii     -      ii vvi   i  v iv    vv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_98583045_9   4792 GT----AGTCAACCCAAAGAATGAGAGAAATTAGTTGCAATCTATGCATC 4837
                           ----  v       v      i      v  v      vii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_98583045_9   4838 CAACAAAGAATTAAGGTGCTGATTCTACAAGGAATGCAAACAGATCAGCA 4887
                         ii i  i i i vivi v v  v v  i  i   iv vv   iv   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_98583045_9   4888 AGAACAAAACAAATTATCCCATTTAAATGTGGGCAAGTGACATGAATGGA 4937
                          v  v  i      v i  v   ?   vi       iv  iv     i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_98583045_9   4938 CATT-CTC---AGAAGATATACAAATGGCCAAAAAACGTATGAGAA-ATG 4982
                             -   ---                     v  i ii    i  -   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_98583045_9   4983 CTCAACATGACTAATAAT 5000
                                 v ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (148 / 105)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.88 (32 / 17)  


2356 25.92 2.33 4.42  chrX_98605604_98609826      492  1305 (2918)  C L1M4_orf2#LINE/L1   (0)   908   112  

C chrX_98605604_9   1305 TTCTTCACAGAACTAGAAAACGTAATCTTAAA-TTTATATGGAAACACAG 1257
                           i  ii     v v  v  vv i   i    -  i         ii  i
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

C chrX_98605604_9   1256 AAGGCCAAGAATAGCCAAAGCTATCCAGAGCAAAAATAAAAACAA--CTG 1209
                         ii i  v            i v   iv  ---    v  i     --i  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGA---AAAAGAAGAACAAAGTTG 208

C chrX_98605604_9   1208 AAGTAATCACATTACCTGGCTTC------TACTATAA-GCTACAGTAACC 1166
                         i  v v     i v  iiii   ------     i  -          i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

C chrX_98605604_9   1165 AATACAACATGGTACTGGCATAAACACACACACACACACACACACACACA 1116
                           v   iii              iv i v   i i --------------
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATA-------------- 294

C chrX_98605604_9   1115 CACACACACACACACAGATCAGTGGAGCACAACATAGAATGCAGAAACAA 1066
                         ----------------     i    ii v  ivv   i v      i  
  L1M4_orf2#LINE/    295 ----------------GATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

C chrX_98605604_9   1065 ATCCATACATCTACAGTGAACTCATTTCCAATAAAGATGTCAAGAAAAAT 1016
                          i        i  ii  v  i v    i i i  i i  i     vv v 
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

C chrX_98605604_9   1015 CACTGGGGAAAGGGAAGTCTCTTCATTAAACGGTGCTAGGAAAAATGGAT 966
                           v         iiv     i    vi   i      i   v  v     
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

C chrX_98605604_9    965 ATCCATACGCAGAAGAATAAAACTGGAGTCCTATCTGTTGCCATTTACAA 916
                          ?   i i   i      i  ii    vi    i  vvii    v     
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

C chrX_98605604_9    915 AAATCAAATTAAAATGGATTAAAAAC--AAATCTAAGGGCTGGACCTCTG 868
                             i  v i         i ? i  --    v    i   ii v  v i
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

C chrX_98605604_9    867 AAACTACTACAAGAAAACTTTGAGGCAGCTCTCCAGTACATTGGACTGGG 818
                              vi  v        v v i? i iv   i ivv  v    ii i  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

C chrX_98605604_9    817 CAAAGAGTTTTTGAGTACTACTTTACAAGCACAGGGAGCCAATGCAAAAA 768
                            v iv  i  iii  iv  vii v       i v i v  v v     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

C chrX_98605604_9    767 TGGACAAATGGTATCACATCAA--CTGAAAAAGTTTCCACATAGCAAAG- 721
                          i  i    v v iiv      --i i    vv   vii v --     -
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGG 676

C chrX_98605604_9    720 -CA--ATCAACAAAATGAAGAGAAAACCCACAGAAGGGGGGAAAATATTT 674
                         -  --     v   i    i   v           v   i          
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

C chrX_98605604_9    673 GCAGTCTCTCTATCTAACAAGGGATTAATAACCAGAACACATAAAAAGCA 624
                            iviiv v     i i      i vi  v      i i     i i v
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

C chrX_98605604_9    623 TAAACAATTCTATATGAAAAAAATCTAATAATTCAATT-AAAAATGGTCA 575
                         ivv    i  v   vv     i - v     ii     -        v  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCA 825

C chrX_98605604_9    574 AAAGATCTGAATAGACATTTCTCAAAAGAAGACATACAAATGGAAAATAG 525
                           i   i                v        i          vv    i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

C chrX_98605604_9    524 GTATATGAAAAGGAGGTCAATATCATTAATGAT 492
                          i i        iv v    i    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (126 / 82)
Gap_init rate = 0.02 (13 / 797), avg. gap size = 4.23 (55 / 13)  

2700 22.97 3.57 0.86  chrX_98605604_98609826     2536  3236 (987)    L1M4_orf2#LINE/L1        3   722 (186)  

  chrX_98605604_9   2536 GAAAGATATCCTATGTTTATTTACTGGAAGACTTAATATTATTAAAATGG 2585
                                    i     i  vv i                i    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_98605604_9   2586 CACTACTACCCAAAGTGACAAAGATATTCAATAAAATCCTTATCAAAATT 2635
                           v    v      v   ivv v v      iiv     i         i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_98605604_9   2636 CCAACGGCCTGTTTTGAAGAAATAAAATAAATAAATCTTCAAATGAATAT 2685
                            i v    v     v      vi -i  iivi   i v    vv    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATAT 151

  chrX_98605604_9   2686 GTAAGTGCAAGAAGCCTCAAGTAGTCAAAAAAATTTAGTAAAAG-----C 2730
                          v  i      iii  ivi i   i     v   i v v     ----- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_98605604_9   2731 AAATGTAGGAGAACTCACACTTACTGATTTCAAAACTTATTATAAGTCTA 2780
                            -  v    i          v ii             i  i  iv   
  L1M4_orf2#LINE/    202 AAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_98605604_9   2781 CAGTAGTCAATACAGTGTGATACTTGCATAAAAATGGACATATAGACCCA 2830
                              i    v        i    v      ii  i          i v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_98605604_9   2831 TGGAATAGCAA--AAGCATTCAGAAACAAACCCACTTACCTATGG--AA- 2875
                                 -  --i  vi i      i       ivi ii     --  -
  L1M4_orf2#LINE/    301 TGGAATAG-AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_98605604_9   2876 -GATTTTCAGCAAAG-TCCAAAGAAAATTAAACAGAAAAAATAATAGTCC 2923
                         -       ii   i - v v    vv   v  ii ii   i-       i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCT 398

  chrX_98605604_9   2924 CTTCAAAACAGGATGCTGGAACAACTAAATATCCACATACAAAGGGATGA 2973
                         i     v v v i      i      ii   ?      i    i i    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_98605604_9   2974 ACTTGGACCCCTACTTCACACAACGTACAAAAAAGTAACTCAAA-TAAAC 3022
                          v            i      v ii        -v         - ii i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGAT 497

  chrX_98605604_9   3023 CCATGACATAGATCGCAGAGCAAAAACCACAAATCTCTTAGAAGAAAAGA 3072
                          v?v   v  i  vvv     v     i i   v              v 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_98605604_9   3073 TAGAGATAAGTTTTCATAACTTTTAATTTGGCATTAATTTCTTAAATATG 3122
                            i?i   i i   i i  i  vii  v    v ii       i     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_98605604_9   3123 ACACAGAAAGCATGAGCAGTGAAAGAAAAAAATTGATAAATTTGACTTTA 3172
                             vi      ii    iii          - v        v     i 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCA 646

  chrX_98605604_9   3173 TCAAAATTAAAAACTTC-GTGCATGAAAGAACATTATCAAGA-------- 3213
                                         i-    v v    i   i        --------
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_98605604_9   3214 ---CAATCTAATGAATGGCAGAAAAT 3236
                         ---   i i vv      v       
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAAT 722

Transitions / transversions = 1.55 (96 / 62)
Gap_init rate = 0.02 (14 / 720), avg. gap size = 2.21 (31 / 14)  

 742 18.48 5.21 0.47  chrX_98605604_98609826     3521  3731 (492)    L1M4_orf2#LINE/L1      688   908 (0)  

  chrX_98605604_9   3521 AAAGAAAAAAAAAAA-----AAAA-GGCAGAAAATATTTCCAAATCGTAT 3564
                             vi    i v  ----- i  -  v           v      i   
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_98605604_9   3565 ATCT---AAGAGTCTAGTATCCACAAAATA-AAAGTAATGTTTACAAGTC 3610
                             ---   i v  v       v  v   -    -  ivi      v  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAG-AACTCTTACAACTC 786

  chrX_98605604_9   3611 AGTAACAAAAAGGCAATAAATTCCACTTAAAAATGGGCGAAATAATTCAA 3660
                          i   i      i   vv  ii v i ?          i  iv v  v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_98605604_9   3661 TAGACATCTCTCCAAAGAAGATACACAAATGACCAGCAAACACATGAAAA 3710
                                i               i       i   ii  i          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_98605604_9   3711 TATGCTCAACAT-ATTTAGTCA 3731
                         v           - ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (21 / 17)
Gap_init rate = 0.03 (6 / 221), avg. gap size = 2.00 (12 / 6)  


2099 27.61 2.24 5.44  chrX_98619964_98623796     2409  3346 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98619964_9   2409 TAGAAAAACATTCTATGTTCATGAATAAAAATAATTAATATCTTTAAAAT 2458
                          i    i i  i i         i  vii  v v       iv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98619964_9   2459 GACCATACAGCCCAAAGCAATTGGC---TTCAATGCTATTTTTATCAAAA 2505
                          i v    vv      vii  ivi ---     i  v  iii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98619964_9   2506 TACCAATGAGATATTGT-CATGGAATAAGAAAAACT-ATTGTAAAATTCA 2553
                          v   iivivv v  v -  - i   v-  v  i  -  iv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATT-GACAAGCTGATCCTAAAATTCA 148

  chrX_98619964_9   2554 TATGGAACAACAACAAAAAAACTA-AATAGCCAAAGCAATCCTCAGCAAA 2602
                                -- ii-   iii v i -          i     i ----i  
  L1M4_orf2#LINE/    149 TATGGAA--ATG-CAAGGGACCCAGAATAGCCAAAACAATCTT----GAA 191

  chrX_98619964_9   2603 AAAATAAAAATAAAAAAATAAAATAAATAAAAAATAAACAACCCAGAGAC 2652
                            i---------  i  i   i --- ii i---------------   
  L1M4_orf2#LINE/    192 AAAG---------AAGAACAAAGT---TGGAG---------------GAC 214

  chrX_98619964_9   2653 ATCACACTACCCAATATCAAACTGTACTTCAAAGTTAGAGTAATCAAAAC 2702
                         -       v      v     viv    v     i  v         i  
  L1M4_orf2#LINE/    215 -TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_98619964_9   2703 AGTATGATATTAGTACAAAAACAGACATGTAGAGACCAATGGAACAGAAT 2752
                            i  i  i i i i  ii i      i    --i        i     
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGA--TCAATGGAATAGAAT 311

  chrX_98619964_9   2753 AGAGAGCCCAAAAACAATGCCACACGCCTACAACCACCTGATCTTGGACA 2802
                         v     i   i   i  vv   i  iii  iiii  vi    i  v    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_98619964_9   2803 GAGTTAACAACAACAAGCAATGGGGAAGGGCCTCTCTATTTAATAAACAG 2852
                         ii v iv   v v  vv          i ivivv   v  i  i   ii 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_98619964_9   2853 TGCTGGAATAAATGGCTGCCAAAATGCCAAAGCTTGAAACCAGGCTCCTT 2902
                               i i  v   v i? v v    v    vv    iiii i i   v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_98619964_9   2903 CCTTTCATTATATCTAAAAATCACATCAATATTAATGAAAGACTTAAATG 2952
                            iv  ii    vi      i vv    v  vi  v ?    i      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_98619964_9   2953 TAAAATTTAAAACTATAGAAACCCTAGTAGAAAACCTAGG---AAAT--- 2996
                            i vi          i  vi i   v       v    ---    ---
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_98619964_9   2997 -ACCATTCTGGATATAGGCCCTGG---CAAAAATTGTATGACAAAGACTT 3042
                         -iiv iii   i -     vv   --- vv i  ---      ---- i-
  L1M4_orf2#LINE/    562 CGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT---ATGACA----CC- 602

  chrX_98619964_9   3043 AAAAAGCAATTGCAACAAAGGCAAAATTTGACAAGTGGGACCTAACTAAA 3092
                         -       vvv        i v    v v  i  i v    i v ii   
  L1M4_orf2#LINE/    603 -AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_98619964_9   3093 CTATAGAGCTTCTGCACAATAAAAGAAACTATCAACAGAGCAGAGAGACA 3142
                         v vv i i   i  ii vvi   i  v        v i  iii i     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_98619964_9   3143 GCCTACCGAATGGAAGAAAATATTTACAAACTTTACATCTTATTAAAGTC 3192
                         i  i  v      i           i    iiv  i    v  v ii v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_98619964_9   3193 TACTATCCAGAATCCCTGAGGAACTTAAACCAATCAGCAAGCAAAAAACA 3242
                          vv          viv i i     ivv  v v   ii  vv    i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_98619964_9   3243 A-----CCACATTAAAAAATGGGCAAAGGACATCAACAAACATTTTTGAA 3287
                          -----   -   ?                iv v  i i      i vv 
  L1M4_orf2#LINE/    802 AATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_98619964_9   3288 AAGAAGACGTACATGTGGACAACAAGCATAGGAAAAAAATGCTCAAGATT 3337
                                ii    vi   v   i     i v     i -       v  i
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATC 899

  chrX_98619964_9   3338 ACTAATCAT 3346
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.49 (153 / 103)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.00 (72 / 24)  


1554 26.74 1.39 7.24  chrX_98639698_98643828.rev      503  1220 (2911)    L1M4_orf2#LINE/L1      233   908 (0)  

  chrX_98639698_9    503 AAATTGTAGTACAAAACTATAGTAACTAAAACATCGTGTTACTGCCATTA 552
                            i -  v      i   i     ii  i   vi   v     v   v 
  L1M4_orf2#LINE/    233 AAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_98639698_9    553 GAAACAGACATATAATCCAGCAGAAGAAAATATAGAATACATAAATAAAT 602
                          i -i         ivi  iii   v i   vv   i v  v       i
  L1M4_orf2#LINE/    282 GGA-TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_98639698_9    603 TCACACATTTAGAATCAACTCATTCTTGACAAAGATGCCAAAAGCATATA 652
                         i  i       vii    i v   i i     i i      i v   vi 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_98639698_9    653 TTTGGGAAGGAATAGACTTTTCAATAAATTGTTATAGGA-ACCTGGATAT 701
                         v v     i      v        i    v  vv i   - v       ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_98639698_9    702 ATATTTGCCAAAGAATGAAACTAGATGCCTATCTCTCACCACATGCAAAA 751
                         vi iv   v          ii i  iv    i   v     i  i     
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_98639698_9    752 ATCAAA--GAAATACTTGATTAAGTACTTAACTGTAAGACATGAAACTAT 799
                           i  v--i    i---   i ?iv  i   v       vv i       
  L1M4_orf2#LINE/    481 ATTAACTCAAAATG---GATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_98639698_9    800 GAAACTAGTGAGACAATACATAGG-GCAAATACATGGGGACATTGGTCTG 848
                         i     vv iii v  v       - i    - v v v   v    vi i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTA 576

  chrX_98639698_9    849 GGCAAATATTGCTTGAGTAAGACTGCAAAAGCATAGGCAACCAAACTTAA 898
                              vvi  v   iii  v   vv        i i     v   vvv  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_98639698_9    899 AATGGACAAATGGGATCACATCAAGCTAATAAGCTTTTGCATAGCCACGG 948
                            i  i    v   iiv      iv v v  i      iiivv v v  
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_98639698_9    949 AAATAATTAATAAA-TGAAGAGATAATCTACAGAATAAGAAAAAATACTT 997
                          v iv  i  v   -    i   i  i i       ii  i      i  
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_98639698_9    998 GCTGACTGTTCAACTTACAAAGGAATAATGACCAGAATATACGAGAAACT 1047
                           vi iii vi v  v i  i   v vi iv          ii ii    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_98639698_9   1048 C----AACTCAATATCAAAACAAAAACAAAAACAAAAAAACAAAAACAAA 1093
                          ----         ----------------- i     i     ------
  L1M4_orf2#LINE/    777 CTTACAACTCAATA-----------------ATAAAAAGACAAA------ 803

  chrX_98639698_9   1094 ATCAAAACATAGCAGAAACCAAATAATCCTGGTATCAAATGAACAAAATA 1143
                         ---------  i -----    v ? ------- --     ii    iv 
  L1M4_orf2#LINE/    804 ---------TAAC-----CCAATTWA-------A--AAATGGGCAAAGGA 830

  chrX_98639698_9   1144 TATGAATAAACATTTATCAAAAGGTGATATACAAGTCGCTAACAGGTGTC 1193
                          v      i      v  v    iv         i v  i  i i iiiv
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_98639698_9   1194 TTAAAA-ATGTTGAAAATCACAAATTAT 1220
                          v    -   i v  v    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (108 / 81)
Gap_init rate = 0.02 (15 / 676), avg. gap size = 4.13 (62 / 15)  

3501 23.62 1.91 0.22  chrX_98639698_98643828.rev     2082  2970 (1161)  C L1M4_orf2#LINE/L1   (0)   908     5  

C chrX_98639698_9   2970 AAAATATTACGTAT-CATAAAATGACAAACGTGGTATTGTCAAGGTGTGA 2922
                           i    iv i i -   ii v  iv i  v ii      i   i  vv 
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

C chrX_98639698_9   2921 ATACTACCATAAATGATCTACAAATTCAATGCAATCTGTATCAAAATCTT 2872
                              v  vv  v         i      i      iv          ii
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

C chrX_98639698_9   2871 AATGACCATTTTAGCAGAAATGAAAAAGCTGATTCTCAAATTCATATGGA 2822
                          iivi  v    v        vi v        i  v             
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

C chrX_98639698_9   2821 ATTTCAAGAGCCCCA-AATAGTCAAATCAATCCTGCAAA----GAACAAA 2777
                          v v    i v    -     i    v     i  v   ----       
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

C chrX_98639698_9   2776 GTTGGAGAATTTATACTTCGTTATTCCAAAACTTACTGTAAAGTTACAAT 2727
                                i i i i     viv   i           ii    i    i 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

C chrX_98639698_9   2726 AATCAAG----TGTTGTGCAGTTATAAGGATACACATATAGTACAATGCG 2681
                                ----   v  i v vi         v        vv     vi
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

C chrX_98639698_9   2680 ATAGAACTGAATCGCCAGAAGTAAACCCATAAATCTATGGTCAATTGACT 2631
                               i   ivvv      i          v  i             i 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

C chrX_98639698_9   2630 TTCATCAAGGGTACCAAGACCATTCAGTGAGGAAAGAATTTTTTCTTCAA 2581
                            iv       i             i  i         vv i i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

C chrX_98639698_9   2580 CAGATGACACTGAGAAAATTTTATATCTACAT--AAAAACATAAATTTGG 2533
                           i   iii   i  v  i vv   ? i    --    iv  i  v    
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

C chrX_98639698_9   2532 ATGCCTATATCATACAATATACACAAAATACCTCAAAACAAATTGATAAC 2483
                          iv    iv   i  v       v   v  v       iii  ii?vi  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

C chrX_98639698_9   2482 ATAAATATTACAGCTATGATTTTATAAAACTCTTAGAAGAAACCATAGGG 2433
                         v     i v v     vi i --                   v      ?
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACT--ATAAAACTCTTAGAAGAAAACATAGGN 552

C chrX_98639698_9   2432 ATAAATATTTACGATTTTGAATTTTGCATTGGACTC--AGATATAACACC 2385
                         i     v  iii  ii   ii  vv   v   vi  --      i     
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

C chrX_98639698_9   2384 AAAAGTATGAAAAACAA--TGAAAAATAGATAAATTTGAACCCATCAAAA 2337
                              i ii iv     --vi               v  vii        
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

C chrX_98639698_9   2336 TTAAATACATTTGTGCATCAAAAGATGTTATCAAGAAAGTAAAAACACAA 2287
                              v  v       v     i  iii            i    v    
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

C chrX_98639698_9   2286 TATAGACAATGAAAAGGAATATTTCCAAATTTTATATCTGATAATGTTCC 2237
                         ivi v v    ii iii       v     iv            v vv i
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

C chrX_98639698_9   2236 AGTATCCAGAATATATAAAGAATTTTTGTAATTCAGCAACAAAAAC-CAA 2188
                         v                     i i  ii  i   ii  i     v-   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

C chrX_98639698_9   2187 ACAACCCAATTAAAAAATTAGAAAAGCATTCGAATGGAAATTTTTCCAAA 2138
                          i         ?      vi v    v   i    i  v    i      
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

C chrX_98639698_9   2137 AACGATAGATAAATGGGCAATAAGCACATGGAAAGAAGTGTAACATCACT 2088
                         i v    v i      v             i     v ivi       ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

C chrX_98639698_9   2087 AGACAT 2082
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.37 (119 / 87)
Gap_init rate = 0.01 (9 / 904), avg. gap size = 2.11 (19 / 9)  


3057 27.43 1.22 0.77  chrX_98655384_98660387.rev     3610  4513 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98655384_9   3610 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3659
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98655384_9   3660 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3709
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98655384_9   3710 TACCAATGACTTTCTTCACAGAATTGGAAAATCT-ACTTTAAAGTTCGTA 3758
                          v   iivi i  i  ii     v v  v  v  - iii    i   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_98655384_9   3759 TGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAGAA 3808
                              viiv  ii  v  viv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_98655384_9   3809 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAACGCTA 3858
                              i      vv    i  v  ii i      viv        v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_98655384_9   3859 CAGTAACCAAAACAGCATGGTACCGGTACCAAAACAGAGATATAGATCAA 3908
                               i   i    ii      i  i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_98655384_9   3909 TGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACTAT 3956
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_98655384_9   3957 CTGATCTTTCACAAACCTGAGAAAAACGAGCAATGGGTGCTGTTTTTAAT 4006
                         i    i  iv    ivv  vv  i v ivv       vivv -----   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-----AAT 393

  chrX_98655384_9   4007 AAATTT---AATAAATG-TGCTGGGAAAACTGGCTAGCCATATGTAGAAA 4052
                          ivi  ---  i     -        v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_98655384_9   4053 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 4102
                         iv    ii    i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_98655384_9   4103 GAATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 4152
                          i  i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_98655384_9   4153 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 4202
                            v    ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_98655384_9   4203 TAAAACACCAAAAGCAATGGCAACAAAAGCCAACATTGACAAATGGGATC 4252
                           vi            vvi          vv  v  v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_98655384_9   4253 TAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTG 4302
                          v  i   v v  i i   i  iiivv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_98655384_9   4303 AACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGA 4352
                           v  i     i   i             v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_98655384_9   4353 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 4402
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_98655384_9   4403 AAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 4448
                             i    ----   v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_98655384_9   4449 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 4498
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_98655384_9   4499 ACCATCACTGGCCAT 4513
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.57 (18 / 7)  


2854 26.15 1.87 2.09  chrX_98688408_98690634      825  1734 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98688408_9    825 TGGGAAAACATTCCGTGCTCATGGATAGAAGAAATCAATATTGTTAAAAT 874
                            i  i i  i  i  i        v i ii v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98688408_9    875 GGCCATACTGCCCAAAGCAATTTATAGATTCAATGCTATGCCTATTAAAT 924
                            v     v      vii  i  i        i  v  v     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98688408_9    925 TACCA-CTGACACTCTTCACAGAACTAGAAAAAAATATTTTAAAATTTAT 973
                          v   -   v -i i  ii     v v  v  ivvv  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_98688408_9    974 GTGGAACCA-AAGAAAGGCTGAATAGCCAAGGCACTCCTAAAGCAGCGGG 1022
                         i     vii-   ii vv v          ii  v  i i  iv  -ii 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG-AAG 198

  chrX_98688408_9   1023 GGCGGAAAGCTGGAGGCATCATGCTATCCCACTACCCAACTTCAAACTAT 1072
                         ii --    i      vv   --------    v     i      viv 
  L1M4_orf2#LINE/    199 AAC--AAAGTTGGAGGACTCA--------CACTTCCCAATTTCAAAACTT 238

  chrX_98688408_9   1073 ACTGCAGAGC---AGTAAGCAAAACAGCATGGTGCTGGTACAAGAACAGA 1119
                            i  i   ---     v   i    ii    i    i i   i i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_98688408_9   1120 CACATAGACCAATGGAACAGAATAGACAACCCAGAAATAAGACCACACAC 1169
                           i     i        i     v  v ii          iv   i   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_98688408_9   1170 CTAGAGCTATCTGATCTTCAACAAACTTGACAAAACCAAGCAGTGGGGAA 1219
                         i  vi ii vi    i   i    ivv  v   i    vv  i       
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_98688408_9   1220 AGGAATC-CCTATGTAATAAATGGTGCTCGGAAAACTGGCTAGCCATATG 1268
                           -   v-i  v vi  i          v   v      v  ?   i   
  L1M4_orf2#LINE/    389 AG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_98688408_9   1269 TGGAAGATTGAAACTGGATCCCTTCCTTATACCATATACAAAGACTAACT 1318
                         iii    v    ii    i    v   i i            i i     
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_98688408_9   1319 CAAGATGGATGAAAGACTTAAATGTAAAACCAAAAACTATAAAATCCCTG 1368
                            i      v ?    i         i v v            ii i i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_98688408_9   1369 GAGGAAAATCTAGGTG-ATACCATTCTGGACATAAGAATTGGCACAGATT 1417
                           i     iv    ? - v i -   vv   v vi iv v    vv i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_98688408_9   1418 TCATGCCGAAGACACAAAAGGCAATTGCAACAAAAACAAAGATTGACAAA 1467
                           v ivvv v     v   i   vvv         iv   i  v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_98688408_9   1468 TGAGATATCATTAAA-TTAAGGAGCTCCTGCACAGCAAAGGAAACTATCA 1516
                          vi  iv    i   -    ii -  ii  ii vv       v       
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_98688408_9   1517 ACAGATTAAATAGAGAACCTACAGGATGGGAGAAAATGTTTGCAAACTAT 1566
                          v i v i  v   v    i    i            i        ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_98688408_9   1567 GCATCTGAAAAAGGTCTAATATTCAGCATCTATAAGGAACTTAAATTTAC 1616
                         ii      v  i  v  vi   i   v  v     i     i----    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC----TTAC 781

  chrX_98688408_9   1617 AAGAAAACAA-AACAAAACAAA-AA---AATTAAAAATTGGCCAAAGGAC 1661
                           vvv  i  -  v  i     -  ---    ?    v   v       i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_98688408_9   1662 ATGAA----CACTTTTCAAAAGAAGACATAAATGTGGCTAACAATCATAT 1707
                         v    ----  i  i  v        i   v vi    i  i  v  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_98688408_9   1708 GAAAAACAGCTCAGCATCACTGACCAT 1734
                              ivv     i     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.00 (36 / 18)  


3819 21.30 2.24 0.78  chrX_98694126_98698161     2652  3543 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_98694126_9   2652 AAAAAT---TCAAGTTTATTAATTTGAGGATATAATCTTGTGAAGATGTT 2698
                            i  ---i  v   i  vi   v  i  iv    v    v      vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_98694126_9   2699 AATACCATCCAAAGAGAGGTGAAAAATCAACGTAATCTCTCTCAAAATCC 2748
                              ivi     vv  vv iv i v      i    i  v         
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_98694126_9   2749 CAATGACATTATTT-CAGAAATAGAAAAA-TAATCGTAAAATTCATGTGG 2796
                           iivi v  v   -       v  v  i- i   v          i   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_98694126_9   2797 A--TGCTTAAGGGACCTGGAATAGCCGAAACAATGTTGAAAAAGAA---C 2841
                          --   --        ii        i       v           --- 
  L1M4_orf2#LINE/    154 AAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_98694126_9   2842 AAAGTTGGAGGTCTCATACTTCCTGATTTCAAATACT-ACTATGAA-TGA 2889
                                    v    i      ii        -   -    ii  -iv 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAA-ACTTACTACAAAGCTA 250

  chrX_98694126_9   2890 CATTAATCAAAACAGTATGTTACCAGCATAAAAACAGATATACAAAACTC 2939
                           v       i     i  v   ii      ii i   i   i i v vv
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_98694126_9   2940 CAGAATAATATAGAGAGCCCAGACATACACCCTTGCATATATAGTCAAAT 2989
                         ii     iv  v     i     v   v    v i   v   i     v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_98694126_9   2990 GATTTTTGATAATAATTCTAAGACCATTCAATGGGGAAATAATAAGTTTT 3039
                               i  i  vii v i                    v    ivi   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_98694126_9   3040 TCAACAAATTGTGTGGGGGAAAACTGGACATCCACGTGAAAAATAATGAA 3089
                                  v   iv   - v       i ?    i  v    v      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGG-ACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_98694126_9   3090 GTTAGACCCTTAACTTATACCATAGACAAAGA--------AAATTGATCA 3131
                            i     i  v  i i      v     i --------    v     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_98694126_9   3132 AAGACCTACATTTAAAAGCAGAAACTATGATACTCCCAGAAGGAAGTAAT 3181
                         ?       v  v   i   vi       i v    ii     i  ii - 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-T 548

  chrX_98694126_9   3182 ATGGGGAAACCTTCATGATATTGTGTTTGGCAATAATTTCTTGGCTATGA 3231
                          v ? v   i    i   iv   v   v      ii      i v     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_98694126_9   3232 TACCAAAAGCACAGGCAATAACACAACAAAAATAGGTAAGTTGGATTTCA 3281
                         i            i    i  v v  --       i   i     i    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAA--AAAATAGATAAATTGGACTTCA 646

  chrX_98694126_9   3282 TCAAAATAAAATACATTTGTGCATCAAATGACACTATCAGGAGAGTAAAA 3331
                                v   v  v       v     v          i  i   i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_98694126_9   3332 TGTCAATGTACAGAATAGAAGAAAATATTCACAAATCATATATCTGGTAC 3381
                         v v   ivi       i i          ii               i  v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_98694126_9   3382 AGGCTTAACATTCAGGATATGTAAAGGACTCCTACAAGTCAACAGTAACA 3431
                         i  vi vii  i   i    i     i    i     v    i i   v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_98694126_9   3432 AAGCAAGCAACCCAATTCAAAAATGGGCAAATGATTTTAATAGACATTTC 3481
                          ii   ii         ?             v     v            
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_98694126_9   3482 TCTAAATAAGATATACAGATGACCAATAAGCATATGGAAAGATGCTCTAC 3531
                           i   v          i   i          i   i          v  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_98694126_9   3532 ATCACTACTTGT 3543
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (109 / 77)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 2.08 (27 / 13)  


1513 27.29 6.35 5.88  chrX_98699934_98701911      628  1477 (501)    L1M4_orf2#LINE/L1       13   866 (42)  

  chrX_98699934_9    628 CCAAGGTCATGGATAAGAGGACTTCATATTGTTATAATGTCAGTTCTCCA 677
                            v v        vi  i     v         vi   v  i v    v
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_98699934_9    678 AAAATTTATCTATAGATTC----CAATC------AAAATCTCAACAGGCT 717
                         v     v     i      ----     ------      i  i v v  
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_98699934_9    718 TTTTATTGTGTCCAG----TGA---GCTGATTTTAAAATTTATATAGAAA 760
                             ----  --   ----   ---      ii       i    i    
  L1M4_orf2#LINE/    113 TTTT----TG--CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_98699934_9    761 TGCAAATGGCAAAGAATAACCAAGGCAATCT------GGAAGAACAAAGC 804
                              iv i vv      i    ii      ------i           i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_98699934_9    805 TGGAGAATTTATACTACAAAAGT-CATGGCCTCTTACTGAAATTTAATAA 853
                              i i i i   v vv  v -  vii i vi   vi iv vi i   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_98699934_9    854 -------AGTTTAATATTGACACAAGAATAAACAAATAGAACAACGGACA 896
                         -------   v ii  i  i  i   i   i   v     v   i   --
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA-- 304

  chrX_98699934_9    897 ATCTAA--GAGGGTCCACAAATAGATGCATACCTGTATTGATCATCTAGT 944
                           vv  --   i     v     i iv     v v   - i   vi ii 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT-GGTCAATTGAT 353

  chrX_98699934_9    945 ATATGATAAAGTTG---AAACTACATAGCACTGTGGAAAGTATCAT-TTT 990
                         v vi  i  i v  --- i  --   -v  v  v      v  vi -   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGAC--CAT-TCAATGGGGAAAGAATAGTCTTT 400

  chrX_98699934_9    991 TCAGTAAATGAGTCACAGGGTCAATATGATATCCA---ACATAGGGATTA 1037
                            ii     -  -i v   v   ivv    ?   ---i  v i i  v 
  L1M4_orf2#LINE/    401 TCAACAAATG-GT-GCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_98699934_9   1038 ATTTTTGCTCTTACATGACATCATAAAAAGGCCAGATAAACAGAGGACCT 1087
                          v  vvi i i   v v   i    v v i--- i  v   ------i v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAA---AAATTAAC------TCA 489

  chrX_98699934_9   1088 AAAT--ATCAAAGAATTTCCATAAAAATAGAAATATCAAAGAATTTCTTT 1135
                             --    ?   vi -------------    i --    ii -----
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCT-------------AAATGT--AAGAGCT----- 519

  chrX_98699934_9   1136 AAAAAATAGAAAATT--TACGTGAAAGTATATAAAGACACCTTTATGACT 1183
                         -    v  v    i --  viv    ii   vi?iv v i   ii    i
  L1M4_orf2#LINE/    520 -AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_98699934_9   1184 TTGGAGTAGACACATATTTTC--AAACAAGACATTAAGATTACCAATGAT 1231
                             iv   i  -  iv    -- i i v    ii  i vi  v iii i
  L1M4_orf2#LINE/    569 TTGGGTTAGGCA-ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_98699934_9   1232 AAA-TAGAAAATTGATAAATTGGACTATATTATGACTTAAA--CTTCTGT 1278
                            -v i     v             vi  i -i v     --   i   
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCA-AAATTAAAAACTTTTGT 666

  chrX_98699934_9   1279 TCATCAGAAGACGCCAATAGGAAGAGTGAATAGATAGCCCACAAAGTGGG 1328
                         v v   i i   i i vi i   -      v   i i      i i    
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAA-AGTGAAAAGACAACCCACAGAATGGG 715

  chrX_98699934_9   1329 AAAAGGTATTTACAAAACATATTCCCCTCAAAAAAGGTTTAGATCCAGAA 1378
                          i  ii     i    v     --vi  v v  ii ii  iv        
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATAT--ATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_98699934_9   1379 TATATAAAGAGCTTTTATCAAATAAATAG-GAAAAGAGAAA-ATCTTTTT 1426
                                   i  i   -   v v    i-i      v   - v iivv 
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTA-CAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_98699934_9   1427 TTAAA--TGAGCAAAAAACTCAAATAAGTACCT-TACAGAAATGATATTT 1473
                          ?   --  i     ii i ii    iii ii - v  i i v     vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_98699934_9   1474 AAAT 1477
                             
  L1M4_orf2#LINE/    863 AAAT 866

Transitions / transversions = 1.48 (136 / 92)
Gap_init rate = 0.04 (38 / 854), avg. gap size = 2.74 (104 / 38)  


2306 26.26 2.57 5.25  chrX_98726094_98728469.rev      959  1891 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98726094_9    959 TGGAAAAACATTTCATGCTCATGAATAGGAAGAATCAGTAT-G--AAAAT 1005
                               i i  ii    i     i  v      v i i   - --  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98726094_9   1006 GGCCATATTGCCCAAAGCAATTTACAGATTCAATGCTATTCCCATTAAAC 1055
                            v   i v      vii  i           i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98726094_9   1056 TACCAATGACATTCTTCACAGAACTAGAATAAACT-ATTACAAAATTCAT 1104
                          v   iivi v  i  ii     v v  -i  i  -  ivi         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_98726094_9   1105 AT---AAT-CAAAACAGAGCCTGAATAGGCAAGACAATTCTAAGCAAAAA 1150
                           ---   -   ii--  v  v      v   i     ii i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_98726094_9   1151 GA-CAAAACTGGGAGCATAACATTACCCAACTTCAAACTATACTACAGGG 1199
                           -    ii   ii vv v   i v     i      viv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_98726094_9   1200 CTACAGTAACCAAAACAGCACGTTACTGGTACAAAAAATAAAACACATAG 1249
                                  i   i    iii v      i i  ii -  i -  i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGA-CATATAG 295

  chrX_98726094_9   1250 ACAAATGGAACAGAATAGAAAGCCCAGAAATAATGCTGCACACATACAGT 1299
                          iv       i     v  i  i          vv iii   iv  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_98726094_9   1300 -AATCTGATCTTCAATAAAGTTGCCAAAAACAAGCGATGAGGAAAGGACT 1348
                         -   -    i   i i  i v      i v  vv i   i      i iv
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_98726094_9   1349 CCCCATTCAATAAATGGTGAGAGGATAACTGGATATCCATATGCAGAATA 1398
                         vi iv     i        vvi   i         ?   i     i  v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_98726094_9   1399 TTGAAACTGGGCCCATACCTTAAACCACATATGAAAATTAACTCAAGATA 1448
                         v    ii   i   v     i v    i   ii             i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_98726094_9   1449 GAACAAAGACTTAAACATAAAACCCAAAACTAAAAAAAAAAAAAAAAAAA 1498
                           v  ?    i    ii   i v i       v    -------------
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA------------- 531

  chrX_98726094_9   1499 AAAAAAAAAAAAAAGAAATGCAGTCT-GTAAGACAACCTAGGAAATACCA 1547
                         -------------------- --   -iv    v   v    ?i----i 
  L1M4_orf2#LINE/    532 --------------------C--TCTTAGAAGAAAACATAGGNG----TA 555

  chrX_98726094_9   1548 TACCATTCTGGACATAGGACCTGGCAAAGCTTTTGTGATTATGTCACCAA 1597
                         v i -   vv   v v  iiiv     v v   iv iiv    v      
  L1M4_orf2#LINE/    556 AATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_98726094_9   1598 AA---TAATGGCAACAAAAAACAAAGATTGAGAAATGAGACCTAATTAAA 1644
                           ---i  --         i -   i  v  v    vi   i v  i   
  L1M4_orf2#LINE/    605 AAGCACAA--GCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_98726094_9   1645 CTAGAGAGCTTCTGTACAGCAAAAGAAACTATGACAAGAGTAAACAGACA 1694
                         v vi i i   i   i vv    i  v     v vi i   i  v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_98726094_9   1695 ACCTATAGAAGGGAAGACAACATGTGCAAACTGCGCATCCAACAAAGGTC 1744
                            i i    v  i   v  i  v      iiiiii   ii i  i  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_98726094_9   1745 TAATATTGAGAATCCATAAGGAACA--TGAAATTCA-CAAGCAAAATA-A 1790
                          vi   iv     vi    i    v-- iv  i   -i  vv    v - 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_98726094_9   1791 AGCAACCCCATTAAAAAGTGGGCAA-GGACATGAACAGACACTTCTCAAA 1839
                          ii     v   ?    i       -   iv    i     i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_98726094_9   1840 AGAAGACAT-CATGTGGCCAAGAAGCATATGAAAAAACG---AA-ATTAA 1884
                               i  -  vi       v     i       i i ---  -  i ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_98726094_9   1885 ATAAAGA 1891
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.74 (153 / 88)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.70 (73 / 27)  


2605 27.25 1.32 2.64  chrX_98735665_98737756.rev      692  1601 (491)    L1M4_orf2#LINE/L1       11   908 (0)  

  chrX_98735665_9    692 TTTCATCCTCATGGATAGGAAGAATCAATATCGTGAAAATGGTCATACTG 741
                          ii   vi        v      v i     i  v  i    iv     -
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT- 59

  chrX_98735665_9    742 CCCAAAGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAACTAC 791
                            ------    v i  i  i        i  v  i  i      v v 
  L1M4_orf2#LINE/     60 CCC------CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_98735665_9    792 CATTGATG--TTCTTCACAAAAAAAACAAAACAAAACAAAAAAACT-ACC 838
                           -- v  --  i  ii  i   -------------ivi v  i  - i 
  L1M4_orf2#LINE/    104 CA--GCTGCCTTTTTTGCAGAAA-------------TTGACAAGCTGATC 138

  chrX_98735665_9    839 TTAAATTTCTTATGGAA-T-CAAAGAAGACCAGGTAAAGCAAAGACAATG 886
                         i    v   v       - -   i --    vi v v   v  i     v
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATC 186

  chrX_98735665_9    887 CTAAGAAAAAAAAA---AGCCAGAGGCATCATGCTACCTGACTTCAAACT 933
                         i i i   i  i  ---  iii    vv   ii  v  ii i      vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_98735665_9    934 ATACTCCAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACA 983
                         v    v   i          i   i    ii         i iv ii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_98735665_9    984 GACATATAGACCAATGGAACAGAGTAGAGACCTCAGAAATAACACCACAC 1033
                                   i        i   i v    vii         vv   i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_98735665_9   1034 ATCTACAAGCATCTGATGTTCAACAATCCTAACAAAAACAAGCAATGGGG 1083
                           i  iiiv  vi    v   i    vvv iv   i v  vv        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_98735665_9   1084 AAAGGATCTCCTATTCAATAAATGGTTCTGGGAAAACTGGCTAGCCATAT 1133
                             i  vvi  v     i       v      v      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_98735665_9   1134 GCAGAAAACTGAAACTGAACCCCTTACTTACACTTTACACAATAATTAAC 1183
                            i  i v    ii  i      vv  i    iv  i    v       
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_98735665_9   1184 TCAATACAGATTACAGATTTCAATGTAAAAGCTAAAACCATAAAAACCCT 1233
                             v ii   i ?   ii v       i         i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_98735665_9   1234 AGGAGCAAACCTAGGCAATACTATTCAGGACATATGAATGGGCAAAGACT 1283
                           i  v    v    ?ivv v v   iv   v vv iv i     v ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_98735665_9   1284 TCATGAAGAAAACACCAGAAGCAATTGCAACAAAAGCAAAAATTGATAAA 1333
                           v ii v vi      i     vvv          v      v      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_98735665_9   1334 TGGGATCTAATTAAACTAAAGAGATTCTGCATAGCAAAAGAAACTATCAT 1383
                          v   ii v  i   v v  i iv  i  iiivv    i  v       v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_98735665_9   1384 CAGAGTGAACAGGCAACCTAGAAAATGGGAGAAAATTTTTGCAATCCACC 1433
                         v i      v  i     i v i             v       vi  iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_98735665_9   1434 CATCTGACAAACGTCTAATATCCAGATTTTACAAGAAACATAAACAAATT 1483
                         i      i  iv v  vi        v v  i  ii   vivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_98735665_9   1484 TACAAGAAAAAAGCAAACCACCCCATCAAACAGTGGGCAAAGGATATGAA 1533
                         v i  v     ii    iv    v  i?  v i            v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_98735665_9   1534 CAGACACTTTTCAAAAAAAGAAATTTATATGATCAACAA--ACATGAAAA 1581
                         i     i  i  v   i    v  vi v   ii   i  --         
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_98735665_9   1582 AAAGC--AACATCACTGATCAT 1601
                         i v  --       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (135 / 109)
Gap_init rate = 0.01 (12 / 898), avg. gap size = 3.00 (36 / 12)  


 216 23.08 0.00 0.00  chrX_98787230_98789052.rev      463   514 (1309)  C L1M4_orf2#LINE/L1   (0)   908   857 *

C chrX_98787230_9    514 ATTTGTAGATTGCCAACAAGTATATGAAAAAACGCTCAGCACCACTAATG 465
                           v ii i  v     i   i i       i i     i  i  ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

C chrX_98787230_9    464 AT 463
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 5.00 (10 / 2)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.00 (0 / 0)  

2919 26.14 0.96 0.36  chrX_98787230_98789052.rev      505  1338 (485)    L1M4_orf2#LINE/L1       70   908 (0)  

  chrX_98787230_9    505 ATCTACAAATGCAACACAATCCCCATCAAAATACCATCATCATTATTCAC 554
                                i  v    i       i        v   v vv v  v  ii 
  L1M4_orf2#LINE/     70 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 119

  chrX_98787230_9    555 AGAATTAGAAAAAACAATTCTAAAGTTCATATGGAACCAAAAAAGAGCAT 604
                             v v  v  ivii  i     i           viiv  ii  v vv
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_98787230_9    605 GCACAGCCAAAGCAAGACTAAGTAAAAAGAACAAATCTGGAGGCATCACA 654
                          v i       i   vvi i iv  i         vi      vv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_98787230_9    655 CTACCTGATTTCAAAGTAAGCTATAAGGCCATAGTCACCAAAACAGCATG 704
                           v  ii        iivvi   i  i  i i   v i   i    ii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_98787230_9    705 GTACTGGTATAAAAATAGGCACATAGACCAATGGAACAGTATAGAGAAAA 754
                                i    ii    i  i     i        i  v  v    ivv
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_98787230_9    755 CAGAAATAAACCCAAATACCTACAGCCAACTGATCTTCGACAAAGCAAAC 804
                                       v i ii  ii i   i    i        i vviv 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_98787230_9    805 AAAAAAAATAAAGTGGGGAAGCAATCCCCTTTTCAACAAACGGTGCTGGG 854
                           i vv v v  -       iv   vvi            i         
  L1M4_orf2#LINE/    370 AAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chrX_98787230_9    855 ATAATTGGCTAACCATATGTAGAAGAATGAAACTGGATCCTCATCTCTCA 904
                          i  i   v  ?   i   i i         ii    i  ii i   v  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_98787230_9    905 CCTTATACAAAAATCAACTCAAGATGGATTAAAGACTTAAATCTAAGACC 954
                           v           i       i      i ?    i     v     v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_98787230_9    955 TGAAACTATAAAAATGCTAGAAGATAACATTGGAAAAACCCTTCTAGATA 1004
                          i           v vi       v     v  ?iv  vi    vv  iv
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_98787230_9   1005 CTGGCTTAGGCAAGGATTTCAT-GACCAAGGAC-TCAAAAGCAAATGCAC 1052
                         i   v        v i    v -  i-- v   -i        v v   v
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGAT--ATGACACCAAAAGCACAAGCAA 616

  chrX_98787230_9   1053 TAAAAACAAAGATAAATAGCTGGGACTTAATTGAACTAAAGAGTGTTTGC 1102
                         i    iv   i   i   iv v      v  ii  v v  i iiv    i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_98787230_9   1103 ATGGCAAAAGGAACAATCAGCAGAGTAAACAGACAACCCACAGAGTGGGA 1152
                         iivv    i iv  v    iv i   i  v              i     
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_98787230_9   1153 GAAAATCTTCACAATCTATACATCTGACAAAGGACTAATATCCAGAATCT 1202
                               v  ii   vii   i      i  i     vi          v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_98787230_9   1203 ACAATGAACTCAAACAAATCAGCAAGAATAAAACAA----TCCA--TCAA 1246
                          i  v      vv    v   ii  v  v  i    ----i   -- ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_98787230_9   1247 AATTGGGCTAAGGATATGAATAGACAGTTCTCAAAAGAAGAAATACAAAT 1296
                           v     v      v          v     v        v        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_98787230_9   1297 GGCCAACAAACATATGAAAAAATGCTTAGTCTTGATTTCTAA 1338
                               i  i  i       i     i iiv ii????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (121 / 93)
Gap_init rate = 0.01 (6 / 839), avg. gap size = 1.83 (11 / 6)  


3238 25.85 0.44 0.99  chrX_98824512_98831590     2837  3749 (3330)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98824512_9   2837 TGGAAAAACATTTCATGTTCATGGATTGGAAGAATCTATATTATTAAAAT 2886
                               i i  ii                    v iv     i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98824512_9   2887 GTCCATACTACACAAAGCAATTCACAGATTAAATGCAATTCTTATTAATA 2936
                          v v     v v    vii  ii       v  i     i i   i  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98824512_9   2937 CGTCAAATGACATTCTTCACAGAAATTAAAAAAAAAACT-ATCCTAAAAT 2985
                         ivi  iv  v -  i  ii        i v  i----  -          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG----CTGATCCTAAAAT 145

  chrX_98824512_9   2986 TTATATGGAATAACAAGAGATCCAGAATAGGCAAAGCTATCCTAAGCAAA 3035
                          i        vvi    i  i         v    i v   i i --   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAA 193

  chrX_98824512_9   3036 AAAAGAACAATACGGGATAAATCATACTACATGACTTCAAATTATACTAC 3085
                          i        viiv   vi v   i   v vii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_98824512_9   3086 AGAGCTATAGTAACCAATGCAGCATGATACTGGCATAAAAACAGACACAT 3135
                          i     i     i   vi   ii  i           ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_98824512_9   3136 AGATCAATAGAACAGAATAGAGAACCCAGAAACAAATCCGTACAACTACA 3185
                                 i   i     v    ii       i   i  i    vi  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_98824512_9   3186 GTGAATTTATTTTTACCAAAGTTGCCAAGACCACACACTGGGAAAAAGAC 3235
                           v    v     iiv   i v           iv  v    i   ii i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_98824512_9   3236 AGTCTCTTCAATAAATGGTGCTGCAAAACCCGGATATCCATAGGCAAAAA 3285
                              i     i           vi v v i     ?   i v      i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_98824512_9   3286 AATAAAATTAGGTCTCTATGTGTTGCCATATACAAAAATCAAATCAAAAT 3335
                            i  i  i ii i   iv vvii              i  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_98824512_9   3336 GGACGAAACACTTAAATCTAAGACATCACACTATAAAATTACTACAAGAA 3385
                            iv ? v  i     v     vv v v         i vi  v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_98824512_9   3386 AACATTGAAGAAACTGTCAAGGACATTGGAGTGGGCAAAGATTTCTTGAG 3435
                              v i? v  v v iviv   v    iv i     v i      iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_98824512_9   3436 TAATAAC-TCATAACCATAGGCAACCAAAGCAAATATGGACAAATGGGAT 3484
                           - i  -i  v  v  i i     v    v   v  i  i    v   i
  L1M4_orf2#LINE/    594 TA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_98824512_9   3485 CACATCGAGCTAAAAAGCTTCTGCACAGCAAATGAAACAATCAATAA-GT 3533
                         iv    i iv v    i   i  ii vv    v  v  v     v  -  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_98824512_9   3534 GAAGAGATAACAGACAGAATGAGAGAAAATTCTTACAAACCACCTCTCTG 3583
                            i   i   vv        i        vi  i    i  iv v    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_98824512_9   3584 ACAAGGAATTAATAACCAGAATATATAAGGAGCTCAACCAACTCTGTAGG 3633
                          i    i i vi  v             i  i   vvv      vi  iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_98824512_9   3634 AAAAAAATCTAATAATTTGATC-AAAAATGGGCAAAATATTTGAATAGAA 3682
                              i - v     iiii  i-             iv           v
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_98824512_9   3683 TTTTCTCAAAAGAAGACATACGAATGGCAAATAGGCATATTAAAACATTC 3732
                         v      v        i    i      v    i   i  v    v  v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_98824512_9   3733 TCAACATCATTGGTCAG 3749
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  

3409 23.09 1.88 1.55  chrX_98824512_98831590     5682  6586 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98824512_9   5682 TGGAAAGATACCCCATGAACATG-ATTGGAAGATATAATATTGTTAATAT 5730
                                   i      vv    -         iv            v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98824512_9   5731 GTCCATACTGCCCAAAGTGAGCTACATATTCAATGCAATCCCTATCAAAA 5780
                          v v     v      v   v     v      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98824512_9   5781 TCCCTGTGACAATTATTACAGACATAGAAAAAAGC-AATGCTAAAATTTA 5829
                             v ivi vv  v  i    v  v  v  --  -i  v        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chrX_98824512_9   5830 TATGAAACCA-AAAGGACACCAAATAGTCAAAACTATATTGAGAAGAAAG 5878
                             i  vii-  i    v vi     i      v  v    i  ii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_98824512_9   5879 ACCAAAGCTGGAGACCAAATCACAGTTCCTGATTTCAAAACATA-TATAA 5927
                          v     i     iv ---     v    ii          v  -  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGAC---TCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_98824512_9   5928 AGCTACAGTAAGAAAAACAGTATGGTACTGGCATAAAGACAGACATATAG 5977
                                    vv  i     i              i  i          
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_98824512_9   5978 GCCAATAAAACAGAATACAGAACCCACAAATAAAACTACACATACATGGT 6027
                         ii    ii  i     vv   ii   v       v i i    vi     
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_98824512_9   6028 CAACTGGTCTTTAACTTCAGTGCCAAGGAAACACAATAGGGAAAGGACAG 6077
                            i  i i  ii  vvvi        ivv iv    i       i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_98824512_9   6078 TCTCTTTAGCAAGTGGTTCTGAGAACACTGGGCATCCACATGCAAAAGAA 6127
                            i  i i   i    v   i  vv     ii ?               
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_98824512_9   6128 TAAAATTGTACCCATATTTTTAGTCTGTATGCAAAAATCAACTCAAAAT- 6176
                          i  i   v    v  ii i- vv ii   i       i          -
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTC-ACACCATATACAAAAATTAACTCAAAATG 494

  chrX_98824512_9   6177 ----ATAGGTTTAAATGTAAGAACTGAATCTGTAAAACTGCTAAGTGAAA 6222
                         ---- ?  iii           i  i  v  i       vi  iiv    
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_98824512_9   6223 ATATAGGGGAAAAGCTTTCTGACACTGGATT-GACAATGATTTGTTAGAT 6271
                          i     ? v   v   iv    vi   i  - i     i   v      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_98824512_9   6272 ATGGCATCATAAGCACAGGAAACAAAAACAAAAATATAAATAAATGGGAC 6321
                            i  i  v       i v       i-     -   i      v    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAG-AAAAA-ATAGATAAATTGGAC 642

  chrX_98824512_9   6322 TACATCAAA-CTAAAAATTTCTGAACAGCAAAGGAAAC----AAAAGAAT 6366
                          v       -i      i  i  vi vv       v  ----  i i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_98824512_9   6367 GAAAAGCCAAATTATAAAATGGAAGGCAATATT-ACAAACCATATGTATG 6415
                               v   vii i i     i  iv      -i    i     i v  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_98824512_9   6416 ATAAGGAGTTAATATTACAAATACAGAAACAACACCTATGACTTTATGGC 6465
                               iii vi   ivvi    i v   v   v i  ii   iv  iii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_98824512_9   6466 ATAAAAACAAATAACCTGATTTAAAA-TAGGCAAAGGACTTGAATTTGCA 6514
                          v   i          ii   ?    - i         i      vvi  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_98824512_9   6515 TTTCCCCAAAGAAGACATACAAATGGATGACAGTATATGGTATATGAAAA 6564
                             i          i          v---  i  ---i i i       
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGC---CAATA---AGCACATGAAAA 886

  chrX_98824512_9   6565 GATGCTCAACACCATTAAATGA 6586
                                    i  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (126 / 79)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.82 (31 / 17)  


3255 24.32 1.10 1.64  chrX_98833375_98837576.rev     2800  3712 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98833375_9   2800 TAAAACAATATTTCATGTTCATGGATTAGAAGAATCAATATTGTTAAAAT 2849
                          ii  vi    ii              i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98833375_9   2850 TTCCAAT-TTACCCAAAGCCATATACATTTTCATTGCAATTCTTATCAAA 2898
                         vv -   -i v      viv  v    vv    vi     i i       
  L1M4_orf2#LINE/     51 GGC-AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_98833375_9   2899 ATACCAATAACATTTTTTATAGTAATAGAAAAAAAAATCCTAAAATTTAT 2948
                           v   iivi v      ii  v   v  v  ivvi           i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_98833375_9   2949 ATGAACTCACAAAAG-CCGAATTCAACAGAATAGCCAACGCTATCCTGAG 2997
                            i vvii   ii -  --------            vi v   i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACC--------CAGAATAGCCAAAACAATCTTGAA 191

  chrX_98833375_9   2998 CAAAAAGAAAAAAACTTGAGGAATCACATTGCCTGACTTCAAATTATACT 3047
                         v  i     v   ii v     v     i v  ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_98833375_9   3048 ACAGAGATATAGTAACCATGACAGCATGTTA-TGGCTTAAAAACAGTTAT 3096
                            i  v  i     i  v     ii  v  -    v   ii i  vi  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_98833375_9   3097 ATAGGCCAACGGAACAGAATAGAGAACCCAGAAACAAATCCACATACCTA 3146
                             ii   i    i     v    ii       i   i   i i ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_98833375_9   3147 CAGTCAACTAATTTTCAACAAAGGTGCCAGGAACATAGAGTAGGGAAACA 3196
                         ii     i i      i    i       i  v   vv i i      v 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_98833375_9   3197 G-AGTCTCTTCAATAAATGGTGCTGGGAAAACTGTATATCCATATGCAGG 3245
                         i-     i     i              v     v   ?   i     ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_98833375_9   3246 TGAATAAAACTAGACCCCCATCTCTCACCATATACAAAATTCAAATCAAA 3295
                         v    i  ii i      i i   v              v i  v     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_98833375_9   3296 ATGATTTAAACACTTAAATCTAAAACATTAAATTATGAAACTACTACAGG 3345
                            iv i ? v  i     v   i vv v   i   i     vi  v i 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_98833375_9   3346 AAAACATTGGGGAAAATCTCCAAGGCATTTGTCTGGATAAAAATTTCTT- 3394
                                v  ? v      i iv i v  v vi i ii  vii      -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_98833375_9   3395 GACA-AACACTGCAGTAGCAGAGGCAATCAAAGCAAAAATGGACAAATGG 3443
                           i -i    --  iv    v i    iv    v      i  i    v 
  L1M4_orf2#LINE/    592 GATATGACAC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_98833375_9   3444 AATAACATCAAG-TTAAAAAGCTTCTGCACAGCAAAAGAAACAATCAACA 3492
                         i ivv      i-       -   i  ii vv    i  v  v     v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_98833375_9   3493 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCATATTACCCA 3542
                                                                  v  i ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_98833375_9   3543 TGTGACAAGGAATTAATAACCAGAATATATAAGGAGCTCAAACAACTCTA 3592
                          v   i    i i vi  v             i  i   vv       v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_98833375_9   3593 TAGGAAAAA-ACGTAATAATCTGAT--AAAAATAGGGGCAAATGATTTGA 3639
                           iv     -  i-     i ii  --      --       v       
  L1M4_orf2#LINE/    789 TAATAAAAAGACA-AATAACCCAATTWAAAAAT--GGGCAAAGGATTTGA 835

  chrX_98833375_9   3640 ATAGACATTTCTGAAAAGAAGACATAAGAATGGCAAACAGGCATATGAAA 3689
                                     vv        i   vi      v  i i   i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_98833375_9   3690 AGTTGCTCAACATCTTTGATCCT 3712
                           v           v????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (130 / 89)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


3070 20.95 4.05 0.68  chrX_98846598_98848321.rev      494  1233 (491)    L1M4_orf2#LINE/L1      144   908 (0)  

  chrX_98846598_9    494 ATTCAGGAGGAATCTCAAGGGAGCCCCAAGGAACCAAAACAATTTTGAAA 543
                              viv    viv       -   vi iv i          i      
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_98846598_9    544 AAGATGAACAAAGTTAAAGGACTCACACTTTGCAATTTCAAAACATATAA 593
                             v          ii             iv            v  iv 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_98846598_9    594 CAAAGCTATAGTAA-CAAAACAGTGTGTCACAAGCA---GAAT-GACACC 638
                                 i     -   i        vi  vi   --- i  -    iv
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_98846598_9    639 CAGGCCAAGGCAATGGGAATCAAA---CAGACAACAAAC----------- 674
                         i  ii   v v   i i v v i ---    -  i    -----------
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGA-AATAAACCCATACATTTA 341

  chrX_98846598_9    675 -----AAATGATTTTCCATGAGGATACCAAGACCACTCAATGGAGAAATG 719
                         -----  v        v ii   i i         i       i    vi
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_98846598_9    720 ACAGTCTCTTCAACAAGTGGTGTTGAAAACACTGGATATCCACAAGCAAA 769
                          i     i        i     i  ii vv        ?     v     
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_98846598_9    770 AGAATGCAGTTGGACTCTTATTTTACAC---ATACAAAAATTAACTGGAA 816
                               v        i i  ii i    ---               vi  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_98846598_9    817 ATGGATTAAACACTTAAATGTAAGAACTGAAATTACAAAACTCCTAAAAG 866
                               i ? v  i           i  i   i  i       i  i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_98846598_9    867 AAAACATAGAAG-ACAGTTTCATAACATTGGATTTGATAATGATTTCTCT 915
                                  i? - v vi   i i  v    i  v ii    i     iv
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_98846598_9    916 GATATGATACCAAAAGCACAAGCAACAAAAGCAAAAATAGACAAGTAGGA 965
                                i                       v         i  i v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_98846598_9    966 CTACCTCAAACTAAAAACCTTCTGCACAAGAAAGGAAACAATCAACAGAT 1015
                           v v     v v    v   i  ii vvv      v  v     v i v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_98846598_9   1016 TGAAAAAGCAACCTACAAAATGGGAGAAAATATTTGCAAATCATAAATCT 1065
                               ii     i   i                           v    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_98846598_9   1066 GGTAAAAAGTTAATATCCACAATATA--AAGAGCTCTTACAACTCAATAG 1113
                          i   iiiii vi      v      --    i                i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_98846598_9   1114 CAAAAAATTTTAAATATCTTTATTTTTGAAATGTGTAAAAGACTTGTATA 1163
                         i     ivi--     v iiv   ?v-i     v i   i  i   v   
  L1M4_orf2#LINE/    792 TAAAAAGAC--AAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATA 838

  chrX_98846598_9   1164 AATATATCTCCAAGGATGATATGCAAATGACCAATAAGCATATTAAAAGA 1213
                         i i  v       i  v     i      i          i  v      
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_98846598_9   1214 TGCTCAACATCACTGGAGGA 1233
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (94 / 57)
Gap_init rate = 0.02 (12 / 765), avg. gap size = 2.92 (35 / 12)  


2336 26.36 5.34 2.39  chrX_98848770_98854083.rev     3944  4823 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_98848770_9   3944 GAAAAATGTTCCATTTTCATGGATTGAAAGAATCAATATTATTAAAATGG 3993
                             i  i i    v           i    v i      i    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_98848770_9   3994 CCATAGTGACCAAAGCAAGCTAAAAATTTCACACTATTTCTATCAAGCTA 4043
                          v   v vv     vii v   v i   iv  i v  ii       iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_98848770_9   4044 CCAACATCATTTTTCTCAGAACTAGAAAAAAAACT-ATTATAAAATTCAT 4092
                            i vv v     iv     v v  v  i---  -  iv          
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCAT 149

  chrX_98848770_9   4093 GTGGAACCAAAAAGAGCCCA-AATAACCAAAACTATTCTAAGAAA-AAGA 4140
                         i     viiv  i ii    -    i       v  ii i i   -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_98848770_9   4141 AGGAAATCAGAGGCTTCACATTACCTATACTATAGACTATACTATAAGGC 4190
                          vi  i ii    vi     i v  i - i vi i viv     i  i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGC 248

  chrX_98848770_9   4191 TACAGTAACCAAAAGAGCATGGTGCTGCTACAAA-ATACACACATAGACC 4239
                                 i   i v  ii    i   vi i  i-   v   i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_98848770_9   4240 AATGGAACAGAATACAGAACACAGTAATAAATCCACATGACTACAGCCAT 4289
                                i     vv   iiv   v      i   i iivi  ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_98848770_9   4290 CTGATCTTCCACAAAGTTAACACAAATAAGCAATGGGGAAAGCACTCCCT 4339
                         i    i   v    i v iv  vi vi vv            v ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_98848770_9   4340 ATGCAATAAATGGTTCTGGGATTGCTGGCTAGCCATATGCAGAAGACTGA 4389
                         v v   i       v      ivi    v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_98848770_9   4390 AATT-------TA------ACCATATACAGAAATTAACTCAAGGTGGATC 4426
                          i  -------  ------          i            ii      
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_98848770_9   4427 AAAGATTTAAAATTACAACTTCAAACTATAAGAATCCTGGAGGAAAACCT 4476
                          ?   ii    vv  vi vi v         i v  i i  i      v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_98848770_9   4477 AGGAG-ACACCATTCTGGATACTAGTCTTGGGAAACAATTTATCAC---T 4522
                            ? - v i -   vv  i-  v vv  i  v  iii   v i v--- 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_98848770_9   4523 GAGTCCTCAAAA--ACAATTGCAGCAAAAGCAAAAATTGACAAGTGGGAC 4570
                           -- vi     --    --   i      v      v  i  i v    
  L1M4_orf2#LINE/    597 GA--CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_98848770_9   4571 CTAATTAAA-CTAAAGACTTTCTGCACAGCAAAATAAACTATCAAAAGAG 4619
                         i v  i   -i    i     -  ii vv    iv v        i i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_98848770_9   4620 TAAACAGGCAAGCTACACAATGGTAGAAAATATTTGCAATCCATGTAGCT 4669
                          i  v  i   v i   v     v               vi   i  v  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_98848770_9   4670 GACAAAGATCTAATATCCAGAATCTATAAG----TCGTGTAAACAATTGA 4715
                           i  i iv  vi          v     i----  v ----    i v 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT----ACAACTCA 787

  chrX_98848770_9   4716 ACAAGGAATTTAAAAAAA----------AATTTAAAAATGAGCAAAAGAC 4755
                          i  ------      i ----------    ?       i     i  i
  L1M4_orf2#LINE/    788 ATAA------TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_98848770_9   4756 ATGACCACACATTTCTCAAAAGAAAAAATACAAGTGGCCAACAA--ATAT 4803
                         v   vi v         v      i v      i       i  -- i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_98848770_9   4804 CA-------CTCATCATCAGAGAAATA 4823
                         v -------    v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (130 / 98)
Gap_init rate = 0.03 (23 / 906), avg. gap size = 2.96 (68 / 23)  


3239 26.40 0.66 0.77  chrX_98866200_98872242     4642  5550 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98866200_9   4642 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4691
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98866200_9   4692 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4741
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98866200_9   4742 TACCAAGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4789
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_98866200_9   4790 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4839
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_98866200_9   4840 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4889
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_98866200_9   4890 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATACACC 4939
                                 i   i i  ii         i iv ii i   v     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_98866200_9   4940 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACT 4987
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_98866200_9   4988 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5037
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_98866200_9   5038 CTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5087
                           v  v  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_98866200_9   5088 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5137
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_98866200_9   5138 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 5186
                          i ?    i       v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_98866200_9   5187 TCTAGGCA-ATACCATTCATGACATAGGCATGAGCAAGGACTTCATGTCT 5235
                         iv    ?i- v i -   i    v v  vv ii    v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_98866200_9   5236 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5285
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_98866200_9   5286 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5335
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_98866200_9   5336 ACAGGCAGCCTACAGAATGGGAGAAAATTGTTGTAATCTACTCTTCTGAC 5385
                          v  i  i  i                 vv   i  vii iviv     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_98866200_9   5386 AAAGGGCTAATATCTAGAATCTACAAAGTACTCAAGCAAATTTACAAGAA 5435
                           i  i  vi    i     v  i    v    vvi   v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_98866200_9   5436 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 5485
                            i -    i     v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_98866200_9   5486 TCCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5535
                          i   v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_98866200_9   5536 ATCATCACTGGCCAT 5550
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2987 23.40 0.93 7.63  chrX_98930361_98934534     2712  3681 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_98930361_9   2712 AAAGATATTGCATGTTCACAAATTAGAAGAATCAATATTGTTAAAATGTC 2761
                                 iv        iii   i     v i           i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_98930361_9   2762 CATACTACCCAAAGCGATCTAAAGAGCCAATGCAATTTCTATCAAAATAA 2811
                         v     v      vi      v   vi   i     ii          vv
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_98930361_9   2812 CAATTACATTCTTTATAGAAATAGAAAAACCTATCCTGTAATTTATATGG 2861
                           ii i v  i   ii      v  v  i iv     iv    i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_98930361_9   2862 AATCATAAAAGACCAAGAATAGCCAAAGTTATGCTAAACAAAAAGGA--- 2908
                           viii  ii    v            iiv  vi i  v  i   i ---
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_98930361_9   2909 AACTGGAAAAATTGCATTAGTTGACTTCAAATTATACTACAAAGCTATAG 2958
                          ii    ii v ii  i vviii i      viv             i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_98930361_9   2959 TAACTAAAACAGCATGACACTGGCATAAAATCAGACACACAGACCACTGG 3008
                            ii  i    ii  ii          iivi     i i   i  v   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_98930361_9   3009 AACAGAATAGAGAACCTAGAAACAAATCCAAACACCTAGAGTGAACTCAT 3058
                           i     v    ii i     i   i   v   ii  vi  v  i v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_98930361_9   3059 TTTTGAAAAAGGTGCCAAGGCCATAAACATATACACCTAATATGTATCCA 3108
                            i  v  i         i    ----------------------  --
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCAT----------------------TC-- 379

  chrX_98930361_9   3109 CAAAAATTAAAAATTAAAAAATGAAATAACAAACATACACACTGGGAAAT 3158
                         -------------------    --------------------      v
  L1M4_orf2#LINE/    380 -------------------AATG--------------------GGGAAAG 390

  chrX_98930361_9   3159 GACAGTCTCTTTAATAAATGGTTGGTGCTGGGAAAACTGTATATCCATAT 3208
                         i i     i  i  i       ----       v     v   ?   i  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGT----GCTGGGACAACTGGATAKCCACAT 436

  chrX_98930361_9   3209 GCAGAAGAAAGAAACTAGATCTCTACCCCTTGCCATATACACAAATCAAA 3258
                            i     v   ii i  i i     i vii         v    i  v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_98930361_9   3259 TTAAAATGGATTAAATGTTTAAATCTAAGACCCCAAACTATAAAACTACT 3308
                          i         i ? viii     v     v iv             vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_98930361_9   3309 ACAAGAAAACATTGGAGAAATTCTCCAGGACTTTGGAGTGAGCAAAGATT 3358
                          v          v  ? v  v   i iv   i    iv ii    v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_98930361_9   3359 TATTGAGTAATACTCCATAAGCACAGGAAACCAAAGCAAACATGGACAAA 3408
                          v  iii  vv  v   v       i v   v    v   v  i  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_98930361_9   3409 TGGGA-----TCAAACCAAGTAAAACAGCTTCTCCACAGCAGAAGAAACA 3453
                          v   -----     --- v     --i   i vii vv  i i  v  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAA---ATTAAAA--ACTTTTGTGCTTCAAAGGACACT 681

  chrX_98930361_9   3454 AATCAACAAAATGAAGAGACAACCAACAGAATGGGAAAATATATTTGCAA 3503
                          -    v   i    i        v           i  v          
  L1M4_orf2#LINE/    682 A-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_98930361_9   3504 -TCTTCCCACCTGACAAGGGATTAATAACCAGAATATATAAGGAGCTCAA 3552
                         -  v vi- i    i      i vi  v             i  i   vv
  L1M4_orf2#LINE/    731 ATCATAT-ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_98930361_9   3553 ACAACTCTGTAGGAAAAAATCTAATAATCTGATAAAAAAAAGGGCAGAAG 3602
                                vi  iv     iv v     i ii  v?     v     i i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_98930361_9   3603 ATTTGAATAGACATTGCTCAAAAGAAGACATACAAATGGCAAATAGACAT 3652
                                        v   v        i           v    ii  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_98930361_9   3653 ATGAAAAGGTGCTCAACATCACTGATCAT 3681
                                 i            ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (137 / 86)
Gap_init rate = 0.01 (11 / 905), avg. gap size = 7.55 (83 / 11)  


2791 25.72 2.44 1.77  chrX_98941792_98947535     4357  5258 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98941792_9   4357 TAGAAAAACATTCCATGCTCATGGATAAAAAGAATCAATATCGTGAAAAT 4406
                          i    i i  i     i        vii    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98941792_9   4407 GGTCATACTGCCTAA-----TCTATAGATTCAATGGTATTCCCATTAAAC 4451
                           iv     v  i  -----    i        i vv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98941792_9   4452 TATCATTGACATTCTTCACAGAATTAGAAAAACT-ACTTTAAAATTCATA 4500
                          vi  vivi v  i  ii     v v  v  i  - iii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_98941792_9   4501 TGGAACCAAAAAAGAGT--GCATATCATCAAAACAGTCCTAAGCAA-AAG 4547
                              viiv  ii  vi-- v   v --       i  i i iv  -   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGC--CAAAACAATCTTGAAAAAGAAG 198

  chrX_98941792_9   4548 AACAAAGCTGGAAGCATCACATTACCAGACTT-GAAACTATACTACAAGC 4596
                                i    i vv     i v  vi i  -i     -        iv
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_98941792_9   4597 TTACAGTAACCAAAACAGCACAGTACTGGTACAAAAACAGACACACAGAA 4646
                         i        i   i    iiii       i i  ii i     i i   v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_98941792_9   4647 CAAAGAAATGGAATAGAGA-TCTGAGAAACAAGACCGCACATCTACAACC 4695
                            v i   i    v    -  i-     i  iv  ii    i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC-AGAAATAAACCCATACATTTATGGTC 346

  chrX_98941792_9   4696 ATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGAAGAAAGAAT--T 4743
                          vi    i  i     i v  v   i v  vv     ii        -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_98941792_9   4744 CCCACCATTAATAAATGGTGTTGGGAGAACTGGCTAGCCATATGCAGAAA 4793
                          iiv--- i  i        i     v      v  ?   i     i  i
  L1M4_orf2#LINE/    397 CTTT---TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_98941792_9   4794 ACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAG 4843
                          v    ii         v   i     v              i    i v
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_98941792_9   4844 GGATTAAAGACTTAAATGTAACACCCCAAATTATAAAAACCCTACAAAGC 4893
                             i ?    i         v v iv   i       vi i  -i   v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA-GAAGA 542

  chrX_98941792_9   4894 AAATCTAGGCAGTA--CCATTCAGGACATAGGCTCAGGCAAAGATTTCAT 4941
                            iv    ?-   --i -   iv   v v  v i      v i    v 
  L1M4_orf2#LINE/    543 AAACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_98941792_9   4942 -GATGATAACATCAAAAGCAATTGCAACAAAAGCTAATATTGACAAATGG 4990
                         -   -  i   i        vvv          vv  v  v  i    v 
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_98941792_9   4991 GATCTAATTAAACTAAAGAGCTTCTGCACACAAAAGAAC-CTATCAACAG 5039
                           ii v  i   v v  i i   i  ii viv    i  -       v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_98941792_9   5040 AGTAAACAGACAACCTACACGATGGGAGAAAAATTTTGCAA--TATATAT 5087
                            i  v        i   vi           vv       --i      
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_98941792_9   5088 CCATTTGATGAGGGGCTAATATCCAGAATCTGCAAGAAACTTAAACAAAT 5137
                          ----    i    i  vi          v ii  ii    ivv    v 
  L1M4_orf2#LINE/    740 C----TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_98941792_9   5138 TTACAAGAAAAAAAACAAACAACCCA-TTAAAAAGTGGGCAAAGAACATG 5186
                         iv i  v     i -    i      -  ?    i         i iv  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_98941792_9   5187 AACAGACATTTCTCAAGAGAAGACATTCATGAGGCCAAGAA--ACATGAA 5234
                           i           v i      i  v  viv      v  --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_98941792_9   5235 AAAAAGCTCCACTTCACTGATCAT 5258
                           i v    v  v   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (139 / 89)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.65 (38 / 23)  


3169 26.94 0.89 0.22  chrX_98962889_98965086      804  1705 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_98962889_9    804 TGGAAACACATCCCAAGCTCATGTATAGGTAGAATCAATATTGTGAAAAT 853
                               v i      v i     v  v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_98962889_9    854 GACCATACTGCCAAAAGCAATCTACAAATTCAAC-CAGTTTTCATCAAAA 902
                          i v     v  v   vii       i       -  i iiii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_98962889_9    903 TATCATCATCATTCTTCACAGAATTAGAAAAAAACAATCCTAAAATTTAT 952
                          vi  v vv v  i  ii     v v  v  iv-ii           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_98962889_9    953 ATGGAACCAAAGAAGAGCCAACATAGCCAAAGCAAGACTAAACAAAAAGA 1002
                               viiv iii  v   iv         i   vvi i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_98962889_9   1003 ACAAATCTGGGGGCATCACATTACCTGATTTCAAAGTATACTATAAGGCC 1052
                              vi   i  vv     i v  ii        iiv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_98962889_9   1053 ATAGTCGCCAAAACAGCATGATACTGGTATAAAAATAGGCACCTAGACCA 1102
                          i   vii   i    ii  i      i    ii    i  iv    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_98962889_9   1103 ATGGAACAGAATAGAGAACTGAGAAATTAACCCAAATACTTATAGCCAAC 1152
                               i     v    iiiv      v      v i i    i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_98962889_9   1153 AGATGTTTGACAAAGCAAACACAAATATAAAGTGGGAAAAGGACACCCTA 1202
                         v   v  i     i vviv  vi vi  vv i    i    i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_98962889_9   1203 TTCAACAAATGGCACTGGGATAATTGGCTAGCCACATGTAGGAGAGCGAA 1252
                                     ii      i  i   v  ?       i ii   ii   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_98962889_9   1253 ACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAAATAGATTA 1302
                         ii    i  ii i   v    v           i          i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_98962889_9   1303 AGGACTT-----TAAGACATGAAACTATAAAAATTCTAGAAGATAACTTT 1347
                         ?i   i -----     vv i           v ii       v   v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_98962889_9   1348 GGAA-AAACCTTTCTAGACATTGGCTTAGGCAATGACTTAATGACCAAGA 1396
                           ?i-   i   iv -   v    v          ii  vv iivi v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_98962889_9   1397 ACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATT 1446
                         vv         v v    i    iv   i   i   iv v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_98962889_9   1447 AAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAG 1496
                            v v  i i      ii vv    i iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_98962889_9   1497 ACAACCCACAGAGTGGGAGAAAATCTTCACAATTTATACATCTGACAAAG 1546
                                     i           v  ii   v i   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_98962889_9   1547 GACTAATATCCAGAATCTACAACGAACTCAAACAAATTAGCAAGAAAAA- 1595
                             vi          v  i  v      vv    v i ii  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_98962889_9   1596 ACAAACAATCCCATCTAAAAGTGGGCTAAGGACATGAATAAACAATTCTC 1645
                              i  i  v  i?    i     v     iv      i   v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_98962889_9   1646 AAAAGAAGATACACAAATGACCAATAAGCATATGGAAAAATGCTCAATAT 1695
                         v          i       i          i   i   i        i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_98962889_9   1696 CACTAATGAT 1705
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3362 26.65 0.44 0.44  chrX_99111428_99117818     4991  5898 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99111428_9   4991 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5040
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99111428_9   5041 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5090
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99111428_9   5091 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5138
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_99111428_9   5139 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGTCAAAAG 5188
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_99111428_9   5189 AACAAAGCTGGAGGCAACATGCTACCTGCCTTCAAACTATACTACAAGGC 5238
                                i      vvv  ii  v  iivi      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_99111428_9   5239 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGATATATAGATC 5288
                                 i   i i  ii         i iv ii i   i         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_99111428_9   5289 AATAGAACAGAAC--AGAGCCCTCAGAAACAATGCCACATATCTACAGCT 5336
                            i   i    i--    i  --     i  vv   i i  i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_99111428_9   5337 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5386
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_99111428_9   5387 CTATTTAACAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5436
                           v  i          i      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_99111428_9   5437 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5486
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_99111428_9   5487 TTAAAGACTTGAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5536
                          i ?    i i     v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_99111428_9   5537 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5586
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_99111428_9   5587 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5636
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_99111428_9   5637 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAA 5686
                          i   v v  i i   i  ii vv    i  v  i i  vv i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_99111428_9   5687 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5736
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_99111428_9   5737 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5786
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_99111428_9   5787 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5836
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_99111428_9   5837 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5886
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_99111428_9   5887 ATCACTGGTCAT 5898
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2810 27.69 1.55 1.11  chrX_99153510_99158937     4033  4935 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_99153510_9   4033 GAAAAAACGTTCCATGCTCATGGATAGGAAGAATCAATATTATTAAAATG 4082
                          i   i ii i     i        v      v i      i    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_99153510_9   4083 GTCATACTGCCTAGAGCAATTTACATATTCGGTGCTATACCTATCCAACT 4132
                          iv     v  i i vii  i    v    iii  v  v      v  v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_99153510_9   4133 ACCAATGACATTCTCCACAAAACTAGAAAAAGCT-ATTTTAAAACTTATA 4181
                         v   iivi v  i iii  i  v v  v  -   -  ii     i i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATA 150

  chrX_99153510_9   4182 TGGAACTAAAAAAAAAAAGAGCCCA-AACAGCCAAGGCAATCCTAAGCAA 4230
                              v iv  iii ------    -  i      ii     i i iv  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA------CCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_99153510_9   4231 AAAGAACAAAGCTGGAGGCATCATGTTACCTGACTTCAAACAATATTACA 4280
                         i          i      vv   iii v  ii i      vvv  i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_99153510_9   4281 GGGCTACAGTAACCAAAAAAGCATGATACTG-TACAAAAACAGACATATA 4329
                         ii          i   i v  ii  i     -i i  ii i         
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_99153510_9   4330 GACCAATGAAACAGAATAGAGAACCCAGAAATAAGGCCACACACCTACAA 4379
                           i     i  i     v    ii          iv   i   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_99153510_9   4380 CCATCTGATCTTCAACAAAGCTGACAATAACAAGTAATGGAGAGAAGACT 4429
                         i  vi    i   i    i v  v   v v  vvi     i  i ii iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_99153510_9   4430 CCCTATTCAATAAATTGCGTGGAGTTAACTGGGTAGCAATATGCAGAAGA 4479
                         vi  v     i    v i iv i vi      i  ? v i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_99153510_9   4480 CTGAAACTGGACCCCTTCCTTAAACCATATACAAAAATAAACTCAAGATG 4529
                         v    ii         v   i v               v       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_99153510_9   4530 GATTAAACGCTTAAGTGTAAAACCCATAACTATAAAAACCCTGGAAAACA 4579
                            i ? vi i   i     i v i v          vi i i   i v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_99153510_9   4580 ACCTAGGCA-ATACCATCCTGGACATAGGAACAGACAAAGATTTTAT-GA 4627
                           v    ?i- v i v  v  -  v v  ivi  i   v i   iv -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_99153510_9   4628 AA-GACACCAAAA--ACAATTGCAACAAAAGCAAAACTTGACAAATTGGA 4674
                         v -          --    --          v    v v  i        
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_99153510_9   4675 TCTAATTAAACTAAAGAGTTTCTGCACAGAAAAAGAAACT--CAACAGAG 4722
                         ii v  i   v v  i ii  i  ii vvv   i  v   --   v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_99153510_9   4723 TAAACAGACAACCTACAGAATAGGATGAAATATTTGCACACTATGCATCT 4772
                          i  v        i       i   vi           v ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_99153510_9   4773 CACAAAGGCCTAACATCCAGCATTTATAAGGAACT--TA-AATTTA-CAA 4818
                         v i  i  v  vii      v  v     i     --  -  i i -i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_99153510_9   4819 GAGAAAAACAAACAACCCAATTAAAAAGTAGGCAAAGGACATGAACAAAC 4868
                         v i   i     i         ?    i i         iv    i i  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_99153510_9   4869 ACTTTTCAAAAGAAGACATACATGTAGCCAAAAAGCATGTGGAAAAAAGC 4918
                          i  i  v        i     vi i     v     ii  i   i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_99153510_9   4919 TCAATATCACTGATCAT 4935
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (160 / 86)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 1.60 (24 / 15)  


3312 26.46 0.55 0.44  chrX_99195581_99201860     4881  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99195581_9   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99195581_9   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99195581_9   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_99195581_9   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_99195581_9   5079 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_99195581_9   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_99195581_9   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_99195581_9   5227 GTCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5276
                         ivi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_99195581_9   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_99195581_9   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_99195581_9   5377 TCAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                            ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_99195581_9   5427 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_99195581_9   5477 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5526
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_99195581_9   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_99195581_9   5577 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5626
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_99195581_9   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_99195581_9   5677 A-ACAAACAACCCCATCAAAAAGAGGGCGAAGGACATGAACAGACACTTC 5725
                          -     i     v  i?    iv    i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_99195581_9   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5775
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_99195581_9   5776 ATCACCGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2844 27.06 1.78 0.67  chrX_99218001_99224658.rev     5270  6167 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99218001_9   5270 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5319
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99218001_9   5320 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATTCCCATCAAGC 5369
                            v     v      v i  i  i       ii  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99218001_9   5370 TACCA-TTGAGTTTCTCAACAGAACTAGAAAAAGCT-ACTCTAAATTTCA 5417
                          v   -i  vv   i ii-     v v  v  -   - ii     v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_99218001_9   5418 AATGGAAGCAAAAAAGAACCTGTACAGCCAAGACAATCCTAAGCAAAAAG 5467
                         v      iiiv  ii  v  v v i      i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_99218001_9   5468 AACAAAGCTGGAGGCCTCATGCTACCTGACTTCAAACTATACTACAAGGC 5517
                                i      v    ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_99218001_9   5518 TACAGTAACCAAAACAGCATGGTACTGGTATTGAAACAGATATATATACC 5567
                                 i   i    ii         i  viii i   i     v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_99218001_9   5568 AATGGTACATAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCAT 5617
                              v i v  iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_99218001_9   5618 CTGATCTTCAAGAAATCTGACAAAAACAAGCAATTGGGAAAGGAAT-TTC 5666
                         i    i   i v  ivv  v   i v  vv    v       -   -v  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTC 397

  chrX_99218001_9   5667 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGCAGAAAACAG 5716
                          v  i  i              v      v  ?         i  i vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_99218001_9   5717 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAAGTCAAGGTGGAT 5766
                           ii         v   i     v              v    ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_99218001_9   5767 TAAAGACTTAAATGTATAACCTAAAATCACAAACACCCT-GGAAGAAAAC 5815
                         i ?    i        vi v      ii i   -  i  -i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chrX_99218001_9   5816 CTA--TGCAATACCATTCAGTACATAGGCATGGTCAAATACTTCATGACT 5863
                         v  --? i  - i -   ivv  v v  vv i v   vvii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_99218001_9   5864 AAAACACCAAAAGCAACTGCAACAAAAGGAAAATT-GACAACAGGGATCT 5912
                          vi            vvv          i    v -  i  vvv   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_99218001_9   5913 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAGTATCATCAGAGTGA 5962
                         v  i   v v  i i   i  ii vv    i  v v     vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_99218001_9   5963 ACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACCCGTCTGAC 6012
                          v  i     i                vv       vii ivii     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_99218001_9   6013 AAAGGTCTAATATCCAGAATCTACAAGGAACTTAAACGAAT--ATACTAG 6060
                           i  v  vi          v  i  i     ivv  i v --   v  i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_99218001_9   6061 AAA---AAA-GACC--ATCAAAATGTGGGTGAAGGACATGAACAGACACT 6104
                            ---   -i   --  i?   vi    ii     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_99218001_9   6105 TCTCAAAATAAGACATTTATGCAGCCAGCAAACATATAAAAAAA-GCTCA 6153
                             v   v    i  vi viii    ii  i  i  i    i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_99218001_9   6154 TCATCACTGGTCAT 6167
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (138 / 101)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.29 (22 / 17)  


3014 27.30 1.44 0.67  chrX_99270202_99276881.rev     5292  6192 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99270202_9   5292 TGGAAAAACATTCCATGCCCATGGATAGGAAGAGTCAATTTCGTGAAGAT 5341
                               i i  i     ii       v      v i   v i  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99270202_9   5342 GGCCATACTGCCCAAAGTAATTTATAGACTGAATACTATTCCCATCAAGT 5391
                            v     v      v i  i  i   i v  ii v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99270202_9   5392 TACCATTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTCA 5440
                          v   vivi i  i  ii     v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_99270202_9   5441 TATGGAACCAAAAAAGAGCCCGCATGGCCAAGACAATTCTAAGCAAAAAG 5490
                                viiv  ii  v  v v  i     i     ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_99270202_9   5491 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAA--CTA-TACAAGGC 5537
                                i      vv       v  ii i      --i  -     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_99270202_9   5538 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACT 5587
                                 i   i    ii         i iv ii i   i       ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_99270202_9   5588 AATGGAACAGAACAGAGGCCTCAGAAATCACACCACACGTCTACAAGCAT 5637
                                i    iv   ivii       v vv   i  i i  iiiv  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_99270202_9   5638 CCAATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5687
                         iii  i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_99270202_9   5688 ATATAATAAATGGTGTTGGGAAAACTGGCTAGCTATATGTAGAAAACTGA 5737
                         v vi  i        i     v      v  ? i i   i i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_99270202_9   5738 AACTAGTCCTCTTCCTTACACCTTATACAAAAATTAA-----GGTGGATT 5782
                          ii i v  i  v   i     v              -----ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_99270202_9   5783 AAAGACTTAAACGTAAGACCTAAAAACATAAAAACCCTAGAAGAAAACCT 5832
                          ?    i    i      v      vi      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_99270202_9   5833 AGGC---AATACGATTCAGGACATAGGCGTAGGCAAAGACTTGATGACTA 5879
                            ?---   - --   iv   v v  vv       v ii  vv iiv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT-C--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_99270202_9   5880 AATCACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAAATGGAATCTA 5929
                         viv           vvi          vv     v  i    v i ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_99270202_9   5930 ATTAAACTAAAGACCTTCTGCACAGCAAAAGCAACTATCATCATAGTGAA 5979
                           i   v v  i v   i  ii vv    i vv       vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_99270202_9   5980 CAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTATTCATCTGACA 6029
                         v  i     i i               v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_99270202_9   6030 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAA-AAA 6078
                          i  i  vi          v  i        ivv    v iv i  -   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_99270202_9   6079 AAGCACAAACAACCCCATCAAAATATGGGCAAAGGATATGAACAGACACT 6128
                            -     i     v  i?   v             v    i     i 
  L1M4_orf2#LINE/    796 AAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_99270202_9   6129 TCTCAAAAGAAGATATGTATGCAGCCAACAAACATATGAAAAAAAGCTCA 6178
                             v           ii viii     i  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_99270202_9   6179 CCACTGGTCATTAG 6192
                         v  iii????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


2578 26.80 1.38 5.19  chrX_99311394_99322522     4301  5244 (5885)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99311394_9   4301 TGAAAAAGCATTCCATGCTCATGGAGAGGAAGAGTCAATATCATTTAAAA 4350
                           i   iii  i     i       vv      v i     ii  -  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAGA 49

  chrX_99311394_9   4351 TGGCCATACTGCCCAAAGCAATTTATAGGTTCAACACTATTCCTATTAAA 4400
                             v     v      vii  i  i  i      i v  i     i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_99311394_9   4401 CTACCAATGATATGCTTCACAGAACTAGAAAAAAAACT-ATTTTGAAATT 4449
                         v v   iiviiv vi  ii     v v  v  i---  -  ii i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chrX_99311394_9   4450 CATGTGTAACCAAAAAAGAGCCCAAATGGCCAAGGCAATCCTAAGCAAAA 4499
                            i  v  viiv  ii  v  vi   i     ii     i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_99311394_9   4500 AGAACAAAGCTGAAGGCATCATGCTATCTAACTTCAAACTGTATTACAGT 4549
                                  i  i   vv   ii  vi i  i      viv  i    iv
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_99311394_9   4550 GCTACAGTAGCCAAAACAACATGGTACTGGTAGAAAAACAGACAGAAAGA 4599
                                  ii   i   iii         i v  ii i     v v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_99311394_9   4600 CCAATGGAACAGAATAGAAAATCCAGAAATAAGGCCAATCACCTACAACT 4649
                         i        i     v  i i           iv   vv  ii  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_99311394_9   4650 ATCTGATCTTTGAAAAACCTGACAAAAAATAAGCAATGGGGAAAGAATTC 4699
                          vi    i  i  v  ivv  v   i v-i vv               vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAG 395

  chrX_99311394_9   4700 CCTATGCAATAGATGGTGCTGGGATAACTGGCTAGCCAAATGCAGAAGAT 4749
                         i  v v   i i            i      v  ?   v     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_99311394_9   4750 TGAAACTGGACCCCTTGCTTACACCATATACAAAAGTTAACTCAAGATTG 4799
                             ii         vv  i               i         i  v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_99311394_9   4800 AGTAAAGACTTAAATGTAAAACCCAAAAGTA-AAAACTCAATTTAAACCG 4848
                          vi ?    i         i v i    v  -       ---   i v- 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC---TTAGAA-G 541

  chrX_99311394_9   4849 AAAAC-TAAATTTAAAGACTTAAATGTAAAACCCTGGAAGACAACCTAGG 4897
                              -  ii?v    v-   ---i  i --  i   i-------i    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT-CTT---CGTGA--CCTTGGG-------TTAGG 578

  chrX_99311394_9   4898 CAATACCATTCTGAACATAGGCATGAGCAAAGATTTCCTAATGAAGACGC 4947
                             --------------------------- i    i  ivv v   i 
  L1M4_orf2#LINE/    579 CAAT---------------------------GGTTTCTTAGATATGACAC 601

  chrX_99311394_9   4948 CAAAAGCAATTGCAACAAAAGCAAAAATTGGCACATGAGATCTAATTAAA 4997
                                 vvv          v      v ii v  vi  ii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_99311394_9   4998 CTAAAGAGCTTCTGCACAACAAAAGAAACTATCAACTGAGTGAACAGACA 5047
                         v v  i i   i  ii vv    i  v        vvi      v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_99311394_9   5048 ATGTACAGAGTGGGAGAAAATTTTTGCAATCTATTAATCTGACAAAGGTC 5097
                          ivi     i           v       vii  vv      i  i  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_99311394_9   5098 TAATGTCCCACATCTATAAAGTACTTAAACAGATTTACACGAAAAAAA-- 5145
                          vi i   viv  v       v   ivv   iv iv i vv     i --
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_99311394_9   5146 ---AAC---ATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAAA 5189
                         ---   ---   ?    i           iv    i     i  i  v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_99311394_9   5190 AGAAGACATATGAA--GTCAAGAATCGTATTTTAAAAAGCTCAACATCGA 5237
                               i   ii  -- i   v  v ii  vvv  i v          i?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_99311394_9   5238 GCCAAGA 5244
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.88 (62 / 16)  

3154 26.73 1.56 0.45  chrX_99311394_99322522     9739 10636 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99311394_9   9739 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 9788
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99311394_9   9789 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 9838
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99311394_9   9839 TACCAATGACTTTCTTCACAGAA-TTGGAAACAA-CT-ACTTTAAAGTTC 9885
                          v   iivi i  i  ii     -   ---    -  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_99311394_9   9886 ATATGGAACCAAAAAAGAGCCCAAATCGCCAAGTCAATCCTAAGCCAAAA 9935
                                 viiv  ii  v  vi   v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_99311394_9   9936 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 9985
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_99311394_9   9986 CTACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGAT 10035
                                  i   i i  ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_99311394_9  10036 CAATGGAACAGAACGGAACCCTCAGAAATAATACCACACATCTACAACCA 10085
                                 i    iv  ivvii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_99311394_9  10086 AACTAACCT--GACAAAAA---CAGGA------AATGGGGAAAGGATTCC 10124
                          -i i ii --     iii---  i  ------           i  vvi
  L1M4_orf2#LINE/    348 A-TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_99311394_9  10125 CTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 10174
                           v  v  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_99311394_9  10175 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 10224
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_99311394_9  10225 TTAAAGACTTAAATGTTAGACCTTAAACCATAAAAACCCTAGAAGAAAAC 10274
                          i ?    i       v   v  v    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_99311394_9  10275 CTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTAA 10324
                         v    ?i v viv   iv   viv  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_99311394_9  10325 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 10374
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_99311394_9  10375 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 10424
                          i   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_99311394_9  10425 AGGCAACCTACAAAATGGCAGAAAATTTTCGCAACCTACTCATCTGACAA 10474
                           i     i   i     v       v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_99311394_9  10475 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 10524
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_99311394_9  10525 AAACAAACAACCCCTTCAAAAAGTGGGCAAAGGACATAAACAGACACTTC 10574
                          i     i     vv i?    i           iv i  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_99311394_9  10575 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 10624
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_99311394_9  10625 ATCACTGGCCAT 10636
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.25 (18 / 8)  


2870 27.69 1.91 0.11  chrX_99365520_99370433     3530  4421 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99365520_9   3530 TGGAACCATATCCCATGCTCATGGAGGGGTAGAATCAATATTGTGAAAAC 3579
                              vv          i       vv  v   v i        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99365520_9   3580 GACCATACAGCCAAAAGCAATCTACAAGTTCAATGCAATTCCCATCAAAA 3629
                          i v    vv  v   vii       ii     i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99365520_9   3630 CACCACCATTATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCATA 3679
                         iv   v vviv  i  ii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_99365520_9   3680 TGGAACCAAAAAAGAGCCCACATAGCAAAAACAAGACTAAACAA-AAGAA 3728
                              viiv  ii  v  viv     v       vvi i  v  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_99365520_9   3729 CAAATCTGGAAACTTCAGATTACCCGACT--AGAACTATACTATAAGGGC 3776
                             vi    iivi   v i v   i i -- i    -     i  i vi
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_99365520_9   3777 ATAGTCACCAAAACAGCATGATACTGGTATAAAAATAAGTACGTAGGCCA 3826
                          i   v i   i    ii  i      i    ii   iii ii   ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_99365520_9   3827 ATGGAACAGAATAGAGAACCCAGGAATAAAGGTAAA----TACAGCCAAC 3872
                               i     v    ii    i      vvi v ----  ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_99365520_9   3873 TGATCTTCAACAAAGCAAACAAAAACA--AAGTGGGGGAAAGACACTCTA 3920
                             i   i    i vviv   i v  --v i     i  ii i v   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_99365520_9   3921 TTCAACAAATGGTGCTGGGATCATTGACAAGTCACACTTAGAAGAATGAA 3970
                                             iv i  ivv ?i    ivi i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_99365520_9   3971 ACTGGATCTTCATCTCTCATCTTATACAAAAATCAACTCAAGGTGCATCA 4020
                         ii    i iii i   v  i v           i       ii  v    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_99365520_9   4021 AGGACTTAATTCTAAGACCTGAAACCATAAAAATTCTA-AAGGTAACATC 4069
                         ?i   i   v v     v  i    i      v ii  -   iv     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_99365520_9   4070 GGAAAAACTCTTACAGACATTGGCTTAGGCAAAGACTTCATGACCAAGAA 4119
                           ?iv  v    vvv   v    v        v ii   v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_99365520_9   4120 CCCAAAAGCAAACACAGCAAAAACAAACATAAATAGATGGGACTT----- 4164
                         v         v vi  i     iv   v   i   i  v      -----
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_99365520_9   4165 -AATTAAAG-CTTCTGCACAGCAAAAGAAATAATCAGCAGAATAAACAGA 4212
                         -       i-   i  ii vv    i  v iv    iv i i i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_99365520_9   4213 CAACCCACAGAGAGGGAGAAAATCTTCACAATCTATACATTTGACAAAGG 4262
                                    iv          v  ii   vii   i  i   i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_99365520_9   4263 ACTAATATCCAGAATCTACAAGGAACTCAGACAAATCAGCAAGAAGAAAA 4312
                            vi          v  i  i      vv    v   ii  v  i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_99365520_9   4313 CCAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCA 4362
                          v  i  i  v  i?    i     v     iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_99365520_9   4363 AAAGAAGATGTACAAATGGCCAACAAGCATATGAAAAAATGCTCAACATC 4412
                                  i             i     i       i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_99365520_9   4413 ACTAATTAT 4421
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.25 (18 / 8)  


2202 24.62 0.30 4.41  chrX_99382164_99384631.rev      745  1402 (1066)    L1M4_orf2#LINE/L1        1   631 (277)  

  chrX_99382164_9    745 TGGAAATACATCCCATGCTCATGAATGAGTAGAATCAATATTGTGAAAAT 794
                               v i        i     i  vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99382164_9    795 GACCATAATGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAAA 844
                          i v   v v  v   vii       i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99382164_9    845 TACTACCATCATTCTTTGCAGGATTAGAAAAAACAATACTAAAATTCATA 894
                          v i v vv v  i       i v v  v  ivii  v            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_99382164_9    895 TGAAACCAAAAAAGAGCCTGCGTAGCCAAAGCAAGACTAAGCAAAAACAA 944
                           i  viiv  ii  v  v vi        i   v-  ------------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CT------------ 187

  chrX_99382164_9    945 AACAAAACAAAACAAAAAACAAAAAAACAAATCTGGAGGAATCACACTAC 994
                         ------------ii     --i  i      vi       v       v 
  L1M4_orf2#LINE/    188 ------------TGAAAAA--GAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_99382164_9    995 CTGATTTCAAGCTATACTATAAGGCCATAGTCACCAAAACATCATGGTAC 1044
                          ii       iviv     i  i  i i   v i   i   vii      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_99382164_9   1045 TGGTATAAAAATAGGCACATAGACCAATGGAACAGAATAGAGAACCCAGA 1094
                            i    ii    i  i     i        i     v    ii     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_99382164_9   1095 AATAAACCCAAATACTTAACAGCCAACTTATCTTCAACAAAGCAAACAAA 1144
                                   v i i   -ii i   i v  i   i    i vviv   i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTA-TGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_99382164_9   1145 AACATAAAGTTGGGGAAGGACACCCTTTTCAAAAAATGGTGCTGGGATAA 1194
                          v   vv i v   i   i i vi        v              i  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_99382164_9   1195 TTGGCTAGCCACATGTAGGAGAATTAAACTGGATCCTCATCTCTCACCTT 1244
                         i   v  ?       i ii     v  ii    i  ii i   v    v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_99382164_9   1245 ATACAAAAATCAACTCAAAATAGATCAAGGTCTTAAATCTAAGACCTGAA 1294
                                   i          i     ?i v i     v     v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_99382164_9   1295 ACTATAAAAATTCTAGAAGATAACATTGGAA-AAACCTTCTAGACATTGG 1343
                                  v ii       v     v  ?i-   i    vv   v    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_99382164_9   1344 CTTAGGCAAGGATTTCATTACCAAGAAC-CCAAAAGCAAATGCAATAAAA 1392
                         v        v i    -   vvv vi  -         v v    i    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTC-TTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_99382164_9   1393 ACAAAGATAG 1402
                         iv   i    
  L1M4_orf2#LINE/    622 GAAAAAATAG 631

Transitions / transversions = 1.37 (92 / 67)
Gap_init rate = 0.01 (7 / 631), avg. gap size = 4.43 (31 / 7)  

 969 23.18 3.46 0.35  chrX_99382164_99384631.rev     1689  1977 (491)    L1M4_orf2#LINE/L1      611   908 (0)  

  chrX_99382164_9   1689 AAAAAAAAAAAAAAAAAAAAGAATAGGTGGGACTTAATTAAACTAAAGAG 1738
                           iv  v    i      v   -  ii v      v  i   v v  i i
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGA-TAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_99382164_9   1739 CTTTTGCACTGCAAAAGAAACAGTCAGCAGAGTAGACAGGCAACTCATAG 1788
                               ii  v    i  v  vi   iv i   ii v  i    i  i  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_99382164_9   1789 AGTGGGAGAAAATCTTCACAA----TGTATGCA------GACTAATATCC 1828
                          i           v  ii   ---- i   vii------    vi     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_99382164_9   1829 AGAATCTACAACGAACTCAAACAAATCAATGAGAAACAAACAAACAATCC 1878
                              v  i  v      vv    v     i v   v i     i  i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_99382164_9   1879 CATCAAAAAATGGGCTAAAGACATGAACAGATAATTCTCAAAAGAAGATA 1928
                         v  i?          v  i  iv    i   i v     v          
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_99382164_9   1929 TACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCACTAATGAT 1977
                                      i  i  i       i             ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (39 / 27)
Gap_init rate = 0.01 (3 / 298), avg. gap size = 3.67 (11 / 3)  


1651 26.35 1.58 0.90  chrX_99511642_99520087     6649  7092 (1354)    L1M4_orf2#LINE/L1       10   456 (452)  

  chrX_99511642_9   6649 ATTCCACACTCATGGATAGGAAAAACCAATATTGTTTTAATGGCCATACT 6698
                           i   iii        v    i vii         vvi     v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_99511642_9   6699 GCCCAAAGCAATTTACAGATTCGATGCTATTCCTATCAAGCTACCAATGA 6748
                         v      vii  i         i i  v  i        iv v   iivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_99511642_9   6749 CATTCTGCACAGAA-TTAGGAAAAACT-ATTTTAAAATTCATATGGGACC 6796
                          v  i vii     -  --  v  i  -  ii              i vi
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_99511642_9   6797 AAAAAAGAGCCCAGAA-AGCCAAGGCAATCCTAAGCAAAAAGAACAAAGC 6845
                         iv  ii  -       -      ii     i i iv  i          i
  L1M4_orf2#LINE/    158 GCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_99511642_9   6846 TGGAGGTATCACACTACCCAACTTCAAACTATACTGCAAGGCTACAGTAA 6895
                               vv       v     i      viv    i   i          
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_99511642_9   6896 CCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACTAGAGGAAC 6945
                         i   i    ii         i i  ii i     i     ii iv    i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_99511642_9   6946 AGAATGGAGAGCCCAGAAATAATACCACACACCTACAACCATCTGACCTT 6995
                              v     i          vv   i   ii  iiii  vi   ii  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_99511642_9   6996 TGATAAATTTGACCAAAATAAG-CAATAGGGAAAGGACTCCCTATTCAAC 7044
                         i  i  ivv  -    i iv v-    i       i ivvi  v      
  L1M4_orf2#LINE/    357 CGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_99511642_9   7045 AAATAGTGCTGGGTTAACTGGCTAGCCACATGCA---GGTTGAAACTGGA 7091
                             i        vi      v  ?         --- iv    ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_99511642_9   7092 C 7092
                          
  L1M4_orf2#LINE/    456 C 456

Transitions / transversions = 2.14 (79 / 37)
Gap_init rate = 0.02 (8 / 447), avg. gap size = 1.38 (11 / 8)  

1140 23.48 1.01 9.72  chrX_99511642_99520087     7460  7953 (493)    L1M4_orf2#LINE/L1      458   908 (0)  

  chrX_99511642_9   7460 CCTTCTTTACACCATATACAAAAATCAATTCAAGATGGATTAAAGACTTA 7509
                            v i i                 i  i    i      i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_99511642_9   7510 GACGTAAAACTGAAAATTCTAAAAACCCTGGAAGAAGAAAAATAAGAAAA 7559
                         i i    i viv    i v     vi i i      --  v   i ?---
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA--AACATAGGN--- 552

  chrX_99511642_9   7560 TTCAAAAAAAAAAAAAAAACCCTGGAAGATAACCTAGGAAATACTCTTC- 7608
                         ------------------------------------ v    ---    -
  L1M4_orf2#LINE/    553 ------------------------------------GTAAAT---CTTCG 563

  chrX_99511642_9   7609 TGAACATAGGTCCTAG-CAAAGACTTCACAATTAAGACACCAAAATCAAT 7657
                            v v i   --   -   v ii   vi iv  v          v  vv
  L1M4_orf2#LINE/    564 TGACCTTGGGT--TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_99511642_9   7658 TGCAACAAAACCAAAATT-GACAAATGGAACCTGGTTAAACTAAAGGGCT 7706
                         v         vv    v -  i    v i  i vi i   v v  iii  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_99511642_9   7707 TCTGCACAGCAAAATAAGCTATCAAGAGAGTAAACAGACAACCTACAGAA 7756
                          i  ii vv    iv vi         i   i  v        i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_99511642_9   7757 AGGGAGAAAATATTTGCAAACTGTGCATTTGACCAAGGTCTAATATCTAG 7806
                         v                   iii ii  i   iv i  v  vi    i  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_99511642_9   7807 AATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAGCAAACAACCCA- 7855
                            v  i  i     ivv    v iv i  v     ii    i      -
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_99511642_9   7856 TTAAAAAAGTGGGCAAAGGACATGAATAAATATTTTTCAAAAGAAGACA- 7904
                           ?     -           iv      i i    i  v        i -
  L1M4_orf2#LINE/    812 TTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_99511642_9   7905 ACACGCAGCTAACAAGCATATGAAAAAATCACTGACCATTAAAGAAATG 7953
                            viii  i  i     i       i  -i  v v   i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (69 / 44)
Gap_init rate = 0.02 (11 / 451), avg. gap size = 4.82 (53 / 11)  


2829 18.05 4.08 1.88  chrX_99576261_99577889.rev      502  1138 (491)    L1M4_orf2#LINE/L1      258   908 (0)  

  chrX_99576261_9    502 CAAGA---TGTGATGCTGGCATA-GTATAGAGATATAGATCAATGAAATA 547
                              ---    i i        - v     v             i    
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_99576261_9    548 AAATTGAAAGTGCTGAAATATGCTTTAATATTTATGATCAATTGATTTTT 597
                         i      i   v v      vi iivv i       i            i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_99576261_9    598 TACAAAGGGACCATGACAATTCACTGAACACAGAATAGCATTTTCAACAG 647
                         v    i  vi   v   v     v  iiv v       iv         i
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_99576261_9    648 ATAGTGCTGAGACAA-TGGATACCCATATACAAAAGAGTAAATTTGAAAC 696
                           i      i     -      ?   i  i       i i  v   i v 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_99576261_9    697 CCCATAGTACACCATACACAAAAATTAACTCAAAAGGGATCATAGACCTA 746
                           i ivvi        i                  v      ?       
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_99576261_9    747 CATGTAAGATGTAAAAGTATAGAACTCTTACAAGGAGACATAGGAGTAAA 796
                         v        vv     v    i        v   i i       ?     
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_99576261_9    797 TTTTTTGTGACCTTGGGTTAAGCAGCATTTTCTTAGATATGATACGAATA 846
                          i  i-              i   iiiv              i  v  v 
  L1M4_orf2#LINE/    558 TCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_99576261_9    847 ACAGCAGCCATTAAAAAAAAAA-AGATAA-CTGAATTTCATTAAAGTTAC 894
                         i  vv   v iv   i      -      -i  i i     i   i   v
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_99576261_9    895 AA-TTTTTGTCTTTTAAATGA---TATTGAAAAGGTGAAAAGATAGCTCC 940
                           -i      vi  i   v  ---   ii i  i         i i i v
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_99576261_9    941 CAGACTGGGAGAAAATATTTGTAAAGTCATATATAAGACTTGGAACTGGT 990
                             v                i   -        vv  ivv  i   v  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATAAGGGACTTGT 755

  chrX_99576261_9    991 ATCCAGAACATGTAAAGAACTC---------AGTAATAAAAAGACAA--- 1028
                                 i  i          --------- i              ---
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_99576261_9   1029 -CTCAATTTTTAAAAACAAAAACAGGCAAAGG-TTTGAATAGACGTTTTT 1076
                         - i     ?--------     ii        -           i   --
  L1M4_orf2#LINE/    806 ACCCAATTW--------AAAAATGGGCAAAGGATTTGAATAGACATTT-- 845

  chrX_99576261_9   1077 CTCCAAAGAAGATATACAAATGGCCAATA-GCATGTGAAAAGATGCTCAA 1125
                                                      -   ii               
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_99576261_9   1126 TATCATTAGTCAT 1138
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (69 / 42)
Gap_init rate = 0.02 (15 / 651), avg. gap size = 2.53 (38 / 15)  


 470 29.89 13.49 3.17  chrX_99583234_99585548.rev      702  1079 (1236)    L1M4_orf2#LINE/L1        1   417 (491)  

  chrX_99583234_9    702 TGGAAAGATGTACTCTATTCTTGAGTAGGGAAGACTCA-CGTTATAAAGA 750
                                  i v iv i   v  ii -v        i -ii  i v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-TGGAAGACTTAATATTGTTAAGA 49

  chrX_99583234_9    751 TGTTAGTTTTCTCTAAATTAATTTATAAATTTAATGCACTTCCAAT-AAA 799
                           vi i vi  i i     i  i  i i   i  i   v i  v  -   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_99583234_9    800 CTACCATCT--TTTCTTTTCTGAAAG-GA------AATTCTAAAGCTCAT 840
                         v v   v  --i  i   v v    v-  ------i  i     ii    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_99583234_9    841 ATGGAAA-ATAAGCAAGCAAAAATAGCCAGGA--ATCTTTGCAATTGAAA 887
                                -ii   vi v v i        ii --     - v  vv   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT-GAAAAAGAAG 198

  chrX_99583234_9    888 AATCATATATTAAAAATGAAAAA-TAATAT------ATT--AAAA----- 923
                           i--------   iv  i ii - v i i------   --    -----
  L1M4_orf2#LINE/    199 AAC--------AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_99583234_9    924 TGTAAAGCCTCAAAAGTTAAGA--GTATGGTACTGGTGAATGAAGAGACG 971
                          ii     iv  iv i i    --  i         iiv v i v    i
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_99583234_9    972 ---GG------GGAACAGGACAGAAAGTCCTGAAATAGACGTAAATAGAT 1012
                         ---i ------    i  i iv  i     v      i  vi v i vv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_99583234_9   1013 ATGG------GAATTTAGTATAGGGCATTTCAAA-----TCAATGTGGTA 1051
                             ------  v   v - i i  -i vi   i-----      v  v 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCG-ACAAGG-GTGCCAAGACCATTCAATGGGGAA 388

  chrX_99583234_9   1052 AAAA-GGAATTTTTGATAAATGATACTGG 1079
                          i  -i vv    ii i     i i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGG 417

Transitions / transversions = 1.76 (72 / 41)
Gap_init rate = 0.05 (22 / 417), avg. gap size = 2.86 (63 / 22)  

 500 30.00 10.45 2.95  chrX_99583234_99585548.rev     1385  1824 (491)    L1M4_orf2#LINE/L1      436   908 (0)  

  chrX_99583234_9   1385 TGGAAAAAGATAAAGTTGGATCCACATCTCATGCCATATACCAGGCTAAA 1434
                           v    ii  i        i  vi i    ii        v iiv v  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_99583234_9   1435 CTCTAAGTAGATTGATGTTGTAAATTTAAAGAGAAATTAAGCCACAAAAG 1484
                            v  i i   ii?v viv     v   ---  iv v  i i i    v
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAA---GAGCTAAAACTATAAAAC 532

  chrX_99583234_9   1485 AACTGGAAGAAAACATAGGT-CAATTCCTCTACAGTCTTAGAGTGGGAGA 1533
                         vvi i              ?-i  v  i  -iiiii   i iv i  vi 
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAA 581

  chrX_99583234_9   1534 AGGCCTTTTTAACTATGATTCAAAATCCAGAAGCCATTAAGGAAAAA--- 1580
                         v  i-  i   iv     iv v   vv  v    v iv  i      ---
  L1M4_orf2#LINE/    582 TGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_99583234_9   1581 GATTAGGGCATTTGACTACATT----TTAAAAAAGTCTTTGTGA--CAAA 1624
                            v ----   v    v   i----       --ii      v--    
  L1M4_orf2#LINE/    631 GATAA----ATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAA 674

  chrX_99583234_9   1625 AAGCAACAT-AAGCAATGCAAAAAAAGAAAG-ACAAACTG--ATAAAATA 1670
                         iii  vi  -   v  - ii    i v  vv-   i v  -- v      
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAA-GTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_99583234_9   1671 TTTGCAATT--TGTGTC--ACAAAGAGCTGCTCTCT------CATAGAAA 1710
                                v -- i i  -- i  i ii  vv v  i------i   i i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_99583234_9   1711 ATGTC------------AAGAAAAAGGCCAACAACCCAATAGAAAAATCG 1748
                          i-  ------------  v      i v  i        v?      v 
  L1M4_orf2#LINE/    774 AC-TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_99583234_9   1749 ACATGGGACATTAACA---ATTT----AAAGAA---AGGGAAAGATCTCT 1788
                         i  vi   iv v  i ---    ----      --- viv   viv ivv
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_99583234_9   1789 TAAAAATATGAAAAGATGCCCAACCTCATTCACAAT 1824
                            iv i            i    v   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (72 / 57)
Gap_init rate = 0.04 (21 / 473), avg. gap size = 2.81 (59 / 21)  


 539 31.01 1.27 0.00  chrX_99587488_99589162       21   178 (1497)  C L1M4_orf2#LINE/L1   (534)   374   215  

C chrX_99587488_9    178 TCACCCTACATGACTTCAAA--CTATAGTAAGGCCACAGTAACCAAAATA 131
                             v  v vii i      --i  ivii  i  i       i   i i 
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

C chrX_99587488_9    130 GCATGGTACTGGTATAAAAACAGACACATAGACCAATGGAACAGAATAGA 81
                          ii         i    ii i     i     i        i     v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

C chrX_99587488_9     80 AAACTCAGAAATAAAGCCGCACACCTGCAATCATTGGATCTTTGATAAGG 31
                         i iii          v  ii   ii iiii   v v   i  i  i    
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

C chrX_99587488_9     30 CCAACAAAAC 21
                         viiv   i  
  L1M4_orf2#LINE/    365 GTGCCAAGAC 374

Transitions / transversions = 3.90 (39 / 10)
Gap_init rate = 0.01 (1 / 160), avg. gap size = 2.00 (2 / 1)  

2012 18.01 6.44 10.54  chrX_99587488_99589162      500  1182 (493)    L1M4_orf2#LINE/L1      254   908 (0)  

  chrX_99587488_9    500 TAAACAAGACAGTATGGTACTGGCATAAAGACAGACATGTAGACCGACAT 549
                            v         i              i  i      i    i i iiv
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_99587488_9    550 AATAGAAAAGAAAGCCCAGAAATCAATCCACACACATATATAGTCAAGGG 599
                                vv  i  i        v  i   i   -- v   i     vv 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACA--TTTATGGTCAATTG 351

  chrX_99587488_9    600 ATCTTCCACAAGGGTACCAAGACTACACAATGGGGAAAGGACAGTCTCTT 649
                           i   v        i       i iv            i i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_99587488_9    650 CAATAAA-GGTGTTAAGAAAACTGGGTATCCACAT--AAAAGAATGAAAC 696
                            i   -    i ii  v      i  ?      --           ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_99587488_9    697 TGGACCC-TATCTTATGTCATACACAAAAATCAATGCAAAATGGAATCAA 745
                                -  i  i iii    i        i  iv         -----
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA----- 496

  chrX_99587488_9    746 TTCAAAAAAGCACATGTACTCACATGTTCATCGCTGCACTATCCACCACA 795
                         -   ? --------------------------------------------
  L1M4_orf2#LINE/    497 -TCAWA-------------------------------------------- 501

  chrX_99587488_9    796 GCAAACCACACTAAAGACCTAAGCGTAAGACTTGAAACCATAAAACTTAT 845
                         ---------------       ii      vi i    i        iv 
  L1M4_orf2#LINE/    502 ---------------GACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_99587488_9    846 AAAATAAAACATAAGAACAAGCTCTT--TGACATTGGCCTTAGCAA-AGT 892
                          i  v        i ?ii  i-    --    v    vi vi    -i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_99587488_9    893 TTTTTTTTTATGACACCAAAAGCTCAA-CAACTAAAGCAAAAACAAACAA 941
                           i  vvv               v   -    v    v     i i i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_99587488_9    942 ATGGGACTACATCAAACTAAAAAGCTTCTG-----CAAAGGA----AGCA 982
                           v     v       v v    i   i  -----       ---- v  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_99587488_9    983 AGCAA-TAAAAAG----CCTATGGATTGGGAGAAAATACTTGCAAATCAT 1027
                           v  - i     ----  i ii  v            i           
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_99587488_9   1028 ATATCTGATAGGGAGTTAATTTCCAAAAT-TAACCAAGAAACTC--ACA- 1073
                                   i  iii vi v    i   -  --i  ii     --   -
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATA--TAAAGAACTCTTACAA 783

  chrX_99587488_9   1074 --TAATAGGAAAAAATCA--TAACTTA-TTAAAAGATGGGCAAAGGACCA 1118
                         --i    iv     iv  --    ii -  ?   i            iiv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_99587488_9   1119 GAATAGACATTTCTCCAAAAAAGA------------CAATAGGTATTTTT 1156
                                            i    ------------     i i iv --
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-- 881

  chrX_99587488_9   1157 GAAAA-ATGTTCAACATCACTAATCAT 1182
                              -   i         ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.22 (82 / 37)
Gap_init rate = 0.04 (23 / 655), avg. gap size = 5.04 (116 / 23)  


2907 24.68 2.07 1.03  chrX_99590325_99596461.rev     4190  4963 (1174)    L1M4_orf2#LINE/L1       30   811 (97)  

  chrX_99590325_9   4190 AAAATTTAATACTGTTAAAATGTCA-TACTACCCAAGCTGATCCACAGAT 4238
                           i i      i      i   v  -    v     ii     i      
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGAT 79

  chrX_99590325_9   4239 TCAATATAATTCCTATCAGAATTCTCATGGCAGTCTTTTT-ATAGAAACA 4287
                             iii   i       i   i -  --  v i      -ii     iv
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCC-CA--GCTGCCTTTTTTGCAGAAATT 126

  chrX_99590325_9   4288 GAAAAAATAATATTAAAATTCATATGGAGCCATAAAAGATCCA-AATAAC 4336
                           v  iv i  vi               iviii  ii  i   -    i 
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chrX_99590325_9   4337 CAAAATAATCTTCAAAAAGGAGAACAAAGTTGCAGCCATCACATTTTCTG 4386
                              i      v      i            v  vvv     i  i ii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_99590325_9   4387 ATTTCAAAATATGTTACAAAGCTTCAGTAAATGAAATAATTTGATACTGG 4436
                                  iv ii         v      vii i i i v  i      
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_99590325_9   4437 CATAAAGACAGACATACAGATTAACGGGACAGGAAAGAGAGCCAAGAAAT 4486
                              i  i       i    i  i  i i  i vv     i v      
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_99590325_9   4487 AAATCTACCTGTATAAAGTCAACAGATCTTCAACAAGCATTCCAGGAATG 4536
                            i i ivii v  vi     iv   i   i     vi v   i  vii
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_99590325_9   4537 CACAATGGGAAAAAGAT-------TCAACAAATGGTGCTGGGAAGAGTGG 4579
                         iv       i   ii  -------                   vi v   
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_99590325_9   4580 ATATGCACATAAAAAAGAATGAAATTGGACCCTTGTTTTACACCATACAC 4629
                            ?v     iv           i        i iii i        i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_99590325_9   4630 AAAAATCAACTCAAAATGGATTGAAGACTTAAACATAATACCAGAAACTG 4679
                               i              ii?    i    ii   v v vi     i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_99590325_9   4680 TAAAACTCCTAGAAGAAAACATAGGGAAAAGACTTCTTGATACTGGTCTT 4729
                                 i                ?iv  iv    v   ivi   vi v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_99590325_9   4730 GGCAATGATTTCATGGGTACTACACCAAAAACATATGCAACAAAAGCAAA 4779
                                i    v i i  iv         i  i v          v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_99590325_9   4780 AATAGACAAGTGAGCCCAGGTCAAAGTAAAAAGCTTCTGCACGGCAGAGG 4829
                               i  i vi v ivvi     i v    i   i  ii vv  i   
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_99590325_9   4830 AAAAAAACTTGATAGAGTGAAAAAGGAAAACT---AGAAATGGGAGAAAT 4876
                          v vv -- ii v i        --  v   i---    -         v
  L1M4_orf2#LINE/    677 ACACTA--TCAAGAAAGTGAAAA--GACAACCCACAGAA-TGGGAGAAAA 721

  chrX_99590325_9   4877 AATTTGCAAACCACATATTTGATAAGGGATTAATTTCCAAAATATATAAG 4926
                         v         i  i    i          i vi v    i         i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_99590325_9   4927 GAACTTCTATAACGCAATAACAAAAA-ACACAC--CCCAA 4963
                              ii  i   v      i     -   v i--     
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

Transitions / transversions = 1.98 (125 / 63)
Gap_init rate = 0.02 (12 / 782), avg. gap size = 2.00 (24 / 12)  

 406 20.88 0.00 0.00  chrX_99590325_99596461.rev     5561  5651 (486)    L1M4_orf2#LINE/L1      818   908 (0)  

  chrX_99590325_9   5561 AATGGGCTAAATACTTGAATATAAATTTCCCCAAAGAAGACAAACAAATG 5610
                                v  iv i       v v     i          i v       
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_99590325_9   5611 GTCAACAGGTATATGAAAATGTGCTCAATGCCACTAATCAT 5651
                          i   i i i i       vi       iii  ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.00 (0 / 0)  


1373 27.05 2.20 1.20  chrX_99602154_99604173        1   499 (1521)  C L1M4_orf2#LINE/L1   (98)   810   307  

C chrX_99602154_9    499 AGAATAAAGAACACAGAAATAACACCACACACCTACAACTATCTGATCTT 450
                              vi   iiv         vv   i   ii  iiiii vi    i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

C chrX_99602154_9    449 CAATAAATCTAACAAAAACAAGCAATGGTGAAAAGGAATC-CCTATTCAA 401
                          i i  ivv iv   i v  vv      v    --    v-i  v     
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAA--GAATAGTCTTTTCAA 404

C chrX_99602154_9    400 TAAATGGTGCTGGGAGAACTGACTAGCCAAATGCAGAAGATTGAAACTGG 351
                         i              v     iv  ?   v     i    v    ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

C chrX_99602154_9    350 AGCCCTTCCTTAAACCATATACAAAAATTCATTCAAGATCATTTGAAGAA 301
                          v    v   i v                v i    i  viv ii?   v
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

C chrX_99602154_9    300 TTAAATGTAAAATCCAAAACTATAAAAATCCTAGAAGACAACCT--GAGC 253
                         i         i v i            v  i       v   v -- ? i
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

C chrX_99602154_9    252 AATGCCATTCA-GGTCATAGGCATGGGCAAAGATTTCAT-GATGAGGATG 205
                           vv --   i- ii v i  i- i     v i    v -   - v  ii
  L1M4_orf2#LINE/    555 AAATC--TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT-ATGACA 600

C chrX_99602154_9    204 CCAAAAGCAATTGCAACAAAAACAAAAATCAACAAATGAGATCTAATTAA 155
                                  vvv         iv      vi i    vi  ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

C chrX_99602154_9    154 A-CTAAAGATCTCTGAACAGCAAAAGAAACTGTCAACAGAGTAAACAGAC 106
                          -i    i ii i  vi vv    i  v   i    v i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

C chrX_99602154_9    105 AATGTACAGAATGGGAGAAAATTTTTGCAAACTATGTATCTGACAAAGGT 56
                           ivi                 v        ii  i       i  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

C chrX_99602154_9     55 GTAATATCCAGCCTCTATAA-GAA-TCTTAAAA---AAAATTTACAAGAA 11
                         v vi       vv v     -   -     v  ---  v v v v    v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

C chrX_99602154_9     10 AAAAAACCCA 1
                            v      
  L1M4_orf2#LINE/    801 AAATAACCCA 810

Transitions / transversions = 1.10 (69 / 63)
Gap_init rate = 0.02 (12 / 504), avg. gap size = 1.42 (17 / 12)  

 443 25.00 3.33 0.00  chrX_99602154_99604173      500   619 (1401)    L1M4_orf2#LINE/L1      176   299 (609)  

  chrX_99602154_9    500 CCAACACAATATTGAA---GAAGAATAAAGTCAGAAGACTGACACTACCT 546
                             v     v     ---      i     ii  i    v     v  i
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_99602154_9    547 GAATTC-TTGCTTGCTATAAAGCTACAATAATGCAGTAAGTGTGGTACTG 595
                         i v   -vvi   i   i         i    vv  vv            
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_99602154_9    596 GTGAAAGAATAGATAAATAAGCCA 619
                          iiv   i     i v   iii  
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCA 299

Transitions / transversions = 1.31 (17 / 13)
Gap_init rate = 0.02 (2 / 124), avg. gap size = 2.00 (4 / 2)  

2003 23.99 3.08 1.13  chrX_99602154_99604173      911  1527 (493)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_99602154_9    911 AAGAATAGAAAAATAGATCAAGTGGG-CAAAATACAAAGCCCAGCAAATA 959
                            i     v v         -   i-i i   vv i  i    -     
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAA-TGGAATAGAATTGAGAGTCCAG-AAATA 327

  chrX_99602154_9    960 GACCACAAAAAA--ATAGTCAGCTGATGCTTGACAAGGGAGCATAGGCAA 1007
                         i   -  v v v--  i    ii    vi i        v  vv  i v 
  L1M4_orf2#LINE/    328 AACC-CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_99602154_9   1008 TACAATGGAGCAACGATAGTCTTCTCAACAAATGATGCTGGAACAACTAG 1057
                          v      i v  vi        i          i      i      i 
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_99602154_9   1058 ACATCCACATGCAAAAGGAAAAATCTAGACAAAGACTTTATACCTCTCAT 1107
                          i ?             i vi  vi i   vvvv  i i i   vivi i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_99602154_9   1108 AAAAATTAACTTAAAATGGATTATAGAGTTAAATGTAAAA--TATAAACT 1155
                                    i         i ?   vi         i --  -     
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAACT 525

  chrX_99602154_9   1156 ACACAACTCT-GGATTATAACATAGGAGAGAACCTAAATGACCCTGGATA 1204
                          i v      -i  vv v        ? vi  i  vvi     i   i v
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_99602154_9   1205 TGGCAATGACATTTTTGATTTAGCACCAAAAGCATAATCCATGAAA-AAA 1253
                         v       iiv i  v   v ii           i  v v ii   -   
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_99602154_9   1254 AAATTGATAAGCTGAAACCCATTGAAATTTAAAACTTCTGCTCTGCTTCA 1303
                             v     ii  i vii   ii     v       i  ---       
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG---TGCTTCA 672

  chrX_99602154_9   1304 ---GACACTGTTGAGAGAATGAAAA-ACAAGCCAAAAACTGGGAGAAAAT 1349
                         ---      i ii   i i      -    v   v i v           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_99602154_9   1350 ATTTGTAAAAGACATATCTGATAAAGGATTATTATCCAAAATATACAAAG 1399
                              i   vv i           i   i vv      i      i    
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_99602154_9   1400 AACACTTA-ACCTCAACAATAACAAAA-AAAC--CCTGATTTTAAAATGA 1445
                            v    - v     i     v  i -   i--  ii   ?v      i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_99602154_9   1446 GCAAAAGACTC----AGACATCTCATCAACGAATACATGCAGACAGAAAA 1491
                              i  i i----      i  vi   v   v i  i  i ii vv  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_99602154_9   1492 TAAACAAATGAAAAGATGCTCAACATCATATGTCAT 1527
                            i  v                     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (86 / 58)
Gap_init rate = 0.03 (16 / 629), avg. gap size = 1.62 (26 / 16)  


4188 16.44 4.68 1.03  chrX_99624884_99626974      725  1600 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99624884_9    725 TGGAAAGACATCCTGGGTTCATAGATTGGGAGACTTAAT-TTGTTAATAA 773
                                 i    iiv      i      i         -       v v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99624884_9    774 GGCAACATTAGCAAAATTGATCTACAAATTCAGAGCTATCA-TATCAAAA 822
                              i i vv v             i     iv  v   v-        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99624884_9    823 TTCTAACTGACTCATTTGCAGAAATTGACAGGCTGATCTTAAAATTAAGA 872
                          i i i   v  iv                i       i       v v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_99624884_9    873 TGAAAAGGCAAGAAACCTATAATAGGTAAAACAATCTTGAAAAAGAAAAA 922
                           i   v     ii   i v     vi                    i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_99624884_9    923 CCAAGTTGGATGACTCATTCTTTCTGATTTCAAAAC----------GGTA 962
                          v        v      iv   i ii          ---------- v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_99624884_9    963 CAGTAATCAAGACAGTGTTGCAATGGAATAAT-ACAGGCATATAGACCAA 1011
                                           v i v   v    v- i  i        i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_99624884_9   1012 TTGAATAGAATAGAAAGCCCAGAAACAAACCTTCGTGTATATGGTCCAAT 1061
                          v         v  i  i       i     iviiii v       v v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_99624884_9   1062 AATTTTTGAGAAGGGTACCAAGATCATTCAATGGAAAAAGGACAGTCTTT 1111
                         i     i  v      i      i          ii    i i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_99624884_9   1112 TCAAGAAATGGTGCTGTGAAAACTAGAT--------------GAATGAAT 1147
                             v           v  v    i   --------------       v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_99624884_9   1148 TTGTATCCCTACCTCACACACCATATATAAAAACTAACTCGAAATGGATT 1197
                            v i             --      i     i      i        i
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACAC--CATATACAAAAATTAACTCAAAATGGATC 498

  chrX_99624884_9   1198 AAAGATCTAAATGTAAAATCCAAA-CCATAAAACTCTTAGAAGAAAACAC 1246
                          ?   i          i v i   - i                      i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_99624884_9   1247 GGAGGTAA-TCATTCATGACCTTGGATTTGGCAATGAAGTCTTAGATATG 1295
                         i i?    -  -   i         i  v       ivv           
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_99624884_9   1296 ACACCAAAAGTACAAGCAACAAAAGAAAAAA-AAATATGTAATGTGGAAT 1344
                                   i                    - i   ---   -    v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA---AAT-TGGACT 643

  chrX_99624884_9   1345 TCATGAAAATCCAAA-CTTTTACAGATCAAAAAACATTATCAAAAAAGTG 1393
                             v     iv   -     iiivv     ii   i      i      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_99624884_9   1394 AAAAGGTCACCTATAAAATGGAAGAAAATATTTACAAATTAAATGCATGA 1443
                              iiv   i i i     i           i     i v  iiv   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_99624884_9   1444 CAAGGGACTT-TATCCAGAACACATAAGAAAACCTCTTACAACTCAATAA 1492
                         i         -         i i    ii  --                 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAA--CTCTTACAACTCAATAA 791

  chrX_99624884_9   1493 TAAAAATACAAATAACCCAATTTAAAAACT--CAAGAGATTTGAATAGAC 1540
                               v               ?     iv--   ii             
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_99624884_9   1541 ATT------AAGAAGATATACAAATGGCTAATAAGCACATGAAAA-ATGC 1583
                            ------                   i                -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_99624884_9   1584 TCAACATAATTAGTGAT 1600
                                v ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (90 / 51)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.78 (50 / 18)  


1009 22.55 11.41 5.98  chrX_99721889_99723786.rev      499   866 (1032)    L1M4_orf2#LINE/L1      245   632 (276)  

  chrX_99721889_9    499 AAG-TATAGTAATCAAGACAGTGTGGTGTTGGT----GAAAAGACAAATA 543
                            -  i                    ii   i---- i v     v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_99721889_9    544 GGTCAATGGAAAAAAATAGAGAGCCCAGAAGTAAACCCACACAGGTGTGT 593
                          i         v i   v     i      i        i   vv i  v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_99721889_9    594 TGAAATGATTTTTGACAAAAGTGCAAAAACAATTAAGTGGAAGAAAGATA 643
                          v  v       i     ii    v  i  v   v i   iii  ii   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_99721889_9    644 GCCTTC-AAACAAACGGTGCTGGAGCACTTGTACTTCCATATGCAAAAAA 692
                          i   i-v      i        ii  vi  v iv?   i        i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_99721889_9    693 AAAAAAAAAAAAAAAAAAAACCCCACCTCGACCTAAGTCTCACACCTTAT 742
                          vi  i--------------------i v    ivvii        v   
  L1M4_orf2#LINE/    445 ATGAAG--------------------TTGGACCCCTACCTCACACCATAT 474

  chrX_99721889_9    743 ACAAAAATTAACTCAAATGGGATCATGGACTTGAA----------AAAAC 782
                                          vv      ?i   i i  ----------     
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_99721889_9    783 ------------AGGAGAA------GG------TCACTGGGATTTAGGGC 808
                         ------------  i    ------  ------  vii v  ii v   i
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_99721889_9    809 TAAGCAAAGTGGT--CTGAGGTATGACACCAACAGCAGAATTAATAAAAG 856
                           i    --    --  v  i           v    v  vi  i     
  L1M4_orf2#LINE/    575 TAGGCAA--TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_99721889_9    857 AAAAATTAAA 866
                              v  i 
  L1M4_orf2#LINE/    623 AAAAAATAGA 632

Transitions / transversions = 1.61 (50 / 31)
Gap_init rate = 0.03 (10 / 388), avg. gap size = 6.40 (64 / 10)  

 581 23.27 3.14 0.00  chrX_99721889_99723786.rev     1249  1407 (491)    L1M4_orf2#LINE/L1      745   908 (0)  

  chrX_99721889_9   1249 AAGGGACTAGTATTTAAAATATAGAAAGAACTCTCAAAAC---AT--TGA 1293
                                 v    ii i      v          i v   ---  -- i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_99721889_9   1294 AAAAGCAAACAATCCAGTTAGAACATGGACAAAAGATATAAGCACACATG 1343
                            ii    i  i   i  ?i  v    i    i   v i ii v    v
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_99721889_9   1344 GCACTGAATAGGCTACACCGATGGCAAATAAGCACATGAAAAGATGTTCA 1393
                         v v ii  v i v  i  vi     v                    i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_99721889_9   1394 GCATCATTAATCAT 1407
                         i     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (23 / 13)
Gap_init rate = 0.01 (2 / 164), avg. gap size = 2.50 (5 / 2)  


1250 20.49 27.08 3.47  chrX_99772975_99774542      500  1075 (493)    L1M4_orf2#LINE/L1      197   908 (0)  

  chrX_99772975_9    500 AGAACAAAGC-GGAA-ACTTA-AC---CTGATTTTAAGAGACACTATAAA 543
                                  i-   i-   i -  --- ii    i  i vvi    i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_99772975_9    544 TCCACAGTAATCAAGTCAATGTGGTACTGGGCAGGAAGACAGACAAATAA 593
                         v i            v  i           -  vi i  i     v   i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGG-CATAAGGATAGACATATAG 295

  chrX_99772975_9    594 AC-----GAACAGAATAGAGAGTATGGAAATAAGCCCTCATGTTTATAGT 638
                          i-----   i     v      vii       i   vi ii     i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_99772975_9    639 CACTTGATTTTTTAAATAAAGGT--TAAGGGAAGTTTAGTGGAGAAATGG 686
                           v        i--i i  i   --i   ivv -  i i   i    vii
  L1M4_orf2#LINE/    346 CAATTGATTTTC--GACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAA 392

  chrX_99772975_9    687 CAGTCTTTTCAACAAGTAGTGCTGGAAAAACTAGATATCCATATG-AAA- 734
                         i              i i       i v    i    ?   i   -   -
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_99772975_9    735 ---------------------------------CAAAAA----------- 740
                         ---------------------------------      -----------
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_99772975_9    741 ----------------------------------------------AAGC 744
                         ----------------------------------------------   v
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_99772975_9    745 AAGCAT-------------------------------------TTCT--G 755
                           i   -------------------------------------    -- 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_99772975_9    756 ACATGACACGTAAAACGTGATC--CAGAAC------TTGATAAATTAGGC 797
                          i       vv   i iii v --  i  v------ v        i i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_99772975_9    798 TTCATCAAAATTTAAAACCTCTG--CTTTGTAAGAACTTTATTA-GAAAA 844
                                     v     i i  --   ii-   i  vi   i -    i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAGAAAG 691

  chrX_99772975_9    845 TAAAAAGATAAGCAGTATACTGGAAGAAAATATTTGCAACTAGTATATCT 894
                          i      i  v vii v v   i               v vi       
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_99772975_9    895 GATAAGG-ACTTATATCCAGCATATATAAAGAACTCTCAGAACTCTACAA 943
                                -    i       v                i v     v i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_99772975_9    944 TATTTTTAAAAACACAAATTTAAAAAATAGACAATGATATGAATAGACAA 993
                           ------    v      ------  iv--    v?v -i   i i   
  L1M4_orf2#LINE/    792 TA------AAAAGACAAAT------AACC--CAATTWAA-AAATGGGCAA 826

  chrX_99772975_9    994 AAGATATGAATAAACATATCACCAAAGAAGATATACAAATAGCAAATAAA 1043
                          i   v      i    v  v                   i  v     i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_99772975_9   1044 CACATGAAAACATGATCAACATCATTAATCAT 1075
                                   v   v         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (75 / 41)
Gap_init rate = 0.03 (24 / 712), avg. gap size = 7.33 (176 / 24)  


3288 26.19 0.44 0.11  chrX_99837979_99842469.rev     3096  4000 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99837979_9   3096 TGGAAACACATCCAATGCTCATGGATGGGTAAAATCAATATTGTGAAAAT 3145
                               v i    v   i        v  v i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99837979_9   3146 GACCATACTGCCAAAAGCAATCTACAAACTCAATGCAATTCCCATGAAAA 3195
                          i v     v  v   vii       i i    i     i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99837979_9   3196 TACCACCATCATTCTTCACAGAATTGGAAAAAACAATTCCCAAAATCATA 3245
                          v   v vv v  i  ii     v v  v  ivii  i iv   v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_99837979_9   3246 TGGAACCAAAAAAGAGCCTGTATAGCCAAAGCAAGACTAAACAAAAAGCA 3295
                              viiv  ii  v  v v         i   vvi i  v  i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_99837979_9   3296 CAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGCCA 3345
                             vi      vv       v  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_99837979_9   3346 TAGTCATCAAAACAGCATGGTACTGGTATAAAAATCGGCACATAGACCAA 3395
                         i   v     i    ii         i    ii  v i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_99837979_9   3396 TGGATCAGAATAGAGAACCCAGAAATAAACCCAAATACTTATGGCCAACT 3445
                             vi     v    ii               v i i      i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_99837979_9   3446 GATCTTCCACAAAGCTAACAAAAACGTAAAGTGGGGGAAAGGACACCCTT 3495
                            i   v    i v iv   i v i vv i     -    i i vi   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTT 399

  chrX_99837979_9   3496 TTCAACAAATCGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAA 3545
                                   v         i  i   v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_99837979_9   3546 ACTGGATCCTTATCTCTCATCTTATACAAAAATCAACTCAAGATGGATTA 3595
                         ii    i  i  i   v  i v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_99837979_9   3596 AGGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGGTAACATT 3645
                         ?i   i    iv     v  i           v ii      iv     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_99837979_9   3646 GGAAAAACCCTTCTATACATTGGCTTAGGCGAGGACTTCATGACCAAGAA 3695
                           ?iv  vi    vvv  v    v      i v ii   v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_99837979_9   3696 CCCAAAAGCAAGTGCAACAA---CAAAAATTAATAGCTGGGACCTAATTA 3742
                         v         viv       ---v      vi   iv v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_99837979_9   3743 AACTAAAGAGCTTTTACACAACAAAAGGAACAGTCAGCAGAGTAAAAAGA 3792
                           v v  i i     iii vv    i iv  vi   iv i   i      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_99837979_9   3793 CAACCCACAGAGTGGGAGAAAAGCTTTACAATCTATACATCTGACAAAGG 3842
                                    i          vv   i   vii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_99837979_9   3843 ACTAATATCCAGAATCTACAACCAACTCAAACAAATCAATAAGAAAAAAA 3892
                            vi          v  i  vv     vv    v       v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_99837979_9   3893 TAA-CGATCCCATCAAAAAGTGGACTAAAGAGATGAATAGACAAGCCTCA 3941
                         i  -ii i  v  i?    i   i v  i  vv          vvi   v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_99837979_9   3942 AAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATC 3991
                                                i  i  i       i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_99837979_9   3992 ACTAATAAT 4000
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.26 (130 / 103)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.67 (5 / 3)  


3107 25.34 2.70 0.45  chrX_99867603_99872683.rev     3703  4590 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99867603_9   3703 TGGAAACATCTCCCATGCTCATGGATGGGTAGAATTAATATTGTGAAAAT 3752
                               v  v       i        v  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99867603_9   3753 GACCATACTGCCAAAAGCCATCTACAAATTCAATGCAATCTCTATCAGAA 3802
                          i v     v  v   viv       i      i      i      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99867603_9   3803 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCCCAAAATCATA 3852
                          v   v vv v  i  ii     v v  v  ivii  i iv   v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_99867603_9   3853 TGGAACCAAAAAAGAGCCCGCATAGCCAAAGGAAGACTAAGCAAAAAGGA 3902
                              viiv  ii  v  v v         iv  vvi i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_99867603_9   3903 CAAATGTGGAGGCATCACACTAGCTGATTTCAAACTATACTATAAGGCCA 3952
                             vv      vv       vv ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_99867603_9   3953 TAGTCACCAAAACAATGTGGTACTGGTATAAAAATAGGCACGTAGACCAA 4002
                         i   v i   i   i           i    ii    i  ii    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_99867603_9   4003 TGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTAGAGCCAACT 4052
                              i     v    ii               v i i   vi i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_99867603_9   4053 GATCTTCAACAAAGCAAACAAAAACA--AAGTGGGAAAAGGGCACCTTTT 4100
                            i   i    i vviv   i v  --v i    i    iii vii   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_99867603_9   4101 TCAACAAATGGTGCTGGGGTAATTGGCTAGCCACATGTAGGAGAATGACA 4150
                                           ii  i   v  ?       i ii       vi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_99867603_9   4151 ATGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTAA 4200
                         v    i  ii i   v    v           i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_99867603_9   4201 GGACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATTG 4250
                         i   i    iv     v  i           v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_99867603_9   4251 GAAAAACCCTTCTAGACATTGGCTTCAGCAAGGATTTCATGACCAAGAAC 4300
                          ?iv  vi    vv   v    v  vi    v i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_99867603_9   4301 CCAAAAGCAAATGCAATAAAAAGATAAATAGCTG----GGATCTAATTAA 4346
                                  v v    i    ii v      v i----   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_99867603_9   4347 ACTAAAGAGCTTTTGCACAGAAAAGGA-ACAGTCAGCAGAGTAAACAGAC 4395
                          v v  i i      ii vvv      -  vi   iv i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_99867603_9   4396 AACCCACAGAGTGGGAGAAAAGCTT--CAGAATCTATACATCTGACAAAG 4443
                                   i          vv  --  -    -   i      i  i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGATAAGG 748

  chrX_99867603_9   4444 GACTAATATCCAGAATCTACAACGAACTCAAACAAATCAATAAGAAAGAA 4493
                             vi          v  i  v      vv    v       v   -- 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA--A 796

  chrX_99867603_9   4494 AAACCCACAATCCCATCAAAAAGTGGACTAAGGAGATGAATAGACAATTC 4543
                          i  vv i  i  v  i?    i   i v     vv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_99867603_9   4544 TC---AAAAGATACACAAATGGC------------GAAAAAATGCTCAAC 4578
                           --- i      i         ------------     i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_99867603_9   4579 ATCACTAATGAT 4590
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (120 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.11 (28 / 9)  


2940 24.50 0.83 6.15  chrX_99918265_99920432.rev      720  1678 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_99918265_9    720 TGGAAAAACATTCCATACTAATGGATAGGAAGAATCAATATCATTAAAAT 769
                               i i  i    ii v      v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_99918265_9    770 GGCCCTACTGCCCAAATCAATTTACAGATTCAACACTATTCCTACCAAAC 819
                            vv    v       ii  i            i v  i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_99918265_9    820 TACCAATGACATTCTTCACAGAATAAGAAAAAAAAACT-ATTTCAAAATT 868
                          v   iivi v  i  ii     ---- vvi v  i  -  iii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA----ATTGACAAGCTGATCCTAAAATT 146

  chrX_99918265_9    869 CATATGAAACCAAAAAAGAGCCCAAATAGCCAAGGCAATCCTAAGCAAAA 918
                               i  viiv  ii  v  vi         ii     i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_99918265_9    919 AGAACAAAGCTGGAGGCATCATGTTACCCAACTTCAAA--CTA-TACAAG 965
                                  i      vv   iii v     i      --i  -     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_99918265_9    966 GCTACAGCAACCAAAACAGCATAGTACTGGTATAAAAACAGACACACAGA 1015
                                i  i   i    ii i       i    ii i     i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_99918265_9   1016 CTGATGGAACAGAATAGAGAGCCCAGAAATAATGTTGCATATCCATGACC 1065
                         iii      i     v     i          vviiii i  ii   ii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_99918265_9   1066 ATGTGATCTTTAACAAAGTCAACAAAAATAAGCAATGGGGAAAGGAC--T 1113
                          vv    i  ii    i viiv   i vi vv            i i-- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_99918265_9   1114 CTGTTCAATAGGTGGTGCTGGGATAACCGGCTAGCCATATGAAGAAGATT 1163
                           v     i ii           i   i  v  ?   i   v i    v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_99918265_9   1164 GAAACTGGACTCTTTCCTTACACCATATACAAAAACCAACTCAAAATGGA 1213
                            ii     i i v   i                ii             
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_99918265_9   1214 TTAAAGACTTAAATGTAAAACCCCAAACTATAAACACCGTAGAAGACAAC 1263
                          i ?    i         i v iv          --------------  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA--------------AC 532

  chrX_99918265_9   1264 CACCCTGGAAGACAACCTAGGCA-ATACCATTCAGGACATAGGCCCTGGC 1312
                         i-- i i     v   v    ?i- v i -   iv   v v  viiv   
  L1M4_orf2#LINE/    533 T--CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGC 579

  chrX_99918265_9   1313 AAAGATTTCAT-GATGAAGATACCAAAAGCAAATGCAACAAAAATAAAAA 1361
                           v i    v -   - v  i          v v         iv     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_99918265_9   1362 TTGATGAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGCA 1411
                          v   i   v   ii v  i   v v  i i   i  ii vv    i vv
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_99918265_9   1412 ACTACCAAGAGAGTAAACAAACAACCTACAGAATGGGAGAAAATATTTGC 1461
                             i     i   i  v i      i                       
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_99918265_9   1462 AAACTACACATCCGACAAAGGTCTAATATCTAGCATCTATAAGGAACCTA 1511
                            ii i i   i  i  i  v  vi    i  v  v     i    iiv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_99918265_9   1512 AACAAATTAACAACAACAACAAAAAAACACAAATTATCCCATAACAAAGT 1561
                         v    v ------   i  i     i   --   v i  v  --------
  L1M4_orf2#LINE/    779 TACAACT------CAATAATAAAAAGACA--AATAACCCAAT-------- 812

  chrX_99918265_9   1562 GTGCAAAGTCTCAAAAAAAAAAAAAAAGTGGGCAAAGGACATAAAGAAAC 1611
                         ---------- ?     -----------           iv i  v i  
  L1M4_orf2#LINE/    813 ----------TWAAAAA-----------TGGGCAAAGGATTTGAATAGAC 841

  chrX_99918265_9   1612 ACTTTTCAAAAGAAGACACACACGCAGCCAACAAGCATATGAAAAAATGC 1661
                          i  i  v        i i   viii     i     i       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_99918265_9   1662 TCAACATCGCCGATCAT 1678
                                 i????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (155 / 76)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.47 (67 / 15)  


 598 12.40 1.65 4.13  chrX_100213819_100217323.rev     1474  1594 (1911)    L1M4_orf2#LINE/L1        1   118 (790)  

  chrX_100213819_   1474 TGGAATGACATATGATGTTCATGCATTGGAAGACTTAATATTATTAAGAT 1523
                              v  i  viv         v                  i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100213819_   1524 GGCAATACTACCCAAATT--TCTACAGATTACAAGCCATTATCTATCAGA 1571
                                  v        --          -   vv  v vi      i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT-CAACGCAATCCCTATCAAA 99

  chrX_100213819_   1572 ATCGCAGCTGGATCCGTTTTTTG 1594
                            v      ---  -       
  L1M4_orf2#LINE/    100 ATCCCAGCTG---CC-TTTTTTG 118

Transitions / transversions = 0.50 (5 / 10)
Gap_init rate = 0.03 (4 / 118), avg. gap size = 1.75 (7 / 4)  

3461 17.54 3.54 0.57  chrX_100213819_100217323.rev     1899  2605 (900)    L1M4_orf2#LINE/L1      102   829 (79)  

  chrX_100213819_   1899 CCCGGCCTGGATTCTTTATAGAAATTAATAAGCTGGTCCTAAAATTCATA 1948
                            i  -  vv  i   ii       i i      i              
  L1M4_orf2#LINE/    102 CCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_100213819_   1949 TGGAATTTCAAAGAACCAACAATAGCCAAAACAATCTTGAAAAAGAAGAA 1998
                              v v   i i   v v                              
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_100213819_   1999 CAA-GTTGGGGAACTCACATTTTCTGATTTCAAAGCTTACTACAAAGCTA 2047
                            -     i i       i  i ii        i               
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_100213819_   2048 TACGGATCAAGACAGCATT-TACTGGCATGAGGATAGACATATAGATCCA 2096
                         i vvi          ii v-         i                  v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_100213819_   2097 TAAAATAGAATTAAGAGTCCA------------TACATCTATGGTCCATT 2134
                          ii         i        ------------     i       v   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_100213819_   2135 GATTTTAGACAAGGGTGCCAAGACATTTTAATGGG-AAAGAGTAGCCTTT 2183
                               v                 vv  i      -     i   i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_100213819_   2184 TCAACAAATGGTGTGGGTACATTTGTGTACTCACACACACAAAAATGAAG 2233
                                      iv  v   vi  vi  ?i    ii  v  i       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_100213819_   2234 TTGTATACTTAAATCACAACATATACAAGAGATAA-----AATTGATTTA 2278
                            v iv i  vv     v         i iv   -----   v   i--
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC-- 498

  chrX_100213819_   2279 AAAAACCCAAATATAAGAGTTAAAACTATAAAATTCTCAGAC-AAAACAG 2327
                          ? i   i    i      i             i   i   v-      v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_100213819_   2328 AGGAGTAAATCTTTGTAACCTTGGGTTAGGCAGTGATTTCTTAAGCTCTG 2377
                            ?         i  i               i  i       - v v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-GATATG 597

  chrX_100213819_   2378 ACAACAAAAGCATAAGCAATAG--GAAAAAAAAGTGAAATTTCATTTCAT 2425
                            v        i      i i--       v  vv     vv i     
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_100213819_   2426 CAAAATTAAAAACCTTTGTAAATCAAAAGACATTAACAAAAAAGTGAA-- 2473
                                      i     ivv     i    i  v   i        --
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_100213819_   2474 GACAACCCACAAAATTGGAGAAAACTTTTGCAAATTACATATTTGATAAA 2523
                                    i   v        iv         i i    i      i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_100213819_   2524 GGATTTGTATCTAGAATATAAAAAGAACCATTATAACTTGATAATAAAAT 2573
                            i       i        v       iv   i    ii         v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_100213819_   2574 CACAAATAAACTCATTAAAAAATGAGCAAAGG 2605
                         v        v iv   ?       i       
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.55 (73 / 47)
Gap_init rate = 0.02 (11 / 728), avg. gap size = 2.64 (29 / 11)  

 513  9.47 4.21 0.00  chrX_100213819_100217323.rev     2920  3014 (491)    L1M4_orf2#LINE/L1      810   908 (0)  

  chrX_100213819_   2920 AATTTAAAA-TGAGCAGAG--TCTGA-TAGACATTTCTCCAAAGAAAATA 2965
                             ?    -  i   i  -- i   -                   i   
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_100213819_   2966 TATAAATGTTCAATAAGCACATGAAAAGATGCTAAACATCAATAGCTAC 3014
                           i     vi                       v       ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.33 (4 / 3)  


 450 18.68 2.20 0.00  chrX_100231145_100233700      537   627 (1929)    L1M4_orf2#LINE/L1        1    93 (815)  

  chrX_100231145_    537 TGCAAATATATCCTATATTCATAGATTAGAAGAC--AATATTGTTAAGAT 584
                           v   v      i  i     i    i      --              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100231145_    585 AGCAATACACCCCAAACTGATATACATTTCCAAAGCAGTCTTT 627
                         i       v       i    v    vv i   v   i  ii 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

Transitions / transversions = 1.43 (10 / 7)
Gap_init rate = 0.01 (1 / 93), avg. gap size = 2.00 (2 / 1)  

1422 18.41 2.91 14.15  chrX_100231145_100233700      920  1435 (1121)    L1M4_orf2#LINE/L1       79   536 (372)  

  chrX_100231145_    920 TCCAATGCAGTCTCTATTGAAATCCCAACTGGCATTTT-ACAGAAATTGA 968
                          i   i   i  i    ii        i   v v    -i          
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chrX_100231145_    969 CAAGGTGAACCAAAAATTCAAATGGAACTG--AGGGACCCAGAACAATAT 1016
                             v   v  v        v      v  --            i ii--
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC-- 176

  chrX_100231145_   1017 ATTTTTCAATATTATTTCAATAATCAAAACAATATTGAAAAAACTTGGAA 1066
                         ------   v iv  i ii -----    v  ----   v   v     i
  L1M4_orf2#LINE/    177 ------CAAAACAATCTTGA-----AAAAGAA----GAACAAAGTTGGAG 211

  chrX_100231145_   1067 AATTCACATTTCTCAACTTCAAAGT---CTACAGCGCTATATTAATCAAG 1113
                         i i     i   i   i      ii---     iv    i v        
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_100231145_   1114 ACAGTGTGATACTGGCATAAGGGTAGACACA--GGTCAATGGGATGGAAT 1161
                                 i             i      i -- i       i  i    
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_100231145_   1162 TGAGAGTTGAGGAATAAACCCATACATTTAGGGCCAATGTGATTTTCCAC 1211
                                iv  i                  v  i    -        v  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT-TGATTTTCGAC 360

  chrX_100231145_   1212 AGGGGAGCCAACACAGTTCAATGGG--AAGAATAGTCCCCCATTGTACTG 1259
                          i   v     v  vi         --          -----  v ----
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-----TTTT---- 401

  chrX_100231145_   1260 GGACGGTATAATAGTTGAAAAGATTATAAAACAATTTTTTTTAAAATGAA 1309
                         --------i  i -----  v i vv iii    i --------------
  L1M4_orf2#LINE/    402 --------CAACA-----AATGGTGCTGGGACAACT-------------- 424

  chrX_100231145_   1310 AAGACTATAGTATTTCATTATGGTACTGTGACAATAGAATCCAGTTGGGT 1359
                         -i  ---  ?i----  i-   ---------   v     vv      ii
  L1M4_orf2#LINE/    425 -GGA---TAKC----CAC-ATG---------CAAAAGAATGAAGTTGGAC 456

  chrX_100231145_   1360 CTCTGTGTCACACCATAAATAAAAATTAA-----AATGGATTTAAAAAAC 1404
                          i  iiv          v i         -----       i- ? i v 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC-AWAGACC 505

  chrX_100231145_   1405 TAAATATAAAGCCCCAAACCAGAAAACTTTT 1435
                              i   iiv iv    i v      i  
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTT 536

Transitions / transversions = 1.82 (60 / 33)
Gap_init rate = 0.04 (19 / 458), avg. gap size = 4.63 (88 / 19)  

1152 17.58 14.70 4.03  chrX_100231145_100233700     1717  2063 (493)    L1M4_orf2#LINE/L1      525   908 (0)  

  chrX_100231145_   1717 TATAAAACTTTTAGA-TAAAACATAGGAGTATATCGTTGTGACATGGGGT 1765
                                  i     -v          ?   v   v i     -------
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC------- 567

  chrX_100231145_   1766 GACATGGGGTTGGGCAGTGATATCTTAGCTATGGCAGCAAAGGCATACAT 1815
                         -- - v     i    i  i v      v    i  v    i   i vii
  L1M4_orf2#LINE/    568 --C-TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_100231145_   1816 AACAGAAAAAAA-----------TGAACTTTATCATAGTTAAAAACATTT 1854
                             i  i    -----------  i    i    v i        v   
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_100231145_   1855 GTGCTTCAAATGACACCATTAAGTGAGGTGGAAA---------CAAAATG 1895
                                   v     i  i   -i i   i   ---------  i    
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAG-AAAGTGAAAAGACAACCCACAGAATG 713

  chrX_100231145_   1896 AGAGGAAATATTTGCAAATCATAC--CTGATAAA--ACTATTTTATTCCG 1941
                         i   i                  i--       i--   -- v   i v 
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT--TGTATCCAG 761

  chrX_100231145_   1942 AATATATAAA-------TA------AATAATGA---------TGACCCAA 1969
                                   -------  ------      i --------- i      
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_100231145_   1970 TTTAAAAACGGACCAAATATCTGAATA----TTTCTCCCCAGGAAGATAT 2015
                           ?     i  i v  iv  i      ----       v- i        
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA-AAGAAGATAT 860

  chrX_100231145_   2016 GCGAATGGATAATAAGAACATGGAACAATGCTGAACATTATGAGTCAT 2063
                         i i     vi      v     i  vi     v     i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (39 / 20)
Gap_init rate = 0.04 (14 / 384), avg. gap size = 4.64 (65 / 14)  


 359 24.03 3.88 3.10  chrX_100261545_100264394.rev      553   681 (2169)    L1M4_orf2#LINE/L1        8   137 (771)  

  chrX_100261545_    553 ATATATTATGCTTATTGGTTAGAAAACTCATTATT-TTAA--TGTTAATT 599
                             vii   i i  v i  i   i   i v    -    --  vi   v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_100261545_    600 TTACCCAAATTGATATATAGGTTAAACACAATCTCAA--AAGTAATACCA 647
                         i v           v  i  i  v   i     i v --  --   v   
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA--AATCCCA 105

  chrX_100261545_    648 GCACGCTCTTTTTTCTGGAAATCAACAAGATGAT 681
                           -i  -       vii     ii     v    
  L1M4_orf2#LINE/    106 GC-TGC-CTTTTTTGCAGAAATTGACAAGCTGAT 137

Transitions / transversions = 1.58 (19 / 12)
Gap_init rate = 0.05 (6 / 130), avg. gap size = 1.50 (9 / 6)  

 926 30.37 4.87 2.01  chrX_100261545_100264394.rev     1122  1470 (1380)    L1M4_orf2#LINE/L1      166   524 (384)  

  chrX_100261545_   1122 CTCAAAATAACAACAACAACAAC----AACAACAACAACGAAGCTGGAGG 1167
                          i  i    i --   -     i----  v  v  v   i   i      
  L1M4_orf2#LINE/    166 CCCAGAATAGC--CAA-AACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_100261545_   1168 GCTTACACTATTAGGTATCAAGACTTGTTATAATGCTACAGTGATTAAGA 1217
                         i  i     viivii v    i    ii  i  v        i  i    
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_100261545_   1218 CCATATGGTATTTATGCAATGATAGTCAAATAGACCAATGGAGCACTATA 1267
                          vi i     i viiii  v     v  v     i       ii vv  v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_100261545_   1268 TAGAATATAGAAAGAGAACCACCCATATCCAGTCATCAGATGTATGGTGA 1317
                         v   i vi     v i v   iv   v vii    viv   v vi iii 
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_100261545_   1318 AGGCACCATTACAATTCAGTGGGAAAGGGTTAGAGTTTTTTTTTTTTTAA 1367
                         i  ii   vv  v     i    i  i iv   ---- i    ivviv  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAG----TCTTTTCAACAAA 408

  chrX_100261545_   1368 TAGTGATGGGTTAACTGGATATCTATATAGAAAAAAATGAA--------- 1408
                          i   v    vi         ? i i  iv    i      ---------
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_100261545_   1409 CTATCTCAAACCACACACAAAAATTAATTTGAGATGGGTAATAGATCTAA 1458
                            i    v    i i           i ii i    i v ?   i    
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_100261545_   1459 ATG----ATCTAGAAC 1470
                            ---- v   i   
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAAC 524

Transitions / transversions = 1.67 (65 / 39)
Gap_init rate = 0.02 (6 / 359), avg. gap size = 4.00 (24 / 6)  

 714 24.67 6.61 0.44  chrX_100261545_100264394.rev     1680  1906 (944)    L1M4_orf2#LINE/L1      536   776 (132)  

  chrX_100261545_   1680 TAGCAAAACACATAGAAGAGTATCTTCTTGATCTTAGGGATAGGCAAGGA 1729
                            v i  v      i? viv      v   i   -   v       v i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT-GGGTTAGGCAATGG 584

  chrX_100261545_   1730 TTTTTAAAGTAGGGCATCAAAAGTAC---TAACTAA-TAAGAAAT-GATA 1774
                            i v ii  v i  i      i  ---i   v  -v  i    -    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_100261545_   1775 AATTGGACTTAATTAAAATTAAGAACTTCTG-G--TCAAATGATATCATT 1821
                                   v  i        i     i  - --     v  i ii  i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_100261545_   1822 AAGAATACGAAAATTCAAGCCATAGACTGGGAGA-----TTTCTGAA--A 1864
                              vii     vv   v   i   v       -----   vii  -- 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_100261545_   1865 TACATACGACTAAGGACTTGCAGTTAGAATATGTAAAGAACT 1906
                           i  vi  iv i       i vii       i         
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.50 (33 / 22)
Gap_init rate = 0.03 (8 / 241), avg. gap size = 2.00 (16 / 8)  

 529 20.29 2.90 0.00  chrX_100261545_100264394.rev     2222  2359 (491)    L1M4_orf2#LINE/L1      767   908 (0)  

  chrX_100261545_   2222 ATATAGAAATCTTACAA---AACAATAGAAAGACAAA-AACTCAGTAATA 2267
                            v    v        ---  i    i         -   i  i v?v 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_100261545_   2268 AAATAGGTAAAATACCTGAACAGGCATTTTACGAAAGAAGATATCCATAT 2317
                             i  i   iv ii    i  i     iv v           v  v  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_100261545_   2318 GGTCAATAAACCTATGAAGAGATGCTCACCATCATTAATCAT 2359
                           i      i vi     i         v     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (16 / 11)
Gap_init rate = 0.01 (2 / 142), avg. gap size = 2.00 (4 / 2)  


 674 23.61 0.00 0.00  chrX_100339815_100342023      501   644 (1565)    L1M4_orf2#LINE/L1       13   156 (752)  

  chrX_100339815_    501 CTGTGTTCATGGATTGGAAGACTCAATATAGTAAAAATGTCAGTTCTCCC 550
                          ii                    i     v  v  i   v  i v     
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_100339815_    551 CAAATTGATCTACAAGTTTAATGTAATTCCTGCCAAAATTCTAGCAAGGT 600
                                       ii  i  i i   i   ii      i i   vivv 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_100339815_    601 TTTCTATAGCTATAGACAAGCTTATTCTAAAATTTATATTAAAA 644
                            i ii  vv  v        v  i        i    vi   
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

Transitions / transversions = 1.83 (22 / 12)
Gap_init rate = 0.00 (0 / 144), avg. gap size = 0.00 (0 / 0)  

1827 22.62 7.90 8.03  chrX_100339815_100342023      974  1720 (489)    L1M4_orf2#LINE/L1      163   908 (0)  

  chrX_100339815_    974 GGACTCTAGAATGGCTAAA-CAATATTGACAAAGAAAAGTAAAGTCAGAG 1022
                             i -     i  i   -    v    v      i ii     ii   
  L1M4_orf2#LINE/    163 GGACCC-AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_100339815_   1023 CAATCA-GCCTTCTAATTTCAGGACCAATTATATAGC------------G 1059
                         v v   -i i i i       ii  iv i  i v   ------------ 
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_100339815_   1060 ACACTGTGATATTGGTGGAGGGATTGACAGATGGATCAGTGGAGGAGAAT 1109
                            v    i  i   iiv i    v    v  i     i    iv     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_100339815_   1110 GGAGAACCCAGAAACAGACCCATAAAACCAAGCCCAACTGATATTTCACA 1159
                         v    ii       i i       v vii v vi   i    v  iv   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_100339815_   1160 AAGGTGCAAAAGCAATACAACAGAGGAAGAATAGCCTTTTCAACAAATAG 1209
                          i     v  ii v  v   ii i i        i             i 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_100339815_   1210 TGCGAGAGCAATTAGACATCCTTTGGCAAGAAAAGCAAAAACAAACAAAC 1259
                            vi ii   i i  i ?  ---------------------------  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCC---------------------------AC 434

  chrX_100339815_   1260 AAACAAAAACAAAACAACAACAACAACAAAAAAAAAACCTTGAACTAAAC 1309
                          vi     i---------------  ii  ivvii v  i -------  
  L1M4_orf2#LINE/    435 ATGCAAAAG---------------AATGAAGTTGGACCCCT-------AC 462

  chrX_100339815_   1310 CTCATAGCTTTTACAAAAATTAAGTCGAAAATGGGCATCA--GGCTTAAA 1357
                             i v v v            v  -       --    -- i i    
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTC-AAAATGG--ATCAWAGACCTAAA 509

  chrX_100339815_   1358 ---AAGATGTAAAA----AAAA------AAAAAAAGCA--GGAGAAAATC 1392
                         ---    vv     ----    ------i  i   i  --  ? v     
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_100339815_   1393 TTCAGGATCT-GGGCTAGGCAAAGAGTTCTTAGATTTACTATAAAAAGCA 1441
                            iv  i  -   i       v iv         v ivi iv       
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_100339815_   1442 AGATCGTTTTCAAAA----AAATCAATATATTGTACTTCATCAAAACTAA 1487
                         vi v iv---     ----    vi   v    v            i   
  L1M4_orf2#LINE/    610 CAAGCAA---CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_100339815_   1488 AAACTTTTGCTCTCTGAAAGACCCTACGAAGAGGATGGAAAGACAAGCTA 1537
                                  iv  iii  i   v   iv    iii  i        v i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_100339815_   1538 CAGACTGGGAGAATATATTTGCAAACTACATATCTGATAAAACACTGGTA 1587
                             v        v           ii i           iiv   -- -
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT--T- 753

  chrX_100339815_   1588 GTATTTAAAATATAAAAAGAACTCTCAAAATTCAATAATAAAAA-----A 1632
                             ii i      v          i v  i             ----- 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_100339815_   1633 T----CAATTTAGAAAATAGGCAAAAGGCATGAGCAGACATTTCGCTGAA 1678
                          ----     ? -     i      i iiv   ii         v ii  
  L1M4_orf2#LINE/    804 TAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_100339815_   1679 GTGGA---ATAGATGGC--------ACATGA---GATGCTCAACCCCGTT 1714
                          vi  --- i i     --------      ---          vi i??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_100339815_   1715 AACCAT 1720
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.86 (108 / 58)
Gap_init rate = 0.03 (25 / 746), avg. gap size = 4.76 (119 / 25)  


 347 19.78 12.09 0.00  chrX_100370980_100374390.rev      504   594 (2817)    L1M4_orf2#LINE/L1        3   104 (804)  

  chrX_100370980_    504 GAAACATATCT--TGTTCATGGATTGGAAGATTCAGCAGAGT-AAGATGT 550
                             v     i--                  i i ii vv  -      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_100370980_    551 CAATTCTCACCAAATTGAT--ATAG------CGGGGATCCTATCAAGATC 592
                             v   v          -- i  ------  viivi        i   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_100370980_    593 CC 594
                           
  L1M4_orf2#LINE/    103 CC 104

Transitions / transversions = 1.25 (10 / 8)
Gap_init rate = 0.04 (4 / 102), avg. gap size = 2.75 (11 / 4)  

1208 22.16 10.27 1.08  chrX_100370980_100374390.rev     1565  1934 (1477)    L1M4_orf2#LINE/L1      127   530 (378)  

  chrX_100370980_   1565 GACAAGATCGTTCTAAAAATCATAAGGAAAGGCAAAGGAATTAGAATAGC 1614
                               v vi i      v     v     v    i   vii        
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chrX_100370980_   1615 AAAAACAATTTTGCAAAGGAAGAGAAAAGTGGGAGGAATCAATATACTT- 1663
                         v        i   v   i     iv     v      v   ---i    -
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA---CACTTC 223

  chrX_100370980_   1664 --AATTTCAAGAC--ATTAGAGAACTACAGTAATCAAGACTCTGTGGTAG 1709
                         --        i  -- i  v i i                vv       v
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_100370980_   1710 TAGTGGAAGGGCAGACAGACAGATAAGAGGAACAGAATGGACAACCCAGA 1759
                          i iiv    ii     v i    v iv    i     v  v ii     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_100370980_   1760 AGCAGACCCACATAAATATGTCCAACTGATTTT-GACAAAGGCAC----- 1803
                          ii i     i i vv    vi   i       -     i  ii -----
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_100370980_   1804 ------------AAAAGAA----CT------CAAATGGTACTGGAGCAAT 1831
                         ------------i      ----  ------        i    ii   i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_100370980_   1832 TGGACA---AAATGGCAAAA--ATGAACCTTGACTTAGACCTCACACCGT 1876
                             i --- v   -     --     vi v   iivv          i 
  L1M4_orf2#LINE/    424 TGGATAKCCACATG-CAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_100370980_   1877 ATACAAAAATTAACTCAAAGTGGATCACAGACTCAAATTTATAATATAAA 1926
                                            i       ?    ii    v  vi vv    
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_100370980_   1927 AGTATAAA 1934
                          v      
  L1M4_orf2#LINE/    523 ACTATAAA 530

Transitions / transversions = 1.38 (47 / 34)
Gap_init rate = 0.02 (10 / 404), avg. gap size = 4.20 (42 / 10)  

1018 25.96 6.78 0.59  chrX_100370980_100374390.rev     2230  2568 (843)    L1M4_orf2#LINE/L1      520   879 (29)  

  chrX_100370980_   2230 AAAAGTGTAAAACTTTTAGGAAAAAATACAAGA--AAGTCTTCAGGATCT 2277
                             v i       i    i i    i i i ?--  i     iv  i  
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_100370980_   2278 AGGGTTAGGCCAAGAGTTCTCAGATATGACAC---------GATCCATAA 2318
                         v         v v iv    i           ---------i v v i  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_100370980_   2319 AAGGAAAAATTGATTAATTGGGCCTCATGAAGATTTAAAACTTTTGCTCT 2368
                            i      v   v      i i    v  i   v          iv  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_100370980_   2369 TTGATAGAGCCTGCTAAGAGGATGAAAAGACAAGCTACGGACTAGGAGAA 2418
                          ii vi  vv  iii    iii           v i  i  v i      
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_100370980_   2419 AATATTTCCAAACGATATAACTGTCGAAAAATTT------AGAATATATA 2462
                                v    iv     v   vii iii i  ------          
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_100370980_   2463 TATATATATCTCGAAACTCAACAGCAAAAAAAAAAAT---CCATTTAGAA 2509
                         v v - i-   iiv       i ii     i v    ---   v  ?i  
  L1M4_orf2#LINE/    770 AAGA-AC-TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_100370980_   2510 AATTGGCAAAAGACATGAACAGAAATGTA-CCAAAGAAGATAGACAGATG 2558
                            v      i  iv    i   v  v v-            v   i   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_100370980_   2559 GGC--TGAGCGC 2568
                          v -- i   i 
  L1M4_orf2#LINE/    868 GCCAATAAGCAC 879

Transitions / transversions = 1.53 (52 / 34)
Gap_init rate = 0.02 (8 / 360), avg. gap size = 3.12 (25 / 8)  

 217 15.52 1.72 0.00  chrX_100370980_100374390.rev     2863  2920 (491)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_100370980_   2863 AAAAAAGA-AGACAGATTGCAAATAAACAGATGAAAAGATGTGCAACATC 2911
                            i    - v   i  v  v     i  v           iv       
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_100370980_   2912 ATCAGCCAT 2920
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 0.80 (4 / 5)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1)  


 303 18.64 0.00 0.00  chrX_100377778_100382791.rev     3315  3373 (1641)    L1M4_orf2#LINE/L1        1    59 (849)  

  chrX_100377778_   3315 TGAAAAGATATTCCATGTTCATGAACTGGTAAAATAAATGTTGTTAAAAT 3364
                           i        i           i i   v i v v   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100377778_   3365 GTCAATACT 3373
                          v       
  L1M4_orf2#LINE/     51 GGCAATACT 59

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  

2839 24.19 2.78 2.78  chrX_100377778_100382791.rev     3675  4538 (476)    L1M4_orf2#LINE/L1       45   908 (0)  

  chrX_100377778_   3675 TAAAA-GTCAATACTATCCAAAGCAATCTACAGATTCAATGCAATCCCTA 3723
                            i - v       vi     vii              i          
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chrX_100377778_   3724 TCTAAGTACCAATGACATTC---ACAGAAATAGAAAAAAAAATCCTAAAA 3770
                           v  i v   iivi v  i---i       v  v  ivvi         
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_100377778_   3771 CTTTTATGCAACCATAAACGACCCAGAATAGCCAAAACCATACCCAGCAA 3820
                         i iv    v  viii  iv                   v  viiv iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_100377778_   3821 AAAGAACAAAACTAGAGGAATTACATTACCTGACTTCAAATTATACTACA 3870
                         i         ii i     v i   i v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_100377778_   3871 GAGCTATAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACATATG 3920
                         i     i     i   i    ii              ii i        i
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_100377778_   3921 TGGACCAATGGAACAGCATAGTGTAACAAATCCATACATACATAGAGAAA 3970
                         --  i        i  v  ---- i -i i    ------------    
  L1M4_orf2#LINE/    295 --GATCAATGGAATAGAAT----TGA-GAGTCCA------------GAAA 325

  chrX_100377778_   3971 CAAATCCATACATCTACAGGAAACTCATTTTCGACAAAGTTGCCAAGAAA 4020
                         i   i        i  ii vv  i v           i v        vv
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_100377778_   4021 ATAGGCTGGGGAAAAGACAGTCTCTTCAATAAATGGTGCTGGGAAAACTG 4070
                           vviv        ii i     i     i              v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_100377778_   4071 GATATTCATAAGCAGAAAAAATGAAATTAGGTCCCTATCTGTCACCATCT 4120
                             ?i  i v   -   i      i  i ii     i  vv      v 
  L1M4_orf2#LINE/    426 GATAKCCACATGCA-AAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_100377778_   4121 ACAAAAATCAAATCAAAATGGATTAAAGACTTAAATCCAATACCTCAAAC 4170
                                 i  v           i ?    i     vi  v v  v    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_100377778_   4171 CATGAAACTACTACAAGAAAACACTGGGGAAGCTCTCCAGGATGTTGGTC 4220
                         i  i     vi  v         iv  ? v iv   i iv  iv    vi
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_100377778_   4221 TGGGCAAAGATTTCTTGAGTA--AC-CCACAAGCACAGTC--CAAAGCAA 4265
                          i     v i      iii  --  -   v       iv --    iv  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_100377778_   4266 AA--TGGGCAAGT--GATTT----AAAA-----AGCTTCTGCACAGGAAA 4302
                           -- i ii  i --  i  ----    ----- i   i  ii vvv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_100377778_   4303 GGAAACAATCGACAAAGTGAAGAGACAACCCA-AGGGTGGGAGAAAACAT 4351
                            v  v   i v        i          -  ii          i  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_100377778_   4352 TTGCAAAGTACTCATCTGACAAGGGATTAATAACCAGAACATGTAAGGAG 4401
                                vi ivi      i      i vi  v      i  i   i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_100377778_   4402 TTCAAACAACTCTATAAGAAAAAAAAAACTAATAATCCAATT-AAAAATG 4450
                         i  vv       v    v     i v  ---    i      -       
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAA---ATAACCCAATTWAAAAATG 821

  chrX_100377778_   4451 GGCCAAATATCTGAATAGACGTTTATCACAAGAAGACATACCAATGGCAA 4500
                            v  iv  i         i   v  vv       i    v      v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_100377778_   4501 ACAGGTTTATGAAAAGGTCATTGATCATCAGAGAAATG 4538
                          i i ivi        i -ii v v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (126 / 80)
Gap_init rate = 0.02 (18 / 864), avg. gap size = 2.67 (48 / 18)  


2977 26.54 2.13 0.45  chrX_100388845_100395753     5524  6416 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100388845_   5524 TAGAAACACATCCCATGCTCACGGATGGGTAGAATCAATATTGTGAAAAT 5573
                          i    v i        i   i    v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100388845_   5574 GACCATCCTTCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 5623
                          i v  v  i  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100388845_   5624 TACCA-CGATCATTCATCACAGAATTAGAAAAAACAATTCTAAAATTCAT 5672
                          v   - vii v  i- ii     v v  v  ivii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_100388845_   5673 ATGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAAACTAAGCAAAAAGA 5722
                               viiv  ii  v  viv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_100388845_   5723 ACAAATCTGGAGGCATCAGATTACCTGATTCCAAGCTATACTATAAGGCC 5772
                              vi      vv   v i v  ii   i   iviv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_100388845_   5773 ATAGTCAGACAA-ACAGCATGGTACTGGTATAAAAATAGGCACATAGATG 5821
                          i   - iv   -    ii         i    ii    i  i      v
  L1M4_orf2#LINE/    250 ACAGT-AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_100388845_   5822 AATGGGACAGAATAGAGAACCCGGAAACAAACCCAAATACTTACATCCAA 5871
                              i i     v    ii  i    i       v i i   iivi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_100388845_   5872 CTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGAGAAAGGACACCCT 5921
                         i    i   i    i vviv   i v   vv i   i     i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_100388845_   5922 TTTCAACAAATGATGCTGGGATAATTGGCTAGCCACATGTCAGAGAATGA 5971
                                     i        i  i   v  ?       iv i       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_100388845_   5972 AACTGAATCTTCATCTCTCACCTTATACAAAAATCAACTCAAGATAGATT 6021
                          ii  i i iii i   v    v           i       i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_100388845_   6022 AAGGACTTAAATCTAAGACCTGAAACTATTAAAATTCT-AGAAGATAACA 6070
                          ?i   i     v     v  i       -    i   -      v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chrX_100388845_   6071 TTAGAAAAACCCTTCTAGACATTGGCTTAGGCAAGAACTTCATGACCAAG 6120
                          vi ?iv  vi    vv   v    v        viii   v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_100388845_   6121 AACCCAAATGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTT--- 6167
                          vv     v   v v    i    iv   i   i   iv v      ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_100388845_   6168 --AAACTAAAGAGCTTTTGCACGAAAAAAGGAACAGTCAGCA--GTGTAA 6213
                         --   i    i -      ii vvv   i iv  vi   iv --   v  
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_100388845_   6214 AGAGAACCCACAGAGTGGGAGAAAAGCTTCACAATCTATACATCTGACAA 6263
                            v          i          vv  ii   vii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_100388845_   6264 AGGAATAATATCCAGAATCTACAATGAACTCAAACAAATCAGCAAGATAA 6313
                         i   v vi          v  i  v      vv    v   ii  v v  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_100388845_   6314 AAACAAACAATTCCATCAAAAAGTGGGCTAAGGACATGAAAAGACAATTC 6363
                          i     i  ii v  i?    i     v     iv    v     v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_100388845_   6364 TCAAAAGAAGATATACAAATG---------CATATGAAAAAATGCTCAAC 6404
                           v                  ---------  i       i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_100388845_   6405 ATCACCAATGAT 6416
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.30 (23 / 10)  


3151 26.94 0.55 1.10  chrX_100496022_100502755.rev     5331  6243 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100496022_   5331 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCCTGAAAAT 5380
                              ii i  i     i      i v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100496022_   5381 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5430
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100496022_   5431 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5478
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_100496022_   5479 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5528
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_100496022_   5529 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAGCGATGCTACAAGGC 5578
                                i      vv    i  v  ii i     ivvv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_100496022_   5579 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5628
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_100496022_   5629 AATAGAACAGAAC--AGAACCCTCAGAAATAACGCCACATATCTACAACT 5676
                            i   i    i--   ii  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_100496022_   5677 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5726
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_100496022_   5727 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5776
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_100496022_   5777 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGA 5826
                            ii    i    v   i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_100496022_   5827 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5876
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_100496022_   5877 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5925
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_100496022_   5926 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5975
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_100496022_   5976 ATTAAACTAAAGAGCTTCTGCACAGCAAAAAAAAAAAACTACCATCAGAG 6025
                           i   v v  i i   i  ii vv    ii v ----   i  vv i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA----CTATCAAGAAAG 691

  chrX_100496022_   6026 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCT 6075
                             v  i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_100496022_   6076 GACAAAGGGCTAACATCCAGAATCTACAATGAACTCAAACAAGTTTACAA 6125
                           i  i  i  vii         v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_100496022_   6126 GAAAAAAATCAAACAACCTCATCAAAAAGTGGGCGAAGGATATGAACAGA 6175
                         v     i -    i    iv  i?    i     i      v    i   
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_100496022_   6176 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATG 6225
                           i     v        i  vi viii     v ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_100496022_   6226 CTCATCATCACTGGCCAT 6243
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3123 27.34 0.66 0.55  chrX_100584977_100591377     5002  5908 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100584977_   5002 TGGAAGTACTTTCCAAGCTCATGGATGGGAAGAATCAATATCTTCAAAAT 5051
                              iv iv i   v i        v      v i     iv i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100584977_   5052 GGCCATACTGCCCAAGGTAACTTATAGATTCAGTGCCATCCCCATCAAGC 5101
                            v     v     iv i ii  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100584977_   5102 TACCAATGACTTTCTTCACAGAACTGGAAAAAAATACTTTAAAGTTAATA 5151
                          v   iivi i  i  ii     v v  v  ivvv iii    i  v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_100584977_   5152 TGGAACCAAAAAAGAGCCCGTATTGCCAAGACAATCCTAATCAAAAAGAA 5201
                              viiv  ii  v  v v  v     i      i i vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_100584977_   5202 CAAAGCTGGAGGTATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5251
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_100584977_   5252 CAGTAACCAAAACAGCATGGTACTCGTACCAAAACAGAGATATAGACCAA 5301
                               i   i    ii       v i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_100584977_   5302 TGGAACAGAAC--AGAGCCCTCAGAGATAATAACACACACAT--ACAACC 5347
                              i    i--    i  --   i    --  v  i    -- iiii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAA--ACCCATACATTTATGGTC 346

  chrX_100584977_   5348 ATCTGATCTTTGACAAACCTGACAAAACAAG-CAATGGGGAAAGGATTCC 5396
                          vi    i  i     ivv  v   i  v v-            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_100584977_   5397 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5446
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_100584977_   5447 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 5496
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_100584977_   5497 TTAAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5546
                          i ?    i     i v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_100584977_   5547 CTAGGCA-ATACCATTCAGGACGTAGGCATAGTCAAGGACTTCATGTCTA 5595
                         v    ?i- v i -   iv   v v  vv   v   v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_100584977_   5596 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCCA 5645
                         vi            vvi          vv     v  i    v   iiiv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_100584977_   5646 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5695
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_100584977_   5696 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5745
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_100584977_   5746 AAGGGCTAATATTCAGAATCTACGAAGAACTTAAACAAATTTACAAGAAA 5795
                          i  i  vi   i      v  ii       ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_100584977_   5796 AAATCAAACCACCCCACCAAAAAGTGGGCAAAGTATATGAACAGACACTT 5845
                           iv    iv    v ii?    i         v  v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_100584977_   5846 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5895
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_100584977_   5896 CATCAATGGTCAT 5908
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3305 25.99 0.77 0.77  chrX_100601557_100607247     4291  5198 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100601557_   4291 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4340
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100601557_   4341 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4390
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100601557_   4391 TACCAA-TGCCTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4437
                          v   i-       i  -ii    -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_100601557_   4438 ACATGGAACCAAAAAAGCGCCTGCATTGCCAAGTCAATCCTAAGCCAAAA 4487
                          i      viiv  ii vv  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_100601557_   4488 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 4537
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_100601557_   4538 CTACAGTAACGAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 4587
                                  iv  i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_100601557_   4588 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 4635
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_100601557_   4636 TATCTGATCTTTGACAAAGCTGAGAAAAACAAGCAATGGGGAAAGGATTC 4685
                         i vi    i  i     i v  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_100601557_   4686 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 4735
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_100601557_   4736 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAAATGG 4785
                             ii    i    v   i     v           i  i         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_100601557_   4786 GTTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCCAGAAGAAAA 4835
                         i i ?    i    i  v   v       i      vi ii         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_100601557_   4836 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4885
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_100601557_   4886 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4935
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_100601557_   4936 ATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGTGAA 4985
                           i   v v  i i   i  ii vv       v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_100601557_   4986 CAGGCAACCTATAGAATGGGAGAAAATTTTCGCAA--CGTACTCATCTGA 5033
                         v  i     i i               v  i    -- i  i--      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chrX_100601557_   5034 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAATAAATTTACAAGA 5083
                         i  i  i  vi          v  i  v      vv i  v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_100601557_   5084 AAAAAACAAACAACCCCACCAAAAAGTGGGTGAAGGACATGAACAGACAC 5133
                             i     i     v ii?    i    ii     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_100601557_   5134 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5183
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_100601557_   5184 ACCATCACTGGCCAT 5198
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2716 27.80 2.91 1.12  chrX_100636638_100638704.rev      685  1576 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100636638_    685 TGAGGAAACATTCCACACTCATGAATTGAAACAATCAATATCGTTAAAAT 734
                           iii i i  i   iii     i    i  v v i     i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100636638_    735 GGTCATACTGCCTAAAACAATCTATAAATTCAATGGTATTCCTATGAAA- 783
                           iv     v  i   vii     i i      i vv  i     v   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100636638_    784 --CTA--TGTCATTTTATCACAGAA-TTAAAAAAAAAACT-ATTCTAAAT 827
                         -- i --  i -    - ii     -  i v  i----  -  i     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTT-TTGCAGAAATTGACAAG----CTGATCCTAAAA 144

  chrX_100636638_    828 TTCATATAAAACCAGAAAAGAGCCCAAATAGCCAAAAGCAATTCTAAGCA 877
                                ii  viiv  ii  v  vi           -    ii i iv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAA 193

  chrX_100636638_    878 AAAAGAATAAAGCCAGAGGTATCACATTACCTAACTTCAAACTATACTAC 927
                          i     i    iii    vv     i v  i  i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_100636638_    928 GATGCTACAGTAAGCAA-ACAGCATGGTATTGGTACACAAATAAACACAT 976
                         i v          v   -    ii     i   i i vii   i   i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_100636638_    977 AGACTAATGGGACAGAATAGAGAACCCAGAAACAAAGCTGCACACCTACA 1026
                            ii     i i     v    ii       i   v iii   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_100636638_   1027 GCCATCTGATCTTTGACAAAGTCAACAAAAGTAAGCAATGGAGAAAGGAC 1076
                          i  vi    i  i     i viiv   i vi vv      i     i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_100636638_   1077 TCCCTTTTCAATAAATAATGTTGAGATAGCTAG----CCATATGCAGAAG 1122
                         vvi        i    ii  i  i  i i  i ----   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_100636638_   1123 AATGAAATTTGATCACTACCTATCGCCATATA-AAAAATTAACTCAAGAT 1171
                               i  v  i v      vv i       -              i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_100636638_   1172 GAATTACAGACTTAAATCTAAGGCCTCCAACTATAAAAATCCTAGGAGAA 1221
                          i  i ?    i     v    iv  vv          v  i   i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_100636638_   1222 AATCTAAG---AAATGCCCTTCTTGACATCAACCTTGGCAAAGAATTCAT 1268
                           iv  i ---    ---    v    v iiivi v     v iv   v 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_100636638_   1269 GGCTAAATCCTCAAAAGCAATTACACCAAAAACAAAAATTGACAAGGAGG 1318
                         i v  viv vi        vvvi  v     iv      v  i  ivv  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_100636638_   1319 ACCTAATTAAACTAAGGAGCTTCTGTACAGCGAGAAAAACTGTCAACAGA 1368
                           i v  i   v v ii i   i   i vv i iii v   i    v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_100636638_   1369 ATAAACAGACAATCTTCAGATTGGGAGAAAATATTTGCAAACTATGCTTC 1418
                         i i  v      i iv    v                    ii  iiv  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_100636638_   1419 TGACAAAGGTCTAATATCCAGAATCTATAAGGAATTTAAATCATTAAGCA 1468
                            i  i  v  vi          v     i   i ivv iv i v ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_100636638_   1469 A-AAAAAGA-AAATAT-----TTAAGAAGTGGACAAAGGACATGAACAGA 1511
                          -       -     v-----  ? i  i   i       iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_100636638_   1512 CACTTCTCAAAAGAAGACATGCAAGTAGCCAGTAA--ACATGAAAA-ATG 1558
                           i     v        i  i   i i    i   --         -   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_100636638_   1559 CTCATCATCACTAATCAT 1576
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (162 / 84)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.00 (36 / 18)  


3199 26.79 0.77 0.66  chrX_100641410_100647702.rev     4896  5802 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100641410_   4896 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4945
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100641410_   4946 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4995
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100641410_   4996 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5043
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_100641410_   5044 TATGGAACCAAAAAAGAGCCTGCATTACCAAGTCAATCCTAAGCCAAAAG 5093
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_100641410_   5094 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5143
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_100641410_   5144 TACAGTAACGAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5193
                                 iv  i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_100641410_   5194 AATGGAACAGAAC--AGAGCCCTGAGAAATAACGCTGCATATCTACAACT 5241
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_100641410_   5242 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGAGGAAAGGATTCC 5291
                          vi    i  i     ivv  vv  i v  vv     i      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_100641410_   5292 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA-AGT 5340
                           v  i  i              v      v  ?   i   i i  - i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_100641410_   5341 GAAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGGA 5390
                            ii    i    v   i     v i            i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_100641410_   5391 TTAAAGACTTAAACGTTAGACCTAAAACCACAAAAACCCCAGAAGAAAAC 5440
                          i ?    i    i  v   v       i i    vi ii          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_100641410_   5441 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5490
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_100641410_   5491 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5540
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_100641410_   5541 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATGAGAGTGAAC 5590
                          i   v v  i i   i  ii vv    i  v    i  v  i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_100641410_   5591 AGGCAACCTACAAAATGGGAGAACATTTTCACAA--CGTACTCATCTGAC 5638
                           i     i   i          v  v  ii   -- i  i--      i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGAT 744

  chrX_100641410_   5639 AGAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATGTACAAGAA 5688
                          ii  i  vi          v  i  v      vv    v vv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_100641410_   5689 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACGGACACT 5738
                            i     i     v  i?    i           iv    ii    i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_100641410_   5739 TCACAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5788
                           v v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_100641410_   5789 TCATCACTGGCCAT 5802
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2897 27.00 1.89 1.00  chrX_100648658_100655017.rev     4970  5869 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100648658_   4970 TGGAAA-ACATTCCATGCTCATGAATAGGAAAAATCAATATTGTTAAAAT 5018
                               - i  i     i     i  v    i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100648658_   5019 GGCCATACTGCCCAAGC-AATTTATAGATTCAATGCTATTCTTATTAAAC 5067
                            v     v     ii-i  i  i        i  v  i i   i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100648658_   5068 TACCATTGATATTCTTCACAGAACTAGAGAAAACT-ATTTTAAAAATCAT 5116
                          v   viviiv  i  ii     v v  v  i-  -  ii     v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_100648658_   5117 ATGGAA---CCAAAAACCT-GAAGAGTCAAGGCAATCCTGAGCAAAAAGA 5162
                               --- v iii   i-   v  i   ii     i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_100648658_   5163 ACAAAGCTACAGTCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5212
                               i iv  vvv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_100648658_   5213 ACAGTAACCAAAACAGCATGGTGCTGGTACAAAAACAGACACATAGACCA 5262
                                i   i    ii    i    i i  ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_100648658_   5263 ATGGAACAGAATAGAGAACCCAAAAATAAGAGCACACACCTACAACCATC 5312
                               i     v    ii   i      ivv  i   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_100648658_   5313 TGATCTTTGACAAACCTGACAAG------CAATGAAGAAAGGATTCCCTA 5356
                             i  i     ivv  v    ------     ii     i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_100648658_   5357 TCTGATAAGTGATGTTGGAATAACTGGCTAGCCATACGCAGAAGACTGAA 5406
                          iii i  i  i  i   i i      v  ?   i i   i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_100648658_   5407 ACTGGATCCCTTCTTTACACCATATACAAAAGTTAATGCAAGATGCATTA 5456
                         ii    i    v i i               i    iv   i   v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_100648658_   5457 AAGACTTAAATGTAAGACTCAAAACTACTAAAAACCCTGAAATACAACCT 5506
                         ?    i           vii       -     vi i ii  v v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTA-TAAAACTCTTAGAAGAAAACAT 548

  chrX_100648658_   5507 AGGCA-ATACCATTCAGGACATAGGTACGGGCAAAGATTTCAT-GATAAA 5554
                            ?i- v i -   iv   v v  vvii     v i    v -    v-
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT- 596

  chrX_100648658_   5555 GATGCCAAAAGCAATGACAACAAAAGCAAAAATTGACAAATGGGATCTAA 5604
                           ii         vvii         v      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_100648658_   5605 TTAAACTAAAGAGCTTCTGCACAGGAAAAGAAACTATCAAGAGAGTAAAC 5654
                          i   v v  i i   i  ii vvv   i  v          i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_100648658_   5655 AGACAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCAATCCGACAA 5704
                                 i                 v       vii  vv   i  i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_100648658_   5705 AGTTCTAATAAACAGAGACTACAAGGAACTTAAATTTACAACAACAACAA 5754
                         i vv  vi  vv    ivv  i  i     i----       v-   i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTC----TTACAACT-CAATAA 791

  chrX_100648658_   5755 CAACAACA-AAATAACCCTGT-AAAAAGTGGGCAAAGGACATGTACAGAC 5802
                         i  v  v -         vi -?    i           iv  v i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_100648658_   5803 ACTTCTTAAAAGAAGACATACATGAAGACAACAAGCATATGAAAAAAACC 5852
                          i    iv        i     vivi v   i     i       i vv 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_100648658_   5853 TCAACATCACTGATCAT 5869
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (150 / 89)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.62 (26 / 16)  


3226 27.61 0.22 0.33  chrX_100772444_100778724.rev     4882  5790 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100772444_   4882 TGGAAGAACATTCCATGCTCATGTGTAGGAAGAATCGATATCGTGAAAAT 4931
                              ii i  i     i     vi v      v ii    i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100772444_   4932 GGCCATACTGCCCAAGTTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     i  i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100772444_   4982 TACCAAGGACTTTCTTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5029
                          v   ivvi i  i   -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_100772444_   5030 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAGTACTGAGCCAAAA 5079
                                 viiv  ii  v  v v  v     iv  i vi   ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_100772444_   5080 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5129
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_100772444_   5130 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5179
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_100772444_   5180 CAATGGAACAGAACAGAGCCTTCAGAAATAACACCGCATATCTACAACTA 5229
                                 i    iv   vv i         vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_100772444_   5230 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5279
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_100772444_   5280 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5329
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_100772444_   5330 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5379
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_100772444_   5380 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5429
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_100772444_   5430 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5479
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_100772444_   5480 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5529
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_100772444_   5530 TCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5579
                         iv  v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_100772444_   5580 GGCAACCTACAAGATGGGAGAAAATTTTTGCAACCTACTCATCTGACGGA 5629
                          i     i   ii            v       vii ivi      iiii
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_100772444_   5630 GGGCTAATATCCAGAATCTACAATGAACACAAATAAATTTACAAGAAAAA 5679
                           i  vi          v  i  v    v vv i  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_100772444_   5680 AACAAACAGCCCCATCAAAAAGTGGGCAAAGGACATGAACGGGCACTTCT 5729
                         i     i i   v  i?    i           iv    ii i  i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_100772444_   5730 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCA 5779
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_100772444_   5780 TCACTGGCCAT 5790
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.42 (145 / 102)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.25 (5 / 4)  


3994 15.50 2.08 7.60  chrX_100785232_100787925.rev     1245  2205 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100785232_   1245 TGGAAAGGCATTG-GCGTTCATGGATTGGAAAGCTTAATATTCTTAAGAT 1293
                                ii  iv-ii               ii         v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100785232_   1294 AACAGTACTCCTCAAATTGATCAACACTTTCAATACAATCCCTATCAAAA 1343
                         ii  i      i          v   vv     ii               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100785232_   1344 TCTCAGCTGAGTTTTT-ACAGAAATACACAAGCTGATTCTAAAATTAATA 1392
                           i      vv     -i       vv          i        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_100785232_   1393 TGGAAATGCAGGGTACACCCAATAGCTAAAAAAAAATTTTGAAAAAGAAA 1442
                                   i  v  v vv      i    v  -- i           i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAA--TCTTGAAAAAGAAG 198

  chrX_100785232_   1443 AAAACAAAGTTAGAGGACTCACACATTTCAATTTCAAA-CTTACTACAAA 1491
                           --       i            v ii          -           
  L1M4_orf2#LINE/    199 AA--CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_100785232_   1492 GCTACTATAATCAAGACTGTGTGGCAATGATATAAAAGGATAGACATATA 1541
                              vi          v      i v  ii    --             
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAA--GGATAGACATATA 294

  chrX_100785232_   1542 GATGAACAGATCAGAAATGAGAATCCAGAAATAAACCCTAACGTTAATGG 1591
                            v  ii  vi    v     i               vv  i  v    
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_100785232_   1592 ACAATTAACTTTTAACAAAGGTTTCAAGGCCATTCAATGGGGAAAGAATA 1641
                         v     i i   ii    i   vi    i                     
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_100785232_   1642 GTCTTTGCAACAAATGGTACTGGGATAAATAGATATTCTCATGCAAAAGA 1691
                               v           i      i  v i    ?i v           
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_100785232_   1692 ATTAATGTGCACCCCTACTTCACATCATTTTCTTTCTTTTTTTTTTTAAC 1741
                           v  vv  v        i     i   v ------------------  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATAT------------------AC 476

  chrX_100785232_   1742 TTTTCTTAAACTTTAATATTATTAGTCTATATCACATCCTGGGTAACCCA 1791
                         -------   ----   --------------------------    i  
  L1M4_orf2#LINE/    477 -------AAA----AAT--------------------------TAACTCA 489

  chrX_100785232_   1792 AAGTGTATCAAAGACTTA----TAAGAACTAAAACTGTAAAACTCTTAGA 1837
                           i  v    ?    i  ----     i        i             
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_100785232_   1838 AGAAAACTTAGAGAGAAATCTTTATGAACTTGATCTAGGCAGTGATTTCT 1887
                                v   i?iv       ii   v    ivi      i  i     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_100785232_   1888 TAAATATGACACCAAAATCTCAGGCAACGAAAGAGAAAATAAATACATTT 1937
                           i              v v  i     i     i      i   v   v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_100785232_   1938 TACTTCAGAAAACTTTAAATTTTTTGTGCTTCAAAACTTAGGAAAAAATC 1987
                         v      vv   v  v   vi              -----   v ---- 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA-----GGACA----C 680

  chrX_100785232_   1988 TTTCATCAA---GAAAAGACAACCCATAGGATGGGTTGAAAATATTTTCA 2034
                          v   vv  ---              i  i     v-          v  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA-GAAAATATTTGCA 729

  chrX_100785232_   2035 AAT-A-ATACCTGATAAGAGTTTAGTATCTAGGATATACAAAGAACTATT 2082
                            - -   i        i vi v     i  i     i        v  
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_100785232_   2083 ACAACTCAACAATAATAAAAGACAA----CACAATCTAAAC-TAGGTAAA 2127
                                  i     --        ---- v    i?   v- i  i   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAA--AAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_100785232_   2128 GTGTTTGAATAGATATTTCTTCAAAGA---TATGCAAATGGTCAATAAGT 2174
                          vi          i      i      ---   i       i       i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_100785232_   2175 ACATGAAAAGATGCTCAACATAATTAGTCAT 2205
                                              v ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (82 / 63)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.43 (93 / 21)  


2660 23.01 8.64 2.57  chrX_100821302_100823158.rev      511  1366 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100821302_    511 TGGAAAAATATCCCATGTTCACAGAAAAGAATAATTAATATCATTAAAGT 560
                               i              ii  vvi   v v       ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100821302_    561 GGCCATACTGACCAAAGCAATCTACAGATTTAACACTATTCTTA-----A 605
                            v     vv     vii           i   i v  i i  ----- 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100821302_    606 T-----------TTTTCACAGAACTAAAAAAAAAAAAATCTG-TTCTAAA 643
                          -----------    ii     v vi v  i-------   - i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-------CTGATCCTAAA 143

  chrX_100821302_    644 ACTCATATAGAA---CAAAGTGCCCA-AATAGCCAAAGCAATCCTAAGCA 689
                          i      i   ---   i vi    -          i     i i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_100821302_    690 AAAGGAACAATGCTGGAGTCATCACACTACCCGACTTCAAACTATACTAT 739
                          i i      v i     vvv       v   i i      viv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_100821302_    740 AAGGCTGCAGTAACCAAAATAGCATGGTACTGCTACAAAAACAGACACAT 789
                           i   i      i   i i  ii        vi i  ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_100821302_    790 AGACCA-TGAACCGGAATACAGAACCCAGAAATAAGACCACATACCCACA 838
                            i  -  i vii    vv   ii          iv   i i iii ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_100821302_    839 GTCATCTGATCTTTGACAAAGTTGC-----------AATGGGGAGAGGGC 877
                             vi    i  i     i v   -----------        i  iii
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_100821302_    878 TCCCTATTCAATAAATTGTGCTGGGATGCCTGGCTAGCCATATGCAGAAG 927
                         vvi  v     i    v         iiv    v  ?   i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_100821302_    928 AA----ACTGGACCCCCTACCTCTCAACATATATTAGTACAAAAATTAAC 973
                           ----ii        -      v  v      ------           
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCC-TACCTCACACCATATA------CAAAAATTAAC 486

  chrX_100821302_    974 TAAAAATAGATTAAAGATTTAAAAGTAAGACCTCAAA-TATAAGAATCTT 1022
                          v     i   i ?   ii    v      v  v   -     i v    
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_100821302_   1023 AGGAAGACAACCTAGG---AAATGCCATTCTGGACATCAGCCTTGGGAAA 1069
                           -    v   v    ---    -- -   vv   v ii v-  i  v  
  L1M4_orf2#LINE/    537 AG-AAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGG-TTAGGCAA 581

  chrX_100821302_   1070 GTGTTTAT--GAC-TGAGTCCTCAAAAGCAATTACAACAAAAACAAAAAT 1116
                         vv    v --  i-   -- vi        vvvi        iv      
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGA--CACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_100821302_   1117 TGACAAATGGGACCTGATTAAA-TTAAAGAGCTTCTGCACCGCAAAAGAA 1165
                         v  i    v    i v  i   -     i -   i  ii iv    i  v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chrX_100821302_   1166 GCTATCAGCAGAGTAAATAGACAACCTACAGAATGGGAGAAAATATTTGC 1215
                         i      iv i   i  v        i                       
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_100821302_   1216 AAACTATGAATCTAACAAGGC-CTAATATCCAGTATCTATAAAGAACTT- 1263
                            ii  iv    i i    v-  vi       v  v           i-
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_100821302_   1264 ---AAATCAA--------------------CAAGCAAAAA----GTAAAG 1286
                         ---  v    --------------------   vi?    ---- i    
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_100821302_   1287 GACATGAACAGACATTTCTAAAAAGAAGATATGCATGTGGCCAACAAGCA 1336
                           iv    i          vv           i  vi       i     
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_100821302_   1337 TATGAAAAAATGCTCAACATTACTTATTAG 1366
                         i       i           i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (120 / 74)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.69 (96 / 26)  


 283 28.77 0.00 0.00  chrX_100829594_100834272.rev     2868  2940 (1739)    L1M4_orf2#LINE/L1        1    73 (835)  

  chrX_100829594_   2868 TGGGAATATATTTCACATTTATGGACTGAAAGAATTCATATGGTTAAAAT 2917
                            i  v    ii  ii  i     i  i    v  v    v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100829594_   2918 GTCCATACTACCTGCATTAGTCT 2940
                          v v     v  iiv   ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCT 73

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.00 (0 / 0)  

3099 24.65 1.17 0.94  chrX_100829594_100834272.rev     3337  4188 (491)    L1M4_orf2#LINE/L1       55   908 (0)  

  chrX_100829594_   3337 ACACTACCCAAGC-AATCTATAGATTCAATGCAATCTCTATCAAAATACC 3385
                          i   v     ii-i     i        i      i          v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_100829594_   3386 AATGACATTCTTCTCAGACACTGAAAAAA-AATCCCAAAATCTATATAGA 3434
                          iivi v  i  iv    v i   v  iv-i    i     ii    i  
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_100829594_   3435 ATCACAATAAAACCAGAATAGCCAAAGCTATCCTAAGCAAAAAGAACAAA 3484
                          vii   vii v              i v   i i iv  i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_100829594_   3485 TCTGGGGGAATCACATTACCTAACTTCAAATTATAGTACAGAGCTATAGT 3534
                         vi   i   v     i v  i  i      viv  v    i     i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_100829594_   3535 AACCAAAACAGCATAGTACTGGCATAAAAACAGACACATAGACCAAGGAA 3584
                           i   i    ii i            ii i     i     i   v i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_100829594_   3585 CCAGAATAGAGAACCCAGAAACAAATCCATACACCTACAGTGAATTCATT 3634
                         vi     v    ii       i   i       ii  ii  v    v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_100829594_   3635 TTCGACAAAAAGTGCCAAGAACTTACGCTGGGGAAAAGAACA-TCTCTTC 3683
                                 ii-         v v v iv        -   i -   i   
  L1M4_orf2#LINE/    355 TTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTC 402

  chrX_100829594_   3684 AATAAATAGTGCTGGGAAAACTGGATATCCACATGCAGAAAAATAAAACT 3733
                           i    i         v         ?         i  i   i  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_100829594_   3734 GGACCTTTATCTCTTGCCATATACAAAAATCAAACCAAAATGGATTAAAA 3783
                              ii  i   vii              i  vi          i ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_100829594_   3784 ACTTAAATCTAAGTCTTTAA-TCAAACTATCAAACTACT-GCAAAAAAT- 3830
                           i     v    ----- i- v       v     vi - v i    i-
  L1M4_orf2#LINE/    503 ACCTAAATGTAAG-----AGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_100829594_   3831 --GGGGAAAATCTTCAGGACATTGT-TCGGGCAAAACTTTCTTGAGCAAT 3877
                         --  ? v        iv   v   v- ii     viv      iiii vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_100829594_   3878 ACCCTTCAAGCACAGGCAACTAAAGCAAAAATGGACAAATGGGATCACAT 3927
                           v ivv       i     v    v      i  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_100829594_   3928 CAAG-TTAAAAAGCTTCTGCACAGCAACAGATCCAATCAACAAAGTGAAG 3976
                            i-       -   i  ii vv   vi  iv v     v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_100829594_   3977 AAACAACCCACAGAATGGGAGAAAACACGTGCAAGTTACCCATCTGACAA 4026
                          i                       i iv     i i ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_100829594_   4027 GGGATTAATTACCATAATATATAAGGAACTCAAACAACTCTATAGGAAAA 4076
                             i vi vv   v         i      vv       v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_100829594_   4077 AATCTAATAATCCTATAAAAAACCAAGCAAAAACTTTGAATAGACAGTAC 4126
                          iv v     i  v  v?    viii     iiv            v v 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_100829594_   4127 TCAACAGAAGACATACAAATGGCAGACATGCATATGAAAAGGTGCTCAAC 4176
                           v v      i           vi i v   i        i        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_100829594_   4177 ATCATTGATCAT 4188
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (127 / 79)
Gap_init rate = 0.01 (12 / 854), avg. gap size = 1.50 (18 / 12)  


2902 25.06 2.43 2.21  chrX_100857079_100859314      839  1744 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100857079_    839 TGGAAAAACATTCCATGCTCATGGATAGGAAGATTCAATATTGTTAAAAT 888
                               i i  i     i        v      i i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100857079_    889 GTCCATGCTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTTTCAAGC 938
                          v v  i  v      vii  i           i  v  i   v    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100857079_    939 TACCAGTGACACCCATCACGGAATTAGAAAAAACTG-TTTTAAAATTCAT 987
                          v    ivi viiiv ii i   v v  v  i-   - ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_100857079_    988 ATGGAACCATA-AAAGAAGCCA-AATAGCCAAG-CAATCATAAGCAAAAA 1034
                               --  i-  i i v   -         i-     v i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_100857079_   1035 GAACAAAGCTGGAGACATCACATTACCTGACTTCAAACTATACTACGAGG 1084
                                 i     ivv     i v  ii i      viv      i i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_100857079_   1085 CTACAGTAACCAAAACAGCATGGTGT--GCATACAAAAATAGGCACATAG 1132
                                  i   i    ii    ii--     -- ii    i  i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATATAG 295

  chrX_100857079_   1133 AAAAAGAGAACAGAATCTAGAGCCCAGAAATAATGCCACACACTTACAAC 1182
                          vv  vi   i     iv    i          vv   i   i   iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_100857079_   1183 CATCTGATATTCAACAAAATCGACAAAAACAAGCAATGGGGAAACAACTT 1232
                           vi    v   i    iivi v   i v  vv           v  ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_100857079_   1233 CCTATTGAATAAATGGTGCTGAGATAACTGGCTAGCCATACACAGAAGAC 1282
                         i  v  v  i           i  i      v  ?   i ii  i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_100857079_   1283 TGAAACTGGACCCCCTTCTTACACCATATAGAAAAATCAACTCAAAATGG 1332
                             ii        ivi  i          v      i            
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_100857079_   1333 GTTAAAGACTTAAATGTAAAACTTAAAACTGTAAAGATGCTGAAAGATCA 1382
                         i i ?    i         i vi       i    iv vi ii    vv 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_100857079_   1383 CCTAGG---AAATACCATTATGGACATAGGTCCTGGAAAATA-TTTCAT- 1427
                          v    ---    -- v ii  iv v i   -- i iv   i-    v -
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--CTTCGTGACCTTGGGT--TAGGCAATGGTTTCTTA 591

  chrX_100857079_   1428 GATGAAGATGCCGAA-GCAATTTCAACAAAAACAAAAATTGACAAATAGG 1476
                            - v  ii  i  -   vvvv        iv      v  i    v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_100857079_   1477 ACCTGATTAAAG-----AGCTACTGCATAGCAAAAAA-ACTATCAACAGA 1520
                           i v  i   i----- i  vi  iiivv    ii -        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_100857079_   1521 GTAAACAGACAACTCACAGAATGTGAGAAAATACTTGCAAACTATGCATC 1570
                           i  v       i         v         i       ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_100857079_   1571 TCATAAATATCTAATATCCAGAATCTATAAAGAACT--TA-AAC-CAATA 1616
                          v    iviv  vi          v           --  -   -     
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_100857079_   1617 ATCAAAAACCAACTAATCCCATTCAAAAATGGGCAAAGGACATATAGTAA 1666
                           v    iv   v   i  v   ?                i------ --
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT------T-- 832

  chrX_100857079_   1667 AGTGAACAAACACTTTTCGAAAGAAGACATACACACAGCCAACAAGTATA 1716
                         --    i i   i  i  v        i     v ii     i   i i 
  L1M4_orf2#LINE/    833 --TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_100857079_   1717 TGCAAAAAAGCTCAACATCGTGAATCAT 1744
                           v   i v          i????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (140 / 84)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.91 (42 / 22)  


2839 25.97 1.30 3.03  chrX_100877953_100884594.rev     5228  6151 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100877953_   5228 TGGAAAAAAAATCCATGCTTATGGATAGGAAGAATCAATATTGTGAAAAT 5277
                               i v vi     i i      v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100877953_   5278 GGCCATACGGCCAAAAGTAATTTATAGATTCTATGCTATTCCTATCAAGC 5327
                            v    vv  v   v i  i  i      v i  v  i        iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100877953_   5328 TACCAGTGACTTTCTTTGTAGAATTAGAAAAAAACT-ACATTAAACTTCA 5376
                          v    ivi i  i    i    v v  v  i--  - ivi    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_100877953_   5377 TATGGAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAA 5426
                                viiv  ii  v  v v        i      i i --------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-------- 190

  chrX_100877953_   5427 TAAAAAATAAAAAAAATAAAAATAAAAGAGCTGAAGGTATCATGCTACCT 5476
                         ------------    v  i  i   --- i  i   vv   ii  v  i
  L1M4_orf2#LINE/    191 ------------AAAAGAAGAACAAA---GTTGGAGGACTCACACTTCCC 225

  chrX_100877953_   5477 GACTTCAAACTATACTACAAAGCTACAGTAACCAAAACAGCATGGTACAG 5526
                         i i      viv                   i   i    ii      v 
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_100877953_   5527 GTAGCAAAACAGATATACAGACCAACACAACAGAACAGAGACTTCAGAAA 5576
                          i vv ii i   i   i   i   iiv  i    iv    v i      
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_100877953_   5577 TAACACCACACATCTACAACCATCTGATCTTCAACAAATCTGACAAAAAC 5626
                            vv   i    i  iiii  vi    i   i    ivv  v   i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_100877953_   5627 AAGCAATAGGGAAAGAATTCCCTATTTAATAAATGGTGCTGGGAAACCTG 5676
                          vv    i          vvi  v  i  i              v v   
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_100877953_   5677 GCTAGCCGTATACAGAAAACAGAAACTGGACCCCTTCCTTACACCTTATA 5726
                          v  ?  ii  i  i  i vv   ii         v   i     v    
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_100877953_   5727 CAAAAATTAACTCAAGATGGATTAAATACTTAAATGTAAAACCCAAAAAC 5776
                                        i      i ? v  i         i v i    - 
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-C 524

  chrX_100877953_   5777 CATAAAAATCTTAGAAGAAAACCTAGGCAGTA--CCATTCAGGACGTAGG 5824
                         i      v              v    ?-   --i -   iv   v v  
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGN-GTAAATC-TTCGTGACCTTGG 572

  chrX_100877953_   5825 CCTGAGCAAAGAATTCATGACTACAACACCAAAAGCAATTGCAACAAAAG 5874
                         vi ii    v iv   v iiv  ii            vvv          
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_100877953_   5875 CCAAAATTGACAAACGGGATCTAATCAAACTAAAGAGCTTCCGCACAAAA 5924
                         vv     v  i   iv   ii v      v v  i i   ii ii vvv 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_100877953_   5925 AATGAAACTATCATCAGAGTGAACAGGCAACCAAAAGAATGGGAGAAAAT 5974
                           v  v       vv i      v  i     v v               
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_100877953_   5975 TTTTGCAATCTACCCATCTGACA--GGTCTAATATCCAAAATCTGCAAGG 6022
                         v       vii ivi      i --  v  vi      i   v ii  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_100877953_   6023 AACTTAAACAAATTTACAAGAAAAAAACAA----CCCCTTCAAAAAGTGG 6068
                             ivv    v iv i  v     i    ----   vv i?    i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_100877953_   6069 GTGAGGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGTGGCCAA 6118
                          ii i    v    i     i     v        i  vi vi       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_100877953_   6119 CAA--ACATGAAAAAA-GCTCATCATCACTGGTCAT 6151
                         i  --         i -     v     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (130 / 106)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.33 (40 / 12)  


4188 20.07 3.99 0.46  chrX_100894284_100896437.rev      787  1663 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_100894284_    787 TGGAAAGACATCCCTTGTTCATAGATTGGAAGACTTAGTATCAATAAGAT 836
                                 i     v       i              i   iiv      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_100894284_    837 GGCAATATCACCCAGAACAATCTACAGATTCATTGCAGTCCCTGACAGAA 886
                                iiv    i vii             vi   i     iv  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_100894284_    887 TCCCAACTGGCTTCTTTGCAGAAATTGACAAGATAATTTCAAAATTCATG 936
                              i   v   i                  v i  iii         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_100894284_    937 TGGAAATACAGTGGACCCCAAACAACCAAAACCATCTTGAAAGAGAAGAA 986
                                i  iv      vi  i i       v         i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_100894284_    987 CAATGTTAGAAGACTAACACTTCCTGATTTCAAAACTTGCTACAAAACTA 1036
                            v   i  i    v        ii            i       i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_100894284_   1037 CATTAATCAAGACTGCGTGGTACCGATATAGGAAGAGACGTGGGCATCAG 1086
                           v          v i       i ii   i i v    i iviv    i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_100894284_   1087 TGGAACAGAGTTCAGAATTCACAGATAATCTCACACATTTATATCCAGTT 1136
                              i   i  v   i i  v i    v i  i        ivi  i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_100894284_   1137 GACTATCATTCTGGGTGCTGAAAAAAAATCCAATAGAAAAA-AATAGTCT 1185
                           i v  ivivv      i--  i vv  i    i ii   -        
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCC--AAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_100894284_   1186 TTTTAACAAATGATGCTGTAACAATTGGATATCAACTTGTAAAACAATGA 1235
                            i        i     vi    i      ? v  v  i    v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_100894284_   1236 ATGTTG-ACACCTGCCTCACATGATGTGCAAACACTGACTGAAAAATGGG 1284
                          -    -  v   i       iv  i i    v i i   v    -   i
  L1M4_orf2#LINE/    449 A-GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGA 496

  chrX_100894284_   1285 TCAAGGATCTAAAAGTAAGAGCTAGAACTGTAAAACTCT----------- 1323
                            ?i  i     v          i    i         -----------
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_100894284_   1324 ATAGGTGTACATCTTCATGACCTTGAATTAGGCAACCATTTCTTACATAT 1373
                              ?   v      i        ii        ivi       v    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_100894284_   1374 GAAATGAAAAGCACAAGCAACCAAAGGAAAAATAGGTAAATCAGACTTCG 1423
                           v iv               v    i        i     ii      i
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_100894284_   1424 TCTAAATTAAAAGCTTTTGTGCATCAACAGATACTATCAAGAAAGTTGAA 1473
                           v         i         v    vi  i              vi  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_100894284_   1474 AACTGACTGATGAAACAAGAGAAAATGTTTGCAAATTACATTGCTGACAA 1523
                          ivii  iv iii  iii        i         i i  vv    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_100894284_   1524 G----------------------AAGAACCCTTACAACTCAACAATAAAC 1551
                          ----------------------      i            i      v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_100894284_   1552 AGACAAACCACCCAATTAGAAAATGGGGAAAGGATTTGAATAGACTTTTC 1601
                                iv        ?i        v                 v    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_100894284_   1602 TCCAAAGAAGATATACAAATAACCAACAAGCACATGAAAAATTTCTCAAC 1651
                                             ii    i             iv v      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_100894284_   1652 ATCATTAGTCAT 1663
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (115 / 57)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 5.57 (39 / 7)  


2640 26.17 0.67 0.67  chrX_100927619_100929356.rev      503  1247 (491)    L1M4_orf2#LINE/L1      164   908 (0)  

  chrX_100927619_    503 GAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGC 552
                           v  v v  vi    iv     i i ivv i          i      v
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_100927619_    553 ATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAAC 602
                         v    i  v  ii i      viv        i          i   i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_100927619_    603 AGCATGGTACTGGTACCAAAACAGAGGTATAGATTAATGGAACAGAAC-- 650
                           ii         i iv ii i   vi       i       i    i--
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_100927619_    651 AGAGCCCTCAGAAATAACGCCACATATCTACAACTATCTGATCTTTGACA 700
                             i  --        vv   i i  i  iiiii vi    i  i    
  L1M4_orf2#LINE/    314 AGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_100927619_    701 AACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGG 750
                          ivv  vv  i v  vvv           i  vvi  v  i  i      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_100927619_    751 TGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTT 800
                                 v      v  ?   i   i i  iiv    ii    i    v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_100927619_    801 CCTTACATCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAATG 850
                            i   i v              i    i      i ?    i      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_100927619_    851 TTAGACCTAAAACCATAAAAACCATAGAAGAAAACCTAGGC---AATGCC 897
                          v   v       i      vi v           v    ?---   -- 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C 559

  chrX_100927619_    898 ATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGC 947
                         -   iv   v v  vv i     v ii   v ivv  vi           
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_100927619_    948 AATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGA 997
                          vvi          vv     v  i    v   ii v  i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_100927619_    998 GCTTCTACATAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACA 1047
                         i   i iiiivv    i  v    i  vv i      v  i     i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_100927619_   1048 GAATGGGAGAAAATTATTGCAACCTACTCATCTGACAAAGGGCTAATATC 1097
                                       vv      vii ivi      i  i  i  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_100927619_   1098 CAGAATCTGCAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACC 1147
                               v ii  v      vv    v iv i  v     i     i    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_100927619_   1148 CCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGAC 1197
                          v  i?    i            v    i     i     v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_100927619_   1198 ATTTATGCAGCCAAAAAACACGTGAAAAAATGCTCATCATCACTGGCCAT 1247
                           vi viii     v  i   i      i       v     ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (109 / 82)
Gap_init rate = 0.01 (5 / 745), avg. gap size = 2.00 (10 / 5)  


1023 23.28 4.60 2.87  chrX_100931211_100937205     2354  2701 (3294)  C L1M4_orf2#LINE/L1   (0)   908   555  

C chrX_100931211_   2701 AAACCATTCAGGACATAGGCATAGGCAAAGACTTC------ATGACAAAA 2658
                            i -   iv   v v  vv       v ii   ------      ---
  L1M4_orf2#LINE/    555 AAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA--- 600

C chrX_100931211_   2657 ATTCCAAAAGCAATCGCAACAAAAGCCAAAATTGAGAAATGGAATCTAAT 2608
                         ---         vvv          vv     v  v    v i ii v  
  L1M4_orf2#LINE/    601 ---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

C chrX_100931211_   2607 TAAACTAAAGAGCTTCTGTATAGCAAAAGAAACTATCATCGGAGTGAACA 2558
                         i   v v  i i   i   iivv    i  v       vvii      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

C chrX_100931211_   2557 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATTTACCCATCTGACAAA 2508
                          i     i                 v       v i ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

C chrX_100931211_   2507 AGTCTAATATCCATAATTTACAAGGAACTTAAACAAATTTACAAGAAAAA 2458
                         i v  vi      v   v  i  i     ivv    v ---   v  v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAA 794

C chrX_100931211_   2457 AAAGACA----------TCAAAAAGTGGGCAAAGTTTATGAACAGACACT 2418
                                ---------- i?    i         vv v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chrX_100931211_   2417 TCTCAAAAGAAGACATTTACATGGCCAAGAAACATATGAAAAAAGGCTCA 2368
                             v        i  vi v        v  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chrX_100931211_   2367 ACATCACTGACCAT 2354
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 0.86 (37 / 43)
Gap_init rate = 0.01 (5 / 354), avg. gap size = 5.20 (26 / 5)  

2750 26.74 0.72 1.56  chrX_100931211_100937205     2902  3735 (2260)    L1M4_orf2#LINE/L1       82   908 (0)  

  chrX_100931211_   2902 AATCCAACCCC-ATCAAGTTATCAATGACTTTCTTCACAGAA-TTGGAAA 2949
                           iv   i   -     iv vi  iivi i  i  ii     -   --- 
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG---A 128

  chrX_100931211_   2950 AAAACT-ACTTTAAAGTTCATATGAGACCAAGAAAGAGCCCGCATTGCCA 2998
                         v  i  - iii    i        ii viivi ii  v  v v  v    
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chrX_100931211_   2999 AGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCATGCTACCTGAC 3048
                          iv     i i ivv i          i      vv   ii  v  ii i
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_100931211_   3049 TTCAAACTATACTAGAAGGCTACAGTAACCAAAACAGCATGGTACTGGTA 3098
                               viv     v  i          i   i    ii         i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_100931211_   3099 CCAAAACAGAGATATAGACCAATGGAACAGAACAGAACAGAGCCCTCAGA 3148
                         iv ii i   v       i        i    iv  ---   i  --   
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGA---GAGTCC--AGA 323

  chrX_100931211_   3149 AATAATACCACACATCTACAACCATCTGATCTTTGACAAACCTGACAAAA 3198
                              vv   i    i  iiii  vi    i  i     ivv  v   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_100931211_   3199 ACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAAC 3248
                         v  vvv           i  vvi  v  i  i              v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_100931211_   3249 TGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACATCTTA 3298
                            v  ?   i   i i  iiv    ii    i    v   i   i v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_100931211_   3299 TACAAAAATTAATTCAAGCTGGATTAAAGACTTAAATGTCAGACCTAAAA 3348
                                     i    iv     i ?    i       v   v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_100931211_   3349 CCATAAAAACCCTAGAAGAAAACCTGGGC---AATGCCATTCAGGAGACA 3395
                          i      vi i           v i  ?---   -- -   -- v   v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTC--GTGACC 568

  chrX_100931211_   3396 TAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACA 3445
                          v  vv i     v ii   v ivv  vi            vvi      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_100931211_   3446 AAAACCAAAATTGAGAAATGGGATCTAGTTAAACTAAAGAACTTCTGCAC 3495
                            ivv     v  v    v   ii vi i   v v  i     i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_100931211_   3496 AGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGA 3545
                         vv    i  v    i  vv i      v  i     i             
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_100931211_   3546 AAATTTTTGCAATCTACCCATCTGACAAAGGGCTAATATCCAGAATCTAC 3595
                             v       vii ivi      i  i  i  vi          v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_100931211_   3596 AAAGAACTTAAACAAATTTATAAGAAAAAATCAAACAACCCCATCAAAAA 3645
                                 ivv    v iv    v     iv    i     v  i?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_100931211_   3646 GTGGGCGAAGCATATGAACAGACACTTCTCAAAAGAAGACATTTATGCTG 3695
                         i     i   v  v    i     i     v        i  vi viiv 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_100931211_   3696 CCAACAGACACATGAAAAAATGCTCATCATCACTGGCCAT 3735
                             i ii          i       v     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (128 / 91)
Gap_init rate = 0.01 (10 / 827), avg. gap size = 1.90 (19 / 10)  

3332 23.84 1.88 1.44  chrX_100931211_100937205     4601  5502 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_100931211_   4601 GAAAG-T-TTCCATGTTCATGGATTGGAGGAATCAATATTGTAAAAATGT 4648
                              - - i                  i  v i        v  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_100931211_   4649 CCATACCACCCAAAGCAATCTAGAGATTCAATGCAATCCCTATCAAATTA 4698
                          v    iv      vii     v        i               v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_100931211_   4699 CCAATGACATTCTTCACAGAAGTAGA-AA----ATCCTAAAATTCATGTG 4743
                            iivi v  i  ii     i v  -  ----              i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_100931211_   4744 GATCCACAAAGTACATAGAGTATCTGAAGCTATCCTAAGCAAAAAGAATA 4793
                           vvii   i v  vi   i  v ii  i v   i i iv  i     i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_100931211_   4794 AAACTGGAAGAATCACATTACCTAACTTCAAA--TTATCCTACAGAGCTA 4841
                           ii    i  v     i v  i  i      --   --     i     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGCTA 250

  chrX_100931211_   4842 TAGTAACCCAAACAGCATGGTACTGGCATAAAACCAGACACATGGATCAA 4891
                         i     i v i    ii              iivi     i  i      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_100931211_   4892 TGGAATGGAATACAGAACCAATAAACAAGTCCACACACCTATGGTGAACT 4941
                               i    vv   ii v v   i  ii   i   ii      v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_100931211_   4942 CATTTTTGACAAAGGTGACCAGGACATACTC--TGAGGATAAGACCA-TC 4988
                         v     i     i    -   i   -i i  --  i   -    vi -  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTG-CCAAGAC-CATTCAATGGGGA-AAGAATAGTC 397

  chrX_100931211_   4989 TCTTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAAAG 5038
                          i     i              v         ?   i     i     v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_100931211_   5039 AAACTAGACCCCCATATACATATCTTTCCATATACAAAAATCAAATCAAA 5088
                           ii i      i iv -  i -----              i  v     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCT-CACA-----CCATATACAAAAATTAACTCAAA 491

  chrX_100931211_   5089 ATGGATTAAATACATAAATCTAAGACCTCAAACTCTGAAAGTACTACAAG 5138
                               i ? v  v     v     v  v     v i   v vi  v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_100931211_   5139 AAAACATTGAGGGAAAATCTCCAGGACATTGGTCTTGGCAAAAATTGCTT 5188
                                v - ? v      i iv   v    vi v     vii  v   
  L1M4_orf2#LINE/    542 AAAACATAG-GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_100931211_   5189 GAGCAATACCCCAAAAACATAGACAACCAGAGCATAAATGGACAAATGGG 5238
                         iiii vv  v      i  i ii    v i  v v    i  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_100931211_   5239 ATCATATCAAG-TTAAAAAGCTTCTACACAGCAAAGGAAACAGTCAACAA 5287
                          iivi     i-       -   i iii vv       v  vi    v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_100931211_   5288 AGTGAAGAAACAATCCACAGAACGGGAGAAAATATTTGCAAACTACCCAT 5337
                               i i    i        i                   ii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_100931211_   5338 CTGACAAGGGGTTAATCACCAGAAGATATAAGAAGCTCAAACAACTCTGC 5387
                             i     ii vi vv      v      ii i   vv       vii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_100931211_   5388 AGGAAAAAATTTAATAATCCAAT-AAAAAATGGGCACAAGATTTGAATAG 5436
                          iv     iviv     i     -?           v i           
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_100931211_   5437 ACATTTTTCTAAAGA---TATATAAGTGGCAAACATGCATATGAAAAGGT 5483
                               i  i     ---    i  i    v  i v   i        i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_100931211_   5484 GCCGAACATCACTGATCAT 5502
                           iv       ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (132 / 79)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 1.67 (30 / 18)  


3039 27.62 0.58 0.58  chrX_101001301_101004115     1458  2315 (500)    L1M4_orf2#LINE/L1        1   858 (50)  

  chrX_101001301_   1458 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1507
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101001301_   1508 GGCCATACTGCCGAAGGTAATTTATAGATTCAATGCCATCTCCATCAAGC 1557
                            v     v  v  iv i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101001301_   1558 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1605
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_101001301_   1606 TATGGAACCAAAAAAGGGCCTGCATCGCCAAGTCAATCCTATGCCAAAAG 1655
                                viiv  ii iv  v v  v     iv     i ivivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101001301_   1656 AACAAAACTGAAGGCATCACGCCACCTGACTTCAAACTATACTACAAGGC 1705
                               ii  i   vv    i iv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101001301_   1706 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1755
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101001301_   1756 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 1803
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_101001301_   1804 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1853
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_101001301_   1854 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 1903
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_101001301_   1904 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGCA 1953
                            ii    i    v   i     v              i    i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_101001301_   1954 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2003
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_101001301_   2004 CTAGGCATTACCATTCA-GGTCATAGGCATGGGCGAGGACTTCATGTCTA 2052
                         v    ?i v viv   i- ii v i  i- i   i v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chrX_101001301_   2053 AAATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2102
                         vi i          vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101001301_   2103 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 2152
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101001301_   2153 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 2202
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_101001301_   2203 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 2252
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_101001301_   2253 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAGTT 2302
                           i     i     v  i?    i     i     iv    i     v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_101001301_   2303 CTCAAAAGGAGAT 2315
                            v    i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGAT 858

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.01 (7 / 858), avg. gap size = 1.43 (10 / 7)  


3041 27.00 2.47 0.34  chrX_101010497_101017194     5317  6205 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101010497_   5317 TGGAAAAACATTACATCCTCATGGATAGGAAGAATGAATATCGTGAAAAT 5366
                               i i  iv   vi        v      v v     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101010497_   5367 GGGCATACTGCCAAAAGTAATTTATAGATTTAATGGTATTCCCATCAAGA 5416
                           vv     v  v   v i  i  i     i  i vv  i  i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101010497_   5417 TACCATTCACTTTCTTCACAGAACTTGAAAAAACT-ACTTTAAATTTCAT 5465
                          v   viii i  i  ii     v    v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_101010497_   5466 ATGGAACGAAAATGGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 5515
                               vviv  v   v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_101010497_   5516 ACAAGGGTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAGGGCT 5565
                             i v      vv   ii  v  ii i      viv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_101010497_   5566 ATAGTAACCAAAACAACATGGTACTGGTACCAAAACAGATATATAGACCA 5615
                          i     i   i   iii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_101010497_   5616 GTGGAACAGAA------GCCTCAGAAATAATACCACACATCTACATCCAT 5659
                         i     i    ------ i -         vv   i    i  iivi  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_101010497_   5660 CTGATTTTTGACAAACCTGACGAAAACAG-CAATGGGGAAAGGATTTCCT 5708
                         i       i     ivv  v i i v  v-            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_101010497_   5709 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAACAGA 5758
                         v  i  i              v      v  ?   i   iii  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_101010497_   5759 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAAGTGGATT 5808
                          ii         v   i     v                    i     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_101010497_   5809 AAAGACTTAAACCTAAAACCTAAAACCATAAAAACCCTAGAAGGAAACCT 5858
                          ?    i    iv   i v       i      vi i      i    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_101010497_   5859 AGGCA-ATACCATTCAGGAGATAGGCATGGGCAAAGACTTCATGACTAAA 5907
                            ?i- v i -   iv  vv v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_101010497_   5908 ACACCAAAAGCAATTACAACAAAAGCCAAAATTGACAAATGAGATCTCAT 5957
                                     vvvi         vv     v  i    vi  ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_101010497_   5958 TAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATCATCAGAGTGAAAA 6007
                         i   v v  i i   i  iv vv    i  v       vv i        
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_101010497_   6008 GACCACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA- 6056
                            v   i                 v       vii  vi      i  -
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_101010497_   6057 ------------AGAATCTACAAGGAACTTAAACAAATTTACAAGGAAAA 6094
                         ------------     v  i  i     ivv    v iv i  vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_101010497_   6095 AACAAACAACCCCATCAGAAAGTGGTCGAAGGATGTGAACAGACACTTTT 6144
                         i     i     v  i?i   i   v i      v    i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_101010497_   6145 CAAAAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCTCATCA 6194
                          v        i  vi vii      i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_101010497_   6195 TCACTGGTCAT 6205
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.12 (25 / 8)  


2780 27.47 1.54 1.76  chrX_101033926_101038202.rev     2877  3786 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101033926_   2877 TGGAAAAACATTCCATGCTCAGGGAAAGGAAGAATCAGAACTGTTAAAAC 2926
                               i i  i     i   v   vv      v i iv i      i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101033926_   2927 GGCCATACTGCCCAAAGCAATTTAGAGGTTCATTGATATTATTGTCAAAA 2976
                            v     v      vii  i  v  i    vi vv  ivi i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101033926_   2977 ACTACCAAATGATATTCTTCACAGAATTAGAAAAAACT-ATTCTAAAATT 3025
                         v --   iv  vi-  i  ii     v v  v  i-  -  i        
  L1M4_orf2#LINE/    101 TC--CCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chrX_101033926_   3026 CATATGGGACCAAAAAGGAACCTGAATAGCTGAAAAAATCCTAAGTGATA 3075
                                i viiv  i   v  v       ii   v    i i ivi v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_101033926_   3076 ACAACAAAGCCAGAGGCATCACACTACCTGACTGCAAGCAA--TACTATA 3123
                          v       iii    vv       v  ii i v   --  --     i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA--AACTTACTACA 244

  chrX_101033926_   3124 AGGCCATGGTAGCCAAAGCAGCATGGTATTGGTATAAAAACAGATACATA 3173
                          i  i ii   ii   ii   ii     i   i    ii i   i i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_101033926_   3174 AACCAAAGGAATATGTTAGAGAACCCAGAAATAAAGCTGCACACATACAG 3223
                         i i   v      viv v    ii           v iii   iv  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_101033926_   3224 TCATCTCATCTTCAACAAAGATGACAATAACAGTCAATGGGGAAAG--CA 3271
                            vi v  i   i    i i  v   v v  v             --i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_101033926_   3272 GTCCCTATTCAGTAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAA 3321
                            -- v    ii              i      v  ?   i     i  
  L1M4_orf2#LINE/    395 GTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_101033926_   3322 GATTGAAACTGGACCCCTTTCTTACACCATA--CAAAAATCAACTCAAAG 3369
                           v    ii         vi  i        --       i        i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_101033926_   3370 TTGATTAAATACTTAAATGTAAAACCCCAATTTATAAAAGCCCTGGAAGA 3419
                          v   i ? v  i         i v iv  vi       vi i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_101033926_   3420 CCACCTAGGCA-ATACCATTCTGGACATGGGAACAGGCAAAGATTCCAT- 3467
                         vv  v    ?i- v i -   vv   v v  ivi      v i  i v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_101033926_   3468 GATGAAGATGCCAAAAGCAATTACAACAAAAGCAAAAATTGACAAAAGGG 3517
                            - v  ii         vvvi         v      v  i   vv  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_101033926_   3518 ATCCAATTAAACTGAACAGCTTTTGCACAGCAAATAA-ACTATTAACAGT 3566
                          iiiv  i   v v  v i      ii vv    vi -     i  v iv
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_101033926_   3567 GTAAAGAGACAACCTATGGAATGGGAGAAAATATTTACAAATGATGCATC 3616
                           i  i        i ii                  i     v  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_101033926_   3617 CAACAAAGGTCAAATATCCAGAATCTAAAAGGAATTT----AAATTAACA 3662
                         ii i  i  v vvi          v  v  i   i i----  v i  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_101033926_   3663 AGCAAAAAGCAAACACCCCTATTAAAAAAAAATTATGAGCAAAGGACTTG 3712
                          vv    ii    i v   v   ?     ------  i        i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAA------TGGGCAAAGGATTTG 834

  chrX_101033926_   3713 ATCAGATGCTTCTCAAAAGAACACATACTTGTGGCCAACAAACATTTGAA 3762
                          vi   iii     v      v i    vvi       i  i  iv    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_101033926_   3763 AAAATGTTCAACATCACTCATCAG 3786
                           i   i         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


4234 17.38 5.33 0.35  chrX_101042641_101044498      505  1367 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_101042641_    505 GAAAATTTTTCCATGTTAATGGATTGGAAGATGTAATATTGTTAAGATGG 554
                             iv v i       v             iv                 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_101042641_    555 CAATACTACTCAAACTGATCTACAGATTTATCACAATCTTGGTCAACATC 604
                                v i    i             i v i     iivi    v   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_101042641_    605 ACAGCTGATTATTTTGTAAGAATTGACAAGGTAGTCCTAAAATTCACATG 654
                         v      vi v     i ii          v ii            i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_101042641_    655 GAAATACAAAGGGACCCAGAACAGCCAAAGCAGTATTGAAAAAAAAAAAA 704
                              i   -           i       i  i v        i  i  v
  L1M4_orf2#LINE/    153 GAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_101042641_    705 AAGAAGTTGAAGGATTCACACTTCCTGATTTTGAAGCTTACTACAAACCT 754
                           --     i    i          ii    ii  i           v  
  L1M4_orf2#LINE/    202 AA--AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_101042641_    755 ACAGTAATAAAGGATTTGTCGTACTAGTAGAAGGATAGACATATAGCTCA 804
                                 v   ivvv   v     i i v                v   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_101042641_    805 AT-----------------------ATGTACT--TACATTTGTGGTCAAT 829
                           -----------------------  iv  i--       i        
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_101042641_    830 TAATTTTCAACAAGGGTGTGTAGACTGTTAAATGGA-AAAGAATAGTTTT 878
                          i      i         ivv    ii  v     i-          i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_101042641_    879 TTCAACAAATGGTGCTTGGACAACTGGATGTCCACATGCTAAAGAATGAA 928
                                         v            i?        v          
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_101042641_    929 GTTGAACCCCTACCACACATCATATGCAAAAATTAACTCAAAATAAATAA 978
                             i         v    i     i                  ii  v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_101042641_    979 T-GACCTAAATGTAAGAGCTACAACTATAAAACTCTTAGAAGAAAGTGTA 1027
                         ?-                   v                       iii  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_101042641_   1028 AGGGCAAATATTCATTAGCTTGAGTTAGGCGATGCTTTCTTAGTTATGAC 1077
                         i ? i    v   i v v    i       i   v        v      
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_101042641_   1078 ACTTAAAGCACAAA-ATCAAAAGAAAAA-TAGTTAAAATGAAC---ATTG 1122
                           iv         i- v           -   v    v  i  ---  ii
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_101042641_   1123 AAATTAAAGTATTTTGTGCTGCATAGGACACTATCAAGTAAATAAAAAGA 1172
                                 ivv         v  v              v  i i      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_101042641_   1173 TAACCTACAGAATAGGAGAAAATTTTTGCAAATCATATATCTGATAAGGG 1222
                         i    i       i         v                          
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_101042641_   1223 ATAAGCAACTACAATGTATGAAGACCCC--ATAATTCAACAATAGAAAGA 1270
                          ivv i v i v   i   i    v i -- i  i    i    i     
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_101042641_   1271 CAAATAACTCGTTTTTAAATTGGACAAAGGGTTTG-----------CTCC 1309
                                 i iv  ?v   v   i      i    -----------    
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_101042641_   1310 AAA-AACATGTACAAATGACCCTTGAGCATATAAAAAGATGCTCATCATA 1358
                            -  v  i        i  vv i    i  i            v   v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_101042641_   1359 AGTCATCAA 1367
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.47 (87 / 59)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 4.08 (49 / 12)  


3325 26.32 0.55 0.55  chrX_101054819_101058267     2049  2956 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101054819_   2049 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 2098
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101054819_   2099 GGCTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2148
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101054819_   2149 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2195
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_101054819_   2196 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 2245
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_101054819_   2246 AAACAAAGCTAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 2295
                         i       i i    vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_101054819_   2296 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 2345
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_101054819_   2346 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACTGCATATCTACAAC 2393
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_101054819_   2394 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 2443
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_101054819_   2444 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 2493
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_101054819_   2494 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 2543
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_101054819_   2544 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2593
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_101054819_   2594 CCTAGGCATTACCATTCAGGACATAGGCATGGGTAAGGACTTCATGTCTA 2643
                          v    ?i v viv   iv   v v  vv i  i  v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101054819_   2644 AAATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2693
                         vi i          vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101054819_   2694 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 2743
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101054819_   2744 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 2793
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_101054819_   2794 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 2843
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_101054819_   2844 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 2893
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_101054819_   2894 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 2943
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_101054819_   2944 CATCACTGGCCAT 2956
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2163 24.56 3.07 10.13  chrX_101061332_101067481     4681  5657 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101061332_   4681 TGGGAAAACATTCCATGCTCATGGATAAGAAGAATCAATATTGTTAAAAT 4730
                            i  i i  i     i        vi     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101061332_   4731 GGCCATATTGCCCAAAGCAATGTATGGATCACAGTGCAATATTATATAAA 4780
                            v   i v      vii  v  ii   i-  ii     ----------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT-CAACGCAAT---------- 89

  chrX_101061332_   4781 TAAATACTAAGAAAATCACTCAAAAACCATAGAACTATATGAAAATTAAA 4830
                         ------------------ i ----------------   v     i---
  L1M4_orf2#LINE/     90 ------------------CCC----------------TATCAAAATC--- 102

  chrX_101061332_   4831 CCACTATTTCTATCAAACTACTAATGAGATTCTTCACAGAATTAGAAAAA 4880
                            -------------i  i i-------  i  ii     v v  v  i
  L1M4_orf2#LINE/    103 CCA-------------GCTGCC-------TTTTTTGCAGAAATTGACAAG 132

  chrX_101061332_   4881 AATATTTTAAAATTCATATGGAATCAAAAAGAGCCCTAAA-AGCCAAGGC 4929
                         vvv  ii                viiv  i ii   vi  -      ii 
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chrX_101061332_   4930 AATCCTAAGCAAAAAGAACA--GTCAGAGGCATCACATTACCTGACTTCA 4977
                             i i iv  i       --  ii    vv     i v  ii i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_101061332_   4978 AACTATACCACAAGGCTACAGTAATGAAGACAGCATGGTGCTGGTACAAA 5027
                           viv   i    i           v       ii    i    i i  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_101061332_   5028 AATAGACA-------CAAAGAAACAGAATAGAGAGCCCAGAAACCATGCC 5070
                         i       -------   v i  i     v     i       iv vv  
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_101061332_   5071 ACACAACTACAACCATCTGATATTTGACAAATTTGACAAAAACAAGCAAT 5120
                          i   vi  iiii  vi    v  i     ivv  v   i v  vv    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_101061332_   5121 TGGGAAA-AGTTCTCTCTATTTAAAAAATGGTGCTGTGATAACTGGCTAG 5169
                         v      - i vv   i -- i  v           v  i      v  ?
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_101061332_   5170 TATTATGCAGAAGGTTGAAACTGGACCCATTCCTTATACCATATA----- 5214
                         ivvi     i   iv    ii       v v   i i        -----
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_101061332_   5215 ---------AGATGTATTTAAGGCTTAAATGTAAAACCTGCATCAAAATA 5255
                         --------- i   v  iv?  i i         i v  -----    iv
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-----AAAACT 525

  chrX_101061332_   5256 AAAAAAGCTACTGGAAAATAACCTAGG---AAATGCTATTCTGAACATAG 5302
                          v    -  vi i   i v   v    ---    -  - iv   v v i 
  L1M4_orf2#LINE/    526 ATAAAA-CTCTTAGAAGAAAACATAGGNGTAAAT-CT-TCGTGACCTTGG 572

  chrX_101061332_   5303 ACTCTGGAAAGATTTCACAACAAAGATGTCAAAAGCAATTGCAACAAAAG 5352
                         ii vv v  v i    vi ivv v  iii        vvv          
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_101061332_   5353 CCAAGAATTGACAAATGGGACCTAATTAAACTAAAGAACTTCTGCAAG-C 5401
                         v-  i   v  i    v    i v  i   v v  i     i  iivv- 
  L1M4_orf2#LINE/    623 A-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_101061332_   5402 AAAAGAAACTACCAAAAGAGTAAACAGACAACCTACAGAGTAAACAGACA 5451
                            i  v    i   i i   i  ------------------  --    
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAA------------------AA--GACA 701

  chrX_101061332_   5452 ACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCCAATAAAGGTC 5501
                            i                          ii  ii   ii    i  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_101061332_   5502 TAATATCCAGAGTCTATAAGGAACTGAAATAAATTAACAAGCAAAACCCA 5551
                          vi        i v     i     vvv i  v i  i  vv    vv  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_101061332_   5552 AACAACCCG-TTAAAAAGTGGGCAAAGGATATGAGCAGAGACTTCCCAAA 5600
                           i     i-  ?    i            v   ii   v i   i v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_101061332_   5601 GGAAGGCATACACATGGCTAACAAGCCTATGAAAAAATGTTCAACATCAC 5650
                         i    ii     v     i  i    vi       i   i         ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_101061332_   5651 CAATCAT 5657
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 5.86 (129 / 22)  


4027 18.72 5.33 0.36  chrX_101073032_101076857     2491  3334 (492)    L1M4_orf2#LINE/L1       23   908 (0)  

  chrX_101073032_   2491 GGATTGGAGATCTTAATATTGTTAAGATGGCAACATTATC--AATGTGAT 2538
                                 iiv                      i i vi --   -    
  L1M4_orf2#LINE/     23 GGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT-TGAT 71

  chrX_101073032_   2539 CTAATGACTCAGTGCAATCCTTATTGAAATCACAACTGTCTTTTTTTTTC 2588
                            vv  i   ii       i   ii     v  i   i       v-- 
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG--C 119

  chrX_101073032_   2589 AAAAATGGCAAAAGTGATCCTGAAAGTCATATGAAACAGAAAGGGACCT- 2637
                          i    v vv  iv       i   v       i  vv v        i-
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_101073032_   2638 GAATGTCCAAAATAATCT-GATAAAGAAAAATAAAATTTGAAGGCTCACA 2686
                             iv      i     -  v      i  i   i  v  i i      
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_101073032_   2687 CTTTCTGGTCCCAAAACTTACTGCAAAGCTACAATAATCAAGA--GTGTA 2734
                            i iii ii           i          i         --    i
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_101073032_   2735 ATGTTGATATAAGGAGAGTCATATAGACTAATTGAATAGAATTTTGAGTC 2784
                         i ii  ii       v  v        ii   v          vv     
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_101073032_   2785 TAGAAATAAACCTCTTCATCTATGGTCAATTAATTTTCCACAAGGGTGAC 2834
                         i           iv v   i           i      v         v 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_101073032_   2835 AAGACCATTCAATGGGGAAAGGCTAGTCTTTTCAACAAATTGTGCTGGGA 2884
                                              iv                 v         
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_101073032_   2885 CAACTGGAGATTTGCATTCCAAACAGTGAAGCTGGACTCTCATGTCACAC 2934
                                 v ?iii   v v   v i     i     i ii iv      
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_101073032_   2935 CATACAGGAAAATTAACTC------------------------------T 2954
                             i vi           ------------------------------ 
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_101073032_   2955 AAAACTACAACATTCTTACAAAAAAA----GGGGTAAATCTTCATGACCT 3000
                                i  v i     v  i    ----  ?          i      
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_101073032_   3001 TGAATTTGATAATGGATTATTAGAAACAATATCAGAAGCATGGGCAGCAA 3050
                           ii  v ii     v  v     v ii i i  i     iii   i   
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_101073032_   3051 AAGAAAGA-CAGATAAATTAGGCTTCATCAAAATTAAAATATTTTGTGCA 3099
                               i -i         i i                 vv        v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_101073032_   3100 TCAGAGTTCACTATAAAGAAAGTGAAAACACATTCTACAGAATGGGAGAA 3149
                            i  vv      v             v   vi i              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_101073032_   3150 AATATTTGCTAATTATATATCTGATAAAGGTCTACTATGCAGTATCTATG 3199
                                  v   i             i  v  vv   v   v  v   i
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_101073032_   3200 AAGACCTCTTATAACTCAA----AAAGAGACCAACAATGCAATTAAAAAA 3245
                             v      i       ----   i    v  i  iv     ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_101073032_   3246 TGGACAAAGGACTTGAATAGTCATTACTCCAAAGAAGATATATAAATGAC 3295
                            i       i        v    v                i     i 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_101073032_   3296 CAATAGTCACATGAAAAGATGCTCAACATCTTGAGTCAT 3334
                              iv                       v????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (93 / 62)
Gap_init rate = 0.01 (10 / 886), avg. gap size = 4.80 (48 / 10)  


3106 27.10 1.11 0.66  chrX_101092064_101102201     4996  5899 (4238)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101092064_   4996 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5045
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101092064_   5046 GGCCATACTGCCCAAGGTAGTTTATAGATTCAATGCCATCCCCATCGAGC 5095
                            v     v     iv ii i  i        i  v     i   i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101092064_   5096 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5143
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_101092064_   5144 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCGTAAGCCAAAAG 5193
                                viiv  ii  v  v v  v     iv     v i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101092064_   5194 AACAAAGCTGGAGGCATCACGTTACCTGACTTCAAACTATACTACAAGGC 5243
                                i      vv    ii v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101092064_   5244 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5293
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101092064_   5294 AATAGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5341
                            i   i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_101092064_   5342 ACCTGATATTTGACAAACCTTAGAAAAACAAGAAATGGGGAAAGGATTCC 5391
                          vi    v  i     ivv vvv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_101092064_   5392 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5441
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_101092064_   5442 GAAACTGGATACCTTCCTTACACCTTATACAAAAATTAATTCAAGATGCA 5491
                            ii    iv   v   i     v              i    i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_101092064_   5492 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAGGAAAAC 5541
                          i ?    i       v   v       i      vi i    i      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_101092064_   5542 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5590
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101092064_   5591 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGGTCTA 5640
                         vi            vvi          vv     v  i    v  iii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101092064_   5641 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA-CAATCAGAGTGA 5689
                           i   v v  i i   i  ii vv    i  v    -   v- i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGA 694

  chrX_101092064_   5690 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACTCATCTGAC 5739
                          v  i     i                 v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_101092064_   5740 AAAGGGCTAATATCCAGAATCTACAAAGAAATCAAACAAATTTACAAGAA 5789
                           i  i  vi          v  i      v  vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_101092064_   5790 AAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5835
                            i    ----   v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_101092064_   5836 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAGATGCTCA 5885
                             v        i  vi viii     v ii                  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_101092064_   5886 TTATCACTGGCCAT 5899
                         vi    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  

2722 27.30 1.89 1.11  chrX_101092064_101102201     8765  9665 (472)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101092064_   8765 TGGAAAAACATTCCATGCTCATTGATAGGAAGAATCAATATCATGAAAAT 8814
                               i i  i     i    v   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101092064_   8815 GGCCATATTGCCCAAAGTAATTTATAGATTTAATGCTATTCCCATCAAAC 8864
                            v   i v      v i  i  i     i  i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101092064_   8865 TACCATTGACATTCTTCACAGAATTAGAAAAAAAACT-ACTTTAAATTTC 8913
                          v   vivi v  i  ii     v v  v  i---  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_101092064_   8914 ATATGGAACCAAAGAAGAGCCTGTATAGCCAAGACAACCCTAAGCAAAAA 8963
                                 viiv iii  v  v v        i    i i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_101092064_   8964 TAACGAAGCAGGAGGCACT-ATACTATCTGACTTCAAACAATACTACAAG 9012
                         v   i   iv     -   - i   vi ii i      vvv        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_101092064_   9013 CCTACAGTAACCAAAACAGCATGGTTCTGGTAAAGAGAAAGAAATATGTA 9062
                         v         i   i    ii    v    i v ii  v   v    -- 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT--A 294

  chrX_101092064_   9063 GATCAATGTAACAGAACAGAGACCTCAAAAATAAGACTTCACATCTGCAA 9112
                                 v  i    iv    vii  i      iv ivi    i iiii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_101092064_   9113 TCATCTGATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 9162
                            vi    i        ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_101092064_   9163 CCCTATTTAACAAATGGTGCTGGGGGAAACTAGCTAGCCATATGCAGAAA 9212
                         vi  v  i                iv  -  i v  ?   i     i  i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAG 443

  chrX_101092064_   9213 ATTGAAACTGGACCCCTTCCTTAAACCTTATA--AAAATTAGTTCAAGAT 9260
                          v    ii         v   i v   v    --       ii    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_101092064_   9261 GGATTAAAGACTTAAATATAAAACCCAAAACCATAAAAACCCTAGAAGAA 9310
                             i ?    i     i   i v i     i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_101092064_   9311 AACCTGGGCA-ATACCATTCAGGACATAGGTGTGGGCAAAGACTTCAT-G 9358
                            v i  ?i- v i -   iv   v v  vv i     v ii   v - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_101092064_   9359 ATGAAGATGCCGAAAGCAATTGCAACAAAAGCCAAAATTAACAAACAGCA 9408
                           - v  ii  i      vvv          vv     vi i   iv v 
  L1M4_orf2#LINE/    593 AT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_101092064_   9409 TCTAA-CTAAATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGA 9457
                         ii v - v        i -   i  ii vv    i  v       vv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_101092064_   9458 GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAAAT-ATCCATC 9506
                              v  i     i                 v         -  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_101092064_   9507 TGACAAAGGTCTAATATCTAGAATCTACAAGGAACTTAAACAAATTTACA 9556
                            i  i  v  vi    i     v  i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_101092064_   9557 AGAAAAA-------AATCCCATCAAAAAGTGGGCAAATTGTATGAACAGA 9599
                          v     -------  i  v  i?    i        vvi v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_101092064_   9600 CAATTCTCAAAAGAAGACATTTATGCAGCCAACAA--ACATGACAGAAAG 9647
                           v     v        i  vi viii     i  --      v ii v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_101092064_   9648 TGAAACATCACTGATAAT 9665
                         ivv       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (137 / 105)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.69 (27 / 16)  


 443 30.26 0.00 0.66  chrX_101107141_101112933.rev      285   436 (5357)    L1M4_orf2#LINE/L1        1   151 (757)  

  chrX_101107141_    285 TGGAAAAACATTCCATGTTCATTGATAGGAAGTATCAATATCATGAAAAA 334
                               i i  i          v   v     vv i     ii v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101107141_    335 GACCATACTGCCCTCAGTAATTTATAGATTCAACGCTATCCCCATCAAGC 384
                          i v     v   vv v i  i  i           v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101107141_    385 TACCATTGACATTCTTCACAGAATTAGAAAAAACTACATTTAAAGTTAAT 434
                          v   vivi v  i  ii     v v - v  i  ivvii    i  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chrX_101107141_    435 AT 436
                           
  L1M4_orf2#LINE/    150 AT 151

Transitions / transversions = 1.00 (23 / 23)
Gap_init rate = 0.01 (1 / 151), avg. gap size = 1.00 (1 / 1)  

3142 26.85 0.88 0.55  chrX_101107141_101112933.rev     2845  3749 (2044)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101107141_   2845 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2894
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101107141_   2895 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2944
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101107141_   2945 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 2991
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_101107141_   2992 ATATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAA 3041
                                 viiv  ii  v  viv  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_101107141_   3042 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 3091
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_101107141_   3092 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 3141
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_101107141_   3142 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACTGCATATCTACAAC 3189
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_101107141_   3190 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 3239
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_101107141_   3240 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTACAAAGC 3289
                         i  v  i  i              v      v  ?   i   i v  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_101107141_   3290 TGAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGC 3339
                             ii    i    v   i     v     v        i    i   v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_101107141_   3340 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3389
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_101107141_   3390 CCTAGGCATTACCATTCAGGACATAGGCATGGGTAA-GGATTCATGTCTA 3438
                          v    ?i v viv   iv   v v  vv i  i  -  v   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101107141_   3439 AAATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3488
                         vi i          vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101107141_   3489 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3538
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101107141_   3539 CAGGCAACCTGCAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 3588
                         v  i     ii  i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_101107141_   3589 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 3638
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_101107141_   3639 AAAACAAACAACACCATCAGAAATTGGGCGAAGGACATGAACAGACACTT 3688
                           i     i   v v  i?i   v     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_101107141_   3689 CTCAAAAGAAGACATTTATGCAGCCAAAAA--ACATGAAAAAATGCTCAT 3736
                            v        i  vi viii     v  --         i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_101107141_   3737 CATCACTGGCCAT 3749
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  

2671 24.81 0.90 1.55  chrX_101107141_101112933.rev     4529  5302 (491)    L1M4_orf2#LINE/L1      140   908 (0)  

  chrX_101107141_   4529 TAAATTTCATATGGAACCAAAAAAGAACCCGTATAGCCAAGACAATCCTA 4578
                             v           viiv  ii  v  v v        i      i i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_101107141_   4579 AGCAAAAAGAACAAGGCTGGAGGCATCACACTACCTGACTTCAAAGTATA 4628
                          iv  i        i i      vv       v  ii i      iiv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_101107141_   4629 CTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAT 4678
                               i          i   i    ii         i iv ii i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_101107141_   4679 ATATAGACCAATGGATCAGAACAGAGGCCTCAGAAATAATGCCACACATC 4728
                                i       vi    iv   ivii         vv   i    i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_101107141_   4729 TACA-TCAAAAACCATCTGATCTTTGACAAACCTGACCAAAACAAG-CAA 4776
                           ii-    -------i    i  i     ivv  -    i  v v-   
  L1M4_orf2#LINE/    340 TATGGTCAA-------TTGATTTTCGACAAGGGTG-CCAAGACCATTCAA 381

  chrX_101107141_   4777 TGGGGAAAGGATTCACTATTTAATAAATGTTGTTGGGAAAACTGGCTAGC 4826
                                  i  vvv  v  i  i     v  i     v      v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_101107141_   4827 CATAAGCAGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAA 4876
                           i v   i  i v    ii         v   i     v          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_101107141_   4877 TTAACTCAAGATGGATTAAAGACTTAAATGTATGGTTTTAAACCATAAAA 4926
                                  i      i ?    i        v ivi v    i      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_101107141_   4927 ACCCTCGAAGAAAACCTAGACA-ATACCATTCAGGACATAGGCATGGGCA 4975
                         vi i v         v   i?i- v i -   iv   v v  vv i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chrX_101107141_   4976 AAGACTTCATGACTGAAACACCAAAAGCAATGGCAACAAAGGCAAAAATT 5025
                          v ii   v iiv ivi            vvi        i v      v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_101107141_   5026 GACAAAT-GGAATCCAATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAA 5074
                           i    -   v i  - i   v v  i i   i   i vv    i  v 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCA-TCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_101107141_   5075 CTATCATCAGAGTGAACAGGAAACCTACAGAATGGGAGAAAATTTTTGCA 5124
                               vv i      v  iv    i                 v      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_101107141_   5125 A--TATATCCATCTGACAAAGGGCTAGTAAGCAGAATCTACAAGGAACTT 5172
                          --i    --      i  i  i  v   vv      v  i  i     i
  L1M4_orf2#LINE/    730 AATCATAT--ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_101107141_   5173 AAACAAATTTACAAGAAAAA-ACAAACAACCACATCAAAAAGTGGGCAAA 5221
                         vv    v iv i  v     -     i    vv  i?    i        
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_101107141_   5222 TGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAAAC 5271
                         v   v    i     i     v        i  vi viii     i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_101107141_   5272 ATATGAAAAAAAGCTCATCATCACTGGTCAT 5302
                          i       i v     v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (107 / 81)
Gap_init rate = 0.01 (11 / 769), avg. gap size = 1.73 (19 / 11)  


1330 28.76 3.92 0.65  chrX_101117603_101120704.rev     1368  1826 (1276)    L1M4_orf2#LINE/L1        1   474 (434)  

  chrX_101117603_   1368 TGGAAACACATCCTATGCTCATGGATGGGTAGAATCAATACTGTGAAAAT 1417
                               v i    i   i        v  v   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101117603_   1418 TACCACACTACC-AAA---------AG---CCGTGCAATTTCCATCAAAA 1454
                         vi v i   v  -   ---------  --- vii     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101117603_   1455 TGCCTTCATTATTCTTCACAGAACTAGAAGAAACAATCCTACAATTTATA 1504
                          v  vv vviv  i  ii     v v  vi ivii      v    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_101117603_   1505 TAGAACAAAAAAGAGCCCACA-TAGCCAAAGCAAGACTAAGCAA-AAGAA 1552
                          i   vviv  i ii    v -        i   vvi i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_101117603_   1553 CAAATCTGGAGGCATCACATTACCCAACTTCAAACTGTACTAAAAGGCTA 1602
                             vi      vv     i v     i      viv     v  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_101117603_   1603 TTGTTGCCAAAACAGCATGGTACTGGTATAAAAATAGGCATACAGACCAA 1652
                         iv  vii   i    ii         i    ii    i    i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_101117603_   1653 TGGAGCAGAATAGAGAA-CCACAAAATAAAGTCTAATAC-TTAACAGCCA 1700
                             ii     v    i-   -i       vi --    -  v ii i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCA-GAAATAAACCC--ATACATTTATGGTCA 347

  chrX_101117603_   1701 ACTGATCTTC-ACAAGGCAAACAAAAACATAAAGTGGGGAAAGGACACCC 1749
                          i    i   -      vviv   i v   vv i         i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_101117603_   1750 AATTCAACAAATGGTGCAGGTGTAATTGGCAAGCCACATGTAGAAGAATA 1799
                         vv               v  vii  i   vv ?       i i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_101117603_   1800 AAACTGGATCCTCATCTCTCACTGTAT 1826
                           ii    i  ii i   v   ii   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATAT 474

Transitions / transversions = 1.47 (78 / 53)
Gap_init rate = 0.02 (10 / 474), avg. gap size = 2.10 (21 / 10)  

1222 23.94 5.63 0.23  chrX_101117603_101120704.rev     2186  2611 (491)    L1M4_orf2#LINE/L1      460   908 (0)  

  chrX_101117603_   2186 TATCACTCACCTTATACAAAAATCAACTCAAGATGGATCAAAGACTTAAA 2235
                           i v v    v           i       i        ?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_101117603_   2236 TCTAAGATCTGAAACTGTGAAAATTATAGAAGATAACACCTGAAAAACTC 2285
                          v     v  i     i i   v iv       v    ivv ?iv  v  
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_101117603_   2286 TTTTAGACATTGGCTTAAGCAAATAGTTTGTAAGCAAGTAC-CCAAAAGG 2334
                           ivv   v    v   i    - i    v v  vv vv  -       v
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_101117603_   2335 AAATGCAACAGAAACAAAGATAAATAGATGGGAGATAGTTAAACTAAATA 2384
                          v v      i  iv   i   i   i  v   vv vi i   v v  v 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_101117603_   2385 GCTTCTGCACAGCAAAAGAAATAATCAGTAGAGCAAACAGACAACTCACA 2434
                         i   i  ii vv    i  v iv    iv i  ii  v       i    
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_101117603_   2435 GAGTGTGAGAAAATATTC-----TCA----------AAAGGACTAATATC 2469
                           i  v           i-----   ----------  i     vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_101117603_   2470 CAGAATCTACAAGGAAGTCAAATAAATCAACAAGAAAAA---AAAT--CC 2514
                               v  i  i   v  vv i  v    i  v     ---    --  
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_101117603_   2515 CA-TCAAAAAGTAGGCAAAGAACATGAATAGACAATTCTCAAAAGAAAAT 2563
                           - i?    i i       i iv          v     v      i  
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_101117603_   2564 ATACAAATGGCCAAAAA--ACATGAAAAAATAATCAACATCACTAATTAT 2611
                                       v  --         i  iv         ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.90 (47 / 52)
Gap_init rate = 0.02 (8 / 449), avg. gap size = 3.12 (25 / 8)  


2871 27.18 2.13 0.56  chrX_101177490_101182773     3898  4791 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101177490_   3898 TGGAAAAACATTCCATCCTCATGAATAGGAAGAATCAGTATTGTTAAAAT 3947
                               i i  i    vi     i  v      v i i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101177490_   3948 GACCATACTATCCAAAGCAATTTATAGATTCAATACTATTTCTATTAAAC 3997
                          i v     vi     vii  i  i        ii v  ii    i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101177490_   3998 TGGCAATGACATTCCTCACAGAATTAGAACAATCT-ATTTTAAATTTTAT 4046
                          vv  iivi v  ii ii     v v  -   v  -  ii    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_101177490_   4047 ATGAAACCAAAAAAGGCCT-GAATAGCCAAAGCAATGCTAAGCAAAAA-A 4094
                            i  viiv  ii i  i-           i    vi i iv  i  - 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_101177490_   4095 ACAAAGCTGCAGGTGTCATGTTACCTGATTTCAAACTATACTACAGGGCT 4144
                               i  v   vv   iii v  ii        viv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_101177490_   4145 ACAGTAACCAAAATAGCATGATATTGGTACAAAAACAGACACATAGTCCA 4194
                                i   i i  ii  i  i   i i  ii i     i    vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_101177490_   4195 ATGGAGCAGAATAGAGAG--CAGAAATAATGCCATGCATCTACAACCATA 4242
                              ii     v     --         vv    i   i  iiii  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_101177490_   4243 TGATCTTTGACAAAGTCAGCAAAAACAAGCAATGGGGAAAGGACCCCCTA 4292
                             i  i     i viiv   i v  vv            i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_101177490_   4293 TTCAATAAATGGTGCTGGGATAGGTGGCTAGCCATATGCAGAAGACTGAA 4342
                              i              i iv   v  ?   i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_101177490_   4343 ACTGGATCCCTTCCTTTCACCATA--CAAAAATCAACTCAAGACAGATTA 4390
                         ii    i    v   iv       --       i       i ii   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_101177490_   4391 AAGTCTTAAATGTAAAACCTGAAAGTATAAACACCCT-GGAATATAACCT 4439
                         ?  v i         i v  i   v      -  i  -i   v v   v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACAT 548

  chrX_101177490_   4440 AGGTAATAGCATTTTGTG-CATAGGACCTGGCAAAGATTTCACAATGAAG 4488
                            ?i-  ivvi  i   - v v  iiiv     v i    vi ivv v 
  L1M4_orf2#LINE/    549 AGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_101177490_   4489 ACACCAAAAGCGATTA-CAACAAAACCAAAAACAGACAAATGGGACCTAA 4537
                                    - iv -        vv     i   i    v    i v 
  L1M4_orf2#LINE/    598 ACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_101177490_   4538 TTAAACCAAAGAGCTTTTGCACAGCAAAAGAAACTATCAACAGAATAAAC 4587
                          i   viv  i i      ii vv    i  v        v i i i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_101177490_   4588 AGACAACCTCCAGAATGAGAGAAAATTTTTGCAAACAATGCATCTGACAA 4637
                                 iv       i        v        iv  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_101177490_   4638 AGGTGTAATATCCAGAATCTATAAGGAACT--TA-AAC---ATATTTCCA 4681
                         i  vv vi          v     i     --  -   ---   v vvv 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_101177490_   4682 GGAAAAA-AATCTCATT-AAAAATTGGCAAAGGACATGAGCAGACACTT- 4728
                         i  v   -  i iv   -      v         iv   ii     i  -
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_101177490_   4729 TCAAAAGAAGACATACAGGCAACCAAAAAGCATATGAAAAAAATTTTCAA 4778
                           v        i     iiiii    v     i       i - vi    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

  chrX_101177490_   4779 CATCACTAATCAT 4791
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (149 / 91)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.26 (24 / 19)  


2952 27.67 0.88 0.77  chrX_101247557_101258825.rev     5000  5906 (5363)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101247557_   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5049
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101247557_   5050 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5099
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101247557_   5100 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5148
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_101247557_   5149 ATGGAACCAAAAAAAAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGA 5198
                               viiv  iii v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_101247557_   5199 ACAAAGCTAGAGGCATTGCGGTACCTGACTTCAAACTATACTACAAGGCT 5248
                               i i    vv ii iv v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_101247557_   5249 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5298
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_101247557_   5299 ATGGAACAGAAC--AGAGCCCTCACAAA-AAACGCTGCATATCTACAACT 5345
                               i    i--    i  -- v   -    - iii i  i  iiiii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAAC-CCATACATTTATGGTC 346

  chrX_101247557_   5346 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5395
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_101247557_   5396 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTATATGTAGAAAGCT 5445
                           v  i  i              v      v  ? i i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_101247557_   5446 GAAACTGGATACCTTCCTTACACCTCCTACAAAAATTAATTCAAGATGTA 5495
                            ii    iv   v   i     viv            i    i   v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_101247557_   5496 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5545
                          i ?    i       v   v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_101247557_   5546 CTAGGCATTACCATTCAGGACACAAGCATGGGCAAGGACTTCATGTCTAA 5595
                         v    ?i v viv   iv   vivi vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_101247557_   5596 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAA 5645
                         i            vvi          vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_101247557_   5646 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 5695
                          i   v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_101247557_   5696 AGGCAACCTACAAATTGGGAGAAAAT-TTT-CAAAACCTACTCATCTGAC 5743
                           i     i   i v           -   -    v v  i--      i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGAT 744

  chrX_101247557_   5744 AAAGAGCTAATAGCCAGAATCTACAATGAACTCAAACAAACTTA-CAAGA 5792
                           i ii  vi  v       v  i  v      vv    -  i -i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chrX_101247557_   5793 AAAAAACAAACAACCCCATC-AAAAATGGGCAAAGGATATAAACAGACAC 5841
                             i     i     v  i-                 v i  i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_101247557_   5842 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5891
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_101247557_   5892 ATCATCACTGACCAT 5906
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (150 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.25 (15 / 12)  

3056 27.46 1.56 0.33  chrX_101247557_101258825.rev     9883 10778 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_101247557_   9883 GAAAAAATATTCCATGCTCATAGATAGGAAGAATCAATATCCTGAAAATG 9932
                          i   i    i     i    i   v      v i     iv v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_101247557_   9933 GCCATACTGCCCAAAGTACTTTATAGATTCAGTGGCATCCCCATCAAGCT 9982
                           v     v      v iv i  i       ii vv     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_101247557_   9983 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 10030
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_101247557_  10031 ATGAAACCAAAAAAGAGCCCGCAAT-GCCAAGTCAATCCTAAGTCAAAAG 10079
                            i  viiv  ii  -   iv   -     iv     i i ivv i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101247557_  10080 AACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTACAAGGC 10129
                                i     ivv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101247557_  10130 TACAGTAACCAAAACAGCATGATACTGATATCAAAACAGATATATAGGCC 10179
                                 i   i    ii  i     ii  v ii i   i      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101247557_  10180 AATGGAACAGAACAGAGGCCTCAGAAATAACATCACACATCTACAACCAT 10229
                                i    iv   ivii         vvi  i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_101247557_  10230 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGAATTCCCT 10279
                         i    i  i     ivv  v   i v  vvv              vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_101247557_  10280 ATTTAATAAATGGTGCAGAGAAAACTGACTAGCCATATGTAGAAAGCTGA 10329
                         v  i  i         v i  v     iv  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_101247557_  10330 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 10379
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_101247557_  10380 AGAGACTTAAATGTTAGACCTAAAACCATAAAAATCCTAGAAGAAAACCT 10429
                          ?    i       v   v       i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_101247557_  10430 AGGCAATACTATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 10479
                            ?ivv v v   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_101247557_  10480 CACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGAGATCTAATT 10529
                                    vvi          vv        i    vi  ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_101247557_  10530 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 10579
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_101247557_  10580 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAG 10629
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_101247557_  10630 GGCTAATATC-------TACAAAGAACTCAAACAAATTTACAAGAAAAAT 10672
                          i  vi    -------  i         vv    v iv i  v     v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_101247557_  10673 ACAAA---CCCA-TCAACAAGTGGGCGAAGGATATGAACAGACACTTCTC 10718
                              ---    - i? v  i     i      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_101247557_  10719 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTGGTCAT 10768
                         v        i  vi viii     i ii          i     viv   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_101247557_  10769 CATTGGCCAT 10778
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 2.12 (17 / 8)  


 531 23.61 5.56 0.69  chrX_101262361_101266067.rev     1530  1673 (2034)    L1M4_orf2#LINE/L1        1   151 (757)  

  chrX_101262361_   1530 TGAAAAGGCAT-TTGTGTTCATTAATTGGAAAAATTAATATCATTAAGAT 1578
                           i    ii  -iii       vi       i v       ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101262361_   1579 GTTGCTACTCCCCTAAATTGATCTACCGATCTAATAAAATAACTTTCAAA 1628
                          viiv        -            v   ii  iiv   vv  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_101262361_   1629 ATTCCAACTGCATTTT-CACAGAAATGGGAAAGCT------AAAATTCAT 1671
                           i   i    v    -ii       v iv     ------         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_101262361_   1672 GT 1673
                         i 
  L1M4_orf2#LINE/    150 AT 151

Transitions / transversions = 1.83 (22 / 12)
Gap_init rate = 0.03 (4 / 151), avg. gap size = 2.25 (9 / 4)  

1462 18.14 13.97 3.92  chrX_101262361_101266067.rev     2052  2459 (1248)    L1M4_orf2#LINE/L1      148   596 (312)  

  chrX_101262361_   2052 ATGTGGAAATAGAAGGCGCCCTGAATAACCAACACAATCTTTAAAAAGTA 2101
                           i       iv    vi   v     i    v        v      v 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_101262361_   2102 GAACAAATTTGGAGAACTTGCACTCCTGGATTTCAAAACT---------- 2141
                                v      i   ii    i ivi           ----------
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_101262361_   2142 --GTAGTAATCAGTACAGTGTGATACTGATGTTTCCATAAGGATA--TAT 2187
                         --ii        iv        i     i------          --i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGG------CATAAGGATAGACAT 291

  chrX_101262361_   2188 ATA----AGTAAAATAAAATTGAGAGCCCAGATATAA-CCCATACATCTA 2232
                            ---- i ii    i         i     v    -         i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_101262361_   2233 TGGTAAATTGGTTTTC---------------------------------A 2249
                             v     i     --------------------------------- 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_101262361_   2250 ATAATCTTTTCAA-AAATGGTCCTGGGACAAATGGTTATACACATAGTGG 2298
                            i         -       v         v   v  ?v     -----
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT----- 436

  chrX_101262361_   2299 TTGCAAAATAATGAATTTGGTCACTTTCCTCACATTCCATTAAAAAAAAA 2348
                         --      v      v    v v i v       --    vv v     v
  L1M4_orf2#LINE/    437 --GCAAAAGAATGAAGTTGGACCCCTACCTCACA--CCATATACAAAAAT 482

  chrX_101262361_   2349 AAACATTAAAATGGATGGAAGACCTAAATGCAAGAATTAAATTTATAAG- 2397
                         v   - i         vi?           i    ii    vi     i-
  L1M4_orf2#LINE/    483 TAAC-TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_101262361_   2398 CTACTGGAAGAAAA---AGATGTAAATCTTTGTGACTTTGGACTAAGAAA 2444
                           vi i        ---  i?         i     i    ii  i v  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_101262361_   2445 TGGTTTCCTTGATAT 2459
                                i v     
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATAT 596

Transitions / transversions = 1.37 (41 / 30)
Gap_init rate = 0.03 (12 / 449), avg. gap size = 6.08 (73 / 12)  

 939 10.88 3.89 22.02  chrX_101262361_101266067.rev     2831  3216 (491)    L1M4_orf2#LINE/L1      593   908 (0)  

  chrX_101262361_   2831 ATATGACATCAAAA-CGCAA-CAACCAAAGAAAAAGTA----AACTGGAC 2874
                                 i     - i   -    v         i  ----  i     
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_101262361_   2875 ATCATCAAAATTTAAAACTTTTGTGCATCAAAGGACACTATCAAGATAAC 2924
                         v           v             v                   ----
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA---- 688

  chrX_101262361_   2925 ACATGTTTATCCATGTAACAAACCTGCACATCCTGCTCATGTACCCCAGA 2974
                         --------------------------------------------------
  L1M4_orf2#LINE/    689 -------------------------------------------------- 688

  chrX_101262361_   2975 ACTTAAAATAAAAATTTAAATTTAAAAAATATAATGAAAAGATAAC--AC 3022
                         --------------------------  i -----       i   --  
  L1M4_orf2#LINE/    689 --------------------------AAGT-----GAAAAGACAACCCAC 707

  chrX_101262361_   3023 AGAGGAGGAGAAAATATTTGCAAATATTTTATGTAATAAAAATCTAGTAT 3072
                            ivi                   vv v   v i    iiiv  v    
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_101262361_   3073 CCAGAATATATAAAGAACTCTTACAATTCAATAATAAAAA--CAAA---C 3117
                                                   i             --    --- 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_101262361_   3118 CCAATT-AAAGCTGAGAAAATAATTTGAATAGCTATTTCTATGAAGAAGA 3166
                               -   iv  i v   vi          vi      vii       
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_101262361_   3167 TACACAAGTGGCCAGTAAGCACAT-AAAAGAGGATCAGTATCATTAGTCA 3215
                           i    i      i         -      v v   ii    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_101262361_   3216 T 3216
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.33 (24 / 18)
Gap_init rate = 0.03 (10 / 316), avg. gap size = 10.00 (100 / 10)  


3142 27.75 0.44 0.44  chrX_101291868_101298252.rev     4987  5894 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101291868_   4987 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5036
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101291868_   5037 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5086
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101291868_   5087 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5134
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_101291868_   5135 CATGGAACCAAAAAAGAGCCCGCATTGCCACGTCAGTCCTAAGCCAAAAG 5184
                         i      viiv  ii  v  v v  v    viv  i  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101291868_   5185 AACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGGC 5234
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101291868_   5235 TACAGTAACCAAAACAGCATGGTACCGGTACCAAAAAAGGGATATAGACG 5284
                                 i   i    ii      i  i iv ii v  iv       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101291868_   5285 AATGGAACCAAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 5332
                                ivi  i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_101291868_   5333 ATCTGATGTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5382
                          vi    v  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_101291868_   5383 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCCTATGCAGAAAGCT 5432
                           v  i  i              v      v  ?  vi     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_101291868_   5433 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5482
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_101291868_   5483 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5532
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_101291868_   5533 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5582
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_101291868_   5583 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5632
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_101291868_   5633 TCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 5682
                              v v  i i   i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_101291868_   5683 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5732
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_101291868_   5733 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5782
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_101291868_   5783 AAACAAACGATCCCATCAAAAAGTGGGCGAAGGACATGAACAGGCACTTC 5832
                          i     ii i  v  i?    i     i     iv    i  i  i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_101291868_   5833 TCAAAGGAAGACATTTATGCAGCCAAAAAACACGTGAAAAAATGCTCATC 5882
                           v  i     i  vi viii     v  i   i      i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_101291868_   5883 ATCACTGGCCAT 5894
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1013 28.46 6.45 4.17  chrX_101312281_101314458.rev      500  1026 (1152)    L1M4_orf2#LINE/L1       16   554 (354)  

  chrX_101312281_    500 TGTCC-TAGATGGAATAATCCAGCATTAAAAAGATGTCGGTTCTTCCTAA 548
                            i - i   v i vi iii ii   ivv      v ii v  i  i  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_101312281_    549 ATTGGTGTATAAATTTAATTCAGTCGC-A--AAAACGCCAGCACACATTT 595
                             i v  i i   i  iv  i  v - --    iv     -ii v   
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCTTT 114

  chrX_101312281_    596 TTATGCA----TTTAGGCAAATTGATAATAAAGTTAATATATTTGTGAAA 641
                           -    ----  -- i   ii    vv    i  v    ------ i  
  L1M4_orf2#LINE/    115 TT-TGCAGAAATT--GACAAGCTGATCCTAAAATTCATAT------GGAA 155

  chrX_101312281_    642 ACATGCAAG-----CA---TAGCCAGGAAACA--CGTGAAAAAGAAAATC 681
                          --      -----  ---      --     -- v          i v 
  L1M4_orf2#LINE/    156 A--TGCAAGGGACCCAGAATAGCCA--AAACAATCTTGAAAAAGAAGAAC 201

  chrX_101312281_    682 TATGAGAGGGGACTTATGATATCAGCCAG---AAAAGCACACTATAAAGC 728
                         v v vvi i     i i- iv  --   i---v   i vi    i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCAC-ACTTC--CCAATTTCAAAACTTACTACAAAGC 248

  chrX_101312281_    729 CTCTGTAATTACGACATTGTGGCACTGGTGCAAGAATAGACTAATAGCCC 778
                         iv v     i v    v     i     iii   i      vv    vi 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101312281_    779 AGTGGACTAGAATAGAAAACTCAGAAATACAACCAAATCAT--ATGA-CA 825
                          i    v      v  i iii        v v   v -   --   i-  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGTCA 347

  chrX_101312281_    826 GTTAGTACATGATAAAGATGGCACATAAACTCTTTA--GGGCAAAGA-TG 872
                         i  ii vivi  i  i i  v  --- i  iv  i --   v     - i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCA---AGACCATTCAATGGGGAAAGAATA 394

  chrX_101312281_    873 GACATTT-AATAAATGGTCCTGGAACAACTGAG-----ACGTCTGGAAAA 916
                          v v   -  i       v    i       ii-----  i viii  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_101312281_    917 ATAAAGGTAGATCCATATAACACAGCATGCACAAGAATAAACTGCAAATG 966
                           i   v i  i  v  ivv    v   ii    i   v    vv     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_101312281_    967 GGTTAGGGATCTAAACATAACAAATGAAACCATGTAAGTTCTT-GAAGAA 1015
                          i i ?i  i     ii   v iv i    i  i-  ii    -      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAA 543

  chrX_101312281_   1016 AACATGGCAGT 1026
                              i v?  
  L1M4_orf2#LINE/    544 AACATAGGNGT 554

Transitions / transversions = 1.69 (93 / 55)
Gap_init rate = 0.05 (26 / 539), avg. gap size = 2.15 (56 / 26)  

 264 30.00 4.44 3.70  chrX_101312281_101314458.rev     1410  1679 (499)    L1M4_orf2#LINE/L1      611   882 (26)  

  chrX_101312281_   1410 AGGCAATGAAAGAAAAAAATAATCAATCCATTTGACCACATAAGGATAAA 1459
                          i    ii          -  ivi  ---   v   iv   v ii  v  
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAA-TAGATAA---ATTGGACTTCATCAAAATTAA 656

  chrX_101312281_   1460 CGAAA-----GTGATGCAAATG-CATCATAAATAAA-TCAAAAGGCAACT 1502
                         --   -----   v v    v -  ii  v  v   - v     i    i
  L1M4_orf2#LINE/    657 --AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_101312281_   1503 GACAAATTGATGTAAAGTACTTGCAGCACATATCGCAGACAACTGGA-TA 1551
                         v   i v  iviv   i  i     ivv     vv v  i  v-   - v
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG-GGACTT 753

  chrX_101312281_   1552 ATATTCCAAATATATAGAGAGCTCTTAAATATTGAGGGATGAAG-GACCA 1600
                         i   i vi        i   i      v - i v ivi  i  i-   v 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACA-ACTCAATAATAAAAAGACAA 802

  chrX_101312281_   1601 -CAACAGCAATAGAAATATGGGGGAAAGATATGAACAGATAATTC--CAA 1647
                         -i   v-    v?   v     vi  i   v    i   i v   --   
  L1M4_orf2#LINE/    803 ATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_101312281_   1648 CAAAAAGTATAAAAACAGTCCTCAAATATATG 1679
                         - i  ii    v   ii i vvi  ii i   
  L1M4_orf2#LINE/    852 -AGAAGATATACAAATGGCCAATAAGCACATG 882

Transitions / transversions = 1.22 (44 / 36)
Gap_init rate = 0.05 (14 / 272), avg. gap size = 1.57 (22 / 14)  


3064 27.75 0.66 0.66  chrX_101327523_101330345     1423  2330 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101327523_   1423 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1472
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101327523_   1473 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1522
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101327523_   1523 TACCAATGATTTTCTTCACAGAA-TTGGAAAAAACT-ACTGTAAAGTTCA 1570
                          v   iiviii  i  ii     -   -- v  i  - iiv    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_101327523_   1571 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1620
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101327523_   1621 AACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGGC 1670
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101327523_   1671 TACAGTAACCAAAACAGCATGGTACCGGTACCAAAACAGAGATATAGACC 1720
                                 i   i    ii      i  i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101327523_   1721 AACGGAACAGAAC--AGAGCCCTCAGATATAATGCCACATATCTACAACT 1768
                           i    i    i--    i  --   v    vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_101327523_   1769 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 1818
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_101327523_   1819 CTATTTTGGAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGAAAGCT 1868
                           v  iviv              v      v  ?  ii   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_101327523_   1869 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1918
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_101327523_   1919 TTGAAGACTTAAATGTTAGACCTAAAACCATAGAAACCCTAGAAGAAAAC 1968
                          ii?    i       v   v       i   i  vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_101327523_   1969 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 2017
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101327523_   2018 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2067
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101327523_   2068 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAA 2117
                           i   v v  i i   i  ii vv    i  v    i ivv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101327523_   2118 CAGGCAACCTACAGAATGGGAGGAAAAT-TTTGCAATCTACTCATCTGAC 2166
                         v  i     i            -     -       vii ivi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAG-AAAATATTTGCAAATCATATATCTGAT 744

  chrX_101327523_   2167 AAAGGGCTAATATCCAGAATCTACAACGAACTCCAACAAATTTACAAGAA 2216
                           i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_101327523_   2217 AAAAACAAACCACCCCCTCAACAAGTAGGCGAAGGATATGAACAGACACT 2266
                            i     iv    vv i? v  i i   i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_101327523_   2267 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 2316
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_101327523_   2317 TCATCACTGGCCAT 2330
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (148 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3643 24.13 0.44 1.31  chrX_101336026_101340320.rev     2889  3804 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101336026_   2889 TGGAAAAATATTCCACGCTCATGGATTGAAAGAATCAATATTGTTAAAAT 2938
                               i    i   i i          i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101336026_   2939 GTCCATAATACCCAAAGCAATCTACAGGTTCAATGCAATCCCTATCAAAA 2988
                          v v   v v      vii        i     i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101336026_   2989 TACCTATTTTGATACTATTTCTATTCACAGAAATAGAAAAAAAAATTCCT 3038
                          -  i -------i  iii i -  ii       v  v  ivvi  -   
  L1M4_orf2#LINE/    101 T-CCCA-------GCTGCCTTT-TTTGCAGAAATTGACAAGCTGAT-CCT 140

  chrX_101336026_   3039 AAAATTTATATGGAACCACAAAAGACCCAGAATAGCTAAAGCTATCCT-- 3086
                               i        vii   ii             i   i v   i --
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_101336026_   3087 -AAGCAAGAACAAACCTGAAGGAATCTCGTTACCTGACTTCAAATAATAC 3135
                         -  iv         vi  i    v  v ii v  ii i      vvv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_101336026_   3136 TACAGAGCCATAGTAACCAAGACAGCATGGTACTGGCATAAAAACAGATG 3185
                             i   i i     i        ii              ii i   ii
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_101336026_   3186 CATGGAACAATGGAACAGAATCGGGAGTCCAGAAAGAAATCCATACACCT 3235
                         i  i  v        i     i i           v   i       ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_101336026_   3236 ACAGTGATCTCATTTTTGACAAAGGTGCCAAGAACATATACTGGAGAAAG 3285
                          ii  v vi v     i     i          v   vi v   i     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_101336026_   3286 GACAGTCTCTTCGATAAATCGTGCTGGAAAACCTGGACCACCCATATGCA 3335
                         i i     i   i i    v       i v v     i- ?   i     
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCA 439

  chrX_101336026_   3336 GAAAAATGCAACTAGACCCCTATCTCTCCCCACATACGAAAATCAAATCA 3385
                         i  i    v ii i        i   v v   i    i     i  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_101336026_   3386 AAATAGATTAAAGACTTAAATGTAAGACCTCAAACTCTGAAACTACTACA 3435
                             i   i ?    i           v  v     v i     vi  v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_101336026_   3436 AGAAAACATTGGGAAAAATCTCCAGGACATAGGTCTGGGCAAAGACTTCT 3485
                                  v  ?iv      i iv   v v  vi i     v ii    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_101336026_   3486 TGAGCAACACCCCACAAGCACAGACGACCAAAGCAAACATGGACAAACGG 3535
                          iiii vv  v   v       ii i  v    v   v  i  i   iv 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_101336026_   3536 GATCACGTCAAG-TTAAAAAGCTTCTTCACAGCAAAGGATACAATCAACA 3584
                           iiv i    i-       -   i vii vv       i  v     v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_101336026_   3585 AAGTGAAGTGACAACCCACAGAATGGGAGAAAATATTTTCAAACCACTCC 3634
                                iv                             v    i  iviv
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_101336026_   3635 TCTGACAAGAGATTAATAACTAGCATATACAAGGATTTCAAACAACTCTA 3684
                              i   i  i vi  v i  v     i  i  vi  vv       v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_101336026_   3685 TAGGAAAAAATCTAATAATCTGATCGAAAGATGGGCAAAAGATTTGAATG 3734
                           iv     iv v     i ii  i?   i         i         i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_101336026_   3735 GACGTTTCTCAAAAGAAGACACACAAATGGCAAACAGGCATATGAAATGG 3784
                            i      v        i i         v  i i   i      v i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_101336026_   3785 TGTTCAACATCATTGATCAT 3804
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


4367 19.04 3.88 0.34  chrX_101384598_101386750      785  1661 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101384598_    785 TGGAAAGGCATCCCACGTTCATAGATTGGAAGACTTAATATCATTACGAT 834
                                ii      i      i                  ii   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101384598_    835 GGCAGTACCACCCAGAACAATCTACAGATTCATTGCAGTCCCTGACAGAA 884
                             i   iv    i vii             vi   i     iv  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101384598_    885 TCCCAACTGACTTCTTTGCAGAAATTGACAAGGTAATCCCAAAATTCATG 934
                              i   v   i                  v i    i         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_101384598_    935 TGGAAATGCAGTGGACCCCAAACAGCCAAAACCATCTTGAAAGAGAAGAA 984
                                   iv      vi  i         v         i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_101384598_    985 CAACGTTAGAAGACTCACACTTCCCGATTTCAGAACTTGCTACAAAACTA 1034
                            v   i  i              i      i     i       i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_101384598_   1035 CATTAATCAAGACTGTATGGTACCGACATAGGAACAGACGTGGGAATCAA 1084
                           v          v  i      i i    i i i    i ivii     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_101384598_   1085 TGGAATATAATTGAGAGTCCACAGATAATCTCACGTATTTATGTCCAGTT 1134
                                v             v i    v i  iii       vi  i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_101384598_   1135 GATTATCATTCAGGGTGCTGAAAAAATCCAATGGAGAAAAAAAATAGTCT 1184
                             v  iviv       ii i vv  i      i    i  --      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA--TAGTCT 398

  chrX_101384598_   1185 TCTTAACAAATGGTGCTGGGAGAAGTGGATATCCACTTGCAAAACAATTA 1234
                          i i                 v  v      ?    v       v   v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_101384598_   1235 ATTTTGACCCCTAACTCACATCACGTGCAAACACTGGCAGAAAATGGATC 1284
                          v  v        v      i  ii i    v i ii vv          
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_101384598_   1285 AATGACCTAAA-ATAAGAGCCAGAACTGTAAAACACT-----------GT 1322
                          ?v        -i       i i    i      v  -----------i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_101384598_   1323 AAGTGTACATCTTCATTACCTTGAATTAGGCAACCATTTCTTACATATGA 1372
                          i ?   v      i v      ii        ivi       v      
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_101384598_   1373 AACCAAAAGCACAAGCAACCAAAGAAAAAATAGGTAAATTGGACTTCATC 1422
                         v                  v             i                
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_101384598_   1423 TAAATTAAAAGCTTTTGTGCATCAGCAGACACTATCAAGAAAGCGGAAAA 1472
                         v         i         v   ivi                i i   i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_101384598_   1473 CCGACTGGTGGGAACAAGGGAAAATATTTGCAAATCACATCGCCGACAAG 1522
                         v i  ivii-i   iii i                  i  vv i  i   
  L1M4_orf2#LINE/    699 ACAACCCAC-AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_101384598_   1523 ----------------------AAGAACCCTTACAACTCAACAACAAACA 1550
                         ----------------------      i            i  i   v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_101384598_   1551 GACAAGCCACCGAATTAAAAAATGGGGAAATGATTTGAATAGATGTTTCT 1600
                              iiv   v    ?         v   v            ii     
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_101384598_   1601 CCAAAGGAGATATACAAATGACCAAGAAGCACGTGAAAATCTTCTCAACA 1650
                               i             i    v      i      vv v       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_101384598_   1651 TCGTTAGTCAT 1661
                           i????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.81 (105 / 58)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 7.40 (37 / 5)  


4367 19.04 3.88 0.34  chrX_101422490_101424642.rev      787  1663 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101422490_    787 TGGAAAGGCATCCCACGTTCATAGATTGGAAGACTTAATATCATTACGAT 836
                                ii      i      i                  ii   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101422490_    837 GGCAGTACCACCCAGAACAATCTACAGATTCATTGCAGTCCCTGACAGAA 886
                             i   iv    i vii             vi   i     iv  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101422490_    887 TCCCAACTGACTTCTTTGCAGAAATTGACAAGGTAATCCCAAAATTCATG 936
                              i   v   i                  v i    i         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_101422490_    937 TGGAAATGCAGTGGACCCCAAACAGCCAAAACCATCTTGAAAGAGAAGAA 986
                                   iv      vi  i         v         i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_101422490_    987 CAACGTTAGAAGACTCACACTTCCCGATTTCAGAACTTGCTACAAAACTA 1036
                            v   i  i              i      i     i       i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_101422490_   1037 CATTAATCAAGACTGTATGGTACCGACATAGGAACAGACGTGGGAATCAA 1086
                           v          v  i      i i    i i i    i ivii     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_101422490_   1087 TGGAATATAATTGAGAGTCCACAGATAATCTCACGTATTTATGTCCAGTT 1136
                                v             v i    v i  iii       vi  i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_101422490_   1137 GATTATCATTCAGGGTGCTGAAAAAATCCAATGGAGAAAAAAAATAGTCT 1186
                             v  iviv       ii i vv  i      i    i  --      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA--TAGTCT 398

  chrX_101422490_   1187 TCTTAACAAATGGTGCTGGGAGAAGTGGATATCCACTTGCAAAACAATTA 1236
                          i i                 v  v      ?    v       v   v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_101422490_   1237 ATTTTGACCCCTAACTCACATCACGTGCAAACACTGGCAGAAAATGGATC 1286
                          v  v        v      i  ii i    v i ii vv          
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_101422490_   1287 AATGACCTAAA-ATAAGAGCCAGAACTGTAAAACACT-----------GT 1324
                          ?v        -i       i i    i      v  -----------i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_101422490_   1325 AAGTGTACATCTTCATTACCTTGAATTAGGCAACCATTTCTTACATATGA 1374
                          i ?   v      i v      ii        ivi       v      
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_101422490_   1375 AACCAAAAGCACAAGCAACCAAAGAAAAAATAGGTAAATTGGACTTCATC 1424
                         v                  v             i                
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_101422490_   1425 TAAATTAAAAGCTTTTGTGCATCAGCAGACACTATCAAGAAAGCGGAAAA 1474
                         v         i         v   ivi                i i   i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_101422490_   1475 CCGACTGGTGGGAACAAGGGAAAATATTTGCAAATCACATCGCCGACAAG 1524
                         v i  ivii-i   iii i                  i  vv i  i   
  L1M4_orf2#LINE/    699 ACAACCCAC-AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_101422490_   1525 ----------------------AAGAACCCTTACAACTCAACAACAAACA 1552
                         ----------------------      i            i  i   v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_101422490_   1553 GACAAGCCACCGAATTAAAAAATGGGGAAATGATTTGAATAGATGTTTCT 1602
                              iiv   v    ?         v   v            ii     
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_101422490_   1603 CCAAAGGAGATATACAAATGACCAAGAAGCACGTGAAAATCTTCTCAACA 1652
                               i             i    v      i      vv v       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_101422490_   1653 TCGTTAGTCAT 1663
                           i????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.81 (105 / 58)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 7.40 (37 / 5)  


3643 24.13 0.44 1.31  chrX_101468964_101473258     2887  3802 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101468964_   2887 TGGAAAAATATTCCACGCTCATGGATTGAAAGAATCAATATTGTTAAAAT 2936
                               i    i   i i          i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101468964_   2937 GTCCATAATACCCAAAGCAATCTACAGGTTCAATGCAATCCCTATCAAAA 2986
                          v v   v v      vii        i     i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101468964_   2987 TACCTATTTTGATACTATTTCTATTCACAGAAATAGAAAAAAAAATTCCT 3036
                          -  i -------i  iii i -  ii       v  v  ivvi  -   
  L1M4_orf2#LINE/    101 T-CCCA-------GCTGCCTTT-TTTGCAGAAATTGACAAGCTGAT-CCT 140

  chrX_101468964_   3037 AAAATTTATATGGAACCACAAAAGACCCAGAATAGCTAAAGCTATCCT-- 3084
                               i        vii   ii             i   i v   i --
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_101468964_   3085 -AAGCAAGAACAAACCTGAAGGAATCTCGTTACCTGACTTCAAATAATAC 3133
                         -  iv         vi  i    v  v ii v  ii i      vvv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_101468964_   3134 TACAGAGCCATAGTAACCAAGACAGCATGGTACTGGCATAAAAACAGATG 3183
                             i   i i     i        ii              ii i   ii
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_101468964_   3184 CATGGAACAATGGAACAGAATCGGGAGTCCAGAAAGAAATCCATACACCT 3233
                         i  i  v        i     i i           v   i       ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_101468964_   3234 ACAGTGATCTCATTTTTGACAAAGGTGCCAAGAACATATACTGGAGAAAG 3283
                          ii  v vi v     i     i          v   vi v   i     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_101468964_   3284 GACAGTCTCTTCGATAAATCGTGCTGGAAAACCTGGACCACCCATATGCA 3333
                         i i     i   i i    v       i v v     i- ?   i     
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCA 439

  chrX_101468964_   3334 GAAAAATGCAACTAGACCCCTATCTCTCCCCACATACGAAAATCAAATCA 3383
                         i  i    v ii i        i   v v   i    i     i  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_101468964_   3384 AAATAGATTAAAGACTTAAATGTAAGACCTCAAACTCTGAAACTACTACA 3433
                             i   i ?    i           v  v     v i     vi  v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_101468964_   3434 AGAAAACATTGGGAAAAATCTCCAGGACATAGGTCTGGGCAAAGACTTCT 3483
                                  v  ?iv      i iv   v v  vi i     v ii    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_101468964_   3484 TGAGCAACACCCCACAAGCACAGACGACCAAAGCAAACATGGACAAACGG 3533
                          iiii vv  v   v       ii i  v    v   v  i  i   iv 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_101468964_   3534 GATCACGTCAAG-TTAAAAAGCTTCTTCACAGCAAAGGATACAATCAACA 3582
                           iiv i    i-       -   i vii vv       i  v     v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_101468964_   3583 AAGTGAAGTGACAACCCACAGAATGGGAGAAAATATTTTCAAACCACTCC 3632
                                iv                             v    i  iviv
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_101468964_   3633 TCTGACAAGAGATTAATAACTAGCATATACAAGGATTTCAAACAACTCTA 3682
                              i   i  i vi  v i  v     i  i  vi  vv       v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_101468964_   3683 TAGGAAAAAATCTAATAATCTGATCGAAAGATGGGCAAAAGATTTGAATG 3732
                           iv     iv v     i ii  i?   i         i         i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_101468964_   3733 GACGTTTCTCAAAAGAAGACACACAAATGGCAAACAGGCATATGAAATGG 3782
                            i      v        i i         v  i i   i      v i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_101468964_   3783 TGTTCAACATCATTGATCAT 3802
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


3072 27.64 0.66 0.66  chrX_101478985_101483791.rev     3409  4316 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101478985_   3409 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3458
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101478985_   3459 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3508
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101478985_   3509 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTGTAAAGTTCA 3556
                          v   iivi i  i  ii     -   -- v  i  - iiv    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_101478985_   3557 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 3606
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101478985_   3607 AACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGGC 3656
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101478985_   3657 TACAGTAACCAAAACAGCATGGTACCGGTACCAAAACAGAGATATAGACC 3706
                                 i   i    ii      i  i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101478985_   3707 AACGGAACAGAAC--AGAGCCCTCAGATATAATGCCACATATCTACAACT 3754
                           i    i    i--    i  --   v    vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_101478985_   3755 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 3804
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_101478985_   3805 CTATTTTGGAAATGGTGCTGGGAAAACTGGCTAGCCGTATGTAGAAAGCT 3854
                           v  iviv              v      v  ?  ii   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_101478985_   3855 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 3904
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_101478985_   3905 TTGAAGACTTAAATGTTAGACCTAAAACCATAGAAACCCTAGAAGAAAAC 3954
                          ii?    i       v   v       i   i  vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_101478985_   3955 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 4003
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101478985_   4004 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4053
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101478985_   4054 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAA 4103
                           i   v v  i i   i  ii vv    i  v    i ivv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101478985_   4104 CAGGCAACCTACAGAATGGGAGGAAAAT-TTTGCAATCTACTCATCTGAC 4152
                         v  i     i            -     -       vii ivi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAG-AAAATATTTGCAAATCATATATCTGAT 744

  chrX_101478985_   4153 AAAGGGCTAATATCCAGAATCTACAACGAACTCCAACAAATTTACAAGAA 4202
                           i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_101478985_   4203 AAAAACAAACCACCCCCTCAACAAGTAGGCGAAGGATATGAACAGACACT 4252
                            i     iv    vv i? v  i i   i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_101478985_   4253 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 4302
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_101478985_   4303 TCATCACTGGCCAT 4316
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (147 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3169 27.39 0.44 0.55  chrX_101511062_101517447     4985  5893 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101511062_   4985 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5034
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101511062_   5035 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5084
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101511062_   5085 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5132
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_101511062_   5133 TATGGAACCAAAAAAGAGCCCGCATTGCCACGTCAGTCCTAAGCCAAAAG 5182
                                viiv  ii  v  v v  v    viv  i  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101511062_   5183 AACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTATACTACAAGGC 5232
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101511062_   5233 TACAGTAACCAAAACAGCATGGTACCGGTACCAAAAAAAGGGATATAGAC 5282
                                 i   i    ii      i  i i-  ii v  iv       i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGAT 297

  chrX_101511062_   5283 GAATGGAACCGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5330
                         v       iv   i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_101511062_   5331 CATCTGATGTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5380
                           vi    v  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_101511062_   5381 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCCTATGCAGAAAGC 5430
                         i  v  i  i              v      v  ?  vi     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_101511062_   5431 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5480
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_101511062_   5481 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5530
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_101511062_   5531 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5580
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101511062_   5581 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5630
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101511062_   5631 ATCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 5680
                               v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101511062_   5681 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5730
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_101511062_   5731 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5780
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_101511062_   5781 AAAACAAACGATCCCATCAAAAAGTGGGCGAAGGACATGAACAGGCACTT 5830
                           i     ii i  v  i?    i     i     iv    i  i  i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_101511062_   5831 CTCAAAGGAAGACATTTATGCAGCCAAAAAACACGTGAAAAAATGCTCAT 5880
                            v  i     i  vi viii     v  i   i      i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_101511062_   5881 CATCACTGGCCAT 5893
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


 531 23.61 5.56 0.69  chrX_101543234_101546939     1527  1670 (2036)    L1M4_orf2#LINE/L1        1   151 (757)  

  chrX_101543234_   1527 TGAAAAGGCAT-TTGTGTTCATTAATTGGAAAAATTAATATCATTAAGAT 1575
                           i    ii  -iii       vi       i v       ii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101543234_   1576 GTTGCTACTCCCCTAAATTGATCTACCGATCTAATAAAATAACTTTCAAA 1625
                          viiv        -            v   ii  iiv   vv  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_101543234_   1626 ATTCCAACTGCATTTT-CACAGAAATGGGAAAGCT------AAAATTCAT 1668
                           i   i    v    -ii       v iv     ------         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_101543234_   1669 GT 1670
                         i 
  L1M4_orf2#LINE/    150 AT 151

Transitions / transversions = 1.83 (22 / 12)
Gap_init rate = 0.03 (4 / 151), avg. gap size = 2.25 (9 / 4)  

1462 18.14 13.97 3.92  chrX_101543234_101546939     2049  2456 (1250)    L1M4_orf2#LINE/L1      148   596 (312)  

  chrX_101543234_   2049 ATGTGGAAATAGAAGGCGCCCTGAATAACCAACACAATCTTTAAAAAGTA 2098
                           i       iv    vi   v     i    v        v      v 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_101543234_   2099 GAACAAATTTGGAGAACTTGCACTCCTGGATTTCAAAACT---------- 2138
                                v      i   ii    i ivi           ----------
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_101543234_   2139 --GTAGTAATCAGTACAGTGTGATACTGATGTTTCCATAAGGATA--TAT 2184
                         --ii        iv        i     i------          --i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGG------CATAAGGATAGACAT 291

  chrX_101543234_   2185 ATA----AGTAAAATAAAATTGAGAGCCCAGATATAA-CCCATACATCTA 2229
                            ---- i ii    i         i     v    -         i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_101543234_   2230 TGGTAAATTGGTTTTC---------------------------------A 2246
                             v     i     --------------------------------- 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_101543234_   2247 ATAATCTTTTCAA-AAATGGTCCTGGGACAAATGGTTATACACATAGTGG 2295
                            i         -       v         v   v  ?v     -----
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT----- 436

  chrX_101543234_   2296 TTGCAAAATAATGAATTTGGTCACTTTCCTCACATTCCATTAAAAAAAAA 2345
                         --      v      v    v v i v       --    vv v     v
  L1M4_orf2#LINE/    437 --GCAAAAGAATGAAGTTGGACCCCTACCTCACA--CCATATACAAAAAT 482

  chrX_101543234_   2346 AAACATTAAAATGGATGGAAGACCTAAATGCAAGAATTAAATTTATAAG- 2394
                         v   - i         vi?           i    ii    vi     i-
  L1M4_orf2#LINE/    483 TAAC-TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_101543234_   2395 CTACTGGAAGAAAA---AGATGTAAATCTTTGTGACTTTGGACTAAGAAA 2441
                           vi i        ---  i?         i     i    ii  i v  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_101543234_   2442 TGGTTTCCTTGATAT 2456
                                i v     
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATAT 596

Transitions / transversions = 1.37 (41 / 30)
Gap_init rate = 0.03 (12 / 449), avg. gap size = 6.08 (73 / 12)  

 939 10.88 3.89 22.02  chrX_101543234_101546939     2828  3213 (493)    L1M4_orf2#LINE/L1      593   908 (0)  

  chrX_101543234_   2828 ATATGACATCAAAA-CGCAA-CAACCAAAGAAAAAGTA----AACTGGAC 2871
                                 i     - i   -    v         i  ----  i     
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_101543234_   2872 ATCATCAAAATTTAAAACTTTTGTGCATCAAAGGACACTATCAAGATAAC 2921
                         v           v             v                   ----
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA---- 688

  chrX_101543234_   2922 ACATGTTTATCCATGTAACAAACCTGCACATCCTGCTCATGTACCCCAGA 2971
                         --------------------------------------------------
  L1M4_orf2#LINE/    689 -------------------------------------------------- 688

  chrX_101543234_   2972 ACTTAAAATAAAAATTTAAATTTAAAAAATATAATGAAAAGATAAC--AC 3019
                         --------------------------  i -----       i   --  
  L1M4_orf2#LINE/    689 --------------------------AAGT-----GAAAAGACAACCCAC 707

  chrX_101543234_   3020 AGAGGAGGAGAAAATATTTGCAAATATTTTATGTAATAAAAATCTAGTAT 3069
                            ivi                   vv v   v i    iiiv  v    
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_101543234_   3070 CCAGAATATATAAAGAACTCTTACAATTCAATAATAAAAA--CAAA---C 3114
                                                   i             --    --- 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_101543234_   3115 CCAATT-AAAGCTGAGAAAATAATTTGAATAGCTATTTCTATGAAGAAGA 3163
                               -   iv  i v   vi          vi      vii       
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_101543234_   3164 TACACAAGTGGCCAGTAAGCACAT-AAAAGAGGATCAGTATCATTAGTCA 3212
                           i    i      i         -      v v   ii    ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_101543234_   3213 T 3213
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.33 (24 / 18)
Gap_init rate = 0.03 (10 / 316), avg. gap size = 10.00 (100 / 10)  


2686 25.87 4.39 2.25  chrX_101583005_101586921     2536  3424 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101583005_   2536 TGGAAAAACAGTCCATCCTCGGGGATAGGAAGAATCAATATCATGAAAAT 2585
                               i i vi    vi  iv    v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101583005_   2586 GGCCACACTACCCAAAGTAATTTATAAATTCAGTGCTATTCCCATCAAAC 2635
                            v i   v      v i  i  i i     ii  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101583005_   2636 TACCATTGACATTCTTCACAGAATTAGAAAAAAACTAGTTTTAAT-TTCA 2684
                          v   vivi v  i  ii     v v  v  i--  ii ii   v-    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_101583005_   2685 TATGGAACAAAAAAAGAGCCCT--ATAGCGAAGACAATCCTAAGCAAAAA 2732
                                - viv  i ii   v--     v  i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_101583005_   2733 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 2782
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_101583005_   2783 CTACAGTAACCAAAATAGCATGGTCCTGGTACCAAAACAGACATATAGAC 2832
                                  i   i i  ii    v    i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_101583005_   2833 CAATGGAACAGAGTAGAAAACTCAGAAATAACACCACACATCTACAACCA 2882
                                 i   i v  i iii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_101583005_   2883 TCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAG------- 2925
                         vi    i   i    ivv  v   i v  vv            -------
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_101583005_   2926 ------------GATTCTGGGAAAACTGGCTAGCCTTATTCAGAAAACTG 2963
                         ------------ i v      v      v  ?  vi  v  i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_101583005_   2964 AAACTGGCCCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 3013
                           ii   v     v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_101583005_   3014 TAAAGACTTAAATGTAAAACCCAAAACCATAAAAGCCCTAGAAGAAAACC 3063
                         i ?    i         i v i     i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_101583005_   3064 TAGG--TAATACCATTCAGGACATAAGCATGGGCAAAGATTTC------A 3105
                             --   - i -   iv   v vi vv i     v i    ------ 
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101583005_   3106 TGACAAAAATGTCAAAAGCAATTGCAACAAAAGCAAAAGTTGACAAATGG 3155
                              ------i        vvv          v    i v  i    v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_101583005_   3156 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAATCTATCAGCAG 3205
                           ii v  i   v v  i i   i  ii vv    i  vv      iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_101583005_   3206 AGTGAACAGGCACAGGCAACCTACACAATGGGAGAAAAATTTTGCAATCT 3255
                               ----- -  i     i   v            vv       vii
  L1M4_orf2#LINE/    690 AGTGAA-----A-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_101583005_   3256 ACCCTTCTGACAAAGGTCTAATACCCAGAATCTTCAAGGAACTTAAACAA 3305
                          iviv     i  i  v  vi  i       v vi  i     ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_101583005_   3306 ACTTA-CAAGAAAAAAACAG----TCCCATCTAAAAGTGGGCAAAGAACA 3350
                         -  i -i  v     i   i----i  v  i?    i         i iv
  L1M4_orf2#LINE/    784 -CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_101583005_   3351 GGAACAGACACTTCTCAAAAGAAAATATGC----GGCCAACAAACATATG 3396
                         v   i     i     v      i    i ----      i  i  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_101583005_   3397 AAAAAAAAAGCTCAACATCACTGATCAT 3424
                             i v--           ????????
  L1M4_orf2#LINE/    883 AAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (136 / 91)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.47 (59 / 17)  


3288 25.91 1.11 0.55  chrX_101634874_101641270     5002  5904 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101634874_   5002 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5051
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101634874_   5052 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101634874_   5102 TACCAATGACTTTCTTCACACAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_101634874_   5150 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101634874_   5200 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5249
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101634874_   5250 TACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATATAGATC 5299
                                 i   i    ii i       i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101634874_   5300 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5347
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_101634874_   5348 ATCTGGTCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5397
                          vi  i i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_101634874_   5398 CTATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCT 5447
                           v  i  i              v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_101634874_   5448 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5497
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_101634874_   5498 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAACCCT-AGAAGAAAAC 5546
                          i ?    i       v   v       i       i  -          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_101634874_   5547 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTGATGTCTA 5595
                         v    ?i- v i -   iv   v v  vv i     v ii  vv ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101634874_   5596 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5645
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101634874_   5646 ATCAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAA 5695
                               v v  i i   i   i vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101634874_   5696 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5745
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_101634874_   5746 AAGGGCTAATATCCAGAATCTACAATGAACTTAAACAAATTTACAAGAAA 5795
                          i  i  vi          v  i  v     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_101634874_   5796 AAAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5841
                           i    ----   v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_101634874_   5842 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5891
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_101634874_   5892 CATCACTGGCCAT 5904
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (137 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2473 12.64 3.10 25.11  chrX_101652591_101654979.rev      736  1898 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_101652591_    736 GAGAAAATTTCC--TGTTCATGGATCTGAAGACAGAATATTATTAAGATG 783
                          ii  i  v   --           iv      vv      i        
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_101652591_    784 GCATTATGCCCCAATTTTATCTACAGATTCCACACAACCCGTATCAAAAT 833
                            v  iv      v  v            v  i   i  v         
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_101652591_    834 ACCACTTCACTTCTTTTCTGAAAATGACAAGTTCATTCTAAAATCCAAAT 883
                         v   vi vv   i   v v    v       i v  i       i  v  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_101652591_    884 A-AAATGCA-TGGATTCAGAATAGCCAAA-CAATCGTGGAAAATAA---- 926
                         i-       -v   ii             -     v  i    v  ----
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_101652591_    927 AAAGTTGGAGGAATTCA-ATTTCCCAATTTTAAAACTTACTACAAAGCTA 975
                                     -i   - i          i                   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGA-CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_101652591_    976 CATTTATCA---CAATGGTGGTATTGGTAAAAAGATAGACATATAGATGT 1022
                           v v    ---  i  -     i   i v  i               --
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTG-TGGTACTGGCATAAGGATAGACATATAGAT-- 297

  chrX_101652591_   1023 CTGTTGGAGTACAGTTGAGAATCCAGAAATAAACCTATATATTTATGGTT 1072
                         -iiv    i  v i      i              i   i         i
  L1M4_orf2#LINE/    298 -CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_101652591_   1073 ATCTGATATAAGAAAAGAGTGCCAATACCATTTAGTGGAGGAAATTGGTG 1122
                          vi    v vv  v   i       v      i i   -     ----- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAA-----G 390

  chrX_101652591_   1123 TGTTGTCTT-----CAAATGGTGTAGGGACAACTGACTATCCACATGCAA 1167
                         vi v     -----         iv          iv  ?          
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_101652591_   1168 ATATACAAAAACTGGCCGGGCGCAGTAGCTCACGCCTGTAATCCCAGCAC 1217
                          ------ i  ---------------------------------------
  L1M4_orf2#LINE/    441 A------AGAA--------------------------------------- 445

  chrX_101652591_   1218 TTTGGGAGGCCGAGATGGGTGGATCATCTGAGGTCAGGAGTTGGAGACCA 1267
                         ----------------------------   -------       -----
  L1M4_orf2#LINE/    446 ----------------------------TGA-------AGTTGGA----- 455

  chrX_101652591_   1268 GCCTGGCCAACATGGCGAAACCCCATCTCTACTAAAAATACAAAAATTAA 1317
                         --------------------    --------------   ---------
  L1M4_orf2#LINE/    456 --------------------CCCC--------------TAC--------- 462

  chrX_101652591_   1318 TGGGGCGTGGTGGTGCGTGCCTGTAATCTCAGCTAGTCGGGAGGCTGAGG 1367
                         ---------------------------    -------------------
  L1M4_orf2#LINE/    463 ---------------------------CTCA------------------- 466

  chrX_101652591_   1368 CAGGGGAATTGCTCGAACCTGGGAGGTGGAGGTTGCAGTGAACCCAGATT 1417
                         --------------------------------------------------
  L1M4_orf2#LINE/    467 -------------------------------------------------- 466

  chrX_101652591_   1418 GCACCACTGCACTCCAGCCTGGGCCACAGAGCGAGGCTCTGTCTCAAATA 1467
                         -     --------------------------------------------
  L1M4_orf2#LINE/    467 -CACCA-------------------------------------------- 471

  chrX_101652591_   1468 TATATACATATATAAAAATTAATTCAAAATG-ATCAAAGATCTAAAAGTA 1516
                         --------    i         i        -    ?   i     v   
  L1M4_orf2#LINE/    472 --------TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_101652591_   1517 AGAGATAAA-CTCTAAAAGTCTTAGAAGGAAACAAAAGTC---GTCTTTG 1562
                             v    -  v     v         i     v i ?v---i    i 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_101652591_   1563 TGACTTTGAATTAAGAAATGGTTTATTTTTTATGACAACAAAAATGTAAG 1612
                             i   ii   i v        v  vvv       v     iiii   
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_101652591_   1613 TAACAAAATAAAAAGTACATAAATTGGATTT-ATCAAAAT-AAAAGCTTT 1660
                         i       v     i  v          i  -        -    i    
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_101652591_   1661 TATGCTTCAAAGGATACCATCAAG---GTGAAAAGGCAACCCACAGAATT 1707
                          i            i  i      ---        i             v
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_101652591_   1708 AGAGAACATTTTTGCAAATCATATGTATTAAAAGGAAATTGTATATGGAA 1757
                         i     v  v              i v v v    i v      vii   
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_101652591_   1758 TATATAAATAAATGCTTACAACTCAAAAGTTATAAGACA-----CCTGAA 1802
                                 -i  iv            v i v v      -----  i-  
  L1M4_orf2#LINE/    764 TATATAAA-GAACTCTTACAACTCAATAATAAAAAGACAAATAACCC-AA 811

  chrX_101652591_   1803 CTTAAAA-TGGGCAAAGGAACTGGATAGAGACATTTTTCCAAAGGAGATA 1851
                         i ?    -           vi  i     --     i       i     
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGA--CATTTCTCCAAAGAAGATA 859

  chrX_101652591_   1852 TACAAATGGCCAATAAGCAGATGAA--GATACTCAACATCATTAGCCAT 1898
                                            v     --   i          ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (78 / 65)
Gap_init rate = 0.04 (33 / 907), avg. gap size = 9.94 (328 / 33)  


1555 19.35 32.53 0.86  chrX_101667911_101671958.rev     2430  3013 (1035)    L1M4_orf2#LINE/L1        1   769 (139)  

  chrX_101667911_   2430 TGGAAGGGCATTATGTCTTTATAGATTGGAA-ACTAAATATTATAAAGAG 2478
                              i ii  ivii v  i  i        -   v      i v    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101667911_   2479 GGCAATAC-CCCCAAG--------CAAAATTTCAATG---------TGAA 2510
                                 -      i--------  i --     i --------- v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGA--TTCAACGCAATCCCTATCAA 98

  chrX_101667911_   2511 AATTCCAAA-GACTTTTTTGTATAAGTGGAAAAGCTGACTCTAAAATTGA 2559
                            i   iv- v        i v  i v  v       ii        v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_101667911_   2560 CATGGAATGGAAAGGGACTTAGAATAACAAAAACAATCTTGAAGCAGAAG 2609
                         i      vv v       ii      i v              iv     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101667911_   2610 AACAAAGTTGGAGCACATACACTTCCTGATTTCAAAATGTACTACAAAAC 2659
                                      v  vi        ii         iv         i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101667911_   2660 TACTGTAATCAAAATTCTGCAGTACTTG---------------------- 2687
                            v        i ivv  ii     v ----------------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101667911_   2688 -ATGAGATA------------CAGA-------------------GGTC-- 2703
                         -   ii   ------------    -------------------    --
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_101667911_   2704 -TAGTTT-------------------CATTC---------------GTCT 2718
                         - ii   -------------------     ---------------    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_101667911_   2719 ------------GT------ATA--TGGATATCCA--------------- 2733
                         ------------  ------ i --      ?   ---------------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_101667911_   2734 ----GGTTTCCTA----GCAC--------------AACTCAAAATGGATT 2761
                         ----  vii    ----i   --------------              i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_101667911_   2762 ATAGACCTAAATGTAA---------CTATGAAACTACTAGAAAAAGAAAA 2802
                          ?              ---------    i     vi     ---     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA---GAAAA 545

  chrX_101667911_   2803 CATAGGAG-AAAT-------ACATTGGTCTGGGCAATGATTTTATGGATA 2844
                               ? -    -------  v    vi i       i   iv i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101667911_   2845 AGACCTCAAAAGCACAGGCAA-AATAGCAAAAATAGACAAATGGGAT--- 2890
                         v   vi          i    -  v  v         i    v   i---
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101667911_   2891 ATCAAACTAAAAAGCTTCTGCACAGCAAAAGAAACAATCA-GAGAGTGAA 2939
                               v v    i   i  ii vv    i  v  v    -  i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101667911_   2940 GAGATAATCTACAGAATGGGAGAAAATACTTGCAAACTATTCATCTGACA 2989
                         i   i  i i                  i       ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_101667911_   2990 AGGGACTAATATCCAGAATATATA 3013
                                vi               
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATA 769

Transitions / transversions = 1.62 (68 / 42)
Gap_init rate = 0.03 (25 / 769), avg. gap size = 7.80 (195 / 25)  

 632 19.59 0.00 0.00  chrX_101667911_101671958.rev     3410  3557 (491)    L1M4_orf2#LINE/L1      761   908 (0)  

  chrX_101667911_   3410 GACTACACAAGGAGCTCAAACAGCTAAACAACAAAAACACAAATAATTCA 3459
                           v  i i  i  i   vv   i  v  i  i     v        ii  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_101667911_   3460 ATTTAAAAATTGGCAAATGATCTGAATAGGCATTTCTCAAAAGAAGACAT 3509
                            ?      v      v   i       i        v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_101667911_   3510 ACAAGTGGCCAAAAATTATATGAAAAAACACTCAACATCACTAATCAT 3557
                             i       v  vi i       i ii          ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.00 (0 / 148), avg. gap size = 0.00 (0 / 0)  


3216 27.06 0.45 0.45  chrX_101676879_101678755      487  1384 (493)    L1M4_orf2#LINE/L1       11   908 (0)  

  chrX_101676879_    487 TCCTGTGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATACTG 536
                            ii  i      i v      v i     i  v  i     v     v
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chrX_101676879_    537 CCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACCAATGAC 586
                              iv i  i           i  v     i     iv v   iivi 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_101676879_    587 TTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCA 634
                         i  i  ii     -   -- v  i  - iii    i           vii
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_101676879_    635 AAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTG 684
                         v  ii  v  v v  v     iv     i i ivv i          i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_101676879_    685 GAGGCAGCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACC 734
                             vvv      v  ii i      viv        i          i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_101676879_    735 AAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAG 784
                           i    ii         i iv ii i   v                i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_101676879_    785 AAC--AGGGCCCTCAGAAATAACGCCGCATACCTACAACTATCTGATCTT 832
                           i--  i i  --        vv  ii i ii  iiiii vi    i  
  L1M4_orf2#LINE/    309 AATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_101676879_    833 TGACAAACCTGAGAAAAACAAGCAATGGGGAAACGATTCCCTATTTAATA 882
                         i     ivv  vv  i v  vv           vi  vvi  v  i  i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_101676879_    883 AATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGAT 932
                                      v      v  ?   i   i i  iiv    ii    i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_101676879_    933 CCCTTCCTTACACCTTATACAAGAATCAATTCAAGATGGATTAAAGATTT 982
                             v   i     v       i   i  i    i      i ?   ii 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_101676879_    983 AAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTA 1032
                            i  v   v       i      vi i           v    ?i v 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_101676879_   1033 CCATTCAGGACATAGGCATGGGCAAGGATTTCATGTCCAAAACACCAAAA 1082
                         viv   iv   v v  vv i     v i    v ivvi vi         
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_101676879_   1083 GCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTAAA 1132
                            vvi           v     v  i    v   ii v  i   v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_101676879_   1133 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCCA 1182
                         i i   i  ii vv    i  v    i  vv i      v  i       
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_101676879_   1183 CAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATA 1232
                           i             v  i    vii ivi      i  i  i  vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_101676879_   1233 TCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAA 1282
                                 v  i  v      vv    v iv i  v     i     i  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_101676879_   1283 CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAG 1332
                            v  i?    i     i     iv    i     i     v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_101676879_   1333 ACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCATCACTAGCC 1382
                          i  vi viii     v ii          i       v     ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_101676879_   1383 AT 1384
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (5 / 898), avg. gap size = 1.60 (8 / 5)  


2935 26.07 3.39 0.90  chrX_101680268_101685614.rev     3971  4856 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101680268_   3971 TGGTAAAATACTCCATGCTCAT--------AGAGTCAATATTGTTAAAAT 4012
                            v  i   ii     i    --------   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101680268_   4013 AGCCATAAGGCCCAAAGCAATTTACAGATTCAATGCTATTACTATT---- 4058
                         i  v   vvv      vii  i           i  v  iv    i----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101680268_   4059 ---TAACTACCATT------GAGATTTTAGACAAAAACT-ATTTTAAAAT 4098
                         ---i i  i  v  ------  i   ---     i--  -  ii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAG--CTGATCCTAAAAT 145

  chrX_101680268_   4099 TCATATGGAACCAAAAAAGAACCTGAATAGCAAAGGCAATCCTAAGAAAA 4148
                                   viiv  ii  v  v       v  ii     i i i   i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_101680268_   4149 AAGAATAAGGCTGAAGGCATCACATTACCCAACTTCAAACTATACAACAG 4198
                              i  i i  i   vv     i v     i      viv   v   i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_101680268_   4199 GGCTACGATAACCAAAACAGCATGGTACTGGTACAAAAACAGA-A---AG 4244
                         i     ii   i   i    ii         i i  ii i   - ---  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_101680268_   4245 ACCAATGAAATAGAACAGAGAGCCCAGAAATAATGCCACACACCTACAAT 4294
                          i     i       iv     i          vv   i   ii  iii 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_101680268_   4295 TATCTGATCTTCAACAAAACTGACAAAAACATGCAATGGAAAAAGGATTT 4344
                         i vi    i   i    iiv  v   i v   v      ii    i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_101680268_   4345 CCTATTCAATAAATGGTGCTAGCATAACTGGCTAGCCATATGCAGAAAGT 4394
                         i  v     i          i v i      v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_101680268_   4395 TGAAAATGGATCCCTTCCTTACATCATATACAAAAATCAACTCAAGGTGG 4444
                             iv    i    v   i   i             i       ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_101680268_   4445 ATTGAAGACTTAAATGTAAGACCTAAAACTATAAAAATCCTGCAAGATAA 4494
                           ii?    i           v              v  i iv    v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_101680268_   4495 CCTAGG---AAATACCATTCTGGACACAGAAACGGGCAAAGATTTCATGA 4541
                          v    ---    -- -   vv   viv iivii     v i    v ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_101680268_   4542 CAAAGATGCCAAAAGCAATTGCAACAAAAGCAAAAATTGATAAAAGAGAA 4591
                         vv v  ii         vvv          v      v      vvi  v
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_101680268_   4592 CTAAGTTAACTAAAGAGCTTCTGCAAG-CAAAATAAACTATCAGCAGAGT 4640
                         i v viv  v v  i i   i  iivv-    iv v       iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_101680268_   4641 AAACAGACAACCTATAAAATGGGAGAAAATATCAGCAAACTATGCATCTG 4690
                         i  v        i i i               iv     ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_101680268_   4691 ACAATGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAG 4740
                          i  v  v  vi       v  v     i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_101680268_   4741 CAAAAAGCAAACAACCCCATTAAAAAGTGGGTGAAGGAAATGAACAGACA 4790
                         v    ii    i     v   ?    i    ii     vv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_101680268_   4791 CTTTTCAAAAGAAGCCATACATGTGGCCAACAAGCACATGAAAAAATGCT 4840
                         i  i  v       vi     vi       i             i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_101680268_   4841 CAACATCATAAATCAT 4856
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (139 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.17 (38 / 12)  


 206 24.44 0.00 0.00  chrX_101704150_101706566.rev      457   501 (1916)    L1M4_orf2#LINE/L1      409   453 (455)  

  chrX_101704150_    457 TGGTAATGAGAGAACCAGATATCCACAGATAAAAGAATAAAGTTG 501
                             iv  i  v   ii    ?     vii        i      
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.00 (0 / 0)  

3107 26.30 2.93 0.45  chrX_101704150_101706566.rev     1043  1928 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101704150_   1043 TGCAGAGATATTCCATGTACATGGATAGGAGGATTCAATATTGTCAAGAT 1092
                           v i      i      v       v   i  i i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101704150_   1093 ATTAATTCTTCCAAATTTAATCTATAAATTCAGTGCGATCCCAACCAAAA 1142
                         ivi   v  i  v  v  i     i i     ii  i     v i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101704150_   1143 TTGCAGCAAGTTGTTTTGTAAGTACTGACAAACTGATTCTAAAGTTTATA 1192
                          iv    vivi v     i iiv i      i     i     i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_101704150_   1193 TGGAGAGGCAAAAGGCCCATAGTAGCTGACACACTATTGGA---GAAGAA 1239
                             i v    ii i    v i    ii v   v v   i ---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_101704150_   1240 CAAAGTTGGA---CCAACACTACCCAACTTTAAAAATTACTATAAAGCTA 1286
                                   --- iv     v     i  i    v      i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_101704150_   1287 TAGTAATCAAAACAGTGTGGTATCAATGAAAGGACAGGCGAATA----AA 1332
                         i         i           iiiiiiv     i  i iv   ----  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_101704150_   1333 TGCAACAGAACAGAGAGCCCAGAAACAGACCCATGTAAATATGGCCAACT 1382
                           v  i    iv     i       i i      ii vv     i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_101704150_   1383 GATCTTTAACAAAGGAGCAAAGGCAATACAACAGAGAAAAGAGAGTCTTT 1432
                            i  ii    i  v  v   i v  v   ii i    ii v       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_101704150_   1433 TCAATAAATTATACTGAAACAACTCAACACCCACATGCAAAAAAA---AT 1479
                             i    vi i   ii      vi i ?            i  --- v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_101704150_   1480 CTAGACACAGACTCTACAC-ATGTCACAAAA-TTAACTCAAAATGGCTAA 1527
                         i i   v vv  iii    -  i -      -              v v 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGATCA 499

  chrX_101704150_   1528 CAGAACTAAAAGTAAAATGC-AAAACTACAG--CTCCTAGATGGTTACAT 1574
                         ?   v     v    i -  -       i i--   i    v ivv    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_101704150_   1575 -TTTCTAAAAGTCTAGATTACCTTGTGTAGGGTGACAATTCTCTAAATAT 1623
                         -vv?v    --   vvi v      v  vi  ii iii  iii  i    
  L1M4_orf2#LINE/    549 AGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_101704150_   1624 AATACCAAAGGTATGATTCACAAAATAAGGTATTGGTTAGCGGGACTTCA 1673
                         i i      i i ii viv      v  iiv  v i v iiv        
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_101704150_   1674 TTAAAAGTAAAAACTTCTACTCTGAGAAAGGCACTGTTATC----TGAGA 1719
                          i    v         i iiv  vvi  i i    i i vv----   i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_101704150_   1720 AGATAAGCCACAAACCAGGAGAAAATATTTGCAAAAGACATATGTGATAA 1769
                            i  v     i vii                  vv i    v      
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_101704150_   1770 AGAACTGTTATCTATAATATATGAAGAACTCTTAAAACCCAACAATACGA 1819
                         i i   vv    i v       i           v   i   i    vi 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_101704150_   1820 AAACAAACAG---GATTAAAAAATGGGCTAAGGACCTTAACAGACACCTC 1866
                          i     i i---i   ?          v     ii v  i     ii  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_101704150_   1867 ACCTAAGAAGATATACAGATGGCAAATAAACATATGAAAAGATGCTCCAC 1916
                         v  v             i     v     i  i              v  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_101704150_   1917 ATTGTATGTCAT 1928
                           ii????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (147 / 82)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


3058 25.82 1.87 2.09  chrX_101724983_101730939.rev     4557  5466 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101724983_   4557 TGGAAAAACATTCTATACTCATGGATAGGAAGAATCAATATTGTGAAAAT 4606
                               i i  i i  ii        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101724983_   4607 GGCCATACTGCCCAAAGTGATTTATAGATTCAGTGCTATTCCCATTAAAC 4656
                            v     v      v    i  i       ii  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101724983_   4657 TACCATTGGCATTCTTCACAGAATTAGAAGAAACAATTTTAAAATTCACA 4706
                          v   viv  v  i  ii     v v  vi ivii  ii         i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_101724983_   4707 TGGAAGCAAAAAAGAGCTCGTGTAGCCGGGAAAGTCCTAAGTAAAAAGAA 4756
                              iiiv  ii  v iv vi     iii v i  i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_101724983_   4757 CAATGCTAGAGGCATCACGCTACCTGACTTCAAACTATACTATAAGGCTA 4806
                            v i i    vv    i  v  ii i      viv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_101724983_   4807 CAGTACTACAGTAACCAAAACAGCATGGTACTGGCACAAAAACAGGCACA 4856
                              -------- i   i    ii           i  ii i  i  i 
  L1M4_orf2#LINE/    251 CAGTA--------ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_101724983_   4857 TAGACCAATGGAACAGAATACAGAACTCAGAAATAAAACTGCACATCTAC 4906
                             i        i     vv   iii          v iii    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_101724983_   4907 AACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGA 4956
                         iii  vi    i  i     ivv  v   i v  vv     i      i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_101724983_   4957 TTCCCTATTTAACAAATGGTGCTGGCAGAACTGGCTAGCCATATGCCAAA 5006
                          vvi  v  i               v v      v  ?   i    v   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_101724983_   5007 AATTGAAAATGGACCCCTTCCTTACACCATATACAAAAATTAACTCAAAA 5056
                         i v    iv         v   i                           
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_101724983_   5057 TGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACTGTAGAAGA 5106
                              i ?    i         i v i            viiv       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_101724983_   5107 AAATCTGGGCA-ATACCATTCAGGATGTAGGGATGGGCAAAGATTTC--- 5152
                            iv i  ?i- v i -   iv  iv v   v i     v i    ---
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_101724983_   5153 ---ATGACAAAAATGTCAAAAGCAACTGCAACAAAAGCAAAAATTGACAA 5199
                         ---      ------i        vvv          v      v  i  
  L1M4_orf2#LINE/    592 GATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_101724983_   5200 ATGGGATCTAAT-AAAACTAAAGAGCTTCTGCACAGCAAAATAAACCATC 5248
                           v   ii v  -    i    i -   i  ii vv    iv v  i   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chrX_101724983_   5249 ATCAGAATGAACAGACAACCTACAGAATGGGAGAAGACTTTTACAGTCTG 5298
                          vv i i    v        i              i iv   i  iviii
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_101724983_   5299 TCCATCTGACAAAGGTCTAATATCCAGAATCTACAAGAAACT--TA-AAT 5345
                          vi      i  i  v  vi          v  i  ii    --  -  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_101724983_   5346 TTA-CAAGAAAAAACTAAACAACCCCATTAAAAAGTGGGCAAAAGA---- 5390
                          i -i  v     ivi   i     v   ?    i        i  ----
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_101724983_   5391 AATGAACAATTTTCAAAAGAAGACATAAATGCGGCCAA-AAACACATATG 5439
                            ii   v  i  v        i   v vii      -  i     i--
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-- 882

  chrX_101724983_   5440 AAAAAAAAGCTCAACATCACTGATCAT 5466
                         -    i v           ????????
  L1M4_orf2#LINE/    883 -AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (145 / 86)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.77 (36 / 13)  


2618 26.55 4.94 0.57  chrX_101735472_101738606.rev     1775  2644 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101735472_   1775 TAGAAAAACATTCCATGCTCATGGATAGGAAGAATTAATATCGTGAAAAT 1824
                          i    i i  i     i        v      v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101735472_   1825 GGCCACACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCTATTAAAC 1874
                            v i   v      vii  i  i        i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101735472_   1875 TACCATTGATATTCTTCACAGAATTAGAAAAAACT-ACATTAGAATTCAT 1923
                          v   viviiv  i  ii     v v  v  i-  - ivi  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_101735472_   1924 ATGGAACCA-AAAAGAGCCAGTATAGCCAAGACAATCCTAAGCAAAAAGA 1972
                               vii-  ii  v    v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_101735472_   1973 AAAAAGTTGGAGGCATCACACT-----ACTTCAAACTATACTACAAGGCT 2017
                          v           vv       ----- i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_101735472_   2018 ACA-TA-----GAC-------TAC------------AGACTCATAGACCA 2042
                            -  -----   -------   ------------    vi     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_101735472_   2043 ATGGAACAGAATAGAGATCTCAGAAATCAGACTGCACATCTACAACCATC 2092
                               i     v    vii       v iv iii    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_101735472_   2093 TGATTTTCAACAAATCTGACAAAAGCA----ACAGGGAAAGGATTGCTTA 2138
                                 i    ivv  v   i v  ---- ii       i  v ii v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_101735472_   2139 TTTAATAAATGGTGCTGTAAAAACTGTCTAGTCATATGCAGAAAACTGTA 2188
                           i  i           vi v     vv  ?i  i     i  i v  v 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_101735472_   2189 ATTAGACCCCTTCCTTACATCATATACAAAAATTAACTCAAGATGGATTA 2238
                         i  i       v   i   i                     i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_101735472_   2239 AACACTTAAATGTAAAACCCCAAACCATAAAAACCC-AGAAGAAAATCTG 2287
                         ? v  i         i v iv    i      vi i-         iv i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_101735472_   2288 GGCA-ATACCACTCAAAATGTAGGGACGGGCAAAGATTTCACAACAAAAA 2336
                           ?i- v i -i  ivi iv v   vii     v i    vi ivv vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_101735472_   2337 TGTCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTAATT 2386
                         iii        vvv          v      v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_101735472_   2387 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATAATCAGAGTGAACAG 2436
                            v v  i i   i  ii vv    i  v     v vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_101735472_   2437 ACAACGTACAGGTTGGGAGAAAATTTTTG-AAATCTATTCATCTGAAAAA 2485
                              vi    iv           v    -     -  vi      v  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAG 747

  chrX_101735472_   2486 AGTCTAATATTCAGAATCTACAAGGAACTTAAACAAATT--TAGCAAAAA 2533
                         i v  vi   i      v  i  i     ivv    v i--  ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_101735472_   2534 ACCCCAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACACACACTT 2583
                         iv --   i     v   ?    i           iv    i v   i  
  L1M4_orf2#LINE/    798 GAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_101735472_   2584 CTCAAAAGAAGACATTTATACAGCCAACAA-C-CATGAAAAAAAGCTCCA 2631
                            v        i  vi v ii     i  - -        i v    v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_101735472_   2632 CATCACTGATCAT 2644
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.67 (48 / 18)  


3009 27.38 1.22 0.55  chrX_101747208_101753596.rev     4997  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101747208_   4997 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCGTGTAAAT 5046
                              ii i  i     i        v      v i i   i  vv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101747208_   5047 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCTATCCCCATCAAGC 5096
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101747208_   5097 TACCAATGACTTTCTTCACACAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5144
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_101747208_   5145 CATGGAACCAAAAAAGAGCCCGCACTGCCAAGTCAATCATAAGCCAAAAG 5194
                         i      viiv  ii  v  v v iv     iv     v i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101747208_   5195 AACAAAGCTGGAGGCATGACGCTACCTGACTTCAAACTATACTACAAGGC 5244
                                i      vv v  i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101747208_   5245 TACAGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5294
                                 i   i v  ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101747208_   5295 AATGGAACACAAC--AGCGCCCTCAGCAATAATGCCACATATCTACAACC 5342
                                i v  i--  v i  --  v     vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_101747208_   5343 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5392
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_101747208_   5393 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 5442
                           v  i  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_101747208_   5443 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5492
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_101747208_   5493 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAAACCTAGAAGAAAAC 5542
                          i ?    i       v   v       i      vv i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_101747208_   5543 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5591
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101747208_   5592 AAACAC-AAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5640
                         vi    -       vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101747208_   5641 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5690
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101747208_   5691 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTGCTCATCTGACA 5740
                         v  i     i                 v   i   viiiivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_101747208_   5741 AAGGGCTAATATCCAGAATCTACAATGAATTCAAACAAATTTACAAGAAA 5790
                          i  i  vi          v  i  v   i  vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_101747208_   5791 AAAACAA----CCCCATCAAAAAGTGGGTGATGGATATGAACAGACACTT 5836
                           i    ----   v  i?    i    ii v    v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_101747208_   5837 CTGAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAA-ATGCTCAT 5885
                           vv        i  vi viii     v ii          -       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_101747208_   5886 CATCACTGGCCAT 5898
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (139 / 104)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


4034 19.14 3.62 0.79  chrX_101756911_101759065      780  1662 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101756911_    780 TGGAAAGACACCCCATGTTTATGGATTGTGAGACTTAATATTATTAAAAT 829
                                 i i        i        vi            i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101756911_    830 ATTGATACCAGCTAAATTGATCTACAGACTCAGTGTAATCCTTACCAAA- 878
                         ivii    ivv i               i   ii i     i  i    -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101756911_    879 -TTCAGCTGCCTTTTC-GTAGAAATTCAGAAGCTGCTCTCAAAATTTATA 926
                         -ii            i- i       v v      v  ii      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_101756911_    927 TG------CAAGTGATCCACAGTATCCAAAATAATC----AATAAAAGAA 966
                           ------    v  i   v i  v      i    ----  v i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_101756911_    967 CAAAGTTGGAGGACTCACACTATTTGATTTCAGTGCTTACTATGAAACTA 1016
                                              viiii      ivi       ii  i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_101756911_   1017 CAGTAATCCAAACTATGTGGTACTGACATAACGGTAAACATAAATATGAA 1066
                                 v i  vi          i     v i  i     v v  v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_101756911_   1067 TGAAAAAGTATTGAGAGTCCAGAAATAAATCCTCACAT-----GT--ATT 1109
                           i  v  v                    i  vi    -----  --   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_101756911_   1110 GAGTTT-GACAAGAGCATGAGAGCCATACAACAGGGTAAGAATTGTCTTT 1158
                           v   -      i iiiv iii    v   ii   v      v      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_101756911_   1159 TCAACAAATGGTGTTGGGATAATTGGACAGGCACCTGCAAAATAATGACT 1208
                                      i     i  i    i ?v   v       v     vv
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_101756911_   1209 TTTAATCCCTGCCTCACACTGTATATAAAAATGAACTAGAAATTGTTCAA 1258
                           vi i    i        ii    i      v    vi    v v   ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_101756911_   1259 AAACCTAAATGTAAGAGCTAAATCTATAAAACCCTTAGAAGAAAACACAT 1308
                          i                    v         i              i -
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA- 549

  chrX_101756911_   1309 GGTATAAATCTTTGTGACTATGGACCTTTGTGACATTTGGTGACTCACAT 1358
                           ?i        i     iv   i---  i- i  v -   vv  i v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGG---TTA-GGCAAT-GGTTTCTTAGAT 594

  chrX_101756911_   1359 ATGACACCAAA-GCACAAAGAACAAAGGGAAAAATAGGCAAACTGTACGT 1407
                                    -      iv      i i        ii   i  v  v 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_101756911_   1408 CATCGAAATTAAAGACTTTTCTGCTTCAAAGGACAT----AAGTAAGTGA 1453
                             i        i      v              i----   v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_101756911_   1454 AAACCCACCCCAGAGAATGGGAGACAATATTT-CAAATCATATACTTAGC 1502
                            vv  v    v           v       -           ii iii
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_101756911_   1503 AAGGAACTTCAATCTAGAATGAATAAA-AACTGTTTCAACTCAAAAATAA 1551
                             i    vv   i     iv     -    v  v        v     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_101756911_   1552 AAAGACAA----CCCAATATAAAAATGGTCAAAAGATCTGGATAAATATT 1597
                                 ----      v?        v    i   i  i   i i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_101756911_   1598 TCTCCAAAGAAAATACAAAAAATTGCAAGTAAGCACATGAAAAGATGCTT 1647
                                    i   i v   - v  v i                    i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_101756911_   1648 AACATCATGAGCTAT 1662
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (101 / 64)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.29 (39 / 17)  


2771 25.67 6.53 0.58  chrX_101768372_101770484      764  1620 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101768372_    764 TGGAAAAATATTCCTTTTTTTT---TTTATCATAACATAATATCATGAAG 810
                               i    i  v v  iv ---  vi-- vi  v      ii v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGG--AAGACTTAATATTGTTAAG 48

  chrX_101768372_    811 ATGTCAGTTCATCTGCACTTGATCTATAGACTCAATGCACTCCCAATCAA 860
                            v  i v vi ivv v        i   i    i   v    v     
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_101768372_    861 AATCCCTGCAAGTTATGTTGTGGATATTGGCAAACTGATTATAAAGTTTA 910
                               v  vivi v v   ii  v    i   i     iv    i  i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_101768372_    911 TGTGGAGAAGCAAAAGACACAGAATAGCCAACACAATATTCAAGAAGAAG 960
                          i    i v    ii   v            v     v  v  i      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101768372_    961 GACAAGGTCAGAGGACTGACACTACCCAACTTTAAGACCTACTATAAAGC 1010
                         i    i  ii       v     v     i  i  i  i     i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101768372_   1011 T----TAAGTAAGAGGGTTTGATATTGGTG-AAAAACAGACAAGTAGATC 1055
                          ----   vi    vi  v  i  i   ii-  ii i     vi      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101768372_   1056 AGGGCAACAGAAGACAGAGCCCAGAAGTAGACCCACAGAAATACGGTCAA 1105
                          iv v  i    vvv    i      i  i     i v vv  i      
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_101768372_   1106 CTAATCTTTGACAAAGGAGCAAAGGTAATTTAATGGGGAAAGGATAGTTG 1155
                         i i  i  i     i  v  v   iiv   i           i     iv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_101768372_   1156 TTTCAACAAATAGTGCTAG-----------ATTCACATGCAAAAAAA--A 1192
                                    i     i ----------- ?i           i  -- 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_101768372_   1193 A--TAGACAAAGACCTTACCCCTTTCACAGATACTAAC------------ 1228
                          -- i   vvvv    i  v  v vi   i v i    ------------
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_101768372_   1229 ------CTAAGTTTAAAAGGCAAAACTATGAAACTTCTAGAAGATAACAT 1272
                         ------    i v   i  vi        i     ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_101768372_   1273 AATAGAACATCTAGGTAACTTTGGGTTTGTCAACAACTTTTTAGATA--- 1319
                          iv? v v    vv  i  i       v v   iiii  i       ---
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_101768372_   1320 CAACAAAAGCATGATCCATGAAAGAACAAATTGATAAGTTGGGTCTCATT 1369
                           v        ii v v ii      v    v     i    iii    i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_101768372_   1370 AAAGATTA-----TTCTCCTCTACAAAATAAACTGTTAAGAGATTGAAAA 1414
                            -    -----  i viv  v    iv v   i i    i v      
  L1M4_orf2#LINE/    649 AAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_101768372_   1415 AGAGAAGCCACAGA------GAAACTATTTGCAAAACAGACATCTGATAA 1458
                         -  v  v       ------    v          v  v i         
  L1M4_orf2#LINE/    698 -GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_101768372_   1459 AAGATTGCTATCCAAAATATACATAAGAATTCTTA-AACTTAACAATAAG 1507
                         ii  i vv      i      i -     i     -    i  i     i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATA-AAGAACTCTTACAACTCAATAATAAA 795

  chrX_101768372_   1508 AAAACAATCAACCCATTTTAAAATTGGGTAAATGATGGGAACAGACACTT 1557
                           i    vi      v  ?    v    i   v   vv   i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_101768372_   1558 GGCCAAAAAACATATTCAGATGGCAAATGAGCATATGAATACATACTAAA 1607
                         vv     i  v    v  i     v   i    i     v v  i  v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_101768372_   1608 TATCACATGTCTG 1620
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (122 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.07 (61 / 15)  


3282 26.65 0.55 0.55  chrX_101838440_101843739.rev     3902  4809 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101838440_   3902 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAGAAT 3951
                              ii i  i     i      i v      v i     ii v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101838440_   3952 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4001
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101838440_   4002 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4049
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_101838440_   4050 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 4099
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101838440_   4100 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 4149
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101838440_   4150 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4199
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101838440_   4200 AATGGAACACAAC--AGAGCCCTCAGAAATAATGCCACATATCTATAACC 4247
                                i v  i--    i  --        vv   i i  i   iii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_101838440_   4248 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATTCC 4297
                          vi    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_101838440_   4298 CTATTTAATAAATGGCATTGGGAAAACTGGCTAGCCACATGTAAAAAGCT 4347
                           v  i  i      iii     v      v  ?       i    iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_101838440_   4348 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4397
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_101838440_   4398 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4447
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_101838440_   4448 CTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCTA 4496
                         v    ?i- v i -   iv   viv  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101838440_   4497 AAACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4546
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101838440_   4547 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4596
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101838440_   4597 AAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 4646
                            i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_101838440_   4647 AAGGGCTAATATCCAGAACCTACAATGAATTCAAATAAATTTACAAGAAA 4696
                          i  i  vi         iv  i  v   i  vv i  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_101838440_   4697 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATAGACACTT 4746
                           i     i     v  i?    i            v          i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_101838440_   4747 CTCAGAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 4796
                            vi       i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_101838440_   4797 CATCACTGGCCAT 4809
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2850 25.17 2.32 2.10  chrX_101852740_101857802.rev     3667  4572 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101852740_   3667 TGGAAAAACATTCCATCTTCATGGATAGGAAGAATCAATATCACGAAAAT 3716
                               i i  i    v         v      v i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101852740_   3717 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTTCCATCAAAC 3766
                            v     v      v i  i  i        i  v  ii i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101852740_   3767 TACCATTGACATTCCTCACAGAATTAGAAAAAAAAACT-ACTTTAAATTT 3815
                          v   vivi v  ii ii     v v  v  i----  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chrX_101852740_   3816 CATATGGAA-T-CAAAGAAGACCCTGTATAGCCACGACAATCCTAAGCAA 3863
                                  - -   i --     v v       vi      i i iv  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_101852740_   3864 AAATAACAAAGCTGGAGGCAC-CATGCTACCTGACTT-AAAACTATACTA 3911
                         i  v       i      -  -  ii  v  ii i  -      -     
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACT-TACTA 242

  chrX_101852740_   3912 CAAGGCTACAGTAACCAAAACAGCATGGTAGTGTTACCAAAACAGATATA 3961
                            i          i   i    ii     v  vi iv ii i   i   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_101852740_   3962 TAGACCAATAGAACAAAACAGAGACCTCAGAAATAACACCACACATCTAC 4011
                             i    i   i i  iv    vii         vv   i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_101852740_   4012 AA-CATTCTGATCTTTGACAAACCAGACAAAAACAAGCAATGGGGAAAGG 4060
                         ii-  v -    i  i     ivvv v   i v  vv            i
  L1M4_orf2#LINE/    343 GGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_101852740_   4061 ATCTCCTATTCAGTAAATGGTGCAGGGAAAACTGGCTAGCCATATGCAGA 4110
                           vvi  v    ii         v    v      v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_101852740_   4111 AAACTGAAACTGGACCCCTTCCTTACACATTATACAAAAATTAACTCAAG 4160
                          i v    ii         v   i    vv                   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_101852740_   4161 ATGGATTAAAGAATTAAATGTAATATCCCAAACCATAAAAACTCT-GGAA 4209
                               i ?   vi         v v iv    i      -    -i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAA 540

  chrX_101852740_   4210 GAAAACCAAGGCAGTACGAT--TCAGGACATAGGCATGGGCAAAGACTTC 4257
                               vv   ?-   -i  --  iv   v v  vv i     v ii   
  L1M4_orf2#LINE/    541 GAAAACATAGGN-GTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_101852740_   4258 ------ATGACAAAAATGCCAAAAGC-CATTGTGACAAAAGCCAAAATTG 4300
                         ------      ------        -  v- ii       vv     v 
  L1M4_orf2#LINE/    589 TTAGATATGACA------CCAAAAGCACAA-GCAACAAAAGAAAAAATAG 631

  chrX_101852740_   4301 ACAAATGGGATCTAATTAAACCGAAGAGCTTCTGCACAGCAAAAGAAACT 4350
                          i    v   ii v  i   viv  i i   i  ii vv    i  v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_101852740_   4351 ATCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAAATTTTGTAAT 4400
                             vv i      v  i     i                vv    i  v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_101852740_   4401 CCACCCATCTGACAAGTATTTAATGCCCAGAATTTACAAGGAACTTAAAC 4450
                         i  ivi      i   vivi vi ii       v  i  i     ivv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_101852740_   4451 ATATTTACAAGAAAAAGA----TAACTCCATCAAAAAGTGGGCAAAGGAT 4496
                          vv iv i  v       ----    i v  i?    i            
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_101852740_   4497 ATGAACAGACACTT-TCAAAAGAAGACATTTACACAGCCAACAAACATAT 4545
                         v    i     i  -  v        i  vi v ii     i  i  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_101852740_   4546 GAAATAAAGCTCAACATCACCGATCAT 4572
                             vi v           ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (129 / 95)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.82 (40 / 22)  


1092 25.99 1.64 0.99  chrX_101870967_101874015.rev      621   924 (2125)    L1M4_orf2#LINE/L1        4   309 (599)  

  chrX_101870967_    621 AGAGACATACTGTCTTCATGAGTTTGAAGACTCAGTGTTGTTAAGATGCC 670
                          i   i  v ii v      ii  v       i i i           v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_101870967_    671 TGTTCTGTTTAAACTGATCTATATATTCAGAACAATCCCAATAAAAATCC 720
                         vi v  viii   i       i v     ivi       v  v       
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_101870967_    721 TAACTGATATAGTTTTAACAGAAAGTAAAATGCTGTTTCTAAAATTCATG 770
                         i i   viv --    i-      v i v v    v i           i
  L1M4_orf2#LINE/    104 CAGCTGCCTT--TTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_101870967_    771 TAAAAATACAAAGGATCTAGACTA-TGAAAACAACATTGAGAAAGAA--- 816
                          ii    i   i   i i   v  -iv       iv    i      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_101870967_    817 CAAAAC-GGATGACAAACACTACCTAATTTTAAGACTTCTTACAAACCCA 865
                             ii-   v   vv     v  i     i  i    vi      v i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_101870967_    866 TAGTAATCAAGACAGTGTGCTACTGGCATCAAGGCAGAAAGGTAGATCAA 915
                         i                  v         v i ii   v vi        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_101870967_    916 AAGAACAAA 924
                         vi   i i 
  L1M4_orf2#LINE/    301 TGGAATAGA 309

Transitions / transversions = 1.55 (48 / 31)
Gap_init rate = 0.02 (5 / 306), avg. gap size = 1.60 (8 / 5)  

1125 24.44 0.00 0.00  chrX_101870967_101874015.rev      925  1235 (1814)    L1M4_orf2#LINE/L1      598   908 (0)  

  chrX_101870967_    925 ATACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 974
                          i          vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_101870967_    975 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1024
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_101870967_   1025 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 1074
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_101870967_   1075 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 1124
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_101870967_   1125 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 1174
                         i     i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_101870967_   1175 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCA 1224
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_101870967_   1225 TCACTGGCCAT 1235
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.34 (43 / 32)
Gap_init rate = 0.00 (0 / 311), avg. gap size = 0.00 (0 / 0)  

1713 24.26 7.80 2.77  chrX_101870967_101874015.rev     1982  2558 (491)    L1M4_orf2#LINE/L1      303   908 (0)  

  chrX_101870967_   1982 GAACAAAATAAACCACCAAAAAATTGACCTACATATAT-TGGACAACTGA 2030
                            i i   vi vvii v i    vi   i i i  v -   v   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_101870967_   2031 CTTTTAACAAAGGTGCAGAAGCCATTCAATGTATAAAGGATGGTATCTTC 2080
                         i   ii    i     vi ii          viv    i  i  v i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_101870967_   2081 AATATATTGTGCTGAAACAAGTAGATATTCATATACACAATTATATACT- 2129
                           i v  v      ii    v i    ?i  i  i  v  vv  iv v -
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_101870967_   2130 -GATCTATATATTGTACCATGTACAAAAGACAATTCAAAAGGCAATTCAT 2178
                         -  i iv  iv iii     i       ----   --------  i   v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAA----ATT--------AACTCAA 490

  chrX_101870967_   2179 AATGGATCATAGATGTAAATATAAAACCTAAAGCTGTAAAACTTGTAGAA 2228
                                  ?   iv     i   i v     i  i       iv     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_101870967_   2229 GAAAACATGGGAGAGCAAAATT--GTGACCCTGAGTTAGGTAAAGATTTC 2276
                                 i  ? --i   vi --      i  i      i  v i    
  L1M4_orf2#LINE/    541 GAAAACATAGGNG--TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_101870967_   2277 TTAGAT---------------------------GAATAAATCAATAATTT 2299
                               ---------------------------   v    vi    v  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_101870967_   2300 GGAATGTGTCAAAGTTAAAAACTCT-GCATCTTACAAAGACATTGTTAAG 2348
                            v vii     i         i - iiii i -  i    i i i   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTATCAAG 687

  chrX_101870967_   2349 AGAATGAAAAGACAAGCCCCTGATTGGGAGAAAATGTTTGAAAATCATAT 2398
                          i i           v  v v  v           i    v         
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_101870967_   2399 --CTGATAAAGTACTTGTATCCAAAATATAGAAAAATATCACAAAATTCA 2446
                         --       i v           i      v   i vv  vi v  i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_101870967_   2447 AT----------TAAACACTCCAATAAATAAATAGGCAAAAGAGTTGAAT 2486
                           ----------i   i vi     v? v    i      i  v      
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_101870967_   2487 AGACACTCATCTATAGAAGATAAACAACTGTCAAATAAGCACATGAAAAT 2536
                              i iv  i v        v    v  v v                v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_101870967_   2537 ATACTCAAACATCATTAATCAA 2558
                           i     -     ????????
  L1M4_orf2#LINE/    888 ATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (82 / 54)
Gap_init rate = 0.02 (12 / 606), avg. gap size = 5.08 (61 / 12)  


2240 23.33 0.67 14.19  chrX_101914541_101918592.rev     2512  3561 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101914541_   2512 TGGATACACATCCTATGCTCATGGATGAGTACAATCAATATTGTGAAAAT 2561
                             v v i    i   i        vi v v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101914541_   2562 GACCATACTGTCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 2611
                          i v     vi v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101914541_   2612 TACTACCATCATTCTTCACGGAACTAGAAAAAAACAATCCTAAAATTCAC 2661
                          v i v vv v  i  ii i   v v  v  iv-ii             i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_101914541_   2662 ATGGAACCAAAAAAGAGCCTGTATAGCCAAAGCAAGACTAGGCAAAAAGA 2711
                               viiv  ii  v  v v         i   vvi iiiv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_101914541_   2712 ACAAATATGGAGGCATCACATTACCTTACTTCAAACTATACTATAAGGCC 2761
                              vv      vv     i v  iv i      viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_101914541_   2762 AGAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACTA 2811
                          v   v i   i    ii         i    ii    i  i     ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_101914541_   2812 TATATGAAACATTTATATACATATATATATATATATATATATATATATAT 2861
                         --------------------------------------------------
  L1M4_orf2#LINE/    300 -------------------------------------------------- 299

  chrX_101914541_   2862 ACACACACACACACACACACATATATATACACATATATATACACACACAC 2911
                         --------------------------------------------------
  L1M4_orf2#LINE/    300 -------------------------------------------------- 299

  chrX_101914541_   2912 ACAAACACACACACACACACACACACATATATATATATATATATATAAAA 2961
                         --------------------------------------------  ii  
  L1M4_orf2#LINE/    300 --------------------------------------------ATGGAA 305

  chrX_101914541_   2962 CAGAATAGAGAACCCAGAAACAAAGCCAAATACTTAGAGCCAACTGATCT 3011
                         i     v    ii       i   v   v i i   vi i   i    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_101914541_   3012 TCGACAAAGCAAACAAAAAC-TTCAAGTAGGGAAAGGACACCCTATTCAA 3060
                                i vviv   i v -     - i       i i vi  v     
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCAA 404

  chrX_101914541_   3061 CAAATGGTGCTGGGATAATTGGCAAGCCACATGCAGAACGATGAAACTGG 3110
                                        i  i   vv ?         i  vi     ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_101914541_   3111 ATCCTCATCTGTCATCTTATA-AAAAATCAACTAGAGATGGATCAAAAAC 3159
                          i  ii i  vv  i v    -      i    vi i        ? i  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_101914541_   3160 TTAAATCTAAGACCTGAAACTACAAAAATTCTAGAAGGTAACATCAGAA- 3208
                         i     v     v  i      i    v ii      iv     vi ?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_101914541_   3209 AAACCATTCCAGGCATTGGCTTGGGCAAGGATTTCAT-GATAAGAAACCG 3257
                            i -   vv i v    v  i     v i    v -    v  v   i
  L1M4_orf2#LINE/    555 AAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_101914541_   3258 AAAGCAAATGCAATAAAAACAAAGATGAACTGCTGGGACTTAATTAAA-C 3306
                               v v    i    iv   i  ii iviv v      v  i   -i
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_101914541_   3307 TAAAGAGTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAACAGACAAC 3356
                             i v     iiivv    i iv  vi   iv i   i  v       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_101914541_   3357 TCACAGAGTGGGACAAAACCTTCACAATCTATACATCTGATAAAGGACTA 3406
                         i      i     v    iv  ii   vii   i         i     v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_101914541_   3407 ATATCCACAACCTACAACAAACTCAAACAAATTAACAAGAAAAAAAAACA 3456
                         i      v  iv  i  vi     vv    v i  i  v     i --  
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA--CA 801

  chrX_101914541_   3457 AACAATCCCATCAAAAAGTGGGCCTAGGACATGAATAGACAATTCTCAAA 3506
                           i  i  v  i?    i     vv    iv          v     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_101914541_   3507 AGAAGATATACAAATGGCCAACAA--ACATGAAGAAAAGCTCAACATCAC 3554
                                              i  --       i i v           ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_101914541_   3555 TAATGAT 3561
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 14.18 (156 / 11)  


3298 26.43 0.55 0.55  chrX_101932502_101938894.rev     4995  5902 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_101932502_   4995 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5044
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_101932502_   5045 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 5094
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_101932502_   5095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5142
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_101932502_   5143 TATGGAAACAAAAAAGATCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5192
                                 iiv  ii  i  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_101932502_   5193 AACAAAGCTGGAGACATCACACTACCTGACTTCAAACTACACTACAAGGC 5242
                                i     ivv       v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_101932502_   5243 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5292
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_101932502_   5293 AATGGAACACAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACC 5340
                                i v  i--    i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_101932502_   5341 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAATGATTCC 5390
                          vi    i  i     ivv  v   i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_101932502_   5391 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5440
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_101932502_   5441 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATCAATTCAAGATGGA 5490
                            ii    i    v   i   i v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_101932502_   5491 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5540
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_101932502_   5541 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5589
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_101932502_   5590 AAACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATGTA 5639
                         vi            vvi          vv     v  i    v   iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_101932502_   5640 ATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGTGAA 5689
                           i   v v  i i   i  ii vv       v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_101932502_   5690 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCGGACA 5739
                         v  i     i                 v  i    vii ivi   v  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_101932502_   5740 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5789
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_101932502_   5790 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5839
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_101932502_   5840 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5889
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_101932502_   5890 CATCACTGGCCAT 5902
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2973 25.23 3.64 1.25  chrX_101946264_101948271.rev      638  1517 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_101946264_    638 ATATACTGTGTTCATGGATGAGAAGACTCAGTATTGTTAAGATATTAATT 687
                             v ii           vi       i i            ivi   v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_101946264_    688 CTCCCCGATCTCATCTATAAATTTAATGCAAACTGAATAAAAAATTTTAC 737
                               i vi v     i i   i  i    v ivv  v    - iii v
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA-TCCCAG 106

  chrX_101946264_    738 CAAAGTTTTAAAAAGGGAATTGATAGGCTGATTCTAAAATTCATGTGAAA 787
                          vivv    vviv  i-      i i      i           i  i  
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_101946264_    788 ATTTAATGGATCTAGCTGATA---AAAACAACTTTGAATAA-AAGGTCAA 833
                           vi  v   i i  --i   ---       ii     v  -   iv   
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAG--AATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_101946264_    834 AGTCAGAGAACAAACACTACCTGACTTCAAGACTCTTTACAAATCTACAG 883
                            ii   i  vv     v  ii i     i   ivi      v      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_101946264_    884 TAATCAAGAC--TGTGCTGTTGGCATCAAGGTAGAAAAGCAGATCAAAGG 931
                                   --    v ii      v i i    v vii       v  
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_101946264_    932 AATAGAATAAGGAATCCAAAACCGA--CCAAACCTACATGGATAACTGTT 979
                                 vii  i    i  vii --   v  v vi    vi  i  v 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_101946264_    980 TTTTTGACAAAGATGCAAAGGCAATTCAGTGGAGCAAAGATACTCTTTTC 1029
                            i-     i i   v   i v     i   i v  ii   v       
  L1M4_orf2#LINE/    354 TTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_101946264_   1030 AACAAATTGTGCTGGGAGAAGTGGTTATCTATATTCACAAATACAAACAG 1079
                                v         v  v   v  ? i i  v  v  iv ii  -- 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA--G 450

  chrX_101946264_   1080 T--GATCCAAATATCATACTATATACAAAAGTCAACTCAAAGTGGATCAT 1127
                          --  i  vv iv   i  i          i i        i       ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_101946264_   1128 AGATATACATATAAAACCTAAAACTATAAGACTTCTACCAGAAAATACAG 1177
                            iv  v  i   i v            i   ii  vv      i i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_101946264_   1178 GAGAAAATCCTTGTGACTTTGGGTTAGGTAAAGACTTCATTAG---TGAG 1224
                          ? v     i i     i          i  v ii   -    ---   v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGAC 599

  chrX_101946264_   1225 AC-AAAACTACAATCTGTAGGTGAAGAAATCAATAAATTAGACTTC-CCA 1272
                           -    vi    v vii iiv   i    vi       i      -i  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_101946264_   1273 AAAGTTAAAAACTTT-GTTCTTCCAAAGATACTGTT-------------G 1308
                            -           -  v    v  i  i   i i------------- 
  L1M4_orf2#LINE/    650 AAA-TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_101946264_   1309 ACAAGCCCTTGTCTGGAAGAAAATGTTTGGAAACCATTTATCTGGTAAAA 1358
                             v  viv vv   i       i    v   i   v      i   ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_101946264_   1359 GGCTTATATCCAGAATACAGAAAA---TCTCACAAAGCTCCTTAAGGAAA 1405
                          i   i           i v   i---   i    --   vv   vi   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAA--CTCAATAATAAAA 796

  chrX_101946264_   1406 AAACAGACACTCCAATAAATAAATGGACAGAAGAGTTGAAAAGACACTCC 1455
                          i   i i vi     v? v      i  i i  v     v     i i 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_101946264_   1456 ACTATAGAAAATATACAGATGTCAAATAAGCATATGAAAAGATATTCAAC 1505
                         v i v    i       i   v v        i          ii     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_101946264_   1506 ATCATTAATAAT 1517
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (131 / 87)
Gap_init rate = 0.02 (19 / 901), avg. gap size = 2.26 (43 / 19)  


2995 25.40 2.93 0.68  chrX_101982265_101984142.rev      502  1387 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_101982265_    502 GAAAAATATTCCATGCTCATGGATAGGAAGAATCAATATTGTTAAAATGG 551
                             i    i     i        v      v i           i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_101982265_    552 TCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTC-TATTAAACTA 600
                         iv     v      vii  i           i  v  i -   i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_101982265_    601 CTAGCAATGTTTTTCACAGAACTAGAATAAA--AATTCTAAAATTCACTT 648
                          i   viiv     ii     v v  -i  i--i  i          iv 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATAT 151

  chrX_101982265_    649 GGAACCAAAAGAGAGCCTGAATAACCAAAGCAATCCTAAATGAAAAGTGC 698
                             viiv   i  v  v     i     i     i i  vi i   vi 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_101982265_    699 AAAGATGGAGGCATCACACTACCTGACTTCAAACTATAATACAAGGCTAT 748
                             v      vv       v  ii i      viv  v     i    i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_101982265_    749 AGTAATTAAAACAGCATGGTACTGGTACAAA-ACAGACACGCAGACAAAT 797
                               i  i    ii         i i  i- i     iii   iv   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_101982265_    798 GGAACATAATAAAGAACACAGAAATAAAGCCACACACCTACAACCATCTG 847
                             i v   vi   iiv          v   i   ii  iiii  vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_101982265_    848 ATCTTCAACAAAGTTAACAATAACAAGCAATGGGGAAAGGACTTCCTATT 897
                           i   i    i v iv   v v  vv            i ivvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_101982265_    898 CAATAAATGGTGCTAGAATAACTGGCTAGACATATGCAGAAGATTGAAAC 947
                            i          i i i      v  ?v  i     i    v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_101982265_    948 TTCACCTTTACCC---------TTCAAAAATCAACTCAAAATGCATTAAA 988
                          vv   ii    i--------- v       i           v  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_101982265_    989 GACTTAAATGTAAAACATAAAACTATAAATACCCT-AGAAGAAAACTTAG 1037
                            i         i vv            -  i  -          v   
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAG 550

  chrX_101982265_   1038 G---AAATACCATTCTAGACATCAGCCCTGGCAAAGACTTCAT-GATGAA 1083
                          ---    -- -   vv   v ii viiv     v ii   v -   - v
  L1M4_orf2#LINE/    551 GNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chrX_101982265_   1084 GACACCAAAAGCAACTGTAGTAAAAACAAATATTGACAAGCAGGACCTAA 1133
                                      vvv i ii    iv   v  v  i  iiv    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_101982265_   1134 TGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGCAGAC 1183
                          v   v v  i i   i  ii vv    i  v        v i  iii v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_101982265_   1184 AGACAACCTACAGAATGGGAGAAAACATCTGTAAACTATGCATCTTCCAA 1233
                                 i                i  i  i   ii  ii    vvi  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_101982265_   1234 AGGTCTAATATCCAGGATCTATAAGGAACT-----AAATCAACAA---GC 1275
                         i  v  vi       i  v     i     -----  v    i  ---iv
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_101982265_   1276 AGAAAAACAACCCCATTAAAAAATGGGCAAAGGACATGAACAGACACTAC 1325
                            v   i     v   ?                iv    i     i v 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_101982265_   1326 TCAAAAGAAGATATACACATGACCAACAAGCATATGAAAAAATGTTCAAT 1375
                           v              v   i    i     i       i   i    i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_101982265_   1376 ATCACTAATCAT 1387
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (134 / 88)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 2.29 (32 / 14)  


1719 27.77 2.00 3.81  chrX_102013756_102019609.rev     4129  4679 (1175)    L1M4_orf2#LINE/L1        1   541 (367)  

  chrX_102013756_   4129 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATTGCTATTGTTAAAAT 4178
                               i i  i     i        v      v  iv         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102013756_   4179 GGCCATACTACC-AAAGCAATTTATAGATTCAATGCTATTCCAATCAA-- 4225
                            v     v  -   vii  i  i        i  v  i  v     --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102013756_   4226 --TCAATGACATTCTTCACAGCATTAGAAAAAACTG-TTTTAAAATTCAT 4272
                         --i  iivi v  i  ii   v v v - v  i   - ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chrX_102013756_   4273 ATGTAACCAAAATAGAGCCCAAATAGCCAAGGCAATTCTGAGGAAAAGTA 4322
                            v  viiv  vi  v  vi         ii    ii   ii  i iv 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_102013756_   4323 ACAAAGCCAGAGACATCATGTTACCTGGCTTCAAACTATGCTACATAGCA 4372
                               iii   ivv   iii v  iiii      viv i     v   -
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC- 248

  chrX_102013756_   4373 TACCTGACTTTGAGCGGCTACAGTAACCAAAACAGCATCGTACTGGTACA 4422
                         ------------------        i   i    ii v       i i 
  L1M4_orf2#LINE/    249 ------------------TACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_102013756_   4423 AAATCAGACACAGAGACCAATATAACATAACAAAGAGCCCAGAAATAAAG 4472
                          iivi     i v   i    iv  i v  ivi    i           v
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_102013756_   4473 CCACACACCTACCACCATCTGATCCTTAACAAAGTCATCAGAAATAAGCA 4522
                            i   ii  ivii  vi    ii ii    i viii  ii vi vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_102013756_   4523 ATGGGAAAATAACCCCCTATTCAATAAATGGTGCTGGTATAACTGGCTAG 4572
                              i   v  ivvi  v     i            v i      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_102013756_   4573 CCATATGCAGAAGATTGAAACTAGACCCCTTCCTTACATCATATACTAA- 4621
                            i     i    v    ii i       v   i   i       v  -
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_102013756_   4622 ----GCTCAAGATGGATTAAAGACTTAAATGTAAAACCTAAAACTATAAA 4667
                         ----i     i      i ?    i         i v             
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_102013756_   4668 AAGTCTTGAAAG 4679
                          -v    ii   
  L1M4_orf2#LINE/    531 A-CTCTTAGAAG 541

Transitions / transversions = 1.96 (100 / 51)
Gap_init rate = 0.01 (7 / 541), avg. gap size = 4.57 (32 / 7)  

1055 27.20 2.13 0.53  chrX_102013756_102019609.rev     4989  5363 (491)    L1M4_orf2#LINE/L1      528   908 (0)  

  chrX_102013756_   4989 AAAAGTCTT-GAAAAAAGCCTGGGAAATAGTATGCTAGACATTGGCCCTG 5037
                             v    -   i   i v i  ?ivv i v v vv   v    viiv 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_102013756_   5038 GCAA--ATATTTTATGATGAAGAAACCAAAAGCAATTGCAACAATACCAA 5085
                             --i v i   -   - v  v          vvv       v vv  
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTA-GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_102013756_   5086 AAATTAACTAATGGAACCTAA-CTAAATTAATAGCTTCTGCACAGCAAAA 5134
                             vi iv   v i  i v - v       v i   i  ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_102013756_   5135 GAAACTATCAACAGAGTAAACATACAGCCTACAGAATGGGAGAAAATACT 5184
                           v        v i   i  v v   i  i                  i 
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_102013756_   5185 TGCAAACTATGCATCCAACAATGATCTAATATCCAGAATCTATAAGGAAC 5234
                               ii  ii   ii i  v iv  vi          v     i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_102013756_   5235 TTCAACAAACGTATAAGCAAAAAACAG----CCCTATTAAAAAGTGGGCA 5280
                          iiv    vivv    vv    i   i----   v   ?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_102013756_   5281 AAGAACATGAACAGATACTTTTCAAAAGAAAACATATGCGTGGCCAACAA 5330
                            i iv    i   i i  i  v      i i   iivi       i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_102013756_   5331 GCATATGAAAAAGTGCTCAACATCACTAATCAT 5363
                            i       ii            ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (54 / 46)
Gap_init rate = 0.02 (6 / 381), avg. gap size = 1.67 (10 / 6)  


2303 25.47 8.69 2.11  chrX_102034333_102036731     1055  1906 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102034333_   1055 TGGAAAGATATCCCATGCTCATGGATCAGAAGAACCAACATCATTTTTAA 1104
                                          i        ii     vii  i  --- v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT---TGTTAA 47

  chrX_102034333_   1105 AATGGCCATATTGCCAAAAGCAATCTACAAGAACAATACAATTCCTATCA 1154
                         i     v   i v  v   vii       iivv   ii    i       
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_102034333_   1155 AA---CTA-CTGTCATTCTTCACAGAC-TTAGGAAA--AATTTTAAG-TT 1196
                           --- i -   i -  i  ii    v-  iiv  i--i  ii   i-  
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_102034333_   1197 CATATGGAACTAAAAAAAAGAGCCCA-AACAGCCAAAGCAATCCTAAGCA 1245
                                  v iv  iii ---    -  i       i     i i iv 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_102034333_   1246 AAAGGAACAAAGCCAGAGGCAC-CATACTACCTGACTTCAAA-----CTG 1289
                          i i        iii    -  -  i   v  ii i      -----  i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_102034333_   1290 TAAGGCTACAATAACCAAAGTAGCATGGTACTAGTA----GATAGACACA 1335
                         i  i      i   i   iii  ii       i i ----        i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_102034333_   1336 TAAGCCAATGGAACAGAATAGAGAGCCCAGAAATAAAGCTACACACCTAT 1385
                           iii        i     v     i           v i i   ii   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_102034333_   1386 ACCCATTTGATCTTTGACAAAGTCAACAATAACAAACAATGGGGGAAG-- 1433
                         ivi  v     i  i     i viiv   v v  vv        i   --
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_102034333_   1434 --GTGCCCCCTATTCAATAAGTGGTTCTGAGATAACTGATTATCCATATG 1481
                         --  -----  v     i  i    v   i  i     iv  ?   i   
  L1M4_orf2#LINE/    393 TAGT-----CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_102034333_   1482 ---AAGAATGAAACTGGACCCCTACATTTTAGCATACTCCAAAATTAAGT 1528
                         ---         ii           v ivi v    iv v        v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_102034333_   1529 CAAGATGGGTTAAATACTTAGATGTAAGACCTCAAACTATAAAAATCCTA 1578
                            i    i i ? v  i  i        v  v           v  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_102034333_   1579 AAAGAAATTCTAGG---AAAT------GGCCTTGG------CAAAGAATT 1613
                         i      viv    ---    ------ i      ------   v iv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_102034333_   1614 --TGACTGTATCCCTAAAA---CAAGTGAAACAAAA-AACAAATTGACAA 1657
                         -- iiv i iv v i    ---    i--       -  v    v  i  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGC--AACAAAAGAAAAAATAGATAA 635

  chrX_102034333_   1658 GTGGGACGTAGTTAAACTAGAGGGCTTCTGCAC---AGAAGA----ATCT 1700
                         i v    v vi i   v vi iii   i  ii --- i i  ----   v
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_102034333_   1701 AGA--GTAAACAAACCACCTACAGAATGGGAGAAAATTGTTGCAAACTAT 1748
                            --  i  v i  v   i                 vv       ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_102034333_   1749 TCATCTGACAAAACTCTAGTATCCAGAATCTATACAGAACT--TAAAAC- 1795
                         vi      i  iivv  v           v    v      --  v   -
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_102034333_   1796 ----AATTCAAGAAGA--AACAATCCTGTCATAAAAATGGGCAGAGGAC- 1838
                         ----   --  i    --  i  i  vi i?-           i    i-
  L1M4_orf2#LINE/    786 CAATAAT--AAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATT 832

  chrX_102034333_   1839 ---ATGGACATTTCTTAGTAGAACCCACACACGCAGCCAACAA----ATA 1881
                         ---  i         iviv    vvi i   viii     i  ----  i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_102034333_   1882 AAAA-ATACTTATCATTAATCAAAGA 1906
                             -  i  i v   i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (144 / 70)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 2.71 (92 / 34)  


3104 28.08 0.44 0.44  chrX_102081785_102088189.rev     5007  5914 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102081785_   5007 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCGATATCGTGAAAAT 5056
                              ii i  i     i      i v      v ii    i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102081785_   5057 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5106
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102081785_   5107 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5154
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_102081785_   5155 TATGGAACCAAAAAAGAGCCCACATCACCAAGTGAATCCTAAGCCAAAAG 5204
                                viiv  ii  v  viv  vi    ivv    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_102081785_   5205 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5254
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_102081785_   5255 TACAGTAACCAAAACAGCATGGTACTGGTACCACAACAGAGATACAGATC 5304
                                 i   i    ii         i iv vi i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_102081785_   5305 AATGGAACAGAAC--AGAGCCCTCATAAATAATGCCGCATGTCTACAACT 5352
                                i    i--    i  -- v      vv  ii ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_102081785_   5353 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5402
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_102081785_   5403 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5452
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_102081785_   5453 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATGCAAGATGGA 5502
                            ii    i    v   i     v              iv   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_102081785_   5503 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAAAAAAC 5552
                          i ?    i       v   v       i      vi i     i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_102081785_   5553 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5602
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_102081785_   5603 AACACAAAAAGCAATAGCAACCAAAGCCAAAATTGACGAATGGGATCTAA 5652
                         i    v       vv      v    vv     v  ii   v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_102081785_   5653 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5702
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_102081785_   5703 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5752
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_102081785_   5753 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5802
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_102081785_   5803 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACCTACACTTC 5852
                          i     i     v  i?    i     i      v    ivv   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_102081785_   5853 TCAAAAGAAGACATTTATGCAGCCAAAAGACATATGAAAAAATGCTCATC 5902
                           v        i  vi viii     v ii  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_102081785_   5903 ATCACTGGCCAT 5914
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (148 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 279 21.74 8.70 3.26  chrX_102096114_102098935.rev     1129  1220 (1602)    L1M4_orf2#LINE/L1        1    97 (811)  

  chrX_102096114_   1129 TGAAAAGATAGTCC-TTTTCATGGGTTGAAAGA----ATATTGTCAAAAT 1173
                           i       vi  - v       i   i    ----       i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102096114_   1174 GTCCATACTACCCAA-TT--CCTACTGAAATTTCAATGTCATTTTTTTCA 1220
                          v v     v     -  --i    v  ---     i iv  iii v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGA---TTCAACGCAATCCCTATCA 97

Transitions / transversions = 1.50 (12 / 8)
Gap_init rate = 0.05 (5 / 97), avg. gap size = 2.20 (11 / 5)  

2800 24.15 2.02 2.28  chrX_102096114_102098935.rev     1541  2331 (491)    L1M4_orf2#LINE/L1      120   908 (0)  

  chrX_102096114_   1541 AGAAATAGAAAAAACAATCCTAAAACTTACAAAAACAAACAAAACACCCC 1590
                               v  v  ivii         i i i vii v vi   iiv    v
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_102096114_   1591 AAAGAGCCAGAGCAATCTTGAACAAAAGGAACGAATCTGAATTGATCACA 1640
                         i  v     i i          v  i i    i  vi  i vviv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_102096114_   1641 CCACTTGACTTCAAAATATACCACAGTGCTGTATTAAACGAAACAGTATG 1690
                          iv iii i       iv   i   iv   ii v   v i i     i  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_102096114_   1691 GTACTAGCATAAAAACAGACTCAGAGGCAAATGGAACAGAATATAGAGCC 1740
                              i      ii i    vi v  iiv       i     vv    i 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_102096114_   1741 CAGAAATAAATCCATGCATATATGGTCAATTAA-----------GGTGCC 1779
                                   i    i   v           i -----------      
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_102096114_   1780 AAGAACACACAATGAAGAAAGGATAGGTTCTTTGATAAAGGGTGTTAGGA 1829
                             v  iv     ii     i    vi i  ii i   v    i i   
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_102096114_   1830 CAACTGTGTATCTGTATATCTACATGCAGAAAAATTAAACTGAACCCTTA 1879
                               ------- -   ? i       i  i   v  ii  i    i  
  L1M4_orf2#LINE/    420 CAACTG-------G-ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_102096114_   1880 GCTCACAC-ATTTAAAAAAA--AACTCAAAATGTATTAAAGAGTTAAATG 1926
                         v       -  v  v     --           v  i ?   vi      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_102096114_   1927 TAAGACCTGAACGTGTAAAACTACTAGAAGAAAACATATGGGTAAAACTC 1976
                              v  i  vv i       vi              v ?     v  i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_102096114_   1977 CATTGTGTTGGTCTGGACGATAATTT-TTGGACTATAGAC-CCAAAAGCA 2024
                          i viiv    vi i i i  ii   -  i  -   -   -         
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TAT-GACACCAAAAGCA 609

  chrX_102096114_   2025 TAGACAACAAAAGCAAAAAAAAAAAATAGACAAACCAGACTACATCAAAC 2074
                         i ii         -------          i   iii    v       v
  L1M4_orf2#LINE/    610 CAAGCAACAAAAG-------AAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_102096114_   2075 TAAAAAGTTTCTGTACAGCCAAGGAAACAATGAACAGAGTGAAGTGACCA 2124
                          v    ii  i   i vv v     v  v  v  v i      iv   v 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_102096114_   2125 TCTACAGAATGGGAGAAAATATTTGCAAACTATACATCTGATAAAGGGTT 2174
                         i i                          ii   i         i  ii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_102096114_   2175 AATATCCAAAGTATGTAGGAAACTCAAACAACTTTATAGAAAAAAAACAA 2224
                         vi      i i   i  iii     vv      iv   iv     i    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_102096114_   2225 ATAATCCAATTAAAATATGAGCAAGGGACCTGAATAGACATTTTTCAAAA 2274
                             i      ?   v   i    i   ii             i  v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_102096114_   2275 GAAGACATACAAATGGCCAACAGATATATGATAAAAATGCTCAAAATCAC 2324
                              i              i iii i    -   i        v    ?
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTCAACATCAZ 901

  chrX_102096114_   2325 TAATCAT 2331
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.92 (123 / 64)
Gap_init rate = 0.01 (11 / 789), avg. gap size = 3.09 (34 / 11)  


1119 26.69 0.34 0.68  chrX_102105559_102110809.rev     3552  3847 (1404)    L1M4_orf2#LINE/L1        1   295 (613)  

  chrX_102105559_   3552 TGTAAAGATATTCAAAATTCACAAATTGGAAGAATCAATATTGTTAAAAT 3601
                           v        i v vi    iii         v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102105559_   3602 GTCCATACTACTCAAAGAAATCTACGGATTCAATGCAATCCCTATCAAAA 3651
                          v v     v i    vvi      i       i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102105559_   3652 TACCAATGAGATTCTTCACAGAAATTTAAAAAAACT-ATTCTAAAATGTG 3700
                          v   iivivv  i  ii        --i v  i  -  i       vii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_102105559_   3701 TATTCAATCACAAAAGACCCAGAATAGCCAAAGCTGTCCTGAGTAAAAAG 3750
                            vv  vii   ii                 i vi  i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_102105559_   3751 AACAAAACAGGAAGAATAACATTTCCTGACTTCAAATTATACTACAGAGC 3800
                               iiv   i  v v   i    ii i      viv       i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_102105559_   3801 TATAGCAACCAAAACAGCATGGTGTTGGAATAGAAACAGACACATAG 3847
                           i  i  i   i    ii    ii   v   iii i     i    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 2.04 (53 / 26)
Gap_init rate = 0.01 (2 / 295), avg. gap size = 1.50 (3 / 2)  

2287 21.85 2.71 3.03  chrX_102105559_102110809.rev     4134  4760 (491)    L1M4_orf2#LINE/L1      284   908 (0)  

  chrX_102105559_   4134 ACAGACATATAGATCAATGGAACAGAATAGAGAACTCAGAAACAAGTCCA 4183
                          i                    i     v    iii      i  ii   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_102105559_   4184 TGCATCTGTACTGAACTCATTTTCGACAAAGCTGCCAAAA------AAT- 4226
                          i   i i iv v  i v           i v      i ------   -
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_102105559_   4227 -----ACACT-GTCTCTTAAATAAACGGTCCTGGGAAAACTGGTTA-CCA 4269
                         ----- v v -    i  v  i   i   v      v      v  -   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_102105559_   4270 TATGCAAAAGAATGAAACTAAACCCCTATCTCTCACCATATACAAAAATC 4319
                         i               ii ii       i   v                i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_102105559_   4320 ATATCAAAATGGATTAAAGACTTATACCTAATAACTCAAACTATGAAACT 4369
                          vv           i ?    i  v iv   v i  v       i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_102105559_   4370 ACTACAAGAAAAAGTTGGGGCGAATCTCCAGGACATTGGACT-GGTAAAT 4418
                         vi  v       vi v  ? ii     i iv   v    ii -  i  vv
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_102105559_   4419 ATTTGTTGAGTAATATCCTACAAGCACAAGCAACCAAAGCAAAAATGGAC 4468
                         i   v  iii  vv iv i v             v    v      i  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_102105559_   4469 AGATAGGATCACATTGTTACCTTTGCTGTGCAGAAGTTACAAAGCTTCTG 4518
                          i  v   iiv   ----------------  i  -   -   i   i  
  L1M4_orf2#LINE/    634 AAATTGGACTTCAT----------------CAAAA-TTA-AAAACTTTTG 665

  chrX_102105559_   4519 CACAGCAAAGGTAATTATCAACAAAGTGAAGAGACAACCCACAGAATAGG 4568
                         ii vv      vv i      v        i                i  
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_102105559_   4569 AGAAAATATTTGCAAACTATCTATCTGACAAGAGATTAACCACCAGAATA 4618
                                         ii  v       i   i  i viivv        
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_102105559_   4619 TATAAGGAGCTCAAACAACTCTATAGGAAAAAAATCTAATCATCCAATTA 4668
                              i  i   vv       v   iv     i - v   v i      ?
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTW 814

  chrX_102105559_   4669 AAAA--GGGGAAAAGATCTGAATAGACACTTCTCAAAAGAAGACATACAA 4716
                             --   v   i   i          i     v        i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_102105559_   4717 ATGGCAAATAGCTATAAGAAAAGGTGCTCAATATCACTGATCAT 4760
                              v    ivi i v      i       i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (79 / 55)
Gap_init rate = 0.02 (10 / 625), avg. gap size = 3.60 (36 / 10)  


1680 16.75 1.50 8.00  chrX_102127478_102129419.rev      501   900 (1042)    L1M4_orf2#LINE/L1      298   671 (237)  

  chrX_102127478_    501 CAATGGAATTGTTTTGAGAGTCCAAAAGTAAAACTATGTGGCTAATCTCA 550
                                  v vv           i  i    v i  iiivi  vvv   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_102127478_    551 AATGAATTTTGACAAGGGTTCCAAGACAATTCAGTGGAGAAATA-TAGTC 599
                          v   v   i         v       v     i   i    v -     
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_102127478_    600 TTTTCAACAAATGGTGCTTGGCCAACTGCATAGCCACATATAAAAGAATG 649
                                           v  v      v   ?      ii         
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_102127478_    650 AAGTTACACTCTTACCTCCCGCCTTATA-AAAAACTAATTCAAACTGGGT 698
                              iv  i i      v i  v    -     i   i     v   i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_102127478_    699 CAAAGACCTAAATGGAAGAGCTAGAAGTATAAAACTCTTGGAGGAAAATA 748
                           ?           v        i  v            i  i     i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_102127478_    749 TAGGGATAAATATTTGTGACCTTGGATTACAAAGGATTCTTAGATTCAAA 798
                             ?i     v  i          i   ----  ---------------
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTA----GG--------------- 578

  chrX_102127478_    799 TGACTCTTGAATTCAAAAGATTCTTAGATATGACACCAATACCAGGAGCA 848
                         -------------   vi v                   v v  vi    
  L1M4_orf2#LINE/    579 -------------CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_102127478_    849 GCAAA-GAAAAA---GGTAATCTAGACTTCATCAAAATTAAAAATTATTG 894
                         i    -      --- i   vi i                    i v   
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_102127478_    895 TGTTTC 900
                           i   
  L1M4_orf2#LINE/    666 TGCTTC 671

Transitions / transversions = 1.13 (34 / 30)
Gap_init rate = 0.02 (6 / 374), avg. gap size = 6.33 (38 / 6)  

1219 17.46 0.79 0.00  chrX_102127478_102129419.rev     1200  1451 (491)    L1M4_orf2#LINE/L1      655   908 (0)  

  chrX_102127478_   1200 AAACACCATTGTGTTTCAAAAGGCACCATTATGAAACTGATTAAAAAACC 1249
                            v  iv     i      i i   i  i v    v   vv i v    
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_102127478_   1250 CACAGAATGGGCTAAAATATCTGCAGATCATATATGTAGTGAGGGATTTC 1299
                                    vv       i    i         v ii i     i  v
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_102127478_   1300 TGTCTAGAATATATAAA-AACTCTTGCAACTCAATAATAAAAAGAAAAAT 1348
                          i  i            -       i                   v    
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_102127478_   1349 AACTCAAATAAAAAGTGCACAAAG-ATCTGAATAGACATTGATCCAAGGA 1397
                            i   v ?    i  vi     -  i            vv     i  
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_102127478_   1398 GGATATACAAATGACCTATAAGCACATGAAAAGATGCACCACATTATTAG 1447
                         i            i  v                    v v    i ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_102127478_   1448 TCAT 1451
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.26 (24 / 19)
Gap_init rate = 0.01 (2 / 254), avg. gap size = 1.00 (2 / 2)  


3923 17.51 5.05 0.59  chrX_102131902_102134836     1585  2435 (500)    L1M4_orf2#LINE/L1        1   889 (19)  

  chrX_102131902_   1585 TGCAAAGACATCCTCTGTTCATGGATTAGAAGACATTGTATTGTTAAAAT 1634
                           v     i    iv            i      v vi         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102131902_   1635 ATTAATACTACCCAAAGTGATCTATGGATTCAATGCAATCCCTATCAAAA 1684
                         ivi      v      v       ii       i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102131902_   1685 TCACAA-TGACGTTCTTGCAGAAATCAA-AATCT-ATCCTAAAATTCATA 1731
                           v  i-  v v  i          ii -  v  -               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_102131902_   1732 TGGAAACTCAAAGGACCT-GATTAGCCAAAACAATCTTGAAAAAGAA--- 1777
                               iv   i     i-  v                         ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_102131902_   1778 CAAAATTTGAAGTCTCCCACATCCTGATTTCAAAGCTTAATACAATGCTA 1827
                             i  v  i v   v   v   ii        i    v     v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_102131902_   1828 CAGTAATCAAAACAGTG--GTACTGGCAGAATGGCAGACATGTAAA-CAA 1874
                                   i      --         v  v ii      i  i -   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_102131902_   1875 ----ATAGAATTGGTAGTCTAAAAACAAATCCTGGCATAAATGGTCAAAT 1920
                         ----         iv    i i   i   i  vvi   vv        v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_102131902_   1921 GCTTTTCAA--AGGGTGCAAAGACTGTCCAATGAGGAAAATACAGTCTT- 1967
                          v     i --       v     ii i     i     iv i      -
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_102131902_   1968 -CAACAAATGTTGCTGGGGAAACTGGATATCCACACAGAAAAGAATGAAG 2016
                         -         v       iv         ?     iiv            
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_102131902_   2017 TTATACCTTTACATTATACCATATACAAAAATTAACTCAAAATGGATGAA 2066
                           iv   ii   v i i                              v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_102131902_   2067 AGACCAAAATATAAGAGCTAAAAGCATGAAACTCTTAGCAGAAGACACAG 2116
                              v    i            vi  i          v    i   i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_102131902_   2117 GGACAAGCCT-CATAATATTGGATTTCACAATGATTTCTTGGATATGACA 2165
                          ?ii  ii  - i i iv    i  vvi     i      i         
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_102131902_   2166 CTAGAAGAACAGGAAACAAAAGAAAATAACAGATAAATTGTACTACATCA 2215
                          i i   v   i v            -  i          v   v     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCA 649

  chrX_102131902_   2216 AAATGAAAGACTTTTGTGCATCAGAGGATG-TAGCAA-----TGGAATGA 2259
                             v   i          v   i    ii-  v   -----  i  v  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_102131902_   2260 ----------AACGGGA--AAATATTTTCAAATCATGTATCCGATAAGAG 2297
                         ----------  i    --        v        i    i      i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_102131902_   2298 ATTAATAGCTAGAAAATATAAAGAACTCCTACAACTCAGCAAAAACAACA 2347
                          i vi  v i    v             i         ii  v  v  -i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA-G 798

  chrX_102131902_   2348 ACAGAAAACAACCCAATTCAAAAATGGGCAAAGGACTT----AGACATTT 2393
                            ---  i         ?                i  ----        
  L1M4_orf2#LINE/    799 ACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_102131902_   2394 CTCCAAAGAAGATATACAAGTAGC-AATAAACACATGAAA-GAT 2435
                                            i i  -     i         -   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

Transitions / transversions = 1.59 (89 / 56)
Gap_init rate = 0.02 (21 / 889), avg. gap size = 2.29 (48 / 21)  


1429 25.19 0.56 9.44  chrX_102180003_102182133.rev      502  1041 (1090)    L1M4_orf2#LINE/L1      178   669 (239)  

  chrX_102180003_    502 AAAGCAATCCTAGGCAAAAAGAATAAATCTGGAGGCATCACATTATTAGA 551
                            i     i iiiv  i     i   vi      vv     i viivi 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_102180003_    552 CTTCAAAGTATGCTACAAGGCTATAGTTACCAAAACAGTATGGTACTGGT 601
                         i      iiv i      i    i   v i   i     i         i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_102180003_    602 ATAAAAGTAGGCACAAAGGCCAATGGAACAGAATAGAGAACCCAGAAATA 651
                             iii   i  i v  ii        i     v    ii         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_102180003_    652 AAGCTGAATACTTACAGCCAACTGATCTTCAAAAAGCATACAAAAGCATA 701
                           v iiv i i   ii i   i    i   i v   vi i -----  - 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC-----CA-A 371

  chrX_102180003_    702 AATTGTTCTACTTAAATGGTGTGCAATAGGAGAAATTTTTTAAAAACATA 751
                         i iii   ------     ---------   -------------------
  L1M4_orf2#LINE/    372 GACCATTC------AATGG---------GGA------------------- 387

  chrX_102180003_    752 AATTGAAGAATGGACAACCTATTTAATAAATGGTGCTGGAAAAACTGGCA 801
                         -----      ---- ii  v  i  i            i v      vv
  L1M4_orf2#LINE/    388 -----AAGAAT----AGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_102180003_    802 AGCCGCATGTAGAAGAATGAAACTAGATCTCTATCTCTCACCTTGTAGAA 851
                          ?  i    i i         ii i  i i   i   v    v i  v  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_102180003_    852 AAATCAACTCAGGATGGATCAAAGACTAAAATATAAGACCTGAAACTATA 901
                             i      ii        ?    iv    i     v  i        
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_102180003_    902 AAAATTCTAGAAGACAACATTGGAAAAACTCTATTATAGACATCGGCCTA 951
                            v ii       v     v  ?iv  v   - ii -   v i  vi  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCT-TCGT-GACCTTGGGTTA 576

  chrX_102180003_    952 GGCAAAGAATCTATGACTAAGACTCCAGAAGCAAATACAACAAAACCAAA 1001
                              v iv iiv iiv  v   v   i     v vi        vv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_102180003_   1002 AATAAATAAATGGAACCTAATTAAA-CCAAAAA--TCTGTGTT 1041
                             i      v i  i v  i   -ii     -- i    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

Transitions / transversions = 2.17 (91 / 42)
Gap_init rate = 0.02 (10 / 492), avg. gap size = 5.40 (54 / 10)  

 930 21.54 0.00 2.69  chrX_102180003_102182133.rev     1381  1640 (491)    L1M4_orf2#LINE/L1      656   908 (0)  

  chrX_102180003_   1381 AACACTTCTGCACAACAAAAGAAACAATCAGCAGAGTAAACAGACAATTC 1430
                           v    i  ii vv    i  v  v    iv i   i  v      ii 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_102180003_   1431 ACAGAAAGGGATACAATATTTGTGAACTATGCATCTAACAAAGGACTAAT 1480
                               v    v v        ii  ii  ii    i i  i     vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_102180003_   1481 ATACAAAATCTACAAGGAATTCAAACAACTCAGGGATAAAAAAAATAAAA 1530
                           v  i   v  i  i   i  vv        ---    v     ----i
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCA---ATAATAAAAA----G 798

  chrX_102180003_   1531 ACAAAGAATCCCATCAAAAAGTGGGCAAATGACATGAGTAGACATTTCTC 1580
                              v  i  v  i?    i        v  iv   i            
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_102180003_   1581 AAAAGAAGATATACAAATGGCTAATAAACATATGAAAAAATTCTCAACAT 1630
                         v                    i     i  i       i  v        
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_102180003_   1631 CACTAATTAT 1640
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.50 (33 / 22)
Gap_init rate = 0.01 (2 / 253), avg. gap size = 3.50 (7 / 2)  


3207 27.20 0.55 0.55  chrX_102191981_102198368     4988  5895 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102191981_   4988 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5037
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102191981_   5038 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5087
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102191981_   5088 TACCAATGACTTCCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 5135
                          v   iivi i ii  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_102191981_   5136 TATGGAATCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5185
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_102191981_   5186 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAATCTATACTACAAGGC 5235
                                i      vv   ii  v  ii i     vviv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_102191981_   5236 TACAGTAACCAAAACAGCATGGTACTGGAACCAAAACAGATATATAGACC 5285
                                 i   i    ii         v iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_102191981_   5286 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5333
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_102191981_   5334 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5383
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_102191981_   5384 CTATTTAATAATTGGTGCTGGGAAAACTGGCTTGCCATATGTAGAAAGCT 5433
                           v  i  i  v           v      v v?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_102191981_   5434 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5483
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_102191981_   5484 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5533
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_102191981_   5534 CTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5582
                         v    ?i- v   -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_102191981_   5583 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5632
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_102191981_   5633 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5682
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_102191981_   5683 CAGGCAACCTACAGAACAGGAGAAAATTTTTGCAATCTACTCATCTGACA 5732
                         v  i     i      ii         v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_102191981_   5733 AAAGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5782
                          ii i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_102191981_   5783 AAAACAGACAACCCCATCAACAAGTGGGCGAAGGACATGAACAGACACTT 5832
                           i   i i     v  i? v  i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_102191981_   5833 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5882
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_102191981_   5883 CATCACTGGCCAT 5895
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2360 22.71 2.91 5.26  chrX_102247094_102249348.rev      502  1223 (1032)    L1M4_orf2#LINE/L1       22   726 (182)  

  chrX_102247094_    502 TGAGTCAGAAGGCTTAATATTGTTAAGATGAAAATTGGTAAGAGGAAAAA 551
                           ii ii    i                  iv   ------------- v
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAAT-------------AC 58

  chrX_102247094_    552 TCCCCAAACTGTTCTATGAATCCAGTG-----------AAAATCCTAGTG 590
                                 i  v    iii  i  ii -----------       i  i-
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC- 107

  chrX_102247094_    591 TGTGTTTTTTTCAAAAGAAATGGAGGAGCTGATTCTAAAATTCATGTGGA 640
                           iv      v  ---     v  vi       i           i    
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCA---GAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_102247094_    641 GGTGCAAAAGATCTACACTAGAAAAAAAAAACCTTGAAAAAGAA---CAA 687
                         ii     ii  i i v v   vv    v  -i            ---   
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAACAA 203

  chrX_102247094_    688 AATTGGAGAACAAACACCACCTGATTTCAAGACTCACTCCAAACTTACAG 737
                          i      i  vv    iv  ii       i   i   v    vi     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_102247094_    738 TAATTAAAACAGTGTGCTGTTGGCATCGAGGTAGACAATTAGATCAATGG 787
                             i  i        v ii      vii i      vv           
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_102247094_    788 AACAGAATAAAGAGTCTCAAAATAGATCC-TGCCAATATGGAAAAGTGAT 836
                           i     vi      ivi     i i  - i vvv     vv  v    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_102247094_    837 TTTTGACACAGGCACAAAGGCAATTTAGTGAGGAAAGGATCTTCTTTTCA 886
                            i    vi  ii v   i v   i i  i      i  vv        
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_102247094_    887 ACAAATGGTGCTGGGATAAGAGGATATTCATATGCACAAATATAAA-TTG 935
                                         i  vv     ?i  i     v  iv  i  -   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_102247094_    936 TGATCTATATATCATGCCATATGCAAAAGTCAATGCAAAATGGATCATAG 985
                         -  i iv  iv   ii      i     i i  iv            ?  
  L1M4_orf2#LINE/    454 -GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_102247094_    986 ACCTAAATGTAAAACGTAGAGCTACAGAAAC-ATTGGAAAAAACACAAAA 1034
                                     ------      ---    -  -----     v vv -
  L1M4_orf2#LINE/    503 ACCTAAATGTAA------GAGCTA---AAACTAT-----AAAACTCTTA- 537

  chrX_102247094_   1035 GAAGAAAAC-TAGGAGAAAATTCTTGCTATCATTGATTAGGCGAAGATTT 1083
                                  -    ? v    ii i iv i v v i      i v i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_102247094_   1084 CCTAGATGTCACAACAAAACTACAGTCCATACATGAACAAATTGATAATT 1133
                          i     i v   v     vi   iv v i v v   v    v     v 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_102247094_   1134 TAGATCT-ACTTAAATTAAAAATGTCTGCTCTTCCCAAAG--CACTATTC 1180
                          i  ii - iiv          iv i  iv    --    --      iv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTC--AAAGGACACTATCA 685

  chrX_102247094_   1181 AGAGAATGAAAAGACAAAGCCACTGACTGGGAGAAAAATATTT 1223
                            i i           v-    v  v          -     
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAAC-CCACAGAATGGGAGAAAA-TATTT 726

Transitions / transversions = 1.44 (95 / 66)
Gap_init rate = 0.03 (20 / 705), avg. gap size = 2.95 (59 / 20)  

 536 19.57 8.70 1.63  chrX_102247094_102249348.rev     1581  1764 (491)    L1M4_orf2#LINE/L1      712   908 (0)  

  chrX_102247094_   1581 TGGAGAAAAATATTTTTAAATCATATATCTGATAAAGGACTTGAA---AG 1627
                            iii         vi                  i       v ---  
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_102247094_   1628 AATAT--------CTCACAAAACTTCATAGAACAAAATAGACA--TTCTC 1667
                              --------   vi v    iv   -- i    -     -- vvi 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATA--ATAAAA-AGACAAATAACC 808

  chrX_102247094_   1668 CAA--AACAAATATGAAAAGGATTTTAATGGTTACTTTATCAA-GAAGAT 1714
                            --? v    iv v         v   i vi i  ivi   -      
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_102247094_   1715 CTAAAAATGTCAAATAAGCACACGAAACTATGCTCAACATCATTAGTCAT 1764
                         v  v     v v          i    vv             ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.84 (16 / 19)
Gap_init rate = 0.04 (7 / 197), avg. gap size = 2.71 (19 / 7)  


 382 19.48 2.60 0.00  chrX_102323408_102326246.rev       57   133 (2706)    L1M4_orf2#LINE/L1        2    80 (828)  

  chrX_102323408_     57 GGAAAGGCAACTTATGTTTAAGGATGGGAAGACTTAATATTTTTAAAATA 106
                               ii v ii     i v    v               v    i  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_102323408_    107 CTAATACTTTCCA--TTGATCTACAGATT 133
                         vi      ii   --              
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATT 80

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.01 (1 / 79), avg. gap size = 2.00 (2 / 1)  

1193 12.45 1.83 10.26  chrX_102323408_102326246.rev      136   408 (2431)  C L1M4_orf2#LINE/L1   (597)   311    62  

C chrX_102323408_    408 CTAAATTTATGGATCTATAGGTTCAATGCAGTCCCTATCAGAATCCCAGC 359
                          i     ----      i  i     i   i         i         
  L1M4_orf2#LINE/     62 CCAAATT----GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

C chrX_102323408_    358 TGGAATTTTTTTTAAAGAATTTGACATGCTAATTCTAAAATTCATATGCC 309
                           ---ii      iv    v      v   i  i              vv
  L1M4_orf2#LINE/    108 TG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

C chrX_102323408_    308 ATTGCAAGGAACCCTCAATA-TCAAAA-AGTTTTCAAAATAAACAAAACA 261
                          v       i    vv    -i     - i i  v    -----------
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA----------- 193

C chrX_102323408_    260 AGAAGAAACAAAGCAGCAAAGTTGGAAGGAGTCACACTTCT-GATTTCAA 212
                                ---------          -   v         i-i       
  L1M4_orf2#LINE/    194 AGAAGAA---------CAAAGTTGGA-GGACTCACACTTCCCAATTTCAA 233

C chrX_102323408_    211 A-CTTACTACAAAGC-ACAATAATCAAGACAATGCAGTACTGGCATAAGG 164
                          -             -   i           i  ii              
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

C chrX_102323408_    163 ATGGACACTTAGATCAATGGAATAGAAT 136
                           i    iv                   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAAT 311

Transitions / transversions = 2.09 (23 / 11)
Gap_init rate = 0.04 (10 / 250), avg. gap size = 3.30 (33 / 10)  

 269 28.38 2.70 0.00  chrX_102323408_102326246.rev      891   964 (1875)    L1M4_orf2#LINE/L1        1    76 (832)  

  chrX_102323408_    891 TGGAAA--CATTCTGTGTTTATAGATTGGAGGAGTCAGCATTATTAAGAA 938
                               --i  i ii    i  i       i  v i ii   i      v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102323408_    939 GTCAGTACTTCTCAATTTGGTGTATA 964
                          v  i    i i   v   i v  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA 76

Transitions / transversions = 3.20 (16 / 5)
Gap_init rate = 0.01 (1 / 76), avg. gap size = 2.00 (2 / 1)  

2578 24.58 3.60 1.16  chrX_102323408_102326246.rev     1573  2349 (490)    L1M4_orf2#LINE/L1      113   908 (0)  

  chrX_102323408_   1573 TTTTTGTAGATATCAACAAGCTAGTTGCAAAATTGAAATG-AAATGTCAA 1621
                               i   v  ii       ii ivi      v v   -     -   
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG-CAA 161

  chrX_102323408_   1622 AGGAAATAGAATAACCAAAACA-TACAGAAAAAGAAGGACAAAATTGGAG 1670
                         i   vvi      i        - viv          i     i      
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_102323408_   1671 GACACACACTAACCAATTTCAATACTTTTTATAAAGCTACATTAAGCAAG 1720
                            v      vv          v    vi  i         v   v    
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_102323408_   1721 ATGGTTTGGTAACAGAAAAATAGTAGGTACATAGATCAATGAAACAA--- 1767
                          ii  v     vii v v  vii   ii i           i  i i---
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_102323408_   1768 -GACAGCTCAGAAATAAACCCACACAAATATAGTCTACTAATATTTGACA 1816
                         -  v  ii              i   vv   i   v i i  v  i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_102323408_   1817 AATGCACAAGGGTAATTCAAGGAAGAAAGAATTGTCTTTTCAACAAATGA 1866
                          iv ii v i iiv      v ii        v                i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_102323408_   1867 CACTGAAACAACTAAACATCTATCTGCAAAA-AATGAACCTTATCTCATA 1915
                         ii   ii      ii i ? i iv       -      vi viv i v  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_102323408_   1916 CATAATATCTTGCACAAAAATTAAATCAAA-TATATCAAAGACCTAAATG 1964
                          v v i i v ii           v     - iv    ?           
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_102323408_   1965 TAAAATGTAAAATTATAACATGTCTAGAAGAAAATATTGGAGAAAATCTA 2014
                            i vv     i     v ivii          i  v  ? v      v
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_102323408_   2015 TATGATCTTAGGTGTGGTGATGAGTTTTTAGATATAATACCAAAAGC-TA 2063
                         ii   i   i   vv  ii   iv  i        i i         -i 
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_102323408_   2064 A-CAAC-----------TTTAAAAACTGGATATCATGAAAATTAAGAACT 2101
                          -    ----------- vv v   i    iv    v        i    
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_102323408_   2102 TTTG--CTTCATGAAAGACACTGTTATGAGAATGAAAATACAAGCCACCC 2149
                             --     --  i      i i v  i i      v    v    vv
  L1M4_orf2#LINE/    662 TTTGTGCTTCA--AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_102323408_   2150 ACTAGAAGAAAATATTTGCACATCACATATCTGATAAAAGATTTTTATCC 2199
                          v i i              v    i           ii  i  v     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_102323408_   2200 AGAAGAAATAAATGACTCTTAAAACCCAATAATAGAAAAGCAAAC--CCC 2247
                             v v     vi       v   i        i   ii    i--   
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_102323408_   2248 AA---AAAAGGCTACGGGAAGTAAAGATATGAACAGAGACTTCATTAAAG 2294
                           ---    ---- i   v --  i   v    i   v i   vii    
  L1M4_orf2#LINE/    810 AATTWAAAA----ATGGGCA--AAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_102323408_   2295 TATATATTCAGACAACAGATATGCACGTGAAAAGATGCTTAGCATCGTGA 2344
                         v v    v  i iii vi   v    i            i i    i???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_102323408_   2345 GTAAT 2349
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.47 (112 / 76)
Gap_init rate = 0.02 (15 / 796), avg. gap size = 2.47 (37 / 15)  


3183 27.09 0.55 0.55  chrX_102343072_102349471     5000  5907 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102343072_   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5049
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102343072_   5050 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5099
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102343072_   5100 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5147
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_102343072_   5148 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5197
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_102343072_   5198 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5247
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_102343072_   5248 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAAGATATAGACC 5297
                                 i   i    ii         i iv ii i i v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_102343072_   5298 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGTCACATATCTACAACT 5345
                                i    i--    i  --        vvi  i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_102343072_   5346 ATCCGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACAATTCC 5395
                          vii   i  i     ivv  v   i v  vvv          v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_102343072_   5396 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5445
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_102343072_   5446 GAAACTAGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGA 5495
                            ii i  i    v   i     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_102343072_   5496 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5545
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_102343072_   5546 CTAAGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5594
                         v  i ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_102343072_   5595 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACCAATGGGATCTA 5644
                         vi            vvi          vv     v  iv   v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_102343072_   5645 ATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGTGAA 5694
                           i   v v  i i   i  ii vv       v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_102343072_   5695 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCCACTCATCTGACA 5744
                         v  i     i                 v       vi  ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_102343072_   5745 AAGGGCTACTGTCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5794
                          i  i  vv i        v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_102343072_   5795 AAAACAGACAACCCCATCAACAAGTGGGCGAAGGACATGAACAGACACTT 5844
                           i   i i     v  i? v  i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_102343072_   5845 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5894
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_102343072_   5895 CATCACTGGCCAT 5907
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2145 25.73 5.31 0.93  chrX_102372436_102376606      501  1254 (2917)    L1M4_orf2#LINE/L1      122   908 (0)  

  chrX_102372436_    501 AAATATTACAAACGTACTCATAAA-TTTATTTGAAAATGCAAAGGACCTA 549
                             - v    i - iv  v    -  i  v  i        i     i 
  L1M4_orf2#LINE/    122 AAAT-TGACAAGC-TGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_102372436_    550 GAATAGACAAA-TAATTTTTTTAAAATATCCTACAAATCTTGAG-AGTTA 597
                               v    -i   i  vvv   iv vv--     vi v   - v i 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGA--ACAAAGTTGGAGGACTCA 217

  chrX_102372436_    598 CATTATATTATTTCAAGACTTA------AGGTGTAATAATAAAGTTAGTG 641
                           i viviv       i     ------  v ii i    v   vi    
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_102372436_    642 TAGTA-----GTAAACATAGACCTGTAGATCAATAGAACAGAAT--AGAC 684
                          i   -----i   iv      v i         i   i     --   v
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_102372436_    685 TCCAGAAATAGACCCATACGTATGTTGTTAATTAGTTTTTGACAAAGATA 734
                                   i        i v i v  i    ii    i     i i i
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_102372436_    735 TCAAAGTAATTCTATATGGAAAGTATAGTCTTTTAAACTAATGGTGCTGA 784
                         i   iiiv    v  iv      v          v   v          i
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_102372436_    785 AATAACAGAATTCTTAAAGG-AAAAAAAGGAGCCTTGCCTTTTATTT-AT 832
                         i i   v i  v?ii v v -    i  v  ivi v v iii  ii - i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_102372436_    833 AC--TATACACAAATTAATTCAAAATGGATCCTAGGCCTAAATGTAAAAG 880
                           --      v       i            v?  i           i  
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_102372436_    881 CTCAAATTAGAAAACTTCTAGAATAAAACATACAGAAAAA-CTTTACAAT 929
                           v   i  v      ii     v        vi?iv   -   iiii i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_102372436_    930 CTTTG---AGAAAACAATTCCTTAG----GACACAAAAAGAACAGATCAC 972
                            v ---  iv  iii  i     ----     v     v   iiiv  
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_102372436_    973 AAAAGAAAAAAATAAGAAATTGGATTT-ATCCAAATTAAAAACTTCTACC 1021
                                    vvi v        i  -   v             i iiv
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_102372436_   1022 ATTTAAAACACATGGTTAAGAAAATGAAGTGAGAAGC-------TGGGAG 1064
                         v  i   iv   ivi i      i    iv  v  v -------      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_102372436_   1065 TAAATATTCACAGTATT-TGTATCTGACAATGGTTTTGAATTCAGAGCAT 1113
                         v       ii  i-  i- i       i  v  vi   v  i    --  
  L1M4_orf2#LINE/    718 AAAATATTTGCAA-ATCATATATCTGATAAGGGACTTGTATCCAGA--AT 764

  chrX_102372436_   1114 ATATAAAGAACTTCGAAAACATAA-AATAAGAAGGCAAATAATGCAGT-- 1160
                                     iiv v   vi  -     i   i       iv  i --
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_102372436_   1161 AAAAATGATCAAAAGATCTGAATAAACATTTCACAAAACTACACACACAA 1210
                                iv    i   i      i       v v   vv v i i    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_102372436_   1211 ATTACCAATGAGCTCATGAAAAGATGTTCAACCTCATTAACTAT 1254
                           vi     i   v            i     v   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (112 / 79)
Gap_init rate = 0.03 (22 / 787), avg. gap size = 2.14 (47 / 22)  

 493 24.34 4.61 2.63  chrX_102372436_102376606     2115  2266 (1905)    L1M4_orf2#LINE/L1       13   167 (741)  

  chrX_102372436_   2115 CCATGATCATAGATGAAAACACTCAATATT-TTAAGGATGTCAATTATAC 2163
                              v    i   vii  v   i      -     -   v    vv v 
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-ATGGCAATACTCC 61

  chrX_102372436_   2164 CCAAATTCATCTGTAAATTCAGTGCAATCCATATGAAAATCTCAACAGGT 2213
                                v    ii i     ii       v   v      i  i v --
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG-- 109

  chrX_102372436_   2214 CACTTTTTG------TTGATAAGCAGACTCCAAATATGTGTATGAAAATA 2257
                          vi      ------    i    v  ii i   -  vii    i    i
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA-ATTCATATGGAAATG 158

  chrX_102372436_   2258 CAAAGAGCC 2266
                            i ii  
  L1M4_orf2#LINE/    159 CAAGGGACC 167

Transitions / transversions = 1.64 (23 / 14)
Gap_init rate = 0.03 (5 / 155), avg. gap size = 2.20 (11 / 5)  

 560 27.48 6.54 11.78  chrX_102372436_102376606     2562  3096 (1075)    L1M4_orf2#LINE/L1      152   658 (250)  

  chrX_102372436_   2562 GAAAATACAAAGAGTCAAATATAGCTAAGACAGCCTTTTAGATGGAGAA- 2610
                          i    i   i iii v iv     i  i   ii   vv i v i    -
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_102372436_   2611 --AGCTCCAAAACGTCCACTATTAGATATCAAAATTTAATACAATTTTAT 2658
                         --  i vv ii  viv    viivi  v      i   v     vvi  i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_102372436_   2659 G-----------AGTATGATATTGTCTCAAAGATTAAAATGTG--TCTGT 2695
                         i-----------   i  i  i  v vi  i   vi v  i i--  vi 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_102372436_   2696 GT--TTGTGTGTGTGTGTCTATCTTATATGGACCTGTGAAACATACC--T 2741
                          v-- v vi -  v v   i ----------------    i v   -- 
  L1M4_orf2#LINE/    302 GGAATAGAAT-TGAGAGTCCA----------------GAAATAAACCCAT 334

  chrX_102372436_   2742 ACCTATACAGTCACCTAATTTATGATAAAGATGACAG-----TTCAATGA 2786
                           v v  ii    vi i    vi  i  i i  v  i-----       -
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG- 383

  chrX_102372436_   2787 AGTGGGGGAAAGCATTTTTCTTTTCAA-AAGTGGTTTTGAAAAGATTAGT 2835
                         -----       v  vv -        -  i    vi  ii ----i ii
  L1M4_orf2#LINE/    384 -----GGGAAAGAATAGT-CTTTTCAACAAATGGTGCTGGGA----CAAC 423

  chrX_102372436_   2836 TGGATATCCATATGGGGAAAAGA-TGTATATTGATTCC-ACCTTACATAA 2883
                               ?   i   v--      -  v vv v  ii  -    i   iv 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGC--AAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_102372436_   2884 TACATTAAAAACAAAAACGAAAAAAAAAAAAAAAAAAAAAAAACCTCAGT 2933
                           i -------      iv  vvv    --------------------- 
  L1M4_orf2#LINE/    472 TATA-------CAAAAATTAACTCAAAA---------------------T 493

  chrX_102372436_   2934 GGATTGCAGACCCAAATGGGAAAGGTAAAAATGTAA---TCCTAATGTAA 2980
                             ii?     i     vi i  v     v i   ---  i  i---  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG---AA 540

  chrX_102372436_   2981 AAAAACTCAGGGGATCACCTTCATGACTCTGGAGTAAGCAGT--TTTCTT 3028
                         i     vi   ? vvv i    i    ii   iv  i   i --      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_102372436_   3029 AAACAGGACACAAAAAGCACTAAGCA-TGAAGGAAAAAGAT-TATGGATT 3076
                          i i v     v        -     -ii  i      -  -v  ii   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCAC-AAGCAACAAAAGAAAAA-ATAGATAAATT 638

  chrX_102372436_   3077 GCACTTTATTCATATTAAAA 3096
                          v    i  iv v       
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAA 658

Transitions / transversions = 1.44 (85 / 59)
Gap_init rate = 0.05 (24 / 507), avg. gap size = 4.08 (98 / 24)  

 580 22.30 2.60 5.95  chrX_102372436_102376606     3410  3678 (493)    L1M4_orf2#LINE/L1      649   908 (0)  

  chrX_102372436_   3410 AAAA--AAAAA---TTGTTTATCATACAACACCATTAAAAGAATGAGAAA 3454
                             --     ---    viv   v vi    i  i  i i i   i  i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_102372436_   3455 GCAACCTGCAAACTGGGAGAAGATATTTGCAACAAATATATCTAACAAAT 3504
                         i     ii  i v        i          vvv        i i  iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_102372436_   3505 GACTCATGTCCATAATGTATTATATAAAGAACTCTTAAAAATAAGTAAGA 3554
                             ii i    v   -----                v  v v i   v 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAAT-----ATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_102372436_   3555 AAAGGAAAGATAATACAATGGAAAAATGGG-AAAATATCTTTAAAAACAA 3603
                            i  v i    iv    v?         -   iv  --  i  v -i 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT--TTGAATA-GA 840

  chrX_102372436_   3604 CACTTCACAAAACAGAACATTTAATACAATAAATGTTCAATAATTTT-TG 3652
                           i   v v   --   v  ---      ---   vi      vivi-  
  L1M4_orf2#LINE/    841 CATTTCTCCAAA--GAAGAT---ATACAA---ATGGCCAATAAGCACATG 882

  chrX_102372436_   3653 AAAAGTTGTTCAACTTCATTACTTTT 3678
                              v  i     v   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (32 / 27)
Gap_init rate = 0.04 (10 / 260), avg. gap size = 2.30 (23 / 10)  


2908 25.06 2.22 1.88  chrX_102512874_102514896.rev      634  1535 (488)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_102512874_    634 AAGGACATACTGTGTTCATGAGTCAGAAGAGTCAGTATTGTTAAGACGTT 683
                           i  i  v ii        ii ii     v i i           i vi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_102512874_    684 TATTCCCCACAAACTAATATACAGATTCAGTGCAATCCCAATAAATGTTC 733
                         v  v i  v    i i  v          ii        v  v  vi i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_102512874_    734 TA--TACATTTTTCAAAGAAATTGGCAAGTGGATATTAAAAT-CATATAC 780
                         i -- i v     iiv        i    iv   vi      -     iv
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_102512874_    781 AAATACAGAACACCTAAACTGTGAAAAACAA-CTGTAAAATG--GAACAA 827
                             i  iiiv   i i v ivvv       -  vv    v --      
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_102512874_    828 AGGTATAGGACAAACACTACCTAATTTCAAAACTCATTATAAACCTACAG 877
                           v iv     vv     v  i            i i  i   v      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_102512874_    878 TAATCAAGACAGTGTGCTATTGCCATTGAAGGG--GAAAAGTAGATCAAA 925
                                         v  i  v   --    i--  v vi        v
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGATCAAT 301

  chrX_102512874_    926 AGGACAGAATAAGGAATCCAGAAGTAAACCTATGCACACACGGACAACTG 975
                         i i i     vii  i       i      i  i  ivi i  v   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_102512874_    976 ATTTTTGACAATGATGTAAAGACTATTCAGTGGAAAAGTAAATAGTCTTT 1025
                              i     v i  iv     i     i   ii  i-i          
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTT 400

  chrX_102512874_   1026 TCAACGAATGGTTCTGTAATAAGTAGATATCCATATACATACACAAAAAT 1075
                              i      v   vi i  v i    ?   ----   i  v  i   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCA----CATGCAAAAGAAT 446

  chrX_102512874_   1076 AAACTGTAATCCATATATCACAACATATACAAAA-TCAACTCAAACTGAA 1124
                         i  v vvi i  v  iv     v           - i        v  i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_102512874_   1125 TATGAGACCTAACTATAAAATCCAAATGTATAAA-CTCCTACAAGAAAAG 1173
                          vv?        v i   i v i   vv      -   i  v       v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_102512874_   1174 ACAGGAGTAAATCCTTGTGACTGTGAGT-AGGTAAACATTTTTTAGATAG 1222
                          i   ?       i i     iv  i  -   i  vvi   i       v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_102512874_   1223 GACATCAATAAAAACATCTTAACCCTAAATAAAAAAAT-TATAAATGGCA 1271
                             i   -  iv   ---- i vvi   vi       -v      v v 
  L1M4_orf2#LINE/    597 GACACCAA-AAGCACA----AGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_102512874_   1272 CTTCCTCAAGGTTAAAAATTTCTGCTCTTCTAAAAGCCACTGTTGAGAGA 1321
                             v    ii       i  i  iv    -   i v    i ii   i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTC-AAAGGACACTATCAAGAAA 690

  chrX_102512874_   1322 ATGAAAAGATAAGTCAATGACTGGGAAAAAGTATTTGAAGAATCGTATAA 1371
                         i        i  vi  vv  v     i   i      v -    i    v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATCATATAT 739

  chrX_102512874_   1372 CTGACAAAGAATTTATATCCAGAATATATAAAA---TC-----ATTTAAA 1413
                             i  i i i  i                 i---  ----- i i  v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_102512874_   1414 AGTAAAAAGTAAACAGACACTCCAATAAATAAATGGGAAAATAATAGAAA 1463
                          i       ---   i i vi     v? v       v   vi  vvi  
  L1M4_orf2#LINE/    790 AATAAAAAG---ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_102512874_   1464 CAGAAACTTTACCAAAGAATATATACAAATGGCAAGTAATCACATGAAAA 1513
                         i   v i  iv        v             v i   v          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_102512874_   1514 GATGTTTAACAATAATAGTCAT 1535
                             i i    vi ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (130 / 92)
Gap_init rate = 0.02 (19 / 905), avg. gap size = 1.95 (37 / 19)  


3224 27.20 0.55 0.55  chrX_102515870_102522244.rev     4977  5884 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102515870_   4977 TAGAAGAACATTCCATGCTCATGAGTAGGAAGAATCAATATCATGAAAAT 5026
                          i   ii i  i     i     ii v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102515870_   5027 GGCCATACTGCCCAAGGTAATTTATACATTCAGTGCCATCCCTATCAAGC 5076
                            v     v     iv i  i  i v     ii  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102515870_   5077 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5124
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_102515870_   5125 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5174
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_102515870_   5175 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5224
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_102515870_   5225 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5274
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_102515870_   5275 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGTCACATATCTACAACT 5322
                                i    i--    i  --        vvi  i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_102515870_   5323 ATCTGATCTTTGACAAACCCGACAAAAACAAGCAACGGGGAAAGGATTCC 5372
                          vi    i  i     ivvi v   i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_102515870_   5373 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5422
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_102515870_   5423 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5472
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_102515870_   5473 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5522
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_102515870_   5523 CTAAGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5571
                         v  i ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_102515870_   5572 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5621
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_102515870_   5622 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCACAGTGAA 5671
                           i   v v  i i   i  ii vv    i  v  i i  vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_102515870_   5672 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAAGCTATTCATCTGACA 5721
                         v  i     i                 v       iii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_102515870_   5722 AAGGGCTAATATCCAGAATCTACAATGAACTCAAATGAATTTACACGAAA 5771
                          i  i  vi          v  i  v      vv ii v iv i vv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_102515870_   5772 AAAACAAACAACCCCATCAAAAAGTAGACGAAGGATATGAATAGACACTT 5821
                           i     i     v  i?    i i i i      v          i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_102515870_   5822 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5871
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_102515870_   5872 CATCACTGGCCAT 5884
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3590 23.39 2.82 0.23  chrX_102554759_102557009.rev      876  1760 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102554759_    876 TGGAAAAGTATTTCATGTTCATTGATTGGAAGAATCAATATTGTTAAAAT 925
                               ii   ii         v          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102554759_    926 GTCCATTCTACTCAAAGCAATCTACAGATTTAATACAATCCCTATCAAAA 975
                          v v  v  v i    vii           i  ii               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102554759_    976 TACCAATGACATTCTCCACAGAAA----CAGAACAATCCTAAAATTCATA 1021
                          v   iivi v  i iii      ----  iivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_102554759_   1022 TAGAATCACAAAAGACCCAGAATTCCCAAAGCTATCTTGAGCAAAAAGAA 1071
                          i   vii   ii          vv     i v       iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_102554759_   1072 CAAAACTGGAGGAATCACAATACCTCACTTCAAATTATACTACAGAGCTA 1121
                             ii       v     v v  iv i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_102554759_   1122 TA-TCACCAAAACAGCATGGTACTGGCATAAAAACAGACACATAGACCAG 1170
                         i - v i   i    ii              ii i     i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_102554759_   1171 TGGAACAGAATAAAGAACCCAGAAACAAATCCACACACCTACAGTGAACC 1220
                              i     vi   ii       i   i   i   ii  ii  v  ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_102554759_   1221 CATTTTCAACAAAGA-ACCTATAC-------TGAGGAAAAGACAGTCTCT 1262
                         v      i    i i-i  v v  -------  i     ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_102554759_   1263 TCAATAAGTGGTGCTGGGAAATCTGGAAATCCATACGCAGAAGAATGAAA 1312
                             i  i           v v     v ?   i i   i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_102554759_   1313 ATAGACCCTCTATTTCTTGCCATATACAAAAATTAAATCAATATCAGTTA 1362
                         v i     -   ii  vii                 v    v  vii i 
  L1M4_orf2#LINE/    451 TTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_102554759_   1363 AAGGCTTAAATCTAAGACTTCAAACTATGAAACT------ACAAGACTTT 1406
                         ?  i i     v     vi v       i     ------ v  i  v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_102554759_   1407 GGGGAAACTCTCCAGGACATTGGTCTGGGCAAAGATTTCT-AGA-GTAAT 1454
                           ? v  v   i iv   v    vi i     v i     -   -i i i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_102554759_   1455 ACCCCAA-CACAGGCAACCAAAGCAAAAACGGACAAATGGAATCACATCA 1503
                            vv  -    i     v    v     ii  i    v i iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_102554759_   1504 AG-TTAAAAAGCTTTTGCACAGCAAAGGAAACAATCAACAAAGTGAAGAG 1552
                          i-       -      ii vv       v  v     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_102554759_   1553 ACAACCCACAGAATGGGAGAAAATATTTGCAGACTACCCATTTGACAAGG 1602
                                                        i ii ivi  i   i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_102554759_   1603 GATTAATAACCAGAATATATAATGAGCTCAAACAACTCTATAGCAAAAA- 1651
                           i vi  v             v  i   vv       v   ii     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_102554759_   1652 -TAACTAAACTGATTAAAAGGTGGGCAAAAGATTTGAATAGACATTTCTC 1700
                         -i  v   v ii   ?   ii        i                    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_102554759_   1701 TAAAGAAGACATACAAATGGCAGACAGGCATATGAAAAGGTGCTCAACTT 1750
                         i        i           vi i i   i        i        v 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_102554759_   1751 CATTGATCAT 1760
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.90 (133 / 70)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.25 (27 / 12)  


 625 18.50 2.89 10.98  chrX_102581912_102584312      636   808 (1593)    L1M4_orf2#LINE/L1       13   171 (737)  

  chrX_102581912_    636 CCATGCTCATGGGTCACAAACAATACTGAGAAGATTCAGTATTGTTAAGA 685
                              i      i ------------  -     i i i           
  L1M4_orf2#LINE/     13 CCATGTTCATGGAT------------TG-GAAGACTTAATATTGTTAAGA 49

  chrX_102581912_    686 TGTCAATTCTTCCAAAACTGATCTATAGATTCAGAGCAATTCAAATGGAA 735
                           v    v  i  v   i       i       iv     i vv  vi  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_102581912_    736 ATCCTA-----TTAAAAAATTTTTAAAGAAACCGACAGGCTGATTCTAAC 780
                             i -----i ------     iv     ii    i      i    v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCT------TTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_102581912_    781 ATTCATATGGACATGTAAAAGACCTAGA 808
                                    v   i  ii    i   
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGA 171

Transitions / transversions = 2.20 (22 / 10)
Gap_init rate = 0.03 (4 / 159), avg. gap size = 6.00 (24 / 4)  

2564 24.90 2.36 1.11  chrX_102581912_102584312     1190  1908 (493)    L1M4_orf2#LINE/L1      181   908 (0)  

  chrX_102581912_   1190 ACAACTTTGATAAAGAA---CAAAATTAGAAGACAAACACTACCTGATTT 1236
                             ii    v      ---    i  i  i   vv     v  ii    
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_102581912_   1237 CAAGACTCCTTACAAACATACAGTAATCCAGACAGTGTGCTATTGGCATC 1286
                            i   ivi      vv          v          v  i      v
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_102581912_   1287 AAGATGGAT-TAGTAGATCAAAGGAACAGAATAAAGAGTCCAGCTATAGA 1335
                          i   i  i-  -        v    i     vi         vv   i 
  L1M4_orf2#LINE/    281 AGGATAGACATA-TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_102581912_   1336 CCCACAAGTATATGGACAACTGAGTTT-GACAAAGATGCAATGGTGATTC 1384
                             i vi v     v   i   v   -     i i   v v iiv    
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_102581912_   1385 AGTGGAGAAAGGATTATTGTTTCAACAAATGGTGCTGGGACAAGTGAATA 1434
                          i   i     i  vi iv                        v  i   
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_102581912_   1435 TTGACATGCACAAATATAAACTGTGACTCAGATATCACACTATATACAAA 1484
                         ?iv       v  iv  i  v vv   i vv iv      i         
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_102581912_   1485 AGTCTATTCAAAATGGACCTGAGATCTAAATATAAAATTTGATGCTATAA 1534
                          i iv i          i v?   i      i   i vi i vi      
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_102581912_   1535 AACTTCTAGCAGAAAAAAAAAAAACAGGAGAAAATCTTTTTGACAATGGG 1584
                             ii   ------  i    v i   ? v       iv    vv    
  L1M4_orf2#LINE/    530 AACTCTTAG------AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_102581912_   1585 TCAGGTGAAGATTTCATAGATGAGACAACAAAACCACAATCTATAAGCAA 1634
                          i   ii v i    v     iv    v     v     v v i  ivi 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_102581912_   1635 AGAAATTGAAAAATTGGACTTCCTCAAAGTTAAAAACTTTAGC-TTTCCA 1683
                          i    v  v            v     i           v i-i   v 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_102581912_   1684 ACTACATGGTTGAAAAAATAGACAAGTAAGCTGCTGACCGGGGTAAAATG 1733
                          vv   ivi ii i   i ii v iii  v ii v  vi   iv     i
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_102581912_   1734 TTTGAAAATTATATATTTAATAAAGGACTTGTATCCAGAATATGT----- 1778
                             v    i      i i    i                   i -----
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_102581912_   1779 ----TTAAAATCTTAGTAAGAAGAAAACACACA--CCAGTAAAGAAACAG 1822
                         ----   v  -  i i   v  i  i   v i --   i v? i   ii 
  L1M4_orf2#LINE/    774 ACTCTTACAA-CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_102581912_   1823 GCAAAATATTTGAATAGACATTCCACTAAAGAAGACATACAAATATCATG 1872
                              iv               i v i        i        iv vvi
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_102581912_   1873 TAAGCACAGGAAATGATGCTCAGCATCACTCGTTAT 1908
                                 v    v        i     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (100 / 75)
Gap_init rate = 0.01 (9 / 728), avg. gap size = 2.78 (25 / 9)  


2962 23.41 1.80 2.64  chrX_102605603_102609613     2686  3518 (493)    L1M4_orf2#LINE/L1       83   908 (0)  

  chrX_102605603_   2686 ATGCAATCCCTATCAAAACTCCCA--TGACTTTTTTCATAGAAAAAGAAA 2733
                          i                -     --  v       -ii     vv  v 
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAA-TCCCAGCTGCCTTTTTT-GCAGAAATTGACA 130

  chrX_102605603_   2734 ACACAATCCTAAAATTTATAAGAAACCACAAAAGACCCTGAATAGCAAAA 2783
                          vvii           i   v i  vii   ii     v       v   
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chrX_102605603_   2784 GCAACCTTGAGAAAGAAGAACAAAGCAGGAAGCATCACATTCCCTGATTG 2833
                         i   i     i              iv   i vv     i i  ii   v
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_102605603_   2834 CAAACTATAGGACAAAGATATAGTAATCAAAACAGCATGGTACTGGCATA 2883
                             viv  vv      v  i         i    ii             
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_102605603_   2884 ATAAAAACAGTCACATAGACTAATAGAACAGAGT--ATAGCCGAGAAATA 2931
                          ---ii i  v  i     ii   i   i   i -- v  i v       
  L1M4_orf2#LINE/    281 A---GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_102605603_   2932 AGTTCACACATACAGGGTCAACTAATCTTTGACAAGGGCACCAAGAATAC 2981
                          iii  i    vi v      i i  i  i        ii      vi i
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_102605603_   2982 ACAATGATGAAAGGAAT-GTGTCTTCAATAAATAGTGTTGGGAAAACTGA 3030
                         v     iv     -   -  v i     i    i   i     v     i
  L1M4_orf2#LINE/    378 TCAATGGGGAAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_102605603_   3031 ATATCCACATGCAAAAAAAAATGAAATTGGACCATTGTTTCATACCATAT 3080
                            ?            i  --    i       vi iii   i       
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAA--TGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_102605603_   3081 TCAAAAATTAATTCAAA-TGCATTAAAGACTTAAACATAAAATCTGAATC 3129
                         v          i     -  v  i ?    i    ii   i v  i  v 
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_102605603_   3130 CGTAAACCTCCCAGAAGATGACATAGGGAAAAAGCTCCTTGACAT-GGGT 3178
                         ii    v   ii      vi       ?iv   v  i v    v -    
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_102605603_   3179 CTTGGCAATTTTTTTTT-GATATGACTCCAAAAGCAAAGGCAACTAAAGC 3227
                         - v      vv   i  -        v         v i     v    v
  L1M4_orf2#LINE/    575 -TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_102605603_   3228 AAAAATAAACAAGTAGAATTACATCAAACTAAAAAATTTCTGCATGGCAA 3277
                                i i  i v i i v       v v     i  i  iiivv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_102605603_   3278 AGGAAAC----AACAAAATGAAAAGGCAACCTATGGGATGAGAGAGAATA 3323
                             v  ----  v   i       i     i ii i   i    i    
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_102605603_   3324 TCTGCAAACCACATAGCTGATAAAGAGTTAACATCCAAAACATGTAAGGA 3373
                          i      i  i   v       i iii vii     i  i  i   i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_102605603_   3374 ACTCACACCATGCAATAGGAAAAAAAAAAAAAACCCAAACAACTCAAT-A 3422
                             vi  v iv     iv     i ---------    i   i    -?
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGA---------CAAATAACCCAATTW 814

  chrX_102605603_   3423 AAAAATAG-CAAAGAACCTGAATTGGTACTT-TCCAAAGAAGATATAAAA 3470
                               i -     i ii     v ii i  -               v  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_102605603_   3471 ATGGCCAACAGTATAGTGTAGGAAAAGGTGCTCAATATCACTAATCAT 3518
                                 i ----  iii v      i       i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATA----AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (127 / 64)
Gap_init rate = 0.02 (18 / 826), avg. gap size = 2.06 (37 / 18)  


4527 15.34 2.91 1.23  chrX_102627984_102630340      972  1864 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102627984_    972 TGGAAATGCATTCTGTGTTCATGGATTGAAAGACTTAATATTGTTAAGAT 1021
                               vii  i ii             i                     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102627984_   1022 GTCAGTACTAACAAAAGTGATCTATAGATTCAA-----TCCCTATCAAAA 1066
                          v  i    vv v   v       i        -----            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102627984_   1067 TCTCAATGATGCAATGATGTTTTTTGCAGGAATAGAAAAATGCATCCTAA 1116
                           i  -- v   v------          i   v  v  iivv       
  L1M4_orf2#LINE/    101 TCCCA--GCTGCC------TTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_102627984_   1117 AATTCATATGGAATCTCAAGGGATACTGAATAACTAAAACAATCTTGAGA 1166
                                      viv       iv v     i i             i 
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_102627984_   1167 AAGAAGAACAAAGTTGGAGGTCTCACACTACCAGATTTTAAAACTTACCA 1216
                                             v        v  vi    i         i 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_102627984_   1217 AAAATCTACAGTAATCAAAATAGTATGGTACTGGCATTAAAGACAGACAA 1266
                         v   v             i i   i            -  i  i     v
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACAT 291

  chrX_102627984_   1267 ATAAACTAATGAGATAGAATAGAGAGCCTAGAAATAAACTCTCACTTATA 1316
                            i ii    ii       v     i i          i vi  v v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_102627984_   1317 TGAT-AATTGATTTTTGACAAGGGTGCCAAGACCATTCCATGAGGGAAAG 1365
                           i -          i                      v   -       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAG 390

  chrX_102627984_   1366 GACAGTCTCTTTAATGAATA-TGTGAGGAAAACTGAATATCCACATGCCA 1414
                         i i     i  i  ii   i-  ivi   v     i   ?        v 
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_102627984_   1415 AAGAATGAATTTAGATACTTCCCTTACACCATATACAAAAATAAACTCAA 1464
                                  v  i  iv i v   i                 v       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_102627984_   1465 AATAGATCAAAGCCCTAAATGTAA-ATCTAAAACTATCAAACTCTTAGAA 1513
                            i     ?  v           - v          v            
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_102627984_   1514 GAAAACATGGGGGGGAACCTTCATGACATTAGTTTTGGCAATGATTTCTT 1563
                                 i  ? vi  i    i    v  i v  v       i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_102627984_   1564 GGATA--ACA---AAAGCACAGGCAACAAAA-----AATAGATAAATTGG 1603
                         i    --   ---        i         -----              
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_102627984_   1604 ATTT-ATCAAAAT---AAACTTATGTGCATCAAAGGACACTAACAACATG 1649
                          i  -        ---      v     v             v   v vi
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_102627984_   1650 GTGAAAATGCAATCCATGCAATGGGAGAAAATATTTGCAAATCATATATC 1699
                                vi   i   iiv                               
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_102627984_   1700 TCATAAGGGACTAATATTTAGAATATATAAATAACTCCTACAACTCAACA 1749
                          v          vi   ii            v     i          i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_102627984_   1750 ATAAAAA---AAATAATCGAATTAAAAACTCGGCAAAGGACCTGAAT-GA 1795
                                ---      i v    ?    v v         ii     -  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_102627984_   1796 CTATTACTCCAAAGGAGATATACAGATTGCCAATAAGTACACGAAAAGAT 1845
                          -   v        i         i  v         i   i        
  L1M4_orf2#LINE/    841 C-ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_102627984_   1846 GCTCAACATCACTAATTAG 1864
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (77 / 56)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.31 (37 / 16)  


4178 16.01 8.96 0.48  chrX_102639167_102641346.rev      853  1689 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102639167_    853 TGGAAAACCATTCTATATTCATAGATCTGAAGACTTAGTATT-------- 894
                               ivi  i i  i     i   iv         i    --------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102639167_    895 ---------TCCAAAATTGATCCATAGAATCAGTGTAATCTCTATCAAAA 935
                         ---------i  v         i i   v   ii i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102639167_    936 TCTTATCTGGCTTCTTTGCAGAAATTGGTAAGCTGATCCCAAAATCCACA 985
                           ii v   v   i             ii          i     i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_102639167_    986 TGAAAATGCAGGAAACCCAGAATATACAAAACAATATTTAAAAAAAAGGA 1035
                           i       i ii          vv         v  v     i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_102639167_   1036 AAACATTGGAGGTCTCACACTTCCAGATTTC------TA----------- 1068
                         v  vi       v           vi     ------  -----------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_102639167_   1069 ------TCAAGGCAGTGTGGTACTGGCATAAGGA----CATATAGATCAA 1108
                         ------     i                      ----            
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_102639167_   1109 TGGAATATAATTGAGAGTCCAGAAATAAGCCCTCATACCTA----CAGTT 1154
                                v                    i   vi i ii  ----  i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_102639167_   1155 G--------------TGCCAAGAAAATTCAACTATGAAAGAATAGTCTTT 1190
                          --------------        vv      iviv               
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_102639167_   1191 TTAACAAATGGTGCTGAGACAAATGGATATCTACCTGCAGAAAAAATGAA 1240
                          i              i     v      ? i  v    -   i      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAATGAA 449

  chrX_102639167_   1241 TTTGGGCCTCTTTTTCACACCATCTACAAAA--CAATTCAAAATAGATTA 1288
                         v    i  i  vii         v       --i  i       i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_102639167_   1289 AAGTCCTAATTGTAAGAGCTAAAACTATCAAATTCTTAGAAGAAAACTTA 1338
                         ?  v     v                  v   i              v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_102639167_   1339 GGTGTAATTCTTTATGACCTTGGATTAGGCAATGGTTTTTTAGATATGAC 1388
                           ?    v    ii         i              i           
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_102639167_   1389 AACAAAAGCTCAAGAAACAAAAGAAATA-TAGATAAATGAGGCTCCATCA 1437
                          v       v    v           v -         vi i  i     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_102639167_   1438 AAATGCACAATTTTTATGATTCAAAGGACATCATCAGGAAAGTGAGAAGA 1487
                             vv v  i    i  v           ii    i        i    
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_102639167_   1488 CAACTAACAGAATAGGA-AAAATTTTTGCGAGTAATGTATCTGATAAGGG 1536
                             iv       i   -     v     i i v  i             
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_102639167_   1537 ACTTGTATCTATAATACATAGAGAATACTTACAACTAAATAATTTTAAAA 1586
                                  i v    i   i    iv         v      ---    
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT---AAAA 796

  chrX_102639167_   1587 A---------CCCAATTTTAAAATGGGCAAAGGATCTGAATAGGTATTTC 1627
                          ---------       ?v                i       ii     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_102639167_   1628 TCCAAAGAAAATATACAAATGGCCAATAAATACATGAAAATGTGCCCAAC 1677
                                  i                   ii         vi   i    
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_102639167_   1678 ATCATTAGCCAT 1689
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (83 / 47)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 6.58 (79 / 12)  


 764 26.09 13.74 2.96  chrX_102667245_102668796      500  1074 (478)    L1M4_orf2#LINE/L1      272   908 (0)  

  chrX_102667245_    500 ACTGGTATATGGATAG-CAAACAGACCAATGAAATAGAATAAAAAGCCCA 548
                              i   v      -  v i   i     i        vi i  i   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_102667245_    549 GAAGGTTTTCCAAGTACAT--ATGGATATTTGATATGTAATAAAGGTGGT 596
                            ivvvvi   --     --    vi v     v vii i  i    --
  L1M4_orf2#LINE/    322 GAAATAAACCCA--TACATTTATGGTCAATTGATTTTCGACAAGGGTG-- 367

  chrX_102667245_    597 ATCTCAAATCCCTAAA---GCAAAGA-TGGACTTTC-------TGATGCC 635
                         -- iv i i vi v  --- v     - i v    i-------  i   i
  L1M4_orf2#LINE/    368 --CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_102667245_    636 AGAACAACTGAGAAACCGATTGGAAAAAGAAAACAAAAGATCCATCAATA 685
                         i i       -  v ? v ivv v       vi---   v vv i vv  
  L1M4_orf2#LINE/    416 GGGACAACTG-GATAKCCACATGCAAAAGAATG---AAGTTGGACCCCTA 461

  chrX_102667245_    686 CTTTATGCCATACACAAATATAAACTC-----------------TAAATG 718
                          i i ii     i     v  v     -----------------      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_102667245_    719 TAA-AG--AAAACCATATGAATACTAGAAGAAAACATGGGTG--AATGCT 763
                            -  --     i   vi v vi             i  ? --   -  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CT 560

  chrX_102667245_    764 TCTTGGACCTTATGT-AGGAAAAGATTTCTTAACTATGA-ATCGAAATCT 811
                           v  -     iv  -   v  v i       iv     - i i   v -
  L1M4_orf2#LINE/    561 TCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC- 608

  chrX_102667245_    812 AGAGGCAATAAAAGT-----TAAATAAATTTGACTACTT-----TT---- 847
                          v i    i     v-----  i       v    v v -----  ----
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_102667245_    848 --TTTAATGCATGGCAGAAAAACACCATAAACAAAGCCAAAAAGCAACTG 895
                         --   vi   v --  -  ii    i  v  v    iv    ii    iv
  L1M4_orf2#LINE/    659 ACTTTTGTGCTT--CA-AAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_102667245_    896 ACAAACTGGAGAGAAAAT---TGCAA--CATATAT-----AACAG--TT- 932
                            i v   -        ---     --       -----  vi --  -
  L1M4_orf2#LINE/    706 ACAGAATGG-GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_102667245_    933 -------AATGTATTAAGAAAACTTGAAAATTGAGGTGAGAAGGACCAAC 975
                         -------   i   v     vv   iv  v ii vivv i  i   v  i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_102667245_    976 AACCCACTAGAAAAATGTGGAAAAGACATGAACCGACAATTCACAAAGAA 1025
                               v v?       v v   i  iv    iv    v   v v  ii 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_102667245_   1026 AGATATTTAAATTGTCCTTAAACACA-GATAAGG----CAAAATAAAATG 1070
                               vi    v i vv   i    -  v   i----   v  v ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_102667245_   1071 CCAT 1074
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 0.93 (71 / 76)
Gap_init rate = 0.05 (31 / 637), avg. gap size = 3.10 (96 / 31)  


4187 17.97 3.16 0.56  chrX_102672972_102675082      741  1625 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102672972_    741 TGGAAATAAATTCAATGTTCATTGATTGAAAGACTTAACATTGTTCAGAT 790
                               v v  i v        v     i         i      v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102672972_    791 GGCAATATTCCCTAA-TTGATTTACAGACTTAAGGCAATCACTATCAAAA 839
                                i    i  -     i      i i  v      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102672972_    840 TCTCCCCTGGCTTCTTTGCAGATAATAACAAAGTGATCCTAAA--TTATA 887
                           i vv   v   i        v v i    iv          -- i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_102672972_    888 -----ATG------ACCCAAAACAGACAAAACAATCTTGAAAAACAATAA 926
                         -----   ------     i  i  v                  v  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_102672972_    927 CAAA--TGGAGTTCTTACACTTTCTAACTTCAAAACTTACCACAAAGCAA 974
                             --     vv  i      i i  i            i       v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_102672972_    975 TAGTAATCAAGACAGGGTGGTCCTACCATAAGGATAGATATATAAATCAA 1024
                         i              v     v  iv            i     i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_102672972_   1025 TGGAATAGAATTGGGAATCCAGAAGTAAACTCTCACTTTTATGCTCAATG 1074
                                      i  i       i     i vi  v      v     v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_102672972_   1075 GATTTTCAACAAGTCTGCCAAGACAATTCAAAGGGAAGATAATAGT-TTT 1123
                                i     vv         v      v   i i v      -   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_102672972_   1124 TAAACAAATTGTGATGAAACCATTAGATATCCACATGCCAAAGAATGAAT 1173
                          v       v   v  ii  v i i    ?        v          v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_102672972_   1174 TTAGAACATTATGTCACACCCTACATCAAAGTGAACTCAACACAGATCAT 1223
                           i  v vi  iv       v  i iv   i v       v ii     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_102672972_   1224 AAATATAAATGAAAGAGCTAAAACTATACAGCTCTTAGAAGAAAACATAT 1273
                          i iv      v                v i                  v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_102672972_   1274 GCATAAATATTCATGACCTTGAGTTAGGCAAT--TTTACTTAGATACAAT 1321
                          ?i     v   i        i          --   -        ii i
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-CTTAGATATGAC 599

  chrX_102672972_   1322 AACAAAATCATATATGACAAAAGA---------TACATTCTACTTCATGA 1362
                          v     v  i viii        ---------  v   vv       v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_102672972_   1363 AAATGGAAACGTTTTGTGCTTCAAATGATAACATCGAGAAAATGAAAAGA 1412
                             vi   vv              v  i vi   i     i        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_102672972_   1413 TGATCCACCAGATGGGAGAAAATAACTGCAAATAATACATTTGATAAGGA 1462
                         ii i    vii             vi       v   i  i        i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_102672972_   1463 GCTAATTTCCAGAATATATAAAAAACTCTTACAACTCAACCATTAAAAAA 1512
                         i  vi v               i                iv  -     i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAAAAG 798

  chrX_102672972_   1513 AAAGAGAACCCAATTTTAAAATGGGCAAATGATTTGAATAGATATTTCTC 1562
                          v i v         ?v            v            i       
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_102672972_   1563 CCAAGAAGATATACAAATGTCCAATAGGCATATGAAAAGAAGCTCAACTG 1612
                          v                 v      i   i         v       --
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC-- 896

  chrX_102672972_   1613 TATTAGTCACTAG 1625
                         -  i ????????
  L1M4_orf2#LINE/    897 -ATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (81 / 74)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.00 (33 / 11)  


4116 15.66 0.88 3.54  chrX_102864027_102868369.rev     2627  3418 (925)    L1M4_orf2#LINE/L1        2   772 (136)  

  chrX_102864027_   2627 GGAAAGGTGTTCTGTTTTCATGAATTGAAAGGCTCAATATTGTTAAGGTG 2676
                               i i i ii v      i    i   i  i            i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_102864027_   2677 GCAATATTCCCCAAATTGATCTATAGAATCAATATAATCCCTGGCAAAAT 2726
                               i                i   v    iii       iv      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_102864027_   2727 CCAAGCTGTTTTGTTTTGTCTTGTTTTGTTTGCAAAAACTGACAAGCTGA 2776
                           v     ii  -     --------------  i   i           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTT-TTTTG--------------CAGAAATTGACAAGCTGA 136

  chrX_102864027_   2777 TGCTGAAATTGATGTTGAAATTGATATGGAAGTGCAAAGAGCTCAGAATA 2826
                          v  i     v  ------------      i     i ii i       
  L1M4_orf2#LINE/    137 TCCTAAAATTCAT------------ATGGAAATGCAAGGGACCCAGAATA 174

  chrX_102864027_   2827 GCTAATACAAACTCGGAAAAGAA---TAAAGTTGGAGGACTCACATTTGT 2873
                           i  v    v  i i       ---i                  i  vi
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_102864027_   2874 TGATTTCAAAACTTACTACAAAACTACAGTAATCAAGACAGTGTAATAAT 2923
                         ii                    i                     ii  v 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_102864027_   2924 GACATAATAATAGACACATAGGTCAATGGGATAGAATTGAGAACCAAGAA 2973
                          i     vi       i    i       i            ii v    
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_102864027_   2974 ATAAACCCTTACATTTATGATGAATCTATTTTCAAAAAGACTGCCAGGAT 3023
                                 v          i v   iv      i v   iv     i  i
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chrX_102864027_   3024 AATTTAATGGGGGAAAGAATAATCTTTTCAACAAATG-TGCTGGGATGCC 3072
                         v   i       -        i               -        iiv 
  L1M4_orf2#LINE/    375 CATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_102864027_   3073 TGAATATCCACATGGAAAACAATGAAATTGGACTCCTGCCTCACAGTATA 3122
                           i   ?       v    v      i      i   i       vi   
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_102864027_   3123 AACAAAAATTAACTCAAAATGAATTATAGATGTAAAGGTAAGTGTTAAAA 3172
                         v                    i  i ?   iv    v     v i     
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_102864027_   3173 CTATAAAACTCTTAGAAGAAAACATAGGTAAAAATCTGTGTGACCTTAGA 3222
                                                     ?iv      vi        i i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_102864027_   3223 TTAGGCAATGATTTCTTAGATATGATAGCAAAAACAAGAGCGACAAAAGA 3272
                                   i              i v     i  vi   i        
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_102864027_   3273 AAAAATAGATAAATTTGACTTCATCTAAGTTAAATACTTTTTTGCTTCAA 3322
                                        v         v  i     v      v        
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_102864027_   3323 AG-CCACCATCAAGAAAGTTAA--GACAACACAAAGAATGGGAGAAAATA 3369
                           -v   i           v  --      v  v                
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_102864027_   3370 TTTGAAAATCATGTATCTGACAAGGAACTGGTAGCTAAAATATGTAAAG 3418
                             v       i       i    i   v   v i i     i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

Transitions / transversions = 1.95 (80 / 41)
Gap_init rate = 0.01 (8 / 771), avg. gap size = 4.38 (35 / 8)  

 531 13.43 11.19 0.00  chrX_102864027_102868369.rev     3719  3852 (491)    L1M4_orf2#LINE/L1      760   908 (0)  

  chrX_102864027_   3719 AAAATATGTAAAGTACTC--ATAACACAATAATA----GACAAATAA--- 3759
                          i     i     v    -- i   v        ----         ---
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_102864027_   3760 --TTTTAAAATTGGCAAAATATCTCA-TAGACATTTCTCTAAAGA---TA 3803
                         --  ?v     v      iv  i v -            i     ---  
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_102864027_   3804 TACAAATGGACCATAAGTACATGAAAAGATGTTTAACATCATTAGTCAT 3852
                                  v v     i             i i       ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.03 (5 / 149), avg. gap size = 3.00 (15 / 5)  


3007 27.81 0.99 0.77  chrX_102874129_102878416     2890  3795 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102874129_   2890 TGGAAAAACATTCCACGCACATGGATATGAAGAATCAATATCATGAAAAT 2939
                               i i  i   i iv       vv     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102874129_   2940 GGTCTTACCGCCCAAAGTAATTTATAGATTCGATGCTATCCCCATCAAGC 2989
                           ivv   iv      v i  i  i      i i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102874129_   2990 TATCAATGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTATACTTCA 3037
                          vi  iivi i  i  ii    i-   -- v  i  - iii  v v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_102874129_   3038 TATGGAACCAAAAAAGAGCTCGCATAGCCAAGACAATCCTGGGCAAGACG 3087
                                viiv  ii  v iv v        i      i  iiv    v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_102874129_   3088 AACAAAGCTGCAGGCATCAAGCTACCTGACTTCAAACTTTACTACAAGAC 3137
                                i  v   vv   vi  v  ii i      vi         ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_102874129_   3138 TACAGTAACCAAAACAGCATGGTACCGGTACCAAAACAGATATATAGACC 3187
                                 i   i    ii      i  i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_102874129_   3188 AATGGAACAGAACAGAG-GTCTCAGAAATAACACCACACATCTACCACCA 3236
                                i    iv   -   -         vv   i    i  ivii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chrX_102874129_   3237 TCTGATCTTTGGCAAACCTGACAAAAATAAGAAATGGGGAAAGGATTCCC 3286
                         vi    i  i i   ivv  v   i vi vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_102874129_   3287 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAGCTG 3336
                          v  i  i              v      v  ?   i   iii  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_102874129_   3337 AAACTAGACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 3386
                           ii i       v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_102874129_   3387 TAAAGTCTTAAACGTAAGACCTAGGACCATAAACATCCTAGAAAAAAACC 3436
                         i ?  v i    i      v   ii  i     vv  i     i     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_102874129_   3437 T--GAGCAATACCATTCAGGACATAGGCATGGGCAAAGACTTC--AAGTC 3482
                          -- ? i  - i -   iv   v v  vv i     v ii   -- ii v
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_102874129_   3483 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 3532
                          i --           vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    596 TGA--CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_102874129_   3533 TAATTAAACTAAAGAGCTTCTGCACAGAAAAATAAACTATTATCAGAGTG 3582
                          v  i   v v  i i   i  ii vvv   iv v     i vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_102874129_   3583 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGA 3632
                           v  i     i                 v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_102874129_   3633 CAAAGGGCTAATATCCAGAATCTATACAGAATTTAAACAAATTTACAAGA 3682
                         i  i  i  vi          v    v    i ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_102874129_   3683 AAAAATCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 3732
                             iv    i     v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_102874129_   3733 TTCTCAAAAGAAGACATTTATTCAGCCAACATACATATAAAAA--TGCTC 3780
                              v        i  vi vvii     i vi  i  i    --     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_102874129_   3781 ATCATCACTGGTCAT 3795
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


4635 14.42 6.68 0.35  chrX_102896850_102898863      669  1521 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_102896850_    669 GGAAAGATATCATATGTTTGTGGATTGAAAGAC--AATATTTATAAGGTG 716
                                    vi     ii       i     --      vv    i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_102896850_    717 GAAATACTCTTCAAATTGATCTACAGATTCAACGCAATTCCTGTCAGAAC 766
                          v       ii                           i   i   i  i
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_102896850_    767 CCCAGCTGGCTTCTTTGTAGAAATTTACAAGCTGATCCTAATATTCTTAT 816
                                 v   i    i       v               v    v   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_102896850_    817 GGAAACTCAAGGAACCCAGAATAGCCAACACAATCCCG-----------C 855
                              iv     i               v      ii ----------- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_102896850_    856 AA-----GAGAACTCAGCCTTTTCAATTTCAAAACTTACTACAAAACTAC 900
                           -----   i     vv   ii                      i    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_102896850_    901 AGTTACCAAAATAGTGTGGTACTGGCATAAGGCTA-ACATGTAGATCAGT 949
                            v i   i i                    v  -    i       i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_102896850_    950 AAAATATAATTGAGAATCCAGAAATAAACACACGTGTCTATGGTCAATTG 999
                         ii    v        i             v  iiii i            
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_102896850_   1000 ATTTTCAACAAAGCTGCCAAGGCCATTTAATGGGGAAAGAATAGATTTTT 1049
                               i    i v       i     i                - i   
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG-TCTTT 400

  chrX_102896850_   1050 TCAACAAAGTGTGCTGGAATAACAGGATAGCCACATGCAGAAGAATGAAG 1099
                                 vv       i i   v     ?         i          
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_102896850_   1100 TGGGACCCTCACCTCACAGCACATACAAAA-TTAACTAAAAATGGATTAT 1148
                          v      ii        v  i        -      v         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_102896850_   1149 A----------------------CTATAAAATTGTTAGAAGAAAGCA--G 1174
                          ----------------------        i v          i  -- 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_102896850_   1175 TAGTAAGTCT----GGTCTTGAGTTAGGCAATGGATTCTTAGATATGACA 1220
                         v?    i   ---- ii    i            v               
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_102896850_   1221 CCAAAAGCAAGGGCAACAAAAGAAAAAATAAATAAATTGGACTTCATGAA 1270
                                  vii                  i                v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_102896850_   1271 AATGAGAAATGTTTGTGCTTCAAAGAACACTATCAGAAATGTAAAAAGAC 1320
                            v i   iv              i         ii  v  i       
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_102896850_   1321 AACTCACAGAATAAGGGAAAATATTTGCAAATAATATACTTGATAAGGAA 1370
                            i        ii i                v     ii        i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_102896850_   1371 GTT--ATCTAGAACATATTTAAAAAAATCTTACAACTCAAAGATAAAAAG 1418
                         v  --   i    i    --   i  v             vi        
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATAT--AAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_102896850_   1419 A----TAACCCAATTTAAAAATGAGCAAAGCATCTGAATAGACTTTTCTT 1464
                          ----          ?       i      v  i         v     i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_102896850_   1465 C---GCAGATGTACAAATGATTAATAAGCACATAAAAAGATGCTCAGCAT 1511
                          --- v    i        iii           i            i   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_102896850_   1512 CATTAATTAT 1521
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.13 (81 / 38)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 4.62 (60 / 13)  


3178 27.45 0.55 0.44  chrX_102928269_102934195     4528  5434 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102928269_   4528 TGGAAGAACATTCCATGCTCATAGGTAGGAAGAATCAGTATCATGAAAAT 4577
                              ii i  i     i    i i v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102928269_   4578 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4627
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102928269_   4628 TACCAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4675
                          v   iivi    i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_102928269_   4676 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4725
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_102928269_   4726 AACAAAGCTGGAGACATCACGCTACCTGACTTCAAACTATGCTACAAGGC 4775
                                i     ivv    i  v  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_102928269_   4776 TACAGTAACCAAATCAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4825
                                 i   iv   ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_102928269_   4826 AATGGAACAGAGC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 4873
                                i   ii--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_102928269_   4874 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCACTGGGGAAGGGATTCC 4923
                          vi    i  i     ivv  vv  i v  vv  v       i i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_102928269_   4924 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4973
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_102928269_   4974 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5023
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_102928269_   5024 T-AAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5072
                          - ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_102928269_   5073 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5122
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_102928269_   5123 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5172
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_102928269_   5173 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGCGAAT 5222
                          i   v v  i i   i  ii vv    i  v    i  vv i  i   v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_102928269_   5223 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5272
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_102928269_   5273 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAT 5322
                         i  i  vi          v  i  v      vv    v iv i  v   v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_102928269_   5323 AAACAAAGAACTCCATCAAAAAGTGGGCAAAGGAGGTGAACAGACACTTC 5372
                          i     v   i v  i?    i           vv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_102928269_   5373 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5422
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_102928269_   5423 ATCACTGGCCAT 5434
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2968 26.43 1.43 1.43  chrX_102952825_102964832.rev     5004  5911 (6097)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102952825_   5004 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5053
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102952825_   5054 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5103
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102952825_   5104 TACCAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5151
                          v   iivi    i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_102952825_   5152 TATGGAAC--CAAAAAACAGCCTGCTTTGCCAAGTCAATCCTAAGCCAAA 5199
                                v--   iii  --  v vv v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_102952825_   5200 AGAACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAG 5249
                                  i      vv   vi  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_102952825_   5250 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5299
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_102952825_   5300 CCAATGGAACAGAAC--ACAGCCCTCAGAAATAATGCCACATATCTAGAA 5347
                         i        i    i-- v  i  --        vv   i i  i  vii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_102952825_   5348 CCATCTGATCTTTGACAAACCTGACAAAAAAAAGAAATGGGGAAAAGATT 5397
                         i  vi    i  i     ivv  v   i vv vvv          ii  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_102952825_   5398 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5447
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_102952825_   5448 CTGAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCACGATG 5497
                         v    ii    i    v   i     v     v        i   vi   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_102952825_   5498 GATTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5547
                            i ?   ii       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_102952825_   5548 ACCTA--CACAATACCATTCAGGACATAGGTATGGGCAAGGACTTCATGT 5595
                           v  --?ii  - i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    545 ACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_102952825_   5596 CTAAAACACCAAAGGCAATGGCAACAAAAGTCAAAATTGACAAATGGGAT 5645
                         v  vi        i   vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_102952825_   5646 CTAATTAAACTAAAGAGCTTCTGCACAGGAAAAGAAACTATCATCGGAGT 5695
                         i v  i   v v  i i   i  ii vvv   i  v       vvii   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_102952825_   5696 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTG 5745
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_102952825_   5746 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 5795
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_102952825_   5796 AAAAAAACAAATAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGCCA 5845
                              i           v  i?    i           iv    i  v  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_102952825_   5846 CATCTCAAAAGAAGACATTTATGCAGCCAA-AACCACAATGA---GATAC 5891
                         iv    v        i  vi viii     -  v    -   ---   i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA-TGAAAAGATGC 891

  chrX_102952825_   5892 CATCTCA-CACCAGTTAGAAT 5911
                         ----   -  i  ????????
  L1M4_orf2#LINE/    892 ----TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  

3256 26.98 0.44 0.44  chrX_102952825_102964832.rev    10610 11517 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_102952825_  10610 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 10659
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102952825_  10660 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 10709
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102952825_  10710 TACCAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 10757
                          v   iivi    i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_102952825_  10758 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 10807
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_102952825_  10808 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 10857
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_102952825_  10858 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 10907
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_102952825_  10908 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 10955
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_102952825_  10956 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 11005
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_102952825_  11006 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 11055
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_102952825_  11056 GAAACTGGATCCCTTCCTTACACCTTATATAAAAATCAATTCAAGATGGA 11105
                            ii    i    v   i     v    i      i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_102952825_  11106 TTAAAGATTTAAAAGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 11155
                          i ?   ii    v  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_102952825_  11156 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 11205
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_102952825_  11206 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGCCAAATGGGATCTAA 11255
                         i            vvi          vv     v vi    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_102952825_  11256 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 11305
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_102952825_  11306 AGGCAACCTACAACATGGAAGAAAATTTTCGCAACCTACTCATCTGACAA 11355
                           i     i   iv    i       v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_102952825_  11356 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 11405
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_102952825_  11406 AAACAAACAACCCCATCAAAAATTGGGCGAAGGACATGAACAGACACTTC 11455
                          i     i     v  i?    v     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_102952825_  11456 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 11505
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_102952825_  11506 ATCACTGGCCAT 11517
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 569 27.56 0.64 1.28  chrX_102995312_103001775.rev     4758  4913 (1551)    L1M4_orf2#LINE/L1        1   155 (753)  

  chrX_102995312_   4758 TGGAAAAACATTCCATGCTCATGGATAGGAAGAGTCAATATCATGAAAAT 4807
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_102995312_   4808 GGCCATACTGCCCAAAGTAGTTTATAGGTTCAATGCTATTCCCTTCAAGC 4857
                            v     v      v ii i  i  i     i  v  i  iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_102995312_   4858 TACCATTGACTTTCTTCACAGAATTAGAAAACAACT-ACTTTAAATTTCA 4906
                          v   vivi i  i  ii     v v  v  --i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chrX_102995312_   4907 TATGGAA 4913
                                
  L1M4_orf2#LINE/    149 TATGGAA 155

Transitions / transversions = 1.69 (27 / 16)
Gap_init rate = 0.01 (2 / 155), avg. gap size = 1.50 (3 / 2)  

2405 27.01 1.98 1.05  chrX_102995312_103001775.rev     5216  5974 (490)    L1M4_orf2#LINE/L1      143   908 (0)  

  chrX_102995312_   5216 AACTCCTATGTAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGC 5265
                           i  v    v  viiv  ii  v  v v  v     i      i i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_102995312_   5266 AAAAAGAACAAAGCTGAAGG---CATGCTATCTGACTTCAAAATATACTA 5312
                           i          i  i   ---  ii  vi ii i       iv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_102995312_   5313 CGAGGCCACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATA 5362
                          i i  i       i   i    ii         i iv ii i   i   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_102995312_   5363 TAGACCAATGGAACAGAGCAGAGGCCTCAGAAATAACACCACACACCTAC 5412
                             i        i   iiv   ivii         vv   i   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_102995312_   5413 AACCATCTGATCTTTGACAAATCTGACAAAAGCA----ATGGGGAAAGGA 5458
                         iii  vi    i  i     ivv  v   i v  ----          i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_102995312_   5459 TTCCCTATTTAATAAATGGTGTTGGGAAAACAGGCTAGCCATATGCAGAA 5508
                          vvi  v  i  i        i     v   v  v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_102995312_   5509 AACTGAAACTGGACCCTTTCCTTACACCTTATACAAAAATTAACTCGAAT 5558
                         i v    ii       i v   i     v                 i  v
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_102995312_   5559 TGGATTAAAGATTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGA 5608
                              i ?   ii    i      v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_102995312_   5609 AAACCTAGGCA-ATACCACTCAGGACATAGGCATGGGCAATGACTTCATG 5657
                             v    ?i- v i -i  iv   v v  vv i       ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_102995312_   5658 ACTAAAATGCAAAAAGCAATTAA--AACAAAAGCCAAAATTGACAAATGG 5705
                         iv  vi ii v       --i  --        vv     v  i    v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_102995312_   5706 GATCTAACTAA--CTAAAGAGCTTCCGCACAGCAAAAGAAACTCTCATCC 5753
                           ii v ii  --i    i -   ii ii vv    i  v   v   vvv
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_102995312_   5754 AAGAGAACAGGCAACCTACAGAATGGGGGGAAATTTTTG-ACATCTATCC 5802
                            v   v  i     i          i i    v    - v   -  vi
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATAT 737

  chrX_102995312_   5803 ATTTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATGT 5852
                           i   i  i  i  vi          v  i  i     ivv    v vv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_102995312_   5853 ATAAGAAAAAAACAAA-AACCCCATCAAAAAGTGGGCACAGGATATGAAC 5901
                             v     i     -     v  i?    i      v     v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_102995312_   5902 AGACACTTTTCAAAAGAAGACATTTATGCGGCCAACAAACACACACACAA 5951
                              i  i  v        i  vi vii      i  i    ii---  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG---AA 884

  chrX_102995312_   5952 AAAA-GCTCATCATCGTTGGTCAT 5974
                           i -     v    i????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (125 / 76)
Gap_init rate = 0.02 (13 / 766), avg. gap size = 1.77 (23 / 13)  


1605 29.93 3.40 2.72  chrX_103002091_103003817.rev      502  1236 (491)    L1M4_orf2#LINE/L1      169   908 (0)  

  chrX_103002091_    502 AGAATAGTTAAGAAACTCTTGAGGAATAAGAATGAGGTGGGAAGACTTCC 551
                                ii  i v v      ii  v     ii i  v   i    iv 
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chrX_103002091_    552 CCTATCAGATATCAAGACATTTATTAGTATTACTGTTACAGGTAAT-AAG 600
                         v  vi vi  v    i  --   i  ----i vv i     -    -   
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAAC--TTACTA----CAAAGCTACAG-TAATCAAG 261

  chrX_103002091_    601 GCAATGCTGTATTGGCACATGATTAGATAAATAAACTGGTAGAATAGAAC 650
                         i  i  iv   i     i v iv    i v   i iiii i        i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_103002091_    651 AGACAGGTCAGAAATCTTCCCAAAAATATATGAACACTTGATATTTGACA 700
                         v  v  vi       vvv    v v  v    iv  v     v  i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_103002091_    701 GAGTTGGCATTGTAACTGAATGGGAGAAGAAAAGGCTTTTCAGCAAATGA 750
                         ii v  v  vviiv i v      ii     v  v       i      i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_103002091_    751 TATTGGGGCAATTGGATATTCATA-----AAGAA-AACATTGGACCTCTA 794
                          ii    i   i      ?i  i -----     -i vi       i   
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_103002091_    795 TTCTCATATTCTACATGAAAATCAATTCCAAGTATATTAAAAACATAGAT 844
                         i-    i iiv  i ii     i  i  v  i iv  i ? i  v  i  
  L1M4_orf2#LINE/    462 C-CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_103002091_    845 GTGAAAGTCAAAACCATAAAAATTTTAAATGTTATTATAGTATAAAGGAA 894
                           i i  ii     i      v i   i v ----- v ii   ii? v 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAG-----AAAACATAGGNGTA 555

  chrX_103002091_    895 TATCTTCATGATATTGGGGTATAGAACGATTTCATTGAAAAGACACAAAA 944
                         v      i   iv     v  viv  i i    v v  v v     v   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_103002091_    945 AGCAC--TTACCATAAAAAAGGATTGATAACTTCGGTATCTATCTTATAA 992
                              --vi v  v  i   ii  v     v  v iiv  -   -- v  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC-ATC--AAAA 652

  chrX_103002091_    993 TTAGAA---TTTATGTTTATCAAAAGAAATCATTAAAA---TGGAAAAAT 1036
                            i  ---   i  i  --    i  v ii  i  i ---  i   i i
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_103002091_   1037 AAGTGACAAAGTGGGGAGAGATATATGGAACACATATAAAGGAGAAAGAA 1086
                           viv   i i    iii i    v  v  vv      vvv  v  i i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_103002091_   1087 CT-------AAAAT-TA-AAACAGCTTCTACAAATTAATTTGAAAAAGTT 1127
                           ------- i   -  -   v i  ii     v i   vvv      vi
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_103002091_   1128 ACACAACTCAACAGGAAAAAATGG-CAAATGTCTTGAATAAATGCTTCAC 1176
                          v i   i   i--v?        -    v vi       i iii   v 
  L1M4_orf2#LINE/    801 AAATAACCCAAT--TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_103002091_   1177 AAAAGAGGAAATACTAACGTTCAATAGGCATGTGAAAAGATGCTCAACAT 1226
                         v     i  v    v  i vi     i   ii                  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_103002091_   1227 TATTAGTAAT 1236
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.45 (128 / 88)
Gap_init rate = 0.03 (19 / 740), avg. gap size = 2.37 (45 / 19)  


2350 25.33 10.30 1.45  chrX_103015354_103020713     4043  4867 (493)    L1M4_orf2#LINE/L1       11   908 (0)  

  chrX_103015354_   4043 TTCCACGCTCATGGCTAGGAAGCATCAATATCATTAAAATGATCATACTG 4092
                          i   i i      v v     vv i     ii    i   iiv     -
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT- 59

  chrX_103015354_   4093 CCCAAAGCAAATTATATTAATAGATTCAATGCTATGCCTATTAAACTAAC 4142
                            ----      i-  iv i        i  v  v     i   v vv 
  L1M4_orf2#LINE/     60 CCC----CAAATTG-ATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_103015354_   4143 A-CTGACATTCCTCACAGAACTAGAAAAAAT-ATTTTAGAATTCACATGG 4190
                          -   v -  ii ii     v v  v  iv -  ii  i      i    
  L1M4_orf2#LINE/    105 AGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_103015354_   4191 AAC--CAA-------AAAATAGCCAAGGCAATCCT-AAGCAGAATGAACA 4230
                           v--   ------- i         ii     i -  iv    -     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GAACA 202

  chrX_103015354_   4231 AAGTTGGAGG------------------CAAACCATGCTACAGGGCTACA 4262
                                   ------------------    v v i     ii      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_103015354_   4263 GTAACCAAAACCTCATGGTACTGATACAAAAACAGGGACATAGACCAATA 4312
                             i   i  vvii        ii i  ii i  iv i     i    i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_103015354_   4313 GAGCAGACTAGAGAAGCCAGAAATAAGAACATATATCTACAATTATATGA 4362
                           ii   v v    iv          ivv    i  i  iii i vv   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_103015354_   4363 TCTTTGACAAACGTGACAAAAACAAGCAATGGAGGAAAGGATC-CCTGTT 4411
                          i  i     iv   v   i v  vv      -      i  v-i  v  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTT 401

  chrX_103015354_   4412 CAACAAATTATGCTGGCATAACTGGCTAGCCATATGCAGAAGGTTAAATC 4461
                                 vi      v i      v  ?   i     i   iv i  vi
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_103015354_   4462 TTGACTCTTTCCTTACATCATATAGAAAAATTAACTCAAGATAGATTGAA 4511
                          v   i i v   i   i      v              i  i   ii? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_103015354_   4512 GACTTAAATGTAAAACCCAAAACTATAAAAC-CTTGGAAGACAACCTAGG 4560
                            i         i v i             -   i     v   v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_103015354_   4561 C---AAT-------ACCATTCAGGTACGAGCAAATATTTCATGAAAAAGA 4600
                         ?---   -------   -- ii   -iii    vvi    v ii v v  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACC--TTGGGT-TAGGCAATGGTTTCTTAGATATGA 598

  chrX_103015354_   4601 TGCCAAAAGCAATTGCAACAAAAG-------------------------- 4624
                         ii         vvv          --------------------------
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_103015354_   4625 -----------CTTCTGCACAACAAAAGAAACT--TGGTAGAGTAGACAG 4661
                         -----------   i  ii vv    i  v   --iiiv i   ii v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_103015354_   4662 ACAACCTACGGAATAGGAGAAAAGTTTTGCAAACCATGCATCTGAGAAAA 4711
                               i  i    i        vv        i   ii      v  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_103015354_   4712 GTCTAGTATCCAGCATCTATAAGGAACTTAAATAAATGTATAAAAGAAAA 4761
                          v  v        v  v     i     ivv i  v vv    v i   i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_103015354_   4762 ACAAA---CCCCATTAAAAAGTGGACAAAGGATGTTAACAGACACTTTTC 4808
                              ---   v   ?    i   i        v v  i     i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_103015354_   4809 AATAGAAGACATACATGTAGCCAATAATCATATAAAAAAA-GCTCAACAT 4857
                         v v      i     vi i        v  i  i    i -         
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_103015354_   4858 CACTGATCAT 4867
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.53 (124 / 81)
Gap_init rate = 0.02 (22 / 898), avg. gap size = 4.41 (97 / 22)  


3267 27.09 0.33 0.33  chrX_103087832_103094110.rev     4881  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103087832_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103087832_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_103087832_   4981 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCAT 5029
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_103087832_   5030 ATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5079
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_103087832_   5080 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAAGCT 5129
                               i      vv       v  ii i      viv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_103087832_   5130 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5179
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_103087832_   5180 ATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATCTACAACTA 5227
                               i    i-- v  i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_103087832_   5228 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTTCC 5277
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_103087832_   5278 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5327
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_103087832_   5328 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5377
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_103087832_   5378 TAAAGATTTAAAAGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5427
                         i ?   ii    v  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_103087832_   5428 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAA 5477
                             ?i v viv   iv   v v  vv i     v ii   v ivvi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_103087832_   5478 ACACCAAAAGCAATGGCAACATAAGCCAAAATTGACAAATGGGATCTAAT 5527
                                     vvi      v   vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_103087832_   5528 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5577
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_103087832_   5578 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5627
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_103087832_   5628 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5677
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_103087832_   5678 AACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCT 5727
                         i     i     v  i?    i     i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_103087832_   5728 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCG 5777
                          v        i  vi viii     v  i          i       v i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_103087832_   5778 TCACTGGCCAT 5788
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


1492 29.58 3.39 2.99  chrX_103147846_103149574      500  1236 (493)    L1M4_orf2#LINE/L1      169   908 (0)  

  chrX_103147846_    500 AGAATAGTTAAGAAACTCTTGAGGAATAAGAATGAAGTGGGAAGACTTTC 549
                                ii  i v v      ii  v     ii    v   i    iv 
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chrX_103147846_    550 CCTATCAGATATCAAGACATTTATTATTATTACTGTTACAGGTAAT-AAG 598
                         v  vi vi  v    i  --   i  iv -- -- i     -    -   
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAAC--TTACTACAA--A--GCTACAG-TAATCAAG 261

  chrX_103147846_    599 GCAATGCTGTACTGGCACAAGGTTAGATAAATAAACTGATGGAATAGAAC 648
                         i  i  iv         i    v    i v   i iii           i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_103147846_    649 AGACAGGTCAGAAATAGTCCCAATA-ATATATGAAAACTTGATATTTGAC 697
                         v  v  vi        iv    -  -  v    ivv v     v  i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCA-TACATTTATGGTCAATTGATTTTCGAC 360

  chrX_103147846_    698 AGAGTTGGCATTGTAACTGAATGGGAGAAGGAAAGACTTTTCAACAAATG 747
                          ii v  v  vviiv i v      ii   i v  v              
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_103147846_    748 ATATTAGGGTA-TTGGATATTCATAAGGAAAAAAAT-----TAGACCTCT 791
                         i ii i  ii -i      ?i  i v v    i   ----- i    i  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_103147846_    792 ATTCTCATACGCTACACGAAAATTAATTCCAAGTATATTAAAAACCCAAA 841
                          i-    i  vv  i  i        i  v  i iv  i ? i   i   
  L1M4_orf2#LINE/    461 AC-CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_103147846_    842 TATGAAAGTCAAAACCATAAAATTGT-AAATGTTATTATAGTATAAAGGA 890
                          i i i  ii     i      i v - i v ----- v ii   ii? v
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAG-----AAAACATAGGNGT 554

  chrX_103147846_    891 ATATCTTCATGATATTGGAGTATAGAAAGATTCCTTTGAAAAGACAC-AA 939
                          v      i   iv    iv  viv  v i  i   v  v v     -  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_103147846_    940 AAGCAC--TTACCGTAAAAAAGGATTGATAACTTCGATATCTATCTTATA 987
                               --vi v iv  i   ii  v     v  v  iv  -   -- v 
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC-ATC--AAA 651

  chrX_103147846_    988 ATTAGAA---CTTATGCTTATCAAAAGA-A--ATCACTAAAATGGAAAAA 1031
                             i  ---i  i     --    i  - --    vv   i  i   i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_103147846_   1032 TAAGTGGCAAGGTGGGGAGAGATGTATGGAACACATATAAAAGAGGAAGA 1081
                         i  vivi  iii    iii i  i v  v  vv      vvv  vi i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_103147846_   1082 ACT-------AAAATTAAAACAAATAACTTCTACAAATTAATTTGAAAAA 1124
                            ------- i   -- v i   v    ii     v i   vvv     
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAAT--ATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_103147846_   1125 GTCATACAACTCAACAGGAAAACATGACAAATGTCTAGAATAAATGCTTC 1174
                          v  v i   i   iv?i    ii- i    v vi v     i iii   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATG-GGCAAAGGATTTGAATAGACATTTC 846

  chrX_103147846_   1175 ACAAAAGAGGAAATCCTAATGTTCAATAGGCAAGTGAAAAGATGCTCAAC 1224
                         v v     i  v  v v    vi     i   vi                
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_103147846_   1225 ATTATTAGTCAT 1236
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (126 / 88)
Gap_init rate = 0.03 (23 / 740), avg. gap size = 2.04 (47 / 23)  


 956 15.06 1.20 0.60  chrX_103228009_103231066.rev      962  1127 (1931)    L1M4_orf2#LINE/L1       10   176 (732)  

  chrX_103228009_    962 ATCTCATATTAATGAATCGGAATATTTAATATTGTTAAGATGGCAATACT 1011
                            i   i  v   i  i    v i                         
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_103228009_   1012 CCCCAAAGCAATCTACAGATTCAATGTGATCTCTACCAAAATCCCAACTA 1061
                                vii              i ii   i   i          i  i
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_103228009_   1062 CTCTTTTTTG-AAAAACGGGCAACCTGATCCTAAAATTCATATGGAATTG 1110
                          -        - i   iv i   v                       v  
  L1M4_orf2#LINE/    110 C-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_103228009_   1111 CAAGGACCCCA-AATAGC 1127
                              iv    -      
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGC 176

Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.02 (3 / 167), avg. gap size = 1.00 (3 / 3)  

1605 15.96 0.65 1.30  chrX_103228009_103231066.rev     1353  1659 (1399)    L1M4_orf2#LINE/L1      149   453 (455)  

  chrX_103228009_   1353 TATCAAAGTGCT-GGGATTACAGATGTGAGCCTAAACAATCTCTATAATG 1401
                            vi  i   v-    ii-    -i -    v         iv v  v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACC-CAGA-AT-AGCCAAAACAATCTTGAAAAAG 195

  chrX_103228009_   1402 AACAGCAAAGTGGGAGAACTAACACATCTCAATTTCAAAACTTACTGAAA 1451
                           v i      v    i   v    v  i                 iv  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_103228009_   1452 AGCTATAATAACTAAAACAGTGTGGTACTAGCGTTAAGGACAGACACATA 1501
                              i i   ii  i             i  i -     i     i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATA 294

  chrX_103228009_   1502 CATCAATGGAATATAATTTAGAGTCCAAAAATAAACCCACACATCTATGA 1551
                         v            v    v        i           i    i    i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_103228009_   1552 TTAATTCATTTTCGA-AAGGGTGCCAAGATGATTCAATGAGGAAAGAATA 1600
                          i    v        -             iv        i          
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_103228009_   1601 ATATTTTCAACAAATGGTGCTGGGACAACTGGATACCTACATGCAAAATA 1650
                         i v                                ? i          v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_103228009_   1651 ATAAATTTG 1659
                           i  v   
  L1M4_orf2#LINE/    445 ATGAAGTTG 453

Transitions / transversions = 1.53 (29 / 19)
Gap_init rate = 0.02 (6 / 305), avg. gap size = 1.00 (6 / 6)  

2198 14.04 3.19 3.40  chrX_103228009_103231066.rev     2098  2567 (491)    L1M4_orf2#LINE/L1      440   908 (0)  

  chrX_103228009_   2098 AAAGAATGAATCTGGACTCCTATCTTACATATCATATACAAAAAGTAACT 2147
                                   vi     i    i  i   i--            v     
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACAC--CATATACAAAAATTAACT 487

  chrX_103228009_   2148 CAAAATGG-TCAAAGACCTACATGTAAGAACTAAAACTCTAAAAGTCTGG 2196
                                 -   ?       v        i        v     v   vi
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_103228009_   2197 GAAGGAAACA--GGTGAAAATCTTCCTCATCTTGGATTACACAGTGGTTT 2244
                             i     --  ? v        v v i     i   vi  i      
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_103228009_   2245 TTAAAATATGACATCATAAGTACA-GC--CAAAAAAAA-----GATAAAT 2286
                         i v i        i  v   i   -  --     i   -----       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_103228009_   2287 TAGACTTCATCAAAATTAAAAACTTTGGTG--TCAAAGGACACTATCAAG 2334
                          i                        v   --                  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_103228009_   2335 TGAACAAATGCTAACAAGCAAAAAGACAACCTGCAGAATA--AAAACATT 2382
                         -----   --------- ii           ii      i-- i  v  v
  L1M4_orf2#LINE/    688 -----AAA---------GTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_103228009_   2383 TTTGCAAATCATATATCTGATAAGGGTCTAGTAGCCAGAATATAGAAAGA 2432
                                                   v  v   v          v     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_103228009_   2433 ACTCTTACAACGCAACCATAAAAAGTAAAATAACACAATTTTAAAAGCAG 2482
                                    v   iv        vv       v     ?v    vvi 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_103228009_   2483 CAAGGTATCTGAATAGATATTTCCCCAAAGAGGACACACAAATGGCCAAT 2532
                            i v  i        i     i       i  i i             
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_103228009_   2533 AAGCACATGAAAAGATGCTCAAAACCATAATGAAA 2567
                                               v i  ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (34 / 29)
Gap_init rate = 0.02 (10 / 469), avg. gap size = 3.10 (31 / 10)  


3165 26.77 1.00 0.55  chrX_103411719_103418113.rev     5001  5904 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103411719_   5001 TGGAAGAACATTCCATGCTCACGGATAGGAAGAATCAATATCCTGAAAAT 5050
                              ii i  i     i   i    v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103411719_   5051 GGCCATATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5100
                            v   i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_103411719_   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5148
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_103411719_   5149 TATGGAACCAAAAAAGAGCCCACATTGCCAACACAATCCTAAGCCAAAAG 5198
                                viiv  ii  v  viv  v     v      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_103411719_   5199 AACAAAGCTAGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5248
                                i i    vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_103411719_   5249 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5298
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_103411719_   5299 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5346
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_103411719_   5347 ATCCGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5396
                          vii   i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_103411719_   5397 CTATTTAATAAATGATGCTGGAAAAACTGGCTGGCCATATGTAGAAAGCT 5446
                           v  i  i     i      i v      v i?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_103411719_   5447 GAAACTGGATCCCTTCCTTACACCTCATACAAAAATTAATTCAAGATGGA 5496
                            ii    i    v   i     vi             i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_103411719_   5497 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAAC 5546
                          i ?    i       v   v       i      vi i   i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_103411719_   5547 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5595
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_103411719_   5596 AAACACCAAAAGCAATGGCAACAAAAGCCAAACTTGACAAATGGGATCTA 5645
                         vi            vvi          vv   v v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_103411719_   5646 ATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5695
                           i   v v  i     i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_103411719_   5696 CAGGCAACTTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5745
                         v  i    ii                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_103411719_   5746 AAGGACTAATATCCAGAATCCACAAAGAACTTAAACAAATTTACAGGAAA 5795
                          i     vi          vi i        ivv    v iv i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_103411719_   5796 AA---AAA-AACCCCATCAAAAAGTGGGTAAAGGATATGAACAGACACTT 5841
                           ---   -     v  i?    i    i       v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_103411719_   5842 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5891
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_103411719_   5892 CATCACTGGCCAT 5904
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2947 26.43 2.46 0.78  chrX_103465183_103470585     4018  4910 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103465183_   4018 TGGAAAAATATTTCACGATCATGAATTGGAAGAATCAATATTATTAAAAT 4067
                               i    ii  i v     i         v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103465183_   4068 GTTCGTAATAC---CCAAAGCAATCTATAGATTCAATGCAATCACCAT-G 4113
                          --- i     ---     vii     i        i      v i  -i
  L1M4_orf2#LINE/     51 G---GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_103465183_   4114 AAATATCAATAACATTCTTCACAGAAAGAGAAAGAAACAATCCT----TT 4159
                             vi  iivi v  i  ii      vv  v - ivii     ----  
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATT 146

  chrX_103465183_   4160 ---GTGGAATCACCAAAGACCCAGAATAGCCAAAGCTATCCTATGCAAAA 4206
                         ---i     vii v ii                 i v   i iviv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_103465183_   4207 TGAACAAATCTGGAGGAATCACATTTCCTGACTTCAAATTATACTACAGA 4256
                         v       vi       v     i    ii i      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_103465183_   4257 GTTATAGTAATCAAAACAGCATGGTACTGGTATCAAAACAGACCCACAGA 4306
                          i  i         i    ii         i  v ii i    vi i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_103465183_   4307 GCAGTGGAAAAGAATAGAGAACCCAGAAACAAATCCACACACCTACAATG 4356
                         v  i     v     v    ii       i   i   i   ii  iii v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_103465183_   4357 AGCTCATTTTTGACGAAGGTGTCAAGAACATACATTGGGGAAAGAACAGT 4406
                          ii v     i   i i    i     v   v  v           i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_103465183_   4407 CTCTTTAATAAATG-TCTTGGAATA-CTGGATATCCATATTCAGACAAAT 4454
                           i  i  i     - vi   i i -       ?   i  v  i vi   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_103465183_   4455 GAAGCTACACCCCTATCTCTCTCCAGATTTAAAAGTCAAATAAAAATGGA 4504
                             i iv       i   v v   v  vi    i i  v v        
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_103465183_   4505 TTAAAATCTT-----TAAGACATCAAAATATGAAATTACTACAAGAAA-C 4548
                          i ? iv i -----     vv v   v   i   i vi  v      - 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_103465183_   4549 TTTGGGGAAAATCTTCAGGACATTAGTCTGGGCAAAAATTTCCTGAGTAA 4598
                         v v  ? v        iv   v  i vi i     vii    i iii  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_103465183_   4599 TAC-CCAACAAGTACAGGCAACCAAAGCCAAAAATGGACAAATGGGATAA 4647
                         v  -    -   i   i     v    v-      i  i    v   ivv
  L1M4_orf2#LINE/    597 GACACCAA-AAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTT 644

  chrX_103465183_   4648 CATCAAG-TTAAAATACTTTTGCACAGCAAAGGAAACAATCAACAAAGTG 4696
                               i-      -       ii vv       v  v     v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_103465183_   4697 AAGGGACAACCCATAGAATGGTAGAAAGTATATGCAAACTAACCATTTGA 4746
                           ii         i       v     i   v      ii vvi  i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_103465183_   4747 CAAAGGATTAATAACTAGAATATATAAGGAGCTCAAATAACTGTATAGGA 4796
                         i  i   i vi  v i           i  i   vv i    vv   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_103465183_   4797 AAATATCTAATAATATGATTAAAAAATGGGCAAAACATCTAAATAGACAT 4846
                            viv v     ivii   ?             iv  i i         
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_103465183_   4847 TTATA-AAAGCACACGTACAAATGGCAAACAGTTACATGAAAATGGGCTC 4895
                           v v-    v v ii          v  i ivi         viv    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_103465183_   4896 AACATTAGAAGGCCC 4910
                              i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (141 / 91)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.81 (29 / 16)  


3331 25.80 0.77 0.66  chrX_103506177_103508261      686  1592 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103506177_    686 TGGAAAAACATTCCATGCTCATGGGTAAGAAGAATAAATATTGTGAAAAT 735
                               i i  i     i      i vi     v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103506177_    736 GGCCATACTTCCCAAAGTAATTTATAGATTCAATGCTATCCCAATTCAAG 785
                            v     i      v i  i  i        i  v     v  -   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT-CAAA 99

  chrX_103506177_    786 CTACCACTGGCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTC 833
                         v v   viv  i  i  ii     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_103506177_    834 ATATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAA 883
                                 viiv  ii  v  viv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_103506177_    884 GAACAAAACTGGAGGCCTCATGCTCCCTGACTTCAAACTATACTACAAGT 933
                                ii      v    ii  i  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_103506177_    934 CTACGGTAACCAAAACAGCATGGTACCAGTATCAAAACAGATATATAGAC 983
                             i    i   i    ii      ii i  v ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_103506177_    984 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACTA 1033
                                 i    iv   ivii         vv   i    i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_103506177_   1034 TCTGATCTTTGACAAACCTGACAAAAACCA-GCAATGGGGAAAAGATTCC 1082
                         vi    i  i     ivv  v   i -   -v           ii  vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAGT 396

  chrX_103506177_   1083 CTATTTAATAAATGGTGTTGGAAAAACTGGCTAGCCATATGCAGAAAACT 1132
                           v  i  i        i   i v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_103506177_   1133 GAAACTGGGCCCCTTCCTTACACCTTATGCAAAAATCAACTCAAGATGGA 1182
                            ii   i     v   i     v   i       i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_103506177_   1183 TTAAAGACTTAAACGTAAGACCTAAAACCATAAAAATCCTAGAAGAAAAC 1232
                          i ?    i    i      v       i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_103506177_   1233 -CAGGGAAATACCATTCAGGACATAGGCATGTGCAAAGACTTCATGTCTA 1281
                         -i   ?iv v i -   iv   v v  vv iv    v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_103506177_   1282 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 1331
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_103506177_   1332 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 1381
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_103506177_   1382 CAGGCAACCTAGAGAATGGGAGAAAATTTTTG-AAATCTATCCATCTGAC 1430
                         v  i     i v               v    -     -  vi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGAT 744

  chrX_103506177_   1431 AAAGGGCTAATATCCAGAATCTACAAAGAACTTATACAAATTTACAGAAA 1480
                           i  i  vi          v  i        iv     v iv i iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_103506177_   1481 AAAGA--AACAACCCCATCAAAAAGTAGGCGAAGGATATGAACAGACACT 1528
                              --  i     v  i?    i i   i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_103506177_   1529 TCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAATGTTCA 1578
                             v        i  vi viii     i  i  i       i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_103506177_   1579 TCATCACTGGTCAT 1592
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (144 / 86)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.18 (13 / 11)  


2453 27.73 3.95 1.58  chrX_103566508_103568589.rev      705  1591 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103566508_    705 TGGAAAAAAATACTATGTTCATAGATTGGAAGACTAAACATAGTAAAGAT 754
                               i v  v i        i            v  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103566508_    755 ACTGATTCTCCTCAACTTGATTTATAGGTTTAATACAATTCCTATCACAG 804
                         ivii  v    i   v     i  i  i  i  ii    i       v i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_103566508_    805 TCACAACAAAAATTTTTATAGATATAGACAAGATTATTTTAAAATGTATA 854
                           v  i vivvv     ii   v  v      v v  ii      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_103566508_    855 TGGAAAAACAAAGGAACTACAAAAGCTATAGCAATTTTGGAAAAAGAAAA 904
                               vi   i   v i v  v   i v i    i   -        i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-AAAAAGAAGA 199

  chrX_103566508_    905 ATAGAGT-----AAATCAGTCTACCTCATTTTAAGATTTATTATACAACT 949
                          i i   -----i v   vv  v  iv    i  i i   i  i v i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_103566508_    950 ACAGCAAT-AAGACTGTGTGG---------AGGGACAAGCATACAGATAA 989
                             i   -     v      --------- i   i ii    i    v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_103566508_    990 AAGGAACAGAATAAGGAACTC-GAACTCAGAGACCCACACAAATATATCC 1038
                          v    i     vii  iii -   v --- i     i   vv   ivi 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAAT---AAACCCATACATTTATGGTC 346

  chrX_103566508_   1039 AACTGCTTTT-GACAAAGGTATAAAAGCAATTTGATGGAGGTAGGATAGT 1087
                           i  v    -     i   iiv  ii v   ii    i iv  i     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_103566508_   1088 CTCT-CAACAAGTGGTGTTAGAAACATTGGAAATGTATAAGTAAAAGAGA 1136
                           i -      i     i i i vv i    v ?vi i v i      - 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-A 445

  chrX_103566508_   1137 TGAAAC--GACTTAAATTTCAAACCTTATACAAAGATTAACTCAAAATAG 1184
                             ii--   iivv ii   v   v        i             i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_103566508_   1185 ATTACGAATTTAAATGTGAAATGTAAAACTA--AAAGTTTTAGAAAATTA 1232
                           i ?ii ii       i i vv        --   v i      i vv 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_103566508_   1233 CA-AAAC---AATCTTCAGGATCTAGGATTAGGCAAAGAGTTCTTAGATT 1278
                           - ii?---       iv  i  v  i        v iv         v
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_103566508_   1279 TAATACCTAAAGCATGGTCTATAATAGGAAACCTTGATAAATTGGACCTA 1328
                          i i   v      iiiv v i  v  i   vv v            i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_103566508_   1329 TTCAAAAGTAAAAACTTTTGCTCTGCAATTGACTCT-T----AAAATGAT 1373
                         v      v            iv  v   vv   v  - ----   i   -
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA- 694

  chrX_103566508_   1374 TTTTTAAAAATAAGCTAGGGAACGGGAGAAAATATTTATAAAGTATATAT 1423
                         -----   i i  v i vi   i              ii   vi      
  L1M4_orf2#LINE/    695 -----AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_103566508_   1424 ACAACAAAAAACTAGTATCTATAATATTTTTTAAAG---TCTCAAAAATC 1470
                         vii i  iii   v     i v     v ---    ---   i v  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATAT---AAAGAACTCTTACAACTC 786

  chrX_103566508_   1471 AGCAATAAAAAAATAAGCCATCCATGTAGAAAATGGACAAAAGACATGAA 1520
                          ii        i i  iiv i   vv ?i       i    i  iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_103566508_   1521 CAGATATTTCACCAAAGAGGATAGAGAGATGACAGATATGCACTTTAAAA 1570
                         i   i     v       i    v v i   i vi   v    v v    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_103566508_   1571 -ATGTTTGACGTCATTAGCCAT 1591
                         -   i ii  i   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.58 (49 / 19)  


2599 27.17 1.81 1.09  chrX_103652368_103658970     5283  6110 (493)    L1M4_orf2#LINE/L1       75   908 (0)  

  chrX_103652368_   5283 CATACTCATTGCTACCCCCATCAAGCTACCA-CTGACTTTCTTAATAGAA 5331
                           v i   vi  v i   i     iv v   -   v    i  i-i    
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG-CAGAA 123

  chrX_103652368_   5332 -TTGGAAAAAAACT-ACTTTAAATTTCATATGGAACCAAAAAAGAGCCCG 5379
                         -   --- v  i  - iii    v           viiv  ii  v  v 
  L1M4_orf2#LINE/    124 ATTG---ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chrX_103652368_   5380 CATAGCCAAGACAATCCTGGGCAAGAAGAATAAAGTTGGAGGCATCACTC 5429
                         v        i      i  iiv        i           vv    v 
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_103652368_   5430 TACCTGACTTCAAACTATACTACAAAGCTACCATAATCAAAACAGCATGG 5479
                          v  ii i      viv              vi       i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_103652368_   5480 TGCTGGTACCAAAACAGACCTATAGACCAATGGAACAGAACAGAGGCCTC 5529
                          i    i iv ii i    v      i        i    iv   ivii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_103652368_   5530 GGGAACAACACCACACATCTACAACCATCTGATCTTTGACAAACCTGACA 5579
                         i i  i  vv   i    i  iiii  vi    i  i     ivv  v  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_103652368_   5580 CAAACCAG-CAATGGGGAAAATATTCCCTATTTAATAAATGGTGTTGGGA 5628
                         - i    v-           iv  vvi  v  i  i        i     
  L1M4_orf2#LINE/    371 -AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_103652368_   5629 AAACTGGCTAGCCAGACACAGAAAACTGAAACTGGACCCCTTCCTTACAC 5678
                         v      v  ?   v ii  i  i v    ii         v   i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_103652368_   5679 CTTATGCAAAAATCAACTCAAGATGGGTTAAAGACTTAAATGTAAGAACC 5728
                          v   i       i       i    i i ?    i           i i
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_103652368_   5729 AGGACCATAAAAATCCTCGAAGAAAACCTGGGCAGTA--CCATTCAGGAC 5776
                          ii  i      v  i v         v i  ?-   --i -   iv   
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGN-GTAAATC-TTCGTGAC 567

  chrX_103652368_   5777 ATAGGCATGCACAAAGACTTCATGTCTAAAACACCAAAAGTAATGGCAAC 5826
                         v v  vv ivi   v ii   v ivv  vi          i vvi     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_103652368_   5827 AAAAGCCAAAATTGACG--TGGGATCTGATTAAA-TTAAAGAGCTTCTGC 5873
                              vv     v  ii-- v   ii v  i   -     i -   i  i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGT 666

  chrX_103652368_   5874 ACAGCAAAATAAATTGTCATTAGAGTGAATAGGCAACCTAGAGAATGGGA 5923
                         i vv    iv v i i   vv i      v  i     i v         
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_103652368_   5924 GCAAAAT-TTTGCAATCTATACATCTGAAAAACG-CTAATATCCAGAATC 5971
                          -     -       vii   i      v  iv -  vi          v
  L1M4_orf2#LINE/    717 G-AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_103652368_   5972 TACAAAGAATTTAAACAAATTTACAAGAATAAAACAA----CCCCATCAA 6017
                           i      i ivv    v iv i  v  v  i    ----   v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_103652368_   6018 AAAGTCGGCAAAGAATATGAACATACACTTCTCTAAAGAAGACATTTATG 6067
                            i v       i  v    i v   i     i        i  vi vi
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_103652368_   6068 CAGCCAACAAACATACGAAAAAATGCTCATCATCACTGGTCAT 6110
                         ii     i  i  i i     i       v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (132 / 89)
Gap_init rate = 0.02 (17 / 834), avg. gap size = 1.41 (24 / 17)  


 511 26.32 1.17 1.17  chrX_103662282_103668903.rev      956  1126 (5496)    L1M4_orf2#LINE/L1      479   649 (259)  

  chrX_103662282_    956 AAGTTAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCCAAACTATA 1005
                           i         i      i ?    i         i v iv        
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_103662282_   1006 AAAACCCTAGAAGGGAATCTAGGCA-ATACCATTCAGGACATTGGCATAG 1054
                            vi i      ii  iv    ?i- v i -   iv   v    vv   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG 577

  chrX_103662282_   1055 GCAAAGATTTCAT-GATGAAATCACCAAAAGTAATTGCAACAAAAACAAA 1103
                             v i    v -   ivi -         i vvv         iv   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_103662282_   1104 ATTTGACAAATTGTATCTAATTA 1126
                          v v  i      v ii v  i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCA 649

Transitions / transversions = 1.15 (23 / 20)
Gap_init rate = 0.02 (4 / 171), avg. gap size = 1.00 (4 / 4)  

 813 22.61 3.04 0.43  chrX_103662282_103668903.rev     1879  2108 (4514)    L1M4_orf2#LINE/L1      673   908 (0)  

  chrX_103662282_   1879 AAAAACAACTATCATCAGAGTGAACAGGGAACATACAGAGCGG-AGAAAA 1927
                           ii   -      vv i      v  iv   vi     ii  -      
  L1M4_orf2#LINE/    673 AAGGACA-CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_103662282_   1928 TTTTTGCAATCTATCCATTTGACAAAGGTCTAGTATCCAGAATCTACAAG 1977
                          v       vii  vi  i   i  i  v  v           v  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_103662282_   1978 GAACTTAAACAAATTTTTT-TAAAAAAGCAA----CCCCATT-AAAAGTA 2021
                              ivv    v ivv v-      ii   ----   v   -    i i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_103662282_   2022 GGCAAAGGACCTGAACAGACATTTCTCAAAAGAAGACATTCATGTGGCCA 2071
                                  ii    i           v        i  v  vi      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_103662282_   2072 ACAAACATATGAAAAAAAGCTCAACATCACTGATCAT 2108
                          i  i  i       i v           ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (30 / 22)
Gap_init rate = 0.02 (5 / 236), avg. gap size = 1.60 (8 / 5)  

2677 28.40 2.58 0.67  chrX_103662282_103668903.rev     5253  6143 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103662282_   5253 TGGAAAACCATTCCATGCTCATTGATTGGAAGAATCAATATCATTAAAAT 5302
                               ivi  i     i    v          v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103662282_   5303 AGCCATACTGCCTAAAGCAATCTACAGATTCAATGCTATTCCTATCAAAC 5352
                         i  v     v  i   vii              i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_103662282_   5353 TACCAA-TGTCATTTTTCACAGAACTAGAAAAAAAAACT-ATTCAAAAAT 5400
                          v   i-  i -     ii     v v  v  i----  -  i v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG----CTGATCCTAAAAT 145

  chrX_103662282_   5401 TCAAATGGAAACAAAAAAGAGATTGACTACCCAAAGCAATCCTAAACAAA 5450
                            v       iiv  ii  vviv  v  v     i     i i  v  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_103662282_   5451 AAGAA---AGCTGGAGGCATCACATGACCTGGCTTCAAACTGTACTATAA 5497
                              ---  i      vv     ivv  iiii      viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_103662282_   5498 GGCTATAGCAACCAAAACAGCATGGTACTGGTACAAAAACAGACCCATAA 5547
                         i    i  i  i   i    ii         i i  ii i    vi   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_103662282_   5548 ACCAATGGAACAGAATACAGAACGTAGAAATAAGGCTGCGCACCAA--AT 5595
                          i        i     vv   iivi        iv iiii  iiv --i 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_103662282_   5596 C---TGATCTTTGACAAAGTGAACAAAAATAAACAATGGGGAAAGGACTC 5642
                          ---    i  i     i vviv   i vi vv            i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_103662282_   5643 CCTATTCAATAAATTGTGCTGGGATAAGTGGCTATCCATATGCAGAAGAA 5692
                         i  v     i    v         i  v   v  ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_103662282_   5693 TGAAACTGGACCCCTATCTTTCATCATATACAAAAATTAACTT----TAG 5738
                             ii          i  iv  i                  i---- i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_103662282_   5739 ATTAAAGATTGAAATATAAGACCTGAGATTATAGGAATCCTGAAAGAAAA 5788
                           i ?   iiv    i     v  i i i    ii v  i ii       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_103662282_   5789 CCTAGGCA-ACACCACTCTGGACATTGGCTTTGGGAAAGAATTTATGACT 5837
                          v    ?i- v i -i  vv   v    v  v  v  v iv  iv iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_103662282_   5838 AAGTCCTCAAAAGCAATTTCGACAAAAACAAAAATTGACAAGTGGGACTG 5887
                          v v vi        vvvv i      iv      v  i  i v     v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_103662282_   5888 AATTAAACTAAACAGCTTCTGCACAGCAA-GAAC-CTATCAACAGAATAA 5935
                         v  i   v v  v i   i  ii vv   - i  -       v i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_103662282_   5936 ACAGACGACCTACCTATTGGGAGAAAATATTTGTAAACTATACACCCAAT 5985
                          v    i   i  vv v                i   ii   i i ii  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_103662282_   5986 GAAGGTTCAATATCCAGAATCTATAAGCAACTTAAACAAATGAACAATCA 6035
                         i i  viivi          v     iv    ivv    v v  i   v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_103662282_   6036 AAAAACAAACAACCTCATTAAAAACTGGGCAAAG-ACATGAAAAGATCCT 6084
                            i     i    iv   ?    v         - iv    v   ivi 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_103662282_   6085 TCTC---ATAAGACATACAAGTGGCCAAGAAACATTTTAAAA--TGGTCT 6129
                             --- v    i      i       v  i  iv v    --  v  v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_103662282_   6130 GCATCCCAGGAGAT 6143
                         i    v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (145 / 104)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.93 (29 / 15)  


3214 26.70 0.55 0.77  chrX_103679605_103688315.rev     5000  5909 (2802)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103679605_   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5049
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103679605_   5050 GGCCACACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5099
                            v i   vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_103679605_   5100 TACCAATGACTTTCTTCGCAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5147
                          v   iivi i  i  i      -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_103679605_   5148 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5197
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_103679605_   5198 AACAAAGCTGGAGGCATCGAGCTACCTGACTTCAAACTATACTACAAGGC 5247
                                i      vv  ivi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_103679605_   5248 TATGGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5297
                           ii    v   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_103679605_   5298 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 5345
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_103679605_   5346 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACAATCCC 5395
                          vi    i  i     ivv  v   i v  vvv          v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_103679605_   5396 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5445
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_103679605_   5446 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCATGATGGA 5495
                            ii    i    v   i     v              i   vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_103679605_   5496 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5545
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_103679605_   5546 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5594
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_103679605_   5595 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5644
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_103679605_   5645 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5694
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_103679605_   5695 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5744
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_103679605_   5745 AAGGGTCAGAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5794
                          i  iiiv --          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    746 AGGGACTTG--TATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_103679605_   5795 AAAAAACAAACAACCCCATCAACAAATGGGCAAAGGATATGAGCAGACAC 5844
                             i     i     v  i? v               v   ii     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_103679605_   5845 TTCGCAGAAGAAGACATTTATACAGCCAAAAGACACATGAAAAAATGCTC 5894
                            v vi       i  vi v ii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_103679605_   5895 ATCATCACTGGCCAT 5909
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  

 710 25.85 1.46 0.98  chrX_103679605_103688315.rev     6689  6893 (1818)    L1M4_orf2#LINE/L1        1   206 (702)  

  chrX_103679605_   6689 TGAAACAATATTCTATGCTCATGCATAGGAATAATTAACATTGTTAAAAT 6738
                           i  vi    i i   i     v  v    v v    i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103679605_   6739 GACCACAGTACCCAAAGCAATCTACAGATTTGATGCAGTGCCTATCAAAA 6788
                          i v i v v      vii           ii i   i v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_103679605_   6789 TACCAA-TGTCATTTTTACTGAAATAGAAAACACAATCCTACAATTTGCA 6837
                          v   i-  i v     i v     v  v  vvii      v    iii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_103679605_   6838 TGAAAC--CAAAAAATGGCCTGAATAGCCACAGCAATCTTAAATAAAAAG 6885
                           i  v--   iii i--  v         v i       i  v  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_103679605_   6886 AACAAAGT 6893
                                 
  L1M4_orf2#LINE/    199 AACAAAGT 206

Transitions / transversions = 1.41 (31 / 22)
Gap_init rate = 0.01 (3 / 206), avg. gap size = 1.67 (5 / 3)  

2711 23.03 1.79 1.10  chrX_103679605_103688315.rev     7496  8220 (491)    L1M4_orf2#LINE/L1      179   908 (0)  

  chrX_103679605_   7496 AAACAAAC---AAAAAAAAGAACAAGGCTTGAGGCATCACACTACCTGAT 7542
                               v ---     i        i i v    vv       v  ii  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_103679605_   7543 TTCAAAATATATTACAACACTATAGTAACCAAAATAGCACGTTATTGGTA 7592
                                iv  i     vi   i     i   i i  iii v  i   i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_103679605_   7593 TAAAAACAGACACATAGACCAATGAAATAGAATACAGAACCCAGAAGTAA 7642
                            ii i     i     i     i        vv   ii      i   
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_103679605_   7643 ATTCATATATTTACAGTCAACTTATTGTCAATAAAGGCTCTAAGAACACA 7692
                          ii    i     ii     i v   v  i i  i  iv i    v  iv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_103679605_   7693 CATTGGGGAAAGGACA--CTCTTCAATATATGGTGCTGGGAAAATTGGAT 7740
                           v         i i --  i     i v            v  i     
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_103679605_   7741 AACCATATGCAGAAGAATGAAACTGGATCCCTATCTCTCACCATATATAA 7790
                          ?   i     i         ii    i     i   v         i  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_103679605_   7791 AGATCAACTCAAAATGGATTAAAGACTTAAATGTAAAATCCCAAACAATA 7840
                          i  i              i ?    i         i v iv    v   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_103679605_   7841 AAACTACTGGAATAAAACAGAGG---AAACACTTCAAGACATTGGCCTAG 7887
                              vi i   v      v   ---   i-    iv   v    vi   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAG 577

  chrX_103679605_   7888 GAAAATAATTTAT-GGCTAAGACCTCAAAAGTATAAGCAACAAAAACAAA 7936
                          v  - ii   v -i v  v   vi      i i           iv   
  L1M4_orf2#LINE/    578 GCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_103679605_   7937 AATAGACAAATGAAAC--CATTATAAACTAAAAAGCTTCTGGACAGCAAA 7984
                               i    vii  --   i -   i      -   i  vi vv    
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCA-AAATTAAAAA-CTTTTGTGCTTCAAA 674

  chrX_103679605_   7985 GGAAACAAGAAACAGAGTGAAAGGACAACCCGTCAAATGGGAGAAAATAT 8034
                            v  v vv  v i       i        iivi               
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_103679605_   8035 TTACAAACTAT-TCCCTAACAAGAGACTAATATACAGAATACACAAGGAG 8083
                           i    ii  - vi  i i   i    vi   v       i i  i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_103679605_   8084 CTCAAACAATTCAACCTCACAAAGAAAGAAACAATCTCATT-AAAAATAG 8132
                            vv    i    -- v i   i i v   i  i iv   -      i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAA--TAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_103679605_   8133 GCAAAAGCTCTAAATAGACATTTCTCAAAAGAAGACATACAAATAGCCAA 8182
                              i v i i              v        i        i     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_103679605_   8183 CAGGTATATGAAAAAAACTGCTCAACACCATTAATCAT 8220
                         i i i i       i --         i  ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (111 / 54)
Gap_init rate = 0.02 (13 / 730), avg. gap size = 1.62 (21 / 13)  


3157 26.87 0.66 0.66  chrX_103723174_103729448.rev     4877  5784 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103723174_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103723174_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATACCATCCCCATCAAGC 4976
                            v     v     iv i  i           ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_103723174_   4977 TACCAAA-GCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5023
                          v   iv-      i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_103723174_   5024 ATATGGAACCAAAAAAGAGCCCACATCGCCAAATCAATCCTAAGCCAAAA 5073
                                 viiv  ii  v  viv  v      v     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_103723174_   5074 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5123
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_103723174_   5124 CTACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGAT 5173
                                  i   i    ii       v i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_103723174_   5174 CAATAGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5221
                             i   i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_103723174_   5222 TATCTGATCTTTGACAAAACTGAGAAAAACAAGCAATGGGGAAAGGATTC 5271
                         i vi    i  i     iiv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_103723174_   5272 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTACAAAGC 5321
                         i  v  i  i              v      v  ?   i   i v  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_103723174_   5322 TGAAACTGGATCCCTTCATTACACCTTATACAAAAATCAGTTCAACATGG 5371
                             ii    i    v v i     v           i ii    v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_103723174_   5372 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5421
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_103723174_   5422 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5471
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_103723174_   5472 AAACACCAAAAGCA-ATGTCAACAAAAGCCAAAATTGACAAATGGGATCT 5520
                         vi            - v -         vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_103723174_   5521 AATTAAGCTAAAGAGCTTCTGCACAGCAAAAGAAATGACCATCAGAGTGA 5570
                         v  i  iv v  i i   i  ii vv    i  v iv i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_103723174_   5571 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5620
                          v  i     i   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_103723174_   5621 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5670
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_103723174_   5671 AAAAACAAACAATCCTATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5720
                            i     i  i  v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_103723174_   5721 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCG 5770
                             v        i  vi viii     v ii          i      i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_103723174_   5771 TCATCACTGGTCAT 5784
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3069 27.40 0.55 0.22  chrX_103887804_103895181.rev     5983  6887 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103887804_   5983 TGGAAAAACATTCCATGCTCATGGATAGGAAAAATCAATATCGTGAAAAT 6032
                               i i  i     i        v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103887804_   6033 GACCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 6082
                          i v     v      v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_103887804_   6083 TACCA-CTGACTTTCTTCTCAGAATAAGAAAAACT-ACTTTAAATTTAAT 6130
                          v   -   v    i  v-     vvv  v  i  - iii    v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_103887804_   6131 ATGGAACAAAAAAAGAGCTTGTATAGCCAAGAAAATTCTAAGCAAAAAGA 6180
                               vviv  ii  v iv v        i v   ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_103887804_   6181 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAGCTATACTACAAGGCT 6230
                               i      vv       v  ii i     iviv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_103887804_   6231 ACAGTAACCAAAACAGCA-AGTAGTGGTACCAAAACAGACATCTAGACCA 6279
                                i   i    ii-i   v   i iv ii i      v    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_103887804_   6280 ATGGAACAGAACAGAGACCTCAGAAATAACATGATACACTTACAACCAAC 6329
                               i    iv    vii         vviv     i   iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_103887804_   6330 TGGTCTTCAACAAACCTGACAAAAACAAGCAATGGTTAAATGACTGCCTA 6379
                           i i   i    ivv  v   i v  vv      vv   vi iv i  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_103887804_   6380 TTTAATAAATGGTCCTGGGAAAACTGGTTAGCCATATGTAGAAAACTAAA 6429
                           i  i       v      v      v  ?   i   i i  i v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_103887804_   6430 ACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGGTTA 6479
                         ii         v   i     v                   i    i i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_103887804_   6480 AGGACTTGAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAACCTA 6529
                         ?i   i i       i v i     i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_103887804_   6530 GGCA-ATACCATTCAGGACATAGGTATGGGCAAAGACATCATAACTAAAA 6578
                           ?i- v i -   iv   v v  vv i     v iiv  v  iv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_103887804_   6579 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 6628
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_103887804_   6629 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAGGGTGAACAA 6678
                            v v  i i   i  ii vv    i  v    v  vv ii     v i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_103887804_   6679 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATTGGACAAAG 6728
                         i     i                 v       vii ivi  iv  i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_103887804_   6729 GTCTAATATCCAGAATCTATAAGAAACTTAAACAAGTTTACAAGAAAAAA 6778
                          v  vi          v     ii    ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_103887804_   6779 ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 6828
                              i     v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_103887804_   6829 AAAAGAAGACATTTATGCAGCCAACAAACATATGAAGAAA-GCTCATCAT 6877
                         v        i  vi viii     i  i  i     i i -     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_103887804_   6878 CAGTGATCAT 6887
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.00 (7 / 7)  


3136 27.31 0.55 0.55  chrX_103940875_103947260.rev     4988  5895 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103940875_   4988 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5037
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103940875_   5038 GGCAATACTGCCCAAGGTAATTTATAGATTCAATGCGATCCCCATCAAAC 5087
                                  v     iv i  i  i        i  i     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_103940875_   5088 TACCAATGACTTTCTTCACA-AAATTGGAAAAAACT-ACTTTAAAGTTCA 5135
                          v   iivi i  i  ii  -      -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_103940875_   5136 TATGGAACCAAAAAAGAACCCGCATTTCCAAGACAATCCCAAGCCAAAAG 5185
                                viiv  ii  v  v v  vv    i      iii ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_103940875_   5186 AACAAAGCTGGAGGCATCATGCTGCCTGACTTCAAACTATACTGCAAGTC 5235
                                i      vv   ii  v  ii i      viv    i   iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_103940875_   5236 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAGA 5285
                                 i   i    ii         i iv ii i   v       vv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_103940875_   5286 AGTGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATATACAACC 5333
                          i     i    i--    i  --        vv   i    v  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_103940875_   5334 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5383
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_103940875_   5384 CTATTTAACAAACGGTGCTGGGAAAACTGGTTAGCCATATGTAGAAAGCT 5433
                           v  i      i          v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_103940875_   5434 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAGGGA 5483
                            ii    i    v   i     v              i    i v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_103940875_   5484 GTAAAGAATTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5533
                         vi ?   vi       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_103940875_   5534 TTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5582
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_103940875_   5583 AAACACCAGAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5632
                         vi      i     vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_103940875_   5633 ATTAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTACCATCAGAGTGAA 5682
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_103940875_   5683 CAGGCAACCTATAGAATGGAATAAAATTTTTGCAATCTACTCATCTGACA 5732
                         v  i     i i       i v     v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_103940875_   5733 AAGGGCTAATATCCAGAATTTACAAAGAACTCAAACAAATTTACAAGAAA 5782
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_103940875_   5783 AAAACAGACAATCCCATCAAAAAGCAGACAAAGCATATGAACAGATATTT 5832
                           i   i i  i  v  i?    iii i     v  v    i   i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_103940875_   5833 CTCAAAAGAAGACATTTATGCATCCAACAGACCCATGAAAACATGCTCAT 5882
                            v        i  vi viiiv    i ii v        v       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_103940875_   5883 CATCACTGGCCAT 5895
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3252 26.76 0.55 0.55  chrX_103955380_103961704.rev     4927  5834 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_103955380_   4927 TGGAAGAATATTCCATGTTCACGGGTAGGAAGAATCAATATCATGAAAAT 4976
                              ii    i         i  i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_103955380_   4977 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5026
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_103955380_   5027 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5074
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_103955380_   5075 TAGGGAACCAAAAAAGAGCCCAGA-TCGCCAAGTCAATCCTAAGCCAAAA 5123
                           v    viiv  ii  -      - v     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_103955380_   5124 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5173
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_103955380_   5174 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5223
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_103955380_   5224 CAGTGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAAC 5271
                           i     i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_103955380_   5272 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5321
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_103955380_   5322 CCTATTTAATAAATAGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGC 5371
                         i  v  i  i    i         v  i   v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_103955380_   5372 TGAAACTGGATCCCTTCTTTACACCTTATACAAAAATCAACTCAAGATGG 5421
                             ii    i    v i i     v           i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_103955380_   5422 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5471
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_103955380_   5472 CCTAGGCATTACCATTCAGGACATAGACATGGGCAAGGACTTCATGTCTA 5521
                          v    ?i v viv   iv   v v ivv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_103955380_   5522 AAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTA 5571
                         vi            vvii         vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_103955380_   5572 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATTAGAGTGAA 5621
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_103955380_   5622 CAGGAAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5671
                         v  iv    i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_103955380_   5672 AAGGACTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5721
                          i     vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_103955380_   5722 AAAACAAACAACCCCATCAAAAAGTGGGGGAAGGACATGAACAGACACTT 5771
                           i     i     v  i?    i    vi     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_103955380_   5772 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5821
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_103955380_   5822 CATCACTGGCCAT 5834
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1017 25.60 8.06 10.57  chrX_104017427_104021098     2267  3184 (488)    L1M4_orf2#LINE/L1       14   908 (0)  

  chrX_104017427_   2267 CATGTTCATGGA-----AGACTCACTATGATAAAGATGACAGTTCTCTCC 2311
                                     -----     i v   vi v      i  i v   i  
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chrX_104017427_   2312 AC-TTAATCTATATATTCAATGCAATTCCAATCAAAATCCCAACAGGGTT 2360
                          v-  i     i v      i     i  v            i ------
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC------ 107

  chrX_104017427_   2361 TTGTTTTTTGCCTTTTGCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 2410
                         -  ii    -----    --------------------------------
  L1M4_orf2#LINE/    108 -TGCCTTTT-----TTGC-------------------------------- 119

  chrX_104017427_   2411 TGTGTGTGTGTGTAAGTAAAAAT--ATAAGCTGATTCCAAAATAAATACA 2458
                         ----------------- i    -- i        i i     vv   ii
  L1M4_orf2#LINE/    120 -----------------AGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_104017427_   2459 GAAG-GAAAAAGACCTCAGGATAGCCAAGAAAATTTTTATGAAG--GGAC 2505
                            i- v  ii    -   i        i v   i  v vi   -- i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_104017427_   2506 A----TGG----------CTTATCAGCTATCAAGGCTTATTAGTAAAGCT 2541
                          ----   ----------   vi  ii -    ii    i  -i      
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATT-TCAAAACTTACTA-CAAAGCT 249

  chrX_104017427_   2542 AGAATAAATAAGCTAATTC--T-CTTACATAAAAACTAGGCCAATAGAAT 2588
                          v i   vi   vi i vi-- -  vi     ii -   i vv     --
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGA-- 296

  chrX_104017427_   2589 TCAATATAATA---T--AGA-TCCAGGAGAAAGTCCTTTCCATATATAAA 2632
                              iv    --- --   -     i iv  ii  v -v   v   iiv
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGGT 345

  chrX_104017427_   2633 AACTTAGTATGAGTCGACA---TTG--AAGA----TTAGCTGGGAAAGAA 2673
                         v v  ii v ---      ---v  --    ---- i iiv         
  L1M4_orf2#LINE/    346 CAATTGATTT---TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_104017427_   2674 CAGGCTGTTCAATAAATGGCACTGGAATCACTGGTTAATACACGTTTAAA 2723
                         i  v  v     i      ii    i iv     v  ?i-   i vi   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC-CACATGCAAA 441

  chrX_104017427_   2724 AG---GGGGTT--ATCTTGACGTCACACCATAGACAAATATAAGTTCCAA 2768
                           --- ii   -- i iiv  v          v     v  v ii  v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_104017427_   2769 ACATTTAAAAGATCTAAATGTAAAAAGAAAACCTTTAAAATGTTTAGAAC 2818
                          iivv v ?   i          i ivv   v  v     ivi      v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_104017427_   2819 AATATAAAAGAGACTAA--CTTTATGACA--GAGTAGAAAAATAGTTCTT 2864
                           v i v i ? --   --   ii    v-- i  viiiv   i   ii 
  L1M4_orf2#LINE/    542 AAAACATAGGNG--TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_104017427_   2865 TGAAAGGTTTTATAACAT--AAAACATAA-------AGGAAAATATTAAT 2905
                          ii ------   i   i--   i  i  ------- i     v  vi  
  L1M4_orf2#LINE/    590 TAGA------TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_104017427_   2906 TCATTTTACTATAATAGAAGTAAAATATTCTGATCATCAAAAG-CACCAC 2954
                         vv   vv   vi vi i  v     vv  i  vv v     i -   i i
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_104017427_   2955 TTA-AAAGTAAAAAAGATAATGAAAAACCTGGGGAAAGATATTTGCAAGG 3003
                         iv -     i    -  i  ivv v ivv    ii  i          iv
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAA-GACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_104017427_   3004 CATAAAATTAATAA----TTAGAATCCA---T-TCTAAAAATGTTTTACT 3045
                             v vi i    ----i v v     --- - v    i vv i    v
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_104017427_   3046 ACT-AATC-TACAAGAGA-AAACAACTCAAGAGAAAATTAGGCAAAGGTT 3092
                            -   v-  -  i   -   i   i   vv?    v i        v 
  L1M4_orf2#LINE/    783 ACTCAATAATA-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_104017427_   3093 ATGAGCAGGTGTAACCTTTCATAACCTCTCACAGGAGAGGAAACATGAAT 3142
                         v   ii  -----  v    ------  iv ----   i  v i ii   
  L1M4_orf2#LINE/    832 TTGAATAG-----ACATTTC------TCCAA----AGAAGATATACAAAT 866

  chrX_104017427_   3143 GGCCAATAAACACAGGAAAAGTTGTTTAATTTGACATGTAAT 3184
                                  i    v      v  i i  iv v ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (132 / 99)
Gap_init rate = 0.05 (47 / 895), avg. gap size = 3.64 (171 / 47)  


2968 26.74 1.44 1.10  chrX_104065393_104068653.rev     1866  2770 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104065393_   1866 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 1915
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104065393_   1916 GGCCATACTGATCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 1965
                            v     vvi    v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104065393_   1966 TAACA-CTGACTTTCTTCACAGAA-TTGGAAAAAACTGCTT-TAAATTTC 2012
                          vv  -   v    i  -i     -   -- v  i   v i-    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_104065393_   2013 ATATGGAATCAAAAAGAGCCC-GCATAGCCAAGACAATCCTAAGCAAAAA 2061
                                 viiv  i ii   - v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_104065393_   2062 GAACAAAGCTGGAGGTATCATGCTACCTGACTTCAAACAATACTACAAGG 2111
                                 i      vv   ii  v  ii i      vvv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_104065393_   2112 CTATAGTAACCAAAATAGCATAGTACTGGTACCAAAACAGATATACAGAC 2161
                            i     i   i i  ii i       i iv ii i   i   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_104065393_   2162 AAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 2209
                         v       i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_104065393_   2210 CATCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAGGAT-- 2257
                           vi    i  i     ivv  v   i vi vv            i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_104065393_   2258 TCCTTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAGGCACAAA 2307
                           i  -- i  i        i     v      v  ?   i v   v  i
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_104065393_   2308 GCTGAAACTAGTTCTCTTCTTTACGCCTTATACAAAAATTAACTCAAGAT 2357
                         iv    ii i vi i  v i i  i  v                   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_104065393_   2358 GGATTGAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAA 2407
                             ii?    i           v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_104065393_   2408 AACCTAGGCA-ATACCATTCAGGACACAGGCATAGGCAAAGACTTCATGA 2456
                            v    ?i- v i -   iv   viv  vv       v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_104065393_   2457 CTAAAACACCGAAAGCAGTATGGCAACAAAAGCCAAAATTCACAAACGGG 2506
                         v  vi     i      vv --          vv     vv i   iv  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_104065393_   2507 ATCTAATTAAACTAAAGAGCTCCTGCACAGCAAAAGATACTATCATCAGA 2556
                          ii v  i   v v  i i  ii  ii vv    i  i       vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_104065393_   2557 TTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATC 2606
                         v    v  i     i                 v       vii  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_104065393_   2607 TGACAAAGGGCTAATATCTAGAACCCACAAATAACTTAAACAAATTTACA 2656
                            i  i  i  vi    i    ivi i   v    ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_104065393_   2657 AGAAAAA---AAA-AACCCCATCAAAAAGTAGGCAAAAGATATGAACAGA 2702
                          v     ---   -     v  i?    i i      i   v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_104065393_   2703 CACTTCTCAAAAGATGACATTTATGTAACCAAGAAACATATTAAAAAAAG 2752
                           i     v     v  i  vi vi ii    v  i  i  v    i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_104065393_   2753 CTCATTATCACTGGTCAT 2770
                             vi    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.53 (23 / 15)  


2939 27.73 1.67 0.56  chrX_104080330_104086718.rev     5001  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104080330_   5001 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5050
                              ii i  i   i i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104080330_   5051 TGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCTATCAAGC 5100
                         v  v     v     iv i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104080330_   5101 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTA----TAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  i----    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_104080330_   5146 TATGGAACCAAAAAAGAGCCCACATTTCCAAGTCAATCCTATGCCAAAAG 5195
                                viiv  ii  v  viv  vv    iv     i ivivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_104080330_   5196 AACAAAGCCGGAGGCATCACTCTACCTGACTTCAAACTACACTACAAGGC 5245
                                ii     vv    v  v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_104080330_   5246 TACAGTAACCAAAAAAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5295
                                 i   i v  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_104080330_   5296 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGGTGCATATCTACAACC 5343
                                i    i--    i  --        vvviii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_104080330_   5344 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATAATTCC 5393
                          vi    i  i     ivv  v   i v  vvv          v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_104080330_   5394 CTATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATATAGAAAGCT 5443
                           v  i  i              i      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_104080330_   5444 GAAACTGGATCCCTTCTTTAAACCTTATACAAAAATTAATTCAAGATGGA 5493
                            ii    i    v i i v   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_104080330_   5494 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5543
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_104080330_   5544 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5592
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_104080330_   5593 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5642
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_104080330_   5643 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5692
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_104080330_   5693 CAGGCAACTTACAGGATGGGAGAAAATTTTCGCAACCTACTCATCTGTCA 5742
                         v  i    ii    i            v  i    vii ivi     vi 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_104080330_   5743 AAGGGCCAATATCTAGAATCTACAATGAACA---ACAAATTTACAAGAAA 5789
                          i  i ivi    i     v  i  v    v---    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_104080330_   5790 AAAACAAA---CCCA-TCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5835
                           i     ---    - i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_104080330_   5836 CTCAAAAGAAGACATTTATGCCCCCAAAAAACACATGAAAAAATGCTCAT 5885
                            v        i  vi viivv    v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_104080330_   5886 CATCACTGACCAT 5898
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2783 26.44 1.30 2.93  chrX_104124118_104132666.rev      975  1897 (6652)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104124118_    975 TGGGAAAACATTCTATGCTCATGGATAGGAAGAATCAATATCATGAAAAC 1024
                            i  i i  i i   i        v      v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104124118_   1025 GGCCATACTGACCAAAGTAGTTTATAGATTCAATGCTATCCCCATCAAGC 1074
                            v     vv     v ii i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104124118_   1075 TAACA-CTGACTTTCTTCACAGAA-TTGGAAAAAACTACTTC--AATTTC 1120
                          vv  -   v    i  -i     -   -- v  i  iv i --  v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_104124118_   1121 CTACGGAACCAAAAAAGAGCCCGCATAGCCAAGGCAATCCTAAGCAAAAA 1170
                         v  i    viiv  ii  v  v v        ii     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_104124118_   1171 GAACAAAGCTTGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 1220
                                 i v    vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_104124118_   1221 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGGTATATAGAC 1270
                                  i   i    ii         i iv ii i  ii       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_104124118_   1271 CAATG-AACAGAACAGAGGCCTCAGAAATAACACCACATATCTGCAACCA 1319
                              -  i    iv   ivii         vv   i i  i iiiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_104124118_   1320 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT--TC 1367
                         vi    i  i     ivv  v   i v  vv            i  --  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_104124118_   1368 CTTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 1417
                         i  -- i  i        i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_104124118_   1418 CAACATTGGACTCTTTTCTTACCCCTTATACAAAAATTAACTCATA-TGG 1466
                         ii vi      i i vi  i  v  v                  v -   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_104124118_   1467 ATTAAAGAATTAAACGTAAGTCCTAAAACCATAAATACCCT-AGAAGAAA 1515
                           i ?   vi    i     vv       i     -  i  -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAA 544

  chrX_104124118_   1516 ACCTAGGCAATAACATTCAGGACATTGGCATGGGCAAAGACTTTATGACT 1565
                           v    ?ivv  iv   iv   v    vv i     v ii  iv iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_104124118_   1566 AAAAGACCAAATTCAATGGCAACAAAAGCCAAAATAGACAAATGGGATAT 1615
                          vi v      vv  vvi          vv        i    v   iv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_104124118_   1616 -ATTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTG 1664
                         -  iv   i    i -   i  ii vv    i  v       vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_104124118_   1665 AACAGGCAACCTACAGAATGGTAGAAAATTTTTGCAATCTGTCCATCTGA 1714
                           v  i     i         v       v       viii vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_104124118_   1715 CAAAGGGCTAATATCCGGAATCTACAAAGGGCTAATATCCAGAATCTATA 1764
                         i  i  i  vi     i    v  i    ii  ------------  -  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACT------------CT-TA 780

  chrX_104124118_   1765 AAGTTAAACAAATTTAAAAGAAAAATAAAACAACGCCATCAAAGATCAGG 1814
                         v ii v  i  -- v      v      vv   i---- ?   i  -i  
  L1M4_orf2#LINE/    781 CAACTCAATAA--TAAAAAGACAAATAACCCAAT----TWAAAAAT-GGG 823

  chrX_104124118_   1815 TGAAGGATATGAACAGACACTTCTCAAAAGATGATATTTATGTGGCCAAC 1864
                         ii      v    i     i     v     v     vi vi       i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_104124118_   1865 CA--ACCTGAATAAAAGCTCATCATCACTGGTCAT 1897
                         v --  v    v i v     v     ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (139 / 101)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.05 (39 / 19)  

3198 26.76 0.66 0.66  chrX_104124118_104132666.rev     7151  8058 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104124118_   7151 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 7200
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104124118_   7201 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 7250
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104124118_   7251 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 7298
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_104124118_   7299 TATGGAACCAAAAAAGAGCCAGCATTGCCAAGTCAATCCTAAGCCAAAAG 7348
                                viiv  ii  v    v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_104124118_   7349 AACAAAGCCGGAGGTATCACGCTACCTGACTTCAAACTATACTGCAA-GC 7397
                                ii     vv    i  v  ii i      viv    i   -  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_104124118_   7398 TACACTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 7447
                             v   i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_104124118_   7448 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 7495
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_104124118_   7496 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATCCC 7545
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_104124118_   7546 CTATTTAATAAATGGTGCTGGGAAAACGGGCTAGCCATGAGTAGAAAGCT 7595
                           v  i  i              v   v  v  ?   iiv i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_104124118_   7596 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 7645
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_104124118_   7646 TTGAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 7695
                          ii?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_104124118_   7696 CTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 7744
                         v i  ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_104124118_   7745 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 7794
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_104124118_   7795 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 7844
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_104124118_   7845 CAGGCAACCTACAGAATGGGAGAGAATTTTTGCAACCTACTCATTGGACA 7894
                         v  i     i             i   v       vii ivi  iv  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_104124118_   7895 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 7944
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_104124118_   7945 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 7994
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_104124118_   7995 CTCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAAAATGCTCA 8044
                            v        i  vi viii     v  i-          i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCA 894

  chrX_104124118_   8045 TCATCACTGGCCAT 8058
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3489 15.50 2.43 0.46  chrX_104145776_104147425      500  1157 (493)    L1M4_orf2#LINE/L1      238   908 (0)  

  chrX_104145776_    500 TATTACAAAGCTACAGTAATTATGACTGTGTGGTAATGGCATAAGAGTAG 549
                           i                 i v   v        v         ii   
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_104145776_    550 GCATAAAGTTCAGCGGAATAGAATTGAGAGTGCAGAAATAAACTCATATA 599
                         i    v  v   ii                 v           i    i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_104145776_    600 TCTATG-TCAATTT-TTTTTTACAAGGATGCCAAAAGCATTCAATGGGAA 647
                          i    -      v-    iv      i      i v           i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_104145776_    648 ATCAATAGTCTTTTCAACAAATAGTGCTGAAACAGCTGGATATCCACATG 697
                          vv                   i      ii   i       ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_104145776_    698 CAAAAGAATAAATTTGGACCACTTTCTCATGCCATATACAAAAA----CG 743
                                  i  v       v  vi    ii             ---- v
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_104145776_    744 TAAACTAGCTCAAAGAGGTAGATATAAGAGCTAAAACAATAAAACTCTCA 793
                         i   v i v   ?   vv  i  i             v          i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_104145776_    794 GAAGAAAACATAGGCATAAATCTTTGTGATCTTTGATTGGACAATGGTGT 843
                                       ?i        i    i   v i  i i       v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_104145776_    844 CTTAAATATGACATCTAAAACACAAGCAACCAAAGAAAAA-TACATAAAT 892
                             i        i v   i          v         -  v      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_104145776_    893 GAGACTTCATAAAAATTAACAACCTTTATGCATCAAAGGACACTAGCAAG 942
                         vi        v        v   i   i   v             v    
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_104145776_    943 AAAATGAAAAGATCGCCCACAGAATGGGAGAAAATATTTACAGATCATAT 992
                            i        ivi                        i  i       
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_104145776_    993 ATCTGGCAAGAGTCTAGTATCCAGAATATATCATGAGCTCTTATAACTCA 1042
                              ii   i v  v               v v  i      i      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_104145776_   1043 ACAATGAAAACACAC----CTTAAATTTTTAAAAA--GGCAAATGATTTG 1086
                          i   i    v   v---- ii  ---  ?     --      v      
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAA---TTWAAAAATGGGCAAAGGATTTG 834

  chrX_104145776_   1087 AATAGCCATTTCTCCAAAGA---TCTACAGATCAACAATAAGCACATGAA 1133
                              v              --- v    i  viv               
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_104145776_   1134 AAGATGCTCAAGATCATCAGTCAT 1157
                                    v    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (55 / 43)
Gap_init rate = 0.01 (8 / 671), avg. gap size = 2.38 (19 / 8)  


3098 27.49 1.00 0.33  chrX_104229073_104233978.rev     3514  4415 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104229073_   3514 TAGATAAACATCCTATGCTCATGGATCAGAAGAATTAATATCGTTAAAAT 3563
                          i  v i i    i   i        ii     v       i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104229073_   3564 AAACATATTGCCCAAAGCAATCTACAGATTCAATATAATCCTTATCAAAA 3613
                         iivv   i v      vii              iii     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104229073_   3614 TACTGACATCATTCTTTACAGAATTAGAAATAAC-AACCCAAAAACTCAT 3662
                          v iii vv v  i   i     v v  v - i -i i  v    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_104229073_   3663 ATGAACCCAAAAATGAGCTGAAATAGCCAAAGCAATCCTGAGCAAAAAGA 3712
                            i vviiv  iv  v iii          i     i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_104229073_   3713 ACAAAGCTGCAGGCATCACATTACGTGATTTCAAAATATATTACAAAGCC 3762
                               i  v   vv     i v vii         iv  i        i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_104229073_   3763 ACAGTAACCAAAACAGCATGACACTGGTATACAAATAGACACACAGACCA 3812
                                i   i    ii  ii     i   vii       i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_104229073_   3813 ATGGAACAGAAGAGAGAACCCAGGAATAAAACTACATATTTAAAGACGAA 3862
                               i    vv    ii    i      v i i i     vi v i v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_104229073_   3863 TGATCTTTGACAAAGCCAACAGGAACTTATATTGGGAAAAGAACACCCTC 3912
                             i  i     i viiv  i  v v vi v    i      i vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_104229073_   3913 TTCAATAAATGGTGCTGGGAAAATTGGATAGCCACATGCA---GAATAAA 3959
                              i              v  i      ?         ---    i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_104229073_   3960 ACTGAATTCCTATCTCTTACCAAATACAAGGAGAAACTCAACAAGGATTA 4009
                         ii  i ii    i   vi    v      ii vv       v v    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_104229073_   4010 GAGACTTAAATGTAAGACCTGAAACTA-AAAATACTAAGA-GATGACCTA 4057
                         ?    i           v  i      -    iv  v   -  vi  v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_104229073_   4058 AGGAAAACTCTCCTGGGCATTAGTCTAGGCAAAGAATTTATGGCTAAGAC 4107
                         i ?iv  v   i vv i v  i vi       v iv  iv i v  v   
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_104229073_   4108 CTCTAAAACATAGACAGTAAGAACAAAAGTAGACAAATAGAACTTGATTA 4157
                         vi v   i  i ii  ii  i iv    i    i    v i    v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_104229073_   4158 AATTAAAAAACTCCTTCACAGTAGAAGTAATAATCAATAGAGTAAAGAGA 4207
                           v v       ii vii vvi i i vv iv     v i   i  i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_104229073_   4208 TAACCTGTTGAATGGGAGAAAATATTTATAAATTATTAATCTGATAGGAG 4257
                         i    iiiv                  ii    i  vv        i i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_104229073_   4258 ACTAGTTAATCCAGAATACACAAGGAACTCAAACAACTCAGTAAGAAAAA 4307
                            v  --          i i  i      vv        i   v     
  L1M4_orf2#LINE/    750 ACTTGT--ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_104229073_   4308 AACA--TAACTCCATTGAAAAGTGGGCAAAAGACACAAATAGACACTTCT 4355
                         i   --    i v   ?    i        i  ivii        i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_104229073_   4356 CAAAAGAAGACATATAAATGGCTAACAGATATATGAAAA-ATGCTCAATA 4404
                          v        i   i       i  i iii i       -        i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_104229073_   4405 TCACTAATCAT 4415
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.80 (157 / 87)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3419 24.97 0.88 0.99  chrX_104262004_104268688     5284  6192 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104262004_   5284 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATTAATATTGTGAAAGT 5333
                               i i  i     i        v      v          v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104262004_   5334 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATTCCCATCAAGC 5383
                            v     v      v i  i  i       ii  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104262004_   5384 TACCAGTTACTTTCTTCACTGAATTAGAAAAAAAAAAACT-ACTTTAAAT 5432
                          v    i i i  i  ii ------     vvi v  i  - iii    v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGC------AGAAATTGACAAGCTGATCCTAAAA 144

  chrX_104262004_   5433 TTCATATGGAACCAAAAAAGGGCCCGCATAGCCAAGACAATCCTAAGCAA 5482
                                    viiv  ii iv  v v        i      i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_104262004_   5483 AAAGAACAAAACTGGAGGCATCACACTACCTGACCTCAAACTATACTACA 5532
                         i         ii      vv       v  ii ii     viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_104262004_   5533 AGGCTACAGTAACAAAAACAGCATGGTACTGGTACCTAA--ACAGATATA 5580
                          i          iv  i    ii         i --   -- i   i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATA 292

  chrX_104262004_   5581 TAGACCAATGGAATGGAACAGAGACCTCAGAAATAACACCACACATCTAC 5630
                             i         i   iv    vii         vv   i    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_104262004_   5631 AACCATCTGATCTTCGACAAACCTCACAAAAACAAGCAATGGAGAAAGAA 5680
                         iii  vi    i        ivv vv   i v  vv      i       
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_104262004_   5681 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGATAGCCATATGCAGAA 5730
                          vvi  v  i  i              v         ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_104262004_   5731 AACTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 5780
                         i v    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_104262004_   5781 TGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGA 5830
                              i ?    i       v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_104262004_   5831 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 5879
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_104262004_   5880 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5929
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_104262004_   5930 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5979
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_104262004_   5980 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCT 6029
                             v  i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_104262004_   6030 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAA 6079
                           i  i  i  vi          v  i  v      iv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_104262004_   6080 GAAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGAC 6129
                         v     i     i     v  i?    i    ii     iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_104262004_   6130 ACTTCTCAAAAGAAGACATTTATGCAGCCAA----CACATGAAAAAATGC 6175
                          i     v        i  vi viii     ----          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_104262004_   6176 TCATCATCACTGGCCAT 6192
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (133 / 90)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.43 (17 / 7)  


3052 25.56 2.68 1.34  chrX_104304631_104310105.rev     4089  4984 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104304631_   4089 TGGAAAAACATCCCATGCTTATGGATAGGAAGAATCAATATTATTA---T 4135
                               i i        i i      v      v i      i   --- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104304631_   4136 AGCCCTACTACCCAAAGCAATTTATAGATTCAATGCTATTCCTATCAAAT 4185
                         i  vv    v      vii  i  i        i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104304631_   4186 TACCAATGATATTCTTCACAGGACTTGA--------------AATTCATA 4221
                          v   iiviiv  i  ii   i v    --------------        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_104304631_   4222 AGGAACCAAAAAAGAGCCCAGCCCAAATAGACAAGGCAATTCTGAGCAAA 4271
                         v    viiv  ii  -     ----     v   ii    ii   iv  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAG----AATAGCCAAAACAATCTTGAAAAAG 195

  chrX_104304631_   4272 CAGAACAAAACTGTAGGCATCACGTT---AAATGACTTGAAACTATACTA 4318
                         v        ii  v   vv    ii ---v   --i ii     -     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAAT--TTCAAAACT-TACTA 242

  chrX_104304631_   4319 CAGGGGTACAGCAACTAAAATAGCAGGGTGCTAGCACAAAAACAGGCACA 4368
                           ii v     i  ii  i i  iiv   i  i   i  ii i  i  i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_104304631_   4369 TAGACTAATGGAAAAGAATAGAGAG-CCAGAAATAAGACAACACATCTAT 4417
                             ii       v     v     -          iv v i    i   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_104304631_   4418 AACCATCTGATCTTCGACAAAGCTGCCAAAAACAAGCAATGGGGAAAAGA 4467
                         iii  vi    i        i v      i v  vv           ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_104304631_   4468 CTCCCTTTTCAATAAATGATGCTGGGACAACTGGCTAGTCATATGCAGAA 4517
                         ivvi        i     i               v  ?i  i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_104304631_   4518 GATTGAAGGTGAACCCCTTCCTTACATCATATACAAAAATTAACTCAAAA 4567
                           v     v  i      v   i   i                       
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_104304631_   4568 TGGTTTAATGAATTAAATGTAGAACCCCAAACTATAAAAACTCT-GGAAG 4616
                            v i ?v  vi        ii v iv           -    -i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAG 541

  chrX_104304631_   4617 ATAACCTAGGCAACAGCATTCAGGACATAGACACAGGCAAAACTTTCATG 4666
                          v   v    ?ivv iiv   iv   v v ivvi      viv    v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_104304631_   4667 ACAAAGACACCAAAAGCAATCA--CAACAAAAGCAAAAATTGACAAGTAG 4714
                         ivv v             --  --         v      v  i  i v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_104304631_   4715 GGTCTAATTAAACTTAAGAACTTCTGCATAGCAAAAGAAACTTTCAACAA 4764
                          iii v  i   v    i     i  iiivv    i  v   v    v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_104304631_   4765 TATAAACAGGCAATCTACAGAATGGGAGAAAAATTTTGCAAATTATGCAT 4814
                         vi i  v  i   i i                vv         i  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_104304631_   4815 ATGACAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATCTCC 4864
                         v   i  i  v  vi       v  v     i     ivv    v  vvi
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_104304631_   4865 AAGAGAAAAATAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAT 4914
                           v i   i i   i     v   ?    i           iv    i v
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_104304631_   4915 ACACTTTTCAAAAGAAGACATACATGTGGCCAATAAACATATGAAAAAAA 4964
                            i  i  v        i     vi          i  i       i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA- 888

  chrX_104304631_   4965 TGCTCGACATCACTGATCAT 4984
                              i      ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.77 (36 / 13)  


2361 20.14 8.16 1.22  chrX_104376157_104378253.rev      498  1073 (1024)    L1M4_orf2#LINE/L1       91   706 (202)  

  chrX_104376157_    498 CCTATCAAAATCTTAGTAGGCTTTTTTTGGCAAAAATTGACAAGCTACTC 547
                                     ii  iv v       --   i             iv  
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATC 138

  chrX_104376157_    548 CTAAAATCTGTATGAGAAGGCAAATGTTCAAGAACAGCCAGAACAATCTT 597
                                iii    ii  v    iv vi v    i     i         
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chrX_104376157_    598 GGTAAAGAA---CAAAG------AACTTACACTTGCCAAGTTCAAAAAGT 638
                          iv      ---     ------i   i      v    v       vv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_104376157_    639 ACTATAAAGTTACAGTAATTAAGACAGTCTTGTATTGGCATAAGGATAGA 688
                             i    i         i        v v   i               
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_104376157_    689 CGTATAGATCAATGGAATA---------------AAAAAAACCC-TACAT 722
                          i                 ---------------   v      -     
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_104376157_    723 TTATTATTAAT--ATTTTTTACATAGGTACAAAGGCATTTCAATGGGATA 770
                             vi i   --     iv   vi   i v   i vv         i- 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-A 387

  chrX_104376157_    771 AAAAATAGTTTTT-----AGATGGTGCTAGAACAA-------------TG 802
                           i      i   ----- i        i i    -------------  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_104376157_    803 CAAAAAGATTAATTCTAACTTCTACCTGATACCATACACAAGTCTTTACT 852
                              ii  v  v ivi  ii      v i      i    ivv  v   
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_104376157_    853 CAAAATGGACCAAAGACCTACATGTAAGAGCTAAAAGTGTAAAACTCTTA 902
                                  i  ?       v               v i           
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_104376157_    903 GTAGAAAACATTGGAGCAAATCTTTGTAATATTGGGTTAGACAAAGATTT 952
                          v         v  ? i       i  i iv         i   v i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_104376157_    953 TGTAGGTAAGACAACAACA-CGCAAGCAACAAGATAAAAATTAGGTCAAT 1001
                         iv   i  v    v   v - i          i v     v   i v   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_104376157_   1002 TGGACTTCGTAAAAAATTTTCAAAAATTGTTGTGCTTCGAAAGTTACCAT 1051
                                 i v    ---- i     i v         i  i vi  i  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAA----TTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_104376157_   1052 TAAAAAAA-AAGAAGACAGGCCA 1073
                         i  i   i-i i      iv   
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCA 706

Transitions / transversions = 1.53 (69 / 45)
Gap_init rate = 0.02 (12 / 616), avg. gap size = 4.50 (54 / 12)  

 933 17.39 1.74 3.04  chrX_104376157_104378253.rev     1377  1606 (491)    L1M4_orf2#LINE/L1      682   908 (0)  

  chrX_104376157_   1377 ATAAAATAAG-GAAAATTAACATGAATCACAGACTGGGAGAAAATATTTC 1425
                           v  iv   -     --i   -- vi      v               v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAA--GACA--ACCCACAGAATGGGAGAAAATATTTG 727

  chrX_104376157_   1426 CAAATCATACATTCGGTAAAAAACATTCACCTTAAATATATAAAAAG--- 1472
                                  i  ii i   iii  v vi i ivi          i i---
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_104376157_   1473 TCATAACTCAAATAATAAAAAGACAAATAACCTGATTTTAAAAAATGGTC 1522
                          i i       -                    ii   ?--        v 
  L1M4_orf2#LINE/    778 TTACAACTCAA-TAATAAAAAGACAAATAACCCAATTW--AAAAATGGGC 824

  chrX_104376157_   1523 AAAGGACCTGAACAGTCATTTCTTCAGAGAAGACATTCAAATGGCCAATA 1572
                               ii    i  v       i  i      i  v             
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_104376157_   1573 AGCATATGAAAAGATGCCCAACATCATTTAGTCA 1606
                             i            i        ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.55 (28 / 11)
Gap_init rate = 0.03 (6 / 227), avg. gap size = 1.83 (11 / 6)  


3217 26.43 0.88 0.88  chrX_104403004_104405440.rev     1039  1946 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104403004_   1039 TGGAAGAACATTCCATGCTCATGGATAGGAAGAAGCAATATCGTGAAAAT 1088
                              ii i  i     i        v      vvi     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104403004_   1089 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 1138
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104403004_   1139 TTCCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 1186
                          i   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_104403004_   1187 ATATGGAACCAAAAAAGAGCCCGCGTTGCCAAGTCAATTCTAAGCCAAAA 1236
                                 viiv  ii  v  v vi v     iv    ii i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_104403004_   1237 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGC 1286
                                 i      vv       v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_104403004_   1287 CTACAGTAACCAAAACAGCATGGTACTGGTACCTAA--ACAGATATATAG 1334
                                  i   i    ii         i --   -- i   i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATAG 295

  chrX_104403004_   1335 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCGTATCTACA 1382
                          i        i    i--    i  --        vv  iiii  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_104403004_   1383 ACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT 1432
                         iii vi    i  i     ivv  v   i v  vvv           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_104403004_   1433 TCCCTATTTAATAAATGGTGCTTGAA-AACTGGCTAGCCACATGTAGAAA 1481
                         vvi  v  i  i          v i -      v  ?       i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_104403004_   1482 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 1531
                         iv    ii    i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_104403004_   1532 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 1581
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_104403004_   1582 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGA 1630
                            v    ?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_104403004_   1631 CAAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 1680
                         vv vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_104403004_   1681 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 1730
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_104403004_   1731 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTG 1780
                            v  i     i                 v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_104403004_   1781 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 1830
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_104403004_   1831 AAAGAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACA 1880
                            i i     i     v  i? v  i     i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_104403004_   1881 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCT 1930
                         i     v        i  vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_104403004_   1931 CATCACCACTGGCCAT 1946
                           v  i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3206 24.06 4.10 0.57  chrX_104414015_104418645.rev     3266  4142 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104414015_   3266 TGGAAAAATATACCCTGTACA--GATTGAAGGA----ATATTATTAAAAC 3309
                               i    v  v   v  --     i i  ----     i    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104414015_   3310 ACCTGTAATACCCAAAGTGATCTAAAGATTCAGTGTAATCCCTATCAAAT 3359
                         iv vi  v v      v       v       ii i             v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104414015_   3360 TTCTAACATCATTTTTTCACAAAAATAGAAAAAACAATCCTAAAATTCAT 3409
                          i i i vv v      -i  i    v  v  ivii              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_104414015_   3410 ATGGAACCAGAAAAAAACCCCAAAGAGCCAAAGCAATCTCTAGCATAAAG 3459
                               vi- v  iii    vi  v       i      iv iv vi   
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_104414015_   3460 AAAAAATCTGGAGGCATCATGCTGCCTGATTTCAAAATATACTATAAAGC 3509
                           v   vi      vv   ii  v  ii         iv     i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_104414015_   3510 TATTGTAATCAAAACAGCATTGTACTGGCATAAAAAGAGATACATTGACC 3559
                           iv        i    ii v            ii v   i i  v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_104414015_   3560 AATGGAAAAGGACAGAAAGCACAGAAATAAAATCAAGTATTTATAGTGAA 3609
                                v  i iv  i  iv          vi  vii      i  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_104414015_   3610 TTAATTTTTGATATAGGTGCCAAGAACATACAACGGGGAA-GAATAGTCT 3658
                           i     i  i vi          v   v   i      -         
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_104414015_   3659 CTTCAATAAATTGTGTTGGGAAAACTGAATAGCCACAGGTAGAAGAACGA 3708
                         i     i    v   i     v     i   ?     v i i     i  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_104414015_   3709 AATTGGACCCCTATCTTCCATCATAAACAAAAATCAAATCAAAATGGATA 3758
                          i           i  iv  i    v        i  v           v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_104414015_   3759 AAAGACTTAAACGTAAGACCTGTAACTGTAAAGCCGCTATAAGAAAACAC 3808
                          ?    i    i      v  iv    i    i ivi  v         i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_104414015_   3809 AGGGA-AAAGCTCC-----------------AATGATTTCTTGAATAGAA 3840
                            ?i-   v  i -----------------    i      ii   vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_104414015_   3841 CTACAAAAGCATAGGCAACAAGAGCAAAAATA--TA--TTAGATTGCATC 3886
                          vv        i i       i  v       --  --  i  i v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_104414015_   3887 AAACTAAAAAGAATTTGCACAGCAAAAGAAAC-------AGAGTGAAGTG 3929
                            v v    ivv    ii vv    i  v  ------- i      iv 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_104414015_   3930 ATAACCCATGGATTGGGAGAAAATATTTGCAAACAATACATCTGATAAGG 3979
                          i      ii  v                    iv   i           
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_104414015_   3980 GGCTAATATCAAAAACATATAAGGAACCCAAATAACTCAATAGCAAGGAA 4029
                          i  vi    v i  i      i    i vv i         ii  ii i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_104414015_   4030 ACAAATCACCAGGTTTAAAAAATTGGGCAAAGGATCTAAATATATATTTC 4079
                               v   vii  ?     --            i i    v i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_104414015_   4080 TTAAAAGAAGAGATATGAATGGCCAAGAGATATATAAAAAATATGCTCAA 4129
                          iv        v   ii         v iii i  i    i-        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG-ATGCTCAA 895

  chrX_104414015_   4130 AATTTCTAATTAT 4142
                         v  iv????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (126 / 81)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.42 (41 / 12)  


3112 27.01 0.77 0.66  chrX_104434175_104436601.rev     1029  1935 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104434175_   1029 TGGACAGCTACCCCATGTTCATGGATTAGAGGAATGAATGT-GTTAAAGT 1077
                             v  v  i                i  i  v v   i -     ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104434175_   1078 GTCCATACTACCCAAAGCAGTCTACAGATTCAATATAATCTCTATCAAAT 1127
                          v v     v      viii             iii    i        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104434175_   1128 TACCAATGATATTCTTCACAGAAATAGAAAAAAAAATCCTAAAATTTATA 1177
                          v   iiviiv  i  ii       v  v  ivvi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_104434175_   1178 TGGAACCACAAAAGACCCAGAATAGTCAAAGCAGTCCTGAGTAAAATGAG 1227
                              vii   ii            i    i  i  i   iv  i v  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_104434175_   1228 CAAAGCTAGAGGTATCATAGTCCTTGACTTCAAATTATACTACAAAACTA 1277
                              i i    vv   i v i iii i      viv         i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_104434175_   1278 TAGTAACCAAAACAGCATGCTACTGGCATAAAAATAGACACATAGACTAA 1327
                         i     i   i    ii  v           ii       i     ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_104434175_   1328 AATAACAGAATAGGGAAACCAGAAATAAATTGACACAGCTACAGGCAACT 1377
                         viv  i     v i  iv           iiv i   vi  ii v   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_104434175_   1378 TATTTCAAACAAAGGCACCAAAAATAGACATTGGGGAAAGGATCGTCTAC 1427
                         v    ivi    i  ii    i vi vv  v         i  v    vi
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_104434175_   1428 TCAAAAAATGGTGCTGGCAAAACTGGATATCCATATGCAAAATAATAAAA 1477
                             v            v v         ?   i        v   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_104434175_   1478 CTAGGTCCCTATCTCTAGCCAAATACAAAAACCAAATCAAAAACAAATTA 1527
                         i i ii     i   vvi   v         ii  v      -iii  i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGATCA 499

  chrX_104434175_   1528 AAGAC--AAATGTGGGACCTGAAACTATACAACTGCTAGAAGAAAACTTT 1575
                         ?    --      ii  v  i        v    vi           v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_104434175_   1576 GGGG-AAATGCTTCAGGACATTGGTCTGGGAAAGGAATTCCTGAGTAAGA 1624
                           ? -    -    iv   v    vi i  v  v iv   i iii  v  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_104434175_   1625 CCTCAAAAACACAGGCAACCAAAGCAAAAAATGGATGAATGAGATTATAT 1674
                          vi     i    i     v    -       i   i   vi  i vi  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCAT 647

  chrX_104434175_   1675 TACACTAAGAAGCTTCTGCACAGCAAAAGAAACAATTGACAATGTAAAGA 1724
                         i v v v i  i   i  ii vv    i  v  v  ii v  v  i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_104434175_   1725 GACAACCTACAAAATGGAAAAAAA-AT--GTAAACTATTCAACTGAATAG 1771
                                i   i     i i    -  -- i   ii  vi v    vv  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_104434175_   1772 GAATTAATAATCAGACTATATAAAGGACTCGAGCAACTCAATAGCAAAAA 1821
                          i i vi  vi    v         i    vvi          ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_104434175_   1822 ACACAAATAATCCAATCTATAAATGGGCAAAAAAATCCTAATAGACATAT 1871
                         i-        i     i? v           ii - iiv         v 
  L1M4_orf2#LINE/    798 G-ACAAATAACCCAATTWAAAAATGGGCAAAGGA-TTTGAATAGACATTT 845

  chrX_104434175_   1872 TTCAAAAGAAGACATATAAATGGCCAGTGGGTATATGAAAAAAATTTTCC 1921
                         i  v        i   i         i ii i i       i - vi  v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCA 894

  chrX_104434175_   1922 ACATCACCAATCAT 1935
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (153 / 88)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.18 (13 / 11)  


2886 25.00 3.49 1.24  chrX_104588313_104590569      877  1764 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104588313_    877 TGGAAAAATATTCCATGCTCATGGACTGGAAGAATCATTATCATTAAAAC 926
                               i    i     i       i       v i v   ii    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104588313_    927 AGCCATACTCCCCAGAGCAAAGTACAGATGCAGTGCTATTCCTATCAAAC 976
                         i  v          i vii vv       v  ii  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104588313_    977 TACCAA-TGTTATTTTTCACAGAAA-----AA--TGTTCC-AAAATTCAT 1017
                          v   i-  ii-     ii      -----  --  v   -         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_104588313_   1018 ATGGAACCAAAAAAGAGCCCAAACATCCAAAGCAATCCTAAACAAAAAGA 1067
                               viiv  ii  v  vi  i v     i     i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_104588313_   1068 ACAAACCCTGAGGCGTCACATTACCTGACTTCAAACTATACTGTATGGCT 1117
                              viiv    vv     i v  ii i      viv    ii vi   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_104588313_   1118 ACAGTAACAAAAATAGGATGGTATAGGTACAAAAACAGACCCATAGACCA 1167
                                iv  i i  vi     iv  i i  ii i    vi     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_104588313_   1168 ATGCAACAGAATAGAGAACCCAGAAA---ATC-ATAC--TGACAG-CATC 1210
                            v  i     v    ii       --- i -    -- v ii -  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_104588313_   1211 TGATATTCGACAAAGTAGACAAAAATAAGCAATGGGGAAAGGACC-TCTT 1259
                             v        i vv v   i vi vv            i iv-    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_104588313_   1260 ATTCAATAAATGGCGCTGGGATAGCTGGCTAGCCACATACAGAAGAATGA 1309
                         -     i      i       i i    v  ?      i  i        
  L1M4_orf2#LINE/    400 -TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_104588313_   1310 AACTGGATACCTTCCTTACACCATATACAAAAATTAACTCAAGATGGATT 1359
                          ii    iv   v   i                         i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_104588313_   1360 AAAGATTTAAATTTAAGACCTTAAACAGTAAGAATCGTAGAAGAAAACCT 1409
                          ?   ii     v     v  v    vi   i v  v           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_104588313_   1410 AGG---AAATACCATTCTGGACATAGGTCCTGGCAAAGATTT------TA 1450
                            ---    -- -   vv   v v  viiv     v i   ------  
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_104588313_   1451 TGACAAAGGTTCCAAAAGCAATTGCAACAAAACCAAAAATTGACAAGTGG 1500
                              ------         vvv         vv      v  i  i v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_104588313_   1501 TATCTAATTAAA-CTAAAGAGCTCTGCACAGCAAAAGAAACTATTAACA- 1548
                         v ii v  i   -i    i vi i  ii vv    i  v     i  v -
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_104588313_   1549 -GTAAACAGAAAATCTACACAATGGGAGAAAATATTTGCAAACTATACCT 1597
                         -  i  v   v  i i   v                      ii   iv 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_104588313_   1598 CTGAAAAAGTTCTAATATCCAGAATGTGTGATGAACTTAAACAATTGTAC 1647
                             v  i vv  vi          i i i v     ivv    i vv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_104588313_   1648 AAGCAAAAAACAAAAAATCCCATTAAAAAGTGGACAAAAGACATGAACAG 1697
                           vv    i     v  i  v   ?    i   i    i  iv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_104588313_   1698 ACACTTCTCAAAAGAAGACACACAAGCAGTCAACAA--ACATGAAAACAT 1745
                            i     v        i i    iii i   i  --         v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_104588313_   1746 GCTCAGCATCACTAATCAT 1764
                              i     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (127 / 92)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.21 (42 / 19)  


2602 28.24 2.23 0.89  chrX_104638776_104644233.rev     4072  4967 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104638776_   4072 TGGAAAAACATCCCACGCTCATGGATAGGAATAATCAATATTGTTAAAGT 4121
                               i i      i i        v    v v i           ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104638776_   4122 GGCCATATTGCTCAAAGCAATTTATAGATTCACTGCTATTCTTATCAAAC 4171
                            v   i v i    vii  i  i       vi  v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104638776_   4172 TACCAAGAACACTTTTTACAAAATCAGAAAAAAAGTATTCTAAAATTCAT 4221
                          v   ivvi vi     i  i  viv  v  ivv -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chrX_104638776_   4222 ---GAAACCAAAAAGAGCTTAAATAGCTAAAGCAATCCTAAGCAAACAGA 4268
                         ---    ivv  ii  v ivi      i   i     i i iv  iv   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_104638776_   4269 GCAAAGCTGAAGGCATAATATTACCCATCTTCAAACTATACTCCAAGGCT 4318
                         i     i  i   vv v i i v    vi      viv    v   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_104638776_   4319 ACAATAACCAACAGAGCATGGTACAGGTGCAAAAACAGACATATAGACCA 4368
                            i   i   v v  ii      v  iii  ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_104638776_   4369 AAGGAACAGAATAGAGGTCCCAGAAATAAAGCTGCATACCTACAACTCTC 4418
                          v    i     v   ivi           v iii i ii  iiiiivvi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_104638776_   4419 TGATCTTTGACAAAGTTCACAACAACAGGCAATAGGGAAAAACTC-CCTA 4467
                             i  i     i v vv   v v  vv    i      i v v-i  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_104638776_   4468 TTCAAAAAATGCTGCTGGGATAACTTAGCTAGCCATATAGAAAAGATTGA 4517
                              v     v        i    -i v  ?   i  iv      v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACT-GGATAKCCACATGCAAAAGAATGA 448

  chrX_104638776_   4518 AACTGGACCCCTTCTTTTCACCATATA-AAAAATTTCAACTAAAAATGGA 4566
                          ii         v i iv         -       --    v        
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATT--AACTCAAAATGGA 496

  chrX_104638776_   4567 TTAAAGACTTAAATATAAAACCCAAAACTACGAAAAACCCTAGGATAAAA 4616
                          i ?    i     i   i v i       i-    vi i   i v    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chrX_104638776_   4617 CCTAAA---AAATACCATTCTGAATGTAGGCCCTGGCAACAATTTC---- 4659
                          v  ii---    -- v iv   viv i  iiv-     iii    ----
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--CTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAG 592

  chrX_104638776_   4660 --ATGACA---AAAGCAATTGCAACAAAAACAAAAATTGACAAGTGGTGC 4704
                         --      ---      vvv         iv      v  i  i v vi 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_104638776_   4705 CTAATTAAACTAAGGAGCTTCTGCACAGCAAAAGAAACCATCAATAGAAT 4754
                         i v  i   v v ii i   i  ii vv    i  v  i     v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_104638776_   4755 AAACAGACAACCTACAGGATAGGAGAAAATTTTTGCCAACTAAGAAACTG 4804
                         i  v        i    i  i         v     v  ii viv v   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_104638776_   4805 ACAAAGGTCTAATATCTAACATCTATAAGGAACTTAAACAAATTTACAAG 4854
                          i  i  v  vi    i iv  v     i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_104638776_   4855 AAAAA---AAATTACCCCATTAAAAAGTGAGCAAAGGACATGAACAGATA 4901
                              ---    v    v   ?    i  i        iv    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_104638776_   4902 CTTTTCAAAAGAAAACATACATATGGCCAACAAATATATGAAAAAATGCT 4951
                         i  i  v      i i     v        i  ii i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_104638776_   4952 CAACATCACTAATAAT 4967
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (148 / 102)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.15 (28 / 13)  


2925 24.97 6.27 0.81  chrX_104652292_104656951     3307  4167 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104652292_   3307 TGAAAAGTCATCTTATATTCATGGAATTAGAAGAATCAATACTGTTAAAA 3356
                           i    vi   ii  i        -  i     v i    i      i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGA-TTGGAAGACTTAATATTGTTAAGA 49

  chrX_104652292_   3357 TAATG-TACTACCCAAAATAATCTATAGATTCAATACAATCCCTATCAAA 3405
                          iiii-    v      v i     i        ii              
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_104652292_   3406 ATACCAATGAAGTTCTTCACAGAAATATTTTTTA-AAATTG----TAACA 3450
                           v   iivivv  i  ii       ----- v -  ii  ----   v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAAT-----TGACAAGCTGATCCTAAAA 144

  chrX_104652292_   3451 TTTGTTTGGAACCAGAAAAGACCCCAAATAGCCAAAGCAATCTTGAACAA 3500
                           ii v     viiv  ii     vi          i          v  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_104652292_   3501 AAAGAACAAAGTTGGAGGCAGTGCACTACCTGAATTCAAATTATGCCACA 3550
                         i                 vvvii    v  ii v      viv i i   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_104652292_   3551 AAGCTATAGTAACCAAAACAGCATGGTGCCAGCATAAAAACAGACACATA 3600
                               i     i   i    ii    i ii      ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_104652292_   3601 GACAAATAGAACAGAATGGAGAACTTAGAAGCAAATCCATGTATTTACAG 3650
                           iv   i   i     v    iiii    ii   i    ii     ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_104652292_   3651 CCAAATGATTTTCAATAGAGGTGCCAAGGAACATACATTGGGGAAAGA-C 3699
                         i   v        i i ii         - v   v  v          -i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAG-ACCATTCAATGGGGAAAGAAT 393

  chrX_104652292_   3700 AGTCTCTTCAATAAATGGTGATGGAAAAACTGTATATTCATATGCAGAAA 3749
                              i     i        v   i v     v   ?i  i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_104652292_   3750 GATGAAACTCAACCTCTATCTTTCACCAAATACAAAAATAATCTCAAAAT 3799
                         i     ii vi   i   i  iv     v          v v        
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_104652292_   3800 AGATTAAAGAC--AAACATCAAACTTCAAACCATAAAACGACTAGAAAAA 3847
                         i   i ?    --   ii v i vi v    i       vvi     i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_104652292_   3848 TGCATAGAGG-AAAT-------ACCTCAGG----ACATTGGT--CTGAGA 3883
                         vi     i? -    -------    ii  ----i  v    --  v   
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_104652292_   3884 ----------------------ACAAAAGCAAAATTAGGTAAATGAGATT 3911
                         ----------------------       v    v   i     vi  i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_104652292_   3912 ATACCAAA-TTAAAAAGCT--GCACAGCAAATGAAACAATTAATAGAATG 3958
                         vi i    -       vi -- ii vv    v  v  v  i  v i i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_104652292_   3959 AAGAGACAACTTGCAAAATGGGGAGAAATATTTGCACACCATTAACCTGA 4008
                           i       iii  i      iii           v i   vv i    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_104652292_   4009 CAAGTAATTAATATGCAGAATATACAAAGAACTC--AAAACT---TAGCA 4053
                         i   vi i vi   v         i         -- v    ---  ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_104652292_   4054 CAGAAACCAATAATTCCATT-AAAAATGGGCTAATGATCTGAATAGACAT 4102
                         v i i  v     ii v   -          v  v   i           
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_104652292_   4103 TTCTCAAAAGAAGACACACAAATGGCCAGCCAGTATATGAAAAAGCGCTC 4152
                              v        i i           iiv  i i       iii    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_104652292_   4153 AACATCACTGATCAT 4167
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (143 / 69)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.39 (61 / 18)  


3005 28.05 1.11 0.44  chrX_104736613_104740117     2111  3012 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104736613_   2111 TGGAAGAACATTCCATGCTCATGAAGAGGAAGAATCAATATCATGAAAAT 2160
                              ii i  i     i     i vv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104736613_   2161 GGCCATGCTGCCCAAAGTAATTTATAGATTCAATGCCAACCCCATCAAGC 2210
                            v  i  v      v i  i  i        i  v v   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104736613_   2211 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2258
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_104736613_   2259 TATGGAACCAAAAAAGAGCCTGCATTGCCAGGACAATCCTAAGCAAAAAG 2308
                                viiv  ii  v  v v  v    ii      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_104736613_   2309 AACAAAACTGGAGGTATCACGCTACCTGACTTCAAACTGTACTACAAGGC 2358
                               ii      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_104736613_   2359 TACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGATTTATAGACC 2408
                                 i   i    ii i       i iv ii i   iv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_104736613_   2409 AGTGGAGCAGAACAGAGGCCTCAGAAATAACATCACACATCTATAA-CAA 2457
                          i    ii    iv   ivii         vvi  i    i   ii-   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_104736613_   2458 TCTGATCTTTGACAAACCTGACAAAAACAAGAAAGGGGGAAATGATTCCC 2507
                          -    i  i     ivv  v   i v  vvv  v       vi  vvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_104736613_   2508 TGTGTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCTG 2557
                          v vi  i              v      v  ?i  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_104736613_   2558 AAACTGGATCCCTTCCTTAAACCTTATACAAAAATTAATTCAAGATGGAT 2607
                           ii    i    v   i v   v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_104736613_   2608 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 2657
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_104736613_   2658 TAAGCA-ATACCATTCAGGACATAGGCATGGGGAG-AACTTCATGACTAA 2705
                           i ?i- v i -   iv   v v  vv i  v i-iii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_104736613_   2706 AACAACAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGGGATCTAA 2755
                         i   v        vvi          iv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_104736613_   2756 TTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAGTGAAC 2805
                          i   v v  i i   i  iiivv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_104736613_   2806 AGGCAACCTATAAAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 2855
                           i     i i i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_104736613_   2856 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 2905
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_104736613_   2906 A--CAAA--ACCCCATCAAAAAGTGGACAAAGGATATGAACAGACACTTC 2951
                          --    --    v  i?    i   i        v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_104736613_   2952 TC-AAAAAAGACATTTATGCAGCCAACAGACGCATGAAAAACTGCTCATC 3000
                           -   i    i  vi viii     i ii i        iv      v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_104736613_   3001 ATCACTGGTCAT 3012
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (154 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3095 27.23 1.79 0.45  chrX_104846545_104852813     4881  5776 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_104846545_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104846545_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_104846545_   4981 TACCAGTGACTTTCTTCACATAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v    ivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_104846545_   5029 AATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                         v      viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_104846545_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGAC 5128
                                i      vv       v  ii i      viv        ii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_104846545_   5129 TACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii i       i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_104846545_   5179 AATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGTATATCTACAACT 5226
                                i    i-- v  i  --        vv  i  i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_104846545_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_104846545_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_104846545_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAA------------TGGA 5364
                            ii    i    v   i     v         ------------    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_104846545_   5365 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5414
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_104846545_   5415 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5464
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_104846545_   5465 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5514
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_104846545_   5515 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5564
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_104846545_   5565 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTATTTATCTGACAA 5614
                           i     i   i             v  i    vii  v       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_104846545_   5615 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAG 5664
                         i  i  vi          v  i  v      vv    v iv i  v   i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_104846545_   5665 AAACAAACAATCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5714
                          i     i  i  v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_104846545_   5715 TCAAAAGAAGACATTTATGCAGCCAAAAAACTTATGAAAAAATGCTCATC 5764
                           v        i  vi viii     v  i vi       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_104846545_   5765 ATCACTGGCCAT 5776
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 3.33 (20 / 6)  


2545 23.22 4.47 7.88  chrX_104975837_104980168.rev     2905  3843 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_104975837_   2905 GGAGAGGCAACATATGCTCATGGACTAGAAGAATTAATATTGCTAAAATG 2954
                            i  ii v vi   i       i i     v         i   i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_104975837_   2955 ACCCTACTATCCCAAGCAATATCCAGATTCTATGCAATCCTTATGAAAAT 3004
                         i vv    vi  v  vii  v v       v i       i   v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_104975837_   3005 ACCAATGACATTCTTCACAGAAATAGGAAAAA-AATCCTAAAATTTGCAT 3053
                         v   iivi v  i  ii       v iv  iv-i           iii  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_104975837_   3054 GGAACCAAAAAAGACCTAGAATAGCCAAAGCAATCCTGAGGAAAAAGAAT 3103
                             viiv  ii    i            i     i   ii  i     i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_104975837_   3104 AATACTAGAGGCATCACAATATCAGATTTCAAAATATACTACAAAACTAC 3153
                           vii i    vv     v vi vi         iv         i    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_104975837_   3154 AGCAACCAAAA--------------------AACAGACACACATACCAAT 3183
                           i  i   i --------------------i i     i i v i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_104975837_   3184 GGAACGGTATAAAGGACCCATAAATAGATCCACATATTCATTTATC-TCA 3232
                             ii v  vi  iii   v     i i   i ----       v-   
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATA----CATTTATGGTCA 347

  chrX_104975837_   3233 TTGTGGTTGATTTTTGATAAAGGCATCAAGAATATTCACTGGGGAAAGAA 3282
                         -----i        i  i  i  iii     vi     v           
  L1M4_orf2#LINE/    348 -----ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_104975837_   3283 CAATGTCTTCAATAAATGGTGCTGGGAGAACTAAATATCCATATGCAAAA 3332
                         i i v i     i              v    ii   ?   i        
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_104975837_   3333 GACTGAAATTAGACCCCTATTTCTCACCTTATAAAAAAATCAACTCAAAA 3382
                           v    i  i        ii  v    v    v      i         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_104975837_   3383 TAGATTAGAGACTTAAATGTAAGATCTGAAACCATAAAACTACTAGAA-- 3430
                          i   i ?    i           v  i    i        vi     --
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_104975837_   3431 -AATATAAGA--AAATGCTTGTGGACATTGGTTTGGGAAAAA-------A 3470
                         -  i   i ?--    vi i   -  v    v  i  v  vi------- 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_104975837_   3471 GA-ATAGGACCAAA-GCACAGGCAACAAAAGCAAAAATAGACAAATAGAA 3518
                           -  iiv      -     i          v         i    v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_104975837_   3519 TTATATCACACTAAAAATCTTCTGCACAGAAAAGGAAATGATCAACAAAG 3568
                         i vi    v v v    v   i  ii vvv      v iv     v    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_104975837_   3569 TGAAGAAACAACCTGAAGAATGAGAGAAAATATCTGCAAACTCTTCGTCC 3618
                             i i      iiv      i          i      iiv vii  i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_104975837_   3619 AACAAGGGATTAAAATCCTGAATGTA--AGAAACTCAAACAACTCAACAG 3666
                         i i      i viv    v    i  -- ii     vv         i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_104975837_   3667 AAAAAAG-CAAATAATCCAACATGTATACATATGTAACAAACCTGCACGT 3715
                         v      -       i    ------------------------------
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAA------------------------------ 811

  chrX_104975837_   3716 TGTGCACATGTACCCTAGAACTTAAAGTATAATAAACAAAATGGACAAAT 3765
                         ---------------------  ?  ------------      i    v
  L1M4_orf2#LINE/    812 ---------------------TTWAA------------AAATGGGCAAAG 828

  chrX_104975837_   3766 GATTTGAATAGACATTTCTC---AAAAGACTTAGAAATAACCAACAGATA 3812
                                             --- i    iv  v    ii    i iii 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_104975837_   3813 GATGAAAAAAAATTTCAACATAATTAATCAT 3843
                         v       i vii -      v ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCT-CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (138 / 76)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 6.82 (116 / 17)  


3585 17.27 2.81 1.47  chrX_104992121_104994351.rev      541  1287 (943)    L1M4_orf2#LINE/L1        1   757 (151)  

  chrX_104992121_    541 TGGAAAAAGTTTTCCTGTTCATAGATAGGTAGATTTAACATTGTTGAAAT 590
                               i vv ii v       i   v  v   i    i      i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_104992121_    591 AGCAATACGGTCCAAAATTGTCTCCATAGATTCAATGCAATCCCTATTAA 640
                         i       vvi     -   -v  i i        i           i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTG-ATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_104992121_    641 AATCCCAATGGCCTTTTATTGAAGAAATGGAAAAGTTGATCCTATATTTC 690
                                iiv       -   v      v  v   i        v v   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_104992121_    691 ACGTGGAATCTTAAGAAGCTCCTAATAGCCAAA-CAATGTTGAAAAAGAA 739
                          ii     vivi   iii i vv          -    v           
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_104992121_    740 AATCTAAGTTGGAGAACTCACACTTTCCAATTTCAAAGCTTACTGCAA-G 788
                         i v v         i          i           i      i   - 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_104992121_    789 TTACAGTAATCAAAGCAGTATGGTACTAAATAACATAAGGAGAGACATAT 838
                         i            ii    i       ----ii        v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACT----GGCATAAGGATAGACATAT 293

  chrX_104992121_    839 AGATCAATGGAATAAAATTGGGAGTTGGCAAATAAACCCATACATCTATG 888
                                       i     i    iviv                i    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_104992121_    889 GTCAAT--------------GGTGTT-ATACCATTCAATAGGGAAAAAAC 923
                               --------------    ii- v          i      i  i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_104992121_    924 AGTCTTTTCAACAAATGGTGCTGGGACAAGCGGATATACCTATGCAAAAC 973
                                                      vi     ?v vi        v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_104992121_    974 AATAAGGTTGGAGTCCAAATTTCACACCATATACAAAA-TTAACTCAAAA 1022
                            i i      vi  -v ii                 -           
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_104992121_   1023 TTGATCAAACACCTAAATGTAATAGCTAAAACAATAAAATTCTTGGAAGT 1072
                          v     ? v            v         v      i    i    v
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_104992121_   1073 AAACATAGGGATAAATCTTGATGACCTTGAATATAGCAATGAATTCTGAT 1122
                                  ?i        vi        ii vvi      iv    v v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_104992121_   1123 ATTTGACACCCAAA-TATAAGGCAAGAAAAGGAAAAAAAAGATAAATTAG 1171
                           v       v   -i i   -   v     -      v         i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAG-CAACAAAAG-AAAAAATAGATAAATTGG 640

  chrX_104992121_   1172 GCTTCATCAAAAATTAAAAA-TTTGGGGCACCAAGGGAAACTATCAAGGA 1220
                         i           -       -   v v  vi   i   v         i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_104992121_   1221 AGTGAAAATACAACATACAGAATAGGAGAAAATATTTGCAAATCATAT-T 1269
                                 v     vi       i                        - 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_104992121_   1270 CTGATGAGAGTCTAGTAT 1287
                              i  i v  v    
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTAT 757

Transitions / transversions = 1.33 (72 / 54)
Gap_init rate = 0.02 (16 / 757), avg. gap size = 2.00 (32 / 16)  

 597 20.26 8.50 1.31  chrX_104992121_104994351.rev     1587  1739 (491)    L1M4_orf2#LINE/L1      745   908 (0)  

  chrX_104992121_   1587 AAAAGACTCTAGTATATGGAATACTTAAAGAATGTTTACAATTCAACAGC 1636
                           ii    i--    vii     iv       ivi      i    i ii
  L1M4_orf2#LINE/    745 AAGGGACTT--GTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_104992121_   1637 AAAAGGATAAGCAAACCAATTAAAAAACAGGCAAAGGACTTGAATAGACA 1686
                             i  i  ii  v      ?     ii         i           
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_104992121_   1687 TGTCTCCAAA-------------TGGTCAGTAAACATATGAAAAGATACT 1723
                          v        -------------   i  i   i  i          i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_104992121_   1724 CAACAACATTAATCAT 1739
                              v  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 4.00 (24 / 6)
Gap_init rate = 0.01 (2 / 164), avg. gap size = 7.50 (15 / 2)  


3177 27.57 0.89 0.33  chrX_105009339_105015628     4895  5797 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105009339_   4895 TGGAAGAACATTCCATGCTCATGGGTAGAAAGAATCAATATCGTGAAAAT 4944
                              ii i  i     i      i v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105009339_   4945 GGCCGTACTGCCCAAGGTAATTTACGGATTCAATGCCATCCCCATAAAGC 4994
                            vi    v     iv i  i   i       i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105009339_   4995 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5042
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_105009339_   5043 ATATGGAACCAAAAATGAGCCTGTGTTGCCAAGTCAATCCTAAGCCAAAA 5092
                                 viiv  iv  v  v vi v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_105009339_   5093 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5142
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_105009339_   5143 CTACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGAC 5192
                                  i   i    ii         i  v ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_105009339_   5193 CAATGGAACAGAACAGAGGCCTCACAAATAATGCTGCATATCTACAACTA 5242
                                 i    iv   ivii  v      vv iii i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_105009339_   5243 TCTTATCTTTGAGAAACCTGACAAAAACAGGAAATGGGGAAAGGATTTCC 5292
                         vi v  i  i  v  ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_105009339_   5293 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5342
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_105009339_   5343 AAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGGAT 5392
                           ii    i    v   i     v i            i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_105009339_   5393 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACT 5442
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_105009339_   5443 TAGGA-T-AACATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5490
                             ?- -  iv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_105009339_   5491 ACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAAT 5540
                                     vvi      i   vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_105009339_   5541 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5590
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_105009339_   5591 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5640
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_105009339_   5641 GGGCTAGTATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5690
                           i  v           v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_105009339_   5691 AACAA----CCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTTCT 5736
                         i    ----   v  i? v  i     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_105009339_   5737 CAAAAGAAGACATTTGTGCAGCCAAAAGACACATGAAAAAATGCTCATCA 5786
                          v        i  viiviii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_105009339_   5787 TCACTGGCCAT 5797
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (144 / 101)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


2866 25.69 4.70 0.57  chrX_105100248_105102604      993  1864 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105100248_    993 TGGAAAAATGTCCTGTATTCATGGATTAGAAAAATAAATATCATTAAAAT 1042
                               i  i   ii i          i   i v v     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105100248_   1043 GTCTACATTATCCAAAACTATCTAAAGATTCAATGAAATCCATATCAAAA 1092
                          v v i i vi     viv     v        i v     v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105100248_   1093 TACCAATGACATTCTTTACAAAAATAGAAAAA--AATTCTAAAATTTGTA 1140
                          v   iivi v  i   i  i    v  v  i--i  i        ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_105100248_   1141 TGGAACCACAAAAGACTCCAAACAGCCAAAGCAGTCCTGAGTAAAGAGAA 1190
                              vii   ii   i vi  i       i  i  i   iv  ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_105100248_   1191 CAAAACTGGGGGTATCACATTACTTGACTTCAAAATATACAGTACAAAGC 1240
                             ii   i  vv     i v iii i       iv   --        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGC 248

  chrX_105100248_   1241 TATAATAACTAAAACTGCATGGCACAGGCATAAAAACATACACATAAACC 1290
                           i i   ii  i  v ii   i  v       ii i v   i   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_105100248_   1291 AGTGGAATAGAATAGAGAACCCAGAAATAAATCCATGCATTTACAGCCAA 1340
                          i           v    ii           i    i      ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_105100248_   1341 CTGATAT-CAAAAAAGGTGCCAAGAACACAGATTGGGGAAAAAACAGTCT 1389
                         i    v - i v  i          v  ivv v        i  i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_105100248_   1390 CTTCAATAAATGGTGCTGGGAGAATTGG-TATCCACATGCAGAATAATGA 1438
                         i     i              v  i   -  ?         i  v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_105100248_   1439 AATTAGACTTGTGTCTCTCACCATATACAAAAAT-----CAAAATGAATT 1483
                          i  i   iiv ii   v                -----       i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_105100248_   1484 AAAGACTTAAATTTAAGACCTGAAGCAATGAAATTACTAGAAAAAAAATT 1533
                          ?    i     v     v  i  i v  i   i vi     i    vv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_105100248_   1534 AAGG--AAATGCTTC-------------AGGAAAT--TTTTTTAGGTAAA 1566
                          i ?--    -    -------------   v   --   i    i  vi
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_105100248_   1567 AC-CTTAAATCACAGGCTA-AAAAGCAAAACTAAACACATGGGATTACAT 1614
                           - iv   v    i  v -     v    v  i i v  v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_105100248_   1615 CAAACTAAAAAATGCTTTTGCACATGAAATGAAAC----AACAGAGTGAA 1660
                             v v     --      ii v v   v  v  ----  v i      
  L1M4_orf2#LINE/    648 CAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_105100248_   1661 AAAGCAATCTACAAAATTTGAGAAAATATTTTTAAACTATGCATCCAACA 1710
                           ii   i i   i   vv            vi   ii  ii   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_105100248_   1711 AAGAA----TATCCAGAATATATAAGAAACTCA-ATAGC-AAATAATAAT 1754
                          i i ----                ii     v- i i -v        v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_105100248_   1755 AA--CAA-TAATTTGATTTTAAAATAGGCAAAATACCTGAACAGACATTT 1801
                           --   -   iiii   ?v     i      iv ii    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_105100248_   1802 CTCAATAGAAGACGCATAAATTTCCAGCAGGTATATGTCAAAATGCTCAG 1851
                            v v      iii i    vv   ii i i i   vv  i       i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_105100248_   1852 TATCACTAATCAT 1864
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (147 / 73)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.56 (46 / 18)  


2942 25.96 3.59 0.60  chrX_105131236_105133445.rev      876  1711 (499)    L1M4_orf2#LINE/L1        1   861 (47)  

  chrX_105131236_    876 TGGAAATATATTCCATGTTCATGAACTGGAAGAGGCAATATTGTTAGAAT 925
                               v    i           i i       vvi          ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105131236_    926 ATCCACAGTACCCAAAGCAATCTACAGATTCAATACAATCCCCAACAAAA 975
                         iv v i v v      vii              ii       i v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105131236_    976 TGCCAATGACATTATTCATAGAAATAGGAAAAACAATTCTAAAATGTATA 1025
                          v   iivi v  v  iii      v iv  ivii  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_105131236_   1026 TGGAACCACAAAAGCCCCAGAATAGCCAAG-CTATCCTGAGAAAAAAGAA 1074
                              vii   ii v              i- v   i   i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_105131236_   1075 CAAAACTGAAGGAATCACATTACTTGGCTTCAAATTATACTACAGGCCTA 1124
                             ii  i    v     i v iiiii      viv       iiv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_105131236_   1125 TAGAAACCAAAACATCATAGTACTGGCACATAAACAGACACATAGACCAT 1174
                         i  v  i   i   vii i         i vii i     i     i  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_105131236_   1175 TTGAACAGAAGAGAGAACCCAGAAACAAATCCATGTGTCTTTAGTGAACT 1224
                          v   i    vv    ii       i   i    iii i v i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_105131236_   1225 CATTTTTGACAAAGGTGCCAAAAACATGCATTGGGGAAAGGACAGTTTGT 1274
                         v     i     i        i v   v  v         i i   i v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_105131236_   1275 TC--TAAATGGTGCTGCGTAAACTGGATATCCATATGCAGAAGAATGAAA 1322
                           --i           v vv         ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_105131236_   1323 CTAGACTCCT----------------------TAAGTCAAA-TAGATAAA 1349
                         i i   i   ----------------------   v     - i   v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_105131236_   1350 ATACTTAAATCTATGACCTCAAAGTATGAAACTACTAAAAACAAAACTTT 1399
                          v  i     v  v  v  v   v   i     -  v i  v     v v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATA 549

  chrX_105131236_   1400 GAGG--AATCTGTACAGGACACTGGTGTGGGCAA--ATTTTTTGAGTACT 1445
                          i? --     - - iv   vi   vv i     --i   i  iii  iv
  L1M4_orf2#LINE/    550 GGNGTAAATCT-T-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_105131236_   1446 ATGCAACAAGCACAAGCAACCAAAGCAAAAGTGGACAAATGGGATCACAT 1495
                          ii v v             v    v    i i  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_105131236_   1496 GAAGTTAAAAAACTTCTGCACAGCCAAGGAAACAATCAACAAATTGAAAA 1545
                         v  iv v        i  ii vv v     v  v     v   v      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_105131236_   1546 GACAACTCACAGAATGGGAGAATGTATTTGCAAAGTATCCATCTGACAAG 1595
                               i               vi          vi  vi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_105131236_   1596 GGATTAATAACCAGAATGTAAAAGGAGCTCATACAACTCTACAGGAAAAA 1645
                            i vi  v       i  v  i  i   v        v i iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_105131236_   1646 AAATCTAATAATCTGATCAAAATATGGGCAAAAGATCTGAATAGACATTT 1695
                         i -- v     i ii  i?   v         i   i             
  L1M4_orf2#LINE/    798 GA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_105131236_   1696 CTCAAAAGAAGACATA 1711
                            v        i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATA 861

Transitions / transversions = 1.45 (126 / 87)
Gap_init rate = 0.01 (10 / 861), avg. gap size = 3.50 (35 / 10)  

 769 26.83 0.98 0.98  chrX_105131236_105133445.rev     2006  2210 (0)    L1M4_orf2#LINE/L1        1   205 (703)  

  chrX_105131236_   2006 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2055
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105131236_   2056 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2105
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105131236_   2106 TCCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2153
                              iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_105131236_   2154 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 2203
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_105131236_   2204 AACAAAG 2210
                                
  L1M4_orf2#LINE/    199 AACAAAG 205

Transitions / transversions = 1.89 (36 / 19)
Gap_init rate = 0.01 (3 / 205), avg. gap size = 1.33 (4 / 3)  


2998 25.91 1.66 1.11  chrX_105144173_105147702.rev     2137  3039 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105144173_   2137 TAGAAAAACATCCCATGTTCATGTATAAGAAGAATCAAGATTATTAACAT 2186
                          i    i i              v  vi     v i  v   i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105144173_   2187 GGCCATGCTGTCCACAGCAATTTTCAGATTCAATGCTATTCCTATCAAAC 2236
                            v  i  vi   v vii  i v         i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105144173_   2237 TGCCAATGACATCCTTCCTAGAATTAGAAAAAGCT-ATTTTAAAATTCAT 2285
                          v   iivi v ii  ivi    v v  v  -   -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_105144173_   2286 ATGGAAC--CAAATGAGCCTGAATAGCCAAGGCTGTACTAAGCAAAAAGA 2333
                               v--   iv  v  v          ii vi vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_105144173_   2334 ACAAAGCAGGAGGCATCATGCTACCCAACTTCCAACCATATTACATGGAT 2383
                               iv     vv   ii  v     i   v  v v  i    vi v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_105144173_   2384 GTGGTAATAAAAACAGCATGGTACTGGTACAAAAACAGACATACA--CCA 2431
                         iii     v  i    ii         i i  ii i       i --i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_105144173_   2432 ATGGAACAGAATAGAGAGCCTAGAAATAAGGCTGCACACCTACAATCATC 2481
                               i     v     i i        iv iii   ii  iii   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_105144173_   2482 TGATCCTCCACAAAGCTGACAAAAACAAGCAATAGGGAAAGGACTTCCTT 2531
                             ii  v    i v  v   i v  vv    i       i ivvi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_105144173_   2532 ATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATTTGCTGAAGACTGA 2581
                         -     i              i      v  ?   iv   vi    v   
  L1M4_orf2#LINE/    400 -TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_105144173_   2582 AACTGGACCCTTTCCTTTCACCATATACAAAAATCATCTCAAGATGAATT 2631
                          ii       i v   iv                i v     i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_105144173_   2632 AAAGACTTAAATGTAAAACTCAAAACAATAAAAGCTCTGTGA-GATAACC 2680
                          ?    i         i vii     v      -    vv  -  v   v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chrX_105144173_   2681 TA--TGCAATACCATTCTGGACATAGGGATGGGCAAAGATTTCATGAGGA 2728
                           --? i  - i -   vv   v v   v i     v i    v iiiv 
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_105144173_   2729 AGACACCAAAAGCAATTGTAACAAAACCAAAAATGGACAAATGGGACTTA 2778
                         v             vvv i       vv      i  i    v      v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_105144173_   2779 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGTAACTATCAACAGAGTAAA 2828
                           i   v v  i i   i  ii vv    i vv        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_105144173_   2829 CAGACAACCTACAGGAAGGGAGAAAATTTTTGCAAACTATGTGTGTGACA 2878
                         v        i    i v          v        ii  i i v   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_105144173_   2879 AAGGTCTAATATTCAGTATCTATAAGGAACT--TA-AAC-CAATTTGCAA 2924
                          i  v  vi   i   v  v     i     --  -   -    ----  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT----AA 791

  chrX_105144173_   2925 GAAAAAAA--AACAACCCCATTGAAAAAGTAGGCAAAGGACATGA-CAGA 2971
                         v     i --  i     v   ?     - i         iv   -i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGA 840

  chrX_105144173_   2972 CACTTTTCAAAGGAGGACATACATTTGGACAACAAGCATATGAAAAATAG 3021
                           i  i  v  i  i  i     vv   v   i     i       ivv 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_105144173_   3022 CTCAATATCACTAATCAT 3039
                              i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (130 / 100)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.47 (25 / 17)  


3108 26.49 1.32 1.10  chrX_105191158_105194643     2088  2993 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105191158_   2088 TGAAAAAACATTCCATGCTCATGGATAGGAAGGATCAATAGTGTTAAAAA 2137
                           i   i i  i     i        v     iv i    v      i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105191158_   2138 GGCCATACTGTCCAAAGCAGTTTACAGATTCAATACTATTCCTATCAAAC 2187
                            v     vi     viii i           ii v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105191158_   2188 TACCAATGACATTCTTCACAGAACTACAGAAAACC--ATTTTAAAATTAA 2235
                          v   iivi v  i  ii     -- iv  v  v --  ii       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chrX_105191158_   2236 TACAGAAGCATAAAAAAATTCTGAATAGCTAAGGCAATCCTAAGCAAAAA 2285
                           ii   iiii  iii -ii v       i  ii     i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_105191158_   2286 GAACAAATTTGGAGGCATCACATTACCCAATTTCCAACTATATTACAGGG 2335
                                v       vv     i v         v  viv  i    ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_105191158_   2336 CTACAGTAACCAATATAGCATGGTACTGGTACAGAAACAGACATATAGAC 2385
                                  i   v i  ii         i i iii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_105191158_   2386 CAATGAAACAAAAGAGAGAGCCCAGAAATAAGGCCTCACACCTACAACCA 2435
                              i  i i  vv     i          iv  vi   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_105191158_   2436 TATGATATTTGACAAAGCTAACAAAAGCAAGCAATGGGAAATTGAC--TC 2483
                         vv    v  i     i v iv   i v  vv       i  vvi i--  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_105191158_   2484 TTCATTCAACAAATGGTGCTGTGATAACTGGCAAGCCATATGCAGAAGAT 2533
                           --                 v  i      vv ?   i     i    v
  L1M4_orf2#LINE/    398 TT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_105191158_   2534 AGAAACTGAACCCTTTCCTTTCACCATATACAAAAATCAACTCAAGAT-- 2581
                         v   ii  i    i v   iv                i       i  --
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_105191158_   2582 ---AAAGCCTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGACAA 2628
                         --- ?  v i         i v i            vi i i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_105191158_   2629 CCTAGGCA-ATGTCATTCTGGACATAGGAACAGGCAAAGATTTCATGAGG 2677
                          v    ?i- vi  -   vv   v v  ivi      v i    v iiiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_105191158_   2678 AAGACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGAGACCT 2727
                          v             vvv          v      v  i    vi   i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_105191158_   2728 AATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTATCAACAGAGTGA 2777
                         v  i   v v  i i   i  ii vv       v        v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_105191158_   2778 ACAGACAACCTGCAGAATGGGAGAACATTTTTGCAAACTATGCATCTGAC 2827
                          v        ii             v  v        ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_105191158_   2828 AAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAA 2877
                           i  v  vi       v  v     i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_105191158_   2878 AAA--TGAACAATCCCATTAAAAAGTGGACAAAAGACGTGAATACACACT 2925
                            --ii  i  i  v   ?    i   i    i  iv      v   i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_105191158_   2926 TTTCAAAAGAAAGCATACAGGTGGCCAACAAGGAAGCATATGAACAACTG 2975
                          i  v      iii     ii       i   ----  i     v iv  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAG----CACATGAAAAGATG 890

  chrX_105191158_   2976 CTCAACATCACTGATCAT 2993
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.20 (22 / 10)  


2201 25.55 10.88 2.20  chrX_105196892_105199671     1462  2279 (501)    L1M4_orf2#LINE/L1        1   889 (19)  

  chrX_105196892_   1462 TGGAAAG-TATTGGAAATTGTGTTCATGGATTGAAAGTCTCAATA----- 1505
                                -   i-----iii             i   v  i    -----
  L1M4_orf2#LINE/      1 TGGAAAGATATC-----CCATGTTCATGGATTGGAAGACTTAATATTGTT 45

  chrX_105196892_   1506 AAGATATCAGTTATCCCCAAATGGATCT-TAGATTTAATTGATTTCCTAT 1554
                              iv  i vv         v     -i     i  ivv v i     
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_105196892_   1555 CAAAATCCCAGCATG---TTTTTGCAGGCATAGACAAGCTTATTTTCAAA 1601
                                     -  ---         iv  v        v  ii v   
  L1M4_orf2#LINE/     96 CAAAATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_105196892_   1602 TTTGTATGGAAAGGCAAGGGAACTAAAGTAGCTGAATTACTCT------- 1644
                           ii        v        v i i i    ii  vi v   -------
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_105196892_   1645 ------------------ACTGACATT----AGT------ACTTAATATA 1666
                         ------------------   v   i ---- i ------     v  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_105196892_   1667 CAGC-ACAGTAATCAAAACAATCAAAATGTGGTATTTGCA-ATGACATAG 1714
                         v   -           i   i ------      i v   - v i-    
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGT------GTGGTACTGGCATAAGG-ATAG 287

  chrX_105196892_   1715 ACACAAGGATCAATGGGACAGAATGGAGAACCCAGAAATAGTCCCAAACA 1764
                            i vi         i i     v    ii         iv    v   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_105196892_   1765 AATATGCTTAATCAAGTTTTGACAAG----CAAAAGCAATTTAAGGGGAG 1810
                         vv    v i   ii v   i      ---- v  ii v   i  v   ii
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_105196892_   1811 AAGGATAATCTTTTTCAACAAAGGGTCCTGGAGCTATTGGACATCCATAG 1860
                            i   i      -       v   v    ii v i    i ?   i v
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_105196892_   1861 GCAAAGAAGCAAAATC---CACCTTAAACTTCACACCTTATATGAAAATT 1907
                              ii iii  i i--- v   ---  i       v    ii      
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCT---ACCTCACACCATATACAAAAATT 483

  chrX_105196892_   1908 AACTCAAAGTGCATCATGATCTTAAGTCTGACATGTAAATCTATACAACT 1957
                                 i  v    ?iiv i   i v i v vv    v     v    
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_105196892_   1958 TTTAG--GAAAA-----------ATCTTCAGTATTTAGTGCTAAGCAATT 1994
                         i    --     -----------      ivv ii v v i  i     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_105196892_   1995 GTT----AGACTTGAAACCAATGCCACTATTCATAAAAACAAAAAACAAA 2040
                            ----   iv   v     viv   v viv i    i-      i i 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGA 632

  chrX_105196892_   2041 GAATTCGAACTT-GTCAAAATTAAACACTTTGGTTCTGACAAAGTCA-TG 2088
                         v  v i i    -i           v     v  v  vvv  i v  - i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_105196892_   2089 TTAAGAGGATGAAAGAATAAACTATACACTACAAGAATATATTTGCACA- 2137
                          i    iii     ii i  v i i v v ivi    v         v -
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_105196892_   2138 CACCCATATTATAATGGACTAATATTTAGAATATATAAAGGACTCTCAAA 2187
                           ivi  v v    v     vi   ii             i     i v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_105196892_   2188 ATTTAATAGTAACAA-ACAAGCAATCCAATTAGAAAATAAGCA------- 2229
                          i i    i   v  -    ii  i      ?i     ii   -------
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_105196892_   2230 ------GGTATTTCACTGAATAGGATTTG-AAATGGCAAATAAGCATATG 2272
                         ------ ii     v ii  v i   v i-       v        i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_105196892_   2273 AGAAGAT 2279
                          i     
  L1M4_orf2#LINE/    883 AAAAGAT 889

Transitions / transversions = 1.45 (122 / 84)
Gap_init rate = 0.03 (27 / 889), avg. gap size = 3.96 (107 / 27)  


2485 24.94 7.52 0.95  chrX_105204080_105205923      514  1351 (493)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_105204080_    514 TGTTTATGTATCAGGACACTCAAT-TT-TTAAGGTCTCAATTCCACTTAA 561
                             i   v  ii i v   i   -  -     i vv    v iv ii  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_105204080_    562 ATTGATCAGTAGAGTCACTACAATTCCAGTCAATATCCCAGCAGTCTCTT 611
                                vii   v   vii    i  vi    v        v i  i  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_105204080_    612 T-GTAGAAATTAACTAGGAGATTCTAAAATTCACATGAAAATGCAAAGAA 660
                          - i       i  v  vv   i          i   i        i i 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_105204080_    661 GATTGAATAGCCAAAACAACTTTGATAAGGAA---CAAAGTTGGAGAAC- 706
                         vviv               ii    v  i   ---           i  -
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_105204080_    707 -ATACTTCCTGACTTC--------TTGCAAAGGTGCGTTAATCAAAATAG 747
                         - i      ii i   --------i i     v i iv       i i  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_105204080_    748 TGTAGTGCTATTGTAAAAATAAACA-ATAGAGCAATGAAATAGAAGAGAA 796
                            i  i  ivii   ii   i   -     v     i       vv  i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_105204080_    797 AGTTCAGAAATATATTACTCATACATGAACAATTGATATGATATTTTACA 846
                            i        - --  i       vv iii ii  -    v  iv   
  L1M4_orf2#LINE/    316 AGTCCAGAAATA-A--ACCCATACATTTATGGTCAAT-TGATTTTCGACA 361

  chrX_105204080_    847 AAGATGCAAAGGCAATTCA--GAAGAAGAAACATTCTTTTCAGCAAATGA 894
                          i i   v   i v     -- ii   ii  i v        i      i
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_105204080_    895 CACAGGAACAATTGAATATACACAT----AAAAAT--------------- 925
                         ii v  i    i  i   ?v     ----  i   ---------------
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_105204080_    926 -CTCACATTATGTTCAAAAAATTAA----------ACCATAGAACTAAAT 964
                         -      ii  i v      -    ---------- i  ?   v      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_105204080_    965 GTGA-AGTATAAAACCACAAAACATT--GTAAACAA-ATAGAAGAAAACC 1010
                           i -  i-      i i     vi -- v i v  -    i? v   i 
  L1M4_orf2#LINE/    511 GTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_105204080_   1011 TTGATGGCTTTCAGTTAGGCAGAGACTTCTTATATATGACAGCATT-GCA 1059
                           vi  i i  vi        iv ii      v        v  vv-   
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_105204080_   1060 TAATCCTTAAGGGAATAAAATA-ATAAATCAGACTTCAAGAAAATTTAAA 1108
                         i  v vvi  ii   -      -      ii       vv      v   
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAA-AAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_105204080_   1109 AGTTGTGCTCTTTGAAGAGC--TAT-AAGAGGATGAAAAGAC--TTCATA 1153
                          v  v  iv   ii   ii --   -    iii         --ii  i 
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_105204080_   1154 AACCAGAAGAAAAATTTTTTAAAATGATATATCAGATAAAGGACTTCTAT 1203
                         i vii i      - v   vv    v       v     i      v   
  L1M4_orf2#LINE/    709 GAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_105204080_   1204 ACAGAATGTATACAGAACTCTCAAGATTAAATAAAATGAAAACAAATTAC 1253
                         v      i    v        i vi i v     v vi  i      v  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_105204080_   1254 CAAAT--AAAAATAGGGAAAATATTTGAATCGACACTTCACTCAGGAAGA 1301
                          v   --      i  v   iv        v    i   v iv i     
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_105204080_   1302 TATATGAATGGCAAATAAGCACATGAAA-GTTGTTCAACATCATAATAAG 1350
                             ii      v               - v  i         ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_105204080_   1351 G 1351
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.64 (128 / 78)
Gap_init rate = 0.03 (28 / 893), avg. gap size = 2.54 (71 / 28)  


2390 23.26 10.55 1.68  chrX_105239933_105247470.rev     1391  2224 (5314)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105239933_   1391 TAGAGAAATATACCATGTTCTTTGACTGAATAACTGAAATACTAATTTTT 1440
                          i  i i    v        v v  i  i vi   v  ----  -  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAA----TA-TTGTT 45

  chrX_105239933_   1441 AGGATGTTA-TATCTCCCCAACATT--TCTGTAGAATTATTGCAATCTCA 1487
                          i    vi -  -        -   --   ii   v i vi      i v
  L1M4_orf2#LINE/     46 AAGATGGCAATA-CTCCCCAA-ATTGATCTACAGATTCAACGCAATCCCT 93

  chrX_105239933_   1488 ATCAAAATCCCAGTAGG-TTTTTCATAGAAATTGAGAAGCTAATTCCAAA 1536
                                      iv v-     iii         v     i  i i   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_105239933_   1537 ATGTATGTGGAAAGAGCAAAGGAACCAGAACAGCCAGACAAATTTTGAGA 1586
                           vi  i      v-    i   v      i     i vv   i    i 
  L1M4_orf2#LINE/    144 ATTCATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_105239933_   1587 AAAAAATACAAAAGTTAGAAGATTCATACTACCTGATTTCAAG------- 1629
                           i  iv     -   i  i  i   i   v  ii       i-------
  L1M4_orf2#LINE/    193 AAGAAGAACAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_105239933_   1630 -----GCTATGGTAATTAAGACAGTTTCTTATTGACATA-GGATTGACCT 1673
                         -----    ii     i        v vv  i  i    -    v   v 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_105239933_   1674 ATAGATCAATAGAATGCAA---AGAGACCA---------TCAAA----TA 1707
                                   i    iv  ---    v   ---------i  v ----  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_105239933_   1708 TAGCCAACAGATTTTGGACAAAGGTA--------ATTAAATGAAGAAATG 1749
                          i i   iv      v     i   i--------   v    ii    vi
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_105239933_   1750 GCGGTCTTTTCAACAAATGGTAC-GGAACAACTGGACATC-ACACACCAA 1797
                         iii                  i -  i         i ? -   ii v  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_105239933_   1798 AATATTCTTCTTGACCCCTCAGCTAAGAAGATATACAAAA-TTA-CTCAA 1845
                          iv  vvvvi v       - v  v v vv          -   -     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_105239933_   1846 AATGGGTTAGCGACCTAAATATAAAACCAAAAATTATAA----CTTGTAA 1891
                              i i ?v         i   i v v    i     ----   iv  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_105239933_   1892 AAAAAAGTAGA---AAATCTTTAAGATTTTGGTCTAGGCAAAGATTTATT 1938
                         i    vi   i---       iiv  ii    vi       v i   v  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_105239933_   1939 AG----GATTTAAAAAGCATGGACCATAAAA-----AATTAATAAATTGG 1979
                           ----  iviv       iiii v i    -----   vi         
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_105239933_   1980 ACTTGA---AAAC---AAGTTCTT----TTCAAAAAA---TAACA----- 2011
                             v ---   i---  ii i  ----      ii ---  v  -----
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_105239933_   2012 -TGAAAAGAAAACCCA--GATTGGGAGACAATACTTGCAAAACACCTATG 2058
                         -        v      --  v       v    i       v  iv   v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_105239933_   2059 TGATGAAGGACTTTTATCCAAAATATATAAAGAACTCTCAAAATTCAATA 2108
                             i i      v      i                 i v  i      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_105239933_   2109 ATAAGATTATTATTGAATAACCAAAT--AAAAATAGT----GAATTTAAA 2152
                             i vv i----i       v   --      i v---- i    i  
  L1M4_orf2#LINE/    791 ATAAAAAGAC----AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_105239933_   2153 CAGACACCTCATCAGAAAAGACATATGAATAGCAAGTGAACACATGAAAA 2202
                         i     ii  vi  i i    i   ii   i  v i i i          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_105239933_   2203 TATGCTCAACAGCATTAGTAAT 2224
                         v          v  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (117 / 75)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 3.09 (102 / 33)  

3208 27.09 0.55 0.55  chrX_105239933_105247470.rev     6140  7047 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105239933_   6140 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 6189
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105239933_   6190 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 6239
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105239933_   6240 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6287
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_105239933_   6288 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 6337
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_105239933_   6338 AACAAAGCTGGAGGCATCACGCCACCTGACTTCAAACTATACTACAAGGC 6387
                                i      vv    i iv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_105239933_   6388 TACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 6437
                            i    i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_105239933_   6438 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 6485
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_105239933_   6486 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAACGATTCC 6535
                          vi    i  i     ivv  vv  i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_105239933_   6536 CTATTTAATAAACAGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6585
                           v  i  i   ii         v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_105239933_   6586 GAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGA 6635
                            ii    i    v   i     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_105239933_   6636 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 6685
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_105239933_   6686 TTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCACATCTA 6734
                         v    ?i- v   -   iv   v v  vv i     v ii   vi vv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_105239933_   6735 AAACACCAAGAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 6784
                         vi       i    vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_105239933_   6785 ATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAA 6834
                           i   v v  i i   i   i vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_105239933_   6835 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 6884
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_105239933_   6885 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 6934
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_105239933_   6935 AAAACAAACAACCCCATCAAAAAGTCGGCGAATGATATGAACAGACACTT 6984
                           i     i     v  i?    i v   i  v   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_105239933_   6985 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 7034
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_105239933_   7035 CATTACTGGCCAT 7047
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2756 25.85 1.75 2.30  chrX_105280269_105282790     1117  2029 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105280269_   1117 TGAAAACATATCCCGTGTTCATGGATGGGTAGAATCAATATTGTGAAAAT 1166
                           i   v       i           v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105280269_   1167 GACCACACTGCCAAAAGCAATCTACAAATTCAAGGCAATTCTCATCAAAA 1216
                          i v i   v  v   vii       i      v     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105280269_   1217 TGCCA-CTGTTATTCTTCACAGAACTAGAAAAACAG-TTCTAAAATTCAT 1264
                          v   -   ii-  i  ii     v v  v  i v - i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_105280269_   1265 ATGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGA 1314
                               viiv  ii  v  viv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_105280269_   1315 ACAAATATGGAGGCATTGCGTTACCCAACTTCAGACTATACTATAAGGCT 1364
                              vv      vv ii ii v     i    i viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_105280269_   1365 ATAGTCACCAAAACAGAATGCTACAGGTATAAAAAAAATAGGCACATAGA 1414
                          i   v i   i    vi  v   v  i    ii ---   i  i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA---TAGACATATAGA 296

  chrX_105280269_   1415 CCAATGGAACAGAATAGAGAACGCAGAAATAAAGCCAAATACTTAACAGC 1464
                         i        i     v    iiv          v   v i i   -ii i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGT 345

  chrX_105280269_   1465 CAAATGATCTCTGAAGAAGCAAACAAAAACTTAAAATGGGGGAAAGGACA 1514
                            v    i ii  vi i vviv   i v v vv       -    i i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chrX_105280269_   1515 CCCTATTCAACAAATAGTGCTGGGATAATTGGCAAGCCACCTGTAAAAGA 1564
                         vi  v          i         i  i   vv ?    v  i      
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_105280269_   1565 ACGAAACTGGGTCCTCATCTCTCACCTTATGCAAAACATCAACTCAAGAT 1614
                          i   ii   ii  ii i   v    v   i     -  i       i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAAT 493

  chrX_105280269_   1615 GGATCAAAGACATAAATCTAAGACCTAAAACCATCTAGATTCTAGTACAG 1664
                               ?    v     v     v       i  v- i i   ----i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCT----TAG 538

  chrX_105280269_   1665 AAGACAGCATCAGGAAAATATTTCCA-GACATTGACTTAGGCAAAGACTT 1713
                             v i   -   ?iv v  i i i-   v   iv        v ii  
  L1M4_orf2#LINE/    539 AAGAAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_105280269_   1714 C------ATGAC--CAAGAACTCAAACGCAAATGCAAAAAAAAAAAGGTA 1755
                          ------     --   i i v   --    ---     i      --  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAA--GCAA---CAAAAGAAAAAA--TA 630

  chrX_105280269_   1756 AATAGATAGGACTTAATTAAACTAAGACGCTTCTGAACAGCAAAAGCAAT 1805
                         i   i  v      v  i   v v i vi   i  vi vv    i vv i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_105280269_   1806 AATCAGCAGAGTTAACAAACAACCCATCAAGGGGGAGAAAATCTTCACAA 1855
                         v    iv i   v  v i        ivi iv          v  ii   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_105280269_   1856 TCTATATATCCGAAAAAGAACTAATATTCTGAATCTACAAATAACTC--- 1902
                         vii       i  v  i i   vi   i v    v  i   v     ---
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_105280269_   1903 -AAATCAGCAAGAAAAAAGCAAACAACCCCCTCAAAATGTGGGCTAAGGA 1951
                         -  v   ii  v     ii    i     vv i?   vi     v     
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_105280269_   1952 CGTGAATAGACAATTCCCAAAAGAAGATATACAAATGGCCAA-AAGCATA 2000
                         iv          v   i v                       -     i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_105280269_   2001 CGGAAAAAATGTGCAACATCACTAATTAT 2029
                         i -    i   iv        ????????
  L1M4_orf2#LINE/    881 TG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (134 / 98)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.95 (37 / 19)  


3002 27.23 1.67 0.33  chrX_105284952_105287357     1018  1913 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105284952_   1018 TGGAAACACATCCTATGCTCATGAATGGGTGGAATCAATATTGTGAAAAT 1067
                               v i    i   i     i  v  vi  v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105284952_   1068 GACCATAAGCCAAAAACT-ATCTACAAATTCAATGCAATCCCCATTAAAA 1116
                          i v   vv  vv   i -       i      i        i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105284952_   1117 TACCATCATCATTCTTCACAGAATTAGAAAAAA-AATTTTTAAGTTCATA 1165
                          v   v vv v  i  ii     v v  v  iv-i  ii v  i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_105284952_   1166 TGGAACCAAAAAAAGCCCACA-TAGCTAAAGCAAAACTAAGCAAAAAGAA 1214
                              viiv  iiii    v -    i   i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_105284952_   1215 CAAATCTAGAGGCATCACACTACCTGATTT-AAAACTATACTATAAGCCC 1263
                             vi i    vv       v  ii    -      -     i  iv i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_105284952_   1264 ATAGTCACCAAAACAGCCTGGTACTGGTATAAAAACAGGCAGAGAGACCA 1313
                          i   v i   i    iv         i    ii i  i  v v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_105284952_   1314 ATGGAACAGAATAGAGGACCCAGAAATAAGCCCAAATACTTACAGCCAAC 1363
                               i     v   iii          i    v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_105284952_   1364 TGATCTTTGACAAAGCAATCAAAAACATAAAAAAGGGAAAGGACACCCTT 1413
                             i  i     i vvii   i v   vv  vi       i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_105284952_   1414 TTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAA 1463
                                             i  i   v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_105284952_   1464 ACTGGATCCTCATCTTTCACCTTATACAAAAATCAACTCAAGATGGATTG 1513
                         ii    i  ii i  iv    v           i       i      ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_105284952_   1514 AGGACTTAAATCTAAGACCTGAAACTATAAAAATTATAGAAGATAACATT 1563
                         ?i   i     v     v  i           v iv       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_105284952_   1564 GGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCAT-GACCAATA 1612
                           ?iv  vi    vv   v    v        v i    v -  i--  i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATG 597

  chrX_105284952_   1613 AC-TCAAAAGCAAATGCAATAGAAGCAAAGATAAATAGCTGAGACTTAAT 1661
                           -i        v v    i i   v   i   i   iv vi     v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_105284952_   1662 TAAGCTAAAGAGCTTTTGCATGGCAAAAGGAACAGGCAGCAGAATAAACA 1711
                         i  iv v  i i      iiivv    i iv  viv  iv i i i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_105284952_   1712 GACAACCCACAGAGTGGGACAGAATTTTCATAATCTATATATATGACAAA 1761
                                      i     v i   v  iii  vii      v   i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_105284952_   1762 GGAATAATATTCTGAATCTACAATGAACTCAAACAAATCAGCAA-AAAAA 1810
                            v vi   i v    v  i  v      vv    v   ii  -     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_105284952_   1811 -------AATCTTATCAAAAAGTGGACTAAGGACAC-AATAGACAATCCT 1852
                         -------  i iv  i?    i   i v     ivi-        v i  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_105284952_   1853 GTAAAGAAGATATACAAGTGGCCAACAAATATAGGAAAAAATGCTCAACA 1902
                         vi               i       i  ii i v     i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_105284952_   1903 TCACTAATGGT 1913
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


3201 26.47 0.89 0.33  chrX_105301450_105306101.rev     3258  4160 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105301450_   3258 TGGGCAAAAATTCCATGTTCATGGATTGGAAGAATCAGTATTATTAAAAT 3307
                            iv i v  i                     v i i    i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105301450_   3308 GTCCATACTACCTAAAGCAATGTACAGATTCAATGCAATCCCTATCATGA 3357
                          v v     v  i   vii  v           i             vi 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105301450_   3358 TACCAATGACATTCTTCATAGAAATAGAAAAAAAAATCCTAAAATTTATA 3407
                          v   iivi v  i  iii      v  v  ivvi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_105301450_   3408 TGGAT-CACAAAAGAAGCAGAATAACCAAAGCTATCCTAAGCAAAAAGAA 3456
                             v-ii   ii  vv       i     i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_105301450_   3457 CAAAACTGGAAGAATCCCATTACCTGACTTCAAATTATACTACAGAGCTT 3506
                             ii    i  v  v  i v  ii i      viv       i    v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_105301450_   3507 TAGTAACCAAAACAGCATGGTACTTGCATGAAAACAGACACATAGGGCAA 3556
                         i     i   i    ii       v    i ii i     i    iv   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_105301450_   3557 TGTAACAGACTAGAGAACCAAGAAA-AAATCCACACACCTACAGTGAACT 3605
                           v  i   v v    ii v     -   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_105301450_   3606 CATTTTTTATGAAGGTGCCAAGAACATACACTGGGAAAAAGACAGTCTCT 3655
                         v     iv ii i          v   v  v    i   ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_105301450_   3656 TCAATAAATGGTGCTAAGAAAACTGGATATCCATATGCAAAATAATGAAA 3705
                             i          ii  v         ?   i        v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_105301450_   3706 CTAGACCCCTCTGTCTCACCATATATAAAAATCAAATAAAAATTGATTAA 3755
                         i i       viv  v         i      i  v v     v   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_105301450_   3756 AGACTTAAATCTCAGACCTTAAGCTATGAAACTACTACAAGAAAACACTG 3805
                             i     v v   v  v  i    i     vi  v         iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_105301450_   3806 GGAAAACTCTCCAGGACACTGCTCTGGGCAAAAATTTCTTGAGCAACACC 3855
                          ?iv  v   i iv   vi  vvi i     vii      iiii vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_105301450_   3856 CCACAGCCACAGGCAACTAAAGCAAAAAGGGACAAATAGAATCACATCAA 3905
                            v iv    i     v    v     vi  i    v i iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_105301450_   3906 G-TTAAAAAGTTTCTGCACAGCAAAGGAAACAATCAACAAAGCTAAGAGA 3954
                         i-       v   -  ii vv       v  v     v    iv  i   
  L1M4_orf2#LINE/    651 AATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_105301450_   3955 CAACCCACATAACTTGC----AAACACTTGCAAGCTAC-CATCTGACAAA 3999
                                  v  --  v----   i i      iii i-i      i  i
  L1M4_orf2#LINE/    700 CAACCCACAGAA--TGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_105301450_   4000 GGATTAATAACCAGAGTATATAAGGAGCTCAAACACCTCTTTAGGAATCA 4049
                            i vi  v     i       i  i   vv   v   vv  iv  vv 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_105301450_   4050 ACCTAATAATCCAATTTAAAAATGAGCAAGAGATCTGAATAGACATTTCT 4099
                         iv v     i      ?       i    ii   i               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_105301450_   4100 CAAAAAAAGACATACAAATGAGAAACAGGCATATTAAAAGGTGCTCAACA 4149
                          v   i    i         ivv  i i   i  v     i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_105301450_   4150 TCATGGATCAT 4160
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3317 24.54 1.09 2.07  chrX_105352976_105356712.rev     2330  3246 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105352976_   2330 TGGAAAAATGTTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 2379
                               i  i i                     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105352976_   2380 GTCCATACTACCCAAAGCAATCTACAGAGTCAATGCAATCTCTATCAAAA 2429
                          v v     v      vii         v    i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105352976_   2430 TACCAA-TGCCATTTTTTTTTTCAAAAA---ACAAAATAGAAAAAAACAG 2475
                          v   i-    ----      v  i   ---    iv -  ---------
  L1M4_orf2#LINE/    101 TCCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCT-GA--------- 136

  chrX_105352976_   2476 TCCTAAAATTTGTATGGAC-TACCAAAGATCCAGAATCACCAAAGCTACC 2524
                                   ii      v- i v ii  i       vi     i v i 
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_105352976_   2525 CTGAGCAAAAAGAACAAAACTGGAGGGATTTCATTACCTGACTTCAAATT 2574
                         i   iv  i         ii      iv iv  i v  ii i      vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_105352976_   2575 ATACCGCAGAGCTATAGTAACCTAAACAGCATGGTACTGGCATAAAAACA 2624
                         v   ii  i     i     i v i    ii              ii i 
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_105352976_   2625 GACACATA-ACCAATGGATCAGACTAGAGAAACCAGAAACAAATTCACAC 2673
                             i   - i       vi   v v    iv       i   ii  i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_105352976_   2674 ACCTACAGCAAACTCGTTTTCAACAAAGATACCAAGAAAATACATTGGGG 2723
                          ii  ii iv  i vi     i    i i i      vv  v  v     
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_105352976_   2724 AAAAGACGGTCTCTTCAATAAATGGTGCTGGGAAAACTGGATATTCGTAT 2773
                            ii ii    i     i              v         ?i ii  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_105352976_   2774 GCAGAAGAATGAGACTAGACCCTTACATCTTGCCATATACAAGAATAAAA 2823
                            i        iii i     i   v  vii          i   v  v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_105352976_   2824 TAAAAGTGGATTGAAGACTTAAATATAAGACCTCAAACTATCAAACTACT 2873
                          v   i     ii?    i     i     v  v       v     vi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_105352976_   2874 ACAAGAAAACTTCGAGAAAAATCTGCAGGACATTGGTCTGGCCAAAAATT 2923
                          v        v v i?iv      v iv   v    vi i v   vii  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_105352976_   2924 TATTGAGCAATACCCCACAAGCACAGACAACCAAAGCAAAACGGGATAAA 2973
                          v  iiii vv  v   v       ii    v    v    vvi      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_105352976_   2974 TGGGATCACATCAAG-TTAAAAAGCTTCTGCACAATGAAGTATATAATCA 3022
                          v   iiv      i-       -   i  ii vvii   v i iv    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_105352976_   3023 ACAAAGTGAAAAGAAAACCCACATAATGGGATAAAATATTTGCAAACTAC 3072
                          v            v        v       v              ii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_105352976_   3073 CAATCTGACAAAGGATCAATAACAAGAATATATAACGAGCTCAAACAACT 3122
                         vv      i  i   iivi  v v           v  i   vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_105352976_   3123 C--TA-TAAAAAATCTAATAATTCGATCTAATAAAAATTAGACAAGTGAT 3169
                          --  -      iv v     ii i  ---- ?    v i i   iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAAT----TWAAAAATGGGCAAAGGAT 831

  chrX_105352976_   3170 TTGAACAGATATTTCTCAAAAGAAGACATACAAATGACAAACAGGAATAT 3219
                              i   i       v        i         i v  i i v i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_105352976_   3220 TAAAAGGTGCTCAACATTATTGATCAT 3246
                         v     i          i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (136 / 85)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  


1816 27.12 1.35 1.15  chrX_105406905_105412600.rev     4002  4521 (1175)    L1M4_orf2#LINE/L1        4   524 (384)  

  chrX_105406905_   4002 AAAAAAATTCCAAGCTTATGGCTAGGAAGACTCAATATCATTAAAATAGC 4051
                            i v  i   v i i    v v        i     ii    i  i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_105406905_   4052 TATTCTGCCCAAAGCAAT-TATAGAATTAATGCTATTTCTATTAAACTAC 4100
                         v  v  v      vii  -  i   v i  i  v  ii    i   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_105406905_   4101 CA-TTGACTTTTTTTTGCAGAATTAGAAAAAAGTATTTTAAAATTCATAT 4149
                           -i  v       --      v v  v  ivvv  ii            
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_105406905_   4150 GGAA---CAAAAGAAGAGCCC-GAATAGCCAAGGCAAGCCTAAGCAAAAA 4195
                             ---   ii  ----   -          ii   v i i iv  i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_105406905_   4196 GAACAAAGCTGGAGTCATCACATTAACTCACTTCAAACTGCACTACAGGG 4245
                                 i     vvv     i vv iv i      vivi      ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_105406905_   4246 CTACAGTAAGCAAAACAGCATGATACTGG-ACAGAAACAGACGCACAGAA 4294
                                  v   i    ii  i      - i iii i    ii i   v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_105406905_   4295 CAATGGAACAGAACAGAGAACCCAGATACAAGGCCACACACCTACAACCA 4344
                                 i    iv    ii     v i  iv   i   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_105406905_   4345 TCTGATCTTCAACAAACCTGTTAAAAATAAGCAATGGGGGAAGAATTCCC 4394
                         vi    i   i    ivv  ii  i vi vv        i      vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_105406905_   4395 TATTTAATAAATAGTGCTGGGATAACTGGCTAGCCATACGCAGAAGACTG 4444
                          v  i  i    i         i      v  ?   i i   i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_105406905_   4445 AAACTGGACCCCTTCCATACACCATATACAAAAATTAACTCAAGATGGAT 4494
                           ii         v  vi                         i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_105406905_   4495 TGAAGAATTACATATAAAACCGAAAAC 4521
                         ii?   vi  v  i   i v v     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAAC 524

Transitions / transversions = 1.73 (88 / 51)
Gap_init rate = 0.01 (7 / 521), avg. gap size = 1.86 (13 / 7)  

1111 26.04 1.56 0.52  chrX_105406905_105412600.rev     4822  5205 (491)    L1M4_orf2#LINE/L1      521   908 (0)  

  chrX_105406905_   4822 AAACAACAGAAACCCTGGAAGACAACCTAGGCA-ATACCATTCTGGACAT 4870
                             v i i  vi i i     v   v    ?i- v i -   vv   v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT 569

  chrX_105406905_   4871 AGGAACAGGCAAATGTTTC--AGATGAAAACATCAAAAGCAATTGCAACA 4918
                         v  ivi      vv     --    - vi   i        vvv      
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACA 618

  chrX_105406905_   4919 AAAGCAAAAATTGACAAGTGGGATCTGATTAAACTAAAGACCCTCTGCCC 4968
                             v      v  i  i v   ii v  i   v v  i v i i  iv 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_105406905_   4969 AGAAAAGGAAACTATCAACAAAGTGAACAGACAACCTAAAGAGTGGGAGA 5018
                         vvv      v        v        v        i v   i       
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_105406905_   5019 AAATGTTTGCAAACTATGCATCCGACAAAGT-CTAATATCCAGCATCTAT 5067
                             i        ii  ii   i  i  i v-  vi       v  v   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_105406905_   5068 AAGGAACT-TAACAAATTTACAAGAAAAAAACAAACAACCTCATTAAAAA 5116
                           i     - v    v iv i  v     i     i    iv   ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_105406905_   5117 GTGGACAAAG-ACATGAACAGACACTTTTTAAAAGAAGACATACATGCAA 5165
                         i   i     - iv    i     i  i iv        i     viiii
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_105406905_   5166 CCAACAAACATATGGAAAAAAGCTCAACATCACTGATCAT 5205
                             i  i  i   i   i v           ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (54 / 44)
Gap_init rate = 0.02 (7 / 388), avg. gap size = 1.14 (8 / 7)  


2717 28.68 1.55 1.44  chrX_105420584_105425676     3699  4601 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_105420584_   3699 AAAATATTCAATACTCATGGATAGGAAGAATCAATATCATTAAAATGGTC 3748
                           i    i v  ii        v      v i     ii    i    iv
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_105420584_   3749 ATACTGCCCAAAGCCAGTTATAGATTCAATGCTATTTCTGTCCAACTACT 3798
                              v      viv vi  i        i  v  ii  i  v  v v i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_105420584_   3799 AATGACATTCTTCACAGAACTAGAAAAATGCT-ATTTTAAAATTCATATG 3847
                          iivi v  i  ii     v v  v  --   -  ii             
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCATATG 152

  chrX_105420584_   3848 GAACCAAAAAAGAGCCCAAATAGCCAAGGCAATCCTAAGCAAAAATAAAA 3897
                            viiv  ii  v  vi         ii     i i iv  i  v  v 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_105420584_   3898 AAGCTGGAGGCATCATATTAGCTGTCTTCAAACTATACTGCAGGGCTATA 3947
                            i      vv   i i vv iivi      viv    i  ii    i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_105420584_   3948 GTAACCAAAACAGCATGGTCCTGGTACAAAAGTAGACACACAGATCAATG 3997
                             i   i    ii    v    i i  iii      i i         
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_105420584_   3998 AAACAGA-----GAGCCCAGAAATAAGGTCACACATCTACAACCATCTGA 4042
                         i  i   -----   i          ivi  i    i  iiii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_105420584_   4043 TCTTCGACAAAGTGGACAAAAATAAACAAGAGAGAAAGGAC--TCCTTAT 4090
                          i        i vv v   i vi vv   vi i     i i--  i  --
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT-- 400

  chrX_105420584_   4091 TCAATAAGTAGTGCTGGGATAACTGCCTAGCCATATGCAGAAGACTGAAA 4140
                             i  i i         i     vv  ?   i     i    v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_105420584_   4141 CTGGACCACTTTCTTACACCATATACAGAAATTATCTCAAGATGGATTCA 4190
                         i      v  vi  i            i      v     i      -  
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT-CA 499

  chrX_105420584_   4191 AAGCCTTAAATATAAAACCCAAAATGATAAAAATCCTGGAAGACAACCTA 4240
                         ?  v i     i   i v i    iv      v  i i     v   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_105420584_   4241 GGCAATAATGTTATTGACATAGGAACAGGCAAAGATTTCATGACAAAGAT 4290
                           ?ivv   v  vv    v v  ivi      v i    v iivv v  i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_105420584_   4291 GCCAAAAGCAATTGCTACAAAACCAAAAATTGACAAATGGGATTTGATTA 4340
                         i         vvv  v      vv      v  i    v   i  v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_105420584_   4341 AAG-----AGCTTCTGGACAGCAAAAGAAACTATCTACAGAGTGAACAGA 4385
                           i----- i   i  vi vv    i  v      v v i      v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_105420584_   4386 CAACCCATAGAATGGGATAAA-TATTTTGTGAACTATGAATCTGACAAAG 4434
                                i         v   -     - ii  ii  iv      i  i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGATAAGG 748

  chrX_105420584_   4435 TTCTAGTATTCAGCATCTATAAGGTATTTAAACAAATTTACAAGAAAGAA 4484
                         vv  v    i   v  v     i v i ivv    v iv i  v   i i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_105420584_   4485 ACAACTCATTTTTAAAGTAATTTTTAAAAGGGCAAAGGACATGAACAGAC 4534
                             v v iii-------    ?vv   v          iv    i    
  L1M4_orf2#LINE/    799 ACAAATAACCC-------AATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_105420584_   4535 ACTTTTCAAAAGAAGACATATATGCCACAAACAAGCATATGAAAAAAAAC 4584
                          i  i  v        i   i viivi v  i     i       i vi 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_105420584_   4585 TCATCATCTGTTATTAG 4601
                            v    v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (147 / 108)
Gap_init rate = 0.01 (10 / 904), avg. gap size = 2.70 (27 / 10)  


3187 26.67 0.66 0.99  chrX_105455923_105462290     4965  5875 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105455923_   4965 TGGAAGGACATTCCATGCTCATGGATAGGAAGAATCACTATCATGAAAAT 5014
                              i  i  i     i        v      v i v   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105455923_   5015 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5064
                           iv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105455923_   5065 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAATTC 5112
                          v   iivi i  i  ii     -   --- v  i  - iii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_105455923_   5113 ATATGGAACCAAAAACAGAGCCCGCATTGCCAAGACAATCTTAAGCCAAA 5162
                                 viiv  i-i  v  v v  v     i        i ivv i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_105455923_   5163 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5212
                                  i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_105455923_   5213 GCTACAGTAACCAAAAACGGCATAGTACTGGTACCAAAACAGAGATGTAG 5262
                                   i   i - i ii i       i iv ii i   v  i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_105455923_   5263 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACA 5310
                          i        i    i--    i  --        vv   i    i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_105455923_   5311 ACCATCTGATCTTTGACAAACCTGACACAAACAAGCAATGGGGAAAGGAT 5360
                         ii  vi    i  i     ivv  v  vi v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_105455923_   5361 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5410
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_105455923_   5411 GCTGAAACTGGATCCCTTCCTTACACCTTATACAATAATTAATTCAAGAT 5460
                         iv    ii    i    v   i     v       v      i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_105455923_   5461 GAATTAAAGACTTAACTATTAGACCTAAAACCATAAAAACCCTAGAAGAA 5510
                          i  i ?    i   v i v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_105455923_   5511 AACCTAGGCAGTA--CCATTCAGGACACAGGCATGGGCAAGGACTTCATG 5558
                            v    ?-   --i -   iv   viv  vv i     v ii   v i
  L1M4_orf2#LINE/    544 AACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_105455923_   5559 ACTAAAACATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5608
                         iv  vi   i        vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_105455923_   5609 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAGACTACCATCAGAG 5658
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_105455923_   5659 TGAAAAGGCAACCTACACAATGGGAGAAAATTTTTACAATCTACCCATCT 5708
                                i     i   v             v   i   vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_105455923_   5709 GACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAA 5758
                           i  i  i  vi          v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_105455923_   5759 GAAAACATCAAACAACCCCATTAACAAGTGGGCGAAGCATATGAACAGAC 5808
                         v    viv    i     v   ? v  i     i   v  v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_105455923_   5809 ACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGC 5858
                          i     v        i  vi viii     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_105455923_   5859 CCATCATCACTGGTCAT 5875
                         i  v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2023 22.77 15.79 4.65  chrX_105503316_105504993      385  1201 (477)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105503316_    385 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTCTTAAAAA 434
                               i i  i     i        v      v i      v    i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105503316_    435 GGTCATATTGCTCAAAACCATTTGCAGATTCAATGCTATTCCTA----AA 480
                           iv   i v i    viv  i i         i  v  i    ----  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105503316_    481 T------------TTTTATAACAA------AGTTG--------------- 497
                          ------------    ii iv  ------  i  ---------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_105503316_    498 -------------------------------------TGAAAA----GAA 506
                         -------------------------------------      ----   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_105503316_    507 CAAAGCTGGAGGCATCACACTACCTGACTTCAAA-----CTATA---CTA 548
                              i      vv       v  ii i      -----   i ---   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_105503316_    549 CA------AAAACAG------AC--GCATAA--------------ACCAA 570
                           ------  i    ------  --      -------------- i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_105503316_    571 TGGAACAGAATAGAGAACCCCAAAATAAATTTGCACATCTACAACCATAT 620
                              i     v    ii  vi       iiiii    i  ---------
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA--------- 341

  chrX_105503316_    621 AATCTTTGACAAAGTCAACCAATCATATGATCTTCGACAAAGTCAACCAA 670
                         ------  -----     i--------    i        i vii-    
  L1M4_orf2#LINE/    342 ------TG-----GTCAAT--------TGATTTTCGACAAGGGTG-CCAA 371

  chrX_105503316_    671 AAT--TTCAATGGGGAAAGGACTCCCTATTCAATAAATGATGCTGGGATA 718
                         i i--              i ivvi  v     i     i        i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_105503316_    719 ACTAGCTAGCCATATGGAGAAGATTGAAACTGGACCCCTACCTTTCACCA 768
                            i v  ?   i   v i    v    ii             iv     
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_105503316_    769 TATACAAAAATCAACTCACAGTGGATTAAAGACTTAAATGTAAAACCTAA 818
                                    i      v i     i ?    i         i v    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_105503316_    819 AACTGTTAAAATCCTATAAGTTAACCTAAG---AAATACCATTCTGGACA 865
                             i v   v  i  v   vv   v  i ---    -- -   vv   v
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACC 568

  chrX_105503316_    866 TATGACCT-GGCAAAGTCTTCATGACAAGGACTCCAAAAGCAATTGCAAC 914
                          -  ivi -     v vi   v iivv v   v         vvv     
  L1M4_orf2#LINE/    569 T-TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_105503316_    915 AAAAACAAAAATTGACAAGTGGGACCTAACTAAACCAAAGAGCTTCTGCA 964
                             iv      v  i  i v    i v ii   viv  i i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_105503316_    965 CAGCAAAAGAAACTATCAACAGAGTAAA----CAGTCTACAAAATGGGAG 1010
                          vv    i  v        v i   i  ----  ii i   i        
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_105503316_   1011 AAAACATTTGCCAACTATGCGTCTGACAAAGGTCTAATATCCAGAATCTG 1060
                             i      v  ii  iii     i  i  v  vi          v i
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_105503316_   1061 TAAGGAACTT----AAATCCATAAGCAAAAAACAAGCAACCCCATTTAAC 1106
                            i     i----  v  v    vv    i    ii     v   ?  -
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA- 816

  chrX_105503316_   1107 AAACAGGCAAAGGACATAAACAGAGATTT-TCAAAAGAAGACATACACAC 1155
                            ii         iv i  i   v    -  v        i     v i
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_105503316_   1156 AGCCAACAAGCATATGAAAAAAAAAAGACTCAATATCACCAATCAT 1201
                         i     i     i       i ----vi     i    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGA----TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (114 / 69)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 6.42 (167 / 26)  


3278 27.09 0.44 0.44  chrX_105518161_105524442     4882  5789 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105518161_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105518161_   4932 GGCCATACTGCCCACGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v    viv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105518161_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_105518161_   5030 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_105518161_   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_105518161_   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_105518161_   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAGCT 5227
                                i    i--    i  --        vv  ii i  i  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_105518161_   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_105518161_   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_105518161_   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_105518161_   5378 TTAAAGATTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_105518161_   5428 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_105518161_   5478 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5527
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_105518161_   5528 TTAAACTAAAGAGCTTCTGCACAGCAGAAGAAACTACCATCAGAGTGAAC 5577
                          i   v v  i i   i  ii vv  i i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_105518161_   5578 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5627
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_105518161_   5628 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_105518161_   5678 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_105518161_   5728 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAGAAATGCTCATC 5777
                           v        i  vi viii     v ii        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_105518161_   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


 477 24.54 1.84 4.91  chrX_105571004_105576249.rev     3485  3647 (1599)    L1M4_orf2#LINE/L1        1   158 (750)  

  chrX_105571004_   3485 TGGAAAGATAATTTGTGTTCATGGATTGATGGATTGGAAGAATTAGTATT 3534
                                   viiii             --------     v   i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTG--------GAAGACTTAATATT 42

  chrX_105571004_   3535 GTTAAAATGTCCATATTACTCAAAGGGATAAACAGCTTCAGAGCAAACCC 3584
                              i   v v   i v i    vv   vv    v    iv    v   
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chrX_105571004_   3585 TATCAAAATTAAAATGGCATTTTTCACAAAAACTTAAAAAATAAT---AA 3631
                                  ivv iiv  v     ii  i   i v v  iv i  ---  
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_105571004_   3632 AATTCATACTGATATG 3647
                                 iv  v   
  L1M4_orf2#LINE/    143 AATTCATATGGAAATG 158

Transitions / transversions = 0.90 (19 / 21)
Gap_init rate = 0.01 (2 / 158), avg. gap size = 5.50 (11 / 2)  

2772 23.92 1.44 2.22  chrX_105571004_105576249.rev     3991  4755 (491)    L1M4_orf2#LINE/L1      150   908 (0)  

  chrX_105571004_   3991 ATGGACTAATACTCAAAAGACCCTGAATAGCCAAAACAATCTTGAGGAAG 4040
                              --   i --  ii     v                     ii   
  L1M4_orf2#LINE/    150 ATGGA--AATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_105571004_   4041 AAAAACAAA-TTAGATACATCATACGTTT-AATTTCAAATTATATTAAAC 4088
                           i      -  i  vivv   i  v ii-         viv  i  ---
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA--- 242

  chrX_105571004_   4089 AATGTAAAACAAAGCTCTAGTAATCAA-ACAGCATGGTATGGGCATA--- 4134
                         ---------       vi         -    ii     iv      ---
  L1M4_orf2#LINE/    243 ---------CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_105571004_   4135 -CAAAC-CAAAGACCAATAGA-CAGAATTGAAAGCCCAGAAATAAACTCA 4181
                         -i i  -i v   i    i  -i        i  i            i  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_105571004_   4182 AGCATATATGGTCAACTAATTTTCAACATGGGAACCAAGAATGCATAATA 4231
                         vi   v         i i      i   v   vi      viiivi   i
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_105571004_   4232 GGGAAAGGATAGTTTCTTGAATAAATAGTGTTGGAAAAGCTGGACATCCA 4281
                                i     i i  v  i    i   i   i v i     i ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_105571004_   4282 CATGCAAAATCATGAAATTGCACCCTTATTTTACACCATACTTAAAAATC 4331
                                  vv     i   v    i  ii i        ivi      i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_105571004_   4332 AGCTCAAAATGGATGAAAGATGTAGACATAAGACTTGAAATCATAAAACT 4381
                          i            v ?   iv  i ii     vi i   ii        
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_105571004_   4382 CTTAGATGAAAACATAGAGG-AAAGCTATGACACATTGACCCTGGCAATA 4430
                               v          i? -   v  vi vv  v   iviiv      i
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_105571004_   4431 ATTTTTTGAATATTCTACCAAAAGCTCAGGCAGCTAAAGCAAAAATAAAC 4480
                         i   i  ii    vvi         v  i   i v    v       i i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_105571004_   4481 AAGTAGGGCTATATCAAGCTAAAACCCTTCTGAACAGAAAAGAAAACAAT 4530
                           i v  i  vi     iv v   vv   i  vi vvv    i v  v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_105571004_   4531 CAACAGAGTGAAAAGGCAATCCACAGAATGGGAGAAA-TATTTGCAAACC 4579
                            v i         i   i                 -          i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_105571004_   4580 ATATATTTGATAAAGGGATAATATCCAAAATACATAAGAAACTCAGAGAG 4629
                               i      i  iv vi      i    i    ii     vv v i
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_105571004_   4630 GTCAATAGCCAAAAATCCAAATAACCAAATTACAAAATGGATAAAAGTCC 4679
                         v      ii-     vv         v    ?v       ii   i vii
  L1M4_orf2#LINE/    784 CTCAATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_105571004_   4680 TGAATAGATATTTCTTTAAAGAAGACATATAAATGGCCAAATGGTATATA 4729
                                 i      ii        i   i          vvi i i  i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_105571004_   4730 AAAAGGTGGTCAACATCACTAATCAT 4755
                              i  v         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (114 / 65)
Gap_init rate = 0.02 (12 / 759), avg. gap size = 2.33 (28 / 12)  


2597 25.72 3.76 1.51  chrX_105582909_105584695.rev      502  1298 (489)    L1M4_orf2#LINE/L1       94   908 (0)  

  chrX_105582909_    502 ATCAAAATCCCAGTAAATAATTGTGTGGATATCAATAAACTGACTCTAAA 551
                                      ivivivv  v  ii  v  ii i  i    ii     
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_105582909_    552 GTTTATATGGAGAGGCAAAAGGCCTCCAAATAGCCAACACAATATTGAAG 601
                         i  i       i v    ii i  - vi         v     v     i
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAA 192

  chrX_105582909_    602 GAGAC-AACAAA-TGAGAGGACTGACTCTACCTGACTCCAAGACTCACAA 649
                         i   v-      - vi       v  v  v  ii i i   i   i  v 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_105582909_    650 TAAAGCTACAGTAATCAAGGCAATGTGGTATTGGTGAAAGAATAGATAAA 699
                         i                  i  i       i   iiv   i     i v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_105582909_    700 TAGATCAACAGAACAGAATAGAGAGCCCAGAAATAGACCCACGTAAATAT 749
                                 ii   i     v     i         i     iii vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_105582909_    750 AGCCAACTGAACTTTGACAGAGAAGCAAAGGCAATACAATGGAGAGA--- 796
                         i i   i   vi  i    ii iv  v   i v  v      i  i ---
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_105582909_    797 -----------ACAAACGATGCTACAAGAACTAGACAACCAAATTCAAAA 835
                         -----------     i i    ivi v    i  i ?   v  v     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_105582909_    836 AAAAGAAGAAGAATTTAGATACAGACCTTATACCTTTCATAAAAGTTAAC 885
                         i  v    ------  i  iv vv    i i   v vi i    i     
  L1M4_orf2#LINE/    443 GAATGAAG------TTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_105582909_    886 TAAAAATGCATCA-AGACATAAATGTAAATCACAAAACTATAAAACTCCT 934
                          v      v    -    v         ivvvi               i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_105582909_    935 GGAAGATAACA--GGAGAAAACCAAAGTGACCTTGGGTGTGGCAATGACT 982
                         i     v    --  ? v   i vvv            vv       ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_105582909_    983 TTATAGGTA-----CTAAAGGCACAATCTATGAAAGAAATAATTGATAAA 1027
                          iv   i  ----- i   i      v v ii       v   v      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_105582909_   1028 CTGGACTTCATTAAAATTAAAAAATTCTTCTCTGTGAAAGATACTGTCAA 1077
                         i          i           v  i viv  vii  i  i   i    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_105582909_   1078 GAGAAAAAGAAGACAATTCACACAGCAGACTGGAAAAATATGTTTGCAAA 1127
                           i ivi i       ii    -----  v   i i  v  i        
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACA-----GAATGGGAGAAAATATTTGCAAA 731

  chrX_105582909_   1128 --AGACATGTGAGAAAAGACTGCTCTCCAAAATATCCAA----CTCTTCA 1171
                         -- v i  v   v  ii    vv v    i     vi  ----     vv
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_105582909_   1172 AACTCAACGATACGAAAATGAGCAAGCTGATTAAAAAATGGGCAAAAGAC 1221
                                ii   vi  i ii ii  v ii   ?             i  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_105582909_   1222 CTAAACAGATACCTCACCAAAGAAGATATACAGATGGAAAATAAGCATAT 1271
                         i i  i   i ii  v                i    vv        i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_105582909_   1272 GAAAAGATGTTTAACATGACCATGTCA 1298
                                  i i     v ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (126 / 76)
Gap_init rate = 0.01 (11 / 815), avg. gap size = 3.82 (42 / 11)  


 242 12.50 0.00 6.25  chrX_105592245_105594941      625   672 (2025)    L1M4_orf2#LINE/L1        1    45 (863)  

  chrX_105592245_    625 TGGAGAGATATCCCAAGTGCATGGATTGGAAGATTCACTACTTTTGTT 672
                             i          v  v              i i v  ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA---TTGTT 45

Transitions / transversions = 1.00 (3 / 3)
Gap_init rate = 0.02 (1 / 45), avg. gap size = 3.00 (3 / 1)  

2095 25.87 6.57 2.10  chrX_105592245_105594941      998  1712 (985)    L1M4_orf2#LINE/L1       31   777 (131)  

  chrX_105592245_    998 AGCCTCAATACTCTTAAGATGTTAATTCTCTTCAAAGTGTTCTATGGAAT 1047
                           v  i    i v        vi   v   ii    v  v    ii  v 
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chrX_105592245_   1048 CAATGCCACCTCAATCAAAATCACAGAAAGCTTTTATTTGTAAAAATTGA 1097
                            i  v i i v         v   vv-  i   -    i i       
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCT-GCCTTT-TTTGCAGAAATTGA 128

  chrX_105592245_   1098 AGGGCTGCTTCTAAAATGTATATGTAAATGC---GAACTTTGAATAACAA 1144
                         vii    v i       vi     v      --- i  iiv     i v 
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chrX_105592245_   1145 AGACAAT-------------GACAAAGTTGGAGGACTTACCCAATCTTAA 1181
                          i     -------------i                i  v -- iiiv 
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC--TTCCCA 226

  chrX_105592245_   1182 ATTGTAAGGTTTGCCACAAAGCTGCAGTGATCAGTACAGTACTGTGTTGG 1231
                            vi  iii  i i        i    i    iv     iiv  ii   
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_105592245_   1232 CTTAAAGAAAGATGTATAGATTTAAAAGGGCAGAAT--AGAGTCCAGAAA 1279
                          v   i  v   ii       i-  vi iii     --            
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATC-AATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_105592245_   1280 CAGACCTGCACTTTGATGATCAATC-ACTTTAGGCAAAGGAATCAATACA 1328
                         i i   iii  v  v   i     i- i   v i   i  vii   v  v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_105592245_   1329 ATTCAATGGGAGAAAGAATAGTCTTCTCGTCAAATGGTGTCAGGAGAACT 1378
                                   -              i  iv         iii   v    
  L1M4_orf2#LINE/    376 ATTCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_105592245_   1379 AGGTATCCGTA---AGAAAAGTGAATCTCAAGCCCTAAATCACATCATTC 1425
                         i i  ?  ii --- i  i i    vi vi v     vv     i   vi
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_105592245_   1426 ACAAAAATTAATT-A----GAATTATAAACCTAAATGCAAAAGATA---T 1467
                                    i - ---- i  i ? i         i  i  v  ---i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_105592245_   1468 TTT----TTTCTAGAAAACAGCATAGGAGAAAATTTTCATACACTTGGGG 1513
                          v ----i ii     i v i      ? v    i   i ivv      v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_105592245_   1514 TAGGTAAGGATTTCTTAAAGATAACACAAAACGCGC---CAATAGAATAA 1560
                             i  v i       i v  i    v   v  i ---   i i  v  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_105592245_   1561 AATATTTTAAAATTGGACTTCACTCATGTTTAA---CTTTTCTTGATA-T 1606
                           v  vvvv             -   viv    ---     ----i i- 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCA-TCAAAATTAAAAACTTTT----GTGCT 669

  chrX_105592245_   1607 TCAATAAACATTA---AGAAAATAAAAAGGCAAGCCAATTCA--ATGCGA 1651
                             vii   i  ---     i i     i   v   ---  --   v  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA---CAGAATGGGA 716

  chrX_105592245_   1652 TAAAATATTCACAATAAATTTATCTGACAATTGACTAG-ATCCCAGGATA 1700
                         v        ii   vvv  v       i  vv    v -    -  i   
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC-AGAATA 765

  chrX_105592245_   1701 TATAAATAACTC 1712
                               v     
  L1M4_orf2#LINE/    766 TATAAAGAACTC 777

Transitions / transversions = 1.56 (111 / 71)
Gap_init rate = 0.03 (24 / 747), avg. gap size = 2.58 (62 / 24)  

 388 23.36 7.30 0.00  chrX_105592245_105594941     2068  2204 (493)    L1M4_orf2#LINE/L1      762   908 (0)  

  chrX_105592245_   2068 AATAAATAAATAACTATTTCAACTCAATAATGGGAATACAA----CCCAA 2113
                             v     v    v  v            iii  v    ----     
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_105592245_   2114 T-AAAAAATGGATACAAGACTTGAACAGAAAGCTC---AGAGAAGACATG 2159
                          -?        ii v i  i     i   v vi  --- i      i  i
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_105592245_   2160 --AAGGGTCAATGAACATATAAAAGTCTCCCCAACATCATTAGTCAT 2204
                         --  v  i    i i  i  i   ivv v i        ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (19 / 12)
Gap_init rate = 0.03 (4 / 147), avg. gap size = 2.50 (10 / 4)  


2208 26.80 5.57 1.97  chrX_105595612_105597666.rev      703  1564 (491)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_105595612_    703 TGTTGATGGATTGAAAGAATCAGCATAGCAAAGCTTTCAATTCTATCCAA 752
                             v        i    v i ii  v iv   v vv    v  vi    
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_105595612_    753 ATTATTACGTGGATTTAATTCAGTTTCTATCAAAAT---ATCTGCAATAT 799
                            iv viiii    i  iv  i ii          --- v    vv - 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT-T 114

  chrX_105595612_    800 TTTGTAAATATGTATGAAT--ATTTTAAAAAATTTATATGGAAAGTGGGA 847
                             i i v  vv ii ii--  ii     --  i         -  vi 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAA--TTCATATGGAAA-TGCAA 161

  chrX_105595612_    848 GAAACT-AACATAGATAAATACA-TTTTGAAAAAGAA---TAAAGTGGGA 892
                          ii  i- iv    vi   -   - i           ---i     v   
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_105595612_    893 GGAAATCAGTCTACCTGATCTCAAGACTTACTATATAAGTACAGTAATCA 942
                            v-   vv  v  ii  i    i        i v iv           
  L1M4_orf2#LINE/    211 GGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_105595612_    943 ---------------------------GATACATAGATCAATGGAACACA 965
                         ---------------------------  i i              i v 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_105595612_    966 ACAGAGAATCCAGAAATATAACTGCTGAAAT-ATGCCCAACTGATTTTTA 1014
                          iv    i          -   ivv iv v -   vi   i       ii
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATA-AACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_105595612_   1015 ACACAGTTGTTGCAAAAGCAATTTAATAGAGTAAATATAGCCTTTTAAAC 1064
                            -  -- v   v  ii v   i   i i v  iv    i     v   
  L1M4_orf2#LINE/    359 ACA-AG--GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_105595612_   1065 AACCGATGCTAGAGCAATTGAATATACACAGGCCATCAAATGAAGTTTGG 1114
                           vi i    i ii   i  i   ?v    v  v vvi         v i
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_105595612_   1115 TCCAATTA--TCGTAACTTATACAAAA-TTAGC-CATTTTGGACCACAGA 1160
                         i  --i  --  ii v v         -   i -  vvv    i  ?   
  L1M4_orf2#LINE/    456 CCC--CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_105595612_   1161 CTCAAATGTGACATGTACAATTTTAAACATTTTAGAAGAAAACA--GGAA 1208
                          ii      i v vv  v  i v    vv i             --  ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_105595612_   1209 AAAACTTTCAGAACTATGGGT-AGGCAAAGAGTTCTTAGATTTGACAT-A 1256
                         v   ii   ivi  iv     -      v iv         v     i- 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_105595612_   1257 AAAGTGCAATACATACAAGGAAAAACTGACAAATTAGACCTCCTCGAAAT 1306
                             ii   vvv i v   i     iv  i     i   i  v  i    
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_105595612_   1307 TAAAAACTTTTGCTCTGAAAAGCATCCTGTGAAGAGAATTAAAAAATATG 1356
                                     iv  vv    v iv  i v    i i v    i i vv
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_105595612_   1357 CTACAGAGGGTGAGAAAATATTTGTAAACCACATGTATAAAAAACGACTA 1406
                          i     iv v             i   i  i  i v i v  iv    v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_105595612_   1407 GTATA-AGAATATATAAAGAACTCTCAAAACTCAACAGTAAAATCA-AAA 1454
                             v-                   i v       i i     vv -   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_105595612_   1455 CAATATAATTAGAAAATGGACAAAATACAGAAAGAGGCATTTTTTCAAAA 1504
                         i  ivi    ?i       i    iv ivvi  v  i     i i    i
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_105595612_   1505 CTAGATATACAGATGACAAAGAAGCCCATGCTTGAAAAGATGTTCAACAT 1554
                         v-         i   i v  v    v    ----        i       
  L1M4_orf2#LINE/    854 A-AGATATACAAATGGCCAATAAGCACATG----AAAAGATGCTCAACAT 898

  chrX_105595612_   1555 CATTAGCTAT 1564
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.27 (127 / 100)
Gap_init rate = 0.03 (26 / 893), avg. gap size = 2.50 (65 / 26)  


3239 27.31 0.44 0.44  chrX_105622766_105629165.rev     5002  5909 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105622766_   5002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5051
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105622766_   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCTTCAGTC 5101
                            v     v     iv i  i  i        i iv     iv   ivv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105622766_   5102 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_105622766_   5150 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_105622766_   5200 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5249
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_105622766_   5250 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5299
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_105622766_   5300 AATGGAACAGAACAGAGGCCTCATAAATAATGCTGCATATCTACAACTAT 5349
                                i    iv   ivii  v      vv iii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_105622766_   5350 CTGATCTTTGACAAACCTGACAAAAACAAGAAGTGGGGAAAGGATTTCCT 5399
                         i    i  i     ivv  v   i v  vvv i         i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_105622766_   5400 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5449
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_105622766_   5450 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5499
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_105622766_   5500 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAACC 5548
                          ?    i       v   v       i      -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chrX_105622766_   5549 TAGGCA-ATACCATTCAGGACATAGGCATGCGCAAGGACTTCATGTCTAA 5597
                             ?i- v i -   iv   v v  vv iv    v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_105622766_   5598 AACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAA 5647
                         i            vvi      i   vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_105622766_   5648 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5697
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_105622766_   5698 AGGCAACCTACAACATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5747
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_105622766_   5748 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5797
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_105622766_   5798 AAACAAACAGCTCCATCAACAAGTGGGCAAAGGATATGAACAGACACTTC 5847
                          i     i i i v  i? v  i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_105622766_   5848 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5897
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_105622766_   5898 ATCACTGGCCAT 5909
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


1571 26.91 9.40 2.70  chrX_105642319_105646427.rev     2775  3625 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105642319_   2775 TAGAGAATTATACATTGATTGTGAATTGGAAGACTTTATATTTTAAAGAT 2824
                          i  i iv   v vv  v ii  i            v     v v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105642319_   2825 ATTATTTTTTCCTAATTTGATCT-CTGATTCAAAATAAT---------AA 2864
                         ivi v vi i  i  v       - v       vii   ---------  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105642319_   2865 TTCCAGTAGGGTTATTTTTCAAGGAAATTGACAAATGAATTCTAAATCTT 2914
                          i    iv vv  -    v  --           iivi  i     vi i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCA--GAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_105642319_   2915 AAATAGAATTGCAAATG-TCAAGAGCAGCACTGAA-AATATTGAA---GA 2959
                          v  i   v     iv -i v   ii   - vi  -   v     ---  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGC-CAAAACAATCTTGAAAAAGA 196

  chrX_105642319_   2960 AAAACAAAGTTTAATGATTTACA------GAAATCAAGATATTTTACACA 3003
                          i         vi v  i i   ------i vv    i iv vi    v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_105642319_   3004 GCCACAATAGTTAAACCAATAAATTATTGTTATAAATATAGAAAAATGGC 3053
                           i   i  i i  iv  i iviv  i  vi    iv     v v  i v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_105642319_   3054 ACAATGGACTAGAAT----AGTCCAAAAAGAGGACTATACA--------- 3090
                         v       v      ----      i   v iiv i     ---------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_105642319_   3091 AATTCTCTTTATGACAAAGAATTCATAACAATGCAGTGGGGGAAAGAATG 3140
                             vvi   -i     i ivvi  vi  v  v  i     -       i
  L1M4_orf2#LINE/    347 AATTGATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chrX_105642319_   3141 GTCATTTTAATAAGTAGATCTTGATCAACTGGGTATCCAAATGGATCCAA 3190
                            v   i  i  i i vv  v iv       i  ?   v   ----   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG----CAA 440

  chrX_105642319_   3191 AAGAA--ACTTTG--CACCTATTTCAAACTGCATACGACATTTAATTCCA 3236
                              -- vv   -- v    ii   v  iii    i v v    i  v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_105642319_   3237 AATGAATTGTAGGG-TAAATGTCAAAGGTGAAACAAATAAAAGTTACTGG 3285
                             i  ii?  iv-       v i  v i    v -     v iviv i
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA-TAAAACTCTTAGA 539

  chrX_105642319_   3286 ATATAACATAGGA--AAATGCCTTAATGGTCTTGATGTAGTCAAGCATTC 3333
                          v v        ?--    --   vi  ii    ivv   v   vvi  i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_105642319_   3334 CTTTAAAAAGACACAAAAAGCACTAACTCTAAACAAAAATA-AAATAAAT 3382
                            vi v v     v        v i vvi   vi    v - i      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_105642319_   3383 TTGACTT------AATTAAAA-----------TCAA--TACACTATTGG- 3412
                          v     ------        -----------    --v       iii-
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_105642319_   3413 --AGTTAAAAGACAAGTCACAGAGTGGAA-AAAATATTTGCAATACTTAT 3459
                         --   v         vi      i   i -             vv v   
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_105642319_   3460 ATCTGAGAAATGGCTTGTATTCAGAATACATACAGAACT---ATAAATCA 3506
                               v  iv i       i       i   v      --- i  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_105642319_   3507 ATAAATAAAAAG-----CAACCCAATTGTTGTTTTAAAATGA-CAA--GT 3548
                             -       -----i         ------?v      i-   -- v
  L1M4_orf2#LINE/    788 ATAA-TAAAAAGACAAATAACCCAATT------WAAAAATGGGCAAAGGA 830

  chrX_105642319_   3549 CTTGAACAGCCAGATC---AAAAACAGTATATCCAAATGGTCAAGGCAAC 3595
                         i     i  v  vv  ---   i -  -    v       i   vi- i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGA-AG-ATATACAAATGGCCAATA-AGC 877

  chrX_105642319_   3596 A-ATAAAAAGGTGTTCGATTTTATTATTTGA 3625
                          -  i     i  i  i iv i ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.08 (117 / 108)
Gap_init rate = 0.04 (37 / 908), avg. gap size = 2.78 (103 / 37)  


2866 24.27 6.68 0.23  chrX_105691957_105696118.rev     2819  3671 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105691957_   2819 TGGAAAAATACTGTATGATCATGTATTGGAAGAATCAAT-TTATTACAAT 2867
                               i   iivi   v     v         v i   -  i   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105691957_   2868 GTCTATACTGCCCAAAGCAATCTACATATTCAATGCAATCCCTGCCAAAA 2917
                          v v     v      vii       v      i         ii     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105691957_   2918 TACCAATGACATTCTTCACAGAAACAGAAAAAACAATCCTAAAATTTAGA 2967
                          v   iivi v  i  ii      iv  v  ivii           i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_105691957_   2968 TGGACCCACAAAAGACCCAGAATAGCCAAAGCTATCCTAATCAACATATG 3017
                             vvii   ii                 i v   i i vv  v vivi
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_105691957_   3018 CAAA--TCAATG--TGATATATC---ATATCAA---------CAGA-TTA 3050
                             -- vi v -- v i iv  ---  v    ---------  i -i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_105691957_   3051 AAG-GATCAAAAC-------------------------CATAC-GATCAT 3073
                         v  -i     i  -------------------------    i-     v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_105691957_   3074 T----TC-AATTGA---TCAACACACAAATCCACACACCTAAAGTGAACT 3115
                          ---- v-      ---  v v v i   i   i   ii  vi  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_105691957_   3116 CATTTTTAACAAAGGTGCCAAGAACATACACTGGGGTAAAGACAGTCTTT 3165
                         v     ii    i          v   v  v     v  ii i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_105691957_   3166 CCAATAAATGGTGCTGGGAAAACTGGATATCCATATTCAGAAGAATGAAA 3215
                         i   i              v         ?   i  v  i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_105691957_   3216 CTATACCCCTATCTCTTGCCATATACAAAAATCAACTCAAAATGGATTAA 3265
                         i iv       i   vii              i              i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_105691957_   3266 AGACCTAAATCTAACACATTGAGA-TATGAAACTACTACAGGAAAACATT 3314
                                   v   v -ii i i -   i     vi  v i        v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_105691957_   3315 GGGCAAAATCTACAGGACATTCGTCTGGGCAAAAATTTCTTGAGTAATAC 3364
                           ?vv      v iv   v  v vi i     vii      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_105691957_   3365 CCCACAAGAACAGGCAACCAAAGCAAAAATGGACAAAT-AGATTGACATC 3413
                         v   v   v   i     v    v      i  i    -i  i v-    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATC 648

  chrX_105691957_   3414 AAGGTGAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAAGAG 3463
                           ii v    i   i  ii vv       v  v     v        i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_105691957_   3464 ACAACCCACAGAATGGGAGGAAATACTTGCAAACTACCCATCTGACAAGC 3513
                                            i     i       ii ivi      i   v
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_105691957_   3514 GATTAATAACCAGAATGTATAAGGAGCTCAAACAACTTA-TAGGAATAAA 3562
                           i vi  v       i     i  i   vv      i -  iv  v  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_105691957_   3563 TCTAATAATGCAAT-AAAAAGCGGGCAAAAGATTTGAATAGACGTTTCTC 3611
                         v v     iv    -?    ii       i             i      
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_105691957_   3612 AAAAGAAGGTATACAAATGGCAAACAGGCACATGAAAAGGTGCTCAACAT 3661
                         v       i            v  i i            i          
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_105691957_   3662 CACTGATCAT 3671
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.33 (116 / 87)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.28 (59 / 18)  


3314 24.48 1.32 1.32  chrX_105736619_105739044     1027  1933 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_105736619_   1027 GAAAAGATAGTCCATGTTTATGGATTGGAAGAACCAATATTGTTAAAATG 1076
                          i       vi       i             vii           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_105736619_   1077 TCCACAATACCCAAAGCGATCTATGGGATTCAACACAATCCCTACTAAAA 1126
                         v v i v v      vi      ii -       i         ii    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAG-ATTCAACGCAATCCCTATCAAAA 100

  chrX_105736619_   1127 TACCAATGACATTCTTCACAAA----GAGAAAATGAAAATTCCTAATATT 1172
                          v   iivi v  i  ii  i ----  v  iv   ----      v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA----TCCTAAAATT 146

  chrX_105736619_   1173 TATATAAAACCCCACAAGATTCAGAATAGCCAAAGTGATCATGAACAAAA 1222
                         i    ii  viv  vii  ii             iii   v    v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_105736619_   1223 AGAACAAAACTGGCGGAATCACATTACCTGACTTCAAATTGTACTACACA 1272
                                 ii   v   v     i v  ii i      viv       v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_105736619_   1273 GCTATAGTATCCAGAACAGCATGGCACTGGTATGAAAACAGACACAGAGA 1322
                             i    vi  ii    ii   i     i  i ii i     i v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_105736619_   1323 CCAAAGGAACAGAATAGACAAACCAGAAATAAATCCATACATCTAAAGTG 1372
                         i   v    i     v  v iv           i        i  vi  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_105736619_   1373 AACTCATTTTCAACAAATATGCCAAGAACCTACATTGGGGAATGGACAGT 1422
                           i v      i    ivi        v v v  v       v i i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_105736619_   1423 CTCTTCAATAAATGGTGATGGGAAAACTGGATATCCATACGCAGAGGAAT 1472
                           i     i        v     v         ?   i i   i i    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_105736619_   1473 AAAACTAGACCC-TATCTCTCACCATATACAAAAATCAAATCAAAATCAA 1521
                         i  ii i     -  i   v                i  v       vi 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_105736619_   1522 TTAAAGACTTAAATCTAAGACTTCAAACTCTGAAACTACTGCAAGAAAAC 1571
                          i ?    i     v     vi v     v i     vi iv        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_105736619_   1572 ATTGGGGAAACTCTCCAGGTCATTGGACAGGGCAAAGATTTCTTCAGTAA 1621
                           v  ? v  v   i iv v v    iivi     v i      vii  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_105736619_   1622 TACTCTACAAGCACAGGCAATCAAATAAAAAATGGACAAAT--GAGTTCA 1669
                         v  v i v       i    iv   v       i  i    --  v    
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_105736619_   1670 CATCAAG-TTAAAAAGCTTCTGCACAGCAAAGGAAGCAATCAACAAAGTG 1718
                         --    i-       -   i  ii vv       vi v     v      
  L1M4_orf2#LINE/    647 --TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_105736619_   1719 AAGAGACAATTCACAAAATGGGAGAAAATATTTGCAAACTATTCATCT-A 1767
                           i      ii    i                      ii  vi    - 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_105736619_   1768 TAAACTAGGGATTAATAACCAAAATATATAAGGAACACAAGCAACTTA-C 1816
                            ----    i vi  v   i         i    v vvi     i -i
  L1M4_orf2#LINE/    744 TAA----GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_105736619_   1817 AGGACAAAATCTAATAATCCAATC--AAAATGGGCAAAAGATCTGATAAA 1864
                          iv v   iv v     i     i--            i   i   vv i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_105736619_   1865 AGATTTCTCAAAAGAAGACATACAAATGGCAAGCAGATTCACGAAAATGT 1914
                          v       v        i           v ii iiiv  i     vi 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_105736619_   1915 GCTCAACATCACTGATCAT 1933
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (131 / 88)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 2.00 (24 / 12)  


3368 25.80 0.77 0.66  chrX_105815340_105821751.rev     5014  5920 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105815340_   5014 TGGAAGAACATTCCGTGTTCATGGATAGGAAGAATCAATATTGTGAAAAT 5063
                              ii i  i  i           v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105815340_   5064 GGCCATTCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5113
                            v  v  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_105815340_   5114 TGCCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5161
                          v   iivi i  i  iii    -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_105815340_   5162 TATGGAACC-CAAAGAGCCC-GCATCGCCAAGACAATCCTAAGTCAAAAG 5209
                                vi-   i ii   - v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_105815340_   5210 AACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGGC 5259
                                i      vv    v  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_105815340_   5260 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5309
                                 i   i i  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_105815340_   5310 AATGGAACAGAAT--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5357
                                i     --    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_105815340_   5358 ATCCGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5407
                          vii   i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_105815340_   5408 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGCT 5457
                           v  i  i              v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_105815340_   5458 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 5507
                            ii    i    v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_105815340_   5508 TTAAAGACCTAAATATTAGACCTAAAACCATAAAAATCCTAGAAGAAAAC 5557
                          i ?          i v   v       i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_105815340_   5558 CTAGGCAAATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGACC 5606
                         v    ?iv v i -   i- i  v i  i- i     v ii   v iivi
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_105815340_   5607 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5656
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_105815340_   5657 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGA 5706
                         v  i   v v  i i   i  ii vv    i  v    i ivv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_105815340_   5707 ACAGGCAACCTACAGAATGGGAGAAAAGTTTTACAATTTACCCATCTGAC 5756
                          v  i     i                vv   i   v i ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_105815340_   5757 AAAGGGCTAATATCCAGAATCTACAATGAACTTGAACAAATTTACAAGAA 5806
                           i  i  vi          v  i  v     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_105815340_   5807 AAAATCAAACAACCCTATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5856
                            iv    i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_105815340_   5857 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGTTCA 5906
                             v        i  vi viii     v ii          i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_105815340_   5907 TCATCACTGACCAT 5920
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (141 / 89)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


3312 21.86 2.25 4.93  chrX_105834762_105836736      550  1482 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_105834762_    550 TGGAAACATATACCATGTTCATGGGTCAGAAGACTTGCTGTTGTTAAGAT 599
                               v    v            i ii        iv i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_105834762_    600 GTCGGTTCCCCACCAAACTAATTTATGGATTTGATGCAGTTTCAATAAAA 649
                          v ii v i  -     i i  i  ii    ii i   i ii v  v   
  L1M4_orf2#LINE/     51 GGCAATACTCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_105834762_    650 ATCCTAGTGTAAATCTTTTATAGAAATTGACAGGCTGATTCTAAGCTT-A 698
                             i  i- ivv i    ii           i      i    iv  - 
  L1M4_orf2#LINE/    100 ATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_105834762_    699 GATGAAAATGCAAAAGAACTAGAATGAACAAAACAATTTTGATAAAGAAC 748
                         v   i        ii  v i     iiv         i    v      v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_105834762_    749 AAC---TTTGGATGATTCATGCTACCTGATTTCAAGAATTATTTTAAAGT 795
                            ---v     v  i   ii  v  ii       i v   i vi    i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_105834762_    796 CACAGCAGTCAAGATAGTGTCGTATTGGAAAAAGGATAGATTTATAGATC 845
                         i    i i      i     v   i   v v         iv        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_105834762_    846 AAAGAAACAGAAGAGAGAGTACAGAAATAAACCCATATATATATGGTCAG 895
                           v i  i    vv      v                i  v        i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_105834762_    896 TTGATTTTCCATAAAAGTGCAAAAGCAATTCAATGAAGAAAGGATAGCCT 945
                                  v i  ii    v  ii v        ii     i    i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_105834762_    946 TTTCAGGAGGATAGCCCTTTGTTGGCTATCCATATGCAGTGATTGGATAT 995
                              iv i-  i -----  i   ------------iiii i      ?
  L1M4_orf2#LINE/    399 TTTCAACAA-ATGG-----TGCTGG------------GACAACTGGATAK 430

  chrX_105834762_    996 CCTTAAGCAAAAAACAAGCAAACAGACAAAAAAGAACTTAAATCCATTCT 1045
                           -----------   v     ------ i  v   v  ii i  v v i
  L1M4_orf2#LINE/    431 CC-----------ACATGCAAA------AGAATGAAGTTGGACCCCTACC 463

  chrX_105834762_   1046 TCATACCCTATGTAAACATTATTTCAA--TAGATCATAGACCTTAACATA 1093
                            i   v   ii   v    vi    -- i     ?      v  ii  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_105834762_   1094 AAACCTAGAACTATGAAATTTTTAGAACAAAACGTTAAAGAAAAATATTT 1143
                          i v   i      i   i i      v     i -- i ?iv  -  i 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT--AGGNGTAA-ATCT 560

  chrX_105834762_   1144 TCATGAC-TTGGGT--GACAAATATTTCTTAGATATAACTCCAAAA--AC 1188
                           i    -      -- i   vvi            i  v      --  
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_105834762_   1189 AAGTCCAA-AAAAGAAAAAAGTTGATACATTTGGCCTTGTCAAAATTAAG 1237
                            --   -           - v    v   v i i ii          i
  L1M4_orf2#LINE/    611 AAG--CAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_105834762_   1238 AATTTCTGTTCTTTGAAAGGCACTGTTAAAAGAAGGAAAAGATAAGGTAC 1287
                           i  i   v   ii  i i    i i  i i iv       i  vvi  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_105834762_   1288 AGACTGGGAGAAAATATTTGCAAATCATATGTCTGTTAAAGGGCT-GTAC 1336
                            v                          i    v   i  i  -   i
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_105834762_   1337 CCAGAATATA--AAGAACTCTTAAAACTTAACAGTAAGAATACAAACAAC 1384
                                   --           v    i  i i   i  v     i   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_105834762_   1385 CTAAT-AGAAAACTGGCAAGCAA----AACAGACAATTCACCAAAAAAAT 1429
                          i   -?i    iv     ivi ----  i     v   v     i  i-
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG- 856

  chrX_105834762_   1430 ATATATATGAATGGCAAATAAACACAT-AAAAGATGTTCAACATCATTAA 1478
                         --     ii      v     i     -        i         ????
  L1M4_orf2#LINE/    857 --ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_105834762_   1479 TAAT 1482
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.12 (136 / 64)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.79 (67 / 24)  


3270 26.68 0.44 0.55  chrX_105863672_105865660.rev      592  1498 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_105863672_    592 GGAAGATCATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATG 641
                          i     -  i     i      i v      v i     i  v  i   
  L1M4_orf2#LINE/      3 GAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_105863672_    642 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCT 691
                           v     v     iv i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_105863672_    692 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 739
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_105863672_    740 ATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGGCAAAAGA 789
                               viiv  ii  v  v v  vi    iv     i i iiv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_105863672_    790 AAAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACACGGCT 839
                          v    i      vv       v  ii i      viv       vi   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_105863672_    840 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 889
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_105863672_    890 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTA 937
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_105863672_    938 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 987
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_105863672_    988 TATCTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAAAAAGCTG 1037
                          v ii  i              v      v  ?   i   i    iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_105863672_   1038 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGAT 1087
                           ii    i    v   i     v              i    ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_105863672_   1088 TAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1137
                         i ?    i    ii v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_105863672_   1138 TTGGCATTACCATTCAGGACATAGGAATGGGCAAGCACTTCATGTCTAAA 1187
                          v  ?i v viv   iv   v v  iv i     vvii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_105863672_   1188 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1237
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_105863672_   1238 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1287
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_105863672_   1288 GGCAACCTACAGAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAA 1337
                          i     i                 v  ii   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_105863672_   1338 GGGCTAATATCCAGAATTTACAATGAACTCAAACAAATTTAGAAGAAAAA 1387
                           i  vi          v  i  v      vv    v iv v  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_105863672_   1388 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 1437
                         i     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_105863672_   1438 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 1487
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_105863672_   1488 TCACTGGCCAT 1498
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (6 / 906), avg. gap size = 1.50 (9 / 6)  


3902 16.05 1.54 2.05  chrX_105885571_105887329      488  1266 (493)    L1M4_orf2#LINE/L1      134   908 (0)  

  chrX_105885571_    488 TGTTCATAAAGTTTTATGTGGAAATACAAAAGACTCAGAGTAACTAAAAC 537
                           v  v    i  i-  i       i   ii   i    i  i i     
  L1M4_orf2#LINE/    134 TGATCCTAAAATTC-ATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chrX_105885571_    538 AGTATTGACAAGGAAAAACAAAGTTGGAAGACTCATGCTTTCCAATTTCA 587
                          i v    v  i   i            i      ii   i         
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_105885571_    588 AAACTTATTATACAGCTATAGTAAACAAGACATTGTGATACTGGCATAAG 637
                                i  i v     i     v       v    i            
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_105885571_    638 GGGAGACATGTAGATCAATGTAATATAGTTGAGACTCTAGAAATACATTC 687
                          iv      i          v    v i      v  i       v ii 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_105885571_    688 TTACATTTATGGTCAGTTAATTTTCAACAAGAAGGCCAAGCTAACTCAAT 737
                         v              i  i      i     iiv      viv i     
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_105885571_    738 GGGGGAAAGAAC--TATTTTCAACAAATGGTGCTGAAACAA-TGGACAGC 784
                             -      i-- v                   ii    -    i ? 
  L1M4_orf2#LINE/    383 GGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_105885571_    785 AACATACTCCCCACCCCCAAAAAGATG---TTGTACTCTTTTCTTAAAAC 831
                         v    i -----------    ii   ---   v  i i vi  i v v 
  L1M4_orf2#LINE/    432 CACATGC-----------AAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_105885571_    832 ATACACAAAAATTAAATTAAAATGGATCAAAGACCAAAATGTAAGAGCTG 881
                            i           v i           ?     v             i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_105885571_    882 AAACTATGAAACTCTCAGA-GAACACATAGGAGTTAATCTTCATGATCTT 930
                                i       i   -   v       ?  v       i   i   
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_105885571_    931 GAATTAGGCAATTGTTTAT-AGATATGACAACAAAAGCAT--GTGACCTT 977
                          ii         v    v -          v        i-- ii  v--
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA-- 618

  chrX_105885571_    978 AAAGAAAAAATAGGTAAATTGGATTACATCAAAATTAAAAACTTTTGTGC 1027
                                      i         i v                        
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_105885571_   1028 TACAAATGATATCATCAAGAAAGTGAAAAGACAACCCACAGAATGG-AGG 1076
                          v    v  i ii                                 -  i
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_105885571_   1077 AAATATTTGCCAATTATATGTCTGGTAAGGGACTGCTGTCTAGAATGTAT 1126
                                   v   i    i    i         vv i  i     i   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_105885571_   1127 GAAGAACTCTTACAACTAAATAATAAAAGG-CAAACAACCCAATTTTAAA 1175
                         i                v          i -    i         ?-   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AAA 817

  chrX_105885571_   1176 AATGGTTAAAGGATTTGAATAGACTTTTCTCCAAAGAAAATAAAGAAATG 1225
                              vi                 v             i   v v     
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_105885571_   1226 GCCAATAAGCACATTAAAAGATTTTTCATATCATTAGTCAA 1266
                                       v       vi iv i    ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (77 / 44)
Gap_init rate = 0.02 (13 / 775), avg. gap size = 2.15 (28 / 13)  


2607 26.38 1.57 0.92  chrX_105907051_105912180.rev     3451  4212 (918)    L1M4_orf2#LINE/L1        3   769 (139)  

  chrX_105907051_   3451 GAAAAACATTCCATTCTCATGGATAGGAAGAATCAATATTGTTAAAAAGG 3500
                             i i  i    vi        v      v i           i v  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_105907051_   3501 CCATACCAACCAAAGCAATTTAAAGATTCAGTGCTATTCCTATCAAACTA 3550
                          v    ivv     vii  i  v       ii  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_105907051_   3551 CCAATGACATTCTTCACAGAATTAGAAAAAACT-ATTCTAGAAAATTCAT 3599
                            iivi v  i  ii     v v  v  i-  -  i   --        
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTA--AAATTCAT 149

  chrX_105907051_   3600 ATGGAACCAGAAAGGAGCCCAAATAGCCAAAGCAATACTAAGCAAAATGA 3649
                               viiv  i   v  vi          i    vi i iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_105907051_   3650 ACAAAGCTAGAGGTATCACGTTATTCACCTTCAAACTATACTACAAGGCT 3699
                               i i    vv    ii vii  vi      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_105907051_   3700 ACAGTAACCAAAACAGCATGGTACAGGTACAAAAACA--CACATAGTCTA 3747
                                i   i    ii      v  i i  ii i --  i    vii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_105907051_   3748 ACGGAACAGAATGGAGTGCCCAGAAATAAAGCTGCACACCTATAACCATC 3797
                          i    i     v   v i           v iii   ii   iii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_105907051_   3798 TGATCTTTAACAAAGTCAACAATAACAAGCAATGGGGAAAGGACAACCTA 3847
                             i  ii    i viiv   v v  vv            i i ii  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_105907051_   3848 TTCAATAAATGGTGCTGGGATAACTGGCTAACCACAGGTAGAAGATTGAA 3897
                              i              i      v  ?     v i i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_105907051_   3898 ACTAGATCCCTACCTTCCACCATATACAAAAATCAACTCAAGATGGATTA 3947
                         ii i  i        iv                i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_105907051_   3948 AAGACTTAAATGTAAAACCTACAACTATAAAAAGCCTTGAAGAAAACCTA 3997
                         ?    i         i v   v          vv i v         v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_105907051_   3998 GGGAGTA--CCATTCTAGATATAGGCGGT--GGCAAAGATTTCACAACAA 4043
                           ?-   --i -   vv  iv v  --  --     v i    vi ivv 
  L1M4_orf2#LINE/    550 GGN-GTAAATC-TTCGTGACCTTGG--GTTAGGCAATGGTTTCTTAGATA 595

  chrX_105907051_   4044 AAATGCCAAAAGCAATTGCAACAAAAATAAAATTTGACAAATGGGACT-A 4092
                         vi ii         vvv         iv    v v  i    v     -v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_105907051_   4093 ATTAAACTAAGGAGCATTTGCACAGTAAA----ACTATCAACAGAGTAAA 4138
                           i   v v ii i v    ii vvi   ----        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_105907051_   4139 CAGACAACCTACAGAGTGGGAAAAAATATTTGCAAACTATGCATCTGACA 4188
                         v        i     i     i              ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_105907051_   4189 AAGGTCTAATATCCAGAATCCATA 4212
                          i  v  vi          vi   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATA 769

Transitions / transversions = 1.48 (118 / 80)
Gap_init rate = 0.01 (11 / 767), avg. gap size = 1.73 (19 / 11)  

 378 20.56 7.48 0.00  chrX_105907051_105912180.rev     4542  4648 (482)    L1M4_orf2#LINE/L1      794   908 (0)  

  chrX_105907051_   4542 AAAAATCAAACAACTCCATAAAAAAGTGGGCAAAGGACATGGACAGACAC 4591
                             iv    i   i v  v?    i           iv  i i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_105907051_   4592 TTTTCAAAAGAAGACCTACATGCAGCCAACAAGCACATGA--------TC 4633
                           i  v        iv    viii     i          --------  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_105907051_   4634 AACATCACTAAATAT 4648
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.01 (1 / 115), avg. gap size = 8.00 (8 / 1)  


3307 25.96 0.44 0.55  chrX_106015193_106021604     5011  5919 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106015193_   5011 TGGAAAAACACTCCATGCTCATGGATAGGAAGAACAAATATTGTGAAAAT 5060
                               i i ii     i        v      viv        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106015193_   5061 GGCCTTAGTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5110
                            vv  v v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106015193_   5111 TACCA-CTGACTTTCTTCACAGAATTGGAAAAACCTACTTTAAACTTCAT 5159
                          v   -   v    i  -i     v v  v  i iv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_106015193_   5160 ATGGAAGCAAAAAAGAGCCCGCATAGCCAAGACAGTCCTGGGCAAGAAGA 5209
                               iiiv  ii  v  v v        i   i  i  iiv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_106015193_   5210 ACAAAGCTGGAGGCATCACACTACCAGACTTCAAACTTTACTACAAGGCT 5259
                               i      vv       v  vi i      vi         i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_106015193_   5260 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATACAGATTA 5309
                                i   i    ii         i iv ii i   i   i    i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_106015193_   5310 AAGGAACAGAACGGAGGCCTCAGAAATAATACCACACATTTACCACCATC 5359
                          v    i    iv   ivii         vv   i       ivii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_106015193_   5360 TGATCTTTGACAAACCTGACACACACAAGCAATAGGGAAAAGAT--TCGA 5407
                             i  i     ivv  v  vivv  vv    i      ii  --  --
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-- 397

  chrX_106015193_   5408 TATTTAATAAATGGTGTTAGGAAAACTGGCTAGCCATATGCAGAAAACTG 5457
                          v  i  i        i i   v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_106015193_   5458 AAACTGGACCACTTCCTTACACCTTATACAAAAATCAACTCAAGATGGAT 5507
                           ii      v  v   i     v           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_106015193_   5508 CAAAGACTTAAATGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAACC 5557
                           ?    i           v   ii  i      v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_106015193_   5558 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAA 5606
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_106015193_   5607 AACACCAAAAGCAATGGCAACAAAAGCCAACATTGACAAATGGGATGTAA 5656
                         i            vvi          vv  v  v  i    v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_106015193_   5657 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAATGAAC 5706
                          i   v v  i i   i  ii vv    i  v       vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_106015193_   5707 AAGCAACCTACAGAATGGGAGAAAAATTTTGTAAACTATCCATCTGACAA 5756
                          ii     i                vv    i   ii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_106015193_   5757 ACGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAATGAAA 5806
                         iv i  vi          v  i        ivv    v iv i   i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_106015193_   5807 AAGCAAACAACCCCATCAAAAAATGGGCAAAGCATATGAACAGACACTTC 5856
                          ii    i     v  i?              v  v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_106015193_   5857 TCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAAATGCTCAT 5906
                           v        i  vi viii     i ii  i       i -      v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

  chrX_106015193_   5907 CATCACTGGTCAT 5919
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (133 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


1659 27.23 5.56 3.07  chrX_106072414_106075177.rev      777  1459 (1305)    L1M4_orf2#LINE/L1        1   700 (208)  

  chrX_106072414_    777 TGGAGGAATTTACTAAGTTC-----TTGAAGAACTCAATATTGCAAAGAT 821
                             iii  v v i v    -----   i ii   i       iv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106072414_    822 GTGAGTTCTGCCCAAATTGATTTATAAACATAATATAGTCCA-ATTAAAA 870
                          vv i v  v           i  i i ivi  iii i   v-  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106072414_    871 TCTCAGCACATTCTTTCTTCAGGGAGTGGAAATTGACACGCTCACTCTAA 920
                           i    --- v i  i  i----- ii          v   v ii    
  L1M4_orf2#LINE/    101 TCCCAGC---TGCCTTTTTT-----GCAGAAATTGACAAGCTGATCCTAA 142

  chrX_106072414_    921 AATTTAGAAAGTGATGCAAAGAGCCAAGAATAGCCAAGACAATCCTAAAG 970
                             i v vi vi      i ii  v           i      i i  i
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_106072414_    971 TAGAAGAACAAAG--GGAAGATTAACAC----AGATAGCAATACTTAT-- 1012
                         v            --   i  i v    ----vi  vv   v     i--
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_106072414_   1013 -AAAACTACATTAATAAAGAC--TGTGGCCTTTTCAAAAGGACAGACAAA 1059
                         -   i     v    v     --     ivi vv  v     i     v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_106072414_   1060 TAGACTAATAGAACAGAAC--ACAGTCCAGAAATAGGTCCACACACATAT 1107
                             ii   i   i    i-- v            iii   i   iv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_106072414_   1108 GA-CATTTGATTTGTGACAAAGATAACACTGCAGAGCA----GTGGGAAA 1152
                          i-  v       vi     i i iv  ----   v  ----i    i  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGAA 388

  chrX_106072414_   1153 AGGA-ATTCTTTTAAATTAATTGTTCTAGGTCTA-TAGA-AG--GAATGA 1197
                           i - v      v  iv   v  v  i  v v - i  - ?--iv   v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_106072414_   1198 AGGAAGAAATGAATCTCAGCCACAACCTCACACC-TATACAAAAATGATT 1246
                          --  ii      vi vii  v v          -           v vi
  L1M4_orf2#LINE/    439 A--AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_106072414_   1247 TCAAGGTGGATTGTAGATCTAAATGTGAGAGGCAAAACAGTAAAGCTTCT 1296
                             ii     ii?   i        i    vi     vi    i  ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_106072414_   1297 AGAGCATAACATAA---TAAAGCATATTTATGATTTTTGGAATAACAAAT 1343
                            iv v      i---    v ---  ii   ii  -  iv  ivv   
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC---TTCGTGACCTT-GGGTTAGGCAAT 582

  chrX_106072414_   1344 A--TTTTTAAATGGGAGGCAAAAATAACACTAACCATTAAAGGGAAATAT 1391
                         i--  i   i  iv  vi v    --i   -  v  vi   i i   v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAA--GCAC-AAGCAACAAAAGAAAAAAT 629

  chrX_106072414_   1392 ---TAAATTGGAATATATTAAAATTAAGAACTTCTGATCATCAAATTGTA 1438
                         ---         v vi  i        i     i  vv v     vvii 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_106072414_   1439 CCATTAAGAGAGTGAAAAGGC 1459
                          i  i    i         i 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGAC 700

Transitions / transversions = 1.56 (112 / 72)
Gap_init rate = 0.04 (25 / 700), avg. gap size = 2.36 (59 / 25)  

 298 20.18 7.02 2.63  chrX_106072414_106075177.rev     1777  1890 (874)    L1M4_orf2#LINE/L1      685   803 (105)  

  chrX_106072414_   1777 AAAAGAGTGAAAAAGCAAGCCACAGAGTAGGA---AATGTTTGAAAA--A 1821
                           i i        ii   v       i i   ---   i    v   -- 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_106072414_   1822 TATATTGCTGACAAAGTACTCATATACTATACAAAATAAAGAACT---AC 1868
                              --    i  i v   ii   - i v vv v          ---  
  L1M4_orf2#LINE/    735 TATAT--CTGATAAGGGACTTGTAT-CCAGAATATATAAAGAACTCTTAC 781

  chrX_106072414_   1869 AAATCAGTAAGAAAAAGACAGA 1890
                           v   i   v         i 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAA 803

Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.04 (5 / 119), avg. gap size = 2.20 (11 / 5)  

 307 23.40 0.00 0.00  chrX_106072414_106075177.rev     2194  2287 (477)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_106072414_   2194 AAAAAAGGGCAAAAGACTTGAAGAGGCACTTAATAAAAAAAGATATACAA 2243
                              v       i  i     v  i  i  vviv   i           
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_106072414_   2244 ATGGCCAAAAAACATATTAAAAACTGGGCCATGTCATTAATCAT 2287
                                 v  i  i  v    iv  vv v ii   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (11 / 11)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3403 25.73 1.57 0.22  chrX_106120275_106125519     1614  2507 (2738)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_106120275_   1614 GAAAGATATTCCATGCTCATGGACTGAAAGA----ACATTGTTAAAATGA 1659
                                  i     i       i  i    ---- i        i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_106120275_   1660 CCATACTATCCAAAGCAACCTACAGAATTAATGCAATCCCTATCAAAATA 1709
                          v     vi     vii i       v i  i                 v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_106120275_   1710 CCAATGACACTCTTCATAGAAAAAGAAAAAA-AATCTTAAAATTTTTATG 1758
                            iivi vi i  iii     vv  v  iv-i   i       iv    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_106120275_   1759 AAACCACAAAAGACTCTGAA--GCCACAGCAATCCTGAACAAAAATAACA 1806
                         i  vii   ii   i v   --    v i     i    v  i  v    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_106120275_   1807 AAGCTGGAGGAACTGCACTACCAGACTTCAAAATGTACTACAAAACTGTA 1856
                            i       viii    v  vi i       iv         i  ii 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_106120275_   1857 GTAACCAAAACAGCATGGTACTGACATAAAAAGAGACACATGTAACTGTG 1906
                             i   i    ii        i     ii v     i  iv v vi  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_106120275_   1907 GAACAGAATAGGGAACTCAGAAACTGACCCATGTATCTACAGCCAACTAA 1956
                            i     v i  iii      ivi      ii  i  ii i   i i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_106120275_   1957 TATTTTAATAAAGACACCAAGAACAT-CAGTTGGGAAAAGACAGTCTCGT 2005
                          -   ii i  i iii      v   -  i v      ii i     iv 
  L1M4_orf2#LINE/    353 T-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_106120275_   2006 CAATAAGTGGTGCTGAGAAAACTGGATACCTATATGCATGAAGAATGAAA 2055
                            i  i        i  v         ? i i     -i         i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAATGAAG 450

  chrX_106120275_   2056 CCAGACCCCCATCTCTCATCCTATACAAAAATCAACTCAAAACAGATCAA 2105
                         iii      i i   v  i v           i         ii     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_106120275_   2106 AGACCTAAACGTAAGACCGGAAACTAAAAAACTACTAGGAAAAAACATAG 2155
                                  i      v vi      v      vi   i i         
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_106120275_   2156 GGGAAACATTTCAGGACACTGGTCTGGGAAAAGATTTCATGAATAAGACC 2205
                          ? v  vvi   iv   vi   vi i  v  v i    v ii   v   v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_106120275_   2206 TCAAAAGCACAGGCAACGAAAGCAAAAATAAACAAACGGGATTATATTAA 2255
                         i          i     i    v       i i   iv   i vi  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_106120275_   2256 A-CTAAAATCTTCTGCACATCAAAGGAAAC----AACAGAGTGAAAAGAC 2300
                          -i     v   i  ii v        v  ----  v i           
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_106120275_   2301 GAACTACAGAATGGGAGAAAATATTTGCAAACTACTCACCCAACAGGGGA 2350
                         i v i                          ii ivi i ii i i    
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_106120275_   2351 TTAATATCCAGACTATACAAGGAATTC-AACATCTTAACAGCATCAAAAC 2399
                         i vi        v    i  i   i  -v   v  i  i ii vv  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_106120275_   2400 AAACAACCTGATTTAAAAATGGGCAAATGATCTAAACAGCTATTTCTCTA 2449
                            i    ii   ?             v   i i  i  vi       i 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_106120275_   2450 AAGAAGACATACAAATTGCCAACAAATATATGAAAAAATACTCAACATCA 2499
                                i        v     i  ii i       i  i          
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_106120275_   2500 CTAATCAT 2507
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.42 (160 / 66)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 1.78 (16 / 9)  

3779 22.43 3.89 0.00  chrX_106120275_106125519     3879  4752 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106120275_   3879 TGAAAAGGTATCCTGTGTTCATGGATTAGAAGACTTAATATT---AATAT 3925
                           i    i     ii            i              ---  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106120275_   3926 ATCCGAACTATCCAAAGCGGTCTACAGATTCAATGCAATCTCTATCAAAG 3975
                         iv viv   vi     vi i             i      i        i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106120275_   3976 TCCCAATGGCATTTTTTACAGAAATAGAAAAAACAATCCCCAAATTCATA 4025
                              iiv  v      i       v  v  ivii    iv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_106120275_   4026 TAGAACCACAGATGATACCAAGTACCCACAACAATCTTGGGAAAGAA--- 4072
                          i   vii  iiv  iv vi i  v   v          ii      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_106120275_   4073 CAAAGCTAGAGGCCATACACTTTCTTATTTCACAACATATTACAAAGCTA 4122
                              i i    v vi      i iv      v   v  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_106120275_   4123 CAGTAATCAAAACAGTATGGTACTGGCATAAAACTGGACACATAGGCCAA 4172
                                   i     i              iiv i    i    ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_106120275_   4173 TGGAACCAATTTGAGAGTCTAGAAATAAACCCATGAAGCTACAGTCAACT 4222
                              ivi v         i              iv vi  ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_106120275_   4223 GATCTTCTACAAGTGTCCCAAGAATATAACATGAGAAAAAGATAGTCTCT 4272
                            i   v     v  v      vi  vvv   i i   ii       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_106120275_   4273 TTAACAAA--ATGTTGAGAAGACAAGACAGCCACATGCTAAATAATGAAA 4320
                          i      --i  i  i  vi  vi  i ?        v   v      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_106120275_   4321 TTGGACCCTTATCTTACGCCATACACACAAGTCAATTCAAAATGGATTAA 4370
                                 i  i  i  i     i   v  i i  i           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_106120275_   4371 AGATTTAAATATACGACCTGAGACTGTAAAACTCCTAGAAGAAAACATAG 4420
                            ii     i  v  v  i i   i        i               
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_106120275_   4421 AGGAAAACCTTCTTCACATTAGTCTTGGCAATGATTTCTTTGCTATGACA 4470
                         i? v   i    v v  v  i vi v       i      v v       
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_106120275_   4471 CCAAAACCACATGCAACAAAAGCAGAAATAGATAAGTGGGACTGCATCAA 4520
                               v    v          v i          i v     v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_106120275_   4521 A-CTAAAAAGCCCTGCACAGCAAAGGAAAC----AATAGAGTGAAAAGGC 4565
                          -i      viii  ii vv       v  ----  v i         i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_106120275_   4566 AACCTATGGAGTAACAGAAAATATTTGCAAACCATAT--TTAATA----- 4608
                             i ii  i iiv                i     --i i   -----
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_106120275_   4609 ------TCTAAAATATATAAGGAACTCT-ACAACTTGATGGCAAGAAAAC 4651
                         ------  i i         i       -      ii  iii  i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_106120275_   4652 AA----CCTCATTAAAATATGGGCAAAAGACTTAAACAGACATTTCTCCA 4697
                           ----  iv   ?   v         i  i  i  i             
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_106120275_   4698 AAGA-GATATA--AATAGCCAACAGGTATATGAAAAGATGCTCAATATTA 4744
                             -      --   i     i i i i                i  i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_106120275_   4745 CTATCAAC 4752
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.05 (129 / 63)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.09 (34 / 11)  


3114 23.71 3.71 2.02  chrX_106129656_106132503.rev     1474  2363 (485)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_106129656_   1474 AGAGACATTTTGTGTTCTTGGATTGAAAGACTTAATATTGTTAAGATATC 1523
                          i   i  iiii     v       i                     iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_106129656_   1524 AGTTCTTCTCAAATTGATTTGTAGATTCCACACAATCCCAAT-GAAATCC 1572
                          i v  i i         i ii      v  i       v  -i      
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_106129656_   1573 CAGAATGT-TATTTTGTGGATATTTAGGAACTTAATCTAAG-TTTATATG 1620
                            v-  i- v     ii  v   v vi i  v vi    i-  i     
  L1M4_orf2#LINE/    104 CAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_106129656_   1621 AAAAGACAAAAGACCCAGAACATGTAACACACTCCTGAA---GAAGAACA 1667
                         i   vi   ii         i vvi  v   v  i    ---        
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_106129656_   1668 AATTTGAAGGACTGACACTACCCAACTTCAAGAGTTACTA---------- 1707
                           v   i      v     v     i     i v      ----------
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_106129656_   1708 -TAATCAAGTAGCATGGTGTGGTGTTGCTGAGGGAAAAGA-AGACATACA 1755
                         -        ---- ii       ii  ---- viv  i  -       i 
  L1M4_orf2#LINE/    253 GTAATCAAG----ACAGTGTGGTACTG----GCATAAGGATAGACATATA 294

  chrX_106129656_   1756 GATCAATGGAGTAGAATAGAGACCCAAGGATTAGACCCACATAAATACAG 1805
                                   i      v    vi v  i v  i     i i vv  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_106129656_   1806 TAAATTGATACTTGACAAGGG-ATCAAGGACAGTTTAGTAGAGAAAGAAT 1854
                          v       vi i        -ii    iv  -  i i i i        
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAAT 393

  chrX_106129656_   1855 AGTCTTTTCAACAAATGGTGCTAGAACAACTGAATAGCCACATGTAAAAA 1904
                                               i i       i   ?       i    i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_106129656_   1905 AAAAATGAATCTAGATACAAACCTTACATCCTTCATAAAAATTAACTCGT 1954
                           ---    vi i  iv vv    i   i v vi i            iv
  L1M4_orf2#LINE/    444 AA---TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_106129656_   1955 AATGG-TCATAGACCTAAATATAA-AGCACAATACGATAAAACTTCTAGA 2002
                              -   ?          i   -   -i  v  v        ii    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGA 539

  chrX_106129656_   2003 AGAAAA---AGATTAAAATCTAAGTGACCTTGTGTTTGATGATGTATTTA 2049
                               ---  i?vv      vv         v   v iii   -i   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTC 588

  chrX_106129656_   2050 TCAGATATATCACCAAAAGTACAATATATGTAAGGAACAATTGGTAAGTC 2099
                          i      iv         i    vvv iiv   i  v   v i   i i
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_106129656_   2100 AGACTTTATTAACATTATAAACTTCTGCTATATGAAAAACACTTTTAAGA 2149
                         i     i  i  v    v      i  ivv vii  ii     v i    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_106129656_   2150 GAATCAAAAGACAAGCCACAGACTAGAA--AAATATTTGCAAAACTCACG 2197
                         i i v         v       v i i --             v vi ii
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_106129656_   2198 TCTAATAAAAAACTTGTATCCAAAATACACAAAGAATTCCCAAAATTCAA 2247
                            i    iii           i    i i      i  ii v  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_106129656_   2248 CAGTATTAAAA-------AACTCAATTTAAAAAATGGGTAAAAAATAAGA 2290
                         i i  --    -------   i     ?     -    i   ii  vv  
  L1M4_orf2#LINE/    789 TAATA--AAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGA 835

  chrX_106129656_   2291 ACAAACACGTCACCACAGAAGATATATACATGGCAAATAAGCATACGAAA 2340
                          i i   iv  v   v          i v     v        i i    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_106129656_   2341 AGAAGCTCATCTTTATTTGTCAT 2363
                            v     v v i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (130 / 77)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 2.43 (51 / 21)  


3857 15.80 7.32 1.97  chrX_106143873_106146858     1633  2493 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_106143873_   1633 GGAAGAGACATTCTATTTTCTTGTATTAAAAGA-TTAATGATTA--AAGA 1679
                             -   i  i i  v   v  v   ii    -     -   i--    
  L1M4_orf2#LINE/      2 GGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAAT-ATTGTTAAGA 49

  chrX_106143873_   1680 T--CAGTTTTCTCCAAATTGAATTATAGATTCAACTCAATCCTTATTAAA 1727
                          --  i vi  i         vi  i         v      i   i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_106143873_   1728 -TTCCAGCAGGCTTATTTTTCTTAAAATATTGGCAAGCTGTTTCTAAAAT 1776
                         - i     v v   -    v -- i  -    i       v i       
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTT-TTTTGC--AGAA-ATTGACAAGCTGATCCTAAAAT 145

  chrX_106143873_   1777 TTACATGGAAATACAAAGCACCTAGAATAG--AAAAGAGTGATTTTAAAA 1824
                          i i        i   i v   i       --    v ---  i  i   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA---ATCTTGAAA 192

  chrX_106143873_   1825 AAGAGAAACAAAGTTGGAGGAGTCATACTACCCAATTTCAAAACTTACTA 1874
                             ii               v   i   v                    
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_106143873_   1875 TAAAGGTACAGTAA-AAAGA---TTTAG----AGTATAAGGATAGGCATA 1916
                         i    v        -v    --- v i ----i i          i    
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_106143873_   1917 TAGATCAATGGAACCAAGTTGAGTGTCCAGAAATAAAGCCTTACATTTAT 1966
                                      ivi i     v             v  v         
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_106143873_   1967 GGTCAATTGATTTTTCCACAAAGGTGCCAAGAC-----AATGGGAAAAAT 2011
                                       - v    i           -----      i   i-
  L1M4_orf2#LINE/    343 GGTCAATTGATTTT-CGACAAGGGTGCCAAGACCATTCAATGGGGAAAG- 390

  chrX_106143873_   2012 AACAGCCTTT-----AAATAGTGCTGGAACAACTGGACATCCATATACAA 2056
                           i  i    -----    i       i         i ?   i  i   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_106143873_   2057 AAATATGAACTTGGACCCTTTACTTCACAC-----ATAAAAATCAACTCA 2101
                           iv     v        i -  i      ----- i      i      
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCA 489

  chrX_106143873_   2102 AA-TGTATAATATATCTAGATGTAAAATCTAAGACTATAAGTACTCC-AG 2149
                           -  v  v ? v i   i      i v    i       i-    i-  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAG 538

  chrX_106143873_   2150 AAAAAAAAATAGA---ATATCTTTCTGACCTTGAGTTCAGCAATGATTTC 2196
                           i    v    i--- v     iv        i   vi      i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_106143873_   2197 TTAGATATGACACCAAAAGCACAAGCCATAAAA-------TA-ATGAATT 2238
                                                   v i    -------  -  i    
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_106143873_   2239 GAACTTCATTAAAATTAAAAACTTCTGTGCTTCAAAAGACACCATTAAGA 2288
                          i       i              i           i     i  i    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_106143873_   2289 AAAT--AAAGACAAGCTACAGACTGGAAGAAAACATTTGCAAATCATATA 2336
                           i --        v i     v   i      i                
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_106143873_   2337 TATACCTTATAAAGGACTTGTATTCAGAATA----AAGAATTCTTATA-C 2381
                          ----  v    i          i       ----     i     i - 
  L1M4_orf2#LINE/    739 T----CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_106143873_   2382 TCAG------------AAACAACCCAATCAAAAAATGGGCAAAAGACTTG 2419
                            i------------   i        i?             i  i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_106143873_   2420 AATAGACATTTCACCAAAAAAGACATATTGATGGCTAATGAGCAGATGAA 2469
                                     v     i    i   ivi     i   i    v     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_106143873_   2470 AAAGTATTCAAGATCATTTGTTAT 2493
                           ii ii    v    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (93 / 40)
Gap_init rate = 0.03 (31 / 907), avg. gap size = 2.58 (80 / 31)  


 715 26.15 4.84 6.78  chrX_106159276_106161176      116   528 (1373)    L1M4_orf2#LINE/L1      309   713 (195)  

  chrX_106159276_    116 AATTATGAGGTTAAGTATTAACACACAAATTC--GGCCAATTGATTTCTG 163
                             iv   vii iiv  v   v  i v   i--  i          ii 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_106159276_    164 ACAAAAATGCAAAGGCAAGTAAATGGAGAAAGGATACTCTTTT-AACAGT 212
                             iii   v   i v v v     i     i   v      -    iv
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_106159276_    213 TGGTTCTAAAACAACAGGACATTTGAAGCCAAAAAAAAAAAATAAGTGAA 262
                             v  iii     v   i ?iiiv vv     i  vi  i ---  i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT---TGGA 455

  chrX_106159276_    263 CTTTAACCTAAACTTCATACCTTATATAAACATCAAGTAGTCAAAATGGA 312
                          i----    -- i   i   v    i   v  i  v ---         
  L1M4_orf2#LINE/    456 CC----CCTA--CCTCACACCATATACAAAAATTAACT---CAAAATGGA 496

  chrX_106159276_    313 TCATAGATCTAAATGTAAAATGTATAACTATATAACTATCAGAAGAAAAC 362
                            ?   i          i vv  v       v    v i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_106159276_    363 ATAGGAAAATATCTTTTTCATGAAC--AGGT-AG--AGTTGTTAGATACA 407
                              ?iv v     --- i   v --i   -  -- i v   vvv  v 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTT---CGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_106159276_    408 TATAAATGCACATACATAAAAG-GCAACCCATGAAAGGATCAACTGATAA 456
                            i ---   -----i     -i   v v ii    i vv  iv     
  L1M4_orf2#LINE/    594 TATGA---CAC-----CAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_106159276_    457 ACAAGATTTGAAACAATACTTGAAAACATTTTCTGTGAGGTAAAAGAC-T 505
                          ivi  i  v v-   - v  i     ---  i    vvvi   i   -i
  L1M4_orf2#LINE/    636 ATTGGACTTCAT-CAA-AATTAAAAAC---TTTTGTGCTTCAAAGGACAC 680

  chrX_106159276_    506 TAT----ACACTGAAAA------CTACAAAATG 528
                            ---- v v      ------ i   i    
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

Transitions / transversions = 1.19 (57 / 48)
Gap_init rate = 0.05 (19 / 405), avg. gap size = 2.53 (48 / 19)  

3830 18.20 8.04 1.30  chrX_106159276_106161176      563  1408 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_106159276_    563 AGACATCCCATGTTCATGACTTAGAAGAC--AATACTGTTAAGACATCAA 610
                            i              iv  i      --    i        iiv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_106159276_    611 TACTAACCAAAGTGATATACAGATTCAATGTAAGTCCTACCAAAACGTCA 660
                             vv     v    v           i i  vi    i     ivi  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_106159276_    661 ATAACATTTTTTTACAGGAATAGAAAAATCCATTCTAAAATTCATATGGA 710
                         iivi -i      i   i   v  v  iiiv  i                
  L1M4_orf2#LINE/    106 GCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_106159276_    711 ATCTCAACCAATCCCCAAATATCCAAAACAATTTTGAAAAAGAA---CAA 757
                          viv   vvi -   vi    v          i           ---   
  L1M4_orf2#LINE/    155 AATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_106159276_    758 AGTTGGAGTTCTCACACTTCCTGATTTCAAAACTTACTACAAGGTTACAG 807
                                 vv           ii                   i i     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_106159276_    808 TAATTAAAACAGTGTGGTACTGGCATAAAGACAGGTATATA--------- 848
                             i  i                    i  i  ii     ---------
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_106159276_    849 --------------------------------------TAGTCAAATGAT 860
                         -------------------------------------- i     v    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_106159276_    861 TTTTGAATAGGGTGCCAGGATCATTCAGTGTGGAAAGAACAGTCTTTTTT 910
                            i  vv         i  i      i  v        i        --
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT-- 401

  chrX_106159276_    911 CAACAACTGGCACTGGGAAAACTGAATATCAACATG-AAAATAATAAAGC 959
                               v   ii      v     i   ? v     -    v   i   i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_106159276_    960 TGAATTTTTACCTTAATACCATATACGAAAATTAACTCAAAA-GGTTCAA 1008
                           i iiii     i -i         i               -  v   ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_106159276_   1009 AGACCTAAACATGAGAGCTAAAGCTATAACACTCTCAGAAGATAACATAA 1058
                                  ii i         i      v     i      v      i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_106159276_   1059 GGAAAAGCCTTCATTTCATAACAATGGATTTGGCAATGATTTCTTGGATA 1108
                          ?iv  ii    i -----i  vv   i  v       i      i    
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGT-----GACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_106159276_   1109 TGACACCAAAAGCATAGACAACAAAAGAAAAAAATCAACAAATTGGACTT 1158
                                       i ii               - vi i           
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTT 644

  chrX_106159276_   1159 CATCGAAATTAAACACTTT-GTGCATCAAAGGACA---------GAGTGA 1198
                             i        v     -    v          ---------i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_106159276_   1199 AAAGGCAATTCTTGGAATAGGAGAAAATATTTGCAAGTCATATATCTTAT 1248
                             i   ii vii    i                 i          v  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_106159276_   1249 AAGGAATTAATATACAGAATATATATAGAACTTCTACAACTCAACAACAA 1298
                             i i vi   v           v      ii          i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_106159276_   1299 A----CAAGAAACTTATTTTAAAAATGGACAAGAGATCTGAACAGATACA 1344
                          ----   iv   ii v  ?        i   ii   i    i   i iv
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_106159276_   1345 TCTCCAAAGAAGATATACAAATGGCCAAAAAGCATGTGAAAAGATGCTCA 1394
                                                     v     ii              
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_106159276_   1395 ACAGCACTAATCAT 1408
                            v  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (102 / 48)
Gap_init rate = 0.02 (14 / 903), avg. gap size = 5.64 (79 / 14)  


2247 24.18 11.49 3.39  chrX_106184854_106188446     2274  3100 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_106184854_   2274 ATGTTCATAGATGGGAAGACTCAACACAGTAAAGATGTTAATTCTCCCCA 2323
                                 i   v        i  i iv  v      vi   v       
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_106184854_   2324 AATTGATCTATAGGTTAAATGCAATTCCTATCAAA-TCCCAG-------- 2364
                                   i  i  v  i     i         -      --------
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_106184854_   2365 ------GACATT------------------TTCAT--GGAAA-------- 2380
                         ------  v   ------------------     --     --------
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_106184854_   2381 -----------CTAAAACAATCTTGACAGAGTAGAATAAAGTGAGAAGAA 2419
                         ----------- i             v i  v    i     vi  i  v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_106184854_   2420 TCATTCTACCAGATACTAAGGCTTCTTACTGTATGGCTATAGTAATGAAA 2469
                            iv  v  vi  vii  ii   ---   ii vi    i      v  i
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTT---ACTACAAAGCTACAGTAATCAAG 261

  chrX_106184854_   2470 GCATTG-GG-----------GGAAAGACACATAGACCCATAGTATAGA-- 2505
                         i  v  -  -----------   v     i     i v  i v     --
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_106184854_   2506 ---GACCTCAGAAAAAGACCCACACAAATATG-TCAAACAGGTTTTTTGT 2551
                         ---  vii      v i     i   vv    -    -------------
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA------------- 348

  chrX_106184854_   2552 TGTTGTTGTTTTTTAA----GGCACAAAAGCAATTTAATTGAGGAAGGAT 2597
                         -----   v    ii ----  ii v  ii v   i   v i i   i  
  L1M4_orf2#LINE/    349 -----TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_106184854_   2598 ACT-TTTTCAA-AAATGGTGCTGGAACAACTGGATATTTGTAGGAAAAAA 2645
                          v -       -            i           ?iiii v v    i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_106184854_   2646 AA-GAAG---AATCTTAATCTAAGCCTCCTATCTTATATAAAAATTAAAT 2691
                           -    ---i i i----   --    vi i v    i         v 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCC----CTA--CCTCACACCATATACAAAAATTAACT 487

  chrX_106184854_   2692 CAAAATGGGTCACAGCCTTAAATGTAA-------AATGATAAAACTTGTA 2734
                                 i   ?  v i         -------  iv        iv  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_106184854_   2735 GAAAAAAGATATAGGAAAAAATCTTGGGGATATGGGGCTAGGCAAAAAGT 2784
                            i   - i     ?iv       v v  iv v   i       viiv 
  L1M4_orf2#LINE/    538 GAAGAAA-ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_106184854_   2785 TCTTAGACTGGACACCATAAACATAATCCATAAAATAAAA--CTGATCAA 2832
                                ivv       v  i  i  v v i    v    --iv   v  
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_106184854_   2833 ATGCATTGCATCAAAATTAAAAAACTTTGTTCTGTGAACAACTCTACTAA 2882
                         v  v i v               vi     v  vii  vi  v   ii  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_106184854_   2883 GAAAATGAATAGATAGGCTACAGACTGCGAGAAAATATTTGCAAACCACA 2932
                             i    v   i iv i     v  v                 i  i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_106184854_   2933 TATGTGACAAAAGACTTGCATCTAGAACACATGAAGA-TTCTCAAAACAC 2981
                            v   i  ii      i   i    i i  i    -i   i v   v 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_106184854_   2982 AACAGTAAAAA-ATAAACAATTTGATTAGAAAATGGACAGAGGACACAAA 3030
                           i i      - i   i  iiii   ?i       i  i    ivii  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_106184854_   3031 CAGGCATTTCACTGAAAAGTTTATACTGATGGGAAGTAAGTACAGGAAAA 3080
                         i  i      v ii  i ivv     vi    vv i    i   v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_106184854_   3081 G--GTTCAGCACCATCATTCAT 3100
                          -- i   i  i  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (120 / 76)
Gap_init rate = 0.03 (24 / 894), avg. gap size = 5.12 (123 / 24)  


3181 28.34 0.33 0.22  chrX_106204643_106210918     4877  5783 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106204643_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106204643_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106204643_   4977 TACCAATGACTTTCTTCACAGAATTGGAAAAAACGACTTTAAAGTTCATA 5026
                          v   iivi i  i  ii     v v  v  ivi  iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_106204643_   5027 TGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGAA 5076
                              viiv  ii  v  v v  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_106204643_   5077 -AAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5125
                         -    i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_106204643_   5126 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5175
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_106204643_   5176 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACTAC 5223
                              i    i--    i  --        vv  ii i ii  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_106204643_   5224 CTGATCTTTGACAAATCTGAGAAAAACAAGCAATGGGGAAAGGATTTCCT 5273
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_106204643_   5274 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5323
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_106204643_   5324 AACCGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5373
                          iii   i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_106204643_   5374 AAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGGAAACCT 5423
                          ?   ii    i  v   v       i      vi i      i    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_106204643_   5424 AGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAA 5473
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_106204643_   5474 CACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAATT 5523
                                    vvi     v    vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_106204643_   5524 AAACTAAAGAGCTTCTGCACAGTGGGGGAAACTACCATCAGAGTGAACAG 5573
                            v v  i i   i  ii vviiii   v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_106204643_   5574 GCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5623
                         i     i   iv            v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_106204643_   5624 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5673
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_106204643_   5674 ACAAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGACACTTCTC 5723
                              i     v  i?    i     i i   iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_106204643_   5724 AAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 5773
                         v        i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_106204643_   5774 CACTGGCCAT 5783
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.56 (154 / 99)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.67 (5 / 3)  


3584 24.26 0.33 1.09  chrX_106329961_106334552     3185  4099 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106329961_   3185 TGGAAAGATATTCCATGTTTATGGACTAGAAGAATCAATGTTGTTAAGAT 3234
                                    i       i     i i     v i   i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106329961_   3235 GTCCATACAGCCAAAA-CAATCTACAGATTCAATTCATTCCATGTCAAAT 3283
                          v v    vv  v   -ii              iv  v   v i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106329961_   3284 TACCAATGACATTCTTCACAGAAATAGAAAAAACACTCCTAAAATTTATA 3333
                          v   iivi v  i  ii       v  v  iviiv          i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_106329961_   3334 TGGTACCACAAAAAGACCCAGAATAGCCAATGCTATCCTGAGCAAAAAGA 3383
                            v vii -  ii                vi v   i   iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_106329961_   3384 ACAAAACTGGAGGAATCACATTACCTGACTTCAAATTATGCTACACAGGT 3433
                              ii       v     i v  ii i      viv i     v  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_106329961_   3434 ATAGTAGCCCAAACAGCATGATACTGGGATAAAAACAGACACAGACACAT 3483
                          i    ii v i    ii  i      v    ii i     i ------ 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA------T 293

  chrX_106329961_   3484 AAGCCAATGGAACACAATGGAGAACCGAGAAACAAATCCATACATCTACA 3533
                          iii        i v   v    ii v     i   i        i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_106329961_   3534 GTGAACTCATTTTTGACACAGGTATCAAAAACATACATTGGGGAAAGGAC 3583
                           v  i v     i    vi   ii   i v   v  v         i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_106329961_   3584 AGTCTCTTCAATGAATGGTTCTGGGGAAACAGGATATCTATATGCAGAAG 3633
                              i     ii      v     iv   v     ? i i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_106329961_   3634 AATGAAACTAGACCTCTGTCTCTTGCTTTATACAAAAATAAAGTCAAAAT 3683
                               ii i    i  ii   vii iv           v  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_106329961_   3684 ACATTAAATACTTAAATCTAAGACCTCAAACTGTGAAACTCCTAAAAGAA 3733
                         iv  i ? v  i     v     v  v     i i      i  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_106329961_   3734 AATATTAAGGAAACTCTCCAGGACATTGGACTGGGGAAAGATTTCT-AGA 3782
                           i  vii? v  v   i iv   v    ii i  v  v i     -   
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_106329961_   3783 GTAATACCCCTCAAGCACAGGCAGCCAAAGAAAACATGGACAAATGGGAT 3832
                         -  vv  v  vv       i   i v        v  i  i    v   i
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_106329961_   3833 CACATCAA-GTTAAAAAGCTTCTGCATAGCAAAGGAAACAATCAATAAAG 3881
                         iv      -i       -   i  iiivv       v  v     v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_106329961_   3882 TGAAGAGACAACACACAGAATGGGAGAAAATATTTGCAAAGTATCTATCT 3931
                             i       v                           vi  v     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_106329961_   3932 GACAAGGGATTAATAACCAGAATATATAAGGAACTCAAACAACTATATAG 3981
                           i      i vi  v             i      vv      vv   i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_106329961_   3982 GAAAAAATCTAATAATCCAATTTAAAAAATGGGCCAAAGATTTAAATAGA 4031
                         v     iv v     i      ?     -     v  i     i      
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGA 840

  chrX_106329961_   4032 CATTTCTCAAAAGAAGACGTACAAATGGCAAATAGGTTTATGAAGAAGTG 4081
                                 v        ii          v    i ivi     i ii  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_106329961_   4082 CTAAATATCACTGATCAT 4099
                           v  i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (129 / 89)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3356 25.33 0.88 0.88  chrX_106413212_106419488     4877  5784 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106413212_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4926
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106413212_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106413212_   4977 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5023
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_106413212_   5024 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5073
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_106413212_   5074 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5123
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_106413212_   5124 CTACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATATAGAT 5173
                                  i   i    ii        vi iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_106413212_   5174 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5221
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_106413212_   5222 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 5271
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_106413212_   5272 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5321
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_106413212_   5322 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5371
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_106413212_   5372 ATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5421
                           i ?    i  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_106413212_   5422 CCTAGGC---AATCCCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 5468
                          v    ?---    ---   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_106413212_   5469 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5518
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_106413212_   5519 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5568
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_106413212_   5569 GAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTG 5618
                            v  i     i                 v  i    vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_106413212_   5619 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 5668
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_106413212_   5669 AAAAAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACA 5718
                              i     i     v  i? v  i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_106413212_   5719 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 5768
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_106413212_   5769 CATCATCACTGGCCAT 5784
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (133 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


2750 27.41 3.85 1.02  chrX_106425673_106429843.rev     2798  3680 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106425673_   2798 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 2847
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106425673_   2848 GGCCATATTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAAC 2897
                            v   i v      v i  i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106425673_   2898 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTTAT 2946
                          v   vivi i  i  ii     v v  v  i-  - iii    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_106425673_   2947 ATGGAACCAAAAAAGAGCCTGTATAGCCAAGACTATCCTAAGAACAAAGA 2996
                               viiv  ii  v  v v        i  v   i i i  vi    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_106425673_   2997 ATGAAGCTGGAGGCATCATGGTTACCTGACTTCAAACTATATTATAAGGC 3046
                          ii   i      vv   iiv  -  ii i      viv  i  i  i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAAGC 248

  chrX_106425673_   3047 TACAGTAACCAAAACAAGCATGGTACTGGTACCAAAACAGATATATAGAC 3096
                                 i   i   - ii         i iv ii i   i       i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACA-GTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_106425673_   3097 TGATGGAACAGAAC--ACAGTCCTCAGAAATAATGCCACATATCTACAAT 3144
                         ii      i    i-- v     --        vv   i i  i  iii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_106425673_   3145 CATCTGATCTATGACAAACCTGACAAAAACAAGCAACAGGGAAAAGATCC 3194
                           vi    i vi     ivv  v   i v  vv   ii      ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_106425673_   3195 CCTATTTAATAAATGATGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 3244
                         i  v  i  i     i  i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_106425673_   3245 TGAAACTGGACCCCT----------------------TAACTTAAAATGT 3272
                             ii         ----------------------     i      v
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_106425673_   3273 ATTAAAGATGTAAACGTTAGACCTAAAACCAGAAAAACCCTAGAAGAAAA 3322
                           i ?   iv    i  v   v       i v    vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_106425673_   3323 CCTAGGC---AATCCCATTCAGGACATAGGCATGGACAAAGACTTCATGA 3369
                          v    ?---    ---   iv   v v  vv i i   v ii   v ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_106425673_   3370 CTAAAACACCAAAAGCA-ATGTCAACAAAAGCCAAAATTGACAAATGGGA 3418
                         v  vi            - v -         vv     v  i    v   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_106425673_   3419 TCTAATTAAACTAAAGAGTTTCTGCATAGCAAAACAAACTATCATCAGAG 3468
                         ii v  i   v v  i ii  i  iiivv    iv v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_106425673_   3469 TGAACAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCCATCCATCT 3518
                             v  i     i i               v       vi   vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_106425673_   3519 GACAATGG-CTAATATCCAGAATCTACCAGGAACTTAAACAAATTTAAAA 3567
                           i  v  -  vi          v  iv i     ivv    v iv v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_106425673_   3568 GAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGAATGTGAACAGAC 3613
                         v     i    ----   v  i?    i         i  v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_106425673_   3614 ACTTCTCAATAGAAGACATTTATGCAGCCAACGAACATATGAAAAAAAGC 3663
                          i     v v      i  vi viii     ii i  i       i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_106425673_   3664 TCATCATCACTGGTCAT 3680
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.31 (43 / 13)  


3238 27.39 0.33 0.44  chrX_106471715_106476986     3871  4779 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106471715_   3871 TGAAAGAACATTCCATGCTCATGGATAGGAAAAATCAACACTGTGAAAAT 3920
                           i  ii i  i     i        v    i v i  i i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106471715_   3921 GGCCATACTGCCCAAGGTAATTTATAGATTCAATACCATCCCCATCAATC 3970
                            v     v     iv i  i  i        ii v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106471715_   3971 TACCAATAACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4018
                          v   iivi i  i   i     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_106471715_   4019 TATGGAACCAAAAGAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAG 4068
                                viiv   i  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_106471715_   4069 AACAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4118
                                i i    vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_106471715_   4119 TACAGTAACCAAAACAGCATGGTAGTGGTACCAAAATAGATATATAGGCC 4168
                                 i   i    ii     v   i iv ii     i      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_106471715_   4169 AGTGGAACAAAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 4218
                          i     i i  iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_106471715_   4219 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGAGAAAGGATTCCCT 4268
                         i    i  i     ivv  v   i v  vvv     i     i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_106471715_   4269 ATTTAATAAATGGTGCTGGGAAAACTGGTTAGCCATGTGTAGAAAGCTGA 4318
                         v  i  i              v      v  ?   ii  i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_106471715_   4319 AACTGGATCCCTTCCTTACCCCTTATACAAAAATTAATTCAAGATGGATT 4368
                          ii    i    v   i  v  v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_106471715_   4369 AAAGACTTAAGTATTAGACCCAAAACCATAAAAACCCTAGAAGAAAACCT 4418
                          ?    i   i i v   v i     i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_106471715_   4419 AGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCATGACTAAA 4467
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_106471715_   4468 ACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAAT 4517
                                     vvi          vv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_106471715_   4518 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 4567
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_106471715_   4568 GGCAACCTACAGAATGGGAAAAAATTTTTGTAATCTACTCATCTGACAAA 4617
                          i     i           i     v    i  vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_106471715_   4618 GGGCTAATATCCAGAATCTACAGAGAACTTGAACAAATTTACAAGAAAAA 4667
                           i  vi          v  i i      ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_106471715_   4668 AAACAAACAACCCTATCGAAAAGTGGGCAAAGGATATGAACAGACACTTC 4717
                         i -    i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_106471715_   4718 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 4767
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_106471715_   4768 ATCATCATCACT 4779
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (153 / 92)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


 469 25.73 3.51 1.75  chrX_106478434_106480586      500   670 (1483)    L1M4_orf2#LINE/L1      152   325 (583)  

  chrX_106478434_    500 GAAAAGGCAAAGGAATTAGAAAAGCCAAGACATTATTTGTGGAAAA---- 545
                          i   v    i   vii    v      i   --  i -  i    ----
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACA--ATCT-TGAAAAAGAAG 198

  chrX_106478434_    546 AATAAAATTAGAGGAATCACATTGAATGATTTTAAGATTTA-TAGAAAGT 594
                           i   i  i     v     i vvvii    i  i i   -  v    i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_106478434_    595 TA-AGTAATCAATACTGAGTGTTACTAGTGAAGAGATAGGCACATAAATC 643
                           -         v  v v   v    i iiv ii     i  i   i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_106478434_    644 AATGAGATGGAAAAGAGAGTTCAGAAA 670
                             ii  i   vv      i      
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAA 325

Transitions / transversions = 1.93 (29 / 15)
Gap_init rate = 0.03 (5 / 174), avg. gap size = 1.80 (9 / 5)  

1782 24.71 0.23 0.92  chrX_106478434_106480586      993  1429 (724)    L1M4_orf2#LINE/L1      358   791 (117)  

  chrX_106478434_    993 GACAAAGATGCAAGAACAATTCAGCAGAGAAAACATCATCTTTTCAACAA 1042
                              i i   v ii  v     iii i    iv  vi            
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_106478434_   1043 ATAATGCTGAAACAGTTGAACATCCACAGTTTTAAAAAAAGAACATTG-A 1091
                           ii     ii   ii  i i ?     -- vi    i  vi vi   - 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACA--TGCAAAAGAATGAAGTTGGA 455

  chrX_106478434_   1092 CCTAAATATTATACCTTATATAAAAGTGAATTCAAAATAGATATTAGATC 1141
                           ivv iv i i   v    i    i v  i       i   vv?   i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_106478434_   1142 TAAATGCAAAACCTAAAACTATAAAACTTTTAGAAGAAGATGTAAGGGAA 1191
                               i  i v                i         i ii  i ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_106478434_   1192 AATCTTTGTGACCTTGGGTTAGGCAAAGAACTTTTGGATATACCACCAAA 1241
                               i                   v ivi i  i     iv       
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_106478434_   1242 AGCTTGATCCATAAAAAAGAAAAATTGGTAAATTGGACTTTATTAAAAGG 1291
                            vii v v i    i -      v i            i  i    vv
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_106478434_   1292 TAAAACTTTTGCTCTGTGAGAGATACTGTTAAGAGAATAAAAAGACAAGC 1341
                         v          iv  vii ii  i   i i    i i i         v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_106478434_   1342 TACAAATTGGGAGAAAATATTTGCAAATCACATATCTGACAAAGAACTTG 1391
                         i   i v                       i        i  i i     
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_106478434_   1392 TATCTAGAATATGTAAAGAGGCTATTAAAACTTAGTAA 1429
                             i       i      i-  v   v    i i   
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAA-CTCTTACAACTCAATAA 791

Transitions / transversions = 2.28 (73 / 32)
Gap_init rate = 0.01 (4 / 434), avg. gap size = 1.25 (5 / 4)  


3523 19.98 2.33 6.87  chrX_106606098_106608218.rev      685  1630 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_106606098_    685 AGAAATACTGTGTTCAGGGATTGGAAGGCTCAATATTGTTAGGATGTCAA 734
                            v  v ii      v          i  i          i    v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_106606098_    735 TTGTCCCCAAATTGATCTATAGTTTCAACACAATCCTAATCCAAATCACA 784
                          vv                i  v      i      iv   v     v  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_106606098_    785 GCAGG--TTTTGGTAGAAATTATCATGGTGATTCTAAAATTCACATGAAA 832
                           v v--    v i       iv  v v    i          i   i  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_106606098_    833 ATGCAAAGGACCTATAATAGCCAAACCAACTTTGAAAAAGAA---CAAAG 879
                               i     i v          v   ii           ---     
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_106606098_    880 TTGGAGAACAAATACTTCCTGATTTCAAGAATTATTATAAAGCTCCAGTA 929
                               i  vv i      ii       i v   i  i      v     
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_106606098_    930 ATCAAGA--GTGTGATGTTGACATAACGACAGACAAGTAGACCAACAGAT 977
                                --     i ii  i     v  i     vi    i   ii  v
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_106606098_    978 CAGAATAGAGAGTACAGGAATAGATCTATATATATATATATATATATATA 1027
                         i     v      v   i    i i i   i  -----------------
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACAT----------------- 338

  chrX_106606098_   1028 TATATATATATATATATATAGACAACAGATTTTTAACAAAAGTACAAAGG 1077
                         -------------- -   i v   iv      ii    ii  i v   i
  L1M4_orf2#LINE/    339 --------------T-TATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_106606098_   1078 CAATTCAGTGGAGGAAGGATACTCTTCTCAACAAAAGGTGCTATAACAAT 1127
                          v     i   i i   i   v    i        v      ivi    i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_106606098_   1128 TGGATATCCATATGCAAAAAAAAACACACACACACACACACACACACACA 1177
                               ?   i        i  ----------------------------
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAA---------------------------- 445

  chrX_106606098_   1178 CACGAAACTTTGATGGATACCTTGCACCACATACAAAAGTTAATTCAAA- 1226
                         --i   i-  v  ivvv     ii     i        i    i     -
  L1M4_orf2#LINE/    446 --TGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_106606098_   1227 TGGATCATAGGCCTAAATATAAAA-CTGTAAATGATAAAACATCTAGAAA 1275
                                ?  i       i   i -  i-   iv       vii     i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAG 541

  chrX_106606098_   1276 AAAA--TAGGGGAAAATTCTTGTAACCTTGGGTTAGACAAAGATTTTTTA 1323
                             --    ? v    ii i  i            i   v i   i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_106606098_   1324 GATATGACACCAAAAGCACTGTCCATAAAAGAACAAATTAGCAAACTGGA 1373
                                            viv v i       v    viii   i    
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_106606098_   1374 CTTCATCAAAATTCACA-CATTTGCTCTGTGAAAGACGTTGTTTAGAGAC 1422
                                      v v - v    iv  vii  i   ii i iv   i v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_106606098_   1423 TGAAAAGGAAAGCTACACACTGGAAGAAAATATTTGCAAATAATATATCT 1472
                                iv  v i   v v   i                 v        
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_106606098_   1473 AACAAACAGCTTGTATCCAGAGTATATAAAGAACTCTCAAAACTCAATAA 1522
                         i i  ivii            i               i v          
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_106606098_   1523 ------GA-AAACAACCCAATAAAAAAGCAGGCAAAG-ATCTAAATGGAC 1564
                         ------  -   i        v?    iii       -  i i   i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_106606098_   1565 ACTTCCCCCGAGAAGATGCGTAGCAT--CAAATAAACACATGAAAAGATG 1612
                          i   i  vi       iiii i-  -- v     i              
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAA-ATGGCCAATAAGCACATGAAAAGATG 890

  chrX_106606098_   1613 CTCAACATCATTAGTCAT 1630
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (121 / 64)
Gap_init rate = 0.02 (17 / 903), avg. gap size = 5.12 (87 / 17)  


3013 26.04 1.54 1.76  chrX_106633075_106639140.rev     4674  5583 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106633075_   4674 TGCAAAAACATTCCATTCTCATGGACAGGAAGAATTAATATTGTGAAAAC 4723
                           v   i i  i    vi       iv      v          v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106633075_   4724 GGCCATACTGATCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 4773
                            v     vvi    v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106633075_   4774 TACCATTGATGTACTTCACTGAATTAGAAA-----AAACTAGTT-TAAAT 4817
                          v   -- v  i-   ivi  ---i     -----  i  ii i-    v
  L1M4_orf2#LINE/    101 TCCCA--GCTGC-CTTTTTTG---CAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_106633075_   4818 TTCATATGGAATCATCAAAGACCCTGTATAACCAAGACAATCCTAAGCAA 4867
                                    viiiv ii     v v   i    i      i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_106633075_   4868 AAAGAACAAAGCTGGAGGCATCATGCTACCTGACCTCAAACTATACTACG 4917
                         i          i      vv   ii  v  ii ii     viv      i
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_106633075_   4918 AGGCTACAGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGACATATA 4967
                          i          i   i    ii     v   i iv ii i         
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_106633075_   4968 GACAAGTGGAACAGAACAGAGACTTCAGAAATAACACCACACATCTACAA 5017
                           iv i     i    iv    v i         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_106633075_   5018 CCATCTTATCTTCATTGAACCTGATAAAAACAAGCAATGGGGAAAGGATC 5067
                         i  vi v  i   ivii ivv  vi  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_106633075_   5068 TCCTATTCAATACATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAA 5117
                         vi  v     i v            v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_106633075_   5118 CTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATG 5167
                         v    ii         v   i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_106633075_   5168 GATTAAAGACTTAAATGTAAAACCCCAAATCATAAAAACTCT-AGAAGAA 5216
                            i ?    i         i v iv   ii      -    -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chrX_106633075_   5217 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTC---- 5261
                            v    ?i- v i -   iv   v v  vv i     v i    ----
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_106633075_   5262 --ATGACAAAAATGCCAAAAGCAATTACGACAAAAGCCACAATTGACAAA 5309
                         --      ------         vvvi i       vv v   v  i   
  L1M4_orf2#LINE/    593 ATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_106633075_   5310 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAT 5359
                          v   ii v  i   v v  i i   i  ii vv    i  v       v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_106633075_   5360 CAGAGTGAACAGGCAACCTACAGAATGAGAGAAAATTTTTGCAATCTATC 5409
                         v i      v  i     i        i        v       vii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_106633075_   5410 CACCTGACAAAGGTCTAATAACCAGAATTTACAAGGAACTTAAACAAATT 5459
                         i i    i  i  v  vi  v       v  i  i     ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_106633075_   5460 TACAAGGAAAAAAAACAAACAATCCCATAAAAAAGTGGGCAAAAAATATG 5509
                         v i  v--     i     i  i  v  v?    i        ii  v  
  L1M4_orf2#LINE/    787 AATAAT--AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_106633075_   5510 AACAGACACTTCTCAAAAGAAGACATTTACGCGGCCAACGAACATATGAA 5559
                           i     i     v        i  vi vii      ii i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_106633075_   5560 AAAATGCTCAACAACAACAACAAC 5583
                           i          v  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (137 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.50 (30 / 12)  


3103 26.30 3.05 0.56  chrX_106642023_106644274.rev      876  1761 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106642023_    876 TGAAAACACAGCCTATGCTCATGGGTGTGTGCAA---TCAATATTGTGAA 922
                           i   v i v  i   i      i ---  v  --- i        v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT---TGGAAGACTTAATATTGTTAA 47

  chrX_106642023_    923 AATGACCATACTGCTAAAAGCGATCTGCAAATTCAACGCTATTCCCATCA 972
                         i   i v     v iv   vi     i  i         v  i  i    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_106642023_    973 AAATGCCATCATCATTTTTCACAGAACTAGAAAAAAAAATCCTAAAATTT 1022
                             v   v vv v     ii     v v  v  ivvi           i
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_106642023_   1023 ATATGGAACCAAAAAAGAGCCCGCATAGCAAAAGCAATCCTAAGCAA-AA 1071
                                 viiv  ii  v  v v     v   i     i i iv  -  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_106642023_   1072 GAACAAATCTGGAGGCATCACATTATCAGATTTCAAACTATACTACGAGG 1121
                                vi      vv     i vi vi        viv      i i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_106642023_   1122 C------------------ATGGTACTGGTATAAAAATAGGTACATAGGC 1153
                          ------------------i         i    ii    ii i    ii
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_106642023_   1154 CAATGGAACAGAATAGAGAACCCAAAAATAAACCCAAATACTTACAACCA 1203
                                 i     v    ii   i           v i i   iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_106642023_   1204 ACTGATCTTCGACAGAGCAAACAAAAACATAAAGTGGGGAAAGGACACCC 1253
                          i    i       ii vviv   i v   vv i         i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_106642023_   1254 TTTTCAACAAATGGTGTTGGGACAACTGGCTAGCCCCATGTAGGAGAATG 1303
                                         i            v  ?  v    i ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_106642023_   1304 AAACTGGATCCTCATCTCTCACATTGCACAAAAATTAACTCAAGAGGGAT 1353
                           ii    i  ii i   v   vv ii                i v    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_106642023_   1354 TAAGGACTTAAATCTAAGACCTGAAACCATAAAAGTTCTAAAAGATAACA 1403
                         i ?i   i     v     v  i    i      v ii  i    v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_106642023_   1404 TTGGA--AAACCCCTACTAGACATTGGCTTACACAAGGATTTCATGACCA 1451
                          v  ?--   i iiiii--   v    v   vi   v i    v iivi 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGT--GACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_106642023_   1452 GGAACCCAAAAGCAAAAGCAATAAAAATAAAGATAAATAGTTGGGACTTA 1501
                         v  vv         v      i    iv   i   i   iv v      v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_106642023_   1502 ATTAAACTAAAGAGCTTTTGCACAGCAAAAGGTACAGTCAACAGAGTAAA 1551
                           i   v v  i i      ii vv    i ii  vi    v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_106642023_   1552 CAGACAACCCACAGAGTGGGAGAAAATCTTTGCAAACTATGCATCCAACA 1601
                         v              i           v        ii  ii   ii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_106642023_   1602 AAGGACTAATATCCAGAATCTACAAGGAGCTCAAACAAATCAGCAAGAAA 1651
                          i     vi          v  i  i  i   vv    v   ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_106642023_   1652 AAAACAAACAATCCCACCAAGAAGTTGGCTAAGGACATGAATAGACAATT 1701
                           i     i  i  v ii? i  i v   v     iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_106642023_   1702 CTCAAAAGAAGGTATACAAATGGCCGA---GCATAGGGAAAAATGTGCAA 1748
                            v       i             i ---   i v i   i   iv   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_106642023_   1749 CATCACTAATTAT 1761
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 4.57 (32 / 7)  


3568 11.95 0.26 21.65  chrX_106849223_106851972     1103  2257 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106849223_   1103 TGGAAAGATATTCCATATTCATGGATTGGAAGACTTAATATTGTTAAGAG 1152
                                    i    i                                v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106849223_   1153 GACAATAACCCACAAATTAATCTATAGATTCAGTGCAATTCCTATCAAAA 1202
                          i     vi  v      i     i       ii     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106849223_   1203 ATTTCAGCTGGCTTTTTTTGTAGAAATTGATAAGCTCTTAAGTGATTTTT 1252
                         - ii      - i       i         i     --------------
  L1M4_orf2#LINE/    101 -TCCCAGCTG-CCTTTTTTGCAGAAATTGACAAGCT-------------- 134

  chrX_106849223_   1253 CAAACTACTAGGAAAAAAACAAAAAAATTTGACAAGCAGATCCTAAAATT 1302
                         --------------------------------------            
  L1M4_orf2#LINE/    135 --------------------------------------GATCCTAAAATT 146

  chrX_106849223_   1303 CATATGGAAATGCAATAG--TCAGCATAGCCAAAACAATCTTGAAAGAGA 1350
                                        vi --i   v                     i   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_106849223_   1351 AGAACAAAGTTGGAGGACTCACACTTCCTGATTTCAAAACTTACTACAAA 1400
                                                     ii                    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_106849223_   1401 GCTACAATACATAAGACAGCATGGTACTGGCATAAGAATAGACATGTAGG 1450
                               i  vvi       ii               i        i   i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_106849223_   1451 TCGGTGGGATAGAATTGACAGTCCAGAGGTAA-CTCTCATATTTACAGTC 1499
                           ii   i          v        ii   - i vi i     ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_106849223_   1500 AATTGATTTTTGATAACAGTGTTAACGACCATTAAATGGGAGAAAGAAGA 1549
                                   i  i  vi   ii  -       v      -       v 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGG-GAAAGAATA 394

  chrX_106849223_   1550 GCCTTTTAAGCAAATGGTGCACAACTGGGTAGACACATGGTGGACAATGG 1599
                          i     v i          -----    -----   ------  --   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGC-----TGGG-----ACA------AC--TGG 426

  chrX_106849223_   1600 ACACACATGTGCAAAAGAATAAATTTGGGTCTATACTTCACACCATATAC 1649
                          i ?v  ii           i  v    ii iv   i             
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_106849223_   1650 TAAAATTAACCCAAAATGGTTCAATGAGCTAAATGTAAGAGCTAATACAA 1699
                         v         i        v   ?v  v                 v  v 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_106849223_   1700 TAAAATTCTTGGAAGAAAACATAGATATACATTTTCAAGACCTTGGGCCG 1749
                              i    i             i?i  v  i   iv         iii
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_106849223_   1750 GGTGCAGTGATTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGG 1799
                           --  i  i  i------------------   ----------  i i-
  L1M4_orf2#LINE/    577 GG--CAATGGTTT------------------CTT----------AGATA- 595

  chrX_106849223_   1800 GTGGACTGCTTGAACTCACGAATTCAAGACCAGCCTGGGCAACATGGCAA 1849
                         ----------   ---   -----   i ---  viii      ----  
  L1M4_orf2#LINE/    596 ----------TGA---CAC-----CAAAA---GCACAAGCAACA----AA 620

  chrX_106849223_   1850 AACCCTGTCTCTACAAAAATACAAAAATTAGCAGAGCGTGGTGGCACATA 1899
                          i---------- -       v v     i ------------------ 
  L1M4_orf2#LINE/    621 AG----------A-AAAAATAGATAAATTGG------------------A 641

  chrX_106849223_   1900 CCTGTATTCCCAGCTACTCAGGAGCTGAGGTGGGAGGATGGCTTGAACTT 1949
                          i -------  -----   ii -i i i----------------     
  L1M4_orf2#LINE/    642 CTT-------CA-----TCAAAA-TTAAA----------------AACTT 662

  chrX_106849223_   1950 GGGAGGCAGAGGTTGTAGTGAGCTGAGATCATGGCACTGCATTCCAGCCT 1999
                         ------------    -----   ----   -------------------
  L1M4_orf2#LINE/    663 ------------TTGT-----GCT----TCA------------------- 672

  chrX_106849223_   2000 GGGTGACAGAACAAGACTCAATCTCAGAAAAAAAAAAAAAGTAGAAAGAC 2049
                         ----- -  i   ---  --   -----------  i     ii      
  L1M4_orf2#LINE/    673 -----A-AGGACA---CT--ATC-----------AAGAAAGTGAAAAGAC 700

  chrX_106849223_   2050 AGCCCACAGAATGGGAGAAACAGTTTGCAAATCATACATGTGATAAGGGG 2099
                          i                  vvi             i  v         i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_106849223_   2100 CTTGTATCTAGAATATGTAAAGAACTCTGAGAACTCAACAATAAAAAGAC 2149
                                 i       i           v v       i           
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_106849223_   2150 AAATAACCCAATTTAAAAATGGGCAAAGGGTCTGAATAGACATTTCTTTA 2199
                                      ?               i i               ii 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_106849223_   2200 AAAAAGAGATACACATAGCCAATAAGCATGTAAAAAGATCTTCAACATCA 2249
                           i    v     v  i           ii i       vi         
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_106849223_   2250 TTAACCAT 2257
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.83 (99 / 35)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 7.44 (253 / 34)  


3299 26.98 0.33 0.33  chrX_106934748_106941139.rev     4994  5901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106934748_   4994 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5043
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106934748_   5044 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5093
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106934748_   5094 TACCAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTGAAAGTTCA 5141
                          v   iivi    i  ii     -   -- v  i  - iiiv   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_106934748_   5142 TATGAAACCAAAAATGAGCCTGCACTGCCAAGACAATCCTAAGCCAAAAG 5191
                             i  viiv  iv  v  v v iv     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_106934748_   5192 AATAAAGCTGGAAGCATCACGCTACCTGACGTCAAACTATACTACAAGGC 5241
                           i    i    i vv    i  v  ii iv     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_106934748_   5242 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5291
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_106934748_   5292 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCGCATATCTACAACTGT 5341
                                i    iv   ivii         vv  ii i  i  iiiiiiv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_106934748_   5342 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5391
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_106934748_   5392 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAGGTAGAAAGCTGA 5441
                         v  i  i              v      v  ?   i v i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_106934748_   5442 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5491
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_106934748_   5492 AAAGACTTAAATGTTAGACCTAAAAGCATAAAACTCCTAGAAGAAAACCT 5541
                          ?    i       v   v      vi         i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_106934748_   5542 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5590
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_106934748_   5591 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5640
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_106934748_   5641 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5690
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_106934748_   5691 GGCCACCTACAGAATGGGAGAAAATTTTTCCAATCTACTCATCTAACAAA 5740
                          i v   i                 v   v   vii ivi    i i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_106934748_   5741 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5790
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_106934748_   5791 AACAAATAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5840
                         i           v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_106934748_   5841 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 5890
                          v        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_106934748_   5891 TCACTGGCCAT 5901
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


3162 26.84 0.88 0.99  chrX_106993191_106999556.rev     4967  5875 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_106993191_   4967 TGGAAGAACATTCCATGCTTACGGATAGGAAGGATCAATATCATGAAAAT 5016
                              ii i  i     i i i    v     iv i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_106993191_   5017 GGCCATACTCCCCAAGGTAATTTATAGATTCAATGCCACCTCCATCAAGG 5066
                            v           iv i  i  i        i  v i i i     ii
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_106993191_   5067 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5114
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_106993191_   5115 TATGGAACCAAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAA 5164
                                viiv  ii-  v  v v  v     i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_106993191_   5165 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5214
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_106993191_   5215 CTACAGTAACAAAAATAGCATGGTACTGGTACTAAAACAGAGAGATAGAA 5264
                                  iv  i i  ii         i iv ii i   v v     v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_106993191_   5265 CAATGGAACAGAAT--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5312
                                 i     --    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_106993191_   5313 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5362
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_106993191_   5363 CCTATTTAAAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAA 5412
                         i  v  i  --i        i     v      v  ?   i   i i  i
  L1M4_orf2#LINE/    396 TCTTTTCAA--CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_106993191_   5413 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 5462
                         iv    ii    i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_106993191_   5463 GAATTAAAGACCTAAATGTTAGACCTAAAACCATAAAACACCCTAGAAGA 5512
                          i  i ?            v   v       i       -i i       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGA 542

  chrX_106993191_   5513 AAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATG 5561
                             v    ?i- v i -   iv   v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_106993191_   5562 ACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5611
                         iv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_106993191_   5612 TCTAATTAAACTCAAGAGCTTCTACATAGCTAAATAAACTACCATCAGGG 5661
                         ii v  i   v i  i i   i iiiivv v  iv v    i  vv ii 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_106993191_   5662 TGAGCAGGCAACCTACAGAATGGGAGTAAACTTTTGCAATCTACCCATCT 5711
                            iv  i     i            v   iv       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_106993191_   5712 GACAAAGGGCTAATATCCAGAATCTACAAAGACCTTAAACAAATTTACAA 5761
                           i  i  i  vi          v  i     v  ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_106993191_   5762 GAAAAAAACAAA---CCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 5808
                         v     i     ---   v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_106993191_   5809 ATTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAGATGC 5858
                                v        i  vi viii     i ii               
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_106993191_   5859 TCATCATCACTGGTCAT 5875
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (149 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


2951 27.70 0.88 0.66  chrX_107003225_107010247.rev     5627  6532 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107003225_   5627 TGGAAAAATATTCCATGCTCATGGATAGGATAAATCAATATCATGAAAAC 5676
                               i    i     i        v   vi v i     ii v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107003225_   5677 AGTCATGCTGCCCAAAGTAATTTATAGATTCCATGCTATTCCCATCAAGC 5726
                         i iv  i  v      v i  i  i      v i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107003225_   5727 TACCATTTACTTTCTTTGCA-AAATTAGAAAAAAACT-ACTTTAAATTGC 5774
                          v   vi i i  i      -     i--- v  i  - iii    v v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_107003225_   5775 ATATGGAACCAAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAA 5824
                                 viiv  ii-  v  v v        i      i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_107003225_   5825 AGAACAGAGCAGAAGGCATCAGGCTACACAACTTCAAACTATACTACAAG 5874
                               i  iv i   vv   vi  v v   i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_107003225_   5875 ACTACAGTAACCAAAGCTGCATGGTACTAGTACCAAAACAGATATATAGA 5924
                         i         i   ii v ii       i i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_107003225_   5925 CCAATGGAACAGAATAGAGACCTCGGAAGTAAGAGCACACATCTACAATC 5974
                         i        i     v    vii i   i   ivv  i    i  iii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_107003225_   5975 ATCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGAATTCC 6024
                          vi    i   i    ivv  v   i v  vv               vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_107003225_   6025 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6074
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_107003225_   6075 GAAACTGGACCCTTTCCATACACCTTATACAAAAATTAACTCAAGATGGA 6124
                            ii       i v  vi     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_107003225_   6125 TTAAAGACTTAAATGTAAAACCAAAAAGCATATAAACACT-AGAAGAAAA 6173
                          i ?    i         i v v    vi   -    v  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAA 545

  chrX_107003225_   6174 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAACACTTCATGGCT 6222
                          v    ?i- v i -   iv   v v  vv i     vvii   v i v 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_107003225_   6223 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 6272
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_107003225_   6273 ACTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 6322
                         vv i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_107003225_   6323 ACAGGCAACCTACAGAATGGGAGAACATTTTTGCAACCTATCCGTCTGAC 6372
                          v  i     i              v  v       vii  vii     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_107003225_   6373 AAAGATCTAATATTCGGAATCTACAA-GAACTTAAACAAATGTACAAGAG 6421
                           i iv  vi   i i    v  i  -     ivv    v vv i  v i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_107003225_   6422 AAA---AAACAACCCCTTCAAAAAGTGGGCAAGGGATATGAACAGACACT 6468
                            ---   i     vv i?    i       i    v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_107003225_   6469 TCTCAAAAGAAGACATTTATGTAGCCATCAAACATATGAAAATAAGCTCA 6518
                             v        i  vi vi i    vi  i  i       v v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_107003225_   6519 TTATCACTGGTCAT 6532
                         vi    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (141 / 106)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


3212 26.76 0.66 0.66  chrX_107016186_107018214      629  1536 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107016186_    629 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 678
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107016186_    679 GGCCATACTGCCCAAGGTAATTTATAGATCCAATGCCATCCCCATCAAGC 728
                            v     v     iv i  i  i    i   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107016186_    729 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 776
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_107016186_    777 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 826
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_107016186_    827 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 876
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_107016186_    877 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGATC 926
                                 i   i    ii         i iv ii i   v v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_107016186_    927 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 974
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_107016186_    975 ATCTGACCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT--T 1022
                          vi   ii  i     ivv  vv  i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_107016186_   1023 CCATATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 1072
                          -- v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_107016186_   1073 CTGAAACTGGATCCCTTCCTTACACCTTGTACAAAAATAAATTCAAGATG 1122
                         v    ii    i    v   i     v i         v  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_107016186_   1123 GATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 1172
                            i ?    i  v    v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_107016186_   1173 ACCTAGGAATTACCATTCAGGACATAGGCACGGGCAAAGACTTCATGTCT 1222
                           v    ?i v viv   iv   v v  vvii     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_107016186_   1223 AAAACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCT 1272
                          vi            vvi     i    vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_107016186_   1273 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 1322
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_107016186_   1323 ACAGGCAACCCACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 1372
                          v  i         i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_107016186_   1373 AAAGGGCTAATACCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1422
                           i  i  vi  i       v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_107016186_   1423 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 1472
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_107016186_   1473 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 1522
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_107016186_   1523 CCATCACTGGCCAT 1536
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


3299 25.58 1.10 0.99  chrX_107035703_107041472.rev     4373  5279 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107035703_   4373 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4422
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107035703_   4423 GGTCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 4472
                           iv     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107035703_   4473 TATCA--TGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4518
                          vi  --  v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_107035703_   4519 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAA 4568
                                 viiv  ii  v  viv  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_107035703_   4569 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATTACAAGG 4618
                                 i      vv   ii  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_107035703_   4619 CTACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGAGATATAGAC 4668
                                  i   i   iii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_107035703_   4669 CAATGGAATAGAAC--AGAGCCCTCAGAAATAGTACCACACATCTACAAC 4716
                                      i--    i  --       ivv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_107035703_   4717 CATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGAT-- 4764
                           vi    i  i     i v  v   i v  vv            i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_107035703_   4765 TCCATATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 4814
                           -- v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    396 TC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_107035703_   4815 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 4864
                         iv    ii    i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_107035703_   4865 GGATTAAAGACTTAAATGTTAGATCTAAAACCATAAAAACCCTAGAAGAA 4914
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_107035703_   4915 AACCTAGGCA-ATACCATTCAGGACATGGGCATGGGCAAGGGCTTCATGT 4963
                            v    ?i- v i -   iv   v v  vv i     v  i   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_107035703_   4964 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5013
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_107035703_   5014 CTAATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGT 5063
                         i v  i   v i  i i   i  ii vv    i  v    ii vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_107035703_   5064 GAACAGGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACTCATCTG 5113
                            v  i     i i               v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_107035703_   5114 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAACTTA-CAA 5162
                          i  i  i  vi          v  i  v      vv    -  i -i  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAA 791

  chrX_107035703_   5163 GAAAAAAACAAACAGCCCCATCAAAAAGTAGGCGAAGGACATGCAAAGAC 5212
                         v     i     i i   v  i?    i i   i     iv  v v    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_107035703_   5213 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGC 5262
                          i     v        i  vi viii     v ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_107035703_   5263 TCATCATCACTGGCCAT 5279
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (141 / 87)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


2830 26.73 3.02 1.45  chrX_107051126_107056469     3958  4851 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107051126_   3958 TGGAAAAACATTCCACACTCATGGGTTGGAAGAATCAATATTTGTAAAAA 4007
                               i i  i   iii      i        v i      -  v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-GTTAAGA 49

  chrX_107051126_   4008 TGACCACATTGTCCAAAGCAATCTATAGATTCAACACTATTCCTATCAA- 4056
                           i v i i vi     vii     i         i v  i        -
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_107051126_   4057 ------GCTACCAAAATAATTTTTCACAGAA-TTAAAAAAA-AATTGTAA 4098
                         ------   i  -------     ii     -  i v  iv-i  iv   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-------TTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_107051126_   4099 ACTTCATATCGAACCAAGAAAGACCCTGAATGGCCAAAGCAATCCTAAAC 4148
                          v       v   viivi ii     v    i      i     i i  v
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_107051126_   4149 AAAAAGAACAAAGCCAGAAGCATCATATTACCTGACTT-AAAATTATACT 4197
                           i          iii  i vv   i i v  ii i  -    i -    
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACT 241

  chrX_107051126_   4198 ATAA-GCTACAGTAGCCAAAATGGCCTGGTACTGGTATAAAAACAG-CGT 4245
                          i  -         ii   i ii iv         i    ii i  - i 
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_107051126_   4246 ATAGACCAATGGAACAAAATGGAGAACCCAGAAATAAAGCCATACACCTA 4295
                              i        i i   v    ii           v       ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_107051126_   4296 CAGCCATCTGATCTTTGACAAAGTTGACAAATATAAGCAATGAGGAAAGG 4345
                         ii i  vi    i  i     i v  v   ivvi vv     i      i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_107051126_   4346 ACTTCCTATTCAATGAATGGTGCTGGGATAGCTAGCTAGCCATATGCAGA 4395
                          ivvi  v     ii             i i  i v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_107051126_   4396 ACAAGGAAACTGGACCCCTATATTTCACCAAATACAAAAAATAACTCAAG 4445
                          v  v   ii          iv iv     v         v        i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_107051126_   4446 GTGGATTAAAAATTTAA-TGTAAGACTTCAAACTA-AGAA-TCCTAGAAG 4492
                         i     i ? i ii   -       vi v      - i  -  i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_107051126_   4493 AAAACCTAGG---AAATACCTTTCTGGACATCAGCCTTGGGAAATAATTT 4539
                              v    ---    --   iv  -  v ii v-  i  v   ii   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT--CTTCGTG-ACCTTGGG-TTAGGCAATGGTTT 587

  chrX_107051126_   4540 GT--GAC-TAAGTCCTCAAGCAATTGTAACAAAACCAAAAATTGACAAGT 4586
                         v --  i- i vv  vv     vvv i       vv      v  i  i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_107051126_   4587 GGGGTCT-ACTTAAATAAAGAGCTTCTGCACAGCAAAAGGAACCATCAAT 4635
                         v  iii - iiv    v  i i   i  ii vv    i iv  i     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_107051126_   4636 AGAGTAAACAGACAACTCACAGAATGGGAGAAAATATCCACAAAGTACGC 4685
                          i   i  v       i                    iii    vi iii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_107051126_   4686 ATCTGACAAAGT-CTAATATCCAGAATCTATAAGGAACAATTATAA---G 4731
                               i  i v-  vi          v     i    vv   i  ---i
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_107051126_   4732 A-AGCAAAAAACCTAATTACTCCATTAAAAAGTGGGCAAAAGACATGATC 4780
                          - ii     iv v   v  i v   ?    i        i  iv   vi
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_107051126_   4781 AGACACTTTTCAAAAGAAGGCATATGAGCGGCCAATAAACATAAGAAAAA 4830
                              i  i  v       ii   ii ii         i  i v     i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_107051126_   4831 ATGTTCATCATCACTAATTAT 4851
                            i   v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.99 (157 / 79)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.82 (40 / 22)  


2863 25.84 5.54 0.92  chrX_107148124_107151434.rev     1958  2824 (487)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_107148124_   1958 GGAGAGACATATGGTGCTCATGGATTGGAAGACTCAGCATAGTAAAGATG 2007
                            i   i  vivi  i                 i ii  v  v      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_107148124_   2008 TCAGTTTTCCCCAAACTGATACACAGGTCTAATACAATTCCTATCAATAT 2057
                         v  i vi        i    vi    i ii  ii    i        v  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_107148124_   2058 CTCAGCTAACTTTTTT-CAGATATAGGCAAGTTTATTCTAAAATTTATAG 2106
                          i     iv       -    v  v i    i v  i        i   v
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_107148124_   2107 GGAAAGTTAAAGGA------ACAG-----GCAATATTGAAAAC----AAT 2141
                              vvi  i   ------ i  -----i    v       v----  i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_107148124_   2142 AAACTAGGAGGAATCACTCTATCAAATTTTAAGATTTATTATAGAGCTAC 2191
                            v v      v    v  vi v     i  i i   i  i i      
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_107148124_   2192 AGTATTCAACACTGTGTGGTA-TGGCAGAGGGACACATACGTAGATCAAT 2240
                             v    v  v        -     v i   i v i ii         
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_107148124_   2241 GAATCAGATTAGAAAACTCAGAAATAGATATACACAAGTACGG-CATACT 2289
                          i vi   v v  i iii        i ivi i   vv  i  -  - i 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA-ATT 350

  chrX_107148124_   2290 TATATTTTACAACAGTGCAAAAGCAATTCAATGGAG-------------- 2325
                         v  v  iv    vi    v  ii v         i --------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_107148124_   2326 -------------CTGAAGTAACTAGATATCAATAATCCAAAAAAATTAA 2362
                         -------------   iiii    i    ? v i - v     i   v  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACA-TGCAAAAGAATGAA 449

  chrX_107148124_   2363 CCTTGACCTAAACTTCACATTTTATGCCAAATATTAACTTAAAATGGATC 2412
                         vi v    ivv  i     iiv   i v   -       i          
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATGGATC 498

  chrX_107148124_   2413 ATGGACTTGAATGTAAAATGTAAAACTATAACATTTTCAGAAGAAAATCT 2462
                          ?i   i i       i vv           v i i i         iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_107148124_   2463 AGGAGAAAATATTTGAGACCTACGACTTGGTGAAGACTTCTTAGATGTAA 2512
                            ? v    v  i v     vv ii v  ii v ii         i i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_107148124_   2513 CAACAAAAGCACAATCTATAATAGGGAAAAAAATCAATAAGTTGAATGTC 2562
                           v           v v i  v  ---       vi    i   i iv  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAG---AAAAAATAGATAAATTGGACTTC 645

  chrX_107148124_   2563 ATCAAAATTAAAAGCTCTTTCTCTGTGGAAAATCCTATTAAGA---TGAA 2609
                                      i  i  viv  viii ii iv    i    ---    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_107148124_   2610 AAGACAAGCCACAGACTGGAAGAGAATATTTGCAAGCTACATATCTGACA 2659
                                v       v   i   i           iii i        i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_107148124_   2660 AAGAACTGGTATCTAGAATACATAAAGCACTCTGAAAACTCAACAGTAAA 2709
                          i i   v     i      i      v     v v       i i    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_107148124_   2710 ACAAACAATACAATACAATTAGAAAATGGGCCAAAGATATAAAGAGATAT 2759
                          - i    - i  iv     ?i         v  i   v i  v   i  
  L1M4_orf2#LINE/    796 A-AGACAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_107148124_   2760 TTAAATGAAGAAGATATGGGGATGACAAATAAACACATGAAAAGATGTTG 2809
                           vvvii          ivii   i v     i              i v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_107148124_   2810 AACTTTATTAGCCAT 2824
                            v i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (133 / 87)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 4.00 (56 / 14)  


 504 20.34 3.39 0.85  chrX_107158121_107160772.rev      561   678 (1974)    L1M4_orf2#LINE/L1       23   143 (765)  

  chrX_107158121_    561 GGACTGGAAGACTTAATATTGTTATGATGTCCATACTACTTGAAGCAATA 610
                            i                    v    v v     v iii  vii  v
  L1M4_orf2#LINE/     23 GGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATC 72

  chrX_107158121_    611 CGCACATTCAACACAATCCCTATCAAAATCCTAAC-AC---TTTTGCAGA 656
                         ii  v       i                  i i -i ---         
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chrX_107158121_    657 AATAGAAAAAATGCATTCTAAA 678
                            v  v  iv  -  i     
  L1M4_orf2#LINE/    123 AATTGACAAGCTG-ATCCTAAA 143

Transitions / transversions = 1.40 (14 / 10)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 1.67 (5 / 3)  

3683 17.13 4.08 0.13  chrX_107158121_107160772.rev     1403  2161 (491)    L1M4_orf2#LINE/L1      120   908 (0)  

  chrX_107158121_   1403 AGAAAAGGA-AAATTCATCCTAAAACTCATATGAAATCTCAAGAGATCCT 1451
                              vv  -  ii v         i       i  viv    i  i  v
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_107158121_   1452 GAAATGCTAAAACAATTTTGAAAAAGAA---CATTGTTAGAGGACTCAAA 1498
                            vv  i        i           ---  vv   i         v 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_107158121_   1499 CTTCCCAATTTCAAAAGA-ATTATAAAGTTACAGTAATCAAAAAAGTATG 1547
                                         vv- i  i    i            i v   i  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_107158121_   1548 GTACTGGCATAAAGGTAGACACATAGCTCAAGGAAATAGAATAGAAAGCT 1597
                                     i i      i    v    v i        v  i  ii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_107158121_   1598 CACACATAAACCC-TG---TCATATTCAAATGATCTTCAACA-GGGTGCC 1642
                           v v        - i--- i  iv    v    i   i   -       
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_107158121_   1643 AAGACCATTCAATGGGTAAAGAACAATCTCTTTAACAAATGATTTTGGGG 1692
                                         v      i i   i  i        i vi    -
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG- 418

  chrX_107158121_   1693 ACAA-TGGATATCCACATACAGAAGTATGAAGTTGGACCCTTAGCATATA 1741
                             -      ?      i  i   v              i  v vi i 
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_107158121_   1742 CCATATACAAAAATTAACTCAATATAGATTAAAGACCTAAACATAAGACC 1791
                                               v  i   i ?         ii     v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_107158121_   1792 TAAAACTGTAAAATGCCTAGAAGAACACATATGAGAAAAGCTTCAAGACA 1841
                                i     iv i        v     v ? v   v    iv   v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_107158121_   1842 TTGGATTTGGTGATGATTTCTTGGATATGACATCAAAAGCACAGGCAACA 1891
                             i  v  ii   i      i         i          i      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_107158121_   1892 AGAACAAAAATAGACAAATGGGACTACATCAAACTTAAGATCTTTTGTGC 1941
                          i iv         i    v     v       v    i v         
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_107158121_   1942 ATCAAAGGATGCAACCAACAGAGTGAAAAGGCAACTTCCAGAATGGGAGA 1991
                         v        ii v i   v i         i    iiv            
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_107158121_   1992 AAATATGTGCAAATCACATATCTGATAAGGGGTTAATATCCAGAATATAT 2041
                               v         i              ii vi              
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_107158121_   2042 AAAGAAC--------------AACAAAAAATCAAATAACCTGATT-AAAA 2076
                                --------------  i     iv         ii   -    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_107158121_   2077 ATGGGCAAAGAATT-GAATAG----TTATCTAAAGATGATATACAAATGG 2121
                                   i   -      ----  v  i     v             
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_107158121_   2122 CCAAAAAGCATATAAAAAGATGCTCAACATCAACTTTCAG 2161
                             v     i  i                  ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (76 / 51)
Gap_init rate = 0.02 (12 / 789), avg. gap size = 2.67 (32 / 12)  


3052 28.30 0.44 0.44  chrX_107327523_107332283     3361  4268 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107327523_   3361 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATCGTGAAAAT 3410
                              ii i  i     i      i v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107327523_   3411 GGCCATACTGCCCAAGGCAATTTATAGATTCAATGCCATCCCCATCAAGC 3460
                            v     v     ivii  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107327523_   3461 TACCAACGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3508
                          v   i vi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_107327523_   3509 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAGGCCAAAAG 3558
                                viiv  ii  v  viv  v     iv     i iiivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_107327523_   3559 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 3608
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_107327523_   3609 TACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGATATAGATC 3658
                                 i   i    ii   i     i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_107327523_   3659 AATGGAACACAAC--AGAGCCCTCAGAAATAACGCCGCATGTCTACAACT 3706
                                i v  i--    i  --        vv  ii ii i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_107327523_   3707 ATCTGATCTTTAACAAACCTGAGAAAAAGAAGCAATGGGGAAAGGATTCC 3756
                          vi    i  ii    ivv  vv  i vv vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_107327523_   3757 CTATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3806
                           v  i  i       i      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_107327523_   3807 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCGAGATGGA 3856
                            ii    i    v   i     v              i  i i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_107327523_   3857 TTAAAGACTGAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3906
                          i ?    iv   i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_107327523_   3907 CTAGGCATTACCATTCAGGACATACGCATGGGCAAAGACTTCATGTCTAA 3956
                         v    ?i v viv   iv   v vv vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_107327523_   3957 AACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTAA 4006
                         i            vvii         vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_107327523_   4007 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAATACCATCAGAGTGCAC 4056
                          i   v v  i i   i  ii vv    i  v v  i  vv i    v v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_107327523_   4057 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 4106
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_107327523_   4107 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4156
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_107327523_   4157 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 4206
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_107327523_   4207 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAGTGCTCTTC 4256
                           v        i  vi viii     v  i          ii     vv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_107327523_   4257 ATCACTGGCCAT 4268
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (151 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1921 24.17 5.37 1.90  chrX_107381477_107383089.rev      490  1122 (491)    L1M4_orf2#LINE/L1      254   908 (0)  

  chrX_107381477_    490 TGATCATGATGTAGCATAGTTCTAGTATAAAAATAGACACATAGATTAGT 539
                          i    v  i--  ii i  v  i i    ii       i      i i 
  L1M4_orf2#LINE/    254 TAATCAAGAC--AGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_107381477_    540 GGAATAGAATAGAGAACCCAGAAGGAAAGCCACATACCTACAACCAACTG 589
                                   v    ii      iv   v   i i ii  iiii   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_107381477_    590 ATCTTTGACAAAATTGACAAGAATATTCATTGAGGAAAG--TGCCCTCTA 637
                           i  i     iiv  v     vi     v  i      -- ivi  i -
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT- 400

  chrX_107381477_    638 TCAATAAATAAGGCTGGAAAAATTGGACAGCCATATGCAGAAGAATGAAA 687
                             i    iiv     i v  i    i ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_107381477_    688 CTGAACCCATATCTATCACCATATCCTAAAATTAACTCAAGATAGAT--- 734
                         i  i    v  i  vv        v v             i  i   ---
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_107381477_    735 -----TAAATGCAAGATCTCAAACTATAAAAATTCTAGAAAAAAAAACTA 779
                         -----      i    v  v           v ii     i    v -  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-TA 549

  chrX_107381477_    780 GGAA-AAATACTTCTGAACATTGGCCTAGGAGAAAAATTTATTACTAAT- 827
                           ?i-    -    vvi  v    vi    v-  vii   v   --i  -
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGC-AATGGTTTCTTA--GATA 595

  chrX_107381477_    828 ---CCTCAGAAGCAAACATAACAAAAACAAAAATAGACACATGTGACTTA 874
                         --- vi  i     v vii       iv         i v  vv     v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_107381477_    875 ATGCAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATTGACAGAGTAAA 924
                           vv  v v    i   i  ii vv    i  v iv  ii v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_107381477_    925 AAGATAACCTATGGAATGGGAGAAAATATTTGCAAACTATGCATCTAATG 974
                             i    i ii                       ii  ii    i  i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_107381477_    975 -----------TCTAGAATCTACAAGGAACT---A-AACTAAAAAA-AAA 1008
                         -----------  i     v  i  i     --- -    v  v  -   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_107381477_   1009 AACTAACAAATAACTCTATT-AAAAATGGGCAAAGGACATGAACAAATGA 1057
                           --i         i v   -                iv    i i i- 
  L1M4_orf2#LINE/    796 AA--GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC-A 842

  chrX_107381477_   1058 TTTTTTCAAAAGAAGAAATGCAGGTGGCCAACAA--ACATGAAAACATGC 1105
                            i i    -     v  i  ii       i  --         v    
  L1M4_orf2#LINE/    843 TTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_107381477_   1106 CCAACATCACTAATCAC 1122
                         i        ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (99 / 52)
Gap_init rate = 0.03 (19 / 655), avg. gap size = 2.42 (46 / 19)  


2591 15.80 2.49 0.21  chrX_107435346_107441850.rev       18   498 (6007)  C L1M4_orf2#LINE/L1   (72)   836   345  

C chrX_107435346_    498 TCAGTTGATTTTTAACAAAGGTGCCAAGACCATTCAATGAGGAAGGAA-- 451
                            i        ii    i                    i    i   --
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

C chrX_107435346_    450 GTCTTTTCAACAAATGGCG-TGGAACAACTGGATATCCACATGCAAGAGA 402
                                          i -   i           ?          i   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chrX_107435346_    401 ATGAACTCGGACTGCTACATCACACAATATGTAATAATTAACTGAAAATG 352
                              v i    iv    v      v    ii  v        v      
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chrX_107435346_    351 GATCAAAGCCCTAAATGTAAGCGCTAAAACTATAAAACTTTTAGAAGAAA 302
                              ?  v            v                 i          
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chrX_107435346_    301 ACATA----TAAATATTTAGGACCTCAAATTTGGCAATGGATTCTTGTAT 256
                              ----     v  iiv     iiii  v        v     iv  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

C chrX_107435346_    255 ATGACTCCAAAAGCATGAACAACAAGAAAAAGAATAGA----GTGGATTT 210
                              v         ii i      i i   i      ----v    i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

C chrX_107435346_    209 TATTATAATTAAACATTTTCATACCTCAAAAGACACTATCAAGAAATTGA 160
                         i  i v       v i   ii i i     i               v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

C chrX_107435346_    159 AAAGATAACCCACACAATGGGAAAAAATATTTGCAAATCATCTATCTGAT 110
                              i        v       i                  v        
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

C chrX_107435346_    109 AAGGAGCGTGTAATCTAGAACAGATAAAGAACTCTCACAACTGGACATCA 60
                             ii v    -  i    i v            i      vi i vi 
  L1M4_orf2#LINE/    745 AAGGGACTTGTA-TCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

C chrX_107435346_     59 AAAAGACAATTAACCCAATT-AAAAATGGACAAATGATCTGAA 18
                                  v          -        i    v   i    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

Transitions / transversions = 1.85 (48 / 26)
Gap_init rate = 0.01 (6 / 492), avg. gap size = 2.17 (13 / 6)  

3004 26.50 1.77 1.11  chrX_107435346_107441850.rev     5113  6014 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107435346_   5113 TGGAAAAACATTCCATGTTCATGGATAGGAAGAATCAATATTGTGAAAAT 5162
                               i i  i              v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107435346_   5163 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAGC 5212
                            v     v      v i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107435346_   5213 TACCA-TTGACTTTCTT-CACGGAATTGGAAAAAACTACTTC-AAATTTC 5259
                          v   -i  v    i  -  - i     -- v  i  iv i -   v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_107435346_   5260 ATATGGAAACAGAAAAGAGTCCACATAGCCAAGAAAATCCTAAGCAAAAA 5309
                                  iiv  ii  vi viv        i v    i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_107435346_   5310 GAACAAAGCTTGGAGGCCTCATGCTGCCTGACTTCAAACTATACTACAAG 5359
                                 -       v    ii  v  ii i      viv        i
  L1M4_orf2#LINE/    198 GAACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_107435346_   5360 GCTACAGTAACAAAAACAGCATGGTAATGGTACCAAAATA--TATATAGA 5407
                                   iv  i    ii     v   i iv ii   --i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_107435346_   5408 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACATATCTACAAGC 5457
                         i        i    iv   ivii         vv   i i  i  iiiv 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_107435346_   5458 ATCTGATCTTTGACAAACCAGACAAAAGCAAGCAATGGGGAAAGGAT--T 5505
                          vi    i  i     ivvv v   i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_107435346_   5506 CCTTATTTAATAAATGGTGTTGGGAGAGCTGTCTAGCCATATGCAGAGAG 5555
                          i  -- i  i        i     v i   vv  ?   i     i -  
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA-AG 443

  chrX_107435346_   5556 CA-GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGAT 5604
                         v -   ii    i    v   i     v                   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_107435346_   5605 GGATTAATGACTTAAGCATAAGACCTAAAACCATAAAAACCCTAGAAGAA 5654
                             i ?v   i   iii     v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_107435346_   5655 AGCCTAAGCA-ATACCATTCA-GAGCATAGGCATGGGCAAACACTTCATG 5702
                          i v  i ?i- v i -   i-  v v i  i- i     vvii   v i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTA 591

  chrX_107435346_   5703 ACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGA 5752
                         iv  vi            vvi          vv        i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_107435346_   5753 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCACAG 5802
                         ii v  i   v v  i i   i  ii vv    i  v       vv v  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_107435346_   5803 TTACCAGGCAACCTACAGAATGGGAGAAAATTTTTGTGATCTATCCATCT 5852
                          v vv  i     i                 v    ii vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_107435346_   5853 GACAAAGGGCTAATATCCAGAATCTACAAAGAACGTAAACAATTTTACAA 5902
                           i  i  i  vi          v  i       vivv    i iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_107435346_   5903 GAAAAAAA-----AACCCA-TCAAAACGTGGGCGAACGATATGAACATTC 5946
                         v     i -----      - i?   vi     i  v   v    i vv 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_107435346_   5947 ACTTCTCAAAAGAAGACGTTTATGCAGCCAACAAATGTATGGAAAAATTG 5996
                          i     v        ii vi viii     i  iiii   i   i  - 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-G 890

  chrX_107435346_   5997 CTCATCATCACTGGTCAT 6014
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.44 (26 / 18)  


1611 26.78 6.51 3.48  chrX_107543795_107545447      492  1152 (501)    L1M4_orf2#LINE/L1      183   863 (45)  

  chrX_107543795_    492 AATATTGGAAAAGAA---TATAGTGGGAGGAATCACTCTACATGATATTA 538
                            v   i       ---i v   v      v    v  v vii  v i 
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_107543795_    539 TGACCTACTATATAGCTGTAGTTAATTAAAACAGTTGCAGTAGTAG-AGA 587
                         vi  i     i v    ii   -   i  i     - ii   v i - v 
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGT-AATCAAGACAGT-GTGGTACTGGCATA 280

  chrX_107543795_    588 AGGAATAGACACATAGATCAATATGATAGAAGGGAGAATTAAGAAATAGA 637
                             -      i          ivi      vv    i iv       i 
  L1M4_orf2#LINE/    281 AGGA-TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_107543795_    638 CCTTTACAAT-ATGCCCAGCTATTTTTTGACAAAGGAGCAAAAGCAATTT 686
                           iv    v -   vi  ii iv    i     i  v  v  ii v   i
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_107543795_    687 AATAGAGGAAGAATAACTTTTTTTTTCAACAAATGATTCTGGAACAATTG 736
                            i i i       i---- i             i v    i    i  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAG----TCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_107543795_    737 AGCATCCATAGACAAAAATATGAACCTTGACCTAAGCCTCACACCTTACA 786
                         iii ?   i vi     iv     vi v    ivvi         v  i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_107543795_    787 AAAAAGTTAACTCAGAATGGATCATGGGTTTAAATATAAAAAG-AAAACA 835
                         v    i        i         ?i iii     i   i iv-     v
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_107543795_    836 ATAAAACGTTTAGAAAAAAATA-------AAATCATC---ACCTAGAGCT 875
                                vi      i    i -------     v  ---    v i i 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_107543795_    876 AGATGAAGAATTCTTAGACGTAATACCAAAAGCCTAGTTCATGAAA---- 921
                           iii v iv        ii i i         vi iviv ii   ----
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_107543795_    922 -------TAA-----------TCAAAATTTAAAAATGTTTATTCTGTGAA 953
                         -------   -----------        -     iv   i v  vii  
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAA 674

  chrX_107543795_    954 AGTCCTTGTTAAACAGAGAATGAAAACACTAGCTATAAAC--GGAGAAAA 1001
                         i v vi i i  ---  i i      v  v v i i i v--        
  L1M4_orf2#LINE/    675 GGACACTATCAA---GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_107543795_   1002 TATTTGCAAAACACATATCCAGTAGAAGATTATTATTTAGAATATATATT 1051
                                   v  i     iii  iii  i vv   ii          v-
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA- 770

  chrX_107543795_   1052 TTTAAAACTCCCAAAACTGATCAGTTCAATAAAACCCCCCCAAAT--CCC 1099
                         --- i     ii v    ---  i --       vvv ---    --   
  L1M4_orf2#LINE/    771 ---AGAACTCTTACAACT---CAAT--AATAAAAAGAC---AAATAACCC 809

  chrX_107543795_   1100 A-TTAGAAAATGGACAAAAGATATGATCATACATTTCATGTAAGAGGATA 1148
                          -  ?i       i    i   v   vi v       vivv    i    
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_107543795_   1149 TACA 1152
                             
  L1M4_orf2#LINE/    860 TACA 863

Transitions / transversions = 1.68 (109 / 65)
Gap_init rate = 0.03 (21 / 681), avg. gap size = 3.14 (66 / 21)  


2421 25.44 1.38 5.14  chrX_107555817_107559436     1959  2756 (864)    L1M4_orf2#LINE/L1        1   768 (140)  

  chrX_107555817_   1959 TGGAAAAACATTCCATGCTCATGGATAGGAAAAATCAATATCATTAAAAC 2008
                               i i  i     i        v    i v i     ii    i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107555817_   2009 GGCCACACTGCCCAATGCAATTTACAGATTCAGTGCTATTCCTATCAGAC 2058
                            v i   v     vvii  i          ii  v  i       i v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107555817_   2059 TACCAGTGACATTCTTCGCAGAACTAGAAAAAACTAGTTTTAAA-TTCAT 2107
                          v    ivi v  i  i      v v  v  i-  ii ii    -     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_107555817_   2108 GTAGGACCAAAAAAAAAAAAAAAAAAAAAAAAGACAAGAAAGAGCCTGCA 2157
                         i i -------------------------   vi    i--  v  v v 
  L1M4_orf2#LINE/    150 ATGG-------------------------AAATGCAAGG--GACCCAGAA 172

  chrX_107555817_   2158 TAGCCAAGGTAATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCACATCA 2207
                                iii    i i iv  i          i      vv     iiv
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_107555817_   2208 CCCAACTTCAAACTACACTACAGGGCTACAGTAACCAAAACAGCATGGTA 2257
                              i      vivi      ii          i   i    ii     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_107555817_   2258 CTGGTATAAAAAACAGGCACATAGACCAATGGAACATAAT----AGCCCA 2303
                             i    ii -i  i  i     i        i v   ----  i   
  L1M4_orf2#LINE/    273 CTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_107555817_   2304 TAAATAAGGCTTCAC-TCTGCAACCATCTGATTTTAGACAAATATGACAA 2352
                         v      iv ivi  - i iiiii  vi       v     ivi  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_107555817_   2353 AAGCAAGCAATGGGGAAAAGACTTTATATTCAATAAATGGTGCTGGGATA 2402
                         i v  vv           ii ivv v v     i              i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_107555817_   2403 ACCAGCTAGCCATAAGCAGAAGATTGAAATTGGACCCCTTCCTTACATCA 2452
                           ii v  ?   i v   i    v    i          v   i   i  
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_107555817_   2453 CATACAAAAATCAACTCAAAATGTATTAAACAATTAAATGTAAAACTCAA 2502
                         i          i           v  i ? v vi         i vii  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_107555817_   2503 AACTGTAAAAACCCTAGAAGACGATCTAGGCAATACCAATCT--G-GACA 2549
                             i     vi i       vi iv    ?i-  --     -- -   v
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNG-TA--AATCTTCGTGACC 568

  chrX_107555817_   2550 TGGGCATGGGCAAAGATTTCATGACAAAGACACCAAAAGCAATTGCAACA 2599
                          v  vv i     v i    v iivv v             vvv      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_107555817_   2600 AAAGCAAAAATTGGCAA--TGCGATCTAATTAAACATAAGAGATTCTGCA 2647
                             v      v ii  --  -  ii v  i   vv   i iv  i  ii
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTG-GACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_107555817_   2648 CAGCAAAGAGCAAAAGAAACTATCAACAGACTAAAAAGACAACCTACAGA 2697
                          vv     -------  v        v i v i           i     
  L1M4_orf2#LINE/    668 CTTCAAAG-------GACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_107555817_   2698 ATGGGAGAAAATAGCTTGCAGACTATGCATCTGACAATGGTCTAATATCC 2747
                                      -i     i ii  ii      i  v  v  vi     
  L1M4_orf2#LINE/    711 ATGGGAGAAAATA-TTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_107555817_   2748 AGCATCTAT 2756
                           v  v   
  L1M4_orf2#LINE/    760 AGAATATAT 768

Transitions / transversions = 1.56 (122 / 78)
Gap_init rate = 0.02 (15 / 768), avg. gap size = 3.47 (52 / 15)  

 383 23.62 2.36 0.79  chrX_107555817_107559436     3007  3133 (487)    L1M4_orf2#LINE/L1      780   908 (0)  

  chrX_107555817_   3007 ACAAATTTACAAGAGAAAAACCAACAACCTCATTAATAAGTGGCCAAAGG 3056
                             v iv i  v i   i  v  i    iv   ? v  i   v      
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_107555817_   3057 ACATAAACAGACACTTTTC-AAAGAAGACAAAACATGCGGCCAACA--CA 3103
                          iv i  i     i  i  -        i -v   vii      i --  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATA-TACAAATGGCCAATAAGCA 878

  chrX_107555817_   3104 CATGAAAAAATGCTCAATGTCACTGATCAT 3133
                                 i        ii   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.02 (3 / 129), avg. gap size = 1.33 (4 / 3)  


1602 22.59 9.36 8.02  chrX_107562363_107564032.rev      507  1179 (491)    L1M4_orf2#LINE/L1      227   908 (0)  

  chrX_107562363_    507 ACTTCCAGACTTATTATAAAGGTACAGTAATTAAGACGGTGTGGTATCAT 556
                          i   v i     i  i    v         i     i        iiiv
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_107562363_    557 CTTAAGAATCAGCAAATAAATCAATGAAACAGAAT---------AGAGAT 597
                          v    i  vii  v   i       i  i     ---------   i  
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_107562363_    598 AG---TGTAC------------TTGATTTTCAACAAAGGTGCCAAAGCAA 632
                          i---ii   ------------         i    i        ii v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_107562363_    633 TCCAATAGGGAAAAAACA---TATTCCAAAAATGGTACTGGAATA-CTGG 678
                          i    i      i  i --- v   v v       i    i i -    
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_107562363_    679 ATATCCCTATTGGAAAAAAATGAGCCTGAATCCCTACTTCATTACTAAGT 728
                            ?  vi  - v    i     ivi  i i      i   i-  i vi 
  L1M4_orf2#LINE/    427 ATAKCCACAT-GCAAAAGAATGAAGTTGGACCCCTACCTCAC-ACCATAT 474

  chrX_107562363_    729 GCAAAAATTATTTGAGAA-AGATCATCGATTAAAACATAAAAGGTCATGG 777
                         i         vi v i  -i     ?v  iiv   ii   i  -------
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG------- 517

  chrX_107562363_    778 ATTAGAAACATAAAACATAAAAACCTACAAAACTTTTACAGGAACACAGA 827
                         -------- -      ---------  i      i   v i   v   v 
  L1M4_orf2#LINE/    518 --------C-TAAAAC---------TATAAAACTCTTAGAAGAAAACATA 549

  chrX_107562363_    828 GGAAAAAACCTTTATAAACAAACATATAAAAAACAAAACATGACTTGAGA 877
                           ?iv   i   -------------------------- i    i vi i
  L1M4_orf2#LINE/    550 GGNGTAAATCTT--------------------------CGTGACCTTGGG 573

  chrX_107562363_    878 TTAAGCAG-GATTTTTTGGACAGGGCA----AAG-ACAGGAAAAACCACA 921
                            i   i- i   i  i  i v i  ----   -   i v  v vv v 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_107562363_    922 AAAAGTGGATAAAT--AACT-CATCAAAATATA---------------CA 953
                             i i       --i   -         -  ---------------  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTTTGTGCTTCA 672

  chrX_107562363_    954 A------TTATTAATA---TGAATAAGCAAGCCAGAGACTGAAAGAAGAT 994
                          ------i   i  v ---    v ii   v   v   v  ii    i  
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_107562363_    995 ATTCACAATACATACATCTGACAAAAAACTGGTATCCAAGATATAAAAGG 1044
                            ii   vv    i      i  iii   v       ii     v  i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_107562363_   1045 AATTACTACAGCTCAACAATAAAAATACAAACAACCCAATTGACATATAG 1094
                           i vi    i     i        v     i         ? v v  i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_107562363_   1095 GCACAAGATTTTAACAGACTCCTCACAAAAGAAAATACACAAATGTCCAA 1144
                            v i     v  i    vii  v v      i   i       v    
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_107562363_   1145 TAAGCACATGAAAAGG-GCTCGACATCACTAGTCAT 1179
                                        i-    i      ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (100 / 48)
Gap_init rate = 0.03 (22 / 682), avg. gap size = 5.32 (117 / 22)  


2886 18.20 1.39 2.08  chrX_107571414_107574224.rev     1106  1682 (1129)    L1M4_orf2#LINE/L1        1   573 (335)  

  chrX_107571414_   1106 TAAAAAATTATCCCATGTTCATGGATCAGAAGACTTAATATTGCTAAGAT 1155
                          ii   iv                  ii               i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107571414_   1156 GATAATGCTCCCTACATTTTTCTGCACCTTCAAGGCAATCCTTATAAAAA 1205
                          ii   i     i v   vv   i  vv     v       i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107571414_   1206 TTCCAACCGCCCTCTTTGCAGAAATGGAAAAGCTGATCATAAAACTGACA 1255
                          i   i i   i i           v  v         v     ------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA------ 144

  chrX_107571414_   1256 TGAAATTCATAGGGAATTGCAAGGAACCCCAAA-GGCCAAAATAATATTT 1304
                         -----      v    v       i    vi  -i       i   v  v
  L1M4_orf2#LINE/    145 -----TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_107571414_   1305 AAA-----GAACAAAGCTGAAGGATTTACACTTTCCAATTTCAAAATTTG 1349
                            -----        i  i    i i      i            i  i
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_107571414_   1350 CTACAAACCTACAATAATCAAACCAGTGTGGTACTGGCAAAAGGACAGAC 1399
                                v     i       iv                v     i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_107571414_   1400 GTGTAGATCAATGGGACAGAATTGAGATTACAAAAATAAACCCATACATC 1449
                         i i           i i          v v  i                i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_107571414_   1450 TATGGTGAATAGATTTTTGACAAAGGTGCCAAGGACATTCACTGAGGGAA 1499
                               v   v      i     i         iv      v  -     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAA 388

  chrX_107571414_   1500 GGAATAGTATTA-CAACAAACACTGCTGGAACAACTGGATACCTATATGC 1548
                         i       v  v-       iiv      i           ? i i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_107571414_   1549 AAATGAATAAACTTGGACCTCTTCTACACACTATACATAGAAATTAACTT 1598
                            v    i  v       i  v iv     i   i i i         i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_107571414_   1599 AAAACAGATCAAAGAT-TAAACACAAGAACTAAAACTATAAAACTCTTAG 1647
                             ii     ?   i-    iii    i                     
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_107571414_   1648 AAGAAAACACAGAGCTAAATATTCTTGGGCCGGGG 1682
                                  i  i?v     v   v  iv iv   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

Transitions / transversions = 1.76 (65 / 37)
Gap_init rate = 0.01 (6 / 573), avg. gap size = 3.33 (20 / 6)  

1266 20.57 5.47 2.60  chrX_107571414_107574224.rev     1938  2321 (490)    L1M4_orf2#LINE/L1      514   908 (0)  

  chrX_107571414_   1938 AGAGC-AAGACTCTG----TCTCAAAAAAAAAAA-AAAAGTAATTTTTTT 1981
                              -  i   v i----   i i  i    v - ii?    v i  iv
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_107571414_   1982 TTTACCTTTGTTTAGTCAAAGCCTTCTTAGATATTATAGCAACAGTACAA 2031
                          v-     v v    v   v vi           v i v   v  i    
  L1M4_orf2#LINE/    564 TG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_107571414_   2032 GTAACAAAAAAA------GTTAAAAACAATTTTATCAAAATTGTAAAAGT 2075
                          i       i  ------ v    vvvi i  i         iv   vv 
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_107571414_   2076 TTGAGCTTCAAAGGACACTACCAAGAAAGTGAAAAGACAACCTACAGAAT 2125
                            v                i                     i       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_107571414_   2126 GGGAAAATGTATTTGCCAATCATATACCTTACAGGAGAATCATATCAAGA 2175
                             i  vi       v         i  v i i i  v ii    v   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_107571414_   2176 ATATATAAAGAATTCTTATAAT---GTACTAGAAAG-CAAATAATACAAT 2221
                                     i     i  i---i  v  i    -       iv    
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_107571414_   2222 TTATAA-TGGGCAAAAGATTTGAATAGACATTTTTC---AAAATATATAT 2267
                          ? v  -        i                 i  --- i  v     i
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_107571414_   2268 ATATCTTTTTATGGGCTTATT-GTACATAAATATATGCTCAACATCGTTA 2316
                          v  ---------   iv  v- i    i  v v            i???
  L1M4_orf2#LINE/    863 AAAT---------GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_107571414_   2317 ATAAT 2321
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.20 (42 / 35)
Gap_init rate = 0.03 (11 / 395), avg. gap size = 2.82 (31 / 11)  


 967 25.90 0.00 0.00  chrX_107578410_107583825     1313  1590 (3826)    L1M4_orf2#LINE/L1      631   908 (0)  

  chrX_107578410_   1313 GACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAC 1362
                           i    v   ii v  i   v v  i i   i  ii vv    i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_107578410_   1363 TACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAA 1412
                           i  vv i      v  i     i   i             v  i    
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_107578410_   1413 CCTACTCATCTGACAAAGGGCTAATATACAGAATCTACAATGAACTCAAA 1462
                         vii ivi      i  i  i  vi   v      v  i  v      vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_107578410_   1463 CAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGA 1512
                            v iv i  v     i     i     v  i?    i     i     
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_107578410_   1513 CATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACA 1562
                         iv    i     i     v        i  vi viii     v  i    
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_107578410_   1563 TGAAAAAATGCTCACCATCACTGGCCAT 1590
                               i       v     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (42 / 29)
Gap_init rate = 0.00 (0 / 278), avg. gap size = 0.00 (0 / 0)  

2337 20.59 2.17 16.43  chrX_107578410_107583825     3866  4924 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107578410_   3866 TGGAAAAATATTTTATACTCATGGATCAGAAGAATTAATATTGTTAAAGT 3915
                               i    iii  ii        ii     v             ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107578410_   3916 CATCGTATTGCCCAAAGGAATCTATACATTCAACATAATCGCTATCAAAA 3965
                         viivi  i v      vvi     i v       ii    v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107578410_   3966 TGCCAA-TGCAATTTTTTCACAGAATTAGA-AAACAAATCCTAAAATGTA 4013
                          v   i-   --i     ii     v v  -  i vi          vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_107578410_   4014 TATGAAACCAAAAAAGAGCCTGAATAGCCAATGCAACCCTGACC--TAAA 4061
                             i  viiv  ii  v  v          vi   i i   vv--v  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_107578410_   4062 AACAAAGCTGGAGGCATCACATTACCTGACTTCAAAATATATTACAAGGC 4111
                                i      vv     i v  ii i       iv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_107578410_   4112 TGTAGTAACCCAAACTGCATTATATTGTTATGAAAATA------TAGACC 4155
                          ii     i v i  v ii vi  i  vi  i ii   ------    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_107578410_   4156 AATGGAACAGAATAGAGAACCCAGAAATAAAGCCACATCTTCATAGCCAA 4205
                                i     v    ii           v   i iv  i  i i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_107578410_   4206 TTGATCTTCAACAAAGCTGACAAGAGCTTACACTGGGGAAAGG-TAATCC 4254
                              i   i    i v  v     v v v  v         i-  i  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_107578410_   4255 TCTTCATTAAATGGTGCTGGAAAAATTGGATAGCCACATGTAGAAGAATG 4304
                          -    vi            i v  i      ?       i i       
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_107578410_   4305 AAACTGGACCCGTATTTCTCACCATATACAAAAATTAACTCAGGATGGAT 4354
                           ii       v  ii  v                       ii      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_107578410_   4355 TAAAGACTTAAATCTTCTTTTGCACAGGAAAAGAAACTATCAACAGAGTA 4404
                         i ?    i     ----------------------------------   
  L1M4_orf2#LINE/    498 CAWAGACCTAAAT----------------------------------GTA 513

  chrX_107578410_   4405 AACAGACAACCTACAGAATGGGAGAAAATATTCGTGAACTGTGCATCCAA 4454
                          i------------------------------------------------
  L1M4_orf2#LINE/    514 AG------------------------------------------------ 515

  chrX_107578410_   4455 CAAAGGTCTAATATCCAGAATCTACAAGGAACTTAAGCAATTCAACAAGC 4504
                         -----------------------------------------------   
  L1M4_orf2#LINE/    516 -----------------------------------------------AGC 518

  chrX_107578410_   4505 TAAAATTTTATGTAAATATAAGACCTGAAAATATAAAACTACTAGAAGAA 4554
                              i -------------------------        vi        
  L1M4_orf2#LINE/    519 TAAAACT-------------------------ATAAAACTCTTAGAAGAA 543

  chrX_107578410_   4555 ATTCCAGGGGAAAACTCTCCTGGACATTGGTCTAGGCAAAGAATT--TGA 4602
                          vivi   ? v   -   i vv   v    vi       v iv  -- ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_107578410_   4603 CTAAGACCTCAAAAGCACAGGCAACAAAAACAAAAATAGCCAAATGGGGC 4652
                         v  v   vi          i         iv        vi    v  i 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_107578410_   4653 TATATTAAA-TAAAAAGCTTCTGAACAGCAAACGAAGCAATCAACAGAGG 4701
                          vi  i   - v    i   i  vi vv    v  vi v     v i  v
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_107578410_   4702 GAATAAACAACTTGTTGAATGGGAGACAATTTTTGCAAAGTATTTATCTG 4751
                            v i     iiiiv          v   v        vi  v      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_107578410_   4752 ACAGGGGACTAATATTGAGAATACAAAAGGAACTCAAACAACAGGAAAAA 4801
                          i i      vi   iv      i v  i      vv     --vv  v 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC--TCAATA 790

  chrX_107578410_   4802 ACAAACAAAACAAAATAAAACTCCAATTAATCCCGTTTAAAGTAAGCAAA 4851
                          i   -  i     -   ---i      ? --------   i ii     
  L1M4_orf2#LINE/    791 ATAAA-AAGACAAA-TAA---CCCAATTWA--------AAAATGGGCAAA 827

  chrX_107578410_   4852 AGACCTGAATAGACATTTCTCATAAAAAAGACATACAAATGGT------- 4894
                         i  ii                -i   i    i          i-------
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTC-CAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_107578410_   4895 -ATATGTAAA-ATGCTCAACATCGCTAATCAT 4924
                         - i   v   -            i????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (131 / 83)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 9.38 (197 / 21)  


3102 27.34 0.66 0.55  chrX_107591734_107598130.rev     5000  5906 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107591734_   5000 TGCAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5049
                           v  ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107591734_   5050 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5099
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107591734_   5100 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5147
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_107591734_   5148 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAGTCCTAAGCCAAAAG 5197
                                viiv  ii  v  v v  v     iv  i  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_107591734_   5198 AACAAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGGC 5247
                                i      vv   i   v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_107591734_   5248 TACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACA 5297
                               v i   i    ii         i iv ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_107591734_   5298 AATGGAACACAGC--AGAGCCCTCAGAAATAATACCACACATCTACAACT 5345
                                i v ii--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_107591734_   5346 TTCTGATCTTTCACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5395
                         vvi    i  iv    ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_107591734_   5396 CTATTTAATAAATGGTGCTAGGAAAACTGCCTAGCCATATGTAGAAAGCT 5445
                           v  i  i          i   v     vv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_107591734_   5446 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTTATTCAAGGCAGA 5495
                            ii    i    v   i     v            v i    iiii  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_107591734_   5496 TGAAAGACTTAAATGCTAGATCTAAAACCATAAAAACCCTAGAAGAAAAC 5545
                          v ?    i      iv   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_107591734_   5546 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5594
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_107591734_   5595 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5644
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_107591734_   5645 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATCAGAGTGAA 5694
                           i   v v  i i   i  ii vv    i  v    ii vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_107591734_   5695 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTAT-TATCTGACA 5743
                         v  i     i   i             v       vii  -       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_107591734_   5744 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACATATTTACAAGAAA 5793
                          i  i  vi          v  i  v      vv   vv iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_107591734_   5794 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5843
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_107591734_   5844 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5893
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_107591734_   5894 CATCACTGGCCAT 5906
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2860 21.97 7.86 2.89  chrX_107601342_107603383      685  1549 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107601342_    685 TGGAGATATATATCATATTCATGAATTGGAAGACTCAATATTGTTAAGTT 734
                             i v    vi   i      i           i            v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107601342_    735 GACAATTGGCCCCAA-TTTATCTATAGATTCAGTGCAACTCCAATCAAAA 783
                          i    vvv      -  v     i       ii    ii  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107601342_    784 TTCTTGTGGTTTTCTGGGGCTACA-AATTTAACAAGCTGATCCTAAGAGT 832
                          i iv iv ii  i ----i i  -  v  i               i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT----TTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_107601342_    833 TAGATGGAAATACAA---AT-----ACAGC--------TTTTATAAAA-- 864
                         i v        i   --- i----- i   -------- i  iv    --
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_107601342_    865 --AACAATGTTGGAGGATTTACAGTACACAATTCCAAGACTTAGTATAAA 912
                         --     v         i i   v v v     i   i     v  i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_107601342_    913 ACCACAGTAAACAAGATAGTGTGCTATTAGCCAAATGATAGACATATAGA 962
                         i i       v     i      v  i i  vv  v              
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_107601342_    963 TGAATGGGACATAATAGAGACTCACAGG--TAAA------------TAGT 998
                          v     i i v   v    v  -   i--    ------------ i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chrX_107601342_    999 GAATCTGTTTTTTGACAAAAATGCAAAGGT-----AGTGGAGAAAG---- 1039
                         v   -  v    i     iii   v   ii----- i   i     ----
  L1M4_orf2#LINE/    346 CAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_107601342_   1040 -TCTTTTCAATAAATAGTCCTGGAAGGGTTGCATATGCGTATGCACAAAA 1088
                         -         i    i  v    i viii  v   ?v ii     v  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_107601342_   1089 ATGG--------------CTCACACTTTATATAAAAGTTAACTCAAAATG 1124
                            i--------------       iv    i    i             
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_107601342_   1125 CATCATAGACCTAGATGTAAAATCTAAACCT-TAAAGTCTTTAAGGAGGA 1173
                         v    ?       i      i v     v  -    i-  i v  i  i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chrX_107601342_   1174 AACAAAGGGGAAAATCCTTGTGACTTTGGGTTAGGCAGATA-TTTCCTAG 1222
                             v   ? v     i i     i            -  i-    i   
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAG 592

  chrX_107601342_   1223 ATCTGATATCAAAAACACGATCCACCAAAGAAAATACTGTTAAGTTGTAT 1272
                           v   i i     i   i v v  v        v iv v   i   v i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_107601342_   1273 TTCCTCAAAAGTAATAACTTGTTCTCCTCTAAAAG-TATTGTTAAAAGAA 1321
                            v      v   v     -  v v  ii   i -i i i i  i i i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTT-TTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_107601342_   1322 TAAAAAGATAATCCACAGTGCAGGAAAAATAATATTTGCAAATTACATAT 1371
                          i      i  i      viii   i   --            i i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAA--ATATTTGCAAATCATATAT 739

  chrX_107601342_   1372 CTGATAGAAGACTTGTATCCAGAATATATAAAGAACTCTAAAAATTTAAT 1421
                               iii                              v v  i i   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_107601342_   1422 AATAAAACATACAGCTCCACATAA---AATTTAATTATAAACAAATTGGA 1468
                                - v   i------    ---    ?  vv  iii    --   
  L1M4_orf2#LINE/    790 AATAAAA-AGACAA------ATAACCCAATTWAAAAATGGGCAAA--GGA 830

  chrX_107601342_   1469 A--GAATATTTTGACACTTAAATAAAAGCAGATATATAGATGGCAAATAG 1516
                         v--     ----    i  vvvi   - v       i i     v    i
  L1M4_orf2#LINE/    831 TTTGAATA----GACATTTCTCCAAA-GAAGATATACAAATGGCCAATAA 875

  chrX_107601342_   1517 ATACACGAAAAGATCCTCAACATTATTAATTAG 1549
                         ii   i        v        i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (117 / 69)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.32 (93 / 28)  


1755 19.63 5.00 17.61  chrX_107660391_107663567     1648  2686 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107660391_   1648 TGGAATGGTATATTGTGTTCATGGAT-------------ATTGTTAAGAT 1684
                              v i   viii           -------------           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107660391_   1685 ATCAGTTTTCTCCAAATCAATCCATAGATTGAAAATATTCTCAAGGAGAA 1734
                         iv  i vi  i      ii   i i     v  vii v  i v vv i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107660391_   1735 -CACA-CAATTTTTCTT---------------------CTAAAATTTATA 1761
                         - v  - viii   i  ---------------------        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_107660391_   1762 TGGAAAAACAAATGGCCTAGAATAGCCAAAACAATTTTGAGAAAGAAGTA 1811
                               vi   iv i  i                 i    i       v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_107660391_   1812 CAAAGTTGGACAATTCATAGTACTTGATGTTAAGACTTAAAATAAAGCTA 1861
                                   vi i   i v v iii  v i  i     vv i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_107660391_   1862 CAATAGTTAAAATAGTGTGGTAT--GTGTGAAATACAGACTAATAGATCA 1909
                           i  i i  i i         i-- ii -  iv i    vv        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATCA 299

  chrX_107660391_   1910 TTGTAACATAATAGAGAGTCTAGAAATACACCCACATATTTA-------- 1951
                         v  v  i v   v       i       v     i i     --------
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_107660391_   1952 --ATTTTTGACAAAGTTGCTAAGGCAATCTCAACAG--AAAGGTAAGTCT 1997
                         --     i     i v   i   i v  -    ii --    ivv     
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAGTCT 398

  chrX_107660391_   1998 TTTCAACAAATGTTGCTAAAATATAAAGCAATTGGACATCCATATGCAAA 2047
                                     v    iii -------   i    i ?   i       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGA-------CAACTGGATAKCCACATGCAAA 441

  chrX_107660391_   2048 AAAAAATATAAACAAACCAACATAACAAACCTCTACCTGCACTTCCTACC 2097
                          i  ---- i  ---------i --iii   i      -   -----   
  L1M4_orf2#LINE/    442 AGAA----TGAA---------GT--TGGACCCCTACCT-CAC-----ACC 470

  chrX_107660391_   2098 TTGCACAAAATTTAACTCCCAATGGATCACAGACCTAAATGTAAAACCTA 2147
                         v ii      v       vv         ?              i v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_107660391_   2148 ACATTATCAAACTTCTGGAACAGAAGCAGGCAAACTTTTTCTGCAAAGAG 2197
                          v i   v     ii -----     v ii  ------------------
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTT-----AGAAGAAAACA------------------ 547

  chrX_107660391_   2198 CTAGAGAGTAAATATTT-TAGTCTTTATGGGCTACATATATGGTCTCTGT 2246
                         -   - ?      v  i- iii   ---   i  vii -     i   --
  L1M4_orf2#LINE/    548 -TAG-GNGTAAATCTTCGTGACCTT---GGGTTAGGCA-ATGGTTTCT-- 589

  chrX_107660391_   2247 CACATATTCTTTTTTAAACAACCCTCTAAAAATGTAAAAACCATTCTTAG 2296
                         i v    ---------i   ----- i    ------------------ 
  L1M4_orf2#LINE/    590 TAGATAT---------GACA-----CCAAAA------------------G 607

  chrX_107660391_   2297 CATGTAGGCAGCACAAAAAGAGGCCTATAGGCCATATTTAGCCATGGGAA 2346
                           i-- i   i  v  i  i i----    ---   --- ---  v   -
  L1M4_orf2#LINE/    608 CAC--AAGCAACAAAAGAAAAA----ATAG---ATA---A---ATTGGA- 641

  chrX_107660391_   2347 GTACTTTGTCATCCCTTGTTTTAGATGAAGAAGCATAAGAGAAAACTCTG 2396
                         ---   ii   ----------- i  ---------   ---   vi i  
  L1M4_orf2#LINE/    642 ---CTTCATCA-----------AAAT---------TAA---AAACTTTTG 665

  chrX_107660391_   2397 TGATCAGATGTTAGGCAAAAAC-TTGTTAGAATACCAAAAAGACAATTCA 2445
                           v ------ i ---  ii  -i i i ii v vii         ii  
  L1M4_orf2#LINE/    666 TGCT------TCA---AAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_107660391_   2446 TAAAAGAAAAATTGGATATATTGGACTTTATTAAAATTAACTGTATTTTC 2495
                         i i  ------ v   -------  --------    -------    v 
  L1M4_orf2#LINE/    707 CAGAA------TGGGA-------GA--------AAAT-------ATTTGC 728

  chrX_107660391_   2496 ATATCATATATCTGACAAAGGACTTATAAGCAGAATATATAATGAACTCT 2545
                          v             i  i      i  vv            v       
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_107660391_   2546 CAAAACTCAATAAGAAAACAAACAACCAACTTTTAAAATATAGTTGGAAA 2595
                         i v          v    - i    vi   ii----   ---- ?--   
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAA-AGACAAATAACCC----AAT----TW--AAA 817

  chrX_107660391_   2596 AATGAGCAAACAATTTGAGTAGATACCTTACCAAAGAAGACACCCAAATG 2645
                             i     vi      i    i ii iv          i iv      
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_107660391_   2646 TCTAATAAGCACATGTAAAGATGCTCAGTATAATTTATCAT 2686
                         v i            v           ii  v ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (134 / 66)
Gap_init rate = 0.05 (45 / 908), avg. gap size = 5.22 (235 / 45)  


1557 16.90 3.91 14.41  chrX_107685516_107689673        1   562 (3596)    L1M4_orf2#LINE/L1      406   908 (0)  

  chrX_107685516_      1 AAATCATGCTGGGAAAAGAGGATACCTGTCTGCAAAAGAATGAATCTGGA 50
                             vi        v  vv     ? iiiv              vi    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_107685516_     51 CCCCTATCTCATACTGTATACAAATATTAACTCCAACTGGATTACTGACC 100
                               i    i  ii        v        v  v     i ?v    
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_107685516_    101 TAAATATAAGAACTAAA-CCATAAACATATTAGGATAAAAGAT--GACTA 147
                              i     i     - i     vv v    i v    v  -- ?v  
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_107685516_    148 AATTCTTGTGACCTTGCATTAGGTAATGGTTTCTTAGCTATGACACTAAA 197
                            ii i         vi     i             v        i   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_107685516_    198 AGCACAAACAACTAAAGGAAAAATAAATTGGGCTATATTAAAATTCATTA 247
                                i    v    i       i  ------------     -----
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGAT------------AAATT----- 638

  chrX_107685516_    248 GGTAATGGTTTCTTAGCTATGACACTAAAAGCACAAACAACTAAAGAAAA 297
                         --------------------------------------------------
  L1M4_orf2#LINE/    639 -------------------------------------------------- 638

  chrX_107685516_    298 AATAAATGGGGCTTTATTAAAATTTAATGTGTTTTCTGTTGCAAATGATA 347
                         --------  i   i  i      v  vii-    v  i v    v  i 
  L1M4_orf2#LINE/    639 --------GGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACA 679

  chrX_107685516_    348 CCATCAAGAAAGTGAAAAGACAGCTCACGAGATGAAAGAAAATATTTGCA 397
                          i                    i i   iii   ii              
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_107685516_    398 AATCATATATGAGATAAAGGATTTGTATACAGAATATATAAAGAATTCTT 447
                                   vv     i   i      v                i    
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_107685516_    448 ATAATTCAACGG---AAAG-CAAATAACTCAGTTTTTAAAAGTGCACAAA 493
                          i  i    iii---    -        i  i  ?--    i  vi    
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTW--AAAAATGGGCAAA 827

  chrX_107685516_    494 G----TGAATTGGAC------CTAACAAACATATACAAAATATTCTAT-- 531
                          ----     -i   ------ i  vi  v         - ivi v  --
  L1M4_orf2#LINE/    828 GGATTTGAAT-AGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAA 875

  chrX_107685516_    532 -C-CAAGAAAA-ATGCAGAATATACATTTTTGCA 562
                         - -  v     -    vv  i  -  ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACAT-CAZZZZZZZZ 908

Transitions / transversions = 1.60 (56 / 35)
Gap_init rate = 0.03 (16 / 503), avg. gap size = 6.44 (103 / 16)  

3671 20.16 3.23 1.61  chrX_107685516_107689673     2798  3665 (493)    L1M4_orf2#LINE/L1       27   908 (0)  

  chrX_107685516_   2798 TGGAAGATTTAATACTGTTAAAATGTCCATACTACCCAAAGCAATACACA 2847
                                i      i      i   v v     v      vii  vi   
  L1M4_orf2#LINE/     27 TGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACA 76

  chrX_107685516_   2848 GATTCAATGCAACGCCTATCAAAACTCCAATGGCATTTTTTTTTCCAGAA 2897
                                i    iv          ii   iiv  ---i      v     
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGC---CTTTTTTGCAGAA 123

  chrX_107685516_   2898 AC-GAAAAACTTAGTCTAA--TTCACAAGGAAATCTCAAGGGACCCCAAC 2944
                          i-  v  i  v vi    --    i v      v-          vi v
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATG-CAAGGGACCCAGAA 172

  chrX_107685516_   2945 TAGCCAAAACAATTCTAAAAAAGAA---CCAGGTTGGAGGACTCATAATA 2991
                                      ii i        --- v i             i v -
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT- 221

  chrX_107685516_   2992 ATTTTTTATTAGAAAACATATTACAAAGTTATAGTAATCAAAGCGGTGTG 3041
                         -- iiiv   vv     v  i       i  i         ii i     
  L1M4_orf2#LINE/    222 --TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_107685516_   3042 GTGCTGACATAAAGACAG-CAAATAGACCAATGTAATAGA-T--AGA--C 3085
                           i   i     i  i  -  v     i     v      - --   -- 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_107685516_   3086 CAGAGATAAAATCTCTGGTCTGTAGTTGAATGATCTTTGACAAGGGTGC- 3134
                             i     vi vivvi i i i  ii v    i  i           -
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_107685516_   3135 --------TCAATGGGGAAAGG------CGTTCAACAAATGCATGCTGGG 3170
                         --------             i------iv           -i       
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG-GTGCTGGG 418

  chrX_107685516_   3171 TAAAATGAATGTCCATATGCAGAAGAATGGAGTTGAACCATTTTCTTACA 3220
                         vv  v  i  i?   i     i       i     i   vi vi  i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_107685516_   3221 TCATATATAAAA-TTAATTCAAAAAAGAATGAAGACCTAAATGTAAGACC 3269
                         i      i    -    i      vi  vii?                v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_107685516_   3270 TAAAACTATAAAACTCTTAGAAGAAAACATGGGACAACATGCCTCATGAC 3319
                                                       i  ?vv v  - i  i    
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGAC 567

  chrX_107685516_   3320 ATTAGATTTTTTTCAATGATTTCTTGGATATGACACCGAAATCACAGGCA 3369
                         v  i i  vvv--     i      i           i   v    i   
  L1M4_orf2#LINE/    568 CTTGGGTTAGG--CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_107685516_   3370 ACAAAAGAAAAAATAGATTAATTGGACAACATCAAAATGTTAAGCTTTTG 3419
                                           v        vv         vvv  i      
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_107685516_   3420 TGCATCCAAGAACACTACTAATAGAGTGAAAAGGCAACTCATGGGATGGA 3469
                            v  v   i      ii  v i         i    i  ii i    i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_107685516_   3470 AGAAAATATTTGTAAATTGTATATCTGGTAAAAGATTAATTTCCAGAATT 3519
                                     i    ii        i   ii  i vi v        v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_107685516_   3520 TTAAAAAGAACTCCTACAAGTCAATAACAAAAGCCATCAAACAACCCAAT 3569
                          - v         i     v       i    i--iv    i        
  L1M4_orf2#LINE/    766 T-ATAAAGAACTCTTACAACTCAATAATAAAAA--GACAAATAACCCAAT 812

  chrX_107685516_   3570 TCAGAAATAAGCAAATGACTTGAATAGACCTTTCTTCAAAGATGATATAC 3619
                          ? i    ii     v  i          v     i      v       
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_107685516_   3620 AAATGGCAAATTAGTACATGAAAAGATGGTCAACATCACTAATCAT 3665
                                v   v  i             v         ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (105 / 66)
Gap_init rate = 0.02 (18 / 882), avg. gap size = 2.33 (42 / 18)  


1719 28.57 6.12 3.17  chrX_107705636_107709790.rev     2786  3667 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107705636_   2786 TGGAGAGATA--ACATGTTCATTTCATTGGAAGGTTGAATACTGTCAAAA 2833
                             i     --v         vv-        ii v    i   i  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGG-ATTGGAAGACTTAATATTGTTAAGA 49

  chrX_107705636_   2834 TATCAATTCTCCTCTACCTTACCTAGAGAGTTATTGCAA-ACTTA--AAA 2880
                          iv    v    i v vi v i   v   v i vi    -v i  --   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_107705636_   2881 ATCCCTACAGATACTTTAAATG--GAAATTGATAAACTGAT-------TT 2921
                              ---  v i i  vvv  --        i  i     -------  
  L1M4_orf2#LINE/    100 ATCCC---AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_107705636_   2922 CCCCTG------CAAAAAAATTAGAATAGCCAAGACAAGCTTTAAAAAAC 2965
                          viv  ------   iii vii           i    v   v     iv
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_107705636_   2966 TGAAACAAATTTCTAGTACTTACCC--ACCATTTTTCAAGGCTTAATATA 3013
                         v   -    v  vv  v   i  v --v   v   -   ii    v  i 
  L1M4_orf2#LINE/    197 AGAA-CAAAGTTGGAGGACTCACACTTCCCAATTT-CAAAACTTACTACA 244

  chrX_107705636_   3014 AATTTACAGTAATT----CAGTGTTGTGTTAAAGCAGCAATAGAAA-ATA 3058
                           vi         i----      v  ii iivii ivi     v -   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_107705636_   3059 AACCATTGGAACAGTACACAGAGTCTGGAAATAG-CCCACCACATGTACA 3107
                         i i  v     i  v ivv      ii      i-    i-    v  ii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATG 343

  chrX_107705636_   3108 GTCATTTGGCTTTCTTACAAAGGTGT---GACTGTAATTTATTGGATGCG 3154
                             v   ii    v-    i    i---   ii -- iv  v  iviv 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCG-ACAAGGGTGCCAAGACCAT--TCAATGGGGAAAG 390

  chrX_107705636_   3155 TTTAGGTTCTTTAAAAAAAAAATAGTGTAGGGAGCAATTGGATAACTG-- 3202
                         vv   vi i  i  v   ---- i   iv    -   i      ? ii--
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAA----TGGTGCTGGGA-CAACTGGATAKCCACA 435

  chrX_107705636_   3203 TGCTGGAAAAAAAATGAACCTTGACCCCTACCTCACAC--TGTAAAAATA 3250
                            ----    i      vi v                -- i  v   v 
  L1M4_orf2#LINE/    436 TGC----AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_107705636_   3251 TTTTTATTTGAGATAGCTCATAAGCC-AAATATGAAAGTTTAAAC-ATGA 3298
                           v-- i ii i  i v   ? ii  -    i i i  i v    -  i 
  L1M4_orf2#LINE/    482 TTA--ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_107705636_   3299 AACATGTTATAA-AAATTAGAAGATTA--TTTCCATAACCTCAAAT-AGA 3344
                            - v   v  -   vi v i ?v  -- i i i i    iiii -  i
  L1M4_orf2#LINE/    530 AAC-TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_107705636_   3345 CAAATATTTATTGAATTGGATAAAAAAATCACTATTCATGAAAGGAAAGA 3394
                            vvi   v  ii  vv  i vv    v   v viv ii    i   i 
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_107705636_   3395 TTGATACACTGGATTTTATTAAAATTAACAACTTTTGTTCATTACACAAC 3444
                          v    v i    i  i  i        v         v v i v vi  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_107705636_   3445 AGCATTAGGAAAG-GCAAATCTGAGGCACAGA------GAATAGATTTGC 3487
                          vi  i i     - v   vvii vv      ------   v v      
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_107705636_   3488 AATATATGTATCTGACAAAGGACTCATATCTTGAGTATATAAAGAACTAC 3537
                           vvi  i       i  i     ii    iv  i             - 
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT-C 777

  chrX_107705636_   3538 TCTGAATCTATTTGAAAAAGGACAGACAATTCAAT-AAAAAATGAACAAA 3586
                          ivv  iii v viv    i    i i  ii    -?       ii    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_107705636_   3587 AGTACTTAAGAAGAAACTTC----AAAAAGATGCTATCCAAATGGCCAAT 3632
                         i - i  i iv   v i   ----  i     ---  v            
  L1M4_orf2#LINE/    828 GG-ATTTGAATAGACATTTCTCCAAAGAAGAT---ATACAAATGGCCAAT 873

  chrX_107705636_   3633 A-GTATAATAAAAAGATGATTAATACTATTATTCAT 3667
                          - i i - i        v i  i ii ????????
  L1M4_orf2#LINE/    874 AAGCACA-TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.04 (39 / 908), avg. gap size = 2.10 (82 / 39)  


 534 26.80 1.31 1.31  chrX_107713075_107714695       54   206 (1415)    L1M4_orf2#LINE/L1       46   198 (710)  

  chrX_107713075_     54 AAGATGCCAGTTGCCTCTAAAGTCATTCATAGATTCAAAGTGATTCCAGT 103
                               v  i vvi i i   v v  ii i        v ii  i  vi 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_107713075_    104 TTAA--CCCAACAACCTTTATTTGGTAACAGTTGACAAATGGATTCTAAA 151
                         iv  --    i vi     -    -i iv i       iiv   i     
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTT-TTTG-CAGAAATTGACAAGCTGATCCTAAA 143

  chrX_107713075_    152 ATGTGTATGGAAATGAAAGGGACATAGAATATCCAAAACAATATTGAAAA 201
                           vii          v       vi      v          v       
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_107713075_    202 CGAGG 206
                         v  i 
  L1M4_orf2#LINE/    194 AGAAG 198

Transitions / transversions = 1.41 (24 / 17)
Gap_init rate = 0.02 (3 / 153), avg. gap size = 1.33 (4 / 3)  

1827 25.71 4.13 1.90  chrX_107713075_107714695      500  1129 (492)    L1M4_orf2#LINE/L1      265   908 (0)  

  chrX_107713075_    500 GTGTGGTACTTG-ATAAGGATTGAGAAATAGATCAATGAAACAGAATTTG 548
                                   v -        v  v v           i  i      vi
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_107713075_    549 GAGGATAAAAA-AGACTAATA----TACAATAAATTGACTTTTGATAAAG 593
                            vvi i   - i  iv   ----  iii v      i   i  i  i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_107713075_    594 GTATCAAATAAATTTTTTAGAGAAAGCAAATTCTTTTCAACAAATGGCCC 643
                           ii   ivvv   ivv i i     v v v                iv 
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_107713075_    644 TGAAACATCTAGATATTCGTATGGGGAAAAAACAAAACTTAATTCATACA 693
                           ii   v  i    ?i ii   vi-   i  ii  ii vi ii v   v
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCA-AAAGAATGAAGTTGGACCCCTACC 463

  chrX_107713075_    694 TTACATCATACAGAAAAAAAAATGTTTTTAATTAGATCTTAG-TCTGAAC 742
                          i   i    i v     vv  i--- iv  v i    v?  -i  i  i
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAAC---TCAAAATGGATCAWAGACCTAAAT 510

  chrX_107713075_    743 ATAAAAGCTAAAACCATAATGCTTTTAGAGGAAAACATAGATAGATATTT 792
                         i   i         i    vi  i     i          i?iv v  i 
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_107713075_    793 CCGTGAC-TTGGCATAGGCAGAT--TTTCTTAG----GATACAAAAAGCA 835
                         i      -    vv      -  --        ----  i  v       
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCA-ATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_107713075_    836 GTAACTGTAAAAGAAAAAAATTGATAGATTAGATTT-----AAATTTTTA 880
                         vv i vii           - v    i   i  i  -----     --- 
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATT---A 655

  chrX_107713075_    881 AACTACTTTTAT----CAGAAAACACCGCTAGGAAAATGAATAGGAAAGC 926
                           v-      i ----  i ii    iiii i    i    v  iv  v 
  L1M4_orf2#LINE/    656 AAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_107713075_    927 CACAGACAAGGAGAAAATATTTGCAAA--ACATAACTGACAAATTACTGA 974
                               vvi                  -- i   v    i  ivv   vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_107713075_    975 TATCTAGGATATGTAAAAAACTTCAATAACTCAATAATAACAAGATGTAT 1024
                             i  i    i    i    iiv i             v    iiv  
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_107713075_   1025 TATCCAATTTTGAAAAATGGAGAAAAC-TTTGAATAGATACTTCACGAAA 1073
                         v i      ?--        iv   iv-          i i   v v   
  L1M4_orf2#LINE/    805 AACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_107713075_   1074 GAAGATATACAAGTGGCCGATAATCACATGAAAAGGTGATCGATGTCGTT 1123
                                     i     i    v           i  v  i ii  i??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_107713075_   1124 AGCCAT 1129
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.68 (99 / 59)
Gap_init rate = 0.03 (18 / 644), avg. gap size = 2.11 (38 / 18)  


1280 14.34 2.94 5.51  chrX_107754495_107757622.rev     1485  1756 (1372)    L1M4_orf2#LINE/L1       16   280 (628)  

  chrX_107754495_   1485 TGTTCATGGGTCAGAAGACTTAATACTGTTAAAATA-CGATACTCCCCAA 1533
                                  i ii            i      i  i- i           
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_107754495_   1534 AGTGATGTACAGATTCAATGTAATC--TATTAATATCCCAGTTGTCTTCT 1581
                          v    v           i i    --   i  v       i  i   --
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT-- 113

  chrX_107754495_   1582 TCTTCTTTTATTTTTTGGCAGCAATTGACAAGCTGAGACTAAA-TGCATA 1630
                         ------------     -   v              vv     - v    
  L1M4_orf2#LINE/    114 ------------TTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_107754495_   1631 TGGAATTGCAAGGGAGCCTGAATAGCCAAAACAATCTTGAAAAAGAA--- 1677
                              v         v  v                            ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_107754495_   1678 CAATGTTGAAAGACTGGCACTTGACTATTTCAAAACTTACTGCAATGTTA 1727
                            v    i i    vi     vv v               i   v i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_107754495_   1728 CTGTAATCAAGACTGTGAGGC-CAGGCACA 1756
                          v           v   v  i- v    i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATA 280

Transitions / transversions = 0.95 (19 / 20)
Gap_init rate = 0.03 (7 / 265), avg. gap size = 3.29 (23 / 7)  

2863 17.41 7.06 0.49  chrX_107754495_107757622.rev     2029  2637 (491)    L1M4_orf2#LINE/L1      260   908 (0)  

  chrX_107754495_   2029 AGACTGTGTAGTACTGGCATAAACACAGACATATCGATCTATGGCACAGA 2078
                             v    i            iv i        v    v    v i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_107754495_   2079 -----GAATCCAGAAATAAAGCCATACTTCTGTGGTGGATCCGTTTTTGA 2123
                         -----  i            v      v i i    vi  ivi    i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_107754495_   2124 CAAGTGTATCAAGACAATTTAATAGAGGAAAGAAAAAGTCTTTTCAACAA 2173
                             v  ii      v   i   i -        v -             
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATA-GTCTTTTCAACAA 407

  chrX_107754495_   2174 ATGGTGCTGGGACAACTG--------CATGCAGAATAATAAATTTGAAAT 2215
                                           --------      i  v   i  v   i vi
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_107754495_   2216 CTTACTTCACACTATGTTTAAAAATTAACTCAATATAGATTAAAGACTTA 2265
                          i   i      i  i vi              v  i   i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_107754495_   2266 AATGTATGAGCCAAAAC----------------------ATAGGAGTTAA 2293
                               v    i     ----------------------     ?  v  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_107754495_   2294 ACATTGTGCACTTGGATTAGGCAATGATTTCTTACATGTGACACCAAAAG 2343
                         v v i   vv     i          i       v  i            
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_107754495_   2344 CAAAAGTAACAAAAGGAAAA-TATTT---TTGATATTTCGTTAAAACTAA 2389
                           v   i        i    -  vv ---   i- i   i i    i   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGG-ACTTCATCAAAATTAA 656

  chrX_107754495_   2390 AATATCCTGTGCTTTAAAAGACACCATCAAGAAAGTAAAAAGATAACCCT 2439
                           vv ii       i   i     i           i      i     v
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_107754495_   2440 CAGAATGAGAGAAAATATTCAGAAATCATATATCTGATAAAGGATAGGTA 2489
                                i           iiv                  i   ivv   
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_107754495_   2490 TCTATAATATATAAAGTACTCTTACAACTCACCAGTGAAAAGACAAATAA 2539
                           i v           v              vi i i             
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_107754495_   2540 CCCAATT-GAAAATGGGCAAAGCATTTACATTGACATTTCTCTAAAGAAG 2588
                                -i             v    iv  v          i       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_107754495_   2589 ATACACAAACGGCCAACAAGCACAT---AAGACTCTCAGAATCATTAGTC 2635
                            i     i      i        ---    iv    iv    ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_107754495_   2636 AG 2637
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.54 (63 / 41)
Gap_init rate = 0.02 (10 / 649), avg. gap size = 4.60 (46 / 10)  


1345 26.50 10.75 0.50  chrX_107800291_107805416      609  1008 (4118)    L1M4_orf2#LINE/L1        1   441 (467)  

  chrX_107800291_    609 TAGAAAAATGTTTTATGTTCACGGATTGAAAGACTCAATAGTCTTAATAT 658
                          i    i  i iii       i      i      i    v v    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107800291_    659 GTTGAAACTCCCTAATCTTATCCATAGATTCAATGCATTTTCAATAAAAA 708
                          vii v      i  vi v   i i        i   v ii v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107800291_    709 TCTTAGCAAGATCTTTTGTAGATATCAGCAAGTCAATTTCTAGAATTTAT 758
                           ii   vivv i     i   v  iii    iii  -i   i    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chrX_107800291_    759 ACGGGAA-GCAACTAAATTAGAATAGCCAAAACAACTTTGAAAAA---TA 804
                          i  i  -    vvi vii                ii        ---v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_107800291_    805 TTTAAGTAGGAGGGCTCACA--TCCTGAATTCAAAATTCACTATAAATTT 852
                         viv    v     i      --   ii v       i i    i   vi 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_107800291_    853 ATAGTAATCAAGACAGTGTGATATTTGTGAAAGAGCGTACGTATGGATCA 902
                          i                  i  i v iiv   iiiiv  i   i     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_107800291_    903 ATGGACAAAAGATAGAGA--CCAGAAGCAA-------------------- 930
                              - v ii  v    --      ii  --------------------
  L1M4_orf2#LINE/    300 ATGGA-ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_107800291_    931 ---------------GGTGCAAAGGCAATTGAATGGAGAAAGAGTAATCT 965
                         ---------------     v   i v   v     i      i  i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_107800291_    966 TTTCAACAAACGGTGCTGAAAAAATTGGACATCCATGTGCAAA 1008
                                   i       ii v  i    i ?   ii      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

Transitions / transversions = 2.28 (73 / 32)
Gap_init rate = 0.02 (7 / 441), avg. gap size = 6.43 (45 / 7)  

3443 25.50 0.89 0.22  chrX_107800291_107805416     2270  3171 (1955)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_107800291_   3171 TAAAAAGATATTCCATGTTCATGGATTGAAAGAATCAATATTGTTAAAAT 3122
                          ii        i                i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_107800291_   3121 GTTTATATTAGTTGAAGCAATCTACAGATTAGATGCAATCTCCATCGAAA 3072
                          viv   i vviii  vii           vi i      i i   i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_107800291_   3071 TACTAATGACATTGTTCACAAAAATAGAAAAA--AATTGTAAAATGTATA 3024
                          v i iivi v  v  ii  i    v  v  i--i  iv      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chrX_107800291_   3023 TGAAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAAAGAA 2974
                           i  vii   ii                 i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chrX_107800291_   2973 TGAAATGGGAGGAATCACATTACCTGACTTCAAACTATACTACAGAGTTA 2924
                         ii  i v      v     i v  ii i      viv       i  i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chrX_107800291_   2923 TAGTACGCAAG---GTATGGTACTGTCATAAAAACAGACATA--AACCAA 2879
                         i    vv    ---  i        v     ii i       --i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

C chrX_107800291_   2878 TGGAACAGAATGGAGAACCCAGAAATAAATCCATACACCTACAGTGAACT 2829
                              i     v    ii           i       ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

C chrX_107800291_   2828 CATTTTTGACAAAGTTGCCAAGAACACACGTTGGGGAAAGGACAATATCT 2779
                         v     i     i v        v  iv iv         i i i v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

C chrX_107800291_   2778 TTAATAAATGGAGCTGGGAAAACTAGATATCTATATGCAGAAGAATGATA 2729
                          i  i      v       v    i    ? i i     i        vi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

C chrX_107800291_   2728 CTAGACCCCTATCTCTAGCCATATGCAAAAATGAAATTAAAATGGATTAA 2679
                         i i        i   vvi      i       v  v i         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

C chrX_107800291_   2678 AGAGTTAAATCTAAGACCCCAAACTATGAAAGTACTACAAGAAAACATTG 2629
                            vi     v     v iv       i   v vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

C chrX_107800291_   2628 GGGAATATATCCAGGACACTCGTCTCGGCCAAAATTTCTTGAGCAATACC 2579
                          ? v v  v i iv   vi v vi v   v vii      iiii vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

C chrX_107800291_   2578 CCACAAGCACAGGCAACCAAAGCAAAAATGGACAAACAGGATCACATCAA 2529
                            v       i     v    v      i  i   iv   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

C chrX_107800291_   2528 GTTGGAAAGCTGCTGCACAGCAAAGAAAACAATCAACAAAGTGAAAAGAC 2479
                         iv vi   i  vi  ii vv     i v  v     v             
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

C chrX_107800291_   2478 A-CCCACAGAAGGGGAGAAAATATGTGCAAAATACCCATCTGACAAGGGA 2430
                          -         v            v      vi ivi      i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

C chrX_107800291_   2429 TTAATAACCAGAATATATAAAAAGGGCTCAAACAACTCCATAGGAAAAAA 2380
                         i vi  v              i i--   vv       v   iv     i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAA--CTCTTACAACTCAATAATAAAAAG 798

C chrX_107800291_   2379 TCAAATAATACAATTTAAAAATGGGCAAAAGATCTGAATAGACATTTCAC 2330
                         v       iv     ?             i   i              v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

C chrX_107800291_   2329 AAAAGAAGACATACAAGTAGTAAATAGCTATGTGAGAAGATGCTCAACAT 2280
                         v        i      i i iv    ivi ii   i              
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

C chrX_107800291_   2279 CAGTGATCAT 2270
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (135 / 91)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.00 (10 / 5)  

1482 24.12 1.54 1.75  chrX_107800291_107805416     4179  4634 (492)    L1M4_orf2#LINE/L1      454   908 (0)  

  chrX_107800291_   4179 GATCTTTACCTTGCATCCTGTAAAAAAATTAACTCAAAATGTGTGTTACA 4228
                           i ii     ii  i v i  v                  vi vv? v 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_107800291_   4229 CCTAAATGTAAAACCTAAACCTACAAAAATTCCAGAAGAAAACATATAAG 4278
                                    i v     v   i    v iii             vi? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_107800291_   4279 AAAATGTCTGTTAACCTTCAGTTAGGCAAAAATTTTTTGCATATGACACT 4328
                         v    v ii  -i     vi         vii   i  iv         i
  L1M4_orf2#LINE/    554 TAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_107800291_   4329 AAGCACATGATCCATAAAAGAAAAACTTG-TAGATTTGCCTTCTTCAAAA 4377
                           ivi  ii v v i          v v -  i   v v    v      
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_107800291_   4378 TTTAA---TTTTCTGCTCTGTGAAAGACACTTTTAAGAGAAATGAAAAGG 4424
                           v  ---    v    iii--  i      v i    -  i       i
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGA-AAGTGAAAAGA 699

  chrX_107800291_   4425 CAAGAAATGAACTGGGA-AAAATATTTGCAAAACATACATCTGATCAAAC 4473
                            vvv iii v     -              v    i       v iiv
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_107800291_   4474 ACTTGTATTCAGAATATGTAAAGCATTCTCAAAATTCAATAAAAAGAAAA 4523
                                 i        i     v i   i v  i       v  i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_107800291_   4524 TGAACAATTCCAATATAAAAGATGT-TAAAAG-TTTGAATGGACACTATA 4571
                         ii  i  i-     - ?   i   v-i   i -       i    i - v
  L1M4_orf2#LINE/    800 CAAATAAC-CCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACATT-TC 846

  chrX_107800291_   4572 TACCTAAGAAGATACACAGATGACAAAAAAGCACATGAATAAATTCTCAG 4621
                          -  v         i   i   i v  v           v i  v    i
  L1M4_orf2#LINE/    847 T-CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_107800291_   4622 CATCTTAGTCATT 4634
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (63 / 44)
Gap_init rate = 0.03 (12 / 455), avg. gap size = 1.25 (15 / 12)  


1017 26.13 1.39 0.35  chrX_107810600_107815241.rev      565   851 (3791)    L1M4_orf2#LINE/L1       14   303 (605)  

  chrX_107810600_    565 CATGTTCATAGATTGGAGG-CTCAATATTGTTAAAATGG--ATGTTTTCC 611
                                  i       i -  i           i    --  ii ii  
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chrX_107810600_    612 TGTAGTGCCTTATAGAGTTGATGAAATCTCTGTAAAAATTTGAGCAGCCT 661
                         -iv v  vii  i   v ii i v    i  i v     iiv   v    
  L1M4_orf2#LINE/     64 -AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_107810600_    662 TATT-GGAAAAATTAACAAGCTGATGCTAAGTCCCATATGGAAATGCAAT 710
                          v  - v i     i          v    ivii               v
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_107810600_    711 GTACCAAGAATAGCCTAAATGATTTTGAAAGTGAAGAAAAATGTGAGAGA 760
                          v   v         v   ii  i      iv      v  v  vi   i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_107810600_    761 CGTTAAACTACCACATTAAAAAATTTACGATAAATCTACATTAATAAAGA 810
                         vv i v   v  vv   vv    i    v i   v     v    v    
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_107810600_    811 CAGAATGATCCTGGCTTAATGATAGACACGTATATCAATAG 851
                            vi  i v     v   v        ii  v      i 
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

Transitions / transversions = 1.03 (38 / 37)
Gap_init rate = 0.01 (4 / 290), avg. gap size = 1.25 (5 / 4)  

1131 23.92 1.53 3.82  chrX_107810600_107815241.rev     3270  3662 (980)    L1M4_orf2#LINE/L1      300   683 (225)  

  chrX_107810600_   3270 ATGAAAAATAATAGAAAGCACAGAGAATA---TCATTGTATTTATGCTAA 3316
                            i  v v   v  i  iv    -    ---i   -ii       v v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGA-AATAAACCCAT-ACATTTATGGTCA 347

  chrX_107810600_   3317 ATTGATGTTCATTAAAGTTATTGAACCAAATTGCTAAGGGAAGAATAGTC 3366
                               v   ivi  i v iiii iv v v iiv ii  i          
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_107810600_   3367 TTTTCAACAAATAGTACTGAGACAATTTGATAACCATATGCATAAAACAA 3416
                                     i  i   i     i v    ?   i     --   v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA--AAAGAA 445

  chrX_107810600_   3417 AGTGAACCTAGATCATTACCAAAAACCGTATGTAAAAATTAACTCTCAAT 3466
                         --    vi i  i vi    vv v   i   ii            vv   
  L1M4_orf2#LINE/    446 --TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_107810600_   3467 TTATTATAGCTCAAAATATAAAAGCTAAAACTATAGAATTTATAGAAGAA 3516
                         vv  i ?  vi v    i   i             i  i iv        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_107810600_   3517 AACAAAGATGGAAAATTTGTTTTGACCTTGGGATAAGCAAAGGTTTCCTA 3566
                             v  i? v   - i - iv          v  i    v      i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAA-TCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_107810600_   3567 -ATATTACACTAAAATCATG-GCA-CAAAAGAAAATAAAATTAATGAATT 3613
                         -    v    i    v  ii-   -          ---   vi  i    
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAA---AATAGATAAATT 638

  chrX_107810600_   3614 GGAATTCATGAAATTTAAAATATGTTTGCTCTTCTTCAAAAGACATTAT 3662
                            v     v   v      - iv    --- v       i    i   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAA-ACTTTTG---TGCTTCAAAGGACACTAT 683

Transitions / transversions = 1.27 (51 / 40)
Gap_init rate = 0.03 (13 / 384), avg. gap size = 1.62 (21 / 13)  

 468 18.30 17.65 0.00  chrX_107810600_107815241.rev     4014  4166 (476)    L1M4_orf2#LINE/L1      729   908 (0)  

  chrX_107810600_   4014 AAATCATATACGCGACAAAACAATATTATTCAGAATATATAAAGAAAACT 4063
                                   ivi  i  iiv v vv   i                vv  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_107810600_   4064 TACAGCTCACTAATAAGAAGATAAATAACTTAATC--AAAATGGG-AAAA 4110
                             i    v      i    i       ii   i--        -   i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_107810600_   4111 TATTTG----GACATTGCACCACAGAAGTTACACAAA------------- 4143
                         v     ----      v v   v     v  i     -------------
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_107810600_   4144 -------AGATGCTCAACATTATTAGTCAT 4166
                         -------             i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (15 / 13)
Gap_init rate = 0.02 (4 / 180), avg. gap size = 6.75 (27 / 4)  


3433 18.51 6.64 2.25  chrX_107815246_107818555.rev     1987  2829 (481)    L1M4_orf2#LINE/L1       29   908 (0)  

  chrX_107815246_   1987 GAAGATTTAATATTCTAAAAGTGGCACTGACCTCCCCCGAATTAATCTAT 2036
                              i        v v  ii     v i--      -i    i     i
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATA--CTCCCC-AAATTGATCTAC 75

  chrX_107815246_   2037 AGATTCAGCAAAATTTCTATTAAAATCCCAGCTGTTTGGAAGTTTTTGCT 2086
                                i iv   ii    i             ii -----       -
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT-----TTTTTGC- 119

  chrX_107815246_   2087 TGCAAATATTTACTAGCTAATCCTAAAATTCATATGGAAATTCAAGAGAT 2136
                         --- i v   v  v    i                      v    i  i
  L1M4_orf2#LINE/    120 ---AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_107815246_   2137 ----AATA-------------TGGAGAA-------AATGTTTGAGGATGC 2162
                         ----    -------------  i i  -------  v   v     iv 
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_107815246_   2163 -CATTTAC-AATTTCAAAACTTGCTACAGAGCTGCAGGGATCAAGAC--- 2207
                         -  i  v -             i     i    i   vi        ---
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_107815246_   2208 ---GTACTAGCATAAGGATAGATACGT-GATAGTTGAGACAAAATTGAGA 2253
                         ---     i             i ii -   viv  ii i i        
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_107815246_   2254 ATCCATAAATACACACTTTCAGT-ATGGTCAATTGAGTTTCAGTAAGGTT 2302
                         i    v     v  v v v  v -            v    iii    v 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_107815246_   2303 -CCAAGATAGTGCAATAGGGGAAAGAATAATTTATTCAACAAATGGCAAT 2351
                         -      ivi v    -            i i v            iiv 
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_107815246_   2352 GAAATAACTGGATATCCACATGCAAAAAAATAAAGTTGTACCCCTTTCTT 2401
                          ii i         ?            i   i      v      vi  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_107815246_   2402 AAACCATACACGAAAATTAACTAAAACTCGATCATGGACCTAA-TGTAAA 2450
                          v      i  i          v   v v     ?i       -     i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_107815246_   2451 AGCTAAAACTAGAAAATTCTTAGAAGAAACCGTAGGAGTTAATCCACATG 2500
                                    v    i            v i    ?  v    iv i  
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_107815246_   2501 CTCTTGAGGTAAGCAAAGACTTTATAGATAATGACACCAAAAGCATAAGC 2550
                         vi    i v  i    v ii  iv      -              i    
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGACACCAAAAGCACAAGC 614

  chrX_107815246_   2551 AACAAAAGAAAAAA---ATAAATGTTTGACTTCATCACAACTTAAAACTT 2597
                                       ---      -- v          v  i v       
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAAT--TGGACTTCATCAAAATTAAAAACTT 662

  chrX_107815246_   2598 TC-TGCTACAAACAATTCCATCAAA----CGAAAGGACAATATACAGAAT 2642
                          i-    v    vi iv i     i----i    i     ivi       
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_107815246_   2643 GGGACAAAATATTTGCAAGC-----ATCTGATAAGGGATTTGTATCTGTA 2687
                             v             ii-----             i       iiv 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_107815246_   2688 ATATATAAAAAA----TATAATTCAATTATAAAGACATAAATATCCCATT 2733
                                  i  ----  i  i     v     i v i     v    v 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_107815246_   2734 TTATAA-TGGGCAAAACATTTGAATAGATATTTCTCTAAAGAGTACATA- 2781
                          ? v  -        iv           i       i     iv i   -
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_107815246_   2782 AAATGGCCA-TAAGCATATGAAAAGATGCTCCAGAATATTAGCCACTAA 2829
                                  -      i              ---  i  i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTC---AACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (95 / 57)
Gap_init rate = 0.03 (26 / 880), avg. gap size = 2.88 (75 / 26)  


1462 21.41 2.54 18.03  chrX_107829056_107831886.rev     1276  2340 (491)    L1M4_orf2#LINE/L1        9   908 (0)  

  chrX_107829056_   1276 TATATCACGTTTTTGAATTGGAAGACTTAACATTGTTAAGATATCAGTTG 1325
                            vi  i   iv  i              i           iv  i vv
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chrX_107829056_   1326 TAACCAAATTGAACTACAAATTTGGTACAATCTAAATGAAATTCCCAGGA 1375
                          vv         v     i   iiiii     ivv  v   v      vv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chrX_107829056_   1376 AGAATATTTGTCAAAATTGATAAACTAACTTTAAAATTTATATTAAAATA 1425
                         ivvv v    ivi       i  i  i iii       i    vi    i
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_107829056_   1426 TAAAGGGTCTAGTATAACCAAGAAAATCTTGAA---GAAGAACAAAGTTG 1472
                         i  i  ii i  v   i    i v         ---              
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_107829056_   1473 GAGGATTTACACTGTTTATTGGATTATAAAATTTACAATAAAACTATAGT 1522
                              i i     viii ----   vi    i    v i   i   i   
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCA----ATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_107829056_   1523 AATTCAGAATGGTGTGGCATTGGCAGAAAGGTAGACAAGTAGATTAATGA 1572
                            -  ii ii      i i     v  i i      vi     i    i
  L1M4_orf2#LINE/    255 AAT-CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_107829056_   1573 AAGAGAAT--GGAATCCAGAAATAGGCTACCCTGACAACAACCTCATACC 1620
                           v     --i  i          ---------------    -     -
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATA---------------AACC-CATAC- 336

  chrX_107829056_   1621 ATACAGAAAAACTAATTCAAAATATATCATATTTCTAAATGTAAAATAAA 1670
                           vi ------- ii i---   --- v  -    v v -------- ii
  L1M4_orf2#LINE/    337 ATTTA-------TGGTC---AAT---TGAT-TTTCGACA--------AGG 364

  chrX_107829056_   1671 GTGAAAAAGCTCTAAAAGAAAACATAAGGAAACAACTTAATAACCTTGCA 1720
                            vv  ii iv vv  ------- ii     v  -----  ii   ---
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAA-------TGGGGAAAGAA-----TAGTCTT--- 399

  chrX_107829056_   1721 TAGACAAAGATTTCTTAAGACCCAAAAAGCAATAATAATTTTAAAATAAA 1770
                         -----------   ------------- i   --  ii vi iii i  -
  L1M4_orf2#LINE/    400 -----------TTC-------------AACAA--ATGGTGCTGGGACAA- 422

  chrX_107829056_   1771 AAACTGGTCTTTATTGACATTAAAAACTGTTCAAATATAATCATTAAAGT 1820
                         ---    v---  ?iv    vv    ------i   i---------    
  L1M4_orf2#LINE/    423 ---CTGGA---TAKCCACATGCAAAA------GAATG---------AAGT 451

  chrX_107829056_   1821 CGG-----TGGCTCACGCC-TGTAATCCCAACACTTTGGGAGACCCGAGG 1864
                         i  ----- iv     i  - i  ----   v v  -----i  i i ii
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATA----CAAAAATT-----AACTCAAAA 492

  chrX_107829056_   1865 TGGGTGGATTACCTGAGGTCTGGAGTTTGAGACCAGCTGACCAACATGGT 1914
                            ----  i ?---  ii  ii - v i   ---   i --   - i- 
  L1M4_orf2#LINE/    493 TGG----ATCAW---AGACCTAAA-TGTAAGA---GCTAA--AAC-TA-T 527

  chrX_107829056_   1915 GAAACCCCATCTCTACTAAAAATAGAAAAAAGTAGCCGGACATGGTGGCA 1964
                         i    ------   --------     i   --------    i v? i 
  L1M4_orf2#LINE/    528 AAAAC------TCT--------TAGAAGAAA--------ACATAGGNGTA 555

  chrX_107829056_   1965 CATGCTTGTAATCCCAGCTACTTGGGAGGCTGAGGTAGGAGAATCTCTT- 2013
                         v  vi i  i i --------     ---- v   i -- vii i    -
  L1M4_orf2#LINE/    556 AATCTTCGTGACC--------TTGGG----TTAGGCA--ATGGTTTCTTA 591

  chrX_107829056_   2014 GA----ACCCTGGAGGCAGAGGTTGCAGTGAGCCAAATTCACGCCATTGC 2059
                           ----  v iii i   v i ivi  i-i  vv   --------  v v
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAA-AAGAAAAA--------ATAGA 632

  chrX_107829056_   2060 GCCATTGCACTCCAGCCTGGGCAAAAAGAACAAAACTCC---GTCTCAAA 2106
                         vvv    v   i  --- ---     vv  --     ii--- ii     
  L1M4_orf2#LINE/    633 TAAATTGGACTTCA---T---CAAAATTAA--AAACTTTTGTGCTTCAAA 674

  chrX_107829056_   2107 CAA-ACAAACAAAACCCTTTGTTTGTGAAAGTACA--CCACGAAAAGAGA 2153
                         vi -  v v   i vv--------      iv   --    ii  v i  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAA--------GTGAAAAGACAACCCACAGAATGGGA 716

  chrX_107829056_   2154 GAAAGG----GCAAGTCATATATCTGACAAGGGCCTTATATACAAAATAT 2199
                             iv----    i            i     v   i   v  i     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_107829056_   2200 ACAAACAATTTTTACAACTCAACAATAAAAAGAGAAATAACCCAATT-AA 2248
                          i   v  i i           i          v             -  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_107829056_   2249 GTATGGGCAAATAATTTGAATACACATTTCTGCAAAGAAGATACACAAAC 2298
                         iv         vi         v        v           i     i
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_107829056_   2299 GGCCAATAAATACATGAAAAGATGCTCAACATCATTAGCCCT 2340
                                  ii                       ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (144 / 81)
Gap_init rate = 0.06 (51 / 900), avg. gap size = 4.29 (219 / 51)  


3092 26.29 1.79 0.45  chrX_107836775_107841462.rev     3304  4197 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_107836775_   3304 GAAATATATTCCATG------AATTAAAAGAACCAATATTGTTAAAATGC 3347
                             v    i     ------i   ii    vii           i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_107836775_   3348 CAATATTACCCAAAGCAATCTACAGATTCAACACAATCTCTATTAAAATA 3397
                              i v      vii               i     i    i     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_107836775_   3398 CTAATGACATTCTTCACAGAAATAGAAAAAA-AATCCTAAAATTTATATG 3446
                          i iivi v  i  ii       v  v  iv-i           i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_107836775_   3447 GCATCACAAAAGAC--AGAACAGCCAAAGCTAACCTTAGCAAA-AAGAAC 3493
                          v vii   ii   --    i       i -  i   iiv   -      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAAC-AATCTTGAAAAAGAAGAAC 201

  chrX_107836775_   3494 AATACTAGAAGAATCACGTTACCTGACTTCAAATTATACTGCACAGATAT 3543
                           vii i  i  v    ii v  ii i      viv    i  v  v  i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_107836775_   3544 A-TAACCAAAACAGCATCTAACTGGCATAAAAACAGACACATAGACCAAT 3592
                          -   i   i    ii vvv          ii i     i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_107836775_   3593 GGAACAGAGTAGAGAACCTAGAAACAAATTCATACGCCTACAGCGAACTC 3642
                             i   i v    ii i     i   ii     iii  ii iv  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_107836775_   3643 ATTTTTGACAAAGGTGCCAAGAACACACACTGGGGAAAGGACAGTCCCCT 3692
                              i     i          v  iv  v         i i    iii 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_107836775_   3693 AAATAAATGGTGCTGGGAAAACTTGAAATTCATATGCAGAAGAATGAAAC 3742
                         v  i              v    v  v ?i  i     i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_107836775_   3743 TAGACATCCATCTCTTGTCATATACAAAAATGCAACT-AAAATTGATTAA 3791
                          i   vi i i   viii             -i    -     v   i ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAAT-TAACTCAAAATGGATCAW 500

  chrX_107836775_   3792 AGAGTTAAATCTAAGACCTCAAACTATGAAAATACTACAAGAAAACATTG 3841
                            vi     v     v  v       i   v vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_107836775_   3842 AGAAAACTCTCCAGGACATTGGTCTGGGCAAACATTTCTTGAACAATACC 3891
                         i?iv  v   i iv   v    vi i     vvi      ii i vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_107836775_   3892 CTACAAGTACAGGCCACCAAAGCAAAAATGCACAAATGGGATTACATCTA 3941
                          i v   i   i  v  v    v      iv i    v   i v    v 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_107836775_   3942 G-TTAAAAAGCTTCTGCAAAGCAAAAGAAACAATCAACAAAGTGAAGAGA 3990
                         i-       -   i  iivvv    i  v  v     v        i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_107836775_   3991 CAACCCATAGAATGGAAGAAAATATTTGCAAACTACCCATCTGACAAGAG 4040
                                i       i                ii ivi      i   i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_107836775_   4041 ATTAATACCCAGAGTAGATAAGAAGGTCAAACAACTCTATAGGAAAAA-A 4089
                          i vi  i     i  v    ii iv  vv       v   iv     - 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_107836775_   4090 TATTGTAATCCAGTC-AAAAATGGGTAAAATATTTAAATAGATATTTCTC 4138
                         i v-i   i   i i-         i   iv    i      i       
  L1M4_orf2#LINE/    800 CAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_107836775_   4139 -AAAGAAGACATAGGAATGGCAAGCAGGCATATGAAAAGGTGCTCAGTGT 4187
                         -        i   vi      v ii i   i        i      iii 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_107836775_   4188 CATTGATCAT 4197
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.86 (151 / 81)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 1.43 (20 / 14)  


2983 27.73 1.10 0.77  chrX_107868861_107874977.rev     4722  5626 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107868861_   4722 TGGAAAAACATTTCATGCTCATGGATAAGAAGAATCAATATCGTGAAAAT 4771
                               i i  ii    i        vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107868861_   4772 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATTCCCATCAAGC 4821
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107868861_   4822 TACCATTGACTTTCTTCACAGAACTGGAAAAAACT-ACTTTGAATTTCAT 4870
                          v   vivi i  i  ii     v v  v  i-  - iii i  v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_107868861_   4871 ATGGTACCAAA---AAAAGAGCCTGCACAGCCAAGACAATCCTAAGCAAA 4917
                             ----   ---  ii  v  v v i      i      i i iv  i
  L1M4_orf2#LINE/    150 ATGG----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_107868861_   4918 AAGAACAAAGCTGGAGCCATCATGCTACCTGACTTCAAACTATATTACAG 4967
                                   i     vvv   ii  v  ii i      viv  i    i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_107868861_   4968 -GCTACAGTAGCCAAAATAGCATGGTACTGGTACCAAAACAGATGTATAG 5016
                         -         ii   i i  ii         i iv ii i   ii     
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_107868861_   5017 ACCAATGGAACAGAACAGAG-GTCTCAGAAATAACATCATATATCTA--A 5063
                          i        i    iv   -   -         vvi    i  i  --i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGG 344

  chrX_107868861_   5064 CCATCTGATCTTTGACCAATCTGACAATAACAAACGACGGGGAAAGGATT 5113
                         i  vi    i  i   v ivv  v   v v  vv i i        i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_107868861_   5114 CTGTATTTAATAAATGGTATTGGGAAAACTGGCTAGCCATATGCAGAAAA 5163
                         v v v  i  i       ii     v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_107868861_   5164 CTTAAACTGAATCCCTTCTTTACACCTTATACAAAAATTAACTCAAGATG 5213
                         v v  ii  i i    v i i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_107868861_   5214 CATTAAAGACTTAAATGTAAGACTGAAAACCATAAAAACCCTGGAATAAA 5263
                         v  i ?    i           viv     i      vi i i   v   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_107868861_   5264 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAC 5312
                           v    ?i- v i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_107868861_   5313 TAAAACACCGAAAGCAATAGCAACAAAATCCAAAACTGACAAATGGGATC 5362
                           vi     i      vv          vvv    iv  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_107868861_   5363 TAATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTATCATCAGAGTG 5412
                          v  i   v v  i i   i  ii vv       v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_107868861_   5413 AACAGGCAACCTACAGGATGGGAGAAAATTTTTGCAATCTACCCATCTGA 5462
                           v  i     i    i            v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_107868861_   5463 CAAAGGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAGA 5512
                         i  i  i  vi          v  i   v    ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_107868861_   5513 AAAA-AGATACAACCCCATCAAAAAGTGGGCAAAAGATATGAACAGACAC 5561
                             - v v i     v  i?    i        i   v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_107868861_   5562 TTCTCAAAAAAAGCCATTTGTGTGGCCAACAAATATATGAAAAAAAGCTT 5611
                              v   i   vi  viivi       i  ii i       i v   i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_107868861_   5612 ATCATCACTGGTCAT 5626
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


1968 22.87 1.86 14.47  chrX_107875145_107877170      511  1533 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_107875145_    511 ATATTAATGAATTGGAAGACTCAATATAATAAAAATGTCAGTCCTCTACA 560
                           i  v   i           i     vi v  i   v  i v   iv  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_107875145_    561 A-TTGATCTGTAGATTTAATGCAATCTCTATTCAAATTGTAGCGAAGATT 609
                          -       ii     i  i      i    iv    ivi   vivvv  
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_107875145_    610 TT---AAAATATAGAAAAACTTATTCTAAAAATTATATAGAAAGACACAG 656
                           --- i  -  v  v  i  v  i      v i    i    vi  -  
  L1M4_orf2#LINE/    115 TTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA-AG 162

  chrX_107875145_    657 GCCCTAGCCCTAGAATAGCTAAAACAATCTTGAAAA-GAAGAGTAAAGTG 705
                          ----- v  i        i                -     ii     v
  L1M4_orf2#LINE/    163 G-----GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_107875145_    706 GGAGAAATCATTATATCTTACAGT---AGGAATTATTATATAATAGGTAC 752
                             i v   i--- ii iv  i --- ii v   i  i -  -- v   
  L1M4_orf2#LINE/    208 GGAGGACTCAC---ACTTCCCAATTTCAAAACTTACTACA-AA--GCTAC 251

  chrX_107875145_    753 AGTAATCAAGA--GTGTCATATTGGTGGAGTAACAGATGTGTGGATTAAT 800
                                    --    vi  i   iiv ivi i   ii i i   i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_107875145_    801 GGAAGAGAATATG-GAATCTAAAAATAGACCCACAAAAATATGCCCAACA 849
                             v     -  -  i  i i     i     i v vv    vi   iv
  L1M4_orf2#LINE/    302 GGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_107875145_    850 TATTCCTGACAAAGGTGTAAAAGCAGTTCAACGGAAGAAGAATATACTTT 899
                         v   iii     i    iv  ii vi     i  iii       vv    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_107875145_    900 TCAATAAATGATGGTGGAGCAGTTGGCTCCCACAGACAACAACAAAAAAT 949
                             i     i  v   ii  ii   ----------------------  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGG----------------------AT 428

  chrX_107875145_    950 TTGACTTAAACTCACATCTTATTAAAAAAAAATGCCTCAAAGTGGGGCTC 999
                         --------- ?i     vi------    i    -----    v  i i 
  L1M4_orf2#LINE/    429 ---------AKCCACATGC------AAAAGAATG-----AAGTTGGACCC 458

  chrX_107875145_   1000 AGTTTGCAGTACATATGCTAGATTTGGAATGATACAGAGAAAATTAGCAT 1049
                         -----------------   ------------------------------
  L1M4_orf2#LINE/    459 -----------------CTA------------------------------ 461

  chrX_107875145_   1050 GGCACCTGCACAAGGATGACATGCAAATTTGTAAAACATTTTGTATTTGA 1099
                         ----   -    ----iv i  i    -----------------------
  L1M4_orf2#LINE/    462 ----CCT-CACA----CCATATACAAA----------------------- 479

  chrX_107875145_   1100 AAAAAGAAAATAATTACCTGAAAATGGATTATGGTCTTAAATGAAAAACA 1149
                         -----------     v  v         i ?i v i      v  i vv
  L1M4_orf2#LINE/    480 -----------AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_107875145_   1150 TAAAACTATTAAATTTTTAGGGAAAAACATAGTAGAAAATCTTCAAGATC 1199
                                  v   i i    iii         v? v        iv  i 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_107875145_   1200 AAGGGGTAGGAAAAGGGTTCTTGAAT-TAAGACTAAAAGCACAATCTAGA 1248
                         vv   v    v  v  v     ii  - i v  i          v v v 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_107875145_   1249 AAATCAAAAATTGATCA-TTAGACCTCATTCATTTAAAAAAACTTTGCTC 1297
                            vv      v   v -  i   i    iv vv v     vi    iv 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_107875145_   1298 TGTGAAATACACTGT--AGAGGATAGAAAGACAAGCTACATAGACTTGGA 1345
                          vii  iv     i --   iii ii        v i   --  v v   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA--GAATGGGA 716

  chrX_107875145_   1346 AGAAATATTCACAAACTCTACATCTGACAAATGACTAGTGTCTAGAATAT 1395
                         ii       ii    iiv  i      i  iv    v  i  i       
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_107875145_   1396 ATGAAGAGTTCTCAAAATTCAACAGTGAAA-GACAAACAATTCAATTAGA 1444
                           i    ii   i v  i    i i i   -      i  ii     ?i 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_107875145_   1445 AAACGAGCAAAAGACATTAATAGATATTTCACCTAAGAGGATATATGAAT 1494
                            i i     i  iv v      i     v  v    i      ii   
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_107875145_   1495 GTCAAATAAGCATATAAAAA-AT--TCAACATCACTAGCTAT 1533
                          v v        i  i    -  --         ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (144 / 86)
Gap_init rate = 0.03 (29 / 894), avg. gap size = 5.76 (167 / 29)  


2644 27.69 1.32 1.65  chrX_107900609_107907110     5100  6009 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_107900609_   5100 GGAAAAACATTCCATACTAATGGATAAGAAGAATCAATATTGTGAAAATG 5149
                              i i  i    ii v      vi     v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_107900609_   5150 GCCATACTGCCACAAAT-AATTTATAGATTTAATGTGATTTCCATTAAAC 5198
                           v     v  -     -i  i  i     i  i ii  ii i  i   v
  L1M4_orf2#LINE/     52 GCAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107900609_   5199 TACCATTGACATTCTTCACAGAATTAGAAAAAAT-ACTTTAAAATTTATA 5247
                          v   vivi v  i  ii     v v  v  iv - iii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_107900609_   5248 TGGAACCAAAAAATAGCCTATATAACGAAGACAATCCTAAGGAAAAAGAA 5297
                              viiv  iiv v  viv   i v  i      i i ii  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_107900609_   5298 CAAAGCTGGAAGCATCATGCCACCCAACTTCAAACTGTACTACAAGGCTA 5347
                              i    i vv   ii iv     i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_107900609_   5348 CGGTCACTAAAACAGCATGGTCCTGGTACAAAAAAGGACACACAGACCAA 5397
                          i  v ii  i    ii    v    i i  ii vi    i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_107900609_   5398 TGGAAGAGAATAGAGA-TCACAGAAATGAGACCACACATCTAAAAACATC 5446
                              v     v    -  -       i iv   i    i  viiv  vi
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_107900609_   5447 TCATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAAGATTCTCTA 5496
                          v  i   i    ivv  v   i v  vv           ii  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_107900609_   5497 TTTAATAAAAGGTGCTGGAAAAACTGGCTAACTGTATGCATGCAGAACAT 5546
                           i  i   v        i v      v  ? iii     --- i iv  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA---AAAGAAT 446

  chrX_107900609_   5547 AGAAACTGAATCCCTTCCTTACACCTTAAACAAAAATAAACTAAAGATGG 5596
                         -   ii  i i    v   i     v  v        v    v  i    
  L1M4_orf2#LINE/    447 -GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_107900609_   5597 GTTAAAGACTTAAACGTAAAACCTTAAACTGTGAAAATCCTAGAAGAAAA 5646
                         i i ?    i    i    i v  v     i i   v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_107900609_   5647 TCTAGGCAATATTATTCAGGACATAAGCATGGGCAAAGATTTCAT-GATG 5695
                         iv    ?ivv v v   iv   v vi vv i     v i    v -   -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chrX_107900609_   5696 AAAATATCAAAAGCAATTGCAACAAATGCAAACATTGACAAATGGGATCT 5745
                          vi i i        vvv        v v   v  v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_107900609_   5746 AATTAAACTAAGGAGCTTCTGCACAGCAAAAGAAATTATTATCAGAGTGA 5795
                         v  i   v v ii i   i  ii vv    i  v i   i vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_107900609_   5796 ACAGACAACCTACAGAATGGAAGAAAGTTTTTGCAG--TATATCCATCTG 5843
                          v        i         i     i v      i--i    --     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTG 742

  chrX_107900609_   5844 AGAAAGGTCTAATATCCAGAATCTATAAGGAACTTAAAGAAATTTACAAG 5893
                          v  i  v  vi          v     i     ivv v  v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_107900609_   5894 AAAAAAAATAAACAACCCTATCAAAAAGTGGGCAAAGAATATGAACAAGC 5943
                              i -i   i     v  i?    i         i  v    i - v
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA-GA 840

  chrX_107900609_   5944 CGCTTCTCAAAAGAAGACTTTTATTCA----GCCAACAA--ACATGAAAA 5987
                          ii     v        ----   v  ----     i  --         
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_107900609_   5988 AAAGCTCAACATCACTGATCAT 6009
                         i v           ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (143 / 105)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 1.69 (27 / 16)  


3206 24.35 3.64 0.34  chrX_107936061_107939314     1883  2761 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107936061_   1883 TAGAAAAATATCTCATGCTCATGGATTAGAAGAATTAATACTGTTAAAGT 1932
                          i    i     i    i         i     v      i      ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107936061_   1933 GCCCATACTACCCAAAGCAATACACATATTCAGTGCAATCTCAATCAATA 1982
                          v v     v      vii  vi   v     ii      i v     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107936061_   1983 TCCTGGTGGCATTCTTCACAGAAATAGAAAAACAAATCCTAAAATTCAAA 2032
                            ii iv  v  i  ii       v  v  i vi             v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_107936061_   2033 TGGAAACTCAAAAGACCCCAAATAGCGAAAGTAATTCTGAGATAGAAAAA 2082
                               iv   ii     vi      v   ii   ii   i v    i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_107936061_   2083 -AAAGTTAGAGTCATAACACTTCCTGATTTCCAATTTTATTTACAATGCT 2131
                         -      i   vvv v        ii     v  vi   i -    v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT-ACAAAGCT 249

  chrX_107936061_   2132 ACAATAATAAAAACAGTGAA--ACTGGCATAAA-ATAGACACATAGACCA 2178
                            i    v  i      vi--          i-       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_107936061_   2179 GAGGAACAGAATACAGAGCCCAGTAATAAATCCAAACTTATATTGTCAAC 2228
                         iv    i     vv    i    v      i   v  v v   v     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_107936061_   2229 TAATTTTTGACAAAGGAACTAAGAATACACAATGGTGAAAGGATAATCTC 2278
                          i     i     i  vi i    vi iv      v     i   i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_107936061_   2279 TTAAATAAGTGGTGTTAGAA-AACTGGATTTCCGCATGCAAAAGAATAAA 2327
                           v  i  i     i i i -        v?  i             i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_107936061_   2328 ATTGAACCCTTACTCCATACCA------AAGTTTAACTCAAAATGGACAA 2371
                         i   i    i   ii  i    ------  iv               iv 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_107936061_   2372 AAGACCTAAATATAATACCTGAAACCATAAAACTCCTAGAAGAAAACATA 2421
                         ?          i   v v  i    i         i              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_107936061_   2422 GGTGCAGATATACA--ACTTT----------------TTTTGGATATGAC 2453
                           ? i i  v v i--  i  ---------------- i  i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_107936061_   2454 ACCAAAAGCTTAGTATACCAAATAAAAAAACAAATAAATAGAACTACATC 2503
                                  vi i-ii v    vi      i i      v i   v    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_107936061_   2504 AGACTAAAAAGCTTCTGCATAGCAAAGGAAACAATTAACAAAATGAAAAT 2553
                          i v v    i   i  iiivv       v  v  i  v   i      v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_107936061_   2554 GCAACCTGTGGATTGGGGAAAAATATTTGCAACCTGTATACATGATAAGG 2603
                         i     iiii  v    ii             viii    iv        
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_107936061_   2604 AGTCAATATCCA--ATGTATAAGGAACTCATAAATCACAATA-TAAAGAA 2650
                         iiiivi      --  i     i      v  v v v     -    -  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AA 797

  chrX_107936061_   2651 AACATATAATCCAAGTGAAAAATGGGCAAAAGACCCAAATAGACATTTCT 2700
                         i   v    i    v ?             i  iiii             
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_107936061_   2701 CAAACAAAGACACACAAATGAAAAACAAGTATCTGAAAAGTTGTTAAACA 2750
                          v  vi    i i       ivv  i   i iv       v  i v    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_107936061_   2751 TCATTAGTCAT 2761
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.69 (132 / 78)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.92 (35 / 12)  


3123 26.76 0.77 0.77  chrX_107952769_107958922     4754  5661 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107952769_   4754 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4803
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107952769_   4804 GGCCATAGTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4853
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107952769_   4854 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4901
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_107952769_   4902 TATGGAACCAAAAAATAGCCTGCATTGTCAAGACAATCCTAAGTCAAAAG 4951
                                viiv  iiv v  v v  v i   i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_107952769_   4952 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5001
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_107952769_   5002 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGCTATAGACC 5051
                                 i   i    ii         i iv ii i   vv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_107952769_   5052 AATGGAACACAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5099
                                i v  i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_107952769_   5100 ATCTGATCTTTGACAAACCTGACAATAACAAGAAATGGGGAAAGGATTCC 5149
                          vi    i  i     ivv  v   v v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_107952769_   5150 CTATTTAATAAATTGTCCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5199
                           v  i  i    v  v      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_107952769_   5200 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTATTTAAAGATGGT 5249
                            ii    i    v   i     v  i          vi v  i    v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_107952769_   5250 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 5298
                          i ?    i       v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_107952769_   5299 CCTAGGCA-ATACCATTCAGGATATAGGCATGTGCAAGGAATTCATGTCT 5347
                          v    ?i- v i -   iv  iv v  vv iv    v iv   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_107952769_   5348 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGATAAGTGGGATCT 5397
                          vi            vvi          vv     v     i v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_107952769_   5398 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5447
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_107952769_   5448 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5497
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_107952769_   5498 AAAAGGCTAATATCCAGAATCTACAAAGAACTCAAACAAACTTA-CAAGA 5546
                           ii i  vi          v  i         vv    -  i -i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chrX_107952769_   5547 AAAAACCAAACAACCCCATCACAAAGTGGGCAAAGGATATGAACAGACAC 5596
                             iv    i     v  i?v   i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_107952769_   5597 TTCTCAAAAGAAGACATTTATGCAGCCGACAGACACATGAAAAAGTGCTC 5646
                              v        i  vi viii   i i ii          ii     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_107952769_   5647 ATCATCACTGGCCAT 5661
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (138 / 101)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


 258 30.56 6.94 0.69  chrX_107973901_107979169.rev     2982  3125 (2144)    L1M4_orf2#LINE/L1        1   153 (755)  

  chrX_107973901_   2982 TGGATAAATGTT--GTGTTATTGGATTGGAAGACTCAGAAAAATAAAGAT 3029
                             v i  i i--i    vv              i iv vvi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107973901_   3030 ACCTACTTTTCCCAAACTGATGTGTA----TAATA-AATTTCTATCAAT- 3073
                         iv v ivi i      i    v ii ----i  ii-   ii       v-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107973901_   3074 TCTCAGCAAGTTTGTTTTCAGTTATAGACAAGACTG-TTCTAAA-TATAT 3121
                           i    vivi  v   v   vv  v      -   - i     - vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_107973901_   3122 ATGG 3125
                             
  L1M4_orf2#LINE/    150 ATGG 153

Transitions / transversions = 1.20 (24 / 20)
Gap_init rate = 0.05 (7 / 153), avg. gap size = 1.57 (11 / 7)  

 299 28.26 1.09 0.00  chrX_107973901_107979169.rev     3473  3564 (1705)    L1M4_orf2#LINE/L1      147   239 (669)  

  chrX_107973901_   3473 CATGTGAAAAAGCAAAGACACTGGAAGAGATAAAACCATTTTGAAAAACA 3522
                            i  i   v    i ivv ii   v  vi     v  i        v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_107973901_   3523 AGAATAAAG-TGGAAAAATCACTCTATCTGATTTCAACGCTTA 3564
                             i    -    ii v    v  vi ii       vi    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

Transitions / transversions = 1.36 (15 / 11)
Gap_init rate = 0.01 (1 / 93), avg. gap size = 1.00 (1 / 1)  

1717 25.99 5.20 3.82  chrX_107973901_107979169.rev     4139  4792 (477)    L1M4_orf2#LINE/L1      246   908 (0)  

  chrX_107973901_   4139 AGTCATACTAATCAAGGCTATATGGTATTGGTTTAGGGAAAGACACAAAG 4188
                           ii i v        i vi i     i   iv  i   v     i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_107973901_   4189 ATCAATAGGATAGAATAGAGAACCCAGAAGTAAACCCACACATGTACACC 4238
                               i i       v    ii      i        i    v  iivi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_107973901_   4239 CAACTGACTTTTGACAAAGATGCAAAAAGAAAAAAAGCAATTCAATAGAG 4288
                            i   i   i     i i   v  i --------- v       i i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGA---------CCATTCAATGGGG 386

  chrX_107973901_   4289 GAAAGACA---TCTTCATCAAACAGTGTTAGAGAAAATAGACATTCATA- 4334
                         i  ii i --- i    v    ii   i i iiv  v i  i ?i  i -
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_107973901_   4335 GCAAAA--ATCAA-TTGA---CCTAAGTGTCACATGTTGTACAAATGGTA 4378
                               --  v  -   i---    --iv     ivv i      viv  
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTA--CCTCACACCATATACAAAAATTA 484

  chrX_107973901_   4379 TCTCAAAATAGATTACAGAATTAAATGT--GAACTGTAAAATATAAAAAT 4426
                         v        i   i ?   vi       --  i  i-   v       v 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACT 533

  chrX_107973901_   4427 TTTA--AGAAAA-----------ACCTTCAGGGTCTAGGTCTAGGCCAAG 4463
                         i   --      ----------- i    iv ii  v  vi     v v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_107973901_   4464 AGTTCTTAGACAAAATATCAAAAGTACAATACACAAAAGCAAAAATTGAT 4513
                         iv        i vi i i      i    vvv       v      v   
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_107973901_   4514 AAATTGGACCTCATCCAA-TTAAGAAGCTTTTGCCCTGTGAAAGAGCCTA 4562
                                  i     v  -    i  -      iv  vii  i  vv   
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA 682

  chrX_107973901_   4563 GTTAAGATTTTTAGAGGGTTAAAAGGCAAGGTATAGACTTGGAGGAAATA 4612
                         - i    --------ii  v     i   vvi i   v v    i     
  L1M4_orf2#LINE/    683 -TCAAGA--------AAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_107973901_   4613 TCTGTAAGCCAGAAACCTGACAAATTACTTGTTTTCAGAACATA---AGA 4659
                          i  i  ii  v v i    i  ivv      v i     i   ---   
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_107973901_   4660 ATTATTAAAACCCAGCAGTAGGGGAA-----AATCCGATTAGAAAATAGA 4704
                          i v   v   i  ii i  iiiii -----  i  i   ?i     i i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_107973901_   4705 CAAAGGACATGAATAGACATTTCACCAAAGACTATATACAGATAGAAAAT 4754
                                iv              v       vv       i  i vv   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_107973901_   4755 AAGCACCTTAAAAGATAATAGTCAAAATCACTTAACCA 4792
                               v v       iv ---   v    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCT---CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (105 / 62)
Gap_init rate = 0.03 (18 / 663), avg. gap size = 3.28 (59 / 18)  


3162 27.42 0.66 0.66  chrX_107980831_107987187.rev     2460  3367 (2990)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107980831_   2460 TGGAAGAACATTCCCTGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2509
                              ii i  i  v  i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107980831_   2510 GGCCATGCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2559
                            v  i  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107980831_   2560 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2607
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_107980831_   2608 TATGGAATCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAAGCCAAAAG 2657
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_107980831_   2658 AACAAAGCTGGAGGCTTCACGCTACCTGACTTCAAACTATACTACAAGGC 2707
                                i      vi    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_107980831_   2708 TGCAGTAACCAAAACAGCGTGGTACTGGTACCAAAACAGAGATATAGATC 2757
                          i      i   i    i          i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_107980831_   2758 AATGGAACAGAAC--AGAGCCCTCAGAAGTAACGCCGCATATCTACAACT 2805
                                i    i--    i  --    i   vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_107980831_   2806 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2855
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_107980831_   2856 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGGCATATGTAGAAAGCT 2905
                           v  i  i              v      v  ?v  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_107980831_   2906 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATTGA 2955
                            ii    i    v   i i   v              i    i  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_107980831_   2956 TTAAAGCCTTAAACGATAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3005
                          i ?  v i    i vv   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_107980831_   3006 CTAGGCA-ATACCATTCA-GAACATAGGTGTGGGCAAGGACTTCATGTCT 3053
                         v    ?i- v i -   i-  v v i   - i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_107980831_   3054 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3103
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_107980831_   3104 AGTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 3153
                         vi i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_107980831_   3154 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 3203
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_107980831_   3204 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 3253
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_107980831_   3254 AAAAACACACAACCTCATCAAAAAGTGGGCAAAGGACATGAGCAGACACT 3303
                            i   v i    iv  i?    i           iv   ii     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_107980831_   3304 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 3353
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_107980831_   3354 CCATCACTGGCCAT 3367
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (150 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  

3307 24.23 1.21 1.21  chrX_107980831_107987187.rev     4959  5866 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_107980831_   4959 TAGAAAAATATCCCATGCTCATAGATTGGAAGAATTAATATTGTTAAAAT 5008
                          i    i          i    i          v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_107980831_   5009 GTTCATACTACCCAAAGTAATCTGCAGATTCAATGCAATCTCTGTCAAAA 5058
                          viv     v      v i    i         i      i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_107980831_   5059 TGCAAACAACATTCTTCTCAGAAATTGAAAACACAATCCTAAAATTTACA 5108
                          v v i vi v  i  iv          v  vvii           i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_107980831_   5109 TGGAACTTCCAAAGACCAAGAATAGCCAAAGCCATCCTAAGCAAAAAAGA 5158
                              v v v ii    v            i v   i i i-   i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chrX_107980831_   5159 ATAAAACTGGAAGAAATGCATTGCCTGACTTCAAATTACACTACAGAGAT 5208
                          i   ii    i  vvii  i v  ii i      vivi      i  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_107980831_   5209 ACAGTAAACAAAACTGCATGGTACTGACATAAAAACAGACACATAGACTA 5258
                                v   i  v ii        i     ii i     i     ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_107980831_   5259 ATGCAACACAATAGAGAACCCAAGAACAAATCCACACAGCTACAGTGAAC 5308
                            v  i v   v    ii   ii  i   i   i   vi  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_107980831_   5309 TCATTTTCAGCACAGGAACCAAGAACATAAACTGGGGAAAAGACAGTCTC 5358
                          v      ii  vi  vi      v   vv v        ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_107980831_   5359 TTCAACAAATGGTGCTGGGA-AACCGAATATCCATATGCAGAAGAATGAA 5407
                                             -   i i   ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_107980831_   5408 ATGAGACTCC-ATCTATCACCATATAAAAAAAGCAAATCAAAATGAATTA 5456
                         i vi   i  - i  vv         v     vi  v        i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_107980831_   5457 AAAACATAAATCTAAGACCACAAACTATGGTACT---ACAAGAAAACTTT 5503
                         ? i  v     v     v vv       iiv   --- v        v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_107980831_   5504 AGGGAAACTCGGCAGGACATTGATTTGGGCAAAAATTTATTGAGCAATAT 5553
                         i ? v  v  vv iv   v   iv  i     vii   v  -  --    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AG--ATAT 596

  chrX_107980831_   5554 GCCAC---AAGTACAGGCAACCAAAGCAAGAATTGAAAAATGGGATCACT 5600
                          v   ---   i   i     v    v  i   v  v    v   iiv v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_107980831_   5601 TCAAG-TTAAAAAGCTTCTGCACAGCAAAGGAAACTATCAATGAAGTAAA 5649
                             i-       -   i  ii vv       v        vi    i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_107980831_   5650 GGGACAACCCACAGAATGGGAGAAAATATTTGCAAA--ATACTAATCTGG 5697
                         ii                                  --   i--     i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chrX_107980831_   5698 CAGGGAATCAATAACTAGAGAATATATAAGGAGTTCAAACAACTGTATAG 5747
                         i i  i iivi  v i   --        i  ii  vv      vv   i
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGA--ATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_107980831_   5748 GGAAAAAATCTAAAAATTTGATTTTAAAAATGGGCAAATAATTTGAATAG 5797
                         vi    i - v  v  iiii   ?-             vi          
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAG 839

  chrX_107980831_   5798 GCATTTCTCAAAAGAAGACTTGCAAATGGCAAACAGGCATATGAAAAGAT 5847
                         i        v        iv i        v  i i   i          
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_107980831_   5848 ACTCAACATCATTGATCCT 5866
                         i          ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (129 / 87)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.57 (22 / 14)  


2666 26.95 1.59 2.60  chrX_107988050_107994703.rev     5278  6160 (494)    L1M4_orf2#LINE/L1        4   877 (31)  

  chrX_107988050_   5278 AAAAAAATTCCATGCTCATGGGTAGGAAGAATCAGTATTGTGAAAGTGGC 5327
                            i v  i     i      i v      v i i      v  ii    
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_107988050_   5328 CACACTGCCCAAAGTAATTTATAGATTCAATGCTATTCTCATTAATCTAC 5377
                         v i   v      v i  i  i        i  v  i ii  i  vv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_107988050_   5378 CATTGATTTTCTTCACAGAATTAGAAAAAATGACTTTAAATTTCATGTGG 5427
                           viviii  i  ii     v v  v  iv   iii    v     i   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_107988050_   5428 AACCAATA-AAGAGAAAAAAGAGCTC-GTATAGCCAAGACAATCCTAAGC 5475
                           ---  i-   i  -------- i - v        i      i i iv
  L1M4_orf2#LINE/    154 AA---ATGCAAGGGA--------CCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_107988050_   5476 AATA-GAACAAAGCTGAAGGCATCACACTATCTGACTT-GAAGCTATATT 5523
                           v -        i  i   vv       vi ii i  -i  i  -  i 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACT 241

  chrX_107988050_   5524 ACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATAT 5573
                             i          i   i    ii         i iv ii i   i  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_107988050_   5574 ATAGACCAATGAAACAGAA--GACCAACCTCAGAAGTAACACCACACATC 5621
                              i     i  i    --  --i vii     i   vv   i    i
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGA--GAGTCCAGAAATAAACCCATACATT 339

  chrX_107988050_   5622 TATAACCATCTGGTCTTCAACAAACCTGACAAAAACAAGCAATTGTGAAA 5671
                            iii  vi  i i   i    ivv  v   i v  vv    v v    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_107988050_   5672 G--TATTCCTTATTTAATAAATGGTGCTAGGAAAACTGGCTAGTCATATG 5719
                          --  v  i  -- i  i          i   v      v  ?i  i   
  L1M4_orf2#LINE/    390 GAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_107988050_   5720 CAGAAAATGGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACT 5769
                           i  i vv   ii         v   i     v                
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_107988050_   5770 CGAGGTGGATTAAAGACTTAAATGTAAAACCCCAAACCCAAAAACACT-A 5818
                          i ii     i ?    i         i v iv    ivv     v  - 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_107988050_   5819 GAAGAAAACCTAGGC-CATACCATTCAGGACATAGGCATTGGCAAACACT 5867
                                  v    ?-i v i -   iv   v v  vv v     vvii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_107988050_   5868 TAATGACTAAAACACCAAAA--ACAATTGCAACAAAAGGCAAAATTGACA 5915
                          vv iiv  vi         --    --          iv     v  i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATA 634

  chrX_107988050_   5916 AATGGGATCTAAGTAAACTAAAGAGCTTCTCCACAGCAAAAGAAATTATC 5965
                            v   ii v vi   v v  i i   i vii vv    i  v i    
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_107988050_   5966 ATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTA 6015
                          vv i      v  i     i                 v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_107988050_   6016 CCCATCTGACAAAGGTCTAATATCCAGAATCTACAAGGAAATTTAACAAA 6065
                         ivi      i  i  v  vi          v  i  i   v i v    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_107988050_   6066 TGTACATT--TAAAAAAACCAGACAACCGCATCAACAAGTGGGTGAAGGA 6113
                          ---  v --      i  - i i    vv  i? v  i    ii     
  L1M4_orf2#LINE/    785 T---CAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_107988050_   6114 TATGAACAGACACTTCTCAAAAGAAGACATTTATGTGGCCAACAAAC 6160
                          v    i     i     v        i  vi vi       i  i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.02 (19 / 874), avg. gap size = 1.95 (37 / 19)  


4184 20.04 1.46 0.22  chrX_107997096_107999186.rev      708  1600 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_107997096_    708 AAGTCATTCTTTGCTCACAGATTAGAAGATTTAATATTGTTAAGACAGTA 757
                            vi  i iv  i   ii    i     i               ii i 
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_107997096_    758 ATACTCCCCAAAGTAACCTACAAATTTAATGCAATAGCTATAAATATCTC 807
                                     v i i     i   i  i     vv    v  v   i 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_107997096_    808 AACAACTTTTTTTGTAGAAATGGAAAGGTTGACACCAAAATTCATAATGG 857
                          i vi i       i      v  v i i   iv i          -   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA-TGG 153

  chrX_107997096_    858 TATTTCCAGGGACCCA-AATAACCAAA-CAACCTTGA----GAAAAAGAA 901
                         v v v v         -    i     -   i     ----   i  v  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_107997096_    902 AATTGGAAAACTCACACTTCCCCATTTCAAAACTCATTACAA-GCTATAG 950
                          i     ii             v           i i     -    i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_107997096_    951 TAATCAAAACAGTGTATTACTGGCATAAATATACACATATATATTAATAG 1000
                                i       iv           iv   v       v  i   i 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_107997096_   1001 AATAAAATAGAGATTATAGAAATAAACCCTCAAATGTATGGTTGATTGAT 1050
                             i   v    v vi            vi v  v      ii      
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_107997096_   1051 CTTCAGTAAGGGAGACAAGATCATTCAATGAAGAAAGAATTGTCTCTGCA 1100
                         i   iii     v v     i         ii        v    i v  
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_107997096_   1101 ACAAATTATGTTGAGACAAATTGATGGCCATAGGCAAAAGGATGAAAATG 1150
                               vi  i  i     v v   i?   i v       i     iv  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_107997096_   1151 GACTCTTACCTCACACTATATACAAAAATTTATTCATCATAGAAAAAAGA 1200
                            i i          i             v i   vv  i  vv ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_107997096_   1201 CCTGAATATAAGAGCTAAAAACACCAAACTGTTAGAAGAAATCATAGGGG 1250
                            i   i            vi iv     v          v      ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_107997096_   1251 TAAATCTT-G-GGTCCTGGATTTGGCAATGGTTTCTTAGGAATGACACTA 1298
                                 - - ii i   i  v                iv       i 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_107997096_   1299 AAAGCACAAGCAATT---TAAAATACAGATAACTTAGACTTCACCAAAAT 1345
                                      iv---v    v i      v  i       i      
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_107997096_   1346 TAACAAACATTTGTGTATCAAATGATATAACCAAGAGAATAAAAAGACAG 1395
                            -    v      iv     v  i iv i     i i i        i
  L1M4_orf2#LINE/    654 TAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_107997096_   1396 CCCATACAATGGAAGAAAATATTTACAAATCATGTATTTGATAAGGATCT 1445
                             i v     i           i        i   i        iv  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_107997096_   1446 AGTATCCAGACTATATAAAAGACACTTACAACTCAACAACAGAATGACAA 1495
                         v         v        ii  v            i  i i  v     
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_107997096_   1496 ACAACCCAATATAAACATGT-CAACAGACTTGAATAGACATTTCTCCAAA 1544
                          i        v?   v   v-   vi  i                     
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_107997096_   1545 GAAGATTTACAAATGGCCCACAAGCACACAAGAGGTTTCTCAGCATCACT 1594
                               v           v i       ii i i v v    i     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_107997096_   1595 GGTTAT 1600
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.54 (106 / 69)
Gap_init rate = 0.01 (10 / 904), avg. gap size = 1.50 (15 / 10)  


 495 18.10 0.00 3.81  chrX_108023612_108026402       34   138 (2653)    L1M4_orf2#LINE/L1        1   101 (807)  

  chrX_108023612_     34 TGGAAAGATATTCCACGTTCATGAATTGGAAGAATCAATATTGTTAAAAT 83
                                    i   i       i         v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108023612_     84 GTTTGTACTACCCAAAGTAATCTATAGATTAAATGCACCCCTCCTCTAAC 133
                          vivi    v      v i     i     v  i   vi  ----   v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC----CTATC 96

  chrX_108023612_    134 AAAAT 138
                              
  L1M4_orf2#LINE/     97 AAAAT 101

Transitions / transversions = 1.38 (11 / 8)
Gap_init rate = 0.01 (1 / 101), avg. gap size = 4.00 (4 / 1)  

2894 25.41 2.31 2.42  chrX_108023612_108026402     1390  2298 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108023612_   1390 TGGAAAGATACTCCATGTTCATGAATTGGAAAAATCAATATTGTTAAAAT 1439
                                   ii           i       i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108023612_   1440 GTTTGTAATAC---CCAAAGAAATCTA--GATTTAATGCACCCCTCCTCT 1484
                          --- i     ---     vvi     --    i  i   vi  ----  
  L1M4_orf2#LINE/     51 G---GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC----CT 93

  chrX_108023612_   1485 ATCAAAATGC-AATGATATTGTTCATAGAAACAGATAAAACAATCCTAAA 1533
                                 v - iiviiv  v  iii     iv  i  ivii        
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_108023612_   1534 ATTTGTATGGAACCTAAAAAAAAACAAAATAGCCATAGCTATACTGAGCA 1583
                            ii       vivv  iii vv  i        v i v  vi   i- 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-A 192

  chrX_108023612_   1584 AAAAAGAATAAATATGGAGGAATCACATTACCTGACTTTAAATTACACTA 1633
                           i     i   vv       v     i v  ii i  i   vivi    
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_108023612_   1634 CAGGGGTATAGTAAACAAAGCAGCATAGAATTGGCATAAAAGGAGACACA 1683
                           ii v  i     v   ii   ii i v i        iiiv     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_108023612_   1684 TAGACCAATGAAACAGAATAGAGAACCTAGGAACAA-TCCATACATCTAC 1732
                             i     i  i     v    ii i  i  i  -i        i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_108023612_   1733 AGTGAATTCATTTACAACAAAGGTGCCAAGAACATACATCAGGGAACTAA 1782
                         i  v    v    v i    i          v   v  vii     vv  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_108023612_   1783 CAGCCTCTTCATTAAATGATGCTGGGAAAACTAGATATCCATGTGCAGAG 1832
                         i  i  i    vi     i        v    i    ?   ii    i i
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_108023612_   1833 GAATGAAACTAGACCCTTGTCTTTTACCATATACAAAAATCAAATTAAAA 1882
                                ii i     i ii  ivi               i  v i    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_108023612_   1883 TGGATTAATGACTTAAATCTATAACCTCAAACTACGGAACTGCTAAAAGA 1932
                              i ?v   i     v  vi v  v      iii    vi  i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_108023612_   1933 AATATTTGGAGAAACTCTCCAGGACATTGCACTGGGCAAATATTTCTT-G 1981
                           vvv v  ? v  v   i iv   v   vii i     vvi      - 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_108023612_   1982 AC-TGATACCCCACAGGCCCAGGAAAACAGAGCAAAAATAGAAAAAT-GG 2029
                          i-   i   -- v i  v  i v  vv i  v         v    -  
  L1M4_orf2#LINE/    593 ATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_108023612_   2030 A----ATCAAATGAAGTAAAAAAGCTTCTGCACAGCAAAGGAAAAAATCA 2075
                          ----      --- v      --   i  ii vv       v vv    
  L1M4_orf2#LINE/    641 ACTTCATCAAA---ATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_108023612_   2076 ACCAACTGAAGAGACAACCCACAGAATGGGAGAAAATATTTGCAAACTAC 2125
                          vv  v    i                                   ii i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_108023612_   2126 TCATCTGACAAGGGATTAATAATCAGAATACATAAGGAGCTCAAACATCT 2175
                         vi      i      i vi  vi       i    i  i   vv   v  
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_108023612_   2176 CTATAGGAAAAAAATCTAGTTATACGATTTAACAATAAAATGGACAAAAA 2225
                          v   iv     i - v i v iv i   ?  -----      i    ii
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA-CAAATAACCCAATTWAA-----AAATGGGCAAAGG 829

  chrX_108023612_   2226 GTCCGAATAGATATTTCTC-----AAGATTTACAAA--GCCAAATACGTA 2268
                         i ii       i       -----     v      --     -  v i 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCA 878

  chrX_108023612_   2269 TATGAAAAGATGCTCCACATCATAGATCAT 2298
                         i              v      ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (139 / 88)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.26 (43 / 19)  


2055 25.61 0.56 0.37  chrX_108032579_108036741.rev     2383  2917 (1246)    L1M4_orf2#LINE/L1        1   536 (372)  

  chrX_108032579_   2383 TAAAAAAATATTTTATGTTCATGGACAGGAGAAATTAATATTATTAAAAT 2432
                          ii   i    iii           iv   ii v        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108032579_   2433 GTCTATACTACCCAACGCAATCTACAGATTCAATGAAATCATTATCAAAA 2482
                          v v     v     vvii              i v    vi        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108032579_   2483 TACCAGCAATATTTTTCACATAAATAGAAAATATAATGCTAAAATTTAGA 2532
                          v     viiv     ii  v    v  v  vv i  v        i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_108032579_   2533 TGGAACACCCAAG--ACCCAGAATAGCCAAAGTCATCCTGAGCACAAAGA 2580
                              - iv    --                iiv   i   iv vi    
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_108032579_   2581 ACAAAATGGGAGAAATCACATTACCAGACTTCAAATTATGCTACAGAGCT 2630
                              i v    i v     i v  vi i      viv i     i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_108032579_   2631 ATAGTAAACAAACCAACATAGAACTGCCATAAAAACAGACACACAGAATA 2680
                          i     v   iv  iii i v    v     ii i     i i   vi 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_108032579_   2681 GTGATACAGAAT-AAGAGCCCAGAAATGAATCCATAAATCTACAGTGACC 2729
                         i  iv i     -i    i        i  i     v  i  ii  v vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_108032579_   2730 TCATTTTTCACAAAGGTGCCAAGAATATACACTAGGAAAAGGACGGTCTC 2779
                          v     iv    i          vi  v  v i  i    i ii    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_108032579_   2780 TTCAGTAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAA 2829
                             ii              v         ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_108032579_   2830 ACTAGACTACTATCTCTCACCATATACAAAAACCAAAAGAAAATGGATTT 2879
                         ii i   iv   i   v               ii  vvv         iv
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_108032579_   2880 CAAACTTAAATCTAAGACCTCAAACTATGAAACTACTT 2917
                         ? i  i     v     v  v       i     -   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTT 536

Transitions / transversions = 1.55 (82 / 53)
Gap_init rate = 0.01 (4 / 536), avg. gap size = 1.25 (5 / 4)  

1258 22.57 3.41 1.57  chrX_108032579_108036741.rev     3292  3672 (491)    L1M4_orf2#LINE/L1      521   908 (0)  

  chrX_108032579_   3292 AGACTATATCATTACTAAAAGAAAACTTAGAGA-AACTCTGCAGAA--TT 3338
                          i      vv i vi  i        v   i?i-  v   v ivi --  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_108032579_   3339 GGATGGGGCAAAGATTTCTT-GAC-TGATAGCCCACAAGCACAGGCAACC 3386
                           i vi     v i      -  i-   i --   v       i     v
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACA--CCAAAAGCACAAGCAACA 618

  chrX_108032579_   3387 AAAGCAAAAATGGACAAATGGAATCACATCAAG-TTAAAAAGATTCTTCA 3435
                             v      i  i    v i iiv      i-       v-  i vii
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGTG 667

  chrX_108032579_   3436 CAGCAAAGAAAACGATCAACAAAGTGAAGAGATAACC-ACAGATTGGGAG 3484
                          vv     i v  v     v        i   i    -     v      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_108032579_   3485 AAAATATTTACAAATTACCCATCTGACAAGGGATTAATAATCAGAACACA 3534
                                  i     i ivi      i      i vi  vi     i i 
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_108032579_   3535 TACAAAGCTCAAACAACTCAACAAGAAAACAAGCCCAAATAATCCCATCA 3584
                           v i i   vv         i  v    vi ---       i  v  i?
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGA---CAAATAACCCAATTW 814

  chrX_108032579_   3585 AAAAGTAGGCAAAG------AATAGACATTTCTCAAAAGAAGACATACAA 3628
                             i i       ------              v        i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_108032579_   3629 ATGGCCAACAGGTATATGAAAAGATGCTAAATATTACTAATCAT 3672
                                 i i i i             v  i  i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (51 / 33)
Gap_init rate = 0.03 (10 / 388), avg. gap size = 1.90 (19 / 10)  


2305 26.68 1.17 1.31  chrX_108059279_108065962     4972  5657 (1027)    L1M4_orf2#LINE/L1        1   685 (223)  

  chrX_108059279_   4972 TAGAAGAAGATTCCATGCTCATAGAGAGGAAGACTCAATATCATGAAAAT 5021
                          i   ii v  i     i    i  vv        i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108059279_   5022 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5071
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108059279_   5072 TACCAA-TGCCTTCCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5118
                          v   i-      ii  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_108059279_   5119 ATATGGAACCAAAAAATAGCCTGCATTGCCAAGACAATCCTAAGCCAAAA 5168
                                 viiv  iiv v  v v  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_108059279_   5169 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGT 5218
                                 i      vv   ii  v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_108059279_   5219 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAATAGAGATATAGAC 5268
                                  i   i    ii         i iv ii     v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_108059279_   5269 CAGTGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5316
                           i     i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_108059279_   5317 CATCTGATCTTTGACAAACCTCACCAAAACAAG-AAATGGGGAAAGGATT 5365
                           vi    i  i     ivv -i    i  v v-v           i  v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_108059279_   5366 TCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5415
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_108059279_   5416 GTGAAACTGGATCCCTTCCTTACACCTTATACAAAATATTAATTCTAGTT 5465
                         i    ii    i    v   i     v         -     i  v iv 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAAT 493

  chrX_108059279_   5466 GGATTAAGGACTTAAATGTTAGACCTAAAACCATAAAAAACCTAGAAGAA 5515
                             i ?i   i       v   v       i      vv i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_108059279_   5516 AACCTAGG--TAATACCATTCAGGACCAAGGCATGGGCAAGGACTTCATG 5563
                            v    --   - i -   iv    vv  vv i     v ii   v i
  L1M4_orf2#LINE/    544 AACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_108059279_   5564 TCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5613
                         vv  vi            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_108059279_   5614 TCTAACTAAACTAAAGAGCTTCTGCAGAGCAAAAGAAACTATCA 5657
                         ii v ii   v v  i i   i  iivvv    i  v       
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

Transitions / transversions = 1.48 (108 / 73)
Gap_init rate = 0.02 (13 / 685), avg. gap size = 1.31 (17 / 13)  

 965 21.52 0.42 0.42  chrX_108059279_108065962     5955  6191 (493)    L1M4_orf2#LINE/L1      672   908 (0)  

  chrX_108059279_   5955 AAAAGAAACTATCATCAGAGTGAACAGGCAACCTATAGAGTGGGAGAAAA 6004
                            i  v       vv i      v  i     i i   i          
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_108059279_   6005 TTTTTGCAATCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAAA 6054
                          v       vii ivi      i  i  i  vi          v  i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_108059279_   6055 GAACTCAAACAAACTT-ACAAGAAAAAAACAAACAACCCCATCAAAAAAT 6103
                               vv    -  i- i  v     i     i     v  i?      
  L1M4_orf2#LINE/    772 GAACTCTTACAA-CTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_108059279_   6104 GGACAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCC 6153
                           i        v    i     i     v        i  vi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_108059279_   6154 AACAGACACATGAAAAAATGCTCATCATCACTGGCCAT 6191
                           i ii          i       v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (32 / 18)
Gap_init rate = 0.01 (2 / 237), avg. gap size = 1.00 (2 / 2)  


3114 26.74 0.99 0.66  chrX_108068946_108075347.rev     5007  5911 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108068946_   5007 TGGAAGAACATTCCATGCTCATGGATAGGAAGACTCAATATCACAAAAAT 5056
                              ii i  i     i        v        i     iiiv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108068946_   5057 GCCCATACTGCCCAAGGTAATTTATACATTCAATGTTATCCCCATCAAGC 5106
                          v v     v     iv i  i  i v      i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108068946_   5107 TGCCA-CTGACCTTTTTCACAGAA-TTGGAAAAAACT---CCTTTAAAGT 5151
                          v   -   -       ii     -   -- v  i  ---   --   i 
  L1M4_orf2#LINE/    101 TCCCAGCTG-CCTTTTTTGCAGAAATTG--ACAAGCTGATCCT--AAAAT 145

  chrX_108068946_   5152 TCCCTTGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAGGCAAA 5201
                           viv     viiv  ii  v  viv        i      i iiiv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_108068946_   5202 AAGAACAAAGCTGTATGCATCAAGCTACCTGACCTCAAACTATACTATAA 5251
                                   i  v v vv   vi  v  ii ii     viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_108068946_   5252 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAT-T-G 5299
                         i          i   i    ii         i iv ii i   v  - - 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_108068946_   5300 ACCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAC 5349
                          i        i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_108068946_   5350 CATCTGATCTTTGACAAACCTGACAAAAACAAGTAATGGGGAAAGGATTT 5399
                           vi    i  i     ivv  v   i v  vvi           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_108068946_   5400 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5449
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_108068946_   5450 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGG 5499
                             ii    i    v   i     v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_108068946_   5500 ATTAAAGACTTAAATATAAGACCTAACACCATAAAAACCCTAGAAGAAAA 5549
                           i ?    i     i     v    v  i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_108068946_   5550 CCTAGGCA-ATACCATTCAGGACCTAGGCATGGGCAAAGTCTTCATGAAT 5598
                          v    ?i- v i -   iv     v  vv i     v vi   v ii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_108068946_   5599 AAAACACCAAAAGCAATGGCAACAAAAGCTACAATCGACAAATGGGATCT 5648
                          vi            vvi          vv v   v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_108068946_   5649 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGTCATCAGAGTGA 5698
                         v  i   v v  i i   i  ii vv    i  v   i   vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_108068946_   5699 ACAGGTAACCTACAGAATGGGAGAAAATCTTTGCAATCTACCCATCTGAC 5748
                          v  ii    i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_108068946_   5749 AAAGGGCTAGTATACAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5798
                           i  i  v    v      v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_108068946_   5799 ATAAACAAACAACCCCATCAAAAATTGGGCAAAGGATATGAACAGAC-CT 5847
                          v i     i     v  i?    v            v    i    -i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_108068946_   5848 TCTCAAAAGAAGACATTTATGCAGCCAACAGACATAAGAAAAAATGCTCA 5897
                             v        i  vi viii     i ii  i v     i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_108068946_   5898 TCATTACTGCTCAT 5911
                         v   i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


3206 27.64 0.22 0.22  chrX_108103466_108107917     3052  3959 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108103466_   3052 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATGAATATCGTGAAAAT 3101
                              ii i  i     i      i v      v v     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108103466_   3102 GGCCATACTGCCCAAGGTAATTTACAGATTGAATGTCATCCCCATAAAGC 3151
                            v     v     iv i  i        v  i iv     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108103466_   3152 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3199
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_108103466_   3200 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3249
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_108103466_   3250 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3299
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_108103466_   3300 TACAGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3349
                                 i   i v  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_108103466_   3350 AATGGAACAGAACGGAGCCCTCAGAAATAACGCCACATATCTACAACTAT 3399
                                i    iv   vvii         vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_108103466_   3400 CTGATCTTTGACAAACCTGGGAAAAACAAGCAATGGGGAAAGGATTCCCT 3449
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_108103466_   3450 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3499
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_108103466_   3500 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATG 3549
                          ii    i    v   i     v           i  i    i      v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_108103466_   3550 AAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3599
                          ?   ii    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_108103466_   3600 AGTCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAA 3649
                           v?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_108103466_   3650 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 3699
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_108103466_   3700 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 3749
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_108103466_   3750 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 3799
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_108103466_   3800 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 3849
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_108103466_   3850 ACAAACAACCGCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 3899
                              i    vv  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_108103466_   3900 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 3949
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_108103466_   3950 CACTGGCCAT 3959
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.35 (142 / 105)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


2609 26.18 3.71 1.69  chrX_108110242_108115011     3388  4277 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108110242_   3388 TGGAAAAATCTTCCATGCTCA-AGATTAGGAGGAAGCAATATTATTAAAA 3436
                               i  v i     i   -i    -   i  vvi      i    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT-GGAAGACTTAATATTGTTAAGA 49

  chrX_108110242_   3437 TGGTCATACTGCCCAAAGCAATTTATAGATTCAATGTCATTTCTATTAAA 3486
                            iv     v      vii  i  i        i iv  ii    i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_108110242_   3487 CTACCTACTACATTCTTCCTATGACTCAAAAAA-AAAAAACT-ATTTTAA 3534
                         v v  vi  i v  i  ----  ---  i   v-i v  i  -  ii   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTT----TG---CAGAAATTGACAAGCTGATCCTAA 142

  chrX_108110242_   3535 AATTCCTATGGAAC--CAAAAAACAGCCTGAATAGCCAATACAATTCTAA 3582
                              v       v--   iii  --  v          v     ii i 
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGA 190

  chrX_108110242_   3583 GCAA-AAGTACAAAGCCAGAAGCATCAAATTACCTGACTTCAAACTATAT 3631
                         iv  -   v      iii  i vv   v i v  ii i      viv  i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_108110242_   3632 TACAAGGCTTCAGTAATGAAAACAGCATGGTACTGACACAAGAACATACA 3681
                              i   v       v  i    ii        i  i   i i v   
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_108110242_   3682 CATAGACCAATGGAACAGAATAGAGAACCTAGGAATAAGACTGCACAACT 3731
                         i     i        i     v    ii i  i     iv iii   vi 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_108110242_   3732 ACAACCATCTGATCTTTGACAAACCTGACAAAAACATGCAATGAGGAAAT 3781
                          iiii  vi    i  i     ivv  v   i v   v     i     v
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_108110242_   3782 GATTCCCTATTTAATAAGTGGTGCTGGGATAACTGGTTAGCCATATGCAG 3831
                         i  vvi  v  i  i  i           i      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_108110242_   3832 AAAGTTGAAACTGGAC----ACCTTACACCATATACAAAAATAAACTCAA 3877
                           iiv    ii     ----    i                 v       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_108110242_   3878 AATAGATTAAAGATTTACATGTAAAATCCAAAACTATGAAAACTCT-AGA 3926
                            i   i ?   ii  v      i v i        -        -   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGA 539

  chrX_108110242_   3927 AGAAAATCTAGGCA-ACACCATTCAAGACATAAGCACAGGAGAACATTTC 3975
                               iv    ?i- v i -   iv   v vi vvi   vi vvi    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_108110242_   3976 AT-GATGAAGATGCCAAAAGCAATGACAACAAAAGCAAAAAGTGACAAAT 4024
                         v -   - v  ii         vvii         v     vv  i    
  L1M4_orf2#LINE/    589 TTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_108110242_   4025 GGGATCTAATTAAGCTAAAGAGTTTCTGCACAACAAAAGAAACTATCATC 4074
                         v   ii v  i  iv v  i ii  i  ii vv    i  v       vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_108110242_   4075 AGAGTTAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAA-TC---T 4120
                          i   v  v  i     i                 v       -  --- 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_108110242_   4121 ATCC--------------ATCCAGCATCTATAATGTACTTAAACAAATCA 4156
                            i--------------      v  v     v v   ivv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_108110242_   4157 CCAAGCAAACAACAAACAACCCCATTAAAGTGTTGGCAAAGGACATTGAA 4206
                         vi  vv   vi     i     v   ?  ivi v         i-     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAA 836

  chrX_108110242_   4207 TAGACACTTCTCAAAAGAAGACATACA--TGCAACAACAATCAGACAAAA 4254
                               i     v        i     --  -iv   i  v  v ii   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATG-GCCAATAAGCACATGAAA 885

  chrX_108110242_   4255 AAAAGCTAAACATCATTAGAGAT 4277
                          i v   v       ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (134 / 95)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.18 (48 / 22)  


2663 27.12 1.76 1.87  chrX_108116269_108127459.rev     3650  4556 (6635)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_108116269_   3650 GAAAAGCATTCCATGCTTATGGATAGGAAGAATCAATTTTGTGAAAATGG 3699
                             iii  i     i i      v      v i   v    v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_108116269_   3700 CCAGAATGACAAAAGTAATTTATAGATTCAATGTTATCCCCATCAAGCTA 3749
                          v v v vv v   v i  i  i        i iv     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_108116269_   3750 CCATTGACTTTCTTCACATAATTGGAAAAAAAAGTCCTTTAAATTTCATA 3799
                            vivi i  i  ii  v  v v  v  ivvii    --   v      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCATA 150

  chrX_108116269_   3800 TGGAAACAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAA-AA 3848
                               iiv  ii  v  viv        i      i i iv  i  -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_108116269_   3849 CAAACCTGCATGCATCATGCTACCTGACTTCAAACTATACTACAGGGCTA 3898
                             vi  v v vv   ii  v  ii i      viv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_108116269_   3899 AAGTAACCAAAACAGTATGGCACTGGTTCCAAAACAGATATATAGATCAA 3948
                         v     i   i     i   i     iviv ii i   i           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_108116269_   3949 TGGAACAGAA--GAGAGGCCTCAGAAATAACATCACACATCTAAAATCAT 3996
                              i    --     v  --        vvi  i    i  vii   v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_108116269_   3997 CTGATCTCTGATAAACCTGACCAAAACAAG-CAATGGGGAAAGGGTTCCC 4045
                         i    i ii  i  ivv  -    i  v v-            ii vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_108116269_   4046 TATTTAATAAATGGTGC-AGGAAAACTGACTAGCCATATGTAAAACACTG 4094
                          v  i  i         -i   v     iv  ?   i   i    v v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_108116269_   4095 AAATTGGATCCCTTCCTTACACATTATACAACAATTAATTCAAGATGGAT 4144
                           i     i    v   i    vv       v      i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_108116269_   4145 TTAAGACCTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4194
                         iv?         i      v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_108116269_   4195 TAGGCA-ATACCATTCAGGAGGTAGGCATGGGCAACGACTTCATGACTAA 4243
                             ?i- v i -   iv  vv v  vv i     i ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_108116269_   4244 AACACCAAAAGTAATGGCAACAAAATCCAAAATTGACAAATGAGATCTAA 4293
                         i          i vvi         vvv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_108116269_   4294 T--AAACTAAAGGGCTTCTGCACAGCAAAGGAAACTATCATCATAATGAA 4341
                          --   i    ii-   i  ii vv       v       vv v i    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_108116269_   4342 CAGGCAACCTACAGAATGCCAGAAAAAA-ATTTGCAA--TATATCCATCT 4388
                         v  i     i        --i  i    -        --i    --    
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATG--GGAGAAAATATTTGCAAATCATAT--ATCT 741

  chrX_108116269_   4389 GACTAATGG-TTAATATCAAGAATCTACAAAGAACTTAAACAAATTTACA 4437
                           -   v  -i vi    v     v  i        ivv    v iv i 
  L1M4_orf2#LINE/    742 GA-TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_108116269_   4438 ATGAAAAATCAAACAACCCCATCAAAAAGCAGGTGAAGGATATGAACAGA 4487
                           i    iv    i     v  i?    iii  ii      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_108116269_   4488 CAATTCCCAAGGGAAGACATTTTTTGCA----GCCAACAAACATTTGAAA 4533
                           v   i v ii     i  -----i  ----     i  i  iv     
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATAT-----ACAAATGGCCAATAAGCACATGAAA 885

  chrX_108116269_   4534 AAATACTCATCATCACTGGTCAT 4556
                          i  i    v     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 1.74 (33 / 19)  

3267 26.66 1.11 0.66  chrX_108116269_108127459.rev     9797 10700 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108116269_   9797 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 9846
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108116269_   9847 GGCCATACTGCCCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 9896
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108116269_   9897 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 9944
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_108116269_   9945 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 9994
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_108116269_   9995 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 10044
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_108116269_  10045 TACAGTAACCAAAAGAGCATGGTACTGGTACCAAAACAGAGATATAGATC 10094
                                 i   i v  ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_108116269_  10095 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 10142
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_108116269_  10143 ATCTGATCTTTGACAAACCGGAG--AAAAACAAGCAATGGGGAAAGGATT 10190
                          vi    i  i     i--  v --  i v  vv            i  v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAG--GGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_108116269_  10191 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 10240
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_108116269_  10241 GTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCGAGATG 10290
                         i    ii    i    v   i     v              i  i i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_108116269_  10291 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 10340
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_108116269_  10341 ACCTAGGCATTACCATTCAGGACATAGGAATGGGCAAGGCCTTCATGTCT 10390
                           v    ?i v viv   iv   v v  iv i     v vi   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_108116269_  10391 AAAACACCAAAAGCAATGGCAACAAAGGCCAAAATTGACAAATGGGATCT 10440
                          vi            vvi        i vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_108116269_  10441 AATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 10490
                         v  i   v v  i ii  i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_108116269_  10491 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 10540
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_108116269_  10541 AAAAGGCTAATATCCAGAATCTACAAGGAATTCAAACAAATTTACAAGAA 10590
                           ii i  vi          v  i  i   i  vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_108116269_  10591 AAAAACAA----CCCCATCAACAAGTGGGTGAAGGATATGAACAGACACT 10636
                            i    ----   v  i? v  i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_108116269_  10637 TCTCAAAAGAAGACATTTATACAGCCAAAAGACACATGAAAAAATGCTCA 10686
                             v        i  vi v ii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_108116269_  10687 TCCTCATTGGCCAT 10700
                         v v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


1447 24.41 3.21 1.71  chrX_108132960_108139589.rev       24   490 (6140)    L1M4_orf2#LINE/L1      355   828 (80)  

  chrX_108132960_     24 TTTGACAAAGTCAACCAAAACCAG-CAATGGGGAAATGACT--CCTTATT 70
                           i     i vii-    i    v-           -  v --i   -  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAA-GAATAGTCTT-TT 401

  chrX_108132960_     71 CAATAAATGGTGCTGTGATAACTGGTTAGCCATATACA---GATTGAAAC 117
                            i           v  i      v  ?   i  i  ---  v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_108132960_    118 TGGACCCCTTTCTTAAACCATAGACAAAAATTAACTCAAGATGGATTAAA 167
                                  vi  i v      v                i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_108132960_    168 GACTTACAAT-TAAAACCCAAAACTATAAACACCCT-GTAAGAGAGCCTA 215
                            i  -   -   i v i           -  i  -iv    i i v  
  L1M4_orf2#LINE/    502 GACCTA-AATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATA 549

  chrX_108132960_    216 GGCA-ATACCATTCTGGACATAGGAACAGGCAAAGATTTCAT-GATGAAG 263
                           ?i- v i -   vv   v v  ivi      v i    v -   - v 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chrX_108132960_    264 ATGCCAAAAACAAATGCAATGAAAACAAAATTTGACAAATAAGACCTAAT 313
                          ii      i  v v    ii   iv    v v  i    vi   i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_108132960_    314 TAAACTAAAGAGCTTCTGCATTGCAATAGGA-ACTATCAACAGAGTAAAC 362
                         i   v v  i i   i  iii v   -    -        v i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAA-AGGACACTATCAAGAAAGTGAAA 696

  chrX_108132960_    363 AGAAAATCTACAGAATTGGAGAAAATATTTGGAAATTATGCATCCAACGA 412
                            v  i i       v              v    i  ii   ii ii 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_108132960_    413 AGATGTAATATCCAGAACATATAATGAAC----ATAAATTAACAAGTAAA 458
                         i ivv vi         i      v    ---- i  v i  i  vv   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_108132960_    459 AAACAAACAACCTCATTAAAAAGTGGGCAAAG 490
                          i     i    iv   ?    i         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.50 (66 / 44)
Gap_init rate = 0.04 (17 / 474), avg. gap size = 1.35 (23 / 17)  

2956 27.15 1.21 1.32  chrX_108132960_108139589.rev     5234  6139 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_108132960_   5234 AAAAAAATTCCATGCTCATGGATAGGAAGAATCAATATCATGTAAATGGC 5283
                            i v  i     i        v      v i     ii vv i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_108132960_   5284 CATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATTGAGCTAC 5333
                         v     v      v i  i  i        i  v     i  ii iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_108132960_   5334 CATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTTATATG 5382
                           vivi i  i  ii     v v  v  i-  - iii    v  i     
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATG 152

  chrX_108132960_   5383 GAACCAAAAAAGAGCTTGTATAGCCAAGACAATCCTAAGCAAAAAGCACA 5432
                            viiv  ii  v iv v        i      i i iv  i   v   
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_108132960_   5433 AAGCTCGAGGCAC-CATGCTACCTGACTTCAAACTATACTACAAGGCTAC 5481
                            i v    -  -  ii  v  ii i      viv        i     
  L1M4_orf2#LINE/    203 AAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_108132960_   5482 GGTAACTGAAACAGCATGGTACTTGTACCAAAACAGAGATATAGACCAAT 5531
                         i    iii i    ii       v i iv ii i   v       i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_108132960_   5532 GGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTGCCACCATCTG 5581
                             i    iv   ivii         vv   i    i iivii  vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_108132960_   5582 ATCTTTGACAAACCTGGCAAAAACAAGCAATTGGAAAACGATTCCCTATT 5631
                           i  i     ivv  v   i v  vv    v  i   vi  vvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_108132960_   5632 GAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAACTAGAAC 5681
                         v  i        i     v      v  ?   i   i i  i v ii ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_108132960_   5682 TGGACCTCTTCTTTACACCTTATACAAAAATTAACTCAAGATGGATTTAT 5731
                               i  v i i     v                   i      iv?v
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_108132960_   5732 GACTTAAATATAATACCTAAAACCATAAAAGCCCTAGAAGAAAACCTAGG 5781
                            i     i   v v       i      vi i           v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_108132960_   5782 C---AATGCCATTCAGGACATAAGCATGGGCAA-GGCTTCATGACTAAAA 5827
                         ?---   -- -   iv   v vi vv i     -  i   v iiv  vi 
  L1M4_orf2#LINE/    552 NGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_108132960_   5828 CACCAAAAGCAATGGCAACAGAATCCAAAATTGACAAATGGGACCCAATT 5877
                                    vvi      i  vvv     v  i    v    iiv  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_108132960_   5878 AAA-CTAAATAGTTT----CTTCACACACAAAAAAAAACTATCATCAGAG 5922
                            -i    v v   ----     -------  ii v       vv i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCA-------AAGGACACTATCAAGAAAG 691

  chrX_108132960_   5923 TGAAAAGGGAACCTACAGAATGGGAGAAAAATTTTGCAATCTATCCATCT 5972
                                iv    i                vv       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_108132960_   5973 GACAAAGGGCTTATATCCAGAATCTACAATGAACTTAAACAAATTTACAA 6022
                           i  i  i   i          v  i  v     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_108132960_   6023 GAAATAAACAAAGAACCCCATCTAAAAGTGGGCAAAGGATATGAACAGAC 6072
                         v   v i     v     v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_108132960_   6073 ACTTCTCAAAAGAAGACATTTATGTGGCCAACAACGATATGAAAAAATCC 6122
                          i     v        i  vi vi       i  vv i       i  v 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_108132960_   6123 TTATCATCACTGGTCAT 6139
                          i v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (138 / 104)
Gap_init rate = 0.01 (11 / 905), avg. gap size = 2.09 (23 / 11)  


3200 26.19 0.89 0.44  chrX_108146166_108150369.rev     2813  3713 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_108146166_   2813 AAAAGTATTCCATGTTCATGGATTGGAAGAATCAATATTGTTGAAATGTC 2862
                            ii   i                     v i         i i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_108146166_   2863 CATATGACCCAATGCAAGCTACAGATTCAATGCAATCCCTATCAAAATAT 2912
                         v   ivv     vvii v            i                 vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_108146166_   2913 CAATGACACTCTTCACAGAAGTAGAAAAAAGAATCCTAAGCTTCATGTGG 2962
                           iivi vi i  ii     i v  v  ivvi       iv     i   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_108146166_   2963 AATCATAAAAGGCCCAGAATAGCTGCAGCTATTCTAAGTAAAAATAAAAA 3012
                           viii  ii i           iiv i v  ii i iv  i  -i  v 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GAACA 202

  chrX_108146166_   3013 AAACTGGAGGAATCACATTACCTGATTTCAAATTATACTACAGAGATATA 3062
                           ii       v     i v  ii        viv       i  v  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_108146166_   3063 ATAATGAAAACAGCATAAAACTCACATAAAAACAGATACGTAGACCAAAG 3112
                         i    v  i    ii iiv   vi     ii i   i ii    i   v 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_108146166_   3113 GGACAGAATAAAGAACCCAGAAAAAAATCTACACACCTACAGTTAACTCA 3162
                          i i     vi   ii       v   i i i   ii  ii  i  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_108146166_   3163 TTTT-GACAAAGGT-CTAAGAACATACACTGGGGAAAAAGACAGTTTCAT 3210
                             -     i   - i    v   v  v        i - i   i iv 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTT 401

  chrX_108146166_   3211 CAATAAATGGTGCTGGCAAAACTGGATATCCATAAGCAGAGGAATGAAAA 3260
                            i            v v         ?   i v   i i       iv
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_108146166_   3261 TAGAATCCTATCTATAACTATATACAAAAATCAAATCAAAATGGATTTAA 3310
                          i  vi    i  vvv  i            i  v           iv? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_108146166_   3311 GACTTAAATCTAATACCTCAAAGTATGCAACTTCCACAAGGAAACATAGG 3360
                            i     v   v v  v   v   iv    iii v   i         
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_108146166_   3361 GGAAAATCTCCAGGTCATTGGCCTGGGCAAAGATTTCTTGAGCAATACTC 3410
                         ? v      i iv v v    vi i     v i      iiii vv  v 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_108146166_   3411 CACAAGCACAGGCAACCAAAGCAAAAATGGACAAAGGGGATCACA-CTAA 3459
                           v       i     v    v      i  i   vv   iiv  - v  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_108146166_   3460 GTTAAAAAGCTTCTGCACAGCAAAGAAAATAATCAACAAAGTGAAAAGAC 3509
                         i       -   i  ii vv     i v iv     v             
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_108146166_   3510 AACCCACAGGTTGGAGGAAAATATTCGCAAACCACCCATCTGACAAGGGA 3559
                                  iv   ii         i     i  ivi      i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_108146166_   3560 TTAATAACCAGAATATATAAGTAACTCAAACAACTCTGTACTAAAAAGTC 3609
                         i vi  v             iv     vv       vi  v       v 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_108146166_   3610 TAAATA-TCTAAT--AAAAACGGGCAAAT-ATTTGACTAGATATTTCTTT 3655
                         -     -i i   --     i       v-      v    i      ii
  L1M4_orf2#LINE/    801 -AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_108146166_   3656 AGAAAA-ACCTACAAATGACAAACAGGCATATGAAAAGGTGCTCAACTTC 3704
                          i i  - iv        i v  i i   i        i        v  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_108146166_   3705 ATTTATTAT 3713
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.01 (11 / 905), avg. gap size = 1.09 (12 / 11)  


3242 25.99 0.77 0.77  chrX_108162183_108168456     4874  5781 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108162183_   4874 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4923
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108162183_   4924 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCGTCCCCATCAAGC 4973
                            v     v     iv i  i           i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108162183_   4974 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5020
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_108162183_   5021 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5070
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_108162183_   5071 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATGCTACAAGG 5120
                                 i      vv       v  ii i      viv i      i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_108162183_   5121 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATTGAT 5170
                                  i   i    ii         i iv ii i   v    v   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_108162183_   5171 CAATGGAACAGAAC--AGAGCCCTCAGAAAGAATGCCGCATATCTACAAC 5218
                                 i    i--    i  --     v  vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_108162183_   5219 TATCTGATCTTTGACAAACCTGGGAAAAACAAGCAATGGGGAAAGGATTC 5268
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_108162183_   5269 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5318
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_108162183_   5319 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5368
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_108162183_   5369 ATGAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5418
                           v ?   ii    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_108162183_   5419 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5468
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_108162183_   5469 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5518
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_108162183_   5519 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAATGACCATCAGAGTGAA 5568
                           i   v v  i i   i  ii vv    i  v iv i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_108162183_   5569 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5618
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_108162183_   5619 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATCTACAAGAAA 5668
                          i  i  vi          v  i  v      vv    v  v i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_108162183_   5669 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5718
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_108162183_   5719 CTCAAAAGAAGACATT--AATGCAGCCAAAAAACACATGAAAAAATGCTC 5766
                            v        i  v--    --     v  i          i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTC 893

  chrX_108162183_   5767 ATCATCACTGGCCAT 5781
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (135 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


1339 20.00 12.62 1.19  chrX_108188952_108192301       83   502 (2847)    L1M4_orf2#LINE/L1      385   852 (56)  

  chrX_108188952_     83 GAAAAAAATGATCTTTTCAACAAATGGTACAGGGACAAC---ATA----- 124
                          i   i   ii                 i v        ---   -----
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_108188952_    125 ----AAAATAATGAATTTGGATGCCTA--------------------TTG 150
                         ----    v      v     iv    --------------------  i
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_108188952_    151 ACTTGGAATGAATCACAGACCTAAATGAAAGAATGAAAACTGTAAAACTC 200
                            iii    i    ?           v    iiv      i        
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_108188952_    201 TTAGAAGAAAATATAGGGCTAAAT----ATGACCTTGTGTTTCACAAAAG 246
                                    i     ?v     ----i        v   vvi   vi 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_108188952_    247 ATTATTAGATATATGAGAAAAAAAG-ATGTGTAA--AAAGAAAAAATA-- 291
                         v  v        --  v vv     - iiv i  --            --
  L1M4_orf2#LINE/    585 TTTCTTAGATAT--GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_108188952_    292 --AATTGGATTTCACCAGAACTAAATTATTCTGTGTTTCAAAGGACATCA 339
                         --       i    i  i  i    vvv  i    i           ii 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_108188952_    340 ACAAGAAAGTGAAAAGGCAACTCACAGAA-GGGTGAAAACATTTGCATAG 388
                         v               i    i       -   v     i       v v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_108188952_    389 CATGTA----ATAAAGGACTTGTAACTCAAAAATATAAAGAATATTTAAA 434
                            i  ----    i         v ivi  v          ivi   v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_108188952_    435 ACTAAGTAATAAAAAGATAAATAAT--GATT--AAAATGGACAAATATAA 480
                            v i           i      i--i   --       i    ---ii
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA---GG 829

  chrX_108188952_    481 AGTTAAA-AAATCTTTTTCCAGA 502
                          v  i  - i iv   i    i 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAA 852

Transitions / transversions = 1.56 (50 / 32)
Gap_init rate = 0.03 (14 / 468), avg. gap size = 4.14 (58 / 14)  

3379 25.78 1.22 0.33  chrX_108188952_108192301     1960  2859 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108188952_   1960 TGGAAAAAGAGTTCATGTTCATGGGTTGGAAGAATCACTATTGTTAA-AT 2008
                               i v vii           i        v i v         -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108188952_   2009 ATCCATACTATGCAAAGTAATCTATAGATTCAAATGCAACCCCTATCAAA 2058
                         iv v     viv    v i     i      -  i    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTC-AACGCAATCCCTATCAAA 99

  chrX_108188952_   2059 ATACCAATAACATTCTTGTCAGAAATAGAAAACACAATGTTAAAATTTAT 2108
                           v   iivi v  i  vv       v  v  vvii  vi       i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_108188952_   2109 ATAGAACCATGAAAGACCCAGAATGGCCAAAGCTATCCTGAACAAAAAGT 2158
                           i   viiii ii          i      i v   i    v  i   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_108188952_   2159 ACAAAACTGGGGAAAACGCATTGCCTGATTTCAAAATGTATTATGGAGTT 2208
                              ii   i i vv i  i v  ii         iv  i  iii  i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_108188952_   2209 GTAATAACCAAAACAGCATGGTACTGGTGCAATAACAGACACATACACCA 2258
                         ii i   i   i    ii         iii  vi i     i   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_108188952_   2259 ATGAAAGAGAATAGAGAACCCAGAAACAAATCCACACACCTATAGTGAAT 2308
                            i  v     v    ii       i   i   i   ii   i  v   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_108188952_   2309 TTATTTTTGACAAAGATGCCAAGAACATACACTCGGAAAAAGACAATCTC 2358
                          v     i     i i        v   v  v v  i   ii i i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_108188952_   2359 TTCAATAAGTGGTGCTGGGAAAACTGGATATCCAAGTGCAGAAAAATGAG 2408
                              i  i           v         ?   vi    i  i     i
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_108188952_   2409 ATTAGACCTTTATCTCTTGCTATATATAAAA-TTAAATTAAAGTGGACTA 2457
                         i  i    ii  i   vii i     i    -    v i   i    ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_108188952_   2458 AACACTTAAATCTAAGACCTCAGATGATGAAACTTCTAGAAGAAAACATT 2507
                         ? v  i     v     v  v i iv  i     ii             v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_108188952_   2508 GGAGACACTCTCCAGGACATTGGTCTGGGCAAAAATTTCTTAAGTAATAC 2557
                           ? vv v   i iv   v    vi i     vii       ii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_108188952_   2558 ATCATAAGCATAGGCAACCAAAGCAAAAATGGACAAACAGGATCACATCA 2607
                          i  v     i i     v    v      i  i   iv   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_108188952_   2608 A-GTTAAAAAGCTTCTGCACAGTGAAAAAAACAATCAACAAAGTGAAGAG 2656
                          -i       -   i  ii vvii  ii v  v     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_108188952_   2657 ACAACCCACAGAATTGGAGCAAATATTTGCAAACTACCCATCTGAAAAGG 2706
                                       v    v             ii ivi      v    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_108188952_   2707 GATTAATAACCAGAATATATAAGGACCTCAAAC-ACTCTATAGGAAAAAC 2755
                           i vi  v             i  v   vv  -    v   iv     v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_108188952_   2756 ATCTAATAACTCCAT--AAAAATGGGCAACTGATTTGAATAGGCAATTCT 2803
                          - v      i v  --            vv           i  v    
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_108188952_   2804 CAAAAGAAGACATA-AAATGGC----AGGCATATAAATAAGTGCTTAACA 2848
                          v        i   -       ---- i   i  i  v ii    i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_108188952_   2849 TAATTGGTCAT 2859
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.66 (143 / 86)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


1887 24.52 1.34 0.38  chrX_108193976_108198556     3567  4088 (493)    L1M4_orf2#LINE/L1      382   908 (0)  

  chrX_108193976_   3567 TGGGGAAATGACATTCTATTCAACAAATGGTGCTGGGATAATTAGCAAGC 3616
                                 vi i v   v                    i  i i vv ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_108193976_   3617 CACATGTAGA-GAATAAAACTGGATCCTCATCTCTCATCTTATACAAAAA 3665
                               i i -    i  ii    i  ii i   v  i v          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_108193976_   3666 TCAACCCAAGATGGATCAAGGACTTAAATCTAAGACCTGAAACAGCAAAG 3715
                          i   i   i        ?i   i     v     v  i    vii   i
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_108193976_   3716 ATCCTAGAAGATAACATTGGAAAAACCCTTCTAGACATTGGATTAGGCAA 3765
                         v  i       v     v  ?iv  vi    vv   v    i        
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_108193976_   3766 AGACTTCATGACCAAAAACCCAAAAGCAAATGCAATAAAAACAAAGATAA 3815
                         v ii   v iivi vi vv         v v    i    iv   i   i
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_108193976_   3816 ATAGATGGCACCTGATTGAACTAGAAAGCTTCTGCACAGCAAAACAAATA 3865
                            i  v v  i v  ii  v vi   i   i  ii vv    iv v iv
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_108193976_   3866 ATCAGCAGAGTTAACAGACAACCCACAGAGTGGTAGAAAATCTTCA-AAA 3914
                             iv i   v  v              i   v       v  ii-   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_108193976_   3915 TGGATACATCTGACAAGGGACTAATATCCAGAATCTACAAAGAACTC--- 3961
                          -v   i      i        vi          v  i         ---
  L1M4_orf2#LINE/    732 T-CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_108193976_   3962 -AAATCAGCAAGAAAAAG-CAAACAATCCCATCGAAATGTGGACTAAGGA 4009
                         -  v   ii  v      -    i  i  v  i?   vi   i v     
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_108193976_   4010 CATGAACAGACAATTCTCAAAAGAAGATATACAAATGGCCAACAAGCATA 4059
                         iv    i     v     v                       i     i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_108193976_   4060 TGGAAAAAATGCTTAACATCACTATGTAT 4088
                           -    i     i       ????????
  L1M4_orf2#LINE/    881 TG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (71 / 53)
Gap_init rate = 0.01 (6 / 527), avg. gap size = 1.50 (9 / 6)  


3195 25.17 2.47 0.45  chrX_108240590_108247253     5282  6171 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108240590_   5282 TGGAAAAACATTCCATGCTCATAGATAGGAAGAATCAATATTGTGAAAAT 5331
                               i i  i     i    i   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108240590_   5332 GGCCATACTGCCCAAATTAATTTATAGATTCAATGCTATCCC-ATCAAGC 5380
                            v     v        i  i  i        i  v     -     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108240590_   5381 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 5428
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_108240590_   5429 TATGGAACCAAAAAAGAGCCTGCATAGGAAAGACAATCCTAAGGAAAAAG 5478
                                viiv  ii  v  v v    vv  i      i i ii  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_108240590_   5479 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGTC 5528
                                i      vv       v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_108240590_   5529 TACAGTAATCAAAACAGTGTGGTACTGATACCAAAACAGATATATAGATC 5578
                                     i              ii iv ii i   i         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_108240590_   5579 AATGGAACAGAACAGAGAGCTCAGAAATCACACAACACGTCTGCATCCAT 5628
                                i    iv     ii       v vv v i  i i iiivi  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_108240590_   5629 CTGATCTTTGACAAACCTGAAAAAAACAAGAAATGGGGAAAGGAT----- 5673
                         i    i  i     ivv  vv  i v  vvv           i  -----
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_108240590_   5674 --TTAATAAATGGTGTTGGGAAAACTGTCTAGCCATATGCAGAAAACTGA 5721
                         -- i  i        i     v     vv  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_108240590_   5722 AACTTCGACCCCTTCCTTACAACTTATACAAAAATTAACTCAAGATGGAT 5771
                          i-  v       v   i   v v                   i      
  L1M4_orf2#LINE/    449 AG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_108240590_   5772 TAAAGACTTAA-TGTAAGACCTAAAACCATAAAATCCCTAGAAGAAAATC 5820
                         i ?    i   -       v       i      ii i          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_108240590_   5821 TAGGCA-ATACCATTCAGGACATAGGCATGAGCAAACACTTCGTGAATAA 5869
                             ?i- v i -   iv   v v  vv ii    vvii   v ii   v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_108240590_   5870 AACACCAAAAGCAATGGCGACAAAAGTCAAAATACACAAATGGGACCTAA 5919
                         i            vvi  i       vv      v i    v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_108240590_   5920 TTAAACTAAAGAGCTTCTGCACAGCTAAAGAAACTATCATCAGAGTGAAC 5969
                          i   v v  i i   i  ii vv v  i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_108240590_   5970 AGGCAACCTACAGAATAGGAGAAAAATTTTGCAAACTATGCATCTGACAA 6019
                           i     i       i        vv        ii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_108240590_   6020 ATGACTAATATCCATTATCTACAAAGAACTTAAACAAATTTACAAGAAAA 6069
                         iv    vi      vv  v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_108240590_   6070 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 6115
                          i    ----   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_108240590_   6116 TCAAAAGAAGA------AGTGGCCAGCAAACATATGAAAAAATCCTCATC 6159
                           v        ------ i      ii  i  i       i  v    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_108240590_   6160 ATCACTGGTCAT 6171
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (126 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.36 (26 / 11)  


2220 30.56 0.99 0.62  chrX_108252294_108258776.rev     4421  5225 (1258)    L1M4_orf2#LINE/L1        1   808 (100)  

  chrX_108252294_   4421 TGGAAAAACATTCCATTCCTAAAGATAGGAAGAATCAATATCATGAAAAT 4470
                               i i  i    viii vi   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108252294_   4471 GGCCATAC-ACCCAAGGTAATTTGTAGATTCAATGCTATTCCCATCAAGC 4519
                            v    -v     iv i  i ii        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108252294_   4520 TAACATTGGCTTTCTTTACAGAACTAGAAAAACTACTTTTAA-TTTCTTA 4568
                          vv  viv  i  i   i     v v  v  i  iv ii   -v   v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_108252294_   4569 CGGAACCAAAAAATAGCCCGTATAGTCAAGACAATCCTAAGCAAAAAGAA 4618
                         i    viiv  iiv v  v v    i   i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_108252294_   4619 CAAACCTGGAGGCATCATGCTACCTGACTTCAAACTGTACTACAAAGCTA 4668
                             vi      vv   ii  v  ii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_108252294_   4669 TGGTAACCAAAACAGCATGGTATTAATACAAAAACAGAAATATAGACCAA 4718
                         ii    i   i    ii     i iii i  ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_108252294_   4719 TGGATCAGAACAGA-AGCCCAAGAAATAATGCCACACATCTACAACCTTC 4767
                             vi    iv  -  i   -       vv   i    i  iiii vvi
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATGGTCAAT 349

  chrX_108252294_   4768 TGATCTTTGGCAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCCA 4817
                             i  i i   ivv  v   i v  vvv           i  vvi iv
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_108252294_   4818 TTTAACAAATGATGCTGAGAAAACTGGCTAGCCATATGCAGAAAACAGAA 4867
                           i        i     i  v      v  ?   i     i  i vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_108252294_   4868 ATTGGAATACTTTTTAACACTTTATACAAAAATTAACTCAAGATGGATTA 4917
                         i     viv  vii v    iv                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_108252294_   4918 AAGACTTACATGTAAAACCTAAAATGATAAAAACCCTT-GAAGAAAACCT 4966
                         ?    i  v      i v      iv      - i   -         v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chrX_108252294_   4967 AGGCAGTAACATTCAGAACATATGCATGGGCAAAGAGTTTATGACTAAAA 5016
                            ?ivv  iv   ivi  v vv vv i     v iv  iv iiv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_108252294_   5017 CACCAAA--TACAATTACAACAAAACCCAAAATTGACAAATGGGATCTAA 5064
                                --i    --i        vvv     v  i    v   ii v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_108252294_   5065 TTAATGTAAAGATCTTCTGCTCAGGAAAAGAAAATATCATCAGAGTGAGC 5114
                          i  vi v  i v   i  iv vvv   i  v v     vv i     iv
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_108252294_   5115 AAGCAACCTACAGAATGGGAGAAAATTTTTGCCATCTATCCATCTGACAA 5164
                          ii     i                 v     v vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_108252294_   5165 ATGTCTAATATCCAGAATCTACAAGGAATTTAAACAAATTTACAAGTAAA 5214
                         iv v  vi          v  i  i   i ivv    v iv i  -    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAA 795

  chrX_108252294_   5215 AA--TAAACAACC 5225
                           --i   i    
  L1M4_orf2#LINE/    796 AAGACAAATAACC 808

Transitions / transversions = 1.27 (136 / 107)
Gap_init rate = 0.01 (10 / 808), avg. gap size = 1.30 (13 / 10)  

 361 22.05 8.66 0.00  chrX_108252294_108258776.rev     5866  5992 (491)    L1M4_orf2#LINE/L1      771   908 (0)  

  chrX_108252294_   5866 AGAACT--TAAAGTATAATAATTAAAAAAAAAAT----CAA----AAAGT 5905
                               --  v iivi      v    i v    ----   ----   i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_108252294_   5906 GGGCAAATGATATGAACAGACATTTCTCAAAAGAAGGCACTTATGCAGCC 5955
                                v   v    i           v       ii ivi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_108252294_   5956 AACAAACATATGATAAAA-GCTCATCATCACTGCTCAT 5992
                           i  i  i    v  i -     v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (17 / 11)
Gap_init rate = 0.03 (4 / 138), avg. gap size = 2.75 (11 / 4)  


3549 24.18 2.71 0.11  chrX_108292616_108302942.rev     2776  3660 (6667)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108292616_   2776 TGAAAATACATTCCATGATTGTTGATCAAAACAACCAATATTATCAAAAT 2825
                           i   v i  i     v ii v   iii  v vii      i i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108292616_   2826 GTCCATGTTACCCAAAACAATCTATAGATTTAATGCGATCTGTATAAAAA 2875
                          v v  ii v      vii     i     i  i  i   iv   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108292616_   2876 TTCCA-TGGCATCTTTCACAGAAATTTCTGAA--AATCCTAAAATTTGCA 2922
                          i   -iv  v i   ii        vvii i--i           iii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_108292616_   2923 TAGAAACATAAAAGAGCCTGAATAGCTAAAGCAATCTTGAGCAAGAAGAA 2972
                          i    iii  ii  v  v       i   i         iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_108292616_   2973 ---AGCTGAAGACATCATACTTCTTCATTTCAAATTTTATTACAAAGCTA 3019
                         ---  i  i  ivv   i     iiv        vi   i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_108292616_   3020 TAATATTTAAAACAGTATGGTACTGGCATAAAAATAGACACACTGACCAA 3069
                         i i  v i  i     i              ii       i iv  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_108292616_   3070 TAGAACAGAATAGAGAGACCAGAAATAAATCCATGCATTTATGGTCAATT 3119
                          i   i     v     v           i    i               
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_108292616_   3120 GATTTCAAACAAATGTGCCAAGAACACATAATGGGAAAAGAAGAGTTTGT 3169
                              ivi    iv         v  ivi      i      v   i v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_108292616_   3170 TCAATAATTAGTGTTGGAAAAACTGGATATCCACATGCAGAAGAATTAAA 3219
                             i  v i   i   i v         ?         i      v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_108292616_   3220 ATGGACACTCATGTCACACAATATACAAGAATCAACTCAAAATGGATTAA 3269
                         v     v ii iv      v        i   i              i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_108292616_   3270 AGGCTTGAACATAAGACGTGAAGTCCATAAAACTAC-AGAAGAAAACATG 3318
                           i i i  ii     - iv  iv i        vi-            i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_108292616_   3319 GAGGAAAAACTACATAACATTGGTCTGGGCAATGATTCTTTGGATTTGGC 3368
                          i? v   v  v i i  v    vi i       i  ii  i   v  i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_108292616_   3369 TCCAAATGTCCAGGCATCAAAAGTAAAAATAGGCAAATGGAAACACATCA 3418
                         v     v iv  i   v      v        ii    v i viv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_108292616_   3419 AACTAAAAAGCTTCTGCACAGCAAAGAAAACAATTAACAGAGTGAAGAGA 3468
                           v v    i   i  ii vv     i v  v  i  v i      i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_108292616_   3469 GAACCTATGAACTGGGAGAAAATATTTGCAAGTCATAGATCTG------- 3511
                         v    i iii v                   i     v     -------
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_108292616_   3512 ----GTATCCAAAAT-TATAAGGATCTCATACAACTCAATACCAAGAAAA 3556
                         ----       i   -     i  v   v            vi  i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_108292616_   3557 CAAATAACCCAATTAAAAAATGGGCAATGGACCTCAATAGACATTTATC- 3605
                                       ?            v   ii v           v  -
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_108292616_   3606 --AAAAGACATA--AATAGCCAATAGATATATGAAAAAATGCTCAACATC 3651
                         -- i    i   --   i       iii i       i            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_108292616_   3652 ATTAAATAT 3660
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.92 (138 / 72)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.78 (25 / 9)  

3018 26.00 1.08 2.71  chrX_108292616_108302942.rev     8914  9836 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108292616_   8914 TGGAAGAATATTCCATGATCATGGATAAGAAGAATCAATATCACTATAAT 8963
                              ii    i     v        vi     v i     iii  vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108292616_   8964 GGCCATACTGCCCAAAGAAATTTATAGATTCAATGCCATCCCCATCAAGC 9013
                            v     v      vvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108292616_   9014 TACCAA-TGACTTTCTT-CAGAGAACTGGAAAAAACT-ACTTTAAAGTTC 9060
                          v   i-  v    i  -    -  i  -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_108292616_   9061 ATATGGAATCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAA 9110
                                 viiv  ii  v  viv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_108292616_   9111 GAACAAAGCTAGAGGCATCATACTACCTGACTTCAAACTATACTACAAGG 9160
                                 i i    vv   i   v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_108292616_   9161 CTACAGTAAACAAAAACAAAACAAACCAAACAGCATGGTACTGGTACCAA 9210
                                  v   i ---------------   ii         i iv i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGA---------------CAGTGTGGTACTGGCATAAG 282

  chrX_108292616_   9211 AACAGAGATATAGACCAATGGATCACAAC--AGAGCCCTCAGAAATAATG 9258
                         i i   v       i       vi v  i--    i  --        vv
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAAC 330

  chrX_108292616_   9259 CCACATATCTACAGCTATCTGATCTTTGATAAATCTGACAAAAACAAGAA 9308
                            i i  i  ii ii vi    i  i  i  ivv  v   i v  vvv 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_108292616_   9309 ATGGGGAAAGGATTCCCTACTTAATAAATGGTGCTGGGAAAACTGGCTAG 9358
                                   i  vvi  vi i  i              v      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_108292616_   9359 CCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAA 9408
                            i   i i  iiv    ii    i    v   i     v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_108292616_   9409 ATTAATTCAAGATGGATTAAAGACTTAAATGTTAGACATAAAACCATAAA 9458
                              i    i      i ?    i       v   vv      i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_108292616_   9459 AACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGGCATAGGCATGGGA 9507
                          vi i           v    ?i- v i -   iv i v v  vv i  v
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGC 579

  chrX_108292616_   9508 AAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAAT 9557
                           v ii   v ivv  vi            vvi          vv     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_108292616_   9558 AGACAAATGGGATTTAATTAAACTAAAGAGCTTCTGCAGGGCAAAAGAAA 9607
                            i    v   i  v  i   v v  i i   i  iivvv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_108292616_   9608 CTACCATCAGAGTGGACAGGTGACCTACAGAATGGGAGAAAATTTTTGCA 9657
                            i  vv i    i v  iii   i                 v      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_108292616_   9658 ATCTACCCATCTTACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAA 9707
                          vii ivi    v i  i  i  vi          v  i         vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_108292616_   9708 ACAAATTTCCAAGAATA----GATCAAACAACCCCATCAAAAAGTGGGCA 9753
                             v ---   v    ----  -    i     v  i?    i      
  L1M4_orf2#LINE/    780 ACAACT---CAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCA 825

  chrX_108292616_   9754 TAGGATATGAACAGACACTTCTCTGAAGAAGACATCTATGCAGCCAATAG 9803
                         v     v    i     i     ii       i  vi viii       i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_108292616_   9804 ACATGTGAAAAAATGCTCATCATCACTGGTCAT 9836
                         i  ii      i       v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.69 (35 / 13)  


3023 27.38 1.33 0.67  chrX_108307570_108311797.rev     2836  3737 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108307570_   2836 TGGAAAAATATTCCATGTTCACAGATTGGAAGGATCAATATTTTTATAAT 2885
                               i    i         ii         iv i      v   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108307570_   2886 GCCTGCACTACACAAAGCAATCTACAGATTCAATGCAACCCCTATCAAAA 2935
                          v vii   v v    vii              i    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108307570_   2936 TACAAATGATGTTCTTCACAGCAACAGAAAAAACAATCCTAAAATGTATG 2985
                          v v iiviiv  i  ii   v  iv  v  ivii          vi  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_108307570_   2986 TGGAGCCACAAAAAATCCAGAGTAGTCAAAGCTATTCTAAGCAAAAAGAA 3035
                             ivii   iii i     i   i    i v  ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_108307570_   3036 CAAAACTGGAAGAATCACATTACCTGACTTCAGATTATACTACAGAACTT 3085
                             ii    i  v     i v  ii i    i viv       i i  v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_108307570_   3086 TAGTAATCAATACTGCATGTTACTGGCATGAAAACAGACATGTACACCAA 3135
                         i         v  v ii  v         i ii i      i  v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_108307570_   3136 TGAAACAGAATAGAGAACCCAGAAAAAAATCCACACACTGACAGTGAACT 3185
                           i  i     v    ii       v   i   i   i v ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_108307570_   3186 CGTTTCTAACAATGATGCCAAGAACATATACTGGGAAAAGA-CAATGTCT 3234
                         vi   iii    v i        v   vi v    i     -i i v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_108307570_   3235 TAAATAAATGGTGTTAGGAAAAATAGGATATTCATATGTAGAAGAATGAA 3284
                          v  i        i i   v  v -     ?i  i   i i         
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACT-GGATAKCCACATGCAAAAGAATGAA 449

  chrX_108307570_   3285 -CTGGACCCCTGTGTCTTGCCATATACAAAAATCAAATCAATATGGCTTA 3333
                         -i         iiv  vii              i  v    v    v i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_108307570_   3334 AAGACTTAA------GACCTCAAGCTATGAAACTACTAAAAGAAAACATT 3377
                         ?    i   ------  v  v  i    i     vi  i          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_108307570_   3378 GGG--AAATCTCTCAAGGACATTTGTCTGGGCAAACCTTTTTCGAGTAAT 3425
                           ?--      -  i-v   v  v vi i     vvv   i iiii  vv
  L1M4_orf2#LINE/    550 GGNGTAAATCT-TCG-TGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_108307570_   3426 ACCCCACAAGCACAGATAACCAAACCAAAAATGGACAGATGCGATCATAT 3475
                           v   v       iii   v   vv      i  i i  vv  iivi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_108307570_   3476 CATG-TTAAAAAGCTTCTGCGTAGCAAAGGAAACAATAAACAAATTGAAG 3524
                           vi-       -   i  i ivv       v  v  v  v   v    i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_108307570_   3525 AGATAACTCAGAGAATGGGAGAAAATATTTGCAAGCTACCTATCTAACAA 3574
                            i   i  v                       iii iv     i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_108307570_   3575 GAGATGAATAACCAGAATATATAAGGAGCTCAAACAACTCTATAGGAAAA 3624
                          i  ivvi  v             i  i   vv       v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_108307570_   3625 AT-CTAGTAATCCAATCAAAAGATGAGCAAAATATTTGAAAAGGCGTTAC 3673
                          v- v i   i     i?   i   i     iv       v  i i  v 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_108307570_   3674 TCAAAAGAAGACATATACAAATGTCAAACAGGCACATGAAAAGGTGGGCA 3723
                           v        --          v v  i i            i  vv  
  L1M4_orf2#LINE/    847 TCCAAAGAAGA--TATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_108307570_   3724 ACATTAGTGATCAT 3737
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


3399 26.33 0.88 0.44  chrX_108337796_108342011.rev     2822  3725 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108337796_   2822 TGAAAAGGGATTCCATGTTCATGGATTGGAAGAACCAATATTGTTAAAAT 2871
                           i    iv  i                     vii           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108337796_   2872 GTTTGTACTACCCAAAGCAACCTACATGTTCAATGAAATCTCTAGCAAAA 2921
                          vivi    v      vii i     vi     i v    i   v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108337796_   2922 CACCAATGATATTCTTCACAGAAATAGAAAAA--AATTCTAAAATTTTTA 2969
                         iv   iiviiv  i  ii       v  v  i--i  i        iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_108337796_   2970 TAGAACAACAAAAGATCCAGAATAGCCAAAGCTACCCTAAGCAAAAATAA 3019
                          i   vvi   ii  i              i v i i i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_108337796_   3020 CAGAACTGCAGAAATCATATTATCTGACTTCAAGTTACACTACAGAGCTA 3069
                           i ii  v  i v   i i vi ii i     ivivi      i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_108337796_   3070 TAGTAAACAAAACAGCATGGTGCTGGCATAAAAACAGACACATACTTTAA 3119
                         i     v   i    ii    i         ii i     i   vv i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_108337796_   3120 TGGAACAGAATAGAGAACCTAGAAACAAATTCACACACTTACAGTGAACT 3169
                              i     v    ii i     i   ii  i   i   ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_108337796_   3170 CGTTTTTGACAAAGGTGCTGAGAACATACACTGGGTAGGGAAGAGTCTTT 3219
                         vi    i     i     ii   v   v  v    v ii   v       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_108337796_   3220 TCAGTGAATCATGGTGGGAAAACTGGATATCCATATGCAGAAGAATGAAC 3269
                            iii   vi  v     v         ?   i     i         v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_108337796_   3270 CTATAGCCCTATCTCTCACCATATACAAAAATTAAATAAAAAATGGATTA 3319
                         i iv v     i   v                   v v    -     i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGATCA 499

  chrX_108337796_   3320 AAGACTTAAATCTAAG-GCCACAAACTAGAAAACTACTACAAGAAAACAT 3368
                         ?    i     v    -  i -      v      vi  v          
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_108337796_   3369 TGGGGCAAATCTCTAGGACATTGGTCTGGGCAAAAATTTCTTGAGTAATG 3418
                         v  ? i      iiiv   v    vi i     vii      iii  -  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TG 597

  chrX_108337796_   3419 CC-CCACAAGTGCAGGTGACCAAAGCAAAAATAGACAAATGGGATCATAT 3467
                         v -   v   ii  i ii  v    v         i    v   iivi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_108337796_   3468 CAAG-TTAAAAAGCCCCTGCATAGTGAAAGAAACAATCAACAAAGTGAAG 3516
                            i-       - iii  iiivvii  i  v  v     v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_108337796_   3517 AGACAATCCATAGCATGGTAGAAAATATTTGCAAACTACCCATCTGGCAA 3566
                               i   i  v    v                ii ivi     ii  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_108337796_   3567 AGGATTAGTAATCAGATTGTATAAGGAGGTCAAACATCTCCATAGGAAAA 3616
                         i   i v   vi    v i     i  iv  vv   v   v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_108337796_   3617 AAAT---TAATCAAATTTTAAACTGGGCAAAAGATGTGAATAGACATTTC 3663
                          i i---   i v    ?v   v        i   v              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_108337796_   3664 TCAAAAGAAGATGTGAAAATGGCTAACAAGCATATGAAAATGTGTTCAAC 3713
                           v         i iv       i  i     i       vi  i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_108337796_   3714 ATCATTGATCAT 3725
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (150 / 84)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


3057 28.71 0.22 0.33  chrX_108364494_108369614.rev     3722  4630 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108364494_   3722 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATTAATATCGTGAAAAA 3771
                              ii i  i     i        v      v       i  v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108364494_   3772 AGCCATACTGCCCAAGGTAATTTATAGACTCAATGCTATCCCCATCAAGC 3821
                         i  v     v     iv i  i  i   i    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108364494_   3822 GACCATTAACTTTCTTCACAGAATTGGAAAAAACAACTTTAAATTTCATA 3871
                         vv   vivi i  i  ii     v v  v  ivii iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_108364494_   3872 CGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAAGAA 3921
                         i    viiv  ii  v  viv  v     i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_108364494_   3922 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 3971
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_108364494_   3972 CAGTAACCAAAACAGCATAGTAATGGTACCAAAACAGATATATAGATCAA 4021
                               i   i    ii i   v   i iv ii i   i           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_108364494_   4022 TGGAACAGAACAGAGGCCTCAGAAATAACCCCACACATCTACAACCATCT 4071
                              i    iv   ivii         v    i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_108364494_   4072 GGTCTTTGACAAACCTGACAAAAACAAGCAATGGGGGAAAGGATTCCCTA 4121
                          i i  i     ivv  v   i v  vv        -    i  vvi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTT 399

  chrX_108364494_   4122 TTTAAAAAATAGTGTTGGGAAAAATGGCTAGCCATATGCAGAAAACTGAA 4171
                           i  v    i   i     v  v   v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_108364494_   4172 ACTGAATCTGTTCCTTACACCTTATACAAAAATTAACTGAAGATGGATTA 4221
                         ii  i i iv v   i     v                v  i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_108364494_   4222 AAGACTTAAATGTAAGGCCTAAAACTATACAAAGTCT-AGAAGAAAACTT 4270
                         ?    i          iv           -   v   -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACAT 548

  chrX_108364494_   4271 AGGCA-ATATCATTCAGTACATAGGCTTTGGCAAAGACTTCATGACTGAA 4319
                            ?i- v   -   ivv  v v  v  v     v ii   v iiv ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_108364494_   4320 ACATCAAAAGTAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCTT 4369
                            i      i vvi          vv     v  i    v   ii  v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_108364494_   4370 TAAACTAAAGAGCTTCTGCACAGTGAAAGAAACTGTCATTAGAGTGAACA 4419
                         i   v v  i i   i  ii vvii  i  v   i   vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_108364494_   4420 GGCAACCTACAGAATGGGAAAAAATTTTTGCAATCTATCCTTCTGGCAAA 4469
                          i     i           i     v       vii  viv    ii  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_108364494_   4470 TGGCTAATATGGAGGGTCTACAAAGAACTTCAACAAATTTACAAGAAAAA 4519
                         v i  vi   vv  ii v  i        iiv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_108364494_   4520 AACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCT 4569
                         i     i     v  i?    i    ii      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_108364494_   4570 CAAAACAAGACATTTATGCGGCCAACAAACATATGAAAAAAAACTCATCA 4619
                          v   v    i  vi vii      i  i  i       i vi    v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_108364494_   4620 TCACCAGTCAT 4630
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (153 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


3115 26.51 0.99 1.10  chrX_108379439_108385843.rev     5006  5914 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108379439_   5006 TGGAAGAACATTCCATGCTCATGGATAGGAAGACTCAATATCGTGAAAAT 5055
                              ii i  i     i        v        i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108379439_   5056 GGCCATACTGCCGAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5105
                            v     v  v  iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108379439_   5106 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTGAAGTTC 5153
                          v   iivi i  i  ii     -   --- v  i  - iii i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_108379439_   5154 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGATAATCCTAAGCCAAAA 5203
                                 viiv  ii  v  v v  v     i i    i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_108379439_   5204 GAACAAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTACAAGT 5253
                                 i      vv   i   v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_108379439_   5254 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAAGAGAGATATAGTT 5303
                                  i   i    ii         i iv ii v   v      v 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_108379439_   5304 CAATGGAACACAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5351
                                 i v  i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_108379439_   5352 CATCTGATCTTTGACCAACCTGACCAAAATAAG-AAATGGG-AAAGTATT 5399
                           vi    i  i   v ivv  -    i iv v-v      -    v  v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_108379439_   5400 CTCTATTTAATAAGTGGTGCTGGGAAAACTGTCTAGCCATATGTAGAAAG 5449
                         v   v  i  i  i           v     vv  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_108379439_   5450 CTGAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAAATG 5499
                         v    ii    i    v   i   i v              i        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_108379439_   5500 GATTAAAGACTTAAATGTTAGGCCTAAAACCATAAAAACCCTAGAAGAAA 5549
                            i ?    i       v  iv       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_108379439_   5550 ACCTAGGCCTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5599
                           v    ?v v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_108379439_   5600 AAAACACCAAAAGCAATGGCAAAAAAAGCCAAAATTGACAAATGGGATCT 5649
                          vi            vvi    v     vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_108379439_   5650 AATTAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5698
                         v  i   -     i -   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_108379439_   5699 AACAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGA 5748
                           v  i  i  i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_108379439_   5749 CAAAGGGCTAATATCCAGAATCTACAAAGACCTTAAACAAATTTCAA--A 5796
                         i  i  i  vi          v  i     v  ivv    --i    -- 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CTCAATAA 791

  chrX_108379439_   5797 GAAAAAAATCAAACGGCCCCATCAAAAAGTGGGCAAAGATTATGAACAGA 5846
                         v     i -    iii   v  i?    i         iv v    i   
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_108379439_   5847 CACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACCCATGAAAAAATG 5896
                           i     v        i  vi viii     i ii v        i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_108379439_   5897 CTCACCATCACTGGCCAA 5914
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


3603 19.17 4.15 2.35  chrX_108558155_108562398     2868  3759 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108558155_   2868 TGGGAAGACATTCCATGTTCATGGATTGGAAGACTTAGTATTGTTAAAAT 2917
                            i    i  i                         i         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108558155_   2918 GTCCATACTATTCAAAGAAATCTGCAGATT-AATGCAATCCCTGTCAAAA 2966
                          v v     vii    vvi    i      -  i         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108558155_   2967 TCCCAACGGCATTTTTCTTCAGAAATGGAATAA--TAATCCTAAAATTCA 3014
                              i v  v     - v       v  -i  -- i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chrX_108558155_   3015 TATGGAATCTCAAAGAACTATAAATAGCCAAAGCAATCTTTAAAAAAATA 3064
                                viv   i i  ivvi          i       v     i --
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA-- 196

  chrX_108558155_   3065 AAGAAAGAAAGAAAACTAGTGGCCTCACACTTCCTGACATCAAAACATAT 3114
                         -----    v-   ii i v  v           ii iv       v  i
  L1M4_orf2#LINE/    197 -----AGAAC-AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_108558155_   3115 TATAAGTTTACAGTAATCAAAACAGTATG-TAGTAGCATAAAGACAGGCA 3163
                           i  ivi            i     i  -  v i      i  i  i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_108558155_   3164 TATAGACCAATGAAACAGAAGAGAGAACCCAGAAATAAATCTTCACATAT 3213
                               i     i  i    vv    ii           i ivi    v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_108558155_   3214 ATGGTCAAAGAATCTTCGACAAAAGTGCCAAGGC--TTCAAAATGGGGAT 3261
                                 vvi  i        ii        i --     --      v
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAA 388

  chrX_108558155_   3262 AGGATAGTTTCTTC-------GG-----------CTGGATATTACAAATA 3293
                           i     i i   -------  -----------       ?i-  v  i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC-CACATG 437

  chrX_108558155_   3294 CAAAA-AATAAAGTTGGACACTTACCTTAAACCATATACAAAC-TTAACT 3341
                              -   i         v i     i v            v-      
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_108558155_   3342 CAAAATGGATTAAACACATAAATATAAGACCTGAGACTATGAAACTCCTA 3391
                                   i ? v  v     i     v  i i     i      i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_108558155_   3392 GAAGAAAACAT-GGTGAAAAGCTTCATTACATTGGATTAG-CAATGATTT 3439
                                    -  ? v   v    i v  v    i    -     i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_108558155_   3440 CTCCAATATGCACACCATACGCACAGGCAACAAAAGCAAAAATAGACAAA 3489
                           ivi     -      v v     i          v         i   
  L1M4_orf2#LINE/    588 CTTAGATATG-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_108558155_   3490 AGAGAATACATCAACCTTAAGAAACTTCTACAGAGCAGAGAAGACAGCCA 3539
                         vvi  v v      vv    -      i iiivvv  i  i v  vii  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_108558155_   3540 ACAGAGGAGAAAGGCAATCCATAAAATTGGAGAAA-TATTTGCAAACCAT 3588
                          v i  vii    i   i   i i   v       -          i   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_108558155_   3589 ACATCTGATAAGGAGTTAATATCCAGAATATGTAAAGAACT---ACAACT 3635
                          i           iii vi            i         ---      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_108558155_   3636 TATCAACAACAAAAAGA-----AATCCAATTTAAAACTGGACAAAATACT 3680
                         ---   i  i       -----  i      ?    v   i    iv i 
  L1M4_orf2#LINE/    786 ---CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_108558155_   3681 TGAATAGACATTTATCCAAAGAAGATAAAGAAATGGCTAAAAAGCAAATG 3730
                                      v             v v       i  v     v   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_108558155_   3731 AAAAGATGCTCAATCGCATTAATCATTAC 3759
                                      ---   i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAA---CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (102 / 65)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.52 (58 / 23)  


3193 27.34 0.55 0.44  chrX_108569350_108574885     4137  5043 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108569350_   4137 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4186
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108569350_   4187 GGCCGTACTGCCCAAGGTAATTTACGGATTCAATGCCATCCCCATCAAGC 4236
                            vi    v     iv i  i   i       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108569350_   4237 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4284
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_108569350_   4285 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAACCCTAAGCCAAAAG 4334
                                viiv  ii  v  v v  v     iv   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_108569350_   4335 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATCCTACAAGGC 4384
                                i      vv    i  v  ii i      viv v      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_108569350_   4385 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGTTATAGATC 4434
                                 i   i    ii         i iv ii i   vv        
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_108569350_   4435 AATGGAACAAAAC--AAAGCCCTCAGAAATAAGACCGCATATCTACAACT 4482
                                i i  i-- i  i  --        iv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_108569350_   4483 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGCGGAAAGGATTCC 4532
                          vi    i  i     ivv  v   i v  vv     v      i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_108569350_   4533 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4582
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_108569350_   4583 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4632
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_108569350_   4633 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAACCCCTAGAAGAAAAC 4682
                          i ?    i       v   v       i       i i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_108569350_   4683 CTAGGCAATAGCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4732
                         v    ?ivv iiv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_108569350_   4733 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4782
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_108569350_   4783 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4832
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_108569350_   4833 AGGCAACATACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4882
                           i    vi   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_108569350_   4883 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4932
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_108569350_   4933 AT-CAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 4981
                          v-    i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_108569350_   4982 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5031
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_108569350_   5032 ATCACTGGCCAT 5043
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


1760 27.22 6.15 7.24  chrX_108633086_108637846     3358  4268 (493)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_108633086_   3358 ATGTATCATGTTCATAATTAGGCACACTCAATAC-----------CAATT 3396
                           i vi         iiv v  v v   i    i-----------    v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_108633086_   3397 CTTCTCAAATTAATCTCTAGAGTCAATGAAATTTCAATTCAAATTTCAAC 3446
                           i i      i    vi   v    i v   ii v  iv    ii  i 
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_108633086_   3447 AGGGCTTTTCATTGAATTTGGCAA-CAAATTTTAAAATTTATATAGGAGA 3495
                         v vvi    iiiv   v   i   - vi  ii       i    i i iv
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_108633086_   3496 ACAGAGTGCCAAGAATAGTGAAGACTATTCCTGAAAGAAAAAGAATCAAG 3545
                         i  ii vi  v       iv  i  v  - i     -  i     iv   
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAA-AAGAAGAACAAAG 205

  chrX_108633086_   3546 TAGGGAGATTTGCCTGAACAAATATTGAGACTTAATATAAAGCCATAGGG 3595
                          v  ii  i ii ----------------    ---------  ------
  L1M4_orf2#LINE/    206 TTGGAGGACTCAC----------------ACTT---------CC------ 224

  chrX_108633086_   3596 GCATATGTTCTCAGGACCTCCGTCATGGAAAAAAAAAAAAGCTACAGTAA 3645
                         -  ---i  -   ii  i v ---- --------- v             
  L1M4_orf2#LINE/    225 -CA---ATT-TCAAAACTTAC----T---------ACAAAGCTACAGTAA 256

  chrX_108633086_   3646 ATAAGACAATATGCTATTGAGGCAGGGGTTTACCAATGGACTAATGGAAC 3695
                         vi      i i  v  i  ivii i  i vv  vv  i  ii       i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_108633086_   3696 AAAAT-GGGGGCTCAGAAATAGATCCATAAATATATGG--AACTG----- 3737
                          i   - i i ii        i i     v  v     --  i  -----
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_108633086_   3738 TGACA----TATCAGAGATCACTGCAGATCATTGAGGAAGGAGT-GACTA 3782
                         i    ---- ii  -   i  i ------  v  i    i  i - v  v
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCA-AGACCATT------CAATGGGGAAAGAATAGTCTT 399

  chrX_108633086_   3783 TTCAATAACTGGTTCTGGGACAGGTGATTATCCATATGCCAAAAAC---A 3829
                              i  v    v        iv  iv  ?   i    v   i v--- 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_108633086_   3830 ATTAGATCCCTATTATACACCATACATAAAA-TAAAGTCCAGATGGACTG 3878
                         i  i  i     iivi        i i    - v  v  v i     iii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_108633086_   3879 AAGACTTAAATGTGAAAAGC-AAAATTTTTAAACTTTTAGAAGAAAACAT 3927
                         ?    i       -  i   -    i v v     i              
  L1M4_orf2#LINE/    500 WAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_108633086_   3928 AAGAGAATATCTTGTTGACTTTAATGTAGTAAAGGATTTTTTGAACAAGG 3977
                          i ? v v     vv    i  iivv   vv  v i   i  ii i v i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_108633086_   3978 CTGAAAAAGCACTAACCATAAAAATAAAGACTGACTAATTAGACTACATT 4027
                          vvv        v i v i    iv   i iv  iv    i    v   i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_108633086_   4028 AACATTTTGAATTTCTGTTTGACAAAAGGCATCATAAAGAAAATGGAGAG 4077
                           v   vvi  i  i   vivv    i i  ii  v      i  i i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_108633086_   4078 ACAAGCTACA-AACGTGGAGGAGGTATTTACAA----CATAACCAAAAAA 4122
                             v i   -  i -    i ii     i   ----i   v ii v  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATG-GGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_108633086_   4123 AGATTCCTATCCAAAAATATAAATATAAATAATTCCTACAGATTTTTT-- 4170
                         i  i iv      i  -    ----    v  i  i    - i ivv --
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAA-TATA----TAAAGAACTCTTACA-ACTCAATAA 791

  chrX_108633086_   4171 TAAA----------------TGTAAAAATGGGCATAGGCCATGAACATTC 4204
                             ---------------- v?           v   viv    i vv 
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_108633086_   4205 ATTTTAC---AGAAGAAACACAAATGGTCAATAAGCATATGAAAAGATGC 4251
                             iv ---      v i        i         i            
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_108633086_   4252 CAAACTTCATGAATAAT 4268
                         iv   v   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (151 / 93)
Gap_init rate = 0.03 (31 / 901), avg. gap size = 3.94 (122 / 31)  


3238 26.73 0.55 0.66  chrX_108652829_108658680     4451  5359 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108652829_   4451 TGGAAAAACATTCCATGCTCATGGATAGGAAGAGTGAATATTGTGAAAAT 4500
                               i i  i     i        v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108652829_   4501 AGCCATACTCCCCAAAGTAATTTATAGACTCAATGCTATTCCCATCAAGC 4550
                         i  v            v i  i  i   i    i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108652829_   4551 TATCA-CTGACTTCCTTCACAGAATTAGAAAAAAAACT-ACTTTAAATTT 4598
                          vi  -   v   ii  -i     v v  v  i---  - iii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chrX_108652829_   4599 TATATGGGACCAAAAATAGCAC-GTATAGCCAAGACAATCTTAAGCAAAA 4647
                         i      i viiv  ivii v - v        i        i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_108652829_   4648 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAATTATACTACAAG 4697
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_108652829_   4698 GCTACGGTAACCAAAGCAGCAAGGTACTTGTACAAAAACAGATATATAGA 4747
                              i    i   ii   iiv      v i i  ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_108652829_   4748 CCAGTGGAACAGAACAGAGACCTCAGAAATAATACCACACATCTACAACC 4797
                         i  i     i    iv    vii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_108652829_   4798 ATCTGATCCTTGACAAGCCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4847
                          vi    ii i      vv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_108652829_   4848 CTATTTAATATATGGTGCTGTGAAAACTGGCTAGCCATATGTAGAAAGCT 4897
                           v  i  i v         v  v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_108652829_   4898 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 4947
                            ii    i    v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_108652829_   4948 TTAAACACTTAAACGTGAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4997
                          i ? v  i    i  i   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_108652829_   4998 CCAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAAGACTTCATGACT 5045
                         vi   ?-   --i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_108652829_   5046 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5095
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_108652829_   5096 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5145
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_108652829_   5146 ACAGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTATCCATCTGAC 5195
                          v  i     i       i         v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_108652829_   5196 AAAGGGCTAATATCCAGAATCTATAAGGAACTTAAACAAATTTACAAGAA 5245
                           i  i  vi          v     i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_108652829_   5246 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5295
                            i     i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_108652829_   5296 TTTCAAAAGAAGACATTTATGCGGCAAACAAACATATGAAAAAAAGCTCA 5345
                          i  v        i  vi vii   v  i  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_108652829_   5346 TTATTACTGGTCAT 5359
                         vi  i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3190 27.97 0.22 0.22  chrX_108693541_108699812     4872  5779 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108693541_   4872 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4921
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108693541_   4922 GGCCACACTGCCCAAGGTAATTTACGGATTCAATGCCATCCCCATCAAGC 4971
                            v i   v     iv i  i   i       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108693541_   4972 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5019
                          vi  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_108693541_   5020 TATGGAACCAAAAAAGAGCCAGCATCGCCAAGTCAATCCTAAGCCAAAAG 5069
                                viiv  ii  v    v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_108693541_   5070 AACAAAGCTGGGGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5119
                                i   i  vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_108693541_   5120 TACAGTAGCCAAAACAGCATGGTACTGGTACCAACACAGAGATACAGATC 5169
                                ii   i    ii         i iv iv i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_108693541_   5170 AATGGAACAGAACAGAGGCCTCACAAATAACGCCACATATCTACAACTAT 5219
                                i    iv   ivii  v      vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_108693541_   5220 CTGATCTTTGACAAACCTAAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5269
                         i    i  i     ivv ivv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_108693541_   5270 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5319
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_108693541_   5320 AACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAAATGGATT 5369
                          ii    i    v   i     v  i        i  i           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_108693541_   5370 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5419
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_108693541_   5420 AGACATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5469
                           i?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_108693541_   5470 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAACTAATT 5519
                                    vvi          vv     v  i    v   vi v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_108693541_   5520 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5569
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_108693541_   5570 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTGCTCATCTGACAAAG 5619
                         i     i   i             v  i    viiiivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_108693541_   5620 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5669
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_108693541_   5670 ACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCTC 5719
                              i     v  i?    i    ii     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_108693541_   5720 AAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5769
                         v        i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_108693541_   5770 CACTGGCCAT 5779
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.53 (151 / 99)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


3699 23.65 2.13 0.34  chrX_108803427_108808059     3249  4140 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108803427_   3249 TGGAAAAATATTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 3298
                               i    i                     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108803427_   3299 GTCCATATTACTCAAAGCAATCTACAGATTCAATGCAATCTTGATCAAAA 3348
                          v v   i v i    vii              i      iiv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108803427_   3349 TACCAATTACATTCTTAACAGAAAT--ACAAAAAAAATCCTAAAATTTAT 3396
                          v   ii i v  i  vi       --    ivvi -          i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_108803427_   3397 ATGGAACCACAAAAGACCTAGAATAGCCAAAGCTATCCTGAGCAAAAAGA 3446
                               vii   ii    i            i v   i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_108803427_   3447 ATAAAACTAGAGGAATCACATTACCTGACTTCAAATTATACTACAGAACT 3496
                          i   ii i     v     i v  ii i      viv       i i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_108803427_   3497 ACAGTAACAAAAATAGCATGGTACTGGCATAAAAATGGACACATAGACTA 3546
                                iv  i i  ii              ii  i    i     ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_108803427_   3547 ACGGAACAGGACAGACAACTCAGAAACAAATCCATACATCTACAGTGAAC 3596
                          i    i  i iv  v iii      i   i        i  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_108803427_   3597 TCATTTTCAACAAAGGTGACAAGAACATACATTAAGGAATAGACAGTCTC 3646
                          v      i    i    v     v   v  v ii    vii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_108803427_   3647 TTCAATAAATGGTGTTGTGAAAACTGGATATCCACATGCAAAGGAAAAAA 3696
                              i        i  v  v         ?           i   vi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_108803427_   3697 ACTAGACCCTTGTCTCTCACTATATACAAAAGTCAAATCAAAATGAATTA 3746
                         ii i     i ii   v   i          i i  v        i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_108803427_   3747 AAGACTTAAATCTAAGACCTCAAATTATGAAACTACTACAAGAAAA---- 3792
                         ?    i     v     v  v   i   i     vi  v       ----
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_108803427_   3793 -------ATCTCCAGGACATTTGGAGTTGGCAAAGATTTCTCGAGTAGTA 3835
                         -------    i iv   -i    iv v     v i     iiii  vv 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_108803427_   3836 CCCCACAAGCACAGGCAACCAAAGCAAAAGTGGACAAATGGAATCACATC 3885
                          v   v       i     v    v    i i  i    v i iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_108803427_   3886 AAG-TTAAAAAGCTTCTGCACAGTAAAAGAAACAATCAACAAAG-----A 3929
                           i-       -   i  ii vvi   i  v  v     v    ----- 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_108803427_   3930 AACAACCCACAGAATGGTAGAAAATGTTTGTAAACTACCCATCTGACGGG 3979
                         i                v       i    i   ii ivi      iii 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_108803427_   3980 GGATTAATAACCAGAATATATAAGGAGCTCAAACATCTCTATAGGAAAAA 4029
                            i vi  v             i  i   vv   v   v   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_108803427_   4030 ATCTAATAATTCAATTTAAAAATTGGCAAAAGATTTGAGTAGACATTTCT 4079
                         iv v     ii     ?      v      i       i           
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_108803427_   4080 CAAAAGAAGACATACAAATGGCAAACAGGCGTATGAAAAGGTGCTCAATA 4129
                          v        i           v  i i  ii        i       i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_108803427_   4130 TCATTGATCAT 4140
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.01 (139 / 69)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.14 (22 / 7)  


1020 23.35 8.17 1.17  chrX_108816298_108820102     1973  2229 (1576)    L1M4_orf2#LINE/L1        3   277 (631)  

  chrX_108816298_   1973 GAGGGATATTCCATGTTCA----------------ATATTGTCAAGATAT 2006
                           ii     i         ----------------       i     iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_108816298_   2007 CAGTTCTTCCCAACAACTTAATAAATAGATTCGATGCAATCCCAATCAAA 2056
                           i v  i     -- -  i  vv i      i i        v      
  L1M4_orf2#LINE/     53 CAATACTCCCCAA--A-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_108816298_   2057 ATCCCAGAGAGTTATGTTGCGGATATCAGCAAATTGATTCTAAAGTTTAT 2106
                                vvivi v v    i  v  iii   ii    i     i  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_108816298_   2107 AAAGAGAGACAAAAGTCCCAGAATAGCCAACATAATATTGGA---GAAGA 2153
                          vi  i vi   ii v              v i   v   i ---     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_108816298_   2154 GCAAAGTTGGAGTACTGACACTACCCAACTTTAAGACTTACTATAAAGCT 2203
                         i           v   v     v     i  i  i        i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_108816298_   2204 ATGGTAATTAAGATGATATGGT--TGGC 2229
                          ii     i    iii i    --    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGC 277

Transitions / transversions = 2.16 (41 / 19)
Gap_init rate = 0.02 (5 / 275), avg. gap size = 4.80 (24 / 5)  

 552 23.08 2.96 3.55  chrX_108816298_108820102     2521  2689 (1116)    L1M4_orf2#LINE/L1      259   426 (482)  

  chrX_108816298_   2521 AAGATGGTATGGCATTGGTAAAAGAA-AGACAAATAGATTAATTGAATAG 2569
                             ii  i   i i   i v   i -     v      i   v      
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_108816298_   2570 AATAGACTAAAGAGCATAGAAATAGATTCACATAAACATAGTCAACTGAT 2619
                            v  -----   ivi       i ii  i i vvi  i     i    
  L1M4_orf2#LINE/    309 AATTGA-----GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_108816298_   2620 CTTTCACAAAGGAGCAAGGACAATACAATTGAGCAAAGAA-AGTATTTTC 2668
                         i  iv    i  v  v i   v  v    v i -      -   v     
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTC 402

  chrX_108816298_   2669 AACAAACGGTGCTG---CAGCTGG 2689
                               i       ---  i    
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGG 426

Transitions / transversions = 1.79 (25 / 14)
Gap_init rate = 0.03 (5 / 168), avg. gap size = 2.20 (11 / 5)  

1880 23.56 0.99 0.79  chrX_108816298_108820102     2809  3313 (492)    L1M4_orf2#LINE/L1      403   908 (0)  

  chrX_108816298_   2809 AAAAAATGGTACTTGAACAACTGAACATCCACATGCAAAAAACAGAATCT 2858
                           v       i  v i       i i ?            i vv   vi 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_108816298_   2859 AGAC----ACGACTTACACTTTTCACAAAGATTAGCACAAAATGAATCAT 2904
                         i   ----  --  i    iv vi     i    i v       i    ?
  L1M4_orf2#LINE/    453 GGACCCCTAC--CTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_108816298_   2905 AGAGCTAAATGTTAGATGC-AAAAGTGTAAAACTCCTAGAAGGTAACATA 2953
                            v        v   -  -    v i        i      iv      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_108816298_   2954 GGAGAAAATCAAGATGACCTTGGGTATGGTGATGACTTTTTAGATATAAC 3003
                           ? v     vvvi           vv  ii   ii  i        i  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_108816298_   3004 ACCAAAGGCACAGTCCACAAAAGAAATAATTGATAGATGGGATTTCATTA 3053
                               i     iv v          v   v    i  v   i     i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_108816298_   3054 AAATAAAAAACACACGCTCCTCAAAAGATACTGTTAAGAGAATGACAAGA 3103
                             v      vivi iv i     i  i   i i    i i   v    
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_108816298_   3104 CACAACACAGGCTAGGAGAAAATATTTGGAAAAAACATATCTGATTTAAA 3153
                           vvv     iv i              v   vv i         vviii
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_108816298_   3154 AATTGTTATCCAAAATTTGCAAATAACTGTCAAAACAGAACAATAAGAAA 3203
                          v    -     i   v ii   v    v i v   vv  i     i  i
  L1M4_orf2#LINE/    750 ACTTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_108816298_   3204 ACAAACAATTCAATTGAAAAATGGGCAAAAGACCTGAACAGACACCTAGT 3253
                              i  ii     ?             i  ii    i     ii vvi
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_108816298_   3254 CAAAGAAGATATACAGATGGCAAATAAGCGTGTGAAAAGATGTTCCACAT 3303
                                        i     v       iii          i  v    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_108816298_   3304 CTTATATCAT 3313
                          v????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.35 (66 / 49)
Gap_init rate = 0.01 (5 / 506), avg. gap size = 1.80 (9 / 5)  


3357 26.34 0.33 0.66  chrX_108945091_108951502.rev     5011  5921 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_108945091_   5011 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5060
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_108945091_   5061 GGCCATACTGCCCAAGGTAATTTATAGATTTAATGCCATCCCCATCAAGC 5110
                            v     v     iv i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_108945091_   5111 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5158
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_108945091_   5159 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAGG 5208
                                viiv  ii  v  v v  v     iv     i i ivv i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_108945091_   5209 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5258
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_108945091_   5259 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5308
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_108945091_   5309 AATGGAACAGAACGGAGCCCTCAGAAATAATGCCACATATCTACAACCAT 5358
                                i    iv   vvii         vv   i i  i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_108945091_   5359 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATTCCCT 5408
                         i    i  i     ivv  v   i v  vvv          vi  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_108945091_   5409 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAGAAAGC 5458
                         v  i  i              v      v  ?   i   i ii    ---
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--- 445

  chrX_108945091_   5459 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5508
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_108945091_   5509 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5558
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_108945091_   5559 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5607
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_108945091_   5608 ACAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5657
                          ii            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_108945091_   5658 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGTGA 5707
                         v  i   v v  i i   i  ii vv    i  v    i  vv v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_108945091_   5708 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGAC 5757
                          v  i     i                 v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_108945091_   5758 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 5807
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_108945091_   5808 AAGAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACACT 5857
                           ii     i     v  i? v  i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_108945091_   5858 TCTCAAAAGAAGACATTTATACAGCCAAAAGGCACATGAAAAAATGCTCA 5907
                             v        i  vi v ii     v i           i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_108945091_   5908 TCATCACTGGCCAT 5921
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2948 18.33 1.45 14.84  chrX_109017529_109022873.rev     3824  4854 (491)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_109017529_   3824 TGTTCATGGGTTGGAAGACTAAATATTGTTAAGAGGTCAATTGTCTTTCA 3873
                                  i          v             v v    vv  iiiv 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_109017529_   3874 TTTTTTCAACATATTTACCATAATTTCAATAAAAATTTCAGAAGGCTTTC 3923
                         v  vv  v   v   i v ii   ii v  v     ii   vv v    i
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_109017529_   3924 TTATGGCATTTGACAATATGACTCTAAAAATCACATAGAAATGCAAAGTA 3973
                           iii v v       vv   ii      v   i  i         i v 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_109017529_   3974 CCTAGAATAGCCATAACAATTTTGAAAA----GAACAAAGGTGAAAGACT 4019
                           i          v      i       ----        v  i i    
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_109017529_   4020 AACACTATCTGATTTTAAGGCTTCTTATAAGGCTACAGTAATTCAGACAG 4069
                         v     vi ii    i  ii   vi  i  i           iv      
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_109017529_   4070 TGTGGTACTGGCATAAAGATAGACAAATAAATCAACGGGACAGAATAGAG 4119
                                         i        v   i     i  i i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_109017529_   4120 AGACCAGAGATAGACCTACACATATATGAACAACTGATTTTTTTGAGAGA 4169
                           v     i   i   i i    v    iv   i       i--------
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC-------- 357

  chrX_109017529_   4170 TGGGGTCTTGCTATGTTGCCCATTGCCCAGGCTGGTTTCAAACTCCTGGC 4219
                         --------------------------------------------------
  L1M4_orf2#LINE/    358 -------------------------------------------------- 357

  chrX_109017529_   4220 CTCAGACAATCCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGTA 4269
                         ----     ----------------------------   ----------
  L1M4_orf2#LINE/    358 ----GACAA----------------------------GGG---------- 365

  chrX_109017529_   4270 CACACCACTGCACCAAGATAGCAACAACTGATTTTTGACAAAGCTGCAAA 4319
                         --------   --     i-------------------------------
  L1M4_orf2#LINE/    366 --------TGC--CAAGAC------------------------------- 374

  chrX_109017529_   4320 AGCATTTCAGTGGAAAAAGTGTAGTCTTTTCAACAAATGGTACTGAAAAA 4369
                         --    -  i   ii    vi                    i   ii v 
  L1M4_orf2#LINE/    375 --CATT-CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_109017529_   4370 GTTAGCTATCCAAATGCATAAAAATAAACTTTGATTCATATCCCACTATG 4419
                         ii i v  ?   v     v  i   i  v  v  ii v  i i   vvii
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_109017529_   4420 TATATAAAAATTAACTAAAAATGGATCATAGACCTAAATGTAAAAGAGAA 4469
                             i           v           ?              i  ----
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG---- 517

  chrX_109017529_   4470 AACCTAAAACTA-AAAGTTCT-AGAAGAAAACATAGGAGAAAATATTTGT 4517
                         ---         -   ii   -               ? v    v  i  
  L1M4_orf2#LINE/    518 ---CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_109017529_   4518 GACTTTGGATTAGGGAATGATTTCTTAGGTATGACATGAAAAA-ATGATT 4566
                            i    i     v    i        i       iv    i- ii v-
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG- 613

  chrX_109017529_   4567 CATCAGAGAAAAAAATTGAAAAATTTGATTTCACCAAAATTAAAAACTTC 4616
                           v  i ii       v  v     v  i    i               i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_109017529_   4617 TGCTCATCTAAAGATACTGTTAAAAGAATGGAAAAACAATTGACAGA-TG 4665
                           iv v  v  i  i   i i  i i i  i   i    iiv     -  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_109017529_   4666 GGA-AAAATATTTGCAAATAATATGTCTGATAAAGAATTTGTATCTAGAA 4714
                            -               v    i        i i i       i    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_109017529_   4715 CATATAAA-ATCTCTCAAAA-TCCATAATAAGAAC-C---TAATCCAATT 4758
                         i       - v    i v  -  v       i  v- ---   i      
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_109017529_   4759 TTTAAAGTGGGAATAAGATTTGAATAGACACATCACCAAAGATGATATAC 4808
                         ?v-   i    v v i              iv  v       v       
  L1M4_orf2#LINE/    814 WA-AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_109017529_   4809 ATCTGGCAAACAAGTGCATGAAAAGATGCTCACCATTATCAGTCAT 4854
                          vv    v  i   ii                v   i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (112 / 73)
Gap_init rate = 0.02 (19 / 893), avg. gap size = 8.84 (168 / 19)  


2809 27.04 1.21 0.99  chrX_109123083_109128056.rev     3578  4483 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109123083_   3578 TGGAAAAGTATTAGATTCTCATGGATTAGAATAATCAACATTGTTCAAAT 3627
                               ii   ivv  vi         i   v v i  i      v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109123083_   3628 GGCCATACTACCCGAAGCAATCTACAGATTCAATGCTACTCCTATCAAAC 3677
                            v     v   i  vii              i  v ii         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109123083_   3678 TACCAAAGTCATTCTTCACAGAATTAGAAAAAACT-ATTCTAAAATCCAT 3726
                          v   ivvv v  i  ii     v v  v  i-  -  i       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_109123083_   3727 A-GATAAC-CAAAAAACAGCCCAAATAGCCAAAGCAATCCTGAGTAAAAA 3774
                          - iv  i-   iii  --  vi          i     i   iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_109123083_   3775 GAACAAACCCAGAGGTAC-CGCATTACCTGACTTCAAACTATACTACAAG 3823
                                viii    -  - i  i v  ii i      viv        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_109123083_   3824 GCTACAGTAACCAAAACAGCATGGTAGTGGTACAAAAACAGATACAAAGA 3873
                                   i   i    ii     v   i i  ii i   i i v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_109123083_   3874 CTAAAGGAATAGGATAGAGAACACAGATATAAAGCCATACACCTACAACT 3923
                         ii  v       i  v    iiv    v     v       ii  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_109123083_   3924 ATGTGATGTTCAGCAAAGTCAACAGAAGTAAACAATGGGGAAAGAACTCC 3973
                          vv    v   ii   i viiv  ii vi vv              ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_109123083_   3974 CTATTAAATAAATGGTGCTGAGAAAACTGGCTATACACGTGCACAAGAAT 4023
                           v  v  i           i  v      v  ?v   i    v      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_109123083_   4024 GAAACTGCACTCCTTCCTATCATGATATACAAAAATTAACTCAAGATGAC 4073
                            ii  v  i   v   vv  iv                    i   iv
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_109123083_   4074 TTAAACATTTAAATGTAAGCTCTCAAACTGTAAAAATCCTAGAAGAAAAC 4123
                          i ? v ii          vv  v     i     v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_109123083_   4124 CCAGA---AAATACCTTCTTGACATTGGCCATGGCAAGGAATTTATAGCT 4170
                         vi  i---    --    v    v    vivv     v iv  iv   v 
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_109123083_   4171 AAGTCCTCAAAAGCAACTAA--AACAAAAACAAAAATTGACAAGTGGGAC 4218
                          v v vi        --i  --       iv      v  i  i v    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_109123083_   4219 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTTATCAGCAGAG 4268
                         i v  i   v v  i i   i  ii vv    i  v   -    iv i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGAAAG 691

  chrX_109123083_   4269 TAAACAGACAACATACAGAATGGGAAAAAATATTCACAAACTACGCATCT 4318
                          i  v       vi           i        ii    ii iii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_109123083_   4319 GACAAAGATCTAATAACCCAAATCTATAAGAAACTTAAACAAATCAACAA 4368
                           i  i iv  vi  v  vi   v     ii    ivv    v    i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_109123083_   4369 GCAAAAAACAAATAACCTGACTAAAAAGTGGGCAAAGGACGTGAACAGAC 4418
                         vv    i          ii i ?    i           iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_109123083_   4419 ACTTCGCAAAAGAAGGCATACAAGCAGCCAACAAGCACATGAAAAAAT-C 4467
                          i   v v       ii      iii     i             i  - 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_109123083_   4468 TCT-TATCACTAACAGA 4483
                           v-i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.43 (20 / 14)  


 235 31.84 11.74 5.69  chrX_109131730_109133583.rev      530  1355 (499)    L1M4_orf2#LINE/L1        5   880 (28)  

  chrX_109131730_    530 AACATATC--ATGTCTTTTCCTGGAT-GACAGACTCTGTGTTGTGATGAT 576
                           v     --    ----  v     - iv     ivi i    v v   
  L1M4_orf2#LINE/      5 AAGATATCCCATGT----TCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109131730_    577 GTCAATG------AAATT---TTA--GGTTTAAAGTAGTTCCAATCAAAA 615
                          v    i------     ---i  -- i  i  v i i i  v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109131730_    616 TCCTGGTAGGATTTTGAGGAGAACCTGACAGAAAC--ATTCTAAG-TTCA 662
                            ii iv vv    vv v    vi     -- i --  i    i-    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA--AGCTGATCCTAAAATTCA 148

  chrX_109131730_    663 TTTGGACGAAAAAATGGTTGAGACTAGCTAAGA--------AAAAAGTGT 704
                          v    viviv  iv iiiv   v    i  i --------      ---
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG--- 195

  chrX_109131730_    705 GGGTAATGCGCTAGGCTGCAGAGAAAGCAAAAG---AAATCT---GGTTT 748
                         ----  - vi v i i  --   i vv  v vv---v   i ---iii  
  L1M4_orf2#LINE/    196 ----AA-GAACAAAGTTG--GAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_109131730_    749 ACCA----GCTGTTGCATATATAAGG--GTATGAAACTGATGGAAAACCC 792
                           i ----   iiv i -  -i   i--  i  iv    iiiv  iiviv
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTA-AT-CAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_109131730_    793 AAGAGAGAGATCAATG-AATAA---TACAAG--CTGAAA-AAATCC-TAG 834
                         i v v v         -    i--- ivi  -- v    -   i  -  -
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA- 335

  chrX_109131730_    835 CATATA-GAAGAATTTATGTATGATAAAAGTAT-AATAGCAATAATCATA 882
                            v  - ivv    v  v vi  i  ii  ii-  v v  v v --  i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA--ATG 383

  chrX_109131730_    883 GGAAAA---TAGTTATTT-GATGAATGGTGCTCAAATAAATGACTCTCTA 928
                           i   ---    iv   -i ii         vii i  v  iv v? i 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_109131730_    929 GGGG--AAAATAT-AAGCTATACTC-TACTTCATACTAGTCACAAAA-TG 973
                         viv --   iv  -   i iv  i -   i   i  i vvi      - v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_109131730_    974 AATTTTTGATGGACTGACAAGTTAAATATT---TTTAAAACTAT------ 1014
                           i ivvi     iii?vi vi     i v---vi         ------
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_109131730_   1015 TTTA-----AAACTGGATTGTTTTAAATCCCATTC-TAACCTTAGAATGG 1058
                         i   -----    ---  v v?v      ---   - i     i iv i 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAAC---ATAGGNGTAAATC---TTCGTGACCTTGGGTTAG 577

  chrX_109131730_   1059 GAAATGTCTTTTCAAGTGTAAAAGCAATGGAAGAAATTACCATGATCTGA 1108
                          v    vi  i i ii i i v v   vi v v  iiv  v ------- 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA-------A 620

  chrX_109131730_   1109 AGGGGGTTTAGAAATCAATCAATTTGAC--CAATAAAAATGTAAACCAAA 1156
                           i------ i    vi  v    v   --  vi    v iv    i---
  L1M4_orf2#LINE/    621 AGA------AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT--- 661

  chrX_109131730_   1157 TCTAT-TATCAAAAG-CATCATTAA-AAAGTTAGAAGACAATC------- 1196
                          i i -iv     i -  ii  i  -     v i       i -------
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_109131730_   1197 TGGG-GAAAACATTTACTGCAAA--AG-----TGATAAAAGATTAACACT 1238
                             -     i    ---     -- v-----      ii  i vii ii
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTT---GCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_109131730_   1239 CTTTATATATGTAAAACTCATACAAATCAACAAGGGAAACACCTGTA--- 1285
                          vvv      iv i     v     v    i  vii   v  vvi  ---
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_109131730_   1286 CA--TCAAAATTCAGCAGAGACCATGAGCTGACAAT-CTACAGAATAAAA 1332
                           -- ?    v vi   i  iviv   iiv    v -  v  -  v  i 
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA-AAGAAGA 857

  chrX_109131730_   1333 TATGTAAATAGCTAATAGATATA 1355
                            ii    i  i    iii i 
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACA 880

Transitions / transversions = 1.35 (149 / 110)
Gap_init rate = 0.06 (56 / 876), avg. gap size = 2.57 (144 / 56)  


3201 27.64 0.44 0.44  chrX_109140333_109146685.rev     4956  5863 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109140333_   4956 TGGAAGAACATTCCATGCTCATGGATAGGAAGTATCGATATTGTGAAAAT 5005
                              ii i  i     i        v     vv ii       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109140333_   5006 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5055
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109140333_   5056 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5103
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_109140333_   5104 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5153
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_109140333_   5154 AACAAAGCTGGAGGCATCATGCTATCTGACTTCAAACTATACTACAAGGC 5203
                                i      vv   ii  vi ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_109140333_   5204 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATGGACC 5253
                          i      i   i    ii         i iv ii i   v    i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_109140333_   5254 AATGGAACAGAAC--AGAGCCCTCAGAAATAGCACCACACATCTACAACC 5301
                                i    i--    i  --       ivv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_109140333_   5302 ATCTGATCTCTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTAC 5351
                          vi    i ii     ivv  v   i v  vvv           i  vii
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_109140333_   5352 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAACCATATGTAGAAAGCT 5401
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_109140333_   5402 GAAATTGGATCCCTTCCTTACACCTTATGCAAAAATTAATTCAAGATGGA 5451
                            i     i    v   i     v   i          i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_109140333_   5452 TTAAAGACTTAAATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAAC 5501
                          i ?    i       v   v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_109140333_   5502 CTAGGCAATAGCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTGA 5551
                         v    ?ivv iiv   iv   v v  vv i     v ii   v iiv iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_109140333_   5552 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5601
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_109140333_   5602 TTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACCAACATCAGAATGAAC 5651
                          i   v v  i ii  i  ii vv    i  v  i v  vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_109140333_   5652 AGGCAACCTACACAATGGGAGAAAATTTTTACAATCTACCCATCTGACAA 5701
                           i     i   v             v   i   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_109140333_   5702 AGGGCTAATATGCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 5751
                         i  i  vi   v      v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_109140333_   5752 AATCAAACAGCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5801
                          iv    i i   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_109140333_   5802 CCAAAAGAAGACATTTATGTAGCCAAAAGACACATGAAAAAATGCTCATC 5851
                         i v        i  vi vi i     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_109140333_   5852 ATCCCTGGCCAT 5863
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (151 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2291 25.26 8.73 1.59  chrX_109147622_109152306.rev     3083  3838 (847)    L1M4_orf2#LINE/L1        1   810 (98)  

  chrX_109147622_   3083 TGGAAAGACATACCTTGTCCAAGGACTGAAAGGCTCAACATAGGAAAGAT 3132
                                 i  v  v   i  v   i  i   i  i  i  v vv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109147622_   3133 GTCATTTCTCACCAAAACGATCTATAGAGTCAAAGCAATTCTGATCAAAA 3182
                          v  v v   v     vi      i   v    v     i iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109147622_   3183 TCCCAACAGGATATTTTATAGA------TAGACTGACTCTAAAGTGTATA 3226
                              i v vv v    ii   ------i ii    ii     i vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_109147622_   3227 TGGAAGGTCAAAGAAACAGGAATAGCTAAAATAATTCTGTAAAAGAAGCA 3276
                              ivv   i i v vi       i    i   ii  v        v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_109147622_   3277 GATAAT-GAAGGAGTCACATTGCCTGATTTTAAGGCTTACTACAAAGTTA 3325
                         v v i - i    v     i v  ii    i  ii            i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_109147622_   3326 AAGCAACCGAAACAATGCAGTATTGCC-CAAGAATAGACACATCAATCAA 3374
                         v  i  i i i   i  ii   i  v -i   i       i  vi     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_109147622_   3375 TGAAACATAAT----AGTCCAGAATTTGACCCACACAAATATAATCATTT 3420
                           i  i v   ----         v vi     i   vv   ii   v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_109147622_   3421 GATTTTTGA------------------------------AAATAGTGT-- 3438
                               i  ------------------------------i      v --
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_109147622_   3439 -----AAATGCGGTTGAAGCAATTGGACATTCATATGTAAAATAACAAAC 3483
                         -----     vv i  iii   i    i ?i  i   i    v  ii  v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_109147622_   3484 TTA-ACCTAAACCTCACAACTTATATAAAAGCTAA----------GTCAT 3522
                           i-   ivv        v v    i    ii   ----------i   ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_109147622_   3523 AAATCTAAATAGAAAATATAAAACTATAAG--TCTTAGAAGGAAATATAT 3570
                          i i      iv  i vv           i--         i   i   v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_109147622_   3571 GAAAAAATCT--GTGATCTTCAGTTAAGCAAACAGTTCTTAGACATGACA 3618
                          ?iv      --    i   vi    i    vviv        i      
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_109147622_   3619 CCAAAAACACAATACATAAAAGAAAAAAAAAATGATAAACTGACATTAAT 3668
                               i     vvv i           v ---      i  ivv  v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATA---GATAAATTGGACTTCAT 647

  chrX_109147622_   3669 CAAAATGAAAAACTTTTGATCTGTGAAAGACACT-TTAAGACAATGAAAA 3717
                               v           vv  vii  i      - i    v i      
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_109147622_   3718 GATAAGCTATATAACATATAACATGGGATAAAATATTTGCAAATCACATA 3767
                           i  v i i v  ---------     v                 i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAA---------TGGGAGAAAATATTTGCAAATCATATA 738

  chrX_109147622_   3768 TCCAACAAAGAACTTTTATCCAGAATATATAAAGAATCCTGA-AATTCAA 3816
                           ii i  i i    v                    ii  v -  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_109147622_   3817 CAATAAGAAAACACACAACTCA 3838
                         i     i  i   v i   i  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCA 810

Transitions / transversions = 1.54 (114 / 74)
Gap_init rate = 0.02 (14 / 810), avg. gap size = 5.57 (78 / 14)  


3608 15.11 3.26 0.59  chrX_109171554_109173211.rev      493  1167 (491)    L1M4_orf2#LINE/L1      216   908 (0)  

  chrX_109171554_    493 CACACT---CAGTTTCAAAGCTTTCTACAAAGCTACAGCAATCAAGACAG 539
                               ---  i       i   v              i           
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_109171554_    540 TGTGGTGCTGGCATATGGATAGACATATAGAGAAATGAGATAGAACTGAG 589
                               i        v               vv    ii      i    
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_109171554_    590 GGTCTAAAAATAAACCTTCACATTTATTTTTCATTGATTTTTAGAAAGGA 639
                         i   i i         ivi        vv iv         iiiv    i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_109171554_    640 TACCAAGATATTTCAATGGGGATGGATAGAAGAGTCTTTTCAACAAATGG 689
                          i      ivv           --- -    v                  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGA---A-AGAATAGTCTTTTCAACAAATGG 411

  chrX_109171554_    690 TGCTGGGACAACTGGATATCCACATG-AAAAAAATGAATTTGGACCCCTT 738
                                           ?       -    i      v          v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_109171554_    739 CCTCACACTACACATAAAGATTAACTCAAAATGGATCATAGACCTAAATG 788
                                 i i i i   i                   ?           
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_109171554_    789 TAAGAGCCAACACTATGAAACTCTTAGAAGAAAACA--GTCATATATCTT 836
                                i  v     i                   -- v?i  v     
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_109171554_    837 CATGATCTTGGACTAGACAACAGTTTCTTAGATGTGATACCAAAAGCACA 886
                          i   i     ii   i   ii           i   i            
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_109171554_    887 AGCAGCCAAATCAAAAATAGAGAAATTAGACTTTATCAAAATTAAAATAT 936
                             i v   vv         v     i     i             vv 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_109171554_    937 TTTGTGCCTCAAAGGATACAATCAAGCAAATGCAATGACAACCCACAGAA 986
                                i        i  v      v  i  v  v              
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_109171554_    987 TGGGAGAAAATGCTT-CAAATTATATATCAGATAAGGGTTTAATATCCAG 1035
                                    ii  -     i       v        vi vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_109171554_   1036 AA-------AGAACAATTATAACTGAACAATGAAAA------CAACCCAA 1072
                           -------     vv   i    v  i   i    ------i       
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_109171554_   1073 TTAAAATTTGGG-AAAGGATCTGAAAAGATATTTCTCCAAA-AAGACATA 1120
                           ?   vv    -       i    v   i           -    i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_109171554_   1121 CAAATAGCTAGTAAGTACATGAAAAAGTGTTCAACATCATTAGTTAT 1167
                              i  i i    i         ii  i         ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (62 / 36)
Gap_init rate = 0.01 (10 / 693), avg. gap size = 2.60 (26 / 10)  


4018 16.26 2.80 1.40  chrX_109234416_109237348     1232  2018 (915)    L1M4_orf2#LINE/L1        1   798 (110)  

  chrX_109234416_   1232 TGGAAAGGCATCCTGCTTTCATGTATTAGAAAA---AATAT---CCAAAT 1275
                                ii    iiiv      v   i   i ---     ---iv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109234416_   1276 GGCAATAGTCTCCAAAGCCATCTACAGTTTCAGTGCAATCCCTATCAAAA 1325
                                v  i     viv        v    ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109234416_   1326 TTCCAATGGCCTTTTTTTTTTTTGCAACAATGGAAAAGCCAATCTTCAAA 1375
                          i   iiv         ------   iv   v  v    ii   i v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT------GCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_109234416_   1376 ATCATAAGGAAACTCAAGGGGCCTTGGACAGCCAAAACAGTATTGAAAAA 1425
                         v     v     iv      i  iv i i          i v        
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_109234416_   1426 GAAAAACAAAGT---AGGATT-ACACTTCCTGATCTCAAAACTCACTGCA 1471
                            i        ---    i -        ii  i        i   i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_109234416_   1472 AAGCTACAGTAATCAAAACAGTGTGGTACTGGCATAAAGGTGGACATATA 1521
                                         i                    i i i        
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_109234416_   1522 GAGCAATGGAATAAGATTGAGA-------AATAAACGCAGACCTCTATGG 1564
                           v          ii       -------       v  v  v i     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_109234416_   1565 TCAACTGATTTTCAACAAGGATTCCAAGAACATTCAATGGGGGAAAGAAT 1614
                             i        i      i v      v            -       
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAAT 393

  chrX_109234416_   1615 AGTATT---AACAAATAGTGTTGAGACAATTGGATAACCACATGCAAAAG 1661
                            v  ---       i   i  i     i      ?             
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_109234416_   1662 AATGAAGTTGGACTGCTACCTCACTACACATACAAAA--TAGCTCAAAGT 1709
                                      iv         vv  i        --  i      i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_109234416_   1710 AAGTCAAAGACCTAAATATAAGGAATAAAACTATACAACTAATAGAAGAA 1759
                         iii   ?          i    iiv          v    vv        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_109234416_   1760 AACATAGAAGTAAATCTTCATGATCTCAGATTTGGCAGTGGATTCTTAGA 1809
                                i?          i   i  ii i  v    i   v        
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_109234416_   1810 TTTGACACCAAAAACATTAGCAACAATAGAAAAAAATAGATAAATTGGAC 1859
                          v           i  iv        v        -              
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGAC 642

  chrX_109234416_   1860 TTCATAAACATGAAAAACTTTTGTCCGTCAAAGGATATTATCAAGAATAT 1909
                              v  v  v            v v        i i         vi 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_109234416_   1910 GAAAGACAAACTACATACAGAGTGAGAGAAAATATTTGCAAATCATATAT 1959
                             --- i  v  vi     i  i                         
  L1M4_orf2#LINE/    693 GAAA---AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_109234416_   1960 CTGATAATGGTTTAATATCCTGAATATATGAAGAACTCTTACAACTCAAC 2009
                                v  vi vi     v        i                   i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_109234416_   2010 AATAAAAAG 2018
                                  
  L1M4_orf2#LINE/    790 AATAAAAAG 798

Transitions / transversions = 1.60 (77 / 48)
Gap_init rate = 0.01 (11 / 798), avg. gap size = 3.00 (33 / 11)  

 626 14.52 0.00 1.61  chrX_109234416_109237348     2317  2440 (493)    L1M4_orf2#LINE/L1      787   908 (0)  

  chrX_109234416_   2317 AATAATAATAAAAGTCAAACAGTCTGATTAAAAACTGGGCAAAGTACTAG 2366
                                 --    v    i ii ii   ?    v         v i v 
  L1M4_orf2#LINE/    787 AATAATAA--AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_109234416_   2367 AATAGACATTTTTCCAAAGAAAATATACAAATAGCCAATAAGCACATGAA 2416
                                    i         i          i                 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_109234416_   2417 AAAGTGTTCAATATCAATGATCTT 2440
                           ii  i    i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 2.00 (2 / 1)  


3220 26.73 0.99 1.10  chrX_109282068_109285115     1647  2555 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109282068_   1647 TGGAAGAATATTCTATGCTCATGGATAGAAAGAATCGATATCGTGAAAAT 1696
                              ii    i i   i        v i    v ii    i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109282068_   1697 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1746
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109282068_   1747 TACCAATGACTTTCTTCACAGAACTGGAAAAAAACT-ACTTTAAAGTTCA 1795
                          v   iivi i  i  ii     v v  v  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_109282068_   1796 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 1845
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_109282068_   1846 AACAAAGCTGGAGGCATCACACTTCCTGACTTCAAACTATACTGCAAGGC 1895
                                i      vv          ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_109282068_   1896 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1945
                           i     i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_109282068_   1946 AATGGAACACAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACC 1993
                                i v  i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_109282068_   1994 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATAGGGAAAGGATTCC 2043
                          vi    i  i     ivv  v   i v  vvv   i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_109282068_   2044 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAGAGCT 2093
                           v  i  i              v      v  ?   i   i i iiiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_109282068_   2094 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 2143
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_109282068_   2144 TTAAAGACTTAAATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAAC 2193
                          i ?    i       v   v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_109282068_   2194 CTA--TGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACT 2241
                         v  --? i  - i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_109282068_   2242 AGAACATCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 2291
                          vi   i        vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_109282068_   2292 AATTAAACTAACGAGCTTCTGCATGGCAAAAGAAACTGGCATCAGCGTGA 2341
                         v  i   v v vi i   i  iiivv    i  v   iv  vv iv    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_109282068_   2342 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 2391
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_109282068_   2392 AAAGGGCTAATTAATATCCAGAATCTACAAAGAACTTAAACAAATTAACA 2441
                           i  i  --- i-          v  i        ivv    v i  i 
  L1M4_orf2#LINE/    745 AAGGGACT---TG-TATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_109282068_   2442 AGAAAAAAACCA----CCCTGTCGAAGGGTGGGCAAAGGATATGAACAGA 2487
                          v     i  v ----   vi i?  iii            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_109282068_   2488 CACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATG 2537
                           i     v        i  vi viii     i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_109282068_   2538 CTTATCATCACTGGTCAT 2555
                           i v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (148 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


4446 15.24 4.18 1.69  chrX_109399169_109401861     1317  2202 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109399169_   1317 TGGAAAGAAATTCCATGTTCGTGGTGTGCAGGAGAC--AATATTGTTAAG 1364
                                 v  i        i   vv  -- i    --            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTG--GAAGACTTAATATTGTTAAG 48

  chrX_109399169_   1365 ACAGCAATACTACTCTAACTGATCTATAGATTCAACACAATCCCTATCAA 1414
                          ii        v i v  i       i         i             
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_109399169_   1415 AATCTCAG-TGGCTTCTTTGCAAAAAATGACATGATGATCTTAAAATTCA 1463
                             i   -  v   i      i   v     v v     i         
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_109399169_   1464 TCTGGAAATGCAAGGGCTCCAGAATAGCCAAAACAATCTTAAAAAAGA-- 1511
                          v              vi                      i       --
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_109399169_   1512 --CATTAGTTGGAGGATGCACACTTCCCAATTTCAAAACTTACTAAAAAG 1559
                         --  v-          iv                           v    
  L1M4_orf2#LINE/    199 AACAA-AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_109399169_   1560 CTACAACAATCA-----GTATGGTACTGACATAAGGATAGACATATAGAT 1604
                              ii     -----  i        i                     
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_109399169_   1605 CAGTGGAATAGAATGAAGGGTCCAGAGATAAACTCTTACATTTATGTTTG 1654
                           i           vi  i       i      i v          v ii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_109399169_   1655 ATAGATTTTCATCAAGGGCACCCAGACATTTCCACGAGGAAAACAGAGTA 1704
                           v       iv      ii  v    vv   v i i     iv v   v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_109399169_   1705 TTTTTAACAAATAGTGCTGAGACAACTGCATCTTCACATGCAAAAGAATG 1754
                             i       i      i        v  v?i                
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_109399169_   1755 AGGTTGTACCCCTTCCTCACACTATATACAAAAATTAACTCAAAATGGAG 1804
                          i    v      v        i                          v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_109399169_   1805 CAAAGATCCAAATGTAAGGGCTAAAATTATAGCACTATTAAAAGGAAACA 1854
                           ?   i i         i       i    iv   v   i   i     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_109399169_   1855 TAGATGTAAATCTTCATAGCTTTGAATTAGGCCATACTTTCTTAAATAGG 1904
                            i?          i ii i   ii      v  iv       i   v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_109399169_   1905 ACACCAAAAAACACAAGCAATAAGAGAAAAAAATGATAAACTG-ACTAAA 1953
                                  i-         i  i        vv      i  -   vv 
  L1M4_orf2#LINE/    598 ACACCAAAAG-CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_109399169_   1954 TCTTAATTAAAAACTTTAATGAATCAAAGGA------------AATGAAA 1991
                           vv             vi  vv        ------------ i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_109399169_   1992 AGACAACCCAGAGAATAAGATGTGAAAGTGTTTGCAAACCATGT--TTGA 2039
                                   v     ii  ---    i i        i   i --i   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGA---GAAAATATTTGCAAATCATATATCTGA 743

  chrX_109399169_   2040 TAAGT-ACTTGTATCCAGAATATATAA----TTCTTACACAACTCAATAA 2084
                             v-                     ----i       --         
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA--ACTCAATAA 791

  chrX_109399169_   2085 -AAAAAGACAA----CCCAATTTAAAAACAGGCAAGGCAAAAGATCTGAA 2129
                         -          ----       ?     ii     ----- i   i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAA-----AGGATTTGAA 836

  chrX_109399169_   2130 TGTATGTTTCTACAAAGAAGATACACAAATGGCCAATTAGCACAAGAAAA 2179
                          iv ii     v           i             v      v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_109399169_   2180 AGATGTTCAGCATAATTGTTAGA 2202
                         -    i   i   v ????????
  L1M4_orf2#LINE/    887 -GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (79 / 52)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.89 (52 / 18)  


2663 25.72 2.66 2.00  chrX_109527578_109529849.rev      880  1781 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109527578_    880 TGGAAAAACATTCCATGCTCATTGATAGGAAAAATCAATATTGTTAAAAT 929
                               i i  i     i    v   v    i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109527578_    930 GGCCATACTGCCCAAAGCAATGTCCAGATTCAGTGCTACTCCTATCAAAC 979
                            v     v      vii  v v        ii  v ii         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109527578_    980 TACCAACAATGTCTATCACAGAATTTGAAAAAAAAAAAAACT-ATTCTAA 1028
                          v   i viiv i v ii     v    v  i--------  -  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--------CTGATCCTAA 142

  chrX_109527578_   1029 AATTCATGTGGAATGAAAAAAAGAGCCCA-AATAGGAAAACCAATCCTAA 1077
                                i     -- viv  i ii    -     vv   v     i i 
  L1M4_orf2#LINE/    143 AATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_109527578_   1078 GCAAAAAGAAGAAAATCGGAGGCAC-CAAACTACCCAACTTCAAGCTACA 1126
                         iv  i     v   i i     -  -  v   v     i     ivivi 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_109527578_   1127 TTACAT-GCTATGGTAACAAAAACAGCATGGTACTGGTACAAAAACAGAC 1175
                         i    v-    ii    iv  i    ii         i i  ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_109527578_   1176 TAATAGAACAATGGAACAGGTTAGAGAACCCAGGAATAAAGCCACACACC 1225
                         vv     v        i  iv v    ii    i      v   i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_109527578_   1226 TAAAACCACCTG-TCTTTGACAAAGTTGAAAATAACAAGCAATGGGGAAA 1274
                           viii  vi  - i  i     i v  vv  v v  vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_109527578_   1275 TGACT--TCCTATTTGATAAATGGTGCTGGGGTAACTGGCTAGCCATATG 1322
                         -  v --  i -  ii i             ii      v  ?   i   
  L1M4_orf2#LINE/    390 -GAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_109527578_   1323 CAGAAGATTGAAACTGAATTCCTTCTTTTCACCATATAAACAGATCAATG 1372
                           i    v    ii  i ii   v i iv         v v i  i  iv
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_109527578_   1373 CAAGATGGATTAAAGACTTAAATGTAAAACCTAAAACTATAAAAATCCTA 1422
                            i      i ?    i         i v              v  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_109527578_   1423 TCATAAAACCAAGG---AAATTCCATTCTGGACATAGACCCTGGAAAAGA 1469
                         vv v     vv   ---    i---   vv   v v iviiv  v  v i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC---TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_109527578_   1470 CTTCA-AGACAAAGACTCCAAAAGCAATTGCAACAATAACAAAAATTGAA 1518
                         i   v-   i v-   v         vvv       v iv      v  v
  L1M4_orf2#LINE/    585 TTTCTTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_109527578_   1519 AAGTCGGACCTAATTAAAGTAAAGAGCTTCTGCACAGCAAAAGAAGGAAT 1568
                           i i    i v  i   i v  i i   i  ii vv    i  vivv  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_109527578_   1569 AAACAGAGTAAACAGACAA--------ATGGGAGAAAATATTTGCAAACT 1610
                         v  v i   i  v      --------                     ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_109527578_   1611 ATGCATCTGACAAAGGCCTAATATCCAGAATCTATAAGGAACT--TA-AA 1657
                           ii      i  i  v  vi          v     i     --  -  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_109527578_   1658 C-CAACAAGCAAAACAACAAACAAGCCCATT-AAAAATGTGCAAAAGATA 1705
                          -   i  -i    vi     i  v  v   -       v     i   v
  L1M4_orf2#LINE/    784 CTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_109527578_   1706 TGAACAGATACTTCTCAAAAGAAGACATACATGAGACCAACAAGCATATG 1755
                             i   i i     v        i     viv i    i     i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_109527578_   1756 AAAAAGTGCTCATCATCATTAATCAT 1781
                             ii      v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (131 / 99)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.00 (42 / 21)  


 243 15.91 2.27 0.00  chrX_109534117_109540027.rev      375   418 (5493)    L1M4_orf2#LINE/L1       10    54 (854)  

  chrX_109534117_    375 ATCCCATGTTCAC-AATTGGAAGACTCAATATCATTAAGATATCA 418
                                     i-i           i     ii       iv  
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

Transitions / transversions = 6.00 (6 / 1)
Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1)  

2829 26.47 2.11 1.11  chrX_109534117_109540027.rev     3163  4061 (1850)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109534117_   3163 TGGAAACACATCCCATG------GATGAGTAGAATCAATATTGTGAAAAT 3206
                               v i        ------   vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109534117_   3207 GACTATACTGCCAAAAGCAATATACAAATTCAATGCAGTTCCCATCAAAA 3256
                          i v     v  v   vii  v    i      i   i i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109534117_   3257 TACCA--T-CATTCTTCACAGAACTAGAAGAAGC-AATCCTAAAATTCAT 3302
                          v   -- - v  i  ii     v v  v-    -i              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_109534117_   3303 ATGGAACCAAAAAAGAGCCTGCATACCTGAAGCAAGACTAAGCAA-AGGA 3351
                               viiv  ii  v  v v   v ii  i   vvi i iv  - i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_109534117_   3352 ACAAATCGAGAGGTATCACATTACCCAACTTCAAACTATATTATAAGGCC 3401
                              vivi    vv     i v     i      viv  i  i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_109534117_   3402 ATAGTCACCAAAACAGCATAGTACTGGTATAAAAATAGGCACATAGCCCA 3451
                          i   v i   i    ii i       i    ii    i  i    vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_109534117_   3452 ATGGAACATAATACAGAACCCAGAAACAAAGCTAAATACTTACAGCCAAC 3501
                               i v   vv   ii       i   v i v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_109534117_   3502 TGATCTTCGACAAAGCAAACAAAAACATGAAGTGGGGAAAGGACACTCTA 3551
                             i        i vviv   i v   vv i         i i v   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_109534117_   3552 TTCAACAAATGGTACTGGGATAACTGGCAAGCCACATGTAGGAGAATGAA 3601
                                      i      i      vv ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_109534117_   3602 ACTGGATCATCCT--CTCTTACTTTATAGAAAAATCAACCCAAGATGGAT 3649
                         ii    i --   --   vi  iv    v      i   i   i      
  L1M4_orf2#LINE/    450 GTTGGACC--CCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_109534117_   3650 CAAAGACTCAAATATAAGACCTGAAACCATA------CCAGAAGATAACA 3693
                           ?    ii    i     v  i    i   ------ii      v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_109534117_   3694 TCAGCAAAACCCTTCTAGACATTCGCTTAGACAAAGACTTCATGACCAAG 3743
                          vi ?iv  vi    vv   v  v v    i   v ii   v iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_109534117_   3744 AACCCAAAAGCAAATGCAACAAAAACGAAGATAAATAGATGGGACTCGAT 3793
                          vv         v v         ivi  i   i   i  v     iv  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_109534117_   3794 TAAACTAAAAAGTTTCTGCACAGCAAAATAAATAATCAACAGAGTTAACA 3843
                         i   v v    ii  i  ii vv    iv v iv     v i   v  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_109534117_   3844 GACAGCCCACAGAATGGGAGAAAATCTTCACAATCTACATATCCAACAAA 3893
                             i                    v  ii   vii i     ii i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_109534117_   3894 GGACTAATATCCAGAATCTACAAAGAACTCAAACAAATCAGCAAAAACAA 3943
                              vi          v  i         vv    v   ii  v  v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_109534117_   3944 AACAAATCAAAAATTCCAATTAAAAAATAGTCTAAGGACATGGATAGCCA 3993
                         i      ----  i-      ?      i v v     iv  i    v  
  L1M4_orf2#LINE/    798 GACAAAT----AAC-CCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_109534117_   3994 ATTCTCAAAAGAAGATATACAAATGGTCAACATGCATATGGGAAAATGCT 4043
                         v     v                   i   i v   i   ii  i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_109534117_   4044 CAACTAATTATCAGGGAA 4061
                             --  i ????????
  L1M4_orf2#LINE/    893 CAAC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.42 (29 / 12)  

3390 19.15 9.14 1.13  chrX_109534117_109540027.rev     4622  5420 (491)    L1M4_orf2#LINE/L1       46   908 (0)  

  chrX_109534117_   4622 AAGATATTAATGCTTCCCAAAGCAACCTATACATTCAATGCCATCCCTAT 4671
                              ivi   i  i      vii i   i v      i  v        
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_109534117_   4672 AAATATCCCAAGTATTTTTTTTTGCGGAAATAGAAAAACCCATTCTAAAA 4721
                         v  v      iv iii      -  i     v  v  i iv  i      
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_109534117_   4722 TTTTTATATGGTATCTCAAGAAACCCTGAATAGTCAAGACAATCTTGAAA 4771
                           i--      v viv    ii    v      i   i            
  L1M4_orf2#LINE/    145 TTC--ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_109534117_   4772 AAGAAGAACAAAGTTGGAGGTCTCATATTTCCTGATTTAAAAACTTACTA 4821
                                             v    i i    ii    v           
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_109534117_   4822 CAAAGCTATAATAATAAAAATAATGTGGTATTGGAACAAAGACAGACATA 4871
                                 i i    v  i i i       i   v i  i  i       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_109534117_   4872 TAGACCAGTGGAATAAAAT--AGAGTCCCCAGAAATAAGTCC-TAGAATA 4918
                             i  i       i   --       --        ii  -  v v -
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATT- 339

  chrX_109534117_   4919 TATGATCAAAAGATTTTCTAGAAAAGTGCCAGGATCATTCAATGGGGGAA 4968
                             i    vv       v v  ii      i  i            -  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AA 388

  chrX_109534117_   4969 AGGAAAGTTTCTTCAACAAATGGTATTGGAA-ATTTGGATATCTACATAT 5017
                           i v   i i             ii   i - vi      ? i    ii
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_109534117_   5018 GAAAGAACAAAGTTAGACACTTACCT---------TACAAAAGTTA---- 5054
                         i      ii     i   v i     ---------       i   ----
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_109534117_   5055 -------------------------------------------------G 5055
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_109534117_   5056 AAGAAAACACAGGGGAAAAGCTACATGACATTGGATT-GGTAATGATTTA 5104
                                  i   ? v   v  v i    v    i  -  i    i   v
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_109534117_   5105 TTGGCTATGACACCAAAAACACAGGCAACAAAACAAAAAATTAATAAATC 5154
                           i v             i    i         v       vi      i
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_109534117_   5155 AGACTTTATTAAAATTAAAAACGTTTGTGCCTCAAATGTCATTATCAACA 5204
                         i     i  i            v       i     v v  i      v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_109534117_   5205 GAATGAAAACACAAACCAGTGAATGGAAGAAAATATTTGCAAATCACATG 5254
                         i i      v    v   vv      i                   i  i
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_109534117_   5255 TCTGATAAGAAGTTAATATCCAGAATATGTAAAGAAACCTGA-AATTCAA 5303
                                  iiii vi            i       vi  v -  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_109534117_   5304 CAACAACAAAAGACAA----CCCAATTTAAAACTAGGCAAAGGATTTGAA 5349
                         i  i  --        ----       ?    v i               
  L1M4_orf2#LINE/    789 TAATAA--AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_109534117_   5350 TAGATATTTCTCCAAAGAAGTTATACAGATGGTCAGTGAAC-CATGAAAA 5398
                             i               v      i    i  i i i -        
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_109534117_   5399 TATACTCAACACCAGTAATTAT 5420
                         v  i       i  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (101 / 49)
Gap_init rate = 0.02 (15 / 863), avg. gap size = 5.47 (82 / 15)  


 493 22.94 9.41 5.29  chrX_109554794_109557310       50   219 (2298)    L1M4_orf2#LINE/L1      405   581 (327)  

  chrX_109554794_     50 CAAA--GTGTTGGGATTACAGGCGTTAGCCAC-TGCACCAG--------- 87
                             --   i     iv  v  v--  ?    -    vv  ---------
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGA--TAKCCACATGCAAAAGAATGAAGTT 452

  chrX_109554794_     88 -GCTTCATACCTCATTTCATACA-AAAAATTAACTTAAAGTGAATCATGG 135
                         - vii v       ivi    i -           i   i  i    ?i 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_109554794_    136 ACCCAAATATAAAATATAAAAGCTAAA--TATAAAAATTCTAGCAGGAAA 183
                            i    i   i -------      --       v ii   v  i   
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGA-------GCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_109554794_    184 TATAAAAGAAATTCTTCATTATCTTGGGGTAGGCAA 219
                         i   ii? v  v     i v i      v       
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

Transitions / transversions = 1.57 (22 / 14)
Gap_init rate = 0.04 (7 / 177), avg. gap size = 3.57 (25 / 7)  

3192 24.92 1.99 1.44  chrX_109554794_109557310     1122  2024 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109554794_   1122 TGGAAAGGTATTTCATGTTCATAAAAAGGAGGACTCAATATTAGTTAGAT 1171
                                i   ii         ii vv   i    i      iv v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109554794_   1172 GTCAACTTTCCCAAACTTGA-CTATAGATTCAGTGCAATCCCAGTCAAA- 1219
                          v   ivi    v  v    -   i       ii        vi     -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109554794_   1220 TCCCAG-TGT-TATTTTGTGGGTATTGATAAACTGATTCTAATGTTTCTA 1267
                               -  i- v     ii iv     i  i     i    vi  iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_109554794_   1268 CGGAAAGGCAAAAAGATCTATATTGGCCAACACAATATTGAAGCAGAAGA 1317
                         i     v    ii-  i i v v i     v     v     iv      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_109554794_   1318 ACAAAGTTGGAGGGCTGGCACTACCCAACTTCAAGACTTACTGTAAAGCT 1367
                                      i  vi    v     i     i       ii      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_109554794_   1368 ACAGCAAT-AAGACAGTGGCTTATTGGTGAAAGAATAGACAAATGGACCA 1416
                             i   -         vvv  i   iiv   i       v  i  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_109554794_   1417 ATGGAACAGAATAGAAAGCCCACACAGAGACTTACACAAATACAGTCAAC 1466
                               i     v  i  i   v v v i  ii i   vv  ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_109554794_   1467 AAATCTTTGACAAAGGAGTGAAGGCAATCTAATGGGGGAAAGGATAGTC- 1515
                         vi  i  i     i  v iv   i v  ii       -    i      -
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCT 398

  chrX_109554794_   1516 ---CAAAGAGACTAAATGGTTCTGGAACAACTGGATATCAAACATGCACA 1562
                         ---   ------i       v    i           ? v -      v 
  L1M4_orf2#LINE/    399 TTTCAA------CAAATGGTGCTGGGACAACTGGATAKCCA-CATGCAAA 441

  chrX_109554794_   1563 CGAAAAAATCCAGATATAGACCTTACACCCTTCAGAAAAATTAACTCAAA 1612
                         v   vi  viii  ivivv    i     v vi v               
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_109554794_   1613 ATGAATCATAGATTTAAATGTAAAACACAAAACTGTAAAACTCCTAGAAG 1662
                            i    ?   ii         i vvi      i        i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_109554794_   1663 ATAACATAGAAGAAAATCTAGATAACCTTGGGTCTGGCGATGACTCTCAT 1712
                          v       i? v      vvi i         iv   i   ii -  v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT-TCTT 590

  chrX_109554794_   1713 TGATTGTGCCTTTGATA----AAATATCTGAA--AAAAGTTGATAAGTTA 1756
                         v   -i  v viii v ----  ii v vi  --    i v     i  i
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_109554794_   1757 GACTTTCATTAAAATTAAAAAGTTCTACTCTGTGAAAGAAGCTAGGAAGA 1806
                              -   i           v  i iiv  vii  i  vi   vv    
  L1M4_orf2#LINE/    640 GACTT-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_109554794_   1807 GAGTTAGAAGATAAGGCACAGACTGAAAAAAAAT--TTGCAAAT-ATATA 1853
                         i   v i    i  vv      v  ii i     --        -     
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_109554794_   1854 TTTGATAAAGGACTGTTACTTTAAATGTACAAAGAACCCACAAAACTAAA 1903
                          i      i     vv  iiivi   i  i       i vi v    v  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_109554794_   1904 CAATAAGAAAATGAAAAACCCAATTAAAAAATGGGCAAAAGGTCTAAACA 1953
                         i     i  i ii  v         ?             i i i i  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_109554794_   1954 GACACCTCATCAAAGAAGATATACAGATGGCAAATTAAACTTATGAAAAG 2003
                             ii  vi               i     v   -  i vi        
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCACATGAAAAG 887

  chrX_109554794_   2004 GTGCTCAAAATCAAATTTTAC 2024
                         i       v    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (137 / 84)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.72 (31 / 18)  


3145 23.99 2.88 2.08  chrX_109577263_109579122      501  1367 (493)    L1M4_orf2#LINE/L1       35   908 (0)  

  chrX_109577263_    501 TTATTTTTGTTAAAATGACCACACTGTCTAAAGCAATCTACACATGTAAT 550
                            v v       i   i v i   vi i   vii       v  vi  i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chrX_109577263_    551 GTAATCCCTATAAAAATACCAATGTTAACTTTTCATTG----AATTAGAA 596
                          i         v     v   -- i iv     --   ----    -  v
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCA--GCTGCCTTTT--TTGCAGAAATT-GAC 129

  chrX_109577263_    597 AAACTAATTCTAAAATTCATATGCAACCAAAAAAAAAGCCCA-AATAACC 645
                           i  i  i              v  viiv  iii --    -    i  
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA--CCCAGAATAGCC 177

  chrX_109577263_    646 AAAGCAATCCTGAGTAAAAAGAATAAAGCTGGAGGCATCACATTACCTGA 695
                            i     i   iv  i     i    i      vv     i v  ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_109577263_    696 CTTCAAATTATATTACAAGGCTGTAGTAACCAAAACAGCATGGTACTGGT 745
                         i      viv  i     i   ii     i   i    ii         i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_109577263_    746 ATAAAAA--GACACATAGATCAATGGAACAGGACAGAGAACCCAGAAATA 793
                             ii --    i              i  i iv    ii         
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_109577263_    794 AAGCCATATATTTACAGGCCATTGATCTTTGACAAAGCCATCAAAAGCAT 843
                           v     i     ii v v      i  i     i viii   i v   
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_109577263_    844 ATACTGGGAAAAGGACACTCTCTTCAATAAATGGTGCTGGGAATATTATA 893
                         vi v    i    i i v   i     i              vv i iv 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_109577263_    894 TTGCCATATGCAGAACAATGAAGGTGGAACCCTACCTCTTACCATGTACA 943
                          v?   i     i  v       v    v         vi     i    
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_109577263_    944 AAAATGAACACAAGATGGACTAAAGACTTAAACATAAGACTCAAAACCAT 993
                              v   v   i     ii ?    i    ii     vii     i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_109577263_    994 AAAAAACT-AGAAGAAAACCTAGGGAAAACTCTTCTGGACATTGGTCTTG 1042
                             vv  -          v    ?iv  v     vv   v    vi v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_109577263_   1043 GCAA---------AGA----ACCTCAAAAGCACAGGCAACAGAAACAAAA 1079
                             ---------   ----  vi          i      i  i--   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG--AAA 625

  chrX_109577263_   1080 AAATAGACAAATGAGACTTTGTTAAACTAAGAAGCTTCTGCACAGCAAAG 1129
                                i    vi     ii i   v v i  i   i  ii vv     
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_109577263_   1130 GAAATTATCAACAGAATGAACAGACAGCCTGCAGAATTTGAGAAAATATT 1179
                           v i      v i i    v     i  ii      vv           
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_109577263_   1180 TGCAAACTATTCATTCAACAGGAGATTAATATCCAGAATATACAAGGAAC 1229
                               ii  vi  iii i i i  i vi             i  i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_109577263_   1230 TCAAACAACTCAACAACAACAACAAAAACCACAGAGATAATCCCATTTAA 1279
                           vv         i  i  ----   i  ----- i    i  v   ?  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAA----AAAGAC-----AAATAACCCAATTWAA 816

  chrX_109577263_   1280 AAGTGGGCAAAGGACATGAACAGATATTTTTCAGAAGAAGA----CAAAT 1325
                           i           iv    i   i    i  vi       ----     
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_109577263_   1326 TACCAACGCATATATGAAAAAATGCTGAACATCACTAATCAC 1367
                         vi    iivii i       i     v       ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (133 / 71)
Gap_init rate = 0.02 (14 / 874), avg. gap size = 3.07 (43 / 14)  


4165 18.05 2.77 0.72  chrX_109614082_109615904.rev      502  1332 (491)    L1M4_orf2#LINE/L1       61   908 (0)  

  chrX_109614082_    502 CCCAAAGCAATCTACAGGTTCAATGCAA-CTCAAT---AAT--------- 538
                               vii        i     i    - i v  ---   ---------
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_109614082_    539 ----TTTACAGAAATAGAAAAATCACTCCTAAAATTTATGTAGAATCTCT 584
                         ----   i       v  v  iiiiv          i  i i   viv v
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_109614082_    585 AGAGACCTAGAATAGCCAAAACAACCTTGAAAAAGAGGAACAACATTGGA 634
                           i    i                i           i      vi     
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_109614082_    635 AGACTCAGACTTTCTGATTTCAAAGTTTACTACAGAGCTATAGTAATCAA 684
                         i      v    i ii        ii        i     i         
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_109614082_    685 AACAGTATGGTACTGGCATAAAGACAGACATATGGACATATTCATTGGAA 734
                         i     i              i  i        i  -----   v     
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGA-----TCAATGGAA 305

  chrX_109614082_    735 TAGAATCAAGAGGCCAAAAACAAACTCATGCATCTATGGTCAAATGATTT 784
                               ii    v   i   i    i   i   i         v      
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_109614082_    785 -CAACAAGGGTGCCAAGACCACTCAATGGGAAAAGGACAGTCTCTTTAAC 833
                         - i                  i        i    i i     i  i   
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_109614082_    834 AACTGGTGGTGGGAAAACTGGATATTCACATGCAAAAGAATAAAGATGGA 883
                           v     v     v         ?i               i   v    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_109614082_    884 GCT-TATTTTATACTGCATATAAACATTAACTTAAAATGGATTAAAGATC 932
                         v i-  ii i i  iii   i   v       i         i ?   i 
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_109614082_    933 TAAACATAAGAGCTAAAATTATACAACTC--AGAAGAAAATATAGAGGAA 980
                             ii            i    v     --         i    i? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_109614082_    981 AAGTTTCATGACATGGGATTTTGCAGTGACTTCTTGTGTAT-ACATCAAA 1029
                           vi   i    v v  i  vv   i  ii     ivi   -   i    
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_109614082_   1030 AGCACAGACAACAAAAGAAAAAAGAAAGAAATTGAACTTCCTCAAAACTA 1079
                               ii               v i v      i     v      i  
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_109614082_   1080 AAAA-TTTTGTGAATCAAAGGACACTATTAACACAGTGAAAAGTCATTCC 1128
                             -       vv              i  v v         v  vi  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_109614082_   1129 ATGGAATGAAAGAAAATATTTGTAAATCATATATCTGATAAGGGTTTAGT 1178
                          ii     ii            i                     vi v  
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_109614082_   1179 ATCCAGGATATATAAGGAACTCCTACAATTCAACAACTAAGAAACAAGCA 1228
                               i        i      i     i    i  iv  i i    ii 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_109614082_   1229 ACCCAGTTCAAAAATGGGCAAATAATTTGAATTGGCATTTCTCCAAAAAA 1278
                              i  ?             vi        v i            i  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_109614082_   1279 GATATACAGATGGCCAAAAAACACATGAAAAAAATGCTCAACATCACTAA 1328
                                 i        v  i          i -            ????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZ 904

  chrX_109614082_   1329 TCAT 1332
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.48 (104 / 42)
Gap_init rate = 0.01 (10 / 848), avg. gap size = 2.90 (29 / 10)  


3125 27.73 0.88 0.55  chrX_109654702_109663842     4877  5781 (3360)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109654702_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4926
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109654702_   4927 GGCCATACTGCGCAAAGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v v    v i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109654702_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5024
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_109654702_   5025 ATATGGAACCAAAAAAGATCCCACATCCCCAAGTCAATCCTAAGCCAAAA 5074
                                 viiv  ii  i  viv  vv    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_109654702_   5075 GAACAAAGCTGGAGGCATCACACTTCCTGACTTCAAACTGTACTACAAGG 5124
                                 i      vv          ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_109654702_   5125 CTACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGAAATAGAC 5174
                                  i   i    ii     i   i iv ii i   v v     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_109654702_   5175 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCGTATCTACAAC 5222
                                 i    i--    i  --        vv  iiii  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_109654702_   5223 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGAGAAAGGATTC 5272
                         i vi    i  i     ivv  vv  i v  vv      i     i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_109654702_   5273 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAGC 5322
                         i  v  i  i              v      v  ?   i   iii  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_109654702_   5323 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5372
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_109654702_   5373 ATTAAAGACTTAAACGTTAGACCTAAAACAATAAAAACCCTAGAAGAAAA 5422
                           i ?    i    i  v   v       v      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_109654702_   5423 CCTAGGCATTACCATTCAGGACATAGGTATGGGCAAGGACTTCATGTCTA 5472
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_109654702_   5473 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5522
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_109654702_   5523 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5572
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_109654702_   5573 CAGGCCACTTATAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5622
                         v  i v  ii i i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_109654702_   5623 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5672
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_109654702_   5673 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5718
                           i    ----   v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_109654702_   5719 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAACAATGCTCAC 5768
                            v        i  vi viii     v  i         vi       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_109654702_   5769 CATCACTGGCCAT 5781
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.17 (13 / 6)  

3083 27.35 1.00 0.44  chrX_109654702_109663842     7746  8648 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109654702_   7746 TGGAAAAACATTTCATGCTCATGGATAGGAAGAATCAGTATCGTGAAAAT 7795
                               i i  ii    i        v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109654702_   7796 GGCCATACTGCCCAAAGTAATTTATAGATTATATGATATCCCCAGCAAGC 7845
                            v     v      v i  i  i     vv i vv     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109654702_   7846 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCT 7893
                          v   vivi i  i  ii     -   -- v  i  - iii    v   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_109654702_   7894 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 7943
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_109654702_   7944 AACAAACCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 7993
                               vi      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_109654702_   7994 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 8043
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_109654702_   8044 AATGGAAC-GAACAGA-AGCCTCAGAAATAGCCCCACACATCTACAACCA 8091
                                i-   iv  -  i -        iv    i    i  iiii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCA 347

  chrX_109654702_   8092 TCTGATCTTTGACAAACCTAACAAAAACAAGCAATGGGGAAAGGATTCCC 8141
                         vi    i  i     ivv iv   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_109654702_   8142 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCTG 8191
                          v  i  i              v      v  ?   i     i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_109654702_   8192 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 8241
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_109654702_   8242 TAAAGACTTAAATGTTAGACCTAAAACCATGAAAACCCTAGAAGAAAACC 8291
                         i ?    i       v   v       i  i   vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_109654702_   8292 TAGACA-ATACCATTCAAGACATAGACATGGGCAAAGACTTCATGACTAA 8340
                            i?i- v i -   iv   v v ivv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_109654702_   8341 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 8390
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_109654702_   8391 TTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCAGAGTAAAC 8440
                          i   v v  i     i  ii vv    i  v       vv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_109654702_   8441 AGGCAACCTGCAGAATGGGAGAAAATTTTTGCAATCTATCCATTTGACAA 8490
                           i     ii                v       vii  vi  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_109654702_   8491 AAGGCTAATATCCTGAATCTACAAAGAACTTAAACAAAT---TTACAAGA 8537
                         ii i  vi     v    v  i        ivv    v --- v i  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_109654702_   8538 AGA-AAACAATCCCATCAAAAAGTGGGCAAAAGATATGAACGGACACTTC 8586
                            -   i  i  v  i?    i        i   v    ii    i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_109654702_   8587 TCAAAAGAAGACATTTATGCAGCCCACAAATATATGAAAAAAAGCTCATC 8636
                           v        i  vi viii   v i  ii i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_109654702_   8637 ATCACTGGCCAT 8648
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


2921 28.23 2.25 0.11  chrX_109665680_109669949.rev     2891  3779 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109665680_   2891 TGGAAACACATCCCATGTTCATGGATGGGTAGAATTAATATTGTGAAAAT 2940
                               v i                 v  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109665680_   2941 GAACTTACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 2990
                          ivvv    v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109665680_   2991 TACCACCATCATTCCTCACAGAACTAGAAAAAGCACTCCTAAAGTTCATA 3040
                          v   v vv v  ii ii     v v  v  iviiv       i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_109665680_   3041 TGGAACCAAAATAGAGCCTGCATATCCAAAGCAAGACTAAGCAAAAAGAA 3090
                              viiv  vi  v  v v   v     i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_109665680_   3091 CAAATCTAGAGGCATCACATTACCTGATTTCAAACTATATTATAAGGCCA 3140
                             vi i    vv     i v  ii        viv  i  i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_109665680_   3141 TAGTCACCAAAACAGCATGATACTGGTATAAAAATGGGCACATCGCCCAA 3190
                         i   v i   i    ii  i      i    ii  i i  i  v vi   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_109665680_   3191 TGGAACAGAAAAGAAAACCCAGAAACAAAGCCAAATACTTACAGCCACCT 3240
                              i    vv  i ii       i   v   v i i   ii i  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_109665680_   3241 GATCTTTGATAAAGCAAACAAAAACATAAAGTGGGGGAAAGACACGCTAT 3290
                            i  i  i  i vviv   i v   vv i     i  ii i vv  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_109665680_   3291 TCAACCAATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAGAATAAAA 3340
                              v             i  i   vv ?       i ii     i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_109665680_   3341 CTGGATTCTTATCTCTCACCTTATAAAGAAATCAACTCAAGATGGATCAA 3390
                         i    ii i  i   v    v    v i    i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_109665680_   3391 CAACTTAAATCTAAGTCCTGAAACTATAAAAATTATAGAAGATAACTTTG 3440
                         vi  i     v    vv  i           v iv       v   v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_109665680_   3441 GAA-AAATCCTCCTAGACATTGGCTTAGGCAAAGATTTCATGACCAAGAA 3489
                          ?i-     i  v -   v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_109665680_   3490 CCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGGTGAGTCTTAATTA 3539
                         v         v v         iv   i   i   ii vi v   v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_109665680_   3540 AGGTAAAGAGCTTTTGCATGGCAAAAGAAAGAGTCAGCAGTGTAAACAGA 3589
                          ii v  i i      iiivv    i  v vvi   iv iv  i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_109665680_   3590 CAAACCACAGAGTTGGAGAAAATCTTCACAATCTGTACATTTGACAAATG 3639
                            v       i v         v  ii   viii  i  i   i  iv 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_109665680_   3640 ACTAATATCCAGAATCTACAATGAAC-------------------GAAGA 3670
                            vi          v  i  v    -------------------i    
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_109665680_   3671 CAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGATAATTCTCA 3720
                             i  i  v  i?    i     v     iv        i v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_109665680_   3721 AAAGAAGATATACATTTGGCCAACAAACATATAAAAAAATGTTCAACATC 3770
                                       vv       i  i  i  i    i   i        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_109665680_   3771 ACTAATTAT 3779
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.29 (139 / 108)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 7.00 (21 / 3)  


3050 27.89 1.33 0.44  chrX_109674891_109681589     5307  6206 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109674891_   5307 TGGAAAAGCATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5356
                               iii  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109674891_   5357 GGCCATACTACCCAGA--G---TATAGATTCAATGCTGTCCCCATTAAGC 5401
                            v     v    i -- ---  i        i  vi    i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109674891_   5402 TACCATTGACTTTCTTCACAGCATTAGAAAATACT-ACTTTAAATTTCAT 5450
                          v   vivi i  i  ii   v v v  v  -i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_109674891_   5451 GTGGAACCAAAGAAGAGCCCGTATAGCCAAGACAATTCTGAGCAAAAAGA 5500
                         i     viiv iii  v  v v        i     ii   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_109674891_   5501 ACAAAGCTGAAGATAC-CATGCTACCTGACTTCAAACTATATTACAAGGC 5549
                               i  i  i-  -  ii  v  ii i      viv  i     i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_109674891_   5550 TACAGTAACCAAAACAGCATGGTACTGGTACCAGAACAGATATATAGACC 5599
                                 i   i    ii         i iv  i i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_109674891_   5600 AATGAAACAGAACGGAGGCCTCAGATGTAACGCCACACATCTGCAACCAT 5649
                             i  i    iv   ivii    vi   vv   i    i iiiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_109674891_   5650 CTGATCTTTGATGAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5699
                         i    i  i  ii ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_109674891_   5700 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGCAGAAAACTGA 5749
                         v  i  i              v      v  ?i  i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_109674891_   5750 AACTGAACCCCTTCCTTACATCTTATACAAAAATTAACTCAAGATGTATT 5799
                          ii  i      v   i   i v                   i   v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_109674891_   5800 AAAGGCTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5849
                          ?  i i           v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_109674891_   5850 AGGCA-ACACCATTCAGGGCATAGGCATGGGCAAAGACTCCATGACTAAA 5898
                            ?i- v i -   iv i v v  vv i     v ii i v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_109674891_   5899 ACACCAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGGGATCTAAT 5948
                                     vvi          iv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_109674891_   5949 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCTTCAGCATGAACA 5998
                         i   v v  i i   i  ii vv    i  v      vvv ivi    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_109674891_   5999 GGCAACCTAAAGAATGGGAGAAAATTTTTGCAATCTATCAATCTGATAAA 6048
                          i     i v               v       vii  vv         i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_109674891_   6049 AGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 6098
                         i i  vi          v  i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_109674891_   6099 AACC--T--CTCCATCAAAAAAATGGGTGAAGGATATGAACAGACACTTC 6144
                         i  v-- -- i v  i?     -    ii      v    i     i   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_109674891_   6145 TTAAAAGAAGACATTTATGTGGCCCACAAACATATGAAAAAAAGTTCATC 6194
                          iv        i  vi vi     v i  i  i       i v i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_109674891_   6195 ATCACTGGTCGT 6206
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (151 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3024 27.87 0.55 1.31  chrX_109689633_109693157.rev     2120  3034 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109689633_   2120 TGGAAGAACATTCTGTGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2169
                              ii i  i ii  i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109689633_   2170 GGCCATACTGCCTAAGGTAATTTATAGATTCAATACCATCCCCATCAAGC 2219
                            v     v  i  iv i  i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109689633_   2220 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 2267
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_109689633_   2268 CATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 2317
                         i      viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_109689633_   2318 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 2367
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_109689633_   2368 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATGGAAC 2417
                                 i   i    ii         i iv ii i   i    -----
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT----- 293

  chrX_109689633_   2418 AGACCAGTGGAACAGAAC--ACAGCCCTCAGAAATAATGCCACATATCTA 2465
                            i  i     i    i-- v  i  --        vv   i i  i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chrX_109689633_   2466 CAACCCTCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGATAGG 2515
                         iiii vvi    i  i     ivv  v   i v  vvv        v  i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_109689633_   2516 ATTCCCTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGA 2565
                           vvi  v  i                 v      v  ?   i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_109689633_   2566 AAGCTGAAACTAGATCCCTTCCTTATCCCTTATACAAAAATTAATTCATG 2615
                          iiv    ii i  i    v   i iv  v              i   vi
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_109689633_   2616 ATGGATTAAAGACTTAAATGTTAGACCTAAAACCATGAAAACCCTAGAAG 2665
                               i ?    i       v   v       i  i   vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_109689633_   2666 AAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCAT 2714
                              v    ?i- v i -   iv   v v  vv i     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_109689633_   2715 GTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGG 2764
                         ivv  vi            vvi          vv     v  i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_109689633_   2765 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA 2814
                          ii v  i   v v  i i   i  ii vv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_109689633_   2815 GTGAACAGGCAACCTATGGAATGGGAGAAAATTTTTGCAATCTACTCATC 2864
                              v  i     i ii              v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_109689633_   2865 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACA 2914
                            i  i  i  vi          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_109689633_   2915 AGAGAAAAACAAAAAAAACCCCATCAACAAGTGGGCAAAGGATATGAGCA 2964
                          v i   i     v  --   v  i? v  i            v   ii 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAA--CCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_109689633_   2965 GACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAGAAA 3014
                             i     v        i  vi viii     v ii        i i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_109689633_   3015 TGCTCATCATCACTGGCCAT 3034
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (151 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


3608 22.52 1.85 3.05  chrX_109700947_109702931      574  1492 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109700947_    574 TGGAAAAATATTT-GTGTTCATGAATTGGAAGAATTAATATTGTTAAAAT 622
                               i    ii-i        i         v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109700947_    623 GTCCATATTACTGAAAGTGACTTACAGATTCAAAATAATCTCTATCAAAA 672
                          v v   i v iv   v   ii           vii    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109700947_    673 TACCAAAGGCATTTTCCACAGAAATAGAAAAAACAATCCTAAAGTTTGTG 722
                          v   ivv  v    iii       v  v  ivii        i  ii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_109700947_    723 TGGAACCACAAAAGAGCCAAAATATCCAAG-CAATCTTGAGCAAAGAGAA 771
                              vii   ii  v   i    v    i-         iv  ii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_109700947_    772 CAAAGCTGGAGGCATCACACTACTTGTTCTCAAAATCTACTTCAAAGCTA 821
                              i      vv       v iiiv i      ii    v        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_109700947_    822 TAGTAATCAAAACAGCATGGTACTGACATAAAAACAGACATACAGACCAA 871
                         i         i    ii        i     ii i       i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_109700947_    872 TGAAATAGAATAGAGAGCACAGAAATTAGTCCATACATTTTACATCCAAC 921
                           i        v     iv       v ii          - iivi   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT-ATGGTCAAT 349

  chrX_109700947_    922 TGATTTTTGACAAAGGTACCAATAATATGCAATGAGAAAAGAATAGTACC 971
                                i     i   i    v vi  v     i i          vii
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_109700947_    972 TTCAACAATTGGTGTTGGAAAAACTAAATATCCACATGCAAAAAAAAAAA 1021
                                 v     i   i v    ii   ?            i  v---
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT--- 446

  chrX_109700947_   1022 AAAAAGAAAGAAAGAAAGAAAAAGAAATTGGACTTTTATCTAAGACCACA 1071
                         -----------------------   i      iii  i  v v    i 
  L1M4_orf2#LINE/    447 -----------------------GAAGTTGGACCCCTACCTCACACCATA 473

  chrX_109700947_   1072 CACAAAAATCAACTCAAAATGGATTAAAGATTTAGACATAAGACCTGATG 1121
                         i        i              i ?   ii  i ii     v  i vi
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_109700947_   1122 CTGTAAAACTACTAGAAGAAAATACAGGTGAAAAGTTTCTTGACATTAAT 1171
                           i       vi          i i   ? v   vi   v    v  iiv
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_109700947_   1172 TTGGGCAATGATTTCTTGGCTATCACACCAAAAGCACAGGCAAAAAAAGC 1221
                           i       i      i v   v              i    v     v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_109700947_   1222 AAAAATATACAAATGGCACTGCATCAAACTAAAATGCTTCTGCATAGCCA 1271
                                v i    v v   v       v v   vi   i  iiivv v 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_109700947_   1272 AGGAGACAGTCAAGAGAGCAAAGAGACAGCCAACAGAATGGGAGAAAATA 1321
                             v  vi      i  ii  i     i  v                  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_109700947_   1322 TTTGCA-----TATATTGGATAAGAGGTTAATATCCAAAATATATAAAAA 1366
                               -----     iv      i ii vi      i          i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_109700947_   1367 AACTCAAACAACTTAGCAGCAAGAA---AAATCACCCGATTAAAGAATGA 1413
                          -   vv      i ii ii  i  ---    v    i   ?  i    i
  L1M4_orf2#LINE/    774 A-CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_109700947_   1414 -TAA-----TTGAGTAGACATTTCTCAAAAGAAGACATACAAATGGCCAA 1457
                         -i  -----    i            v        i              
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_109700947_   1458 CAGGTGTATAAAAA-ATGCTCAGCATCACTAATCAT 1492
                         i i iii  i    -       i     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (136 / 67)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 4.50 (45 / 10)  


3090 27.28 0.66 0.77  chrX_109705779_109712173     4994  5902 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109705779_   4994 TGGTAGAACATTCCATGCTCTTGGATAGGAAGAATCTATAT-GTTGAAAA 5042
                            v ii i  i     i  v     v      v iv    -   -  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAGA 49

  chrX_109705779_   5043 TGGCCATACTGCCCAAGGTAAATTATTGATTCAATGCTATCCCCATCAAT 5092
                             v     v     iv i vi  iv       i  v     i     v
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_109705779_   5093 CTACCC--CTGACTTTCTTCACAGAATTGGATAAAACTGCTT-TAAAGTT 5139
                         v -   --   v    i  -i     v v  i  i-   v i-    i  
  L1M4_orf2#LINE/    100 AT-CCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATT 146

  chrX_109705779_   5140 CATATAGAACCAAAAAAGAGCCTGCAAAGCCAAGACAATCCTAAGCAAAA 5189
                              i   viiv  ii  v  v v v      i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_109705779_   5190 AGGACAAAGCTGGAGGCATCATGCTACCTGACTTCAACGTATACTACAAG 5239
                           i      i      vv   ii  v  ii i     viiv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_109705779_   5240 GCTACAGTAACCAAAACAGAATGGTACTAGTATCAAAACAGATATATAGA 5289
                                   i   i    vi       i i  v ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_109705779_   5290 CCAGTGGAATAGAACAGAGGCCTCAGAAATACCACCACACATCTACAACC 5339
                         i  i          iv   ivii        vvv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_109705779_   5340 ATCTGATCTTTGACAAACCTGACAAAAACAGGAAATGGGAAAATGATTCC 5389
                          vi    i  i     ivv  v   i v  vvv      i   vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_109705779_   5390 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5439
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_109705779_   5440 GAAACTGGATCCCTTCCTTACATCATATACAAAAACTAACTCAAGATGGA 5489
                            ii    i    v   i   i            i        i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_109705779_   5490 TTAAAGACTTAAATGTAAGACCCAACACTATAAAAACCCTAGAAGAAAAC 5539
                          i ?    i           v i  v         vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_109705779_   5540 CTAGGCA-ACACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5588
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_109705779_   5589 AAACACCAAAAACAACATCAACAAAAGCCAAAATAGACAAATGAGATCTA 5638
                         vi         i  vv v         vv        i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_109705779_   5639 ATTAAACTAAAGGGCTTCTGCACAGTTAAAGAA-ACTACCATCAGAGTGA 5687
                           i   v v  iii   i  ii -v i    i -    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_109705779_   5688 ACAGGTAACCTACAGAACGGGAGAAAATCTTTGCAATCTACCCGTCTGAC 5737
                          v  ii    i      i          v       vii ivii     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_109705779_   5738 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5787
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_109705779_   5788 AAAAATAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5837
                            i i   i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_109705779_   5838 TCTCAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAACCCTC 5887
                             v        i  vi viii     i  i  i       i -iv   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chrX_109705779_   5888 ATCATCACTGGTCGT 5902
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.08 (13 / 12)  


2628 27.33 0.38 0.76  chrX_109756144_109757928      499  1292 (493)    L1M4_orf2#LINE/L1      118   908 (0)  

  chrX_109756144_    499 GCACAAAATTAGAAAAAACT-ACTTTAAATTTCAAATGGAACCAAAAAAG 547
                            -i     i-- v  i  - iii    v    v      viiv  ii 
  L1M4_orf2#LINE/    118 GCA-GAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_109756144_    548 AGCCCATATAGCCAGGACAATCCTAAGCAAAAGGAACAAAGCTGGAGGCA 597
                          v  viv       ii      i i iv  i i        i      vv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_109756144_    598 TCACACTATCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACA 647
                                vi ii i      viv        i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_109756144_    648 GCATGGTACTGGTACCAAAACAGATATATAGACCAATGGAACAGAACAGA 697
                          ii         i iv ii i   i       i        i    iv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_109756144_    698 GGCCTCAGAAATAATGCCACTTATCTGTAACCATCTGATCTTTGACAAAC 747
                          ivii         vv   ivi  i i iii  vi    i  i     iv
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_109756144_    748 CTGAGAAAAACAAGCAATGGAGGAAAAGATTCCCTATTTAATAAATGGTG 797
                         v  vv  i v  vv      -     ii  vvi  v  i  i        
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_109756144_    798 TTGGGAAAACCTGGCTAGCCATATGCAGAAAAATGAAACTGGACCCCTTC 847
                         i     v   -   v  ?   i     i  i      ii         v 
  L1M4_orf2#LINE/    414 CTGGGACAAC-TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_109756144_    848 CTTACACCTCATGCAAGAATTAACTCAAGATGGATTAAAGGCTTAAACGT 897
                           i     vi  i   i           i      i ?  i i    i  
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_109756144_    898 AAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCA-ACACCATT 946
                             v       i      vi i           v    ?i- v i -  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TT 561

  chrX_109756144_    947 CAGGGCATAGGCATGGGCAAAGACTCCATGACTAAAACACCAAAAGCAAT 996
                          iv i v v  vv i     v ii i v iiv  vi            vv
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_109756144_    997 GGCAACAAAAGCCAAACTAGACAAATGGGATCTAATTAAACTAACGAGCT 1046
                         i          vv   v    i    v   ii v  i   v v vi i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_109756144_   1047 TCTTCACAGCAAAAGAAACTATCATCAGAGTGCACAGGCAACCTACAGAA 1096
                          i vii vv    i  v       vv i    v v  i     i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_109756144_   1097 TGGGAGAAAATTTGTGCAATCTATCTATCTGACAAAGAGCTAATATCCAG 1146
                                    v v     vii  v       i  i ii  vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_109756144_   1147 AACCTACAAAGAACTTAAACAAATTTACAAGAAAAAAA-AACCAACCCCA 1195
                           iv  i        ivv    v iv i  v     i -  vi     v 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_109756144_   1196 TCAAAAAGTGAGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATT 1245
                          i?    i  i         v    i     i     v        i  v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_109756144_   1246 TATATGGCCCACAAACATATGAAAAAGAGCTCATCATCACTGGTCAT 1292
                         i v      v i  i  i       iiv     v     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (127 / 86)
Gap_init rate = 0.01 (8 / 791), avg. gap size = 1.12 (9 / 8)  


1288 22.56 2.36 0.34  chrX_109812875_109815553.rev      504   800 (1879)    L1M4_orf2#LINE/L1      268   570 (338)  

  chrX_109812875_    504 TGGTACTGGTATAAAAATAGGCATATAGACCAATGGAACAGAATAGAGAA 553
                                  i    ii    i        i        i     v    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_109812875_    554 CCCAGAAATAAACCCAAATACTTACAGCCAACTGATCTTCAGCAAAGCAA 603
                         i               v i i   ii i   i    i   ii   i vvi
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_109812875_    604 ACAAAAACAT-AAATGTGG---GGGT--CCTTTTCAACAAATAGTGCTGG 647
                         v   i v   -v    v  --- ii --i             i       
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_109812875_    648 GATAACTGGCAAGCCACATGTAAGAGAATGAAACTGGATCCTCGTCTCTC 697
                           i      vv ?       i  i        ii    i  iiii   v 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_109812875_    698 ACCTTATACAAAAATCAACTCAAGATGGATTAAGGACTTAAACCTAAGAC 747
                            v           i       i      i ?i   i    iv     v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_109812875_    748 CTGAAACTATAAAAACTCT-AGAAGATAACATTGGAAAAACCCTTCTAGA 796
                           i           -    -      v     v  ?iv  vi    vv  
  L1M4_orf2#LINE/    518 CTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_109812875_    797 CATT 800
                          v  
  L1M4_orf2#LINE/    567 CCTT 570

Transitions / transversions = 2.05 (43 / 21)
Gap_init rate = 0.02 (5 / 303), avg. gap size = 1.60 (8 / 5)  

1105 24.62 3.30 0.00  chrX_109812875_109815553.rev     1856  2188 (491)    L1M4_orf2#LINE/L1      565   908 (0)  

  chrX_109812875_   1856 GACATTGGCTTAGACAAGGATTTCATGACCAAAAACCCAAAAGCAAATGC 1905
                            v    v    i   v i    v iivi vi vv         v v  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_109812875_   1906 AATAAAAACAAAGATAAATAGCTGTGACCTAATTAAACTAAAGAGCTTTT 1955
                           i    iv   i   i   iv vv   i v  i   v v  i i     
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_109812875_   1956 GCATGGCAAAAGGAACAGTCAACAGAGTAAACAAACAACCCACAGAGTGG 2005
                          iiivv    i iv  vi    v i   i  v i            i   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_109812875_   2006 GAGAAAATCTTCACAATCTATACATCTGACAAAGGACTAATATCCAGAAT 2055
                                 v  ii   vii   i      i  i     vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_109812875_   2056 TTACAATGAAC------AAATCAGTAAGAAAAAAA-----AATCCTATCA 2094
                         v  i  v    ------  v   i   v     i -----  i  v  i?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_109812875_   2095 AAAAGTGGGCCAAGGACATGAATAGACAATTCTCAAAAGAAGATATACAA 2144
                             i     v     iv          v     v               
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_109812875_   2145 ATGCCCAACAAACATATGAAAAAATGATCAACATCACTAAAGAT 2188
                            v    i  i  i       i   v         ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (44 / 37)
Gap_init rate = 0.01 (2 / 344), avg. gap size = 5.50 (11 / 2)  


1955 24.91 4.91 1.40  chrX_109826478_109829519.rev      317   886 (2156)    L1M4_orf2#LINE/L1        1   590 (318)  

  chrX_109826478_    317 TGGAGAGATACTCCATGTTTGTGTTTAGGAAAACTCGATATTGTCAAGAT 366
                             i     ii       ii  vv v    i   ii       i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109826478_    367 ATCAGTTTTTCCCAACTTGATGAATAGATGCAATACAATATC-AGTAAAA 415
                         iv  i vi i     v     vv i    v   ii    vi - vi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_109826478_    416 TCCCAGCAAGTTATTTTGTGGATGTCAACAAACTGACTCTAAAGTGTATA 465
                                vivi v     ii  vi ii    i    ii     i vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_109826478_    466 TGGTAAGGCAAA--ACCCAGAACAGCCAACACAATATT---AAAGGAGAA 510
                            v  v    i--        i      v     v  ---    i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_109826478_    511 CAAA---------CTCAC--TACCCAACTTCAAGACTTACTATTAAGCTA 549
                             ---------     -- v     i     i        iv      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_109826478_    550 TGGTAATCAAAGTTATGAGATATTGGCA-AAGTAATAGAAAAATAGATCA 598
                         ii        iiivi  v i  i     -   -i     v v        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATATAGATCA 299

  chrX_109826478_    599 AGGGAATGTAATAGAGAGCCCAGAAATAGACCCAAATAAACATCATCAAC 648
                          v     iv   v     i         i     v i vvi  vi    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_109826478_    649 TGATCTTTAACAAAG----TAA-----TTCAATGGAGAAAAAATAGTCTT 689
                             i  ii    i ----i  -----        i    i         
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_109826478_    690 TTGAATAAATGGGTGCTGGAACAACTGGGCATCCATATCCAAAATGTAAA 739
                           v  i      -      i        ii ?   i  v     ---i  
  L1M4_orf2#LINE/    400 TTCAACAAATGG-TGCTGGGACAACTGGATAKCCACATGCAAAA---GAA 445

  chrX_109826478_    740 TAAATCTAGACATAGATTTCACACCCTTCACCAACATTTACTCAAAATGG 789
                          i  vi i   vivv ii       v vi  v  v   v           
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_109826478_    790 AACACAGACATGAGTGTCAAATGC-AAAGCTAAAGAACCCTTAGAGGATA 838
                          v  ?    v i i   v i -  -   i   v i   i      i  v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_109826478_    839 ATATAAGAGAAAAATTTAGGTAACCTTGGATTTGGCAATGACTTGCTT 886
                          i   i ? v   vi  v - i       i  v       ii  -   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTT-CTT 590

Transitions / transversions = 1.62 (86 / 53)
Gap_init rate = 0.03 (15 / 590), avg. gap size = 2.40 (36 / 15)  

1822 26.80 2.68 1.17  chrX_109826478_109829519.rev     1627  2223 (819)  C L1M4_orf2#LINE/L1   (0)   908   303  

C chrX_109826478_   2223 GAACAGAATAAGAAGCCCAGAAATAATGTCACA-------GACCATTTGA 2181
                            i     viii  i          vvi  i ------- ii  v    
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

C chrX_109826478_   2180 TCTTCGACAAAGTCAACAAAAACAAGCAATGGAGAAAGGAATC-CCTATT 2132
                          i        i viiv   i v  vv      i     -   v-i  v  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTTTT 401

C chrX_109826478_   2131 CAATACGTAGTGTTAGGATAACTGGCTCGCCATATGCAGAAGACTGAAAC 2082
                            i vi i   i i   i      v v?   i     i    v    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

C chrX_109826478_   2081 TAGACCCCTTCCTTAAACCATGTACAAAAAGTCAACTCAAGATGGGTTAA 2032
                          i       v   i v     i        - i       i    i i ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAW 500

C chrX_109826478_   2031 AGACTTAAATGTAAAACCTAAAACTATAAAAACCCTGGAAGATAACCTAG 1982
                             i         i v              vi i i     v   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

C chrX_109826478_   1981 G---AAATGCCATTCTAGAAAAAGGAACTGGCAAAGATTTCATTACAAA- 1936
                          ---    -- -   vv  vvvv  iviv     v i    -   v v -
  L1M4_orf2#LINE/    551 GNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATAT 596

C chrX_109826478_   1935 GATGCCAGAAGCAACTGCAACAAAAATAAAAATTAGCAAGTGGAATCTAA 1886
                           ii   i     vvv         iv      viii  i v i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_109826478_   1885 TCAAACTAAAGAGCTTCTGCACAGCAAAAGAAAGCATCCACAGAGTAAAC 1836
                              v v  i i   i  ii vv    i  v vi   v v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_109826478_   1835 AGATAGCCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCTGACGA 1786
                            i i  i                          ii  ii      ii 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chrX_109826478_   1785 AGGTCTAATATCAAGAATCTGTAAGGAACTTAAACAAACTTA-TAAGCAA 1737
                         i  v  vi    v     v i   i     ivv    -  i -   vv  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAA 795

C chrX_109826478_   1736 AAAACAAATAACCTCATTAAAAAGCAGATAAAGGACATGAATAGACACTT 1687
                           i          iv   ?    iii ii      iv          i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

C chrX_109826478_   1686 TTC---AAAAGACACGCATGTAGTCAACAAGCACATGAAAATGTGCTCAG 1640
                         i  --- i    i ii  vi i i   i             vi      i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

C chrX_109826478_   1639 TATCACTGATCAT 1627
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (97 / 60)
Gap_init rate = 0.02 (12 / 606), avg. gap size = 1.92 (23 / 12)  

1453 20.12 1.83 0.00  chrX_109826478_109829519.rev     2224  2551 (491)    L1M4_orf2#LINE/L1      575   908 (0)  

  chrX_109826478_   2224 TGGGCAATTACTTTTTAGATACAACACCAAAGGTTCTATCCAAGAAAGAA 2273
                          i      vii  i       ii        i iv v v v vi      
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_109826478_   2274 AGAATTGATAAATTTGACTTCATGAAAATTAAAAATTTCTGCTCTGCAAA 2323
                          i   v        v        v           i  i  iv  v    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_109826478_   2324 TGACACTGTCAAGAAAATAAAAAG-----CCACAGACTGGGA-AAAATAT 2367
                         v      i        i i     -----       v     -       
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_109826478_   2368 TTGCAAGAGACATATCTGATAAAGGACTGTTATCCAAAATATACAAAGAA 2417
                               ivv i           i     vv      i      i      
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_109826478_   2418 CTCTTCAAACTCAACAATAAGAACACAAACAGCTCTATTTAAAAATGGAC 2467
                              vv       i     i  v     i i i v   ?        i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_109826478_   2468 CAAAGACCTTAGCAGACACCTCACCCAAGAATGTATACAGATGGCAAATA 2517
                         v  i  ii v ii     ii  v  v     vi      i     v    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_109826478_   2518 AGCATATGAAAAGATGCTCTACATCATATGTCAT 2551
                             i              v      ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (37 / 28)
Gap_init rate = 0.01 (2 / 334), avg. gap size = 3.00 (6 / 2)  


3197 26.43 0.99 0.99  chrX_109866379_109872646.rev     4870  5777 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_109866379_   4870 TGGAAGAACATTCCACGCTCATGGGTAGGAAGGAAGAATCAATATAGTGA 4919
                              ii i  i   i i      i v     ---- v i     v  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAG----ACTTAATATTGTTA 46

  chrX_109866379_   4920 AAATGGCCATACTGCCCAAGGTAATTTATAGATTCAACGCCATCCCCATC 4969
                          i     v     v     iv i  i  i           v     i   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_109866379_   4970 AAGCTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAG 5017
                           iv v   iivi i  i  ii     -   -- v  i  - iii    i
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAA 144

  chrX_109866379_   5018 TTCATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCA 5067
                                    viiv  ii  v  v v  vi    iv     i i ivv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_109866379_   5068 AAAGAACAAAGCTGGAGGCATCACTCTACCTGACTTCAAACTACACTACA 5117
                         i          i      vv    v  v  ii i      vivi      
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_109866379_   5118 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 5167
                          i          i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_109866379_   5168 GATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTAC 5215
                                    i    i--    i  --        vv  ii i  i  i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTAT 342

  chrX_109866379_   5216 AACTATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGTAAGGA 5265
                         iiii vi    i  i     ivv  v   i v  vv        v   i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_109866379_   5266 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 5315
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_109866379_   5316 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGA 5365
                         iiv    ii    i    v   i     v           i  i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_109866379_   5366 TGGATTAAAGACTTACATGTTAGACCTAAAACCATGAAAACCCTAGAAGA 5415
                              i ?    i  v    v   v       i  i   vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_109866379_   5416 AAACCTAGGCATTACCATTGAGGACATAGGCATGGGCAAGGACTTCATGT 5465
                             v    ?i v viv  viv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_109866379_   5466 CTAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGAT 5515
                         v  vi            vvi           v     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_109866379_   5516 CTAATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5565
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_109866379_   5566 GAAAAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTG 5615
                               i     i   i             v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_109866379_   5616 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAACTTA-CAA 5664
                          i  i  i  vi          v  i  v      vv    -  i -i  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAA 791

  chrX_109866379_   5665 GAAAAAAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGAC 5710
                         v     i    ----   v  i?    i     i     iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_109866379_   5711 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGC 5760
                          i     v        i  vi viii     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_109866379_   5761 TCATCATCACTGGCCAT 5777
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


 675 24.21 3.68 0.53  chrX_109875178_109879331     2107  2296 (1858)    L1M4_orf2#LINE/L1        1   196 (712)  

  chrX_109875178_   2107 TGGATGGAAATACCATATTTGTATCTTGAAAGACTTG----TCTTAAGAT 2152
                             vi  v  v    i  ii ivv   i       i---- v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_109875178_   2153 GTTCAT-TTCCCCAAAATGATCTAGGGATATAAC-CATATGCCAAACATA 2200
                          viv  -i        v       vi   vi   -  -  v  v v  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCA-ATCCCTATCAAA 99

  chrX_109875178_   2201 ATCCCATCTGGCTCTTTCATAGAAATGTACAAACTAATTCTAAAATTTAT 2250
                               v   v  i   iii      vv    i  i  i        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_109875178_   2251 TTGGAAATACAAAGGACCTAGA-TATCCAAAGCAATCTTAAAAAAAA 2296
                         v       i   i     i   -  v     i       i     i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

Transitions / transversions = 1.19 (25 / 21)
Gap_init rate = 0.03 (5 / 196), avg. gap size = 1.60 (8 / 5)  

 858 28.11 5.22 0.00  chrX_109875178_109879331     2652  2900 (1254)    L1M4_orf2#LINE/L1      214   475 (433)  

  chrX_109875178_   2652 CCTATACTT---GACTTCAATGTTTATTGTAAAACTACTGTAATCAAGAC 2698
                          ii i    ---i i     vii   i ii   i    v           
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_109875178_   2699 CATATATCATTGGCATAAGGACTGACAAATAAGGTGATGGAACAAAATAT 2748
                         vi i ivi i           iv    v   iivii      i i   vv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_109875178_   2749 AGAGTCTACAAATAGACACACACTTATATAGTCATCTGATTTTTGACAAA 2798
                               i v     i  v  i  v v   i    vi       i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_109875178_   2799 GATGCTAAAACAATTCAATGAGAAAAGTAAAGAATCCTCAACAAATGGTG 2848
                          i   i  i  v        i i    v v  vv ii             
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_109875178_   2849 CTGGAA-AACTGGATATACAAATA---------GAAACTTAATCTCTACC 2888
                             i -         ?v  v  i---------   ii vi i i     
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_109875178_   2889 TCAAACTACATA 2900
                            v  i i   
  L1M4_orf2#LINE/    464 TCACACCATATA 475

Transitions / transversions = 2.00 (46 / 23)
Gap_init rate = 0.01 (3 / 262), avg. gap size = 4.33 (13 / 3)  

1004 21.97 13.38 1.52  chrX_109875178_109879331     3266  3661 (493)    L1M4_orf2#LINE/L1      466   908 (0)  

  chrX_109875178_   3266 ACACCATA--CAAAAATTAATTTGCATAGGATTACATATCTAATGATAAA 3313
                                 --          i iiv vv    i ? v i    vvi   i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_109875178_   3314 A-CTTAAGCCATAAAAATTCTC----GAAAATATAGGAGCATATCTCTAT 3358
                          -  v  i i      -i   i----     i     ? i v    iii 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_109875178_   3359 GAACCAGGAGTAGGCAAAAGTTTCTTAG----GACAC-AGAA--ATAATT 3401
                           v iv  iv       vi         ----     - i  -- i  vi
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_109875178_   3402 ATATAATA---AAAATTGATACATTAAACATCATCAAAATTAAAAACAGC 3448
                          - i  v ---     v    v   ii  v                 --i
  L1M4_orf2#LINE/    615 A-ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC--T 661

  chrX_109875178_   3449 TTTTTA--TCAAAATACACCATTAAGAAAATGAACAGACAAGCCACATTC 3496
                            v i--     iv    i  i      i    v      v     vvv
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_109875178_   3497 TAAGAGAAAGTATCC-CAAAGCATATATCAGATAAAGAAATGGTATTCAG 3545
                          ii      i   ii-    v        v     i i v v    i   
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_109875178_   3546 AATATATAAAGA--------------------------CAAATAACCTAA 3569
                                     --------------------------         i  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_109875178_   3570 TC--AAAACAGGCAAAATGTTTAAACAGA-AT--CTTCACAAAAGATATG 3614
                          i--    ii      ivi   i  i   -  --  i  v i       i
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_109875178_   3615 TGAATGACCAATAAGCACATGAC--TATGCAGTCAACATCATTAGATAT 3661
                         ii    i               v--v    --         ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGC--TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (53 / 32)
Gap_init rate = 0.04 (18 / 443), avg. gap size = 3.28 (59 / 18)  


4730 16.22 1.01 1.12  chrX_109916647_109918707      667  1560 (501)    L1M4_orf2#LINE/L1        3   895 (13)  

  chrX_109916647_    667 GGAAGACATTCTGTGTTCATGTAATGGAAGGCTTAATATTGTTA-GATGG 715
                          i    i  i ii        v v      i             -     
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_109916647_    716 CAGTACTCCCCAAAGTGATATACAGATTCAGCGCAATCCCTATCAAAACC 765
                           i           v    v          i                 i 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_109916647_    766 CCAACAGTCTTTTTTTTTGCACAAATGTAAAAGCTGATTCTCAAATTCAT 815
                            i v i       ---   v    vv v        i  v        
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_109916647_    816 ATGAAATTGTAAGGAACCTCAAGTAGCCCATA-AATCTTTAAAAAAAAGT 864
                            i  v  i    i   ivi i     v v -      v     i   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_109916647_    865 ACAAAGTTGGAGAACTCACACT-CCTGACTTCAAAACTCATTACAAAGAT 913
                                     i         -  ii i         i i       v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_109916647_    914 ATAGTAATCAAAACAGAGTGGTACTGGCAAAAAGACAGACATATAGATCA 963
                          i         i    v            v  i  i              
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_109916647_    964 ATGGAATAGAATTGAGCACCCAGAAATAAACCCCTCCGTCTATGGTCAAT 1013
                                         vii              v v i i          
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_109916647_   1014 TGATTTTTTAGAAAGATGTCAAGATCATTCAGTACAGAAAGAATAGTCTC 1063
                                iv v  i i  i     i      i ivi             i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_109916647_   1064 TTTA-CAAATGGTACCGAGACAACTAGATATCTACATGCAAAATAATGAA 1112
                           i -        i i i       i    ? i          v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_109916647_   1113 GCTGGATCTTTATCTTATACCATATACAAAAATTAACTCAAAATGGATCA 1162
                          i    i ii  i  i i                                
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_109916647_   1163 AAGACCTAAATATAAGAGCTACAACTACAAAACTCTTAGAA---AACATA 1209
                         ?          i         v     i             ---      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_109916647_   1210 GTGGACATGAATCCTTCATGTCCCTGAATTTGGCAATGGTTTCTTAGCTA 1259
                          v? --- i    -   i  v  i  ii  v                v  
  L1M4_orf2#LINE/    550 GGNG---TAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_109916647_   1260 TAATACCAAAAGCACAAGCAATGAAAGAAAAAATGGATAAACAGGACTTT 1309
                          i i                 ii           i      iv      i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_109916647_   1310 ATCAAAATTAAAAACTTTTTGTGCATCAAAGCATACTGTAAACAGAGTGA 1359
                                            -    v      v i   i v  v i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_109916647_   1360 AAAGACATACCACAGAATACGAAAAAGTATTTGCAAATCATATATCTGAT 1409
                                vv         iv  i   i                       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_109916647_   1410 AAAGTTCTCCTATCCAGAATATATAAAGAACTCTAGCAACTCAACAACAA 1459
                           i vv  iv                        vi        i  i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_109916647_   1460 AAGG-CAAACAACCCA-TTAAATGAAAGATTCAAACAATTTGCATAGATA 1507
                           i -    i      -  ?  --   vivv    vi     v     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAA--AAATGGGCAAAGGATTTGAATAGACA 842

  chrX_109916647_   1508 TATCTCAGAAGAAGATATGCAAATGGCCAAAAAGCTCATGAAAAGTTGTT 1557
                          v    vi          i           v    v         v  i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_109916647_   1558 CAA 1560
                            
  L1M4_orf2#LINE/    893 CAA 895

Transitions / transversions = 1.66 (88 / 53)
Gap_init rate = 0.01 (12 / 893), avg. gap size = 1.58 (19 / 12)  


3151 26.99 1.00 0.66  chrX_109948019_109954335.rev     4923  5826 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_109948019_   4923 GGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAATG 4972
                             ii    i     i        v      v i     ii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_109948019_   4973 GCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCGCATCAAGCT 5022
                           v i   v     iv i  i  i        i  v    vi     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_109948019_   5023 ACCAATGACCTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTCA 5070
                         v   iivi    i  ii     -   --- v  i  - iii    i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCA 148

  chrX_109948019_   5071 TATGGAACTAAAAAGGAGCCCACATTGCCAAGACAATCCTAAGCAAAAAG 5120
                                v iv  i   v  viv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_109948019_   5121 AACAAACCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5170
                               vi      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_109948019_   5171 CACCATAATCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5220
                         i  vi       i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_109948019_   5221 AATGGAACAGAA--AAGAGGCCTCAAAAATAACACCACACATCTACAATC 5268
                                i    --i    v  -- i      vv   i    i  iii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_109948019_   5269 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAACGGGGTAAGGATTCC 5318
                          vi    i  i     ivv  v   i v  vvv  i    v   i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_109948019_   5319 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCCCATGTAGAAGGAT 5368
                           v  i  i              v      v  ?  v    i i   i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_109948019_   5369 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGG 5418
                            ii    i    v   i     v  i           i    i    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_109948019_   5419 TTAAAGAGTTATATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5468
                          i ?   vi  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_109948019_   5469 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5517
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_109948019_   5518 AAACATCAAAAGCAATGGCAGCAAAAGCCAAAATAGACAAATGGGATCTA 5567
                         vi   i        vvi   i      vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_109948019_   5568 ATTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACTACCATCAGAGTGAA 5617
                           i   v v  i i   i vii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_109948019_   5618 CAGGCAGCCTACAGAATGGGTGAAAATTTTTGCAATCTACCCATCTGACA 5667
                         v  i  i  i          v      v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_109948019_   5668 AAGAGCTAATATCCAGAATCTACAAACAACTCAAACAAATTTACAAGAAA 5717
                          i ii  vi          v  i   v     vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_109948019_   5718 AAAACAA----CCCCATCAAAAAGTGGACAAAGGATATGAACAGATACTT 5763
                           i    ----   v  i?    i   i        v    i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_109948019_   5764 CTCAAAAGAGGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5813
                            v     i  i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_109948019_   5814 CATCACTGGCCAT 5826
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (8 / 907), avg. gap size = 1.88 (15 / 8)  


3857 17.76 4.22 1.24  chrX_110065863_110069682     2119  2923 (897)    L1M4_orf2#LINE/L1        1   829 (79)  

  chrX_110065863_   2119 TGGAAATACATCTCATGCTCTTAGATTGAAAGACTTAACATATTTATGAT 2168
                               v i   i    i  v i     i         i  vv   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_110065863_   2169 GTCA---CTACCCAAAGTGATCTACAGATTCAGTGCAATCCTTATCAAAA 2215
                          v  ---  v      v               ii       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_110065863_   2216 CCCCAGTGACTTTTGTTGCAGAAATAGGAAAATCCATCCTAAAATTTATA 2265
                         i     ivi i   v          v iv  iiiv           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_110065863_   2266 TGGAATCTCAAGGGACCCCAGATGAGTGAAACAATCATGAAACAGAG--- 2312
                              viv          vii  iivii        v     v   i---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_110065863_   2313 CAAAGTTGGAGAACTCACACTTCTTAATTTCAAAACATACTACGAAGCTT 2362
                                    i           ii           v      i     -
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT- 249

  chrX_110065863_   2363 ACAGTAATCAAAATATTGTGGCACTGTCATAATGACAGACACATATACCA 2412
                                    i i v     i    v     v  i     i   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_110065863_   2413 ATGGAGTAGAA--GAGAGCCCAGAAATAAACCC-T-CATTAGATGGTACC 2458
                              i     --     i              - -    -v     -- 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGGT--C 346

  chrX_110065863_   2459 TTTTTGTACCCTTTTGACAAGGGCACAAAGTCCATTCAATAGGGAAAGAG 2508
                         vv  vi ----   i        ii v   v         i        i
  L1M4_orf2#LINE/    347 AATTGAT----TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_110065863_   2509 CAATCTTTCCAACAAATGGTGGCTGGGAAAACTGGATATCCACATGCAAA 2558
                         i i     i            -      v         ?           
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTG-CTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_110065863_   2559 GGAATGATGTTGGGCCTTTACCTTACACCATATACATAAATTAACTTAAA 2608
                         i      v     i  ii     i            v         i   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_110065863_   2609 ACAGATAAAACACCTAACCATAATAACTAAAACTATAAAACTCTTAGAAG 2658
                          ii   v ? v      vii   v i                        
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_110065863_   2659 AAAACATAGGGGAAAATCTTCGTGACATTGGATTTGGCAATGATTTATTG 2708
                                   ? v             v    i  v       i   v  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_110065863_   2709 TATATGACATCAAAAGCATAGGCAACAAAA----AAATGGATAAGTTGGA 2754
                         v        i        i i         ----    i     i     
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_110065863_   2755 TGTCATTAAAATTAAAAACCTTTATGTATCAAAAGACAATATCAG---AG 2801
                         iv    i            i   i  iv     i    v     i---  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_110065863_   2802 TGAAAAGGCATCCTACAGAATGAGAGAAAGTATTTGCAAATCCTATATCT 2851
                                i  v  i        i      i            v       
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_110065863_   2852 GGTAAGGGATTGATATCCAGAAT-TGTAAA------------CTCAACAA 2888
                          i       i vi          - i    ------------     i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_110065863_   2889 CAACCA--CAAA--ATTCGATTATAAAATTATGCAAAGG 2923
                         i  vv --    -- ii i   ?v     vi-       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGG-GCAAAGG 829

Transitions / transversions = 1.67 (87 / 52)
Gap_init rate = 0.02 (17 / 829), avg. gap size = 2.59 (44 / 17)  

 548 10.23 0.00 0.00  chrX_110065863_110069682     3240  3327 (493)    L1M4_orf2#LINE/L1      821   908 (0)  

  chrX_110065863_   3240 GGGCAAATGATTTGAATATACATTTCTCCAAAGAAGATATACAAATGACC 3289
                                v          v                            i  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_110065863_   3290 TATATACACATGAAAAGGTGCTTGACATCACTAGTCAT 3327
                         v   vi           i    ii      ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (5 / 4)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.00 (0 / 0)  


 335 24.39 4.27 2.44  chrX_110107309_110110502.rev       17   180 (3014)    L1M4_orf2#LINE/L1      742   908 (0)  

  chrX_110107309_     17 GATAAG--ATTTTTATCTAGAATATAATAATAAACACCTTCAAATCAATA 64
                               -- i  v    i        -   vi   v i v   v      
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATA-TAAAGAACTCTTACAACTCAATA 790

  chrX_110107309_     65 AGACAAAGATGATCAACACAATAGCAAGATAGGCAAAGAAT---AAAAGC 111
                          v v     ii vi   v    v?v  i  i       i  ---  v  -
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG- 839

  chrX_110107309_    112 CAACAGTTCACGGAATAAGAAACCCAAATGGCCAATAAGT-C-TAAAAAT 159
                         --   v   v vi  v    v iv               i- - i    v
  L1M4_orf2#LINE/    840 --ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_110107309_    160 CTATTCAATTTTACCACTAAT 180
                         v ii    iv i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.86 (18 / 21)
Gap_init rate = 0.04 (6 / 167), avg. gap size = 1.83 (11 / 6)  

 618 17.54 3.51 0.88  chrX_110107309_110110502.rev     1546  1659 (1535)    L1M4_orf2#LINE/L1        1   117 (791)  

  chrX_110107309_   1546 TGAAAAGACATCCTATGTTCATGGATTGGAAGGTTTAACATT---AACAT 1592
                           i     i    i                  ii    i   ---  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_110107309_   1593 GGCAACACTCTTCAAATTGACCTATAGATGCGATGCAATCCCCATCAAAA 1642
                              i    ii        i   i    v i i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_110107309_   1643 CTCTAA-TGCTCTTTTTT 1659
                         ii i i-   -       
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTT 117

Transitions / transversions = 9.00 (18 / 2)
Gap_init rate = 0.03 (3 / 117), avg. gap size = 1.67 (5 / 3)  

2859 15.71 14.29 1.57  chrX_110107309_110110502.rev     2004  2703 (491)    L1M4_orf2#LINE/L1      120   908 (0)  

  chrX_110107309_   2004 AAAAAAGGAAAAGTTGATCCTAAAATTCATATGGAAATACCAGGGCCTCG 2053
                          i   vv  v   i                        i v    v i i
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_110107309_   2054 TGATAGGCAAAACAATCTTGAAAAAGATC--TAAAAT--GAAGACTCATA 2099
                         vi    v                    vv--i   i --  i      i 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_110107309_   2100 ATTCCCAGTTTCAGAACTTACTACAAAGTGACAGTAACCAAG-------- 2141
                         v      i     i              iv       i    --------
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chrX_110107309_   2142 ----TGGCATAAGGATAGATAGCTATGTCAG-TCAATGGAACAGAATTGA 2186
                         ----               i --   ---  -         i        
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACA--TAT---AGATCAATGGAATAGAATTGA 314

  chrX_110107309_   2187 GAGTCCA------------------------------------------- 2193
                                -------------------------------------------
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_110107309_   2194 ------AGACCATTCAAAGGAGAAA-AGCAGTTTCTTCAACAAATGGTAC 2236
                         ------           v  i    - ii   i i             i 
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_110107309_   2237 TGAGACAACTGGATATCCACATGCAAAAGAATAAATTTTGACCACTGTCT 2286
                           i            ?                i  v  v    v  ii  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_110107309_   2287 TA-----TATACAAAACTTTACTTGAAATGG-TCAAAGACCTAAATGTAA 2330
                         i -----         v  v   ii      -   ?              
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_110107309_   2331 TAGCTAAAACAATGAAACTC--AGAAGAAAATATAGGGGTCAATATTTTG 2378
                         v         v  i      --         i     ?  v   -i  i 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCG 563

  chrX_110107309_   2379 TG--TTTGGACTAGGCATCATTTTCTTAAATATGATGCCAAAAGTGAAAG 2426
                           --i    ii      viiv       i      ii       iiv   
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_110107309_   2427 CAACCAAAGAAAAAAACTCAATAAGTTGAATTACTT-----TT------T 2465
                             v          -- vi    i   i i v v -----  ------ 
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAA--TAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_110107309_   2466 TTGGGTGTGTGTCAAAGGGCACTATCAAGAAA-TGAAAAGACAACCCACA 2514
                           ---    iv       i             -                 
  L1M4_orf2#LINE/    662 TT---TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_110107309_   2515 GAATGGAAGAAAATATTTGTAAATCGTAAATCTCCTGAAGCACTTTTATC 2564
                               i            i     i  v    vv i i v    v    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_110107309_   2565 TAGAATATATAAGGAACACTTACAACTCCATAA--GAAAGA----TAACA 2608
                         i           i    v          v    --i     ----    v
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_110107309_   2609 CAATT-AAAAATGG-CAAAT-ATCTGAATGAACATTTCTTCAATGAAGAT 2655
                              -        -    v-  i     ii        i   v      
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_110107309_   2656 ATACAAATGGTGAAAAACTACA--AAAAGATATTCAACATTATTAATCAT 2703
                                   iv  v  vi   --       ii       i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (66 / 41)
Gap_init rate = 0.03 (24 / 789), avg. gap size = 4.62 (111 / 24)  


3683 16.82 4.57 5.01  chrX_110284371_110286236      476  1373 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_110284371_    476 ATGTTGATAAGTTAAATGCCCTGTAATATTGTTAAGATGGCAATATTCCC 525
                              v  iii  ii v v i --                     i    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTT--AATATTGTTAAGATGGCAATACTCCC 62

  chrX_110284371_    526 CAAATTAATATACAGATTCAATTCAATGCCTATCAAAATCCTAGCTGGCT 575
                               i  v           iv    v             i     v  
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_110284371_    576 TCTTTGCAGAAATTGA-AA----------AAATT----TGA-----CAAG 605
                          i              -  ----------     ----  i-----    
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_110284371_    606 CTGACCCAAAATAACAAAAAT--TATTCAAAGATAAGGAAACAGTTGGAG 653
                         v-      i    i v    i-- v  v   i v   i v v        
  L1M4_orf2#LINE/    163 G-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_110284371_    654 GTCTCACACTTTCTAATTTCAAAATTTACTACAGAGCCATAGCAATCAAA 703
                          v         i i          i        i   i i  i      i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_110284371_    704 ACAGCATGGTACTATCATA-GGATAGACATA--GAT-AATAGAATATAAT 749
                             ii       iv    -           --   -   i     v   
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_110284371_    750 TGAAAATCCAGAAATAAATCCACACATTTGTGGTCCATTGGTTTTCAACA 799
                            i i            i   i      i     v    i     i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_110284371_    800 AGAGTGCCAACACTATTCAATGGGTAAAGAATGGTCTTTTCAAACAAGTG 849
                           i       v  i          v       i          -   i  
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA-CAAATG 410

  chrX_110284371_    850 AAATAAACCATTTGCACA--TGGATATCCACATGCAAAAAAAAAAAAAAA 897
                         i-------iii v v   --      ?            i  vi  i---
  L1M4_orf2#LINE/    411 G-------TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG--- 450

  chrX_110284371_    898 AAACAAATTTGGATTCTTGCAGTACATCATATACAAAAATTAACTCAAAA 947
                         --------     ii i i vvi   i                       
  L1M4_orf2#LINE/    451 --------TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_110284371_    948 TGGATTAAAGTCCTTAACATAAAAGCTAAAACAACAAATCTCTTAGAACA 997
                              i ?  v   v  ii   i         v i   v         v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_110284371_    998 ---CATAGGCATAAATCTTTGTGACATCGGATTAAGCAATGATTTAAACA 1044
                         ---      ?i        i     v i  i   i      i   --- -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT---C- 588

  chrX_110284371_   1045 GTGGATTAAGCAATGATGTAAGCTGTCACACCAAAACCACAAGCAGCAAA 1094
                         -----   ------   i i -------        v        i    
  L1M4_orf2#LINE/    589 -----TTA------GATATGA-------CACCAAAAGCACAAGCAACAAA 620

  chrX_110284371_   1095 AGAACAAACAGATAAATTGGGCATCATCAAAATTAAAAATGTTTGTGCAT 1144
                             v   i           i v                iv       v 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_110284371_   1145 GAAAGGACAA-ATCAAGAAATAGAAGGAACAACCCAGAAAATGGCAGATA 1193
                         v        v-         vv   iii        v i     v   v 
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_110284371_   1194 ATATTTGCCAAGCATAT--CTGTTAAATGGCTTAGATCCAGAATATATAT 1241
                                 v  v     --   v   iv i   iv              v
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_110284371_   1242 ATAAAGTCT-ACAACTCAATAA--AAAAGACAA----CCCATTTTTAACA 1284
                          -i  v   -            --         ----    v  ?v  v 
  L1M4_orf2#LINE/    771 A-GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_110284371_   1285 TGGGCAAAGGATCTGAATACATATTTTTCTGAGTAAGATGTACAAATTTC 1334
                                     i      v i    i  ii iv     i       vv 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_110284371_   1335 TAATAAGGGCATAAATAGATGCTCAACATCATTAGCCAT 1373
                         i      vi   i  v               ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (88 / 59)
Gap_init rate = 0.03 (25 / 894), avg. gap size = 3.44 (86 / 25)  


2894 27.31 0.77 0.77  chrX_110389388_110395527     4740  5647 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_110389388_   4740 TGGAAAAACATTCCATCCTCATGGATAGGAAAAATCAATATCGTGAAAAT 4789
                               i i  i    vi        v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_110389388_   4790 GGCCATACTGCCCAAAGTAATTTATATATTCAGTGCTATTCCCATCAAAC 4839
                            v     v      v i  i  i v     ii  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_110389388_   4840 TACCATTGACATTCTTCACAGAATTAGAAAAAAAACACTTTAAATTTCAT 4889
                          v   vivi v  i  ii     v v  v  ivvi- iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCAT 149

  chrX_110389388_   4890 ATGGAA-T-CAAAGAAGACCCTGTATAGCCAAGACAATCTTAAGCAA-AA 4936
                               - -   i --     v v        i        i iv  -  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_110389388_   4937 GAACAAAGCTGGAGGCATCACGCTACTTGACTTCAAACTATACTAGAAGG 4986
                                 i      vv    i  v iii i      viv     v  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_110389388_   4987 CTACAGTAACCAAAACAGCACGTTACTGGTAGCAAAACAGTCATATAGAC 5036
                                  i   i    iii v      i vv ii i  v        i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_110389388_   5037 TGATGGAACAAAACAGCAACCTCAGACATAATACCACACATCTACAACCA 5086
                         ii      i i  iv vi vii    v    vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_110389388_   5087 TCTGATCTTCGACAAACCTGACAAAAACAAACAATGGGGAAAGCATCTCC 5136
                         vi    i        ivv  v   i v  vv            v  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_110389388_   5137 TATTCAATAAATGGTACTGGGAAAAACTGGCTAGCCATATGTAGAAAACT 5186
                          v     i       i      v  -    v  ?   i   i i  i v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAAT 446

  chrX_110389388_   5187 GAAACTGGACCCCTTCCTTATATCTTACACAAAAATTAACTCAATATGGA 5236
                            ii         v   i i i v  i                v     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_110389388_   5237 TTAAAAACTTAAATGTAAAACCCAAAACCATAAGAACCCTAGAAGAAAAC 5286
                          i ? i  i         i v i     i    i vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_110389388_   5287 CTAGGCA-ATACCATTCAGGACATAGGCACGGACAAAGACTTCACGACAA 5335
                         v    ?i- v i -   iv   v v  vvii i   v ii   viiivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_110389388_   5336 AAACGTCAAAAGCAATTGCAACAAAAGCCAAAAAT-GACAAATAGGTTCT 5384
                         vi  ii        vvv          v-      -  i    v  vii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTT 644

  chrX_110389388_   5385 AATTAAACTAAAGAGCTTCTGCAAGGCAAAAGAAACTATCATCAGAGTGA 5434
                         v  i   v v  i i   i  iivvv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_110389388_   5435 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATGTACCCATCTGAC 5484
                          v  i     i                 v       vvi ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_110389388_   5485 AAAGGTCTAATATCCAGAATTTACAAGGAACTTAAACAAAATTTACAAGA 5534
                           i  v  vi          v  i  i     ivv    v- iv i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAATAATA 793

  chrX_110389388_   5535 AAAAAACAAACAACCCCATGAAAAAGTGGGCAAAGGATATGAACAGAC-- 5582
                             i     i     v  v?    i            v    i    --
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_110389388_   5583 TTCTCAGAATAAGACGTTTACATGGCCAACAAACATAGGAAAAAAAGCTC 5632
                              vi  v    ii vi v        i  i  i v     i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_110389388_   5633 AACATCACTGATCAT 5647
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (137 / 107)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.17 (14 / 12)  

 500 22.09 4.91 0.00  chrX_110389388_110395527     5972  6134 (6)  C L1M4_orf2#LINE/L1   (0)   908   738  

C chrX_110389388_   6134 ATCTGACAAAGGTCTAATATCCAGAAT-TACAAGAAACTTAAACAAATTT 6086
                               i  i  v  vi          -  i  ii    ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

C chrX_110389388_   6085 ACAAGAAAAA---AAAAAACCCA-TGAAAAAGTGGGCAAGGGATATGAAC 6040
                          i  v     ---   v      - v?    i       i    v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

C chrX_110389388_   6039 AGAC--TTCTCAAAATAAGACAT-TATGTGGCCAGCAAACATAGGAAAAA 5993
                             --     v   v    i  -i vi      ii  i  i v     i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

C chrX_110389388_   5992 AAGCTCAACATCACTGATCAT 5972
                          v           ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (20 / 15)
Gap_init rate = 0.03 (5 / 171), avg. gap size = 1.60 (8 / 5)  


4152 15.24 6.17 0.60  chrX_110428826_110430641.rev      501  1327 (489)    L1M4_orf2#LINE/L1       36   908 (0)  

  chrX_110428826_    501 TAATATTATTAATGTAATAATATTCCCCAAATTGACCTACTGATTCAATG 550
                                i    vi iii    i            i    v       i 
  L1M4_orf2#LINE/     36 TAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACG 85

  chrX_110428826_    551 AAATTCCTATGAAAATACTGACTGACTTT---GCAGAAATTGATAAACTA 597
                         v   i     v     v iii   v    ---           i  i  i
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chrX_110428826_    598 ATCCTAAAATTCATTTGGAAATTCAAGGGATCCAGAATAGCAAAAACAAT 647
                                       v       v       i          v        
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_110428826_    648 ATTGAAAAAAAGAGGGATAAAGT---AAAACTTATACTTCCTAATTTCAA 694
                         v        --  i i i     --- ii   i i      i        
  L1M4_orf2#LINE/    186 CTTGAAAAA--GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_110428826_    695 A-CTTACCACAAGTTTACAGTTATCAAAACAGTGTGGTACTGACATA--- 740
                          -     i    ivi      v     i              i    ---
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_110428826_    741 ---GACACATAAATCAATGGAATAAAATTGAGAGTTCAAAAATAAACTCT 787
                         ---    i   i            i          i  i        i v
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_110428826_    788 TACATTTACAACCAATTGATTTTCAA-AA---TACCAATGTAATTCAATA 833
                                 iiii            i -  --- i    viiv       i
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_110428826_    834 GGGAAAAAAGTAGTCTTTTCAGCAAACAGTGCTGGAACAACTGGATATCC 883
                               i  -           i    ii       i           ?  
  L1M4_orf2#LINE/    384 GGGAAAGAA-TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_110428826_    884 ACATGGACAAGAATGAAGTTAAATCCCCACCTCACAGCATATATAAAAAT 933
                              v v            ii i   i        v      i      
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_110428826_    934 TAACTCAAAATGAATCAAAGACCCAAATGTAAG--------CTATGAAAT 975
                                     i    ?     i         --------    i   i
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_110428826_    976 TCTTA-AGGAAAA-ATATGTATAAATCTT---GAATTTAGATTAGGCAAT 1020
                              - i     -   v ?i        ---  vi  i i         
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_110428826_   1021 GGTTTCTTAGATATGATACCAAAAACACAAGCAACCAAAGAAAAAATAGA 1070
                                         i       i          v              
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_110428826_   1071 CAAATTGGACTTCATAAGAATTAAAAACTTCTGTGCTGCACATGATAC-A 1119
                         i              v i            i      v  v v  i  - 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_110428826_   1120 TCAATAAAGTGGAAATATGACTCACAAAATGGAAGAAAATATTTGAAAAT 1169
                             v      i   v ii  i    i     i            v    
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_110428826_   1170 CATATGTCTGACTAGGGACTTGTACCTAGAATATATACACAGAACTCTTA 1219
                              i     iv           i i          - -          
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATA-A-AGAACTCTTA 780

  chrX_110428826_   1220 CACATCAATAATAAAAAGATAA-TAGTCCAATTTTAAAATGG-CAGAGC- 1266
                           vv               i  -  ii      ?v       -  i  v-
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_110428826_   1267 CTTGAATAGATATTTCTCCAAGGA-------------GC----ACGTACA 1299
                         i         i          i  -------------  ---- v i   
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_110428826_   1300 TGAAAAGATGCTCAACATAATTAGCCAT 1327
                                           v ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.49 (87 / 35)
Gap_init rate = 0.02 (20 / 873), avg. gap size = 2.80 (56 / 20)  


1036 17.42 0.35 9.76  chrX_110497985_110500939      203   489 (2466)    L1M4_orf2#LINE/L1      395   654 (254)  

  chrX_110497985_    203 GTTATTTTAAAAAATGATGCTGGAACAATGATATATCCATATACAGAAAT 252
                           iv   i  v     i      i    iviv   ?   i  i  -----
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA----- 439

  chrX_110497985_    253 AAACAAACAATACATCTCAACCCTTTTCTCATAACATATATTAATACAAA 302
                         ----   v   iv vi vi    i vi    i v      ------    
  L1M4_orf2#LINE/    440 ----AAAGAATGAAGTTGGACCCCTACCTCACACCATATA------CAAA 479

  chrX_110497985_    303 AATTAACTTAAAATGGATTATAGACCTAAATGTAAGTGTTAAA-CTATAA 351
                                 i         i ?               v i    -      
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_110497985_    352 AAGTCTTATAGGAAAACCTAGGAAACATGATAAACATAACTCTTTATTAC 401
                           v     v i      v    ?i------    ------    ii v  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNG------TAAA------TCTTCGTGAC 567

  chrX_110497985_    402 CTAGAGTTAGTCAACGGTTTCTTAGATATGACAATGAAAGCATACGCAAC 451
                           v i     v   i                  vii      i v     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_110497985_    452 AAAAGAAAAAAGTAGAAAAACTGGACTTCATCAAAATT 489
                                    -    v   i                 
  L1M4_orf2#LINE/    618 AAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATT 654

Transitions / transversions = 1.35 (27 / 20)
Gap_init rate = 0.02 (6 / 260), avg. gap size = 4.83 (29 / 6)  

1996 21.26 12.71 4.99  chrX_110497985_110500939     1621  2462 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_110497985_   1621 GGAAACACATCCTGTTTTCAAGGACTGGAAGACTTAATATTGTTAAGATA 1670
                              v i    ii v    v   i                        i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_110497985_   1671 GCAATACTACCCAAAGGAATCTACAGATTCAATGCAATCTCTATCAAAAT 1720
                                 v      vvi              i      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_110497985_   1721 TCCAATGGCCTTTTC-ATAGAAATGGAAAAGCAAATTTTAAAATTAGTAT 1769
                         i   iiv       i-ii      v  v    vi  ii       vi   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_110497985_   1770 GGAATTGCAAGGGGCCCCAAATACCCAAAACAATTTTGAAAAAGTAGGAC 1819
                             v        i   vi    v          i         v  i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_110497985_   1820 AAAGGTAGAGGATACACACTTCCCTATTT----ATTGGGCCATCTAAAG- 1864
                             v i     iv          v    ---- i vi- i i--    -
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA-CTAC--AAAGC 248

  chrX_110497985_   1865 -ACATGAAATACTGATA-CATGCTACAATGTAAAAGAACCTTAAAAATAT 1912
                         -   - v   vvv  i -ii  v   vi- i v   i ---  i v    
  L1M4_orf2#LINE/    249 TACA-GTAATCAAGACAGTGTGGTACTG-GCATAAGGA---TAGACATAT 293

  chrX_110497985_   1913 TACAGCAAGTGAA--------AGAAACCAGATATAAAAAGTCACATATTG 1954
                         - v v   vv   --------   iv     v     v--i  i i   -
  L1M4_orf2#LINE/    294 -AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC--CCATACATT- 339

  chrX_110497985_   1955 TATCATTCCATTTATCTGAATTGTCAAGAAT----AGGTAATCCA-TAAA 1999
                            vi - v   v  i --- i v    ii ----  iiv  i  - iii
  L1M4_orf2#LINE/    340 TATGGT-CAATTGATTT---TCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_110497985_   2000 GACAGAATA--------AA-GAATGGTA----GATGCCAGGG--GCTAGA 2034
                           v      --------  -i      i----  iiv v  i--? i v 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_110497985_   2035 GG-AAAGGA--GGAGT-GGAG--------------------AACAACTG- 2059
                         v -   i  -- i   -   v--------------------  v  i i-
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_110497985_   2060 CTTAA--TGGGT-----AC---------AGTGTT------------TCCT 2081
                           i  --   i -----  ---------  v i ------------ii  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_110497985_   2082 TTGGAGATGA--TAAAAATA---TTTTGTTACCAGAGGTTGTGGTTACCC 2126
                          v i   vi --  ii?i  ---i  i  v   -----   -     vv 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACC-----TTG-GGTTAGGC 579

  chrX_110497985_   2127 AACA---TTTTAAATG---CACTAAATGCCACTGAATTGTTCACTTTAAA 2170
                           ii--- i   i  i---   i   v  -  --  vii---  ---   
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGC-AC--AAGCA---AC---AAA 620

  chrX_110497985_   2171 ATGATTAATTTTATGTTATGTGACTTTCACCTCAATAAAAAAAGGTAAAA 2220
                          vi vv   -------- vi i v  vv  i   vi    vv ---    
  L1M4_orf2#LINE/    621 AGAAAAAAT--------AGATAAATTGGACTTCATCAAAATTA---AAAA 659

  chrX_110497985_   2221 CTTTTGTGCTTCAAAGAATACCATCAAGACAGTGAAAATACAAGCCACAG 2270
                                         i i  i       v        v    v      
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_110497985_   2271 AGTGGGAGAAA-TATTTGCAAATCATATATCTGATAAGGAAATTATATCC 2319
                          i         -                           i v  i     
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_110497985_   2320 AAAGTA-AT---GAAATTTTATAGCTCAACAATAAAAAAACAAATAACCC 2365
                          i i  -  ---   v i   i i     i        i           
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_110497985_   2366 AATT-AAAAATGGGCAAAGTATTTACA-AGACAGTTCTTCAAAGAATATA 2413
                             -              v    iv -     v    i       v   
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_110497985_   2414 TGCAAATGTCCAATAAGCGCATGAAAAGATGTTCAACATCAGTAGTCAT 2462
                          i      v         i            i         ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (103 / 74)
Gap_init rate = 0.05 (47 / 907), avg. gap size = 3.17 (149 / 47)  


3376 25.70 0.45 0.45  chrX_110533249_110535541.rev      909  1795 (498)    L1M4_orf2#LINE/L1        1   887 (21)  

  chrX_110533249_    909 TGGAAAGATTTTCCATATTCGTGGATTGGAAGAATCAATATTGTTAAAAT 958
                                  v i    i   i            v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_110533249_    959 ATTCATATTACTCAAAGCAATCTATAAAATGAATGCAAGCCCTATCAAAA 1008
                         iviv   i v i    vii     i i v v  i    v           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_110533249_   1009 TACCAATGACATTCTTCACAGAAATAGAAAAAC-AATCCTAAAAGTTATA 1057
                          v   iivi v  i  ii       v  v  i -i         v i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_110533249_   1058 TGGAACCACAAATGCCCCAGAAAAGCCAACGCTACCCTCAGCAAAAATAA 1107
                              vii   iv v       v      vi v i i v iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_110533249_   1108 CAAAACTGGAGGAATCACATTACCTAATGTCAAATTATACGATAGAGCTA 1157
                             ii       v     i v  i   v     viv   v i i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_110533249_   1158 TAGTAACCAGAACAGCATGGTACTTGCATAAAAACAGACACATAGACCAA 1207
                         i     i  ii    ii       v      ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_110533249_   1208 TGGAACACAAAAGAGAACCCACAAATAAATCCATACATCTAAAGTGAACT 1257
                              i v  vv    ii   v       i        i  vi  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_110533249_   1258 TATTTTCAACAAAGGTGTCAAGAACATATATTGGAGAAAAGACAGTCCCT 1307
                         v      i    i    i     v   vi v   i    ii i    ii 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_110533249_   1308 TCAATAAATAGTACTAGGAAAACTGGACATCCATATGCAGAAAAATTAAA 1357
                             i    i  i  i   v       i ?   i     i  i   v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_110533249_   1358 TTGAATCCCTATCTCTCATCACAAACAAAAATCAATTCAAAATAGATTAA 1407
                            i i     i   v  i  i v        i  i       i   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_110533249_   1408 AGACTTAAATCTAAGACCTTAAAGTATGAATCTACTACAAGAAAACTTTG 1457
                             i     v     v  v   v   i  v  vi  v        v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_110533249_   1458 GGGAAGATCTCTAGGATGCTGGTTTGGGCAAAAATTTCTTGAGCAATATC 1507
                          ? v i    iiiv  ivi   v  i     vii      iiii vv iv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_110533249_   1508 CCACGAGCACAGGTAACCAAAGTAAAAATGGACAAATGGGATCATATCAG 1557
                            vi      i i   v    v      i  i    v   iivi    i
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_110533249_   1558 G-TTAAAAAGCTTCTGCACAGCAAAGGAAAACAATA-AAAAAAAATGAAG 1605
                         i-       -   i  ii vv       ---  v  -v  i   i    i
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGA---CACTATCAAGAAAGTGAAA 696

  chrX_110533249_   1606 AGACAACCCACATAATGGAAAAATGTATTTGCAAACTATCCATTTGACAA 1655
                                     v     i i  vi          ii  vi  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_110533249_   1656 GGGATTAATAACCAGAATATATAAGGAGCTCAAACAATTAAAGAGGAAAA 1705
                             i vi  v             i  i   vv    i v  v iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_110533249_   1706 AATCAA-TAATCCAATTTAAAAATGGGCAAAAGATGTGAATAGACATTTC 1754
                          iv   -   i      ?             i   v              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_110533249_   1755 TCAAAAGAAGACATACAAATGGCAGACAGGCAGATGAAAAG 1795
                           v        i           vi i i   v        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.01 (6 / 887), avg. gap size = 1.33 (8 / 6)  


2796 20.69 6.71 5.70  chrX_110588619_110591269     1265  2158 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_110588619_   1265 AGGTAGTCCTTGTTCATGGATTGGACAACTCAATATTGTTAAGGTGTCAA 1314
                           i  vi  v               vi   i            i  v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_110588619_   1315 CTCTTTACAAAACTGATCTATAAATTCAACACAATCCCAATCAAAATCCC 1364
                         iv  iiv    -i       i i       i       v           
  L1M4_orf2#LINE/     56 TACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_110588619_   1365 AGCAGACTTTTTTTTTTCTTAGGAATTGATGAGCAGGTTTTAAACATCAT 1414
                            v v       vi-----  i      ii   v i ii    vv    
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGC-----AGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_110588619_   1415 AAGGAAATGCAGAAGACCTAGAATAGCCAAAAGAATTCTGAAAATAAAAT 1464
                          v         iii    i             v   ii      vi  i-
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG- 198

  chrX_110588619_   1465 TGGGGGTAACATCTGATTTTGCAGCACT---ATTTGTCAATTAAAATAAA 1511
                         -------    ---- vv   v  v   --- i  vi     v---i   
  L1M4_orf2#LINE/    199 -------AACA----AAGTTGGAGGACTCACACTTCCCAATTT---CAAA 234

  chrX_110588619_   1512 ATCTATTTTTTAAAAGCTACAG-AATAAAGACAGTGTGTTATTGGCATAA 1560
                          ii  i vi---          -   v           v  i        
  L1M4_orf2#LINE/    235 ACTTACTAC---AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_110588619_   1561 AAGTAGACAAATAGGTTAATGAAACATAAC--AGAGTCCATACATAAACC 1608
                         iii      v    i i    i  i v  i--        v v       
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_110588619_   1609 CACCTCTATATGGACAACAGATTGTGGTTATGGACAGCAGATTTTTGACA 1658
                           ----  i  ----------------      v  iiv      i    
  L1M4_orf2#LINE/    332 CA----TACAT----------------TTATGGTCAATTGATTTTCGACA 361

  chrX_110588619_   1659 AATATGC-AAAATCA---AAGGAGTGGCGAGAGAAAAGCCTTTTTAACAA 1704
                          ivi   -  i i  ---  ----   v  i    v  i     i     
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAA----TGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_110588619_   1705 ATGCTGCTGAAACAATCGGATGTCCATAT--------------------- 1733
                            v     ii    ii    i?   i  ---------------------
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_110588619_   1734 -----TTTGCATGATATACAAGAATTAACTCAAAATGGATCTTACATCTA 1778
                         -----i ii  iv        i                   v? v i   
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_110588619_   1779 AATGTAAAACCTAAAACT-------TCT-AGAACAAAACA---GAATAAA 1817
                                i v        -------   -    v      --- ?i    
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_110588619_   1818 ATCTTTGTGACCTTGGGATAAGAAAAGATTTACTGAACTTGAAAACAAAA 1867
                         -    i           v  i v  v i   vi ii iv   v v     
  L1M4_orf2#LINE/    558 -TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_110588619_   1868 GCACAATCCATAAGAGAAAAAAAATGATAAATTGGATTTCGTCTAAATTA 1917
                               v v i  i        v -           i   i  v      
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTCATCAAAATTA 655

  chrX_110588619_   1918 AAAACTTTGGATCTTCAAAAGAAACTGATAAGAGAATGAAAA-ACAAGCC 1966
                                 v vv       i  v   ivi    i i      -    v  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_110588619_   1967 ACAGACTGTGAGAAAATCTTTGCAAAGCATGTAACTGACAA--------- 2007
                              v  v        v        v   i  v    i  ---------
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_110588619_   2008 ATCCAGTATTCATAAAGAACTCTCAAAACTGAAGAAAAAGATAATAACTT 2057
                               v  vi            i v    v  v  v  i vi i  v v
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_110588619_   2058 ACCCAATTTGAAAAACTGGAAAAATATTTGAATAGACATTTCTTT---GA 2104
                                 ?-     iv  v   iv                  ii---  
  L1M4_orf2#LINE/    806 ACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_110588619_   2105 AGATGTATGAGTGAAAAATAAGCACATAAAAAGTTGTTTATCATCATTAG 2154
                             i  ii i  ivv           i     v  i i v     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_110588619_   2155 GAAA 2158
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.32 (103 / 78)
Gap_init rate = 0.03 (24 / 903), avg. gap size = 4.62 (111 / 24)  


3254 27.48 0.44 0.22  chrX_110638323_110644600.rev     4882  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_110638323_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_110638323_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_110638323_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGCTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_110638323_   5030 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_110638323_   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_110638323_   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_110638323_   5180 AATGGAACAGAACAGAGCACTCAGAAATAACACCACATACCTACAACTAT 5229
                                i    iv   viii         vv   i i ii  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_110638323_   5230 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5279
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_110638323_   5280 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5329
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_110638323_   5330 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5379
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_110638323_   5380 AAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5429
                          ?   ii    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_110638323_   5430 AGGCATTACCATTCAGGACACAGGCGTGGGCAAGGACTTCATGTCCAAAA 5479
                            ?i v viv   iv   viv  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_110638323_   5480 CACCAAAAGCAATGGCAACAAGAGCCAAAATTGACAAATGGGATCTAATT 5529
                                    vvi       i  vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_110638323_   5530 AAACT--AGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5577
                            v -- i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_110638323_   5578 GCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5627
                         i     i   iv            v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_110638323_   5628 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5677
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_110638323_   5678 ACAAACAACCCCATCAAAAAGTGGGCGAGGGACATGAACAGACACTTCTC 5727
                              i     v  i?    i     i i   iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_110638323_   5728 AAAAGAAGACATTTATGTAGCCAAAAAACACATGAAAAAATGCTCATCAT 5777
                         v        i  vi vi i     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_110638323_   5778 CACTGGCCGT 5787
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.53 (148 / 97)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3297 22.06 3.07 3.40  chrX_110651541_110654779.rev     1838  2748 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_110651541_   1838 TGGAACAGCATACTTTGGTCATGTGTTGGAAGACTCAGTATTATTAAGA- 1886
                              viii  v iv  v     vi          i i    i      -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_110651541_   1887 -GCTTAATTCTCCCAAAATAGTTCTATAGAGTCAATGCAATCTCAATTAA 1935
                         -  --   v     v    v v    i   v    i      i v  i  
  L1M4_orf2#LINE/     51 GGC--AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_110651541_   1936 GATCCCAGTTTGTTATTTTTTAAAAATTGGCAAGTTAATCCTAAAATGCA 1985
                         i       i vvi v    vi i      i    i i          v  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_110651541_   1986 GATGGAAATGCAAAAAACCTAGAATAGGCAAAACTAGGCTGAAAAAGAAG 2035
                         v            iii   i       v      v vvi           
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_110651541_   2036 GTCAAATTTGGGGG---CACAA----CAATGATTTCAAGTCTGTTATAAT 2078
                         iv    v    i  ---    v----    --  iv  iii ii  i  v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAAT--TTCAAAACTTACTACAAA 246

  chrX_110651541_   2079 GGTACAGTAATCAAAACAATGTG-TACTGCCATCACAATAGACAAATAGG 2127
                          v            i   i    -     v   v vi       v    i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_110651541_   2128 TCAGTGGAACAGAAC--ACAGTCCA-AAATAGACT--TACATATGTGGAC 2172
                            i     i    i-- v      -     i  i--     v i   v 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_110651541_   2173 ATCTGATTTTTGACAAATATTCAAAGGCAATTCAATGAAGAAAGCATTGT 2222
                          vi       i     ivi v v   i v        ii     v  v  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_110651541_   2223 CTTTTTAACAAATGCTGCTGAAATAAGTGGCTATCCATATGCAAAAAAAA 2272
                              i        v     ii i  v   v  ?   i        i  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_110651541_   2273 AAAA----ACCCATAAAACTTCACAACATACATACACAAAAATTAACTCA 2318
                         i  i----    v  --- i     - ---    i               
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTA---CCTCACA-C---CATATACAAAAATTAACTCA 489

  chrX_110651541_   2319 AAGTGTATCATAGACCTAAATGTAA-AGCTAATACTATAAAGATTTTCAA 2367
                           i  v    ?              -      v        iv i  vi 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_110651541_   2368 AGAAAAAACAGGAGAAGACCTTTGTGACCTTTGATTAGGGAACATTCACT 2417
                               v i   ? v i i   i        v i     v  iiv iv  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_110651541_   2418 TAGATACAACACAATAAGCACAGCCAATGAAAGAAAAAATA--TAAA--A 2463
                               ii    v v       iv   ii            --    --i
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_110651541_   2464 GACTTTGTGAGAAATGAAAACGTTTGCTCTTCAAAAGACATGGTTAAGAG 2513
                              ii v i  v i     v    iv       i    ivi i    i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_110651541_   2514 GCTGAAAAGTCAAGCTATGGATTGGGAGAAAATATTTGCAAAGCATACAT 2563
                         iv       v   v i ii  v                    v    i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_110651541_   2564 ATCATAAAAGACTTGTGTGCGGGGTATATAAAGAACACTCAAAACCTAAT 2613
                         v v    ii       i v i ii            v  i v   ii   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_110651541_   2614 AAGAAA----CAAACAACTCAATAAAAAAGTGGGCAAAAGGCTTAAATAG 2659
                           v   ----    i   i    v?    i        i ii  i     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_110651541_   2660 ACACTTTACCAAGGAAGATACATGGATTGCAACAAAAACAAAAAACAACA 2709
                            i  iv    i       i iii  v  ---------------   i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGC---------------CAATA 874

  chrX_110651541_   2710 AAAATCACATGTGAAAAGATGCTCAACATCATTAGTCAC 2748
                          i---      --                  ????????
  L1M4_orf2#LINE/    875 AG---CACATG--AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (119 / 78)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.95 (59 / 20)  


1290 25.95 12.60 2.10  chrX_110683199_110684845      631  1154 (493)    L1M4_orf2#LINE/L1      330   908 (0)  

  chrX_110683199_    631 CCCACAAAT--ATGTCCAATTAATTTCTGACAAAGAAGCAAAAGCAATTC 678
                             i v  --   vi     i    ii     i iv  v  ii v    
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_110683199_    679 AAT-----------------------AAATGGTGCTGAACAAATTGGATA 705
                            -----------------------           iivv  i      
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_110683199_    706 TCCATTAGCAAAAAAAAAAAAAAGAACCTTGACCTAAACTTCATACTTTA 755
                         ?   ivv      i  vi  ivv i   ----    -- i   i  iv  
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACC----CCTA--CCTCACACCATA 473

  chrX_110683199_    756 TATTAAAATTAACTCAAAATGTATAATGAACATAAGTGTAAAATGTAAAA 805
                           iv                 v  v ?ii  v   i     i vv     
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_110683199_    806 CTACAAAACTTCTAAAAATATATATAGGAAAAAATCTTTGAGACCTAGAT 855
                            i      ii  i  iv v i     ?iv       i v     v --
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG-- 571

  chrX_110683199_    856 AAGACTAAGCAA--ATTTCTTAGAATTGACACAAAATAACATGATTGATT 903
                         -- ii  i    --i         vv      v   - i  ii vii iv
  L1M4_orf2#LINE/    572 --GGTTAGGCAATGGTTTCTTAGATATGACACCAAA-AGCACAAGCAACA 618

  chrX_110683199_    904 GAATGAAAAATTGATAAATTGGACCTCAACAAAATTTTGAAATTTTGC-C 952
                         i  vi      v            i   v       vvi  v     i- 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_110683199_    953 TACAAACGATTCTGTTAGAAGAATGAAAAGACAA---------------- 986
                          v    v  iv  i i ii i i           ----------------
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_110683199_    987 ------------GTTCTATGTCCAATAAAGGCTTTGTATC-------TAT 1017
                         ------------i iv   i  ii    i  vi       -------   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_110683199_   1018 AAAGGACTCTCAAAACTCAACATCAAAA---CAAGCAATTCAATTAAGAA 1064
                             i     i v       i vi    ---   ii  ii     ? i  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_110683199_   1065 ATTGGCAAACAATATGCATAGATATTTAATCAGTGATGATATACAGATGG 1114
                           v      vi  v  v     i    vvi  iv  v        i    
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_110683199_   1115 CAAATAAGCATATGGAAAGATGTTTAATATCATTAGCCAT 1154
                          v        i   i       i i  i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (81 / 51)
Gap_init rate = 0.02 (11 / 579), avg. gap size = 7.00 (77 / 11)  


1037 25.05 20.12 2.05  chrX_110797387_110799336.rev      351   837 (1113)    L1M4_orf2#LINE/L1        7   581 (327)  

  chrX_110797387_    351 GATA--CTATGTTCATGAATTCAAAGAGACCATACTGTTAAGAATTGGCA 398
                             -- i         i   vi    vviv   i        --     
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA--TGGCA 54

  chrX_110797387_    399 TT-CTCCCCAAATTGAGCCATAGATTATAAACACAATCCCTA----ATTT 443
                         v -             v i i     v--   i         ---- v i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTC--AACGCAATCCCTATCAAAATC 102

  chrX_110797387_    444 CCAGACGTTTTTTTTTT-----TT-------TGGT---AAAATT----TG 474
                             vi ii      vi-----  -------  i ---      ----  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_110797387_    475 ATAGTGTAAGAGAC-----AT-GC--AAATGACCCT-----------AC- 504
                         iv i  i   i   -----  -  --   ii i i -----------  -
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_110797387_    505 -----------CTTAC----------TTCAAACCTTACTA-AAA------ 526
                         -----------  i  ----------      v       -   ------
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_110797387_    527 -------AGACAGTATAGTACTGATGTAAGGATTAAAAAATTGATCAATG 569
                         -------       i i      iii       vi v v  v        
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_110797387_    570 CAACAAAA--GAGGGCACAGAAATAGACC--TGCACTTAAAACAGTCATT 615
                         v  i i  --   i iv        i   -- i  i   ---ii    v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA---TGGTCAAT 349

  chrX_110797387_    616 TGATTTTTGACTAAAACACCAAAGTGATCCAACGAGGAAAGGAAAATCTT 665
                                i   v iiiii    iiiv  i   i i      i v i    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_110797387_    666 TTTCACAAATGGTACTGCTGGAATACTGGAGATCCATA-----AAGAAAA 710
                           iv         i   --   vv      v ?   i -----     vi
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTG--GGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_110797387_    711 AAA---AATC---ACCTC-CACCATCCACAAAAATGAATTTGAGATGAAT 753
                           i---i i ---     -      vi        v  i ii i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_110797387_    754 AGTGGACTTAAACATAAAA-CTAAATGAATTAAGCTTTTAAAGGAAAACA 802
                         vi?i   i    ii   i -     vvv  v  i  i   i i       
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_110797387_    803 TAGGAAACAATCATAACGACTTTGGAGTAAGACAA 837
                             ?ivv    v vii   i    -  v  i   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAA 581

Transitions / transversions = 2.05 (80 / 39)
Gap_init rate = 0.05 (27 / 575), avg. gap size = 4.00 (108 / 27)  

 730 24.18 11.72 1.83  chrX_110797387_110799336.rev     1166  1438 (512)    L1M4_orf2#LINE/L1      584   883 (25)  

  chrX_110797387_   1166 GTTGCTTAGAT----TACAGAAAGCAATACACACCAAAA-----AAT-GA 1205
                            v       ----i  vi      -i vi  v     -----   -  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGA 632

  chrX_110797387_   1206 TCAATTAGATTCCATCAGAATTAAAATCCTCTACCCATCAAAAGGCACCA 1255
                          v    i  i i     i        v i i iiv v     i i   i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_110797387_   1256 TGAAGAAAAT----AGATAAGCCACAGAATAGGAGCAGATATTCACGAA- 1300
                          v      i ----   i  v         i    v i     ii i  -
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_110797387_   1301 -ACATACCTGACAAAAGACTAGCATAGAGAATATGCAGAGAACGTCTGCA 1349
                         - i   i    i  ii    v i  vv       ii i     vii i  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_110797387_   1350 ACTCAATAACAAG----CA-----CCCAATAAAAAAGAAAGTAGTCAAAA 1390
                                  i  i----  -----      v?    i---- i v    i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA----TGGGCAAAG 828

  chrX_110797387_   1391 TATGTGAACA-------CTTTACAAAAAATATGCAAATGGCCAATAAGCA 1433
                         v  v    i -------  ii v i  i    i                 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_110797387_   1434 CATGA 1438
                              
  L1M4_orf2#LINE/    879 CATGA 883

Transitions / transversions = 2.25 (45 / 20)
Gap_init rate = 0.03 (10 / 300), avg. gap size = 3.70 (37 / 10)  

1654 23.46 4.32 0.82  chrX_110797387_110799336.rev     1439  1924 (26)    L1M4_orf2#LINE/L1      406   908 (0)  

  chrX_110797387_   1439 AAAAAGTACTCAAACAACTGGACATCCACATGCAAAAATATGAATCTACA 1488
                            vi  i  vii         i ?            iv     vi iv 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_110797387_   1489 CAC--ACTTTACATACTTCACAAAAAGGTCACTCAAAATGGATCACAGAC 1536
                          v --  i i   ivv vi       v- v               ?    
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAAT-TAACTCAAAATGGATCAWAGAC 504

  chrX_110797387_   1537 CTAAAAGTAAAATGC-AAAAC-ATAAAACTCCTAGACGATAACATAGGAG 1584
                              v    i -  -     -         i    v  v        ? 
  L1M4_orf2#LINE/    505 CTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_110797387_   1585 AAAATCTAGATGACCCCAAGACTGGCGATTACTTTTTAGATACAATACCA 1634
                         v      vvi     iiii viv   i  vii  i       ii i    
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_110797387_   1635 TAGGCATGATCCATAAAAGAAATAATTTATATGTTAGAGTTCTTTAAAAT 1684
                         v i   ii v v i        v   vv   vi  i  v   v i     
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_110797387_   1685 TAAAAACATCTGCTCTGTGAAAGACACT--TAA-----TGAAAAGACAAG 1727
                                v i  iv  vii  i      --i  -----           v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_110797387_   1728 CCACAGACTTGGAAAAAATACTTGCAAAAGACATACCTGATATAATGGAC 1777
                                v v   i      i       vv i   i      -- v    
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA--AGGGAC 751

  chrX_110797387_   1778 TGTTACCCAAAATATACAAAGAACTCTTAGAACTCAATAA-------GTA 1820
                          vv  i   i      i            v          -------ii 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_110797387_   1821 AACTACCTGAATTAAAAATGGGCCAAACATCTTAACAGATGTTTCACCAA 1870
                           iv   ii v ?          v  iv  i v  i   ii    v    
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_110797387_   1871 AGA---TATATAGATGGCAAATAAGCACATGAAAAGATGCTCTACGTCGG 1917
                            ---    i i     v                       v  i  i?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_110797387_   1918 ATTTCAT 1924
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.24 (61 / 49)
Gap_init rate = 0.02 (10 / 503), avg. gap size = 2.50 (25 / 10)  


 229 30.19 2.83 3.77  chrX_110833329_110839693       16   121 (6244)  C L1M4_orf2#LINE/L1   (463)   445   341  

C chrX_110833329_    121 ATGCCCCACTGATGTTCGGCAAAGGGG--AAAAGCAGTTCAATGGAGAAA 74
                            vi v i    v    i   i  v --  i v  -        i    
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAA 389

C chrX_110833329_     73 TGAGAGT-TGTCCAACAAATTGGGTCAGAGCAATTGTTCACTCATATTTT 25
                         vi v   - v i        v v iii ii   i  vvi ?i  i  vi-
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC- 438

C chrX_110833329_     24 CAAAAAGAA 16
                         --       
  L1M4_orf2#LINE/    439 --AAAAGAA 445

Transitions / transversions = 1.38 (18 / 13)
Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.75 (7 / 4)  

1729 16.67 2.82 0.28  chrX_110833329_110839693      121   474 (5891)    L1M4_orf2#LINE/L1      412   774 (134)  

  chrX_110833329_    121 TGCT-GGACTACTAGACATCCACATTCAAAAGAGTAGAGTTAAACACCTA 169
                             -    v   i  i ?      v       i ii    ii  v    
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_110833329_    170 CTTTATACCACGTACAAAA-----CTCAAAATGGATCATAGACCTATACT 214
                          i i i    ii       -----              ?       v iv
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_110833329_    215 TAACAGATAAAAACTATAAAACTCTAATAGGAAAGCATAGGAGTAAATCT 264
                            v  v     -            v v i    i      ?        
  L1M4_orf2#LINE/    512 TAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_110833329_    265 TTGTGACCTTGGATAAAACAACGATTTCTTAGATATGACACCAGAAAC-C 313
                          i          i v ii   i i                   i  i - 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_110833329_    314 AAGTGACAAAAGAAAA--TAGGTAAATTTGACTTAATCAAAATTAAAAAC 361
                            ii           --   i      v     v               
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_110833329_    362 ATTTTTACATCAAAGGACAGCATAAAGAAAATGAAAAGATAACTCATAGA 411
                         v   v i v          vi  v      i        i   i  i   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_110833329_    412 ACGTGAGAAAATAATTTAATATCATATATCTGATAAGGGACTTGTATC-A 460
                          i v         v  vv v                            - 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_110833329_    461 CAATATATAAAGAA 474
                         v             
  L1M4_orf2#LINE/    761 GAATATATAAAGAA 774

Transitions / transversions = 1.43 (33 / 23)
Gap_init rate = 0.02 (6 / 363), avg. gap size = 1.83 (11 / 6)  

3119 26.97 1.22 0.44  chrX_110833329_110839693     4972  5872 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_110833329_   4972 TGGAAGAATATTCCATGCTCATAGATAGGAAGAATCATTATCGTGAAAAT 5021
                              ii    i     i    i   v      v i v   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_110833329_   5022 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCGTCAAGC 5071
                            v     v      v i  i  i        i  v     ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_110833329_   5072 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5119
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_110833329_   5120 CATGGAACTAAAAAAGAGCCCACATTGCCAAAACAATCCTAAGCAAAAAG 5169
                         i      v iv  ii  v  viv  v            i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_110833329_   5170 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5219
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_110833329_   5220 CACTGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5269
                         i  v    i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_110833329_   5270 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5319
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_110833329_   5320 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5369
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_110833329_   5370 ATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5419
                         v  i  i       i      v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_110833329_   5420 AACTGGATCCCTTACTTACACCTTATACAAACATTAATTCAAGATGGATT 5469
                          ii    i    vv  i     v        v     i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_110833329_   5470 AAAGACTTAAACGTTATACCTAAAGCCACAAAAATCCTAGAAGAAAACCT 5519
                          ?    i    i  v v v     i i i    v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_110833329_   5520 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 5568
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_110833329_   5569 ACACCAAAAGCA-ATGCCAACAAAAGTCAAAATAGACAAATGGGATCTAA 5617
                                     - v  -        vv        i    v   ii v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_110833329_   5618 TTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGAGAAC 5667
                          i   v v  i i   i  ii vv       v    i  vv i  v   v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_110833329_   5668 AGGCATCCTACAGAATGGGAGAAAATTTGTGCAATCTGCCCATCTGACAA 5717
                           i  v  i                 v v     viiiivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_110833329_   5718 AGGGCTAATATCCAGAATCTACAAAGAACTCAAGCAAATTTACAAGAAAA 5767
                         i  i  vi          v  i         vvi   v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_110833329_   5768 AAGCAA----CCCCATC-AAAAATGGGCAAAAGATATAAACAGAC--TTC 5810
                          ii   ----   v  i-             i   v i  i    --   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_110833329_   5811 TTAAAACAAGACATCTATGCAGCCAACAGACACATGAGAAAATGCTCACC 5860
                          iv   v    i  vi viii     i ii       i  i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_110833329_   5861 ATCACTGGTCAT 5872
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


3771 17.96 4.59 0.64  chrX_110850516_110852274.rev      484  1268 (491)    L1M4_orf2#LINE/L1       93   908 (0)  

  chrX_110850516_    484 TATAAAAATATAATTTGC---TTTTGCATAAATTGACAAGCTGCTCCTAA 530
                            v     viv vi   ---       v              v      
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_110850516_    531 AATTCATATACAAATATAAGAGACCCCAAAGAACCAATATAATCTTGAAA 580
                                  iv    ii   i     vi  v i    v i          
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_110850516_    581 AATCA--ATGAAGTTTGAGGATTTATACTTCCAAGTTTCAAAACTTACTA 628
                           vv -- ii     v     i i i      v i               
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_110850516_    629 CAAAGCTATAGTAATCAAAACAGTGTGGTAGTGGCATAAGAATTGACATA 678
                                 i         i           v         i  v      
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_110850516_    679 AAGACCAACAGAATAGAATTAAAGGTCCAGAAGAAATAAATTT-----TT 723
                         v   i   ii          i ii        ---     iii-----  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAA---ATAAACCCATACATT 339

  chrX_110850516_    724 TATGA-------GTTTCTGTCAAGGGTACCAAGACAATTCAATGGAGAAA 766
                             i-------i   ii v       i       v         i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_110850516_    767 GACTAGTCTTTTCTAACAAACGGTGCTGAGACAACTGGATTTCCACATGC 816
                           v          -      i       i           v?        
  L1M4_orf2#LINE/    390 GAATAGTCTTTTC-AACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_110850516_    817 AAAAGAGTAAAGTAAGGCTCCTTTTTCATACCATACACAAAAACTAACTC 866
                               i i    vi i i   vii   i      i       i      
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_110850516_    867 TATATTGAGCACAGACCTAAATGTAAGTG--------ATAAAACTCTTAG 908
                         v v  v  v  ?               v --------             
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_110850516_    909 AAGAAAACCTAGGAGTAAATCTTTGTGACCATGGGTTAGACAATGATTTC 958
                                 v    ?         i      v        i     i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_110850516_    959 ACAGATATGACACTGGAAGCACAAGTGATAAAAGAGATGATTCATAG-TT 1007
                         vi           iii         ii i      i vi  vv   i-  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_110850516_   1008 GAGTTTCATTAAAGTTAAAAACTTTT-TGCCTCAACATATACTATCAAGA 1056
                          iii     i   i            -   i    viv i          
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_110850516_   1057 AA-TCAGAAGACAGCCCACAGAATAGAAGAGAATATTTGCAAATCATAGA 1105
                           - v i      i          i i   i                 v 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_110850516_   1106 TCTAATAAGTGACTGGTATCCAGAACACACAATG----TTTACGTCTCAA 1151
                            i     v    v          i i i  v ----i    iv     
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_110850516_   1152 TAATACAAAGACAA----CCTGATTTTTTAAGTGGGCAAAGGATATGAAA 1197
                              v        ----  ii   ?vv-  i            v    v
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAAT 837

  chrX_110850516_   1198 TGACATTTCTCCAAATAAGATGTACAAATGGTCAATGAGCACATTGTAAC 1247
                         v              v     i         i    i       viv  v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_110850516_   1248 ATCCTCAACATCATTCGGCAT 1268
                           v          ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (84 / 53)
Gap_init rate = 0.02 (13 / 816), avg. gap size = 3.15 (41 / 13)  


3097 26.05 1.66 1.00  chrX_111011712_111018109     5004  5905 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111011712_   5004 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5053
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111011712_   5054 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5103
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111011712_   5104 TACCAATGACTTTCTTCACAGAACTGGAAAAAAACT-ACTTTAAAGTTCA 5152
                          v   iivi i  i  ii     v v  v  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_111011712_   5153 TAGCGACCAA---AAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCCAAA 5199
                           vv  --  ---  ii  v  v v  i     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_111011712_   5200 AGAACAAAGC---A----TCACACTTCCTGACTTCAAACTATACTACAAG 5242
                                  i--- ----          ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_111011712_   5243 GCTACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGA 5292
                                       i    ii         i iv ii i   v   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_111011712_   5293 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAA 5340
                                  i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_111011712_   5341 CCATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5390
                         i  vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_111011712_   5391 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5440
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_111011712_   5441 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAGGATG 5490
                         v    ii    i    v   i     v              i   ii   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_111011712_   5491 TATTAAAGACTTAAATGTTAGCCCTAAAACCATAACAACCCT-AGAAGAA 5539
                         v  i ?    i       v  vv       i    -   i  -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAA 543

  chrX_111011712_   5540 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 5588
                            v    ?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_111011712_   5589 CTAAAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGAT 5638
                         v  vi            vvi     v    vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_111011712_   5639 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGT 5688
                         i v  i   v v  i i   i  ii vv    i  v  i i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_111011712_   5689 GAACAGGCAACCTACAGAATGGGAGAAAATTTTTTCAACCTACTCCTCTG 5738
                            v  i     i                 v   v   vii iviv    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_111011712_   5739 ACAAAGGGCTCATATCCAGAATCTACAATAAACTCAAACAAATTTACAAG 5788
                          i  i  i  ii          v  i  vi     vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_111011712_   5789 AAAAAAACAAAAAAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGAC 5838
                              i     v  -   v  i?    i     i      v    i    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_111011712_   5839 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGC 5888
                          i     v        i  vi viii     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_111011712_   5889 TCATCATCACTGGCCAT 5905
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


3266 24.12 3.87 0.57  chrX_111024811_111027750     1570  2448 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111024811_   1570 TGAGATGAGATCCCAAGTTTATGGACTAGAATAATTAATATTTTCAAAAT 1619
                           ii v  v      v   i     i i   v v        v i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111024811_   1620 GTCCATACTACCCAAAGTGATCTACAGATTCAATGCAATTCCTATCAAAA 1669
                          v v     v      v                i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111024811_   1670 TCCCAAATGGCCTTT---AAAAAATAGAAAAAAAAATCCTAATATTTGTA 1716
                              iv  v i   ---v i    v  v  ivvi       v   ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_111024811_   1717 TGGAACTACAAAAGACCTGAAACAGCCAAAGCAGTCTTGTGCAA-AAGGA 1765
                              v i   ii    iii  i       i  i     viv  -   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_111024811_   1766 TAA-GCTGGAGGCATCATATTTCCTGACTCTAAG--TTA-TAT-----TA 1806
                         i  - i      vv   i i    ii i ii  i--   -  i-----  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_111024811_   1807 TAGTAATTAAAACATTACGGTACCAGCATAAAAGTAGACATACCGATCAA 1856
                         i      i  i   v ii     ii      iii        iv      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_111024811_   1857 TAGAATAGAACAGATAACCAAAAAATAAACGCACACATTTATGGTCAACT 1906
                          i        iv  v ii v i        v  i              i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_111024811_   1907 GATCTTCG----GAGTGTCAAAAACGCAAAATGGAAAAAGGATAGACTCT 1952
                            i    ---- i   i   i v iivv     ii    i    v  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_111024811_   1953 TCAACAAATGGTATTGGGAAAACTGGATATCCAAATGCAAAA-ATTGAAA 2001
                                     ii     v         ?   v        - v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_111024811_   2002 TTAAATTCATATCTTACACTGTACACAAAA-----CTTAAA------TAA 2040
                           ii ii v  i  i    ii  i      -----  i   ------i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_111024811_   2041 AGATTTAAACATAAGACGTGAAACTACAAAACTGCTAGAAGAAAACATAG 2090
                            ii    ii     vv i      i      vi               
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_111024811_   2091 GGAAAAACCTTCTTAACATTGATCTTGTCTATAATTTTTAGGATGTAACT 2140
                          ?iv   i    v i  v   ivi v v v  ii   i vi   i i  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_111024811_   2141 CCGAAAGCACAGACAACAAAAGCAAAAATAGACAAGAGTT--ATTACACC 2188
                           i        ii         v         i  i--  -- i v  i 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA--TTGGACTTCATC 648

  chrX_111024811_   2189 AA--CTAAAAAGCTTC-TGCCTGGCAAAGGAAAAAATCAAGAAAACAAAA 2235
                           --i      vi  i-   i --       v vv         iii   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_111024811_   2236 AGGCAACTCACAGAATGGGAAAAAGTATTGGCAAACTATGTATCAAATAA 2285
                           i    i            i   i    v     ii  i    vi    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_111024811_   2286 GTGGTTAGTATCCAACATATATAAGAAACTCATAACAACTCAATACCAAA 2335
                          v ii v       iv        ii     v  -          vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATAAA 795

  chrX_111024811_   2336 AATACAAATAACCCAATTAAAAAATGGGCAAAGAACCTAAATAGACGCTT 2385
                           v               ?              i ii i       ii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_111024811_   2386 CTCAAAAGAAGAAACGCAGATGGCCAACAGGCATATGCAAAGGTGTTAAA 2435
                            v        v ii  i        i i   i   v    i  i v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_111024811_   2436 CATCTCTAATCAT 2448
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (140 / 68)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.44 (39 / 16)  


2374 22.78 3.17 1.51  chrX_111027957_111029604      493  1155 (493)    L1M4_orf2#LINE/L1      235   908 (0)  

  chrX_111027957_    493 ACTTTTGATAAAGGTATAGCAATCAAGA-AATGTGGTAGTAGCATCAAGA 541
                             viv i    v  i  i        - i       v i    v i  
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_111027957_    542 GAGACAAATAGATTAATGGAA-AAAA---AGAGTCCAGTAGTATGCCTAC 587
                         v     v      i       - i  ---         v i  vi  i i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_111027957_    588 ACATATATACAAAACTGATGTCTGAAAAAGGTA--AAGGCAATTCG-TGG 634
                             v   ivvv  i    v ii  v  i   i--   i v    i-   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_111027957_    635 ATAAAGAAGGGTCTTTTTCAACAAAAGGTGCTGGAACAATTGGATTTCCA 684
                         iv      vi       -       v        i    i     v?   
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_111027957_    685 TGTG-AAAATAAGGACCTTTGAGCCATACTTTACACCATATGCAAAACTT 733
                         ii  -    v  v  vv  v  v  v   i i         i     v  
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_111027957_    734 AATTCAAAATGGATCACAGACCTATGTGTAAGGCCTAAAATCATAAATGA 783
                           i             ?       vi      iv      ii     -- 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA--A 531

  chrX_111027957_    784 CT---AGAATAAGATATAATGAAAAATCTTTGTGACCACGAGCTAAGCAA 830
                           ---    v  i i   iv?iv       i      vi i i  i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_111027957_    831 TGATTTCTTCGATATAACATCAAAAGTATAATCTATAATAGATGAAAGGA 880
                           i      v     i   i      i i  v ---  i i v    ii 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGC---AACAAAAGAAAAAA 628

  chrX_111027957_    881 AAGATTAATCACACTCCATCAAAATTAAAATTATCTGTTGTTCTAAAGAC 930
                         v    v   iiv   i              viv i   vv   v  i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_111027957_    931 ACTATTGAGAAAATGAAAACATGAGTTACAGACTGGGA--AAATATATGC 978
                              ii     i      v ii vii     v     --      v   
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_111027957_    979 AAATCATA-ATCTGATAAAGGACTC--ATTCAGAACATATAAAGA-CTCT 1024
                                 -         i     i--  i     i         -    
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_111027957_   1025 TAAAACACCCCAA-AATTGAAA--CAAATAATCTGGTTTTTAAGTTGGGC 1071
                           ---  v i   -   vi   --       i iii  ?vv  i -    
  L1M4_orf2#LINE/    779 TA---CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT-GGGC 824

  chrX_111027957_   1072 AAAATATTTGAAAAGATACTTCACCAAAAAGGATATATAAATGGAAAACA 1121
                            iv       v   i i   v     i i      i      vv  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_111027957_   1122 GGCATATGAGAAGTTGCTCAGCATCACTAGTTTT 1155
                         i   i    i   v      i     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (88 / 59)
Gap_init rate = 0.03 (18 / 674), avg. gap size = 1.72 (31 / 18)  


3112 27.97 0.33 0.33  chrX_111042526_111048033.rev     4110  5017 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111042526_   4110 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 4159
                              ii    i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111042526_   4160 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4209
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111042526_   4210 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 4257
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_111042526_   4258 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 4307
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_111042526_   4308 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4357
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_111042526_   4358 TACGGTATCCAAAACAGCATGGTAATGGTACCAAAACAGATATATAGACA 4407
                            i   vi   i    ii     v   i iv ii i   i       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_111042526_   4408 AACGGAACAGAACAGAGGCCTCAGAAATAATACTACACATCTACAACCAT 4457
                           i    i    iv   ivii         vv i i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_111042526_   4458 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 4507
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_111042526_   4508 ATTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCTGA 4557
                         v  i  i              v     iv  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_111042526_   4558 AACTGGATCCCTTACTTACACTTTATACAAAAATTAATTCAAGATGGATT 4607
                          ii    i    vv  i    iv              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_111042526_   4608 AAAGGTTTAAATGTTAGTCCTAAAACCATAAAAACCCTAGAAGAAAACCT 4657
                          ?  iii       v  vv       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_111042526_   4658 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 4706
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_111042526_   4707 ACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGAGATCTAAT 4756
                                     vvi          vv        i    vi  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_111042526_   4757 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 4806
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_111042526_   4807 GGCACGGCACAGAATGGGAGAAAAATTTTGCCATCTACCCATCTGACAAA 4856
                          i  vvv                 vv     v vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_111042526_   4857 GGGCTAATAGCCAGAATCTACAAAGAACTCAAACAAATTTACCAGAAAAA 4906
                           i  vi  v       v  i         vv    v iv iv v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_111042526_   4907 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATACAAACAGACACTTTT 4956
                         i     i     v  i?    i            vii  i     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_111042526_   4957 CAAAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5006
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_111042526_   5007 TCACTGGTCAC 5017
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (148 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


3275 14.77 2.57 12.75  chrX_111081744_111084395.rev      747  1640 (1012)    L1M4_orf2#LINE/L1        1   803 (105)  

  chrX_111081744_    747 TGAAAAGACATTCTGCAT-CATGGATTGCAAAACTTAATATTGTTAGGAT 795
                           i     i  i iiii -         v  i              i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111081744_    796 TTCAATACTGCTTAAAAGGATCTACAGATTCAGTGCAATTTATATCAAAA 845
                         vv       v ii   vv              ii     iiv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111081744_    846 TC--AATGGCATTTTTTGGCAGAAATGGAAAACCTTATCCTCAAATTCAT 893
                           -- iiv  v       -       v  v  v  v     v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_111081744_    894 ATCAAATTGCAAGGGTCCCCAAAAAT-GTCAAAACAATCTTAAAAAATAA 942
                           vi  v        v   -- i   - i            i     v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCC--AGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_111081744_    943 GAATAAGTTTCGTGTGCTCACATTTTCTGTTTTTAAAAACTTACTACAAA 992
                            i  iv  v v vi      i  i iiv   i    -           
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA-CTTACTACAAA 246

  chrX_111081744_    993 GC-ATAGTCCTAAAAACTAATGTGGTACTGGCATAAGGAGAGACATACAC 1041
                           - i   vv v  i  - i                   v       i v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGAC-AGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_111081744_   1042 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACTCATAGATCAATGGC 1091
                                                            i    v  iv    i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_111081744_   1092 CTATTGCTTTTTAACAAGGGGGAAACAATAGCCTTCTCTTTTTTATTGAG 1141
                          v    v    ii       ------------------------------
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGG------------------------------ 365

  chrX_111081744_   1142 ATGGGGGTCTTGCTCAAACTTGCTTGTGGGCTCAAGCAATTTTCCTGCCT 1191
                         --------------------   ---------    --------------
  L1M4_orf2#LINE/    366 --------------------TGC---------CAAG-------------- 372

  chrX_111081744_   1192 CAGCCTCCTTATTAGTTGGAATCACAGGCACATGCCATTGTGCCTGGCAA 1241
                         -----------------------  -----   v v  v -----  v  
  L1M4_orf2#LINE/    373 -----------------------AC-----CATTCAATGG-----GGAAA 389

  chrX_111081744_   1242 GAATAGTCTTTTCAACAAATGGTGCTGAGATAACTAAATATCCACATGCA 1291
                                                    i  i    ii   ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_111081744_   1292 AAAAGACGAAATTG--CACATACTTCACACCATATACAAAA--------- 1330
                            ii i   i   -- v v   i                 ---------
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_111081744_   1331 ---TGGGGCAGCAACCTAAATATAAGAGCTAAAACTATAAAACTCTTACA 1377
                         ---   iv  ?vi        i                          v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_111081744_   1378 AGAAAACATAAGGGTAAAATCTTCATGAAGTTGAATTTCACAAAGGATTC 1427
                                   i ?     -     i   vv   ii  vvi   v  v   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_111081744_   1428 TTAGATATGAATACCTAAAGCATAAGCAACAAAAGAAAAACATAAATAAT 1477
                                   -i   v      i                 -   i    v
  L1M4_orf2#LINE/    589 TTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAA 636

  chrX_111081744_   1478 TTGGACTTCATCAAAATTAAAACCTTCTGTGCATCAAAGGATATTATCAA 1527
                                               v   i     v        i i      
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_111081744_   1528 GAGAGTAAAAAGACAACCTATAGAATGAGAGAAAATATTTTCAAATCATA 1577
                           i   i           i i      i            v         
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_111081744_   1578 TCTCTAATAAGGATCTGGTATGCAGAATA----AAGAACTCCTGCTACTC 1623
                          v   i      iv  v    v       ----        i i v    
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_111081744_   1624 AATAACAAAAAGATAAA 1640
                              i       i   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAA 803

Transitions / transversions = 1.26 (72 / 57)
Gap_init rate = 0.02 (19 / 803), avg. gap size = 7.21 (137 / 19)  

 488 18.10 0.00 0.95  chrX_111081744_111084395.rev     2057  2161 (491)    L1M4_orf2#LINE/L1      805   908 (0)  

  chrX_111081744_   2057 AACCTCTATTTTAAATTGGGCAAAAAACTTGACTATGCATTTCTCCAAAG 2106
                             - v   ?v   v        ii i    v  vi             
  L1M4_orf2#LINE/    805 AACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_111081744_   2107 AAGATATATGTATGGCCAAAAAGCATATGAGAAGATGTTTATCATCATTA 2156
                                 iiv        v     i    i      i i v     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_111081744_   2157 GTCAT 2161
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.25 (10 / 8)
Gap_init rate = 0.01 (1 / 104), avg. gap size = 1.00 (1 / 1)  


2778 16.88 5.03 1.79  chrX_111101250_111102849.rev      495  1110 (490)    L1M4_orf2#LINE/L1      273   908 (0)  

  chrX_111101250_    495 CTGGCACACAAAGGCAGACATATATGCCAATGGAATAGAATAGAGTACCC 544
                               i -- i ii         vii              v   vii  
  L1M4_orf2#LINE/    273 CTGGCATA--AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_111101250_    545 AGAA------TCA--CTTATATGGCCAAATGATTTTTGACAAGAGTGCCA 586
                             ------i  -- v v     i   v       i      i      
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_111101250_    587 AGACCATTCAATGGGGAAATAACAGTCTTTTCAACAAATAGAGTTGAGAA 636
                                            v  i                i v i  i  v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_111101250_    637 AAGTGGATATCAATATGCAAAAGAATGAAGTTGGACCCTTACCTTACACC 686
                           v      ? v i                        i     i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_111101250_    687 AAGTACAAAAATTAACTCTAAATAAATCAAAGACCTAAATATAAGAGTTA 736
                          vi               v    ii    ?          i      i  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_111101250_    737 AAAGCACAGACCTCC--------------GGGGGGAAGCTTCATGATATT 772
                            vi i i v   i--------------  ? vi  v    i   iv  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_111101250_    773 GATTT-GAAAATGGTTTCTTGGATATGACACCAAAAGCACAGGCAATCAA 821
                          iv  - iv           i                    i    -   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA-CAA 619

  chrX_111101250_    822 AAGTAAAAACAGAGAAATTATACTACATCAAAATTTAAAACATCTGTGCA 871
                            v     i   v     iv   v          v     v i     v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_111101250_    872 TCAAAGGAC----TCAACAGAGTGAAAAGGCAACCTATAGAATGAGTGAA 917
                                  ----    v i         i     i i      i v   
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_111101250_    918 AAATATTTGTAAAT-ATCATATCTGATAAGATGTTAATATCCAAAATATA 966
                           -      i    -  -            ivii vi      i      
  L1M4_orf2#LINE/    720 AA-TATTTGCAAATCAT-ATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_111101250_    967 TAAAGAACTCCTACAACTCAACAACAAAATATTCCCCAAAAAAATCAATT 1016
                                   i          i  i    vi----v    v  vi     
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAG----ACAAATAACCCAATT 813

  chrX_111101250_   1017 TTAAAAAATGGACAAAGGACTCAAATATATATTTCTCTAAAGA---TATA 1063
                         ?--        i       i ii    v i       i     ---    
  L1M4_orf2#LINE/    814 W--AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_111101250_   1064 CAAATGGCCAGTAAGCACATGAAAAGATGAACAACATCCCTAATCAT 1110
                                   i                  vv       v????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (61 / 39)
Gap_init rate = 0.02 (13 / 636), avg. gap size = 3.23 (42 / 13)  


2042 16.31 1.71 24.17  chrX_111175256_111178971     2053  3223 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111175256_   2053 TGGAAAGATATTCCATG------GATTAGAAGATTTAATATCATTAAAGT 2096
                                    i     ------    i     i       ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111175256_   2097 GACAATATAAACTGAAATAGTCTACAAATTCAATGTAATATATATCAAAA 2146
                          i     ivvv ii  v ii      i      i i   viv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111175256_   2147 TTCCA-TTGCCCTTTTTTGTAGAAATGGAAAAGCTGA-CCTACAAATGCT 2194
                          i   -i    -       i      v  v       -    -    v v
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTA-AAATTCA 148

  chrX_111175256_   2195 TAAGGATTTACAAGGGGCCTTAATTATCCTAAATATCCCTTAAAAAGAAG 2244
                           v   vv i      i  ivi v  v  v   i vi i v         
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_111175256_   2245 AAAAAAGGTGGGAAGACTCATATTTCCAAATTTAAAATCTTATTAAAAAG 2294
                           v    v   - i      i i    v     v   v    i  v    
  L1M4_orf2#LINE/    199 AACAAAGTTGG-AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_111175256_   2295 CTAGAGGAATCAAAACAGTGTGGTACTGGCATAAGGACATATCTGTAGAC 2344
                            v  v      i                       i v iv i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_111175256_   2345 TAGTGTAATAGAATTGAGACTCCAGAAATAAACCTGTACATTTAGAGCCG 2394
                         i i  v             v              ii        vi i i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_111175256_   2395 ATTGATTT--GACAAGGGTGCCAAGGCCAT-CAATAAGGAGAGAATATTC 2441
                                 --               i    -    ii   i      v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_111175256_   2442 TCTTCGACAAGAAATGCTGGCGTGACTGGATATCCACGTTTAAAAGAATG 2491
                          i   i    ivii      viii        ?    i vi         
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_111175256_   2492 AACTTGGGGCCCGGCGCGGTGGCTCACGCCTCTAATCCTGGCACTTTGGG 2541
                           v    i--------------------  i   --   vi   ------
  L1M4_orf2#LINE/    448 AAGTTGGA--------------------CCCCTA--CCTCACAC------ 469

  chrX_111175256_   2542 AGGCCGAGGCGGGCGGATTATCTGAGGAGTTCGAGACCAGCCTGGCCAAC 2591
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    470 -------------------------------------------------C 470

  chrX_111175256_   2592 ATGGTGAAACCCTGTCGCTACTAAAAATACAAAAAGTAGCCAGGCGCAGT 2641
                           ------------------------         v  ------------
  L1M4_orf2#LINE/    471 AT------------------------ATACAAAAATTA------------ 484

  chrX_111175256_   2642 GGCACGCGCCTGTAGTCCCAGCTACTTGGGAGACTGAGGCAGGAGACTCG 2691
                         -----------------------   i--- i v  iiv  ?-    ---
  L1M4_orf2#LINE/    485 -----------------------ACTC---AAAATGGATCAW-AGAC--- 504

  chrX_111175256_   2692 CTTGAACCCGGAAGTGGAGGTTGCAGTGAGCAGAGATTTTGTCACTGCAC 2741
                           ---------  i  v i --------   vi i i ------------
  L1M4_orf2#LINE/    505 CT---------AAATGTAAG--------AGCTAAAACT------------ 525

  chrX_111175256_   2742 TCCAGCCTGGGAGACAGAGTGAGACTCTGTCTCACAAAAAAAAAAAAAAA 2791
                         ------------------i i i     --- ------ i  i    v v
  L1M4_orf2#LINE/    526 ------------------ATAAAACTCT---T------AGAAGAAAACAT 548

  chrX_111175256_   2792 AAAAGTAAAAGAACTTAGAAGTTGGGTCCCTACCTTCTATTATGTACAAA 2841
                          ii?     --------------------------   - ii  ------
  L1M4_orf2#LINE/    549 AGGNGTAAA--------------------------TCT-TCGTG------ 565

  chrX_111175256_   2842 AATTAACCCAAATTAAGTCTAATCCTAATATAAGAGATAAACTATAAAAC 2891
                         -----   ----  ii  -  iv --   ------ i -----------i
  L1M4_orf2#LINE/    566 -----ACC----TTGGGT-TAGGC--AAT------GGT-----------T 586

  chrX_111175256_   2892 TCTTAGAATAAAACTTTGGCTATGACACCAAAAGCTTAGGCAATAAAC-- 2939
                                -------------               vi i    i   v--
  L1M4_orf2#LINE/    587 TCTTAGA-------------TATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_111175256_   2940 --AAATAAATAAATTAGACTTCATCAAAATTAGTCTTCTGTCTTCTGTGC 2987
                         --     i       i                iv-----iv   i     
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAA-----AACTTTTGTGC 668

  chrX_111175256_   2988 ATCAAAGGACATTATCAACAAA-TGTAAAAGATAGCCTACTCAATAGGAG 3036
                         v          i      v   -  -      i i  i  vv   i    
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTG-AAAAGACAACCCACAGAATGGGAG 717

  chrX_111175256_   3037 AAA---TTTATAAATCATATGTCTGATAAGGATCTAATGTCAACAATGTA 3083
                            ---   ii         i          iv  vi i  v v   i  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_111175256_   3084 TAAAGAACACTTAGAACTCAACAACAAAAGGGCAAACAATCCACTT-AAA 3132
                                 v    v       i  i    i i    i  i   v  -   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_111175256_   3133 TGTAGTCAAAAGAATTGAATAGACGTTTACCCAAAGAAGATGTAAAAAGG 3182
                         vi i v    i  v          i   vi           i  v   v 
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_111175256_   3183 GCCAAGAAGGAAATAAAAAGATATTCAACATCATTAGTTAT 3223
                              v   v v  i       ii         ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (118 / 70)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 8.42 (303 / 36)  


1602 21.84 28.23 1.95  chrX_111185341_111187135      584  1302 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111185341_    584 TGGAAAAACATCCCATATTCGTGGACTGTAAAAGT-AATATTATTAAAAT 632
                               i i       i   i    i  v  i v -      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111185341_    633 GTCCACACTACCCAAAGTGATCTACAGATTAAATGCAATTCCTATCAAAA 682
                          v v i   v      v             v  i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111185341_    683 TCCCAGTAGCATTTTT-ACAGAACTGGAAAAAACTG-TCCAAAAATTCAA 730
                               iv  v     -i     v v  v  i-   -   v        v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_111185341_    731 ATGGAATCAGCAAAGATCCCAGC-TACTCAAAGCAGATTGGAGGAAGAAT 779
                               vi-    i iv     v-  vi    i  ivi v  ii     v
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_111185341_    780 AACAAAGCTAGAGGCAC-CATACTTCCTGATTTCAAAATATATTGCAAAG 828
                                i i    -  -  i      ii         iv  i i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_111185341_    829 CTGTAGTAATTAAAACTGTTT----------TTATGCCAGTTTTATA--- 865
                           ii      i  i  v  v ---------- v v vi  viv    ---
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_111185341_    866 ---------------------CCAG-----------------TATGGC-- 875
                         ---------------------    -----------------     i--
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_111185341_    876 ATTGA--------------------------CAAT-----AAAAACAG-- 892
                              --------------------------    -----  i  i  --
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_111185341_    893 -----------------------------------ACATATA-------- 899
                         -----------------------------------    ii --------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_111185341_    900 ------GACC---------------------------------AATGGAA 910
                         ------    ---------------------------------      v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_111185341_    911 CA-------AAATG-GAGACCTGAAACTGTAAAAGTTCTAGAAGAAAACA 952
                           -------     -i   v  i     i     v ii            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_111185341_    953 TAAGGA-AAATCTTCTTGACATTGGCCTTAGCAATGATTTCTTCAATAGG 1001
                           i ?i-        v    v    vi vi      i      vi   v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_111185341_   1002 ACACTAAAAGCATAGGCAACAAAAGCAAAAATAGACAAGTGAAATTATAT 1051
                             i       i i          v         i  i vii i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_111185341_   1052 CAAA-CTAAAATGCTCTGCACAACAAAGGAAACAATTAACAAAATGTAAA 1100
                             -i     vvi i  ii vv       v  v  i  v   i  v   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_111185341_   1101 GGCAAACTCCAGAATGGGGAAAAGTATTTTCAACCCATACATCTGATAA- 1149
                          i   v iv         ii   i     v   vi    i         -
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_111185341_   1150 ---------------ATATATAG-GAATTCCTAGAACTCAATATTTAAAA 1183
                         ---------------       i-   i  i  v         v v    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_111185341_   1184 AAAAAGAAACCCACAAATACTTGTATT--AAAGTGGGCAAAAAACT-GCA 1230
                         i v  iv      -----------   --   i        ii i - v 
  L1M4_orf2#LINE/    798 GACAAATAACCCA-----------ATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_111185341_   1231 GATGCATTTCTCCAAGGAAGACATACAAATAGCCAACAGGTATATGAAAA 1280
                         v vi           i     i        i     i i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_111185341_   1281 TGTGCTCAACATCACTGATCAT 1302
                         vi            ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (94 / 62)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 8.35 (217 / 26)  


2777 25.39 3.90 2.78  chrX_111251890_111254926.rev     1649  2546 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111251890_   1649 TGGAAAGACATATCACATTTATGGATTGGGAGATTCAAC-TAGTAAAGAT 1697
                                 i  vi  ii  i         i   i i  i- v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111251890_   1698 GTCAGTTTTCCCTGAATTGTTTTATTTTGTGTTTAA-GCAATTATTATCA 1746
                          v  i vi    ii     v i  i---ivi  i  -     ivi     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTAC---AGATTCAACGCAATCCCTATCA 97

  chrX_111251890_   1747 AAATCCTAGCAAAATTATTT-TAGACATGGACGAGCTTATTCTAAAATGT 1795
                               i   vivv  v   -i   v  v   i    v  i       vi
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_111251890_   1796 ACATGGGAAGTCATAGGCCCTAGAATAGCTAAAATAACCTCAACAAAGAA 1845
                          i    i  vv  vi  v  i        i    i  i  ii v      
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_111251890_   1846 GAATAAAGTGGGAGGAATCACTCTACCTGATATGAAGGCTTACTATATAG 1895
                            i     v      v    v  v  ii  v v  ii       i v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_111251890_   1896 CTATATAGCTGATACAACCAAGACAGAGTTGTATCAGTGGAGGGACAGAC 1945
                            i --------ii  i        v  v   iii iiv i   i    
  L1M4_orf2#LINE/    248 CTACA--------GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_111251890_   1946 ACATAGATCAATGGAACAGAACAGAGAAGCCAGAAATCGACCCATATGAA 1995
                          i              i    iv    iv        vi       iivv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_111251890_   1996 TATGCCCAAC--ATATGAGAAAAAGG----AAGAAAATTCAATCAAAGGA 2039
                             vi   i--  v vv  v  i  ----    vv       ----  i
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT----GGG 385

  chrX_111251890_   2040 GGAAAAGAAGTCTTTTTAACAAGTGGTGCTAGAACACTTGGACA-CTAGG 2088
                          i  i iv        i     i       i i   vi    i - i vi
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_111251890_   2089 -GCATAAAAATGAATCCTGACCTAAACCTCACTCCCTATACAGAAAGTAT 2137
                         -   v  i      viiv    ivv       v  v      i   v  v
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_111251890_   2138 CTCCAAATGGATTATAGACTTAAATATAAAA-CTAAAAATGTAA---TTT 2183
                            v        i ?    i     i   i -      v i   --- i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_111251890_   2184 TGAAGAATAAAAAATAAGAGGAAATCTTCATACTCTAGGAATAGGCAAAG 2233
                          --    v    v   i ? v        i ivi  v  iv       v 
  L1M4_orf2#LINE/    536 T--AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_111251890_   2234 ATGTCTTAGCTTTAATCATCTA---CAAAAGCAATTCAGAAAAGAAAAAT 2280
                         i v      v v i -  i v ---  v      i----          v
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGA-CACCAAAAGCACAAGCAAC----AAAAGAAAAAA 628

  chrX_111251890_   2281 GTGATAAACTGGACTCCATCAAAATTAAATACTTTT-T-CTTTGTGAAAG 2328
                         vv      i      i             v      - -   i---    
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC---AAAG 675

  chrX_111251890_   2329 AAC----TTAAGAGGATGCAATGACAAATTACAGGTGGAGAGAAAATATT 2374
                         i  ---- i    iii  v  v     vii    ivv i           
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_111251890_   2375 CGCAACCCCTATGTTCAACAAAGGACTAGTATTTAGAA-----------C 2413
                         i    vi v   i iii i  i     v    ii    ----------- 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_111251890_   2414 TCTCAAAACTCAACAATAAAAATACAAACCATCCAAGTAGAACATGGGCA 2463
                            i v       i        v     iv i    v ?i  v       
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_111251890_   2464 AGAGATACGAAGAGACAGTTCTCTGAAAAAGATATGCAGAGGATAAATAA 2513
                          ii   vi   v     v     ii  i       i  i v iiv     
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_111251890_   2514 GCACATGAAAAGATGTTCGACATTATTAATCAG 2546
                                        i  i    i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (134 / 91)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.86 (60 / 21)  


3090 27.25 0.66 0.88  chrX_111290317_111296724.rev     5008  5917 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111290317_   5008 TGGAATTACATTCCATGCTCATGAATAGGAAGAATCAATATCATGAAAAT 5057
                              vv i  i     i     i  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111290317_   5058 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5107
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111290317_   5108 TACCAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5155
                          v   iivi    i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_111290317_   5156 TGTGGAATCAAAAAAGAGCCCGCATTGCCAAGACAATACTAAGCAAAAAG 5205
                          i     viiv  ii  v  v v  v     i     vi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_111290317_   5206 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5255
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_111290317_   5256 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5305
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_111290317_   5306 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5355
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_111290317_   5356 CTGATCTTTGACAAACCTGACAAAAATAAGAAATGGCAAAAGGATTCCCT 5405
                         i    i  i     ivv  v   i vi vvv     vi    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_111290317_   5406 ATTTAAGAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5455
                         v  i  v              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_111290317_   5456 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5505
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_111290317_   5506 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5555
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_111290317_   5556 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTGAA 5604
                            ?i- v i -   iv   v v  vv i     v ii   v iiv ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_111290317_   5605 ACAACAAAAGCA---ATGACAAGAGAAGCCAAAATTGACAAATGGGATCT 5651
                            v        ---iii    i    ---     v  i    v   ii 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAA---AAAATAGATAAATTGGACTT 644

  chrX_111290317_   5652 AATTAAACTAAAGAGCTTCTCCACAGCAAAAGAGATTACCAACAGAGTGA 5701
                         v  i   v v  i i   i vii vv    i  v i  i   v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_111290317_   5702 ACAGGCAACCTACAGAATGGGAGAAAATTTGTGCAATGTACCCATTTGAC 5751
                          v  i     i                 v v     vvi ivi  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_111290317_   5752 AAAGGGCTAATAGCCAGAATCGACAAAGAACTTAAACAAATTTACAAGAA 5801
                           i  i  vi  v       vv i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_111290317_   5802 AAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGTATATGAACAGACAC 5851
                            i -    i     v  i?    i         v  v    i     i
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_111290317_   5852 TTTTCAGAAGAAGAGATATATGCAGCCAACAGACACATGAAAAAAATGCT 5901
                           i  vi       v   i viii     i ii          i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chrX_111290317_   5902 CATCATCACTGGTCAT 5917
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3122 27.54 0.88 0.44  chrX_111373828_111381292      708  1611 (5854)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111373828_    708 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 757
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111373828_    758 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATTCCCATCAAGC 807
                            v     v     iv i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111373828_    808 TACCAATGACATTCTTCATAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 855
                          v   iivi v  i  iii    -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_111373828_    856 ATATGGAATCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAA 905
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_111373828_    906 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 955
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_111373828_    956 CTACAGTAACCAAAACAGCATGATACTGGTACCAAAACATTGATATAGAC 1005
                                  i   i    ii  i      i iv ii i vvv       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_111373828_   1006 CAATGGAACAGAACGGAGCCCTCAGAAATAATACCACACATCTACAACTA 1055
                                 i    iv   vvii         vv   i    i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_111373828_   1056 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 1105
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_111373828_   1106 TATTTAAGAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGGAAGCTG 1155
                          v  i  v              v      v  ?   i  ii ii iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_111373828_   1156 AAACTGGATCCCTTCCTTATGCCTTATACAAAAATTAATTCAAGATGGAT 1205
                           ii    i    v   i ii  v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_111373828_   1206 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1255
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_111373828_   1256 TAGGCA-ATACCATTCAGGGCATATGCATGGGCAAGGACTTCATGTCTAA 1304
                             ?i- v i -   iv i v vv vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_111373828_   1305 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTCACAAATGGGATCTAA 1354
                         i            vvi          vv     vv i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_111373828_   1355 TTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAAC 1404
                          i   v v  i i   i   i vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_111373828_   1405 ACGCAACCTACAGAATGGGAGAAAATGTTTGCAACCTACTCATCTGACAA 1454
                          vi     i                 i       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_111373828_   1455 AGGGCTAATATCCAGAATCTACAAAGAACTC----AACACATTTACAAGA 1500
                         i  i  vi          v  i         ----   v  v v i  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_111373828_   1501 AAA-AAACAACCCCATCAACAAGTGGGCAAAGGACATGAACAGACACTTC 1549
                          i -   i     v  i? v  i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_111373828_   1550 TCAAAAGCAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 1599
                           v    v   i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_111373828_   1600 ATCACTGGCCGT 1611
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  

3294 26.54 0.44 0.44  chrX_111373828_111381292     6065  6972 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111373828_   6065 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 6114
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111373828_   6115 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 6164
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111373828_   6165 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6212
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_111373828_   6213 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCTTAAGCCAAAAG 6262
                                viiv  ii  v  v v  v     iv       i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_111373828_   6263 AACAAAGTTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6312
                                       vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_111373828_   6313 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 6362
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_111373828_   6363 AATGGAACAGAAC--AGAGCCCTCAAAAATAACACCGCATATCTACAACT 6410
                                i    i--    i  -- i      vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_111373828_   6411 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 6460
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_111373828_   6461 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6510
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_111373828_   6511 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 6560
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_111373828_   6561 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 6610
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_111373828_   6611 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 6660
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_111373828_   6661 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 6710
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_111373828_   6711 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 6760
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_111373828_   6761 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCAACTGACAA 6810
                           i     i   i             v  i    vii ivi v    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_111373828_   6811 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 6860
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_111373828_   6861 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 6910
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_111373828_   6911 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 6960
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_111373828_   6961 ATCACTGGCCAT 6972
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1795 24.77 4.54 10.84  chrX_111435981_111441069.rev     3630  4598 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111435981_   3630 TGGAAA-ACATTCCATGCTCATGAATAGGAAGAATCAATATTATTAAAAT 3678
                               - i  i     i     i  v      v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111435981_   3679 GGCCATAATGCCCCAAAC-AATATATAAATTCCATGC--TCTTCTATCAA 3725
                            v   v -       i-i  v  i i    v i  --  i-       
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCC-CTATCAA 98

  chrX_111435981_   3726 ACTACTAATGACATTCTTCATAGAACTAGAAAAAACCTATTTTAAAGTTC 3775
                          v v i iivi v  i  iii    v v  v  i- iv  ii    i   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chrX_111435981_   3776 ATAAAGAACCATAAAAGAGCTCAGA-TAGCCAAGGCAATCATAAACAAAA 3824
                            vi   viii  ii  - i    -       ii     v i  v  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_111435981_   3825 AGAGCAAAGCTGGAGGCATCATGTTACCCAACTTCAAACTATACTATGGG 3874
                            i     i      vv   iii v     i      viv     iiii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_111435981_   3875 GATATACAAACCAAAACAGCATGGTACTGGTACACAACCAGACACGTAGA 3924
                          v  i vv  i   i    ii         i i viivi     ii    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_111435981_   3925 CCAATGGAAGAGAATAGACAGCCCAGGAATAAGACTGCACAACTACAACC 3974
                         i        v     v  v  i    i     iv iii   vi  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_111435981_   3975 ATCTGATATTCAACACAGCAGACAAAAACAAAAACAAGCAATGGGGAAAA 4024
                          vi    v   i   -  vivi v  i  -----  vv           i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACA-AGGGTGCCAAGAC-----CATTCAATGGGGAAAG 390

  chrX_111435981_   4025 GAC--TCCTTATTCAATAAATGGTGCTGAGATAACTGGCTAGTCATATGT 4072
                         i i--  i  --    i           i  i      v  ?i  i   i
  L1M4_orf2#LINE/    391 AATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_111435981_   4073 AAAAGAATGAAGCTGGACCCCTTCATCACATTCAGATTC-----TTTTGT 4117
                                     i         v v     i-  v  v -----  vvv 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACAC-CATATACAAAAATTAACT 487

  chrX_111435981_   4118 CCCACTGGCTGATCCCTTGATCTGGTGCTCTCTCCCTTTCCCTAGGAATG 4167
                          vv v   ---   v-?v  --------------------    --    
  L1M4_orf2#LINE/    488 CAAAATGG---ATCA-WAGA--------------------CCTA--AATG 511

  chrX_111435981_   4168 GGTCTTCCTGAGAGCCAGA-CTGCAGTGATTTTTATTGCCCTTCTGGGTC 4216
                         -------- i     i i -  ii i-i i i   ---------------
  L1M4_orf2#LINE/    512 --------TAAGAGCTAAAACTATAA-AACTCTTA--------------- 537

  chrX_111435981_   4217 TGGCCATCCAGCAGGGCTACCAGGCTCCAGGATGGTGCTGAGAAATGTCT 4266
                         ---------- v  ii-- v  -----i   ?--  ------    v ii
  L1M4_orf2#LINE/    538 ----------GAAGAA--AACA-----TAGGN--GT------AAATCTTC 562

  chrX_111435981_   4267 GCAAAAAGTCCT---GTGATGTGATCTGTCTTTAGGTCTCCCAGCCATGG 4313
                          ii -----   ---  v v ii  ---------   i  ii  vi   -
  L1M4_orf2#LINE/    563 GTGA-----CCTTGGGTTAGGCAAT---------GGTTTCTTAGATATG- 597

  chrX_111435981_   4314 ATACTAGCAGTGAAA--AAAAAAAAAAAAGATAAATAGGTGGGACTT--- 4358
                          i  i iv  iiv  --  v    i    i   i   ii v      ---
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_111435981_   4359 ---AATTAAAGAGCTTCTGCACAGCAAAAAGAACAGTCAGCAGAGTAAAC 4405
                         ---       i -   i  ii vv    iiiv  vi   iv i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_111435981_   4406 AGACAACCCACAAAGTGGGAGAAAAT-TTCACAATCTATACATCCAACAA 4454
                                     i i           -  ii   vii   i   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_111435981_   4455 AGCACTAATATCCAGAATCTACAACGAACTC----AAATCAG----AAAA 4496
                         i v   vi          v  i  v      ----  v   i----    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_111435981_   4497 A---AAA------AATCAAAAAGTGGGCTAAGGACATGAATAGACAATTT 4537
                          ---   ------   i?    i     v     iv          v  i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_111435981_   4538 TCAAAAGAA--TATACAAATGGCCGACAAATGTATGAAAAAAATGCTCAA 4585
                           v      --             i i  iiii       i -       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

  chrX_111435981_   4586 CATCACTAATGAT 4598
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.99 (157 / 79)
Gap_init rate = 0.04 (40 / 908), avg. gap size = 3.73 (149 / 40)  


3407 25.36 0.66 0.55  chrX_111458740_111462989     2851  3757 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111458740_   2851 TAGAAATATATTTTATGTTTATGGATTGGAAGAATCAATATTGTTAAAAT 2900
                          i    v    iii     i             v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111458740_   2901 CTCCATAATACCCAAAACAATCTACAAGTTCAACAGAATATCTATTAAAA 2950
                         vv v   v v      vii       ii      iv   vi    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111458740_   2951 TAACAATGATATTCTTCACAGGAATGGAAATAAC-AATTGTCAAATTTAT 2999
                          vv  iiviiv  i  ii   i   v  v - i -i  iv v     i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_111458740_   3000 ATAAAAACGCAAAAGACCCAGAATAGCCAAAGCTATCATGAGCAAAAAGA 3049
                           ii   i    ii                 i v   v   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_111458740_   3050 ACAGAACTGGAAGAATCACATTACCTGACTTCAAATTATACTACAAAGCT 3099
                            i ii    i  v     i v  ii i      viv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_111458740_   3100 ATATTAACCAAAACAGCATGGTACCAGCATAACAACAGACACCTGGACCA 3149
                          i v   i   i    ii      ii      vi i     iv i  i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_111458740_   3150 ATCAAGCAGAGTAGAAAAGTCAGAAACAAATTCATACATGTACATTAAAC 3199
                           vi ii   i v  i ivi      i   ii       v  iiv v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_111458740_   3200 TCATTTTAAACAGAGGTGCCAAGAACATACATTAAGGAAAGGTCAGTCTC 3249
                          v     vi   ii          v   v  v ii      ivi     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_111458740_   3250 TTCAATAAATGGTGGTGGGAAAACTGGATATCCATATGCAGAAGAATGAA 3299
                              i        v     v         ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_111458740_   3300 ACTAGACCTCTATCTCTCACCATATACAAACACCAAATCAAAATGGATTT 3349
                         ii i    i   i   v             v ii  v           iv
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_111458740_   3350 GAATCTTAAATCTAAGACCTCAAGCTATCAAACTATTAAAGGAAAATCTT 3399
                         ? iv i     v     v  v  i    v     v   i i     iv v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_111458740_   3400 GAGGAGACTCTTCAAGACATTGGGTGGGGCAAATATATTTTGAGTAATAC 3449
                          i? vi v     iv   v      vi     vvi v i  iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_111458740_   3450 TCCACAAACACAGGTAACCAAAGCAAAGACGGTTAAATGGTA--TCA-CA 3496
                         v   v  i    i i   v    v   i ii v     v v --   -  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_111458740_   3497 GTAAGTTACAAAGCTTCTGCACAGTAAAGGAAACAATCAACAAAGTGAAG 3546
                         --  i   -   i   i  ii vvi      v  v     v        i
  L1M4_orf2#LINE/    650 --AAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_111458740_   3547 AGACAACCCACATAATAGGAGAAAATACATGTAAACTATCCATCTGACAA 3596
                                     v   i          iv  i   ii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_111458740_   3597 GGGATTAATAACTAGAATATATAAGGAGCTCAAACAACTCAATATGAAAA 3646
                             i vi  v i           i  i   vv           vv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_111458740_   3647 AGTATAAATAATC--ATATAAAAATGGGCAAAAGATTTGAATAAACATTT 3694
                           - i      i --  v?             i          i      
  L1M4_orf2#LINE/    797 AG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_111458740_   3695 CTCAAAGGAAGACATGCAAATGGCAAACAGGCATATGAAAAGATGCTCAG 3744
                            v  i     i  i        v  i i   i               i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_111458740_   3745 CATCACTGACCAT 3757
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (138 / 88)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2654 26.29 7.51 1.29  chrX_111474553_111476240.rev      346  1197 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_111474553_    346 AAAGAGCTATTCCAGATTCAAGGATAGGAAGATTCAATAT-GTTCGAGAT 394
                              --   i   vi    v    v      i i     -   -i    
  L1M4_orf2#LINE/      4 AAAGA--TATCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAGAT 50

  chrX_111474553_    395 GTCAGTTCTTTCCAACTTGATCTATGTATTCAACACAATCCCAAATCAAA 444
                          v  i v  ii    v        iiv       i       v -     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAAA 99

  chrX_111474553_    445 AATCATAGCAAGCTGTTTAGTGGCTATCATCAGACTAATTCTAAAATGTA 494
                          -  vi   viv  v   v ii vv  iiv  ii  i  i       vi 
  L1M4_orf2#LINE/    100 A-TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_111474553_    495 TATGGA----------------------------------------GAAG 504
                               ----------------------------------------    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_111474553_    505 AACAAAATCAGAGGACTGATACTACTGGATTTCAAATTTTAATATAAAGA 554
                               i ii       v i   v ivi        vi   v  i    v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_111474553_    555 TA-----------ACAATGTGGTATTGGTGAAAGAATAAATGAATAAATT 593
                           -----------   i       i   iiv   i   i iiv   i  i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_111474553_    594 AATGAAATAGAATAGAGATCTCAGAAATAGACCTATATA------GCCTA 637
                             i        v    vii        i   i   i ------ i v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_111474553_    638 CTGATCTTTGATAAAAGCACAAAGGCAATACACTGGAGTAAAGACAGTCT 687
                         i    i  i  i  ii ii v   i v  v  v   i v  ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_111474553_    688 TTTCAACAAATGGTGCTAGAACAACTGGACATCCACATGCAAAAATCATG 737
                                          i i         i ?            i-v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AATG 447

  chrX_111474553_    738 AATCTAAACACAGACCTTATAC-ATGTCAAAAAATTAACACTAAATGTAT 786
                           vi ii  v vv    i i  -  i vv          v v     v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_111474553_    787 CATAGACCTAAAT-TAAAAATGAAAAACAATAAAACTCCCAGAAGACAAT 835
                           ?          -   i iiv    - v         ii      v  i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAAC 546

  chrX_111474553_    836 ATAGGAGAAAACCTTTATGACCTTGGATATGGCGATGACTT--TAGATAC 883
                              ? v   i   ii         i vv   i   ii  --      i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_111474553_    884 AACATCATATGTGCAAACCAAGAAATAAATAATTGAGAAGCTGGACTTCA 933
                         i   i  v v ii   i v vi   v   v   v  v  ii         
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_111474553_    934 TTAAAATAAAAACCTTCTGCTCTGTGAAAGACAATGTTAAGAGAGTGGGA 983
                          i     v    v   i  iv  vii  i    v i i    i    ii 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_111474553_    984 AGATAAGCTGAAGATTGGGA-AAAATATTTATAAAAGGCACAGCTGATAA 1032
                            i  v iiv   v     -         ii   vvii i v       
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_111474553_   1033 AGGACTGTTGTCCAAAATATACCAAGAATCTTTAAAACTCAACAATAAGG 1082
                         i     vv i    i      iv     iii   v       i     ii
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_111474553_   1083 AAATTTTTAAA-AACCTGATTAAAAAGTAAGCAAAATATCTGAACAGATA 1131
                          i i----   -    ii   ?    i ii     iv  i    i   i 
  L1M4_orf2#LINE/    797 AGAC----AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_111474553_   1132 TCTCACCAAAGAAGATATATAGATGGTAGGAAAGCATATAAAAGGGTATT 1181
                          i  v              i i    iviiv     i  i   i i ii 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_111474553_   1182 CAACATCATATGTCAT 1197
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (144 / 76)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 4.69 (75 / 16)  


3085 26.93 0.88 0.66  chrX_111510686_111517098     5017  5922 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111510686_   5017 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAGTATCATGAAAAT 5066
                               i i  i     i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111510686_   5067 GGCCTTACTGCCCAAAGTAATTTACAGATTCAATGCTATCCTCATCAAGC 5116
                            vv    v      v i  i           i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111510686_   5117 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 5164
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_111510686_   5165 TATGGAACCAAAAAAAGAGCCTGCATAGCCAAGATAATCCTGGGCAAGAA 5214
                                viiv  ii-  v  v v        i i    i  iiv     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_111510686_   5215 GAACAAAGATGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5264
                                 v      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_111510686_   5265 GTACAATAACCAAAACACCATGGTACTGGTACGAAAACAGAACTTTAGAC 5314
                         v    i   i   i   vii         i ii ii i   vv v    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_111510686_   5315 CAATGGAACAGAAC--GGAGTCCTCAGAAATAACACCACACATCTACCAC 5362
                                 i    i--i      --        vv   i    i  ivii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_111510686_   5363 CATCTGATCTTTGACAAACCTGACACACACAAGCAATGGGGAAAAGATTC 5412
                           vi    i  i     ivv  v  vivv  vv           ii  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_111510686_   5413 CCTATTTGATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 5462
                         i  v  ii i        i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_111510686_   5463 TGAAACTGGACCCCGTCCTTACACATTATACAAAAATCAACTCAACATGG 5512
                             ii        vv   i    vv           i       v    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_111510686_   5513 ATCA--GACTTAAACATAAGACCAAGGACCATAAAAATCCTAGAAGAAAA 5560
                             --   i    ii     v v ii  i      v  i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_111510686_   5561 TCTGGGC-CATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCT 5609
                         iv i  ?-i v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_111510686_   5610 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5659
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_111510686_   5660 AATTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTATCATCAGAGTGA 5709
                         v  i   v v  i i   i  iiivv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_111510686_   5710 ACAGGCAACTTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGAC 5759
                          v  i    ii                 v       vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_111510686_   5760 AAAGGGCTAATATCCAGAATCTACAAAGGACTCAAATAAATTTACAAGAA 5809
                           i  i  vi          v  i    i    vv i  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_111510686_   5810 AAAAGCAAATACCCCCATCAAAAAATGGGCAAAGGATATGAAAAGACACT 5859
                            ii      v   v  i?                 v    v     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_111510686_   5860 TATCAAAAGAAGACAT-TATGTAACCAACAGACGTATGAAAAAATGCTCA 5908
                          v  v        i  -i vi ii    i ii ii       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_111510686_   5909 TCATAACTGGTCAT 5922
                         v   v ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (138 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2740 21.57 12.01 0.74  chrX_111531437_111533259.rev      517  1332 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111531437_    517 TGGAATGATATCCTGTGCTCATGGATTGGGGGAATTAATATTGTTAAAAT 566
                              v       ii  i           ii  v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111531437_    567 GTCCATACTAGGCACAGCAATATATAGATTCAATGCAATCACTATCAAAA 616
                          v v     vvv  v vii  v  i        i      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111531437_    617 TTTCAA-TGCTATCCTTCACAAAAATGGAAAAGA-AATCCCTGAAATTTG 664
                          ii  i-   i- ii  ii  i    v  v   v-i    - i     ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCC-TAAAATTCA 148

  chrX_111531437_    665 TATAGAAA--CAAAATACCCCCAAATATCCAAAACAATTCTGTGAAAGAA 712
                            i    --   iiv    v-i    v          ii  vi      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_111531437_    713 AAACAAAGTTGGAGGTATCACAGTTCTTAATTG-AAAATTATATTACAAA 761
                         i              vv     v   ii    v-    i -  i      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chrX_111531437_    762 GCTATAGTAAT-AAAACAGTGCGGCACTGGCATAAATACAGTCATATAGA 810
                             i      -  i      i  i          iv i  v        
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_111531437_    811 TGAGTGGATTAGGATAGAGAGCCCAGAAATAAATCCAAACATATATGGTC 860
                          v i    v   i  v     i           i   v    v       
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_111531437_    861 ACCTAATTTTTTGCAAGAGCACCAAGAAGACACA-TGGGGAAAGGACTAT 909
                          vi i     ivi    i ii      vv iv  -         i ivi 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_111531437_    910 CTCTTCAATAAGTGGTGCTGGGTAAACTGGACTTACACATGCAAAAGAAT 959
                           i     i  i          vv       iv?v               
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_111531437_    960 GAAGTTGGACCCTTATCTTACACCAAACACAAAACTTAAGTAAAAATGAA 1009
                                     i  i  i      v i      v    v v      i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_111531437_   1010 T-AAAGACCTAAATTTAAGA-CTAGAAACTTTAAAACTTCTAGAAGATAA 1057
                          - ?          v     -   -     v       ii       v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAA 545

  chrX_111531437_   1058 CA-AGG--TAA-----CATAA----GGATAAAGC-------TCTT----- 1083
                           -   --   ----- i i ----  i v i  -------    -----
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_111531437_   1084 ------------------CTACA---GAATATATATATACAT-------- 1104
                         ------------------ v   ---   v v   v   v  --------
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_111531437_   1105 ATGTAAAT----------------------------------AAAATAAA 1120
                           vv    ----------------------------------   i i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_111531437_   1121 ATAGCAACCTATC-ATTTGGAAAAAA-ATTTGCAAGCCATATGTCTGATA 1168
                          vii     i iv- v v   i    -        ii     i       
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_111531437_   1169 AGGGGTTACTATTCAAAATATATTAAGAATTCATACACCTAAATAGTAGA 1218
                             ii vv   i  i       v     i  v    v  v    i  i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_111531437_   1219 AAAACAAATAATATAATCATAAAAATAAGCATATGATCTAAATAGACATT 1268
                           i        ivi   i?-      ii   v v   i i          
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_111531437_   1269 TCTTCAATGAAGACATACAAATGATCAATGGGTACATAAAAACATGCTCA 1318
                            i   v     i         ii    ii i    i    v       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_111531437_   1319 ACATCATTAATCAT 1332
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (104 / 69)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 4.16 (104 / 25)  


2970 27.07 0.65 1.96  chrX_111535360_111538281.rev     1512  2431 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111535360_   1512 TGGAAACACATCCCATGCTCATGGATGGGTAGAGTCAATATTGTGAATAA 1561
                               v i        i        v  v   v i        v  v v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111535360_   1562 GACCATATTGCCAAAAGCAATCTACAAATTTAATGTAATCGCCACCAAAA 1611
                          i v   i v  v   vii       i   i  i i    v i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111535360_   1612 TACCACCATAATTCCTCACAGAATTAGAAAAAAAACAATTCTAGAATTCA 1661
                          v   v vvvv  ii ii     v v  v  iv--ii  i   i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chrX_111535360_   1662 TATGGAACCAAAAAAGAGCCTGCATAGCCACAGCAAGACTAAACAAAAAG 1711
                                viiv  ii  v  v v       v i   vvi i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_111535360_   1712 AACAAATCTGGAGGCATCACACTACCCGATTTCAAACTCTACTATAAGGC 1761
                               vi      vv       v   i        vii     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_111535360_   1762 CAGATTCTCCCAAACAGCATGGTACTAGTGCAAAAATAGGCACATAGACC 1811
                         i v v vvi v i    ii       i iii  ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_111535360_   1812 AGTGGAATAGAGAATAGCAGAATAGAGAACCCAGAAATAAATCCAAATAC 1861
                          i         ----------  v    ii           i   v i i
  L1M4_orf2#LINE/    299 AATGGAATAGA----------ATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_111535360_   1862 TTACAGCCAACTGATCTTTGATAAAGCAAAGAAAAACATAAAGTGCAGAA 1911
                            ii i   i    i  i  i  i vvivv  i v   vv i  vi   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_111535360_   1912 AGGGCACCCTTTTCTACAAATGGTGCTGGGATAATTGGCTAGCCACATGT 1961
                           iii vi      v                i  i   v  ?       i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_111535360_   1962 AGGAGAATGAAACTTGATTCTTATCTCTCACTTTATACAAAAATCAACTC 2011
                          ii        ii v  ii i  i   v   iv           i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_111535360_   2012 AAGATGGATTAAAAACTTAAACCTAATACCTGAAACTATAAAAATTCTAG 2061
                           i      i ? i  i    iv   v v  i           v ii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_111535360_   2062 AATATGACATTGGA--AAATCTCTTCCAGATATTATCTTAGGCAAGGATT 2109
                           v vi    v  ?--      --  vv  iv  ivv        v i  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCT--TCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_111535360_   2110 TCAT-GACCAAGGAC-CCAAAAGCAAATGCAATAAAAACAAAGATAAATA 2157
                           v -  i-- v   -         v v    i    iv   i   i   
  L1M4_orf2#LINE/    587 TCTTAGAT--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_111535360_   2158 GCTGGGACCTAATTAAACTAAAGAGCTTTTGCATGACAAAAGGAACAGTC 2207
                         iv v    i v  i   v v  i i      iiivv    i iv  vi  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_111535360_   2208 AGCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCCTCACAATCTA 2257
                          iv i   i  v              i           vi ii   vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_111535360_   2258 TACATCTGACAAAGGACTAATATCCTGAATCTACAATGAACTCAAATACA 2307
                           i      i  i     vi     v    v  i  v      v--    
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT--TACA 782

  chrX_111535360_   2308 --TCAGTAAGAAAAAACTAAACAATCCCATCCAAATGTGGGCTAAGGACA 2355
                         --   i   v     ivi   i  i  v  i?   vi     v     iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_111535360_   2356 TGAATAGACAATTCTTAAAAGATCATGTACAAATGGCCAATAAACGTACG 2405
                                   v    iv     vv  i                i ii i 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_111535360_   2406 AAAAAATGCTCAACATCACTAATGAT 2431
                             i             ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  


3358 26.46 0.55 0.44  chrX_111554793_111557186      995  1901 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111554793_    995 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1044
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111554793_   1045 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1094
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111554793_   1095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1142
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_111554793_   1143 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1192
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_111554793_   1193 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1242
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_111554793_   1243 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGATC 1292
                                 i   i    ii         i iv ii ii  v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_111554793_   1293 AATGGAACAGAAC--AGAGCCCTCGGAAATAACGCCACATATCTACAACT 1340
                                i    i--    i  --i       vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_111554793_   1341 ATCTGATCTTTGACAAACCTGACAAAACCAAGCAATGGGGAAAGGATTCC 1390
                          vi    i  i     ivv  v   i    vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_111554793_   1391 CTATTTAATAAATGGTGCTGGGAAAACGGGCTAGCCATATGTAGAAAGCT 1440
                           v  i  i              v   v  v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_111554793_   1441 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1490
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_111554793_   1491 TTAAAGACTTAAACATTCGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1540
                          i ?    i    ii vv  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_111554793_   1541 CTAGGCATTA-CCTTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1589
                         v    ?i v -i    iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_111554793_   1590 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGATAAATGGGATCTAA 1639
                         i            vvi           v     v       v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_111554793_   1640 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1689
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_111554793_   1690 AGGCAACCTATAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAAAA 1739
                           i     i i i             v  i    vii ivi      v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_111554793_   1740 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 1789
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_111554793_   1790 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 1839
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_111554793_   1840 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 1889
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_111554793_   1890 ATCACTGGCCAT 1901
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2460 24.18 1.75 8.33  chrX_111604916_111610726     4347  5318 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111604916_   4347 TGGAAAAACATTTCATGCTCATAGATAGGAAGAATCAATATCATGAAAAT 4396
                               i i  ii    i    i   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111604916_   4397 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCACACCAAA- 4445
                            v     v      v i  i  i        i  v  i vi i    -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111604916_   4446 TTACATTGACATTCTTCACAGAATTAGAAAAAAAAACT-ACTTTAAAATT 4494
                          iv  vivi v  i  ii     v v  v  i----  - iii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chrX_111604916_   4495 CATATGGAACCAAAAAAAAAAGCCTGTATAGCCAAGACAATCTTAAGCAA 4544
                                  -- viv  iii v  v v        i        i ----
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---- 190

  chrX_111604916_   4545 AGAAAAAAAAAAGAACAAACAAACAAACAAAAAAACAAAGCTGGAGACAT 4594
                         -----    i         -------------------- i     ivv 
  L1M4_orf2#LINE/    191 -----AAAAGAAGAACAAA--------------------GTTGGAGGACT 215

  chrX_111604916_   4595 CATGCTACCCAATTTCAATCTATACTACAAGGCTACAGTAATCAAAACAG 4644
                           ii  v           vviv        i              i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_111604916_   4645 CATTGTATTGGTACAAAAACAGACACATAGACCAATGGAAAAGAAC--AG 4692
                         ii v   i   i i  ii i     i     i        v    i--  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_111604916_   4693 AGTTCTCAGAAATAAGATTGCACATCTACAATCATCTGATCTTTCACAAA 4742
                            i --        iviiii    i  iii   vi    i  iv    i
  L1M4_orf2#LINE/    316 AGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_111604916_   4743 CCTGGCAAAAGAAAGCAATTGGGAAAGATTC-CCGATATAATAAATGGTG 4791
                         vv  v   i vv vv    v        v v-i vv vi  i        
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_111604916_   4792 CTGGGAGAACCGG-TAGCCATATGCAGAAAGCTGAAACTGGACCATT-CC 4839
                               v   i  -  ?   i     i  iiv    ii      vi -  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_111604916_   4840 TTACACCTTATACAAAAATTAACTCAAGATGGATTAAAGACTTAAATGTA 4889
                          i     v                   i      i ?    i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_111604916_   4890 AAACCCAAAACTATAAAAACCTTAGAAGAAACCCTAGAC---AATACGAT 4936
                          i v i            vi           v v   i?---   - -- 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-C--T 560

  chrX_111604916_   4937 TCAGGACATAGGCATGGGCAAAAATTTCAT-GACAAAACTTCAAAAGCAA 4985
                           iv   v v  vv i     vii    v -  i vi  vi        v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_111604916_   4986 TTGTAACAAAAGCAAAAATTGACAAATGGAATCTAAGTAAACTAAAGAGC 5035
                         vv i        v      v  i    v i ii v vi   v v  i i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_111604916_   5036 TTCTGCACAGCAAAAACAAAACAAAACAAAACAAACAAATAAACAAAAAA 5085
                           i  ii ------------------------------- v--    ii 
  L1M4_orf2#LINE/    661 TTTTGTGC-------------------------------TT--CAAAGGA 677

  chrX_111604916_   5086 CAAAAAAAAACTATCATCAGAGTGAACAGACAACCTACAATATTGGAGAA 5135
                           --------      vv i      v        i   iv  v      
  L1M4_orf2#LINE/    678 CA--------CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_111604916_   5136 AATTTTTACAATCTATCCACCTGACAAACATCTAATATCCAGAATCTACA 5185
                            v   i   vii  vi i    i  iviv  vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_111604916_   5186 AGGAACTTAAACAAATTTACAAGAAAAAAACAA----CCCCATGAAAAAG 5231
                          i     ivv    v iv i  v     i    ----   v  v?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_111604916_   5232 TGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGTGGC 5281
                                    iv    i     i     v        i  vi vi    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_111604916_   5282 CAACAA--ACATGAAAAAAAGGTCAATATCACTGATCAT 5318
                            i  --         i v v    i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (134 / 97)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.90 (98 / 20)  


 473 25.00 0.86 0.00  chrX_111616235_111618646.rev      711   826 (1586)    L1M4_orf2#LINE/L1        1   117 (791)  

  chrX_111616235_    711 TGGAAAGATGTTCCATGTTCATGCAGTGGAAGAAATAATATCATTACAAT 760
                                  i i           v v       vv      ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111616235_    761 CATTGTACTGCCCAGAACAATCTAGAGATTCAATGCAACACCTATCAAAA 810
                         viivi    v    i vii     v        i    iv          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111616235_    811 CACCAAC-GTCATTTTT 826
                         iv   i - i v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT 117

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.01 (1 / 117), avg. gap size = 1.00 (1 / 1)  

2746 28.45 0.38 0.50  chrX_111616235_111618646.rev     1124  1921 (491)    L1M4_orf2#LINE/L1      112   908 (0)  

  chrX_111616235_   1124 TTTCTTG--GAAATAGATAAAACAATCATAAAATTTGTATGGAACCACAG 1171
                            i   --     v  i  ivii   v       ii       vii  i
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_111616235_   1172 AAGAGCTCAAATAGCCAAAGCCATCCTGAGCAAAAATAACAAAGCTGGAG 1221
                         ii  v ivi          i v   i   iv  i  v       i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_111616235_   1222 ACATTACACCACATGACTTCAAAATATATTACAAGGTTATGTTAGCCAAG 1271
                         ivv i    iv vii i       iv  i     i i  iiv  ii    
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_111616235_   1272 ACATCATGGTTTTGGCATAAAAACAGACACGTAGACCAAGAGAATGAAAT 1321
                            vii    vi        ii i     ii    i   vi    ii   
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_111616235_   1322 TGAAAATCCAGAAGTAAATCTACATATTTACAGCCAGCTGATTTTCAACA 1371
                            i i       i    i i i i     ii i  ii        i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_111616235_   1372 AAGTTACCAAGAACATACAATGGGTAAAGGATACCTTCTTCATTAAATGG 1421
                          i v i      v   v       v    i   vii i    vi      
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_111616235_   1422 TGCTGCGAAAATTGGATTGTCATATGCAGAAGAATAAAGCTGTACTCCTA 1471
                              v  v  i     v?i  i     i      i   i  v  i    
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_111616235_   1472 TCTTTCAACATATACCAAAATCAATTCAAGATGGTTTAAAGACTTAAATG 1521
                         i  iv  v       v     i  i    i    v i ?    i      
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_111616235_   1522 TAAAACATGAAACTATAACACTACCAGAAGAAAACATAGGGAAAACACTT 1571
                            i vv i         v   vii               ?iv  vv   
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_111616235_   1572 CAGGATATTGATCTAGATAAAGATTTTATGTCTAAAACTTCAAA-GCACA 1620
                          iv  iv   ivi   ii  v i   iv ivv  vi  vi    -     
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_111616235_   1621 GGCAACACAAACAAAAGTAGATGAATGTGACTATATTAAACTAAAAAGCT 1670
                         i      v  iv    i     i   vv    vi  i   v v    i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_111616235_   1671 TCTGAACAGCTAAGAAAATAATCAACAGAGTAAACAAAGAACCTGTTGAA 1720
                          i  vi vv v   i v iv     v i   i  v i v    iiiv   
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_111616235_   1721 TGAAAGAAAATATTGGCAAAATATTCATTTGTCAGGGGAGTAATATCCAA 1770
                           ii          v     vi  vi  i  vi i    v vi      i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_111616235_   1771 AATATACAGGCAACTTAAACAATTAAACAGTAAAGAAACAATTAATAATT 1820
                               i iiv    ivv    i v  i i    i i    ---    ii
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA---ATAACC 808

  chrX_111616235_   1821 TCATTTAAAAGTGGGTAAAGAACATGAATAGACATTTCTCAAAAGAAGAC 1870
                         iv   ?    i    i    i iv                v        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_111616235_   1871 ATACAAGTGGTCAACAGGCATATGAATAAAATGCTCTACATCACTTATCA 1920
                               i   i   i i   i     -  i      v      ???????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAA-AAGATGCTCAACATCAZZZZZZZ 907

  chrX_111616235_   1921 T 1921
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.82 (144 / 79)
Gap_init rate = 0.01 (4 / 797), avg. gap size = 1.75 (7 / 4)  


3159 27.13 1.00 0.44  chrX_111638997_111645402     5011  5913 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111638997_   5011 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATAATGTGAAAAT 5060
                              ii i  i     i      i v      v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111638997_   5061 GGCCATACTGCCCAAGGTAATTTATAGATTCGATGCCATCCCCATCAAGC 5110
                            v     v     iv i  i  i      i i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111638997_   5111 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5158
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_111638997_   5159 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5208
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_111638997_   5209 AATAAAGTTGGAGGCATCAGGCTACCTGACTTCAAACTGTACTACAAGGC 5258
                           i           vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_111638997_   5259 TACAGTAACCAAAACAGCATGGTAGGGGTACCAAAACAGAGATATAGATC 5308
                                 i   i    ii     vv  i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_111638997_   5309 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5356
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_111638997_   5357 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGAATTCC 5406
                          vi    i  i     ivv  vv  i v  vvv              vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_111638997_   5407 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5456
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_111638997_   5457 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 5506
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_111638997_   5507 TTAAAGACTTAAAGGTA-GACCTAAAACCATAAAAACCCTAGAAGAAAAC 5555
                          i ?    i    v   -  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_111638997_   5556 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5605
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_111638997_   5606 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5655
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_111638997_   5656 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5705
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_111638997_   5706 AGGCAACCTACAAAATGGGAGAAAATTTTCTCAACCTACTCATCTGACAA 5755
                           i     i   i             v  iv   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_111638997_   5756 AGGGCTAATATCCAGAATCTATAATGAACTCAATCAAATTTACAAGAAAA 5805
                         i  i  vi          v     v      vvv   v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_111638997_   5806 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5851
                          i    ----   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_111638997_   5852 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5901
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_111638997_   5902 ATCACTGACCAT 5913
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3204 27.77 0.55 0.11  chrX_111645703_111648605     1507  2410 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111645703_   1507 TGGAAACACATTTCATGCTCATGGACAGGTAGAATCAATATTGTGAAAAT 1556
                               v i  ii    i       iv  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111645703_   1557 GACCATACTGCCAAAAGTGCTCTACAAATTCAATGCAGTTGCCATCAAAA 1606
                          i v     v  v   v  v      i      i   i iv i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111645703_   1607 TACCAGCATCATTCTTTGCAGAGCTAGAAAAAGCAATTTTATAATTCATA 1656
                          v     vv v  i        iv v  v  ivii  ii  v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_111645703_   1657 TGGAACCAAAAAAGAGCCCACTTAGCTGAAACAAGACTAAGCACAAAGAA 1706
                              viiv  ii  v  vivv    ii      vvi i iv vi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_111645703_   1707 CAAATCTGGAGGCATCACACTACCAGATTTCAAAGTATACTGTAAGGCCA 1756
                             vi      vv       v  vi        iiv    ii  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_111645703_   1757 TAGTCACCAAAACAGCATGGAACTGGTATAAAAATAGGCACATAGATCCA 1806
                         i   v i   i    ii   v     i    ii    i  i       v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_111645703_   1807 CGGAACAGAATAAAGAACCCAGAAATAAACCCAAATACTTACAGCCAAAT 1856
                         i    i     vi   ii               v i i   ii i   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_111645703_   1857 GATATTCGACAAAGCAAACCAAAA-TATAAAGTAGGGAAAGGACACCCTT 1905
                            v        i -ivi    i -i  vv i i       i i vi   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_111645703_   1906 TTCAACAAATGATGCTGGGATAATTGGCTAGCCATATGTAGGAGAAGGAA 1955
                                    i        i  i   v  ?   i   i ii    v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_111645703_   1956 ACTGGATCCTCATCTCTCACGTTACACAAAAATCAACTCAAGATGGATTA 2005
                         ii    i  ii i   v   vv  i        i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_111645703_   2006 AGGACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGAAAACATT 2055
                         ?i   i     v     v  i           v ii             v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_111645703_   2056 GGAAAAACCCTTCTAGACATTGGCTTAGGTGAAGATTTCATGACCAAGAA 2105
                           ?iv  vi    vv   v    v     ii v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_111645703_   2106 CCCAAAAGTAAATTCAATAAAAACAAAGCTAAATAGCTGGGACTTAATTA 2155
                         v       i v vv   i    iv   iv  i   iv v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_111645703_   2156 AACTGAAGAGCTTTTGCATAGCAAAAGGAACAGTCAGCAGAATAAACAGA 2205
                           v v  i i      iiivv    i iv  vi   iv i i i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_111645703_   2206 CAACCCATAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGG 2255
                                i   i           v  ii   vii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_111645703_   2256 ACTAATATCCAAAATCTACAATGAGCTCAAGCAAATCGTTAAGAAAAAAA 2305
                            vi      i   v  i  v  i   vvi   v  iv   v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_111645703_   2306 CAA----TCCCGTCAAAAAGTGGGCTGAGGACATGAATAGACAATTCTCA 2351
                            ----i  vi i?    i     vi    iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_111645703_   2352 AAAGAAGTTATACGAATGGCCAACAAACATATGAAAAAGTGCTCAGCATC 2401
                                v     i         i  i  i       ii      i    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_111645703_   2402 ACTAATGAT 2410
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.47 (147 / 100)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 2.00 (6 / 3)  


4189 16.09 2.03 2.98  chrX_111704874_111708418     1804  2642 (903)    L1M4_orf2#LINE/L1        1   831 (77)  

  chrX_111704874_   1804 TAGAAAGTCATCTCAGGTTCATGGATTGGAAAACTTCATATTATTAAGGT 1853
                          i     vi   i  v               i    v     i     i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111704874_   1854 AGCAATACTCCCCAAACTAATCTACAGATTCAATACAATTCCTATCAAAA 1903
                         i               i i              ii    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111704874_   1904 TATCAGCTTGATTTTGTGTAGAAATTGACAAGCTAAATCTAAAATTCCGA 1953
                          vi     vvv    v  i               i vi         vv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_111704874_   1954 TGGAAATGCAAAGGAATCAGAATAGCCAAAGCAGTATTAAAAGAGAAG-- 2001
                                    i   vi             i  i v  i   i     --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_111704874_   2002 --------GAAAACTCATACTTCC-GATTTCAGAACTTGCTACAAATCTA 2042
                         --------  ii     i      -i      i     i       v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_111704874_   2043 TGATAATCAATACAGTGTGGTACTGGCATAGGAATACACATATATATCAA 2092
                         iii       v                   i i   v       v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_111704874_   2093 TGGAATAGAACGAAGAATCCAGATATAAACCCTTACATTTATGGACAATT 2142
                                   ivi   i      v        v           v     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_111704874_   2143 GACTTTTCAACAAGGATACCAAGACCATTCAATGAGGGGAAATAATAGAC 2192
                           -     i      i i                --      v     v 
  L1M4_orf2#LINE/    351 GA-TTTTCGACAAGGGTGCCAAGACCATTCAATG--GGGAAAGAATAGTC 397

  chrX_111704874_   2193 TTTTCAAGAAATGGTGCTACAACAACTGGATATTCACATCCAAAAGAATG 2242
                                v          ivi           ?i     v          
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_111704874_   2243 AATATGGACCTATATCTCATACCACTTTCAAAA-TTAACTCAAAACAGAA 2291
                           vv      iv  i    i    iv v     -           ii  v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_111704874_   2292 CAAAGGCCTAACTATAAGAGCTAAAATTATAAAACTCTTAGAGGAAAACC 2341
                           ?  i     v i            i               i      v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_111704874_   2342 TAGGGGTAAATCTTTTTGATGTTGGATTTATCAATGTATTCTTAAATATG 2391
                             ?         iv   iv    i  viv     vv      i     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_111704874_   2392 ACACCTAAAACAGAAGCAAAAAAAAAAAAAAGAAAAAGGAAAATAGATAA 2441
                              v   i  v      v    i      ------------       
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAA------------TAGATAA 635

  chrX_111704874_   2442 ATTAGATTTGATCAAAATTA----TTTTTGTACTTCAAAGAATGTCATCA 2487
                            i  i  v          ----i      i        i iiii    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_111704874_   2488 AGAAAGTGAAAAGACAACCTACAGAATGGGAGAAAATATTTAAAAATCAT 2537
                                            i                     iv       
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_111704874_   2538 ATATCCAAAAAGGGTCTTGTATCCAGAACACATAAAACAATCTTACAGCT 2587
                              ii v     v             i i     iv v       i  
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_111704874_   2588 CAACAACAACGAGGACAACAACAGCAAATAACCCAATT-AAAAATAAGCA 2636
                            i  i  ----------  vii              -      ii   
  L1M4_orf2#LINE/    786 CAATAATAA----------AAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_111704874_   2637 AAGGAT 2642
                               
  L1M4_orf2#LINE/    826 AAGGAT 831

Transitions / transversions = 1.64 (82 / 50)
Gap_init rate = 0.01 (9 / 831), avg. gap size = 4.67 (42 / 9)  

 376 19.44 7.41 0.00  chrX_111704874_111708418     2945  3052 (493)    L1M4_orf2#LINE/L1      793   908 (0)  

  chrX_111704874_   2945 AAAAAGAAAAAAAA--------AAAACCAAGCAAATGATTTCAATGCACA 2986
                                v   v  --------    viii     v     v   iv   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_111704874_   2987 TTTCTCCAAAGGAGATGTAAAAACAGCCAATAAGTACACAAAAAGATGTT 3036
                                    i    i  v   ii         i   ii        i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_111704874_   3037 CGAAATCATCAGTCAT 3052
                          i v    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.01 (1 / 116), avg. gap size = 8.00 (8 / 1)  


2432 26.52 1.83 0.14  chrX_111722873_111724570      497  1205 (493)    L1M4_orf2#LINE/L1      188   908 (0)  

  chrX_111722873_    497 TGAAGCAAAAAGAACAAATCTGGAAGCATCATACTACCTGATTTCAAACT 546
                             i-  i         vi    i vv   i   v  ii        vi
  L1M4_orf2#LINE/    188 TGAAA-AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_111722873_    547 ATACTATAAGGCCATAGTCACCAAAACAGCGTGGCACTGGTATAAAAATA 596
                         v     i  i  i i   v i   i    i    i     i    ii   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_111722873_    597 GGCGCATAGACCAATGGAACAGAATAGAGAACCCAGAAA--AACCCAAA- 643
                          i ii     i        i     v    ii       --      v -
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_111722873_    644 ---TACAGCCAACTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGG 690
                         ---  ii i   i    i   i    i vviv   i v   vv i     
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_111722873_    691 AAAGGACATCCTTTTCAACAACTAGTGCTGGGATAATTGGCTAGCCACAT 740
                             i i vi           v i         i  i   v  ?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_111722873_    741 GTAGGAGAATGAAACTGGATCCTTATCTCTCACCTTATACAAAAATCAAC 790
                          i ii        ii    i  i  i   v    v           i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_111722873_    791 TGAGGATGGAATAAGGACTTAAACCCAAGACATGAAACCATAAAGATTCT 840
                          v ii     vi ?i   i    ivi    vv i    i     iv ii 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_111722873_    841 AGAAGATAACATTGAAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATT 890
                               v     v i?iv  vi    vv   v    v        v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_111722873_    891 TCATGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGC 940
                           v iivi v  vv         v v    i    iv   i   i   iv
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_111722873_    941 GGGGACCTAATTGAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAG 990
                         vv    i v  ii  v v  i i      ii vv    i iv  vi   i
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_111722873_    991 CAGAGTAAGCAGACAACCCACAGA--GAGAGAAAATCTTCACAATCTATA 1038
                         v i   i iv              -- i        v  ii   vii   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_111722873_   1039 CATCTGACAAAGTACTAATATCCAGAATCTACAACGAACTCAAACAAATC 1088
                         i      i  i v   vi          v  i  v      vv    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_111722873_   1089 AGTAAGAAAAAAA-AAAT--CCCA-TCAGAAAGTAGGCTAAAGACATGAA 1134
                          i   v     i -    --    - i?i   i i   v  i  iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_111722873_   1135 TAGACAATTATT-AAAAAAGATATACAAATGGCCAACAGATATATGAAAA 1183
                               v  v i-   i                   i iii i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_111722873_   1184 AATGCTCAACATCACTAATGAT 1205
                         i             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (115 / 69)
Gap_init rate = 0.01 (8 / 721), avg. gap size = 1.75 (14 / 8)  


3680 19.08 5.86 1.49  chrX_111743984_111748013.rev     2670  3539 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111743984_   2670 TGGAAAGATATCCTGTGTTCATGGATTAGAAGACTTAATATTGTTAAGAT 2719
                                      ii            i                      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111743984_   2720 ATCCATAATACTCAATGCAATCTACAGATTCAATACAATCCCTATCAAAA 2769
                         iv v   v v i   vvii              ii               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111743984_   2770 TCCCAATGGGATATTTTGCAGAAATAGAAAAATCCATCCTAAAATTTACA 2819
                              iiv vv v            v  v  iiiv           i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_111743984_   2820 TTGAATCTCAAG---CCTA-AAGAGCCAAAACAATTTTGAAAAAGAAGAA 2865
                          v   viv    ---  i -  v            i              
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_111743984_   2866 CAAA-TTGAAAGATTCACAATTCCTGATTTCAAAACATATTACAAAAATA 2914
                             -   i i  i     v    ii          v  i      iv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_111743984_   2915 CAGTAATCAAAACAGTATGGTACTGGCATAAAGACAGACATATAGACCAA 2964
                                   i     i              i  i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_111743984_   2965 TGGAATGGAATAGACAGCCCAGAAATAAATTCTCATGTATATGATGAAAT 3014
                               i    v  v  i           ii vi ii v    i v  v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_111743984_   3015 AATCCTC---AAGGTTGCAAAGACATCCCCCTCAAGTGGGGGAAGAAACA 3061
                         i  ii  ---    v   v     ---- vi    -     i     -i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGAC----CATTCAA-TGGGGAAAGAA-TA 394

  chrX_111743984_   3062 GTCTCTCCAAAAAATGGTGCTAGGAAAACTGGGTATTCACATGTGAAAGA 3111
                             i i   v          i   v      i  ?i      ii     
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_111743984_   3112 GTAGAGTGGGAACACTGTCTTATACAATACAGCATACAAAAATTGACTCA 3161
                         i ii   v   v v  ii  i i  v   -----          i     
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATA-----TACAAAAATTAACTCA 489

  chrX_111743984_   3162 AAGTGTATTAAATTCCTAAACATAAAACCCAATACTATAAAACTCCTAGA 3211
                           i  v  i ? vv      ii   i v i  v            i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_111743984_   3212 ATA---CAT-----TA---------GACCT-GAG---AATAAT--TTTTT 3238
                          v ---   -----  ---------     - i ---iii   --   i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_111743984_   3239 TGGATATGACAACAAAAGCACAGGTGACAAAAACAAAAATAGACAAATGG 3288
                          i         v          i ii      iv         i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_111743984_   3289 GACTGCATCAAACTGATGAACATTTTT-CATCAAAGG----T-------- 3325
                             v       v v vi   v   v - v       ---- --------
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_111743984_   3326 --TGAAAGGGCAATCTATGGAATGGAAGAATATATTTGCAAATCACATAC 3373
                         --     i i   i i ii      i    v              i   i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_111743984_   3374 CTGATAAAGGGTACT---ATCCAAAGTATA--AAGAACTTCTACAATTCA 3418
                                i  --   ---     i i    --       ii     i   
  L1M4_orf2#LINE/    740 CTGATAAGGG--ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_111743984_   3419 ACAACAAAAAGCCAAATCACCAGATTAAAAGATGGGCAAAAGACTTAAAT 3468
                          i  i      v     v   vi   ?   i         i  i  i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_111743984_   3469 AGACATTTCTCCAAAGATAATATACAACTGGCCAAAAAGCATATGAAAAG 3518
                                          vi        v       v     i        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_111743984_   3519 ATGCTTGACATCACTAATCAT 3539
                              ii      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (105 / 58)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.20 (64 / 20)  


2999 27.29 1.88 0.35  chrX_111749974_111752748.rev     1427  2276 (499)    L1M4_orf2#LINE/L1        1   863 (45)  

  chrX_111749974_   1427 TGGAAACATATTCCATATTTATGGATTGGAAGAGCTAATATTGTTAAAAT 1476
                               v    i    i  i             vi            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111749974_   1477 GTTCATACTACCTAAAGCAATCTACAGATTTTATGCAATCTCCATCAAAA 1526
                          viv     v  i   vii           iv i      i i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111749974_   1527 TACCAATGACATTCTTCATAGCAACAGAAAAAC-AATTGTAAAATTTATA 1575
                          v   iivi v  i  iii  v  iv  v  i -i  iv       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_111749974_   1576 TGGAACCACAAAATACCCAGAATAGCCAAAGATATTCTGAGCAAAATAAA 1625
                              vii   iiv                ivv  ii   iv  i vi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_111749974_   1626 CAAAACTGGAGGAATTACTTTATCTGACTTCAAATTATGCTATAGAGCTA 1675
                             ii       v i  vi vi ii i      viv i   i i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_111749974_   1676 TAGCAACCAAAACAGCATGATATTGATATGAAAACAGACACATAGACCAA 1725
                         i  i  i   i    ii  i  i  ii  i ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_111749974_   1726 TGGAACAGAATAGAGAACCCAGACACAAATCCCTGTATCTATGGTCAACT 1775
                              i     v    ii     v i   i  v ii  i         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_111749974_   1776 CATTTTTTGCAAAGGTGCCAAGAACATACATTGGGAAAAGGACA-----T 1820
                         v     ivi   i          v   v  v    i    i i ----- 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_111749974_   1821 TCAATAAATGGTGCTGGGAAAACTAGATATTCATATGCAGAAGAATGAAA 1870
                             i              v    i    ?i  i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_111749974_   1871 CTTGACTCCTCTCTCTTGCCATACACAAAAATCAAATCAAAATTGAATAA 1920
                         i v   i   vi   vii     i        i  v       v  vi ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_111749974_   1921 AGACTTAAATCTAAGTCCCAAAA---TGAAGCTGCTACAAGAAAACTTAG 1967
                             i     v    vv i    --- i  i  vi  v        v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_111749974_   1968 GAGAAACTCTCCAGAACATTGGTCGGGGCAAAAATTTCTTGAGTAATACC 2017
                          ? v  v   i ivi  v    vivi     vii      iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_111749974_   2018 CCACAAGCACAGGTGATCAAATAAAAAATGAACAAAT-GGA----ATCAC 2062
                            v       i ii iv   v       ii i    -   ----    -
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA- 649

  chrX_111749974_   2063 AAGTTAAAAAGTGTCTGCACAACAAAGGATACAATCAACAAAGAGAAGAG 2112
                           i       v - i  ii vv       i  v     v    v   i  
  L1M4_orf2#LINE/    650 AAATTAAAAACT-TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_111749974_   2113 ACAATCCACAGAATGAGAGAGAATTTTTCCAAACTACCCATCTAACAAAA 2162
                             i          i    i   v   v    ii ivi    i i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_111749974_   2163 GATTAACAAC--AAATGTAGAAAAGAGCTCAAACAAGTCTATAGAAGAAC 2210
                           i vii v --i   i  v   -  i   vv    v  v   iv i  v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAA-GAACTCTTACAACTCAATAATAAAAA 797

  chrX_111749974_   2211 ATCTAATAATCTGATTTAAAAATGGGCAAAAGATTTGAACAGCCATTTCT 2260
                         iv v     i ii   ?             i        i  v       
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_111749974_   2261 CAAAAGAAGTCATACA 2276
                          v       vi     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACA 863

Transitions / transversions = 1.78 (146 / 82)
Gap_init rate = 0.01 (9 / 863), avg. gap size = 2.11 (19 / 9)  


4214 17.35 2.65 2.32  chrX_111756482_111759794.rev     1927  2831 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111756482_   1927 TGAATAGATACTCCATGCTCATGAGTCAAAAGACTTAATATTTTCAAGAT 1976
                           i v     ii     i     ii iii             v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111756482_   1977 GGCAATATGCCCTAAATTGATCTACAGCTTCAATGTAATCCCTATCAAAA 2026
                                iv   i              v     i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111756482_   2027 TCCTCACTGCCTTTTTTACAAAAATTGAGGCGCTGATTTTAAAATTCATG 2076
                            ivi           i  i       viv      ii          i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_111756482_   2077 TGGAAAT-CACAGGGATTTCAAATAGCCAAA-TAATCCTGAAAAAGAA-- 2122
                                -  -     iiivi          -i    i          --
  L1M4_orf2#LINE/    151 TGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_111756482_   2123 -CA--GCTAGAGGAGTAACACTTCCTGATTTCAAAAATTATTACAAAGCC 2169
                         -  -- i i     v v        ii         v   i        i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_111756482_   2170 ACAGTAGCCAATTCTGCGTGGCATTTCCATAAGGAAAGACATGTAGATCA 2219
                               ii   vv v i    i i vv        v      i       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_111756482_   2220 ATGGAATGGAATTGAAAGTTCAGAAAGAAACCAATGTAACTATGGTCAAT 2269
                                i       i   i      v     v  ii vi          
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_111756482_   2270 TGATTTTCAGCAAGGGTACAAAAGCTATCCAATGGGGGAAGACTAGTCTT 2319
                                 ii       i v  ii i  i        i    v       
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_111756482_   2320 TACAACATATGGTACTGGCACAGCTAGATATCTACATGTAAAAGAAAGAA 2369
                          v     v     i    v   i  i    ? i     i       v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_111756482_   2370 TTTGGACCCCTACCTCACCTCACCTCATACATATAGAAAAATTAACTCAA 2419
                         v                 ---   ------     v              
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCAC---ACC------ATATACAAAAATTAACTCAA 490

  chrX_111756482_   2420 AATGAGTCAAAGACCTGAATGTAAGTGT--AAACTATAACTCTAATCCTT 2467
                             ii   ?      i        v i--         ----  ii   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA----AACTCTT 536

  chrX_111756482_   2468 AGAAGAAAATTTAGGTTTAAATATTTGTGACCTTGCATAAGGCAATGTTT 2517
                                  iv    ?v     v  i         vi v        v  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_111756482_   2518 TCTTAGATAAGAAACCAAAAACACAATGGCAA-AAAAAAAAAAATGG-TG 2565
                                  v  v       i     --    -    i       i - i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATA 634

  chrX_111756482_   2566 AATAGGACTTCATCAAAATTTTTAAAATTTT---GCTTCAAATGACA--A 2610
                            v                v--    i   ---        v    -- 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTA--AAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_111756482_   2611 TCAGGAAACTGAAAAGACAATGCACAGAGTGGGAGAAAAATATTTGTAAA 2660
                            i    v           iv      i          -      i   
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAA 731

  chrX_111756482_   2661 TAATAACATTTT-TAAGGGTGCAGTATCCAGAATATATGAGGAACTCTTG 2709
                          v   -i  i v-      vviv               i i        i
  L1M4_orf2#LINE/    732 TCATA-TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_111756482_   2710 CAACCCAATAGCAAAAAGACAAATGGCTTAATTTAAAAATTGGCAAAAAA 2759
                             i     ii            ii ii    ?      v      ii 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_111756482_   2760 CTTAAA---ACATTTCTCCATAAAAGATA---AGACTGGCCAATACATGC 2803
                         i  i  ---           v i      --- i -         viii 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCAC 879

  chrX_111756482_   2804 ATTAAAAGATG-TGAAAATTATTTAGCTA 2831
                           v        - v  v  i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (100 / 53)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.05 (45 / 22)  


3250 26.43 0.55 0.55  chrX_111767483_111773761     4879  5786 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111767483_   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111767483_   4929 GGCCATACTGCCCAAGATAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111767483_   4979 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5025
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_111767483_   5026 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 5075
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_111767483_   5076 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5125
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_111767483_   5126 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5175
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_111767483_   5176 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCAGCGTATCTACAAC 5223
                                 i    i--    i  --        vv viiii  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_111767483_   5224 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGAGAAAGGATTC 5273
                         i vi    i  i     ivv  vv  i v  vv      i     i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_111767483_   5274 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5323
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_111767483_   5324 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5373
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_111767483_   5374 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCCAGAAGAAAA 5423
                           i ?    i       v   v       i      vi ii         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_111767483_   5424 CCTAGGCATTACCAATCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5473
                          v    ?i v vivv  iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_111767483_   5474 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5523
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_111767483_   5524 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5573
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_111767483_   5574 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5623
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_111767483_   5624 AAGAGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5673
                          i ii  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_111767483_   5674 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5723
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_111767483_   5724 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5773
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_111767483_   5774 CATCACTGGCCAT 5786
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3216 26.95 0.44 0.55  chrX_111964007_111965885.rev      480  1388 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_111964007_    480 TGGAAGAACATTCCATGCTCAAGGATAGGAAGAATCAATATCATGAAAAT 529
                              ii i  i     i   v    v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_111964007_    530 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGACATCCCCATCAAGC 579
                            v     v     iv i  i  i        i vv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_111964007_    580 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 627
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_111964007_    628 TATGGAACCAAAAAAGAGCCTGCATTGCCAAAACAATCTTAAGCAAAAAG 677
                                viiv  ii  v  v v  v              i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_111964007_    678 AACATAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 727
                             v  i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_111964007_    728 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 777
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_111964007_    778 AATGGAACAGAACAGAGGCCTCAGAAGTAACATCACACATCTACAACCAT 827
                                i    iv   ivii     i   vvi  i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_111964007_    828 CTGATCTTTTACAAACCTGACAAAAACAAGAAATGGGGAAACGATTCCCT 877
                         i    i  iv    ivv  v   i v  vvv          vi  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_111964007_    878 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 927
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_111964007_    928 AACTGGATCCCTTCCTTACACCTTATACAAAAATTCATTCAAGATGGATT 977
                          ii    i    v   i     v            v i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_111964007_    978 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1027
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_111964007_   1028 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 1076
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_111964007_   1077 ACACCAAAAGCAATGGCAACAAAAGCCAAAGTTGACAAATGGGATGTAAT 1126
                                     vvi          vv   i v  i    v   iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_111964007_   1127 TAAA-TTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAGC 1175
                         i   -     i -   i  ii vv    i  v    i  vv i     iv
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_111964007_   1176 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 1225
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_111964007_   1226 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAGGAAAA 1275
                         i  i  vi          v  i        ivv    v iv i iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_111964007_   1276 AAATCAAACAACCCCATCAAAAAGTGGGCAAAAAATATGAACAGACACTT 1325
                          i -    i     v  i?    i        ii  v    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_111964007_   1326 TTCAAAAGAAGACATTTATGCAGCCAACAGACAAATGAAAAAATGCTCAT 1375
                         i  v        i  vi viii     i ii  v       i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_111964007_   1376 CATCACTGGTCAT 1388
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


3117 25.29 2.22 0.59  chrX_112077569_112079871.rev      951  1804 (499)    L1M4_orf2#LINE/L1        1   868 (40)  

  chrX_112077569_    951 TAGAAAGATAGTACATGTTCATGGATTGGAAGAATGAATATTGTTATCAA 1000
                          i        viv                    v v          -- i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA--AG 48

  chrX_112077569_   1001 AT--CCACACTATTTAAAGCAATCTACAGATTCAATACAACCCCTGACAA 1048
                           -- v i   viii   vii              ii   i    iv   
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_112077569_   1049 AATACCAATGACATTCCTTGTAGAAATAGAAAAA-TAATCATAAAATTTA 1097
                            v   iivi v  ii   i      v  v  i- i   v       i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_112077569_   1098 TATGGAA----------TCCGGAATAGTCAAAGCTATCCTGAACAAAATG 1137
                                ----------i  i      i    i v   i    v  i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_112077569_   1138 GATCAAACTGGAGAAATCACATTTCCTGACTTCAAATTATATTACAGAGC 1187
                         i iv  ii     i v     i    ii i      viv  i    i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_112077569_   1188 TATAGTAATCAAAACAGCATGGTGCTGTCATAAAAACAGACACA--GACC 1235
                           i         i    ii    i   v     ii i     i --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_112077569_   1236 AATGGAACAGAATAGAAAACCCACAAACAAATCCATGCACCAATG-TGAA 1284
                                i     v  i ii   v   i   i    i  iiv   - v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_112077569_   1285 CTCATTTTTGA-AAGATATGCCAAGAACATACACTGGGAAATAGAGAATC 1333
                         i v     i  -   i-i        v   v  v    i  vii v i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_112077569_   1334 TCTTCAATAAACAGTGTTATAAAAACTGGATATCCATATGCAGAAGAATG 1383
                          i     i   ii   i ivi v         ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_112077569_   1384 AATCTTCACCCCTTTCTCCTGCCATATACAAAAATCAAATCAAAATGGAT 1433
                           vi vv      vi   vii              i  v           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_112077569_   1434 AGAAGACTTAAATCTAAGACCTCAAATCATGAAACTACTACAAGAAAACA 1483
                         vi?    i     v     v  v   ii  i     vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_112077569_   1484 TTAGGGAAAATCTCCAGGACATTGGTCTAGGAAAACATTTCTTGCACAAT 1533
                          vi ? v      i iv   v    vi    v  vvi      iv i - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-T 596

  chrX_112077569_   1534 AAC-CCACAAGTACAGAAAACCAAAGACAAAAAGGACAAATGGGACCACA 1582
                         i  -   v   i   iiv   v     v    vi  i    v    iv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_112077569_   1583 TTAAG-TTAAAAAGCTTCTGCACAGCAAAGGTTACAATCAGCAAAGTGAA 1631
                          i  i-       -   i  ii vv      vi  v    iv        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_112077569_   1632 GTGACAACCTACAGAATGGGAGAAAATATTTGCAAACTACCCATCTGACA 1681
                         iv       i                          ii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_112077569_   1682 AGCGGTTCATAACCAGAATATATAAGGAGCTCAGACAACTCTACACGAAA 1731
                           v ii ii  v             i  i   vv       v i vv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_112077569_   1732 AAGCCTAACAATCCGATAAAGAAATGGGCAGAAGTTTTGAATAGACATTG 1781
                            v v  i  i  i  v? i         i i v              v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_112077569_   1782 CTCAAAAGAAAACATACAAATGG 1804
                            v      i i          
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGG 868

Transitions / transversions = 1.59 (130 / 82)
Gap_init rate = 0.01 (12 / 868), avg. gap size = 2.00 (24 / 12)  


3235 27.68 1.45 0.11  chrX_112113981_112119026.rev     3660  4555 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112113981_   3660 TGAAAATATATTTCATGTTCCTAAATTGGAAGAATCAACATTGTTAAAAT 3709
                           i   v    ii       v ii         v i  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112113981_   3710 GTCCATATTACCCAAAGCAATCTACACATTTAATGTAATCTCTATCAAAA 3759
                          v v   i v      vii       v   i  i i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112113981_   3760 TACCATTGATATTCTTCACAGAAATAAAAAAA--AATCCTAAAATTTATG 3807
                          v   viviiv  i  ii       vi v  i--i           i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_112113981_   3808 TGGCATCACAAAAGATTCAGAATAGCCAAAGCTATCATAAGAAAAATGAA 3857
                            v vii   ii  ii             i v   v i i   i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_112113981_   3858 CAAAACTGAAGGAACCATATTAACTGACTTCAAATTATACTACAGAGTTA 3907
                             ii  i    vi  i i vv ii i      viv       i  i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_112113981_   3908 TTGTAACTAAAACAGCATGGTACTGGCATAAAAACAGATGCATAGACCAA 3957
                         iv    ii  i    ii              ii i   iii     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_112113981_   3958 TGGGACAGAATAGAGAACCCAAGAACAAATCCACACACCTACAGTGAACT 4007
                            i i     v    ii   ii  i   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_112113981_   4008 CATTTTTGGCAGAGGTGCCAAGAATCTACAGAGGGGAAAAGAGAGTCTCT 4057
                         v     i i  ii          viv v  iv       ii v     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_112113981_   4058 TCAATAAATGATGCTGGGAAAAATGGATATCCACATGCAGGCAAATTAAA 4107
                             i     i        v  v      ?         iivi   v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_112113981_   4108 CTAGACACCTATCTCTTGCCATATACAAAAATCAAATCAAGATGGATTAA 4157
                         i i   v    i   vii              i  v    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_112113981_   4158 AGACTTAAATCTAAGATCTTAAGCTACAAAACTACTATAAAAAAGTATTG 4207
                             i     v     v  v  i   i      vi  v  i   ii  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_112113981_   4208 GAAAAACTCTCCAGGGCATTGGACTGGGCAAAGACTTCTTGAGTAATACC 4257
                          ?iv  v   i iv i v    ii i     v ii     iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_112113981_   4258 CCACGAGTACAGACAACCAAAGCAAAAATGAACAAATGGGA--TCATGTT 4305
                            vi  i   ii    v    v      ii i    v   --    vvv
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_112113981_   4306 AATTTAAAACTCTTCTGCACAGAAAGA---------AAAAGTGAAGAGAA 4346
                             v      i  v   vivi  i  ---------i        i   v
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_112113981_   4347 AACCCACAGAATGGGAGAAAACATTTGCAAACAACCCATGTGACAAAGGA 4396
                                              i         iv ivi  v   i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_112113981_   4397 TTAAAAACCAGAATATATAAGAAGTTTAAACAACTCTGTAAGAAAAAAAT 4446
                         i viv v             ii ii ivv       vi   v     i i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_112113981_   4447 ATAATAATTAAATCAAAAAATAGATGAAAGATCTGAATAGACATTTTTCA 4496
                          -     iiv   i?      i iii  i   i             i  v
  L1M4_orf2#LINE/    801 A-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_112113981_   4497 AAAGAAGACATACAAGTAGCAAACAGGCATATGAAAAGGTACTGAACATC 4546
                                 i      i i  v  i i   i        i i  v      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_112113981_   4547 ATTGATCAG 4555
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.05 (164 / 80)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 3.50 (14 / 4)  


1047 19.29 16.14 0.39  chrX_112125055_112127600      868  1121 (1425)    L1M4_orf2#LINE/L1        1   294 (614)  

  chrX_112125055_    868 TGGAGAGACAACTAATGTTCATGGATCGAAAGAGTCAATATTGCTAAAAT 917
                             i   i v iv            i i    v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112125055_    918 GGCAA---------AATTGATATACAGATTAAATAAAATCGCTCTTAAAA 958
                              ---------       v        v  iiv    v  v i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112125055_    959 ATTCTAATTGCTTCTTTTGCAGAAACAAATGGGCTGATCCTAAAATTCAC 1008
                         - i i ii   i i           ivi iii                 i
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_112125055_   1009 ATAGAAATGGCAGGACCCCTGAATAGCCAAAACAATCTTGAGAAAGAA-- 1056
                           i      vv   iv   v                     i      --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_112125055_   1057 -CAAAATTGGAGGACTCACA---------------------------GCT 1078
                         -    i              ---------------------------   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_112125055_   1079 ACAGCACTAAATAC--TGTGGTATTGCTATAAGAATAGACATTTA 1121
                             i v v  v  --       i  vi     i        v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

Transitions / transversions = 1.72 (31 / 18)
Gap_init rate = 0.02 (5 / 294), avg. gap size = 8.40 (42 / 5)  

3064 17.95 1.10 0.94  chrX_112125055_112127600     1419  2053 (493)    L1M4_orf2#LINE/L1      273   908 (0)  

  chrX_112125055_   1419 CTGGC-CAAGAGTAGAGATTTAGATCATTGGAATGGAATTGAGAATTCAG 1467
                              -i   ii    v  v       v      i         i i   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_112125055_   1468 AAATAAACCCATATACCTATGGTCAATTAGTATTTGACAAGGGTGCCAAG 1517
                                      i ii           ii v  i               
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_112125055_   1518 CTCCTTCAATGGGCAAAGAATAGGCTTTTCAACAAATGATTCTGGGAAAA 1567
                         vi v         v         v              i v      v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_112125055_   1568 CTGCATATTCACATGCTAAAGAATAATGTTGGATCATTACCTCACAACAT 1617
                            v   ?i       v       i v      i vi         v   
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_112125055_   1618 GTACAAAAATTAGCTCAAAATGGATTATAGACCTAAATAAAATGGCTAAA 1667
                         i           i            i ?          iv  vi      
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_112125055_   1668 ACTATAAAATCTTTAGAAAGAAATTATAGGTAAAAATATTTGTTACCTTG 1717
                                  iii      -    vi     ?iv    v  i  v      
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAA-GAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chrX_112125055_   1718 AATTAGGCAATGGTTTCTTAAATATGACCCCAAAAGCACAAACAACAGAA 1767
                         ii                  i       v            i     i  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_112125055_   1768 GAAAAAAAAGATATATTAGACTTAATAAAAATTACAGACATTTGTGTATC 1817
                                v     v   i     v  v       v i  v      iv  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_112125055_   1818 AAAGCAGACTATCAGGGAAATGAAAAGATAATTCACAAAATAGGAGAAAA 1867
                             v v       i i  i        i  ii    i   i        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_112125055_   1868 CATTTGCAAATCATAT--TTGAAAAGGGCCTAGCATCCAAAATATATTTT 1915
                         i               --i   v     v  v i     i       ---
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT--- 768

  chrX_112125055_   1916 AAAAG---TTTTACAACCTGATAACAAAAC-ACAAATAAATCAAATAAAA 1961
                         -    --- i       iii    i    v-        vi   v ?   
  L1M4_orf2#LINE/    769 -AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_112125055_   1962 AATGAACATAGAGGTAGAAGAGACATTTTGCTAAAAAAAGATTCATAAAT 2011
                             ii  v  iiv v   v        iv i   i  -   vi i    
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-GATATACAAAT 866

  chrX_112125055_   2012 GGCCAAAAAGCACATGAAAAGATACTCAATATCACTAGTCAT 2053
                               v                i     i    ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (66 / 44)
Gap_init rate = 0.01 (7 / 636), avg. gap size = 1.86 (13 / 7)  


3039 26.67 1.67 0.33  chrX_112138145_112143171     3639  4534 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112138145_   3639 TGGAAACACATTCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3688
                               v i  i     i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112138145_   3689 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATCTCCATCAAAA 3738
                          i v     v  v   vii       i      i      i i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112138145_   3739 TACCACCATCATTCTTCACAGAATTAGAAAAAA-AATTCTAAAATTCATA 3787
                          v   v vv v  i  ii     v v  v  iv-i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_112138145_   3788 TGAAACTAAAAAAGAGTCCACATAGCCAAAGTAAGACTAAGCAAAAAGAA 3837
                           i  v iv  ii  vi viv         ii  vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_112138145_   3838 CAAATCTGGAGGCATCACACTATTTGATTTCAAATTATACTCTAAGGCCA 3887
                             vi      vv       viiii        viv    vi  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_112138145_   3888 TAGTCACAAAAACAGCATAGTACTGGTATAAAAATAGTCACATAGAACAA 3937
                         i   v iv  i    ii i       i    ii    v  i     v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_112138145_   3938 TGGAACAGAA-------CCCAGAAGTAAACTCAAATACTTACAGCCAACC 3980
                              i    -------i      i     i  v i i   ii i   ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_112138145_   3981 GAATTTCCACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTAT 4030
                           v    v    i vviv   i v   vv i         i i vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_112138145_   4031 TCAAAAAATGGTGCTGGGATAATTGGCTAGCCACATGTATAAGAATGAAA 4080
                             v              i  i   v  ?       i v         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_112138145_   4081 CTGGATCCTCATCTCTCACCTTATACAAAAATAAATTCAAGATGGATTAA 4130
                         i    i  ii i   v    v           v  i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_112138145_   4131 GGACTTAAACCTAAGACCTGAAACTCTAAAAATTCTAGAAGACAACATTG 4180
                         i   i    iv     v  i     v     v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_112138145_   4181 GAAAAAACCCTTATAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAA 4230
                          ?iv   i i ii -   v    v        v i    v iivi v  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_112138145_   4231 CCCAAAAGCAAATACAATAAAAACAAAGAGAAATA--TTGGGACCTAATT 4278
                         v         v vi   i    iv   i v i   --    -  i v  i
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG-ACTTCATC 648

  chrX_112138145_   4279 AAACTAAAGAGCTTTTGCACAGTGAAAGGA-ACAGTCAGCAGAGTAAAGA 4327
                            v v  i i      ii -v v      -  vi   iv i   i  i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_112138145_   4328 GACAACTCACAGACGGGGAGAAAATCTTCACAATCTGTATATCTGACAAA 4377
                               i      vv          v  ii   viii         i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_112138145_   4378 GGACTAATATCCAGAATCTACAACGAACTGAAACACATCAGTAAGAAAAA 4427
                              vi          v  i  v     vvv   vv   i   v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_112138145_   4428 AACAA----TCTCATCAAAAAGTGGGCTAAGGATATTAGTAGACAATTGT 4473
                         i    ----i iv  i?    i     v      v v i      v  v 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_112138145_   4474 CAAATGAAGGTATACAAATGGCAAACAAACATTTGAAAAAATGCTCAACA 4523
                          v  v    i            v  i  i  iv      i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_112138145_   4524 TCAGTAATGAT 4534
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.28 (132 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.25 (18 / 8)  


2838 27.72 2.81 0.90  chrX_112148093_112152977.rev     3504  4394 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112148093_   3504 TGGAGAAGCATTCCATGCTC--GAATTGAAAGAATCAATATCATTAAAAT 3551
                             i iii  i     i  -- i    i    v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112148093_   3552 GACCACACTGCCAAAAGCAATCTACAGATTCAACGTTATTCCTAGCACAC 3601
                          i v i   v  v   vii                iv  i    v  v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112148093_   3602 AACCAA-TGCCATTTTTCACAGAATGATTAAAAAAAC-ACTCTATGATTC 3649
                         vv   i-    -     ii     --   i v  ivi- ii   vi    
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chrX_112148093_   3650 ATATGGAA-TGAAAAAAAGAGCGGGAATAGCCAAAGCAATTCTAAGCAAA 3698
                                 -  v  ii--  v vi           i    ii i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_112148093_   3699 AAGAACAAAGCCAGAGGCATCACATTACCTGACTTCAAA-CTG--TACAA 3745
                                   iii    vv     i v  ii i      -  v--     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_112148093_   3746 GGCCACAGTAAACACAACAGCATGGTACTTGGTACAAAAACAGACACATA 3795
                         i  i       v  vi    ii       -  i i  ii i     i   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACT-GGCATAAGGATAGACATATA 294

  chrX_112148093_   3796 GACCAATGTAACAAAATAGAGAACCCAGAAGTAAAGCCTCACACCTACAA 3845
                           i     v  i i   v    ii      i    v  vi   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_112148093_   3846 CCATCTGATTTTTGACAAAAAT---AAG------CAATGGGGAAAGGAC- 3885
                         i  vi       i     iii ---   ------            i i-
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_112148093_   3886 -TCATAATTTAATAAATGGTACTGGGATGGCTTGCTAATTGTATGCAGAA 3934
                         -  v --  i  i       i      iii  v v  ?iiii     i  
  L1M4_orf2#LINE/    395 GTCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_112148093_   3935 GAATGAAACTGGACCCCTACCTTTCACCGTATACAAAAATCAACTCCAGA 3984
                                ii             iv    i           i     v i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_112148093_   3985 TGAATTAAAGATTTAAATATAAGAAATTAAACTCTAAGAATCCTAGAAGA 4034
                           i  i ?   ii     i     iv v     v   i v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_112148093_   4035 GAACCCAGGAAACACTATTCTGAACATTGGCCTTGGCAAAAAATTTATGA 4084
                         i   vi   ?ivv v v   vvi  v    vi v     viiv  iv ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_112148093_   4085 CTAAGTCCTCAAAAGCAATTGCAATGAAAACAAAAATTGACAAGTGAGAC 4134
                         v  v v vi        vvv    ii   iv      v  i  i vi   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_112148093_   4135 CTCATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAAT 4184
                         i    i   v v  i i   i  ii vv    i  v        v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_112148093_   4185 AAACAGACAATCTACAGAATGCAAGAGGATAGTCACAAACTCTGCCTCTG 4234
                         i  v      i i        vi   ii   v ii    iiv iiv    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_112148093_   4235 ACAAAGGTCTAATATCTAGAATCTATAAGGAAC------AATTCAATGAG 4278
                          i  i  v  vi    i     v     i    ------  i     i v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_112148093_   4279 CAAAAAACAAATAACTGCATTAAAAAGTGGGCAAACAACTGGAACAGACA 4328
                         v    i         ivv   ?    i        vi i v   i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_112148093_   4329 CTTCTCAAAAGAAGACATACAAGTGGCCATCAAACATACGAAAAAATGCT 4378
                         i     v        i      i      vi  i  i i     i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_112148093_   4379 CAGCATCACTAATCAG 4394
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (160 / 83)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


1252 27.19 8.44 3.12  chrX_112163345_112164932      456  1095 (493)    L1M4_orf2#LINE/L1      235   908 (0)  

  chrX_112163345_    456 ACCTATTATAAAACTGTAGT--TAAAAACTGTACTGATTAAACTAAGTAT 503
                           i  i  i   i  ii   -- v  i  v  i-  i ---   i- i  
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTG-TGGT---ACTG-GCAT 279

  chrX_112163345_    504 AAGAATGGATAAAC-TATCAAATGGAACAGAATTCAGTG---AAAAACAA 549
                            i  i  i v i-v     -     i      v  v --- i   i  
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAA-TGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_112163345_    550 CAACAATACTTTCCTTATATAAAGTCACCTGATTCATGACAAAA-TG--- 595
                         - v v    v  -----   i--    vi     ivi     ii-  ---
  L1M4_orf2#LINE/    329 -ACCCATACATT-----TATG--GTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_112163345_    596 AAACTGTAGTGCATTAGGGGTAAGATGCTCTTTTGAATAAATGGTGTTAG 645
                          i  ii -- -  v i   iv ii  iv      v  i        i i 
  L1M4_orf2#LINE/    371 AGACCAT--T-CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_112163345_    646 CTCAATCAGATATCCAAGTGGGAAAAACTGAATCTTGACTCTTACCTTAC 695
                         vv   iii    ?   vi  vi   i v    vi v   i i     i  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_112163345_    696 ACCATACACAAAAATCAATTCCAGATGTATTATAG--------GTGAAAT 737
                               i        i  i  v i   v  i ?  --------  i i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_112163345_    738 ATAAATCAGTGAAAGATTTTAGAGGAAACCAT-GATAAAATATCTTTTTT 786
                         v    v vi i   v- i     i    v   - i?iv  -     iv v
  L1M4_orf2#LINE/    518 CTAAAACTATAAAAC-TCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTG 565

  chrX_112163345_    787 ATCTTGAAGTAGGCAAAGATTTCTTAAA----------GAAGC-----TA 821
                          i    iiv       v i       i ----------i    -----i 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_112163345_    822 ACCAGA-AAAAAAT-GACAAATTGTACTACATTAAAATTTATAACTTTTA 869
                           v i -       -  i      v   v   i      v v       i
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_112163345_    870 T----CAAAAAAT-CCATTCAGAGAATTAAGAATTAACTCACTAAATGGG 914
                          ----    ii i- i  iv   i i v  i ivi   i   vi      
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_112163345_    915 AGA---TATTTGTGAGACAACGTAACTAACAAATGACTATTAATAAGAAT 961
                            ---      ii iv  -ii  v  i i  iv    vv  viv     
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCA-TATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_112163345_    962 ATATAAATAACTCTCACAAAT---TAATAGAGTGCTAAA------AATAG 1002
                                v      i    v ---     i iv vi   ------   v?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_112163345_   1003 AAAAATGGGCAAAAGATTTAAACAGATATTTTACAATAGAGGATATCCGA 1052
                                      i     i  i   i    iv v v   i     v i 
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_112163345_   1053 -TGACCAATAAAAATAAGAAAAGTTACTCAACTTCATTAGTCAC 1095
                         -  i       iv i v      v i      v   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (106 / 64)
Gap_init rate = 0.04 (29 / 674), avg. gap size = 2.55 (74 / 29)  


3060 27.36 1.56 0.56  chrX_112191334_112193157.rev      435  1333 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112191334_    435 TGGAAGAACATTCCACGCTCATGGGTTGGAAGAATCAATAT--------- 475
                              ii i  i   i i      i        v i     ---------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112191334_    476 --CCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 523
                         -- v     v     iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112191334_    524 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 571
                          v   iivi i  ii ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_112191334_    572 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATTCTAAGCCAAAT 621
                                 viiv  ii  v  viv  v     iv    ii i ivv i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_112191334_    622 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 671
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_112191334_    672 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 721
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_112191334_    722 CAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACATATCTACAACCA 771
                                 i    iv   ivii         vv   i i  i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_112191334_    772 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 821
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_112191334_    822 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAAGCTG 871
                          v  i  i              v      v  ?   i i i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_112191334_    872 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 921
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_112191334_    922 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 971
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_112191334_    972 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGAACTTCATGTCTAA 1020
                             ?i- v i -   iv   v v  vv i     viii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_112191334_   1021 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1070
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_112191334_   1071 TGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1120
                          v   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_112191334_   1121 AGGCAACCTACACAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 1170
                           i     i   v             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_112191334_   1171 AGCGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1220
                         i vi  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_112191334_   1221 AAACAAACAACCCCATCAAAAAGTGAGCAAAGGATATGAACAGACACCTC 1270
                          i     i     v  i?    i  i         v    i     ii  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_112191334_   1271 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAAATGCTCAT 1320
                           v        i  vi viii     v  i          i -      v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAA 895

  chrX_112191334_   1321 CATCACTGGCCAT 1333
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.71 (19 / 7)  


1585 25.00 1.56 1.12  chrX_112210285_112211998.rev       53   500 (1214)    L1M4_orf2#LINE/L1      377   826 (82)  

  chrX_112210285_     53 TTGAATGGGGAAA--ATACTCTCTATTTAATAAATGGTGCTGGGATAGCT 100
                           v          --   v   i -- i  i              i i  
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACT 424

  chrX_112210285_    101 GGCTAGCCATATGCAGAAGAATGAAACTGGATCACTGCCTTTCACCATAT 150
                           v  ?   i     i         ii    i v  i   iv        
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_112210285_    151 ACAAAAATTAACTCAATATGGGTTAAAGATTAAAATGTAAGACCTGAAAC 200
                                         v    i i ?   iiv          v  i    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_112210285_    201 TATAAGAATCCTAGAAGAAACCCTAGGAA-ACACCATTCTAGACCTCAGC 249
                              i v  i         v v    ?i- v i -   vv     ii v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

  chrX_112210285_    250 TTTGAGAAAGAATTTATGCCTAAGTCCTCAAAA--ACAATTGTGATAAAA 297
                           v iv  v iv  iv ivv  v v vi     --    -- ii i    
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GCAACAAAA 621

  chrX_112210285_    298 CCAAAAATTGACAAGTGGGATTTAATTAATA--AAGAGCTTCTCTACAGC 345
                         vv      v  i  i v   i  v  i  v --  i i   i v i vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_112210285_    346 AAAAGAAACTATCATCATGGTAAACAGACAACCTATAGAATGGGAAAAAA 395
                            i  v       vv vi  i  v        i i         i    
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_112210285_    396 TATTAGCAAACTATGCATCTGATAAAGGTATAATATCCTGAATCTATAAG 445
                             v     ii  ii         i  vv vi     v    v     i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_112210285_    446 GAACTTCAACAATTCAACAAACAAAAAACAAATAGCCCATTTAAAAAGTG 495
                              iiv    i    i  vv    i       i    v  ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_112210285_    496 GGCAA 500
                              
  L1M4_orf2#LINE/    822 GGCAA 826

Transitions / transversions = 1.20 (59 / 49)
Gap_init rate = 0.02 (7 / 450), avg. gap size = 1.71 (12 / 7)  

2291 25.76 3.05 0.69  chrX_112210285_112211998.rev      502  1223 (491)    L1M4_orf2#LINE/L1      170   908 (0)  

  chrX_112210285_    502 GAATAGCCAAAGCAATCCTAAGCAAAAAAGAACAAATTTAGGAGCATCAC 551
                                    i     i i i-   i         v  i ii vv    
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAA-AAAGAAGAACAAAGTTGGAGGACTCAC 218

  chrX_112210285_    552 ATTACCCAGCTTCAAATTATACTAAAAGGTTATAGTAACCAAAACAGCAT 601
                          i v    ii      viv     v  i i  i     i   i    ii 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chrX_112210285_    602 GACGATGGCATAAAAGTAGATACATAGATCAATGGAACAGAATCA----C 647
                          iiiv        iii    i i              i     ii----i
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_112210285_    648 CAAGAAGTAAAGCCAAA----TACAACCAATTAAGCTTTGACAAAGCATA 693
                          v    i    v   v ----  iiii     i vi  i     i -i i
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTG 367

  chrX_112210285_    694 CAGAAAC-ATAAACTGCAAAAAGGACACCCTATTCAATAAATGGTGCTAG 742
                          vi i  -  vv v  vii    i i vi  v     i          i 
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_112210285_    743 GAAAATTGGATAGCCACATGTAGAAGAATGAAACTTGATCCCTAATTTTC 792
                           v  i      ?       i i         ii v  i     vi iv 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_112210285_    793 ACCATATATAAAAATTAACTCAAGATGGATCAAAGACTTAAATCTAAGAC 842
                                 i              i        ?    i     v     v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_112210285_    843 CTGAGACCACAAAAATTCTAGAAGAAAACAAAAA---AAATCTTCCAGAC 889
                           i i  i i    v ii            v ii---        vv   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_112210285_    890 ATTGGCCTAGGCAAAGAATTTATGACTAAGATCCCAAAAGCAAATGCAAC 939
                         v    vi       v iv  iv iiv  v  iv         v v     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_112210285_    940 AAAAACAAAAATAAATACATAGGACCTAATTAAA-TTAAAAAGCTTCTGC 988
                             iv       i   v  v    i v  i   -       -   i  i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGT 666

  chrX_112210285_    989 ACAGCAAGAGATATAATCATCAGAGTCAACAGGCAACATACAGAATGGAA 1038
                         i vv   ii  i iv    vv i   v  v  i    vi         i 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_112210285_   1039 GAAAATATTTTCAAGCTATTCATCTGACAAAGGACTAATATCTAGAATCT 1088
                                   v   iii  vi      i  i     vi    i     v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_112210285_   1089 ACAAGGAACGCAAACAAATCAGCAAGAAAAAAA--AAT--CTC--T---A 1129
                          i  i    v vv    v   ii  v     i --   -- i -- --- 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_112210285_   1130 AAGTGGGCAATTCACATGAATACACATTTCTCAAATGAAGATATATAAAT 1179
                           i       vvv iv      v         v  v         i    
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_112210285_   1180 GGCCAAGAAACATATAAAAAAAACCCCTCGACATTACTAATCAG 1223
                               v  i  i  i    i --iv   i    i ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (115 / 69)
Gap_init rate = 0.02 (13 / 739), avg. gap size = 2.08 (27 / 13)  


3420 20.23 6.13 1.16  chrX_112240081_112242112      689  1553 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112240081_    689 TGGGAAGGCACTCCATGCTCATGCATTGAAGGACTTAATATTGTTAATAT 738
                            i   ii ii     i     v    i i                v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112240081_    739 GACAATACTACCCAAAGGTATTTACAGATTCAACTCAATCTCTAGGAAAA 788
                          i       v      vvv  i            v     i   vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112240081_    789 --CCAACAGCACATTTTT-CAGAAATTGAACAAAA-AATTTTAAAAGTCT 834
                         --   i v  - v     -          -   iv-i  ii     v  v
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chrX_112240081_    835 TATAGAATTGTAAGCAATGCTGTATAGCCAAAACAGTCTTAAAAA----T 880
                            i   v  i   vi iv v v            i    i    ----v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_112240081_    881 AGTAAAGTTGGAAGACTCAGGCTTTCTGATTTCAAAACT-ACTACAAAGA 929
                          ii         i      vi   i ii           -         v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_112240081_    930 TACTGTAATTAAAA--GTGTTGGACTGGCATATGGATAGCCTTATAGATG 977
                            v     i  i --    v v         v      v v       v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_112240081_    978 AATGGAAGAAAATTAATAGTATAAAAACAAGCCCATATATT-ATGGTCAA 1026
                                v i    i v   vi i   i  i      i   -        
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_112240081_   1027 TTGATTTTTGACAAGGGTA----------------GGAGAAGAATACTGG 1060
                                 i         i----------------  ii       v vv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_112240081_   1061 CTTCAACGAATGATACTGTGACAACTGTATATCCATATTAACAAGAATAA 1110
                         i      i    i i   v        v   ?   i  vv v      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_112240081_   1111 A------------CCTCAGCACAATATATTAAAAATAAGTCAAAATAAAA 1148
                          ------------     -   v     iv    v   v       ii v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_112240081_   1149 CAAAAATATAAATGTAAGAGCTAAAACTATAAAACTCATGAAAGAAAACA 1198
                           ? i iv                             v ii         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_112240081_   1199 TACCGGTAAATTTTCCTGACATTGGATTTAGCAGTGGATTCTTAGACAAG 1248
                           vv?      i   v    v    i  vi   i   v        i v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_112240081_   1249 ACATTAGAAACACAAGCAAAAAGAGGAAAAACTAGATCAATTGGGTTTCA 1298
                            ii i  i         v  i  i     -     v      ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCA 646

  chrX_112240081_   1299 TCAAAATTATAAATGTTTGTGC-----------CTATCAAGAACATGAAA 1337
                                  v   iv       -----------          vi     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_112240081_   1338 ATAAAACTTCTAGAATAGGAGAAAATATTTGTAAATCATATATATGATAC 1387
                          v v   iivi     i              i           v     v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_112240081_   1388 AG--TTTGAACATCCAGAATATATAAAACCAACCCTTAAAACTCAACAAT 1435
                         i --i   --i                i--   i    v       i   
  L1M4_orf2#LINE/    747 GGGACTTG--TATCCAGAATATATAAAG--AACTCTTACAACTCAATAAT 792

  chrX_112240081_   1436 AAAAAGACAAAAAAACACTGTTAGAAAACGGGCAAAGAACTTGAATAGGC 1485
                                    v  v - vi  ?i    i        i i        i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_112240081_   1486 ATTTGTTTGAAGAACATATACAAATGACCCACAGGCACGTGAAAAGTATA 1535
                             v iii     v           i  v i i    i       -  i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG-ATG 890

  chrX_112240081_   1536 TTAGTCATTATGAAAATG 1553
                         i viv   i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (98 / 73)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.32 (63 / 19)  


2929 28.00 0.44 1.53  chrX_112246773_112252555.rev     4375  5292 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112246773_   4375 TGGAAAAACATTCCATGCTTATAGATAGGAAGAATCAATATCGTGAAAAT 4424
                               i i  i     i i  i   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112246773_   4425 GGCCATACTCCTCAAAGCAATTTATAGATTCAATGCTATTCTCATTATAC 4474
                            v       i    vii  i  i        i  v  i ii  i v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112246773_   4475 TGTCATTGGCATTCTTCACAGAATTAGAAAAAACCACTTTAAAATTCATA 4524
                          vi  viv  v  i  ii     v v  v  iviv iii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_112246773_   4525 TGAAACCAAAAAAGAGTCCATATAGTCAAGACAATCCTAAGCAAAAAGAA 4574
                           i  viiv  ii  vi viv    i   i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_112246773_   4575 CAAAGCTGGAGGCATCACACCTTCAGAGAGAGGGAGAATTCAAACTATAC 4624
                              i      vv      i i vi v----------      viv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAAT----------TTCAAAACTTAC 240

  chrX_112246773_   4625 TACAAGGTTACAGTAACCAAAACAGCATGGTGCTGGTACAAAAACAGACA 4674
                              i i        i   i    ii    i    i i  ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_112246773_   4675 TATAGACCAATGGAACAGAACAGAGATCTCAGAAATAAGACTGCACATCT 4724
                               i        i    iv    vii         iv iii    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_112246773_   4725 ATAACCATCTGATTTTTGACAAACCTGACAAAAACAAGTAATAGGCAAAA 4774
                           iii  vi       i     ivv  v   i v  vvi   i  v   i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_112246773_   4775 GATTCCCCATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAG 4824
                         i  vvi iv  i  i              v      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_112246773_   4825 AAAATTGAAACTGGATCCCTTCATTACACCTTATACAAAAATTAACTCAA 4874
                           i v    ii    i    v v i     v                   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_112246773_   4875 GATGGATTAAAGACTTAAATATAAAACCCCAAACTGTAAACACTCT-AGA 4923
                         i      i ?    i     i   i v iv     i    -     -   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGA 539

  chrX_112246773_   4924 AGAAAATCTAGGCA-ATACCATTCAGGACATAGGCACGGGCAA-GATTTC 4971
                               iv    ?i- v i -   iv   v v  vvii     - i    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_112246773_   4972 ATGACAAAAACATCAAAAGCAATTGCAACAAAAGCAAAAATTGAGAAATG 5021
                         v iivv vi   i        vvv          v      v  v    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_112246773_   5022 GGATCTAATTAAA-TTAAAGAGCTTCTGCACAGCAAAATAAACTATCATC 5070
                            ii v  i   -     i -   i  ii vv    iv v       vv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_112246773_   5071 AGAGTTAACAGACAATCTACAAAATGGGAGAAAAATTTTGCAATCTACTC 5120
                          i   v  v      i i   i            vv       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_112246773_   5121 ATCTAATGAAGGTCTACTATCCAGAAATTACAAGGAACTTAAACAAATTT 5170
                             i  i i  v  vv         vv  i  i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_112246773_   5171 ACAGGAAAAAATTAAAATGACCCCATTAAAAAGTAGGCAAAAAACATGAA 5220
                          i iv     ivi   - i    v   ?    i i      ii iv    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_112246773_   5221 CAGACACTTTGCAAAAGAAGACATTTATGTGGCCAGCAAACATATGAAAA 5270
                         i     i  iv v        i  vi vi      ii  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_112246773_   5271 AAAGCTCAACATCACTCATCAT 5292
                         i v           ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (153 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


 371 26.25 0.00 0.00  chrX_112256235_112262548.rev     5005  5084 (1230)    L1M4_orf2#LINE/L1        1    80 (828)  

  chrX_112256235_   5005 TGGAAGAACACTCCATGCTCACGGATTGGAAAAATCAATATCGTGGAAAT 5054
                              ii i ii     i   i         i v i     i  vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112256235_   5055 GGCCATACTGCCCAAGGTAATTTATAGATT 5084
                            v     v     iv i  i  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT 80

Transitions / transversions = 3.20 (16 / 5)
Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.00 (0 / 0)  

2633 27.14 0.14 0.14  chrX_112256235_112262548.rev     5087  5823 (491)    L1M4_orf2#LINE/L1      172   908 (0)  

  chrX_112256235_   5087 ATTGCCAAGTCAATCCTAAGCAAAAAGAACAAAGCTGCAGGTGTCATGCT 5136
                           v     iv     i i iv  i          i  v   vv   ii  
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_112256235_   5137 ACCTGACTTCAAACTATACTACAAGGCTACAGTAGCCAAAACAGCATGGT 5186
                         v  ii i      viv        i         ii   i    ii    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_112256235_   5187 ACTTGTACCAAAACAGATATATAGACCAATGGAACAGAACAGAGGCCTCA 5236
                            v i iv ii i   i       i        i    iv   ivii  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_112256235_   5237 GAAATAACACCACACATCTACAACCATATGATCTTTGACAAACCTGACAA 5286
                                vv   i    i  iiii  vv    i  i     ivv  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_112256235_   5287 AAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGATGCTGGGAAA 5336
                         i v  vvv           i  vvi  v  i  i     i        v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_112256235_   5337 ACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCT 5386
                              v  ?   i   i i  iiv    ii    i    v   i     v
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_112256235_   5387 TATACAAAAATTAATTCAAGATGGATTAAAGACTTAAATGTTAAACCAAA 5436
                                       i    i      i ?    i       v i v v  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_112256235_   5437 AACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGCACATA 5485
                            i      vi i           v    ?i- v i -   ivv  v v
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTT 570

  chrX_112256235_   5486 GGCATGGGCAAGGATTTCATGACTAGAACACCAAAAGCAATGACAACAAA 5535
                           vv i     v i    v iiv  vi            vvii       
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_112256235_   5536 AGCCAAAATTGATAAACGGGATCTAATTAAACTAATGAACTTATGCACAG 5585
                           vv     v      iv   ii v  i   v v vi     v  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_112256235_   5586 CCGAGGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAC 5635
                          vi    v    i  vv i      v  i     i              v
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_112256235_   5636 ATTTTTGCAATCTACACATTTGACAAAGGGCTAATATCCAGAATCTACAA 5685
                           v       vii i i  i   i  i  i  vi          v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_112256235_   5686 AGAACTTAAGCAGATTTACAAGAAAAAAACAAACAACCCCATCAACAAGT 5735
                               ivvi  iv iv i  v     i     i     v  i? v  i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_112256235_   5736 GGGCAAAGGATATGAACAGACATTTCTCAAAAGAAGACATTTATGCAGCC 5785
                                    v    i           v        i  vi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_112256235_   5786 AACAGACACATGAAAAAATGCTCATCATCACTGGTCAT 5823
                           i ii          i       v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (113 / 83)
Gap_init rate = 0.00 (2 / 737), avg. gap size = 1.00 (2 / 2)  


3106 27.13 0.78 0.22  chrX_112283778_112287180.rev     2012  2914 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112283778_   2012 TGGAAAAATATTCCATGTTAATGGAGTAAAAGAATCAATATTATTTAAAT 2061
                               i    i       v     v ii    v i      i  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112283778_   2062 GTCCATATTGCCCACAACAATCTACAGATTAAATACAATCCTTAGCAAAA 2111
                          v v   i v    v vii           v  ii      i  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112283778_   2112 TACCAAGGATATTCTTCACAGAAATAGA-AATCACAATCCTAAAATTTAT 2160
                          v   ivviiv  i  ii       v  -  v -ii           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_112283778_   2161 ATGAAACCACAAAAGACCCAGAATAGCCAGAGCTATACTAAATTAAAAAA 2210
                            i  vii   ii               i i v  vi i  vv i  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_112283778_   2211 AAAAAACTGGAAAAATCACAGTACCCGACTT-AAAATTATACTACAGAGC 2259
                          v   ii    ii v     v v   i i  -    i -       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_112283778_   2260 TATAGTGACCAAAACAGCATTGTAATTGCATAAAAACAGACATATAGATC 2309
                           i   i i   i    ii v   v v      ii i             
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_112283778_   2310 AATGAAGCAGAATAGAGAACCCAGAAACAAATCAACACACTT---GCAAA 2356
                             i ii     v    ii       i   i v i   i  --- iv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_112283778_   2357 CTCATTTTCCACAAAGGGGCCATGAACAAACACTGGGGAAAAGACAGTCT 2406
                         i v      v    i  v    v  v  vv  v        ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_112283778_   2407 CTTCAACAAATGGCACTGGGAAAACTGTATATCAGTATGCAGAGGAATAA 2456
                         i            ii      v     v   ? vii     i i    i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_112283778_   2457 AACTAAACCTCAATATCTCACCATATACAAAAGTCAAATCAAAGTGGATT 2506
                          ii ii   i v iv  v              i i  v     i     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_112283778_   2507 AAAGACTTAAATCTGAGACCTCAAACTATAAAACTAGCACAAGAAAACAT 2556
                          ?    i     v i   v  v             vvi v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_112283778_   2557 TGGGGAAAATCTCCAGGACATTAGTCT-GACCAGACTTTCTCAAGCAATA 2605
                         v  ? v      i iv   v  i vi - i v viv     i iii vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_112283778_   2606 CCCCACAAGTGCCTGCATCCAAAGCACAAATGGACAAATGAGATCACAAC 2655
                          v   v   ii vv   v v    v v    i  i    vi  iiv  v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_112283778_   2656 AAGTTGAAAAGTTTCTGCACAGCAAAGGATACGATCAACAAAGTCAAGAG 2705
                           iv v    ii  i  ii vv       i  v     v     v  i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_112283778_   2706 ACAACCCACAGAATGGGAGAAAATATTTGTAAACTACCCATCTGACAAGG 2755
                                                      i   ii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_112283778_   2756 AATTAATAAGCAGAATATATAAGGAGCTCAAAGAACTCTATTGGACAAAA 2805
                         i i vi  vv            i  i   vv v     v  viv v   i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_112283778_   2806 TCTAATAATCTGAACCACAAATGGGCAAAAAATTTGAGTAGGCATTTTTC 2855
                         v v     i ii vi? v           ii      i   i     i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_112283778_   2856 -AAAGAAAACATACAAATGGGAAACAGGCATATGAAAATGTGCTCAATAT 2904
                         -      i i          vv  i i   i       vi       i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_112283778_   2905 TGTTGACTAT 2914
                         ii????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3290 25.12 1.87 0.35  chrX_112296197_112300020.rev     2466  3321 (503)    L1M4_orf2#LINE/L1        1   869 (39)  

  chrX_112296197_   2466 TGGAAAGATATTCCATGTTCATCGATTGAAATAATCAATATTGTTAAAAT 2515
                                    i          v     i  v v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112296197_   2516 GTCTATACTATCCAAAGCATTTTACAGATTCAGTGCAACCCCTATCAAAA 2565
                          v v     vi     viiv i          ii    i           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112296197_   2566 TACAAATGATATTCTTCACAGAAATAGAAAAAACAATCCTAAAATTTATA 2615
                          v v iiviiv  i  ii       v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_112296197_   2616 TGGAACCACAAG--ACCCAGAATAGCCAAAGCTATTTTAAGCAAATAGAA 2663
                              vii    --                i v  i  i iv  iv    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_112296197_   2664 CAAAACTGGAGGAATCACATTACCTGATTTCTAGTTATACTA-AGACCTA 2712
                             ii       v     i v  ii     v iviv     - i v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_112296197_   2713 TAGTAGCCAAAACAACATGGCAATGGCATAAAAACAAACATGTAGACCAA 2762
                         i    ii   i   iii   i v        ii i i    i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_112296197_   2763 TGGAATAGAACATAAAATTCAGAAACAAATTTGCACACCTACAGTGAACT 2812
                                   ivv i i i      i   iiiii   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_112296197_   2813 TATTTTCGACAAAGGTGCCAAGAACACT----GGGGAAAAGATAACCACT 2858
                         v           i          v  i ----       ii   ii vi 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_112296197_   2859 TCAATATATGGTTCTGGGAAAACTGGATATCAATAGGCAGCAGAATGAAA 2908
                             i v     v      v         ? v i v   iv        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_112296197_   2909 GTTGACCCCTATCTCTCACCGTATACAAAAATCAAATCAAAATGGATTAT 2958
                         v v        i   v    i           i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_112296197_   2959 AAACTTAAATGTAAGTCCTCAAATTATGAATCTACTACAAGAAAACATCA 3008
                          i  i          vv  v   i   i  v  vi  v          vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_112296197_   3009 GTGAAACTCATCAGGATATTGGTCTTGGCACAAATTTCTTGAACA--ATA 3056
                          ? v  v  v  iv  iv    vi v    vvii      ii i -- i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_112296197_   3057 C---AAGCACAGGCAACCAAAGGAACAATGGACAAATAGGATCACATGAA 3103
                          ---       i     v    i  v   i  i    v   iiv   v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_112296197_   3104 GTTGAAAAGCTTCTGCAAAG----AAAGGATACAATAAAAAAAGTGAAAA 3149
                         iv v    i   i  i--- ----      i  v  v  i          
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGT---GCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_112296197_   3150 GACAACCCACAGGATGGGAGAAAATATTTACAAACTACCCATCTGACAAG 3199
                                     i                i    ii ivi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_112296197_   3200 GGATTATTAACCTGAATATATAAGGAGCTCAAACAACTCTATAAGATCAA 3249
                            i vv  v  v          i  i   vv       v    v vv  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_112296197_   3250 ATCTAATAATCAGATCCGAAAATGGGCAAAAGATTTGAAAAGACATTTCT 3299
                         iv v     i vi  i?i            i        v          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_112296197_   3300 CACAAGAAGACATGTAAATGGC 3321
                          vv       i  ii       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGC 869

Transitions / transversions = 1.51 (127 / 84)
Gap_init rate = 0.01 (7 / 869), avg. gap size = 2.71 (19 / 7)  


2708 27.10 3.36 1.68  chrX_112305538_112309888.rev     2968  3860 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112305538_   2968 TGGAAGAACATTCTAGGTTCATGAGTAGGAAGAATCAATATTGTTAAAAT 3017
                              ii i  i i v       ii v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112305538_   3018 GGCCATAATGGCCAAAGCAACTTACAGAATTAATATTATTCCTGTCAAAC 3067
                            v   v vv     vii ii      v i  iiiv  i   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112305538_   3068 CACCAATGACATTCTTCACAGACTTGAAAAAACT-ATTCTAAAATTCATA 3116
                         iv   iivi v  i  ii    vv vi v  i  -  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_112305538_   3117 TGAATAAACAACAACAAAAAAACAGCCCA-AATGGCCAAGGCAATCCTAA 3165
                           i -----  ii-   iii ----    -   i     ii     i i 
  L1M4_orf2#LINE/    151 TGGA-----AATG-CAAGGGA----CCCAGAATAGCCAAAACAATCTTGA 190

  chrX_112305538_   3166 GCAACAAGAACAGCACTGTAGGCATCACATTATCTGTCTTCAAACTATAC 3215
                         iv  v       ivii  v   vv     i vi iivi      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_112305538_   3216 TACAG-GCTAGAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAAC 3264
                             i-    v     i   i    ii         i i  ii i   - 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA-C 289

  chrX_112305538_   3265 ACATAGAATAATGGAACAGAATGGGGATTTGAGAAATAAAGTCGCACACC 3314
                          i     vi       i     v i  v iv         vi ii   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_112305538_   3315 TACAACCATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGAAAA 3364
                           iiii  vi    i  i     i v  v   i v  vv       i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_112305538_   3365 GGACGCCCTCTTTAATAAATGGTGCTGGGATACCTGGG-----ATATGCA 3409
                          i iivi  i  i  i              i v    i----- i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_112305538_   3410 GAAGACTGAAATGGAACCCCTTCCTTACACCATATACAAAAAACAACTCA 3459
                         i    v    i v i      v   i                vi      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_112305538_   3460 AGATGGATTAAGGACTTAAATATAAAACCCAAAACTATAAAATACCTGGA 3509
                          i      i ?i   i     i   i v i            iv i i  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_112305538_   3510 AAATAACCTAGGCA-ACACCATTCAGGACATAGGCATGGGCAAAATTTTC 3558
                          i v   v    ?i- v i -   iv   v v  vv i     viv    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_112305538_   3559 ATGAAGAAGACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATG 3608
                         v ii v v             vvv          v      v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_112305538_   3609 GGATCT------AATTAAAGAGCGTCTGCAC---AAATAA-ACTATCAAC 3648
                            ii ------       i - v i  ii ---   vi -        v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_112305538_   3649 AGAATAAACAAACAACCTACAGGATGGTAGAAAATATTTGCA--TGCTGC 3696
                          i i i  v i      i    i    v              -- vv ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_112305538_   3697 ATCCAATAAAGGTCTAATATCCAAAATCTACAAGGAACTTAAACAAATTT 3746
                            ii    i  v  vi      i   v  i  i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_112305538_   3747 ATGAGAAATTAA---AAAGAACCCCATTAAAATGTGGGTAAAGGAC---- 3789
                           i v   --  ---   v     v   ?   vi    i      i----
  L1M4_orf2#LINE/    788 ATAATAAA--AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_112305538_   3790 --AGATAGTTTTCAAAAGAAGACATACATGTGGCCAAGAAACATATGAAA 3837
                         --   i v  i  v        i     vi       v  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_112305538_   3838 AAATGTTCAACATCACTAATTAT 3860
                          i   i         ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (150 / 89)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.50 (45 / 18)  


3499 23.41 3.64 0.45  chrX_112368920_112373310     3021  3900 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112368920_   3021 TGGAAAGATATCCTGTGCTCATGGATAGGAAGAGTTGATAGTGTTAAAAT 3070
                                      ii  i        v      v  i   v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112368920_   3071 GTCCATAGTATCCAAAGCTATCTATAAGTTCAATGCAGTTTCTATCAAAA 3120
                          v v   v vi     viv     i ii     i   i ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112368920_   3121 TTTTGATAGCATTTTTTTTACAGAAATAGAAAAAAGCAAATC-TAAAATT 3169
                          iiiiiiv  --i      i       v  v  --  vi   -       
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATT 146

  chrX_112368920_   3170 CATATGGAACCACAGATGACTCA-AATAGCCAAATCAGTCTTGAAAAAGA 3218
                                  vii  iiv   i  -          v  i            
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_112368920_   3219 ATAACAAAGCTGGAGATAACACATGTCCTGATTTCAAAATATACTATAAA 3268
                          v       i     ivvv    iv   ii         iv     i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_112368920_   3269 GCTATAGTAATTAAAACAGTGTGGTACTGGCATAAATACAGATATATAGC 3318
                             i      i  i                    iv i   i      v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_112368920_   3319 TCAATGAAACAGAAT--AGAGCCCAGAAGCAAACCCATGTACATATGATT 3366
                               i  i     --    i      ii        ii iv    i i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_112368920_   3367 AAGTGATCTTTGCTAAGGGTGGTAAGAATACATAGTAGGAAAAATATTGT 3416
                           v    i  i vi       vi    vi ivi i i  i   iv  v  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_112368920_   3417 CTTTTTGACAAATGGTGCTGGGAAAACTGGATATGCACATGCAAAAGAAT 3466
                              ii                v         ?v               
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_112368920_   3467 GAAATTGGA-----GACTTATGCCATACACAGAC-TCAACTAAAAATAGA 3510
                            i     -----iv  i ii     i   i v- i    v     i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_112368920_   3511 TTAAAGGCTTAAATGTAAGACCTAAAACTGTCAAACTC--AGAAGAAAAC 3558
                          i ?  i i           v        i v      --          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_112368920_   3559 ATAGAAG---AGCTTCATGACATTGGTCTCAGGAATGATTTCTTTGATAT 3605
                             i? --- v    i    v    vi vi v    i      v     
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_112368920_   3606 GGCACCCAAAGTAGAGGTAACAAAAGCAAAA-TAAACAAGGGGAACTACA 3654
                          i    v    i v i i        v    -  i i  ivv i   v  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_112368920_   3655 TTGAACTTAAAAGCTTCTGCAGAGTGAAGGAAAC----AACAGAGTGAAA 3700
                          ii  v      i   i  iivvvii     v  ----  v i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_112368920_   3701 AGGCAACCTATAAAATGGGAGAAAATATTTGCTAACCATACATCAGATAA 3750
                           i     i i i                   v  i    i   v     
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_112368920_   3751 ATGGTTAATATTCAAAATATAGAAAGATCTTCTACAACACAACATGAAAA 3800
                         iv ii vi   i  i      v     v  ii      v   i vv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_112368920_   3801 AAA----------GATTTAAAAATGGGCAAAGGGCTTGAATAAACATTTA 3840
                          i ----------i   ?               ii       i      v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_112368920_   3841 TTCAAATAATACATACATTTGCCCAA--GTCATATGAAAAGATGTGCAAA 3888
                          i    v  v i     vv  v    --iv  i           iv   v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_112368920_   3889 ATTGCTAATCAT 3900
                           ii????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (127 / 75)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.77 (36 / 13)  


2064 23.51 0.55 8.16  chrX_112382416_112384076.rev      448  1170 (491)    L1M4_orf2#LINE/L1      241   908 (0)  

  chrX_112382416_    448 TACAATATCCTCAAGAATCAA-ATAA-ATAATATTGATCCCAGGAAAAAT 495
                              - v iv  iv      - i i-i ii  i  iiviv    v i i
  L1M4_orf2#LINE/    241 TACAA-AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_112382416_    496 GATTTCAGACCTGTGGAACAGAATAGAGAACCCAGAAATAAATCTAATCA 545
                         -  v -   i vi     i     v    ii           i i vv  
  L1M4_orf2#LINE/    290 -ATAT-AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_112382416_    546 GTTACAGCCAACTCATTTTTTACAAAGGTGCCAAGAACATACATTGAGGA 595
                         v   ii i   i v     iv    i          v   v  v  i   
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_112382416_    596 AAGAAGAGTCCCTTTAATACATGATGCTGGGAAAAATGGATATTCATATA 645
                              v    ii  i  i v   i        v  v      ?i  i  i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_112382416_    646 CGTAAGAATGAAGCTAGATCCCCATGTTTTACCGTATATAAAAGTCAACT 695
                          iv          i i  i   i iv ivi   i    i    i i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_112382416_    696 CAAAATGGACTAAAGACTTAAATGTAAGGCCTAAAATTATAAAACTATTA 745
                                  ii ?    i          iv      i         v   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_112382416_    746 GAAGAAAACATCTGGG-AAATGCTACGTAACGT-GGGTCTGGGCAAAAAT 793
                                    vv ? -    -  v   i  v -    - i     vii 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGT-TAGGCAATGGT 585

  chrX_112382416_    794 GTTTTGGCCAAGACCTCAAAAGCCTATACTTACAATATAATATCTGACTG 843
                         v i  i vi v   vi       --------    ---------------
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGC--------ACAA--------------- 612

  chrX_112382416_    844 AAATGCAGTCTAAATGCAATAAAAGCAAAAATAGACAAATGGGATTACAT 893
                         ---------------    i     v         i    v   i v   
  L1M4_orf2#LINE/    613 ---------------GCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_112382416_    894 CAAGCTAAAAAGCTTCTGCACAGCAAATGAAACAACCAACAAGGTAGAGA 943
                            iv v    i   i  ii vv    v  v  v i   v  i  ii i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_112382416_    944 AACGACCTATAGAATGGGATAAAAATTTTGCAAACTATCCATTTGGTAAG 993
                         i  i   i i         v    vv        ii  vi  i  i    
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_112382416_    994 AGATTAATAACTATAATATATAAGGAATTCAAACAACTCAATAGCAAAAT 1043
                         i  i vi  v i v         i   i  vv           ii    -
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA- 796

  chrX_112382416_   1044 AAAAACCCTCAAGTAAGCCAATTAGAACATGGGCAAAAAAAAAAAAAAAA 1093
                         -- i  ----  i   v      ?i  v         ii v---------
  L1M4_orf2#LINE/    797 --AGAC----AAATAACCCAATTWAAAAATGGGCAAAGGAT--------- 831

  chrX_112382416_   1094 CCAAACAGTTATTTTTCAAAAGAAAATATACAAATGGCCAAGAAGTACAT 1143
                         iii  i  vi    i  v      i                v   i    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_112382416_   1144 GAAAAAATGCTCACCATCATTTATCAT 1170
                              i       v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (104 / 62)
Gap_init rate = 0.02 (14 / 668), avg. gap size = 4.50 (63 / 14)  


3331 27.20 0.22 0.22  chrX_112387448_112393725.rev     4880  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112387448_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112387448_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTTAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i        i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112387448_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_112387448_   5028 TATGGAATCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_112387448_   5078 AACAAAGCGGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                iv     vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_112387448_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_112387448_   5178 AATGGAACAGAACAGAGCACTCAGAAATAACACCGCATATCTACAACTAT 5227
                                i    iv   viii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_112387448_   5228 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTTCCT 5277
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_112387448_   5278 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5327
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_112387448_   5328 AACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 5377
                          ii    i    v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_112387448_   5378 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5427
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_112387448_   5428 AGGTATCACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAA 5477
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_112387448_   5478 CACCAAAAGCAATTGCAACAAAAGACAAAATTGACAAATGGGATCTAATT 5527
                                    vvv           v     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_112387448_   5528 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5577
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_112387448_   5578 GCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAG 5627
                         i     i   i             v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_112387448_   5628 GGCTAATATCCAGAATCTACAATGAACTCCAATAAATTTACAAGAAAAAA 5677
                          i  vi          v  i  v      iv i  v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_112387448_   5678 ACAAACAACCCCATCAACAAGTGGGCGAAGGACATGAACAGACACTTCTC 5727
                              i     v  i? v  i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_112387448_   5728 AAAAGGAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCAT 5777
                         v    i   i  vi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_112387448_   5778 CACTGGCCAT 5787
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


3200 26.10 0.77 0.77  chrX_112409991_112412392.rev     1004  1911 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112409991_   1004 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTAAAAAT 1053
                               i i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112409991_   1054 GGCCACACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAAC 1103
                            v i   v      v i  i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112409991_   1104 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 1152
                          v   vivi v  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_112409991_   1153 ATGAAACCAAAGAAGAACATATA-TAGCTAAGACAATCCTAAGCAAAAAG 1201
                            i  viiv - i i  vi v -    i  i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCA-AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_112409991_   1202 AACAAAGCTGGAGGCATCACACTACCTGACTTCAGACTATACTGCAAAGC 1251
                                i      vv       v  ii i    i viv    i      
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_112409991_   1252 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACC 1301
                                 i   i    ii         i iv ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_112409991_   1302 AATGAAACAGAACAGAGACCTCATAAATAACACCACACATCTACAACCAT 1351
                             i  i    iv    vii  v      vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_112409991_   1352 CTGATCTCTGACAAACCTGACAAAAACAAGCGATAGGGATAGGGTTTCCT 1401
                         i    i ii     ivv  v   i v  vv i  i    v  ii vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_112409991_   1402 TTTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACGGA 1451
                               i              v      v  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_112409991_   1452 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGAATT 1501
                          ii         v   i     v                   i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_112409991_   1502 AAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAACCT 1551
                          ?    i         i v i     i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_112409991_   1552 AGGCA-ATACCATTCAGGACAT--AGTCATGGGCAAAGACTTCATGACGA 1598
                            ?i- v i -   iv   v --i  i --     v ii   v iivv 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATA 595

  chrX_112409991_   1599 AAACGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1648
                         vi  i         vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_112409991_   1649 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 1698
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_112409991_   1699 CAGACAACCTATAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 1748
                         v        i i               v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_112409991_   1749 AAGGTATAATATTTGGAATCTACAAGGGACT--TAACCAAATTTACAAGA 1796
                          i  vv vi   iii    v  i  i i   --  --   v iv i  v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATA 793

  chrX_112409991_   1797 AAAAAACAAACAACTCCATTAAAAAGTGGGCAAAGGATATGAACAGAAAC 1846
                             i     i   i v   ?    i            v    i   v i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_112409991_   1847 TTCTCAAAAGAAGACATTTATGTGGACAACAAACATATGAAAAAAAGCTC 1896
                              v        i  vi vi   v   i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_112409991_   1897 AACATCACTGATCGT 1911
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


 426 25.55 10.95 0.73  chrX_112421282_112424565.rev      482   618 (2666)    L1M4_orf2#LINE/L1      172   322 (586)  

  chrX_112421282_    482 ATGGTCATAAACAA------AAAACCAGAGCAAAGTTGGAGGACTTACAT 525
                           i i  -      ------    vv   i               i   i
  L1M4_orf2#LINE/    172 ATAGCCA-AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_112421282_    526 TTTCAGATCTCAAGGTCAATTATAAAGCTATA-------AGATAATGTGA 568
                           i vi  i    iiiiv i  i       i -------   i i    i
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_112421282_    569 TACTGGCAAAAGAATATATAAGCTAACCAATTGAATAAAAT--AAAGTCC 616
                                 v   i   v i viivi i    v     i   -- i     
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_112421282_    617 AG 618
                           
  L1M4_orf2#LINE/    321 AG 322

Transitions / transversions = 2.89 (26 / 9)
Gap_init rate = 0.03 (4 / 151), avg. gap size = 4.00 (16 / 4)  

 569 26.73 15.84 1.32  chrX_112421282_112424565.rev      929  1231 (2053)    L1M4_orf2#LINE/L1      314   660 (248)  

  chrX_112421282_    929 AGAGTACAGCAACAGTCCCA--CATCTATAGTCATCTGATTTATG-CAAA 975
                              v   v  i iv    --   i   i    vi      vi -   i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_112421282_    976 AATTCCACTAGAACA--CAGTGAGCAAATGAAGAA-CTTTTCAATAAATA 1022
                         ii v   --   v  --  i  i v   -   v i-        i    i
  L1M4_orf2#LINE/    364 GGTGCCA--AGACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATG 410

  chrX_112421282_   1023 GTACTGGGTCAATTGGATATTCATATAAGAAAAAAT--ATTTTGATCCCT 1070
                           i     v   i      ?i  i  ivi   i   -- v  v  i    
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_112421282_   1071 ACCTCATATTAAACATAAAAATCAATTCCAAATATAT------------T 1108
                               i ii v i i      i  i  v    iv  ------------ 
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_112421282_   1109 GTA----CTTGAAATATAAAA----------------TAAGTCTA--TCT 1136
                            ----  vi  v       ----------------  i ?v  --   
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_112421282_   1137 TAGTGGACTTAGATTAGCCAACACTTTTTGAAA-AGGAAACCAAACAGCA 1185
                          v   iv   i i    v   iiv   i v i - v  v      -    
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA-AGCA 609

  chrX_112421282_   1186 T--TCATCATAA--AACAATA-ATAATTTAGATTCTATTAAACTTAAGAG 1230
                         i--v  v  v  --  v    -    v  i  i ii  i   v    i i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_112421282_   1231 C 1231
                          
  L1M4_orf2#LINE/    660 C 660

Transitions / transversions = 1.47 (47 / 32)
Gap_init rate = 0.05 (16 / 347), avg. gap size = 3.25 (52 / 16)  

1873 26.02 1.02 1.36  chrX_112421282_112424565.rev     1989  2576 (708)  C L1M4_orf2#LINE/L1   (0)   908   323  

C chrX_112421282_   2576 AAATAGGACACCACACATATACAACCATTTAATCTTTGACAAACCTGACA 2527
                              i-  -   i    v  iiii  v  i  i  i     ivv  v  
  L1M4_orf2#LINE/    323 AAATAA-AC-CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

C chrX_112421282_   2526 AAAACAAGCAATGAGAAAAGGATTCCCTATTTAATAAATGGTGCTGGGAA 2477
                          i v  vv     i i    i  vvi  v  i  i              v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

C chrX_112421282_   2476 AACTGGCTAGCCATATGCAGAAAACTGAAACTGGACCCCTTCCTTACACC 2427
                               v  ?   i     i  i v    ii         v   i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

C chrX_112421282_   2426 TTATATAAAAACTAACCCAAGATGGATTAAAAACTTAAATGTAAGACCTA 2377
                         v    i     i    i   i      i ? i  i           v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

C chrX_112421282_   2376 ACAAACACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGG 2328
                          --   --i      vi i           v    ?i- v i -   iv 
  L1M4_orf2#LINE/    521 A--AAC--TATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTG 565

C chrX_112421282_   2327 ACATAGGCATGAGCAAAGACTTCATGACTAAAACACCAAAAGCAACGACA 2278
                           v v  vv ii    v ii   v iiv  vi            vvii  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

C chrX_112421282_   2277 ACAAAAGCCAAAATTCACAAATGAGATCTAATTAAACTAAAGAGCTTCTG 2228
                                vv     vv i    vi  ii v  i   v v  i i   i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

C chrX_112421282_   2227 CACAGCAAAAGAAACTCATCAG---AGTGAACAGGCAACCTACAGAATGG 2181
                         ii vv    i  v   -    i---      v  i     i         
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACT-ATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

C chrX_112421282_   2180 GAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAAT 2131
                                 v       vii  vi      i  i  i  vi          
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

C chrX_112421282_   2130 CTACAAAAAACCTAAATAAATTTACAAGAAAAAAGCAAACAACCCCATCA 2081
                         v  i   i   iivv i  v iv i  v     ii    i     v  i?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

C chrX_112421282_   2080 ACAAGTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGACGTTTAT 2031
                          v  i     i      v    i     i     v        ii vi v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

C chrX_112421282_   2030 GTGGCCAACAA--ACATGAAAAAAAGCTCATGATCACTGGTCAT 1989
                         i       i  --         i v     vv    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (87 / 62)
Gap_init rate = 0.02 (9 / 586), avg. gap size = 1.56 (14 / 9)  

 354 29.25 8.96 1.42  chrX_112421282_112424565.rev     2574  2785 (499)    L1M4_orf2#LINE/L1      669   896 (12) *

  chrX_112421282_   2574 TTTAAAAAATCACCCTTAAAGGAGTAAAAA-AGAATTCTTAGAGTAGG-G 2621
                           i   ii -   iv i  iii   i    - v  ii vi   i i  - 
  L1M4_orf2#LINE/    669 TTCAAAGGA-CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_112421282_   2622 TAAATATTTACAATACTTATATCCAATAAAAGACTACCATCCATAATATT 2671
                         v        i   vv v      ii    ii    vvi     v     v
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_112421282_   2672 TGTAAGA-----TA----TCAATTACAAAAAAGACAGACAAGCCAA---G 2709
                          i-    -----  ----     v i     -    i i  v    ---i
  L1M4_orf2#LINE/    768 TA-AAGAACTCTTACAACTCAATAATAAAAA-GACAAATAACCCAATTWA 815

  chrX_112421282_   2710 AGAA-----GAAAGACTAGAATAGGCAATTTACCCAAGAAGACATGCAAG 2754
                          i  -----i  i  i v      i  v  iv  v       i  i   i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_112421282_   2755 TTAATGATAAACATATAACAAGAAACTCAAC 2785
                          vivii    i  i  i v    vi      
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAAC 896

Transitions / transversions = 1.95 (41 / 21)
Gap_init rate = 0.04 (9 / 228), avg. gap size = 2.44 (22 / 9)  


3181 24.97 1.78 0.56  chrX_112430087_112432523     1048  1944 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112430087_   1048 TGGAAATACATCCCATGTGCATGGACTGGAATAATCAATATTGTGAAAAT 1097
                               v i         v      i     v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112430087_   1098 GACCATACTCCCCAAAGCAATCTACAGATTCAATGCAATTTCCATCAAAA 1147
                          i v            vii              i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112430087_   1148 TACCAACATCATGTTTTACAGAA-TTAAAGAGAAAATAATCTTAAAATTC 1196
                          v   i vv v v    i     -  ---  v  iv i   i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chrX_112430087_   1197 ATATGGAATTCAAAAAGAGCCTGAATAGCCAAAGCAATTCTAAAGAAAAA 1246
                                 v vv  ii  v  v           i    ii i  i  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_112430087_   1247 TAATAAATTTGGAGGCATCATATTACCCCACTTCCAATTATACTGCAAGG 1296
                         v  i   v       vv   i i v   v i   v  viv    i   i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_112430087_   1297 CTATAGTTACCAAAACCACATGGAACTGCTATAAAAGTAGATACAAAGAC 1346
                            i   v i   i  viii   v    vi    iii    i i v   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_112430087_   1347 CAATGGAAAAGAATAGAGAGCACAGAAATAAAGCCAAATACTTACAACCA 1396
                                 v     v     iv          v   v i i   iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_112430087_   1397 ACTGATTTTTGACAAAGCATACAAACACAAAT---TGGAGAAAGGCTACC 1443
                          i       i     i -i i v  v  v v ---   i     iv  vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_112430087_   1444 CTATTTAATAAATGGTGCTGGGAAAACTGGATAGCCTCATGTAGAAGAAT 1493
                           v  i  i              v         ?  v    i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_112430087_   1494 AAAACTGGATCCCAATCTTTCACCACATAGGAAAATTAACTCAAGATTGA 1543
                         i  ii    i   v i  iv     i   vi             i  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_112430087_   1544 TTAAAGACTTAAA-----GACCTGAAGCCATACAGATTGTAGAAGAAAAC 1588
                          i ?    i    -----  v  i  i i   v iv iv           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_112430087_   1589 ATAGAAAAAACTCTTC-TGCACGTTGGCCTATGCAAAGAATTTATGACTA 1637
                             i?iv  v     -  -  v    vi  v    v iv  iv iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_112430087_   1638 AGACCCCAAAAGCAATTGCAACAAAAACAAATATAAATACATAGGACCTA 1687
                         v   v         vvv         iv   v   i   v  v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_112430087_   1688 ATTAAACTAAAAAGCTTCTGCATAGCAAAAGACATAATCCAGA--GTAAA 1735
                           i   v v    i   i  iiivv    i    iv   v   --  i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_112430087_   1736 CAGGCAACCTATAAAATGGGAGAAAATACTTGCAAATTATACATCTAAAA 1785
                         v  i     i i i              i        i   i    i v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_112430087_   1786 AAGGACTAATTTCAAGAATCTACGAGGAACTCAAAAAAGTCAGCAAGAAA 1835
                          i     vi v  v     v  ii i      vv v  v   ii  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_112430087_   1836 AA-ACA--TAATTCA-TTAAAAAGTGGGAAAAGAACATGAATCGACATTT 1881
                           -   --   ii  -  ?    i    v    i iv     v       
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_112430087_   1882 CTCAAAAGAAGATATACAAATGGCCAACAAACATATTTAAAAATGCTTAA 1931
                            v                       i  i  i  vv   i     i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_112430087_   1932 CATCACTAATCAT 1944
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (123 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.91 (21 / 11)  


3205 26.74 1.10 0.77  chrX_112435030_112440414.rev     3990  4894 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112435030_   3990 TGGAAAAGCATGCCATGCTCATGGATTGTAAAACTTGATATCATTCAAAT 4039
                               iii  v     i          v  i    i    ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112435030_   4040 GGCCGTGCTGCCTAAAGCAATTTACAGATTCAAAGCTATTCCTATCAAAC 4089
                            vi i  v  i   vii  i           v  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112435030_   4090 CACCAATGACATTCTTTACAGAACTAGAAAAAAAACT-ATTTTGAAATTC 4138
                         iv   iivi v  i   i     v v  v  i---  -  ii i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_112435030_   4139 ATATGGAACCACAAAAGTGCTCGAGTAGCCAAGCCAATCCTAAGCAAAAA 4188
                                 vii   ii vv iv  i       iv     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_112435030_   4189 GAACAAAGCTGGAGGCATCACATTTCCTGACTTCAAACTATAATACAAGG 4238
                                 i      vv     i    ii i      viv  v     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_112435030_   4239 CTACAGCAACTATAACAGTATGGTACTGGTACAAAAACAGGCATATAGAT 4288
                               i  ii vi     i         i i  ii i  i         
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_112435030_   4289 CAATGGAACAGAACAGAGAGCCTAGAAATAATGCCACACACCTACAACCA 4338
                                 i    iv     i i        vv   i   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_112435030_   4339 TCTGATCTTTGACAAAGTTGACTAGAACAAGCAATGGGGAAAGGACTCTC 4388
                         vi    i  i     i v  v v   v  vv            i ivv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_112435030_   4389 TAGTCAATAAAGGGTGTTGGGATAACTGGCTAGCCATGTGCAGAAAATTG 4438
                          vv    i   v    i     i      v  ?   ii    i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_112435030_   4439 AAATTGGACTCCTTCCTTATACCATATATAAATATCAATTCAAGGTGGAC 4488
                           i      i   v   i i        i   v  i  i    ii    i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_112435030_   4489 TAAAGACTTAAATGTAAAACCCCAAACTATAAAAACCCTGAAAGACAACC 4538
                         i ?    i         i v iv           vi i ii    v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_112435030_   4539 TA--TGCAATACCATTCTGGACATAGGG--AGGAACAAAGATTTCATGAC 4584
                           --? i  - i -   vv   v v   --   --   v i    v iiv
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGG--CAATGGTTTCTTAGA 593

  chrX_112435030_   4585 AAAGATGCCAAAAGCGATTGCAACAAAAGCAAAAATTGACAAATTGGATC 4634
                         v v  ii        ivvv          v      v  i        ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_112435030_   4635 TAATCCAACTTAAGCATTTCTGCACAGCAAAAGAAACTATCAACAAAGTA 4684
                          v   v  v    iv i  i  ii vv    i  v        v     i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_112435030_   4685 AACAGACAACATACAGAATGGGAGAAGATTTTTCCAAACTATGCATCTAA 4734
                           v       vi              i  v   v    ii  ii    i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_112435030_   4735 CAAATGGCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACCAGA 4784
                         i  iv i  vi       v  v     i     ivv    v iv iv v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_112435030_   4785 AAAAAACAA----CTCCATTAAAAAGTGG-CAAAGAACATGAAGAGACAC 4829
                             i    ---- i v   ?    i   -     i iv    v     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_112435030_   4830 TTCTCAAAAGAAGACATTCATGTGGCCAGCAAACATATGAAAAAAATCTC 4879
                              v        i  v  vi      ii  i  i       i vv   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_112435030_   4880 AACATCACTCATCAT 4894
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.89 (17 / 9)  


3395 24.59 0.43 2.06  chrX_112480831_112485053     2808  3730 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112480831_   2808 TGGAAA-ATATTCCATGCTCGCTCATGAATTGGAAGAATTAATATCATTA 2856
                               -    i     i  ----   i         v       ii   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTC----ATGGATTGGAAGACTTAATATTGTTA 46

  chrX_112480831_   2857 AAATGTCCATACTACCGAAAGCAATCTACAGATTCAATGCAATCCCTATG 2906
                          i   v v     v  v   vii              i           v
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_112480831_   2907 AAAATACCAATGACATCGTTCACAGAAATAGAAAAAACGATCCTAAAATT 2956
                              v   iivi v iv  ii       v  v  ivi            
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_112480831_   2957 TATGTGAAACCACAAAAGTCCCAGAATAGCTAAAGCTATCCTAAGCAAAA 3006
                         i  i  i  vii   ii v           i   i v   i i ---   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAA 193

  chrX_112480831_   3007 AGAAAAA-AAAACTGGAGGAGGAAGAATCACATTACCTGACTTCAAATCA 3055
                             i  -   ii       v------     i v  ii i      v v
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGAC------TCACACTTCCCAATTTCAAAACT 237

  chrX_112480831_   3056 TAGTACAGAGCTATAGTAATCAAAACAGCATGATACTGGCATAAAAAGAG 3105
                           v    i     i         i    ii  i           ii v  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_112480831_   3106 ACACGTACATCAACGGAACAAAATAGAGAACTCAGAAGCAAATCCACACA 3155
                            ii  v     i    i i   v    iii     ii   i   i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_112480831_   3156 CCTACAGTGTGGACACCTACATTTTGACAAAGGTGCCAAGAATATACACT 3205
                         ii  -----   v  vi ivv   i     i          vi  v  v 
  L1M4_orf2#LINE/    338 TTTA-----TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_112480831_   3206 GGGGAAGGGACAGTCTCTTCAATAAATGGTGCTTGGAAAACTGAATATCC 3255
                               i i i     i     i          v   v     i   ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_112480831_   3256 TT-TGCAATGGAATGAAACTAGACCCTTTTCTCTAATCATATTCAAAAAT 3304
                         vi-     vi       ii i     i vi   vv i     v       
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_112480831_   3305 CAAATCAAAATGGGTTAAATACTTAAATCTAAAACCCCAAACTATGAAAC 3354
                         i  v         i i ? v  i     v   i v iv       i    
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_112480831_   3355 TACCACATAAAAACATTGGGGAGAATCTCCAGGATATTAGAGTTGGTAAA 3404
                          vii v vi       v  ? vi     i iv  iv  i iv v  i  v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_112480831_   3405 AATTTCTTAAGCAATACCCCACAAGCACAGAAAACCAAAGCAAACATGGA 3454
                         ii       iii vv  v   v       iiv   v    v   v  i  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_112480831_   3455 CAAATGGGATTACATCAAG-TTAAAAACTTCTGCATAGCAAAGGATACAA 3503
                         i    v   i v      i-          i  iiivv       i  v 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_112480831_   3504 TCAACAAAGGGAAGAGACAACTCACAGAATAGCAGAAAATATTTGAAAAC 3553
                             v    v   i       i        i v            v   i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_112480831_   3554 TATCCATCTGACAAGGGATTAACAACTAGAATATGTAAGGAGCTCAAACA 3603
                         i  vi      i      i vii v i       i   i  i   vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_112480831_   3604 ACTCTATAGGAAAAACATTTAATAATCTGATCAAAAAATGGGCAAAAGAT 3653
                             v   iv     v iv-     i ii  i?             i   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_112480831_   3654 TTGAATAGACATTGCCCAAAAGAGGACATACAAATGGGAAAAAGGCATAT 3703
                                      v i v     i  i          vv  v i   i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_112480831_   3704 GAAAAGTTACTCAACATCATTGATCAC 3730
                               v i          ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (136 / 87)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.56 (23 / 9)  


2858 20.57 6.34 2.07  chrX_112491398_112500619     2598  3370 (5852)    L1M4_orf2#LINE/L1        1   806 (102)  

  chrX_112491398_   2598 TGGAAACACATCTAGTGGTCATGAATTAGAAGTCTTAACATTGTTAAAAT 2647
                               v i   ivi  v     i   i    v     i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112491398_   2648 G-CATTATTTCCTGAATTGGTTTACAATGCCAATGCTACCTCTTTCAAAC 2696
                          -  v  i i  ii     i i    ivvi   i  v i i  v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112491398_   2697 TCCTAGTTGCCATTTTTTC------------------CCTTAAACT---- 2724
                            i  i    v     v ------------------   v   i ----
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_112491398_   2725 -GACAATGCAACTGACCCAGAATAATAAAAAAAACCTGTTTTTTGA---- 2769
                         - iv       vv           iiv    v  ------ i    ----
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAA------TCTTGAAAAA 194

  chrX_112491398_   2770 ---GTACTAAATTGGAGGAT----ACTTCCTGATTTCAAAACTTACTACA 2812
                         --- v  v  i        i----      ii                  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_112491398_   2813 AAGCTAAAATAACAAAGACATTGTGTTACTGGCATAAGAATCTGCATGTA 2862
                               v i   iv      v    v            i  vvi   i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_112491398_   2863 GATTAATGGAATAGTATATGTGTGT--AGAAATAAATTCATA--TTTATG 2908
                            i          v  -  v v  --         ii    --      
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_112491398_   2909 GCCAATTTCTTTTCAACAAGAATGCCAAGACAATTCAATGGAAGAATGAA 2958
                          i     vv     i     ii         v         i-   v   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAA 392

  chrX_112491398_   2959 TAGGGTTTTCAACAGATACTGTTGG-ACAATTGGATATCCAAATGCAAAA 3007
                            vv         i  iv  i   -    i      ?   v        
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_112491398_   3008 TAATGAAGTTGG--CACCACCGTAAACATCTTGCACAAAGGGTAACTCAA 3055
                         v           -- v i   vi --  i v ii     iiv        
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCA--CACCATATACAAAAATTAACTCAA 490

  chrX_112491398_   3056 AACGGTTAATATATCCAAACGTATGAGCTAAAATTATAAAACTCTTAGAA 3105
                           i  v v ? v i i   i   v         i                
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_112491398_   3106 G----CAGAGTAGTACATCTTCTTGGCCTTGT-TTATGCAAAGGCTTCCT 3150
                          ----  v  v?   v      v  i     v-   v    v  i   i 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_112491398_   3151 AGATACAAAAACAAAAGCACAAGTGACAAAAGAAAAAAACAGATGT-TTA 3199
                              ii v v            ii             -i    iv-  i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTG 639

  chrX_112491398_   3200 GACTTCTTCAAAATTAAAATATTTTGTGTTGCTAACAATAATATCAAGAA 3249
                               v            vv       i v v  vi i v         
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_112491398_   3250 AGTTTAAA-ATGATCCAGAAATAATGGGAGAAAATATTTGCAAATCATAT 3298
                            vv   - ii i   v i --                           
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGA--ATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_112491398_   3299 ATATGATATGGGACTTATATCCAGAAAAAAAAAAAAAGAGCTGTTACTAA 3348
                           v     v       i         v v v   i  ---  v    v v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA---CTCTTACAAC 784

  chrX_112491398_   3349 TCAACAAGTAAAAGAAAAAAAA 3370
                             i  vv      v   v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAA 806

Transitions / transversions = 1.00 (78 / 78)
Gap_init rate = 0.02 (20 / 806), avg. gap size = 3.25 (65 / 20)  

 389 19.05 12.93 2.04  chrX_112491398_112500619     3649  3795 (5427)    L1M4_orf2#LINE/L1      746   908 (0)  

  chrX_112491398_   3649 AGAGACTCTGTCTCCAAAA-----AAACAA-----ACAAC--AACAACAA 3686
                           i    -   v    i  -----   v  -----     --  i  i  
  L1M4_orf2#LINE/    746 AGGGACT-TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_112491398_   3687 AAAAA-----AAC--AATGTTATAAATGGGCAAAGGGTCTGAATAAATAT 3729
                            i -----   --   - ? v             i i      i i  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAAT-TWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_112491398_   3730 TTTTTCAATTTAAGGTATACTAATGGTCAATAAACACATTAAAAAATATT 3779
                           i i   vv-   i     v     i      i     v    i  ii 
  L1M4_orf2#LINE/    844 TTCTCCAAAG-AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_112491398_   3780 CAATTCCATAGGCATT 3795
                            ivi  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (19 / 8)
Gap_init rate = 0.05 (8 / 163), avg. gap size = 2.75 (22 / 8)  

3280 26.76 0.44 0.44  chrX_112491398_112500619     7822  8729 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112491398_   7822 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 7871
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112491398_   7872 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 7921
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112491398_   7922 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 7969
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_112491398_   7970 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 8019
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_112491398_   8020 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATGCTACAAGGC 8069
                                i      vv       v  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_112491398_   8070 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 8119
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_112491398_   8120 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 8167
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_112491398_   8168 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAACGATTCC 8217
                          vi    i  i     ivv  v   i v  vvv          vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_112491398_   8218 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 8267
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_112491398_   8268 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 8317
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_112491398_   8318 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 8367
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_112491398_   8368 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAA 8417
                         v    ?i v viv   iv   v v  vvii     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_112491398_   8418 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 8467
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_112491398_   8468 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 8517
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_112491398_   8518 AGGCAACCTACCAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 8567
                           i     i  vi             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_112491398_   8568 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 8617
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_112491398_   8618 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAAAAGACACTTC 8667
                          i     i     v  i?    i     i     iv    v     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_112491398_   8668 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 8717
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_112491398_   8718 ATCACTGGCCAT 8729
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3315 25.25 1.10 0.99  chrX_112524551_112534571      492  1398 (8623)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_112524551_   1398 TAGAAAAATATTCTATGCTCATAAATTGGAAAAATCAATATTGTGAAAAT 1349
                          i    i    i i   i    ii       i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_112524551_   1348 GGACATATTGGCCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 1299
                           vv   i vv     vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_112524551_   1298 TACCAATGACGTTCTTCACAGAAATAGAAAAAAAAAAAAACCTAAAACTT 1249
                          v   iivi v  i  ii       v  v  ivvi v---       i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT---CCTAAAATTC 147

C chrX_112524551_   1248 ATATGGAACCACAAAAGGCCCAGAATAGCCAAAGCTATCCTAAGCAAAAA 1199
                                 vii   ii i               i v   i i ---    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAA 194

C chrX_112524551_   1198 AAAAAAAAAAAAAGGAGAAATCACATTACCTGACTTCAAATTTTACTACA 1149
                         i  i  v   ivv    i v     i v  ii i      vi        
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

C chrX_112524551_   1148 GAGCTATAGTAAACAAAACAGCATGGTACTGACATAAAAACAGACACATG 1099
                         i     i     v   i    ii        i     ii i     i  i
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

C chrX_112524551_   1098 GACCAAAGGAACAGAATAGAGAACCCAGAAACAAATCCACACTTCAACAG 1049
                           i   v    i     v    ii       i   i   i  v iv ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

C chrX_112524551_   1048 TGACTTCCTTTTTGACAAAGGTGCCAAAAATATAAACTGGGGAAGGGACA 999
                          v v  vv    i     i        i vi  vv v       i i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

C chrX_112524551_    998 TTCTCTTCAATAAATTGTGCTAGGAAAACTTGATATCCATATGCAGAAAA 949
                         v   i     i    v     i   v    v    ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chrX_112524551_    948 ATGAAACTAGATCCCTATCTCTTGCCATATACAAAAATCAAATCAAAATG 899
                              ii i  i     i   vii              i  v        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chrX_112524551_    898 GGTTGAAGACTTAAATCTAAGACCTTAGACTATGGAAATACTACAAGATA 849
                          i ii?    i     v     v  v i     ii  v vi  v    v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chrX_112524551_    848 ACATTGAGGAAAATCTCCAT----TTTGTCTGGACCAAAACGTCTTCAAG 803
                             v i? v      i i ----  v vi i i v viiiv    --  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--AG 592

C chrX_112524551_    802 CAAT-ACCCCAGAAGCAAAGGCAGCCAAAGCAAATGTGGACAAATGGGA- 755
                         vv  -  v   i     v i   i v    v   vi i  i    v   -
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

C chrX_112524551_    754 -TCAC--AAGTTAAAAAGCTTCTACACAGCAAATGTTACAATCAACAAAA 708
                         -   i--  i       -   i iii vv    v vi  v     v   i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

C chrX_112524551_    707 TGAAGAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTATCCATCT 658
                             i        i                          ii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

C chrX_112524551_    657 GACAAGGGATTGATAACCCAAATATATAAGGAGCTCAAACAATTCAATGG 608
                           i      i vi  v  vi         i  i   vv    i     ii
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

C chrX_112524551_    607 GAAAAAATCTAATAATCCTATCTAAAAATGGGCAGAAGATT-GAATAGAC 559
                         v     iv v     i  v  i?           i i    -        
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

C chrX_112524551_    558 ATTTCTCAATACAAGACATACAAATGGAAAACAGGCATATGAGAAGGTGC 509
                                v v v    i          vv  i i   i    i   i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

C chrX_112524551_    508 TCAACAGCACAGATCAT 492
                               v  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (139 / 86)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  

3158 27.31 0.55 0.55  chrX_112524551_112534571     8621  9528 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112524551_   8621 TGGAAGAACATTCCACGCTCATGGGTAGGAAGACTCAATATCGTGAAAAT 8670
                              ii i  i   i i      i v        i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112524551_   8671 GGTCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 8720
                           iv     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112524551_   8721 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 8768
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_112524551_   8769 TATGGAATCAAAAAAGAGCCCCCATTGCCAAGTCAATCCTAAGTCAAAAG 8818
                                viiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_112524551_   8819 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 8868
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_112524551_   8869 TACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGATATAGACC 8918
                                 i   i    ii   i     i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_112524551_   8919 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACATATCTACAACC 8966
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_112524551_   8967 ATCTGATCTTTGACACACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 9016
                          vi    i  i    vivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_112524551_   9017 CTATTTAACAAATTGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 9066
                           v  i       v         v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_112524551_   9067 GAAACTGGATCCCTTCTTTACACCTTATACAAAAATTAATTCAAGATGGA 9116
                            ii    i    v i i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_112524551_   9117 TTAAAGACTTACACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 9166
                          i ?    i  v i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_112524551_   9167 CTAGGCA-ATACCATTCAGGACATAGGGATAGGCAAGGACTTTATGACTA 9215
                         v    ?i- v i -   iv   v v   v       v ii  iv iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_112524551_   9216 AAACACAAAAAGCAATGGCAACAAACGCCGAAATACACAAATGGGATCTC 9265
                         vi    v       vvi        v vvi     v i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_112524551_   9266 ATTAAACTAAAGCACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 9315
                           i   v v  iv    i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_112524551_   9316 CAGGCAACCTACCAAATGGGAGAACATTTTTGCAATCTACTCATCTGACA 9365
                         v  i     i  vi          v  v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_112524551_   9366 AACGGCTAATATCCAGAATCTACAAAGAACTCAAACATATTTACAAAAGA 9415
                          iv i  vi          v  i         vv   vv iv i  v i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_112524551_   9416 AAAACAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTT 9465
                           i     i     v  i? v  i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_112524551_   9466 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 9515
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_112524551_   9516 CATCACTGGCCAT 9528
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 377 32.33 6.04 4.53  chrX_112589409_112591957      663   993 (1556)    L1M4_orf2#LINE/L1        3   338 (570)  

  chrX_112589409_    663 GAAATCTATC--ATGTTCATAAGTGGGAAAATTCAGTATGAT--AGACAT 708
                             vv    --        iii v    i i i i   vi --   iiv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_112589409_    709 TAACTGTCACCAACATAGA-CTATA-ATCCAACACAATATCGTTTAAAAT 756
                         i  ivv  v    -  v  -   i -  i    i    vi vv i     
  L1M4_orf2#LINE/     53 CAATACTCCCCAA-ATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_112589409_    757 CTTAGAAGATATTTTCCCCATAGACCTTAAAAAAACGTTATTTTAAAATT 806
                          ii  v--- iii  iiiiii   vv  i v  ivi --  ii       
  L1M4_orf2#LINE/    102 CCCAGC---TGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATT 146

  chrX_112589409_    807 CATATGGAAGACTACAAGT--CTAAGAAATTTCAAAATTTGCACAAT--T 852
                                  i-- i    v-- iv    vvvi     ------    -- 
  L1M4_orf2#LINE/    147 CATATGGAAA--TGCAAGGGACCCAGAATAGCCAAAA------CAATCTT 188

  chrX_112589409_    853 AACAAAAAATAAGCAAAGT----GGTTTTAT--TTTGTTAT----AGGTT 892
                         i v   i  v  -      ----  vi i i--  iviv  ---- iii 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAA-CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_112589409_    893 GGTTATAAATCTATGGTAATTAACAAAGTGAGATATTAACCCATGGACAG 942
                         vii  i   v   ii     i  v v    v i  i ii vi v   i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_112589409_    943 AAAAATACATTAATGGAACAGAACAGATAACAAAGAAATAGACCCATGCA 992
                          v v   v  i       i    iv  v iivv       i      i  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_112589409_    993 T 993
                          
  L1M4_orf2#LINE/    338 T 338

Transitions / transversions = 1.61 (66 / 41)
Gap_init rate = 0.04 (15 / 336), avg. gap size = 2.33 (35 / 15)  

 268 32.01 4.37 7.95  chrX_112589409_112591957     1546  2048 (501)    L1M4_orf2#LINE/L1      401   885 (23)  

  chrX_112589409_   1546 TCAGTAAATGATGTTTTGAAAACTGCTTGTCCATATAGAAAACAATTA-- 1593
                            ii     i  i vv  v     vv i?   i  iv    v   v --
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_112589409_   1594 -TGTATCTCATTAACCTATATCATATATATATTATATATAAATAACCTAT 1642
                         -  v i i --  v ii i i      i v --------  v    ----
  L1M4_orf2#LINE/    451 TTGGACCCC--TACCTCACACCATATACAAA--------AATTAAC---- 486

  chrX_112589409_   1643 ATCATATATATATAAATAAACCCAGACTAGTCAAAAACTCAAATTTTTGA 1692
                         -   v -  iv  v ?- i   i i i--  -  i i  v   i v -i 
  L1M4_orf2#LINE/    487 -TCAAA-ATGGATCAW-AGACCTAAAT--GT-AAGAGCTAAAACTAT-AA 529

  chrX_112589409_   1693 CAATTTTAGGGGAAGAGAATGTTATTAGGAGAATGTTATTATGACTTTAG 1742
                         v v i    ---    i  ii ----   ? v vi iv ii    i  i 
  L1M4_orf2#LINE/    530 AACTCTTAG---AAGAAAACAT----AGGNGTAAATCTTCGTGACCTTGG 572

  chrX_112589409_   1743 CATCAAAAAA-AGTTTCTTAAACACAATGTAAAATGTCTAAATCCTAATG 1791
                         -i i iiv  -i        i i ii iiiv   v ivi  iivvi  vi
  L1M4_orf2#LINE/    573 -GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_112589409_   1792 GAAAAATATGGATAAAGTTGGCAAAATTTTA--AAAAGCAAAA--TCCGA 1837
                               -  i      -    ---- i  i --    vi    -- iivi
  L1M4_orf2#LINE/    622 GAAAAA-ATAGATAAA-TTGG----ACTTCATCAAAATTAAAAACTTTTG 665

  chrX_112589409_   1838 CACT--AGAAAAAGCCATAAACCAATTTAAAATTTAAGCCACAGATTGGG 1885
                         ii  -- i ii vi i  v  vv  v v    vvi  v       v    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_112589409_   1886 AGTCAATGTTCTCATGTGA-ATAATT-ATAAAAGACTTTGTATCTGAAAT 1933
                           vv   i  iv  vi v -   vi -    ii     -     iii   
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTT-GTATCCAGAAT 764

  chrX_112589409_   1934 ACGTAA----TTACTGCAAAACAATTACACAAAAACA-----CTCAATTA 1974
                          ii   ----i vi i   vv    v i v   i   ----- i     ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_112589409_   1975 AAAAACAAACAGGCGAGTGATGTGAAAAGCCAATTAACCAAAAGAAAC-T 2023
                              ii----   i iv   v    v  v  v  vv     ii i i- 
  L1M4_orf2#LINE/    815 AAAAATG----GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_112589409_   2024 ATAAATGGCTGAAAAACATATTAAA 2048
                          i       ii v  i  i  v   
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAA 885

Transitions / transversions = 1.57 (96 / 61)
Gap_init rate = 0.05 (26 / 485), avg. gap size = 2.38 (62 / 26)  


3159 23.15 3.36 1.79  chrX_112648561_112652782     2838  3731 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112648561_   2838 TGGAAAAACATCCTATGTTCCGGAATTAAAAGACTCAATACTATCAAAAT 2887
                               i i    i      vv i   ii      i    i i i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112648561_   2888 GTCCAATGTACCC--AAGTGATCTACAGACTCATGACAATCCCCATAAAA 2935
                          v -   iiv   --  v           i   vvi       i  v   
  L1M4_orf2#LINE/     51 GGC-AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_112648561_   2936 AACCCAATTGCATTTTTCTCAGAAATAGAACAAA--AATCCCAAAATTAA 2983
                          v    ii   v     iv       v  -   i--i    i      v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chrX_112648561_   2984 TATGTAATCTCAATGGACACTGAATAGCCAAAAAATTCTTGAAAAGGAAG 3033
                             v  viv   v    v v            v v         i    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_112648561_   3034 AACAAAACTAGAGGACT-----TTCCTGATTTCAAAACACATTATAAAGT 3078
                               ii i       -----    ii          vi i  i    i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_112648561_   3079 TACAGTAATCAAATCAATGTATTATTGACATAAAAACAGAAATGTAGACC 3128
                                     iv  i   iv  i  i     ii i   v  i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_112648561_   3129 AATGGAACAAAATAGAGAACAGAGAAATAAACCTTCATATATTT--GGTC 3176
                                i i   v    iivv           --    i    --    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTC 346

  chrX_112648561_   3177 CACTAATCATCAACAAGGGCTCCAAGACTACACAATGGAGAAAAAATCAT 3226
                         v i i  iv  i       iv       i iv      i    i   vi 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_112648561_   3227 CTTTTCAACCAATAGTGCTTGGAAAATCTGGAAATCTACAGGAAAAAGC- 3275
                                  v   i     v   v  -     v ? i   v v     v-
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAA 445

  chrX_112648561_   3276 TGAAATTGAACCTTTATTGTATAC-AGACGTATAAATTAATTAAAAATGG 3324
                             i   i   ii  iivi i  - v iii v       i v       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_112648561_   3325 ATTAAAAGCCTGAAAATAAGACCTGAAACTATAAAATCCCTAAAGGAAAA 3374
                           i ? ii   i  vi     v  i           ii i  i i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_112648561_   3375 CCTTGAGGAAATTATTCCTGACATTGGACTGGGCAATTATTTATTTGGAT 3424
                          v v i? v  v v   v    v    ii i      vi   -i  i   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-CTTAGAT 594

  chrX_112648561_   3425 AAGATGCCATAAACACAGTTAACAAAAGCAAAAATAGATAAACAGGACTG 3474
                          v  ii   v  i    ivi        v             iv     v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_112648561_   3475 CATCAAACTTAAAA--TTATTTGCAGCACAGGAAACAATCCAGA--GTGA 3520
                                v      --  v v   vv  v    v  v   v   --    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_112648561_   3521 AAAAGCAAACTACAGAACGAGAGAAAATATT------------ATCTAAT 3558
                            ii   v i      i i           ------------    i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_112648561_   3559 AAGGGGTTAAAATCCAAGACATACAAAGAACTCTTACAACTCAATAACAA 3608
                              ii viv     ii i   i                       i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_112648561_   3609 CAACA-AAATGAAACCTAGTTAACAAACAGGCAAATAAACTGAATAAGAA 3657
                         v  v -    --    i i  ? v   ii      ------ i  vv   
  L1M4_orf2#LINE/    795 AAAGACAAAT--AACCCAATTWAAAAATGGGCAAA------GGATTTGAA 836

  chrX_112648561_   3658 TATATGTTTCTCCAAAGAAGACATACAAATGGCTAACAGGTATATGAAAA 3707
                           v ii               i           i  i i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_112648561_   3708 AAGATGCTCAAGATAATTAATTAT 3731
                         --         v  v ????????
  L1M4_orf2#LINE/    887 --GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (123 / 80)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.56 (46 / 18)  


3366 24.67 1.67 0.33  chrX_112672827_112675678.rev     1466  2361 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112672827_   1466 TGGAAAGATATTCCATGTTCATGGGTTAGAAGAATCAATGTTGTTAAAAT 1515
                                    i            i  i     v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112672827_   1516 GTTTATACAGCCCAAAAGAATCTACAGATCCAATGCAATCTCTATCAAAA 1565
                          viv    vv      vvi          i   i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112672827_   1566 T---AA-TG--TTCTTCACAAAAATAGAAAAAGCAATCCTATAATTTATG 1609
                          --- i-  --  i  ii  i    v  v  ivii      v    i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_112672827_   1610 TGGAGCCACAAAAGACCCAAAATAGCCAAAGCTATCCTAAGCAAGAAGAA 1659
                             ivii   ii      i          i v   i i iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_112672827_   1660 CTAAACTGGAGGAATCACATTACCTGGCTTCAAATTATATTATAAAGCTA 1709
                          v  ii       v     i v  iiii      viv  i  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_112672827_   1710 CAGTAACCGAAACAACATGGTACTGGCATAAAAACAGACACAGGGACCAA 1759
                               i i i   iii              ii i     i vi  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_112672827_   1760 GGAAATAGAACAGAGAACTCCAAAATAGATTCATGCATTTATAGTCAGCT 1809
                         v i       iv    iii vi     i ii   i       i    ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_112672827_   1810 CATTTTTCACAAAAGCGCCAAAAACATACACTGAGGAAAGAACAGCATCT 1859
                         v     iv    ii i     i v   v  v  i        i  iv i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_112672827_   1860 TCAATAAATTGTGTAGAAAAAACTGGATATCCACATGCAGAAGGATGAAG 1909
                             i    v   iv ii v         ?         i   i      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_112672827_   1910 CTGAATCCC-ATCTCTCATCATATACAAAAATCAAATAAAAA---AT-AA 1954
                         i  i i   - i   v  i             i  v v    ---  - ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_112672827_   1955 AGACTGAAATGTAAGACCCCAAATTATAAAACTATTAGAAGAAAACAT-T 2003
                             iv          v iv   i         v              -v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_112672827_   2004 GAACAAACACTCCTGCACATTGGCCTGGGCAAAGATTTCTTGAGTAAGAC 2053
                          ?ii   ivi  v  -  v    vi i     v i      iii  v   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_112672827_   2054 ATTAAAAGCACAGGCAATCAAAGCACAAATGGATAAATGATATCACACCA 2103
                          ii         i    iv    v v    i       viv iiv  i  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_112672827_   2104 AGATAAAAAGCTACTTCACAGCAAAGGAAACAATTAACAAAGTGAAAAGA 2153
                          i  v    i  vi vii vv       v  v  i  v            
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_112672827_   2154 GAATCTACAGAATGGGAGAAAACATTTGCTAACTACTA-ATCTGAGACGG 2202
                         v  i i                i      v  ii -  -      v v  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGATAAGG 748

  chrX_112672827_   2203 GATTAATAACTAGAATATATAAGGAGCTCAAACAACACAATAAGAATAAA 2252
                           i vi  v i           i  i   vv     v      v  -   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AAA 797

  chrX_112672827_   2253 ACCAAATAATCCAACTTAAAAATTTGCAAAAAATATGAATAAACATTTCT 2302
                         iv       i    i ?      vv     ii  v      i        
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_112672827_   2303 CAAAAGGAGACATGCAAATGCCCAACAGGTATATAAAAAAC--CTCAACA 2350
                          v    i   i  i      v    i i i i  i    iv--       
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_112672827_   2351 TCACTAATCCC 2361
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.82 (140 / 77)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


3710 18.24 6.71 0.47  chrX_112688737_112690872.rev      798  1647 (489)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_112688737_    798 AAACATCTTGTGTTTATGAATAAGAAGGCTTAATATTAGTAAGATACCAA 847
                          i i   iii    i   i  vi    i         iv      iv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_112688737_    848 TAACCCTCAAAGTGATCTGTAGATTGAATGCAATTCTTATCGAAATTACA 897
                           vi  i    v      ii     v  i     i i    i    iv  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_112688737_    898 GCTGGCTTTTT-GCAGAAGTTGACAAGCTGATTCTAAAAGTCA---AAAA 943
                             v      -      i             i      v   ---ii  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_112688737_    944 ATTCAAGTGATCCAGAATA-CCAAAGACAACCTTGAAAAGACATAACAAA 992
                           v    v  i        -     -    i        iiv v      
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGAACAAA 204

  chrX_112688737_    993 ATTGAAAAACTCACACTTCCTGATTTCAAAACTTACTACAAAGTCACAGT 1042
                         i   i ii            ii                     ii     
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_112688737_   1043 AATCAACAC--TGTGCTACTGGCATAAAGATAGACCCATAGACCAATGGA 1090
                               v  --    v           i       vi     i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_112688737_   1091 ATAGA-------GTCTAGAAATGGAC------ATTTATG-----TT---T 1119
                              -------   i      ii  ------       -----  --- 
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_112688737_   1120 TTCTACCAGGGTATCAAGAAAATACAATGAATAAAGAATAGTCTTTTTAA 1169
                            v  v     ii     vv  v     iiv               i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_112688737_   1170 AGAACGGAGCTGGGA-AAC--GATCTCCACATACAAACAAAGGAAGTTGG 1216
                         vi  i  v       -   --   v?      i    vi  v        
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_112688737_   1217 ATACCTCCACCT---ACCATATCCAAAAATTAACTCAAACTAGATTGAAG 1263
                          --  i i    ---       v                v i   ii?  
  L1M4_orf2#LINE/    455 A--CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_112688737_   1264 ACTTAAATGTAAAAGCTAAATTTATAAGCTTCTTAGAAGAAAATATAGGT 1313
                           i         i       vi     ivi             i     ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_112688737_   1314 GTAAATGTTTGTGACCTTAGATTAGGCAATGATTTCTTACATATGACACC 1363
                               v  i        i i          i       v          
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_112688737_   1364 TAAAAACATA--CAATCAAA----AAATA-ATAAATTGGACGGTAGTAAA 1406
                         -    i  i --   iv   ----     -           vvi vi   
  L1M4_orf2#LINE/    603 -AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_112688737_   1407 ATTAAAAGTGTTTGTGCATCAAAGGACATTCTCAAAGAAGTGAAAAGACA 1456
                                iiv       v          i v    ii             
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_112688737_   1457 AACTACTGAATTATAGAAAACATTTGCAAATTATATGTTTAATAAGGGTC 1506
                          v i  v    viv      i          i    i i i       v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_112688737_   1507 AAATATTCAGAATCTATAAAGAATTCTTACAAATCAATAA----AAG-CA 1551
                         vvi   i      v         i        v       ----   -  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_112688737_   1552 AATAACC-AACTCAAAA-TAA-TAATATATTTGAATAAACATTTATACAA 1598
                                -  i ?    - ii-i  viv         i      v v   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_112688737_   1599 A-----TA---AAATGGTCCATATGTACATGAAAAGATGCTCGACATAAT 1640
                          -----  ---      i v   v i                i    v ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_112688737_   1641 TATAAAT 1647
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.70 (95 / 56)
Gap_init rate = 0.03 (24 / 903), avg. gap size = 2.54 (61 / 24)  


 709 24.61 11.72 0.78  chrX_112726920_112729373.rev      502   757 (1697)    L1M4_orf2#LINE/L1      252   535 (373)  

  chrX_112726920_    502 AATAATTGAGACACTGTGGTTTTAGTGAAAGATTAGACACATAGATCAAT 551
                          i    ii     v      vi i iiv   iv      i          
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_112726920_    552 GCCACAAAATAAAAAGTTCAGAAATAGACATATATGTATATGACCTATTG 601
                          vv i i   vi i   i        i  vi   ii v    ii v    
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_112726920_    602 ATTTTTGACAAAGATGCAAGGGCAATTTCAATGGAGAGAGGATAGTCTTT 651
                              i     i i   v i i v   -      i  i  i         
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAGTCTTT 400

  chrX_112726920_    652 TTATCCAAAT---------ACAAAAGGAAA---------AAAAGAATCAT 683
                          i -v     ---------    vv   v ---------        v v
  L1M4_orf2#LINE/    401 TCA-ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_112726920_    684 AATCAAC----ACTTCACCCTTTATACAAAAACTCACTCAAA-TGGACCA 728
                         iv vi  ----  i    v iv          i v       -    i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_112726920_    729 CAGAC-TAAAT-CA-----TAAATTTATAAAACTTT 757
                         ?    -     -i -----    vi         i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

Transitions / transversions = 1.58 (38 / 24)
Gap_init rate = 0.03 (9 / 284), avg. gap size = 3.56 (32 / 9)  

 497 24.84 3.11 0.62  chrX_112726920_112729373.rev     1288  1448 (1006)    L1M4_orf2#LINE/L1      527   691 (217)  

  chrX_112726920_   1288 TACAACTTTTAGAAGAAACAAAAGGAGGAAATCTTTGTGACCCTGGGTTA 1337
                           v    i          vv v   ? v       i      i       
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_112726920_   1338 GATAAACATTTATTGAGTATGACATTAAAAGCATGACCCATTAAAGAAAA 1387
                          ii  vvi   v  iii       ii       ii v v iv        
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_112726920_   1388 AA---ATTGA-TGTATTTAATCAAAATTTAAAA-TTTTGCTCTGTGAAAG 1432
                           ---  vi -  v i  v         v    -     iv  vii  i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_112726920_   1433 ACAATATAAAGACAAG 1448
                            v   v    -   
  L1M4_orf2#LINE/    677 ACACTATCAAGA-AAG 691

Transitions / transversions = 1.05 (20 / 19)
Gap_init rate = 0.02 (4 / 165), avg. gap size = 1.50 (6 / 4)  

 526 19.58 13.76 0.00  chrX_112726920_112729373.rev     1775  1963 (491)    L1M4_orf2#LINE/L1      694   908 (0)  

  chrX_112726920_   1775 AAAAGAAAAGCTGTAGACAGAGA-AAAATATTTGCAAGTCA--------- 1814
                               v  v iii   vv i  -             i   ---------
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_112726920_   1815 -------CTTTTATCC-TAATATTTAAAGGTCACTCAAAACTTAACTATA 1856
                         -------   v     -v     v     iv v  i v    i  iv   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_112726920_   1857 GAAA---AAA-AACCCAATGAAAAAATAGACAA----TATGAACTGACAC 1898
                         i   ---   -        v?      i i   ---- v    iv    i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_112726920_   1899 TTCACAAAAGAAGATATTTTAATGGCAAATAAGCACATGAAAAGATGTTC 1948
                            v v           viv      v                    i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_112726920_   1949 AAAATCATTAGTCAT 1963
                           v    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 0.80 (16 / 20)
Gap_init rate = 0.03 (6 / 215), avg. gap size = 4.33 (26 / 6)  


2944 27.54 1.56 0.33  chrX_112741293_112747963.rev     5284  6180 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112741293_   5284 TGGAAAAACATTCCATGATCATGGATAGGAAGAATCAGTACTGTGAAAAT 5333
                               i i  i     v        v      v i i  i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112741293_   5334 GGCCATACTGCCAAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5383
                            v     v  v   v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112741293_   5384 TACCATTGACTTTCTTCACAGAG-TTGGAAAAAACTGCTT-TAAATTTCA 5431
                          v   vivi i  i  ii    i-   -- v  i   v i-    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_112741293_   5432 TATGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAA-AAG 5480
                                viiv  ii  v  v v        i      i i iv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_112741293_   5481 AACAAA-CTAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGTC 5529
                               -i i    vv   ii  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_112741293_   5530 TACAGTAACCAAAACAGCATGGTACTGGTAACAAAACAGACATATAGACC 5579
                                 i   i    ii         i vv ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_112741293_   5580 AATGGAACAGAACAGAGGCCTCAGAAAGAACTCCACACATCTACAACCAT 5629
                                i    iv   ivii      v  vi   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_112741293_   5630 CTGATCTTCAACAAACCTGACAAAAACAAGCAACAAGGAAAGGATTCCCT 5679
                         i    i   i    ivv  v   i v  vv   iii      i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_112741293_   5680 ATTTAATAAATGGTCTTGGGAAAACTGGCTAGCCATATGCAGAAAGCTGA 5729
                         v  i  i       vi     v      v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_112741293_   5730 AACTGGATCCCTTCCTTACACCTTATACAAAAATGAACACAAGATGGATT 5779
                          ii    i    v   i     v           v   v   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_112741293_   5780 ATAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5829
                          ?    i    ii     v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_112741293_   5830 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 5878
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_112741293_   5879 ACACCAACAGCAATGGCAACAAA-TCCAAAATTGACAAATGGAATCTAAT 5927
                                v    vvi        -vvv     v  i    v i ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_112741293_   5928 TAAGCTAAAGAGCTTATGCACAGCAAAAGAAACTGTTATCAGAGTGAACG 5977
                         i  iv v  i i   v  ii vv    i  v   i i vv i      vi
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_112741293_   5978 GGCAACCTACCGAATGGGAGAACATTTTTGTAATCTATCCATCTGACAAA 6027
                          i     i  v           v  v    i  vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_112741293_   6028 GAGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTAC-----AAGA 6069
                          ii  vi          v  i        --  -  i i v-----  i 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_112741293_   6070 GAAAAACAACCCCATCAAAAAGTCGGCAAAGGATACGAACAGAAAGTTCT 6119
                           v   i     v  i?    i v          vi   i   v v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_112741293_   6120 CAAAAGAACACATTTATGTGGCCAATAAACATATGAAAAAAAGCTCATCA 6169
                          v      v i  vi vi          i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_112741293_   6170 TCAGTGGTCAT 6180
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


 542 27.09 9.03 3.68  chrX_112762817_112765082.rev       66   364 (1902)    L1M4_orf2#LINE/L1      248   562 (346)  

  chrX_112762817_     66 CTACAATAATTAGGACATTGTGGGATTGGCATAAATGTAGACATGAGGAC 115
                              i    i i    v     v i        ivi       ivi  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_112762817_    116 TAAAGGAAAATAATAGAATGTC-AGAAATAAATACATACATATAT---TA 161
                         i  v    v v   v  iv   -         iv       v   ---i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_112762817_    162 ACTGATTT----CAAA--T-TCAA-----TTCAATGGGTAAAGAA-AATG 198
                          i      ----   i-- -i   -----         v      - i v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_112762817_    199 TTTCACAACAAATTGTGCTGCAAGAA---GATATTCGCATG---AAAAAC 242
                            i-        v      vi v  ---    ?i i    ---  i  i
  L1M4_orf2#LINE/    398 TTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_112762817_    243 AAAG---GAACTCTATCTTCTGCTATGTACCAAAAAGTA-TTTAGATGTT 288
                         i   ---  v i   i  ivii i  i   -     v  -i i i ----
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATAC-AAAAATTAACTCAAA---- 491

  chrX_112762817_    289 TGTTATTTATTATGCACCTAAATATACCAATCTAATATTTTAATGATTTT 338
                         ----  vv  i ?iv        i  vv i-    v i v   viv i  
  L1M4_orf2#LINE/    492 ----ATGGATCAWAGACCTAAATGTAAGAG-CTAAAACTATAAAACTCTT 536

  chrX_112762817_    339 AGATTAGAATGTAGGAAAAAAATTTC 364
                            vv i  ii    ?iv   vi   
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTC 562

Transitions / transversions = 1.44 (46 / 32)
Gap_init rate = 0.05 (15 / 315), avg. gap size = 2.53 (38 / 15)  

2240 27.53 6.39 0.93  chrX_112762817_112765082.rev      915  1775 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112762817_    915 TGGAGATACATAACATGTCCATGGAATGAAAGACTTAACGTAACAAAGAT 964
                             i v i  vv     i      v  i         ii viiv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112762817_    965 GATAATTATCCCCAAAGTGATATATAGACTTAATGCAATGCCTATTAAAA 1014
                          ii   vv        v    v  i   i i  i     v     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112762817_   1015 TTCTATCAAGAGTTTGGGTAGATACTGACAAGCTTAAACTAAAATTTATA 1064
                          i i v vivvv   vv i   v i         v vv        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_112762817_   1065 TAAAAAGGCAAAATAGCTAGCACAGCTAAAACAATTTTCTAAAAAAAGAA 1114
                          ii   v    iiv v i  v i   i        i  vv    i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_112762817_   1115 TAAAACTGGATGAATCA---TTC--GATCTGA-----TGCTA-ATAGC-- 1151
                         i   ii    v  v   ---   --i  i v ----- i   - v   --
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_112762817_   1152 -----ATCAAGAGAGTGTATTATTGACAGAGAGACAGATACATAGATCAA 1196
                         -----       v     iv  i  i  v ii  i   i i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_112762817_   1197 TGCAACAGAATTGAGAGACCAGAAACAGACCCACACAAATACC-CCAGCT 1245
                           v  i           v       i i     i   vv  iv-i  ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_112762817_   1246 GATTTTTGACGAAGGTATAAAAACAATTCAGAAGAGGAAAGGCC-GTCTT 1294
                               i   i i   iiv  i  v     - v i      ivi-     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCA-ATGGGGAAAGAATAGTCTT 399

  chrX_112762817_   1295 TTCAACAAATACTTGTGGAGTAA-TAGA----------CAAAATA-TGAA 1332
                                   iv vv   iii  - i  ----------     v -    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_112762817_   1333 CTTCAGCCTAAAGCTCTCACATTATACACAAATTATTTGAAAATAGGTTA 1382
                         v  vii  ivv v   v   vv      v      vi v     i i i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_112762817_   1383 TGAGTTTAAATGTAAAATGTAAATCTATCAAACATTTAGAAGAATTCTTA 1432
                         ?iiiii         i vv    v    v    vi         vv v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_112762817_   1433 GAAGAAAATCTTTGGAACTGGAGGCCAAGTGATGAGTCCTTACCCATGAC 1482
                          i? v       i vi  ivvi  ii i ii   iv i    vvi     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_112762817_   1483 ACCAAAAGCATGATCCTTCAAAAGGAAAAAT-GATAAATTTCACTCTATC 1531
                                   ii v vv-      i      -        vv   ii   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAA-CAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_112762817_   1532 AAAATTTAAAAGTTTTG--CTTTGAGAAAGGCTGTTAAGAGAATAAAAAG 1579
                               v    v     --   ii iii vi  i i    i i i     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_112762817_   1580 ACAGGCTCCAGATTTGTGAGAAA-TAT---CA---CACACA----ACAAA 1618
                            iv iv    v v -      -   ---  ---  i i ---- i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGG-GAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_112762817_   1619 GAACCTGTATCTAGAATGAATAAATGATGCTCAAAATTAAAAAATATCCC 1668
                          i  i      i     iv     vi iv  i v  i v  v    ----
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA---- 793

  chrX_112762817_   1669 AAAAGAT-------TGAATTAGAAAATATGCAAAAGATATGAAGAGACAT 1711
                               i-------iv    ?i     iv     i   v    v      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_112762817_   1712 TTGACTAAAGA-GATATATGGAATG-CAAATAAGCATGTGAAAAGATGTT 1759
                           vv i     -      ii-    - v        ii          i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACA-AATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_112762817_   1760 CAATATCACCTATAAA 1775
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (135 / 99)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.62 (63 / 24)  


2949 27.18 2.13 0.56  chrX_112778970_112784067.rev     3714  4607 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112778970_   3714 TGGAGAAACATTCCATGCTCATGGATAGGAAGAATCAGTATTATGAA-AT 3762
                             i i i  i     i        v      v i i    i v  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112778970_   3763 GGCCATACTGCCAAAAGTGATTTATAGATTCAATGCTATCCCCATCAATT 3812
                            v     v  v   v    i  i        i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112778970_   3813 TACCA-TTGTATTTCTTCACAGAATTAGAAAAATCTACTTTAAATGTCAT 3861
                          v   -i  iv   i  -i     v v  v  iiiv iii    vv    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_112778970_   3862 ATGGAACCAAAAAAGAGTCAGTATAGCCAAGACAATCCTAAGCAAAAAGA 3911
                               viiv  ii  vi   v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_112778970_   3912 ACAAAGCTGTAGGCATCATGCTACCTGACTTCAAACTATGCTACCAGGCT 3961
                               i  v   vv   ii  v  ii i      viv i    v i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_112778970_   3962 ATGGTAACCAAAACAGCATGGTACTCGTACCAGAACAGATATCTAGACCA 4011
                          ii    i   i    ii       v i iv  i i   i  v    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_112778970_   4012 ATGGAAAAGAACATAGGCCTCAGAAATAATGCCACACATCTACAACCATC 4061
                               v    ivv  ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_112778970_   4062 TGATCTTTGACAAACCTGATAAAAACAAGCAATGGGGAAAGGATTCCCTA 4111
                             i  i     ivv  vi  i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_112778970_   4112 CTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATACAGAAAATTGAA 4161
                         i i  i        i     v      v  ?   i  i  i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_112778970_   4162 ACTGGACCCCTTCCTTACAACTTACACAAAAATTAACTCAAGATGGATTA 4211
                         ii         v   i   v v  i                i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_112778970_   4212 AAGACTTATATGTGAGACCTAAAAC---------CCTAGAAGAAAACCTA 4252
                         ?    i  v    i   v       --------- i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_112778970_   4253 GGCAGTA--CCATTCAGGACATAGGCATTGACAAAGAGTTCATGACTAAA 4300
                           ?-   --i -   iv   v v  vv v i   v iv   v iiv  vi
  L1M4_orf2#LINE/    550 GGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_112778970_   4301 ACACCAAAAGCA-ATGTCAACAAAAGCCAAAATTGACAAATGGAATCTAA 4349
                                     - v -         vv     v  i    v i ii v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_112778970_   4350 TTAAACTAAAGAGCTTCTACACAGCAAAAGAAACTATCGTCAGAGTGAAC 4399
                          i   v v  i i   i iii vv    i  v      ivv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_112778970_   4400 AGGCAACTTACAGAATGGGAGAAAAGTTTTACAATCTATTCATCTGACAA 4449
                           i    ii                vv   i   vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_112778970_   4450 AGGGCTAATATCCAGAATCTACAAAGAACTGAAACAAATTTACAAGAAAA 4499
                         i  i  vi          v  i        vvv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_112778970_   4500 A---AAA-AACCCA-TCAAAGAATGGGTGAAGGATATGAACAGACACTTC 4544
                          ---   -      - i?  i      ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_112778970_   4545 CTCAGAAACAGATATTTATGTGGCCAACAAACATATGAAAAAAAGCTCAT 4594
                         ii  i i -      vi vi       i  i  i       i v     v
  L1M4_orf2#LINE/    847 TCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_112778970_   4595 CATCACTGGTCAT 4607
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


2985 27.92 0.99 0.77  chrX_112868481_112876945      492  1397 (7068)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_112868481_   1397 TGGAAAACCATTTCATGCTCCTGGATAGGAAGAATCAATATTGTGAAAAT 1348
                               ivi  ii    i  v     v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_112868481_   1347 GGCCAAT-CTACTCAAAGTCATTTATAGATTCTATGCTATTCCCATCAAG 1299
                            -   -  v i    v v  i  i      v i  v  i  i     i
  L1M4_orf2#LINE/     51 GGC-AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

C chrX_112868481_   1298 CTACCATTGACTTTCTTCACAGAATTAGAGAAAACT-ACTTTATATGTCA 1250
                         v v   vivi i  i  ii     v v  v  i-  - iii  v vv   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

C chrX_112868481_   1249 TATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCC-AAGCAAAAAG 1201
                                viiv  ii  v  v v        i      i-i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_112868481_   1200 AACAAAGCTGGAAGCATCATGCTACCTGACTTCACACTATACTACAAGGT 1151
                                i    i vv   ii  v  ii i    v viv        i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_112868481_   1150 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAAATAGATATGTAGAC 1101
                           i     i   i    ii         i i-  ii     i  i    i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGAT 297

C chrX_112868481_   1100 CAATGGAACAGAACAGAG-GTCTCAGGAAGAATGCCACACATCTACAACC 1052
                                 i    iv   -   -   i  v  vv   i    i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTC 346

C chrX_112868481_   1051 ATTTGATCTTTGGCAAACCCGACAGAAACAAGCAATGGAGAAAGGATTCC 1002
                          v     i  i i   ivvi v  ii v  vv      i     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_112868481_   1001 CTATTTAATCATTGGTGTTGGGCAAACTGGCTAGCCATATGTAGAAAACT 952
                           v  i  iv v     i    vv      v  ?   i   i i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_112868481_    951 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTTGAGATAGA 902
                            ii         v   i     v                ii i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_112868481_    901 TTAAAGTCTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 852
                          i ?  v i    ii     v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_112868481_    851 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 802
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_112868481_    801 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 752
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_112868481_    751 TTAAACTAAAAAGTTTCTGCACAGCAAAAGAAACTATCATCAGAATGAAC 702
                          i   v v    ii  i  ii vv    i  v       vv i i    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_112868481_    701 AGGCAACCTATAGAATAGGAGAACATTTTTGCCATCTATCCATCTGACAA 652
                           i     i i     i      v  v     v vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chrX_112868481_    651 AGGGCTAATATCCAGAATCTACAAAGAATTTAAACAAATGTACAAGAA-- 604
                         i  i  vi          v  i      i ivv    v ---   v  --
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATA 793

C chrX_112868481_    603 AAAAAACAAACAACCCCATCAAAAAGTGTGTGAAGGATATGAACAGACAT 554
                             i     i     v  i?    i  v ii      v    i      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

C chrX_112868481_    553 TTCTC---AGAAGACATTTATGTTGCCAACAAACGTATGAAAAAAAGCTC 507
                              ---      i  vi vi v     i  i ii       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

C chrX_112868481_    506 ATCATCACTGGTCAT 492
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (145 / 104)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  

4212 17.95 2.42 2.42  chrX_112868481_112876945     7065  7972 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112868481_   7065 TAGAAACACATTGCATGTTCATTGATTAGAATACTTAATATTGTTCAGAT 7114
                          i    v i  iv         v    i   v             v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112868481_   7115 GGCAATACTTCCCAA-TCAGTCCACAGATTCAACAGAATCCCCAT-AAAA 7162
                                  i     - iii  i           iv      i  -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112868481_   7163 TCATAGCTGGATTTTT-GCATAAATGGATAAACTGATCCTAAGATTCATA 7211
                           vi     vv     -   v    v  i  i          i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_112868481_   7212 TGGATATTTAAAGGATCAAGAAAAGCCAAGCTAATATTGGAAAGAAAGAA 7261
                             v  vi  i   i v    v      ivi   v   i   ii     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_112868481_   7262 TAAAGTTGAAGAATTCTTGCTTCTGAATTTCAAAATTTGCCACAAAACTA 7311
                         i       i  i i  vii    iv          i  i i     i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_112868481_   7312 CAGTAATAAAGAAAATGTAGTGCTGGCATCAGTTTAGACATATAATTCAA 7361
                                v    v i   i  i       v  vv          iv    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_112868481_   7362 TGGAATAAAATTGAGCATACAGAAATAA--TTGTGCATTTATGCACAACT 7409
                                i       vi v         --iii i        vv   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_112868481_   7410 GATGCTTGACAAAGGTGCCAAGAAAATTCAATGGGAAAAGAATAGTCTTT 7459
                            vi i     i          vv          i              
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_112868481_   7460 TCAACAATTGGTGCTGGGACAATTGGATATTCATATGTGAAAGAATGAAA 7509
                                v              i      ?i  i   ii          i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_112868481_   7510 TTAAACTTACTCTTTACC--ACACCACACACTAAAATTTACTCAAAATGG 7557
                           ii  ----- ii    --      i i  v      v           
  L1M4_orf2#LINE/    451 TTGGAC-----CCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_112868481_   7558 ATCACTGATCTAAACGTAGTAGCTAAAAATAATTTTTAAAAAAACTTTTA 7607
                             ?v  i     i   iv        v  -----     ---  i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTA-----TAAAA---CTCTTA 537

  chrX_112868481_   7608 AAAGAAAACATTGGCATAAATTTTTGTGACCTCGAGTTAGGCAAAGCACA 7657
                         i          v  ?i     i  i       i i         ------
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA------ 581

  chrX_112868481_   7658 AGTGACATCT-AGATATGACAACAAAACTTCAAATGACAAAAAAAAA--- 7703
                         --  iiv   -          v     viv   iii      i    ---
  L1M4_orf2#LINE/    582 --TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_112868481_   7704 -GACAAATTGAACTTCATCAAAA------ACTTTTGTGCTTCAAAGGATA 7746
                         -  i      i            ------                   i 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_112868481_   7747 CTATCAAGAATGTGAAAAGTCCACCC-CAAAATGGAAGCAAATATTTGTA 7795
                                   v        v v    -  i     i  v         i 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_112868481_   7796 AATTACATATCTGATAAGGGACTTGTATGTAGAATATAAGAGAAACTCAT 7845
                            i i                      vi        vi ii     v 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_112868481_   7846 GT--CTCAATATTGTAAAGACAAATAAGCCAACTTTAAAAATGG-CAAGA 7892
                         ii--       v iv            v    -  ?        -   ii
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAA-TTWAAAAATGGGCAAAG 828

  chrX_112868481_   7893 AATCAGAATAGATATTTATCTGAAGAAAATATACAAATTGCCAATAAGCA 7942
                         i  iv       i    v  ii     i          v           
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_112868481_   7943 CATGAAAAGATGTTCAACACCATTAGTCAT 7972
                                     i      i  ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (103 / 56)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.75 (44 / 16)  


2760 26.87 2.09 2.09  chrX_112907049_112913130.rev     4684  5591 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_112907049_   4684 TAGAAAAACCTTCCATGCTCATGGATAGGAAGAATGGATATCGTGAAAAA 4733
                          i    i iv i     i        v      v vi    i  v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_112907049_   4734 GATTATACTGCCCAAAGTAATTTATAGATTCAATGCTATTTCCATTAAAC 4783
                          iiv     v      v i  i  i        i  v  ii i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_112907049_   4784 TACCC--CTG--------ACAGAA-TAGAAAAATAACT-ACTTTAAAATT 4821
                          -   --   --------i     - v  v  i---  - iii       
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chrX_112907049_   4822 CATATGGAACTAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGGGGAA 4871
                                  v iv  ii  v  viv        i      i i ------
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------ 190

  chrX_112907049_   4872 AAAAAAAAAAAAAAAAAGCTGGAGGCATCACACTACCTGGCTT-AAAGCT 4920
                         ---    i  i  v    i      vv       v  iiii  -   i  
  L1M4_orf2#LINE/    191 ---AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_112907049_   4921 ATACTACAAGGCTACTGTAACCAAAACAACATGGTACTGGTACAAAAACA 4970
                         -        i     v    i   i   iii         i i  ii i 
  L1M4_orf2#LINE/    238 -TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_112907049_   4971 GACACATAGACCAATGGAACAGAATAGAGATCTCAGAAATAAGACTGCAC 5020
                             i     i        i     v    vii         iv iii  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_112907049_   5021 ACCTACAACCATCTGATCTTC---AAACCTGACAAAAACAAGCAATGGGG 5067
                          ii  iiii  vi    i   ---  ivv  v   i v  vv        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_112907049_   5068 AAAGGATTCTCTATTTAATAAATAGTGCTGGGAAAACTGGCTAGCCATAT 5117
                             i  vv   v  i  i    i         v      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_112907049_   5118 GCAGCAAATTGAAACTGGGCCCCTTCTGTACATCTTCTACAAAAATTAAC 5167
                            iv i v    ii   i     v ivi   i v v             
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_112907049_   5168 TCAAGATGGATTAAAGACTTAAATGTAAAACCTAAAACTATAAAAATCCT 5217
                             i      i ?    i         i v              v  i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_112907049_   5218 AGAAGAAAATGTTGGCA-ATACCATTCAGGACATAGGCATGAGCGAAGAT 5266
                                  ii v  ?i- v i -   iv   v v  vv ii  i v i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_112907049_   5267 TTCAT-GATAAAAACATCAAAAGCAATTGCAGGAAAGGCAAAAGTTTGCA 5315
                            v -    vi -  i        vvv   iv   i v    i vvii 
  L1M4_orf2#LINE/    586 TTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_112907049_   5316 AATGGGATCTAATTAAGCTAAAGAGCCTCTGCACAGCAAAAGGAACCATC 5365
                            v   ii v  i  iv v  i i i i  ii vv    i iv  i   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_112907049_   5366 ATCAGAGCGAACAGACAACTTACAGAATTGGAGGAAATTTTTGCAATCTA 5415
                          vv i  i   v       ii       v    i    v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_112907049_   5416 TACATCTGACAGAGGTTTACTATCCATCATCTACAAGGAACTTATACAAA 5465
                           i      i ii  vi vv      vv  v  i  i     iv     v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_112907049_   5466 TTTACAGGAAAAAAAAACAAACAACCCCATTAAAAAGTGGCCAAAAGACA 5515
                          iv i -- v     i     i     v   ?    i   v    i  iv
  L1M4_orf2#LINE/    785 TCAATA--ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_112907049_   5516 TGAAGAGA-ACTTCTCAAAAGAAGACATTTATACAGCAAACAAGCATATG 5564
                             v   - i     v        i  vi v ii  v  i     i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_112907049_   5565 AAAACAAAGCTCAACATCACTTATCAT 5591
                             -i v           ????????
  L1M4_orf2#LINE/    883 AAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  


 354 14.75 0.00 0.00  chrX_112972896_112976757.rev     2555  2615 (1247)    L1M4_orf2#LINE/L1        6    66 (842)  

  chrX_112972896_   2555 AGATATTCCATGTTCATGGATTGGAAAAATCATTATTGTTAAAATGTCCA 2604
                               i                   i v i v         i   v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_112972896_   2605 TACTACCCAAA 2615
                             v      
  L1M4_orf2#LINE/     56 TACTCCCCAAA 66

Transitions / transversions = 0.80 (4 / 5)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.00 (0 / 0)  

2678 26.92 2.39 0.53  chrX_112972896_112976757.rev     2618  3371 (491)    L1M4_orf2#LINE/L1      141   908 (0)  

  chrX_112972896_   2618 AAAATTTATACGGAACTATGAAAGATTCAGAATGACCGAAACAATCCTCA 2667
                               i   i    v iii ii  ii      ii  i        i v 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_112972896_   2668 GCTAAAAGAACAAAACTGGAAGTATCACATTACCTGACTTCAAATTATAC 2717
                         ivv i         ii    i vv     i v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_112972896_   2718 TACAAAGCTATAGTAACCAAAACATAATGGTACTGGCATAAAAACAGACA 2767
                                   i     i   i   vvi              ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_112972896_   2768 CATAGACCGATGGAACAGAATATAGAACCCAGAAACAAATCTATGCATTT 2817
                         i     i i      i     vv   ii       i   i i  i     
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_112972896_   2818 ATAGTCAATTTGTTTTTCATAAAAGGACCAATGAC-ATACAATGGGGAAA 2866
                           i       vi    iv i  ii vi    -   -  v           
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAA 389

  chrX_112972896_   2867 GGACAGTGTCTTCAATACATGGTGTTGGGAAAATTAGATATCCATATGCA 2916
                          i i   v i     i v      i     v  i i    ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_112972896_   2917 GAAAAATGAAATTAGATCCCAATCTCTTGATACATAAAAAAGTCAAATCA 2966
                         i  i      i  i  i   v i   viivi i   v    i i  v   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_112972896_   2967 AAATTGATTAAACACTTACATCTAAGACCTGGAGCTATGAAACTACTAGA 3016
                             v   i ? v  i  v  v     v  ii i    i     vi    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_112972896_   3017 ACAAAACATTGGGGAAGCACTCCAGGACATTGGGCTAGGCCAAGATTTCT 3066
                          v       v  ? v ivv  i iv   v     i     v v i     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_112972896_   3067 TGAGTAAGACCTCAAAAGCACAGGTAAACAAAGTAGAAATGGACAAACAG 3116
                          iii  v   vi          i i  vv    v i    i  i   iv 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_112972896_   3117 GATTATATCAAGCTAAAAAGCTTCCGCATAAGAAAGGAAACAGTCAACCA 3166
                           i vi     iv v    i   ii iiivvv      v  vi    vv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_112972896_   3167 AGTGAACGGACAACGCACAGAATTGCAGAAAATATTAATAAACTACCCAT 3216
                               vi      v        v v          vii   ii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_112972896_   3217 TTGACAAGGGCTTTATGACCAGAATATACAAGGAGCTCAAACAACTCAAT 3266
                         i   i     vi  i iv          i  i  i   vv          
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_112972896_   3267 AGGAAAAGAAACCCAAATAATCCCATTTAAAAATGGGCAAAATATTTGAA 3316
                          iv    ii ---       i  v   ?             iv       
  L1M4_orf2#LINE/    790 AATAAAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_112972896_   3317 TAGATATTCTTTGAAAGATGACATATA-----------------TGAAAA 3349
                             i   ii iv     v  i   i -----------------      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_112972896_   3350 AATTCTTAACATCATTAATTAT 3371
                         i  v  i       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (127 / 72)
Gap_init rate = 0.01 (4 / 768), avg. gap size = 5.50 (22 / 4)  

 490 21.26 2.36 5.51  chrX_112972896_112976757.rev     3468  3594 (268)  C L1M4_orf2#LINE/L1   (434)   474   352  

C chrX_112972896_   3594 ATTTTTCCCAAAGGGACCAATGAC-ATACAATGGGGAAAGGACAGTGTCT 3546
                              ivv   i  vi    -   -  v            i i   v i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCTTT 400

C chrX_112972896_   3545 TCAGTACATGGTGCTGGGAAAACTAGATATCCATATGCAGAAAAATGAAG 3496
                            ii v            v    i    ?   i     i  i       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

C chrX_112972896_   3495 CCCACCAAGGGCTCC--CCTTTCAACATAT 3468
                         ii------  i i  --   iv  v     
  L1M4_orf2#LINE/    451 TT------GGACCCCTACCTCACACCATAT 474

Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.03 (4 / 123), avg. gap size = 2.50 (10 / 4)  


2424 19.60 11.96 1.16  chrX_112980635_112982228.rev      502  1103 (491)    L1M4_orf2#LINE/L1      242   908 (0)  

  chrX_112980635_    502 ACAAAGCTGTAGTAATCAAGACAGTGTGTTACTGTCATAAAGGCAGACAT 551
                                 ii                  v     v     i ii      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_112980635_    552 ATAGACCAGTGGAATAGAATAGAGAGCTCAGAAATAAATTCTCACATACA 601
                              i  i           v     ii          ii vi    vi 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_112980635_    602 GGGTCAAATGATTTTTGACAAGATTACTGAGAC-ATTCAGTGGGGAAAGT 650
                         v      v       i      iv i ii    -     i         v
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_112980635_    651 ATAGTCCTTTTGACAAATGATGCTGGGAAAACTGGATAGGTAAATACAAA 700
                               i   ii       i        v         ?vi v  i    
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_112980635_    701 AGAATAAAGTCGGACTAGTATCTTACACTATATCCAAAAA--ACCTCAAA 748
                              i    i    ivv  i  i    i    v      -- v      
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_112980635_    749 ATTGATCAAACACCTAAATGTAGTAGATAAAACTATAAAACTCTTAGAAG 798
                           v     ? v           iv  v                       
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_112980635_    799 AAAACATAAG---------------------------------------- 808
                                 i ----------------------------------------
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_112980635_    809 -------------AAG----------AAAAGAAAAAACTGGGAAGTTGGA 835
                         -------------   ----------           iv iv  i     
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_112980635_    836 CTTTATCAAAATGTAAAACTTCCATGTTTCAAACGACACTATCAGCAGAG 885
                            i        vv       iii  i      v          iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_112980635_    886 TGAAAGAGCAGTCTGTGAAATGGAAGAAAATGTTTGCAAATCATATATTT 935
                              iii  ii iiiii     i       i                i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_112980635_    936 AATAAGGGATTAACATCCAACATATAAAAAAAAAAAACTCGTACAACTCA 985
                         i        i vii     iv     v   i  ----   v         
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAA----CTCTTACAACTCA 787

  chrX_112980635_    986 ACAACAAAAA------CAACCAGATCGAAAAGTGGGTAAAGGACTTGAAT 1029
                          i  i     ------i    vi  i?    i    i      i      
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_112980635_   1030 AAACATTCAACATCTGTACATCTTATACAGATGGCCAATAAACACAAGAA 1079
                          i     i-- -  iiv v vvv      i           i    v   
  L1M4_orf2#LINE/    838 AGACATTT--C-TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_112980635_   1080 AAGATTCGCAACATCACTAATCAT 1103
                              v v        ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (76 / 39)
Gap_init rate = 0.01 (8 / 667), avg. gap size = 9.88 (79 / 8)  


1512 17.47 1.71 0.34  chrX_113016354_113018691      223   514 (1824)  C L1M4_orf2#LINE/L1   (80)   828   533  

C chrX_113016354_    514 TTTTGAAAGAAAATGTAAGTGAAAATCTTCCTG-----GAATTTGGCAAT 470
                          i  ii       ii  i ? v        v  ----- ii  v      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

C chrX_113016354_    469 GGATTCTTAGAAATGACACCAAAAGTATAAGTAACAAAAGAAAAAAAATG 420
                           v        v             i i   i              v - 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-G 631

C chrX_113016354_    419 ATAAGTTAGAGTTTATCAAAATCAAAAACTTTTATGCTTCAAAGGACCCC 370
                             i  i  v  i        i          i             v i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

C chrX_113016354_    369 ATCAAAAATGTGAAAAGACCACCCACAGAATGGGAGAAAATGTTTGTCAG 320
                              i  v          v                     i    iv i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

C chrX_113016354_    319 TTATATATTTGATAAGGGATCTGTATCCAGAATATATAGTAAACTCTTAC 270
                          i      i          ii                 ivi         
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

C chrX_113016354_    269 AAATCAAAAACAAAAAGGCAGATGACCTGATTTACAAATGGTCAAAG 223
                           v    v  i      i  i  i   ii   ? v      v     
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 2.06 (33 / 16)
Gap_init rate = 0.01 (2 / 296), avg. gap size = 3.00 (6 / 2)  

3316 26.76 0.44 0.44  chrX_113016354_113018691      938  1845 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113016354_    938 TGGAAGAACATTCCATGCTCATGGATACGAAGAATCAATATCATGAAAAT 987
                              ii i  i     i        vv     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113016354_    988 GGCCATACTGCCCAAGGTACTTTATAGATTCAATGCCATCCCCGTGAAGC 1037
                            v     v     iv iv i  i        i  v     ii v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113016354_   1038 TACCAATGACTTTCTTCATAGAAATGGAAAAAACT-ACTTTAAACTTCAT 1086
                          v   iivi i  i  iii      v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_113016354_   1087 ATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAGA 1136
                               viiv  ii  v  v v  v     i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_113016354_   1137 ACAAAGCTGGAGGCATCACACTACCTGACTTCCAACTATACTACAAGGCT 1186
                               i      vv       v  ii i   v  viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_113016354_   1187 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAGTAGATATATAGATTA 1236
                                i   i    ii         i iv iii    i        i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_113016354_   1237 ATGGTACAGAAC--AGAGCCCTGAGAAATAACACCACACATCTACAACCA 1284
                             v i    i--    i  --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_113016354_   1285 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 1334
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_113016354_   1335 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 1384
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_113016354_   1385 AAACTGGATCCCTTCCTCACACCTTATACAAAAATTAATTCAAGATGGAT 1434
                           ii    i    v         v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_113016354_   1435 TAAAGACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1484
                         i ?    i     i v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_113016354_   1485 TAGGCA-ATACCATTCAGAACATAGGCATGGGCAAGGACTTTGTGACTAA 1533
                             ?i- v i -   ivi  v v  vv i     v ii  iv iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_113016354_   1534 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 1583
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_113016354_   1584 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1633
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_113016354_   1634 AGGCAACCTACAGAATGGGAGAACATTTTTGCAACCTACCCATCTGACAA 1683
                           i     i              v  v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_113016354_   1684 AGAGCTAATATCCAGAATCTACAAAGAATTTAAACAAATTTACAAGAAAA 1733
                         i ii  vi          v  i      i ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_113016354_   1734 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 1783
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_113016354_   1784 TCAAAAGAAGACATGTATGCAACCAACAGGCACATGAAAAAATGCTCATC 1833
                           v        i  ii viiii    i i           i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_113016354_   1834 ATCACTGGTCAT 1845
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2591 11.71 2.47 27.62  chrX_113057781_113060835.rev     1352  2564 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113057781_   1352 TGGAAAGACATTTCATGTTCATGTATCAGAAAACTTAGT-TTATTTACAT 1400
                                 i  ii          v  ii   i     i -  i  v v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113057781_   1401 AGCAATACTCCCCAAAATGATCTACAGATTCAGTGTGATCCCTACTAGAA 1450
                         i               v               ii ii       ii i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113057781_   1451 TCCTAGCAGCTAACTTTTTTATAGAAATTGACAAGCTGATCCTAAAATTT 1500
                            i   v  ---       ii                           i
  L1M4_orf2#LINE/    101 TCCCAGCTGC---CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_113057781_   1501 ATATGAGAACTTGAGGAACCCCAAATAACCAAAA-ACTCCTAAAAAAGAA 1549
                              ii  ivii   i    vi    i      - v  i i        
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_113057781_   1550 ---CCCAGTTGTCAGACTTACATTTCTCAATTTCAAGGCTTACTGCAAAG 1596
                         --- vv     vvi    i   i   i         ii      i     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_113057781_   1597 CAACTGTAATCAGGACACTATGGTACTAGCATTAAGGATAGACATATAGA 1646
                          v  v       i    v i       i    -                 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGA 296

  chrX_113057781_   1647 TTAATTGAATTTAATTTAGAGTCCCTAGGTAAATGTATGTATCAACTGAT 1696
                          i   v    vv    v       --------------------------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC-------------------------- 320

  chrX_113057781_   1697 TTTCTTTTTCTTTTTTCCTTTTTTTTTTTTTTTTTTTTTGAGACAGTCTG 1746
                         ----------------------------------------   -------
  L1M4_orf2#LINE/    321 ----------------------------------------AGA------- 323

  chrX_113057781_   1747 GCTCTGTGACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAA 1796
                         --------------------------------   ---------------
  L1M4_orf2#LINE/    324 --------------------------------AAT--------------- 326

  chrX_113057781_   1797 CCTCTGCCTCCTGGGTTCAAGCCATTCTCGTGCCTCAGCCTCCAGAATAG 1846
                         ------------------  i  ---------------------------
  L1M4_orf2#LINE/    327 ------------------AAACC--------------------------- 331

  chrX_113057781_   1847 CTGGGATTACAGGCGCTCGCCACCATACCCGGCTGAATTTTTTTTTTGTA 1896
                         -----------------------     --------------------- 
  L1M4_orf2#LINE/    332 -----------------------CATAC---------------------A 337

  chrX_113057781_   1897 TTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACT 1946
                            ---------    ----------------------------------
  L1M4_orf2#LINE/    338 TTT---------ATGG---------------------------------- 344

  chrX_113057781_   1947 CCTGACCTCAAATGATCCGCCTGCCTCGGCCTCCCAAAGTGCTGGGATTA 1996
                         -------    v    ----------------------------------
  L1M4_orf2#LINE/    345 -------TCAATTGAT---------------------------------- 353

  chrX_113057781_   1997 CAACTGTTTTAGCAAGT-TGCCAAGACCATTCAGTTGGGGGAAGAATAGT 2045
                         ------   iii    v-               i -    i         
  L1M4_orf2#LINE/    354 ------TTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGT 396

  chrX_113057781_   2046 CTCTTCAACAAATAGTGATGGGGCAACTAGAT--CCACTCATGCCAAA-A 2092
                           i          i   v    i     i   --    --    v   - 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC--ATGCAAAAGA 444

  chrX_113057781_   2093 AT--ACTTGGACACCTAACTCATACCATACACCAAATTTAACTCAAAATG 2140
                           -- v      v    v    i      i  v   v             
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_113057781_   2141 AATCAAAGACCTAAATGTAAGAGCTAAAGTGATAAAATTCTTAGAAGAAA 2190
                         i    ?                      iiv      i            
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_113057781_   2191 ACA--GGCATAAATTGT-GTGAACTTAGGTTAGGTGGTTGCTCATTAGAT 2237
                            --  ?i     iv -    v   i       iii v i iv      
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_113057781_   2238 ATGACACCAAAAGCACAAGCAATTACAGAAA-------TAAATT-----T 2275
                                               iv v     -------      ----- 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_113057781_   2276 AATTAAAATTTAAAAACTTTTATTTTTCAAAGAATGCAATCAAAAAAGTA 2325
                         v  i      -          i vi       i ii v     i     i
  L1M4_orf2#LINE/    645 CATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_113057781_   2326 AAAAGACAACCCACAGAAAAGGAGAAAACATTTGCAAATCATATACCCCT 2375
                                           vi        i                i ivv
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_113057781_   2376 TAAAGGTGTAGTATACAGAATATATAAAGAACTCCGTA-AACTCAATAA- 2423
                            i  vv v    v                   i-  -          -
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCT-TACAACTCAATAAT 792

  chrX_113057781_   2424 AAATAGACAAA-AACC-AATTTAAAGATGAGCAAAATAATAATAATAATA 2471
                            v       -    -    ?   i   i     ---------------
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAA--------------- 827

  chrX_113057781_   2472 CGGATGAGCAAAGGGATAGGATAGACATTTATCCGAAGAAGATATACAAA 2521
                         -    ----------- v i          v   i               
  L1M4_orf2#LINE/    828 -GGAT-----------TTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_113057781_   2522 TGGCCAGTAAACACACGGAAATATGTTTAACATCATTAATCAT 2564
                               i   i    i i   v   i i       ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (90 / 49)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 11.77 (365 / 31)  


3612 24.73 0.22 0.88  chrX_113138041_113142589     3143  4056 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113138041_   3143 TGGAAAGATATTTCATGTTCGTGGATATGAAGAATCAATATGGCTAAAAA 3192
                                    ii       i     vv     v i     v i   i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_113138041_   3193 TGTTCTTACTACCCAAAGCAATCTGCAGATGCAATGCAATCCTTATCAAA 3242
                           vivv    v      vii    i     v   i       i       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_113138041_   3243 ATACCAATGACATTCTTCATAGAAATAGGAAAAAAAAACCTAAAATTTAT 3292
                           v   iivi v  i  iii      v iv  ivvi v         i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_113138041_   3293 ATACAACCACAAAAGACCCTGAATAGCCAAAGCTATCCTGAGCAAAGAGA 3342
                           iv  vii   ii     v           i v   i   iv  ii   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_113138041_   3343 ACAAAGCTGGAGGAATCTTGTTACCTAACTTTAAATTATACTACAGAGCT 3392
                               i       v  viii v  i  i  i   viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_113138041_   3393 ATAGTAACCAAAACAGCATGGTACTGGCATAAAAAAAGAAAAGCCACATG 3442
                          i     i   i    ii              ii v   -----  i  i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA-----CATATA 294

  chrX_113138041_   3443 GACCAATAGAACAGAATAGAGAACCCAGAAACAAATCCACACACCTACAG 3492
                           i    i   i     v    ii       i   i   i   ii  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_113138041_   3493 TAAACTCATTTTTGACAATGTTGCCAAGAACATACACTGGGAAAAAGACA 3542
                          v  i v     i     v v        v   v  v    i   ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_113138041_   3543 GTCTCTTCTATAAATTGTGCTGGAAAAACTGGATATCCATATGCCGAAGA 3592
                             i   v i    v       i v         ?   i    vi    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_113138041_   3593 ATGAAACCACAACTCTTATCTGTCGCTGTATATGAAAATCAAATCAAAAT 3642
                              iiii-i  i i  i  vv i ii    ii     i  v       
  L1M4_orf2#LINE/    445 ATGAAGTTG-GACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_113138041_   3643 GGATAGAAGACTTAAATCTAAGACCTCAAACTATAAAACTACTACAAGAA 3692
                             vi?    i     v     v  v             vi  v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_113138041_   3693 AACTTTGGGGAGACTCTTCAGGACATTCAATTGGGCAAAGATTTCTTGAG 3742
                            v v  ? vi v     iv   v  vii  i     v i      iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_113138041_   3743 TAATATCCCATAAGCACAGGCAACCAAAGCAAAAATGGACAAATGGGATC 3792
                           vv iv   v       i     v    v      i  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_113138041_   3793 ACATCAAA-TTAAAAAGCTTCTGCACAGCAAAGGATAGAATCAGCAAAGT 3841
                         v       -       -   i  ii vv       i vv    iv     
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_113138041_   3842 AAAGAGACAACCCACAGAATGGGAGAAAATATTTGCAAACTAC-CATCTG 3890
                         i  i                                   ii i-i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_113138041_   3891 ACAAGAGACTAATAACCAGAATATATAAGGAGCTCAAACAACTCTATAGT 3940
                          i   i    vi  v             i  i   vv       v   i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_113138041_   3941 AAAAAATCTAATAATATGATTTTAAAATGGACAAAAGATTTGAATAGACA 3990
                              iv v     ivii   ?v       i    i              
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_113138041_   3991 TTTCCCAAAAGGCGATACACAAATGGCAAACAGCTATATGAAAAAATGCT 4040
                             i v    iv    i         v  i ivi i       i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_113138041_   4041 CAATATCATTGATGGT 4056
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (138 / 84)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3123 27.62 0.88 0.55  chrX_113171058_113177727.rev     5275  6179 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113171058_   5275 TGGAAAAACAGTCCATGCTCATGGATAAAAAGAATTGATATCATGAAAAT 5324
                               i i vi     i        vii    v  i    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113171058_   5325 GGCCATACTGCCCAAAGTAGTGTATAGATTCAATGCTATCCGCATCAAGC 5374
                            v     v      v ii v  i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113171058_   5375 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5422
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_113171058_   5423 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTGGGCAAGAAG 5472
                                viiv  ii  v  viv        i      i  iiv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_113171058_   5473 AATGAAGCTGAAGGCATCATGCTGCCTGACTTCAAACTATACTACAAGGC 5522
                           ii   i  i   vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_113171058_   5523 TACAGTAACCAAAACAACATAGTACTGGTACTGAAACAGATATATAGACC 5572
                                 i   i   iii i       i iviii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_113171058_   5573 AATGGAACAGAGCAGAGACCTCAGAAATAACACCACACATCTACAACCAT 5622
                                i   iiv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_113171058_   5623 CTGATCTTTGACAAACCTGACACAAGCAAGCAATGGGGAAAAGATTCCCT 5672
                         i    i  i     ivv  v  vi v  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_113171058_   5673 ATTTAATAAACGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5722
                         v  i  i   i    i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_113171058_   5723 AACTGGAGCCCTTCCTTACACCTTATACAAAAATCAACTCACGATGGATC 5772
                          ii    v    v   i     v           i      vi       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_113171058_   5773 AAAGACTTAAACGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAACCT 5822
                          ?    i    i      v   ii  i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_113171058_   5823 GGGC---AATACGATTCAGGACATAGGCATGAGCGAAGACTTCATGTCTA 5869
                         i  ?---   - --   iv   v v  vv ii  i v ii   v ivv  
  L1M4_orf2#LINE/    549 AGGNGTAAAT-C--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_113171058_   5870 AAACACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5919
                         vi    i       vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_113171058_   5920 GTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5969
                         i i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_113171058_   5970 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACA 6019
                         v  i     i                 v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_113171058_   6020 AAGGGCTAATATCCACAATCTGTAAAGAACTTAAACAAATTTACAAGAAA 6069
                          i  i  vi      v   v i         ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_113171058_   6070 AAAACAAACAACCTCATCAAAAACTGGGCCAAGGATATGAACAGACACTT 6119
                           i     i    iv  i?    v     v      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_113171058_   6120 CTCAAAAGAAGACATTTATGCAGCCAACAG--ACATGAAAAAA-GTTCAT 6166
                            v        i  vi viii     i i--         i - i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_113171058_   6167 CATTACTGGTCAT 6179
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (150 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2371 26.98 5.51 1.26  chrX_113194307_113196421      756  1626 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113194307_    756 TGGAGAGGCCTACTATGTTT-TA---TGGAAAATTCAAAGTAGCAAAGAT 801
                             i  iiv v i     i- i---     i i i  vi v iv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113194307_    802 GTTAATTTTCCCCAAATTTATT-----ATTTAATATGATCCCTATCAAAA 846
                          vi   vi          v  i-----   i  iiii             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113194307_    847 CCCCAGCAGGATTTTGTGTAGATATCTTTAAAATGCTGATTTTAAAACGT 896
                         i      v vv    v  i   v  --- i v v      ii     ivi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT---TGACAAGCTGATCCTAAAATTC 147

  chrX_113194307_    897 ATATGGAAAAACAAAGAAGGTGGAATACCTAAAACAATTTTTAAAAAGAA 946
                                  vi   i i vvii     v i        i  v        
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_113194307_    947 GAATAAAGTGGGAAGAATCA-ATTACCTTATTTTAAGACT---------- 985
                            i     v   i  v   - i v  iv    i  i   ----------
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_113194307_    986 ---CAGTAATTAAGAAAGTGTGG------CAAATGAATAGATCTGTA--T 1024
                         ---       i    v       ------  v v i     iv i  -- 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_113194307_   1025 CAATGGAACAGAATACAGAGTCCAGTA-TACACCCAAATAAGTATGGTGA 1073
                                 i     vv         v -  v     v i vv      v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_113194307_   1074 ATTAATTTTTGACAAAGGTGCAAAAGCAATTCAAAGGAAGAAGGATAGAT 1123
                            i     i     i     v  ii v      v  i-   i  ---  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGA---AT 393

  chrX_113194307_   1124 AGTCTTTT-AACAATTAGATATTG--ACAGGTTAAAAAAGGAAAGG--AA 1168
                                 -     v i - ii  --   i-i ii v ?vv v v --  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGG-TGCTGGGACAA-CTGGATAKCCACATGCAAA 441

  chrX_113194307_   1169 AAAAGAAAGTTTCAACTTAACTATTACAAGTTACATGAAAATTAACTCAA 1218
                          i  vi     vv v iiv  i- i   vvv  i ii             
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACC-TCACACCATATACAAAAATTAACTCAA 490

  chrX_113194307_   1219 C-TGGATTACAGCTCTAAACGTTAAGTG-TAAAACCATAAAAGTTTTAGA 1266
                         v-     i ?  vi     i  -   v -      i      v i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_113194307_   1267 ATAAAGAACAGGAGAAAACACTCATGATTTAGAATTAGGCATTAAGTTCC 1316
                          v   iv i   ? v   ivi  i   ii v ii       v iiv   i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_113194307_   1317 TAGACTTGACACCAAAGATATGATCTATAAAAGGAAAAATTGA-AAATTG 1365
                             iv          iii ii v v i     i      v  -      
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_113194307_   1366 GATTTTGTCAAAATTAGAAACCTTTGCACTTGAAAAACCA-TGTTAAGAG 1414
                           i  ii         i    i    ii   v   iiv  - i i    i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_113194307_   1415 AATTAAAACGTAAGCCACAGACTGGGAGGAAATATTTGCACATCACATTT 1464
                          i v    vii  v       v      i           v    i  v 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_113194307_   1465 CCAACAAAGGACTTACATACCAAACATTTAAAGAATACTTTAAAATCAAC 1514
                          ii i  i      ii  v vi  i  v       iv   vv  v    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_113194307_   1515 AG----AAAATAAA--ATCCAGTTCAAAAATTGGCAAAAGACAGGACAAG 1558
                          i----  i i   -- i   i  ?      v      i  ivv  vv  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_113194307_   1559 ACACCTA-CCAAAGAGGATATACAGATGGTAAATATGCACATGTAGGGGT 1607
                            ii v-       i        i    iv    v       v ii i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_113194307_   1608 GTTCAACTTGATTAGCCAT 1626
                          i     v v ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.36 (59 / 25)  


3290 27.21 0.55 0.11  chrX_113231650_113238338     5293  6196 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113231650_   5293 TGGGAAAACAGTCTGTGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5342
                            i  i i vi ii  i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113231650_   5343 GGCCATACTGCCCAAAGTAGTTTATAGATTCAATGTTATCCCCATCAAGC 5392
                            v     v      v ii i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113231650_   5393 TACCAGTGGCTTTCTTCACAGAATTGGAAAAATCTACTTTAAACTTCATA 5442
                          v    iv  i  i  ii     v v  v  iiiv iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_113231650_   5443 TGGAACCAAAAAAGAGCCCACATAGCCAAGACAATTCTGGGCAAGAAGAA 5492
                              viiv  ii  v  viv        i     ii  iiv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_113231650_   5493 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5542
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_113231650_   5543 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATGTAGACCAA 5592
                               i   i    ii         i iv ii i   i  i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_113231650_   5593 TGGGACAGAACAGAGACCTCAGAAATAACACTACATATCTACGACCATCT 5642
                            i i    iv    vii         vv i i i  i  i ii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_113231650_   5643 GATTTTTGACAAACCTGACACAAACAAGCAATGGGAAAAGATTC-CCTAT 5691
                               i     ivv  v  vi v  vv       i     v v-i  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_113231650_   5692 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGCAGAAAACTGAAA 5741
                          i  i              v      v  ?         i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_113231650_   5742 T-GGACCCCTTCCTTACACCTTATACAAAAATCAACTCAAGATGGATTAA 5790
                          -        v   i     v           i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_113231650_   5791 AGGCTTAAATGTAAAACCCACAACCATAAAATCCCTAGAAGAAAACCTAG 5840
                           i i         i v i v   i      ii i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_113231650_   5841 GCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAGTAAAAC 5889
                          ?i- v i -   iv   v v  vv i     v ii   v iii  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_113231650_   5890 ATCAAAAGCAATAGCAACAAAATCCAAAATTAACAAATGGGATCTAATCA 5939
                          i        vv          vvv     vi i    v   ii v    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_113231650_   5940 AACTAAAGAGCTTCTGCACAGCAAAAGAAAGTATCATCAGAGTTAACAGG 5989
                           v v  i i   i  ii vv    i  v v     vv i   v  v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_113231650_   5990 CAATCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGG 6039
                            i i                 v       vii  vi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_113231650_   6040 ACTAATATCCAGAATCTACAAAGAACTTAAACAAATTTGTAAGAAAAAAA 6089
                            vi          v  i        ivv    v ivi   v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_113231650_   6090 CAAACAACCTGGTCAAAAAGTGGGCAAAGCATATAAACAGACACTTCTCA 6139
                             i    iii i?    i         v  v i  i     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_113231650_   6140 AAAGAAGACACTTATGCAGCCAACAA--ACATGAAAAAAAGCTCATCATC 6187
                                 i ivi viii     i  --         i v     v    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_113231650_   6188 ACCAGTCAT 6196
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


2774 26.22 0.76 3.68  chrX_113242502_113244444      528  1450 (493)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_113242502_    528 CCATGTTTATGGATAGAAAGACACAATATTATCAAGATGTTGGTTCATTG 577
                                i      v i     vi      i i      viii v viiv
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_113242502_    578 TTACTAGATCTATAGATCTAACATAATCCCAAACAAAATCCCAGAAGGTA 627
                         iv v v      i    ii   ii      v v           vv viv
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_113242502_    628 ATTTTGTGTGTATCAACAAAC--ATTCTAAAATTTATATGAAGATTCAAA 675
                         v     iiviv  ii    i --  i        i     i i  v   i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_113242502_    676 AGACAATGATTAGCCACCACAGTATTGAAGAAGAATAACAAAGTTGGAGG 725
                         i   vvv  v      vv   i v     i     v              
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_113242502_    726 ACTGACATTGTTCTACTTTAAGACTTACTATAAATCTAAAGTAAACAAGA 775
                            v   i vii v i  i  i        i   v   v     v     
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_113242502_    776 TAGTGTAGTTTCAGCAAATGAATAAACAAATAGATCCGTTTAGAACAGAA 825
                         i     i  viii   v v i   i   v       vi --i   i    
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT--GGAATAGAA 310

  chrX_113242502_    826 TAGGGAGCTGAGAAAGAGACCCAAATGAATACTGTCAACTGAATTTTGAC 875
                          v i   iiv     v i     v iivv  iv     i   v   i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_113242502_    876 AAAGGAGCAAAGTCAGTGTAATGAAGCAAAGATAGTGTTT-CAACAAATG 924
                           i  v  v   v vi vi    ii v  ii     v   -         
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_113242502_    925 GTGCCGGAACAACTGGACATCTATACACCAAAAAAGGTGGGAGGAGTCTA 974
                             i  i         i ? i i ii v   i  --  i----   - i
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--TGA----AGT-TG 453

  chrX_113242502_    975 GATACAGATCTTACATCTTTCTTAAAACAATAACTCAAAATGGACCACAG 1024
                           iv vv i  i   i v vivi    - v              i  ?  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATGGATCAWAG 502

  chrX_113242502_   1025 ACCTAAATGTGAAATGC-AAAACTATAAAAATTCCTTCAAGATAATATAG 1073
                                   i i -  -            -i  i vv    v  i    
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGA-GCTAAAACTATAAAA-CTCTTAGAAGAAAACATAG 550

  chrX_113242502_   1074 GAGAAAATCTCAATGACCTTGCGTTTGGTAATGGCTTTTTAGAAACAACA 1123
                          ? v      ivi        v   v  i     i  i     v ii   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_113242502_   1124 TCATATGCACTATCAATAGAAGAAAGAACTGATAA-CTGGCTTTTATTAA 1172
                         i  v v    v v   i i      i  iv     -i   vi  i  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_113242502_   1173 AGTTAAAAATGTCTGAGTCTGTGAAGACACAATCAAGAGAAGAGAAAGAA 1222
                          i       iv i  v ii vvi i     v       i ivii     v
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_113242502_   1223 AAGCCACAGATTGGGA-AAAACGTTTGCAGAATACATTTATCTGATAAAG 1271
                           v       v     -    ii      -   -   v          i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCA-AAT-CATATATCTGATAAGG 748

  chrX_113242502_   1272 GACTGTTATTTAAAATGTGCAAAGAACCCTTAAAACTGAAGAGTAAGAAA 1321
                             vv   ii i   i ii       i    v    v  v i   i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_113242502_   1322 ACAAATAACCATATTAAAAAATGAGCAAAGACCTT-AACAGATACCACAC 1370
                                   vv   ?       i      ivi  -  i   i iiv v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_113242502_   1371 CAAAGATTTTATATATATATATATATATATATATATATAGCAAACAAGCA 1420
                               -------------------- v     i v  i  v  i     
  L1M4_orf2#LINE/    849 CAAAGA--------------------AGATATACAAATGGCCAATAAGCA 878

  chrX_113242502_   1421 TATTAAAAGATGCTCCATATCATGTGTAGT 1450
                         i  v           v i    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.02 (16 / 896), avg. gap size = 2.56 (41 / 16)  


4081 19.20 2.22 1.44  chrX_113292545_113295656     1730  2630 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113292545_   1730 TGGAAAGATATTTTATGTGCATGGGTTAGAAGACTTAATATT---AAGAT 1776
                                    iii    v     i  i              ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113292545_   1777 G-CAATTACTCCTCAAATTAATCTGCAGATTCAACGCAATCATTATCAAA 1825
                          -    -     i      i    i                vi       
  L1M4_orf2#LINE/     51 GGCAAT-ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_113292545_   1826 ATCCCAGATGGCATTTTTGGAGAAACTGATGAGATGCTCTTAAAATTCAT 1875
                                v  v v      v     i   ii  v  v  i          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_113292545_   1876 ATGAAAATCCAAGGGACTCCAAATAACTCAAACTATCTTTAAAAAAGAAC 1925
                            i    v        i vi    i iv    v     -i        v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT-GAAAAAGAAG 198

  chrX_113292545_   1926 AACAAAGG-GGAGAACTTACCCTCCCTGATTTTCAAACTTATTACAAAGC 1974
                                v-    i   i  v  i  ii    iv       i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_113292545_   1975 TACACTAATCAAGACTGCATAGTATTGACATAAGGATAGACTTACAGTTC 2024
                             v          v ii i   i  i             v  i  v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_113292545_   2025 AATGGAATAAGAT-GAGAGTCCAGAAATAAACCCATACCTCTATGG-CAA 2072
                                  ii  -                        v i     -   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_113292545_   2073 CTGATTTTTGACAAGAGTGCTAAGGCAATTCAGTGGAGACAGAATAGTTT 2122
                         i       i      i    i   i v     i   i  v        i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_113292545_   2123 CTTCAA-AAACACTGCTGGGACAACTGGAGGTACACATGTAAATGAATAA 2171
                         i     -   iiv                vi?v      i   v    i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_113292545_   2172 AGGTGAACCCCT-CCCCATATCATACAGAAAAATTAACTCAAAATAGATT 2220
                           v  i      -  i  i i    i v                 i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_113292545_   2221 AAAGACACAAGTGTAAGA----AAATTATAAAACCCTTGAAAGTAAGTAT 2266
                          ?    vi  i       ----   i        i   ii   v  ii  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_113292545_   2267 AGGGGTACACCTTTCTGTCTTTGACTTCA-CAATGGTTTCCTTATATATG 2315
                            ?   v i   iv  v i   iv  vi-          -   v     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATG 597

  chrX_113292545_   2316 ACACCAAAAGCATAAGAAAAATAAATAAAAAAAATAAAAATAGATAAATG 2365
                                     i   v  ------i    i   ---            v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAA------CAAAAGAAA---AAATAGATAAATT 638

  chrX_113292545_   2366 AGACTTCATCAAAATGAGAAACCCCTGTGCTTCAAAGTACATTATCAGGA 2415
                         i              v i    iii            v   i     i  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_113292545_   2416 CAAGAAAAACAGAAACCACAGAATGGAAGAAAATAATTGTCAGTCATATT 2465
                         v ivi    v v  v           i        v   iv i      v
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_113292545_   2466 TAAGATAAAGGTCTAGTATCCACAATATGTAAAGAATTATTACAACTCAA 2515
                          vv     i  v  v       v     i       i v           
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_113292545_   2516 CAACAAAAAGTCAAACGACTCAATTAATAAA-GGACAAATGACTTGAATA 2564
                         i  i      v    ii  i     ? v   -  i    v  i       
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_113292545_   2565 GCTAATTTTTAAAAGAAAATCTGCAAATGGCCATCAGAGAACATGAA--- 2611
                          vi v  i iv      i  v i          vi -  v       ---
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATA-AGCACATGAAAAG 887

  chrX_113292545_   2612 --GTTTGTCATTAAAACAATG 2630
                         -- i iiv   i ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (104 / 65)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.94 (33 / 17)  


3282 24.25 2.68 1.23  chrX_113310507_113312637      746  1640 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113310507_    746 TAGAAAGATATCACATGTTCAGGAATTGAAATAACTAATATCGTTAAAAT 795
                          i          v        v i    i  v vi      i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113310507_    796 GATCAGGGCATCTAAAGTGAGATACAGATTCAGTGCAATCCTTATCAAAG 845
                          iiv vivivi i   v   vv          ii       i       i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113310507_    846 TACCAATGACATTATTTACAGGAA--GACAAAATGCAATCCTAAAATTTG 893
                          v   iivi v  v   i   i  --     iv  --           ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCA 148

  chrX_113310507_    894 TACGAAACCACAGAAGACCCTGGATAGCCAAAGCAAACTTGAGCAAAAAG 943
                           i i  vii  iii     v i         i   v     iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_113310507_    944 AATAAAGCTGGTGGCATCACGCTACTTGAGTTCAAAACATACTACAAACC 993
                           i    i   v  vv    i  v iii v        v         v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_113310507_    994 TAGAGTAAGCAAAACAGCATTGGACTGGCATAAAAATAGACACATAGACC 1043
                           v     v   i    ii v v          ii       i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_113310507_   1044 AATGAAATAGAATAGAGAGCCAAGAAATAAATTCACACATCTATAGCTAA 1093
                             i        v     i v         ii  i    i   i ii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_113310507_   1094 CCGATTTTTGACAAGG-TGCCAAGAACACACATTAAGGAAAGGACAGCCT 1142
                         ii      i       -        v  iv  v ii      i i  i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_113310507_   1143 CTTCAATAA-CAATGCTGAGAAAACTGGATATCCACATGAGAAAGAATGA 1191
                         i     i  -iii     i  v         ?       vi         
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_113310507_   1192 TATTAGAGCTTTCTCTCTCACCATAAGCAAATATTATCTCAAAACAGATT 1241
                         vi  i  v ii vi   v       vi    v    v       ii   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_113310507_   1242 AAAGACTTAAAATGTAACACCCGAAACTAC--------TAGAAGAAAATA 1283
                          ?    i    -     v v ii      i--------          i 
  L1M4_orf2#LINE/    499 AWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_113310507_   1284 TAGGGGAAAAGCTTCATGACAGTGGTCTAGACAAAGATTTTTTAGATAAA 1333
                             ? v   v    i    vv   vi   i   v i   i       vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_113310507_   1334 ACCTCAAAAGCAAAGGTAATCAAAGCAAAAATGGACAAATAGGATCACAT 1383
                           vi        v i i  iv    v      i  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_113310507_   1384 CAGG-TTAAACAGCTTCTGCACAACTAAGAAAACAATCAACAGAGCTTAA 1432
                           ii-     - i   i  ii vv v   i v  v     v i  -- i 
  L1M4_orf2#LINE/    648 CAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAG--TGA 694

  chrX_113310507_   1433 AAAGACAACCCACAGAATGGGAGAATATATTTGCAAACTATATACCTGAT 1482
                                                  v           ii     i     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_113310507_   1483 ACGGGGTTAATAACCAAAATATATAAGGAACAAAAATAACTCAATATTTT 1532
                          v   ii vi  v   i         i    vvvv i         v --
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-- 792

  chrX_113310507_   1533 TTTAAAAAA---------CTGATT-AAAAATGAACAAAAGATCTGAATAA 1572
                         ---     i--------- ii   -       ii    i   i      i
  L1M4_orf2#LINE/    793 ---AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_113310507_   1573 ACATTTCTCAGAAGAAGACATACAAATGGACAACAGATATGTGAAAA-AT 1621
                                  vi       i          v   i iii ii      -  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_113310507_   1622 GCTCAACATTCCTAATGAT 1640
                                  iv????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (136 / 78)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.69 (35 / 13)  


3935 19.12 2.81 0.67  chrX_113430897_113433007      730  1618 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113430897_    730 TGGAACAATATCCTGTGCTCATGGATTATAAGATTTAATTTGGTTAAGAT 779
                              vi      ii  i         iv    i     v v        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113430897_    780 GGCAATAATCCCCAAGTCGATCTAGAGATTCAAAGAAATTACTATCAGA- 828
                                v       i i      v        v v   iv      i -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113430897_    829 TCCGCAGCTGACTTCTTTTTAGAAATTGTCAAGATAATCCTAAAATTGAT 878
                            -      v   i   vi        v    v i           v  
  L1M4_orf2#LINE/    101 TCC-CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_113430897_    879 ATGGAAACTCAAAGGACCCATAGTAGCCAAA-TAATGTTGAAAATGAA-- 925
                                iv   i       v i        -i   v       v   --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_113430897_    926 -CTCAGTTGGAAGAC--ATAATTCCTGATTTCAAAACTTCCTGCAAAGCT 972
                         - vv       i   -- i v    ii            v  i       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_113430897_    973 ACAATGATTACGTTGATGTGGTACTGCCATAGAAATAGAAATATGGATTA 1022
                            i i  i v viii          v    iii     v    i   i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_113430897_   1023 AAGGAACATAATTCAGAGTCCAGAAGTAAACCTTTATGTT-ATGGTCAAT 1071
                          v    i v    v           i      iv  ii  -         
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_113430897_   1072 GTATTTTTCACCAGGATGCCAAGAAAACTCAATGGCAAAAGACTGAAAT- 1120
                         vv     iv  v   i        vv i       vi     v -- i -
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT--AGTC 397

  chrX_113430897_   1121 ---TCAAAACATGGTGCTGGCACAACTGGATATTCACATACAAGATGATG 1167
                         ---    v v          v           ?i     i   i vi   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_113430897_   1168 AATTTAGATGGCTACCTCATACCGCTATA---AAATTAACCCCAAATATA 1214
                           v  i  ivv        i   i-    ---        i v    iv 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCA-TATACAAAAATTAACTCAAAATGGA 496

  chrX_113430897_   1215 TCATAGACATAAATAT--GAGGTAAAAGTATAAAACGCTTAGAAATAAAA 1262
                            ?    v     i --   v     v        v       i-    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG-AAAA 545

  chrX_113430897_   1263 CATAAAAGTAAATATTCATGACCTTGGATTATGCAGTGGTTTCTTAGCTA 1312
                             ii?      v   i         i   v   i           v  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_113430897_   1313 TGACATCAAAAGCACAAGTGACTGAAGAAAAAA---ATAGATTGGACTTC 1359
                              i            ii  vi         ---   i          
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_113430897_   1360 ATGAACAATAAAAACGTTTGAGCTGCAAATGATACCACCAAGGAAGTGAA 1409
                           v  v v       v    v   v    v  i  i i    i       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_113430897_   1410 GA-ACAACCTACAAAATGGCAGATGATATTTGCAAATCATATATCTG-TA 1457
                         i -      i   i     v   vi                      -  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_113430897_   1458 ATGAAGCTTGTGTTCCAAATATAGTAAGAACTCTTACAACTCAAAATTTA 1507
                          v i -     i i vi      vv                   v v v 
  L1M4_orf2#LINE/    746 AGGGA-CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_113430897_   1508 AAAGACAA-TAATCCAATC-AAAACTTTGCAATGGATCTCAATACATATT 1555
                                 -   i     i-    v vv    v    i v    v i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_113430897_   1556 TATCCTAAAAAGATATACAAATG-CCAATAAGCATATTCAAGGATGCTCA 1604
                          v   v  i              -          i  vv  i        
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_113430897_   1605 ATGTCATTAGTTAT 1618
                          ii   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.06 (86 / 81)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.63 (31 / 19)  

 649 18.99 5.03 0.56  chrX_113430897_113433007     1893  2071 (40)    L1M4_orf2#LINE/L1      695   881 (27)  

  chrX_113430897_   1893 AAAGA-AACCCAGAGGATG--AAAAAATGTTTTTAAATCATTTATCTCTT 1939
                              -      v  i   -- i     i   vi       v     vv 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_113430897_   1940 AAGTGTCTAGTACCTTGAATATATAAAGAGCTC--ATCATTCAATAATAA 1987
                            v v  v   i iv             i   -- iv i          
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_113430897_   1988 AAGGG--AATAACTGAATTTAAAA-TGAGCAAAAGACTT-AATGGACATT 2033
                           i i--      iv    ?    -  i     i  i  -   i      
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_113430897_   2034 TATCCAAAGAATATATAGAAATTACCAAGAAGCAGCAT 2071
                          v         v     v    vi    v     -   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCA-CAT 881

Transitions / transversions = 1.06 (17 / 16)
Gap_init rate = 0.04 (7 / 187), avg. gap size = 1.43 (10 / 7)  


3701 21.12 3.65 0.23  chrX_113499363_113501721.rev      995  1870 (489)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_113499363_    995 GAAAGACACTCCTATAT--ATGAATTGGAGGAATTAATATTGTTAAGATG 1042
                               i -   i  i --   i      i  v                 
  L1M4_orf2#LINE/      3 GAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_113499363_   1043 TTGATACTATCCAAATGAATCTAGAAATTCAGTGCAATCCATATAAAAAG 1092
                         vii     vi      vi     v i     ii       v   v    v
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_113499363_   1093 TCCAGTGATGATTTTTGCAGAAAGAGAAAAATTCTTTCCAAAATTAATAT 1142
                         i    iviivv            vv  v  ii vv i i      v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_113499363_   1143 AGAATCTCAAAGCACCCTGAATAACCAAAATAATCTTGAAAAGCAGGAAT 1192
                         i   viv   i v    v     i      i           iv i   i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_113499363_   1193 GTAGT-GAAGCTCTCACAGTTTCTGATTTCAAAATTTACTACAAATCTGT 1241
                         iv   - i  vv      v  i ii         i          v  ii
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_113499363_   1242 AGTAATCAGAATGTCGTGGTACTGATATGAAGACGGACATATAGACTGAT 1291
                                 ii iivi         ii  i i  ii          iii  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_113499363_   1292 GGAATAGG-----GACTTCAGGAATAAACCC------TCATGGTCCGATG 1330
                                i-----  v i   i         ------ i      viv  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_113499363_   1331 ATTTTCTATAAGGATGCCAAGACCACTCAATGG----AGAACAGTCTTTT 1376
                               v i    i           i       ----    i        
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_113499363_   1377 CAACAAATTGTGTTGGAAAAATGGAATACTCACACACAAAAGAATGTAGA 1426
                                 v   i   i v  iv i   ?i    ii          v  v
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_113499363_   1427 CAGAAACTTACCTTAGAGCATATGCAAAAATTAACCCCAAATGGATCAAA 1476
                         ii  vv i     i v v     i           i v          ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_113499363_   1477 GACCTGAACATATGAGCTAATACTATAACATTCTTTAAAATAAGCTTAGG 1526
                              i  ii  v       v       v i    vi  iv  i v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_113499363_   1527 CA-AAAGCTTCATGACATTGGATTTGGCAATTATTTCTTCAATATGAAGC 1575
                         ?i-   v    i    v    i  v      vi      vi      vi 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_113499363_   1576 CAAAAGTATAAGGCACAAAAGAAAAAATAGATAAATTTGACAACACCAAT 1625
                               i i   vv                       v   vv  i   v
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_113499363_   1626 ATTAAAAA-TTTTGTGGATTAAATAATACT--CAACAGAGAGAAAAGGCA 1672
                                 -       vv i   vi i   --   v i  v      i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_113499363_   1673 GCTCACATAATGTGAGGAAATATTTGCAAATCATATATCAAATAAGGGAT 1722
                         i i    v    v   i                      vi        i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_113499363_   1723 TT----CCAGAATACATATAAAAACTCTTACAACTTAACAACATAAA-AC 1767
                           ----        i   -  i             i  i  i v   -  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATA-AAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_113499363_   1768 AAACAATC-AA---AAAAGTGGGCAAAGAAATTGAATAC-CATTTCTCCA 1812
                            i  i -  ---    i         i v       v-          
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_113499363_   1813 AAGAAGATACACAAATGGCCAATAAGCTCATGAAAAGATGCACAACATAA 1862
                                  i                 v             v      v 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_113499363_   1863 TCATTAGT 1870
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.46 (108 / 74)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 2.27 (34 / 15)  


3434 22.02 1.18 3.65  chrX_113559726_113565181     2155  3085 (2371)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113559726_   2155 TGGAAAAACATCCTGTATTCATAAACTGGAAGAGCTAATATTGTTAAAAG 2204
                               i i    ii i     ii i       vi            i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113559726_   2205 GTCCACACTACCCAAAGTGATCTACAGATTCAATGCCATCCCCATCAAAA 2254
                          v v i   v      v                i  v     i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113559726_   2255 CTCCAACTGGATATTTTACAAAAATGGTAAAAAC-AATCCTAAAATACAT 2303
                         ii   i   vv v    i  i    v - v  i -i          v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chrX_113559726_   2304 AAAGAACAACAAAGGACCCTGAATAGCCATAACAATATTGAGAAAGAAGA 2353
                          vi   vvi   i      v         v      v    i        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_113559726_   2354 GCAAAGCTGGAGTCATCACACTTCCTGATTTGAAAATATATTACAAAGCC 2403
                         i     i     vvv          ii    v    iv  i        i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_113559726_   2404 ACAGTAGTTGAAAAATTGTGGGAACAGCGTAAACACAGACAGTTACACCA 2453
                               i ii i v v     v vii  i   iv i     vv  v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_113559726_   2454 ATGGAAGAGAATAAAGAGCCCAGAAATGAGTCCATGCATATACAGTCAAC 2503
                               v     vi    i        i ii    i   v  ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_113559726_   2504 TGATAGTCAACAAGAATTCCATGAATACACAATGTGAAAAGGATAATGTC 2553
                             vv  i     ii v   v  vi iv     v i    i   i v i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_113559726_   2554 TTCAACAAATCATGCTGGAAAAACTAGATATATAACTGCATAACTGCAAA 2603
                                   vi      i v    i    ?---- ii   ----     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAK----CCACAT----GCAAA 441

  chrX_113559726_   2604 AGAATGAAATTGAACCTTTATCTTACAATATACACAAAATGTGGTT-AAA 2652
                                 i   i   ii  i  i   vi   i      vv iii -   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_113559726_   2653 ATATATTAAAAACTTAAACTTAAGACCTGAAATTATAAAAGTCTCAAAAG 2702
                           iv  i ? i  i    iv     v  i   i       v   i i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_113559726_   2703 AAAAGGTAGGAG-AACGATATCTT---GACATTGGTCTTGGCAATGATTT 2748
                             vi    ? -  ----     ---   v    vi v       i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAA----ATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_113559726_   2749 CTTGGATATGACACCAAAAGGATAGGCAATAGTAGCAAAAATAGACACTT 2798
                            i                v i i    i iv  v         i vv 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_113559726_   2799 GGGACTACATCAAACTAAAAAGTTTCTATATAGCCAAAAAAAAAAAAATC 2848
                         v     v       v v    ii  i i ---  ivv   ii v vv   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGT---GCTTCAAAGGACACTATC 684

  chrX_113559726_   2849 ATCAGAGTTGAAAAGACAACCTATGCAATGGGAGAAAATATCTGCAAAGC 2898
                          vv i   -            i iiv               i      v 
  L1M4_orf2#LINE/    685 AAGAAAGT-GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_113559726_   2899 ATATATCTGATAAGGGGCTAATATAAAAAAAA---AAGGAACTTTTACAA 2945
                                         i  vi   vv i  v ---  i     i      
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_113559726_   2946 CTCAATAGCAAAAAAAGAGAAAAAAAAAACAACAAATAACCCTCATT--A 2993
                                ii     i ----------------          -v   -- 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGA----------------CAAATAACCC-AATTWAA 816

  chrX_113559726_   2994 AAATGGGCAAAAAATTTGAAAAGACATTTTTCCAAAGAAGACATACAAAT 3043
                                    ii       v        i           i        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_113559726_   3044 GGCCAACTGGTACATGAAAAGAAGCTCAACATCACTGATGAT 3085
                               ivi i           v           ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (120 / 82)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.21 (45 / 14)  

3666 18.73 2.43 3.16  chrX_113559726_113565181     3776  4597 (859)    L1M4_orf2#LINE/L1       16   831 (77)  

  chrX_113559726_   3776 TGTCCATAGCTTGGAAATCTTAATATTGTTAAGATAGCAATATCACTCAA 3825
                            i   i v      iv                 i      iiv i   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_113559726_   3826 ATTGAACTACAGATTCAATGCAATCCCTGTCAAAATTCTAGCTGTCTTAA 3875
                              v            i         i       i i     i   vv
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_113559726_   3876 TTGCAGAAATTGATAAGGTTATCTTAAAATTCATATGGAAATGTAAATGA 3925
                                      i   v v   i                   i  iv  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_113559726_   3926 CCCCAAATAGTCAAAATAATCTTGTAAAAGAA---CAGTGTT------CT 3966
                            vi     i     i       v       ---  iv   ------  
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_113559726_   3967 TTTACATGCTTTTGGATTTCAGAACTTTCTACAAAGCTACAGCAATCAAG 4016
                         ----  ii   iivi      i     v              i       
  L1M4_orf2#LINE/    216 ----CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_113559726_   4017 AC--TCTGGTGCTGGCATTAAAATAGGCATATATATCAATGGATTAGAGT 4064
                           -- v    i       v ii    i      v         v    i 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_113559726_   4065 TGAAAGTTAGGAAATAAAATCTGACATTTATGGTCAATTGATTCTTGACA 4114
                            i   ivi        vi vv                    i i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_113559726_   4115 AAGATGTCAAAACTATTCAACAGGGAAA-AATGGTGTTTTCAACAAGTGG 4163
                          i i  i   i  i      ii      -   i  v          i   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_113559726_   4164 TGCTGGAATAACTGCATATCAACGGGCAAATAAATTAAATTGGTCCCCAA 4213
                               i i     v   ? v  iv     vi   v  i    v    v 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_113559726_   4214 CTTCACACCATATACAAAAATTATCACAAAATGTTAACAAAAATGGAAAC 4263
                          i                     v v       -----------------
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATG----------------- 494

  chrX_113559726_   4264 TATAAAATCAAAGACCTTAATGTAAG-GCTAAAACCATCAAACTCTCATA 4312
                         -----i    ?      v        -        i  v       i v 
  L1M4_orf2#LINE/    495 -----GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_113559726_   4313 A-AAAATATAGGCATAAACCTTTGTAATCTTCAATTAGTAAATGATATCT 4361
                          -    i     ?i    i   i  i i   vii    vv    i v   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_113559726_   4362 TAGAAATGACATCAAAAATATAAGCAACAAAATAAAACATACATAA---- 4407
                             v      i     ii i           v    v   v    ----
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_113559726_   4408 GGTTTCATCAAAATTAAACATTTCTGTGCTTCAAAGGACATTATCAATAA 4457
                          ii               v i  i                i      v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_113559726_   4458 ATGGAAAAGACTACCAACAGAATGGGAAAGAATATTTGCAAATCATATTT 4507
                          vv        v   v           i i                  v 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_113559726_   4508 ATTATAAAGAATTCATATGCAGAATATACGAATAACT--TATAACCCCAA 4555
                         v v    i i i ii   v         ii  v    --  i   i v v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_113559726_   4556 AATTAATATATAACTAATGCAACTTAAAAATGGACAAAGGAT 4597
                            v  v v i  v   iv   i ?        i        
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 1.46 (89 / 61)
Gap_init rate = 0.01 (10 / 816), avg. gap size = 4.60 (46 / 10)  

 307 21.74 0.00 0.00  chrX_113559726_113565181     4887  4955 (501)    L1M4_orf2#LINE/L1      815   883 (25)  

  chrX_113559726_   4887 AAAAAAGGACAAAGGATGCGAATAAACATCTCTTCAAAAAACATACACAA 4936
                              v  i        vi     i    i   i    i  v   i    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_113559726_   4937 GTGGTTAATAAGGACTTGA 4955
                         i   ii      v  v   
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGA 883

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.00 (0 / 0)  


3287 26.02 0.88 0.77  chrX_113577831_113582064     2835  3741 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113577831_   2835 TGGAAGGACATTCCATGCTCATGGGTAGGAAGAATTAATATCGTGAAAAT 2884
                              i  i  i     i      i v      v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113577831_   2885 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2934
                            v     vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113577831_   2935 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2982
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_113577831_   2983 TATGGAACCAAAAAAGAGCCTGCGTTGCCAAGTCAATCCTAAGCCA-AAG 3031
                                viiv  ii  v  v vi v     iv     i i ivv -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_113577831_   3032 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3081
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_113577831_   3082 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3131
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_113577831_   3132 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 3179
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_113577831_   3180 ATCTGATCTTTGACAAACGTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3229
                          vi    i  i     iv   vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_113577831_   3230 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 3279
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_113577831_   3280 GAAACTGGATCCCTTCCTTACACCTTATAGAAAAATTAATTCAAGATGGA 3329
                            ii    i    v   i     v    v         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_113577831_   3330 TTAAAGACTTACTTGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3379
                          i ?    i  vv   v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_113577831_   3380 CTAGGC---AATGCCATTCAGGACATAGGCATGGGCAAGTACTTCATGTC 3426
                         v    ?---   -- -   iv   v v  vv i     vvii   v ivv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_113577831_   3427 TAAAACACCAAAATCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 3476
                           vi         v  vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_113577831_   3477 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 3526
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_113577831_   3527 AACAGGCAACCTACAGAATGGGAGAACATTTTTGCAACCTACTCATCTGA 3576
                           v  i     i              v  v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_113577831_   3577 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 3626
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_113577831_   3627 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAC 3676
                             i     i     v  i?    i     i     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_113577831_   3677 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 3726
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_113577831_   3727 ATCATCACTGGCCAT 3741
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (135 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


1826 26.38 14.16 0.15  chrX_113600421_113602077      494  1164 (493)    L1M4_orf2#LINE/L1      144   908 (0)  

  chrX_113600421_    494 ATTC-TATGGAACCAAAAAAGAGTCCACATAGCCAAAGGAAGACTAAGCA 542
                             -       viiv  ii  vi viv         iv  vvi i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_113600421_    543 AAAAGAACAAGTCTGGGGGCATCACATTACCCAACTTCAAACTATACTAC 592
                          i        ivi   i  vv     i v     i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_113600421_    593 AAGGGTATAGTCACCAAAACAGCAGGGTACTAGTATAAAAGTAGACATAT 642
                           i v  i   v i   i    iiv      i i    iii         
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_113600421_    643 AGACCAATGGAACTGAATAGAGAACCCAGAAATAAAGCCAAATACTTCCA 692
                            i        iv    v    ii           v   v i i  vii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_113600421_    693 GCCAACAGTTCTTCGACAAAGCAAACAAAAACATAAAGTGAGGAAATGAC 742
                          i   iv v i        i vviv   i v   vv i  i     vi i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_113600421_    743 ACCCTATTCAAAAAATGGTGCTGGGATAATTGGAAAGCCACATGTAGAAG 792
                          vi  v     v              i  i    v ?       i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_113600421_    793 AATGAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGAT 842
                               ii    i  ii i   v    v           i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_113600421_    843 GGATCAAAGACTTAAATCTAAGACCTTAAACCATATAAACTCT-AGAAGA 891
                               ?    i     v     v  v    i   -       -      
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGA 542

  chrX_113600421_    892 TGACATTGGAAAAACTCTTCTAGACATTGGCTTAGGCAAAGAGTTCATGA 941
                         vi    v  ?iv  v     vv   v    v        v iv   v ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_113600421_    942 CCAAGAACCCAAAAACAAATGCAACAAAAACAAATGTAGATAGACAGGAC 991
                         vi v  vv      i  v v         iv   vi      i iv    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_113600421_    992 TTAATTAAACTAAAAATCTTCTGCACAGCAAAAGAAATAATCAGCAGAAT 1041
                           v  i   v v    v   i  ii vv    i  v iv    iv i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_113600421_   1042 TAACAGACCACCCAC----------------------------------- 1056
                         v  v    v      -----------------------------------
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_113600421_   1057 -----------------------------GAAC----------------- 1060
                         -----------------------------    -----------------
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_113600421_   1061 ------------AACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACA 1098
                         ------------     v  i?    i     i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_113600421_   1099 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 1148
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_113600421_   1149 CATCATCACTGGCCAT 1164
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (93 / 80)
Gap_init rate = 0.01 (5 / 765), avg. gap size = 19.20 (96 / 5)  


3318 23.26 1.74 3.04  chrX_113628794_113632816     2613  3532 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113628794_   2613 TGGAAAGATATCTTGTGTTCATGGATTAGAAGGCTTAACATTATTAAAAT 2662
                                     iii            i    i     i   i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113628794_   2663 AGCTATACTACCACAAAC-AATCTACAGATT----GTTATTCCAATCCAA 2707
                         i  v     v  -    i-i           ---- iv  i  v   v  
  L1M4_orf2#LINE/     51 GGCAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_113628794_   2708 ATCCCCAAAGTATGTTTTACAGAAATAGAAAACACCATCCTAAAATTCAG 2757
                              vivv iv v    i       v  v  vviv             v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_113628794_   2758 ATGCAATGACAAAAGAGC---AATAGCCAAAGCAATCTCGAGAAGGAAAA 2804
                            v  vvi   ii  v ---          i      i  i  i   i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_113628794_   2805 ACATAGTTGGAGGTATCACATTTCCTGGTTTGAAAATAGATTACAAAGTC 2854
                            v         vv     i    iii   v    ivv i       ii
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_113628794_   2855 ATGGTAATTAAAACAGTATGGCACAGGCATAAAGACA--CATATAGACCA 2902
                          ii     i  i     i   i  v       i  i --        i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_113628794_   2903 ATGGAATAGAATACAAAGCCCAGAATGAAATTCACACACATATGGTCAAC 2952
                                     vv i  i      vv   ii  i   iv         i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_113628794_   2953 TGCCTTT-GACAAAGGTTCGAAAAGTACACAACAGGGAAAAGATAGCCTC 3001
                           vi   -     i   v v  i vi iv   ii      ii    i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_113628794_   3002 TTCAGCAAATGGTGTTGGTAAAATTGTATATCTGCATGAAGAAGAATGAA 3051
                             i         i   v v  i  v   ? ii    v i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_113628794_   3052 ATTGGACCCTTATCTTATACCATATACAAAAATAAACTCAAAATGGAATA 3101
                         i        i  i  i i               v             vi 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_113628794_   3102 AAGACTTAAATGTCAGTCCAGAAACTA--GAACTTCTAGAGGAAAACATA 3149
                         ?    i       v  vv vi      --i    ii    i         
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_113628794_   3150 AAGGAAAAGCTTCTTGACACCTGTCTT-GGCATTGATTTCTTGGATACAA 3198
                         ii? v   v    v    - i  vv  -    v  i      i    ii 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_113628794_   3199 CACCAAAGGCACAAACGACAAAAGCCAAAATAGATAAGTGGGATTACATC 3248
                                i      i i       vv           i v   i v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_113628794_   3249 AAACTAAACAGCTCATGCACAGCAAAGGAAACAATCAATAGAATGAAAAG 3298
                            v v  v i  iv  ii vv       v  v     v i i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_113628794_   3299 GCAACCTACATAAAGGGGAAACATATGTAAAAATAAACATATGTTTATTT 3348
                         i     i   v  v   ii  v    v iv    ---     i i i---
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAAT---CATATATCTG--- 742

  chrX_113628794_   3349 TTAAACATAAATGGAAAGATGTCTTTATTAACATCCAAAATATTTAG-GA 3397
                         ------    --  i -------i  i ----     i     v  i-  
  L1M4_orf2#LINE/    743 ------ATAA--GGGA-------CTTGT----ATCCAGAATATATAAAGA 773

  chrX_113628794_   3398 ACTCCTATAAGTCAATAGAAAAAAGA-AACCAACTCAATATAAAAACAGG 3446
                             i  i  v      iv       -  vi   i    v?     ii  
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_113628794_   3447 CAACAAAACTTGAATAGGCATTTTTCCAAAGAAGACACACAAGTGGCCAA 3496
                            - ii i        i     i           i i    i       
  L1M4_orf2#LINE/    824 CAA-AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_113628794_   3497 AAAATCTATGAAAATATATTCAACATTGCTAATCAT 3532
                         v  iivi       v  ii       ii????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (131 / 79)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.59 (44 / 17)  


3234 26.13 0.66 0.55  chrX_113757473_113763865     4994  5900 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113757473_   4994 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5043
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113757473_   5044 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5093
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113757473_   5094 TACCAA-TGACTTTCTT-CACAATATTGGAAAAAAAT-ACTTTAAAGTTC 5140
                          v   i-  v    i  -  v  -    -- v  iv - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_113757473_   5141 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAACCAAAA 5190
                                 viiv  ii  v  v v  v     iv     i i  vv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_113757473_   5191 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5240
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_113757473_   5241 CTACAGTAACCAAAACAACATGGTACTGGCACCAAAACAGAGATATAGAT 5290
                                  i   i   iii           iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_113757473_   5291 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCTCATATCTACAAC 5338
                                 i    i--    i  --        vv  vi i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_113757473_   5339 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5388
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_113757473_   5389 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5438
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_113757473_   5439 TGAAACTGGATCTCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5488
                             ii    i i  v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_113757473_   5489 ATTAAAGACTTAAAGGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5538
                           i ?    i    v  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_113757473_   5539 CCTAGGCATTACCATTCAGCACATAGGCATGGGCAAGGACTTCATGTCTA 5588
                          v    ?i v viv   ivv  v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_113757473_   5589 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5638
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_113757473_   5639 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5688
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_113757473_   5689 CAGGGAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5738
                         v  iv    i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_113757473_   5739 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5788
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_113757473_   5789 AA-ACAAACAACTCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5837
                           -     i   i v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_113757473_   5838 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5887
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_113757473_   5888 CATCACTGGCCAT 5900
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (132 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3144 27.20 0.55 0.55  chrX_113778157_113784420.rev     4866  5773 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113778157_   4866 TGGAAGAACATTCTATGCTCATAGGTAGGAAGAATCAATATCGTGAAAAT 4915
                              ii i  i i   i    i i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113778157_   4916 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4965
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113778157_   4966 TACCAA-TGACTTTCTT-CACAATATTGGAAAAAAAT-ACTTTAAAGTTC 5012
                          v   i-  v    i  -  v  -    -- v  iv - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_113778157_   5013 ATATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAA 5062
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_113778157_   5063 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5112
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_113778157_   5113 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5162
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_113778157_   5163 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAAC 5210
                                 i    i--    i  --        vv  ii i ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_113778157_   5211 TATCTGATCTTTGACAAACCTGAGAAAAATAAGAAATGGGGAAAGGATTC 5260
                         i vi    i  i     ivv  vv  i vi vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_113778157_   5261 CCTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5310
                         i  v  i  i   i          v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_113778157_   5311 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5360
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_113778157_   5361 ATTAAAGATTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5410
                           i ?   ii    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_113778157_   5411 CCTAGGCATTACCATTCAGCACATAGGCATGGGCAAGGACTTCATGTCCA 5460
                          v    ?i v viv   ivv  v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_113778157_   5461 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5510
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_113778157_   5511 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5560
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_113778157_   5561 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5610
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_113778157_   5611 AAGGGCTAATATCCAGAATCTACAATGAACTTAAACAAATTTACAAGAAA 5660
                          i  i  vi          v  i  v     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_113778157_   5661 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5710
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_113778157_   5711 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5760
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_113778157_   5761 CATCACTGGCCAT 5773
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2664 24.85 5.98 1.06  chrX_113803015_113807047     2680  3532 (501)    L1M4_orf2#LINE/L1        1   895 (13)  

  chrX_113803015_   2680 TGGAGAGATATATCCTGATTATGGATTAGAAGAAGAATCAATATTATTAA 2729
                             i      vi v  v i       i     v--- i      i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC---TTAATATTGTTAA 47

  chrX_113803015_   2730 GATGTCAGTTTGCCCCCAAATGATCTGTAGATTCAACACAATTGCAACCA 2779
                             v  i viv    v  v      ii         i    iv v i  
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_113803015_   2780 AAACTCTCAGCAGGTTTTTTT-----AATCAAAAAGCTGATCCTAAAATT 2824
                            -  i    v vi      -----   ii v                 
  L1M4_orf2#LINE/     98 AAA-TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_113803015_   2825 TATGCAGAAAGGCAAAAGAACTACAATAGCTGAAACAGTTTTGAAAAACA 2874
                         i  iii    v    ii  v i v      ii     i i        v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_113803015_   2875 -GCACAA--TTGGAGAACTCATAATACTGGAATTTAGGACTTACTGTCAA 2921
                         - v    --      i     i v v ivi v  i ii       iiv  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_113803015_   2922 GCTACAGTAATCAAGA-AGAATGGTATTGTTGGAAAGAAAAGTGCATATA 2970
                                         -  vi     i  viiv  i  v iiiii   v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_113803015_   2971 TGAATGGATATA-AATAGAGGATCCAGAAATCAAC----AAAT--ATAAT 3013
                          v      -   -   v   ii         v   ---- v  --  ii 
  L1M4_orf2#LINE/    297 TCAATGGA-ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_113803015_   3014 CAATTAATATTTTTACTAA------AAGGCATTTCAATGGAGAAAGAATA 3057
                              i  -   iv  v i------   i vv        i         
  L1M4_orf2#LINE/    346 CAATTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_113803015_   3058 GTCTTTTCAACAAATG------------TTGGAAATCCACATTCAGAAAA 3095
                                         ------------i    v ?      v  i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_113803015_   3096 A-AAACCTGAATTCATATTTTACACCTTCTACAAAAATAAACTCAAAATG 3144
                          -i  vi  i ii v  ii i     v v         v           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_113803015_   3145 GAATATAGAGCTAAATTTAAAATGC-AAAACTACTAAACTTCTGGAAGAA 3193
                           vi ?   v      v   i -  -       iv     ii i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_113803015_   3194 AACAGAAGA--AAATCTTTAATGATATTGGGTTAGGCCAAGAGCTCTTAC 3241
                             v i ?--       ii-   iv           v v ivi     v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_113803015_   3242 CTATGATGTCAAAAACCACAAGCCATAAAA---AGAATGGGTAAATTGGA 3288
                         v     iii     i -      v i    --- i   i i         
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_113803015_   3289 CTTCATCAAAATTAAAAGCTTTTGCTCTTTGAACAACAGGATTGAGCCAA 3338
                                          i      iv   ii  vi   vv  ii  vv i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_113803015_   3339 TGAA--GAAAAGCCACAGATTGATAAAGAATATTCAGCAGTAACATATTC 3386
                             --  v  v       v  iv i i      iivv i v i    ii
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_113803015_   3387 AGTAAACGATTTGTATCCTGAATAGATAAAGAACTCTCAAAACTCAA-AA 3435
                         ii   iv  i        v     v            i v       -  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_113803015_   3436 TAAGAA---AAATGGCT-AATT-AAAAATAAG-AAGTTATTTGAACAGAC 3479
                            i  ---    ii i-    -      ii -  ivv       i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_113803015_   3480 ACTTCACCAAGGAAGATATGTAGCTATCAAATAAATAGACAATAAAATG- 3528
                          i   v    i        ii iv iv v     ii v ii v  i   -
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_113803015_   3529 TCAA 3532
                             
  L1M4_orf2#LINE/    892 TCAA 895

Transitions / transversions = 1.58 (128 / 81)
Gap_init rate = 0.03 (27 / 895), avg. gap size = 2.22 (60 / 27)  


 246 25.42 0.00 0.00  chrX_113810364_113813723      843   901 (2459)    L1M4_orf2#LINE/L1        4    62 (846)  

  chrX_113810364_    843 AGAGGCATACCCTGTTCATGGATTGGAAGAGTCAACATAGTAAAGATATC 892
                          i  ii  v  v                  v i  i  v  v     iv 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_113810364_    893 AGTTCTTCC 901
                          i v  i  
  L1M4_orf2#LINE/     54 AATACTCCC 62

Transitions / transversions = 1.14 (8 / 7)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  

1902 25.50 7.64 2.45  chrX_113810364_113813723     1250  1943 (1417)    L1M4_orf2#LINE/L1       21   750 (158)  

  chrX_113810364_   1250 ATGAATTTAGGGGGACACAAT-----TCAGCTCATAACACTTCTCAAATT 1294
                            i   --  ii   vi   ----- v  v vii  i   i i      
  L1M4_orf2#LINE/     21 ATGGATT--GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chrX_113810364_   1295 ----TA----TTTAATGCAATTCCTACCAAAACTCCAAAAAGGATTTT-- 1334
                         ----  ----  i  i     i    i     -   v ivv vv    --
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAA-TCCCAGCTGCCTTTTTT 117

  chrX_113810364_   1335 -AAGACATGATCAAGCTTGTTTTAAAATTTATATAGAAAGACACAGGTAG 1383
                         -v   v  viv      vi ii       i    i    vi  -   v -
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA-AGGGA- 165

  chrX_113810364_   1384 GTCCTTGAAGAACTAAAATAACCTTGAAAAAGAATGCATTAAG----AGG 1429
                         --  iv   v i i    i  i            - v iv   ----   
  L1M4_orf2#LINE/    166 --CCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GAACAAAGTTGGAGG 212

  chrX_113810364_   1430 AATCACTGTACCTGATATTAAGGATTACAAGACAGCTGCAGTAATCAAGA 1479
                          v    vv v  ii  v i  iiv    v v v    i            
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_113810364_   1480 TAATATCATATTTGCAGAGGAAGGGACACATAGATCAATGGAACAGAACA 1529
                         i i i vi  i v   v i i vi    i              i    iv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_113810364_   1530 AAGAATTCAGAAATATACCCACATAAATATGTCCAATTGATTTTTGACAA 1579
                         i   i i        v     i i vv    vi           i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_113810364_   1580 AGGTGCAAAAGTAATTCAATAGAGGAA---------------CAAATGGT 1614
                         i     v  iiiv       i i i  ---------------        
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_113810364_   1615 GCCAAAGAAAATGGTCCTCCATAGGTAAAAACAAATGAACTTTGATCTA- 1663
                           iiiiiv  v   viv?   i v i    i--      v  v  i iv-
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAG--AATGAAGTTGGACCCCT 460

  chrX_113810364_   1664 ACTTGATACC-TATACAAAAATTAA-----AACAGACCATAGACTTAAAT 1707
                           i v i   -              -----  ii  i  ?    i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_113810364_   1708 GTACAATGTAAAACTATAAAACTTTTAGAAAAAAAAAACACA-----AAA 1752
                            vi vv               i      i    ---  i -----   
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA---CATAGGNGTAAA 557

  chrX_113810364_   1753 TTTTCAGAATCTAGGGCTTGG----GGTAGTTCTTAGATTTGACAGCAAA 1798
                          i   ivi i  v   i v  ----   --         v     v    
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGT--TTCTTAGATATGACACCAAA 605

  chrX_113810364_   1799 AGCCCAATCCATAAAATGTAAAAATGTGTAAATTGGACTTTATCAAAATG 1848
                            v   v v i    - v      ivi            i        v
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_113810364_   1849 AAAAACTTTTGCTCTGCAAAAGAGCCCTTTAAAGGAATTGGAAA-ACCAT 1897
                                    iv  v    i  - v  v v   i  v  i   -  v i
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGA-CACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_113810364_   1898 CTACAGCGTGAGAGAAA-TATTTGTAAATGATACATCCAACAAAAGA 1943
                          i    vi  i      -      i    v   i   ii i  ii  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

Transitions / transversions = 1.43 (103 / 72)
Gap_init rate = 0.03 (23 / 730), avg. gap size = 3.04 (70 / 23)  


3314 26.32 0.55 0.55  chrX_113888492_113891148.rev     1259  2166 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113888492_   1259 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1308
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113888492_   1309 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATACCCATCAAGC 1358
                            v     v     iv i  i           i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113888492_   1359 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAGAACT-ACTTTAAAGTTC 1405
                          v   i-       i  -i     -   iv   --  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_113888492_   1406 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 1455
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_113888492_   1456 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 1505
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_113888492_   1506 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 1555
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_113888492_   1556 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 1603
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_113888492_   1604 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 1653
                         i vi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_113888492_   1654 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1703
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_113888492_   1704 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATCCAAGATGG 1753
                             ii    i    v   i     v           i  ii   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_113888492_   1754 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1803
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_113888492_   1804 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1853
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_113888492_   1854 AAACATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1903
                         vi   i        vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_113888492_   1904 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1953
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_113888492_   1954 CAAGCAACCTGCAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 2003
                         v ii     ii  i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_113888492_   2004 AAGGGCTAATATCCAGAATCTACAATAAACTCCAACAAATTTACAAGAAA 2053
                          i  i  vi          v  i  vi     iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_113888492_   2054 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 2103
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_113888492_   2104 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 2153
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_113888492_   2154 CATCACTGGCCAT 2166
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1760 26.81 9.72 4.22  chrX_113914541_113918623.rev     2739  3592 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_113914541_   2739 ATATGCATACGTACATGGATTGGAAGCCATAGTATTGTTAAGACA--AAT 2786
                             v -i i  v             v v  i           ii--   
  L1M4_orf2#LINE/      8 ATATCC-CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_113914541_   2787 CCTCACTTAGCTGACTTATAGATTTAATGCAATACCAATTTTAAAACAAT 2836
                         v   v iv ii   ii  i     i  i     v  v  i--    ivvi
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC--AAAATCCC 104

  chrX_113914541_   2837 AGCATATTTTGTTTTG--GGGGTTGACAAGCTAATTTTAGT-TTTATATG 2883
                            - iii  -     -- iii          i  ii  iv-  i     
  L1M4_orf2#LINE/    105 AGC-TGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_113914541_   2884 AAAATGAAAAGGCCTTAGGCTAGCCCAGAAAATTTTGAA---GAAGAACA 2930
                         i     v  i  v ii  iv     v i v   i     ---        
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_113914541_   2931 CAGCTGACAGACTTACTCAACTAGATTAGAAGACTTAGTATAAAGCTATA 2980
                         v  i  ivi    i  v vv ivi   vv  i     v  i       i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_113914541_   2981 GTAATTAGGACATTGTAATACTAGTACAAGGACAGA-ATATTAGATCAAT 3029
                              i i    v   ii    i i i     i   -    -        
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT-AGATCAAT 301

  chrX_113914541_   3030 AGAACAGAACTTATAGCCCAGGAG-AAACAACATATAT--AAGGTAACCT 3076
                         i   i    i v v  i    i i-    v-    i  -- v   v vi 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACC-CATACATTTATGGTCAATT 350

  chrX_113914541_   3077 GACTTATGAGAATGACGCCATTGTAATTCGGTAGGCAA-GAATAATCTTT 3125
                           i  vi  v  v ii    vviiv    ii i  v  -     i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_113914541_   3126 CCAATAAATGATGCTGAGTCAACTGGATATTCACAT---AGGGAA-AAAA 3171
                         i   i     i     i v          ?i     --- ii   -i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_113914541_   3172 TTCAATCTCTAGCTCGCATCAGACGTATACATTAAGTTAAGATGGCTCCT 3221
                           vi i i   v   i  i  v iii v v     v i  i    v  v?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_113914541_   3222 GGACCTAAATGTGAAAGCTAAGATGATCAAACACTTAAGAAAGGAAGGAA 3271
                         i           i i      i iv  v    v    ------    i  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA------GAAGAAA 544

  chrX_113914541_   3272 ATACAAAGACAGAGGAGGTTATCCTCTTGAATATCCTCTTGAACTCTGGA 3321
                          --------  v   ? ---------- i   -- i  v   v  -   i
  L1M4_orf2#LINE/    545 A--------CATAGGNG----------TAAAT--CTTCGTGACCT-TGGG 573

  chrX_113914541_   3322 TGAGAAAACT-TTTCATAAACCGGATAA-AAAATCACTGGCCATTAAAGA 3369
                          v  iv  iv-    v  i ivv  i v-    v   vi  v iv     
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_113914541_   3370 AAACGCTGACAAATTGAACTTTA-----------AACGAGTGT------A 3402
                            viiv  i      i    i -----------   vvv   ------ 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_113914541_   3403 AGG------TCA------TG-----------CACAGATTGGGAAAAAATA 3429
                            ------   ------  -----------      v     i      
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_113914541_   3430 TTTTCACTATACATATCCGACAAAGAACTCTTATCTAGACTATACAAAAA 3479
                            v  vvvi i     i  i  i i   iv    i   v    i   i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_113914541_   3480 A-----ACA-CT--AGAATTAAAA------------AATT-GAAAATAGG 3508
                          -----   -  -- v   v    ------------    -i     i  
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_113914541_   3509 CAAATGGTGT---TAAAAATTCATCACAAAAGAGGACGTCGAAATGCTTA 3555
                             v i v ---  i v   --  v v     i  ii vv     vii 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATT--TCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_113914541_   3556 AAAACCATAACAAAAAGTGCCCAACATTATGAGTCAG 3592
                          v  v  i vv    ii   i      i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.04 (35 / 901), avg. gap size = 3.40 (119 / 35)  


2824 26.97 1.26 0.80  chrX_113918776_113920642.rev      502  1376 (491)    L1M4_orf2#LINE/L1       30   908 (0)  

  chrX_113918776_    502 AAGAATTAATATTGTTAAAATGTTCATACTGCCCAAAGCAATATAGAGAT 551
                             v             i   viv     v      vii  v  v    
  L1M4_orf2#LINE/     30 AAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGAT 79

  chrX_113918776_    552 TCAACACAACCCTTTTAAAAATCCC-GATGCCTTCCTTATCAGAAATAGC 600
                              i   i  i v v        - v      ii  i-       v -
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG-CAGAAATTG- 127

  chrX_113918776_    601 AAAAGC-AATAATAAAATTTGTATGGAATAATAAAAGACCCCAAATAGCC 649
                          v    -i  vv       ii       vvii  ii     vi       
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chrX_113918776_    650 AAAATAATTCTGAGAACAAA---TGAAGTTGGAGGCATCATACTTCCTT- 695
                             i   ii   i  vi  ---ii          vv   i      iv-
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_113918776_    696 TTTTAAGATAGTATTACAAAACTATAGTAATCAATATCGTATGGTCCAGG 745
                            i  i i-v  i      i   i         v iv  i    v v  
  L1M4_orf2#LINE/    228 TTTCAAAAC-TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_113918776_    746 CAGAAATACAGACACACAGACCAGTAAAACAGAATAGAGAGCCCAGAGAT 795
                           v  iv i     i i   i  i ii  i     v     i     i  
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_113918776_    796 AAATCCAAACACAAATTGTCAATTTGTTTTTGACAAGGGCATCAATAAAG 845
                            i   v   ivv  v       vi    i        iii   v vvi
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_113918776_    846 CCCAATAGGAAAAGGATAATTTCTTAAATAAATGATGCTGTAAAAACTCT 895
                         ii    i  i    i   i i i  v  i     i     vi v    vv
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_113918776_    896 ATTTCCATATGCAAAAGAATGAAATTTGACCCTTATCTGACATCATGCAC 945
                           v?   i               i  v     i  i  v   i   ii  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_113918776_    946 AAAAATCAACTCAAAATGTATAAAAGGCCTACATACAACA-CTAGACACT 994
                               i           v  v ?  i    v  ii  v -   i -   
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA-ACT 525

  chrX_113918776_    995 GTAAATCTCTTAGAAGAGAACATAAAGGAAAAGCTCTTGT-ACATTAGGC 1043
                         i    v           i      ii? v   v  - i  -  v  i  i
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT-TCGTGACCTTGGGT 574

  chrX_113918776_   1044 TTGGAAATGAATTTTTGTATATCATGTCAAAAGTGCAGGCTACAAAAGCA 1093
                          v  v    iv  i  iv    v iii      ii  i  v       v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_113918776_   1094 AAAATAAATAAATGGGATTAAATCGAA-TTAAAAAGCTTCTAAACAGTGA 1142
                               i      v   i vv   i  -       -   i ivi vvii 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chrX_113918776_   1143 AGGAAATAATCCACAAGATGAAATGGTT-CCTATGAATTGAGAAAAAAAT 1191
                             v iv   v v  ii     v iiv-  i iii v  i  i    - 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-T 722

  chrX_113918776_   1192 ATTTGCAAACCATATATCTGTTAAAGGGTTAATATCCAAAATTTATCAAT 1241
                                  i          v   i  ii vi      i   v   v  v
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_113918776_   1242 AACTTGTTCA-CACAATAATGGAAAAACAAATATCCTGTTTAAAAATTAG 1290
                             iv v  - v       ii   i       v  iiv  ?    v i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_113918776_   1291 AAAAAAGACAAGAATAGACACTTCTCTGTGGAAGACATAAAAATCTCCAA 1340
                         iv   i  ivv         i     iivi     i   v    vv    
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_113918776_   1341 CAGGTATATGTAGAGGTGCGCAACATCAATTAATCA 1376
                         i i i i   v i  i   v        ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.02 (16 / 879), avg. gap size = 1.12 (18 / 16)  


3669 20.25 3.94 1.80  chrX_113938155_113941685.rev     2152  3040 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_113938155_   2152 TGGACATAAATCCTCATGCTCATGGATT---AGATTTGAAATACTTAAGA 2198
                             v v v    -    i         ---   i  i v  vv      
  L1M4_orf2#LINE/      1 TGGAAAGATATCC-CATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_113938155_   2199 TGACAATACTTCCCAAAGTTACCTAAAAACTCAACAAAATTACTATCAGC 2248
                           i       i      v v i   v i i     iv   iv      iv
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_113938155_   2249 ATCCCAGATGACTTCTTTGTAGAAATTGTCAAGCCTATTATAAAATTCAT 2298
                                v  v   i    i        v     iv  iv          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_113938155_   2299 ATGAAATTGCAAAGGACTCAGAGTAGCCAGAGTAATAGTAATCTTGAGAT 2348
                            i  v     i    i    i      i ii   ------     i v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT------CTTGAAAA 193

  chrX_113938155_   2349 AAAAGAGCAAAGTACGAGGACTCGCACTACCTGATTTTCAAACCAACTAC 2398
                          i    i      vv        i    v  ii    iv    iv     
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_113938155_   2399 AAAGCAGTGGTATTCAAGACCAGGTGGTACTGACATATATATAGACATAT 2448
                              viii   v       viv         i    viv          
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_113938155_   2449 AGATAAATGGAATAGAATTGAGAGGCTACAAGTAAACACATGGTTTCTAT 2498
                             v                   v i v  i     v   ivv  -   
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TAT 342

  chrX_113938155_   2499 G--TAACTGATTTTCAACA-GAGTGTCAAGACAATTCAGTGAAGGAAATA 2545
                          --i  i        i   - i   i      v     i  i-     v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGA 391

  chrX_113938155_   2546 ATAGTCTTTTCAACAAATGGTGCTAGGATAACTGAATACCAACATGCTAA 2595
                                                 i   i     i   ? v      v  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_113938155_   2596 ACAATAAAATCATACCCTTATCTTGCACCATTCACAGAAAAAAAAAAACC 2645
                          v   i  i iiv    i  i  ii      vi   i   vv  ------
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA------ 485

  chrX_113938155_   2646 CTCAAAATAGTTCAAAGACCTAAAAGTAAGGGGTAAGACTGTACAACTTT 2695
                                 i v   ?         v     i v   i   i  v    i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_113938155_   2696 TAGATGAAAACATAGGACTAAATCTTCATGACTCCAGCTATGACAATGTT 2745
                             v           ?v         i    iiii v vv i     v 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_113938155_   2746 TTCTTGAATATGACACTAAAAGCACAAACAACAA--GGTAAAATAAA--- 2790
                              ii         i          i      -- iv      i ---
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_113938155_   2791 ----GACTTTATCGAAATTAAAAAATTTTACACTGCAAATGATGCCATCA 2836
                         ----     i   i          v    iii  v    v  ii i    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_113938155_   2837 AG----------GACAACTAAAATAATGGGAGACAATAATTTCAAATCAT 2876
                           ----------      iv v v         v    v  v        
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_113938155_   2877 -TATGTG-T------CTTTCATCCAGAATATTTGTTACAATCCTGACAAT 2918
                         -   v  - ------   vi           v iv- v  ii  v    i
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAA-AGAACTCTTACAAC 784

  chrX_113938155_   2919 TCAGTAGTAAGA-GATAAATAACCCAATT-AAAATTGGGCAAAGGATCTG 2966
                            i  i   i -  i             -    v            i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_113938155_   2967 AAAACACATTTCTCCAAAGAAGATATGCAGATGGCCTATATGTATGTGAA 3016
                           v v                     i  i      v   v i ii    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_113938155_   3017 AATATGCTCAACATCATTAGCTAT 3040
                           v             ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (100 / 77)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.00 (51 / 17)  


 250 26.67 2.67 3.33  chrX_113949445_113951984      852  1001 (1539)    L1M4_orf2#LINE/L1        1   149 (759)  

  chrX_113949445_    852 TGGAATGATATTACATGTTTTTGAATTGAAAATCTAAAAATTAAAATATA 901
                              v     iv      iv  i    i  iv  v  v   ---i -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT---GT-TA 46

  chrX_113949445_    902 ATATATTAATA-TATCTAAATTAATCTATAGATTCATATTAATCC--AAA 948
                          v  ivi    - vi i     i     i       vvvi     -- vv
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_113949445_    949 AATAATCACATCAGGCTAGTTT-CAGAAACTGACAAACTGATTTTATTAT 997
                           -    v  v v v  vv   -      i      i     ii  vv  
  L1M4_orf2#LINE/     97 AA-AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_113949445_    998 TTAT 1001
                          i  
  L1M4_orf2#LINE/    146 TCAT 149

Transitions / transversions = 0.82 (18 / 22)
Gap_init rate = 0.04 (6 / 149), avg. gap size = 1.50 (9 / 6)  

1689 26.46 7.06 1.76  chrX_113949445_113951984     1311  2047 (493)    L1M4_orf2#LINE/L1      133   908 (0)  

  chrX_113949445_   1311 CTGATTTTAAAATTTATAAGGAAAAGTAATGGACCTAGGAGAGTTAAAAT 1360
                              ii       i   v     v i  v     i  i v  ii    i
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chrX_113949445_   1361 AATTTTGAAAAAAAAT--CTA----GGAGCATTTAT-----CTGATCTCA 1399
                            i        i  v-- v ----    v i i i----- ii  i   
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_113949445_   1400 AGACATACAATATAGCTAAAGTAATCAAGAGAGTG-GTTATTGGCACAAG 1448
                          i  v   v i v     v           v    - v  i     i   
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_113949445_   1449 AATAAAGAAATAAATCAATGCAATTTTTAAAA--AATAGTCCAGAAATAT 1496
                         i   i v v   i       v   ---- i  --i v            v
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAAT----AGAATTGAGAGTCCAGAAATAA 328

  chrX_113949445_   1497 ACTCACACATAAACTATCAGTT---TTCCAAAAAAAGTGCCAAGATAATT 1543
                           i  i    vv ivi   i  ---  i i v  ii         iv   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_113949445_   1544 AAATAAGAAAA--ATGTTTTTTTCAATAAATGTT-CTGAGGC--TTATGT 1588
                         v   ii i   --  iv i       i     v -   i i --i ivi 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_113949445_   1589 A--CAAATTGGTATAAAAGAATTAACCTTGACTTCAACCTCATAGTATAT 1636
                          --  v  ----ii        v  vi v   ii v      i vi    
  L1M4_orf2#LINE/    429 AKCCACAT----GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_113949445_   1637 ACAAAA-TTACCTTAAGCCAGATCATCAATCTAAATATAAAATCTAAAA- 1684
                               -   v  i  ivii     ?vi i      i   i v      -
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_113949445_   1685 -GCAAAATTATTATAGATAAAATATAAAAGAATATCTTCATAACCTTGCC 1733
                         -ii    i v   v - v    i   ii? v v      i i      vv
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGA-AGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_113949445_   1734 ATAGGCCAATA-TGCTTTGAATAGGAAACAAAACACATAAATTAAGAAAT 1782
                         v     -   i- vii  ii   v  v  v   vi  i  iiv vi   v
  L1M4_orf2#LINE/    574 TTAGGC-AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_113949445_   1783 TAAAAGTTGACAAATCAAACTTCA---AAATTAAAAACTGCTCT--TTGA 1827
                         v    i v  i    iii      ---            vi v --  v 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_113949445_   1828 AAGACGACAATATTAAGGAAATAAAAAAGACAAGCCAAAGACTCAGAGAA 1877
                            --    v   i   i  i i    -     v   v   v vi     
  L1M4_orf2#LINE/    673 AAG--GACACTATCAAGAAAGTGAAAA-GACAACCCACAGAATGGGAGAA 719

  chrX_113949445_   1878 AATATAGGCAAG--ATATATCTGACAAAAGACGTGTATGCAAAATATATA 1925
                              vv    i--          i  ii   v     v  i        
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_113949445_   1926 AAGAGCTCTTA-AA---AATAA------GTCAAACAACTCAACT-GAAAA 1964
                             i      -  ---     ------ v    i   i   i -i    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_113949445_   1965 TGGG-AAAAATCTTGAA----CACTTTATAACAGAGTATATCCAAATGGC 2009
                             -   iivi     ----  i  iviv v   iv    v        
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_113949445_   2010 -AGTAAGTATATGAGACATTGTTCAGTGTCATAGACTGT 2047
                         - i    i i    i viv  i   iii   ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (117 / 76)
Gap_init rate = 0.04 (29 / 776), avg. gap size = 2.24 (65 / 29)  


 468 26.72 0.76 0.76  chrX_113994741_114001667.rev     5200  5330 (1597)    L1M4_orf2#LINE/L1        1   131 (777)  

  chrX_113994741_   5200 TGGAAAAACAATCCATGCTTATGGACAGGAAGAATCAAGATCGTGAAAAT 5249
                               i i vi     i i     iv      v i  v  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_113994741_   5250 GGCCATACTGTCCAAAGTAATTTATAGATTCATTGCTATCCCCATCAAGC 5299
                            v     vi     v i  i  i       vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_113994741_   5300 TACCA-CTGACTTTCTTCACTGAAGTAGAAAA 5330
                          v   -   v    i  -i v   i v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA 131

Transitions / transversions = 1.19 (19 / 16)
Gap_init rate = 0.02 (2 / 131), avg. gap size = 1.00 (2 / 2)  

2442 26.62 1.15 2.93  chrX_113994741_114001667.rev     5652  6436 (491)    L1M4_orf2#LINE/L1      138   908 (0)  

  chrX_113994741_   5652 CTTTAATTTCATATGGAACCAAAAAAGAACCTGCATAGCCAAGACAATCC 5701
                          i v  v           viiv  ii  v  v v        i      i
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chrX_113994741_   5702 TAAGCAAAAAGAACAAAGCTGGAGGCTTCACCCTACCTGACTTCAATCTA 5751
                          i iv  i          i      vi    v  v  ii i     vviv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_113994741_   5752 TGCTACAAGTCTACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAG 5801
                          i      iv      i  i   i    ii         i iv ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_113994741_   5802 ATATATAGACCAACGGAACAGAA--AAGAGGCCTCAGAAATAATGCCACA 5849
                          i       i   i    i    --i    v  --        vv   i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATA 335

  chrX_113994741_   5850 CAGCTACAACCATCTGATCTTTGACAAACCTGACAAAACAAG-CAATGGG 5898
                           vi  iiii  vi    i  i     ivv  v   i  v v-       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_113994741_   5899 GAAAGGATTCCCTATGTAATAAATGGTGACGGGAAAACTGGCTAGCCATA 5948
                              i  vvi  v vi  i        vi    v      v  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_113994741_   5949 TGCTGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAA 5998
                            vi  i v    ii         v   i     v              
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_113994741_   5999 CTCAAGATGGATTAAAGTCTTAAATGTAAGACCTAAAACCATAAAAAACC 6048
                              i      i ?  v i           v       i      vv i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_113994741_   6049 TAGAAGAAAACCTAGGCAATAACTTTCAGGACATAGGCATAGGCAAAAAC 6098
                                    v    ?ivv  ii   iv   v v  vv       viii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_113994741_   6099 TTCATGACTAAAACACTGAAAGCAATGGCAACAAAAGCCAAAATTGACAA 6148
                            v iiv  vi    ii      vvi          vv     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_113994741_   6149 ATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAAAAAAAAAAA 6198
                           v   ii v  i   v v  i i   i  ii vv    ii v ------
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA------ 679

  chrX_113994741_   6199 AAAAAAAAAAAAAAACTATCATCAGAATGAACAGGCATTCTACAGAATGG 6248
                         ---------------      vv i i    v  i  vi i         
  L1M4_orf2#LINE/    680 ---------------CTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_113994741_   6249 GAGAAAAATTTTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGATT 6298
                                vv       vii  vi      i  i  i  vi        v 
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_113994741_   6299 CTACAAAGAACTTAAACAAATTTACAAGAAAAAACCAA----CCCCACCA 6344
                         v  i        ivv    v iv i  v     iv   ----   v ii?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_113994741_   6345 AAAAGTGGGTGAAGGATATAAACAGACATTTCTCAAAAGAAGACATGTAT 6394
                             i    ii      v i  i           v        i  ii v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_113994741_   6395 GCAGCCAACAA--ACATGAAAAAAAGCTCATCATTACTGTTCAT 6436
                         iii     i  --         i v     v   i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (117 / 88)
Gap_init rate = 0.01 (6 / 771), avg. gap size = 5.33 (32 / 6)  


1800 27.38 8.46 2.70  chrX_114025672_114027640      641  1491 (478)    L1M4_orf2#LINE/L1        9   908 (0)  

  chrX_114025672_    641 TATATCATGTTAATGAATTGGAAGGCTCAATGTTATGATTATGAGACTCC 690
                            vi      v   i        i  i   i  i v vv   iv v v 
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chrX_114025672_    691 TCCCCAAAGTAATCTATATATTCAGTGCAATCCCAATACAAATATCAGCA 740
                                 v i     i v     ii        v  vv    vi    v
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chrX_114025672_    741 GGGTTTTTTGTGGAAATTGGCAAACCAGTGCTAGAGTATATACGGGAATG 790
                          vv       ii       i   i iii v   i i vi   i  i    
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_114025672_    791 CAAAGGGCCAAGAATATTCAGA-CAATTTTGTGTAAGAAACAGAACAAAA 839
                            i  i  v      vi  i -    i   ---  i  iv        i
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTG---AAAAAGAAGAACAAAG 205

  chrX_114025672_    840 CTGGAGGATTTATACAACCAGATATCAAAACTCAT---AAAGCTATAGTA 886
                         i       i i i  vv  vi  v        i i---       i    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_114025672_    887 ATTTAGACATTGTGGTACTG-CAAAAAGATAACAAAATAGACCAATGGAA 935
                           iv     v          -  v  i    ivv v     i        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_114025672_    936 CAGAAT--AAAGTCCA-AAATAGATCC-------CATGGTGGCACTGAA- 974
                         i     -- i      -     i i  -------i     --  v vi -
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT--CAATTGAT 353

  chrX_114025672_    975 ----GAGAAGTGGGTGAAGACTTTTT-------------TTTTTTTTTTA 1007
                         ----  v   v v iv     iv  i------------- vv i    i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_114025672_   1008 ACAATAAGTGGTGCTACATCAATT---TA---ACATGAGAAACA--GAAA 1049
                             ---i       iviv   i ---  ---     vi   v --   i
  L1M4_orf2#LINE/    404 ACAA---ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_114025672_   1050 ---AATCCTTGTCTT-TACTGGAGATAAAAGTTAATTCTAGGTAGACTGT 1095
                         ---i i  i ii  i-i  iiv v i    i    i  v ii i  iii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_114025672_   1096 AGATCTAAATATAAATAGTAAAACAACAAAGCTTACAGAGGAAG---TAG 1142
                            i      i   iviv      v i   i  ivi   i   i---   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_114025672_   1143 CATTGAATATATTGTGTCCTTGAGGTAAGAAAAGCTTTCTTAAACAGGAC 1192
                         v?v i   v - i   v     i v  i v  v v       i i v   
  L1M4_orf2#LINE/    551 GNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_114025672_   1193 GTATAAAAG-ACGAACCAAAAAGGAAATGATTGATAAAC--AAC---ATT 1236
                         ii-i     -  i i v v   i    vi  v      i--i  ---  i
  L1M4_orf2#LINE/    600 AC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_114025672_   1237 AAAATTAAGGACATCTGTTCATTGA-GCTCACAACAAAGAGACTACAAAG 1285
                                 ii  v i   v v ii - vv   v iv    i v iv    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_114025672_   1286 GCAAGCCACAG--TAAGAAAAGATATTTATTTGCAATGCATA-AT-TAGC 1331
                         i   v      -- ii  i  i      ----    vv    -  - iii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTT----GCAAATCATATATCTGAT 744

  chrX_114025672_   1332 AAAGAATTCATATCCATAAGGTATAATATAAAAAACTCATAACAA-TAAA 1380
                           i i i ii      v  --    ---    i     v  -   - v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAA--TATA---TAAAGAACTCTTA-CAACTCAA 788

  chrX_114025672_   1381 TAATAAAT-GACAGATATACCAATATAAAATTAAGCAGAAGACTTTAACA 1429
                                v-    i   vv     v?    v ii   i i  i  v  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_114025672_   1430 AGTATTTTGCAAAAGAA--TAT------GGCCAATAA--ACATAAAAAG- 1468
                         iii    iv v      --   ------         --    i     -
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_114025672_   1469 TCCTTAATCACATTACTAATAAT 1491
                          v  i  ---   i ????????
  L1M4_orf2#LINE/    889 TGCTCAA---CATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (141 / 89)
Gap_init rate = 0.04 (37 / 900), avg. gap size = 2.57 (95 / 37)  


2417 18.75 8.10 6.68  chrX_114029040_114030735      500  1203 (493)    L1M4_orf2#LINE/L1      195   908 (0)  

  chrX_114029040_    500 GAAGAAGAAAGTTGGAAGACTCATACTTTCTGATTTCAAAACATACTACA 549
                               v         i      i    i ii          v       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_114029040_    550 AACCTACACAAATTAAGACAATGTGGCACTGGTACAGAGTTAGGCATGTA 599
                           v     vv   i      i     i     i i ii v   i   i  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_114029040_    600 GATCCAAGGAACAGAATTGAGAGTACAGAAACAAA-------ATTTCAGG 642
                             v v    i            v      i   -------    vv  
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_114029040_    643 TCAACTGATTT-CAACAAAGGAGTCAGAAAAATTCAATAAGGAAAACATA 691
                             i      - i    i  v i  ii vv       ii     iv   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_114029040_    692 GCCTTGTCAGCAAATGATAGTAGGACAAATGAATATCAACATGCAAAAGG 741
                          i   v   i      i iv i      v  i   ? v           i
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_114029040_    742 ATGAA-TTGGACC----------AACATACACAAAAAT-AATTCAAATTC 779
                              -       ---------- v    i        -  i     v v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_114029040_    780 AATTATAGATATGAGCATCAGAGTTAAATCTATAAAAATCTTAGAAGAAA 829
                         i  i ?   iv i iii v    i    v        v            
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_114029040_    830 ATATTGGAGTGAATCTTCATGACCTTG---------------------AT 858
                          i  v  ?  i       i        ---------------------  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_114029040_    859 ATGACACCAAAATTACAAGCGATAAGTGA-----TTGATTACAGTTTGCT 903
                                     vi      i i  iv  ----- v   - - i  v vi
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT-A-AATTGGAC 642

  chrX_114029040_    904 TTCATCAACATTAAAGATGTTTGTAATTCAAAGGCCACCACCAAGAAAAT 953
                                 v      i iv     iv        v   i i       i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_114029040_    954 AAAAAGACAG----------GGGAGATAATTTTTGCAAATAATATACCTT 993
                         i        i----------      v   v         v     i  v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_114029040_    994 ATAAATTTTCATTTGAACACCTATTTTCAATTCTCTTGGGTATATATCTA 1043
                             i--------- i  -----------------   ------    i 
  L1M4_orf2#LINE/    743 ATAAG---------GGAC-----------------TTG------TATCCA 760

  chrX_114029040_   1044 GGGATATATAGTAGAATATATAAAGAAAACTTACAACTTCACAGTAAAAT 1093
                          -------------             vv         iv i i     v
  L1M4_orf2#LINE/    761 G-------------AATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_114029040_   1094 GATATGCAACTCAATT-AAAAATGGGCAAAGGTTTCAAAGAGGCATTTCT 1142
                           i vii   i     -               v  ii  v  i       
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_114029040_   1143 CCAAAGAACATATACAAATGGGCAGCAAGCACTTGAAGAGATGTTCAATG 1192
                                 v            v  ii      v    i     i    ii
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_114029040_   1193 TCATTAGGCAT 1203
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.58 (79 / 50)
Gap_init rate = 0.02 (15 / 714), avg. gap size = 6.93 (104 / 15)  


2114 26.49 3.26 2.31  chrX_114045952_114047679      500  1235 (493)    L1M4_orf2#LINE/L1      166   908 (0)  

  chrX_114045952_    500 CCCCAAATAGCCAAAGCAATCATAAGCAAAATGAAAAAATCTGGAGGCAT 549
                            vi          i     v i iv  i v   v   vi      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_114045952_    550 CATATTGCTGGATTTCAAGTTATACTACAAGGTTATAATTACCAAAGCAG 599
                           i i v ivi       iviv        i i  i i v i   ii   
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_114045952_    600 GATGGAACTGGTATAAAAGTAGTCACATAGACCAACGGAACAGAATAGAG 649
                         vi   v     i    iii   v  i     i   i    i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_114045952_    650 AACCCAGAAGTAAAGACAAATATGTACAACCGATTGACCCTTGAAAAAGC 699
                          ii      i    vv  v i  v  iiii i     iii i  v  i -
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG- 364

  chrX_114045952_    700 ATACAAAAAC-ATAAATTGGAGAAAAGACACCATATTTAATAAATGGTGC 748
                         i i v  i  -  vv v   i    ii i viv v  i  i         
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_114045952_    749 TGGGAAAATTGGCCAGTCACATGTAGAAGAATGAAACTGGATCCCTATCT 798
                              v  i   vi ?i      i i         ii    i     i  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_114045952_    799 CCCAACATATACAGAAATCAACTCAAGATGGATCA-AGACCTGAA----- 842
                          v  v        i    i       i        -      i  -----
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_114045952_    843 --------ACCATACAAATTCT-GGAAGAAAGTCTAGCAAAAACTCTTCT 883
                         --------  i   -   i   -i       iiv   v?iv  v     v
  L1M4_orf2#LINE/    515 GAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_114045952_    884 GGGCATTGTCCTAGACAAAGAATTCTTGACTAAGACCCCAAAAGACCCCA 933
                         v i v   vvi   i   v iv     -----   i----- v   v   
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTT-----AGAT-----ATGACACCA 603

  chrX_114045952_    934 AAAGCAAAGGCAACAGAAACAAAAATAAATAAATGGGATCTCGT-AAAAT 982
                               v i      i  iv       i      v   ii  i -     
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_114045952_    983 TAAAAAGATTCTGCACAACAAAAGAAATAATTTTGA--GTAAAGAGACAA 1030
                               v-  i  ii vv    i  v iv  ivv  --  i  i      
  L1M4_orf2#LINE/    654 TAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_114045952_   1031 ACCACAGAATGTGAGAAAATATTTGCAAACTATGCATTCAACAAAAGACC 1080
                         v          v                 ii  ii  iii i  ii   i
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_114045952_   1081 AGTATCT-GAATCTATGAGGAACGCAAACAAATCAGCAAGAAAAAAAAAA 1129
                         v     i-    v   i i    v vv    v   --- v  v     i 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCA---ATAATAAAAAGA 799

  chrX_114045952_   1130 CAAATAATCCCATCAAAAAGTGGGCAAAGGACATGAATGGACATTTATCA 1179
                                i  v  i?    i           iv     i       v  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_114045952_   1180 AAAGAAGA----CAATCAACCAACAAACATTTGAAAAAAATGTTCAACGT 1225
                                 ----   viii    i  i  iv      i -  i     i 
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACAT 898

  chrX_114045952_   1226 CACTAATCAT 1235
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.67 (120 / 72)
Gap_init rate = 0.02 (15 / 743), avg. gap size = 2.73 (41 / 15)  


3125 26.23 0.77 1.10  chrX_114138232_114144654.rev     5022  5932 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_114138232_   5022 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5071
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_114138232_   5072 GGCCATACTGCCCAAGACAATTTATAGATTCAATGCCATCCCCATCAATC 5121
                            v     v     ivii  i  i        i  v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_114138232_   5122 TACCAAAGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5169
                          v   ivvi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_114138232_   5170 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5219
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_114138232_   5220 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTAGAAGGC 5269
                                i      vv    i  v  ii i      viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_114138232_   5270 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGATC 5319
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_114138232_   5320 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 5367
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_114138232_   5368 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGGAAAGGATTC 5417
                          vi    i  i     ivv  vv  i v  vv        -    i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAG 395

  chrX_114138232_   5418 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5467
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_114138232_   5468 TGAAACTGGATCCCTTTCTTACACCTTATAAAAAAATTAATTCAAGATGG 5517
                             ii    i    vi  i     v    v         i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_114138232_   5518 ATTGAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5567
                           ii?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_114138232_   5568 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCT 5616
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_114138232_   5617 AAAACATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5666
                          vi   i        vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_114138232_   5667 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5716
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_114138232_   5717 ACAGGCAACCTACAAAATGGGAGAAAAT-TTT-CACATCCTGCTCATCTG 5764
                          v  i     i   i             -   -  v   v ii--     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTG 742

  chrX_114138232_   5765 ACAAAGGACTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 5814
                          i  i     vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_114138232_   5815 AAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACA 5864
                              i     i     v  i?    i     i     iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_114138232_   5865 CTTCTCAAAAGAAGACATTTTTATGCAGCCAAAAAACACATGAAAAAATG 5914
                         i     v        i  vivv   --     v  i          i   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATG 890

  chrX_114138232_   5915 CTCATCATCACTGGCCAT 5932
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


2982 23.80 3.59 0.53  chrX_114151239_114155562     2509  3260 (1064)    L1M4_orf2#LINE/L1        1   775 (133)  

  chrX_114151239_   2509 TGGAAAAATATCCTGTACTCATGAGTTGGAAAAATTAATATTGTTAAAAT 2558
                               i      ii ii     ii      i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_114151239_   2559 GTCCATACTACACAAAGTGATCTGCAGCTTGAACACAATCCCTATCAAAA 2608
                          v v     v v    v      i   v  v   i               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_114151239_   2609 TTTCAATGACATTTTCCATAGAGATCAAACAAAATAATCATAAAATTCAT 2658
                          ii  iivi v    iiii   i  ii -   iv i   v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_114151239_   2659 ATGGAGCCACAATACACCCAGAATAGCCAATGCAACTGTT----ACCAAG 2704
                              ivii   viv               vi   - v  ---- vv   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAG 198

  chrX_114151239_   2705 AACAAAGCAAGAGGCATCATATTACCTGATTTCAAAATATACTACAAAAG 2754
                                ivi    vv   i i v  ii         iv         - 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-G 247

  chrX_114151239_   2755 CTATAGCAATCAAAACAGCATAGTACTGAAATAAAAACAGACACATCAAC 2804
                            i  i      i    ii i      iv    ii i     i  vi i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_114151239_   2805 CAATAGAATAGGATAGGAAGCCAATAAATAAGCCTACATATCCATGGTCA 2854
                             i      i  v ii  i v v      i  i i i  ii       
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_114151239_   2855 ACTCATTTTTGACAAAGGCCCTAAGAACACATAATGGGAAAAAAACAGTC 2904
                          i v     i     i  iv i    v  ivi      i   i  i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_114151239_   2905 TTCTCAATAA-CAGTGTTGGGACAACTGGATATCAACATGTAGAAGAATG 2953
                           i    i  -ii   i               ? v     i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_114151239_   2954 AAACTGGACCCTAATCTCACACCATATACAAAAAAACAACTCAATACGGA 3003
                           ii       iv i                   v-i       v i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAACTCAAAATGGA 496

  chrX_114151239_   3004 TTAAAGACTTAAATGTAAGACCTGAAACTGTAAAACACT-AGAAGAAAAC 3052
                          i ?    i           v  i     i      v  -          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_114151239_   3053 ATAGGGGCAAAGCATCTAAACATTGGTCTGGACAAAGAATTTTTGAATAT 3102
                              ? i   v v  vvi  v    vi i i   v iv  i  ii    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_114151239_   3103 GACCCCAAAAGCA---------------AAAATAGACAAATGGGTTTGTG 3137
                            v         ---------------        i    v  vi vii
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_114151239_   3138 TCAAACTAAAAAGCTTCTGTGCTG-AAAAGA----ATCAACGAAGGGAAG 3182
                              v v    i   i      v-   i  ----     vi   v   i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_114151239_   3183 AGACAACCTTTGGTATGG-AGAAAATATTTGCAAACTATATATCTGATAA 3231
                                 ivii v    -                ii             
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_114151239_   3232 GGGGCTAATATCCAAAATAAATAAGAAAC 3260
                            i  vi      i    v    ii   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAAC 775

Transitions / transversions = 1.93 (116 / 60)
Gap_init rate = 0.01 (11 / 775), avg. gap size = 2.82 (31 / 11)  

1108 21.31 6.53 0.00  chrX_114151239_114155562     3541  3831 (493)    L1M4_orf2#LINE/L1      599   908 (0)  

  chrX_114151239_   3541 CATCAAAAA-------AAAAAAAAAAGAAACAAACAAACAGGGTTGCATC 3583
                           i     i-------  v    i  i   i i i   iv  ii v    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_114151239_   3584 AGACTAAAAAGCTTCTGCACAGCAAAGGAAACAATGAACAAAGTGAAGGG 3633
                          i v v    i   i  ii vv       v  v  v  v        ii 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_114151239_   3634 ACAACCTATGGTATGGAAGAAAATATTTGCAAACTATACATCTGACAAGG 3683
                               i ii v    i                ii   i      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_114151239_   3684 GGCTAATATCCAAAATATATAA-GAA--------ACTCACTAGCAGGAAA 3724
                          i  vi      i         -   --------     v  ii ii  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_114151239_   3725 ACAAATAACCTGATTAAAAAATCGTCAAAGGACCTGAATAGACATTTCTC 3774
                                   ii   ?      v v       ii                
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_114151239_   3775 ---AAAAGACATACAAATGATCAATAGGCATATGAAAAAATACTCAACAT 3821
                         --- i    i         ii     i   i       i  i        
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_114151239_   3822 CACTAATGAT 3831
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.81 (45 / 16)
Gap_init rate = 0.01 (4 / 310), avg. gap size = 4.75 (19 / 4)  


2711 28.21 0.68 1.02  chrX_114156693_114161675     3608  4486 (497)    L1M4_orf2#LINE/L1        1   876 (32)  

  chrX_114156693_   3608 TGGGAAAACATTCCATACTCACAGATAAGAAGAAGAAATACTGTGAAAAT 3657
                            i  i i  i    ii   ii   vi     vvv    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_114156693_   3658 GGCCAAACTGCCCAAGGTAATTTATAGATTAATTGGTATTCCCATTAAAC 3707
                            v v   v     iv i  i  i     v vi vv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_114156693_   3708 TACCA-TTGACACTCTT-CAAAGAATTAGAAAAAAAACT-ACTTTAAAAT 3754
                          v   -i  v vi i  -  i -    i---- v  i  - iii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG----ACAAGCTGATCCTAAAAT 145

  chrX_114156693_   3755 TAATATGGAACCAACAGAGAGCCCACA-TAGCCAAGACAATTCTAAGGCA 3803
                          v        vii-  ii ii    v -       i     ii i iiv 
  L1M4_orf2#LINE/    146 TCATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_114156693_   3804 AAAGAACAGAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTGCA 3853
                         i       i  i      vv    i  v  ii i      viv    i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_114156693_   3854 AGCCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATA 3903
                          iv         i   i    ii         i i  ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_114156693_   3904 GACCAATGGAACAGAATAGAGATTTCAGAAATAAGACTGCACACCTACAA 3953
                           i        i     v    v i         iv iii   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_114156693_   3954 CTATCTGATCTTCAACAAAGCTGACATAAACAAGCCAATGGGGAAAGGAT 4003
                         ii vi    i   i    i v  v  - i  v vi            i  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAAT 393

  chrX_114156693_   4004 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCCAAAA 4053
                         vvi  v  i  i              v      v  ?   i    v   i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_114156693_   4054 ATTGCAACTGGACTCCTTCCTTACACCTTATACAAAAAATAACTCAAGAT 4103
                          v  v ii     i   v   i     v          v        i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_114156693_   4104 GGATTAAAGACTTAAATATACATCCCAAAACGAGGAAAACCCGAGAAGAA 4153
                             i ?    i     i  vivv i     v vi   vi iv       
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_114156693_   4154 AATCTAGGAAATAGTATTCAGGACATAGGCACAGGCAAAGATTTCAT-GA 4202
                           iv    ?ivv i v   iv   v v  vvi      v i    v -  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_114156693_   4203 TGAAAACATCAAAGGCAATTGCAAGAGAAGCAAAAATTCACAAATGGGAT 4252
                          - vi   i    i   vvv    v i   v      vv i    v   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_114156693_   4253 CTAAATAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGT 4302
                         i v vi   v v  i i   i  ii vv    iv v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_114156693_   4303 GAACAGACAACCTACAGAATGGGAGAAAATTTCTGCAA-TCAATCCATCT 4351
                            v        i                 v i     -   - vi    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCT 741

  chrX_114156693_   4352 GACAAAAGTCTAATAGCCAGAATCTACAAGGAACTTAAACAAATTTACAA 4401
                           i  ii v  vi  v       v  i  i     ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_114156693_   4402 GAAAAAAAGAAACAACCCCATTAAAAAGTGGGCAATGGACATGAACAGAC 4451
                         v     i v   i     v   ?    i       v   iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_114156693_   4452 ACTTCTCAAAAGAAGACATTTATGTGGCCAATAAG 4486
                          i     v        i  vi vi           
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.01 (12 / 876), avg. gap size = 1.25 (15 / 12)  


4659 14.88 2.91 1.34  chrX_114171821_114174000      794  1687 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_114171821_    794 TGGAAAGATGTCTCATGTTAATGGATCACAGGAATAAACATTGTGAAGAT 843
                                  i  i      v      iiv i  v v  i     v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_114171821_    844 GACAATATTCCCCAAATC-ATTT-TAGATTCG--GTAATCCC-AGCAAAA 888
                          i     i         i-  i -i      i-- i      - v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_114171821_    889 TCCCAAGTGGCTTTTTTGCAGAAATTGACAAGCTAATCAATCCTAAAATT 938
                              iv  v                        i   ----        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC----CTAAAATT 146

  chrX_114171821_    939 GATATGGAAATGCAAGGGACTCAGTATAGCCAAAACAACCTTGATACAGA 988
                         v                   i   v             i     v v   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_114171821_    989 A---CAAATGTGGAAGACTCACACTTCTTGATTTCAAAATGCATCACAAA 1035
                          ---    vv    i            iii         ivi ii     
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_114171821_   1036 ATTACAGTAAGCAAGACAGTGTGATACTGGAATAAGGA-----ATTTAG- 1079
                         ii        v            i      v       -----  v   -
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_114171821_   1080 ----TGGTAAAAAAAACTGAGAATCCAGAAATAAAGCCTTATATTTATGG 1125
                         ----   --  v i  i     i            v  v  i        
  L1M4_orf2#LINE/    297 TCAATGG--AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_114171821_   1126 TCACCTGATTTTTGACAAAGGTGCTAAGACAGACAATTCAATGGGGAAAA 1175
                            vi       i     i     i     ---  -             -
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGAC---CA-TTCAATGGGGAAA- 389

  chrX_114171821_   1176 GAAGAGTCTTATCAACAAATGGTGCTGGGAAAATTGGATATCCACATGTG 1225
                            v      v                   v  i      ?       ii
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_114171821_   1226 AAAGAATGAATTTGGATCCGTACCTCATACCATGCACAAAACTGATCTCA 1275
                                   v     i  v       i     ii      v v v    
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_114171821_   1276 AAATGGATCACAGACAAAAAGGTAAGCCCTAAAACTATAAAACTTTTAGA 1325
                                   ?    vv   v     vv                i     
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_114171821_   1326 AGAAAACACAGGTGTAAATCTTTGTGACCCTGAATTACACAATGTTTTCT 1375
                                 i   ?         i      i  ii   vi     v     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_114171821_   1376 TAGATATGATATCAAAATCATAAGCAGCAGAAGAAAAAATGGGATAAACT 1425
                                  i i     v  i     i  i          i -     i 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG-ATAAATT 638

  chrX_114171821_   1426 ACACTTCATCAAA-TTAGTAACTTTTGTGCTGTAAATGATACCATCAAGA 1474
                         iv           -   iv            vi   v  i  i       
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_114171821_   1475 AAGTGAAAAGACAACCTGCAGAATGGGAGAAAATATTTGCAAATCATGTA 1524
                                         ii                             i  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_114171821_   1525 TCTCTTAGGCAATTTGTATCCAGAATACATAAGGAACT---ACAACTCAA 1571
                            vv  i vi i              i    i     ---         
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_114171821_   1572 AAA-AAAAAGATAAATAATCTAACTCAGAAATGAACACAGGGTTTCAATA 1620
                         v  -       i      i i  i ? i     ii  v   i   v    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_114171821_   1621 GACATTACTCCAAAGAACATATACAAAT---CAATAAGCACAAGAAAAGA 1667
                               v          v          ---           v       
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_114171821_   1668 TGCTCAACATCATTAACTAC 1687
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (78 / 51)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  


3800 16.06 6.45 3.73  chrX_114279118_114281627     1134  2017 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_114279118_   1134 TGAAAAGACATCCCCTATTCATGGATTGGACAACTTAATATTGATAAGAT 1183
                           i     i     v i             vi           v      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_114279118_   1184 GGCAAAATTCCCCCAAATTGAT-----GATTCAACACACTCCTTTTCAAA 1228
                              v i     -        -----        i  v   i v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_114279118_   1229 ATCCCAACTTGCATTCTGCATTTTCCAAAGAAATTGTGTAGCTTATCCTG 1278
                               i  -  v  -----    v  --       vvv    v     i
  L1M4_orf2#LINE/    100 ATCCCAGCT-GCCTT-----TTTTGCA--GAAATTGACAAGCTGATCCTA 141

  chrX_114279118_   1279 AAATTCAT--------GCAAGGGTCCCAGAATAGCCCCAAAAATCTTGAA 1320
                                 --------       v            vv  v         
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_114279118_   1321 AAA-------AATGTCGGAAAATTCACACTTCCCAATTACCAAACTTACT 1363
                            -------  v  i   ii i               v v         
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_114279118_   1364 GCACAGCTACAATAATCAATACAGTGTGGTATTGGGTTAAGAACAGAAAT 1413
                         i  v       i       v           i   vv    i i   v  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_114279118_   1414 ATAGATCAATGAAATACAATTGAGAGTTCAGAAATAAATCTTGACATTTA 1463
                                    i    v          i          i ivv       
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_114279118_   1464 TGGTCAACTGATTTTAAACAAGGGTCACAAGACAATCAGATGAAGAAAAA 1513
                                i       vi        vv      v  ivi   ii    i 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_114279118_   1514 AATGACCTTTTCAAAAAATGGTGCTAGGACAACTAGATACCCACATGTAA 1563
                          - iii        v          i        i    ?       i  
  L1M4_orf2#LINE/    392 A-TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_114279118_   1564 AAGAATGAAGTTGGACCCTGATCTTACATGACACACAAAAATCAACTTAA 1613
                                           iv i  i   iv i i        i    i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_114279118_   1614 ATAAGCAGTAAAG--CTAAATGTAAAAAAATGAAAGAGCTAAAACTATAA 1661
                          - v v vi ?  --          ----------               
  L1M4_orf2#LINE/    491 A-ATGGATCAWAGACCTAAATGTAA----------GAGCTAAAACTATAA 529

  chrX_114279118_   1662 A-CTC-----AGAATACATAAGGATAAATCGTTCTGACCCTGGGTTAGGC 1705
                          -   -----    v     i ?i      v iv     i          
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_114279118_   1706 AATGCTTCCTTAGACATGACACAAAAAGCACAAGCAACATAAGAAAA--T 1753
                             v  i      i       v                v       -- 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_114279118_   1754 AGATAAAATAGGTGATATCAGTATGTTTTAA----TTTTGTGTTTCAGAG 1799
                                v i iivvi    iv  ----   ----       i    i  
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAAT----TAAAAACTTTTGTGCTTCAAAG 675

  chrX_114279118_   1800 -----TA----GA---TGAA-------CCAACAGAATAGGAAAGAAATAT 1830
                         -----  ----  ---    -------  v       i   i -      
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA-AAATAT 724

  chrX_114279118_   1831 TTGCAAGTGATATATCTGATAAAAAACTTGAATATAGAATTTTTTTTTTA 1880
                               i v             iii     v  vi     v v ------
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT------ 768

  chrX_114279118_   1881 AAAAAACCTCTTACAACTCAGTAATGAAAAGACAC----CCCAATTAGTA 1926
                            i   -            i    i        v----       ?iv 
  L1M4_orf2#LINE/    769 AAAGAAC-TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_114279118_   1927 AATGGACAAAGGGTCCTAATAGACATTTTGCTTATGAAAATATACAAATA 1976
                              i      i iiv           iv iv v   i          i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_114279118_   1977 GTCAATAAGCACATGAAAAGATGTTCAACATCATTAGTCAT 2017
                          i                     i         ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (78 / 60)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.75 (90 / 24)  


3177 26.90 0.77 0.66  chrX_114299346_114301243.rev      501  1407 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_114299346_    501 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTCATGAAAA 550
                              ii i  i     i      i v      v i      -i v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-GTTAAGA 49

  chrX_114299346_    551 TGGCCATACTGCCCAAGGTAATTGATAGATTCAATGCCATCCCCATCAAG 600
                             v     v     iv i  iv i        i  v     i     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_114299346_    601 CTACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTC 648
                         v v   iivi i  i  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_114299346_    649 ATAAGGAACCACAAAAGAGCCCGCATGGCCAAGTCAATCCTAAGCCAAAA 698
                            v    vii   ii  v  v v  i     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_114299346_    699 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 748
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_114299346_    749 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 798
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_114299346_    799 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATGTCTACAAC 846
                                 i    i--    i  --        vv  ii ii i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_114299346_    847 CATCTGATCTTTGACAAACTTGAGAAAAACAAGCAATGGGGAAAGGATTC 896
                           vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_114299346_    897 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 946
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_114299346_    947 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 996
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_114299346_    997 ATTAACGACTTAAAGGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1046
                           i ?v   i    v  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_114299346_   1047 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1096
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_114299346_   1097 AAACACCAAAAGC-CATGGCAACAAAAGCCAATATTGACAAATGGGATCT 1145
                         vi           -  -i          vv  v  v  i    v   ii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_114299346_   1146 AATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGTGA 1195
                         v  i   v v  i i   i  ii vv       v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_114299346_   1196 ACAGGCAACCTACACAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 1245
                          v  i     i   v             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_114299346_   1246 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1295
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_114299346_   1296 AAAAACAAACAACCCCATCAAAAAGTGGGTGAATGACATGAACAGACACT 1345
                            i     i     v  i?    i    ii  v  iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_114299346_   1346 TCTCAAAAGAAGACATTTATGCAGCCAAGA--CACATGAAAAAATGCTCA 1393
                             v        i  vi viii     v --          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_114299346_   1394 TCATCACTGGCCAT 1407
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


2663 22.19 1.02 1.75  chrX_114308259_114309941      506  1190 (493)    L1M4_orf2#LINE/L1      229   908 (0)  

  chrX_114308259_    506 TTCAAAATATATTACCAAACTATAGTAACCGAAATAGCATGATATTGGCA 555
                                iv  i   v  i   i     i i i i  ii  i  i     
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_114308259_    556 TAAGAATAGACACATAGAACAATGGAACAAAATAGACAGCCCAGAAATAA 605
                             i       i     v        i i   v  v  i          
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_114308259_    606 ATCCATGCATTTACAGCCAACTGATTTTCAACAAAGTTGCCAAAAACACA 655
                          i    i      ii i   i        i    i v      i v  iv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_114308259_    656 CACTGGGGAAAAGATTGTCTCTTCAATAAATGGTGCTGGGAAAATTGCAT 705
                           v        ii  v    i     i              v  i  v  
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_114308259_    706 ATCCATATGCAGAAGAATGAAACCAAACCTGTATCTATCACCATATACAA 755
                          ?   i     i         iiiii   iv  i  vv            
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_114308259_    756 AAAA-AACTAAAAATGGATTAAAAACTTAAATATTAAGATGTGAAATTAT 804
                            v-    v         i ? i  i     i -    vv i   i   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTAT 527

  chrX_114308259_    805 GAAGCTACTAGAAGAAAACATAGCAGAAACACTTCAAGACATTGGATGGG 854
                         i  i  vi               v? v  vv    iv   v    i vi 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_114308259_    855 GCAAGGATATTTTTGGATAAGACCTCAAAAGTACAAGAAACAAAAGCAAA 904
                             v i -  i  i    v   vi      i     v        v   
  L1M4_orf2#LINE/    578 GCAATGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_114308259_    905 AATAGACAAATGAGATTACATCATACCAAAAAGCTTCTGTGCAGCAAAGG 954
                               i    vi  i v     v viv    i   i     vv      
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_114308259_    955 AAAGACTCAACAGAGCAAACAGGCAACCCACAGAAT---AGAAAATATTT 1001
                          v vvv    v i  ii  v  i             ---           
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_114308259_   1002 GCATA-CACTACATCTAACGAGGAGTTAATATCCAGAATATGTAAGGAAC 1050
                            v -  -  i    i ii   iii vi            i   i    
  L1M4_orf2#LINE/    727 GCAAATCA-TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_114308259_   1051 AA--ACAACTCAATAGCAAGAAAATATGAAAACAAATAATCCAAAGAAAA 1098
                         vv--           --------   vi  i        i    vv?   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATA--------ATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_114308259_   1099 AATAGCTAAAAGATCTTAATAGATATTTCTCAAAAGAAGACATACAAATG 1148
                            i vi   i   i v      i       v        i         
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_114308259_   1149 GCCAACAGGTATATGAAAAAAATGTTCAACATCACTAACCAT 1190
                              i i i i       i -  i         ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (93 / 55)
Gap_init rate = 0.01 (9 / 680), avg. gap size = 2.11 (19 / 9)  


2826 19.29 4.82 0.32  chrX_114367518_114369131.rev      502  1123 (491)    L1M4_orf2#LINE/L1      259   908 (0)  

  chrX_114367518_    502 AAAATGGCATCATACTGGCATAAAGACAGAC-TACAG-------GAATAG 543
                           i ii ii vi           i  i    -  i  -------      
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_114367518_    544 AATAAAAAGCCCAGAAATAAACCTTTGGTTATATGATTAAATGATCTTCA 593
                            vi i  i             iv ivv v    i i  v    i   i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_114367518_    594 ACCAGGGTGCCAAGACCACTCACCGGGGAAAAGACAATCTTTTCAACAAA 643
                           v               i   vi       ii i i             
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_114367518_    644 TGGTATTAGGAAAACTGAATATCCACATGCGAAAGAATGGAGTTTGACCC 693
                             ii i   v     i   ?        i        i    v     
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_114367518_    694 TTATCATATACCATATACAAAAATTAATTGAAAATGGATTAAAGATCTAA 743
                         i  i vi i                  i v         i ?   i    
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_114367518_    744 A-------------ACAATAAAACTCCTA-AAGAAAACATAGGGG-AAAG 778
                          -------------  v         i  -             ? -   v
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_114367518_    779 CTTCATGATACTGGAATTAG-TAATAATTTCTTGGAACGGACATCAAAAG 827
                             i   i-  v ii    -i   ii      i  vvv    i      
  L1M4_orf2#LINE/    559 CTTCGTGAC-CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_114367518_    828 TACAAGCAATAAGAACAAAAAATATGCAAATGAGACTATATTAAAGTTAA 877
                         i        i  -  v        vii    vi    vi  i   i    
  L1M4_orf2#LINE/    608 CACAAGCAACAA-AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_114367518_    878 GAACTTTTGTGCATCAAAAGACACAATCAACAGGGTGAAATGACAACCTA 927
                         i           v     i     v     v ii      v       i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_114367518_    928 TGCAATGGGAGAAAATATTTGCAAATCATGTATC-AATAAAAGGTTAATA 976
                         iiv                          i    -i    ii ii vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_114367518_    977 TCCAGAATATATAAGGAACTCCTACAAC---AT--CAAAAACTCAAATAA 1021
                                       i      i      ---  --i     vv       
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_114367518_   1022 CCCAATTAAAAAGCAGGTAAAGGACTTGAACAGCCATTTCTCCAAAGATG 1071
                                ?    iii  i      i     i  v              v 
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_114367518_   1072 ATATACAAATGCACAACAAGCATGTGAAAAGATGCTCAACATCACTAATC 1121
                                    vv   i     ii                    ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_114367518_   1122 AT 1123
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.31 (81 / 35)
Gap_init rate = 0.02 (11 / 650), avg. gap size = 2.91 (32 / 11)  


1889 27.26 7.75 1.00  chrX_114636450_114638390.rev      383  1079 (862)    L1M4_orf2#LINE/L1       86   829 (79)  

  chrX_114636450_    383 CAATTCCTCTCAAAATCCTAGA-ACAGTTTTTGTAGTTATAGACAAGCTT 431
                             i   v         i  v-i vv      i  vv  v        v
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chrX_114636450_    432 CTTTTAAAAATTAACATGGAAAGGAACAAGCCTTAGAACATCTAAAAC-- 479
                         v ii     -  v i       v v vii v ii    i v i     --
  L1M4_orf2#LINE/    136 ATCCTAAAA-TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_114636450_    480 TGTTGAAAAATAAGG-------TGAATAGACTC-CACCTGGCA---TTAA 518
                          v        v   i-------  i -i     -   i vv  --- i  
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGA-GGACTCACACTTCCCAATTTCAA 233

  chrX_114636450_    519 GTCAGACTATGTAGCTACAGTAATCAAGACAGTGTGATACTGACAGAGCA 568
                         iv vv    iiv                        i     i  v ivi
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_114636450_    569 ACAGATACTCAAAACAACGGAACAGAA--GAGAACCCAGAAACAGATTTA 616
                          i   i ivi i v   i    i    --    ii       i i iii 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_114636450_    617 CACAAATATATTCAAT-GATTTTTCACAAGGGTGCAAAAAACCATGTCAG 665
                         i   vv   iv     -      iv          v  i -    -   i
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA-CCAT-TCAA 381

  chrX_114636450_    666 TAGACGAGGA----------CAA-ACACAGT-CCAAAACAA--------- 694
                          i ivi i  ----------   - v ii  - iiii    ---------
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_114636450_    695 -------AAAATAAGAAACTTCAACCCAAACTTCACACCTTACACAAAAG 737
                         -------    v  vi  v  vi    vv  i       v  i      i
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_114636450_    738 TTAGCTCAAAACAGATCACAGACCTAAATGTAAAACATAAAACTATAAAA 787
                            i       ii     ?              i vv             
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_114636450_    788 CT-TTAGGGGGGAA----AGAGAAATTCTTCAGGAACCTGATTT-GATGA 831
                           -    ii ii  ----i ? v  v     iv  v i  iv  - iii 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_114636450_    832 AGAGTTCTCGGACATGACACCAAAAAT-CAATCCATAAAAGGAAATACTG 880
                         v iv    ii  i            ii-   v v i     i   v iv 
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_114636450_    881 ATAAAGTGGGCCTCACCAAA--TAAATCCTTTTGTTCTATGAAAGATTCT 928
                              v   i i   i    --    vv       v  vii  i  iv  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_114636450_    929 GTTCAGAAGATGAAAAGATAAGCTACAGGCGAGGAGAAAATATTTGTATG 978
                         i iv    ii        i  v i    ivvi              i vi
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_114636450_    979 CCACATATCTGATAAAGAATTAGACTCTAGAATACATAAAGACCTCTTAA 1028
                         i  i           i i i v vv  i      i       v      v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_114636450_   1029 AATTCCACAACAGTAAAAACACAAATAATCCAATTAGAAAACAGACAAAA 1078
                           i  ---  i i      v        i      ?i    ii i    i
  L1M4_orf2#LINE/    782 AACTC---AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_114636450_   1079 G 1079
                          
  L1M4_orf2#LINE/    829 G 829

Transitions / transversions = 1.63 (116 / 71)
Gap_init rate = 0.03 (21 / 744), avg. gap size = 2.90 (61 / 21)  

 329 22.83 1.09 0.00  chrX_114636450_114638390.rev     1359  1450 (491)    L1M4_orf2#LINE/L1      816   908 (0)  

  chrX_114636450_   1359 AAAATAGGTAAAAGACATGAACAGACATTTCACTGAAGAGGGCAAACAGA 1408
                              i  i   i  iv    i         v ii    i ii v   i 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_114636450_   1409 TGGGAAATAAGTGCATAAAAA-ATGTTAAACATCATTAGTTAT 1450
                            vv      ii   i    -   i v       ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.01 (1 / 93), avg. gap size = 1.00 (1 / 1)  


2626 24.34 4.65 1.55  chrX_114851938_114854669     1402  2239 (493)    L1M4_orf2#LINE/L1       45   908 (0)  

  chrX_114851938_   1402 TAGAATGACCATAACTGCCTAA-----TCTACAGATTCAATGCAATTCCC 1446
                           ii   i v   -  v  i  -----             i     i  i
  L1M4_orf2#LINE/     45 TAAGATGGCAATA-CTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chrX_114851938_   1447 ATCAAAATACCAG-TGTCGCTTTTCACAGAATTAGAAAAAACAACCATAA 1495
                                 v    -  i -i    ii     v v  v  ivii i v   
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_114851938_   1496 GATTCATATGGAACCAAAACAAAG--CCCA-AGTAACCAAAGCAATCTTA 1542
                         i            --- vi   i --    - i  i     i       i
  L1M4_orf2#LINE/    143 AATTCATATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_114851938_   1543 AGCAAAAAGATCACAGCTGGAAGCATCACTTTATTTGCC---TTCAAATA 1589
                          iv  i    v  v  i    i vv    --- i  v  ---      vv
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCAC---ACTTCCCAATTTCAAAAC 236

  chrX_114851938_   1590 ATATTACAACGCTCTAGTAAGCAAAATAACATGATAGTGATATAAAAATA 1639
                         v  i     v   vi     v   i i iii  i  v  ii    ii   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_114851938_   1640 G-TATACAGATTAATATAAAAGAATAGTGAATCCAGAAATAAAGCCACAT 1688
                          -i   i    i   iv  v     v v  i            v   i i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_114851938_   1689 ATTTACAGCCAACTGATTTTTGACAAAA---CCAACAACACATACAGTGG 1735
                              ii i   i       i     ii---    -i  -   v  i   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GAC-CATTCAATGG 384

  chrX_114851938_   1736 GGGAAAGAAGACCCGCTTTAATAAATGG--CTTAAA-AATTGAATATCTA 1782
                           -      v vi vi  i  i      --  vii -  i  i   ? i 
  L1M4_orf2#LINE/    385 GG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_114851938_   1783 T-TGCAGAAAAATGAAACTGAATCCTTATCTCTCACCACATACAAAAACC 1831
                         i-    i  i      ii  i i  i  i   v     i         ii
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_114851938_   1832 ATCTCAAGATGGATTA-AAACTTACATGTAAGACCCAATACTTTAAAAAT 1880
                          v     i      i - i  i  v        v i  v   v     v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_114851938_   1881 GTTAGAAGGAAACCTAG-AGTAAACTCTTCTGGACATTGATCTAGGCACC 1929
                         v       i    v   -?     -     vv   v   ivi      vi
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_114851938_   1930 AAATTAATGATTAAGAACTCAAAAGCACAGGCAACAGAAGAAAAAATAGA 1979
                         iiv  vv iiv  v  vvi          i      i             
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_114851938_   1980 CAAATGGGACTTAATTAAACTAAAAAGCTTCTTCGCAGCAAAGGAAACAA 2029
                         i    v      v  i   v v    i   i vi  vv       v  v 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_114851938_   2030 TCAACATAGAGAAGAGACAACCTGTTATATGGGAGAAAATATTTTCAAAC 2079
                             v v  v   i        iiiviv                v    i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_114851938_   2080 TATCAATCCAACAGAGGACTAATATCCAGAATATACAAGGAACTC----A 2125
                         i  vv   ii i ii     vi             i  i      ---- 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_114851938_   2126 A----ACAATAAAAT--CAAATAATCCCAT------GTGGGACAAAAGAC 2163
                          ---- i       v--       i  v  ------i    -    i  i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG-CAAAGGAT 831

  chrX_114851938_   2164 ATGAACAGACATTTTTCAAAAGA-GACATACAAATGGCCAACAGGTATAT 2212
                         v    i        i  v     -  i              i i i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_114851938_   2213 GAAAAAATGCTCATCATTAATCATCAG 2239
                              i       v   i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (126 / 76)
Gap_init rate = 0.03 (26 / 864), avg. gap size = 2.00 (52 / 26)  


3247 24.97 2.69 1.12  chrX_114857508_114861844.rev     2954  3846 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_114857508_   2954 GAAAATGGATAGTCTATGTTTATGAATTGGAAGAGTCAATATTGTGTAAA 3003
                          i   --    vi i     i   i         v i        -   i
  L1M4_orf2#LINE/      2 GGAAA--GATATCCCATGTTCATGGATTGGAAGACTTAATATTGT-TAAG 48

  chrX_114857508_   3004 ATTCCA-TACTACCCAAAGCAATCTACAGATTCAGTGCAATCCCTATCAA 3052
                           vv  -    v      vii             ii              
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_114857508_   3053 AATACCAA-TGTTATTTTT-CAATGAAATAGATAAAACAATCTTAAAATT 3100
                            v   i-  iiv     -  --     v  i  ivii   i       
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCA--GAAATTGACAAGCTGATCCTAAAATT 146

  chrX_114857508_   3101 TCTATGTAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTAGGCAAAA 3150
                         iv    v  vii   ii                 i v   i iiiv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_114857508_   3151 AGAACAAACCTGGAGAATTCATATTACCTGACTTCAAATTATACTACAGA 3200
                                 vi     i i   i i v  ii i      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_114857508_   3201 GCTATACTAACCAAACCAGCTTAATGCTGGTATAAAAACAGACACA--GA 3248
                             i v   i   iv   iv ii i    i    ii i     i --  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_114857508_   3249 CCAATGGAACAGAATAGAGAATCTAGAAACA--TTCACACTCCTATAGTG 3296
                         i        i     v    i  i     i --ii  i  vii   i  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_114857508_   3297 AACTCATTTTCAATAGAAGTGCCAAGAACATACGCTGAGGAAAAGACAGT 3346
                           i v      i i iii         v   v iv  i     ii i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_114857508_   3347 CTCTTCTTTGATAAATGGTGCTGTAAAAACTGGATATCCATATGCACAAG 3396
                           i   ---i i           vi v         ?   i     v   
  L1M4_orf2#LINE/    397 CTTTTC---AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_114857508_   3397 AATGAAACTAGATCCCTATCTCTCATTGTATACAAAAAT-----CAAAAT 3441
                               ii i  i     i   v  iii           -----      
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_114857508_   3442 GGATTAAAAACGTAAA-----GATCTCAAACTATGAAACTACTACCAGAA 3486
                             i ? i  v    -----  v  v       i     vi  vv    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_114857508_   3487 GTCATTGGGGAAAATCTCCAGGACATTGTTCTCAGCAAAAATTTCTTAAG 3536
                         iv   v  ? v      i iv   v   vvi vi    vii       ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_114857508_   3537 TAATTCTCCACAACGACAGGCAACCAAAGCACAAATGGACAAATGGGATC 3586
                           vvv v   v  vv   i     v    v v    i  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_114857508_   3587 TCATCAAG-TTAAAAAGCTTCTGCACAGCCAAGGAAACAAACAAAAAATT 3635
                                i-       -   i  ii vv v     v  v v   i   v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_114857508_   3636 GAAGAGAGAACCCACAGAATGAGAGAAAATATTTACAAGCTACCCATTTG 3685
                            i   v             i            i   iii ivi  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_114857508_   3686 ACAAAGGATTAATAACCAGAATATATGAAAAGCTCCAACAACTCTATAGG 3735
                          i  i   i vi  v           i  i i   iv       v   iv
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_114857508_   3736 AAAAAAATCCAATAACCTGACCAAAAAATGGGCAAAATATCTGAATAAAC 3785
                              i - v       ii ii?             iv  i      i  
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_114857508_   3786 ATTTCTTCGAAGAAGACATGCAAATG------AAAAACATGAAAAGGTGT 3829
                               i i       i  i      ------  iv          i  i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_114857508_   3830 TCAACATCATTGATCAT 3846
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (143 / 76)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 2.27 (34 / 15)  


3132 25.67 2.47 0.67  chrX_114890477_114894761     2901  3792 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_114890477_   2901 TGGAAACACATCCCATGCTCATTGATGAGTAGAATCAATATTTTGAAAAC 2950
                               v i        i    v   vi v   v i      v v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_114890477_   2951 GACCATACTGCCAAAAGCAATCTATAAATTCAATGCAATCTCCACCAGAA 3000
                          i v     v  v   vii     i i      i      i i i  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_114890477_   3001 ---CA-CTACCATAATTCTTCACAGAGTTAGAAAAATCAATCCTAAAATT 3046
                         ---  -  i  ----  i  ii    iv v  v  iiii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_114890477_   3047 CATATGGAATCAAAAAAGATCCCACATAGCCAAAGCAAGACTAAGCAAAA 3096
                                  viiv  ii  i  viv         i   vvi i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_114890477_   3097 ATAACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAG 3146
                          v      vi      vv       v  ii        viv     i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_114890477_   3147 A--ACAGTCACCAAAACAGCGTGATACTGGTATAAAAATAGGCACATAGA 3194
                         i--     v i   i    i   i      i    ii    i  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_114890477_   3195 CCAATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCC 3244
                         i        i     v    ii               v i i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_114890477_   3245 AACTGATCTTCGACAAAGCAAACAAAAACA--AAGTGGGGAAAGGACACA 3292
                           i    i        i vviv   i v  --v i         i i vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_114890477_   3293 CTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGAGGAAA 3342
                                                i  i   v  ?       i i i   v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_114890477_   3343 GAAACTGGATCCTCATATCTCACCTTACACAAAAATCAACTTAAGATGGA 3392
                            ii    i  ii iv  v    v  i        i    i  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_114890477_   3393 TTAAGAACTTGAACCTAAGA-CCAAAACTATAAAAATTCTAGAAGATAAC 3441
                          i ?ii  i i  iv     - i            v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_114890477_   3442 ATTGGA--AAATCCCTTCTAGACATTGGCTTAAGCAAGGATTTCATGACC 3489
                           v  ?--     --   vv   v    v   i    v i    v iivi
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_114890477_   3490 AAGAACCCAAAAGCAAATGTAATAAAAACAAAGATAAATAGCTGGGACCT 3539
                          v  vv         v v i  i    iv   i   i   iv v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_114890477_   3540 AATTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAT 3589
                         v  i   v v  i i      iiivv    i iv  vi   iv i   iv
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_114890477_   3590 ACACAAAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGAC 3639
                          v v v          i           v  ii   vii   i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_114890477_   3640 AAAGGACTAATATCCAGAATCTACAATGAACTC----AAATCAGTAAGAA 3685
                           i     vi          v  i  v      ----  v   i   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_114890477_   3686 AAAAACAA----TCCCATTAAAAAGTCGGCTAAGGACATGAATTGATAAT 3731
                            i    ----i  v   ?    i v   v     iv     v  i v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_114890477_   3732 TCTT---AAAAGATATACAAATGGCCAATAAACATATGAAAAAATGCTCA 3778
                            i--- i                      i  i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_114890477_   3779 ACATCACTAATGCT 3792
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (138 / 87)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.55 (28 / 11)  


3182 26.06 0.76 2.17  chrX_114957972_114967996      492  1412 (8613)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_114957972_   1412 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1363
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_114957972_   1362 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1313
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_114957972_   1312 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 1265
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

C chrX_114957972_   1264 ATATGGAACCGAAAAAGAGCCCACATTGTCAAGACAATCGTAAGCCAAAA 1215
                                 vi v  ii  v  viv  v i   i      v i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chrX_114957972_   1214 GAACAAAGCTGGAGGCATCATGCTACCTAACTTCAAACTATACTACAAGG 1165
                                 i      vv   ii  v  i  i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chrX_114957972_   1164 CTACAGTAACCAAAAGAGCATGGTACTGGTACTAAAACTGAGATATAGAC 1115
                                  i   i v  ii         i iv ii iv  v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chrX_114957972_   1114 CAATGGAACAGTACAGAGCTCTCAGAAATAATGCCACACATCTACAACTA 1065
                                 i  v iv   vvii         vv   i    i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

C chrX_114957972_   1064 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 1015
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chrX_114957972_   1014 TATCTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACTG 965
                          v ii  i              v      v  ?   i   i i  i ---
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA--- 444

C chrX_114957972_    964 GCTAGCCATATATGAAACTGGATCCCTTCCTTACACCTTATACAAAAATT 915
                         -----------     ii    i    v   i     v            
  L1M4_orf2#LINE/    445 -----------ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

C chrX_114957972_    914 ATTTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAACC 865
                          vi    i      i ?    i       v   v       i       i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

C chrX_114957972_    864 CCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAA 816
                          i           v    ?i- v i -   iv   v v  vv i     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

C chrX_114957972_    815 GACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGA 766
                          ii   v iiv  vi            vvi          vv     v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

C chrX_114957972_    765 CAAATGGGATTGAATTAAACTAAAGCACTTCTGCACAGCAAAAGAAACTA 716
                         i    v   i vv  i   v v  iv    i  ii vv    i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

C chrX_114957972_    715 CCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATC 666
                         i  vv i      v  i     i                 v   i   vi
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

C chrX_114957972_    665 TACCCATTTGACAAAGGGCTAATATCCAGAATCCACAAAGAACTTAAACA 616
                         i ivi  i   i  i  i  vi          vi i        ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

C chrX_114957972_    615 AATTTATAAGAAAAAATCAAACAACCCCATCAAAAAGTGGGTGAAGGATA 566
                          v iv    v     iv    i     v  i?    i    ii      v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

C chrX_114957972_    565 TGAACAGACATTCCTCAGAAGACAGTTATGCA----GCCAACAAACACAT 520
                             i       i   vi    -  v   i  ----     i  i     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCACAT 881

C chrX_114957972_    519 GAAAAAAATGCTCATCATCACTGGCCAT 492
                              i -      v     ????????
  L1M4_orf2#LINE/    882 GAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.00 (27 / 9)  

3147 26.70 2.01 0.56  chrX_114957972_114967996     8638  9532 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_114957972_   8638 TGAAAAGCTCTTTCATGTTCATGAATTGGAAGAATCAACATTGTTAAAAT 8687
                           i    v v ii          i         v i  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_114957972_   8688 GTCCATACAATCCAAG-CAATCTATAGATTCAATACAATTCCTATCCAAA 8736
                          v v    vvi    i-ii     i        ii    i      v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_114957972_   8737 TTACCAATGATATTTTTCACAGAAATCGGAAAATCAATCTTAAAGTTTAT 8786
                          i-   iiviiv     ii       i iv  iiii   i    i  i  
  L1M4_orf2#LINE/    101 TC-CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_114957972_   8787 GTGAAACCATATAAG--ACCCAGGATAGACAATGCTATTCCAAGCAAAAA 8834
                         i  i  --  ii   --      i    v   vi v  iiii iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_114957972_   8835 GAACAAAACTGGATGAATCGCATCACCTGACTTCAAATTATACCGCAAAG 8884
                                ii    v  v  i  iiv  ii i      viv   ii     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_114957972_   8885 CTATAGTAACCAAAACAGTGGGATATTGGCATAAAGATAGACAAATAAAC 8934
                            i     i   i      v i  i        i        v   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_114957972_   8935 CAATAGGACAAAATAGAGAACCCAGAAATAAATCCACAGACCTACAGTGA 8984
                             i i i i   v    ii           i   i v ii  ii  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_114957972_   8985 AGTCATTTTTGACAGAAGGGTCAAGAACATACAATGGGAAAA----AGTC 9030
                          v v     i    iii v i     v   v       i   ----    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_114957972_   9031 TCTTCAATAAAGGGTGCTGTGAATACTGGATATTCATATGCAGAAGAATG 9080
                          i     i   v       v  vv        ?i  i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_114957972_   9081 AAACTAAACCTCTATCTCTCACTATATACAAAA------TGAAAATGTAT 9124
                           ii ii   i   i   v   i          ------ v      v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_114957972_   9125 CACAGAATAAAATCTAAAACTTTAAACTATGAAATCACCACAAGAAAACA 9174
                           ?   viv    v   i vi v       i   iivii v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_114957972_   9175 TTGGAGAACATCTCTAGGACATTGGGCTGGCCCAAAATTTCTTCAGCAAT 9224
                          v  ? v v    iiiv   v     i i v v vii      -  vv  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATAT 596

  chrX_114957972_   9225 TAC-CCACAAGCACAGGCAACCAAAGCAAAAATAAACAAATGGAATCATA 9273
                         v  -   v       i     v    v       i i    v i iivi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_114957972_   9274 TCAA-GTTAAAAACCTTCTGCACAACAAAGGATACAAGCAATGAAGTGAA 9322
                             -i        i  -  ii vv       i  v v   vi       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_114957972_   9323 GAGACAGCTCCAAAAATGGCAGAAAATGTTTTTATACTACCCATCTGATG 9372
                         i     i i vv i     v       i   vi v ii ivi       i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_114957972_   9373 AGGAATTAATAATCAGTATACATAAGGAACTCAAACAATTCTATAGGAAG 9422
                            i i vi  vi   v   i    i      vv    i  v   iv  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_114957972_   9423 AATG-AAATAATCCAA--AAAAAATGGACAAAAGACTTGAATAGACATTT 9469
                           vi-      i    --?        i    i  i              
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_114957972_   9470 CTCAGAAGAAGGCACACAAATGGCAAACAAACGTATGAAAAGGTGCTCAA 9519
                            vi      ii i         v  i  i ii        i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_114957972_   9520 CATCATTGATCAT 9532
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (154 / 81)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  


2922 25.30 2.21 1.88  chrX_114976167_114978273      710  1614 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_114976167_    710 TGCAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTAAAAAA 759
                           v   v i        i        v  v   v i        v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_114976167_    760 TCACCATACTGCCAAAATGAATCTGCAAATTCAGTGCAATCCCCATCAAA 809
                          vi v     v  v    vi    i  i     ii        i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_114976167_    810 ATACCA-CTGTCATTCTTCACAG---TTAGAAAAAC-AATTCTAAAATTC 854
                           v   -   i -  i  ii   ---  -  v  i -i  i         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTC 147

  chrX_114976167_    855 ATATGGAACCAAAAAAGAGCCCACATAGCTAAAGCAA----GAAGAAGCA 900
                                 viiv  ii  v  viv     i   i   ----   i   --
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG-- 195

  chrX_114976167_    901 AAAAGAACAAATCTGGAGACATCA-ATTACCTGATTTCAAACTATACTAT 949
                         --         vi     ivv   - i v  ii        viv     i
  L1M4_orf2#LINE/    196 --AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_114976167_    950 AAGGCCATAGTCACCAAAACAGCATGGTACTCGTATAAAAATAGGCACAT 999
                           i  i i   v i   i    ii       v i    ii    i  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_114976167_   1000 AGACTAATGGATCAGAATAGAGAACCCAGAAATAAACCCAAATATTTACA 1049
                            ii      vi     v    ii               v i     ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_114976167_   1050 GCCAACTGATCTTTGACAAATGAAACCAAAAC-ATAAAGTGAGGAAATGA 1098
                          i   i    i  i     i- ivi    i  -  vv i  i     vi 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAG-GGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_114976167_   1099 CACCCTCTCCAACAAATATTGCTGGGTTAATTGGCAAGCCACATGTAGGA 1148
                         i vi  i i        iv       vi  i   vv ?       i ii 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_114976167_   1149 GAATGAAACTGGATTCTCTTCTCTCACCTTATACATAAATCAACTCAAGA 1198
                                ii    ii iivi   v    v      v    i       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_114976167_   1199 TGTATCAAGCACTTATATCCAAGACCTGAAACTATGAAAATTCTAGAAGA 1248
                           v    ?iv  i  v  vi    v  i       i   v ii       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_114976167_   1249 TAACATTGGAAAAATGTTTTCTAGACATCAGCTTAGGCAAGGATTTC--- 1295
                         v     v  ?iv  -i i   vv   v ii v        v i    ---
  L1M4_orf2#LINE/    543 AAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_114976167_   1296 ---ATGACAAAAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGC 1342
                         ---      -----         v v    i    iv   i   i   iv
  L1M4_orf2#LINE/    592 GATATGACA-----CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_114976167_   1343 TGAAACTTAATTAAA-TTAAAGAATTTTGCATGTCCAAAGGA-ACAGTCA 1390
                          vii    v  i   -     i v     iii- i       -  vi   
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCA 685

  chrX_114976167_   1391 ACAGAGTATAGAGAAACCCCACAGAGTAGGATAAAA-ATCTTCATAATCT 1439
                          v i   iv i   v v        i i   v    -  i v  -    -
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC- 733

  chrX_114976167_   1440 ATGCATCTAACAAAGGACTAATATCCAGAATCTACAATTAACTCAAACAA 1489
                           ii    i i  i     vi          v  i  vv     vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_114976167_   1490 ATTAGCAAGAAAGAAACAAACAATCCCATCAAAAAGTGGGATAAGGACAT 1539
                         v i ii  v   i i     i  i  v  i?    i    vv     iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_114976167_   1540 GAATAGAAAATTCTCAAAAGAAGATGTATAAATGGCCAAAAAACATATGA 1589
                                v v     v         i  i          v  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_114976167_   1590 AAAAATGCCCAACATCACTAATAAT 1614
                            i    i        ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (139 / 86)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.85 (37 / 20)  


3039 28.19 0.55 0.55  chrX_115007277_115013216.rev     4542  5449 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115007277_   4542 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4591
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115007277_   4592 GGCCATACTGCCCAAGGTAATTCATAGATTCAATGCCATCCCGGTCAAGC 4641
                            v     v     iv i  ii i        i  v     vi    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115007277_   4642 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4689
                          v   vivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_115007277_   4690 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 4739
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_115007277_   4740 AACAAAGCTGGAGGCATCAGGCTACCTGACTTCAAACTATACTACAAGGC 4789
                                i      vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_115007277_   4790 TACAGTAACCAAAAGAGCATGATGCTGGTACCAAAACTGAGATATAGACC 4839
                                 i   i v  ii  i i    i iv ii iv  v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_115007277_   4840 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 4887
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_115007277_   4888 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4937
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_115007277_   4938 CTATCTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCT 4987
                           v ii  i              v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_115007277_   4988 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5037
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_115007277_   5038 TTAAGGACTTAAATATTAGACCTAAACCCATAAAAACCCTAGAAGAAAAC 5087
                          i ?i   i     i v   v     v i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_115007277_   5088 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5136
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_115007277_   5137 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5186
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_115007277_   5187 ATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5236
                           i   v v  i ii  i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_115007277_   5237 CAGGGAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5286
                         v  iv    i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_115007277_   5287 AAGGGCTAATGTCCAGAAACTACAATGAACTCAAACAAATTTACAAGAAA 5336
                          i  i  vi i       vv  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_115007277_   5337 AAAAGAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAAACACTT 5386
                           i v   i     v  i? v  i     i      v    i i   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_115007277_   5387 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5436
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_115007277_   5437 CATCACTGGCCAT 5449
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (149 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2382 28.25 4.00 3.00  chrX_115016044_115020683     3249  4147 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115016044_   3249 TGGCAAAACATTTCTTGCTCATGGATAGGAGGAATCAGTTTTGTTAAAAT 3298
                            v  i i  ii v  i        v   i  v i i v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115016044_   3299 GGCA-TGCTGTCCAAAGCAATTTATGGGTTCAATGCTATTTCTATCAAAA 3347
                             - i  vi     vii  i  ii i     i  v  ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115016044_   3348 TACCAGTGACATTCTGCATAGAATTAGAAAAAA-AATTCTAAAATACATG 3396
                          v    ivi v  i viii    v v  v  iv-i  i       v   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115016044_   3397 GGGAACCAAAAAAAAAAAAAAAAAGCCCA-AATGGCCAAAGTAATCCTAG 3445
                         v    viiv  iii ----------    -   i      ii    i ii
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA----------CCCAGAATAGCCAAAACAATCTTGA 190

  chrX_115016044_   3446 GCAAAAAGAACAAAGATAGTGGCATCACATTATTCCACTTCAAACTATGC 3495
                         iv  i          v i v  vv     i vii v i      viv i 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_115016044_   3496 TACAAGACTATAGTAACCAGAAGCAATATGACACTGGTACAAAAATGGAT 3545
                              ii   i     i  ii -  i i  ii     i i  ii  i  i
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_115016044_   3546 GCATAGACCAATGGAACAGAAT--AGAGTTCCCAGAAATAAAGCTGCACA 3593
                         ii     i        i     --     --           v iii   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGT--CCAGAAATAAACCCATACA 337

  chrX_115016044_   3594 TCTACAACTATCTGTTCATTAAGAAAATTGACAAAACCA----GTGGGGA 3639
                          i  iiiii vi  v iv ii v  iiv  v   i    ----i      
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_115016044_   3640 AGGCACCGTCCATTCAATAAATGGTGCTTTAATAACTAGCTAGGCATTTG 3689
                          i v iv   iv     i          vvi i    i v  ?v  iv  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_115016044_   3690 CAGAAGATTGAAACTAAACCCCTTCCCTTCCACTATATACAAAA-TCAAG 3738
                           i    v    ii ii      -v   iv   i          - i  v
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAAC 486

  chrX_115016044_   3739 TCGAGATGGATTAAAGACTTAAATGTAAAACCTAAAACCATAAAAACCCT 3788
                           i i      i ?    i         i v       i      - i  
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCT 535

  chrX_115016044_   3789 T-GAAAATTACCTAGGCAAAACAATTCTATACATAGGCCCTATCTAAAAT 3837
                          -   i vv  v    ?iv  --  ii --- i - i  i ivv v iii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAA--ATCTT---CGT-GACCTTGGGTTAGGC 579

  chrX_115016044_   3838 A-TGGT------GATAAAGATGCTAAAAGCAATTGCAACAACAACAAAAA 3880
                          -    ------    v-  ii i       vvv       -  v     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAACAA-AAGAAAAA 627

  chrX_115016044_   3881 AT-GATAAATGAGACCTAATTAAACTAAAGGGCTTCTGCCCAGCTATTAA 3929
                           -       vi   i v  i   v v  iii   i  i---   - i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT---GCT-TCAA 673

  chrX_115016044_   3930 A-----TTATCAACAGATTAAGCAGACAGCCTACAGAATGGGAGAAAATA 3974
                          -----i      v i v i iv     i  i                  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_115016044_   3975 TTTGCAACCTATGCATCCAACAAAGGTCTAGCGTCCAGAATTTGTAATGA 4024
                                vii  ii   ii i  i  v  v ii        v i   v  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_115016044_   4025 ----------TTCAACAAGCAAAAAACAAATAACCCCATTAAAAAGTTGA 4064
                         ----------i    i  vv    i           v   ?    i v i
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_115016044_   4065 CAAATAGCATGAACAGACACTTCTCAAAAGAAGATAGTTAAGCAGCCAAC 4114
                             viiiv    i     i     v          vvi  iii     i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_115016044_   4115 AA--ATAAGAAAAAATGCTCAACATCACAAATTAT 4147
                           -- i v     i             ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (167 / 83)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.52 (63 / 25)  


2849 26.73 2.46 0.82  chrX_115026088_115028116      676  1528 (501)    L1M4_orf2#LINE/L1        1   867 (41)  

  chrX_115026088_    676 TGGAAAAACATCCCATGCTCATGGACTGGAAGAATCAATATCATTAAAGT 725
                               i i        i       i       v i     ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115026088_    726 AACCATACTCTTTAAAGCAATCTACATGTTCAATGCAATCCCTATCAAAT 775
                         ii v      iii   vii       vi     i               v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115026088_    776 TACCAGCCTTGTTTTTCACAAAATTAGAAAAAATGATGGTAAAATTAATA 825
                          v     iviv     ii  i  v v  v  iv    vv       v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115026088_    826 TGAAACCAAAAAGGGTCT-GAATAACCAAAGCAATCCTAAACAAACAGAA 874
                           i  viiv  i  ii i-     i     i     i i  v  iv    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115026088_    875 CAAAGCTGAAGGCATGACATTACCTGACTTCAAATTATACTGTGAGACTA 924
                              i  i   vv v   i v  ii i      viv    iii ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_115026088_    925 TAGGAACCAAAACAGCATGGTACTGGAATAACAAACAGACACATAGATCA 974
                         i  v  i   i    ii         v    -ii i     i        
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAA-GGATAGACATATAGATCA 299

  chrX_115026088_    975 ATGGAACAGAATAGAAAAGC-AGAAATGAAGCCACAAACCTATAACCAAC 1023
                               i     v  i iv -      i  v   i v ii   iii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_115026088_   1024 TGATCTTCAACAAAGTCAACAAAAATATACACTGGTGACAGGA-AATCGC 1072
                             i   i    i viiv   i vi  v  v   v  v  i - i  vi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_115026088_   1073 --CAATAAATGGTCCTGGGAAAATTGGATTGCCATATGCAAAAGAATGAA 1120
                         --   i       v      v  i     v?   i               
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_115026088_   1121 CCTAGGCTCATACAACTCACCATATGCAAAAATTAACTCAAGATGGACTA 1170
                         vi i i i v   vv v        i               i     ii 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_115026088_   1171 AAGACCTAAATGTAGGACCTGAAACTATGAAAATCCTAGAAAACAGTCTA 1220
                         ?             i  v  i       i   v  i     i v iiv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_115026088_   1221 GGAA-AATTCTTCTGGACATTGGTCTAGGCAATGAATT------TATGAC 1263
                           ?i-  v     vv   v    vi         iv  ------      
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_115026088_   1264 CAAGTTCTTAAAAGCA-----AACACAAGAAAAA-TAGAAAAGTGGGACT 1307
                         -- ----ii       -----    v        -    v  i v     
  L1M4_orf2#LINE/    600 --A----CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_115026088_   1308 TAATTAAACTGAAAACCTTCTGCACAGTAAAATAAACAATCAACAGAATA 1357
                          v  i   v v    v   i  ii vvi   iv v  v     v i i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_115026088_   1358 AACAGACAATCTACAGAATGGGAAGACACTTTTGCAAACTATGCATCTAT 1407
                           v      i i           ii v iv        ii  ii    iv
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_115026088_   1408 AAAAGGGCTCATATCTAGAATCTACAAGGAGCTCAAACAGCTCAAGAAGA 1457
                         v  i  i  ii    i     v  i  i  i   vv   i     v  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_115026088_   1458 AAA---CAAATAACGTCATTAAAAAGTGGGCAAAGGACATGAACATACAT 1504
                            ---        viv   ?    i           iv    i v    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_115026088_   1505 TTTTCAAAGGAAAACAAACAAATG 1528
                           i  v  i   i i v       
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATG 867

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.01 (12 / 867), avg. gap size = 2.33 (28 / 12)  


1774 15.64 3.28 23.97  chrX_115039127_115041194.rev      502  1569 (499)    L1M4_orf2#LINE/L1       43   889 (19)  

  chrX_115039127_    502 GTTAAGATGTTCATATTTCCAAAAGTGA---ACAAATTCAACAAAATCCC 548
                                  viv   i i  v   v   ---   i       iv      
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chrX_115039127_    549 TATCAAACTTTCAACAGCCTTTTTTGTAGAAATAAAAAAAAGCTAGTAAT 598
                                v ii  i v          i      vi v  --   ii vv 
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCT 140

  chrX_115039127_    599 CAAATTTATATAGGATTCCTAGGGCCCTTGAAAAAGCAAACCAATCTTGA 648
                         v     i    i i v v v    v  iv   v iv    v         
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_115039127_    649 AAAAAAAAAACAAATAAAGTCAGAGGGCTAACATTTCTCCAATTCAAAAC 698
                             i  i      ----  ii    i  v   i   i v v        
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAA----GTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chrX_115039127_    699 TTACCATAAAGCTGCAGTAATCAAAACCATTTGATACTAGCATAAGAATA 748
                             i i      i          i  vi v  i    i       i   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_115039127_    749 GATATATAGACAAATTGAATCAAAAAAAGAGTGCAGATATAAAC--ATAC 796
                           i       iv   v    vi  vvi     v    v      --    
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_115039127_    797 AGATATGGCCAATT----TTTGACAAGATTGCCAAGTACATTCAATGGGG 842
                          vv     i     ----  i      iv       vv            
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_115039127_    843 AAAGGACAATCTTTTCAACAAATGGTTTCAGCACAACTGAATATCCAAAT 892
                             i i i                 viii v       i   ?   v  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_115039127_    893 GCAAAAGAATGAAGTTGGATTCCTACCTCACATAATACAGTTGACTCTTG 942
                                            ii           ------------------
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACA------------------ 468

  chrX_115039127_    943 AACAACAAGAGATTGAACTGTATGGATCCACTTATGCACAGCTTTTATTC 992
                         --------------------------------------------------
  L1M4_orf2#LINE/    469 -------------------------------------------------- 468

  chrX_115039127_    993 AACCAAACATAGATTGAAACTACAGTATTTGTGGTATGCAAAACCCACAT 1042
                         --------------------------------------------------
  L1M4_orf2#LINE/    469 -------------------------------------------------- 468

  chrX_115039127_   1043 ATGGGAAAGGCTGACTTTTTATATATGAGGGCTTCACAGGGCCAACTGCA 1092
                         -----------------------------------------   ------
  L1M4_orf2#LINE/    469 -----------------------------------------CCA------ 471

  chrX_115039127_   1093 GTACTTGCGTATGTGTAGATTTGGTTCTATATAGGCAGTCCCGCAACAAA 1142
                         --------------------------------------------------
  L1M4_orf2#LINE/    472 -------------------------------------------------- 471

  chrX_115039127_   1143 TCTCCCTCATATTGTGAGGGACAACTGTATACAAAACTTAACTTTAAATA 1192
                         ---------------------------         v      iv    i
  L1M4_orf2#LINE/    472 ---------------------------TATACAAAAATTAACTCAAAATG 494

  chrX_115039127_   1193 GATCAAAGTCCTAAATATAAAA-CTGAAACTTTAAAAATGTTA-----AA 1236
                              ?  v       i   i -  i     v     v v   -----  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_115039127_   1237 ACATAG-CATATAATGTT-ATAAA-TTGGATTTGGCAAATAATTATTGGA 1283
                               -?i  -   v  -i i v-    i  v     vviv  v  i  
  L1M4_orf2#LINE/    545 ACATAGGNGTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_115039127_   1284 TATAACACCAAAA-CATAAAGAACAAAAGAAAATAATTGATAAATCAAAC 1332
                            i         -  i  iv            -   v       iii  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGAC 642

  chrX_115039127_   1333 TTCATCAAGGTTAAAAACTTATGTGAATCAATGG-CATTTT----AGAGT 1377
                                 ii          v    vv    v  -  i v ---- i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_115039127_   1378 GAAAAGACAGCATACAGAATG--AAAAGATATATACAAATCACATCTGCT 1425
                                  i vi        -- i  i    v i       i  v -  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT-CT 741

  chrX_115039127_   1426 GATAA----TTTAGTATCCAGAA-ACTTAAAAAACTACTAGAAATCAAAA 1470
                              ----i  -          - iv    i    vi  v  v    v 
  L1M4_orf2#LINE/    742 GATAAGGGACTT-GTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_115039127_   1471 ACAAAAAAAGACAAATTACTCCCAATATAAAA-TGGG-AAAAAAT--AAA 1516
                          i     --       v  --     v?    -    -   ii  --i  
  L1M4_orf2#LINE/    791 ATAAAAA--GACAAATAAC--CCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_115039127_   1517 TAGGGATTTCTTCAGAGAAGATACTCAAATAGCCAATAAGCACACAAAAT 1566
                            iv      i  i        iv     i             ii   v
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_115039127_   1567 GAT 1569
                            
  L1M4_orf2#LINE/    887 GAT 889

Transitions / transversions = 1.23 (90 / 73)
Gap_init rate = 0.03 (27 / 847), avg. gap size = 10.78 (291 / 27)  

1699 22.85 4.40 1.47  chrX_115039127_115041194.rev     1577  2053 (15)    L1M4_orf2#LINE/L1      418   908 (0)  

  chrX_115039127_   1577 GAAAACAAGATATCCACA----AAATGATGACATTGGACCCTTACCT--- 1619
                           v   vi    ?     ----   vi    vi        i     ---
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_115039127_   1620 ----TATACAAAAGTCAACTCAAAATAGATTAAAGGCTTAAGGTTAAGAG 1665
                         ----         i i          i   i ?  i i   ivv      
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_115039127_   1666 CAACTACTATGAAACTCCTAGGAAAAAAACACAGTGAAAAAGCTTTTTGA 1715
                          v vv     i      i   -  i      i  v?iv   v   iv   
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAG-AAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_115039127_   1716 AATTGGTCCTGACAA-GGTTTTTTTTTGGTGTGGCACCAAAAGCACAGGC 1764
                         vv    viiv i   -     i  v-- i i  i             i  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTA--GATATGACACCAAAAGCACAAGC 614

  chrX_115039127_   1765 AATGAAAGCAAAAATAAACAACTGGAGGTACATCAAG-CTAAAAACTTT- 1812
                           ii    v       i i  v v iiv v      i-i          -
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_115039127_   1813 GTGCTCAGCAAAAAAAAC-A--AACAAAATCAAAAGGCAATCTATGGAAT 1859
                              i--    ii v  - --  v   i v     i   i i ii    
  L1M4_orf2#LINE/    665 GTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_115039127_   1860 GGGAGAAAATATTTGCAGACAGCATATCAGAAAAGGAGTTTAGTATTCAA 1909
                                          i ivii     v  v    iii  -    i  i
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT-GTATCCAG 761

  chrX_115039127_   1910 AATATATAAGGAACTCTTACAACTCAATAGCAAC----TAAATAAGCTTA 1955
                                  i                   ii  v----i      - ii 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA-CCCA 810

  chrX_115039127_   1956 TTTTTAAAATGGACAAAGGACTTAAATAGATATTTTTCTAAAGAAGACAT 2005
                         v  ?v       i       i  i      i    i  i        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_115039127_   2006 ACAAATTACCAATAGTTATATGAAAAGATGTTCAATATTACTAACCTT 2053
                               vi      ivi i           i    i  i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (71 / 34)
Gap_init rate = 0.03 (13 / 491), avg. gap size = 2.15 (28 / 13)  


1980 26.09 4.92 7.21  chrX_115042270_115044138.rev      507  1380 (489)    L1M4_orf2#LINE/L1       55   908 (0)  

  chrX_115042270_    507 ATATTACTCAA--TGCCAACTACGGTTTCAGTGCAATCCCTATCAAAATA 554
                            i v i   --  -- v    i v    ii                 v
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_115042270_    555 TCAATGATATTTTTCACAGAAATAAAAACAAAC-AATCCTAAAATTTGTA 603
                         i  iiviiv     ii       vi --   i -i           ii  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCATA 150

  chrX_115042270_    604 TGGAATCATGAAAGACCCAGAATAGGTAAAGTTATCCCGAGCAAAAGAAA 653
                              viiii ii            vi   iiv   ii  iv  i ii  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115042270_    654 CAAA-CTAGAGAAATCACATTACCTGACTTCAAATTATAGTACGGAATTA 702
                             -i i   i v     i v  ii i      viv  v   ii ii  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_115042270_    703 TAGTAACCAAAA-ATCATGGTACTGGCATAAAAACAGA------------ 739
                         i     i   i - vii              ii i   ------------
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_115042270_    740 -----------TGA---CTCAGAAACAAATCTACACACCTACAGGTAACT 775
                         -----------   ---ii      i   i i i   ii  ii vi  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_115042270_    776 AACGTTTAACAAATGTGTGAAGAACATACACTGGGGAAAAGACAACTTCT 825
                         i iv  ii    iv   iv    v   v  v        ii i iii i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_115042270_    826 TCAATAAATGGTGCTTTAAAAACTGGATATCCAAGGGCAAAAGAATGAAA 875
                             i          vvi v         ?   viv             i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_115042270_    876 CCAGACCCCTATCTCTCACTATATAAAATAAACCAAATCAAA-TGAATAA 924
                         iii        i   v   i     v  -   ii  v     -  i  v 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAA-AAATTAACTCAAAATGGATCA 499

  chrX_115042270_    925 TAGAAGAAAATCTAAGAATTCAAACTATGAAACAACTACAAGAAAACATT 974
                         ?   vvv    v     ii v       i    vvi  v          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_115042270_    975 GGGGAAAATATCCAAAAAGTTGGTCTGGGCCAAAAAAAAAATATATGTAT 1024
                           ? v    v i ivi vv    vi i   ---------   i-------
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGC---------AATG------- 583

  chrX_115042270_   1025 ATATAATTATTATTTTTTATATATATATATAATATATATATAGCAATACA 1074
                         -----------i   i   v    i----------------------   
  L1M4_orf2#LINE/    584 -----------GTTTCTTAGATATG----------------------ACA 600

  chrX_115042270_   1075 TCACAAGCAAAGGCAACCAAAGCAAACATAAACAAATGGGATCACATCAA 1124
                         i  v     v i     v    v   v   i i    v   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_115042270_   1125 C-TTAAAAAGCTTCTGCCCAACAAAGGATACAATCAACAAAC-----AGA 1168
                         v-       -   i  iv vv       i  v     v   v-----   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_115042270_   1169 CAACCCACAGAATGAGAGAAAATATTTGCCAACTTTTCATCTGGCAAAGA 1218
                                       i              v  iiv vi     ii  i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_115042270_   1219 ATTAATAACCAGAATATATAAGGAGCTCAAACAACTCTGTTTTAAAAAAG 1268
                          i vi  v             i  i   vv       vi vv      ii
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_115042270_   1269 TCTAGGTATAC---ATTCAAAA-TAGGTGAAAGATTTAAATAGGCATTTC 1314
                         i-- ii  -  ---   ?    - i  ii  i     i     i      
  L1M4_orf2#LINE/    800 C--AAATA-ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_115042270_   1315 TCAAAAAAAAGCAAAACATGCAAATGGTGAA-GAGAAGGTGAAAAGGTGT 1363
                           v   i  i----- i  i       iv  -i  v vi       i  i
  L1M4_orf2#LINE/    847 TCCAAAGAAG-----ATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_115042270_   1364 CCAACATTGTTAATCAT 1380
                         i      ii????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (147 / 77)
Gap_init rate = 0.03 (22 / 854), avg. gap size = 4.82 (106 / 22)  


2297 28.39 0.64 1.79  chrX_115045506_115047984.rev     1207  1988 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_115045506_   1207 ATTCTAAAATTCATATGGAA-T-CAAAAAAAGCACACATAGCCAAAGCAA 1254
                           i                 - -   iii vv  v -         i   
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA-ATAGCCAAAACAA 184

  chrX_115045506_   1255 GTCTAAGCAAAAGAA-AACAAATCTAAAGGAATTATATTACCTGACTTCA 1303
                         vii i --       -      vi ii    v i i i v  ii i    
  L1M4_orf2#LINE/    185 TCTTGA--AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_115045506_   1304 AACTGTATTATAAGGCCATAGTCACCAAAACAGCATGACACTGGTATAAA 1353
                           viv  i  i  i  i i   v i   i    ii  ii     i    i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_115045506_   1354 AATAGGCACATAGGCCAATAAAACAGAATAGAGAATCCAGAAGTAAACAC 1403
                         i    i  i    ii    ii  i     v    i       i     v 
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_115045506_   1404 AAATACTTATAGCCAACTGATCTTTGGCAAAGAAAACAAAAACATAAAGT 1453
                          v i i    i i   i    i  i i   i iviv   i v   vv i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_115045506_   1454 GGTGAAAGGACACACTATTCAACAAATGGTGCTGGGATAATTGGCAAGTT 1503
                           v     i i vv  v                    i  i   vv ?ii
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_115045506_   1504 ACGCGTAGAAGAATGAAACTGGATCTTCATCTCTCACCTTATACAAAAAT 1553
                           ii i i         ii    i iii i   v    v           
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_115045506_   1554 CAATTCAAGATGGATTAAAAAAAACCTTAAATGTAAGACCTGAAACCATA 1603
                         i  i    i      i ? i ---- i           v  i    i   
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGA----CCTAAATGTAAGAGCTAAAACTATA 528

  chrX_115045506_   1604 AAAATTCTAGAAGATAACGTTAAAAAAAAGAAACCCTTCTAAACACTGGC 1653
                            v ii       v   i ----- ii? v  vi    vvi  vi   v
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACAT-----AGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_115045506_   1654 TTAGGTGAAGACTTCATGACCAAAAACCCAAAAGCAAATGCAACAAATAC 1703
                              ii v ii   v iivi vi vv         v v        viv
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_115045506_   1704 AAAGATAAATAGATGGGACTTGATTAAACCAAAAAGCTTCTACAAAGCAA 1753
                            i   i   i  v      v  i   viv    i   i iiivvv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_115045506_   1754 AAGAAATAATCAGCAGAGCAAACAGACAACACACAGAGTGGGAGAAAA-A 1802
                          i  v iv    iv i  ii  v       v      i          - 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_115045506_   1803 TCTTCATTATCTATACATCTGACAAAAGACTAATATTCAGAATCTACAAG 1852
                          i v  v-   -   i      i  ii    vi   i      v  i  i
  L1M4_orf2#LINE/    724 TTTGCAA-ATC-ATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_115045506_   1853 GAATTCAAACAAATCAGCAAGGAAAAG-CAAACAATCCCATCAAAAGACA 1901
                            i  vv    v   ii  vi     -    i  i  v  i?   i ii
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_115045506_   1902 GACTAAAGGCATGAATAGACAACTCTGAAAAGAAAATGTACAAATGGTCA 1951
                          i v  i iiv          vi   vv      i  i         i  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_115045506_   1952 GCAAACATATGAAAAAATTCTCAACATTACTAATGAT 1988
                         ii  i  i       i  v        i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (146 / 72)
Gap_init rate = 0.01 (11 / 773), avg. gap size = 1.73 (19 / 11)  


3129 27.99 0.77 0.33  chrX_115063837_115071991     5000  5903 (2252)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115063837_   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5049
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115063837_   5050 GGTCATACTGTCCAAGGTAACTTATAGATTCAATGCCATCCCCATCAAGT 5099
                           iv     vi    iv i ii  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115063837_   5100 TACCAATGACTTTCTACACAGAATTGGAAAAAAATACTTTAAAGTTCATA 5149
                          v   iivi i  i vii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115063837_   5150 TGGAAACAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5199
                               iiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115063837_   5200 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATGCTGCAAGGCTA 5249
                              i      vv    i  v  ii i      viv i  i   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_115063837_   5250 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACTGAGATATAGACCAA 5299
                               i   i    ii         i iv ii iv  v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_115063837_   5300 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACCAT 5347
                              i    i--    i  --        vv   i i  i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_115063837_   5348 CTGATCTTTGACAAAGCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5397
                         i    i  i     i v  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_115063837_   5398 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5447
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_115063837_   5448 AACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGATT 5497
                          ii    i    v   i i   v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_115063837_   5498 AAGGACTTAAATATTAGACCTAAAACCATGAAAACCCTAGAAGAAAACCT 5547
                          ?i   i     i v   v       i  i   vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_115063837_   5548 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGTACTTCATGACTAAA 5596
                            ?i- v i -   iv   v v  vv i     vvii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_115063837_   5597 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5646
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_115063837_   5647 TAAACTAAAGAGCTTCTGCACAGCAAAAGCAACTGCCATCAGATTGAACA 5696
                         i   v v  i i   i  ii vv    i vv   ii  vv i v    v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_115063837_   5697 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5746
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_115063837_   5747 GGGCTAATATCCAGAATCTATAATGCACTCAAACAAATTTACAAGAAA-- 5794
                           i  vi          v     v v    vv    v iv i  v   --
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_115063837_   5795 --CAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACTTCT 5842
                         --    i     v  i? v  i     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_115063837_   5843 CAAAAGAAGATATTTATGCAGACAAAAGACACATGAAAAAATGCTCATCA 5892
                          v           vi viii v   v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_115063837_   5893 TCACTTGCCAT 5903
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.42 (146 / 103)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.00 (10 / 5)  

3211 23.30 3.28 0.57  chrX_115063837_115071991     6788  7671 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115063837_   6788 TGGAAAGACATTATGTATTCATAAATTGCAAGA--TAATATTGTTAAGAT 6835
                                 i  ivii i     ii    v    --               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115063837_   6836 GTCCATTCTACCTAAAGTGCTCCACGCA--CAAGGAAATCTCTATCAAAA 6883
                          v v  v  v  i   v  v  i  iv --   v v    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115063837_   6884 TAATAATAA--TTTTTTGCATTAATAGAAAAAAACAATTTTAAAATGTAT 6931
                          vvi iivi--         vv   v  v  iv-ii  ii      vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_115063837_   6932 ATGAAATCTCAAAAGTCTCTGAATAGCCAAAACAATCTTTAAA------- 6974
                            i  viv   ii v i v                   v   -------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_115063837_   6975 -TAAAATTGAATGTCTTACACTTCTTGATTTCAAAACTGCCTATTATGCT 7023
                         -i   i   i v v  i       iii           vv   iv v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_115063837_   7024 AGACTAAACAAAATATTGTGGTAATGGCACAAAGGCATAAACATA--GAC 7071
                          v v   v   i i v       v     i  i --   i     --  i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGG--ATAGACATATAGAT 297

  chrX_115063837_   7072 CAATGGAATAGAAT-ACGGGCCACAGAAAGAAATCCTAACATGTATGATC 7120
                                       -iv i i -      v   i  vv    v    i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTC 346

  chrX_115063837_   7121 AAATGATTTTTGA--AGTTTGCCAAGACCATTCAATAA--AAAACACAAT 7166
                           v       i  --  vv                 ii--   iv i i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_115063837_   7167 CTTTTCAACAAATGGTGGTGAGA-AACCTTATATGCACATGCAATAGAAG 7215
                                          v  i  -   ivv   ?v         v    v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_115063837_   7216 GAAATTGGACCCTTAACTTACATTATATATGAAAATTAATTCAAAATGGA 7265
                            i        i  v  i   ii     ii        i          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_115063837_   7266 CCACAAATCTAAACATAAGAGCTAAAACTATAAAATTCTTAGACAAAAAC 7315
                         i  ? i i     ii                    i       vi     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_115063837_   7316 ATAGGGATA--TCTTTATGTCATTAGGTTTGGCAAAAATTGTTTTGGATA 7363
                              ?i  --    ii  v v  i    v     vii  - i  i    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAGATA 595

  chrX_115063837_   7364 TGACCTCAAAAACACAGGTAAGAGAAAAAAAGTTA-ATAAATAAGACTTT 7412
                             vi     i    i i  v i  i    iv  -      vi     i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_115063837_   7413 GTCAAAATTAAAAACTTTTGTGTATCAAAGTACAGTGTCAGCA--GTGAA 7460
                         i                     iv      v   v i   iv --     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_115063837_   7461 AAGACAACCCATACAGTTGAAGAAAGTATTTGCAAATCATATATGTGATA 7510
                                    i v i v i     i                  v     
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_115063837_   7511 TGCAATTAGTATCAATAATATATTTAAAAATCTTACAACTCAATAACAAA 7560
                         v vi i v     v v       vv i  v                i   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_115063837_   7561 AAATCAAACAATCCAATGTTAAAATGGGTGAAGTACTTGTACAGAAATTC 7610
                           iv    i  i     v?v        ii   v i   v i   v   i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_115063837_   7611 ATCTGAAAAAGAAATATAGATG-CCAATGAACCTATAAAAAGATGACAAA 7659
                         v  ii  i    v   i i   -     i i vi  i        viv  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_115063837_   7660 CA-CAACTAATCA 7671
                           -  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (115 / 87)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.89 (34 / 18)  


3181 28.11 0.33 0.22  chrX_115101837_115108241     5006  5912 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115101837_   5006 TGGAAGAACATTCCATGCTCACAGGTAGGAAGAATCAATATCGTGAAAAT 5055
                              ii i  i     i   ii i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115101837_   5056 GGCCACATTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5105
                            v i i v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115101837_   5106 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5154
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115101837_   5155 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5204
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115101837_   5205 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5254
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_115101837_   5255 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGTTATAGATCAG 5304
                               i   i    ii         i iv ii i   vv         i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_115101837_   5305 TGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 5352
                              i    i-- v  i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_115101837_   5353 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5402
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_115101837_   5403 ATTTAATAAATGGTGCTAGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5452
                         v  i  i          i   v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_115101837_   5453 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5502
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_115101837_   5503 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5552
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_115101837_   5553 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5602
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_115101837_   5603 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5652
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_115101837_   5653 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5702
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_115101837_   5703 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 5752
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_115101837_   5753 AGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5802
                         ii  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_115101837_   5803 ACAAACAACCCCATCAAAAAGTGGGCAAACGATATGAGCAGACACTTCTC 5852
                              i     v  i?    i        v   v   ii     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_115101837_   5853 AAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCAT 5902
                         v        i  vi viii     v ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_115101837_   5903 CACTGGCCAT 5912
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.51 (151 / 100)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.67 (5 / 3)  


2149 23.39 2.21 11.04  chrX_115135711_115138470     1272  2267 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115135711_   1272 TAGAAAAATATCCCATGCTCATGGAATAAAAGAATTAACATTGTTAAAAT 1321
                          i    i          i       v ii    v    i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115135711_   1322 AACCATATTGCCCAAAGCCATCTAAAGATTCAATGCAATCTCTATCAAAA 1371
                         ii v   i v      viv     v        i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115135711_   1372 TATCAG-TATCATTTTTACAGAGTTAGAAAGAAATG-TAC-AAAATTATA 1418
                          vi   - ii v     i    iv v  v - iv  - v -      -i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATT-CA 148

  chrX_115135711_   1419 TATGAAACAAAACAAAACAAAACAAAAAACCT-GTATGGCCAAAGCAATC 1467
                             i  ------------ vi   iii   i- v  i      i     
  L1M4_orf2#LINE/    149 TATGGAA------------ATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_115135711_   1468 TTAAGCAAAAAGAACAGAGCTGAAGCA-TAATATTACCTGATTTCAAATT 1516
                           i iv  i       i  i  i  v - v i i v  ii        --
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-- 234

  chrX_115135711_   1517 ATACTACAAAACTTCAAATTATCCTACAAGACTATAGTAACCAAAACATA 1566
                         ----------    ------ --      ii   i     i   i   --
  L1M4_orf2#LINE/    235 ----------ACTT------A--CTACAAAGCTACAGTAATCAAGACA-- 264

  chrX_115135711_   1567 CCATACTACAAGACTTCAAATTATTCTACAAGACTGGAGTAACCAAAACA 1616
                         --------------------------------------  i---------
  L1M4_orf2#LINE/    265 --------------------------------------GTG--------- 267

  chrX_115135711_   1617 GCATTGGTACTGGTATAAAAATAGGTTCATAGGCAAATAGAACAAAATAG 1666
                         ----         i    ii    iivi    iiv   i   i i   v 
  L1M4_orf2#LINE/    268 ----TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_115135711_   1667 ATAATCCAGGAGTAAGGCCACACACCTACAACCCTCTGATCTTTGACAAA 1716
                          v i     i i   iv   i   ii  iiii vvi    i  i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_115135711_   1717 GTTGACAATAATAAGTAATGGAGAAAGGAATC-TCTATTCAATAAATGGT 1765
                          v  v   v vi vvi     i     -   v-   v     i       
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAAATGGT 412

  chrX_115135711_   1766 GCTGGGATAACTGGCTCACTATGTGCAAAAGAATAAAACTGGATCCCTGT 1815
                                i      v v? i ii           i  ii    i    ii
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_115135711_   1816 CTTTCACCATAGATAATA-TCAACTCAAAATAGAT-AAAGA----AATTT 1859
                           iv       v i  v - i          i   - ?   ----   v 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_115135711_   1860 -----TTAAGACT-TGAAACTGTTAGTGTATACTGCAATAAAATCTATGG 1903
                         -----i   i   - i     v    ----------  v    iv  v ?
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAG----------AAGAAAACATAGGN 552

  chrX_115135711_   1904 A-AAATGTTATTGGATATTTGCCTAGGCAAAGAATTAATGACTAAGACCT 1952
                         i-    v  vv  - iv  v vi       v iv  vv iiv  v   vi
  L1M4_orf2#LINE/    553 GTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_115135711_   1953 CAAAAGCAAGAGCAACGAA-GTAAAAATAGACAAATGTGACTTAATTAAA 2001
                                 vi      i  - v         i    vv     v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_115135711_   2002 -CAAAAAGCTTATACACAGCAACAAA-ATTAACCAACAGAGTGAAAAGAA 2049
                         -iv    i   v iii vv   vii - i  -i   v i          v
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAAAAGAC 700

  chrX_115135711_   2050 AACCTACAGAATGGGAGAAACTATTTACAAAATATGCATCCAACAAAGGT 2099
                             i               v     i    vi  ii   ii i  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_115135711_   2100 CTAATATCTAGAATATACAAGGAACACAAACAACTCAACAATCACAAAAC 2149
                           vi    i        i  i    v vv         i   v v  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_115135711_   2150 TTCAAATAGTCTCTTTAAAAAAGTGAGCTAAAGAGAGAAATAGACTTTTT 2199
                         ---     ii ivv  ?     -  i  v  i  vvvi       v   i
  L1M4_orf2#LINE/    801 ---AAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_115135711_   2200 TTTTTTGCAAAGAAAGACATACAAATGGCCAATGAGTATATGAAAAAATG 2249
                          i-----       -  i               i  i i       i   
  L1M4_orf2#LINE/    847 TC-----CAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_115135711_   2250 TTCAACATTACTCATCAT 2267
                         i       i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (143 / 86)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 4.26 (132 / 31)  


2898 26.59 2.22 1.22  chrX_115142349_115144348.rev      611  1509 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115142349_    611 TGGAAAGATAGTCCATGTTTCTGAATTACAAGGGTCAATATTCTTAAAAT 660
                                   vi       iv  i   iv   iv i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115142349_    661 GTC--TACTC---AAATCAGTCTACAGATTCAGTGCAATCTCTATCAAGA 705
                          v --     ---    iii            ii      i       i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115142349_    706 AACCAATGACATTTTATACAGAAATATTTTAAA--AATCCTAAATGTATT 753
                         vv   iivi v    v i       - vvi  i--i        ---   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAA---ATT 146

  chrX_115142349_    754 TATA----ATCACAAAAAACCCAGAATAGCCAAAGTTATCTTGAGCAAAA 799
                         i   ---- vii   iii                iiv       iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_115142349_    800 AGAACAAAACTGGAGAAATCACATTACCTGACCTCAAATTATACCACATA 849
                                 ii     i v     i v  ii ii     viv   i   v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_115142349_    850 GCTACAGCAACAAAAACAGCATGGTGCTGGCATAGAAACAGATACACAGA 899
                                i  iv  i    ii    i        iii i   i i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_115142349_    900 CAAATGGAACAGAATAGAGAACCCAGAAATAAATACACACATCCACAGTG 949
                         iv       i     v    ii           iv  i    ii ii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_115142349_    950 AACATACACCTTTTTGACAAAGATGCCAAGAACATACATTGGGAAAAGG- 998
                           ivv ----    i     i i        v   v  v    i    i-
  L1M4_orf2#LINE/    347 AATTGA----TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_115142349_    999 CAGTCTCTTCAATAAATGGTGCTAGGAAAGCTGGATATCTATATGGAGAA 1048
                         i     i     i          i   v i       ? i i   v i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_115142349_   1049 GAATGATACTTGACCCTTATGTCTTTTCTTATACAAAAATCAAATAAAAA 1098
                               vii v     i  iv  vivi v           i  v v    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_115142349_   1099 TGGA-CATAAAATGAAATTTAAAGCCTCAAACTATGAAACTGCTACAAGA 1147
                             -  ? i viv    v   iiv  v       i     vi  v    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_115142349_   1148 AAACATTGGAGAAACTCTCCAGGACATCAGCGTGAGTCAA-GATTTCTTG 1196
                               v  ? v  v   i iv   v ii -  v  v   - i      i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTA 591

  chrX_115142349_   1197 AGTAGTTCCCTGCAAGCACAGGTAATCAAGACAACAATGGACAAATGGTA 1246
                         ii  vvv v iiv       i i  iv  iiv  v   i  i    v v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_115142349_   1247 --TCATACCAAGTTAAAAAGCTTCTGCACGACAGAGGAAACAAGCAACAC 1294
                         --    - v  i       -   i  ii vv  i    v  v v   v v
  L1M4_orf2#LINE/    642 CTTCAT-CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_115142349_   1295 AGAGTAAAGACAACTCACAGAATGAGAATAAAAATTTGCAAACCACTCAT 1344
                           v v         i         i  iv   v         i  ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_115142349_   1345 CAGGAAAGGTATTAATAACTAGAATATATGAGTAGTTCAAACCAATCTAT 1394
                          v iv    v i vi  v i         i iv ii  vv  v v  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_115142349_   1395 AA-AAAAAATC---TAACCGGCTTTAAAAATGGAGAAAAGATTTAAATAG 1440
                           -     iv ---     viv  ?        iv   i     i     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_115142349_   1441 ACATTTCTCAAAAGAAGACATACAAATGGCAAACAGGTATATGAAGGGGT 1490
                                  v        i           v  i i i i     ii i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_115142349_   1491 GCTCAACATCATTGATCAT 1509
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.94 (31 / 16)  


2778 26.05 0.65 2.91  chrX_115148448_115155446     1033  1961 (5038)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115148448_   1033 TGGAAATACATCCCATGCTCATGAATTGGAAGAATCAATATGATGAAAAT 1082
                               v i        i     i         v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115148448_   1083 GACCATATTGCACCAAGCAATCTACAGATTCAATGCAATTCCCATCAAAA 1132
                          i v   i v v v  vii              i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115148448_   1133 TACCAACATCATTTTACTCATTTTACACAGAATTAGAAAAAAAAATC-TA 1181
                          v   i ------- i iiv    i  v -    -  v  ivvi   -  
  L1M4_orf2#LINE/    101 TCCCAGC-------TGCCTTTTTTGCAGA-AATT-GACAAGCTGATCCTA 141

  chrX_115148448_   1182 AAATTTATATGTAAGCAAAAAAGAGCCTGAATAGCCAAAGCGATCTTAAG 1231
                              i     v  iiiv  ii  v  v           i i     i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_115148448_   1232 CAAAAAGAATCAATCTGGAGGCATCATATTACCCAAGTTCAAATTATACT 1281
                         v  i     iv  vi      vv   i i v     v      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_115148448_   1282 ACAAGAGTATAGTAACCAAAACAGCATGGTTCTGCTGTAAAAGTAAATCC 1331
                             iiv  i     i   i    ii    v   vii   iii  i ivi
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_115148448_   1332 ATAGACCCATGGAAAAGGACAGAGAACCCAGGAATAAAGCCAAATACTTA 1381
                              i v      v  i iv    ii    i      v   v i i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_115148448_   1382 CAACCAAATGATATTTCACAAAGCATACAAAAAT-ATAAATTAGGGAAAG 1430
                         iiii   v    v  iv    i -i i v  i i-  vv v i       
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_115148448_   1431 GACACCCTACTCAATAAACGGTGCTAGGAAAATTGGATAACCACATGTAG 1480
                         i i vi  vi    i   i      i   v  i      ?       i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_115148448_   1481 AAGAATGAAACTGAATCCCTCAACTCAC--CATATATGAAAATTAACTCA 1528
                                  ii  i i    - v     --      ii            
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCA 489

  chrX_115148448_   1529 AGATGGATCAAAGAGTTAAATGTAAGACCTGAAACAAAAAAAAAAAATCC 1578
                          i        ?   vi           v  i    v v    v----  i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC----TCT 535

  chrX_115148448_   1579 -AGAAGAAAACCTAGGAAACACTCTTCTGAACATTGCCCTATGCAAAGAA 1627
                         -          v    ?ivv v     vvi  v   vvi  v    v iv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_115148448_   1628 TTTAT-GATGAAGACCCCAAAAGCAAATGCAACAAAAACAAATACAAGTA 1676
                           iv -   - v   v         v v         iv   v i ii  
  L1M4_orf2#LINE/    586 TTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_115148448_   1677 AATTGGACCTAATTAAACTAAAAAGCTTCTGCACATCAATATAAAAGATC 1726
                                 i v  i   v v    i   i  ii v    viv v vv   
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_115148448_   1727 ATTAGAGTAAACAGACAACCCACAGAGTGGGACAAAATATTTGCAAATTA 1776
                          vv i   i  v              i     v               i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_115148448_   1777 TACATCTGACAGAATACTAGTATCCTGAACCTGCAAGGAGCTCAAACAAA 1826
                           i      i iiiv   v      v   iv ii  i  i   vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_115148448_   1827 TCAGCAAGGAAAAAAAAAACAAAACAAAATAATGTCATTAAAAAGTGGGC 1876
                            ii  v----     i     ------   iviv   ?    i     
  L1M4_orf2#LINE/    785 TCAATAAT----AAAAAGACAAA------TAACCCAATTWAAAAATGGGC 824

  chrX_115148448_   1877 AAAAAGCATGAGTAGACTTTTCTCAAAAGAAGATGTACAAATGGCCAAAT 1926
                            iiiiv   i     v      v         i             vv
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_115148448_   1927 GACATATGAAAAAAATGATTAACATCACTAATCAT 1961
                         ii  i       i -  v i       ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (137 / 101)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  

3327 23.52 2.80 1.12  chrX_115148448_115155446     3996  4888 (2111)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115148448_   3996 TAAAAATACATCCTGTATTCATGGATTAGATAACTTAATATTGTTAAAAT 4045
                          ii   v i    ii i          i  vi               i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115148448_   4046 GTCCATCTTACCTATAGCAATCTACAGATTCAATGCAATACTTGT-AAAA 4094
                          v v  vi v  i v vii              i     v i i -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115148448_   4095 TCACGATGGCATTTCCTTTTGCAGAAATAGATAAAAAGTCATCCTAAAAT 4144
                           v iiiv  v   ---           v  i  ivv --          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT---TTTGCAGAAATTGACAAGCTG--ATCCTAAAAT 145

  chrX_115148448_   4145 TCGTATGCATTCTCAGATGACTTAAAATAACCAAAGCAATCTTGGGAAAA 4194
                           i    v vviv  iiv   ii i    i     i        ii   i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_115148448_   4195 AAGAACAAAGCCAGAGCTGAGATTACACACTTCCTTATTTCAAAACATAT 4244
                                   iii   ----  i -         iv          v  i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAG----GACT-CACACTTCCCAATTTCAAAACTTAC 240

  chrX_115148448_   4245 TACAAAGTTACACTAATCAAGA--GTGTGTTACTGGCCTAAAGACAGACA 4292
                                i    v         --     v       v   i  i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_115148448_   4293 TAAAAATTCATGCTACAGCATAGAAAGACCAGAAATAAACTCACACATAT 4342
                           v i  iv   vv i  v  v  i  v            i  i    v 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_115148448_   4343 ATGGGCAACTGATCTTCAACAGGAATGCCAATACC---CAATGGGGAAAG 4389
                             v   i    i   i   i ii      v   ---            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_115148448_   4390 GATAGTCTCTTCAACAAATAGCATTGGGAAAGCT--ATATCCACATTCAA 4437
                         i       i          i iii     v i  --   ?      v   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_115148448_   4438 AAGAATAAAATTTGACCCTCTTCTTACATTATATA-AAAAATGAACTCAA 4486
                               i  i  v     iivi  i   ii     -      v       
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_115148448_   4487 AATCGATTAAAGACCTAAGTATAAGACCTGAAACTGTAAGACTAGAAAAA 4536
                            v   i ?        i i     v  i     i   i   vvv i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_115148448_   4537 AAAAATTTAGGA--AAAGATTTAAGACATTGGAATGGGCAATGACTTC-- 4582
                         i    iv    ?--   vv  iiv   v    iv i       ii   --
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_115148448_   4583 -AATGTGACAACAAAAGCAGAA-TAACAAAAACAAAAATAGACAAATAGA 4630
                         -i  i     v        v  -i       iv         i    v i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_115148448_   4631 AATAACTCTCACTTAAAAACTTCTATGCAGAAAAAGAAAC--------AA 4672
                          v vvv  vv v          i i   vvv   i  v  --------  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_115148448_   4673 GTAAAAAGACAACCTACAGAATGGAAGTAAATGTTTGCCAACTGTGTATT 4722
                           i           i         i  v    i     v  iii i   i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_115148448_   4723 GTATTAGGCGTTAATAATGAAAGTATAAAAAGAATTCTCATAGCTCAACA 4772
                         vv  v   vii vi  viv i i    v      i   i i i     i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_115148448_   4773 ACAGCAACA-AAATAACCTTATT-AAAAATGGGCAAAGAACTTGAGTAGA 4820
                          i iv  v -        iv   -              i i    i    
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_115148448_   4821 TATTTTTCCAAAGATGAGATATAAATGGTCAACAAGTACATGAAAAGATA 4870
                         i    i        v  v   i      i   i   i            i
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_115148448_   4871 CTCAACATCATTAATTAT 4888
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (126 / 81)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.33 (35 / 15)  

 247 30.96 6.95 6.64  chrX_115148448_115155446     5860  6492 (507)    L1M4_orf2#LINE/L1      255   889 (19)  

  chrX_115148448_   5860 AATCTAAGACAATGTGGTATTGGCCAATGAAATGGTAGGCTT---GA-CA 5905
                             -      i       i    --  --  v i   i v ---  -  
  L1M4_orf2#LINE/    255 AATC-AAGACAGTGTGGTACTGGC--AT--AAGGATAGACATATAGATCA 299

  chrX_115148448_   5906 CTGGCACAAAATAGAATATGGAAG--CAGTCAAATA----CATACAGAAA 5949
                         v   -----        -  ii  --   --     ----      vvv 
  L1M4_orf2#LINE/    300 ATGG-----AATAGAAT-TGAGAGTCCAG--AAATAAACCCATACATTTA 341

  chrX_115148448_   5950 TA--TAAT--ATTTT--A-AAATCTGTCA------TTCA-TAGAAACAGA 5985
                          i--i   --     -- -  ivv  i  ------    - i i----  
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG----GA 387

  chrX_115148448_   5986 GAAAATTGAATTATTT--ACAAGTAGT-TTGGAACAAATGGATAGTCATC 6032
                         i i   -- i iv   --    i i  -i   i    v      ?i  - 
  L1M4_orf2#LINE/    388 AAGAAT--AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA-C 434

  chrX_115148448_   6033 ATA-AAGAAAATAAAGTTAGATTCTGACAATTTGCTCCTTTGAATAAAAT 6081
                           i-  i i   i     i  ii iv  --i ii v  v vv vv     
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTAC--CTCACACCATATACAAAAAT 482

  chrX_115148448_   6082 ATATTCCAAAAATAATAAAGGATTTAAACATAAAAATAAAAACCCAAAGG 6131
                         -  vii     vvi  v ?i  ii    ii   i iiv     ivv  ii
  L1M4_orf2#LINE/    483 -TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_115148448_   6132 CATT----AGAACACATGAAAGAATAGTCTCATAATCTTAGTGTGGG-GA 6176
                          vi ----    v    iii? v v vii  i i i   i vv i  -i 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_115148448_   6177 TGATATTTCTAAGCATGTCACAAATTCTAGAAGCCATTTTTTAAAAAGCT 6226
                           i -  ii  iii   v   v  vvvi v    v ivvvvv     i- 
  L1M4_orf2#LINE/    582 TGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-T 629

  chrX_115148448_   6227 AAATAAATTTAACTAACAT-AAAATTACAAAAACATGCATGGCTCTAAAT 6275
                          i       vi   v-   -       --     v vii  vi  v  iv
  L1M4_orf2#LINE/    630 AGATAAATTGGACTT-CATCAAAATTA--AAAACTTTTGTGCTTCAAAGG 676

  chrX_115148448_   6276 ACTCACCACAAATGAAATAAAAAGACAAATCATAATCTGC-ATAAACTGT 6324
                           --  i iv  vi  i i         vi  i ivv  v- v   v i 
  L1M4_orf2#LINE/    677 AC--ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_115148448_   6325 TTAAAATATTAAATTTATATTAGTCAAAAGCCTAATTTTTGTT---AACA 6371
                           iv  -  i ----     iv vi  ii ---- i  v i i---  i 
  L1M4_orf2#LINE/    725 TTGCAA-ATCA----TATATCTGATAAGGG----ACTTGTATCCAGAATA 765

  chrX_115148448_   6372 CACAAAAAGATTTTACAAATAAATAAGTAAAAGGTAGATAACCTAACAGG 6421
                         i i   i iv i      v v     vv     ii i      i  iv?i
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_115148448_   6422 AATACTGG---AAGACTTATGTAGGCAGTTG---AAAGAAATGGAAATAC 6465
                           v iv  --- i  i  ivi   i  v  v---      ---  v    
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA---GATATAC 862

  chrX_115148448_   6466 AAATGTCTTTTTAAAATATTAAAAGAT 6492
                              v ivv v iv i  v       
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGAT 889

Transitions / transversions = 1.40 (112 / 80)
Gap_init rate = 0.06 (40 / 635), avg. gap size = 2.15 (86 / 40)  

 930 25.44 3.35 8.88  chrX_115148448_115155446     6493  6999 (0)    L1M4_orf2#LINE/L1      390   868 (40)  

  chrX_115148448_   6493 GAACATTCTT--CAACAGACGGTACTAGATAAATTGGATATCCCCATGGC 6540
                            i v    --     i i   i  i ivv  i      ?  v    - 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-C 438

  chrX_115148448_   6541 AATAG--TGTATTTTGAATCCTACCTGACATTATAAATATAAAATATAAA 6588
                           v  --  v v  v  vi       v   ii   --  i    -  v  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATA--TACAAAA-ATTAA 485

  chrX_115148448_   6589 TATAAAATATCAATTGCAGATCGGTTGCAGACCTAAAAGTGAGAAGTA-- 6636
                         ivi     i---------    i?----         v  i   iv  --
  L1M4_orf2#LINE/    486 CTCAAAATG---------GATCAW----AGACCTAAATGTAAGAGCTAAA 522

  chrX_115148448_   6637 -TTAAAATACTTTGTGTAGAGAAAGACATGGGG---AATCTTTGAAACCT 6682
                         -i  v  v   i ---    ii  i    i  ?---      i vi    
  L1M4_orf2#LINE/    523 ACTATAAAACTCT---TAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_115148448_   6683 CGGAGTTGGCAAATATTTGTTAAATAGGGCATAAAATATAAAACGTTAAC 6732
                         i  iv v     vvi   v   i   v i  iv   ----- i iiv i 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA-----AGCACAAGC 614

  chrX_115148448_   6733 TACAAAAAAAATCAAACA-ACAAATTGAATCCTATTTTAATTGAGAAAAT 6781
                         v      i   --   i - i      i iiii  ivv    i i  vv 
  L1M4_orf2#LINE/    615 AACAAAAGAAA--AAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_115148448_   6782 TTGTTCACCAAAAGATGCCATCAAGAAGGTGAAAAAGTAAGCCACAG--T 6829
                             v vi    i  ii i        i       iii  v      -- 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_115148448_   6830 GGGAGACATTATTTGGTACATATAGCAACTTTTACATACATCTGAGTA-- 6877
                               v v      ----------   v ----    i      -  --
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTG----------CAAAT----CATATATCTGA-TAAG 747

  chrX_115148448_   6878 -TATTTGTATCTAGAAGATATTAAAATTTCCTGGGAATCAATAAAAAGTA 6926
                         -v i       i    v    v  i vi  i ivi v       v  -- 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA--A 795

  chrX_115148448_   6927 AAGATGTTTAATTTAATTTAAAAATGTGCAAAACACTTTAAATGGACACT 6976
                             iivv   iii    ?       v     iv -   i   i    i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGA-TTTGAATAGACATT 844

  chrX_115148448_   6977 TCACAATAGAGGATAAGCAA-TGG 6999
                           v v v   i    vi   -   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGG 868

Transitions / transversions = 1.45 (74 / 51)
Gap_init rate = 0.04 (21 / 479), avg. gap size = 2.95 (62 / 21)  


2408 24.70 9.88 0.84  chrX_115243692_115248084.rev     3073  3902 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_115243692_   3073 AAAAAT-TTTCATGTACATGAAATGGAAGAATCAATATTGTTAAAATATT 3121
                            i  - ii     v    i v       v i           i  ivi
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_115243692_   3122 CATACAACCCAAAGCAATCTACAGGTTCAATGGAAACCCTATCCAAATAC 3171
                         v    vv      vii        i     i v  v       v    v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_115243692_   3172 CAATAAAAATTCTTCAGAGAAATATTTTTAAA--AATCCGGAAATTTATA 3219
                           iivivv-  i  iiv      -- vvi  i--i    vi     i   
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCATA 150

  chrX_115243692_   3220 TGGAA-----------CCA-------CAAAGCTATCTTGAATAAAAAGAA 3251
                              -----------   -------    i v        v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115243692_   3252 CAAAACTGGAAGAATCACATTACCTGACTTCAAAATATACTACAGAGTTA 3301
                             ii    i  v     i v  ii i       iv       i  i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_115243692_   3302 TAGTAACCAA-ATGATGTGGTGCTGGCATGAAAACAGACACATTGACCAA 3350
                         i     i   - iii      i       i ii i     i  v  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_115243692_   3351 TAAAACAGAATAGAGAACCAAGAAACAAATCCACACATCTACAACGAACT 3400
                          ii  i     v    ii v     i   i   i    i  iiiiv  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_115243692_   3401 --TTGTCGACCAAGATGCCAAGGACATACACAGGGACAAGGACAGTCTTT 3448
                         --  v     v i i       iv   v  vv   iv   i i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_115243692_   3449 TCCAATAAATGGTACAGGGAAAACTGGATATCCATATGCAAAAGAATGAA 3498
                           -  i       i v    v         ?   i               
  L1M4_orf2#LINE/    401 TC-AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_115243692_   3499 ATTGGA----------AAACTTTA---AGAA-----CTCAAAGT------ 3524
                         i     ---------- v  iv  --- i  -----      i ------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_115243692_   3525 ---------ATGAAAGTAGTTAAAACT---------TTGGGAGAAAA--- 3553
                         ---------   v   -  i       ---------  i i      ---
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAG-AGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_115243692_   3554 ---------TCTCCTGGACATTGTACTGGGCAAAGATTTCTTGAGTAATA 3594
                         ---------   i vv   v   vii i     v i      iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_115243692_   3595 CTTCACAATCA-AGGCAACTGAAGCAAAAATAGACAAATGGGATCACGTC 3643
                          vi  v  v  - i     vi   v         i    v   iiv i  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_115243692_   3644 AAG-TTAAAAAGCTTCTGCACAACAAAGGAAACAATCAAGAAACTGAAGA 3692
                           i-       -   i  ii vv       v  v         v    i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_115243692_   3693 TACAACCCACGGAATGGGAGAAAATATTAGAAAACTACACATCTGATAAG 3742
                         v         i                 v v   ii i i          
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_115243692_   3743 TAATTAATAACCAGAATATA--AGGAGTTCAAACAACTCTATAGGAAACA 3790
                         vi i vi  v          -- i  ii  vv       v   iv   v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_115243692_   3791 ATCTAATAATCCAACCTAAAAATGGAAAAAAAGATGTCAATAGACATTTC 3840
                         iv v     i    ii?        iv   i-   v v            
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAG-GATTTGAATAGACATTTC 846

  chrX_115243692_   3841 TCAAAAGAAGACATACAAATGAAAAACAGTCATATGAAAATGTTCTCAAA 3890
                           v        i         ivv  i iv  i       vi v     v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_115243692_   3891 ATCATTTATCAT 3902
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (121 / 82)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 4.24 (89 / 21)  


3213 27.53 0.44 0.44  chrX_115253789_115256707     1519  2426 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115253789_   1519 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAC 1568
                              ii i  i     i      i v      v i     i  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115253789_   1569 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1618
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115253789_   1619 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1666
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_115253789_   1667 TATGGAACTAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1716
                                v iv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_115253789_   1717 AACAAAGCTGGAGGCATCATGCCACCTGACTTCAAACTATACTACAAGGC 1766
                                i      vv   ii iv  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_115253789_   1767 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGATC 1816
                                 i   i    ii         i iv ii i   v  i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_115253789_   1817 TATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCTCATATCTACAACT 1864
                         v      i    i--    i  --        vv  vi i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_115253789_   1865 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1914
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_115253789_   1915 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1964
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_115253789_   1965 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 2014
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_115253789_   2015 TTAAAGACTTAAACTTTAGACCTAAAACCATAAAAACCCTGGAAGAAAAC 2064
                          i ?    i    iv v   v       i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_115253789_   2065 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2114
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_115253789_   2115 AACACCCAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 2164
                         i     v      vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_115253789_   2165 TTCAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAAC 2214
                          iv  v v  i i   i   i vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_115253789_   2215 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 2264
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_115253789_   2265 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2314
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_115253789_   2315 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 2364
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_115253789_   2365 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 2414
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_115253789_   2415 ATCACTGGCCAT 2426
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2470 27.42 1.28 4.78  chrX_115279377_115283090     2282  3222 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115279377_   2282 TGGAAGAAGAGTTCATGCTCATGGATAGGTACAATCAATATCATGAAAAT 2331
                              ii v vii    i        v  v v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115279377_   2332 GACCATGCTACCTAAAGCAATTTAAAGATTAAATGCTATTCCTATCAAAG 2381
                          i v  i  v  i   vii  i  v     v  i  v  i         i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115279377_   2382 TACCAATCATATTTTTCACAGAA-TTATAAAAAAAAACT-ATTCTAAAAT 2429
                          v   iiiiiv     ii     -  i----- v  i  -  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-----ACAAGCTGATCCTAAAAT 145

  chrX_115279377_   2430 TTATTTGGAACCAGAAAAGAGCTCATATAGCCAAAGCAATCCTAAGCAAA 2479
                          i  v     viiv  ii  v iviv         i     i i -----
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA----- 190

  chrX_115279377_   2480 AGACAAAAAAAAAAAAAAAATGACAACAACAAAAACACAGTCACAAGCAT 2529
                         ----    i  i  v   iv  i-------- ii  ----     -----
  L1M4_orf2#LINE/    191 ----AAAAGAAGAACAAAGTTGG--------AGGAC----TCACA----- 219

  chrX_115279377_   2530 CAAACTATCTGACTTCAAAGTGTACTACAAAGTTACCATAATTAAAACAG 2579
                         ----  vi ii i      iiv          i   vi    i  i    
  L1M4_orf2#LINE/    220 ----CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_115279377_   2580 CATAGTACTGGAACAAAAGCAAACACATAGATCAATGGAACAGAGTAAAG 2629
                         ii i       v i  iiii i   i              i   i vi  
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_115279377_   2630 AACCCAGAAATAAAGCCAAACACCTGCAGCCATCTGATCTTCAACAAATT 2679
                          ii           v   v   ii iii i  vi    i   i    ivv
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_115279377_   2680 TGACAATAACAAGCAATGAAGAAAGGACCCTCTATTCAATAAATGCTGCT 2729
                           v   v v  vv     ii     i ivv   v     i     v    
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_115279377_   2730 AGAATAACTAGCTAGCCATATGCAAATTACTGAAATTGGACCCCTTTCTT 2779
                         i i i    i v  ?   i       vv v    i          vi  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_115279377_   2780 TTACCATATAGAAAAATTAACTCAAGATGAAGTAAAGACTTATATGTAAA 2829
                         vi        v              i   i vi ?    i  v      i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_115279377_   2830 TCCTAGCACTGTAAAAACCCTAGAAGAAAATGTAGG---AAATACAATTC 2876
                         vv   iv   i     vi i          ii    ---    - --   
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-C--TTC 562

  chrX_115279377_   2877 TGGACATCAGCCCTGGCAAAAACTT----GATGACAAGGACTCCAAAAGT 2922
                         vv   v ii viiv     viii  ----   ---- v   v       i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGAT----ATGACACCAAAAGC 608

  chrX_115279377_   2923 AATTGCAAAGAAAACAAAAATTAACAAATGAAACTTAATTAAACTAAAGA 2972
                          vvv    vi   iv      vi i    vii    v  i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_115279377_   2973 GCATCTAGACAGCAAAGGAAACTATCTATAGAGTAAACAGACAGCCTACA 3022
                         i v i ivi vv       v      v v i   i  v     i  i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_115279377_   3023 GAATGGGAGAAAATATTTGCAAACTATGCACCAGACTAAG--ATTTAATA 3070
                                                ii  ii i v  -    -- i  i-  
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGA-TAAGGGACTTG-TA 756

  chrX_115279377_   3071 TACAGAATCTATAAGGAACTTAAATAAGTCAACTAGCAAAAA-ACAAACC 3119
                          v      v     i     ivv i  v    -  ii     -     iv
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAA-TAATAAAAAGACAAATA 805

  chrX_115279377_   3120 AACCTATTAAACAATGGGCAAAGAACGTGAGCAGATACTTCTCAAAAGGA 3169
                          v  v   ?  v           i iv   ii   i i     v    i 
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_115279377_   3170 GTCATATATGCAGCCAGCAAGCATATGAAAAAATGCTCAATATCCCTAAT 3219
                          vi   i viii    ii     i       i        i   v?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_115279377_   3220 GGA 3222
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.63 (158 / 97)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.35 (57 / 17)  


2744 26.55 0.65 3.26  chrX_115339918_115341828.rev      502  1420 (491)    L1M4_orf2#LINE/L1       14   908 (0)  

  chrX_115339918_    502 CATGCTCATGGATAGGACAAATCAATATCATTAAACTGGCCATACTTCCC 551
                             i        v   vi v i     ii    iv    v     i   
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chrX_115339918_    552 TAAGCAATTTACAGATTCAGTACTGTTCTTGTCAAAATTACCAATATCAT 601
                         v  vii  i          iii vi i i i       i-   iivv v 
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC-CCAGCTGCCT 112

  chrX_115339918_    602 TTTTCATAGAAAGAGAAAAAAACT-ATTCTAAAAATCATATGGAACCAAA 650
                             iii     vv  v  i--  -  i      v          viiv 
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_115339918_    651 AAAAGAGTCTGAATAGCCAAAGCAGTCCTAAAGCAAAAAGAACAAAGCTG 700
                          ii-  vi v           i  i  i i  i-  i          i  
  L1M4_orf2#LINE/    161 AGG-GACCCAGAATAGCCAAAACAATCTTGAAA-AAGAAGAACAAAGTTG 208

  chrX_115339918_    701 GAGGCATCACAGTAACCAAATTCAAACTACACTATAAGTGCTATAAGACT 750
                             vv     v vv    v      ----   ----- i   i  ii  
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAA----ACT-----TACTACAAAGCT 249

  chrX_115339918_    751 ACAGGAACTGAAACAGCATGGTATTAGTACAAAAACAAACATATAGAGCA 800
                             v  iii i    ii     i i i i  ii i i         v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_115339918_    801 ATGGAACAGAATAGAGAATCCAGAAAGAAATCTACACAACTACAGACATC 850
                               i     v    i        v   i i i   vi  ii v  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_115339918_    851 TGATCAACTTTTGACAAAGTTGACAAAAATAAGCAATAGGGAAAGGAC-- 898
                             ----   i     i v  v   i vi vv    i       i i--
  L1M4_orf2#LINE/    350 TGAT----TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_115339918_    899 TCCCTATCAATAAATGGTTCTGGGATAAGTGGCTAGCCATATGCAGAAGA 948
                           ii -    i       v      i  v   v  ?   i     i    
  L1M4_orf2#LINE/    396 TCTTT-TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_115339918_    949 ATGAAACTTGACCCCCTACCTTTTACCATGTACAAAAATTAACTCAAGAT 998
                              i-   iv         ivi     i                 i  
  L1M4_orf2#LINE/    445 ATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_115339918_    999 AGACCAAAAATTTAAATGTAGGAATTCAAACTATGAAAATCCTAGAAGAA 1048
                         i  i  ? i ii        i  ii v       i   v  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_115339918_   1049 AACCTAGGAAATAACCTTCTTGACATCAGCTTTAGCAAAGAATTTATGGG 1098
                            v    ?ivv  i    v    v ii v  vi    v iv  iv i i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_115339918_   1099 TAACTCCCCAAAAGCAATTGCAACAAAACCAAGAATTGACAGGTTGGACC 1148
                           vvv v         vvv         vv  i   v  i ii      i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_115339918_   1149 TAATTAAACTAAAGAGCTTCTGCACAGCAGAAGTAACTAT-AACAGAGTA 1197
                          v  i   v v  i i   i  ii vv  i i vv     -  v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_115339918_   1198 AACAGACAACATATAGAATGGGAGGAAAATATTCACCAACTATGCATCTT 1247
                           v       vi i          -        ii v  ii  ii    v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAG-AAAATATTTGCAAATCATATATCTG 742

  chrX_115339918_   1248 ACCAAGGTCTAATATCGAGAATCTACAAGTAACTTAAATCAACAAGCAAA 1297
                          iv i  v  vi    v     v  i  iv    i--- i -----   v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTC---TTA-----CAAC 784

  chrX_115339918_   1298 ATAATAATAATAATAATAATAATTCAATTAAAAAATAGGCAAAGGACATG 1347
                         vi        v  v vv     ii     ?      i         iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_115339918_   1348 AACAGACACTTCTCAAAAGAAGATATACATGCACCCAACAA--ACATGAA 1395
                           i     i     v              viiiv    i  --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_115339918_   1396 AAAAATACTAATCACCACTAATCAT 1420
                           i - i  v v  i  ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (17 / 895), avg. gap size = 2.12 (36 / 17)  


 700 26.73 8.14 9.09  chrX_115357794_115359416      394  1130 (493)    L1M4_orf2#LINE/L1      179   908 (0)  

  chrX_115357794_    394 AAACAAGCAT--AAAATAAAAAT----TTAAAGGA-TAACA-TTCACAAT 435
                               v v --    v  i  i----  ii    - v   -   v    
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_115357794_    436 ACCATAAATATGTCAAATACCTAGAGAGATCA-GACAAAATA-TA-TAAC 482
                         vi  -   iv iii v v v   v  vi    -    ivi i-  - ii 
  L1M4_orf2#LINE/    229 TTCA-AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_115357794_    483 AGATCAATACATACAATTAGAACATTAGAACA--ATGGGGA------AAA 524
                          v vvi   v i i --    v  v i   i --  v i  ------   
  L1M4_orf2#LINE/    278 ATAAGGATAGACATA--TAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_115357794_    525 TAGAGTTCCATCTACACATATG--TAATTTACGATTTATGTCAAAAGCGC 572
                           i --i    --   iv    --i    ---     vi v   ii i  
  L1M4_orf2#LINE/    326 TAAA--CCCAT--ACATTTATGGTCAATT---GATTTTCGACAAGGGTGC 368

  chrX_115357794_    573 CACTGCAGTGCAGCAGGGAAGGA-TGACCTTGCCAATAAATGGTGCTGGA 621
                           vvi vi v  iii     i  - iii   vi   i            i
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chrX_115357794_    622 TTTATAGTCTATTG---AGCTACAAATAGAAAAAAAGGAAATT------T 662
                         --- i ---- i  --- ? i   -- iv    i  v   i  ------i
  L1M4_orf2#LINE/    419 ---ACA----ACTGGATAKCCACA--TGCAAAAGAATGAAGTTGGACCCC 459

  chrX_115357794_    663 TACCTCTATATTATAAACAAAGA--AATTTCATATGGACTGTAGATCTAA 710
                               - i ii   v     i --  i iv v     iii?   i    
  L1M4_orf2#LINE/    460 TACCTC-ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_115357794_    711 ATATGAAAGGTAAAATAATACAGCTTCTGTGAAAAAATATAAGCGAATAC 760
                           i i i  v     iv   v i  ii ivi i    i   i ? v v i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_115357794_    761 CTCACTGACTTCG--T---GCAAAGATTTTTTAAACA--ACACACAAAAG 803
                           ivv    i i -- ---    v i   i   i i --    -      
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC-CAAAAG 607

  chrX_115357794_    804 CAC--TTAATAAAAGAAGATGCTATA-AAATTGGAC---ATTAAAATTAA 847
                            --vi  i       i -iv  v -         ---  i        
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_115357794_    848 GAACTTATATTAATCAAAAG-CATCATTAAGAACGTGAAAAAAGCCAAAA 896
                         i     v i vvv     i -  ii  i     v       i --   --
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA--CAA-- 702

  chrX_115357794_    897 AAAGAAAAAGAAAAACAAAAAGAAAATGAAAAAGCCAGCTGCATACTGGG 946
                         --------------- ------------------   ----  v v    
  L1M4_orf2#LINE/    703 ---------------C------------------CCA----CAGAATGGG 715

  chrX_115357794_    947 ATAAGATGTTTATAAAAACTATGATC-AACAAAGTTGGA---GTAATGAG 992
                          v  i  i   ii   vvv   -   -i i  i ---  ---   viv  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATAT-ATCTGATAAGG---GACTTGTATCCAG 761

  chrX_115357794_    993 AACATCTAAAGAACT---ACAAATCAACAAT-----GACAGACAACTCAA 1034
                           i  v         ---    v    i   -----    i i   i   
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_115357794_   1035 TAAACAAATTGGTAAAATACTCGACCAGATACTTTGTAAGATAGGATATC 1084
                          v? v    v  i   iv i i  vi   i i  iviv i v i     v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_115357794_   1085 CCAATAGCCAATG-GAATATGAAAAGCCTCTGAGCATCATCAGTCAT 1130
                          v   i      i- v i        viv  v i     ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (119 / 74)
Gap_init rate = 0.06 (43 / 730), avg. gap size = 2.95 (127 / 43)  


1339 27.01 14.96 0.18  chrX_115408459_115412486.rev      500  1047 (2981)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_115408459_    500 AGGGATAGACA----GATGAATGAAACAAAATACAGAGACCAGAAACAGA 545
                          i         ----   v    i  i i   vv    v       i i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_115408459_    546 CCCACATAAATATAGTTGACTGATCTTTGACAA--------------TAC 581
                             i i vv   i  ii i    i  i     -------------- v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_115408459_    582 AATGGAGCAAACATAATCTTT-CAATTAATGGTGGCAGAATAACGGGACA 630
                              i v  iv   i     -   iv       vii i i   v   i 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_115408459_    631 TCCACATGCACAA-AATAAATCCACAGACAGACCCTACGACCTT-CATAA 678
                         ?         v  -   i  viiiv vv vv   ii  -   v -i i  
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC-ACCATATACAA 478

  chrX_115408459_    679 AAATGAGCTCAAGATGAATCACAGATCTAAATGTAAA------------- 715
                             v i     i   i    ?   i          i-------------
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_115408459_    716 ----------------------------------GTGA------GTTTGG 725
                         ----------------------------------    ------   v  
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_115408459_    726 TGATGACATTTTAGATGCAACACCAAAGGCACAGTCCAT----GAAAACA 771
                         ii   iiv i      iii        i     iv v i----     v 
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_115408459_    772 -AGATAAGCTGAATTTTATTCAAATTAAAATTTCCTCCTCTGTGAAAGGC 820
                         -      ii  i i  i  iv         vi ii viv  vii  i i 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_115408459_    821 ACAGTCAAGGTAATAAAAAGATAAGCCAAAGACTAGGAGAAAAGATTTTC 870
                           vi     iv i i      i  v   v   v i        v    v 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_115408459_    871 AAA-CA-ATATCTGATACTGGACTGCTATCCAAAATATACAAAAAACTGT 918
                            -  -          vv     vv      i      i   i    v 
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_115408459_    919 TAAATCTCAATAATAAGAAAACAAAAAATCTGATTTTAAAACGAGACAAA 968
                           v v           i  i     v  i ii   ?v    i i vv  i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_115408459_    969 AATCTTAACTGATACCTCACCAAAGAA-ATATACAGATGGCAAATAAGCA 1017
                         i  i v  iv  i ii  v        -       i     v        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_115408459_   1018 TACAAAAATATGCCAAGCATCAGATATCAT 1047
                         i ii    v    iv i     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (90 / 55)
Gap_init rate = 0.02 (13 / 629), avg. gap size = 6.38 (83 / 13)  

3668 20.63 3.85 0.91  chrX_115408459_115412486.rev     2679  3560 (468)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115408459_   2679 TGAAAATATATACCATAATATTGGGGTGAAAGTGTTAATAATCTTAAAAT 2728
                           i   v    v    iv vv   iv  i   vv      v v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115408459_   2729 GTCGATACCACCCAAAGTGATCTACAGAGTCAAAGCAAGACTTACGAAAA 2778
                          v i    iv      v           v    v    vv i  iv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115408459_   2779 TCCCAAAGATG--TTTTTCGCAGAAATATCAAAATCC-ATGCTAAAATTT 2825
                              -- v  --     i        - v v  v i-  v        i
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTC 147

  chrX_115408459_   2826 ACTTGGAAACACAAGAGACATTAAATGGCCAAAATTATCTTGAGAAATAA 2875
                          iv      ii    i   vivi   i       iv       i   v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_115408459_   2876 GAACAAAGTTAGAGGACACACATTTGTTGATTTCAAAACTTACCACAAAG 2925
                                   i      v    i  viii              i      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_115408459_   2926 CTATGGTAATAAAAAAAAAAATGTGCTACTAACATAAAGACA--CACATG 2973
                            ii     v  i v i---    v    ii     i  i --  i  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAG---TGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_115408459_   2974 AGCCAACGGAACAGA-----GAGCACAGAAATAAACCCTTGAATGTATGG 3018
                         iii   i    i   -----   iv             v iv  v     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_115408459_   3019 TCAATTGATTGTCAACAAGGGTACCCAGACTATTCAATGAGGAATAATTA 3068
                                   v  i        i  v    i        i    vi v  
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_115408459_   3069 GTGTTTTCCATAAATGGTGCTGGGAAAACTGGATCTCCATATGCTAAAGA 3118
                           v     v i              v        v?   i    v     
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_115408459_   3119 ATAAAGTTGGACCCTT----TAGAAAATATGCAAAAATTAACTCAAGG-G 3163
                           i           i ----i v vv    i               ii- 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_115408459_   3164 AATCAAATACCTAAACTTAAGGGGTAAGACAATAAGACTCTTAGAAGGAA 3213
                         i    ? v       iv    i v   i  v    i           i  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_115408459_   3214 -CATTTGAAAAAAGCTTCATGATGTTAGATTTGGCAGTGATTTTCAAGAT 3262
                         -   vv ?iv   v    i   iv  i i  v    i  i   iiv    
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_115408459_   3263 ATGACACCAAAATTACAGGCAACAAAAGAAAAAGTAGGTAAAGTGGAGTT 3312
                                     vi   i               i   i    v    v  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_115408459_   3313 CATCAAAATTAAAAGCTTT-GTGCCTTAAAGGACGTTATTAAAACAGTGA 3361
                                       i    -    i i       ii   i  i v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_115408459_   3362 AAAAGCAACTCACAGGAAGAAATAAAATATTTGCAATGCAAATATCTGAT 3411
                            ii    i     i v ii v             vv  v         
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_115408459_   3412 AAGAGATTGGTATCCAGAATATATAAAGAACTTTTACAACTCAGTAACAA 3461
                            i  i v                       i          i   i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_115408459_   3462 CAGAAAACAAACAAACAAATTAAAAACCAGG-AAAGGACTTGAATAGAGA 3510
                         --i  i     i  v v    ?    vii  -      i         v 
  L1M4_orf2#LINE/    795 --AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_115408459_   3511 TTTCTCCAAAGAAGATATA-------------AGCACAT---AAGACATT 3544
                                            -------------       ---    iii 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_115408459_   3545 CAATATCACTAATCAT 3560
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (104 / 74)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.80 (42 / 15)  


3035 25.06 3.13 1.79  chrX_115425110_115431201     2766  3659 (2432)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_115425110_   2766 GAAAGATGTTTCATGTTCATTGATTGGAAGAAGAATTAATATTGTTAAAA 2815
                                i ii         v          v---             i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGAC---TTAATATTGTTAAGA 49

  chrX_115425110_   2816 TGCCCTTGCTTCCCAAAGCAATCTAGAGATTTAATGCAACCCCTATAAAA 2865
                           v vv i  i      vii     v     i  i    i      v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_115425110_   2866 ATACCACTGATGC--TCTTCACAGAAATACAATAAA-TAATCCTAAAATT 2912
                           v   -- v   -- i  ii       -ii i  i- i           
  L1M4_orf2#LINE/    100 ATCCCA--GCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATT 146

  chrX_115425110_   2913 TGTATAGAAACGAAAAAGACCCAGAACAGTCAAAACTATCCTAAGCAAAC 2962
                         ii   i    i v  ii         i  i      v   i i iv  iv
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_115425110_   2963 AGAACAAAACTGGAGGAATCACATTATCTGACTTTAAATTTTTCTACAAA 3012
                                 ii       v     i vi ii i  i   vi  v       
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_115425110_   3013 GCTGTAGTAACCAAAACAGCATGGTACTGGAATAAAAAACAGA-ATCATA 3061
                            ii     i   i    ii         v    ii -i   -  -   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACAT-ATA 294

  chrX_115425110_   3062 GATCAAGGAAACAGAATAGAAAACCCAGAAACATATCCATTCACCTACAG 3111
                               v i  i     v  i ii       i v i    v  ii  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_115425110_   3112 TAAACTCATTTTTGACAAAGGTGCCAAAAGCATACACTAAGGAAAAGACA 3161
                          v  i v     i     i        i v   v  v ii     ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_115425110_   3162 GTCTCTTCAATAAATGGTGCCAGGAAAACTGGATATTCATTTACAGAAGA 3211
                             i     i         ii   v         ?i  iv i  i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_115425110_   3212 GTAAAACTAGAGCACTATCTATCTCTCACCATGTACAAAAATCAAATGAA 3261
                         i i  ii i  v ----i   i   v      i         i  v v  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACC----CCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_115425110_   3262 AATGAGTTAAAGACTTAAATCTAAGACCTCAAACTGTAAAACTACTACAA 3311
                             ii i ?    i     v     v  v     i       vi  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_115425110_   3312 GAAAACTTAGGGAAGAATCT-CAAGTACATTGTTCTGGGCAAAAATATCT 3360
                               v    ?ivi     - iv -  v   vvi i     vii v   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_115425110_   3361 TGAGTAATGCC-CCACAATCACGGGCAACCAAACCAAGAAGGAACATATG 3409
                          iii  -  v -   v  v   ii     v   vv  i  vii i v  v
  L1M4_orf2#LINE/    590 TAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_115425110_   3410 GGATCCAATCAAC-TTAGAAAACTCCTGGACAGCAAAGGAAAC------- 3451
                            iiiv     v-   -      ii  vi vv       v  -------
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_115425110_   3452 AAAGTAAAGAGACAACCTACAGAATGGGAGAAAATATTTGCAAACTACCC 3501
                              i  i        i                          ii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_115425110_   3502 ATCTCA--------------CCAGAATATATAAAACGCTCAAACAACTCT 3537
                             v --------------              ivi   vv       v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_115425110_   3538 ATAGGAAAAAAATCTAATAATCCAACAAGAAAATGAACTCGATATTTGAA 3587
                            iv     i - v     i    iv?i      ii vviiv       
  L1M4_orf2#LINE/    788 ATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_115425110_   3588 TAAGTATTTCTCAAAAGAAGACATACAAATGGCAAACAGGCTTATGAAAA 3637
                           iii       v        i           v  i i  vi       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_115425110_   3638 GGTGCTCATCATTGATCATCAG 3659
                          i      v   ii????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (142 / 78)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 2.44 (44 / 18)  

2910 25.95 0.74 4.96  chrX_115425110_115431201     4652  5599 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115425110_   4652 TGTAAAGATATTCCATGCTTATGGATTGAAAGACTTAATATTAATAAAAT 4701
                           v        i     i i        i             iv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115425110_   4702 ACCTGCATTATGCAAAAGTATGTACAGATTCAATACAATTCCTACAAAAG 4751
                         iv vii i viv    vvv  v           ii    i    iv   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115425110_   4752 TCCAAAGGGCATTTTTCACAGACAAAGAGAAAACAATCCTCATGTTTGTA 4801
                            v ivv  v     ii    v vv  v  ivii     v vi  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115425110_   4802 TGGAACAACAAAAGACCCCAAATAACCAAAGAAATCTTGAGAAAGGAAAA 4851
                              vvi   ii     vi    i     iv        i    i i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115425110_   4852 CAGAGCTAGAAGCCTCACATTTCTTGATTTCAAACTTTATTACAATCCTA 4901
                           i  i i  i v      i   iii        vi   i     vv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_115425110_   4902 TTGTAATAAAAAGAATATGATACTTTCAGTGAAAAAAGACACAGAAACCA 4951
                         iv     v  i v i i  i    vv  - i ii v     i v i i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCA-TAAGGATAGACATATAGATCA 299

  chrX_115425110_   4952 ATGAAACAGAATTGATTGTCCAAAACTAAACCCACGCATATACAGTCAAC 5001
                            i  i        vv     i  v        ii   v  ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_115425110_   5002 TAATCTTC---AAGGGTTTCAGGAACACACATTAGGAAAGTGATAGTCTC 5048
                          i  i   ---      vi  i  v  iv  v i  i  ivi       i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_115425110_   5049 TTCCAAAAATGGTGTTTGTAAAACTGGATATCTACATGCAAAAGAATAAA 5098
                            v v        i v v v         ? i              i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_115425110_   5099 -CAGAACCCTTGTCTTATACCATATACAATAATAAACTCAAA-TATATTA 5146
                         -iv i    i ii  i i           v   v        - iv  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_115425110_   5147 AAGACCTAAAAGTAACGTG-TGAAGCAATAAAATTTGTAGGAGAAATCAT 5195
                         ?         v    - v - i  i v      i iv   i     v   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAA-GAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_115425110_   5196 AGAGAGAAAGCTCCTTAACAGTGAGTTTGAAAATGTTTATTTGGATGTGA 5245
                           i?iv   v  i v i  vv  i   v iv    v  vi  i   i   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_115425110_   5246 TGTCAAAAGCACAGGCAACAAGAGCCAAAAAAAAAAAAAAAAAAAAAAAA 5295
                         iii          i       ---------------------------- 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAA----------------------------A 620

  chrX_115425110_   5296 AAAAAAAATCCCAAAACAAAAAACAAGTGAGATTACATCAAACTAAAAAA 5345
                          i       ----------- i i  i vi  i v       v v     
  L1M4_orf2#LINE/    621 AGAAAAAAT-----------AGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_115425110_   5346 TCTTCTGCACAGCAAAGGAAATAATCAACAGAATAAAGAAGCAACCTATG 5395
                         -   i  ii vv       v iv     v i i i  i ii     i ii
  L1M4_orf2#LINE/    660 -CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_115425110_   5396 GAATGAGAGAAAATGTTTGCAAACCATAAACTATCTCCTATGAAGTTAAT 5445
                              i        i        i    ---     vv  v iiii vi 
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATA---TATCTGATAAGGGACTTGT 755

  chrX_115425110_   5446 GTCCAAAATATATAAGGAGCTCATGCAATTAAATAG-AAAAAAACAAAAA 5494
                         i    i         i  i   v i   i v    i-     i     --
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA-- 803

  chrX_115425110_   5495 TAACCTGATTAAAATATGGGCAAAGGACATGGATAAACATGTTTCCAAAG 5544
                              ii   ?   v            iv  i   i    v i       
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_115425110_   5545 AAGACATACGAATGGTTAACCAATACATGAAAAGGTGCTCAATGTCACTA 5594
                             i    i     ii  iv ii          i       ii   ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_115425110_   5595 ATCAT 5599
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.75 (154 / 88)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 4.50 (54 / 12)  


1882 27.54 2.21 2.21  chrX_115438085_115440149.rev      502  1180 (885)    L1M4_orf2#LINE/L1      150   828 (80)  

  chrX_115438085_    502 ATGGAACCACAAAAGACCCAGACTATCCAATGCTATCCTAAGCAAAAAAG 551
                               vii   ii        v  v    vi v   i i ----     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA----AAAAG 195

  chrX_115438085_    552 AAGAACA---TTGGAGGAATCACATTATCTGACTTCAAA--TTA-TATGA 595
                                ---        v     i vi ii i      --   -  i--
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC-- 243

  chrX_115438085_    596 AAAAAAAAATAGTAACCAAAACAGCATGGTAGTGGCATAAAAACAGAAAT 645
                         --   ivv i     i   i    ii     v        ii i   v  
  L1M4_orf2#LINE/    244 --AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_115438085_    646 ATAGACCAATGGAACAGAATACAGAACCCAGAAAGAAATCCACACACCTA 695
                              i        i     vv   ii       v   i   i   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_115438085_    696 CAGTGAACTCATTTTCAACAAAGGTGCCAAAAACCTATACTAAGGAAAAT 745
                         ii  v  i v      i    i        i v v vi v ii     iv
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_115438085_    746 ACAGTGTCTTCAGTAAATGGGGCTGGGAAAACAAGATATCTATACACAGA 795
                          i   v i    ii      v       v   vi    ? i i ii  i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_115438085_    796 AGAATCAAACTCAACCACT--CTCTCGCCATATATAAAAATCTAA-TAAA 842
                              v  ii vi   v  --   v i       i      -   - v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAACTCAA 490

  chrX_115438085_    843 AACAGACTAAACACTTAAATCTAAGACCTCAGACTATGAAACTACTACAA 892
                           ii  ii ? v  i     v     v  v i     i     vi  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_115438085_    893 GCAAACGTTGAAGAAACTCTTCAGGGTATTGTACTGGGCAAAACTTTCTT 942
                          v    i v i? v  v     iv iiv   vii i     viv      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_115438085_    943 GAGTAACACCCCACAAGCACAGGCAACCAAAGCAAAAATGGACAAATAGT 992
                         iii  vv  v   v       i     v    v      i  i    v v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_115438085_    993 ATCACA-CGAAGTTCAAAAACTTCTGCACAGCAAAGGAAACAATCAGCAC 1041
                          iiv  - i  i  -        i  ii vv       v  v    iv v
  L1M4_orf2#LINE/    641 ACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_115438085_   1042 AGTGAAGAGACAAC----AAAATGGAAAAAAATATTTGCAAACTACCCAT 1087
                               i       ---- i     i i              ii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_115438085_   1088 TTGACAAGGAGTTAATGACCACAATATATGAGAAGCTCAAACAATTCTAT 1137
                         i   i    iii vi iv   v       i ii i   vv    i  v  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_115438085_   1138 AG-GAAAATATATAATAATCTGAGCAAAAAAAAATGAGACAAAG 1180
                          i-i    v i -     i ii vi?     ---  i -     
  L1M4_orf2#LINE/    790 AATAAAAAGACA-AATAACCCAATTWAAAAA---TGGG-CAAAG 828

Transitions / transversions = 1.65 (114 / 69)
Gap_init rate = 0.02 (15 / 679), avg. gap size = 2.00 (30 / 15)  

 392 16.30 2.17 0.00  chrX_115438085_115440149.rev     1483  1574 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_115438085_   1483 AAAAAGGAACAAA--ATTTGAATAGACATTTCTCAAAAGAAGACATAAAA 1530
                              v ii    --                   v        i   v  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_115438085_   1531 ATGGCAAACAGGCATATAAAAAGGTCTTGAACATCATAGATCAT 1574
                              v  i i   i  i     i vi v       ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 2.00 (2 / 1)  


 811 28.35 7.86 3.54  chrX_115443888_115445523.rev      502  1150 (486)    L1M4_orf2#LINE/L1      232   908 (0)  

  chrX_115443888_    502 AAAACTAATTATAA-GCCATAATAATTAAAACAGTGTGATACTGGCA-AA 549
                               v i  i  -  i i i    i  i        i        -  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_115443888_    550 --ATTGAGCAATTAGACTAATGAAACAA---TGC-AGCCTAGAAATGCAG 593
                         --  v  -  vv    ii    i  i i---  v-  i i      iv v
  L1M4_orf2#LINE/    282 GGATAGA-CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_115443888_    594 T-ATGCATGTTTTAA--AATTTAGCATATAGCAAAAATGACATTAAAATT 640
                         i-  i   -  v ii--    v viv -iii   iii  v  --- i ii
  L1M4_orf2#LINE/    331 CCATACAT-TTATGGTCAATTGATTTT-CGACAAGGGTGCCA---AGACC 375

  chrX_115443888_    641 ATT----GAAGAGAGTACAAGTTTTCCATTAAATAGAGTTGGATCAATTG 686
                            ---- ii  i  v i ivi   i  vi    i v i   iv   i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_115443888_    687 AGTGTATATATGAAGAAAAATTAAGTTG-ATCCCTGCAATAACAAAATCA 735
                         ii i?vi i   v i  i   v      - i    i ----- ----   
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC-----C----TCA 466

  chrX_115443888_    736 TGCAATA-ACAAAAAATCAATTTCAAATGTATTTAAATACCTAAATGT-- 782
                         ii v   -       - i  i iv     v  i- ? v          --
  L1M4_orf2#LINE/    467 CACCATATACAAAAA-TTAACTCAAAATGGATC-AWAGACCTAAATGTAA 514

  chrX_115443888_    783 GAACAAAAA--ATAAAACATTTAGACAAAAACATAGGAGAATATCTTTAT 830
                           i v    --       vi     vi          ? v v     ii 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_115443888_    831 GAC--TGGAGCATGTCAATAGCTTTCTAAGACAAGA-ACCCAAAGTTAAA 877
                            --   ivi v -    i -     v   i v  -   v    ivv  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGG-CAATGG-TTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_115443888_    878 GTAATAAA-GAAAAAGTTCA-AAATTTGAGTATGTAATAATTTAAAG-TA 924
                          i  i   -      i vv -     v  v vii v v    v   i- v
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_115443888_    925 TCG-GCATGATAAAAAATTTT----AAATTCGAAGATACAAC-------- 961
                          i -  v v v ii v i v ----   v -   i v     --------
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGT-GAAAAGACAACCCACAGAA 711

  chrX_115443888_    962 TGGGAGAAGATATTTACAACACCTATGAGCCAAAAACAAATTGGTGATGA 1011
                                 i      i   vv v   - v ii v  vii i v  -  vv
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGGGACTTGT-ATCC 759

  chrX_115443888_   1012 AGAAAACATAAATAACTC--ACATATTCATTTTTTAAAAACCAA----CT 1055
                             v i     v     --   - i   v vv v    iv   ---- i
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACA-ACTCAATAATAAAAAGACAAATAACC 808

  chrX_115443888_   1056 CAA----AAAACAGGGAAGGGATGTGGACAAGCAATTC-ACAGAGAAGGA 1100
                            ----    ii  v  i    v  i i ii  v   -v  i     iv
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_115443888_   1101 ATATGAATGATCAATAAACATATGAAAAGATGATCAAACTTAGTCAGAAA 1150
                            ii    ii      i  i           v    vv i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (105 / 76)
Gap_init rate = 0.06 (38 / 677), avg. gap size = 1.95 (74 / 38)  


1441 28.52 3.19 4.69  chrX_115452667_115455767.rev     1386  1918 (1183)    L1M4_orf2#LINE/L1        1   525 (383)  

  chrX_115452667_   1386 TAGAAAAGTATTTCATGCTCATTGATAGGAAGAATCATTATTGTTATAAT 1435
                          i    ii   ii    i    v   v      v i v        vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115452667_   1436 AGCCATACTGCTCAAAGCAAGTTACACATTCAATGCTATTTCTATGAAAG 1485
                         i  v     v i    vii vi    v      i  v  ii    v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115452667_   1486 TACTAATGACATTCCTCACCAAATTAGAAAATACT-ATTTTAAAATTCAT 1534
                          v i iivi v  ii ii vi  v v  v  -i  -  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_115452667_   1535 AAGGAGCCAAACAAAAG--CCTGAATAGCCAAAGCAATCCTAAGCAAAAA 1582
                          v   i-- vi   ii --  v           i     i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_115452667_   1583 TAAATAAATAAATAAATAAATCAAAGCTGGATGCATCACATTACCTCACT 1632
                         v  ------------------     i    v vv     i v  iv i 
  L1M4_orf2#LINE/    198 GAA------------------CAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_115452667_   1633 TCAAACTATACCAAAAGGCTATAATAACTCAAACAGCATGGTACTGGTAC 1682
                              viv   i v  i    i i   iiv i    ii         i i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_115452667_   1683 AAAAAGATACACATTGACCAATGGA----------GCTCCCAGAAATAAA 1722
                           ii v v   i  v  i       ---------- vvi           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_115452667_   1723 GCCGTACACAGACAACCACCTGATCTTTGACAAAGTTGGCAAAAACAAGC 1772
                         v  i    ivv iiii  vi    i  i     i v  v   i v  vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_115452667_   1773 AATGGAAAAA----AGTCTCTCTATTCAATAAATGGTAGTGGGGTGACAG 1818
                              ii   ----     i ----    i       iv    iii  v 
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTT----TCAACAAATGGTGCTGGGACAACTG 425

  chrX_115452667_   1819 GTTAGTCATATGCAGAAGAATGAAACTAGATACCTTCTTTACACCATCTA 1868
                          v  ?i  i     i         ii i  iv   v i i       v  
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_115452667_   1869 CAACAATCAACTCAAGATGGAGTAAAGATTTAAATTTAAAACCTAAAACT 1918
                            v   i       i     vi ?   ii     v   i v        
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

Transitions / transversions = 1.63 (93 / 57)
Gap_init rate = 0.02 (8 / 525), avg. gap size = 5.25 (42 / 8)  

 698 27.36 6.97 2.49  chrX_115452667_115455767.rev     2211  2612 (489)    L1M4_orf2#LINE/L1      489   908 (0)  

  chrX_115452667_   2211 AAAATAAAT---AAA--TAAATGTAAAA--TAAAA---TAAAAC-CT--- 2246
                              ii  --- i --         i --     ---      -  ---
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_115452667_   2247 ---AAAACTATAAAAAAAAA-ATTCTAGACCTAGGCCTTGGCAAGTATTT 2292
                         ---     -   ii?iv   -v   vv     v  vi v     vvi   
  L1M4_orf2#LINE/    539 AAGAAAAC-ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_115452667_   2293 CATGACAAAGATGACA---AAAGCAATTGCAA-CAACAACA-AAAAAATT 2337
                          v --- i v      ---      ----   -      v -       v
  L1M4_orf2#LINE/    588 CTT---AGATATGACACCAAAAGCA----CAAGCAACAAAAGAAAAAATA 630

  chrX_115452667_   2338 GGCAAATGGGACCTAATTAACCTAAAGAGCTTCTACACAGCAAAAGAAAA 2387
                          ii    v    i v  i  vv v  i i   i iii vv    i  v v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_115452667_   2388 TACCAACAGAATAAACAGACAACTTACAGA-TGGGAGAAAATATTTGCAA 2436
                           i   v i i i  v       ii     -                   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_115452667_   2437 ACTGCGCATCCAACAAATGCCTAATATCCACAATCTATAAGGAACTTAAA 2486
                          iiiiii   ii i  iv v  vi      v   v     i     ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_115452667_   2487 TAAATTAGCAAGCAAAAAACAA----TCCCATTAGAAACTGGGCAAAGGA 2532
                         i  v i ii  vv    i    ----i  v   ?i   v           
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_115452667_   2533 CAGGAACAGACAGTTTTAAAAGGAAGATACACTGGCAGCCAACAAGCTTA 2582
                         ivv   i     v  i vv  i       i  viiii     i    vi 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_115452667_   2583 CGAAAAAAAATGTTTACCATTTCTAATCAT 2612
                         i     i --  i i v   iv????????
  L1M4_orf2#LINE/    881 TGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (63 / 45)
Gap_init rate = 0.04 (16 / 420), avg. gap size = 2.38 (38 / 16)  


3315 26.35 0.66 0.55  chrX_115457899_115461166.rev     1871  2777 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115457899_   1871 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1920
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115457899_   1921 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1970
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115457899_   1971 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2018
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_115457899_   2019 TATGGAACCAAAAAAGAGCCTGCATAGCCAAGTCAATCCTAAGCCAAAAG 2068
                                viiv  ii  v  v v        iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_115457899_   2069 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2118
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_115457899_   2119 TACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGATC 2168
                                 i   i    ii    i    i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_115457899_   2169 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 2216
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_115457899_   2217 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 2266
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_115457899_   2267 CTATTTAATAA-TGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2315
                           v  i  i  -           v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_115457899_   2316 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 2365
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_115457899_   2366 TTAAAGACTTAAAGGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2415
                          i ?    i    v  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_115457899_   2416 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 2464
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_115457899_   2465 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTC 2514
                         vi            vvi           v     v  i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_115457899_   2515 ATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAA 2564
                           i   v v  i i   i   i vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_115457899_   2565 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 2614
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_115457899_   2615 GAGAGCTAATATTCAGAATCGGTAATGAACTCAAACAAATTTACAAGAAA 2664
                         ii ii  vi   i      vvi   v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_115457899_   2665 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 2714
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_115457899_   2715 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTGAT 2764
                            v        i  vi viii     v  i          i     v v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_115457899_   2765 CATCACTGGCCAT 2777
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2485 27.96 1.51 3.87  chrX_115483834_115489582.rev     4329  5258 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115483834_   4329 TGTAAAAACATTCCATACTCATGGATAGGAAAAATCAATGTCTTCAAAAT 4378
                           v   i i  i    ii        v    i v i   i iv i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115483834_   4379 GGCCATACTGCTTAGAGTAATTTACAGATTCAATGATATTCCCATTAAAC 4428
                            v     v ii i v i  i           i vv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115483834_   4429 TACCA-TTGACATTCTT-CAGTGAATTAGGAAAAAAAAAACTC-TTTTAA 4475
                          v   -i  v v  i  -   -i    i------- v  i  v- ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG-AAATTG-------ACAAGCTGATCCTAA 142

  chrX_115483834_   4476 ATTTCATATGGAACCAAAAAAGAGCCCGAATAGCCAAGACAATCCTAAGC 4525
                          v           viiv  ii  v  v          i      i i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_115483834_   4526 AAAAAGAACAAAGCTGGAGGCATCATGCTATCCAACTTCAAACTATACTA 4575
                           i          i      vv   ii  vi    i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_115483834_   4576 CAAGGCTACAGCAACCAAAACAGCATAGTACTGGTACAAGAACAGACACA 4625
                            i       i  i   i    ii i       i i   i i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_115483834_   4626 TAGAATGATGAAACAGAATAGAGATATCAGAAATAAGACCACACACCTGT 4675
                             vii   i  i     v    vvi         iv   i   ii i 
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_115483834_   4676 AACCACCTGATCTTCAACAAACCTTACAAAAACAAGCAATGGGGAAAGGA 4725
                         iii  vi    i   i    ivv vv   i v  vv            i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_115483834_   4726 AAGGATTCCCTATTTAAAAAATGGTGGTGGGAGAAATGAGTAGCCCAATG 4775
                         v  -----i  v  i  v        v     v  v  ii  ?  vv   
  L1M4_orf2#LINE/    393 TAG-----TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_115483834_   4776 CAGAAAATTGAAACTGGACCACTTCCTTACACCTTATACAAAAATTACCT 4825
                           i  i v    ii      v  v   i     v             v  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_115483834_   4826 CAAAATGGATTAAAGACTTATATGTACAAACCTAAACTATAAAAAACCCT 4875
                                   i ?    i  v     vi i iv           v-i i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTT 536

  chrX_115483834_   4876 AGAAGAAAATCTAGGCAATACCTTTCAGGACACATGCATAGGCATAGGAC 4925
                                  iv    ?ivv vii   iv   ------------------ 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGAC------------------C 568

  chrX_115483834_   4926 ATAGGCATAAGCAAAGATTTCAT-GATGAAAATGCCAAAAGCAATTTCAA 4974
                         v i  i-  i    v i    v -   - vi ii         vvvv   
  L1M4_orf2#LINE/    569 TTGGGT-TAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAA 616

  chrX_115483834_   4975 CAAAAGCAAAACTTGACAAATGGGATCTAATTAAGGTGAAGAGCTTCTAC 5024
                               v    v v  i    v   ii v  i  ii v  i i   i ii
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_115483834_   5025 ACAGAAAAAGGAACTACCATCAGTGTGAGCAAACAACCTACAGAATGAAA 5074
                         i vvv   i iv    i  vv iv    iv i      i        ii 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_115483834_   5075 GAAAATTGTTGTAATCTATCTGTCTGACGAAGGTCTGATATACAGAGTCT 5124
                               vv   i  vii  v i     ii i  v  vi   v    i v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_115483834_   5125 ACAAAAAACTTAAACAAATT-----TCCAAGAACAA----CCTCATTAAA 5165
                          i   i    ivv    v i----- vv  ii    ----  iv   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_115483834_   5166 AAGTAAACAAAGGACATTAACAGACACTTCTC-AAAAAAAATAAATACAT 5214
                           i iii       iv v  i     i     -   i  i   --    v
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA--TACAA 864

  chrX_115483834_   5215 GTAGCCAAGAAACATATGAGAAAAAGCTCAAAATCATTGATCAT 5258
                         i i     v  i  i    i  i v      v    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (153 / 103)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.33 (50 / 15)  


3249 24.62 1.09 1.75  chrX_115527633_115530069     1031  1944 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115527633_   1031 TGAAAAGACATGTCATGTTCATGTATAGGATGAATTAATATTATTAAAAT 1080
                           i     i  vi          v  v   v  v        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115527633_   1081 GTCCATACTACTCAAAATAATCTACGGATTTAATTCAATCCTTATCAAAA 1130
                          v v     v i    v i      i    i  iv      i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115527633_   1131 TTCCAATGACATTGTTCACAGAAATAGAAAATAAAATTCTGAAATTCATA 1180
                          i   iivi v  v  ii       v  v  vvvi  i  i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115527633_   1181 TGAAATTACAAAAGACTCCTTAATTGCCAAAGTGATCTTAAGAAAGAGGA 1230
                           i  v i   ii   -  vv   v      iii     i i     i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_115527633_   1231 ACAAAGTAAGGGAAATCACACTTCTTGAATGTAAAATATATTACATAGTT 1280
                                vi i i v         iii v vi    iv  i    v  i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_115527633_   1281 AGAGTAATTAAAACCG-GTGATAATGACATAGAGACAGGCATGTAGATGA 1329
                          v      i  i  v -   i  v  i    ii  i  i   i     v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_115527633_   1330 ATGAAACAGAATAGAGAGCCCAGAAATATATCTGTACATGTATTGTCAAT 1379
                            i  i     v     i         v i ii     v   v      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_115527633_   1380 TGATCTTTGATAAGGGTGGGAAGAGTACACAATGGGGAAAGTTTAGTCTC 1429
                             i  i  i       vv    vi iv            vv      i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_115527633_   1430 TTAAACACATGGTGCTGGGAAAACTGGATATCCACATATAAAAATGAATT 1479
                           v    v            v         ?      ii    --    v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA--GAATG 447

  chrX_115527633_   1480 AAATTGGACTTTTATCATACACTCTACACAAAAATAAACTCAGAATAGAT 1529
                           i      iii  i vi    iv  i        v      i   i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_115527633_   1530 TAAAGAG--AAATGTAACACTTGAAACTCTTATGCTCCTAGAAGAAAACA 1577
                         i ?   v--        v vi i     v v vi   i            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_115527633_   1578 TAGGGAAAAAAGTTTATTGACGTTTGTCCAGGCAATGATTTCATGGATAT 1627
                             ?iv   vv  ii -   v  v vii        i    v i     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_115527633_   1628 GACACCAAA-GTACAGGCATCAAAGACAAAAATA---AAATGGGACTAT- 1672
                                  - i   i   v    iiv       ---    v     vi-
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_115527633_   1673 TTAAAACTAAAATCTTTTGCACAGAAAAGGTAACAATCAGTGGACTGTAA 1722
                          i    i     v      ii vvv     vv  v    ivii v  v  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_115527633_   1723 AGGCAACATGTAGAATTGCAGAAAAACAATCCCAAACCATATACCAAATG 1772
                           i    viii     v v      -i v iv    i      i vi  i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATA 745

  chrX_115527633_   1773 AGAAATTAATATC-AAAATATATAAGAAACTCCTACAACTCAATAGCAAG 1821
                           ii i vi    - i         ii     i            -----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA----- 790

  chrX_115527633_   1822 AATAAATAAATCAATACATAACTCAACTTGAAAGTGGGCAAAGGTCTTGA 1871
                         -     v i -   ---     i   i ?i   i          vi    
  L1M4_orf2#LINE/    791 -ATAAAAAGA-CAA---ATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_115527633_   1872 ATAGATATTTCTTCCAAGAAAAACA-ACAAATGGGCAATAGGTATATGTT 1920
                              i      -    ii  i i -        v     i i i   vv
  L1M4_orf2#LINE/    836 ATAGACATTTCT-CCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_115527633_   1921 GATATGCTCTACACCACTAAAGTT 1944
                         i v      v   i  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (131 / 90)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.73 (26 / 15)  


2708 27.95 1.34 0.22  chrX_115565063_115569652.rev     3202  4099 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115565063_   3202 TGGAAACACATCTCATGCTCATGAATGGGTAGAATCAATATTGTGAAAAA 3251
                               v i   i    i     i  v  v   v i        v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115565063_   3252 GACCATACTGCCATAAGAAACTTACAAATTCAATGCAATTCCCATCAAAA 3301
                          i v     v  vv  vvi ii    i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115565063_   3302 TACCA--T-CATTCTTCACAGAACTAGAAAACACAATCCTAAAATTCATA 3348
                          v   -- - v  i  ii     v v  v  vvii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115565063_   3349 TAGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGTAA-AAGAG 3397
                          i   viiv  ii  v  viv         i   vvi i iv  -    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115565063_   3398 CAAATCTGTAGACAC-CATATTACCCAACTTCAAACTATACTATAAGGCC 3446
                             vi  v  i-  -  i i v     i      viv     i  i  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_115565063_   3447 ATAGTAACAAACATAGCATGGTACTGGTATAAAGATAGGCATATAGACCA 3496
                          i     iv  v i  ii         i    i     i        i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_115565063_   3497 ATAGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACATCCAAC 3546
                           i   i     v    ii           v   v i i   iivi   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_115565063_   3547 TGATCTTTAACAAAGCAAATAAAAACATAAAGTGGGGTAATGACACCCTA 3596
                             i  ii    i vvivi  i v   vv i     v  vi i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_115565063_   3597 TTAAACAAATAGTCCTGGTATAATTGGCAAGCCACATGTAGAAGAATGAA 3646
                           v       i  v    v i  i   vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_115565063_   3647 ACTGGATCCTAATCTCTCACCTTATACAAAAATCAACTCCAGTTGGATCA 3696
                         ii    i  iv i   v    v           i     v iv       
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_115565063_   3697 AAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACATG 3746
                         ?    i     v     v  i    i      v ii       v     i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_115565063_   3747 GGAA-AAACCCT-GTAGACATTGGCTTAGGCAAAGACTTCATGACCAAGA 3794
                           ?i-   i i -  -   v    v        v ii   v iivi v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_115565063_   3795 AACCAAAAGCAAATGTGCCATAAACAATGATAAATAGATGGGACTTAATT 3844
                         v          v v iiv  v  iv  vi   i   i  v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_115565063_   3845 AAACTAAAAAGTTTCTCCACAGCAAAAGAAA-TAT-AGCAGATTTAACAG 3892
                            v v    ii  i vii vv    i  v -   - iv i v v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_115565063_   3893 ACAACTCACAGAATGGGAGAAAGTCTTCACAATCTATAGATACAACAAAA 3942
                              i                i v  ii   vii   v  vii i  ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_115565063_   3943 CACTAATATCTAGAATCTGCAAGGAACTCAAACAAATCAGCAAGAAAAAA 3992
                         v   vi    i     v ii  i      vv    v   ii  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_115565063_   3993 TCAAGCAATCCCATCAAAAAGTTGGCTAAGGACATGAATAGATCATTCTC 4042
                         v   ii  i  v  i?    i v   v     iv        ivv     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_115565063_   4043 AAAAGAAGATATACAAATA-TCAACAA--ACATGAAGAAATGCTCAACAT 4089
                         v                 i-i   i  --       i i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_115565063_   4090 CACTAATAAT 4099
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.33 (141 / 106)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.17 (14 / 12)  


 442 27.93 4.90 11.74  chrX_115589798_115591456.rev      489  1161 (498)    L1M4_orf2#LINE/L1      231   857 (51)  

  chrX_115589798_    489 CAATATTTA-TATA---CTGTACTAATTAAAATAGTGAGTTGTTAGCATA 534
                            v i   -  i ---  ii v    i  i i    v v ii i     
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_115589798_    535 GGTATAGGTATATAGGCCAATGGAACAGGATAGTAATCTCAGAAATAGAT 584
                         i v    ii      ii        i  i  v vi vii        i i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_115589798_    585 TAAAAAACAAATGG--AACTTGGCATGTGGCAGAGGTGGCAATGCAGATC 632
                         iv v v ivv    --  -   iiv vi i  ii    v   vi viv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAA-TTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_115589798_    633 AATAGGGAAAGGGATAATCATCCAATTGATAGAGTTGATATCTAATTGAT 682
                            i       i----------------    --------   ------ 
  L1M4_orf2#LINE/    380 AATGGGGAAAGA----------------ATAG--------TCT------T 399

  chrX_115589798_    683 TTAATTGATAATATCAATTATCCTTGAACAATTG-ATATCC-TATTTAGG 730
                           ------i  i --   vi v  v i    i  -   ?  -i  vi ii
  L1M4_orf2#LINE/    400 TT------CAACA--AATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_115589798_    731 AAACACCATCAGTTGGAAATTTCACATATCATTCACATATCACATAAATT 780
                          i - iv --       ---ii vi iv   iv -     -   v     
  L1M4_orf2#LINE/    442 AGA-ATGA--AGTTGGA---CCCCTACCTCACAC-CATAT-ACAAAAATT 483

  chrX_115589798_    781 GATATGCACAATGTCAATATTAGGTGAATTGAAAATTTGACAATATAGG- 829
                         i i----------    v  ----- i  ii? i ii i --  i  i -
  L1M4_orf2#LINE/    484 AAC----------TCAAAAT-----GGATCAWAGACCTAA--ATGTAAGA 516

  chrX_115589798_    830 -CAAAAACTTGAATTCTTTTAGAAGAACATATAGAA-TAGTACCTTTATA 877
                         - v      vv  vv  i         v i    i?-  i- i   ii i
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGTG 565

  chrX_115589798_    878 ACCTTGGGCTAAGCA---GTTT-TTAAAAGTAACAGAGATCAAGGGCA-A 922
                                 i  i   ---    -   i vi i   ----i   ii   - 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA----CCAAAAGCACA 611

  chrX_115589798_    923 TACA-TATAATCAAAGATGGATACCTTCATTTTCAGTAAACCCACAACAA 971
                         vi  -i v  vv   i  i    vv  vivi    vi   vii -  -  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA-AA-AA 659

  chrX_115589798_    972 CTGTGGTTAATCAAAGGATACAATGTTAA-AAGGTAAAAAAAATAAGCCA 1020
                           v v  vvv        i  -- i i  -  i  i    i -i  v   
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACAC--TATCAAGAAAGTGAAAAGA-CAACCCA 706

  chrX_115589798_   1021 CAAATTGGGAGGCAAAAAAT---CAA--CATATATAATAGACAAAGAATT 1065
                           i v      --    v  ---   --       --iv  i  i i i 
  L1M4_orf2#LINE/    707 CAGAATGGGAG--AAAATATTTGCAAATCATATAT--CTGATAAGGGACT 752

  chrX_115589798_   1066 AGAATCCAAAAGACATCAATAATTATTAGAAACCAAGTAACACAG-GCCA 1114
                         v v     i  v i  v  v  i v   v  vi   -   i v i- v  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAA-TAATAAAAAGACA 801

  chrX_115589798_   1115 AA----CCAA-----AAACTGGCAAAAGACATAAACAAGAATTTCACAGA 1155
                           ----    -----   iv      i  iv i  i iiv     v vi 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_115589798_   1156 AAAAAA 1161
                          i  i 
  L1M4_orf2#LINE/    852 AGAAGA 857

Transitions / transversions = 1.64 (115 / 70)
Gap_init rate = 0.06 (40 / 627), avg. gap size = 2.80 (112 / 40)  


2087 22.84 2.33 14.58  chrX_115613326_115617422.rev       85  1113 (2984)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_115613326_     85 AGATATTTTATGTTCATAGATAGAAAGAGTCAATATTGTCAAAATGTCAG 134
                               iii        i   v i    v i        i  i   v  i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_115613326_    135 TTCTTCTCAGATTGAT----AGTTTCAGAGAAATCCCGACAAAAATCTCA 180
                          v  i i  i      ----  v    iv v      v iv      i  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_115613326_    181 G--AACATGAATTTGTGGACATCAATAAATTGATTATTAAGTTTGTATGA 228
                          --iv v v--    ii  v  ii i  ii    iv v  i  ii    i
  L1M4_orf2#LINE/    106 GCTGCCTTT--TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_115613326_    229 GGAGGTAAAAGACATAGAATAGACAACAGTATTATTGAATGAAAATCACA 278
                         ii v i  ii   vi       v   - ii v v     vi i  vv   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAA-AACAATCTTGAAAAAGAAGAACA 202

  chrX_115613326_    279 ATGTTGGAGGACTGACGCTACCCTTCTTCAAAACTTACTATACAGTTACA 328
                          v           v  i  v   vvi              i v  i    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_115613326_    329 GTAATCAAGACAGTGTGATATTGGCAAGAAGAGTAGACAGATAAGTCTGG 378
                                          i  i     ------------------------
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCA------------------------ 278

  chrX_115613326_    379 CACTGTCATGGCAGTGCATGTCTGTAGTGCCAGTTATTTCAGAAGCTCAG 428
                         --------------------------------------------------
  L1M4_orf2#LINE/    279 -------------------------------------------------- 278

  chrX_115613326_    429 TGGGGAGTATTTCTTGAGCCCAGAAGTTTAAGTCCAGCCTAGGCAACATA 478
                         ----------------------------    ------------------
  L1M4_orf2#LINE/    279 ----------------------------TAAG------------------ 282

  chrX_115613326_    479 GCAAGATCTCATCTCAATAACATGGATAGACAAATAGATAAATGAAACAG 528
                         ------------------------        v      v    i  i  
  L1M4_orf2#LINE/    283 ------------------------GATAGACATATAGATCAATGGAATAG 308

  chrX_115613326_    529 AATACAGAGACCAGAAACAGACCAAGATATATATAGTTGACTGATCTTTG 578
                            vv    v       i i   v v i  v   i  ii i    i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_115613326_    579 ACAAAGGAATAAGGTCGATAAAATGGAGCAAACATAGTCTTT-CAATTAA 627
                             i  viiv i v v  vv     i v  iv         -   iv  
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_115613326_    628 TGGTGCTGAAATAACTGGGCATCCATGTACACAA-AATAAATCCACAGAC 676
                                 ii i      ii ?   ii i  v  -   i  viiiv vv 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_115613326_    677 AGACCTTAAAACCTTCATAAAAATGAGCTCAGAATGAATCACAGATCTAA 726
                         vv    i v v v vi i      v i    i    i    ?   i    
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_115613326_    727 ATGTAAAACGGAAAAATATATAACTCATAGCAGA-----TAAGAGAAAAT 771
                               i vvv    v    v     v   v   -----  i ? v    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_115613326_    772 CTGGATGACCTTGGGTTTGGTGATGACAACTTAGATGCAACACCAAAGGC 821
                           vvi            v  ii   iivv       iii        i  
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_115613326_    822 ACAGTCCATGAAA---AAAGGGGATAAGGTGGATTTCATTCAAATTAAAA 868
                            iv v ii   ---   ivi     iv    i     iv         
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_115613326_    869 --TTTTCTCCTCTATGAAAGACACAGTCAGGGCAATAAAAAGATAAGCCA 916
                         --    v v  ii --  i     vi   i iv i i      i  v   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCA--AAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_115613326_    917 AAGA-TAGGAGAAA-TATTTTCAAA-CAT-TATCTGATAATGGACTGCTA 962
                         v   - i       -     v    -   -          v     vv  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_115613326_    963 TCTAAAATACACTAAGAACTATTAAAACTCAATAATAAGAAAACAAAAAG 1012
                           i i    i iv       v   v             i  i     v i
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_115613326_   1013 CCTAATTTTTAAATGAGACAAAAACCTTAACT-GACACCTCACCAAAGAA 1061
                           i    ?vv     i -    iivi  i v -    ii  v        
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGG-CAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_115613326_   1062 -ATATACAGATGGCAAAGAGGCATACAAAAATATGCCCAGAATCAGATAT 1110
                         -       i     v  v i   i ii    v    i  iv    ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_115613326_   1111 CAC 1113
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.33 (132 / 99)
Gap_init rate = 0.02 (19 / 903), avg. gap size = 9.16 (174 / 19)  

3585 22.64 2.93 0.68  chrX_115613326_115617422.rev     2735  3622 (475)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115613326_   2735 TAAAAATATATACTGTAATATTGGAGTGAAAGGCTTAATAATCTCAAAAT 2784
                          ii   v    v ii iv vv    v  i   i       v v i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115613326_   2785 GTCAATATTACCCAAAGGGATCTACAGAGTCAATGCAAACCCTATGGAAA 2834
                          v     i v      vv          v    i    v      vi   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115613326_   2835 CATCCCAAAGACGTTTTTTGCAGAAA--AATCAAAATCCATCCTAAAATG 2882
                         --     ivvi v             --i i--  iiiv          v
  L1M4_orf2#LINE/    101 --TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATT 146

  chrX_115613326_   2883 TATTTGGAAACACAAGAGAAATCAAGTTGCCAAAACTATCCTGAGAAATA 2932
                         i  v      ii    i  vvivi i v        v   i   i   v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_115613326_   2933 AGAATAAAGTTAGAGGACTCACATTTGTTGATTTCAAAACTTACCA-AAC 2981
                             i      i           i  viii              i -  v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_115613326_   2982 ACTATGGTAGTCAAAACAATTTGCTACTAACATAAAGACACACATGAAG- 3030
                         i   ii   i    i   i v  v    ii     i  i v    iv  -
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_115613326_   3031 -TAATGAAACAGAACAGAGA-TCACAGAAATAAACCCTTGAATACGTGGT 3078
                         -i    i  i    iv    -  -             v iv  vii    
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chrX_115613326_   3079 CAATTGATTTTCATCAAGGGTGCCCAGACTATTCAATGAGGAATAATTAG 3128
                                     iv          v    i        i    vi v   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_115613326_   3129 TCTTTTCCATAAATGGTGCTGGGAAAACTGGATCTCCACAGGCCAAATAA 3178
                                v i              v        v?     v  v   v  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_115613326_   3179 TAAAGTTGGACC---ATTT-ACACTATGTACAAAAATTAACTCAAAAGTG 3224
                          i          --- ii -    i  i                   vv 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_115613326_   3225 ATCAAGAAACTAAACTTAAGGGGTAAGACTAAAATATTCTTAGGGGAAA- 3273
                             ?ii v     iv    i v   i    v  v i      ii    -
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_115613326_   3274 CATTTAAGAAAAGCTTCATGATTTTAGATTTGGCGGTGATTTCCTGGATA 3323
                            vvi? v   v    i   ii  i i  v   ii  i    i i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_115613326_   3324 TGACAACAAAATTACAGATGACAAAAGAAAAAGTAGGTAAAGTGGACTTC 3373
                              v     vi   iiii            i   i    v        
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_115613326_   3374 ATTTAAATTATAAGCTTTTGTGCATTAAGGGACACTATTAAAAGAGTGAA 3423
                           iv      v  i         v i  i         i  i i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_115613326_   3424 AAAGCAACACACAGGAACAAAGAAAATACTTACAAGTCATATATCTAATA 3473
                           ii    v     i vvii        i  i   i          i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_115613326_   3474 AGAGATTGGTATCCAGAATATATAAAGAACTTCTACAACTCAACAACAGA 3523
                           i  i v                       ii          i  i i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_115613326_   3524 AA-ACAAACTAACA-AATTAAAAACCGGGCAGAGGACTTCAGTAGAGGTT 3571
                           -     -    v-    ?    vi     i    i  v i    vi  
  L1M4_orf2#LINE/    796 AAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_115613326_   3572 TCTTCAAAGAAGATATA-------------AGCACATGACATGACACTGA 3608
                            i             -------------         v v  ii  v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_115613326_   3609 ACATCCATCACTAA 3622
                              v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (120 / 77)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.29 (32 / 14)  


3115 25.88 3.16 0.56  chrX_115618220_115622470.rev     2876  3760 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115618220_   2876 TGGAAA----TTCTTTGTTCATAGATTGGAAGAATCAATATTGTTAAAAT 2921
                               ---- i iv       i          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115618220_   2922 GTCCATACCACCCAAAGCAATATACATATTCAATGTAATCCTTATCTAAA 2971
                          v v    iv      vii  v    v      i i     i    v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115618220_   2972 TACCAA-TGTCATTCTTCACAGAAATGGAAAGAAAACAG-TCCTGAAATT 3019
                          v   i-  i -  i  ii       v  v --- i v -    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACA---AGCTGATCCTAAAATT 146

  chrX_115618220_   3020 TATGTAGAACCACAAGAGATTCAGAATTGCCAAAGCTATTCTAAACAACA 3069
                         i  i i   vii    i  ii      v      i v  ii i  v  v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_115618220_   3070 ACAACAAAAACTAGAGGAATTGCATTACCTCACTTTAAATTATACTACAG 3119
                          v      i-i i     v ii  i v  iv i  i   viv       i
  L1M4_orf2#LINE/    197 AGAACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_115618220_   3120 AGCTATAGTAACCAAAACAGCATGTTACTGGCATAAAAACAGACACA--G 3167
                              i     i   i    ii  v           ii i     i -- 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_115618220_   3168 ACCAATGAAACAGAACAGAGAAGCT-GAAAGAAATCCACACAGCTACAGT 3216
                          i     i  i    iv    iv i-    v   i   i   vi  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_115618220_   3217 TAACCTATTTTTGAGAAAGATGCTAAAAACATATACTGAGGAAAGGACAG 3266
                         i  iiv     i  v  i i   i  i v   vi v  i      i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_115618220_   3267 TCTTTTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGGAGAA 3316
                                  i              v         ?   i     ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_115618220_   3317 GAAAACTAGACCCTTATCTCTCATCAGATACAAAAATCAAGTCAAAATGG 3366
                         vi  ii i     i  i   v  i  v          i  v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_115618220_   3367 ATTAAAGACTTAAATCTAAGACCTCACACTATGAAGCTACTACAA---AA 3413
                           i ?    i     v     v  v v     i  i  vi  v  ---  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_115618220_   3414 TTT-GGGGAAAGCCTCCAGGACATTGTTCTAGGCAAAAGTTTATTG---- 3458
                         iv -  ? v  ii  i iv   v   vvi       vi    v  i----
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_115618220_   3459 ----------AGCACAGAAAACAGAAGTAGACCTGAACAAATGGAATCAC 3498
                         ----------      iiv    i   v i vv ii i    v i iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_115618220_   3499 ATCAAGCTAAACAGCTTGTGTAAAGCAAAGGAAACAATCAACAAAGTGAA 3548
                              iv v  v i   v   ivvv       v  v     v        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_115618220_   3549 GAGTCAACCCACAGAAAGGAAGAAAATATTTCTGAACTATCTATCTGACA 3598
                         i  v            v  i           vii  ii  v       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_115618220_   3599 AGGGATTAACAACCAAAACATATAAAGATCTCAAACAACTTTATAGGAAT 3648
                              i vii v   i  i         v   vv      iv   iv  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_115618220_   3649 AAATCCAATAATACAATAAAAAAA-GAGCAGAGGATTTGAATAGGCATTT 3697
                           iv v     iv    v?     - i   i             i     
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_115618220_   3698 CTCAGAAGAAGACATACAAATGGTAAATAGGCATATGGAAAGGAGCTCAA 3747
                            vi       i          iv    i   i   i    iv      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_115618220_   3748 CATCATTGATCAT 3760
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (137 / 88)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.75 (33 / 12)  


2020 27.87 2.55 5.96  chrX_115623846_115629587.rev     4340  5279 (463)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115623846_   4340 TGGAAAAGGATTTCATGCTCGTGGAGAAAAAGAACCAATATCATCAAAAT 4389
                               iiv  ii    i  i    vvii    vii     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115623846_   4390 GGCCATACTTCCCAAAGCAAATTATAGATTCAATGTTATTCCTATTGAAC 4439
                            v     i      vii vi  i        i iv  i     ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115623846_   4440 TACTATTGAGATTCTTCAAAGAACTAGAAAGAAAACT-ATTTTAAAATTC 4488
                          v i vivivv  i  iiv    v v  v --- i  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA---AGCTGATCCTAAAATTC 147

  chrX_115623846_   4489 ATATGGAA---CAAAAAAAGTCC-GAATAGCCAAGGCAATTATAAACAAA 4534
                                 ---   iii --i  -          ii    iv i  ----
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAA---- 191

  chrX_115623846_   4535 TGAAACAAAGCCAAGGCAATTATAAGCAAATGAAACAAAGCTGGAGACGT 4584
                         ------    -------------   -------       i     ivv 
  L1M4_orf2#LINE/    192 ------AAAG-------------AAG-------AACAAAGTTGGAGGACT 215

  chrX_115623846_   4585 GATGCTACCAGACTTCATA--CTACGATACAGTGCTACATTAACTAAAAC 4632
                         v ii  v  vi i    v --i   --    iv      v   ii  i  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTAC--TACAAAGCTACAGTAATCAAGAC 263

  chrX_115623846_   4633 AGCATAGTACTGACACAAGAAGAGACACATAGACTAATAAAACAGAATAG 4682
                           ii i      i  i   i v     i     ii   ii  i     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_115623846_   4683 AGATTCCAGAAATAAGGCTGCATACTTACAACTATCTGATTTT-GACAAA 4731
                            v           iv iii i i   iiiii vi       -     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_115623846_   4732 CCTTACA-GAAAATAAAAAAGCGATGGAGTAAGGATTTCCTATTCAATTT 4780
                         vv vv  -  vv  ------v i    i v   i  vvi  v     ivv
  L1M4_orf2#LINE/    364 GGTGCCAAGACCAT------TCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_115623846_   4781 ATGGTGCTGGGATCACCGGCTAGCCATAAGCAGAAGATTGAAACTGGAAT 4830
                                     iv  i  v  ?   i v   i    v    ii    vi
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_115623846_   4831 CCTTCCTTATATCATATACAAAAATCAACTCAAGATGGATTAAAGACTTA 4880
                            v   i i i             i       i      i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_115623846_   4881 AATGTCATACCAAAAACTATAGACACCCTAAGA-GACAACCTAGGCA-AA 4928
                              v v v v         i -  i  v   -  v   v    ?i-  
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_115623846_   4929 ACCACTCAGGACATAGGCATGGGCAAATATTTAACAATGGAGATG---CC 4975
                          i -i  iv   v v  vv i     vvi   -- v- i  v   ---  
  L1M4_orf2#LINE/    557 ATC-TTCGTGACCTTGGGTTAGGCAATGGTTT--CT-TAGATATGACACC 602

  chrX_115623846_   4976 AAAAGCAATTGCAAAAAAAGCAAAAAAAAAAAATTGACAAATGGGATCTA 5025
                                ----   iv  --     i      - v  i    v   ii v
  L1M4_orf2#LINE/    603 AAAAGCA----CAAGCAA--CAAAAGAAAAAA-TAGATAAATTGGACTTC 645

  chrX_115623846_   5026 ATTAGACT--AGAGCTTCTGCATGGCAGAAGAAACTGTCAACAGAGTAAA 5073
                           i i v -- i i   i  iiivv  i i  v   i    v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_115623846_   5074 CAGACAACCTACAGAATGGGAGACATT-TTTGCAAACTATGCATTCAACA 5122
                         v        i             v v -        ii  ii  iii i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_115623846_   5123 TAGGTCTAAAGTCTAGCATCTATAAAGAATTTAAACAAATTTACAAGATA 5172
                         vi  v  vivi  i  v  v         i ivv    v iv i  v v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_115623846_   5173 AAAACAA----CCCCATTAAAAAGTGTGCAAAGTACAGGAACAGGAACTT 5218
                           i    ----   v   ?    i  v      v ivv   i  iv i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_115623846_   5219 TTCAAAAGAAGACATACATG-GGCCAGCAATTATAATTTAAAAATGA--A 5265
                         i  v        i     vi-     ii  vi i - vv   i   v-- 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACA-TGAAAAGATGCTCA 894

  chrX_115623846_   5266 ACATTACTGATTAT 5279
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (155 / 103)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.76 (80 / 29)  


3276 27.01 0.55 0.44  chrX_115630144_115634952     1645  2551 (2258)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115630144_   1645 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1694
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115630144_   1695 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCGAGC 1744
                            v     v     iv i  i  i        i  v     i   i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115630144_   1745 TACCAATGACTTTCTTCACAGAATTGAAAAAACT-ACTTTAAAGTTCATA 1793
                          v   iivi i  i  ii     v vi v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115630144_   1794 TGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAGAA 1843
                              viiv  ii  v  viv  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115630144_   1844 CAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 1893
                              i i    vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_115630144_   1894 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 1943
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_115630144_   1944 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACCAT 1991
                              i    i--    i  --        vv   i i  i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_115630144_   1992 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 2041
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_115630144_   2042 ATTTAATAAATGATGCTGGGAAAACTGGCTCGCCATATGTAGAAAGCTGA 2091
                         v  i  i     i        v      v v?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_115630144_   2092 AACTGGATCGCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATT 2141
                          ii    i v  v   i     v           i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_115630144_   2142 AAAGACTTAAATGTTAGACCTAAAACTATAAAAACCCTAGAAGAAAACCT 2191
                          ?    i       v   v              vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_115630144_   2192 AGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2239
                            ?-   --i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_115630144_   2240 AACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTAA 2289
                         i            vvi     i    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_115630144_   2290 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2339
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_115630144_   2340 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCACCTGACAA 2389
                           i     i   i             v       vii ivi i    i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_115630144_   2390 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2439
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_115630144_   2440 AAACAAATAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGATACTTC 2489
                          i           v  i?    i     i      v    i   i i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_115630144_   2490 TCAAAAGAAGACATTTATGCAGCCAAAAAACGCATGAAAAAATGCTCATC 2539
                           v        i  vi viii     v  i i        i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_115630144_   2540 ATCACGGCCATC 2551
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  

2004 26.59 3.34 5.60  chrX_115630144_115634952     3394  4322 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115630144_   3394 TGGAAAAACAT------TACATGGATAAGAAGAGTCAATATTCGTTTAC- 3436
                               i i  ------ v       vi     v i      -   v v-
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-GTTAAGA 49

  chrX_115630144_   3437 TGTCCATACTGCACAAAGCAATTTACAGGTTCAATGCTATTTCTATTAAA 3486
                           v v     v v    vii  i     i     i  v  ii    i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_115630144_   3487 TTTCCAACGACATTGTTCACAGAATTAAATATATATATATATTCGAAAAT 3536
                         v i   i vi v  v  ii     v vi i --- vv i-  i v     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACA---AGCTG-ATCCTAAAAT 145

  chrX_115630144_   3537 TTATGTGAAACCA-AAAAAAGCCTGAAAAACCAAAGCAATACTAAGAAAA 3585
                          i  i  i  vii-  iii v  v   v i     i    vi i i   i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_115630144_   3586 AAAAA---AGTCAGAGGCCTCACACTTCTTCTTGACTTTAAAATATATTA 3632
                           i  ---   ii    v          ii---i i  i    iv  i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCC---AATTTCAAAACTTACTA 242

  chrX_115630144_   3633 AAAGATGACAGTAACCAAAACAGCGTGGTACTGGTATAAA-ACAGACACA 3681
                         v  iiiv       i   i    i          i    i- i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_115630144_   3682 TAGACCACAGAAACACAAAAGAGAGCCCAGAAGTAAAGCCACACACCTAA 3731
                             i  vv i  i v  vv     i      i    v   i   ii  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_115630144_   3732 AACCATCTGATCTCTGATAAGATTGACAAAAACAAGCAAGAGGGAAAAGA 3781
                         iii  vi    i ii  i   iv  v   i v  vv   vi      ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_115630144_   3782 CTCCCTGTTCAACAAATTGTGCTGG--CA------TAGCCAAATGCAGAA 3823
                         ivvi  v          v       --  ------  ?   v     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_115630144_   3824 TATTGAAACTGGACACCTAATTTATACCATGTAAAAATAACAACTCAAAA 3873
                         v v    ii     v    vi i i     i  v   v vi         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_115630144_   3874 TGAATTACAGAACTAAATGTAAAACCTAAAACTATAAAAACCCCA-ATGA 3922
                           i  i ?   v          i v              vi ii - v  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_115630144_   3923 AAACCTAGG---AAATAC-CATGA---TGGACATAGGCCCTGG---CCAA 3962
                             v    ---    vi- i   ---   ii-     vv   --- iv 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTA 591

  chrX_115630144_   3963 GATTTAATAATGAAGATGTCAATCGCAATTGCAACAAAAGCAAACACTGA 4012
                            v i i vii  ------- v i   --          v   v iv  
  L1M4_orf2#LINE/    592 GATATGACACCAAA-------AGCACAA--GCAACAAAAGAAAAAATAGA 632

  chrX_115630144_   4013 CAAATGGAACTTAATTAAACTAAAAAGATTCTGCACTGCAAAAGAAACTA 4062
                         i    v i    v  i   v v    iv  i  ii  v    i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_115630144_   4063 TCAACACTGCAAAAAGAAGACCTACAGAATGGAAGAAAATACTTGCAAAC 4112
                             v vv ii      vi   i         i        i       i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_115630144_   4113 TATGCATGTGAGAAAGGTCTAATAACCATGATCTATAAGAAACTTCAAGC 4162
                         i  ii  v   v  i  v  vi  v   vi  v     ii    ----- 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT-----C 777

  chrX_115630144_   4163 TGTACAACAAACTAGACAAACTACAAACTATGCAAATTAGCAAGCAAAAC 4212
                          -      ---------------------- -   --  ii  --   iv
  L1M4_orf2#LINE/    778 T-TACAAC----------------------T-CAA--TAATAA--AAAGA 799

  chrX_115630144_   4213 CAAACAACCCTATTACAAATTAGGCAAAGGTCATGAACAGGCATTTAAAA 4262
                             i     v   ?v   v i        viv    i  i     vvvv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_115630144_   4263 AAAAAAAGACACATAAGTGGCCAAAAAGCATATGAAAAAATACTCAAAAT 4312
                            i  -  i i i  i       v     i       i  i     v  
  L1M4_orf2#LINE/    850 AAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_115630144_   4313 TTCTAACCAC 4322
                         iv????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.19 (83 / 26)  


2625 28.52 2.59 0.79  chrX_115658696_115660720.rev      648  1534 (491)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_115658696_    648 AAACATTCCATGTTCATGCATTAGAGGAATCAATATTGCTAATATGGCCA 697
                          i i  i           v   i  i  v i       i   v     v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_115658696_    698 CATTTCCCAAAAGATTCTACAGATTTAATAGTATTCCTATAAAACTCCCA 747
                         i i i      vviv          i  iivv  i     v   v     
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_115658696_    748 A-TGTCATTTTT-CATAAAATGAGAAAAAAACT-ATTCTAAAATTCACGT 794
                         i-  i v     -  v   v   v  ----i  -  i          ii 
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAA----GCTGATCCTAAAATTCATAT 151

  chrX_115658696_    795 GGAACTATAAAAGCCCCCAAATAGCCAAAGCAATCTTAAAAAAAAAGAGC 844
                             v ii  ii v   vi          i       i     i    i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_115658696_    845 -----TGGAGGCATCACATTGCCCAACTT-AAAACT-ACTACAAGTCTAC 887
                         -----      vv     i v     i  -      -       iv    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_115658696_    888 CTTAGCCAAAACAGCATGGTACTGTTACAAAAAACAGATACATATACCAG 937
                         vv  ii   i    ii        vi i  ii -i   i i   v i  i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAA 300

  chrX_115658696_    938 TAGAACTGAATAGAGAGCCAAGTAATAAAGCTTCACACTTACAACCATCT 987
                          i   iv    v     i v  v      v ivi   i   iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_115658696_    988 GATCTTTGACAAAGATGAAAATAACAAGCAATGGAGAAAAGATTTCCTAT 1037
                            i  i     i i  vv  v v  vv      i    ii  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_115658696_   1038 TTAATAAGTGGTGCTGTGATAACTGGATAGTCATCGGCAGAAGAATGAAG 1087
                          i  i  i        v  i         ?i  ivv   i          
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_115658696_   1088 ----ACCTCTACCTTTCATCATATATAAAAATTAACTCAATGTGGATTAA 1133
                         ----   i      iv  i      i              vi     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_115658696_   1134 AGATTCCAATATAAGACTTCAAATTGTAAGATTCCTAGCAGAAATCCTAC 1183
                            iiiv   i     vi v   i i   i i  i   v     v v  v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_115658696_   1184 AAA-ACACCATTCTTGATTCCAGCCTTGGGAAGGAATTTATAAATAAATC 1232
                         i?i- v i -   v   iiiii vi v  v  v iv  iv  i   viv 
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_115658696_   1233 CCTAAAAGCTATTGCAATAAAAATAAAAATTGACAAGTGGGAGCTAATTG 1282
                         v i      vvvv    i    iv      v  i  i v   vi v  ii
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_115658696_   1283 AACTAAAGAACTTCTGCACAGCAAAAAGAAATTTTCA-----GCAAACAG 1327
                           v v  i     i  ii vv    -i  v i v   ----- ii  v  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAAAG 698

  chrX_115658696_   1328 ACAAACTACAGAGTGGGACAAAATATTCATAAACTGTGAATCTGACAAAG 1377
                             v i     i     v        iii   iii iv      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_115658696_   1378 GTCTAATATCCAGAATCTATAAGGAATTTAAACAAATCAAAAAGCAAAAT 1427
                          v  vi          v     i   i ivv    v    v  vv    v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_115658696_   1428 ACAAATAAACTCATTAAAAATTGGGCAAAGAACATGAACAGACACTTCTC 1477
                                 v iv   ?    v         i iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_115658696_   1478 AAAAGAAGACACACATGCATTCAACAAACA---GAAAAAAAGCTCAACAT 1524
                         v        i i   viiivi   i  i  ---     i v         
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_115658696_   1525 CACTAATTAT 1534
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.02 (14 / 903), avg. gap size = 2.14 (30 / 14)  


2303 31.50 0.88 0.88  chrX_115675196_115677090      501  1408 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115675196_    501 TGGGAAAATACTCCATGCTCATGGATAGGAAGAATCGATATCATTAAAAT 550
                            i  i   ii     i        v      v ii    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115675196_    551 GGCCATAACACCCAAAGCATTTTGTAGACTCAATGCTATTTTTATTAATC 600
                            v   viv      viiv i ii   i    i  v  iii   i  vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115675196_    601 TACCATGGTGA-TTCTTCACAGATCTAGAAAAAAGTATTTTAAAATTGAT 649
                          v   - v  v-  i  ii    vv v  v  ivvv  ii       v  
  L1M4_orf2#LINE/    101 TCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_115675196_    650 ATAGAACCAAAAAGAGCCCA-AATAGCCAAGGCAATCCTAAGCAAAAAGA 698
                           i   viiv  i ii    -         ii     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_115675196_    699 ACAAAGCTGAAGGCATCATGCTACTTGACTTCCAACCATAATACTGGGCT 748
                               i  i   vv   ii  v iii i   v  v v  v   vii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_115675196_    749 ACAGTAACCAAAACAGCATGGTACTGGTACAAAAATAAGCACATAGATCA 798
                                i   i    ii         i i  ii   ii  i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_115675196_    799 AGGAAACAGAATGGAAAGCCCAGATGTATGGCAGCAAACAT--ACAATCA 846
                          v i  i     v  i  i     vi  viv --  v    -- iii   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCA 347

  chrX_115675196_    847 TCTTATCTTTGACAAAGCTGAAAAAAGCTATCAATGGGGAAACAACTCCC 896
                         vi v  i  i     i v  vv  i v vv            v  ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_115675196_    897 TATGCAATAAATGATCCTGAGATAACTGACTAGCCATATGGAGAAAATTG 946
                          v v   i     i v   i  i     iv  ?   i   v i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_115675196_    947 AAGCCAGACCCATTCCTTACACCATATAAGGAAATCAACACCAGATGGAT 996
                            iii     v v   i          vii    i   v v i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_115675196_    997 TAAAGACTTAAATATAAAACCCAAAAGTATAAAAACCCTGGAAGACAATC 1046
                         i ?    i     i   i v i    v       vi i i     v  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_115675196_   1047 TAGACA-ATACCATGCTGGACATAAAAATGAGCAAAGATTTCACAACAAA 1095
                            i?i- v i - v vv   v viiiv ii    v i    vi ivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_115675196_   1096 GACACCAAAA--ACGATTGCAACAAAAGTAAAATTTGACAAATGGGATCT 1143
                                   --  i --          v    v v  i    v   ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_115675196_   1144 ATTTAAACTTAGGAGCTTCTGAACAGCAGAAGAAACTATCTACAGAGTAA 1193
                         vv i   v   ii i   i  vi vv  i i  v      v v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_115675196_   1194 ACAAAAAACCTTCAGAATGAAAGACATTTTCTTTGCAATCTATGCATATG 1243
                          v i v    iv       ii   v v --v       vii  ii  v  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAAT--ATTTGCAAATCATATATCTG 742

  chrX_115675196_   1244 ACAAAGATCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTATAAG 1293
                          i  i iv  vi       v  v     i     ivv    v iv    v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_115675196_   1294 AGAAAAGCAAAAAACTTTCTTAACAAGTAAGCAAAGTACATAAATGGACA 1343
                          i   ii    v   iivv  ? v  i ii      v iv i   i    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_115675196_   1344 CGTTACAAAAGAAGACATATATCTAGCCAACAAGCATATGAGAAAA-GCT 1392
                         iv iv v        i   i vv i     i     i    i  i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_115675196_   1393 CAATACCACTAATAAT 1408
                            i i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (164 / 118)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


 458 26.16 2.33 1.16  chrX_115682229_115684650.rev      249   420 (2002)  C L1M4_orf2#LINE/L1   (0)   908   735  

C chrX_115682229_    420 TATATCTGTCAAAAAAACTAGTATCTAAAAAATATAAAGGA-TATTCCAA 372
                                 vi  iii -  v     i i  v        i - v  v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGA-CTTGTATCCAGAATATATAAAGAACTCTTACAA 783

C chrX_115682229_    371 ACTCAACAGTTGAAAAACAGACAATCCAACTAGAAAATGTGCAAAAGACA 322
                         -     i i vi   i   i i  i    i ?i      v     i  iv
  L1M4_orf2#LINE/    784 -CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

C chrX_115682229_    321 TCAGGAGGCATTTCACAAAAGAGGATGTTCTACTGGCAAATAGGGACAT- 273
                          v iv  i      v v     i   i v v v    v    i v    -
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

C chrX_115682229_    272 --AATATGTTCTACATGAATAGCCAT 249
                         --  v   i  v    v ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (24 / 20)
Gap_init rate = 0.02 (4 / 174), avg. gap size = 1.50 (6 / 4)  

2208 27.99 4.18 1.69  chrX_115682229_115684650.rev     1054  1939 (483)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115682229_   1054 TGGAAAAATATCGGATTCTCATGGAT-GGAAGAATCAATGTTGTTAAAAT 1102
                               i     vv  vi        -      v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115682229_   1103 TATTATACTACTCAAAGCAATCTACAGATGCAACACAACTTCTTTCAAAT 1152
                         viiv     v i    vii          v    i   iii  v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115682229_   1153 TACCAAAT-CATTTTTTACAGTATCAGAAAAAAAATCCTAAAATCCTAAA 1201
                          v   iv - v      i   v viv  v  i-----  i --       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGA--TCCTAAA 143

  chrX_115682229_   1202 ATTCATATGGGATGGAAAAAGAGCCTGAATAGCCAAAGCAATTCTAAGCA 1251
                                   i vv v  ii  v  v           i    ii i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_115682229_   1252 AAAGGAACAAACCTGGAATCATCACATTATCTGACTT-AAAATTATACTA 1300
                          i i       vi    ivvv     i vi ii i  -    i -     
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTA 242

  chrX_115682229_   1301 TACAACTGCAGTAACAAAAACAGCATAGTACCAGTATAAA-ATG---ATA 1346
                         i v i  i      iv  i    ii i    ii i    i-  i---   
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_115682229_   1347 CAGATCAATGAAACAGAATAGAGAACCCAAAAATAAATCCACCCCT---- 1392
                         i         i  i     v    ii   i       i   iv v ----
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_115682229_   1393 GACCAACCTAT----GACAAAGTCAACAAAAATATACACTGAGGAAAGGG 1438
                          ii   iiv  ----     i viiv   i vi  v  v  i      ii
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_115682229_   1439 CACCCTGTTCAATAAATGATACTGAAAAAAATTGGATAGCCATAGGCAGA 1488
                         i vi  v     i     i i   ii v  -i      ?   i v   i 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAA 441

  chrX_115682229_   1489 AGAATAAAACTCGACCCATATCTCTCACTATATACAAAAATTAACAAAAG 1538
                              i  ii v     v  i   v   i                vv  i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_115682229_   1539 ATGGATTA-AAACTTAAATGTAAAACCTGAAGCTATACAAAACCTAGGAG 1587
                               i - i  i         i v  i  i     v  vv i   i  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_115682229_   1588 GAATTTTCAAAAACTACTCTTCTGGGCATTGGCCTAAGCAAAGAATTTAT 1637
                         i  viv - ii?iiv v     vv i v    vi  i    v iv  iv 
  L1M4_orf2#LINE/    542 AAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_115682229_   1638 GAGTAATATCTCAAAAGCAAACAAAACAAAAACAAAAGTAGACAAATAGG 1687
                         iii  vv ivi        v viv       iv    i    i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_115682229_   1688 ACTT------AACTAAAAAGCTTCTAAACAGCAAAAGAAATAAT---GAA 1728
                             ------  i      -   i ivi vv    i  v iv  ---   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_115682229_   1729 TAGTGAACTGAAAACCTACAGAATTGGAGAAAATATTCGCAAACTATATA 1778
                         -      vv  v    i       v            i     ii     
  L1M4_orf2#LINE/    690 -AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_115682229_   1779 TCTTACAAATGGCTAATAACCAGACTCTAAAACTAACTCAGACAACTCAA 1828
                            v i  iv i  vi  v     v v  v  vv     vv         
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_115682229_   1829 CAACAACCACA-AAACAACCCTACTAAAAAGTGGGCA-----T---AACA 1869
                         i  i  vv v -   i     v i ?    i      ----- ---  i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_115682229_   1870 CACATCTTTTAAAAGAAGGCGACATACAAATGGTGAACAAACATATGAAA 1919
                         v    i i iv       --- i          iv  i  i  i      
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAG---ATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_115682229_   1920 AAAT---TAGTATCATCACTAAC 1939
                          i  ---i ii    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.36 (52 / 22)  


 542 26.56 4.69 1.56  chrX_115687877_115691162        5   196 (3090)    L1M4_orf2#LINE/L1      553   750 (158)  

  chrX_115687877_      5 GCAAATCTTTATGATGTTAGATTTGACAAT----TCTTAAACATGACAAT 50
                          i       ii   iv  i i  v i    ----     i i      vi
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_115687877_     51 ACAAACACAATTCATGAAAGAATAATGTAGTTAAATCAGACCTCAACAAA 100
                          v  i     viv ii      v  -i   v     ii   i   v    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAA 651

  chrX_115687877_    101 AATTTCAAAA-----ATAGATTAAAGGACACTACCAAGAAAATGGAAAGT 145
                          --  v    -----i ivv i           i       i  i    v
  L1M4_orf2#LINE/    652 A--TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_115687877_    146 CAATCTAAAAATTGAGAGAAAACATGTGCTAATCATACATCAGCTAACAG 195
                            i i v i v  i       i  v   v       i   v v   vi 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_115687877_    196 A 196
                          
  L1M4_orf2#LINE/    750 A 750

Transitions / transversions = 1.55 (31 / 20)
Gap_init rate = 0.02 (4 / 198), avg. gap size = 3.00 (12 / 4)  

2919 27.54 1.56 0.33  chrX_115687877_115691162     1897  2793 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115687877_   1897 TGGAAACACATCCCATGCTCATGAATGGGTATAATCAATATTGTGAAAAT 1946
                               v i        i     i  v  v v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115687877_   1947 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 1996
                          i v     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115687877_   1997 TACCACCATCATTCTTCACAGAAGTAGAAAAAAAAATCCTAAAATTCACA 2046
                          v   v vv v  i  ii     i v  v  ivvi             i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115687877_   2047 TGGAACCAAAAAAGGATCCACA-TAGCCAAAGCAAGACTAAGCAAAAAGA 2095
                              viiv  i-   i   v -        i   vvi i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_115687877_   2096 ACAAATCTGGATGCATCACATTATCTAACTTCAAACTATACTGTAAGACC 2145
                              vi    v vv     i vi i  i      viv    ii  ii i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_115687877_   2146 ACAGTCACCAAAACAGCATGGTACTGGTATAAAAATAAGCACATAGACCA 2195
                              v i   i    ii         i    ii   ii  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_115687877_   2196 ATAAAACAGAATAGAGAATCCAGAAATAAACCAA-ATACTTACGGCCAAC 2244
                           ii  i     v    i              v - i i   i  i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_115687877_   2245 TGATTTTCAACAGAGCAAACAAAAACATGAAGTAGGGAAAAGACACTCTA 2294
                                 i   ii vviv   i v   vv i i      ii i v   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_115687877_   2295 TTCAGCAAATAGTGCTGGGATAATTAGCAAGCCACATATAGGAGAATAAA 2344
                             i     i         i  i i vv ?      ii ii     i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_115687877_   2345 AGTGGATCTTTTTCTCTCCCCTTATACAAAAATCAACACAATATGGATTA 2394
                         iv    i ii vi   v v  v           i   v   v      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_115687877_   2395 ATGACTTAAATCTAACATGTGAAACTATAAAAATTCTAGACGATAACATT 2444
                         ?v   i     v   v vv i           v ii    v  v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_115687877_   2445 GGAAAAACCCTTCTAGATTTTGGCTTAGGCAAAGACTTCATGAGCAAGAA 2494
                           ?iv  vi    vv  ii    v        v ii   v iiii v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_115687877_   2495 CCCAAAAGCAAATGCAACGAAACCAGAGATAAATAAGTGGGACTTCAT-- 2542
                         v         v v     i   vv i i   i    i v         --
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_115687877_   2543 ----TAAGAGCCTGTGCACAACAAAAGGAACTGT--AGGCAGTATAAACA 2586
                         ----   i i i v  ii vv    i iv   i --  iv   i-   - 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG-AAA-A 697

  chrX_115687877_   2587 GACAACCCACAGAGTGGGAAAATATCCTCACAATATAGACATCTGACAAA 2636
                                      i     i  v  vi ii   vvi v i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_115687877_   2637 GGATTAATATCCAGAATCTACAAGGAACTGACACAAATCAGCAAGAAAAA 2686
                            i vi          v  i  i     vvi    v   ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_115687877_   2687 ----AAGAATCCCATCAAAATGTGGGCTAAGGACATGAATAGACAATTCT 2732
                         ----  v  i  v  i?   vi     v     iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_115687877_   2733 CAAAATAAGATATACAAATGACCAGTGAAGATATGAAAAAATGCTCCACA 2782
                          v   v              i   i i iv i       i      v   
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_115687877_   2783 TCACTAATAAT 2793
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


2600 27.43 2.32 1.88  chrX_115712835_115715668.rev     1456  2359 (475)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115712835_   1456 TGGAAAAACATTCCATCCTCATGAATAGGAAGAGTCAATATAGTGAAAAT 1505
                               i i  i    vi     i  v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115712835_   1506 TGCCATAGTGCCCAAAGTAATTTACATATTCATAGGTATTCCC-ATCAAG 1554
                         v  v   v v      v i  i    v     - v i v    -     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCA-ACGCAATCCCTATCAAA 99

  chrX_115712835_   1555 CTACCATTGACATTCTTCACAGAATTCGAAAAATCTGCTT-TAAATTTAA 1603
                         v v   vivi v  i  ii     v i  v  i-   v i-    v  v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_115712835_   1604 TATGGAAGTAAATAAGACCTCGTATTGCCTAGACAATCCTAAGCAAAAAG 1653
                                i iv vii    iv v  v   v i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_115712835_   1654 AAAAAACCTGGAGGCATCATGCTACCTGATTTCAAACTATGCTACCAAGG 1703
                           v   vi      vv   ii  v  ii        viv i    -  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC-AAAG 247

  chrX_115712835_   1704 CTACAGTAACCAAAACAGCATGGTACTGACACCAAAACAGACAGACATAT 1753
                                  i   i    ii        i  i--  i--  i        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCAT--AAG--GATAGACATAT 293

  chrX_115712835_   1754 AGACCAATGGAGCAGAATAAAGACCTAAGAAATAACAAACACCACACATC 1803
                            i       ii     vi   viiv        ---  -   i    i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAA---AC-CCATACATT 339

  chrX_115712835_   1804 TACAACCATCTGGTCTTTGACAAACCTGATAAAAACAAGCAATGGGGACA 1853
                           iiii  vi  i i  i     ivv  vi  i v  vv         v 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_115712835_   1854 TGAT-TTCATATTCAGTAAATGGTGCTGGGAAAACTGGCTAGTCATATTC 1902
                         vi  -v  v -    ii              v      v  ?i  i  v 
  L1M4_orf2#LINE/    390 GAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_115712835_   1903 AGAAAACTGAAACTGGACCCCTTCGTTACACCTTATACAAAAATTAGCTC 1952
                          i  i v    ii         v v i     v             i   
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_115712835_   1953 AAGATGGATTAAAGACTTAAATGTAAAACCTAAATCCATACAAATCTTAG 2002
                           i      i ?    i         i v     v i   v  v      
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_115712835_   2003 AAGAAAGCCTAAACA-ATACCATTCAGGACATAGGCATGGACAAAGACTT 2051
                               i v  ii?i- v i -   iv   v v  vv i i   v ii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_115712835_   2052 CATGAAAAAAACGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAAA 2101
                          v ii v vi  i         vvv          vv     v  i   v
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_115712835_   2102 TGGATCTAATTAAA-TTAAAGAGCTTCTACACAGCAAAAGAAACTATCAT 2150
                             ii v  i   -     i -   i iii vv    i  v       v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_115712835_   2151 TAGAGTGAACAGGCAACTTATAGGATGGGAGAATATTTTTGCAAGCTACT 2200
                         v i      v  i    ii i  i         v  v       iii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_115712835_   2201 CATCTGA---------------CAGAATGTACAAGGAACTTAAACATATT 2235
                         i      ---------------      i  i  i     ivv   - i 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACT 785

  chrX_115712835_   2236 TACTAG-AAAAAAACAAAAAACCCCATCAAAAAGTGGGTGAAGTATATGA 2284
                         i v  i-     i     v     v  i?    i    ii   v  v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_115712835_   2285 ACAGGCACTTCTCCAAATAAGACATTTATGAGGCCAGCAAACACGAAAAA 2334
                          i  i  i         v    i  vi viv     ii  i   -- vi 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC--ATGA 883

  chrX_115712835_   2335 AAAAAAACTCAATGTCATTAATCAT 2359
                            i vi     ii   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.00 (38 / 19)  


2792 28.48 2.69 0.90  chrX_115715944_115720132.rev     2807  3698 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115715944_   2807 TAGAAAGGTACTCCATATTTATGAATTGGAAGAATCAATGTTATTAAAAT 2856
                          i     i  ii    i  i   i         v i   i  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115715944_   2857 TTTTGTACTACCCAAAGAAATCCACTAATTCAATGAAATTCATGTCAAAA 2906
                         vvivi    v      vvi   i  vi      i v   i v i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115715944_   2907 TTCCAA-TGCATTCTTCACACAAATAGAAAAAAAACCCATAATTTTAAAA 2955
                          i   i-   v  i  ii  v    v  v  i----- - i  ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----C-TGATCCTAAAA 144

  chrX_115715944_   2956 TGTAGGTGGAACTACAGAAGACCCAGAATAGCCAAATCTATTATAAGCAA 3005
                          vi vi     v i  iii                 v v  iv i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_115715944_   3006 AAAGAACAAAACTGGAGAAATCACATTACCTGACTTCAATTTATACTACA 3055
                         i         ii     i v     i v  ii i     vviv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_115715944_   3056 GAGTTATAGTAACCAAAATGGCATGGTACTGACATAAAAATAGACACACA 3105
                         i  i  i     i   i ii ii        i     ii       i i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_115715944_   3106 CACCAGTGGAGCAGAATAGATAACTCAGAAACAAATCCACACACCTACAG 3155
                         v i  i    ii     v  v iii      i   i   i   ii  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_115715944_   3156 TGAACTCATTTTCAATAAATATGCCAAGAATGTACACTGGGGACAAGACA 3205
                          v  i v      i i  ivi        vii v  v      v ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_115715944_   3206 GTCTCTTTAATAAATTATGCTGGGAAAACTGGATATCCAAATGCAGAAGA 3255
                             i  i  i    vi        v         ?   v     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_115715944_   3256 ATAAAACTAGACCCTTCTCTTTCACCA------AAAATCAAATCAAACTT 3299
                           i  ii i     i vi  iv     ------     i  v     v v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_115715944_   3300 AATTCAAGACTTAAATCTAAGACCTCAAAGTATGAAACTACTAAAATAAA 3349
                         i  iv?    i     v     v  v   v   i     vi  i  v   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_115715944_   3350 ACATTGAGAAAACTCTCCAGGACATTAGTCTCAGCAAAAATGTCTTGAGT 3399
                             v i?iv  v   i iv   v  i vi vi    vii v    iii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_115715944_   3400 AATACCCTACAAGCACAGGCAACCAAAGCACAAATGGACAAATGGAACCA 3449
                          vv  v i v       i     v    v v    i  i    v i  iv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_115715944_   3450 CATCAAG-TTAGAAAGCTT----CTTCACAGAAAAAAAAGTTAATAAAGT 3494
                               i-   i   vi  ----     v  i v vv -- i  v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA--TCAAGAAAGT 692

  chrX_115715944_   3495 GAGGAGAAAACCCACAGAATGGGCCAAAACTTTTGCGAACTATCCATCTA 3544
                           ii   v               vv    iv     i  ii  vi    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_115715944_   3545 ACAAAGGAGTAATAAATAGACTATATAAGGAGCTTCAACAACTCTATAA- 3593
                          i  i   v vi  vvi   v       i  i  iiv       v    -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_115715944_   3594 ----AAATTAATAATCTGATT-AAAAATGGGTAAAAGATTTGAATAAACA 3638
                         ---- i iv     i ii   -         i   i          i   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_115715944_   3639 TTTTTC--AAGAAAGCACACAAATGGCAAACAGGTA--TGAA--GGTGCT 3682
                            i  --     iii i         v  i i i --    -- i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_115715944_   3683 TATTATCATTGATCGT 3698
                         i vi    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (161 / 90)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.67 (32 / 12)  


1760 26.38 17.41 1.15  chrX_115737835_115739971      864  1644 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115737835_    864 TAGAAAAACATCTCATGTTCATGGATTAGAAGAATTAATATTGTTGAAAT 913
                          i    i i   i              i     v           i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115737835_    914 GACAATATTACCCAAAGCAATCCACAGATTCAATGCAATCTTTATCAAAA 963
                          i     i v      vii   i          i      ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115737835_    964 TACCAATAACATTCTTCACAAAATTAGAAAAA---ATCCTAAAATATTT- 1009
                          v   iivi v  i  ii  i  v v  v  i---          viv -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115737835_   1010 TGGAACCACAAAATACTCCAAATAGCCAATGTGATTCATAGCAAAAAGAA 1059
                              vii   iiv  i vi         viii  iivv iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115737835_   1060 CAAAGCTGGAGGTATCATACTTTCAGACCTCAAATTATACTACAAGGCTA 1109
                              i      vv   i    i vi ii     viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_115737835_   1110 TAGTAACCAAAACAGCATGATACTAGCATAAAAAGAGACACAAAGGGCAA 1159
                         i     i   i    ii  i    i      ii v     i v  iv   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_115737835_   1160 TGGAGCAGAGTAGGTAACATAAACATTAATCGACATATCTACAGCCCACT 1209
                             ii   i v iv iivi i v  v  i v i i  i  ii i v i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_115737835_   1210 GATTTTTGACA-TAGTGCCAAGGACATTCATTGAAGAAAGGATTGTCTCG 1258
                               i    -vi        iv      v  ii     i  v    iv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_115737835_   1259 TCAATAAGCAGTGCTTAAGAACAA----A-----ACATA-AAGAAAATG- 1297
                             i  iii     --i i    ---- -----    i-  i i    -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCT--GGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_115737835_   1298 ----------CTAC---A----------GGAAATTGGCC-----TGGGGG 1319
                         ----------    --- ----------ii     ii i-----   ivv
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_115737835_   1320 AAAAA----ATTGTGA-----------ATAAGACCTTTAAAA-------T 1347
                          ? i ---- v   i -----------    i  ii   i  ------- 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_115737835_   1348 AG-------------------------AGGCAATG--------------- 1357
                           -------------------------        ---------------
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_115737835_   1358 -----AAAGCA-----------AAAATAAATAGAGTAAA----AC----- 1382
                         -----      ----------- i  v       -    ----  -----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGA-TAAATTGGACTTCAT 647

  chrX_115737835_   1383 --AAATTAAAAATCTTCTCCACAGCAAAGCAAACAAGCAACAGAGTGAAA 1430
                         --          -   i vii vv     v v  v v   v i       
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_115737835_   1431 TGACAGCCTATAGGATGGAAAAAGAATCTTTGCAAGCTACTCGTCTGACA 1480
                         v    i  i i  i    i i  -   v       iii ivii     i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCATATATCTGATA 745

  chrX_115737835_   1481 AAGGATTAATATCCAGAACTTTCAATGAACTCAAACATGTCAACAACAAC 1530
                          i   i vi         iv vi  v      vv   vv    i  i  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_115737835_   1531 AACA-AAATA-TCTGATT-AAAAATGAGCAAATGATCTGACCAGACATTT 1577
                           v -     -i ii   -       i     v   i   vi        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_115737835_   1578 CTCAAAAGCAGACATACAAATGGTCAACAAATATATGAAAAATAAAATGC 1627
                            v    v   i          i   i  ii i       i----    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG----ATGC 891

  chrX_115737835_   1628 TCAACATCACTAATCAT 1644
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (138 / 67)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 5.58 (145 / 26)  


 906 22.99 0.60 10.15  chrX_115770496_115772619.rev       11   345 (1779)  C L1M4_orf2#LINE/L1   (177)   731   429  

C chrX_115770496_    345 ATCCATATGCAAAAGAATAAAACTCAATCCATATCTCTCACCATATGCAA 296
                          ?   i            i  ii vi i  v  i   v        i   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

C chrX_115770496_    295 AAAATCCAATCAAAATAGATAAAGGACTTAAATCTAAGACCTCAGACTAT 246
                            - iv v       i   v ?i   i     v     v  v i     
  L1M4_orf2#LINE/    479 AAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

C chrX_115770496_    245 AAAACTGCTAAACAAAACAAAACAAAACAAACAAACATAAAACATTAAGG 196
                               vi  i ------------------------ v       vii? 
  L1M4_orf2#LINE/    528 AAAACTCTTAGA------------------------AGAAAACATAGGNG 553

C chrX_115770496_    195 AAAATCTCCAGGATGCTGGTCTGGGCAACACCTCAAAGATTTCTTGAGCA 146
                         v      i iv  ivi   vi i     i-------- i      iiii 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAAT--------GGTTTCTTAGATA 595

C chrX_115770496_    145 ATACCCTAAGGGCACAGGCAACCAAAGCAAAAATGAACAAATGGGATCAT 96
                         vv  v i  ii     i     v    v      ii i    v   iivi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chrX_115770496_     95 ATCAACTTTAAAATCGTTTGCACG-CAAAGGA-ACTAATCGACAAAGTGA 48
                              vv      v v    ii v-       -    -  i v       
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGA 694

C chrX_115770496_     47 AGAGACAACACATAGAATGGGAGAAAATATTTGCAAA 11
                          i       v  i                        
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

Transitions / transversions = 1.47 (44 / 30)
Gap_init rate = 0.02 (6 / 303), avg. gap size = 6.00 (36 / 6)  

1105 25.64 0.37 0.37  chrX_115770496_115772619.rev      508   780 (1344)    L1M4_orf2#LINE/L1      238   510 (398)  

  chrX_115770496_    508 TACTACAGAGCTATAGTAAACAAAACAACATAGTAATCACATAAAAGCAG 557
                                i     i     v   i   iii i   v vi     iiii  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_115770496_    558 ACACATGGATCAATGGAACAGACTAAAGAAACCAGAAAAAAAATTATACA 607
                            i  i           i   v vi   iv       v   vii     
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_115770496_    608 TCTACAGTGAACTTATTTTCAACAAAGTTGCCAAGAACATACATTGAGAA 657
                          i  ii  v  i v      i    i v        v   v  v  i i 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_115770496_    658 AAATATAATCTCTTCAATAAGTGGTTCTGGGAAAACTGGATATCTACCTG 707
                           iv   i   i     i  i    v      v         ? i  v  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_115770496_    708 CAGAAGAATGGAACTAGACCCTTATCATTCACCATATGCAAAAATATAAT 757
                           i       i ii i     i  i viv        i       -   i
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT-TAAC 486

  chrX_115770496_    758 T-AATATGGATTAAGAACTTAAAT 780
                          -  v      i ?ii  i     
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAAT 510

Transitions / transversions = 2.24 (47 / 21)
Gap_init rate = 0.01 (2 / 273), avg. gap size = 1.00 (2 / 2)  

1171 26.13 6.09 1.77  chrX_115770496_115772619.rev     1125  1633 (491)    L1M4_orf2#LINE/L1      378   908 (0)  

  chrX_115770496_   1125 TCAA-GGTGATAAAATAGTCTTTACACCAAAC--TTCTGTGACA--TGC- 1168
                             -  v  v i          v  v    i-- v   v    --  v-
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_115770496_   1169 CATTTACCTTCATAGGTAT----------CCCTGGATCTAAAATAA-ACA 1207
                         i ?ii  v v  v i v  ----------    -- i  v v iv - i 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCT--ACCTCACACCATATA 475

  chrX_115770496_   1208 TAAAAA--AA---AAATTAGA--AAAGACTTAAATCTAAGATCTCATACT 1250
                         i     --  ---   v i  -- ?    i     v     v  v v   
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_115770496_   1251 AGGAAACTACTAAGAGAAAACCTTGGGGAAACTCTCTAGGACATTGGACT 1300
                          vi     vi  ii       v v  ? v  v   iiiv   v    ii 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_115770496_   1301 GGGCAAAGGAACCTTGAGTA--ATACTGCACAAGCACAGGCAACCAAAGT 1348
                         i     v  vvi   iii  -- i  --  v       i     v    v
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACAC--CAAAAGCACAAGCAACAAAAGA 623

  chrX_115770496_   1349 AAAA-TGGATAAATTGTATCTAATTAAG-TCAAAAAGCTTCTGCACAGCA 1396
                             - i         v ii v  i  i- i     -   i  ii vv  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCA 672

  chrX_115770496_   1397 AAGGAAACAATCAAGAAAAAAAAAAAAGAAAACTCATGAAATAGGAGAAA 1446
                              v  v         ivi    --  v   i  iii   i       
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAA--GACAACCCACAGAATGGGAGAAA 720

  chrX_115770496_   1447 -TATTTCCAAAATGTCCATCTGACAAGGAATTAATTACCAGAATATGTAA 1495
                         -     v    vii vi      i    i i vi vv         i   
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_115770496_   1496 GGAATTTAAACAACTTTATAGGATATAAAT-CTCATAATCGGATTCAAAA 1544
                         i   i ivv      iv   --   v   v- vv    i vi   ?    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATA--ATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_115770496_   1545 CTGGGCAAAAGATCTGAATAGACATATCTC-AAAAATGGCATTCAAATAG 1593
                         v        i   i           v    -   i v ii  v     i 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_115770496_   1594 CAAGCAAGTATATGAAAAGATGCTCAGCATCAATGATCAT 1633
                          v ii   i i               i     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.15 (69 / 60)
Gap_init rate = 0.04 (20 / 531), avg. gap size = 2.00 (40 / 20)  


2956 26.10 2.08 2.52  chrX_115792491_115796604.rev     2712  3623 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115792491_   2712 TGGAAAAATTTCC-------ATGGGTTGGAAGAATCAATATTATTAAAAT 2754
                               i  v   -------    i        v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115792491_   2755 GTCCATACTCCC-AAAGCAATCTACATATTCAGTGAAACCCCTATTAAAA 2803
                          v v        -   vii       v     ii v  i      i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115792491_   2804 TACCAA-TAATATTCTTGAAATATAAATAGAAACAAAATGGAAATAGAAA 2852
                          v   i- iviv  i   v i---    v  --   iv  ----------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAG---AAATTGA--CAAGCTG---------- 135

  chrX_115792491_   2853 AAAATCCTAAAACTTATATGGAACTATAGAAGACCCAGAAAAGCTAAAGC 2902
                         ---         i i        v ii iii         v   i   i 
  L1M4_orf2#LINE/    136 ---ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chrX_115792491_   2903 TATCT-AAGCAAAATGAACAAAACTTAAGAAATCACATTACCTGACTTCA 2951
                         v    -i iv  i v       ii vi  i v     i v  ii i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_115792491_   2952 AATTATAGTACAGAGCTATAGTAAGCAAAACAACATGATACTGGCACAAA 3001
                           viv  v    i     i     v   i   iii  i        i  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_115792491_   3002 AACAAACTTATAGA-CAAAGGAA-AAAATAGAAAACCCAGAAACAATTCA 3049
                         i i i  v      -   v    - i   v  i ii       i  vi v
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_115792491_   3050 GCAAGTTTACAGCGAAGTCATTTTTGACAAAGGTGCCAAGAACATACACT 3099
                         ii vi    ii iv  v v     i     i          v   v  v 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_115792491_   3100 GGGGAAAAAGACAGTCTCTTCAATGAATGGTGCTGGAAAAAACTTGATAG 3149
                                i - i     i     ii           i v  -  v    ?
  L1M4_orf2#LINE/    383 GGGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAK 430

  chrX_115792491_   3150 CCATATGCAGAAGAATGAAGCTAGACCACTGTTTATTTCCATATACAAAA 3199
                            i     i          i i    v  iii vviv            
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_115792491_   3200 ATCAAATCAAAATGGATTAAGGACTTAAATCTAAGACCTCAGCCTACGAA 3249
                           i  v           i ?i   i     v     v  v iv   ii  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_115792491_   3250 ACCACTACAAGAAGACATTGGGGAAAATCTCCAGGGCATTGGTCTGGGCA 3299
                           ivi  v     i    v  ? v      i iv i v    vi i    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_115792491_   3300 AAGATTTCTTGAGCAATACCCCACAAGCGCAGGCAACCAAAGCAAACATG 3349
                          v i      iiii vv  v   v    i  i     v    v   v  i
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_115792491_   3350 AACAAATGGGACTCACAT-GAAGTTAAAAAGCTTCTGCACATCAAAGGAT 3398
                         i i    v     i-   -i  i       -   i  ii v        i
  L1M4_orf2#LINE/    631 GATAAATTGGACTT-CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chrX_115792491_   3399 ACCGTCGACAAAGTGA-----TAATCCACAGGATGGTAGAAAATATTTGC 3443
                           ii  i v       -----i  i      i    v             
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_115792491_   3444 AAACTACCCCTCTGACAAGGGATTCATAACTATAACATGTAAGGAGCTCA 3493
                            ii iviv     i      i ii  v i v  i  i   i  i   v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_115792491_   3494 AACAATTCTGCAGGAAAAATATCTAGTCATCCAATTAAAAAGTGGGCAAA 3543
                         v    i  vii iv     v - v i v i      ?    i        
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_115792491_   3544 ATATTTGAATATACATTTCTCAAAAATAGACACATGATTGGGAAATAGGC 3593
                         iv         v         v   iv   i i ii v   vv    i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_115792491_   3594 ATATGAAAGG-TGTCTGACATCATTGATCAT 3623
                          i      i -  iiii      ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (149 / 85)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.47 (42 / 17)  


2813 25.72 1.59 5.10  chrX_115802325_115806579.rev     2825  3765 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115802325_   2825 TAAAAAGATAGCCAATGTTTATGGATTGAAAAAATTAACATTGTTAAAAT 2874
                          ii       v  v     i        i  i v    i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115802325_   2875 GGCCATACTACCGAAAACGATCTAGAGATTCAGTGCAATTTTTAT-AATA 2923
                            v     v  v   vi      v       ii     iii   -  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115802325_   2924 TTTTAACAACATTTTTTATTGAAGTAGA-AAG--AATCCTAAAACTTGTA 2970
                          iii i vi v      iiv   i v  -   --i         i ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115802325_   2971 TGGAAGCACAAAAGACTCAAACTAACCAAAACTGTCTTGAGCAAAAATAA 3020
                              iii   ii   i  i v  i       vi      iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115802325_   3021 CAAAGCTGGAGGCAC-CAAGTTACCTGACTTAAAAAAGTACTGAATGGCT 3069
                              i      -  -  vii v  ii i  v    vv    iv vi   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_115802325_   3070 ATAATAATGAAAACAGCCTGGTGCTGGCGTTAAAATAGACACATACATAA 3119
                          i i    v  i    iv    i     i v ii       i   v  v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_115802325_   3120 ATGGAATAGAATGAAGACCCCAGAAATAAACCCAGATATTTACAGCCAAT 3169
                                     vi   vi               v i     ii i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_115802325_   3170 TGATTTTCTACA--GTTGTCAAGGACACTAAATGAAGAAAGGACTGCCTC 3217
                                 v   -- v  i    iv  i v    ii     i iv i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_115802325_   3218 TTCAATAAATATTGGTGGGGAAATTGGATATCCACACACAGAAGAATGAA 3267
                              i    iv  v    iv  i      ?     ii  i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_115802325_   3268 ATTAGACCCTTATCTCATCCCATGTACAAAAATAAATTGAATATGGATGG 3317
                         i  i     i  i    iv    i         v  i v  v      vi
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_115802325_   3318 AAGACTCAAATGTAAGTCCTGAACATGTAAAACTGCTGAAACAAAATTTA 3367
                         ?    ii         vv  i  vv i       vi ii  v    iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_115802325_   3368 GGGGGAAG-CTCTATTACATTGGTCTTTGTAATGATTTTTTGGATATGAC 3416
                           ? v  i-  iii v  v    vi vv i    i   i  i        
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_115802325_   3417 CTCAAAAGCACAGGCAACAAATGCAGAAAT-GACACATGGGA--TCATAG 3463
                         vi          i        v v i    -  i v  v   --    --
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT-- 647

  chrX_115802325_   3464 CAAACTAAAAAGCTTCTACACAGCAAAAAAAAAAAAAAAAAAAAAAAAAA 3513
                             v v    i   i iii vv    ii v vv ---------------
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA--------------- 682

  chrX_115802325_   3514 AAAAAAAAAAAAAAAAAAAAAAAAAAAATCAATCAAGTGAAGAGAAAACC 3563
                         ----------------------------    vv       i   v    
  L1M4_orf2#LINE/    683 ----------------------------TCAAGAAAGTGAAAAGACAACC 704

  chrX_115802325_   3564 TATGAAATG----AAAATATTTTAAAACCTTACATCTGATAAGAGGTTAA 3609
                         i iii    ----         vv   i v  i          i ii vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_115802325_   3610 TATTCAAAATATATAAGAAACTCAAACAACTCAATAGCAATCAAACAAAT 3659
                            i  i         ii     vv           ii  vv i      
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_115802325_   3660 AACACAAATTTAAGAATGAACAAATGATCTGAATCAATGTTTTTCCAAAT 3709
                            v   -  ?  i    ii    v   i     vi ii   i      v
  L1M4_orf2#LINE/    805 AACCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_115802325_   3710 AAGACATATCATTGATCAGCAGGTATATTAAAAAAATGGTCAAAATCTCT 3759
                             i   iv v  ii  ii i i i  -i    i   v    v   v??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACAT-GAAAAGATGCTCAACATCAZZ 902

  chrX_115802325_   3760 AATAAA 3765
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.64 (148 / 90)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.50 (63 / 14)  


3180 26.99 0.88 0.44  chrX_115857381_115863636.rev     4862  5765 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115857381_   4862 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4911
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115857381_   4912 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4961
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115857381_   4962 TACCAATGACTTTCTTCACAGAA-TTGGAAGAAACT-ACTTTAAAGTTCA 5009
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_115857381_   5010 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5059
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_115857381_   5060 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5109
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_115857381_   5110 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5159
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_115857381_   5160 AATGGAACAGAAC--AGAGCCCTCAAAAATAATGCCACATATCTACAACT 5207
                                i    i--    i  -- i      vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_115857381_   5208 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5257
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_115857381_   5258 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5307
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_115857381_   5308 GAAACTGGATCCCTTCCTTACA----ACACAAAAATCAATTCAAGATGGA 5353
                            ii    i    v   i   ---- i        i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_115857381_   5354 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5403
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_115857381_   5404 CTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATATCTAA 5453
                         v    ?v v viv   iv   v v  vv i     v ii   v  vv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_115857381_   5454 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5503
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_115857381_   5504 TTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGAAC 5553
                          i   v v  i i   i  ii vv v  i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_115857381_   5554 AGGCAACCTACACAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5603
                           i     i   v             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_115857381_   5604 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5653
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_115857381_   5654 AAACAAACAACCCCATCAAAAATTGGGTGAAGGACATGAACACACACTTC 5703
                          i     i     v  i?    v    ii     iv    i v   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_115857381_   5704 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGTTCATC 5753
                           v        i  vi viii     v  i          i   i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_115857381_   5754 ATCACTGGCCAT 5765
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (141 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


1889 25.85 5.11 1.70  chrX_115870179_115871874      500  1203 (493)    L1M4_orf2#LINE/L1      181   908 (0)  

  chrX_115870179_    500 ACAATTTTTTAAAACAAG--CAAAGTTGGAGGAGTTAC--TACCTTATTT 545
                              i  vv    v   --             v i  -- v  iv    
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_115870179_    546 CTAATCT-ATTCTAAAGATAGAGTAATCATGAAAATGCAGTATTTGTGAA 594
                          v  v  - i vi    v  v        v  v i  ii   i v iiv 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_115870179_    595 AACATAGACATATAGATCAACAGAATAGAAC--AGATTCTAGACATAA-- 640
                          iv                 ii        i--   v  i   v    --
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_115870179_    641 CCTTACATCTATTTGGTCAATTGATTTTTGAGAAATTTGCCAACATAAGT 690
                           v     i   --              i  v  ivv      v iv v 
  L1M4_orf2#LINE/    331 CCATACATTTAT--GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_115870179_    691 -AATGTGGAAAAAATA--TTTTTGAACAAATA-TGTTGGAACAATTTGAT 736
                         -    v     i    --i    v       i-  i   i    i v   
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_115870179_    737 AGGCATACATATGCAAAAAAAT-----TGAACCTCAACCATGTCTCACAC 781
                          ?- ---  i        i   -----  i   i v   -----      
  L1M4_orf2#LINE/    429 AK-C---CACATGCAAAAGAATGAAGTTGGACCCCTACC-----TCACAC 469

  chrX_115870179_    782 TCTATATAAAAATTAATAGAAAATGTGTCACAGACCCAAATATAAGAATG 831
                         iv    i         ivv      vi   ?     i    i     iiv
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_115870179_    832 AAAATTATAAAAATTTTAGGACAAAA--TAGGAGATAAGCTTAGCAACCT 879
                             i       v i    i v    --    ? vv  v   v ii    
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_115870179_    880 TGGATTTGACAAAAATTTCTTAAATACAA----AAAAGAACAAATTAATG 925
                            i  v i   vii       i   ii ----     v    ii-  ii
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC-AACA 618

  chrX_115870179_    926 AAGAAAGTAATAAA-AAATCACAGTTTATTAATATTAAAG-CTTTTCT-T 972
                           ii  iv    i -    iiv v  i  i  v      i-     v -i
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_115870179_    973 TTTAAAAGGCACTGCTACAAATGTGAAAAGGTGAGCCATGGGCTTGAAGA 1022
                           i   i i    iii vi  v        iii v   ii iv v i   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_115870179_   1023 AAATACTTGCAAAGCAAATATCTGAAAAATAACTTCTGTGTAGAATACCT 1072
                              i       v  v        v  ivi    v i vi      iv 
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_115870179_   1073 AAATTACCTTTACAGTTTAATTGTTAGAACACAAAAAACAGAATT--AAA 1120
                            vv  ii     ii i   vi v i  v     v   vv    --   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_115870179_   1121 ATGGGCAAAATATTTGAATAG----TTAACCAAAGA---CACTCAGGTAA 1163
                                  iv          ----  vv       ---i iv  ii ii
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_115870179_   1164 TAAATAAGCACATTAAGTGCTGCTTACTATCATTAGCCAT 1203
                         iv           v  iv v    i vi    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (102 / 77)
Gap_init rate = 0.03 (22 / 728), avg. gap size = 2.18 (48 / 22)  


3220 26.14 1.67 0.67  chrX_115880931_115887185.rev     4866  5764 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115880931_   4866 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4915
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115880931_   4916 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4965
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115880931_   4966 TACCAA-TGCCTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5012
                          v   i-       ii -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_115880931_   5013 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 5062
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_115880931_   5063 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5112
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_115880931_   5113 CTACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGAT 5162
                                  i   i    ii         i  v ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_115880931_   5163 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAC 5210
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_115880931_   5211 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGTGAAAGGATTC 5260
                         i vi    i  i     ivv  vv  i v  vv      v     i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_115880931_   5261 CCTGTTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5310
                         i  v  i  i   i          v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_115880931_   5311 TGAAACTGGATCCCTTTCTTACACCTTATACAAAAATCAATTCAAGATGG 5360
                             ii    i    vi  i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_115880931_   5361 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5410
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_115880931_   5411 CCTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5460
                          v    ?v v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_115880931_   5461 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5510
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_115880931_   5511 ATTAAACTAAAGAGCTTCTGCACTCTG-------CCATCAG---AGTGAA 5550
                           i   v v  i i   i  ii  iii------- i    i---      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_115880931_   5551 CAGGCAACCTACAAAGTGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5600
                         v  i     i   i i           v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_115880931_   5601 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5650
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_115880931_   5651 AAAACAAACAACCCCATCATAAAGTGGGCAAAGGACATGAACAGACACTT 5700
                           i     i     v  i?v   i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_115880931_   5701 CTCAAAAGAAGACATTTATGCAGCCAAAAATCACATGAAAAAATGGCTCA 5750
                            v        i  vi viii     v  v          i   -    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG-CTCA 894

  chrX_115880931_   5751 TCATCACTGGCCAT 5764
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  


2895 28.12 0.44 1.09  chrX_115895235_115897336      696  1609 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115895235_    696 TGGAAAAACAAACATTCCATGCTCATGGATAGGAAAAATCAATATCATCA 745
                               i i ---- i     i        v    i v i     ii i 
  L1M4_orf2#LINE/      1 TGGAAAGATA----TCCCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chrX_115895235_    746 AAATGACCATACTGCCCAAAGTAATTTATAGATTCAATGCTGTCCCAATC 795
                          i   i v     v      v i  i  i        i  vi    v   
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_115895235_    796 AAGCTACCA-TTGACTTTCAT-CAGAGAATTGGAAAAAACT-ACTTTAAA 842
                           iv v   -i  v    iv -    -     -- v  i  - iii    
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAA 143

  chrX_115895235_    843 TTTCTCATGGAACCAATAAAGAGCCTGCATAACCAAGACAATCCTACGCA 892
                         v   vi      viivv ii  v  v v   i    i      i iviv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_115895235_    893 AATGGAACATAGCTGCAGGCATCAGGCTACCTGACTTCAAACTATACTAC 942
                          ivi     v  i  v   vv   vi  v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_115895235_    943 AAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATACAT 992
                           i          i   i    ii         i iv ii i   i i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_115895235_    993 AGACCAATGGAACAAAACAGAGGCCTCAGAAATAATGCCACAGATCTACA 1042
                            i        i i  iv   ivii         vv   i v  i  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_115895235_   1043 ACCATCTAATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAACGAT 1092
                         ii  vi i  i  i     ivv  v   i vi vv           vi  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_115895235_   1093 TCCCTATTTAATAAATGGTGCTGGGAAAACTAGCTAGCCATATGCAGAAA 1142
                         vvi  v  i  i              v    i v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_115895235_   1143 GTTGAAACTGGATCCCTTCCTTACACCTTATACAATAATTAACTCCAGAT 1192
                         iv    ii    i    v   i     v       v         v i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_115895235_   1193 GGCTTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAA 1242
                           v i ?    i           v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_115895235_   1243 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGA 1291
                            v    ?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_115895235_   1292 CTAAAACACCAAAAGCAATGACAACAAAAGCCAAAATAGACAAATGGGAT 1341
                         v  vi            vvii         vv        i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_115895235_   1342 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGT 1391
                         i v  i   v v  i i   i  ii vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_115895235_   1392 CAACAGGCAACCTACAGAATGGGAGAAAACTTTTACAATCTATCCATCTG 1441
                         v  v  i     i                iv   i   vii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_115895235_   1442 ACAAAGGGCTAATATCCAGAATCTACAAAGAAATTAAACAAATTTACAAG 1491
                          i  i  i  vi          v  i      v ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_115895235_   1492 AAATAAAACAAACAACCCTATCAAAAAGTGGGTGAAGGATATGAACAGAC 1541
                            -  i     i     v  i?    i    ii      v    i    
  L1M4_orf2#LINE/    793 AAA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_115895235_   1542 ACTTCCCAAAGGAAGTCATTTATGCAGTCAACAAACATATGAAAAAAAAG 1591
                          i   i v  i    vi  vi viii i   i  i  i       i v- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-G 890

  chrX_115895235_   1592 CTCATTATCACTTGTCAT 1609
                             vi    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (150 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


2413 27.46 2.19 2.84  chrX_115939600_115943794.rev     2794  3707 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115939600_   2794 TAGAAAACT-TTCCATGCTTATGGATAGAAAAAAATCAATATTGTTAAAA 2842
                          i    iv - i     i i      v i  i v- i           i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chrX_115939600_   2843 TGGCCATACTACCTAAAGCAGAAGCAATTTACAGACTCATTGCTATACCT 2892
                             v     v  i   vii------  i      i   vi  v  v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTG------ATCTACAGATTCAACGCAATCCCT 93

  chrX_115939600_   2893 ATCAAACTACCAGTGACATTGTTCACATAATTAGAAAAAAAATCT-ATTC 2941
                               v v    ivi v  v  ii  v  v v  v  i----  -  i 
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCC 139

  chrX_115939600_   2942 TAAAATTCATAAGGAATCAAAAAAAAAAAAAAAACCTGAATAGCCAAAGC 2991
                                    v    ------- viv  iii v  v           i 
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAA-------ATGCAAGGGACCCAGAATAGCCAAAAC 182

  chrX_115939600_   2992 AATCCTAAGCAAAAAGAACAAAGATAGAGGCATCACACTACCCGACTTCA 3041
                             i i iv  i          v i    vv       v   i i    
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chrX_115939600_   3042 AACTATACTGCAAGGCTAGAGTAAGCCAAACAGCATTGTACTGGTGCAAA 3091
                           viv    i   i    v     v v i    ii v       iii  i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_115939600_   3092 AACAGACACATAGACCAATCAAACAGAAT--AGAGTCCAGAAATAAAGCT 3139
                         i i     i     i    vi  i     --                v i
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_115939600_   3140 GCACACCTACAGCTATCAT--ATCTTCAAAAAAATTGACAAA--CATAAG 3185
                         ii   ii  ii ii --  --  i   i v  iiv  v   i--   --v
  L1M4_orf2#LINE/    333 ATACATTTATGGTCA--ATTGATTTTCGACAAGGGTGCCAAGACCAT--T 378

  chrX_115939600_   3186 CAATGGGGAAAGGACTCCCTATTCTATAAATAATACTTGGATGACTGGGT 3235
                                     i ivvi  v   v i    ii i  v   ii     i 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_115939600_   3236 AGTGATG-GCAGAAGACTGAAACTGTACCAGTTTCTTAAACCACATATGA 3284
                          ?iv ii-   i    v    ii  v   vv vi  i v    i   ii 
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_115939600_   3285 AAATTAACTAAAGATGGATTAAAGATGTAAATTTAACACCTAAACCTGTA 3334
                                  v  i      i ?   iv     v   v v     v  i  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chrX_115939600_   3335 AAAATCCTTGAAGATAAGCTTGGAAATATTATTCT--GT-ACATAGTCTC 3381
                            v  i v     -  i v i i?i  -- v   --  -  v v vv i
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGA-AAACATAGGNGTA--AATCTTCGTGACCTTGGGTT 575

  chrX_115939600_   3382 TGGCAAAGATTTCATGACGAAGACTCCCAAAGCAATTGCAACAAAAACAA 3431
                         v     v i    v iivv v   v  v      vvv         iv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_115939600_   3432 AAATTGACAAATGGAACTT-----AAACTAAAGGGCTTCTGCACAGCAAA 3476
                             v  i    v i    -----   i    ii-   i  ii vv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAA 674

  chrX_115939600_   3477 AGAATCTATCAACGGAGTAAACAAACAACCTACTGAATGGGAGAAAATAT 3526
                         i  vv       vii   i  v i      i  v                
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_115939600_   3527 TTGCAAACTATGGATCCAACAGATGTCTAATATCCAGAATCTATAAGGAA 3576
                                ii  iv   ii i iiv v  vi          v     i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_115939600_   3577 TTTGAACAAATCAACAAACAAAAATTAAACAACCTCATTAAAAAGTGGTC 3626
                         i ivv    v    i  vv    ivi   i    iv   ?    i   v 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_115939600_   3627 AAAGGATATGAACAGACATGTTTCAAAAGA-GACATAGATGCAGCCAAAA 3675
                                v    i      v i  v     -  i   v viii     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_115939600_   3676 AGCATATAAAAA--TACTCAACAATATTCATCAT 3707
                             i  i    -- i       vi ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (140 / 107)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.30 (46 / 20)  


2928 25.71 1.94 1.60  chrX_115957036_115958902      500  1374 (493)    L1M4_orf2#LINE/L1       31   908 (0)  

  chrX_115957036_    500 AGAATCAATATTGTTAAAATGCTCACACCACACAAAGCAATCTACAGATT 549
                            v i           i   viv i  iv v    vii           
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATT 80

  chrX_115957036_    550 CAATGCAATCCCTACCAAAATACCAATTGACATTCTCCACAGAAATAGAG 599
                            i          i      v   ii  v -  i iii       v  v
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGAC 129

  chrX_115957036_    600 AAAACAATTCTAAAATTAGTACAAAATCACAAAAGACTGAGAATAGTCAA 649
                           ivii  i        vi  iii  vii   ii   iv       i   
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_115957036_    650 TGCTATGCTAAGCAAAAAGAACAAAACTGGAGGAATCACATTACCTGACT 699
                         vi v  vi i iv  i         ii       v     i v  ii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_115957036_    700 TTGAA--TTA-TACAAAAGAGCTATAGTAACCAAAACAGCATGGTACTGG 746
                          ii  --   -      ---    i     i   i    ii         
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAA---GCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_115957036_    747 TATAAAAACAGACACATCAGATACATATACTAATAGAAT---------AG 787
                         i    ii i     i  -    -  -  iv-        ---------  
  L1M4_orf2#LINE/    277 CATAAGGATAGACATAT-AGAT-CA-ATGG-AATAGAATTGAGAGTCCAG 322

  chrX_115957036_    788 AAAT----CTACACACCTACAGTGAATTAATTTTCAACAAAGGTGCCGAG 833
                             ---- i i   ii  ii  v    i      i    i      i  
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_115957036_    834 AACATACACTGGGGAAAAGACCATCTCTTTAATAAGTGGTGCTGAGAAAA 883
                          v   v  v        ii ivi   i  i  i  i        i  v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_115957036_    884 GTGGATGTCCATATGCAGAAGGATGAAACTAGGACACTTATCTCTCATCA 933
                         v     i?   i     i   i     ii -    v i  i   v  i  
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTT-GGACCCCTACCTCACACCA 471

  chrX_115957036_    934 TATACAGAAATAAAATCAGAAAGCATTAAAGACTTAAATTTAGTAACTCA 983
                               i    v  v   i  v v  i ?    i     v  iv i  v 
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_115957036_    984 AACTATGAAACTACTACTACAACAAAAACATTGAATAAAATCTCCAGGAT 1033
                               i     -  --  v  -i       v i?vv      i iv  i
  L1M4_orf2#LINE/    522 AACTATAAAACT-CT--TAGAA-GAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_115957036_   1034 ATTGGTTTTGGCAAAGATTTCTTGAGTAACACCCCACAAGCACAGGCAAC 1083
                         v    v  v     v i      iii  vv  v   v       i     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_115957036_   1084 CAAAGTAAAAATGGGCAAGTGAGATCACATCAAA-TTAAAAAGCTTCTGC 1132
                         v    v      i ii  i vi  iiv       -       -   i  i
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGT 666

  chrX_115957036_   1133 ATAGCAAAGGATCCAATCAGCAAAGTAAAGAGAAAATACACAGAATGGGA 1182
                         iivv       iv v    iv     i  i   v  iv            
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_115957036_   1183 GAAAATATTTGTAAACTGCTTTTCTGGTAAGTAATTAATAATCAGAATAT 1232
                                    i   iiiiv v    i    vi i vi  vi        
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_115957036_   1233 GTAAGGTGCACAAACAACACCATAGGAAAATATCTAATAATCCAACCCCA 1282
                         i   i vi v vv     v v   iv    viv v     i    ii?v 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_115957036_   1283 AAATGGGCAAAATATTTGAATACACATTTCTCAAAAGAAGACATACAAAT 1332
                                    iv         v         v        i        
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_115957036_   1333 GGCAGACAGGTATATGAAAAGGTGCTCAACATCACTGATCAT 1374
                            vi i i i i        i            ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (140 / 81)
Gap_init rate = 0.02 (16 / 878), avg. gap size = 1.94 (31 / 16)  


3001 26.38 1.09 2.50  chrX_115962950_115967165     2803  3723 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_115962950_   2803 TGGAAAGATAATTCATGTTCATGGATCGAGTGAATCAATATTGTCAA-AT 2851
                                   vii             i iiv  v i        i  -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_115962950_   2852 ATCCACACTACCTAAAGCAATATACAGATTCTATGCAATCTCCTTCAAAA 2901
                         iv v i   v  i   vii  v         v i      i iv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_115962950_   2902 TACCAATGATATTCATTACTGAAATAGAAAAA--AATGCTAAAATTTATA 2949
                          v   iiviiv  iv  i v     v  v  i--i  v        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_115962950_   2950 TGAAACCTCAAAAGACCTGGAATAGTCAAAGCTATCCTAAGCAAAAAGAA 2999
                           i  viv   ii    ii      i    i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_115962950_   3000 TAAAACTGGAGAAATCACATTACCTGACTTCAAATTATATGAAAGAGGTA 3049
                         i   ii     i v     i v  ii i      viv  iv v i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_115962950_   3050 TAGTAACCAAAACAGCATGGTACTTCCATAAAAACAGACACACAGACCAA 3099
                         i     i   i    ii       vv     ii i     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_115962950_   3100 TGGAACAGAATGGAGAACTCAGAAAAAAATTTACACACCTACAGTGAAGT 3149
                              i     v    iii      v   iii i   ii  ii  v  v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_115962950_   3150 AATTTTTGATAAGGGTGCCAAGAACATATACTGGGAAAA--AGAATCTCT 3197
                         i     i  i             v   vi v    i   -- v i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_115962950_   3198 TCAATAAATGGTGCTGGGTAAGCTGAATATTTATATGCAGAAGAGTAAAA 3247
                             i             vv i   i   ?ii i     i    i i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_115962950_   3248 CTGGATCTTTATCTGTTGTTGCATACAGAAATCAAATCAAAATGGATTAA 3297
                         i    i ii  i  vviiiiii     i    i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_115962950_   3298 AGACTTAAATCTAAGACTTTAAATTATGAAACTTCTACAGGATGTAATTG 3347
                             i     v     vi v   i   i     ii  v i  vivv  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_115962950_   3348 GAGAAAATCTCCAGGATATTTTCCAGGGCAAATTCTTCTCCAGGGCAAAG 3397
                          ? v      i iv  iv  -----   -------  -----i     v 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTT-----GGG-------TT-----AGGCAATG 583

  chrX_115962950_   3398 ATTTCTTAAGAAAT-ACCCCACAAGAACAGGCAACCAATGCAAAAATGGA 3446
                         i       -  v  -  v   v   v   i     v  v v      i  
  L1M4_orf2#LINE/    584 GTTTCTTA-GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_115962950_   3447 TAAATAGGATCACATGAAGTTATTATAAAAATCCTCTGCACATTAAAGAA 3496
                              v   iiv   v  i--    --    - i i  ii v i    i 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAA--ATTA--AAAA-CTTTTGTGCTTCAAAGGA 677

  chrX_115962950_   3497 AACAATCAACAAAATGAAAAGACAATCCACAGAATGGAAGAAAATATTTG 3546
                         v  v     v   i           i           i            
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_115962950_   3547 CAAACTACCCATCTGACTAGGGATGAATAACGAGAATATATAAAGACCTC 3596
                             ii ivi      iv     ivvi  v v              v   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_115962950_   3597 AACTAATGCTATAGGAAAAATTCTAATAATCTGATTTAAGA-TGGGCAAA 3645
                         vvvi  iv v   iv     vv v     i ii   ?  i -        
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_115962950_   3646 ATATTTAAATAGACATTTCTCAAAATAAGATATACAAATGGCAAACAGGC 3695
                         iv    i              v   v                v  i i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_115962950_   3696 ATATGAAAAGGTGATCA---TCAGAGAAATG 3723
                          i        i  v   ---   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (148 / 91)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.54 (33 / 13)  


 341 16.95 0.00 0.00  chrX_116026653_116030074     1775  1833 (1589)    L1M4_orf2#LINE/L1        1    59 (849)  

  chrX_116026653_   1775 TGGAAAAATATGCCACGTTTATGGATTGGAAGAATTAATATTGTTAAAAT 1824
                               i    v   i   i             v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116026653_   1825 GACCACGCT 1833
                          i v ii  
  L1M4_orf2#LINE/     51 GGCAATACT 59

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  

2781 24.53 4.46 2.23  chrX_116026653_116030074     2078  2929 (493)    L1M4_orf2#LINE/L1       38   908 (0)  

  chrX_116026653_   2078 ATATATTTAAAATGACTATACCACCTAAAGTGATCTACAGATTCAATGCA 2127
                             vv    i   i v    iv  i   v                i   
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chrX_116026653_   2128 ATCTCCATCAG--TTACAA-TGCCATTTTTTACAGAAATTTTAAAAAG-- 2172
                            i i    i-- iv  i-    -      i        --i v   --
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATT--GACAAGCT 134

  chrX_116026653_   2173 --TCCTAAAATAAGTATGAAACCTCAAGAGTTTCTGAA--------GCAA 2212
                         --         vvi    i  viv    i vii v   --------i   
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_116026653_   2213 TCTTGAACAAAAATAAATAAATAAATAAAATTGGAAGCCTCACATAGACC 2262
                                v  i  ---------i  i   i     i v      ivvv  
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAA---------GAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_116026653_   2263 AATCTTATAAATATACTAAAAAGCTATAGTAATAAAAACAGCATGATATT 2312
                            i i -   iv     v       i      v  i    ii  i  i 
  L1M4_orf2#LINE/    226 AATTTCA-AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_116026653_   2313 GGCATAA----AAACAGATAGACTAAGGAAACATAATAGAGAGCTCAGAA 2358
                                ---- i   v     ii  v i  i v   v     ii     
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_116026653_   2359 ATAAATCTACACATTTACTCTCATTTGACTTCCTACAATGATTCCCAAAA 2408
                              i i i       ivv   v    i  i v    v i v  v i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chrX_116026653_   2409 CACCCAA--GAGA-----CAGTCTCTTC--C-----GTGCCGGGAAAACT 2444
                           ii   -- i  -----i     i   -- -----    i    v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_116026653_   2445 GGATCTCCATATGCAGAATAATGAAATTAGGCCTTAATCTCACACTATAT 2494
                             v?   i     i  v      i  i i  iiv i       i    
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_116026653_   2495 ACAAAAATCAACTCAAAATGGATTAAAGATGTAAATGTAATACCCGAAAC 2544
                                 i              i ?   iv         v v ii    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_116026653_   2545 TGTAAAACTTTTAGAAAAACACATATG-GTAAAGCTCTATGACATTCATC 2593
                          i       i      i  v     v -     v  iii    v  vivi
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_116026653_   2594 TGGAAAATTATTTTTTGGATATGACTCCAAAAGCACAGGCAACAAAAGCA 2643
                          i iv   vi   i  i        v           i          v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_116026653_   2644 AAAATAGACAAATGGGATGACATCAAACATAAAAGCTCTTCCACAGCCAA 2693
                                 i    v   ivv       vv     i  i  vii vv v  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_116026653_   2694 GGAAATGATCAACAGAGTGAAGATGTGACCTACTATACAGGAAAAAATAT 2743
                            v iv     v i      i viii   i  viv ii   i       
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_116026653_   2744 TTGCAAACCATATAGCTGATAAGAAGTTAATGTCTAAAACATA--AGGAA 2791
                                i      v        iiii vi i  i i  i   -- i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_116026653_   2792 TTCAAACCACTTAATAG--AAAAGAAAAATCCCAAACACCTGATTACAAA 2839
                         i  vv  v   i    i--      v    ----   -- ii   ?v   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAAT----AAC--CCAATTWAAAA 818

  chrX_116026653_   2840 ATGAGCAAAGGATCTGAATAGACATTTCTCCAAAGAAACCATGAAAATAG 2889
                            i         i                       ivi  iv    i 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_116026653_   2890 CCACTAGGAATATGAAAACATCTTTATCATTACTAATCAT 2929
                            v  i v i       v  vi i v   i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (127 / 79)
Gap_init rate = 0.02 (18 / 871), avg. gap size = 3.17 (57 / 18)  


2767 27.29 2.46 0.89  chrX_116059481_116061127.rev      264  1157 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116059481_    264 TGCAAAAACATTCTATACTCATGCATAGGAAGAATCAATATCGTGAAAAT 313
                           v   i i  i i  ii     v  v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116059481_    314 GGCCATACTGCCCAAAGTAATTTATACATTGAGTGCTATCCCCATCGAGC 363
                            v     v      v i  i  i v   v ii  v     i   i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116059481_    364 TCCCATTGACTTTCTTCACAGAATTAGAAAAAAAACT-ACTTTAAATTTC 412
                              vivi i  i  ii     v v  v  i---  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_116059481_    413 ACATGGAACCAGAAAAGGGTCT-GTATATCCAAGACA--TTTCAAAGCCA 459
                          i      vi- v  i  ii i- v   v    i   --i  v   i-- 
  L1M4_orf2#LINE/    148 ATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA--A 194

  chrX_116059481_    460 AAAGTACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACA 509
                         i   v      i      vv    i  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_116059481_    510 AGGTTACATTAACCAAAACAGCATGGTACTTGTACCAAAACAGATATATA 559
                          i i    v   i   i    ii       v i iv ii i   i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_116059481_    560 GACCAATGGAATAGAACAGAGGCCTCAGAAATGACACCACACATGTACAT 609
                           i             iv   ivii       i vv   i    v  iiv
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_116059481_    610 CCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 659
                         i  vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_116059481_    660 CCCTATTTAATAAATTGTGTTGTGAAAACTGGCTAGACAGATGCAGAAAA 709
                         vi  v  i  i    v   i  v  v      v  ?v  v     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_116059481_    710 TTGAAACTGGACCCCTTCCTTACAACTTGTGCAAAAATTAACTCAAGGTG 759
                         v    ii         v   i   v v i i               ii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_116059481_    760 GATTA-AAACTTAAATGTAAGACCAAAAACCATAAAAACCCTAGAAGAAA 808
                            i - i  i           v v     i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_116059481_    809 ACCTAGGCA-ATACCACTCAGGACATAAGCATGGGCAAACACTT------ 851
                           v    ?i- v i -i  iv   v vi vv i     vvii  ------
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_116059481_    852 TATGACT---AAAGCAC------CAAAAGCCAAAATTGACAAATGGGATT 892
                               v---       ------      vv     v  i    v   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_116059481_    893 TAATTAAACTAAAAAGCTTCTGCAAAGCAAAAGAAACTATCATCAGAGTG 942
                          v  i   v v    i   i  iivvv    i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_116059481_    943 AACAGGCAACCTACAGAATGGGAGAAAATTTTGGCAATCTATCCATCTGA 992
                           v  i     i                 v  v    vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_116059481_    993 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTAGAAGA 1042
                         i  i  i  vi          v  i        ivv    v iv v  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_116059481_   1043 AAAAAACCAAACAACTCCATCAAAAAGTAGGCAAAGGATATGAACAGACA 1092
                             i  -   i   i v  i?    i i          v    i     
  L1M4_orf2#LINE/    794 AAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_116059481_   1093 CTTC-AAAAAGAAGAAATTTATGTGGCCAACAAACATATGAAAGAAAGCT 1141
                         i   -vv        v  vi vi       i  i  i      ii v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_116059481_   1142 CATCATCCCTCTTCAT 1157
                           v    v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (134 / 107)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


2801 25.47 2.88 2.33  chrX_116064600_116066774.rev      782  1684 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116064600_    782 TGGAAAAATATTCCATGCTCATGGATTGGAAGAATCAAT-TCATTGCAAT 830
                               i    i     i               v i   - ii  ivi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116064600_    831 GGCCACACTGCACAAAGCAATGTACAGATTCAATTCTATTTCTATAAAAC 880
                            v i   v v    vii  v           iv v  ii    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116064600_    881 TACCAACATCATTTTTCACAGAA-TTAGAAAGAAAAACT-ATTCTAAGAT 928
                          v   i vv v     ii     -  -----  v  i  -  i    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-----GACAAGCTGATCCTAAAAT 145

  chrX_116064600_    929 TCATATGGAAACAAACAAAATATAGGCCA-AATAGACAATATAATCCTAA 977
                                    ii--   iiv i---   -     v   v i    i i 
  L1M4_orf2#LINE/    146 TCATATGGAAATG--CAAGGGAC---CCAGAATAGCCAAAACAATCTTGA 190

  chrX_116064600_    978 ACAAAAAGAACAGAGCTGGAAGCATTACACTACTCGACTTCAAATTATAT 1027
                          v  i       i  i    i vv i     v i i i      viv  i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_116064600_   1028 TGCAATGCTATAGTAACTAAAACAATG--GTACTGGTATGAAAACAGACA 1075
                          i   v    i     ii  i   i  --       i  i ii i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_116064600_   1076 AATAGACTAATGGAATAGGTTATAGAACACAGAAATAAAGTCACACACCT 1125
                         v     ii          iv vv   iiv          vi  i   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_116064600_   1126 ACAACTACCTGATCTTCAACAAAGTTGACAATAACAAGCAACAGGGAAAG 1175
                          iiiii vi    i   i    i v  v   v v  vv   ii       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_116064600_   1176 ----GTCTCCCTATTAAACAAATTGTGCTGAGATAACTGGCCAGCTATAT 1221
                         ----    i----  v       v      i  i      vi ? i i  
  L1M4_orf2#LINE/    391 AATAGTCTT----TTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_116064600_   1222 GCAGAAGATTGAAGCTGGACCTCTTCCTTTCACCACATACAGAAATTAAC 1271
                            i    v     i      i  v   iv     i     i        
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_116064600_   1272 TCAAGATGGATTAAAGACTTAAATATAAAATCTAAAACTAT------CTT 1315
                             i      i ?    i     i   i v          ------   
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_116064600_   1316 AAAAGG---CCTATG---AAATGTCATTCTGGACATAGGCCTTGGCAAAG 1359
                          i   i--- v  v ---    -- -   vv   v v  vi v     v 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATG 583

  chrX_116064600_   1360 ATTTCGTGACAAAGTCTCCAAAAGCAATTGCAACAAAAATAAAAGTTGAC 1409
                         i    v iivv v v v         vvv         iv    i v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_116064600_   1410 AAGAGGGACCGAACTAAGCTAAAGAGCTTCTGCACAGTAAAAGGAC--TA 1457
                           ivv    ivv ii  iv v  i i   i  ii -v v       --  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTA 682

  chrX_116064600_   1458 TCAATAGATTAAACAGACAGCCAACAGAATGGGAGAAAATATTTGCAAAC 1507
                             v i v i  v     i  v                          i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_116064600_   1508 TATACATCTGACAAAGGTCTAATATTCCAAATCTATAAGCCATTTAAACA 1557
                         i   i      i  i  v  vi   i vi   v     ivv i ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_116064600_   1558 AATCAACAAGCAAAAAACAAACAGCGCCATCTAAAAAAAATGGGCAAGGG 1607
                          v    i  vv    i     i i -   vi ?     --       i  
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAAC-CCAATTWAAAAA--TGGGCAAAGG 829

  chrX_116064600_   1608 ACATGAACAGACATTTCTCAAAAGAAGACATACATGTGGCCAACAA--AC 1655
                          iv    i           v        i     vi       i  --  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_116064600_   1656 ATAAAAAACTGCTTAACATCACTAATCAT 1684
                           i    iv    i       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (133 / 94)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.35 (47 / 20)  


2849 27.14 1.89 0.89  chrX_116168385_116172810.rev     3037  3935 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116168385_   3037 TGGAAAAACTTTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3086
                               i iv i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116168385_   3087 GGCCAAAATGCCCAAAGTAATTTATAGATTCAACACTATCCCCATCAATC 3136
                            v v v v      v i  i  i         i v     i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116168385_   3137 TACCAGTGACTTTCTTCACA-AAATTAGAACAAATCTACTTTAAATTTCA 3185
                          v    ivi i  i  ii  -     i--    iiiv iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_116168385_   3186 TATGGCACCAAAAAAGACCACATATAGCCAAGACAATCTGAAGCAAAAAG 3235
                              v viiv  ii    vviv        i       vi iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_116168385_   3236 AAATAAGCCACAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGA 3285
                           vv   iiiv   vv    i  v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_116168385_   3286 TACAGTAACCCAAACTGCATGGTATTTGTACCAAAACAGGTATACAGACC 3335
                                 i v i  v ii     i v i iv ii i  ii   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_116168385_   3336 AATGGAATAGAACAGAGGCCTCAGAAATAACGCCACACATTTACAACCAT 3385
                                     iv   ivii         vv   i       iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_116168385_   3386 CTGATCTTTGACAAGCCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 3435
                         i    i  i      vv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_116168385_   3436 ATTTAACAAATGGTGTTAGGAAAACTGGCTAACCATATGCAGAAAACAAA 3485
                         v  i           i i   v      v  ?   i     i  i vvi 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_116168385_   3486 AACTGGATCCCTTCTTTACACTTTATACAAAAATTAACTCAAGATTCATT 3535
                          ii    i    v i i    iv                   i  vv  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_116168385_   3536 AAAGACTTAAACATAAGACCTAATACCATCAAAACCCT-AGAAAAAAACC 3584
                          ?    i    ii     v    v  i  -     i  -    i     v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACA 547

  chrX_116168385_   3585 --GAGGTAATACCATTCA-GAACATAGGTATGGGCAAAGGCTTCATGACA 3631
                         -- i?    - i -   i-  v v i   - i     v  i   v iivv
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_116168385_   3632 AAAACACCAAAAGCAACGGCAACAAAAGCCAAAATAGACAAATGGGATCT 3681
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_116168385_   3682 AATTAAACTAAAGAACTTCTGCAAAGCAAAAGAAACTATCATCAAAGTGA 3731
                         v  i   v v  i     i  iivvv    i  v       vv       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_116168385_   3732 ATAGGAAATCTACAGATTGGGAGAAAATTTTTGCAATCTATCTATCTGAC 3781
                          v  iv  i i     v           v       vii  v       i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_116168385_   3782 AAAGGGCTACTATCCAGAATCTACAAAA-----TTAAACAAATTTACAAG 3826
                           i  i  vv          v  i   i-----   --   v iv i  v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAAT 792

  chrX_116168385_   3827 AAAAAAA-----AACC--ATCAAAAAGTGGGCTAAGGATATGAACAGACA 3869
                              i -----    --  i?    i     v      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_116168385_   3870 CTTCTCAAAAGAAGACATTTATGGGACCAATAAATATATGAATAAATGCT 3919
                         i     v        i  vi viv i       ii i     v i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_116168385_   3920 CATCATCACTGGTCAT 3935
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (137 / 103)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.92 (25 / 13)  


3181 27.35 1.00 0.44  chrX_116176037_116182414     4983  5885 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116176037_   4983 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCAAGAAAAT 5032
                              ii i  i     i      i v      v i     iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116176037_   5033 GGCTATACTGCCCAAGGTAACTTATGGATTCAATGCCATTCCCATCGAGC 5082
                            v     v     iv i ii  ii       i  v  i  i   i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116176037_   5083 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5130
                          vi  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_116176037_   5131 TATGGAACCAAAAAGAGCCC-GCATCGCCAAGTCAATCCTAAGCCAGAAG 5179
                                viiv  i ii   - v  v     iv     i i ivv     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_116176037_   5180 AACAAAGCCGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5229
                                ii     vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_116176037_   5230 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5279
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_116176037_   5280 AATGGCACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5327
                              v i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_116176037_   5328 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5377
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_116176037_   5378 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5427
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_116176037_   5428 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5477
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_116176037_   5478 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5527
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_116176037_   5528 CTAGGCGTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5577
                         v    ?  v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_116176037_   5578 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5627
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_116176037_   5628 TGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5677
                          v   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_116176037_   5678 GGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5727
                         i i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_116176037_   5728 AGGGCTGATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5777
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_116176037_   5778 AAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5823
                          i    ----   v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_116176037_   5824 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5873
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_116176037_   5874 ATCACTGGCCAT 5885
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (148 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2972 28.41 0.44 0.44  chrX_116183420_116190099     5281  6188 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116183420_   5281 TGGAAAAACATTCCATGCTCATGGAGAGGAAGAATCAATATCATGAAAAT 5330
                               i i  i     i       vv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116183420_   5331 GACCATAATACCCAAAGTAATTTATAGATTCAATGCTATCTCCATCAACC 5380
                          i v   v v      v i  i  i        i  v   i i     vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116183420_   5381 TACCATTGACTTTCTTCACAGAATTATAAAAAACT-ACTTTAAATTTTAC 5429
                          v   vivi i  i  ii     v - i v  i  - iii    v  i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_116183420_   5430 AGGGAACCAAAAAAGAGCCCGTATAGCCAAGGCACTCCTAAGCAAAAAGA 5479
                          v    viiv  ii  v  v v        ii  v  i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_116183420_   5480 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGGCT 5529
                               i      vv   ii  v  ii i      vivi       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_116183420_   5530 ATGGTAACCAAAACAGCATGGTACTGGTATCAAAACAGATATATAGACCA 5579
                          ii    i   i    ii         i  v ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_116183420_   5580 ATGGAACAGAATAGAGGCCTCAGAAATAACGCCACACATCTACAACCATC 5629
                               i     v   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_116183420_   5630 TGATCTTTGACTAACCTGACAAAAGCAATCAATGGGGAAAAAATTCTCTA 5679
                             i  i   v ivv  v   i v  v            i   vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_116183420_   5680 TTTAATAAATAGTGTTAGGAAAACTCGCTAACCATATGCAGAAAACAGAA 5729
                           i  i    i   i i   v    v v  ?   i     i  i vv   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_116183420_   5730 ACTGGATCCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGATTA 5779
                         ii    i    v   i    iv                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_116183420_   5780 AAGACTTAAACATAAGACCGAATACCATCAAAACCCT-AGAGAAAAACCT 5828
                         ?    i    ii     v v  v  i  -     i  -   ii     v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chrX_116183420_   5829 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGGCTTCATGACAAAA 5877
                            ?i- v i -   iv   v v  vv i     v  i   v iivv vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_116183420_   5878 ACACCAAAAGCAATGGTAACAAAAACCAAAATAGACAAATGGGATCTAAC 5927
                                     vvi i       ivv        i    v   ii v i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_116183420_   5928 TAAACTAAAGTGCTTCTGCACAGCAAAAGAAACTATCCTCAGAGTGAACA 5977
                         i   v v  ivi   i  ii vv    i  v      vvv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_116183420_   5978 CGCAACCTACAGAATGGGAGAAAAT-TTTTCAATCTATCCATCTGACAAA 6026
                         vi     i                 -   v   vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_116183420_   6027 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 6076
                           i  vi          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_116183420_   6077 AACAAACAACCTCATCAAAAAGTAGGCAAAGGATATGAACATACACTTCT 6126
                         i     i    iv  i?    i i          v    i v   i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_116183420_   6127 CAAAAGAAGACATTTATGTGTTCAATGAACATATGAAAAAAAAGCTTATC 6176
                          v        i  vi vi  vi    i i  i       i v-   i v 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAAC 896

  chrX_116183420_   6177 ATCGCTGGTCAT 6188
                            i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (151 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.00 (8 / 8)  


 904 28.86 0.00 2.35  chrX_116213850_116216181.rev      627   924 (1408)    L1M4_orf2#LINE/L1        1   291 (617)  

  chrX_116213850_    627 TGAAAAAACATTTCATGATCATGGATAGGAAGAATCAACATTGTTTAGAT 676
                           i   i i  ii    v        v      v i  i      v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116213850_    677 GGACATCCTGCAGAAAGCAATGTACGGAGTCAATGCTGTTCCTATTAAAC 726
                           vv  v  v vv   vii  v   i  v    i  vi i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116213850_    727 TACCAATGACATTCTTGACAGAATTAGAAAAAAATCAACTTTAAAATTTA 776
                          v   iivi v  i  vi     v v  v  i--iii iii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_116213850_    777 AACGGAACCAAAAAAGAGCCCGAATAGCCAAGACAATCCTAAGAAAAAAA 826
                         v i    viiv  ii  v  v          i      i i -----   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-----AAA 193

  chrX_116213850_    827 AAAAAAAAAAAGCTGAAGGTATCACATTACCCAAATTCAAACCATACCAC 876
                          i  i  v    i  i   vv     i v     v      v v   i  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_116213850_    877 AAGGCTACAGTAACCAAAACAGCACGATACTGGTATAAAAACAGACAT 924
                           i          i   i    iii i      i    ii i      
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

Transitions / transversions = 1.53 (52 / 34)
Gap_init rate = 0.01 (2 / 291), avg. gap size = 3.50 (7 / 2)  

1917 26.86 2.27 0.49  chrX_116213850_116216181.rev     1224  1841 (491)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_116213850_   1224 AAAAAAAGACACATGGACCGATGGAACAGAGTAGAGAGCACAGAAATAAA 1273
                           ii v     i  i  i i      i   i v     iv          
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_116213850_   1274 GCCATACACCT-CAATCATTTGATCTTTGACAAAGCTAACAAAAACAAGC 1322
                         v       ii -iii   v     i  i     i v iv   i v  vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_116213850_   1323 AATGGGGAAATGACTTTCTATTCAGTAAATAGTGGTAGGATAACTGGCTA 1372
                                   vi ivv   v    ii    i   v i   i      v  
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_116213850_   1373 ACCATATGCAGAAGATTGAAAATGTATCATTTCCTTTCACCATATACAGA 1422
                         ?   i     i    v    iv  v i vi v   iv           i 
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_116213850_   1423 AACCAATTCAAGGTGCATTATAGAC--AAATGTGAAACCCAAAGCTATAA 1470
                           ii  i    ii  v  i ?    --      i i v i   i      
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_116213850_   1471 AGACTCT-AGAAGTAAAC-TAGGAAGTACAT--TCTGGACATAGGCCCTG 1516
                          -     -     v    -    ?-   v  --  vv   v v  viiv 
  L1M4_orf2#LINE/    530 A-ACTCTTAGAAGAAAACATAGGN-GTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_116213850_   1517 GCAAAGATTTCAT-GATAAGGAC-TCAAATGCAATTGTAACAACAACAAA 1564
                             v i    v -    -v   -i    v   vvv i     v iv   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_116213850_   1565 AATTGACAAGTAGGACCTAATTTTA-CTAAGAGCTTCTGCACAGCTAAAG 1613
                            v  i  i v    i v  ivv -i   i i   i  ii vv v  i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_116213850_   1614 AAACTATCAACAGAGTAAACATATGACTTACAGAATGGGCGAAAATATTT 1663
                          v        v i   i  v v ii  ii          v          
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_116213850_   1664 GCAAACTATGCATTTGACAAAGATCTAATATCCAGCATCTATAAGCAACT 1713
                              ii  ii  i   i  i iv  vi       v  v     iv    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_116213850_   1714 T----AAATCAACAAGCAAGAAACAAACAACCCCATTGAAAAATGGGCAA 1759
                         i----  v    i  vv  i i     i     v   ?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_116213850_   1760 AGAACATGAACATACACTTTTGAAAAGAAGACATACATGTGGCCAACAAG 1809
                           i iv    i v   i  i vv        i     vi       i   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_116213850_   1810 CATATGAAAAAACGATCAACATTACTGATCAT 1841
                           i       i i v       i ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (93 / 69)
Gap_init rate = 0.02 (12 / 629), avg. gap size = 1.42 (17 / 12)  


3234 25.44 1.33 0.88  chrX_116268703_116272894.rev     2798  3701 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116268703_   2798 TGGAGAAATATTTCATTTTCATGGATTGGAAAAATCAATATTGTTAAAAT 2847
                             i i    ii   v              i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116268703_   2848 GTTCATAGTACCCGAAGC-ATCAACAGATTCAATGCCATCCCTATCAAAA 2896
                          viv   v v   i  vi-   v          i  v             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116268703_   2897 TACAAATGACATTCTCTACAGAAATAGAAAAAATTTTCCTAAAATTTATA 2946
                          v v iivi v  i i i       v  v  iv vv          i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116268703_   2947 TGGAATCACAAAAGACCTAGAATAGCCAAAGCTATCCTAAGAAAAAAGAA 2996
                              vii   ii    i            i v   i i i   i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_116268703_   2997 -AAAACTGGAACAATCACATTGCCTGACTTCAAATTATGCTACAGATGGA 3045
                         -   ii    iv v     i v  ii i      viv i     i ----
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA---- 246

  chrX_116268703_   3046 GCTATAGTAACCAAAACAGCATGGTATTGGCATAAA-ACAGGTACACAGA 3094
                             i     i   i    ii     i        i- i  ii i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_116268703_   3095 TAAATGGAACAGAATAGAGAACCCAGAAACAAATTCACACACCTCCAGTG 3144
                          v       i     v    ii       i   ii  i   ii vii  v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_116268703_   3145 AGCTCATTTTTGACAGAAGTTGCAAGAACATACACTGGGGACAT--TAGT 3192
                          ii v     i    iii  vv     v   v  v      v v--    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_116268703_   3193 CTGTTCAATAAATAGTGATGGGAAAACTGGATATCCATATGTAGAAGGAT 3242
                           v     i    i   v     v         ?   i   i i   i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_116268703_   3243 GAAAGTAGACCCCTATCTCCTACCATATACAAAAATCAAATCAAAATGAA 3292
                            iv i        i   vi               i  v        i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_116268703_   3293 TGAAATACTTAAATCTATGACATCCAACCTTGAAACTACTACAAGAAAAC 3342
                          v ? v  i     v  v  vv vv   iv i     vi  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_116268703_   3343 ATTGGGAAAAATCTCCAGGACATTGGTCTGGGCAAAAATTTCTTGAGGAA 3392
                           v  ?iv      i iv   v    vi i     vii      -  iv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATA 595

  chrX_116268703_   3393 T-AGACCACAAGCATAGGCAGCTAAGGCGAAATTGTACAAATGGGATCAC 3441
                          - v    v     i i   i v  i vi   v iv i    v   iiv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_116268703_   3442 AGCAGG-TTAATAAGCTTCTGTACAGCAAATGATACAATCAC-AAAGTGA 3489
                          v  ii-    -  i   i   i vv    v  i  v    v-       
  L1M4_orf2#LINE/    646 ATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_116268703_   3490 AGAGACAACCCACAGAATGGGAGAAAATATTTGCAAACTATCCATTTGAC 3539
                          i                                   ii  vi  i   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_116268703_   3540 AAAAGATTAATCACCAGAATATATAAGGAGCTCAAACAACTCTATAGGGA 3589
                           ii  i vi vv             i  i   vv       v   ivi 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_116268703_   3590 AAAATCTAAGTTGATCAAA---AAAAATGGGCAAAAGATCTGAATAGACA 3636
                            iv v  -- i i v  ---             i   i          
  L1M4_orf2#LINE/    795 AAAGACAAA--TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_116268703_   3637 TTTCTT-ACAGAAGACATAGAAATGCAAAACAGGCATACGAAAAAGTACT 3685
                              i- v      i   v     vvv  i i   i i     ii i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_116268703_   3686 CAGCATCACTGATCAT 3701
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (136 / 91)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.54 (20 / 13)  


1525 27.70 2.60 0.93  chrX_116275157_116279031      497  1034 (2841)    L1M4_orf2#LINE/L1      289   835 (73)  

  chrX_116275157_    497 CACATAGACCAATGAAATAAAATAGAGAACCCAGAAATAAGGCAGCACAC 546
                           i     i     i    i   v    ii          iv vii   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_116275157_    547 CTACAGCCATCTGACCTTTGGCAACCCTGACAAAAATAAGCAATGGTGAA 596
                         i  ii i  vi   ii  i i   vvv  v   i vi vv      v   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_116275157_    597 AGGACTCCCTATTTAATAAATGGTGCTGGGAGAACTGACTAGCCATCTGC 646
                           i ivvi  v  i  i              v     iv  ?   iv   
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_116275157_    647 AGAAAATTGAAACTAGACCCCTTTCTTATACCATATACAAAAATCAACTC 696
                          i  i v    ii i       vi  i i               i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_116275157_    697 AAAATGGATTAAAGAGTTAAATGTAAAACCCACAACTATAAAAACTCT-G 745
                                  i ?   vi         i v i v          -    -i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTA 537

  chrX_116275157_    746 GAAAACAACCTAGGCA-ATATCATTCAGGACATAGGCAT-GGAAAAGATT 793
                            i v   v    ?i- v   -   iv   v v  vv -  v  v i  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_116275157_    794 TCATGAAAAAGACACTGAAAGCAATCA--CAACAAAAGTCAAAACTGACA 841
                           v ii v v     ii      --  --         vv    iv  i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATA 634

  chrX_116275157_    842 AATGTAATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATC 891
                            vvi ii v  i   v v  i i   i  ii vv    iv v      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_116275157_    892 AACAGAGTAAACAGACAACCTACAAAATGGGAGAACATTTTTGCAATCTA 941
                           v i   i  v        i   i          v  v       vii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_116275157_    942 TGCGTCTGACAAAGGTGTAATATCCAGCATCTATAAGAAAC----ATAAG 987
                          iii     i  i  vv vi       v  v     ii   ---- i  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_116275157_    988 CAAAT--TTACAAGAAAAAAAAC---ATTAAAAAGTGGGCAAAGAACATT 1032
                         iv   -- v v    v   v   ---   ?    i         i i-  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TT 833

  chrX_116275157_   1033 GA 1034
                           
  L1M4_orf2#LINE/    834 GA 835

Transitions / transversions = 1.27 (81 / 64)
Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.73 (19 / 11)  

 311 26.21 0.00 2.91  chrX_116275157_116279031     3280  3382 (493)    L1M4_orf2#LINE/L1      809   908 (0)  

  chrX_116275157_   3280 CAGCTTGAAAATGGACTAATACAGACATGAACCAATACTTCTCAAAAGAA 3329
                           ii ?i       i v  ---i  iv    ivi i i     v      
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAA---GGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_116275157_   3330 GACACACATGCAGCCAACAAGCATGTGAAAAAAAGCTCACCATCACTGAT 3379
                           i i   viii     i     ii      i v     v     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_116275157_   3380 TAT 3382
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.71 (19 / 7)
Gap_init rate = 0.01 (1 / 100), avg. gap size = 3.00 (3 / 1)  


2757 27.57 1.90 0.67  chrX_116325496_116330770     3887  4782 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_116325496_   3887 GGAATAAACATTCCATGTTCACGAACAGGAATAATCAATATTGTTAA-AG 3935
                             - i i  i         i i iv    v v i           - v
  L1M4_orf2#LINE/      2 GGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116325496_   3936 GGCCATACTTCCCAAAGCAATTTATAGATTCAATGTTATTCTTATCAAAC 3985
                            v     i      vii  i  i        i iv  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116325496_   3986 TACCAATGACATTCTTCACAGAACTAGACAAAACT-ATTTTAAAATTCAC 4034
                          v   iivi v  i  ii     v v     i-  -  ii         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_116325496_   4035 ATG-AAACAAAAAAGAGCCTGAGTAGCCAAGGAAATCCTAAGCAAAAAGA 4083
                            -   iiv  ii  v  v  i       iiv    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_116325496_   4084 ACAAATCTGGAAGCATCACACCACCTGACTTTA-----TACTACAAAGCT 4128
                              vi    i vv      iv  ii i  i -----            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_116325496_   4129 ACAGTAACCAAAACAGCATGGTAATAGTACACAATCAGGTGCATAGACCA 4178
                                i   i    ii     v i i i viivi  iiii     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_116325496_   4179 ATGGAACAGAATAGACAGCCCAGCAATAAGGCCACACACCTATAGCCATC 4228
                               i     v  v  i    v     iv   i   ii   i i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_116325496_   4229 TGATCTTCCACAAAACTAACAAAAAAAG-CAATGGGGAAGAGATC-TCAA 4276
                             i   v    iiv iv   i vv v-          iii  v-  vv
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_116325496_   4277 TTCAATAAATGGTTCTGGGATAACTGGCTCAACAAATGCAGAAGACTGAA 4326
                              i       v      i      v v?v  v     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_116325496_   4327 GTTGCACCCCTTCCTTACACCTTATACAAAAATGAACTCAAAATGGATTA 4376
                             v      v   i     v           v              i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_116325496_   4377 AAGACTTAAAT-TAAAAAAACCCAAAACTATAAAAACCCTGGAAGATAAC 4425
                         ?    i     -   i i--- i            vi i i     v   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAG---CTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_116325496_   4426 CTAGGCA-ATATCCTCCTAGACATAGGAATGGACAAACATTTCATGTGGA 4474
                         v    ?i- v   i  v -   v v  iv i i   vvi    v iviv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_116325496_   4475 AGATATCAAAAGCAATTGCACCAAATTAAAAATT-GACAAATGGGATTGA 4523
                         v  i i        vvv   v    vv     v -  i    v   i vv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_116325496_   4524 ATTAAACTAAAGAGATTCTGCAAAGCAAAAGAAACTGTCAACAGAGTAAA 4573
                           i   v v  i iv  i  iivvv    i  v   i    v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_116325496_   4574 CAAGCAACCTATATAATGGGAGAAAATTTTCGCAAACTATGCGTCTGACA 4623
                         v ii     i i v             v  i     ii  iii     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_116325496_   4624 AAGGTCTAATATCCACCATCTGTAAGGTACATAAACAAATTTACAAGAAA 4673
                          i  v  vi      vv  v i   i v  vivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_116325496_   4674 AAAACAAACAGCCTCATTAAAAAGTGGGCAAAGGACATGAA----CACTT 4719
                           i     i i  iv   ?    i           iv    ----  i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_116325496_   4720 TTCAAAAGAAGACATACATGTGGCCAAAAAGCATATGAATAAAAGCTCAA 4769
                         i  v        i     vi       v     i     v i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_116325496_   4770 CATCACTGATAAT 4782
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 1.64 (23 / 14)  


3040 27.91 0.89 0.33  chrX_116332034_116333857.rev      431  1333 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116332034_    431 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 480
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116332034_    481 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGATATACCCATCAAGC 530
                            v     v      v i  i  i        i vv  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116332034_    531 TATTATTGACATTTTTCACAGAATTAGAAAAAAGCT-ACTTTAAATTTTG 579
                          vii vivi v     ii     v v  v  --   - iii    v  ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chrX_116332034_    580 TATGGAACCATAAAAGAGCCCGTATAGCCAAGACAATCCTAAGCAA-AAG 628
                                viii  ii  v  v v        i      i i iv  -   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_116332034_    629 AACGAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 678
                            i   i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_116332034_    679 TACAGTTACCAAAACAGTATGGCACTGGTAACAAAACAGATATATAGACC 728
                               v i   i     i   i     i vv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_116332034_    729 AATGGAACAGAGTAGAGGCCTCAGAAATAGCACCACACATCTACAACCAT 778
                                i   i v   ivii        ivv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_116332034_    779 CTGATCTTTGACAAACCTGACAAAAGCAAGCAATGGGAAAAATATTCCCT 828
                         i    i  i     ivv  v   i v  vv       i   iv  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_116332034_    829 ATTTAATAAATGATGTTGGGAAAATTGTATAGCTATATGGAGAAAACTGA 878
                         v  i  i     i  i     v  i  v   ? i i   v i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_116332034_    879 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAGT 928
                          ii         v   i     v                   i     vi
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_116332034_    929 AAAGACTTAAATGTAGGACCTAAAACCATAAAAAGCATAGAAAAAACCCT 978
                          ?    i        i  v       i      vv v     i   v v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_116332034_    979 AGACA-ATACCATTTAAGACATAGGCATGGGCAAAGACTTCATGACTAAA 1027
                           i?i- v i -  iiv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_116332034_   1028 ACACGAAAAGCAATGGCAACAAAAGCCAAAATTGGCCAATGGGATCTAAT 1077
                             v       vvi          vv     v iiv   v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_116332034_   1078 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 1127
                         i   v v  i i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_116332034_   1128 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 1177
                          i     i                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_116332034_   1178 GGGCTAATATCCAGAATCTACAAAGAACTTAAATAAATTTACAAGAAAAA 1227
                           i  vi          v  i        ivv i  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_116332034_   1228 -----ACAACCCCATCAAAAAGTGGGCAAAGGAGATGAACAGACACTACT 1272
                         ----- i     v  i?    i           vv    i     i v  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_116332034_   1273 CAAAAGAAGACATTTATGCAACCAACAAACATATGAAAAAAAGCTCATCA 1322
                          v        i  vi viiii    i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_116332034_   1323 TCACTTGTCAT 1333
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (143 / 105)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


 817 21.86 6.07 1.21  chrX_116358500_116365171       15   261 (6411)    L1M4_orf2#LINE/L1      650   908 (0)  

  chrX_116358500_     15 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAT-----GACTAAACAG 59
                            i    i -   i  ii vv    i  v     -----i v i  v  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_116358500_     60 ACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGAATCTGATAAAT 109
                               i                          ii  iv         iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_116358500_    110 GTCTAATATTCAAAATTTATAAG---------CAACTTAA-AACAAAAAG 149
                          v  vi   i  i   v     i---------     i  -  i      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_116358500_    150 CAAAAAAGAACCCCATTAAAAAGTGGGTAGAGGACATTAACAGACACATT 199
                         -- v   v     v   ?    i    i i    iv v  i     iv i
  L1M4_orf2#LINE/    799 --ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_116358500_    200 TTGAAAGAAGACATACATATGGACAACAAGCATATGAAAAAATGCTCATC 249
                          iv        i     v    v   i     i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_116358500_    250 ACTAACCATTAG 261
                          ii ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (33 / 20)
Gap_init rate = 0.02 (5 / 259), avg. gap size = 3.60 (18 / 5)  

2841 28.19 1.33 0.78  chrX_116358500_116365171     5279  6179 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_116358500_   5279 GAAAAACATTTTGTGCTCACGCATAGGAAGAATCAATATCATGAAAATGG 5328
                             i i  iiii  i   i v  v      v i     ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_116358500_   5329 CCATACTTCCCAAAGTAATTTATAGATTCAATGTTATCCCCATCAAGCTA 5378
                          v     i      v i  i  i        i iv     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_116358500_   5379 CCA-CTGACTTTCTTTACAGAA-TTGGAAAAAAACT-ACTTTAAACTTCA 5425
                            -   v    -   i     -   --- v  i  - iii    v    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTT-TTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCA 148

  chrX_116358500_   5426 TATGGAACAAAAAAAGAGCCCATA-TAACCAAAACAATCATAAGCAAAAA 5474
                                - viv  i ii    v -  i           v i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_116358500_   5475 GAACAAAGCTGGAGGCATCCTGACTACCTGACTTCAAACTATACTACAAG 5524
                                 i      - ii vv   v  ii i      viv        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_116358500_   5525 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATACAGA 5574
                                   i   i    ii         i iv ii i   i   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_116358500_   5575 CCAGGGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACC 5624
                         i  iv    i    iv   ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_116358500_   5625 ATCTGATCTTTGACAAACCTGGCACAAATAAGCAATAGGGAAATGATTCC 5674
                          vi    i  i     ivv  v  vi vi vv    i      vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_116358500_   5675 CTATTTAATAAATGGTGTTGGGAACACTGGCTAGCCATATGCAGACAACT 5724
                           v  i  i        i     vv     v  ?   i     i vi v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_116358500_   5725 GAAACTGGACCCCTTCCTTACACCTTATGTAAAAGTTAACTCAAGATGGA 5774
                            ii         v   i     v   ii    i         i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_116358500_   5775 GTAAAGACTTGAATGTAAGACCCAAAACCATAAAAACCCTAGAAGAAAAC 5824
                         vi ?    i i         v i     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_116358500_   5825 CTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTA 5873
                         v i  ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_116358500_   5874 AAACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGAGAAATGGGATCTA 5923
                         vi            vvi   i      vv     v  v    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_116358500_   5924 ACTAAACTAAAGAGCTTCTGCACAGCAAAGAA-ACTATCATCGGAGTCAA 5972
                          ii   v v  i i   i  ii vv     i -       vvii   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_116358500_   5973 CAGGCAACACACAGAATGTGTGAAAACTTTTGCAATCTGTCCAT-TAACA 6021
                         v  i    v         v v     iv       viii vi  - i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_116358500_   6022 AAGGGCTAATATCTAGAATCTACAAAGAACTTAAACAAATTTACAAGAGA 6071
                          i  i  vi    i     v  i        ivv    v iv i  v i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_116358500_   6072 AAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 6117
                           i    ----   v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_116358500_   6118 CTCAAAGGAAGACACTTATGCAGCCAACAAACATATGAAAA-ATAGTCAT 6166
                            v  i     i ivi viii     i  i  i       -  iv   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_116358500_   6167 CATCACTGTTCAT 6179
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (152 / 98)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 1.36 (19 / 14)  


1505 26.13 0.50 1.26  chrX_116378297_116383862.rev       35   432 (5134)    L1M4_orf2#LINE/L1        1   395 (513)  

  chrX_116378297_     35 TGGAAAAGTATTCCATGTTTATGCATTGGAAGAATCAATATGGTTAAAAT 84
                               ii   i       i   v         v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116378297_     85 GTCCATACTACCCAAAGTGATCTAGAGATTCAATGAAATCCCTATCAAAA 134
                          v v     v      v       v        i v              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116378297_    135 TACAAAGGACATCCTTCACAGAAATAGAGAAAC-AATTCTAAAATGTATA 183
                          v v ivvi v ii  ii       v  v  i -i  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116378297_    184 TGGAACCACGAAAGGCCCAGAATATCCAAAGCTAACCTAAGCAAACAGAA 233
                              vii i ii i         v     i v v i i iv  iv    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_116378297_    234 CAAAACTGGAAGAAGCATATTACCTGATTTCAAATTATACTACACACCTA 283
                             ii    i  vv  i i v  ii        viv       v v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_116378297_    284 TGGTACCCAAAACAGCATGATGCTGGCATAAAAACAGACACATAGCTCAA 333
                         ii   vi   i    ii  i i         ii i     i    v    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_116378297_    334 TGGAACAGAATAGAGAACCTAGAAACAAATCCACATACCTATACTGAACT 383
                              i     v    ii i     i   i   i i ii   iv v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_116378297_    384 GATTTTCAACAAGG-TATCAAAAACATACAGTGGGAAGATGGCCGAATAG 432
                                i      - ii   i v   v  i    i i -----      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-----GAATAG 395

Transitions / transversions = 1.81 (67 / 37)
Gap_init rate = 0.01 (3 / 395), avg. gap size = 2.33 (7 / 3)  

3010 26.70 1.67 0.67  chrX_116378297_116383862.rev     4177  5075 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116378297_   4177 TGGAAAAACATTTCATCTTCACAGATAGGAAGAATCAATATCGTGAAAAT 4226
                               i i  ii   v    ii   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116378297_   4227 GGCCATACTGACCAAAGTAATTTATAAATTCAATGCTATCCCCATCAAGC 4276
                            v     vv     v i  i  i i      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116378297_   4277 TACCA-CTGACTTTCTTCACAGAATTGGAAAACACT-ACTTTAAACTTCC 4324
                          v   -   v    i  -i     v v  v  -i  - iii    v   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_116378297_   4325 -----AAA---AAGAG--CTTGCATAGCCAAGACAATCCTGGGCAAGAAG 4364
                         -----   ---   i -- iv v        i      i  iiv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_116378297_   4365 AACCAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTATAAGGC 4414
                            v   i      vv    i  v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_116378297_   4415 TACAGTAACCAAAAGAGCATGGTACTGATAACAAAACAGATATATAGACC 4464
                                 i   i v  ii        ii vv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_116378297_   4465 AATGGAATAGAACAGAGGCCTCAGAAATAACACCACGCATCTACAACCAT 4514
                                     iv   ivii         vv   ii   i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_116378297_   4515 CTGATATTTGACAAACCTTTCACAAACAAGCAATGGGGAAAAGAATC-CC 4563
                         i    v  i     ivv vi  vi v  vv           -    v-i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTC 397

  chrX_116378297_   4564 TATTTAATAAATGTTGTTGGGAAAATTGGCTAGCTACATGCAGAAAACTG 4613
                          v  i  i     v  i     v  i   v  ? i       i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_116378297_   4614 AAACTGGACCCCTTCCTTACACTTTATACAAAAATCAACTCAAGATGGAT 4663
                           ii         v   i    iv           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_116378297_   4664 CAAAGACTTAAATGTGAGACCTAGGACCATAAAAAATCCTGGAAGAAAAC 4713
                           ?    i       i   v   ii  i      v-  i i         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAAC 546

  chrX_116378297_   4714 CTGGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATATGTA 4762
                         v i  ?i- v i -   iv   v v  vv i     v ii   v  vi  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_116378297_   4763 AAACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATGTA 4812
                         vi            vvi   i      vv     v  i    v   iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_116378297_   4813 ATTAAACTGAAGAGCTTCTGCACAGCAAAATAAAGTATCCTCAGAGTGAA 4862
                           i   v v  i i   i  ii vv    iv v v    vvv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_116378297_   4863 CAGGCAACCTACAGAATGGGAGAAAATTTTTTGCAATCTAGCCATCTGTC 4912
                         v  i     i                 v   -    vii vvi     vi
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTT-GCAAATCATATATCTGAT 744

  chrX_116378297_   4913 AGAGGGCTAATATCCAGAATCTACAAA-AACTTAAATAAATTTACAAGAA 4961
                          ii  i  vi          v  i   -    ivv i  v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_116378297_   4962 AAAAACAAACAACCCCATCAAGAAGTGGGCAAAGGATATGAACAGACACT 5011
                            i     i     v  i? i  i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_116378297_   5012 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5061
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_116378297_   5062 TCATCACTGGCCAT 5075
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (136 / 100)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


1023 24.83 3.31 0.33  chrX_116413857_116419088     2195  2496 (2736)    L1M4_orf2#LINE/L1      598   908 (0)  

  chrX_116413857_   2195 ACATCAAAGGCAATTGCAACAAAAGCAAAAATTGACAAATGAGATGTTAC 2244
                            i    i   vvv          v      v  i    vi  iv i i
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_116413857_   2245 TAAAACTAAAAAGCTTCTGCACAGCAAAAGAAACTATTATCAGAGTGAAC 2294
                         i    i      -   i  ii vv    i  v     i vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_116413857_   2295 AGACAACCTACAGAATGGGAGAAAGCTTTTGCAATCTATCCATCTGACAA 2344
                                 i               iiv       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_116413857_   2345 AAGTCTAATATCCAGAATCTACAAGGAACTTAAGCAAATTTACAAGAAAA 2394
                         ii v  vi          v  i  i     ivvi   v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_116413857_   2395 AAACA----------TTAAAAAGTGGACAAAGGACATGAACAGACACTTC 2434
                          i   ----------  ?    i   i       iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_116413857_   2435 TCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAACAAAGCTCAAC 2484
                           v        i  vi vi       i  i  i      vi v       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_116413857_   2485 ATCACTGATCAT 2496
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (44 / 30)
Gap_init rate = 0.01 (2 / 311), avg. gap size = 5.50 (11 / 2)  

3105 22.91 1.80 5.51  chrX_116413857_116419088     3797  4739 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116413857_   3797 TAGAAATATATCCCCTGTTCATGGGTTGAAAAAATTAATTTTGTCAAAAT 3846
                          i    v       v         i   i  i v     v    i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116413857_   3847 GAACATACTACTCAAAGAGATCTACAGATTTAATGCAATCCCTATCAAAA 3896
                          ivv     v i    vv            i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116413857_   3897 TACCAAAGACATTCTTCACAGAAATATAAAATATAATCCTAAAATTTGTA 3946
                          v   ivvi v  i  ii       vv v  vv i           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116413857_   3947 TAGAACCACAAAAGATACCAAATAGCCATAGCAATCTTGAGCTAAAACAA 3996
                          i   vii   ii  iv vi        v i         ---    ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAA--- 194

  chrX_116413857_   3997 ACCAAATTAAACAAGCAAACAAAAAACAAAGCCGGAGGCATCACACTACC 4046
                         --------------------i  i       ii     vv       v  
  L1M4_orf2#LINE/    195 --------------------GAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_116413857_   4047 TGACTTCAAAATATGCTGCAAATCTATAGCAACCCAAACAGCATGGTATT 4096
                         ii i       iv i  i    v   i  i  i v i    ii     i 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_116413857_   4097 GGCATAAAAATAGACACATAGAACAATGAAACAGAATAGGGAATACAGAA 4146
                                ii       i     v     i  i     v i  i v     
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_116413857_   4147 ATAAATCAATGTATCTATAGCCAACTAATTTTTTGACAATGGTACCAGGA 4196
                              i v  ii  i   i i   i i     i-     v   i   i  
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTC-GACAAGGGTGCCAAGA 373

  chrX_116413857_   4197 ACAA-AAATTGGGAAATGACAATCTCTTCAATAAATATTGTTGGGAAAAC 4245
                         v  v-v   v      vi i i   i     i    iv  i     v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_116413857_   4246 TGGATATCCATATGCACAATAATGAAACTGGACCCCTATCATTCACCATA 4295
                               ?   i     v  v      ii          i viv       
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_116413857_   4296 TTTGAAAATCAACTCAAAATGGATT---GACTTAAAAGTAAGACCCAAAA 4342
                          vii     i              i---   i    v      v i    
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_116413857_   4343 CTGTGAAAGTACTAGAAGAAAACATAGGGG-AAATGCTTCATGACATTGG 4391
                           i i   v vi                ? -    -    i    v    
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGG 572

  chrX_116413857_   4392 ACTAGGCAATAATTTTTTAGATAAAGTCTCAAAAGCACAGGAAACAAAAA 4441
                         ii        ii   i       viiivi          i v       i
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_116413857_   4442 CAATAATAGACAAATGGGATTACATCAAACCAAAATGCTTCTGCACAGCA 4491
                         v  v      i    v   i v       viv   vi   i  ii ----
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC---- 668

  chrX_116413857_   4492 TTTTCTGCACAGCAAAATGCTTCTGCACT--CAACAGAGTGAAGAGACAG 4539
                         --   ---------   v -----i    --   v i      i     i
  L1M4_orf2#LINE/    669 --TTC---------AAAGG-----ACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_116413857_   4540 CCTACAAAATGGGAGAAAATATTTCCATGCTATACATCAGACAAGGAGTC 4589
                           i   i                 v  viii   i   v  i    iiii
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_116413857_   4590 AGTATCCAGAATATATAAGGAACTC----AACTTAAAAGCAAAAAG-CAA 4634
                         v                 i      ----    i  v ii      -   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_116413857_   4635 ACAATCTGATT-AAAAATAGCAATAAAAAGCACTTGA-TAGGCATTTTTC 4682
                          i  i ii   -      i ----iv    v i    -   i     i  
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGG----GCAAAGGATTTGAATAGACATTTCTC 848

  chrX_116413857_   4683 --AAAAAAATGTAGAAAAGGAAAACA-GTATATTGAAAAACATTCAACAT 4729
                         --  i  i  i  v   v  vv  i - i i  vi   i iii       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_116413857_   4730 CACTATCATC 4739
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.89 (140 / 74)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.83 (69 / 18)  


3246 26.27 1.22 0.55  chrX_116419297_116421705     1015  1916 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116419297_   1015 TGGAAGAACATTCCATGCTCATGGATAGGAAAAATCAATATCGTGAA--- 1061
                              ii i  i     i        v    i v i     i  v  ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116419297_   1062 ---AATACTGCCCAAGTTAATTTATAGATTCAATGCCATCCCCATCAAGC 1108
                         ---      v     i  i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116419297_   1109 TACCAATGAATTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1156
                          v   iivivi  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_116419297_   1157 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAG 1206
                                viiv  ii  v  v v  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_116419297_   1207 AAAAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1256
                           v    i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_116419297_   1257 TACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1306
                                     i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_116419297_   1307 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCATACATCTACAACC 1354
                                i    i--    i  --        vv        i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_116419297_   1355 ATCTGATCTTTGAAAAACCTGATAAAAACAAGAAATGGGGAAAGGATTTC 1404
                          vi    i  i  v  ivv  vi  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_116419297_   1405 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTTGAAAGCT 1454
                           v  i  i              v      v  ?   i   ivi  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_116419297_   1455 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1504
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_116419297_   1505 TTAAATACTTAAATATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1554
                          i ? v  i     i v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_116419297_   1555 CTAGGCA-ATACCATTCAGGACCTAGGCATGGGCAAGGACTTCATGACTA 1603
                         v    ?i- v i -   iv     v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_116419297_   1604 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1653
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_116419297_   1654 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCACAGTGAA 1703
                           i   v v  i i   i  ii vv    i  v    i  vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_116419297_   1704 CAGGCAACCTACAGAATGGGAGAAGATTTTTGTAATCTACCCATCTGACA 1753
                         v  i     i              i  v    i  vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_116419297_   1754 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 1803
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_116419297_   1804 AAATCAAAGAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACGCTT 1853
                           iv    v     v  i?    i     i      v    i    ii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_116419297_   1854 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 1903
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_116419297_   1904 CATCACTGGTCAT 1916
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


3254 27.20 0.44 0.44  chrX_116471037_116477396     4960  5867 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116471037_   4960 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5009
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116471037_   5010 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCTCCATCCAGC 5059
                            v     v     iv i  i  i        i  v   i i   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116471037_   5060 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5107
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_116471037_   5108 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTGAGCAAAAAG 5157
                                viiv  ii  v  viv  v     iv     i   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_116471037_   5158 AATAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5207
                           i    i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_116471037_   5208 TACAGTAACCAAAACAGCATGGCATTGGTACCAAAACAGAGATATAGACC 5257
                                 i   i    ii   i i   i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_116471037_   5258 AAAGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATGTCTACAACC 5305
                           v    i    i--    i  --        vv  ii ii i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_116471037_   5306 ATCTGATCTTTGGCAAACCTGACAAAAACAAGCAATGGGGAAATGATTCC 5355
                          vi    i  i i   ivv  v   i v  vv           vi  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_116471037_   5356 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAAAAAGCT 5405
                           v  i  i              v      v  ?   i   i    iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_116471037_   5406 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5455
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_116471037_   5456 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5505
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_116471037_   5506 CTAGGCAATAACATTCAGGACATAGGCATGGGCAAGGACTTCACGTCTAA 5555
                         v    ?ivv  iv   iv   v v  vv i     v ii   viivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_116471037_   5556 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5605
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_116471037_   5606 TGAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTACCATCATAGTGAAC 5655
                          v   v v  i i      ii vv    i  v    i  vv v      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_116471037_   5656 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATATGACAA 5705
                           i     i                 v       vii ivi  v   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_116471037_   5706 AGGGCTAATATCCAGAATCTACAAAGAATTCAAACAAATTTACAAGAAAA 5755
                         i  i  vi          v  i      i  vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_116471037_   5756 AAACAAACAATCCCATCAAAATGTGGGCAAAGGATATGAACAGACACTTC 5805
                          i     i  i  v  i?   vi            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_116471037_   5806 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5855
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_116471037_   5856 ATCACTGGCCAT 5867
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2616 27.06 2.12 1.00  chrX_116492781_116498567.rev     2824  3721 (2066)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116492781_   2824 TGGAAACAGATCCCATGCTCATGAATAGGAAGAATCAATATTGTGAAAAT 2873
                               v v        i     i  v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116492781_   2874 CAACATACTGCCCAAAGTAATCTACAGATTTGGTGCAATTCCCATCAAAA 2923
                         vivv     v      v i           iiii     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116492781_   2924 TACCACCATCATTTTTCACAGAAATAGAAAAAACAATTCTAGAATTCATA 2973
                          v   v vv v     ii       v  v  ivii  i   i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116492781_   2974 TGGAACCAATA-AAGAGCCCTC--ATAGCCAAAGCAATACT-AAACAGAA 3019
                              ---  i-   i v  iv--         i    vi -   v    
  L1M4_orf2#LINE/    151 TGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_116492781_   3020 AAA--AATCTGGAGGCATTACATTACAAGACTTCAAATTATACTACAAAG 3067
                         i  --  vi      vv i   i v vvi i      viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_116492781_   3068 CTATAGTTAACAAAGCAGCATGGTACTTGTATAAAAATAGGCACTTAGAA 3117
                            i   v v   ii   ii       v i    ii    i  iv    v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_116492781_   3118 CAATGGAACACAATAGATAACCCAGAAATAAAGCCAAATA--------CA 3159
                                 i v   v  v ii           v   v i --------  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_116492781_   3160 ACAAATCTTTGACAAAGCATACAAAAAC-ATAAATTGGGGAAAGAACACC 3208
                          ivi  i  i     i -i i v  i  -  vv v           i vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_116492781_   3209 CTATTCAATACATGATGCTGGGAAAACTGAAAAGCCAGATGTAGAAGAAT 3258
                           v     i v   i        v     i v ?   v   i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_116492781_   3259 GAAACTAGATCCTCATCTGTTACCTTCTATAAAAATCTATTCAAGGTGGA 3308
                            ii i  i  ii i  vvi   v v  i      iv i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_116492781_   3309 TTAAAAACTTAAATCTAAGATTGGAAACCATAAAAATTCTAGAAGATAAC 3358
                          i ? i  i     v     vivi    i      v ii       v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_116492781_   3359 ATCGGA--AAATCTCTTCTGGACATTGGCCTAGGCAAAGAATTCATAACT 3406
                           v  ?--      --  vv   v    vi       v iv   v  iv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_116492781_   3407 GAGACCTCAAAAGCAAATACAAGAAGAACAAAAATAAATAAGG-GAAGCT 3455
                         iv   vi        v vi   v  i iv       i    iv- i vi 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_116492781_   3456 AATTAAACTGAAAAGGTTTC-TGCATAGCAAAAGAAATAATCAGCAGAGT 3504
                         v  i   v v    iv   i-   v --    i  v iv    iv i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGT 692

  chrX_116492781_   3505 AACCAGACAACCCACAGAGTGAGAGAAAATATTTGCAAACTTTGCATCAG 3554
                         i vv              i  i                 iiv ii   v 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_116492781_   3555 AGAAATTACTATTATCCAGAATCTACCAGGAACTCAAACAAATTAGCAAA 3604
                          v  ivv   vv          v  iv i      vv    v i ii  -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA- 791

  chrX_116492781_   3605 TAATAATAATAATCATCCCATCAAAAAGTGGGCAAAAGTCGTGACTAGAC 3654
                            v  v vv   v i  v  i?    i        i viv   v     
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_116492781_   3655 ATTTACTAAAAGAAGATATACAAACAGTGAACAAACAAATGAAAATATGC 3704
                             viiv                ii iv  i  i  v       v    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_116492781_   3705 TCAACATCACTAATCAT 3721
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (125 / 114)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  

2974 24.56 2.14 0.71  chrX_116492781_116498567.rev     4454  5296 (491)    L1M4_orf2#LINE/L1       54   908 (0)  

  chrX_116492781_   4454 AATATTTTTTAAA---ATTTAAAAAT--AATA-AATTATAATAAAAATAC 4497
                             i iiii   ---  i  v i  --  ii-   iviv  v     v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_116492781_   4498 CAACAATATTCTTCACAGAAATAGAAAAAAAAATTCTAAAATTTATATGG 4547
                           i viiv  i  ii       v  v  ivvi  i        i      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_116492781_   4548 AATCGCAAAG-ACCCAGAATAGCCAGAGTTATCCTAAGCAAAAGAAATGA 4596
                           vi    i -              i iiv   i i iv  i ii  ii 
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_116492781_   4597 AACTGGAGGAATCTGATTACCTGATT-AAAAATTATACTAGAGAGCTGTA 4645
                          ii       v  vv i v  ii   -v    i -     v i    ii 
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACA 252

  chrX_116492781_   4646 GTAACCAAAACAGCAAGGTACTGGCATAGCAATAGACACATAGACCAACA 4695
                             i   i    iiv            ivi       i     i   ii
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_116492781_   4696 GAACAGAATGGATAATCCAGAAACAAATCCACATAACTACAGTGAATTCA 4745
                            i     v  v i        i   i   i i vi  ii  v    v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_116492781_   4746 TTTTCAACAAAGCGT-CCAAGAACATATACTGGGGAAAAGACAGTCTCTT 4794
                              i    i -  -      v   vi v        ii i     i  
  L1M4_orf2#LINE/    353 TTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_116492781_   4795 CAATAAATGGTGCTTGGAAAACTGGATATCAATATGCAAAAGAATGAAAA 4844
                            i          v   v         ? v i               iv
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_116492781_   4845 TAGACCCCTAACTCTCACCATATACAAAAATCAAATCAACATGGATTAAA 4894
                          i        v   v                i  v    v      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_116492781_   4895 AACTTAAATCTAAAACCTCAAACTATGAAACTAGTGCAAGAAAACATTAG 4944
                         i  i     v   i v  v       i     vv iv          -  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AG 550

  chrX_116492781_   4945 GAA-AAATTTCTAGGACATTGGTCTTGGCAAAGATTTCTTGAGGAATATC 4993
                          ?i-    i iiiv   v    vi v     v i      -  iv  iv 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGAC 599

  chrX_116492781_   4994 -CCACAAACACAGGCAACTAAAGCAAACATGGACAAATGGGATCACATCA 5042
                         -   v  i    i     v    v   v  i  i    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_116492781_   5043 AG-TTAAAAAGCTTCTGGATAGCAAAGGGTACAATCAGCAAAGTGAAGTG 5091
                          i-       -   i  viivv      ii  v    iv        iv 
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_116492781_   5092 ACAACCCACAGAATGTGAGAAGATATTTGCAAACTACCCATCTGACAAGG 5141
                                        v     i           ii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_116492781_   5142 GATTAATAACTAGAATATA-AAAGAAGCTCCAACAATTCTATAGGAAAAA 5190
                           i vi  v i        -      -   iv    i  v   iv     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATAATAAAAA 797

  chrX_116492781_   5191 AATAA-TAATCCAATTTAAAAATGGGTGAAATGTTTGAATAGAAATTTCT 5239
                         i i  -   i      ?         ii  ivi          v      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_116492781_   5240 CAAAAGAAGA----CAAATGGCAAACAGGCATATGCCAAAGTGCTCAACA 5285
                          v        ----        v  i i   i   vv  ii         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_116492781_   5286 TCATTGATCAT 5296
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.67 (127 / 76)
Gap_init rate = 0.02 (18 / 855), avg. gap size = 1.33 (24 / 18)  


2779 27.84 1.67 0.89  chrX_116505426_116511096     4281  5178 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_116505426_   4281 AAAAACATTCCATGCTTATGGATAGAAAGAATCAATATCATGAAAATGGC 4330
                            i i  i     i i      v i    v i     ii v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_116505426_   4331 CATACTGCCTAAAGTAATTTATGGATTCAGTTCTATTCCCTTTAAACTAC 4380
                         v     v  i   v i  i  ii      iiv v  i  iv i   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_116505426_   4381 CAGTGACACTCTTCACAGAA-TTAGAAGAAAAGCT-ACTTTAAAATCCAT 4428
                            ivi vi i  ii     -  ----  v     - iii      i   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATT----GACAAGCTGATCCTAAAATTCAT 149

  chrX_116505426_   4429 ATGGAACCAAAAAGGAACCTGTATAGCCAAGACAATCCTAGAGAAAAAGA 4478
                               viiv  i   v  v v        i      i ii i  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_116505426_   4479 ACAAAGAGGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGGCT 4528
                               vv     vv   ii  v  ii i      vivi       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_116505426_   4529 ACAGTAACCATAACAGCATGGTACTGGTACAAA-ACCGAAACATAGACAA 4577
                                i  vi    ii         i i  i- iv  v i     iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_116505426_   4578 ATTGAACAGAATAGAGATCTCAGAAATAAGACTGCATATCTACAAGCATC 4627
                           v   i     v    vii         iv iii i  i  iiiv  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_116505426_   4628 TGATCTTCAACAAACCTGACAAAAAGAAGCAACGGGGAAAGAATCTCCTA 4677
                             i   i    ivv  v   i vv vv   i           vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_116505426_   4678 TTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAAATTGAA 4727
                           i  i              i      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_116505426_   4728 ACTGGTTGCCTTCCTTACACCTTATACAAAAATTACCTAAAGATGGATTA 4777
                         ii   viv   v   i     v             v  v  i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_116505426_   4778 AAAACTTAAATGGAAAGCCCAAAGTTATAAAAACCCTAGAAGAAAATCTA 4827
                         ? i  i      v  iiv i   ii       vi i          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_116505426_   4828 GCCA-ATACCATTCAGAACATAAGCACAGGCAAAGATTTCATGACAAAGA 4876
                          v?i- v i -   ivi  v vi vvi      v i    v iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_116505426_   4877 TGTCAAAA--ACAATTGCAACAAAAGCAAAAATTGATGAATGGGATCTAA 4924
                         iii     --    --          v      v   i   v   ii v 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_116505426_   4925 TTAAACTAAAGAGCTTCTGCACACCAAAAGAAACTATCATCAGAGTGAAC 4974
                          i   v v  i i   i  ii vi    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_116505426_   4975 AGACAGCCTAAAAAATGAGAGAAAATTTTTACAATCTATCCATCTGACCA 5024
                              i  i v i    i        v   i   vii  vi      iv 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_116505426_   5025 AGGTCTAATACCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 5074
                         i  v  vi  i       v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_116505426_   5075 AAA-----AACC--ATTAAAAAGTGGGCAAAGGAAATGAAGAGACATTTC 5117
                          i -----    --   ?    i           vv    v         
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_116505426_   5118 TCAAAAGAAGACATTTATATGGCCAACAA--ACATGAAAAAAAAGCTCAA 5165
                           v        i  vi v        i  --         i v-      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAA 895

  chrX_116505426_   5166 CATCACTCATCAT 5178
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (145 / 101)
Gap_init rate = 0.01 (12 / 905), avg. gap size = 1.92 (23 / 12)  


2810 26.07 1.39 3.97  chrX_116532801_116539905.rev     5683  6614 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116532801_   5683 TGGAAAAACATTCCATGCTCATAGATAGGAAGAATCCATATTGTGAAAAT 5732
                               i i  i     i    i   v      v iv       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116532801_   5733 GGACATACTGCCTAAAGTAATTTATAGATGCAATGCTATCCCCGTCAAGG 5782
                           vv     v  i   v i  i  i    v   i  v     ii    --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA-- 98

  chrX_116532801_   5783 AATTTATAGATTCAATGCTCTCCCCATCAAGCGCCTATTGACTTTCTTCA 5832
                         -------------   ------    ------  ----  v    i  -i
  L1M4_orf2#LINE/     99 -------------AAT------CCCA------GC----TGCCTTTTTT-G 118

  chrX_116532801_   5833 CAGAA-TTGGAAAAAAACTG----TAAATTTCATATGGAACCAAAAAGAG 5877
                              -   --- v  i   ----    v           viiv  i ii
  L1M4_orf2#LINE/    119 CAGAAATTG---ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_116532801_   5878 CCCATA-TAGCCGAGATAATCCTAAGCAAAAAAAACAAAGCTGGAGGCAT 5926
                             v -     i i i    i i iv  i  i       i      vv 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_116532801_   5927 CATGCTACCTGACTTCAAACTGTACTACAAGGCTATCGTAACCAAAACAG 5976
                           ii  v  ii i      viv        i    iv    i   i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_116532801_   5977 CATGGTACTGGTACCAAAACAGTTACATAGACCGATGGAACAGAACAGAG 6026
                         ii         i iv ii i  vi i     i i      i    iv   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_116532801_   6027 GCTGCAGAAATAACACCACACATCTACAACCATCTGATCTTTGACAAACC 6076
                         iv v         vv   i    i  iiii  vi    i  i     ivv
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_116532801_   6077 TGACAAAAACAAGCAATGGGGAAAGGATTCCCTTTATAATAAATGCTGTT 6126
                           v   i v  vv            i  vvi    vi  i     v  i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_116532801_   6127 GGGA-AACAGGCTAGCCATATGCAGAAAACTGAAACTGGACCCCTTCCTT 6175
                             -   v  v  ?   i     i  i v    ii         v   i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_116532801_   6176 GCACCTTATACAAAAATTAACTCAAGATGGATTAACGACTTAAATGTAAT 6225
                         i    v                   i      i ?v   i         v
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_116532801_   6226 ATCTAAAACCATGAAAACCCAAGAAGAAAACCTAGGCAATAACATTCAGG 6275
                          v       i  i   vi iv          v    ?ivv  iv   iv 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_116532801_   6276 ACATAGGCATGGGAAAAGACTTCATGAGTAAAACACCAAAA--ACAATTG 6323
                           v v  vv i  v  v ii   v iii  vi         --    -- 
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--G 613

  chrX_116532801_   6324 CAACAAAAGCCAAAATTGACCAATGGGATCTAATTAAACTAAAGAGCTTC 6373
                                  vv     v  iv   v   ii v  i   v v  i i   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_116532801_   6374 TGCACAGCAAAAGAAACTATCATCAGCATGAACAGGAAACCTACAGAATG 6423
                           ii vv    i  v       vv ivi    v  iv    i        
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_116532801_   6424 GGAGAAAATTTTGGCAATCTATCCATCTGACAAAGGGCTAATATCCACAG 6473
                                  v  v    vii  vi      i  i  i  vi      v i
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_116532801_   6474 TCTACAAGGAACTTAAATAAAT---TTACAAGAAGA-AAACAACCCCATC 6519
                          v  i  i     ivv i  v --- v i  i    -   i     v  i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_116532801_   6520 AAAAAGTGGGTGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTA 6569
                         ?    i    ii     iv    i     i     v        i  vi 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_116532801_   6570 TGTGGCTGAGAAACATATGAAAAAAAGCTAATCATCACTGGTCAT 6614
                         vi    ii v  i  i       i v   v v     ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.57 (50 / 14)  


2293 27.34 6.81 2.08  chrX_116590903_116596742     4481  5347 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116590903_   4481 TGAAAAAGTATTTCATATTCATGGACAAAAAGAATCAACATTGTTAAAAT 4530
                           i   ii   ii   i        ivii    v i  i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116590903_   4531 GGCCATACTGCCCAATGCAATTTACAGATTTGGTGTTATTCCTATCAAAC 4580
                            v     v     vvii  i        iiii iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116590903_   4581 TATTGATGACATTTTTCACAGAATTCGGAAAAAT-ATTCAGAAATTCATA 4629
                          viiiiivi v     ii     v i iv  iv -  i vi         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116590903_   4630 TGGAACTAAAAAAGAGCCCAAATAACCAAAACAATCCTAAGAAGCAAAAA 4679
                              v iv  ii  v  vi    i           i i i  --- i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA---AGAA 197

  chrX_116590903_   4680 GAACAAAGCTGGTGGAATCACACTACCCAACTTCAAAATATACTACAGGG 4729
                                 i   v   v       v     i       iv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_116590903_   4730 ATACAATAA-CAAAACAGCATTGT-CCAATAGAAAAATTGACACATAAAT 4777
                         v    i   -   i    ii v  - iiii v  ii  v    i   i  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_116590903_   4778 CAATGCTACATGTTAGAGAACCCAGAAATAAAGCAGCACACCTACAACCA 4827
                              vv i viv v    ii           v vii   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_116590903_   4828 TCTGGTCTTCAACAAAGTCAACAAAAACAAGCAATGGGGAAAGGACTCCC 4877
                         vi  i i   i    i viiv   i v  vv            i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_116590903_   4878 TAGTCAATAAATAGTGCAGGGTTAACTGTCTAGCTATGTGCAGAAGATTG 4927
                          vv    i    i    v   vi     vv  ? i ii    i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_116590903_   4928 AAAATGGATCACTTCCTTTCACCATA-AC--------------------- 4955
                           iv    i v  v   iv       -  ---------------------
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_116590903_   4956 ------CCTAAA--------------CTATAAATACCCT-AGAATAAAAC 4984
                         ------      --------------       -  i  -    v     
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chrX_116590903_   4985 CTAGGAATACCATTCTGCACACAGACCCTGG------CAAGGATTTCAT- 5027
                         v    ?i  -- v   v ii---    i   ------   v i    v -
  L1M4_orf2#LINE/    547 ATAGGNGTA--AATCTTCGT---GACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_116590903_   5028 GATGAAGATTCCAAAAGCAATGGCATCAAAA-ACAAAATTGAAAAGTGGG 5076
                            - v  iv         vvi   v     - v     v  v  i v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_116590903_   5077 ACCTAATCAAACTATAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGA 5126
                           i v      v vv i i   i  ii vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_116590903_   5127 GTAAACAGACAACCTACAGAATGGGAGAAAATATTCACAATCTATGCATC 5176
                           i  v        i                    ii   vii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_116590903_   5177 TGAAAAAGATCTAACATCCAGAATACATTAATATATGGGATTT----AAA 5222
                            v  i iv  vii          i  v  ------ i i i----  v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAA------GAACTCTTACAAC 784

  chrX_116590903_   5223 TCAACAAGCAAAAAAACCGAACAACTCCATT-AAAAATGGGCAAAGGACA 5271
                             i  -i     i  -i  i   i v   -                iv
  L1M4_orf2#LINE/    785 TCAATAA-TAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_116590903_   5272 TAAACAGACACTTCTCAGAAGAAGACATACCTGTGGCCAACAAGTATATG 5321
                          i  i     i     vi       i    vvi       i   i i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_116590903_   5322 AAAAAGTTTTCAACACCATTAATCAT 5347
                             ii vi      i  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (146 / 89)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.85 (77 / 20)  


3013 23.53 2.83 3.92  chrX_116608499_116610533.rev      627  1544 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116608499_    627 TGGAGAGAGATGTCATATACTTGGATAAGGAGACTTAATATTGTGAATAT 676
                             i   v  vi   i v v     vi i              v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116608499_    677 GTCAGT-CTTCCCAACTTGATCTGTAGTGTTAATGCAACCTCAATAAAAA 725
                          v  i -  i     v       ii  vv i  i    i i v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116608499_    726 ATCCCAGC-ACATTATTTTGTGGGTATTGATAAACTGATTCTAAAATTAT 774
                         -       -i v  -     ii iv     i  i     i        -i
  L1M4_orf2#LINE/    101 -TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATT-C 147

  chrX_116608499_    775 ATTTGGA---GGAAAATACCCCAAATAGTCAACATAATATTGAAGGAGGG 821
                           v    --- v  iiv    vi     i   v i   v     ii  i-
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA- 196

  chrX_116608499_    822 AAAATA----TGGAGAACTCACACTATACAATTGTAAGGTTTACTATACA 867
                          i  i ----     i         viv     vi  iii      i v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_116608499_    868 GCTACAGTAATCAAGACTCTGTTGCATTGGTAAAAGAATAGACAAATAGG 917
                                          vv   v i i   i v   i       v    i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_116608499_    918 TTAATGAGACAACA--GAGAGCCCAGAAATAGACCCACACAAATATAGTC 965
                          i    ii i iv --     i         i     i   vv   i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_116608499_    966 AACTAAACTTTGACAAGAA-GCAAAGGCAAGTCAACAGAGAAAATATGGT 1014
                           i i vi  i      ii-  v   i v v    ii i    iv  i  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_116608499_   1015 CTTTTCAACAAATGGTCCTGGAACAATGAGACACGCACAGGCAAAAAGTA 1064
                                         v    i    ivi  i ?v    v      ii--
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-- 444

  chrX_116608499_   1065 AATAAATACATAAATAAATACACTATGAATCTAAACACATACCTAATGCC 1114
                         ------------------------     vi ii  v v     v ii  
  L1M4_orf2#LINE/    445 ------------------------ATGAAGTTGGACCCCTACCTCACACC 470

  chrX_116608499_   1115 TTTCACAAAAATGAACTCAAG-TAGATCATAGATTTAAATGTGAAATAGA 1163
                         v vi        v       i- i     ?   ii       i i vvv 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_116608499_   1164 AAACTA--AAACTTCTGAAATATAACAC--GAGAAAATCTAGGTGTCCTT 1209
                               --     ii ii  v v    i-- ? v      vv   v    
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_116608499_   1210 GAGTT---TAATGATGACTTTAAAAAAATATAACACCAAAAACATGATCC 1256
                          i   ---i    i vv   ----- i    i         i  ii v v
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTT-----AGATATGACACCAAAAGCACAAGCA 615

  chrX_116608499_   1257 ATTGAAGAAAAAATTGGTATGTTGGACTTCATAAAAATTAAAAACTTATC 1306
                          ivi          v i  vi           v              v v
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_116608499_   1307 TGC--CAAAG-ACACCGTTA-TACAATGAAAAGACAAGGCACAGATTGGG 1352
                            --     -    ii i -v v i           vv      v    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_116608499_   1353 AGAAGATTCTTTGCTAAACACATATCTGATAGAGAACTGGTATTTGAAAT 1402
                             i  -v     v  v  i          ii i   v    iiii   
  L1M4_orf2#LINE/    716 AGAAAAT-ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_116608499_   1403 ATATAAA-ACCTCTTAAAACTCAACAATAACAGAATAAACAACCCAATT- 1450
                                - v      v       i     v ii i   i         -
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_116608499_   1451 AAAAATGGGCTAAAGATCTGTACATACACCTCGCCAAAGAAAATATACAG 1500
                                   v  i   i  v i v   ii  v        i       i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_116608499_   1501 ATGGCAAATAAGCATATAAAAAGATGTTCTACATCATACGTTAT 1544
                              v        i  i        i  v      ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (127 / 86)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.82 (62 / 22)  


3366 23.95 0.64 3.11  chrX_116613605_116617864     2837  3767 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116613605_   2837 TGGAAAAATAGTCCATGTACATGGATTGGAAAAATCAATATTGTTAAAAT 2886
                               i   vi      v            i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116613605_   2887 AGCCATAGTACCCAAAGCAATCTGCAGATTCGATACAATCCCTATCAAAA 2936
                         i  v   v v      vii    i       i ii               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116613605_   2937 CACCAAAGACATCCTTCAAAGAAATAGAAAAAACCATCTTAAATTTTATA 2986
                         iv   ivvi v ii  iiv      v  v  iviv   i    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116613605_   2987 TGGAATCACGAAAGACACAAAATAGCCACAGTTATCCTAAGCAAAAGGAG 3036
                              vii i ii   v  i        v iiv   i i iv  i i  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_116613605_   3037 CAAAACTGGAGGAATCTGATTACGTGATTTCGAATTTTACTACAGAGCTA 3086
                             ii       v  vv i v vii     i  vi        i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_116613605_   3087 TAGTAATCAAAACAGCATGGTACTGGCATAACAACAGACAAATAGACCAA 3136
                         i         i    ii              vi i     v     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_116613605_   3137 GGGAACAGAATGGAGAATTCAGAAACGAATCCACATACTTACAGTCAACT 3186
                         v    i     v    i i      ii  i   i i i   ii     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_116613605_   3187 CATTTTTGACAAAAGTGCCAACAATATACACTGGGAAAAATAGAGTCTCT 3236
                         v     i     ii       v vi  v  v    i   iv v     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_116613605_   3237 TCAATAAATGGTGCTGGAAAAACTGGATATCCATATGCAAAAGAATAAAA 3286
                             i            i v         ?   i            i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_116613605_   3287 CTAGACACCTATCTCTCACCATATACAAAAATCAAATCAACATGGATTAA 3336
                         i i   v    i   v                i  v    v      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_116613605_   3337 AGACTTAAATTGAAGACCTGAAACTATTAAACTACTACAAAAAAAACATT 3386
                             i     vv    v  i       v     vi  -i  i       v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA-GAAGAAAACATA 549

  chrX_116613605_   3387 GGAA-AAATCT--AGCACATTGGTCTGGGCAAAGACTTCTTGAGCAATAC 3433
                           ?i-      --ivv  v    vi i     v ii     iiii vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_116613605_   3434 CCCACAAGCACAGGCAACCAAAGCAAACATGGACAAATGGAATCTTATCA 3483
                         v   v       i     v    v   v  i  i    v i ii i    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_116613605_   3484 AG-TTAAAAAGCATCTGCCCAGCAAAGGATAAAATCAACAAAGTTAAATG 3532
                          i-       - v i  iv vv       i vv     v     v   v 
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_116613605_   3533 ACAACCCACAGAATGGGAGAAAACATTTGCAAGCTACTTATCTGACAAGG 3582
                                                i        iii iv       i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_116613605_   3583 GTTTAATAACCCATTGTCAGGACTAATAATATATATCAGAAAATATAGGT 3632
                          --------------------   ----- i   -i     v     iiv
  L1M4_orf2#LINE/    749 G--------------------ACT-----TGTAT-CCAGAATATATAAAG 772

  chrX_116613605_   3633 AGCTCAAACAACTCTATAGGAAAAAAATCTAATAATCTGATTTAAAAATG 3682
                          i   vv       v   iv     i - v     i ii   ?       
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATG 821

  chrX_116613605_   3683 GGCAACATATTTGAA--GACATTTTTTAAAAGAAGACATATAAATGGCAA 3730
                              viv       --       i iv        i   i       v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_116613605_   3731 ACAAGAATATGCAAAAGTGCCCAACATCATTGATCAT 3767
                          i   v i   v   ii   i        ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (133 / 86)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.50 (35 / 10)  


1785 21.35 19.70 3.16  chrX_116656053_116657707      500  1164 (491)    L1M4_orf2#LINE/L1      134   908 (0)  

  chrX_116656053_    500 TGACTATAAAATTTGTATGGAAAGGCAAAGTAACTAGAATACTGAATACA 549
                            iiv       ii        v    i v v i      viv  v   
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_116656053_    550 ATCTTTTAAAAAAATAAGAACAACGTTGGAGGCCTCATAT------AT-- 591
                              ---i     v        v        v    i i------  --
  L1M4_orf2#LINE/    184 ATCTT---GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_116656053_    592 -AAGACTTACTATACATCTACAGTAATAATGAAAGCACAGAATTTGAAGA 640
                         -  i        i v v          v v  v  iiii v i v v v 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_116656053_    641 CAGTAAAGACATACAGATTAACAGAAAAGAATCAAGAGTCC--------- 681
                         -  v v       i    i  ii   v     ii       ---------
  L1M4_orf2#LINE/    281 -AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_116656053_    682 ------------TG------------------------------------ 683
                         ------------  ------------------------------------
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_116656053_    684 --------------------------------TGCTACAACAACCGAATA 701
                         --------------------------------    ivi     i i   
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_116656053_    702 CTCACATGTAAAATGATAAGCCTGGACCTCTACTTCATACCATACAGATA 751
                         ?i      i    vi  i ivi      i    i   i      i v v 
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_116656053_    752 AACAAACTCAAAATGGATCACAGGCCTAAATATAAAATTCAATATAAAAA 801
                           iv                ?  i       i   i ------------i
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA------------G 517

  chrX_116656053_    802 CTCAAATTATAAAATTCTTATGATAAAACATAGGAGTAAATGTTCATGAC 851
                           v   i       i     vi v          ?      v   i    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_116656053_    852 GTTGGGTTGGGCAACAATTTCTTAGATATGGGAGATGCT----GCACAAG 897
                         v       i     iii             ---- ii i----       
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATG----ACACCAAAAGCACAAG 613

  chrX_116656053_    898 CAATAAAATAACAAAATATCTAAGTAGAATTTCACCAAATTTTAAAACTT 947
                            i    v  -      vv   i v i i    i    v  v       
  L1M4_orf2#LINE/    614 CAACAAAAGAA-AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_116656053_    948 TTGATCTTCAAAGGATACAATCAAGAAAGC--AATGTCT-TCAAGAGAGT 994
                            vv          i  v          i--  v v v-i v v   i 
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_116656053_    995 GGAA-AGAATATCTGTAAACAATATCCGTGGTAAAGGAC----------- 1032
                           i - i     i  i   iv    viv  i   i    -----------
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_116656053_   1033 --ATATAATGAACTCTTACAACTCAATAA------GA-AAATAACCCAAT 1073
                         --      v                    ------  -            
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_116656053_   1074 TAAAACTTG--TAAAAGATTTAAATAGATATTTCTCT---GAGGATATCT 1118
                          ?   vv  --i   i     i      i       i---  i     vi
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_116656053_   1119 GAATGGCCAATAAACCCTTGAATATATGCTCAACATGATTAGTCAT 1164
                         i            i v v    v v           v ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (79 / 59)
Gap_init rate = 0.02 (18 / 775), avg. gap size = 8.44 (152 / 18)  


3222 26.32 0.99 0.99  chrX_116673274_116679676.rev     5005  5912 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116673274_   5005 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5054
                              ii    i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116673274_   5055 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5104
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116673274_   5105 TACCAA-TGCCTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5151
                          v   i-       ii -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_116673274_   5152 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5201
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_116673274_   5202 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATAGTACAAGG 5251
                                 i      vv   ii  v  ii i      viv  v     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_116673274_   5252 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5301
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_116673274_   5302 CAATG-AACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5348
                              -  i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_116673274_   5349 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5398
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_116673274_   5399 CCTGTTTGCTAAATGGTGCTGGGAAAACTGTCTAGCCATATGTAGAAAGC 5448
                         i  v  iivi              v     vv  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_116673274_   5449 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5498
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_116673274_   5499 ATTAAAGACTTAAACATTAGACTTAAAACCATAAAAACCCTAGAAGAAAA 5548
                           i ?    i    ii v   vi      i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_116673274_   5549 CCTAGGCGTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5598
                          v    ?  v viv   iv   v v  vv i     v ii   ----i  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC----TTA 591

  chrX_116673274_   5599 AA---AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA 5645
                         i ---i            vvi          vv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_116673274_   5646 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 5695
                         ii v  i   v v  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_116673274_   5696 TGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCT 5745
                             v  i     i   i             v  i    vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_116673274_   5746 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAA 5795
                           i  i  i  vi          v  i  v      iv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_116673274_   5796 GAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGAC 5845
                         v     i     i     v  i?    i     i     iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_116673274_   5846 ACTTCTCAAAAGAAGACACTTACGCAGCCAAAAAACACATGAAAAAATGC 5895
                          i     v        i ivi viii     v  i          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_116673274_   5896 TCACCATCACTGGCCAT 5912
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


3114 26.09 2.01 0.78  chrX_116725338_116731442      806  1702 (4403)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116725338_    806 TGGAAACACATCCCATGCTCATGGATCAGCAGAATCAATATTGTGAAAAT 855
                               v i        i        ii v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116725338_    856 GACA-TACTACCAAAAGCAATCTACAAATTCATGGCAACTTCCATCAAAA 904
                          i  -    v  v   vii       i     vv    iii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116725338_    905 TGCCACCATCATTCTTCACAAAACTAGAAAAAACAATCCTAAAATTCATA 954
                          v   v vv v  i  ii  i  v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116725338_    955 TGGAACCACAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 1004
                              vii   ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_116725338_   1005 CAAATCTGGCGGCATCACATTACATGATTTCAAACCATACTATAAGGTCA 1054
                             vi   v  vv     i v vii        v v     i  i ii 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_116725338_   1055 TTGTCACCAAAACAGCATG-TACTGGCATAAAAATAGGCATATAGGCCAA 1103
                         iv  v i   i    ii  -           ii    i       ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_116725338_   1104 TGGAACAGAATCAAGAACCCGGTAATAAGCCCAAATACTTACAGCCAACT 1153
                              i     ii   ii  i v     i    v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_116725338_   1154 GATCTTCAACAAAGCAAACAAAAACATGAAGTGGGGAAAGGACACTCTAT 1203
                            i   i    i vviv   i v   vv i         i i v   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_116725338_   1204 TCAACTAATGGTGCTGGGATAATTGGCAAGCCACATATAGGAGAATGAAA 1253
                              v             i  i   vv ?      ii ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_116725338_   1254 CTGGATCCTCATTTCTCCTGTTATATAAAAATCAACTCAAGATGGATCAA 1303
                         i    i  ii ii  v vivv    i      i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_116725338_   1304 GGACTTAAATCTAAGACCTGAAACTATAACAATTCT-GGAAGATAACATT 1352
                         i   i     v     v  i         -  i   -i     v     v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACATA 549

  chrX_116725338_   1353 GGAAAAACCCTTCTAGACATTGGCTTAGGCAAAGATTT------TATGAC 1396
                           ?iv  vi    vv   v    v        v i   ------      
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_116725338_   1397 CAAGAACCCAAAGCAAATACAACAAAATCAAAGATAAATAGGTGGGACTT 1446
                         -----   v      v vi        vv   i   i   ii v      
  L1M4_orf2#LINE/    600 -----ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_116725338_   1447 -----AAACTAAAGAGCTTTGGCAAGGCAAAAGCAACAGTCAGCAGAGTC 1491
                         -----   i    i -    v iivvv    i vv  vi   iv i   v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_116725338_   1492 AACAGACAACCCACGGAGTGGGAGAAAATCTTCACAATCTATACATCTGA 1541
                           v           i  i           v  ii   vii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_116725338_   1542 CAAAGAACTAATATCCAGAATCTGCAAGGAACTCAAACAAATTAGCAAGA 1591
                         i  i i   vi          v ii  i      vv    v i ii  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_116725338_   1592 AA----TAAACAATTCCATCAAAAAGTGGGCTAAGGACATGAATAGACAA 1637
                           ----i   i  ii v  i?    i     v     iv          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_116725338_   1638 TTCTCAAAAGAAGATATACAAATGGCCCACAAACATCTGAAAAAAGGCTC 1687
                              v                     v i  i  iv      i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_116725338_   1688 AACATCACTAATGAT 1702
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (135 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.78 (25 / 9)  

3069 25.34 1.35 0.61  chrX_116725338_116731442     4415  5231 (874)    L1M4_orf2#LINE/L1        1   823 (85)  

  chrX_116725338_   4415 TGGAAAGATATTCCATGTTTGTGCATTGAAGAAATCAATATTGCTAAAAT 4464
                                    i       ii  v    i ii v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116725338_   4465 GTTCATGCTACTTAAAGCAATGTACAGATTACATGCAATCCTTATCAAAA 4514
                          viv  i  v ii   vii  v        vv i       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116725338_   4515 TACCAATGACATTCTTCAAAGAAATAGAAAAAA-AACCCTAAAATTCATA 4563
                          v   iivi v  i  iiv      v  v  iv-i i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116725338_   4564 TGAAACCACAAAAGACCCAGAATAGTCAAAGCATTTCTGAGCAAAAAGAA 4613
                           i  vii   ii            i    i  v ii   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_116725338_   4614 CAAAACTGGAGGAATCACATTACCTGATTTCAAATTATACTACAAAGCTA 4663
                             ii       v     i v  ii        viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_116725338_   4664 TAGTAACCAAAACAGCATGATACTGGCATAAAAAGAGACAAATAAACCAA 4713
                         i     i   i    ii  i           ii v     v   i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_116725338_   4714 TTGAATAGAATAGAGAACCCAGAAAAAAATCCATACTTCTACAGTGAACA 4763
                          v         v    ii       v   i      v i  ii  v  iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_116725338_   4764 AATTTTCAGCAAAGATGTCAACAACATACATTGAGGAAAGAAGAGTCTCT 4813
                         i      ii   i i  i   v v   v  v  i        v     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_116725338_   4814 TCAATAAATGGTTCTGGGAAAACTGGATATCCATATGCAGAAGAATAAAA 4863
                             i       v      v         ?   i     i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_116725338_   4864 CTAGAACCCTATTTCTTGCCATATACAAAATTCAAATCAAAATGAATTAA 4913
                         i i  v     ii  vii            v i  v        i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_116725338_   4914 AGACTTAAATTTAAGACTTCAAACTATGAAACAACTAAAAGAAAACATTG 4963
                             i     v     vi v       i    vvi  i          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_116725338_   4964 AGGAAACTCTCCAGGACACTGGGCTGAGCAAATATTTCTTGAGCAATACC 5013
                         i? v  v   i iv   vi    i ii    vvi      iiii vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_116725338_   5014 CCGCAAGCACAGACAACCAAAGTAAAAATGGACAAATGGGATCACATCAA 5063
                           iv       ii    v    v      i  i    v   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_116725338_   5064 TGTAAAAAGCTTCTGCACAAGAAAGGAAAC----AGCAAAGTGAATAGAC 5109
                         vi v    i   i  ii vvv      v  ---- iv        v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_116725338_   5110 AACCCACAGAATGGGAGAAAATATTTGCCAACTATCT---TGACAAAGGA 5156
                                                     v  ii  v ---   i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_116725338_   5157 TTAATAACCAGAATACATAAGGA--TTGTAAACAACTCTATAGGAAAAAA 5204
                         i vi  v        i    i  -- iv  --      v   iv     i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAAAAG 798

  chrX_116725338_   5205 GAAACTAATAATCTGATT-AAAAATGGG 5231
                         ---  v     i ii   -         
  L1M4_orf2#LINE/    799 ---ACAAATAACCCAATTWAAAAATGGG 823

Transitions / transversions = 1.62 (126 / 78)
Gap_init rate = 0.01 (7 / 823), avg. gap size = 2.29 (16 / 7)  

 433 18.09 0.00 0.00  chrX_116725338_116731442     5519  5612 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_116725338_   5519 AAAAATGGGTGTAATATCTGTAGAGACATTTATCAAAAGAAGACATACAA 5568
                                  iiv iv  i  v v        v  v        i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_116725338_   5569 ATGGCAAACAATCATATGAAAAGGTGCTCAGCATCACTGATCAT 5612
                              v  i  v  i        i      i     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


2617 25.21 3.01 1.10  chrX_116731929_116736388     2757  3486 (974)    L1M4_orf2#LINE/L1        1   744 (164)  

  chrX_116731929_   2757 TGTAACAACATCCCATGTTTATTGATTGAAAGAATTAATATTGTTAA--T 2804
                           v  vi i          i  v     i    v             -- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116731929_   2805 GTTAAT------TGAAGCAATCTACAAATTCAATGCAATTCCTATCAAAT 2848
                          vi   ------ii  vii       i      i     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116731929_   2849 TACTAAG-GCCCTTTTCCCAAAAATAGAAAAA--AATTCTAAAAGTTGTA 2895
                          v i iv-   i    iv  i    v  v  i--i  i      v ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116731929_   2896 TGGAACCACAAAAGACCCAGAATAACCAATGCATTTCTGAGCAAAAAGAA 2945
                              vii   ii           i    vi  v ii   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_116731929_   2946 CAAATCTGGAGGCATCACACTACCCGACTTCAAAATATGCTACAAAAAGC 2995
                             vi      vv       v   i i       iv i       --  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA--GC 248

  chrX_116731929_   2996 TATAGTAAACAGAACAGCATGGTACTGGCATAAA-AGAGACACATAGACT 3044
                           i     v  ii    ii              i- v     i     ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_116731929_   3045 AATGGAACAGAATAGATAACCCAGAAATAAATCCATGTATATACATCCAA 3094
                                i     v  v ii           i    ii  v  iivi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_116731929_   3095 CTGACTTTCAACAAAAGCAGCACGAACATACAACGGGGAAAGGACAGTCT 3144
                         i   i    i    ii iiv  v  v   v   i        i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_116731929_   3145 CTTCAATAAATGGCGCTGGGAAAACTGGATGTTCATATGCAGAATACTAG 3194
                         i     i      i       v        i?i  i     i  v v ii
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_116731929_   3195 ACTAGGCTAGACTCCCACCTTTCATCATATACCAAAATTAACTCAAAATG 3244
                          ---- i i   i  i    iv  i       v                 
  L1M4_orf2#LINE/    449 A----GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_116731929_   3245 GATTAAAAACTT-----TAAGA-CAATAAACTATAAAACTCCCAGAAGAA 3288
                            i ? i  i -----     - v -              ii       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAA 543

  chrX_116731929_   3289 AACACACAAGAAACATTTCAGAACATTGGTCTGGGCAAAGAT--CGTATG 3336
                             i vi? v  vvi   ivi  v    vi i     v i -- v  - 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA-G 592

  chrX_116731929_   3337 CTAAAACCTCAAAAGCTCTGGCAACAGAAGTAAAAATAGACAAATGAGAT 3386
                         v  vi  vi       v vi      i   v         i    vi  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_116731929_   3387 TATATCAGACTAAAAAGCTTTTGCACAGCAAAGGAAACAGTTAACAGAAT 3436
                          vi    i v v    i      ii vv       v  vi i  v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_116731929_   3437 GAAGAAACAACTGGCAGGATGGGA-AAAATATT-GCAAGCCATTCATCTG 3484
                            i i     ivi   i      -        -    ii   vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_116731929_   3485 AT 3486
                           
  L1M4_orf2#LINE/    743 AT 744

Transitions / transversions = 1.83 (117 / 64)
Gap_init rate = 0.02 (14 / 744), avg. gap size = 2.14 (30 / 14)  

 574 20.90 8.46 1.99  chrX_116731929_116736388     3768  3968 (492)    L1M4_orf2#LINE/L1      695   908 (0)  

  chrX_116731929_   3768 AAAAACAACAACAACAAAA---AAAAAAAAACCTAT---TCATAT----G 3807
                            i     -- v   i  ---i i    v ii ii---      ---- 
  L1M4_orf2#LINE/    695 AAAGACAAC--CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_116731929_   3808 ACACGGGATTAATATCCAAAATACATAAGGAACTG----AACACAACAGC 3853
                          i v    i vi      i    i    i     v----   v   i ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_116731929_   3854 AGAAAAACCCAAATAACCTCATTTAAAAATGTGCAATTGATCTGAACAGA 3903
                          i   i  --        iv   ?       v    vv   i    i   
  L1M4_orf2#LINE/    793 AAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_116731929_   3904 CATTTCTC---AAAAGACATACAAATGGCCAACAGGTACATAAATAAATG 3950
                                 --- i    i              i i i    i  v i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_116731929_   3951 CTCAACATCTCTAATCAT 3968
                                  v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.42 (29 / 12)
Gap_init rate = 0.03 (7 / 214), avg. gap size = 3.00 (21 / 7)  


2713 26.69 4.35 0.34  chrX_116737323_116742945.rev     2454  3326 (2297)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116737323_   2454 TGGAAACACATCCCATGCTTATGGATAGGAAGA-TCAATATCATAAAAAT 2502
                               v i        i i      v      - i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116737323_   2503 AGCCGTACTGCCCAAAGCAATCTAGAGATTCAATGCAATCCCTATCAAAA 2552
                         i  vi    v      vii     v        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116737323_   2553 TACCAACAACATTTTC-ACAGAATTAGAGAAAACAAGCCTAAAATTCATA 2601
                          v   i vi v    i-i     v v  v  ivii v             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116737323_   2602 TGGAACCAAAAAAGAGCCTGAATAGCTAAAGCAATCCTGAGCAAAATGAA 2651
                              viiv  ii  v  v       i   i     i   iv  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_116737323_   2652 CAAATCTGTAAGCATCACATTACCAGACTTCAAGTTATACCGCAAGGCTA 2701
                             vi  v i vv     i v  vi i     iviv   ii   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_116737323_   2702 GAGTTACCAAAACAGAAGGATACTGTTATAAAAGTAGACACGTAAACCAA 2751
                         v   v i   i    viv i     vi    iii      ii  i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_116737323_   2752 TGGAACAGAATAGAGAACCCAAGAGTGAAGACAAATACTTATAACCAACT 2801
                              i     v    ii   ii i i  vv  v i i    iii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_116737323_   2802 GATCTTTGACAAAGCTGACAAAAATAT-AAATCAGGGAAAGGACACCCTA 2850
                            i  i     i v  v   i vi  -v   -i       i i vi  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTCTT 399

  chrX_116737323_   2851 TTGAATAAATCATCCTGGGAAAACTGGAT--------------------- 2879
                           v  i    vi v      v        ---------------------
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_116737323_   2880 -------CCCTGTCTTTTACCTTATACAAAAATCAACTCAAGATGGATCA 2922
                         -------    ii  ivi   v           i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_116737323_   2923 AAGACTTAAATCTAAGGCCTGAAACCCATAGACATTCT-AGAAGATAACC 2971
                         ?    i     v    iv  i    i-   i - i   -      v   v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACT-ATAAA-ACTCTTAGAAGAAAACA 547

  chrX_116737323_   2972 TAGGAAAAATTCTTCTAGACATTGGCCTAGGCAAAGAATTGATGACTAAG 3021
                             ?iv  v     vv   v    vi       v iv  vv iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_116737323_   3022 ACCCCAAAAGCAAATGTAACTAAAATAAAAAGAAATAAATGAGACCTAAT 3071
                           v         v v i   v   iv     v i      vi   i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_116737323_   3072 TAAACTAAAAATCTTCTTTATAGCAAAAGAAGTAATCATCAGAGCAGACA 3121
                         i   v v    v   i v iivv    i  viiv    vv i  iii v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_116737323_   3122 GATGACCTACAGAATGGGAGAAAATATTTGTAAACTATGTATCTGACAAA 3171
                           ii   i                      i   ii  i       i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_116737323_   3172 GGACTAATACCCACAATCTGCAAGGAACTCAAACAAATGAGCAAGAAAAA 3221
                              vi  i   v   v ii  i      vv    v v ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_116737323_   3222 -AC---TAATCCCATGAAAAAGTAGGCAAATGACATGAACAGACATTTCT 3267
                         -  ---   i  v  v?    i i      v  iv    i          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_116737323_   3268 CACAAGAAGATATACAAATGTCCAACAA--ACATGAAAAAATGCTCAACA 3315
                          vv                 v    i  --         i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_116737323_   3316 TCACTAATTAT 3326
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.30 (130 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.73 (41 / 11)  

2839 27.64 1.07 0.47  chrX_116737323_116742945.rev     4285  5127 (496)  C L1M4_orf2#LINE/L1   (0)   908    61  

C chrX_116737323_   5127 CCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAATGAC 5078
                              iv i  i  i        i  v     i     iv v   iivi 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

C chrX_116737323_   5077 TTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACAA 5030
                         i  i  ii     -   -- v  i  - iii    i           vvi
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATG 158

C chrX_116737323_   5029 AAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGAACAAAGCTG 4980
                         v  ii  v  v v  vi    iv     i i ivv i          i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

C chrX_116737323_   4979 GAGGCATCACGTTACCTGACTGCAAACTATACTACAAGGCTACAGTGACC 4930
                             vv    ii v  ii i v    viv        i        i i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

C chrX_116737323_   4929 AAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATG-AACAG 4881
                           i    ii         i iv ii i   v             -  i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

C chrX_116737323_   4880 AAC--AGAGCCCTCAGAAACAACGCCGCATATCTACAACTATCTGATCTT 4833
                           i--    i  --     i  vv  ii i  i  iiiii vi    i  
  L1M4_orf2#LINE/    309 AATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

C chrX_116737323_   4832 TGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCTGTTTAATA 4783
                         i     ivv  vv  i v  vvv           i  vvi  v  i  i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

C chrX_116737323_   4782 AATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGAT 4733
                                      v      v  ?   i   i i  iiv    ii    i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

C chrX_116737323_   4732 CCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTT 4683
                             v   i     v              i    i      i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

C chrX_116737323_   4682 AAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCGTTA 4633
                            i  v   v       i      vi i           v    ?  v 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

C chrX_116737323_   4632 CCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAA 4583
                         viv   iv   v v  vv i     v ii   v ivv  vi         
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

C chrX_116737323_   4582 GCAATGGCAACAAAAGTCAAAATTGACAAATGGGATCTAATTAAACTAAA 4533
                            vvi          vv     v  i    v   ii v  i   v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

C chrX_116737323_   4532 GAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAGCAGGAAATCTA 4483
                         i     i  ii vv    i  v    i  vv i   i iv  iv  i i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

C chrX_116737323_   4482 CAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAGGGCTAATA 4433
                                         v       vii ivi      i  i  i  vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

C chrX_116737323_   4432 TCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAC--- 4386
                                 v  i  v      vv    v iv i  v     i    v---
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

C chrX_116737323_   4385 CCCAAC-AAAAAGTAGGCAAAGGTTATGAACAGACACTTCTCAAAAGAAG 4337
                              i-?    i i        v v    i     i     v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

C chrX_116737323_   4336 ACATTTATGCAGCCAATAGACACATGAAAAAGTGCTCATCATCACTGGCC 4287
                          i  vi viii       ii          ii      v     ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

C chrX_116737323_   4286 AT 4285
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.01 (8 / 848), avg. gap size = 1.62 (13 / 8)  


3196 27.89 0.33 0.22  chrX_116743544_116749937.rev     4997  5903 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116743544_   4997 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5046
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116743544_   5047 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116743544_   5097 TACCAATGACTTTCTTCACAGAATTGGAAAAAAT-ACTTTAAAGTTCATA 5145
                          v   iivi i  i  ii     v v  v  iv - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116743544_   5146 TGGAACAAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5195
                              vviv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_116743544_   5196 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5245
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_116743544_   5246 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGATCAA 5295
                               i   i    ii         i iv ii i   v i         
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_116743544_   5296 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT 5343
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_116743544_   5344 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5393
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_116743544_   5394 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5443
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_116743544_   5444 AACTGGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5493
                          ii    i  i v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_116743544_   5494 AAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5543
                          ?    i    ii v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_116743544_   5544 AGGCATTACCATTCAGAACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5593
                            ?i v viv   ivi  v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_116743544_   5594 CACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTAATT 5643
                                    vvi     i    vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_116743544_   5644 CAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAATGAACAG 5693
                         v  v v  i i   i  ii vv v  i  v    i  vv i i    v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_116743544_   5694 GCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5743
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_116743544_   5744 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 5793
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_116743544_   5794 GGAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 5843
                         iv   i     v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_116743544_   5844 AAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCAT 5893
                         v        i  vi viii     v ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_116743544_   5894 CACTGGCCAT 5903
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.67 (5 / 3)  


3239 27.01 0.55 0.44  chrX_116790094_116800210      492  1398 (8719)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_116790094_   1398 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1349
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_116790094_   1348 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1299
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_116790094_   1298 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1251
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_116790094_   1250 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1201
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_116790094_   1200 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATAGTACAAGGC 1151
                                i      vv       v  ii i      viv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_116790094_   1150 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1101
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_116790094_   1100 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 1053
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chrX_116790094_   1052 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1003
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_116790094_   1002 CTATTTAATAAATGGTGCTGGAA-AACTGGCTAGCCATATGTAGAAAGCT 954
                           v  i  i            i -      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_116790094_    953 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 904
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_116790094_    903 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 854
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_116790094_    853 CTAGGCATTACCATTCAGGACATAGGCATAGGCAAGGACTTCATGTCCAA 804
                         v    ?i v viv   iv   v v  vv       v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_116790094_    803 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 754
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_116790094_    753 TGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 704
                          v   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_116790094_    703 AGGTAACCTACAAAATGGGAGAAAATTTTTTCAACCTACTCATCTGACAA 654
                           ii    i   i             v   v   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chrX_116790094_    653 AGGGCTGATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAAA 604
                         i  i  vi          v  i  v      vv    v iv i  vi   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chrX_116790094_    603 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 554
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chrX_116790094_    553 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATTAAAAAATGCTCATC 504
                           v        i  vi viii     v  i     v    i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chrX_116790094_    503 ATCACTAGCCAT 492
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  

3396 24.24 0.87 1.75  chrX_116790094_116800210     8709  9624 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116790094_   8709 TGGAAAGGTATTTCATGATCATGGATTGGAAGAACCAATATTATTAGAAT 8758
                                i   ii    v               vii      i   ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116790094_   8759 AGCCA-ACTACTCAAAGCAATCTACAGATTCGATGCAATCCCTAACAATA 8807
                         i  v -   v i    vii            i i          v   v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116790094_   8808 TACCAATGACATTCTTCACAGAAATAGAAAAAA-AATCCTAAAATCCATA 8856
                          v   iivi v  i  ii       v  v  iv-i          i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_116790094_   8857 TGGAACCACAAAAGACCCAGAATAGTCAAAGCTATCCTGAGCAA-AATAA 8905
                              vii   ii            i    i v   i   iv  -  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_116790094_   8906 AAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCTA 8955
                         v   ii       v     i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_116790094_   8956 TAGCAACCAAAACAGCATGGTACTATCATAAAAACAGACACATAGATAAA 9005
                         i  i  i   i    ii       iv     ii i     i      v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_116790094_   9006 TAGAACAGAATAGAAAACCCAGAAACAAATCCA--CATTCCTACAGTAAA 9053
                          i   i     v  i ii       i   i   --    --  ii  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAA 348

  chrX_116790094_   9054 CTCATTTTCAACAAAGGTGCCAAGAACATGTGCTGGGGAAAAGACAGTCT 9103
                         i v      i    i          v   viiv        ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_116790094_   9104 GTCTTCAATAATTGATGCTTGGAAAACTGGATATCCATATACAGAAGAAT 9153
                         --i     i  v  i    v   v         ?   i  i  i      
  L1M4_orf2#LINE/    399 --TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_116790094_   9154 GAAACCAGATCCCTATTTCTCCCCATATGCAAAAGTCAAATCAAAATGGA 9203
                            iiii  i     ii  v v      i     i i  v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_116790094_   9204 TTAAAGACTTAAAGCTAAGACTTCAAACTATGAAACTTCCATAAGAAACC 9253
                          i ?    i    vv     vi v       i     iii v      v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_116790094_   9254 ATTGGGGAAAATCTCCAGCACATTTCACTGGGCAAAAATTTCTTGAGA-- 9301
                           v  ? v      i ivv  v  vvii i     vii      -   --
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATA 595

  chrX_116790094_   9302 -AACACCCTGCAACTACAGACAACCAATGCAAAAATGGACAAATGGGAAT 9350
                         -i     --iv  vi   ii    v  v v      i  i    v   v 
  L1M4_orf2#LINE/    596 TGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_116790094_   9351 CATATCAAGCTAAGAGGTTTCTTCACAGCAAAGGAAGCAATCAATAAAGT 9400
                         i-i     iv v i iii  i vii vv       vi v     v     
  L1M4_orf2#LINE/    644 T-CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_116790094_   9401 GATTGTCAATTATTTAACCCACAGAATGGAAGAAAATATTTCCAAACTAC 9450
                           -----  vv i--              i           v    ii i
  L1M4_orf2#LINE/    693 GA-----AAAGAC--AACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_116790094_   9451 CCATCTGGCAAGGGATTAGTAACCAGAATATATAAGGAGCTCAAACAACT 9500
                         vi     ii      i v   v             i  i   vv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_116790094_   9501 CAATAGGAAGAAGTCTAATAATCCCATCAAAATAAGGGACAAAATATTTG 9550
                              iv  i   v v     i  v  i?   -  v  i    iv     
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTG 834

  chrX_116790094_   9551 AATAGACATTTCTCAAAAGAAGACATACAAATGGCAAACGGGCACATGAA 9600
                                       v        i           v  iii         
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_116790094_   9601 AAGGTGCTCAACATCACTGATCAT 9624
                            i            ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (137 / 81)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


 260 18.07 9.64 2.41  chrX_116924393_116926303.rev      451   533 (1378)  C L1M4_orf2#LINE/L1   (0)   908   820  

C chrX_116924393_    533 TGAGCAGTGG-TTTG--TAG----TTCTCCTTGAAGAAGACATTTATGCA 491
                           i   iv  -    --   ----      --i       i  vi viii
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCC--AAAGAAGATATACAAATG 867

C chrX_116924393_    490 GCCAAAAAACA-ATGAAAAAATGCTCATCATCACTGGCCAT 451
                              v  i  -       i       v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.06 (5 / 89), avg. gap size = 2.00 (10 / 5)  

3033 27.48 0.47 0.47  chrX_116924393_116926303.rev      560  1407 (504)    L1M4_orf2#LINE/L1        1   848 (60)  

  chrX_116924393_    560 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 609
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116924393_    610 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 659
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116924393_    660 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTTA 707
                          v   iivi i  i  ii     -   -- v  i  - iii    i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_116924393_    708 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 757
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_116924393_    758 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 807
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_116924393_    808 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 857
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_116924393_    858 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 905
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_116924393_    906 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 955
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_116924393_    956 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1005
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_116924393_   1006 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1055
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_116924393_   1056 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1105
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_116924393_   1106 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 1155
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_116924393_   1156 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1205
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_116924393_   1206 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1255
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_116924393_   1256 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 1305
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_116924393_   1306 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1355
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_116924393_   1356 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 1405
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_116924393_   1406 TC 1407
                           
  L1M4_orf2#LINE/    847 TC 848

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.01 (5 / 848), avg. gap size = 1.60 (8 / 5)  


3086 27.54 0.56 0.56  chrX_116934602_116936748.rev      763  1648 (499)    L1M4_orf2#LINE/L1        1   886 (22)  

  chrX_116934602_    763 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 812
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116934602_    813 GACCATACTGCCCAAGGTAATTTACAGTTTCAGTGCCATCCCCATCAAGC 862
                          i v     v     iv i  i     v    ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116934602_    863 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 910
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_116934602_    911 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 960
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_116934602_    961 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1010
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_116934602_   1011 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1060
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_116934602_   1061 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCTCATATCTACAACT 1108
                                i    i--    i  --        vv  vi i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_116934602_   1109 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1158
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_116934602_   1159 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1208
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_116934602_   1209 GAAACTGGACCTCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1258
                            ii      i  v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_116934602_   1259 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGGAAAC 1308
                          i ?    i    i  v   v       i      vi i      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_116934602_   1309 CTAGGCA-ATACCATTCAGAACATAGGCATGGGCAAGGACTTCATGTCTA 1357
                         v    ?i- v i -   ivi  v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_116934602_   1358 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1407
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_116934602_   1408 ATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCACCAGAGTGAA 1457
                           iv  v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_116934602_   1458 CAGGCAACCTACAAAATGGGAGAAAATTTTTTCAACCTACTCATCTGACA 1507
                         v  i     i   i             v   v   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_116934602_   1508 AAGGGCTAATATCCAGAATCTACAATGAGCTCAAACAAATTTACAAGAAA 1557
                          i  i  vi          v  i  v  i   vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_116934602_   1558 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 1607
                           i     i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_116934602_   1608 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAA 1648
                            v        i  vi viii     v  i          
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (7 / 886), avg. gap size = 1.43 (10 / 7)  


3099 27.34 0.77 0.66  chrX_116947075_116953350     4877  5783 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_116947075_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116947075_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4976
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_116947075_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_116947075_   5025 TATGGAACCAAAAAAGAGCCCGCATCACCAAGGCAATCCCAAGCCAAAAG 5074
                                viiv  ii  v  v v  vi    ii     iii ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_116947075_   5075 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_116947075_   5125 TACAGTCACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGATC 5174
                               v i   i    ii    i    i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_116947075_   5175 AATG-AACAGAAC--AGAGCCCTCAGAAACAACGCCGCATATCTACAACT 5221
                             -  i    i--    i  --     i  vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_116947075_   5222 ATCTGATCTTTGACTAACCGGAG--AAAAACAAGAAATGGGGAAAGGATT 5269
                          vi    i  i   v i--  v --  i v  vvv           i  v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAG--GGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_116947075_   5270 CCCTATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5319
                         vi  v  i  i     i        v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_116947075_   5320 CTGAAACTGGATCCCTTCCTTATACCTTATACAAAAATCAATTCAAAATG 5369
                         v    ii    i    v   i i   v           i  i        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_116947075_   5370 GATTAAAGACTTAAATGTTAGACCCAAAACCATAAAAACCCTAGAAGAAA 5419
                            i ?    i       v   v i     i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_116947075_   5420 ACATAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5469
                                ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_116947075_   5470 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5519
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_116947075_   5520 AATTCAACTAAAGAACTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5569
                         v  iv  v v  i     i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_116947075_   5570 ACAGGAAACCTAAAAAATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5619
                          v  iv    i v i             v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_116947075_   5620 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5669
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_116947075_   5670 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5719
                            i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_116947075_   5720 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5769
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_116947075_   5770 CCATCACTGGCCAT 5783
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2916 23.67 1.18 3.31  chrX_116957212_116961828     2877  3721 (896)    L1M4_orf2#LINE/L1        1   827 (81)  

  chrX_116957212_   2877 TGGAAAGATATTTCATCTTCATGGATTGGAGGAATCAATATTGCTAAAAT 2926
                                    ii   v             i  v i       i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_116957212_   2927 GTCCATACTACCCAA--TGCTATTTACAGATTCAATGTAACCCCTATCAA 2974
                          v v     v     --  --  i           i i  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTG--ATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_116957212_   2975 AATACCAATGACATTCTTCACAGAAATAGAAATAATAATCCAAAAATTAA 3024
                            v   iivi v  i  ii       v  v viv i    v      v 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_116957212_   3025 TA-AGAACCACAAAAGACC-AGAATTGCCAAAGTTACTCTGAGGAAAAAA 3072
                           -i   vii   ii    -     v      ii- v   v--      i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAAC-AATCTT--GAAAAAG 195

  chrX_116957212_   3073 AAAAAAAAAGGAAAATCAGAAGAATCACATTACCTCACCTCAAATTATAC 3122
                           i  v    ----- ii  i  v     i v  iv ii     viv   
  L1M4_orf2#LINE/    196 AAGAACAAAG-----TTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_116957212_   3123 TCTAGAGCTACAGTAACCAAAACAGCATGGTGCTGGAATAAGAAAAGACA 3172
                          vi i           i   i    ii    i    v     i v     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_116957212_   3173 CATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAATCCATACATCT 3222
                         i     i        i     v    ii           i        i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_116957212_   3223 TCAATGAACTCATTTTTTACAAAGGTGCCAAGAATATGCATTAGGGAAAG 3272
                         viii v  i v     iv    i          vi  v  v i       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_116957212_   3273 GACAGTCTCTTCAATAAATCATGCTGAGAAAACTGGGTATCCATATGCAG 3322
                         i i     i     i    vi     i  v      i  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_116957212_   3323 AAGAATGAAAGTAGACCCCTATCTCTCACCATATAGAAACATCAAATCAA 3372
                                  iv i        i   v         v   v  i  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_116957212_   3373 AATGGATTAAAGACATAAATCTAAGACCTCAAACTATGAAACTTCTAAAA 3422
                                i ?    v     v     v  v       i     ii  i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_116957212_   3423 GAAAACATTGGGGAAAGACTCCAGAATATTGGTCTAGGCAAAGATTTCTT 3472
                                 v  ? v  iv  i ivi iv    vi       v i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_116957212_   3473 GAGCA--ATACCTGATAAGCACAGACAACCAAAGCAAAAATGGACAAATG 3520
                         iiii -- i   -- v       ii    v    v      i  i    v
  L1M4_orf2#LINE/    591 AGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_116957212_   3521 GGATCACATCAAG-TTAAAAAGTTTCTACACAGCAAAGAAAACAATCAAC 3569
                            iiv      i-       v   - iii vv     i v  v     v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAG 687

  chrX_116957212_   3570 AAAATGAAGAGACAACG-ATAGA-TGGATAATTTGCATCTATTTTTTCCC 3617
                            i    i       v- i   -   ivi ----- vv     ------
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGA-----AAATATTT------ 726

  chrX_116957212_   3618 ACATGTAAACCATCCATCTGACAAGTGATTAATAACCAAAATATGTAAGG 3667
                         ---- i   i   vi      i   v  i vi  v   i     i   i 
  L1M4_orf2#LINE/    727 ----GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_116957212_   3668 AGCTCA-GCAACTCTATAGAAAAAATTCTAATAATCCAATTAAGAAATGG 3716
                          i   v-i      v   iv     vv v     i      ? i      
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_116957212_   3717 GCAAA 3721
                              
  L1M4_orf2#LINE/    823 GCAAA 827

Transitions / transversions = 1.51 (118 / 78)
Gap_init rate = 0.02 (16 / 827), avg. gap size = 2.38 (38 / 16)  

 348 22.95 1.64 0.00  chrX_116957212_116961828     4003  4124 (493)    L1M4_orf2#LINE/L1      785   908 (0)  

  chrX_116957212_   4003 TCAAAAAAAAAAAAAAAAAGAAAGAAA--AAGAAATGGGCAAACTATCTG 4050
                             v  v     i v   v  vvv  --? i           vv  i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_116957212_   4051 AATAGACATTTCTCAAAAGAAGACATACATATGGCAAACAGGCCAATAAA 4100
                                       v        i     v     v  i i  vv  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_116957212_   4101 AAGGTGGCTGATATCATTGATCAT 4124
                            i  viii i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.80 (12 / 15)
Gap_init rate = 0.01 (1 / 124), avg. gap size = 2.00 (2 / 1)  


3097 26.72 1.66 1.00  chrX_117009313_117014672     3975  4876 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_117009313_   3975 TGAAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4024
                           i  ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_117009313_   4025 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4074
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_117009313_   4075 TACCAATGACTTTCTTCACAGAA--TGGGAAAAAACT-ACTTTAAAGTTC 4121
                          v   iivi i  i  ii     --  --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_117009313_   4122 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCGATTCCAAGCCAAAA 4171
                                 viiv  ii  v  v v  v     iv i  iiii ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_117009313_   4172 GAACAAAGCTGGAGGCATCACACTACCTG-CTTCAAACTATACTACAAGG 4220
                                 i      vv       v  ii-i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_117009313_   4221 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 4270
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_117009313_   4271 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 4318
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_117009313_   4319 TATCTGATCTTTGACAAACTGGAGG--AAAACAAG-CAATGGGGAAAGGA 4365
                         i vi    i  i     ---  iv --  i  v v-            i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAA---GGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_117009313_   4366 TTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 4415
                          vvi  v  i  i              v      v  ?   i   i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_117009313_   4416 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 4465
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_117009313_   4466 TGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGG 4515
                              i ?    i    i  v   v       i      vi i      i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_117009313_   4516 AAACCTAGGCA-ATACCATTCAGAACATAGGCATGGGCAAGGACTTCATG 4564
                             v    ?i- v i -   ivi  v v  vv i     v ii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_117009313_   4565 TCTAAAACACCAAAAGCAATGGCAACAAAAACCAAAATTGACAAATGGGA 4614
                         vv  vi            vvi         ivv     v  i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_117009313_   4615 TCTAATGAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAG 4664
                         ii v  v   v i  i i   i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_117009313_   4665 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATTG 4714
                             v  i     i                 v       vii ivi  iv
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_117009313_   4715 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAAAAATTTA-CAG 4763
                           i  i  i  vi          v  i  v      vv v  i i -i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_117009313_   4764 GAAAAA----AATAACCCCATCAAAAAGTGGGCAAAGGCTATGAACAGAC 4809
                         v     ----        v  i?    i          v v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_117009313_   4810 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAGGACACATGAAAAAATGC 4859
                          i     v        i  vi viii     viii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_117009313_   4860 TCATCATCACTGGCCAT 4876
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


3409 17.80 4.02 1.47  chrX_117053039_117055180.rev      905  1651 (491)    L1M4_orf2#LINE/L1      143   908 (0)  

  chrX_117053039_    905 AATTCATATGGAATTTCAAGGGACGCTGAATAGCTAAAATAATCTTGAAA 954
                                      v v        v v       i    i          
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_117053039_    955 AAGAAAAA---AGTTGGACATCTCACATTTCCTGATGCCAAAACATGTTA 1001
                              i  ---       viv      i    ii  vi      v ii  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_117053039_   1002 CAAAGCTGTAGTAATCAAAATGGTGTGGTTCTGACGAAAAGGCAAACACG 1051
                                ii         i ii       v   i iv  i ii i   ii
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_117053039_   1052 TAGAACAATGGAATAGAATAGACAGCCCAGAAATAAGCCCTAGTGAAT-- 1099
                             v              v  v  i          i   --i iv  --
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC--ATACATTT 340

  chrX_117053039_   1100 ATGGTCAAATGATTTTTGACAAGGGTGCTA-GATCACTCAATGGAGAAAG 1148
                                 v       i           i -  i  i       i     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_117053039_   1149 TACAGTCTGTACAAAAAAAAAAAGGTTTTGGGAAAAT--AATATCTGCAT 1196
                         v i     v v   v   v----   vi     v  i--i   ? ii   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAAT----GGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_117053039_   1197 GCAAAAGAATAAAGTTGGACCCCTACCTTACATTATATACAAAAATTAAC 1246
                                   i                 i   ii                
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_117053039_   1247 TCAAAATG-ATTAAAGATCTAA-TGTAACACCTAGAACTATAAAACTAAA 1294
                                 -  i ?   i    -     v v   i            ---
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT--- 533

  chrX_117053039_   1295 CTGCTAGAAGAAAACATAGAGGAAAA-CTTCACGACATTGCATTTGACAA 1343
                           --               i? v   -    ii   v   vi  v i   
  L1M4_orf2#LINE/    534 CT--TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_117053039_   1344 TTGTTTATTGGATATGGCAC-ATAAGTACAGCCAACAAAAGCAAAAATAG 1392
                          v    v  i      i   - v   i   iv         v        
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_117053039_   1393 ACTAA---------ATCAAACTTTAAAACTTTTGTGCATTATAGGTCACA 1433
                          iv  ---------      v  v             v i v   v   v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_117053039_   1434 ATCATTAGAGTGAAAAGGCAACCTATGGAATGGGAGAAAATATTTGCAAG 1483
                             vv i         i     i ii                      i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_117053039_   1484 TCATATATTCAATAAGTGGTTAATATCCAGAATATATAAAGAA---TTAC 1530
                                 iii     v ii vi                    ---    
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_117053039_   1531 AACTCAACAACAAAAA------CAACACAGTTATAAAATGGGCAAATGAC 1574
                                i  i     ------i   v  i  ?v            v  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_117053039_   1575 TTAAATAGGCATTTCTCCAAAGATGATGGACAAATGGCCAACAGGCACAT 1624
                           i     i              v   iv            i i      
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_117053039_   1625 GAAAAGATGTTCAGCATCACTAATCAC 1651
                                  i   i     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (80 / 49)
Gap_init rate = 0.02 (15 / 766), avg. gap size = 2.73 (41 / 15)  


2963 27.89 0.88 0.77  chrX_117157052_117163463     5013  5919 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_117157052_   5013 TGGAAGAACATTCCATCCTCATTGGT-AGAAGAATCAATATCATGAAAAT 5061
                              ii i  i    vi    v i -i     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_117157052_   5062 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5111
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_117157052_   5112 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 5159
                          v   iivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_117157052_   5160 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5209
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_117157052_   5210 GACAAAGCTAGAGGCATCACGCTACCTGACTTCAAACTATACTATAAGGC 5259
                         i      i i    vv    i  v  ii i      viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_117157052_   5260 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGGCC 5309
                                 i   i    ii         i iv ii i   v      ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_117157052_   5310 AATGGAACAGAAC--AGAGCCATCAGAAATAACGCCACATATCTACAACT 5357
                                i    i--    i --         vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTC 346

  chrX_117157052_   5358 ATCTGATCTTTGACAAACCTGACAAAAAAAAAGAAATGGGGAAAGGATTC 5407
                          vi    i  i     ivv  v   i vv v-vv           i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGGGGAAAGAATAG 395

  chrX_117157052_   5408 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5457
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_117157052_   5458 TGAAACTGGATCCCTTCTTTGCACCTTATACTAAAATTAATTCAAGGTGG 5507
                             ii    i    v i ii    v     v        i    ii   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_117157052_   5508 ATTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5557
                           i ?   ii       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_117157052_   5558 CCTAGG--TAATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTC 5605
                          v    --   - i -   iv   viv  vv i     v ii   v ivv
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_117157052_   5606 TAAAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATC 5655
                           vi            vvi      i   vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_117157052_   5656 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5705
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_117157052_   5706 AACAGGCAACCTAAAAAATGGGAGAAAAATTTTGCTATCTACCCATCTGA 5755
                           v  i     i v i            vv     v vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_117157052_   5756 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5805
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_117157052_   5806 AAAA-ACAAACAACCCCATCAACAAGTGGGGGAAGGATATGAACAGACAC 5854
                             -     i     v  i? v  i    vi      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_117157052_   5855 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5904
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_117157052_   5905 ATCATCACTGGCCAT 5919
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (149 / 101)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


1908 27.26 6.60 3.55  chrX_117582318_117584797.rev     1172  1989 (491)    L1M4_orf2#LINE/L1       66   908 (0)  

  chrX_117582318_   1172 ATTGATTGAGAAATTCAATAT------TGTTAAACTCTCCATTCTCAGGC 1215
                               iv v i      iii------ i i   v  i vii ---- v 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT----GCC 111

  chrX_117582318_   1216 TATTTTGAGGAAGTAGAAAAGATGATTCTAAAGATTATATGGAAATTCAA 1265
                          v     vi   i v  v   v    i     iv i          v   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_117582318_   1266 AGGACGTAGAATAGCCAAAACAACTTTGAAAAAGAA---TAAAGCTGGAG 1312
                         i    vi                ii           ---i    i     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_117582318_   1313 GGCTAACACTACTTGATTTCAAGACTTA------AGTTATAGTAATCAAG 1356
                          i  v     v iii       i     ------  i  i          
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_117582318_   1357 ----TGTGATATTGGCATCAAGATGGGCAAATAGATCAGTGGAAGAGAAC 1402
                         ----    i  i      v i   i i  v        i     v    i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_117582318_   1403 CGAGAATCCAGAAATAG-CCCACACAAATATGAAAAACCGAACTTTTGAC 1451
                         i    i          i-    i   vv    ivv  ii  -i   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA-TTTTCGAC 360

  chrX_117582318_   1452 CAAGGTGCCAAAGTAAATTCAACGTGACAAAAGGAAAGTCTTGTTTTTCC 1501
                         v i        iiiv -     --  ivi    i v      ----   v
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCA-TTCAA--TGGGGAAAGAATAGTCTT----TTCA 403

  chrX_117582318_   1502 CCAAATGGTACGTCTTAAAAAAAAAAAAAACTGTCT-TAAAAAAA-GAGC 1549
                         v        i --- vii v  vvii v ? iiiv -i    i  -  iv
  L1M4_orf2#LINE/    404 ACAAATGGTGC---TGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_117582318_   1550 TTTGACCTCTATTTCATTCCACA------AATGAACTTTAAATATATTAT 1593
                           v    i   ii   iv   i ------   v    iv    iv  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_117582318_   1594 AGACCTAAAC---AAAACTCGGAAAC----AAGTTTCTAGGAGAAAACAC 1636
                                  i--- i i  --i    ----  ii ii   i        i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCT--AAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_117582318_   1637 AGGACAACACTATCAGGATCTTGAGGTAGGCACAGATTTTTGGGACCAGA 1686
                            ?vv v iiv  iv  i    i v      vv i   i vi  ivv  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_117582318_   1687 TACAAAAAGAACAAATTAT----TATAAAATA-ATAAACTGGATTTCATC 1731
                         i  v     v    iiv i----v v      -     i    i      
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_117582318_   1732 AATTACAACCAAAACCAAAATTTTCTGCTCAACCACAGACTCAATTAAGA 1781
                           ----  ii    v ----    v    i-- v vi   v v  i    
  L1M4_orf2#LINE/    649 AA----AATTAAAAAC----TTTTGTGCTT--CAAAGGACACTATCAAGA 688

  chrX_117582318_   1782 AAGTGAATGGTCAAGTCAGAAGCTGGTAAAGAA-ATATACAGCACATATA 1830
                                vi v   vi  v iiv   v i i  -  v i  ivv      
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_117582318_   1831 TCTTGACAAAGGATTTATATCCAGGA------AAGAACTCCCACAAAACA 1874
                            -  i  i   i  i       i ------        ii    vv  
  L1M4_orf2#LINE/    739 TCT-GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_117582318_   1875 ACAATAAAAAG-TAAGCAATGTGATTTCTAAAACGGATAAAAGAC----- 1918
                          i         -i  ii  ivii   ?v-    i  ii   i  i-----
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAA 836

  chrX_117582318_   1919 -AAACATTTCACAAAAGAAAATACAAAAGAGGCCAAGGAACACCTGAAAA 1967
                         - i       v v      i   i v  iv      vi i   v      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_117582318_   1968 AGTGGTAGACATCATCGGTTAT 1989
                         ii  v vi      ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (136 / 83)
Gap_init rate = 0.03 (28 / 843), avg. gap size = 2.96 (83 / 28)  


 559 19.49 0.85 1.69  chrX_117606560_117610248.rev     1373  1490 (2199)    L1M4_orf2#LINE/L1        1   117 (791)  

  chrX_117606560_   1373 TAGAAAAACATCCTAT-TTCATGGGGGCTGGAACACTTATTATTATTGAG 1421
                          i    i i    i  -       i--i     v     v    i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGA--TTGGAAGACTTAATATTGTTAAG 48

  chrX_117606560_   1422 ATGGCAATACTCTGCACATTGAATTACAGATTCACAGCAAATCCTGCCAA 1471
                                     iv  v     vi          vv    vi   ii   
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_117606560_   1472 AATCCCAGCGGCCATTTTT 1490
                                  v   v     
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTT 117

Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.02 (2 / 117), avg. gap size = 1.50 (3 / 2)  

3299 14.46 4.92 2.09  chrX_117606560_117610248.rev     2154  2824 (865)    L1M4_orf2#LINE/L1      140   829 (79)  

  chrX_117606560_   2154 TAAAATAAAAATGGAAATGCGAGGGGCCTAGAATATACAAAACAATTTTG 2203
                               vv v          i    i  i      vv         i   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_117606560_   2204 AAAAAGAA---TAAAGTTGGAGGACTCACACTTCCAAATTTCAAAATCTT 2250
                                 ---i                       v          -   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA-CTT 238

  chrX_117606560_   2251 ACTACAAAGCTATAGTAATTAAGACTTTGTGGCACTAGCGTAAGGACAGA 2300
                                     i      i     vv     i   i  i      i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_117606560_   2301 TACAGAGGTCAATAGAATAGAACTAAGAGTCCAGAA-TAAACCCACATAT 2349
                         i i v  i     i        i i           -        i i  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_117606560_   2350 TTTTGGTCAATTGATTTTTTATAAGGGTGCCAAGGCAATTGGATGGGGGA 2399
                           v               iv i            i v   vi      i 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_117606560_   2400 AAGAT--TCTTTTCAACAAATGGTGCAGGGAAAACTGGTTATCCACATGC 2447
                          ii  --                   v    v      v  ?        
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_117606560_   2448 AAAAGAATGAATCTGAATCCCTACAACACACCATATACAAAA-TTAGCTC 2496
                                    vi  i i      vv                -   i   
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_117606560_   2497 AAAATGGACCAAAGACCAAAA-GTAAGAGTTAAGATTATAAAACTCTTAA 2545
                                 i  ?     v   -       i   i i             i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_117606560_   2546 GAGAAAACATAGGTGTAAATTTCTGTGAAATTGGATTACGCAA-GGTCTT 2594
                         i            ?      i ii    vv    i   v    -   -  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TT 587

  chrX_117606560_   2595 CTTAGATACAATGCCAAA-GCACAGGCAACAAAAGAAAA--TA--TAAAT 2639
                                 ii ii     -     i              --  --     
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_117606560_   2640 TGGACTGCATCAAAATTTTTAAAAACTTGAATGCTTCAAAGAACACCATC 2689
                               v          ---        vvi          i    i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATT---AAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_117606560_   2690 ATGAAAGTGAAAAGGCAACACACAGAACAGGAGAAATATGTTT--AAATC 2737
                          v            i    v       ii       -  i   --     
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA-ATATTTGCAAATC 733

  chrX_117606560_   2738 ATATA------------CTTGCATCTCGAATA----AAGAACCCT-GCAA 2770
                              ------------    i   iv     ----      i  -i   
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_117606560_   2771 CTCAACAATAATAGTAATAATAGTAAAGCAACCTGATTTAAAAATGGGCT 2820
                              i     -------  -  vv  ii    ii   ?          v
  L1M4_orf2#LINE/    784 CTCAATAATAA-------AA-AGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_117606560_   2821 AAGG 2824
                             
  L1M4_orf2#LINE/    826 AAGG 829

Transitions / transversions = 1.91 (61 / 32)
Gap_init rate = 0.03 (19 / 690), avg. gap size = 2.47 (47 / 19)  

 433 17.20 0.00 1.08  chrX_117606560_117610248.rev     3106  3198 (491)    L1M4_orf2#LINE/L1      817   908 (0)  

  chrX_117606560_   3106 AAATGGTCTAAGGACTTAAAAGAGATATTTCTCTGAGGAAGATACAAAAA 3155
                               v v     i  -i  v   i       ii i       i v   
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTT-GAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_117606560_   3156 TGGCCAGTAACCACATGAAAGAATTCTCAACATCATTAGACAT 3198
                               i   v         ii  v          ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1)  


4102 17.35 3.74 0.79  chrX_117648734_117650608.rev      503  1384 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_117648734_    503 TGGAAACACATCCCATGTTCACGTATTAGAACACTTAATATTGTTAAGAT 552
                               v i            i v   i   v                  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_117648734_    553 GTCAATACTATCCAAAGTGATATATAGATTCAATTCAATCCTTATCAAAA 602
                          v       vi     v    v  i        iv      i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_117648734_    603 TCTTAATGGCATAGTTTTGCAGAAATAGAAAAATCCATCCTAAAATTCTT 652
                           ii iiv  v -v            v  v  iiiv            v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_117648734_    653 ATGAAATCTCAAGGAACCCTGAATAGCCAAA-CAGTCTTGAAACGGAAAA 701
                            i  viv     i    v           -  i        vi   i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_117648734_    702 ACAAAGCTGTAGGACTCACACTTCCTGATTTCTGAACTTACTACAAAGCT 751
                               i  v               ii     vi                
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_117648734_    752 GCAATAATCAAAACAGTGTG-TACTGGCATAAAGACAGACATACTGATCA 800
                         i  i       i        -           i  i       iv     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_117648734_    801 ATGTAATAGAATAGACAGTCCAGAAATAAACC-ATCACATGTATGGTCAA 849
                            v        v  v                -  -    v         
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACATTTATGGTCAA 348

  chrX_117648734_    850 ATGATTTT-GACAACAGTGCCAAGACCACTCAATGCAGA-----CAATCT 893
                         v       -     vi            i      vi  -----i i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_117648734_    894 TTTCAACAAATGGTGCTGGGAAAACTGGATATCCATATGAAAAAGAATGA 943
                                              v         ?   i   v          
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_117648734_    944 AATTGGACGCTTACCCAATACCAAGTAAAAAAAA-AATTCAAAATGGATC 992
                          i      v i    iv i    vi  v     v-  i            
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_117648734_    993 AGAGACTGAAATTTTAAGA-CTAAAACTATAAAATTTTTAGAAGAAAACA 1041
                          ?    iv    v -    -              i i             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_117648734_   1042 TAAGACAAAAGCTTCATACCATTGGATTCAGCAACAATTTCTTGGATATG 1091
                           i ?vv   v    i iv v    i  vi    iii      i      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_117648734_   1092 ACACCAACAATGTAGGTAACAAAAGAAAAAATTGACGAATTGGATTTCAT 1141
                                v iiii i i               v  ii       i     
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_117648734_   1142 GGAAAAAATTAAAA---CGTGTGCATCAAA--ATATT--CACAGAAA--- 1181
                         v---          ---iv     v     -- i i --  -     ---
  L1M4_orf2#LINE/    648 C---AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA-AGAAAGTG 693

  chrX_117648734_   1182 -AAAG-TGACTCACAGAATGGAA--AAATATGTGTAAATCATATATCTGA 1227
                         -    -ii  i          i --      v  i               
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_117648734_   1228 TAAGGGATTAATATCCAGAATATACAGAGAATGCCTAAAACTCAACAATA 1277
                                i vi             i i    iv i  v       i    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_117648734_   1278 AAAAAA-----AATTCAATTCAGAAATAGGCAAAGG-CTTAAATAGATAT 1321
                             i -----  ii     ? i    i        -i  i      i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_117648734_   1322 TTCACCAACAAAGATAAGGAAATAGCCAATAAGCACATGAA--GGTGTTC 1369
                            v    vi      viv    i                 -- i  i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_117648734_   1370 ATCATCACTAATATT 1384
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (91 / 58)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.90 (40 / 21)  


 697 25.93 1.85 0.00  chrX_117730906_117733786.rev      781   942 (1939)    L1M4_orf2#LINE/L1        3   167 (741)  

  chrX_117730906_    781 GAAAGACATTTGATCATCCTGGTTTAGAGGGCCAAATATTGATAAAATGG 830
                               i  iiv  vv  v   v  i  i i iv       v   i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_117730906_    831 CAAT---CTACAGATTGATCTGTAGATTCAATGTTATGTCTAGCATAATT 877
                             --- iv  i        ii        i iv  vi   v  v   i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_117730906_    878 TCAGCTGGCTTCTTTGTAGAAACTGAGAAACTGATCCTAAAATTCACACA 927
                         i      v   i    i     i   v  i                i ii
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_117730906_    928 GAAATACAGGGAGCC 942
                              i  i  ii  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACC 167

Transitions / transversions = 2.00 (28 / 14)
Gap_init rate = 0.01 (1 / 165), avg. gap size = 3.00 (3 / 1)  

2920 12.65 1.38 1.58  chrX_117730906_117733786.rev     1255  1760 (1121)    L1M4_orf2#LINE/L1      153   657 (251)  

  chrX_117730906_   1255 GAAATGCAGGAAACCCAGAATAGTCAAAACAATCTTGAAAAAGAAAAACA 1304
                                 i ii           i                     i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_117730906_   1305 GAGTTGGAGAACTGACACTTCCCAATTTCAAAACCTACTACAAAGCTGCA 1354
                         i        i   v                    i            i  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_117730906_   1355 GTAATCAAAATCGTGTGGTCCTGGAATAAGGATAG-TATATAGATCAGTG 1403
                                 i iv       v    v          -i          i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_117730906_   1404 GAATAGAATTGAGAGTCCAAAAATAAACTCATACATTTATGGTCAGTTAA 1453
                                            i        i                i  i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_117730906_   1454 TTTTTGACAAGGATGACAAGACCATTCAATGGGGAAACAAAAGTCTGTTC 1503
                             i       i  v                     v  v     v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_117730906_   1504 AACAAATGGTGCAGGGACAAATGGAT-GTCACAAGCAAA-GAATGAATTT 1551
                                     v       v     -?i    v     -       v  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_117730906_   1552 GGACTACCACCTCACACCATGTACAAAAATTAACTCAAAATGAATCATAG 1601
                             iv i            i                     i    ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_117730906_   1602 ACCTAAGTATAAAAGCTAAAATTATAAAAACTCT---AAGAAGTCATAGA 1648
                               i i   i        i       -    ---     iv     i
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGG 551

  chrX_117730906_   1649 AGTAAATGTTTGTGTCTTTGAGTTAGGCAAAGCATTCTTAGATATGACAC 1698
                         ?      v  i   v i   i         v vv                
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_117730906_   1699 CAAA-GTATAAGCAACAACAACAACAACAACAAACAGAAAAACTAGACTT 1747
                             - i i         -------  v  v   i   v   i i     
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAA-------AAGAAAAAATAGATAAATTGGACTT 644

  chrX_117730906_   1748 CATCAAAATTTAA 1760
                                   v  
  L1M4_orf2#LINE/    645 CATCAAAATTAAA 657

Transitions / transversions = 1.65 (38 / 23)
Gap_init rate = 0.01 (7 / 505), avg. gap size = 2.14 (15 / 7)  

 236 13.95 2.33 0.00  chrX_117730906_117733786.rev     1831  1873 (1008)    L1M4_orf2#LINE/L1      644   687 (221)  

  chrX_117730906_   1831 TCA-CAAAATTTAAAATTTTTGTGCATCAAAAGACACTGTCAGG 1873
                            -       v    i        v     i      i   i 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

Transitions / transversions = 2.00 (4 / 2)
Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1)  

1062 14.98 7.49 3.08  chrX_117730906_117733786.rev     2164  2390 (491)    L1M4_orf2#LINE/L1      672   908 (0)  

  chrX_117730906_   2164 AAAAGACACTGTCAGGAAGGGGAAAAGACAATCCACAGAATGAAAGAAAG 2213
                            i      i   i   i v          i          ii     i
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_117730906_   2214 TATAGGGAAATTATATATCTGATGAAGGATCTTTATCTAGTATATATAG- 2262
                            vv v    i           i i   ii v    i  v       i-
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_117730906_   2263 ----TTTTACAACTCAACAATAAAAAGACAA----CTTAATTTTAAAATG 2304
                         ---- i           i             ---- ii    ?v      
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_117730906_   2305 GACAAAGGATCTGAGTAAACATTTCTCCAGGGAATATATATGATATACAA 2354
                          i        i   i  i           ii   -------         
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-------GATATACAA 864

  chrX_117730906_   2355 ATGGCCAAT--------GAAAAGATGCTCAACATTATTTGGTCA 2390
                                  --------                 i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.71 (26 / 7)
Gap_init rate = 0.02 (4 / 237), avg. gap size = 6.00 (24 / 4)  


2197 14.88 2.53 28.29  chrX_117821640_117827753.rev     4402  5624 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_117821640_   4402 TGGAAAGACATCCCCTGTTCACAGACTGGCAGAATTAATATTGTTAAAAT 4451
                                 i     v      ii  i   v   v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_117821640_   4452 GTCCATACTAGCCAAAGCAATCTACAGATTCAATGCAATCCCTACCAAAA 4501
                          v v     vv     vii              i          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_117821640_   4502 TCCCAATTA--TTTTTTACAGAAATAGGAAAAGGAATCCTAAAATTCGTA 4549
                              ii i--      i       v iv  ivvi            i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_117821640_   4550 TAG----------GACACCAAATAGCCAAAGCAATCAT--ACAAGAAG-- 4585
                          i ----------   v vi          i     v -- v      --
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_117821640_   4586 -----CTAGAAGCATCATACTCCCTGACTTCAAATTATATTACACAGCTA 4630
                         -----i i  i vv   i   i  ii i      viv  i    v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_117821640_   4631 TAGCAATCAAAACAGTATAGTAATGACAGAAAAACAGACATATAGACCAA 4680
                         i  i      i     i i   v  i  v  ii i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_117821640_   4681 TGGAACAGAATAGAGGGCCCAGAAATAAACCCATTCATTTATGGTTAACG 4730
                              i     v   i i                v          i  iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_117821640_   4731 GATCTTCAACAAGGGTGCCAAGAATACACAATGAGGAAAAGACAGTCTCT 4780
                            i   i               vi iv     i     ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_117821640_   4781 TCAACAAACGGTGTTGGGGAAACTGGATATTCACATGCAGAAGAATGAAA 4830
                                 i    i    iv         ?i        i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_117821640_   4831 TTGGACCCTGCTATAATTTGAATGTTCCCTCCAAAACTCATGTTGAAATT 4880
                                 ------------------------------------------
  L1M4_orf2#LINE/    451 TTGGACCC------------------------------------------ 458

  chrX_117821640_   4881 TAATTGCCATTGTCAGAGTATTAAGAAGTGGGATCTTAAGAGATGATTAG 4930
                         --------------------------------------------------
  L1M4_orf2#LINE/    459 -------------------------------------------------- 458

  chrX_117821640_   4931 GACATAAGGGCTTCAACTTCATGGATTGATTAATGCTGCTATCAATGGAG 4980
                         --------------------------------------------------
  L1M4_orf2#LINE/    459 -------------------------------------------------- 458

  chrX_117821640_   4981 TATGTAGTTATTGTGGGAGTTCAGTCCCCTTATTTTCTGTCTTGCCCTTC 5030
                         --------------------------------------------------
  L1M4_orf2#LINE/    459 -------------------------------------------------- 458

  chrX_117821640_   5031 TGCCATGAGATAATAGAGCACGAGGGCCATTGCCAGATGCAGGTGCCATG 5080
                         --------------------------------------------------
  L1M4_orf2#LINE/    459 -------------------------------------------------- 458

  chrX_117821640_   5081 CTCTTTGACTTCCCAGCTTCCAGACCATGAGTCAAATAAACTATTGTTTA 5130
                         --------------------------------------------------
  L1M4_orf2#LINE/    459 -------------------------------------------------- 458

  chrX_117821640_   5131 TAAATTATCCAATCTTTGGTATTCTGTTACAGCATCAGAAAAAGACTAAG 5180
                         --------------------------------------------------
  L1M4_orf2#LINE/    459 -------------------------------------------------- 458

  chrX_117821640_   5181 ACCCCTAGCTCACACCATATACCAAA-TCAACTCAAAATGGATTG----C 5225
                         ----   v              v   - i              ii---- 
  L1M4_orf2#LINE/    459 ----CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_117821640_   5226 TTAAACATAAGATCTGAAACCACAAAACTCT-AGAAGAAAACAGAGAA-- 5272
                         i    ii     v  i    i i        -           v  i?--
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_117821640_   5273 AAGCCTTTTTGACATTGGTCTTGGCAATGACTTTTT-GATATGACAGCAA 5321
                           ii   iv    v    vi v       ii  i  -         v   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_117821640_   5322 AAGCACAGGCAACAAAAGAAAAA-TAGACAAGCGAGTCTTCATCAAACTA 5370
                                i               -    i  iivi v          v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_117821640_   5371 AAAATCTTCTGCACAGCAAAGGAAACAATCAACAAAATGCAAAGGCAACA 5420
                             v   i  ii vv       v  v     v   i  v    i    v
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_117821640_   5421 TACAGAATGGGAGAAAATATTTGCAAACTATATATCCAATAAGGGATTAA 5470
                         i                          ii       ii        i vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_117821640_   5471 TACCCAAAATATATAAGGAACCTGTATAGCTCAATGCCAAAAACACAAAT 5520
                           i   i         i    iiv  i i      ivi     v      
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_117821640_   5521 AAGCCAATTAAAAAGTGGGCAAAGGACCTAAATAGACACTTCTCAAGAAA 5570
                           v      ?    i           ii i        i     v i i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_117821640_   5571 AGAAATTAAAATTGCTAATAGGTATATTAAATGATTCTCAATATCTCTAA 5620
                            v  vv    v  i    i i i  v   v   v     i   v????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_117821640_   5621 TCAG 5624
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.80 (115 / 64)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 34.27 (377 / 11)  


 703 20.90 0.75 0.00  chrX_117871764_117877303     3586  3719 (1821)    L1M4_orf2#LINE/L1        1   135 (773)  

  chrX_117871764_   3586 TGGAAACACATTCTATGTTCATAGGTCAGGAGACTTAATATTGTTAAAAT 3635
                               v i  i i        i i ii i                 i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_117871764_   3636 GGTAATACTTCCCAAAGTAATCAACATATTCAATGCAATCTTTAT-AAGA 3684
                           i      i      v i   v   v      i      ii   -  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_117871764_   3685 TCCCAGCTAGTTTTTCTTTAGAAATTGGCAAGATG 3719
                                 ivi    i vi        i    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

Transitions / transversions = 3.00 (21 / 7)
Gap_init rate = 0.01 (1 / 135), avg. gap size = 1.00 (1 / 1)  

2287 10.44 5.12 27.49  chrX_117871764_117877303     4033  5047 (493)    L1M4_orf2#LINE/L1      121   908 (0)  

  chrX_117871764_   4033 GAATTTGGCAAGCTGATTCCAAAATTCATATGGAATTGCAAGTGACCCAG 4082
                            v   i         i i               v      v       
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chrX_117871764_   4083 AATACTTAAAACAATCTGGAAAAAGAAGAACAAAGTAGAAGGACTCACAT 4132
                             vii          v                  v i          i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_117871764_   4133 TTCCTGATTTCAAATTTTACAACAAA----CGGTAATCAAGACAGTGCAG 4178
                             ii        vi    v     ---- i               ii 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_117871764_   4179 TAGTGGTATAAGGATA----TAT--------GGCATAGAATTGAAAGTCC 4216
                           v   i         ----   --------  v          i     
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_117871764_   4217 AGAAATAAAACCATGTGTCTATGGTCAACTGATTTT-GACAAGAGTGTCA 4265
                                  v    iii i         i       -      i   i  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_117871764_   4266 AGACCATTCAATGAGAAAAGAATAGTGTTTTCAACAAATAGTGCTGGGAC 4315
                                      i i          v            i          
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_117871764_   4316 AACTGCATAGCCACACAGAAAAGAATGACGTTGGATCA-TGCCCCACACT 4364
                              v   ?     iiv          v      i v- i  i     i
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_117871764_   4365 ATATATAAAAATGAACTCAAA-TGGATCAAAAACCTAAATATGGCCGGGT 4413
                              i      v        -       ? i        i --------
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-------- 512

  chrX_117871764_   4414 GCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGAAGGGTG 4463
                         --------------------------------------------------
  L1M4_orf2#LINE/    513 -------------------------------------------------- 512

  chrX_117871764_   4464 AATCACCTGAGGTCAAGAGTTTGAGACCAGCCTGGCCAACATGGTGAAAC 4513
                         --------------     -------------------------------
  L1M4_orf2#LINE/    513 --------------AAGAG------------------------------- 517

  chrX_117871764_   4514 CCCGTCTCTACTAAAATTACAAAAATTAGCCGGGTATGGTGGTGGGCGCC 4563
                         ----------      i  i    --------------------------
  L1M4_orf2#LINE/    518 ----------CTAAAACTATAAAA-------------------------- 531

  chrX_117871764_   4564 TGTAATTCCAGCTACCCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCCG 4613
                         --------------------------------------------------
  L1M4_orf2#LINE/    532 -------------------------------------------------- 531

  chrX_117871764_   4614 GGAGGTGCAGGTTGCAGTGAGCCGAGACGTTTTCATTGCACTCTAGCCTG 4663
                         ----------------------------------------    ------
  L1M4_orf2#LINE/    532 ----------------------------------------CTCT------ 535

  chrX_117871764_   4664 GGCAACAAAGAGCAAAACTCCGTAAAAAACAAACAAACAACAACAAAAAA 4713
                         ----------------------  i  i -----     -----------
  L1M4_orf2#LINE/    536 ----------------------TAGAAGA-----AAACA----------- 547

  chrX_117871764_   4714 ACCCCATAAGATTAAATGTTCATGACCTCAGCTTTGGCAAGGAATTGTTA 4763
                         ------  i ?v     v   i      ii v  v     v iv  v   
  L1M4_orf2#LINE/    548 ------TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_117871764_   4764 TTTATGATACCAAAAGGACAAGCAACAAAATAAAAAATAGATAAATTTGA 4813
                         vv     i        v             v                v  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_117871764_   4814 TCTCTTCAAAATGTAAAAC------------AAGGACACCATCATGAAAG 4851
                         ii  v       vv     ------------        i    v     
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_117871764_   4852 TGAAAAGTCAACCCACAGAATGGGGGAAA-TATTTTCAGTTCAT-----T 4895
                                v                i    -     v  iv    ----- 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_117871764_   4896 AATAAGGGAGTGGTATCTAGACTATATAAA----------AACCCAATAA 4935
                         i        v v     i   v        ----------   i      
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_117871764_   4936 TAAAAAGAAAAA----CCAATT-AAAAATGGGCAAAGGATCTGAATAGAC 4980
                                 v   ----      -                 i         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_117871764_   4981 ATTTCTTTGGGGAAGAAGTACAAATGGACAATAAACACATGAAAAGTTGC 5030
                               iiiii     vi         v      i           v   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_117871764_   5031 TCAACATCATCAGGGAG 5047
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (60 / 43)
Gap_init rate = 0.02 (18 / 788), avg. gap size = 18.39 (331 / 18)  


2763 14.08 2.73 1.47  chrX_118025397_118028926     1257  1732 (1798)    L1M4_orf2#LINE/L1        1   482 (426)  

  chrX_118025397_   1257 TGAAAGGAAATCCCATGTTCATTCATTGGAAGACTTAAACTTGTTAAGAT 1306
                           i  i  v             vv              vv          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_118025397_   1307 GGCAGTACTTCACAAAATGATCTACAGATTCAATGCAATAGCTATTGAAT 1356
                             i    i v    v                i     vv    ii  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_118025397_   1357 TTCATGCTGGCTTTTTTTTTTTTTCCAGAAA-------ATTGATCTTAAA 1399
                          i vv    v       v-------      -------ii     i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-------CAGAAATTGACAAGCTGATCCTAAA 143

  chrX_118025397_   1400 ATTCATAGTGAAATGCAAGGGACCACAAATAGCCAAAATAATCTTGAACA 1449
                                vv               vvi           i         v 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_118025397_   1450 AGAAGAACAAAGTTGGATAACTTATACTTC--AATTTCAAAGCTTACTAT 1497
                                          vi   i i     --         i       i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_118025397_   1498 AAAACTACAGTAATCAAGACAGTGTAGCACTAGCATAAAGATAGACATAT 1547
                            i                     i i   i      i           
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_118025397_   1548 AGATCAATGAAATAGAGTTGAGAGTTCAGAAATGAACCTATACATCTATG 1597
                                  i      i        i       i    i      i    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_118025397_   1598 GT----TGATTTTCAGCAAGGGTGCCAAGACTATTCAATGAAAAAAGAAT 1643
                           ----        ii               i        iii       
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_118025397_   1644 AGTCTCTTCAACATATGGTGCTGGAGCAACTGGGTATCCACATGCAAAAG 1693
                              i       v          ii       i  ?             
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_118025397_   1694 AATTAAGTTGGACCTTTATCTCACAACATATATAAAAAT 1732
                            v          ii  i      v      i      
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

Transitions / transversions = 1.87 (43 / 23)
Gap_init rate = 0.01 (4 / 482), avg. gap size = 5.00 (20 / 4)  

 996 11.25 0.62 0.00  chrX_118025397_118028926     2206  2365 (1165)    L1M4_orf2#LINE/L1      477   637 (271)  

  chrX_118025397_   2206 AAAAATTAACTCAAAATGGATTAAAGGCCTAAATATGAGAGCTAAAACTA 2255
                                              i ?  i       i i             
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_118025397_   2256 TAAAATTCTTAGAA-AAAACATAGGAGTAAATCTTTGTGATCTTGGATTT 2304
                              i        -          ?         i    i     i  v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_118025397_   2305 GGCAATGGATTTTTAGATATGACACCAGAAGCTCAAGTAACAAAAGAAAA 2354
                                 v  i               i    v    i            
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_118025397_   2355 AATAAATAGAT 2365
                             i   i  
  L1M4_orf2#LINE/    627 AATAGATAAAT 637

Transitions / transversions = 4.33 (13 / 3)
Gap_init rate = 0.01 (1 / 161), avg. gap size = 1.00 (1 / 1)  

1046 12.20 1.19 18.75  chrX_118025397_118028926     2702  3037 (493)    L1M4_orf2#LINE/L1      632   908 (0)  

  chrX_118025397_   2702 ACAAAT-GGATTTCATAAAAATTAAAAATGTTCGTGCATCAAAGGTTACT 2750
                          i    -   i     v           iv  i    v       vi   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_118025397_   2751 AGGAAGAAAATGAAAAGATGACCTACGTAATGGAAGAATATATTTGCAAA 2800
                          vv      i        ii   i  iv     i    v           
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_118025397_   2801 TTATATATCTGATAAGT--CTTGGATCTGAAACATATAAAGAACTCTTTC 2848
                          i              v--    v   iii  i               --
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT-- 779

  chrX_118025397_   2849 TTACTAATAGGAATTCTTTTTATTGAATTCTTAAGGAATTCAATAATAAA 2898
                         --  --------------------------------  i           
  L1M4_orf2#LINE/    780 --AC--------------------------------AACTCAATAATAAA 795

  chrX_118025397_   2899 AATTTAAATAACCCAATTAGAAAATAAA-AAAAGATGTGAATAGACATTT 2947
                           vvi             ?i     iii-   i   v             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_118025397_   2948 CTCCAAACAAGAAAGATATACAAATATATTTTCCAAAGATATATAAATGG 2997
                                ---------------------------i        i      
  L1M4_orf2#LINE/    846 CTCCAAA---------------------------GAAGATATACAAATGG 868

  chrX_118025397_   2998 CCAACAAGTACATGAAAAGATGCTCAACATCACCAGTTGG 3037
                             i   i                       ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (27 / 13)
Gap_init rate = 0.02 (6 / 277), avg. gap size = 11.17 (67 / 6)  


2242 24.48 11.33 0.56  chrX_118097934_118099625      487  1201 (491)    L1M4_orf2#LINE/L1      117   908 (0)  

  chrX_118097934_    487 TGCAGAATCCCATCAAGCTTATTC-AAAATGTATATGAAGAGCCAGCGGA 535
                                viiv -      v  i -     vi     i i vv  i-  i
  L1M4_orf2#LINE/    117 TGCAGAAATTGA-CAAGCTGATCCTAAAATTCATATGGAAATGCAA-GGG 164

  chrX_118097934_    536 ACTTATGAATAGACAAAACAATTTCGATAAAGAA---CAAACTGGGAGGA 582
                           ii -      v         i i  v      ---    v v      
  L1M4_orf2#LINE/    165 ACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_118097934_    583 ATCATTCTATCTGATTTCAGGACTTGCTACATAGCTACAGTAATCAATAC 632
                         v   iv  vi ii      ii    i     v               v  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_118097934_    633 AATGTGGTATTAGCAGGGGGGTGGACACATTGATTAATG-AATAAAATAG 681
                          i       i i   vii  i i    i  v   i    -    i   v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_118097934_    682 AGAAGCCAGAACTAGACCCACACAAATATGCCCAATCGATTGTTGACAAA 731
                            iv      v  i     i   vv    vi    i    v i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_118097934_    732 GGTGCAAAAGAAATTTAATGTAGAAAAGATGGCCTTTTCAACAAATGGCA 781
                              v  iivv   i    vi    ii  i i               ii
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_118097934_    782 TTGGAACAAATGGGCATCAATAGGCCAAAAAA--------GAT------- 816
                         i   i    v   ii ? v i v  v   i  --------  i-------
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_118097934_    817 --------------AAAAT-AACGCAAAATGGATGATGGATTTAAATATA 851
                         --------------     -   v          v ?i  ii     i  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_118097934_    852 ACATGTAAAACTAGAAGGCTTTTAGAAAAAAA-ACAGGAGGAAATTTTCA 900
                          v vv        v  ii  i      i    - i   ? v    i   i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_118097934_    901 GGATCCAGGTGTAGGCAAAAGTT-CTCAGATGTGACACCAAAAGCACAAT 949
                         v  i iv  vv       vi   -  i    i                 v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_118097934_    950 CCATGAAAGGAAAAATTGATAAGTTGGACTTTATCAAAAT-AAAACCTTT 998
                          v ii    i      v     i        i        -    v    
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_118097934_    999 TTCTCTGTGAAAGACCCTGTTAAGAGGATGAAAAGAC-----------TA 1037
                          viv  vii  i   v  i i    iii         ----------- i
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_118097934_   1038 GGAGAAAATAT---------------CCAATAAAGGACTAGTATCTAGAA 1072
                                    --------------- ii    i     v     i    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_118097934_   1073 TATATAAAGAATTCTCA-AACTTAACAGTAGAAAAACAA----TCCAATT 1117
                                    i   i -    i  i i  i   i    ----i      
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_118097934_   1118 AGAAAATGACCAAATGACACGAACATATAC-----------ACATATACA 1156
                         ?i      iv    v  ivi   i v i i----------- v       
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_118097934_   1157 GATGGCAAACTAGTATATGAAAATGA-GTTCAATATTGCTAGACAT 1201
                         i     v  iv  i i       -  - i    i  ii????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (111 / 60)
Gap_init rate = 0.02 (19 / 792), avg. gap size = 4.47 (85 / 19)  


2542 25.74 3.49 4.47  chrX_118208803_118211515.rev     1312  2228 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_118208803_   1312 TGGAGAGACATACCATG------GAT-GGAAAACTGAACACAGTAAAGAC 1354
                             i   i  v     ------   -    i   v  i iv  v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_118208803_   1355 ATCAATTCTCCCCAAATTGATATACAAGTTTAATGCAATAATTATTAGAA 1404
                         iv    v              v    ii  i  i     vvi   i i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_118208803_   1405 TCATAGCAAGAACTTTTGTAGACAAAGACATGTTTATTTTAAAATTTATA 1454
                           vi   vivvvi     i   v vv    v i v  ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_118208803_   1455 TGTAAA-GCAACAGGCCCTAGAATAGTTAAAACG-TAGTGAAAATAAGTT 1502
                           v   -    -i  v  i       ii     i- vv      --  --
  L1M4_orf2#LINE/    151 TGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGAAAA--AG-- 195

  chrX_118208803_   1503 AATAAGATTAAAGTATATGGAATCAC--TT----GTGTTATGACTTAATA 1546
                         ---    vi     vviv   v    --  ----i v i vi     v  
  L1M4_orf2#LINE/    196 ---AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_118208803_   1547 TGATGCTACGGTAGTCAAGATAGTGTGGTATTGGTGGAGGGATAAACACA 1596
                         ii v     i   i      i         i   iiv i     i   i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_118208803_   1597 --GATTGGAGGGACAGAAGAGAGAATCCAGGA-CAGACTCTTAAAAACAA 1643
                         --   iiiv  i i    vv    i     i -i i  i v  ----  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA----CAT 338

  chrX_118208803_   1644 ATATGGCAAACTGATTTTTGACAAA--TGCACAAAAGAATGTCAATGGAG 1691
                         v     iv  i       i     i--   -   i vv  -       i 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGC-CAAGACCAT-TCAATGGGG 386

  chrX_118208803_   1692 GAAATATAGCTTTTTCAACAAATGATGCTAAAACAATTGGATATCCACAG 1741
                         i  iv    ii             i    iii    i      ?     v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_118208803_   1742 GCAAAAAACAAACAAACAAACAAACAAACACCTTGACCTATATATCACAT 1791
                               i --------------- ii  v--i v    iv  iv     i
  L1M4_orf2#LINE/    437 GCAAAAGA---------------ATGAAG--TTGGACCCCTACCTCACAC 469

  chrX_118208803_   1792 CTTACACAAAAATCAACTCAAAATGGATTATGAACTTAAGTGTAAAACAC 1841
                          v  i        i              i ?ii  i   i     i vvi
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_118208803_   1842 AAAACTATAAAGGTTTTAGAAAAAAAAACACAGGAGAAAATCTTTGGGAT 1891
                                    iv i      i    --  i   ? v       i v  i
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATCTTCGTGAC 567

  chrX_118208803_   1892 CTAGGGCTATGTGAATAGTT-CTCATACCTGACACCAAAGGCATTAGCCA 1940
                           v   i  v i-   i   -  i v iv          i   iv   v 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGC-AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_118208803_   1941 TAAAAGGAAAAATTTATAAATTGGACTTAATCAAAATGAAAAACTTCTGC 1990
                         i     i      vv             v        v        i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_118208803_   1991 TTTGCGAA-----------AGAGGATGAAAAGGCAAGCTATAAGCTTGGA 2029
                         vi v i  -----------   iii       i   v i i iiv v   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_118208803_   2030 GAAAATATTTGCAAACCACATATCCAACAAAGGACCTGTATACAGAATAT 2079
                                        i  i     ii i  i    i     v        
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_118208803_   2080 TTAAAGAACTCCCAAAAACTTAACAGTTAAAAAATAAAACCAATCAATTC 2129
                         v          ii v  -  i  i i v    i i   ------i  ii 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAA-CTCAATAATAAAAAGACAAA------TAACCC 809

  chrX_118208803_   2130 AATCAGAAAATGAACAAAAGTCATGAAGAGTCATTCCATGAATGAGGAGA 2179
                            i?i      ii    i viv    v  v    i viv  v  i  v 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_118208803_   2180 TATAGATAGCAAATAAGCATAGTTAATGATGTTCATTGTAAGGGAAATG 2228
                           i i  i  v        i vvv  v    i   vii v ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (144 / 88)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.17 (73 / 23)  


3311 22.68 2.00 6.22  chrX_118213572_118216231.rev     1222  2169 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_118213572_   1222 TGGAAAGATATTCCATGTTCACAGGTTGGAAAA-TTAATATTGTTAAAAT 1270
                                    i         ii i      i -             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_118213572_   1271 ATCTATACTACCCAAAGCAATCTATTGATTCAGTGAAATGTCTATCAAAA 1320
                         iv v     v      vii     iv      ii v   vi         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_118213572_   1321 TTTCAG--ACATTTTTCACTAAAATAGAAAAAGCAATCCTAAAATTTGTA 1368
                          ii   --i v     ii vi    v  v  ivii           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_118213572_   1369 TGAAACCACAAG--ACCCCAAACTGCCAAAACAATCTTGAAAAAGAA--- 1413
                           i  vii    --    vi  iv                       ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_118213572_   1414 CAAACCTGGAGGCATCACACTACCTCACTTCAAAATCTACTATATAGCGA 1463
                             vi      vv       v  iv i       ii     i v   v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_118213572_   1464 TAGTAATCAAAACAGCGTGATACTGGCATAGAAACAGACACATAGACCAA 1513
                         i         i    i   i          iii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_118213572_   1514 TAGAACAGAATACGGAGCCCTGAAATAAATCCACCCATTTATGGTCAATT 1563
                          i   i     vvi   i  v        i   iv               
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_118213572_   1564 GATTTT-GACAAAGGTGCTAAGAACATACAATGGGGGAAATGGGGAAAAG 1612
                               -     i     i    v   v        --------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-------------- 386

  chrX_118213572_   1613 CATAATGGGGAAAGCAGGAAAGGAGAGTCTCTTTAATAATTGGTGTTTGA 1662
                         ------------------    i v     i  i  i  v     i v i
  L1M4_orf2#LINE/    387 ------------------AAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chrX_118213572_   1663 ACAATT----ATTTATGTACAAAAGAATGAAATTAGATCCTTGTCTCACG 1708
                             i ---- ?ii ii i            i  i  i  i ii     i
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_118213572_   1709 CTATATACAAAA-TCAACTCAGAATGGAGTAAAGTGTTAAATGTAAGAAC 1757
                          i          - i      i      vi ?  vvi           i 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_118213572_   1758 TGATACTATGAAACTACTAGAAGAAAACA--GGGG-AAATAACCATGACA 1804
                          i v     i     vi            --  ? -    vvi i    v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_118213572_   1805 TTGGTCTAGGCAATTATTT-TTGCATATGACCTGAAAAACATAGGCAATA 1853
                             vi        vi   -  iv       viv    i  i i    i 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_118213572_   1854 AAAGTGAAGATAGGCAAATGGGATTACATCAAACCGAAAAGCTCCTGTAC 1903
                             vi  i    ii    v   i v       viv    i  ii   i 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_118213572_   1904 AGCAAAGGAAACAATAAACAGAGTGAAAAGATAATGTATGTAATGAGAGA 1953
                         vv       v  v  v  v i          i  ivi iiv    i    
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_118213572_   1954 AAACATTTGCAAAGCGTATGTCCTATAAGGGGTTAATAGCCAAAATATAT 2003
                            i         v i   i  iv       ii vi  v   i       
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_118213572_   2004 GAGAAACTAAAATAACTCAGCAGCAAGAATACAAATAACCTGATTAAAGA 2053
                         i ii    vvv i      ii ii  i  v          ii   ?  i 
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_118213572_   2054 ATACAAAAATACAGGAATACAAAAAACCTGGGCAAAGGACCTCAATAGAT 2103
                           ---------------------------          ii v      i
  L1M4_orf2#LINE/    819 AT---------------------------GGGCAAAGGATTTGAATAGAC 841

  chrX_118213572_   2104 GTTTCTCAAAAGAAAACATGCAAATGATGAACAGGTATATGAAAA-ATGC 2152
                         i      v      i i  i      iiv  i i i i       -    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_118213572_   2153 TAAGCATCACTAATTGT 2169
                          v i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (142 / 69)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 6.00 (78 / 13)  


3297 26.87 0.44 0.44  chrX_118351566_118357838.rev     4875  5782 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_118351566_   4875 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4924
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_118351566_   4925 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4974
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_118351566_   4975 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5022
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_118351566_   5023 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5072
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_118351566_   5073 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5122
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_118351566_   5123 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5172
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_118351566_   5173 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5220
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_118351566_   5221 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5270
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_118351566_   5271 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5320
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_118351566_   5321 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5370
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_118351566_   5371 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5420
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_118351566_   5421 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5470
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_118351566_   5471 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5520
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_118351566_   5521 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5570
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_118351566_   5571 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5620
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_118351566_   5621 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5670
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_118351566_   5671 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5720
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_118351566_   5721 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5770
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_118351566_   5771 ATCACTGGCCAT 5782
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1162 24.48 1.03 0.69  chrX_118424733_118427019.rev      567   856 (1431)    L1M4_orf2#LINE/L1        1   291 (617)  

  chrX_118424733_    567 TGGAAACACATTCTATGCTCATGGATGGGTAGAATCAATATCGTGAAAAT 616
                               v i  i i   i        v  v   v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_118424733_    617 GACCATACTGCCCAAAGCAATCTACAGATTCAGTGCAATTCCTATCAAAA 666
                          i v     v      vii             ii     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_118424733_    667 TACCAACATCATTTTTCACAGAATCAGAAAAA---ATCCTAAAATTCATA 713
                          v   i vv v     ii     viv  v  i---               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_118424733_    714 TGGAACTAAAAAAGAGCCAGAATAGCCAAAGCAATCCTAAGCAAAAAGAA 763
                              v iv  ii  v              i     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_118424733_    764 CAAATCTGGAGGTATCACATTACCGGACTTCAAATTATACTACAAGGCTA 813
                             vi      vv     i v  vi i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_118424733_    814 TAGTTACCAAAACAAAATAGTACTGATATAAAAGTAGTTACAT 856
                         i   v i   i   ivi i      ii    iii   --    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG--ACAT 291

Transitions / transversions = 1.54 (43 / 28)
Gap_init rate = 0.01 (2 / 291), avg. gap size = 2.50 (5 / 2)  

2113 23.20 1.72 2.82  chrX_118424733_118427019.rev     1159  1796 (491)    L1M4_orf2#LINE/L1      278   908 (0)  

  chrX_118424733_   1159 ATAAAAGTAGTTATATTAGACCAATGGAACAGAATAGAGAACCCAGAAAT 1208
                             iii   vi    -   i        i     v    ii        
  L1M4_orf2#LINE/    278 ATAAGGATAGACATAT-AGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_118424733_   1209 AAAGCCAAATACTTACAAACAACTGATATTTGACAAAGCATACGAAAACG 1258
                            v   v i i   iiiv   i    v  i     i -i i v  i  v
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACC 375

  chrX_118424733_   1259 ---TAAGTTGGGGAAAGGATACCCTATTCAATAAATGGTGCTGGGCAAAC 1305
                         ---i  --         i   vi  v     i             vv   
  L1M4_orf2#LINE/    376 ATTCAA--TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_118424733_   1306 TGGCTAGCCCCATGTAGAAGAATGAAACTGTATCCCTATCTCTCACCTTA 1355
                            v  ?  v    i i         ii  v i     i   v    v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_118424733_   1356 TGCAAAAATCAACTTGAGATGGATCAAAGACTTAAATCTAAGACCTGAAA 1405
                          i       i    ii i        ?    i     v     v  i   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_118424733_   1406 TCATAAAAATTCTAGAAGAAAACCTAGGAAAAACTCTTCTGGACATTCTT 1455
                         ii      v ii           v    ?iv  v     vv   ------
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC------ 567

  chrX_118424733_   1456 TGCCTAGGC-AGGCAAAGAATTTATGACTAAGACCCGAAAAGCAAATGCC 1504
                         -- i i  i-      v iv  iv iiv  v   v v       v v  v
  L1M4_orf2#LINE/    568 --CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_118424733_   1505 ACAAAAACAAAAATA----AATGGGACCTAATTAAACTGAAAAGCTTCTT 1550
                               iv       ----   v    i v  i   v v    i   -  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT-TT 664

  chrX_118424733_   1551 GCACAGCAAAAGAAAAAATCATCAGAGTAAACAGA--ACCCACAGAATGG 1598
                          ii vv    i  v vv    vv i   i  v   --             
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_118424733_   1599 AAGAAAATATTTGCAAACTATGCGTCCAACAAAGGAGTAATATACAGAAT 1648
                         i                ii  iii  ii i  i   v vi   v      
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_118424733_   1649 CTACAAGGAACTCAAACAAATCAGCAAGAAAACAAATAAACAAATAATCC 1698
                         v  i  i      vv    v   ii  v    ----- i        i  
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAA-----AGACAAATAACCC 809

  chrX_118424733_   1699 CATTAAAAAGGGGGCAAATGACACGAAGAGACATTTCTCAAAAGAAGATA 1748
                         v   ?    iv       v  ivi   v           v          
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_118424733_   1749 TACAAACGGCCAACACACACATAAAAA-ATGCTCAACATCACTAATCAT 1796
                               i      i vi     i    -             ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (81 / 63)
Gap_init rate = 0.02 (11 / 631), avg. gap size = 2.64 (29 / 11)  


1811 21.95 6.50 2.64  chrX_118443942_118446143.rev      498   989 (1213)    L1M4_orf2#LINE/L1      287   797 (111)  

  chrX_118443942_    498 GATGCATCGATCAATGAAACAGAATAGTGAGCCCAGAAATAAATCCACGC 547
                           iii  v        i  i     v v   i           i   ii 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_118443942_    548 ATCTATAGCCAACAGATTTTCAACAAAAGCGCCAATAACACACATTAGGG 597
                           i   i i   iv       i    ii i     v v  iv  v i   
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_118443942_    598 AAAGGACAGTCTCTTCAATAAATGTTGCTGGGAAAACTGCATATCTATAT 647
                             i i     i     i     v        v     v   ? i i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_118443942_    648 GCAGAAGAATAAAACCAGACCCCTCTCTCTCACCATATACAAAAACTAAC 697
                            i      i  iiii       vi   v               i    
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_118443942_    698 CCAG--TGGATTAAAGGCTTAAATGTAGGATCTGAAACTG--AAACAGCT 743
                         i  i--     i ?  i i        i  v  i     i--    vvi 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_118443942_    744 AGAAGAAAA----GGG--AAATGCTTTATGACATTGGGCTGGGCAA-GGT 786
                                  ----  ?--    -   ii    v     i i     -   
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_118443942_    787 TTTTTTTTTTTTTTTTTTCATATGA-ACT--------------CAAAAGC 821
                           i  vv------------      -  i--------------      v
  L1M4_orf2#LINE/    586 TTCTTAG------------ATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_118443942_    822 AAAAATAGACAAGTAGGATTACATCAAACTAAAAAGCT---GTCCACCAA 868
                                  i  i v   i v       v v    i  ---  v vi   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_118443942_    869 AGGAAACAGTCCACAGAGTGAAGATATAACCTACATAATGAGAGAAAATA 918
                             v  vi  v v i      i v i    i   v    i         
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_118443942_    919 TTTGCAAATTCTACATCTGACAAGGGGTTAATATCCAGACTGTATAAGGA 968
                                  iv  i      i     ii vi        v i     i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_118443942_    969 ATTC--A-AACTCAATAGCAAAAA 989
                          i  -- -         ii     
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAA 797

Transitions / transversions = 2.00 (70 / 35)
Gap_init rate = 0.02 (12 / 511), avg. gap size = 3.75 (45 / 12)  

 430 20.95 0.00 0.95  chrX_118443942_118446143.rev     1607  1711 (491)    L1M4_orf2#LINE/L1      805   908 (0)  

  chrX_118443942_   1607 AATCTGATTTTTAAACGGGCAAAATACCTTTATAGACATTTCTGAAAAGA 1656
                           i ii   ?vv   i       iv ii vv            vv     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_118443942_   1657 AGGCATACAGAATGGCCAACAAGTATATGAAAAAATGCTGAACATCACTA 1706
                           ii     -         i   i i       i     v       ???
  L1M4_orf2#LINE/    855 AGATATACA-AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_118443942_   1707 ATCAG 1711
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.01 (1 / 104), avg. gap size = 1.00 (1 / 1)  


1963 11.82 6.34 0.86  chrX_118630051_118635748     3365  3711 (1987)    L1M4_orf2#LINE/L1        2   367 (541)  

  chrX_118630051_   3365 GGAAAGACATTCTGTGTTCATGAATTGGAAGACT-AATACTGTTAAAATG 3413
                                i  i ii        i           -    i      i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_118630051_   3414 ACAATAATCTCCAAACT-AGCTA-AGAT-AGATGCAATCTCTATCAAAAT 3460
                         i     v  i     i - v   -    -vi i      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_118630051_   3461 CCAAGGTACCTTTTCTTTCCAGAAATTGACAGGCTGATCCTAAAATTAAT 3510
                           v  v i      --  v            i               v  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTT--TTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_118630051_   3511 ATGGAAATTCAAATGACCCAGAATAG---------TCTTGAAAAA----- 3546
                                 v   iv            ---------          -----
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_118630051_   3547 -CAAAGTTGGAGGACTCACAGTTCCCCATTTCAAAACTTACTACAAAGCT 3595
                         -                   v     v                       
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_118630051_   3596 ACAGTAATCAAGACAGTGTGGTCCTAGCATAAGGATAGACATA--GATCA 3643
                                               v  i                 --     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_118630051_   3644 ATGGAATCGATTTAACAGTCCAGAAATAAACCT-TGTAGTTTACAGTCAA 3692
                                v  v  i v                i- ii -    ii     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA-TTTATGGTCAA 348

  chrX_118630051_   3693 TCGATTTTCAACAAGAGTG 3711
                          i       i     i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTG 367

Transitions / transversions = 1.73 (26 / 15)
Gap_init rate = 0.03 (10 / 366), avg. gap size = 2.50 (25 / 10)  

 820 12.31 3.85 0.00  chrX_118630051_118635748     4033  4162 (1536)    L1M4_orf2#LINE/L1      365   499 (409)  

  chrX_118630051_   4033 GTATCAAGACAATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGATGC 4082
                           ii      v                                   i   
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_118630051_   4083 TGGGACAACTGGATATTCACATGCAAAAGAATGAAACAGGACCCCTACTA 4132
                                        ?i                  iiv          iv
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_118630051_   4133 CATACCATATATAAAAATGAA-----AATGGGCCA 4162
                           i        i      v  -----     ii  
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCA 499

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.01 (1 / 135), avg. gap size = 5.00 (5 / 1)  

1979 17.26 4.04 0.90  chrX_118630051_118635748     4760  5205 (493)    L1M4_orf2#LINE/L1      449   908 (0)  

  chrX_118630051_   4760 AGTGAGACCC-TGTCTC---TCAAAGAAAAAAAAAAAATTAAAATGAATC 4805
                            vi     - ii   ---i  v v v     vv  v i      i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_118630051_   4806 AAAGACCTTAATGTAAGAACTAAAATTTAAAAAC----AGAAGAAAACA- 4850
                          ?      v         i      i vv     ----           -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_118630051_   4851 -AGAGTAAACCTTCATGACCATGTATTAAGCAATGAATTATTAGATGTGA 4899
                         -i ?     i    i     v  vi   i      iv  v      i   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_118630051_   4900 CACCAAAGGCACAAGCAAGAAAAGAAAAAACAGATAAATTGGACTTCATT 4949
                                i          v           i                  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_118630051_   4950 AGAATT-------TTTGTTCCTTATAGGATACCAGCAATAAAGTGAGAAG 4992
                          i    -------     v i i v    i  i v   v       i   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_118630051_   4993 ACATCCCACAGAGTCGGGGAGAAATATTTACAAATCATATATCTAATAAG 5042
                            v        i v  i  -        i              i     
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGA-AAATATTTGCAAATCATATATCTGATAAG 747

  chrX_118630051_   5043 AGACTTATAAATGAAAATGTATGAAAAACTCTTACAACTCAAAAATAAAA 5092
                         i     i  vvi- i   i   i  i                v       
  L1M4_orf2#LINE/    748 GGACTTGTATCC-AGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_118630051_   5093 AGCAAAATAACTCAATTTTTAAAAAGGGG-AAAAGATCTGAATAGACATT 5141
                           vv       i     ?--     v   -   i   i            
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_118630051_   5142 TCTCTAAGGAAGATAGACAAGTGGCCAATGAGCTTATGAAAAGATGCTCA 5191
                             i  i       v    i        i   vi               
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_118630051_   5192 ATACCATTGGGCCA 5205
                          i i  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (45 / 29)
Gap_init rate = 0.02 (9 / 460), avg. gap size = 2.44 (22 / 9)  


2089 23.87 3.91 0.98  chrX_118866709_118873796.rev     5112  5622 (1466)    L1M4_orf2#LINE/L1        1   526 (382)  

  chrX_118866709_   5112 TGAAGAGAGATTCTATGTTCACGAATAGGAAGACTCAATATTGTTTAGAT 5161
                           i i   v  i i       i i  v        i         v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_118866709_   5162 GTCACTTCTTCCCAACTTGACCTGTAGATTGAATGCAATTCCCATCAAAA 5211
                          v  v v  i     v    i  ii     v  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_118866709_   5212 TCCCTGCAAATCATTTTGTGGAAGTCAACTAACTGATTTTAAAGTTTATA 5261
                             v  viviiv     ii   i ii  v i     ii    i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_118866709_   5262 TAAAAAATCAAATGACCCAGAAATTGCCAAATTAATTCTCAAGAATAAGA 5311
                          ii   vv   iv         - v      vi   ii v  i  v    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAA-TAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_118866709_   5312 ATAAAGTGAGAGGACTGACATTTCCCAACAACAAGATATTACTATTATAA 5361
                          i     vi       v   i       ivv   i i-      i---  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC-TTACTAC---AA 245

  chrX_118866709_   5362 AGCTACAGTAATCTAGACAGTGGGGTATTGGT-----GAAAGA---ATAG 5403
                                      v        v    i   i-----  v   ---    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_118866709_   5404 ATTGATGAGACATAACAGACAGCTCAGAAATAGGCCCACACAAATATAGT 5453
                           ii   ii i v  iv  v  ii        ii    i   vv   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_118866709_   5454 TAACTGATCTTTGATAAAGGAACAAAGGCAATCCAATGGAGAAAGGATAG 5503
                         i  i    i  i  i  i  vi v   i v  i      i     i    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_118866709_   5504 TCTTCTCAACAAATGGTGCTGGAAAAACTGGACAGCTACATGCAAAAAAA 5553
                             i                 i v       i ? i          i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_118866709_   5554 TGAA------------TCTTACACCTTTCACAAAGAGTAACTCAAAATGG 5591
                             ------------i  i     v vi     i v             
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_118866709_   5592 ATCACAGATTTAAATATAAAATGTAAAACTA 5622
                             ?   ii     i   i vv        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

Transitions / transversions = 1.93 (79 / 41)
Gap_init rate = 0.01 (6 / 526), avg. gap size = 4.17 (25 / 6)  

 544 28.16 0.57 0.00  chrX_118866709_118873796.rev     5927  6100 (988)    L1M4_orf2#LINE/L1      519   693 (215)  

  chrX_118866709_   5927 TAAAGCTATAAAACTTCAAGAAGATAACATATGAAAAAATCTGGGTGACT 5976
                             i          iiv      v      v ?iv      vv     i
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_118866709_   5977 TGGGGTTTGTCAATAAGTTTTTAGGTAAAAAGCAAACAGAATATTCCATG 6026
                          v     v v    iiv  i    i  vi vi v  v  v i vv v ii
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_118866709_   6027 AAA-AAAAAATTGATAACTTGGACTTCATTAGGATTAAAAACATCTGTCC 6075
                            -       v     v           i ii         v i   v 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_118866709_   6076 TACAAAAAACATCATTAAGAGAATG 6100
                          v    ii   ii  i    i i  
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTG 693

Transitions / transversions = 1.09 (25 / 23)
Gap_init rate = 0.01 (1 / 175), avg. gap size = 1.00 (1 / 1)  

 729 15.03 15.54 0.00  chrX_118866709_118873796.rev     6405  6597 (491)    L1M4_orf2#LINE/L1      686   908 (0)  

  chrX_118866709_   6405 AGAGAATGAAAATACAAGCCACTGACTGAAAGGAAGTATTTTCAAA--AT 6452
                            i i      v    v    v  v  ii  i  i     v    --  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_118866709_   6453 ACAT---ATAAAAGGCTTGTATCCACAATACACAAGGAACTCTT-CAACT 6498
                          i  ---    ii i          v    i i  i        -     
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_118866709_   6499 CAACAATAAGAA----AATAACCCAATTAAAAA----------GATGTGA 6534
                            i     i  ----            ?    ----------   v   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_118866709_   6535 AC---CA-------AAAGAAGACATACACATGGCAAACAAGCACATGAAA 6574
                          i---  -------        i     v     v  i            
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_118866709_   6575 AGATGTTCAACATCATATGTAGT 6597
                              i         ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (19 / 9)
Gap_init rate = 0.03 (7 / 223), avg. gap size = 4.29 (30 / 7)  


4369 16.33 3.13 1.57  chrX_118942961_118944853      507  1400 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_118942961_    507 TAAAAAGATATCCCATGTTCATGTATTAAAAGACCTGATAGTGTTAAGAT 556
                          ii                    v   ii     i i   v         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_118942961_    557 GGCAATACTGTTTAATTTGATCTACTCCCCAGATTGATTCAGTGAAATCT 606
                                  viii  v         -----     ----  ii v    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTAC-----AGATT----CAACGCAATCC 91

  chrX_118942961_    607 CT--CAAAATCCCAGCTAACGTCATTTG--GAAATTGACAAGCTGATCCT 652
                           --             iv v i-    --                    
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCT 140

  chrX_118942961_    653 AAAATGTACTTGAACACTG-AAGTGACCAAGAATTGCCAAAATAATCTTG 701
                              vi iv  i v -  -   v    v     v       i       
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_118942961_    702 AAAAAGTTAAACA--TTTAGAAGACTCACACTTCCTGATCTTAAAACACA 749
                               vvi    --v  i  i             ii  i i     vi 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_118942961_    750 CTACAGAGCTACAGTAATCAAAACAATGGGATACTACCATAAGGATAAGC 799
                              i               i   i  v i    iv          ii 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_118942961_    800 ATATAGACCAATGGAATAGAATTTAGAGTCCAGGAATACACTCATATATG 849
                                i               v         i    v  i    i  v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_118942961_    850 TATGGGTAATTGATTTTCAACATGGGCATTAAAGCCATTCAATGGGGAAA 899
                              vi           i   v   iiii  ii                
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_118942961_    900 -AATAATCTTTTTAAGAAATGGTTCTGGGAAAACTGGATATCCACATGCA 948
                         -    i      i  v       v      v         ?         
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_118942961_    949 AAAGAATGAAGTTGGACCC-TGTATAACACCATATACAAAAATTAATTCA 997
                                            - iiv v                    i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_118942961_    998 AAAGGAAT-AAAAACTT-----TAAGAGCTAAAACTATAAAACTCTTAGA 1041
                            v i  - ? i  i -----                            
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_118942961_   1042 AGAAAATATAGATGCAAA-ATTCATGACCTTTCTATAGTCAATGGATTCT 1090
                               i    i? i   -v   i       vvvv   v      v    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_118942961_   1091 TAGATATGACACCAAAAGCACAAGCA-CAGAAGAAAGA-TAGATAAACTG 1138
                                                   -  i      i -        i  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_118942961_   1139 GACATCATCAAAATTTAAAACTTGTGTGCCTCGATGGACACTATTGGCAA 1188
                            v           v       v     i  i v         ii-- i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--AG 687

  chrX_118942961_   1189 AAAGTGAGGAGGCAAACCACAGAGTTGGAGAACAAT-TTTGCAAATCACA 1237
                                ii  i   v       i v      -   -           i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCATA 736

  chrX_118942961_   1238 CATCTGATAAAA----TATATCTAGAATATGTAAAGAATGCTTA-AACTT 1282
                         i         ii---- i    i       i       iv    -    i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_118942961_   1283 GATAATAAAAAGACAA----TCCAGTTAAAAAGGGGGCAAAGGATCTGAA 1328
                         i               ----i   i  ?    iv           i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_118942961_   1329 TAGACAGTTCTCTACAGAAAGTATACAGATGCACAATAAGCACAAGAAAA 1378
                               v     i v    ii      i   vv           v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_118942961_   1379 CCTGTTCAGTATCATTAGCCAT 1400
                         vv  i   ii    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (90 / 52)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.00 (42 / 21)  


3125 26.35 2.59 0.34  chrX_118962502_118968865.rev     4986  5873 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_118962502_   4986 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5035
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_118962502_   5036 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5085
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_118962502_   5086 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5133
                          v i iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_118962502_   5134 TATGGAACCAAAAAAGAGCTTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5183
                                viiv  ii  v iv v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_118962502_   5184 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5233
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_118962502_   5234 TACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5283
                                     i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_118962502_   5284 AATGGAACAGAAC--AGAGTCCTGTTAT---C---TACAACTAT------ 5319
                                i    i--       v vv  --- ---    vi   ------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_118962502_   5320 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5369
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_118962502_   5370 ATTTAATAAATGGTGCTGGGAAAACTGGCTTGCCATATGTAGAAAGCTGA 5419
                         v  i  i              v      v v?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_118962502_   5420 AACTGGATCCCTTCCTTACGCCTTATATAAAAATTAATTCAAGATGGATT 5469
                          ii    i    v   i  i  v    i         i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_118962502_   5470 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC-C 5518
                          ?    i       v   v       i      vi i           -i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_118962502_   5519 AGGCA-ATACCATTCAGGACATAGGCATGGTCAAGGACTTCATGTCTAAA 5567
                            ?i- v i -   iv   v v  vv i v   v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_118962502_   5568 ACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTAAT 5617
                                     vvi     i    vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_118962502_   5618 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5667
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_118962502_   5668 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 5717
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_118962502_   5718 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5767
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_118962502_   5768 AACAA----CCCA-TCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5812
                         i    ----    - i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_118962502_   5813 TGAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 5862
                         iv        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_118962502_   5863 TCACTGGCCAT 5873
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (136 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.17 (26 / 12)  


1820 23.83 1.66 7.69  chrX_119057149_119058808.rev      507  1169 (491)    L1M4_orf2#LINE/L1      286   908 (0)  

  chrX_119057149_    507 AGACACATAGACCAATGGAAAAGAATAGAGAGCCCAGAAATAAAGCTGCA 556
                              i     i        v     v     i           v iii 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_119057149_    557 CACCTATGGCCATTTGATCTCTTACAAACTTGACAAAAATAAGCAATGGG 606
                           ii     i  v     i iiv    ivv  v   i vi vv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_119057149_    607 GAAAGGACTCCCTATTCAGTAAATGGTGCTGAGATAGCTAACTAGCTATA 656
                              i ivvi  v    ii           i  i i  iiv  ? i i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_119057149_    657 TGCAGAAGAATGAAACTGGGCCCCTACATATCATATACAAAAATTATCTG 706
                             i         ii   i       --------------------  -
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTAC--------------------CT- 464

  chrX_119057149_    707 AAGATGGGTTATCATATACAAACATTTTATCATATACAAAAATTAACTGA 756
                         ------------------  v  -------                  v 
  L1M4_orf2#LINE/    465 ------------------CACAC-------CATATACAAAAATTAACTCA 489

  chrX_119057149_    757 AGATGGGTTAAAGATTTAAATGTAAGATATCAAACTATAAGAACCCT--- 803
                          i    i i ?   ii           vv v         -   i  ---
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAG 538

  chrX_119057149_    804 -AGAAAATCTAGGAA-ACACCATTCTGGACATCAGCCTCAAGAAAGAGTT 851
                         -      iv    ?i- v i -   vv   v ii vi - i v  vi   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTT-AGGCAATGGTT 586

  chrX_119057149_    852 TGTGAG-TAAGTCCTCAAAAGCAATTGCAACAAAAACAAAAATTGACAAT 900
                          v v  -  v v vi        vvv         iv      v  i  v
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_119057149_    901 TGGGACCCAAGTAAACTAAAGCACTTTTGCATAGCAAAAGAAGCTATAAA 950
                          v    iiv vi   v v  iv       iiivv    i  vi    v  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_119057149_    951 CAGAGTAAATAGACAACCCACAGAATGGGAGAAAATATTCACAAACTATG 1000
                         v i   i  v                             ii    ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_119057149_   1001 CATCCAACAAAGGCCTACTATCCAGAATCTATAAGGAA-----ACAATTC 1045
                         i   ii i  i  v  vv          v     i   -----    i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_119057149_   1046 AAGAAATAAAAAACAAGTAACTCCATTAAAAAGCAGGCAAAAAACACATG 1095
                           v  vv    i    i    i v   ?    iii      ii iv--  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT--TG 834

  chrX_119057149_   1096 AACAGACACTTTTCAAAAGGAGACATACAAGTGGCCAACAAACATTTGAA 1145
                           i     i  i  v    i   i      i       i  i  iv    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_119057149_   1146 AAAATGTTCAATATCACTAATCAT 1169
                           i   i    i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (92 / 62)
Gap_init rate = 0.02 (11 / 623), avg. gap size = 5.64 (62 / 11)  


3188 26.94 1.22 0.55  chrX_119099069_119105445     4984  5885 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_119099069_   4984 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5033
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_119099069_   5034 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5083
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_119099069_   5084 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5131
                          v i iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_119099069_   5132 TATGGAACCAAAAAAGAGCTTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5181
                                viiv  ii  v iv v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_119099069_   5182 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5231
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_119099069_   5232 TACAGTAATCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5281
                                     i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_119099069_   5282 AATGGAACAGAAC--AGAGTCCTCAGAAATAATGCCGCTTATCTACAACT 5329
                                i    i--       --        vv  iivi  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_119099069_   5330 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5379
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_119099069_   5380 CTATTTAATAAATGGTGCTGGGAAAACTGGCTTGCCATATGTAGAAAGCT 5429
                           v  i  i              v      v v?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_119099069_   5430 GAAACTGGATCCCTTCCTTACGCCTTATATAAAAATTAATTCAAGATGGA 5479
                            ii    i    v   i  i  v    i         i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_119099069_   5480 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5529
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_119099069_   5530 -CAGGCA-ATACCATTCAGGACATAGGCATGGTCAAGGACTTCATGTCTA 5577
                         -i   ?i- v i -   iv   v v  vv i v   v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_119099069_   5578 AAACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTA 5627
                         vi            vvi     i    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_119099069_   5628 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5677
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_119099069_   5678 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5727
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_119099069_   5728 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5777
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_119099069_   5778 AAAACAA----CCCA-TCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5822
                           i    ----    - i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_119099069_   5823 CTTGAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5872
                           iv        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_119099069_   5873 CATCCCTGGCCAT 5885
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


 846 10.98 10.37 4.88  chrX_119239063_119242946.rev     1884  2047 (1837)    L1M4_orf2#LINE/L1        1   173 (735)  

  chrX_119239063_   1884 TGGAACATTATCCCATTATCATGTATTGGAAGACTTAATATTGTTAAGGT 1933
                              viv        vv     v                        i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_119239063_   1934 GGCAATACTCTCTAAACTGATATACAGACCCAAGGCAATTCCTATTAAAA 1983
                                   i i   i    v      ii   v     i     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_119239063_   1984 TCCCAGCTACCTTTTTTTTTTTTTGGCAGAAATTGACAA----------A 2023
                                 i        --------              ---------- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--------GCAGAAATTGACAAGCTGATCCTAA 142

  chrX_119239063_   2024 AAT------GGAAATGTAAGGGACC-AGAAT 2047
                            ------       i        -     
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAAT 173

Transitions / transversions = 1.57 (11 / 7)
Gap_init rate = 0.02 (4 / 173), avg. gap size = 6.25 (25 / 4)  

 909 14.86 2.86 1.14  chrX_119239063_119242946.rev     2363  2537 (1347)    L1M4_orf2#LINE/L1      179   356 (552)  

  chrX_119239063_   2363 AAGCAATCCTGAAAAAGAA---CAAAGGCAGAGGCCTCACACTTAACCAA 2409
                           i     i          ---     vii    v         v-    
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC-CCAA 227

  chrX_119239063_   2410 TTTCAAAGCTTACTACAAAGTAACAGTAATCAAGAGTGCATGGTACCTGC 2459
                                i            iv             vv ii      iv  
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_119239063_   2460 ATAAGGATAGACATATAGATCAATAGAATGTAACTGAGAATCCAGAAATA 2509
                                                 i    iv  i     i          
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_119239063_   2510 AGAGTCA--CTTTTATGGTTAACTGATTTT 2537
                          - vi  -- v        i  i       
  L1M4_orf2#LINE/    328 A-ACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 1.60 (16 / 10)
Gap_init rate = 0.02 (4 / 178), avg. gap size = 1.75 (7 / 4)  

2895 16.28 1.42 1.24  chrX_119239063_119242946.rev     2829  3393 (491)    L1M4_orf2#LINE/L1      343   908 (0)  

  chrX_119239063_   2829 GGTTAACTGATTTTTGACAAGTGTGCCAAGATCATTCAATTGAGAGAAAA 2878
                            i  i       i      v         i        --i i    i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT--GGGGAAAG 390

  chrX_119239063_   2879 AAGAGTGTTTTCAACAAATGGTGCTGAAACAACTGAATATGCACAT-CAA 2927
                           v   v                   ii       i   ?v     -   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_119239063_   2928 AAGAATGAAGTTGGACCCCCTACTTCATACCACATACATACATTAACAAA 2977
                                            -   i   i    i     v v      vv 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCA 489

  chrX_119239063_   2978 AGATGGATCAAAGACGTAA--GCACAAGTTACATCTAGAAAACTTTTAGA 3025
                          i        ?    v   -- i vi  i  v v   v      i     
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_119239063_   3026 AGAAAACGTAAGCACAAATCTTTGTGGTTTTTGGATTAAACAATGGATTT 3075
                                i  i ?ii       i   iii  -  i   ii      v  i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTT-GGGTTAGGCAATGGTTTC 588

  chrX_119239063_   3076 TTAAACATGACACCAAAAGCACGAGTGACAAAAGAAAAAAATAGATAA-T 3124
                            i i                i  ii             -       - 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAAT 637

  chrX_119239063_   3125 TGAACTTTATCAGATTTTAAAACTTCCATTCTTAAAAGGACACCACCAAG 3174
                           i    i    i v  v       iii v   v         i i    
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_119239063_   3175 AAAGTAAAAACTGACAACCCACAGAATGGGAGAAAATTTTTGGAAATCAT 3224
                              i    --                         v    v       
  L1M4_orf2#LINE/    688 AAAGTGAAAA--GACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_119239063_   3225 ATATCTGATGAGAGACTTGTATCTAGAATATATTAAAAACAGTTACAACT 3274
                                  i  i          i         v  i   vv        
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_119239063_   3275 TAATAACAAAAGGACAAGTAACCCAATTAAAAGATGGTTAAAGGGTCTGA 3324
                         i     i    i     i          ?   i    vi     i i   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_119239063_   3325 ATATACAGTTCTCCAAAGA---TACACAA-TGACCAATAAGCAAATGAAG 3370
                            v   v           ---  i    -  i          v     i
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_119239063_   3371 GGATGCTCAATATCATTAGTCAC 3393
                         i         i    ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.26 (61 / 27)
Gap_init rate = 0.02 (10 / 566), avg. gap size = 1.50 (15 / 10)  


3255 26.32 0.77 0.77  chrX_119259473_119265895     5023  5930 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_119259473_   5023 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5072
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_119259473_   5073 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5122
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_119259473_   5123 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5170
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_119259473_   5171 TATGGAGCCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCCAAAG 5220
                               iviiv  ii  v  viv  v     iv     i i ivvvi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_119259473_   5221 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATGCTACAAGGC 5270
                                i      vv    i  v  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_119259473_   5271 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACC 5320
                                 i   i    ii         i iv ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_119259473_   5321 AATGGAACAGAAC--AGAGTCCTCAGAAATAATGCCATATATCTACAACC 5368
                                i    i--       --        vv     i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_119259473_   5369 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAACAA--GT 5416
                          vi    i  i     ivv  v   i v  vv           v  --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_119259473_   5417 CACTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAG 5466
                          -- v  i  i              v      v  ?   i  ii i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_119259473_   5467 CTGAAACTGGATCCCTTCCTTACGCCTTATACAAAAATTAATTCAAGATG 5516
                         v    ii    i    v   i  i  v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_119259473_   5517 GATTAAAGACTTAAATGTTAGACCTAAAACCTTAAAAACCCTAGAAGAAA 5566
                            i ?    i       v   v       iv     vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_119259473_   5567 ACCTAGGCA-ATACCACTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5615
                           v    ?i- v i -i  iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_119259473_   5616 TAAAACACCAAAAGCAATGACAACCAAAGCCAAAATTGACAAATGGGATC 5665
                           vi            vvii    v    vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_119259473_   5666 TAATTAAACTAAAGAGCCTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5715
                          v  i   v v  i i i i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_119259473_   5716 AACAGGAAACCTACAAAATGGGAGAAAATTTTTGCAATTTTCTCATCTGA 5765
                           v  iv    i   i             v       v ivivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_119259473_   5766 CAAAGGGCTAATACCCAGAATCTACAATGAACTCAAACAAGTTTACAAGA 5815
                         i  i  i  vi  i       v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_119259473_   5816 AAAAGACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATGGACAC 5865
                                   i     v  i?    i            v     i    i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_119259473_   5866 TTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTC 5915
                              v        i  vi viii     v ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_119259473_   5916 ATCATCACTAGCCAT 5930
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3071 28.41 0.33 0.33  chrX_119301052_119307445.rev     4996  5903 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_119301052_   4996 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCGATATCATGAAAAT 5045
                              ii i  i     i        v      v ii    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_119301052_   5046 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5095
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_119301052_   5096 TTCCAATGAGTTTCTTCACAGAATTGGAAAAAAATACTTTAAAGTTCATA 5145
                          i   iivivi  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_119301052_   5146 TGGAGCCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCCAAAGAA 5195
                             iviiv  ii  v  v v  v     iv     i i ivvvi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_119301052_   5196 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5245
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_119301052_   5246 CAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGACATATAGACCAA 5295
                               i   i    ii i       i iv ii i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_119301052_   5296 TGGAACAGAAC--AGAACCCTCAGAAATAATACCACACGTCTACAACTAT 5343
                              i    i--   ii  --        vv   i  i i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_119301052_   5344 CTGATCTTTGACAAACCTGACAAAAGCAAGAAATGGGGAAACAATTCCCT 5393
                         i    i  i     ivv  v   i v  vvv          v   vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_119301052_   5394 ATTTAACAAATGGTGCTGGGAAAACTGGCTTGCCATATGTAGAAAGCTGA 5443
                         v  i                 v      v v?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_119301052_   5444 AACTGGATCCCTTCCTTACACCTTATACAAAAATTCATTCAAGATGGATT 5493
                          ii    i    v   i     v            v i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_119301052_   5494 AAAGACTTACATCCTAGACCTAAAACCATAAAAACACTAGAAGAAAACCT 5543
                          ?    i  v  viv   v       i      vivi           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_119301052_   5544 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5592
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_119301052_   5593 ACACCATAAGCGATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAAT 5642
                               v    ivvi     v    vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_119301052_   5643 TAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGTGAACA 5692
                         i   v i  i i   i  ii vv    i  v    i ivv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_119301052_   5693 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAGAAA 5742
                          i     i                 v       vii ivi      v  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_119301052_   5743 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAA 5792
                           i  vi          v  i         vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_119301052_   5793 AACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAAACCCTTCT 5842
                         i     i     v  i? v  i            v    i i  vi    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_119301052_   5843 CAAAAGAAGACATTTATGCACTCAACAGACACATGAAAAAATGCTCATCA 5892
                          v        i  vi viiivi   i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_119301052_   5893 TCACTGGCCAT 5903
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.37 (147 / 107)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


1118 18.75 4.78 4.78  chrX_119434929_119437609        1   272 (2409)    L1M4_orf2#LINE/L1       99   370 (538)  

  chrX_119434929_      1 AATCCCAATGGCCTTTTTTGCAGAAATGAAAAAGCTGATCCTAAAATCCA 50
                                iiv                 vi v                i  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_119434929_     51 TATGGAATTATATGTAAGGCACCTA-AATAGTTAAAACAATCTTGAAAAA 99
                                ----   i    v   i -     ii                 
  L1M4_orf2#LINE/    149 TATGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_119434929_    100 GAGGAA---AGGTGAAACATTCACATTTTCTGATTTCAAAATTTACCAAA 146
                           i   ---  v  i iv i     i  i ii         i    i v 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_119434929_    147 AAGCTATAGTAATCAAAACAGTGTAGCACCAGTGTAAG-ACGGACATATA 195
                               i         i       i i  ii ii    - ii        
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_119434929_    196 AGAAGAATGGAATAGAATTAAGA-------AATAAACCC-CATCTCTGTG 237
                         -  vv              i   -------         -i iv i i  
  L1M4_orf2#LINE/    295 -GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_119434929_    238 GTTTTATCTACCTTTGGTCTTTGATGATGGTGACA 272
                           ----- v ---   i i  i  ii v    v  
  L1M4_orf2#LINE/    344 GT-----CAA---TTGATTTTCGACAAGGGTGCCA 370

Transitions / transversions = 2.92 (38 / 13)
Gap_init rate = 0.03 (9 / 272), avg. gap size = 2.89 (26 / 9)  

3151 26.83 1.11 0.44  chrX_119434929_119437609     1287  2188 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_119434929_   1287 TGGAAGAACATTCCATGCTCATAGATAGGAAGAATCAATATCGTGAAAAT 1336
                              ii i  i     i    i   v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_119434929_   1337 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1386
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_119434929_   1387 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAA--CTAAAGTTCATA 1433
                          v   iivi i  i  ii     -   iv  ivvi --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_119434929_   1434 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCCAAAGAA 1483
                              viiv  ii  v  v v  v     iv     i i ivvvi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_119434929_   1484 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATGCTACAAGCCTA 1533
                              i      vv    i  v  ii i      viv i      iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_119434929_   1534 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACCAA 1583
                               i   i    ii         i iv ii i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_119434929_   1584 GGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAATCAT 1631
                         v    i    i--    i  --        vv   i    i  iii   v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_119434929_   1632 CTGATCTTTGACAAACCTGACAAAAAACAAGAAATGGTGAAAGGATTCCC 1681
                         i    i  i     ivv  v   i v-  vvv     v     i  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTC 397

  chrX_119434929_   1682 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCTG 1731
                          v  i  i              v      v  ?   i     i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_119434929_   1732 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 1781
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_119434929_   1782 TTAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1831
                         iv?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_119434929_   1832 TAGGCA-ATACCACTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA- 1879
                             ?i- v i -i  iv   v v  vv i     v ii   v ivv  -
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_119434929_   1880 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1929
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_119434929_   1930 TTAAACTAAAGGGCTTCTGCACAGCAAAAGAAACTACGATCAGAGTGAAT 1979
                          i   v v  iii   i  ii vv    i  v    iv vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_119434929_   1980 AGGCAACCTACGGAATGGGAGAAAATTTTTGCAAGCTACACATCTGACAA 2029
                           i     i  i              v       iii i i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_119434929_   2030 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 2079
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_119434929_   2080 AAACAAA---CCCCATCAAAAAGTGGGTGAAGGATATGAACAGATACTTC 2126
                          i     ---   v  i?    i    ii      v    i   i i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_119434929_   2127 TAAAAAGAAGACATTTATGCAGCCAACAGACACAGGAAAAAATGCTCATC 2176
                          vv        i  vi viii     i ii    v     i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_119434929_   2177 ATCACTGGCCAT 2188
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2117 20.10 2.23 14.02  chrX_119502989_119504785      500  1305 (492)    L1M4_orf2#LINE/L1      198   908 (0)  

  chrX_119502989_    500 GAACAAAGCTGGAGGCATCATACTATGTGACTTCAAATTATATTACAAGG 549
                                 i      vv   i   vivii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_119502989_    550 CTATAGTGACCAAAACAGCATGGTATTGTTATAAAAACAGACACATAGAC 599
                            i   i i   i    ii     i  vi    ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_119502989_    600 CAATTGAACAGAATAGATAATCCAGAAATAAATCCATGTATTTATAGCCA 649
                             v   i     v  v i            i    ii      i i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_119502989_    650 ACTGATTATAGACAAAGGCACCAAGAACATACATTGGAGAAAAGACACTG 699
                          i     v v     i  ii      v   v  v   i    ii i v v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_119502989_    700 CCTTCAATAAATGGTGCTGGTGTTGTTACATGGATATATTGGGACACCCA 749
                         ii     i            ----------------------    ----
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGG----------------------GACA---- 421

  chrX_119502989_    750 CACACACACACACACACACACACACACACACACACACACCACAAATAAAT 799
                         --------------------------------------------------
  L1M4_orf2#LINE/    422 -------------------------------------------------- 421

  chrX_119502989_    800 GGTCCTGCAAAAATTGGATATTTATATTCAGAAGAATGAAATCCGACCCC 849
                         ------------ i      ?ii i  v  i         i iv      
  L1M4_orf2#LINE/    422 ------------ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_119502989_    850 TATCTCTCACCATATACAAAAATT----TAAGATGGATTAAAGACTTAAA 895
                           i   v                 ----i  i      i ?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_119502989_    896 CATAAGATCCAAAACTATAAAACTACTAGAGGAAAA--TGGGAGGAACAC 943
                         ii     v i              vi    i     -- i  ? v  vv 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_119502989_    944 TTCTGGACATTTATCTAGGCAAATATTTTATGGCTAAGACCTCAAAAGCA 993
                            vv   v  vivi       vvi   iv i v  v   vi        
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_119502989_    994 CAGGCAACAAAAACAAACAAACAAAAAGGACAAATGTGACTTAATTAAA- 1042
                           i         i-   -   i -----  i    vv     v  i   -
  L1M4_orf2#LINE/    610 CAAGCAACAAAAG-AAA-AAATA-----GATAAATTGGACTTCATCAAAA 652

  chrX_119502989_   1043 CAAAAAGCTTTTGCATAGCAAAGGAAAC-----ACAAAATAAAAAGGCAA 1087
                         iv    i      iiivv       v  ----- v   i i     i   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_119502989_   1088 CCTACGGAATGAGA-AAAACATTTGCAAACTAGGTATCTGATAAGGGTTT 1136
                           i  i     i  -    i         ii vi             vi 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_119502989_   1137 AATATTCAAAATATATAAGGAACTC----AACACCATAGTAAAAACAATG 1182
                         vi   i  i         i      ----   v v   i      ---- 
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA----G 798

  chrX_119502989_   1183 ACAAAAACAACAACAAAGTAATTCTATTAAAAAAGTGGTCAAAGGGCATG 1232
                              -------------   ii v   ?     -   v      iiv  
  L1M4_orf2#LINE/    799 ACAAA-------------TAACCCAATTWAAAAA-TGGGCAAAGGATTTG 834

  chrX_119502989_   1233 AATAGACATCTCTCCAAAGAAGACACACAAATGGCCAAAAGATATATAAA 1282
                                  i             i i            v iii i  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_119502989_   1283 AA-ATGCTCAATGTCGCTAATTAT 1305
                           -        ii  i????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (105 / 53)
Gap_init rate = 0.02 (15 / 711), avg. gap size = 8.73 (131 / 15)  


3346 26.21 0.33 0.77  chrX_119613322_119618373     3648  4559 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_119613322_   3648 TGGAAAAACATCCTGTGCTCATTGATAGGAAGAATCAGTATTATTAAAAT 3697
                               i i    ii  i    v   v      v i i    i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_119613322_   3698 GGCTATACTGTGCAAAGCAATTTACAGATTTAATGCTATTCCTATCAAAC 3747
                            v     viv    vii  i        i  i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_119613322_   3748 TACCAACAACATTCTTCACAGAACTAGAAAAAATTATTTTAAAATTTCTA 3797
                          v   i vi v  i  ii     v v  v  iv v  ii       iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_119613322_   3798 TGGAACCAAAAAAGAGTCTGAATAGCCAAGGCAATCCTAAGCAAAAAGGA 3847
                              viiv  ii  vi v          ii     i i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_119613322_   3848 CAAAGCTGGAGGAATCACATTACCCAACTT-GAAACTATACTACAAGGTT 3896
                              i       v     i v     i  -i     -        i i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_119613322_   3897 ACCGTGACCAAAATAGCATGGTACCGGTGCAAAAACAGGCACATAGATGA 3946
                           v  i i   i i  ii      i  iii  ii i  i  i      v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_119613322_   3947 ATGGAACAGAATAGAGAGCCCAGAAATAAGGCTTCACATTTACGACCATC 3996
                               i     v     i          iv ivi       i ii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_119613322_   3997 TGATCTTTGACAAAGCTGACAAAGACAAGCAATGGGGAAAAGACTCCCTA 4046
                             i  i     i v  v   iiv  vv           ii ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_119613322_   4047 TTCAATAAATGATGCTGGGATAACTGGCTAGCCATATGCAGAAGATTGAA 4096
                              i     i        i      v  ?   i     i    v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_119613322_   4097 GCTGGACCCCTTCCTTACACCATATACAAAAATTAACTCAAGATGAATTA 4146
                          i         v   i                         i   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_119613322_   4147 AAGACTTAAATGTAAACCCCAAAACTATAAAAACCCTGGAAGACAACTTA 4196
                         ?    i         ivv i            vi i i     v   v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_119613322_   4197 GGCA-ATACCATCCTGGACATAGGAGTGAGCAAAGATTTCATGACAAAGA 4245
                           ?i- v i v  v  -  v v  iv ii    v i    v iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_119613322_   4246 CACCAAAAGCAATAGCAACAAAAGCAAAAAATTGACAAATGAGATCTAAT 4295
                                    vv           -       v  i    vi  ii v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCAT 647

  chrX_119613322_   4296 TAAACTTAAGAGCTTCTGCACAGAAAAAGAAACTATCAACAGAGTAAACA 4345
                         i   v    i i   i  ii vvv   i  v        v i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_119613322_   4346 GACAACCTACAGAATGAGAGAAAACATTTGCAAACTATGCATCTGTCAAA 4395
                                i        i       i         ii  ii     vi  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_119613322_   4396 GGTCTAATATCCAACATGTATATGAAACGTAAGCAAATTTACAAGAGAAA 4445
                           v  vi      iv  i    vii   vivvi   v iv i  v i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_119613322_   4446 AACAAACAATCCCATTAAAAAGTGGGCAAAGCACATGAACTGACACTTCT 4495
                         i     i  i  v   ?    i         v iv    iv    i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_119613322_   4496 C-AAAGAAGACACTTCTCAATGCGACCAACAAGCATATGAAGAAAAGCTC 4544
                          -        i -- viv    --i    i     i     i i v    
  L1M4_orf2#LINE/    848 CCAAAGAAGATA--TACAAATG--GCCAATAAGCACATGAAAAGATGCTC 893

  chrX_119613322_   4545 AATATCACTGATCAT 4559
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (147 / 88)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


 292 20.83 4.17 0.00  chrX_119743057_119749750.rev        1    72 (6622)    L1M4_orf2#LINE/L1      834   908 (0)  

  chrX_119743057_      1 GAACAGACACTTTTC---AAAAGACATACATGCAGCCAATGAGCATATGA 47
                            i     i  i  --- i    i     viii      i    i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_119743057_     48 AATAAAGTTCAACATCACTGATCAT 72
                           vi v i         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.01 (1 / 75), avg. gap size = 3.00 (3 / 1)  

2819 26.48 3.75 0.57  chrX_119743057_119749750.rev     5324  6203 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_119743057_   5324 TGGAAAAACATTCCATCCTCATGGATAGGAAGA----AT-CTG--AAAAT 5366
                               i i  i    vi        v      ----  -i  --  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_119743057_   5367 GGCCATATTACCCA--TT--------------------TCTTCATCAAGC 5394
                            v   i v    --  --------------------  iii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_119743057_   5395 TACCATGGACTTTCTTCACAGAATTAAAAAAACT-ACTTTAAATTTCATA 5443
                          v   vvvi i  i  ii     v vi v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_119743057_   5444 TGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTACGTAAAAGGAA 5493
                              viiv  ii  v  viv        i      i iviv  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_119743057_   5494 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACATTACTACAAGG 5543
                              i      vv   ii  v  ii i      --  -         i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--AC-TTACTACAAAG 247

  chrX_119743057_   5544 CTGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGAC 5593
                           i      i   i    ii         i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_119743057_   5594 CAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAATCA 5643
                                 i    iv   ivii         vv   i    i  iii   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_119743057_   5644 TCTGATCCT-GGCAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5692
                         vi    ii - i   ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_119743057_   5693 TATTTAACAAATGGTGCTGGGAAAACCGGCTAGCCATATGCAGAAAACTA 5742
                          v  i                 v   i  v  ?   i     i  i v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_119743057_   5743 AAACTGGACACCTTCCTTACACCTTATACAAAAATTAACTCAAGATGAAT 5792
                           ii     v   v   i     v                   i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_119743057_   5793 TAAAGACTTAAATGTAAGACCTAAAACCATCAAAACCCT-AGAAGAAAAC 5841
                         i ?    i           v       i  -     i  -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAAC 546

  chrX_119743057_   5842 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5890
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_119743057_   5891 AAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5940
                         vi    v       vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_119743057_   5941 ATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCATCACAGTGAA 5990
                           i   v v  i     i  ii vv    i  v       vv v      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_119743057_   5991 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTGCCCATCTGACA 6040
                         v  i     i                 v       viiiivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_119743057_   6041 AAGGGCTAACATCCAGAATCTACAATGAATTTAAACAAATGTAGAAGAAA 6090
                          i  i  vii         v  i  v   i ivv    v vv v  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_119743057_   6091 AAAGCAAACAACCCCATCAAAAAGTGGGCAAAAGAAACGAAGAGACACTT 6140
                           ii    i     v  i?    i        i  vvi   v     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_119743057_   6141 CTCAAAAGAAGACATTTTTGCCGCCAACAAGCATATGAAAAAAAGCTCAT 6190
                            v        i  vivviiv     i     i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_119743057_   6191 CATCATTGGTCAT 6203
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (132 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.92 (38 / 13)  


1913 19.18 0.34 24.29  chrX_119759976_119764849.rev     3190  4383 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_119759976_   3190 TGGAAACATATCCCATGCTCATGGATAGGTAGAATCAACATTGTGAAAAA 3239
                               v          i        v  v   v i  i     v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_119759976_   3240 TAACCATAGTGTCAAAAGCAATCTGCAAATTCAATGCAATTCTCATCAAA 3289
                          ii v   v vi v   vii    i  i      i     i ii      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_119759976_   3290 ATACTA-CTATCATTCTT-CAAAGAATTAGAAAAAACAATTCTAAAATTC 3337
                           v i -  ii v  i  -  i -    -  v  ivii  i         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGA-AATT-GACAAGCTGATCCTAAAATTC 147

  chrX_119759976_   3338 ATATGGAACTGAAAAAGAGCCTGCATAGCCAAAGCAAGACTGAGCAAAAA 3387
                                 v  v  ii  v  v v         i   vvi   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_119759976_   3388 GAACAAATCTGGAGGCATCACATTACCTGATTTCAAACTATACTATAAGG 3437
                                vi      vv     i v  ii        viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_119759976_   3438 CCATAGTCACCAAAACAGCATGGTACTGGTATAAAAAAAAAGGCACATAG 3487
                          i i   v i   i    ii         i    ii v i --  i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA--CATATAG 295

  chrX_119759976_   3488 ACCAATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGC 3537
                          i        i     v    ii               v i i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_119759976_   3538 CAACTGATCTTCAGCAAAGCAAACAAAAACATAAAGAGGGGAAAGGACAC 3587
                            i    i   ii   i vviv   i v   vv iv        i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_119759976_   3588 ACTTTTCAACAAATGGTGCTAGGATAATTGGTTAGCCACATGTAGGAGAA 3637
                         v                   i   i  i   v  ?       i ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_119759976_   3638 TGAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCTGGTGGC 3687
                             ii    i  ii i   v    v           i     -------
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC------- 488

  chrX_119759976_   3688 TCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGTGGGGGTGGATCACC 3737
                         --------------------------------------------------
  L1M4_orf2#LINE/    489 -------------------------------------------------- 488

  chrX_119759976_   3738 TGTGGTCAGGAGTTCAAGACCAGACTGGCCAACATGGCAAAACCCTGTCC 3787
                         --------------------------------------------------
  L1M4_orf2#LINE/    489 -------------------------------------------------- 488

  chrX_119759976_   3788 CTACTAAAAATACAAAAACAGGCAGGCGCCTGTAATCCCAGCTACTTGGG 3837
                         --------------------------------------------------
  L1M4_orf2#LINE/    489 -------------------------------------------------- 488

  chrX_119759976_   3838 AGGCTGAGGTAGGAGAATTGCTTGAGCCTGAAAGGAGGTTGCATTGAGCC 3887
                         --------------------------------------------------
  L1M4_orf2#LINE/    489 -------------------------------------------------- 488

  chrX_119759976_   3888 AAGAACGTGCCACTGCACTCCAGTCTGGGTGACAAACTGAGAGTCCGTCT 3937
                         --------------------------------------------------
  L1M4_orf2#LINE/    489 -------------------------------------------------- 488

  chrX_119759976_   3938 CAAAAAAGAAAAAAAAAATCAACTCAAGATGGATCAAGGACTTAAATCTG 3987
                         -------------------------  i        ?i   i     v i
  L1M4_orf2#LINE/    489 -------------------------AAAATGGATCAWAGACCTAAATGTA 513

  chrX_119759976_   3988 AGACCTGAAACTATAAAAATTCTGGAGGATAACATTGGAAAAACCCTTCT 4037
                            v  i           v ii i  i  v     v  ?iv  vi    v
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_119759976_   4038 AGACTTTGGCTTAGGTTAGGATTTCATGACCAAGAACCCAAAAACAAATG 4087
                         v   i    v     iv v i    v iivi v  vv      i  v v 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_119759976_   4088 CAATAAAAACAAAGATAAATTACTAGGACTTAATTAAACTAAAGAGCTTT 4137
                            i    iv   i   i  v v v      v  i   v v  i i    
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_119759976_   4138 TGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAGACAACCCACTGAGTG 4187
                           ii vv    i iv  vi   iv i   i  v           v  i  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_119759976_   4188 GGAGAAAAT--CTACAAAATCTATACATCTGACAAAGGACTAATATCCAG 4235
                                  --i i    -  -   i      i  i     vi       
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAA-TC-ATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_119759976_   4236 AATCTACAAGGAACTCAAATAAATCAGCAGGAAAAAAACCAAACAACCCC 4285
                            v  i  i      vv i  v   ii iv     i  -   i     v
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCA 810

  chrX_119759976_   4286 ATCAAAAAGTAGGCTAAGGACATGAATAGACAATTCTCAAAAGAAGATAT 4335
                           i?    i i   v     iv          v     v           
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_119759976_   4336 GCAAATGACCAATAATCATATGAAAAAATGCTCAACATCACTAATCAT 4383
                         i      i       v  i       i             ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (136 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 26.73 (294 / 11)  


2934 26.06 1.53 2.51  chrX_119899031_119901254      815  1731 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_119899031_    815 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 864
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_119899031_    865 GGCCATACTGCTCAAAGTAATTTATAGATTCAGTGCTATTCCGATCAAGC 914
                            v     v i    v i  i  i       ii  v  i  v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_119899031_    915 TACCA-TTGACTTTATTCGCAAAATTAGAAAAAAAAACTTTAAATTTCAT 963
                          v   -i  v    -  i   i  v v  v  ivvi iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_119899031_    964 ATGGAACCAAAAAAGAGCTTGTATAGCAAAGACAATCCTAAGCGAAAAGA 1013
                               viiv  ii  v iv v     v  i      i i ivi i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_119899031_   1014 ACAAAGGTGGGGGGCACCACGCTACCTGACTTCAAACTATGCTACACTAT 1063
                               v   i  i -i   i  v  ii i      ---------   - 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAA---------ACT-T 238

  chrX_119899031_   1064 ACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGA 1113
                                i          i   i    ii         i iv ii i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_119899031_   1114 TATATAGACCAATGAAACAGAACAGAGGCCTCAGAAATAACGCCATACAT 1163
                         i       i     i  i    iv   ivii         vv        
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_119899031_   1164 CTACAACCATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAA 1213
                         i  iiii  vi    i  i     ivv  vv  i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_119899031_   1214 AGGATTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCATTATGC 1263
                           i  vvi  v  i  i        i     v      v  ? vvi    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_119899031_   1264 AGAAAACTGAAACTGGACCCCTTCCTTACACCTTATAAAAAAATTAACTC 1313
                          i  i v    ii         v   i     v    v            
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_119899031_   1314 GAGATAGGTTAAAGACTTAAACCTAAAACCTAAAACCATGAAAACCCTAG 1363
                         i i  i i i ?    i    iv   i v       i  i   vi i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_119899031_   1364 AAGAAAACCTAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAAGACT 1411
                                 v    ?-   --i -   iv   v v  vv i     v ii 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_119899031_   1412 TCATGACCAAAACACCAAAAGTAATGGCAACAAAAGCCAAAATTGACAAA 1461
                           v iivi vi          i vvi          vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_119899031_   1462 TGGGATCT------AATTAAAGAGCTTCTGCACAGCAAAAGAAACTATCA 1505
                          v   ii ------       i -   i  ii vv    i  v       
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_119899031_   1506 TCAGAGTGAATAGGCAACCTACAGAATGGAAGAAATTTTTTTGCATCTGA 1555
                         vv i      v  i     i         i     v v   -   -----
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT-GCA----- 729

  chrX_119899031_   1556 AATTTTATCCATCTGACAAATGTCTAATATCCAGAATCTACAAGGAAGTT 1605
                            iv   --      i  iv v  vi          v  i  i   v i
  L1M4_orf2#LINE/    730 AATCATAT--ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_119899031_   1606 AAACAAATTTACAAGGAAAAAA--ACCAACCCCATCAAAAAGTGGGTGAA 1653
                         vv    v iv i  vi    i -- vi     v  i?    i    ii  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_119899031_   1654 GGATATGAGCAGACATTTCTCAAAAGAAGACATGTATTTGGCCAAGAAAC 1703
                             v   ii           v        i  ii vv       v  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_119899031_   1704 ATATGAAAAAAAGCT-AA--TCACTGGTCAT 1731
                          i       i v   -  --   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.31 (37 / 16)  


3262 25.36 1.45 0.44  chrX_119917265_119921467.rev     2814  3712 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_119917265_   2814 TGGAAAAACATTCCATGCTCATGGATTGGAAAAATCAATACTGTGAAAAT 2863
                               i i  i     i             i v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_119917265_   2864 GACCATACTGCCCAAAGCAATCTACATATTCAATGCAATTCCTATCAAA- 2912
                          i v     v      vii       v      i     i         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_119917265_   2913 TCACCAATATCATCATGCACAGAATTAGAAAAA--AATCTTAAAATTCAT 2960
                           -   iivv v iv vii     v v  v  i--i   i          
  L1M4_orf2#LINE/    101 TC-CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_119917265_   2961 ATGGAACCAAAAAAGAGCCTAAATAGCCAAAGCAATCCTAAGCAAAAAGA 3010
                               viiv  ii  v  vi          i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_119917265_   3011 ACCAAGCCAGAGACATCACATTACCTAACTTCAAATTATACTACAAGGCT 3060
                           v   iii   ivv     i v  i  i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_119917265_   3061 ATAGTAGCCAAAACAGCATGGTACTGGTATAAAAGTAGATACATAGACCA 3110
                          i    ii   i    ii         i    iii    i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_119917265_   3111 ATATAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAAAACAG 3160
                           iv  i     v    ii           v   v i i   iiiv-  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT-CAA 348

  chrX_119917265_   3161 CTGATCTTTGACAAAGCAGACAAAAGCATGCACTGGGGAAAGCACACTCT 3210
                         i    i  i     i vv v   i v   v  v         v i v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_119917265_   3211 TTTCAATAAATGATGCTGAGAATATTGGACAGCCACATGCAGAAGAATGA 3260
                               i     i     i  vv i    i ?         i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_119917265_   3261 AACTGGACCCTTAACTCTTACCATATACAAAAATTAACTCAGGATGGATT 3310
                          ii       i  v   vi                      ii      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_119917265_   3311 AAATACTTACATATAAGACCTGAAACTATAAAAATTCTAGAAGAAAACCT 3360
                          ? v  i  v  i     v  i           v ii           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_119917265_   3361 AGGGAAAGCTTTTCTGGACATTGGCCTAGAAAAGTAATTTATCAG-TAAG 3409
                            ?iv iv i   vv   v    vi   iv  - ii   v i  -  v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATG 597

  chrX_119917265_   3410 GCCTCAAAAGCAAATGCAGCAAAAACAAAAATAAATAAATGGGACTTCAT 3459
                         i vi        v v   i     iv       i      v         
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_119917265_   3460 TAAACTAAAGAAGCTTCTGCACAGCTAAAGAAAT----AACAGAGTAAAC 3505
                         i   v v  i  -   i  ii vv v  i  v i----  v i   i  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_119917265_   3506 AGAAAACCTGCAGAATAGGAAAAAATATTTGCAAGCTATACATCCAACAA 3555
                            v    ii      i   i             iii   i   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_119917265_   3556 AAGGCTAACATCCAGAATATGCAAGGAAATC----AAATCAGAAAGAAAA 3601
                         ii i  vii           ii  i   v  ----  v   iv  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_119917265_   3602 AGACAAATAATCCCATTAAAAAGTAGGGAAACAACATAAATAAACACTTC 3651
                                   i  v   ?    i i  v   vi iv i    i   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_119917265_   3652 GCAAAAGAAAATATACAAATGGCCAACAAACATATAAAAA-ATGCTCAAC 3700
                         v v      i                i  i  i  i    -         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_119917265_   3701 ATTATTAATCAT 3712
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (143 / 81)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


 339 17.46 1.59 0.00  chrX_119929713_119934035.rev      442   504 (3819)    L1M4_orf2#LINE/L1        1    64 (844)  

  chrX_119929713_    442 TGAAAAGACAGCCTATGTTTTTGGA-TATAAGATTTAATATTGTTAAGAT 490
                           i     i v  i     iv    - iv    i                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_119929713_    491 GGCAATACCCCACA 504
                                 i  v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCA 64

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1)  

3374 24.56 0.66 0.77  chrX_119929713_119934035.rev     2925  3832 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_119929713_   2925 GAAAAGATATTCCATGTTAATGGATTGAAAGAATCAATATTGTTAAAAAT 2974
                          i        i       v        i    v i         -  i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAGAT 50

  chrX_119929713_   2975 GTCCACATTACACAAAGCAATCTACAGATTCAATGTAATCCTTATCAAAA 3024
                          v v i i v v    vii              i i     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_119929713_   3025 TACCAATGACATTCTTCATAGAAATAGAAAAAAAAATCCTAAAATGTAGA 3074
                          v   iivi v  i  iii      v  v  ivvi          vi v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_119929713_   3075 TGGAACCAAAAAAGACCCAGTGTAGCAAAAGCTATCCTAAGTAAAAAGAA 3124
                              viiv  ii       vi    v   i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_119929713_   3125 TATAACTGGAGAAATCACATTGCCCGACTTCAAATCATACTACAGAGCTA 3174
                         i v ii     i v     i v   i i      v v       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_119929713_   3175 TAGTAACCCAAAACAGCATGATATTGACATAAAAATAGACACATAGTCCA 3224
                         i     i -  i    ii  i  i  i     ii       i    vi  
  L1M4_orf2#LINE/    251 CAGTAATC-AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_119929713_   3225 ATGGAACAGAATATAGAACTCAGAAACAAATCCACACACCTACAGTGAAC 3274
                               i     vv   iii      i   i   i   ii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_119929713_   3275 TCATTTTTGACAAAGGTGCTAAGAACATACACTGGGGAAAAGACAGTCTC 3324
                          v     i     i     i    v   v  v        ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_119929713_   3325 TTCAACAAATGGTGCTGGAAAAACTGGATATCCAAATGCAGAAGAATGAA 3374
                                           i v         ?   v     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_119929713_   3375 ACTTGACCTCTATTTTCCCCCATATAAAAAAAATCAAATCAAAATGGATT 3424
                         ii v    i   ii iv v       v     - i  v           i
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATC 498

  chrX_119929713_   3425 AAAGAC--AAATCTAGTACCTCACACTATGAAACTACTACAAGAAAACAT 3472
                          ?    --    v  iv v  v v     i     vi  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_119929713_   3473 TGAGAAAAATCTCCAGGACATTGGTCTAGGCAAAATTTTCTGGAGCAATA 3522
                         v i?iv      i iv   v    vi       viv     viiii vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_119929713_   3523 CCCCACAAACACAAGCAACCAAAACATAAATGGACAAATGATATCACATC 3572
                          v   v  i          v   iv v    i  i    viv iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_119929713_   3573 -GAGTTAAAAAGCTAATGCACTGCAAAGAAAACAATCAACACAATGAAGA 3621
                         -i i       -  vv  ii  v     i v  v     v v i    i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_119929713_   3622 -ACAACCCACAGAATGGGAGAAAATATTTGCAAAATACTCATCTGACAAG 3670
                         -                                 vi ivi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_119929713_   3671 AGATTAATAACCAGAATATATAAGGAGCTCGAACAACT--GTATTAAAAA 3718
                         i  i vi  v             i  i   vv      --i  v      
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_119929713_   3719 AATCTAATAATCTGATCAAAAGATGGGCAAAATATTTGAACAGACATTTC 3768
                         i - v     i ii  i?   i         iv       i         
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_119929713_   3769 TCAAAAAGAAGACCTATAAAGTGACAAACAGGCATATGAAAAGGTGCTCA 3818
                           v   -     iv  i   -  i v  i i   i        i      
  L1M4_orf2#LINE/    847 TCCAAA-GAAGATATACAAA-TGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_119929713_   3819 ACATCATTTATCAT 3832
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (133 / 86)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 1.18 (13 / 11)  


3012 25.77 0.99 1.43  chrX_120059581_120062705.rev     1724  2635 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120059581_   1724 TGGAAATAGATCCCATGCTTATGGATTGGAAGAATGGATATTGTAAAAAT 1773
                               v v        i i             v vi       v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120059581_   1774 GACCATACTGTC-AAAGCAATCTACAGATTCAATGCAATTCCTATCAAAA 1822
                          i v     vi -   vii              i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120059581_   1823 TACCAACTTCATTTTTCACAGAACTAGAAAAAACAGTCCTAAGATTCATA 1872
                          v   i  v v     ii     v v  v  iviii      i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_120059581_   1873 ATGGAACTAAAAAAGACCCCAAATATCCAAAGCAATCGTAATCAAAATGA 1922
                         -     v iv  ii     vi    v     i     v i vv  i v  
  L1M4_orf2#LINE/    151 -TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_120059581_   1923 ACAAATCTGGAGGCATTAT-CTTCCTCAACTTCAAATCATATAATACTAC 1971
                              vi      vv i i-     -   i      v --- --      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCC-CAATTTCAAAAC---T--TACTAC 243

  chrX_120059581_   1972 AAGGCTATAGTAACCAAAACAGCATAGTACTGGTACAAAAGTAGATACAC 2021
                           i    i     i   i    ii i       i i  iii    i i i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_120059581_   2022 AGACTAATGGAACATAACAGAGAGCCCAGGAATAAATTCGTACATTTACA 2071
                            ii       i v  iv     i    i      ii i        ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_120059581_   2072 ACCAACTGATCTTTGACAAAGCATACAAAAAC-ATAAACTGGGAAAAGAA 2120
                         ii   i    i  i     i -i i v  i  -  vv v    i      
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_120059581_   2121 CACCATATTCAATAAATGGTGCTAGGAAAATTGAAGAGCCACACGTAGAA 2170
                         i viv v     i          i   v  i  i v ?     i i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_120059581_   2171 GAATAAAACTGGATCCCTATCTCAT--CTTATACAAAAATTTAATGCCGA 2218
                             i  ii    i     i    i-- v            v v vvvi 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_120059581_   2219 TGGATTAAAGACTTAAATCTAAGGCCCGAAATCACAAATATTCT--GAGG 2266
                              i ?    i     v    iv ii   ii i   - i   --  i 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAG 541

  chrX_120059581_   2267 AAAACTTAGGGAAAAAACCCTTCTGGACATTGGCATAGGCAAAGAATTTA 2316
                              v    ?iv   --i    vv   v    vv       v iv  iv
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_120059581_   2317 TGATTAAGACCCCAAAAGCAAATGCAACAAAAACAGAAATAAATAAATGG 2366
                          iiv  v   v         v v         iv i     i      v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_120059581_   2367 AAACTAATTAAA-TTAAAAAGCTTCCACACAGCAAAAGAAATAATCATCA 2415
                         i vi v  i   -       -   iiiii vv    i  v iv    vv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_120059581_   2416 AAGTAAACGTACAACTCACAGCATGGGAGAAAATATTTGGAAATTATACA 2465
                             i  viv     i     v                 v    i   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_120059581_   2466 TCTGACAAAGAACTAATGTCCAGAATCTACAAGGAACTCAAGTAAATCAG 2515
                              i  i i   vi i        v  i  i      vvii  v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_120059581_   2516 CAAAAAACCCACAAATAATCCCATCAAAAAGTGGGCAAATAACATGAATA 2565
                         i  v   vvv        i  v  i?    i        vi iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_120059581_   2566 GACAGTTTTTCAAAAGAAGATATACAAAGGGCCAAGAAACATATAAAAAT 2615
                             -   i  v                v      v  i  i  i    v
  L1M4_orf2#LINE/    839 GACA-TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_120059581_   2616 -CACCCAACACCTCTAATAAT 2635
                         -ii i     i v????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (139 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.38 (22 / 16)  


3422 23.37 1.90 0.59  chrX_120127299_120129133.rev      502  1344 (491)    L1M4_orf2#LINE/L1       55   908 (0)  

  chrX_120127299_    502 ATACTACTCAAAGAAATCTACAGATTCAATGCAATCCCTATCAAAATTCC 551
                              v i    vvi              i                 i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_120127299_    552 CATAGTATTTTTCACCTAAAT----AAACT-ATCCTGAAATTTGTATGGA 596
                         viiv iv     ii vv    ----  i  -     i     ii      
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_120127299_    597 AACACAAGAGACCCTGAATAGCTAAAGCAACCTTGAATAAGAGAAACAAA 646
                           ii    i     v       i   i   i      v    ii      
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_120127299_    647 GCTAGAATTATCACACTTTCTGATTTTAAGTTATATAACAAAACTGTAAT 696
                          i i  ivvv        i ii    i  iviv  iv     i  ii i 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_120127299_    697 AATCAAAGCAATATAGTACTGGCATAAAAACAAGCACACAGACCAATG-A 745
                               ii  i i i            ii i ii  i i   i     - 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_120127299_    746 ATAGAA---AGCAAC--AAAATTAAGCCATAAATATACAGCTAACTAATC 790
                               ---  viv --i    v  v     v  v  ii ii  i i  i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_120127299_    791 TTTAACAAAGGTACCAATAATACACAATGGAGAAAAAAATAGTCTCTTCA 840
                           ii    i   i    v vi iv      i    i  -      i    
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTTTTCA 403

  chrX_120127299_    841 ATAAATGGTGCTGGGAAAACTGGGCATCCACATGCAAAAGAATGAAATTG 890
                          i              v      ii ?                   i   
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_120127299_    891 GACTCTAACCTTGCAACATAGA-AAAAATCAACTCAAGATGGATTAAAGA 939
                            i iv    ii  v    v -      i       i      i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_120127299_    940 TTTTTAAATGTGAGAATTGAAAGTTTAAAACTCTTAGAATAAAACACAGG 989
                         ii --      i   ii i   v v              v      i   
  L1M4_orf2#LINE/    504 CCT--AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_120127299_    990 GGAAAATCTCCTTGACATCAGGCTGGGCAATGAATTTTTGGGTATGACAC 1039
                         ? v      i v    v ii  i i       iv  i  i i        
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_120127299_   1040 CAAAAGCACAGGCAACTAAAGCAAAAATACGTAAGTGAGACTATGTGAAA 1089
                                   i     v    v       vi   i vi    vii v   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_120127299_   1090 CTAAAAAGTTTCCATACAGCAAAAAAAATAATTCAACAGAAAGAAAAGGC 1139
                         v v    ii  iii i vv    ii v iv  -   v i iv      i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTAT-CAAGAAAGTGAAAAGAC 700

  chrX_120127299_   1140 AACCTATGGAATTGGAGAAAATATTTGCAAGCCATATATCTGATAAGG-A 1188
                             i ii    v                 ii                - 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_120127299_   1189 TTTGATATCCAAAATATATGAGGAACTGATATAACTCAATAACAAAAATA 1238
                         i   -      i       i i     vv  i          i     v 
  L1M4_orf2#LINE/    751 CTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_120127299_   1239 ---ATATTCCAATTAAAAAATGAACAAAGAACTTGAACAGACATTTTTCC 1285
                         ---   vi      ?       ii     i i     i        i   
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_120127299_   1286 AAAGAAGACATAAAAATTGCCACCAGGTATATGAAAGGATGCTCAACATC 1335
                                 i   v    v    vi i i i      i             
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_120127299_   1336 ACTAATCAT 1344
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.33 (135 / 58)
Gap_init rate = 0.01 (12 / 854), avg. gap size = 1.75 (21 / 12)  


3638 22.55 2.93 0.56  chrX_120135708_120140186     3100  3986 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120135708_   3100 TGGAAAGATATTTCATGTTCATGGATTGAAAGAATCAATATTGTTAAAAT 3149
                                    ii               i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120135708_   3150 GTCCATATTACCCAAAGAAATCTACAGATTTAGCTCAATCCCTATTAAAA 3199
                          v v   i v      vvi           i i v          i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120135708_   3200 TACCAA-TGTCATTCTTGACAGAAATAGAAAAGAACAG-TCCTAAAATTA 3247
                          v   i-  i v  i   -       v  v   -- v -          v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_120135708_   3248 ATATGGAA----------CCGAGAATAGCCAAAGCTATTCTAAGCAAAAA 3287
                                 ----------  v            i v  ii i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_120135708_   3288 GAACAAAACTGGAGGAATTACATTACCTGGCTTTAAATTATGCTACAGAG 3337
                                ii       v i   i v  iiii  i   viv i     i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_120135708_   3338 CTACAGTAACCAAAAGAGCATGGTACTGG-ATAA-AACAGATACATAGAC 3385
                                  i   i v  ii         -    -i i   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_120135708_   3386 CAATGGAACAGAATAGAGAACCCAGAAAGAAACCTACACACCTACAGTAA 3435
                                 i     v    ii       v     i i   ii  ii  v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_120135708_   3436 ACCCAGTTTTGACAAAGGTGTAAAGAACATTTATCGCAGAAAGGACAGTC 3485
                          iiv v   i     i    iv    v    i vi vi     i i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_120135708_   3486 TCTTCATTAAATGATGCTGAGAAAACTGGATATTCATATGCAGAAGAATG 3535
                          i    vi     i     i  v         ?i  i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_120135708_   3536 AAACTAGACCCCTGTCTCTCACCATGTACAAAAAT-----CAAAATGAAT 3580
                           ii i       ii   v      i         -----       i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_120135708_   3581 TAAAGACTTAAATCTAAG-GCCACAAACTATGAAACTACTACAAGAAAAC 3629
                         i ?    i     v    -  i -       i     vi  v        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_120135708_   3630 ATTATGGAAACTCTCCAGGACATTGGTCTAAACAATGATTTTTTGAGTAC 3679
                           viv? v  v   i iv   v    vi  ii     i   i  iii  i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_120135708_   3680 TATTCCACAAGCACAGGAAAGAAAAGCAAAAATGGACAAATGGGATTTTA 3729
                         v iv   v       i v  v     v      i  i    v   i  i 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_120135708_   3730 TCAA-GTTAGAAAGCATCTGTACATCAAATGAAACAATCAGCAAAGAGAA 3778
                             -i   i   - v i   i v     v  v  v    iv    v   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_120135708_   3779 GAGATAACCCACAGAATGAGATAAAACATTTGCAAACTACCCATCTGACA 3828
                         i   i             i  v    i         ii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_120135708_   3829 AGGGATTAATAACCAGAATATATAAGGAGCTCAAACAACTCTATAGAAAT 3878
                              i vi  v             i  i   vv       v   iv  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_120135708_   3879 AAATCAGATAATTCAA----ATAATGGGCAAGAGATTTGAATAGACATTT 3924
                           iv  i    ii   ---- v         ii                 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_120135708_   3925 CTCT-GAGAAGACATACAAATGGCCAACAAGCATATGAAAAGGTGCTCCA 3973
                            i-i      i              i     i        i     v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_120135708_   3974 TATCATTGGTTAT 3986
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (128 / 69)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.21 (31 / 14)  


2931 27.15 0.48 0.48  chrX_120158512_120160339.rev      502  1337 (491)    L1M4_orf2#LINE/L1       73   908 (0)  

  chrX_120158512_    502 TATAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTCACAGA 551
                           i        i  v     i     iv v   iivi i  i  ii    
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chrX_120158512_    552 A-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCG 599
                          -   -- v  i  - iii    i           viiv  ii  v  v 
  L1M4_orf2#LINE/    123 AATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chrX_120158512_    600 CATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTTGAGGCATCACGC 649
                         v  v     iv     i i ivv i          i v    vv    i 
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_120158512_    650 TACCTGACTTCAAACTATACTAGAAGGCTACAGTAACCAAAACAGCATGG 699
                          v  ii i      viv     v  i          i   i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_120158512_    700 TACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCC 747
                               i iv ii i   v                i    i--    i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_120158512_    748 TCAGAAATAACGCCGCATATCTACAACTACCTGATCTTTGACAAACCTGA 797
                         --        vv  ii i  i  iiiii vi    i  i     ivv  v
  L1M4_orf2#LINE/    321 --AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_120158512_    798 CAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGG 847
                            i v  vv            i  vvi  v  i  i             
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chrX_120158512_    848 AAAACTGGCCAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCCTACA 897
                          v      vi ?   i   i i  iiv    ii    i    v  ii   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_120158512_    898 CCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGACC 947
                           v              i    i      i ?    i       v   v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_120158512_    948 TAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACA 997
                               i      vi i           v    ?i v viv   iv   v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_120158512_    998 TAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACA 1047
                          v  vv i     v ii   v ivv  vi            vvi      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_120158512_   1048 AAAGCCAAAATTGACAAATGGGATCTAATTCAACTAAAGAGCTTCTGCAC 1097
                             vv     v  i    v   ii v  iv  v v  i i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_120158512_   1098 AGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGA 1147
                         vv    i  v    i  vv i      v  i     i   i         
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_120158512_   1148 AAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTAC 1197
                             v  i    vii ivi      i  i  i  vi          v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_120158512_   1198 AATGAACTCAAACACATTTATAAGAAAAAAACAAACAACCCCATCAAAAA 1247
                           v      vv   vv iv    v     i     i     v  i?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_120158512_   1248 GTGGGTGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAG 1297
                         i    ii     iv    i     i     v        i  vi viii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_120158512_   1298 CCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCAT 1337
                             v  i          i       v     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (131 / 92)
Gap_init rate = 0.01 (5 / 836), avg. gap size = 1.60 (8 / 5)  


2736 24.40 3.05 1.19  chrX_120216715_120220530      492  1245 (2571)  C L1M4_orf2#LINE/L1   (0)   908   141  

C chrX_120216715_   1245 AAAATTCATTTGGAACCATACAAAAGACCCTGATTACTTAAAGCAATCTC 1196
                                  v     --  i   ii     v  v  vii   i      i
  L1M4_orf2#LINE/    141 AAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

C chrX_120216715_   1195 ATGCAAGAGAAATTAAGCTGGAGTAA--ACAGTTTCTGATTTCAAATGGT 1148
                         iviv    ii  iv   i     v v--   v  i ii        vvv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

C chrX_120216715_   1147 ATTACAAAGTAATAGTAATCAA-ACAACATGGCAGTGACATAAAACCAAG 1099
                          i       iv i         -   iii   i v  i     iivi ii
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

C chrX_120216715_   1098 TACACAGACCAATGGAATAGAATATAGAGCTCAGAAATAAACCTATGCAT 1049
                         i i i   i              vv    ii            i  i   
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

C chrX_120216715_   1048 ATGCAGCCAACTATTCTTCCACCAAGTCACCA----CAT---ATGGGGAA 1006
                         v iii i   i iv i   v  v i vii   ----   ---        
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

C chrX_120216715_   1005 AGGATAGTCTCTTCAATAAATGGTGCTAGGAAAATGGGATA-CCACATGC 957
                           i       i     i          i   v  iv     -        
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

C chrX_120216715_    956 AAAAGAATGGAATTGGACCT-TACCTTAAACTATACATAAAAATAAACTC 908
                                  i i       i-     i v  i   i i      v     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

C chrX_120216715_    907 AAAATCAATTCAAGACTTAAACATAAAACCTGAAACTGTAAAAATCCTAC 858
                              vi  iv?    i    ii   i v  i     i     v  i  v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

C chrX_120216715_    857 AAGAAAACATGGAGCAGGGAAAGCTTCTTGACATTGGTCTTCACAATGAT 808
                                   i i?--- v   v    v    v    vi vvi     i 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGN---GTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

C chrX_120216715_    807 GTTTTTGGTTAGGACACCAAAAGTATAGGTAACAAAAACAAAAATAAACA 758
                         -  i  i v  v           i i i i       iv       i i 
  L1M4_orf2#LINE/    586 -TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

C chrX_120216715_    757 AGTGGGACCACATCAAACTAAAAAGTTTCTGCACATCATGAAAATA--AT 710
                          i v    iv       v v    ii  i  ii v   -i ii i --  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGACACTAT 683

C chrX_120216715_    709 CAATGAACTAAAAAGGCAAACTACAGAATGGGAAAAAAT--TTGCAAATC 662
                            vi  v i     i   v i           i     --         
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

C chrX_120216715_    661 ATATATCTGGTAAGGTGTTAATATCTAATATACATAAGGAAACTC----A 616
                                  i     vii vi    i iv   i    i   -   ---- 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACA 782

C chrX_120216715_    615 ATTCAATGGCAAGCAAACTAATAACCCAATTAAAAAAATGGGTAAAGAAC 566
                          i     iii  iv i  v            ?     -    i    i i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGAT 831

C chrX_120216715_    565 CTGAATAGACATTTTGTCAAAGA---CATACAAATGGCCAACAGCTGTAT 519
                         i             ivi      ---i              i iviii  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

C chrX_120216715_    518 GAAAAGATGCTCAACATCACTAATCAT 492
                                            ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.18 (124 / 57)
Gap_init rate = 0.02 (16 / 768), avg. gap size = 2.00 (32 / 16)  

 687 22.37 0.00 0.00  chrX_120216715_120220530     1505  1656 (2160)  C L1M4_orf2#LINE/L1   (753)   155     4  

C chrX_120216715_   1656 AAAGATATCCCTTGTTCATGGTTGGGAAGAATTAATATTGTTAAAATGTC 1607
                                    v         v v      v             i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

C chrX_120216715_   1606 CATACTACCCAAAGCAATCTACACATTCAGTGAAATGTCTATCAATATTC 1557
                         v     v      vii       v     ii v   vi       v  i 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

C chrX_120216715_   1556 CAGTGGTATTCTTCCCAGAGATAGAGAAAGCAATCCTAAAATTCATTTGG 1507
                            iv iv  i  iv    i  v  v  ivii              v   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

C chrX_120216715_   1506 AA 1505
                           
  L1M4_orf2#LINE/    154 AA 155

Transitions / transversions = 0.79 (15 / 19)
Gap_init rate = 0.00 (0 / 152), avg. gap size = 0.00 (0 / 0)  

2629 26.62 3.91 2.35  chrX_120216715_120220530     2430  3323 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120216715_   2430 TGGAAAAACATTCCATGCTAATAGATGGGAAGAATCGATATTGTTAAAAT 2479
                               i i  i     i v  i   v      v ii          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120216715_   2480 GGCCATAGTGCCAAAAT-AATTTATAGAATCAATGCTATTCCTATTAAAC 2528
                            v   v v  v    -i  i  i   v    i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120216715_   2529 TATCATTGACATTCTTTACAGA--TCGAGAAAAAACT-ATTTCAAAATTC 2575
                          vi  vivi v  i   i    -- i  v  i---  -  iii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_120216715_   2576 ATATGGAACCAAAAAGTAGTGCAAATAGCCAAAGCAATCCTAAGCAAAAA 2625
                                 viiv  i v vivvi          i     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_120216715_   2626 GAACAAAGCTGAAGA---CATGCTACTTGACTTCAAATTATACTATAG-G 2671
                                 i  i  i---  ii  v iii i      viv     i i- 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_120216715_   2672 CATACAGTAACCAAATCAGCATGGTACTAGTACAAGAACAGACACATAGA 2721
                          -        i   iv   ii       i i i   i i     i     
  L1M4_orf2#LINE/    248 C-TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_120216715_   2722 TCAATGGCACAGAATAGAGAGCTCAGAAATAAGACCATAC--CTACAA-C 2768
                                v i     v     ii         iv      --i  iii- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_120216715_   2769 AATCTGATCTTTGACAAACCTAACAAAAACAAGCAGTGGGGAAAG--TAA 2816
                            -    i  i     ivv iv   i v  vv  i         --  i
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_120216715_   2817 TCCTTATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAG 2866
                           i  -- i  i              i      v  ?   i     i   
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_120216715_   2867 ATTTAAACTTGACCCCTTACTTACACCATATTACACAACAATTAACTCAA 2916
                          v v  ii v       vv  i         ---    v           
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATAT---ACAAAAATTAACTCAA 490

  chrX_120216715_   2917 GATAGATTAAAGACTTAAATGTAAAATC-AAAGCTATAAAAGCCCTGGAA 2965
                         i  i   i ?    i         i v -   i        vi i i   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_120216715_   2966 TACAATCTA--TGCAATATCATTGTGCATATAGATATGGGCAAATATTTC 3013
                         v v  iv  --? i  -   v i   vviv i i - i     vvi    
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGT-TAGGCAATGGTTTC 588

  chrX_120216715_   3014 ATGACAAAGACATCAAGAGCAATTGCGACAAAAGCAAAAATGGACAAATG 3063
                         v iivv v    i   i    vvv  i       v      i  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_120216715_   3064 GGATCTTATTAAACTAAGGACCTTCTGCACAGAAAAAGGAACTATCAACA 3113
                            ii i  i   v v ii v   i  ii vvv   i iv        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_120216715_   3114 GAAAGAGCATACAACCTATAGAATGGTAGAAAATTTTTGCAAACTATGCA 3163
                         i iv  iv v      i i       v       v        ii  ---
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT--- 735

  chrX_120216715_   3164 AAATAGATATCTGACAAAAGTCTAATATCTAGCACCTATAAAGAACT--T 3211
                         ------        i  ii v  vi    i  v iv           -- 
  L1M4_orf2#LINE/    736 ------ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_120216715_   3212 A-AATTTATTAA--------------ACC--ATTAAAAAGTGGGCAAATG 3244
                          -  i i v   --------------   --   ?    i        v 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_120216715_   3245 ACATGAACAAATACTTTTCAAAATAAGACATACATGCAGCCAATGATAAT 3294
                          iv    i i i i  i  v   v    i     viii      i vv i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_120216715_   3295 ATGAAAAAAAGTTCCACATCACAGGTTAT 3323
                                i v i  v      ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (145 / 89)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.55 (56 / 22)  


3126 26.03 1.67 0.89  chrX_120320301_120324859.rev     3170  4068 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_120320301_   3170 GAAAGAAATTCCATGTTCATGGACTGGAAGAGTTAATATTGTTAAAAATC 3219
                               v  i             i       v             i vvv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_120320301_   3220 TACATACTACTCAAAGCAATCTACAGACTTCATGCAATCTCTACCAAAAC 3269
                         i -     v i    vii         i iv i      i   i     i
  L1M4_orf2#LINE/     53 CA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_120320301_   3270 ATCTATGATATTCTTAACAGAAATAGAAAAAACAATTTTAAAATTTGTAT 3319
                         vi viiviiv  i  vi       v  v  ivii  ii       ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_120320301_   3320 AGATACACAAAAGACCCAGAATAGCCAAAGTCATCCTGACCAAAAAGAAC 3369
                         i  v ii   ii                 iiv   i   vv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_120320301_   3370 AAAACTGCAGGAATAACATTACCTGACTTTA-----TACTACAGAGCTAG 3414
                            ii  v    v v   i v  ii i  i -----       i     v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_120320301_   3415 AGAAACCAAAACAGGACAGTACTGGCATAAAAACAGACACATAGATCAGT 3464
                           v  i   i    viii            ii i     i        i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_120320301_   3465 GGAACTGTTTAGGAAACCCAGAGGCAAATCGATACATCTACAATAACTTC 3514
                             iv vv v ii ii     iii   i v      i  iii v v  v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_120320301_   3515 AGTTTTGATAATGTTGCCAAGAAGTTACACTGGAGAAAGGACAGTCTCTT 3564
                          v   i  i  v v        vvv v  v   i     i i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_120320301_   3565 CAAAAAATGGTGCTAGGAAAACTGAATATCCACGTGCAAAAGAATGAAAC 3614
                            v          i   v     i   ?    i              ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_120320301_   3615 CAGACCACTATCTCTCACCATTTATCAAAAGCAAATAAAAATGGATTAAA 3664
                         ii    v   i   v      v  iv    vi  v v         i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_120320301_   3665 TACTTAAATCTAAGACCTCAAACTCAGAAACTACTAAAAGAAAACTTTGG 3714
                         v  i     v     v  v     vvi     vi  i        v v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_120320301_   3715 AAGAAA-CTTCAGGACATTAAACTGGGCAAAGATTTCTT-GAC-TAATAC 3761
                         ?iv   -    iv   v  iiii i     v i      -  i- i i  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_120320301_   3762 CCGGGAAGCACAGGCAACCAAGGCAAAAATGGACATGTGGGATCACTTCA 3811
                          --ii       i     v  i v      i  i vi v   iiv v   
  L1M4_orf2#LINE/    602 C--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_120320301_   3812 AG-TTAAAAAGCTTCTGCACAGAAAAGGAAACAATCAACAAGGGGAAGAG 3860
                          i-       -   i  ii vvv      v  v     v  i v   i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_120320301_   3861 ACAACCCACCGAATGGGAGAAAATACTTTCCAACTACTCATCTGACAAGG 3910
                                  v               i  v v  ii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_120320301_   3911 TATTAATAACCAGAATATACAGGGAGCT--TA-AACT--ATTATATGGGA 3955
                         v i vi  v          i ii  i  --  -    --  v   ---- 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA----A 794

  chrX_120320301_   3956 ACAAATGAATAATCCAATT-AAAAATGGACAAAATACTTGAATAGGCATT 4004
                          v i ii     i      -        i    iv i        i    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_120320301_   4005 TCTCCGAAGAAGACATACAAATGGCAAACAGGCATACGAGAAGGTGCTCA 4054
                              i       i           v  i i   i i  i   i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_120320301_   4055 ACATCACTGATCAT 4068
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (142 / 89)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 1.77 (23 / 13)  


3158 27.24 0.89 0.33  chrX_120331579_120333725.rev      758  1660 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120331579_    758 TGGAAAAACATTCCATGCTCATAGAAAGGAAAAATCAATATCATCAAAAT 807
                               i i  i     i    i  vv    i v i     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120331579_    808 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTGTCCCCATCAAGC 857
                            v     v      v i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120331579_    858 TACCATGGACTTCCATCACAGAATTAGAAAAAAACT-ACTTTATATTTCA 906
                          v   vvvi i iiv ii     v v  v  i--  - iii  v v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_120331579_    907 TATGGAACGAAAAAAGAGCCCACATATTCAAGACAATCCTAAGCAAAAAG 956
                                vviv  ii  v  viv   vi   i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_120331579_    957 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1006
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_120331579_   1007 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATACATAGACA 1056
                                 i   i    ii         i iv ii i   i i     iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_120331579_   1057 AATGGAACAGAACAGAGGCCTCAGAAATAACGCCATACATCTACAATCAT 1106
                                i    iv   ivii         vv        i  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_120331579_   1107 CTGATCTTTCACAAACCTGATAAAAACAAGCAATGGGGAAAAGATTCCCT 1156
                         i    i  iv    ivv  vi  i v  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_120331579_   1157 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAGCTGA 1206
                         v  i  i        i     v      v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_120331579_   1207 AACCGGATCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGGATT 1256
                          iii   i    v   i i   v                   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_120331579_   1257 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1306
                          ?    i           v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_120331579_   1307 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 1355
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_120331579_   1356 ACACCAAAAGCAATGGCAGCAAAAGCCAAAATTGACAAATGGGATCTGAT 1405
                                     vvi   i      vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_120331579_   1406 TAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTATCATCAGAGTGAACA 1455
                         i   v v  i i   i  iiivv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_120331579_   1456 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATTTATCCATCTGACAAA 1505
                          i     i                 v       v i  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_120331579_   1506 GGGCTAATATCCAGAATCCACAAAGAA-----ACAGGTTTACAAGAAAAA 1550
                           i  vi          vi i      -----   iv iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_120331579_   1551 AACAAATAACCCCATC-AAAAATGAGCAAAGGATATGAACAGACACTTCT 1599
                         i           v  i-       i         v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_120331579_   1600 CAAAAGAAGACATTTATGCAGCCAACAAACATATGAAAAAAAGCTCATCG 1649
                          v        i  vi viii     i  i  i       i v     v i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_120331579_   1650 ACACTGGTCAT 1660
                         v  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


2459 19.46 1.95 0.19  chrX_120350606_120356559.rev     2894  3407 (2547)    L1M4_orf2#LINE/L1        1   523 (385)  

  chrX_120350606_   2894 TGGAAAGACATTG-ATGATGATGAATTGAAAGACTTAATATTATTACAAT 2942
                                 i  iv-   v v   i    i             i   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120350606_   2943 GGCAATATTTCTGAAACTGATATACAGATTAAATATAATCTTCATAAAAA 2992
                                i i iv   i    v        v  iii    iii  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120350606_   2993 TACCATCTACCATGTTTGAAGAAATTGGCAACCTAATCCAAATTTTTATA 3042
                          v   v  i  v v    v        i   v  i    v  vv  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_120350606_   3043 TGGAAATGCAAGAGACCCAGGATAGCCAAAACAATTTTGAAAAAGAA--- 3089
                                     i       i              i           ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_120350606_   3090 TGAAGTTGCA--ACACATATTTTCTTATTTCAAAACATACGAAAAAGCTA 3137
                         ii      v --  v  i i  i iv          v   v v       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_120350606_   3138 CAGTAGTCAAGA--GTGTAGTACTGGCCTAAGGATAGACATATAGATCAA 3185
                              i      --    i        v                      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_120350606_   3186 TGGAATGGAACTGAGAGACCAGAAATAAACCCAAGTATTTATTGTCTACT 3235
                               i   i      v               vii      v   v i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_120350606_   3236 AATTTTTGACAAGGGTGCCCAGACAATCTAACAGG-AGAGAATAGTCTTT 3284
                         i     i            v    v  ii  ii  - i            
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_120350606_   3285 CCAACAAGTGGTAATGGGAGAAATTAATATCCACTTGTAAAAGCAAT-AA 3333
                         i      i    iv     v  v vi   ?    v  i     -   -  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AATGAA 449

  chrX_120350606_   3334 GTTGGACCCATATATCACACTGTATACAAAAAGTACCTCAAAATGGACTG 3383
                                  v  iv      ii          v  v           iii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_120350606_   3384 TATACTGAAGTGTAAGAGATAAAA 3407
                         ? v  iv  i        v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAA 523

Transitions / transversions = 1.33 (56 / 42)
Gap_init rate = 0.01 (7 / 523), avg. gap size = 1.57 (11 / 7)  

 387 21.60 8.00 0.80  chrX_120350606_120356559.rev     3819  3943 (2011)    L1M4_orf2#LINE/L1      539   672 (236)  

  chrX_120350606_   3819 AAACAAACA-AAAAG-AAATGCCTATGACAGTGGGTTGAGCAATGATTTC 3866
                           iv     - ii? -    viiii    vv      ii      i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_120350606_   3867 TTAG----GGCACCAAAAGCATAAGCAGAAATTTAAAAAA---ATAAATT 3909
                             ---- i           i     iv  vvv      ---       
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_120350606_   3910 AGACTGCAT-AAAATTGTAAAAGATTTGTGCTTCA 3943
                         i    v   -      i-    vv           
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTA-AAAACTTTTGTGCTTCA 672

Transitions / transversions = 1.36 (15 / 11)
Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.83 (11 / 6)  

1143 24.00 5.00 2.50  chrX_120350606_120356559.rev     3944  4343 (1611)    L1M4_orf2#LINE/L1      499   908 (0)  

  chrX_120350606_   3944 ATAAACTTAAATCTAAGACCTCAACCTATGAAACTACCACAAAGAAACTT 3993
                          ? i  i     v     v  v  v    i     vii v  ii    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_120350606_   3994 TGGGGAAAATCTTCATGATATTGGTCTGTGCAAAAATTTCTTGAGTATTA 4043
                         v  ? v        i   iv    vi iv    vii      iii   v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_120350606_   4044 TCCTACAAGCACAGGCAACCAATATAAAAATGAACAAATGAACAAATGGT 4093
                         iv i v       i     -------    -   v    ii i    v v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAAC-------AAAA-GAAAAAATAGATAAATTGG 640

  chrX_120350606_   4094 ATCACAG-AAAGTTAAAAAGCTTCTGCACGGCAAAA-ACA--ATCAACAA 4139
                          iiv  v-   i       -   i  ii vv    i-   --     v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_120350606_   4140 AGTGAAG-GACATCCCACAAAACCGGAGAAAATATTTGTAAACTACCCAT 4188
                               i-    v      i  iv              i   ii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_120350606_   4189 CT--------ACCTA---CCAGAATCTATAAGGAGCTCA-AAAACCC--T 4224
                           --------  i i---       v     i  i   v- v   i -- 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_120350606_   4225 A-TAAATATATCTAATAATCTTATCAAAATATGGACAAAATATTTGAATA 4273
                          -    v v - v     i iv  i?   v    i    iv         
  L1M4_orf2#LINE/    790 AATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_120350606_   4274 GGCATTTCTCAAAAGAAGACATACAAATGGCAAACAGGTATATGAAAAGG 4323
                          i        v        i           v  i i i i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_120350606_   4324 TGTTCAACATCATTGATCAT 4343
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (55 / 38)
Gap_init rate = 0.03 (13 / 410), avg. gap size = 2.31 (30 / 13)  

 819 22.08 1.25 2.50  chrX_120350606_120356559.rev     5224  5463 (491)    L1M4_orf2#LINE/L1      672   908 (0)  

  chrX_120350606_   5224 AAAGAATATCTATTAAGGAAGTAAAATAACAACCCAGAAAATGAGAGAAA 5273
                             i i -    i   i    i   vi        v i    i      
  L1M4_orf2#LINE/    672 AAAGGACA-CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_120350606_   5274 AAATTTTTCAAATCATATATCTGATAAGAGGCTTGTATCTAGAATACATA 5323
                          v    -v                    i i        i      i   
  L1M4_orf2#LINE/    721 ATATTT-GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_120350606_   5324 AATCATACTTCTAATTAAACAATAAAAA---AGACAACTCAATTTATAAG 5370
                           vv iv   vi  i v  i        --- i i   i     ? v  i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_120350606_   5371 CAAGCAATAGACTTGTTTTGACTTTTTTCTAAATAAGATACAGAAATGTC 5420
                         iii    vi  i   vv v   v   i  i   v      i v     v 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_120350606_   5421 CACTATGCACACACACGAAAAAATGCTAAATATCATTAGTCAT 5463
                           v  v     ----i     i     v  i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACA----TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (31 / 21)
Gap_init rate = 0.02 (4 / 237), avg. gap size = 2.25 (9 / 4)  


2288 23.49 8.49 3.37  chrX_120360755_120364022.rev     1931  2790 (478)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_120360755_   1931 AAGACCTCTACCAAATTCATGGATTGAAAGACTTAGTATTG----GGTGT 1976
                             iv  --   vi           i        i     ---- i  v
  L1M4_orf2#LINE/      5 AAGATATC--CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_120360755_   1977 --GTTTTCTGCAAATATATCTATACATTTAATGTTATACTGATAAAGAT- 2023
                         --i vi  iv     vv     i v   i  i iv  v iv  v  i  -
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_120360755_   2024 ---------TTGTTTGCATATATTGAAAAGTCAATACTAAAATTTATCTA 2064
                         ---------  v      v v     v   iii  v        i  v i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_120360755_   2065 GAATAACCAAAAGTATCTAGAATAACCAAAACAAT--TAAAAAAG----- 2107
                            - vv   ii - i i      i          -- i      -----
  L1M4_orf2#LINE/    153 GAA-ATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_120360755_   2108 -----TTTGGGAAGTCATAGCACCTGATTTCAAAGCATGTCATAAAGCTA 2152
                         -----  v i i v   i viv  ii        i v iii i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_120360755_   2153 CAGTAATTAAGAAAGCATAATACTGGCAGAAGGATAGACATATAAGC--A 2200
                                i    v  ii ii        v               iii-- 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_120360755_   2201 T---ATAGAAC--AGAGTCTAGAAACAAGACCTTATATAAATATGTAGTC 2245
                          ---      i--      i     i  -   i---   v  v i i   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAA-ACCC---ATACATTTATGGTC 346

  chrX_120360755_   2246 AATTGATTTATGGCAAAGATGACAA-----TTCAATGAGGAAAAGGTAGT 2290
                                  vi i   i i  v   -----       i     iii    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_120360755_   2291 TTTTTCAACAAATAGTGATACAGCAATTGGAT--CCATAAGAAAAAAAGA 2338
                         i            i   v ivii   i     --   i v v    i --
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-- 444

  chrX_120360755_   2339 AAAGAACTTCAGAACTTAAGAGCTTACCTCACACTATATACAAAA-TTAA 2387
                         - v   v  -- i  i------ i          i          -    
  L1M4_orf2#LINE/    445 -ATGAAGTT--GGACC------CCTACCTCACACCATATACAAAAATTAA 485

  chrX_120360755_   2388 CTCAAAGTGTATTGAATTTATAGATGTAAGATCTGAAATGATCAAACTTC 2437
                               i  v  ii? vviv  i        v  i   iv  v     ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_120360755_   2438 TTTAA-AAAACAT----GAAATTCCTTATGACCTTGGGTAAGGCAAAGAT 2482
                          vv  -       ---- v  v  i ii           v      v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_120360755_   2483 GT---AAAAATGATGCCAAAATGCACAAACAG-------AAAATTTGATG 2522
                         v --- i v    ii      -      i  i-------    v v   i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_120360755_   2523 AATTGAATTACACTTCATTGAAATTGAAATCTTTTGCTCCTCAAAAGACA 2572
                              i -----      ii     i   v      iv i     i    
  L1M4_orf2#LINE/    635 AATTGGA-----CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_120360755_   2573 TCAGTAATGAAATGATAAAAAACAAGTTACAGAATGGGAGATAATATTTG 2622
                         ii vi  vi  i   --   i    vii             v        
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGA--AAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_120360755_   2623 CAAA--ACATATCTAATAAAGTACTTGTGTCCAGATTACATACATACGTT 2670
                             -- i      i    i v      i      v  i   v v vv i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_120360755_   2671 TTCCAAT------GTAAGAAAACAAA----CCAAT-AAAAAATAAGCAAA 2709
                           v   i------i   i  i     ----     -?      ii     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_120360755_   2710 ATAATTGAATAGCCACTTCACCATAGAAGATAATTAAATGA--AATACAT 2757
                         iv v        v  i   v   v        vvi     i--    - -
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA-A- 875

  chrX_120360755_   2758 ACACATGAAAAGTTTCTAATCATAATTAGCCAT 2790
                         i           v v  v v   v ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (121 / 79)
Gap_init rate = 0.04 (33 / 904), avg. gap size = 3.09 (102 / 33)  


3299 26.32 0.88 0.88  chrX_120390844_120397250.rev     5009  5916 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120390844_   5009 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5058
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120390844_   5059 GGCCATACTGCCCAAGGCAATTTATAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v     ivii  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120390844_   5109 TACCAATGACTTTCTTCACAGAA-TTGGAATAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- i  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_120390844_   5157 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5206
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_120390844_   5207 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5256
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_120390844_   5257 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATGGACC 5306
                                 i   i    ii         i iv ii i   v    i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_120390844_   5307 AATGGAAGAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5354
                                v    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_120390844_   5355 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5404
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_120390844_   5405 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5454
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_120390844_   5455 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATCAATTCAAGATGGA 5504
                            ii    i    v   i i   v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_120390844_   5505 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5554
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_120390844_   5555 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5604
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_120390844_   5605 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5654
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_120390844_   5655 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5704
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_120390844_   5705 AGGCAACCTATAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5754
                           i     i i i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_120390844_   5755 AGGGCTAATATCCAGAATCTACAATGAACTCAAACACATTTATAAGAAAA 5804
                         i  i  vi          v  i  v      vv   vv iv    v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_120390844_   5805 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5854
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_120390844_   5855 TCAAAAGAAGACAGTTATGCA----GCCAACAAACACATGAAAAAATGCT 5900
                           v        ----   i  ----     i  i          i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_120390844_   5901 CACCATCACTGGCCAT 5916
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


3286 24.58 2.00 1.00  chrX_120412010_120416224     2824  3722 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120412010_   2824 TGGAAAAATATTCCATGTGCATGGATTGAAAAAAAAATTAATATTGTTAA 2873
                               i    i      v         i  i v---             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC---TTAATATTGTTAA 47

  chrX_120412010_   2874 AATGTTCCTGCTACCCAACACAGTCTACAGATTCAATGCAATCCCAATCA 2923
                         i   vivv i  v     vviii             i        v    
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_120412010_   2924 AAATACCAATGATATTTTTCACAGAAATAGA-AAGAAAAAGTCATATAAT 2972
                             v   iiviiv     ii       v  -   vvi --  v  v   
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAAT 145

  chrX_120412010_   2973 TTATATGGAACCACAAAAGACCCAGAATAGCCAAAACTATTCTAAAGAAA 3022
                          i        vii   ii                   v  ii i  i  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_120412010_   3023 AAGAGCAA-GCAGGAGGAATCACACTACCTGACTTCAGTTTGTGCTACGG 3071
                             i   - iv      v       v  ii i    ivviv i    ii
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_120412010_   3072 AGCTA--GTAACCAAAACAGCATGTTACTGACATCAGAACCAACACGTAG 3119
                              --    i   i    ii  v     i   v  i ivi   ii   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_120412010_   3120 ACCAATGGAACAAAATAAAGAACCCAGAAACAAATCCATACACCTACTGT 3169
                          i        i i   vi   ii       i   i       ii  iv  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_120412010_   3170 AAACTCATTTTCAACAAAGGCACCAAGAACATACGCTGGAGGAAAAGACA 3219
                         v  i v      i    i  ii      v   v iv   -     ii i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATA 394

  chrX_120412010_   3220 GTCTCTTAAATAAATAGTGCCAGGAAAACTGGATAGTTGTATGCAGAATA 3269
                             i  v  i    i    ii   v         ?iiii     i  v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_120412010_   3270 ATGAAATTAGACCCCTGTCTCTCATCATATACAAAAAATCAAATCAAAAT 3319
                              i  i       ii   v  i            - i  v       
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAAT 493

  chrX_120412010_   3320 GGTTTGAAGACTTAAATCTCAGAGTTCAAACTATAAAGCTACTACAAGAA 3369
                           v ii?    i     v v    i v          i  vi  v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_120412010_   3370 AACATTGGAGAAAATCTCCAGGAGATTGGTCTTGGCAAAAATTTCTTTAA 3419
                              v  ? v      i iv  vv    vi v     vii      vi 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_120412010_   3420 CAATAGC-CCACAAGCACAGGCAACCAAAGCAAAAATGAACAAAAGGGGT 3468
                         i - ii -   v       i     v    v      ii i   vv  ii
  L1M4_orf2#LINE/    594 TA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_120412010_   3469 CACATCAAG-TTAAAAAGCTTTTACACAGAAAAGAAAAC----AACAAAG 3513
                         iv      i-       -     iii vvv    i v  ----  v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_120412010_   3514 TGAAGAGACAACCCACAGAATGGGAGAAAATATTTTCAAACCACTCATTT 3563
                             i                              v    i  ivi  i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_120412010_   3564 GAGAAGG-ATTAATAACCAGAATATACAAGAAACTCAAACAACTCTATAG 3612
                           v    - i vi  v          i  ii     vv       v   i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_120412010_   3613 GAAAAA---AAA----CTGATCAAAACATAAGTGAAAGATTTGAATAGAC 3655
                         v     ---   ---- ii  i?   v  ii ii  i             
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_120412010_   3656 ATTTCTCAAAAGAAGACATACAAATGACAAATGGGCATATAAAAAGGTGC 3705
                                v        i         i v   ii   i  i     i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_120412010_   3706 TCAATGTCATTGATCAT 3722
                             ii   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.80 (27 / 15)  


 230 17.65 0.00 0.00  chrX_120431750_120434287      749   799 (1739)    L1M4_orf2#LINE/L1        1    51 (857)  

  chrX_120431750_    749 TGAAAATATATTTCATGTTAATGGATTGGAAGAATTGGTATTGTTAAAAT 798
                           i   v    ii      v             v  ii         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120431750_    799 G 799
                          
  L1M4_orf2#LINE/     51 G 51

Transitions / transversions = 2.00 (6 / 3)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.00 (0 / 0)  

2945 24.09 1.40 1.75  chrX_120431750_120434287     1226  2080 (458)    L1M4_orf2#LINE/L1       57   908 (0)  

  chrX_120431750_   1226 ACTACCCAAAGCAATCAACAGATTCAATGTGATTCCTATGAAAATACCAA 1275
                            v      vii   v          i ii  i     v     v   i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_120431750_   1276 TAATATTCTTTACAGAAATAGAAAAATTAATCCTAAAATTTATATGGAAC 1325
                         iviiv  i   i       v  v  ii i           i        v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_120431750_   1326 CAGAAAAGACTCATAATGGCCAAAACCACCTTGGACAAGAAGAATAAAAC 1375
                         iiv  ii   i  v   i        v i    i v        i   ii
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_120431750_   1376 TGGAGGAGTCACAATCATTGACTTCAAA--TTACAATACAGAGCTATAGT 1423
                                v     v iviii i      --    --    i     i   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGCTACAGT 254

  chrX_120431750_   1424 AAACCAAAGATCATGGTACTGGCATAAAAACAGAAACATAGACCAATAGA 1473
                           v v i v vii              ii i   v i     i    i  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_120431750_   1474 TCAGAATATAGAACCCAGAAAGAAATCCTGACATCTACAGTGAACTCATT 1523
                         vi     vv   ii       v   i  vv    i  ii  v  i v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_120431750_   1524 TTTGATGAAGGTGTCAAGAACATACATTGGGGAAATGATAATCTCTTCAA 1573
                           i  ii i    i     v   v  v        vi   i   i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_120431750_   1574 TAAATGGGGCTGGGAAAACTGCATATGTATATGGAAAAGAATGAAACTAG 1623
                         i      v       v     v   ?vi i   v           ii i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_120431750_   1624 ACTGCTGTCTCCTGCCATATACTAAAATCAAATCAAAATGGATTAAATAA 1673
                           iv  ii   vii        v     i  v           i ? v v
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_120431750_   1674 TTAAATTTAAGACCTAAAACTATGAAACTGCTTAAAAGGAAACTTTGGGG 1723
                         i     v     v          i     -    i   i    v v  ? 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNG 553

  chrX_120431750_   1724 -AAATGCTTCAGGACATTGGTCTGGGCAATTTTTTCTTTAGTAATATCCC 1772
                         -    -    iv   v    vi i      vv      vii  vv iv  
  L1M4_orf2#LINE/    554 TAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_120431750_   1773 ACAAGCACAGGCAACCAAAGCAAAAATAAACAAATGGGATCACGTCAAG- 1821
                          v       i     v    v       i i    v   iiv i    i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_120431750_   1822 TTAAAAAGCTTTTTCACAACAAAGAAAACAATCCACAAAG-----ATACA 1866
                                -     vii vv     i v  v   v v    ----- v   
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_120431750_   1867 ACCAACAGAATGGGA-AAAATATTTGCAAACTATCCATCTGACAAGGGAT 1915
                            v           -              ii  vi      i      i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_120431750_   1916 TAATAACCAGAATATATAAGGAGCTCAAACTACTTAATAGGAAAAAAATC 1965
                          vi  v             i  i   vv  v   i    iv     i - 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-C 800

  chrX_120431750_   1966 TAATAATCTGATT-AAAAATGGGCAAAATATCTGAATGATCATTTCTCAA 2014
                         v     i ii   -             iv  i     iiv        v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_120431750_   2015 AAGAAGACATACAAAAGACAAACTAAAAATA-GAGCTACCATATGATCCG 2063
                                i       v i v  -   iv i -  i-- -- v   v  --
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAA-TAAGCACATGAA--A--AGATGCTC-- 893

  chrX_120431750_   2064 ACAACATCAAAGGGATA 2080
                         --       ????????
  L1M4_orf2#LINE/    894 --AACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (115 / 88)
Gap_init rate = 0.02 (16 / 852), avg. gap size = 1.69 (27 / 16)  


2712 26.58 4.05 1.80  chrX_120486460_120489247     1408  2295 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120486460_   1408 TGGAAAAATATTCTATGTTCATGGATTAGAAGAATCAATATTGTTAAAAT 1457
                               i    i i             i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120486460_   1458 GTCCATACTACCCAAAGCAACCTACAGATCCAGTGCAATTCCTATGAAAA 1507
                          v v     v      vii i        i  ii     i     v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120486460_   1508 TACCAATGATATTCTTTCAACACATAGAAAAA-TAATCCTAAAATTTATA 1556
                          v   iiviiv  i   vv v v  v  v  i- i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_120486460_   1557 TGGTACTACAGTAGTTTCGTAATAGCCAAAGCTATCCTGAGCAAAAAGAA 1606
                            v v i  ivi vii iv          i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_120486460_   1607 CAAAACTGGAAGAATCATGTTACTTGACTTCAAATTATACTACCGGATTT 1656
                             ii    i  v   iii v iii i      viv      viiii v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_120486460_   1657 TTTTTTTTTTCAAAAA--AAGA--GCATGATAGTGGCATAGAAGGAGACA 1702
                         ----------  iv  --    -- ii  i  v       iiiiv     
  L1M4_orf2#LINE/    251 ----------CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_120486460_   1703 CATAGACCAGTGCAACAGAATAGAGTATCCAGAAATGAATCCATACATCT 1752
                         i     i  i  v  i     v   vi         i  i        i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_120486460_   1753 TCAGTGAACTCATTGTTAACAAAGATGCCAAAAACAATCACTAGGGAAAG 1802
                         vii  v  i v   v ii    i i      i v  v   v i       
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_120486460_   1803 G-CATTCTCTTTAATAAATGGATATT-----AAATAAATATCCACTTGCA 1846
                         i-i v   i  i  i      - ii -----  v ii   ?    v    
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGG-TGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_120486460_   1847 GAACAATGAAACTGGATGCCTGTGTTGTACCATGTAGAAAAAT-----CA 1891
                         i  v      ii    iv   iiv iii     i  v      -----  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_120486460_   1892 AAAT---------ATTCAAATCTAAGACCTCACACTATGAAACTACTAAA 1932
                             --------- iii    v     v  v v     i     vi  i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_120486460_   1933 AAAAAACATTACAGAAACACTGAAGAACATTGGTCTGAGCAAATGTTTCT 1982
                          i       viv? v  vv  vvivi  v    vi ii    vv      
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_120486460_   1983 TGGGTAATAC-CCACATGCACAGGCAATCAAAGCAAAAA-GGACAAAATG 2030
                          i i  vv  -   v v     i    iv    v     -i  i   v  
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_120486460_   2031 GATCACATCAAGTTTAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAA 2080
                           iiv      iv      i   i  ii vv       v  v     v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_120486460_   2081 AGTTAAGAGATAACCTGGAGAATGGGAAAAGTTATCTGCA--TCCTATCC 2128
                            v  i   i    iiv         i  iv   i    --  v   --
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-- 737

  chrX_120486460_   2129 ATCTGACAAGGGATTAATAACCAGAATATATAAGGAGCTCAAAGAACTCA 2178
                               i      i vi  v             i  i   vv v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_120486460_   2179 ATAG-----AAACAAATTATAATGCAATTTAAAAATGAGCAAAAGATCTG 2223
                            i----- i      ---  iv     ?       i     i   i  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAAT---AACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_120486460_   2224 AATAAACATTTCTCCAAA-AAGACATACAAATGGGAAACAGGTATATAAA 2272
                             i             -    i          vv  i i i i  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_120486460_   2273 AA-ATGCTCAACATTATTGATCAT 2295
                           -           i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (142 / 91)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.06 (52 / 17)  


 826 20.14 16.38 2.05  chrX_120546382_120549219.rev      723  1015 (1823)    L1M4_orf2#LINE/L1        1   335 (573)  

  chrX_120546382_    723 TGGAAGAACATAATATATTCATGGATTTGAAGAATTTATATTGTTGAATT 772
                              ii i  vvi  i          v     v  v        i iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120546382_    773 GTCAGTACTCTCCAAAGC-ATCTACAGACTCAACGCAATCCTTATCAAAA 821
                          v  i     i     vi-         i            i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120546382_    822 TCCCAATGACCTTTTCT-CAGAAATAGAAAACACAACTCTAAAATTCATA 870
                              iivi      i -       v  v  vvii ii            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_120546382_    871 CAGAATCTCAAGGGA---------GC----------TTGAA--------- 892
                         ii   viv       ---------  ----------     ---------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_120546382_    893 CAA----------C---CACTTCCCAATTTCAA--CTTACTCCAAATCTC 927
                            ---------- ---                --      v    v  v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_120546382_    928 TA-TAGTCAAAATACAATGGTAATG-CATAAAAATAGACATATTAATCAA 975
                         i -  i    i i vvi     v  -     ii          vi     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_120546382_    976 ATGGA-TAAAATTGAAATAAACTACAAATAGAACTACCATA 1015
                         -    -  i      i --iv i v     -   --     
  L1M4_orf2#LINE/    301 -TGGAATAGAATTGAGA--GTCCAGAAATA-AAC--CCATA 335

Transitions / transversions = 1.46 (35 / 24)
Gap_init rate = 0.04 (15 / 335), avg. gap size = 3.60 (54 / 15)  

2465 18.52 4.24 4.87  chrX_120546382_120549219.rev     1712  2348 (490)    L1M4_orf2#LINE/L1      276   908 (0)  

  chrX_120546382_   1712 GTACAAGTAT-TATGTGTAAATTAATAAAAAAGAAATTAAGAATTGGGAG 1760
                          i i   v  -v ii i  i  i   ------ i   --       i   
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAAT------GGAAT--AGAATTGAGAG 317

  chrX_120546382_   1761 TCCAGAAATAGGCCCATACATCTACGGTCAATTTATTTTTTACAAAGGTG 1810
                                   ii         i  i        v     iv    i    
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_120546382_   1811 CTAAGATAATTCAATGGAGAACGA-TGGTCTTTTCAACAAATAGTTCTGG 1859
                          i    iv         i   v  - i               i  v    
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_120546382_   1860 GACA------------CATGCAAAAGAATGAAGTTGAGTACTTAACTCAT 1897
                             ------------                    iiiv i  v    i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_120546382_   1898 ATCACATA--AAAATTAAGTCAAAATGGAGTGCAAGCCTAAATATAAAAG 1945
                          i  i   --        v          vii? ii       i   i  
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_120546382_   1946 CTACAATTATGTAACTCTTAAAAGAAAACATTCTGGTAAATTTTCATGAT 1995
                            v  i   iv        i          vvv?      i   i   i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_120546382_   1996 CTTAAATTTGGCGATGTTTTCCTAGATGTGATACCAAAAACACAAGCAAC 2045
                            iii  v   i   v    i     i   i       i          
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_120546382_   2046 AATGGAAAAAATA----AATCGGAATTCCTCAAAATTGAAAACTTT-GCA 2090
                           vi         ----   i   v   v        i        - ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_120546382_   2091 CATCAAAGGACACTATCAAGATAGT-ATAAGCCAACCCACAGCATAAGAG 2139
                          v                   v   - v   v          v  ii   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_120546382_   2140 AAGATATTTTCAAATTGTGTATTTGGCAAGGC-CCTGACTATCCAGAATA 2188
                           i      v     ii i   i  ii    v- i  --           
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTG--TATCCAGAATA 765

  chrX_120546382_   2189 TATATATGTATGTATATATATATATATAACTCTTACA-CTAAAAAACAAA 2237
                             v ----- ---------------          -  v  v  i   
  L1M4_orf2#LINE/    766 TATAAA-----G---------------AACTCTTACAACTCAATAATAAA 795

  chrX_120546382_   2238 A-GTCATACAATTAAATTAATAAAGTGGGGAAACGACTTGAA--GACACT 2284
                          - v  v i  iiv    ? -   i    v   v  i     --    i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_120546382_   2285 TCTGCAAAGAAGACAAAAAAATTGCCAACAAGCACATTAAAAGATATTCA 2334
                            v         i v v    v     i        v       ii   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_120546382_   2335 ACATCCTTAGATGT 2348
                              v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (73 / 42)
Gap_init rate = 0.03 (17 / 633), avg. gap size = 3.41 (58 / 17)  


3035 27.62 0.47 0.47  chrX_120553621_120557787.rev     2039  2896 (1271)    L1M4_orf2#LINE/L1        1   858 (50)  

  chrX_120553621_   2039 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2088
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120553621_   2089 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2138
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120553621_   2139 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2186
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_120553621_   2187 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAACG 2236
                                viiv  ii  v  v v  v     iv     i i ivv i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_120553621_   2237 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2286
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_120553621_   2287 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2336
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_120553621_   2337 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 2384
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_120553621_   2385 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 2434
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_120553621_   2435 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 2484
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_120553621_   2485 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATCAATTCAAGATGGA 2534
                            ii    i    v   i i   v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_120553621_   2535 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2584
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_120553621_   2585 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 2634
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_120553621_   2635 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAA 2684
                         i            vvi          vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_120553621_   2685 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 2734
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_120553621_   2735 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACCA 2784
                           i     i   iv            v  i    vii ivi      iv 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_120553621_   2785 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 2834
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_120553621_   2835 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 2884
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_120553621_   2885 TCAAAAGAAGAT 2896
                           v         
  L1M4_orf2#LINE/    847 TCCAAAGAAGAT 858

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (5 / 858), avg. gap size = 1.60 (8 / 5)  

2472 24.06 3.76 2.69  chrX_120553621_120557787.rev     2925  3668 (499)    L1M4_orf2#LINE/L1      139   890 (18)  

  chrX_120553621_   2925 CTAAAATTCATAGGGAAGCACAAAATGCCACTAATAACCAAGGCAATCTT 2974
                                     v    iii   iivi  vvv    i    ii       
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chrX_120553621_   2975 GAGAAAAACAAAAACAAAAAACAAAGCTAGAGGCATCTCACTACCTAATT 3024
                           i   i --------- i       i i    vv  v    v  i    
  L1M4_orf2#LINE/    189 GAAAAAGA---------AGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_120553621_   3025 TCAAAATCTACTAAAATGCTATAGTAATTGAAACAGCATGGTCCTGGAAC 3074
                               ii     v  v    i      ii i    ii    v    v i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_120553621_   3075 AATCATAACCACATAGACCAATGGAATGGAATAGAGAGGCCAGAAATAAA 3124
                           vv   iv  i     i         i    v     v           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_120553621_   3125 TTCACATATTTATGGTCAATTCATTTTCTACAAAGGTGCCAAGAACACAT 3174
                         ii  i i              v      v    i          v  ivi
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_120553621_   3175 GATAGGAAAAGAACAGTCTCTTCAATAAATGATATTGGAAAAACTGGATA 3224
                         i  i  i      i     i     i     i ii   i v         
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_120553621_   3225 TCCATATGCAGAAGAATGAAATTAGATCCTTATCTTAGACCA-------A 3267
                         ?   i     i         i  i  i  i  i  i v    ------- 
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_120553621_   3268 AATCATAC-CAACATAGATTAAATATTAAAAGGTAAAAACTGAAAAATGT 3316
                            i -  -   v  i   i ? v iiv   v    i i  -    v i 
  L1M4_orf2#LINE/    480 AATTA-ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTAT 527

  chrX_120553621_   3317 AAAACTACTAGAAGAAAACAT-GAGGTAAACGTTCCCTGACATTGTTCTG 3365
                               vi             - i?     iv   v-    v   vvi i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTA 576

  chrX_120553621_   3366 GGTAATCGTTTTTTAAAATATAACCCCCAAATCACTGGCAATATAAGCAT 3415
                           i   v    i   i -   i  v  v   v   vi    i v   ---
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAG--- 622

  chrX_120553621_   3416 TTTAAAAAATGGA---ATTA-----TAT-AAAACTAAAAAGCTATATAA- 3455
                         ---       i  ---   i-----i  -    i      vi v i iv-
  L1M4_orf2#LINE/    623 ---AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_120553621_   3456 -CAAGGGAAATAATCAACGGAGTAAAAGAGACAACCTA---GATGGAAGA 3501
                         -   i   v iv     vii   i   -        i ---i    i   
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAA-AGACAACCCACAGAATGGGAGA 718

  chrX_120553621_   3502 AAACATTTGCAAACTATGTATCTGATGAGAAGTTAGTACCCCCTAAATAT 3551
                            i         ii  i        i  iiii v   i  vvv v    
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_120553621_   3552 AAGGAACTCAAACAACGCAATATTTGGAAAACAA----CACAATTAAAAA 3597
                           i      vv     v     v vii  i    ---- v     ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_120553621_   3598 ATGAGCAA-TTATCTGAATAGACATTTTTCAAAAAATGACAGGCAAATGG 3646
                            i    -vv  i             i  v   i v  i vi       
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_120553621_   3647 CCAACAGGTATATGAAAAAATG 3668
                             i i i i       i   
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATG 890

Transitions / transversions = 1.78 (112 / 63)
Gap_init rate = 0.02 (17 / 752), avg. gap size = 2.82 (48 / 17)  


3114 26.53 1.23 0.67  chrX_120559821_120561910.rev      704  1600 (490)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_120559821_    704 GATATTCCATGTTCATAGATTGGAAGAATGAATGCTGTTAAAATATTCAT 753
                              i          i          v v   ii      i  iviv  
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_120559821_    754 ACTTCCCAAAACAATCCACAGATTTAATGCAATTCCTATCAAAATACTA- 802
                            i      vii   i       i  i     i           v i -
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_120559821_    803 -TGATATTCTTCACAGAAATGGAAAAAG-AATCCTAAAATTTACGTGCAA 850
                         -  vi-  i  ii       v  v  iv-i           i ii  v  
  L1M4_orf2#LINE/    107 CTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_120559821_    851 TCACAAAAGATCGAGAATGGCCAAAGCAATCCTTTACAAAAAGAATAAA- 899
                         vii   ii  i v     i      i     i vv v  i     i   -
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_120559821_    900 CTGGAGAGATAACATTAGCAGACTTCAAATTATAGTACTAAGTTATAGTA 949
                         i     iiv v   i vv vi i      viv  v   v   i  i    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_120559821_    950 ACCAAAATAGCATGCTACTCACATAAAAACAGACACTTAGACTAATGGAA 999
                          i   i i  ii  v    vi     ii i     iv    ii       
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_120559821_   1000 AGGAATAGAGATCCTAGAAGCAAATCTACACATTTACAGTCAGCCCATTT 1049
                         vi    v    vi i    ii   i i i       ii    iiiv    
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_120559821_   1050 TTGAAAAAGGTGCCAAGAACATATATTGTGGAAAGAAGAGCCTCTTCAAT 1099
                          i  v  i          v   vi v  v        v  i  i     i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_120559821_   1100 GAATGGTGCTAAGAAACCTGGATATACACATGCATAAAAATGAAACTAGA 1149
                         i         ii  v v       ?v        v  i      ii i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_120559821_   1150 CCCCAATCTCTTCTTATATACAAACCTCAAATCAAAATAGATTA--AACT 1197
                             v i   vivii         vv i  v       i   i --i  i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_120559821_   1198 TAAATCCAATACCTGAAACTATGAAACTACTAAAATAAAATATAGGGAAA 1247
                              vi  v v  i       i     vi  i  v    i     ?iv 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_120559821_   1248 ACACTCTG-GGTCATATGTCTTGGCAAAGGTTTCTTGAGTAAGATTTCAA 1296
                          vv  ii - ii v iv  - v     v        iii  v  ivi   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_120559821_   1297 AAATATACGCAACTAAAGTAAAAATGGACAAATGGGAACACATCAAGCTA 1346
                           ii i v     v    v      i  i    v   viv      iv v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_120559821_   1347 AACAGCTTCTGCATAGCAAACGGAACAACAT--ACAAAGTGAAGAGACAA 1394
                           v i   i  iiivv    -- i   vi  -- v        i      
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAA--GGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_120559821_   1395 CCCATAGAATGGGAAAAAATATTTGCAAACTATCCATTTGACAAGGAATT 1444
                             i         i              ii  vi  i   i    i i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_120559821_   1445 AATAACCAGAATATATATAAGGAGCTCAAACAACTAAATAGGAGAAA-AC 1493
                         vi  v            -- i  i   vv      v    iv i   -  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATA--AAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_120559821_   1494 AAATAATCTGATTTTAAAATGGGCAAAATATTTGAATAGAAATTTCCTGA 1543
                               i ii   ?v            iv           v     iiv 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_120559821_   1544 AAGAAGACATACAAATAGCCAACAAGTATATGCAAA-ATGCTCAACATCG 1592
                                i        i     i   i i   v   -            i
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_120559821_   1593 TAACCATC 1600
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.70 (148 / 87)
Gap_init rate = 0.01 (12 / 902), avg. gap size = 1.42 (17 / 12)  


2921 26.70 1.50 1.96  chrX_120623301_120625161      500  1368 (493)    L1M4_orf2#LINE/L1       44   908 (0)  

  chrX_120623301_    500 TTAAAAGGATATATACTACCCAA-CTAATCTACAGAGTTGATGTAATCAC 548
                             i v ii -     v     -i i         v ii i i    v 
  L1M4_orf2#LINE/     44 TTAAGATGGCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chrX_120623301_    549 AATCAAATTCCAAACAGCAAATTTACTGATGTAGTAA--AACAATTTTAT 596
                         v      v   v i v  ---i  vi --  i  v  --i    vi v  
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGC---CTTTTT--TGCAGAAATTGACAAGCTGAT 137

  chrX_120623301_    597 C-----ATTCATATGGAACCACATAAAAGATCCTGAGCAGCCAAAGCATC 641
                          -----            -- iii  ii  i  v  ii       i  vi
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_120623301_    642 TTTGAAGAAAGAGGAGAAAACTGGAGACATCGAACTTCCCAATTTTGAAA 691
                         i     i  ii  i v   ii     ivv  iv            ii   
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_120623301_    692 TATCATACACAGCTACAGTAATAAAAAAAGTATGGTGCTAGCATCAAAAC 741
                         iv vv    v            v  i v   i    i  i    v ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_120623301_    742 AAACATATAGATCAATAATAAAAAATAGAGATATCAGAAATAGGCCTACT 791
                          i              iiv v i   v    vvi        ii  i iv
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_120623301_    792 CAC--ATGATAAACTAATTTTTGACAAGGGTGCCAGGAATACACAATACA 839
                           i--   i v  i i     i             i  vi iv    ivi
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_120623301_    840 AAAAATGTAATATTGACAATAAATAGTGTTGGGAAAACTAGATATCCAGA 889
                         i   ivi  i v  vv   i    i   i     v    i    ?   v 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_120623301_    890 TGCAAAGGAATGAAATTGGATCCTTATCTTACACCATACACAAAAATCAA 939
                               i       i     i  i  i  i        i        i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_120623301_    940 CTCAAAACGGATTAAATAATTAAATGTAAGACCCATAAATATACAACATG 989
                                i    i ? v vi           v i v  v    v   viv
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_120623301_    990 TAGAAGTAAGCATAGGAAAAACTTCTTGTAA--TTGGCCTTGTCAGTGAT 1037
                               v  i      ?iv  v ii i  i --    vi v v  i  i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_120623301_   1038 TTTTTGGATATGATCTTGTATACGCCAAA-GCACAATGAAGAGAAGTAAA 1086
                           i  i       --------- i     -      vv  v i   v   
  L1M4_orf2#LINE/    586 TTCTTAGATATGA---------CACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_120623301_   1087 AATAAACAAGTGCAGCTACATCAAAATAAAAATCTTCTGCACAGCAAAGA 1136
                             i i  i vvii  v         v    v   i  ii vv     i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_120623301_   1137 ATACGATCAACAAAGTGAAAAGGCAACCTTTGAAATGGGAGAGAACATTT 1186
                          i  v     v           i     iviii         i  i    
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_120623301_   1187 GCAAACCATGTATCTGTTAAGGGGTTAATATCCAAAATACGTAAGAAACT 1236
                              i   i      v      ii vi      i    ii   ii    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_120623301_   1237 TCTACAAGTTAACAGCAATAAAACAAATAACCTGATTTAAAAATGTACAA 1286
                         ii     v i  i ii  v  i          ii   ?       vi   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_120623301_   1287 AGGATTTGAATAAATATTTCTTTTAGAAGGACATACAAGTGGCTAGCAAG 1336
                                     i i      iiv ii i  i      i    i ii   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_120623301_   1337 TATATGAAAAGGTCATCAGAATCATCAATTAT 1368
                         i i        i vv   iv    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (150 / 78)
Gap_init rate = 0.01 (11 / 865), avg. gap size = 2.73 (30 / 11)  


2442 25.58 4.23 3.23  chrX_120630211_120637629.rev     3266  4164 (3255)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120630211_   3266 TAGAAACACATGCTGTGTGCATGGAATGGAAGAATCAATGTCATGAAAAT 3315
                          i    v i  v ii   v      v       v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120630211_   3316 GACCATACTGCATGAGTATGGT-------------GCAGTTCCT--CAAA 3350
                          i v     v vii i -  i -------------   i i   --    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_120630211_   3351 ATGCCAACATAATTTTGCACAGAATTAGAAAAATACATTCTCAAAATTCA 3400
                           v   i vvvv    vii     v v  v  iivv  i  -        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAATTCA 148

  chrX_120630211_   3401 TATGGAACCATAAAATGG-CCC-GAATGGTCAAAGCAATTCCAAGCAGAA 3448
                                --  iv  v  -   -    i i    i    iiii iv ii 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_120630211_   3449 AGAAAAAATCTGGAGGAATTACCCAACTTCAAATCTGGAGGAATTACCCA 3498
                             v   vi       v i  ---     -----------------   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCAC---ACTTC-----------------CCA 226

  chrX_120630211_   3499 ACTTCAAATTATACTACAA-GTTGATAGTAACCAAAAGAGCATGGTTCTG 3547
                          i      viv        - i - i     i   i v  ii    v   
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCT-ACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_120630211_   3548 GTGTAAAAGTAGATTAATGGACCAATGGAACAGGATAGAGAACCCAGGAA 3597
                          ii   iii    ivv  i  i        i  i  v    ii    i  
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_120630211_   3598 TAAAGCCAAATGCTTACAACCAACTGATCTTTGACAAAGCATACAAAAAC 3647
                             v   v iii   iiii   i    i  i     i -i i v  i  
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGAC 374

  chrX_120630211_   3648 -ATAAATTGGGGAAT--ACACCCTATTTGA--AATAATGCTGGGAAAATT 3692
                         -  vv v       v-- i vi  v  ii --   ii        v  i 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_120630211_   3693 CAATAGCCATATGTAGAAGAATGAAATTGGAACCCTAAACTCAT--TATA 3740
                         vi   ?   i   i i         i     v     v-    i--i   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC-CTCACACCATA 473

  chrX_120630211_   3741 TACAAAAATTAAATCGTGATGGATCAAAGACTTAAATCTAAGACCTAAAA 3790
                                     v  ivi        ?    i     v     v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_120630211_   3791 CCCTAAAAACTGTAGAAGAAAACCTAGGAAAAACTCCTCTGGACACTGTC 3840
                          iv     viiv           v    ?iv  v  i  vv   vi  vv
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_120630211_   3841 CTAGGCAAATAATTTATGACAAA-GACCTCAAAAGCAAATGCAACAAA-G 3888
                         i       - ii   v v v v -   vi        v v        - 
  L1M4_orf2#LINE/    574 TTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_120630211_   3889 CAAAAATAAGTAAATGGGACCTAATTAAACTAAAATCCTTCTGCACAGCA 3938
                         v       ii     v    i v  i   v v   vv   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_120630211_   3939 AAAGA-AGTATTCATTAGAGTAAACAGACAACCCACAGAAAGGGAGAAAA 3987
                           i  - v   -  vv i   i  v               v         
  L1M4_orf2#LINE/    673 AAGGACACTAT-CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_120630211_   3988 TATTTGCCAATTAT-TATCTGATAAAGGACTAATATCCTGAGTCTACAAG 4036
                                v   i  -          i     vi     v  i v  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_120630211_   4037 ---CTCAAATGAATCAGCAAGAAAAAAACAAATAATCTTATT-AAAAGTT 4082
                         ---   vv ii v   ii  v     i        i iv   -    i v
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_120630211_   4083 TACAAA-----TGAGTAGACATTTCTCAAAAGAATACATATAAACGGCCA 4127
                         vi    -----   i            v      v i   i   i     
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_120630211_   4128 ACGAACATATGAAAAAATGCTCAATATCACTAATCAT 4164
                          ii i  i       i        i    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.58 (67 / 26)  

3388 23.05 2.23 1.11  chrX_120630211_120637629.rev     6031  6928 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120630211_   6031 TAAAAATACATACTGTATTCATTGATTAGATGTCTTAATACTGTTAAAAT 6080
                          ii   v i  v ii i     v    i  v v       i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120630211_   6081 GTTCATCTTAACTAAAGCAATCTACAAATTTA-TGCAATCTGTAT-AAAA 6128
                          viv  vi vv i   vii       i   i -i      iv   -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120630211_   6129 TCACAAAGGTCTTTTTTCTTTTGCAGAAATAGAAAAAAAATCATCCTAAA 6178
                           v  ivv i       -----        v  v  iv-- v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-----GCAGAAATTGACAAGC--TGATCCTAAA 143

  chrX_120630211_   6179 ATGTATATGCATTCTCAAATGATCCAAAATAACCAAAACAATCTTGAGAA 6228
                           vi     v vviv   iv  i   i    i               i  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_120630211_   6229 AGAAGAATAAAGCTGGAGGTTTCACACTTCCTTATTTCAAAGCATATTAC 6278
                                i    i      vi          iv        i v  i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_120630211_   6279 AAAGCTACAGTAATTAAGA--GTATGCTACTAGCATGAAGACAAACATAA 6326
                                       i    --  i  v    i    i i  i i     v
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_120630211_   6327 AAATCAATACCACAAAATAGAGAGCTTAGAAATAAACTCA-ATATATATG 6375
                          i      ivv i i   v     iii          i  - i  v    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_120630211_   6376 GGCAACTAATCTACAACAAAGATGCCAAGAACACACAATGAGGAAAAGAT 6425
                          v   i i  i v i    i i        v  iv     i     ii  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_120630211_   6426 AGTCTCTTTAACAAATAGCATTGGGAAAA--GTATATCCACATACAAAAG 6473
                              i  i       i iii     v  -- v   ?      i      
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_120630211_   6474 AATGAAATTGGACCCTTTTCTTACATTATATA--AAAACTAACTCAAAAT 6521
                               i        i vi  i   ii     --    i           
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_120630211_   6522 AGATTAAAGACCTAGGTATAAGTACCAAAACTATAAGACTAG-AAAAAAA 6570
                         i   i ?       ii i    vi i          i   vv- i  i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_120630211_   6571 AACATAAGGAAAAGACTT-ATGACATTGGAATGGGCAATGACTTCTTCAA 6619
                               i ?iv  iv   -i    v    iv i       ii     vi 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_120630211_   6620 TATGACAAAAGAAGCA-GAGTAACAAAAGCAAAAATATACATAAGGGAAT 6668
                                vv i     -i  i        v       v i v vv   v 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_120630211_   6669 AACTCTAACTTAAAAACTTCAGTGCAGAAAAAGAAACAATCAAG----TA 6714
                         vvv  v  v          iv    vvv   i  v  v      ---- i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_120630211_   6715 AAAAGACAACCTGCAGAATGGAAGAAAATATTTGCAAACAGTGTATTGGA 6764
                                    ii        i                ivi i   iv  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_120630211_   6765 TTAGGGGTTAATAATCAGAGTATATAAAGAACTC--ATAACTCAACAACA 6812
                          v    ii vi  vi    i              -- i       i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_120630211_   6813 AAAACGACAACAATGGTT--ATTAAAAAATGGGCAAAGAATTTGAGTGGA 6860
                             -     --  iiii--   ?              i      i i  
  L1M4_orf2#LINE/    794 AAAA-GACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_120630211_   6861 CACTTTCCCAAAGATGAGATACAAATGGCCAACAAGTATATGAAAAGATG 6910
                           i  ii       v  v              i   i i           
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_120630211_   6911 CTCAACATCACTAATCAT 6928
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (128 / 75)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


3042 25.70 1.78 0.78  chrX_120656785_120662632.rev     4459  5357 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120656785_   4459 TAGAAAAACATTCCATCCTCATGAATTGGAAGAATCAATATTGTGAAAAT 4508
                          i    i i  i    vi     i         v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120656785_   4509 GGCCATACTGCCCAAAATAATTTATAGATTAAATGTTATTCCCATCAAAC 4558
                            v     v      v i  i  i     v  i iv  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120656785_   4559 AACCATTGACATTCTTCAAAGAATTATAAAAAACT-ACTTTAAATTTCAT 4607
                         vv   vivi v  i  iiv    v - i v  i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_120656785_   4608 TTGGAA-T-CAAAGAAGACCCCATATAGCCAAGGCAATCCTAAACAA-AA 4654
                         v     - -   i --     viv        ii     i i  v  -  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_120656785_   4655 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 4704
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_120656785_   4705 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAAGAGACATATAGAC 4754
                                  i   i    ii         i iv ii v           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_120656785_   4755 CAATGGAACAAAAC--AGAGTCCTCAGAAATAACACCACACATCTACAAC 4802
                                 i i  i--       --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_120656785_   4803 CATCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAGGATCT 4852
                           vi    i  i     ivv  v   i vi vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_120656785_   4853 CCTATTCAATAAATGGTTCTGGGAAAACTGGCTAGCCTTAGGCAGAAAAC 4902
                         i  v     i       v      v      v  ?  vi v   i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_120656785_   4903 TGACATGAGACCCCT----TACACCTTATATAAAAATTAACTCAAGATGG 4948
                            vi vi       ----i     v    i              i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_120656785_   4949 ATTAAAGACTTAAATATAAAAACCCAAACCATAAAAACCCTAGAAGAAAA 4998
                           i ?    i     i   i i iv    i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_120656785_   4999 CCTAGGCA-ATACCATTCAGGGCATAGGCATAGGCAAAGACTTCAT-GAT 5046
                          v    ?i- v i -   iv i v v  vv       v ii   v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_120656785_   5047 GAAAATGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATC 5096
                         - vi ii         vvv          vv     v  i    v   ii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_120656785_   5097 TAATTAAACTAAAGAGTTTCTGTACAGTAAAAGAAACCATCATCAGAGTG 5146
                          v  i   v v  i ii  i   i vvi   i  v  i    vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_120656785_   5147 AACAGGGAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGT 5196
                           v  iv    i                 v       vii ivi     v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_120656785_   5197 CAAAGGTCTAATATCCAGAATTTACAAGGAACTTAAACAAATTTACAAGA 5246
                         i  i  v  vi          v  i  i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_120656785_   5247 AAAA-ACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 5295
                             -     i     v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_120656785_   5296 TTCTCAAAAGAAGACATTTATGTGGCCAACAA--ACATGAAAAAA-GCTC 5342
                              v        i  vi vi       i  --         i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_120656785_   5343 AACATCATTGATCAT 5357
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (131 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.44 (23 / 16)  


2858 26.84 1.75 1.28  chrX_120669928_120674608.rev     3328  4184 (497)    L1M4_orf2#LINE/L1        1   861 (47)  

  chrX_120669928_   3328 TGAAGAAATATCCCATGTCCATTGATAGGTAGATTCAATAATGTCAAGAT 3377
                           i i i           i   v   v  v   i i    v   i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120669928_   3378 GTCAGTTATCTCCAGCTTCATCTACAGTTTCAGGAGAATCTCAATTTTAA 3427
                          v  i vv  i   iv  v        v    iviv    i v  ivv  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120669928_   3428 TCCCAGAAAGTTA--TTTTTTG--GATATCAATAAAATGATTCTAAACTT 3473
                               ----i i--       --  v  ii i  iv    i     v  
  L1M4_orf2#LINE/    101 TCCCAG----CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_120669928_   3474 TATATGGAGAGACAAATGACTCAGAATAGCCAATACGATCTTGAAGAAAA 3523
                         i       i vi   iv   i            v  i        i  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_120669928_   3524 AGATGAAAGTTGAAGTATTGACACTACTTGACAACAAAACTTCCTA---- 3569
                            vv       i  v i v     v iii ivv        v   ----
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_120669928_   3570 --TATAGTAATTAAGACATTGTAGTATTGGTAAAATAAAAGACATATATG 3617
                         --  i      i      v   i   i   i v  vi v         vi
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_120669928_   3618 TCAATGAATCAGAATAGAGAGCCTGGAAATAGACCCACATAAATACGGCT 3667
                               i vi     v     i ii      i     i i vv  i  ii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_120669928_   3668 AACTGAATTGTGACAAGGGAGCAAAGACAATACAATGAGTAAAAGATAAT 3717
                           i   v  vi        v  v     v  v     i v   ii   i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_120669928_   3718 CCTTTTAGCAAATTGTGCTGGAGGAAGTGGACATCCGCATGCAAAAAAAA 3767
                          i   i i     v       iiv  v    i ?  i         i  v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_120669928_   3768 TAAATAAATATAAACACAGATGTTATAACCTTCCCAAAAGTTAATTCAAA 3817
                         v  i ----- ii  v vv iv i i v v viv     i    i     
  L1M4_orf2#LINE/    447 GAAGT-----TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_120669928_   3818 ATGGATCATAGACCAAAATATAAAATGC--AAACTATAAAGCTCCTAGAA 3865
                                 ?     v    i   i -  --          i   i     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAA 540

  chrX_120669928_   3866 GATAACATAGGAAAAAATCTATATGACCTTGGGTTTGGCAATGGCTTTTT 3915
                           v        ?iv      vii            v        i  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_120669928_   3916 AGCTACAATACCAAAGGCACAATCCATGAAATAAATAATTGATAAGCTGG 3965
                           v  ii i      i      v v ii   v   v   v     ii   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_120669928_   3966 TATTCATTAAAACTAAAATGTTCTGCTCCACAAAAGACAATGTCAAGAGA 4015
                         vv     i    i     vv  i  iv iv    i    v i      i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_120669928_   4016 ATCAAAAGACAAGCCATAGGTCAAGATAAAATATTTGCAGA--GGACATT 4063
                         i v         v   i  iviii  v            i --iv i  i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_120669928_   4064 TAATAAAGGA-TTATAATTCAAAATACATAAATAACTCTTACAGTTCAAC 4112
                          i    i   -  i  - i  i    i     v          ii    i
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTA-TCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_120669928_   4113 AATAAGAAAACTAAAAACTAAGTTAAGTAATGGGTCAAAGACCTTTACAG 4162
                              i  i  v  v   iv i  ? iv      iv  i  ii vv i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_120669928_   4163 ATAGATTAACAAAGAAGATACA 4184
                          i vv ivv           i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATA 861

Transitions / transversions = 1.43 (133 / 93)
Gap_init rate = 0.01 (10 / 861), avg. gap size = 2.60 (26 / 10)  


2262 30.47 2.34 1.34  chrX_120683231_120686339     1721  2616 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_120683231_   1721 AAAAACATTTCATGCTCGTGGATCGGAAAAATCAGTATCATTAAAACGGC 1770
                            i i  ii    i  i     i    i v i i   ii    i i   
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_120683231_   1771 CATGCTGCCTAAAGCAATACACAGATTAAACACTATTCATATCATGCTAC 1820
                         v  i  v  i   vii  vi       v   i v  i v     viv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_120683231_   1821 CAACATCATTTTTCACCAAATTGGAAAAACT-ATTCTAAAATTGATATGG 1869
                           i vv v     ii vi  v v  v  i  -  i        v      
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_120683231_   1870 AACCAAAAAAGAGCCTGATTAGCCAAAGAAATCCAAAACAACAAGAACAA 1919
                           viiv  ii  v  v  v        iv    ivi  v  v        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_120683231_   1920 AACCAGAGGCATCACATTACCCAGCTTCAAACTATACT-ATTATAAGGCT 1968
                          iiii    vv     i v    ii      ----   - i  i  i   
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAA----ACTTACTACAAAGCT 249

  chrX_120683231_   1969 ACCATTAACCACAAGAGCATAGTACTCGTACAAAAAT-GACACATAGACC 2017
                           - v   i  vi v  ii i     v i i  ii  -    i     i 
  L1M4_orf2#LINE/    250 AC-AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_120683231_   2018 AGTGAAACAGAATATAGAACACAGAAATAAAGCCTAACACCTACAACCAT 2067
                          i  i  i     vv   iiv          v  vv   ii  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_120683231_   2068 CTGATCTCTGACTAAGTGAACAAAAATAACCAAAAAAGAAAGGACTCCCT 2117
                         i    i ii   v i vviv   i vi vi   viii     i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_120683231_   2118 ATTCAATAAATGA---------AGCTGGCTAGCCATATGCAGAAGAATGG 2158
                         v     i     i--------- i    v  ?   i     i       i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_120683231_   2159 AACTGAACCCTTAACTTTTAACATATGAAACATAAAAAATGAACTCAAGA 2208
                          ii  i    i  v  ivi v     ---   ---     v       i 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATAT---ACA---AAAATTAACTCAAAA 492

  chrX_120683231_   2209 TGAATTGTAGTTTTAAATGTAAGAACTCAAACCATAAGAATCTTAGAAGA 2258
                           i  ii?  vii           i  v    i    i v          
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_120683231_   2259 AAACCTAGGAA-ACACCATCTGGAC--TGGCCTTGGGAATGAATTTATGA 2305
                             v    ?i- v i v  vv   --   vi v  v    iv  iv ii
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_120683231_   2306 CTAAGTCCTCAAAAGCAATTGCAACTAAC--AAACATTGACAGCTGGAAC 2353
                         v  v v vi        vvv     v  v--   v  v  i iv v i  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_120683231_   2354 CTGATTAAACTAAAGTGCTTCTGCACAGCAAAAGAAACTATCAACAGAGT 2403
                         i v  i   v v  ivi   i  ii vv    i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_120683231_   2404 AAA----CAATCTACAGAATGGGAGAAAATATTTGCAGTCTCTGCATCTG 2449
                         i  ----   i i                        iviiv ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_120683231_   2450 ACAAAGATCTAATATACAGAATCTATAAGGAACTTAAACAATTGAACAAG 2499
                          i  i iv  vi   v      v     i     ivv    i v  i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_120683231_   2500 TAAGAAACAAGTAATTCCATTCAAAAGTGTACAAAAGACATGAACAGACA 2549
                         v  i i    i   ii v   ?    i  vi    i  iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_120683231_   2550 CTTCTCAAAAGAAGACATACATGCGGCTAACAAATATATGAAAATAAAGC 2599
                         i     v        i     vii   i  i  ii i       -i v  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGC 891

  chrX_120683231_   2600 TCCGCATCACTTACCAT 2616
                           vi     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (160 / 109)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 2.54 (33 / 13)  


3334 26.43 0.44 0.44  chrX_120736245_120742657     5013  5920 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120736245_   5013 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5062
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120736245_   5063 GGCCATACTGCCCAAGGTACTTTACAGATTCAATGCCATCCCCATCAAGC 5112
                            v     v     iv iv i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120736245_   5113 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5160
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_120736245_   5161 TATGGAGCCAAAAAAGAGCCCACATTGCCAAATCAATCCTAAGCCAAAAG 5210
                               iviiv  ii  v  viv  v      v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_120736245_   5211 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5260
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_120736245_   5261 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5310
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_120736245_   5311 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5358
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_120736245_   5359 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5408
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_120736245_   5409 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5458
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_120736245_   5459 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5508
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_120736245_   5509 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5558
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_120736245_   5559 CTAGGCATTACCATTCAAGACATAGGCATGGACAAGGACTTCATGTCTAA 5608
                         v    ?i v viv   iv   v v  vv i i   v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_120736245_   5609 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5658
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_120736245_   5659 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5708
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_120736245_   5709 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5758
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_120736245_   5759 AGGGCTAATATCCAGAATATACAATGAACTCAAACAAATTTACAAGAAAA 5808
                         i  i  vi             i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_120736245_   5809 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5858
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_120736245_   5859 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5908
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_120736245_   5909 ATCACTGGCCAT 5920
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2195 27.00 4.25 1.77  chrX_120760204_120762019.rev      502  1349 (467)    L1M4_orf2#LINE/L1       40   908 (0)  

  chrX_120760204_    502 ATTACTAAAATGCCAATTATCCCTAACTTGATTTATAGGTTCAATG-AAT 550
                            ii   i   v    vv    i  v     i  i  i     i -   
  L1M4_orf2#LINE/     40 ATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

  chrX_120760204_    551 TCACATTCAAAATTCCAGAAAACTATTTTGTAAATATTAGCAAATTGACT 600
                         i vi  -      i    vviv  v     i i v   ii   ii   ii
  L1M4_orf2#LINE/     90 CCCTAT-CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC 138

  chrX_120760204_    601 CTAAAGTTTATATGGAAAGGCAAAATTCCTAGAATAGATGACACTATT-- 648
                              i  i         v    iivv  i       vii v  v  i--
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chrX_120760204_    649 -AAAGAGAAG--CAAAGTTGGAAGACTAA-ACTTATCTAATTTCAAGACT 694
                         -   i     --          i    v -    -i i        i   
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAAACT 237

  chrX_120760204_    695 TACCATAA-GTTAAGACAATAATCAAGACAGTGTGTTATTGGCAAAATAA 743
                            i i  - i  ---  i                v  i     v  vi 
  L1M4_orf2#LINE/    238 TACTACAAAGCTA---CAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_120760204_    744 TAAACAACTTGATCAGTGGAATAGCATAGAGAGCCTAGAAATCAACGCAC 793
                           i   vv v     i        v  v     i i      v   v  i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_120760204_    794 ACACCTACAGTTACTTGATCTTTGACAATGAAGGGAAG-----TCAATGA 838
                            ii  ii  i v     i  i     v iv vv   -----      i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_120760204_    839 AGAAAAGATACTCCTTTTAATAA-TGGTGCTAGGAAGACTGGTCATCTAT 887
                         i    ii   v  i   i  i  -       i   vi     vi ? i i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_120760204_    888 ATGCAAAATAATGAATTTAGACACATAAATTATAGTTAATTTTACTAAGA 937
                                 v      v  i   v v  vv i i -ii -- v   v  i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACA-CCA--TATACAAAAA 481

  chrX_120760204_    938 TTAACTCACA-TAAATTATTGACCTAAA-ATACAATGTAAAATTATAAAA 985
                                 v - ii  i ?v        -i  vi vv     i       
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_120760204_    986 TTTGCACAAGAAAATATATAA--AAATTCTCAATTACCTTGCATTTATTG 1033
                         i ivi v       i   vi?--    ii  i- v      vi  vivii
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCA 580

  chrX_120760204_   1034 ATGAATTTTTAGATACAACAT--GAGCCATGAAAAACAAAA----ACATT 1077
                            iv  i       ii   i--i iv  ii iv       ---- v  v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_120760204_   1078 GCAAATTTGGATTTTATTAAAATCTAAAATTTCTGCTCTTCAAAAGAC-C 1126
                          vv  v     i  i  i     iv    i  i  iv       i   - 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_120760204_   1127 TATTAAGAAAATGAAAAGATTAGCCACAAACATGG-AGAATATATTTATA 1175
                            i      i        iv v     i -    -    v      ii 
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGA-ATGGGAGAAAATATTTGCA 729

  chrX_120760204_   1176 AAACACACACCTGATTA---ACTGGCATCCAAATTATACAAAAGACTCTT 1222
                           v  i i i     v ---   v i     i v    i   ii      
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_120760204_   1223 AAAACTGAACAATTAAAA-ACAAATAACTCAA----AATGTGTGCAAAAC 1267
                          v    v  i   v    -         i   ----  vi  v     iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_120760204_   1268 ATAAAACCAGACCCCTCACAAATGAAGATCTATAGGTAG--AAAAAGGAC 1315
                           vvi vi    vii  v v  v      v  i ii i --  v   v  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_120760204_   1316 ATTAGATACATACTAATAAAACATAAATATAGTA 1349
                           v i - v  i  v ----    v ????????
  L1M4_orf2#LINE/    880 ATGAAA-AGATGCTCA----ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.03 (27 / 869), avg. gap size = 1.89 (51 / 27)  


2497 26.60 5.91 0.95  chrX_120782547_120787558     3666  4511 (501)    L1M4_orf2#LINE/L1        1   888 (20)  

  chrX_120782547_   3666 TAGAAAAGCATTCCATATTCATGGATACAGAGAATCAATATTATTATCAT 3715
                          i    iii  i    i         vvii   v i      i   vv  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120782547_   3716 GACCATACTGCCCAAA------------------GCAAT---TATAAACA 3744
                          i v     v      ------------------     ---   v  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120782547_   3745 TTC-----------TTCATAGAATTAGAAAACACT-ATTTTAATATTCAT 3782
                          i -----------  iii    v v  v  -i  -  ii   v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_120782547_   3783 ATGGAACCAAAAAGGAGCCTGAATAGCCAAGGCAATCCTATACAATAACA 3832
                               viiv  i   v  v          ii     i iv v  v  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_120782547_   3833 GCAAAGC-AGAAGACATGCTGCTGCCCAACTTCAAACTATATTACAGGGC 3881
                         i     i-i  i   vii -i  v     i      viv  i    ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_120782547_   3882 TACAATAACCAAA------TGGTAGTGGTACAAAAACAGACACATGGACA 3925
                             i   i   i------     v   i i  ii i     i  i  iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_120782547_   3926 AATGGAACAGAATTGGCAGCCCAGATGTAAGACCACAGACTTAACAATCA 3975
                                i       iv  i     vi   iv   i v i   -iii   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCA 347

  chrX_120782547_   3976 TATGATCTTTGACAAAGCTGACAAAAACAAACAATGAGGAAAGGATTCCC 4025
                         vv    i  i     i v  v   i v  vv     i      i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_120782547_   4026 TATTCCATAAATGGTGCTGGGTTAACTGGTTAGCCATATGCAGAAGATTA 4075
                          v   v i             vi      v  ?   i     i    v i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_120782547_   4076 AAACTGTACCCCTTTCTTACACAATTTACCAAAGTCAACTCAAGATGCAT 4125
                           ii  v      vi  i    v  v   v   i i       i   v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_120782547_   4126 TAAAGACTTAAATGTAAAATCTAAAACTATATAAAGATTGGAAGGCAACC 4175
                         i ?    i         i v           v  vvv  i    iv   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_120782547_   4176 TAGG--TAACACCATTCTGGACATAGGAGCTGGCAAAGATTTCATA-ACA 4222
                             --   - i -   vv   v v  iviv     v i    v  - i 
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_120782547_   4223 AAATGCCAAAAGCAATGGCAGCAAAAGCAAAAATTGAAAAATTGGATCTA 4272
                         vi ii         vvi   i      v      v  v        ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_120782547_   4273 ATTGAACAAAAGAGCTTCTGTGCAGCAAAAGAAACTATCAACAGAGTAAA 4322
                           ii  vvv  i i   i     vv    i  v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_120782547_   4323 CAGAAAACCTACAGAATGGGAGAAAACATTTTCAAACTCTATATTTGACA 4372
                         v   v    i                i    v    iiv     i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_120782547_   4373 AGGGTCTAACATCCAGCATCTATAAGGA--TTTTA-AATTTACAAGAATA 4419
                             v  vii      v  v     i  -- i   -  i --   v    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--CAATAATA 793

  chrX_120782547_   4420 AAA---CAAGCAACTGCATTAAAAAAGTGGGCAAAGAAGT-GAACAGACA 4465
                            ---   ii   ivv   ?     -         i v -   i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chrX_120782547_   4466 CTTTTGCAAAGAAGACTCACGTGTGGCCAACAAGCATATGAAAAAA 4511
                         i  i v         ivi  ivi       i     i       i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

Transitions / transversions = 1.34 (127 / 95)
Gap_init rate = 0.02 (19 / 888), avg. gap size = 3.05 (58 / 19)  


2742 25.48 4.78 1.71  chrX_120809147_120811320      805  1683 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_120809147_    805 GAAACACATCCTGTGTTCATAGATTGTAAGACTTAA---------AATGT 845
                             v i    ii       i     v         ---------i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_120809147_    846 CCTCACTACTCA----GATCCATAAATTCAATGCTATCCCAAACAAAATC 891
                          vvi   v i  ----    i i i      i  v     v v       
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_120809147_    892 CCAATAATATTTTTTTACAGAAATAAAAAA----ATTCTAAAATTTATAT 937
                            iivii-i      i       vi v  ----  i        i    
  L1M4_orf2#LINE/    103 CCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_120809147_    938 GGGACCACAAAAGACT--GAATAGTCAAATCAATCTTGAGAAGGAAGAAC 985
                           i vii   ii   i--      i    v         i  i       
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_120809147_    986 GAAGATG-AGGCTTTGTTTCTTCTCCTGATTTCAAAACCTATTACAAAGC 1034
                         i   v  -   vi ii--- vii   ii          i  i        
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCA---CACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_120809147_   1035 TTCAGTAGTTAAAA--GTACTAGGTACTGTCATAAAGACTAGATGTAAAT 1082
                          v     i i  i --  ii--       v     i  -    ii  v v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGT--GGTACTGGCATAAGGA-TAGACATATAG 295

  chrX_120809147_   1083 AGCTATGAAACAGGATATGAC-GCCCACAAATAAATTCACAC-------G 1124
                          v v   i  i  i  -   v- i   v       ii  i  ------- 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_120809147_   1125 TCAACTGATTATCAACAAGAATGTCAATAATATGTAATGGCAAAAAATAG 1174
                             i     v  i     ii  i   v vi  vi     vi   i - v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-AT 393

  chrX_120809147_   1175 AGTCTCTATAACAAGAGATAGGCTTGGAAAACTGGATATTCACATGCCAA 1224
                              i vi     iv i --   v   v         ?i       v  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGT--GCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_120809147_   1225 AAAATCAAACTGGTCCTGTATCTTCTACCATACTCTAAGAGAAACTCAAA 1274
                          i   v  ii   v  iv  i  ivi      iv v  i vv        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_120809147_   1275 GTAAGTTAACAATGTACATATAAGACCTAAAACCGTAACACTCTTAGAAG 1324
                         i iii i ?vi iv  v  i     v       ii   v           
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_120809147_   1325 AAAACATAGGGTAAAATCTTCATGAAATTGGTCTTGACAATGATTTCAAG 1374
                                   ?vv        i   vv    vi v i     i    vvi
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_120809147_   1375 AATATGACACCAAAAGCACTGGCAACAAAAACAAAAATAAGCAAGTTTAT 1424
                         i                  vi         iv       iii  i  ---
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT--- 638

  chrX_120809147_   1425 GAGACTACGTCAAGTTCAAAGGCTTT-ATA----AAAGGAAACAATGAAA 1469
                         -i    v i    iv i   ii    -i i----      v  v  v  i
  L1M4_orf2#LINE/    639 -GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_120809147_   1470 AAAATGAAAAGGCAATTAATGTACAGGAAGAAAATACTTGCAAACCATAT 1519
                            i       i   iiv iiv vv  i        i       i     
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_120809147_   1520 GTATGATAAGTGCTTAATATTCAAAATATAGGATGGACTCATAAAAC--A 1567
                         i v       v vi vi   i  i      vi v i    v  v   -- 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_120809147_   1568 ATAGTAAAAA---ATATAACT-ATTTTAAAAACAGGACAAGAACTTGAAT 1613
                            i      --- v     i- v  ?     ii  vv   i i      
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_120809147_   1614 AGACATTTCTTCAAGGCAGACATACAAATGTCCAATGGGCATATAAAAA- 1662
                                   i   i v   i         v     ii   i  i    -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_120809147_   1663 ATGCTCAACATAACTAATCAT 1683
                                    v ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (137 / 83)
Gap_init rate = 0.02 (22 / 906), avg. gap size = 2.59 (57 / 22)  


2968 28.21 1.45 0.45  chrX_120840079_120842509     1047  1943 (488)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_120840079_   1047 GAGAGATATCCTATGTTAATGGATTGAAAGAATTAACATTGTCAAAATGC 1096
                           i        i     v        i    v    i     i  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_120840079_   1097 CATTACTACCCACAGAAATCTATGGATTCAGTGCAATTCCTATCAAAATT 1146
                           v    v    v vvi     ii      ii     i           i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_120840079_   1147 CTAATGACGATTTTTACCCAAATAGAAAAG--AATTTTCAAATTTGTATG 1194
                          i iivi vv     i vv    v  v   --i  ii v     ii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_120840079_   1195 GAACCACAAAAAACCTTGTATAGTCAATACAACCTTGAGCAAAAATAGTA 1244
                            vii   iii   iv v    i   v    i     iv  i  v ii 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_120840079_   1245 AAGCTGAAAATATTACACTACCTGACTTCAAAATATACTATAAAATGATA 1294
                            i  i iivv i     v  ii i       iv     i   iiv i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_120840079_   1295 GGAATTGAAACAGCATCATACTGTCATTAAAACAGACACATAGATCAATA 1344
                          v   ii i    ii vi     v   v ii i     i          i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_120840079_   1345 GAACAAAACAGAAAATCCAAAAATAAATCCATATAATTAAGATGTATTTA 1394
                            i i  iv  i i    i       i     i v   v i vv   v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_120840079_   1395 TTTTCAACTAAAGTTGCAAGAACATGGGATAGGGAAAGGTTAGTCTCTTA 1444
                              i  v ii  vv     v   vvi  i       iv      i  v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_120840079_   1445 AATAAACGGTGTTGGGAAAGCTGGATATATACATAAAGAAGAATAAACTT 1494
                           i   i    i     v i       ?vi    iv i      i  v  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_120840079_   1495 AGGGTCGTATATCAAACCATATACAAAAATCAAAT-ATAATAGATTAAAG 1543
                         i ivi v  iv   v               i  v - v   i   i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_120840079_   1544 ACTTAAATACAAGACCTGAAACTGTAAAGCTACTAGAAGAAAACTTAGAG 1593
                           i     ii    v  i     i    i  vi           v   i?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_120840079_   1594 AAGAAGGCTCATGGCATTGGTCTGCACAATAATTTATTTGACCTCACTCC 1643
                         ivi  vvi  i  i v    vi ivi    ii   v  v  iv v  v  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_120840079_   1644 AACAGCACAGGTGACAACAGCAAAAGTAGACAAATATGATTACAACAAAC 1693
                           v      i ii    v  v    i    i    vv  i v  v    v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_120840079_   1694 TAAAAAATTTCTGAGTATTGAAGGAAAC-------AGAGTGAAGAGACAA 1736
                          v     i  i  v iv ii     v  ------- i      i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_120840079_   1737 CCTATAAAGTGGGA-AAAATATTTATAAACTATACATCTGATAAAGGGTT 1785
                           i i i i     -         ii   ii   i         i  ii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_120840079_   1786 AGTACCTAAGAATTTATAAGAAACTCAAACAACTCAATAGCAAGAAAACA 1835
                         v   i i -    v     ii     vv           ii  i  i   
  L1M4_orf2#LINE/    753 TGTATCCA-GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_120840079_   1836 AATTACCCAATTAAAAAAATGAGCAAAGGGCCTGAATAGACATTTCTCAA 1885
                            v        ?     -  i       iii                v 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_120840079_   1886 AATAGGCTA--CAGATGGCCAACAGTTGTATTTTTAAAAATGCTTAATCT 1933
                           v i v  --  i        i i-- i iv vv   i     i  iv 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAA--GCACATGAAAAGATGCTCAACAT 898

  chrX_120840079_   1934 CTATTGTGTA 1943
                          v????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.65 (155 / 94)
Gap_init rate = 0.01 (8 / 906), avg. gap size = 2.12 (17 / 8)  


2975 27.08 1.22 0.44  chrX_120857680_120863751.rev     4680  5580 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120857680_   4680 TGGAAAAACATCCCATCCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4729
                               i i       vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120857680_   4730 GGCCATACTGCCCAAAGTAATTTGTAGATCCAATGCTATTCCCTTCCAAC 4779
                            v     v      v i  i ii    i   i  v  i  iv  v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120857680_   4780 TACCA-TTGACGTTCCTCAAGGAATTAGAAAAATCTATTTTAAATTTTAT 4828
                          v   -i  v v  ii vv  i    -  v  iiiv  ii    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chrX_120857680_   4829 ATGGAATAAATG-AAG--ACCCTGTATAGCCA---CATTTCTAAGCAAAA 4872
                               ---   -   --    v v       ---  v ii i iv  i 
  L1M4_orf2#LINE/    150 ATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_120857680_   4873 AGAACAA-GCTGGAGGTGTCACACTACCTGACTTCAAACTATACTACAAG 4921
                                - i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_120857680_   4922 GATACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGA 4971
                          v        i   i    ii         i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_120857680_   4972 CCAATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACACCC 5021
                         i        i    iv   ivii         vv   i    i  iivi 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_120857680_   5022 ATCTGATCTTTGACAAACCTGACACACACAAGCAATGGGGAAAAGATTCC 5071
                          vi    i  i     ivv  v  vivv  vv           ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_120857680_   5072 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATACAGAAAACT 5121
                           v  i  i        i     v      v  ?   i  i  i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_120857680_   5122 GAAATTGGACCTCTTCCTTACACCTCATAAAAAAATTAACTCAAGATGGA 5171
                            i       i  v   i     vi   v              i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_120857680_   5172 TTAAATACTTAAATGTAAAACTCAAAACAATAAAAACCCTAGAAGAAAAC 5221
                          i ? v  i         i vii     v      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_120857680_   5222 ATAGGCAATACTATTCAGGACATAGGCATAGGCAAAGACTTCATAACAAA 5271
                              ?ivv v v   iv   v v  vv       v ii   v  ivv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_120857680_   5272 AACAGCAAAAGCAATTGCAACAAAAGCCAACATTGACAAATGGAATCTAA 5321
                         i   v        vvv          vv  v  v  i    v i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_120857680_   5322 TTAAGCTAAAGAGCTTCTGCACAGCAAAAGAAACTGTCATCAGAGTGAAC 5371
                          i  iv v  i i   i  ii vv    i  v   i   vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_120857680_   5372 AGGCAACCTACAGAATGGGAGAAAATTTTTGCCATCTACCCATCTGACAA 5421
                           i     i                 v     v vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_120857680_   5422 AGTTCTAATATCCAGAATGTACAAGGAACTTAAATATATTTACAAGAAAA 5471
                         i vv  vi          i  i  i     ivv i vv iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_120857680_   5472 AAACAC-CAACACCATCAAAAAGTGAGCAAAGGATATGAACAGACACTTC 5520
                          i   v-i   v v  i?    i  i         v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_120857680_   5521 TCAAAAGAAGACATTTACGTGGCCAACAA--ACATGAAAAAAAGCTCAAC 5568
                           v        i  vi vi       i  --         i v       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_120857680_   5569 ATCACAGATCAT 5580
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (130 / 110)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2724 26.30 1.52 3.15  chrX_120896311_120902126.rev     4406  5325 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_120896311_   4406 AAAAAAATCCCATCCTCATGGAAAGGAAGAATCAATATCGTGAAAATGGC 4455
                            i v       vi       vv      v i     i  v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_120896311_   4456 CATACTGCCCAAAGTAATTTGTAGATTCAATGCTTTTCCCATCAAACTAC 4505
                         v     v      v i  i ii        i  vv i  i      v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_120896311_   4506 CATTGACATTCTTCACGGAATTAGAAAAAAAAACT-ACTTTAAATTTCAT 4554
                           vivi v  i  ii i   v v  v  i----  - iii    v     
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATTCAT 149

  chrX_120896311_   4555 ATG-AAATGAAAAAAAGAGCACATA-TAGCCAAGACAATCCTAAGCAAAA 4602
                            -     v  iii --- v  v -       i      i i ------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGA------ 190

  chrX_120896311_   4603 AAAAAAAAAAAAAAAAAAAAAGCTGGGGGGGCATTATGCTACCTGACTTC 4652
                         -------    i  i  v    i   i  i- - i ii  v  ii i   
  L1M4_orf2#LINE/    191 -------AAAAGAAGAACAAAGTTGGAGGA-C-TCACACTTCCCAATTTC 231

  chrX_120896311_   4653 AAACTATACTACAAGTCTGCAGTAACCAAAACAGCATGGTACTGGTACCA 4702
                            viv        iv  i      i   i    ii         i iv 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_120896311_   4703 AAACAGACATACAGCCCAACAGAACAGAACAGAGATGTTGGAAATAACAC 4752
                         ii i       i  vi   ii   i    iv    vviii       vv 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_120896311_   4753 CGCACATCTACAATCATCTGATCTTCGACAAACCTGACAAAAACAAGCAA 4802
                          ii    i  iii   vi    i        ivv  v   i v  vv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_120896311_   4803 TGGGGAAAGGA--GTCCCTATTTAATAAATGGTGCTGGAAAAACTGGCTA 4850
                                  i --   -- v  i  i            i v      v  
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_120896311_   4851 GCCATATGCAGAAAACTGAACCTGGACCCCTTCCTTACACCTTAAACAAA 4900
                         ?   i     i  i v    vi         v   i     v  v     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_120896311_   4901 AATTAATTCAAGATGTATTAAAGACTTAAATGTAAAACTCAAAACCATAA 4950
                               i    i   v  i ?    i         i vii     i    
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_120896311_   4951 AAACCCTAGAATAAAACTTAGGC---AATGCCATTGAGGACATAGGCCTG 4997
                           vi i     v     v    ?---   -- v i -v   v v  vi i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCG-TGACCTTGGGTTA 576

  chrX_120896311_   4998 GGCAAAGATTTCAT-GACG-AACATGCCAAAAGCAATTGCAACAAAAGCT 5045
                              v i    v -  ii-i   --         vvv          vv
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACA--CCAAAAGCACAAGCAACAAAAGAA 624

  chrX_120896311_   5046 AAAATTGACAAATGGGATCTAATTGTGCTAAAGAGCTTCTGCACAGCAAA 5095
                              v  i    v   ii v  iiviv v  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_120896311_   5096 AGAAACTATCATCAGAGTGAAA-GACAACCTATAGAATGGGAGACAATTT 5144
                         i  v       vv i       -       i i           v   v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_120896311_   5145 TTGCAATCTATTTATCTGACAAAGGTCTAATATCCAGAATTTGCAAGAAA 5194
                               vii  v       i  i  v  vi          v ii  ii  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_120896311_   5195 CTTAAACAAATTTACAAGAAAAA---AAAAGACCCCATCAAAAAGTGGGC 5241
                           ivv    v iv i  v     ---   vi    v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_120896311_   5242 AAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACA 5291
                                v    i     i     v        i  vi viii     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_120896311_   5292 GACTTTTGGAAAAAAGCTCAACATCACTGATCAT 5325
                         ii viv  i   i v           ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.02 (18 / 905), avg. gap size = 2.39 (43 / 18)  


2877 29.09 0.33 0.66  chrX_120922768_120926678     2508  3418 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120922768_   2508 TGAAAAAACATTCCATGGTCATGGATAGAAAGAATCAATATTGTGAAAAT 2557
                           i   i i  i     v        v i    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120922768_   2558 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 2607
                            v     v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120922768_   2608 TACCATTGACTTTCTTCACAGAATTATAAAAAACT-ACTTTAAATTTCAT 2656
                          v   vivi i  i  ii     v - i v  i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_120922768_   2657 ATGGAACCAAAAAAGAGCTGATATAGCCAAGACAATCCTAAGCAAAAAGA 2706
                               viiv  ii  v iiiv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_120922768_   2707 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATAGTGCAAGGCA 2756
                               i      vv   ii  v  ii i      viv  v i   i  v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_120922768_   2757 ACAGTAAAAAACACAGTATGGTACTTGTACTGAAACAGATATATAGACCA 2806
                                vv  v     i       v i iviii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_120922768_   2807 ATGGAACAGAACAGAGGCCTCAGAAATAATGTTACACATCTACAACCATC 2856
                               i    iv   ivii         vvii i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_120922768_   2857 TGATCATTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 2906
                             iv i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_120922768_   2907 TTAAATAAATGGTGTTCAGAAAACTGGCTAGTCATATACAGAAAACTGAA 2956
                           v  i        i vi  v      v  ?i  i  i  i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_120922768_   2957 ACTGGACTCTTTCCTTACACCTTATACAAAAATTAACTCACAGTGGATTA 3006
                         ii     i i v   i     v                  v i     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_120922768_   3007 AAGACTTAAACATCAGACCTAAAACCACCAAAACCCT-AGAAGAAAACCT 3055
                         ?    i    ii v   v       i -i     i  -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTA-TAAAACTCTTAGAAGAAAACAT 548

  chrX_120922768_   3056 GGGAA-ATACCATTCAGGACATAGACATGGGCAAAGACTTCATGACAAAA 3104
                         i  ?i- v i -   iv   v v ivv i     v ii   v iivv vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_120922768_   3105 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGGATGTAAT 3154
                                     vvi          vv     v  i    v   iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_120922768_   3155 TAAACTAACGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 3204
                         i   v v vi i   i  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_120922768_   3205 GGCAACCTACAGAGTGGGAGAAAATTTTTGCAATCTATTCATCTGACAAA 3254
                          i     i     i           v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_120922768_   3255 GGGCTGATATCCTAAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 3304
                           i  vi     vi   v  i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_120922768_   3305 AAAAAACAAACACCCCATCAAAAAGTAGGTGAAGTATATAAACAGACACT 3354
                         i v   i  ---   v  i?    i i  ii   v  v i  i     i 
  L1M4_orf2#LINE/    798 GACAAATAA---CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_120922768_   3355 TCTAAAAAGAAGACATTTAGGTGGCCAACAAACATACGAAAAAAAGCTCA 3404
                            vv        i  vi ii       i  i  i i     i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_120922768_   3405 TTGTCACTGGTCAT 3418
                         vii   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (155 / 106)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3049 26.11 0.87 2.49  chrX_120998889_121005312     5009  5931 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_120998889_   5009 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATCATGAAAAT 5058
                              ii i  i     i i    i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_120998889_   5059 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5108
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_120998889_   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_120998889_   5157 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5206
                                viiv  ii  v  v v  vi    iv     i i ---     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAAAG 195

  chrX_120998889_   5207 AACAAAGTTGGAGGCATCAAAGTTGGAGGCATCACGCTACCTGACTTCAA 5256
                           v  ------------            vv    i  v  ii i     
  L1M4_orf2#LINE/    196 AAGAA------------CAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_120998889_   5257 ACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAA 5306
                          viv        i          i   i    ii         i iv ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_120998889_   5307 ACAGAGTTATAGATCAATGGAAGAGAAC--AGAGCCCTCAGAAATAATGC 5354
                          i   vv               v    i--    i  --        vv 
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACC 331

  chrX_120998889_   5355 CAAATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAA 5404
                           v i  i  iiiii vi    i  i     ivv  vv  i v  vv   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_120998889_   5405 TGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACCGGCTAGC 5454
                                  i  vvi  v  i  i              v   i  v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_120998889_   5455 CATATGGAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAA 5504
                           i   v i  iiv    ii    i    v   i     v          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_120998889_   5505 TTAATTCAAGATGGATTAAAGACTTACATGTTAGACTTAAAACCATAAAA 5554
                             i    i      i ?    i  v    v   vi      i      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_120998889_   5555 ACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCA 5603
                         vi i           v    ?i- v i -   iv   v v  vv i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chrX_120998889_   5604 AGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT 5653
                          v ii   v ivvi vi            vvi          vv     v
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_120998889_   5654 GACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAC 5703
                           i    v   ii v  i   v v  i i   i  ii vv    i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_120998889_   5704 TACCATCAGAGTGAACAGGCAAGCTACAGAATGGGAGAAAATTTTCGCAA 5753
                           i  vv i      v  i   v i                 v  i    
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_120998889_   5754 CCTATCCATCTGAGAAAGGGCTAATATCCAGAATCTACAATGAACTC--A 5801
                         vii  vi      v  i  i  vi          v  i  v      -- 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_120998889_   5802 -AACGCATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGCTGAA 5850
                         -   v  --- i  v     i     i     v  i?    i   vii  
  L1M4_orf2#LINE/    781 CAACTCA---ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_120998889_   5851 GGTTATGAACAGATCCTTCTCAAAAGAAGACATTTATGCAGCCAAAAAAC 5900
                           v v    i   ivi     v        i  vi viii     v  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_120998889_   5901 ACATGAAAAAATGCTCATCATCACTGGCCAT 5931
                                  i       v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.58 (31 / 12)  


2367 20.82 5.36 1.26  chrX_121013885_121015506      496  1129 (493)    L1M4_orf2#LINE/L1      249   908 (0)  

  chrX_121013885_    496 TACAGTAATCAAAACAATGAGGTACTGGCATGAAAATAAAAATATGTACC 545
                                     i   i  v           i ii   i v    iv i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_121013885_    546 AATGGAACACA-CTGAAA-TTCAGAAAATACATCTAGCAATATATGATCA 593
                                i v -i   i - i      -  v i i vvv  v    i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATGGTCA 347

  chrX_121013885_    594 ATTGATTTTTG-CAAGAGTTCTAAAAC-ATTCAATGCAGAAGAGAGAGCC 641
                                  i -    i  v i  i  -        vi   iii v  i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_121013885_    642 TTTTCAACAATTGATGTTAAAAAAAGCTGGAAATCCACATGCAAAATAAT 691
                                   v  i  i iii v  -     v ?            v   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAAT 446

  chrX_121013885_    692 AAAGTTGGACCCTTATCTCACATCATATACAAAAATTAAATCATAATGGA 741
                         i           i  i      i                v   v      
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_121013885_    742 TTGAAGACCTAAATTTAAGAGTTAAAACTATTAAACCCTT---------C 782
                          ii?          v      i         v    i   --------- 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_121013885_    783 ACGGGGGCAAATTTTCCTGACCTTTTATTTGGCGAAGAGTTTTCAGATGG 832
                          ii  ? i    i   v       vvi  v   i v iv  i i    iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_121013885_    833 GGCACCAAAAGTTCAAG-AATAAAACAAGAAATAGATAA-TTACACTTCA 880
                          i         iv    -  i    v  i          -  iv      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_121013885_    881 CTGACAATTAAAA-CTTATGTGCATCAAAGAAAGCACTTTTAAGAAAGTA 929
                         iii -        -   v     v      i --    v i        i
  L1M4_orf2#LINE/    647 TCAA-AATTAAAAACTTTTGTGCTTCAAAGGA--CACTATCAAGAAAGTG 693

  chrX_121013885_    930 AAAAGTCAACTTTCAACATGGGAAAAAAATATTTGCAAATCA-ATATTTG 978
                              v    iiv  iv      i    -             -    i  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTG 742

  chrX_121013885_    979 GATAAGAATCTAGT-TTCAGAATGTACAAGGGACTCTTAAAGC--AACAA 1025
                         -     iiv  v  - i      i  i  i i       v i --  i  
  L1M4_orf2#LINE/    743 -ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_121013885_   1026 CAAAATGTCAAACAAACTAATTTTTAAAATTAGCAAA----------AGA 1065
                         i    v v    i  v i    ?v-     vi     ----------   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGA 840

  chrX_121013885_   1066 CATT-CTCCAAAGA---TATACAAATGTTCAATAAGCATATATAATAATG 1111
                             -         ---          vi         i  iv  vi   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_121013885_   1112 TTCAACATCATTAGTCAT 1129
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (81 / 47)
Gap_init rate = 0.03 (21 / 660), avg. gap size = 2.00 (42 / 21)  


 777 23.87 2.25 2.70  chrX_121023033_121025079      500   721 (1326)    L1M4_orf2#LINE/L1      286   506 (402)  

  chrX_121023033_    500 AGACAAATAGACCAATTAAAGAGAATAAATAGATCCCAGAAATAAATCCA 549
                              v     i    vi  v     vi v  --i           i   
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAG--TCCAGAAATAAACCCA 333

  chrX_121023033_    550 CACATGTATGCTAAATTTTATTTTTTGAAAAAGATGCCAAGA--ATGCAC 597
                         i    v    v v    --iv    i  v  i i        --  v  -
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATT--GATTTTCGACAAGGGTGCCAAGACCATTCA- 380

  chrX_121023033_    598 TGTGGGGAAGTGATTGTGTCTTCAGTAAATGATATTGGGAACACTGGATA 647
                         -i       ivi  v  v i    ii     i ii     vv        
  L1M4_orf2#LINE/    381 -ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_121023033_    648 TCCAAATGTAAAA---TAAAATTAGACCTGCATCTCACACCACATACAAA 694
                         ?   v   i    --- i  i  i    ivi i         i       
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_121023033_    695 AATAAACTCAAAGGGTATTAGAGACTT 721
                            v        iv v  i ?    i 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCT 506

Transitions / transversions = 1.43 (30 / 21)
Gap_init rate = 0.02 (5 / 221), avg. gap size = 2.20 (11 / 5)  

1371 25.18 1.19 1.19  chrX_121023033_121025079     1134  1554 (493)    L1M4_orf2#LINE/L1      488   908 (0)  

  chrX_121023033_   1134 CGAACTGTATCA-AGACTTAAATGTAAATTGTAAAACAA-AAAACTACTG 1181
                          i  v  v    -    i         ivvv      v -      vi i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_121023033_   1182 GAACAAAATATAGGGAAAAAGCTCCATGACATTGGCCTTGGGAATTACTT 1231
                            v    i     ?iv   v  i i    v    vi v  v   vii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_121023033_   1232 TTTGGATATAATGCCAAAAACACAGGCAACGAAAGCAAAACTAGATATGT 1281
                         i  i     i ii      i    i     i    v    v      vi 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_121023033_   1282 GGAATTGCATC-AAACTAAAAAGATTTGCACAGCAAAGGAAGCAATAAAC 1330
                         v i i v    -   i      vv    ii vv       vi v  v  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_121023033_   1331 AGAGTGAAGAGACAATCTATGTTATAAGAGAAACTATTTGCAAATCATAT 1380
                          i      i      i i iivv  ii      v                
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_121023033_   1381 ATCTAATAAGGGGTTAATATCCAAAATATATTAGAAACTAAAACAACTCA 1430
                             i       ii vi      i       v ii    vvv        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_121023033_   1431 ATAGAAAGAAAATAAATAACTTTAATT--AAAATAAGCAAATGACCTTAA 1478
                            iv  i  i i       -ii    --     ii     v  ii v  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAAC-CCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_121023033_   1479 CAGACATTTCTATAAAGAACACATACAAATGGCTAGCCAACAAGTATGTA 1528
                         i          vi      v i           ----   i   i ii i
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGC----CAATAAGCACATG 882

  chrX_121023033_   1529 AAGAAACACTCAACATCACTAATCAT 1554
                           i i ii          ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (64 / 41)
Gap_init rate = 0.01 (6 / 421), avg. gap size = 1.67 (10 / 6)  


2885 26.87 1.10 1.10  chrX_121027197_121029138      542  1449 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121027197_    542 TGGAAACTCATCTCATGCTCATGGATGGGAAGAATGAATATTGTGAAAAC 591
                               vvi   i    i        v      v v        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121027197_    592 AACCATACTGCCTAAAGCAGTTTGCATATTCAATGCAATTCCCATCAAGC 641
                         ii v     v  i   viii i i  v      i     i  i     i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chrX_121027197_    642 ATGCCATCATCATCCTTCACAGAACTAGAAAAATCCATTGCAAAATTCAT 691
                           v   v vv v ii  ii     v v  v  iiiv  ivi         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_121027197_    692 ATGGAACCAAAAAAAACCCCACATAGCCGAAGCAATGCTAAGCAAAAAGA 741
                               viiv  iii    viv      i  i    vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_121027197_    742 -TGAATCTGCAGGCATCACATTACCTGACTTCAAATTATGCTACAAGGCT 790
                         -ii  vi  v   vv     i v  ii i      viv i      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_121027197_    791 GTAGTTACCAAAACAGCATGGTACTGGTATAAAAATAGGCATACAGACCA 840
                         ii   v i   i    ii         i    ii    i    i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_121027197_    841 ATGGAACAAAATACAGAATGTGGAAATAAAGCCAAATACTTACAGCCAAC 890
                               i i   vv   i vii        v   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_121027197_    891 TGATCTTTGACAAA----CCATATGAAAACATAAATTGGGGAAAGGACAC 936
                             i  i     i----   ---- i v   vv v         i i v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGAAAGAATAG 395

  chrX_121027197_    937 CCTATTCAATAAATAGTGCTGGGAAAATAGGCAAGCTACATGTAGAAGAA 986
                         i  v     i    i         v  iv  vv ? i     i i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_121027197_    987 TGAAAGTGGATCCCCATCTCAC--CTTATACAAAAATCAACTCAAGATGG 1034
                             iv    i   i i     -- v           i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_121027197_   1035 ATCAAAGACTTAAATTTAAGACCTGAAACCATAAAAATTCTAGAAGATAA 1084
                             ?    i     v     v  i    i      v ii       v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_121027197_   1085 CATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAACTACTTCATGACCA 1134
                            v  ?iv  vi    vv   v    v        ivii   v iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_121027197_   1135 AGA-ACCCAAAGCAAATGCAACAAAAACAAAGATAAATAGATTGGAATTA 1183
                         v  -   v      v v         iv   i   i   i      v  v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_121027197_   1184 ATTAAACTAAAAAGCTTATGTGCAACAAAAGAAATAAT-AGGCAGAGTAA 1232
                           i   v v    i   v     vv    i  v iv  - i - i   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGA 694

  chrX_121027197_   1233 ACAGACAACCCACAGAATAAAAGAAAATCTTCTCAAACTAAGCAACCAAC 1282
                          v                iii       v  iv    ii vii v ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_121027197_   1283 AAAGTACTAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAAGAA 1332
                           i v   vi          v  i  i      vv    v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_121027197_   1333 AAAAA-AATTAACGATCCCATTAAAAAGTGGGCTAAGGATATGAATAGAC 1381
                            i -  v    ---  v   ?    i     v      v         
  L1M4_orf2#LINE/    795 AAAGACAAATAAC---CCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_121027197_   1382 AATTCTGAAAAGAAGATATGCAAACAGCCAACAAACATATGAAAAAAATT 1431
                          v    vv           i    ii     i  i  i       i - v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chrX_121027197_   1432 CTCAAAATCACTAATCAT 1449
                              v    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


2726 28.54 2.36 0.34  chrX_121090985_121095517.rev     3153  4042 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121090985_   3153 TGGAAACACATCCCA----CATGGGT----AGAATCAATATTGCGAAAAT 3194
                               v i      ----     i ----   v i       iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121090985_   3195 GACCATGTTGCC-AAATGCAATCTACAAATTCAATGCAATTCCCATCAAA 3243
                          i v  ii v  -    -ii       i      i     i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_121090985_   3244 ACGCCACCATCATTCTTCACAGA--CTTATAAAAATATCCTAAAATTAAT 3291
                          iv   v vv v  i  ii    --i v i  ivvv           v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_121090985_   3292 ATGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGA 3341
                               viiv  ii  v  v v         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_121090985_   3342 ACAAATATGGAGGCATCACACTACCTGATTTTAAACTATACTATAAGGCC 3391
                              vv      vv       v  ii    i   viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_121090985_   3392 ATAGTCACCAAAACAGCATGGTACTGTTACAAAAATTGTCACACAGACCA 3441
                          i   v i   i    ii        vi i  ii  v v  i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_121090985_   3442 ATGGAACAGAATAGAGAACCAAGAAATAAACCCAAGTACTTACAACCAAC 3491
                               i     v    ii v             vii i   iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_121090985_   3492 TGATCTTTGACAAAACAAACAAAAACA-------GAGAAGGGACACCCTT 3534
                             i  i     iivviv   i v  ------- i   i i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_121090985_   3535 TTCAACAAATGGTGCTGGGATAATTGGCTGGCAACATGTAGGAGAATGAA 3584
                                             i  i   v i? v     i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_121090985_   3585 ACTGGATCTTCATCTCTCATATTATACAAAAATTAACTCAAGATGGATTA 3634
                         ii    i iii i   v  ivv                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_121090985_   3635 AGGACTTAAACCTAAGACCTGAAACCAGAAATATTCT-AATAGATAACAC 3683
                         ?i   i    iv     v  i    i v   - i   - iv   v    i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACAT 548

  chrX_121090985_   3684 TGGAAAAACTCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGA 3733
                         v  ?iv  v     vv   v    v        v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_121090985_   3734 AGCCAAAAGCACATGCAATAAAAACAAAGATAAATAGCTGAAGCCTAATT 3783
                         vi           v    i    iv   i   i   iv viii i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_121090985_   3784 AAACTAAAGAACTTTTGCACGGGAAAAGGAACAGTCAGCAGAGT--AAAC 3831
                            v v  i        ii vvv   i iv  vi   iv i   --   v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_121090985_   3832 ACAACCTACAGAGTGGGAGGAAATCTTCACAATCTATACATCTGACAAAG 3881
                               i     i      i    v  ii   vii   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_121090985_   3882 CACTAATATTCAAAATCTACAACAAACTCAAGCAAATCAGTAAGAAAAAA 3931
                         v   vi   i  i   v  i  vi     vvi   v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_121090985_   3932 ACAAAAAATACCATCATAAAGTAGGCTAAGGACATGAATAAACAATACTC 3981
                              v  iv v  i?v   i i   v     iv      i   v v   
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_121090985_   3982 AAAAAAAGATATGCTAATGGCCAACGAACATGTGAAAAAAATGCTCAGCA 4031
                         v   i       i v         ii i  ii      i -      i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACA 897

  chrX_121090985_   4032 TCACTAATGAT 4042
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (152 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.40 (24 / 10)  


2971 26.24 0.32 2.27  chrX_121120032_121124406.rev     2959  3884 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121120032_   2959 TGACAAAATATTCCATGTTCATGGATTGAAAGAATTAATATTGTTAAAAT 3008
                           iv  i    i                i    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121120032_   3009 GTCCATACTACCCAAGGCATCCTATGGAATCAATGCAATCCTTATCAAAA 3058
                          v v     v     iviivi   ii  v    i       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121120032_   3059 TACCAATGACATTCTTCACTTAAATAGAAAAAAAAAATCTTAAAATTTAT 3108
                          v   iivi v  i  ii vv    v  v  ivvi -  i       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_121120032_   3109 ATGAAACCACAGAAGACACAGAATATCCAAAGCTTTCATAAGCAAAACAA 3158
                            i  vii  iii   v       v     i vv  v i iv  i - i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA-AG 198

  chrX_121120032_   3159 AACAAAACAACTGGAACAATCACATTATCTGACTTCAAATTTGAAGCTAT 3208
                               ii---    iv v     i vi ii i      vi v --   i
  L1M4_orf2#LINE/    199 AACAAAGT---TGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTAC 243

  chrX_121120032_   3209 AGAGCTATAGTAACCAAAACAGCATGATACTGGCATAAAAACATGATACT 3258
                          i     i     i   i    ii  i           i-----    --
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-----GATA-- 286

  chrX_121120032_   3259 GGCATAAAAATAGACCAATAGAACAGAATTGAGAACCCAGAAGCAAATCC 3308
                          i    ----    i    i   i          ii      ii   i  
  L1M4_orf2#LINE/    287 GACATA----TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_121120032_   3309 ACACACCTACAGTGATCTTATTTTTGTTAAAGGTGCCAAGAACATACACT 3358
                          i   ii  ii  v vi v     i vi  i          v   v  v 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_121120032_   3359 GGAGAACAGACAGTCTCTTCAGTAAATGGTGCTGGGCAAACTGGACATCT 3408
                           i   vii i     i    ii             vv       i ? i
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_121120032_   3409 GTATGCAAAAGAATAAAACTACACCCCTATCTCTCACCATATACAAAAAT 3458
                         ii            i  ii iv       i   v                
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_121120032_   3459 CAAATCAAAATAGATTAAATACATAAATCTAAGACCTCAAACTCTGCAGC 3508
                         i  v       i   i ? v  v     v     v  v     v iv i 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_121120032_   3509 TACTACAAAAAAAAATTTCAGAAAATCTCCAGGACATTGAACTGGGAAAA 3558
                          vi  v  i    v  vvv? v      i iv   v   iii i  v  v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_121120032_   3559 AATGTCTGGAGTAATACTCTACAAGCACAGGCAACTAAAGCAACA-TGTA 3607
                         ii v   viii  vv  v i v       i     v    v  v - iv 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_121120032_   3608 CAAATGAGATCACAGCAAG-TTAAAAAGCTTTTGCACGATAAAGAATACA 3656
                         i    vi  iiv  v   i-       -      ii vvi    i i  v
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT 681

  chrX_121120032_   3657 ATCAACAAAGGGAAGAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 3706
                              v    v   i                                   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_121120032_   3707 CTACCCATCTAACAAGGAAATAATAACCAGATTATATAAAGAGCTCAAAC 3756
                         ii ivi    i i    i v vi  v     v          i   vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_121120032_   3757 AAATGTATAGGGAAAAAATTATAATAATCACATCAAGAAATGGGCTAAAA 3806
                           v vv   ivi    i i- -     i vv  i? i        v  ii
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGAC-A-AATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_121120032_   3807 ATTTGAATACACATTTCTCAAAAGAAGATATACAAATAACAGACAGGCAT 3856
                                  v         v                 ii vi i i   i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_121120032_   3857 ATTAAAA-ATGCTCAAAATCATTGATCAT 3884
                           v    -        v    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


3358 20.98 3.55 3.11  chrX_121135830_121138773.rev     1553  2453 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_121135830_   1553 AAAAGTACATCATGTTCAAGGATTGAAAGACTTAATAATTCTAGAATGGC 1602
                            ii  ivi        v      i           v vi  ii     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_121135830_   1603 AGTACTGCCCTATTTGATCTGCAGATTTAACACAATTCATGTCAAAATAC 1652
                          i    v   v v       i      i   i    i v i       v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_121135830_   1653 CAAATACATTTTGTGCAGTAATTGACAAATTAAATTTAAA-TGTATATAA 1701
                           iv i v    v     v         ii i vii    - vi    ii
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_121135830_   1702 AAATGCAAAGGATCCAAGTTAGCCAAAATAACATAAAAAAAAAAAAAGAA 1751
                                 i   i   iiv         i  iv vi     i  i  v  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_121135830_   1752 AAAAAAATGAAACTTTGGGGGACTCATATTTTCCACTTTTAAAACTAGTT 1801
                          i------------    i       i i  i   v   i      vii 
  L1M4_orf2#LINE/    204 AG------------TTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_121135830_   1802 TCAATGATGCAATAATGAAGACAGAGAGGTACTGACATAAGGATAGACAG 1851
                         v   v v i  i    v       v v       i              v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_121135830_   1852 GTAGATCAATGGAATAGAATTGAGAGTCTAGAAATAAACCCTAGAATACA 1901
                         i                           i            ----     
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC----ATACA 337

  chrX_121135830_   1902 ---A-GGTCAGTT-ATTTTCAACAAAGGTATAATGACTTTAAAAAGGAGA 1946
                         --- -     i  -      i    i   iiv v   iv vv  v  i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_121135830_   1947 AATAATATTCCTTTTAAAAGATATTACTGGGATAACTGGATATTTACATG 1996
                           v    v  i   i  v i  iv i      i         ?ii     
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_121135830_   1997 TAAAAGAATGAAGCTGGAGGCCTACCTTAAACAATTTACAGA--TTAACT 2044
                         i            i    vv       i v  v  v    i --      
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_121135830_   2045 CAAAATGGATCATAGACCCAGATGTAAGTGATAAAACTATAAAACTTATA 2094
                                     ?     i i       v v               iv  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_121135830_   2095 GAAGAAAAT-------TAACTTTTCATGACCTTGGTGTAGACAATTTTAT 2137
                                 i-------   v i   i         vv   i    vv v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_121135830_   2138 CTTGAATATGACAC--AAAGTGCAAGCCACAAAA------ATAAATGAAT 2179
                            ii         --    ii     v      ------   i  i   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_121135830_   2180 TGAACTACATCATA-TGAAAAACTTCTAAGCTGTAAA---TACCACCTAG 2225
                           i   v     v - v        i iv   vi   ---i  i i v  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_121135830_   2226 AAAATAAAAATATG--TCAGAGAATGAGGAAAAATATTATCAAATCATAT 2273
                            i i    v ii--i  v      i ii        vv          
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_121135830_   2274 ATCTAATAAAGGACTTATATCCTGCATATAAACAGAATGCTTACAACTCA 2323
                             i    i      i     v v     v v    iv           
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_121135830_   2324 GTAATGAAAAGATAGATGATAGCCTGAATTTTAAAAATGG-TAAATTACC 2372
                         i    i      i i  i ---  ii --  ?        -i   vv ii
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAA---CCCAA--TTWAAAAATGGGCAAAGGATT 832

  chrX_121135830_   2373 TGA-TAGACATTTCTCCAAGGAGAGAT-TAAAAATGGCCAGTAAGAGATA 2420
                            -               i  -    -  v         i    -----
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGA-AGATATACAAATGGCCAATAAG----- 876

  chrX_121135830_   2421 CAAATGGCCAGTATGCTTAACTTCATTGGTGAT 2453
                           v   ivv  -     i   v   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (111 / 75)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 2.86 (60 / 21)  


2464 27.29 0.43 0.14  chrX_121146388_121148080      501  1200 (493)    L1M4_orf2#LINE/L1      207   908 (0)  

  chrX_121146388_    501 TGGAGGCATCACATTTCCTGATTTCAAACTATACTATAAGGCCACAGTCA 550
                               vv     i    ii        viv     i  i  i     v 
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_121146388_    551 CCAAAACAGTATGGTATTGGTATAAAAATAGGCACATAGGCCAATGGAAC 600
                         i   i     i     i   i    ii    i  i    ii        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_121146388_    601 AGAATAGAGAACCCAGAAATAAACCCAAATATTTACAGCCAACTGATCTT 650
                              v    ii               v i     ii i   i    i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_121146388_    651 TGACAAAGAAAACGAAAACACAAAGTGAGGAAAAGACACCCTTTTCAACA 700
                         i     i iviv i i v  ivv i  i     ii i vi          
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_121146388_    701 AATGGTGATGGAATAATTGGCTAGCAACATGTAGGAGAATGAAACTGGAT 750
                                v   i i  i   v  ? v     i ii        ii    i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_121146388_    751 CCTCATCTATCACCTTATACAATAACTAACTCAAGATGGATTAACGACTT 800
                           ii i  vv    v       v  i        i      i ?v   i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_121146388_    801 AAACCTAAGACCTGAAACTGTAAAAATTCTAGAAGATAACATTGGAAAAA 850
                            iv     v  i     i     v ii       v     v  ?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_121146388_    851 CCCTTCTAGACATTGGCTTAAGCAAGGATTTCATGACCAAGAACTCAAAA 900
                         vi    vv   v    v   i    v i    v iivi v  vvi     
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_121146388_    901 GCAAATGCAATAAAAACAAAGATAAATAGCTGGGACATAATTAAACTAAA 950
                            v v    i    iv   i   i   iv v    v v  i   v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_121146388_    951 GAGCCTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAACAGATAACCTA 1000
                         i i i    iiivv    i iv  vi   iv i   i  v   i    i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_121146388_   1001 CAGAGTAGGAGAAAATCTTCACAATATATACAAGTGACAAAGGACTAATA 1050
                             i i         v  ii   vvi   i vv   i  i     vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_121146388_   1051 TCCAGAATCTACAACCAACTTAAACAAATCAGTAAGAAAAA---AAATCA 1097
                                 v  i  vv    ivv    v   i   v     ---    - 
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT-A 805

  chrX_121146388_   1098 ATCCCGTTAAAAAGTCGGCTAAGGACATGAATAGACAATTCTCAAAAGAA 1147
                          i  vi  ?    i v   v     iv          v     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_121146388_   1148 GATATACAAATGGACAGCAAACATATGAATAAATACTGAACAACACTAAT 1197
                                      v  ii  i  i     v i  i  v    v  ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_121146388_   1198 GAT 1200
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.46 (111 / 76)
Gap_init rate = 0.00 (2 / 702), avg. gap size = 2.00 (4 / 2)  


2842 26.77 2.10 1.66  chrX_121153894_121160065.rev     4778  5681 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121153894_   4778 TGGAAAAACATTCCATGTTCATGGATAGGAAGAATCAATATCGTGAAAAT 4827
                               i i  i              v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121153894_   4828 GGCCGTACTGCCCAAAGTAATTTATAGATTCAATGCTACTCCCATCAAA- 4876
                            vi    v      v i  i  i        i  v ii  i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121153894_   4877 TCACCATGGACTTTCTACACAGAAGTAGAACAAACT-ACTTTAAATTTCA 4925
                           v viiv v    i -ii     i v  -   i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chrX_121153894_   4926 TATGGAACCAAAAAAGAACTCTTATAGGCAAGACAATTCTAAGCAAAAAG 4975
                                viiv  ii  v ivvv    v   i     ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_121153894_   4976 AACAAAGCTGGAGGCAC-CACGCTGCCTGACCTCATACTATACTACAATT 5024
                                i      -  -   i  v  ii ii   v viv        vv
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_121153894_   5025 CTACAGTTAAAAAAAAAAAAAAAAGCATGATACTGGTACCAAAACAGATA 5074
                                -------  vv  i v  ii  i      i iv ii i   i 
  L1M4_orf2#LINE/    248 CTACAGT-------AATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_121153894_   5075 TATAGACCA-TGGAATGGAACAGAGGCCTCAGAAATAATGTTACACATCT 5123
                               i  -      i   iv   ivii         vvii i    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_121153894_   5124 ACAACCATCTGATCATTGACAAACCTGACAAAAACAAGCAATGGGGAAAG 5173
                          iiii  vi    iv i     ivv  v   i v  vv            
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_121153894_   5174 GATTCCCTATTTAATAAATGGTATTGGGAAAACTGGCTAGCCATATGCAG 5223
                         i  vvi  v  i  i       ii     v      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_121153894_   5224 AAAGCTGAAACTGGACCCCTTCCTTACACCCTATTCAAAAATTAACTCAA 5273
                           iiv    ii         v   i     v   v               
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_121153894_   5274 GATGGATTAAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAA 5323
                         i      i ?    i    ii     v       i      vi i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_121153894_   5324 GAAAACCTAGGC---AATGCCATTCAGGACATAGGCATGGGCAAAGACTT 5370
                               v    ?---   -- -   iv   v v  vv i     v ii  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_121153894_   5371 TATGACTAAAACACCAAAAGCGATGGCAATAAAAGCCAAAATGGACAAAT 5420
                         iv iiv  vi           ivvi    i     vv     i  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_121153894_   5421 GGGATCT------AATTAAAGAGTTTCTGCACAGCAAAAGAAACTATCAT 5464
                         v   ii ------       i v   -  ii vv    i  v       v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAA 686

  chrX_121153894_   5465 TAGAGTGGACAGGTAACCTACAGAATGGGAGAAAATTTTTGCAATCTATC 5514
                         v i    i v  ii    i                 v       vii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_121153894_   5515 CATCTGACCACGGGCTAATATCCAGAATCTACAAAGAACATAAAGAAATT 5564
                         i      iv v  i  vi          v  i       vivv v  v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_121153894_   5565 TACCAGAAAAGAACAA----CCCCATCCAAAAGTGGGCAAAGGATATAAA 5610
                         v iv v    ii    ----   v  i?    i            v i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_121153894_   5611 CA--CACTTCTCAAAAGAAGACATTTATGTGGCCAACAAACCCATGAAAA 5658
                         i --  i     v        i  vi vi       i  i v        
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_121153894_   5659 AAAAGCTCATCATCACTGGTCAT 5681
                         i v-     v     ????????
  L1M4_orf2#LINE/    887 GAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.12 (34 / 16)  


2356 27.22 3.43 1.30  chrX_121186053_121190196     2809  3653 (491)    L1M4_orf2#LINE/L1       46   908 (0)  

  chrX_121186053_   2809 AAAATG---ATATTTCCCAAAGCAATCTACAGATTCAACAAAATTCCTCT 2855
                           i   ---   i i      vii               iv   i   v 
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_121186053_   2856 TAAA-TACCAA-TGTCATTTTCACAGAATTACTTTTAAGAAGTCAATTAT 2903
                         i   - v   i-  i v    ii     -- ---  i v   iii  iv 
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAA--A---TTGACAAGCTGATCCT 140

  chrX_121186053_   2904 AAGGTTCATATGGAACCCAAG-AAGAGACT--GAATAGCCAAATCAATCC 2950
                           ii           --- v -   i   i--           v     i
  L1M4_orf2#LINE/    141 AAAATTCATATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chrX_121186053_   2951 TAAACAAAATGAACAAAGCCTGAGACATCATATTACCCATCTTCAAGCTA 3000
                          i  v  i v        iiv   ivv   i i v    vi     iviv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_121186053_   3001 TACTACAAGGCTATAGTAACCAAAGCCACATGCTACTGGTAGAAAAATAC 3050
                                 i    i     i   ii viii  v      i v  ii   v
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_121186053_   3051 ACACATAGTTCAGTAAAACAGAATAGAGAATGTAGAAATAAATCCACATA 3100
                            i    v   i ii  i     v    i vi         i   i i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_121186053_   3101 CCTACAACCAACTGAACTTTGACGAAGTCTACAAAAATAAAT-AATGGAA 3149
                         ii  iiii   i   vi  i   -   vv i v  i iv v -     ii
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGAC-AAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_121186053_   3150 AAACTATCCTCTATTCAACAAATCTTGCTGGGGAAACTGGTTAGCCATTT 3199
                            vv  vv   v          vv       iv      v  ?   iv 
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_121186053_   3200 CCAGAATAATGAGACTGGACCCCTATCTCTCACCATACACAAAAATTAAC 3249
                         v  i  v     iii          i   v       i            
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_121186053_   3250 TAAACATTGAGTAAAGATGTAAATGTAAGACCAGAAACCAGAAAAGTCCT 3299
                          v  v  v  vi ?   iv           v vi    i v    v  i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_121186053_   3300 AAAAGAAAACCTAGGA--AAATTTTTCTGGACATTGGTCTAGGCAAATAA 3347
                          i        v    ?--    i  iv  -  v    vi       - ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAA-TGG 584

  chrX_121186053_   3348 TTTATGAG-TAAGACCTCAAAAGCAAATGTAACATAAACAAA----GACA 3392
                            v v  -  v   vi        v v i    v  iv   ----  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_121186053_   3393 AATAGGACATAATTAAACTAAAGTACTTCTGGACATAAAAAGAAGCAGTA 3442
                            v    v v  i   v v  iv    i  vi v v   i  vi vi v
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_121186053_   3443 AACAGATTAAACAGTCAACCTACAAAACGGAAATAAATATTTATGAACTA 3492
                           v i v i  v  v     i   i  i  i iv        iii  ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_121186053_   3493 TGCACCTGACAAAGTACTAATATCCAGAATCTATAAGCAATTT----AAA 3538
                          ii i    i  i v   vi          v     iv  i i----  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_121186053_   3539 TCAACAAGAAAAA----AATAACCCCATTAAAAAGTGGACAAAGGACTTG 3584
                             i  v     ----        v   ?    i   i       i   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_121186053_   3585 AACAGACAATTCTC---AAAAGACATAAAAGTGGTCAACAAACATATAAA 3631
                           i     v     --- i    i   v  i   i   i  i  i  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_121186053_   3632 AA--TGTACAACATTTCTAACTGT 3653
                           --  iv      iv????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (133 / 93)
Gap_init rate = 0.02 (19 / 863), avg. gap size = 2.11 (40 / 19)  


2902 23.98 1.15 6.47  chrX_121212680_121215834     1706  2664 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121212680_   1706 TGGAAAGATATTCCACGTTTATAAATTGGAAGAATTAATATTGATAAAAT 1755
                                    i   i   i  ii         v         v   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121212680_   1756 GTCCATGCTATGCAACGCAATCTACAAATTCAATGCAATCTCTATCTAAG 1805
                          v v  i  viv   vvii       i      i      i     v  i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121212680_   1806 TTCCAACGACATTCTTCACAGAAATAGAGAAAAGC--ATTTAGAAAATAT 1853
                          i   i vi v  i  ii       v  v  --  --  ii-v     vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCC-TAAAATTC 147

  chrX_121212680_   1854 ATAGGGAACTACAAAAGACCCAGAAGAGTCACAGTTATCCTAAGCAAAAG 1903
                            v    v i   ii         v  i  v iiv   i i iv  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_121212680_   1904 GAACAAAACTGGGGGAATGACATTACCTGATTTCAAA--TTACGTTGCAT 1951
                                ii   i   v v   i v  ii        --    -- i  v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAA 245

  chrX_121212680_   1952 AGCCATAACAAAATCTGATGAAGATAGAGAGTATATTGGTATTTTTATGA 2001
                            i i -------------------------------------------
  L1M4_orf2#LINE/    246 AGCTACA------------------------------------------- 252

  chrX_121212680_   2002 CAGTGTCATAGTGTAACCAAAACAGCATGACACTGGCATAAAAACAGACA 2051
                         ------------    i   i    ii  ii          ii i     
  L1M4_orf2#LINE/    253 ------------GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_121212680_   2052 CATAGAGCAATGGAACAGAATAGAAAACCCAGAAATAAATCCACACACCT 2101
                         i     v        i     v  i ii           i   i   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_121212680_   2102 ACAGTGAACTCATTTTTGACAAAGGTGCCAAGAACATACACTGGGGAAA- 2150
                          ii  v  i v     i     i          v   v  v        -
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_121212680_   2151 AACAGTCTTTTAAATAAATGATGCTGATAAAACTGAATATCCATATGCAG 2200
                           i        v  i     i     iv v     i   ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_121212680_   2201 AAGAATGAAACTGGACCCCTATCTGTTGCCATATACAAAAATCAAATCAA 2250
                                  ii          i  vvii              i  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_121212680_   2251 AATGAATTGAAGACTTAA-TGTAAGATGTTAAACTATGAACCTTGTACAA 2299
                             i  ii?    i   -       vv v       i  v  iv  v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_121212680_   2300 CAAAACTTTGGGA-AACTCTCCAGAACATCGATCTGGGCAAAAATTTCTT 2348
                         v     v v  ?i-  v   i ivi  v i ivi i     vii      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_121212680_   2349 -GATCATAAACCCATAAACCCAGGCAATCC--TACAAAATGGACAACTGG 2395
                         -   -  i vv   v  i v  i    ivv--v v     i  i  v v 
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_121212680_   2396 GATTATATCAAG-TTAAGAATCTTCTGCACAGCAAAATAAACAATCAACA 2444
                           i vi     i-    i  -   i  ii vv    iv v  v     v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_121212680_   2445 AAGTGAAAGGACAACCCATAGAATGGGAGAATATATCTGCAAACTACCAA 2494
                                 i         i            v    i      ii ivv 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_121212680_   2495 TCTGACAAGAAATTAATAACCAAAATATATAAGCAGCACAAACAACTGTA 2544
                              i   ii i vi  v   i         iv i v vv      vv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_121212680_   2545 TAAGAAAAAAATTAATAATCCAATAAAAAACCAGGCAATATATTTGAATA 2594
                            v     i iv     i     v?    vii     viv         
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_121212680_   2595 GACATTTCTCAAAAGAAGACATAAAAATGGCAAATATGCAACTAAATAGG 2644
                                   v        i   v       v    v   vv i  v  i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_121212680_   2645 TGCTCAACATAATTGATTAT 2664
                                   v ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (132 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 5.21 (73 / 14)  


2266 28.27 3.22 2.55  chrX_121217399_121222803.rev     4013  4914 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121217399_   4013 TGAAAACACATTCCATGCTCATGGATAAGAAAAATCAATATCATTAAAGT 4062
                           i   v i  i     i        vi   i v i     ii    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121217399_   4063 GGCCAGACTGCCCAAAGCAAT-TATTGATTTAATGCTATTTCTGTTAAA- 4110
                            v v   v      vii  -  iv    i  i  v  ii  i i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121217399_   4111 CCACAATTGACATTCTTCACAGGATAGAAA--AAAAAACT-ATTGTAAAA 4157
                         i v  ii  v -  i  ii   -----   --i v  i  -  iv     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAG-----AAATTGACAAGCTGATCCTAAAA 144

  chrX_121217399_   4158 TTCACATG--AACCCAAAAAGAACCAAAACATTCAAATCAATTATAAGCA 4205
                             i   --  iv   ii-  v   i  i vi    v    iv i iv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_121217399_   4206 AGAATAACAAAGCTGGAGGCATTATGCTACCTGACCTTAAACTATACCGC 4255
                             v       i      vv i ii  v  ii ii i   viv   ii 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_121217399_   4256 AGGGCTACAGTAACCAAAATAGCATGGTACTGGTGCA-AAAAACAGGCAC 4304
                          ii          i   i i  ii         --  -  ii i  i  i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGG--CATAAGGATAGACAT 291

  chrX_121217399_   4305 ACAGACCAATGGAACAGAGCAGAAAACCCAAAAATAAGACCATACACCTA 4354
                          i   i        i   iiv  i ii   i      iv       ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_121217399_   4355 CAGTTATCTGATCTTTGACAGACCTGACAAAAACAAGCAATGGAGAAAGA 4404
                         ii  i vi    i  i    iivv  v   i v  vv      i      
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_121217399_   4405 ATTTCCTACTCAATAAATGGTACTGTAATAGAATAACTGGCAAGCCATAT 4454
                           vvi  vi    i       i   ----- i i      vv ?   i  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTG-----GGACAACTGGATAKCCACAT 436

  chrX_121217399_   4455 GGAGAAGATTGAAACTGGATCCTTTCCTTGCCCCATATACAAAAATCAAC 4504
                          v i    v    ii    i  i v   ii v              i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_121217399_   4505 TCAAGATAGATTAAAGACTTAAATGTAAAACCCAAAATGA-AAAGCCCT- 4552
                             i  i   i ?    i         i v i    iv -   i i  -
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_121217399_   4553 AGAAAACAACCTAGGCAGTA--CCATTCAGGACTTAGGCACGGGTAAAGA 4600
                             i v   v    ?-   --i -   iv   i v  vvii  i  v i
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_121217399_   4601 TTTTAT-GATGAAGATGCCAAAAGCAATTTCAAGAAAAGCAAAAATTGAC 4649
                            iv -   - v  ii         vvvv   v     v      v  i
  L1M4_orf2#LINE/    585 TTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_121217399_   4650 AAGCAGAACCTAATTAAGGTAAAGAGCTTCTGAACAGGAAAAGAAATT-T 4698
                           iiv i  i v  i  ii v  i i   i  vi vvv   i  v i - 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_121217399_   4699 ----AGAGTAAACTACACAACATACATAGTGGGAGAAACTTTTTGCAAAC 4744
                         ---- i   i  v- v     vi   v i         v v        i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_121217399_   4745 TATCTATCTGACAAAGGTGTAATATCCAGCATCTGTAAGGAACT--TA-A 4791
                         i  v       i  i  vv vi       v  v i   i     --  - 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_121217399_   4792 ATTCAA-AAGAAAAA---AAATG--CCA--TAAACAAATGGGTAAAAGTC 4833
                          i    -  v     ---    i--   -- ?  -       i   i vi
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGAT 831

  chrX_121217399_   4834 ATAAACAGACACTTTTCAAAAGAAAAGTGTCATTCATGTGGCCAACAATC 4883
                         v i  i     i  i  v      i ----i  v  vi       i  v 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGA----TATACAAATGGCCAATAAGC 877

  chrX_121217399_   4884 ATATGAATAAAAGTTCAACATCACTGATCAT 4914
                          i     v i v i         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (161 / 90)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 1.79 (52 / 29)  


 229 29.73 0.00 1.35  chrX_121226863_121229750     1210  1283 (1605)    L1M4_orf2#LINE/L1        1    73 (835)  

  chrX_121226863_   1210 TGAAGACACACACCTTGTTTACGGTTTTGAAAGACTCAAAATTGTTAACA 1259
                           i i v i iv  v    i i  v-   i      i  v        v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGA-TTGGAAGACTTAATATTGTTAAGA 49

  chrX_121226863_   1260 TGCTAATTTTCTTCAAAGTGATTT 1283
                           vi   vi  ii    v    i 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCT 73

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1)  

2252 26.26 5.40 1.35  chrX_121226863_121229750     1581  2395 (493)    L1M4_orf2#LINE/L1       61   908 (0)  

  chrX_121226863_   1581 CCCAAAGTGATCTACTGATTTATCATAATTCCAATCAAAATTCTAAAGGA 1630
                               v        v    i v ii   i  v        i i ivv v
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_121226863_   1631 AATTTTTTGCATAAATTGGCACACTGATTATAAAATGCACACTGAAATGT 1680
                         v-         v      i  vi     iv      v  i iv      i
  L1M4_orf2#LINE/    111 C-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_121226863_   1681 AACGGAACTGGAATAGTTAAAATTAAGTTTTGAAAAAGAG---CAAAGTT 1727
                           v   v ii      ii    i-- i i          i---       
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAAC--AATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_121226863_   1728 TAAGGACTAACTTTACCTCATTT-AAGACTTATTATAAAGCCA-AATACT 1775
                         vi      v  vi v  iv    -  i     i  i     i - i  v 
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_121226863_   1776 CAATATAGTGCGCCATTTAACA-AAAAATTGACAAAGAGATCAGCAGAAC 1824
                            v i    i vi i -ii  -  ii  v    v v      iii   i
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACT-GGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_121226863_   1825 AGGATAGAGAG-ACAGAAATGGACCCACACATACATATAATTCAGTTAAT 1873
                           i  v     -v       ii     i    v--   ii -  i  i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGT-CAATTGAT 353

  chrX_121226863_   1874 TTTTTATGAAAATATAAAGACAATTCATTGGAGAAAGA-----TTTTTTA 1918
                            iv ii iii iiv     v     v   i      -----i    i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_121226863_   1919 ACAAATATTTCTGAAACAACTCAATAATTATATTTAAACG--TGAAAC-A 1965
                               iv v   ii      vi   ?ii i  vi   v --    ii-i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_121226863_   1966 TATCCATAACCCACACCATACACAAAAATTAAAT-AAAATGGATTTTAGG 2014
                         v i  v  v i         i           v -         iv?  i
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_121226863_   2015 TCTAAATGTAAAA-CTTAAATCGTAAGACT--TATAAAAACTCATAGAAA 2061
                         i          i -  v   iii   i   --  v  i  vv     i?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_121226863_   2062 -AAATCTTTATGATCTTTGGTTAGGTAAATATTTTGCAGGCATATGAC-- 2108
                         -       ii   i   v       i  vvi   ivi  --       --
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG--ATATGACAC 601

  chrX_121226863_   2109 CAAAAGCACAATC--CAAAGAAAAAAATTGATAAATCAGAATTCATCAGA 2156
                                    v --    ii       v       ii  v       i 
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_121226863_   2157 ATGTAAAACTTTGGCTGTTGACAATGCAC-CCAT-AAGAGAGTGAAAAG- 2203
                           vv        v -  i v-   v v  - i  -    i         -
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTG-TGCTT-CAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_121226863_   2204 CAAGCCACAGACTAGGAGACCATATTTGCATATCATATTT---------- 2243
                            v       v i     vv         v       v ----------
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_121226863_   2244 --TCACATGCAGAATATATTAATACCTCTCAAAACTTAATGAGGAAACCG 2291
                         -- iii  v          v  v v    i v    i   i vi   vvi
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_121226863_   2292 CAA----TTCAGTAAATAAA-GAGAAAAGGATGTTAACAGGCACTTCTCA 2336
                            ----ii  i v? v   - i v       v v  i  i  i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_121226863_   2337 CAGGAAGATATCTGGATGACACATAAGCTCATGAAAAAATGTTCGAAATC 2386
                         v i        viii   i vv      v        i   i  i v   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_121226863_   2387 ATTAGTCAT 2395
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.44 (124 / 86)
Gap_init rate = 0.03 (28 / 848), avg. gap size = 1.96 (55 / 28)  


 543 23.28 0.86 0.00  chrX_121230896_121236939.rev     4344  4459 (1585)    L1M4_orf2#LINE/L1        1   117 (791)  

  chrX_121230896_   4344 TGGAAAGATATTGTGTGTTCACAAATTGAAAGAGTTAATATTGCTAAAAT 4393
                                    ivii      iii    i    v         i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121230896_   4394 GGCCATACTACCAAAAGCAATCTAGAGATTTGATACAATCCCTATCTAAA 4443
                            v     v  v   vii     v     ii ii           v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121230896_   4444 TTCCAA-TACTTTTTTT 4459
                          i   i- i i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT 117

Transitions / transversions = 2.38 (19 / 8)
Gap_init rate = 0.01 (1 / 117), avg. gap size = 1.00 (1 / 1)  

2488 28.87 0.62 0.74  chrX_121230896_121236939.rev     4747  5553 (491)    L1M4_orf2#LINE/L1      103   908 (0)  

  chrX_121230896_   4747 CCAG-TGTCACTCTTCACTGAAATAGAAAAAACAATCCTAAAATATATAC 4795
                             -  i -i i  ii v     v  v  ivii          vi   i
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_121230896_   4796 GGAATCACAAAAGACCCAGAATATCCCAAGCTATCCTGAGCAAAAAGAGC 4845
                             vii   ii           v  v  i v   i   iv  i    i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_121230896_   4846 AGAGCTGAAAGAATCACACTACTTGACTTCAAA--TTACATTATAGAGTT 4893
                          i  i  i i  v       v iii i      --    --  i i  i 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAGCT 249

  chrX_121230896_   4894 AAAATAACCAAAGCAGCATGGTACTGGCAAAAGAACAGACACATAGACTG 4943
                          v i   i   ii   ii           v   i i     i     iii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_121230896_   4944 ACGGAACAGAATAGAGAACCCAGAAATACATTCACAGAGCTACAGCGAAC 4993
                          i    i     v    ii         v ii  i v vi  ii iv  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_121230896_   4994 TCATTTTCAAAAAAGCTACCAAGAACATAGACTGGGTAAAAGAGAGCCTC 5043
                          v      i v  i v i      v   vv v    v   ii v  i  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_121230896_   5044 TTCAATAAATGGTGCTGGTTAAACTGGATATCCTTCTGCCAAAGAATGAA 5093
                              i            vvv         ?  viv   v          
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_121230896_   5094 ACTTGGTCCATAACTCTCACCTTATACAAAAATCAAATTCAAATGGATTA 5143
                         ii v ii  v  v   v    v           i  v iv        i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_121230896_   5144 AATACTTAAAATTAAAACTTTAGTCTATGAAACTGCTACATGAAAACATT 5193
                         ? v  i    vv   i vi v iv    i     vi  v v        v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_121230896_   5194 GGAGAAACTCTCTAGGGCATTCTTCTGGGAAAAAATTTCTTGAGCAATAC 5243
                           ? v  v   iiiv i v  vvvi i  v  vii      iiii vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_121230896_   5244 CCCACAAGCACAGGCAACCATACAAAAA-TGGACAAACAGGATCACATCA 5292
                         v   v       i     v v v     - i  i   iv   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_121230896_   5293 AG-TTAAAAGCTTCTGCACAGCAATGGAAACTATCAACAAAGTCAAGAGA 5341
                          i-      i   i  ii vv   v   v        v     v  i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_121230896_   5342 CAAATATTATATTGTGGGAGAAAATATTTGCAAACAACCCATCTGACAAG 5391
                            vi--i i vvi                    iv ivi      i   
  L1M4_orf2#LINE/    700 CAACC--CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_121230896_   5392 GGATAAACAATCAGAATATGTAAAGAGCTCAAACAACTCTGTAGGGAAAA 5441
                            ivvii vi        i      i   vv       vi  ivi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_121230896_   5442 AATGTAATAATTTGATCAAAAAATGGTCAAAATATTTGAATAGCTATTTC 5491
                         i ii-     iiii  i?        v    iv          vi     
  L1M4_orf2#LINE/    798 GACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_121230896_   5492 TCAAAAGAAGGTATACAAATAGCAAACAGGTATATGAAAAGGTGATCATC 5541
                           v       i         i  v  i i i i        i  v   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_121230896_   5542 ATTAATCATTAG 5553
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.01 (8 / 806), avg. gap size = 1.38 (11 / 8)  


3086 25.99 3.52 0.45  chrX_121248579_121251074.rev     1125  2005 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121248579_   1125 TGGACAAATAAACCATGTTCATGGATTGAAAGAATTAATATTGTTGAAAT 1174
                             v i   vv                i    v           i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121248579_   1175 ATCCATATTACCCAAAGCAATCTATGGATTCAGTGCAAACCTTATCAAAA 1224
                         iv v   i v      vii     ii      ii    v  i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121248579_   1225 TTCTAA-TGTCATTTTTTACAAAAATAGAAAAAACAAAAATGATAATTTA 1273
                          i i i-  i -      i  i    v  v  ivii vvv i -    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAA-AATTCA 148

  chrX_121248579_   1274 AATGAAATTCCAAAAGACCCTGAATAGCCAAAGCTATCTTGAGCAAAAAT 1323
                         v   i  v v   ii     v           i v       iv  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_121248579_   1324 AACAAAGCTGGAGACATTATACTACCTGACTTCAAACTATATTACAAAGC 1373
                                i     ivv i i   v  ii i      viv  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_121248579_   1374 TATACTAATTCAATA-GGCATGACAAAGGCATAAAAACAAACATGTTGAG 1422
                           i v    -   v -i ii  ii vv       ii i i    i v  v
  L1M4_orf2#LINE/    249 TACAGTAAT-CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_121248579_   1423 CAATAGAGCTGGATGGAGAGCCTGGTAATAAACCCACACATTTATGGTTA 1472
                             i  iiv i  v     i ii v          i           i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_121248579_   1473 ATTGACTTTCAACAAAGGTGCAAAGGACACACAATAGAGAAAATAAAGTC 1522
                              i    i    i     v   iv  iv    i i    iv v    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_121248579_   1523 ACTTCAATAAATGGTGTTGGGAAAACTGGATAGCC--------------- 1557
                         vi     i        i     v         ?  ---------------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_121248579_   1558 ----------CTTATCTCATACCATGTATGAAATTCAACTCAAAATGAAC 1597
                         ---------- i  i    i     i  ii   v i           i i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_121248579_   1598 TAAAGATGGAAGCATAAAACTTGAAACTGTGAAATTACTAGAAGAAAACA 1647
                         i ?   ivv  iii   i vi i     i i   i vi            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_121248579_   1648 GGGAAATA---CTCCACAACAATGGTCTGGACAATGATATTTTGGATATG 1694
                         vi i?i  ---  i iii  vv   vi i i     i v i  i      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_121248579_   1695 ACCTCAAAAGTACAGGCAACAAAAGCAAAAATAAACAAATAGGACCACAT 1744
                           vi      i   i          v       i i    v    iv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_121248579_   1745 -AAAACTAAAAAGTTTCTGCACAGCAGAGGGAACAATTAACAAAGAGAAG 1793
                         -    i      v   -  ii vv  i   iv  v  i  v    v   i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_121248579_   1794 AGAAAACACTCGTATTGTGAGAAATTAGTTGCAAATCAAACATTTGATGA 1843
                            v   v v iv v  v      v  v          v i  i    i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_121248579_   1844 TGGGCTGTTATTCAAAATATATGAGAAACTCAAACAACTCAATAGCAAGT 1893
                         v  i  vv   i  i       i ii     vv           ii  iv
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_121248579_   1894 AAACAAATATCCCAATTAAAAATTGAGCAAAGGACCTGAATAGACATTTC 1943
                          i       v       ?    v  i        ii              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_121248579_   1944 TCAAAAGAACAAATACAAATGGCCAACAGGTATATAAAAAAATACTCAAC 1993
                           v      v v              i i i i  i    i  i      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_121248579_   1994 ATCACTGATCAT 2005
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (141 / 84)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.89 (35 / 9)  


2001 26.87 3.82 1.98  chrX_121288877_121290558.rev      485  1191 (491)    L1M4_orf2#LINE/L1      189   908 (0)  

  chrX_121288877_    485 GAAGAAAGAAAATAAAA----AGGCATCGTGCTACCTAACTTCAAACTAT 530
                            i  ii i  i   i----   vv  iii  v  i  i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_121288877_    531 GCTACAGGGCTACAGTAACCAACAGTAACCTAAACAGTATGGTGTGGGCC 580
                         i     ii          i   ----------i     i    iiv   v
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAA----------GACAGTGTGGTACTGGCA 278

  chrX_121288877_    581 TAAGTACGGACACATAGACCAATGGAACAGAATAGAGAACCAGGAAATAA 630
                             v ii    i     i        i     v    ii vi       
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_121288877_    631 GTTTGCACACCTACAACTGTCTGATCTTTGACAAACCTGAAAGAAACAAG 680
                         iiiiii   ii  iiiiiivi    i  i     ivv  vv ii v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_121288877_    681 CAATGGAGAAAGGACTCG-CTATTCAATAAATGGAGCTGGGATAACTGGC 729
                               i     i - v -  v     i      v       i      v
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAA-TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_121288877_    730 TCGCCATGTGCAGAAAATTGAAATTGGACCCCTCCCTTACACCATGTACA 779
                          v?   ii    i  i v    i          v   i       i    
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_121288877_    780 AAAATTAACTCAAGATGGAT--------TAAATGTAAAATACAAAACCAT 821
                                      i      --------         i vvi     i  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_121288877_    822 AAAAACCATGGAAGACAACCTAGGCAATACTATTCAGGACATAGGCATGT 871
                             vi v i     v   v    ?ivv v v   iv   v v  vv iv
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_121288877_    872 GTGAGGATTTCAT-GATGAAGATGCCAAAAGCAATTACAACAAAAGCAAA 920
                          ii v i    v -   - v  ii         vvvi         v   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_121288877_    921 AGCTGACGAAAGGAATTTAATTAAA-CTAAAAACCTCATGCACAGCAAAA 969
                          iiv  ii  vv i i  v  i   -i       i i-  ii vv    i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAG 675

  chrX_121288877_    970 GAAACTATCAACAGAGTAAA----CAGCCTACAGAATGGGAGAAAATTTT 1015
                           v        v i   i  ----  i  i                 v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_121288877_   1016 AGCAAACTATGCATCTGACAAAGGTCTAATATCAAGCAACTATAGGGAAC 1065
                         v     ii  ii      i  i  v  vi    v  v vv    ii    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_121288877_   1066 TTAAACAAATTTACAAGAAAAAAA-----AAGCCA-TTAAAAAGTGGGCA 1109
                          ivv    v iv i  v     i -----  v   -  ?    i      
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_121288877_   1110 A-GGACATGAACAGACACATCTCAAAAGAAGACATACATGTGGCCAACAA 1158
                          -   iv    i     iv    v        i     vi       i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_121288877_   1159 GCATATGAAGAAAAT-CTCAACATCACCGATTAT 1191
                            i     -  i  -          ????????
  L1M4_orf2#LINE/    876 GCACATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (113 / 74)
Gap_init rate = 0.02 (15 / 720), avg. gap size = 2.73 (41 / 15)  


 228 21.57 0.00 0.00  chrX_121293402_121297067.rev     2232  2282 (1384)    L1M4_orf2#LINE/L1        1    51 (857)  

  chrX_121293402_   2232 TGGAAAAACATTCTATGCTCAGAGATTGGAAGAATTAAAATAGTTAAAAT 2281
                               i i  i i   i   vi          v    v  v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121293402_   2282 G 2282
                          
  L1M4_orf2#LINE/     51 G 51

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.00 (0 / 0)  

2390 26.65 4.03 3.92  chrX_121293402_121297067.rev     2283  3175 (491)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_121293402_   2283 ATATTTAT---TTATAAAACTTAATCTTGTCATAAAATA-CAATAGTGCC 2328
                           i  i  ---  iv  i       v    --   i  i-     v v  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGT--TAAGATGGCAATACTCCC 62

  chrX_121293402_   2329 CAAAGCAATCTACATATTCAATCCAATCCCTATCAAAATACCAATATCAT 2378
                             vii       v      iv                v   iivv v 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_121293402_   2379 TTTTCACAGAATTACAGCAAAC-AATCTTAAACTTTATATGGAACCA-AA 2426
                             ii     v -iii   i -i   i    v  i        vii-  
  L1M4_orf2#LINE/    113 TTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_121293402_   2427 TAGACACCTGAATAGCTGCAACAACCCTAAGCAAAAATAACAAAACTTGA 2476
                         vi   -  v       iiv     i i i iv  i  v      ii v  
  L1M4_orf2#LINE/    162 GGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_121293402_   2477 GGCATCACATTATCTAATCTCAAATTATATTACAAGAACATAGTAACCCA 2526
                           vv     i vi i   i     viv  i     iivi i     i v 
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_121293402_   2527 G-CACTATGGTACTGGTATAAAAATAGACACATAAATCAATGGAACAGAA 2575
                          -  v i         i    ii       i   i          i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_121293402_   2576 TAGAGAACCCAGAAATAAAGTCACGTATTTATAGCCAACTTATCTTTGAC 2625
                          v    ii           vi  iii      i i   i v  i  i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_121293402_   2626 AAAAGCAATAAGAACATACACTGGGAAAAGGACACCCATTTTAAAAAACA 2675
                           ii iivi    v   v  v    i    i i vi v   i  v   ii
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_121293402_   2676 GATCTGGGAAAATTGGGT---------TAAA----TAAAACTGGACCTCT 2712
                          vv      v  i   i ---------i   ---- i  ii      i  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_121293402_   2713 ACGTT-CACCATATACAAAAATCAACACAAGATGGATTAGAGACTTAAGT 2761
                           v i-                i   v   i      i ?    i   i 
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_121293402_   2762 GGAAGATCAATTAGTACAAAAATACTAGAAGGAAACTTATGGAAAACTCT 2811
                          v    v v vv v  i    v vi      i    v  v ?iv  v   
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_121293402_   2812 TCTTTGCCATGG------CAAAGAATTCATGACTAT-ACCTCAAAAGCAC 2854
                           v vi  v   ------   v iv   v iiv   -  vi         
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_121293402_   2855 AGATAATAAAAACAAAAATAGACAAACAGGACTTGATTAAACTAGATAGC 2904
                          iii  i    iv         i   iv      v  i   v vi v i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_121293402_   2905 TTCTGCACAGAAAAATAGATAATCAAACATTTTCTGCACAGCAAAATAAT 2954
                           i  ii vvv   iv v iv     i----------------   ----
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAG----------------AAA---- 690

  chrX_121293402_   2955 CAGCAGTGTGAGCAGATAACCTGCAGAAAGGGAGAAAATATTTGCAA--- 3001
                         -------    iv   i    ii     v                  ---
  L1M4_orf2#LINE/    691 -------GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_121293402_   3002 -----TCTGACAGAGGACTAATATTCAAAATACACAAGGAATTCGAACAA 3046
                         -----     i ii     vi   i  i    i i  i   i  vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_121293402_   3047 TTCAACAACAGTAACAAACCAAATAATTCTATTAAAAATTTGATAAAGGA 3096
                         i    i  ---   v  iv       ii v   ?    v v ii      
  L1M4_orf2#LINE/    784 CTCAATAA---TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_121293402_   3097 CCTAAATAGATATTTTTTCAGAAGAAGACATGCAAATAGCCAAAAGACAT 3146
                         ii i      i    i i  -       i  i     i     v ii  i
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCA-AAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_121293402_   3147 GTAAGAAAATGCTCAACATTACTAATCAT 3175
                         i i i  i           i ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (149 / 86)
Gap_init rate = 0.02 (18 / 894), avg. gap size = 3.94 (71 / 18)  


2250 25.24 2.37 0.95  chrX_121342225_121345486      499  1132 (2130)    L1M4_orf2#LINE/L1      266   908 (0)  

  chrX_121342225_    499 TATGGCACTAGCATGAAAATAGGCACATAGATCAATGAAACAGAATAGAG 548
                          i   i   i    i ii    i  i           i  i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_121342225_    549 AACTCAAAAA----GCCACATATCTACAGCCAACTGATCTTTGACAAAGT 594
                          iii  i   ----v   i i  i  ii i   i    i  i     i v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_121342225_    595 TGACAAAAACATACACTGGG-AAAGGATGTCCTTTTCAATAAATGGTGCT 643
                           v   i v   v  v    -    i  ivi        i          
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_121342225_    644 GGAAAAACTGGATTTCCATATGCAGAAGAATAAAACTGGGCCCCTATCTC 693
                           i v        v?   i     i      i  ii   i      i   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_121342225_    694 TCACCATATACAAAAATTGACTCAAGATG--------ATTTAAATGTAAG 735
                         v                 i      i   -------- ii          
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_121342225_    736 AACTGAAAGTATTAAAATACTAAAAGAAAACATAGGGAAAACTCTTCTGG 785
                          i  i   v   v   v vi  i             ?iv  v     vv 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_121342225_    786 ACATTGGTCTAGATGAAGAATTCATAACTGAGAACTCAAAAGCACAAACA 835
                           v    vi   iii v iv   v  iv iv  vvi           i  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_121342225_    836 ACAAAAACAAAAATAGACACATGGGATTTAATTAAACTAGAAAGCTTCAG 885
                               iv         i v  v   i  v  i   v vi   i   iv 
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_121342225_    886 CACAGCAATAGAAATAATCAACAGAATGGACAAACAACCTAGGGAATGGG 935
                         ii vv   vi  v iv     v i i  i v i      i vi       
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_121342225_    936 AGAAAATATTTGCCAAATACACATATGGCAAGGAACTGATATCCAGAATT 985
                                      v  vi i i  v  ii    i   vi          v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_121342225_    986 TATAAGGAACTTAAACAACTCAACAAAAACAACAACAAAATAAATAACCC 1035
                              i     ivv         i  ------i  v  i i         
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAA------TAAAAAGACAAATAACCC 809

  chrX_121342225_   1036 CATTAAAAAGTTGGCAAAGGACATGTATAGA--TTTTTCAATATAAGGCA 1083
                         v   ?    i v         iv  v     --   i  v v v   ii 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_121342225_   1084 TACAAATGGTCAAAAAGCATGTGAAATAATGAACAACTTCACTTATCAT 1132
                                  i   v     ii     vi   vv    v   ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (94 / 63)
Gap_init rate = 0.01 (5 / 643), avg. gap size = 4.20 (21 / 5)  

2837 23.19 5.66 2.94  chrX_121342225_121345486     1897  2780 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121342225_   1897 TGTAGAGATATCCTGTGTTTATGGGTTGGAAGACTTAATATTGTTAAAAT 1946
                           v i        ii    i    i                      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121342225_   1947 GT---TAGTTCTCAAATTGATGTAGAAATTCAATACAATCCCAATCAAGA 1993
                          v---  v i i         v  v i      ii       v     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121342225_   1994 TCTCAGCAAGTCTTTTTGTAGAAATAGACAAGACAATTCTAAACTTCATA 2043
                           i    vivii      i      v      vii  i     v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_121342225_   2044 TGGAAATGTGAAAGATGTAGAATATTCAAGCCAAT-TTGAAAAAGAA--- 2089
                                 ii ii  ivi      vi   iv    -           ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_121342225_   2090 TGAAGTTGAAGGAATTACATGGCCCTATTTCAAGACTTACTATAAATCTA 2139
                         ii      i    v i   ivv   v       i        i   v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_121342225_   2140 CAGCCATAAATATAGTGTGTTATTGGCATAAAGACAGACGTGCTTATTAA 2189
                            iv  v  v i      v  i        i  i    i iivv  i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_121342225_   2190 TGGAACAAAATTAAG--TACAGAAATAGGCCGGCTATAAA---A-GGTCA 2233
                              i i    i  -- v        ii  ---i   v --- -     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACC---CATACATTTATGGTCA 347

  chrX_121342225_   2234 ATTGATTTTTTATAGAGATTCAAAGGCAGGTCAATGGGGAAAGGATAGTC 2283
                                  iv i ii i v v   i viv             i      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_121342225_   2284 TTTTCAAAAACAAATA-TACTGGAACATTTAAATATTCATATTCGAAAAC 2332
                                ---     i- i    i   vi ii   ?i  i  --------
  L1M4_orf2#LINE/    398 TTTTCAA---CAAATGGTGCTGGGACAACTGGATAKCCACAT-------- 436

  chrX_121342225_   2333 AAGAATGAACAAAAGAAAGAAGTCTCAATCAACACCATGCATCATAGACA 2382
                         --------i        v     - vi i vvi   vii  i    v   
  L1M4_orf2#LINE/    437 --------GCAAAAGAATGAAGT-TGGACCCCTACCTCACACCATATACA 477

  chrX_121342225_   2383 AAATTTAACTCAAAATG-ATCATAGGACTAACTGCAAGTGCTAAAACTAT 2431
                            v             -    ?  iv    v  i   v           
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_121342225_   2432 AAACTTCATAAAAGGAAAGATAG-TGTAAATCTTTATGGCCTTGGACTAG 2480
                            vi  v  i   i   v    -?         ii  i      ii   
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_121342225_   2481 GCAATGGTGTCTTAGATACAATAGCAAAAATATCATCTGTAAAATAACA- 2529
                                 v         ii i v     ii iv v vii    v  v -
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_121342225_   2530 -CTGATAAATTGGAGTTTATTAAAGTTAGGAACTTATGTTCTC---AGG- 2574
                         -iv           v  i  i   i   ii     v   v  i---   -
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_121342225_   2575 ------TAAGAAAAAGAAATGACAAGCCACTGACTTGG-GCAAACATTTT 2617
                         ------i      iv    v     v    v  v v  - v   i    v
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_121342225_   2618 TATTTCACATA----ATACTTAATTTGTATCCAAAATATGTAAAATAATC 2663
                         i vv   i   ----   vvvi i         i     i    iv v  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_121342225_   2664 TCAAAATTCAATAATAACAAAATAAATAATACAAT-AAATAACAGACAAA 2712
                          i v  i          v  i i      iv    -?  v  ii i    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_121342225_   2713 ATATTTAAACAGA--TTCAGCACCAAAGAAGATGTA----------ATAA 2750
                         iv    i  i   --  i-- v           i  ----------    
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTT--CTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_121342225_   2751 GCACATAAAAA-ATG---AACAATTAACCATTGA 2780
                               i    -   ---    - i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.58 (123 / 78)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.04 (76 / 25)  


2819 27.44 1.67 0.78  chrX_121352113_121358249      492  1391 (4746)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_121352113_   1391 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATTTCGTGAAAAT 1342
                               i i  i     i        v      v i   v i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_121352113_   1341 GGCCATACTGCCCAAAATAATTTATAGATTCAATGATGTTTCCATTAAGC 1292
                            v     v      v i  i  i        i vvi ii i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_121352113_   1291 TACCA-CTGTCTTCCTTTGCAGAATTAGAAAAAAACTAGTT-TAAATTTT 1244
                          v   -   i   i-         v v  v  i--  ii i-    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

C chrX_121352113_   1243 ATATGGAACCAGAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAA 1194
                                 viiv  ii  v  viv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chrX_121352113_   1193 GAACAAAACTGGTGGTAC-CATGCTACCTGACTTCAAACTATACAATAAG 1145
                                ii   v  -  -  ii  v  ii i      viv   v i  i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

C chrX_121352113_   1144 GCTACAGTAACAAAAACAGCGTGGTACTGGTACCAAAACTGATACATAGA 1095
                                   iv  i    i          i iv ii iv  i i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

C chrX_121352113_   1094 CCAATGGAACAGAACAAAGACCTCAGAAATAACACCACACATCTACAA-C 1046
                         i        i    ivi   vii         vv   i    i  iii- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

C chrX_121352113_   1045 AATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGAT-- 998
                            -    i  i     ivv  v   i v  vv            i  --
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

C chrX_121352113_    997 TCCCCATTATTAAAAGGTGCTAGGAGAACTGGCTAGCCATATGCAGAAAA 948
                           iii- i vi   v      i   v      v  ?   i     i  i 
  L1M4_orf2#LINE/    396 TCTTT-TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chrX_121352113_    947 CTGAAACTGGACCCCTTCCTTACACCTTATGCAAAAATTAACTCAAGATG 898
                         v    ii         v   i     v   i               i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chrX_121352113_    897 GATTAAAAACTTAAATGTAAAACCCAAAACCATAAAAACCACAGAAGAAA 848
                            i ? i  i         i v i     i      vi vi        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chrX_121352113_    847 ACCTAGGCA-ATACCATTCAGGACATAGACATGGGCAAAGACTTCATGAC 799
                           v    ?i- v i -   iv   v v ivv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

C chrX_121352113_    798 TAAAACATTGAAAGCAATTGCAAAAAACGCCAAAATAGACAAATGGGATC 749
                           vi   iii      vvv    v   v vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

C chrX_121352113_    748 TAATCAAACTAAAGAGCTTCTGCACGGCAAAAGAAAGTATCATTAGAGTG 699
                          v      v v  i i   i  ii vv    i  v v     vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

C chrX_121352113_    698 ATCAGGCAACATACAGAGTGATAGAAAAT-TTTTCAATCTACCTATCTGA 650
                          vv  i    vi     i  iv       -   v   vii iv       
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

C chrX_121352113_    649 CAAAGGTCTAATATCCAGAATCTACAAGGTACTT----AAAGGAATT-TA 605
                         i  i  v  vi          v  i  i v   i----  vvv   v-  
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

C chrX_121352113_    604 CAAAAAAAAATACCTCA-TCAAAAAGTGGGCAAAGGATATGAACAGACAC 556
                         v   i v     v i  - i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

C chrX_121352113_    555 TTCTCGAAAGAAGACATTTATGCGGCCAAGAAACATATGAAAAAA-ACTC 507
                              v        i  vi vii      v  i  i       i -i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

C chrX_121352113_    506 ATCATCACTGGTCAT 492
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.29 (22 / 17)  

3117 27.07 0.99 0.66  chrX_121352113_121358249     4740  5644 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121352113_   4740 TGGAAGAGCTTTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAGT 4789
                              iiiiv i     i      i v      v i     i  v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121352113_   4790 GGCCATACTGCCCAACGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4839
                            v     v     vv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121352113_   4840 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4887
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_121352113_   4888 TATGGAACCAATAAAGAGCCC-GCATTGCCAAGTCAATCCTAAGCCAAAA 4936
                                vii-i  i ii   - v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_121352113_   4937 GAACAAAGCTGGAGGCATCAAACTACCTGATTTCAAACTATACTACAAGG 4986
                                 i      vv   v   v  ii        viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_121352113_   4987 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5036
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_121352113_   5037 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5084
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_121352113_   5085 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGGAAAGGATT 5134
                         i vi    i  i     ivv  v   i v  vv        -    i  v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chrX_121352113_   5135 CACTATTTAATAAATGGTGCTGGGAAACCTGGCTAGCCATATGGAGAAAG 5184
                         vv  v  i  i              v v    v  ?   i   v i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_121352113_   5185 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5234
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_121352113_   5235 GATTAAGGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5284
                            i ?i   i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_121352113_   5285 ACCTAGGCCTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5334
                           v    ?v v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_121352113_   5335 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5384
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_121352113_   5385 AATTAAACTAAAGAGCTTCTGCACAGCCAAAGAAACTACCATCAGAGTGA 5434
                         v  i   v v  i i   i  ii vv v  i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_121352113_   5435 ACAGGCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGAC 5484
                          v  i     i   iv            v  ii   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_121352113_   5485 AAAGGGCTAATACCCAGAATCTACAATGAACTCAAACAAATTTAAAAGAA 5534
                           i  i  vi  i       v  i  v      vv    v iv v  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_121352113_   5535 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5580
                            i    ----   v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_121352113_   5581 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5630
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_121352113_   5631 TCATCACTGGCCAT 5644
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (140 / 101)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


2448 29.93 1.55 0.89  chrX_121363171_121365314.rev      758  1659 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121363171_    758 TGGAAAAACATTTCGTGCTCATGGACAGAAATAAGCAATATCATTAAAAT 807
                               i i  ii i  i       iv i  v vvi     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121363171_    808 GGCCATACTGCCCAAAGCAATCTACAGATTCAACAGTATGTTTATCAAAC 857
                            v     v      vii               ivv  vii       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121363171_    858 AACCAACATCATTTTTCACAGAATTAGAAAAAAATGACTCTAAAATTCAT 907
                         vv   i vv v     ii     v v  v  iv-   ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_121363171_    908 ATT-AAATAAAAAAGAGCCTGAATGGTGAAAGTAATCCTAAGCAAAAATA 956
                           v-    iv  ii  v  v    i iv   ii    i i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_121363171_    957 ATAAAGCTGGAAGCTTCACATTACGTCACTTCAAACTATAGTATAAGGCT 1006
                          i    i    i vi     i v viv i      viv  v  i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_121363171_   1007 ACAATAACCAAAACGGCCTAGTA-TAGTTAAAAAAAACAGACACATAGAA 1055
                            i   i   i  i iv i   - i i-- v  ii i     i     v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGC--ATAAGGATAGACATATAGAT 297

  chrX_121363171_   1056 CGATGGAACAGAATAGATAACCCATAAATAAAGCAACACCCCTACAGCCA 1105
                          i      i     v  v ii   v       v v i  vii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_121363171_   1106 TCTGATCTTTAACAAA--TTCTACAAAAATAAGCAATGGGGAAAGGACTC 1153
                         vi    i  ii    i-- v --   i vi vv            i ivv
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGC--CAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_121363171_   1154 CCTATTCAATAAATGG------GATAGGTAGCTAGCTATATGCAAAAGAA 1197
                         i  v     i      ------  i iv i v  ? i i           
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_121363171_   1198 TGGATCTGTACTCCTACCATTCATCATATTAAAAAATTAACTCAAAATGG 1247
                           i vi  v  i      viv  i     vv                   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_121363171_   1248 ATTAATGATTTAAATGTAAGACCTCAAACTATAAGAACCCTAGGAAAAAA 1297
                           i ?v  ii           v  v         i vi i   i i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_121363171_   1298 CCTAAGAA-ACATCATTCTGGATATTCGCCTTGGGAAATAATTTAT--GA 1344
                          v  i ?i- v   -   vv  iv  v v-  i  v   ii   v --  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGA 593

  chrX_121363171_   1345 TTAAGTCCTCAAAAGCAACTGCAACTAAACAAATATT-GACAATTAGGAT 1393
                          - v v vi        vvv     v   v   v v -  i  v v   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_121363171_   1394 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAGCAGAGT 1443
                         i v  i   v v  i i   i  ii vv    i  v       iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_121363171_   1444 AAACAGACAACCTAGAGAATGGAAGAAAATATTTGCAAACTATGTATCCT 1493
                         i  v        i v       i                ii  i    iv
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_121363171_   1494 ACAAAGGTCTAGTGTCCAGAATCTATAAGGAACTTAAACAATTGAACAAG 1543
                          i  i  v  v  i        v     i     ivv    i v  i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_121363171_   1544 CAAAAACCAAACAGCCCCATTAAAAAGTCGATAAAATACATAAACAGGTA 1593
                         v    iv    i i   v   ?    i v ii   iv iv i  i  ii 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_121363171_   1594 TTTCTCAAAGGAAGACATACAAGCAGACAACAAATATTTGTAGAAGTGCT 1643
                               v  i     i      iii v   i  ii iv  v i ii    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_121363171_   1644 CAACGTTGCTAATCAT 1659
                             i ii????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (155 / 111)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


1771 25.34 14.08 3.06  chrX_121372577_121377801     3913  4729 (495)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_121372577_   3913 GGAAAAATATTCCATGCTCACGGATAGGAAGAATCTACTTTGTTAAAATG 3962
                              i    i     i   i    v      v iv iv       i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_121372577_   3963 GCCACACTGGCCAAAGCAATTTACAGATTCAATGCTATTTCTAT--ATAT 4010
                           v i   vv     vii  i           i  v  ii    -- v  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_121372577_   4011 CAAAG--ACATATTTCATGGAATTAGAAAAA--AAT--TAAAATTCATAT 4054
                          vv  --i v v   iiii   v v  v  i--i  --            
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_121372577_   4055 GGAACCACAAAAGAGCCAGAATAGCCAAAGCAATCCTAAGGAAAATTAAA 4104
                             vii   ii  v              i     i i -----------
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA----------- 190

  chrX_121372577_   4105 AAAAAAAAAAAAAAAGCTGGCGGTATCACATTACCCAGTTTCAAACAATA 4154
                         -    i  i  v    i   v  vv     i v    i       vvv  
  L1M4_orf2#LINE/    191 -AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_121372577_   4155 CTACAAGGCTACAGTAACCATAACAGCATACTACCGGTACAAACACAAAC 4204
                               i          i  vi    ii iv   i  i i  iv i i  
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_121372577_   4205 ACACAGACAAATGTAATACAATAGACAACCCATAAATAATGTTGCACACC 4254
                          i i   iv    v    v   v  v ii   v      vviiii   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_121372577_   4255 TGCAACCATCTGATTTTTGACAAGT-TAACAAATGCAACCAATGGGGATA 4303
                          iiiii  vi       i      v- iv   ivv  vi         v 
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_121372577_   4304 GGACTCCCTATTCAATCAATGTTGCTGGGATAACTGACTAGCAATATTCA 4353
                          i ivvi  v     iv    v        i     iv  ? v i  v  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_121372577_   4354 GAAGTTTAAAACTATAACCTTTCATTATACCATATACAAAAATAAACTTA 4403
                         i   vv i  ii iv v  i v v i i               v    i 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_121372577_   4404 AGATGGATTAAAGATTCAAATGGAAAACCTCAAACTATAAAAAC---ACA 4450
                          i      i ?   iii     v  i v  v           vi--- v 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_121372577_   4451 AGAAAACCTAAG---AAATACCATTCTTGACATAGGACCTGGCCAATA-T 4496
                                v  i ---    -- -   v    v v  iiiv   -   i- 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGC-AATGGT 585

  chrX_121372577_   4497 TTC------ATGAC----------------------GA------------ 4506
                            ------     ----------------------  ------------
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_121372577_   4507 ---GGAT---ACCAAAAACAA------TTGTA---------ACACCTTCA 4535
                         ---   i--- i     vi  ------    i---------    iv   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_121372577_   4536 A-----------------------AATGGAAGAAAATATTTGCAAACTAT 4562
                          -----------------------     i                ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_121372577_   4563 GCATCTGACACATCTGACAAAGGTCTAATATCCAGAAGCTATAAGAAACT 4612
                         --------- i      i  i  v  vi         vv     ii    
  L1M4_orf2#LINE/    736 ---------ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_121372577_   4613 --TA-AATTTACAAGTAAAAA-ACAA-----CCTCTTAAAAAATGGGCAA 4653
                         --  -  i i vv i      -    -----  vv  ?            
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_121372577_   4654 AGGACATGAACAGACAGTTCTCAAAAGAAGACACACACA--ACCAA---G 4698
                             iv    i     v     v        i i   v --i    --- 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_121372577_   4699 TACATGAAAAAATGTTCAGC-TCATTAATCAT 4729
                         i         i   i   i -   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (120 / 84)
Gap_init rate = 0.03 (27 / 907), avg. gap size = 5.19 (140 / 27)  


2035 27.67 4.14 1.34  chrX_121394056_121395795      500  1247 (493)    L1M4_orf2#LINE/L1      140   908 (0)  

  chrX_121394056_    500 TAAAATTTATATAAAAAT-CAATGGAATGAAAATAACTAAAACAATTTTG 548
                                i    ii    -   v   viv i    i i        i   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_121394056_    549 AAAA-------TAAA-TTGATAGGACTGAGTATACAAAATTTCAAGA--T 588
                             -------i   -   i-      v vvv v vv        i -- 
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGG-AGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_121394056_    589 ATTCGATAGCTATACTAATCAAGTC--TGTGATATTGTGCA-AGAGATAT 635
                          i vv v     i v        v --    i  i  -   - ii    v
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG-GCATAAGGATAG 287

  chrX_121394056_    636 ACACAGGCATTAATGAGGTAGAAAAAGGAACCTAGAAAGAAAT--GAACA 683
                            i viv  i    iii     vvii  ii i     v   i--iv   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_121394056_    684 TATGTGCCCAACTAATTTTTTGCAATGACATAAAG-CAATTCATTAGAGA 732
                          v i  vi   i i     ivi   v iiiiv   - v     v i i  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_121394056_    733 AAAAAATGGTCTTTTCAACATATTTTCTTAGAACAACTGAACATACATAC 782
                           i  - i            v  vv vi i i       i i ?v  i i
  L1M4_orf2#LINE/    388 AAGAA-TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_121394056_    783 GCAAAAGATATATAGCTCCTCCCTTAAGTCTCACACCTTATACAAAAACT 832
                                 -  iv  i vvv   i  --i        v          i 
  L1M4_orf2#LINE/    437 GCAAAAGA-ATGAAGTTGGACCCCTA--CCTCACACCATATACAAAAATT 483

  chrX_121394056_    833 ACCTCAAAATAAACCAGAAACTTAAATGTAAATCATAAAACTATAAAGCT 882
                          v        ii i  ? i  i         ivvv            i  
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_121394056_    883 TTTAGT-GAAAAAGTAGGAGAAAAACTTCAGGATCTAGGGCTAGGCAAGG 931
                         i    v-     vi    ? v   v    iv  i  v   i       v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_121394056_    932 AATTCTTAGACTTGACACTGAAAATGTCCAAG----------AAAATTTT 971
                         iv        iv      ii   -- iv    ----------    v vv
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAA--GCACAAGCAACAAAAGAAAAAATAG 631

  chrX_121394056_    972 ATGAATTGGACTTCATCAAAATTACAGACTTCTGCTCTTCCAAAAACCAC 1021
                           i                     v i    i  iv    v  ii  -  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC-AC 680

  chrX_121394056_   1022 TAT-AAGAGGGTGAAAATACAAGCTACACATTAGACAAAAATATCTGCAT 1070
                            -    ii       v    v i   v v i ivi       i    v
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_121394056_   1071 GCTGCATATCTGAAAAAAAAACTTGCATCTAGAATATATAAAGAATTCTT 1120
                         iiiii        v  iii -    i   i               i    
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGA-CTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_121394056_   1121 GAAGCTTAACATCAGAAAG-TAAACAATATAGTTAGAGAATAGGCAAAAT 1169
                         iv i  i  i vi i    -i   i  ivi i  ?i i   i      iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_121394056_   1170 ATATGAG-AGACATTTTACTGAAGAGGCTATATATGTGGCATACAAGCGT 1218
                           v   i-        iv ii    i v    i vi    vv i    ii
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_121394056_   1219 ATGGATCTATGTTCAACATCATTAGCCAT 1247
                            i vvv   i         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (124 / 79)
Gap_init rate = 0.03 (21 / 769), avg. gap size = 1.95 (41 / 21)  


1742 26.09 6.89 2.38  chrX_121398424_121400744      542  1296 (1025)    L1M4_orf2#LINE/L1        2   790 (118)  

  chrX_121398424_    542 GGAGAGATATACAGTGATCATACATTACAAAAC--AATAT-ATTAAGATA 588
                            i      v vi  v    iv   iv  i  --     -i       i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_121398424_    589 TCAA-ATTTCC-----TGAT--A-GGAATCAAGACATTCTCAGTCAAAAT 629
                         v   - i i  -----    -- -i  v    vi  v  i vi       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_121398424_    630 TCCATCAGGCTGTTTTATTTTCATAAAAGTTATCAAGCTAAATATAAATT 679
                         i   ----    ii  --   iii i  i  iv      i viv    v 
  L1M4_orf2#LINE/    102 CCCA----GCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_121398424_    680 TTATATGAAAAAATCAAAGAACCTGGAATTATGCAAACAACTTT----AA 725
                          i     i   vi-   i i   ii    viivv      ii  ----  
  L1M4_orf2#LINE/    146 TCATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_121398424_    726 GGAAAATAGAATTCAAGGTATTTTACTATTTAATTTTAAGGCTTAC---A 772
                          i i  i i i  vi   vv ivi   viii     i  ii     --- 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_121398424_    773 AGTTTATAATTATCAAGTCCGTGTGGCATTGATAAAAGGACAGACATAGA 822
                          ivi  i i v      v v      i i  ii v     i       v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_121398424_    823 GATTTATGGAACAAAATAGAGAATCCAGAAATAGAC--ATGGATCTATAT 870
                            iv      i i   v    i          i  --  iv  i   i-
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG- 343

  chrX_121398424_    871 GTCCCATTGATTTCTTTGACAAAC-TGCCAATATAATTCACTGGG-ACAG 918
                            v-        -- i     iv-      v iv     v    - v  
  L1M4_orf2#LINE/    344 GTCA-ATTGATTT--TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_121398424_    919 GATAGTCTTTTGAA-AAATGTTGCTGGGA-AATGTATGGATCTCTAT--- 963
                         i          v  -     v        -  i---     v? i i---
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAAC---TGGATAKCCACATG 437

  chrX_121398424_    964 TAATA-AATGAACCTTGAACCATACATCAAACCACATACAAAAATTAATT 1012
                         i  v -      vi v  v  v   v   v    i             i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_121398424_   1013 AAAAATATATCATA-ACGTAAATGTAA-------AACTATAAAACTTCTA 1054
                         v     iv    ? -  v         -------            ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_121398424_   1055 AAAGCAAACCTAGGGGAAAATATTCCTGAATTTTGACTATCCAAAGATAT 1104
                         i   v    v    ? v    v   v   vi  v ii  vv   v i v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_121398424_   1105 AGTGACTATG----CAAGAATACAAACCATGAAAGAAAAGTAAACA-ATA 1149
                         vv iiv    ----   i ii    i v ii        ---  i -   
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA---AATAGATA 634

  chrX_121398424_   1150 AATAAGACATAATTAAAATTGAAAACTGTAGTTCTTTAAAACACAATTTT 1199
                            vi   v v  i      i      v v  v   i   iv   v v i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_121398424_   1200 ACAAACATTAAAAAG-----CCACAAA----GAGAAAATATTTGCCAAAT 1240
                          vi  - v i     -----     i ----              v  vi
  L1M4_orf2#LINE/    685 AAGAA-AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_121398424_   1241 ACATATCTGATAAAAGACCTATACACAGAATTTAAAAAGAAAACT-ACAA 1289
                          i           ii   i i  iv      v  v      vv  -    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_121398424_   1290 CTCAATA 1296
                                
  L1M4_orf2#LINE/    784 CTCAATA 790

Transitions / transversions = 1.31 (110 / 84)
Gap_init rate = 0.04 (31 / 789), avg. gap size = 2.26 (70 / 31)  

 392 21.09 16.33 0.00  chrX_121398424_121400744     1682  1828 (493)    L1M4_orf2#LINE/L1      738   908 (0)  

  chrX_121398424_   1682 ATTTG-TAAGGGAC--------AAAACATGCAAA----CCATACACTGTA 1718
                           i  -        -------- i  i  ii   ----i v    vivi 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_121398424_   1719 GTAATAAGAGAACAAA-------ATTTATAGA--GGCAA--GATTTGAAA 1757
                         i      i ii     -------   ? v i --     --        v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_121398424_   1758 AGATACTTTATCAAAGAAGAGATACAGATTACAAATAAGCACATGAAAAG 1807
                            i i  ivi         v     i  vi v                 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_121398424_   1808 ATGATCAACACCATTAGCCAT 1828
                            v      i  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.04 (6 / 171), avg. gap size = 4.00 (24 / 6)  


2345 26.68 4.82 3.03  chrX_121418957_121424577     4249  5140 (481)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121418957_   4249 TGGAAA-ACATTTTATGGTCATGGAGAGGAAAAATCAATATTAGTAAAAT 4297
                               - i  iii   v       vv    i v i      iv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121418957_   4298 GGCCATACTGCTCAAAGCAATTTATAGATACAATGCTATTCCCATCAAAC 4347
                            v     v i    vii  i  i    v   i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121418957_   4348 TACCAATGACATTCTTTCCAGAACTAGAAAAAAACT-ATTTTAAAATTCA 4396
                          v   iivi v  i   v     v v  v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_121418957_   4397 TATGGAACCAAACAGAACCAAAAAAAAACAGCCCGGCTGGCCAAAGCAAT 4446
                                viiv vi i   v i  ------------- i      i    
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAA-------------TAGCCAAAACAAT 185

  chrX_121418957_   4447 CCTTTGCAAAA--AGAACAAAGCTGGAGGCATTATGATGCTCGACTTCAA 4494
                          --   v    --         i      vv i iiv v i i i     
  L1M4_orf2#LINE/    186 C--TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_121418957_   4495 ACTGTACTACAGGGCTACAGTAAACAAAACAGCTTGGTACTGGTATAAAA 4544
                          viv       ii          v   i    iv         i    ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_121418957_   4545 ACAGACACAT---CCACAT---ATATAATAAAGGCCCCAGAAATATGACT 4588
                          i     i  ---i  -  ---   v   vi  ivi         -i  i
  L1M4_orf2#LINE/    284 ATAGACATATAGATCA-ATGGAATAGAATTGAGAGTCCAGAAATA-AACC 331

  chrX_121418957_   4589 GA-ACACCTAAAACCATCTGATGTTTGACAAAGCTGCCAAGAACAAATGA 4637
                         v -   ii  viii  vi    v  i     i v        v  vvii 
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_121418957_   4638 TGAAAAAAGGATTCCCTATTCAATAAATGGTTCTGGGATAACTGGCTAGC 4687
                           iii    i  vvi  v     i       v      i      v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_121418957_   4688 CAAATGAAGAAGACTGAAACTAGACCCCTCTCT-ACACCACATGCAAAAA 4736
                           v   v i    v    ii i       vi  -      i  i      
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_121418957_   4737 TCAACTCAAGATCCATTAAAGACTTAAATGTAAAACACAAAACTATAAAA 4786
                          i       i  vv  i ?    i         i vvi            
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_121418957_   4787 ACTCT-GGAAGACAATCTAGACA-ATACCATTCTGGACATAGGAACAGGC 4834
                         -    -i     v  iv   i?i- v i -   vv   v v  ivi    
  L1M4_orf2#LINE/    532 -CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGC 579

  chrX_121418957_   4835 AAAGATTTC------ATGACAAAGAGGCCAAAACCAATGGCAACGAAAGC 4878
                           v i    ------      ------      v  vvi     i    v
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAACAAAAGA 623

  chrX_121418957_   4879 AAAAATTGACAAATGGAACCTAATTGAACT--ATAGCTTGTACACAGCAA 4926
                               v  i    v i  i v  ii  v -- v i   v iii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_121418957_   4927 AAGAAACTATCAGCAGAGTAAACATACAAACTACAGAATGGGAGAAAATA 4976
                          i  v       iv i   i  v v    v i                  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_121418957_   4977 TTTGCA---------TCTA----------TGTATCTAGCACCTATAGGAA 5007
                               ---------   i----------      i  v iv    iii 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_121418957_   5008 ACAA--ACAAATTTACAAGCAAAGAACAAGCAACCCTGTTAAAAAGTGGG 5055
                           vv--    v iv i  vv   ii    ii     vi  ?    i    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_121418957_   5056 CAAAGGACATGAACAGACACTTTATGAAAGAAGACATACATGTGGGCAAC 5105
                                iv    i     i  iviv        i     vi   v   i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_121418957_   5106 ACACATATGAAGAAAAAGTCAATATAACTGATCAT 5140
                          vi  i     i i viv    i  v ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (135 / 99)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.18 (70 / 22)  


1650 27.64 2.68 2.68  chrX_121455915_121457954      500  1096 (944)    L1M4_orf2#LINE/L1      141   737 (171)  

  chrX_121455915_    500 AAAGTTTATATGGGAAGGCAAAAGACCTATAACAGCCAGGGCAAT----A 545
                            i  i      i  v    ii    i v  i     iii    ---- 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_121455915_    546 ATTAAAAGGACAAAGTTGGAATACTCATATTATTAAATTCCAAGACTTGC 595
                          vv i   i           iv     i i viiv    i   i    i 
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_121455915_    596 CATAAAACTGTATTAATCAAGACAGAATAGTGTTGGAGTTAGAACAGACA 645
                         i i   i  ii v            vi i  ii   vi v  i i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_121455915_    646 CACAGATCAGTGGCATTTAATGGACTGCATATAAAAAGATCCACACAAAG 695
                         i i      i   v  vv   v  vv ivi v   v i i   i   vvv
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_121455915_    696 ATAGTCAGTTGATTTTTGCCAGTGATGCAAAGACAATTAAATGGAGAAAA 745
                           i    i        i v  iv i   v     v   v     i    i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_121455915_    746 AACAGTCTTTTCCACAA-TGGTGCCAAAACAATAGAATGTCAAAAGGCAA 794
                           i         v    -      iiii    iv i  i? v v v    
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_121455915_    795 AATAGGGAACCTAGGCACTAAATTTAAATCTTTCA-AAAAATTAAATCAA 843
                           v iv   vi i i v iv vi i v i v vi -         v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_121455915_    844 AATGGATAATACACTTAAATATAACATGC-AAAACTATAACATTTCTAGA 892
                                v ? v  i     i   v -  -          v i ii    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGA 539

  chrX_121455915_    893 AGAAAGCATAGAA-TAGAATCT--G-GATTTTTCGGTTTTGG---TGGTT 935
                              i     i?-  -     -- -  ii  --  v  v  ---     
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTA-AATCTTCGTGACCTT--GGGTTAGGCAATGGTT 586

  chrX_121455915_    936 TTTTTTTTTTTTTTTAATAGAGCACCAAAATCAAGATCTATGAAAGAAAA 985
                          i  v----------i   vii        v  vi v v ii        
  L1M4_orf2#LINE/    587 TCTTA----------GATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_121455915_    986 AATTTGACAAGCTGGACTTCATTCAAGTTTAAAATGTTTGCCTTTTGAAA 1035
                            v-  i  ii          iv  i  v    iv    ivi  ii  i
  L1M4_orf2#LINE/    627 AATA-GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_121455915_   1036 GACAATGTTAAGAAAAT--AAAGACAAGCCACAGACTAGAAAAAAGGTAT 1083
                             v i i      i --        v       v i i i   i-   
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TAT 724

  chrX_121455915_   1084 TTGCAAATCACAT 1096
                                   i  
  L1M4_orf2#LINE/    725 TTGCAAATCATAT 737

Transitions / transversions = 1.57 (99 / 63)
Gap_init rate = 0.03 (15 / 597), avg. gap size = 2.13 (32 / 15)  

 864 18.23 0.55 0.00  chrX_121455915_121457954     1367  1547 (493)    L1M4_orf2#LINE/L1      727   908 (0)  

  chrX_121455915_   1367 GCAAATCATGTATTTGATAAAGGACTTGTATCCAAAACATATAAAATATT 1416
                                  i   i      i             i  i       iv i 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_121455915_   1417 CT-AAAACTCAACAATAAGAAAACAAACAATCCAATTTAAAAATAGATGA 1465
                           - v       i     i  i     i  i      ?      i iii 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_121455915_   1466 AAGATCTGAACAGACACCACTCCAAAGCAGATATACACATGGAAAATAAA 1515
                          i   i    i     iiv        v         v    vv     i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_121455915_   1516 CATATGAAAAGATGCCCAAGATCATCTGTGAT 1547
                           i            i   v    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (24 / 8)
Gap_init rate = 0.01 (1 / 182), avg. gap size = 1.00 (1 / 1)  


3131 22.60 1.71 4.90  chrX_121459795_121463227     2014  2951 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121459795_   2014 TGGAAACATATTCCATGCTCAAGGATTGGAAGAATTAAGATTGTTAAAAT 2063
                               v    i     i   v           v    v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121459795_   2064 GACAACACTACTCAAAGCAATTTAAAAATGCAATGCCATCCCTATGAAAA 2113
                          i   i   v i    vii  i  v i  v   i  v        v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121459795_   2114 TACCAATGACATTCTTTGCAGTAATAGAAAAAA-AATCCTAAAATTTATA 2162
                          v   iivi v  i       v   v  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_121459795_   2163 CGGAACCACCAAAAAC--AGAATTGCCAAAGCAATTCTGTGTGAAAAGAA 2210
                         i    vii v iii  --     v      i    ii  vivi i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_121459795_   2211 CAAAGCTGGAGGCATCACAATACCTGACTTCGAAATTTACTACAAAGTTA 2260
                              i      vv     v v  ii i   i   i           i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_121459795_   2261 TAGTAATCAAAACAGCATGGTGCTGGCATAAAAACAGACACATAGAACAA 2310
                         i         i    ii    i         ii i     i     v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_121459795_   2311 TGGAACAGAATACAGACCCCTGAAACAAATCCATGCATTTAAAATTAACT 2360
                              i     vv   vi  v    i   i    i      vii i  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_121459795_   2361 CATTTTCAACAGCGATGCCAAGAATATACAATGGGGAAAGGACAGTCTTT 2410
                         v      i   iv i        vi  v            i i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_121459795_   2411 TCAATAAATGGTGCTGGGAAAACTGGATAACCATATGCAGAAAAATAAAA 2460
                             i              v         ?   i     i  i   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_121459795_   2461 CTAGACCCTATTTGCAGAAAAATAAAACCAGATCCCTATTTCTCACCATA 2510
                         i i     ---------------------------   ii  v       
  L1M4_orf2#LINE/    451 TTGGACCC---------------------------CTACCTCACACCATA 473

  chrX_121459795_   2511 CAAAAAAAAAGATCAAATCAAAATGGATTAAAGACTT-----TAAGACAT 2555
                         i v     ---- i  v           i ?    i -----     vv 
  L1M4_orf2#LINE/    474 TACAAAAA----TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_121459795_   2556 CAAACTATAGAAATATTAGAAGAAAACATTAGGG-AAATGTTCCAGGACA 2604
                         v        i  v v              vi ? -    v   -iv   v
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACC 568

  chrX_121459795_   2605 TTGGTCTTGGTAA--ATTTTTTTG-TGTGTTAACACTTCAAAAACACAAG 2651
                             vi v  i  --i   i  v - i  ---    --     i      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATG---ACAC--CAAAAGCACAAG 613

  chrX_121459795_   2652 CTACCAGAGCACAAATAGGCAACTGGAATCACATTAAGCTAAGAAGCTTC 2701
                          v  v i  v v      ii  v v i iiv   i  iv v i  i   i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_121459795_   2702 TAAACCACAAAGGAAACAATAAAAAAAAACTGAAGAGACAACTTACAGAA 2751
                          ivi iv       v  v  v  i   i--    i       ii      
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAG--TGAAAAGACAACCCACAGAA 711

  chrX_121459795_   2752 TGGGAGAAAATATTTACAAACTATACATCTGATAAAAGATTAATAACCAG 2801
                                        i    ii   i         ii  i vi  v    
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_121459795_   2802 AATACATAGGGAGTTCAAATAGCTCAATAGCCAAAAAAACCCCTCCAAAT 2851
                             i   ii  ii  vv i i       ii-     i  ------    
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAAT-AAAAAGAC------AAAT 804

  chrX_121459795_   2852 AATCTAATT-AAAAATGGGCAAATGATCTGAACAGACAGTTTTCAAAAGA 2900
                           i i    -             v   i    i     v  i  v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_121459795_   2901 A-ACATCCAAATGGCAAA-GAGTACATGAAAAAAAAAACA-CATCACTAA 2947
                          - i  v        v  -i  i         i vivv  -     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_121459795_   2948 TCAT 2951
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.68 (131 / 78)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.44 (62 / 18)  


3091 26.14 1.67 0.89  chrX_121475502_121481326.rev     4443  5341 (484)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_121475502_   4443 GAAAAACATTCCATACTCA------AGAAGAATCAATATCGTGAAAATGG 4486
                             i i  i    ii   ------i     v i     i  v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_121475502_   4487 CCATACTGCCCAAGGTAATTTGTAGATTCAATGCTATCCCCATCAAGCCA 4536
                          v     v     iv i  i ii        i  v     i     iviv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_121475502_   4537 CCA-TTGACTTTCTT-CACACAATTGGAAAAAACT-ACTTTAAATTTCAT 4583
                            -i  v    i  -  v -     -- v  i  - iii    v     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_121475502_   4584 ATGGAACCAAAAAAGAGCCCACATAGACAAGACAATCCTAAGCAAAAAGA 4633
                               viiv  ii  v  viv    v   i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_121475502_   4634 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 4683
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_121475502_   4684 ACAGTAACTGAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 4733
                                iii i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_121475502_   4734 ATAGAACAGAACAGAGGCCTCACAAATAACACCACACATCTACAACCATC 4783
                           i   i    iv   ivii  v      vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_121475502_   4784 TGATTTTTGACAAACCTGACAAAAATGAGCAATGGGGAAAGGATTTTCTA 4833
                                i     ivv  v   i viivv            i  vv   v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_121475502_   4834 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAGAGCTGAA 4883
                           i  i              v      v  ?   i     i iiiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_121475502_   4884 ACTGGATCCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGATTA 4933
                         ii    i    v   i    iv                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_121475502_   4934 AAGACTTAAACATAAGACCTAAAACCATCAAAACCCT-AGAAGAAAACAT 4982
                         ?    i    ii     v       i  -     i  -            
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chrX_121475502_   4983 AGG--TAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5030
                            --   - i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_121475502_   5031 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5080
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_121475502_   5081 TTGAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAA 5130
                          ii  v v  i i   i  ii vv    i  v       vv i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_121475502_   5131 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 5180
                           i     i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_121475502_   5181 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAAT---TTACAAGA 5227
                         i  i  vi          v  i        ivv    v --- v i  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_121475502_   5228 AGAAAAACAACCCTGTCAAATAGTGGTCAAAGGATATGAACAGACACTTC 5277
                            v   i     vi i?  v i   v        v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_121475502_   5278 TCAAAAGAAGACATTTATGCAGCCAACAAAACATATGAAAAGAATCTCAC 5327
                           v        i  vi viii     i  i-  i         vv    v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCAA 895

  chrX_121475502_   5328 TGGTCATTATAGAA 5341
                         ii-   ????????
  L1M4_orf2#LINE/    896 CA-TCAZZZZZZZZ 908

Transitions / transversions = 1.61 (143 / 89)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 1.64 (23 / 14)  


2963 26.09 2.35 0.67  chrX_121489926_121494247.rev     2939  3831 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121489926_   2939 TGGAAAGGTATTCTGTGTTCATGTATTGGAAGAATCAATATTGTTACAAT 2988
                                i   i ii        v         v i          vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121489926_   2989 TTCCATACTACCTAAAGAAATCTATAGATTCAATGCAATTTATATAAAAA 3038
                         vv v     v  i   vvi     i        i     iiv   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121489926_   3039 TACCAATGACATTCTTCACAGAAATAGAAAAAGCAATCCTAAAATTTATG 3088
                          v   iivi v  i  ii       v  v  ivii           i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_121489926_   3089 TGGAACCAAAAAAGACCTAAAGTAGTCAAACCTGTCCTGAGCAAAAAGAA 3138
                              viiv  ii    i i i   i    v vi  i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_121489926_   3139 CAAAACTGGAGGAATCACATTACCAGACTTCAAATTATACTACAACAGCT 3188
                             ii       v     i v  vi i      viv        -    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA-AGCT 249

  chrX_121489926_   3189 ATAGAAACCAAAACAGCATGGTACTGCAATAAAAACAGATACATAGACCA 3238
                          i  v  i   i    ii        vv    ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_121489926_   3239 ATGGAACTGAATACAGAAACCAGAAACAAATACACAGATCTGCAGTAAAC 3288
                               iv    vv   iv       i   iv  i v  i iii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_121489926_   3289 TCATTTTCAACAAAGG-GCATAGAAAATATATTGGGGGAAAGGACAGTCT 3337
                          v      i    i  -  vv   vv  vi v     -    i i     
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCT 398

  chrX_121489926_   3338 ATTCAATAAATGGTGCTGAAAAAAATGTCTATCCATATGAAGGAGAAAGA 3387
                         v     i           ii v  v  vv  ?   i   v ii    v  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_121489926_   3388 AGCTTGACCTCCGTTTCTCACTACATACAAAAATCAAGTAAAAATTTATT 3437
                           i v    i iiii  v   i i          i  v v     vv  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_121489926_   3438 AAATACTTAAATCTAAGACCTCAAACT-TGAAACTACTTA-AATAAAATA 3485
                          ? v  i     v     v  v     - i     -    -  v    i 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACA 547

  chrX_121489926_   3486 TTGGGGAAGCTCTCCAGGACATTGGTCTAAGCAAAGATTTCTT-GAT-TG 3533
                          v  ? v iv   i iv   v    vi  i    v i      -   -  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_121489926_   3534 TACAC-----ACACAATCAA----AGCACAAATGGACAAATGGGATCACA 3574
                         -    -----i     v   ----  v v    i  i    v   iiv  
  L1M4_orf2#LINE/    598 -ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_121489926_   3575 TCAGG-TTAACAACCTTCTTTACAGTGAAGGA----ATCAATAAAGTGAA 3619
                            ii-    v   i  - v i vvii     ----     v        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_121489926_   3620 GAGACAACCCACAGAATGGGAGAAGATATTTTTAATCTATCCATCTGGCA 3669
                         i                       i      vi  vii  vi     ii 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_121489926_   3670 -GTGATTAATAGCCAAAGCATATAAAGACCTCAAACAACTCAATAGGAAA 3718
                         - v  i vi  v   i ii         v   vv           iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_121489926_   3719 ATAATCTAAGACTCTGATT-GAAGATAGGTAAAACATCTGAATAGACATT 3767
                          vi - v  v vi ii   -i  i  i  i   iv  i            
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_121489926_   3768 TCTCAAAAGAAGACATACAAATAGCAAATGGGTATATGAAAAGATGCTTA 3817
                             v        i        i  v   ii i i             i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_121489926_   3818 ACATCATTGATTGT 3831
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.59 (27 / 17)  


2126 24.29 4.32 1.04  chrX_121508682_121510337      493  1163 (493)    L1M4_orf2#LINE/L1      216   908 (0)  

  chrX_121508682_    493 CATATATCCCAACTTCAAATTATACTGCAAGGCTACAGTA---------- 532
                           i iv      i      viv    i   i         ----------
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_121508682_    533 -------CTGGTATAAA-ATAGGCACATAGACCAATGGAAGAGAATAGAG 574
                         -------    i    i-    i  i     i        v     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_121508682_    575 ATAGCAGAAATAAAGTCAAATACTTACAGTCAACTGATCTTCAACAAAGC 624
                          vvv          vi  v i i   ii     i    i   i    i -
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG- 364

  chrX_121508682_    625 ATAGAAAAAC-ATAAATTGGGGAAAGAACACCCTATTCAATAAATGGTAC 673
                         i ivv  i  -  vv v           i vi  v     i       i 
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_121508682_    674 TGGGAAAACTAGCAAGCCACATGTAGAAGAATGAACCTGGATTCTCATCT 723
                              v    i vv ?       i i         vi    ii ii i  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_121508682_    724 CTCACCTTATACAAAAATCAACTCAAGATGGATCAAAGACTTAAATCTGA 773
                          v    v           i       i        ?    i     v i 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_121508682_    774 GATCTGAAACCATAAAATTTCTAGAAGATAACATCTGAAAAAATTCTTCT 823
                           v  i    i      i ii       v     vv ?iv    -    v
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCG 563

  chrX_121508682_    824 AGACGTTGGCTTAGGCAAAGAATTCATGACTAAGAACTCACAAGCAAATG 873
                         v   v    v        v iv   v iiv  v  vvi  v     v v 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_121508682_    874 CAACAACAACAACAAA---ATAAATGGGACCTAATCAAA-TTAAAAACTT 919
                               -  v  v   ---      v    i v      -          
  L1M4_orf2#LINE/    614 CAACAA-AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_121508682_    920 TCTGCCCAGCAAAAGAAATAATCAGCAGAGTGAACAGAAAATCCACAGAG 969
                          -  iv vv    i  v iv    iv i      v   v  i       i
  L1M4_orf2#LINE/    663 T-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_121508682_    970 TAGGGGAAAATATTCACAAAC--TGCATCCAACAAACGACTAATATCCAG 1017
                          i  i         ii    i-- ii   ii i  iv    vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_121508682_   1018 A-TCTACGAGGAACTCAAACAAATTAGCCAGAAAAGAAAACTGAATAATC 1066
                          - v  ii i      vv    v i iiv v    -- i  -i     i 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAA--AGAC-AAATAACC 808

  chrX_121508682_   1067 CCATCCAAAA-TGGGCAAAGGACATGAATA--CAATCCTCAAAAGAAGAT 1113
                          v  i?    -           iv      --  v i   v         
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_121508682_   1114 ATGTAAACAGCCAACAAACATTTGAAAAAATACTCAACATCATTAATTAT 1163
                           ii   ii     i  i  iv      i  i          ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (91 / 68)
Gap_init rate = 0.02 (15 / 693), avg. gap size = 2.40 (36 / 15)  


3144 26.61 1.34 0.22  chrX_121532819_121537805     3597  4494 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121532819_   3597 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3646
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121532819_   3647 GACCATAATGCCAAAAGCAGCCTGCAAATTCATTGTAATCCCCATCAAAA 3696
                          i v   v v  v   viiii  i  i     vi i      i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121532819_   3697 TACCACCATTTTTCTTCACAGAATTAGAAAAAA-AATTCTAAAATTCATA 3745
                          v   v vvii  i  ii     v v  v  iv-i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_121532819_   3746 TGGAACCAAATAAAAG-CCCACA-TAGCCAAAGCAAGACTAAGCAAAAGG 3793
                              -- vii  ii -    v -        i   vvi i iv  i i 
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_121532819_   3794 AACAAATTTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGC 3843
                               v       vv       v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_121532819_   3844 CATAGTCACCAAAACAGCATGGTACTGATATAAAAACAGGCACATAGACC 3893
                         i i   v i   i    ii        ii    ii i  i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_121532819_   3894 AATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTATAGCCAA 3943
                                i     v    ii               v i i    i i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_121532819_   3944 CTGATCGTCAACAAAGCAAACAAAAACATAAAGTAGGGAAAGGACATCTT 3993
                         i    iv  i    i vviv   i v   vv i i       i i vii 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_121532819_   3994 TTTCAACAAATTATGCTGGGATAATTGGCTAGCCACATGTAGGAGAATAA 4043
                                    vi        i  i   v  ?       i ii     i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_121532819_   4044 AACTGGATCCTCATCTCTCACT-TATA-AAAAATCAATGCAAAATGGATT 4091
                          ii    i  ii i   v   i-    -      i  iv          i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_121532819_   4092 AAGGACTTAAATCTAAGACCTGAAACTATAAAAATTATCGAAGATAACAT 4141
                          ?i   i     v     v  i           v iv v     v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_121532819_   4142 TGGAAGAACCCTTCTAGACACTGGGTTAGGCAAGGATTTCATGACCAAGA 4191
                         v  ?iv  vi    vv   vi            v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_121532819_   4192 ACCCAAAAGCAAATGCAATAAAAACAGAAATAAATAGCTGGGACTTAATT 4241
                         vv         v v    i    iv i     i   iv v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_121532819_   4242 AAACTGAAGAGCTTTTGCACAGCAAAAGAAA--GTCATCAGAGTAAACAG 4289
                            v v  i i      ii vv    i  v --i   vv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_121532819_   4290 ACAACCCATAGAGTGGGAGAAAATCTCCACAATCTATCCATCTGACAAAG 4339
                                 i   i           v iii   vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_121532819_   4340 GACCAATATCCAGAATCTACAACAAACTC----AAATCAGTAAGAAAAAA 4385
                            ivi          v  i  vi     ----  v   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_121532819_   4386 AGAAACAATCCCATCAAAAAGTGTGCTAAG-ACATGAATAGATAATTCTC 4434
                          v   i  i  v  i?    i  v  v   - iv        i v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_121532819_   4435 GAAAGAAGATACACAAATGGCCGACAAACATATTTAAAAATGTTCAACAT 4484
                         v          i          i i  i  i  vv   i   i       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_121532819_   4485 CACTAATGAT 4494
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2991 25.20 2.12 0.89  chrX_121546557_121548818      873  1769 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121546557_    873 TGAAAATACATCTTATGTTCACGGATTGGAAGAATCAATATCATGAAAAT 922
                           i   v i   ii       i           v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121546557_    923 GGCCATACTGCC-AAATAAATCTACAGATTCAATACAATTCGTATCAAAA 971
                            v     v  -    vi              ii    i v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121546557_    972 TATTAGCATCATTTTTCACAGAATTAGAAAAAAAAATCCTAAAATTCATA 1021
                          vii   vv v     ii     v v  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_121546557_   1022 TGGAATCAAAAAAGAGCTCAAATAGCCAAAGCAAACTTAAGCAAAAAAGA 1071
                              viiv  ii  v ivi          i   v   i i-   i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chrX_121546557_   1072 ACAAATCTGGAGGCATCACATTATCCAACTTCAAATTATACTGCAAGGCT 1121
                              vi      vv     i vi    i      viv    i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_121546557_   1122 ATAGTAACTAAAACCACATGGTACTGGTATAAAAGTAGATAGATAGACCA 1171
                          i     ii  i  viii         i    iii    i v     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_121546557_   1172 AGGAAACAGAAT-GAGAACCCAGAAACAACACCACATACCTATAGCCAAC 1220
                          v i  i     -    ii       i  vv   i i ii   i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_121546557_   1221 TGATCTTTCA-AAAGTTGACAAAAATATACACTGGGGAAAGGACACCCTA 1269
                             i  iv -  i v  v   i vi  v  v         i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_121546557_   1270 TTCAATAAATGGTGCTGGTTAAACTGGATAGCCACACAAAGAAGAATTAA 1319
                              i            vvv         ?     iiv i      v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_121546557_   1320 ACTGGATCCTTATCTCTCACCTTATACAAAAGTCAA-TGGAAATGGATTA 1368
                         ii    i  i  i   v    v         i i  - vi        i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_121546557_   1369 AAGACAGAAATCTAAGATCTGAAGCCATACAATTTCTAGGAAATAACCTT 1418
                         ?    vv    v     v  i  i i   v  i ii   i i v   v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_121546557_   1419 GCAAAAACTCTTCTGGACATTGGTCTAGGCAAGGAATTAT--GACTAAGA 1466
                          v?iv  v     vv   v    vi       v iv  v --  -  v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGA 598

  chrX_121546557_   1467 CCTCAAAAGCAAATACAACAAAAACAAAAATAAATAAGTGGGACCT-ATC 1515
                          vi        v vi        iv       i    i v    i -   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_121546557_   1516 TAAACTAAAAAGCTTCTG-----CATAGGAAAATAAATACTCATCAGAGT 1560
                         v   i      -   i  -----  v    v v  -----   vv i   
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTA-----TCAAGAAAGT 692

  chrX_121546557_   1561 AAACAGACAACCCAAAGAATGAGTGAAAATATTTACAAACTATGCGTCCA 1610
                         i  v          v      i v          i    ii  iii  ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_121546557_   1611 ACAAAGAACTAATATCCAGAATCTACAAGGAACTCAAACAAATTAGCAAG 1660
                          i  i i   vi          v  i  i      vv    v i ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_121546557_   1661 AAAAA---AAA-GACC--ATCAAAAAGTGGACAAATGATAGGAATAGACA 1704
                              ---   -i   --  i?    i   i    v   vv         
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_121546557_   1705 TTTCTCAAAAGAAGATACACAAATGGCCAAGAAACATAAGAAAAT-TGCT 1753
                               v          i            v  i  i v     v-    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_121546557_   1754 CAACATCACTAATCAG 1769
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (128 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.80 (27 / 15)  


3018 26.77 1.99 1.55  chrX_121564402_121569987     4190  5093 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121564402_   4190 TAGAAGGATACAAATCCTATGCTCATGGATTGGAAGGATTAATACTGTTA 4239
                          i   i    ----   i   i              iv      i     
  L1M4_orf2#LINE/      1 TGGAAAGATA----TCCCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chrX_121564402_   4240 AAATGGCAATACTACCCAAAGCAATCTACAGATTCAGTGCAATCCCTATC 4289
                          i           v      vii             ii            
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_121564402_   4290 AAAATACCAATAATGTTCTTTACAGAAATAGAACAAA--AATTCTGAAAT 4337
                              v   iiviiv  i   i       v  -   i--i  i  i    
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAAT 145

  chrX_121564402_   4338 TTGTCTGGAGCTACAAAATGCCTCTAATAGCCAAAACAATCATCAGCAAA 4387
                          ii v    iv i   iivi  ivv                v v iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_121564402_   4388 AATAGAAAAACTGGAAGTATCACACTAGCAGATCACAAAATATACTACAA 4437
                           v iv   ii    i vv       vv vi  iv     iv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_121564402_   4438 AGTTGTAGTGAACAAAATGGCAGGATACTAGCATAAAAACAAACATA--G 4485
                           i ii   i v   i ii iiv i    i      ii i i     -- 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_121564402_   4486 ACCAATGGAGCAAAATGGAGAACCCAGAAATTAATACATATATTTACAGC 4535
                          i       ii i   v    ii        v  iv    i     ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_121564402_   4536 CAACTGATTTTTGACAAAGGTAGCAATAACACTCATTAGGGAAAAGGACA 4585
                            i       i     i   iv   v v  i   v i      - i i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATA 394

  chrX_121564402_   4586 GTCCCTTTAATAAGTGGTGCTAGGAAAACTGTATATCTACATGCAAAAGA 4635
                            ii  i  i  i       i   v     v   ? i            
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_121564402_   4636 ATAAAACTAGACTTTCACCTCTCGTCCTACAGAAAAATCAACTCAAAGTG 4685
                           i  ii i   iiii     v ii v  i v      i        i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_121564402_   4686 AATCACATGCCTGAATTTAAGATCCAAAATTATAAAATTACTAGAAGAAA 4735
                         i    ? vi   i   v     v i    i       i vi         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_121564402_   4736 A--TGGGAG-AAATGTTTCAGGACATTGGTCTGGGTAA-GATTGTATGAA 4781
                          -- i  ? -    -i   iv   v    vi i  i  - i  viv ii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_121564402_   4782 TAAGACTTCAAAAGTGCAGGCAATAAACGCAAAGGTAAACAAATAGGATT 4831
                           v   vi      ii  i    i   v v   ii  i i    v   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_121564402_   4832 ATGTTAGA-CTACAGATTTCTGCACAACAAAGAAAGCAATCAACAGAGTG 4880
                         vii i i -i  v i i  i  ii vv     i vi v     v i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_121564402_   4881 TAAAAACAACCTACAGGATGGGAAAAAAATATTTGCAAACTAATCT-TCC 4929
                         v   i      i    i      i    -          - v  v -  i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAA-TCATATATCT 741

  chrX_121564402_   4930 AACAGGGAATTAATATCCGGATTACATAAGGAGCT---GAAGC---ATA- 4972
                         i i i  i i vi     i  v  i    i  i  ---iv i ---   -
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_121564402_   4973 TAAAAAG-CAAAAACACAATCCAATTTAAAAATGAGCCAGTGATTTAAAT 5021
                                -    ----i  i      ?       i  v iv     i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAA----TAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_121564402_   5022 AGGGATTTCTCAAAAGAAAACATATAAATGACAGAGAAATATGTGAAAAA 5071
                           iv       v      i i   i     i vi v  ii ii      i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_121564402_   5072 AATACTCCACATCACTAACCTT 5093
                          - i   v      ????????
  L1M4_orf2#LINE/    888 A-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.31 (166 / 72)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.68 (32 / 19)  


2705 25.59 1.62 1.87  chrX_121570751_121573537     1292  2092 (695)    L1M4_orf2#LINE/L1        2   800 (108)  

  chrX_121570751_   1292 GGAAAGCTATTCTATGTGCATGGATTAGAAGAACCAATATTTTTTA-ATG 1340
                               v   i i    v        i     vii      v  v -   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_121570751_   1341 TCCATTCCACCCAAAGCAATGTACAGATTCAATGCAATCTGTATTAAAAT 1390
                         v v  v iv      vii  v           i      iv   i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_121570751_   1391 ACCAATGACATTCTTCACAGAAAT--ACAAAAAAAAAGACT-ATCCTAAA 1437
                         v   iivi v  i  ii       --    i--------  -        
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG--------CTGATCCTAAA 143

  chrX_121570751_   1438 ATTTCTATGGAACCACAAAACACCCAGAACAGCCAAAGCTATTCTAAGCA 1487
                            iv       vii   iiv        i       i v  ii i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_121570751_   1488 AAAAGAACAAAACTGCAGGAATCACATTACCGCACTTCAAATTATATACT 1537
                          i         ii  v    v     i v  vv i      -- iv    
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACT 241

  chrX_121570751_   1538 GCAGAGCTGTAGTAATCAAAACAGCATGGTATTGCCATAAAAACAGACTC 1587
                         i  i    ii         i    ii     i  v     ii i    vi
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_121570751_   1588 ACAGGCCAATGAAACAGAATAGAGAACCCAGAAACAAATCTACACATTTA 1637
                          i  ii     i  i     v    ii       i   i i i       
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_121570751_   1638 CAGTCAACTTATTGTTTG-CAACAATGCCAAAAACATACATTAAGGAAAG 1686
                         ii     i v   -  i -   vii      i v   v  v ii      
  L1M4_orf2#LINE/    342 TGGTCAATTGATT-TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_121570751_   1687 GACGGCATGTTTAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAG 1736
                         i ii iv v  i  i              v         ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_121570751_   1737 AAAGATGAAACTAGA----TGCCTTTCACCATATACAAAAATCAAATCAA 1782
                           ii     ii i  ---- i   iv                i  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_121570751_   1783 AATTGATTAAAGACTTAAATCTAAGACCTGAAACTATAAAAATACTGAAA 1832
                            v   i ?    i     v     v  i           v vi ii  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_121570751_   1833 GACAACATTGAG--AAACACTCCAAGACAATGGTCTGGGCAAATATTTCT 1880
                           v     v i?--   i-  i iv   vv   vi i     vvi     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_121570751_   1881 TAAGTAAAACCTCAAAAGCAAAGGCAATCAAATAAAAAAATAGACAAA-- 1928
                           ii  vi  vi        v i    -    vi          i   --
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAA-CAAAAGAAAAAATAGATAAATT 638

  chrX_121570751_   1929 GGAGATCAAATCAAGCTGAAAGGCTTCTGCGCAGCAACAGAAACAATCAA 1978
                            vv   --    iv v   ii   i  i  vv   vi  v  v     
  L1M4_orf2#LINE/    639 GGACTTCA--TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_121570751_   1979 GAAAGTGAAGAGACAATACACAGAATGAGATAAAATATTTGCAAACTACC 2028
                                  i      iv         i  v              ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_121570751_   2029 TATCTGACAAAAGATTAGTAACTACAATATGTAAGAGACCCAAATAACTA 2078
                                i  ii  i v   v i v     i   iii  i vv i    v
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_121570751_   2079 AATAGAAAAAAGAC 2092
                             iv        
  L1M4_orf2#LINE/    787 AATAATAAAAAGAC 800

Transitions / transversions = 1.69 (127 / 75)
Gap_init rate = 0.02 (13 / 799), avg. gap size = 2.15 (28 / 13)  

 341 24.11 3.57 0.00  chrX_121570751_121573537     2186  2297 (490)    L1M4_orf2#LINE/L1      793   908 (0)  

  chrX_121570751_   2186 AAAAAGAAAAAGAATCCAATTTTAAAATGTGTAAATGCTCCAAATAAAAA 2235
                                v   v  i      ?v      v i   v v iii    i v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_121570751_   2236 TTTCTCAAAAGACGACATACA--TGGCCAACAGGTATATTAAAAA--GTT 2281
                               v     v  i     --       i i i i  v    i-- i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_121570751_   2282 CACCACTAATACTTAG 2297
                           v  ii ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (15 / 11)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 2.00 (4 / 2)  


2337 24.83 5.12 4.34  chrX_121588426_121591038     1223  2120 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_121588426_   1223 AGAAATATTACATGCTCATGAAAAGGAAGAATCAATGTCATTAAAATGGC 1272
                          i i    iv    i     i vv      v i   i ii    i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_121588426_   1273 CTTACTGCCCAAGGGAATTTACAAGTTCAATGCTATTTCTTCCAAAATGA 1322
                         vv    v     ivvi  i    ii     i  v  ii  vi      vv
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_121588426_   1323 CA------TTGTTCACAGAA-TTAA-----TGATTGTAAAATTCATATGA 1360
                           ------  v  ii     -  i -----    iv             i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_121588426_   1361 AAA--CAAAGAGCCT-GAAGAGCCAAGACTATCCTAAGCAAAAATAAAAA 1407
                            --   i ii  i-   v      i  v   i i iv  i  v  v  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_121588426_   1408 AGCTGGAGGCATCACTCTACCCAACCTCAAACTATACTACACAGCTACAG 1457
                           i      vv    v  v     ii     viv       v        
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_121588426_   1458 TAACCAAAAGAGTGTAGTGCTGGTACAAAAACAGACTCATAGACCAATGG 1507
                            i   i v     i  i    i i  ii i    vi     i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_121588426_   1508 --CAAAGTTAGAAAACCCAGAAATAAAGCCACACACTT-TGCTCTTCAAC 1554
                         --i i i  -  i ii           v   i   i  -  ---------
  L1M4_orf2#LINE/    304 AATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTATG--------- 343

  chrX_121588426_   1555 TAAGTCAACAAAAAGTATCACCTGACCTTTGTCAAAGTCAACAAAAACAA 1604
                         ---     i-------------   ii  i v   i viiv   i v  v
  L1M4_orf2#LINE/    344 ---GTCAAT-------------TGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_121588426_   1605 GGAACAGGGAAATGACACCCTATTCAATAAATAGTGCTGGGATAACTGGC 1654
                         vv  ii      vi i vi  v     i    i         i      v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_121588426_   1655 TAGCCATGTGCAGAAGATTAATACTATGCCCTTTCCTTTCACCATATACA 1704
                           ?   ii    i    v i vii ivi   i v   iv           
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_121588426_   1705 AAAATCAAATCAAGATAGATTAAAGACTTAAATGTAAAACCTAAAAGTAT 1754
                              i  v    i  i   i ?    i         i v      v   
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_121588426_   1755 AAAAATACAAAAAGAAAAACTCAGAA--ACACCATTTGGGACAT-AGATC 1801
                             v viv i       - vi  i?-- v i -  i v   v -i i -
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAA-CATAGGNGTAAATC-TTCGTGACCTTGGGT- 574

  chrX_121588426_   1802 CTAGCAAAGAGTTTAT--GATGAAGACCCCAAAAGAAATTGCAGCAAAAA 1849
                         -   vv  vi    v --   - v   v       v vvv   i     i
  L1M4_orf2#LINE/    575 -TAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_121588426_   1850 CCAAAATTGAAAAAT-GAGCTTCTGCACA---------------GCT--A 1881
                         vv     v  v    - ii    vv  v ---------------   -- 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_121588426_   1882 AAGAA-ACTATCAACAGAGTAAACAGACAACCAACAGAATAGGAAAAAAT 1930
                            i -        v i   i  v        v       i   i     
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_121588426_   1931 ACTTGCAAACTATGCATCCAACAAAGGTCTAGTATCCAGAATCCATAAGG 1980
                          i       ii  ii   ii i  i  v  v           vi    i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_121588426_   1981 AACTTAAACAAATTAACAAGCAAAAAACAAA---CCCACTT-AAAAATGG 2026
                             ivv    v i  i  vv    i     ---    v  -        
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_121588426_   2027 GCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATACATGCATACGT 2076
                                 iv    i     i     v        i     ----- ---
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA-----A--- 864

  chrX_121588426_   2077 ATGGCCAAGAAGCATATAAAAAAAACCCCAATATCACTAAACAT 2120
                                 v     i  i    i vv i   i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (130 / 90)
Gap_init rate = 0.03 (25 / 905), avg. gap size = 3.40 (85 / 25)  


2770 25.60 2.29 3.38  chrX_121619422_121621343      512  1429 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121619422_    512 TGAAAACACATCCCATGCTCATGGATAGGTAGAATCAATATTGTGAAAAT 561
                           i   v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121619422_    562 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 611
                          i v     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121619422_    612 TACCA-CCGTCATTCTTCACAGAACTAGAAAAAGCAATCCTAAAGTTTAT 660
                          v   - i i -  i  ii     v v  v  ivii        i  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_121619422_    661 ATGAAATTAAAAAAGATCCTGCATAGC-ATGAC-----TAAGCAAAAAGA 704
                            i  v iv  ii  i  v v     - vi  ----- i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_121619422_    705 ACAAACCTGGAGGAATCACATTACCTAGGTTCAAAGGATACTATACGGCC 754
                              vi       v     i v  i iv      ivv     i vi  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_121619422_    755 ACAGTCACCAAAACAGCATGGTACTGGTAAAACAAACAAACAAACATAGT 804
                              v i   i    ii         i v  -ii i i   --i    v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAA-GGATAGACA--TATAGA 296

  chrX_121619422_    805 CCAACGGAACAGAATAGAGAAATCAAAAATAAACCCAAATACTTACAGCC 854
                         i   i    i     v    ivi  i           v i i   ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_121619422_    855 AACTGATCTTCAACAAAGCAAACAGAAACATGAAGTGGGGAAAGGACATC 904
                           i    i   i    i vviv  ii v   vv i         i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_121619422_    905 CTATTTAACAAATGATGCTGGGATAACTGGCAAGGCACATGTAGAAGAAT 954
                           v  i        i        i      vv ?v      i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_121619422_    955 GAAACTGGATCCTCACCTCTCATAGTATACAAAAATCAACTCAAGATGGA 1004
                            ii    i  ii     v  ivi           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_121619422_   1005 TCAAAGACTTAAATCTAAGACCTGAAATCATAAGGATTCTAGAAGATATA 1054
                            ?    i     v     v  i   ii    iiv ii       v vv
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_121619422_   1055 ATCAGAA-AAACCCTTGTAGACACTGGCTTAGGCAAAGACTTCAT-GATC 1102
                           vi ?i-   i i i  -   vi   v        v ii   v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chrX_121619422_   1103 AAGAAGCCAAAAGCAAATGCAGCATGAAACAAGATAGATG----GGACTT 1148
                          v  vi         v v   i  vi i v  i      i----      
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_121619422_   1149 AATTAAACCAAAAATCTTCTGCAGAGCAAAAGAAACAATCAGCCAAGTAA 1198
                         v  i   viv    v   i  iivvv    i  v  v    ivv    i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_121619422_   1199 ACAGACAACCCACGGGGTGGGGAAAAATCTTTGCAATCTGTACATCTAAC 1248
                          v           i ii    ii     v       viii  i    i i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_121619422_   1249 AAAGGACTAATATATAGAATCTACAAGGAACTC----AAATCAGCAAGAA 1294
                           i     vi   vi     v  i  i      ----  v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_121619422_   1295 AAAAACAATT---CCA-TAAAAAAGTGGGCTAAGGACATGAATACAAATG 1340
                            i    v ---   - v?    i     v     iv      ----- 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA-----G 839

  chrX_121619422_   1341 TTTCATATTTTTTTGCCCATTTGAATACAAAAAAAAGATAAATAAATGGC 1390
                         ---- i    i ----   ------------  i      v i       
  L1M4_orf2#LINE/    840 ----ACATTTCT----CCA------------AAGAAGATATACAAATGGC 869

  chrX_121619422_   1391 CAAGAAACATATGAAAAAATGCTCAACATCACTATCAGG 1429
                            v  i  i       i             ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (143 / 88)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.89 (52 / 18)  


2824 25.73 3.15 1.12  chrX_121623568_121628400     3451  4340 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121623568_   3451 TAGAAAAACTTCCCATGCTCATGGATTGGAAGAACCAATATCATTATAAT 3500
                          i    i iv       i               vii     ii   vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121623568_   3501 TACCATGCTGCCCATAGAAATCTACAGATTTAATGCAAAGCCTATCAAAA 3550
                         vi v  i  v    v vvi           i  i    vv          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121623568_   3551 TACCAA-TGTCATTTT--CACAAATTAGATAAAACAATCCTAAAATTAAT 3597
                          v   i-  i v    --  v     -  i  ivii           v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chrX_121623568_   3598 ATAGAACCAAAAAAAGAGCTCA-AATAGTCAAAGTAATCCTAAGCAAAAA 3646
                           i   -- viv  i ii i  -     i    ii    i i i-   i 
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGA 196

  chrX_121623568_   3647 GGAACAAAGCTGGAGGCATCACATTACCTGACTTCAAATTCTACAACAAG 3696
                         i        i      vv     i v  ii i      vii   v    i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_121623568_   3697 AGTACAGTAAGCAAAACGGCATGGTACTGGTA----------CTCATAGA 3736
                         iv        v   i  i ii         i ---------- vi     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_121623568_   3737 TCAATGGAACTAGA-TAGAGAGCCCGGAAATAAGGCCACATACGTATAGC 3785
                                  -    - v     i  i       iv   i i iv   i i
  L1M4_orf2#LINE/    297 TCAATGGAA-TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_121623568_   3786 CAACAGGTCTTTGACAAGGTTGACAA---CATACACTGAGCAAAGTACAT 3832
                            iv i i  i       v  v   ---   v  v  i v    v i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_121623568_   3833 TCTATTCAATAAATGGTTCTGGGAAGACTGGATAGCCATATGCAGAAGAA 3882
                            v     i       v      vi        ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_121623568_   3883 TAAAACTGAACTAATATCTTTTACTATATA-AAAAATTAAATCAAA-TGG 3930
                          i  ii  i  ivv  i  ivi  i     -         v     -   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_121623568_   3931 ATTAAAGACTTAAA----AGATCTATAACTATAAAATTTCTAAAAGAAAT 3976
                           i ?    i    ----   v   v          i ii  i      v
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_121623568_   3977 TCTAGGAA-AAACTCTCATTTCCATTGGCTTAGGCAAAAAAATTATGACT 4025
                         iv    ?i-   iii  i vv  -    v        viivv iv iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_121623568_   4026 AAGACCTCAAAAGCAAATAAAACTAAAACAAAAAATAGACTAATGTGACC 4075
                          v   vi        v viv   -    v          iv   vv   i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGGACT 643

  chrX_121623568_   4076 TAATTAAACTGAAAAGCTTCTGCATAGGAAAAGAAATAATTAACAGAGTA 4125
                          v  i   v v    i   i  iiivvv   i  v iv  i  v i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_121623568_   4126 AACAGGCAACCTATAGAGTGGGA-AAAATGTT-GCAA-TTATGCATCCAA 4172
                           v  i     i i   i     -     i  -    - i  ii   ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_121623568_   4173 CAAAGGACTGAAATCCAGAATCTGTAAGGATCTCAAACAACTCAACAACA 4222
                         i  i     viv         v i   i  v   vv         i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_121623568_   4223 ACAAAAATCCAAATAACCCCTCTAAAAAGTGGGCAAAGGACACGAACAGA 4272
                          -   i --          vvi ?    i           ivi   i   
  L1M4_orf2#LINE/    794 A-AAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_121623568_   4273 CATTTTGCAAAAGAAGACATACAAATGGCCAAAAAGCATGTGGAAAAATG 4322
                              iv v        i              v     ii  i   i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_121623568_   4323 CTCAACACCACTAATCCT 4340
                                i  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (138 / 87)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.81 (38 / 21)  


2725 22.06 3.07 3.34  chrX_121665490_121667212      487  1234 (489)    L1M4_orf2#LINE/L1      163   908 (0)  

  chrX_121665490_    487 GAACCCTAATACAATAGCCAAGGAAACCTTGAGAAAATAGAACAAAACAG 536
                          i    ---- v         iiv  i     i   iv        iiv 
  L1M4_orf2#LINE/    163 GGACCC----AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_121665490_    537 GAGG-CACAACACTTGCTGATTTCAAAAC--A-TATAAGGCTACAGTAAT 582
                             - v  -     v ii          -- -  i  i           
  L1M4_orf2#LINE/    209 GAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_121665490_    583 TAAAATAGTATGGTACTGGCATGAAGATGGGCATATAGAACAGTGGAATG 632
                         i  i i   i            i i   i i        v  i      -
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT- 306

  chrX_121665490_    633 CACCAGAATAGAAAGACCAGAGATAAATCCACGCATACACAATCAACTGA 682
                         ----     v  i  v     i     i   ii   vi iii    i   
  L1M4_orf2#LINE/    307 ----AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_121665490_    683 CCATTGACTAGAGTGCCGAGAC-AT--AATGGG---AGAATAGTCTCCTT 726
                         iiv i   v  i     i    -  --      ---          ii i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_121665490_    727 AA---ATGATGTTGGAGAGACTGTATATCATCCCAGTGCACAAGAATGAA 773
                           ---   i  i   iivi    v   ? -- v  -    v         
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKC--CACA-TGCAAAAGAATGAA 449

  chrX_121665490_    774 ATTGGACCCTTATCTTACATTATACTCAAAAATCAACTCAAAATGGTTTG 823
                         i        i  i  i   ii   iv       i            v ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_121665490_    824 AAGATTTAAATGTAAGAGTAAAAAATCTAAAACGCCTGGAAGAAAACATA 873
                         ?   ii            iv    v v      v i i            
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_121665490_    874 GGGAAAAAGCTTCTTGACACTGGACTTGACAATGATTTCAAGGTTGTAAC 923
                           ?iv   v    v    vi   ii v i     i    vvi v i i  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_121665490_    924 ACCAAAAGCACAGGCAACAAGAGCCAAAATAGACCGGCGGGATTACATCC 973
                                     i       i  vv        iviiiv   i v    v
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_121665490_    974 AACTACAAAGCTTTTGCACAGCAAA---------CAACAGAGTAAAAAAG 1014
                           v vv   i      ii vv    ---------   v i   i    ii
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_121665490_   1015 CAATGTACAGAATGGCAGAAAATATTTGCAAACCATACATCAGATAAGGG 1064
                            ivi         v                i    i   v        
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_121665490_   1065 GTTAATTTCTAAAATATATAAATAAGGAACTCAAACAACTCAATAGCAAA 1114
                         ii vi v  i i          ----      vv           -----
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAA----GAACTCTTACAACTCAATA----- 790

  chrX_121665490_   1115 AGAAAAAAAACCCTAATAACCTGACTAAAAAATGGCCAAAGAATTTGAAT 1164
                          v     i --- v       ii i ?        v     i        
  L1M4_orf2#LINE/    791 ATAAAAAGA---CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_121665490_   1165 AAACATTTTTTCAAATAAGACATACAAATAGCCAACCGGTCCATGAAAAG 1214
                          i      i i    v    i        i     ivi iv         
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_121665490_   1215 ATACTCAA-GTCACTAATCAT 1234
                           i     -i   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (106 / 55)
Gap_init rate = 0.02 (17 / 746), avg. gap size = 2.82 (48 / 17)  


2832 26.77 1.09 2.29  chrX_121780017_121783665.rev     2240  3158 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121780017_   2240 TGGAAAAACCTTCCATGCTTATGGATAGCAAGAATCAATATCATGAGAAT 2289
                               i iv i     i i      v v    v i     ii v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121780017_   2290 GGCCATACTGCCTAAAGTAGTTTATAGATTCAATGCTATTCCCATCAAAC 2339
                            v     v  i   v ii i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121780017_   2340 TACCATTTACATTCTTCACAGAATTAGAAAAAACCTG-TTTTAAAATTCA 2388
                          v   vi i v  i  ii     v v  v  i--   - ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_121780017_   2389 CATGGAACAAAAAAAGAGTTCACA-TAGCCAAGACAATCCTAAGCAAAAA 2437
                         i      - viv  i iiii  v -       i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_121780017_   2438 GAACAAAGCTGGAGGCATCATGCTATTTGACTTCAAACTATACTACAAGG 2487
                                 i      vv   ii  viiii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_121780017_   2488 CTACAGTAACAGAAACAGCATGGTACTGGTACCAAAACAGACATATAGAC 2537
                                  ivi i    ii         i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_121780017_   2538 CATTGGAACAGAATAGAGACCTGAGAAATAAGACCACACATCTACAACCA 2587
                           v     i     v    viiv        iv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_121780017_   2588 TCTGATCTTCAGCAAAAATCGACCTGACAAAAACAAACAATGGGGAAAGG 2637
                         vi    i   ii   iii ------ v   i v  vv            i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGT------GCCAAGACCATTCAATGGGGAAAGA 391

  chrX_121780017_   2638 ATTCGATTCCCTATTTAATAAATGGTGCTAGAAAAACTGGCTAGCCATAT 2687
                           --- v  -- v  i  i          i i v      v  ?   i  
  L1M4_orf2#LINE/    392 AT---AGTC--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_121780017_   2688 GCAGAAAACTGAAACCGGACTCCTTCCTCACACCATATACAAAAATTAAG 2737
                            i  i v    iii    i   v                        v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_121780017_   2738 TCAAGATGGATTAAATACTTAAATATAAAACCCAAAACCATAAAAACCCT 2787
                             i      i ? v  i     i   i v i     i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_121780017_   2788 AGAAGAAAACCTAGGCA-ATACCATCAGGACATAGCCAGG---GGCAAAG 2833
                                   v    ?i- v i v  iv   v v ---  ---     v 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG---GGTTAGGCAATG 583

  chrX_121780017_   2834 ATTTTAT-GATGAAATCACCAAAAGCAATTGCAACAAGAGCTAAAATTGA 2882
                         i   iv -   ivi -           vvv       i  vv     v  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_121780017_   2883 CGAATGAGATCAAATTAAACTAAAGTGCTTCCGCACAGCAAAAGAAACTA 2932
                         ii   vi  iivv  i   v v  ivi   ii ii vv    i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_121780017_   2933 TCATCAGAGTGAACAGGCAACCTACAGGTAATTGGAGAAAATTTTTGCAA 2982
                            vv i      v  i     i    --   v         v       
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAG--AATGGGAGAAAATATTTGCAA 730

  chrX_121780017_   2983 TTTACCCATAAGATAAAGGTCTAATATCCAGAATTTACAAGAAATTTAAA 3032
                         v i ivi  vv     i  v  vi          v  i  ii  i ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_121780017_   3033 CAAATTTATAAGAAAAAAAACAAACAACCCCATCAAAAATTAGGCAAAGG 3082
                            v iv    v     i -    i     v  i?    v i        
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_121780017_   3083 ATATGAACAGATACTTCTCAAAAGAAGACAT-TATGCGGCCAA--AACAT 3129
                           v    i   i i     v        i  -i vii      -- i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_121780017_   3130 ATGATAAAAAGCTCAACATCACTGATCAT 3158
                             v  i v           ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (147 / 95)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.94 (31 / 16)  


1629 25.97 14.35 1.72  chrX_121792814_121797568     3568  4264 (491)    L1M4_orf2#LINE/L1      124   908 (0)  

  chrX_121792814_   3568 ATTGACAAACTGACTCTAAAATTTATAGAAAAAAGCAAAGTTACTAGAAT 3617
                                 i    ii        i   vii   v    i vvv i     
  L1M4_orf2#LINE/    124 ATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAAT 173

  chrX_121792814_   3618 AGCCAAGACAATTTTGAAAGA------CAAATTTGGAGAACATACATTAC 3661
                               i     i      i ------    v      i  vi   i v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_121792814_   3662 TCAATTTCAAGAATTACTATAAAGTTCCAACAATCAAGAGAGTGCAACAC 3711
                         i         i v      i    i v  ii        v    iiii  
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_121792814_   3712 TGCTGAAATTATAGATATATTGATCAACG-AACAGAATAGAGTGCCCAGA 3760
                           viiv  vv     i    v      i -  i     v   v i     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_121792814_   3761 AGTAGACATGCACAAATGTAGTCAACTAATTTTTGACAGAGACATGAAGG 3810
                          i  i  viii   vv i i     i i     i    ii iiiiv   i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_121792814_   3811 TAATTCAATAGAGAAAGGATAGTCTTTTCAATAAATGGTACTGAAACAGT 3860
                         iv       i i     i             i       i   ii   ii
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_121792814_   3861 TACAAGTCAATATGTAAAATAATGAATAAATAAGGCTGGATATGAACTTT 3910
                          iv vi? v i   i    v      -------- i    ivivv  i i
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAA--------GTTGGACCCCTACCTC 465

  chrX_121792814_   3911 ACACCTTA---AAAAATTAACTGAAAGTAGACTATACAACTAATTGTAAA 3957
                              v  ---           v   i i  ii ? v v    v     i
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_121792814_   3958 TAGC-ACAATTGTAAAATTTCTAGAAAAAAATACAAG---AAATGCAATG 4003
                         -   - v  i i     i ii     i    i i i ---    - vvi 
  L1M4_orf2#LINE/    516 -AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCG 563

  chrX_121792814_   4004 CTATCTTGGGCTTGATGATGCATT--TATATACAACACTGAAAGCATGAA 4051
                         iv i      i v iii   vv  --  v   ii    ii      ii i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_121792814_   4052 C--CA-----------------------TTTTTTTAAAATGTTAAG---- 4072
                          --  -----------------------i  iv i     --   i----
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT--TAAAAACT 661

  chrX_121792814_   4073 -TTGAACTTCA-------CT-----GAAA-TGAAAAAA------------ 4096
                         -   vi     -------  -----    -      i ------------
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_121792814_   4097 ----AAAAAAGCTTT-TAAACC-----TTT--TAAAG---------CCAG 4125
                         ---- i    vv   -i   i ----- i --   i ---------    
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_121792814_   4126 AATATACAAATGAGACTTAAAAGTCAACAATAAAAAAGCAA----CCCAA 4171
                               i   vi vv    v  v    i        ii   ----     
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_121792814_   4172 CTAAAAAATGAGCAAAAGATTTGAACA---AGTTATC-AAAGAAGATATA 4217
                         i ?       i     i        i --- v  v  -            
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_121792814_   4218 CAAAGAGCAAATAAGCATATAGAAAAATACTCAATATAATTTGTCTT 4264
                             vi  v        i  ii   i  i     i  v ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (121 / 57)
Gap_init rate = 0.03 (24 / 785), avg. gap size = 4.67 (112 / 24)  


3240 25.70 1.45 0.44  chrX_121812328_121814284.rev      570  1468 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121812328_    570 TGGAAACACATCCCATGCTCATGGATGAGTAGAATCAATATTGTGAAAAT 619
                               v i        i        vi v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121812328_    620 GACCAGACTGTCCAAAGCAATCTATAGATTCAGTACAATTTCCATTAAAA 669
                          i v v   vi     vii     i       iii    ii i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121812328_    670 TGCCATCATCATTTTTCACAGAACTATAACAAAC-AATCCTAAAATTTAT 718
                          v   v vv v     ii     v - i    i -i           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_121812328_    719 ATAGAACCATAAAAGAGCCTGCATATCCAAAGCAATACTAAGCAAAAAGA 768
                           i   viii  ii  v  v v   v     i    vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_121812328_    769 GCAAATTTGGAGGCATCACATTATCCAACTTCAAATTATACTACAAGGCT 818
                         i    v       vv     i vi    i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_121812328_    819 ATAGTTACCAAAACAGCATGGTGTTCATATAAA-ATAGGCACATAGACCA 867
                          i   v i   i    ii    ii vii    i-    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_121812328_    868 ATGAAATAGAATAGAGAATCCAGAAATAGAACCAAATACTTACAGCCAAT 917
                            i        v    i          i v   v i i   ii i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_121812328_    918 TGATCTTTGACAAAGCATACACAAA--CATAAATTGGGGAAAGGACACCC 965
                             i  i     i -i i -   i--   vv v         i i vi 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGC-CAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_121812328_    966 TATTCAATAAATGGTGCTGGAAAAACTGGCAAGACACATGTAGAAGAATG 1015
                          v     i            i v      vv ?v      i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_121812328_   1016 AAACTGGATTCTCGTCTCTCACCTTATCCAAAGATCAACTGAAGATGGAT 1065
                           ii    ii iiii   v    v   v    i  i    v  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_121812328_   1066 CAAAGACTTAAATATTAGACCTGAAACCATAAAAATTGTAGAAGATAACA 1115
                           ?    i     i v   v  i    i      v iv       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_121812328_   1116 TAGGAAAAACTCTTCTAGACATTGGCTTATGCAAATAATTCATGACTAAG 1165
                             ?iv  v     vv   v    v   v    vviv   v iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_121812328_   1166 ACCCCCAAAGCAAATACAACAAAAACCAAAAATAAATAAATGGAATCTAA 1215
                           v  v      v vi        iv-       i      v i ii v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCA 646

  chrX_121812328_   1216 TTAAAGTAAAAAGCTTCTGCACAGCAAAGGAAATTATCAGCAGAGGAAAC 1265
                          i   i v    i   i  ii vv       v i     iv i  vi  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_121812328_   1266 AGACAACCCACAGAGCGGGAGAAAATATTAGCAAACTATGCATCTGTCAA 1315
                                       ii             v     ii  ii     vi  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_121812328_   1316 AGGACTAATATCCAGAATCGACAAGGAACTCAAATAG---AGCAAGAGAA 1362
                         i     vi          vv i  i      vv i i--- ii  v i  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_121812328_   1363 AAACAAATAATCTCATCAAAAAGTGGGCAAAGGACATGAATAGACATTTC 1412
                          i        i iv  i?    i           iv              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_121812328_   1413 TTAAAAGAGAATATACA----GCCAACAA--ACATGAAAAAATGCTCAAC 1456
                          iv     ii       ----     i  --         i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_121812328_   1457 ATGACTAGTTAT 1468
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (137 / 90)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


2773 27.26 0.69 1.26  chrX_121869300_121871145      481  1353 (493)    L1M4_orf2#LINE/L1       41   908 (0)  

  chrX_121869300_    481 TTTTTAATAATGGCCACAGTGCCCAAAGTAATTTATAGATTCAATGCTAT 530
                           v    -i     v i v v      v i  i  i        i  v  
  L1M4_orf2#LINE/     41 TTGTTAA-GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

  chrX_121869300_    531 TCCCATTAAACTACTATTGACATTCTTCACAGAATTAGAAAAAAAAACT- 579
                         i  i  i   v v i vivi v  i  ii     v v  v  i----  -
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTG 135

  chrX_121869300_    580 ATTTTAAAATTCATATGGAACCAAAAAAGAGCCCATAG-AACCAAGACAA 628
                           ii                viiv  ii  -    v i- i    i    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAA 184

  chrX_121869300_    629 TCCTAAGCAAAAAGAATAAAGCTGGAGGCATCACCCTACCAGACTTCAAA 678
                           i i iv  i     i    i      vv    v  v  vi i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_121869300_    679 CTATACTATAAGGCTACAATAACGAAAATAGCATGGTACCGGTACAAAAA 728
                         viv     i  i      i   iv  i i  ii      i  i i  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_121869300_    729 CAGACACATAGACCAATGGAACAGAATGAAGAACTCAGAAATAAGATCAC 778
                         i     i     i        i     vi   iii         ivi  i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_121869300_    779 TCATCTACAA-CAATCTGATCTTCGACAAACCCGGCAAACACAAGCAATG 827
                         v   i  iii-    -    i        ivvi v   ivv  vv     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_121869300_    828 GGGAAAGGACTGCCTGTTTAATAAATGGTGCTGGGAGAACTGGCTATCCA 877
                                i iv i  v  i  i              v      v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_121869300_    878 TTTGCAGAAAATTGAAAGTGGACCCCTTCCTCACACCTTATACAAAAATT 927
                         iv    i  i v    iv         v         v            
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_121869300_    928 AACTCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAAC 977
                                i      i ?    i         i v i            vi
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_121869300_    978 CCTAGAAGTAAATCTAGGCA-ATACCATTCAGGACATAGGCACAGGCAAA 1026
                          i      v   iv    ?i- v i -   iv   v v  vvi      v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAAT 582

  chrX_121869300_   1027 GATTTCAT-GATAAAATCACCAAAAGCAGTTTCAACCAAAGCAAAAAAAT 1075
                          i    v -    vi -           vvvv    v    --       
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAG--AAAAAAT 629

  chrX_121869300_   1076 TGACTAATAGGATCTAATTAAACTACAGAGCTTCTGCACAGCAAAAGAAA 1125
                         v  iv   v   ii v  i   v vv i i   i  ii vv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_121869300_   1126 CTATCATCAGAGTGAACAGGCAACCTATGAAGTGGGACAAAATCTTTGCA 1175
                               vv i      v  i     i iii i     v     v      
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_121869300_   1176 ATCTATCTATCTGACAAAGGTCTAATATCCAGCATCTACAAAAAACACAA 1225
                          vii  v       i  i  v  vi       v  v  i   i   v vv
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_121869300_   1226 ACAAATTTACAAGAAAAAAACAGACAATCCCATTAAAAAGTGGGCAAAGG 1275
                             v iv i  v     i   i i  i  v   ?    i          
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_121869300_   1276 ACATGAACAGATGCTTCTCAAAACAAGGCATTCATGCAGCCAACAAACAT 1325
                          iv    i   iii     v   v   ii  v  viii     i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_121869300_   1326 ATAAAATAA-ACTCAACGTCACTGATCAT 1353
                           i   vi -i      i   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.01 (13 / 868), avg. gap size = 1.31 (17 / 13)  


3246 25.41 1.55 1.22  chrX_121880019_121885284     3869  4773 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121880019_   3869 TGGAAACACATCCCATGCTCATGGATAGGTAGAATCAATACTGTAAAAAT 3918
                               v i        i        v  v   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121880019_   3919 GACTCTACTGCCAAAAGCAATCTATAAATTCAATGCACTCTCCATCAAAA 3968
                          i vv    v  v   vii     i i      i   v  i i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121880019_   3969 TACCACCATTG--TTTTTCACAGAATTAGAAAAAGCAATTCTAAAATTCA 4016
                          v   v --  --     ii     v v  v  ivii  i          
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_121880019_   4017 TATGGAACAAAAAAGAGCCCACA-TAGCCAAAGCAAGACTAAGCAAAAAG 4065
                                vviv  i ii    v -        i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_121880019_   4066 AACAAGTCTGGAAGCATCACACTACCTGATTTCAAACTATACTATAAGGC 4115
                              ivi    i vv       v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_121880019_   4116 CATAGTCACCAAAACAGCATGGCACTGGTATAAAAATAGGCACATAGGCC 4165
                         i i   v i   i    ii   i     i    ii    i  i    ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_121880019_   4166 AATGGAACAGCACAGAGAATCCAGAAATAAACCCAAATACTTATAGCCAA 4215
                                i  v iv    i                v i i    i i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_121880019_   4216 CTGATCTTCAACAAAGCAAACAAAAACATGAAGTGGAGAAAGGACACCCT 4265
                         i    i   i    i vviv   i v   vv i   i     i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_121880019_   4266 TTTCAACAAACGGTGCTGGGATAATTGGCTAGCCACATGTAAAAGAATGA 4315
                                   i          i  i   v  ?       i          
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_121880019_   4316 AACTGGATCCTCATCTCTCTTCACCTTATACAAAAATCAATGCATGATGG 4365
                          ii    i  ii i   v ---   v           i  iv  vi    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCAC---ACCATATACAAAAATTAACTCAAAATGG 495

  chrX_121880019_   4366 ATTAAGGACTTAAACCTAAGATCTGAAACTATAAAAATTCTAGAAGTTAA 4415
                           i ?i   i    iv     v  i           v ii      vv  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_121880019_   4416 CATTGGAAAAACTCTTCCAGACATCGGCTTAGGAAAGGATTTC------A 4459
                            v  ?iv  v     vv   v i  v     v  v i    ------ 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_121880019_   4460 TGACAAAGAACTCAAAAGCAAATACAATAAAAATAAAGATAAATAGCTGG 4509
                              ------i        v vi   i    iv   i   i   iv v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_121880019_   4510 GACCTAATTAAACTAAAGAGCTTTTGCACGGCAAAAGGAACAGTCAGCAG 4559
                            i v  i   v v  i i      ii vv    i iv  vi   iv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_121880019_   4560 AGTAAACAGACA-CCCACAGAGTGGGGGAAAATCTTCACAATCTATACAT 4608
                            i  v     -        i    i      v  ii   vii   i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_121880019_   4609 CTGACAAAGGACTAATTTCCAGAATCTGCAACAAACTCAAACAAATCAGT 4658
                             i  i     vi v        v ii  vi     vv    v   i 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_121880019_   4659 AAGACAAAAACAA----TCCCATCACAAAGTGGGCTAAGGACATGAATAG 4704
                           v v   i    ----i  v  i?v   i     v     iv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_121880019_   4705 ACAATTTTCAAAAGAAGACATACAAATGGCCAACAAACATATGAAAAAAT 4754
                            v  i  v        i              i  i  i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_121880019_   4755 GCTCAACATCACTAATGAT 4773
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (135 / 91)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.12 (25 / 8)  


2672 29.62 0.44 1.20  chrX_121981680_121987039     3953  4867 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_121981680_   3953 TGAAAAAACATTCTTTGCTCATGGATAGGAAGAATCAATATCATAAAAAT 4002
                           i   i i  i iv  i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_121981680_   4003 GTCCATACTGCCCAAAGCAATTTATAGGTTCAATGTTGTTCCCATTAAAC 4052
                          v v     v      vii  i  i  i     i ivi i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_121981680_   4053 TACCAGTGACATTCTTCACAGAACTAGAAGAAAACT-ATTTTAAAATTCA 4101
                          v    ivi v  i  ii     v v  v--  i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chrX_121981680_   4102 TATAAAACCCAAAAAGAGCCCAAATAGCCAAGGCAATCCTTAGCAAAAAG 4151
                            ii  vivv  ii  v  vi         ii     i v iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_121981680_   4152 AACAAAGCGGGGGGCATCATGTTACCTAACTTCAAACTATACTACAGGGC 4201
                                iv  i  vv   iii v  i  i      viv       ii  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_121981680_   4202 TCCAGTAAACAAAAGAGCATGGTACTGTTACAGGAACAGACACACAGACC 4251
                          v      v   i v  ii        vi i i i i     i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_121981680_   4252 ATTGGAACAGAATAGAGAACCTAAAAATAAGACTGTACACATACAAGTAT 4301
                          v     i     v    ii i i      iv ii    iv  iiivi v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_121981680_   4302 CTGAACTTCAACCAACCTGACACAAGCAAACAATGGGGAAAGGATTCCCT 4351
                         i   vi   i  v ivv  v  vi v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_121981680_   4352 ATTCAATAAATGGTGTTGGGGTAAACAGCTAGTCATATGCAGAAGATTGA 4401
                         v     i        i    ii  vii v  ?i  i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_121981680_   4402 AACTAGACCCCTTCCTTACACCATATGCAAAAATTAACTCAAGATGGAAA 4451
                          ii i       v   i         i               i     vv
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_121981680_   4452 AAATGACTTAAATGTAAAACCCAAAACTATAAAATCCCTGGAAGACAACC 4501
                          ? -   i         i v i            ii i i     v   v
  L1M4_orf2#LINE/    499 AWA-GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_121981680_   4502 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACAAA 4550
                             ?i- v i -   iv   v v  vv i     v ii   v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_121981680_   4551 GATGCCAAAAGCAATTGCAACAAA-GCAAAAATTGACATATGGGGTCTAA 4599
                           ii         vvv        - v      v  i v  v  iii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_121981680_   4600 TTTGACTAAAGACCTTCTGCACAGCAAAAAAAAAAAAAACTATCAACAGC 4649
                          ivi v v  i v   i  ii vv    ii v ------       v iv
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACA------CTATCAAGAAA 690

  chrX_121981680_   4650 ATAAACAGAAAACCTATAGATCGGGAGAAAATTTTTGAAAACTACGCACC 4699
                         i i  v   v    i i   vi          v    v   ii iii i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_121981680_   4700 TGACAAAGGTCTACTATCCAGCATCTATAAGGAACTTAAACAAATTTACA 4749
                            i  i  v  vv       v  v     i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_121981680_   4750 AGAAAAA-ACAAATGACCCCATTATAATGTGGGCAAAGGACATGAATAGA 4798
                          v     -      i    v   ?v  vi           iv        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_121981680_   4799 TACTTTTCAAAAGAAGACATACATGCAGCCAACAATCATATGAAAAAAAA 4848
                         i i  i  v        i     viii     i  v  i       i v-
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT- 889

  chrX_121981680_   4849 GCTCAACATCACTGATTAT 4867
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (156 / 111)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3955 19.91 1.08 2.81  chrX_122008981_122010899      503  1426 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_122008981_    503 TGGAAAGGCTTCCCATATTTAATGGCTCGGAAAACTTAAT---GTTAAGA 549
                                iiv      i  i -   v i    i       ---       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCA-TGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_122008981_    550 TTCCAGTGCCACCCAAAGCAATCTACAGATTCAGTGTAATCCCATTCAAA 599
                          vv  i i iv      vii             ii i      vv     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_122008981_    600 ATCCCAATTATATTTTTTTCCAGAAAT-AAGAAATCAATCCTAAAACTTT 648
                               ii ii-i      v       -i v  iiii         i iv
  L1M4_orf2#LINE/    100 ATCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_122008981_    649 TATGGAATTTCAAGGTACCAGGAATAACCAAAACAATCTTGAAAATAAAG 698
                                v v     v   vi     i                  vi   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_122008981_    699 AACAAAATTGTAGCACTCACACTTACTTATTTCAAAAGTTACCAGAAAGC 748
                               i   v  v          v iv         v    i v     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_122008981_    749 TACAGTTATTGTAACAGTATGGCACTGGAATAAAGATAGACATATAGATC 798
                               v  iivi     i   i     v    i                
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_122008981_    799 AATT-AATAAAATAGGGAACCCAGAAATAAATCCTCACATATATGATCAA 847
                            v-    i   v i  ii           i  vi    v    i    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_122008981_    848 ATGATCTTTGACAAGTGTTCTAGGACCATTTAAGAGGGGACAAGAGAGTC 897
                         v    i  i      v  v i i       i  v-     v ii v    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGTC 397

  chrX_122008981_    898 TTTTCAACAAAAGGTGCTGAGAAAACTGGATATCCACATGCAAAAGAATA 947
                                    v       i  v         ?                i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_122008981_    948 AAGTCAGACCCTTAACTAATATTATGTACAATTTTTGTACATAGCTAATC 997
                             ii     i  v  v i ii  i     ----------- ---   -
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAA-----------A---AAT- 482

  chrX_122008981_    998 TTTAATTCAAAATGGATCAAAGACTTAAATATAAGAGCTAAAACCATTAA 1047
                         --   i             ?    i     i             i  v  
  L1M4_orf2#LINE/    483 --TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_122008981_   1048 ACTCTTGGAAGAAAA--TAGGCG-AGAGCTTTACAACATTGCATTTGGCA 1094
                               i        --    ? - i v   iiii  v   vi  v    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_122008981_   1095 ATGATTTCTTGGATATGACACCAAAAGTACAAGTAAGTAAGGCAAAAATA 1144
                            i      i                i     i  vv  i v       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_122008981_   1145 AACAAACTAAAAATGATAAAAACTAAAAACTATTATGCATCAAAGAATAC 1194
                         i i   i ii vv v  v    i        v  i   v      i i  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_122008981_   1195 TATCAACATATTGAAAAGGCAATCTGGGCAATGGTATAAAATATCTGCAG 1244
                               v v v       i   i iiviv     v v       i    i
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_122008981_   1245 ATCATATGTCTGCTAACGAATTCATATCCAGAATATACAGAGAACACT-A 1293
                                i    v   v i i ii             i i     v  - 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_122008981_   1294 AAACTCAACAACAAAAACAAAACCCCAAACAATCCAACT-AAAAATGGGC 1342
                         v       i  i     v ------    i  i    i -          
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGA------CAAATAACCCAATTWAAAAATGGGC 824

  chrX_122008981_   1343 AAAAAACTTGAATAGACATTTCTCCAAAGAAGATATATTAATAGCCAATA 1392
                            ii i                              iv   i       
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_122008981_   1393 GGTCCTTGAAAAGATGCTCAACATTAGTAATCAT 1426
                         i iv v                  i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (113 / 68)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.57 (36 / 14)  


3145 26.30 0.66 0.55  chrX_122021701_122024029.rev      934  1838 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_122021701_    934 GAAACACATCCCATGCTCATGGATGGTAAAA-TCATTATTGTGAAAATAA 982
                             v i        i        v v  i - i v      v  i  ii
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_122021701_    983 CCATACTTCCAAAAGCAATCTACAAATTCTGTGCCATCCCCATCAAAATA 1032
                          v     i  v   vii       i    vii  v     i        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_122021701_   1033 CCA-CGATCATTCCTCACAGAATTAGAAAAAAACAATTATAAAATTCACA 1081
                            - vii -  ii ii     v v  v  iv-ii  iv         i 
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATA 150

  chrX_122021701_   1082 TGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 1131
                              viiv  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_122021701_   1132 CAAATCTGGAGGCATCACATTACCTGATTTCAAAGTATGCTATAAGACCA 1181
                             vi      vv     i v  ii        iiv i   i  ii i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_122021701_   1182 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCAA 1231
                         i   v i   i    ii         i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_122021701_   1232 TGGAACAGAATAGAGAATCCAGAAATAAACCCAAATATTTACAGCCAGCT 1281
                              i     v    i                v i     ii i  ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_122021701_   1282 GATCATCGACAAAGCAAACAAAAAGACAAAGTGGGGAAAGGACACCCTTT 1331
                            iv       i vviv   i vv ivv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_122021701_   1332 TCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGAAA 1381
                                            i  i   v  ?       i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_122021701_   1382 CTGTGTCCTCACCTCTCACCTTATACAAAAATCAACTCATGATGGAT-AA 1430
                         i  vii  ii     v    v           i      vi      - ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_122021701_   1431 GGACTTAAATCTAAGACCTGAAACTATAAAAGCTCT-AGAAGCTAACATT 1479
                         i   i     v     v  i           -    -     vv     v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATA 549

  chrX_122021701_   1480 GGAAAAACCCTTCTAGATACTGGCTTAGGCAATGATTTCATGACCAAGAA 1529
                           ?iv  vi    vv  ivi   v          i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_122021701_   1530 CCCAAAAGCAAATGCAATAAAAATAAAGACAAATTGCTGGTACTTAATTA 1579
                         v         v v    i    iv   i i i  viv v v    v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_122021701_   1580 AACTAAAGAGCTTTTGTATAGCAAAAGA-ACAGTCAGCAGAGCAAAGAGA 1628
                           v v  i i       iivv    i  -  vi   iv i  ii  i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_122021701_   1629 CAACCCACAGAGTGGGAAAAAA-ATCTTCACAATCTATATATCTGACAAA 1677
                                    i     i    -  i v  -    -          i  i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGATAAG 747

  chrX_122021701_   1678 AGACTAATATCCAGAATCTACAATGAATTCAAACAAATCAACAAGAAAAA 1727
                         i    vi          v  i  v   i  vv    v    i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_122021701_   1728 AACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGGCAATTCC 1777
                         i     i  i  v  i?    i     v     iv       i  v   i
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_122021701_   1778 AAAAAGAAAGCATACAAATGGCCAACAACTATATGAAAAAATGTTCAATA 1827
                         vv      iii              i  vi i       i   i    i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_122021701_   1828 TCACTAATGAT 1838
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.00 (11 / 11)  


3241 26.15 0.55 0.77  chrX_122141839_122148563     5326  6235 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_122141839_   5326 TAGAAAAACATTCCATGCTCATGGATAGAAAGAATCAATATCGTGAAAAT 5375
                          i    i i  i     i        v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_122141839_   5376 GGCCATATTGCCCAAAGTAATTTATAGATTTAATGCTATCCCCATCAAGC 5425
                            v   i v      v i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_122141839_   5426 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5474
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_122141839_   5475 AAGGGACCAAAAAAGAGCCCATATAGCCAAGACAATACTAAGCAAAAAGA 5524
                          v  i viiv  ii  v  viv        i     vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_122141839_   5525 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTTTACTACAAGGCT 5574
                               i      vv    i  v  ii i      vi         i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_122141839_   5575 GCAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGATATATAGACCA 5624
                         i      i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_122141839_   5625 ATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCATC 5674
                               i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_122141839_   5675 TGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTA 5724
                             i  i     ivv  vv  i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_122141839_   5725 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCATTATGCAGAAAACTGAA 5774
                           i  i        i     v      v  ? vvi     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_122141839_   5775 ACTGGACCCCTTCCTTACACCTTATAAAAAAATTAACTCAAGATGGATCA 5824
                         ii         v   i     v    v              i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_122141839_   5825 TAGACTTAAATGTAAGACCTAAAACCATCAAAACCCT-AGAAGAAAACCT 5873
                         ?    i           v       i  -     i  -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chrX_122141839_   5874 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 5922
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_122141839_   5923 ACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGGATCTAAT 5972
                                     vvi          vv i   v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_122141839_   5973 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCA-TCGAGTGAACA 6021
                         i   v v  i i   i  ii vv    i  v       -vvi      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_122141839_   6022 AGCAACCTACAGAATGGGAGAAAATCTTTGCAATCTATCCATCTGACAAA 6071
                         ii     i                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_122141839_   6072 GGGCTAATATCCAGAATCTACAAGGAACTTAAACAAACTTACAGGA-AAA 6120
                           i  vi          v  i  i     ivv    -  i - vi -   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCA-ATAATAAA 795

  chrX_122141839_   6121 AAAACAAATTACCCCATCTAAAAGTGGGCAAAGGATATGAACAGACACTT 6170
                           i      v    v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_122141839_   6171 ATCAAAAGAAGACATTTACGTGGCCAACAAACATATGAAAAAAAAAGCTC 6220
                         v  v        i  vi vi       i  i  i       i v--    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT--GCTC 893

  chrX_122141839_   6221 ATCACTACTGGTTAT 6235
                          v  ii ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.09 (12 / 11)  


3569 24.92 0.33 1.95  chrX_122245080_122249951.rev     3458  4380 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_122245080_   3458 TGGAAAGACACCCCACGCTCATGGATTGAAAGAATTAATATTGTTAAAAT 3507
                                 i i    i i          i    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_122245080_   3508 GACCATACTACTCAAAACAATCTACAGATTTCATGCAATTCCTGTCAAAA 3557
                          i v     v i    vii           iv i     i   i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_122245080_   3558 TACCAA-TGTCATATTTCACAGAAAATAGAAAAAAAAATCCTAAAATTCA 3606
                          v   i-  i v -   ii      v -  v  ivvi             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCA 148

  chrX_122245080_   3607 CTTGGAA-TGAATAAAGAGTCCA-AGTAGCCAAAGCAACCCTGAGCAAAA 3654
                         iv     -  --i  i iii   - i        i   i i   iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATG--CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_122245080_   3655 AGAACAAAGCTGGAGGCATCATACTACCTGACTTCAAGATGTGTCACCAG 3704
                                  i      vv   i   v  ii i     i iv iii  v i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_122245080_   3705 GCTATAGTAATCAAAATGACACAGTATTCATATAAAGGCAGACACATAGA 3754
                             i         i iiiiiii   i vii    i ii     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_122245080_   3755 TGAATGGGACAGAATAGTGAACCCAGAAATAAATCCACATATTTACAGCC 3804
                          v     i i     v v  ii           i   i i     ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_122245080_   3805 AACTTATTTTCAAAAAAATTTCTAAGGACATACACTGGGGAAAGGGCACC 3854
                           i v      i v  iiv v i   iv   v  v         iii vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_122245080_   3855 CTCTTCAATAAATGGTGCTGGGAAAATTAGATATCCATATTCGGAAGGAT 3904
                           i     i              v  i i    ?   i  v ii   i  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_122245080_   3905 GAAACTGGACTCCTATTTTTCATCATATACAAAAATGAACTCCAGATGGA 3954
                            ii     i    ii iv  i             v     v i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_122245080_   3955 TTGAAGACCTAAACATAAGACTCGAAACTATAAACCTACTAGAAGAAAAC 4004
                          ii?         ii     viii          v  vi           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_122245080_   4005 ATAGGGGAAGCACTTCAGGACATTAGTGTAGGCAAAGATTTTATGGCTAA 4054
                              ? v ivv    iv   v  i vv       v i   iv i v  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_122245080_   4055 GACTTCAAAAGCACAGGCAACAAAAACAAAAACAGACAAGTGAGACTATA 4104
                            vi          i         iv     i   i  i vi    vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_122245080_   4105 TTAAACCAAAAAGCTTCTGCACAGTAAAGGAAACAATCAACAGAGTGAAG 4154
                          i   viv    i   i  ii vvi      v  v     v i      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_122245080_   4155 AGACAACCTGTTGAATGGCAGAAAATATTTGTAAACTATTCATCCAACAA 4204
                                 iiiv      v            i   ii  vi   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_122245080_   4205 GGGACTAATATCCAGAATATACAAGGAACTCAAACAACTCAATAAAAAAC 4254
                               vi             i  i      vv            v   -
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA- 795

  chrX_122245080_   4255 AAAAACAAAAACAAAAACAAATAATCCCGTTAAAAAGTGGGCAAAGAACA 4304
                         -------------  i        i  vi  ?    i         i iv
  L1M4_orf2#LINE/    796 -------------AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_122245080_   4305 TGAATAGAAATTTCTTAAAATAAGACATACAGATTGCCAATAGGTGTATG 4354
                                 v      iv   v    i     i  v       i iii   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_122245080_   4355 AAAAAATGCTCAACATCACTAATCAA 4380
                             i             ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (153 / 73)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.00 (21 / 7)  


2883 27.59 0.92 0.92  chrX_122366201_122368071      500  1369 (502)    L1M4_orf2#LINE/L1       17   886 (22)  

  chrX_122366201_    500 GCTCATGGATAGGAAGAATCAATATCGTGAAAATGGCCATACTCCCCAAG 549
                          i        v      v i     i  v  i     v           i
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA 66

  chrX_122366201_    550 GTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTT 599
                         v i  i  i        i  v     i     iv v   iivi i  i  
  L1M4_orf2#LINE/     67 TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTT 116

  chrX_122366201_    600 CACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAAG 647
                         ii     -   -- v  i  - iii    i           viiv  ii 
  L1M4_orf2#LINE/    117 TGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_122366201_    648 AGCCCGCATTACCAAGACAATCCTAAGCCAAAAAAACAAAGCTGGAGGCA 697
                          v  v v  vi    i      i i ivv i  i       i      vv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_122366201_    698 TCATGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACA 747
                            ii  v  ii i      viv        i          i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_122366201_    748 GCATGGTACTGGTACCAAAACAGAGATATAGAACAATGGAACAGAACAGA 797
                          ii         i iv ii i   v       v        i    iv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_122366201_    798 ACAGAGGCCTCAGAAATAATACCACACACCTAAAACCATCTGATCTTTGA 847
                         ---   v  --        vv   i   ii  viii  vi    i  i  
  L1M4_orf2#LINE/    315 ---GAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_122366201_    848 CAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAAT 897
                            ivv  v   i v  vvv           i  vvi  v  i  i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_122366201_    898 GGTGCTGCAAAAACTGGCTAGCCATATGTAGAAAGCTGAAAACGGATCCC 947
                                vi v      v  ?   i   i i  iiv    ivi   i   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_122366201_    948 TTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAAACTTAAA 997
                          v   i     v              i    i      i ? i  i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_122366201_    998 TGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCG-ATACC 1046
                            v   v       i      vi i           v    ? - v i 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_122366201_   1047 ATTCAAGACATAGGCATGGGCAAGGACTTCATGACTAAAACACCAAACGC 1096
                         -   iv   v v  vv i     v ii   v iiv  vi        v  
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_122366201_   1097 AATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGA 1146
                          vvi          vv     v  i    v   ii v  i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_122366201_   1147 GCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAAGCAACCTACA 1196
                         i   i  ii vv    i  v    i  vv i      v ii     i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_122366201_   1197 GAATGGGAGAAAATTTTTACAGTCTACCCATCTGACAAAGGGGTAATATC 1246
                                       v   i  ivii ivi      i  i  iv vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_122366201_   1247 CAGAATCTACAAAGAACTTAAACAAATTTACAGGAAAAAATCAAACAACC 1296
                               v  i        ivv    v iv i iv     iv    i    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_122366201_   1297 CCATCAAAAAGTGGGCCAAGGATATGAACAGACACTT-----GAGAAGAC 1341
                          v  i?    i     v      v    i     i  -----i      i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_122366201_   1342 ATTTATACAACCAACAGACACATGAAAA 1369
                           vi v iii    i ii          
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAA 886

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (8 / 870), avg. gap size = 2.00 (16 / 8)  


 613 17.65 0.00 1.68  chrX_122382642_122384437.rev      242   360 (1436)    L1M4_orf2#LINE/L1        1   117 (791)  

  chrX_122382642_    242 TGAAAATATGTCCTGTGTTCCTAGGTTGGAAGAGGTAATATTGCTAAGAT 291
                           i   v  i   ii     v i i        vv        i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_122382642_    292 GTCAGTTCTACCCAAAGTTATCTACAGATTCAATGCAATCCCTATCAAAA 341
                          v  i v  v      v v              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_122382642_    342 TCCCAATGGTGTCATTTTT 360
                              -- v  i v     
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTT 117

Transitions / transversions = 0.91 (10 / 11)
Gap_init rate = 0.01 (1 / 117), avg. gap size = 2.00 (2 / 1)  

3643 19.98 0.87 1.50  chrX_122382642_122384437.rev      505  1305 (491)    L1M4_orf2#LINE/L1      113   908 (0)  

  chrX_122382642_    505 TTTTTGCAGAAATAGAAAAATCCATTGTAAAATTCTTGTGTAATTTTAAG 554
                                      v  v  iiiv  iv        v i  v  v vi   
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_122382642_    555 AGGCATTAAATAGCCAAGAAAATCTCTGAAAAGACGAGCAAAGTTGGAGG 604
                         i i vivi         i v     ivi      v  i            
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_122382642_    605 TCTCATACTTTCTAATTTCAAAACTTACAGTACATTATGCTATGGTAATC 654
                         v    i    i i               --    -- v    ii      
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTAC--TACA--AAGCTACAGTAATC 258

  chrX_122382642_    655 AAACCAGTATGATACTGGCATAAAGACAGACATTTAGAACAATAGAGTAG 704
                           iv    i  i           i  i      v    v    i  i   
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_122382642_    705 AAACATAGAGATCAGAAATAAATTTTTACATATATGGCCAAGTTAGTTTT 754
                           vii-    vi          iiiv     v     i   v v v   i
  L1M4_orf2#LINE/    309 AATTG-AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_122382642_    755 GACAAGAGTACCAAGATCATTCAATGGGGAAAGTACAGTCTTTTTGACAA 804
                               i  i      i                v i        ii    
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_122382642_    805 ATAGTGTTGGGAAAACTGGATATCCACATCCAAGAAAATGAA-TTGAATC 853
                           i   i     v         ?      v   i i      -   i i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_122382642_    854 CTTACATTATACCATATACAGAAATTAACTCAAAATGGATTGAAGACTTA 903
                          i   v i i          i                   ii?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_122382642_    904 AACATAAGAGCTAAAACTATAAA-CTTTTAGAAGAAAACATAGGAA-AAA 951
                           ii                   -  i                 ?i-   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_122382642_    952 GCCTCATA---TTAGATTTGGTAATGATTTGTTGGATATGACATGAAAAA 998
                         v i  i i---  i i  v  i    i   v  i         iv    i
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_122382642_    999 CACAGACAACAAAAGAGAAAATAGATAAATTGAACCTCATCAAAATAAAA 1048
                             ii          i               i  i          v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_122382642_   1049 AAGGTTTCTGCATCAAAAGATGCTATCAACAGAGTGAAAAGGCAACCTAT 1098
                           vv   v   v     i  ii       v i         i     i i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_122382642_   1099 GGAATGTGAGAAAATATTTTCAAATCATATATCTGATTAGGGATTGATAT 1148
                         i     v            v                 v     i vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_122382642_   1149 TCCAAATATATAAAGAAATCATACAATTCAACAACAACAATAACAATAAA 1198
                         i vi             v  v     i    i  i  v  -i    ----
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA-GACAA---- 802

  chrX_122382642_   1199 CAACAACCTGGTTAAAAAATGGG-AAAAGAGTCAAGCAGACATATCTCCA 1247
                         -- i    iii  ?         -   i  v ii ii      v      
  L1M4_orf2#LINE/    803 --ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_122382642_   1248 AAGAAGATGTATCAACGGCTAATCAGCACATTAAAAGATAATCAGCATCA 1297
                                 i  iv  i   i   v       v       iv   i     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_122382642_   1298 CTAATCAT 1305
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.94 (103 / 53)
Gap_init rate = 0.01 (10 / 796), avg. gap size = 1.90 (19 / 10)  


2630 23.28 4.98 2.02  chrX_122388662_122395426.rev      499  1241 (5524)    L1M4_orf2#LINE/L1      117   881 (27)  

  chrX_122388662_    499 TGAAGAAATCAGAAAA---ATCCTAAAATTTATATAGAAGCACAAAAGAC 545
                           v      iiiv  i---           i    i   iii   ii   
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_122388662_    546 TCCAAATAGTCAAAGCAATCTTGAGCAAGAA---CAAAGCTGGAGGCATC 592
                         i vi     i    i         iv     ---     i      vv  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_122388662_    593 ATGCTTCCTGAT---GAAATTCTATTACAAAGCTATAGTAATCAAAACAG 639
                          ii     ii  ---i   i -  i          i         i    
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_122388662_    640 TATGATGTTGGCATAAAAACAGGCACATAGAACAATGGAACAGAATAGAT 689
                          i  i ii        ii i  i  i     v        i     v  v
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_122388662_    690 AGCCCAGAAATAAACAAACGTATATACAGTTAACTAATTTT-GACAAAGG 738
                           i            vv iii  v  ii  i  i i     -     i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_122388662_    739 CAC-AA--------AATGGGGAAAGGATAATCTTCTTGACAAATGGTGTT 779
                         ii -  --------           i   i    i ii          i 
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_122388662_    780 GGGAAAACTGGATATCATCCATATGCAACAGAATGAAATTGAACCTATAT 829
                             v         ? ---  i      v        i   i   iv  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKC---CACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_122388662_    830 CTTATACCACACACACAAATCAATTCAAAATAGTTTAAGGACTTAAA-GC 878
                           i i    i i   v    i  i       i v i ?i   i    - i
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_122388662_    879 -----CTAAAATTATAAAACTGATAGAAGAAAACATAGAG--AAATTCCT 921
                         -----      i         vv               i?--    --  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CT 560

  chrX_122388662_    922 CCTTGTCATTGATCTTTGCAATAATTTTTTTTGGATATGATACCAAAAGC 971
                         i v  v v   ivi vv     ii   i  --i       i         
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTT--AGATATGACACCAAAAGC 608

  chrX_122388662_    972 GCAAGCAAAAAAAAAAAAAGCAAAAATAAACAAGTGGGATTACATCGAAC 1021
                         i       v    i     ------   i i  i v   i v    i  v
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAA------ATAGATAAATTGGACTTCATCAAAA 652

  chrX_122388662_   1022 TAAAAATCTTCTGCACGGCAAAGGAAACAATCAATAAAATGAAAAGCCAA 1071
                          v    v   i  ii vv       v  v     v   i       v   
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_122388662_   1072 CTTATGGGATGGGAGAAAATATTTGCAAACCATATATCTGATAAGTGGCT 1121
                          ii ii i                     i               v i  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_122388662_   1122 AATATCCAAAATACGTAAGCAACTACTACAGTT---TAGTGAACAAACAA 1168
                         vi      i    ii   iv    vi    ii ---  i i  v i    
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_122388662_   1169 GTAACTTGATTAAAAAAATGGGCAAAGACT---AACAAAAAGCTTTCCAA 1215
                         i    iii   ?     -         iv ---  i i v vi i     
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_122388662_   1216 AAAAGA-A-ACAAAGAG--AACAATCCCAT 1241
                          i    - -     vi --  i  v v   
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 2.52 (121 / 48)
Gap_init rate = 0.03 (20 / 765), avg. gap size = 2.60 (52 / 20)  

2682 20.44 17.35 0.64  chrX_122388662_122395426.rev     1360  2137 (4628)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_122388662_   1360 TGGAAATATATCTCATGTTCATGGATTGGAAGAATTAATATTGTTAAAAT 1409
                               v     i                    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_122388662_   1410 GTTCATACTACCCCAAAC-AATCTACATATTCAATGCACTCCCTGTCGAA 1458
                          viv     -       i-i       v      i   v     i  i  
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_122388662_   1459 ATTCCAGTGACATTTTTCACAGAAAAAGAAAGAGC-AATCCTAAAATTCA 1507
                           i    ivi v     ii      vv  v -   -i             
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chrX_122388662_   1508 CAAGGAACAACAAGAAACTCTGAATAGCAAAGGCAATCCTGACTCAAAAG 1557
                         i v    vvi    ii  i v       v  ii     i   vvv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_122388662_   1558 AACAAAGCTGGAGGTATCACACTACCTGATTTCAGTCTATACTACAAAGC 1607
                                i      vv       v  ii      ivviv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_122388662_   1608 TGAAGTAATTAAAAGAGCATGTGG--CTGGCATAAAAATAGA-ACATTGA 1654
                          iv      i  i v  --     --         ii     - i  v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAG--TGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_122388662_   1655 CCAATGGAACAGAATAGAGAGCCCAGAAATGAACCCACACAT-------- 1696
                         i        i     v     i        i      i    --------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_122388662_   1697 ----GACTTTTGACAAAAGTGTCAAGAATGCACAATGGG-AAAGGGCAAT 1741
                         ----  i   i     ii   i     viiiv       -    iii i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_122388662_   1742 CTCTTCAATAAATGGTATTGTGAAAAGTTGATATTCGTATACAGAGGAAT 1791
                           i     i       ii  v  v  v v    ?i ii  i  i i    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_122388662_   1792 GAAATTGGACCCTTATCTCACACTATATACAAAAAT-----CAAAATGGA 1836
                            i        i  i       i            -----         
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_122388662_   1837 TAAT-GACTTAAACATAAGACCTGAAACTGTACAACTATTA--------- 1876
                          v ?-   i    ii     v  i     i  v    v   ---------
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_122388662_   1877 ------------CTT------------TTAG----TGG------------ 1886
                         ------------   ------------    ----   ------------
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_122388662_   1887 -----CAAAAAC-C--GCAAT---------------TAATTTTG----CA 1909
                         -----     i - --    i---------------   v  v ----  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_122388662_   1910 TCAAC-CTAATAATT----------------------------AAT-AGA 1929
                             v-i   v  i ---------------------------- i - i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_122388662_   1930 AGAAAACATACAG-----GAGAAAATATGTGCAAGTCATACATCTGATAA 1974
                            v   vi    -----          v     i     i         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_122388662_   1975 GGGGTTAATATCTAGAATATGTAAGCCACCCAAACAACTCTATAGAAAGA 2024
                            ii vi    i       i   ivv  i vv       v   iv  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_122388662_   2025 AAACAAATAATTCAATTAAAAAAATGGGCAAAGGACCTGAATAGATATTT 2074
                          i        ii     ?     -           ii        i    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTT 845

  chrX_122388662_   2075 TTCAAAAGAAGACATACAAACGGCCAACAGACACATGAAAAAATGCCCAA 2124
                         i  v        i       i      i ii          i    i   
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_122388662_   2125 CATCACTAATTAT 2137
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (102 / 54)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 5.83 (140 / 24)  

2904 26.83 1.55 0.89  chrX_122388662_122395426.rev     5374  6275 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_122388662_   5374 TGGAAAAACATTCCA-GCTCATGGATAGGAAGAGTCAGTATCATGAAAAT 5422
                               i i  i   - i        v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_122388662_   5423 GGCCATACTGCCCAAAGTAATTTATAGATTCAGAGCTAATCCC-ATTAAA 5471
                            v     v      v i  i  i       iv  -      -  i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAAA 99

  chrX_122388662_   5472 CTACCC--TTGACATTCTTCACAGAATTAGAAAAAGCT-ATGTTAAAATT 5518
                         v -   --i  v -  i  ii     v v  v  -   -  vi       
  L1M4_orf2#LINE/    100 AT-CCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATT 146

  chrX_122388662_   5519 AATGTGGAACCAAAAAAAGAGCCTGGATAACCAAGACAATCCTAATCAAA 5568
                         v  i     viiv  ii-  v  v i   i    i      i i -v   
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGA-AAAA 194

  chrX_122388662_   5569 AAAGAACAAAGCTGGAGGCATCATGATACCCAACTTCAAA--CTAC-ACA 5615
                         i          i      vv   iiv v     i      --i   -   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_122388662_   5616 AGGCTACAGTAACCGAAATGCCATGGTACTGGTAAAAACACAGACACATA 5665
                          i          i i i iivii         i v  iv i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_122388662_   5666 GACCAATGGAACAGAATAGAGAACTCAGAAATAAGACCACACACCTACAA 5715
                           i        i     v    iii         iv   i   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_122388662_   5716 TCATCTGGTCTTTGACAAACCTGATAAAGATAAGCAATGCGGAAAAGATT 5765
                            vi  i i  i     ivv  vi  iivi vv     v     ii  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_122388662_   5766 CCCTATTTAGTAAATGATGGTGGGAGAACTGGCTAGCCATATGCAGAAAA 5815
                         vi  v  i ii     i  v     v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_122388662_   5816 TTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATG 5865
                         v    ii         v   i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_122388662_   5866 GATTAACGACTTAAATGTAAAACCCAAAACTATAAAAACCCTATAAGAAA 5915
                            i ?v   i         i v i            vi i  v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_122388662_   5916 ATCTTGGCA-ATACCATTCAGGATATAGGCACGGGCAAAGATTTCAT-GA 5963
                          iv v  ?i- v i -   iv  iv v  vvii     v i    v -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_122388662_   5964 TGAAAACACCAAAAGCAATTGCAGCAAAAGCAAGAATTGACAAATGGGAT 6013
                          - vi            vvv   i      v  i   v  i    v   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_122388662_   6014 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGT 6063
                         i v  i   v v  i i   i  ii vv    i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_122388662_   6064 AAACAGACAACCTAAAGAATGGGAGAACATTTTTGCAAACTGTGCATCTG 6113
                         i  v        i v            v  v        iii ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_122388662_   6114 ACAAAGGTCTAATATCCAGAGTCTACAAGGAACTTAAACAAATTTACAAG 6163
                          i  i  v  vi        i v  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_122388662_   6164 AAAAAAACAA----CTCAATTAAAAAGTGGGCAAAGGACAGGAACTGACA 6209
                              i    ---- i     ?    i           ivv   iv    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_122388662_   6210 CTTCTCAAAAGAAGACATTCATGCAGCCAAGAAATATTTGAATAAAAATT 6259
                         i     v        i  v  viii     v  ii iv    v i vii 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_122388662_   6260 CAACATCTCTGATCAT 6275
                                v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.29 (22 / 17)  


3142 26.22 1.22 0.77  chrX_122432098_122439097     5604  6507 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_122432098_   5604 TGGAAAAACATCCCATGCTTATAGATAGAAAGAGTCAATATTGTGAAAAT 5653
                               i i        i i  i   v i    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_122432098_   5654 GGCCATACTGCCCAAAGTAATTTTTAGATTCAATGCTATTCCAATCAAGC 5703
                            v     v      v i  i vi        i  v  i  v     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_122432098_   5704 TACCAGTAACTTTCTTTGCAGAATTAGAAAAAAACT-ACTTTAAATTTCA 5752
                          v    ivi i  i         v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_122432098_   5753 TATGGAACCAAAAAAGAGCCTGTATACCCAAGACAATTCTAAGCAAAAAG 5802
                                viiv  ii  v  v v   v    i     ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_122432098_   5803 AACAAAGCTGGAAGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5852
                                i    i vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_122432098_   5853 TACAGTAACCAAAACAGCATAGTACTGGTATCAAAACAGATATATCGACC 5902
                                 i   i    ii i       i  v ii i   i    v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_122432098_   5903 AATGGAACAGAACAGAGGCCTCAGAAATGACACCACCCATCTATAACCAT 5952
                                i    iv   ivii       i vv   iv   i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_122432098_   5953 CTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGAAAAGGATTCCCT 6002
                         i    i   i    ivv  v   i v  vv       i    i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_122432098_   6003 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACAGA 6052
                         v  i  i              v      v  ?   i     i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_122432098_   6053 AACTGGATCCCTTCCTTATCCCTTATACAAAAATTAACACAAGATAGATT 6102
                          ii    i    v   i iv  v               v   i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_122432098_   6103 AAAGACTTAAACATAAAACCCAAAACCATAAAAACCCTAGAAGAAAACTT 6152
                          ?    i    ii   i v i     i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_122432098_   6153 AGGCA-ATACCATTCAGGACAT--AGTCATGAGCAAAGACTTCATGACTA 6199
                            ?i- v i -   iv   v --i  i --i    v ii   v iiv  
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATA 595

  chrX_122432098_   6200 AAACACCAAAAGCAATTGGAACAAAAGCCAAAATTGACAAATGGGATCT- 6248
                         vi            vvv v        vv     v  i    v   ii -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_122432098_   6249 -----AATTAAAGAGCTTTTGCACAGCAAAAGAAACTATCATCAGAGTGA 6293
                         -----       i -      ii vv    i  v       vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_122432098_   6294 ACAGACAACCTACAGAATGGGAGAAAATTTTTGCAAGCTACCCACCTGAC 6343
                          v        i                 v       iii ivi i    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_122432098_   6344 AAAGGTCTAATATCCAGAAGCTACAAGGAACTTAAACAAACTTA-CAAGA 6392
                           i  v  vi         vv  i  i     ivv    -  i -i  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chrX_122432098_   6393 AAAAAATCAACAACCCCATCAAAAAGTGGGCAAGGGATATGAACAGACAA 6442
                             i iv  i     v  i?    i       i    v    i     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_122432098_   6443 TTCTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTC 6492
                              v        i  vi vi       i  i  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_122432098_   6493 ATCATCACTGGTCAT 6507
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


2892 13.40 0.62 19.23  chrX_122445330_122447737.rev      565  1370 (1038)    L1M4_orf2#LINE/L1        6   661 (247)  

  chrX_122445330_    565 AGATATCCTATATTAATGGATTAGAAGACTTACTAGTATTAATATAGCAA 614
                                 i  i  v       i         v  v i    v  i    
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_122445330_    615 TACTTCCTCAATTGACCTGTAGGTTTAACTCAATTCTTGTCAGAAGCCCA 664
                             i  iv      i  ii  i  i   v    i i i   i  v    
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_122445330_    665 GCTGGCTGCTTTGTAGAAATTGATAAGTTGATCCTAAGATTCATGTGGAA 714
                             v  vi    i         i   i         i      i     
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_122445330_    715 ATTCAAGGGACACAGAATTGCTGAAACAATGTTGAAAAAGAACAAC---G 761
                           v        v      v  ii       v           v   --- 
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_122445330_    762 TTGGAGAGCTTATGCTTTTTGATTTCAAAACTGTCTACAATGCAACAATA 811
                               ii  i ii   iiii           vv      v  v   i  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_122445330_    812 ATCAAGATAGTGTGGTACTGGCATATGGATAGACATACAGATAAATGGAA 861
                                i                 v           i    v       
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_122445330_    862 TAGAATTGAGAATCCAGAAATAAACCCTCACATTTATAGTCAATTGATTT 911
                                    i               vi        i            
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_122445330_    912 -CAGCAAGGATGCTAAAACAATTCAATGAGGAAGGAATGATCTCTTCAAC 960
                         - ii     i   i  i  v        i    i    ii   i      
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_122445330_    961 AAATGGCACTGGGACAACTGGATATCCACGTGCAAAGGAATGAAGTTGGA 1010
                               ii                ?    i      i             
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_122445330_   1011 TGTCTATCCAATTTTTGTATACACTGTATACAAAAATGAACTTGAAATGG 1060
                         ivi   i i----------i    ii           v    ii      
  L1M4_orf2#LINE/    456 CCCCTACCT----------CACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_122445330_   1061 ATCAAAGACCCAAATGTGGCCAGGTGCGGTGGCTCACGCCTGTAATCCCA 1110
                             ?     i      ---------------------------------
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGT--------------------------------- 512

  chrX_122445330_   1111 GCTCTTAGGGAGGCAGAGGCGGGAGGATAGCTTGAGCCCAGGAGTTTGAG 1160
                         --------------------------------------------------
  L1M4_orf2#LINE/    513 -------------------------------------------------- 512

  chrX_122445330_   1161 ACCTGCCTGGGCAATATAGCGAAACCCTGTTCTCCACAAAAAGGAAAAAA 1210
                         --------------------------------------------------
  L1M4_orf2#LINE/    513 -------------------------------------------------- 512

  chrX_122445330_   1211 AAGACCCAAATGTAACAGAACTATAAACCTCTTACAAGAAAACATAGAAG 1260
                             v i   ---------        v      v            i? 
  L1M4_orf2#LINE/    513 AAGAGCTAAA---------ACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_122445330_   1261 TATGTCTTTGTGACCTTGGATTTGTCAATGGTTTCTTAGATAT-ACACCA 1309
                           vi    i          i  v v                  -      
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_122445330_   1310 CATGCATTAGCAAAAAAGGAAAAAAAATAGATAAATTGGACTTGATCAAA 1359
                         v v   iv     v   -- i                      v      
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAA--AGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_122445330_   1360 AGTTAAAAACT 1370
                          -         
  L1M4_orf2#LINE/    652 A-TTAAAAACT 661

Transitions / transversions = 2.00 (70 / 35)
Gap_init rate = 0.01 (8 / 656), avg. gap size = 20.00 (160 / 8)  

1324 13.50 0.00 0.42  chrX_122445330_122447737.rev     1673  1909 (499)    L1M4_orf2#LINE/L1      649   884 (24)  

  chrX_122445330_   1673 AAAATGTAAAAACTTTAATGCATTATAGGATGCTATCAGAAAAGTGAAAT 1722
                              -          vi   v i v    ii      ii         v
  L1M4_orf2#LINE/    649 AAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_122445330_   1723 GACAGCCCATAGAATGGAAGAAAATATTTGCAAATCATATATCTGATAAG 1772
                             i    i       i                                
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_122445330_   1773 GGATTTGTATCTAGACTATATAAAGAACACTTAAAAGTCAATAATAAAAA 1822
                            i       i   v            v    v  v             
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_122445330_   1823 GATACATAACCCAATTTTTTAATGGGCACAGGATCTGAATAGCCATTTCT 1872
                           i v           ?vvv        v     i       v       
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_122445330_   1873 CTAAAGAAGATATAGAAATGTCCAATAAGCACATCAA 1909
                          i            v     v             v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

Transitions / transversions = 0.82 (14 / 17)
Gap_init rate = 0.00 (1 / 236), avg. gap size = 1.00 (1 / 1)  


2900 26.45 2.12 0.78  chrX_122506901_122513561     5273  6168 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_122506901_   5273 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5322
                               i i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_122506901_   5323 GGCCACACCATCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5372
                            v i  ivi     v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_122506901_   5373 TACCAG-TGACTTTTTT-CAGAGTTAGAAAAAACT-ACTTTAAATTTCAT 5419
                          v    -  v       -    iv v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_122506901_   5420 AAGGAACCAAAAAAGAGCTCGTGTACCCAAGACAATCCTAAGCAAAAAGA 5469
                          v    viiv  ii  v iv vi  v    i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_122506901_   5470 ACAAAGCTGGAGGCATCATGCTACCTCACTTCAAACTATACTACAAGGCT 5519
                               i      vv   ii  v  iv i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_122506901_   5520 ACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGATACATAGACCA 5569
                                i   i i  ii         i iv ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_122506901_   5570 ATGGAACAGAACAGA-AGCCTCAGAAATAACACCACACATCTACAACTAT 5618
                               i    iv  -  i -         vv   i    i  iiiii v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_122506901_   5619 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATCCCCT 5668
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_122506901_   5669 ATTTAATAAATGGTGTTGGAA-AACTGGCTAGCCATATGCAGAAAACTGA 5717
                         v  i  i        i   i -      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_122506901_   5718 AACTGGACCCCTTCCTTACACCATATACAACAATTAACTCAAGATGGATT 5767
                          ii         v   i             v           i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_122506901_   5768 AAAAGACTTAAACGTTAAGACCTCAAACCCGAAAAACCCTAGAAGAAAAT 5817
                          ? -   i    i  -    v  v    ivv    vi i          i
  L1M4_orf2#LINE/    499 AWA-GACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_122506901_   5818 TTAGGCA-ATACCATTTAGGACAAAGGCATGGGCAAAGACTTCATGACTA 5866
                         v    ?i- v i -  iiv   vvv  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_122506901_   5867 AAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAACGGGATCTA 5916
                         vi            vvi          vv i   v  i   iv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_122506901_   5917 ATTAAA-CTA-----TTCTGCACAGCAAAAGAAACTATCATCAGAATGAA 5960
                           i   -i  -----  i  ii vv    i  v       vv i i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_122506901_   5961 CAAGCAACCTACAGAATGGGAGAAAATTTTTGTAATCTATCCATCTGACA 6010
                         v ii     i                 v    i  vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_122506901_   6011 AAAGGGCTAATATCCAGAATCTAGAAGGAACTTAAACAAATTTACAAGAA 6060
                          i-  i  vi          v  v  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    746 AG-GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_122506901_   6061 AAA---AAA-AACCCA-TCAAAAAGTGGGCGAATGATATGAACAGACACT 6105
                            ---   -      - i?    i     i  v   v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_122506901_   6106 TCTCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAATGCTC 6153
                             v        i  vi viii     i  --         i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chrX_122506901_   6154 ATCATTACTGGTCAT 6168
                          v   i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.37 (26 / 19)  


 723 23.18 3.86 3.86  chrX_122576923_122579180        3   235 (2023)    L1M4_orf2#LINE/L1        1   233 (675)  

  chrX_122576923_      3 TGAAAAGATATTCCATGCTGATTGATTAGAATAATTAAGATTGTTTAAAT 52
                           i        i     i v  v    i   v v    v      v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_122576923_     53 GTCCATGCTACCCGAAGAGATATAAAGACTCAATGCAATCTCTATCAAAA 102
                          v v  i  v   i  vv   v  v   i    i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_122576923_    103 CACCAA-TGCCATTTTTCACAGAAACAGAAAA----ATCCTAAAATTTAT 147
                         iv   i-    -     ii      iv  v  ----           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_122576923_    148 ATGGAACCAAAAAAAAAAAAAAAACC---AATAGCCAAGGCAATCCTGAA 194
                               -------- viv  iii   ---         ii     i    
  L1M4_orf2#LINE/    150 ATGGAA--------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_122576923_    195 CAAAAAGAAAAAAGCTAAAGTA-TCACACTATTTGACTTCAA 235
                         v  i     v    i ii  v -       viiii i     
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

Transitions / transversions = 1.45 (32 / 22)
Gap_init rate = 0.03 (6 / 233), avg. gap size = 3.00 (18 / 6)  

1861 23.06 0.91 0.46  chrX_122576923_122579180      502   939 (1319)    L1M4_orf2#LINE/L1      238   677 (231)  

  chrX_122576923_    502 TATTACAAAACTAGGGTAATTAAAAGAGCATGGCGCTGGCATAAAAACAG 551
                           i      i   vi     i  i v  ii   ii         ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_122576923_    552 ACACATCAACCAATGGAACAGAATAGAGAGCGCAGATATTAATCCATGCA 601
                            i  vi i        i     v     iv    v  v  i    i  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_122576923_    602 TTTATAGCCAATTAATTTTCAACAAAGGGTACCAAGAACACATAATGGGA 651
                              i i     i      i  -      i      v  ivi      i
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGAC-AAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_122576923_    652 AAAAAGACAGTCTCTTCAATAAAGAATGTTGGGAAAACTTAATATCCACA 701
                            i - i     i     i   vii  i     v    vi   ?     
  L1M4_orf2#LINE/    387 AAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_122576923_    702 TACAGAACAATGAAACTGGACACTTACTTCACACCATATACAAAAATCAA 751
                          i  i  v      ii     v i   i                   i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_122576923_    752 CTCAAAATGAATTAAAGACTTAAATGTAAGACCTGAAACTATAAAAATCC 801
                                  i  i ?    i           v  i           v  i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_122576923_    802 TAAAAGAAAAAATAGGGGAAGAGCTACACAACACTGGTCTGGGCTATAAT 851
                           i       v     ? v i v  v iii  vi   vi i   v  ii 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_122576923_    852 TTTTTAGATTTGACCCCAAAAGCTCAAGTAATTAAAGCAAAAATAGACAA 901
                           i      v    v        v    i  iv    v         i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_122576923_    902 ATGGGATTACATCAAACAAAAAAAGTTT----CTACACAGGA 939
                           v   i v       vvv     v   ----  v  v    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

Transitions / transversions = 1.72 (62 / 36)
Gap_init rate = 0.01 (3 / 440), avg. gap size = 2.00 (6 / 3)  

 361 27.07 0.00 1.50  chrX_122576923_122579180     1219  1351 (907)    L1M4_orf2#LINE/L1      647   777 (131)  

  chrX_122576923_   1219 TCAAAAAAAAAAAGTTTCTACACAGGAAAGGAAACAATTAACAGTGTGAT 1268
                               vv     v   - iii vvv      v  v  i  v iv    -
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGA- 694

  chrX_122576923_   1269 GGAGACAACCTATGGATTCAGAGAAAATATTTGCAAGCCAAACATCAAAT 1318
                         ii        i ii  v vi                ii  v i   vi  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_122576923_   1319 ATGGGGTTAATATCCAAAATATATAAAGAAGTC 1351
                          v   ii vi      i             v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTC 777

Transitions / transversions = 1.12 (19 / 17)
Gap_init rate = 0.02 (2 / 131), avg. gap size = 1.00 (2 / 2)  

 406 13.46 8.65 0.00  chrX_122576923_122579180     1662  1765 (493)    L1M4_orf2#LINE/L1      796   908 (0)  

  chrX_122576923_   1662 AAGA-AAACAACCCAATTTTAAAATGGGCAAAGGACTTGAGTAGACATTT 1710
                             -   i         ?v               i    i         
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_122576923_   1711 CTC---AAAAGACATACAAATGACCAA----CAGAAAAAAAAAC-CTCAA 1752
                            --- i    i         i    ----  v vi    i i-     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_122576923_   1753 AATCATTAATAAC 1765
                         v    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.04 (4 / 113), avg. gap size = 2.25 (9 / 4)  


3098 27.28 1.56 0.45  chrX_122964047_122970222.rev     4788  5685 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_122964047_   4788 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4837
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_122964047_   4838 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4887
                            v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_122964047_   4888 TACCAATGACTTTCTTCACACAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4935
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_122964047_   4936 TATGGGACCAAAAAAGAGCCAGCATTGTCAAGTCAATCCTAAGCCAAAAG 4985
                              i viiv  ii  v    v  v i   iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_122964047_   4986 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAA--CTA-TACAAGGA 5032
                                i      vv    i  v  ii i      --i  -     i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_122964047_   5033 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAAATATAGACC 5082
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_122964047_   5083 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACT 5130
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_122964047_   5131 ATCTGATCTTTGACAAACCTGACAAAAATAAGCAATGGGGAAAAGATTCC 5180
                          vi    i  i     ivv  v   i vi vv           ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_122964047_   5181 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5230
                           v  i  i        i     v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_122964047_   5231 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCGAGAGGGA 5280
                            ii    i    v   i i   v              i  i i v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_122964047_   5281 TTAAAGACTTAAATCTTAGACCTAAAACCATAAAAACCCTATTAGAAAAC 5330
                          i ?    i     v v   v       i      vi i  vv       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_122964047_   5331 CTAGGCAATACTATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5380
                         v    ?ivv v v   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_122964047_   5381 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5430
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_122964047_   5431 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAAC 5480
                          i   v i  i i   i  ii vv    i  v    i  vv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_122964047_   5481 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5530
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_122964047_   5531 AGGGCTAATATCCAGAATCTACAAAGAACTC----AAATTTACAAGAAAA 5576
                         i  i  vi          v  i         ----  v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_122964047_   5577 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATGTGAACAGACACTTC 5626
                          i     i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_122964047_   5627 TCAAAAGAAGACATTTTTGCAGCCAAAAAACACATGAAAAAATGCTCA-- 5674
                           v        i  vivviii     v  i          i       --
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_122964047_   5675 -TCACTGGCCAC 5685
                         -   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (147 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


3287 20.77 3.15 5.37  chrX_123080394_123083185.rev     1080  1936 (856)    L1M4_orf2#LINE/L1        1   838 (70)  

  chrX_123080394_   1080 TGGAGAGGCATTCTGTTTTCATGGATCAGA-GACTCAATAGGGTCAAAAT 1128
                             i  ii  i ii v         ii  -    i    vv  i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_123080394_   1129 GTCAGTTCTTCTCGAATTGGTCTATAGATTCCACACAATCTCAACCAAAA 1178
                          v  i v  i i i     i    i      v  i     i v i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_123080394_   1179 AGACAGCAGGCTGCTTTGTAGAAAATGACAAGCTGATTCTAAACTTTCTA 1228
                         vvv    v v  vi    i     v            i     v  iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_123080394_   1229 TGGAAAAAGTAAAGGACATAAAAGAGCCAAGGCAATTTTTCAAAAGAA-- 1276
                               v- i  i    vi i  v      ii    i  vv       --
  L1M4_orf2#LINE/    151 TGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_123080394_   1277 -CAAAGTTGGAGGACCTACATTTT--AACTTCAAGACTTATTACTAATCT 1323
                         -              ii   i  i--  i     i     i   v  v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_123080394_   1324 ACAATAAACAAGGCAGCGTGGTGTTGGCATAAGGCTAAATATATAGATCA 1373
                            i   v    i   i     ii          v  i i          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_123080394_   1374 ACAGAACAGAATAGAG-GTCTATAAGTAGACCCATATATATGTGGTCACT 1422
                          ii   i     v   -   i v  i  i       i  v i      v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_123080394_   1423 TGATTTTTGACAAAGGTGCAAAAGCAATTCAGTGAAGAAAGGATAGTTTT 1472
                                i     i     v  ii v     i  ii     i     i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_123080394_   1473 TTCAACAAATGTTACTGTGACAATTTGACATCTATATGCAAAAAAATAAA 1522
                                    v i   v     i v  i ? i i        i   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_123080394_   1523 TAAATAAATAAGCCTCAGCCCTTACCTTGTATCATATACAAAA-TTAACT 1571
                         --iv ii ----------   i     iii i           -      
  L1M4_orf2#LINE/    450 --GTTGGA----------CCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_123080394_   1572 CAAAATGGCTCATAGACATGAGTGTAA-ATCTAACACTATAAAGCTTCTA 1620
                                 v   ?    v i i     - v    v        i  ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_123080394_   1621 GAATAAAACATGAGAGAAAACTCTTTGTTCTCAAGAGTTTGCTTCTTTGC 1670
                            v       ii ? v   -    i  ------  --------------
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAA-TCTTCGT------GA-------------- 566

  chrX_123080394_   1671 CTCTCTTTGCCTCAAGTTAGGCAAAGATCTATTAGATATGACTCCAAAAA 1720
                         ---------   iii         v i i v           v      -
  L1M4_orf2#LINE/    567 ---------CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA- 606

  chrX_123080394_   1721 GCATGAACAATAGAAGAAAA----------TTGAACTTCATGAAAATTAC 1760
                            ii i   i i       ----------   i       v       v
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_123080394_   1761 TAACT------CTTCAAAAGATAAGACTAGAAAAATGAAAAGGAGAGCCA 1804
                         v    ------       i  i vv ii ii   i       ivi v   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_123080394_   1805 CAGACTAGAAGAAAATATTTGCAAATCACATATCTGATAAGAGGCATGTA 1854
                             v i i                   i            i i v    
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_123080394_   1855 TTCAGAATATATAATTAACTCTCAAAACTCAATCATAAGAAAACAAACAA 1904
                          i            vv      i v        v    i  i     i  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_123080394_   1905 CCCAGTTTAAAAATCGGCAGCAAGGAT--GAATA 1936
                             i  ?      v    --      --     
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCA--AAGGATTTGAATA 838

Transitions / transversions = 2.00 (116 / 58)
Gap_init rate = 0.02 (17 / 838), avg. gap size = 4.29 (73 / 17)  

 548 12.37 0.00 0.00  chrX_123080394_123083185.rev     2205  2301 (491)    L1M4_orf2#LINE/L1      812   908 (0)  

  chrX_123080394_   2205 TTAAAAAATGGGCAAAAGATTTGAATAGACACTTCACCAAAGAAGAGATA 2254
                           ?             i              i   v          v   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_123080394_   2255 CAGATGACAAATAAGCACATGAAAAGACACTTCACATCATTCATCAT 2301
                           i   i v                  ii  iv      ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.00 (0 / 0)  


3545 24.69 1.56 0.56  chrX_123174157_123178774     3227  4125 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_123174157_   3227 TGGAAAGCTATTTCATGCTCATGGAATAGA-GAATTAGTATTGTTTAAAT 3275
                                v   ii    i       v i  -  v   i       v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_123174157_   3276 GACAATACTACCCAAAGAAATGTACAGATTCAATGCAATCCCTATCAAAA 3325
                          i       v      vvi  v           i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_123174157_   3326 CACCAATGACATTCCTCACAGTAATAGAAAAAAAAATCCTAAAATTTATG 3375
                         iv   iivi v  ii ii   v   v  v  ivvi           i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_123174157_   3376 TGAAACCACAAAAGATCGCAAATAATCAAAGCAATGCTGAGCAAAAAGAA 3425
                           i  vii   ii  i vvi    ii    i    vi   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_123174157_   3426 ---AGCTGGAGGCAC-CATACTACCTGACTTTAATGTTTACTACAAAGCT 3471
                         ---  i      -  -  i   v  ii i  i  vii             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_123174157_   3472 ACACTAACCAAAACCGCATGGTACTGGCATAAAAACAGACACATAGACCA 3521
                            v   i   i  v ii              ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_123174157_   3522 ATGGAACAAAATGGAGAACCTTGATGTAAACCCATACATTTACAAGCAAC 3571
                               i i   v    ii iv  vi                iiiv   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_123174157_   3572 TCATCTTCAACACAGGCACCACAAACATACAAGGGGGAAAGGACAGTCTT 3621
                          v  i   i   vi  ii   vi v   v   v        i i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_123174157_   3622 TTCGGTAAATAGTGCTGGGAAAACTGGATAACTATATGCAGAAGAATAAA 3671
                            iii    i         v         ? i i     i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_123174157_   3672 ACTAGATCCCTCTCTTACATCATACACAAAAATAAAATCAAAATGGATTA 3721
                         ii i  i    vi  i   i    i        v  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_123174157_   3722 AAGACCTAAATCTAAGACCTGCTAAA----TTCAACTACTAGAAGAAAAC 3767
                         ?          v     ---      ---- vv    vi           
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA---GCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_123174157_   3768 ATTGGGGGAAACGCTCTAGGACATTGGTCTGGGCAAAGATTTTTTGTGTA 3817
                           v  ? v   i-  iiiv   v    vi i     v i   i  ivi  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_123174157_   3818 AGACCTCAAAAGCACGGGTGACCAAAGCAAAATTAGGCAATTGGGATTAC 3867
                         v   vi         ii ii  v    v    v   ii  v v   i v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_123174157_   3868 CTCAAG-CTAAAAAGCTTTGCAAAGCAAAGGAAACAATCAACAAAGTGAA 3916
                         v    i-i      vi    iivvv       v  v     v        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_123174157_   3917 GAGACAGACCACAGAATGGGAGAAAATATTTGCAAGCTATCCATTTGACA 3966
                         i     iv                           iii  vi  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_123174157_   3967 AGGGATTAATTATCAGAATATATAAGGAGCTC----AACTCAATAGGAAA 4012
                              i vi vvi            i  i   ----         iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_123174157_   4013 AAAACGAATAATTTGATATAAAAATGGGCAAAAGATCCGAACAAATATTT 4062
                           i  i     iiii  v?             i   ii   i i i    
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_123174157_   4063 CTCAAAAGAAAACATACAAATGGCCAACAGGTATATGAAAAAATTCTCAA 4112
                            v      i i              i i i i       i  v     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_123174157_   4113 CATCACCAATCAT 4125
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (143 / 75)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


3076 28.18 0.88 0.55  chrX_123268198_123270664     1070  1974 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_123268198_   1070 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1119
                              ii i  i   i i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_123268198_   1120 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1169
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_123268198_   1170 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1217
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_123268198_   1218 TGTGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 1267
                          i     viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_123268198_   1268 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1317
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_123268198_   1318 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATTGACC 1367
                                 i   i    ii         i iv ii i   v    v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_123268198_   1368 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 1415
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_123268198_   1416 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 1465
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_123268198_   1466 CTATTTAATAAATGGTGATGGGAAAACTGGCCAGCCATATGTAGAAAGCT 1515
                           v  i  i        v     v      vi ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_123268198_   1516 GAAACTGGATCCCTTCCTTACATCTTACACAAAAACTAATTCAAGATGGA 1565
                            ii    i    v   i   i v  i       i   i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_123268198_   1566 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAAACCCTAGAAGAAAA 1615
                          i ?    i       v   v       i      v-i i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAA 545

  chrX_123268198_   1616 CCTAGGCATTACCATTCAGGACATAGGCATGAGCAAGGACTTCATGTCTA 1665
                          v    ?i v viv   iv   v v  vv ii    v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_123268198_   1666 AAACACCAAAAGCAATGGCAACGAAAGCCAAAATTGAGAAATGGAATCTA 1715
                         vi            vvi     i    vv     v  v    v i ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_123268198_   1716 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1765
                           i   v i  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_123268198_   1766 CAGGCAACCTACAGAACGGGAGAAAATTTTTGCAATCTACTCATCTGACA 1815
                         v  i     i      i          v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_123268198_   1816 AAGGGCTAATATCCAGAATCTACAACGAACCCCAACAAATTTACAAGAAA 1865
                          i  i  vi          v  i  v    i iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_123268198_   1866 AAAACAA----CCCTATCAACAAGTGGGCAAAGGATATGAACAGACACTT 1911
                           i    ----   v  i? v  i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_123268198_   1912 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGTTCAT 1961
                            v        i  vi viii     v ii          i   i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_123268198_   1962 CATCACTGGCCTT 1974
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (154 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


 219 15.15 0.00 0.00  chrX_123441456_123447836      278   310 (6071)  C L1M4_orf2#LINE/L1   (875)    33     1  

C chrX_123441456_    310 TGGAAAAACATTCCATGCTCATAGATTGGAAGA 278
                               i i  i     i    i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA 33

Transitions / transversions = 1.00 (5 / 0)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.00 (0 / 0)  

3244 27.20 0.44 0.44  chrX_123441456_123447836     4981  5888 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_123441456_   4981 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5030
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_123441456_   5031 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5080
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_123441456_   5081 TACCAATGACTTTCTTCACACAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5128
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_123441456_   5129 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAATG 5178
                                viiv  ii  v  v v  v     iv     i i ivv i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_123441456_   5179 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5228
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_123441456_   5229 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATTGACC 5278
                                 i   i    ii         i iv ii i   v    v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_123441456_   5279 AATGGAACAGAAT--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5326
                                i     --    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_123441456_   5327 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5376
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_123441456_   5377 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5426
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_123441456_   5427 GAAACTGGATCCCTTCCTTACACCTTATACAAAAACTAATTCAAGATGGA 5476
                            ii    i    v   i     v          i   i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_123441456_   5477 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5526
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_123441456_   5527 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5576
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_123441456_   5577 AACACCAAAAGCAATAGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5626
                         i            vv           vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_123441456_   5627 TTAAACTAAGGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5676
                          i   v v ii i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_123441456_   5677 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5726
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_123441456_   5727 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5776
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_123441456_   5777 AAACAAACAGCCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5826
                          i     i i   v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_123441456_   5827 TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCACC 5876
                           v        i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_123441456_   5877 ATCACTGGCTAT 5888
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3819 11.65 0.96 22.00  chrX_123518209_123520518      668  1817 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_123518209_    668 TGGAAAGATATCCTATGTTCATGGATCAAAAGACTTATTATTGTTAAGAT 717
                                      i            iii        v            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_123518209_    718 GGCAGTACTTCCCAAATTGATTTACAGATTCAATGCAGTCCCTGTCAAAA 767
                             i    i           i           i   i     i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_123518209_    768 TTCCAACTCTCATTTTTTTTTTAGAAATAGACAAGCTGATGCTAAAATTA 817
                          i   i  vi ---      vi      v           v        v
  L1M4_orf2#LINE/    101 TCCCAGCTGCC---TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_123518209_    818 ATATGGAAATGCAAGGGACTCAGAATAACTAAAGCAATCTTTAAAAAGAA 867
                                            i       i i   i       v        
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_123518209_    868 ---CAAAATTGGAGGCCTCACACTTCCTGATT-CAAAACTGATTACAAAC 913
                         ---    i       v           ii   -       v i      v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_123518209_    914 CTACACTAATCAAGATAATG-AGTACTGGCATTAGGATAGATATATAGAT 962
                              v         i i  -i          v        i        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_123518209_    963 CAATGGAATACAACTGAGAATCTAGAAATGAAACCTCACATTTATGGTGA 1012
                                   v  i     i  i      i  v  vi           v 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_123518209_   1013 ACTGATTTTCGACAAGGTCACCAAGACAATTCAATGGGGGAAAGAATAAT 1062
                          i               vii       v           -        i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGT 396

  chrX_123518209_   1063 ACTTTCAACAAATGATACTGGAACAACTGGATATCCACATGCATAAGAAT 1112
                         vi            i i    i           ?         v      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_123518209_   1113 AAACGTGACCCCCTTCCTCATACCATATACAAAAAACAACTCAAAATGGA 1162
                         i  vv  iv     v     i              vi             
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_123518209_   1163 TCAAATGCCTACATGTAAGGGCTAAAGCTGTACAATTCTCAAATGAAAAT 1212
                            ? vi    v       i      i  i  v  i   i i v     i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_123518209_   1213 ACAGGCATAAATCTTTGTCACCTTGGATTTGTCAATAGTTTCTTAGACAT 1262
                          i   ?i        i  v       i  v v    i          i  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_123518209_   1263 GACATCAAA-GCACAAATAACAAAGAAAAAAATACATAAATTGAACTGGG 1311
                             i    -      ii      ii        v        -------
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG------- 639

  chrX_123518209_   1312 AGGCCGAGACGGGTGGATCACGAGGTCAGGAGATTGAGACCATCCTGGCT 1361
                         --------------------------------------------------
  L1M4_orf2#LINE/    640 -------------------------------------------------- 639

  chrX_123518209_   1362 AACACAGTGAAACCCCGTCTCTACTAAAAAATAGAAAAAATTAGCCAGGC 1411
                         --------------------------------------------------
  L1M4_orf2#LINE/    640 -------------------------------------------------- 639

  chrX_123518209_   1412 GTGGTGGCGGGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAG 1461
                         --------------------------------------------------
  L1M4_orf2#LINE/    640 -------------------------------------------------- 639

  chrX_123518209_   1462 AATGGCGTGAACCCGGGAGGCAGAGGTTGCAGTGAGCCGAGATCGCACCA 1511
                         --------------------------------------------------
  L1M4_orf2#LINE/    640 -------------------------------------------------- 639

  chrX_123518209_   1512 CTGCACTCAAGCCTGGGCGACTGAGCTAGACTCCATCTCCAAAAAAAAAA 1561
                         ----------------------------    i    -------------
  L1M4_orf2#LINE/    640 ----------------------------GACTTCATC------------- 648

  chrX_123518209_   1562 AAAAATTAAAAACTTTTGTGCTTCAAAAGACACTATCAAGAAAGTGGAAA 1611
                         -                          i                  i   
  L1M4_orf2#LINE/    649 -AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_123518209_   1612 AACAGCCCACAGAATGGGAGAAAACATTTGCAAATGATATATTGGATAAG 1661
                         i   i                   i          v      iv      
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_123518209_   1662 GGGCTTGTATCTATGGTATATTAAGGAGGCTTACAACTCAACAATAAAAA 1711
                           i        i vii     v   i vv            i        
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_123518209_   1712 GTTAAATAA-----TTGAAAAAAGAGCAAATGATCTGAATAGACATTTCT 1756
                          vi      -----  ?     v i     v   i               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_123518209_   1757 CCAAAGAAGACAGACTAATGACCAATAAGAACAGTAAATGAAGCTTAACA 1806
                                   i v  v    i        v   vv   v  v   i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_123518209_   1807 TCATTATTCAT 1817
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.65 (81 / 49)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 29.33 (264 / 9)  


1969 27.77 7.85 1.25  chrX_123545373_123547680     1045  1847 (461)    L1M4_orf2#LINE/L1       53   908 (0)  

  chrX_123545373_   1045 CAAAACTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATA-CAA 1093
                            v     ii  ii    vvi  iv    i iv i  i ----  -   
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC----TATCAA 98

  chrX_123545373_   1094 AATC--AA-TG-------TGCAAAAATC-ACAAGC--ATTC-------CA 1123
                             -- i-  -------    i    i-      --  i -------  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_123545373_   1124 TATGAAACCAAAAAAGAGCCCATATAGCCACGACAATCCTAAGCAAAAAG 1173
                             i  viiv  ii  v  viv       vi      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_123545373_   1174 AACAACGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG-- 1221
                              v i      vv   ii  v  ii i      viv        i--
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_123545373_   1222 ----------AAACCAGCATGGTA------TCAAAACAGACATATAGACC 1255
                         ----------  iv   ii     ------ v ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_123545373_   1256 AATGGAACAGAATGGAGACCTCAGAAATAAGACCACATATCTACAACCAT 1305
                                i     v    vii         iv   i i  i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_123545373_   1306 CTGATCTTCGACAAATCTCACAAAAACAAGCAATGGGGAAAGGATTCCCT 1355
                         i    i        ivv vv   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_123545373_   1356 ATTTAATGAATAGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAACTGA 1405
                         v  i  ii   i         v      v  ?   i   iii  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_123545373_   1406 AACTGGACCCCTTCCTTATGCTTTA---AAACTTTAACTCAAGATGGATT 1452
                          ii         v   i ii iv  ---   vv         i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_123545373_   1453 GAAGACTTAAAAGTAAAACCCCAAACCATAAAAACCCTAAAAGAAAATTT 1502
                         i?    i    v    i v iv    i      vi i  i       iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_123545373_   1503 AGGCA-ATACCATTCAGGACATAGGCATGGACAAAGATTTTAT-GATGAA 1550
                            ?i- v i -   iv   v v  vv i i   v i   iv -   ivi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_123545373_   1551 ATCGCCAAAAGCAATTGCAACAAAAGCTAAAATTGACAAATGGGATCTAA 1600
                          - i         vvv          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    598 A-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_123545373_   1601 TTAAACTATAGATCTTCTGCACAGCACAAGAAACTATCATCAGAGTGAAC 1650
                          i   v vv i v   i  ii vv  v i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_123545373_   1651 AGGCAACTTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 1700
                           i    ii                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_123545373_   1701 AGGTCTAATATCCAGAATTTACAAGGAACTTAAACAAATT-----TAAAG 1745
                         i  v  vi          v  i  i     ivv    v i-----    i
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_123545373_   1746 AAAAAAACAACCCCACCAAAAAGTGGGCAAAGGACATGAACAAACACTTC 1795
                          i v   i     v ii?    i           iv    i i   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_123545373_   1796 TTAAAAGAG-----ACAAA--GC----AAGACACA-GAAAGACAAATACT 1833
                          iv     i-----     --  ----   -    -    --- i  i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAA---AGATGCT 892

  chrX_123545373_   1834 --ACATGATCTAGCAC 1847
                         --    v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (131 / 88)
Gap_init rate = 0.03 (23 / 856), avg. gap size = 3.17 (73 / 23)  


 572 18.80 0.00 0.00  chrX_123611128_123617527.rev        3   119 (6281)  C L1M4_orf2#LINE/L1   (131)   777   661  

C chrX_123611128_    119 TTTTGTGCAGCAAAGGAAACAATCAAAAGAGTGAAAAGACAACCTATGAA 70
                                 vv       v  v     i i               i iii 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

C chrX_123611128_     69 ATGGGAGAAAATATTTGCAAACCATACAGCTGAGAAGAGATTAACATCCA 20
                                              i    i v    v   i  i vii     
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

C chrX_123611128_     19 GAATAGAAAAGGAACTC 3
                              v v  i      
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTC 777

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.00 (0 / 0)  

3104 28.35 0.78 0.22  chrX_123611128_123617527.rev     5007  5909 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_123611128_   5007 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5056
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_123611128_   5057 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5106
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_123611128_   5107 TACCAATGACTTTCTTCACACAATTGGAAAAA---A--CTAACGTTCATA 5151
                          v   iivi i  i  ii  v  v v  v  i--- --    vi      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_123611128_   5152 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5201
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_123611128_   5202 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5251
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_123611128_   5252 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5301
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_123611128_   5302 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACTAT 5349
                              i    i--    i  --        vv iii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_123611128_   5350 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5399
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_123611128_   5400 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5449
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_123611128_   5450 AACTGGATCCCTTCCTTACATATTATACAAAAATTAATTCAAGGTGGATT 5499
                          ii    i    v   i   ivv              i    ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_123611128_   5500 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAATCT 5549
                          ?    i    i  v   v       i      vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_123611128_   5550 AGGCATTACCATTCAGGACATAGGCATGAGCAAGGACTTCATGTCTAAAA 5599
                            ?i v viv   iv   v v  vv ii    v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_123611128_   5600 CACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATCTCATT 5649
                                    vvi     i    vv     v  i    v   ii    i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_123611128_   5650 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAGCAGAGTGAACAG 5699
                            v v  i i   i  ii vv    i  v    i  iv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_123611128_   5700 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 5749
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_123611128_   5750 GGCTAATACACAGAATCTACAATGTACTCAAACAAATTTACAAGAAAAAA 5799
                          i  vi  iv      v  i  v v    vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_123611128_   5800 ACAAACAGCCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTC 5849
                              i i   v  i?    i     i     iv    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_123611128_   5850 AAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCACCAT 5899
                         v        i  vi viii     v ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_123611128_   5900 CACTGGCTAT 5909
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (152 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 2.25 (9 / 4)  


3646 23.78 0.77 0.33  chrX_123724529_123728774     2850  3753 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_123724529_   2850 TGGAAAAATATTCCATGTTCATGGACTGGAGGAAACAATATTGTTAAAAT 2899
                               i    i             i    i  vvi           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_123724529_   2900 GACCATACTATCCAAAGCAATCTACAGATTTGATGCAATCCCTATTAAAA 2949
                          i v     vi     vii           ii i           i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_123724529_   2950 TCCCAATGACATTCTTCACAGAAACAGAAAAAA-AATCCTAAAATTTATA 2998
                              iivi v  i  ii      iv  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_123724529_   2999 TGGAACGATAAAAGAGCCAGAATAGCTAAAGCTATCT-AAGCAAAAAGAA 3047
                              vvii  ii  v          i   i v    -i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_123724529_   3048 CAAAACTGGAGGAATAACATTACCTGACTTCAAATTATACTACAGAGCTA 3097
                             ii       v v   i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_123724529_   3098 TAGTAACCAAAACAGCATGGCACTGGCATAAAAACAGACAGATAGA-CAG 3146
                         i     i   i    ii   i          ii i     v     -  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_123724529_   3147 TGGAACAGAATAGAGAACCCAGAAACAAATCCACACACCTACAGTAAACT 3196
                              i     v    ii       i   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_123724529_   3197 CATTTTTGACAAGGGTGCCAGTAACATACACTGGGGAAAGGACAGGCACG 3246
                         v     i             iv v   v  v         i i  v viv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_123724529_   3247 TCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAAA 3296
                             i              v         ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_123724529_   3297 CTAGACCCCTATATCTTGCCATATACAAAAATGAAATCAAAATGAACTAA 3346
                         i i        iv  vii              v  v        i ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_123724529_   3347 AGACTTAAATCTAAGACCTCAGCCTACGAAACTACTACAAGAAAACATTG 3396
                             i     v     v  v iv   ii     vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_123724529_   3397 GGGAAACTCTCCAGGATATTACTCTGGGCAAAAAATTTCTTAAGCAATAC 3446
                          ? v  v   i iv  iv  ivvi i     -vii       iii vv  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGAC 599

  chrX_123724529_   3447 TCCACAAGCACAGGCAACCACAGCAAAAATGGGAAAATGGGATCACATCA 3496
                         v   v       i     v v  v      i iv    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_123724529_   3497 A-GTTAAAAAGCTTCTGTACGGTAAAAGATACAATCAACAAAGTGAAGAG 3545
                          -i       -   i   i vvi   i  i  v     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_123724529_   3546 ACAACCCACAGAATAGGAGAAAATATCTGCAAACTACTA-ATCTCCCACA 3594
                                       i           i      ii -  -    vvi vi
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGATAAG 747

  chrX_123724529_   3595 GGATTAATAACCAGAATATATAAGAAGCTCAAACAACTCTATAAGAAAAA 3644
                            i vi  v             ii i   vv       v    v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_123724529_   3645 ACCTAATAATCCTATCAAAACATGGGCAAAAGATTTGAATAGACATTTCT 3694
                         iv v     i  v  i?   v         i                   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_123724529_   3695 CAAACCCAGACATACAAATGGCAAGCAGGCATATGAAAAG--GCTCAGTA 3742
                          v  vvv   i           v ii i   i        --     ii 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_123724529_   3743 TCATTAATCAT 3753
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (129 / 82)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


 446 29.27 0.00 0.00  chrX_123865306_123871482     4469  4591 (1586)    L1M4_orf2#LINE/L1        1   123 (785)  

  chrX_123865306_   4469 TAGAAAAACATTCCATTCTCAGGGATAGGAAGAATCAATATCTTGAAAAT 4518
                          i    i i  i    vi   v    v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_123865306_   4519 GGCCATACTGCCCAAAGTAATTTTTAGATTCAGTGCTATTCCCATCAAAC 4568
                            v     v      v i  i vi       ii  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_123865306_   4569 TACCATTGACATTCTTCACAGAA 4591
                          v   vivi v  i  ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA 123

Transitions / transversions = 1.25 (20 / 16)
Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.00 (0 / 0)  

2507 27.06 0.52 0.90  chrX_123865306_123871482     4909  5684 (493)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_123865306_   4909 ATTTTAAATTACATGTGGAACCGAAAAAGAGGCCATATAGCCAAGACAAT 4958
                           ii    v v   i     vi v  ii  vv viv        i     
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_123865306_   4959 CCTAAGCAAAAAGAACAAAGCTGCAGGTATCACACTACCTAACTTCAAAT 5008
                          i i iv  i          i  v   vv       v  i  i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_123865306_   5009 TATACTACAAGGTTACAGTTACCAAAACAGCATGGTACTGGTACCCAAAC 5058
                         iv        i i      v i   i    ii         i ivvii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_123865306_   5059 AGACATATAGGCCAATGGAACAGAACAGATACCTCAGAAATAACACCACA 5108
                                   ii        i    iv  v vii         vv   i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_123865306_   5109 CATCTACAACCATCTGATCTTCTACAAACCTGACAAAAACAAGCAATTGG 5158
                            i  iiii  vi    i   v    ivv  v   i v  vv    v  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_123865306_   5159 GAAAGGATTCCCCATTCAATAAATGGTGCTAGGAAAACTGGCTAGCCAAA 5208
                              i  vvi iv     i          i   v      v  ?   v 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_123865306_   5209 TGCAGAAAACTGAAACTGGACCCCTTCCTTACCCCTTATACAAAGATTAA 5258
                             i  i v    ii         v   i  v  v        i     
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_123865306_   5259 CTCGAGATGGATTTAAGAGTTAAATGTAAAACCCAAAACCATAAAAACCC 5308
                            i i      iv?   vi         i v i     i      vi i
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_123865306_   5309 TAGAAGAAAACGTAGG--TAATACCAATCAGGACATGGGCATGGGCAAAG 5356
                                    i    --   - i v-  iv   v v  vv i     v 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAA-ATCT-TCGTGACCTTGGGTTAGGCAATG 583

  chrX_123865306_   5357 ACTTCATGACAAAAACACCAAAAGCTAGTGCAACAAAAGCCAAAATTGAC 5406
                         ii   v iivv vi           vviv          vv     v  i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_123865306_   5407 AAAT-GGATCTAATTAAACTAGAGAGCTTCTGCACAGCAAAAGAAACTAT 5455
                             -   ii v  i   v vi i i   i  ii vv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_123865306_   5456 CATCAGAGTGAACAGGAAACCTACAGAATGGGAGAAAATTTTTGCAATCT 5505
                           vv i      v  iv    i                 v       vii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_123865306_   5506 ACCTATCTGACAAAGGTCTAATATCCAGAATCTACAACAAATTTGTAAAC 5555
                          iv       i  i  v  vi          v  i  vi  i iv  -- 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--C 781

  chrX_123865306_   5556 AAATTTGCCAGAAGAA-ACAAACAACCCCATCAAAAAGTGGGCAAAGGAT 5604
                           v iviiv v  i  -     i     v  i?    i            
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_123865306_   5605 ATGAGCAGACACTTCTCAAAAGAAGACATTTATGTTGCCAACAACAGACA 5654
                         v   ii     i     v        i  vi vi v     i  ---i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA---GCA 878

  chrX_123865306_   5655 TATGAAAAAAAGCTCATCATCACTGGTCAC 5684
                         i       i v     v     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (114 / 93)
Gap_init rate = 0.01 (7 / 773), avg. gap size = 1.57 (11 / 7)  


3257 26.19 0.99 0.66  chrX_123909739_123911990      855  1759 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_123909739_    855 TGGAAGAACATTCCACGCTCATGGGTAGGAAGAATCAATAT-G--AAAAT 901
                              ii i  i   i i      i v      v i     - --  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_123909739_    902 GGCCATGCTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 951
                            v  i  v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_123909739_    952 TACCAATGACTTTCTTCACACAA-TTGGAAAAAACT-ACTTTAAAGTTCA 999
                          v   iivi i  i  ii  v  -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_123909739_   1000 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1049
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_123909739_   1050 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 1099
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_123909739_   1100 TACAGTAACCAAAACAGCATGGTCTTGGTACCAAAACAGAGATATAGACC 1149
                                 i   i    ii    vi   i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_123909739_   1150 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGTATATCTACAACC 1197
                                i    i--    i  --        vv ii  i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_123909739_   1198 ACCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1247
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_123909739_   1248 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1297
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_123909739_   1298 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1347
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_123909739_   1348 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1397
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_123909739_   1398 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1446
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_123909739_   1447 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1496
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_123909739_   1497 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1546
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_123909739_   1547 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAA-CCTTCTCATCTGAC 1595
                         v  i     i                 v       -i v v -      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGAT 744

  chrX_123909739_   1596 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1645
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_123909739_   1646 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 1695
                            i     i     v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_123909739_   1696 TCTCGAAAGAAGACATTTATGCAGCCAACAGATACATGAAAAAATGCTCA 1745
                             v        i  vi viii     i iii         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_123909739_   1746 TCATCATTGGCCAT 1759
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


 256 21.57 0.00 0.00  chrX_123972330_123976526       11    61 (4136)    L1M4_orf2#LINE/L1      145   195 (713)  

  chrX_123972330_     11 TTTACATGACAATGCAAAGGACCTAGAAAAGCCTAAATGATTTTGAAAAA 60
                           i i   iv       i     i    v    v   ii  i        
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_123972330_     61 G 61
                          
  L1M4_orf2#LINE/    195 G 195

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.00 (0 / 0)  

1044 27.40 3.67 1.13  chrX_123972330_123976526       62   415 (3782)    L1M4_orf2#LINE/L1      255   617 (291)  

  chrX_123972330_     62 AATCATGATA-TGTAGTATCAGCATA----TACTACACATAGTCTAATGG 106
                              v  i -   i   iii     ----  v-   i    vii     
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAG-ACATATAGATCAATGG 303

  chrX_123972330_    107 AACAAAATAGGGAGTCCAAAAATATATCCACCTGTATATGGTTAAATGGT 156
                           i i   v i       i     v i   ivii v      i  v  i 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_123972330_    157 TTTTGAATAAAATTCAAAGGTAAAATTCAATGAGAAAAAGATAATATTTT 206
                            i  vv iii v v   -- vv        i i   ii   i v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAG--ACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_123972330_    207 -AATAAATGTTGCTAACATAACTGAATAACCATAAGGAAAA-ATTGAACT 254
                         -  i     v    iiv i     i   ?   i v v    - v    v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_123972330_    255 TCAACTCTTACCTCATGCCAGATA-AAAAATTGTCTCAAAATGTATTATA 303
                          vi  i i       ii   v   -       iv         v  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_123972330_    304 GGCCTAAATGTAAAAGCTAAAACTATAAAACTACCAGAGGAAAATGCAGC 353
                          i           i                  vii   i     iii  v
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_123972330_    354 GGAAAACTGTCATGATCTTGGAATATGCAAGAAC-----ACACAGGACAC 398
                         ? v   iiv  i   i     iv  v    viii----- v i v     
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_123972330_    399 AAAAAAGCACTAGCCAC 415
                         v    -    v   v  
  L1M4_orf2#LINE/    602 CAAAA-GCACAAGCAAC 617

Transitions / transversions = 1.54 (57 / 37)
Gap_init rate = 0.02 (9 / 363), avg. gap size = 1.89 (17 / 9)  

3028 25.81 2.34 1.33  chrX_123972330_123976526     2806  3704 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_123972330_   2806 TGGAAAAATATTCCATGCTCATGAATAGGAAGAATCAATATCTTGAAAAT 2855
                               i    i     i     i  v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_123972330_   2856 GGCCATACTACCCTAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 2905
                            v     v   v  v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_123972330_   2906 TACCATTGACTTTCTTCACAGAA-TTACGAAAAAAAAAAACT-ACTTTAT 2953
                          v   vivi i  i  ii     -  i-------- v  i  - iii  v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--------ACAAGCTGATCCTAA 142

  chrX_123972330_   2954 ATTTCATATGGAACGAGAAAAGAGCCCATA-TAGCCAAGACAATCCTAAG 3002
                          v           -iv v  i ii    v -       i      i i i
  L1M4_orf2#LINE/    143 AATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_123972330_   3003 CAAAAAGAACAAAGCTGGAGGCATCACGCTACTTGATTTCAAACTATACT 3052
                         v  i          i      vv    i  v iii        viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_123972330_   3053 ACAAGGCTACAGTAACCAAAACAGCATGGTAGTGGTACCAAAACAGATAT 3102
                             i          i   i    ii     v   i iv ii i   i  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_123972330_   3103 ATAGACCAATGGAATAGAACATAGGCCTCAGAAATAATGCCACACATCTA 3152
                              i             ivv  ivii         vv   i    i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_123972330_   3153 CAACCATCTGATCTTTGACAAACCTGACGAAAGCA----ATGAGGAAAGG 3198
                         iiii  vi    i  i     ivv  v i i v  ----   i      i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_123972330_   3199 AT--TCCTTATTTAATAAATG---TTGGGAAAATTGGCTAGCCATAGGCA 3243
                           --  i  -- i  i     ---i     v  i   v  ?   i v   
  L1M4_orf2#LINE/    392 ATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_123972330_   3244 GAAAACTGAAACTGGACACTT-CCTTACACCTTATACAAAAATTAACTAT 3292
                         i  i v    ii     v i -   i     v                vv
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_123972330_   3293 AGATGGATTAAAGACTTAAACGTAAAACCTAAACCCATAAAAACCCTAGA 3342
                          i      i ?    i    i    i v     v i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_123972330_   3343 AGAGAACCTAGGCA-ATACCATTCAGGACATAGGCATGGACAAAGACTTC 3391
                            i   v    ?i- v i -   iv   v v  vv i i   v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_123972330_   3392 ATGATTAAAACACCAAAAGCAATGGCAACAAAACCCAAAATTGACAAATG 3441
                         v iiv  vi            vvi         vvv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_123972330_   3442 GGATCTAATTAAAATAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCA 3491
                            ii v  i     v  i i   i  ii vv    i  v       vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_123972330_   3492 GAGTGAATAGGCAACCTACAGAACGGGAGAAAATTTTTGCAATCTATCCA 3541
                         i      v  i     i      i          v       vii  vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_123972330_   3542 TCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACT--TA-AATTTAC 3588
                              i  i  i  vi          v  i  i     --  -  i i v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_123972330_   3589 AAGTAAAAA-ACAAACATCCCCATCAAAAAGTGGGCAAAGGATATGAACA 3637
                         v i      -     i v   v  i?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_123972330_   3638 GACACTTCTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAA 3687
                             i     v        i  vi vi       i  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_123972330_   3688 AGATCA---TCACTGGTCAT 3704
                         v v   ---   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (139 / 89)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.06 (33 / 16)  


2319 26.31 0.83 1.79  chrX_124073125_124074827.rev      497  1222 (481)    L1M4_orf2#LINE/L1      190   908 (0)  

  chrX_124073125_    497 AAGACAAAGAACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATA 546
                           i vi          i      vv    v  v  ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_124073125_    547 CTGCAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCACAACAGAG 596
                           i   i          i   i    ii         i iv vi i   v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_124073125_    597 ACATAGACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACGCA 644
                          i     i        i    i--    i  --        vv   ii  
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACA 337

  chrX_124073125_    645 TCTACAACCATCTGATCTTTGACAAACCTGACAATGACAAGAACAAGAAA 694
                          i  iiii  vi    i  i     i------ii  v     v  vvv  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAG------GGTGCCAAGACCATTCAA 381

  chrX_124073125_    695 TGGGGAAATGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGC 744
                                 vi  vvi  v  i  i              v      v  ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_124073125_    745 CATATGTAGCAAGCTGAAACTAGATCCCTTCCTTACACCTTATACAAAAA 794
                           i   i iv iiv    ii i  i    v   i     v          
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_124073125_    795 TTAATTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAA 844
                             i    i      i ?    i       v   v       i      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_124073125_    845 ACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGACATGGGCA 893
                         vi i           v    ?i- v i -   iv   v v ivv i    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCA 580

  chrX_124073125_    894 A--GTCCTTCATGACTAAAACAGCAAAAGCAATGGCAGCAAAAGCCAAAA 941
                          --  --   v iiv  vi   v        vvi   i      vv    
  L1M4_orf2#LINE/    581 ATGGT--TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_124073125_    942 CTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAACAA 991
                         iv  i    v   ii v  i   v v  i i   i  ii vv    iv v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_124073125_    992 ACTACCATCAGAGTGAACAGACAACCTACAGAATGGGAGAAAATTTTTAC 1041
                             i  vv i      v        i                 v   i 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_124073125_   1042 AATCTACTCATCTGACAAAGGGCTAATATCCAGAATCCACAAAGAACTTA 1091
                           vii ivi      i  i  i  vi          vi i        iv
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_124073125_   1092 AACAAATTTACAAGAAAAAAATCAAACAACCACAAC-AAAAAGTGGGCAA 1140
                         v    v iv i  v     i -    i    -   i-?    i       
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGA-CAAATAACC-CAATTWAAAAATGGGCAA 826

  chrX_124073125_   1141 AGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGA 1190
                              v    i     i     v        i  vi viii     i ii
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_124073125_   1191 CACATGAAGAAATGGACACTTTCATACACTCT 1222
                                 i i   vv  viv   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (111 / 76)
Gap_init rate = 0.01 (10 / 719), avg. gap size = 1.90 (19 / 10)  


2601 23.65 1.41 4.63  chrX_124104867_124106582      489  1266 (450)    L1M4_orf2#LINE/L1      156   908 (0)  

  chrX_124104867_    489 ATGTAGTAGGG--CCGGACTCGCCAAGGTAATACTAAGCAAAAACAACAA 536
                            i --    --  i  v v     iii   vi i iv  i  v     
  L1M4_orf2#LINE/    156 ATGCA--AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_124104867_    537 AACTGGAGGCATCACTTTATCTGACCTCAAATTATACTACAAGTCTACAG 586
                          ii      vv    vi vi ii ii     viv        iv      
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_124104867_    587 TAACCCAAACAGCAAGGTACTGGCATAAAAATAGACACATAGGTCAAGAG 636
                            i v i    iiv             ii       i    i    vi 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_124104867_    637 AACAGAATAGAGAACCCATAAATAAAGCCATGTATCTACAGCTAACCGAT 686
                           i     v    ii   v       v    ii  i  ii ii  ii   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_124104867_    687 CTTTGCCAAAGCTGACAAAAACATAGCCTGGGGAAAGGACACTCTATTCA 736
                         i  i v   i v  v   i v   vvvv         i i v   v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_124104867_    737 ATAAATGGTGTTGGGATGGACTGCCATATTCAGAAGAATGGTGTTGGGAT 786
                          i        i     i-------------------  i---------- 
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGAC-------------------AAC----------T 424

  chrX_124104867_    787 GGATTGCCATATTCAGAAGAATGAAACTGGACCCCTGTCTTTCACCATAT 836
                             v?   i  v  i         ii         ii  iv        
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_124104867_    837 ACAAAAATCAGCTCAAGATGGATTAAAGACTTAAGTGTAAGACCTGAGAA 886
                                 i i     i      i ?    i   i       v  i i v
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_124104867_    887 TATAAAAATACTAGAAGGAAAC-CAAGGGAAAACTTGTCTGGACATTGAT 935
                                v vi      i    -i i ? v   ii -  vv   v   i-
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT-TCGTGACCTTGG- 572

  chrX_124104867_    936 TAGTCTAGGCAAAGAATTCATGACTAAGACCTCAAAAGCACAAAGAACGA 985
                         --  -       v iv   v iiv  v   vi           iv   i 
  L1M4_orf2#LINE/    573 --GT-TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_124104867_    986 AA------ATAAACAAATAGGACTTAATTCAA-CTAAAAGCTTCTGTACA 1028
                           ------   i i    v      v  iv  -i     i   i   i v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_124104867_   1029 GCAAAAGAAATAATCAACAGAGTGAAAAGACAACATACAGAATGGGAGAA 1078
                         v    i  v iv     v i              vi              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_124104867_   1079 AATATTTGCAAACTATTCACCCAACAGGGGACTAATATCCAGAATTTACA 1128
                                     ii  vi i ii i i      vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_124104867_   1129 AGCAACTCAAACAACTCAACAA-AAAAATTCAGATAACCCCATTAAAAAG 1177
                          iv     vv         i  -     vv  i       v   ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_124104867_   1178 TGGGCAAAGGATATGAATAGACATTTCTCCAAAAAAGACATACAAATGGC 1227
                                     v                    i    i           
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_124104867_   1228 CAACTGGAGTATGAAAAAATGATGAATATCATTAATCAT 1266
                            ivi vii       i   v v  i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (111 / 69)
Gap_init rate = 0.01 (11 / 753), avg. gap size = 4.27 (47 / 11)  


2822 26.99 1.63 2.83  chrX_124129246_124132049.rev     1397  2315 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124129246_   1397 TGTAGAGCTATTTTATTTTCATAATTAGGAAGACTCAATATTGTCAAGAT 1446
                           v i  v   iii  v     iiv v        i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124129246_   1447 ACCAGTTCTTTCCAACT----CTGTATATTCAATGCTATACGAGTCAAAA 1492
                         iv  i v  ii    v ----  ii v      i  v  v vvi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124129246_   1493 TATCATCAAGATATTTTGTGGTTATTGACAAACTTATTCTAAAGTTTACA 1542
                          vi  v vivv v     ii vv        i  v  i     i  i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_124129246_   1543 TGGGGAGGTCATATACTCTGATAGTCTTTCCATATAAACCTTAGAATAGC 1592
                            ii v -  -----------  -----------ii   i-        
  L1M4_orf2#LINE/    151 TGGAAATG-CA-----------AG-----------GGACCC-AGAATAGC 176

  chrX_124129246_   1593 CAACCCAATATTGAAGAAGGAAAACAA--TC--AGGATCCTGACACTACC 1638
                            vv    v     i   i i     -- i--    --  v     v  
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA--CTCACACTTCC 224

  chrX_124129246_   1639 CAACTTTGAGACTTACTATAAAGCTACAGTAATAAAAACAGTGTCATCTT 1688
                            i  ii i        i              v  i       vi vi 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_124129246_   1689 GGTGAAAGAATGGACAAGTAAATCAAAGGAACAGAATAAAGAACCCAGAA 1738
                           iiv   i  i    vi  i     v    i     vi   ii      
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_124129246_   1739 ATTGACCCACATAAATATAATCACCTGATTTTTGACAAAGGAGCAAAAGC 1788
                           vi     i i vv   ii   vi       i     i  v  v  ii 
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chrX_124129246_   1789 AATACAATTGAGAAAAGATAGTCTTTTCAACAAATGGTGGTGAAACAATT 1838
                         v  v    v i    ii                      v  ii    i 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_124129246_   1839 GGATATCTATATACCAAAAAGTGAATTTAGACACAGATTTTGTGCCCTTC 1888
                              ? i i  i v   i i    v  i   v vv ii iiii  v vi
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_124129246_   1889 ACAAAACTTAACTCAAG-TGCATCATAGATCTAAATGTAAAATGTAAAGC 1937
                               v         i-  v    ?   i          i vv    i 
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_124129246_   1938 TATAGAACTCCTAGAAGATCACTTAGGAGAAAAACTAGATAACCTCGGAT 1987
                             i     i       vv  v    ? v   v  vvi i    i  i 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_124129246_   1988 ATGATGACAACTTTTTAGATACAACATCAAAGGCATGATCCATGAAACAA 2037
                         vv iii iiii  i       ii   i    i   ii v v ii   v  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_124129246_   2038 AAAATTAATAAGCTAGACTTCATTAAAATTAAAAACTTATGCTCTGCAAA 2087
                              vi    ii i        i              v  iv  v    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_124129246_   2088 AGACAAAGCCAAGAGAATGAAAAGACAAGCTACAGATGGGAAGAAAATAT 2137
                         i    vvii     i i           v i     vv  i         
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_124129246_   2138 TTTCAAAAGACACACCTCATAAGAAA---ATATTCAAAATATATAAAGAA 2184
                           v    vv i i i  v     ii ---i   i  i             
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_124129246_   2185 CTCTTAAAATTCAAGAATAAGAAATTAAA-AGTCTGATT-AAAAATGGGT 2232
                               v  i    v     i  ivi   - ii ii   -         i
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_124129246_   2233 AAAAGACCTGAACATATACTGCAACAAAAGAGATAAACAGATAGCAAGGA 2282
                            i  ii    i v i i v vv    ii     v   i  i  v iv 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_124129246_   2283 AGCATGTGAAAATAT-TTCAATATAATATTTCAT 2315
                             ii      v  -i    i  v ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (152 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.15 (41 / 13)  


 786 25.88 6.61 13.80  chrX_124206738_124208614      500  1376 (501)    L1M4_orf2#LINE/L1       80   893 (15)  

  chrX_124206738_    500 TCAATGCAATTTCAAT-GAAATATCAATAGGCTGCGTTGTT---GGAACT 545
                             i     ii v  -i    vi  ----     v  v  ---i   v 
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCA----GCTGCCTTTTTTGCAGAAAT 125

  chrX_124206738_    546 TGATAAGCTAATTCTAAAACTTACATTGAAATGCAAAAAGCCAAGAATAG 595
                            i     i  i      i i i  v         iiii  v       
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chrX_124206738_    596 TATAAAACAATGTTGAAGA-------TATAGTTCAGAGGATTTGGTCTAC 638
                         i-i        v     i -------i v    -i     i iivv  v 
  L1M4_orf2#LINE/    176 C-CAAAACAATCTTGAAAAAGAAGAACAAAGTT-GGAGGACTCACACTTC 223

  chrX_124206738_    639 TGGATATAAAGGTCCATTTTAACGCTATGACAATAAAGGGAATGTACTAT 688
                         ivi  v v  iiiii i vi  v    iiii   v   iv i   iv  i
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_124206738_    689 TGACACT-GGATCAGATGAATAAACAAATGGGACAGAAT--AGAGTGAAA 735
                           i  iv-    -   iiv   i iv     i i     --     vv i
  L1M4_orf2#LINE/    274 TGGCATAAGGAT-AGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_124206738_    736 AAAATAGACTTGCACATATATGGACAAAGGAC-----ACAC---TGCAGA 777
                            -  i  iiii    v     v   vv  i-----   v---   vi 
  L1M4_orf2#LINE/    323 AAA-TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_124206738_    778 GA------AGTGAGGAAAAGACAATCTCTTCAATAACTGTTGCTGGGTCA 821
                           ------ i  i     ii i i   i     i  v  v       v  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_124206738_    822 G-TGGACATT-ATATGGGAAATAAAGTAGACTTAGATCCC---CTCAC-- 864
                         i-    i ?i- i   vi   v  v v  --  i  i   ---     --
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAG--TTGGACCCCTACCTCACAC 469

  chrX_124206738_    865 CATATGCAAA------CTCAAA-----TTCCACATCTAAAAGTCAAAGGC 903
                              i    ------      ----- iv? v i     v  v i  vi
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_124206738_    904 AAAGCAATAACATGTCTACAGGATAACATGGAA--AACTATCTGCATGAA 951
                            i v    v ivii  v i  v     i i?--  --    v i   v
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA--ATCTTCGTGAC 567

  chrX_124206738_    952 CTAAGGAAATTCAAATAGAAAAATATTTATTAAACAGTAATG--AAAAGC 999
                           vi  ---  -----  iv  vvi   v   i i - i ii--      
  L1M4_orf2#LINE/    568 CTTGGG---TT-----AGGCAATGGTTTCTTAGATA-TGACACCAAAAGC 608

  chrX_124206738_   1000 ACTAATTTAAAATAAATACCTGAAAAATAGACACCATTAAAACCCACTTA 1049
                           v ii----  i   vi---i         i v-   ii -----   -
  L1M4_orf2#LINE/    609 ACAAGC----AACAAAAG---AAAAAATAGATAA-ATTGGA-----CTT- 644

  chrX_124206738_   1050 TGCCTAGCGTTCCATTATTGGAACTCTAAGCATGTGGGAGTTATTTACAT 1099
                         ------------   i ---i  i vv  i v v  ----- ii  -  -
  L1M4_orf2#LINE/    645 ------------CATCA---AAATTAAAAACTTTTG-----TGCTT-CA- 672

  chrX_124206738_   1100 CCTACTGCTGAAGGTCATCGCCAAGGTCTGACTGCAAAATTCAAAAAAAT 1149
                         ----------    v  iiii    ----------   i --i    i -
  L1M4_orf2#LINE/    673 ----------AAGGACACTATCAAG----------AAAGT--GAAAAGA- 699

  chrX_124206738_   1150 TCAACCCCAGGCATAAATAGGTTAATATAGTGAACACCCAAGGCATGGTA 1199
                         -      --------------------------   ----------- v 
  L1M4_orf2#LINE/    700 -CAACCC--------------------------ACA-----------GAA 711

  chrX_124206738_   1200 TGGCAAAAATTATTTGTAACACAAATAACTGACAAAGGGCTTATGTACAG 1249
                            v i   v      i  vv  v   v    i  i  i   i i v   
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_124206738_   1250 AAAATGTAGAAAACTTGCAGAAATAAACAATAAA--GTTAGACAACCTAA 1297
                           v  i  i i    ivi v  v v  i      -- vi i i    i  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_124206738_   1298 T--AAAACTGTTGG----GGATTTAAATGGACACTTCACTATAAGAGGGC 1341
                          --    v  --  ----      i   i    i   v i -    i ii
  L1M4_orf2#LINE/    812 TTWAAAAATG--GGCAAAGGATTTGAATAGACATTTCTCCA-AAGAAGAT 858

  chrX_124206738_   1342 ATTCAAATGACCAGTAAACATATGTAAAGTTGCTC 1376
                           v      i   i   i  i   v    v     
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

Transitions / transversions = 1.73 (142 / 82)
Gap_init rate = 0.06 (45 / 814), avg. gap size = 3.98 (179 / 45)  


2483 26.92 2.95 0.77  chrX_124300044_124301815.rev      502  1281 (491)    L1M4_orf2#LINE/L1      112   908 (0)  

  chrX_124300044_    502 TTTCCTCCAGAACTAGAAAAAACT-ATTTTAAAATTTATATGGAACCAAA 550
                            ii v     v v  v  i-  -  ii       i        viiv 
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_124300044_    551 AAAGAGCCTAAATAGCCAAGGTAA----------AAACAACAAAGTTGGA 590
                          ii  v  vi         iii  ----------i  v            
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_124300044_    591 GGTGTCATGTTACCTGACTTCAAACTATACTACAGGGCTACAGAGACCAA 640
                           vv   iii v  ii i      viv       ii       vi i   
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_124300044_    641 AATAGCATGGTACTGGCACCAAAACAGACACTTAGACCAATGAAACATAA 690
                         i i  ii           iv ii i     iv    i     i  i v  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_124300044_    691 TAGGGAG-CCAGAAACAAAGCTGCTCACCTATGACCACCTGATCTTCAAC 739
                          v i   -       i   v iiiv  ii    ii  vi    i   i  
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_124300044_    740 GAAG---CCGAGAAAATAAGCCACGGGGAAA--ATACTCCCTATTCAATA 784
                         i i ---  i   vv  --v v i       --   v  -- v     i 
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCAT--TCAATGGGGAAAGAATAGTC--TTTTCAACA 406

  chrX_124300044_    785 AATAGTGCTGGGATAAATGGTTAGCCATATGCCAAAGACTGAATCTGAAC 834
                            i         i  v   v  ?   i    v     v    vi  i  
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_124300044_    835 CCCTTCCTTAAATCATATACAAAAATCAACTCTAGATAGATTAAAGACTT 884
                             v   i v i             i     v i  i   i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_124300044_    885 AAATGCAAAACCTAAAACTAGAAAACCCT-GGAAGACAACCTAGGCA-AT 932
                              i  i v         v     i  -i     v   v    ?i- v
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_124300044_    933 ACCATTCCAGACATAGGCACAAGCAAAGATTTCATGGTGAAAACACCAAA 982
                          i -   vv   v v  vvi i    v i    v i vv vi        
  L1M4_orf2#LINE/    557 ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_124300044_    983 AGCAATTGCAACAAAAGCAAAAGTTGACAAATGGGATCTCATTAAACTAA 1032
                             vvv          v    i v  i    v   ii    i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_124300044_   1033 AAAGCTTCTACACAGCAAAAGAAACTATCAACAGAGTAAACAGACAACCT 1082
                            i   i iii vv    i  v        v i   i  v        i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_124300044_   1083 AGAGAATGTTAGAAAATTTTTGCAAACTATGCATCTGACAAAGGTCTAAT 1132
                          v      vv       v        ii  ii      i  i  v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_124300044_   1133 ATCTAGCGTCCATAAGGAACTTAGACAAATTTACAAGAGAAAAACAAACA 1182
                            i  vi vi    i     ivv    v iv i  v i   i     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_124300044_   1183 ACCTTATTAAAAAGTGAGCAAATGACATGAA----CACTTTTCAAAAGAA 1228
                            iv   ?    i  i     v  iv    ----  i  i  v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_124300044_   1229 GACATACATGTGGCCGACAAGCATATGAAAAAATGCTCATTATCATTGCC 1278
                           i     vi     i i     i       i       vi    ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_124300044_   1279 CAT 1281
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.45 (122 / 84)
Gap_init rate = 0.02 (12 / 797), avg. gap size = 2.42 (29 / 12)  


2660 27.60 2.57 1.12  chrX_124303992_124309858     4480  5374 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124303992_   4480 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATATAGTGAAAAT 4529
                               i i  i     i               v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124303992_   4530 GGCCATACTGCCAAAAGTAATGTATAGATTCAATGCTATTCTCATCAAAC 4579
                            v     v  v   v i  v  i        i  v  i ii      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chrX_124303992_   4580 TATCATAGACAC--TCTTCATAGAATTAGAAAA---------AAAATACT 4618
                         -   vi  vii -- i  iii    v v  v  ---------     ---
  L1M4_orf2#LINE/    100 -ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT--- 145

  chrX_124303992_   4619 TTAAATGAAAC--CAAGATAGAGCATGTATAGCCAAGACAATCCTAAACA 4666
                          i v   i  v--    i--  v vv v        i      i i  v 
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_124303992_   4667 AAAAGAAAAAAAACTGGAGGCATCATGCTACCTGACTTCAGACTATACTA 4716
                          i     v   i-i      vv   ii  v  ii i    i viv     
  L1M4_orf2#LINE/    194 AGAAGAACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_124303992_   4717 CAAGGTTACAGTAACTGAAACAGCATGGTACTGGTACAAAAACAGACACA 4766
                            i i        iii i    ii         i i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_124303992_   4767 TAGACCAATGGAAGAGAATAGAGAACTTAGAAATAAGACTGCACATCTAC 4816
                             i        v     v    iiii        iv iii    i  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_124303992_   4817 AAGCATCTGATCTTCCAGAAACCTGACAAAAACAAGCAATGGGGAAAGGG 4866
                         iiv  vi    i   v v  ivv  v   i v  vv            ii
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_124303992_   4867 TCTTCTATTTAATAAATTGTTCTGGGTGAACTGGCTAGCCATATGCAGAA 4916
                          vv   v  i  i    v  v     vv      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_124303992_   4917 AATTGAAACTGGACAACTTCCTTACACCTTATACAAAAATTAACTCAAGA 4966
                         i v    ii     vv  v   i     v                   i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_124303992_   4967 TGGATTAAAAACTGAAATGTAAAACCCACAACTATAAAAACCTTAGAAGG 5016
                              i ? i  iv        i v i v          vi        i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_124303992_   5017 AAGTCTAGGCA-ATATCATTCAGTACATAAGGAAGGGCCAAAATATTATG 5065
                           iiv    ?i- v   -   ivv  v vi  vvi   v vii -  v v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT-TTCTT 590

  chrX_124303992_   5066 ACAAA-AACATCAAAATTAATGACAACTAAAGCAAAAATTGACACATTAG 5114
                          v v -i   i     vi vvii    v    v      v  i v   i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_124303992_   5115 ATCTAATTAAACTAAATAGCTTCTGCACAGCAAAAGAAACTATCATCAGT 5164
                          ii v  i   v v  v i   i  ii vv    i  v       vv iv
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_124303992_   5165 GTGAACAGACAACCGAGAGAATGGGAGAAAATTTTTGCAATCTGTCCATC 5214
                              v        v v               v       viii vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_124303992_   5215 TGACAAAGGTCTAACATCCAAAATCTACAAGGAAGTTAAACAAATTTACA 5264
                            i  i  v  vii     i   v  i  i   v ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_124303992_   5265 AGAACAAAACAA----CCCCATTAAAAAGTGGGCAAAGGACATGAACAGA 5310
                          v  v  i    ----   v   ?    i           iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_124303992_   5311 CAGTTCTCAAAAGAAGACATTTATGTGGCCAACAAACATGTGAAA----G 5356
                           v     v        i  vi vi       i  i  ii     ---- 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_124303992_   5357 CTCAACATCACTGATAAT 5374
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (133 / 110)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.54 (33 / 13)  


3728 25.03 0.11 0.00  chrX_124357969_124362221.rev     2856  3762 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124357969_   2856 TGGAAAGATATTTCTTGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 2905
                                    ii v                  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124357969_   2906 GTATGTACTACCAAAAGCAATCTACAGATTCAATGGAATCCTTATCAAAA 2955
                          vvvi    v  v   vii              i v     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124357969_   2956 TACCTATGACATTCTTCACAGAAATAGAAAAAATAATCCTAAAATTTACA 3005
                          v  viivi v  i  ii       v  v  iv i           i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_124357969_   3006 TGGAACCACAAAAGACCCAGAATAGCCAAAGCTGTTTTAAGCAAAAAGAA 3055
                              vii   ii                 i vi i  i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_124357969_   3056 CAAAACTAGAGGAATCTCATTACCTGACTTCACATTATACTACAGAGCTA 3105
                             ii i     v  v  i v  ii i    v viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_124357969_   3106 TAGTAACCAAAACATCATGGTACTTGCATAAAAGCAAACACATAGACCCG 3155
                         i     i   i   vii       v      iiii i   i     i vi
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_124357969_   3156 TGAAGCAGAATAGAGGACCCAGAAACAAATCCATACATCTACAGTGAACT 3205
                           i ii     v   iii       i   i        i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_124357969_   3206 CACTTTTGACAAAGGTGCCAAGAACGAACATTGAGGAAAGGATAGTCTCT 3255
                         v i   i     i          v ivv  v  i      i       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_124357969_   3256 TCAATAAGTGGTGCTTGGAAAACTGGATATCCATATGCAGAAGAATGAAA 3305
                             i  i       v   v         ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_124357969_   3306 CTAGAACCCTATCTCTCACCATATAGAAAAATCAAATCAAAATGGACTAA 3355
                         i i  v     i   v         v      i  v          ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_124357969_   3356 AGACTTAAATCTAAAGCCCAAAACTATGAAACTACCAAAAGAAAACTTTG 3405
                             i     v   iiv i        i     vii i        v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_124357969_   3406 GGGAAACGCTCCAAGACATTGGGCTGGGCAAAGATTTCTTGAATAATACT 3455
                          ? v  vv  i iv   v     i i     v i      ii   vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_124357969_   3456 CCACAAGCACAGGCAATCAAAGCAAAAATGGACAAATGGGATCACATCAA 3505
                            v       i    iv    v      i  i    v   iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_124357969_   3506 GTTAAAAAACTTCTGCACAGCAAAGGAAACAATCAACAAAGAGAAGAAAC 3555
                         iv v        i  ii vv       v  v     v    v   i i  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_124357969_   3556 AATACACACAATAGAAGAAAATATTTGCAAACTGTCCATCTGATAAGGGA 3605
                           iv    v   i i                iii vi             
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_124357969_   3606 TTAATAACTAGAATATATAAGGAGCTCAGACAACTCTATAA-AAAAAATT 3654
                         i vi  v i           i  i   vv       v    -     ivi
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_124357969_   3655 TAATAATCTTATTTCAAAATGTGCAAAAGATCTAACGAGACATTTCTCAG 3704
                         v     i iv   ?v      v     i   i i vv           vi
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_124357969_   3705 AAGAAAACATACAAATGGTCAACAGGTATATGAAAAACTGCTTGACATCA 3754
                              i i          i   i i i i       iv    ii      
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_124357969_   3755 TTGATCAT 3762
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.62 (138 / 85)
Gap_init rate = 0.00 (1 / 908), avg. gap size = 1.00 (1 / 1)  


3285 26.32 0.55 0.55  chrX_124369995_124375071.rev     3679  4586 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124369995_   3679 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAAGCAATATCGTGAAAAT 3728
                              ii i  i     i      i v      vvi     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124369995_   3729 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3778
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124369995_   3779 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3826
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_124369995_   3827 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 3876
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_124369995_   3877 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3926
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_124369995_   3927 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGATC 3976
                                 i   i    ii         i iv ii ii  v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_124369995_   3977 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 4024
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_124369995_   4025 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4074
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_124369995_   4075 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 4124
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_124369995_   4125 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAAATGGA 4174
                            ii    i    v   i     v           i  i          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_124369995_   4175 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4224
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_124369995_   4225 CTAGGCATTACCATTCAGGACATAGGCATGGGCAA-GGTCTTCATGTCTA 4273
                         v    ?i v viv   iv   v v  vv i     -   -   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATA 595

  chrX_124369995_   4274 AAACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4323
                         vi    v       vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_124369995_   4324 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4373
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_124369995_   4374 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 4423
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_124369995_   4424 AAGGGCTAATATCCAGAATCGACAATGAACTCAAACAAATTTACAAGAAA 4473
                          i  i  vi          vv i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_124369995_   4474 AAAACAAACAACCCCATTAAAAAGTGGGTGAAGGACATGAACAGACACTT 4523
                           i     i     v   ?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_124369995_   4524 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 4573
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_124369995_   4574 CATCACTGGCCAT 4586
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (137 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3510 24.55 1.45 0.11  chrX_124385712_124389902.rev     2805  3700 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124385712_   2805 TGGAAAAATATTCCATTTACACAAGTTGAAAGAATTAATATTGTTAAAAT 2854
                               i    i    v v  iiii   i    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124385712_   2855 GTTCATACTACCAAAAGCAATCTACAGACTCAATGCAATCCCTATCAAAA 2904
                          viv     v  v   vii         i    i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124385712_   2905 TACCAATGACATTCTTCACAAAAATAGAAAAA--AATC-TAAAATTTGTA 2951
                          v   iivi v  i  ii  i    v  v  i--i   -       ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_124385712_   2952 TAGTACCACAACAGACCCAGAATAGCCAACAATATCCTAAGCAAAAAGAA 3001
                          i v vii   vi                v vv   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_124385712_   3002 CAAAACTGGAGGAATTACATTACCTGACTTCAAATTATACTATAGAGCTA 3051
                             ii       v i   i v  ii i      viv     i i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_124385712_   3052 TAATAAGCAAAACTGCATGGTACTGGCTTAAAAACAGACACACAGACCAA 3101
                         i i   v   i  v ii          v   ii i     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_124385712_   3102 TGGAACACAATAGGGAACCCAAAAATAATTCCACACACCTACAGTGAACT 3151
                              i v   v i  ii   i      vi   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_124385712_   3152 CATTTTTGACAAAGGTGCCAAGAACAAACACTGGAGAAAAGACAGTTTCT 3201
                         v     i     i          v  vv  v   i    ii i   i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_124385712_   3202 TCAATAAATGATTCTGGGAAAACTGGATATCCATATTCAAAAGAATGAGA 3251
                             i     i v      v         ?   i  v           ii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_124385712_   3252 CTAGACCCCTGTCTTTCACATTATACAAAAATAGAATCAAAATGGACTAA 3301
                         i i       ii  iv   vv           vi v          ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_124385712_   3302 AGACTTAAATCTAAGATCTCAAACTGTGAAACTACTACAAGAAAAGTTTG 3351
                             i     v     v  v     i i     vi  v       vv v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_124385712_   3352 GGGAAAATCTCCAGGACATGGGTTTGGGCAAAGACTTCTTGAGCA--ACC 3399
                          ? v      i iv   v v  v  i     v ii     iiii --  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_124385712_   3400 CCACAAACACAAGCATTTGAAGAAAATATGGACAAATGGGATTGCATCAA 3449
                            v  i        vivi       v  i  i    v   i v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_124385712_   3450 G-TTAAAAAGCTTCTGTGCAGCAAAGGACACAATCAACAAAGGGAAGAGA 3498
                         i-       -   i     vv          v     v    v   i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_124385712_   3499 CAACCCACAGAACGGGAGAAAATATTTGTATAGTATCCATCTGACAAGGG 3548
                                     i               i v vi  vi      i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_124385712_   3549 ATTAATAACTGGAATATATAAGGAGCTCAAAGAACTC--T--CAAAGAAA 3594
                          i vi  v ii          i  i   vv v     -- --i   i i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_124385712_   3595 CTAATAATCCAATC-AAAAATGGGCAAAAGATTTGAATAGACATTTCTCA 3643
                          v     i     i-             i                    v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_124385712_   3644 AAAAAAGACATA--AATGGCAAACAGACATATGAAAAAGCGCCCAACGTC 3691
                            i    i   --      v  i ii  i       iii  i    i  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_124385712_   3692 ACTGATCAT 3700
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.68 (136 / 81)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2767 28.21 1.67 0.45  chrX_124396339_124401311     3584  4480 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124396339_   3584 TGGAAACAGATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3633
                               v v        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124396339_   3634 GACCCTACTTGCCAAAAGTAATCTACAAATTCAATGCAATTCCCATGAAA 3683
                          i vv    iv     -v i       i      i     i  i  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_124396339_   3684 ATACCA-CCACCATTCTTCACAGAACTAGAAAAAAAAATCCTAAAATTCA 3732
                           v   - ii  -  i  ii     v v  v  ivvi             
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_124396339_   3733 TATGGAACCAAAAAAGAGTCCACATAGCCAAAGCAAGACTGAGCAAAAAG 3782
                                viiv  ii  vi viv         i   vvi   iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_124396339_   3783 AACAAATCTGGAGGCATC-CATTACCTGATTTCAAACTATGCTATATGAC 3831
                               vi      vv  -  i v  ii        viv i   i vii 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_124396339_   3832 CATAGTCGCCAAAACAGCATGGTACTGGCATAAAAATTGGCACATAGACC 3881
                         i i   vii   i    ii              ii  v i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_124396339_   3882 AATGGCACAGAATAGAAAACTCAGAAATAAAGCCAAATACTTAAAGCCAG 3931
                              v i     v  i iii          v   v i i   vi i  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_124396339_   3932 TTGATCTTCAACAAAG-CACACAAAAACATAAAGTGGGGAAAGGACACCC 3980
                              i   i    i -ii -   i v   vv i         i i vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_124396339_   3981 TCTTCAACAAATGGTACTGGGATAATTGGCAAGCCACATATAGGAGAATT 4030
                          i             i      i  i   vv ?      ii ii     v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_124396339_   4031 AAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGAT 4080
                           ii    i  ii i   v    v           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_124396339_   4081 TGAAGACTTAAATCTATGACCTGAAACTATAAAGATTCTAGAAGATAACA 4130
                         ii?    i     v  v  v  i          iv ii       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_124396339_   4131 TTGGAAAAACCCTTCTAGACATTGGCTTATGTAAGAATTTTATGACCAAG 4180
                          v  ?iv  vi    vv   v    v   v i  vii   iv iivi v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_124396339_   4181 AACCCAAAAACAAATGCAATAAAAACAATGATAAATAGCTGGGACTTAAT 4230
                          vv      i  v v    i    iv  vi   i   iv v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_124396339_   4231 TAAACTAAAGAGTTTTTGCACGGCAAAAGAAAC-AGTAGGCAGAACAAAC 4279
                         i   v v  i ii     ii vv    i  v  - vi i - i iii  v
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAA 696

  chrX_124396339_   4280 AGAAAACCCACAAAGTGGGAGAAAATCTTCACAATCTATACATATGATGA 4329
                            v        i i           v  ii   vii   i  v    i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_124396339_   4330 AGGACTAACATCCAGAATCTACAACAAACTCAAACAAATTAGCAAGGACA 4379
                         i     vii         v  i  vi     vv    v i ii  vi v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_124396339_   4380 AAACAAACAACCCA-TCAAAAAGTGGGCTAAGGACATGAAT-------TA 4421
                          i     i      - i?    i     v     iv     ------- v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_124396339_   4422 TCAAAAGAAGATA-ATAA--GAACAACAAACAAAAGAAAAAAAGTTCAAT 4468
                           v          - i  -- iv   i  i  v v     i v i    i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_124396339_   4469 ATCACTAATGAT 4480
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.58 (19 / 12)  


2876 25.63 1.31 1.07  chrX_124406172_124408001.rev      502  1340 (489)    L1M4_orf2#LINE/L1       68   908 (0)  

  chrX_124406172_    502 TAATCTAAAGATTCAACGCAATCCCTATCAAAATACCAATGACGTTTGTC 551
                          i     v                          v   iivi v   v i
  L1M4_orf2#LINE/     68 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTT 117

  chrX_124406172_    552 ACAGAAATTGAAGAAACAATCCTAAAATTTACATGGCACTACAAAAGACC 601
                         i          vi ivii           i i    v v i   ii    
  L1M4_orf2#LINE/    118 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chrX_124406172_    602 CAGAATAGCCAAAGCTATCATAAACAAAAACAAAACAAAAAAACTTGAGG 651
                                      i v   v i  -   i - i      i---i v    
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAA-AAAGA-AGAACAAAG---TTGGAGG 212

  chrX_124406172_    652 AATCACATTACATGACTTCAAATTACACTACAGAGCTATAATAGCCAAAA 701
                          v     i v vii i      vivi      i     i i  ii   i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_124406172_    702 CAGCATCAGACTGGCATAAAAACAGACACAAAGAGCAATGGAATAGAACA 751
                            ii viv          ii i     i v   v             iv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_124406172_    752 GAGAACCCAGAAACCAATTTACATACCTACAATGAACTCATTTTCAACAA 801
                             ii       iv  iii i i ii  iii v  i v      i    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_124406172_    802 AGATGCCAAAAACATACAGTGGGGAAAAGAGAGT---------AAATGGT 842
                         i i      i v   v  i        ii v   ---------       
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_124406172_    843 GGTGGGAAAACTAGATATCCATA-GCAGAAGAATAAGACTAGATCTCCAT 891
                          v     v    i    ?   i -   i      i iii i  i i i i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_124406172_    892 CTATCACCATACACAAAAATCAAATCAAGATGGATTAAAGACTTAAATCT 941
                           vv       i        i  v    i      i ?    i     v 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_124406172_    942 AAGACCTCAAACTATGAAACTACTATGAAAAAGTATTGGGGAAACTCTCC 991
                             v  v       i     vi  vi i   ii  v  ? v  v   i 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_124406172_    992 AGGACATTGGTCTGGGCAAAAATTTCTTAAACAATTCCCCATAAGAACAG 1041
                         iv   v    vi i     vii       i i vvv v   v   v   i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_124406172_   1042 GCAACAAAAGCCAGAAATGGGAAAATGAGATAACATCAAGTTAAAAAACT 1091
                                   v- i    i iv    vi  ivv      iv v       
  L1M4_orf2#LINE/    613 GCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_124406172_   1092 TCTGCACAGTATACAACACAATCAACAAAGTGAAGAGACACCCCACCTAA 1141
                          i  ii vvi v vi    v     v        i     v     vv  
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_124406172_   1142 TGGGAGAAAATATTTGAAAACTACCTATCTGACAAAGAATTTATAACCAG 1191
                                         v   ii iv       i  i i i  i  v    
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_124406172_   1192 AATATATAAGGAACACAAACAACTCTATAGGAAAAAATCTAATAATT-AG 1240
                                  i    v vv       v   iv     iv v     ii- i
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_124406172_   1241 TTCCAAAAATGGGCAAAAGATTTGAATAGACACTTCTCAAATGAAGACAT 1290
                           ?-             i              i     v  v     i  
  L1M4_orf2#LINE/    812 TTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_124406172_   1291 ACAAATGAAAAACAGGCATATGAAAAGGTGTGCTTAACATAATTGATCAT 1340
                                ivv  i i   i        i  --  i     v ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATG--CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (129 / 82)
Gap_init rate = 0.01 (9 / 841), avg. gap size = 2.22 (20 / 9)  


 285 28.12 0.00 0.00  chrX_124409152_124410803      432   495 (1157)    L1M4_orf2#LINE/L1        2    65 (843)  

  chrX_124409152_    432 GAAAAAATATTTCACACTCATGGATTGGAAGTGTCAGTATCTTTAAAGTG 481
                          i   i    ii  iii              vv i i   iv    ii  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_124409152_    482 GCCATATTTCCCAA 495
                           v   i i     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAA 65

Transitions / transversions = 3.50 (14 / 4)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.00 (0 / 0)  

1544 28.77 2.05 1.37  chrX_124409152_124410803      549  1132 (520)    L1M4_orf2#LINE/L1      278   865 (43)  

  chrX_124409152_    549 ACAAAAATCAGATATATAGATCAATGAAACAGAACAGAGAACTCAGAAAT 598
                          i  ii  -   i             i  i    iv    iii       
  L1M4_orf2#LINE/    278 ATAAGGAT-AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_124409152_    599 AAAGCCACCTATCTACAATGAGCTGATCTTCAATAAACCCAGCAAAAATA 648
                            v   ivi  i  iii v ii    i   i i  ivviiv   i vi 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_124409152_    649 AATAATGAGCAAA-AATCTCCCTATTCAGAAAATGGGGCTGTTCTAACTC 697
                         vvi    i v   -   vvi i -    iv      v    vvvi    v
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGGACAACTG 425

  chrX_124409152_    698 ACTAACCACATACAGAAGAATGAAATTGGACCCCTGTTTATCACAATATA 747
                         iv  ?      i  i         i          iii vv   v     
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_124409152_    748 CAAAAATTAATTCAAGATGGAATGAAGATTTAAATGTAGCACCTCAAACT 797
                                   i    i     vii?   ii        iv v  v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_124409152_    798 ATAAAAATCCTAGAAGAAAACCTAGG---AAATACCTTTCTGGACATTGG 844
                               v  i           v    ---    --   iv  -  v    
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTG-ACCTTGG 572

  chrX_124409152_    845 CCTTGGCAAATAATTTAT--GAT-TAACTCCTCAAAAGCAATTACAACCA 891
                         vi v     - ii   v --   - i  v  --       vvvi    v 
  L1M4_orf2#LINE/    573 GTTAGGCAA-TGGTTTCTTAGATATGACACC--AAAAGCACAAGCAACAA 619

  chrX_124409152_    892 AAACAAAAATTGTCAAGAGAGGCCTAGTTAAACTAAAGTGCTTCTGCACA 941
                           iv      v vi  ivvi i i vi i   v v  ivi   i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_124409152_    942 GCAAAATAAACTATCAACAGAGTAAATACTCAACTTACAGAATGGGAGAA 991
                         v    iv v        v i   i  v vv    ii              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_124409152_    992 AATATTTGCAAACTATCCATTCAGCAAAGGTCTAATATCAAGAAACTGGA 1041
                                     ii  vi  iiiii  i  v  vi    v    vv iv 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_124409152_   1042 AGAAACTT----AAATCAGCAA-GAAAATACAAATAACCTTATTAAAAAG 1086
                          ii    i----  v   ii  -i    v          iv   ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_124409152_   1087 TAGGCAAAGGACATGAACAGACACTTCTCCAAGGAAGTTATTTAAA 1132
                          i         iv    i     i        i    v   vi   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

Transitions / transversions = 1.39 (96 / 69)
Gap_init rate = 0.02 (12 / 588), avg. gap size = 1.67 (20 / 12)  


2594 29.13 1.31 1.86  chrX_124434162_124437203     1638  2550 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124434162_   1638 TGGAAAGATATTCCATGTGCATGAATTGGAATACTAAATATTGCTAAAAC 1687
                                    i      v    i       v   v       i   i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124434162_   1688 GTCTATACTACCCAAAATATTCTACAGATTCAGTGCAATCCATATCAAA- 1736
                          v v     v      v iv            ii       v       -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124434162_   1737 TACCAATGACATTCTTCATAAAAGTAGAGAAAATAATCTTAAAATATATA 1786
                          v   iivi v  i  iii i  i v  v  iv i   i      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_124434162_   1787 TGGAACCACAAAAGACCAAAGACAGCGAAAGCCATCCTGAGGAAAAAGAA 1836
                              vii   ii    v ii i   v   i v   i   ii  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_124434162_   1837 CAAAACCATAAGATTCACATTATTAGACTTTGAATTTTACTACAGAGGCA 1886
                             iiiiv i  i     i viivi i  ii  vi        i  vi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_124434162_   1887 TAGTAACCAAAGCAACATAAGACTGACACACAAACAGACACATAGACCAA 1936
                         i     i   ii  iii iiv    i  i vii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_124434162_   1937 TGGAACAAAATATAGAACCCAGAAATAAATCAATACCTCTACAATAAATT 1986
                              i i   vv   ii           i v    v i  iii v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_124434162_   1987 CATTTTCAACAAATGTGTCAGGAACATACATTGGGAAAATGACCATCTCT 2036
                         v      i    iv   i  i  v   v  v    i   vi ivi   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_124434162_   2037 TTAATAAATGAAACTTATTTAATAAATGA-AACTGG-TAACCATATGCAG 2084
                          i  i     ivi  vi----------  -      -  ?   i     i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGG----------GACAACTGGATAKCCACATGCAA 440

  chrX_124434162_   2085 AAAAATAAAATGAGACCACTATTTCTCATCATATACAAAAGTAAAATGAA 2134
                           i   i  i vi    v   ii  v  i           i v  v v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_124434162_   2135 AATTGATTAAAAACTTTAACCTAAAACATCAGACTATGAAAATACTAAAA 2184
                            v   i ? i  i v  iv   i vv v i     i   v vi  i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_124434162_   2185 GAAAACCTTTAGGA-TAC-TCTCCAGAACATTGGCATGGGTA--GATTTC 2230
                               v --   ?-  v-   i ivi  v    vv i  i -- i    
  L1M4_orf2#LINE/    541 GAAAACAT--AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_124434162_   2231 TTGAGTAATACCACGAAAAGCACAGCCAGCAAAAGCGAAAATAGGCAAAT 2280
                           iii  - iv   v         iv  i      vi       ii    
  L1M4_orf2#LINE/    589 TTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_124434162_   2281 GAGATTACATCAAG-TTAAAAAGCTTCTGCATAACAAAGAAAACAATCAG 2329
                         vi  i v      i-       -   i  iiivv     i v  v    i
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_124434162_   2330 TGAAGTGCAGAGAAAACCCACAGAATGGGAGAAAATATTTGTAAACTATT 2379
                         vi     v i   v                           i   ii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_124434162_   2380 CATCTCACTAGAGATTAATAACCAGAATGTACAAGCAGCACAAACCACTC 2429
                         i    v iv  i  i vi  v       i  i  iv i v vv  v    
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_124434162_   2430 --TG-TAGAAAAATATTTAATAATCGGATTCAGAAATGGATTAAAAATTT 2476
                         -- i-  i   i i ---     i vi   ? i      iiv  ii    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACA---AATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_124434162_   2477 AAACTGATGTTCCTCTAAAGAAGACATACAAATGGCCAGCAGATGTTTAA 2526
                         i  iv  ii  i   i        i             ii iiiiiv i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_124434162_   2527 AAAGGTGCCCAAAAT-ATTGATCAG 2550
                             i   i   v  - ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (173 / 89)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.93 (29 / 15)  


3263 26.76 0.44 0.44  chrX_124468730_124475000.rev     4873  5780 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124468730_   4873 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4922
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124468730_   4923 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4972
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124468730_   4973 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5020
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_124468730_   5021 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5070
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_124468730_   5071 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5120
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_124468730_   5121 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGATC 5170
                                 i   i    ii         i iv ii ii  v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_124468730_   5171 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5218
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_124468730_   5219 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5268
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_124468730_   5269 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5318
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_124468730_   5319 GAAACTGGATCCCTTCCTTACAACTTATACAAAAATCAATTCAAGATGGA 5368
                            ii    i    v   i   v v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_124468730_   5369 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5418
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_124468730_   5419 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5468
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_124468730_   5469 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCCAA 5518
                         i            vvi           v     v  i    v   iiiv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_124468730_   5519 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5568
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_124468730_   5569 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5618
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_124468730_   5619 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5668
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_124468730_   5669 AAAGAAACAACCGCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5718
                          i v   i    vv  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_124468730_   5719 TCAAAACAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5768
                           v   v    i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_124468730_   5769 ATCAGAGAAATG 5780
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2585 28.27 1.66 1.00  chrX_124488800_124493747     3554  4455 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124488800_   3554 TGGAAATACATTCTATGCTCATGAATTGGAAGAATCAATATTATGAAAAT 3603
                               v i  i i   i     i         v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124488800_   3604 GACCATACTGCCCAAAACAATCTACAGATTTTATGCGATTCCATTCAAAG 3653
                          i v     v      vii           iv i  i  i  vv     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124488800_   3654 TACCAACATCATTTTTTTTCACAGAATTAGAAAAAAGC-AATTCTAAAAT 3702
                          v   i vv v      ---i     v v  v  --  -i  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT---GCAGAAATTGACAA--GCTGATCCTAAAAT 145

  chrX_124488800_   3703 TCATATGGAA-CAAAAAAGAGCTTGAATAGCCAGTGCTATCCTAAGCAAA 3751
                                   -iiv  ii  v iv         ivi v   i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_124488800_   3752 AATACAAAATTTGGAGGCATCATATTATCTGATTTCGAATTACACTATGA 3801
                           v vv   v       vv   i i vi ii     i  vivi    ii 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_124488800_   3802 AGCTTCAGTAACTAAAAGAGCATGGTAGTGTGAAAAAAATAGACATATAA 3851
                             v      ii  i v  ii     v  vv v  ii           i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_124488800_   3852 ATCAATGGAACAAATTAGAGAAACCAGAAATAAATCTACATGCCTACACC 3901
                                   i i v v    iv           i i i iiii  iivi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_124488800_   3902 CAAATGAACTGCAACAAAGTTGACAAAAATAAACAATGGGAACAGGATAC 3951
                            v   vi v i    i v  v   i vi vv       i v  i   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_124488800_   3952 CCTATTCAATAAATCATGCTAGAAAAACTGGAGAGCCA---GTAGGAGAA 3998
                         i  v     i    vi    i i v       v ?   --- i ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_124488800_   3999 TAAAACTGAATTCTTATGTTTTACCATCTAGTAAAATCAACTCAAGATGG 4048
                          i  ii  i ii i  iv ivi     v  vv     i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_124488800_   4049 ATCAAACATTTAAGTCCAATGCCTGAAATCATAAACATTCT-AGAGGAAA 4097
                             ? v ii   i vi  viv  i   ii     - i   -   i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAA 544

  chrX_124488800_   4098 ACCTAGGAA-AAACATTTCTGAACATTAGCCTAAGCAAAAAATATATAAC 4146
                           v    ?i-   iv  iv   v -  i vi  i    viiv viv  iv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_124488800_   4147 TAAGAGCCCAAAATCAAATGCAACAAAAATGAAAATAAATA----GGACT 4192
                           v  vv      v  v v         ivi      i   ----     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_124488800_   4193 TAATTAAACTAAAAGTCTTCTTCACAGCAAATAAATAATTGTCA-GAA-- 4239
                          v  i   v v   iv   i vii vv    -ii i -i i   -   --
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAA-GGACA-CTATCAAGAAAG 691

  chrX_124488800_   4240 TAAACAGACAACCCACAGAATGAGAGAAAATATTTGCAAACTATGCATCT 4289
                          i  v                 i                 ii  ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_124488800_   4290 GACAAGGGAGCAATATCCAGAATCTATAAGGAACCCAAACTAATCAGCAA 4339
                           i      vivi          v     i    i vv  v v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_124488800_   4340 GAAAAACCCAAATAATTCCATTAAAATGTGGGCAAATGACATAAATAGAC 4389
                         v     vv       ii v   ?   vi        v  iv i       
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_124488800_   4390 ACTTCTCAAAAGAAGATATACAAATGACCAACAAACATATGAAAA-ATGA 4438
                          i     v                  i    i  i  i       -   v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_124488800_   4439 TTAACATCACTCATCAT 4455
                          i       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (146 / 105)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.60 (24 / 15)  


2203 23.65 2.30 11.68  chrX_124507351_124508988.rev      146  1147 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124507351_    146 TGAAACAATATCACATGCTCATGAATCAGAAAAATTAATATTGTTAATAT 195
                           i  vi     v    i     i  ii   i v             v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124507351_    196 GACCATACCACCAAAAGCAATCAACAGATTCAATGCAATCTCTATCAAAA 245
                          i v    iv  v   vii   v          i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124507351_    246 T---AACATCATTTTCCACAGCACCATAAAAAAGTCAGTTCTAACATACA 292
                          --- i vv v    iii   v --  vi v   iiii i    v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chrX_124507351_    293 CACAGAACCAAAAAAGAACCTGAATAAACATAACAATATTACACAAAAAG 342
                         i ii   viiv  ii  v  v     iv  v      v  iv v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_124507351_    343 AGCAAAGCCAAAGGCATCACATTACCTGACTTCAAGTTATATTAAAAGGG 392
                          i     iiii   vv     i v  ii i     ---------------
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAA--------------- 233

  chrX_124507351_    393 TAATATATTTAAACTAGAACTACCATATAATCCAGAAATCCAACTTCTGG 442
                         -----------    -----   ---------------------------
  L1M4_orf2#LINE/    234 -----------AACT-----TAC--------------------------- 240

  chrX_124507351_    443 GTATATATACAAAAGAATTGCAATCAGGATCTAAAAGAAAGATCTACACT 492
                         -------      ------  -----------------------------
  L1M4_orf2#LINE/    241 -------TACAAA------GC----------------------------- 248

  chrX_124507351_    493 ACCATTTTGTACAGTAGACAAAATAGCATGGTTCTTGTCTAAAAATAGAC 542
                         ---------       iv   i i  ii    v  v iv   ii      
  L1M4_orf2#LINE/    249 ---------TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_124507351_    543 ATGTAGATAATTAAAACAGAATAGAGAA-CCAGAAGTGAAGCCACTTATT 591
                           i     v v ii  i     v    i-      i i  v   ivi   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_124507351_    592 AACAGCCAACTAATCTTTGACAAAGTTATCAAGAACATTTATTGGGGAAA 641
                         v ii i   i i  i  i     i v ii     v    i v        
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_124507351_    642 GGACACCCTTTTCAACAAATTGTGCTGGGAAAATTGGATTTCCATATGCA 691
                          i i vi             v         v  i     v?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_124507351_    692 GAAAAATGAAACTGGACTTCTATCCCTCACCATATACAAAAATCAAC-CA 740
                         i  i      ii     ii   i i v                i   -  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_124507351_    741 AGATGGATTAGAAATTTATACATAAGAACGGAGACTATAAAAATCCTGCA 790
                          i      i ? i ii  v ii     i vi i         v  i iv 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_124507351_    791 AGAAAACCTAGGCAATACTATTCTGGACATTGGTCTAGGCAAATAATTTG 840
                                v    ?ivv v v   vv   v    vi       - ii   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTC 588

  chrX_124507351_    841 CT-GCTAAGACCTCAAGAGCACAACCAA--AAAAAAACCCAAATAGACAA 887
                         i - v  v   vi   i       v   --   i   ---       i  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA---AAATAGATAA 635

  chrX_124507351_    888 ATGAGACTTAATTAAACTAAAAAGCTTCTGCAAAGAAAAGGAAATAATCA 937
                           vi     v  i   v v    i   i  iivvvv      v iv    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_124507351_    938 ACAAAGTGAACAGACAACATGCAGAATTGAAAAATATATTTGTAAATTAT 987
                          v        v       vii      v i i  v       i    i  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_124507351_    988 TCATCTAACCAGATACTAATATTCAGAATATGCAAATAACTC----AAC- 1032
                         vi    i iv  iv   vi   i        ii   v     ----   -
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_124507351_   1033 --------AAAAAATAA-TAATTCCATT-AAAAGTTGGCAAAGGACATGA 1072
                         --------    i i  -   ii v   -    i v         iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_124507351_   1073 ATAGATTTTTTTTAAAATAAGAACATACATATGACCAATAAGTATGTGAA 1122
                              iv   i iv   v    -i     v   i        i ii    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGA-TATACAAATGGCCAATAAGCACATGAA 884

  chrX_124507351_   1123 AAAAATGCTCACCATCACTAATCGT 1147
                           i -      v     ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 7.37 (140 / 19)  


2597 26.07 2.13 2.25  chrX_124510255_124513851.rev     1767  2610 (986)    L1M4_orf2#LINE/L1        1   843 (65)  

  chrX_124510255_   1767 TGGAAAGACATCCC-TGTTTCATGGGTTGGAAGAATTAATACTTTTTAAA 1815
                                 i     -    -     i        v      i v  v i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTT-CATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_124510255_   1816 TGTTTATACTATCCAAAACAATCTATGGAGTCAATGTTATCCTCATCAAA 1865
                           viv     vi     vii     ii  v    i iv    ii      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_124510255_   1866 ACTCCAATGGCATTTCTTATAGAAATAGAGAAAACATATAAATAATA-TA 1914
                          ii   iiv  v   i  ii      v  v  i- ------- i  v-  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-C-------TGATCCTA 141

  chrX_124510255_   1915 AAATTCCTATGGAACAACAAAATATGTAGAATAGCCAAAGTGATTTTGAG 1964
                               v       vvi   iiv ivi            iii  i    i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_124510255_   1965 AAAGTAGAACAAAGCTG-AGGCATTAAATTTCCTGATTTCAAA-TATATT 2012
                             v         i  -   vv i v i    ii        -iv  i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_124510255_   2013 ACACA-TTACAGTAATTAAAACAGTATGATACTAGCATAAAGACACACAT 2061
                            v -i         i  i     i  i    i      i  i v    
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_124510255_   2062 ATAGATCAATGAAACATATTAGGGAGACCAGAAATAAACCTATGCACATA 2111
                                    i  i v v v i   v             i  i  iv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_124510255_   2112 TAGTCAACAAATCTTTGACAAGGGTATCAAGAATACATAATGGA-AAAGG 2160
                          i     ivi  i  i         ii     vi ivi     i-    i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_124510255_   2161 ATAGTCTCTTCAATAAATGATGTTGAAAAGACTGGATAGTCACACACAAA 2210
                                i     i     i  i  ii vi        ?i    ii    
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_124510255_   2211 AGAATAAAAT-GGACTTTTTAACTTAAAGCATACACAAAAATCAACCCAA 2259
                              i  i -    iii - v  i v v    i        i   i   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_124510255_   2260 AAAAGATAAAAAACTTAAATATAAGATTTGGAACTGTAAAATTCCTAGAG 2309
                           vi   v ? i  i     i     vi ii    i     i  i    i
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_124510255_   2310 AAAAATATATAAAAATATCTTCTTGATATTGGTTTTTGAAATTATTTATT 2359
                         i    i   vi?iv v      v   iv    v  vv v   vi   v  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_124510255_   2360 GAATCTGACACTAAAAGCACAGGTGACAAAAGCAAATATAAACAG-TAAG 2408
                         ii  v      i         i ii       v   v   i i i- vi 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_124510255_   2409 ATTATATTAAA--TAGAAGCTTCTTGCACAGAAAAGGAAACAATCAACAA 2456
                          i vi  i   --  i  i   -   ii vvv      v  v     v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTT-TTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_124510255_   2457 ACTGAAAAG-CAACATAGGAAATGGGAGAAAATACTTGCAAACTGCATAT 2505
                          v       -    vi vii              i       iiii    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_124510255_   2506 ATGATAAGGGGTTAATTTCCAAAATATATAAAGAA-----A-AACATAAT 2549
                         v         ii vi v    i             ----- -   vi   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_124510255_   2550 AACAAAAACAAATTTTAAAAAATAACCTTATT-AAAAATGAGAGAAAGAC 2598
                           i     --------i v        iv   -       i vi  i  i
  L1M4_orf2#LINE/    790 AATAAAAA--------GACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_124510255_   2599 AGGAGCAGAAAT 2610
                         vv  ii   v  
  L1M4_orf2#LINE/    832 TTGAATAGACAT 843

Transitions / transversions = 1.86 (141 / 76)
Gap_init rate = 0.02 (19 / 843), avg. gap size = 1.95 (37 / 19)  

 456 19.57 0.00 0.00  chrX_124510255_124513851.rev     3015  3106 (490)    L1M4_orf2#LINE/L1      817   908 (0)  

  chrX_124510255_   3015 AAATGGGCAGATAATTTGAATAGACTTTTCTTGAAAGAAGATTTGCAAAT 3064
                                  i vi            v     iv         v i     
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_124510255_   3065 GACCCATAAGTGTATGAAAGAGTGCCCAACATCGTGATTCAT 3106
                          i  v     iii      iii   i       i????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.00 (0 / 0)  


2430 28.12 3.60 1.46  chrX_124524070_124528986     3536  4424 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124524070_   3536 TGGAAAATCATTCTATGCTCATGGATGGAAATAATTTGTCTTATTAAAAT 3585
                               ivi  i i   i        v i  v v  vi v  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124524070_   3586 GGCCACACTGCCCAAAGCAATTTACAGATTCAATGTTATTCCAATCAAAC 3635
                            v i   v      vii  i           i iv  i  v      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124524070_   3636 CACCAATGACATGCTTCACAGAACTAGAAGAAAACT--TGC-AAAATTTA 3682
                         iv   iivi v vi  ii     v v  v--  i  -- v -      i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chrX_124524070_   3683 TGTGGAACCATAAAGGCACCTGAATAACCAAAGCAATCCTGTGGAAAGAG 3732
                          i     viii  i  vv  v     i     i     i  vii  ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_124524070_   3733 AATAAAGTTGGTGATATCACACTACCTAATGTCAAACTATATTATAAGGC 3782
                           i        v ivv       v  i   v     viv  i  i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_124524070_   3783 TACAGTAATGAAAAGAGCATGGTACTGGTACAAAAACAGACA----GATC 3828
                                  v  i v  ii         i i  ii i     ----    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_124524070_   3829 AATGGAACAGG--TAAAAGATACTGGAAGTAAAGCCAGACACCTACAACC 3876
                                i  i-- i i  - - ii   i    v   v   ii  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAG-T-CCAGAAATAAACCCATACATTTATGGTC 346

  chrX_124524070_   3877 ATCTGTTCTTTGGAAAAGAGGACAAAAACAAGCAATGTAAAAAGGA--GT 3924
                          vi  v i  i iv  i iv v   i v  vv     vii    i --  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_124524070_   3925 TTTTATTTAATAAATTGTGCTGGACTAACTGCCTAGCCATATGCAGCAGG 3974
                         i   -- i  i    v       ivi     vv  ?   i     iv  i
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_124524070_   3975 CTGAAAC----CCCCTGCTT-ACACCATATACAAACATTAAGTCAAGGTG 4019
                         v    ii----     i i -              v     v    ii  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_124524070_   4020 GATTAAACACTTGAGTGTAAAATGTAAATCTCTAAAATTCCTGAAAGATA 4069
                            i ? v  i i i     i vv    v  v     i  i ii    v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_124524070_   4070 ACCTAGGA--AAATCCGTTC-TGGACATGGGTCCTTGCAAAGATTTAATG 4116
                           v    ?--     --   -  iv v     ivv-    v i   vv i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC--TTCGTGACCTTGGGTTAG-GCAATGGTTTCTTA 591

  chrX_124524070_   4117 AAAAAGACCACAGGAGAAATTGCAACAAAACCAAAAATTGACAAGTGGCA 4166
                         i v v   vv  ii  v vvv         vv      v  i  i v v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_124524070_   4167 CCTAATTAAACTAAAGAGTTTCTGCACAGCAGGAGAAAATAGCAACAGAG 4216
                          i v  i   v v  i ii  i  ii vv  iii  v v  v   v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_124524070_   4217 TAAACAGACACCCTACAGAATGGGAGAAAGTATTTGCAAACTATGCAGCT 4266
                          i  v     v  i               i          ii  ii v  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_124524070_   4267 GACAAAGGTCTACTATTCAAAATCTATAA-GAATTTCAACAAATTAACAA 4315
                           i  i  v  vv   i  i   v     -   i iiv    v i  i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_124524070_   4316 GCAAAAAACACACAAAAAAACCA-TT--AAAATGGGCAAAGGACATGAAC 4362
                         -i     i---     v  v   -  --               iv    i
  L1M4_orf2#LINE/    792 -TAAAAAG---ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_124524070_   4363 AGACACTTCTCAGAAGAAGACATACAA--------CAAGCATATGAAAA- 4403
                              i     vi       i      --------i     i       -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_124524070_   4404 ATGCTCAACAGCACTAATCAT 4424
                                   v  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (144 / 103)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.05 (45 / 22)  


2135 24.43 3.28 1.15  chrX_124536717_124538319.rev      503  1112 (491)    L1M4_orf2#LINE/L1      286   908 (0)  

  chrX_124536717_    503 AGACATAAAGATCAATAAAGCAGAATAGAGAGCCCAGAAATAAATCTGCA 552
                                v        ii ii     v     i           i iii 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_124536717_    553 TATTTATGGTCACTTGATCTTTAATAAAGGTGCCAAAACACAT--AATAA 600
                         i           v     i  ii i  i        i  -   --   ii
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGG 384

  chrX_124536717_    601 GGAAAGGGAAGTCTTTTCAATAAATTGTGTCAAGGAAACTGAATATCCAC 650
                               iiv           i    v   iiii iv     i   ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_124536717_    651 ATGGGGAAAAAAGAAATAAGACCCTTATCTCCCACAAGA-ACAAAAATCA 699
                            vii  i  v   i vi     i  i   v   v v -        i 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_124536717_    700 ACTTAAAGC-TATTAAAAACTTAAA------ACTTGAAAACGTAAAACTA 742
                            i   ii-v  i ? i  i    ------ vi i   vii       v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_124536717_    743 CTAGAAAAAAATATAGAAA-AAAGCATCTTGACATTGGCCTAGGCAATAA 791
                         i     i    i    i?i-   v v  v    v    vi        -i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT-G 583

  chrX_124536717_    792 ATTTTTTGAATATAATACTAAAAGTACAGGCAACAAAAACAAAAATAAAC 841
                         i   i  ii    i i  i     i   i         iv       i i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_124536717_    842 AAATGGGATTTTATCAAACTAAAATGTTTCTGCACAGCAAAGGAAACAAT 891
                             v   i  i      v v   vii  i  ii vv       v  v  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_124536717_    892 CAACAGAGTGAAGAAACAACCAACAAAATGGGATAAAAT--TTGCAGACC 939
                            v i      i i      v   i       v     --     i i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_124536717_    940 ATATATCTG--CAGGGGTTAATATTCAAAACAT-TAAGAAACTC----AA 982
                                  --v    ii vi   i  i  i  -   ii     ----  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_124536717_    983 CTCAATCGCAAGAAAACAAATAACCCAATTTTTTAAAAAATGAGTGAATG 1032
                               vii  i  i               ----?       i ii  v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATT----WAAAAATGGGCAAAGG 829

  chrX_124536717_   1033 ATCTGAATAGACTTTTCTCAAAAGAAAACATATGAATTACCAACAGGCAT 1082
                           i         v      v      i i   ii   vi    i i   -
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA- 878

  chrX_124536717_   1083 TAGAAAAAAATGCTCAACATTACTAATCAT 1112
                         i vi    i           i ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.54 (104 / 41)
Gap_init rate = 0.02 (13 / 623), avg. gap size = 2.08 (27 / 13)  


2322 27.73 1.28 4.07  chrX_124559486_124561127.rev      220  1153 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124559486_    220 TGGAAAGGCAGTTCCTGCTTATGAATAGGAAGAATCAATATTCACAAAAT 269
                                ii vii v  i i   i  v      v i      vvi  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124559486_    270 TATCATATTGCCAAAAGCAATTTACAGATTAAGCATAATTCTTATCAAAC 319
                         viiv   i v  v   vii  i        v i ii   i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124559486_    320 TACCAA-TGTCACTTTCCACAGTACTATAAAATGCT-ATTCTAAAATTCA 367
                          v   i-  i -i   iii   v v - i v v   -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chrX_124559486_    368 TATGGAACCTAAAAAGAGCCCACC-TAACCAATGAAATCCTAAGCAAAAG 416
                                v- iv  i ii    vv-  i    viv    i i iv  i i
  L1M4_orf2#LINE/    149 TATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_124559486_    417 AAACAAAGCTGAAGGCATCATACTACCCCACTTCACAGGACACTACAAGT 466
                         i       i  i   vv   i   v   v i    v ivvi       iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_124559486_    467 CTACAGTAACCAAAACAACATGGTTCTAGTGTGCAAAAAGACACACATAG 516
                                  i   i   iii    v  i ii --  ii v v   i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAG 295

  chrX_124559486_    517 ACCAATGGAACAGGTTAGCAAACCCAGAAATAAAGCTGCACACTCACAAC 566
                          i        i  iv v vi ii           v iii   i i iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_124559486_    567 CATCTGGTCTTTGGCAATGTTAACAAGGGCAAACAATGAGGAAAGGACTC 616
                           vi  i i  i i   v v iv    iv  vv     i      i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_124559486_    617 CCTATTTAATAAACGATGCTGGAATAACTGGCCAGCCATATGCAGAAGAT 666
                         i  v  i  i   i i      i i      vi ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_124559486_    667 TGAAACTGGACTCCTTCCTTTCACTATACACAAAAATCAACTCAAGTTTG 716
                             ii     i   v   iv   i   i        i       iv v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_124559486_    717 ATTAAATACTTAAACATACAACCTAAAACTATAAAAACCCTAGAAGAAAA 766
                           i ? v  i    ii  vi v              vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_124559486_    767 CCTAGGGAATACAATCCTCA--ACACAGGCATTGACAAAGATTTCAT-GA 813
                          v    ?i-  -    i  i--  viv  vv v i   v i    v -  
  L1M4_orf2#LINE/    546 CATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_124559486_    814 TGAAGACTCCAAAGGCA-AAGATTTCATGATGAAAACTCTAAAAGTAATT 862
                          - v   v     i   -   ----  --------  ---     -----
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAG----CA--------AC---AAAAG----- 622

  chrX_124559486_    863 GGAAACATAACTGACAAGTGGGACCAAA-CTAAACTAAATATTTTCTGCA 911
                         -i   v   ---  i  i v    ivv - v   i    v i   -  ii
  L1M4_orf2#LINE/    623 -AAAAAATA---GATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTG 667

  chrX_124559486_    912 CAGCCAAAGAAACTATCAACAGAACAAATGGACAACCTAAAGAGTAGAAG 961
                          vv v  i  v        v i iii  vi       i v   i i i  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_124559486_    962 AGAATATTTGCAAACTTCATTCACC----AAAGGTGTAATATCCAGAATC 1007
                          i            --    vi i ----  i  vv vi          v
  L1M4_orf2#LINE/    718 AAAATATTTGCAAA--TCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_124559486_   1008 TACAAAGAACTGAAACAAGTCAACAAGCAAAAAAGCAAACGACCCCTTTA 1057
                           i        vvv    v    i  -i     ii    ii    vv  ?
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTW 814

  chrX_124559486_   1058 AAAAATGGGCAAAAGACATGAACAGACATTTCTCAAAATAAGATATACAT 1107
                                      i  iv    i           v   v          v
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_124559486_   1108 GCAGCCAATGAGCATACGAAAAAAAATGCTCAACATGACTAATTAT 1153
                         iii      i    i i     i --          v ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (156 / 99)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.08 (50 / 24)  


2086 23.64 3.75 6.46  chrX_124570545_124572304      494  1267 (493)    L1M4_orf2#LINE/L1      156   908 (0)  

  chrX_124570545_    494 ATGCA---GAGTCAAAACCAGCAAAAGCAAAC-------AGAAAACTAAA 533
                              ---  vi  i  i-   v   i   v -------    i vi   
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAAT-AGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_124570545_    534 GCTGAGGTATTCA-ACT---------CATA---TACTATAAGGCTATAGT 570
                          i  ii v i   -   ---------  v ---     i  i    i   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_124570545_    571 TACCAAAACAGCATCATACTGGCATAAAAATAGGCATGTAGACCAATGAA 620
                         v i   i    ii vi           ii    i   i    i     i 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_124570545_    621 ATAGAATAGAGAACCTAAAAATAAAGCCAAATACTTACAGCCAACTGATC 670
                                v    ii i i       v   v i i   ii i   i    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_124570545_    671 TTTGACAAAGCCTATAAAAATAT--AAGTTAGGGAAAGGACACCCTATTT 718
                           i     i vivvi  i vi  --  -- i       i i vi  v  i
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTCTTTTC 402

  chrX_124570545_    719 AATAAATGGTGTTGGGAAATCTAGAAAGCCACATGTAGAAGAATAAAACT 768
                           i        i     v v  i  v ?       i i      i  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_124570545_    769 GGACTCTTATCTCTCACCCTATAAAAAAATCAACTCAAGATGGATGAAAG 818
                             i i  i   v    v    v      i       i      v ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_124570545_    819 ACTTAAATCTGAGACATGAAACCATAAAAATTCTAGAAGATAACACTGGA 868
                           i     v i   vv i    i      v ii       v    iv  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_124570545_    869 AAAACTCTTCTAGACATTGGCTTAGGCAAAGAATTAATGACTATGACTCC 918
                         iv  v     vv   v    v        v iv  vv iiv      v  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_124570545_    919 AAAAGCAAATGCAACAAAAACAAAAATAAATAAATGTGACCTCATTAAAC 968
                                v v         iv       i      vv   i    i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_124570545_    969 TAAAAAGCTTCCGAACAGCAAAAGAAATAATCAGCCAAGTAAACAGACAA 1018
                          v    i   ii vi vv    i  v iv    ivv    i  v      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_124570545_   1019 CACACAGAATGGGATAAAATATCCATAAACTATGCAGTAAATCCACAACT 1068
                          v            v       i---------    ---    -------
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATT---------TGCA---AATC------- 733

  chrX_124570545_   1069 ATGCAATAAAATATCCACAAACTTCCCAAGGGGGAAGACAAAGGAATAAT 1118
                         -----   ---    i--------------------  i  i   v vi 
  L1M4_orf2#LINE/    734 -----ATA---TATCT--------------------GATAAGGGACTTGT 755

  chrX_124570545_   1119 ATCCGGAATCTACAGGGATCTCAAACAAATTGGCAAGAAAAA-ACAAATA 1167
                             i    v  i ii  v   vv    v iiii  v     -       
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_124570545_   1168 ACTCAATCAAAAAGTGGGTAAAGTACATGAATAGACAATTCTC---AAAA 1214
                           i    i?    i    i    v iv          v     --- i  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_124570545_   1215 GATGTACAAACAGCCAATGAACATATGAAAAAATACTCAACATCACTAAT 1264
                            i      ii      i i  i       i  i          ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_124570545_   1265 TAT 1267
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.56 (109 / 70)
Gap_init rate = 0.02 (15 / 753), avg. gap size = 5.27 (79 / 15)  


2722 26.14 4.91 1.48  chrX_124584457_124586630.rev      809  1684 (490)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_124584457_    809 GAAACATGCTCAGTGTTCATGGATTAGAAGAATCAATATCGTTAAAATGT 858
                             v  iii vi            i     v i     i     i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_124584457_    859 CTATATTACCCAAAGCAATCTACAGATTCAGTGCAATCCCTATAAAAACA 908
                          v   i v      vii             ii           v    iv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_124584457_    909 CCAGCGAAGTTCTTCACAGAAACAGAAAAA-TAATTCTAAAATTTATATG 957
                              vivv  i  ii      iv  v  i- i  i        i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_124584457_    958 GAATCACAAAAGACCCAGAATGTCCAACTTTATTCTGAGCAAAATAATAA 1007
                            vii   ii          iv    vviv  ii   --    v  ---
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAA--- 197

  chrX_124584457_   1008 TAAATAAAAT--GAAGAATCACATTACATTACTTCAAA--TTAAACTATA 1053
                         -i  i   i --  i  v     i v viv i      --   --   i 
  L1M4_orf2#LINE/    198 -GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACA 244

  chrX_124584457_   1054 AAGCTATAGTAACCAAAATGGCATGGTACTGAC-CAAGAAACAACAGAAA 1102
                               i     i   i ii ii        i -i   i ----i   v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA----TAGACA 290

  chrX_124584457_   1103 TTT-GAACAACGGAACAGAACAGAAAACTGAGAAACACATCCATATACCT 1151
                          v -  v   i    i    iv  i iiiv     i v i     i ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_124584457_   1152 ACAGTTAACTCATTTTCAACAAAGGTGCCAAGAACATGTATTGGGGAAAT 1201
                          ii  i  i v      i    i          v   vi v        v
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_124584457_   1202 AACAACCTCTTCAATATATGGTGCTGGGAAAACTGGATATCCATATGCAG 1251
                           i ii  i     i v            v         ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_124584457_   1252 AAAAATGAATGTAGACCCCTATCTTTCCCCATATACAAAAATTAATTCAA 1301
                           i      vv i        i  iv v                 i    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_124584457_   1302 AATAGGTTAAAAACTTAAATCTATGACCTGAAATTATAAAACTACTA--A 1349
                            i i i ? i  i     v  v  v  i   i         vi  -- 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_124584457_   1350 TGAAACATTGGGGAAAGTCTCCAATACGTTGGCCTGTACAAAGATTTCTT 1399
                         vi      v  ? v  i   i ivv  v    vi ivi   v i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_124584457_   1400 GAGTAATACCCTACAAGCACAGACAACCAAAGTAAAAATAGACAA----G 1445
                         iii  vv  v i v       ii    v    v         i  ---- 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_124584457_   1446 AGTATGTCAAATTTAAAAACTCCTGCACAGCAAAGAAAAC----AAAAAA 1491
                          v vii     v         ii  ii vv     i v  ----  i   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_124584457_   1492 GTGAAAAGGCAACACACAGAATGGGGAAAAAATATTTGCAAACTATTCAT 1541
                                 i    v           - i              ii  vi  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGG-AGAAAATATTTGCAAATCATATAT 739

  chrX_124584457_   1542 CTAACAACTGATTAATAACCAGAATATATAATGAGCTCAAACAACTTGAT 1591
                           i i  vv  i vi  v             v  i   vv      ii  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_124584457_   1592 AGGATAAAATCTAAAATTGTGATTTAAAAATTGGCAA------------- 1628
                          iv v   iv v  v vivii   ?      v     -------------
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_124584457_   1629 -------------GAAGACACAAAAATGGCCAACAGGTAAAAGATTAGGT 1665
                         -------------     i i v          i i i v v  vv  i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_124584457_   1666 GCACAACATCCTTGGTCAT 1684
                           v       v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 4.00 (56 / 14)  


2000 23.03 0.90 14.26  chrX_124639692_124641668.rev      484  1486 (491)    L1M4_orf2#LINE/L1       40   908 (0)  

  chrX_124639692_    484 ATTGGTGAGACTGCAACAATACTACCAAAAGCAATCTACAAATTCAATGA 533
                             v i   -  --i       v  v   vii       i      i v
  L1M4_orf2#LINE/     40 ATTGTTAAGA-TG--GCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chrX_124639692_    534 AATTCCCATTAAAATACCATCATCATTCTTCACAGAACTAGAAAAAGCAA 583
                            i  i  i     v   v vv v  i  ii     v v  v  ivii 
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chrX_124639692_    584 TCCCAAAATTCATATGGAACCAATAAAAAGAGCTCACA-TAGCCAAAGAA 632
                            i               ---  iv  i ii i  v -        iv 
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_124639692_    633 AGACTAAGCAAAAAGAACAAATTGGGAGGTATCACATTACCTGACTTCAA 682
                          vvi i iv  i         v v     vv     i v  ii i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_124639692_    683 ACTATACTACAAGGCTA---TAACCAAAACAGCATAGTACTGGTATAAAA 729
                          viv        i    ---   i   i    ii i       i    ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_124639692_    730 ACAGGCATGTAGACCAATGGAACAGAATAGAGAACCCAGAAATAAGGCCA 779
                          i  i   i    i        i     v    ii          iv   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_124639692_    780 AATACTTGTATCCAGCTGATCATCAATGAAGCAAACAAAAACATAAAGCA 829
                         v i i  i ivi  ii    iv  i ii i vviv   i v   vv iii
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_124639692_    830 TGGAAAGGACAAACTCTTCAACAAATATTGCTGGGATAATTGGCAT-GCC 878
                         v      i i iv  i          iv        i  i   -  -?  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG-ATAKCC 432

  chrX_124639692_    879 ACATGTAGAAGAACTGAAACTGCATCCTCATCTCTCACCTCATACAAAAA 928
                              i i     -    ii  v i  ii i   v    vi         
  L1M4_orf2#LINE/    433 ACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_124639692_    929 TCAAATCAAGATGGAACAAAGACTTAAATCTAAGACCTGA--CCATAACA 976
                          i  v    i     v  ?    i     v     v  i -- i    - 
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-A 530

  chrX_124639692_    977 ATTCT-AGAAGATAACATTGGAGAAACTCTTCTAGACATTGGCCTAGGCA 1025
                          i   -      v     v  ? v  v     vv   v    vi      
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_124639692_   1026 AAGAGTTCATGACCAAGA-ACGCAAAAGCAAATGCAACAAAAACAAAGAT 1074
                          v iv   v iivi v  -  -        v v         iv   i  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACAC-CAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_124639692_   1075 AAATAGATGGGATGTTATTAATCCATTTATGCCTGAGGTTGCAATTTTTT 1124
                          i   i  ------------------------------------------
  L1M4_orf2#LINE/    630 AGATAAAT------------------------------------------ 637

  chrX_124639692_   1125 GAATTTTTGCTATCAGACCTTGGCGATGAACTTGATCAGTAGAATATAAA 1174
                         --------------------------  i    v    ------------
  L1M4_orf2#LINE/    638 --------------------------TGGACTTCATCA------------ 649

  chrX_124639692_   1175 TAACTCCCAGATGTTTAACGTTCTAATAATAGAACACTAGGCATAAGTTT 1224
                         --------------------------------------------------
  L1M4_orf2#LINE/    650 -------------------------------------------------- 649

  chrX_124639692_   1225 AAACTAAACAGCTTCTGTACAGCAAAAGAAATAATCAGCAGAGTAAACAG 1274
                            i    - i   i   i vv    i  v iv    iv i   i  v  
  L1M4_orf2#LINE/    650 AAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_124639692_   1275 ACAACCCACAGAGTGGGAGAAAAATCTTTGCAAACTATGTATTGGACAAA 1324
                                     i          - v        ii  i   iv  i  i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAG 747

  chrX_124639692_   1325 AGACTAACATCTAGAATCCACAAGGAACACAAACAAATTAGCAAGGAAAA 1374
                         i    vii   i     vi i  i    v vv    v i ii  vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_124639692_   1375 AAAATAATAATTCCATAGAAAAGTGGGCTAGGAACATGAATAGACAATTC 1424
                         i v -     ii v  v?    i     v i i iv          v   
  L1M4_orf2#LINE/    798 GACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_124639692_   1425 TCAAAAGAAGATATACAAATATCCAGCAAACATATGAATAAATGCTCGAC 1474
                           v                 iv   ii  i  i     v i      i  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_124639692_   1475 ATCACTAATTAT 1486
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (138 / 89)
Gap_init rate = 0.02 (18 / 869), avg. gap size = 8.44 (152 / 18)  


2480 27.81 2.32 2.10  chrX_124655936_124658233      907  1812 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124655936_    907 TGGAAAAATATTCCATACACATGGATTGCAATCACT-AATGTAGCTGAAA 955
                               i    i    iiv         v  v-   -   i v i i i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGA 49

  chrX_124655936_    956 TGGCCATCCTGCCCAAAGTGATTTACATATTTAATGTTATTTCAATAAAA 1005
                             v  v  v      v    i    v   i  i iv  ii v  v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_124655936_   1006 CTACCAA-TATCATTTTTATAGAGTTTTCACAGAGA-AAGCT-ATACTAA 1052
                         v v   i- ii v     ii   iv  -------  -     -  v    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATT-------GACAAGCTGATCCTAA 142

  chrX_124655936_   1053 GATTCATATGGAACCAAAAAGAGCCCA-AATAGTCAAAGCAATCCTTAGC 1101
                         i            viiv  i ii    -     i    i     i v iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_124655936_   1102 AAAAACAACAAAGCTGGAGGCATCACATTACTTGACTTCAAACTACACCA 1151
                           i  v       i      vv     i v iii i      vivi  i 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_124655936_   1152 CAAATACATAGTAACTAAAACAGCATGGTAGTAGTACAAAAACAGACTCA 1201
                             vvi i     ii  i    ii     v i i i  ii i    vi 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_124655936_   1202 TAGACCAATGGAACCGAA--GAGAGCTCAGAATTAAAGCTGTACATTTAC 1249
                             i        iv   --     ii     v    v ii        i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_124655936_   1250 CACGCC--CTGTTCTTTGACAAACTTGACCAAAAAAAG-CAATGGGGAAA 1296
                         v-- i --i  v i  i     ivv  -    i vv v-           
  L1M4_orf2#LINE/    343 G--GTCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAA 389

  chrX_124655936_   1297 GGACTCCCTATTCAGTAAATAGTGAGGGGATAACTGGCTATTCAAATATA 1346
                          i ivvi  v    ii    i   vv    i      v  ?i  v  ii 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_124655936_   1347 GAAGAATAAAACTGGACCCCCTACATATAACCATATACAAAAAATAA--- 1393
                         i      i  ii        -   v vvv              v   ---
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTC 488

  chrX_124655936_   1394 --GGTGGATTATAGACTTAAATGTAAGACCTCAAACTATAAAAATTCCAG 1441
                         --ii     i ?    i           v  v           v iii  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_124655936_   1442 AAGAAAACCTAGGAAGTACCCTTCTCATTATCAAAGG--AGGCAAATAAT 1489
                                 v    ?-   vvii -  i v i vvi  --      - ii 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGN-GTAAATCT-TCGTGACCTTGGGTTAGGCAA-TGGT 585

  chrX_124655936_   1490 TTAT-GGCTAAGTCTCCAAAATCAATTGTGGCAAAATCCAATTT-GCTAA 1537
                           v -i v  v v v      v  vvv iii     vvv  vv - v   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_124655936_   1538 ATGAAATCTAATTAAA-TTAAAGAGCTTCTGCATAGCAAAAGAAACTATC 1586
                           vii ii v  i   -     i -   i  iiivv    i  v      
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chrX_124655936_   1587 AACAGAGCAACAAAA-AACCTACAGAATGGGAGAAAATATTCACAAACTA 1635
                           v i  ii v  i -    i                    ii    ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_124655936_   1636 TGTATCCAACAAAAAAGTCTAATATCCAGAATCTACAAAGAAACTTAAAT 1685
                          i    ii i  iii --  vi          v  i      -  ivv i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGA--CTTGTATCCAGAATATATAAAGAA-CTCTTAC 781

  chrX_124655936_   1686 AATTCAACGAGCTAGTAGCAAATAACCCCATTAAAAAGTGGGCAAAAGAT 1735
                           i    ii vvv ivii          v   ?    i        i   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_124655936_   1736 ATGAACAAACACTTCTCAAAAGAAGACATACAAGTGGCTAACAAACACAT 1785
                         v    i i   i     v        i      i    i  i  i     
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_124655936_   1786 GAAAGAAAGCTCTGTGTCACTAATCGT 1812
                             ii v    viii   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (151 / 97)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 1.60 (40 / 25)  


2503 26.44 3.21 2.77  chrX_124678071_124685647.rev     6183  7086 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124678071_   6183 TGGAAAAACACTCCATTCTCGTTGATTAGAAGAATTAATATCATGGAAAT 6232
                               i i ii    vi  i v    i     v       ii vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124678071_   6233 GACCATGCTGCC-AAAGCAATTTACAAATGCAATGCTATTTCTATCAAAT 6281
                          i v  i  v  -   vii  i    i  v   i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124678071_   6282 TATCAATATCATTCTTCACAGAATTAGAAAAAGT-ATTCTAAAATTTATA 6330
                          vi  iivv v  i  ii     v v  v  iv -  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_124678071_   6331 TGGAATCAAAAAGAGCCTA-AATAGCCAGAGCAATTGTAAGCAAAAAAAA 6379
                              viiv  i ii  i -        i i    iv i ----------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---------- 190

  chrX_124678071_   6380 AAAAAAAAAAAAAAAAAAAAGCTGGAGGCAC-CACGCTACCCAACTACAA 6428
                         ------    i  i  v    i      -  -   i  v     i v   
  L1M4_orf2#LINE/    191 ------AAAAGAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAA 233

  chrX_124678071_   6429 ACTACACTATAAAGCTACAGTAAACAAAACAGCATGATACAGATACAAAA 6478
                          vivi    i             v   i    ii  i   v ii i  ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_124678071_   6479 ACAGACATGTAGACTAATAGAACAGAATAGAAAACTCAGAAATAAAGCTG 6528
                          i      i    ii   i   i     v  i iii          v ii
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_124678071_   6529 CACACTTACAACCATTTGATCTTAAACATGGTTAACAAAAACAAGCAATG 6578
                         i   i   iiii  v     i  vi   v  v iv   i v  vv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_124678071_   6579 GGAAAAGGA--GTCTGTATTAAATAAATGGTCCTGGGATAACTGGCTAAC 6626
                           i    i --    - -  v  i       v      i      v  ? 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCT-T-TTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_124678071_   6627 CATATCCCGAAGGTTGACACCAGACAGTGACCTTTCACCATATACAAAAA 6676
                           i  v vi   iv   viiii   vviv    iv               
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_124678071_   6677 TAAACTCAAAACAGATTAAAGATTTAAATGTAAGACCTTAAACTGTAAAA 6726
                          v         ii   i ?   ii           v  v     i     
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_124678071_   6727 AGTCCTAGAAGGCAACCTAGG---AAATACCCTGCTCAACATCAGCTTTG 6773
                         v-  i      iv   v    ---    ---  v vii  v ii v  v 
  L1M4_orf2#LINE/    532 C-TCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAG 577

  chrX_124678071_   6774 GCCAAGAATTTTTGGTTAACTCCCCCAAAGCATTTGCAACTAAAACAAAA 6823
                           v v iv  i  i v  vvv v  v      ivv     v   iv    
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_124678071_   6824 ATAGACAAATGGAACCTAATTAAACTAAGCAGCTTCTGCACAGCAAAAGA 6873
                              i    v i  i v  i   v v iv i   i  ii vv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_124678071_   6874 AACTATCAACAGAG-GAAA---CAACCTACAGAATGGGAGAAGATATTTG 6919
                         v        v i  -    ---     i              i       
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_124678071_   6920 CAAACTATGTATCTGACAAAGGCCTAATATCAAGAATCTATAGGGAACT- 6968
                             ii  i       i  i  v  vi    v     v    ii     -
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_124678071_   6969 -TA-AACACATCAACAAACTAAGA--AACAACCCCAT-AAAAAATGGGCA 7013
                         -  -   v  vi  i   --    --  i     v  -?           
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAA--AAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_124678071_   7014 AAGG----GCATGAACCCTTCT----GGAAGACATACAAGTGCCCAA-AA 7054
                             ---- v  ii  vi    ----i     i      i  v    -  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_124678071_   7055 ACATATACAAA-ATACTCACCATCATTAATCAT 7086
                         i  i  iv   -  i    v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.35 (54 / 23)  


3257 27.20 0.44 0.44  chrX_124697878_124704281     5004  5911 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124697878_   5004 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5053
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124697878_   5054 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5103
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124697878_   5104 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5151
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_124697878_   5152 TATGGAACCAAAAAAGATCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5201
                                viiv  ii  i  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_124697878_   5202 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5251
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_124697878_   5252 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGATC 5301
                                 i   i    ii         i iv ii ii  v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_124697878_   5302 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCACATCTACAACT 5349
                                i    i--    i  --        vv  ii    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_124697878_   5350 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5399
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_124697878_   5400 CTATTTAATAAATGGTGCTGTGAAAACTGGCTAGCCATATATAGAAAGCT 5449
                           v  i  i           v  v      v  ?   i  ii i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_124697878_   5450 GAAACTGGATCCCTTCTTTACACCTTATACAAAAATCAATTCAAGATGGA 5499
                            ii    i    v i i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_124697878_   5500 CTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5549
                         ii ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_124697878_   5550 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5599
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_124697878_   5600 AACACCAAAAGCAACGGCAGCAAAAGCCCAAATTGACAAATGGGATCTAA 5649
                         i            vvi   i      vvv    v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_124697878_   5650 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAT 5699
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_124697878_   5700 AGGCAACCTACAAAATGGGAGGAAATTTTCGCAACCTACTCATCTGACAA 5749
                           i     i   i        i    v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_124697878_   5750 AGGGCTGATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5799
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_124697878_   5800 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5849
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_124697878_   5850 TCAAAACAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5899
                           v   v    i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_124697878_   5900 ATCACTGGCCAT 5911
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1472 26.49 16.42 0.66  chrX_124705771_124708367.rev     1344  2098 (499)    L1M4_orf2#LINE/L1        8   881 (27)  

  chrX_124705771_   1344 ATATCATATATTTATGGACTTAAGAACA-AAGAGTGATAAGTTGTCAATT 1392
                              vi  i  i     i vi ii  v-  v v  v    v  v    v
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_124705771_   1393 CTTTTCAAATTTATCTATAGATTAAACACAATCTCAATAAAAATCCAAGC 1442
                           iii      v     i     v   i     i v  v       v   
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_124705771_   1443 AGA-TTATTTGCAGAAAGTAACAAGTAGATTCTAAATTTTATATGGATAT 1491
                         v v-  v          v i     iv   i     v  i       v  
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_124705771_   1492 GCAA----------AT--CTAAGGCAATCTTGATTAACAATGATACAGCT 1529
                             ----------  -- i  ii         vv  v  vi i v  i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_124705771_   1530 GAAAGGTTTAGTTACT-----ATTTCAAGATTTAGTGTAAAGCTACAATA 1574
                          i i ii i --i   -----       i i   v ii         i  
  L1M4_orf2#LINE/    208 GGAGGACTCA--CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_124705771_   1575 CTCAAAA---TGTGGTTTTGCCATACGGATCAACAAATAGATCACTGGAA 1621
                         v    i ---      vi  v    v    vi   v        v     
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_124705771_   1622 TAAAATAGAAAGCTTGGAAATAGACACACACATTTATAATCATTTGATTT 1671
                           i   v  i  iiii      i  v  i        ii   v       
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_124705771_   1672 TTGTCAAAGG---CAA-----TCCAATGGAACAAAGAAAAGT--TTTCCG 1711
                          i v   i  ---   ----- i      ii-      v   --    vi
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAA 404

  chrX_124705771_   1712 CAAATTAAATTGAAATAACTGGACATTTACATAGAAAA-AATGAACATTG 1760
                              vivii  ii i       i ?ii    iv    -      vv v 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_124705771_   1761 ACACCTACCTCATGCTCCATAC------TA-CT--------AGCA----- 1790
                           v         ii ivi    ------  -  -------- v  -----
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_124705771_   1791 CTA---GTAGTAG-TAA-----TAG------TAGTAGGAATCATACAGA- 1824
                            ---   iv  -   -----  i------   v  i  v    vi?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_124705771_   1825 AAATA---ATAACC------------AT----------ATAT----TTAA 1845
                             v---i i   ------------  ----------    ----ii  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_124705771_   1846 AA-----AGTAATAACA-------TAG--------GATTT-GCCAAAACA 1874
                           -----  i  i  v -------   --------  i  -ii     iv
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_124705771_   1875 TAAAACTTCTGTTCCTCAAAAAGACACAACTAAAAA--TAAATAAATAAG 1922
                         v       i   v i     i-     v ii  i  -- i  v i i  v
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_124705771_   1923 TCACAATATGGGAGAAAAAAGTCACAAACCATATATTTGAAAAAGAGCTA 1972
                         i    iv           v v ii    i       i   v  i ii  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_124705771_   1973 GTATGCAGGATAAATAAAGACATGTTACAAGTCAATAATAAAAAGA-AAA 2021
                             v   i   v       vv v      v               -   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_124705771_   2022 CACTCCAGTAAAAAAATGGACAAA--ACTTCATATATATACTTGACAACA 2069
                         i vi   i v?        i    -- i  v -   v i i  vv v v 
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGA-ATAGACATTTCTCCAAA 852

  chrX_124705771_   2070 GAAATTATATGGATGGTTATTAATCACAT 2098
                            iv    iii    ii v   v     
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACAT 881

Transitions / transversions = 1.37 (114 / 83)
Gap_init rate = 0.04 (34 / 874), avg. gap size = 3.79 (129 / 34)  


3120 23.40 4.14 2.46  chrX_124713380_124715457.rev      699  1591 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124713380_    699 TAGAAAGTTATTCCATGGTCATGGACTGGAAGAATTTCTATTGTTAAAAT 748
                          i     v   i     v       i       v  vv         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124713380_    749 GGCCATAATAACCAAAT----CTACAGATTCAATGCAATCCCTATCAAAA 794
                            v   v vv      ----            i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124713380_    795 TTCAA--TGTCATTTTTCATAGAAAT--ATAAAAAAATGTTAAATTTTTT 840
                          i v --  i -     iii      -- i  ivvi  vi    v  iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_124713380_    841 AGAGAAGTATAAAAGACCACAGA-TAGTCAAAGCAATCTTGATCAAAAAA 889
                          vi   i ii  ii    -    -   i    i         vv  i  i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_124713380_    890 GATAAAGCTGGAGGCATCACACTACTGGATTTCAAAATTTACTGCAAAGC 939
                         i i    i      vv       v ivi         i     i      
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_124713380_    940 TGCAGTAATTAAAACAGCATGGTACTGGCATAAAAACAGACACATTAATC 989
                          i       i  i    ii              ii i     i  vi   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_124713380_    990 AATGGAATAGGAAAAAGAGCTCAGAAATAAATCCACACATCTACAGTTAA 1039
                                   i vvi    ii          i   i    i  ii  i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_124713380_   1040 TTGATTTGCAACAAAGTTACCAAGAACACCCAATAAGAAAAGGACAGTCT 1089
                                v i    i v i      v  ii    ii i    i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_124713380_   1090 CTTCAATAAACGATGTTAAAAGAACTGGATATCCACATGTGGAAAAATGA 1139
                         i     i   i i  i iii v         ?       iii  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_124713380_   1140 AAATTGATGTTTATCTCACTCCTTATAAAAGAATCAACTCAAAATGGTTG 1189
                          iv v  ivii  i     v  v    v  i   i            ---
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG--- 495

  chrX_124713380_   1190 ATTAAATCAACCATTTCAATCTTAAACATAAGATCTGAAACTGTAAAACT 1239
                           i ? --i   ----------    ii     v  i     i       
  L1M4_orf2#LINE/    496 ATCAWA--GACC----------TAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_124713380_   1240 ACTGGGATAAAATAGAGGGA-AAATCTCCATGACACTGATGTGGGCAGTG 1288
                         vi i i v    i v   ?i-      i i    vi  ivv i    i  
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_124713380_   1289 GTGATATCCTGGATATGACCCCACAAGCACAGGAAACAAAAGCAAAT-TA 1337
                           -- -  i i        v   v       i v        v   v-  
  L1M4_orf2#LINE/    584 GT--T-TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_124713380_   1338 GACAAATGGGATCCCATCAAACTGAAAAGCTTCT-CACAGCAAAGGAAAC 1386
                           i    v   iii       v v    i   i -ii vv       v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_124713380_   1387 AAT-AGGA---TGAGGAGGCAACTTATAGATTTGGAGAAAATATTTACAA 1432
                         v  - i  ---   ii  i    ii i   v v             i   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_124713380_   1433 ATCGTACATTGTTTGAGAGGCTAATATACAAAATATACAAAGAACTTAAA 1482
                            i  i  ivvv i  i i  vi   v  i      i        ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_124713380_   1483 CTACTCAAAAACAAACAAACAAACAA---AA----------GACAA---- 1515
                          v      v  i   v i     i  ---  ---------- i   ----
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_124713380_   1516 ---GAATGGAGATTTCTCAAAAGAAGATATACAAATGGCCAACAAGTATT 1562
                         ---    i  v       v                       i   i iv
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_124713380_   1563 TGAAAAAA-GCTGAACATATCATCAGATAA 1591
                               i -   v     --  ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACAT--CAZZZZZZZZ 908

Transitions / transversions = 1.94 (136 / 70)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.81 (59 / 21)  


 388 27.81 9.27 0.00  chrX_124720796_124726216     3663  3813 (1608)    L1M4_orf2#LINE/L1        1   165 (743)  

  chrX_124720796_   3663 TAAAAAAGCATTCCGTATTCATGGCTTAGAAGAATCAGTATTGTTAAAGT 3712
                          ii   iii  i  i i       v  i     v i i         ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124720796_   3713 ATTTATACAGCCCAAAGCAATCTACAGATTTAATG-AATC--TATCAA-- 3757
                         iviv    vv      vii           i  i -    --      --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124720796_   3758 TTTCA-------TTTTCACAGAA-TT-ACAAAAAAATTTTAAAATTTATA 3798
                          ii  -------    ii     -  -    ivvi  ii       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_124720796_   3799 TGTAATTGAAAAAGA 3813
                           v  v  v  ii  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA 165

Transitions / transversions = 2.50 (30 / 12)
Gap_init rate = 0.04 (6 / 165), avg. gap size = 2.33 (14 / 6)  

1832 26.91 5.05 2.73  chrX_124720796_124726216     4203  4934 (487)    L1M4_orf2#LINE/L1      160   908 (0)  

  chrX_124720796_   4203 AAAGTGTCCA-AATTGCCAAAGCAATCT-GCATAAAAAGAAAAAAGCTGG 4250
                           i vii   -   v      i      - v v  i     v    i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_124720796_   4251 AGGCATCACATTACCTGACTTCAAATTATACTACAAGGTTACAGTAACCA 4300
                            vv     i v  ii i      viv        i i        i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_124720796_   4301 AAACATTATGGTATTGGTACAAAAATAGACACATAGA-CAAGTGAACAGA 4349
                          i   v i     i   i i  ii       i     -   vv   i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_124720796_   4350 ATAGAGACCTCTGAGATAAAGCTGCACAACTATAACTAACTAATATTCAA 4399
                           v    vii v  i     v iii   vi   iiii  i i  v   i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_124720796_   4400 CAAAG-TCCACAAAAATAAACATTTCAAT----AAA-------CTATTCA 4437
                            i - v -   i vi -----      ----   -------  v    
  L1M4_orf2#LINE/    360 CAAGGGTGC-CAAGACCA-----TTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_124720796_   4438 ATAAAATATGCTGGGAAAACTGGCTAACCTAATGCAAAAGAATGAAACTG 4487
                          i   vvi        v      v  ?  vv               ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_124720796_   4488 GACCTCTACCTTTCAGTATATACAAAACATTAATT-AAAATGTGTTAAAG 4536
                             i      iv  vi          -     i -      vi i ?  
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAA-ATTAACTCAAAATGGATCAWAG 502

  chrX_124720796_   4537 ACTTAAAT--AAAGTCT----TTATAAAAATTCTAAACAAAAACCCAGGA 4580
                           i     --  iiv  ----i       v ii  i vi     vi   ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_124720796_   4581 AAAATTCTAAACAAAAAACCTAGACATTTGCCTTGACGAAGAATT--TAT 4628
                         iv  v   ----------i vv   v  v vi v i i v iv  --  v
  L1M4_orf2#LINE/    553 GTAAATCT----------TCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_124720796_   4629 GTAGGTC-CCAAAGGGATATTCAACAAAATAAACACTAGACAAATGAGAC 4677
                         i  v v -     i v i vv        v   v v    i    vi   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_124720796_   4678 CTAATTAAACTAAAGAGATTCTGCAC---AAAATATAAAACTCTCAAAAA 4724
                         i v  i   v v  i iv  i  ii ---   iv i ---  v    i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA---CTATCAAGAA 689

  chrX_124720796_   4725 AGTAAA----CAACCTACAGAATGGGAGAAAATATTTGAAAACTATTCAT 4770
                            i  ----     i                      v   ii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_124720796_   4771 CCAACAAAGGACTGATACCCATAATCTATATAGAA----TGTAAATGAAT 4816
                          ii i  i     vi  i   v   v    v    ---- ii  v v   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_124720796_   4817 CATCGAGAAAAAAAAAATCCTATTAAAAAGTGGGCAAAAGACATGAATAG 4866
                         v  vi i i v   v  i  v   ?    i        i  iv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_124720796_   4867 ATGCTTCTCCATAGAAGACGTACAAGCAGCCGAGGAACACATGAAAA-AT 4915
                          iii       v      ii     iii   i vi i          -  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_124720796_   4916 GCTCAGTGCTACTAATTAT 4934
                              iiiii ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (116 / 77)
Gap_init rate = 0.03 (20 / 749), avg. gap size = 2.85 (57 / 20)  


2140 31.96 1.78 1.00  chrX_124746177_124749334.rev     1770  2667 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_124746177_   1770 AAAAAAATCC-ATGCTTATGGAATGAAAGAATCAATATCATAAAAATGGC 1818
                            i v    -   i i     v  i    v i     ii v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_124746177_   1819 TGTACTGCACAAATCTATTTACAGATTCAATGCTATTTATATCAAACTAC 1868
                         vi    v v     iv  i           i  v  iiv       v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_124746177_   1869 AAACATCATTTTTCACAGAATTAGAAAAACGTATTCTAAAATTCATGTAG 1918
                         v i vv v     ii     v v  v  i vv  i           i i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_124746177_   1919 AACCAAAAAGAAGCCTGAATAGCCAGAGATATCCTAAGAAAAGAGAATAA 1968
                           viiv  i i v  v         i ivv   i i i   ii    i  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_124746177_   1969 AGCCAAAATTATCACACTGTTGGACTTCAAACTATAATGTAAAGCTACAG 2018
                           iiii ivvv       viivi i      viv  v ii          
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_124746177_   2019 TAACCAAAATAGCATGGTACTAGTACAAAAACAGACACATAAACCAATGG 2068
                            i   i i  ii       i i i  ii i     i   i i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_124746177_   2069 AATATAATAAAAAACTCAGATATAAATCTACATGCCTACAACTATTTGAT 2118
                             v   vi i iii    v     i i i iiii  iiiii v     
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_124746177_   2119 TTTTGACAAGGCCAACAAAAACAAGCATTAGACAAAGGATTCTCTACTCA 2168
                            i       viiv   i v  vv  v i iv    i  vv   vi   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_124746177_   2169 ATAAATGATGTTCGAATAACTTACTGACCAGGCATAGAAGATTGGAGGTG 2218
                          i     i  i v i i    viv i?   viiii i    v  i  v  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_124746177_   2219 GACCCTTACCTTTCACCATATACAAAAATTAACTCAAAATGAATTAAAGA 2268
                              i     iv                            i  i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_124746177_   2269 TTTAAGTGTAATACCTCAAACTATTAAAATCATAGATGACAACCTAGGAA 2318
                         ii   i     v v  v       v   v  v    v  v   v    ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_124746177_   2319 ATACTTTTCTTGACATCAGCCTTGGATAAAAAGTTTTTGGCTTAGTCACC 2368
                         vv v i   v    v ii v-  i ii  viiv  i  i v vv v    
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_124746177_   2369 AACAG---AAATTTGAAGGAAAAAAATAGGCAAGTGTGAACT--AGTTAC 2413
                           v  ---  iivvv  iii         ii  i -  i   -- viv v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT-TGGACTTCATCAAA 651

  chrX_124746177_   2414 ACTAAAGAGCTTCATCACAGCAAAAGATATT-TACAGAAA---AACAGAC 2459
                          i    i vi  ii -i vv    i  i i - vv     ---  v    
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGT-GCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_124746177_   2460 AATCTACAGAACTGGAGAAGATATTCATTCACAAACTGTGGATCCAATAA 2509
                           i i      iv      i     ii----    iii iv   ii    
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTG----CAAATCATATATCTGATAA 746

  chrX_124746177_   2510 AAGTCTGATATTGAAGAATATATAG-GAA-----ACAAATCAACTAGAAC 2553
                         ii v  vi   iv -         i-   -----    v    iv v  v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCA-GAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_124746177_   2554 TAAAATAAACAACCTCATTAAAAAGTGACAAAAGTACATGAATGAATCCT 2603
                         -  i i   i    iv   ?    i  ivv    v iv     ii ivi 
  L1M4_orf2#LINE/    796 -AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_124746177_   2604 TCTGAAGAGAAGAAATGTAAGTGACCAACAAACATATAAAAAAATTCTGA 2653
                            vv i      v  ii  i  i    i  i  i  i    i  v  v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_124746177_   2654 ACATCATTAATCAT 2667
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (173 / 110)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 1.92 (25 / 13)  


2710 25.19 2.41 2.96  chrX_124749377_124753655.rev     2876  3788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124749377_   2876 TGGAAACACATCCGATGCTCATGGGTGGGTAGAATCAATATTGTGAAAAT 2925
                               v i    v   i      i v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124749377_   2926 GACCATACTGCCAAAAGCAATCTACAAATTTAATGCAGTCACCATCAAAA 2975
                          i v     v  v   vii       i   i  i   i  v i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124749377_   2976 TAT-AACCATCATTCATCACAGAACCAGAAAAAAAC-AATCCTAAAATAC 3023
                          vi- i iii v  i- ii     -- vvi v  i -i          v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT-TTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chrX_124749377_   3024 ATATGTAACCAAAAAGGGGCCCACA-TAGCCAAAGCAAGACTAAGCAAAA 3072
                              v  viiv  -   i    v -        i   vvi i ---   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAA-GGGACCCAGAATAGCCAAAACAATCTTGA---AAA 193

  chrX_124749377_   3073 AGAACATAAAGAACAAATCTGGAGGCATCACATTACCTGACTTCAAACTA 3122
                             ------       vi      vv     i v  ii i      viv
  L1M4_orf2#LINE/    194 AGAA------GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_124749377_   3123 TACTATAAGGTGACAGTCATCAAAATAGCATGGTACTGGTATAAAAATAG 3172
                              i  i iv     v     i i  ii         i    ii    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_124749377_   3173 GCTCATAGACCAAGTGAACAGAATAGAGAACCCAGAAATAAAGCGAAATA 3222
                         i vi     i   vv   i     v    ii           v v v i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_124749377_   3223 CTTACAGACAATGGATTTTTGACAAAGCAAACAAAAACATAAAATGGGGA 3272
                         i   ii v    v      i     i vviv   i v   vv        
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_124749377_   3273 AAAGGACACCCTATTCAACAAATGGTGCTGGGATAATTGGCAAACCACAT 3322
                           - i i vi  v                    i  i   vv ?      
  L1M4_orf2#LINE/    388 AA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_124749377_   3323 GTA---GAATGAAATTGTATCTTCATCTCTCACCCTATACAAAAATCAAC 3369
                          i ---       i   v i iii i   v    v           i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_124749377_   3370 TCAAGATGGATCAAAGACTTAAATCTAAGACCTGGAACCATGAAAACTCT 3419
                             i        ?    i     v     v  ii   i  -        
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCT 535

  chrX_124749377_   3420 -GTAAGATACCATCGGAAAAACTCTTCTAGATATTGGCTTAGGCACAGAG 3468
                         -iv    v v   v  ?iv  v     vv  iv    v       vv iv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_124749377_   3469 TTCTTGACCAAGAATCCAAAAGCTAATGCAACAGAAACAAAGATAAATAG 3518
                              iivi v  vv        vv v      i  iv   i   i   i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_124749377_   3519 ATGGGACTTAATTTTTCTGCACAGCAAAAT-AAAAA---TAGT------A 3558
                           v      ------------  v      -     --- v  ------ 
  L1M4_orf2#LINE/    636 ATTGGACTT------------CATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_124749377_   3559 ATAATA--ATCAGCAGAGTTAACAGACAACCCACAGAGTGGAAGAAAATC 3606
                          vi i --    iv i   v  v              i   i       v
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_124749377_   3607 TTTATAGTCTATGCTCCTGACAAAGGACTAATATATTGAATCTACAAAGA 3656
                            ii ivii  iivi    i  i     vi   viv    v  i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_124749377_   3657 ACTCAAACAAACTAGCAAGGAAAAAAAAAAT--CCCA-TGAAAAAGTAGG 3703
                             vv    vii ii  vi    i v    --    - v?    i i  
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_124749377_   3704 CTAAGGATATGAATAGGCAATTCTCAAATGAAGATATGCAAATGGCCAAC 3753
                          v      v       i  v     v  v        i           i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_124749377_   3754 AAACAGATTGAAAAATGCTCAACATCACTAATTAT 3788
                           i  v  vi   i             ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (123 / 103)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.58 (49 / 19)  


2644 27.82 3.76 0.34  chrX_124777137_124782939.rev     4436  5312 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_124777137_   4436 GGAAAAAAATTCCATGCTCATGAATAGAAAGAATCAATATCTTGAAAATG 4485
                              i v  i     i     i  v i    v i     iv v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_124777137_   4486 GCCATACTGCCCGCAGTAATTTGTAGATTCAATTCTATTCCCATCAAGCT 4535
                           v     v   iv v i  i ii        iv v  i  i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_124777137_   4536 ACCA-TTGACTTTATTTACAGAACTAGAAAAACT-ACTTTAAATTTCATA 4583
                         v   -i  v    -   i     v v  v  i  - iii    v      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_124777137_   4584 TGGAACAAAAAAGAGCCCATA-TAGCCAAGACAATACCAAGCCAAAAGTA 4632
                              vviv  i ii    v -       i     viii ivv i   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_124777137_   4633 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATATGGCAATGCTA 4682
                              i      vv    i  v  ii i      viv  ivi   v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_124777137_   4683 CAGTAA---------------------------ACAGATATATAGACCAA 4705
                               --------------------------- i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_124777137_   4706 TGGAACAGAACAGAGGCCTCCGAAATAATGCCACACATCTACAACCATCT 4755
                              i    iv   ivii v       vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_124777137_   4756 GATCTTTCACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 4805
                            i  iv    ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_124777137_   4806 TTAATAAATGATGCTGGGAGAACTGGCCAGCCATATGCAGAAAACAGAAA 4855
                          i  i     i        v      vi ?   i     i  i vv   i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_124777137_   4856 CTGCACCCCTTCCTTACACCTTATACAAAAACTAACTCAAGATGAATTAA 4905
                         i  v      v   i     v          i        i   i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_124777137_   4906 AGACTTAAATGTAAGACCTAAAACCATAAAAACTCT-AGAAGAAAACCTA 4954
                             i           v       i      -    -          v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATA 549

  chrX_124777137_   4955 GGCA-ATACCACTCAGGACATAGGCATGGGCAAAGCCTTCATGACTAAAA 5003
                           ?i- v i -i  iv   v v  vv i     v vi   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_124777137_   5004 CATCAAAAGCAATTGCAATAAAAGCCAAAATTGACAAATGGGATCTAATT 5053
                           i        vvv    i     vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_124777137_   5054 AAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTAAACAG 5103
                            v v  i i   i  ii vv    iv v       vv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_124777137_   5104 GCAACCTACAGAATGGAGGAAAATTTTAGCAATCTATCCATCTGAAAAAG 5153
                         i     i         ii      v  v    vii  vi      v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_124777137_   5154 GTCTAATATACAGAATCTACAAGGAACTTAAACAAATCTACAAGAAAAAA 5203
                          v  vi   v      v  i  i     ivv    v  v i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_124777137_   5204 ACAAACAATCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTATC 5253
                              i  i  v  i?    i            v    i     i  v  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_124777137_   5254 AAAGGAAGACATTTATGCAGACAACAAACATGTGAAAAAA-GCTCATCAT 5302
                         v  i     i  vi viii v   i  i  ii      i -     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_124777137_   5303 CACTGGTCAT 5312
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.22 (132 / 108)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 3.60 (36 / 10)  


3240 26.76 0.55 0.55  chrX_124787136_124789490.rev      957  1864 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124787136_    957 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 1006
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124787136_   1007 GGCTATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1056
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124787136_   1057 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 1103
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_124787136_   1104 ATATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAA 1153
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_124787136_   1154 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGA 1203
                                 i      vv       v  ii i      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_124787136_   1204 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGAT 1253
                                  i   i    ii         i iv ii ii  v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_124787136_   1254 CAATGGAACAGAAC--AGAGCCATCAGAAATAACGCCGTATATCTACAAC 1301
                                 i    i--    i --         vv  i  i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGT 345

  chrX_124787136_   1302 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGAAAAGGATTC 1351
                         i vi    i  i     ivv  vv  i v  vv       i    i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_124787136_   1352 CCTATTTAATAAATGGTGCTGGGAAATGTGGCTAGCCATATGTAGAAAGC 1401
                         i  v  i  i              v vv   v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_124787136_   1402 TGAAACTGGATCCTTTCCTTACATCTTATACAAAAATCAATTCAAGATGG 1451
                             ii    i  i v   i   i v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_124787136_   1452 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTACAAGAAAA 1501
                           i ?    i       v   v       i      vi i  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_124787136_   1502 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1551
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_124787136_   1552 AAACACAAAAAGCAATGGCAACAAAAGCCAACATTGACAAATGGGATCTA 1601
                         vi    v       vvi          vv  v  v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_124787136_   1602 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCACCAGAGTGAA 1651
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_124787136_   1652 CAGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 1701
                         v  i         i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_124787136_   1702 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1751
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_124787136_   1752 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 1801
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_124787136_   1802 CTTAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1851
                           iv        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_124787136_   1852 CATCACTGGCCAT 1864
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 203 27.87 0.00 0.00  chrX_124825475_124827559.rev        8    68 (2017)    L1M4_orf2#LINE/L1      198   258 (650) *

  chrX_124825475_      8 GAACAAAGTGAGATTACTGACTCTACCTTACATCAAGAGTTACTCTAAAG 57
                                  vi  vv   v  v  v  iv iv    i v     vi    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_124825475_     58 CTTCAGTAGTC 68
                           v     i  
  L1M4_orf2#LINE/    248 CTACAGTAATC 258

Transitions / transversions = 0.55 (6 / 11)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.00 (0 / 0)  

 599 23.87 1.29 1.94  chrX_124825475_124827559.rev       67   221 (1864)  C L1M4_orf2#LINE/L1   (754)   154     1  

C chrX_124825475_    221 TGCAAAGATATTCTGTGTTCATTGGTTGGAAGAGTTAATATTGTTAAAAT 172
                           v        i ii       v i        v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_124825475_    171 GTCCATACTACCCAAAGCATTCTACATGTTCAGTGCAATCCCTGTAAAAA 122
                          v v     v      viiv      vi    ii         i v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_124825475_    121 TTCCAATGTTGATTTCCATG--GATATGGACAGAAACAATTCTAAAATTT 74
                          i   -- i  vi  iiv  --  v  v    - ivii  i        i
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTC 147

C chrX_124825475_     73 ATATAGA 67
                             i  
  L1M4_orf2#LINE/    148 ATATGGA 154

Transitions / transversions = 1.47 (22 / 15)
Gap_init rate = 0.02 (3 / 154), avg. gap size = 1.67 (5 / 3)  

2492 23.85 3.91 1.89  chrX_124825475_124827559.rev      501  1242 (843)    L1M4_orf2#LINE/L1      114   870 (38)  

  chrX_124825475_    501 TTTCACAGAAATATAAAAAAAAACTCCTAAAATTAATATGGAACCACAAA 550
                            ii       - i v  ivviv          v        vii   i
  L1M4_orf2#LINE/    114 TTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_124825475_    551 A---TCATTGCATAGCCGAACCAATTTTGTGAAAAAAGAACAAAGCTAAA 597
                         i---i  -- v      i  v    i   vi   i          i ii 
  L1M4_orf2#LINE/    163 GGACCCA--GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_124825475_    598 AGTCTCACAATACCTGATTTCAAGCTATATTACAAAGCCACAGTAATCAA 647
                         i v      v v  ii       iviv  i        i           
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_124825475_    648 AGCAATATGGTACTTATATTAAGAGAGATGCATAGACAAATGAAATGGAA 697
                         ii  i i       vii  v i  v   iii     iv    i   i   
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_124825475_    698 GAGAGAGACCAGAAATAAA----TACATGCATAGTCAGCTGGTCTTTGAA 743
                         vv     v           ----     vi  i    ii  i i  i  v
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_124825475_    744 AACAGTGCCAAGTATATACAATGGAGAAAGGACAGTATCTTCAATAAATG 793
                           vi        vvi  v      i     i i   v i     i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_124825475_    794 ATGCTGGGAAAACTGG-TATTCACATTTAAA-TAATAAAATTGGATGACT 841
                         i        v      -  ?i     vi   -v   i  i     ivv  
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_124825475_    842 GTTTTATACCATATACAAAAATTAACTAGAAGTGGACTAAAGATATTAAT 891
                         iii i i                    vi  i    ii ?   iv v   
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_124825475_    892 ATAAGGTCAGAAGCTATAAAACTCCTAGAAGAAAATACAAGA-TAAAAAA 940
                         i    iv vi  i           i          i i i ?-    ---
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA--- 557

  chrX_124825475_    941 GCTCTT--TGGCATTG--TTATTGGTGATAGTCTTTTAGATATAACACCA 986
                         --    --  i v   --   --  ii  i  i i        i      
  L1M4_orf2#LINE/    558 --TCTTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATATGACACCA 603

  chrX_124825475_    987 AAAGCACAGGCAACAAAAGCAAAAATAG-CA----GGATTATATCAAACT 1031
                                 i          v        -i ----   i vi      v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_124825475_   1032 AGAAAGCTTCTGCACAGCAAAGGAAACAATTAACAAAGTGAAAAG-CAAT 1080
                         vi   i   i  ii vv       v  v  i  v           -   i
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_124825475_   1081 CTA--AAATAGAA-AAAATATTTGCAGACCATATATCTTATAAGGTGCTA 1127
                          i --i   i i -            i i         v      vi  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_124825475_   1128 ATATCCAAAGTAAGTAAAAAACTAC-ACAACTCAATAGCAAAAAAAGCAC 1176
                         i      i i  vi    i    vi-           ii     i -  -
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CA- 801

  chrX_124825475_   1177 CTAATAATCCAATT--AAAATCAACAAGAAACCTGACTAGACATTTCTCA 1224
                         --     i      --     vii   iii ii   v            v
  L1M4_orf2#LINE/    802 --AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_124825475_   1225 AAAGAAGACATACA---GGCC 1242
                                 i     ---    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCC 870

Transitions / transversions = 2.11 (118 / 56)
Gap_init rate = 0.03 (21 / 757), avg. gap size = 2.05 (43 / 21)  

 284 16.95 0.00 0.00  chrX_124825475_124827559.rev     1536  1594 (491)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_124825475_   1536 AAAAAAGACATACAAATGGCCAACAAATATATGAAAAAGTTCTCAATATC 1585
                            i    i              i  ii i       ii v     i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_124825475_   1586 ACTGATCTT 1594
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 9.00 (9 / 1)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


2531 30.20 0.44 1.09  chrX_124867233_124872372     3740  4653 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124867233_   3740 TGGAAAGCCATTTTATGCTCATAGATAGGAATAGTCAATGTTATTAAAAT 3789
                                vi  iii   i    i   v    v v i   i  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124867233_   3790 GGCCATACTGCCAAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 3839
                            v     v  v   vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124867233_   3840 TACCAATGACACTCATCACAAAACTAGAAAAAAAAACT-ATTTTAAAACT 3888
                          v   iivi vi iv ii  i  v v  v  i----  -  ii     i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chrX_124867233_   3889 CATATGGAACCAAAAAAGAGCCTGAATAGCCAAAGCAACCCTAGGCAAAA 3938
                                  viiv  ii  v  v           i   i i iiiv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_124867233_   3939 AGAACCAAGCTGGAGGCATCATACTACCCTATTTCAAACTACACTACAGG 3988
                              v   i      vv   i   v   v        vivi      ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_124867233_   3989 GCTACAGTAACTAGAACAGCATGGGACTGGTATTAAAAACAGACACAGAT 4038
                                   ii ii    ii   v     i  -  ii i     i v v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAG 295

  chrX_124867233_   4039 AACAACTGGACAGAATAGAGAGCACGGAAATAAGGCCACAGACCTACAAC 4088
                          v   iv i i     v     iv i       iv   i v ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_124867233_   4089 CATCTGATCTTTAACAAAGCCGAGAAAA--AAGCAATGTGGAAAGGACTC 4136
                           vi    i  ii    i vi vv  i -- vv     v      i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_124867233_   4137 CCTATTCAATAAATGGTGCTGAGATAACTGGCTAGCAATATGTGGAAGAC 4186
                         i  v     i           i  i      v  ? v i   iii    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_124867233_   4187 TGAATGTAGACTCCTTCCTTAAACCATATACAAAAATCAACTTAAGATAT 4236
                             vv i   i   v   i v               i    i  i  iv
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_124867233_   4237 ATTAAAGACTTATGTATAAAGCCCAAAACTATAAGAACCCTGGAAATCAA 4286
                           i ?    i  vi i   iiv i          i vi i i   ivv  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_124867233_   4287 TCTAGGCAATATTATTCTAGACATAGGAATGAGCAAAGATTTCAT-GACA 4335
                         iv    ?ivv v v   vv   v v  iv ii    v i    v -  i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_124867233_   4336 CGGATGCCAAAAGCAATTGCAACAAAAGCAAACATTGACAAATAAGATTT 4385
                         i - ii         vvv          v   v  v  i    vi  i  
  L1M4_orf2#LINE/    596 TG-ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_124867233_   4386 AATTCAACTAAAGAGCTTCAGCACAGCAAAAGAAGCCATCTACAGAGTAA 4435
                         v  iv  v v  i i   iv ii vv    i  vi i   v v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_124867233_   4436 ACAGACAACCTACACAATGAGAGAAAATATTGGCAAACTATACATCTGTT 4485
                          v        i   v    i           v     ii   i     v 
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_124867233_   4486 AAAGGTTTAATTTCCAGCATTTATAAGTAATTTAAACAAATTTCCAAAAA 4535
                           i  vi vi v     v  v     iv  i ivv    --i  v v  v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CTCAATAAT 792

  chrX_124867233_   4536 AAAAACCCAAACAACCCCATTACAAAGTGAACAAAAGAACATGAACTGAC 4585
                              vv    i     v   ?v   i  ii    i  vi-    iv   
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT-TGAATAGAC 841

  chrX_124867233_   4586 ACTTTTCAAAAGAAGACATACATGAGGCCAACAATCATATGAAATGAAAG 4635
                          i  i  v        i     viv      i  v  i      v  v- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-G 890

  chrX_124867233_   4636 CTCAATATTACTAATCAT 4653
                              i  i ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (155 / 117)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


2871 27.40 0.77 0.44  chrX_124872604_124876883.rev     2885  3789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124872604_   2885 TGGAAATATATTTCATGTTCATGGATTGGAAGAGGCCATATCATTAAAAT 2934
                               v    ii                    vviv    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124872604_   2935 ATCCATACAACACAAAGCAATCTACAGATTCAATGAAATACCCACCAAAA 2984
                         iv v    vv v    vii              i v   v  i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124872604_   2985 TACCAATGACATCCTTCACAGAAATAGAAAAAACTATCCTAAAATTTATA 3034
                          v   iivi v ii  ii       v  v  iviv           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_124872604_   3035 TGGAATCACAAAAGACC-AGAATAGCCAAAGCTATCCTGAGCAAAAAGAA 3083
                              vii   ii    -            i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_124872604_   3084 TAAAACTGGAGGAATCACATTACCTGTCTTCAAATTATACTACAGAGCTA 3133
                         i   ii       v     i v  iivi      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_124872604_   3134 TAGCAATAAAAACCGCATGGTACCTGTATAAAAACACACATATAGACGAA 3183
                         i  i   v  i  v ii      iv i    ii i v         iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_124872604_   3184 TGAAACAGAATACAAAACCCATGAAAAAAATCCATACATCTACAGTTAAC 3233
                           i  i     vv i ii   -    v   i        i  ii  i  i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATGGTCAAT 349

  chrX_124872604_   3234 TCATTTTTGACAAAGCTTCCAAGAACATACTTAA-GGGGAAAGACT-GTC 3281
                          v     i     i v v      v   -- i  -         v -   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAATAGTC 397

  chrX_124872604_   3282 TCTTAAATAAATAATGCTGGGA-AACTAGATATCCACATGAAAAAGGATA 3330
                          i  v  i    ii        -    i    ?       v     i  i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_124872604_   3331 AAGGTAGGCCCTTATCTCTCACCATATA-AAAAATCAAATCAAAATGTAT 3379
                            v i i   i  i   v         -      i  v        v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_124872604_   3380 TAAAGATTTAAATTTAATACTTGAAACTATTAAACTACTATAAGAAAACA 3429
                         i ?   ii     v   v vi i       v     vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_124872604_   3430 TCTTGAAAAAGCTCCAGGATATCCATCTGGGAAAATATTTTTTGAGTAAT 3479
                          vvv?iv   v  i iv  iv ivivi i  v  vvi   i  iii  vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_124872604_   3480 ATCCCACAAGCACAGGCAACCAAAACAAAAATGAACAAAT-GGAAAACAT 3528
                          iv   v       i     v   iv      ii i    -   vvv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_124872604_   3529 CAA-GTTAGAAAGCCTCTGCACAACAACAAAAACAATCAACAAAGTAAAG 3577
                            -i   i   - i i  ii vv   vii v  v     v     i  i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_124872604_   3578 AGACAACTTACAGAATTGGAGAAAATCTTTGTAATCTACCCATCTGATAT 3627
                                ii       v         v    i  vii ivi        v
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_124872604_   3628 AGGATTAACAACCAGAAGATATAAGTAGCTCAAACAACTCTACAAGAAAA 3677
                         i   i vii v      v      iv i   vv       v i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_124872604_   3678 TATCTAATAATCAGATTTTAAAATTGGCAAAAGATCTGAATAGACATTTC 3727
                         viv v     i vi   ?v     v      i   i              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_124872604_   3728 TCAAAAGATGACATAAAAATGGCAAACAGATATATAAAAAAGTTATCAAC 3777
                           v     v  i   v       v  i iii i  i    ii vv     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_124872604_   3778 ATTATTGATCAT 3789
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (140 / 104)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.10 (11 / 10)  


2969 20.42 1.33 3.85  chrX_124883563_124885284.rev      482  1235 (487)    L1M4_orf2#LINE/L1      174   908 (0)  

  chrX_124883563_    482 AGCCAAAATGTTTATTTTCTAAAA--AGAACAGGGTTAGAGGACTCACTT 529
                                 ii---  i  vv    --      ii   i          vi
  L1M4_orf2#LINE/    174 AGCCAAAACA---ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_124883563_    530 TTTTTTCTTGATTTCCTGAAACATATTACAAAGTTTCAGTAAACAAAATA 579
                           ---- iii     --i    v  i       i v      v   i i 
  L1M4_orf2#LINE/    221 TT----CCCAATTTC--AAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_124883563_    580 GCATGGTACTGGCATAAAGACAGATCAGTATGTTAATGGAGTAGAATAGA 629
                          ii              i  i   ivvi  vi i      i      v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_124883563_    630 AAACTTTGAAATAAACTCTCATGTATATGGTCAAATAATCTTCAACATGA 679
                         i iiiiv         i vi ii v         v i  i   i   v i
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_124883563_    680 GTGCTAAGACAATTCAGTGGGGGAAAGGACAGAATCTTCAACCAATGATG 729
                             i     v     i     -    i i  vv i      v    i  
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_124883563_    730 CTGGGAAAACTAGATATCCACATTCAAAAGAATGAAGTTGGATCCTTATC 779
                               v    i    ?      v                  i  i  i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_124883563_    780 TTACACCATGTACAAAAATTAACTCAAAATGCATTAAAGAACTAAATGTA 829
                          i       i                     v  i ?   v         
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_124883563_    830 AGACCTAAAACTATAAAACTCTTAGAAGAAAAC-TAGGGGTAAAGCTTCA 878
                            v                             -    ?     v    i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_124883563_    879 --ACATCGGACTTGGCAATGATTTCTTGGATATGACACCAAAAGCATAGG 926
                         --  v i  ii v       i      i                  i i 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_124883563_    927 CAGCAAATGCAAAAAAAAAAAAAAAAGACAAAC-AGACTACTTCAAACTT 975
                           i    --------- i      v   i   i-i    v v     v  
  L1M4_orf2#LINE/    614 CAACAAA---------AGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_124883563_    976 ACAAACTTCAATGCATCAAAGAACAAAACCAATAGAATGAAATGGCAACA 1025
                          v      ivi   v      i   vv i   v i i     v i    v
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_124883563_   1026 TAAAAAATGGGAGAAAATATTTTCAAATTATATATCTGATAAGGAGTTAA 1075
                         i v i                 v     i               iii vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_124883563_   1076 TATCTAGAATACATAAAGAATTCATACAAATGAACAACAAAA-GTCAAAT 1124
                             i      i        i  v     v v  i  i    - v     
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_124883563_   1125 AACTCAATTTTAAAATAGACAATGTTAATAGAGATGTTAACAAATGATTC 1174
                            i     ?v     i i   -------  -   v v  i i iiv   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAA-------AG-GATTTGAATAGACATTTC 846

  chrX_124883563_   1175 TACAAAGATGATACATAAGTGG---ACAAGCATATGTAAAGATGCTTGAT 1221
                          v      v    i i  i   --- i     i   v         ii i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_124883563_   1222 ATATCACCAATCAT 1235
                           --  ????????
  L1M4_orf2#LINE/    897 AT--CAZZZZZZZZ 908

Transitions / transversions = 1.83 (97 / 53)
Gap_init rate = 0.02 (14 / 735), avg. gap size = 2.79 (39 / 14)  


1372 27.79 0.48 1.90  chrX_124922768_124928451     1242  1662 (4021)    L1M4_orf2#LINE/L1        1   415 (493)  

  chrX_124922768_   1242 TGGAAAACCATTCCATGCTCATGGATGGGAAGAATCAATGTCATTAAAAT 1291
                               ivi  i     i        v      v i   i ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124922768_   1292 GGCCATACCGCCCAAAGCAATTTGCAGATTCAATGCAATTCCTATCAAAC 1341
                            v    iv      vii  i i         i     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124922768_   1342 TACAAATGACACTCTTCACAGAACTTGAAAAAAACT-ATTTTAAAATTCA 1390
                          v v iivi vi i  ii     v    v  i--  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_124922768_   1391 TGTGGAACAAAAAAAAAGCCTGAATAGCCAAAGCCATTCTAAGCAAAAAG 1440
                          i     vviv  iii v  v           i v  ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_124922768_   1441 AA-AAAGCAGGAAGCATCACTCTAATGCTAACTGACTTCAAACAATACTA 1489
                           -    iv   i ----    -- ii  vv ii i      vvv     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG----ACTC--ACACTTCCCAATTTCAAAACTTACTA 242

  chrX_124922768_   1490 CAGGGCTACAGTAACCAAAATAGCATGGGACTAGTACCATAACACACATA 1539
                           ii          i   i i  ii   v   i i iv vi i v     
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_124922768_   1540 TAGACCAATGGAAGAGAATAGAGAGGCCAGAAATAAAACAGCACATTCAT 1589
                             i        v     v     v           v vii     i  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_124922768_   1590 AACCATCTGATTTCCCACAAAGATGACAAAAACAAGCAATAGGGAAAGGA 1639
                         iii  vi      i v    i i  v   i v  vv    i       i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_124922768_   1640 CCCCCTATTCAATAAATGGTGCT 1662
                         ivvi  v     i          
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCT 415

Transitions / transversions = 1.66 (73 / 44)
Gap_init rate = 0.01 (5 / 415), avg. gap size = 2.00 (10 / 5)  

1587 23.52 4.91 1.84  chrX_124922768_124928451     3437  3925 (1758)    L1M4_orf2#LINE/L1      405   908 (0)  

  chrX_124922768_   3437 CAAAGGATACTGTGACACAGATAACTGGCTAGCCATATGCAGAAGCTTGA 3486
                             v i i   v    ------     v  ?   i     i   vv   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACA------ACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_124922768_   3487 AGC----------CCTTAAACCGTGTACAAAAATTACCTCAAGATGGATT 3526
                           i----------   i v   i i           v     i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_124922768_   3527 AAAGACTTAAATGTAAAACACAAAAACTATAAAAATACTAGGCAATACCA 3576
                          ?    i         i -i v            v vi   ivi v v  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_124922768_   3577 T---------TCT--G-GACATAGGAATGGGCAAAGATTTTAT-GATGCA 3613
                          ---------   -- -   v v  iv i     v i   iv -   ii-
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT- 596

  chrX_124922768_   3614 GACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTAA 3663
                                      vvv          v      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_124922768_   3664 T-AAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAGCAGAGTAAA 3712
                          -    i    i -   i  ii vv    i  v       iv i   i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_124922768_   3713 CAGACAACCTACAAAATGGGAGAAAATTTTTGCAAACTGTGCATCTGACA 3762
                         v        i   i             v        iii ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_124922768_   3763 AAGGTTTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAA 3812
                          i  vi vi       v  v     i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_124922768_   3813 ATAACAAACAACCCCATTAAAAAATAGGCAAAGGACATGAACAGACACTT 3862
                          vi     i     v   ?      i         iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_124922768_   3863 TTCAAAGGAAGACATACATGTGGCCAACAATCATATGAATAGAAGCTCAA 3912
                         i  v  i     i     vi       i  v  i     v   v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_124922768_   3913 TGTTACTGATCAG 3925
                         ii i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (64 / 48)
Gap_init rate = 0.02 (10 / 504), avg. gap size = 3.30 (33 / 10)  

2318 26.44 1.03 1.18  chrX_124922768_124928451     4515  5191 (492)    L1M4_orf2#LINE/L1      233   908 (0)  

  chrX_124922768_   4515 AAATTATACTACAGAGCCCTGGTAACCAAAACAGCATAGTACTTGCATAA 4564
                            i -       i   ivii    i   i    ii i     v      
  L1M4_orf2#LINE/    233 AAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_124922768_   4565 TGACAAATACATAGTTCAGTGAAACAGAATAGATAACTCAAAGATTTATC 4614
                         v  i i i i    v   i  i  i     v  v iii  i i  vv i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_124922768_   4615 CACACATATACAGTGAACTCATTTTTGACAAAGTTTCCAAGGACATACAT 4664
                           i    v  ii  v  i v     i     i v v     iv   v  v
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_124922768_   4665 TGGAGAAAGTACAGTCTCTTCAATAAATGGTGTTGGCAAAACTGGATATC 4714
                            i     v i     i     i        i   v v         ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_124922768_   4715 CATGTGGAGAAGAATGAAACTAGACCCCTATTTCTTGCCACATACAAAAA 4764
                           ii  v i         ii i        ii  vii   i         
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_124922768_   4765 TCAAATAAAAACAAATTAAAGACTTTTAAATCTAAAACCTGAAACTGTGA 4814
                          i  v v    iii  i ?    i --    v   i v  i     i i 
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCT--AAATGTAAGAGCTAAAACTATAA 529

  chrX_124922768_   4815 AATTACTACAAGAAAACATTGGGGAAAATTTCTAGGACATTGGTCTGGGC 4864
                           i vi  v          v  ? v    i iiiv   v    vi i   
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_124922768_   4865 AAAAATTTCTTGAGCAATACCCCACAAGTATAGGCAACCAAAGCAAAAAA 4914
                           vii      iiii vv  v   v   i i i     v    --     
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG--AAAAA 627

  chrX_124922768_   4915 ATGGGCAAATGGGATCACATCAAG-TTAAAAAAGCTCACGCACAGCAAAG 4963
                           i ii    v   iiv      i-       --  ivi ii vv     
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAA--CTTTTGTGCTTCAAAG 675

  chrX_124922768_   4964 GAAAC----AATGAAGTGAATAGACAATGCGCAGAATGTTAGAAAATATT 5009
                           v  ----  vi       v      iv i       vv          
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_124922768_   5010 TGCAAACTACCCATCTGACAAGAGATTAATAACCAGAATATATAAGGAGC 5059
                               ii ivi      i   i  i vi  v             i  i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_124922768_   5060 TTAAGTCACTCAATAGGAAAAAAATCTAATGATCCAATT-AAAAATGGGC 5108
                          ivviiv        iv     i - v   i i      -          
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGC 824

  chrX_124922768_   5109 AAAATATCTGAATACACATCTCTCAAAAGAAACCATACATATGGCAAACA 5158
                            iv  i      v    i    v      ivi     v     v  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_124922768_   5159 GGTATATGAAAAG-TCCTCAACATCAATGATCAT 5191
                         i i i        - v          ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (112 / 64)
Gap_init rate = 0.01 (9 / 676), avg. gap size = 1.67 (15 / 9)  


 458 28.61 2.78 6.67  chrX_124963895_124970155.rev        7   366 (5895)  C L1M4_orf2#LINE/L1   (165)   743   398  

C chrX_124963895_    366 TTTTCAACAAACCACACTGAAATGAGTTGATAACT-TATGTAAAAAAATT 318
                                    iviii   ii ii v v    ? i-i   i    i   v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chrX_124963895_    317 AACCTTGACT--TACCCCATGCCATAGACAAAAAAAAAAGATGTCAAA-T 271
                           vi v   i--    i  ii     v       vv  v----     - 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC----TCAAAAT 493

C chrX_124963895_    270 GTGTCAAATACCTAATGATAAAAGACAAAACTATAATATTTATGAAAAAA 221
                          vi   ? v      vvi   i  vi          v i iv ii  i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

C chrX_124963895_    220 AATAATATCCTGTCATGAAATGCTTCAGTAAATTCCTAAATCTTTGAAGT 171
                           i -  ---- v?i -    -    -  i ---------- i   iiv 
  L1M4_orf2#LINE/    544 AACA-TA----GGNGT-AAAT-CTTC-GTGA----------CCTTGGGTT 575

C chrX_124963895_    170 AGACAAAGATTTTTTAAGTAGGAGACAAAAAG---GAATTATAAAGCAAA 124
                           i   v i   i   ii  v  v  v     ---i iiv i   iv   
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

C chrX_124963895_    123 AAAATGATAAATTG-ACTTTATTATTTTTTTAAAATTCAGT--TTTGAAA 77
                            vv         -    i  i vvv  vv   v  iv  --  ii  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

C chrX_124963895_     76 GACATTATTAATAAAATTAAAAGACGAAATATAGATTGGGAAAAATACTA 27
                             i   i  v   i v       i vvi i   v     i   - -  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA-A-TA 723

C chrX_124963895_     26 TTAGTAGAACATGTATCTAA 7
                           v i i v   i     i 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGA 743

Transitions / transversions = 1.44 (59 / 41)
Gap_init rate = 0.04 (15 / 346), avg. gap size = 2.27 (34 / 15)  

3237 26.21 0.66 0.66  chrX_124963895_124970155.rev     4863  5770 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_124963895_   4863 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4912
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_124963895_   4913 GGCTATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4962
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_124963895_   4963 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5009
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_124963895_   5010 ATATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAA 5059
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_124963895_   5060 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGA 5109
                                 i      vv       v  ii i      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_124963895_   5110 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5159
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_124963895_   5160 CAATGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCGCATATCTACAAC 5207
                                 i    i--    i  --    i   vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_124963895_   5208 CATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5257
                           vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_124963895_   5258 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAAGTAGAAAGC 5307
                         i  v  i  i              v      v  ?   i v i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_124963895_   5308 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5357
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_124963895_   5358 ATTAAACACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5407
                           i ? v  i    ii v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_124963895_   5408 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5456
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_124963895_   5457 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5506
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_124963895_   5507 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5556
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_124963895_   5557 ACAGGAAACTTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5606
                          v  iv   ii   i             v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_124963895_   5607 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGTA 5656
                           i  i  vi          v  i  v      vv    v iv i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_124963895_   5657 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5706
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_124963895_   5707 TCTCAAAACAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5756
                             v   v    i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_124963895_   5757 TCATCACTGGCCAT 5770
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1984 25.80 3.97 0.46  chrX_124976853_124978852.rev      855  1509 (491)    L1M4_orf2#LINE/L1      231   908 (0)  

  chrX_124976853_    855 CAAACCATACCA-AGAGCTGTAGTAAGCCAAACAGCATGGTACTGGCATA 903
                             v v   i - i    ii     v v i    ii             
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_124976853_    904 AAGTCAGACACATAGAGCAAGGGAACAAAGCATAAAACCCAGAAACAAAT 953
                          i vi     i     v   v    i i iivv i ii       i   i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_124976853_    954 GCACACACCAACAATAAACT-ATTTTCCACAAAGATGCCAAAAATAAACA 1002
                         v  i   iiv iii v  i -      v    i i      i vi vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_124976853_   1003 CTAGGGAAAAAACAGTCTCTTCAATAAATGGTGCTGGGAAAACTGGATAT 1052
                         v i      i  i     i     i              v         ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_124976853_   1053 GGATATGCAGAATAATGAAACTTGACCCATAACTCTCACAAT---CAAAA 1099
                         vv i     i  v      ii v     v  v   v   v  ---     
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_124976853_   1100 --TAAATCAGTAT---TTA-----TTAAATCTAAGACCTGAAACTATGAA 1139
                         --   v   iv  --- i -----i     v     v  i       i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_124976853_   1140 AATACTAGAAGAAAACATTGGGGAAACTCTCCAGGACTTTGGTGTCTGTA 1189
                          v vi             v  ? v  v   i iv   i    -  iv vv
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGC 579

  chrX_124976853_   1190 AAAAATTTCTTGAGTAAAACCCCACAAGCATAGGCAATGAAATAAAAA-T 1238
                           vii      iii  vi  v   v     i i    ii   v     - 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_124976853_   1239 GGACATATAAGATTATATCATG-TTAAAAAGCTTCTGCACAGCAAAA--- 1284
                         i  i v  vi  i vi    vi-       -   i  ii vv    i---
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chrX_124976853_   1285 ATT--CAAGAAAGTGAAGAGAATACTCACAGAATGGGAAAAAA-ATTTGC 1331
                          i --            i   vv  i            i    -      
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_124976853_   1332 AAACTACCCATCTGAAATGAGATTGCTAACCAGACTA-ATTAAGCATCTC 1380
                            ii ivi      v v i  i vv  v     v  -  v   v -   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA-CTC 777

  chrX_124976853_   1381 ATAGAATTCTATAAGGAAAAAATTGATAATCTAATTTAAAAA-GGGCAAA 1429
                         v  v  i  v    vi    i ivi    i i    ?     -       
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_124976853_   1430 G-ATGTGAATAGATATTTCTCAGAAGAAGACATACAGTTAGAAAACAGGC 1478
                          -  v        i       vi       i     iv i vv  i i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_124976853_   1479 ATATGAAAAGGTGCTCAACATCACTGATCAT 1509
                          i        i            ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (95 / 71)
Gap_init rate = 0.03 (17 / 678), avg. gap size = 1.71 (29 / 17)  


2211 28.86 4.09 1.70  chrX_124986797_124989896.rev     1730  2609 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_124986797_   1730 ATATGCCCAATG---ATGG-TTAGACTCAAACATAATA-----AAGATGT 1770
                             -    -  ---    -  i  --- i  v     -----      v
  L1M4_orf2#LINE/      8 ATAT-CCCA-TGTTCATGGATTGGA---AGACTTAATATTGTTAAGATGG 52

  chrX_124986797_   1771 CCACTCTACCCCGAATTT-TATGTAGGTTAAATATAATTATTATAAAAAC 1819
                          v iv  -    i    v- v ii  i  v  iii   ivi   v    i
  L1M4_orf2#LINE/     53 CAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_124986797_   1820 CCCAAAATGT-TTTCTCATAAGTATAAACAAGATTATTCTAAATTGAATA 1868
                             iv-  i-   i iii iiv  vi     v v  i     v vv   
  L1M4_orf2#LINE/    102 CCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_124986797_   1869 TGAAAAGGAAAAAGATCTAGAATAGATAAAACTAT-TTGAAAAAGAA--- 1914
                           i   v v  ii  i i       vi     v  -           ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_124986797_   1915 TACAGTGAGAAGAACCAGTGTTCTTGACTTCAAGGCTTATTATA----TA 1960
                         i v   vi  i  vi  vvv   iii i     ii    i  i ----  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_124986797_   1961 TGGTGATAGAGTC--TGTGCTATTGGT-TGTGAATTTGGCACATA--TCA 2005
                         ii  i  vi  v --    v  i   i- iv i  v- i  i   --   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGATCA 299

  chrX_124986797_   2006 GTAAAACACAATAGCGAACCCTGAAACAAATC--TGGATTAACATACTCA 2053
                         i ii  i v   v v  ii  v    i   i -- iv   --i  iv   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCA 347

  chrX_124986797_   2054 TTTGATTTTTCACAGAAGTGCAAAATCAATTCAATGGAAGGAGGGTATTC 2103
                         v        iv   iii    v  iv v         iiii  ii  v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_124986797_   2104 TTTTCAACATATGGTGCTGGAGAAACTGGACATTCATAGGCCAAAAAAGG 2153
                                  v          iiv       i ?i  i v  v   i  v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_124986797_   2154 AAATGAAACTCTACCTGTCTCATACCTTATATAAAAATGAACTCAAAAAT 2203
                           i vii  i ---  ii    i   v    i      v         - 
  L1M4_orf2#LINE/    448 AAGTTGGACCC---CTACCTCACACCATATACAAAAATTAACTCAAAA-T 493

  chrX_124986797_   2204 GGATCATGGACTTAAATATAAAATGTAAAACTATAAAACATTTATCAAAA 2253
                               ?i   i     i   i vv              vi   vv i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_124986797_   2254 TGCATATGAAAAAATTTTTTGAATCTAGGGCTAGGCAAAGAGTTTTTTAA 2303
                         vi    v ?iv    i  ivvi i  v   i       v -    i   i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCTTAG 592

  chrX_124986797_   2304 TTATGTT-CCAAAAACACACTCCATGAAA-----AATTGGTAAATTGGTC 2347
                         v    vi-      i    vv v ii   -----   v i        v 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_124986797_   2348 TTTATGAAAATTAAAA-CTTTTGCTTTGTGAAAGACTCTGTTAAGAGACT 2396
                           i  v          -      ivi vii  i   v  i i    i v 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_124986797_   2397 GAAAAGACAAGCTAAAAGACTGGGGAAAATACTAGTAAAGCACATATATG 2446
                                   v i v ii iv  i       i v i   v  i    v  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_124986797_   2447 ACAGTGGACTACTATCTAGAATATTTAAAGAACCCTCAAAACTCAAACAT 2496
                          i iv     vv    i       v        i  i v       vv  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_124986797_   2497 GAAAATGTAAACAATTCAAGTAGAATATAGGCAAAAGTCATGAAGATGCA 2546
                         i    vii   i  ii   v ?i  v  i      i viv    v vi  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_124986797_   2547 TTTTACT---GCAGATATACAGATGGTAAATAATCATATGAAGAGCTGTA 2593
                            iv i--- v         i    iv     v  i     i  v  iv
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_124986797_   2594 CAACACCATTAACCAT 2609
                              i  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (148 / 102)
Gap_init rate = 0.03 (26 / 901), avg. gap size = 1.96 (51 / 26)  

 440 26.52 2.27 0.00  chrX_124986797_124989896.rev     2809  2940 (160)  C L1M4_orf2#LINE/L1   (52)   856   722  

C chrX_124986797_   2940 TATTTATGTATTGTGCATCTGACAGGGGATTAATATTCAGTATGTGTAAA 2891
                              iiiv  ii ii      i i    i vi   i   v  i i    
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

C chrX_124986797_   2890 AAGCTAA-AAAATTCAATAACAAAAA--TAAATAATTTGATTAAAAAATA 2844
                         i i  vv- v  i       i     --i      iiii   ?      i
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

C chrX_124986797_   2843 GGCAAATGACTTGAATATACATTTCTCAAAAGAAG 2809
                               v  i       v         v       
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

Transitions / transversions = 2.78 (25 / 9)
Gap_init rate = 0.01 (2 / 135), avg. gap size = 1.50 (3 / 2)  


2531 28.12 3.85 0.91  chrX_125004737_125010546.rev     4438  5319 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125004737_   4438 TGGAAAAACATTCCATGCTCATGGATAGGAAGAAGTAATGTCGTGAAAAT 4487
                               i i  i     i        v      vv    i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125004737_   4488 GGCCATACTACCCAAAGTAATGTATAGATTCAATGCTATTCTCATTAAAC 4537
                            v     v      v i  v  i        i  v  i ii  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125004737_   4538 CACCATTGGCATTCTTCACAGAATTAGAAGAAATTATTTTAAAATTCATA 4587
                         iv   viv  v  i  ii     v v  vi iv v  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_125004737_   4588 CGGAACCAAAAAAGAGCTTGTATAGCCAAGATAATCCAAAGCAAAAAGAA 4637
                         i    viiv  ii  v iv v        i i    ivi iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_125004737_   4638 CAAAGCTGGAGGCATCACACTACCTGGTTTTAAACTAAACTACAAGGCTA 4687
                              i      vv       v  iii   i   vivv       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_125004737_   4688 CAGTAATCAAAATAGCATGGTACTGGTACAGAAAGAGAAACATAGACTAA 4737
                                   i i  ii         i i iii v   v i     ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_125004737_   4738 TGGAACACAATAGAGAACTCAGAAATAAGACCACACAACTACAACTGTGT 4787
                              i v   v    iii         iv   i   vi  iiiiiivv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_125004737_   4788 GATCTTTGACAAACCTGACAAAAACAAACAATGGGGAAAGGAATC-CCTG 4836
                            i  i     ivv  v   i v  vv            -   v-i  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTT 399

  chrX_125004737_   4837 TTTAATAAATGGTGCTGGGAGATCTGGCTAGGTATCTGAATAAAATTAAA 4886
                           i  i              v v    v  ?vi iv  v v  i v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_125004737_   4887 ACTGGACCCCTGTCTTACACCTTACACAATAATTAA-----GATGGATTA 4931
                         ii         ii  i     v  i    v      -----i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_125004737_   4932 CAGAATTAAATGTAAAACCCTAAACTATAAAATCCCTAAAAGAAAATCTA 4981
                         ?   vi         i v iv           ii i  i       iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_125004737_   4982 GGCA-ATACCAGTCAGGACAT--AGTCACGGGCAAAGGTTTCAT-GATAA 5027
                           ?i- v i -v  iv   v --i  i --     v      v -    v
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATAT 596

  chrX_125004737_   5028 AAATGTCAAA-GCAATTACAACAAAAGCAAAAATCAACAAATGGGTTCTC 5076
                         i -iii    -   vvvi         v      vi i    v  vii  
  L1M4_orf2#LINE/    597 GA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_125004737_   5077 ATTAAACTAAAGGGCTTCTGCACAGCAAAAGAAACTCTCATCAGAG---- 5122
                           i   v v  iii   i  ii vv    i  v   v   vv i  ----
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_125004737_   5123 ----CAA---ACAGAA---------ATTTTTTTCAATCTATCCATCTGAC 5156
                         ----   ---      ---------  v   viv    -  vi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGAT 744

  chrX_125004737_   5157 AAAGGTCTAATATCCAGTATCTACACAGGACT--TAACCAATTTACAAGT 5204
                           i  v  vi       v  v  i v  i   --  --   i i vv i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAAT 792

  chrX_125004737_   5205 GAAAA-ACAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACA 5253
                         i    -     i     v   ?    i           iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_125004737_   5254 CTTCTCAAAAGAAGACATTTATCTCACCAACAAACATATGAAAAAAAGCT 5303
                         i     v        i  vi vv vi    i  i  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_125004737_   5304 CAATATCACTGATTAT 5319
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (141 / 103)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.47 (42 / 17)  


3189 27.25 0.44 0.66  chrX_125044989_125051270.rev     4882  5791 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125044989_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125044989_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125044989_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_125044989_   5030 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_125044989_   5080 AACAAAGCTGGTGATATCACACTACCTGACTTCAAACTACACTACAAGGC 5129
                                i   v ivv       v  ii i      vivi       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_125044989_   5130 TACAGTAACCAAAACAGCATGGTACTGGTAGCAAAACAGAGATATTGATC 5179
                                 i   i    ii         i vv ii i   v    v    
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_125044989_   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5227
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_125044989_   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_125044989_   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_125044989_   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_125044989_   5378 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTGGAAGAAAAC 5427
                          i ?    i    i  v   v       i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_125044989_   5428 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_125044989_   5478 AACACCAAAAGCAATGGCAAGAAAAGACAAAATTGACAAATGGGATCTAA 5527
                         i            vvi    v      v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_125044989_   5528 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_125044989_   5578 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5627
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_125044989_   5628 AGGGCTAATATCCAGCATCTACAATGAACTCCAACAAATTTACAAAAAAA 5677
                         i  i  vi       v  v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_125044989_   5678 AACAACAAACAACCCCATCAAAAAGTGGGTGAAGTACATGAACAGACACT 5727
                          i--     i     v  i?    i    ii   v iv    i     i 
  L1M4_orf2#LINE/    797 AG--ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_125044989_   5728 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5777
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_125044989_   5778 TCATCACTGGCCAT 5791
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3086 27.75 0.44 0.44  chrX_125089228_125095445.rev     4820  5727 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125089228_   4820 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4869
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125089228_   4870 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4919
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125089228_   4920 TACCAATGACTTTCTTCACGGAACTGGAAAAAACT-ACTTTAAAGTTCAT 4968
                          v   iivi i  i  ii i   v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_125089228_   4969 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTCAGCCAAAAGA 5018
                               viiv  ii  v  v v  v     iv     i v ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_125089228_   5019 ACAAAGCTGGTGGCATCACACTACCTGACTTCAAACTACACTACAAGGCT 5068
                               i   v  vv       v  ii i      vivi       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_125089228_   5069 ACAGTAACCAAAACAGCATGGTACTGGTAGCAAAACAGAGATATTGATCA 5118
                                i   i    ii         i vv ii i   v    v     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_125089228_   5119 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTA 5166
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_125089228_   5167 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAATGATTCCC 5216
                         vi    i  i     ivv  vv  i v  vv           vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_125089228_   5217 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTATATGTAGAAAGCTG 5266
                          v  i  i              v      v  ? i i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_125089228_   5267 AAACTGGATCCCTTCGTTACAACTTATACAAAAATCAATTCAAGATGGAT 5316
                           ii    i    v v i   v v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_125089228_   5317 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTACAAGAAAACC 5366
                         i ?    i    i  v   v       i      vi i  v        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_125089228_   5367 TAGGCA-ATACCATTCAGGACATACGCATGGGCAAGGACTTCATGTCTAA 5415
                             ?i- v i -   iv   v vv vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_125089228_   5416 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5465
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_125089228_   5466 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5515
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_125089228_   5516 AGGCAACCTAGAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5565
                           i     i v i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_125089228_   5566 AGGGCTAATATCCAGCATCTACAATGAACTCCAACAAATTTACAAGAAAA 5615
                         i  i  vi       v  v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_125089228_   5616 AAACAAACAACCCCATCAAAAAGTGGGCGAAGTACATGAACAGACACTTC 5665
                          i     i     v  i?    i     i   v iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_125089228_   5666 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5715
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_125089228_   5716 ATCACTGGACAT 5727
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (143 / 105)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2724 27.52 2.80 1.23  chrX_125111796_125115374.rev     2195  3088 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125111796_   2195 TGGAAAAATATTCCATGCTCATTGATGGGAAGAATCTATATCATTAAAAT 2244
                               i    i     i    v   v      v iv    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125111796_   2245 AGCCATACGACTCAAA-------GCAGATCCAATGATATTCCTATCAAAG 2287
                         i  v    vv i    -------i     i   i vv  i         i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125111796_   2288 TACTGATGACATTCTTCAC-GCAATTAAAAAA--AATTTTAAAATTCATA 2334
                          v iiiivi v  i  ii - v    i v  i--i  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_125111796_   2335 TGGAACCAAAAAAGAGCCTGAATAGCTAAGGCAATCCTAAGCAAAAATAA 2384
                              viiv  ii  v  v       i  ii     i i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_125111796_   2385 TAAAGCCAGACACAACACATTACCTGACTTCAAACTGTACTACAAGGCTA 2434
                         i    iii  vivvv    i v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_125111796_   2435 CAGTAAACAAAACACCATGGTACTGGCACAAAAACAAACACGTAGACCAG 2484
                               v   i   vii           i  ii i i   ii    i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_125111796_   2485 TGGAACAGAATGGAGAGCCCAGAAATAATGCCTCACACATACAACCACCT 2534
                              i     v     i          vv  vi   iv  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_125111796_   2535 GATCTTTGACAAAGTCGACAAAAACAAACAATGGGGAAAGAACTCTCTAG 2584
                            i  i     i vi v   i v  vv              ivv   vv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_125111796_   2585 TCAGTGAATGGTGCTGGGATTAGTGGCTCGCCATTTGCAGAAGATTGAAA 2634
                            iii             iv v   v v?   iv    i    v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_125111796_   2635 TTGGACCCCTTCCTTAAACCGTACACAAAAATCACCTCAAGATGGATTAA 2684
                                   v   i v   i  i        i v     i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_125111796_   2685 AGACTTAAATGTAAAGCCTAAAAATATAAAAATCCTGGAAGCTAATCTAG 2734
                             i         iiv      v       v  i i    vv  iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_125111796_   2735 GAAGTA---CTATTGTG----TAAAT-AGGCCCTGGCATCCATTTCATGA 2776
                          ?-   ---  - i   ---- iii -    vv   ------    v ii
  L1M4_orf2#LINE/    551 GN-GTAAATCT-TCGTGACCTTGGGTTAGGCAATGG------TTTCTTAG 592

  chrX_125111796_   2777 CAAAGATGCCCAAA--ACAATTTCAACAAAAGCAACATT-GACAAATGGG 2823
                         vv v  ii  v   --    v--         v  v v -  i    v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAG--CAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_125111796_   2824 ACTTAATTAAACTAAAGAGCTTCTGCACAGCAAAATAAGCTATCAACAA- 2872
                             v  i   v v  i i   i  ii vv    iv vi       v  -
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_125111796_   2873 GTAAACAGACAACCTACAGAATGGGAGAAAATATTTGCAAAC--TGCATC 2920
                           i  v        i                          i-- ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_125111796_   2921 CAACAAGTATCTAATATCCAGAATGTATAAGGAACTTAAACAGTGTCACA 2970
                         ii i   viv  vi          i     i     ivv   ii-   vv
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TCAAT 789

  chrX_125111796_   2971 AGCAAAAAG-CAAACAACCCCATTACAAAGCAGACAAAGGACATGAACAC 3019
                          ii      -    i     v   ?v   iii i       iv    i v
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_125111796_   3020 TCACTTTTCAAAAGAAGACATACGCTCAGTCAACAAGCATAGGAAAAAAT 3069
                         v  i  i  v        i    ivvii i   i     i v     i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_125111796_   3070 GCTCAACATCACTAATCAT 3088
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.25 (36 / 16)  


3328 18.52 3.57 0.69  chrX_125152272_125153992      500  1228 (493)    L1M4_orf2#LINE/L1      159   908 (0)  

  chrX_125152272_    500 CAAAAAATTCTAAATAGCCAAAACAATATTTTAAAAAAAGA------CTG 543
                            iii ii vi               v  vv    i    ------i  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_125152272_    544 GAAGACTCACACTTTCCACTTTCAAACCTTACTAAAAAGTGATAGTCAAC 593
                           i           i   v       v       v    iv i   v v 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_125152272_    594 AAGACAATGTAATA---GCATGAGGATATATATATTGATCAATGGAATAT 640
                               i   ii  ---    i      v i    v             v
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_125152272_    641 AACTCAGAGTCCAAAAATAAACCCACATATCTATTGTCAATTGACTTTTG 690
                           i v        i           i i  i   v         i   i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_125152272_    691 GGAAAAATGCCCAGACCACTCGATGGGGAAAAAAATAGTCTTTTCCACAA 740
                         iv  iii    v      i  i         i  -          v    
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTTTTCAACAA 407

  chrX_125152272_    741 ATGG--CTGGAGACAACTAGATATTCACATGGAAAAGGATGAAATCAGAT 788
                             --    -       i    ?i      v     i     i ii  i
  L1M4_orf2#LINE/    408 ATGGTGCTGG-GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_125152272_    789 CCTCACATCACACCATATACAAAACCAAACTCAGAATGCATCAACAACCT 838
                           ii  v                 viv      i    v    ?vi    
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_125152272_    839 --TTATAATAACTAAAACTATAAAACTATTTGAAGAAAGCATAGGAATAA 886
                         --v i   v i                v  v       i      ?i   
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_125152272_    887 ATCTGTATGTATTTGGATTTGTCAACTATTTCTTA--TGTAACACTAGTA 934
                             vii  vvi    i  v v   ivi       -- i i    i iv 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_125152272_    935 ACAGAAGCAGCAAAAGAAAA--CAGATAAATTGGACTTTCTAAAAAATAA 982
                         i  v     i          --i               iv v    v   
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_125152272_    983 AA-CTTTTGTGCATCAATGGACACCATTAAGAAAGTGAAAATAAAATTCA 1031
                           -         v    v      i  i             v v  ii  
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_125152272_   1032 CAGCATGGGAGAAAATATGTGTAAATCATAT--CTGATAAG--ACTTTAG 1077
                            v              v  i         --        --    -- 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT--G 754

  chrX_125152272_   1078 TATCCAGAATATGTAATGAACTCTTATGACTCAACAACAAAAAGACAA-- 1125
                                     i   v         ii      i  i          --
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_125152272_   1126 --CCTAATGAAACAAATAGGCAATAGACTTGAATAGGCATTTCTCAAAAA 1173
                         --  i   v?  -    i     vi  i        i        v   i
  L1M4_orf2#LINE/    805 AACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_125152272_   1174 AAGATATACGAATGGCCAAAAAGCATGTGAAAAGATGCTCAACAGCATTA 1223
                                  i         v     ii                 v  ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_125152272_   1224 GTCAT 1228
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.57 (80 / 51)
Gap_init rate = 0.02 (14 / 750), avg. gap size = 2.21 (31 / 14)  


3005 26.63 0.88 1.33  chrX_125170286_125172184.rev      504  1408 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_125170286_    504 ACATTCCATGCTCATGGACAGGAAGAATCAACATAGTAAAAATGGCCATA 553
                          i  i     i       iv      v i  i  v  v  i     v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_125170286_    554 CTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGTTACCATT 603
                           v      v i  i  i        i  v  i  i     iv v   vi
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_125170286_    604 GACTTTCTTTACAGACTCAGAAAAAAAAAAAAAAAGACTTTAAATTTCAT 653
                         vi i  i   i    --------  vvi v  ivv  iii    v     
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGA--------AATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_125170286_    654 ATGGAACCAAAAAAGAGCCTGTATATCCAAGACAATCCTAACCAGAAAGA 703
                               viiv  ii  v  v v   v    i      i i vv ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_125170286_    704 ACAAACCTGGAGGTGTCATGCTACCTGACTTCAAACTATTCTGCAAGGCT 753
                              vi      vv   ii  v  ii i      viv v  i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_125170286_    754 ACAGTTACCAAAACAGCATGGTGCTGGTACCAAAACAAATATATAGACCA 803
                              v i   i    ii    i    i iv ii i i i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_125170286_    804 ATGGAACAGAACAGAGACCCCAGAAATAAAACCGCACATCTACAA-CAAT 852
                               i    iv    vi           v  ii    i  iii-    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_125170286_    853 CTGATTTTCGACCAACCTGACTAAAATGAG-CAATGAAGAAAGGATTCCC 901
                         -           v ivv  - i  i iv v-     ii     i  vvi 
  L1M4_orf2#LINE/    350 -TGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_125170286_    902 TATTTAATAAATGGTGCTGGGAAAACTAACTAGCCATATGCACAAAACAG 951
                          v  i  i              v    iiv  ?   i     v  i vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_125170286_    952 AAACTGGACCTCTTCCTTACACCTTATACAAAAATTAACTAAAGATGGAT 1001
                           ii      i  v   i     v                v  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_125170286_   1002 TAAAGACTTAAATGTAAAATCTAAAACCATAAAAACCCTAGAAGAAAACC 1051
                         i ?    i         i v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_125170286_   1052 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 1100
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_125170286_   1101 AACACCAAAAGCAATTTCAACCAAAGCAAAAATTGACAAATGGGATCTAA 1150
                         i            vvvv    v    v      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_125170286_   1151 TTAAACTGAAGAGCTTCTGCTCAGCAAAAGAAACTATCAACAAAGTGAAC 1200
                          i   v v  i i   i  iv vv    i  v        v        v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_125170286_   1201 AGGCAGCCTACAGAGTGGGAGAAAATTTCTGCAATCTATCTATCTGACAA 1250
                           i  i  i     i           v i     vii  v       i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_125170286_   1251 AGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACA-TGAAA 1299
                         i  i  vi          v  i  i     ivv    v iv i - i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_125170286_   1300 A--CAAACAACCCTATCAAAAAGTGGGCAAAGGATGTGAACAGACACTTC 1347
                          --    i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_125170286_   1348 TCAAAAGAAAACATTTATGTGGCTGACAA--ACATGAAAAAAAAGCTCAT 1395
                           v      i i  vi vi    ii i  --         i v-     v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAA 895

  chrX_125170286_   1396 CATCACAGGTCAT 1408
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (137 / 100)
Gap_init rate = 0.01 (11 / 901), avg. gap size = 1.82 (20 / 11)  


2559 27.79 2.46 1.45  chrX_125182594_125188343     4362  5257 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_125182594_   4362 AAAAAT-TTCCATGCTCATGGATAGAAAGAATCGATATTGTGCAAATGGT 4410
                            i  - i     i        v i    v ii       vv i    i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_125182594_   4411 CATATGGCCCAAAGTAATTTAAAGGTTCTATGCTATTCCCATTAAACTAC 4460
                         v   ivv      v i  i  v  i   v i  v  i  i  i   v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_125182594_   4461 CA-TTGACATTCTT-CATAAATTAGAAAAGAACT-ATTTTAAAATTTTTA 4507
                           -i  v v  i  -  v     -  v   --  -  ii       iv  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATT-GACAAG--CTGATCCTAAAATTCATA 150

  chrX_125182594_   4508 TGGA--TCCAAGAAAGAGCCCA-AATAGCCAATACAATCCTAAGTAAAAA 4554
                             -- v    ii ---    -         v      i i iv  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_125182594_   4555 GAACAAAGCTGGAGGCATCGCACTACCTGACTTCAAACTCTACTACAAGG 4604
                                 i      vv  i    v  ii i      vii        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_125182594_   4605 CTACGCTAACCAAAACAGCATGGTGCTGGTACAAAAACAGACACGTAGAC 4654
                             iv   i   i    ii    i    i i  ii i     ii    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_125182594_   4655 CAATGGAACAGAATAGAGAACTCTTAAATTAGACAGCACACTTACAAACC 4704
                                 i     v    iii vv    v iv vii   i   iiiv v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_125182594_   4705 ATCTATTTTCGACAAACCTGACAAAAACAAGCAATGGGGAAAGAACTCCC 4754
                           iv           ivv  v   i v  vv              ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_125182594_   4755 TATTAAATAAATGGTGCTGGGAAAGCTGGCTAACCATATGCAGAAAATTG 4804
                          v  v  i              v i    v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_125182594_   4805 AAACTGGACTCCTTCCTTATACCATATACAAAAATTAATTCAGTACGGAT 4854
                           ii     i   v   i i                  i   iv i    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_125182594_   4855 TGAGGACTTAAATGTAAAAACCCAAACTATAAAAACCCTGGAAGAAAATC 4904
                         ii?i   i         i i iv           vi i i        iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_125182594_   4905 TAGGCA-ATACCTTACAGGCCATAGGCATGAGCAAATATTTCAT-GATGG 4952
                             ?i- v i   vvv i  v i  i- ii    vvi    v -   iv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT 596

  chrX_125182594_   4953 AAACACCAAAAGCAATTGTGAGAAAAACAAAAGCTTTGACATGGGGGAAC 5002
                         i -           vvv ii v    iv    i-- v  i vivv   vi
  L1M4_orf2#LINE/    597 GA-CACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAAATTGGACT 643

  chrX_125182594_   5003 TAATTAAGCTAAGGAGCTTCTGCAAAACAAGAGAAAGTATCATCAGAGTG 5052
                          v  i  iv v ii i   i  iivvv   ii  v v     vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_125182594_   5053 AACAGACAACCAACAGAGTGGGAGAAAATTTTTGCAATTTATCCATCTGA 5102
                           v        v     i           v       v i  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_125182594_   5103 CAAAGATCGACT---ATCCTG--TCTACAAGGAATTTAAACAAAT--ATA 5145
                         i  i ---    ---    v -- v  i  i   i ivv    v --   
  L1M4_orf2#LINE/    744 TAAGG---GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_125182594_   5146 CAAGAAAAACAAACAACCTCACT-AAAAGTGAGCAAACGATATTAATAGA 5194
                         vv i   i     i    iv i -    i  i     v   v v      
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_125182594_   5195 CACTTCTC----AAAGACAAACATGTGGTCAAAAAATATGGAAAAAGA-G 5239
                           i     ----i    i v   vi   i   v  ii iivi      - 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_125182594_   5240 CTTAACATCACTGACTAT 5257
                           i       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 1.67 (35 / 21)  


2264 27.89 6.71 1.62  chrX_125190749_125192743.rev      641  1504 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125190749_    641 TGGAAAAACATTCCATTGTCATGGATTGGAAGAATCAACATCATTGAAAT 690
                               i i  i    vv               v i  i  ii  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125190749_    691 GGCCGTACTTCCCAAAGCAATGAACAGATTCAACACTATTCCTATCAAAC 740
                            vi    i      vii  vv           i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125190749_    741 TACCAATATCATTTTTCACAGAA-TTAAAAAA--AATTCTAAAATTCATA 787
                          v   iivv v     ii     -  i v  i--i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_125190749_    788 TAGAACCAAAAAAGAGCCCAAATAAACATAGCAATCCTAAGCCAAAAGAA 837
                          i   viiv  ii  v  vi    iv  v i     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_125190749_    838 CAAAGCCAGAAGCATCACATTACTCAACTTGAAAATATGCTACAAGGC-- 885
                              iii  i vv     i v i   i  v    iv i      i  --
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_125190749_    886 ---------AGACAG----------------------ACACATAGACCAA 904
                         ---------      ----------------------   i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_125190749_    905 TGGAACAGAATAGAGAATGCATAAATAAAGCAGCACACCTACAGCCATTT 954
                              i     v    i v  v       v vii   ii  ii i  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_125190749_    955 GATCTTTAACAAAGACAACAAAA--A--CAATGGAGAAAAGACTTCCTAT 1000
                            i  ii    i iiiv   i -- --      i    ii ivvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_125190749_   1001 TCAATAAATAGCACTGGAATAACTTGCTTGCCATATGCAGAAAAGTGAAA 1050
                             i    i ii    i i    v v v?   i     i  i i    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_125190749_   1051 CTTGACCCATAACTAACACTATATATGAAAATTAACTCAAGGTCAATTAA 1100
                         i v     v  v  v    i     ii             ii vi  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_125190749_   1101 AGACTGAAATGTAAGTCTTCAAACTATAACAATCCT-GAAGAAAATCTAG 1149
                             iv         vvi v         v v  i -        iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_125190749_   1150 ---CAAATGCTCTGCTCAATATGAACCTTGG--CA---AATAATTTAT-G 1190
                         ---i    -  ii -------   -      --i ---   ii   v -i
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCG-------TGA-CCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_125190749_   1191 GCTGAGTCCTCAAAAGCAATTGCAACGATAACAAAAGTTGACAAATTGGA 1240
                          v iv v vi        vvv     i v iv    i v  i        
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_125190749_   1241 CTTAATTAAACTAAGGAGCTTCTGCATAGCGAGAGAAACTATCAAGGGAA 1290
                            v  i   v v ii i   i  iiivv i ii  v         ii i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_125190749_   1291 TGAATAAAGAACCTACAAAATGAGAGAAAATATTTGCAAAATATTCATCC 1340
                             v i v    i   i    i                 ----    vi
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA----TCATAT 737

  chrX_125190749_   1341 ATCCAACACAGGTCTATTATCCAGATTCTATGTGGAACTTAAGCAAATCA 1390
                            ii i vi  v  vv        v v   ivi     ivvi   v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_125190749_   1391 AAGAGCAAAAAACAA----CCTCATT-AAAAGTGGGCAAATGACATTAAT 1435
                          vi vv    i    ----  iv   -    i        v  iv v   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_125190749_   1436 AGACACTTCTC---AAAAGATACACACATGGTATGACAAAAACATGAAAA 1482
                              i     --- i      i   v    i-ii i  iv         
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGC-CAATAAGCACATGAAAA 886

  chrX_125190749_   1483 AATGCTCATTATCACACATCGT 1504
                         i       vi    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (147 / 92)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.79 (72 / 19)  


3025 27.72 0.55 0.66  chrX_125221976_125223928.rev      554  1462 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125221976_    554 TGGTAAAACATTGCATCTTCATGGATAGGAAGAACTGATATCATGAAAAT 603
                            v  i i  iv   v         v      vi i    ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125221976_    604 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCCCATCAAAC 653
                            v     v      v i  i  i       ii  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125221976_    654 TACCATTGACATTCTTCACGGAATTAGAAAAAAAACT-ATTTTAAATTTC 702
                          v   vivi v  i  ii i   v v  v  i---  -  ii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_125221976_    703 ATATGGAA-T-CAAAGAAGACCCTGTATATCTAAAACAATCCTAAGCAAA 750
                                 - -   i --     v v   v i         i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_125221976_    751 AAGAACAAAGCTGGAGGTGTCATGCTAACTGATTTCAAACTATTCCAGAA 800
                                   i      vv   ii  vv ii        viv v i v  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_125221976_    801 GGCTACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGGCATATAG 850
                         i          i   i    ii  i      i iv ii i  i       
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_125221976_    851 ACAAATGGAACAGAACAGAGACCTCAGAAATAACACCACATATCTGCAAC 900
                          iv       i    iv    vii         vv   i i  i iiiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_125221976_    901 CATCAGACCTTCAACAAACCTGACAAAAACAAGCAATGAGGAAAGGATCT 950
                           viv  ii   i    ivv  v   i v  vv     i      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_125221976_    951 CCTATTCAGTAAATGGTGCTGGGAAAACTGGATAGTTATATGCAGAAAAC 1000
                         i  v    ii              v         ?ii i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_125221976_   1001 TGAAACTGGACCCCTTCCTTACACCATATACAAAAATTAACTCAAGATGG 1050
                             ii         v   i                         i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_125221976_   1051 ATTAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAA 1100
                           i ?    i         i v i     i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_125221976_   1101 GCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACT 1149
                         vv    ?i- v i -   iv   v v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_125221976_   1150 AAAATGCCAAAAGCAATTGTAACAAAAGCCAAAGTTGACAAATGGGATCT 1199
                          vi ii         vvv i        vv   i v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_125221976_   1200 AATTGAACTAAAGAGCTTCTGCACAGCAGAAAAAACTATAATCAGAGTGA 1249
                         v  ii  v v  i i   i  ii vv  i ii v     v vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_125221976_   1250 ACAGGCAACCTAAAGAATGGGAGAACATTTTTGCAATCTACCCATCTGAC 1299
                          v  i     i v            v  v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_125221976_   1300 AAGGT-CTAATATCCAGAATTTACAAGGAACTTAAGCAAATTTACAAGAT 1348
                             v-  vi          v  i  i     ivvi   v iv i  v v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_125221976_   1349 AAAAACAAACAAACTCATCAAAAAGTGGGCAAAGGATATGAACAGGCACT 1398
                            i     i  v iv  i?    i            v    i  i  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_125221976_   1399 TCTCAAAAGAAGCCATTTACGTGGCCAACAAACATATGAAAAAAAGCTCA 1448
                             v       vi  vi vi       i  i  i       i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_125221976_   1449 ACATCACTGATCAT 1462
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (144 / 104)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2351 25.96 7.60 1.52  chrX_125229187_125232209     1676  2530 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_125229187_   1676 GGAAAAACATCCCATGCTCATGTACTGGAAGAGTCAATATCATTAAAATG 1725
                              i i        i     v i       v i     ii    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_125229187_   1726 ATCATATTGCCCAAAGCAATCTACAGTTTCAACGTAATTTCTATCAAATT 1775
                         iiv   i v      vii        v       i   ii        v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_125229187_   1776 ACTAAC-ATCACTTTGGAAAGAATTAGAAAAAAAAATCT--AAGTTTATA 1822
                         v i i -ii vi   v v ii    -  v  ivvi   i--  i  i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCATA 150

  chrX_125229187_   1823 TAGAGCCAAATAAAAAG---CCTGAATAGCCAAAGCCATCTTAAGTAGGA 1869
                          i  ----   iv  i ---  v           i v     i iv i  
  L1M4_orf2#LINE/    151 TGGA----AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_125229187_   1870 AGAACAA-GTCCAAAGGCATCATATTACCTGACGTCAAATTATACTACAA 1918
                                -  ivi i i -   i i v  ii iv     viv        
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_125229187_   1919 GGCTATAATAACTAAAACAGCATGGTACTGGTACAAAAATAGACACATGG 1968
                         i    i i   ii  i    ii         i i  ii       i  i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_125229187_   1969 ATCAATGGAACAGAA---AAA----AGAAGGAAAGCCACATACCTAAAAA 2011
                                   i    --- i ----    iv   v   i i ii  viiv
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_125229187_   2012 CAACTGATCTTCAACAAAGTCAACAAAGATATACAGTGAGGAAAAGGTAC 2061
                            i    i   i    i viiv   iivi  v  i  i     iii  v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_125229187_   2062 GCTTTTCAATAAATAGTGTTGGGAAACTTGGGTAATCACAGGCA---GAA 2108
                         v        i    i   i     v vi   i  ?i    v   ---   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_125229187_   2109 TGAAACTGGAAAGCTATCCCTTCAAACCA----CAAAAATTAACTCAAGA 2154
                             ii    vvv   i ---   v    ----               i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACC---TCACACCATATACAAAAATTAACTCAAAA 492

  chrX_125229187_   2155 TTGATTAAAGACCTAAATTTAATACCTGAAACTATAAAAATTCTAGAAGA 2204
                          v   i ?          v   v v  i           v ii       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_125229187_   2205 AAACCTAGGAAAAACTCTTCTGGATATCAGCCTAGACAAATAACTT---- 2250
                             v    ?iv  v     vv  iv ii vi   i   - iii  ----
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA 591

  chrX_125229187_   2251 ---ATGA----------------------AAAAAAAATGGACACATGAGA 2275
                         ---    ---------------------- i       i  i v  vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_125229187_   2276 TTT-----AAAGTAAAAA-TTTCCTGCATAGTAAAAGAAATAATCAACAG 2319
                         i  -----   v      -   iv   v --i   i  v iv     v i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAA 689

  chrX_125229187_   2320 AGTAAACAGACAACCTACAGCATAGGATAAAATATTTGAAAATTATACCT 2369
                            i  v        i    v  i   v          v    i   iv 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_125229187_   2370 CTGATGAAAGCCTAATATGCATAATTTACAAGGAACTCAAACAAC--AAG 2417
                              i ii v  vi   v  v   v  i  i      vv     --  v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_125229187_   2418 AATAAAACAAACAA-TAACTCAATTAAAAACTGGACAAAAGACATGAACA 2466
                                - i    -    i     ?    v   i    i  iv    i 
  L1M4_orf2#LINE/    790 AATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_125229187_   2467 GATATTTTTC-AAAAAC----TACAAGTGGCCAAGAAAAAC-TGAAAAAA 2510
                           i    i  -   i v----     i       v  iv  -      i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_125229187_   2511 TTATCAACATCAATAATTTT 2530
                          vv         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (138 / 80)
Gap_init rate = 0.03 (24 / 907), avg. gap size = 3.25 (78 / 24)  


2945 27.14 2.82 0.56  chrX_125242169_125248544     4996  5883 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125242169_   4996 TGGAAGAACATTACATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5045
                              ii i  iv    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125242169_   5046 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5095
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125242169_   5096 TACCAATGACTTTCTTCATAGAATCGGAAAAA---A--CTAAAGTTCATA 5140
                          v   iivi i  i  iii    viv  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_125242169_   5141 TGGAACCATAAAAGAGCCCACATTGCCAAGTGAATCCTAAGCCAAAAGAA 5190
                              viii  ii  v  viv  v     ivv    i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_125242169_   5191 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 5240
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_125242169_   5241 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5290
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_125242169_   5291 TGGAACATAAC--AGAGCCCTCAGAAATAATGCTATATATCTACAACTAT 5338
                              i v  i--    i  --        vv i   i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_125242169_   5339 CTGATCTTTGACAAACCGGAG--AAAAACAAGCAATGGGGAAAGGATTCC 5386
                         i    i  i     i--  v --  i v  vv            i  vvi
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAG--GGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_125242169_   5387 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5436
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_125242169_   5437 GAAACTG----TCT-----------TATACAAAAATTAATTCAACATGGA 5471
                            ii  ----i  -----------              i    v     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_125242169_   5472 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTACAAGAAAAC 5521
                          i ?    i  v    v   v       i      vi i  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_125242169_   5522 CTAGGCA-ATACCATTCAGTACATAGGCATGGGCAAGGACTTCATGTCTG 5570
                         v    ?i- v i -   ivv  v v  vv i     v ii   v ivv i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_125242169_   5571 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5620
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_125242169_   5621 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCGGAGTGAA 5670
                           i   v v  i i   i  ii vv    i  v    i  vvii      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_125242169_   5671 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5720
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_125242169_   5721 AAGGACTAATATCCAGAATTTACAATGAACACTAACAAATTTACAAGAAA 5770
                          i     vi          v  i  v    v  v    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_125242169_   5771 AAAACAAACAACCTCATCAAAAAGTGAGCGAAGGACATGAACAGACACTT 5820
                           i     i    iv  i?    i  i  i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_125242169_   5821 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5870
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_125242169_   5871 CATCACGGCCATC 5883
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.00 (30 / 10)  


2808 26.59 3.86 0.68  chrX_125277862_125282843.rev     3612  4491 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125277862_   3612 TGGAATGAT-TCCAGTGT-CATGAATTAGAAGAACGAATATTGTTGAAAT 3659
                              v   -   vi   -    i   i     viv         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125277862_   3660 GTCCATACTATCCAAAACCATCTACAGATTCAA-----TTCCTATCAAAA 3704
                          v v     vi     viv              ----- i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125277862_   3705 TACCAATGACATTCTTAACAGAAATACAAAAAACAATCTTAAAATTTGTA 3754
                          v   iivi v  i  vi       vv v  ivii   i       ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_125277862_   3755 TGCAATTAAAAAAGACCCAGAATAGCCATAGTTATCCTGGGGAAGAAGTT 3804
                           v  v iv  ii               v iiv   i  iii      v-
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA- 199

  chrX_125277862_   3805 ACCAAACTGGAGGAATCAAACTATCTAACTTCCAGTTATACTACAGAGCT 3854
                           v  ii       v   v   vi i  i   v iviv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_125277862_   3855 ATAGTAACCAAAACAGCATAGTATTCTCATGAAAACAGACACATAAAACA 3904
                          i     i   i    ii i   i vv   i ii i     i   i v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_125277862_   3905 ATAAAGAAGAATAAAGAATGCTGAAAGGAATCCACATACCTACAGTGAAC 3954
                           ii iv     vi   i v v    vi  i   i i ii  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_125277862_   3955 TCATTTTCGACAAAGGTGCCAAG----------GTGTAAAGA-CAGTCTC 3993
                          v           i         ---------- v v     -i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_125277862_   3994 TTCAATAAATGGTGCTGGGAAAACTGGACATTCATATGCA---GAATGAA 4040
                              i              v       i ?i  i     ---       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_125277862_   4041 ACTAGACTCTT--CTCGTCACATA-AAAAAAATCAAA-CAAAATGGATTA 4086
                         ii i   i i --   iivv    - v      i  v-          i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_125277862_   4087 AAGATTTAAACCTAAGACCTTAAACTATGAAACTACCACAAGAAAACATT 4136
                         ?   ii    iv     v  v       i     vii v          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_125277862_   4137 AGGGAAAATTTCCAGGACATTGGTTTGGGCAAAAATTGTTTGAGTAATAC 4186
                         i ? v    i i iv   v    v  i     vii  vi  iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_125277862_   4187 -CCAAGAAACAGGGGCCACCAA-GCAAAAATGAACAAATGTGATCACTTC 4234
                         -    -  i  vii  v  v  - v      ii i    vv  iiv v  
  L1M4_orf2#LINE/    600 ACCAA-AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_125277862_   4235 AAGTTGAAAGGCTTCTGTACCACAACAGAAACAACCAACAAAGTAAAGAG 4284
                           iv v   ii   i   i iv   vi  v  v i   v     i  i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_125277862_   4285 AGA-------GAATGGGAGAAAATATTTACAAACTACCCATCTGATAAGG 4327
                          v -------                  i    ii ivi           
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_125277862_   4328 AACTATTAACCATAATATATAAAGGGCTCCAACTAATCTATAGGAAAAAA 4377
                         i   vv  v   v           ii   iv  v v  v   iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_125277862_   4378 AAATCTAATAATCTGACTTTAAAAATGGACACAAGATTTGAATAGACATT 4427
                          v ---     i ii -  ?        i  v i                
  L1M4_orf2#LINE/    799 ACA---AATAACCCAA-TTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_125277862_   4428 TCTCGAAAGAAGACATATGAATGGCAAACAGGCATATGAAAAGCTGCTCA 4477
                             v        i   ii      v  i i   i        v      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_125277862_   4478 ACATTATTTGTCAT 4491
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.50 (40 / 16)  


2984 24.21 3.38 1.13  chrX_125293922_125296365     1066  1953 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125293922_   1066 TGGAAAGATATGCCATGTTCATTAACTGGGAGACTCTATGATATCAA--T 1113
                                    v          vi i   i     iv  iv i i  -- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125293922_   1114 AGCAATATTCCC-AAATAGATGTA----TTCAACAACAA-CCCTATCAAA 1157
                         i      i    -    v   v  ----      i-   -          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACG-CAATCCCTATCAAA 99

  chrX_125293922_   1158 ATCCTAGCTCCCTTCTTT-TAGAAACATAATA-GCTAACTCTAATGTTTA 1205
                             i    v    i   -i     i- i i -   i ii    vi  i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chrX_125293922_   1206 CATAGAAATTCAAGGGACCCAGAATAAGCAAAACAATCTTGACAAAGAAT 1255
                         i  i     v                iv              v      v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_125293922_   1256 GAGAATGTTGGAGGGCATGTACTTCT---TTTCAAAATATACTGCAAGGC 1302
                         i v  v        i viii     i---        iv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_125293922_   1303 TACAGTAGTGAATATGATATAGCGCTGGCATAAATGTTGACATC--AATC 1350
                                i v  v iii i i ii         ivi v     v--i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_125293922_   1351 AATGGAATACTTTTTAGAGTCCAAAATGAAACGCTTACATTTTTGGTCAA 1400
                                  vvv  v        i  vv    v v       v       
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_125293922_   1401 CTGATTTT-GACAAAGATTCCAAT-CAACACAACTAGCAATGCATAGTAA 1448
                         i       -     i i v    v- v iv   ivi v  v v     vv
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_125293922_   1449 CCTCAACAAATATTGCTGACACAACTGGATATCTATATGCAAA-GAATAA 1497
                         ii         iv     iv           ? i i       -    i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_125293922_   1498 ATTTAGACGAATACCTCAT--CATACACAAAAAT-AATTCAAAACGAATA 1544
                          v  i   vvv       i--    i        -  i      i i  v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_125293922_   1545 ATAAACATAAAGTTATTCATAAAAACTGAAGAATTTTTAGAAGAAGA-AT 1593
                          ? i  v    vv  vvviiv      iv i  i i         i -  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_125293922_   1594 ATGAGTAAATTTTTTTTATCTTAAGTCAGCTGAAGATTTCTCAGATCTGA 1643
                          v ?      i  iv v i   ii  i  vii v i     i    v   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_125293922_   1644 AACCAAGGGCACAAGAAATAGAAGAAAACTTTTATAAAGTAGCCTTCATA 1693
                         v     ii       v  i i       vv vv     v i v      v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_125293922_   1694 AAAAATTTTAAAAATT-----GCTTCAAAATACTCCATGAAGAAAGTGAA 1738
                             ---       i -----        iv  v i  v           
  L1M4_orf2#LINE/    649 AAAA---TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_125293922_   1739 AATACAAACGATAGATTTGAAGAAAATATTTATACCTCATATGTCTGAGA 1788
                           v    v v i   v v i           ii vv      i     v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_125293922_   1789 AATGACTTAAAAGTAT--AGAATACATAAAGAATGCTTACAATTCAATAA 1836
                          iv     ----    --      i        iv       i       
  L1M4_orf2#LINE/    746 AGGGACTT----GTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_125293922_   1837 TAAGGGGAAAAATC-CCCAAATAAGTAACGGACCAAAGATTTCAGTGGAA 1885
                            iii  v    v-     v ? iv  i  i v  i     v i i  v
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_125293922_   1886 ATTTCATTAAATAAGTATATCTGTATGGTGAATAAGTACATGAAAAGGTG 1935
                              vii   v   -    viiv    iv      i          i  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAG-ATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_125293922_   1936 CTCAACATAATTACTCAT 1953
                                 v ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (115 / 96)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 1.82 (40 / 22)  


2748 27.34 2.34 1.00  chrX_125300437_125304361.rev     2545  3440 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125300437_   2545 TGGAAAGATATGCAGTGTTCATGGACTGGAACAATTATTACTGTCAAAAT 2594
                                    v vi          i     v v   v  i   i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125300437_   2595 ATCTAAACCACTTAAAATAATCTACATATTCAATGCAATCGCTATCAAAA 2644
                         iv v v  iv ii   v i       v      i      v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125300437_   2645 TACCAATGACATTTTCCAGAGAGAGAAAAAATATAATCGTAAAATTCATA 2694
                          v   iivi v    iiiv   i vvi v  vv i   v           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_125300437_   2695 TGGAGCTACAAAAGACCCTAAATAGCCAAATCAATCCTGAGCAAAAAGAA 2744
                             iv i   ii     vi          v     i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_125300437_   2745 GAAAACTGGAGACATTACACAATCTGACATCAAAATATTCTACAAACCTA 2794
                         v   ii     ivv i    vvi ii iv      iv v       v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_125300437_   2795 TAGCAAGCAAAACAGTATGATACTGGCATAAAAACAGGCATCTAGACTAA 2844
                         i  i  v   i     i  i           ii i  i   v    ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_125300437_   2845 TGGAACAGAATAGAGATCCCAGAAATAA--CTGTGGCATTTACAGCGAAC 2892
                              i     v    vi          -- ii i-      ii iv  i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGTCAAT 349

  chrX_125300437_   2893 AGATTTTTTTATAAAGGTTCCAAGAACATATATTGTGGAAAGGACAGTCG 2942
                         v      iv- i  i   v      v   vi v  v      i i    v
  L1M4_orf2#LINE/    350 TGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_125300437_   2943 CTTCAGTA---GGTGGTGGGAATACTGAATATGCATATGCGAAAGAATAA 2989
                         i    ii ---    v     vv    i   ?v  i    i       i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_125300437_   2990 CAAAATTAGACTC--ATCTCTCATGATATTCAAAAATTATCAGAAAGTGG 3037
                         --- i  i   i -- i   v  iv    v         v vv   i   
  L1M4_orf2#LINE/    449 ---AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_125300437_   3038 ATTAAATCTTTAAATGTAAGATCTGAAACACTGAAACTACTGGAAGTAAA 3087
                           i ? vvii           v  i    vv i     vi i    v   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_125300437_   3088 TATAGGACAAAAGCGTC-------TGG---AG--AATTGTTTTCTGGATA 3125
                         i     ?vv   v v  -------   ---  --   v    ii i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_125300437_   3126 TATCCTCCAGAGCGCAAGAAAGAAAAGGAAAAATACGCAAATGAGAATTC 3175
                          iv vi v i   i    v  v     i       vii    vi  v   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_125300437_   3176 GTTAAACTGAGAGGCTTCTGCACAACAAAGGAAGCAATCAACAAAGTGAA 3225
                         i i   v v i ii   i  ii vv       vi v     v        
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_125300437_   3226 GAAACAGCCTACCATATGAGAGAAAATATTAG-AAACCATACATCTGACA 3274
                         i i   i  i  viv   i           v -   i    i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_125300437_   3275 CGGGTTTAATATATAAAATATATTTTAAAACCTCAAACAACTTAATAGCA 3324
                         v   vi vi   vi i       v--  i v   vv      i    ii 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATA--AAGAACTCTTACAACTCAATAATA 793

  chrX_125300437_   3325 AGAAGACAAACAACCCAATTGCTAAATGG-CATAAATACTTGGATAGACG 3373
                          i        i         ?vv      -  -  iv i   i      i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCA-AAGGATTTGAATAGACA 842

  chrX_125300437_   3374 TTTCTAAAAAGAAGACATACAAATTGTCAACAGGTGTATGAAAAAAATAC 3423
                              vv        i        v i   i i iii       i - i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGC 891

  chrX_125300437_   3424 TCAGAATTACAAATTGT 3440
                            iv  i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (138 / 103)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


3215 26.51 0.66 0.77  chrX_125319679_125324556     3477  4385 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125319679_   3477 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGGAAAT 3526
                              ii i  i     i      i v      v i     i  vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125319679_   3527 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3576
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125319679_   3577 TACCAATAACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3624
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_125319679_   3625 TATGGAACCAACAAAGAGCCC-GCATCGCCAAGTCAATCCTAAGCCAAAA 3673
                                vii-   i ii   - v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_125319679_   3674 GAACAAAGCCAAAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 3723
                                 iiii   vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_125319679_   3724 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 3773
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_125319679_   3774 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAAC 3821
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_125319679_   3822 TGTCTGATCTTTGACAAACCTGACAAAAACAATAAATGGGGAAAGGATTT 3871
                         iivi    i  i     ivv  v   i v  v v           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_125319679_   3872 CCTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAACGC 3921
                         i  v  i  i  i           v      v  ?   i   i i  viv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_125319679_   3922 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 3971
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_125319679_   3972 ATTAAACACTTACATGATAGACCTAAAACCATAAAAACCCTAGAAGAAAA 4021
                           i ? v  i  v   vv   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_125319679_   4022 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 4070
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_125319679_   4071 AAAACATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 4120
                          vi   i        vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_125319679_   4121 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 4170
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_125319679_   4171 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 4220
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_125319679_   4221 AAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAA 4270
                           i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_125319679_   4271 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 4320
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_125319679_   4321 TCTCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAAATTGCTC 4370
                             v        i  vi viii     v  i-          iv     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTC 893

  chrX_125319679_   4371 ACCATCACTGGCCAT 4385
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.30 (13 / 10)  


 413 28.63 4.84 5.24  chrX_125360160_125361916.rev        1   248 (1509)    L1M4_orf2#LINE/L1      383   629 (279)  

  chrX_125360160_      1 GGAGAACTGATAGTTTTTCAAAAAAATAA-GCAAAAAAAAAAAAAAACCC 49
                           i   vvi     i   iv  v    ii-  viii v  vvii v ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_125360160_     50 CACACACAAAACAAACAAAAATTGAACCTAGACTGAGGCCTTATACCTTT 99
                         -   ii     -i  ii  i-   i   i---  i---   i i   v v
  L1M4_orf2#LINE/    433 -ACATGCAAAA-GAATGAAG-TTGGACCC---CTA---CCTCACACCATA 473

  chrX_125360160_    100 CATGAAA-TTAACTCAAAAT-----ATAATTCTAAATTCAAATAC-AAAA 142
                         i ii   -            ----- ? ivi      vi  ivi -    
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_125360160_    143 TCATAAAACTTCTAGGAGAAAGCATAGGTGAGAATCTAT-TGACCTTTGA 191
                         ii        ii   i     i      ? vi     vi-       v i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_125360160_    192 TTAGACA-TGGTGTTTTTAGATACAATGCCAGAAGCATGATC--CATGAG 238
                             i  -    -  i       ii ii   i     ii v --  vi  
  L1M4_orf2#LINE/    574 TTAGGCAATGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_125360160_    239 TTTAAAAAAT 248
                         ---       
  L1M4_orf2#LINE/    623 ---AAAAAAT 629

Transitions / transversions = 2.58 (49 / 19)
Gap_init rate = 0.06 (14 / 247), avg. gap size = 1.79 (25 / 14)  

2361 27.47 0.39 1.17  chrX_125360160_125361916.rev      499  1266 (491)    L1M4_orf2#LINE/L1      147   908 (0)  

  chrX_125360160_    499 CACATGAAAACAAAAAGCAGCTTACATAGCCAAAGCAATACTAAACAAAA 548
                           i   i   iiv  i v v iviv         i    vi i  v  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_125360160_    549 AGAACAAATGTGGAGTCATCACATTACCTGACTTTGAACTATAATACAAG 598
                                 vv     vvv     i v  ii i  ii  viv  v     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_125360160_    599 GCTATAGTTACCAAAGCAGCATGGTACTGGTATAAAGGTAGGGACATAGA 648
                             i   v i   ii   ii         i    i i   iv i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_125360160_    649 CCAATGGAACAGAATAGAGAATCCAAAAATGAAGCCAAATAGTTATGGCC 698
                         i        i     v    i    i    i  v   v i v      i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_125360160_    699 AACTTATCTTAGACAAAG-TACACAAAAGTGTAAATTGGGGAAACAACAC 747
                           i v  i  v     i - i -   i vii vv v        v  i v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_125360160_    748 CCTATTCAACAAATAGGGTGCTGGAATAATTGGTAAGCCACACTTAGAAG 797
                         i  v          --        i i  i   vv ?     ivi i   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAAT--GGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_125360160_    798 AATGAAACCGGATCCTCTTCTCCCACCTTGTACAAAAATCAACTCGAGAG 847
                               iii   i  iivi   v    v i         i     i i v
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_125360160_    848 AGATCAAAGACTTAAATCTAAGACCTGAAACCATAAAAAATGTAAAAGAT 897
                         i     ?    i     v     v  i    i      vviv  i    v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_125360160_    898 AACATCAGAAAAACTCTTCTAGACATTGGCTTAGGCAAATAATTCATGAC 947
                              vi ?iv  v     vv   v    v        - ii  iv v v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAG 592

  chrX_125360160_    948 CAAGAACAC-AAAAGCAAATGCAACAAAAGCAAACATAAGTAAATGGTAC 996
                         vv vi    -       v v          v   v   ii     v v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_125360160_    997 ATAAATAAACTAAGAAACTTCTGAACAACAAAATAAATAACTAGCAGAGT 1046
                         v v vi   v v i      i  vi vv    iv v iv ii iv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_125360160_   1047 AGACAGACAACCCACAGAGTGGGAGAAAATATTTGCAAACTATGCATCCA 1096
                         ii v              i                    ii  ii   ii
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_125360160_   1097 ACAAAGGACTAATATCCAGAATCTGCAAGGAACTCAAACAAATTATTT-T 1145
                          i  i     vi          v ii  i      vv    v i v v- 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_125360160_   1146 AAAAAAACCCTCTTAATAATCCCATCAAAAAGTGGACAAGGGACATAAAT 1195
                              i  v-----     i  v  i?    i   i   i   iv i   
  L1M4_orf2#LINE/    793 AAAAAGACA-----AATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_125360160_   1196 AGACAATTCTCAAAAGAAGATACACAAATGGCAAATGTACATATGAGAAA 1245
                              v     v          i         v   ivi  i    i  i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_125360160_   1246 ATGCTCAACATCAATAATTAT 1266
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (117 / 90)
Gap_init rate = 0.01 (7 / 762), avg. gap size = 1.71 (12 / 7)  


3148 25.67 2.01 0.67  chrX_125363349_125366404.rev     1670  2565 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125363349_   1670 TGTAAAGATATTC-ATGTACATGGGTGGGAAGAGTTAGTATTATTAAAAT 1718
                           v        i -    v     i v      v   i    i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125363349_   1719 GTCCATACACCCCAAGT-GATCTCTAGATTCAATGTAATCCCTACCAGA- 1766
                          v v    v      i -     vi        i i        i  i -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125363349_   1767 TCCTAGTAGATTTTATTTTACAGAAATAGA-AAATGAAGCCCAAAATTCA 1815
                            i  iv vi   --   i       v  -  iivi v  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT--TTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_125363349_   1816 TATGGAACTACAAACACTCCA-AACAGCCAAAGAAAT-TAGGAGATGAGG 1863
                                v i   ivivi   -  i       iv   - v i i v  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_125363349_   1864 AACAAAGCCAGAGGCAGCATGCTTT--GATGTCAAAATATATTACAAAGC 1911
                                iii    vvv  ii   i--i  v      iv  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_125363349_   1912 TATGATAATTATAGCAATATTTCACTGACACAAAAACA--CATATGGAAT 1959
                           iii    i vii  i i vvi    i  i  ii i --     i  vi
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_125363349_   1960 AATGGAACAGAATATAAATCCCAGAAATAAACCTACTCACATAGGATTAA 2009
                                i     vv i vi             i iv  iv  v i i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_125363349_   2010 CTGACCTTTGACAATGGTGACAAGAACACAAAATAGAGAAAGTATAGTCT 2059
                         i   ii  i     v    v     v  ivv   i i     v       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_125363349_   2060 TTTCAA---ATATTGCTGGGATAGCTGGGTATCCACATAGAAAAGAATGA 2106
                               ---  iv        i i    i  ?      iv          
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_125363349_   2107 AATTGAACCATTATCTTACTCCATACATAAAAATCAACCCAGAATGTATT 2156
                          i   i   vi  i  i  v     i i      i   i  i    v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_125363349_   2157 AAAGAATTAAATGTAAGTCCTGAAACTGTAAAATTCCTAGTAGAAAACAT 2206
                          ?   vi          vv  i     i     i  i   v         
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_125363349_   2207 AAGAGAAGATCTTTGTGACATTGGTCTTGGCAATGATTTCTTGACCATGA 2256
                          i ? v i     i     v    vi v       i      iivi    
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_125363349_   2257 CACCAAAAATACAAGCAACAAAA-AAAAAATAGACAAGTGGGACTATATC 2305
                                 ii             -          i  i v     vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_125363349_   2306 AAT-TTAAAAAGCTTCTATGCAGCAAAGAATAAAATCAACAGAGTGAAAT 2354
                           v-       -   i i   vv     i i vv     v i       v
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_125363349_   2355 AGCAACCTATGAAAAGTGATAAAATATTTGTAAATTATATATATATATTA 2404
                         ii     i iii  v v  v          i    i      v i-  v 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG-ATAA 746

  chrX_125363349_   2405 AGGTTTTAATTTTTAAAATATTTTTTGAAACCCCTACAACTAAGTAGCTA 2454
                         i  vi  i- v ii i     v vvv   - i i       v i  iiv 
  L1M4_orf2#LINE/    747 GGGACTTG-TATCCAGAATATATAAAGAA-CTCTTACAACTCAATAATAA 794

  chrX_125363349_   2455 AAAAAC---TGACATGATTAAAACATGAATAAATAACTTAAATATACATT 2501
                            i  --- i  vii   ?   v   iii   vi i  i    v     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_125363349_   2502 TCTCCAATGAAGACATACAAATGGCCAATATATATATGAAAAGATGTTTA 2551
                                v     i                vii i           i i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_125363349_   2552 ACATTAATAACTAT 2565
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (144 / 82)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.41 (24 / 17)  


2881 25.26 6.90 0.70  chrX_125399404_125401446      698  1552 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125399404_    698 TAGGAAGATATCCCATGTTCATGGATTGAAAAGTCCA----TATTAA--- 740
                          i i                        i  iiiii ---- i    ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125399404_    741 -----------CCAAAGTGATTTACAGATTCAATGCAATCTCTATCAAAG 779
                         -----------     v    i           i      i        i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125399404_    780 TTCCAA-TGCCATTTCTTACAGAAATAGAAAAAACAATCCTAAAACTAAT 828
                          i   i-    -   i  i       v  v  ivii         i v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_125399404_    829 ATGGAACCACAAAA-ATCCACAAATAGCCAAAGTGATCCTCAGCAAAAAT 877
                               vii   ii- i   -i          iii   i v iv  i  v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_125399404_    878 AACAAAGCTAGAAGCATCGTACTATCTGATGTTAAAATTTACTACAAAGC 927
                                i i  i vv  ii   vi ii  v i    i            
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_125399404_    928 TACAGTAATCAAAATAGCATTGCACTGG---AAAAACATACACATGGAAC 974
                                     i i  ii v i     ---  ii i v   i  i  v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_125399404_    975 AATAGAACAAGATAAAGAGCTCAGAAGAAAACCCATAAATTTATAGCCAA 1024
                            i   i ii  vi    ii     iv         v      i i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_125399404_   1025 TTGATTTTTGAGAAAGAGGCCAAAAACACAGAATGGAGAAAGGACAGTCT 1074
                                 i  v  i iv     i v  ivv     i     i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_125399404_   1075 C--CAAAAACTGGTGTCAGGAAAACTGTATATCCATATGCAGAAGGATGA 1122
                         i--   v  v     iii   v     v   ?   i     i   i    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_125399404_   1123 ATTTGAATCTTTCTTTCATAACATAT------------------------ 1148
                          v   i i ii vii   i v     ------------------------
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_125399404_   1149 ---GACTTAAACATAAGACCTGAAACTCTAAAACTGCTAGAGGAAAACAT 1195
                         ---   i    ii     v  i     v       vi    i        
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_125399404_   1196 ACAGGAAAATTATCTTGACGTTGGTTTGGGCAAAGATTTTTTTTGGATAT 1245
                          vi? v    iv  v    v    v  i     v i   i  --i     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--AGATAT 596

  chrX_125399404_   1246 GACCCTGAAAGCACAAGCAATAAAAAGCAAAAATAGACAA-TGAAATTTT 1294
                            v ii             i    - v         i  - vii i  i
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTC 645

  chrX_125399404_   1295 ATCAGA-TGAAAAAGCTTCTTCACAGCAAAAGAAA--A--AACAGAGTGA 1339
                             i - v     -   i vii vv    i  v -- --  v i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_125399404_   1340 AAACACAACCCACATAGTAGAAGAAAATATTTGCAAGCCATACATCTGAT 1389
                            v          v i i i               ii    i       
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_125399404_   1390 AAGAGGTTAATATCCAAAATATATAAGGAACTCAAACGACTTAATAACAA 1439
                            i ii vi      i         i      vv  i   i     i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_125399404_   1440 GAAAACAAATAACCAGATCAGAAAACGAACAAAAAACCTGAAGAGACATG 1489
                         i  i          vi  i?i    i ii    ii ii    v      v
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_125399404_   1490 TATCATAATAAGACATGCAAATGATCCACAGGTTCATGAAAA-ATTCTCG 1538
                          v  vv  v    i  i      ii v i i iv        -  v   i
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_125399404_   1539 ATATAAGTAAACAT 1552
                          i  v ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.23 (147 / 66)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.82 (65 / 17)  


2772 25.45 1.69 3.49  chrX_125449305_125451686.rev     1004  1891 (491)    L1M4_orf2#LINE/L1       37   908 (0)  

  chrX_125449305_   1004 AATATTGTTAAAATGTCCATACTCCCCAAAGCAATCTACAAATTTAATGC 1053
                                    i   v v            vii       i   i  i  
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chrX_125449305_   1054 AATCCCTATCAAAATACCAATGACATTCTTCACAGAAATAGGAAACAAAA 1103
                                        v   iivi v  i  ii       v ---    iv
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGC 133

  chrX_125449305_   1104 AG-TTCTAAATTTTATATGGAACCACAAAAGACCCAGAATAGCTAAAGCT 1152
                         v - i     v  i        vii   ii             i   i v
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_125449305_   1153 ATTCCAAGCAAAAAGAATATAG---GAGTCACCTTACCTTTTATACCATA 1199
                           iiii iv  i     i v  ---   --iv  i  vi  i---   --
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAG--GACTCACACTTC---CCA-- 226

  chrX_125449305_   1200 CTATCACATTACCTGTTATATAAATTATACTACAGAGCTATAGTATCCAA 1249
                         -------   ----- i ---   i -       i     i    vi   
  L1M4_orf2#LINE/    227 -------ATT-----TCA---AAACT-TACTACAAAGCTACAGTAATCAA 260

  chrX_125449305_   1250 AATAACATGTTACTGGCATAAAAACAGACACACAGACAAATGAAACAGAA 1299
                         i i iii  v           ii i     i i   iv    i  i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_125449305_   1300 TAGATAACTCAGAAAGAAATCCACACACTTACAGAGAACTCATTTCTGAC 1349
                          v  v iii      v   i   i   i   ii vv  i v    ii   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_125449305_   1350 AAAGGTGTCAAGAATGTACACTGGGGAAAAGACAATCTCTTCAATAAATG 1399
                           i    i     vii v  v        ii i i   i     i     
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_125449305_   1400 GTGCTGGAATAACT--ACATCCATATGTAGAATAATGAAACTAGGCCCCT 1447
                                i i    -- i ?   i   i i  v      ii i i     
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_125449305_   1448 GTATCTCACTATACACAAAAAATCAAATAAAAATATATTAAAGACTTAAA 1497
                         iiv  v   i   i       - i  v v     iv  i ?    i    
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_125449305_   1498 TCTAAGGCCTCCAACAATGAAACTACTACAAGTAATCATTGGGGAAAATG 1547
                          v    iv  vv   v  i     vi  v   v  v   v  ? v    v
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_125449305_   1548 TCTAGGACATTGGTCTGGGCAA-AATTTCTTGAGCAATACCCCACAAGCA 1596
                          iiiv   v    vi i     -ii      iiii vv  v   v     
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_125449305_   1597 CAGATAACCAAAGCAAAAGTAGACAAATGTGATCACATCAAG-TTAAAAA 1645
                           iii   v    v    i    i    vv  iiv      i-       
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_125449305_   1646 CTTCTGCACATCTAAGGAAAGCATCGGTAAAGTGAAGAGACAACCCAAAG 1695
                            i  ii v  v     v vi   iiv        i          v  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_125449305_   1696 AATGAGAGAAAATATTTACAAA-CTTACCATCTCACAAGGGATTAATAAC 1744
                             i            i    - v  i-    v i      i vi  v 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGGGACTTGTATC 758

  chrX_125449305_   1745 CAGAATA----AGGAGTTCAAACAACTGTGTAGGGAAAAAAAATATAATA 1790
                                ---- i  ii  vv      vvi  iv--     i i -    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAAT--AAAAAGACA-AATA 805

  chrX_125449305_   1791 ATTCAATATAAAAA--GGCAAAAGATTTTAAGAGATACTTTTCAAAAGAA 1838
                          ii    v?     --      i     v  v   i i  i  v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_125449305_   1839 GACATGCAAATAGCAAATAGGCATATGAAAAGGTTCTCAACATCATTGAT 1888
                           i  i     i  v    i   i        i v          ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_125449305_   1889 CAT 1891
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.81 (143 / 79)
Gap_init rate = 0.02 (19 / 872), avg. gap size = 2.42 (46 / 19)  


2739 20.74 6.62 1.47  chrX_125461443_125465472     2334  3013 (1017)    L1M4_orf2#LINE/L1        5   719 (189)  

  chrX_125461443_   2334 AAGACATCCTGTGTTCATGTAT---AAGACTTGATATTGCTAAGCTGTCA 2380
                             i    ii        v  ---       i      i    v  v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_125461443_   2381 GTACTATACAAAGTATTCTAGAGATTCAGTACA-TGTCCACCAAAATTCC 2429
                         i    viv    v iv    v       iii  - vi i i      i  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_125461443_   2430 AGAAGCCTTTTTTCTACAGAATTGGAAAAGCTGAAAATTCTGAAATTCAT 2479
                           vv         --i     v v  v       --- i  i        
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTT--GCAGAAATTGACAAGCTGA---TCCTAAAATTCAT 149

  chrX_125461443_   2480 ATGGAATTGCAAGGGGCCC----TAACTTGAAAAACTAACTTTTAAAAAA 2525
                               v        i   ----  i i---     -  - i  i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCC---AAAAC-AA-TCTTGAAAAA 194

  chrX_125461443_   2526 GAA-----AAGTTGGAGGATCAACACTTCACAATTTCAAAACATTCTATA 2570
                            -----           iiv       v            v v   i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_125461443_   2571 AAACTATCATAATAAAGACAAT-----ACTTGCATAAGGATGTACATATA 2615
                           i   ivi    v      i -----   v          iv       
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_125461443_   2616 GACCAATGTAATAGAATTGAGATTCCAGAAATAAATCCATAAGTTCATGG 2665
                           i     v             v            i     vi  i    
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_125461443_   2666 CCAGTTGACTTTTTACAAGCATGTCAAGCACATTCAATGTGGAGATA-TG 2714
                         i  i    i   iv     vi  i    vv         v   i v - i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_125461443_   2715 GTTTCTTTAATAAATATTTCTGAGACAACTGAATATCCACATGCAACAGA 2764
                           i i  i  i    iv v   i        i   ?          v   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_125461443_   2765 TTTAAGTTGGACTACTACCTCGCAACATATACAATCCTTAAATGAAAGTG 2814
                         v v         iv       i  v         vvv    v v   i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_125461443_   2815 CATCAACATCTTAAATATAGGAACTAAAATCATAATACTCTTAGA----- 2859
                         v    ?viv i     i  i  i      ii    v         -----
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_125461443_   2860 -------------TTTTCATGATTTTGGATTTGGCAATATATTCTTAGAT 2896
                         ------------- i   i   ii    i  v      ivv         
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_125461443_   2897 ATGACACCAAAAGCATGAG-----AAATAAAAAATAAATAGATTAGAATC 2941
                                        ii  -----   v        i   i   i  v i
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_125461443_   2942 CAGCAAAATTAAAAACATTTTTGTCTTAAAGGACTTTATCAAGGAAGTAA 2991
                           v             v   v  ii i       vi       i    i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_125461443_   2992 AAAGAC---TTAAAGAATGAGAGAA 3013
                               ---ii v      i     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAA 719

Transitions / transversions = 1.40 (81 / 58)
Gap_init rate = 0.02 (14 / 715), avg. gap size = 3.93 (55 / 14)  

 799 20.45 2.73 0.91  chrX_125461443_125465472     3318  3537 (493)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_125461443_   3318 AAAAAAGAGAGAGAGAGAG---AGAGAATGGGAGAAAATATTTACAAACC 3364
                           i    v  i -   v i--- v                   i    i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_125461443_   3365 ATATATCTTATAAGTGTTCAATATCCACAATGTAGAAAGAACT---ACAA 3411
                                 v     v viivi      v   i  v        ---    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_125461443_   3412 CTCAACAACAACAAAAAGCAGGAACTGAACTTAAAAATGGGCAAAGGACT 3461
                              i  i  -   i vv iv   iv  i ?                i 
  L1M4_orf2#LINE/    784 CTCAATAATAA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_125461443_   3462 TAAATTGAACTCTTTCTAAATAATATATACAAATAATCACTAAGCACATG 3511
                          i   v  vv i i  i   v  v          iii  v          
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_125461443_   3512 AAAAGATACTCACCATCATTAGTCAT 3537
                                i    v     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (24 / 20)
Gap_init rate = 0.02 (4 / 224), avg. gap size = 2.00 (8 / 4)  


2933 23.09 4.09 3.76  chrX_125485834_125487908.rev      690  1594 (481)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125485834_    690 TGGAGAGATATTTCACTTACATGCATGGGAAGGTTCAACGTTTTCAAGAT 739
                             i      ii  iv v    v  v     ii i  ii  v i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125485834_    740 GTCAGCTCTTTTCAAATTGGTCTA--ATTTCAATGGAGTCTTAATAAAAA 787
                          v  iiv  iii       i    --iv     i v i  iiv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125485834_    788 CCCTGGTATGA-TTTTTAGTGGATATCAACAATCTGATTTTAAAGTTTAT 836
                         i  ii i-  v-     v ii  v  ii    v     ii    i  i  
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_125485834_    837 ATGGACAAT--AAAAGACCCAGAATAACCACTACAATATTGAAAGAGAA- 883
                              -   --  ii           i   vv     v      i    -
  L1M4_orf2#LINE/    150 ATGGA-AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_125485834_    884 --CAAATTCAGAGGACTGACACTACCTGACTTCATGCCTTACTATAAAGC 931
                         --    v ii       v     v  ii i    viv       i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_125485834_    932 TA--GTT-TCAAGAC--TGTGATTTTGGTGAAAGAATAGACAAATAGACC 976
                           --  v-       --    i vi   iiv   i       v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_125485834_    977 AACAGAACAGAATTGAAAGTCCATAAATAGACCCAAA----TATAATCAA 1022
                           ii   i        i      v     i     v ----   ii    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_125485834_   1023 GTGATCTTTGACAATGGAGGAAAAATGATTCAATAAGAAAAACGTAGTCT 1072
                         v    i  i     v  v vv  i iv       ii i   ivi      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_125485834_   1073 TTTCAACAA-TGGTGCTAAAAAGACTGGACATCCACATACAAAAAATATT 1121
                                  -       iii vi      i ?      i     i -  v
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-ATG 447

  chrX_125485834_   1122 AGTTCTAGACACAGATATTACACCTT-TACGTAA-TTAACTGAAGTGCCC 1169
                          iv - i   v vv iv i     v -   iv  -      ---------
  L1M4_orf2#LINE/    448 AAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACT--------- 487

  chrX_125485834_   1170 ACAAAAAATAAAAATGGGCCACGAGACCTAAACGCAAAACACAAAGCTGT 1219
                         -     --------   ii  ?-         i i  i vvi   i  i 
  L1M4_orf2#LINE/    488 -CAAAA--------TGGATCAW-AGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_125485834_   1220 AAAACTCCTAGAAGATAACA--GGTGAAAATCTCAGTAACCTTGGGCTTG 1267
                                i       v    --  ? v      iv  i        i v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_125485834_   1268 TCAATGATGTTTTAGATATAGCACAAAAAATGTGTTCCATGAAATAAATA 1317
                         v     i v i        ii   v    iiiiivv v ii   v   - 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA-A 626

  chrX_125485834_   1318 AATAGATAAATAGTTGGACTTTATTAAAATTAAAACCT---GCACTTCAA 1364
                                    ---       i  i          v  --- ii      
  L1M4_orf2#LINE/    627 AATAGATAAAT---TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_125485834_   1365 AAGGA----ATTAAGGTAATGAAAAGACAATCCACAGACTGTGAGAAAAC 1410
                          -   ----  i   iv i           i       v  v       i
  L1M4_orf2#LINE/    674 A-GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_125485834_   1411 TTTTGCAAAATATGTATCTGATAAAGAATTGGTAT--AGAA------AAG 1452
                         v        vi  i          i i i v    --    ------   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_125485834_   1453 ACCTCTTATAACTCAACAATAAGTAAACACAAAAAAGCCGACTAAAAGAG 1502
                          v      i       i     --   v     v  v  i i ?   i v
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAA--AAAGACAAATAACCCAATTWAAAAAT 820

  chrX_125485834_   1503 GGGCAAAAGATCTGAAAAGACATTTTACTAAAGAAGATAAACAGATGACC 1552
                                i   i    v        iv i          v   i   i  
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_125485834_   1553 AATGACCTTATGAAAAGATGCTCATGTGCCATTAGGGAATTG 1594
                            i v vi               ----v   i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCA----ACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (129 / 76)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.54 (71 / 28)  


2171 25.96 2.48 4.60  chrX_125502762_125504556      498  1302 (493)    L1M4_orf2#LINE/L1      121   908 (0)  

  chrX_125502762_    498 GAAATTAGAAAAAACT-ATTCTAAAATTCATATGGATCCAAAAGAGAGCC 546
                               i-- v  i  -  i                vviiv   i  v  
  L1M4_orf2#LINE/    121 GAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCC 168

  chrX_125502762_    547 TGAATATCCAGTGTAATCCTACACAAAAAGAATAAAGCTGGAGG-----C 591
                         v     v   ivii    i iv v  i     i    i      ----- 
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chrX_125502762_    592 ATTTACCCAATCT-AAAACTATACTATATGAACTTACCCAGCTTTATACT 640
                          i  -      i -      --------------------------    
  L1M4_orf2#LINE/    219 ACTT-CCCAATTTCAAAACT--------------------------TACT 241

  chrX_125502762_    641 ATAAGGCTAGAGTAACCAAAATAGCATGATACTGGTACAAAAACAGATAC 690
                          i  i    v     i   i i  ii  i      i i  ii i   i i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_125502762_    691 ATAAACCAATGGAACAGAATGGAGAACCCAGAAATAAAGCTACACACGTA 740
                            i i        i     v    ii           v i i   iv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_125502762_    741 CAACCATCTGATCTTTGACAAAGTCAACAAAAACTAGCAATGGGAAAAGA 790
                         iiii  vi    i  i     i viiv   i v vvv       i     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_125502762_    791 TCTCCCTATTCAATAAGTGATGCTAGGATAAGTGGCTAGCCATATGCAGA 840
                         vivvi  v     i  i  i    i   i  v   v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_125502762_    841 AGAATGAAACTGGACAGATATCATTCACCATAGACAAAAATCAACACAAG 890
                                 ii     vvv  i viv       v        i   v   i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_125502762_    891 ATGGATTAAAGATTTAAAGGTAAGCCCTCAAACTATAAAAATCCTAGACG 940
                               i ?   ii    v     vv  v           v  i    v 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_125502762_    941 CAAACCTAGG---AAATATGATTCTGAACATGGGCATTGGGAAAGAATTT 987
                         v    v    ---    v -- iv   v v    --  i  v  vii   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCT--TCGTGACCTTGGG--TTAGGCAATGGTTT 587

  chrX_125502762_    988 AT-GGCTAAGTCCTCAAAAGCA---GTTGCAAAGGAATAAAAATTGACAA 1033
                         v -i v  v v vi        --- ivi    i   --     v  i  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA--AAAATAGATAA 635

  chrX_125502762_   1034 GTGGGATCTAAATAAACTAAAGAGCTTCTGCACAGGAAAACAAAACATCA 1083
                         i v   ii v vi   v v  i i   i  ii vvv   iv v vi    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_125502762_   1084 ACAAAGTGAACAGACAACCTACATAATGGGAGACAATATTCACAAACTAT 1133
                          v        v        i   v         v      ii    ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_125502762_   1134 GCATCTGACAAATATCTAATATCCAGATCCTATGAGGAACT--TAACCAA 1181
                         ii      i  iviv  vi        viv   i i     --  --   
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAA 783

  chrX_125502762_   1182 TTCAATAAGGAAAAATGAAATGACCCCATTAAAAAGTAGGCAAAGAACAT 1231
                         i       vi    ivv    i    v   ?    i i       i iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_125502762_   1232 GAAAAGACACTTCTCAAAAGAAGTCATGCAA----CCAATAAAAATACTA 1277
                            v     i     v       vi  i   ----       iv i iv 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_125502762_   1278 ACAAATGCTCAACATCAATACTCAT 1302
                          v i             ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (120 / 86)
Gap_init rate = 0.02 (15 / 788), avg. gap size = 3.80 (57 / 15)  


2777 28.32 1.44 1.00  chrX_125529941_125537523     6187  7090 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125529941_   6187 TGGAAAAACATTCCATGTTCATGGATAGGAAAAACTGATATTGCAAAAAT 6236
                               i i  i              v    i vi i      iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125529941_   6237 AACCATATTGCCCAAAGTAATTTATACATTCAATGCTATTCCCATTAAAC 6286
                         ii v   i v      v i  i  i v      i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125529941_   6287 TACCATTAACATTCTTCACAGAATTAGAAAAAAAGCCAATG-TGGAATTC 6335
                          v   vivi v  i  ii     v v  v  ---  ii  v- ii     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA---GCTGATCCTAAAATTC 147

  chrX_125529941_   6336 ATGTAGAACCAAAAAGGAGCATGAATAGCCAAGACAATCCTAAGCAGAAA 6385
                           i i   viiv  i   v vv          i      i i iv ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_125529941_   6386 GAACAAAGCTGGAGACATCATGCTATCCAATTTCTAACTATACTACAAGG 6435
                                 i     ivv   ii  vi        v  viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_125529941_   6436 CTACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGACACATAGAC 6485
                                  i   i    ii  i      i iv ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_125529941_   6486 AAATGGAACCGAATAGAGAAGTCAGAAATAAGATTGCATGTCTACAACCA 6535
                         v       iv    v    ivi         iviiii ii i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_125529941_   6536 TCTGATCTTCAATAAACCTGACAAAAACAAGCAATGAGGAAAGGATTTCC 6585
                         vi    i   i i  ivv  v   i v  vv     i      i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_125529941_   6586 TATTTAATAAGTGGTGGTTGGAGTGCTGGCTAGCCATATGCAGAAAATTG 6635
                          v  i  i  i     v v   vvi    v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_125529941_   6636 AAGTTGGACTGCTTCCTTACACCTCCTACAAAAATTAACTCAAGATGGAT 6685
                                  iv  v   i     viv                 i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_125529941_   6686 TAAAGACTTTAATGTAAAACCCAAAACTATAAAAACCCTAGATGAAAAAT 6735
                         i ?    i v       i v i            vi i    v     -i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-C 546

  chrX_125529941_   6736 CTAGGCAATACAAT--TGAGGACATAGGCACAGGCAAAGATTTCATGAGG 6783
                         v    ?i-  -   -- viv   v v  vvi      v i    v iiiv
  L1M4_orf2#LINE/    547 ATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_125529941_   6784 AAAATGCCAAAA--ACAATTGCAATAAAAGCCAAACTTGACAAATGGGGT 6831
                          vi ii      --    --    i     vv   v v  i    v  ii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_125529941_   6832 CTCATTAAACTAAAGAGCTTCTGCACAGCAAAGGAAGCTATCATCAGAGT 6881
                         i    i   v v  i i   i  ii vv       vi      vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_125529941_   6882 GAGCAGACAACCTGAATAATGGGAGAAAGTTTTTGTAAACCTATCCATCT 6931
                           iv        iiv v           i v    i   i -  vi    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCT 741

  chrX_125529941_   6932 GTAAAAGGTCTAATATCCAG--TCTACCAGAAACT--TA-AATTTA-CAA 6975
                          vv  i  v  vi       -- v  iv ii    --  -  i i -i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_125529941_   6976 GAAAAAAGCAAACAACCCCATTAAAAGTTGGGTAAAGAACATGAATAGAC 7025
                         v     ii    i     v   ?   iv    i    i iv         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_125529941_   7026 ACCTCTCAAAAAAATACATACATGTGGCCAACAA--ACATGAAAAAAAGC 7073
                          ii    v   i  v i     vi       i  --         i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_125529941_   7074 TCAACATCACTGATCAT 7090
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (151 / 101)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.57 (22 / 14)  


2979 27.43 0.55 0.11  chrX_125632334_125636337     2608  3511 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125632334_   2608 TGGAAACACTTCTCATGCTCATGGGTAGGTAGAATCAATATTGTAAAAAT 2657
                               v iv  i    i      i v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125632334_   2658 GACCATA-TGCCAAAAGGAATCTACAAATTCAATGCAATTTCCATCAAAA 2706
                          i v   - v  v   vvi       i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125632334_   2707 TACTGTCATCGTTCTTCACAGAACTAAAAAAGACAATCCTAAAATTCTTG 2756
                          v iiv vv v  i  ii     v vi v   vii            v i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_125632334_   2757 TGGAACCAAAAACAAGCCTGTATAGCCAAACTACGGCTAAGCAAAAAGAA 2806
                              viiv  ivi v  v v         vi vvvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_125632334_   2807 CAAATGTGGAGGCATCACATTACCTGACTTCAAACTATACTATAAGGCCA 2856
                             vv      vv     i v  ii i      viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_125632334_   2857 TAGTCACCAAAACAGCATGGTACTGGTATAACAATAGGCACATAGACCAA 2906
                         i   v i   i    ii         i    vi    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_125632334_   2907 TGGAACAGAATAGAGAACCCAGAAATAAAGCAAAATACTTAGGGCCAACT 2956
                              i     v    ii           v v v i i   v  i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_125632334_   2957 GATCTTTGTCAAAGCAAACAAAAACATAAAGTAGAGAAAGAATACTGTAT 3006
                            i  i v   i vviv   i v   vv i i i         v v v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_125632334_   3007 TCAACAAATGGTGATGGGATAATTGGCAAGCCACATGTAGAAGAATAAAA 3056
                                      v     i  i   vv ?       i i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_125632334_   3057 CTGGATCCTCGTTTCTCACCTTATACAAAAATCAACACAAGATGGATCAA 3106
                         i    i  iiiii  v    v           i   v   i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_125632334_   3107 AGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACATTG 3156
                             i     v     v  i    i      v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_125632334_   3157 AAAAAACCCTTCTAGACAAAGGTTTAGGCAAAGAATTCATATCCAAGTAC 3206
                         i?iv  vi    vv   vvv  v        v iv   v  vvi v -  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG-AC 599

  chrX_125632334_   3207 -CCAAAAACAAATGCAACAAAAAAAATAATAAATAGGTGTGACTTAATTA 3255
                         -      i  v v         i   v    i   ii vv     v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_125632334_   3256 AA-CTAAAAGTTTCTGTACATCAAAAGAAACAATCAGTGGAGTAAACAGA 3304
                           -i     ii  i   i v     i  v  v    ivii   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_125632334_   3305 AAACCCACAGAGTGAGAGAAAATGTTCACAATCTATACATCCAATAATGG 3354
                         v          i  i        i  ii   vii   i   ii    v  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_125632334_   3355 ACTAAAATCCAGAATCTACAAGGAACTCAAACAAATTAGCAAGAAAAGGA 3404
                            viv         v  i  i      vv    v i ii  v    i  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_125632334_   3405 --AACAAGCTCATCAAAAACTGGGCTAAGGACAGGAACAGACAATTCTCA 3452
                         --  i  v iv  i?    v     v     ivv   i     v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_125632334_   3453 AAAGAAGATATACAAATTGCCAACAAATATATGAAAGAATGCTCAACATC 3502
                                          v     i  ii i      ii            
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_125632334_   3503 ACTAATGAT 3511
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.20 (133 / 111)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


3053 27.90 1.45 0.11  chrX_125667993_125671926.rev     2548  3443 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125667993_   2548 TGAAAAAATATTCTATGTTCATAAATTGGAAGAATAAATATTGTTAAAAT 2597
                           i   i    i i        ii         v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125667993_   2598 ATTCATACGTCTCAAAGGAATCTACAGAGTCAATGTAATTTTTATTAAAA 2647
                         iviv    vi i    vvi         v    i i   iii   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125667993_   2648 TATTAATGACATTCTTCACAGAAAT--A-AAGC-AATCCTAAAATTTAGA 2693
                          vii iivi v  i  ii       -- -    -i           i v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_125667993_   2694 TGCAACCACAAAAGACACAGA-TAACCAAAGCTATACTGAGCAGAAAGTA 2742
                           v  vii   ii   v    -  i     i v  vi   iv ii   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_125667993_   2743 CAAAACTGGAAGAATTATGGTACCTGATCTCAAA-TTGACCTACAGAGTT 2791
                             ii    i  v i iiv v  ii  i     -i v  -    i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC-TACAAAGCT 249

  chrX_125667993_   2792 ATAGTAACCAAAACAACATGGTACTCA-ATAAAAATAGACACATAGACTA 2840
                          i     i   i   iii       vi-    ii       i     ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_125667993_   2841 ATGGAAAAGGATAGATAACTCAGAAACATATCCAGACATCTGCAGTGAGC 2890
                               v  i  v  v iii      i v i   v    i iii  v ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_125667993_   2891 TCATTTTTGACAAAGATGTCAAAAACATACGTTGGGAAAAGGACAGTCTT 2940
                          v     i     i i  i   i v   v iv    i    i i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_125667993_   2941 TT-AATAAATG---CTAAGAAAATTGGATGTCTTTAGGTGGAAGAATGAA 2986
                           -  i     ---  ii  v  i     i? ivi v iii         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_125667993_   2987 AGTAGATTCTTATCTTTCACCAGATACAAAAATCAAATCAAAATGAATTA 3036
                         iv i  ii i  i  iv     v          i  v        i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_125667993_   3037 AAGACTTAAATATTAGCACTCCAACTATGAAAGTTCTA-AGGGTAACACT 3085
                         ?    i     i v  vi  vv      i   v ii  - i iv    iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_125667993_   3086 GGGGTAACTGTCCAAGACATCGGACTTGGAAAAGATTTCTTGAGTAATAC 3135
                           ?    v v i iv   v i  ii v  v  v i      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_125667993_   3136 ATCAAAAGCACAGTCAACAAAAAAAGAAATAAACAAATGGGACTACTTCA 3185
                          i          iv        i  i     i i    v     v v   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_125667993_   3186 GGATAAAAATCTTTTGGACAGCAAAGGATATAACCAACAAAGTAAAGAGG 3235
                         ii  v    v      vi vv       i iv i   v     i  i  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_125667993_   3236 CAACCCACAGAATGGGAGAAAATATTTACAAACTATCCATCTGACAAAGG 3285
                                                    i    ii  vi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_125667993_   3286 ATTAATAAGCAGAATATATAAGGAGCTCAAACAACTCCATAGGAAGAAAT 3335
                          i vi  vv            i  i   vv       v   iv  i  iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_125667993_   3336 CTAATAGTACAATT-AAAAATGAGGAAAAGATCTGAATAGATATGTCTCA 3384
                          v    iiv     -       i v   i   i        i  v    v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_125667993_   3385 GAAGAAGAAATACAAATGGCAAACAGATGTAAGAAAAGATGCTCAACATC 3434
                         i       v           v  i iiiii v                  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_125667993_   3435 ATTGATCAT 3443
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.91 (162 / 85)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


2838 27.83 2.83 0.45  chrX_125697384_125701843     3084  3967 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_125697384_   3084 AAAAAAATC--ATTTTTATGAATTGGAAAGATCAATGTTGTTCAACATA- 3130
                            i v   --  v  i   i       iiv i   i     -  v  i-
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAGATGG 52

  chrX_125697384_   3131 CA-TACTATCCAAAGCAGTCTACAGATTCAATAAAATCCCTATCAAAATA 3179
                           -    vi     viii             iiv               v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_125697384_   3180 CAAATTACATTCTTCATAAAAACAGAGAAAGCAATTCTAAAATTTATATG 3229
                          v ii i v  i  iii i   iv  v  ivii  i        i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_125697384_   3230 GAGACACAAAAGACCTAGAATAACCAAAGCAATCCTAAGCAAAAAGAACA 3279
                           i ii   ii    i      i     i     i i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_125697384_   3280 AAATGGGAGGAATTATATTACCTGACTTCAAATTGTACTACAGAGCCATA 3329
                           i v      v i i i v  ii i      viv       i   i i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_125697384_   3330 GTCACCACAAGAGCATGGTGCTGGCATAAA-ACAGACACATAGGTAAATG 3378
                           v i  vi v  ii    i         i- i     i    i v    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_125697384_   3379 GAACAAAATATATAACCCAGAAAGAAATCCACTTCCCTAAAGTGAACTCA 3428
                            i i   vv v ii       v   i   ivivii  vi  v  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_125697384_   3429 TTTTTGATAAAGGTGCCAAGGACGCACACTGGGGGGAAGGGCAATCTCTT 3478
                             i  i  i         iv iiv  v     i-   iii i   i  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATAGTCTTTT 401

  chrX_125697384_   3479 CAATAAATGGTGCTGGGAAAACTGGATATTCATATGCAGAAGGATGAACT 3528
                            i              v         ?i  i     i   i     v 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_125697384_   3529 TTG--------------CCATATGGAAAAACTAAACTAAAATGGATTAAA 3564
                          v --------------      iv     i   vii         i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_125697384_   3565 GGCTTAAATATAGGCCCTCAAACCATGAAATTACTACAAGAAAACATTAA 3614
                          i i     i  i vv  v    i  i   i vi  v          - i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AG 550

  chrX_125697384_   3615 GAA-AAATCTTCAGGACATTGGTCTGGGCAAAAACTTATTGAGCAATACC 3663
                          ?i-        iv   v    vi i     viii  v  iiii vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_125697384_   3664 CCACAAGTGCAGACAATGAAAACAAAAATGAAGAAATGGGATTGCATCAA 3713
                            v   ii  ii   ii   iv      ii v    v   i v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_125697384_   3714 G-TTAAAGAGTTTCTGAACAGAAAAGGATACAATCAAAA---T-AAAGGA 3758
                         i-     i v   -  vi vvv      i  v     i --- -   i  
  L1M4_orf2#LINE/    651 AATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_125697384_   3759 TAACCTACAGAATGGGAGAAAATGTTTGCAAACTACCCATCTGACAAAGG 3808
                         i    i                 i        ii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_125697384_   3809 ATTAATAACCAGAATATATAAGGAGCACAAACAACCCTATAGGAAAAAAT 3858
                          i vi  v             i  i v vv     i v   iv     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_125697384_   3859 CTAATAATCTGATCTAAAGATGGCCCAAAGATTTGAATAGTCATTTCTAA 3908
                          v     i ii  i?   i    v v  i           v       vv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_125697384_   3909 AAAGAAGACATACAAAAAACAAACAGACATAAGAAAAGGTGATCAACATC 3958
                                 i       vii v  i ii  i v      i  v        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_125697384_   3959 AATGATCAT 3967
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.92 (159 / 83)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 2.23 (29 / 13)  


2933 25.14 3.27 1.01  chrX_125711129_125715117.rev     2612  3498 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_125711129_   2612 GGAAAAATA----ATATTTCCATGCATTGGAAGAAGTTATATTGTTAATA 2657
                              i   ----  i  --    v         vv v          v 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTT--CATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_125711129_   2658 TGTCCGTACTACCCAAAGCAATCTAGAGACTCAATGTACTGCTTATCAAA 2707
                           v vi    v      vii     v   i    i i v v i       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_125711129_   2708 ATATCAATGACATTATTCACAGAAATAGAAAA----AAC---AAATTAAT 2750
                           vi  iivi v  v  ii       v  v  ---- v ---     v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_125711129_   2751 ATGAAACCAAAAAAAGACCCAGAATAGTCAAAGTTATCCTAAGCAAAATG 2800
                            i  viiv  ii-            i    iiv   i i iv  i v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_125711129_   2801 AACAAAACTGGATGAATCACATTACCTGACTTGAAATTATACTA-AGAGG 2849
                               ii    v  v     i v  ii i  v   viv     - i  v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_125711129_   2850 TATAGTTACCACAACAGCATGGTACTGGCATGAAAACAGACACATAAACC 2899
                           i   v i  vi    ii            i ii i     i   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_125711129_   2900 AATGGAACAGAA--GAGAGTACCCAGAAACAAATCCACACACTTGCAGTG 2947
                                i    --      --       i   i   i   i  iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGT--CCAGAAATAAACCCATACATTTATGGTC 346

  chrX_125711129_   2948 AACTCACTTTCCACAAAGGTGCCAAGAACACACACTGAGGAAA--ATAGT 2995
                           i v i    v    i          v  iv  v  i     --     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_125711129_   2996 GTCTCTTCAATAAATGGTGCTGGAAAAACTAAATATCCATATACAGAAGA 3045
                         --  i     i            i v    ii   ?   i  i  i    
  L1M4_orf2#LINE/    397 --CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_125711129_   3046 ATGAAACTAGGCCCCTATCTATCACTATATATAAAA-TTAAATCAAAATG 3094
                              ii i i      i  vv   i     i    -    v        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_125711129_   3095 GATTAAAGACTTCAATCTAAGACCTCAAACTATGAATCTACTACAAGAAA 3144
                            i ?    i v   v     v  v       i  v  vi  v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_125711129_   3145 ACATTAGGGAAAATATCCAGGAAATTGGCCTGGGCAATGATATCTTAAGC 3194
                             vi ? v    v i iv  vv    vi i       i v     iii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_125711129_   3195 AGTACCCCACAAGGGCAGGCAACCAAAACAAAAATGGACAAATCA-ATCA 3243
                          vv  v   v   vi  i     v   iv      i  i    ii- iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_125711129_   3244 CATCAAT-TTAGAAAGCTTCTGTACAGCAAATGCTATGATCAATAAAGTG 3292
                               v-   i   -   i   i vv    v vi iv     v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_125711129_   3293 AAGAGACAACCCACAACATGAGATAAAATATTTGCAAACTATACCTTTGA 3342
                           i            iv   i  v              ii   iv i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_125711129_   3343 CAAGCAATTAATAACCAGAATATATAAGGAGCTCAAACAACTCCATAG-A 3391
                         i   vi i vi  v             i  i   vv       v   i- 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_125711129_   3392 AAAGTATCTAATAATTCAGTCAAAAAATGGTCAACG-ATTTGAATAGACA 3440
                            iv - v     ii  i i?        v   v -             
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_125711129_   3441 TTGCTCAAAAGAAGACA--------GCACACAGGCATATGAAAATGTGCT 3482
                           v   v        i --------  vv i i   i       vi    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_125711129_   3483 CAACATTATTGATTAT 3498
                               i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (127 / 92)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 2.11 (38 / 18)  


3034 25.93 2.27 0.91  chrX_125716815_125721064     2875  3757 (493)    L1M4_orf2#LINE/L1       14   908 (0)  

  chrX_125716815_   2875 CATGTTCATGTAGTGGAAGAATCAATATTGT-AAAAGGCCCATACTAGTC 2923
                                   v v       v i        -  i v v v     vvi 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chrX_125716815_   2924 AAAGCAATCTACAGATTCAATGCAATCCCTATCAACATACTAATTATATT 2973
                            vii              i              v  v i ii iiv  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chrX_125716815_   2974 ATTCACAAAACTAGAAAAAAACT-ATCCTAAAATTTGTATGGAATCACAA 3022
                         v  ii  i  v v  v  i--  -           ii       vii   
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_125716815_   3023 AAGACCCAGAATAGCCAGAGCTACCTTTAGTAAAAAGAACGAAACTTTAG 3072
                         ii               i i v i   v iv  i      i  ii vv  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_125716815_   3073 GATTCACATTACCTAACTTTAAATCATACTTCAGAGCTTTAGTAACCAAA 3122
                           i     i v  i  i  i   v v    v  i    vi     i   i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_125716815_   3123 ACAGCATGGTACTGGCATAAAAAAAGATTCATAGACCAATGGAACAGAGT 3172
                             ii              ii v   ivi     i        i   i 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_125716815_   3173 AGAGAACCCAGTAACAATTCCACGTACTTATAGCAAACTCATTTTCGACA 3222
                         v    ii    v  i  vi   iii i    i iv  i v          
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_125716815_   3223 AAGATGCCAAAA--ATTTACATTAGGAAAAAGACAGTCTCTTCAATAAAT 3270
                          i i      i --   --  v i  i   ii i     i     i    
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATT--CAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_125716815_   3271 GGTCCTGGGAAAACTGAACATCCATATGCAGAAGTATTAAACTAGACACC 3320
                            v      v     i i ?   i     i   v  v  ii i   v  
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_125716815_   3321 TGTCTTTTGCCATAT-CAAAAA---------AATGGATTA-AGACTTAAA 3359
                          ii  ivii      -      ---------       i -    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_125716815_   3360 TCTAAGACCTCAAACTATGAATCTTCTATAAGAAAACATTGGGGGAAATT 3409
                          v     v  v       i  v  ii  v          v  ? v    i
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_125716815_   3410 TCCAGGACATTGAACTGTGCAAAAATCTCTTGAGA-ACTAC-CCAGGAAG 3457
                          i iv   v   iii iv    vii i    -   - iv  -   i-   
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAA-AAG 607

  chrX_125716815_   3458 CACAGGCAACCAAAGCAAAATTAGAAAAATGAGATCACGTTGAG-TTAGA 3506
                             i     v    v    v    v    vi  iiv i ii i-   i 
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_125716815_   3507 AAGCTTCTGCACAGCAAAGGGTACAATCAACAAAGCAAAGAGACAACCCA 3556
                           -   i  ii vv      ii  v     v    ii  i          
  L1M4_orf2#LINE/    658 AA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_125716815_   3557 CAGAATGGGAAAAAATATTTTCAAACTATCCACCTGGCAAGGCATTAATA 3606
                                   i         v    ii  vi i   ii    v i vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_125716815_   3607 ACTGGAATGTAGAATAAGCTAAAAAAATTCAATAGGAAATAATCAAATAA 3656
                         v ii    i  v  vi i  vvv v  i      iv   v iv       
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_125716815_   3657 TATGATC-AAAAATTGGCACAAAATTTGAATACACATTTCTCAAAAAAAG 3705
                         ivii  i-      v    v ii         v         v   i   
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_125716815_   3706 ATACACAAATGGC-AGTCAGGCATATAAAAAGGTGCTCAACATTATGGAT 3754
                            i         - i - i   i  i     i          i ?????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAAT-AAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_125716815_   3755 CAC 3757
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.77 (145 / 82)
Gap_init rate = 0.02 (17 / 895), avg. gap size = 1.65 (28 / 17)  


 485 29.56 0.63 1.26  chrX_125731062_125735747.rev     2886  3044 (1642)    L1M4_orf2#LINE/L1        1   158 (750)  

  chrX_125731062_   2886 TGGAAACACATCCCATGCTCATGG-TTGGATAGAATCGATATTGCAAAAA 2934
                               v i        i      -     -   v ii      iv  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGA-AGACTTAATATTGTTAAGA 49

  chrX_125731062_   2935 TGACCATTCTGCCAAAAGGACCCTACAGATTTGATGCAATTCCCATCGAA 2984
                           i v  v  v  v   vvivi         ii i     i  i   i  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_125731062_   2985 GTATTATCATCTTTCTTCACAGAACTAGAAAAAACAATCTTAAAACTTAT 3034
                         i vii v vv i  i  ii     v v  v  ivii   i     i i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_125731062_   3035 ATGTGATATG 3044
                            -  v   
  L1M4_orf2#LINE/    150 ATG-GAAATG 158

Transitions / transversions = 1.47 (28 / 19)
Gap_init rate = 0.02 (3 / 158), avg. gap size = 1.00 (3 / 3)  

2157 26.97 2.22 3.82  chrX_125731062_125735747.rev     3384  4195 (491)    L1M4_orf2#LINE/L1      110   908 (0)  

  chrX_125731062_   3384 CCTTTTTAGCAGCA--TGAGAA--TGGACT---AATACAATATGGAAC-- 3424
                                v    v --   v  --  iv i---   v  -       v--
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA-TATGGAAATG 158

  chrX_125731062_   3425 CAAAAAATAGCTCAGA-TAGCCAAAGCAAGACTT-AGTAAGAAGAATAAA 3472
                            iii --- i    -        i   v-   - iv        i   
  L1M4_orf2#LINE/    159 CAAGGGA---CCCAGAATAGCCAAAACAAT-CTTGAAAAAGAAGAACAAA 204

  chrX_125731062_   3473 TCTGGAGGCATCACATTACCTGACGTCAAGCTATACTACAAGGCTGTATT 3522
                         vi      vv     i v  ii iv    iviv        i   ii v 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_125731062_   3523 TACCAAAACGGCATAGTACTGATATAAAAATAGGTGCATAGACCAATGTA 3572
                         v i   i  i ii i      ii    ii    iiii     i     v 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_125731062_   3573 ACAGAATAGAGAACCCAAAAATAAAATGAAATAGTTATAGCCAACTGATC 3622
                          i     v    ii   i       viv v i v    i i   i    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_125731062_   3623 TTTGACAAAGCATAC-AAAAC-ATAAAGTGGGAAAATGACACCCTATTCA 3670
                           i     i -i i -  i  -  vv i    i   vi i vi  v    
  L1M4_orf2#LINE/    355 TTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_125731062_   3671 ATAAATGTTGCTGGTATAATTGGCAT-GCCACATGTAGAAGAATGAAACT 3719
                          i     v      v i  i   -  -?       i i         ii 
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGG-ATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_125731062_   3720 GGATCCTCATCACTCACTTTATGAAAAAATCAACTGAAGATGGATCAAAT 3769
                            i  ii i v v   iv   iv      i    v  i        ? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_125731062_   3770 ACTTAAATCTAAGACCTGAAATTCTAAAAATTATAGAAGATAACATTAGA 3819
                           i     v     v  i   i v     v iv       v     vi ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_125731062_   3820 AAAACTCTTCTAGATGTTGACTTAGGCAAATATTTTGTGACCAAAAACCC 3869
                         iv  v     vv  iv   iv        vvi   iv iivi vi vv  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_125731062_   3870 AAAAGCAAATGCAACGAAAACAAAAATAAACAGATGGGACCTAATTAAAC 3919
                                v v     i   iv       i i i  v    i v  -----
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT----- 647

  chrX_125731062_   3920 TAAACAATAACAACAAAACTTAAAACAAGAGCTTCTGCACAGCAAAAGAA 3969
                         -------------     -      -----i   i  ii vv    i  v
  L1M4_orf2#LINE/    648 -------------CAAAA-TTAAAA-----ACTTTTGTGCTTCAAAGGAC 678

  chrX_125731062_   3970 ATAATCAGCAGAGTAAACAGACATCCCACAGAATGG-AGAAAATATTCAC 4018
                          iv    iv i   i  v     v            -          ii 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_125731062_   4019 AAACTGTGCATTCAACAGAGGACTCATATCCAGAATTTAAAAGGAACTCA 4068
                            iii ii  iii i ii     ii          v  v  i      v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_125731062_   4069 AACAAATCAGCAAGAAAGAAACAGATAATCTCATCAAAAAGGAGGCAAAC 4118
                         v    v   ii  v   i i   i    i iv  i?    ivi      v
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_125731062_   4119 GACATGCATAGACAATTCTC---AGAAGATATACAAATGGTCAACAAACA 4165
                           iv  v       v     ---                 i   i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_125731062_   4166 TACAGTAAAATACTCAACATCACTAATCAT 4195
                         i iiiv  i  i          ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (134 / 81)
Gap_init rate = 0.02 (19 / 799), avg. gap size = 2.58 (49 / 19)  


2352 31.27 1.44 1.10  chrX_125760511_125765897     3990  4894 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125760511_   3990 TGGAAAAATGTTCCATACTCGTGTATAGGAAGAAACAATATTATTAAAAT 4039
                               i  i i    ii  i  v  v      vvi      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125760511_   4040 GGCCTTCCTGCTCAAAGCAATGTATAGGTTCAATGCTATTTCTATCAACG 4089
                            vv v  v i    vii  v  i  i     i  v  ii       vi
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125760511_   4090 TATCAA-TGATATCTTCACAGAACTGGAAAAAAAAACT-ATTTTAAAATT 4137
                          vi  i-  viv i  ii     v v  v  i----  -  ii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chrX_125760511_   4138 CATACGGAA---CCAAAAAGCCAGAAGAGCCAGGGAAATCCCATGCAAAA 4184
                             i    --- v iii v      v     iiiv    iiiviv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_125760511_   4185 AGAACAACACTGAAGACATTAGGCTACCCAACTTCAAA--CTATAATAAA 4232
                                vii  i  ivv i vi  v     i      --i  iv i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_125760511_   4233 TGAATATAGCAACCAAAACAGCATGGTACTGGTACGAAAACAAACACGTA 4282
                         --iv  i  i  i   i    ii         i ii ii i i   ii  
  L1M4_orf2#LINE/    247 --GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_125760511_   4283 GACCGAAGGAACAGAATAAAGAACTTATAAACAAGACTGCACACCTACAA 4332
                           i i v    i     vi   iiii v   i  iv iii   ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_125760511_   4333 CTGTCTGATCTTTGATAAAGTTTACAAAAGCAAGCAATGGGAAAATAATT 4382
                         iiivi    i  i  i  i v vv   i v  vv       i   v   v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_125760511_   4383 CCCTGTTCAATAAATAGTGCTGGGATAACTGGATAGTCACTTGCAGAAGA 4432
                         vi  v     i    i         i         ?i   v    i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_125760511_   4433 TTGAAAACTAGACCCCTTTTTTATATCATATACAAAATCTGCCT-GAAAT 4481
                         v    i-i i       vii i i i           vi iv  -i    
  L1M4_orf2#LINE/    445 ATGAAG-TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_125760511_   4482 GGATTAAAGACTTAAATGTAAAACTCGGAACTATAAAAACCATGGAAGAT 4531
                             i ?    i         i viiii          vi v i     v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_125760511_   4532 TACCTAGGCAATATTATTCTGGACATAGGAACAGACAAAGATTTCATGAC 4581
                         v  v    ?ivv v v   vv   v v  ivi  i   v i    v iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_125760511_   4582 GAAGATACCAAAAGCAATTGCAAAAAAAGTAAAAAATTGACAAATGGGAT 4631
                         v v  i          vvv    v     -       v  i    v   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGAC 642

  chrX_125760511_   4632 CTAATTATACTGAAGAGCTTCTGCACAGAAAAACAAACTATCAACAGAGT 4681
                         i v  i v v v  i i   i  ii vvv   iv v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_125760511_   4682 AAGCACACAACATACAGAATGAGAGAAAATGTTTGCAAACTATGCATCTG 4731
                         i iv v     vi        i        i        ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_125760511_   4732 ACAACGGTCTAATATCTAGCATCTATAAGGCACTTAAACAAATGTACAAG 4781
                          i  v  v  vi    i  v  v     i v   ivv    v vv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_125760511_   4782 AAGAAAAACAAGCAACCTA-TTAAAAACTGGACAAAGGAC----ATCGAC 4826
                           -   i    ii    i -  ?    v   i       i----  v   
  L1M4_orf2#LINE/    793 AA-AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_125760511_   4827 ACTTTTTTAAAAGAAGACATACATGTAGCCAAAAGGCATACGGTGAGAAA 4876
                          -   i iv        i     vi i     v i   i i ivi   vi
  L1M4_orf2#LINE/    842 A-TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_125760511_   4877 CTCAACATCACTGATCAT 4894
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (170 / 109)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.77 (23 / 13)  


2758 27.74 0.88 1.32  chrX_125766135_125770050     2512  3423 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125766135_   2512 TGAAAACACATTCCATGTTCATGAATAGGAAGAATCAGTATTGTAAAAAT 2561
                           i   v i  i           i  v      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125766135_   2562 GGCCATACTGCCCAAAGCAATTTATAAATTCAATGTTATTCCCATTAAAT 2611
                            v     v      vii  i  i i      i iv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125766135_   2612 TACCATTGAGGTTCTTCACAGAATTATAAAAAACT-ATTTTAAAATTTAT 2660
                          v   vivivv  i  ii     v - i v  i  -  ii       i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_125766135_   2661 ATGAAACCAAAAAAGACCCCAAACAGCCAAGACTATCATAAGCAAAAGAA 2710
                            i  viiv  ii     vi  i      i  v   v i --       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAA 197

  chrX_125766135_   2711 -AATAAAGCTGGAGACATCATGCTATCTGACTTCAAACTACACTACAAGG 2759
                         -  i    i     ivv   ii  vi ii i      vivi       i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_125766135_   2760 CTACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGACATCTAGAC 2809
                                  i   i    iii        i iv ii i      v    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_125766135_   2810 CAATGGAACAGAATAGATACCTCAGAAATAAGACCACACATCTACAACTA 2859
                                 i     v  v vii         iv   i    i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_125766135_   2860 TCTGATCTTCGACAAACCTGACAAAAACAAGCAATGGAGAAAGGATTCCC 2909
                         vi    i        ivv  v   i v  vv      i     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_125766135_   2910 TATTTAATAAATGGTGTTGGGAAAACTGGCTAACCATATGCAGAAAAGTG 2959
                          v  i  i        i     v      v  ?   i     i  i i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_125766135_   2960 AAGCTGGACCCCTTCTTTACAATTTATACAAAAATTAAGTCAAGATGGAT 3009
                            i         v i i   viv              v    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_125766135_   3010 TAAAGACTTAAATGTAAAACCCCAAACCATAAAAACTCT-AGAAGAAAAT 3058
                         i ?    i         i v iv    i      -    -         i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chrX_125766135_   3059 GTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTTAT-GATG 3106
                         i    ?i- v i -   iv   v v  vv i     v i   iv -   i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_125766135_   3107 AAATCACCAAAAGCAATTGCAATAAAACCTAAAATTGACAAATGGGATCT 3156
                         vi -           vvv    i    vvv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_125766135_   3157 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCTTCAGAGTGA 3206
                         v  i   v v  i i   i  ii vv    i  v      vvv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_125766135_   3207 ATAGGCCACCTACAGAAAGTGAGAAAATTTTTGCAATCTACCCATGAGGC 3256
                          v  i v   i      v v        v       vii ivi  vv ii
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_125766135_   3257 AAAGGTATAATATCCAGAATTTACAAGAAACTTAAACAAATTTACAAGAA 3306
                           i  vv vi          v  i  ii    ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_125766135_   3307 AAA-ACAAACAACCCCATCAAAAAGTGGTTAAAGGACATGAACAGAACAG 3355
                            -     i     v  i?    i   vi      iv    i   ----
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA---- 840

  chrX_125766135_   3356 ACATTTGTCAAAAGAAGACACTTATGCAGCCAAGAA--AAATGAATAAAA 3403
                         -     v  v        i ivi viii     v  -- v     -  i 
  L1M4_orf2#LINE/    841 -CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGA 888

  chrX_125766135_   3404 AGCTCAACATCACTGATTAT 3423
                         v           ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (145 / 104)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.43 (20 / 14)  


2620 26.64 5.28 1.03  chrX_125783767_125787498.rev     2371  3241 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125783767_   2371 TGGAAACATATCCCATGCCCATGAATGGGTAGAATCAGTATTCTGAAAAT 2420
                               v          ii    i  v  v   v i i    v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125783767_   2421 GACCATATTGCCAAAAGCAACCTA-AAATTCAATGCAATTCTCATCAAA- 2468
                          i v   i v  v   vii i   - i      i     i ii      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125783767_   2469 TACCACCATCATTCTTCACAGAATCAGAAAAAAAC-AATTGTAAATCTCA 2517
                          v   v vv v  i  ii     -- vvi v  i -i  iv    vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chrX_125783767_   2518 TGTGGAACCAAAAAAGAGTCCACATAGCCAAAGCAAGACTAAGCAAAAAG 2567
                          i     viiv  ii  vi viv         i   vvi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_125783767_   2568 GACAAATCTGGAGGCATCACATTATATGATTTCAAA-----CTATAAGGC 2612
                         i     vi      vv     i vivii        -----   i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_125783767_   2613 CACAGTCACCAAAACAACATGGTACTGGTATAAAAATAGGCACATAGACC 2662
                         i     v i   i   iii         i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_125783767_   2663 AATGGAAAAAGAATAGAGAAACCAGAAATAAGT------ATTTACAGCC- 2705
                                v -    v    iv          ii------     ii i -
  L1M4_orf2#LINE/    299 AATGGAATA-GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_125783767_   2706 -TTTGAGATCTTTGACAAAGCAAACAAAAACATAAAGTCGGGAAAGGACA 2754
                         -  ---   i  i     i vviv   i v   vv i v       i i 
  L1M4_orf2#LINE/    348 ATT---GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_125783767_   2755 CCCTTTTCAACAAATGGTGCCGGGATAATTGGCTAGCCAAATGTAGGAGA 2804
                         vi                  i    i  i   v  ?   v   i ii   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_125783767_   2805 ATGAAACTGGATCTTCGTCTTTCACCTTATACAAAAATCAACT------- 2847
                              ii    i iiiii  iv    v           i    -------
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_125783767_   2848 ------------AAATCTAAAATCTGAAACTATAAAAATTCTAGAAGATA 2885
                         ------------    v   i v  i           v ii       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_125783767_   2886 ACATTGGAA-AAACCTTTCTAGACATTGACTTAGGCAAAGATTTCTTGAC 2934
                             v  ?i-   i   iv -   v   iv        v i      iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_125783767_   2935 CAAGAACCCAAAAATAAATGCAACAAAAACAAAGATAAATAGCTGGGACT 2984
                         i v  vv      ii v v         iv   i   i   iv v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_125783767_   2985 TAAATAAGCTAAAGAGCTTTTGCATGGCTTAAGGAACA--GTCAGCAGAG 3032
                          v vi  iv v  i i      --  vi i  i i   --i   iv i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTG--TGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_125783767_   3033 GAAACAGACAATCCACAGAATGGGAGAAAATCTTCACAA-TCA------- 3074
                         vi  v      i                   v  ii   -   -------
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_125783767_   3075 GACAAACAACCGATATCCAGAATCTATAAGGAACTCAAACAAATCAGCAA 3124
                           i  ivi  ivi          v     i      vv    v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_125783767_   3125 GAAAAAAAAAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATATAC 3174
                         v     i v   i  i  v  i?    i     v     iv      v  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_125783767_   3175 AATTCTCAAAAGAAGATATACAAATGGCCAACAAATATATGAAAAAATGC 3224
                          v     v                       i  ii i       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_125783767_   3225 TCAACATCACTAATGAT 3241
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (139 / 90)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.44 (55 / 16)  


3201 26.36 1.22 0.66  chrX_125789915_125793324.rev     2017  2919 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125789915_   2017 TGGAAAAATATTTCACTTTCATAGATTGGAAGAATCAATATTGTTAAAGT 2066
                               i    ii  iv     i          v i           ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125789915_   2067 GTCCATAATACCCAAAGCAATCTACAGATTCAATGCAATCCCTAT-AAAA 2115
                          v v   v v      vii              i           -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125789915_   2116 TACCAA-TGACATTCTTACAAAAATAGAGAAAACAATCATACAATTCATA 2164
                          v   i-  v v  i  i  i    v  v  ivii   v  v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_125789915_   2165 TGGAACCACAAAAGACCCAGAATAGCTAAAGCTATTATAAGTAAGAACAA 2214
                              vii   ii             i   i v  iv i iv     v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_125789915_   2215 -AAATTTAGAAATGATATA-ACCTGTTGA---CAAGTTATACTGTAGAGC 2259
                         -   v  i  i--  ivi -  i viii ---   iviv    ii i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAG--GACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_125789915_   2260 TATAGTGACCAAAGTGGCATGGTACTGTCATAAAAATAGGCATATAGATT 2309
                           i   i i   iiii ii        v     ii    i         i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_125789915_   2310 AACAGAACAGAATAGAAACCCCAGGATCAAATCTGCACACCTACAGTGAA 2359
                           ii   i     v  i vi    i vi   i iii   ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_125789915_   2360 TCTATTTTTGACAAACGTGCCAAGAACATACACTGGGGAAAAGACAGTCT 2409
                          iv     i     iv         v   v  v        ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_125789915_   2410 CTTCAATAAATGATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAA 2459
                         i     i     ---         v         ?   i     i     
  L1M4_orf2#LINE/    399 TTTCAACAAATG---GTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_125789915_   2460 CAAGACTGGAGCCCCATCTCTCCCCATATACAAAAAATCAAATTAAAATG 2509
                         ii iii    v   i i   v v             - i  v i      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATG 494

  chrX_125789915_   2510 GATTA-AAACTTAAATCTAAGACCTCAAACTGTTAAAATACTCCAATAAA 2558
                            i - i  i     v     v  v     i v   v vi vv  v   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_125789915_   2559 ACATAGGGGAAACCCCCCAGGACATTGTTCTGGACAAAGATTTCTTGAGC 2608
                                ? v  vi ii iv   v   vvi i i   v i      iiii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_125789915_   2609 AATACCCTATAAGCACAGGCGACCAAAGCAAACATGGACAAATGTGATCA 2658
                          vv  v i v       i  i  v    v   v  i  i    vv  iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_125789915_   2659 CATCAAG-TGAAAACCTTCTGCACAGCAAAAGATGCAGTCAATGAAATGT 2707
                               i- v    v   i  ii vv    i  ii vi    vi  i  v
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_125789915_   2708 AGAGACAACCCTCAGAATGGGAGAAAATATTTGCCAACTACTTATTTGAT 2757
                          i         v                      v  ii iv   i    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_125789915_   2758 AAGGAGTTAATAACCAAAATATATAGGGAGTTCAAACAACTTTATAGAAA 2807
                             iii vi  v   i        ii  ii  vv      iv   iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_125789915_   2808 AAAATCTAATAATCCAATC-AAAACTGGGCAAAAGACTTGAATAGGCATT 2856
                            iv v     i     i-    v        i  i        i    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_125789915_   2857 TCTCAAAAGAAGATATA-AAATGTCAAACAGGCATATGAAAATGTGCTCA 2905
                             v            -     v v  i i   i       vi      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_125789915_   2906 ACATCATTGATCAT 2919
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (147 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  


3051 27.56 0.66 0.55  chrX_125805798_125812155     4959  5865 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125805798_   4959 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATAAAAAT 5008
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125805798_   5009 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5058
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125805798_   5059 TACCAAGGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCC 5106
                          v   ivvi i  i  ii     -   -- v  i  - iii    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_125805798_   5107 TATGGAACAAAAAAGAACCT-GCATCGCCAAGTCAATCCTAAGCAAAAAG 5155
                                vviv  i i   i- v  v     iv     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_125805798_   5156 AAGAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5205
                           v    i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_125805798_   5206 TACAGTAACCAAAACAGCCTGATACTGGAACCAAAACAGAGATATAGACA 5255
                                 i   i    iv  i      v iv ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_125805798_   5256 AATGGAACATAAC--AGAGCCATCAGAAATTATACCACATATCTACAACC 5303
                                i v  i--    i --       v vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTC 346

  chrX_125805798_   5304 ATCTGTTCTTTGACAAACCTGACAAAAACAAGAAGTGGGGAAAAGATTCC 5353
                          vi  v i  i     ivv  v   i v  vvv i        ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_125805798_   5354 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5403
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_125805798_   5404 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5453
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_125805798_   5454 TTAAAGATGTAATTGTTAGATCTAAAACCATAAAAACCCTTC-AAGAAAA 5502
                          i ?   iv   v   v   v       i      - i   v-       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chrX_125805798_   5503 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5552
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_125805798_   5553 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5602
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_125805798_   5603 ATTAAACTAAAGAGCTTCTGCACAACAAAAGAAACTACCATCAGAGTGAA 5652
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_125805798_   5653 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 5702
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_125805798_   5703 AAGGGCTAATATCCAGAATCTACAAAGAATTTAAACAAATTTACCAGAAA 5752
                          i  i  vi          v  i      i ivv    v iv iv v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_125805798_   5753 AAATCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5802
                           iv    i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_125805798_   5803 CTCAAAAGAAGACATTTATGCAGCCAACAGACACAAGAAAAAATGCTCAT 5852
                            v        i  vi viii     i ii    v     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_125805798_   5853 CATCACTGGCCAT 5865
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (141 / 105)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2252 25.90 1.60 2.14  chrX_125828133_125829873      501  1249 (492)    L1M4_orf2#LINE/L1      164   908 (0)  

  chrX_125828133_    501 GACCCAAGATCTCCAAGTTTATCTTGGTACCTTAAGAGGAGAGAACAAAG 550
                               ii  vv    iviv      -------  i i  -         
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTG-------AAAAAGA-AGAACAAAG 205

  chrX_125828133_    551 GTGGAGGCATCACCCTACCCAACTTCAAACAATACTACAAGGCTATAGTA 600
                         v      vv    v  v     i      vvv        i    i    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_125828133_    601 ACCAAAACAGCATGGTACTTGTACAAGAACAGACATATAGACCAATGGAA 650
                          i   i    ii       v i i   i i           i        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_125828133_    651 CAGAATAGGGAACCCAGAAATAAGACCGCACACCTACAACCATATGATCT 700
                         i     v i  ii          iv  ii   ii  iiii  vv    i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_125828133_    701 TCAACAAACCTGACAAAAACGAGCAATGGGAAAAGGATTCCCTATTTAAT 750
                           i    ivv  v   i v ivv       i    i  vvi  v  i  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_125828133_    751 AAATTATGATTGGATAACTGCTTAGCCACATGCAGAAAACTGAATCTAGA 800
                             vi  v v   i     vv  ?         i  i v    vi i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_125828133_    801 CCCCTTCCCTACAGCTTATACAAAAATTAACTCAAGATGGATTAAACACT 850
                              v  ii   v v                   i      i ? v  i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_125828133_    851 TAAATGTAAAACTCAAAACTGTAAAAACCCTAGAAGAAAATTTAGACAGT 900
                                  i vii      i     vi i          iv   i?-  
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN-GT 554

  chrX_125828133_    901 A--CCATTCAGGACATACGCACAGACAAAGATTTCATGAGGAAAACACCA 948
                          --i -   iv   v vv vvi  i   v i    v iiiv vi      
  L1M4_orf2#LINE/    555 AAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_125828133_    949 AAAGCAATTGCAAAAAAAGCAAAAATTGACAAATATGATCTGATTAAACT 998
                               vvv    v     v      v  i    vv  ii v  i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_125828133_    999 AAAGAGATTCTGCACAGAAAATAA-ACTATCAG---AGTGAACAGACAAC 1044
                         v  i iv  i  ii vvv   vi -       i---      v       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_125828133_   1045 CTACAGAATGGGATAAAATGTTTGCAA--TATATCCATCTGACAAAGGTA 1092
                          i           v     i       --i    --      i  i  vv
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGATAAGGGAC 751

  chrX_125828133_   1093 TAATATCCAGAGTCTACGAGGAACT--TAATCAAATTTACAAGAGAAAAA 1140
                          vi        i v  ii i     --  --   v iv i  v i   i 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAAAAGA 799

  chrX_125828133_   1141 CAAACAACCCCCTATTAAAAAGTGGGCAAAAGAAATGAGCAGACACTTCT 1190
                             i     v--   ?    i        i  vv   ii     i    
  L1M4_orf2#LINE/    800 CAAATAACCCA--ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_125828133_   1191 CAAAAGAAGACATCTATGCTGCCAACAA--ACATGAAAAAAAGCTCAACA 1238
                          v        i  vi viiv     i  --         i v        
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_125828133_   1239 TCCCTGATCAT 1249
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.26 (106 / 84)
Gap_init rate = 0.02 (13 / 745), avg. gap size = 2.15 (28 / 13)  


3421 19.98 6.85 1.63  chrX_125878371_125882052     2329  3189 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_125878371_   2329 GGAAGTCATCC-ATGTTCTGGGATTGGAAGATTTGTTATTGTT-----GA 2372
                          i   vi    -      vv           i  iv       ----- i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_125878371_   2373 CAATGTTAGCCAAATTGATCTATAAATCCATCACAAT------------- 2409
                             ii vv             i i  i  v i    -------------
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_125878371_   2410 ---------------------ATGGAAAAGCTGAGCCTAAAATCTGCATG 2438
                         ---------------------  v  v       v        iiii   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_125878371_   2439 GAAATGCAAGGGAACAAAAACAGCCAAAACAATTTTGAAAAAGTA---CT 2485
                                      v v i  i            i         v --- v
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_125878371_   2486 AAATTGGAGGACTCACACTTCCTGATTTCAAAACTTTCTACAAAATTACA 2535
                           i                   ii            v       ii    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_125878371_   2536 AAGATAAAAACACTATGGTACTGGCATTAGTATAGACATATAGATCAATA 2585
                         ivi  v  i   v i            v  v                  i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_125878371_   2586 GAACAGAATTAAGAATCCAGAAA--ATCTCATATGTCTATGGCCAATTGT 2633
                            i      i   i        -- v i    ii i     i      v
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_125878371_   2634 GTTTTAATAAAAGTGCCAAGACCATTCAATGGAGAAAAAAATAGTCTCTA 2683
                         v   ii i  ii                    i    i  -      i v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTTTT 401

  chrX_125878371_   2684 CAACAAATGACAATAGGGCAACTAAGTAGCCACCTGCAAAC-AATAAA-T 2731
                                  iiiv i  i     iii  ?    v      v-   i  - 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_125878371_   2732 TATTCTTTTCCCTCATTTCATATGTAAAATTTAACTCAAAATTGGTTA-A 2780
                          ivv iii v     ivi     ii    v            v i i - 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_125878371_   2781 AACATAAATTTCAGAGCTAAAAATATAA--TTAATAGATGGAAAT---GG 2825
                         i  v     v v          v     --i vv    v i   i---  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_125878371_   2826 T-TAACTGTTTATGGCCTTGAATTTGGCATTGGTTTCTTAAATATGGAGG 2874
                         ?-   v v  ii  i     ii  v    v          i     iviv
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_125878371_   2875 CAAAAGTGAAGGCAAAAGAAAATAAAAATAGAAACATTGGACCT--TCAA 2922
                               iiv i    v i  i -         v v       i --    
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCATCAA 650

  chrX_125878371_   2923 AATAAAAAACTTTTGTGCTTCAAAGGACACTATCTAGTATGTGAAAA--- 2969
                            v                              v  v v       ---
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_125878371_   2970 AACTCACAAAATGGAAAAATGTATGCAAAATGTATACTATAAAGCATATA 3019
                            i    i     i i  ---------   i v i ---   v      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAA---------AATATTTGC---AAATCATATA 738

  chrX_125878371_   3020 TATGATAAGCATCTAATATCAAGAATATAAAAATAATTGTTACAGCTCAA 3069
                          v       viv  vi    v        v   v  i v     i     
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_125878371_   3070 CAATAAAAAGACAAATGACCCAATTTTAAAATGCACAAATGAATTGAAGA 3119
                         i               i        ?v      vi    v  v     v 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_125878371_   3120 GACCTTTCTCCAAAGAAGATATACAAATGGCCAACATGTCCATGAAAAGA 3169
                            v                              i v iv          
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_125878371_   3170 TGCTCAATATCATTAGACAT 3189
                                i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (97 / 72)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 4.29 (73 / 17)  


2643 23.23 7.78 2.12  chrX_125893225_125895998     1434  2281 (493)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_125893225_   1434 CCATGCTCAAGGATTGGCAGAATCAATATCATCAAAATGACTATACTGTC 1483
                              i   v       v   v i     ii i  i   i v     vi 
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_125893225_   1484 CAAAGCAATCTGTAGATTCAGCGCAATTCTTATTA------CAAATGTAA 1527
                             vii    ii       i      i i   i ------  iv  ivv
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_125893225_   1528 TTTTT-CAAATAATTAGAAAAA--AATTTTAAA-TTCATATGGAATCAAA 1573
                              -  i -    -  v  i--i  ii    -           viiv 
  L1M4_orf2#LINE/    113 TTTTTGCAGA-AATT-GACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_125893225_   1574 AAGGGCCT-GTGTAGTCAAAGGAATCCTATGCCAGAAGAGAAAAGCCAGA 1622
                          i  i  i- vi   i    iv    i ivivv      iv    iii  
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_125893225_   1623 GGCATCACATTACCTAACTTCAAATTATACTGCCAGGCTATAGTACACCA 1672
                           vv     i v  i  i      viv    i v i    i    - i  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA-ATCA 259

  chrX_125893225_   1673 A-ACAGTGTAGTACTGGTACCAAAATAGTCACGTAGATCAATATGACAGA 1721
                          -       i       i iv ii    v  ii         ivi i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_125893225_   1722 CTAGAGATCCCAGAAATAAAGCCACAAACCTACAACCAACTGATTAT-GA 1770
                         v v    vi           v   i v ii  iiii   i     v -  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_125893225_   1771 CAAAG---CCAACACTAATAAACAATGAGGAAAGGACACTCTATTCAATA 1817
                            i ---    v  i v ---     i      i i v   v     i 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATT---CAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_125893225_   1818 AATGGTTCTGGGAAAATTGGATAGCCATATACAAAACAGTGAA------- 1860
                               v      v  i      ?   i  i     v i    -------
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_125893225_   1861 -----------ACTATATACAAAAATTAACTCACGATGGAT--------T 1891
                         -----------  i                   vi      -------- 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_125893225_   1892 AAATATAAGATCCGAAACTATAAAAATGT-ATAGGAAAACCT-------- 1932
                             i     v ii           v v - v i      v --------
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_125893225_   1933 --CTTCTGGATATTGGCCTAGG---TGGTT-----GATGTATGACTAAGT 1972
                         --    vv  iv    vi    ---     -----   --     -- --
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGAC--A-- 600

  chrX_125893225_   1973 TCTCAAAAGCAAATGCAACAAAAACAAAAATAGACAAGT-GGAATTCAAC 2021
                         --i        v v         iv         i  i -   v    v 
  L1M4_orf2#LINE/    601 --CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_125893225_   2022 TAAACTATAAAGCTTCTGCACAGCAAAAGAAATAATCAACAGAGTAAACA 2071
                         v   i  -   i   i  ii vv    i  v iv     v i   i  v 
  L1M4_orf2#LINE/    649 AAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_125893225_   2072 GACAACCTACAGAATGAGAGAAAATATTTACAAATTATACATCCAACAAA 2121
                                i        i            i     i   i   ii i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_125893225_   2122 GAACTAATATCAAGAATTTGCAAGGAACTCAAACAACTCAACAAGTGAAG 2171
                          i   vi    v     v ii  i      vv         i  vvi  i
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_125893225_   2172 GA---ACAACCCA-TTAAAAAGTGGGCAAAGGATTTGAACAGACATTTCT 2217
                           --- i      -  ?    i                 i          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_125893225_   2218 CAAAAGAATACATACAAGTGGTCAACAAACATATGAAAAAAAAATGCTCA 2267
                          v      v i      i   i   i  i  i       i ---      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA---TGCTCA 894

  chrX_125893225_   2268 ACATTACTAATTAG 2281
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (124 / 71)
Gap_init rate = 0.03 (26 / 896), avg. gap size = 3.23 (84 / 26)  


3361 20.60 1.25 7.08  chrX_125905482_125909883.rev     2953  3913 (489)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_125905482_   2953 AAAAAAGTTCTGTGTTATTGGATAGGGAGACTTAATAGTGTTAACATGGC 3002
                            i vi i ii    vv     v  i          v      v     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_125905482_   3003 AATGCATTCCAAATTTATCTATAGATTCATTGCAAAGCCTATTATAATCC 3052
                            i vii       v     i       vi    vv     i v     
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_125905482_   3053 ACACTAGATTTTTTACAGAAATTCACATGGTAATGCTGAAATTCATATAG 3102
                         vvi  ivv      i        v   v v i  v  i          i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_125905482_   3103 AACCCAGAATAAACTCTCCAAATAGGGACTGAAAATATCAAAAATAATGC 3152
                           ------  i-------   ---     iv i    v v    i   vi
  L1M4_orf2#LINE/    154 AA------ATG-------CAA---GGGACCCAGAATAGCCAAAACAATCT 187

  chrX_125905482_   3153 TGAGAAAGAGGAGCAAATTTCAAGGGCTCCTACTTTCCAATTTCAAGAGT 3202
                            i     i  i    v  vi   i   vi    i          i v 
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_125905482_   3203 TGCCACAAAGTTACAGTAAAAAAAATATGTGTTGTGCAGGCAAAAGAGTA 3252
                          i i      i        vv  i i -    v  i v    v   ii  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACA-GTGTGGTACTGGCATAAGGATA 286

  chrX_125905482_   3253 GACATAAAGATCAATGAAATAGAATTGAGGATAGAGAAAGAAACCTATGC 3302
                               v         i            ii vv     v     i  i 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_125905482_   3303 ATTTATGTTTAATTGATTTTCAACAAGGTTGCCAAGACTCTTCAATGAGA 3352
                                v i           i      v         iv       i -
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG- 385

  chrX_125905482_   3353 GAATAAATAGTCTTTTCAACAAATGATGCAGGGACAAATGAATATCCACA 3402
                            vi                    i   v       v  i   ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_125905482_   3403 TGCAAAACTTTGAGTTTGAACCCTTAACTCAAATCATATACAAATATTAA 3452
                                vvv   iv   i    i  v    v i          v     
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_125905482_   3453 CTGAAAGTAGATCAAAGACATAAATGTAAGAGCTAAAACT---------- 3492
                           v   i i     ?    v                    ----------
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_125905482_   3493 TAGAAGATAACATGGAGGTAAGTTTTCATTATTTTAGATTAGGCAATGGT 3542
                                v     i i?    i i   i v ii  i i            
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_125905482_   3543 TTCTTATATATCATACATAAAGCACAAGCAACAAGAGAAAATATAGATAA 3592
                               v    v i  vv                i      v        
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_125905482_   3593 TTTAGAACTCTTCAAAATTACAAACTTTTGTGCATCAAAGGATATTATCA 3642
                         v  i  vi  v         v            v        i i     
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_125905482_   3643 AGAAAGTAAAAAGACAATGCATAGAATCAGAAAATGTATAAAAGTCTAGT 3692
                                i         iv  i     vi  i  vi   ------- v -
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT-------TTG- 727

  chrX_125905482_   3693 ATCCAAAACATATAAACAACACAAATCAATCAAAAGTGATGAATAACAAA 3742
                         ---    v      ---------------  -----    i ivi  ---
  L1M4_orf2#LINE/    728 ---CAAATCATATA---------------TC-----TGATAAGGGAC--- 751

  chrX_125905482_   3743 ATTTTTAAAGAGGAAAAGACATCCAAAGTACACAAAGAACACCTAACACT 3792
                         --  v  --------------    i i  i i       v i  vv   
  L1M4_orf2#LINE/    752 --TTGTA--------------TCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_125905482_   3793 CAACAATAAAAAAG--AACAAGCAAATTAATAAATAGATGAAATATCTCA 3840
                            i        ii--  i  v v    ? v    i iii  iv  i v 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_125905482_   3841 ACGGACACCTCCCCAAAGAAGATATATACATAACAAGTAAACATATTAAA 3890
                          ii    ii  i              i v  ii v i   i  i  v   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_125905482_   3891 AGATGTCCAATATTTTTAATATG 3913
                              ii   i  iv????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (111 / 83)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 6.15 (80 / 13)  


3017 27.99 0.88 0.44  chrX_125910593_125916970.rev     4984  5887 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125910593_   4984 TGGAAGAACATTTCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5033
                              ii i  ii    i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125910593_   5034 GGCCATACTGCCCAATGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5083
                            v     v     vv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125910593_   5084 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5131
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_125910593_   5132 TATGGAACCAAAAAAGAGCCCACATTGCAAAGAGAATCCTAAGCCAAAAG 5181
                                viiv  ii  v  viv  v  v  i v    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_125910593_   5182 GACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5231
                         i      i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_125910593_   5232 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5281
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_125910593_   5282 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAGCC 5329
                                i    i--    i  --        vv   i    i  ii i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_125910593_   5330 ATCTGACCTTTAACAATCCTGACAAAAACAAGAAATGGGGTAAGGATTCC 5379
                          vi   ii  ii    vvv  v   i v  vvv       v   i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_125910593_   5380 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5429
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_125910593_   5430 GAAACTAGAACCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGT 5479
                            ii i  v    v   i     v              i    i    v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_125910593_   5480 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5529
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_125910593_   5530 CTAGGCAATACCCTTCAGGACATAGGCATGGGCAAGGACTTCATGATTAA 5579
                         v    ?ivv vi    iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_125910593_   5580 AACACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAAGGGAATCTAA 5629
                         i         i  vvi          vv     v  i   vv i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_125910593_   5630 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGCGAAC 5679
                          i   v v  i i   i  ii vv    i  v       vv i  i   v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_125910593_   5680 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5729
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_125910593_   5730 AGGGCTAATATCTAGAATCTACAAAGAACATAAACAAATTTCCAAGAAAA 5779
                         i  i  vi    i     v  i       vivv    v ivvi  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_125910593_   5780 AATCAA----CCCCATCAAAAATTGGGCAAAGCATATGAACAGACACTTC 5825
                          iv   ----   v  i?    v         v  v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_125910593_   5826 TCAAAAGAAGACATTTATGCAGCCAACAGACACACGAAAAAATGGTCATC 5875
                           v        i  vi viii     i ii    i     i   v   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_125910593_   5876 ATCACTGGTCAT 5887
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (143 / 106)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


2370 24.94 1.57 4.24  chrX_125930699_125932508.rev      494  1319 (491)    L1M4_orf2#LINE/L1      105   908 (0)  

  chrX_125930699_    494 AGATGCTTATTCTTCACAGAACTAGAAAAAAACAATTCTAAAATTTATAC 543
                           v   i -- i  ii     v v  v  iv-ii  i        i   i
  L1M4_orf2#LINE/    105 AGCTGCCT--TTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATAT 151

  chrX_125930699_    544 AGAACCAAATAAATAAGAGCTCACA-TAGCCAGAAAGAAAAATTAACAAT 592
                         i   ----  iv - i ii i  v -      i  -----------    
  L1M4_orf2#LINE/    152 GGAA----ATGCA-AGGGACCCAGAATAGCCAAAA-----------CAAT 185

  chrX_125930699_    593 ACTAAGAAATTCAATACTAAGAAAAATTAACAAATTTGGGAGCATCACAT 642
                         vi --    ---------     i  ----    v    ii vv     i
  L1M4_orf2#LINE/    186 CTT--GAAA---------AAGAAGAA----CAAAGTTGGAGGACTCACAC 220

  chrX_125930699_    643 TATTAGACTTCAAATTATACTACAAATTTATAGTTACCTAAACAGCATGG 692
                          viivi i      viv         vi  i   v i v i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_125930699_    693 TACTGGTATAAAAATAGGAATATAGACCAATGGAACAGAATAGAGAACCC 742
                               i    ii    iv       i        i     v    ii  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_125930699_    743 AGAAATAAAGACAAATACTTACAGCTGACTGATCTTCTAAAAAGCATACA 792
                                  vv  v i i   ii iii i    i   v v  i -i i v
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCC 369

  chrX_125930699_    793 AAAAC-ATAAATTGGGGAAAGGACACCCTATTCAATAAATGGTGCCGGGA 841
                           i  -  vv v         i i vi  v     i         i    
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_125930699_    842 AAACTGGCAAGCCACATGTAGAAGAATGAAACTGGATTCCCATCTCTCAC 891
                         v      vv ?       i i         ii    ii  i i   v   
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_125930699_    892 CTTATACAAAAATCAATTCAAGATGGATCAAATACTTAAATCTAACACTT 941
                          v           i  i    i        ? v  i     v   v vi 
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_125930699_    942 GAAACCATAAAAGTTCTAGAAGATAACATTGGAAAAATTCATCTAGACAT 991
                         i    i      v ii       v     v  ?iv  v  v  vv   v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_125930699_    992 TGGCTTAGGCAAAGAATTCATGACTAAAATCCCAAAAGCAAATGCAACTA 1041
                            v        v iv   v iiv  vi iv         v v     v 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_125930699_   1042 TAACAAAAATAAATAAATGGGACCTAATTAAACTAAAAAGCTTTTGCACA 1091
                         v iv       i      v    i v  i   v v    i      ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_125930699_   1092 GCCAAAGAAATGATCAACAAAC-----AGACAACCCACAGAGTGGGAGAA 1136
                         v v  i  v iv     v   v-----              i        
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_125930699_   1137 AATATTTGCAAACTACATATCCAACAAAGTACTAATATCCAGAATCTACA 1186
                                     ii i     ii i  i v   vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_125930699_   1187 AGGAACTCAAACAAATCAGCAAGAAAAAGA-----AATTAAATCAAAAAG 1231
                          i      vv    v   ii  v       -----  iiv   i?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_125930699_   1232 TGGGCAAAGGAAT-GAATGGACAGTTCTCAAAAGAAGATTGACAAACAGC 1280
                                    v -    i    v     v         vv     ii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_125930699_   1281 CAACAAACATATGAAAAAATGCCAAACATCACTAATCAT 1319
                            i  i  i       i    iv       ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (116 / 86)
Gap_init rate = 0.02 (14 / 804), avg. gap size = 3.43 (48 / 14)  


 972 29.43 13.92 2.83  chrX_125938564_125940270      413  1224 (483)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_125938564_    413 GATATATTTTGTTGATAGAGTAAAAGACTCAGTATTGAACAAATGTTAAT 462
                              viiv    v  i  v ii      i i     vvv i   vi   
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_125938564_    463 TGTTCCCAAATGAATCTAAATATTGAACATAATTCTAATGAAAATCC--- 509
                         vv i       vi     v v   v   ii   i iv  v       ---
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_125938564_    510 -TG-----------GAAAATGACCAGT----------------------- 524
                         -  -----------    v    v  i-----------------------
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_125938564_    525 --------------AATAGCCAAGGTGAACAT---AAGGAAGCTCAAAGC 557
                         --------------         iiii v v ---  i    vv     i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_125938564_    558 TAGAAAACATACAGTACTGGATTTTAAAAACTATTATAAGATTATAATAA 607
                          i  ii  vi   v v ivi    i    vi  i  i  iii  i i   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_125938564_    608 TTAGAACAGTGTGTTAGTGATGCATA--GATAAACAAACTGAATAATAGA 655
                          i ii        v  v  --     --    i   v iv  vi   i  
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTG--GCATAAGGATAGACATATAGATCAATGGA 304

  chrX_125938564_    656 ACAAAAC--AGAGTTCAGAAACAGACCTATGGATTTACAG-CAACCTGAA 702
                          i i  i--     i      i i   i  iv     ii -   i-   v
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT-TGAT 353

  chrX_125938564_    703 TTTCTATAAAGA---CAACATTAAAGAACAGGGTAGATGAATGACTTGTC 749
                             v i  i i---   v ii vvv  ii   ------  v  v v   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGG------AAAGAATAGTC 397

  chrX_125938564_    750 TTTTTAAAAAATTGCATTGGGTCAATAGAATATCCATCTGGAAAA-ATTG 798
                             i  v    v iii    v   iv i   ?   iv  v    - v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_125938564_    799 AATTTTAA--------TGATACCATATATAAAAATCAATTTCAGAATG-A 839
                           v  vi -------- v i        i      i  i -  i    - 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT-CAAAATGGA 496

  chrX_125938564_    840 TTGCATATTTTAATGTTAAAAGCAAAAA--ATGAAACTTCTATA-GAAAA 886
                          ii? v ii v     -  i   v    --  i     ii  v -     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_125938564_    887 CTTGTAGAATGTA----TTTATGAACTTCTGGA--AGACAAATATTTCTT 930
                          --i   i?-   ----  ii   v   --  i--  i   vvi      
  L1M4_orf2#LINE/    546 C--ATAGGN-GTAAATCTTCGTGACCTT--GGGTTAGGCAATGGTTTCTT 590

  chrX_125938564_    931 AAACAAGGCAGAAAAA--ATAACCA-TAAAAGAATATAATATATA--TTT 975
                          i i v i  vv    -- i  v  -i       v -    v   --  v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTG 639

  chrX_125938564_    976 AATTACATGAAGAATGTAAATCAATAT------AAAGATACCAATAAGAA 1019
                         i i v   v  i v iv   iivv i ------  i  i  i vi     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_125938564_   1020 AATTAAATAACAACTCACAGAGTGAAAAAAGATAT--GCATACC-----T 1062
                          i v   vi     i      i  ii i  i    --   v i ----- 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_125938564_   1063 CTGAGCAAAAAAAAAAAAAGTACTCAGAATACATAAAGAACTCCCATAA- 1111
                             v-----  iii vvv   ii       i           ii i  -
  L1M4_orf2#LINE/    740 CTGAT-----AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_125938564_   1112 ---ATACAAAAAGGATA--CAACT-AATTAGGAAAACAGACAAAAGACTT 1155
                         ---   vv    i  i --i   i-    ?i-    ii i    i  i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWA-AAAATGGGCAAAGGATTT 833

  chrX_125938564_   1156 AAA----CACTTTTCAAAGGAGGATAACCAAATGGCCCCAAAACACACAA 1201
                         i  ----  i  i  v  i  i    vv         vvv  i    ii 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_125938564_   1202 AAAAA--CCCCATTTCACTATCTAG 1224
                            i -- i v iv   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (145 / 90)
Gap_init rate = 0.04 (37 / 902), avg. gap size = 3.68 (136 / 37)  


2479 25.75 2.91 5.06  chrX_125941137_125943151      595  1522 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125941137_    595 TGGAAAAACATTTTATGCTCACAGATTGGAAGAATCAATTTTGTTAAAAT 644
                               i i  iii   i   ii          v i   v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125941137_    645 GGCCAAACAGCCCAGAGAAATCTATAGATTCCATGCCATTTCTATCAAAC 694
                            v v  vv    i vvi     i      v i  v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125941137_    695 TACCAA--GGCTATTTTGCACAGAATTAGAAAAATGATTCTAGAATTCAC 742
                          v   i-- v  v       v -    iiv  iv    i   i      i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_125941137_    743 ATATAACCAATA-AAGAGGCTCAAAA--GCCAGAGCAATACTAAGCAAAA 789
                           iv  ---  i-   i i i  i  --    i i    vi i iv  i 
  L1M4_orf2#LINE/    150 ATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_125941137_    790 AAAACAAAGCTGGAGGTATCACACTATTCAACATCAAACTATACTATAA- 838
                          i       i      vv       vii   iv     viv     i  -
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_125941137_    839 GTTAACAGTAACCAAAACAGCATGATACTGGTATGTAAACAGACACATAG 888
                          i  -      i   i    ii  i      i  ivii i     i    
  L1M4_orf2#LINE/    247 GCTA-CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_125941137_    889 ACCAATGGAATAGAATAGAAAATTAAAAAAAGAAAGAAAGAAAGAAAGAG 938
                          i              v  i i iv i   --------------------
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAA-------------------- 325

  chrX_125941137_    939 AGAGAGAAAGCAAGCAAGCTGCACACCAACAACTATCTGCTTTTCAACAA 988
                         ----------i  i --- iii   iiv iiiii vi  v     i    
  L1M4_orf2#LINE/    326 ----------TAAAC---CCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_125941137_    989 AGTTGACAAAA--ATTAGCAATGGGGAAAGAAC--TCCTTATTGAATAAA 1034
                         i v  v   i --   --              i--  i  -- v  i   
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATT--CAATGGGGAAAGAATAGTCTTT--TCAACAAA 408

  chrX_125941137_   1035 TGG------AATAACTTGTTATCCATATGCAGAAGAAGAAAACTGGACCC 1078
                            ------i i    v v  ?   i     i     vi  ii       
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_125941137_   1079 CTACCTATCACCACATACAAAAATAAACTCAAGATGGATTAACGACCCAA 1128
                               vv     i          v       i      i ?v    i  
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_125941137_   1129 ATGTAAGACTTCAAGCTATAAAAATCCTATAAGAAATCCTAGG---AAAT 1175
                                 vi v  i        v  i  v      v v    ---    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_125941137_   1176 ACCATTCTGGACATTATACATGGCAAATAATTTAT--GATTAGGTCCTCA 1223
                         -- -   vv   v  iviivv     - ii   v --   - v v vi  
  L1M4_orf2#LINE/    559 --C-TTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT-ATGACACCA 603

  chrX_125941137_   1224 AAAGCAATTGCAACAAAAATAAAAATTGACAAGTGGCACCTAATTAAA-C 1272
                               vvv         iv      v  i  i v v  i v  i   -i
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_125941137_   1273 TAAAAGCTTCTGCAAAGCAAAAGAAACTATTAACAGAGTAAAGAGACAGC 1322
                              i   i  iivvv    i  v     i  v i   i  i     i 
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_125941137_   1323 TTACAGAATGGGAGAAAATATTCACAAATTATGCATTTGAGAAAGT-CTA 1371
                         ii                    ii     i  ii  i   v  i v-  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_125941137_   1372 ATATCCTGAATCTGTAAGTAACTTAAGCAATTGGACAAGCAAAAAACAA- 1420
                         i     v    v i   iv    ivvi   i vi i  vv    i    -
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_125941137_   1421 ---CCCCATTAAAAAGTGGACAAAGGATATGAACAGGCACTTCTCAAAAG 1467
                         ---   v   ?    i   i        v    i  i  i     v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_125941137_   1468 AAGACATAAAAGCAGCCAACAAACCTATAGAAAAATACTCATCATCACTA 1517
                             i   v  iii     i  i vi  ii   i  i    v     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_125941137_   1518 ATCAT 1522
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.68 (148 / 88)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.22 (74 / 23)  


3068 27.54 1.11 0.66  chrX_125961270_125967318     4653  5556 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125961270_   4653 TGGAAGAACATTCCATGCTCATGGATAGAAAGAATCAATATCATGAAAAT 4702
                              ii i  i     i        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125961270_   4703 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCGTCCCCATCAAGC 4752
                            v     v     iv i  i  i        i  vi    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125961270_   4753 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 4800
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_125961270_   4801 ATATGGAAACAAAAAAGAGCCCACATAGCCAAGACGATCCTAAGCCAAAA 4850
                                  iiv  ii  v  viv        i  i   i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_125961270_   4851 TAACAAAGCTGGAGGCATCACGCTATATGACTTTAAACTATACCACATGG 4900
                         v       i      vv    i  vivii i  i   viv   i   vi 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_125961270_   4901 CTACAGTAACCAAAAAAGCACGGTACTGGTACCAAAACAGAGATATAGAC 4950
                                  i   i v  iii        i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_125961270_   4951 CAATGGAACAGAAC--AGAGTCCTCAGAAATAACACCACACATCTACAAC 4998
                                 i    i--       --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_125961270_   4999 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGACTC 5048
                           vi    i  i     ivv  v   i v  vvv           i ivv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_125961270_   5049 CCTATTTAACGAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5098
                         i  v  i   i             v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_125961270_   5099 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAAGTAATTCAAGATGG 5148
                             ii    i    v   i     v          v   i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_125961270_   5149 ATTAAAGACTTAAATGTTAGACCTAGAACCATAAAAACCCTAGAAGAAAA 5198
                           i ?    i       v   v   i   i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_125961270_   5199 CCTAGGCA-ATACCATTCAGGACATAGGCATGAGCAAGGGCATCATGACC 5247
                          v    ?i- v i -   iv   v v  vv ii    v  iv  v iivi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_125961270_   5248 AAAACACCAAAAGCAATGGCAATAAAAGCCAAAATTGACAAATGAGATCT 5297
                          vi            vvi    i     vv     v  i    vi  ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_125961270_   5298 AATTAAACTAAAGAGCTTCTGCACAATAAAAGAAACTACCATCAGAGTGA 5347
                         v  i   v v  i i   i  ii vvi   i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_125961270_   5348 ACAGGCAACCTACAGAATGGGAGAAAATATGTGCAACCTACCCATCTGAC 5397
                          v  i     i                   v     vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_125961270_   5398 AAAGGGCTAATATCCAGAATCTACAAAGAATTTAAACAAATTTACAAGAA 5447
                           i  i  vi          v  i      i ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_125961270_   5448 AAAAACAA----CCCTATT-GGAAGTGGGCAAAGGATATGAACAGACACT 5492
                            i    ----   v   -ii  i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_125961270_   5493 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5542
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_125961270_   5543 TCATCACTGGCCAT 5556
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (153 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


2620 27.65 2.54 2.10  chrX_125968223_125971576     1960  2863 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125968223_   1960 TGGAAAAATATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 2009
                               i    i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125968223_   2010 GGCCATAATGCCTAAAGTAATTTATAGATTTAATGCTATTTAAATTAACT 2059
                            v   v v  i   v i  i  i     i  i  v  ii-------  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC-------CT 93

  chrX_125968223_   2060 ATTAAACTACCATTGACATTCTTCACAGAA-TTAGGAGAAACT-ATTTTA 2107
                           i   v v   vivi v  i  ii     -  --  v  i  -  ii  
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTA 141

  chrX_125968223_   2108 AAATTCATGTGGAATTAAAAAAGAGCCTGCATAGCTAAGACAATCCTAAG 2157
                                 i     v iv  ii  v  v v     i  i      i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_125968223_   2158 CAAAAATAACAATGCTGGAGGCATCATAATACCTGACTTCAAACTACACT 2207
                         v  i  v     v i      vv   i v v  ii i      vivi   
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_125968223_   2208 ACAAGGCTATAGTAACAAAAACAACATGGTACTAGTACAAAAACATGCAT 2257
                             i    i     iv  i   iii       i i i  ii i vi   
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_125968223_   2258 ATAGGCCAATGAAACAGAATAGAGAACTCAGAAATAAGACCACACACCTA 2307
                             ii     i  i     v    iii         iv   i   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_125968223_   2308 CAACCATCTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGTAAGG 2357
                         iiii  vi    i   i    ivv  v   i v  vv        v   i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_125968223_   2358 GTTCCCTATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATGTGCAGA 2407
                         i vvi  v  i  i              v      v  ?   ii    i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_125968223_   2408 AAATTAAAACTGGACCTGTTCCTTACCCCTTATACAAAAATTAACTTAAT 2457
                          i v i  ii      iv v   i  v  v                i  v
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_125968223_   2458 ATGAATGAAAGATTTAAAC-------CCAAAACTATAAAAATCCTAGCAG 2500
                            i  v ?   ii    i------- i            v  i   v  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_125968223_   2501 AAAATGTAGACA-ATACCATTCAGGACAT------AGGCAATGG---CAA 2540
                             ii   i?i- v i -   iv   v ------         --- vv
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_125968223_   2541 AGATTTTATGACAAACATGCCAAAAGCAATAGCAACAGAAGCAAAAATTG 2590
                             ---      ------         vv       i   v      v 
  L1M4_orf2#LINE/    591 AGAT---ATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_125968223_   2591 ATAAATGGCATCTCATTGAACTAAAGAGCTTGTGCAGAGCAAAATAAACT 2640
                               v v ii    ii  v v  i i   v  iivvv    iv v   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_125968223_   2641 CTCATCAGAGTGAACAGACCACCTACAGAATGGGAGAATTTTTTTTCTTT 2690
                         v   vv i      v    v   i              vv v   v vvv
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_125968223_   2691 CTATCCATCTGACAAAGGTCTAATATCCAGAGTCTACAAGAAACTTAAGG 2740
                         ii  vi      i  i  v  vi        i v  i  ii    ivviv
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_125968223_   2741 AAATTTACAAGGAAAAAA-AAATAAAACCATTAAAAATTGGACCAAGAGC 2789
                           v iv i  vi    i -      vv v   ?    v   i v   iii
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_125968223_   2790 ATGAACAGTCACTTCTTAAAAGAAGACATTCATAAGGCCAACAA--ACAT 2837
                         v    i  v  i    iv        i  v  v v      i  --    
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_125968223_   2838 GAAAAAA-GCTCAACATAACTGATCAT 2863
                              i -         v ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (139 / 107)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.00 (42 / 14)  


3301 26.32 0.66 0.66  chrX_125976468_125983989      492  1399 (6123)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_125976468_   1399 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1350
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_125976468_   1349 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1300
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_125976468_   1299 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1252
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_125976468_   1251 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1202
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_125976468_   1201 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1152
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_125976468_   1151 TACAGTAACCAAAACAGCATGGTCCTGGTACCAAAACAGAGATATAGATC 1102
                                 i   i    ii    v    i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_125976468_   1101 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATAC--CTACAA 1056
                                i    i--    i  --        -   -     --i  iii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAA-ACC-CATACATTTATGG 344

C chrX_125976468_   1055 CTATCTGATCTTTGACAAATCTGAGAAAAACAAGCAATGGGGAAAGGATT 1006
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

C chrX_125976468_   1005 ACCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 956
                         ii  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

C chrX_125976468_    955 CTGAAACTGGATCCCTTCCTTACATCTTATACAAAAATCAATTCAAGATG 906
                         v    ii    i    v   i   i v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chrX_125976468_    905 GATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 856
                            i ?   ii    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chrX_125976468_    855 ACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTAC 806
                           v    ?i v viv   iv   v v  vv i     v ii   v iv i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

C chrX_125976468_    805 AAAACACCAAAAGCAATGGCAACAAAAGCAAAAATTGACAAATGGGATCT 756
                          vi            vvi          v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

C chrX_125976468_    755 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 706
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

C chrX_125976468_    705 ACAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 656
                          v  i     i   iv            v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

C chrX_125976468_    655 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 606
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

C chrX_125976468_    605 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 556
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chrX_125976468_    555 TCTCAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTCA 506
                             v        i  vi viii     v  ii         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chrX_125976468_    505 TCATCACTGGCCAT 492
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  

2350 25.43 2.88 5.88  chrX_125976468_125983989     6094  7029 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_125976468_   6094 TGGAAAAACACTCCATGATCAAAGATTGGAAGAATCAATATCATTAAAAT 6143
                               i i ii     v   vi          v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_125976468_   6144 AGCCATATTGCCCAAAGAAATCTATAGATAAAGTGCTACTCCTATCAAAC 6193
                         i  v   i v      vvi     i    vv ii  v ii         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_125976468_   6194 TACCAACATCATTTTTTTACAGATTTAGAAAAAC-AATTCTAAA-TTCAT 6241
                          v   i vv -i      i    vv v  v  i -i  i     -     
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_125976468_   6242 ATGGAAC--CAAAAAAATAGCCCA-AATAGCCAAAACAATCCTAAGCAAA 6288
                               v--   iii ----    -                i i iv  i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_125976468_   6289 AAGAACATAGCCAGAGGCATCACATTATCTGACTTCAAATGATATTATTA 6338
                                v  iii    vv     i vi ii i      vvv  i  iv 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_125976468_   6339 GTCTACAGTAAAAAAAAAAAAAAAGTATGGTACTGCTATAAAAACAGATG 6388
                         iv         vv  i v -----  i        vi    ii i   ii
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACA-----GTGTGGTACTGGCATAAGGATAGACA 290

  chrX_125976468_   6389 CATATACTAGTGGAACAGAATAGAGTACTCAGAAATAAAGCTGCACACCT 6438
                         i   v ii i     i     v   viii          v iii   ii 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_125976468_   6439 ACAATCA-----TCTTTGAAAAACTTGACCAAAATTAG-CAATGGGGAAG 6482
                          iii   ----- i  i  v  ivv  -    i ii v-          i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAA 389

  chrX_125976468_   6483 GACTC-CCTATTCAATAAATGGTGCTGAGATAGCTGTCTAACCATATGCA 6531
                           v v-i  v     i           i  i i   vv  ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_125976468_   6532 GAAGAATGAAACTGGGACCCTACCTTTCACTATA----AAAATTAACTGA 6577
                         i         ii   iv        iv   i   ----          v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_125976468_   6578 AGATAAATTAAAGATGTAAATGTAAGACCTCAAACTATAACAAATCCTAG 6627
                          i  ii  i ?   iv           v  v         -  v  i   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAG 538

  chrX_125976468_   6628 AAGAAACCCTAGGAAATACTCTTCTCAGCATCAACCTTGGCAAAGTGTTT 6677
                               v v    ?ivv v     viii v iiivi v     v -    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTT 587

  chrX_125976468_   6678 ACGGCTAAAT----CCTCAAAAGCAATCA--CAACAAAAACAAAAATTGA 6721
                         - --i  i  ---- vi        --  --        iv      v  
  L1M4_orf2#LINE/    588 -C--TTAGATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGA 632

  chrX_125976468_   6722 CAAATTGGCTGTTCA-CAAGCTCTTTAGCTAACTAAGAGATGTTTAGCTT 6770
                         i       vi-    -   -----------  i   i - iv   -----
  L1M4_orf2#LINE/    633 TAAATTGGAC-TTCATCAA-----------AATTAAAA-ACTTTT----- 664

  chrX_125976468_   6771 ACTAAGCTAAAGAGCTTCTGCAAAGCAAAATAAACGATCAACAGAGTAAA 6820
                         ----------- v     --------   iv v  v     v i   i  
  L1M4_orf2#LINE/    665 -----------GTGCTTC--------AAAGGACACTATCAAGAAAGTGAA 695

  chrX_125976468_   6821 CAGACCACCTACAGAATGGGAGACAATATTTGCAAACTATGCATTTGACA 6870
                         v    v   i             v            ii  ii  i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_125976468_   6871 AAGGTCTAATATCCAGACTCTATAAGAAACTTAAATAACTCCACAGGCAA 6920
                          i  v  vi        v v     ii    ivv i     v i ivv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_125976468_   6921 AGAATAAAAAACCCTATC-AAAAGCGGGCAAAC-ACATGAACAGACACTT 6968
                          ii i   v     v  i-    ii       v- iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_125976468_   6969 CTCAGAAGAAGACATGCAAGTGGCTAATGAAAATTTAAAAA--TGCTCAA 7016
                            vi       i  i   i    i   i iv iv i    --       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_125976468_   7017 CATCATTAATCAT 7029
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 2.93 (82 / 28)  


3915 18.52 2.43 2.65  chrX_126009333_126011415.rev      686  1592 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_126009333_    686 AAAGACATCTTATGTTTATGGATTGGAAGACTTAAAATCATTAAGATGTA 735
                              i   ii     i                  v  ii        --
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG-- 51

  chrX_126009333_    736 AGATGTCGATACTACCCAAAGTGATCTA--GATTCAATGCAATCTCTATC 783
                         ---- - i     v      v       --       i      i     
  L1M4_orf2#LINE/     52 ----G-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_126009333_    784 AAAACCCAACAACT-TTTTTTTTGCTGAAAAATC-ATACCCTCACCCCAA 831
                             i  --  i  -ii        -- i    i- i vv  v i  i  
  L1M4_orf2#LINE/     97 AAAATCC--CAGCTGCCTTTTTTGC--AGAAATTGACAAGCTGATCCTAA 142

  chrX_126009333_    832 AGTTTACATGGAATCCCAAAGTACCCTGAATAGCCAAAACAATCTTGAAA 881
                          i  i i      viv   i v    v                       
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_126009333_    882 AAAAGACACAA-GTTAGAGAATTCACACTTCCTGATTTCAAAACTTAGTA 930
                           i iiv    -   i   i i          ii             v  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_126009333_    931 TAAAACTACAGTAATCAAAACGACATGGTACTAGACTAAAAGCAGACATA 980
                         i   i             i  iiii       i vv   iiii       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_126009333_    981 TAGA---ATAAAGCAGAA-----AGCCCAGAAATAAACT-ATACCATATA 1021
                             ---  ii ii    -----  i            i-    -  v  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC-ATTTA 341

  chrX_126009333_   1022 TAGTCAAATAATTTTCAACAAGGGTGTTCAGACCATTCAATGAAGGAAAG 1071
                          i     v i      i         iiv             i-      
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAG 390

  chrX_126009333_   1072 AACTGTCTTTTCAACAAATGGTTTTTGGAAACCTAGACACCCACATGCAA 1121
                           iv                  vi v   v v  i  i ?          
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_126009333_   1122 AATAATGATGTTGGAAACTTACCCTACACCACATACAAAAATTAAGTCAA 1171
                           v     v      vv i    ii      i             v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_126009333_   1172 AACG-ATGAAAGAACTAAACTTAAGAGCTAAAATTTTAAAACTCTTAAAA 1220
                           i -  v ?   v     iv            i v           i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_126009333_   1221 GAAAACATAGGGACAATGCTTCATGATATTGTATTTGGCAGCAAAGTTT- 1269
                                    ?ii  vv    i   iv   vi  v    -- vi    -
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA--ATGGTTTC 588

  chrX_126009333_   1270 --GGATATGACACCAAAGGCACAAGCAAAAAAAGGAAAAACAGATAAATT 1317
                         --i              i          v     i     i         
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_126009333_   1318 AGACTACCTTAAGATAAAATGAAAAAACTTCCATGCATCAAAGGATACAA 1367
                         i    v v i  i  ---- --        iii   v        i  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAAT----T--AAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_126009333_   1368 TCAACACAGTGAAAAGGCAACCCAGAGAGTCAGTGAAAATATTTGAAAAT 1417
                             v v         i       v   i vi v           v    
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_126009333_   1418 CACATATCTGATAAGGAACTGATATTTAAAATGTATGGAGAACACTTAAA 1467
                           i             i   vi   ii i   i   ii     v    v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_126009333_   1468 ACTGAACAACAACAACAAAACAAATAACCTGATTCAAAAATAGGCAAACA 1517
                            ---   i  i  v  i          ii   ?      i      vi
  L1M4_orf2#LINE/    783 ACT---CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_126009333_   1518 GCTTGAATAGACATTTCTCCAAAAT---TATACAAGTGGCCAATAAGCTT 1564
                         ii                     iv---       i            vi
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_126009333_   1565 ATGAATAGATGCT-AACATCACTAATCAT 1592
                              v       -       ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (108 / 56)
Gap_init rate = 0.02 (21 / 905), avg. gap size = 2.19 (46 / 21)  


2970 26.12 3.03 1.23  chrX_126021513_126023437.rev      543  1434 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126021513_    543 TGGAAAGATATCCTGTGTTTTTGAATTTCAAAAATTAAT-TTAATATAAA 591
                                      ii    iv  i   vv  i v     -  iv  - i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGA 49

  chrX_126021513_    592 TGTCTATATTACCCCAAAT-GGTCTATAGATTCAATGTAATCACTATCAA 640
                           v v   i -        - i    i        i i    v       
  L1M4_orf2#LINE/     50 TGGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_126021513_    641 AATAATAATGACATTTTTCACAGAAATAGAAACACCAATTCTATAATTTT 690
                            vvi iivi v     ii       v  v vi ii  i   v    iv
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_126021513_    691 TATGGAACCAGAAAGAACCCA-AACAGCCAAAGCAATGCTGAGCAA---- 735
                                viiv  i i     -  i       i    vi   iv  ----
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_126021513_    736 ----AAGCTTAATGCATCATATTACCTGACTTCAAAATATACTACAAAGC 781
                         ----   i vi v vv   i i v  ii i       iv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_126021513_    782 TATAGTAACCAAAACAGCACGGTACTCACTTAAAACTATCCATATCAATC 831
                           i     i   i    iii      vi v   iiv  vv     vi   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_126021513_    832 AATGGAACAAAATAGAGAATGCAGAAAT----CCACACATGTACAGCCAA 877
                                i i   v    i v       ----   i    v  ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_126021513_    878 TTGAATTTTTGACAAAGGCATCAAGAACATATGTTGGAGAAAGAACAATC 927
                             -    i     i  iii     v   viiv   i       i i  
  L1M4_orf2#LINE/    349 TTGA-TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_126021513_    928 TCTTCAATAGATGGTGCTGGAAAAACTGGATATCCATGTGCA---GAGCA 974
                          i     i i          i v         ?   ii    ---  iii
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_126021513_    975 AAACTAGACTCTTATCTCTCACCACACACAAAAATCAACTCAAAATAGAT 1024
                           ii i   i i  i   v     i i        i          i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_126021513_   1025 TAAGGACTTAAATTTAAGGTCTGAGACTTTGAAAGTAGTAGAAGAAAACA 1074
                         i ?i   i     v    iv  i i   v i   v vv            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_126021513_   1075 TGGAAACA---TTTCAGGACATTGGTGTAGGCAAGAATTTTTTGGATAAG 1121
                          i i?ii ---i   iv   v    vv       vii   i  i    v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_126021513_   1122 GCTTCAAAA-CACAGGCAACAAAAGCAAAAATAGACAAATGGGATTACAT 1170
                         i vi     -    i          v         i    v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_126021513_   1171 CAAA-TGAAGAAGCTTCTGTATGGCAAAGGAAAC----AACAAATTGTAA 1215
                             - v  i  -   i   iivv       v  ----  v   v  v  
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_126021513_   1216 AGAAAACTTACAAAAAAAGAGAAAATATTCACAAACTGTGTCTCTGAGAA 1265
                            v   ii   i  vii           ii    iii i v     v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_126021513_   1266 GATGTTAATATCCAGAATATATAAGCAACTCAAACAACTCAATAGCAAAT 1315
                          ivii vi                iv     vv           ii   -
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA- 795

  chrX_126021513_   1316 AAGCACATATAATCTAACTAAAAATAAGGAACAACTCTGGATCTAAATAA 1365
                            -   v    i i  i ?    -- v ii   v---    i i    i
  L1M4_orf2#LINE/    796 AAG-ACAAATAACCCAATTWAAAA--ATGGGCAAA---GGATTTGAATAG 839

  chrX_126021513_   1366 ACATATCCTGAAGGAAAACATACAAATAGCCAACAGGTATATGATAAAAT 1415
                             v  iiv  i   i i        i     i i i i    v  i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_126021513_   1416 GCCCATCATCACTAATCAT 1434
                           i  v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (149 / 80)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.11 (38 / 18)  


3125 27.52 1.00 0.22  chrX_126060891_126066545     1681  2581 (3074)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126060891_   1681 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 1730
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126060891_   1731 GGCCATACTGCCCAAGGTAGTTTATAGATTCAATGCCATCCTCATCAAGC 1780
                            v     v     iv ii i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126060891_   1781 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 1829
                          v   iivi i  i  ii     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_126060891_   1830 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 1879
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_126060891_   1880 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAAGTATACTACAAGGCTG 1929
                              i      vv    i  v  ii i      iiv        i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_126060891_   1930 TAGTAACCAAAACAGCATGGTCCTGGTACCAAAACAGAGATATAGACCAA 1979
                         i     i   i    ii    v    i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_126060891_   1980 TGGAACAGAACGGAGCCCTCAGAAATAATACCACACATCTACAACCATCT 2029
                              i    iv   vvii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_126060891_   2030 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 2079
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_126060891_   2080 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 2129
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_126060891_   2130 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 2179
                         i    i    v   i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_126060891_   2180 AGACTTAAATGTTAGACCTAAAACCATAAAAACCGTAGAAGAAAACCGAG 2229
                             i       v   v       i      vi v           vv  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_126060891_   2230 GCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGCCTAAAAC 2278
                          ?i- v i -   iv   v v  vv i     v ii   v ivv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_126060891_   2279 ACCAAAAGCAATGGCAAGAAAAGCCAAAATTGACAAATGGGA-TCCAT-- 2325
                                   vvi    v     vv     v  i    v   - i   --
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_126060891_   2326 AAACTATAGAGCTTCTGCACAACAAAAGAAACTACCATCAGAGCAAACAG 2375
                            i  - i i   i  ii vv    i  v    i  vv i  ii  v  
  L1M4_orf2#LINE/    650 AAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_126060891_   2376 GTGACGTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAG 2425
                         iii  vi                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_126060891_   2426 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAA 2475
                          i  vi          v  i  v      vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_126060891_   2476 ACAA----CCCCATCAACAAGTGGGCAAAGGATATGAACAGACACCTCTC 2521
                             ----   v  i? v  i            v    i     ii    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_126060891_   2522 AAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCAT 2571
                         v        i  vi viii     v ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_126060891_   2572 GACTGGCCAT 2581
                         v ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  

1594 28.97 10.94 1.80  chrX_126060891_126066545     4343  5174 (481)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126060891_   4343 TGGAGAAGTGTACTTTATTCATATGTTGGAATACACAAGATTGCTACAAT 4392
                             i ii i v iv i     ivi      v  vi  v    i  vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126060891_   4393 TTGCATT-CTCCCCAAAGTATTTCTACAGATTCCATGCAATTTCAATCAA 4441
                         v-   v -         v iv -          v i     ii v     
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGAT-CTACAGATTCAACGCAATCCCTATCAA 98

  chrX_126060891_   4442 AACTCCAA-TACATGTAATATATCAATTGACAGTATTATTCTAAAA--CA 4488
                           ii   i- i v v vv ii vv        ivv v  i      --  
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_126060891_   4489 TATGTTGAAATTGGAATTTAAATTATCTAGAATAGCCAAATTAAGTGTGA 4538
                             -------- i   vi  ivv i i            vi  viv   
  L1M4_orf2#LINE/    149 TATG--------GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_126060891_   4539 AATAGAAGCAATAAGTTAGAGGACACATGCTACCTTATT-CAAGGCTTAC 4587
                           v     v vv     i      v  ii  v  iv   -   ii     
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_126060891_   4588 TATAAAGCTATGGTAATCAAGACAGTGTGATGTTGGCATAAGAACAGACA 4637
                           i       ii                 i ii         i i     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_126060891_   4638 CATAGTTCAGTGGAAAAAAATTAAGAGTCTAGCAGTAAACCTACCTATCT 4687
                         i    v   i     v i    i      i  v i      i ivi  i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_126060891_   4688 ATGTGCAAATTATATT-GACAAAACCACCAGGGT-----AAAAAGGAAAA 4731
                            vv   v v  v  -     iivii   i ii-----  vii     i
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_126060891_   4732 --------CTTGAACAA-TGATGCTAGGACAACTATATATCTCTACGGAG 4772
                         --------i  v     -  i    i        iv   ? ivi i v i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_126060891_   4773 AA-AAGAAAGATAAACTATTATTGATCACAATACATACACATACAAATTC 4821
                           -  vi   v ii  ivi  ii--     vi i     v v iv  i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACC--TCACACCATATACAAAAATTAACTC 488

  chrX_126060891_   4822 AAAATGGGTTATAGACCTAAAAATAAAA-TTAAATTTAGACAATTTCTAT 4870
                                i i ?         vi   i -i    vi  v v  i ii  v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_126060891_   4871 AAGAAA---TA-------------------TTGCATT-GGCCATCTTTTC 4897
                               ---  -------------------   vi  -   v  vv    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_126060891_   4898 ------ATGA---------------------ATGAAAACATGGATAAATT 4920
                         ------    --------------------- v     v  i        
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_126060891_   4921 TGACTTCATTGGCAGCAGAGACCTGTGCTTTTTAGAAGTTACCAGTTTAA 4970
                         v        iiiv vi i i  i v  ivi  i i i vi  i -- i  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA--TCAA 686

  chrX_126060891_   4971 CAGAATGAAAAGTCAAGCCATTAACTA--AAAACATGTGTGCACTACATA 5018
                         v i i       v   v   ivi v i-- i  v  i v    vvv    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_126060891_   5019 TATCTGACAAAAATCTTGCCTGGAAAATATATAAACAACTTTTA--ACAC 5066
                                i  iiiv    iv vv i          v    i   --  v 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_126060891_   5067 AATAACAAATAAGA-AAAGAAAGAAATT-ACAATTATGCAGAATACTTAA 5114
                              i   -    -   v  vvv    - v  v iv   i iv i  i 
  L1M4_orf2#LINE/    787 AATAATAAA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_126060891_   5115 ACA-----TTCACAAAAGAAGATGTAGAAATGAC-AATA----CGTGAAA 5154
                          i -----   v v         i  v     i -    ---- i     
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_126060891_   5155 CAATA---AGCAGCAATTTTAGT 5174
                         vi  i--- i  v  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (136 / 103)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 3.66 (106 / 29)  


3394 24.23 1.10 1.10  chrX_126073749_126079171     4023  4930 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126073749_   4023 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4072
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126073749_   4073 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4122
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126073749_   4123 TACCAA-TGATTTTCTT-CAGAGAATTGGAAAAAACT-ACTTTAAAGTTC 4169
                          v   i-  vi   i  -    -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_126073749_   4170 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 4219
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_126073749_   4220 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAAACTATACTACAAG 4269
                                 i      vv       v  ii i         -        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chrX_126073749_   4270 GCTACAGTAACCAAAACAGCATGGTATTGGCACCAAAACAGAGATATAGA 4319
                                   i   i    ii     i     iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_126073749_   4320 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAA 4367
                                  i    i--    i  --        vv   i i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_126073749_   4368 CTATCTGATCTTTGACAAACCTGACAAAAACAAGCATTGGGGAAAGATTC 4417
                         ii vi    i  i     ivv  v   i v  vv  v          v v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_126073749_   4418 -CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 4466
                         -i  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_126073749_   4467 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 4516
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_126073749_   4517 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAA 4565
                            i ?    i       v   v       i      -    -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAA 543

  chrX_126073749_   4566 AACCTAGGCA-ATACCATTCAGGACATAGGTATGGGCAAGGACTTCATGT 4614
                            v    ?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_126073749_   4615 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 4664
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_126073749_   4665 CTAATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 4714
                         i v  i   v i  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_126073749_   4715 GAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAA--CATACTCATC 4762
                            v  i     i   i             v       --    i--   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATC 740

  chrX_126073749_   4763 TGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACA 4812
                            i  i  i  vi          v  i  v      vv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_126073749_   4813 AGAAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGA 4862
                          v     i     i     v  i?    i    ii      v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_126073749_   4863 CACTTCTCAAAAGAAGACATTTATGCAGCCAGGAAACACATGAAAAAATG 4912
                           i     v        i  vi viii    iv  i          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_126073749_   4913 CTCATCATCACTGGCCAT 4930
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (129 / 87)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.33 (20 / 15)  


1708 28.65 1.85 1.11  chrX_126079720_126083927.rev      582  1122 (3086)    L1M4_orf2#LINE/L1        6   550 (358)  

  chrX_126079720_    582 AAACATTCCATTCTCATCAATAGGTTGAATCGATATTGTTAAAATGGCCA 631
                          i i  i    vi    vi  v  vv  v ii          i     v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_126079720_    632 TACTGTCCAAAGCAATTTATAGATTCAATGCTATTTCTATTAAACTATCA 681
                             vi     vii  i  i        i  v  ii    i   v vi  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_126079720_    682 ATAACATTCTTCACAGAATTAGAAAAAAACT-ATTCTAAAATTCATATGT 730
                         iivi v  i  ii     v v  v  i--  -  i              v
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATATGG 153

  chrX_126079720_    731 AGCCAAAAAAGAGCCCAAACAGCCTAAGCTATCCTAGGGAAAAAGAATAA 780
                          iviiv  ii  v  vi  i    v  i v   i iiii  i     i  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_126079720_    781 AGCTGG-GGACAGTACATTACCTGACTTCAAACTATACAGCAAGGCTACA 829
                           i   -    -vi   i v  ii i      viv   vi   i      
  L1M4_orf2#LINE/    204 AGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_126079720_    830 GTAACCCAAACAGTACAGGAGTAGTACAAAAAATAGACACATAGACAAAT 879
                             i v i     iii v v i i i  ii -      i     iv   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCAAT 301

  chrX_126079720_    880 GGAAAAAGAAAAAGAGCCCTGGAATAAAGCCACACACCCACAACTATCTG 929
                             v ii vvi    i  v i      v   i   iii iiiii vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_126079720_    930 GTCTTCAACAAAATTAACAAAAGCAAACAATGGGAAAAGGAC--TCATTA 977
                         i i   i    iiv iv   i v  vv       i    i i--  -  -
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-TT- 399

  chrX_126079720_    978 TTCAATTAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGATTTAA 1027
                              iv             i      v  ?   i     i    v v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_126079720_   1028 ACTGGACCCCTTCATTACACCATATACAAAAATCAACTCAAGATGGATTA 1077
                         ii         v v i                 i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_126079720_   1078 AAGACTTAAATGTGAAACCTA----TA-AAAACTCTT-GAAGAAAATCTA 1121
                         ?    i       i i v   ----  -         -        iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_126079720_   1122 G 1122
                          
  L1M4_orf2#LINE/    550 G 550

Transitions / transversions = 1.94 (101 / 52)
Gap_init rate = 0.02 (11 / 545), avg. gap size = 1.45 (16 / 11)  

1023 23.24 3.36 1.83  chrX_126079720_126083927.rev     3392  3718 (490)    L1M4_orf2#LINE/L1      577   908 (0)  

  chrX_126079720_   3392 GGCAAAGATTTTTGAGA-AGGATGCCAAAAGCAATTGCAACAAAAACAAA 3440
                              v i   i v   - v  ii         vvv         iv   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_126079720_   3441 AATTGACAAATGGGAGCTAATGAAACTAAAGAGCTTCCACACAGCATAGG 3490
                            v  i    v   vi v  v   v v  i i   iiiii vv  v   
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_126079720_   3491 AAACTATCAACAGAGTAAATGTAAACAGACAACCCAAAGAATGGGAGAAA 3540
                          v        ------i  v  i  v          v             
  L1M4_orf2#LINE/    677 ACACTATCAA------GAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_126079720_   3541 ATATTTGCAAACTATGCATATGACAAAGTCCTAATATCCAAAATCTATAA 3590
                                    ii  ii  v   i  i vv  vi      i   v     
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_126079720_   3591 AGAACT----TAAATTAATAAGCAAAAAACAA----TCTAATTGAAAAGT 3632
                               ----i  v i     vv    i    ----i i    ?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_126079720_   3633 GGACAAAG-ATATTAACAGATACTTTTCAGAAGAGGACATACGTATGGCC 3681
                           i     -  v v  i   i i  i  vi    i  i    iv      
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_126079720_   3682 AACAAGCATATGAAAAAATGCTCAACAT-AGCTAATTA 3718
                           i     i       i           - ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (42 / 33)
Gap_init rate = 0.02 (6 / 332), avg. gap size = 2.83 (17 / 6)  


3022 28.24 0.55 0.77  chrX_126110233_126116510.rev     4878  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126110233_   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126110233_   4928 GGCCACAGTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v i v v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126110233_   4978 TACCAATGAGTTTCTTCACAGAA-TTGGAAAAAAAACT-ACTTTAAAGTT 5025
                          v   iivivi  i  ii     -   ---- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chrX_126110233_   5026 CATAGGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAA 5075
                             v    viiv  ii  v  v v  vi    iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_126110233_   5076 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTATGAT 5125
                                  i      vv   ii  v  ii i      viv     ii v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_126110233_   5126 GCTACAGTCACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGA 5175
                                 v i   i    ii         i iv ii i   v   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_126110233_   5176 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 5223
                         i        i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_126110233_   5224 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5273
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_126110233_   5274 TCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAAG 5323
                         vi  v  i  i              v      v  ?   i i i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_126110233_   5324 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATG 5373
                         v    ii    i    v   i     v                   i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_126110233_   5374 GATTAAAGACTTAAATGTTAGAACTAAAACCATCAAAAACCTAGAAGAAT 5423
                            i ?    i       v   i       i  v   vv i        v
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_126110233_   5424 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGTC 5472
                           v    ?i- v i -   iv   v v  vv i i   v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_126110233_   5473 TAAGACATCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5522
                           v    i        vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_126110233_   5523 TAATGAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5572
                          v  v   v i  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_126110233_   5573 AACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 5622
                           v  i     i   i             v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_126110233_   5623 CAAAGGGCTAATATCCAGACTCTACAATGAACTGAAACAAATTTACAAGA 5672
                         i  i  i  vi        v v  i  v     vvv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_126110233_   5673 AAAAAACAAACAGCCCTATCAACAAGTGAGCGAAGGATATTAACAGACAC 5722
                             i     i i   v  i? v  i  i  i      v v  i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_126110233_   5723 TTCTCAAAAGAGAACATTTATGCAGCCAACAAACACATGAAAAAATGCTC 5772
                              v     ii i  vi viii     i  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_126110233_   5773 ATCATCACTGGCCAT 5787
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (150 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2862 27.48 1.32 1.10  chrX_126164549_126171218     5272  6177 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126164549_   5272 TGGGAAAACAGTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5321
                            i  i i vi     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126164549_   5322 GGCCATACTGCCTAAAGTAATTCATAGATTCAATGTTATTCCCATCAAGC 5371
                            v     v  i   v i  ii i        i iv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126164549_   5372 TACCAGTGACTTTCTTCACACAATTAGAAAAAAACT-ACTTTAAATTTCA 5420
                          v    ivi i  i  ii  v  v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_126164549_   5421 TATGGAACCAAAAAGAGTGCATA-TAGCCAAGACAATCCTAAGCAAAAAG 5469
                                viiv  i iiiv  v -       i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_126164549_   5470 AACAAAGCTGGAGACATCATGCTACCTGACTTCATACTATACTACAAGGC 5519
                                i     ivv   ii  v  ii i    v viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_126164549_   5520 TACAGTAACCAAAACAACATGGTACTGGTACCTAA--ACAGATATATAGA 5567
                                 i   i   iii         i --   -- i   i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATAGA 296

  chrX_126164549_   5568 CCACAGGAAAAGAACAGAGACATTAGAAATAACAGCACACATGTACAACC 5617
                         i  vv    v    iv    vvii        vvv  i    v  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_126164549_   5618 ATCTGGTCTTTGACAAACCTGACAAAAGCAAGCAACGGGGAAAGGATTCC 5667
                          vi  i i  i     ivv  v   i v  vv   i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_126164549_   5668 CTATTTAATAAATGGTGTTGGGAAAACTGGCTGGCCTTATGCAGAAAACA 5717
                           v  i  i        i     v      v i?  vi     i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_126164549_   5718 GAAACCGGACCCCTTCCTTACACCTTATACAAAAACTAACTCAAGATGGA 5767
                            iii        v   i     v          i        i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_126164549_   5768 TTAAAGACTTAAATGTAAAACCCCAAACCATAAAAACCCTAGAAGAAAAC 5817
                          i ?    i         i v iv    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_126164549_   5818 CTAGGCA-ATACCATTCAGGAAATAAGCATGGGCAAATACTTCAGTATTA 5866
                         v    ?i- v i -   iv  vv vi vv i     vvii   ----   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC----TTA 591

  chrX_126164549_   5867 AA----ACACCAAAAGCAATTGCAACAAAACCAAAATTGACTAA--TGGG 5910
                         i ----            vvv         vv    v iiv   --   i
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_126164549_   5911 CTCTAATCAAACTAGAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGA 5960
                           - v      v vi i i   i  ii vv    i  v       vv i 
  L1M4_orf2#LINE/    642 CT-TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_126164549_   5961 GTGAACAGACAACTTACAGAATGGGAGAAAGTTTTTGCAAACTACCCATC 6010
                              v       ii               i v        ii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_126164549_   6011 TGACAAAGGTCTAATATCCAGAATCCACAAGGAACTTAAACAAATTTACA 6060
                            i  i  v  vi          vi i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_126164549_   6061 AGAAAAAAA-AAACAACTCCATCAAAAAATGGGCAAAAGACATAAACAGA 6109
                          v     i -   i   i v  i?             i  iv i  i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_126164549_   6110 CACTTCTCAAAAGAAGACATTTATGTGGCCAATAAACATATGAAAAATAG 6159
                           i     v        i  vi vi          i  i       ivv 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_126164549_   6160 CTCATCAACACTGCTCAT 6177
                             v  v  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (143 / 102)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


3048 25.14 2.45 1.45  chrX_126196181_126200504.rev     2935  3833 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126196181_   2935 TGGAAAGAT--TCTATGCTCATGGATTAGAAAAATCAAAATTGTTAAAAT 2982
                                  --i i   i         i   i v i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126196181_   2983 ATCCTTACCACCCAAATCAATCTACAGGTTCAATGCAATCCCTATCAAAA 3032
                         iv vv   iv       ii        i     i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126196181_   3033 TACCAATAATATTCTTCACAGAAATAGAAAAAAATAGTCCTAAAATT-AT 3081
                          v   iiviiv  i  ii       v  v  iv- ii          -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_126196181_   3082 ATAGAAACACACACACCAAAAAAC--AGAATAACCAAAGCTATCCTCTAC 3129
                           i    ii  ------- iii  --      i     i v   i v- v
  L1M4_orf2#LINE/    150 ATGGAAATGCA-------AGGGACCCAGAATAGCCAAAACAATCTTG-AA 191

  chrX_126196181_   3130 AAAAAAAAATTAAAATGGGGAAATCAT-CTTACCAGACTTCAAATTGTAT 3178
                            i  i  iv  iv   i i v   i-   v   - i      viv  i
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTAC 240

  chrX_126196181_   3179 TACAGAGATATAGTAACCAAAACAGCATGGTATTGGCATGGAGACAGGCA 3228
                             i  v  i     i   i    ii     i      iii  i  i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_126196181_   3229 TATAGAGCAATGGAACAGAAGAGAGAATGCATAAACAAATCCACACATCT 3278
                               v        i    vv    i v  v   i   i   i    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_126196181_   3279 ACAGTGAACTCATTTTTGACTAAGGTGCCAAGAATATC----GGGGAAAG 3324
                          ii  v  i v     i   v i          vi  i----        
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_126196181_   3325 CATAGTTGTTTCAACAAATGGTGCTGGAAAAACT---TATCAATATGCAG 3371
                         v     iv                   i v    ---  ? v i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_126196181_   3372 TCAAAGGGAACTGAAGTCCTATCTTCCAAT-TATA-AAAAATCAAGTCAA 3419
                         vvi  v i ii  i vi    i  iv  vi-    -      i  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_126196181_   3420 AATGGATTAAAGACTTAAATATCAGACCTCCCTGTATGAAACTGCTAAAA 3469
                                i ?    i     i v   v  vvvvv   i     vi  i  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_126196181_   3470 GAAAACATTGGGAAAACTATTCAGGACATTAAACTGGGCAAAGATTTCTT 3519
                                 v  ?iv  v v   iv   v  iiii i     v i      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_126196181_   3520 GAGTAATACCCCATAAGCATAGGCAACCAAAACAAAAATGGACAACTTGG 3569
                         iii  vv  v   v     i i     v   iv      i  i  v    
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_126196181_   3570 A-TCCAACCAAGTTAAAAGGCTTCTGCACAGCAATGGAAAC----AACAA 3614
                          - i  v v  i      i-   i  ii vv   v   v  ----  v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_126196181_   3615 AGTGGAGAGACAACTCACAGAATGGGAGAAAATATTTGCAAACTACTCAT 3664
                             i i       i                           ii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_126196181_   3665 TTGACAAGAGATTAATAACCAGAATATATAAATAGCTCAAACAACTCAAT 3714
                         i   i   i  i vi  v              v i   vv          
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_126196181_   3715 AGGAAAAAAA-AATTAAACATCTGTTTAAAAACGG-CAATAAATCTGAAT 3762
                          iv     i -  v   v -- vi  ?     i  -   vii  i     
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACC--CAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_126196181_   3763 AGATATTTCTCAAAAGAAGACATACAAATGGTGAACAGGTACATGACCAG 3812
                            i       v        i          iv  i i i      vv  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_126196181_   3813 GTGCTCAACATCACATCTATC 3833
                         i            ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (136 / 86)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.94 (35 / 18)  


2639 26.58 7.14 0.94  chrX_126200817_126204306     2144  2997 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_126200817_   2144 GAAAAAATAATCCCATGTTTATGGATTGGAAGGATTGATATTGCTAAAGT 2193
                          i   i   -         i            iv  i      i   ii 
  L1M4_orf2#LINE/      2 GGAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126200817_   2194 GTCCACACTACCCAAGGCAATTTACAGGTTTAATGCAATCTCTTTCAAAA 2243
                          v v i   v     ivii  i     i  i  i      i  v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126200817_   2244 TACCAATGGCATTCTTCACAGAAATAGAAGAA--------AGAATCC-TA 2284
                          v   iiv  v  i  ii       v  vi i-------- i   i -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_126200817_   2285 T-------------ACTTAG------CAAAAT---------------GAA 2300
                          -------------  ii  ------     i---------------   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_126200817_   2301 CAAAACTAGAGGAATTACATTACTTGACTTCAAGTTACACTATAGAACTA 2350
                             ii i     v i   i v iii i     ivivi    i i i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_126200817_   2351 TAATGAACAAAAGATCATGGTACTGGCATAAAATCAGACACATAGAACAA 2400
                         i i i v   i v vii              iivi     i     v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_126200817_   2401 TGGAACAGAATACAGAACCCAGAAACAAATCCATACACCTAGAGTGAACT 2450
                              i     vv   ii       i   i       ii  vi  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_126200817_   2451 CACTTTTAACAAGA-TGCCAAGAACATTCACTGGAAACAAAGCAGTCTTT 2499
                         v i   ii     i-        v      v   ii v i ii       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_126200817_   2500 TCAATAAATGGTGCTGAGAATATTAAATATCCATATGCGGAAGAATGAAA 2549
                             i           i  vv i ii   ?   i    ii         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_126200817_   2550 CTAGATCCCTATCTTTTGCCATATACAAAA------------TGTATTAA 2587
                         i i  i     i  ivii            ------------  v  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_126200817_   2588 TGACTGAAATTTAAGACCTCAAACTATAAAACTACTACAAGAAAACATTG 2637
                         v   iv    v     v  v             vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_126200817_   2638 GGGGAAATCTCCAGGGAATAGTTCTGGACAAGAATTTCTTGAGCAATACC 2687
                          ? v      i iv ivv v vvi i i   vii      -  vv  iv 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGAC 599

  chrX_126200817_   2688 CCCAA--GCACAGGCAACCAA-GCAAAAATGGAAAAATGGGTTCACATCC 2734
                         v    --     i     v  - v      i  v    v  viiv    v
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_126200817_   2735 AG-TTAAAAATTTTCTACACAGCAAAGGATACAATAAAAAAAATTGAAGA 2783
                          i-       i   - iii vv       i  v  v  i   i -   i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGT-GAAAA 697

  chrX_126200817_   2784 GACAACCCACCAAATAGGAGAAAATATTTGCAAACTACGCATCTGGCAAG 2833
                                   vi   i                  ii iii     ii   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_126200817_   2834 GGATTGATAACCAGAATATAAAAGGAGCTCAAACAACTCTATAGGAAAAA 2883
                            i vi  v          v  i  i   vv       v   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_126200817_   2884 ATCTAATAGTCTGATCCAAAAAAAAATAGGAAAACGATTTGAATAGACAT 2933
                         iv v    ii ii  i----?      i  v   v               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATT----WAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_126200817_   2934 TACTCAAAAGAAGACACCCAAATGGCAAACTGACATAT-AAAATTTGCTT 2982
                          v   v        i iv        v  ivii  i  -    vv    i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_126200817_   2983 AACATCACAGAAATG 2997
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (141 / 82)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 4.31 (69 / 16)  


 239 19.30 0.00 0.00  chrX_126221242_126227520      367   423 (5856)  C L1M4_orf2#LINE/L1   (0)   908   852  

C chrX_126221242_    423 AGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCAC 374
                               i  vi viii     v  i          i       v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

C chrX_126221242_    373 TGGCCAT 367
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.00 (0 / 0)  

3254 27.09 0.44 0.44  chrX_126221242_126227520     4879  5786 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126221242_   4879 TGGAAGAACATTCCATGCTCACGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i   i  i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126221242_   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126221242_   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_126221242_   5027 TATGGAACCAAAATAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  vi  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_126221242_   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_126221242_   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_126221242_   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_126221242_   5225 GTCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                         ivi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_126221242_   5275 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i                 v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_126221242_   5325 GAAACTGGATCCCTTCCTTACACCTTATACCAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v     v     i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_126221242_   5375 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_126221242_   5425 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5474
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_126221242_   5475 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5524
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_126221242_   5525 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5574
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_126221242_   5575 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5624
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_126221242_   5625 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_126221242_   5675 AAACAAATAACCCCATCAAAACGTGGGCGAAGGACATGAACAGACACTTC 5724
                          i           v  i?   vi     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_126221242_   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5774
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_126221242_   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2241 28.16 3.46 2.01  chrX_126233716_126238622     3520  4414 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126233716_   3520 TGAAAAAATACACTCCGCTCATGGATTAGAAGAATCAATAATATAAAAAA 3569
                           i   i   iv ivi i         i     v i    v i v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126233716_   3570 GACCATGTTGCCCAAAGCAATAGCAACCTACACAATAAATGCAATTCCTA 3619
                          i v  ii v      vii  ------     v v v  i     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT------CTACAGATTCAACGCAATCCCTA 94

  chrX_126233716_   3620 TACAAATACCAA-TGCCAGTTTT-CACAAACTTAGGAAAAACT-ATTCTG 3666
                          vv    v   i-    vv    -  v   i ---  v  i  -  i  i
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTA 141

  chrX_126233716_   3667 AAATTTGTAAGGAACGAAAAAAAGAGCCCA-AAGAGCCAAAACAACCCTA 3715
                              ii  v    -- viv  i ii    -  v           i i i
  L1M4_orf2#LINE/    142 AAATTCATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_126233716_   3716 AGCAAAAAGAACAAATCTGGAGGCATTACGTTACATGACTTCAAATTATA 3765
                          iv  i         vi      vv i  ii v vii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_126233716_   3766 CTACAAGGCTATAATAACCAAAACAGTATGGTACTGGTATTAAAATAGAC 3815
                               i    i i   i   i     i         i  v ii      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_126233716_   3816 ACATACATCAGTGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACT 3865
                          i   v    i     i     v    ii           v   v i i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_126233716_   3866 TACAACCAACTGATCTT--GTAAAAGTCATCCAAAAC-ATACACTTGAGA 3912
                           iiii   i    i  --ii  ii  v--    i  -  v  v v i  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTG--CCAAGACCATTCAATGGGGA 387

  chrX_126233716_   3913 CAGGACACCCTATTCAATAAATGGTGCTGGGAAAATTGTATAGGTATATA 3962
                         v  i i vi  v     i              v  i  v   ?vi i  i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_126233716_   3963 CAGAAGAATGAAATTAGACCTGTATATCTTGTCATATA-AAAATTTATCT 4011
                           i         i  i    iv  iv  viii      -    v   v  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_126233716_   4012 CAAGATGGTTTAAAAGCTTAAATATAGGACCAGAAACCATAAGAATTCTA 4061
                            i    v i ? ii i     i  i  v vi    i    i v ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_126233716_   4062 GAAGTAAATCTAGAAAAACCTCTTCTGGATGCTGGCACTATCAAATAATT 4111
                             v   iv   i?iv vv     vv  ivi   -ii  vvv   ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTT 586

  chrX_126233716_   4112 TGTGA-ATAAGTCCTCAAA--TAAAAATTCAACAAAA-----AATAAACA 4153
                          v v -   v v vi    --i v  i--        -----    i i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAG--CAACAAAAGAAAAAATAGATA 634

  chrX_126233716_   4154 AATGGGACTTAATTAAACTGAAGTATTTCTGCATAGCTAAAGA-ACTAAT 4202
                            v      v  i   v v  iv i  i  iiivv v  i  -    - 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-T 683

  chrX_126233716_   4203 CAACAGAATAAATAGACAATCTATAGAATCAAAGAAAATATTCACAAACT 4252
                            v i i i  v      i i i     vii          ii    ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_126233716_   4253 ATACATCCAACAAAGAACTAATATT-----TCTACAAGTAACACAT-CAG 4296
                            i   ii i  i i   vi   i----- v  i  iv   v v -  i
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_126233716_   4297 C--AAGAACAAAATGAATAATAAC---ATTAAAAAGTGGGCAAATGATAT 4341
                          --  v  i    v  vv      ---   ?    i        v   v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_126233716_   4342 GGGTAGATATTTCTCAAAAGAAGACATACAAAGGGTCAA---ACATATGA 4388
                          ii    i       v        i       v  i   ---i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_126233716_   4389 AAAAAATGCTCAACATCAAGAATTAT 4414
                            i -            ????????
  L1M4_orf2#LINE/    884 AAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (152 / 96)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.04 (49 / 24)  


 423 22.01 5.03 9.43  chrX_126239846_126241852.rev      102   260 (1747)    L1M4_orf2#LINE/L1        1   152 (756)  

  chrX_126239846_    102 TGGAAAAATATTCCAGGCTCATGTATAGAATGAATCAGTATTGACAAAAT 151
                               i    i   v i     v  v i v  v i i     vi  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126239846_    152 GGCCATATTCTCCAAAGCCATTTATAGATTCAATGCTATTCCCATCAAAC 201
                            v   i  i     viv  i  i        i  v  i  i      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chrX_126239846_    202 TATAAATAACATTCTTCACAG--ATTTTTTTTTTAAAAA---ACA--CT- 243
                         ----------  i ----   --iii      vi i   ---   --  -
  L1M4_orf2#LINE/    100 ----------ATCC----CAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chrX_126239846_    244 ATTTTAAAATTCATATG 260
                           ii             
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATG 152

Transitions / transversions = 2.18 (24 / 11)
Gap_init rate = 0.04 (6 / 152), avg. gap size = 3.83 (23 / 6)  

1222 27.30 3.51 0.54  chrX_126239846_126241852.rev      504   873 (1134)    L1M4_orf2#LINE/L1      160   540 (368)  

  chrX_126239846_    504 AAATGAGCTCGAATATCCAGGGCAATTTTAAACAAAAGGAATGAAACAGG 553
                           iv  v iv     v   iii    i  i  v  i i   ii  iiv  
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_126239846_    554 AGGCCTCACATTACCCAACTTCAAACTATACTACAAGGCTTCAGTAACTA 603
                            v      i v     i      viv        i   v      ii 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_126239846_    604 AGACAGCATGGTACTGGGACAAAAACAGACACACTGACCAATGGAACAGA 653
                               ii         v i  ii i     i iv  i        i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_126239846_    654 ATAGAAAG-CCA-AAATATAGCCACACACCTACACCCACCTGATGTTCAA 701
                           v  i  -   -     v v   i   ii  iivi  vi    v   i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_126239846_    702 CAAAGTTTACAAAACAAG-CAATGTGGTAAGGAC--TCTGTTCAATAAAT 748
                            i v vv   i  v v-     v  v   i i--   v     i    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_126239846_    749 AGTGCTGGGATAAATG-ACAGGCATATGCAGAATATTGAAGTTGAATCCT 797
                         i         i  v  - i ?v  i     i  v v        i i  i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_126239846_    798 TTTCTTA-----TATACAAAAATCAACTCGAG--GGATTAAAGATTAAAA 840
                          vi  i -----           i     i i--    i ?   iiv   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_126239846_    841 TGTAAAAGCCTACCCTATTTAAAACTCTTGAAA 873
                              i   iv vv    --         ii  
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTAT--AAAACTCTTAGAA 540

Transitions / transversions = 1.75 (63 / 36)
Gap_init rate = 0.02 (8 / 381), avg. gap size = 1.88 (15 / 8)  

 654 27.65 8.38 1.40  chrX_126239846_126241852.rev     1172  1529 (478)    L1M4_orf2#LINE/L1      526   908 (0)  

  chrX_126239846_   1172 ATAAAACCCTT-GAAATAAACCTAGGAAACATAA---TTCTAGACAT-AG 1216
                                i   -   iv    v    ?i---   ---   vv   v -i 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNG---TAAATCTTCGTGACCTTGG 572

  chrX_126239846_   1217 GCCCTGCAAAGATTTTATGAAGAAGATGCCAA---------CAACAAAA- 1256
                          iivv    v i   iv ii v v  ii    ---------        -
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_126239846_   1257 -----ATTGACAAATGGCAATTAAACAAAA----GAACTTCTACACAGCA 1297
                         -----  v  i    v v v  v v     ----i     i iii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_126239846_   1298 CAAAGAAACTATCAA-----TAAACAAACCACCTATAAAATGGGAGGAAA 1342
                         -  i  v        ----- i  v i  v   i i i        i   
  L1M4_orf2#LINE/    673 -AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_126239846_   1343 TATTTGCAAACTGTACATTTCATAAAGGTCTAATACCCAGGATCTGTAAG 1392
                                   iii  i  i v    i  v  vi  i    i  v i   i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_126239846_   1393 GAACTTAGACAAATGAACAAGCAAAAACCAAAGAACCCCATTAAAAAGTG 1442
                              ivv    v v  i  vv    iv    v     v   ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_126239846_   1443 TTGCAAAGAACATGAACAGAGATTTTTCAATGGAAGACATACACACAGCC 1492
                         v-      i iv    i   v    i  v vi     i     v ii   
  L1M4_orf2#LINE/    822 G-GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_126239846_   1493 AACAAGAATATAAAAAGCAGC-CAACAAGAATATAAAA 1529
                           i   v i  i     vv  -     vv ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (51 / 46)
Gap_init rate = 0.03 (11 / 383), avg. gap size = 3.18 (35 / 11)  


2444 25.37 11.95 1.59  chrX_126322598_126324595      686  1505 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_126322598_    686 AAACATATTCCATGTTCATGGATTGGAAAAAATAAACATTGTTAAAATGT 735
                            v    i                   i vv   -i        i   v
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAA-TATTGTTAAGATGG 52

  chrX_126322598_    736 TCATACTACCCAAAGCAATTCACGGATTCAAAGCAATCCTTATCAAAATA 785
                         iv     v      vii  ii  i       v       i         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_126322598_    786 CCAATGACATTCTTCACAGTTATAGAAAAAAAACT-ATCCTAAAATTTAT 834
                            iivi v  i  ii   vv  v  v  i---  -           i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCAT 149

  chrX_126322598_    835 ATGGGGACACAAAAGATGCAGAATAGTCAAATCCATCCTAAGCAAAAATA 884
                             ii ii   ii  iv        i    v v   i i iv  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_126322598_    885 ATAAAACTGGAGGAATCACATTACCTGACTTCAAGTTATACTACAGAGCT 934
                          i   ii       v     i v  ii i     iviv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_126322598_    935 ATAGCAACCAAAACAGGATGGTACTGGCATTAAAACGGGCACATAGACTA 984
                          i  i  i   i    vi            v ii ii i  i     ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_126322598_    985 ATGGAACAGAATAGAGAACCCAGAAATGAA--------TTTGTG------ 1020
                               i     v    ii        i  --------   i  ------
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_126322598_   1021 ----------------TGC--------TT--------------------- 1025
                         ----------------   --------  ---------------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_126322598_   1026 ----ACA----GTG-----------GGATATCCATATGCA---GAATGAA 1053
                         ----   ----   -----------     ?   i     ---       
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_126322598_   1054 ACTGGACTCTTATCTCTCCCCATATACAAAAATCAAATCAAAATAGATTA 1103
                         ii     i i  i   v v              i  v       i   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_126322598_   1104 AAGAC--AAATAAAGGACTTGAAACTATGAAACTACTACAAGAAAACAAA 1151
                         ?    --    iv i  vi i       i     vi  ---------i  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA---------GAA 540

  chrX_126322598_   1152 GAAAACATTGGGGAAAATCTCCAGGACATAGGTCTGGGTAAAAATTTTTT 1201
                                 v  ? v      i iv   v v  vi i  i  vii   i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_126322598_   1202 GAGCAATATCCCAGAAGCACAGGCAACCAAAGCCAAAATGGACAAAAAGA 1251
                         iiii vv iv   i       i     v    vv     i  i   vv i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_126322598_   1252 ATCACGTCAAGTTTAAAGGTTTCTGCATAGCAAATAATACAATCAGCAAA 1301
                          iiv i    iv     iii  i  iiivv    vi i  v    iv   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_126322598_   1302 GTCAAGAGACAACCTACAGAATAGGAGAAAATATTTGTGAAGTATCCATC 1351
                           v  i        i       i              ii  vi  vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_126322598_   1352 TGACAAGAGATTAATAATCAGAATATATAAAAAGCT-------------A 1388
                            i   i  i vi  vi             i i  ------------- 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_126322598_   1389 GGAAAAAATCTGATAATCCAATATAAAAATGGGCAAAT-ATATGAATAGA 1437
                         iv     iv vi    i     v?             v-  v        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_126322598_   1438 TATTTCAGAAAAGAAGACATACGAATGTCAAACAGGCATATGAAAAGGTG 1487
                         i     vvv        i    i    v v  i i   i        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_126322598_   1488 CTCAACAGCATTGATCAC 1505
                                v  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (132 / 72)
Gap_init rate = 0.02 (14 / 905), avg. gap size = 7.93 (111 / 14)  


3126 26.84 1.34 0.22  chrX_126333079_126338138     3670  4567 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126333079_   3670 TGGAAACACATACCATGCTCATGGCTGGGTAGAATAAATATTGTGAAAAC 3719
                               v i  v     i      v v  v   v v        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126333079_   3720 GACCATACTGTTAAAAGCAATCTACAAATTCAATGCAATCCCTATCAAAG 3769
                          i v     viiv   vii       i      i               i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126333079_   3770 TAC--ACCATCATTCTTCACAGAATTAGAAAAAATAATTCTAAAATTTAT 3817
                          v --i iii -  i  ii     v v  v  iv i  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_126333079_   3818 ATGGAACCATAAAAAAGCCAACATAGCCAAAGCAAGAATAAGCAAAAAGT 3867
                               viii  iii v   iv         i   vvv i iv  i   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_126333079_   3868 ACAAATCTGGAGGCATCACACTACCTGATTATAAACTATACTATAAGGCC 3917
                              vi      vv       v  ii   vi   viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_126333079_   3918 ATAGTCACCAAAACAGCATGGTACTGGTGTAAAAATAGGCACATAGACCA 3967
                          i   v i   i    ii         ii   ii    i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_126333079_   3968 GTGAAACAGAATACAGAACCCAGAAATAAACCCAAA----TACAGCCAAC 4013
                         i  i  i     vv   ii               v ----  ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_126333079_   4014 CAATCTTTGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTT 4063
                         ii  i  i     i vviv   i v   vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_126333079_   4064 TTTAACAAATGGTGCTGAGATAATTGGTTAGCCATGTGTAGGAGAATGAA 4113
                           i              i  i  i   v  ?   ii  i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_126333079_   4114 ATTGGATCCTTATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTA 4163
                         i     i  i  i   v    v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_126333079_   4164 AGGACTTAAACCTAAGACCTGAAACTGTAAAAATTCTAGAAGGTAACATT 4213
                         ?i   i    iv     v  i     i     v ii      iv     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_126333079_   4214 GGAAAAACCCTTCTAGACATTGGTTTAGGCAAGGATTTCAAGAACGAGAA 4263
                           ?iv  vi    vv   v    v        v i    vvii iiv  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_126333079_   4264 ACCAAAAGCAAATGCAATAAAAACGAAGATAAATAGCTGGGACTTAATTA 4313
                                   v v    i    ivi  i   i   iv v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_126333079_   4314 AA-CTAGAAGTTCATG-GC---AATAGGA-ACAGACATCAGAGTAAACAG 4357
                           -i  i  ii iv  -  ---  -    -  viv  vv i   i  v  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAA-AGGACACTATCAAGAAAGTGAAAAG 698

  chrX_126333079_   4358 ACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAG 4407
                                     i           v  ii   vii   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_126333079_   4408 GACTAATATCCAGAATCTACAACAAACTCAAACAGATCAGTAAGAAAAAA 4457
                             vi          v  i  vi     vv   iv   i   v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_126333079_   4458 ACAAACAATCCTATCAAAACCTGGGCTAAGGGCAGGTATAAACAATTCTC 4507
                              i  i  v  i?   vv     v    iivv v   i   v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_126333079_   4508 AAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCACAACAT 4557
                         v                       i  i  i       i    v      
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_126333079_   4558 CACTAATGAT 4567
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3069 22.95 2.84 3.61  chrX_126340232_126343506.rev     1870  2784 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126340232_   1870 TGGAAAGATAGTCCATGTTCGTTCATTGGAAGAATCCGTATTGTTAAAAT 1919
                                   vi        i vv         v ivi         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126340232_   1920 GTCTACACTACCCAGACCAATCTACAGATTCAACATAACCCCTATGAAAA 1969
                          v v i   v    i iii               ii  i      v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126340232_   1970 TGCCGATGGCATTCTACACAGAAATAGAAAAAAAAACT-ACCTTAAAATT 2018
                          v  iiiv  v  i vii       v  v  i----  - i i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chrX_126340232_   2019 TATATAAAACCTAAAAAGACCCAGAATAGCCGAAGCTACCGAAGCTATTA 2068
                         i    ii  vivv  ii              i  i -----  v  ----
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC-----AATCT---- 187

  chrX_126340232_   2069 TGAGTAACAAGAAAAAAAAAAAAAAAAACAA-GCTGGAAGAATCACATTT 2117
                            ---------------    i  i     - i    i  v     i  
  L1M4_orf2#LINE/    188 TGA---------------AAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_126340232_   2118 CCTGCCTTCAAATTATATTGAAGAGCTATAGTAACCAAAACAGCCTGATA 2167
                           iivi      viv  i iv i     i     i   i    iv  i  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_126340232_   2168 CTGGCATAAAAACAGACACATAGACTAATGGAACAGAATAGAGGACCCAG 2217
                                  ii i     i     ii       i     v   iii    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_126340232_   2218 AAACAAATCCACACACTTATAGGAAACTTATTTTTGACAATG-TACCAAG 2266
                            i   i   i   i    i vv  i v     i     v - i     
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_126340232_   2267 AATATACACTGGGGAAAAGACAGGC------ACAAATGGTGCTGTGAAAA 2310
                          vi  v  v        ii i  v ------             v  v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_126340232_   2311 CAGGATATCCATAAGCAGAAGAATGAAACTAGAGCCCTATCTCTCATCAT 2360
                          v     ?   i v   i         ii i  v     i   v  i   
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_126340232_   2361 ATA-AAAAATCAAGTCAAAATGGATTATAGACTTAAATTTAAAATCATAA 2409
                            -      i  v           i ?    i     v   i v vv  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_126340232_   2410 ACTATAAAACTACGATAAGAAAACATTGGAGAAACACTCCAGGACATCGG 2459
                                    viv v          v  ? v  vv  i iv   v i  
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_126340232_   2460 -TCAGGGAAAATATTTCTTGAGGAAT-ACAC--AAAGCACAGGCAACCAA 2505
                         - i   v  vi-i      -  iv  -    --        i     v  
  L1M4_orf2#LINE/    573 GTTAGGCAATG-GTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_126340232_   2506 AGCAAAAA--G------TGTGATCATATTAAG-TTAAAAGCTTGTGCACA 2546
                           v     -- ------  -  iivi  i  i-      i   v  ii v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTG-GACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_126340232_   2547 GCAAAGGATACGATCAGCAAAGTGAAGAGACAACCCACCGAATGGGAGCA 2596
                         v       i  v    iv        i           v         v 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_126340232_   2597 AATGTTTGCCACCTACCCATCTCACAAGACACTAATAACCAGAATATATA 2646
                            i     v vii ivi    v i   iv   vi  v            
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_126340232_   2647 AGGCATTCAAACAACTCTATTAGAAAAAAAATCTAATAATCAAATT---A 2693
                          i v i  vv       v  v v     i -- v     i v    --- 
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGA--CAAATAACCCAATTWAAA 817

  chrX_126340232_   2694 AATAGGCAAAAGATCTGAATAGATATTTCTCAAAAGAAGGCATACAAATG 2743
                            i      i   i        i       v       ii         
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_126340232_   2744 GCAAACAGGCATATGAAAAGGTGTTCAACATCACTGATCAT 2784
                           v  i i   i        i  i         ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (123 / 84)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.95 (59 / 20)  


2633 27.11 1.27 5.49  chrX_126355003_126359072     2630  3577 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126355003_   2630 TGGAAAGACATCTCATGCTTATGGATTGCAAGAATTAATATGGTTAAAAT 2679
                                 i   i    i i        v    v       v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126355003_   2680 GACCATACTTCCCAAAGTCATCTACAGATTCAATGCAATCCTTATCAAAA 2729
                          i v     i      v v              i       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126355003_   2730 TACCAACATCATTATTCACAGAA--TCAGAAACAACAATTATAAAATTTG 2777
                          v   i vv v  v  ii     -- v v  i --ii  iv       ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chrX_126355003_   2778 CATGGAACAACAACAACAACAAAGAATTCA-AATAGCCAAAGCAGTTCTG 2826
                         i      -------- ii-   i i ii  -          i  i ii  
  L1M4_orf2#LINE/    149 TATGGAA--------ATG-CAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_126355003_   2827 ACCAAAAAAAAAAAAAAAAAATCCCCCAAAATTAAAAAGCTGCAGTGATC 2876
                          ----------    i  i  -----    i  ii iii  -------- 
  L1M4_orf2#LINE/    190 A----------AAAAGAAGAA-----CAAAGTTGGAGGACT--------C 216

  chrX_126355003_   2877 ACACTACTTGACTTCAAAATATATTACAAGGCTATACCAAACCACCAACC 2926
                              v iii i       iv  i     i    -----------  iiv
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTA-----------CAGTA 255

  chrX_126355003_   2927 ATCCAACCAAGGCATGGTATTGGTATAAAAACAGACACCTATAACAATGT 2976
                            v iv  -- ii     i   i    ii i     iv  v v     v
  L1M4_orf2#LINE/    256 ATCAAGACA--GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_126355003_   2977 TACATAATAGAAAACCCTGAAATAAATGCATATACTCATAGCAAACTGAT 3026
                         v i v   v  i ii  v        iv    i i i  i iv  i    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_126355003_   3027 TTTTCACAGAAGCATCAAGAATATGCAA------AAGGGTGCCCTCTTCA 3070
                            iv   iii iii     vi  v   ------   ii ivi  i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chrX_126355003_   3071 ATAAATGGTGCTGGGTAAATTAGATATCCATATGAAGAAGAGTAAAACTG 3120
                          i             vv  i i    ?   i   v i    i i  ii  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chrX_126355003_   3121 AATCACTACCTCTCATGTCATACAAAAGTCAATTTAAGATGGATTAAAGA 3170
                         i i v       v  ivvi        i i  i i  i      i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_126355003_   3171 CTTAAACATTACACCCCACACTGTAAAACTACTAGATTAAAACATAGGGA 3220
                          i    ii v v v iv v   i       vi    vv          ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_126355003_   3221 AAACACTTCAGGTCATTGATTTAGGTAAAGATTTTACCTTTTGGCTAAGA 3270
                         v  vv    iv v v   iv     i  v i   i-----  i v  v  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-----TTAGATATGA 598

  chrX_126355003_   3271 CCTCAAAAGCACAGACA-CAAAAATAAAAACAAACAAATAAAGCTATATT 3319
                          vi          ii  -     iv     i i i    viii  vi  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_126355003_   3320 AAACTGAAAAGCTTCTGCACCACAAAGGGAACAATCAACACAGTGAAGAG 3369
                            v v    i   i  ii iv      iv  v     v v      i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_126355003_   3370 ACAACCTGTTGAATAGGAGAAAATATTTGCAAACTATTCATCCACCAACA 3419
                               iiiv    i                  ii  vi   iivi  vi
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_126355003_   3420 GACTAATATCTAGCATATACAAGGAACTCAAACAACTCAACAATTAGAAA 3469
                             vi    i  v     i  i      vv         i   v i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_126355003_   3470 ATGAAGAATCCCATTTAAAAGGGGGAAAATGTCATGAATTGACATTTCTC 3519
                          ii  v  i  v   ?    iv   v   v viv     v          
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_126355003_   3520 AAAAGGAAATGAACA--TGCCCAACGGGTATATGGAAACATGCTCAATAT 3567
                         v    i i  iv   --  v    iii i i   i   v        i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_126355003_   3568 CACTGGTGCA 3577
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.81 (163 / 90)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.57 (64 / 14)  


2546 23.58 5.45 4.45  chrX_126376701_126378623.rev      534  1432 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126376701_    534 TAGAGAACTATTCCACACTGATAAATAAGATTATTTAATACTATTAGCAA 583
                          i  i iv   i   iii v  ii  vi  vv i      i i   iv v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126376701_    584 GGTGGTCCTCCCTCAAATTGGTCCACAGTTTCAATGTAATTTACATAAAA 633
                           iii v     -       i  i    v     i i   iivi  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_126376701_    634 ATTCCAGATGGATTTTTTCTTGCAGAAACTGACAAGTTGACTATAAAATT 683
                           i    v  ---ii   i         i       i   iiv       
  L1M4_orf2#LINE/    100 ATCCCAGCTG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_126376701_    684 CATATGGAAATTCAAGGGTCCAAGAATAGCTAAAA--AT----------A 721
                                    v      v  v        i    --  ---------- 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_126376701_    722 AGAACAGTATTGGAAGACTCAGACT-CCCAATTTTAAAACTTACTACAAA 770
                               ivi     i      v   -        i               
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_126376701_    771 -CAGCAGTAACTAAGACTGATTTTCAAATTATT-TAATAGCATACTAAG- 817
                         - vi      ii     v ---------- i v-  v i     -- i -
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAG----------TGTGGTACTGGCATA--AGGA 284

  chrX_126376701_    818 TA-ATATATAGTTACATGGAATGGAATTGAAAGTCCAAAAAACAAACCAA 866
                           - i      v vv       i       i      i   -i     v 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCA 333

  chrX_126376701_    867 TAAATT----GTCAGTTGTTTTTAAACAAAGATACCTGCCATACAATTTA 912
                           v   ----    i   v    vi    i i i  ---v v  v   i 
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCC---AAGACCATTCA 380

  chrX_126376701_    913 ATATGATAA--ATATTTTTTGTAAAATTTGAAACAAATAGTGGTGAGATA 960
                           iv iv  --   v i   ------- i--       i   v  i  i 
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTT-------TC--AACAAATGGTGCTGGGACA 421

  chrX_126376701_    961 ACT--ATCTCT-TATCCTGGTAAGAAAATGAAATCAAAACTCTGTTTCAC 1007
                            --  v? i-i  ---- i  i i      i iii v i  iii    
  L1M4_orf2#LINE/    422 ACTGGATAKCCACAT----GCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_126376701_   1008 ATCACATACAATAAATAACTCAAAATTAATCAAATATCTATATATAAGAG 1057
                          i  i      v  v           vi    ? v i   v  i      
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_126376701_   1058 TTGAAAATATAAAATTCTTAGAAGGAAACA--GATGAAAATCTACATGAC 1105
                         i i   v       i         i     -- i? v      v i    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_126376701_   1106 CCTGAGTTAAGCAACTCTTAATTTTA-ATATGACACCAAAAACACTAGCA 1154
                          i  i    i    ivv  -- i   -              i   v    
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTT--TCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_126376701_   1155 AAAAAAACAAAAAATA-ATAA--------TCATCAAA-TTA----CTGTT 1190
                          v    i-        -    --------        -   ----  v  
  L1M4_orf2#LINE/    616 ACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_126376701_   1191 TTGCTCCAAAAGATACCATAGAGAATGTGAAAAAACAACATTCAAAATAA 1240
                         v    i    i  i  i  vi    v       i     viv  i   ii
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_126376701_   1241 ACAAAAAT-TTTGCAAATCATGCATGTGATAGGGGACTTATATTTAGATT 1289
                         ivi     -            ii  v     i       i   ii   v 
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_126376701_   1290 GTATAACTGCCACTTAGAAGAGTACAAGAAAAAGGCAAGTAATTTGATTT 1339
                         i     vviv v    v  vvvv i  v      i   i   iiii   ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_126376701_   1340 AAAAG-AAGCAAAGTACAGAT----ATTGGCATTTCCCCAAGGGAGCTAT 1384
                             i-ii      ----   ----  v i      i    i i  v   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAG----GATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_126376701_   1385 CAAAATGTTCAGTAAGCATACAAAAAAATACTCAACATTATTAGTCAT 1432
                         vv     vi  i      i ii    i  i        i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (134 / 74)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 2.78 (89 / 32)  


2912 26.98 1.32 1.32  chrX_126379206_126384927     4322  5229 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126379206_   4322 TGGAAAAACATTAGATTCTCATGGATAGGAAGACTCAATATTGTGAAAAT 4371
                               i i  ivv  vi        v        i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126379206_   4372 GGCCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCCATTAAAC 4421
                            v     v      vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126379206_   4422 TGCCC--TTGACTTTCTTCACAGAATTAGAAAAAACTA--CTTAAAAATT 4467
                          -   --i  v    i  -i     v v  v  i-  i-- i     -  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAA-TT 146

  chrX_126379206_   4468 CATATGGAACCAAAAAAGAGCCCAAATAGCCAAGGCAATCCTAAGCAAAA 4517
                                  viiv  ii  v  vi         ii     i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_126379206_   4518 AGAACAAAGCTGGAAGCATCACGCTACCTGACTTCAAACTATACTACAAG 4567
                                  i    i vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_126379206_   4568 GCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAAACACATAAA 4617
                                   i   i    ii         i i  ii i i   i   i 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_126379206_   4618 CCAATAAAACAGAATCAAGAACTCAGAAATAAGACTGTACATCTGAAACC 4667
                         i    ii  i     ii   iii         iv ii     i iviii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_126379206_   4668 ATCTGATCTTTGACAAACCTGACAAAAACAAGGAAAGGGGAAAGGATTGC 4717
                          vi    i  i     ivv  v   i v  vvv  v        i  v i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_126379206_   4718 CTATTTAATAAATGGTGCTGGGAGAACTGGCTAGCCATATGCAGAAAATT 4767
                           v  i  i              v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_126379206_   4768 GAAACTAGACCCCTTCCTTACACCTTATACAAAAGTTAACTCAAGATGAA 4817
                            ii i       v   i     v         i         i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_126379206_   4818 CTACAGACTTAAATGTAAAACCCCAAACTACAAAAACCCTAGAAGAAAAT 4867
                         ii ?    i         i v iv      i    vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_126379206_   4868 CTAG---TCAATACGATTCAAGGCATAGA--CAGGGACAAAGTTTTCATG 4912
                         v   --- v   - --   iv i v v i--i   --   v v    v i
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-C--TTCGTGACCTTGGGTTAGG--CAATGGTTTCTTA 591

  chrX_126379206_   4913 AAAAAAACATCAAAAGCAATTGCAACAAAAGCAAAGATTGACAAATGGAA 4962
                         i v vi   i        vvv          v   i  v  i    v i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_126379206_   4963 TCGAATTAAACTAAAGAGCTTCTGCACAGCAAAACAAACTATCATCAGAG 5012
                         iivv  i   v v  i i   i  ii vv    iv v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_126379206_   5013 TGAAGAGACAACCTATAGAATAAGAGAAAATTTTTGTAATATTTT-CATT 5061
                             i        i i     ii        v    i  -  iv -i  i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATC 740

  chrX_126379206_   5062 GGACAAAGGTCTAATATCCAGAGTCTACAAGGAATTTAATTA-AATTTA- 5109
                         v  i  i  v  vi        i v  i  i   i i--   -  i i -
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--TTACAACTCAA 788

  chrX_126379206_   5110 TAAGAAAAAAACAAACAACCACATTAAAAAGTGGGCAAAGGACACGAACA 5159
                            v     i     i    vv   ?    i           ivi   i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_126379206_   5160 GACACTTCTCAAAAGAAGACATATATGCTTTCAACAAACGTGAAAAAAAA 5209
                             i     v        i   i viivvi   i  i iiivi    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_126379206_   5210 AGCTCAACATCACTGATAAC 5229
                         v           ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (155 / 87)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.50 (24 / 16)  


2513 27.63 3.54 1.30  chrX_126398402_126403017.rev     2806  3652 (964)    L1M4_orf2#LINE/L1        1   866 (42)  

  chrX_126398402_   2806 TGCAGAGATATTCCAGGTTCATGGATTGGAAGAATTAATATTATTAAAAT 2855
                           v i      i   v                 v        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126398402_   2856 GTCCATACTACACAAAGCAATATA----TTCAATGGAATCTCTATCAAAA 2901
                          v v     v v    vii  v  ----     i v    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126398402_   2902 TACCAATGACATTCTTCACAGAAATAGAAAAAAT--TCCTGAAATGTATA 2949
                          v   iivi v  i  ii       v  v  iv --    i    vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_126398402_   2950 TGAAACCATGAAAGACCCAGAATCACCAAAGATATATTAAGCAAATAGAA 2999
                           i  viiii ii          vi     ivv  v  i iv  iv    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_126398402_   3000 CAAAACTGAAGGAATCACATCACCTGACTTCAAATTATACTACAGAGCTC 3049
                             ii  i    v     iiv  ii i      viv       i    v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_126398402_   3050 TGTTAACCAAAACAACATGGTACTGGTATAAAAACAGACACATAGACCAA 3099
                         iiv   i   i   iii         i    ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_126398402_   3100 TGGAACAAAATAGAGAACCCCAAAA---ATCCACACACCTAAAGTGAACT 3146
                              i i   v    ii  vi   --- i   i   ii  vi  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_126398402_   3147 CAGTTTTCACAAAGATGCGAAGAACGTGCC-TGGGGAAAGA-CAGTTTGT 3194
                         v v   iv    i i   v    v i v v-          -i   i v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_126398402_   3195 TCGATAAATGGTTCTGGGAAAACTGGATATATATATGCAGAAGAATGAGA 3244
                           i i       v      v         ?vi i     i        ii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_126398402_   3245 CTAGAGCCCTATATCTTGCCATATACAAAAAAAAAAAAAAATCAAAGTGA 3294
                         i i  v     iv  vii             vv  v-----     i  i
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAAC-----TCAAAATGG 495

  chrX_126398402_   3295 ATTGAAGACTTA--CGTAAGACCTGAAACTATGAAACTGCTATAAGAAAA 3342
                           ii?    i  --i      v  i       i     vi  v       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_126398402_   3343 TATTGAGG-AAACTTTCAAGGTCATTACTTTGGGCAAAAATTTCTT-GAT 3390
                         i  v i? -   ii   iv ii -  ivv  i     vii      -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_126398402_   3391 TCAT-ACCCCACAATCACAAGCAAGCAAACAAAAGAGA-ACAAATGGGAT 3438
                         --  -  v   v  v         vv   v    i v - i    v   i
  L1M4_orf2#LINE/    595 --ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_126398402_   3439 CACATCAAG----------TCTGCACAGCAAAGGAAACAATGAACAAACT 3478
                         iv      i---------- i  ii vv       v  v  v  v   v 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_126398402_   3479 GAAGAGGCAACCCCCACAAAATGGGAGAAAATATTTGCAATGTACCCATC 3528
                            i  i      --   i                     vvi ivi   
  L1M4_orf2#LINE/    693 GAAAAGACAACCC--ACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_126398402_   3529 TGACAGGGCATTAATAATGAGAACATACAAGGGGCTCAAATAATTGTATA 3578
                            i i  v i vi  viv    i   i  i ii   vv i  i vv   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_126398402_   3579 GAAAAAAATCTAATAATCTGATCAAAAACTGAGAAAAGAAATTTGAATAA 3628
                         iv     iv v     i ii  i?    v  i v    i -        i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA-TTTGAATAG 839

  chrX_126398402_   3629 ATATTTCTC---AAAAGACATACAAAT 3652
                          i       --- i    i        
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAAT 866

Transitions / transversions = 1.53 (139 / 91)
Gap_init rate = 0.02 (17 / 866), avg. gap size = 2.41 (41 / 17)  


 964 26.33 1.18 5.92  chrX_126421198_126423231.rev        8   345 (1689)    L1M4_orf2#LINE/L1      190   511 (397)  

  chrX_126421198_      8 AAAAAGAAAAA-AAAACTGGATAAATCACATTACTTGACTTCAAATTTTA 56
                                 i  -   ii    vi v     i v iii i      vi   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_126421198_     57 CTACAGAGCTATAGTAAACAAAACAGCATGGTGTTGGCAAAAACAAACAA 106
                              i     i     v   i    ii    ii     -----------
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA----------- 278

  chrX_126421198_    107 GCAAGCAAACAAACAAAAAAAACAGACCACTGGAAAAGATTAGAGAACCC 156
                         -i   --i i i   v -----i   i  v     v   v v    ii  
  L1M4_orf2#LINE/    279 -TAAG--GATAGACATA-----TAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_126421198_    157 AGAAACAAATCTAGGCACTTACAGCGTACTCATTTTTGACAAAGGTGCCA 206
                              i   i i vi  i   ii ivv i v     i     i       
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_126421198_    207 GGAACATATATTAGAAAAAAAGACGGTCTCTTCAATAAATTGTGCTGGGA 256
                         i  v   vi v i ii   i - ii    i     i    v         
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_126421198_    257 AAACTGAATATCTACATGCAGCAAAATGAAACTATAACCATATCTCTCTC 306
                         v     i   ? i       iv i      ii iv v  v  i   v v 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_126421198_    307 CATATATGAAAATCAAATCAAAA---ATGAAAGACTAATATG 345
                               ii     i  v      ---  v ?    iv v   
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

Transitions / transversions = 2.00 (58 / 29)
Gap_init rate = 0.02 (6 / 322), avg. gap size = 4.00 (24 / 6)  

2705 28.94 1.33 0.67  chrX_126421198_126423231.rev      642  1543 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126421198_    642 TGGAGAAACATTCCATGCTCAGGGATAAGAAGAATCAACATCGTGAAAAT 691
                             i i i  i     i   v    vi     v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126421198_    692 AGCCCTACAGCCCAAAGTAATTTAAAGATTCAGTGCTATTCCCATTAAAC 741
                         i  vv   vv      v i  i  v       ii  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126421198_    742 TACCATCGACATTCTCTACAGAAATAGACAAAACTTACCAGAAAATTCAT 791
                          v   v vi v  i i i       v     i-  v i vv         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_126421198_    792 ATGGAACCAAAAGAGAGCCTGTATAGACAAGACAATCCTAAGTAAAAAGA 841
                               viiv   i  v  v v    v   i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_126421198_    842 ACAAAGCTGGAGGCATCATGCTACATGACTTCAAACTATACCACAAGGCT 891
                               i      vv   ii  v vii i      viv   i    i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_126421198_    892 ACAGTAAACAAAACAGGATGGCACTGGTACAAAAA-AGAGACACATACCA 940
                                v   i    vi   i     i i  ii -   v i i v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_126421198_    941 AAGGAACAGAATAAAGATCTCAGAAGCAAGACTGCACATCTACAACCATC 990
                          v    i     vi   vii     ii  iv iii    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_126421198_    991 TGCTCTTCAGCAAACCTGACAAAAACAAGCAATGGGGAAAAGATTCCCTA 1040
                           v i   ii   ivv  v   i v  vv           ii  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_126421198_   1041 TTTAACAAATGGTGCTGGAGAAACTGGCTAGGTATATGCAGAAAACTGAA 1090
                           i               iiv      v  ?vi i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_126421198_   1091 ACTGGACCCCTTCCTTACACCTTGTACAAAGGTTAACTCAAGATGGATTA 1140
                         ii         v   i     v i      ii         i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_126421198_   1141 AAGACTTAACTGTAAAACCCCAAATTATAAAAAACTTAGAAAAAAATCTA 1190
                         ?    i   v     i v iv   i       vv       i    iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_126421198_   1191 GGCA-ATACCATTCAGGACATAGGCACAGAAAAAGATTTCAT-GATGAAA 1238
                           ?i- v i -   iv   v v  vvi  iv  v i    v -   - vi
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chrX_126421198_   1239 ATGTCAAAAGCAACCGCAACTAAAGCAAAAATGAACAAATGGGATCTCAT 1288
                          iii        vvv     v    v      ii i    v   ii    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_126421198_   1289 TAAACTAAAGAACTACTGCACAGCAAAAGAAACTATCATCAGAGTGAACA 1338
                         i   v v  i    vi  ii vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_126421198_   1339 GACAATCTATAGAATGGAGGGAAATTTTTGCAATTTTTGTACCTGACAAA 1388
                              i i i       ii i    v       v iv i  i    i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_126421198_   1389 GGTCTAATATCCAGAGTCTATAAGGG-CTTGCACAAATTTACAAGAGAAA 1437
                           v  vi        i v     i i-  ivi    v iv i  v i   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_126421198_   1438 AA-----AAC---ATTGAAAAGTGGGCACAGGACATGAACAGACACACTT 1479
                         i -----   ---   ?    i      v    iv    i     i--  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT--TT 845

  chrX_126421198_   1480 TTCAAAAGAAGCCATTTATGCTGCCAACAAACACATGAAAAGAAAGCTCA 1529
                         i  v       vi  vi viiv     i  i            v-     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCA 894

  chrX_126421198_   1530 ACATCACTGATCAT 1543
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (150 / 107)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


2787 27.17 1.87 1.98  chrX_126511628_126514053     1025  1933 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126511628_   1025 TGGAGAAATATTCCACGCTTATGGAT--AAAAAATCAGTATCATGAAAAT 1072
                             i i    i   i i i      --i  i v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126511628_   1073 GGCCATACTGCCCAAAGTAATTTATAAATTCAATGTTATTCCCATTAAAC 1122
                            v     v      v i  i  i i      i iv  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126511628_   1123 TACTATTGACATTCTTCACAGAATTAGAAAGAAACT-ATTTTAAAATTCA 1171
                          v i vivi v  i  ii     v v  v -- i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA--AGCTGATCCTAAAATTCA 148

  chrX_126511628_   1172 TATG-AAACCCAAAAAGAGCCCCAG--TAGCCAGGACAATCCTAGGCAAA 1218
                             -   iv   --- i v     --      ii      i iiiv  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAA---GGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_126511628_   1219 AAGAACAAAGCTGGAGGCATCACGATACCCAAGTTCAAACTATACTACAA 1268
                                   i      vv    iv v     v      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_126511628_   1269 GACTACAGTAACCAAAACAGCATGGTACTGACACAAGATCAAACACTTAG 1318
                         ii         i   i    ii        i  i   ivi i   iv   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_126511628_   1319 ACCAAAAGAACAGAACAGGGAAGGGAACCCAGAAATAAGACCACACACCT 1368
                          i   vi   i    iv i  i-----i          iv   i   ii 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAG-----TCCAGAAATAAACCCATACATTT 340

  chrX_126511628_   1369 ACAACTATCTGACCTTCGACAAATCTGACAAAAAAAG-CAATGGGGAAGG 1417
                          iiiii vi   ii        ivv  v   i vv v-          i 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_126511628_   1418 GATTCCCTATTTAATAAATGGTAAGGAGAGGGCTGGCTAGCCATATGCAG 1467
                         i  vvi  v  i  i       ivv i  vii    v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_126511628_   1468 AAGATTGAAACTGGACCCCTTCCTTACACCACATACAAAAATCAATTAAA 1517
                             v    ii         v   i      i          i  i v  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_126511628_   1518 GATAGATTAAAAACTTAA-TATAAAAACCAGAACTATAAAAATCCTAGAA 1566
                         i  i   i ? i  i   - i   i i i i          v  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_126511628_   1567 GAAAATCTAAGTAATACAAT--TCATGGCATAGACATGGGCAATGGTTTC 1614
                              iv  i ?i-  -   --  i  i v v ivv i            
  L1M4_orf2#LINE/    541 GAAAACATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_126511628_   1615 ATGCCAAACATG---CCAAAAGCAATTGCAACAAAAGCCAAAATAGACAA 1661
                         v --- i i   ---         vvv          vv        i  
  L1M4_orf2#LINE/    589 TT---AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_126511628_   1662 ATGGGATCTAATCAAACTAAAGAGCTTCTGCACAGCAAAAGACACTATCA 1711
                           v   ii v      v v  i i   i  ii vv    i          
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_126511628_   1712 TCAGAGTAAACAGACAACCTACAGAATGGGAGAACATTTTTGCAATCTAT 1761
                         vv i   i  v        i              v  v       vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_126511628_   1762 CAATCTGTCCAAAGTCTAATATCCAGAGTCTACAAGGAACTTAAGCAAAT 1811
                         vv     viv ii v  vi        i v  i  i     ivvi   v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_126511628_   1812 TTGCAAGAATAAAA---CAAGCAACCTCATTAAAAAGTGGGCAAAGGACA 1858
                         ---   v       ---   ii    iv   ?    i           iv
  L1M4_orf2#LINE/    786 ---CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_126511628_   1859 TGAGCAGATACTTCTCAAAAGA-GACATACATGCTTTCAACAAACATAAG 1907
                            ii   i i     v     -  i     viivvi   i  i  i v 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_126511628_   1908 AAAAAAAGCTCAATATCATTGATCAT 1933
                             i v      i    ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (154 / 89)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.06 (35 / 17)  


1371 31.89 5.14 1.37  chrX_126577620_126580457     1472  2346 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126577620_   1472 TGGAAATTTAAACCATCATTATCAATTGAAAGATTCAATGTAGAGAAATT 1521
                               vv  vv    vv i  vi    i    i i   i v vv  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126577620_   1522 ATTATTTTTTCCCAAATTGACTTATTTGTTCTATGCAATTTTGAGTAAAA 1571
                         ivi v vi i          ii  ivvi   v i     iiiv vi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126577620_   1572 TTTCTGCAGAATAATCTATACATAATTTATACAGC-AATTCTAAATTTTA 1620
                          ii v  v vv vv i ii v -    v i -   -i  i     v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTGACA-AGCTGATCCTAAAATTCA 148

  chrX_126577620_   1621 TATGAAAAAGTAAAGAAACTAGAATAG---AAAGAATACTTGAAATTAAA 1667
                             i   v i  i i v i       ---   v   -       vvi  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTGAAAAAGAA 197

  chrX_126577620_   1668 GATTAA---TATATGATGCATGG-----GATATGAAGATTTACTGTGAAC 1709
                           vi  --- iv v  iv  iiv-----i  v v  i i     iii  v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_126577620_   1710 TTATAACAATCAAGAGAGTGCAGTATTGAAGCAATGATAAATCTATATAT 1759
                         i  i ii        v    ii   i  ivii  v    i iv    v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_126577620_   1760 AAATGATACAGAATGGAGAGTCCAGAAGTAAACCCATACATATATAGTTA 1809
                         v    iv i     v            i             v   i  i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_126577620_   1810 ACTTATTTTTAATAACAATGCCCTGGTAATTTAATGAAGGGCATACAGTG 1859
                          i v     ii i  vii    vv iiv   i    ii iiviv i   v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_126577620_   1860 TTTTCAACAAACTGTCATGGAGCAATAAAA-------ATAAGAAAAAATA 1902
                                    iv  vv   ii   ivii -------  ivi   i   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_126577620_   1903 AGACTTACATTTATTCCTATCTCACACTACATACAAATATTAATTCAAAA 1952
                          iii vi----- ii    i       i i       v     i      
  L1M4_orf2#LINE/    448 AAGTTGG-----ACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_126577620_   1953 TGAATCACAGAATTAAAAGTAAAATGTAAAATGATAATATTTATTAAATA 2002
                           i    ?   vi    v    i vv     iv    v i iv vi  v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_126577620_   2003 AAAC---GAGAAAAATACTT--TCATCTTTAGTGCATCACTGATTT-TCA 2046
                             --- i?iv    -   -- v i   vi  vviv  v  i   - i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_126577620_   2047 GAAAGGAGACAATGATTATAA--AATAAAAACAAA----GACAAATTAGA 2090
                           v v  v  v vi vi i  --  i    iv   ----  i     i  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_126577620_   2091 CTTTATCAATATTAAAAATTACTGCTTTATAAAAGACACCATTAAGTAAT 2140
                            i     v        i vi  ivi vi   i     i  i   v  v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_126577620_   2141 TAAAAAGATGGC--AGAAACTAGGTAAAAATATGCACCAAACTCATATCT 2188
                          i      iii -- v i v i  vi       vii v  v vi      
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_126577620_   2189 GAAAAATTAATTGTATACACAACTTATACAAAGG--TCCAACACTTCAAT 2236
                           v  ivv v      v  v  --    i    i--  iv   vi     
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAA--TATATAAAGAACTCTTACAACTCAAT 789

  chrX_126577620_   2237 ACACAAAAA-ATTAATGCTCC--T----AAATGT-CAAAATATTTGAAAA 2278
                          - i     - iv   ivi  -- ----     v-    iv       v 
  L1M4_orf2#LINE/    790 A-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_126577620_   2279 GATACTTCACAAAAAAAGATAAAAAAA-GTCCAATATTCATATGAACA-A 2326
                           i i   v v   i      v v   - v      vv  i     v - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_126577620_   2327 TTTTCAACATCTTTAGACAC 2346
                          vi        v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (153 / 124)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.28 (57 / 25)  


2476 26.26 4.91 1.26  chrX_126596913_126599402     1122  1997 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126596913_   1122 TGCAGAGATGTTACATATTTACGGGTAGGAAGAGACAATATCGTCAAGAT 1171
                           v i    i iv   i  i i  i v      vvi     i  i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126596913_   1172 GTTAGTTCTACCCAACTTGATCTATACATTCAATGAAATCCAAGTCAAAT 1221
                          vi i v  v     v        i v      i v     vvi     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126596913_   1222 TCCTTACAAGTTAATATTT----AGGATATTGGTAAACTGATAC-AAAAT 1266
                            i----  i iviv   ----  i -    ii  i     v -     
  L1M4_orf2#LINE/    101 TCCC----AGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAAT 145

  chrX_126596913_   1267 TTATATGGACAGTCAAAAGACCAGGAA-AACCAACACAAACACTGAAA-- 1313
                          i       v vv   ii    vi   - i    v    v -i     --
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAA 194

  chrX_126596913_   1314 GAA-AACAAATTTGGAAAA-TGACATTACCTGACTTCATGACTTATTATA 1361
                            -      v     ii - v   i v  ii i    vi     i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_126596913_   1362 AAGCTATAGTAATCAATACAGTGTGGTCTTGATGAAAGAATGAACAAATA 1411
                               i         v          vi  iiiv   i  ii   v   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_126596913_   1412 AATTGAGGGAA-AAAATAAAGCATAAAGAAAGAGATCCATACAAATATAG 1460
                         i  ii v    - i   vi  vi vv     v i i       vv   i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_126596913_   1461 TCAACTAAATTTTCAGAAAAAAATA--AAAATAATACAATAGAAAAAAAC 1508
                             i i -     -  v  iii i--  i iv  v    i ii   i v
  L1M4_orf2#LINE/    345 TCAATTGA-TTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_126596913_   1509 TA---TTTCAAACAAACGGTGCTT---TAACTGAATATCTA-ATACAAAA 1551
                           ---   iv      i      v---i     i   ? i -  i     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_126596913_   1552 AAA-AAATCTAAACACAGAACATACACCCTTTACAAAAATTATCCCAAA- 1599
                         i  -i  vi ii  v vv v vi     v v           v i    -
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_126596913_   1600 TTTATCATATACCTAAATGTAAAAATGTAAAATTATAAATCTCCTAAAAG 1649
                          vv    ? v            i ii-     i      v   i  i   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAG 541

  chrX_126596913_   1650 A-----TAAAAG---------GTGACCTTGGTTT-GGTGATCATTCTTCA 1684
                          -----  ii? ---------          v  -  ii  vi  ii i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_126596913_   1685 GATAT---ACCAAAGGCACAGTC--CAAGAAATAAATATATGATAATCTG 1729
                              ---      i     iv --   i i v   -   -     vi  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-ATA-GATAAATTG 639

  chrX_126596913_   1730 TACTTCATTAAAATTAAAAGCCTCTCTTTGCCAAAAGATACTGACAAGAG 1779
                         v       i          i i i v vivi    i  i   iv     i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_126596913_   1780 AATGAAAAGACAAGCCACAGACTGAGAAAAAAAATTTGCAAAAAACATTT 1829
                          i           v       v  i  i    v         vv i  v 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_126596913_   1830 CTGATAAAGGACTCTTAGCTAAAATGTATGCAAAATTCTT-TAATTCAAC 1878
                                i     iv  v i i   i   iv i  i    -i  i    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_126596913_   1879 AATAAGAAAATGAGCAACCCTATTTTAAAATGGACAAAAGATCTGAGCAG 1928
                              i  i ii ii     v   ?v       i    i   i   ii  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_126596913_   1929 ACCCTGCATAAAAGAAGATATATAGATAGCAAATAAGCATATGAAAAGAT 1978
                           vi v viv            i i  i  v        i          
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_126596913_   1979 GCTCAACACCACATATCAT 1997
                                 i  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (142 / 84)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.00 (54 / 27)  


2431 26.50 6.24 0.76  chrX_126625710_126630239     2868  3652 (878)    L1M4_orf2#LINE/L1        1   828 (80)  

  chrX_126625710_   2868 TGGAAAGAGATTCTCTGTTCATGGATTGGAGTAATTAATATTGT-AAAAT 2916
                                 v  i iv               iv v          -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126625710_   2917 GCCTATATTACCCAAAGTGATCTACAGATTTCATACAATCACCATCAAGA 2966
                          v v   i v      v             iv ii     v i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126625710_   2967 TTTCA--------------AAAAAT--AAAAAT--ATC-TAAATTTTGTA 2997
                          ii  -------------- i    -- v  ii--   -    v  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_126625710_   2998 TACAACCACCAAAGATCCCAAATAGCGAAATTATTACTGAACAAAAAGAA 3047
                          iv  vii v ii  i  vi      v   vi v vi    v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_126625710_   3048 CAAAGCTGGATGCATCATACTACCTGACTTCAAA-CACAATACAAAGCTA 3096
                              i    v vv   i   v  ii i      - vi v          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_126625710_   3097 TAGTAATCCAAAGAGTATAGTGTTGCCATAAAAGGAAACACACACACCAA 3146
                         i       v i v   i i  ii  v     iiiv i   i i v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_126625710_   3147 TGGAACAGAATAGGGGGCCCAGAAACAAATCCATGAATTTATGGTTAATT 3196
                              i     v i i i       i   i    iv         i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_126625710_   3197 TGTTTTTTACAAAGATTCCAAGAACACCAAATAGTGAAAGGACAGCCTCT 3246
                         vi    iv    i i v      v  iiv   i v     i i  i  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_126625710_   3247 TCAA-AAGT--CTCCGGGAAAACTGGATATCCACTTG---GAGAATAAAA 3290
                             -  i --iv i    v         ?    v  ---i     i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_126625710_   3291 TTTAACTCTTGTCTCACATCATATACAAAAATCAACTTGAAATGGATTAA 3340
                           vi  i i ii      i             i    ii        i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_126625710_   3341 TGACTTTCAACATAAGACTTAAAACTCTAAAACTACTAGAAGATAACATT 3390
                         v   i -v  ii     vi       v       vi       v     v
  L1M4_orf2#LINE/    501 AGACCT-AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_126625710_   3391 CATGAAAAGTTCCTTGACAGTAGCCAGGGCAATATTTTTTTTTTAATATG 3440
                         vi? v   vi i v    vv i vivi      iv   i  v--i     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA--GATATG 597

  chrX_126625710_   3441 ACCACGAAAACATGGACCACAAAAGCAAAAATAGAGAAATAGGATTATAT 3490
                           vv i   i  iiii v       v         v    v   i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_126625710_   3491 CAAA-TTAGAAA-------GCTTCGCAG-------CCAAGGAAATAATTA 3525
                             -   i   -------     iv  -------i    i  i i v- 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA-A 696

  chrX_126625710_   3526 ACACAACACACAGAATAGGTCAAAATATTTGCAAATCATACATCTGATAA 3575
                          v     v        i  vv                   i         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_126625710_   3576 GAGGTTAACATCCAAAATACATAAGGAACTCAT----TTGAACAGCAAGA 3621
                          i ii vii     i    i    i      v ----i v  i ii  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_126625710_   3622 AAGCAAATA---CAATGATTAAAAATGGGCCAAG 3652
                          ii      ---    -- ?          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAAT--TWAAAAATGGGCAAAG 828

Transitions / transversions = 1.62 (126 / 78)
Gap_init rate = 0.02 (18 / 828), avg. gap size = 3.06 (55 / 18)  

 423 17.20 1.08 0.00  chrX_126625710_126630239     3945  4037 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_126625710_   3945 AAAAATGGGCAAAGGACTTGAATAGATATTTCTCAAAAGATCTCGTACGC 3994
                                         i         i       v     vvvii   iv
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_126625710_   3995 ATGCCCAATAGGAGTATGAAAA-ATGCTCAAAATCACTAATCTT 4037
                            v      i vii       -        v    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (8 / 8)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


2614 26.47 3.99 3.43  chrX_126639197_126642403.rev     1814  2716 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126639197_   1814 TGAAAAGACTTTCTGTGTTTATAGATTGGAAGCTTTAATATTGTTTCAAT 1863
                           i     iv i ii    i  i         vi           vvi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126639197_   1864 GTACACACTACTAAAAGGGATATATAGATTCAATGCAAACTCAGCCAAAG 1913
                          vvv i   v iv   vv   v  i        i    v i vii    i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126639197_   1914 TTCCTGTGGTGTTTACACACACACAGATACACACACACACACACACACAC 1963
                          i  v iv iv   vi-----ii    v ivv   vi v-----------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-----TGCAGAAATTGACAAGCT----------- 134

  chrX_126639197_   1964 ACACAGAGATTCTACAATTCATATGGAACTAAAAAAGAAC--AAATATCC 2011
                         -------   i   v             v iv  ii  v --i    v  
  L1M4_orf2#LINE/    135 -------GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chrX_126639197_   2012 AAATAAATCTTGT----GGAAAACAAAAATTTGCAGGCATTACTCT-CTC 2056
                            vv       v---- i i      i--   v   vv i  v  - i 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAG--TTGGAGGACTCACACTTCCC 225

  chrX_126639197_   2057 AATTTTAAAACATATTA-AAGGCTACAGTTTTGGGAACAGTATGGTATAA 2105
                              i     v  i  -  i        vv viii     i     ivi
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_126639197_   2106 ACATAAAGATACACATTTAGACTAATGGAAGAGAATAGAGAGCCCAGAAA 2155
                         i     i    v    v    ii       v     v     i       
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_126639197_   2156 TAAA------------TGGTCAACTGATCTTCAATAAGATTGCCAAAAAT 2193
                             ------------       i    i   i i   iv      i vi
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_126639197_   2194 ACACAATAGAGAAAAAGGTATTCTGTTCAATAAATCATGCTGGGAAAAGC 2243
                          iv    i i    i i-  v   v     i    vi        v  vi
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAA-TAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_126639197_   2244 GGATATACACATGCAGAATAGGAAAATTAGACCCTTATCTTGAACCATAT 2293
                              ?v        i  v ivi  i  i     i  i  iiv       
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_126639197_   2294 ATAAAATTCAACTCAAAATTGATTAAATGCTTAATTGTAAAACCTGAAAC 2343
                          i    v i          v   i ? vi i   v     i v  i    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_126639197_   2344 TCTAAAACTTCTAAAAGAAAACATAGGGGAGAAT-TTAATGGCATTTTTC 2392
                          v       ii  i             ? vi   -  vi  i v  vvvi
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_126639197_   2393 TTGGCTGTGATTTTATGACTGTGACACCAAAAGCACAGGCAAGAAAAACA 2442
                          v   vi  i   iv iiv i                i    v    iv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_126639197_   2443 AATGTAAACAAGG-GGACTTCATTAAAATAAAAGGCTT-----CTTTAGA 2486
                           vi  i i  iv-         i     v   ii   -----   i --
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA-- 672

  chrX_126639197_   2487 AAAAGGAAACAACTAACAGAGTCAAAAG-CAGTCTTTAGAATAGGAGAAA 2535
                         --     v  v ii  v i   v     -  ii ivi     i       
  L1M4_orf2#LINE/    673 --AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_126639197_   2536 ATATTTTCACACCACATTTCTGATAAATAGTTCACATCCAAAATATATAA 2585
                               v  v i  i  v        iviii iii     i         
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_126639197_   2586 GGCACTTCTACAATTCAATACCAAAAA-----ACAACCCAATTAAAATAT 2630
                         i v   ii     i      vi     ----- i         ?   v  
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_126639197_   2631 GAGCTGAAAGCTTGAATAGACATTTCTCCAAATAAGACAT-CGAATGATC 2679
                          i  vi iiii                     v    i  - i    ii 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_126639197_   2680 AGCAGGTATCATGAAGAAA--ATCAACATCAGTATTCAT 2716
                          ii i i -      i i --v         ????????
  L1M4_orf2#LINE/    871 AATAAGCA-CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.72 (67 / 18)  


2988 27.25 1.45 0.44  chrX_126642685_126646934.rev     2861  3759 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126642685_   2861 TAGGAAAATATTCCATGTTCATGGATTGGAGGAATCAATATTGTCATAAT 2910
                          i i  i    i                  i  v i        i vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126642685_   2911 GTCCGTACAAACCAAAGCAATCTACAGATTCAATGCAATACCTATTAAAA 2960
                          v vi   vvv     vii              i     v     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126642685_   2961 TACCAAAGAAGTTCTTCACAGAA-TAGAAAAAACAATTCTAAAATTTATA 3009
                          v   ivvivv  i  ii     - v  v  ivii  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_126642685_   3010 GGGAAACAAAAAAGATGCAGAATAGCCAAAACTATCCTAAGCAAAAAGAA 3059
                         v     iiv  ii  iv               v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_126642685_   3060 CAATACTGGAGGAATCACGTTACCTC-TATCAAATTATACTATAGTGCCA 3108
                            vii       v    ii v  iv- v     viv     i iv  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_126642685_   3109 TAATAACCAAAACAGCATGGCACTGGCATAAAAACAAATACATAGACCAA 3158
                         i i   i   i    ii   i          ii i i i i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_126642685_   3159 TGCAACAGCATAGAGAACCAAGAAACAAATGTACACACCTACAGTAAACA 3208
                           v  i  v  v    ii v     i   ivi i   ii  ii  v  iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_126642685_   3209 CATTTTTTACAAAGATGCCAAGAATATAC--TGGAGAAAAGATAGCCTCT 3256
                         v     iv    i i        vi  v --   i    ii    i  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_126642685_   3257 TCAATAAATGACATTGGGAGAACTGGATATCTATATGCCAAAGAATGGAA 3306
                             i     iiii     v         ? i i    v        i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_126642685_   3307 CTATACACCTATTTCTCACCATATA-GAAAATGAAATCAAAATGGATTAA 3355
                         i iv  v    ii  v         -i     v  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_126642685_   3356 ATGCTTACATCTATAACCTGAAACTATGAAAATCCTACAGGAAAATATTG 3405
                          vi i  v  v  vi v  i       i   v  i  v i     i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_126642685_   3406 GGGAAAACCTTCAGGACCTT----TGGGCAAAGATTTCTTGAGCA--ATA 3449
                          ? v   i    iv      ---- i     v i      iiii -- i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_126642685_   3450 CCTTACAAGTACTGGAAACCAAAGCAAACATAGACAAATGGGATCACAT- 3498
                           -- v   i  vi v   v    v   v     i    v   iiv   -
  L1M4_orf2#LINE/    601 CC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_126642685_   3499 AACGTTGAAAAGCTTTTGCACAGAATAGGATACAAT-AAGCAAAGTGAAG 3547
                           vi  i    -      ii vvv v    i  v  -   -        i
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAA 696

  chrX_126642685_   3548 ATACAACCCACAGAATGTGAGAAAAGATTTGCAAACTACCCCTCTGACAA 3597
                          v               v       v         ii iviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_126642685_   3598 GGGATTAGTAACTAGAATATATGAGGATCTCAAACAACTCTATAGGAAAT 3647
                             i v   v i         i i  v   vv       v   iv   v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_126642685_   3648 ATTCTACTAATCTGATCAATAAATAGACAAAAGATTTGAATAGACATGTA 3697
                          vv v v   i ii  i? v    i i    i               v v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_126642685_   3698 TAAAAAGAAGACATACCAATGGCAAACAGGCATATGAGAAGTTGTTCAAC 3747
                          vv        i    v      v  i i   i    i   v  i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_126642685_   3748 ATTATTGATCAT 3759
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


3176 26.61 1.22 0.55  chrX_126650038_126654187     2756  3657 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126650038_   2756 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCAACAAAAT 2805
                              ii i  i     i      i v      v i     iivi  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126650038_   2806 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2855
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126650038_   2856 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTAAAGTTCA 2903
                          v   iivi i  i  ii     -   -- v  i  - i i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_126650038_   2904 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 2953
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_126650038_   2954 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3003
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_126650038_   3004 CACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3053
                         i       i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_126650038_   3054 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 3101
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_126650038_   3102 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 3151
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_126650038_   3152 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3201
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_126650038_   3202 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAAC--AAGATGGA 3249
                            ii    i    v   i     v               --  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_126650038_   3250 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAAAAAAC 3299
                          i ?    i       v   v       i      vi i     i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_126650038_   3300 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 3348
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_126650038_   3349 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGGTCTA 3398
                         vi            vvi          vv     v  i    v  iii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_126650038_   3399 ATTAAACTATAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 3448
                           i   v vv i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_126650038_   3449 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACA 3498
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_126650038_   3499 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 3548
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_126650038_   3549 AA----AAGAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACATTT 3594
                           ----  v     v  i? v  i            v    i        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_126650038_   3595 CTTAAAACAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 3644
                           iv   v    i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_126650038_   3645 CATCACTGGCCAT 3657
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


2842 27.46 1.22 0.66  chrX_126676358_126681651     3899  4801 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126676358_   3899 TGGAAACACATCCCCTGCTCATA-ATTGGGTAGAATCAATATTGTGAAAA 3947
                               v i     v  i    i-     i-   v i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGA-AGACTTAATATTGTTAAGA 49

  chrX_126676358_   3948 TGACCACACTGACAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAA 3997
                           i v i   vv v   vii       i      i     i  i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_126676358_   3998 ATACCACCATCATTCTTTACAGAACTAGAGAAAAAATTCCTAAAATTCAT 4047
                           v   v vv v  i   i     v v  v  ivviv             
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_126676358_   4048 ATGGAACCA-AAAAAATTTCACATA-CCAAAAGCAAAACTAAGCAAAAAG 4095
                               vii-  iii iiiviv   -      -   vvi i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAG 198

  chrX_126676358_   4096 AACAAATATGGAGGCATTACATTATCCAACTTCAAACTATAATATAAGGC 4145
                               vv      vv i   i vi    i      viv  v  i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_126676358_   4146 CACAGTCACCAAAACAGCATGGTACTGGTATAAAAATATGCATCTACACC 4195
                         i     v i   i    ii         i    ii   vi   v  v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_126676358_   4196 AATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAGTACTTACAGTCAA 4245
                                i     v    ii           v   vii i   ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_126676358_   4246 CTGATCTTCGACAAAGCAAACAAAAACATAAAGTGGGGAAAGAACACTCT 4295
                         i    i        i vviv   i v   vv i           i v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_126676358_   4296 ATTCAACAAACAGTGCTGGGATAATTGGCAAGGCACATGTAGAAGAATGA 4345
                         v         ii         i  i   vv ?v      i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_126676358_   4346 AACTGAATCCTTATCTCTCACTGTATATAAAAATCAATTCAATATGGATG 4395
                          ii  i i  i  i   v   ii    i      i  i    v      v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_126676358_   4396 AAAGAATTAAATATAAGACGTGTTA---CCATAAAAATTATAAAAGATAG 4442
                          ?   vi     i     --- i  --- i      v iv  i    v i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGA---GCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_126676358_   4443 CATTGGAATAAATCTTTTAGACATCAGCTTAGGCAAAGATTTTATGACCA 4492
                            v  ?i        ivv   v ii v        v i   iv iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_126676358_   4493 AGAACCCAAAAGCAAATGCAACAAAAGTGAAGACAAATTGATGGAACTTA 4542
                         v  vv         v v          vi  i i i  vi  v i    v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_126676358_   4543 ATTAAGCTAAAAAGCTTCTGCACATTCAAAGAA-ATAATCATTAGAGTAA 4591
                           i  iv v    i   i  ii -       i - iv    vv i   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGC-TTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_126676358_   4592 ACAGACAACCTACAGAGTGGGACAAAGTCTTTGCAATCTATACATCCAAC 4641
                          v        i     i     v   i v       vii   i   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_126676358_   4642 AAAGGACTAATACCCAGAAACTACAAGGAACTCAAACAAATCATCAAGAA 4691
                           i     vi  i      vv  i  i      vv    v   vi  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_126676358_   4692 CAAAACAA----TCCCATCAAAAAGTGTGCTAAGGACATAAATAGACAAT 4737
                         v  i    ----i  v  i?    i  v  v     iv i        v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_126676358_   4738 TATCAAAAGAAGATACACAAACGGTCAACAAACTTATGAAAAAATGTTCA 4787
                          v  v          i     i  i   i  i vi       i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_126676358_   4788 GCATCACTAATGAT 4801
                         i     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (142 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


1808 26.96 9.86 2.02  chrX_126682046_126685392     2015  2856 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126682046_   2015 TAGAAGGACATCTGGTGTTCATGTATTGGAAGGCATAATGTCCGTAAGAT 2064
                          i   i  i   ivi        v        i v    i ivv      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126682046_   2065 GTCAATACTATCCCAAGTGATATACACAACAAATGTGACCTCTATAAGAA 2114
                          v       vi  v  v    v    v viv  i ii i i    v i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126682046_   2115 TTCCAATGGGCTTCTTTTCAAAAAATGGAAAACCCTATCCTTAAATTATA 2164
                          i   iiv v   i   v  i   - v  v  v iv     v     ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAA-TTGACAAGCTGATCCTAAAATT--- 146

  chrX_126682046_   2165 CATAT--ATATACATATG-TTTATAATATTATATGTAATAT--------- 2202
                              -- v  i  viv -iii v    vivv vii   v ---------
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_126682046_   2203 ---ACATA--TATATAACATATATGT---GATATGAGATATATGATTGCA 2244
                         ---   v -- iv vi  vi i iv ---i  v v i - i- v i i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-AC-TTACTACA 244

  chrX_126682046_   2245 AGGGGCCTCAAATAGCCAAAATAAC------CTGGAAAAAGAACA----- 2283
                          i ---  vv i  ii   i i ii------    v v   i i -----
  L1M4_orf2#LINE/    245 AAG---CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_126682046_   2284 ------CAACAGAA-AGGCTTACAATACCTGATTTAAA---A---ACTTA 2320
                         ------   ii   -  iv  ivi vv  v  vv    --- --- i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_126682046_   2321 TGA--AA--AAGCTTGAACAA-----TCAAAGT-----AATGTAGTATTA 2356
                           i--  --i vi  vi    -----i   iii-----    vi v -- 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA--A 389

  chrX_126682046_   2357 GCTTGACCCCTTCAACAAATCATTCTGTGACAAATGGACAACCAAATGCA 2406
                          vv iii ii          vi v   v     v    i ?   v     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_126682046_   2407 TAAAAAGGTGGTATG-----CTATCTCACACCATAAACAAAA-TTATCTT 2450
                         v  i  v vi  -  -----   i           v      -   v  i
  L1M4_orf2#LINE/    440 AAAGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_126682046_   2451 AAAATGGAT---ACAC----ATGCTAAAGT--AAACCATAAAATGCTTAT 2491
                                  --- v  ----   iv i  i--    i      iv    v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_126682046_   2492 GAGGAAACATAGGGGTAAGTCTTTATGTCTTTGAATTTGGCAATAAATTT 2541
                         i  i         ?    i    ii  v i   ii  v      ii-   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-TTT 587

  chrX_126682046_   2542 C--AAATAAGACACTAAAATTACTATCAATAAAATAAAAAACTTAGATAA 2589
                          -- i   v     i    vi  v v   i    v      --       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAA 635

  chrX_126682046_   2590 ATTAGATTTCATCAAACACTTAAA------GTACATCAAAA-ACACTGTT 2632
                            i  i         - i v   ------  i v     i-     i i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_126682046_   2633 AAGAAAGTGAAAAAATATCCAACAGAGTGCGATAAAATATTTGCTAACCA 2682
                                      i i v  v     i  v  v           v  i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_126682046_   2683 AATATGTGATAAGGATATCATATTCAGAATATATAAAAATGTATCACAGC 2732
                         v    v        ivv ii   i             i vv v i   i 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_126682046_   2733 TCAGCAACAAAAAGACAAACA-CCCAATTATAAAAATTGGCAGAGAGTTT 2781
                            ii  i           i -       ?-      v    i  ii   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTT 833

  chrX_126682046_   2782 CAGTAGACATTTCTCCAAGGAGGATATACAAATGACCAGCAAGCACATAG 2831
                         v i               i  i            i   ii        ii
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_126682046_   2832 AAAGGTGCTCAACATTGTTAGTCAT 2856
                             i          ii????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (131 / 93)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 2.94 (100 / 34)  

 506 19.10 0.00 0.00  chrX_126682046_126685392     3254  3342 (5)  C L1M4_orf2#LINE/L1   (423)   485   397  

C chrX_126682046_   3342 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 3293
                           v  i  i        i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_126682046_   3292 GAAACTGGACCCCTTCCTTACATCCTATACAAAAATTAA 3254
                            ii         v   i   i v              
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.00 (0 / 0)  


2436 26.58 1.32 0.79  chrX_126695542_126697313      520  1279 (493)    L1M4_orf2#LINE/L1      145   908 (0)  

  chrX_126695542_    520 TTCATATGGAACCAAAAAAGAGCCTGAATAACCAAAGAAATCCTAAGCAG 569
                                    viiv  ii  v  v     i     iv    i i iv i
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_126695542_    570 AAAGAACAAATTTGGAGGCATCATATTACCTGACTTCAAACTATACTACA 619
                         i         v       vv   i i v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_126695542_    620 AGAATACAATAACCCAAACAGCATGAAACTAGTATAAAAGTAGATACATA 669
                          iiv    i   i v i    ii  iv   i i    iii    i i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_126695542_    670 GACCAATGGAACAGAATATAGAAGACAGAAATAAAGCCAGATACTTAAGA 719
                           i        i     vv   ivv          v   v i i   v i
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_126695542_    720 CCAACTTATCTTTGACAAAGAATACAAAAACATAAACTGTAGAAAAGACA 769
                         i   i v  i  i     i ivvv   i v   vv v  vi    ii i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_126695542_    770 TCCTATTCAATAAATGATGCTGGGAAAATTGGACATCCCCAAGTAGAAGA 819
                         vi  v     i     i        v  i    i ?  v  v i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_126695542_    820 ATAAAACTGGATCCCTATCTCTCAGTATATATAAAAATTAACTCAAGATG 869
                           i  ii    i     i   v  vi     i              i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_126695542_    870 GACTAAACACTTAAATGTAAGACCTGAAACCATAGAAATTCTAAAAGAGA 919
                           ii ? v  i           v  i    i   i  v ii  i    i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_126695542_    920 AGAT-GGCAAAAACTCTTTTGGACACTGGCCTAGGCAAATAATT-----G 963
                          v  -  ?iv   -    ivv   vi   vi       - ii  ----- 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAG 592

  chrX_126695542_    964 ATGACGAAGACCCCAAAAGCAAATGCAACAAAAGCAAAAATAAATAAATG 1013
                           ---- v   v         v v          v       i      v
  L1M4_orf2#LINE/    593 AT----ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_126695542_   1014 GAACCTAATTAAACTAAAAAGCTTTGGTACAGCAAAAGAAATAATCTTCA 1063
                          i  i v  i   v v    i    v  i vv    i  v iv   vvv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_126695542_   1064 GAGTAAAAAGAAAACCTACAGACTA--AGGAAATTTTTGCAAATCATGCA 1111
                         i   i      v    i     v i--  i    v            ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_126695542_   1112 TTCGACAAAGAACA-ATATTCAGAATCTACAAGGAACTCAAACAAAACAG 1160
                          ii  i  i i  v-i   i      v  i  i      vv    vv  i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_126695542_   1161 CAAGAAGCAGCCAAATAATCCCATT-AAAATTGGGCAAATGGCATTAATT 1209
                         i  v  iv  v       i  v   -    v        v iiv v   v
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_126695542_   1210 GACACTTCTCAAAAGAAGATATACAAATGGTCAACAAACATATGAAAAAA 1259
                             i     v                   i   i  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_126695542_   1260 TGCTCAACATCACTGTATTA 1279
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (116 / 83)
Gap_init rate = 0.01 (8 / 764), avg. gap size = 2.00 (16 / 8)  


2287 28.42 0.29 0.29  chrX_126702169_126703840      494  1172 (500)    L1M4_orf2#LINE/L1      209   887 (21)  

  chrX_126702169_    494 GAGCATTCATGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACC 543
                            v i   ii  v  ii i      viv        i          i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_126702169_    544 AAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAATGGAACAG 593
                           i    ii         i iv ii i   v       i        i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_126702169_    594 AAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACTATCTCATCTT 641
                           i--    i  --        vv   i i  i  iiiii vi v  i  
  L1M4_orf2#LINE/    309 AATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_126702169_    642 TGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATA 691
                         i     ivv  vv  i v  vv            i  vvi  v  i  i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_126702169_    692 CATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGAT 741
                         v            v      v  ?   i   i i  iiv    ii    i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_126702169_    742 CCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTT 791
                             v   i     v              i    i      i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_126702169_    792 AAACATTAGACCTAACACCATAAAAACCCTAGAAGAAAACCTAGGTATTA 841
                            ii v   v    v  i      vi i           v    ?i v 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_126702169_    842 CCATTCAGGACATAGGCATGTGCAAGGACTTCATGTCTAAAACACCAAAA 891
                         viv   iv   v v  vv iv    v ii   v ivv  vi         
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_126702169_    892 GCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAA 941
                            vvi          vv     v  i    v   ii v  i   v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_126702169_    942 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGGACAGGCAACCTA 991
                         i i   i  ii vv    i  v    i  vv i    i v  i     i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_126702169_    992 CAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAGGGCTAATA 1041
                           i             v  ii   vii ivi      i  i  i  vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_126702169_   1042 TCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAA 1091
                                 v  i  v      vv    v iv i  v     i     i  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_126702169_   1092 CCCCATCAAAAAGTGGGCGAAGGACATGAAAAGACACTTCTCAAAAGACG 1141
                            v  i?    i     i     iv    v     i     v     v 
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_126702169_   1142 ACATTTATGCAGCCAAAAAACGCAGGAAGAG 1172
                          i  vi viii     v  i i  v   i  
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAG 887

Transitions / transversions = 1.36 (109 / 80)
Gap_init rate = 0.00 (2 / 679), avg. gap size = 2.00 (4 / 2)  


1487 21.88 1.25 20.18  chrX_126722240_126724489      638  1757 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126722240_    638 TGGAAACACATTCCATGATCGTGAATGGGAAGAATCAATCGTGTAAGAAT 687
                               v i  i     v  i  i  v      v i   vv   v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126722240_    688 GATACTATTGCACAAAACAATCTATAGATTCAACGTAATTCCCATCAAT- 736
                          ii v  i v v    vii     i          i   i  i     v-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126722240_    737 TACCA-TTATTATTCTTCACAGAA-CAAAAAAATCAATCCTAAAATTTAT 784
                          v   -i iii-  i  ii     -ivi v  iiii           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_126722240_    785 TTGGAATCAAAAAAGAGCCCACATAACCAAATAAATACTAAGCAAAAAGA 834
                         v     viiv  ii  v  viv   i     vv   vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_126722240_    835 AAAAATATGGAG-ACTCACATTACCCAACTTCAAATAATACTACAAGACT 883
                          v   vv     -       i v     i      vvv        ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_126722240_    884 ATACTTACCAAAACATTATGGTATTAACATAATAGTAGGCACATAGATCA 933
                          i v v i   i   v i     i ii     vii   i  i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_126722240_    934 ATGGAACAGAATGGAGAAGCCAGAAGTAAAACCAAATACTTACAGCCAAC 983
                               i     v    iv      i    v   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_126722240_    984 TGTTCGTCAACAGAGCATGTAAAAACTTAAATTGTGGTGGGGTGGGGGGA 1033
                           v iv  i   -  vi  iv  i  ------------------------
  L1M4_orf2#LINE/    350 TGATTTTCGACA-AGGGTGCCAAGAC------------------------ 374

  chrX_126722240_   1034 GGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGATGAGTTA 1083
                         --------------    ------------i    ---------------
  L1M4_orf2#LINE/    375 --------------CATT------------CAATG--------------- 383

  chrX_126722240_   1084 GTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTG 1133
                         --   ---------------------------------------------
  L1M4_orf2#LINE/    384 --GGG--------------------------------------------- 386

  chrX_126722240_   1134 CACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAATAAAAAATT 1183
                         ----------------------------    v   i ------------
  L1M4_orf2#LINE/    387 ----------------------------AAAGAATAGT------------ 396

  chrX_126722240_   1184 AAAAAAAAAACTTAAATTGACAAAAAGACACACTATTCCATAAATGGTGC 1233
                         ----------   ----------------------   v i         
  L1M4_orf2#LINE/    397 ----------CTT----------------------TTCAACAAATGGTGC 414

  chrX_126722240_   1234 TGAGAAAACTGGCAAGCCACATGCAGAAGAATGAAACTGGAACATCGTAT 1283
                           i  v      vv ?         i         ii    v viiiiv 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_126722240_   1284 TGCACTATATAGAAAAATCAACTCAAGATGGATCAAAGACTAAAATATAA 1333
                         ii   i     v      i       i        ?    iv    i   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_126722240_   1334 GACCTGAAAGCACAAAAATTCTAGATGATACCATTTGAAACACTCTTCTG 1383
                           v  i   vi i    v ii    v  v v   vv ?ivv v     vv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_126722240_   1384 GACATTGGCTTAGGTAAACAATTCATGGCTAAGATCCCAAAAGCA-AATC 1432
                            v    v     i  vviv   v i v  v  iv         -  v 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_126722240_   1433 AACAAAAACATAATAACAACTGGAATCTATTTAAACTACAGAGCTTCTGC 1482
                                i------  v  v i  -------    i --- ii    ---
  L1M4_orf2#LINE/    615 AACAAAAG------AAAAAATAGA-------TAAATT---GGACTTC--- 645

  chrX_126722240_   1483 CCAGCAAAATAATAATAATAATAATCATCGT-CATCATCATCATCATCAT 1531
                         -- v      --------   v  iiv i  - v   ----- vviv  i
  L1M4_orf2#LINE/    646 --ATCAAAAT--------TAAAAACTTTTGTGCTTCA-----AAGGACAC 680

  chrX_126722240_   1532 TATCAGCACCAGCAGAGTAAACAGACAACC-GCAAAGTGGGAGAAAATAT 1580
                              -----  - i   i  v        -i  i i             
  L1M4_orf2#LINE/    681 TATCA-----AG-AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_126722240_   1581 TCACAAACTATACATCCTACAAAGGACTAGTGTCAACAATCTACAAAAAA 1630
                          ii    ii   i   iv i  i     v  i  v v   v  i   i  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_126722240_   1631 CTCAAGCAAATCAGCAAGAGAAAAACAAATAATTCCATCAACAAGCGG-- 1678
                            vvi   v   ii  v i   i        ii v  i? v  ii  --
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_126722240_   1679 AAA-----TGAATTGACATTTCTCAAAAGAAGATATACAAACAGCCAACA 1723
                            -----     v          v                ii     i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_126722240_   1724 AACATATGAAAAAATGCTTAATATCACTAATCAT 1757
                          i  i       i     i  i    ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 9.60 (240 / 25)  


 202 26.92 0.00 0.00  chrX_126727202_126729265        1    52 (2012)    L1M4_orf2#LINE/L1      255   306 (602)  

  chrX_126727202_      1 AACCAAAAGAACATGGTACTGGTACAAAAACAGACACATAGACCAATGCA 50
                           i   i v iii         i i  ii i     i     i     v 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_126727202_     51 AT 52
                           
  L1M4_orf2#LINE/    305 AT 306

Transitions / transversions = 6.00 (12 / 2)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.00 (0 / 0)  

2663 24.86 5.20 2.82  chrX_126727202_126729265      687  1571 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_126727202_    687 GAAAGACATCTTCTGTTCCTGGATGGAAAGGTTTA---CTGTTAAATTGC 733
                               i   iiv     v     v i   ii   ---i      iv  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_126727202_    734 CCACATAAGCCAAAACGATCTA-AGTAGTCAATGCAATTCCTATCAAAAT 782
                          v i ivvv     vi      -  - v    i     i           
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAG-ATTCAACGCAATCCCTATCAAAAT 101

  chrX_126727202_    783 TTCATTGGCATTTTTTAAAGAAATAGATAAAACAATCCTAAAATTCATAT 832
                         ii  viv  v      iv      v  i  ivii                
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_126727202_    833 GGAACTACAAAAGACCCTGAATAGCCAAAGCAACCT----GAGCAAGAAC 878
                             v i   ii     v           i   i  ----i iv      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_126727202_    879 AAAGCTGGAAGCAC-CACATTTTCTGATTTCAAATTATTAACATGTTACA 927
                             i    i -  -    i  i ii        ------  v ii    
  L1M4_orf2#LINE/    202 AAAGTTGGAGG-ACTCACACTTCCCAATTTCAAA------ACTTACTACA 244

  chrX_126727202_    928 AAGCTATGGTTA-CAA---AGTATTGTAGTGGAATAAAAACAAGACTTGT 973
                               ii  v -   ---   i v   v   v    ii i -   v i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATAT 293

  chrX_126727202_    974 AGACTAATGGAGCAGACTAAAGAGCCGAGACATCAGTCCTCAAATATATT 1023
                            ii      ii   v vi    i v   v  v ii  vi v  v   v
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_126727202_   1024 GTCAACTGATCTTTTACAAGACTGCTA----TATGCAA----GAATGGAT 1065
                              i    i  iv     iv   i ----i  v   ----   v i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_126727202_   1066 CATCTCTTTAACAAATCGTGATGAAA-AACCAGATATCCAATTGTAAAAG 1114
                         vi   i  i       v   v  ii -   ii    ?   vv  i     
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_126727202_   1115 AATGTAATGGGACCCTTATCTTACATGATAGACAAAAGTCAACTCAAAAT 1164
                             v i v      i  i  i   iv   v      i i          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_126727202_   1165 TAATTAAAGACTT---T-------------CTGTAAAACTCCTAAAAGAA 1198
                         vi  i ?    i --- -------------  i        i  i     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_126727202_   1199 AACA--GGAA-AAATCTCTATGACATTGGTTTTGGTAATGATTTCATGTA 1245
                             --  ?i-      iii    v    v  v  i    i    v iv 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_126727202_   1246 TATGACAACAAAAACACAGGGAAAAACATCAAAAATAGACAAGTGAGGCT 1295
                                v     i    i v  v  v vv         i  i vi i  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_126727202_   1296 ACAGCAAAATAAAAAGCATTTGCACAGCAAATAAAATAATGAACAGAATG 1345
                         v  v      v    i v    ii vv    vi v iv  v  v i i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_126727202_   1346 ATAAGGCAATGTACAGAATGGGAAAATATATTTGTAAACCATATATCAAA 1395
                          v   i   ivi           i  v       i   i        vi 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_126727202_   1396 TGAGACATTAGTTTCCAAAATATATATTAGAACT---GCAACTCAATAGC 1442
                          i  iv i v  v    i        v-      ---i          ii
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAA-AGAACTCTTACAACTCAATAAT 792

  chrX_126727202_   1443 AAAAACAAAAAATAAACAAAATTAATAACCCAATT-AAAAATGGGCTAAC 1491
                              ---------i     -----          -          v  v
  L1M4_orf2#LINE/    793 AAAAA---------GACAAA-----TAACCCAATTWAAAAATGGGCAAAG 828

  chrX_126727202_   1492 AATGTGAACAGACACTTCTCTTAAAAAGACATACAA-TGGTCGACAGTTA 1540
                         i  v    i     i     iv  i    i      -   i i i ivi 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_126727202_   1541 TTATGAAAAGATGATTAGTGTCACTAATCAT 1571
                         i-           v i iii   ????????
  L1M4_orf2#LINE/    879 C-ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (131 / 86)
Gap_init rate = 0.03 (24 / 906), avg. gap size = 2.96 (71 / 24)  


2716 25.79 4.41 1.70  chrX_126769615_126772778     1788  2671 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126769615_   1788 TGGAAATACATCT-GTGTTCATCGATGGGAAGTATTAATATTGCTGAAAT 1836
                               v i   i-i       v   v     vv         i i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126769615_   1837 GTCCATACCACCCAAAGTGGTCTACAGATTCAATGCAATCCCTATCAAAA 1886
                          v v    iv      v  i             i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126769615_   1887 TTCCAA-TACAAATTTTCATGGAAAT--AAAAACAATAGTCCTAAAATTC 1933
                          i   i- i vv-    iiii     -- v  i -- ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTC 147

  chrX_126769615_   1934 ATATGGAACCACAAAAGACTCA-AGTATCCAAAGCACTCTTGAGAAAAAT 1982
                                 vii   ii   i  - i  v     i  v      i   i v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_126769615_   1983 GAACCAACATGGAGGCATCAAAGTACCTGATTTTAAAATATTTTACAAAT 2032
                             v  vv      vv   v v v  ii    i    iv vi      v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_126769615_   2033 CTACAGTATCCAGAACAGTATGATATTGATGTAAAAACAGATATATAGAC 2082
                                 vi  ii     i  i  i  iii   ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_126769615_   2083 TAATGGAACAGAAT--AGAGTCCCAAATCAAATCTACATATTTATAGTCA 2130
                         i       i     --       vi  vi   i i i i      i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_126769615_   2131 ATTTATCTTTGACAAAGATACCAAGATCAT--AAGACAGAAAAAAAAGTC 2178
                            v  i  i     i i i      i   --  vivi    i  v    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_126769615_   2179 TTT--AATAAATAATGTTGGAA-AACTGGTGTGAAAAATCCATACGCAGA 2225
                            --  i    ii  i   i -      ------ v ?   i i   i 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGG------ATAKCCACATGCAAA 441

  chrX_126769615_   2226 ATAATGAAATGCAACCTTTATCTCATATAATAT-CAAAAATTAAGT-AAA 2273
                          v      i vvi   ii  i    i iv    -          v -   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_126769615_   2274 ATGAATTAAA----CAAATATAATAACTGAAACTGTAAAACTACTGGAAG 2319
                            i  i ? ----i    i   v i  i     i       vi i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_126769615_   2320 AAAATATAGGACGAAAGTGTCTTC---ACATTGATCTGGGCTATGATTTA 2366
                             i     ?vv   ---     ---  v   ivi i   v   i   v
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_126769615_   2367 TTGCATATGACACTAAGAACATAGGCAGTGAAAGTTTAAGTGTATGGAAT 2416
                           iv         i  i i  i i   iii    vvv  i iv  i-   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA-AAT 637

  chrX_126769615_   2417 TGCAGT------AAACTAAAATCTTTCTTCACACCAAAGGAAACAACTAA 2460
                           v v ------   i     v    iv -i vi       v  v ii  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGT-GCTTCAAAGGACACTATCAA 686

  chrX_126769615_   2461 TAAAGTGGAGATACAGCATACAGAATGAGAGGAAGTATTTACAGATTATA 2510
                         v      i i v   i vi        i   i  i     i  i  i   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_126769615_   2511 CATCTGATAATGAGTTAATATTTAAAATATAAAAGGAACT-TAACAGC-- 2557
                         i         v iii vi   ii i      v  i     - v   i --
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_126769615_   2558 ---AAGAAAAA--CA--TTACCCATTTTTAA--TGGGCAAGAGACCTAAA 2598
                         ---  v     --  -- v     v  ?v  --       ii  ii i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_126769615_   2599 TAGACATCTATTTAAAAAAGACATATAAATGACCAAGATGTATACAAAAA 2648
                                i v ii   i    i   i     i    v v i i ii    
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_126769615_   2649 CAATGCTCAACAACACTAACCAT 2671
                         -i          v  ????????
  L1M4_orf2#LINE/    887 -GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.99 (149 / 75)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.16 (54 / 25)  


 933 28.84 4.08 0.94  chrX_126811729_126816126.rev      242   560 (3838)    L1M4_orf2#LINE/L1        5   333 (575)  

  chrX_126811729_    242 AAAATATGGGATGCTCATTGATAAGACCACTTAATATTGTTAAGATGTCA 291
                           i    vvv   i    v   vi  vv                   v  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_126811729_    292 ATATTACCCAAAGCAATCTACAGATTCAATAAAATCCCTATCAAAATTTC 341
                            i v      vii              iiv               ii 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_126811729_    342 AACTTTTGTTTCTCCAGAAATAGGCA----GATCTGAACATTTATATAGA 387
                          i  viiv   i v       v i  ----    iv  v   i    i  
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_126811729_    388 ATTACAAAGAACCTTGACTAGC-AAAGGAATCACGAAAAATAA---TAAA 433
                          v i   i i   iv  v    -   iv    vi      v  ---i   
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_126811729_    434 GTTAGATGGCTAATGTTTCTTGACTATAAAACTAGTTACAAAGCAACCAT 483
                            i  v i  v iii   iii i vi      vii        v  vi 
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_126811729_    484 AATTAAAACAATGTGGTGAAAGCATCAAAATATGTGAGGCAAAAACCGAT 533
                            i  i   i      ivvi    v ii   ---  vii v i i i  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATA---GACATATAGATCAAT 301

  chrX_126811729_    534 GGAACTGCATGGAGAAAC-----ATAAATTCA 560
                             iv v  v    iv -----     ii  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

Transitions / transversions = 1.42 (54 / 38)
Gap_init rate = 0.02 (5 / 329), avg. gap size = 3.20 (16 / 5)  

2187 21.99 2.67 5.65  chrX_126811729_126816126.rev     3235  3907 (491)    L1M4_orf2#LINE/L1      256   908 (0)  

  chrX_126811729_   3235 ATTAAAAAACCAAGGTGGTGCCAGCATGTGGACAGA--TAAACATCAATA 3282
                           i  i ---  iv     i ii    iv   i   --  v v      i
  L1M4_orf2#LINE/    256 ATCAAGA---CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_126811729_   3283 AGATGGAATAGAGAGCTCAGAAATAAACCTTCACATATATAGTGAATTGA 3332
                         ii  i    v     ii            ivi    v   i  v      
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_126811729_   3333 TTTTCAACAACAATGTCAAGAGCCTTCAATGAAGAAAGGACAGTCTTTTA 3382
                              i    vii  i     v v       ii     i i        v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_126811729_   3383 AATGAATGGTGCTACAAAAGTTGAATATCCG-ATGAAAAAGGATGAATTT 3431
                           ii         ivi v ii  i   ?  i-   v     i     v  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_126811729_   3432 GAACTGTGACCTTAAAGTATATACAAAA-TTATTTCAAAATGGCTCAAGT 3480
                          i  iviv    i v vi          -   vi         v   ?iv
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_126811729_   3481 ACCTAAACTG-GAGATATAAAATTATAAAACTCTTAGACATAAACATCAG 3529
                                -  -i   vv     i               viv      -  
  L1M4_orf2#LINE/    503 ACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-AG 550

  chrX_126811729_   3530 GA--AAATGTTTACTACATTGGATTGGATATGACATTATGGATATGGATA 3577
                          ?--    v  iiiv  v    i  i ii -------------    ---
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCA-------------ATGG--- 584

  chrX_126811729_   3578 TACACAGATGTGAAAATTTTATGTATATAACACAAAAAGTACAAGCAACA 3627
                         ----------------   iv iv    i    v     i          
  L1M4_orf2#LINE/    585 ----------------TTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_126811729_   3628 GAA----ACATAAATAGAGTGGACGTTTTCACAATTAAAG---TTTATGC 3670
                         i  ---- v   i   i v     v iv   v       i---   i   
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_126811729_   3671 ATCAAAGGTCATTATCAATAAACTGAAAACACAATGTAGAGAATAGGAGA 3720
                         v       v  i      v   v      v    ivi v     i     
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_126811729_   3721 CAACATCTGCAAATAAAATGTCTGGTAAGGGATTAATGTCCAGAATATAT 3770
                         v  i  i       v v  i    i       i vi i            
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_126811729_   3771 AAAGAATATCTATAGCTCAACA-TAAACA---AAACAACCCAATACAAAA 3816
                               ivii  i i     i -    v ---   i        -i?   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT-TWAAA 817

  chrX_126811729_   3817 AATGGGCAAATGACTTGGATAGATATTTCTCCAAAGGAGATATACCAATG 3866
                                   v  i   i     i            i        v    
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_126811729_   3867 GCCAGTAAACAAATAAAAATAAGCCCAACATCATTAGTAAT 3907
                             i   i  v  i    v v  i        ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (88 / 56)
Gap_init rate = 0.02 (15 / 653), avg. gap size = 3.73 (56 / 15)  


2830 25.67 2.68 1.34  chrX_126819305_126823657.rev     2967  3862 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126819305_   2967 TGGAAACATATCCCATACTCATGGATGGATAGAATCAATATTGTGAAAAT 3016
                               v         ii        v iv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126819305_   3017 GACCATACTGCCCACAGCAGTCTACAGATTCAATGCAATTCCTATCAAAG 3066
                          i v     v    v viii             i     i         i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126819305_   3067 TACAATCATCATTCTTCACGGAACTAGAATAAACC-ATC----------- 3104
                          v v v vv v  i  ii i   v v  -i  i i-   -----------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_126819305_   3105 ATGGAACCAAAAAAGAGCCTGCCTAGCCAAAGCAATACTAAGCAAAAAGA 3154
                               viiv  ii  v  v vv        i    vi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_126819305_   3155 ACAAATCTGGAAGCATCACATTACACCACTTCTA----TACTATAA---T 3197
                              vi    i vv     i v v v i   v ----     i  --- 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_126819305_   3198 ACAATAACTATCCAAACTGCAAATGGTACTGGT-TAAAAACAGGCATGTA 3246
                            i   ---  v i  v ii--         i-   ii i  i   i  
  L1M4_orf2#LINE/    250 ACAGTAA---TCAAGACAGTG--TGGTACTGGCATAAGGATAGACATATA 294

  chrX_126819305_   3247 AACCAATGGAACAGAATAGAGACCCTGGAAATAAAGCCCA-ATACTTACA 3295
                         i i        i     v    vi ii        -    - i i   ii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTATG 343

  chrX_126819305_   3296 GTCTACTGATCCTTGACAAAGCAAACAAAAACATAAAGTGGGAAAAGGAC 3345
                            v i    ii i     i vviv   i v   vv i    i    i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_126819305_   3346 ACCCTATTTAACAAATGGTACTGGGATAATTGGCGGGCCACATATAGAAG 3395
                          vi  v  i          i      i  i   vvi?      ii i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_126819305_   3396 AATTCACCTGGATTCTCATCTCTTACCTTATAAAAAAATCAACCCAGCAT 3445
                            vv vi    ii ii i   vi   v    v      i   i  iv  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_126819305_   3446 GGATCAAAGACTTAAATATAAGAACTGAAACCATAAAAATTCTAGAAGAT 3495
                               ?    i     i     i  i    i      v ii       v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_126819305_   3496 AGCATTGGAAAAACTCTTCTAGACATTGGCTTAGGCAAAAAGTTCA-AGG 3544
                          i   v  ?iv  v     vv   v    v        viiv   v-  i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_126819305_   3545 TCAAGAAACCAAAAGCAAATGCAACAAAAACAAAAATAAATAGATTGGAC 3594
                          - v  v          v v         iv       i   i       
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_126819305_   3595 CTAATTAAACTAAAAAGCTGCTGCACAGCAAAAGAAATAATCAGCAGACT 3644
                         i v  i   v v    i  vi  ii vv    i  v iv    iv i v 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_126819305_   3645 AAATAGACAACCCACAGGATGGGAGAAAATATTTGCAAACTATGCATCTG 3694
                         i  v             i                     ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_126819305_   3695 ACAAAGGACAAGTAGCCAGAATATACAAGGAACTCATACAAATCAGCAAG 3744
                          i  i    vv   v          i  i      v     v   ii  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_126819305_   3745 AAAAAAAAAAACAATAATCACATTTAAAAAGTGGGCAAATGACATGAATA 3794
                              i v   ---   i -  v  ?    i        v  iv      
  L1M4_orf2#LINE/    793 AAAAAGACAAA---TAACC-CAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_126819305_   3795 GACAATTATCAAATGAAGATATACACATGGCCAA-AAGT-CATATAAAAA 3842
                             v  v  v  v           v        -   i-   iv   i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_126819305_   3843 TGCTCAAAATCACTAATTAT 3862
                                v    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (127 / 99)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.25 (36 / 16)  


2974 24.57 5.33 1.16  chrX_126838412_126840286      524  1386 (489)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_126838412_    524 ATCCTGTGTTCATGGATTGGAAGACTTAATGTTGCTAAAATGTCCATCCT 573
                             ii                        i   i   i   v v  v  
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_126838412_    574 ACCCAGAAAGCTCTACAGAATCGATGCAGTTCCCATCAAAATCTCAATGG 623
                         v    i vv v        v  i i   i i  i         i  iiv 
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_126838412_    624 TATTTTTTACAAAAATAGAAAAAC-AATTCTAAAACTCATATGAAATCAC 672
                         iv      i  i    v  v  i -i  i      i       i  vii 
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chrX_126838412_    673 AAAAGACCACCAATA-CCAAAATCACTCTTGAGAAAGAA---TAAAATTG 718
                           ii    vvv    -      -  v      i      ---i   i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_126838412_    719 AAGGCATCACATTTCCTGATTCCAAGATATGTTACAGAGCTACAGCAACT 768
                         i   vv     i    ii   i   i iv ii    i        i  ii
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_126838412_    769 AAAAAAGTAAAGAATTGACATAAAGACAAAGATATAGATCAATGCAACAT 818
                           i v   ivi v i  i     i  i i v             v  i v
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_126838412_    819 AATAGAAAGTCCAGAAATAAATTTACATGTATATGTTCGACTGATCTTTG 868
                            v  i              iii i ii v    v  i i    i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_126838412_    869 ACAAGAGTCTCTAAA--ATACAAAATAGACAAGGGTAATCTCTTCAATAA 916
                              i  vi v i --  v   vivi  -   ii  i   i     i  
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGA-AAGAATAGTCTTTTCAACAA 407

  chrX_126838412_    917 ATAATGCCAGATAAAATGGATTTCCACATG-AAAATAATAAGATTAGACC 965
                           ii   ii ivv  v     v?       -    v   i ii  i    
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_126838412_    966 CCTACATTACATTATATACAAAAATCAACTCAAAGTGAATTAAAGGCCTA 1015
                              v i   ii            i        i  i  i ?  i    
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_126838412_   1016 ------------------------------GAAGAAAACATAGGAAGAA- 1034
                         ------------------------------              ?iv  -
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_126838412_   1035 -CTTCTTGACATTTGTCTTGACAATGATTTCTTGAATATGACACCAAGAG 1083
                         -    v    v  v vi v i     i      ii            i  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_126838412_   1084 CACAGGCAACAGAAGCAAAAATAATTAAATGTGG-CT--ATTACAAACTA 1130
                             i      i   v       iv     -   -  --  i -   i  
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAAT-TGGACTTCATCA-AAATTA 655

  chrX_126838412_   1131 ATAAGCTTCTGCAAG-CAAATAAAACAATCAACCGAATAAAAAGTCAACC 1179
                          -  i   i  iivv-    vi v  v     vvi i i     v     
  L1M4_orf2#LINE/    656 A-AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_126838412_   1180 TATGGAATGGGAAAAAA-ATTTGAAAACTATATTATCTGATAAAAGGTTA 1228
                         i ii        i    -     v   ii    -         ii ii v
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGGGACTT 753

  chrX_126838412_   1229 ATTTCCAAAATATGTAAATAGCTTATACAACTCAATAGCAAATAATCATA 1278
                         i v    i     i    v i  iv            ii   v iv  --
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA-- 801

  chrX_126838412_   1279 ATAATAGCCTAATTAAAAAATGGGGAAAGTATTGGAACAGACATTTCCTC 1328
                         --    i  i    ?         v    v   v   i         ii 
  L1M4_orf2#LINE/    802 --AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_126838412_   1329 AAAGTGGACATACAAATGGCCAATATGTATATGGAAAATTGCTCAA-ATT 1377
                             vi  i                v i i   i   iv       -  i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_126838412_   1378 ATTAATTAT 1386
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.01 (139 / 69)
Gap_init rate = 0.02 (19 / 899), avg. gap size = 2.95 (56 / 19)  


3599 21.56 3.05 0.56  chrX_126843557_126847397.rev     2465  3350 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126843557_   2465 TGGAAAGATATTCTTTGTTCATAGGTTGAAAGACTTAATATTATTAAAAT 2514
                                    i iv       i i   i             i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126843557_   2515 GAAAATACTGACAAAACT-ATCTACGGGTGTAATGCAATTCATATCAAAA 2563
                          iv      vv v   i -      i i vi  i     i v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126843557_   2564 TTCCAATGGCATTATTTGAAGATATAGACAAATTTATCCTAAAATCCATA 2613
                          i   iiv  v  v    v   v  v     ii v          i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_126843557_   2614 TG-AAATGTCAACGGTCCCTGAATAGCCAAAACACTCATGATAAATAA-- 2660
                           -     -   v  v   v              v  v   v   v  --
  L1M4_orf2#LINE/    151 TGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_126843557_   2661 -CAAAGTTGAAGGTGTCACACTTTCTGATTTCAAAACTTATTACAAGGGC 2709
                         -        i   vv        i ii             i     i vi
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_126843557_   2710 ACAGTAATTAAGA--GTGTGGTGCTGGCATAAAGACA--TATATAGCCTA 2755
                                 i    --       i         i  i --i      vii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_126843557_   2756 ATGAAAAAGCAT-ATAAATCATAAAAATAAATCCTTGCATATGTGTTCGA 2804
                            i  v  v  -ivi i  -i i       i  v i   v i  v  i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_126843557_   2805 ATAATTTTT-ACAAAGATGCCAAATCCACTCAATAGGGAAAGGACAGTCT 2853
                         v i     i-    i i      iv   i     i       i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_126843557_   2854 T--CACCAAATGGAGTTGGGAAAACTGGATGTCCACATACAAAATAATAA 2901
                          --  v       v i     v        i?      i     v   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_126843557_   2902 AGTTGAATCCTTACTTCAAACAATATATAAAAATAAACTCAAA-TAGATC 2950
                              i i  i   i   v  v     i      v        - i    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_126843557_   2951 AAATACCTAAACATAAGAACTAAAATAATAAAAGTGTTAGAATAAAATAC 3000
                          ? v       ii     i      iv      v v      v    i i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_126843557_   3001 AAGAAAAAA-CTTCATGATGTTGGATTTGGCAATGATTTCTTGAATAAGA 3049
                          i ?iv   -    i   iv    i  v       i      ii   v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_126843557_   3050 CACCAAATGCACCAGCAACAAAAGTGAGAATAGGTAAATTGGACTAGATG 3099
                                v    v           vi i     i           vv  v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_126843557_   3100 AAAAATAAAAGCTTTAGTTCATGAAAAGACACAATTGAG----TGACAAA 3145
                             v     i    v  v v v   i     v  ii  ----   v  i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_126843557_   3146 GCAACATATAAGATGACAGAGTATATTTGTAAATCATTTATCTGCTAAGG 3195
                         i    vi i ii   iv   iv       i       v      v     
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_126843557_   3196 GGTTAAAATCTAGAATTTATAAAGAATTCTTACAACTCAACAAGAAAATA 3245
                          ii viv   i     v         i             i  v    vi
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_126843557_   3246 TCATGCAATATT----TTTAAA----GGTAAAGTATCTGAAAAGACATTT 3287
                         v  ---    vi----  ?   ----  i    v  i    v        
  L1M4_orf2#LINE/    799 ACA---AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_126843557_   3288 CTTCAAAAAAGACATATGAATGGCTAGCAAGCACATGAAAAGATGCTCAA 3337
                           i    i    i   ii      i ii                      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_126843557_   3338 CATCAATAATAAT 3350
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (111 / 76)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.00 (32 / 16)  


2289 26.17 1.67 8.45  chrX_126867085_126868710.rev      177  1135 (491)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_126867085_    177 ATGTTCATGCATTTGAAACAATCAATATTGTCAAAATGTCCATATCACCT 226
                                  v   v   i- v i        i  i   v v   iiv  i
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chrX_126867085_    227 AAAGCAATCTACAATTTCAGTTCAATTCCTATTGAAATACCAATAAAATT 276
                            vii       iv    iiv    i     ii    v   iivivv  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chrX_126867085_    277 ATTCACAGAA-TGGAAAAAATAATCCCAAAATTTACAAGGGGCCACAAAA 325
                         v  ii     - v  v  iv i    i      i i v  iivii   ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chrX_126867085_    326 GACTCAAAATAGCTAAAGCTACCCTAAGCAAAAAGAACAAAACTTGAAGA 375
                            i  i      i   i v i i i iv  i         ii v  i  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_126867085_    376 ATCACATTACCTGACTTCAAATTATGCCACGGAGCTATAGTAAACAAAGC 425
                         v     i v  ii i      viv i i  ii     i     v   ii 
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_126867085_    426 AGCATGATACTGGCATAAAAACAGACACATAGACAAATGTAGCAGCATAG 475
                           ii  i           ii i     i     i----------------
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGAT---------------- 297

  chrX_126867085_    476 AGAACCCTGAAACACAGTGAACACACTGGTACTGCCATAAAAACAGGCGC 525
                         --------------------------------------------------
  L1M4_orf2#LINE/    298 -------------------------------------------------- 297

  chrX_126867085_    526 ATAGACCAATAGAATAGAATAGAGAACTCAAAAAAAAAAATCCACATCCC 575
                         ------    i         v    iii  i   v   --i   i ivii
  L1M4_orf2#LINE/    298 ------CAATGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACATT 339

  chrX_126867085_    576 TACAGTGAACTCATTTTAGACAAAGGTGCTAAGAGTGTATACTGGGGAAC 625
                           ii  v  i v     v     i     i    vii vi v       v
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_126867085_    626 AGACAGTCTTTTCACAATAACTGGTGCTAGGAAATCT--ATATTCATGTG 673
                         ii i          -- i  v       i   v v  --   ?i  ii  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCA--ACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_126867085_    674 CAGAAAAATAAAACTAGACCCCTACTTCTCACCATATATGAAAATCAAAT 723
                           i  i   i  ii i         i  v         ii     i  v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_126867085_    724 AAAAATATATTAAATACATAA-TGT-----CTCAAACTATGAAATTACTA 767
                         v     iv  i ? v  v   -   -----  v       i   i vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_126867085_    768 CAAAAAAACCT----GAAAACCTCTCCATAACATTGTTCTGCACAAAGAC 813
                         v  i     v ---- v   --   i i i  v   vvi ivi   v ii
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_126867085_    814 TTCCTGAGTAACACACTACAAGCACAGACAGCCAAAGCAAACATGGACAA 863
                            i iii  vv    i v       ii  i v    v   v  i  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_126867085_    864 ACAGGA--TCATGTCAAGTTAAGAAGCTTCTGCACAGCAAGGGAAACAAT 911
                          iv   --    -iv  i    i  -   i  ii vv   i   v  v  
  L1M4_orf2#LINE/    636 ATTGGACTTCAT-CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTAT 683

  chrX_126867085_    912 CAACGAAGTGAAAAGACAACTCACAGAATGGGAGAAAATATTTGCAAACT 961
                            vi               i                           ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_126867085_    962 AACCATCTGGCAATGGATTAATAACCAGAATACATAAGGAGCTCAAACAA 1011
                          vvi     ii  v   i vi  v        i    i  i   vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_126867085_   1012 CTATATAGCAAAAAATCATATAATCCAATC-AAAAATGGGCAAAGACTAG 1060
                           vv   ii     iv  v    i     i-              iv vv
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_126867085_   1061 GAATAGACATTTCTCAGAAGAACACATAAAAATGCCAAACAGGCAAATAA 1110
                                        vi     v i   v     v v  i i   v  i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_126867085_   1111 AACAGTGGTCAGCATTATTGATCAT 1135
                           vii  v   i   i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (158 / 91)
Gap_init rate = 0.02 (14 / 894), avg. gap size = 6.93 (97 / 14)  


2825 27.71 2.12 1.23  chrX_126880239_126883538     1913  2807 (493)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_126880239_   1913 AGGTATTTCACATTTATGGATTAGAAGAATTAATATTTTTAAAACATCTG 1962
                           i   ii  ii  i       i     v        v    i iiv vi
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_126880239_   1963 TACTACCCAAAGCAATCTACAGATTCCATGTAATCTCTATCAAAATACCA 2012
                             v      vii            v i i    i          v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_126880239_   2013 ATTACATTCTCCACAGAAATGGAAAAA---ATCCTAAATTTTGTATAGAA 2059
                         ii i v  i iii       v  v  i---        v  ii   i   
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_126880239_   2060 CAACAGAAGACCATAAATAGCTAAAGCAATACTGAACAAAAGGAACAAAG 2109
                         vvi  iii    vvi      i   i    vi    v  i i        
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_126880239_   2110 CTAGAGGTATCATACTATGTGACTTCAAAATATACTACATGTCTGTAATT 2159
                         i i    vv   i   vivii i       iv       viv  ii i v
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_126880239_   2160 ACCAAAACAGCATGGTGTGGGCATAAAAAAAGGCAT-T-GATCAACGGAA 2207
                          i   i    ii    iiv       ii v  i   - -      i    
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_126880239_   2208 GAGAATAGCAAACCCACAAAACAAATTCACACTTCTACAACCAGCTGATT 2257
                         v     v vi ii   -i   i   ii  i  v i  iiii  ii     
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_126880239_   2258 TTCAACAAAGGTAACAAGAATACACACTAGGGAAGGGACAGTTTCCTCAA 2307
                            i    i   iv     vi iv  v i     i i i   i ii    
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_126880239_   2308 TAAATGGTGCTGGGAAAACTGTGTATTCACATGCAAAAGAAAAAATCTAG 2357
                         i              v     vi  ?i              vi  vi i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_126880239_   2358 A-----ATCGATTACTGTATGCACAAATCAACTGAAAATGGGTTAAAGAC 2402
                          ----- i vvvi  ii   i  v    i    v       i i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_126880239_   2403 TTACATGTAAGACCTAAGAGTATAAAACTATCAGAAGTAAATATAAAGA- 2451
                         i  v        v    i v         v i     v   i   ii?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_126880239_   2452 AAGTGCTTCCTGACATTGGTCTGGGCAGGAATTTTAAAAATAAGACTTCA 2501
                           i -    v    v    vi i    ivii   ivv i   v   vi  
  L1M4_orf2#LINE/    555 AAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_126880239_   2502 AAAGCACAGTCAACAAAAGGAAAAATAAACAAATGGGATTTCATCAAA-T 2550
                                 iv         i       i i    v   i         - 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_126880239_   2551 TAAAAAGATTCTTCACAGCAAAGGAAACAATAAACAGAACAAAGAAACAA 2600
                               v-  i vii vv       v  v  v  v i iii  i i    
  L1M4_orf2#LINE/    654 TAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_126880239_   2601 CCTATAGAATGGG-GAAAATATTTGTAAACTATGTATCTGACAAGGGGTT 2649
                           i i        -           i   ii  i       i     ii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_126880239_   2650 AATATCAAGAATATATAAAGTAATCAGGCAAATCAAGAGCAAATAAGCAA 2699
                         vi    v             v v  vvi   v    v ii   v ii   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_126880239_   2700 ATATTTTGATTTTAAAAATGGGCAAAAGACCTAAACAGTCATTTCTC-AA 2748
                            viiii   ?-             i  ii i  i  v        -  
  L1M4_orf2#LINE/    803 ATAACCCAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_126880239_   2749 AAAATACATACACATGGCAAACAGTTCTATAACATATAAA-----GCTAA 2793
                          i  v i     v     v  i ------- i  i  i  -----   v 
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATA-------AGCACATGAAAAGATGCTCA 894

  chrX_126880239_   2794 ATATCACTAATAAT 2807
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (161 / 83)
Gap_init rate = 0.02 (14 / 903), avg. gap size = 2.14 (30 / 14)  


2456 27.72 3.70 1.80  chrX_126901418_126906336.rev     3538  4428 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126901418_   3538 TGGAAAAGCATTCCATGCTTGTGAATAGGAAGAATCAATATTGTTAACAT 3587
                               iii  i     i ii  i  v      v i           v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126901418_   3588 GGCCATACAGACCAAAGCAATCTACAGATTTAATGCTCTTCCTAT-AAAA 3636
                            v    vvv     vii           i  i  vv i     -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126901418_   3637 --CTAACAATATTGTTCGTCATATAATTGGTAAACCTATTCTAAAATGTA 3684
                         -- i i viiv  v  i -  v -     ii  i iv  i       vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGA-AATTGACAAGCTGATCCTAAAATTCA 148

  chrX_126901418_   3685 TATGCAACCAAATAAGAG-CCCA-AATACCCAAAGAAATCCTAAGCAAAA 3732
                             v  -- vii   i -    -    v     iv    i i ----  
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA----AA 192

  chrX_126901418_   3733 AAGAAAAATAAAGCTGGAGTTATCACACTACCTGACTTTAAACTATATCG 3782
                              i  i    i     vvv       v  ii i  i   viv  iii
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_126901418_   3783 TAAAAC---------CAAGACAGCATGGTACTGATACATAAACAGACACA 3823
                         i   i ---------        ii        ii i vii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_126901418_   3824 TAGGCCAATGGAACAAAATAGAAAACTCATATATAAAGCTGCACACTTAC 3873
                            ii        i i   v  i iii  v v     v iii   i   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_126901418_   3874 AACTATCTGATATTCTACAAGACTGACAAAAACTGGCAATGGAAAAAAGA 3923
                         iiii vi    v   v     iv  v   i v vvv      ii   i--
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-- 390

  chrX_126901418_   3924 CCCAATA-----TTCAATAAATAGTGCTGAGATAACTGGCTAGCCATATG 3968
                         ---    -----     i    i      i  i      v  ?   i   
  L1M4_orf2#LINE/    391 ---AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_126901418_   3969 CAGAAGATTAAAACTGGACCTTCACTTTTCAACACATAAAAAAATTAACT 4018
                           i    v i  ii      iii  i iv  v  i   v           
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_126901418_   4019 CAAGATGGATTA-AAATTGAAATATAAGACCTCAAACTGTAAAACTTCTA 4067
                            i      i - i iiv    i     v  v     i       ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_126901418_   4068 CAAGAAAAACTAGG---AAATATGCTTCTTGATATTGACCTTGGCGGAGA 4114
                         v       vv    ---    ---    v   iv   ivi v   iiv i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_126901418_   4115 ATTAT-GGCCAAGTCCCCAAAAGCAATTGCAACAAAAACAAATATTGACA 4163
                         v  v -i vi v v v         vvv         iv   v  v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_126901418_   4164 TGTGAGACGAAATTAAA-CTAAAAGCTTCTGCACAGCAAAAGAAACTATT 4212
                         vi vi   vvv  i   -i     i   i  ii vv    i  v     i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_126901418_   4213 GATAGAGTAAACAGAAAACCTACAGAATGGGGGAAA-CAGTCACAAACTA 4261
                         i v i   i  v   v    i          i    -i v ii    ii 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_126901418_   4262 TGCATCTAACAATGT-CTGATATCCAGAATCTATAAAGAATTT----AAC 4306
                          ii    i i  v v-  vi          v         i i----   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_126901418_   4307 TCAACAAGCAAAAAACAAATAAACTCATTAAAAAGAGGGCAAAAGACATA 4356
                             i  vv    i        v iv   ?    iv       i  iv i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_126901418_   4357 AACAGACACTTCTCAGAAGAAGACATACAGGGTGCCAATA--CACATTAA 4404
                           i     i     vi       i     iivv       --     v  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_126901418_   4405 AAAATGCTCAACATCACTAATCAT 4428
                           i             ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.45 (49 / 20)  


3504 22.00 2.56 1.67  chrX_126911896_126913933.rev      650  1549 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126911896_    650 TGGCAAAATAAAATCACATGTTCATGGGTTGGAAGAGTTGACGTTATTAA 699
                            v  i   ---  v           i        v  i ii  i    
  L1M4_orf2#LINE/      1 TGGAAAGATA---TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chrX_126911896_    700 GATGGTAATATTCCTTAAATTGATCTAATGATTCAAGGCAATCTCTATCA 749
                              i    i   ii           vv       v      i      
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_126911896_    750 AAATTCCATATGACATTTGCGTAGGAATTGGAAAGTTGATCCTAAATTGC 799
                             i   vv  v v   vi i  i     iv   i          v v 
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_126911896_    800 ATACTGAATTGCAAGGGACCCAAAATGGCCAAAACAATCTTGAAAAGGAA 849
                            iv   v             i   i                   i   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_126911896_    850 GAACAAAG---AAGTACTCAAACTTCTTAACTACAGAATTTATTACAGAG 896
                                 ---i  v     v     ii  i v  i  i   i    i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_126911896_    897 TGACAGAAATCAATGCAGTGTGCTACCAGCATGATGATAGACATATAGAT 946
                         iv    v      vi       v   ii    i v               
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_126911896_    947 CAATGGAATAGGGCAGTGAGTCCAGAAATAAACCCAGGTGTCTGTCTATG 996
                                    iiiv v                   ---- vii i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA----TACATTTATG 343

  chrX_126911896_    997 GTCAATTGTTGCTTGAAAAAGATACTAG--TCATTCTATGGGGCAAAATT 1044
                                 v vi i  v  i i i i i--i     v      v  i v 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_126911896_   1045 ATCCTCTTCAGCAAATGGTGCTGGAACAGCCAGATAGAACCATATTCAAA 1094
                          vi  i    i             i   i ii    ?--   i  v    
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK--CCACATGCAAA 441

  chrX_126911896_   1095 AGAATGAAGTTGAAAACTTAATGCACACCATAAATAAAAAATGAACTCAA 1144
                                     i vv i  viv         v i     - v       
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAA 490

  chrX_126911896_   1145 AATTAA-CAAAAAC-TAAATGTAATAGTTAAAAGTTTAAAATTCTTACAA 1192
                            vi -  ? i  -         v  i     v v     i     v  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_126911896_   1193 GAAAACAAAAAGATAAATTTAAG-AATCTTAAATTTTATAATGAATGCTT 1241
                                v ii?i     i vv -i i   iii  vvii    iv v   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_126911896_   1242 ACATATGACAC--AAAATATGAACAACAAATGATAA--CAGAGAAACTGG 1287
                          v         --   ii ii i       v  v  --i   v   i   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_126911896_   1288 ACTCCTTTAAAATTTAAAAGTTTTGTAATTTCAAGAACACTAACAAAAAA 1337
                            i v i      v    v      iv  iv   i      v   i   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_126911896_   1338 GTGAAAAGACAATACA-AGAATAAAAGAACATGTATGCACATAATGTATC 1386
                                     iv  -     iii    v  i v    v  v  i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_126911896_   1387 TGATAAACACCAGACT-----CTTGAATGTGTAAAGAACAGTTACAATGG 1431
                               i----i    ----- iv    i i        vv      ivv
  L1M4_orf2#LINE/    741 TGATAAG----GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_126911896_   1432 AATAATCAAAAAACAA----CCTTAT-AAAAAAGGAACAAAGGGTCTGCA 1476
                               v    i    ----  iv  -?     v ii      i i  v 
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_126911896_   1477 TAGACATTTCTCCCAAGAAGGTATTAGAATGGCCAATAAGCACATAATAA 1526
                                      v      i   vvi                  i -  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AA 885

  chrX_126911896_   1527 AGATTCTCAACATTGATACTTAA 1549
                             v        ii????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (113 / 81)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.24 (38 / 17)  


2735 28.21 1.09 2.18  chrX_126918842_126923827     3576  4493 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_126918842_   3576 TGAAGAAACATTCCATGCTCATGGCTAGGAAGAATAAATGTCGTGAAAAT 3625
                           i i i i  i     i      v v      v v   i i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126918842_   3626 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCTATTCCTATTAAAC 3675
                            v     vi    iv i  i  i        i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126918842_   3676 TAC-AATTGACATTCTTCACAGAATTATGAAAAAAAAAAAACT-ATTTTA 3723
                          v - ii  v -  i  ii     v -   v  i-------  -  ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAG-------CTGATCCTA 141

  chrX_126918842_   3724 AAATTTATGTGGAACCAAAAAAGAGTGAGGATAGCCAAGACAATTCTAAT 3773
                              i  i     viiv  ii  viv  i        i     ii i v
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_126918842_   3774 CAAAAA-AACAATGCTAGAGG---CAT-CTTGCCACCTGAATTACAACTA 3818
                         v  i  -     v i i    ---  i-   v   vi --- i v    -
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT---TCAAAACT- 237

  chrX_126918842_   3819 TATTTCAAGGCTACAGTAACCAAAACAGAATGGTACTGGTACAAAATCAG 3868
                           i v   i          i   i    vi         i i  iivi  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_126918842_   3869 ACACATAGATCAATAAAACAGAATAGAGAACCTGGAAGTAAGACTGCATA 3918
                            i          ii  i     v    ii ii   i   iv iii i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_126918842_   3919 TCTACAATCATTTGATCTTTAACAAACCTGATGAAAACAAGCAATGGTGA 3968
                          i  iii   v     i  ii    ivv  vii i v  vv      v  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_126918842_   3969 AAAGATTCCCTACTTATTATTAATAAGTGGTACTGGGAGAACTGGCTAGT 4018
                           ii  ----- v iv  - i  i  i    i      v      v  ?i
  L1M4_orf2#LINE/    388 AAGAAT-----AGTCTTT-TCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_126918842_   4019 CATATGCAGAAAATTGCAACTGGACCCCTTCCTTACACCTTATATAAAAA 4068
                           i     i  i v  v ii         v   i     v    i     
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_126918842_   4069 TTTGCTCAAAATGGATTAAAGATTTAAATGTAAAACCTACAACTATAAAA 4118
                           vi            i ?   ii         i v   v          
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_126918842_   4119 ACCCTAGAAGAAAATCTAGGCAATACCCTTCAGGACATAGGAATGGGCAA 4168
                         vi i          iv    ?ivv vi    iv   v v  iv i     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_126918842_   4169 AAATTTCAT-GATGAAAACTCCAAAAGCAATTGCAACAAAAGCAAAATTT 4217
                         vii    v -   - vi  v         vvv          v    v v
  L1M4_orf2#LINE/    582 TGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_126918842_   4218 GACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACCGCAAAATAAAC 4267
                           i    v   ii v  i   v v  i i   i  ii iv    iv v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_126918842_   4268 TGTCATCAGAGTGAACAGACAGCCTACAAAATGGAAGAAAATTTTTGCAA 4317
                          i   vv i      v     i  i   i     i       v       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_126918842_   4318 TCTATCCAACTGACAAAAT-CTAAAACCCAGAGTCTACAAGGAACTTAAA 4366
                         vii  vi v    i  iiv-  viv i     i v  i  i     ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_126918842_   4367 CAAATTTACAATAAAAA-ACATATAACCCCATTAAAAAGTGGACAAAGAA 4415
                            v iv i        -   v       v   ?    i   i     i 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_126918842_   4416 CATGAACAGACACTTCTCAAGGGAAGACATTTATGCAGCCAACAAACATA 4465
                         iv    i     i     v ii     i  vi viii     i  i  i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_126918842_   4466 TTAAAAAACCCTCAACATCACTGGTTAT 4493
                          v    i iv          ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (158 / 97)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.88 (30 / 16)  


2357 28.94 3.18 0.34  chrX_126930234_126938275      492  1372 (6670)  C L1M4_orf2#LINE/L1   (0)   908     3  

C chrX_126930234_   1372 GAAATATTTCCCATGTTCATTGACTGGAATAATAAATATCATTTAAGTTA 1323
                             v  v            v  i     v v v     ii  v ii vi
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

C chrX_126930234_   1322 CCATACTGCCCAAAGCAAGCTACAGATTCAGTGCAATTCCTATTAAAATG 1273
                          v     v      vii v           ii     i     i     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

C chrX_126930234_   1272 GCAACATCATTTTTCACA-AAATTACCAAA--AATCCTAAAATTAATATG 1226
                         v  i vv v     ii  -     iv   i--i           v     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

C chrX_126930234_   1225 GAACCAAAAAAGAGTTCAAATAGCCAA-----TCCT-AACAGTAAGTGAA 1182
                            viiv  ii  viivi         -----  i -  v iv   viv 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

C chrX_126930234_   1181 AATGTGGAGGCATTATTTTACCTTACTTCAAATTATACCACAAGGCTACA 1132
                           vv      vv i ivi v  iv i      viv   i    i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

C chrX_126930234_   1131 GTA-CCAAAACTGTATAGTAATGTTATAAAAGTGGACACACAGACAAATG 1083
                            -i   i  v  i i   v  vi    iii i    i i   iv    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

C chrX_126930234_   1082 GAACAGAATAGAGAGCACAGAAATAAAACCAAACAC----AACCAACTGA 1037
                            i     v     iv          v   v   i----iii   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

C chrX_126930234_   1036 TCGTCGACAAAGCATACAACAAC--TTAAATTGGGAAACGGACACCATCT 989
                          iv       i -i i v vi  --  v   v      - i i viv i 
  L1M4_orf2#LINE/    353 TTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTT 400

C chrX_126930234_    988 TTAATAAATGATGCTGGGAAAACTGGGTAGCCACATGTAGAAAAATAAAA 939
                          i  i     i        v      i  ?       i i  i   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

C chrX_126930234_    938 CTGGATTCCTATCTGTCACCATATATAAAAATCAGCTCAAGATGGATTAA 889
                         i    ii    i  vv         i      i i     i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

C chrX_126930234_    888 AGCCACAAATTTAAGGCCTAAAACCATAAAAATTATAGAAGAAAACCTAA 839
                           v vi    v    iv       i      v iv           v  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

C chrX_126930234_    838 GAAAAACTCCTCTGGATATTGGACTAGGCAAATAATTTAT-AACTAAGTT 790
                          ?iv  v  i  vv  iv    ii       - ii   v - iv  v vi
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGAC 599

C chrX_126930234_    789 CTCAAAAGC-CAAT--GCAAAACCAAAAATAAATAAATAGGACCAAATTA 743
                         vi       -   v--i     vv       i      v    ivv  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

C chrX_126930234_    742 AACTCAAAAGCTTCTGCAGAACAAA--ATAGTCTTCAGAC--TAAACAGA 697
                           v i    i   i  iivvv    -- i v v iv   v-- i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

C chrX_126930234_    696 CAATCCATTGAATGGGAGAAAACATTTTCAAACTATGCAGCCAACAAAAG 647
                            i   iv             i    v    ii  ii v ii i  ii 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

C chrX_126930234_    646 GCTAATATCTATAATCTGCAAGGAATTCA-AAAACTCAGCAAGAAAAAT- 599
                         i  vi    i v   v ii  i   i  v- v      ii  v     v-
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

C chrX_126930234_    598 CAAGTAAATACATCAAAAAGTGGGCAAATGACATGAATAGACATTTCTTA 549
                            i   vivv  i?    i        v  iv               iv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

C chrX_126930234_    548 AAAAATGATATACAAATT-TTAAAAAATATGTGAAAAAACACTCA-CATC 501
                            i v           v-ii  v  ii ii      i ii    -    
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

C chrX_126930234_    500 ATTAATCAT 492
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.39 (146 / 105)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 1.63 (31 / 19)  

 658 30.33 1.23 1.23  chrX_126930234_126938275     5949  6192 (1850)    L1M4_orf2#LINE/L1        1   244 (664)  

  chrX_126930234_   5949 TGAAAAAATATTTCATGCTCATGGATTTAAAGAATCAATACTCTTAACAT 5998
                           i   i    ii    i         vi    v i    i v    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_126930234_   5999 GGCCATACTCCCTAAAGCAATCTACAGGTTTAATACTATTCCAATCAAAC 6048
                            v        i   vii        i  i  ii v  i  v      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_126930234_   6049 TACTAACGTCATTTTTTACAGAGTTAGAAAAAAAACT-ATTCTAAAATGA 6097
                          v i i vv v      i    iv v  v  i---  -  i       vv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_126930234_   6098 ATGTGGAACCAAAAAAAGCCCA-ACTAGCCAAAGCAATTTTAAGCAGAAA 6146
                           i     viiv  iiii    - v        i    i  i iv ii  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_126930234_   6147 GATTAAA-TCCAAGGCATCACATTACAGTATTTCAGACTATACTATA 6192
                           vi   - ivi   vv     i v vvv      i viv     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

Transitions / transversions = 1.31 (42 / 32)
Gap_init rate = 0.02 (4 / 244), avg. gap size = 1.50 (6 / 4)  

1651 29.58 2.77 0.46  chrX_126930234_126938275     6901  7549 (493)    L1M4_orf2#LINE/L1      245   908 (0)  

  chrX_126930234_   6901 AGGCTACAGTAACCAAAATACCATTGTACTGGTATAA----AAACATACA 6946
                          i          i   i i vii v       i    ---- i     i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_126930234_   6947 GACCAAAGAAACAGAATAGGCAATACAGAAATAAAGCCACTCACCTACAA 6996
                           i   v i  i     v iv i v          v   iv  ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_126930234_   6997 GTAACTGACCTATGAAAAAGTTGGCAAAAATAAACAGTGGAGAGAAGGCT 7046
                         vi  i   ii vi  v  i v  v   i vi vv  i   i  i iiiiv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_126930234_   7047 CTCTATTCAACAAATGATGCTGGAAAAACTGGCTAGCCATATAGAAAACA 7096
                         v   v           i      i v      v  ?   i  iv    v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_126930234_   7097 ATAAAACTA---CCCTCCATTTCATCATATACAAAAATTAACTGAAGTTG 7143
                           i  ii i---    v v iv  i                  v  iv  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_126930234_   7144 GATTAAAGATGTTAATGTAAGACCTCAAACTACAAAATTCT-AGAACAGA 7192
                            i ?   iv v         v  v      i    i   -    v i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_126930234_   7193 ATCTAGAAAACATTATTCTGGACATTGGGCTTGAGAAATAATTTAT--GA 7240
                          iv   i?ivv v v   vv   v     -  ii v   ii   v --  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGA 593

  chrX_126930234_   7241 CTAAGTCCTCAAAAGCAAATGTAACAAAACAAAAAACTGA-AAGTGGGAC 7289
                         -  v v vi        v v i       v      iv  -  i v    
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_126930234_   7290 CT------AACTAAAGATCTTCTGCAAGGTAAAATAAACTATCAATAGAG 7333
                         i ------  i    i -   i  iivvvi   iv v        v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_126930234_   7334 TAGACAGAAAACCTACAGAATCGGAGAAAATATTCACAAATCATGCATCT 7383
                          ii v   v    i       v            ii        ii    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_126930234_   7384 GACAAAGGTCTAATATCCAGTATTTATAAGGAATATAAAAAAGTTAAGAA 7433
                           i  i  v  vi       v  v     i   ivivv v  v i  v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_126930234_   7434 GAAGAAAACAAATAATCCCATTATAAAGTAAGCAAAA-ACATAAACAGAC 7482
                         v  i  i        i  v   ?v   i ii     i- iv i  i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_126930234_   7483 ACTTCTTAAATGAAGACATACAAGCAACAAACACACGTATGAAAAAAAAT 7532
                          i    iv  v     i      iiii v  i vi ii       i vii
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_126930234_   7533 TCAACATCATGATCATC 7549
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (109 / 79)
Gap_init rate = 0.02 (10 / 664), avg. gap size = 2.10 (21 / 10)  


2817 26.09 1.30 2.72  chrX_126968569_126970221.rev      250  1169 (484)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_126968569_    250 GAAAAGATGTTCCTTGTTCATGGATTAGAAGAATCAATATTGTCAAAATG 299
                          i      i i  v            i     v i        i  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_126968569_    300 TTCATACTACCAAAAGCCATCTACAAATTCAATGTACTCTCTATCAAAAT 349
                         viv     v  v   viv       i      i i v  i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_126968569_    350 ACCAATGACATTCTTTAAATAAATAGAAAAAACAATGCTAATATT-ATAT 398
                         v   iivi v  i   iv v    v  v  ivii  v    v   -    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_126968569_    399 GGAACCACCAAAGACCCAGAATAGCTAAAGCTATCATGAGCCAAAAAAAA 448
                             vii v ii             i   i v   v   -----    i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-----AAAAGA 196

  chrX_126968569_    449 AAAAAAAAATTAAAAAACTAAAACTGGAAGAATCACATTACCTGACTTCA 498
                          i  v   i  --------------   i  v     i v  ii i    
  L1M4_orf2#LINE/    197 AGAACAAAGTT--------------GGAGGACTCACACTTCCCAATTTCA 232

  chrX_126968569_    499 AATTATAC-ACAGAGCTATAGTGACCAAAACAGCATGATTATGGCATAAA 547
                           viv   -   i     i   i i   i    ii  i vv        i
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_126968569_    548 AACAGCCACATAGATCAATGAAACAGAATATAGAGAACCCAGAAACAAAT 597
                         i i  v  i           i  i     - -    ii       i   i
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAAT-T-GAGAGTCCAGAAATAAAC 330

  chrX_126968569_    598 GCACACACT-ACGGTAAACTCATTTTTTACAAAGGTGTCAAGAACATACA 646
                         v  i   i - i   v  i v     iv    i    i     v   v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_126968569_    647 TTGGTGAAAAGACAGTGCCTTCAATAAATGCTGCTGAAAAAACTGGTTAT 696
                         v   v    ii i   vii     i     v     ii v      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_126968569_    697 CCATATGGAGAAAAATATAACTAGACCCCTATCTCTCAACATATACAAAA 746
                            i   v i  i   iv ii i        i   v  v           
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_126968569_    747 CTCAAATCAAAATGCATTAAAGACTTAAATTTGACACCTCACACTATGAA 796
                         v i  v        v  i ?    i     v i v v  v v     i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_126968569_    797 ACTATTACAATAAAACATTTGTGAAATTCTCCAGGACATTTTTCTGGGCA 846
                            v   v  v       vv ? v  v   i iv   v  vvvi i    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_126968569_    847 AAAATTTCCTGAGTAATGCC-CTGTAAGCATAGGCAGCTAAAGCATAAAT 895
                          vii    i iii  -  v - iiv     i i   i v    v v    
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_126968569_    896 GGACAAATGGAATTGCATCAG--TTAAAAAGCTTATTCACAGCAAAGGAA 943
                         i  i    v i i v     i--       -   v vii vv       v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chrX_126968569_    944 CCTATCAAAAAAATGAAGATGCAACCCACAGAATGAAAGAAAATATTTGA 993
                         v       i   i    i vi              ii            v
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_126968569_    994 AAACTACCCATCTGACAA-----TAATAACCGTAATATATAAGGATTTCA 1038
                            ii ivi      i  ----- vi  v  iv         i  vi  v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_126968569_   1039 AACAACTCTATAGGAAAAAAAACTAATAATCTGATTTTAAA-TGAGCAAA 1087
                         v       v   iv     i - v     i ii   ?v   -  i     
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_126968569_   1088 ATATGTGAATAGGCATTTCTCAAAAGAACATATACTAATGGCAAACAGGC 1137
                         iv  v       i        v      v      v      v  i i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_126968569_   1138 ATATGCAAAGGTGTTTATTGATCATCAGACAA 1169
                          i   v    i  i i vi-    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (134 / 102)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 2.47 (37 / 15)  


3422 22.17 3.02 1.68  chrX_126982951_126986671     2336  3228 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_126982951_   2336 AAAGTATATCATTTATGCATATATTGGAATACTTGGCATTATTAAGATAA 2385
                             -     viv i v   iv       v    iii   i       ii
  L1M4_orf2#LINE/      4 AAAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_126982951_   2386 CAATACTAA--AAATGTGATATACAAATTCAACACATTCCTTATTAAAAT 2433
                                vv--    -    v    i       i  v   i   i     
  L1M4_orf2#LINE/     53 CAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_126982951_   2434 TTTAATGGTGTTTGTTACAAAAATGGAGAAACCTGTTCTAAAATCCAAAT 2483
                         iii iiv iv   v  i  i    v  v  i ivi i       i  ---
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA--- 148

  chrX_126982951_   2484 CTATTGGATTTTAAGGTTTTCAAGGGACCCCAAATAACCAAATTAATTCT 2533
                         -   -   ----  v ----          vi    i     vi   ii 
  L1M4_orf2#LINE/    149 -TAT-GGA----AATG----CAAGGGACCCAGAATAGCCAAAACAATCTT 188

  chrX_126982951_   2534 GAAAATGCAGAACAAAATTGGAGAACTCACACTTCCTAATTACAAAATTT 2583
                              v v        i      i            i    v     i  
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_126982951_   2584 ACTGTAAAGCAACTGTAATAAAATCAGTGTGGTCGTAGCATAAAGATAAG 2633
                            ii     v  v     v  iv         vv i      i    ii
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_126982951_   2634 CTTATATATTAATGGAATCGAATTGAGAGTTCAGAAACAAACCTATACAT 2683
                          v    v  i        v           i      i     i      
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_126982951_   2684 ATAAGTTCAATTGATTTTCAACAAGGGTGTCAAGACCATACAATGGGAAA 2733
                         v  v v             i         i         v       i  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_126982951_   2734 A-AACAGTATCTTCGATA----GTGTTGGAAAAACAGGATAGTCATATAC 2778
                          -  i   v i   i i ----   i   i v   v     ?i  i  i 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_126982951_   2779 AAAAGAATGAAGCTGGACAATTATCTCATGCTGCATAAAAAAATTAACTC 2828
                                     i     vvi  i    ii iii   v            
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_126982951_   2829 AAAATGAATAAAAACCCTAAATGTAAGAACTGACACCACAAGATTCTCAG 2878
                               i  v ? iv             i  i v  i i  i i   i  
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_126982951_   2879 AAGAAAACATAGGAGTAAATCTTCATGACCTTGAAATTGGCAATGGTTTC 2928
                                      ?          i        iiv v            
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_126982951_   2929 CTAAATATGATACCAAATGAAAATG------AAGAAAAAA---ATAAATT 2969
                         i  i      i      v v v v ------         ---       
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_126982951_   2970 GGACTTTAACAAAATTAA---TTTTTGCACATCAAATGATAATGTCAAGA 3016
                               i v         ---i     ii v     v  i v i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_126982951_   3017 GAGTAGAAAGCCAAACCAATAAACAGGAGAA------TAAAACTCACATA 3060
                         i   ii    v   v   vvi  ii      ------ iv  v   i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_126982951_   3061 TATTATAGCAGTGTAATATCTGGACTATATAAAGAACTCCTA-AACTAGA 3109
                          v v   ivi vv vi    ii  v              i  -    vi 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_126982951_   3110 CTGCCAAACTACACACAAGCCAATTAAAAAATAGGCTAAGGACT-GACTA 3158
                         iviiv   vv   v i  v      ?      i   v     i -  v  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_126982951_   3159 AATATTTCTCCAAAGAAGATATAGAAATAGTAAATAAGCACATAAAAAAA 3208
                         i i                    v    i iv           i    i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_126982951_   3209 TGCTAGACACCACTAACCAT 3228
                             vi   i  ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (116 / 78)
Gap_init rate = 0.02 (15 / 905), avg. gap size = 2.80 (42 / 15)  


2729 25.68 2.95 3.72  chrX_127007494_127013069     4169  5083 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127007494_   4169 TGGAAAAACATTCCATCCTCTTGAATAGGAAGAATTAATATTGTGAAAAT 4218
                               i i  i    vi  v  i  v      v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127007494_   4219 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATTTCCATCAAAC 4268
                            v     v      v i  i  i       ii  v  ii i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127007494_   4269 TACCA-CTGACATTCTTCATAGAATTAGAAACAACT-ACTTTAAATTTGA 4316
                          v   -   v -  i  iii    v v  v - i  - iii    v  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chrX_127007494_   4317 TATGGAA-TG-AAAAAACAGCCTGTATAGCCAAGACAATCCTAAGCAAAA 4364
                                -  -  iii  --  v v        i      i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_127007494_   4365 AGAACAAAGCTGGAGGCATCACGTTTTCTGACTTCAAACTATACTACAAG 4414
                                  i      vv    ii  i ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_127007494_   4415 GTTATAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGCATGGTACT 4464
                          i  i     i   i    ii       -----------i    i-----
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACT-----------GGCATA----- 280

  chrX_127007494_   4465 TGTACCAAAACAGATATATAGACTAATGGAACAGAACAGAGATCTCAGAA 4514
                         ------ ii i   i       ii       i    iv    vii     
  L1M4_orf2#LINE/    281 ------AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_127007494_   4515 ATAACACCAGACATCTACAACCATCTGATCTTCAACAAAGTTGACAAAAA 4564
                             vv   v    i  iiii  vi    i   i    i v  v   i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chrX_127007494_   4565 CAAGTAATGGGGAAATAATTCCCTATTTAATAAATGGTGTTGGGAAAACT 4614
                           vvi          v   vvi  v  i  i        i     v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_127007494_   4615 GGCTAGCCATATGCAGAAAACTGAAAGTGGACACCTTCCTTACATCTTAT 4664
                           v  ?   i     i  i v    iv     v   v   i   i v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_127007494_   4665 ACAAAAATTAACTCCAGATGGATAAAAGACTTAAATGTAAAACCCAAAAC 4714
                                       v i      v ?    i         i v i     
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_127007494_   4715 CATAAAAACCCGAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGGC 4763
                         i      vi iv          v    ?i- v i -   iv   v v  v
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

  chrX_127007494_   4764 ATGGGCAAAGA---CTTA---ATGACAAGAATGCCAAAA--ACAA-TGGC 4804
                         v i     v i---    ---      ------      --    -iii 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACA------CCAAAAGCACAAGCAAC 617

  chrX_127007494_   4805 AAAAGCTAAAATTGACAAAGGGGATCTAATTAAACTAAAGAGCTTCTGCA 4854
                              vv     v  i   vv   ii v  i   v v  i i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_127007494_   4855 CAGCAAAAGAAACCTAC-------------AGGCAACCTACAGAACGAGA 4891
                          vv    i  v  -  i-------------  i     i      i i  
  L1M4_orf2#LINE/    668 CTTCAAAGGACAC-TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_127007494_   4892 GAAAATTTTTGCAATCTATCCATCTGACAAAAGTCTAATATTCAGAATCC 4941
                               v       vii  vi      i  ii v  vi   i      vi
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_127007494_   4942 ACAAGAAACTTAAAGATATTTACAAGAACAAAACAAACAACCCCATCAAA 4991
                          i  ii    ivv v vv iv i  v  v  i     i     v  i?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_127007494_   4992 AAGTGGGCAAAGGATATGAACAGATGCGTCTCAAAAGAAGACATGTATGT 5041
                           i            v    i   iiiv    v        i  ii vi 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_127007494_   5042 GGCCAAGAAACATATGAAAAAAAGCTCACCACCACTTAGCAT 5083
                               v  i  i       i v     v  i  ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (139 / 92)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.39 (61 / 18)  


2763 27.88 1.33 1.11  chrX_127016963_127021542.rev     3186  4089 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_127016963_   3186 GAAACACATCCTAGGCTCATGGATGGGCAGAATCAATATTGTGAAAATTG 3235
                             v i    i v i        v  v   v i        v  i  v 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_127016963_   3236 CCATACTTCCAAAAGTAATCTACAAATTCAATGCAATTCACATCAAAATA 3285
                          v     i  v   v i       i      i     i vi        v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_127016963_   3286 TCACCATCATTCTTCACAGAACCACAAAAAACAATACTAAAATTCATAAG 3335
                         i  v vv v  i  ii     vivv v  ivii  v            v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_127016963_   3336 GAACCAAAAAAAGACCCCACATACTCAGAGCAAGACTAAGCAAAAGGAAC 3385
                            viiv  ii-     viv   vi  i i   vvi i iv  i i    
  L1M4_orf2#LINE/    153 GAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_127016963_   3386 AAATCTGGAGGGATCACATTACCCAACTTCAAACTATACTATGAGGCCAT 3435
                            vi      iv     i v     i      viv     ii i  i i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_127016963_   3436 AGTCACCCAAACAGCATGGTACTGGTGTAAAAATAGGAACATAGACCAAT 3485
                            v i v i    ii         ii   ii    iv i     i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_127016963_   3486 GGAACAGAATAGAGAACCCAGAATTAAAGCCAAATAAGTACAACCAACTG 3535
                             i     v    ii      v    v   v i vv  iiii   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_127016963_   3536 ACCTTTGACAAAG-CAACAAAAATATAAAATGGGGAAAGGACAACCTATT 3584
                          ii  i     i -iiv   i vi  vv           i i ii  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_127016963_   3585 CAACAAATGGTGTTGGGATAATTGACAAGCCACATGTTGAAGAATGAA-- 3632
                                     i     i  i  ivv ?       ivi         --
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_127016963_   3633 ---ACTC--ATTTCTCACCTTATACTAAAATCAACTCAAGATGGATCAAG 3677
                         ---  i -- ii  v    v     v     i       i        ?i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_127016963_   3678 GACTTAAATCTAAGACTGAAAACTATAAAAATTCTGGAAGATAACATTGG 3727
                            i     v     viv            v ii i     v     v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_127016963_   3728 AAAGACCCTTCTAGACATTGGCTTAAGCAAAGACTTCTTGACCAAGAACC 3777
                         ?ivi vi    vv   v    v   i    v ii     iivi v  vv 
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_127016963_   3778 CAAAAGCAAATGCAACAAAAACAAAAATAAATAGATGGGACTTAATTAAA 3827
                                 v v         iv       i   i  v      v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_127016963_   3828 CTAAAAAGCTTCTGCACAGAAAAAGAAACAATCAGCAGAGTAAACAGACA 3877
                         v v    i   i  ii vvv   i  v  v    iv i   i  --- - 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA---A-A 697

  chrX_127016963_   3878 GACAACCCACAGAGTTGGAGAAAATCTTCATTATCTATACATCTGGCAAA 3927
                                      i v         v  iiiv vii   i     ii  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_127016963_   3928 GGACTAATTAATATCCAGAATCTGCAAGGAACTCAAACAAATCAGCAAGA 3977
                              --- i-          v ii  i      vv    v   ii  v 
  L1M4_orf2#LINE/    748 GGACT---TG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_127016963_   3978 ACAGAACAA----TCCCATCAATAAGTGGGCTAAAAACATGAATAGACAA 4023
                          v ii    ----i  v  i? v  i     v  ii iv          v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_127016963_   4024 TTATTTTAAAAAAGGTATAGAAATGGCCAGCAAACATATGAAAAAATGCT 4073
                           -i ii   i   i    v         ii  i  i       i     
  L1M4_orf2#LINE/    844 TT-CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_127016963_   4074 CAACATCACTAATAAT 4089
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 2.20 (22 / 10)  


2932 27.56 0.56 0.45  chrX_127037319_127043085     4378  5266 (501)    L1M4_orf2#LINE/L1        2   891 (17)  

  chrX_127037319_   4378 GGAAA--CATTCCATGCTTATGGATAGAAAGAATCAATACCATGAAAATG 4425
                              --i  i     i i      v i    v i    iii v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_127037319_   4426 GCTATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATTAAACT 4475
                           v     v      v i  i  i        i  v     i  i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_127037319_   4476 ACCATAGGCATTCTTCACAGAATTAGAAAAAACT-ATTTTAAAATTCATA 4524
                         v   vvv  v  i  ii     v v  v  i-  -  ii           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chrX_127037319_   4525 TGGAACCAAAAAAGAGCCTGAATAACCAAGACAGTCCTAAGCAAAAAGAA 4574
                              viiv  ii  v  v     i    i   i  i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_127037319_   4575 CAAAGCTGGAGGCATCATGCTACCCCACTTCAAAATATACTACAAGGCTA 4624
                              i      vv   ii  v   v i       iv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_127037319_   4625 AAGTAACCAAAAGAGCATGTTACTGGTACAAGAACAGACACATAGAACAA 4674
                         v     i   i v  ii  v      i i   i i     i     v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_127037319_   4675 TGGAACAGAATAGACAAATCGGAAATACGACTGCACACTGAAAAGCATCT 4724
                              i     v  v ivi i      viv iii   i v viiv  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_127037319_   4725 GATCTTTGATAAACTTGAAAAAAACATGCAATGGCGAAAGGATTCCCTAT 4774
                            i  i  i  ivv  vv  i v   v      v     i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_127037319_   4775 TTAATAAATGGTGCTGGGAAAACTGGCTACCCATATGCAGAAAACTGAAA 4824
                          i  i              v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_127037319_   4825 CTGGATCCCTTCCTTACACCTTATAAAGAAAATTAACTCAAGATGGATTA 4874
                         i    i    v   i     v    v -             i      i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACA-AAAATTAACTCAAAATGGATCA 499

  chrX_127037319_   4875 AAGACTTAAATGTAAAACCCCAAACTATAAAATCCCTAGAAGAAAATCTA 4924
                         ?    i         i v iv           ii i          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_127037319_   4925 GGGA-ATACCATTCAGAACATAGGCATGGGCAAAGACTTCAT-GATGAAA 4972
                           ?i- v i -   ivi  v v  vv i     v ii   v -   - vi
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chrX_127037319_   4973 ACACCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTAAT 5022
                                     vvv          v      v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_127037319_   5023 TAAACTAAAGAGCATCTGTTCAGCAAAAGAAACTATCATCAGAGTGAAAA 5072
                         i   v v  i i v i   v vv    i  v       vv i        
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_127037319_   5073 GATAACCTACAGAATGGGAGAAAATTTTTGCAATGGAGTCATTTGCTAAA 5122
                           i    i                 v       vvv vvi  i  v   i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_127037319_   5123 GGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 5172
                           v  vi          v  i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_127037319_   5173 AACAAGAAATCTCATTAAAAAGTGGGCAAAGGACATAATCAGATACTTCT 5222
                         i    iv  i iv   ?    i           iv i vi   i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_127037319_   5223 CAAAAGAAGGCACTCATGTGGCCCACAAAGATATAATAAAAAGC 5266
                          v       ii iv  vi     v i  iv i  i v  i v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

Transitions / transversions = 1.21 (132 / 109)
Gap_init rate = 0.01 (8 / 890), avg. gap size = 1.12 (9 / 8)  


3060 26.76 0.99 0.99  chrX_127059128_127064349     3822  4729 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127059128_   3822 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3871
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127059128_   3872 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3921
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127059128_   3922 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 3969
                          v   iivi i  i  ii     -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_127059128_   3970 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGACAATGCTAAGCAAAAAG 4019
                                viiv  ii  v  v v  v     i     vi i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_127059128_   4020 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4069
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_127059128_   4070 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4119
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_127059128_   4120 AATCGAACAGAAC--AGAGCCCTCAGAAATAATACCGCACATCTACAA-C 4166
                            v   i    i--    i  --        vv  ii    i  iii- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_127059128_   4167 AATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTC 4216
                            -    i  i     ivv  vv  i v  vvv           i  vv
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_127059128_   4217 CCTATTTAATAAATGGTGCTGGAAAAACTGGCTAGCCATATGTAGAAAGC 4266
                         i  v  i  i            i v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_127059128_   4267 TGAAACTGGATACCTTCCTTACAACTTATACAAAAATTAATTCAAGATGG 4316
                             ii    iv   v   i   v v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_127059128_   4317 CTTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTGGAAGCAAA 4366
                         v i ?    i       v   v       i      vi i i    v   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_127059128_   4367 CCTA--TGCAATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGAC 4414
                          v  --? i  - i -   iv   v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_127059128_   4415 TCAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 4464
                          vvi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_127059128_   4465 TAAGTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 4514
                          v vi   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_127059128_   4515 AACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGA 4564
                           v  i     i                 v   i   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_127059128_   4565 CAAAGGGCTAATATCCAGAATCTACAAAGAACAA--ACAAATTTAGGAGA 4612
                         i  i  i  vi          v  i       vv--    v iv vi v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_127059128_   4613 AAAAAAATCAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGAC 4662
                             i --    i     v  i?    i    ii      v    i    
  L1M4_orf2#LINE/    794 AAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_127059128_   4663 ACTTCTCAAAAGAAGACATTTGTGCAGCCAACAGACACATGAAAAAATGC 4712
                          i     v        i  viiviii     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_127059128_   4713 TCATCATCACTGGCCAT 4729
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


2517 26.92 1.18 4.17  chrX_127068012_127074023     4584  5519 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127068012_   4584 TGGAAAAACATCTCATGCTCATGGATGGGTAGACTCAATATTGTGAAAAT 4633
                               i i   i    i        v  v     i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127068012_   4634 GATCATACTGCCAAAAACAATCTAATAATTCAATGAAATTCCCCTCAAAA 4683
                          iiv     v  v   vii     vvi      i v   i  iv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127068012_   4684 TATCACCATCATTCTTCACAGAACACAGA-AAAC-AATCCTAATGGAGGA 4731
                          vi  v vv v  i  ii     - iv  -  i -i       -----i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAA-----AA 144

  chrX_127068012_   4732 TTATTTTCATATGCAACCAAAAAATATCCCACATAGACAAAACAAGACTA 4781
                           -----      v  viiv  iiv i  viv    v        vvi i
  L1M4_orf2#LINE/    145 TT-----CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_127068012_   4782 AGCAACAAGAACAAATCTGGAGGCATCACATCATCTGACTTCAAACTATA 4831
                          iv  v         vi      vv     iivi ii i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_127068012_   4832 CTATAAGGCCATAGTCACCAAAATAGCATGGTACTGGTATAAAAATAAGC 4881
                            i  i  i i   v i   i i  ii         i    ii   ii 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_127068012_   4882 ATATAGAACAATAGAACAGAATAGAGAACCCATGAATAAAGCCAACTACT 4931
                                v    i   i     v    ii   vi      v   vvi i 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_127068012_   4932 TACAGGTGACTGATCTTCAACAAAG-CAACAAAAATATAAAGTTGGGAAA 4980
                           ii vii i    i   i    i -iiv   i vi  vv i v      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_127068012_   4981 GGACACCCTATTCAACAAATTGTGCTGGGATAATTGGCAAGCCAAGTGTT 5030
                          i i vi  v          v         i  i   vv ?   vi  iv
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_127068012_   5031 GAAGAATAAAACTGGATCTTTATTTCTCACCTAATAAAAAAATCAACTTA 5080
                         i      i  ii    i ii  ii  v    vv   v      i    i 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_127068012_   5081 AGATGGATCAAGGACTTAAA-----GACCTGAAAACATAAAAATTCTAGA 5125
                          i        ?i   i    -----  v  i   vi      v ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_127068012_   5126 AGATAATATCGGAA-AAGCCTTTCTAGACATTGGCTTAGGCAAACACTTC 5174
                            v  i  v  ?i-  ii   iv -   v    v        vvii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTC 588

  chrX_127068012_   5175 ATGACCAAGAACCCAAAAGCAAATGCAACAAAAACAAAGACAAATGGAT- 5223
                         v iivi v  vv         v v         iv   i i i  ii  -
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_127068012_   5224 -GACAATTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACAGTCAG 5272
                         -   --  v  i   v v    i   i  ii vv    i  v  vi   i
  L1M4_orf2#LINE/    639 GGAC--TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_127068012_   5273 CAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCACAAACTATA 5322
                         v i   i  v              i           v  ii    ii   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_127068012_   5323 CATCTAGCAAAGGACTAATATCCAGAATCTACAAGGAACTCAGACAAATC 5372
                         i    iii  i     vi          v  i  i      vv    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_127068012_   5373 AGCAAGAACAGGAAAAAAAACAAGAAAACAAACAAAAAAAAACCAATCAC 5422
                          --------------- v  i  i  i     i  v------     ---
  L1M4_orf2#LINE/    787 A---------------ATAATAAAAAGACAAATAAC------CCAAT--- 812

  chrX_127068012_   5423 ATCAATAAGTAGCTAAGGACATGAATAGACAATTCTAAAAAGAAGATATA 5472
                         - ?  v  vvi  v     iv          v    vv            
  L1M4_orf2#LINE/    813 -TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_127068012_   5473 CAAATGGCCAACAAACACATGAAAAAATTCTCAACATCACTAATGGT 5519
                                    i  i          i  v          ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (146 / 102)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.57 (50 / 14)  


1907 27.20 2.81 2.94  chrX_127134909_127136683      500  1282 (493)    L1M4_orf2#LINE/L1      127   908 (0)  

  chrX_127134909_    500 GAAAAGCT-ATTCTAAAATTTATATGGAAAGGCTCAGGCTCTAGAATAGC 548
                           v     -  i        i         v  vvi  vi i        
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chrX_127134909_    549 TAAAATAATCCTGACAAAAAAGAATTAAGTGAGAGGAATCAC-TTTACCA 597
                         i    i    i   v   i     iv    vi     v    -i  v   
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_127134909_    598 GACACTAAGGCTTAGTATGTAGCTACAGTAATCAAGGCAATGGGGTATTG 647
                         - ivii  ii    v  iiv                i  i  v    i  
  L1M4_orf2#LINE/    227 -ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_127134909_    648 -TAGAGGGATGAACACATAGATAAATAAAACAAAATAAAAAAATTAGAAG 696
                         -i v i    ii   i      v   ii  i i   vi i ivii    i
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_127134909_    697 TATACCCAGGAAAATATGCTCAACTGATTTCTGACAAAAATTTAAAAAAA 746
                           v     viv vv    v    i      ii     iii viv  i --
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA-- 373

  chrX_127134909_    747 TGATTAAATGGATAAAGGATCACCTCTTCACCAAATGGTGCTGG-ACATC 795
                         iv   v     iv    i  vii  i    v             -   v 
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_127134909_    796 CATGAGCAAAAAAATG-AAAAGAAATAAATTAAGCCTAAGCCTCAACATC 844
                         --  iii ?vv v   -       vv  i  iii  ivvi     -  i 
  L1M4_orf2#LINE/    424 --TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA-CACC 470

  chrX_127134909_    845 TTATACAAAAATTGACCTAAGATGGATCATGAACATAAGTATAAAATATA 894
                         v            i  ii  i        ?ii  v   i i   i vv  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_127134909_    895 AAACCAGAAAATATTTAGTGAAAAACAGAAAAA-AAATCTTCAGGATCTA 943
                             i v    ivi    vii      v ii?i-        iv  i  v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_127134909_    944 GAACTAGGTGAATAATT-CTTAGGTTTGATACCAAAGGATGATCTATACA 992
                          iii    i-   ii  -     i v   i      i --------i   
  L1M4_orf2#LINE/    571 GGGTTAGGC-AATGGTTTCTTAGATATGACACCAAAAG--------CACA 611

  chrX_127134909_    993 AGGAAACAACAACAACAAAAA-AGATCATTACAACCTCATCGAGATGAAA 1041
                           ----      v iv     -    v v vvi  i     i i  v   
  L1M4_orf2#LINE/    612 AG----CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_127134909_   1042 AACTTT-GCTCTGTGGATGAAGCTGTACAGAAGATGAAA-GAAAAGCTGG 1089
                               - iv  viii v  vi  i vv    ii     -  v  v iiv
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_127134909_   1090 ACACTGAGAGAAATTATT--AAAATTACATATGCAATAAAATGA-TTGTA 1136
                          v v  i      v    --v    i i    vii    ii-  -     
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG-GACTTGTA 756

  chrX_127134909_   1137 TCCAGAATATATAAAAAAGTTTCTA-AACTCAATGATAAGAAAACAA--- 1182
                                        i  v i -  -        i    i  i    ---
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCT-TACAACTCAATAATAAAAAGACAAATA 805

  chrX_127134909_   1183 -TCTAATTAGAGAATGGACAAAATACATAAACAGAAATTT----AAACAA 1227
                         -i i    ?i i     i    iv iv i  i   v    ----   -i 
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA-GA 854

  chrX_127134909_   1228 AGATTTACAGATGGCAAATAAGAACATGAAAAAAATGTTCAACATCATTA 1277
                             v    i     v      v         i -  i         ???
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZ 903

  chrX_127134909_   1278 GCTAC 1282
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.68 (131 / 78)
Gap_init rate = 0.03 (26 / 782), avg. gap size = 1.73 (45 / 26)  


2940 26.26 1.83 0.46  chrX_127148828_127151367     1172  2047 (493)    L1M4_orf2#LINE/L1       21   908 (0)  

  chrX_127148828_   1172 ATGCATTGGAAGAATCAATATTGTTAAAATGTCCATAGTACCCAAAGCAA 1221
                            v         v i           i   v v   v v      vii 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chrX_127148828_   1222 TTCACAGATTCAATGCAATCCCTATAGAAATATCAATGACATTCTTAACA 1271
                          ii          i           vi    vi  iivi v  i  vi  
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chrX_127148828_   1272 GAAATAGAAAAAAAAATCCTAAAATTTGTATGGAACCACAAAAGACCCAG 1321
                              v  v  ivvi           ii       vii   ii       
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chrX_127148828_   1322 AATAGTCAAATCTATCCTAAGAAAAAAGA-CAAAACTGATGGAATCACAT 1370
                              i    v v   i i i   i    -    ii  iv   v     i
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_127148828_   1371 TGTCTGAATTCAAATTATACTACAGAGCTATAGTAACCAAAGCAGCATGG 1420
                          vi ii v      viv       i     i     i   ii   ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_127148828_   1421 TAC------------AGACACATGGAACAATGAAACAGAATAGAAGATGC 1458
                            ------------     i  i  v     i  i     v  iii v 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_127148828_   1459 CGAAAAAAATACACACACCTGCAGTGAACTCATTTGTGATGAAGGTATCA 1508
                         v    v   iv  i   ii iii  v  i v    vi  ii i   ii  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_127148828_   1509 AGAACATACAATGAGGAAAAGACTGTCTTCTCAATATATGATGCTGAGAA 1558
                            v   v     i     ii iv     i    i v   i     i  v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_127148828_   1559 AACTGGATATCCACATGCTGAAGAATTAAACTAGATCCCTATCTC--TCC 1606
                                  ?        vi      v  ii i  i     i   --v  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_127148828_   1607 ATATACAAAAATTAAATCAAAATTGATTAAAGACTTAAATCTAAGACCTG 1656
                                        v       v   i ?    i     v     v  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_127148828_   1657 GAACTATAAAACTACTACAAGAAATAATTGGGGAAAATCTCCAGGACACT 1706
                         i            vi  v      vv  v  ? v      i iv   -  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC-CT 569

  chrX_127148828_   1707 T-TTCTGGGCAAACATATATTGAGCAATACCCCACAAGCACAGGCCACCA 1755
                          -vvi i     vvi v v  iiii vv  v   v       i  v  v 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_127148828_   1756 AAGCAAAAATGCACACATGGGATCACATCAAGTTTAAAAGCTTCTGCACA 1805
                            v      iv i v  v   iiv      iv      i   i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_127148828_   1806 GCAAAGGGCATAATAAACAAAGTGAACATAGAAGACAAAGAATGGGAGAA 1855
                         v      i  iv  v  v        v v v  vv  v            
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_127148828_   1856 AATATCTGCAAACTACCTGTCTGACAAGGGATTAAAAAAACATAATATAC 1905
                              i      ii iv i     i      i -viv vv  v      i
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACT-TGTATCCAGAATATAT 768

  chrX_127148828_   1906 AAGCAGCTCAAAGAACTCTATAGAAAAAAAATCTAATAATCAGATCAAAA 1955
                           iv i   vv v     v   iv     i - v     i vi  i?   
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAA 817

  chrX_127148828_   1956 AAATGGGCAAAAGATTTGCATACACATTTCTCAAAAGAAGACATACAAAT 2005
                           -        i      v   v         v        i        
  L1M4_orf2#LINE/    818 AA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_127148828_   2006 GGCAAATAGGCATATGAAAAAGTGCTTAACATCATTATAGAA 2047
                            v    i   i       ii    i       ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (126 / 100)
Gap_init rate = 0.01 (8 / 888), avg. gap size = 2.50 (20 / 8)  


2500 25.27 3.38 4.47  chrX_127154709_127157257     1139  2056 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127154709_   1139 TAGAAAAATATCCTATTCTCATTGATTAGATGAAGGAATATTGTTCAAAT 1188
                          i    i      i  vi    v    i  v  vvv         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127154709_   1189 ATCCATATTTTCCAAAGTGACCTTCAGATTCAATGCAATCCCTAGCAAAA 1238
                         iv v   i ii     v   i  v         i          v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127154709_   1239 TATCAAT-------------GAAATTATTCACAAAG-AATCATAAAATTC 1274
                          vi  ii-------------      i---    iv-i   v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_127154709_   1275 ACATGAAGTCACAAAAGATGCTGAATAGCTAAAGCAAACCTGAGTAAAAA 1324
                          i   i ivii   ii  iv v       i   i   v i   i-   i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGA 196

  chrX_127154709_   1325 AAAGCAAAGCTG-AGGCATCACACTACCTGACTTCAAACTATAC-AGAAA 1372
                          i i     i  -   vv       v  ii i      viv   - v   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_127154709_   1373 GCTATATAATAACCAAAACACCATGTTACTGACATTAAAAAATCCCCACA 1422
                             i --i   i   i   vii  v     i   --  ii  vvv  i 
  L1M4_orf2#LINE/    247 GCTACA--GTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATA 292

  chrX_127154709_   1423 TATATTAGTGGAACAGAATAAGGGAATGCAGAAATAAACTCACTC-CCTA 1471
                           v  i i     i     v- i  i v           i  iv -ii  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_127154709_   1472 TAGCCAACTGATTTTCAACAAAGGTGCCAAGAACATATATTGAGAAAATG 1521
                          i i   i        i    i          v   vi v  i i   vi
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_127154709_   1522 ACAATTTCTTCAATAAATGGTGCTGGAAAAACTAGATATTCATATGCAAA 1571
                          i i i i     i            i v    i    ?i  i       
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_127154709_   1572 AGGGAAAAACTAGATATTCATATGCAAAAGGGTAAAACTAGACCTCCATT 1621
                           -------------------------  --- i  ii i    i i ii
  L1M4_orf2#LINE/    442 AG-------------------------AA---TGAAGTTGGACCCCTACC 463

  chrX_127154709_   1622 TTTCACTATATACAAAAATCAAATCAAAATAAATGAAATATTTTAAGGTA 1671
                          iv   i            i  v       ii  v ? v ii v  v   
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_127154709_   1672 AGTCCTGGATCTATGAAACTACCAGAAGAAAACATTGAGG-AAATGCTTC 1720
                           vv  ii v    i     vii            v i? -    -    
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTC 562

  chrX_127154709_   1721 ATGATATTGGTCTGGACAAAGAGTTTCTGTG-TAAGACCTTGAAAGCACA 1769
                         i   iv    vi i i   v -      vv -  v   viii        
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATG-GTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_127154709_   1770 GGCAACAAAAGCAAAA-TACAGAAATAGGATTACATCAAGGT-AAAAA-T 1816
                         i          v    -  v v    v   i v      ii -     - 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_127154709_   1817 CTTGTGCA-CAGGAAAAAAAATCAAAAAAGTTAAGTGATAACCTACAGAA 1865
                         i      v-  iiii v vv     i     v  iv  i    i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_127154709_   1866 TAAGAGAAAATATTCACAA-TC---CATCTGAAATGAGATTAATGACCAA 1911
                          ii           ii   -  ---i      v v i  i vi iv   i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_127154709_   1912 AATATATAAGGAACTGAAACTACTCAATAGCAAAATAA-AAATAATCTAA 1960
                                  i     vvv  v        ii    vi -      i i  
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_127154709_   1961 TTTAAAAATTGGCAAATTATCTGAATACACATTTC-AGAAAGAAGATA-- 2007
                           ?      v      vv  i      v       -vv          --
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_127154709_   2008 CTAATGGCCAACAAGTGTATTTTTAGAAATACTCAACATTACTAATGAT 2056
                          v         i   iii  vv-- i i  i        i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGA--AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (142 / 86)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.77 (72 / 26)  


2334 27.44 4.88 2.27  chrX_127158857_127163746     3516  4397 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_127158857_   3516 AAAAAAATTCCTCACTCATGCATAGGAAGAATTAAGTTCATTAAAATGAC 3565
                            i v  i  viii     v  v      v    vv ii    i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_127158857_   3566 AGTACTACCTAAAGCAATCTACAAATACAATGCAATTCCTATCAAATTAC 3615
                          i    v  i   vii       i  v   i     i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_127158857_   3616 CAA-TGCCATTTTTCACATAGTTAGAAGAAATCATTTTAAAATTCATCTG 3664
                           i-    -     ii  v iv v  vi iv v  ii          v  
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_127158857_   3665 GAACCAATAAAAGAG--CCTGAATATCTAAG-CAATCCTAGGCAAAGAGA 3711
                            ---  iv   i --  v     v i  i-     i iiiv  ii   
  L1M4_orf2#LINE/    153 GAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_127158857_   3712 ACAAAGCCAGAGGTGTCACATTACCCAACTTCAGACTATATTGTAAAGCT 3761
                               iii    vv     i v     i    i viv  i ii      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_127158857_   3762 GCAGTAATCAAAATAGCATGGTACTGGTAAACAAATAGACACATTCACTA 3811
                         i          i i  ii         i v vii       i  vv ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_127158857_   3812 ATGCAACAGTATAAAGAACCTAGAATTCAAGCCACACATCTACAACCAAT 3861
                            v  i  v  vi   ii i    v v  v   i    i  iiii    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_127158857_   3862 TGATTTCAATGAAGTCAACAAAAAAAAAAAAAAAAAAAAAAACAATGGAG 3911
                               --------  i    iiivivv  i vv vv-----      i 
  L1M4_orf2#LINE/    350 TGATTT--------TCGACAAGGGTGCCAAGACCATT-----CAATGGGG 386

  chrX_127158857_   3912 AAAGGATATCCTATTCTTTAAACAGTGCTGGGAAAACTAGCTAGCCATAT 3961
                             i   vi  v   vvi   ii         v    i v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_127158857_   3962 GTACAGGAATGAAACTGGACCCCTACCTCTAAGCATATACAAAAATTATC 4011
                          i v i       ii              vv v               v 
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_127158857_   4012 TCAAGATAGATTTAAAAATTAAAAGTAATAACTGAAACTAGAAAAATCCT 4061
                             i  i   iv? i vi    v    v i  i      v    v  i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_127158857_   4062 AGAACAGAGCCTAGGAAATACTCTTCTGGAATATTGATTTAGGCAAATAA 4111
                             v i i v    ?ivv v     - vi iv   iv        - ii
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAA-TGG 584

  chrX_127158857_   4112 TTTATCAC-TAAGACCTCAAAAGCAAATGCAACAAAAACAAATATTGACA 4160
                            v i v-  v   vi        v v         iv   v  v  i 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_127158857_   4161 ACTAGGACCTAATTAAT-CTAAAGATTCTCTTCACAGCAAAAGAAATGAT 4209
                          v v    i v  i  v-i    i i i iv -i vv    i  v iv  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGT-GCTTCAAAGGACACTAT 683

  chrX_127158857_   4210 CAACAGAGTAAAAAGATAACCAACAGAATGGGATAAAATATTTGTAAACT 4259
                            v i   i      i    v           v          i   ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_127158857_   4260 ATAAATCTGA--AAGGACTGATATCC--------TAAA----TCC----- 4290
                            v      -- i     vi     --------    ----  i-----
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_127158857_   4291 ------------------AATAGCCCCTTTAAAACGTGGGAAAAGGACAT 4322
                         ------------------    i   vv  ?   vi    v      iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_127158857_   4323 GAACAGACACCTCTCAAAAGAAGACATGCAAGTGGCCAACAAACAAATTT 4372
                            i     ii    v        i  i   i       i  i  v  vv
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_127158857_   4373 TAAAATGCTCAACATCACTAATTAT 4397
                         v  i             ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (135 / 103)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 3.94 (63 / 16)  


 892 27.99 2.05 1.71  chrX_127186957_127192000.rev     2862  3154 (1890)    L1M4_orf2#LINE/L1        1   294 (614)  

  chrX_127186957_   2862 TAGAAAACTATTCTGTGCTCATGGTTTGGAAGAATCAATATCGTTAATAT 2911
                          i    iv   i ii  i      v        v i     i     v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127186957_   2912 GTCCACATTGTTCAATGCAATCTACAGATTCAAAGCAATTCCTATCAAAT 2961
                          v v i i vii   vvii              v     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127186957_   2962 TATTAA-TGTAATTTTCCATAGAAATTGACAAAGCTC-TTCTAAAAATCA 3009
                          vii i-  iv-    iiii            -   v- i      v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_127186957_   3010 TATGGAACCAAAAGGAATCT-GAATAGCTAATGAAATCCTAAGCAAAAAG 3058
                                viiv    i i i-       i  viv    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_127186957_   3059 AGCAAAACTGGAGGAATCACATTACTGAACT---ATACTATACTATAAGG 3105
                          i    ii       v     i v iv  i --- v   -     i  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_127186957_   3106 CTATATTAAGTAAAACAGCATGTTACAGGTAAGAAAAAATGGACACATA 3154
                            i v   vi  i    ii  v   v  i v--  ii  i    i   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATA 294

Transitions / transversions = 1.83 (53 / 29)
Gap_init rate = 0.03 (8 / 294), avg. gap size = 1.38 (11 / 8)  

1510 25.18 0.96 0.72  chrX_127186957_127192000.rev     3769  4185 (859)    L1M4_orf2#LINE/L1      409   826 (82)  

  chrX_127186957_   3769 TAATGCTGGGAAAACTGGCTAGCCACATGCAGAAGAATAAAACTGGACCT 3818
                          ii        v      v  ?         i      i  ii      i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_127186957_   3819 GTACCTCTCACCATATACAAAAATTAACTCAAGATGGATTAACGATTTAA 3868
                         v      v                        i      i ?v  ii   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_127186957_   3869 ATATAAGCCCTCAAACTATAAAAACCCTAGAAGAAAACGTAGG---AAAT 3915
                           i    vv  v           vi i           i    ---    
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_127186957_   3916 ACTCTTGAACGCAGGCTTAGGCAAAGAATTTATGACTAAGTCCTCAAAGG 3965
                         vi  v   v vii  -        v iv  iv iiv  v v vi    i 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_127186957_   3966 CAAATGAAGCAAAAACAAAAATTCACAATTGGAACCTAATTAAAATAAGG 4015
                           v v v i     iv      vv i  v v i  i v  i     v ii
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_127186957_   4016 AGCTTCTGCATAGCAAAAGAAATGGTCAAAAGAGTGAACAGACAACCTAC 4065
                          i   i  iiivv    i  v ivi    i i      v        i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_127186957_   4066 AGAATGGGAGAAAATATTTG-AAACTATACATCCAACAAAGGACTAATAT 4114
                                             -   ii   i   ii i  i     vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_127186957_   4115 CCAGAATCTACAAGGAGCTTAAACAAATTAACAACAACAAAAAACAAGTA 4164
                                v  i  i  i  ivv    v i  i  i  --   i    i  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAA--AAAGACAAATA 805

  chrX_127186957_   4165 ACCCCATTAAAAAGTGGGCAA 4185
                             v   ?    i       
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAA 826

Transitions / transversions = 1.49 (61 / 41)
Gap_init rate = 0.01 (4 / 418), avg. gap size = 1.75 (7 / 4)  

 330 20.22 0.00 1.12  chrX_127186957_127192000.rev     4465  4553 (491)    L1M4_orf2#LINE/L1      821   908 (0)  

  chrX_127186957_   4465 GGGCAAAGGACATGAATGGAAACTTCTCAAAAGAAGGAATACAATCTGCC 4514
                                   iv     i  v i     v       iv      viv   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_127186957_   4515 AACAAATATACTTTAAAGATGCTCAAAATCACTAATTAT 4553
                           i  ii i - vv            v    ????????
  L1M4_orf2#LINE/    871 AATAAGCACA-TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (9 / 9)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1)  


3312 24.11 2.11 1.22  chrX_127237965_127242198     2844  3743 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127237965_   2844 TGGAAAGACATAACATGTTCATAGGAAGGAAGAATATATATTATTAAAAT 2893
                                 i  vv         i ivv      v vv     i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127237965_   2894 GTGCA-TACTACCCAAGGTGATCTATAGATTCAATGCAATCTCTATCAAA 2942
                          -   -    v     iv       i        i      i        
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_127237965_   2943 ATTACAA-TGTCATTTTCCACAGAAATAGAAAAAAT-ATCCCAAAATGTG 2990
                           iv  i-  i -    iii       v  v  iv -    i     vii
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_127237965_   2991 CATGGAACCAGAAAAGACCCCAAATAACCAAAGCAATCTTGGGCAA--AC 3038
                         i      viiv  ii     vi    i     i        iiv  -- v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_127237965_   3039 AACAAAGCTGGAGGCGTCAAATTACCTGAACTCAAATTATGCTAAAAGGC 3088
                                i      vv   v i v  ii vi     viv i   v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_127237965_   3089 TATAGTAATCAAAACAGCATGGTGTTAGCATAACAAAAGACACATTGACC 3138
                           i         i    ii    ii i      vi v     i  v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_127237965_   3139 AAGAGAACAGGATAGA-AGACCAGGGATAGAAATAATTCCAAGTATTTAT 3187
                           vi   i  i  v  -  v    ------      vi   vii      
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAG------AAATAAACCCATACATTTAT 342

  chrX_127237965_   3188 ATAGTCATTGGATTTTCAACAAATGTACCAAAAACA--CATTGGGGAAAA 3235
                         i--    v v       i    iv  i    i v  --  v        i
  L1M4_orf2#LINE/    343 G--GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_127237965_   3236 GACAATCTCTTCAATAACTGGTACTGAAAAATTTAGACATTCACATGCA- 3284
                         i i i   i     i  v    i   ii v vi i  i ?i        -
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_127237965_   3285 --GAATAAAATTGGACCTCTATCTCACACCATATAGAAAAATCAGCTCAA 3332
                         --    i  i       i   i             v      i i     
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_127237965_   3333 AATGG-CCAAAGACTTAAATGTAAGACCTGAAACTGTAAAGCTACTAGAA 3381
                              -i  ?    i           v  i     i    i  vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_127237965_   3382 GAAAACATAGTGGAAAAGCTCCATGACCTTGGTCTGGGTAATAATTTTTT 3431
                                   v? v   v  i i         vi i  i   ii   i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_127237965_   3432 A-ATAGGATTTCAAAAGCACAAGCAATGAAAGCAAAAATAGACAAATGAC 3480
                          -   v  ivi               ii    v         i    viv
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_127237965_   3481 ACTTTAGCAAA-CTAAAAACCTT----CTGCAAAGAAAAGAAATAACAGA 3525
                             i v    -i       i  ----  v     i v vv vi  v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_127237965_   3526 GTGAAGAGATCACTCATAGATTGGGAGAAAATATTTGTAAACCATGTATC 3575
                              i   iv  i  i   v                i   i   i    
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_127237965_   3576 TGATAAGGGGCTAATATCTAAAATATATAAGATACTCAAACAAGTCAACA 3625
                                  i  vi    i i         iiv    vv    v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_127237965_   3626 GCAGGAAAACAAAAAACCGAATTAGAAAATAAGCAAAG-ATCTGGACAGA 3674
                         ii ii  i     v    v    ?i     ii      -  i  i i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_127237965_   3675 TCTTTCTCAAAAGAAGAGATACAAATGGCCAACTAATATATGAAGAAAAT 3724
                         iv      v        v              iv ii i     -  i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGAT 889

  chrX_127237965_   3725 GTTTAACATTTCTAATAAT 3743
                          i i     iv????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (137 / 76)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.76 (30 / 17)  


3086 26.66 1.00 0.55  chrX_127244211_127249209     3603  4506 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127244211_   3603 TGGAAACATATACCATCCTCATGGATAGGTAGAATCAATATTGTAAAAAT 3652
                               v    v    vi        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127244211_   3653 TACCATAGTGTCAAAAGCAGTCTACAATTTCAATTCAATCTCTATCAAAA 3702
                         vi v   v vi v   viii      iv     iv     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127244211_   3703 TACCACCATCATTCTTCACAGAATTAGAAAAAAAACAATTTTAAAATTCA 3752
                          v   v vv v  i  ii     v v  v  iv--ii  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCA 148

  chrX_127244211_   3753 GATGGAACCAAAAAAGAGCCTGCATAGCCAAGAATGAC--TAAGGAAAAA 3800
                         v      viiv  ii  v  v v        -  ii i-- i ii  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAA-AACAATCTTGAAAAAGAA 197

  chrX_127244211_   3801 GAACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGT 3850
                                vi      vv       v  ii        viv     i  iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_127244211_   3851 CCAAAGTCACCAAAACAGCCTGGTACTGGTATAAAAATAGGCACATAGAT 3900
                          i v   v i   i    iv         i    ii    i  i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_127244211_   3901 CAATGGAACAAAATAGAGAACCCAGAAATAAATCCAGA----TAGAGCCA 3946
                                 i i   v    ii           i   v ----  vi i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_127244211_   3947 GCAGAACTTTGACAAAGCCAACAAAACCATAAAGTGGGGAAAGTACATCC 3996
                         iiv  vi  i     i viiv   i     vv i         v i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_127244211_   3997 TTTTCAACAAATGGTACTGGGATAATTGGCTAGCCACATGTAGGAAAATA 4046
                                        i      i  i   v  ?       i ii i   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_127244211_   4047 AAACTGGATCCTCTTCTCTCACCTTATATAAAAATCAACTTAAGATGGAT 4096
                           ii    i  iivi   v    v    i      i    i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_127244211_   4097 TAAGGACTTAAACCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACA 4146
                         i ?i   i    iv     v  i    i      v ii       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_127244211_   4147 TTGGAA-AAATCCCTTCTAGACATTGGCTCAGGCAAGGATTTCATTACCA 4195
                          v  ?i-     --   vv   v    v i      v i    v vivi 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_127244211_   4196 AGAAACCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTA 4245
                         v  v          v v    i    iv   i   i   iv v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_127244211_   4246 ATTAAACTAAGGAGTTTTTGCATGGTAAAGGA-AGAGTCAGCAGAGTAAA 4294
                           i   v v ii ii     iiivvi      - vvi   iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_127244211_   4295 CAGACAACCCACAGAATGCGAGAAAGTCTTCACAATCTATACATCTGACA 4344
                         v                 v      i v  ii   vii   i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_127244211_   4345 AAGCACTAATATCCAGAATCTACAATGAACTCAAAGAAATCAGTAAGAAA 4394
                          i v   vi          v  i  v      vv v  v   i   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_127244211_   4395 AAACCAAACAATCCAATCAAAAAGTGGGCTAAGGACATAAATAGACATT- 4443
                           iv    i  i     i?    i     v     iv i          -
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_127244211_   4444 CTCAAATGAAGATATACAAATGGCCAACAAATATATGAAAAAATGCTCAA 4493
                            v  v                    i  ii i       i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_127244211_   4494 CATCACTAATGAT 4506
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (136 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2855 26.68 1.54 1.43  chrX_127272201_127275100.rev     1503  2409 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127272201_   1503 TGGAAACACATCCCATGCTTAAGGATGGATAGAATCAATATTGTGAAAAT 1552
                               v i        i i v    v iv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127272201_   1553 GACCATACTGTCAAGAAGAATCTACAGATTCAAGGCAATTCCCATCAAAA 1602
                          i v     vi v i vvi              v     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127272201_   1603 TACCACCATCATTCTTCACAGAACTAGAAAAAA-AATCTTAAAATTCATA 1651
                          v   v vv v  i  ii     v v  v  iv-i   i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_127272201_   1652 TGGAACCAAAAAAGATCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 1701
                              viiv  ii  i  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_127272201_   1702 CAAATCTGGAGGCATCACATTACCTAATTTCAAACTATACTACAAGGCTA 1751
                             vi      vv     i v  i         viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_127272201_   1752 TAGTTACCAAAACAGTATGGTACTGATATAAACATAGGCACGTAGACCAA 1801
                         i   v i   i     i        ii    iv    i  ii    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_127272201_   1802 TGGAACAGAATAGAGAACC----AATAAAGCCAAATATTTACAGCCAACT 1847
                              i     v    ii ----      v   v i     ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_127272201_   1848 GACCTTTTGTTTGCTTTGACAAAGCAAACAAAAACATAAACTGGGGAAAG 1897
                           --    --------i     i vviv   i v   vv v         
  L1M4_orf2#LINE/    351 GA--TTTT--------CGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_127272201_   1898 AACACCCTATTCAACAAATGGTGCTGGGATAATTGGCAAGCCTCATATAG 1947
                           i vi  v                    i  i   vv ?  v   ii i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_127272201_   1948 AAGAATGAAGCTGGATCCTCATCCCTTACCTTATACAAAAATCAACTTAA 1997
                                   i    i  ii i i vi   v           i    i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_127272201_   1998 GATAGATCAAAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGGA 2047
                         i  i     ?    i     v     v  i    i      v ii   i 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_127272201_   2048 GATAACATCTGGAAAACTCTTCTAGTCAC--TGACTTTGGCAAAGAGTTC 2095
                           v     vv ?iv  v     --  v  --  iv  v     v iv   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTC--GTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_127272201_   2096 AT-GACCAGAAATCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGAT 2144
                         v -  ivv  v -         v v         iv   i   i   i  
  L1M4_orf2#LINE/    589 TTAGATATGACA-CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_127272201_   2145 GGGACCTAATTAAACTAAAATGCTTCTGCACAGCAAAAGGAATAATCAGC 2194
                         v    i v  i   v v   vi   i  ii vv    i iv iv    iv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_127272201_   2195 AGAGTAAACAAACAGTTTACAGAGCAAAAGAAAATATTCACAAACTATGC 2244
                          i   i  v i   iiii     iiiii          ii    ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_127272201_   2245 ATCCAACAAAGCACTAATATCCAGAATCTACAAGGAACTCAAATCA-TCA 2293
                            ii i  i v   vi          v  i  i      vv iv -   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_127272201_   2294 AGAATAAA----CAAACAATCCCATCAAAAGGTGGGCAAAGGACA-AAAT 2338
                          v      ----    i  i  v  i?   ii           iv-i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_127272201_   2339 AGACAATTCTCAAAAGAAGAGATACAAATGGTCAACAACGATGAAAAAAA 2388
                              v     v        v          i   i  vv iivi    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_127272201_   2389 AGGCTCAACATCACTCATTAT 2409
                          v           ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.45 (27 / 11)  


3139 23.77 3.12 1.79  chrX_127369279_127372617     1952  2847 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127369279_   1952 TAGGAATATATCCCATGTTCTTGAATTAGAATAACCCATATCTTTAAAAT 2001
                          i i  v             v  i   i   v viiv    iv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127369279_   2002 ATCAATACTACCTAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 2051
                         iv       v  i   vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127369279_   2052 CTCTAATGGCAGTTTTTACATAAATAGTAAAAACT-ATCCTAAAATTCGA 2100
                         ii i iiv  vv     i  v    v - v  i  -            iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chrX_127369279_   2101 ATGTAACCACAAAAGACTCAGAATAGCTAAAGCTATGT---ACAGAAAGA 2147
                            v  vii   ii   i         i   i v  v --- v ii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_127369279_   2148 ACAAACCTGGAGGCATCATATTTCTTA-TTTCAGATTGTATTACAAAGCT 2196
                              vi      vv   i i   ii -     i viv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_127369279_   2197 ACAGCAATCAAAAAGATATGAAATAGGCA-AAAGACAGACATACAGATGA 2245
                             i      i vii i  iv iv    -  i  i       i    v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_127369279_   2246 ATGGAACAGATTTGAGAGCCCAGAAGTAAACCCATGCATATAAGGTAAAT 2295
                               i   v       i      i         i   v  v   v   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_127369279_   2296 TAACCTTTGACAAAGGTGCCAAGAATATTCAATGGAGAAAGAATTGTCTC 2345
                          i ii  i     i          vi         i        v    i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_127369279_   2346 TTCAA-AAA--------------CTAGATAACCACATGCAAAACAATAAA 2380
                              -   --------------  i    ?            v   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_127369279_   2381 ATTGGATACTTTTCTTACACCATATATAAATAT-AATTCAAAATGGATTG 2429
                         i     iv i vi  i          i   v  -  i           ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_127369279_   2430 AAGATTTAAAATGCAGGACCTGAAATCATTAAGCACTTAGAAGAAAACA- 2478
                         ?   ii    -  i i  v  i   ii  v  i v              -
  L1M4_orf2#LINE/    500 WAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_127369279_   2479 GGGAATAAACCCTT-TGACATTGGTTCTTTTTAATGATATTTTAGATGTG 2527
                         i  ?i    i i i-    v    v - vvvi    i v i      i  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATG 597

  chrX_127369279_   2528 ACACCAAAACTAAAAGCAACAAAAACAGAAGTGAACAAATGGGCCTAAAA 2577
                                  vi v           iv i  i ii i    v  v  vv v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_127369279_   2578 CAAATTTAAGG---TTTCTGCATAGTAACAAAATAAAAATTAACAAAAAA 2624
                             v    ii---   v   v -----    i--i v i  v   i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTT-----CAAAG--GACACTATCAAGAAA 690

  chrX_127369279_   2625 AAATTAACAAAAAAGCAACCTACAGAATGGGAGAAAATAGTTGCAAATCA 2674
                         i------ii    ii     i                  v          
  L1M4_orf2#LINE/    691 G------TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_127369279_   2675 TATATCCAATAGGAGATTAGTCTTTAAAATATATTAAAAACTCATACAAA 2724
                               ii   i i  i v  v ii i       v  i     v     v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_127369279_   2725 TCAATA-TAAAAAATCAAACAACCCAATTAAAAAATGAGAAAAGGGATGA 2773
                               -      iv    i         ?       i v     iv vi
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_127369279_   2774 AATACACACTTTTTAGAAGAAGACATAAAAATGGCCAATGGATATATGAA 2823
                             v   i  i ivi       i   v           iiii i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_127369279_   2824 AAGATGCTTAACTTCTCTAATTAT 2847
                                 i   v  v????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (132 / 77)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.59 (44 / 17)  


2789 28.00 1.46 0.90  chrX_127384975_127390414     4055  4947 (493)    L1M4_orf2#LINE/L1       11   908 (0)  

  chrX_127384975_   4055 TTTCATGCTAATGGATTGGAAGGTCCAG-ATCATTAAGAAGGCCATACTG 4103
                          ii    i v            iiii i-  ii      v   v     v
  L1M4_orf2#LINE/     11 TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTC 60

  chrX_127384975_   4104 CCTAAAGCAATCTATACATTCAATGCAATTCAAATCAAAATACCAAAGTC 4153
                           i   vii     i v      i     i vv        v   ivvv 
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_127384975_   4154 ATTTTTCACAGAATTAGAAAAAAAAACCCTAAAATTTGTATGGAACTATA 4203
                         v     ii     v v  v  ivvi i         ii       v ii 
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_127384975_   4204 AAAGAGCCCAAATAGCCAAAGCAATCTTACATTTAGAAAAA--AAGCTAG 4251
                          ii  v  vi          i       iv vv-    i  --   i i 
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAA-AGAAGAACAAAGTTGG 209

  chrX_127384975_   4252 AGTCATCATATTACCTGACTTTAAAGTGTACTACAAAGCTATAGTAACCA 4301
                           vvv   i i v  ii i  i   iiv             i     i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_127384975_   4302 AAACAGCATGGTATTTGGTAGAAAAAAAAAGACACATAGACCAGTGAAAC 4351
                          i    ii     i -  i v  ii v --    i     i  i  i  i
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACT-GGCATAAGGATA--GACATATAGATCAATGGAAT 306

  chrX_127384975_   4352 ACATTATAGAAACCAGAAATAAAGCAGCACACCTACAACCATCTGCTTTT 4401
                          v v vv   iv           v vii   ii  iiii  vi  v    
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_127384975_   4402 CATCAAAGTCGATAATAACAAGCAATGGGGAAAGGACTTTCTTTTCAATA 4451
                          iv   i vi vi  v v  vv            i ivv         i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_127384975_   4452 AATGGAGCTGAGATAACTGGCTAGCTATAGGCAGAACAATGAAACTGGAC 4501
                              v    i  i      v  ? i i v   i  v      ii     
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_127384975_   4502 CTCTACCTATCACCATATACAAAAATTAACTCAAGGTGGATTAAATACGT 4551
                          i      vv                        ii     i ? v  v 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_127384975_   4552 AAATGTAAGACCTTAAACTAGAAAAATCCTAGAAGAAAACTTAA---TAA 4598
                                   v  v      v    v  i           v  i---   
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_127384975_   4599 ATATGCTTCTCCACACTGACCTTGGCAATAAATTTATGGCTAAGTCCTCA 4648
                           ---    viv  vi  ivi v      iiv  iv i v  v v vi  
  L1M4_orf2#LINE/    557 AT---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_127384975_   4649 AAAGCAATTGCAATAAAAATAAAAATTGACAAGTGGGATCTAATTAAACT 4698
                               vvv    i    iv      v  i  i v   ii v  i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_127384975_   4699 AAAGAGCTTCTGCACAGCAAAAGAAACCATCATCAGGGTAAACAGATCAC 4748
                         v  i i   i  ii vv    i  v  i    vv ii  i  v   iv  
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_127384975_   4749 TTATAGA-TGGGAGAAAATATTCACAAACTATGCATCCAATAAAGATCTA 4797
                         ii i   -              ii    ii  ii   ii    i iv  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_127384975_   4798 ATATCCAGAATCTATAAGGACCTT----AAATCAACAAGCAATAAACAAA 4843
                         i          v     i  v  i----  v    i  vv  v i     
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_127384975_   4844 TAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAG 4893
                               v   ?    i           iv    i     i     v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_127384975_   4894 AGAACATACAAGCAGTTAACAA--ACATGAAGAAAATGCTCATCGTCACT 4941
                          ii i      iii ii  i  --       -  i       v i   ??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAA-AAGATGCTCAACATCAZZ 902

  chrX_127384975_   4942 AATTAT 4947
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.45 (146 / 101)
Gap_init rate = 0.01 (11 / 898), avg. gap size = 1.91 (21 / 11)  


2827 26.58 1.88 1.33  chrX_127397066_127403211.rev     4753  5655 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127397066_   4753 TGGGAAAACATTCCATCCTCATGGATAGGAAGAATCAATATTGTGAAAAT 4802
                            i  i i  i    vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127397066_   4803 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTGTTCCCATCGAAC 4852
                            v     v      v i  i  i        i  vi i  i   i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127397066_   4853 TACCATTGACATTCTTCACAGAATTAGAAAATATAGTT-TAAATTTCACA 4901
                          v   vivi v  i  ii     v v  v  vv ii i-    v    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_127397066_   4902 TG-AAAT-CAAAGAAAACCCCGTATAGCCAAGACAATCCTAAGCAAAAAG 4949
                           -    -   i i --   v v        i      i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_127397066_   4950 AACAAAGCTGAAGACATCATGCTACCTGACTTCAAATTATACTACCAGGC 4999
                                i  i  ivv   ii  v  ii i      viv      v i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_127397066_   5000 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5049
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_127397066_   5050 AATGGAGCAGAATAGAGACCTCAGAAATAACACCACACATCTACAACCAG 5099
                               ii     v    vii         vv   i    i  iiii  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_127397066_   5100 CTGATCTTTGACAAACCTCACAAAAACAAGCAATGGG--AAGGGTTCTCC 5147
                         i    i  i     ivv vv   i v  vv       --   ii vv  i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_127397066_   5148 TATTCAATAAATGGTGCTTTGAAAACTGGCTAGCCATATGCAGAAAACTG 5197
                          -     i          vv  v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_127397066_   5198 AAACTGGAACCCTGCCTTACACCTTGTACAAAAATTAACTCAAGATGCAT 5247
                           ii    v    i   i     v i                 i   v  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_127397066_   5248 TAAAGACTTAAATGCAAAACCCCAAACTATAAAAACTGTAAAATAAAACC 5297
                         i ?    i      i  i v iv           viiv  i  v     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_127397066_   5298 TAGTCA-ACACCATTCAGGACACAGGCATGAGCAAAGGCTTC------AT 5340
                            v?i- v i -   iv   viv  vv ii    v  i   ------  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_127397066_   5341 GACG--AAAATGGCAAAGGAATTGCAACAAAAGCTAAAATTGACAAATGA 5388
                            i--    --   v i -----         vv     v  i    vi
  L1M4_orf2#LINE/    597 GACACCAAAA--GCACAAG-----CAACAAAAGAAAAAATAGATAAATTG 639

  chrX_127397066_   5389 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAG 5438
                           ii v  i   v v  i i   i  ii vv    i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_127397066_   5439 AGTGAACAGGCAACCTACAGAATCGGAGAAAACTTTTGCAATCCACCCAT 5488
                               v  i     i       v        iv       vi  ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_127397066_   5489 CTGACAAAGGTCTAATATCCAGAATTTACAAGGAATTTAAACAAATGTAC 5538
                             i  i  v  vi          v  i  i   i ivv    v vv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_127397066_   5539 AAGAAAAA-AGAAACAACTCCATCAAAAAGTGGGCAAAAGTATACGAAAT 5587
                           v     - v   i   i v  i?    i        i -  vi   vv
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG-ATTTGAATA 838

  chrX_127397066_   5588 GACACTTCTCAAAAGAAGACATTTATATTACCAATAA--ACATGAAAAAA 5635
                             i     v        i  vi v  vi       --         i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_127397066_   5636 AGCTCAACATCACTGATCAT 5655
                         v           ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (135 / 101)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.93 (29 / 15)  


2714 26.85 4.10 0.80  chrX_127450875_127457199.rev     4956  5834 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127450875_   4956 TGGAAAAACAGTCCATCCTCATGGATAGGAAGAGTCAATATTGTGAAAAT 5005
                               i i vi    vi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127450875_   5006 GGCTATACTCCCCAAAGTAATTTAAAGATTCAATGCTATTCCCATCAAAC 5055
                            v            v i  i  v        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127450875_   5056 TACCATTGACATTCTTCACTGAATTAGAAAAAATCAGTTTAAATTTTATA 5105
                          v   vivi v  i  ii v   v v  v  iv v vii    v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_127450875_   5106 TGGAA-T-CAAAGAAGACCCCGTTTAGTCAAGACAATCCTAACCAAAAAG 5153
                              - -   i --     v vv   i   i      i i vv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_127450875_   5154 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATGCTACAATGC 5203
                                i      vv   ii  v  ii i      viv i      v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_127450875_   5204 TATAGTAACCAAAACAGCATGGTAGTGGTGCCAAAACAGATATATAGACC 5253
                           i     i   i    ii     v   iiiv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_127450875_   5254 AATGGAACAGAACAGAGACCTCAGAGATAACACCACACATCTACAACCAT 5303
                                i    iv    vii    i    vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_127450875_   5304 CGGATCTTCCACAAACCTGACAAAAACAAGCAATGGGGGAAAGGCTCTCC 5353
                         iv   i   v    ivv  v   i v  vv        -    iv vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTC 397

  chrX_127450875_   5354 TATTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5403
                          v     i              v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_127450875_   5404 AAACTGGAACCCTTCCTTACATCTTATACAAAAATTAACTCAAGATGGAT 5453
                           ii    v    v   i   i v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_127450875_   5454 TAAAGACGTAAATGTAAAACCCCAAACCATAAAAACCCTAGAAGAAAACC 5503
                         i ?    v         i v iv    i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_127450875_   5504 TAATCAGTACTATCCAGGACATAGGCATGGGCAAAAATTTTATG---ATG 5550
                           iv?ivv v v i iv   v v  vv i     vii   iv i---   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_127450875_   5551 AAATTGCCAAAAGCAATTGCAACAAAAGGTAAAATTGACAA-TGGGATCT 5599
                          v ---         vvv          iv     v  i  - v   ii 
  L1M4_orf2#LINE/    598 ACA---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_127450875_   5600 AATTAAA-CGAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGGGTGA 5648
                         v  i   -iv  i i   i  ii vv    i  v       vv ii    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_127450875_   5649 ACAGGCAACCTGCAGAATGGGAAAAAATTTTTGCAA-TCGAAT---TTAC 5694
                          v  i     ii          i     v       -  iv  --- v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_127450875_   5695 ATGGAACTTAAAT---GAATGTACAAG---------------------AA 5720
                          v  i    iv  ---    i  i  i---------------------  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_127450875_   5721 AAAATCAAAGAACCCTATCAAAAAAGTGGGCAAAAGAAATGAACAGACAC 5770
                            iv    v     v  i?     -        i  vv    i     i
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACAT 843

  chrX_127450875_   5771 CTCTCAAAAGAAGACATTTATGTGGCCAACAAACATACGAAAAAA-GTTC 5819
                         i    v        i  vi vi       i  i  i i     i - i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_127450875_   5820 ATCATCACTGAGCAT 5834
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (128 / 104)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.07 (43 / 14)  


3122 27.12 1.56 0.33  chrX_127528800_127535529.rev     5344  6239 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_127528800_   5344 GAAAAAACATTCCATGCTCATGAATAGGAAGAATTAATATAGTGAAAATG 5393
                          i   i i  i     i     i  v      v       v  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_127528800_   5394 GCCGTACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGCT 5443
                           vi    v      v i  i  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_127528800_   5444 ACCA-CTGACTTTCTT-CACACAATTAGAAAAAACT-ACTTTAAATTTCA 5490
                         v   -   v    i  -  v -    i-- v  i  - iii    v    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_127528800_   5491 TATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAG 5540
                                viiv  ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_127528800_   5541 AACAAAGCTGGAGGCATCATGCTATCTGACTTCAAACTATACTAAAAGGC 5590
                                i      vv   ii  vi ii i      viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_127528800_   5591 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGATATATAGACC 5640
                          i      i   i    ii         i iv ii ii  i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_127528800_   5641 AATGGAACAGAACAGAGGCCTCAGAAATAATGCTACACATCTACAACCAT 5690
                                i    iv   ivii         vv i i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_127528800_   5691 CTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5740
                         i    i   i    ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_127528800_   5741 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 5790
                         v  i  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_127528800_   5791 AACTGGACCCCTTCCTTACAC-------AAAAATTAACTCAAGATGGATT 5833
                          ii         v   i    -------              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_127528800_   5834 GAAAACATAAACATAAGACCTAAAACCACAAAAACCCTAGAAGAAAACCT 5883
                         i? i  v    ii     v       i i    vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_127528800_   5884 AGGCAATACTATTCAGGACATAGGCATGGGGAAAGATTTCATGACTAAAA 5933
                            ?ivv v v   iv   v v  vv i  v  v i    v iiv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_127528800_   5934 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5983
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_127528800_   5984 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTGTACAG 6033
                            v v  i i   i  ii vv    i  v        v i    v v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_127528800_   6034 GCAACCCACAGAATAGGAGAAAATTTTTGCAATCTATCCATCTGACAAAG 6083
                         i             i         v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_127528800_   6084 GGCTAATATCTAGAATCTACAAAGAACTTACACAGATTTACAAGAAAAAA 6133
                          i  vi    i     v  i        ivi   iv iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_127528800_   6134 CCAA----CCCCATCAAAAAGTGGGTGAGGGATATGAACGGACACTTTTC 6179
                         v   ----   v  i?    i    ii i    v    ii    i  i  
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_127528800_   6180 AAAAGAAGATATTTATGCGGCCAACAAACATATGTAAAAAAGCTCGTCAT 6229
                         v           vi vii      i  i  i   v   i v    iv   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_127528800_   6230 CACTGGTCAT 6239
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (7 / 907), avg. gap size = 2.43 (17 / 7)  


3199 26.33 1.33 0.88  chrX_127591751_127598155     5009  5912 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127591751_   5009 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGCGAAAAT 5058
                              ii i  i     i      i v      v i     i iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127591751_   5059 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127591751_   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_127591751_   5157 TATGGAACCAAAAAAGAGCCCTCATCGCCAAGTCAACCCTAAGCCAAAAG 5206
                                viiv  ii  v  vvv  v     iv   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_127591751_   5207 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5256
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_127591751_   5257 TATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5306
                           i     i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_127591751_   5307 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5354
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_127591751_   5355 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5404
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_127591751_   5405 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5454
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_127591751_   5455 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5504
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_127591751_   5505 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCTTAGAAAAAAAC 5554
                          i ?    i    ii v   v       i      vi       i     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_127591751_   5555 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATATCTAA 5604
                         v    ?i v viv   iv   v v  vv i     v ii   v  vv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_127591751_   5605 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCGAA 5654
                         i            vvi           v     v  i    v   iivv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_127591751_   5655 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5704
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_127591751_   5705 AGGGAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5754
                           iv    i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_127591751_   5755 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5804
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_127591751_   5805 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5850
                          i    ----   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_127591751_   5851 TCAAAAGAAGACCTTTATGCA----GCCAAAAGACACATGAAAAAATGCT 5896
                           v        ----   i  ----     v ii          i     
  L1M4_orf2#LINE/    847 TCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_127591751_   5897 CATCATCACTGGCCAT 5912
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.50 (20 / 8)  


3141 19.20 3.37 10.62  chrX_127632326_127636680.rev     2886  3864 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127632326_   2886 TGGAAAGATATTGCATGTTTATGGATTGGTAGAATCAATATTGTTAAAAT 2935
                                    iv      i         v   v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127632326_   2936 GTCCATATGACCCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 2985
                          v v   ivv      vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127632326_   2986 TACCAAAGACATTCTTTATAGAAATAGAAAAAATTATCCTAAAATTTATA 3035
                          v   ivvi v  i   ii      v  v  iv v           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_127632326_   3036 TGGAACCGCAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAAAGAA 3085
                              vi    ii                 i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_127632326_   3086 CAAAACTGGAGGAATCATATTCCCTGACTTCAAATTATACTTACAGAGAA 3135
                             ii       v   i i i  ii i      ----      ------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA----ACTTAC------ 240

  chrX_127632326_   3136 CCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAAAAGAACAAAA 3185
                         --------------------------------------------------
  L1M4_orf2#LINE/    241 -------------------------------------------------- 240

  chrX_127632326_   3186 CTGGAGGAATCATATTCCCTGACTTCAAATTATACTTACAGAGTTATAGT 3235
                         ------------------------------------    i  i  i   
  L1M4_orf2#LINE/    241 ------------------------------------TACAAAGCTACAGT 254

  chrX_127632326_   3236 AACCAAAACAGCATGGTAATGTCATAAAAACAGACACATCGACCAATAAA 3285
                           i   i    ii     v  v     ii i     i  v  i    ii 
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_127632326_   3286 ACAAAATAGAGAACCTAGAAGAAAATCCACACACCTTTAGTGAACTCATT 3335
                          i i   v    ii i    iv   i   i   ii v i  v  i v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_127632326_   3336 TTTGACAAAGGTGCCAAGAACACATACACTGGGGAAAGGACAGTCTCTTC 3385
                           i     i          - -   v  v         i i     i   
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGA-C-CATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_127632326_   3386 AATAAATGGTGCTGGGAAAACTGGATACCCCATATGCAGAAGAATAAAAC 3435
                           i              v         ?  - i     i      i  ii
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCC-ACATGCAAAAGAATGAAGT 451

  chrX_127632326_   3436 TAGACCCCTA------------TACAAAAATCAAATCAAAATGGATTAAA 3473
                          i        ------------         i  v           i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_127632326_   3474 TACCTAAATCTAAGACCTCAAACTATGAAACTACTACAAGAAAACATTGG 3523
                         v        v     v  v       i     vi  v          v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_127632326_   3524 GGAAAATCTCCAGGACATTTGTCTGGGCAAACATTT----GATCAAT-AC 3568
                         ? v      i iv   v  v vi i     vvi   ----   --  -  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGAC 599

  chrX_127632326_   3569 CCCACAAGCTCAGGAAACCAAAGCAAAAATGGACAAATGGGATCACATCA 3618
                         v   v    v  i v   v    v      i  i    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_127632326_   3619 AG-TTAAAAACCTCCTGCACAGCAAAGGATATAATCCACAAAGTGAAGAG 3667
                          i-        i i-  ii vv       i iv   v v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_127632326_   3668 ACAACCCACAGAATGGGAGAAAATATTTTCAAACTATTCATCTGA----- 3712
                                                     v    ii  vi      -----
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_127632326_   3713 ----------CAGAATGTATAAGGAGTTCAAACAACTCTATAGGAAAAAA 3752
                         ----------      i     i  ii  vv       v   iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_127632326_   3753 ATCTAATAATTTGATCAAAAAACTGGGCAAAAGATTTGAATAGACATTTC 3802
                          - v     iiii  i?     -        i                  
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_127632326_   3803 TCAAAAGAAGGTAAACAAATGGCATACAGGCATACGAATAAGTACTCAAC 3852
                           v       i  v         vv i i   i i   v ii i      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_127632326_   3853 ATCATTGATCAT 3864
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (113 / 71)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 9.79 (137 / 14)  


3211 26.02 1.10 0.99  chrX_127641668_127647935     4869  5775 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127641668_   4869 TGGAAGAACACTCCACGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4918
                              ii i ii   i i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127641668_   4919 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4968
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127641668_   4969 TACCAA-TGCCTTTCTT-CACAGATTTGGAAAAAACT-ACTTTAAAGTTC 5015
                          v   i-       i  -  v i   ---i v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chrX_127641668_   5016 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 5065
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_127641668_   5066 GAA-AAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGA 5114
                            -    i      vv       v  ii i      viv        ii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_127641668_   5115 CTACAGCAACCAAAACAGCATGGTACTGATACCAAAACAGAGATATAGAT 5164
                               i  i   i    ii        ii iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_127641668_   5165 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5212
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_127641668_   5213 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5262
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_127641668_   5263 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5312
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_127641668_   5313 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5362
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_127641668_   5363 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5412
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_127641668_   5413 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5462
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_127641668_   5463 AAACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTA 5512
                         vi            vvi     v    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_127641668_   5513 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5562
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_127641668_   5563 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTATTCATCTGACA 5612
                         v  i     i   i             v  ii   vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_127641668_   5613 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5662
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_127641668_   5663 AAAACAAACAACCCAATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5712
                           i     i        i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_127641668_   5713 CTCAAAAGAAGACCTTTATGCA----GCCAAAAAACACATGAAAAAATGC 5758
                            v        ----   i  ----     v  i          i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_127641668_   5759 TCATCATCACTGGCCAT 5775
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (140 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


2736 28.06 2.47 0.56  chrX_127651368_127655974     3224  4114 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127651368_   3224 TGGAAAAGCATTCCATCCTCATGCATAGGAAGAATCAATATCGTGAAAAT 3273
                               iii  i    vi     v  v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127651368_   3274 GGCCATACTGCTGAAAGTAATTTATAGATTCAGTGCTATTCCCATCAAAC 3323
                            v     v iv   v i  i  i       ii  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127651368_   3324 TACCATTGACTTTCTTCACAGAATTAGAAAAA--AATACTTTAAATT--- 3368
                          v   vivi i  i  ii     v v  v  i--i  - i v     ---
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCAT 149

  chrX_127651368_   3369 --GGAGCCAGAAAAGAGCCTGTATGGCCAAGACAATCCT-AAGCAGATAG 3415
                         --   iviiv  ii  v  v v  i     i      i -  iv   -  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA-AG 198

  chrX_127651368_   3416 AACAAAGCTAGAGGTATCACACTACCTGACTTCAGACTATACCTCAAGGC 3465
                                i i    vv       v  ii i    i viv   iv   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_127651368_   3466 TACAATAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACC 3515
                             i   i   i    ii         i iv ii i           i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_127651368_   3516 AAGGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCAT 3565
                           v    i    iv    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_127651368_   3566 CGGCTCTTCGACAAATCAGACAAAAACAAGCAATGGGGAAAGGATTTCCT 3615
                         iv v i        ivvv v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_127651368_   3616 ATTTAATAAAGGGTGCTGGGAAAACTGGCTAGCCATGTGCAGAAAACTGA 3665
                         v  i  i   v          v      v  ?   ii    i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_127651368_   3666 AACTGGATCTCTTCCTTACACATTATAGAAAAATTAACTCAAGATAGATT 3715
                          ii    i i  v   i    vv    v              i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_127651368_   3716 AAAGACTTAAATGTAAAACCCAAACCCACAAACACCCT-AGAAGAAAACC 3764
                          ?    i         i v i   v i i   -  i  -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chrX_127651368_   3765 TAGGCA-ATACCATTCAGGACACAGGCATGAGCAAGGACTTCAT-GATGA 3812
                             ?i- v i -   iv   viv  vv ii    v ii   v -   - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_127651368_   3813 AAATGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTA 3862
                         vi ii         vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_127651368_   3863 ATTATACTAAAGAGTTTCTGCACAGCAAAAGAAACTTTCATCAGAGTAAA 3912
                           i v v v  i ii  i  ii vv    i  v   v   vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_127651368_   3913 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACA 3962
                         v  i     i                 v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_127651368_   3963 AAGGTCTAATGTCCAGAATCTACAATGAACTTAAACAAATTTACAAGGAA 4012
                          i  v  vi i        v  i  v     ivv    v iv i  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_127651368_   4013 AAAACAA---------TCAAAAAATGGGCAAAGGATATGAACAGATACTT 4053
                           i    --------- i?                 v    i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_127651368_   4054 CTCAAAAGAAGACATTTATGCAGCCAGCA--CACACGAAAAAAAGCTCAA 4101
                            v        i  vi viii    ii --    i     i v      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_127651368_   4102 CATCACTGATCAT 4114
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (142 / 104)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.08 (27 / 13)  


3336 26.14 1.00 0.44  chrX_127775559_127777487      534  1436 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127775559_    534 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 583
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127775559_    584 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGA 633
                            v     v     iv i  i  i        i  v     i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127775559_    634 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCACA 678
                          v   iivi i  i  ii     v v  v  i--- --     i    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_127775559_    679 TGGAACTAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGAA 728
                              v iv  ii  v  viv  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_127775559_    729 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 778
                              i      vv       v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_127775559_    779 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 828
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_127775559_    829 TGGAACAGAAC--AGAGCCCTCAGAAATAATGTCGCGTATCTACAACCAT 876
                              i    i--    i  --        vvi iiii  i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_127775559_    877 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 926
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_127775559_    927 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 976
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_127775559_    977 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 1026
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_127775559_   1027 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1076
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_127775559_   1077 AGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGCCTAA 1124
                            ?i- v i -   i- i  v i  i- i     v ii   v ivv  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT 596

  chrX_127775559_   1125 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1174
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_127775559_   1175 TTAAACTGAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1224
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_127775559_   1225 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 1274
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_127775559_   1275 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 1324
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_127775559_   1325 AAACAAACAACCCCATCAAAAAGTGGGTGAAGTATATGAACAGACACTTC 1374
                          i     i     v  i?    i    ii   v  v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_127775559_   1375 TCAAAAGAAGGCATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 1424
                           v       ii  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_127775559_   1425 ATCACTGGCCAT 1436
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (141 / 91)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3076 23.93 3.39 0.90  chrX_127846657_127850892.rev     2860  3745 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127846657_   2860 TAGAAATACATCCCATGTTCATGGATTGGAAGAATTAACATT---AAGAT 2906
                          i    v i                        v    i   ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127846657_   2907 GACCATATTAACCAAA---ACCTACAGATTCAATACAATCTCCATTGAAA 2953
                          i v   i vv     --- i            ii     i i  ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127846657_   2954 TAC-AGATGTCATTTTTTTTTACAAAACTATAAAAGACAATCCTAAAATT 3002
                          v -  v  i ----      i  i  v vv v   vii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC----TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_127846657_   3003 CTTACTGAA-T-CAAA--ACTGCCTAAATAGAGAAAGCAATCTTGAGCAA 3048
                          v  iv   - -   i--  --  vi     vv   i         iv  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_127846657_   3049 GAAGA-CAAAGCTAGAGGCATCACAACACATAAGTTCAAAATATATTATA 3097
                              -     i i    vv     viv vi  v       iv  i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_127846657_   3098 AGGTTATAGTAACCCAAAATGCATGATATTGTTATAAAAACAGACACATA 3147
                          i i  i     i v i vv ii  i  i  vi    ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_127846657_   3148 GATCAACGGAATATAATAGAGAACCTAGAAAAAAATTTACATATGTACAG 3197
                               i      v   v    ii i     v   iii i i  v  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_127846657_   3198 CTGAATTGATTTTCAAAAAAGGTGCCAGGAACTTACACTGGGAAAAGAAC 3247
                         - v           i v  i       i  v v v  v    i      i
  L1M4_orf2#LINE/    345 -TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_127846657_   3248 AACCTCCACAATAAATGGTGTTGGGAAAATTGGATACCTATATGTGGGAG 3297
                          ii  iiv   i        i     v  i      ? i i   iiii  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_127846657_   3298 AAAGAAATTGGACCTCT------TACCATATACAAAA-TCAACTGACAAT 3340
                           v   i       i  ------i             - i    v v   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_127846657_   3341 AAATCAAATACTTAAATGTAAGATGCCAAA-CCATAAAAGTACTAGGAGA 3389
                         ii    ? v  i           -  i   - i      v vi   i   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_127846657_   3390 AACCATAGGGGAAACACTTTGGGACACTGGTCTAGGAAAGGATTTTATGG 3439
                           v      ? v  vv   i v   vi   vi    v  v i   iv i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_127846657_   3440 CTAAGACAGCAAAA-CACAGGGAACAAGACAAAAA-TAGACAAATGCGAC 3487
                         v  v    v     -    i v     i v     -    i    vv   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_127846657_   3488 TATATTAAACTAAAAAGCTTCTGCACAGCAAAGGAAAC----AACAAATT 3533
                          vi  i   v v    i   i  ii vv       v  ----  v   v 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_127846657_   3534 GAAAAGACAGCCTGTAGAATGGGAGAAAATATTTGCAAGCTATTCATCTG 3583
                                  i  iii                       iii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_127846657_   3584 GCAAGGGACTTATATCCAGAATATATGAGGAACTCAAACAACTGAACAGT 3633
                         ii         i              i i      vv      v  i i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_127846657_   3634 AAAGAAACA--TAACCCCATTATAAAGTAGGCAAAA-ACATGAATAGATA 3680
                            i i   --      v   ?v   i i      i- iv        i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_127846657_   3681 TTTCTCAAAATAAGACATACAAATGGCCAACGAGTATATTAAAA-ATGCT 3729
                               v   v    i              ii  i i  v    -     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_127846657_   3730 CAACAACACTAATTAT 3745
                              v  ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (125 / 83)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.90 (38 / 20)  


2891 26.02 0.97 3.33  chrX_127876303_127878970.rev     1248  2177 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127876303_   1248 TGGAAATACGTCCCATGCTCATGGATTGGAAGAATCTATACAGTGAAAAT 1297
                               v ii       i               v iv   iv  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127876303_   1298 GACCATACTGCCCAAAGCAATCTACAGATTCAATGCAATTCCCATAAATA 1347
                          i v     v      vii              i     i  i  v  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127876303_   1348 TACCACCATCATTTTTCATA-AAATTAGAAAAAAAACCCTAAAATTTATA 1396
                          v   v vv v     iii -     iiv  ivvi i         i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_127876303_   1397 TGGAGCCAAAAAAGAGCCCAGA-TAGCCAAAGCAATCCTAAGCAAAAAGA 1445
                             iviiv  ii  -      -        i     i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_127876303_   1446 GCAAATCTGTAGGCAGCATATTATCCAATTT--AAATTTATACTACAAGG 1493
                         i    vi  v   vvv  i i vi       --   i   --      i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAG 247

  chrX_127876303_   1494 GTTTAATTACCAAAACAGCATGGTACTGGTATAAAAGTAGACATATAGAC 1543
                         v vi i v i   i    ii         i    iii            i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_127876303_   1544 TAATGGATCAGAGTAGAGAACCCAGCAGTTAAGCCAAATACTTACAACCA 1593
                         i      vi   i v    ii    v i v  v   v i i   iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_127876303_   1594 ACTGATCTTTCACAAAGCATACAAAAAT-ATAAATTGGGGAAAGGACACC 1642
                          i    i  iv    i -i i v  i i-  vv v         i i vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_127876303_   1643 CTATTCAATAAATGGTACTGGGAAAACTGTCAAGACACATGTAGGAGAAT 1692
                           v     i       i      v     vvv ?v      i ii     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_127876303_   1693 GAAACTGGATCCCCATCTCTCACCTTCTACAAAAATCAACTCAAGATGGA 1742
                            ii    i   i i   v    v v         i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_127876303_   1743 TCAAAGACTTAAATATAATATCTGAAACCATAAAAATTCTAGAAGAATAC 1792
                            ?    i     i   v v  i    i      v ii        v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_127876303_   1793 CTGGGAAAAACTCTTCTGAACATTGGCCTTGGCAAAGCATTTATGACTAG 1842
                         v i  ?iv  v     vvi  v    vi v     v -i   v ---   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTCT---TAG 592

  chrX_127876303_   1843 ACAAAAACAAAACAAAACAAACAAACAAACAAAAAAACAAATGCAACAAA 1892
                          i ---------ii v  -----------     iv    --        
  L1M4_orf2#LINE/    593 ATA---------TGACAC-----------CAAAAGCACAA--GCAACAAA 620

  chrX_127876303_   1893 AATAAAGATGAATAGATGGGGCCTAATTAAACTAAAAGGCTTCTGCACAA 1942
                          iv   i  ii   i  v  i i v  i   v v   ii   i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_127876303_   1943 CAAAAGAAATCGTTATCAGAGTTAACAGAGAACACACAGAATGGGAGAAA 1992
                             i  v iii i vv i   v  v   v   v                
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_127876303_   1993 ATACCTTTAAATTATGCACTTGAAAAAAGACTAATATGCAGAATCTACAA 2042
                            ii vi    i  ii ii   v  ii    vi   v      v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_127876303_   2043 GGAACTC----AAATCAGCAAGAAAAAAATCAACTAATCCCATTAAAAAG 2088
                         i      ----  v   ii  v     i -   v   i  v   ?    i
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAA 819

  chrX_127876303_   2089 TGGGCAAAGGACATGCATAGACATTTTTCAAAAGAAGATGTACAAATGGC 2138
                                    iv  v          i  v         i          
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_127876303_   2139 CAACAAATATATGAAAAAATGTTCAACATCACTAATCAT 2177
                            i  ii i       i   i         ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.86 (40 / 14)  


3225 26.98 0.55 0.55  chrX_127903350_127909659     4910  5817 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_127903350_   4910 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4959
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_127903350_   4960 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5009
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_127903350_   5010 TACCAA-TGCCTTTCTT-CACGGATTTGGAAAAAACT-ACTTTAAAGTTC 5056
                          v   i-       i  -  - i v   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_127903350_   5057 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 5106
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_127903350_   5107 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5156
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_127903350_   5157 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5206
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_127903350_   5207 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5254
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_127903350_   5255 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5304
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_127903350_   5305 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5354
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_127903350_   5355 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5404
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_127903350_   5405 ATTAAAGAGTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5454
                           i ?   vi    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_127903350_   5455 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCACGTCTA 5504
                          v    ?i v viv   iv   v v  vv i     v ii   viivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_127903350_   5505 AAACACCAAAAGCAATGGCAACAAAAGACAAAACTGACAAATGGGATCTA 5554
                         vi            vvi           v    iv  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_127903350_   5555 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAA 5604
                           i   v i  i i   i  ii vv    i  v    i  vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_127903350_   5605 CAGGCAACCTAGAAAATGGGAGAAAATTTTCGCAACCTATTCATCTGACA 5654
                         v  i     i v i             v  i    vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_127903350_   5655 AAGGGCTAATACCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAG 5704
                          i  i  vi  i       v  i  v      vv    v iv i  vi i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_127903350_   5705 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5754
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_127903350_   5755 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5804
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_127903350_   5805 CATCACTGGCCAT 5817
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


4742 15.74 1.53 2.30  chrX_128017794_128020239.rev     1041  1955 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128017794_   1041 TGGATAAACATCCTATGTTCATGGATCAGAAGACTTAATATTGTTAAGAT 1090
                             v i i    i            ii                      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128017794_   1091 GGCAATACCCTCCAAACTGATTGATAGATACAATGTGATCCCTA-AAAAA 1139
                                 i i     i    iv i    v   i ii       -v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128017794_   1140 TCCCAGATGGCTTCTTTGCAGTAATTGACAAGCTGATCATTAACTTCATA 1189
                               v  v   i       v                v v  v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_128017794_   1190 TAAAAATTTAAGGGACCTACAATAGCAAAAATAACCATGAAAAAGAA--- 1236
                          ii    vi        i v      v    i  i v          ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_128017794_   1237 CAAAGTTGAAGGGCTCACATTTTCTGATATCAAAACTAAGCACAAGGCTA 1286
                                 i   i      i  i ii  v        v vi    i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_128017794_   1287 TAGTAATCACGACAGTGTGATATTGGCAAAGGGATAGACATGTGGGTCAA 1336
                         i        v         i  i     v i          i i i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_128017794_   1337 TGGAATAGAACTGAGAGTCCAGAAATAAACCCACACATTTATGGTCAATT 1386
                                   i                      i                
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_128017794_   1387 GATATTCAACAAGGATGCCAAGAGAATTTAATAGGGAAAATAACATTATT 1436
                            v   i      i        vv   i   i      i-  i v v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTT 399

  chrX_128017794_   1437 TTTAA-AAATGGTGCTGACACAACTGGATATCCTCATGCAAAAGAGTGAG 1485
                           i  -           iv           ?  v           i   i
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_128017794_   1486 GTTGTTTCCCTCCCAAACACCATATGCAAATATTAACTCAAAATGAATTA 1535
                             vvi    v  vv         i    v              i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_128017794_   1536 AATACCTAAAGTTAACACTTAAAACTATA-CGTATTTATGAGAAAACATA 1584
                         ? v       vv   v vi          -viivi   vi          
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_128017794_   1585 AGGGCAAATATTCATGACCTTGGGTTAGGTAGAGGTTTTTTAGATATGAC 1634
                         i ? i    v   i               i iv     i           
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_128017794_   1635 AACAAAAGCAAAGGCAACTGAGAGAGAGAGAGAGAGAGAGAGAGAGATAA 1684
                          v        v i     -i i   i i ------------- v      
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAAC-AAAAGAAAAA-------------ATAGATAA 635

  chrX_128017794_   1685 ATTGTACTTCATTGAAATTAAGAAAGAAAACTTTTGTGCTTCAAGAG-TA 1733
                             v       ii       ------                 ii -i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAA------AAACTTTTGTGCTTCAAAGGACA 679

  chrX_128017794_   1734 CCATCAAGAAAGTGAAAAAACAACCCACAGAATGGAAGAAGATATTTGCA 1783
                          i                i                i    i         
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_128017794_   1784 AATCATATATCTGATAAGGGATTTGTATACTGAATACATAA-GTACTCTT 1832
                                              i      v v     i    - v      
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_128017794_   1833 ACTGTTCAACAATAAAAAAA------ATCCAATTTAAAAATTGGCAATGA 1876
                           vii    i        i ------ i      ?      v     v i
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_128017794_   1877 ATTTGAATAAACATTTCCCCAAAGAAGATATACAAATGGCTAAGAAGCAC 1926
                                  i       i                      i  v      
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_128017794_   1927 ATGAAAAGATGCTCAACATCATTAGCGGT 1955
                                              ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (87 / 53)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.18 (35 / 11)  


3659 24.06 0.77 0.55  chrX_128032280_128036556.rev     2881  3786 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128032280_   2881 TGTAAAAATATTCCATGTTTATGAATTGGAAGAATCAATATTGTTAAATT 2930
                           v   i    i       i   i         v i           iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128032280_   2931 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTGTCAAAA 2980
                          v v     v      vii              i         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128032280_   2981 TACCAATGACATTCTTCATAGAAATAGAAAAAA-AATACTAAAATTTATA 3029
                          v   iivi v  i  iii      v  v  iv-i  v        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_128032280_   3030 TGGAACTACAAG--ATCTAAAATAGCCAAAGTTATCCTAAGCAAAAAGAA 3077
                              v i    -- i i i          iiv   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_128032280_   3078 CAAAACTAGAGGAATCACATTACCTGACTTCAAATTATATACTACAGAGC 3127
                             ii i     v     i v  ii i      -- iv       i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAGC 248

  chrX_128032280_   3128 TATAGTTACCAAAACAGCATAGTACTAGCATAA--ACAGACACATAGACC 3175
                           i   v i   i    ii i     i      -- i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_128032280_   3176 AATGGAATAGACTGGAGATCTCAGAAACCAATCCGGACATCTATATTGAA 3225
                                    v v    vii      iv  i  iv    i   iv v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_128032280_   3226 CCCATTTTCTACAAAGGTGCTGAGAACATACACTGGGGAAAAGACAGCCT 3275
                         iiv      v    i     ii   v   v  v        ii i  i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_128032280_   3276 CTTCAATAAAGGGTGCTGGGAAAACTGGATATCTCTATGAGGAAAAATGA 3325
                         i     i   v          v         ? ivi   vii  i     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_128032280_   3326 AACTAGACTCCTATCTCTCACCATATACAAAAATCAAATCAAAATGGATT 3375
                          ii i   i    i   v                i  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_128032280_   3376 GAAGACTTAAATCTAAGACCTCAAACTATGAAACTACTACAAGAAAACAT 3425
                         i?    i     v     v  v       i     vi  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_128032280_   3426 TGGGGAAAATCTCCAGGACATTGATTTGGGCAAAGATTTCTTCAGTAATA 3475
                         v  ? v      i iv   v   iv  i     v i      vii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_128032280_   3476 CCCCATAAGCACAGGCATCCAAAGCAAAAATGGGCAAATGGG--TTCATA 3523
                          v   v       i   v v    v      i ii    v  --     -
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT- 647

  chrX_128032280_   3524 TCAAGTTTAAAAGCTCCTGCAAAGAAAAGTAAACAATCCGCAAAATGAAG 3573
                         -   iv      i  ii  iivvvv    v v  v   viv   i    i
  L1M4_orf2#LINE/    648 -CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_128032280_   3574 AGACAACCCACAGAATGGGAGAAAATATTTCCAAACTACCCATCTAACAA 3623
                                                       v    ii ivi    i i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_128032280_   3624 GGGATTAATAACCAGAATACATAAGAAGCCCAAACAATTCTGTAGGAAAA 3673
                             i vi  v        i    ii i i vv    i  vi  iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_128032280_   3674 AAATCTAATAATCTGATTAAAAAGTGGGGAAAAGATTTGAATAGACATTT 3723
                          i - v     i ii   ?    i    v   i                 
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_128032280_   3724 CTCCAAAGAAGACATACAAATGGCAAACAGACATATGAAAATGTGATCAG 3773
                                     i           v  i ii  i       vi  v   i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_128032280_   3774 CATCACTGATCAT 3786
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (132 / 82)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2885 26.74 1.99 1.66  chrX_128064466_128068757.rev     2897  3801 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128064466_   2897 TGGAAACACATCCCATGCTCACGGATGGGTAGAAACAATATTGTGAAAAT 2946
                               v i        i   i    v  v   vvi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128064466_   2947 GACCATACTGCCAAAAGCAATCTACAAATTCAATGTAATTCCCATCAAAA 2996
                          i v     v  v   vii       i      i i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128064466_   2997 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 3046
                          v   v vv v  i  ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_128064466_   3047 TGGAACAAAAAAAGAGCCTACATAGCCAAAGCAAGACTAAGCAAAAAGAA 3096
                              vviv  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_128064466_   3097 CAAATATGGAGGCATCATGTTACCTGATTTCAAACCATACTATGTGGACA 3146
                             vv      vv   iii v  ii        v v     iivi vi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_128064466_   3147 TAGCCACCAAAACAGCATGACATGATACTG-TATAAAAATAGGCATATAG 3195
                         i  iv i   i    --  ---  i     -i    ii    i       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAG--TG---TGGTACTGGCATAAGGATAGACATATAG 295

  chrX_128064466_   3196 ACCAATGGACCAGAATGGAGAACCTAGAAATAAACCCAACTACTTACAGC 3245
                          i       vi     v    ii i             vvi i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_128064466_   3246 CAACAGA------GCAAA-----CAAAAACATAAAGTGGGGAAATGACGC 3284
                            iv  ------i   i-----   i v   vv i        vi iiv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_128064466_   3285 TCTTTTTAACAAGTGGTGCTGGGATAATTGGCTAGCCACCTCTAGGAGAA 3334
                               i     i           i  i   v  ?    v vi ii    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_128064466_   3335 TGAACCTGGATCCTCATCTCTAACCTTATACAAAAATCAACTCAAGATGG 3384
                             vi    i  ii i   vv   v           i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_128064466_   3385 ATTAAGGACTTAAATCTAAGACCTGAAACTATAACTATAAAACTTCTAGA 3434
                           i ?i   i     v     ------i   v            ii    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGA------GCTAAAACTATAAAACTCTTAGA 539

  chrX_128064466_   3435 AGATAACATTGGAAAGACCCTTTTAGACATTGGCTTAGGCAAGGATTTCA 3484
                            v     v  ?ivi vi   ivv   v    v        v i    v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_128064466_   3485 TGACCAAGAACCTAAAAGCAAATGCATTAAAAACAAAGATAAGTAGCTGG 3534
                          iivi v  vv i       v v   vi    iv   i   ii  iv v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_128064466_   3535 GACTTAA--ATAATCTAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGTA 3582
                              v -- v   -   i i      ii vv    i iv  vi   iv 
  L1M4_orf2#LINE/    640 GACTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_128064466_   3583 GAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCATAATCTATACA 3632
                         i   i  v              i           v  iii  vii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_128064466_   3633 TCTGACAAAGGACTAATATCTAGGATCTACAATGAATTCAAACAAATCAG 3682
                              i  i     vi    i  i  v  i  v   i  vv    v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_128064466_   3683 CTAGAAAAA---AAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATA 3729
                         iv v     ---   i  i  v  i?    i     v     iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_128064466_   3730 GACAATTTTCAAAAGAAGATATACAA-TGGTCAACAAACATATGAAAAAA 3778
                             v  i  v               -   i   i  i  i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_128064466_   3779 AATTCCTCAACATCACTAATGAT 3801
                         --- v          ????????
  L1M4_orf2#LINE/    889 ---TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (137 / 101)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.00 (33 / 11)  


3246 26.48 0.44 0.66  chrX_128099874_128106265     4990  5899 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128099874_   4990 TGGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5039
                              ii i  ii    i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128099874_   5040 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5089
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128099874_   5090 TACCAATGACTTTCTTCACAGAACTGGAAAAAACT-ATTTTAAATTTCAT 5138
                          v   iivi i  i  ii     v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_128099874_   5139 ATGGAACCAAAAAAAGAGCCC-GCATTGCCAAGTCAATCCTAAGCCAAAA 5187
                               -- viv  i ii   - v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_128099874_   5188 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5237
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_128099874_   5238 CTACAGTAACCAAAACAGCATGGTACCGATACCAAAACAGAGATATAGAC 5287
                                  i   i    ii      i ii iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_128099874_   5288 AAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTAAAAC 5335
                         v       i    i--    i  --        vv   i i  i  viii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_128099874_   5336 CATGTGATCTTTGACAAACCTGACAAGAACAAGAAATGGGGAAAGGATTC 5385
                           vv    i  i     ivv  v     v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_128099874_   5386 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGC 5435
                         i  v  i  i              v      v  ?   i     i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_128099874_   5436 TGAAACTGGATCCCTTCCTTACACCTTCTACAAAAATTAATTCAAGATGG 5485
                             ii    i    v   i     v v            i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_128099874_   5486 CTTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5535
                         v i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_128099874_   5536 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5585
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_128099874_   5586 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCCA 5635
                         vi            vvi          vv     v  i    v   iiiv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_128099874_   5636 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5685
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_128099874_   5686 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5735
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_128099874_   5736 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5785
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_128099874_   5786 AAAATTAACAACCCCATCAAAAAGCGGGCAAAGGATATGAACAGACACTT 5835
                           i iv  i     v  i?    ii           v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_128099874_   5836 CTCCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5885
                                -     i  vi viii     v ii          i       
  L1M4_orf2#LINE/    846 CTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_128099874_   5886 CCATCACTGGCCAT 5899
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (136 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3317 25.06 1.11 0.44  chrX_128109998_128114258.rev     2869  3770 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128109998_   2869 TGGAAACACATCCCATGCTCATGGATTGGGCAGAATCAATATTGTGAATA 2918
                               v i        i           i-   v i        v  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGA-AGACTTAATATTGTTAAGA 49

  chrX_128109998_   2919 TGACCGTACTGACAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAA 2968
                           i vi    vv v   vii       i      i        i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_128109998_   2969 -TACCA-CTGTCATTCTTCACAGAAATAGGAAAAC-AATTCTAAAATTCT 3015
                         - v   -   i -  i  ii       v iv  i -i  i         v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_128109998_   3016 TATGGAACAAAAAAAAGAGCCCGCATAGCCAAAGCAAGACTAAGCAAAAA 3065
                                - viv  ii  v  v v         i   vvi i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_128109998_   3066 GAACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGT 3115
                                vi      vv       v  ii        viv     i  iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_128109998_   3116 CCATAGTCACCGAAACAGCATCATACTGTTATAAAAATAGGCACATAGAC 3165
                          i i   v i i i    ii vi     vi    ii    i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_128109998_   3166 CAGTGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCA 3215
                           i     i     v    ii               v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_128109998_   3216 ACTGATCTCCGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCG 3265
                          i    i i      i vviv   i v   vv i         i i viv
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_128109998_   3266 TTTACAACAAATGGTGCTGCGATAATTGGCTAGCCGCATGTAGAAGAATG 3315
                            v               v  i  i   v  ?  i    i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_128109998_   3316 AAACTGGATCCTTATCTCTCACCTTATACAAAAATCAACTCAAGATGGAT 3365
                           ii    i  i  i   v    v           i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_128109998_   3366 TAAGGACTTAA------GACCTGAAACTATAAAAATTCTAGAATATAACA 3409
                         i ?i   i   ------  v  i           v ii     v v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_128109998_   3410 TTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCAT-GATCAA 3458
                          v  ?iv  vi    vv   v    v        v i    v -   - v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chrX_128109998_   3459 GAACCCAAAAGAAAATGCAATAAAAACAAAGATAAATAGTTGGGACTTAA 3508
                           vv       v v v    i    iv   i   i   iv v      v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_128109998_   3509 TTAAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAAC 3558
                          i   v v  i i      ii vv    i iv  vi   iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_128109998_   3559 AGACAACCCACAGAGTGGGAGAAAACCTTCACAATCTATACATCTGACAA 3608
                                       i          iv  ii   vii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_128109998_   3609 AGAACTAATATTCAGAATCTACAATGAACTCAAACAAATCAGTAAGAAAC 3658
                         i i   vi   i      v  i  v      vv    v   i   v   v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_128109998_   3659 AAACAAACAATCCCATCAAAAAGTGGGTTAAGGACATGAATAGACAATTC 3708
                          i     i  i  v  i?    i    iv     iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_128109998_   3709 TCAAAAGAAGATATACAAATGGCCAACAAACATATGAAATAATACTCAAC 3758
                           v                       i  i  i      vi  i      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_128109998_   3759 ATCACTAATGAT 3770
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (129 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3287 25.55 1.11 0.66  chrX_128137217_128140120.rev     1510  2413 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128137217_   1510 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 1559
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128137217_   1560 GTTCATACTGCCAAAAGCAGTCTACAAATTCAATGCAATCCCTATCAAAA 1609
                          viv     v  v   viii      i      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128137217_   1610 TACCACCATCATTGTTCACAGAATTAGAGAAAACAATTCTAAAATTTATA 1659
                          v   v vv v  v  ii     v v  v  ivii  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_128137217_   1660 TGGAACAATAAAAGAG-CCCACA-TAGCCAAAACAAGGCTAAGCAAAAAG 1707
                              --  iv   i -    v -            vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_128137217_   1708 AACAAATCTGGAGGCATCACACTACCTGATTGCAAACTATACTATAAGGC 1757
                               vi      vv       v  ii   v    viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_128137217_   1758 CATAGTCACCAAAACAGTGTGGTACTGGTACAAAAATAAGCACACAGACC 1807
                         i i   v i   i               i i  ii   ii  i i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_128137217_   1808 AACAGATCAGAATAGAGAACCCAGAAATAAACCCAAATACTCACAGCCAG 1857
                           ii  vi     v    ii               v i i i ii i  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_128137217_   1858 CTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCT 1907
                         i    i   i    i vviv   i v   vv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_128137217_   1908 TTTCAACAAATCATGCTAGGATAATTGGCTAGCCGCTTGTAGGAGAATGA 1957
                                    vi    i   i  i   v  ?  i v  i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_128137217_   1958 AACTGGGTCCTCATCTCTAATCTTATACAAAAATCAACTCAAGATGGATT 2007
                          ii   ii  ii i   vv i v           i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_128137217_   2008 AAGGACTTAAATTTAAAACCTGAAACTATAAAACTTCTAGAAAATAACAT 2057
                          ?i   i     v   i v  i             ii     i v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_128137217_   2058 TGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCAT-GACCAAT 2106
                         v  ?iv  vi    vv   v    v        v i    v -  i--  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--AT 596

  chrX_128137217_   2107 AAC-CCAAAAGCAAATGCGTTAAAAACAAAGATAAATTGCTGGGACCTAA 2155
                         i  -         v v  ivi    iv   i   i  viv v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_128137217_   2156 TTAAACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGAAGAGTAAAC 2205
                          i   v v  i i      iiivv    i iv  vi   ii i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_128137217_   2206 AGACAATCCACAGAGTGGGAGAA--TATCTGCACAATCTATACATTTGCC 2253
                               i       i        --   i    -    -   i  i  vi
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCA-AATC-ATATATCTGAT 744

  chrX_128137217_   2254 AAAGGACTAATATCCAGAATCTACAATTAACTCAAACAAATCAGTAAGAA 2303
                           i     vi          v  i  vv     vv    v   i   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_128137217_   2304 AAAAACGA----TCCCATCAAAAAGTGGGCTAAGGACAAGAATAGACAAT 2349
                            i  i ----i  v  i?    i     v     ivv         v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_128137217_   2350 TCTTAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCA 2399
                            iv                       i  i  i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_128137217_   2400 ACATCACTAATTAT 2413
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (136 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3139 27.75 0.33 0.33  chrX_128150038_128153359     1922  2829 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128150038_   1922 TGGAAGAACATTCCATGCTCATGGATAGGACGAATCAATATCGTGAAAAT 1971
                              ii i  i     i        v   v  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128150038_   1972 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2021
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128150038_   2022 TACCAATGACTTTCTTCACAGAACTGGAAAAAGCT-ACTTTAAAGTTCAT 2070
                          v   iivi i  i  ii     v v  v  -   - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_128150038_   2071 ATGGAACCAAAAAAGAGCCCACATTTCCAAGACAATCCTAAGCAAAAAGA 2120
                               viiv  ii  v  viv  vv    i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_128150038_   2121 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 2170
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_128150038_   2171 ACAGTAACCAAAACAGCATGGTACAGGTACCAAAACAGAGATATAGACCA 2220
                                i   i    ii      v  i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_128150038_   2221 ATGGAACCAAATAGAGCCCCCGGAAATAATACCACACATCTACAACCATC 2270
                               ivi   v   vvi  i       vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_128150038_   2271 TGATCTTTGACAAACCTGACAAAAACAAGAAAGGGGGAAATGATTCCCTA 2320
                             i  i     ivv  v   i v  vvv  v       vi  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_128150038_   2321 TTTAATAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCTGAA 2370
                           i  i              v     iv  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_128150038_   2371 ACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA 2420
                         ii    i    v   i     v              i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_128150038_   2421 AAGACTTACATGTTAGACCTAAAAACCATAAAAACCCTAGAAGAAAACCT 2470
                         ?    i  v    v   v      - i      vi i           v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACAT 548

  chrX_128150038_   2471 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAA 2519
                            ?i- v i -   iv   v v  vv i     v ii   v ivvi vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_128150038_   2520 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATTGGATCTAAT 2569
                                     vvi          vv     v  i        ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_128150038_   2570 TAAAGTAAAGAGCTTCTGCACATCATAAGAAACTACCATCAGAGTGAACA 2619
                         i   i v  i i   i  ii v   v i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_128150038_   2620 GGTAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 2669
                          ii    i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_128150038_   2670 GGGCTAATATCCAGAATCTACAAAGAACTTAAAGAAATTTGCAAGAAAAA 2719
                           i  vi          v  i        ivv v  v ivii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_128150038_   2720 T-CAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTACT 2768
                         v-    i     v  i?    i            v    i     i v  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_128150038_   2769 CAAAAGAAGACATTTATGCAGTGAACAGACACGTGAAAAAATGCTCATCA 2818
                          v        i  vi viii iv  i ii   i      i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_128150038_   2819 TCACTGGCCAT 2829
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.41 (145 / 103)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.00 (6 / 6)  


3329 25.97 0.88 0.55  chrX_128196068_128202331     4867  5771 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128196068_   4867 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4916
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128196068_   4917 GGCCACACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4966
                            v i   v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128196068_   4967 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5013
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_128196068_   5014 ATATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAA 5063
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_128196068_   5064 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5113
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_128196068_   5114 CTACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGAGATATTGAT 5163
                                  i   i    ii         i iv ii i   v    v   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_128196068_   5164 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5211
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_128196068_   5212 TATCTGATCTTTGACAAACTTGAGAAAAACAAGCAATGGGGAAAGGATTC 5261
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_128196068_   5262 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5311
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_128196068_   5312 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5361
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_128196068_   5362 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5411
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_128196068_   5412 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5461
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_128196068_   5462 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5511
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_128196068_   5512 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5561
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_128196068_   5562 CAGGGAACCTACAAAATGGGAGAAAATTTTCGCAAACTACTCATCTGACA 5611
                         v  iv    i   i             v  i     ii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_128196068_   5612 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 5661
                          i  i  vi          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_128196068_   5662 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5711
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_128196068_   5712 CTC---AGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5758
                            ---      i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_128196068_   5759 CATCACTGGCCAT 5771
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3089 27.50 0.55 0.66  chrX_128211220_128217225     4605  5513 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128211220_   4605 TGGAAGAACATTGCATGCTCATAGATAGGAAGAACCAATATCGTGAAAAT 4654
                              ii i  iv    i    i   v      vii     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128211220_   4655 GGCCATACTGCCCAAGGTAATTTATAGATTCAACGCCATCCCCATGAAGC 4704
                            v     v     iv i  i  i           v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128211220_   4705 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4752
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_128211220_   4753 TATGGAACCAAAAAAGAGCCTGCATCACCAAGTGAATCCTAAGCCAAAAG 4802
                                viiv  ii  v  v v  vi    ivv    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_128211220_   4803 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACGAGGC 4852
                                i      vv       v  ii i      viv      i i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_128211220_   4853 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4902
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_128211220_   4903 AATGGAACAGAAC--AGAGCCCTGAGAAATAATGCTGCATATCTACAACC 4950
                                i    i--    i  --        vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_128211220_   4951 ATGTGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5000
                          vv    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_128211220_   5001 CTATTCAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5050
                           v     i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_128211220_   5051 GAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGA 5100
                            ii    i    v   i     v  i           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_128211220_   5101 TTAAAGACTTACATGTTAGACCTAAAAACCGTAAAAACCCTAGAAGAAAA 5150
                          i ?    i  v    v   v      - ii     vi i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAA 545

  chrX_128211220_   5151 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGAGT 5199
                          v    ?i- v i -   iv   v v  vv i     v ii   v iii 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_128211220_   5200 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5249
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_128211220_   5250 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5299
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_128211220_   5300 ACAGGCAACCTACAGAATGGGAGAAAAATTTTACAATCCACCCATCTCAC 5349
                          v  i     i                vv   i   vi  ivi    v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_128211220_   5350 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAAATTACAAGAA 5399
                           i  i  vi          v  i        ivv    vviv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_128211220_   5400 AAAATCAAACAACCCCTTCAAAAAGTGGGTGAAGGATATGAACAGACACT 5449
                            iv    i     vv i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_128211220_   5450 TCTCAGAAGAAGACATTTATTCAGCCACAAGACACATGAAAAAATGCTCA 5499
                             vi       i  vi vvii    vv ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_128211220_   5500 TCATCACTGGCCAT 5513
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (145 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1588 25.62 3.96 1.25  chrX_128239301_128242268       24   503 (2465)    L1M4_orf2#LINE/L1      225   717 (191)  

  chrX_128239301_     24 CAACTTCAAACTACACTACAAGGCTACAGTAATCAAAACAACATGGTACT 73
                            i      vivi       i              i   iii       
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_128239301_     74 GGTAGAAAAACAGACACATAGACCAATGGAACAGAATAAAGAACACAGAA 123
                           i v  ii i     i     i        i     vi   iiv     
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_128239301_    124 AAAAAGCCACATGACTACAACCAACTGATCCTCAACAAAGTTGACAAAAT 173
                          v   v   i iivi  iiii   i    ii  i    i v  v   i i
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chrX_128239301_    174 AAG-CAATGGGGAAAGGAC---CTATTCA-TAAATGGTGTTGGGATAACT 218
                         v v-            i i---  v    -i        i     i    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_128239301_    219 GGCTGTACATATGCAGAAGAATGAAACTGGACC--TATC----ACCATAT 262
                           v i?v  i     i         ii      --  i ----       
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_128239301_    263 ACAAAAATTAACTTAAGACGGATTAAAGACTTAAATGTAAGACCTCAAAC 312
                                      i  i i    i ?    i           v  v    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_128239301_    313 TATAAAACTCCTAGAAGAAAACATAGA---AAATACCTTTCTCAATAAC- 358
                                   i               i---    ---i   ---i i  -
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTC---GTGACC 568

  chrX_128239301_    359 ---AGCCTGGCAAAGAATTTATGGTTAAGTCCTCAAAAGCAATTGCAACA 405
                         ---i iiv     v iv  iv i v  v v vi        vvv      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_128239301_    406 AAAACAAAAATTAACAAGTGGGATCT-ATTAAACTAAAGAGCTTCTGCAC 454
                            iv      vi i  i v   ii -  i   v v  i i   i  ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_128239301_    455 AGCAAGAAAAACTATCAAAAGAGTAAACAGATAAACTACAGAACAGGAG 503
                         vv   iii v        i i   i  v   i  v i      ii    
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

Transitions / transversions = 2.18 (83 / 38)
Gap_init rate = 0.02 (10 / 493), avg. gap size = 2.50 (25 / 10)  

1751 28.46 1.15 0.19  chrX_128239301_128242268     1274  1793 (1175)    L1M4_orf2#LINE/L1        1   525 (383)  

  chrX_128239301_   1274 TGGAAAAACATTCCATGCTCACGGATAGGAAGAATCAATATCATGAAAAT 1323
                               i i  i     i   i    v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128239301_   1324 AGCCACACTGCCCAAAACAACTTATAGATTCAATGCTATTCTCATTAAAC 1373
                         i  v i   v      vii ii  i        i  v  i ii  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128239301_   1374 TACCATTGACATTCTTCACAGAACTAGAAAAAAATGATTTTGAAATTCAT 1423
                          v   vivi v  i  ii     v v  v  iv-    ii i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_128239301_   1424 ATGGAACCAAAAAAGAGCTTGAATAGGCAAGGCAATACTAAACAAAAAGA 1473
                               viiv  ii  v iv      v   ii    vi i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_128239301_   1474 ACAAAGCTGGAGGCATGACACTACCAGACTTCATACTATACTACAGGGCT 1523
                               i      vv v     v  vi i    v viv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_128239301_   1524 ACAGTAACCAAAACATCATGGTACTGTGACAGCCACAGACACATAGACCA 1573
                                i   i   vii        vv i ivv i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_128239301_   1574 ATGGAACAAAACAGAGAACACAGAAATAAGACCATACACCTACAACCATC 1623
                               i i  iv    iiv         iv       ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_128239301_   1624 TGATCTTCAACAAA----CCAAAACAAG-CAGTGGGAAAAGGATTCCCTA 1668
                             i   i    i----    i  v v-  i    i    i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_128239301_   1669 TTTAATAAATGGTGCTAGCAGAACTGGCTAACCATATGCAGAAAATTGAA 1718
                           i  i          i v v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_128239301_   1719 ACTGGATGCCTTCCTTACACCATATACAAAAATCAACTCAACATGAAT-A 1767
                         ii    iv   v   i                 i       v   i  - 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_128239301_   1768 AAGCCTGAAATGTAAAACCCAAAACT 1793
                         ?  v iv        i v i      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACT 525

Transitions / transversions = 1.65 (91 / 55)
Gap_init rate = 0.01 (4 / 525), avg. gap size = 1.75 (7 / 4)  

1050 25.13 4.66 2.07  chrX_128239301_128242268     2090  2475 (493)    L1M4_orf2#LINE/L1      513   908 (0)  

  chrX_128239301_   2090 AAAAACCCAAACTGTAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATT 2138
                           i i iv     i     vi i           v    ?i- v i -  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TT 561

  chrX_128239301_   2139 TG-GAACATAGGTACAGACAAAGATTTC------ATGACAAAGATTCCAA 2181
                         i -  v v i   -i  i   v i    ------      ------    
  L1M4_orf2#LINE/    562 CGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACA------CCAA 604

  chrX_128239301_   2182 AGGCAATTTCAACAAAAGCAAAAATTGACAAATGTGATCTAATTAAACTA 2231
                          i   vvvv         v      v  i    vv  ii v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_128239301_   2232 AAGAGCTTCTGCACAGCAAAAGAAACTATCAAAAGAGTAAACAGACAACA 2281
                           i i   i  ii vv    i  v        i i   i  v       v
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_128239301_   2282 TGCAGAATGGGAGAAAATGTTTGCAAACAGTGCACTTGACAAAGGTTTAA 2331
                         ii                i        ivi ii ii   i  i  vi vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_128239301_   2332 TATCCAGCATCTATAAGAAACT--TA-AATTTAC-------AAGAAAAAA 2371
                                v  v     ii    --  -  i i v-------    v   v
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_128239301_   2372 AACACCATTAAAAAGTAGGCAAAGGATATGAATAAACACTACTCAAAAGA 2421
                            v v   ?    i i          v      i   i v   v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_128239301_   2422 AGACATACATGCAGCTAACAATCATATGAAAAAAGGCTCAACATCAGTGA 2471
                            i     viii  i  i  v  i       i v           ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_128239301_   2472 TCAT 2475
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.44 (56 / 39)
Gap_init rate = 0.02 (9 / 396), avg. gap size = 2.89 (26 / 9)  


3261 27.07 0.77 0.44  chrX_128247210_128252184     3578  4482 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128247210_   3578 TGGAAGAACATTCTATGCTCATGCGTAGGAAGAATCAATATCGTGAAAAT 3627
                              ii i  i i   i     vi v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128247210_   3628 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3677
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128247210_   3678 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3725
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_128247210_   3726 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 3775
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_128247210_   3776 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 3825
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_128247210_   3826 TACAGTAACCAAAACAGCATGCTACTAGTACCAAAACAGAGATACAGATC 3875
                                 i   i    ii  v    i i iv ii i   v   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_128247210_   3876 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 3923
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_128247210_   3924 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 3973
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_128247210_   3974 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTT 4023
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_128247210_   4024 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 4073
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_128247210_   4074 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4123
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_128247210_   4124 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4173
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_128247210_   4174 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATCGGATCTAA 4223
                         i            vvi          vv     v  i    i   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_128247210_   4224 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4273
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_128247210_   4274 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 4323
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_128247210_   4324 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 4373
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_128247210_   4374 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 4423
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_128247210_   4424 TC---AGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 4470
                           ---      i  vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_128247210_   4471 ATCACTGGCCAT 4482
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


4809 16.41 1.10 1.10  chrX_128268215_128270583      969  1876 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128268215_    969 TGCAAAAACATTCTGTGTTCATGGAGTAGAAGACTTGATATTGTTAAGAT 1018
                           v   i i  i ii          v i        i             
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128268215_   1019 GGCA-TACTGCCCAAATTGATGTATAGATTCAACATAATCTCTCTCCAAA 1067
                             -    v           v  i         ii    i  v  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128268215_   1068 TCCCAGCTGAATTCCTTGTACAAATTGACAAGCTAATTCTAAAATTTATA 1117
                                  vv  ii   i v             i  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_128268215_   1118 TGAAATTGCAAGGCTCCCAGAATAACCAAAACAATCTTGACAAAGAAGAG 1167
                           i  v       vv         i               v        i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_128268215_   1168 CAAAGCAGGAAGACAGGAAGACTCATGTTTTCTGATTTCAAAACTTACTG 1217
                              iv   i   --------   iii  i ii               i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGAC--------TCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_128268215_   1218 AAAAGC---AATGAT-AGGACAATATCAGTATTGGCATA-GGACAGACAC 1262
                         v     --- i i  - i    i i -i   i       -   i     i
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGT-GGTACTGGCATAAGGATAGACAT 291

  chrX_128268215_   1263 CTATATCAATGGAATAGAATTATGAGTCCAGAAGTAAAACCATACATCTA 1312
                         v  v                 iv          i    v        i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_128268215_   1313 GGACTAGCTGATTTTCTACAAGGATGCCAAGACCATTGAATGGAGAAA-A 1361
                         v iii ii        v      i             v     i    - 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_128268215_   1362 ATGTTCTTTTCAATAAATGGTGCAGAGACAACCGGATAACCACATGCAAA 1411
                           iv         i         v i      i     ?           
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_128268215_   1412 AGAATAAAGTTGGACCCAAGCCTCACATCCTACACAAAACTTAACTCAAA 1461
                              i           vvi       i v  i      v          
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_128268215_   1462 ATGGATCAAAGACATAAATGTAAGAGCCGAA-TTGTAATATTCTTAGAAG 1510
                                 ?    v             ii  -i i   v i         
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_128268215_   1511 GAAACATAGAGATAAATCTTCATGAACTTGGATTTGGCAAAGGGTTCTTA 1560
                         i        i?i         i   v     i  v     v  v      
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_128268215_   1561 GATATGACATGAAAAGCATGAGCAAAAAAAGAAAAAATAGATAATTAGTA 1610
                                  iv       ii     v                  v v v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_128268215_   1611 CTTCATCAAATTTTAAAACTTTTATGCTTCAAAGGACATGAAGATAAAAG 1660
                                   v  v         i              iv vv vi    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_128268215_   1661 TGAAAAGAGAACCAACAGAATGGGAAAAAATATTTGCCAGTCACATATTT 1710
                                 v    v           i           v i   i    i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_128268215_   1711 GATAAGGGACTTGTATCTGGACTGTACAAAGAATTCTTATAACTCAACAA 1760
                                          ii  v i  i      i     i       i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_128268215_   1761 TAAAAAG-CAAATAACTCAATTAAAAATATGGTCAAAG-ATCTGAATAGA 1808
                                -        i     ?    -    v     -  i        
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAGA 840

  chrX_128268215_   1809 CATTTCTCTGAAGGAGATACACAAATAGCCACTAAGCACATGAAAAGGTG 1858
                                 ii   i     i      i    v               i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_128268215_   1859 CTCGATACCATTTGCCAT 1876
                            i i i  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (94 / 51)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


3312 24.29 3.16 0.56  chrX_128282599_128286730.rev     2757  3641 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128282599_   2757 TGCAAAGGCATTACATGCTCATGGATTAGAAGAATTACCATTATTAAAAT 2806
                           v    ii  iv    i         i     v   vi   i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128282599_   2807 GACCATAGTACCTAAAGAAAGCTACAGATTTAATGCAATCCCTATCAAAA 2856
                          i v   v v  i   vvi v         i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128282599_   2857 TACCAATTTCATTTTTTACATAAATAGAGAAAACAGTCCTAAAATTTATA 2906
                          v   ii v v      i  v    v  v  iviii          i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_128282599_   2907 TGGAAACAAAAAAGGACCCA-AATAGCCA--GCAATCCTGAACAAAAATA 2953
                               iiv-  i       -        --i     i    v  i  v 
  L1M4_orf2#LINE/    151 TGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_128282599_   2954 ACAAAACTGGAGGCATCACACTACCTGATTTCAAAATATATTACAAAACT 3003
                              ii      vv       v  ii         iv  i      i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_128282599_   3004 ATGGTTACCAAGACAGCATGGTATTGGTATAAAAATAGACACATAGACCA 3053
                          ii  v i        ii     i   i    ii       i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_128282599_   3054 ATGGAACAGAACAGAGAACCCAGAAATAAATGGACTTATTTGTAGCCAAC 3103
                               i    iv    ii           ivv ivi    i i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_128282599_   3104 TGATTTTT-ACAAAGGTACCAAGAACATACACTGGGGAAAGAACA--CTT 3150
                                i-    i   i      v   v  v           i --   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_128282599_   3151 TTCAATAAATGGTGCTGAGGAAATTGGATATCCATATGCAGAAGAATTAA 3200
                              i           i iv  i      ?   i     i      v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_128282599_   3201 CCTGGACCCTTATCTCA-----------AATATCACCTCAAGATGGATTA 3239
                         vi       i  i    -----------  v  i v     i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_128282599_   3240 AAGATTTAAACACAAGACTCCAAAGTATAAAACTACTAAAAGAAAACATA 3289
                         ?   ii    iii    viiv   v         vi  i           
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_128282599_   3290 GGGAAAACATCTTAG-GACATTGATCTAGGCAAAGATTTTATGGCCAAGA 3338
                           ?iv  -     v -   v   ivi       v i   iv i vi v  
  L1M4_orf2#LINE/    550 GGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_128282599_   3339 GCTCAAAAGCACAGGCAGCAACAAAAACAAAACTAGACAAACTAGACTGT 3388
                         vvi          ---          iv    v    i   i i    vi
  L1M4_orf2#LINE/    599 CACCAAAAGCACA---AGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_128282599_   3389 AATAAACAAAAAAGGTTTTGAACAGCAAAGGAAACAATCAACAGAGTGAA 3438
                          vi   vvv    iv     vi vv       v  v     v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_128282599_   3439 GAGACCACCTGTTGACTGGAAGAAAATATTTATCAACTACTTATGTGACA 3488
                         i    v   iiiv  v   i           iiv  ii iv   v   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_128282599_   3489 AGGGACTAATATTTAGAATATACAAGGAACTC---------AACAGTAAA 3529
                                vi   ii        i  i      ---------  i i    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_128282599_   3530 ACACCTAATAGTCTCATTAAGCAGTGGGCATATGACATGAATAGACATTT 3579
                          viv v    ii iv   ? iv i      v v  iv             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_128282599_   3580 CTCAAAAGAAGACATTCAAATGGTAAATAGGCATATTAAAA-ATGCTCAA 3628
                            v        i  v       iv    i   i  v    -        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_128282599_   3629 CATCACTAATCAT 3641
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (127 / 84)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.00 (33 / 11)  


3102 25.68 1.07 0.83  chrX_128312367_128314878      950  1794 (718)    L1M4_orf2#LINE/L1        1   847 (61)  

  chrX_128312367_    950 TAGAAAAACATTCCATGCTCATGGATAGGAAGAATCTATATCGTGAAAAT 999
                          i    i i  i     i        v      v iv    i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128312367_   1000 GGCCATACTGCCCAAAGTAATTTATAGATTAAATGCTATCCCCATCAAGC 1049
                            v     v      v i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128312367_   1050 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 1098
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_128312367_   1099 ATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAACAAAAAGA 1148
                               viiv  ii  v  v v        i      i i  v  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_128312367_   1149 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 1198
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_128312367_   1199 ACAGTAACCAAAACAGCATGATATTGGTACCAAAACAGATATATAGACCA 1248
                                i   i    ii  i  i   i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_128312367_   1249 ATGGAACAGAACAGA-AGCCTCAGAAATAACACCACACATCTACAACCAT 1297
                               i    iv  -  i -         vv   i    i  iiii  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_128312367_   1298 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 1347
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_128312367_   1348 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 1397
                         v  i  i              v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_128312367_   1398 AACTGGACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 1447
                          ii         v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_128312367_   1448 AAAGACTTACACGTAAGACCTAAAACCATAAAAACCTTACAAGAAAACCT 1497
                          ?    i  v i      v       i      vi    v        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_128312367_   1498 AGGCA-ATACCATTCAGGACACAGGCTTGGGCAAAGACTTCGTGAGTAAA 1546
                            ?i- v i -   iv   viv  v  i     v ii   v iii  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_128312367_   1547 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAAT 1596
                                     vvi          vv     v  i    vi  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_128312367_   1597 TAAACTAAAGAGCTTCTACACAGCAAAAGAAACTATCATCAGAGTAAACA 1646
                         i   v v  i i   i iii vv    i  v       vv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_128312367_   1647 GGCAACCTACAGAATGGGAGAAAATCTTTGCAATCTATCCATCTGACAAA 1696
                          i     i                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_128312367_   1697 GGGCTAATATCCAGAATCTACAA------CTTAAACAAATTTACAAGAAA 1740
                           i  vi          v  i  ------    --   v iv i  v   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTCAATAATAAA 795

  chrX_128312367_   1741 AAAACCCAAACAACCCCATTAAAAAGTGGGCGAAGGATATGAACAGACAC 1790
                           i  --   i     v   ?    i     i      v    i     i
  L1M4_orf2#LINE/    796 AAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_128312367_   1791 TTTT 1794
                           i 
  L1M4_orf2#LINE/    844 TTCT 847

Transitions / transversions = 1.51 (128 / 85)
Gap_init rate = 0.01 (9 / 847), avg. gap size = 1.78 (16 / 9)  

 285 23.38 0.00 1.30  chrX_128312367_128314878     1943  2019 (493)    L1M4_orf2#LINE/L1      833   908 (0)  

  chrX_128312367_   1943 TGAACAGACACTTTTCAAAAGAAGACATTTATGCGGCTAACAAACATAAT 1992
                             i     i  i  v        i  vi vii   i  i  i  i - 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA-T 881

  chrX_128312367_   1993 GAAAAAGAGCTCATCATCACTGGTCAT 2019
                              iiv     v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1)  


 594 20.92 3.35 10.88  chrX_128483224_128486167     1161  1399 (1545)    L1M4_orf2#LINE/L1        4   224 (684)  

  chrX_128483224_   1161 AAAAACATTCCATGCTGATGGATTGAAAGAACCAATATTGTGAAAACGAC 1210
                            i i  i     i v        i    vii        v  i i i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_128483224_   1211 CATACTGCCCAAAGCAATCTACAAATTCAATGCAATTCCTATCAAAATGC 1260
                         v     v      vii       i      i     i           v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_128483224_   1261 CAAC-ATCATTTTT-CAAATAATTAGAAAAAATAATCTTAAAATTCATAT 1308
                           i -ii v     -  i -    -  v  iv i   i            
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGA-AATT-GACAAGCTGATCCTAAAATTCATAT 151

  chrX_128483224_   1309 G----TGTATTAGCCTGTTCTCACTCTGCTAATGAAGACATACCCAAAAC 1354
                          ----  i vvi ---------  i ---------   -   v       
  L1M4_orf2#LINE/    152 GGAAATGCAAGGG---------ACCC---------AGA-ATAGCCAAAAC 182

  chrX_128483224_   1355 TGGGTAATTT--ATAAAGAAAAAGAGGTTTAATGGACTTACAGTTCC 1399
                         -----   i -- v      i  v iiv  iiv     i   v    
  L1M4_orf2#LINE/    183 -----AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

Transitions / transversions = 1.78 (32 / 18)
Gap_init rate = 0.05 (10 / 221), avg. gap size = 3.40 (34 / 10)  

2390 25.00 0.90 3.33  chrX_128483224_128486167     1673  2452 (492)    L1M4_orf2#LINE/L1      148   908 (0)  

  chrX_128483224_   1673 ATATGGAA-T-CAAAAAACGGCCAGAATAACCAAAGCAATCCTGGGCAAA 1720
                                 - -   iii  --        i     i     i  iiv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_128483224_   1721 AAGAACAAAGCCAGAGGCGTCACATTACCTGACATCAAATTATACTACAA 1770
                                   iii    vv     i v  ii iv     viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_128483224_   1771 GGGCACAGTAACCAAAAGAGCATGGTGCTGGTACAAAAATAAATACAGAC 1820
                         i vi       i   i v  ii    i    i i  ii   ------   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA------GAC 289

  chrX_128483224_   1821 ACATAGACCAATGGAACAGAATAGAGACCCCTGAAATAAAACTGTACACC 1870
                          i     i        i     v    vi  v        v ii    ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_128483224_   1871 TACAACCAACTGATCTTCAGCAAAGTGGACAAAAATAAACAATGGGGAAT 1920
                           iiii   i    i   ii   i vv v   i vi vv          -
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA- 388

  chrX_128483224_   1921 ACCCAATAGGACACCCTACTCAATAAATGCTGCTGGGAAAACTGGCTAAC 1970
                         -------  i i vi  vi    i     v        v      v  ? 
  L1M4_orf2#LINE/    389 -------AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_128483224_   1971 CATATGCAGAAGAATGAAATTCAACCTCTACCTGTTACCGCATACAAAAA 2020
                           i     i         i  vi   i      vvi   ii         
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_128483224_   2021 TTAACACAAGGTGGAATAAAGACTTAAATGTAAGACCATAAACTATAAAA 2070
                              v   ii    vi ?    i           v vv           
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_128483224_   2071 ATCCTAGAATCAAACTTAAGAAATACTCTTC-TGGCCATTGGCCAAGGTA 2119
                         v  i     vv    v  i ?ivv v     -  i  -    viv   i 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCA 580

  chrX_128483224_   2120 AATAATTTAT-AACTAAGTCCTCAAAAGCAAATGCAACAAAACCAAAAAT 2168
                          - ii   v - iv  v v vi        v v         vv      
  L1M4_orf2#LINE/    581 A-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_128483224_   2169 TGACAAGTAGGACCTGATTAAACTAAACAGCTTCTACACATCAAAAGAAG 2218
                         v  i  i v    i v  i   v v  v i   i iii v     i  vi
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_128483224_   2219 CCATCAACAGAGTAAACAGACAACCCACAGAATGGGAGAAAATAGAGGCA 2268
                          i     v i   i  v                           vvv   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_128483224_   2269 AACTATGCAAACAACAAAGGACTAATTAATATCTGGAATCTATTAGGAAC 2318
                           ii  ii vvii i  i     --- i-    ii    v   v i    
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACT---TG-TATCCAGAATATATAAAGAAC 775

  chrX_128483224_   2319 T--TA-AACTCATCAACAAGGAAAAAAACAAACAACCCCATTAAAAACTA 2365
                          --  -      vi  i  ----   i     i     v   ?    v i
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAA----AAAGACAAATAACCCAATTWAAAAATG 821

  chrX_128483224_   2366 GACAAAGGACATAAACAGACACTTCTCAAAAGAAGACATATGAGTGGCCA 2415
                          i       iv i  i     i     v        i   ii i      
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_128483224_   2416 ACAAACATATGAAAAAATGCTCAACATCGCTAATCAG 2452
                          i  i  i       i            i????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (119 / 72)
Gap_init rate = 0.02 (14 / 761), avg. gap size = 2.36 (33 / 14)  


 428 32.95 1.16 0.58  chrX_128622108_128624362      615   787 (1468)    L1M4_orf2#LINE/L1       29   202 (706)  

  chrX_128622108_    615 GAAGCCTCAATATTATGAAGATATCATTACTCTCTAAATTAATCTATAAA 664
                             v  i      i v     iv  v     i i     i     i i 
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chrX_128622108_    665 TTCAAGATAACCTCAATTCCAGTGCTAACTGGATACTTTTGTA--ACTTC 712
                              vii  i i v  ivv i v i i   vv -i     i -- v  v
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCT-TTTTTGCAGAAATTG 127

  chrX_128622108_    713 ACAAAATGATAGTAAAGTTTATTTGTAAAAATAAACATGCGAAGATAGCT 762
                             iv    vv    i  i  v  v   vii  ivivv v ii     i
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chrX_128622108_    763 AGGAAAATTCTGAAAAAGAAGAGCA 787
                          ii v   ii            i  
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACA 202

Transitions / transversions = 1.38 (33 / 24)
Gap_init rate = 0.01 (2 / 174), avg. gap size = 1.50 (3 / 2)  

 541 31.16 9.21 5.52  chrX_128622108_128624362     1062  1767 (488)    L1M4_orf2#LINE/L1      177   908 (0)  

  chrX_128622108_   1062 CAAAACCCAATCT---AAAAAAAAAGCAA--TAAGAAAAGCCAGTCCTCT 1106
                               --     ---    i  i i   -- vi  ii vi  vv i  i
  L1M4_orf2#LINE/    177 CAAAAC--AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_128622108_   1107 CAAATTTGAA------CACAAA-CTACCATAACTAAAACAGTATGACACT 1149
                            v  ii  ------i     -    vi   ii  i     i  ii   
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_128622108_   1150 GGAGATGAA-ATAGATAGCTGTAA--CAATGAAACAGAACAATCAGTCCA 1196
                           v-  i i-     i -- i  i--     i  i    ivivv      
  L1M4_orf2#LINE/    275 GGC-ATAAGGATAGACA--TATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_128622108_   1197 GAAGTAAACCCTCTTATTCCCATAAACAACATGGGAATTTAGTTTACAAG 1246
                            i       vivi   i--  iiv   i-  ---    -- iv     
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTT--ATGGTCAAT-TG---ATTT--TCGACAAG 363

  chrX_128622108_   1247 AAAGCT--GATTTTGCAAAAAAGTAAGAAAAAAATGAT-TATTCAGCAAA 1293
                         iiv  i--  iiv v   ----- ii i   i   ii - v    i    
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAA-----TGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_128622108_   1294 TGG-ACAGGGGGAACAAATGGCTAATCATTTG--GGGGGATTAAACTGAA 1340
                            -i v   ---    v   v  ?i  iv  --iii i  v  ii  i 
  L1M4_orf2#LINE/    409 TGGTGCTGGG---ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_128622108_   1341 TA---ACCTC----------CAAAATAAAATTCCAGATGGACCAAAGTTT 1377
                         iv---     ----------     vvv  i  v i     i  ?  vii
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_128622108_   1378 TAAG-GTGAGCAATGAGACCACAAAAGATGTAGAGGAAAACCTA--TATC 1424
                            i-  i  viv i i  i i    vviv    i      v  --?i v
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_128622108_   1425 AATTCATTTATAATCTCAGGGTGGAAAAGAGTCTTTC---TGTG----CA 1467
                            i--  ii i i  ii  v i iv  vi  i i i--- i  ----  
  L1M4_orf2#LINE/    556 AATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_128622108_   1468 AGACCAGAAGCCATGAAGGAAAAGATTAATAACTCTGACTAAATAGAAAA 1517
                          i v  v    v ii  i     i  vi    v iv    vv  vi   v
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_128622108_   1518 TGGAAACAATGTTTATGG---AAACAATGCCATAAACAAAGCCAAGAGA- 1563
                          ii    -- -   i  v---   vi ii i  v  v    iv  i   -
  L1M4_orf2#LINE/    654 TAAAAAC--T-TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_128622108_   1564 -----------TGTGTGACAAATATCTCTTGGCTTTGTTTATGGCAT-TG 1601
                         -----------  v v  -      ---------   ivv  vii  - v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGA-AAATAT---------TTGCAAATCATATATC 740

  chrX_128622108_   1602 TGAGAGGGTGAGTTTTCTT---ATTTTACCATGAGCTTTTTACAAATCCG 1648
                            v i  -  v  v v i--- v v  iv v  i  i  -    v  vi
  L1M4_orf2#LINE/    741 TGATAAGG-GACTTGTATCCAGAATATATAAAGAACTCTT-ACAACTCAA 788

  chrX_128622108_   1649 TAAGACAAAAATAGACAAAACAGG-AAAAAATAGGGCAAAGGACATGAAA 1697
                            v v   i i i i  vv  iv-?      -          iv    v
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAAT-GGGCAAAGGATTTGAAT 837

  chrX_128622108_   1698 AGGCAATTCACTAAAATTAACAC-CAAATGGTCCACATGCATGTGGAAAG 1746
                           i  v   v i   ivvi i i-       i v i v   ii  i    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_128622108_   1747 ATGCTCAAGTTCATCCTTAAA 1767
                                 vv   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (131 / 85)
Gap_init rate = 0.05 (39 / 732), avg. gap size = 2.67 (104 / 39)  


5221 14.14 0.88 0.55  chrX_128666859_128668989      734  1638 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128666859_    734 TGAAAATACAGTCCATGTAAATGGCTCAGAATATTTAATCTTGTTAGGAT 783
                           i   v i vi      vv    v ii   v i     v      i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128666859_    784 GGCAATATTTCCCCAAATTGATCTATAGATTCAATGAAATCCCCATCAAA 833
                                i -               i        i v      i      
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_128666859_    834 ATTCCAGCTGGCTTCTTTTCATAAAT-GACAAGTTGATCCTAAGATTCAT 882
                           i       v   i   v  v    -      i         i      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_128666859_    883 ACGGAAATTTAAGGCACCCAGAAGAGCCAAAACAATCATGAAAAAGAAGT 932
                          i      vi    v        v             v           v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_128666859_    933 ATAAAGTTGGAGGACTCACATTTCCTGATTTCAAAACTTACTACAATGCT 982
                          i                  i    ii                   v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_128666859_    983 AAAGTAATCAAGACAGCGTGGTACTAGCATAAGAACAGACATATTGAGCA 1032
                          v              i        i       i i        v  v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_128666859_   1033 ATACAATAGAACTGAAAGTCCAGAAATGAACTCTCACATTTATAG----- 1077
                           iv       i   i           i   i vi        i -----
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_128666859_   1078 --ATTTTCAACAAGGGTGCCAAGACAAGTCTATGGGAGAAGAATAGTCCT 1125
                         --      i                v v  v     ii          i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_128666859_   1126 TTCAACAAATGGTGCAGAGACAACTGGATAGCTACAGGCAAAAGAAAGAA 1175
                                        v i            ? i   v         v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_128666859_   1176 TGTGGACCCTCTACCTCACACCATATATAAAAATTAACTCAAAATGGATC 1225
                         vv       -                 i                      
  L1M4_orf2#LINE/    450 GTTGGACCC-CTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_128666859_   1226 AAAAACCTAAATGTAAGAGCCAAAACTGTACAGCTCTTACAAGAAAACAA 1275
                          ? i                i      i  v i      v         v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_128666859_   1276 GGGCATAAATCTTCATGACTTTGGATTAGGCAACAGTTTCTCAGATATGA 1325
                         i  ?i         i    i    i        ii      i        
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_128666859_   1326 CACCAAAAAGTACAAACAACAAAAGAAAAAAATAGACAAACTGGACTACA 1375
                                 - i    i               -    i   i      v  
  L1M4_orf2#LINE/    599 CACCAAAA-GCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCA 646

  chrX_128666859_   1376 TCAAAATTTAAAAATTTTGTGCTCCAAAGGACACTATCAAGAAAATTAAA 1425
                                 v    v         i                    i v   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_128666859_   1426 AGATAACCCATGGAATAGGAGAAAATATTTGCAAATTGTATATCTGGTAA 1475
                            i      ii    i                   ii        i   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_128666859_   1476 GAGACTTGCATACAGATTACATAAAGAACTCTTACAACTCAACAATAAAA 1525
                          i      i  v    v  i                      i       
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_128666859_   1526 AAGACAAACAATCCAATTAAAAAATAGACAAAAGCTCTGAACAGACACTT 1575
                          -      i  i      ?      i i    i v i    i     i  
  L1M4_orf2#LINE/    797 A-GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_128666859_   1576 CTCCAATGAGCACATAAAAATGGCCAATAAGCACATGAAAAGATATTCGA 1625
                               v  iv i   v                           ii  i 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_128666859_   1626 CATCATTAGTCAT 1638
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (81 / 43)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


3164 28.05 0.22 0.33  chrX_128713410_128719372.rev     4564  5472 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_128713410_   4564 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4613
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_128713410_   4614 GGCCATACTGCCCAAGGTAATTTATGGATTCAATGCCATCCCCATCAAGC 4663
                            v     v     iv i  i  ii       i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_128713410_   4664 TACCAAGGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 4713
                          v   ivvi i  i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_128713410_   4714 CGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAAGAA 4763
                         i    viiv  ii  v  v v  v     i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_128713410_   4764 CATAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 4813
                           v  i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_128713410_   4814 CAGTAACCAAAACAGCATGGTACTGGTTCCAAAACAGAGATATAGACCAG 4863
                               i   i    ii         iviv ii i   v       i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_128713410_   4864 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 4913
                              i    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_128713410_   4914 GATTTTTGACAAACCTGAAAAAAACAAGAAATGGGGAAAGGATTCCCTAT 4963
                               i     ivv  vv  i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_128713410_   4964 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5013
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_128713410_   5014 CTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGATTAA 5063
                         i    i    v   i i   v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_128713410_   5064 AGACTTAAATGTTAGACCTAAAACCATAAAATCCCTAGAAGAAAACCTAG 5113
                             i       v   v       i      ii i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_128713410_   5114 GAATA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATATCTAAAAC 5161
                          ?i  --i -   iv   v v  vv i     v ii   v  vv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_128713410_   5162 ACCAAAATCAATGGCAACAAAACCCAAAACTGACAAATGGGATCTAATTA 5211
                                v  vvi         vvv    iv  i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_128713410_   5212 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAGTAGG 5261
                           v v  i i   i  ii vv    i  v    i  vv i     iv  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_128713410_   5262 CAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAAGG 5311
                              i                 v       vii ivi      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_128713410_   5312 GCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAAAA 5361
                         i  vi          v  i        ivv    v iv i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_128713410_   5362 ATCAAACAACCCCATCAAAAAGTAGGCGAAGGACGCGAACAGACTCTTCT 5411
                         --    i     v  i?    i i   i     ivi   i    vi    
  L1M4_orf2#LINE/    800 --CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_128713410_   5412 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAAAGGTCATCA 5461
                          v        i  vi viii     v ii          i v v   v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_128713410_   5462 TCACTGGGCAT 5472
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (148 / 103)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.67 (5 / 3)  


3415 22.47 1.78 0.83  chrX_129161377_129163687.rev      639  1479 (832)    L1M4_orf2#LINE/L1        1   849 (59)  

  chrX_129161377_    639 TGAAAAGACAT-CTATTTTTATGGACTAAAAGGCTTACTATTGTTAAAAT 687
                           i     i  - i  v  i     i ii   i    v         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129161377_    688 GCCAATATTTCCCAAATTTATTTACAGTTTGAATTCAAGGTTTATCAAAA 737
                          v     i i        v  i     v  v  iv   vvii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129161377_    738 TATGATCTGGTTTTTATGCAGAAATAGATGACCTGATCTTAAAATGTATA 787
                          viv v   vi    v         v  ii v      i      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_129161377_    788 TGTAATTGAAAAGCATCCTGAAGAATAAAAACAATCTTGAGAAAGAATAA 837
                           v  v  v  i v i  v   v iiv             i      v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_129161377_    838 CAAAGT---AGAACTTATTATTCTCAATTCCAAAA--TATTATCAACCTG 882
                               ---  i   i ivv   i     i     --  i  iv  v  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_129161377_    883 CAGTAATCGAAACACTGTGGTCATGCCAT-GGGATTAAAAAGAAAAACAA 931
                                 i i   v      vv  v   -i    -----   v v i i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-----AGACATATAG 295

  chrX_129161377_    932 AGCAGTGACATATAG-TGAGAGTCCAGGAAAAAGCCCATGCATTTATGGT 980
                          v  i  iv   v i-           i  v  i     i          
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_129161377_    981 ACATTGATTTTAAATTTTGTTACCATGACAATTCAATAGAGAAAATATAA 1030
                         vv         vi ivvv v i   v   v       i i    iv   i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_129161377_   1031 TCTTTTCAAAAAATGATTCTGGGAAAACTGGATATCCATGTGCAAAAGAA 1080
                                  v     i v      v         ?   ii          
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_129161377_   1081 TGTATTTGG-CCTCTACCTCATACTGTGTTCAAAAATTAACTCAAAATGG 1129
                           v v    -  i        i  ii i v                    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_129161377_   1130 ATCAAAGATCTCAAATGTAAGACCTAAACACTCTAAAATTCTTAGAAAGT 1179
                             ?   i  -          v     -   v     i        iiv
  L1M4_orf2#LINE/    496 ATCAWAGACCT-AAATGTAAGAGCTAAA-ACTATAAAACTCTTAGAAGAA 543

  chrX_129161377_   1180 AACACAGGTGTGAATCCCCATGAACTTGTATTAGGCAATGATTTCTTTAA 1229
                             i   ?  i    ii i   v    vi          i      vi 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_129161377_   1230 TATAACATTGAAATCACAAACAACAAAAGAAAAAATAGATAAATTGGATT 1279
                            i   iii   v     i                            i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_129161377_   1280 TCATCAAATTGTAAAAGTTCTGTGCCTC-TAGGAAACTATCAAGAAGGTA 1328
                                 v vv    v  i     i  -v    v           i  i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_129161377_   1329 ACAAGACAACTTAGTGGATGG-AGAAAATATATGCAAGACACATATTTCA 1377
                          v        ii vv i    -         v     iv  i    i v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_129161377_   1378 TAAAGTTGTAGTATCCAGAATACATAAA-AACACTTGTAACT---TAATA 1423
                            i vvv v            i     -   v   ii    ---     
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_129161377_   1424 AAAAAATGGGCAACTTCAGAAAAAAATGGGCAAAGGACTTGAATAGACAT 1473
                             i iiiii   iiv vv?                i            
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_129161377_   1474 TTTTTC 1479
                           i i 
  L1M4_orf2#LINE/    844 TTCTCC 849

Transitions / transversions = 1.26 (103 / 82)
Gap_init rate = 0.02 (13 / 849), avg. gap size = 1.69 (22 / 13)  

 374 12.31 0.00 0.00  chrX_129161377_129163687.rev     1756  1820 (491)    L1M4_orf2#LINE/L1      844   908 (0)  

  chrX_129161377_   1756 TTGTTCAAAAAAGATAAACCAATGGCCAATAAGCACATGAAGGGGTGCTC 1805
                           v i    i      v  v                     ii i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_129161377_   1806 AACATCATTAGTCAT 1820
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.00 (0 / 0)  


 505 21.82 0.00 0.00  chrX_129168317_129170851.rev        1   110 (2424)    L1M4_orf2#LINE/L1      478   587 (321)  

  chrX_129168317_      1 AAAATTAACATAAAGAGGATTCAATATCTAACTATAAGACTTAAAACTCT 50
                                  vi   iv    iv? v i    v i     vi       v 
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_129168317_     51 AGAAATCTTAAAAGGAAATATAGACGTAAATCATCGTGACCTTGGATAAG 100
                          i  v     i   i   i    i?       v            i v  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_129168317_    101 GCAATGGTTT 110
                                   
  L1M4_orf2#LINE/    578 GCAATGGTTT 587

Transitions / transversions = 1.20 (12 / 10)
Gap_init rate = 0.00 (0 / 110), avg. gap size = 0.00 (0 / 0)  

2175 17.11 1.43 22.18  chrX_129168317_129170851.rev      610  1655 (879)    L1M4_orf2#LINE/L1        1   829 (79)  

  chrX_129168317_    610 TGGAAAACCATACCAGTTTCATGAACAACAATACTTAACATTGTTAGGAT 659
                               ivi  v   vv      i iviv  v      i       i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129168317_    660 AGCAATAGTCCTCA--TTGATCTACAGTTGAAATGCAAGGTGTATAAAAA 707
                         i      v   i  --           v vv  i    vviv   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129168317_    708 TACAAGATGCTGTTTTTGGCAGAAATGAACTAACTGATCCTAAAATTCAT 757
                          v v  v   iv      -       vi  v i                 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_129168317_    758 GTGGAATTGCAATGGACCCTGAATGTCCGAAAAAAAAAAAAAAAGTCTGG 807
                         i     v     v      v    iv  i   v  ----------   v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA----------TCTTG 189

  chrX_129168317_    808 GAAAAGAA---CGAAGTAGAAGAACTCACAGTTTCTGATTTCAAAACTTA 854
                         i       --- i    v i  i       v  i ii             
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_129168317_    855 CAACACAACACCTCTACAAAACTACAGTAATCACAACCTTATAGTCCTGC 904
                          -------------      i            vi  vv i i  v   v
  L1M4_orf2#LINE/    240 C-------------TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_129168317_    905 CATAAGCATAGAAATATACAGTGGTAGAACAGAAC-AAGGGTCCAGAAAT 953
                               v     v     v viii i   i    i-i  i          
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_129168317_    954 CAGCCCATACATCAATGGAAAGCTGATTTTT-ATAAGGATGCCACAATCA 1002
                         v i         iv    vv ii       i- i    i     vi i  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_129168317_   1003 TTCAATAGGGAAAAA---GTCTTTTCAACCAATGGTTCTGGAACAACTGA 1049
                               i      i ---           v      v    i       i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_129168317_   1050 ATATCCACATGTGAA-GAATGCATTTGG-CCCCTATCTCATACTATATAG 1097
                            ?       ii  -     v v    -      i    i  i     v
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_129168317_   1098 AAAAATTAACTCAAAATGGATCAAAGAACTAAATGTGGGATCTACAACCA 1147
                                                ?   v        --------------
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-------------- 512

  chrX_129168317_   1148 GAAAATTATTTAAAAGAGTGCTCACTTCGGGAGCACATATATTAAAATTG 1197
                         -------------     i-----------------------     i -
  L1M4_orf2#LINE/    513 -------------AAGAGC-----------------------TAAAACT- 525

  chrX_129168317_   1198 GAACGATGCAGAGAAGATTAGCATGGCCCTTGAGCAAGGATGACACGATA 1247
                         --------------------------------------------------
  L1M4_orf2#LINE/    526 -------------------------------------------------- 525

  chrX_129168317_   1248 ATTTGTGAAACATTCTGTATTTTGGGGATTTTTGGAGCAGGGACAGGGAA 1297
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    526 -------------------------------------------------A 526

  chrX_129168317_   1298 TAAGAGCTTGCTCTGTTTTTACTACTATTATTATTTTTTAAATAATAAAA 1347
                            i -----    -------------------------------  i  
  L1M4_orf2#LINE/    527 TAAAA-----CTCT-------------------------------TAGAA 540

  chrX_129168317_   1348 GTTTTTAAAAAATTCTTTAAAAGGAGCATAAATGTAAATAATTATGATTG 1397
                          -----------------    ----    ii?      vv ii   iiv
  L1M4_orf2#LINE/    541 G-----------------AAAA----CATAGGNGTAAATCTTCGTGACCT 569

  chrX_129168317_   1398 TGGATTAGGCAACAATTTCTCAAGTGTGATACCCAATGCTGAAGCAACAA 1447
                            i        iii     i ii i   i   v  v  vv         
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_129168317_   1448 AAGAAAAAACACATGAATTGGACTTAATTAAAAGTAAAAATATTTGTGCC 1497
                                  i v  i          v  i    v      iv       i
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_129168317_   1498 TCAAAAAATATTATCAACAAAGTGAAAATACGACCCATATAGAGGGAGAA 1547
                              ii i i      v          v  i     i v iv       
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_129168317_   1548 AATGTTTGCAAATTCTAAGTCTCATAAGACTCTACTATG-AGAATACATA 1596
                            i         iv  vi   v     ivv  vv   v-      i   
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_129168317_   1597 AAGAAATCTCTCAACTCAAACACAAAAAGAAAAACAGCCC--TGTATAAA 1644
                              v   iv        vv i       v   i i   -- v? -   
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA-AAA 818

  chrX_129168317_   1645 ATGGGTGGAGG 1655
                              iii   
  L1M4_orf2#LINE/    819 ATGGGCAAAGG 829

Transitions / transversions = 1.24 (97 / 78)
Gap_init rate = 0.02 (20 / 829), avg. gap size = 12.35 (247 / 20)  

 339 23.40 0.00 0.00  chrX_129168317_129170851.rev     1950  2043 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_129168317_   1950 AAAAAAGGGTGGAGGACCCAATTAGACACTATTCCAAAGAAGACATAAAA 1999
                              v   iii    iiii v      i vi           i   v  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_129168317_   2000 ATGGCAAATAGATACATGAAAATATAATCAACACCATTAGTCAA 2043
                              v    iii         v  iv      i  ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (15 / 7)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3642 19.33 4.00 3.11  chrX_129172980_129174972.rev      616  1515 (478)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129172980_    616 TGGAAAACCAATCTAGTTTCATGAACTAGAAAGCT-AATATTTTTGAGAT 664
                               ivi vi i vv      i i i   ii  -      v  i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129172980_    665 GGCGATTCTCCCCAAGTTTGTCTGCAATTTGAATGCATGACCTACCAAAA 714
                            i  v        i  vi   i  iv  v  i   vvv    i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129172980_    715 TACCTTTTTTACAGAAATAGACAAGTCTGCCTTTTTTGCAGAAATAGACA 764
                          -  -------   ------------                   v    
  L1M4_orf2#LINE/    101 T-CC-------CAG------------CTGCCTTTTTTGCAGAAATTGACA 130

  chrX_129172980_    765 AGTCTATCCTAAAATTCACGTGTAATTCCAAAAATCCTCGAATAGCCAAA 814
                           iiv             ii  v  v v   iiiv  iv           
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chrX_129172980_    815 ACAATTTTGGAAAAGAA---CAATGGGGAAGAACCCACACTACTGAATTA 861
                              i   i       ---   v vv i  i  i      v iv    v
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_129172980_    862 AACAACTTACTACAAAGCTGCAGAAATCAAAACAGTGTAGATCTGTCATA 911
                         v v                i   v      i       i vv   v    
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_129172980_    912 AAAA-AGAAATATACAGCAATGGAATAGAAT-AAGAGTCTAGATATAAAC 959
                          ii -   v     v v              -i      i   v      
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_129172980_    960 CTATAAATTTATGGTCAATTGATTTTCAGCAAAGGTGCTACACTGATTCA 1009
                          i   v                     ii   i     i viviv     
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_129172980_   1010 ATGGG-AAACAATAGTGTTTTCAACAAATAGTTCTGTGACAACTGGATAT 1058
                              -   v      v            i  v   v            ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_129172980_   1059 TCATGTGAAAAATAATGTATTTGG-TCTCTATCCCATACCATAGACAAAA 1107
                         i  ii  v    v    v v    -i i   i i  i      v      
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_129172980_   1108 AAAAAATCACTCAAAATGGATCAAAGACCTAAAT---ACAGCCTAAAGCT 1154
                          v---- v               ?          --- v   -    i  
  L1M4_orf2#LINE/    481 AT----TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACT 525

  chrX_129172980_   1155 ATGAAACTGT-AGAAGAAAACACATAC-TAAATCTTTATGACCTTGAATT 1202
                           i     v -           i vi?-        ii        ii  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_129172980_   1203 AGGCAATGGTTTCTTAATTATGATACCAAAAGTACAAGTATGAAAATAAA 1252
                                         iv     i        i     i vv    v   
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_129172980_   1253 AAGTAGATGAATTGGGCTTCATTAAAATTAACAATGTTTGTACCTTGAAG 1302
                           i     i      i      i        v  iv     i i ii   
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_129172980_   1303 GACACTATCAAGAAAGTTGACCAGACAATCCACGGAAAGGGAGAAAATAT 1352
                                          -  vv      i    i   v            
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGT-GAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_129172980_   1353 TTGCAAATAATATAACTCATAAGAAGGTGGTATCCAGAATATATAAAGGA 1402
                                 v     v  v     iiiv v                   i 
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_129172980_   1403 TTCT-----CTCA------------CAA-CAGCCCACTTTAAAAGTAGAC 1434
                         i   -----    ------------   -i i    v  ?    i i i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_129172980_   1435 AAAGAACTTGAACAGACATTTTTCCAAAGA---TACACAAA--ATAAATA 1479
                             i i     i        i        ---  i     --iiv    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_129172980_   1480 TGCAAATTAAAAGATAGGCAATTCATTAGTCATTAT 1515
                         v   v  v       ivv   --   i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAA--CATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (96 / 74)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.05 (64 / 21)  


3571 23.40 0.88 0.88  chrX_129297599_129301222.rev     2228  3133 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_129297599_   2228 GGAAGAGATTCCATGTTCATGAATTGGAAGAATCAATATTATTAAAATGT 2277
                          i    v  i           i         v i      i    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_129297599_   2278 CCATACTACCCAAAGCAATCTACAGATTCAATGCAATCTCTATCAAAATA 2327
                          v     v      vii              i      i          v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_129297599_   2328 CCAGATA--TTATTCACAGAAATAGATAAAACAATCCTAAAGTGTACATA 2375
                             v i--  v  ii       v  i  ivii        i vi i  i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_129297599_   2376 GAATCATGGGAGG--CTCAGAATAGCCAAGGCTATCCTAAGCAAAAAGAA 2423
                            --   vi   -- i            ii v   i i iv  i     
  L1M4_orf2#LINE/    153 GAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_129297599_   2424 TAAAACTGGAAGAATCACATTACCTGACTTCAAATCATATTACAGAGCTA 2473
                         i   ii    i  v     i v  ii i      v v  i    i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_129297599_   2474 TAGTAACCAAAACAGCATGGCACTGGCATAAAAACA--CACACAGACCAA 2521
                         i     i   i    ii   i          ii i --  i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_129297599_   2522 TGGAACAGAATACAGAACCCAGAAACAAATACACAAACCTACAGTGAACT 2571
                              i     vv   ii       i   iv  i v ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_129297599_   2572 CATTTTCAACAAAGGTGCCAAGAACATACACTGGGGAAAAGATAGTCTCT 2621
                         v      i    i          v   v  v        ii       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_129297599_   2622 TCAATAAATGGTGCTGGGAAAATTGGATATCCATATGCAGAAGAATGAAA 2671
                             i              v  i      ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_129297599_   2672 CTAGACCCCTATCTCTCACCATATACAAAAATAAAATCAAAATGGATTAA 2721
                         i i        i   v                v  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_129297599_   2722 ATACTTAAATCTAAGACCTCAGATCATAAAACTACTACAAGAAAACTTTG 2771
                          v  i     v     v  v i ii        vi  v        v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_129297599_   2772 GGGAAAAATCTCCAGGACATCAGTCTCAGCAAAAATGTACTGAGTAATAC 2821
                          ? v   -   i iv   v ii vi vi    vii v vi iii  vv  
  L1M4_orf2#LINE/    551 GNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_129297599_   2822 CCCACAAGCACAGGCAACCAAAAGAAAACTGGAGAAATGGGATCACATCA 2871
                         v   v       i     v   ii    v i  v    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_129297599_   2872 AG-TTAAAAAGCTTCTGCACAGCAAAGGATACAATCAACAAAGTGATGAG 2920
                          i-       -   i  ii vv       i  v     v       vi  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_129297599_   2921 ACCACTCACAGAATGGGAGAAAATATTTGCAAAACACCCATATGACAAGG 2970
                           v  i                           v  ivi  v   i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_129297599_   2971 GATTAATAACCAGAATATGCAAGGAGCTCAAACAATTCTATAGGAAAAA- 3019
                           i vi  v         ii  i  i   vv    i  v   iv     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_129297599_   3020 ACATAATCATCCAATCAAAAAAATGGGCAAAAGATCTGAACAGATATTTC 3069
                            -   v i     i?     -        i   i    i   i     
  L1M4_orf2#LINE/    799 ACA-AATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_129297599_   3070 TCAAAAGAAAACATACACAAATAGCAAACAGGCATATGAGAAGGTCCTCC 3119
                           v      i i     --   i  v  i i   i    i   i v   v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACA--AATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_129297599_   3120 ACATCACTGATCAT 3133
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (131 / 77)
Gap_init rate = 0.01 (11 / 906), avg. gap size = 1.45 (16 / 11)  

 450 15.38 0.96 1.92  chrX_129297599_129301222.rev     3489  3592 (32)    L1M4_orf2#LINE/L1      806   908 (0)  

  chrX_129297599_   3489 ACCC-ATTAAAGAAATGGGCAAAGGACCATGAACAGACACTTCTCAAAAG 3537
                             -   ?  -              ii-    i     i     v    
  L1M4_orf2#LINE/    806 ACCCAATTWAA-AAATGGGCAAAGGATT-TGAATAGACATTTCTCCAAAG 853

  chrX_129297599_   3538 AAGACATAAAAGCAGCCAACAAGCATATGAAAAAATACTCAGCATCACTA 3587
                             i   v  iii     i     i       i  i    i     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_129297599_   3588 ATCAT 3592
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 6.50 (13 / 2)
Gap_init rate = 0.03 (3 / 103), avg. gap size = 1.00 (3 / 3)  


3083 27.32 1.22 0.77  chrX_129307270_129313662.rev     4999  5902 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129307270_   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5048
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129307270_   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129307270_   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_129307270_   5147 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5196
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_129307270_   5197 AACAAAGCTGGCAGCATCACACTACCTGACTCCAAACTATATTACAAGGC 5246
                                i   vi vv       v  ii i i    viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_129307270_   5247 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAAACC 5296
                          i      i   i    ii         i iv ii i         i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_129307270_   5297 AATGGAACACAAT--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 5344
                                i v   --    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_129307270_   5345 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATAGGGAAAGGATTCC 5394
                          vi    i  i     ivv  vv  i v  vv    i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_129307270_   5395 CTATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5444
                           v  i  i  i           v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_129307270_   5445 GAAACTGGATCCCTCCCTTACACCTTATACAAAAATTAATTCATGATGGA 5494
                            ii    i    v   i     v              i   vi     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_129307270_   5495 TTAAACACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5544
                          i ? v  i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_129307270_   5545 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5594
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_129307270_   5595 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5644
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_129307270_   5645 TTTAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCGGAGTGAAC 5694
                          iv  v v  i i   i  ii vv    i  v  i i  vvii      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_129307270_   5695 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACTTACTCCTCTGACAA 5744
                           i     i                 v       v i iviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_129307270_   5745 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5794
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_129307270_   5795 AAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 5840
                          i    ----   v  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_129307270_   5841 TCAAAAGAAGACAGTTACACAATG---AAAAAACACATGAAAAAGTGCTC 5887
                           v        i --    -    ---  v  i          ii     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATA--TACA-AATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_129307270_   5888 ATTATCACTGGCCAT 5902
                          vi    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (144 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


3216 27.31 0.44 0.44  chrX_129377313_129382664     3952  4859 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129377313_   3952 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4001
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129377313_   4002 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4051
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129377313_   4052 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4099
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_129377313_   4100 TATGGAACCAAAAAAGAGCCCTCATCGCCAAGTCAATCCTAAGCCAAAAG 4149
                                viiv  ii  v  vvv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_129377313_   4150 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4199
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_129377313_   4200 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4249
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_129377313_   4250 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 4297
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_129377313_   4298 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 4347
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_129377313_   4348 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4397
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_129377313_   4398 GAAACTGGATCCCTTCTTTACACCTTATACAAAAATCAATTCAAGATGGA 4447
                            ii    i    v i i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_129377313_   4448 TTCAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4497
                          iv?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_129377313_   4498 CTAGGCATTACCATCCAGGACAAAGGCGTGGGCAAGGACTTCATGTCCAA 4547
                         v    ?i v viv i iv   vvv  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_129377313_   4548 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 4597
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_129377313_   4598 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAGCAGAGTGAAC 4647
                          i   v v  i i   i  ii vv    i  v    i  iv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_129377313_   4648 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4697
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_129377313_   4698 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4747
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_129377313_   4748 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 4797
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_129377313_   4798 TCAAAAGAAGACATTTATGCTGCCAAAAAACACATGAAGAAATGCTCATC 4847
                           v        i  vi viiv     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_129377313_   4848 ATCACTGGCCAT 4859
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3144 27.75 0.44 0.44  chrX_129427429_129433670.rev     4844  5751 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129427429_   4844 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4893
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129427429_   4894 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4943
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129427429_   4944 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4991
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_129427429_   4992 TATGGAACCAAAAAAGAGCCTGCATCACCAAGTCAATCCTAGGCCAAAAG 5041
                                viiv  ii  v  v v  vi    iv     i iiivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_129427429_   5042 AACAAAGCCAGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5091
                                iii    vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_129427429_   5092 TGCAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5141
                          i      i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_129427429_   5142 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5189
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_129427429_   5190 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATAGGGAAAGGATTCC 5239
                          vi    i  i     ivv  vv  i v  vv    i       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_129427429_   5240 CTATTTAAGAAATGGTGCTGGGAAAACTGACTAGCCATATGTAGAAAGCT 5289
                           v  i  v              v     iv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_129427429_   5290 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5339
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_129427429_   5340 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5389
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_129427429_   5390 CTAGGCATTACCATTGAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5439
                         v    ?i v viv  viv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_129427429_   5440 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5489
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_129427429_   5490 TTTAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAGC 5539
                          iv  v v  i i   i  ii vv    i  v  i i  vv i     iv
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_129427429_   5540 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5589
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_129427429_   5590 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5639
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_129427429_   5640 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5689
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_129427429_   5690 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAAAGCTCATC 5739
                           v        i  vi viii     v  i          i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_129427429_   5740 ATCACTGACCAT 5751
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (149 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1418 29.39 6.53 0.93  chrX_129437668_129439298      500  1142 (489)    L1M4_orf2#LINE/L1      230   908 (0)  

  chrX_129437668_    500 TTAAGACTTATTATAAAACTGTAGTAATTAAGACAGGGTAGTATTTTCAT 549
                          i  i     i  i   i  ii      i       v  i   i vv   
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_129437668_    550 AGGAAGAGACAAATAATCCAATGTAATAGAAT--ACAGCACAGAGAGATA 597
                          i i v     v   ivi     v        -- v  iv    i v v 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_129437668_    598 CATACTGTACATGCTTTGACACTTCATATACAACTGAAATGGCA------ 641
                          --- ii     viv v v  v  v  v v i  viiii  v  ------
  L1M4_orf2#LINE/    330 C---CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_129437668_    642 -----TGAG--AAGCAT-GCATTTTTGATTAATAATGCAGTAAAAACTGA 683
                         -----  i --   v  - iv    ii iv   ii   v vi v     i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_129437668_    684 GTAT----AGG-ACAAAAATGAAAATTGACCCCTACAACACACCATATAT 728
                         i  ?---- v - v  i      iv v         vv           i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_129437668_    729 AAAAATCAACTTTAGGAAGATAAAGGACCAAAATGTGAAA----AAGC-- 772
                               i    iv iivi   v ?i    v      i i ----  i --
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_129437668_    773 -AAAACTTTTAGAA-----CATGGGAGGCTACCTTTGTATCCTCAGGATA 816
                         -      i      -----   i  ? vvv i   i  iv   ii  v  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_129437668_    817 AAGAAGAGTTTATAAAA---GAAGGAAAAAGTAGCAGAACCAAAGGAAAA 863
                         iiv  vi    v v i ---  vivv     i vv  v v    i     
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_129437668_    864 CATTGATACATTCAACTGCATTAAAATTAAGTACTTCTGTTTATCAAGAT 913
                         v  v    v   vi   v   i        iv    i   viv    iiv
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_129437668_    914 ACATCA-CAAAAGAGTGAAAGGACTGGCCACAAGGGGAGAGAAAAT-TTT 961
                            ii -   i i       i   viv     iiiv i        -   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_129437668_    962 GCAG--CATCTATGAGCCAATAAATGACTCATATCCAGAATATACAAATA 1009
                            i--   v   --- ii    iv    ii             i   v 
  L1M4_orf2#LINE/    727 GCAAATCATATAT---CTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_129437668_   1010 ACTTCTGAAAATCAACAAGAAAAAGACAGACAACCTAACAGAAAAATTAG 1059
                            ii iv  v    i  v         i i    i  iv?      vi 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_129437668_   1060 CAAAAGACTTAAATAGACAGTTGATAAAAGGGGAAATTCAAACAGCCAGT 1109
                             i  i  i        v  vviv    ii  v  v    ii    i 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_129437668_   1110 AA--ACATGAAAAGGTACTCAACTTGATTGGAAAA 1142
                           --          i i      v v ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (104 / 81)
Gap_init rate = 0.02 (16 / 679), avg. gap size = 3.00 (48 / 16)  


 358 16.22 14.41 6.31  chrX_129590573_129593294      354   464 (2258)    L1M4_orf2#LINE/L1      331   450 (458)  

  chrX_129590573_    354 CCATACAA--ATAGTCTCAATTGATTTTTGACAAAGGTGC-AAAACCAAT 400
                                v--  i   --          i     i     -  i    - 
  L1M4_orf2#LINE/    331 CCATACATTTATGGTC--AATTGATTTTCGACAAGGGTGCCAAGACCA-T 377

  chrX_129590573_    401 TCAATAG-------------TTTTTAACAAAATATTACTGGAGCAACTGG 437
                              i -------------    i      - iv i    ii       
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAA-TGGTGCTGGGACAACTGG 426

  chrX_129590573_    438 ACATCCACAGTTGGGAAAAGGAGGAGG 464
                          i ?     --  v-     i v  i 
  L1M4_orf2#LINE/    427 ATAKCCACA--TGC-AAAAGAATGAAG 450

Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.07 (8 / 120), avg. gap size = 2.88 (23 / 8)  

3815 20.99 1.29 3.55  chrX_129590573_129593294     1301  2229 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129590573_   1301 TGAAAAGACATTCCATGTTCATGGATT-GAAGACTTAATATTGTTAAGAT 1349
                           i     i  i               -                      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129590573_   1350 GTTCATACTACCCAAAGAGATCTACAGATTCAATGCAAGCCCTATCAAAA 1399
                          viv     v      vv               i    v           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129590573_   1400 CCCCAGTGACATTTTATTTTCACAGAAATAGGAAGAACAATTTTGCAATT 1449
                         i     ivi v    ---- ii       v iv iivii  ii iv    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTT----TTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_129590573_   1450 CATAGGGAAATCCATAAGATCACAAATAGCCAAATCAATATTGAGAAAGA 1499
                             v      v  vii  i vvi          v    v    i     
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_129590573_   1500 AGAA---AGCTGGAAGCATCACATTTCCTGATTTAAAAACT-ATTACAAA 1545
                             ---  i    i vv     i    ii    v      - i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_129590573_   1546 GTCGAAGTAATCAAAACAGTATGGTACTGGCTTAAAGATAGATATGTAGA 1595
                          iiiv         i     i          v   i      i  i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_129590573_   1596 CCAATGGCACAGAATGGAGATCCCAGAAATAAATCCATTCACACACACAC 1645
                         i      v i     v    vi           i    ------------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT------------ 334

  chrX_129590573_   1646 ACACACACACACACACACGTACAGTTAATTGATCTTCAACAAGAGCACCA 1695
                         --------------   iv  ii  i       i   i     i ii   
  L1M4_orf2#LINE/    335 --------------ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_129590573_   1696 AAAATACGCAACAGGGAAAGTACAGTCTCTTTAACAAACAGTGCTGGAAG 1745
                          i vi iv   ii       v i     i  i      ii       i v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_129590573_   1746 AACTGGATATCCACATGCAAAAGAGTACAATTGGACACTTATTTTACACC 1795
                                  ?              i iv i      v i  ii i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_129590573_   1796 ATACACAAAAATCAACTAAAAATGAATTA--GACTTAAATGTAGGACCTG 1843
                            i        i    v      i  i --   i        i  v  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_129590573_   1844 AAA-TGTAAAACTCCTAGATGAAAACA--GGGGGAAAGCTTCTTGACATT 1890
                            - i        i    v       --  ? v   v    v    v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_129590573_   1891 CGACTAGGCAATGATTTCATGTATATGACACCAAA-GCACGTGTAACAAA 1939
                         v ii         i    v iv             -    iv i      
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_129590573_   1940 ACAAA-TATAAACAAGTGGGTCTACATCAAACTAAAAAGTTTCTGTACAG 1988
                          v   -v   i i  i v  v  v       v v    ii  i   i vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_129590573_   1989 CAAAGGAAAAACTCAACAGACTGAAAAGTCAACCTATGGAATAGGATAAA 2038
                                v vvv    v i v       v     i ii    i   v   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_129590573_   2039 ATATTTATAAATCATATATCTGACAAAGGGTTAATCTCTAAAATATATAA 2088
                               ii               i  i  ii vi v  i i         
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_129590573_   2089 GGAACTCCTACAACTCAATAACAAAGAAACTTAACAGCCTAATTTTAAAA 2138
                         i      i             i   i i  -v  i i  i    -?    
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATT-WAAAA 818

  chrX_129590573_   2139 ACAAGTTAAGGACTTGAACAGACATTTCTCCAAAGAAGACACACAAATGG 2188
                          iii iv     i     i                    i i        
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_129590573_   2189 CCAATAGCTATGTGAAAAAAATGCTCAACATCACTAATCAT 2229
                               ivi ii      i -            ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (125 / 67)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.46 (45 / 13)  


 979 26.71 3.86 2.37  chrX_129617824_129623164.rev     3719  4055 (1286)    L1M4_orf2#LINE/L1       15   356 (552)  

  chrX_129617824_   3719 ATGTTCATG---TAGAAATCACAATATAGTAAATATGTCGGTACTCATGA 3765
                                  --- i   iv vi     v  v  v   v ii     viv 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_129617824_   3766 CATCAATCTTTAGATTCAATGCAATCTCTATCAAAATTTTAGCAAGGTAT 3815
                         v  ii    vi        i      i          iii   --v iv 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC--TGCCT 112

  chrX_129617824_   3816 TTCTGAAATAAA--GGCAAGATTATCCTAACATTTATGTAGAAAGGCACA 3863
                           i viv v   -- i    v v       v   i  i i    v   vi
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_129617824_   3864 AGTCCTATAAGAGCTAAATCAATCTCAAAAAAAAAATAAAAATAAAGTGG 3913
                         i v  i v  v   i   v      ii     i  i----  i     v 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG----AACAAAGTTG 208

  chrX_129617824_   3914 GAAGAATCAGTCTACACAATATTAAATTTTGCTATATAGCTACAGTAATC 3963
                           i  v   vv  v v    v i   vi  i   i v             
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_129617824_   3964 AAGACTGTGTGGTGCTTGT----GGACAGA--TACAGATCAATGGAACAG 4007
                              v       i  v i----   i   --  i            i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_129617824_   4008 AATAGAGAA--CAGAGAAAACTACCCACATAAATGCACCCAACTGACTTT 4055
                            v    i--    i v  --     i i vv iiivi   i   i   
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAA--ACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 1.25 (50 / 40)
Gap_init rate = 0.02 (8 / 342), avg. gap size = 2.62 (21 / 8)  

1691 26.62 4.62 0.74  chrX_129617824_129623164.rev     4310  4850 (491)    L1M4_orf2#LINE/L1      347   908 (0)  

  chrX_129617824_   4310 AATTAATTTTT--CAAATGTGCAAAAACAATTCAGTGGAGGGCATCTGAC 4357
                             i     i--   iv    v  i  v     i   i iivivv iii
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_129617824_   4358 CTTTTCAG----TGATACTGGAGAAATTGGACATCCATGGGTAAAATTAA 4403
                                i----  i i    iiv  i    i ?   iiv i    v-  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG-AA 445

  chrX_129617824_   4404 TGAACCTCAATCTAAACCTTACTCC---TGTAAAAATATACTCAAAATGG 4450
                             vi vi i ivv    i  v  --- ii      vv           
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_129617824_   4451 ATCATGGACTTACATTTAAAATATAAAATTATAAAACTTTTAGAGAAAAA 4500
                             ?i   i  v  v   i vv     i         i     ii    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_129617824_   4501 AATAGAAGAAAATTTTCAGGACCTAAGGTTAGACAAATAATTCTTAAACT 4550
                         v    i? v    i   iv     vi      i   vviv      i iv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_129617824_   4551 TGACACCAAAAACACAGTCCATAAAAGAAAAAAATTGATAAATTAGACTT 4600
                                    i    iv v i           - v        i     
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTT 644

  chrX_129617824_   4601 TATCAAAATTACA--TTTTTATTCTGGGAAAGACCGTGTTAGGAG----- 4643
                         i          v --i    i v  vvi  i   vv i i i  i-----
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_129617824_   4644 ---GATAA---ACAGAATGGGAGAAAACATTTGTAAACCACATATCCAAC 4687
                         ---  i  ---                i     i   i  i     ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_129617824_   4688 AAAGAATTAGTATCTAGGATATATAAAGAACTCTCA-AATTCAACGGTAA 4736
                           i i i v     i  i                i -  i    iii   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_129617824_   4737 AAAAAATAAATAATTCAATTAGAAAATTGAAAAAAGACATGAACAGACAT 4786
                            i -i      ii     ?i     v iv   i  iv    i      
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_129617824_   4787 TTCATGTAAAG--TATATGCAGGCGGCAAATAAGTGTTTTAAAAGATGGT 4834
                            - vi    --v    i  iii   v      iiiv v        v 
  L1M4_orf2#LINE/    844 TTC-TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_129617824_   4835 CAATATCATGAACCAT 4850
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (93 / 47)
Gap_init rate = 0.02 (12 / 562), avg. gap size = 2.42 (29 / 12)  


1224 22.14 1.11 0.00  chrX_129672469_129679145      208   478 (6199)    L1M4_orf2#LINE/L1      272   545 (363)  

  chrX_129672469_    208 ACTGGCATAACAACAGATACATATACCAATGGAACAAAATAGAGAGCTTA 257
                                   vi i   i i   v i        i i   v     iii 
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_129672469_    258 GAAATAAATCCATTCCTTTAAAGTCAATTGATTTTCAACAAACGTGCCAA 307
                                 i    v v    vi              i    iv       
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_129672469_    308 GAACACGCAA-GGAGAAAGGACAGTCTCTTCAATAAATGGTGCTGGGAAA 356
                           v  iv   -  i     i i     i     i              v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_129672469_    357 ACCGTATATGCACATTCAGAAGAATGACATTAAACC-TTATCTTACAC-A 404
                           i v   ?v     v  i        vi  ii   -i  i  i    - 
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_129672469_    405 TATACAAAAATCAATGCAATATGGATTAGGGACTTGAATGTAAGACCTAA 454
                                    i  iv   v      i ?i   i i         v    
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_129672469_    455 AGCTATAACATCACTATAAGAAAA 478
                          i      v iivi  v       
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAA 545

Transitions / transversions = 1.90 (38 / 20)
Gap_init rate = 0.01 (3 / 274), avg. gap size = 1.00 (3 / 3)  

3093 25.17 3.85 0.91  chrX_129672469_129679145     5303  6184 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129672469_   5303 TGGAAAAACATCCCGTGCTCATGGATAGGAGGAATCAATATCATGAAAAT 5352
                               i i     i  i        v   i  v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129672469_   5353 GGCCACACTGCCCAAAGTAATTTACAGATTTAATATTATCCCCATCAAGC 5402
                            v i   v      v i  i        i  iiiv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129672469_   5403 TACCA-TTGACTTTCT-GCATGGAATTAGAAAAAACTA--CTTAAAATTT 5448
                          v   -i  v    i -   - i    i-- v  i  i-- i       -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATT- 146

  chrX_129672469_   5449 CATATGGAACAAAAAAGAGCCCATA-TAGCCAAGACAATCCTAAGCAAAA 5497
                                  vviv  i ii    v -       i      i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_129672469_   5498 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAG 5547
                                  i      vv    i  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_129672469_   5548 GCTACGGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATACAGA 5597
                              i    i   i    ii         i iv ii i   i   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_129672469_   5598 CCAATGGAACAGAACAGAGACCTCAGAAATAATGCCACATATCTACAACC 5647
                         i        i    iv    vii         vv   i i  i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_129672469_   5648 ATCTGATTGTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5697
                          vi     v i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_129672469_   5698 CTATTTAATAAATGGTATTGGAAAAACTGGCTAGCCATATGCAGAAAACC 5747
                           v  i  i       ii   i v      v  ?   i     i  i vi
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_129672469_   5748 GAAACTGGACTCCTTCCTTACACCTAATACAAAAATTAACTCAAGATGGA 5797
                            ii     i   v   i     vv                  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_129672469_   5798 TTAAAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5847
                          i ?    i    i      v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_129672469_   5848 CTAGGCA-ATACCATTCATGAC----------------------TAAA-- 5872
                         v    ?i- v i -   i    ----------------------  i --
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_129672469_   5873 --ACACTAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTG 5920
                         --    i    i  vvi          vv     v  i    vi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_129672469_   5921 ATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGAA 5970
                           i   v v  i i   i  iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_129672469_   5971 CAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTATCCATCTGACA 6020
                         v  i     i                vv       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_129672469_   6021 AAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAT 6070
                          i  i  vi          v  i  i     ivv    v ---   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAAT 792

  chrX_129672469_   6071 GAAAA--CAAACAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGGCA 6118
                         i    --    i   i v  i?    i            v    i  i  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_129672469_   6119 CTTCTCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCT 6168
                         i     v        i  vi vi       i  i  i       i v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_129672469_   6169 CATCATCACCAGTCAT 6184
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (139 / 79)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.23 (42 / 13)  


1349 25.52 12.76 1.13  chrX_129794090_129797515     1676  2208 (1218)    L1M4_orf2#LINE/L1       16   610 (298)  

  chrX_129794090_   1676 TGTTCATGGCTTAGAAGACTCAATATT-TTAAGATCTGAAGTTAT--CGC 1722
                                  v  i       i      -       vvv  --  i-- v 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA--TACTCCCC 63

  chrX_129794090_   1723 ACATTCATTCTTGCTTTCAACAGGATTCTGTTAAAAATTCCAGCTGGATT 1772
                          v   v  iiviivv      ivi  i ivv v     i       vv  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chrX_129794090_   1773 TTTTCATAGAAATTGTCAGGATATTTCTAAAATTTCTATGGCCATGCATC 1822
                             -ii        v  i v iv i        iv     vv     -v
  L1M4_orf2#LINE/    114 TTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA-A 161

  chrX_129794090_   1823 TTGACT-AGAATAGGCAAAAACATTCTTGAGAAA-AAGATTAAAGTAGGA 1870
                         vv   i-       v     -  v      i   -    vi     v   
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_129794090_   1871 GTATTTACGCT----GATTTTAATATCTAAAATAAAGCTATGGTAATCAA 1916
                          v i i  i  ----i    i  v ii  vv i       ii        
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chrX_129794090_   1917 GATAATATGGTATTTATATATGAA--AACA----GATCCATGGAACAGAA 1960
                           i i i     i vii   v i --i   ----    v      i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_129794090_   1961 ATAA-AGTCAGGAAATAGACCAACTCACGTATTACCAAGTGATTTTTGAC 2009
                         v i -    vi      i   v iv  iv   vii   v       i   
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chrX_129794090_   2010 AATGACACCAAGGC--------------------GTC--------AAA-- 2029
                           v iii     i --------------------   --------   --
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_129794090_   2030 --------ACAACTAAATATCAGCATTGAAATAAATGAACCTTGTTTCAT 2071
                         --------      ii   ? vi   vv   vi      vi v vii v 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_129794090_   2072 ACCTTATACCATATACAAAAATAAACTCAAAATGGATCA------TAAAT 2115
                             i i               v                ------     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chrX_129794090_   2116 ATAAAAACTAAAACTTTAAAACTCTTAGAAGT---CATAAGAGATTATCT 2162
                         i   i i        v               v---    i ? vvv    
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_129794090_   2163 TTATGAACTGGAGGCTAGGCAAAGTTTTTTTAAATGT-ATA----AAGCA 2207
                          ii   v  v -  i       v v   i   i  i - i ----     
  L1M4_orf2#LINE/    561 TCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_129794090_   2208 C 2208
                          
  L1M4_orf2#LINE/    610 C 610

Transitions / transversions = 1.16 (72 / 62)
Gap_init rate = 0.03 (20 / 595), avg. gap size = 3.70 (74 / 20)  

 749 23.67 5.33 3.33  chrX_129794090_129797515     2637  2936 (490)    L1M4_orf2#LINE/L1      603   908 (0)  

  chrX_129794090_   2637 AAAAGACAAAAGCAAAAAATGATGAAATAAA-AAATGATATGTGTATTTC 2685
                              -  v      v   v  vi     i -    ------  v i   
  L1M4_orf2#LINE/    603 AAAAG-CACAAGCAACAAAAGAAAAAATAGATAAAT------TGGACTTC 645

  chrX_129794090_   2686 ATAAAAACCAAAAATGTCTACTCATCAAAAAACAACATTAAGAAAATAAG 2735
                           v    ii     iv i iiv v     ii   vi  i      i i i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_129794090_   2736 AAGACAAGCCATTGTACTGAAAAATATATTTGTGAAACATATAACTGACA 2785
                                v   iv v iv i i  v       ii  v      v    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_129794090_   2786 AATGACTCACACACAGAACATGTGAAGAACTCTTACAACTCAATGATAAA 2835
                          iv    iii iv     i  i i                    i     
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_129794090_   2836 AA--TAAGCAACCCAAT--AAAAATGT-CTAAGTTTTTAAAACTTAGACA 2880
                           --i  ii        --       v- v   vv   i  ---      
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA---TAGACA 842

  chrX_129794090_   2881 TTTCATAGAAGAGTATCTACCAATGGCCAGTAA----------AGATGCT 2920
                             vivi    iv  v   v        i   ----------       
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_129794090_   2921 CAGCAACGTTAGCCAT 2936
                           i  v i????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (42 / 29)
Gap_init rate = 0.03 (8 / 306), avg. gap size = 3.25 (26 / 8)  


 239 21.21 4.55 13.64  chrX_129812068_129816090.rev     1913  2044 (1979)  C L1M4_orf2#LINE/L1   (783)   125     6  

C chrX_129812068_   2044 AGACATACTCTGTTCATGGATTAGAAGACTTATTAGGAGAGTTAAGATAG 1995
                            i  v iv            i         v  vv---        i 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATT---GTTAAGATGG 52

C chrX_129812068_   1994 TAAATATGTCAGTTCTCCCCCAAATGATCTATA-ACTTAATTCCCCTCCT 1946
                         i  -  --------      v  v       i - i i  iv vvii   
  L1M4_orf2#LINE/     53 CAA-TA--------CTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

C chrX_129812068_   1945 AT-----TCCTAATTTTCTAAAACTTTTTATCATAAAT 1913
                           -----   i ii vi  -----     i-  v    
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCT-----TTTTTG-CAGAAAT 125

Transitions / transversions = 1.33 (16 / 12)
Gap_init rate = 0.06 (7 / 120), avg. gap size = 3.43 (24 / 7)  

2571 23.18 3.22 8.84  chrX_129812068_129816090.rev     2571  3532 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129812068_   2571 TGGAATGGAATAACATGCTCATGGAATAGAAGATTCAACATAGTAAAAAT 2620
                              v iv  vv    i       v i     i i  i  v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129812068_   2621 GTCAATTCTCCCTCCAAAT-GATTTGCAGGTTTAATGCAATTCCTATAAA 2669
                          v    v     --     -   i i   i  i  i     i     v  
  L1M4_orf2#LINE/     51 GGCAATACTCCC--CAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_129812068_   2670 AAT---ATCTGCAAAGTTTCCTTGTAGACATGGAAAAGTTTATTCTAAAA 2716
                            --- v    ----i  ii   i   v  v  v   i v  i      
  L1M4_orf2#LINE/     99 AATCCCAGCTGC----CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_129812068_   2717 TTTATATGGATGGGTGCA--GGCCCTACAATATGTAAAATGATCTCGACA 2764
                           i       --ii    --  v  i v    vvi    ii    i  v 
  L1M4_orf2#LINE/    145 TTCATATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_129812068_   2765 AAGAAAAACAAAGTAGGGATAATCAATCTACCCAATATTAAAGCTTTACT 2814
                              i        v  iiv v   vv  v      v i   i   ----
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT---- 238

  chrX_129812068_   2815 ATTAAATATTAAATACTAAGTATTATTATAAATAATAAATAAATGTTAAA 2864
                         ------------------------ i  i   ------------ i  --
  L1M4_orf2#LINE/    239 ------------------------ACTACAAA------------GCTA-- 250

  chrX_129812068_   2865 TAATATGAAGGTTTTAATATATGCCTTCAATAATCAAGGT--TGTGGAAT 2912
                         ---------------------------  i        ii--     v i
  L1M4_orf2#LINE/    251 ---------------------------CAGTAATCAAGACAGTGTGGTAC 273

  chrX_129812068_   2913 TGGCAGAGGGATAGGCACATAGATCAATGGAACTGAATAGAGAACTCAGA 2962
                              v i      i  i              iv    v    iii    
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_129812068_   2963 AGTGGACCCACACAAATGTGTCCAAGTAATTTTTGACAAAGTTGTCAAAA 3012
                          i ii     i   vv i  vi   v i     i     i v  i   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_129812068_   3013 T-ATATCACTGGAGGAAGGATAAACTTTGTAACAAATGGTGCTAGAGGTA 3061
                         i-  -   v   i i   i   iv    vi             i iivv 
  L1M4_orf2#LINE/    374 CCAT-TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_129812068_   3062 TTGGACATTCATAGACAACA-AATGACCCTTAACTTAAACCTCATACCTT 3110
                         i    i ?i  i vi   v -     vvi vi  iivv      i   v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_129812068_   3111 ATA--AAAGTT----CAAAATGGATCATGGACTTCAATGTAAAACATAAA 3154
                            --   i  ----            ?i   i v       i vv    
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_129812068_   3155 ATTATAAAACTTTTTAAAAAAGTTTTTTAAGTAGGAGAAAATCTTCAGGG 3204
                          i         i  vi  i  i------ vi    ? v        iv i
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAA------ACATAGGNGTAAATCTTCGTGA 566

  chrX_129812068_   3205 TCTAAGGCTAGACAAGGATTTATTAAATTTGACACTAAAAATACAATTTA 3254
                         i  vi  i   i   v i   v   i  v      i    ii    viv 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_129812068_   3255 TAAAAGGAAAAAATTGATAA----GACTTCATCAAAATAAAAAACTTTTT 3300
                         i     -       v     ----              v          v
  L1M4_orf2#LINE/    617 CAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chrX_129812068_   3301 CTCTGCAAAGGACCCTATTAAGAGGATGAAACAACAAGCTACAGAGTGGG 3350
                         iv  v        v    i    iii     vi    v i     i    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_129812068_   3351 AGAAAATATCTGCAAACCACATATCC-AGAAAGGACA-ATATTTAGAGTA 3398
                                  i      i  i     i- v  i    v-i   ii   i  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_129812068_   3399 TAGGAGTAACCC--A-AACTCAGCAGTTTAAA---AAAT---CCAATTAA 3439
                           vi iv   i -- -      ii i vv   ---    ---      ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_129812068_   3440 ATAATAGAAAAAAGACATAAACAGACATTTCACTGAGGATGATATACAGA 3489
                          v   i iv   i  iv i  i         v ii i  v        i 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_129812068_   3490 TGGCAAATAAGTACATGGAAAGATATTCAACATTATTAGTGAT 3532
                             v      i     i      ii       i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (137 / 82)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 4.83 (116 / 24)  


3269 26.54 0.66 0.66  chrX_129817941_129824215     4875  5782 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129817941_   4875 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4924
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129817941_   4925 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4974
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129817941_   4975 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5022
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_129817941_   5023 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5072
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_129817941_   5073 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5122
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_129817941_   5123 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5172
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_129817941_   5173 AATGGAACAGAAT--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5220
                                i     --    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_129817941_   5221 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5270
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_129817941_   5271 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACT 5320
                           v  i  i              v      v  ?   i   i i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_129817941_   5321 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5370
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_129817941_   5371 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5420
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_129817941_   5421 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5470
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_129817941_   5471 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGGCAAATGGTACCTAA 5520
                         i            vvi          vv     v ii    v v  i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_129817941_   5521 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5570
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_129817941_   5571 AGGCAACCTACAACATGGGAGAAAATTTTCGCAA--CGTACTCATCTGAC 5618
                           i     i   iv            v  i    -- i  i--      i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGAT 744

  chrX_129817941_   5619 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5668
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_129817941_   5669 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5718
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_129817941_   5719 TCTCAAAAGAAGACATTTATGCAGCCAAAAAATACGTGAAAAAATGCTCA 5768
                             v        i  vi viii     v  ii  i      i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_129817941_   5769 TCATCACTGGCCAT 5782
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


3492 22.83 4.22 0.57  chrX_129878459_129882815.rev     2991  3866 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129878459_   2991 TGGAAAG-----TTATGTTTATGGATCAGAAAGCTCAATAATGATAAGAT 3035
                                -----ii     i      ii   ii  i    v  v      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129878459_   3036 AGCAGTTTTCTCCAAATTGATCTACAGATTCATCATAATCCCATTCAAAA 3085
                         i   i vi  i                     v ii      vv      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129878459_   3086 TCCCAGTAGGCTTCTGTATAGATATTGACAAGTTGATTCTAAAATTTACA 3135
                               iv v   i v ii   v         i    i        i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_129878459_   3136 TAGGAATTCAAAGGACCTAGATGTGTCAAAAATAACTTTAATAAAAAACG 3185
                          i i   v   i     i   -i iv v    i  ii  i -    i v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGA-ATAGCCAAAACAATCTTGA-AAAAGAAG 198

  chrX_129878459_   3186 AATAA----------------CTGCCTGGTTTTAAGATTTATAGTAAAGG 3219
                           i  ----------------  v  iii   i  i i   ivii    v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_129878459_   3220 TATAATAATCAAGATAGTATAGTATTGGTATAAAAACAGACTTATATATC 3269
                           i i         i   i i   i   i    ii i    v    v   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_129878459_   3270 AATAGAACAGAATAGAGAGTCCA-AAATAGACCCACACATATAAGGTCAT 3318
                            i   i     v         -     i     i    v  v     v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_129878459_   3319 TTGATTTTTCACAAAGATGGCAAGGCAATTTAATGGGGAAA------TCT 3362
                                 iv    i i  v    i v   i          ------   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_129878459_   3363 TTTTCAACAAAC--TTCTGAAACAA-TGGAAAGATCACGTATAAAAAAGT 3409
                            -       i-- v   ii    -    v ?-i   i ii    i i 
  L1M4_orf2#LINE/    399 TTT-CAACAAATGGTGCTGGGACAACTGGATAK-CCACATGCAAAAGAAT 446

  chrX_129878459_   3410 AGGGCCTCAGCCCTTATCTCATGTTATATATAAAAATTAACTCAAAATGG 3459
                         iii i- vii   i  i    iiii     i                   
  L1M4_orf2#LINE/    447 GAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_129878459_   3460 ATCAAAGACTTAAAAGTAAGAGCTAAAACTATAAAACTTCCAGCACAACA 3509
                             ?    i    v                       iii  v v  v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_129878459_   3510 CTTAATAGAAACTCTAAGTGACTTTACATTTGGCAAAGATTTTCTAAATA 3559
                          v  iv? v  v   vv     i  ivi  v     v i   ii  i   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_129878459_   3560 GAATACAATAAGCATGAG-GACTTAAGCAAAA-TCAATAA-TTGGACTTC 3606
                         vi i  v v     ii  -i  vv   v    - vi    -         
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_129878459_   3607 ATCAAAATTAAAAACTATTGTTTCCTAAAAAATACTATTAGTAAAATAAA 3656
                                         v    viiii   ii i     i iv   i i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_129878459_   3657 AAGGCAAGTCACAGA-TGGGAGAAAACATTTACAAATCACATATCCAATA 3705
                            i   vi      -          i    i       i     ii   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_129878459_   3706 AAGGACTTGTATCTAGAATATATAAAGAATTTTTATAACTCAATAATAAG 3755
                          i           i               i i   i             i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_129878459_   3756 AAGATAAGCAATACACT--AAAAATAGGCAATAGATTAGAATAGACACTT 3803
                             i  ii  iv  v --      i     vi    v         i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_129878459_   3804 CACGAAAGAAGAAATACAAATGGCAAATATGTACATGAAAAGATGTTCAA 3853
                          v v        v           v    v i             i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_129878459_   3854 CATCATTTGTCCT 3866
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.18 (135 / 62)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.62 (42 / 16)  


2841 24.38 5.64 3.16  chrX_129964911_129970222.rev      852  1737 (3575)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129964911_    852 TGGAAAGATATTCTATATTCATTGAATGGAAGAATCCTTATTGTTAAAAT 901
                                    i i  i     v  v       v ivv         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129964911_    902 TTCTATCAAGACTACCTAAAGCAACCTACAGATTCAATGCAATCTCCATT 951
                         ----iv   v   v  i   vii i            i      i i  i
  L1M4_orf2#LINE/     51 ----GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_129964911_    952 AAAATACCAATGATATTCTTCACAGAAATAGAAAAAAACTG-TCCTAAAA 1000
                              v   iiviiv  i  ii       v  v  i--   -        
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAA 144

  chrX_129964911_   1001 TTTATATGGAACCACAAAAGACCCAGTATAGCCAAAGCTATCCTAAGCAA 1050
                           i        vii   ii       v         i v   i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_129964911_   1051 AAAGAACAAA-CTGGAGAAATCATATTATCGGACTTCAAATTATACTAAT 1099
                         i         -i     i v   i i vi vi i      viv     -i
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA-C 243

  chrX_129964911_   1100 AAAGCAATAATAACCAAAATAGTATGGTACTGGGATAAAAACAAGCACAT 1149
                              v i i   i   i i   i         v    ii i ii  i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_129964911_   1150 ATACCAATGGAACAGAATAGAGAACTCGGAAAAAAAATCCACATACCTA- 1198
                          v i        i     v    iii i    v   -i   i i ii  -
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA-CCCATACATTTAT 342

  chrX_129964911_   1199 ------------------------------------CACTGGGGAAAGGA 1212
                         ------------------------------------  v         i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_129964911_   1213 TAGTCTCTTAAATAAATGGTGTTGAAAAAACTGGATATCCATAACTATAT 1262
                               i  v  i        i  ii v         ?   i ------ 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA------T 436

  chrX_129964911_   1263 GCAAAAGAATGAAACTAGACAGACCGTATCACACTATATCTCACCATATA 1312
                                      ii i   ---  v  i v   --------        
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGAC---CCCTACCTCAC--------ACCATATA 475

  chrX_129964911_   1313 CAAAAATCAAATACAAATGTATTAAAGTCTTAAATCTAAGACCTCAAACT 1362
                                i  v vv     v  i ?  v i     v     v  v     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_129964911_   1363 GTAGAATTACTACAAGAAAAC-TGGAAAT---TCTCTGGGACATCATTCT 1408
                         i  i  i vi  v        - i i?i ---   ii v   v iivvi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_129964911_   1409 AGGCAAAGATTTCTTGAGTAATACCTCACAAGCATAGGATACCAAAGCAA 1458
                               v i      iii  vv  vi  v     i i vv  v    v  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_129964911_   1459 AAATGGACAAATGGGATCACATCAAG-TTAAAAAGCTTCTACACAGCAAA 1507
                             i  i    v   iiv      i-       -   i iii vv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAA 674

  chrX_129964911_   1508 GGAAACAGTCACCAAAGTGAAGAGACAACCCACAAAATGGGAGAAAATAT 1557
                            v  vi   vv        i            i               
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_129964911_   1558 TTGCAAACTACTCATCTGACAAGGGATTAATTATCAGAATATATAAGGAG 1607
                                ii ivi      i      i vi vvi            i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_129964911_   1608 CTCGAACAACTCTGTAGGGGAAAAAAACTAATGATTTGAGTAAAAAGTGG 1657
                            vv       vi  iv--     i  v   i iiii v ?    i   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAAT--AAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_129964911_   1658 GCAAAATATTTGAATAGACATTTCT-----GAAGACATACAGGTGGCAAA 1702
                              iv                  -----     i     ii    v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_129964911_   1703 CA-GCATATGAAAAGGTGCTCAACTTCACTGATTAT 1737
                         i -   i        i        v   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (135 / 77)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 4.59 (78 / 17)  

3415 23.88 2.23 0.89  chrX_129964911_129970222.rev     3926  4821 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129964911_   3926 TGGAAAGATATCTCATGTTCATGGA-----AGAGTTAATATTGTTAAAAT 3970
                                     i            -----   v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129964911_   3971 GTACATGCTATGAAAAGAAATCCACAGATTTAATGTAATCCCTACCAAAA 4020
                          vvv  i  vivv   vvi   i       i  i i        i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129964911_   4021 CTCCAGTAGCATTTAAAATAAAACATAGAAGAAATAACCCTATAAGTCAT 4070
                         ii    iv  v   vvvii i  -  v  vi iv i i    v  v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_129964911_   4071 TTGAAACTGCAAAAGACTCCAAATAGACAAAGCAATCTTGAGCAAGAATA 4120
                         v  i  v     ii   i vi     v    i         iv     v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_129964911_   4121 ACAAAGCTACAGGCATCACACTTCCAGATTGTAAATTATATTACAAAGCT 4170
                               i iv   vv          vi   vi   viv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_129964911_   4171 ATAGTAATCAAAACAGAGTGGTA-TGGCATAAAAACAGCCATATAGACCA 4219
                          i         i    v      -        ii i  v        i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_129964911_   4220 GTGGAATAGAATAGAGAGCCCAGAAATAAACCCACACATATACAGTCAAC 4269
                         i           v     i               i    v  ii     i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_129964911_   4270 TAATTTTTCACGAGGGTGCCAAGAATACAAAATGAGGAAAGGATAGCTTC 4319
                          i     iv  i            vi ivv    i      i    ii i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_129964911_   4320 TTTAATAAATGATGCTGGGAAAACTGGATATCCACATACAAAATAATTAA 4369
                           i  i     i        v         ?      i     v   v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_129964911_   4370 -TTGGACCTTTAT-----ATCATACACAAAATTCAACTCAAA-TGGATTA 4412
                         -       ii  i----- i    i      v i        -     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_129964911_   4413 AAGACTTAAATATAAGATGAACAACTATCAGGA-----AAAAGAAAACAT 4457
                         ?    i     i     vvv v      - ii ----- i          
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chrX_129964911_   4458 AAGGAAAAAGTTCCTTAATGTTCGTCTTGGCAATTATTTTTAAAATATGA 4507
                          i ?iv   vi i v i iv  v vi v      vi   i v i      
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_129964911_   4508 TACTGAAAGCACAGGCAACAAAAGCAGAAACAAACAAATGGGATCATATC 4557
                         i  ii        i          v i   i i i    v   iivi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_129964911_   4558 AAG-CTAAAAATCTCTGCACAGTAAAGGAAACAATCAACAAAATGAAAAG 4606
                           i-i      ii i  ii vvi      v  v     v   i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_129964911_   4607 GCAGTCTGCACAATGGGAGAAAATATTTGCAAACTGTATATTTGTTAAGG 4656
                         i  ii ii  v                      iii     i  v     
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_129964911_   4657 GGTTAATATTTTAAAAATATATACAAGGAACTCATACAACTGAATGGCAA 4706
                          ii vi   ii-- i        -- i      v       v   iii  
  L1M4_orf2#LINE/    749 GACTTGTATCC--AGAATATATA--AAGAACTCTTACAACTCAATAATAA 794

  chrX_129964911_   4707 AAA-ATAATAACAACCTGATTTTAAAATGGACAAAGAACTTGAATCAATA 4755
                            - i  -- i    ii   ?v       i     i i      vi i 
  L1M4_orf2#LINE/    795 AAAGACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_129964911_   4756 TATCTCAAAAGAAGACATACAAATGGCCTACAGGCATATGAAAAAGTGCT 4805
                          v    v        i            v i i   i       ii    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_129964911_   4806 CAACATCACTAATCAT 4821
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (135 / 75)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.15 (28 / 13)  


 423 26.55 6.55 4.73  chrX_129982975_129989252.rev        8   282 (5996)    L1M4_orf2#LINE/L1      423   702 (206)  

  chrX_129982975_      8 CCAGAAATCTACATAGAAAAAAAATGAGCCATAACCCCTATATCGCACCA 57
                          ii  v ? i    - v    i     ivivvi       iv  i     
  L1M4_orf2#LINE/    423 CTGGATAKCCACAT-GCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_129982975_     58 -----AAAAACTTGATTCAAGATGGAGCACAGAACTAAATATGGAAAACT 102
                         -----     -  i i    i     v  ?   v      i i- i i  
  L1M4_orf2#LINE/    472 TATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTA-AGAGCT 519

  chrX_129982975_    103 AGGACTACAAAGTTTATGGAAGAAAGCACAGAAAAAGAACTTCATAAACA 152
                          ii    i   ii iv i       i  i  i?iv i v    i i v -
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC- 568

  chrX_129982975_    153 TTGAGT-AGGAAAAAATTATACAGAGAAGAGACAAAAA----AAG-AGTA 196
                            i  -   v  vii  vivi   v v  v  v    ----   - ii 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_129982975_    197 AAATAACATTTCTAAAAT-GACACATTGGACTTAATCAAAAT-AAAAATA 244
                            v  -------     -  i v         v        -     iv
  L1M4_orf2#LINE/    619 AAAGAA-------AAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_129982975_    245 TTTCTGCTTGTTAAAAGACAC-----AGATGGGAAAAAGACAA 282
                            v     --i   i     -----   vi vi         
  L1M4_orf2#LINE/    662 TTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

Transitions / transversions = 1.59 (43 / 27)
Gap_init rate = 0.05 (13 / 280), avg. gap size = 2.38 (31 / 13)  

3211 27.31 0.44 0.44  chrX_129982975_129989252.rev     4880  5787 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_129982975_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGCAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v  v   v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_129982975_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_129982975_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_129982975_   5028 TATGGAACCAAAAAAGAGCCCACATTGCCAAATCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  viv  v      v     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_129982975_   5078 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_129982975_   5128 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii       v i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_129982975_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5225
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_129982975_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_129982975_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5325
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_129982975_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_129982975_   5376 TTAAAGACTTAAATGTTAGACCTAAAACCATGAAAACCCTAGAGAAAAAC 5425
                          i ?    i       v   v       i  i   vi i    ii     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_129982975_   5426 CTAGGCTTTACCATTGAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5475
                         v    ?v v viv  viv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_129982975_   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAG 5525
                         i            vvi          vv     v  i    v   ii vi
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_129982975_   5526 TTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAAC 5575
                          i   v v  i ii  i  ii vv    i  v  i i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_129982975_   5576 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5625
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_129982975_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_129982975_   5676 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_129982975_   5726 TCAAAAGAAGACATTTATGCAGCCAAAACACACATGAAAAAATGCTCACC 5775
                           v        i  vi viii     v vi          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_129982975_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1617 24.76 3.67 5.27  chrX_129993486_129995103.rev      502  1127 (491)    L1M4_orf2#LINE/L1      293   908 (0)  

  chrX_129993486_    502 TAGGTTAATG-AACAGAATAGAAAACTCTGAAATGGACCCACACAAATAT 550
                            i i    -  i     v  i iii v     ii     i   vv   
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_129993486_    551 GCTCAGCTGATTTTTGACAAAGATGTGAAGACAATTCAATAAAGCAAGTA 600
                          v   ii       i     i i  iv     v       iii v   v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_129993486_    601 TAGTCCTTCTAACAAATAGTGTTGGAGCAATTGGAATTACAAACATGTGT 650
                              i  ii       i   i   ii   i    --  -----------
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA--TA----------- 429

  chrX_129993486_    651 GCACGCATGCACACACACACACAGAGACAACTTCAACTGAAAATTCAAAC 700
                         ? - i      v ---------   - ii ---- ii  i --ii vv  
  L1M4_orf2#LINE/    430 KC-CACATGCAAA---------AGA-ATGA----AGTTGGA--CCCCTAC 462

  chrX_129993486_    701 CTCACACCTTATGTAAAATTTAAATCAAA------CATTAACTTAAATTT 744
                                 v   ii    v    v     ------  ?vi  i     v 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_129993486_    745 AAAACATAAACCTATAAGACGTCTATAA-AAATCATAGGAGAAAA-CTGC 792
                           i vv    v      i  vii  v  -   v      ? v   -  v 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_129993486_    793 AAGATCTAGGGCTAGGGAATTAATTCTTAGAGTTAACACCAAAAGCATAA 842
                         iv  i  v   i    v   viv        vv i            i  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_129993486_    843 TGCA-TAAAATAATAAATTAACAAACTGGACATCATCAAAATTAAAAATT 891
                         -   -i    v  v    vi i   i     v                --
  L1M4_orf2#LINE/    613 -GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-- 659

  chrX_129993486_    892 CTCTTTTGC---AAAAGCCCAGGTGAAGAACATGAAAA--TAAGGCATAG 936
                           i  v   ---   i v vvvi v     vi      --i  vv  i  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_129993486_    937 ATTTGAAGGAAGTATTTGCAAACCAGCTATCTGACAAAGAACTAATATCT 986
                          v v i  i  i          i  vv       i  i i   vi    i
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_129993486_    987 ATAACATACAAA-AACTTTGAAAACTCAACATTTAAAA-------AATCC 1028
                          v  i   i   -    i v v       i v v    -------  i  
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_129993486_   1029 AATGAGAAAACCAGCAGAGGACATGAGCAGACATTTCACTGAGGAGAATA 1078
                            v?i    ivi   i    iv   ii         v ii i  ii   
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_129993486_   1079 TACAGATGGTAAATAAGCACATTAAAAGCTATTCAACATCATTAGCCAT 1127
                             i    iv           v     v ii         ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (89 / 62)
Gap_init rate = 0.03 (18 / 616), avg. gap size = 3.11 (56 / 18)  


3100 26.22 1.44 1.00  chrX_130001038_130003149      716  1619 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130001038_    716 TGGAAACACATCCCATGTTCATGGATGGGTAGAATCAATATTGTGAAAAT 765
                               v i                 v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130001038_    766 GACCATACTGCCAAAAGCAATCTATAAATTCAATGTAATTTCCATCAAAA 815
                          i v     v  v   vii     i i      i i   ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130001038_    816 TACCGTCATCATTCTTCACAGAAGTAGAAAAAC-AATCTTGAAATTCATA 864
                          v  iv vv v  i  ii     i v  v  i -i   i i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_130001038_    865 TGGAACCAAAAAAGAGCCCGCATGGCCAAAGCAAGACTAAACAAAAATAA 914
                              viiv  ii  v  v v  i      i   vvi i  v  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_130001038_    915 CAAATCTGGAGGCAACACGTTACCTGACTTCAAACTATACTACAAGGCTA 964
                             vi      vvv   ii v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_130001038_    965 TATTTACCAAAACAGCATGGTACTGGTATAA-AACAGGCATGTAGACCAA 1013
                         i v v i   i    ii         i    -i i  i   i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_130001038_   1014 TGGAACAAAATAGAGGACCCAGAAATAAAGCCAAATACTTACAGCCAATT 1063
                              i i   v   iii           v   v i i   ii i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_130001038_   1064 GATCTTTGACAAAGCAAACAAAAACGTAAATTGGGAAAAGGGCACCCTAT 1113
                            i  i     i vviv   i v i vv v    i    iii vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_130001038_   1114 TCAACAAATGGTTCTGGGATAATTGGCAAGCCTCATGTAGAAGAATGAAA 1163
                                     v      i  i   vv ?  v    i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_130001038_   1164 TTGGATCCTCATCTCCTACTTTATACAAAAATTAACTCGTGATAGATCAA 1213
                              i  ii i   vi  iv                 ivi  i     ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_130001038_   1214 AAACTTAAACCTAAGACCCGAAACCATAAATATTCT-AGAATATAACATC 1262
                          i  i    iv     v ii    i     - i   -    v v     v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATA 549

  chrX_130001038_   1263 AGAAAAACTCTTCTAGACATTGGTTTAGGCAAAGAGTTC------ATGAC 1306
                         i ?iv  v     vv   v    v        v iv   ------     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_130001038_   1307 AAAGAACTCAAAAGCAAATGCAATAAAAACAAAGATAAATACATGGGACT 1356
                          ------i        v v    i    iv   i   i   v  v     
  L1M4_orf2#LINE/    600 A------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_130001038_   1357 TAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACAATCAGCAGAGTA 1406
                          v  i   v v    i   i  ii vv    i  v  v    iv i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_130001038_   1407 AACAGACAACCCACAGAGTGGGAGAAAATATTCGCAAACTGTGCATCCAC 1456
                           v              i              i     iii ii   iiv
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_130001038_   1457 CAAAGGACTAATATCCAGAATCTACAAGGATCTCAAACAAATCAACAAGA 1506
                         i  i     vi          v  i  i  v   vv    v    i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_130001038_   1507 ATAAAACAAATTGTCTCATCAAAAACTGGGGTAAGGA----GATAGACAA 1552
                          v  i      vii iv  i?    v    vv     ----i       v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_130001038_   1553 TTCTCAAAAGAAGATATTTAAATGGCCAAAAACCCCATGATAAAAAATGC 1602
                              v           vi          v  v v     --   i    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA--AAAGATGC 891

  chrX_130001038_   1603 TCAATATCACTAATTAT 1619
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (133 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.75 (22 / 8)  


3196 26.66 1.00 0.55  chrX_130012032_130014672.rev     1247  2150 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130012032_   1247 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1296
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130012032_   1297 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1346
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130012032_   1347 TACCAA-TGACTT-----CAAAGAATTGGAAAAAACT-ACTTTAAAGTTC 1389
                          v   i-  v   -----  i -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_130012032_   1390 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGGCAATCCTAAGCCAAAA 1439
                                 viiv  ii  v  v v  v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_130012032_   1440 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGC 1489
                                 i      vv       v  ii i      viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_130012032_   1490 CTACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGAT 1539
                                  i   i    ii       v i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_130012032_   1540 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATGTCTACAAC 1587
                                 i    i--    i  --        vv   i ii i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_130012032_   1588 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 1637
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_130012032_   1638 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1687
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_130012032_   1688 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 1737
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_130012032_   1738 ATTAAACACTTAAACGTTAGACGTAAAACCATAAAAGCCCTAGAAGAAAA 1787
                           i ? v  i    i  v   vv      i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_130012032_   1788 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 1837
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_130012032_   1838 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 1887
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_130012032_   1888 ATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1937
                           i   v v  i ii  i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_130012032_   1938 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 1987
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_130012032_   1988 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 2037
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_130012032_   2038 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 2087
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_130012032_   2088 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAGAATGCTCAT 2137
                            v        i  vi viii     v  i         ii       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_130012032_   2138 CATCACTGGCCAT 2150
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (140 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  


1895 25.00 9.69 0.62  chrX_130041475_130043115.rev      503  1142 (499)    L1M4_orf2#LINE/L1      167   864 (44)  

  chrX_130041475_    503 CTAAAATAGCCAATACAATTTTGAAAAATAACAACA---TTGGAAGACTT 549
                          i i         v     i        v  v    ---     i    i
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_130041475_    550 ACATTGCTTGCTTCCAAGACTTAGTGTAAAGTTACAATG-TCAAGA---- 594
                            i v iiiv  i   i     v ii    i    i i-      ----
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_130041475_    595 -------------AAAAATG-----ATAGATCAATGAAACAAAAC--AGA 624
                         -------------  ii  i-----           i  i i  i--   
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_130041475_    625 GTCTAGAAAGAGATCCAAAATACAT--ATGATCGACCGATTTTCTACAAA 672
                            i     v i i   ---     --   i  i ii       v    i
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCA---TACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_130041475_    673 GGTGACTAAATAAGT-AGTGATGAAAGGATAGTATTCTCAGCAAATAATG 721
                             v v i iv v - i  iv     i     v  i   i     ii  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_130041475_    722 CTGGAACAATAGGACCACCACAAGCTAAA-AATGAGCTTTAACTTATAAG 770
                             i    iv   iv?     v  v   -     iv  vi  iiv  vv
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_130041475_    771 CTGTACCATATTTAAAAACTGACTCCAAAGGGATCATAGTTGTAAATGTT 820
                         iiii       vi     i i    v   v      ?  viv       v
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_130041475_    821 AAACCAAAACCTATAAAACTTGTGG--GGAAATTTA-------AT----G 857
                          i v v   v          iv i -- i   iv  -------  ---- 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_130041475_    858 TGATCT-GGGTTAGGGAAAGATTTCCTAGAAAGGACTCAAAAAACACAGA 906
                            i  -        v  v i    i    v v   v v    i    ii
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_130041475_    907 CAACAAAAGTAAATTTA-ATAAATTTGACTTTATCT---TTCCAAGCCTC 952
                                  v   vv  -       v     i   v---  vv  i i i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_130041475_    953 TACTCTTCAAATGGCACTGTTAAGGAAATAAACAGGCAAGCCACAGGCAG 1002
                          iiv       v i    i i   i  i i  v  i   v      ivv 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_130041475_   1003 ACAGAAA-TATTTTCAGAACACATGTCTGATAAAGGACTTGTATCCAGAA 1051
                         iv     -     v  i v  i  i        i                
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_130041475_   1052 TATATAAATAACTCTCACAGCTCAATAAGAATAAAACAAACAACCCAA-- 1099
                                 v      i   i        v  v  i     i       --
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_130041475_   1100 AGAAAATTTGACAA--GTTTCAAACAGACAATTC-------AAGATATCC 1140
                         ?i     v- i   -- v  ii  i     v   -------       v 
  L1M4_orf2#LINE/    814 WAAAAATG-GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_130041475_   1141 AA 1142
                           
  L1M4_orf2#LINE/    863 AA 864

Transitions / transversions = 1.49 (94 / 63)
Gap_init rate = 0.03 (20 / 698), avg. gap size = 3.30 (66 / 20)  


3245 26.62 0.55 0.66  chrX_130105303_130111583.rev     4882  5790 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130105303_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130105303_   4932 GGCCACACTGCCCAAGGTAATGTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v i   v     iv i  v           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130105303_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCC 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_130105303_   5030 TATGGAACCAAAAAAAGAGCCC-GCATCGCCAAGGGAATCCTAAGCCAAA 5078
                                -- viv  i ii   - v  v     iiv    i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_130105303_   5079 AGAACAAAGCTGGAGGCATCACACTATCTGACTTCAAACTATACTACAAG 5128
                                  i      vv       vi ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_130105303_   5129 GCTACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGAGATATAGA 5178
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_130105303_   5179 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 5226
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_130105303_   5227 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5276
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_130105303_   5277 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5326
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_130105303_   5327 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5376
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_130105303_   5377 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5426
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_130105303_   5427 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCC 5476
                           v    ?i v viv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_130105303_   5477 AAAACATCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5526
                          vi   i        vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_130105303_   5527 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5576
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_130105303_   5577 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAA 5626
                          v  i     i   i             v  i    vii ivi      v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_130105303_   5627 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACACATTTACAAGAA 5676
                           i  i  vi          v  i  v      vv   vv iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_130105303_   5677 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5726
                            i     i     v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_130105303_   5727 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5776
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_130105303_   5777 TCATCACTGGCCAT 5790
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


1035 21.59 3.96 0.88  chrX_130169003_130170781        1   227 (1552)    L1M4_orf2#LINE/L1      185   418 (490)  

  chrX_130169003_      1 TTTTAAAATACAAGAAAAAAAGTTAG----CTCACACTTTTTGGTTTTAA 46
                          i  i   v v     v   -   i ----         iiiii   i  
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAA-GTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_130169003_     47 AACCCTCTTCAAAGCTATAGTAATCAAAATAACATAATTCT-----AAGG 91
                            iiv  v        i         i i iii ii v  -----    
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_130169003_     92 ACAGATACATAGATTAATGGAATAGAATTGAGGCTCCAAAACTATATGCA 141
                          i   i i      i                 iv    i  v  v iv  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_130169003_    142 TACACTTATGGCCAATTGATTTTCAGCAGGTGTGCCAAGACTATTGAATG 191
                             i      i            ii  i v          i   v    
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_130169003_    192 AGGGAAAGAGTAGTTTCATCAACAAATGATGCTGGG 227
                         -        i    i iv          i       
  L1M4_orf2#LINE/    384 -GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

Transitions / transversions = 2.77 (36 / 13)
Gap_init rate = 0.02 (4 / 234), avg. gap size = 2.75 (11 / 4)  

 301 11.11 0.00 0.00  chrX_130169003_130170781      465   509 (1270)    L1M4_orf2#LINE/L1      403   447 (461)  

  chrX_130169003_    465 AAAAAATGATGCTGGGACAACTGGATATCCATATGCAATAGAATG 509
                           v     i                  ?   i      v      
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

Transitions / transversions = 1.00 (2 / 2)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.00 (0 / 0)  

2315 26.38 4.38 2.06  chrX_130169003_130170781      510  1286 (493)    L1M4_orf2#LINE/L1      114   908 (0)  

  chrX_130169003_    510 TTTTATAGATATTGTCTAATCGATGGTAAAATTTATATGGAAATG-AAAG 558
                             ii   v    v v iii   vv       i           -  i 
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chrX_130169003_    559 GACCTAGAAAATTCAAAGCGATTTCAAGAAA--AGAACAAAGTCAGGGGA 606
                             i    v vi    i i  i ii i   --          ii i   
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_130169003_    607 CTTACATAACCCAGTATCGAAACTTACTACTAAGCCATAGTAATCAAGAG 656
                           i   ivv    i v  i           v    i i           v
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_130169003_    657 AGTGTGTTGTTGGCACAAGGACAGGCATTTAGACCAACGGAAGCAAATTA 706
                               v ii     i     i  i   v    i   i    vvi    i
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_130169003_    707 AATTTTCAGAAACAAATTCTCACATATAC---C------TCTTCAACAAA 747
                          ivv i      i   ii vi    v  i--- ------ i   i    i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_130169003_    748 GATCCCAAGACAATTTGACAAGGAAAAGGGTAGATTTTTCAATAACAGAT 797
                          i v       v   ii iii     - ii   vi       i  vv i 
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAATGGT 412

  chrX_130169003_    798 ATTGTGACAATTATATACCCCAATACAAACAAAATGAAAAAAAAAACCTT 847
                         ii  v     i iv   ?  vv  i    - i      i---------  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAA-AGAATGAAG---------TT 452

  chrX_130169003_    848 ACATACTTACCTCACATCATACAAAAAAATTAACTCAAGG-GCATGCTAG 896
                         iv iv i         i    i v              ii- v  vv?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_130169003_    897 TCCTAAATTTAAGAGCTAAAACTACAACATTTTTAGAATGAAGCATAAGA 946
                         v       v               i  v i i      vi  i    i ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_130169003_    947 GAAAATCTTTCTATTTTGGGGTAAGGCTATGATTTCTTTGATACAACGCC 996
                          v       iv ivii v    v    v   i      v    ii  i  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_130169003_    997 AAAGACATG----------GAAAAAATAATTTGTGAATTTGCATTTTATT 1036
                            ii  ii----------         iv ----  v   v i  i  i
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGAT----AAATTGGACTTCATC 648

  chrX_130169003_   1037 AAAATCGGCA---TTTGAACACCAAAAACCATTATTAAGAAAATGAAAAA 1083
                              iiiv ---    vi vi    iiv  i   i      i      i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_130169003_   1084 ACAAACCA--GAACTGGAGGAAAATATTTGCAAATTGTACATCCACTAAA 1131
                             v   --   -   ii                ii  i   iiv   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAA-TGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_130169003_   1132 TC-TTTTTATCCAGAATTTATGAA-AACTATAATATCTCAGTAATAAGAA 1179
                         vv-i  v          v   i  -    v v i v    i      i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_130169003_   1180 TACAAACGACACAATTGACCACT---TAAAG-ATTTAAATAGAAAACTCA 1225
                         v     ii  v     ? vv v ---i    -    i      v vi  v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_130169003_   1226 CTGAAGAAAATAACCAAAGGGCTAGTAAGCACATAAAAAGATACTAAATA 1275
                          ii     i   vv    v   i i         i       i  v  i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_130169003_   1276 TCATTAATCAT 1286
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.72 (127 / 74)
Gap_init rate = 0.02 (17 / 795), avg. gap size = 2.94 (50 / 17)  


1097 31.51 8.44 1.90  chrX_130194712_130196546.rev      504  1344 (491)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_130194712_    504 CCATTTTCAGATATAGCAATACTCAAC-TTA--AAGATGTCCAATGTCCC 550
                             v    viv  v v  v   i  i-  i--      v -   iii  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC-AATACTCC 61

  chrX_130194712_    551 AAAAACTAATCTATAAATTTAATGCAATTCCAGACGTAATTTCAAATG-- 598
                         vv   i i     i i   i  i     i  viv iv   ii  iv  --
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chrX_130194712_    599 --------AGGT-TTAACAAGCTGATCCTAAAATTCATATGAGTAAT-TG 638
                         --------  iv-  i                         - v   -ii
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG-GAAATGCA 160

  chrX_130194712_    639 AAGGACCAAGAATATTCAAGATAATTATGAA---GAAGAACAA-GTAGGA 684
                          i     v      vi   i i   iv    ---         -  v   
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chrX_130194712_    685 AGGACTTGTCCT--ACAGCTATCAAGACTTAG---AAAACTGTAATAATT 729
                         -     iiiv  --v  ii -    i     v---   i  ii i    i
  L1M4_orf2#LINE/    211 -GGACTCACACTTCCCAATT-TCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_130194712_    730 GAAACAGTATAGTACTTATGCAGAGAGACACAAACAGATCAGTGGGA--G 777
                         i i     i i     viiii ii  v v   v i      i   i -- 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_130194712_    778 AAAGGAAAGACCTAGACACAAATCAGAGAATATAAGGAGCCTTGGTATAT 827
                           vv  i  v  -   v i   i viviv  v  v  vvvv   i v vi
  L1M4_orf2#LINE/    309 AATTGAGAGTCC-AGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_130194712_    828 GACAGAATTGGCATTGCAAATCA-TGGGAGAAAAGGATGGATTATTCAAT 876
                             iiiv  v  vvi v v   -    i--    i  i vi v     i
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGG--AAAGAATAGTCTTTTCAAC 405

  chrX_130194712_    877 AAATGGGGTAAGAATGATTGTTTATTCAAAT-CAGAAAAAATACAATTAG 925
                               v ivi i ii i  vv  ?i  v  -  -   i   iv i  i 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAATGAAGTTGG 454

  chrX_130194712_    926 ATTACTATATCACA-----TATAGAAATCAATTTCAGATGGATTTAAAAA 970
                          iiv   iv     -----  i i    i  i iv i      iv? i v
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_130194712_    971 CTAAATCTTAAAAAC--AACTTTTAAAATT--TAAAAGATA-CTTAGAA- 1014
                               v -  i i --  vi v     i --  i    v - v   i?-
  L1M4_orf2#LINE/    505 CTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_130194712_   1015 TAA-----TATGATCTCAGTGTAGGAAAGGATTTCTTGAATAAGACACAA 1059
                            -----ii   i  ii vv    v  v i      ii   v     v 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_130194712_   1060 AAAACACAAATTGTAAATTACAGATTAATTAGAGCATATTGA----TAGG 1105
                            i     iivii   ----   vv  v    -i v    i----i vv
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAA----AGAAAAAATAGA-TAAATTGGACTTCATC 648

  chrX_130194712_   1106 GAAAT--AAAGCCTCTGTCTTTC----TGTATTAT-AAGATAAAGATAAT 1148
                         i    --   i i i   vi   ----vii i   -    --   vv  v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA--AAGTGAAA 696

  chrX_130194712_   1149 AGACAAGTGACAGACTTAGAGAAGACATTTGTAA--CAAATAT---ATAA 1193
                               viv     v vi     i i     i  --  v    ---    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_130194712_   1194 CAAATCAATAT--GGACGACATAAAGTACTCC----ATTTAGT--TAAAA 1235
                         vii iivi   --i  vv i      v    i---- i i i --     
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_130194712_   1236 A-ACAACCAACCTAAATTAACAGTGGGCAATATATT--AATGAACAATGC 1282
                          -    vi    i  v ?  v i       viv   --   ii   v v 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_130194712_   1283 ACAGAAGAGAAAATCTGAATGGCTAGTAAGTAGATAAAAACATACTTATC 1332
                         v vi    ii v  vii      i i    i v  i    v  i  i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_130194712_   1333 TTCATAAATAAT 1344
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (153 / 108)
Gap_init rate = 0.04 (40 / 896), avg. gap size = 2.17 (87 / 40)  


2744 25.85 2.73 3.71  chrX_130209669_130211933      856  1772 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130209669_    856 TGGTGGGACATACCATGAGTATGGATTGGAGGATTCAATGTAATAAAGGT 905
                            vii  i  v     vvi          i  i i   i vi v   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130209669_    906 ATCAATTATCTCTAAAGTGATCTATAGATTTAATGCAATAGTAATAAAAG 955
                         iv    vv  i i   v       i     i  i     vviv  v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130209669_    956 TCCCAGCAGGTTTTTTGTTGCTATTGTTGCTGTAGACAACAGGAATTTCT 1005
                                v vi     --------------  i   -------    vvi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT--------------TGCAGA-------AATTGAC 129

  chrX_130209669_   1006 AAAACTCTAAATTATAAAATTTGTATGAAAGGACAAGAAAAATAAAATAG 1055
                           i---  i - iv       ii    i  ivi    ii vvi i     
  L1M4_orf2#LINE/    130 AAG---CTGA-TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chrX_130209669_   1056 CTAAAACAATTTTGAAAAAAAAGAACAAAGTTGAAGGACTCGTACTACTC 1105
                          i        i        i             i       ii   v i 
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chrX_130209669_   1106 A-TTTTAAGACTTACTATAAAGGTACAGTAATGAATACAGTGTG-CACTG 1153
                          -   i  i        i    v         v  v        -i    
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_130209669_   1154 ACAAAGAAATAAACACAT----CAATGGAAAAGAATGGAGAGTTCAGAAA 1199
                         i  v iii   i   i  ----        v     v      i      
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_130209669_   1200 TAGACCCATACAAATATGGACATTTAATCTTTGAAAAAGGTGTAAAAGCA 1249
                           i         vv     v  v  i  i  i  v  i    iv  ii v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_130209669_   1250 ATTCATTGGGGAAAGAGTAGTCTTTTCAACAAATAG------AACAAGTA 1293
                              v          i                 i ------i    v i
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_130209669_   1294 GTCATTCATACACAAAAAATCGAAAATGAACCTTGACTTTAACCTCACAC 1343
                          vi ?i  i ii     i vi   iv  i   ---- i --         
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACC----CCT--ACCTCACAC 469

  chrX_130209669_   1344 T-TACACAAAGATTAATTGAAAATGGTGGATATATATAAAAATCAAACCC 1392
                         i-  i     i     i v       vvv ? v iv    vi v i v i
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_130209669_   1393 AAATCTTTAAAACTTTTGGACGA---CATAGGTAAAAACCCATATAACCT 1439
                            v  v       i  i  v  ---      ?iv   i ivii i    
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_130209669_   1440 GCATTTGGATGAAAAATTCTTAGAGAGAAAATCAAAA-CACAA-TACCTA 1487
                         vviv  i iii viiv        v vi v i     -     -i v - 
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-A 618

  chrX_130209669_   1488 AAACCAAAAAAGTAGATAAATAATTCTTTGTTAAAATTAAAACCTTTTTC 1537
                            --i     i         vivv   ii i          v     vi
  L1M4_orf2#LINE/    619 AAA--GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_130209669_   1538 CCTTTCAAGGGCACTGTCATGAAAATAAAAAGGGAAGCTAAAGACTGAGA 1587
                         v   iv    i    i   v    i i     iv  v i v   v  i  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_130209669_   1588 AAAAATATTTGCCATTCATATATCCAACAAAGGATTTTTATTTAGAGTAT 1637
                         i           v v         ii i  i   i  v   ii   i   
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_130209669_   1638 ATAGATAACTATGAAAACTCAACAGTAAAA-------TCATCAAATTAGA 1680
                            i v    v v v       i i     ------- v i v    ?i 
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_130209669_   1681 GAATGGGCAAAAGGCATGAACAGACATTTCACTGAAGAGGGTATACAGAT 1730
                         i          i iiv    i         v ii    i i      i  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_130209669_   1731 GGCAAATACATGCAGGAAAGGATGTTCAACATCATTAGCCTT 1772
                            v    viii  v    i    i         ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (143 / 90)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.47 (59 / 17)  


3324 26.21 0.55 0.55  chrX_130238096_130242947.rev     3454  4361 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130238096_   3454 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3503
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130238096_   3504 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3553
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130238096_   3554 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3601
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_130238096_   3602 TATGGAACCAAAAAAGATCCCGCATCGCCAAGTCAATCCTCAGCCAAAAG 3651
                                viiv  ii  i  v v  v     iv     i v ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_130238096_   3652 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGCC 3701
                                i      vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_130238096_   3702 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 3751
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_130238096_   3752 GATGGAACAGAAC--AGAGCCCTCAGAAATAATACCATACATCTACAACC 3799
                         i      i    i--    i  --        vv        i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_130238096_   3800 ATCTGGTCTTTGACAAACCTGAGAGAAACAAGCAATGGGGAAAGGATTCC 3849
                          vi  i i  i     ivv  vv ii v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_130238096_   3850 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3899
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_130238096_   3900 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 3949
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_130238096_   3950 TTAAAGACTTAAATGTTAGACCTAAAACCATAAACACCCT-AGAAGAAAA 3998
                          i ?    i       v   v       i     -  i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAA 545

  chrX_130238096_   3999 CCTAGGCACTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTA 4048
                          v    ?iiv viv   iv   v v  vvii     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_130238096_   4049 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 4098
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_130238096_   4099 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4148
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_130238096_   4149 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 4198
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_130238096_   4199 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 4248
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_130238096_   4249 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 4298
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_130238096_   4299 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 4348
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_130238096_   4349 CATCACTGGCCAT 4361
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2994 26.27 1.55 1.32  chrX_130286993_130293673     5283  6188 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130286993_   5283 TGGAACAACATTCCGTGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5332
                              vi i  i  i  i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130286993_   5333 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5382
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130286993_   5383 TACCATTGACCTTCTTCACACAATTAGAAAAAACT-ACTTTAAATTTCAT 5431
                          v   vivi    i  ii  v  v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_130286993_   5432 ATGGAACCAAAAAAGAGCCCATATAGCCAAGAAAATCCTAAGAATCCTAA 5481
                               viiv  ii  v  viv        i v    i i i  ------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA------ 193

  chrX_130286993_   5482 GCAAACAGAACAAAGCTGGAGGCATCACAGTACCTGACTTCAAA--CTA- 5528
                         -- i -         i      vv     v v  ii i      --i  -
  L1M4_orf2#LINE/    194 --AGA-AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_130286993_   5529 TACAAGGCTACAGTAACCAAAACAGCATGGCACTGGTACCAAGACAGAGA 5578
                              i          i   i    ii   i     i iv i  i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_130286993_   5579 TATAGACCAATGGAACAGAACAGAGGCCTCAGAAATAGCTCCACACATCT 5628
                               i        i    iv   ivii        ivi   i    i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_130286993_   5629 ACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAG 5678
                          iiii  vi    i  i     ivv  v   i v  vvv           
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_130286993_   5679 GATTCCCTATGTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAG 5728
                         i  vvi  v vi  i        i     v      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_130286993_   5729 AAAACTGAAACTGGACCCCTTCCT-ACACCTTATACAAAAATTAACTCAA 5777
                           i v    ii         v   -     v                   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_130286993_   5778 GATGGCTTAAAGATTTAAACCTAAGACCCAAAACCGTAAAAACCCTAGAA 5827
                         i    v i ?   ii    iv     v i     ii     vi i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_130286993_   5828 GAAAACCTAGGCA-ATACCATTCAGGACATAAGCATGGACAAAGACTTCA 5876
                               v    ?i- v i -   iv   v vi vv i i   v ii   v
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_130286993_   5877 TGACTAAAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGG 5926
                          iiv  vi            vvii         vv     v  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_130286993_   5927 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAG 5976
                           ii v  i   v v  i i   i  ii vv    i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_130286993_   5977 AGTGAATAGGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTATCCAT 6026
                               v  i  i  i                 v       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_130286993_   6027 CTGACAAAGGGCTAACATCCAGAATCTATAAGGAACTTAAACAAATT--- 6073
                             i  i  i  vii         v     i     ivv    v i---
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_130286993_   6074 --TACAAGGAAAAAAAACCTG-TCAAAAAGTGGGCAAAGGATATGAACAG 6120
                         --  v  i  v   v    ii- i?    i            v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_130286993_   6121 AGACTTCTCAAAAGAAGACATTTATGTGGCCAAACAA--ACATGAAAAAA 6168
                          v i     v        i  vi vi       -i  --         i 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAGA 888

  chrX_130286993_   6169 AGCTCATCATCACTGCTCAT 6188
                         v     v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.00 (26 / 13)  


3086 27.31 0.66 0.66  chrX_130383500_130389889     4990  5897 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130383500_   4990 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAACATCGTGAAAAT 5039
                              ii i  i     i        v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130383500_   5040 CGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATTCCCATCAAGC 5089
                         v  v     v     iv i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130383500_   5090 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTAAATTTCA 5137
                          v   iivi i  i  ii     -   -- v  i  - i i    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_130383500_   5138 TATGGAACCAAAAAAGTGCCCACATT-GCCAAGTCAATCCTAAGTCAAAA 5186
                                viiv  ii -i    v v -     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_130383500_   5187 GAACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTGCTAGT 5236
                                 i      vv   vi  v  ii i      viv    i v iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_130383500_   5237 CTACAGTAACCAAAACACCATGGTACTGGTACCAAAACAGAGATACAGAC 5286
                                  i   i   vii         i iv ii i   v   i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_130383500_   5287 CAATGGAACACAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5334
                                 i v  i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_130383500_   5335 CATCTAATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTC 5384
                           vi i  i  i     ivv  vv  i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_130383500_   5385 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGC 5434
                         i  v  i  i              v      v  ?   i  ii i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_130383500_   5435 TGAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGG 5484
                             ii    i    v   i   i v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_130383500_   5485 ATTAAAGACTTAATTGTTAGACCTAAAACCATAAACACCCT-AGAAGAAA 5533
                           i ?    i   v   v   v       i     -  i  -        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAA 544

  chrX_130383500_   5534 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAACGACTTCATGTCT 5583
                           v    ?i v viv   iv   v v  vv i     i ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_130383500_   5584 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCT 5633
                          vi            vvi          vv    iv  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_130383500_   5634 AATGAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTACCATCAGAGTGA 5683
                         v  v   v v  i i   i  ii vvi   i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_130383500_   5684 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTGCTCATCTGAC 5733
                          v  i     i                 v       viiiivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_130383500_   5734 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAA 5783
                           i  i  vi          v  i         vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_130383500_   5784 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5833
                            i     i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_130383500_   5834 TCTTAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 5883
                            iv        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_130383500_   5884 TCATCACTAGCCTT 5897
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


4002 19.42 2.55 1.78  chrX_130428185_130430551.rev      975  1875 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130428185_    975 TGGAAAAACTTTCCATTTTCATAGCTTAGAAGACTTAATATTGTTAAGAT 1024
                               i iv i    v     i v  i                      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130428185_   1025 AGCAATACTTACCAAATTGATCCCCAGACTCAACACAATCTCTATCTATT 1074
                         i        iv           iv    i     i     i     v vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130428185_   1075 TCCCTGTTGGAATTTACAACATTCATATAGAAAT--GCAAG--AAACCAA 1120
                             v i  ------- -- v  iv ii      --i    --i v  v 
  L1M4_orf2#LINE/    101 TCCCAGCTG-------C--CTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_130428185_   1121 AAATTGATATA-AAATGCAAGGGATCTAAAACAGCCAAAACTATCTTGAA 1169
                              v    i-            i i i  i         v        
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_130428185_   1170 AAATAAGAATAAAGTTGGAGGAGTCACAATCCCCTACTCCAAAACTTATT 1219
                            v     i            v     v i   v i i         i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_130428185_   1220 AAAAGAATAGGGTAACCAAAGCTGTGTGGTACTGGCCTAAAGACAGACAT 1269
                          v  iiv  vi    i   ii v             v   i  i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_130428185_   1270 ATTAGTGAGTGAAGTAGAGTTGAATATCCAAAAATAAAT--ATGCACATA 1317
                           vii v i  i i    i    ivi    i       i--  i  iv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_130428185_   1318 TGGT--AT--------GACAAGG-TGCCAAAACAAGTAGATGGGGGAAGT 1356
                             --  --------       -      i  v v vi      i   -
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG- 390

  chrX_130428185_   1357 AATAGTTTTTTCAGCAGATGATACTGGGAGAACTGCATCATTCCCTCATG 1406
                               i      i  i   i i      v     v  - ?--  v    
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT-AK--CCACATG 437

  chrX_130428185_   1407 CAAGGGGATGAGGTTTGAACCTTATCTCATATCATATACAAAAGTTAATT 1456
                            ii i    i   v  v  i  i    i i           i    i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_130428185_   1457 CAAAATGGATCAAAGACCTAACTGAAAGAGCTAAAATTTTGTAATTCTTA 1506
                                     ?        v  v           i v iv  i     
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_130428185_   1507 AAAGAAAATATAGAGATAAATATTTGTGACATCAGACTAGGCAATGGTTT 1556
                         i       i    i?i     v  i     v ii ii             
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_130428185_   1557 -TTAGATATGACAACGTAATTATAAGCCACAAAAGGAAG--TGGAACACA 1603
                         -            v iv  vi i    v       i  i-- i  ---i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA---TA 634

  chrX_130428185_   1604 AACTGGACATCATCAAATTTAAAAACTTT-GTGCTTCAAAGGACATTACC 1652
                           i     v        v           -               i  i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_130428185_   1653 AAAAAATTGAAAAGACAACCCATGAAGTGGAACAAAATGTTTGCAAATCA 1702
                           i   v               iii i   i v     i           
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_130428185_   1703 TATATCCCATAAGGAATTTATATTTGGAGGATGTAAATAGCTCTTACAGC 1752
                               iv      i i  i   iii  iv  i    v i        i 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_130428185_   1753 TCAATAATAAAAAGAAAAATAACCCAATT-AAATATGGGCAAATGATATG 1801
                                        v             -   v         v   v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_130428185_   1802 CAAAGACATTTCTCCAAAAAAGATGTACAAATGGCAAATAAGCACATGAA 1851
                         v v               i     i          v              
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_130428185_   1852 AATATATGCAACACCATTAGTGTT 1875
                           v  iiv     i  ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (110 / 62)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.29 (39 / 17)  


3238 25.33 1.10 1.54  chrX_130437690_130443988     4895  5806 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130437690_   4895 TGGAAGAACATTCCATGCTCATGGGTAGGCAGAATCAATATCATGAAAAT 4944
                              ii i  i     i      i v  v   v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130437690_   4945 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4994
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130437690_   4995 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAAAGTTC 5041
                          v   i-       i  -i     -   -- v  i  -  ii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_130437690_   5042 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAGTCCTAAGCCAAAA 5091
                                 viiv  ii  v  v v  v     iv  i  i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_130437690_   5092 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5141
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_130437690_   5142 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5191
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_130437690_   5192 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5239
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_130437690_   5240 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5289
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_130437690_   5290 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5339
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_130437690_   5340 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5389
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_130437690_   5390 ATTAAAGACTTAAACATTCGACCTAAAACCATAAAAACCCTAGAAGAAAA 5439
                           i ?    i    ii vv  v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_130437690_   5440 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5488
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_130437690_   5489 AAAACACCAAAAGCAAAAAGCAATGGCAGCAAAAGACAAAATTGACAAGT 5538
                          vi            -----   --   i       v     v  i  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCA-----CAA--GCAACAAAAGAAAAAATAGATAAAT 637

  chrX_130437690_   5539 GGGATCTAATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATC 5588
                         v   ii v  i   v v  i i   i   i vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_130437690_   5589 AGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTC 5638
                          i      v  i     i   i             v       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_130437690_   5639 ATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTTAAACAAATTT 5688
                               i  i  i  vi          v  i  v     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_130437690_   5689 ACAAGAAAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAAC 5734
                          i  v     i    ----   v  i?    i            v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_130437690_   5735 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAAACACATGAAAA 5784
                              i     v        i  vi viii     v  i-          
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAA 886

  chrX_130437690_   5785 AATGCTCATCATCACTGGCCAT 5806
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (136 / 91)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


 234 16.95 1.69 5.08  chrX_130461005_130463296.rev      679   737 (1555)    L1M4_orf2#LINE/L1        1    57 (851)  

  chrX_130461005_    679 TGGAAAGCTATTCTGTGTTCATAGATTGAAAAA-TTAATATTCTTATCAA 727
                                v   i ii       i     i  i -        v   --- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA---A 47

  chrX_130461005_    728 GATTCCAATA 737
                            vv     
  L1M4_orf2#LINE/     48 GATGGCAATA 57

Transitions / transversions = 1.50 (6 / 4)
Gap_init rate = 0.04 (2 / 57), avg. gap size = 2.00 (4 / 2)  

2322 26.77 1.01 1.16  chrX_130461005_130463296.rev     1111  1801 (491)    L1M4_orf2#LINE/L1      219   908 (0)  

  chrX_130461005_   1111 ATTTCCCAACTTCAAACTGTATGACAAGGCTATAGTAACCAAAACAGAAT 1160
                          i       i      viv  iv    i    i     i   i    vi 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chrX_130461005_   1161 GGTGCTGGGGGAAAAACTGACACATAGACCAATGGAACAGAATAGAGAAC 1210
                            i    viv  ii iv    i     i        i     v    ii
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_130461005_   1211 CCAGAAATAAAGCCATACATCCACAACCACCTGAACTTTGACAAACCTGA 1260
                                    v        ii iiii  vi   vi  i     ivv  v
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_130461005_   1261 CAAAAATAAGCAATGGGGCAATGATTCCCTATTCAATAAATGGTGCTGGG 1310
                            i vi vv        v  vi  vvi  v     i             
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chrX_130461005_   1311 ATAACTGGTTATCCATATGCAGAAGAATGAACCTGGGCCCCTATCTAGTA 1360
                          i      v  ?   i     i         vi   i      i  vii 
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_130461005_   1361 CCACAAGCAAAAATTAACTTGAGATGGATTGATAACTTAAATGTAA-ACC 1409
                            i vi            ii i      ii?vi  i         - v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_130461005_   1410 TCAAACTATAAGAATCCTAGAAAAAAATCTGGGAAATAACATTCTGGACA 1459
                          v         i v  i     i    iv i  ?ivv  iv   vv   v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_130461005_   1460 TCAGCCTTAGGAAATAATTTAT--GACTAAGTCCTTAAAAGCAATTGCAA 1507
                          ii v-     v   ii   v --  -  v v vii       ----   
  L1M4_orf2#LINE/    569 TTGGG-TTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCA----CAA 612

  chrX_130461005_   1508 CTGGAACAAAAACAAAAATTGATAAGTGGGACCTAATTAAACTAAAGAGT 1557
                         -- v       iv      v     i v    i v  i   v v  i ii
  L1M4_orf2#LINE/    613 --GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_130461005_   1558 TTGTGTACAGCAAGAAAAACTATCAAAGGAATAAACAGACAACATATAGA 1607
                           v   i vv   iii v        iii i i  v       vi i   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_130461005_   1608 ATAAAAGAAAATATTTACAAATTAGGTATCTGACAAAGGTCTAATATCCA 1657
                           iii           i     i vi       i  i  v  vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_130461005_   1658 GAATCTATAGGAAAC-CT---AAATCAATGAACAAAAAACAAATAACCCC 1703
                             v    iii   -  ---  v     i vv    i           v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_130461005_   1704 ATTAAAAAGTGTGTAAAGGATGTGAATAGGTACTTCTCAAAAGAAGAAAT 1753
                            ?    i  v i       v       ii i     v        v  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_130461005_   1754 ATAAGTCGCTATCAAATGTATGAAAAAATGCTCATCATCACTGATCAT 1801
                          i  i v  i vi  iiii       i       v     ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (110 / 71)
Gap_init rate = 0.01 (8 / 690), avg. gap size = 1.88 (15 / 8)  


2143 22.69 4.52 11.29  chrX_130498640_130501142     1037  2010 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130498640_   1037 TGGAAAGACATAGTATGTTCATGGACTTGAAGACTCAAAGC-----AGAT 1081
                                 i  vvi           i v       i  vii-----    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130498640_   1082 GTCAACTCTACCCAAATTGACACACATATTTAATGTAATTCCTGTCAAAA 1131
                          v   iv  v          ivi   v   i  i i   i   i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130498640_   1132 TCCAAGCAAAATTTTGTATATATAGGTTATGCATATATATATGTATATAC 1181
                            v   -------  iv v -----  -    v ---------------
  L1M4_orf2#LINE/    101 TCCCAGC-------TGCCTTT-----TT-TGCAGA--------------- 122

  chrX_130498640_   1182 AATAGATAAGTAAATATGTGATAGAGATAGACAATATACCTACAAAAATG 1231
                            v  i   i-------    ----------------    --------
  L1M4_orf2#LINE/    123 AATTGACAAGC-------TGAT----------------CCTA-------- 141

  chrX_130498640_   1232 CCTGGATTTTGGTACGAATTATTGCAAAATTTGTATGAAAAGTCAAAAGA 1281
                         --------------------------     ii    i   vv   ii  
  L1M4_orf2#LINE/    142 --------------------------AAATTCATATGGAAATGCAAGGGA 165

  chrX_130498640_   1282 CTCA-AATAGCTAAAAACAGTTTTTTAAAAGTA---CAAAATGGGAAGAC 1327
                          i  -      i    -  i i  vv     v ---    i v   i   
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_130498640_   1328 TCAGTGTACCCAATTTCGAG-TTTATTATATAACTACAGTAATCAAGACT 1376
                            vvv v         i i-i   i  i v i                v
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_130498640_   1377 GCATGATATTGATAGAGTGATAGACACATAGATCAATGGTGCAGCACACA 1426
                          ii  i  i  ii v iv        i            vii  v ivv 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_130498640_   1427 AAACCCAGAAATAGACACACACAAATATGACCA-TTGATTTTCGGCAAAG 1475
                         i ii         i  v  i   vv    ii  -          i   i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_130498640_   1476 GTGCAAAAGCAGTTCAATGGAGGAAAGATAGCATTTTCAACAAATGGTAT 1525
                             v  ii vi        i i  ii    iv               ii
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_130498640_   1526 TAGAGCAATTGAAAATCCATAGGGTAAAAAGTGAACCTCAACCAAAGACT 1575
                          i ii   i  i v ?   i v vv   i i    vi vi   vvviv  
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_130498640_   1576 CATACCCTATACAAAAATTAACTAAAAATGTATTATGGACTTA--TGTAA 1623
                           i   v                v      v  i ?i   i  --     
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_130498640_   1624 AATGTAAAATTGTAGAACTTTTAGGAAAAAAGCACAAGA--AAAGCTTTG 1671
                         i vv     i i  i    i    i i    -  i i ?--   v   i 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGTAAATCTTCG 563

  chrX_130498640_   1672 GCATATAGGGTTGGGCAAAGAGTTCATACACTTGATACGAAAAGCACAAT 1721
                         vv iv v     i     v iv   v  v iv   i  v          v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_130498640_   1722 CTATAAAAGAAATTAAAT-GATAGTTTGGACTTCATCAATATTAAAAACT 1770
                          v i        --    -    iv              v          
  L1M4_orf2#LINE/    614 CAACAAAAGAAA--AAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_130498640_   1771 TT-G-GCTCCATGAAGAAGGATAAAAAAACTTTGGCTCCATGTTAAAAGG 1818
                           - -   i  -----     i ------  v -----  ---- i  i 
  L1M4_orf2#LINE/    662 TTTGTGCTTCA-----AAGGACA------CTAT-----CA----AGAAAG 691

  chrX_130498640_   1819 ATAAAATACAGTCTATAGAGTAAAAGAAAATATTTGCAAATCACAAATCT 1868
                         vv    v   ii i i   i iii                   i v    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_130498640_   1869 GACAAAATACCTGATATCTATAGTATATATAGAA---------------- 1902
                           i  iiv  i  -    i v i      v    ----------------
  L1M4_orf2#LINE/    742 GATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_130498640_   1903 -----AAAATAAGCAATCCAATTAGAAAATAATGAAAAGAC----ATAGA 1943
                         -----  i i  ii  i      ?i     iivv   i  i----     
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_130498640_   1944 CCTTTCACAGACAAGGATATACAA-TGGTAAATAAGCACATAAACAGATG 1992
                          v    v vi vi i         -   iv           i  v     
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_130498640_   1993 TAAAACATCATTAGTAGT 2010
                         ivv       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (131 / 86)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 5.50 (154 / 28)  


1046 27.74 5.48 0.00  chrX_130508175_130510214.rev      512   803 (1237)    L1M4_orf2#LINE/L1      192   499 (409)  

  chrX_130508175_    512 AAAGA-GAACAAAGCTAGAGGCATCACCTTAGCTGACTGCAAACTATGCT 560
                              -        i i    vv    vi vv ii i v    viv i  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_130508175_    561 ACAGGGCTACAGTAACCAAAACAATATGGTACTGGTACAAAAACAGGCAC 610
                            ii          i   i   i i         i i  ii i  i  i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_130508175_    611 AGAGACCAATGGAACAGAATAGAAATCCCAGAAATAAGGTCACACACCTA 660
                          v   i        i     v  i vi          ivi  i   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_130508175_    661 CAACCATCTAATCTTCGACAAAGCTGGCAAAAGCAAGCAATGGGGAAAGT 710
                         iiii  vi i  i        i v  v   i v  vv            v
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_130508175_    711 AC---------------TGGGGCTGGGATAACTGGTTAGTCATATGCAGA 745
                          i---------------   v       i      v  ?i  i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_130508175_    746 AGATTGAAACTGGACCCTTTCTTTATACCACATACAAAAAACAACTCAAG 795
                            v    ii       i v i i i    i         vi       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_130508175_    796 ACGACTCA 803
                          i iv   
  L1M4_orf2#LINE/    492 ATGGATCA 499

Transitions / transversions = 2.20 (55 / 25)
Gap_init rate = 0.01 (2 / 308), avg. gap size = 8.00 (16 / 2)  

1231 23.93 4.03 1.42  chrX_130508175_130510214.rev     1128  1549 (491)    L1M4_orf2#LINE/L1      476   908 (0)  

  chrX_130508175_   1128 CAAAAA--AACTCAAGATGGAATAAAGACTTAAATATAAAACCCAAAACT 1175
                               --       i     vi ?    i     i   i v i      
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_130508175_   1176 ATAAAACCCT-GGAAGACAACCTAGGCAATGCAATTCT--GGAA--TAGG 1220
                                i  -i     v   v    ?--- i  v   -- vi -- v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGN---GTAAATCTTCGTGACCTTGG 572

  chrX_130508175_   1221 ACCAGGCAAAGATTTCAT-GACAGAGACACCAAAAGCAATTGTGACAAAA 1269
                         iii      v i    v -  i v-             vvv ii      
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAACAAAA 621

  chrX_130508175_   1270 GCAAATATTGGTAAATTGAATCTAAT-GAAACGAAAGAGTTTC-TACATA 1317
                          v   v  v i       i ii v  -i   iv   i v   i- i v -
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT- 670

  chrX_130508175_   1318 GCAAAATAAACTATGAACTGAGCAAACAAACAACCTACAGAATGGAAGAA 1367
                         -    iv v     v  vvi  ii  v i      i         i    
  L1M4_orf2#LINE/    671 -CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_130508175_   1368 AATATTTGCAAACTATGCATCTGACAAAGGTTTAAAATCCAAAATCTATA 1417
                                     ii  ii      i  i  vi viv     i   v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_130508175_   1418 AGGAACT--TA-AATTTA-CAA-AAAAAAACCCAT--CCCCATTAAAAAG 1460
                          i     --  -  i i -i  -     i  vv  --   v   ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_130508175_   1461 TGGTCAAAGGACATGAACAGATACTTTTCAAAAAAAGACATACATGTGGC 1510
                            v       iv    i   i i  i  v   i    i     vi    
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_130508175_   1511 CAGCAAGCATATGAAAAAATGCTCAATATCATGAATCGT 1549
                           ii     i       i        i    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (61 / 37)
Gap_init rate = 0.03 (15 / 433), avg. gap size = 1.53 (23 / 15)  


3173 26.30 1.22 0.88  chrX_130512265_130514662.rev     1005  1909 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130512265_   1005 TGAAAAGATATTCCATGATCATGGATAGGAAGAATCAATGTTGTTAAAAT 1054
                           i        i     v        v      v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130512265_   1055 ATCTATACTACCCAAAGCAATCTATAGATTCAATGCAATCCCTATCAAAA 1104
                         iv v     v      vii     i        i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130512265_   1105 CACCAAAGACATTCTTCACAAAAATAGAATAAACT-ATCCTAAAATT-AT 1152
                         iv   ivvi v  i  ii  i    v  -i  i  -           -  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_130512265_   1153 GTGGAACCACAAATAACCCAGGACCACCTAAACTATCCTGAGCAAATAAA 1202
                         i     vii   ivi      i ivi  v    v   i   iv  iv i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_130512265_   1203 ACTAAAATTGGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGC 1252
                           -   i        v     i v  ii i      viv       i   
  L1M4_orf2#LINE/    200 AC-AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_130512265_   1253 TCTAGTACCCAAAACAGCATGGTATTGGTATAAAAACAGACACATAGACC 1302
                          vi    vi   i    ii     i   i    ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_130512265_   1303 AATGGAACAAAGTAGAGAACCTGGAAACAAATCCATGCAGCCACCATGAA 1352
                                i i i v    ii ii    i   i    i  vii ivi v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_130512265_   1353 CTCATTTTTGGCAAAGCCACCAAAAACATGCACTGAGGAAGAGATAGTCT 1402
                         i v     i i   i vii    i v   v  v  i    iii       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_130512265_   1403 CTTTGATACAATAGTGCTGGGAAAACTGGATATCTTTATGCAAAAGAAGA 1452
                         i  ii i -   i         v         ? ivi           vi
  L1M4_orf2#LINE/    399 TTTCAACA-AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_130512265_   1453 AAACTAGACCCCTGTCTCTCACCACATATAAAAATCAAATCAAAATGAAT 1502
                           ii i       ii   v     i   i      i  v        i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_130512265_   1503 TAAAGACTTAATTCTAAGACCTCAAACTG--AAACTACTACAAGAAAACA 1550
                         i ?    i   v v     v  v     i--     vi  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_130512265_   1551 CTGGCCAAACTTCCCAGGACATTGGTCTCGGCAACAATTTCTTGAGCAAT 1600
                         iv  ?vv  v iii iv   v    vi v     iii      -  --  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AG--AT 594

  chrX_130512265_   1601 ATCTCAC---AAACACAGGCAACCAAAACAAAAATGGACAAATGAGATCA 1647
                           vv   ---  i    i     v   iv      i  i    vi  iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_130512265_   1648 CATCAAGCTACAAGGCTTCTGCACAGCAATGGAAACAATCAATAACACGA 1697
                               iv vv  ii   i  ii vv   v   v  v     v  vii  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_130512265_   1698 AGAGACAACCCACAACATGGGAGAAAATATTTGTAAACTACCCATCTGAC 1747
                          i            iv                 i   ii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_130512265_   1748 AAGGGATTAACAACCAGTAACACATAAGGAGCTCAAACAACTCTACAGGA 1797
                               i vii v    -  i i    i  i   vv       v i iv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAG-AATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_130512265_   1798 AAAAAATATAATAATCCTTTCAAAAAATGGGCAAAAGATTTGAATAGACA 1847
                             i i -     i  vv i?             i              
  L1M4_orf2#LINE/    794 AAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_130512265_   1848 TTCCTCAAAAGAAGGCATATAA-TA---AACAGGTATATGAAAAGGTGCT 1893
                           i   v       ii   i  - i---  i i i i        i    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_130512265_   1894 CAACATAACTGATCAT 1909
                               v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (153 / 81)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


3268 26.43 0.55 0.55  chrX_130523001_130529283     4883  5790 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130523001_   4883 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4932
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130523001_   4933 GGCCATACTGCCCATGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4982
                            v     v    viv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130523001_   4983 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5029
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_130523001_   5030 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAA 5079
                                 viiv  ii  v  v v  v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_130523001_   5080 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5129
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_130523001_   5130 CTACAGTAACCAAAACAGCATGGTACCAGTACCAAAACAGAGATATAGAT 5179
                                  i   i    ii      ii i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_130523001_   5180 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5227
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_130523001_   5228 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5277
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_130523001_   5278 CCTATTTAATAAATGGTGCTGGGAAAACTGTCTAGCCATATGTAGAAAGC 5327
                         i  v  i  i              v     vv  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_130523001_   5328 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5377
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_130523001_   5378 ATTAAAGACTTAAACGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAA 5427
                           i ?    i    i  v   v  i    i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_130523001_   5428 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5477
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_130523001_   5478 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5527
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_130523001_   5528 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5577
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_130523001_   5578 CCGGCAACCTACAAAATGGGAGAAAATTTTTTCAACCTACTCATCTGACA 5627
                         vv i     i   i             v   v   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_130523001_   5628 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5677
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_130523001_   5678 AAAACAAACAACCCCATGAAAAAGTGGGCAAAGGACATGAACAGACACTT 5727
                           i     i     v  v?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_130523001_   5728 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5777
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_130523001_   5778 CATCACTGGCCAT 5790
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2278 25.56 4.50 3.20  chrX_130728726_130730560      500  1344 (491)    L1M4_orf2#LINE/L1       53   908 (0)  

  chrX_130728726_    500 CAATTTTTTCAAATTTGATCTATAAATTAGATGCCACCCCAAACAAAATT 549
                             vi ii v  v        i i   vi i  v i   v v      i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_130728726_    550 TCAGCAGACTTTTTGGTAAGAGATGACTAACTGATTGTAAAGTTCA-ATG 598
                         i    v v      v i ii iv    v i     iv    i    -   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_130728726_    599 GAAATTCAAAGTACCTAAAATAGCCAACAGAACTTTGAAAAAGAAAAAT- 647
                              v   i v   i i         v v  ii           i  i-
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_130728726_    648 --GTTTGAG-ACTAACACTCCCTGATTTTAATATTTATTTTATATCTCCA 694
                         --   v   -   v     i  ii    i  v i   i vi v v  v  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_130728726_    695 GTAAACAAGAT-GTGTATTAATGGTATAAAAA---GCAAATCAATCCATG 740
                             v     i-    iv  v   i    ii ---i  v  vi   v   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_130728726_    741 AAAGAGAA--GCAAATCCAGAAGTAGATCCACATACTTATATTGACAACC 788
                         i  v    -- vi i       i  i i   i i i    iv --   ii
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT--CAATT 350

  chrX_130728726_    789 TATTTTGGACAAGGGCACAGATGCAATTCAGTGGATTAATGATAGCCTTT 838
                         v     v        ii vi vi v     i   ivv  vi    i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_130728726_    839 TCAAGAAATAGTGGTAGAACAATTAGATATTCATATGCAACAAAA-GAGC 887
                             v    i   v i i    i i    ?i  i      v i  -  iv
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_130728726_    888 ATCAATCCATATCTTGCACCATATACAAATAATTAACAGAAAATATGTTA 937
                         v vi i  v  i  ii             -       vv     ivi i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAA-AATTAACTCAAAATGGATCA 499

  chrX_130728726_    938 TAGACCTAAATGTATCACCTAAAACTATTAATCTTCTATATATAAATACA 987
                         ?             vv v          v  v  ii  v viv   i i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_130728726_    988 GGAGAAAACCTCTGTGACCTTGAATTAGGGAAAACTTTCTTAGATACAAC 1037
                           ? v   i  ii         ii     v  viv           ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_130728726_   1038 ACCAAAAGCATAATCCTTATAACAAAC--TA-ATTAATTGGATTTCACCA 1084
                                   i  v vvi v  v   v--  -  v       i    i  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_130728726_   1085 ACATTATAAACTTCTCT-CTTTGAAAGACACAGTTAAGATAAAGAAAACA 1133
                          v    v      i v -   ii  i     vi i    v iv     v 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_130728726_   1134 TAAGCCACAGAC--AGAAAAAAGA---GTAA--------TCTGATAAAG- 1169
                         i  v       v--i  i    v --- i  --------        i -
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_130728726_   1170 ATTTAT-TCCAGAATATATAAAGG---CTTACATTCCTGATATATTTATA 1215
                          i  i -                i---      ---------------- 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACA----------------A 783

  chrX_130728726_   1216 CCCAGAATACATAAATTGGATTAAAATTACCCAATTTTTAAAAGTAAG-A 1264
                          i  --   -     v-i  i--    v        ?--    i ii - 
  L1M4_orf2#LINE/    784 CTCA--ATA-ATAAAA-AGAC--AAATAACCCAATTW--AAAAATGGGCA 825

  chrX_130728726_   1265 AAATATTTGAAGAGGCATTTCACCCACAAAGACAAATGAATGGC-ATTAA 1313
                           iv       v  i      v  v vi    i v ii      - v   
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_130728726_   1314 GCACCTAAAAATATGTTCAAC--CACGTTATTC 1344
                             v i    v   i     --  ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (121 / 91)
Gap_init rate = 0.03 (27 / 856), avg. gap size = 2.41 (65 / 27)  


1653 22.95 1.68 7.84  chrX_130780335_130782370      474  1009 (1027)    L1M4_orf2#LINE/L1      257   759 (149)  

  chrX_130780335_    474 TCAAGACAG-ACAGTACAATAAGATATGCATAGAAACAACAGACATACAG 522
                                  -iii    ------- i-     --- vi i       i  
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTAC-------TG-GCATA---AGGATAGACATATAG 295

  chrX_130780335_    523 AACAATGGAACAGA-------GCCCAGAAAGAAATTTGTACATCTACAGT 565
                          v        i   ------- i       v   iiii     i  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_130780335_    566 GAACTCATTTTTTTACAAATATGCCAAAAACATACACTGGGGGAAAGGAC 615
                         v  i v     iv-    ivi      i v   v  v     -    i i
  L1M4_orf2#LINE/    346 CAATTGATTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAAT 393

  chrX_130780335_    616 AGTCTCTTCAGTAAATGGTGCTGGGAAAACTGGATATACATATGCAGAAG 665
                              i    ii              v         ?v  i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_130780335_    666 AAGGAAACTAGACTCC-ATCTCTTGCCATATACAAAAATCAAATTAAAAT 714
                           v   ii i   i  - i   vii              i  v i     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_130780335_    715 GGATTAAAGACTTCAATCTAAGTCCTCAAACTATGAAACTTTTACAAGAA 764
                             i ?    i v   v    vv  v       i     i   v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_130780335_    765 AACATTGGTGAAACTTTTACAAGAAAACATTGGTGAAACTTTCCAGGACA 814
                              v  ? v  v i  --------- i ----------------   v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTT---------CGT----------------GACC 568

  chrX_130780335_    815 TTGAACTGGGCAAAGATTTCTTGAGTAATACCCCATAAACACAGGCAACC 864
                            iii i     v i      iii  vv  v   v  i    i     v
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_130780335_    865 AAAGCAAAAATGAACAAATGGGATCATATCAAGCTAAAAAGCATTTGCAC 914
                             v      ii i    v   iivi     iv v    i v    ii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_130780335_    915 AGCAAAGGAAACAATCAACAAACTAAAGAGACAACCCACAGAATGGGAGA 964
                         vv       v  v     v   v i  i                      
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_130780335_    965 AAATATTTGCAGACTAGCCATTTGACATGGTTAGGCTTTGTGTCC 1009
                                    i ii vvi  i   i v  ---- vi    i   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGG----GACTTGTATCC 759

Transitions / transversions = 1.55 (73 / 47)
Gap_init rate = 0.02 (11 / 503), avg. gap size = 4.64 (51 / 11)  

 660 22.49 1.78 0.59  chrX_130780335_130782370     1375  1543 (493)    L1M4_orf2#LINE/L1      738   908 (0)  

  chrX_130780335_   1375 ATCTGAAAAGGGATTGATAGCTAGGATATATAGGGAGCTCAAGCAACTCT 1424
                               v      i vi  v i  i       ii  i   vvi      v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_130780335_   1425 ATAAGAAAATAATCTGTAATCCAATTTTAAAATGGACAAAAAGATCTGAA 1474
                             v    vi ivvi   i      ?v       i    -i   i    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA-GGATTTGAA 836

  chrX_130780335_   1475 TAGACAATTCTC---AAAAGGCATACAAATGGCAAACAGGTATATGAAAA 1521
                               v     --- i   ii           v  i i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_130780335_   1522 TGTGCTCAACATCATTGATCAT 1543
                         vi            ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (23 / 14)
Gap_init rate = 0.01 (2 / 171), avg. gap size = 2.00 (4 / 2)  


3138 25.65 0.65 2.38  chrX_130811981_130814781.rev     1390  2313 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130811981_   1390 TAGAAACACATCCCATGCTCATGTATGGGTAGAATCAATACTGTGAAAAT 1439
                          i    v i        i     v  v  v   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130811981_   1440 GACCATACTGCCAAAAGCAATCTACAAATTCAGTGCAATCCTCATCAAAA 1489
                          i v     v  v   vii       i     ii       ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130811981_   1490 TACCACCATCATTCTTCACAGGATTAGAAAAAAGAATTCTAAAATTCATA 1539
                          v   v vv v  i  ii   i v v  v  ivvi  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_130811981_   1540 TGGAACCAAAAAAGAGCCCGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 1589
                              viiv  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_130811981_   1590 CAAATTTGGAAGCATCACACTACCTGATTTCAAACTACACTATAAGGCCA 1639
                             v     i vv       v  ii        vivi    i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_130811981_   1640 TAGTCACCAAGACAGTGTGGCACTGGCATAAAAATAGGCACATAAACCAT 1689
                         i   v i             i          ii    i  i   i i  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_130811981_   1690 TGGAGCAGAGTAGAGAACCCAGAAATAAAGCCAAATACTTATAGTCAACT 1739
                             ii   i v    ii           v   v i i    i     i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_130811981_   1740 GATCTTCGACAAAGCAAACTAAAAC-ATAAAGTGGGAAAAGGACACTCTT 1788
                            i        i -ivi i  i  -  vv i    i    i i v    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_130811981_   1789 TTCAACGAATGGCCCTGGGATAATTGGCTAACCACATGTAGCAGAATGAA 1838
                               i     iv      i  i   v  ?       i iv        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_130811981_   1839 ACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTA 1888
                         ii    i  ii i   v    v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_130811981_   1889 AGGACTTAAACCTAAGACTTGAAACTATACAACTTTTAGAAGATAACATT 1938
                         ?i   i    iv     vi i        v    i        v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_130811981_   1939 GGAAAAACTCTTCTAGACTTTGGCTTAGGCTAGGATTTCATGACCAAGAA 1988
                           ?iv  v     vv   i    v      v v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_130811981_   1989 CCCAAAAGCAAATGCAATAAAAACAAAAATAAAGAGCTGGGATCTAATTA 2038
                         v         v v    i    iv       i v iv v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_130811981_   2039 GACTAAAGAGCTTTTGCACAGCATAAAGAATAGTCATCAGAGTAAACAGA 2088
                         i v v  i i      ii vv  --   i i v -    --------   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCA--AAGGACACT-ATCA--------AGA 688

  chrX_130811981_   2089 CAACCTGCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCACA 2138
                         ---------i   i  v              i           v  ii  
  L1M4_orf2#LINE/    689 ---------AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_130811981_   2139 ATCTGTACATTTGACAGAGGACTAATATTTAGAAACTACAACGAACTG-- 2186
                          viii  i  i   i ii     vi   ii    vv  i  v     v--
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_130811981_   2187 --AAATCAGGAAGAAAAAAAACAAAAAATCCCATCAAAAAGTGACCTAAG 2234
                         --  v   iv  v     i -    v  i  v  i?    i  iv v   
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_130811981_   2235 GACATGAATAGACAATTCTTAAAAGAAGATATACAAATGGCCAACAAACA 2284
                           iv          v    iv                       i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_130811981_   2285 TAAGAAAAAATGCTCAAC-TAAAGACCAGG 2313
                         i v     i         - v ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.11 (28 / 9)  


2411 27.09 1.14 7.24  chrX_130825917_130828812     1437  2403 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130825917_   1437 TGGAAAGACATTCCATGTTCATGGCTTGGAAAAATTCATATTGTTAAGAA 1486
                                 i  i            v      i v  v            v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130825917_   1487 GATCATATTACCTAAGGCAATTTACAGATTCAATGCAATCCCAATAAAAA 1536
                          iiv   i v  i  ivii  i           i        v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130825917_   1537 ACCCAATGACATTCTTCACAGAAATAGAAAAAACAATCCTAAAATTTATA 1586
                         v    iivi v  i  ii       v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_130825917_   1587 TCGAACCACAAAAGACCCAGAATAGTCAAAGCTATCCTAAGCAAAAAAGG 1636
                          v   vii   ii            i    i v   i i i-   i   i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chrX_130825917_   1637 ACAAAACTGAAGTA-TCACATTACCTGATTTCACATTGTACTACAGAGCT 1685
                              ii  i  v -     i v  ii      v viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_130825917_   1686 ATAGTAACCAAAACAGCATGGTACTGGTATAAAAACAGACTCATAGACCA 1735
                          i     i   i    ii         i    ii i    vi     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_130825917_   1736 ATAGAACAGAATAGAGATCCCAGATATAAATTCATGCATTTACAACCAAC 1785
                           i   i     v    vi     v     ii   i      iiii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_130825917_   1786 TCGTTTTTGACAAAGTTTCCAAGAATATGCAATGGGGAATTGCTAGTCTC 1835
                          vi    i     i v v      vi  v          vviv      i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_130825917_   1836 TTCAAGTGATCATAGCTCACTGCAGCCTCAAACTCCTGGGCTCAAGTGAT 1885
                              -ii --  i i--i   vii ----    ----  v ------ ?
  L1M4_orf2#LINE/    400 TTCAA-CAA--ATGGT--GCTGGGAC----AACT----GGAT------AK 430

  chrX_130825917_   1886 CCTCCCGCCTCAGTCTCCCAAGTAGCTGAGATAACAGGTGCACACCGCCA 1935
                           v vi  --- i------   v --   ii --ii iiv vi   -i  
  L1M4_orf2#LINE/    431 CCACATGC---AA------AAGAA--TGAAGT--TGGACCCCTACC-TCA 466

  chrX_130825917_   1936 CACCCGGTTAATTTTTTTTTTGTACAAACGGGGTCTCACTATGTTGACCA 1985
                             ------  ---------i      vivviv    vv   --  i  
  L1M4_orf2#LINE/    467 CACC------AT---------ATACAAAAATTAACTCAAAATG--GATCA 499

  chrX_130825917_   1986 GGCTGGTCTTGAATTCCTGGCCTCAAGCTGTCGTCCCACCTCGACCCCCC 2035
                         ---?i v i i   vivv iv  v  i  i ------ ----i v i ii
  L1M4_orf2#LINE/    500 ---WAGACCTAAATGTAAGAGCTAAAACTAT------A----AAACTCTT 536

  chrX_130825917_   2036 AAAATGCTGGGATTATAAGCATGCGCCACCACG-CC--GAGCCTTGGGCA 2082
                          i  ---- ii vi   i ?i ivii vi ii -  -- i --  i    
  L1M4_orf2#LINE/    537 AGAA----GAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCA 580

  chrX_130825917_   2083 AAGATTTTTTGTGTAAGACCTCAAAAGCATAGGCAACCAAAGTGAAAATA 2132
                          v i   i  ivi  v   vi        i i     v    vi      
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_130825917_   2133 GACAAATGGGATTACATCAAGCTAAAAAGCGTCTGCAC--AGAAAAAAGC 2180
                           i    v   i v      iv v    i v i  ii --vi  ii vi 
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_130825917_   2181 T-TCAACAAAGCAAAGAGGCAACCCATGGGATGGGAGAGAATATTTGCAA 2229
                          -    v    ii  i  i       ii i        i           
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_130825917_   2230 ACTACCCATCTGACAAGGGATTAATAAGAAGAATATATGAAGCATTT--- 2276
                          ii ivi      i      i vi  vvv         i   v i i---
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_130825917_   2277 -AACCCAATAACAAAAAAGCGAATACTGCATTTAAAATATGGGCAAAAGA 2325
                         -   i      i     ii i    viv  v  ?   v         i  
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_130825917_   2326 TCTGATTAGAAATTTCTCAAAAGAAGACGTACAAATGGCCCGCAGATATA 2375
                          i   v    v       v        ii           vii iii i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_130825917_   2376 CGAAAAAATGTTCAGCATCACTAACCAT 2403
                         i     i   i   i     ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (172 / 86)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.12 (81 / 26)  


3222 27.05 0.89 0.22  chrX_130848557_130854964     5014  5915 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130848557_   5014 TGGAAGAATATGCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5063
                              ii    v     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130848557_   5064 GGCCATACTGGCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5113
                            v     vv    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_130848557_   5114 TACCAATGACTTTCTTCACAGAATTGGAGAAAACT-ACTTTAAAGTTCAT 5162
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_130848557_   5163 ATGGAACCAAAAATGAGCCCTCATTGCCATGACAATCCTAAGCAAAAAGA 5212
                               viiv  iv  v  vvv  v    vi      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_130848557_   5213 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATTACAAGGCT 5262
                               i      vv   ii  v  ii i      viv  i     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_130848557_   5263 ACAGTAACCAAAACGGCATGGTACTGGTACCAACACAGATATATAGACCA 5312
                                i   i  i ii         i iv iv i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_130848557_   5313 ATGGAACAGAACAGAGGCCTCAGAAATAA--CCAGACATCCACAACCATC 5360
                               i    iv   ivii         --   v    ii iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_130848557_   5361 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTA 5410
                             i  i     ivv  v   i v  vvv           i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_130848557_   5411 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAA 5460
                           i  i              v      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_130848557_   5461 ACTGGATCCCTTCCTTACACCTTATATAAAAATCAATTCAAGATGGATTA 5510
                         ii    i    v   i     v    i      i  i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_130848557_   5511 AAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5560
                         ?    i    i  v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_130848557_   5561 GGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGCCTAAAA 5609
                           ?i- v i -   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_130848557_   5610 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5659
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_130848557_   5660 AAACTAAAGAGATTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5709
                            v v  i iv  i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_130848557_   5710 GCAACCTACAAAATGGGAGAAAATTTTCGCAATCTACCCATCTGACAAAG 5759
                         i     i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_130848557_   5760 GGCTAATATCCAGAATCTATAAAGAACT--TA-AATTTA-CAAGAAAAAA 5805
                          i  vi          v           --  -  i i -i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_130848557_   5806 AGAAACAACCCCATCAAAAAGTGGGAAAAGGATATGAACAGACACTTCTC 5855
                          v   i     v  i?    i    v       v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_130848557_   5856 TAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCAT 5905
                         i        i  vi viii     i ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_130848557_   5906 CACTGGTCAT 5915
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


3780 19.11 3.80 2.35  chrX_130946648_130949806     1773  2667 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_130946648_   1773 TGAAGAGATAGTTCATGTTCACAGACAAGAAGATTCAATATTGTTATGGT 1822
                           i i     vii        ii  ivi     i i          v i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_130946648_   1823 GGCAATTTTTTCAAAAAATAATCTATAAATTCAATGCAATCCCCATCAAA 1872
                               vi ii v   v- i     i i      i        i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_130946648_   1873 ATCCCAGTAGGCTTTTAAAAATAGAAATTGACAAA-TGACCTTAAAATTT 1921
                                iv v     vvi--i            i-   i i       i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTG--CAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_130946648_   1922 ACATGGAAATGCACAGATCTCAGAATAACCAAA-CTATTTTGAAAAAGAA 1970
                          i           vi iv i       i     - v  i           
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_130946648_   1971 ---CAAAGTTGGGCAATGTGTACACTTCCTTATTTCAAAGCTTACCTCAA 2017
                         ---         ivi i- -i        iv        i     iv   
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGAC-T-CACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_130946648_   2018 AGCTACAGTAATTAAGACAGTGTGGTAATGGCATAAGAATAGAAATATAG 2067
                                     i              v         i     v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_130946648_   2068 ATCAATGGAACATAAGTGAGAGTACAGAAGTAACTCCTTACATTTATGGT 2117
                                   i v  v       v     i   vi  v            
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_130946648_   2118 CAATTGGTTTTTGACAAATGTGCCAAGACAATTCAATGAAGAAAAATAAT 2167
                               i    i     iv          v        ii    i --  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA--AT 393

  chrX_130946648_   2168 ATTCTTTTCAACAAATGTTGCTAGGACAAATGGACATCCACACACAAAAA 2217
                          v               v    i      v    i ?     ii     i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_130946648_   2218 TATGAAGTCGGACCCCTACCTCACACTATACTCCATGCAAGCGTACAAAA 2267
                         v       i                 i   -------------       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATA-------------TACAAAA 480

  chrX_130946648_   2268 AAATAGCTCAAAATGGATCATAGATCTAACTATAAGAGGTAAATTTATAA 2317
                          v-  i              ?   i    v i      v    vi     
  L1M4_orf2#LINE/    481 AT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_130946648_   2318 AAGTTCTAGGAGAAAA------------TCTTTTTGACCTTAAGTTAGGC 2355
                           v ii   i      ------------    iv       ii       
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_130946648_   2356 AAAGAGTTCTTAGATACAACACCGAAAGAATGATCCACTAAA-ACTACAC 2404
                           v iv          ii     i    v ii v v  v   - vv v i
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_130946648_   2405 AGA-AAGTGAAATTCCATCAAATTTTAAAACTGTTGTACTTCAAAAGATA 2453
                            -  i vii i i       v  v      v    i       i  i 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_130946648_   2454 TCCTTACAAAA-TGAAAAGACAAGCCACAGATTAGAAGAGAAAATT-GCA 2501
                         iiv i vi   -           v       v i i   i  v   -   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_130946648_   2502 AATTGTATATCTTATAAAG-ACTTTTAATCAGAATTTATAAAACCCTCTT 2550
                            ii       v    i -    v  vi      v      ivv     
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_130946648_   2551 AAAACTCAATAATAA---TATAAA-AACTCA-TTTAAAAATGGGCAAAAG 2595
                          v             ---v i   -   i  -  ?             i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_130946648_   2596 ATTTGACTAGGCATTTTACCAAAGAAAACAT-----TGG--AATAAGCAC 2638
                               v   i     iv        i i  -----   --         
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_130946648_   2639 ATGAAACTGTGCTCAACATCGTTAGTCAT 2667
                               vvi           i????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (103 / 65)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.62 (55 / 21)  


3296 26.68 0.44 0.44  chrX_130991874_130998071     4799  5705 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_130991874_   4799 GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATG 4848
                             ii i  i     i      i v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_130991874_   4849 GCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCT 4898
                           v     v     iv i  i           i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_130991874_   4899 ACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 4946
                         v   iivi i  i  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_130991874_   4947 ATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAGA 4996
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_130991874_   4997 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCT 5046
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_130991874_   5047 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5096
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_130991874_   5097 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATACCTACAACTG 5144
                               i    i--    i  --        vv   i i ii  iiiiii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_130991874_   5145 TCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCC 5194
                         vi    i  i     ivv  vv  i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_130991874_   5195 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5244
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_130991874_   5245 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5294
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_130991874_   5295 TAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5344
                         i ?   ii       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_130991874_   5345 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAA 5394
                             ?i v viv   iv   v v  vv i     v ii   v ivvi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_130991874_   5395 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5444
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_130991874_   5445 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5494
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_130991874_   5495 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5544
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_130991874_   5545 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5594
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_130991874_   5595 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 5644
                         i     i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_130991874_   5645 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5694
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_130991874_   5695 TCACTGGCCAT 5705
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (5 / 907), avg. gap size = 1.60 (8 / 5)  


3291 26.87 0.44 0.44  chrX_131015959_131022221.rev     4865  5772 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_131015959_   4865 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4914
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131015959_   4915 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4964
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_131015959_   4965 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACCTTAAAGTTCA 5012
                          v   iivi i  i  ii     -   -- v  i  - i i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_131015959_   5013 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5062
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_131015959_   5063 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5112
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_131015959_   5113 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGATC 5162
                                 i   i    ii         i  v ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_131015959_   5163 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5210
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_131015959_   5211 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5260
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_131015959_   5261 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5310
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_131015959_   5311 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5360
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_131015959_   5361 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5410
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_131015959_   5411 CTAGGCATTACCGTTCAGGGCATAGGCATGGGCAAGGACTTCATGTCTAA 5460
                         v    ?i v viv   iv i v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_131015959_   5461 AACACCAAAAGCAATGGCAGCAAAAGACAAAATTGACAAATGGGATCTAA 5510
                         i            vvi   i       v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_131015959_   5511 TTAAAGTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 5560
                          i   i v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_131015959_   5561 AGGCAACCTACAAAATGGGAGAAAATTTTCCCAACCTACTCATCTGACAA 5610
                           i     i   i             v  iv   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_131015959_   5611 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5660
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_131015959_   5661 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5710
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_131015959_   5711 TCAAAAGAAGACATTTATGCAGCCAAAAAACACAAGAAAAAATACTCACC 5760
                           v        i  vi viii     v  i    v     i  i    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_131015959_   5761 ATCACTGGCCAT 5772
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3824 15.84 2.95 1.61  chrX_131090492_131093975.rev     1729  2473 (1011)    L1M4_orf2#LINE/L1        3   757 (151)  

  chrX_131090492_   1729 GAAAAATATCCCATGCTTGTGGATGAGAAGACTTAATAGACTTAATATTG 1778
                             i          i ii     vi            ---------   
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA---------TTG 43

  chrX_131090492_   1779 TTAAGGTGGCAATACTCTTTGAATTGATCTATAGATTCAATGCAATTCCT 1828
                              i           iiii          i        i     i   
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chrX_131090492_   1829 ACCATAATCTCAGGTGGATTCCTTTTAGAAATTGACTAGCTGATTCTAAT 1878
                          i  v    i   v  vv  ii  vi          v       i    v
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_131090492_   1879 ATTCACTTGGAATTGCAAATGACCCAGAATAGCCAAAATAATCATGAAAA 1928
                              iv     v     iv                  i    v      
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_131090492_   1929 AGAAGAACAAACCTGGAAGATTCACACTTCT-GATTTCAAAATGTACTAA 1977
                                    vi    i  i         i-i         iv     v
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_131090492_   1978 AAAGCAGTAGTAATCAAGACAATGTGTTACTGCCATAAGGATAGACATA- 2026
                              vii             i    v     v                -
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_131090492_   2027 AAA-CAATAGAATAGAATTGAGAGTACAGAAATAAACCCATACACCTATG 2075
                          i -    i                v                  ii    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_131090492_   2076 GTCAATTGATTTT---------TGCCAAGACCATTCAACAGGGAA-GAAT 2115
                                      ---------                ii     -    
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_131090492_   2116 AGTTGTTTTAACAAAC--TGCTGGAACAACTAGTTAGCCACATGTGAAAG 2163
                            iv   i      i--      i      i v  ?       ii    
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_131090492_   2164 AGTTAAATTGTACCCTTAC-TCACCCCATATACAAAAATTAACTCAAAAT 2212
                          i v  i   v    i   -    v                         
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_131090492_   2213 TAATCAAAGATGTAAATGTAAGAGCTAAACTTGTAAAACTCTTAGAAGAA 2262
                         vi    ?   iv                 vi i                 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_131090492_   2263 ATTATAAG-GTAAATATTCATGACCTCAAAATTGGCAAAGTATCCTTAGA 2311
                          vi   i -      v   i      iiiiv v     v vv i      
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_131090492_   2312 TACGACACCAAAAACACAAGCAACCAAAGAAAAAAATAGATAAATTAAAC 2361
                           i          i          v          -          ii  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGAC 642

  chrX_131090492_   2362 TTCATCATACTTAAAAAATGTTGTGCTCCAAAAGATACTATCAA-----C 2406
                                v v       v v       i    i  i        -----i
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_131090492_   2407 CCAAAGACAACCTAGAGAATGAGAGATCATATTTGCAAATCATCTATGTC 2456
                         vv          i v      i    vv               --  i  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT--ATATC 740

  chrX_131090492_   2457 TAATAAGGGACTTGAAT 2473
                          i            v  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTAT 757

Transitions / transversions = 1.58 (71 / 45)
Gap_init rate = 0.02 (12 / 755), avg. gap size = 2.83 (34 / 12)  

 945 10.26 2.56 0.00  chrX_131090492_131093975.rev     2838  2993 (491)    L1M4_orf2#LINE/L1      749   908 (0)  

  chrX_131090492_   2838 GACTTATATCTAGGATATATAAAGAACTCTTACAACTCAATGATAAAAAG 2887
                              i    i  i                           i        
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_131090492_   2888 AAAAAGAACCCAATTTGAAAATAGGTAAAGGATCT----AGACATTTCTC 2933
                          v   v         ?i     i  i       i ----           
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_131090492_   2934 CAAAAGAGATATACAAATAACCAATAAGCACATGAAAAGATGCTCAATAT 2983
                             ii            ii                           i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_131090492_   2984 CATTAGTCAG 2993
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 6.50 (13 / 2)
Gap_init rate = 0.01 (1 / 160), avg. gap size = 4.00 (4 / 1)  


3232 26.58 1.11 0.55  chrX_131103850_131106582.rev     1340  2242 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_131103850_   1340 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCATTATCGTGAAAAT 1389
                              ii i  i     i      i v      v i v   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131103850_   1390 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1439
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_131103850_   1440 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1487
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_131103850_   1488 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 1537
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_131103850_   1538 AACAAAGCTGGAGGCATTATGCTACCTGACTTCAAACTATACTACAAGGC 1587
                                i      vv i ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_131103850_   1588 TACAGTAACCAAAACAGCATGGTACTAGTACCAAAACAGAGATATAGACC 1637
                                 i   i    ii       i i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_131103850_   1638 AATGGAACAGAAC--AGAGTCCTCAGAAATAATGCCGCTTATCTACAATT 1685
                                i    i--       --        vv  iivi  i  iii i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_131103850_   1686 ATCTGATCTTTGAGAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 1735
                          vi    i  i  v  ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_131103850_   1736 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1785
                           v  i  i        i     v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_131103850_   1786 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1835
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_131103850_   1836 TTAAAGCCTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1885
                          i ?  v i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_131103850_   1886 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1934
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_131103850_   1935 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1984
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_131103850_   1985 ATTAAACTAAAGAGCCTCTGTACAGCAAAACAAACCACCATCAGAATGAA 2034
                           i   v v  i i i i   i vv    iv v  i i  vv i i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_131103850_   2035 AAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACGTATCTGACA 2084
                            i     i                 v       vii ii       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_131103850_   2085 AAGGACTAATATCCAGAATCTACAATGAACTC----AAATTTACAAGAAA 2130
                          i     vi          v  i  v      ----  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_131103850_   2131 AA-ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 2179
                           -     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_131103850_   2180 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 2229
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_131103850_   2230 CATCACTGGCCAT 2242
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3455 23.48 3.37 1.35  chrX_131134025_131137721.rev     2317  3206 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_131134025_   2317 TGGAAAAATATTCCATGTTCATGGATTGGAAAAATCAATATTGTTAAAAT 2366
                               i    i                   i v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131134025_   2367 GTCCATACTACC------AATCTACAGATTCAATGCAAACTGTATCAAAA 2410
                          v v     v  ------i              i    v iv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_131134025_   2411 TACCAATAATACTCTCCATAGACATAGAAAAAACAATTGTAAAATGTATA 2460
                          v   iiviivi i iiii   v  v  v  ivii  iv      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_131134025_   2461 TAGAACCACAAAAGATCCAGAATAGCCAAAGGTAGCCTAAGCAAAAAGGA 2510
                          i   vii   ii  i              ivv v i i iv  i   i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_131134025_   2511 CAAAATTGGAGGACTCACATTACCTGACTTCAAATTATGCTATGGAGCTA 2560
                             i              i v  ii i      viv i   iii     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_131134025_   2561 TAGTAACCAAAACAACATGGTACTGGCACA------------TAGACCAA 2598
                         i     i   i   iii           i ------------    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_131134025_   2599 TGTAACAGAATAGAGAACGCAGAAACAAATCCACACACATACAGTGAATT 2648
                           v  i     v    iiv      i   i   i   iv  ii  v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_131134025_   2649 CATTTTTGACAAAGGTGTCAAGAACATACACTGGGGAGAAGACAATCTCT 2698
                         v     i     i    i     v   v  v      i ii i i   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_131134025_   2699 TCAATAAATGGTGCTGGGAAAACTGGATATCCATATGTAAAAGAATGAAA 2748
                             i              v         ?   i   i           i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_131134025_   2749 CTAGACCCCTATCTTTCACCATATACAAAAATCAAATAAAAATGGATTAA 2798
                         i i        i  iv                i  v v         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_131134025_   2799 AGACTTATCTCTAAGACCTCAAACTATGAAATTACTACAAGAAAACATTG 2848
                             i  vv v     v  v       i   i vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_131134025_   2849 GGGAAAAATCTCCAGGACATTGGTCTGGGCAAAGACTTCTTGAGTAAG-C 2897
                          ? v   -   i iv   v    vi i     v ii     iii  v - 
  L1M4_orf2#LINE/    551 GNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_131134025_   2898 -CCACACGCACAGACAA-----GTAAACATGGACAAATGTGATCACATCA 2941
                         -   v v     ii   ----- v   v  i  i    vv  iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_131134025_   2942 AG-TTAAAAACCTTCTGCACAGCAAAGGATACAGTCAACAAAGTGAACAG 2990
                          i-        i  -  ii vv       i  vi    v        v  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_131134025_   2991 ACAACCTACAGAATGGGAGAAAATATTTGCAAACTACCCATCTGACAAGG 3040
                               i                          ii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_131134025_   3041 GATTAATAACCGGAATATATAAGGGACTC----AACTCTCCAGGAAAAAA 3086
                           i vi  v  i          i i    ----     vvi iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_131134025_   3087 AATCTAATAATCTGGTCAAAAAATAGGCAAAATATTTTAATAGAAATTTC 3136
                          -- v     i iii i?      i      iv    v      v     
  L1M4_orf2#LINE/    799 A--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_131134025_   3137 TCCAAAGAAGATATACAAATGGGAAACAGGCATATGAAAAGGTACTCTAT 3186
                                               vv  i i   i        i -------
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT------- 889

  chrX_131134025_   3187 TGCTCAACATCACTGATCAT 3206
                         -           ????????
  L1M4_orf2#LINE/    890 -GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (131 / 74)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.82 (42 / 11)  


3825 18.58 7.57 0.24  chrX_131139100_131140743.rev      309  1153 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_131139100_    309 GGAGACAGAATCCATGATCATGGATTGGAAGTCTCAATATTGTCAGGACG 358
                            i v v vi     v              v  i        i i  i 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_131139100_    359 GCAAT-TATCCAAAATTGATGTATAATGTCAATTCAAGTCCTGTCAAAGC 407
                              -ivi  v        v  i ivv    iv   vi   i     ii
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_131139100_    408 CACAGTAAGCTTTTGTGTAGAAATTGACAAGCTGATCCCAAAATTTACGT 457
                          v   iviv     v  i                    i      i ii 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_131139100_    458 AGAAATACAAAGGATATAGAATAGCCAAAACAACTTTGAAAAGG-----C 502
                         i     i   i   ivi                ii       i ----- 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_131139100_    503 AAA--------------ACTTCTTG-TTTTAAAACTTA------------ 525
                            --------------     iii-   i        ------------
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_131139100_    526 -GAAATCAGGACAGTTTAGTACTGTCACAA----AGACAAAGAGATCAAT 570
                         - v     i      v i      v  i  ----     v v        
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_131139100_    571 GGGATAGAATTGAGAGTCCA----------------TTTATGGTCAATTG 604
                           i                 ----------------              
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_131139100_    605 ATTTTTGACAAACATGGTAACACAAGCCAGTGCAGAAAGAATAGTCTTTT 654
                              i     ivi  vi  v  v vi  i  vi                
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_131139100_    655 CAACAAATGGT-CTAGGAGAATTGGATATCCACATGCAAAAAGAGGAGTT 703
                                    -  i   v  i      ?            ii v  iv 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_131139100_    704 TAGATTATTAATGCACACCGTATTAAAAAATTAACTCAAAATGGATTATA 753
                          i  iivi  viv      i   vv                     i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_131139100_    754 GACCTAAATGTATGGGCTAAAGCTATAAAACTTTTAGAAGATAATATAGG 803
                                     v i      i          i        v  i     
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_131139100_    804 AAAAAAAATCCT-GTGACTTCAGATTGGGCA--GAGCTCTTGGATGCAAT 850
                         ?iv   --  i -     i ii i  i    -- ivi    i   iii i
  L1M4_orf2#LINE/    552 NGTAAA--TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_131139100_    851 GCCCAAAGCACTATCCATAAAATTAAAAATTGATAAATTATACTTCATCC 900
                         i  v       v v v i    vv      v        iv        v
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_131139100_    901 AAAT-AAAAACTTTTGTGCTTCAAAGGATGCCATCAAGAAACTGAAAAGA 949
                             -                       ii i         v        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_131139100_    950 CAAATCACAGAGTGGGAGAAAA-ATTTGCAAATCATATATCTCATAAGAG 998
                            vi      i          -                   v     i 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_131139100_    999 -CTTGCATCAAGAATATATAAAGAACTC--ATAACTCAATAAGTAAAAGA 1045
                         -    i   v                  -- i          vv      
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_131139100_   1046 CAAATAATCCAATGAAATGTTGGACAAAGTATCTGGATAGACATTTCTCC 1095
                                i     v?  viv   i     v  i  i              
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_131139100_   1096 AAA-AAGATATATAAATGGCTAATAAGTACATGAAAAGATGCTCAACATC 1144
                            -        i       i      i                      
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_131139100_   1145 AAATTCATC 1153
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.59 (94 / 59)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 4.12 (66 / 16)  


1529 24.95 4.48 1.28  chrX_131144283_131150680.rev        9   477 (5921)    L1M4_orf2#LINE/L1      194   677 (231)  

  chrX_131144283_      9 AGAAAAACAAATCTTGAGGCATCACATTACCTGACTTCAAATTATACTAC 58
                             i      vi v    vv     i v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_131144283_     59 AAGGCTATAGTAACCAAAAGAGCATGGTACTGGTAAAAACGTAGACATGT 108
                           i    i     i   i v  ii         i v  ivi       i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_131144283_    109 A-ACTGATGGAACAGAATAGAG-GTCTCAGGAATAAAGCCA--CATCTTA 154
                          - iii      i     v   -   -   i      v   --   -   
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACAT-TTA 341

  chrX_131144283_    155 CAACCAACTGATCTTTGACAAAGCATAC-AAAAGCATAAATTAGGGAAAA 203
                         iiii   i    i  i     i -i i -  i v   vv v i      i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_131144283_    204 GATATCCTGTTCAATAAATGGTGCTGGGAAAATTGGATAGCTACATGTAG 253
                         i   vi  v     i              v  i      ? i     i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_131144283_    254 AAGAACAAAACCAGATCCCTATATCTTACCATGTACAAAATTTAACTCAA 303
                              ii  iiii  i     iv  vi     i       v         
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_131144283_    304 GATGGATC-------------TAAGAACTGATACCATTAAAAATCT-AGA 339
                         i       -------------     i  i v  i  -    v   -   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGA 539

  chrX_131144283_    340 AGAAAACCTAGGAAAAACTCTTCTGAACATTGGCCTAGGCAAATAATTTA 389
                                v    ?iv  v     vvi  v    vi       - ii   v
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTC 588

  chrX_131144283_    390 T--GACTAAGACCCCAAAAGCAAATGCAACAAAAACAAAACTGAATAAAT 437
                          --  -  v   v         v v         iv    v ii      
  L1M4_orf2#LINE/    589 TTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_131144283_    438 GGGACCTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGA 477
                         v    i v  i   v v    i   i  ii vv    i  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

Transitions / transversions = 1.61 (71 / 44)
Gap_init rate = 0.03 (13 / 484), avg. gap size = 2.08 (27 / 13)  

3142 26.26 0.88 1.10  chrX_131144283_131150680.rev     4998  5907 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_131144283_   4998 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCATTATCATGAAAAT 5047
                              ii i  i     i      i v      v i v   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131144283_   5048 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5097
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_131144283_   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_131144283_   5146 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5195
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_131144283_   5196 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_131144283_   5246 TACAGTAACCAATACAGCATGGTACTGGTACCAAAACAGACTTATAGACC 5295
                                 i   v    ii         i iv ii i    v      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_131144283_   5296 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACT 5343
                                i    i--    i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_131144283_   5344 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5393
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_131144283_   5394 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5443
                           v  i  i        i     v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_131144283_   5444 GAAACTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 5493
                            ii    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_131144283_   5494 TTAAAGACTTATAGGTAAGACCTAAAACCATATAAACCCT-AGAAGAAAA 5542
                          i ?    i  v v      v       i   -    i  -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAA 545

  chrX_131144283_   5543 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5591
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_131144283_   5592 AAAACCCCAAAAGCAATGGCAACAAAATCCAAAATTGACAAATGGGATTT 5641
                          vi  v         vvi         vvv     v  i    v   i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_131144283_   5642 AATTAAACTAAACAGCTTCAGCTCGGCCAAAGAAACTACCATCAGAGTGA 5691
                         v  i   v v  v i   iv iv vv v  i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_131144283_   5692 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5741
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_131144283_   5742 AAAGGGCTAATGTCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5791
                           i  i  vi i        v  i        ivv    v ---   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAA 791

  chrX_131144283_   5792 AAAAAAGA--AACAACCCCATTAAAAAAATGGGAAAAGGATATGAACAGA 5839
                         v       --  i     v   ?     -    v       v    i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGA 840

  chrX_131144283_   5840 CACTTCTCAAAAGAAGACATCTGTGCAGCCAACAGACACATGAAAAAATG 5889
                           i     v        i  viiviii     i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_131144283_   5890 CTCATCATCACTCGTCAT 5907
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (135 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


2420 22.91 3.56 0.62  chrX_131370141_131371778      500  1145 (493)    L1M4_orf2#LINE/L1      244   908 (0)  

  chrX_131370141_    500 AAAGCCATAATAACAAAAACAGCATGATAC----ATAAAAACAAGACACA 545
                              i i i   iv  i    ii  i   ----    ii i -    i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATA 292

  chrX_131370141_    546 CATACCAATGGAACATGATAGAGAACCCAGAAATAAATCCACTCATTTAC 595
                         i v i        i vi  v    ii           i   iv      i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_131370141_    596 AGCCAACTCATTTTTGACAAGGGCACCAAGAACATACATTGGGGAAAGGA 645
                         i i   i v     i        ii      v   v  v         i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_131370141_    646 CTGTCTT--CAATAAATGGTGCTGGAAAAACTGGATATCCATACATAGAA 693
                         iv     --   i            i v         ?   i iii i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_131370141_    694 GAATGAAACTAGATTCCTATCTCTTACCATATATAAAAATCAAATCAAAG 743
                                ii i  ii    i   vi        i      i  v     i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_131370141_    744 TGGATTAAAGACC--AATGTAAGACCTGAAACTATGAAACT---AAAAGA 788
                              i ?     --         v  i       i     --- i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_131370141_    789 AAACATTGGAA-AATTTTTCAGGACATTGGTGTAGGCAAAGATTT--TGG 835
                               v  ?i-  v i   iv   v    vv       v i   -- i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_131370141_    836 GTGTAAGACTTTAAAAGCAGAGGCAACAGAAACAGAAATGGACAAATGGG 885
                         i i i v  i--       v i      i  iv i    i  i    v  
  L1M4_orf2#LINE/    593 ATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_131370141_    886 AACACATCAAGCTAAAACACTTTTGCACAGCCATGGAAAC----AACAAA 931
                          viv      iv v   v       ii vv v v   v  ----  v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_131370141_    932 TTGAAGAGACAACCCACAGAATGGGAAAAAATATTTTCAGGC----TACC 977
                         v    i                    i         v  iii----  i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_131370141_    978 TAACAAGGGATTAATAACCACAATATATAAGGAACTCAAGCAATTCAACA 1027
                          i i      i vi  v   v         i      vvi   i    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_131370141_   1028 GCAAAAAGAAAAAATAATCCAATTTTAAAATGGGCAAATGATGTGAACAG 1077
                         ii       v   -   i      ?v            v   v    i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_131370141_   1078 ACATTTCTCAAAAGAAGAAATAGAAAAGGTCAACAGGTATATGAAAA-AT 1126
                                  v        v   v   v  i   i i i i       -  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_131370141_   1127 GCTCAACACCACTAATCAT 1145
                                 i  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (93 / 51)
Gap_init rate = 0.02 (12 / 665), avg. gap size = 2.25 (27 / 12)  


2466 25.00 2.12 0.45  chrX_131394549_131399278.rev     2646  3305 (1425)    L1M4_orf2#LINE/L1        1   671 (237)  

  chrX_131394549_   2646 TGGGGAGATAT-----ATTCATGAATTAGAAGACTCTATTTTGTTAAGAT 2690
                            ii      -----i      i   i       iv  v          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131394549_   2691 GTCAAATA-TCTCAAAATTTGTCTGTGGATTTAGTGTGATCCCAGTCAAA 2739
                          v   -  -  i v     vi   iii    i ii ii     vi     
  L1M4_orf2#LINE/     51 GGCAA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_131394549_   2740 ATCCCAGCAGACTTTGT-GTAGTGTTTGACAAGCTGCTT-TACAATACAC 2787
                                 v v    v - i  viv           v i-  v   v  i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_131394549_   2788 ATGACATTGCACAGGACCTAGAATATTCAAAATAACTTTTAAAAAGAAGA 2837
                            iv v    vi     i      vi     i  ii  v          
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_131394549_   2838 ACGAAGTTGGAGTGTTAACACTACCTATTTTAAAGTTTTAATGTAAACCT 2887
                           i         vii v     v  i v   v  ivi   v ii   v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_131394549_   2888 ACCATGAGCTAAAAAGTGTGGTACTGCCATAAAGACAGACAAATAAACCA 2937
                           vi i v v i v            v     i  i     v   i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_131394549_   2938 ATAGAACATAACAGAATGTCCAGAAATAGACTTACACAT--ATGCTCAAC 2985
                           i   i v  iv  iv           i  ii i    --   v    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_131394549_   2986 TGATTATTGACAGAGTTGCAAAGGCAATTCACTGGAGAAATAATAGACTT 3035
                              v i    ii v   v   i v     v   i    v     v   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_131394549_   3036 TTCCATAAATGGAGCTGGAACAATTGGATATCTATATGCAAAA-AATGAA 3084
                            v i      v     i    i      ? i i        -      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_131394549_   3085 CTTTTATCA-TACCTTGCACCATATACAAAAAATAACTCGAAATAGCTCA 3133
                         v  vv i v-     ii               v      i    i v   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_131394549_   3134 TTGACATGATTGTGAAACCTAAAACTATAAAACTTTCATCAGGAAATATA 3183
                         ?v   v i v   i i v                i i vv  i   i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_131394549_   3184 GGAGAAATTCATTGAGACCTTGG-TTAGGCAAAGATTTCC-AGGTACAAC 3231
                           ? v  v  v i v        -        v i    i-  i  ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_131394549_   3232 ACCAAAAAGCATAAGTCATAAAATAACAAGTTACATAAATCAGACTTCGC 3281
                                -   i   iv i    v  v  i - v      ii      ii
  L1M4_orf2#LINE/    600 ACCAAAA-GCACAAGCAACAAAAGAAAAAAT-AGATAAATTGGACTTCAT 647

  chrX_131394549_   3282 AAAAATCTAAAACTTCTGCTTTTC 3305
                         v     iv       i  ivi   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTC 671

Transitions / transversions = 1.31 (92 / 70)
Gap_init rate = 0.02 (12 / 671), avg. gap size = 1.42 (17 / 12)  

 478 19.14 14.35 4.78  chrX_131394549_131399278.rev     4033  4241 (489)    L1M4_orf2#LINE/L1      680   908 (0)  

  chrX_131394549_   4033 CTGTTAAGAGAATGAAAATGA-AATCCACAGA-TGATAAGGAAATAATTG 4080
                           i i    i i      -  -  i       -  i-i  i     v   
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAA-GACAACCCACAGAATGG-GAGAAAATATTTG 727

  chrX_131394549_   4081 TAAATGAAATAATTTGCCAAGGGACTTATATCCATAATATCTATCTATCT 4130
                         i    v v   - i  vi         i      v     v  vvv v  
  L1M4_orf2#LINE/    728 CAAATCATATA-TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_131394549_   4131 ATATATCTCAAGCTCCATCAAAAGAAAACAAACAACCCAATCAAAAGATG 4180
                         v -  ---   -   v  v v  i  i     i        i?   i   
  L1M4_orf2#LINE/    777 CT-TA---CAA-CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_131394549_   4181 GGCAAACAGGAT-------------------AAAAGGAT--------GGC 4203
                               --    -------------------  i i   --------   
  L1M4_orf2#LINE/    822 GGCAAA--GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_131394549_   4204 AAATAAGC-CATGAAAATATGTTCAGCATTGTTACCCAC 4241
                         v       -        v   i   i   ii????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (23 / 16)
Gap_init rate = 0.05 (12 / 229), avg. gap size = 3.33 (40 / 12)  


2557 22.76 1.39 2.01  chrX_131415409_131417033.rev      489  1134 (491)    L1M4_orf2#LINE/L1      267   908 (0)  

  chrX_131415409_    489 GTAATGCTATCAGTAAAAACAGACACATAGACCAATGGAATGAAA--GAG 536
                           ii i  iv  -   ii i     i     i         ii  --   
  L1M4_orf2#LINE/    267 GTGGTACTGGCA-TAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_131415409_    537 AGCCCAGAAATAAACCCACACATTTACAACCAACTGATTTTCAACAAAAG 586
                           i               i       iiii   i        i    ii 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_131415409_    587 CACTAAGAACACGTAATAGGGAAAGGGAAA-CTCTTCAATAAATGGTTCT 635
                         ii i    v  ivi   i       iiv i-  i     i       v  
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_131415409_    636 AGGAAAACTGGATATCCATATGCAAAAGAATGAATCTAGACCGCTATCTC 685
                         i   v         ?   i               vi i    v   i   
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTC 465

  chrX_131415409_    686 TCACCATATACAAAAATCAAT----AATTGATTAAATACTTAAATGTAAG 731
                         v                i  i----   v   i ? v  i          
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_131415409_    732 ACCCCAAACTATGAAATTACTAGAAGAAAACATAGGGA-ATATGCTCCAT 780
                          v iv       i   i vi                ?i- v  -  i i 
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGT 564

  chrX_131415409_    781 GAAATTAGATTGGGCAAGGATTTTTTTAATTTGACTTCAAAAGTGCAGGT 830
                           vv  i i  i     v i   i  vi  v    vi      ii  i i
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_131415409_    831 AACCAAGGCAAAAACGGACAATTGGGATTACATCAAA-TAAAAAACCTCC 879
                            v  i v     ii  i  v v   i v       - v      i ii
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_131415409_    880 GCACAGCAAAGGAAACAATCAATAAAGTGAAGAGACAACCTACAGAATGG 929
                          ii vv       v  v     v        i        i         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_131415409_    930 GAGAAAATATTTACAAACTACACATCTGACAAGGGATTAAAAAGGGATTA 979
                                     i    ii i i      i      i ---------- i
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACT----------TG 754

  chrX_131415409_    980 ATAACCAGAATATATAAGGAGCTCAAACCACTCAATAGGAAAACCCCAAA 1029
                         -  v             i  i   vv  v        iv    vvv    
  L1M4_orf2#LINE/    755 -TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_131415409_   1030 TAATCTGATATAAAAATGGGCCAAAGACCTGAGTAGGCATTTATCAAAAG 1079
                            i ii  v?          v  i  ii   i   i     v  v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_131415409_   1080 AAGATATACAAATGGCCAACAGATATATTTAAAAATGTTCAACATCACTC 1129
                                            i iii i  vv   i   i         ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_131415409_   1130 TGATG 1134
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.11 (97 / 46)
Gap_init rate = 0.01 (9 / 642), avg. gap size = 2.44 (22 / 9)  


3192 26.54 0.66 0.66  chrX_131722971_131731248     2313  3220 (5058)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_131722971_   3220 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 3171
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_131722971_   3170 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3121
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_131722971_   3120 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3073
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_131722971_   3072 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 3023
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_131722971_   3022 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 2973
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_131722971_   2972 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 2923
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_131722971_   2922 AATGGAACAGAAC--AGAGCCCTCAGAAATAA-CGC-TGCTATCTACAAC 2877
                                i    i--    i  --        - v - i -  i  iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATAC-ATTTATGGT 345

C chrX_131722971_   2876 TATCTGATCTTTGACAAACCTCAGAAAAACAAACAATGGGGAAAGGATTC 2827
                         i vi    i  i     ivv vvv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

C chrX_131722971_   2826 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCTTATGTAGAAAGA 2777
                         i  v  i  i              v      v  ?  vi   i i  ii 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

C chrX_131722971_   2776 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 2727
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

C chrX_131722971_   2726 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 2677
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

C chrX_131722971_   2676 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 2627
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chrX_131722971_   2626 AAACACCAAAAGCAACTGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2577
                         vi            vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chrX_131722971_   2576 ATTAAACTCAAGAGCTTCTGCACAGAAAAAGAAATTACCATCAGAGTGAA 2527
                           i   v i  i i   i  ii vvv   i  v i  i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chrX_131722971_   2526 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTGCTCATCTGACA 2477
                         v  i     i   i             v  i    viiiivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chrX_131722971_   2476 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 2427
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chrX_131722971_   2426 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 2377
                           i -    i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chrX_131722971_   2376 TCTCAAAAGAAGACATTTATCCAGCCAAAAAACACATGAAATAATGCTCA 2327
                             v        i  vi vvii     v  i         vi       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chrX_131722971_   2326 CCATCACTGGCCAT 2313
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  

3085 25.85 1.31 1.86  chrX_131722971_131731248     6873  7785 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_131722971_   6873 TGGAAAAATATTCAATTTTCATGGATAGGAAGAATGAATATCATGAAAAT 6922
                               i    i v  v         v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131722971_   6923 GGCCATACTGCCCGAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 6972
                            v     v   i  v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_131722971_   6973 TACCATTGGCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTCAAGTTCA 7020
                          v   viv  i  i  ii     -   -- v  i  - iii v  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_131722971_   7021 TATGGAACAAAAAAAGAGCCCATG-TAGCCAAGACAATCCTAAGCAAAAA 7069
                                - viv  i ii    vi-       i      i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_131722971_   7070 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTATAAGG 7119
                                 i      vv    i  v  ii i      viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_131722971_   7120 CTAGAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGATAAATTGAC 7169
                            v     i   i    ii i       i iv ii i   i v  v  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_131722971_   7170 CAATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATCTACAGCCA 7219
                                 i    iv   ivii         vv   i    i  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_131722971_   7220 TCTGATTTT-GACAAAACTATCAAAAACAAGCAATGGGGAAAGGATTTCC 7268
                         vi       -     iiv ii   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_131722971_   7269 TATTTAATAAATGGTATTGGGAAAAC-AGCTAGCCACATGCAGAAAACTG 7317
                          v  i  i       ii     v   -i v  ?         i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_131722971_   7318 AAACTGGGCCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 7367
                           ii   i     v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_131722971_   7368 TAAAGACTTAAACATAAGACCTAAAACCATAAAATCCCTAGAAGAAAACC 7417
                         i ?    i    ii     v       i      ii i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_131722971_   7418 TAGGCA-ATACCATTCA-GGCATTGGCATGGGCAAAGACTTCATGACTAA 7465
                             ?i- v i -   i- i v    vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_131722971_   7466 AAGACCGAAAGCAACTGCAACAAAAGCCAAAATGGACAAACGGAATCTAA 7515
                         i v   i      vvv          vv     i  i   iv i ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_131722971_   7516 TTAAA-CTAAACAGCTGTGCACAGCAAAAAAAAAACTATCATCAGAGTGA 7564
                          i   -i    v vi v  ii vv    ii v --      vv i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACA--CTATCAAGAAAGTGA 694

  chrX_131722971_   7565 ACAGGCAACCTACAGGCAACCTACAGATTGGGAGAAAATTTTTGCAATCT 7614
                          v  i     i    --  ---------           v       vii
  L1M4_orf2#LINE/    695 AAAGACAACCCACAG--AA---------TGGGAGAAAATATTTGCAAATC 733

  chrX_131722971_   7615 ACCCATCTGACAAAGGGCCAATATCCAGAATCTACAAGGAACT--TA-AA 7661
                          ivi      i  i  i ivi          v  i  i     --  -  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_131722971_   7662 TTTA-CAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATAT 7710
                         i i -i  v     i     i     v  i?    i    ii      v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_131722971_   7711 GAACAAACACTTCTCCAAAGAAGACATTTATGTGGCCAACAAACATATGA 7760
                            i i   i              i  vi vi       i  i  i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_131722971_   7761 AAAAAAGCTCATCATCAGTGGTCAT 7785
                            i v     v     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (147 / 85)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.71 (29 / 17)  


3167 26.52 0.99 0.66  chrX_131740441_131742947.rev     1112  2016 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_131740441_   1112 TGGAAGAGCATTCTATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 1161
                              iiii  i i   i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131740441_   1162 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1211
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_131740441_   1212 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1259
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_131740441_   1260 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 1309
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_131740441_   1310 AACAAGGCTGGAGGCATCACGCTACCTGACATCAAACTATACTACAAGGC 1359
                              i i      vv    i  v  ii iv     viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_131740441_   1360 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1409
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_131740441_   1410 AATGGAACAGAAC--AGGGCCCTCAGAAATAATACCACACATCTACAACC 1457
                                i    i--  i i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_131740441_   1458 ATCTGATCTTTGACAAACCTGACAAAAACCAG-AAATGGGGAAGGGATTC 1506
                          vi    i  i     ivv  v   i -   v-v         i i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAG 395

  chrX_131740441_   1507 CCTATTTAATAAATGCTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1556
                         i  v  i  i     v  i     v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_131740441_   1557 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 1606
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_131740441_   1607 ATTAAAGACATACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 1656
                           i ?    v  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_131740441_   1657 CCTAGACA-ATACCATTCAGGACATAAGCATGGGCAAGGACTTCATGACT 1705
                          v   i?i- v i -   iv   v vi vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_131740441_   1706 AAAACACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCT 1755
                          vi            vvii         vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_131740441_   1756 AATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 1805
                         v  i   v i  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_131740441_   1806 ACAGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTACCCATCTGAC 1855
                          v  i     i       i         v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_131740441_   1856 AAAGGGCTAATATCCAGAATCTACAAAGAACTCA-ACAAATTTACAAGAA 1904
                           i  i  vi          v  i         v-    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_131740441_   1905 AAA--CAAACAACCCCATCAACAAGTAGGCAAAGTATATGAACAGACACT 1952
                            --    i     v  i? v  i i       v  v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_131740441_   1953 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 2002
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_131740441_   2003 TCATCACTGGCCAT 2016
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


1905 28.54 0.77 0.38  chrX_131796797_131800753        1   522 (3435)    L1M4_orf2#LINE/L1       28   551 (357)  

  chrX_131796797_      1 GAAAGAATTAATATTGTTAAAATGTCCACACTACCCAAAGCAATCTACAG 50
                          i    v             i   v v i   v      vii        
  L1M4_orf2#LINE/     28 GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAG 77

  chrX_131796797_     51 ATTCAATGCAATCCCTGTCAAAATACCAATAACATTCTTCATAGAAATAG 100
                               i         i       v   iivi v  i  iii      v 
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chrX_131796797_    101 AAAAAACAAATTCTGAAATTTGTATGAAACTACAGAAGACCCTGAACAGC 150
                          v  -i vi  i  i     ii    i  v i  iii     v   i   
  L1M4_orf2#LINE/    128 ACAA-GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chrX_131796797_    151 CGAAGCAATACTGAGCAAAAAGGACAACGCTGGAGGCAAGACACTACATG 200
                          i  i    vi   iv  i   i    v i      vvvv     v vii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_131796797_    201 ACTTCAAATTATACTAGAAAGTTATAGTAACCACAACAACATGACATTGC 250
                          i      viv     v    i  i     i  vi   iii  ii i  v
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_131796797_    251 TGTAAAAACAGATACATAGACCAATGGAACAGAGTAGAGAACCCAGAAAA 300
                         ii   ii i   i i     i        i   i v    ii       v
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_131796797_    301 AAAATCTGTGTATTTACATCTAACTGATTTTCAACAAAGGCACTAAGAAT 350
                            -i ii ii     iivii  i        i    i  ii i    vi
  L1M4_orf2#LINE/    327 AAA-CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_131796797_    351 ATATATTGGGAAAAGGGCACCCTCTTCAATAACTTGTGCTGGGAAAATTT 400
                           vi v    i    iii vi  i     i  v v         v  i v
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_131796797_    401 GATAGCCACATGCAGAAGAATAAAACTGGACCCTTAGCCCTCATCATGTG 450
                             ?         i      i  ii       i  v i v  i   i i
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_131796797_    451 CAAAAATCAACTCAA----GATTAAAGACTTAAACCTAAGACCTGAAACT 496
                                i       ----   i ?    i    iv     v  i     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_131796797_    497 ATGAAAATACTAGAAGAAAATCTAAG 522
                           i   v vi          iv  i 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGG 551

Transitions / transversions = 2.27 (102 / 45)
Gap_init rate = 0.01 (3 / 524), avg. gap size = 2.00 (6 / 3)  

3363 19.75 5.76 3.27  chrX_131796797_131800753     2579  3464 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_131796797_   2579 TGGAAAAATAGCCCATGTTTTTGAATTGAAAAAC--AATATTGTCCATAT 2626
                               i   v        iv  i    i  i  --        iv v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131796797_   2627 GGCAATACTCCCCAAAATTGATCTACAGATTTAATACAATCCCTAAAAAA 2676
                                         -              i  ii         vv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_131796797_   2677 ATCCCAGCCGGCTTCTTTGTGGATATTGATAAGCTGATGCTAAAATTCAC 2726
                                 i v   i    ii  v     i        v          i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_131796797_   2727 AATGAAATTCAAGGTGCCAAGAATAGCCAAAACAATCTAGAGAAAGAAAA 2776
                          vv     v     vi  v                   v  i      i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_131796797_   2777 AATAAA--TAAAAGATTCGCACTTCCTGCTTTCAAAACTAGCTACAAAGC 2824
                          -i   -- ii i  i  i       iiv          vi         
  L1M4_orf2#LINE/    200 A-CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_131796797_   2825 AACAGTAGTCAAGACTGTGTGTCACTTGATTAAAGATAGCTTTATAGACA 2874
                         v      i       v     vi   v vv   i     viv      iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_131796797_   2875 AGTAAAATAGAAT-------CCAGAAATAAATCCAAACATTTATGATCAA 2917
                          i ii        -------           i   v         i    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_131796797_   2918 CCGGTTTTGTATAATGGTACCAAGGAAAATGAATAAAGAAA-AACAGTCT 2966
                         ii i    vv i  v   i     ivv v v   iii    -  i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_131796797_   2967 T--CAACAAAGGATTCTGGGACAAATAT-TACCTAAATAAAAAAGGATAA 3013
                          --       v i v         v iv-  ? i v  iv     i  i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_131796797_   3014 AGTTATACCAATCTTATGGGTGTGTCTCCTTTTTCACAATATGCACAAAA 3063
                             iv   ------------------   vii     vi  ii      
  L1M4_orf2#LINE/    449 AGTTGGACC------------------CCTACCTCACACCATATACAAAA 480

  chrX_131796797_   3064 ATTAACCTGAAATAGATCATTGACCTTACTGTAAAAGGTTAAACTATAAA 3113
                               iii    i     ?v     v v     i  v v          
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_131796797_   3114 ACTCTTAAAAGCAGATATAGGAGTAAATTTTTGTGAAC----ACTAGGCA 3159
                                i   v i i     ?      i  i    v ----ii      
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_131796797_   3160 AAGCCTTC--AGA------------------AGTGACAAAGAAAAAAAT- 3188
                          v vi   --   ------------------  ii     ii       -
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_131796797_   3189 --TAAATTGGACTTCACCAAAATTTAAAACTTTCCTGCTTCAATGGGTAC 3236
                         --              i       v        iv        v  ii  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_131796797_   3237 CTTCAAGAAAGTGAAGCAACAACC-ACTGAATGGGGGTAAAATGTTTGCA 3285
                         iv             ivi      -  v       i -     i      
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG-AAAATATTTGCA 729

  chrX_131796797_   3286 AAGCGTATATCTTATAAGAGACTTGAACCTAGAATATGTTTAAAAAAAAC 3335
                           v i       v     i      v i i       i ----   i   
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATAT----AAAGAAC 775

  chrX_131796797_   3336 -----CAATT-AATATTAAAAAGAAAAAGAAATAACACAATT-AAGAATG 3378
                         -----   i -    v        v   ----    v     -  i    
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAA----TAACCCAATTWAAAAATG 821

  chrX_131796797_   3379 T-CAAACAACCTGTATAGATATTTCTCCAGAGAAGATACTCAAATGGGCA 3427
                         v-    vi ii  v     i         i        iv       v  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_131796797_   3428 ATAGGCACATGAAAAAATGTTTAACATCATTAGCCAT 3464
                            i           i   i i       ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (103 / 69)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.81 (80 / 21)  


3315 25.55 0.99 0.99  chrX_131868722_131875130     5009  5916 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_131868722_   5009 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATTGTGAAAAT 5058
                              ii i  i     i i    i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131868722_   5059 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_131868722_   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_131868722_   5157 TATGGAAATAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5206
                                  iv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_131868722_   5207 AACAAAGCCGGAGGCATCACACTACCTCACTTCAAACTATACTACAAGGC 5256
                                ii     vv       v  iv i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_131868722_   5257 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5306
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_131868722_   5307 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 5354
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_131868722_   5355 ATCTGATCTTTGACAAACTTGACAAAAACAAGAAATCGGGAAAGGATTCC 5404
                          vi    i  i     ivv  v   i v  vvv   v       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_131868722_   5405 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCTTATGTAGAAAGCT 5454
                           v  i  i              v      v  ?  vi   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_131868722_   5455 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5504
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_131868722_   5505 TTAAAGACTTACATGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAAC 5554
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_131868722_   5555 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5603
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_131868722_   5604 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5653
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_131868722_   5654 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5703
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_131868722_   5704 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5753
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_131868722_   5754 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5803
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_131868722_   5804 AAAACAAAGAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGATACTT 5853
                           i     v     v  i?    i    ii      v    i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_131868722_   5854 CTCAAAAGAAGACAATTATGCA----GCCAAAAAACACATGAAAAAATGC 5899
                            v        ----   i  ----     v  i          i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_131868722_   5900 TCATCATCACTGGCCAT 5916
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (134 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.00 (18 / 9)  


2863 27.47 1.56 0.67  chrX_131895977_131902708.rev     5343  6241 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_131895977_   5343 GAAAAAAAATTCCATGTTCATGGATAGGAAGAATCAGTAT-G--AACATG 5389
                          i   i v  i              v      v i i   - --  v   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_131895977_   5390 ACCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGCT 5439
                         i v     v      v i  i  i        i  v  i  i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_131895977_   5440 ACCATTTAG-TTTTTCACATAACTAGAAAAAACT--TCCTTAAACTTCAT 5486
                         v   vi iv-     ii  v  v v  v  i-  --    -   v     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCT-AAAATTCAT 149

  chrX_131895977_   5487 ATGGAACCAAAAAAGAGCCCATATAGCTAAGACAATCCTGAGCAAAAAGA 5536
                               viiv  ii  v  viv     i  i      i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_131895977_   5537 ACAATGCTGGAGGCATCATGCTACCTGAGTTCAAACTATACTACAAGGCT 5586
                             v i      vv   ii  v  ii v      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_131895977_   5587 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 5636
                                i   i    ii         i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_131895977_   5637 GTGGAACAAAAC--AGAGTCTTCAGAAATAACAGCACACATCTACAACCA 5684
                         i     i i  i--      --         vvv  i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGTCA 347

  chrX_131895977_   5685 TCTGATCTTCACCAAACCTGACAAAAACAAACAATGGGGAAAGGATTCCC 5734
                         vi    i   iv   ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_131895977_   5735 TATTTAACAAATGGTGTTAGGAAAACTGGCTAGCCATATGCAGAAAACAG 5784
                          v  i           i i   v      v  ?   i     i  i vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_131895977_   5785 AAACTGGAGCCTCT-TCTTACCTCTTAAACAAAAATTAACTCAAGATGGA 5833
                           ii    -  i  -i  i  vi v  v                i     
  L1M4_orf2#LINE/    448 AAGTTGGA-CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_131895977_   5834 TTAAAGACTTAAATGTAAAACCTAAAACTATAAAAACCCTAGAAGAAAAC 5883
                          i ?    i         i v              vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_131895977_   5884 CTAGGCA-ATACCATTCAGGACATAGGTATGGGCGAAGACTTCATGACTA 5932
                         v    ?i- v i -   iv   v v  vv i   i v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_131895977_   5933 AAACACCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5982
                         vi            vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_131895977_   5983 ATTAAACTAAAGTGCTTCTGCTCAGCAAAAGAATTTATCCTCAGAGTGAA 6032
                           i   v v  ivi   i  iv vv    i  vvi    vvv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_131895977_   6033 CAGGCAACCTACCAAATGGGAGAAATTTTTTGCAATCTATCCATCTGACA 6082
                         v  i     i  vi           v v       vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_131895977_   6083 AAAGTCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 6132
                          ii v  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_131895977_   6133 AAAACAA----CCCCATCAAAAAGTGCGTGAAGGATATAAACAGATACTC 6178
                           i    ----   v  i?    i  v ii      v i  i   i i i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_131895977_   6179 CTCAAAAGAAGACATTTATGTGGCCAACAAACGTATGAATAAAAGCTTGT 6228
                            v        i  vi vi       i  i ii     v i v   iiv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_131895977_   6229 CATCACTGGTCAT 6241
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (136 / 107)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 1.54 (20 / 13)  


2785 28.34 0.99 0.88  chrX_131922768_131927184     3018  3924 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_131922768_   3018 TGGAAAAAAATTCCACACTCATGGAT-AGATGAATCAAAATCATGAAAAT 3066
                               i v  i   iii        -i  v  v i  v  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131922768_   3067 GGCCATACCACCCAAAGTAATTTATAAATTCAATGCTATTTCCATCAAGC 3116
                            v    iv      v i  i  i i      i  v  ii i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_131922768_   3117 TACCATTTACTTTCTTCACAGAACTACAAAAAACT-ACTGTAAATTTCAT 3165
                          v   vi i i  i  ii     v -ii v  i  - iiv    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_131922768_   3166 ATGGAACCAAAAAGCAGCCCACATAACCAAGAGAATCCTAAGCAAAAAGA 3215
                               viiv  i v v  viv   i    i v    i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_131922768_   3216 ACAAAGCTGGAGGCAC-CATGCTACCTGGCTTCAAA--CTAGTCTACAAG 3262
                               i      -  -  ii  v  iiii      --i  --      i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTA--CTACAAA 246

  chrX_131922768_   3263 GCTACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGATACGTAGA 3312
                                   i v i    ii         i iv ii i   i ii    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_131922768_   3313 CCAATAGAACAGAACAGAGGCCTCAGAAATAACTCCACACATATACAACT 3362
                         i    i   i    iv   ivii         vi   i    v  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_131922768_   3363 ATCTGATCTG-GAGAAATCTGACAAAAACAAGCAATGGGGAAAGCATTCC 3411
                          vi    i v-  v  ivv  v   i v  vv            v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_131922768_   3412 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTGATATGCAGAAAACA 3461
                           v  i  i              v      v  ?iv i     i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_131922768_   3462 GAAAGTGAATCCCTTCCTTCCACCTTATGCAAAAATTAACTCAAGATGAA 3511
                            iv  i i    v   iv    v   i               i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_131922768_   3512 TTAAAGACTTAAATGTAAAA-CTCAAAAACCATAAAAACTCT-AGAAGAA 3559
                          i ?    i         i -  --     i      -    -       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCT--AAAACTATAAAA-CTCTTAGAAGAA 543

  chrX_131922768_   3560 AACCTAGGCA-ATACCACCCAGGACATAGGGATGGGCAAAGACTTCATGA 3608
                            v    ?i- v i -ii iv   v v   v i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_131922768_   3609 ATAAAACACCAAAAGCAACTGCAACAAAAGCCAGAATTGACAAATGGGAT 3658
                            vi            vvv          vv i   v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_131922768_   3659 CTAATTAAACTAAAGAACTTCTGCTCAGCAAAAGAAACTATCATCAGAGT 3708
                         i v  i   v v  i     i  iv vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_131922768_   3709 GAACAGGCAACCCACAGAATGGGAAAAAATTTTTGCAGTCTATCCATCTG 3758
                            v  i                 i     v      ivii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_131922768_   3759 ACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACACATTTACAAG 3808
                          i  i  i  vi          v  i  i     ivv   vv iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_131922768_   3809 AAAAAAGCAAACAACCCCATCAAAAATTAGGTGAAGAATATGAACAGACA 3858
                              ii    i     v  i?    v i  ii   i  v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_131922768_   3859 ATTCTCAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAAAGTT 3908
                         v     v        i  vi viii     i ii  i       i v i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_131922768_   3909 CATCATCACTGGTCAT 3924
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (154 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.21 (17 / 14)  


3079 27.53 0.66 0.66  chrX_131968215_131975829      492  1399 (6216)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_131968215_   1399 TGGAAGAACATTCCATGCTTATGGATAGGAAGAATCAATATTGTGAAAAT 1350
                              ii i  i     i i      v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_131968215_   1349 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1300
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_131968215_   1299 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1252
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_131968215_   1251 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1202
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_131968215_   1201 AACAAAGCTGGCGGCATCACACTACCTGACTCCAAACTATACTACAAGGC 1152
                                i   v  vv       v  ii i i    viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_131968215_   1151 TACAGTAACCAAAATATCATGGTACTGCTACCAAAACAGAGACATAGACC 1102
                                 i   i i vii        vi iv ii i   v i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_131968215_   1101 AATGGAACGGAAC--AGGGCCCTCAGAAATAATGCCACACATCTACAACT 1054
                                ii   i--  i i  --        vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chrX_131968215_   1053 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1004
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_131968215_   1003 CTATTTAATAAATGGTGCGGGGAAAACTGTCTAGCCATATGTAGAAAGCT 954
                           v  i  i         v    v     vv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_131968215_    953 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 904
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_131968215_    903 TTAAAGACTTACACGTTAGACCTAAAACCGTAAAAACCCTAGAAGAAAAC 854
                          i ?    i  v i  v   v       ii     vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_131968215_    853 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 805
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chrX_131968215_    804 AAACACCAAAAGCAATGGCAATGAAAGCCAAAATTGACAAATGGGATCTA 755
                         vi            vvi    ii    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chrX_131968215_    754 ATTAAAGTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 705
                           i   i v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chrX_131968215_    704 CAGGCAACCAA-AGAATGGGAGAAAATTTTAGCAACCTACTCATCTGACA 656
                         v  i     v -               v  v    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chrX_131968215_    655 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 606
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chrX_131968215_    605 AAAAACAAACAACCCCATTAAAAAGTGGGTGAAGGACATGAAAAGACACT 556
                           i -    i     v   ?    i    ii     iv    v     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

C chrX_131968215_    555 TCTCAAAAGAAGACATATATGCAGCCAACAGACACATGAAAAAATGCTCA 506
                             v        i   i viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

C chrX_131968215_    505 TCATCACTGGCCAT 492
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (147 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  

3261 26.73 0.44 0.55  chrX_131968215_131975829     6214  7122 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_131968215_   6214 TGGAAGAACATTCCATGCTTATGGGTAGGAAGAATCAATATTGTGAAAAT 6263
                              ii i  i     i i    i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_131968215_   6264 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 6313
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_131968215_   6314 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6361
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_131968215_   6362 TATGGAATCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 6411
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_131968215_   6412 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6461
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_131968215_   6462 TACAGTAAACAAGACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 6511
                                 v        ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_131968215_   6512 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 6559
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_131968215_   6560 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 6609
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_131968215_   6610 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6659
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_131968215_   6660 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 6709
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_131968215_   6710 TTAAAGACTTACACGTTAGACCTAAAACCGTAAAAACCCTAGAAGAAAAC 6759
                          i ?    i  v i  v   v       ii     vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_131968215_   6760 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 6809
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_131968215_   6810 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGTATCTAA 6859
                         i            vvi           v     v  i    v v ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_131968215_   6860 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGATTGAAC 6909
                          i   v v  i i   i  ii vv    i  v    i  vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_131968215_   6910 AGGCAACCTACAAAATGGGAGAAAATTTTAGCAACCTACTCATCTGACAA 6959
                           i     i   i             v  v    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_131968215_   6960 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 7009
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_131968215_   7010 AAAACAAACAACCCCATTAAAAAGTGGGTGAAGGACATGAAAAGACACTT 7059
                          i -    i     v   ?    i    ii     iv    v     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_131968215_   7060 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 7109
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_131968215_   7110 CATCACTGGCCAT 7122
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2342 28.51 0.58 0.44  chrX_132017814_132025901     5603  6286 (1801)    L1M4_orf2#LINE/L1        1   685 (223)  

  chrX_132017814_   5603 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5652
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_132017814_   5653 GGCCATACTGCCCAAAGTAATTTGTAGATTCAATGTTATCCTCATCAAGC 5702
                            v     v      v i  i ii        i iv    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_132017814_   5703 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACTA--CTTAAACTTCA 5749
                          v   vivi i  i  ii     -   -- v  i  i-- i    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_132017814_   5750 TATGGAACCAAAAAAGAGCCCGCATAGCCAAGAAAATCCTGGGCAAGAAG 5799
                                viiv  ii  v  v v        i v    i  iiv      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_132017814_   5800 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5849
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_132017814_   5850 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5899
                                 i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_132017814_   5900 AATGGAACAGAACAGAGGCCTTGGAAATAAAATCACACATCTACAACCAT 5949
                                i    iv   iviiii        vi  i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_132017814_   5950 CTGATCTTTGAGAAACCTGACACAAACAAGCAATGGGGAAAAGATTCCCT 5999
                         i    i  i  v  ivv  v  vi v  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_132017814_   6000 ATATAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 6049
                         v vi  i        i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_132017814_   6050 AACTGGACCCCTTCCTTATACCTTATACAAAAATCAACTCAAGATAGCTC 6099
                          ii         v   i i   v           i       i  i v  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_132017814_   6100 ATATTCTTAAACGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAACCT 6149
                          ? vv i    i      v   ii  i      v  i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_132017814_   6150 GGGCA-ATACCATTCAGGACATAGGCATATACAAAGACTTCATATCTAAA 6198
                         i  ?i- v i -   iv   v v  vv  vi   v ii   v  vv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_132017814_   6199 ACAACAAAAGCAATGGCAATAAAAGCCAAAATTGACACATGGGATCTAAT 6248
                            v        vvi    i     vv     v  i v  v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_132017814_   6249 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCA 6286
                         i   v v  i i   i  ii vv    i  v       
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

Transitions / transversions = 1.43 (113 / 79)
Gap_init rate = 0.01 (5 / 685), avg. gap size = 1.40 (7 / 5)  

 809 21.40 0.00 4.80  chrX_132017814_132025901     7367  7595 (492)    L1M4_orf2#LINE/L1      691   908 (0)  

  chrX_132017814_   7367 GTAAACAGGCAACCTACAGAATTCTCCCTACAGGGAGAAAATTTTTCCAA 7416
                           i  v  i     i       ----------          v   v   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAAT----------GGGAGAAAATATTTGCAA 730

  chrX_132017814_   7417 TCTATCCATCTGACAAAGGGCTACTATCCAGAATCTACAAAGAACTTAAA 7466
                         vii  vi      i  i  i  vv          v  i        ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_132017814_   7467 CAAATTTACAAGAAAAAAACCAAACAACCCTATCAAAAAGTGGGCAAATG 7516
                            v iv i  v     i  -   i     v  i?    i        v 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_132017814_   7517 ATATGAACAGACACTTCTCAAAAGAAGACATGTATGCAGCCAACAAACAT 7566
                           v    i     i     v        i  ii viii     i  i  i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_132017814_   7567 ATGAAAAAATGCTCATCATCACTGGTCAT 7595
                                i       v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (29 / 19)
Gap_init rate = 0.01 (2 / 218), avg. gap size = 5.50 (11 / 2)  


3184 26.98 0.44 0.44  chrX_132137745_132144417     5273  6180 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_132137745_   5273 TGGAAAAATATTCCATGCGCATGGATAAGAAGAATCAATAACATGAAAAT 5322
                               i    i     iv       vi     v i    vii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_132137745_   5323 GGCCATACTTTCCAAAATAATTTATAGATTCAATGCTATGCTCATCAAGC 5372
                            v     ii     v i  i  i        i  v  v ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_132137745_   5373 TACCATTGACTTTCTTCACAGAATTAGAAAAGGCT-ACTTTAAATTTCAT 5421
                          v   vivi i  i  ii     v v  v   -  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_132137745_   5422 ATAGAACCAAAAAAGAGTCCGTATAGCCAAGACAATCCTAAGCAAAAAGA 5471
                           i   viiv  ii  vi v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_132137745_   5472 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCC 5521
                               i      vv       v  ii i      viv        i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_132137745_   5522 ACGGTAACCAAAACACCATGACACTATTACCAAAACAGATATATAGATGA 5571
                           i    i   i   vii  ii   ivi iv ii i   i        v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_132137745_   5572 ATCGAACAGAACAGAGGCCTCAGAAATAACGCCACACATTTACAACCATC 5621
                           v   i    iv   ivii         vv   i       iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_132137745_   5622 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5671
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_132137745_   5672 TTTAACAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAATGAG 5721
                           i           i     v      v  ?   i     i  i     i
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_132137745_   5722 ACTGGGCCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 5771
                         ii   i     v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_132137745_   5772 AAGAGTTAAATGTAAGACCTAAAACCATCAAAACCCT-AGAAGAAAACCT 5820
                         ?   vi           v       i  -     i  -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chrX_132137745_   5821 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGAGTAAA 5869
                            ?i- v i -   iv   v v  vv i     v ii   v iii  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_132137745_   5870 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGTATCTAAT 5919
                                     vvi          vv     v  i    v v ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_132137745_   5920 TAAACTAAAGAGCTTCTGCATAGTAAAAGAAACTATCATCAGAGTGAACA 5969
                         i   v v  i i   i  iiivvi   i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_132137745_   5970 GGCAACCTACAGAATGGGAGAAAATTTTTCCAATCTATCCATCTGACAAA 6019
                          i     i                 v   v   vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_132137745_   6020 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 6069
                           i  vi          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_132137745_   6070 AACAAACAACCCCATCAAAAAGTGGGCAA-TGCTATGAACAGACACTTCT 6118
                         i     i     v  i?    i       -v v v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_132137745_   6119 CAAAAGAAGACATTTATGCAGCCAACAGACATATGAAAAAAATGCTCATC 6168
                          v        i  vi viii     i ii  i       i -      v 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAAC 896

  chrX_132137745_   6169 ATCACTGGTCAT 6180
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (143 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.00 (8 / 8)  


4108 15.90 1.58 1.94  chrX_132376837_132378660.rev      502  1325 (499)    L1M4_orf2#LINE/L1       43   863 (45)  

  chrX_132376837_    502 GTAAAGATGGTAATGCTCTCCAAATTTATCTGCAGATTCAACACAATTTC 551
                           v       i   i   i       v    i          i    ii 
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chrX_132376837_    552 TATCAAAATCCCAGCTGGTTTCCTTTGCAGAAATTGACAAGCCGATCCTA 601
                                          vi  -i                   i       
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_132376837_    602 AAATTCATATGGTAATGCAAAGGACATATAATAGCTCAAACAATATTGAA 651
                                     v       i    vi v      iv       v     
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_132376837_    652 A--GAAGAACAAAGTTGGAGGAATCGCATCTTCCCA-TTTTAAAACTTAA 698
                          --                   v  i  -       -   i        -
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACA-CTTCCCAATTTCAAAACTTA- 239

  chrX_132376837_    699 CTACAAAGCAAGAGTAATCAAGATCAAGATAGCATGGTATTGGCAT-TGC 747
                                  v v           ------i  ii     i      -v v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGA------CAGTGTGGTACTGGCATAAGG 283

  chrX_132376837_    748 ATTGACATATAGATCAATCAAACAGAACTGAG--TCCAGAAATGAACCCC 795
                           v               vi  i    i    --         i     v
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_132376837_    796 TGCTCCTTGAGTCAGTTGATTTTTTTGTACAAGAGAGTCAAGATCATTCA 845
                          i vii vvi    i        --i -     i v i     i      
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTT--CG-ACAAGGGTGCCAAGACCATTCA 380

  chrX_132376837_    846 ATGAGGAAAGAATAGTCCCTTCAACAAATGATGCTGACACATCTGGATAT 895
                            i             ii           i     iv   v       ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_132376837_    896 CTACATGCAAAAGAAGAAAATTGTACCCCTACCTCACACCATACACAAAA 945
                          i             vi  i   v                   i      
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_132376837_    946 ATTAACTCAAAATTGGTCAAAGACTTAAATGTGAGAGCTAAAACTATAAC 995
                                      v i   ?    i       i                v
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_132376837_    996 ATTCTTAGAAAAAAACATAAGGGTGAATTTTTATGACATTGGATTTGGCA 1045
                          i        i        i ?  i   i  ii    v    i  v    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_132376837_   1046 ATGGGTACTTAGATATAACACCAAAAGTACAAGCAACTATAACAAAAATA 1095
                             v v         i          i         - v  v     - 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-AAAAGAAAAA-A 628

  chrX_132376837_   1096 TAGATAAATTAGACATCACCAAAATTAAAGAGTTT-GTGCTTCAAAGAAT 1144
                                   i   v   i          i v   -           i i
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_132376837_   1145 ACCA-GAAGAAAATGAAAAGATAAATCACAGAATGCAAAAATATATTTTA 1193
                           i -v      i        i  vi         vi i  v      vv
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_132376837_   1194 AAATAAAATGTCTGATAAGAAACATGTATCTGGAATACATAAATAATTCT 1243
                             v v  i         ii  v      ii     i     v  i   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_132376837_   1244 TACAATGTGATAATGAAAAGA--AATAAGCCAATT--ATAATGGGCAAAG 1289
                              ivii     i      --     v      -- v           
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_132376837_   1290 GATCTGAATAGTCATTTA-CCAAAGAATGAATATATA 1325
                            i       v     v-        --i     i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAA--GATATACA 863

Transitions / transversions = 1.61 (79 / 49)
Gap_init rate = 0.02 (18 / 821), avg. gap size = 1.61 (29 / 18)  

 251 11.54 0.00 0.00  chrX_132376837_132378660.rev     1374  1425 (399)    L1M4_orf2#LINE/L1      857   908 (0)  

  chrX_132376837_   1374 ATACACATATACCCAATAAGCACATAAAAAGATGCTCAACACCACCATTA 1423
                            i   v  iv             i               i  ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_132376837_   1424 GC 1425
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.00 (4 / 2)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.00 (0 / 0)  


3203 25.69 1.21 1.10  chrX_132480228_132486624     4998  5904 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_132480228_   4998 TGGAAGAACATTCCATGCTCATGGATAAGAAGAATCAATATTGTGAAAAT 5047
                              ii i  i     i        vi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_132480228_   5048 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5097
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_132480228_   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_132480228_   5146 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAG 5195
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_132480228_   5196 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_132480228_   5246 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5295
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_132480228_   5296 AATGGAATAGAAC--AGAGCCCTTAGAAATAATATCACACATCTACAACC 5343
                                     i--    i  --        vvi  i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_132480228_   5344 ATCTGATCTTTGACATACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5393
                          vi    i  i    vivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_132480228_   5394 CTATTTAATAAGTGGTGCTGGGAAAACTTGCTAGACATATGTAGAAAGCT 5443
                           v  i  i  i           v    v v  ?v  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_132480228_   5444 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5493
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_132480228_   5494 TTAAAGACTTAAATGTTAGACCTAAAATCATAAAAACCCTAGAAGAAAAC 5543
                          i ?    i       v   v      ii      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_132480228_   5544 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTTATGACTA 5592
                         v    ?i- v i -   iv   v v  vv i     v ii  iv iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_132480228_   5593 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATGTA 5642
                         vi            vvi          vv     v  i    v   iv v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_132480228_   5643 ATTAAACTAAAGAGCTTCTGCATAACAAAAGAAACTATCATCAGAGTGAA 5692
                           i   v v  i i   i  iiivv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_132480228_   5693 CAGA-AACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTCTCA 5741
                         v   -    i                 v   i   vii ivi    vvi 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_132480228_   5742 AGGGG-TAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAA 5790
                             i- vi          v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_132480228_   5791 AAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5840
                           i -    i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_132480228_   5841 TCTCAAAAGAAGACAGTTATGCA----GCCAACACACACATGAAAAAATG 5886
                             v        ----   i  ----     i vi          i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGA----TATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_132480228_   5887 CTCATCATCACTGGCCAT 5904
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (135 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


3666 14.60 5.92 0.58  chrX_132592508_132596186     2029  2720 (959)    L1M4_orf2#LINE/L1        1   729 (179)  

  chrX_132592508_   2029 TGAAAAGACAT-------TAATATATTAGAAGACTTAAT---GTCAAGAT 2068
                           i     i  ------- v  iv   i           ---  i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_132592508_   2069 GGCAATACCTCCTAAATT-ATCTACAGATTTAACACAATCGCTATCAAAA 2117
                                 ii  i     -           i   i     v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_132592508_   2118 TCTCAGCTGACTTCTTTGCATAAATTGACAAGTTGCTCATAAAATTCATA 2167
                           i      v   i      v           i  v  v           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_132592508_   2168 TGGAATTGCAGGGGGCCCCAAATAGCCAAAACAATCTTGAAAA-GAAGAG 2216
                              v    i   i   vi                       -     i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_132592508_   2217 CAAAGTTGGAGAACTCACACTTCCCATTTTCAAAACTTGCTACAAAG--- 2263
                                    i              v           i        ---
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_132592508_   2264 ---TATTCAAAGCAGCATGGCACTGGCATAATGATAGACATAGAGATCAA 2310
                         ---  v    ii   ii   i          v          v       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_132592508_   2311 TAAAATAGAATTGAGAGTC-AAAAA-AAACCCTACATACATTTATGGTCA 2358
                          ii                - i   -      ---               
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCC---ATACATTTATGGTCA 347

  chrX_132592508_   2359 ATTGAATTTTGATGATAGTGCCAAGACAATTCATGGGGGAAAGAACAGTC 2408
                              v   i  ii vi          v     vv          i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_132592508_   2409 TTTTCAACAAATGGAACTTGGGACAAAAGGATATCCACATATAGAAGAAT 2458
                                       vi  -       vv     ?      ii i      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_132592508_   2459 GAAGTTGTGCCACTACCTCATACCATATACAAAAATTAGCTCAAA-TGAA 2507
                                vi  v        i                 i      -  i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_132592508_   2508 TCATAGACCTATATTTAAGGGCTGATTCTATAAAATTCTTAGAAGAAATC 2557
                            ?       v  v    i   i vv        i            v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_132592508_   2558 ATAGGTATAAATCTTTATGCCCTTGGATTAGGCAGTGATTTCTTAGATAT 2607
                              ?i        ii  v      i       i  i            
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_132592508_   2608 GACACATAAAG------------------AAATATATAAATTGAACTTCA 2639
                              vv    ------------------     v        i      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_132592508_   2640 TCAAAATCATAA-TTTTTGAG-TTAAAAAGACATTATCAGGAAAGTGAAA 2687
                                i v  -i     v -  v   i    i     i          
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_132592508_   2688 AGACATCCCAGAATATAGGAGAAAATAATTATA 2720
                              v    v iv  i          v  ii 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCA 729

Transitions / transversions = 1.51 (59 / 39)
Gap_init rate = 0.02 (13 / 729), avg. gap size = 3.46 (45 / 13)  

 734 16.47 7.06 0.00  chrX_132592508_132596186     3017  3186 (493)    L1M4_orf2#LINE/L1      727   908 (0)  

  chrX_132592508_   3017 GTAAATCATGTATGTGATAAGGGTCTAGTATCCAGAATATGTAAATAATC 3066
                          i       i   v         v  v             i    v  ii
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_132592508_   3067 CTTACAATTGAACAATGAAATGACAAATAGCCCAGTTTAAAATT---TAA 3113
                                i v  i   i   v        i    i  ?    v ---i  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_132592508_   3114 --GATTTCAATAGACGTTTTACCAAAAAAGAT---C---TGGCCAATAAG 3155
                         --     v       i   iv     i     --- ---           
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_132592508_   3156 CACATGAAAAT-CACCCAACATCATTAATCAT 3186
                                   v-ii i        ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.03 (5 / 182), avg. gap size = 2.40 (12 / 5)  


3102 23.04 2.72 4.02  chrX_132618136_132620094      547  1466 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_132618136_    547 TGAAGAGATACTCCATGTTTATGGATAGAAAGACTCAATATTATTAAGTT 596
                           i i     ii       i      v i      i      i     v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_132618136_    597 TTCAATTCTTTCCAACATGATCTATAAATTCAATG-AATCCCAATCAAAA 645
                         vv    v  ii    vv       i i      i -      v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_132618136_    646 TCCCTGCAACTTATTTTGTGGACATCAATAG--------TAAAGTTTATA 687
                             v  vi i v     ii  v  ii i i--------    i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_132618136_    688 TGGAAACATAAAAGACTCAAAATAGCTGTAACAGCACTGCAAAAGAA--- 734
                               iii  ii   i  i      iiv    iivi  v       ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_132618136_    735 CAAAGTTGGAGGACTGGCATGACCTGAATTCAAGAATTCCCATCAAGGTA 784
                                        vi  ivv  ii v     i v  v i iv   v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_132618136_    785 CAGTAATAAAGACAGCTTGGTATTGGTGAAAGAATTGAAAAACAGATCCA 834
                                v       iv     i   iiv   i  v  v v i     v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_132618136_    835 TGGAACAAAATACAGAGCCCAGAAATAGACCCACACAAATACAATAATCA 884
                              i i   vv    i         i     i   vv  --- ii   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA---TGGTCA 347

  chrX_132618136_    885 ACTGATCTTTGACAAAAGAGCAGAGACAATTCAATGGAGAAAGAATAATC 934
                          i    i  i     ii v  vi    v         i         i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_132618136_    935 TTTGCAACAAATAGTGCTGAAACAATTGGACATCCACATGCAAAA-AATG 983
                            v        i      ii    i    i ?            -    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_132618136_    984 AATCTAGATATAGACTTTTCACCTTTCATAAAA-TTAAGTCAAA-TATAT 1031
                           vi i  ivivv  i iv    v vi i    -    v     - iv  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_132618136_   1032 CATAGACATAAACATAAAATGC-AAAACTATAAAACTTATAGAATGTAAA 1080
                           ?    v    ii   i -  -              iv     - v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAA-GAAAA 545

  chrX_132618136_   1081 -GTGGGAGT---TCTTGGTGACTGACCTTAAGTTTAGCAGTAAGTTTTTA 1126
                         -i i  ?  ---    v     ----   ii   vi   i iiv  i   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGAC----CTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_132618136_   1127 GATATAACAGTAAAAGCACAATCTATGAAGTTGAAAATTGATTAGTCAGA 1176
                              i   vi          v v ii  ivvi     v   v i ii  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_132618136_   1177 CTT-ATCAGGCACTAAGCAGAAAAACATCCATTCTGCAATGTTAAGAGAA 1225
                            -    ii- i   ------    v ---  v   ----  v i  i 
  L1M4_orf2#LINE/    642 CTTCATCAAA-ATTAA------AAACTT---TTGTGC----TTCAAAGGA 677

  chrX_132618136_   1226 TGAAGAGTAAAGCATATGTCAAGAAAATGAAAAGACAAGCCACAGACTAA 1275
                         ------------  i- i        i           v       v ii
  L1M4_orf2#LINE/    678 ------------CAC-TATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_132618136_   1276 GAGAAAATATTTGCAAAACACATGTCTGATAAAGGCCTTGTATCCAAAAC 1325
                                          v  i  i        i  v          i  i
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_132618136_   1326 ACTCAAAGAACACTTGCAATTCAACAGTAAGAAAACAA----CCCAATTA 1371
                          ivi       v   i   i    i i   i  i    ----       ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_132618136_   1372 AAAAATGGGCAGAAGATCTGAACAGACATCTCACCAAAGAAGATATACAG 1421
                                    i i   i    i      i  v                i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_132618136_   1422 ATGGGGAAAAAAAACTAGAAAAAGATATTCAATATCATATGTTAT 1466
                             vv  v  iv  - vi       ii    i    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCAC-ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (133 / 75)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.82 (62 / 22)  


2908 19.10 0.48 1.77  chrX_132787733_132789347.rev      502  1124 (491)    L1M4_orf2#LINE/L1      294   908 (0)  

  chrX_132787733_    502 AAACCAGTGGAACAGAATCAAGAACCCAAAAATGAACCCAAACATATGTG 551
                          i i  i     i     ii   ii   i    i      v    v i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_132787733_    552 GTCAACTAATTTTCCACAAGGGCACCAAAAAGGACA--CAATGGAGAAAG 599
                              i i      v       ii    i v---  --      i     
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAAAG 390

  chrX_132787733_    600 AATAGTCTTTTCAATAAATGGTGCTGAGAGAACAGGATTTCCACATGCAA 649
                                       i           i  v   v    v?          
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_132787733_    650 AAGAATTAAATTGGACCCTTATCTTATACTGTACATAAAAATCAACTTAA 699
                               v  i        i  i  i i  ii  i i      i    i  
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_132787733_    700 AATGGATGA-AGACCTAAAAGTAAGACCTGAAACCATAAACCTTTTAGAA 748
                                v -         v      v  i    i     v  i      
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_132787733_    749 GAAAACATAGGGGAAAAGCTCCTTGGCATTGACCTTGGCAATGATTTTAT 798
                                    ? v   v  i v  i v   ivi v       i   iv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_132787733_    799 GGATATCACACCAAAAGCTCAGGCTACAAAAGCAAAAATAAGTAAATGGG 848
                         i     v           v  i  v       v       ii     v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_132787733_    849 ACTACATCAAACTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAGCAAA 898
                            v       v v    i   i  ii vv       v  v    iv   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_132787733_    899 ATGAAAAGGCAACCTACAGATTGGGAAAATGGTTGCAAATATTTACAAAC 948
                         i       i     i     v     i  --------       i    i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAA--------AATATTTGCAAAT 732

  chrX_132787733_    949 CTTATATCTGATAAGGGGTTAATATCCAAGATTTATAAAGAACTCATACA 998
                          v               ii vi      ii  v            v    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_132787733_    999 ACTCAATAGGAAGAAAACATATAACTTGATTTAAAAATGGGCAAAGGACT 1048
                                 iv  i  i   v     iii   ?                i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_132787733_   1049 TGAATAGATATTTCTCCAAAGATGACATAAAAATAGCCAACAGGTACCTG 1098
                                 i             v  i   v    i     i i i  v  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_132787733_   1099 AAAAAATGCTAAACATCACTAATCAT 1124
                             i     v       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (73 / 43)
Gap_init rate = 0.01 (4 / 615), avg. gap size = 3.50 (14 / 4)  


3254 26.13 0.66 0.99  chrX_132903961_132910356.rev     4995  5905 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_132903961_   4995 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATGGTGAAAAT 5044
                              ii i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_132903961_   5045 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCGTCAAGC 5094
                            v     v     iv i  i  i        i  v     ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_132903961_   5095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5142
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_132903961_   5143 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAA 5192
                                viiv  ii  v  v v  v     iv     i i iv-  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA-AAGAA 197

  chrX_132903961_   5193 AAACAAAGCTGGAGGCATCATGATACCTGACTTCAAACTATACTACAAAG 5242
                         i       i      vv   iiv v  ii i      viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_132903961_   5243 CTACAGTAACCAAAACAGCATGGTACTGGTACTAAAACAGAGATATAGAC 5292
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_132903961_   5293 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATTTACAAC 5340
                                 i    i--    i  --        vv  ii i     iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_132903961_   5341 TATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGGGAAAGGAT 5390
                         i vi    i  i     ivv  v   i v  vv        --    i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAAGAAT 393

  chrX_132903961_   5391 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5440
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_132903961_   5441 GCTGAAACTGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 5490
                         iv    ii  i i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_132903961_   5491 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5540
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_132903961_   5541 AACCTAGGCA-ATACCATTCAGGACATAGGCACGGGCAAGGACTTCATGT 5589
                            v    ?i- v i -   iv   v v  vvii     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_132903961_   5590 CTAAAGCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5639
                         v  vii           vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_132903961_   5640 CTAATTAAAGTAAAGCGCTTCTGCACAGCAAAAAAAAACTACCATCAGAG 5689
                         i v  i   i v  ivi   i  ii vv    ii v -   i  vv i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGAAAG 691

  chrX_132903961_   5690 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCT 5739
                             v  i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_132903961_   5740 GACAAAGGGCTTATATCCAGAATCTACAATGAACTCAAACAAATTTACAA 5789
                           i  i  i   i          v  i  v      vv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_132903961_   5790 GAAAAAAA-AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 5838
                         v     i -   i     v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_132903961_   5839 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGGCACATGAAAAAATGC 5888
                          i     v        i  vi viii     v i           i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_132903961_   5889 TCATCATCACTCGCCAT 5905
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


 314  5.77 3.85 0.00  chrX_132916436_132922824.rev      369   420 (5969)    L1M4_orf2#LINE/L1      855   908 (0)  

  chrX_132916436_    369 AGATAGGCAAATGGCCAA--AGCACATGAAAAGATGCTCAACATTATTAG 416
                              vi           --                        i ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_132916436_    417 CTAT 420
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 2.00 (2 / 1)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 2.00 (2 / 1)  

3167 27.47 0.44 0.66  chrX_132916436_132922824.rev     4989  5898 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_132916436_   4989 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5038
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_132916436_   5039 GGCCATACTGCCCAAGGTAATTTATAGATTCGATGCCATCCCCATCAAGC 5088
                            v     v     iv i  i  i      i i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_132916436_   5089 TACCGATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTTA 5136
                          v  iiivi i  i  ii     -   -- v  i  - iii i  i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_132916436_   5137 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5186
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_132916436_   5187 AATAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5236
                           i    i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_132916436_   5237 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5286
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_132916436_   5287 AATGGAACAGAACAGAGCTCTCGGAAATAATACCACACATCTACAACCAT 5336
                                i    iv   vvii i       vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_132916436_   5337 CTGATCTTTGACAAACCTGACAGAAACAAGCAATGGGGGGAAAAGATTCC 5386
                         i    i  i     ivv  v  ii v  vv        ii i  v v  -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chrX_132916436_   5387 CTATTTAATAAGTGGTGCTGGGAAAACTTGCTAGCCATATGTAGAAAGCT 5436
                         - v  i  i  i           v    v v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_132916436_   5437 GAAACTGAATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5486
                            ii  i i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_132916436_   5487 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAACAC 5536
                          i ?    i       v   v       i      vi i        v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_132916436_   5537 CTAGGCA-ATACCATTCA-GGCCATAGGCACAGAGAAGGACTTCATGTCT 5584
                         v    ?i- v i -   i- i  v i  i-i  iv  v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_132916436_   5585 AAAGCACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGAACT 5634
                          vii           vvi          vv     v  i    vi  vi 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_132916436_   5635 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGCGTGA 5684
                         v  i   v v  i i   i  ii vv    i  v    i  vv iv    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_132916436_   5685 ATAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCGGAC 5734
                          v  i     i                 v       vii ivi   v  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_132916436_   5735 AAAGGACTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5784
                           i     vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_132916436_   5785 AAAATCAAACAACCCCATCAAAAAGTGGGGAAAGGATATGAACAGACACT 5834
                            iv    i     v  i?    i    v       v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_132916436_   5835 TCTCAAAAGAAGACATTTATGCAACCAACAGACACATGAAAACATGCTCA 5884
                             v        i  vi viiii    i ii          v       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_132916436_   5885 TCATCACTGGCCAT 5898
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (149 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


3364 25.77 0.77 0.77  chrX_132938541_132944903     4963  5870 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_132938541_   4963 TGGAAGAACATTCCATGCTCATGGATTGGAAGAATCAATATTGTGAAAAT 5012
                              ii i  i     i               v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_132938541_   5013 GGCCATACTGCCCAAGGTAATTTATAGATTCGATGCCATCCCCATCAAGC 5062
                            v     v     iv i  i  i      i i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_132938541_   5063 TACCGATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTCTAAAGTTTA 5110
                          v  iiivi i  i  ii     -   -- v  i  - ii     i  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_132938541_   5111 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATTCTAAGCCAAAAG 5160
                                viiv  ii  v  v v  v     i     ii i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_132938541_   5161 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5210
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_132938541_   5211 TACAGTAACCAAAACATCATGGTACTGGTACTAAAACAGAGATATAGACC 5260
                                 i   i   vii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_132938541_   5261 AATGGAACAGAAC--AGAGCCCTCGGAAATAATACCACACATCTACAACC 5308
                                i    i--    i  --i       vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_132938541_   5309 ATGTGATCTTTGACAAACTTGACAAAAACAAGAAATGGAGAAAGGATTCC 5358
                          vv    i  i     ivv  v   i v  vvv     i     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_132938541_   5359 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5408
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_132938541_   5409 GAAGCTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGA 5458
                             i    i    v   i   i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_132938541_   5459 TTAAAGACTTAAATGTTAGACCTAAAACCGTAAAAACCCTAGAAGAAAAC 5508
                          i ?    i       v   v       ii     vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_132938541_   5509 CTAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGACT 5556
                         v    ?i- v i -   i- i  v i  i- i     v ii   v iiv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_132938541_   5557 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5606
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_132938541_   5607 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5656
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_132938541_   5657 ACAGGCGACCTACAGAATGGGAGAAAATTTTTGCAA-TCTTCCCATCTGA 5705
                          v  i i   i                 v       -  v vi-      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGA 743

  chrX_132938541_   5706 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 5755
                         i  i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_132938541_   5756 AAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5805
                             iv    i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_132938541_   5806 TTCTCAAAAGAAGACATTTATGCAACCAACAGACACATGAAAACATGCTC 5855
                              v        i  vi viiii    i ii          v      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_132938541_   5856 ATCATCACTGGCCAT 5870
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (142 / 88)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


4547 19.23 0.44 1.20  chrX_132971121_132973043.rev      518  1432 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_132971121_    518 TAAAAAAAAGTCCTGTGTTCATGGATTGGAAGACTTAACATTGTTAAAAT 567
                          ii   i vi   ii                       i        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_132971121_    568 GTCAATACTATCCAAAATAATCTACAGAGTTGATGAAATCCTTATTTAAA 617
                          v       vi     v i         v ii i v     i   i-   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC-AAA 99

  chrX_132971121_    618 ATCCCAATGATACTTTTTGCAGAAATAGAAAAATGGACACTAAAATTCAT 667
                               iiviivi             v  v  iiv  iv           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_132971121_    668 ATGGAATCTCAAGGGATCATGAATAGTCTTAAGAAAGAAGAACAATCTTA 717
                               viv       i vv      i ---------- i         i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCC----------AAAACAATCTTG 189

  chrX_132971121_    718 AGAAAGAA---CAATGCTGGAAGTCCCACAACTCCTGATTTCAACAATTA 764
                          i      ---   v i    i v i    vi   ii       v v   
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_132971121_    765 TTACAAAGCTACAGTAGTCAAAACAGTATGGTACTGGCATAAAGACAGAC 814
                         i               i    i     i              i  i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_132971121_    815 ATATAGAAGAGTAAAATAGAAAAGAGAGTCCAGAAATAAACTCTTGCATA 864
                                vv i ii       vv                  i v i   v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_132971121_    865 TATATTCAAACAATTTTCATTAAGGATGCCAAGAGCATCCAAAGAGAAAA 914
                            iv    vii      ivi    i        v   i   v i i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_132971121_    915 AGGCAGTCTCTTCAAAAAATAGTGTTGGGAAAACTGGATATCCGCATGCA 964
                         iiii     i     v    i   i     v         ?  i      
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_132971121_    965 AAAGAATGAAGTTGGATCCTTACCTTAAACCATATACAAAAACTAACTCA 1014
                                         i  i     i v              i       
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_132971121_   1015 AAATGGATCAAGGACCTAATCATAAGGCCTAAAATTATAAAACTTTTGGG 1064
                                   ?i       vii    iv      i         i  i i
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_132971121_   1065 AGAAAACATAGGGGAAAATCTTCATAACGTTGGGTTTGGCAATGATTTAT 1114
                                     ? v        i i  v       v       i   v 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_132971121_   1115 TGGATATAACACCAAAAACACAGACAACAAAGGAAAAA-TAGATAAATCA 1163
                          i     i         i    ii       i      -         ii
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_132971121_   1164 GACCTCATTAAAATTAAAAGCTTTTGTGCACCAAAGGATGCTATCAACAG 1213
                            i    i          i         vi       ii       v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_132971121_   1214 AATAAAAAGGCGACTCATGGAATGGGAGAAAATATGCGAAAGGCATATGT 1263
                          i i     i i  i  ii                vi v  iv     i 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_132971121_   1264 CTGATAAGGCATTAATATCCAGAATATATAAAGAACACTTTCAGGTCAAC 1313
                                  v i vi                     v   v  iv    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_132971121_   1314 AACAACAGAACAAACAACCCAATTAACAAATGGGCAAAGGACTTCAGCAG 1363
                           i  v ii     i         ? v              i  v ii  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_132971121_   1364 ACATTTCTCCAAAGAAAATATACACATGGCCAATAAGCACATGAAAAGAT 1413
                                         i       v                         
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_132971121_   1414 GTTCAACACCATTGATCGT 1432
                          i      i  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (117 / 55)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 3.75 (15 / 4)  

 948 22.18 7.85 3.07  chrX_132971121_132973043.rev     1631  1923 (0)    L1M4_orf2#LINE/L1      424   730 (178)  

  chrX_132971121_   1631 TGGATAACTATATGCAGAAGAAGGAAGTCATACTCTCATCTCTCATTATA 1680
                               ? i i     i     v     iiv  i ii i   v  ii   
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_132971121_   1681 TA-AAAAATCAAAT-GAAATGGATTAAATACTTAAGTCTTAAGACCTGAA 1728
                           -      i  v -i        i ? v  i   i v -    v  i  
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAGAGCTAAA 522

  chrX_132971121_   1729 ATTATAAAACTACAGGAAGAAAATATTGGAATATTGGGGAAATGCTTCGG 1778
                          i         vivi        i  v  ?i  -------   -     v
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTA-------AAT-CTTCGT 564

  chrX_132971121_   1779 GACCTTGGTCTGGGCAAAGATGT-TTGGGTAATACCTCAAAAGCCCAGGC 1827
                                 vi i     v i v -  i i  vv  vi       v  i  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_132971121_   1828 AACAAAAGCAAAAATAGACAAATGTGATTACATCAA-------------- 1863
                                 v         i    vv  i v      --------------
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_132971121_   1864 --GCT----AGAAAACAGTCAACAAAGTGTAGAGACAACCTACAGAATGG 1907
                         --   ----  i v  vi    v      v i        i         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_132971121_   1908 GAAAAAATATTTGCAA 1923
                           i             
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAA 730

Transitions / transversions = 1.38 (36 / 26)
Gap_init rate = 0.03 (8 / 307), avg. gap size = 4.00 (32 / 8)  


3129 26.23 0.99 1.32  chrX_132976230_132982629     4997  5907 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_132976230_   4997 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5046
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_132976230_   5047 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_132976230_   5097 TACCGATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTGAAGTTCA 5144
                          v  iiivi i  i  ii     -   -- v  i  - iii i  i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_132976230_   5145 TATGGAACCAAAAAAGAGACC--ACATTGCCAAGTCAATCCTAAGCCAAA 5192
                                -- viv   i    --iv  v     iv     i i ---   
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA---AAA 193

  chrX_132976230_   5193 AAAAG--CGAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTAC 5240
                          i   -- i   i      vv   ii  v  ii i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_132976230_   5241 AAGGCTACAGTAACCAATACAGCATGGTACTGGTACCAAAACAGAGATAT 5290
                           i          i   v    ii         i iv ii i   v    
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_132976230_   5291 AGACCAATGGAACAGAAT--AGAGCCCTCAGAAATAATGCCGCATATCTA 5338
                            i        i     --    i  --        vv  ii i  i  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTA 341

  chrX_132976230_   5339 CAACTATCTGATCTTTGAAAAACCTGACAAAAACAAGAAATGGGGGGAAA 5388
                         iiiii vi    i  i  v  ivv  v   i v  vvv       --   
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG--AAA 389

  chrX_132976230_   5389 GGATTCCCTATTTAATAAATGGTCCTGGGAAAACTGGCTAGCCATATGTA 5438
                          i  vvi  v  i  i       v      v      v  ?   i   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_132976230_   5439 GAAGGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCA 5488
                         i   iv    ii    i    v   i     v              i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_132976230_   5489 AGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGA 5538
                          i      i ?    i       v   v       i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_132976230_   5539 AGAATACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTC 5587
                             v  v    ?i- v i -   iv   v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_132976230_   5588 ATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATG 5637
                         v ivv  vi            vvi          vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_132976230_   5638 GGATCTAATTAAAGTAAAGACCTTCTGCACAGCAAAAGAAACTACCATCA 5687
                            ii v  i   i v  i v   i  ii vv    i  v    i  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_132976230_   5688 GAGTGAACAGACAACCTACAGAATAGGAGAAAAATTTTGCAATCTACTCA 5737
                         i      v        i       i        vv       vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_132976230_   5738 TCTGACAAAGGGCTAATATTCAGAATCTACAATGAACTCAAACAAATTTA 5787
                              i  i  i  vi   i      v  i  v      vv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_132976230_   5788 CAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACA 5837
                         i  v     i     i     v  i?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_132976230_   5838 AACACTCCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAA 5887
                         i   i i   v        i  vi viii     v ii          i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_132976230_   5888 TGCCCTTCATCACTGGCCAT 5907
                            i vv     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.75 (21 / 12)  


1799 14.68 4.28 0.31  chrX_133070459_133072883      500   826 (1599)    L1M4_orf2#LINE/L1       61   400 (508)  

  chrX_133070459_    500 CCCAACTTGATCCACAGATTCAAGGCAATTCCTATTAAAATCTCAAATGT 549
                              v      i          v     i     i      i  iv  i
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chrX_133070459_    550 -TTTTTTCCAGAAATTCACAAGCTGATCCTAAGATTCTTATGGAAATTCA 598
                         -      v        v               i    v         v  
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_133070459_    599 AGGGAGTCAAAATAGTAAAAAAAAATCCTGAAAAAGAA---CAAAGTTGA 645
                              vi  i     iv    v  -  i          ---        i
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_133070459_    646 AGGACTTACACACC---------AAACTGACTACAGAGTTATAGTAATAA 686
                               i    vi ---------     v      i  i  i      v 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_133070459_    687 GGACAATATGGTACTGGCACAAAGATAGACATATAGATGAATGGAATAGA 736
                         i    i i           i  i               v           
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_133070459_    737 ATTGAGAATCCAAAAATAAACCTTCAAACTTATAGTCAATTGATTTTTGA 786
                                i    i         ivi v i    i             i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_133070459_    787 CAAGGGTGCCAAGATAATTCAATGTGGAAAGAATAG-CTTT 826
                                       iv        v           -    
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

Transitions / transversions = 1.67 (30 / 18)
Gap_init rate = 0.01 (5 / 340), avg. gap size = 3.00 (15 / 5)  

1501 16.10 7.91 2.82  chrX_133070459_133072883     1128  1481 (944)    L1M4_orf2#LINE/L1      387   758 (150)  

  chrX_133070459_   1128 AATGAAAAACCTTTTCAACAAATTGTGCTGGGACA-CTGCAGGTGGATAC 1176
                           v   v ii             v           -   -- i i?vi  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG--GATAKCCAC 434

  chrX_133070459_   1177 CTGCAAAAGGAC-----TGTACTCCTACCTCACATCACATGCAAAAATTA 1221
                         v        i i-----  v  i           i  i  i         
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_133070459_   1222 ACTTAAAATGGACGTTAGATTTAAATTTAAGAGCCTGTAACTATAAAACT 1271
                            i        ivv?   ii     v       - iv            
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACT 533

  chrX_133070459_   1272 CTTAGAAGAAAACATAGGTGTAAGCCTATGTGAACATGGATTAT-CAATC 1320
                                           ?    ii  vi    v v   i   v-    v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_133070459_   1321 ATTTCTTAGAT--GACACCAAA----CAAGCAATGGCA--AAAAATTCAT 1362
                         i          --         ----       iiiv --      vv  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_133070459_   1363 A---------TTATCAAAATTTAAAACTTTTGTGCTTCAAAGGATACCAT 1403
                          --------- i         v                      i  i  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_133070459_   1404 AATGAAAGT-AAAAGGCAACCCGCAGAATGGGAGAAAAAAT---CAAGTC 1449
                         v v      -     i      i               v  ---   ---
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA--- 730

  chrX_133070459_   1450 AGTGATCATATAACTAATAAAGGACTTGTATC 1481
                         ----        v  i    i           
  L1M4_orf2#LINE/    731 ----ATCATATATCTGATAAGGGACTTGTATC 758

Transitions / transversions = 1.35 (31 / 23)
Gap_init rate = 0.03 (12 / 372), avg. gap size = 3.17 (38 / 12)  

 728 16.23 4.55 0.00  chrX_133070459_133072883     1782  1935 (490)    L1M4_orf2#LINE/L1      748   908 (0)  

  chrX_133070459_   1782 GGCCTTGTATCTTGAATATTTAAGGAACTCTTACAA--TAGTAATAAGAA 1829
                           v        iv      v   i            --i i      i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_133070459_   1830 AGTAAAT---CC-ATTTAAAAATAGCCAAAAGATCTGAATGGACATTTCT 1875
                         iii    ---  -   ?      i v    i   i     i         
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_133070459_   1876 CAAAAGAAAACATACATATGATCAACAAGTACATGAAAAGATGCTCAAC- 1924
                          v      i i     v   ii   i   i                   -
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_133070459_   1925 TCATTAGCTAC 1935
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 3.00 (18 / 6)
Gap_init rate = 0.02 (4 / 161), avg. gap size = 1.75 (7 / 4)  


 543 31.89 0.54 0.00  chrX_133137284_133139357.rev      199   383 (1691)    L1M4_orf2#LINE/L1       45   230 (678)  

  chrX_133137284_    199 TACAATATCAGTTCTCCCCAACCTGATTTATAGATTTTACACAATTTCAA 248
                           vi  iv  i v        vi    i  i     iv  i    ii v 
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chrX_133137284_    249 TCAAAATCCCA-CAAGAAATCTTGTAGATATAGGGAAGCCAATTCTAAAA 297
                                    - vivvvv i   i   v  v iv    ii  i      
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_133137284_    298 GTTATGTGAAAAATCAAAGAAACTGTAATATTCAAAACAATTTTGAGAAA 347
                         v i  i  i   vv   i i v iiv    vi         i    i   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_133137284_    348 GAATAATTAAGTGGAAGATCTCACATTGCTTGATTT 383
                            v  iv    v i  iv      i v iii    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

Transitions / transversions = 1.36 (34 / 25)
Gap_init rate = 0.01 (1 / 186), avg. gap size = 1.00 (1 / 1)  

 933 24.66 0.27 10.19  chrX_133137284_133139357.rev      502   874 (1200)    L1M4_orf2#LINE/L1      218   553 (355)  

  chrX_133137284_    502 CATTGCTTGATTTTAAGACTTACCATAAAGCTATAGTGATCAAGACAGGG 551
                           i v iii    i  i      i i       i   i          v 
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_133137284_    552 TAGTATTGGTGAAAAATTAGATGTATAAATCAAAGGAACAAAAAATAAAG 601
                          i   i   iiv  iiv    ii    i     v    i i  vvv i  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_133137284_    602 TCCAGAAATAGACCCAGAGAAATTTGGCCAATTGATTTTTTGATAAAGG- 650
                                   i     v v vv v   i           i-  i  i  -
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC-GACAAGGGT 366

  chrX_133137284_    651 GCAAAGAAAATTCAATTGAGAAATTATAGCATTTCCAACAAATAGTGTTG 700
                           v    vv       v i    vv    iv   i        i   i  
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_133137284_    701 GAACAATTGCACATTCTTATGCCAAAAACAAAAAACAAAACAAAAAAAGA 750
                          i    i  v i ?i vi    ----------------------------
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGC---------------------------- 438

  chrX_133137284_    751 CAGAAAAGAGAAAAAAAGAACCTTGACCTAAACTCCCCTCATTATACAAA 800
                         ---      ivi  ivv i   ----    v-   v vi   -       
  L1M4_orf2#LINE/    439 ---AAAAGAATGAAGTTGGACC----CCTAC-CTCACACCAT-ATACAAA 479

  chrX_133137284_    801 AATTAACTCAAAATAGATTATACATCTCAAGGTCAAATGTAAGAGTATTA 850
                                       i   i ? v i  v  v  v i vv   i v   v 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_133137284_    851 AACATTTATCGAAAAACATAGGAG 874
                            vi   vvii          ? 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNG 553

Transitions / transversions = 1.28 (50 / 39)
Gap_init rate = 0.02 (6 / 336), avg. gap size = 6.50 (39 / 6)  

1256 22.99 3.45 0.29  chrX_133137284_133139357.rev     1236  1583 (491)    L1M4_orf2#LINE/L1      550   908 (0)  

  chrX_133137284_   1236 GGAGAAAATATTTTTGATCACAG-TTAGGCAAGGAGTTCTTAGATATGAC 1284
                           ? v    v  iv   i vii -        v iv              
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_133137284_   1285 ATCAAAAGCATGATCCACAAAA----AAATCAAGAAATTGAACTTTATCA 1330
                          i        ii v v      ----    vi v      i    i    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_133137284_   1331 AAATTTAAA-CTTTTACCCTTAGAAAGGCACTGCTAAGAGAACAAAAAGA 1379
                              v   -     iiv   vi  i i    iii    i iii      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_133137284_   1380 CAAGGTACAATTTGAGAGAAAATAATTGCAAAGCACATATCTGACAAAG- 1428
                            vvi   ivv  i         v       v  i        i  i -
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_133137284_   1429 ACTT-TATCTACAATGTA--AAGAACTCTGAGAAATCAACAGCAAGAAAA 1475
                             -    i v   i  --         v v  v    i ii  i  i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_133137284_   1476 CAAA-AACCCAATTTAAAAAATGGTCAAAACACTTGAGCAGACACTTCAC 1524
                             -         ?     -   v    iv i    ii     i   v 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_133137284_   1525 CAAAGGAGACATGCAA-TAGCAAATGAGCGCATGAAAAGACATTCAACAT 1573
                              i   i  i   - i  v   i   i          iii       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_133137284_   1574 TATTAGCCAT 1583
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.89 (51 / 27)
Gap_init rate = 0.03 (9 / 359), avg. gap size = 1.44 (13 / 9)  


3519 22.41 0.64 3.74  chrX_133161033_133165593     3132  4068 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_133161033_   3132 TGGAAAAATATTACATGTTCATTGATTGGAAGAATCAATATTGTTAAAAT 3181
                               i    iv         v          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_133161033_   3182 TTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTGTCAAAA 3231
                         vv v     v      vii              i         i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_133161033_   3232 TACCAAGGACATTCTTCACAGGAATAGAAAAGTCTATCCTAAAATTCACA 3281
                          v   ivvi v  i  ii   i   v  v   iiv             i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_133161033_   3282 -GGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCCAAGCAAAAAGAA 3330
                         -    vii   ii                 i v   iii iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_133161033_   3331 CAAAACTGGAGGAATCACATTACCTGACTTCAAATTATAGTACGGAGCTA 3380
                             ii       v     i v  ii i      viv  v   ii     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_133161033_   3381 TAGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACACGTAGACCAA 3430
                         i     i   i    ii              ii i     ii    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_133161033_   3431 TGGAACAAAACAGAGAACCCAGAAACAAATCCACACACCTACAGTGAACT 3480
                              i i  iv    ii       i   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_133161033_   3481 CATTTTTGACAGAGGTGCCAAGGT-ATACACTGGGGAAAAGACAGTCTCT 3529
                         v     i    ii         ii-  v  v        ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_133161033_   3530 TCAATACATGGTGCTGGAA-AACTGGATATTCATATGCAGAAGAATGAAA 3578
                             i v          i -         ?i  i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_133161033_   3579 CTAGACCCCTATCTCTCACCATATACAAAAATCAAAGCAAAATTGATTAA 3628
                         i i        i   v                i  vv      v   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_133161033_   3629 AGACTTGAATCTAAGACCACAAACTATGAAACTACTACAAGAAAACGTTG 3678
                             i i   v     v vv       i     vi  v        i v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_133161033_   3679 GGA-AAATGCTCCAGGACATTGGTCTGGGCAAAGATTTATTGAGA-ATAT 3726
                          ?i-    -  i iv   v    vi i     v i   v  -   -  iv
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chrX_133161033_   3727 C-CCACAAGCACAGGCAACCCAAGCAAAAATGGTATCACATCAAGTTAAA 3775
                          -   v       i     vv   v      i ------  -  i  ii 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAG------AT-AAATTGGA 641

  chrX_133161033_   3776 AAGCTTCTGCACAAATGGTATCACATCCATTTAAAAAAAGCTTCGGCACA 3825
                         ---    ------------    v ---   ----    i   iv ii v
  L1M4_orf2#LINE/    642 ---CTTC------------ATCAAA---ATT----AAAAACTTTTGTGCT 669

  chrX_133161033_   3826 GCACAGGATACAATCAACAAAGTGAATAGGCAACCCAAAGAATGGGAGAA 3875
                         v  v    i  v     v        v  i       v            
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_133161033_   3876 AATATTTGTGAACTACCCATCTGACAAAAGATTAATTAACCAGAATATCT 3925
                                 ii  ii ivi      i  ii  i vi - v         v 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGT-ATCCAGAATATAT 768

  chrX_133161033_   3926 AAGGAGCTCAAGCAATTCTATAGGAAAAAAATATATAATAATCCTATGAA 3975
                           i  i   vvi   i  v   iv     i i ---     i  v  v? 
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACA---AATAACCCAATTWA 815

  chrX_133161033_   3976 AAAATGAGTAAAAGTATTGAATAGATATTTCTCAAAAGAAGACATACAAA 4025
                               i i   i vv         i       v        i       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_133161033_   4026 TGGCAAACAGGCATTTGAAAAGGTGTTCAACATCATTAATCAT 4068
                             v  i i   iv       i  i         ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (132 / 74)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.56 (41 / 16)  


 457 23.08 0.00 0.00  chrX_133183803_133188496.rev        1    91 (4603)  C L1M4_orf2#LINE/L1   (816)    92     2  

C chrX_133183803_     91 GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATG 42
                             ii i  i     i      i v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

C chrX_133183803_     41 GCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCC 1
                           v     v     iv i  i  i        i  v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.00 (0 / 0)  

2971 23.28 2.08 6.89  chrX_133183803_133188496.rev     3286  4200 (494)    L1M4_orf2#LINE/L1        1   871 (37)  

  chrX_133183803_   3286 TGGGAAGATATCCGATGCTCATGGATCAGAAGAATTAGTTTTGTTAAAAT 3335
                            i         v   i        ii     v   i v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_133183803_   3336 GACCATACTGCCCAAAGCAGTG-ACAGATTCAGTGTAATTCTTACCAACA 3384
                          i v     v      viii v-         ii i   i i  i   v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_133183803_   3385 TACCAA-TGTCATTTTTCATGAAAATAGAAAAAATAATCCTAAAATTCAT 3433
                          v   i-  i -     iiiii    v  v  iv i              
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_133183803_   3434 ATGGAATCAAGAAAGAG-CCCA-AATAGCCAAAGCAATCCTAAGCAAAAG 3481
                               -- v v   i -    -          i     i i --     
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAG 195

  chrX_133183803_   3482 CAAAACAAACAAACAAACAAACAAACAAACAAAACCCCCAAACCCAAAAA 3531
                         --------------------------------------------------
  L1M4_orf2#LINE/    196 -------------------------------------------------- 195

  chrX_133183803_   3532 ACCCACAAAAAACAAAGCTGGATGCATCACACTACCTGACTTCAAAATAT 3581
                         -------  i       i    v vv       v  ii i       iv 
  L1M4_orf2#LINE/    196 -------AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_133183803_   3582 ATTACAAGACTATGGTAATCAAGACAACATGGTATTAGTATAAAAATAGA 3631
                          i     ii   ii            iii     i i i    ii     
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_133183803_   3632 CACATAGACCAATGGAACAGAAAAGAGAACCCATAAGTAAATCCACATAT 3681
                           i     i        i    vv    ii   v  i    i   i i  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_133183803_   3682 TTACAGCCAACTGATTTTTGACAGGGGCGTCAAGAACATACACTGGGGAA 3731
                            ii i   i       i    i   i i     v   v  v       
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_133183803_   3732 AGGACACCCTCTTCAATAAGTGATGCTGGGAAAATTGGATATCCATATGC 3781
                           i i vi  i     i  i  i        v  i      ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_133183803_   3782 AGAAGAATGAAAGTGGACCCCTCTCTCTCACCATATACAAAAATCAAATC 3831
                          i         iv         vi   v                i  v  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_133183803_   3832 AAGATGGATTAAAGACTTAACCATAAGACCCCAAACTATGAAACCACTAG 3881
                           i      i ?    i   vii     v iv       i    ivi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_133183803_   3882 GAGAAAATGTATGGA-AAATACTTCAGGATATTGGTCTAGGCAAAGATTT 3930
                         i      ii  v ?i-    -    iv  iv    vi       v i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_133183803_   3931 TATGGCTAGGGCCTTAAAAGCACAGACAATTT--TAAAAAATGGACAAAT 3978
                         iv i v  v i vii         ii   ivv--v       i  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_133183803_   3979 GGGAGTATATTAAA-CTGATAACTTCTGCATAGCAAAAGAAACAATCAAT 4027
                         v   v vi  i   -i i v     i  iiivv    i  v  v     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_133183803_   4028 AGAGTGAAGAGATAACCTGTTGAGTGGGTGAAAATATTTGCAAACTATTC 4077
                          i      i   i    iiiv  i    v               ii  vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_133183803_   4078 ATCTGACAAGGGAATAATATCCAGAACA----AGGAAATCAAACAAGTGA 4123
                               i      v vi         i ---- i   v  vv    v v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_133183803_   4124 GCAATAAAAAAA-AAAT---CCTATTGAAAAGTGGGCAAAGAACATGAAT 4169
                         ii        i -    ---  v   ?    i         i iv     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_133183803_   4170 GGATAATTCTATAAAGGAGACATACA---GGCCA 4200
                         i  i v    vi    i   i     ---     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.99 (139 / 70)
Gap_init rate = 0.02 (16 / 871), avg. gap size = 5.12 (82 / 16)  

 252 20.34 0.00 0.00  chrX_133183803_133188496.rev     4399  4457 (237)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_133183803_   4399 AAGGAAGACATACAACTGGCCAACAGGCATATTAAAAAATGTTCATCACT 4448
                           i     i      v       i i   i  v    i   i   v  ii
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_133183803_   4449 AATCACCAG 4457
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


 478 24.95 21.13 4.63  chrX_133267599_133269476.rev      409   905 (973)    L1M4_orf2#LINE/L1      121   699 (209)  

  chrX_133267599_    409 GAAACTTA-AAGTTGATTCTGTGGTTT-TCTGGAAA----ATGGATG-AG 451
                             i v -   i    i  ivii  i- v      ---- v   iv-  
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chrX_133267599_    452 AATACACAAGATGA----AAAAAAGAATACACAA-----GAGTA-TC--- 488
                             vv   i ii ----i        v -    -----   v -  ---
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGA-ACAAAGTTGGAGGACTCACA 219

  chrX_133267599_    489 CTTTTGAAAAGAAGATATCAAAATATACTATAAAGCAATAGCAGTTAAAC 538
                            iiv  ------- v      iv     i     v i  i i i  iv
  L1M4_orf2#LINE/    220 CTTCCCAA-------TTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_133267599_    539 CA--------CTGGCACAAGAATAGACATATA--TCAGTGGAAGAGAATC 578
                           --------      i   i           --   i     v     -
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT- 311

  chrX_133267599_    579 TCCAAGTTTGAAAACAGACCCACGTGCAC--ATGA-AAATTGAAAATAT- 624
                          vvi   iiii   i i     -- i  i--   i-v      --- v -
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAATTGA---TTTT 356

  chrX_133267599_    625 -GATAATGGTGGCAT-----TTCAGATGAGTGGAAAAGACATAAT----- 663
                         -  i  v    v  v-----    -   ---  i     -   i -----
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCA-ATG---GGGAAAGA-ATAGTCTTTT 401

  chrX_133267599_    664 --------------GGCACAACTGGATATCCATTTTTTAAAAA------- 692
                         --------------  v           ?   iv viv   i -------
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_133267599_    693 TGGA----TACCTCATACTATATGAAAAAGTTAG---GAGATGTATTAAA 735
                             ----       i  i    iv    i   i---i i   v  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_133267599_    736 AATCTAATTGTAA-AGT--AAACTATGAATATAATAGGAGAAAATAGCGG 782
                         i i    v     -  i--       i  vv vv   i      i vv  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_133267599_    783 AG--AATTTTAAAAAATAATCTTGGATCAGG------------ACATAT- 817
                         ? --   i  vi---- i i     i i   ------------ v    -
  L1M4_orf2#LINE/    552 NGTAAATCTTCG----TGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_133267599_    818 -------AAG---AAGCCCTAAAGGAAAAGACTGGGATATTTGACT--A- 854
                         -------   ---    vvi   i     i iv iv v   v    -- -
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_133267599_    855 -AAAATTAGTAACTTTTGTACAGCTAAAGGCACCATAAACTAAGTTAAAA 903
                         -       iv         i vv v  i i   i  v  vv    v    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_133267599_    904 GA 905
                           
  L1M4_orf2#LINE/    698 GA 699

Transitions / transversions = 1.37 (70 / 51)
Gap_init rate = 0.06 (35 / 579), avg. gap size = 3.66 (128 / 35)  

 280 21.33 4.67 4.67  chrX_133267599_133269476.rev     1238  1387 (491)    L1M4_orf2#LINE/L1      759   908 (0)  

  chrX_133267599_   1238 CAGAATATCTATATTATAGAGAACACCTGTATATCAATTTTAAAAAGACA 1287
                                 -------   i     v i ii vv     vv          
  L1M4_orf2#LINE/    759 CAGAATAT-------ATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_133267599_   1288 AAC--CCCAAGAGAAAAATGCACAAAGCATAGGAAAAGGCAATTCACAAA 1335
                           i--     vv?       vi     v  vv   v  i  v   v v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_133267599_   1336 AGAA---ACATAAATGACAAAAAA--ACATGAACAGAGGCCCAACCTCAC 1380
                             --- i i     i v  v  --       v   v  i    v   ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_133267599_   1381 CAGTGAT 1387
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 0.55 (11 / 20)
Gap_init rate = 0.03 (4 / 150), avg. gap size = 3.50 (14 / 4)  


1158 25.33 7.92 1.06  chrX_133450950_133455951.rev     2904  3282 (1719)    L1M4_orf2#LINE/L1       46   450 (458)  

  chrX_133450950_   2904 AAGGTGTCAATTATTTCCAAATTGATATACATGTTTGACATAATTCCCAT 2953
                            i  v    vv ii          v    vi  ii  ii   i  i  
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_133450950_   2954 CAAAA---CAGCAACAAGATTTTTGTACAATTTTA-----TG-TC---AA 2991
                              ---    vi vv--      i v  v  v -----  -  ---  
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCT--TTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_133450950_   2992 ATTTATACAGAAAAGTCAAAGGAACACA-AATAGCTAAAGCAAGTTTGAA 3040
                            i   ii    v i--    i  v  -      i   i   vi     
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_133450950_   3041 AAAGAAGAATAAAGTGGGAGGAATCA---------GTT---GACCCTATC 3078
                                  i     v      v   ---------i  ---i v i  ii
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_133450950_   3079 ATATATCTACAGTAATCAAGACTGTGTGGTATTGGTAGAAGGACAGACAC 3128
                          i v v                v        i   i v     i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_133450950_   3129 ATAAATCAACAGAACAGAAC--AGAACCCAGAAATAGTCCCATATAAATA 3176
                            i     ii   i    i--   ii         iv      i vv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_133450950_   3177 TGGCCAACTGACTTTTTA-AAAGATACACACACAATTCAATGGAGGAAAG 3225
                            i   i   i   iv -  i i i vv v  v         i i  ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_133450950_   3226 ATAGCCTTTTAAACAAATGATGATGGAGAAATTGCACATCCATG-GCAGA 3274
                             i     v        i  v   iiv  i  v i ?   ii-   i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_133450950_   3275 -GAAAAAAG 3282
                         -   vi   
  L1M4_orf2#LINE/    442 AGAATGAAG 450

Transitions / transversions = 1.79 (61 / 34)
Gap_init rate = 0.03 (13 / 405), avg. gap size = 2.62 (34 / 13)  

1164 24.06 7.08 1.89  chrX_133450950_133455951.rev     4087  4510 (491)    L1M4_orf2#LINE/L1      463   908 (0)  

  chrX_133450950_   4087 CTCATACTTTATACAAAAAGTATCTGAAAATGGATGATGGAGTTAAACAT 4136
                             i  iv          v  v  v         v ?i  vi    ii 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_133450950_   4137 AAAAACTA---TTTTAAAATGTTTAAAT--AAACAGTAGA---AAATGTT 4178
                           i i   ---i v     ivi   i v--     -   i---    v  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-TAGGNGTAAATCTT 561

  chrX_133450950_   4179 TGGGATCTAGAGCTTAGGCAAAAAGGTCTTAGACTTGAT--CAAAAGCAC 4226
                         i v  i  v i -        viivv       iv   i--         
  L1M4_orf2#LINE/    562 CGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_133450950_   4227 AATCCATGAAAGGAAAAATCAATAAATTGGACCTGACCAAAATATAAAAC 4276
                           v v ii    i      vi           i v i      vv     
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_133450950_   4277 ATTTGCTCTGTGAA-----------AGAAGATGAAAAGACAAGTTATATA 4315
                         v    iv  vii  -----------    ii           vii ----
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA---- 706

  chrX_133450950_   4316 ACATAATGGGAGAAAATATTTTCAAACCACACATCTGACAACTGACACAT 4365
                         -  v                 v    i  i i      i  vv   vii 
  L1M4_orf2#LINE/    707 -CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_133450950_   4366 ATCTAGAATACGTTAAGAACTTTAAAAAACTCAACAGTAAAA---CAAA- 4411
                            i      ii v       i v v  -     i i     ---    -
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAAAAGACAAAT 804

  chrX_133450950_   4412 -ATCCAATTAGAAAATGGGCAAAGGACATAAAGATACATTTAACCAAAGA 4460
                         - i      ?i               iv i  v v      vv       
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_133450950_   4461 GGAAACATGGATTG----TAAAGACATGACAAGATGTTCACCATCATTAA 4506
                         i  v i iii  v ----   iv      v      i   v     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_133450950_   4507 TCAT 4510
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.27 (56 / 44)
Gap_init rate = 0.03 (12 / 446), avg. gap size = 3.17 (38 / 12)  


 519 26.61 0.81 0.00  chrX_133474379_133476825.rev      491   614 (1833)    L1M4_orf2#LINE/L1       64   188 (720)  

  chrX_133474379_    491 AAAGTGATATTCAGATTTGATGTAATCCCTATCAAAATTCCAGCAGCATT 540
                            v    v v      ii i i               i     v  v  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chrX_133474379_    541 TTTCACAGAAAGAGAAAAAC-AATTCTAAAATTTGTGTGGAACCACAAAA 589
                            ii      vv  v  i -i  i        ii i     vii   ii
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chrX_133474379_    590 GACCCCAGATAGCTGAAGCAATTTT 614
                              vii     ii  i    i  
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTT 188

Transitions / transversions = 2.30 (23 / 10)
Gap_init rate = 0.01 (1 / 125), avg. gap size = 1.00 (1 / 1)  

 227 23.08 6.41 5.13  chrX_133474379_133476825.rev      916   993 (1454)    L1M4_orf2#LINE/L1      166   244 (664)  

  chrX_133474379_    916 CCCAGCTAAGGTGAAGCAATCTTGAGAGGGAAAAAGAGAGAAAGTTGGGG 965
                              vvv  vii  i         i ---  i    - v        i 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAA---AAGAAGA-ACAAAGTTGGAG 211

  chrX_133474379_    966 G-----CACTTTCTGATTTCAAATTATATTACA 993
                          -----     i ii        viv  i    
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACA 244

Transitions / transversions = 1.57 (11 / 7)
Gap_init rate = 0.04 (3 / 79), avg. gap size = 3.00 (9 / 3)  

2853 21.58 1.64 0.89  chrX_133474379_133476825.rev     1285  1956 (491)    L1M4_orf2#LINE/L1      232   908 (0)  

  chrX_133474379_   1285 AAAATTATATTAAAAATCTATAGTAATCAAAACAGTATAACTCTGGCATT 1334
                             i -  i  v   v   i         i     i iiiv       v
  L1M4_orf2#LINE/    232 AAAACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_133474379_   1335 AAAA-AAACACATAGACCAATAGAATAGAATAGAGAGCCCATAAATAAAC 1383
                          ii - i   i     i    i         v     i   v        
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_133474379_   1384 CCAAGCATACACAGTCAACTAATTTTTAACAAGGGTGCCAAGAAGACACC 1433
                            vi   vi ii     i i     ii               vv iv v
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_133474379_   1434 ATGGGGAAAGGGCA-TCTCTTCAACAAATGGTGTTGGGAAAACTGGATAT 1482
                                   iii -   i              i     v         ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_133474379_   1483 CCACATTCAAAAGAATGAGATTAGACTTTTAT-----ACCATACATACAA 1527
                               v           ii  i   iii  i-----      i i v  
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_133474379_   1528 ATCAACTCAAAATTGGTTAAAGGCCTACATATAAGACCTGAAACCATAAA 1577
                           i          v i i ?  i    v  i     v  i    i     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_133474379_   1578 GCT---AGAAGAAAACCTAGCAGAAAAGCGCCTTGACATTAGCTTTGGCA 1624
                         i  ---          v   v? v   v vi v    v  i v  v    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chrX_133474379_   1625 ATGATATTTCAGATATCACACCAAAAGCTCAGATTACAAAAGCAAAAATA 1674
                            i v i i      v           v  iiiv       v       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_133474379_   1675 AAGAAGTGAGACTACATCGAG-CTAAAAGCTTCTGTACAGCAAGGAAAAT 1723
                         i v  i vi    v    i i-i     i   i   i vv   i i v i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_133474379_   1724 AATCAACAAAATGAAAAGGCAGCCTACAGATTGGGGGAAAATATTTGCAA 1773
                         v     v   i       i  i  i     v    i              
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_133474379_   1774 ATAATATATCTAATAAGGGGCTAATATCCAAAATATGTAAGGAACACACA 1823
                           v        i       i  vi      i     i   i    v vi 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_133474379_   1824 CAACTCAATGGCAAAATAAATCAATAAATAACCTGATTTAAAAATGGGCA 1873
                                  -----      vvi i        ii   ?           
  L1M4_orf2#LINE/    781 CAACTCAAT-----AATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_133474379_   1874 AAGGATCTGAATAGACATTTATCTAAAGAAAACATACAAATAGCCAACAA 1923
                               i             v  i      i i        i     i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_133474379_   1924 GTATATGAAAAGGTGCACAATATCACTAATCAT 1956
                          i i        i   v   i    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (92 / 49)
Gap_init rate = 0.01 (7 / 677), avg. gap size = 2.43 (17 / 7)  


 461 28.27 7.42 8.83  chrX_133568118_133570291      504   786 (1388)    L1M4_orf2#LINE/L1        2   280 (628)  

  chrX_133568118_    504 GGAGATATATGCCATGTTCATGTATGGGAAGGCTCAACACA---AATATG 550
                            i v    v           v  v     i  i  i iv---  v   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_133568118_    551 GCAATTTTCTTTAAATTGGTCTGTAAATTCTATGCAAGTTCAACCAAAAT 600
                              vi  iii      i   ii i    v i    vii v i      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_133568118_    601 CACAACAGGATTTTT--CTGGATTTTTGACAAGGTAATTTACACAGAAGA 648
                          v  i v vv     -- v i v  --      v i  ----- vv  i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGAT-----CCTAAAA 144

  chrX_133568118_    649 TTTACACAGAGAATAAGATTGTAACAGAATAGTAAGGCATCAAGAATATA 698
                           i i ii  -----------------   - i    v i v      vv
  L1M4_orf2#LINE/    145 TTCATATGGA-----------------AAT-GCAAGGGACCCAGAATAGC 176

  chrX_133568118_    699 CAAGACAATTGTGAA---GAAGAGTAG---TGAAGGGC--ACATTG---- 736
                            i     iv    ---     ii i---  i   i --   i v----
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_133568118_    737 ---TTAAGGCTTATTATAATGTCATGGCA-TTAAAACAACGTAGGCCAGG 782
                         --- i  ii    i  i  v ii ii i - i  i   ii  i vv v  
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_133568118_    783 CACA 786
                           i 
  L1M4_orf2#LINE/    277 CATA 280

Transitions / transversions = 1.76 (51 / 29)
Gap_init rate = 0.04 (11 / 279), avg. gap size = 4.18 (46 / 11)  

 783 29.50 6.62 4.10  chrX_133568118_133570291     1048  1681 (493)    L1M4_orf2#LINE/L1      259   908 (0)  

  chrX_133568118_   1048 AAAACTATATAGTATTGGCAGATGGATAAACAAATAGACCAGTGGAATAT 1097
                           i  vi i i   i     v v     i   v     i  i       v
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_133568118_   1098 AAA-AAGGGCCTACAAACAA-CTCAGGTAAGTCTATGAG-AACTA----- 1139
                           v-i  i i i v   i  - i  --  vi i    iv-  i i-----
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAATTGATTTT 356

  chrX_133568118_   1140 -GGTAAAGG-ACAGAGATTGATTATAAATCGTGGAGGATAAGATATAGAT 1187
                         - ii  i  -i vi   ii-   -i  ----   -   -    -    vi
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACC-ATT-CAA----TGG-GGA-AAGA-ATAGTC 397

  chrX_133568118_   1188 TATTTAATAAATGGCATTAAAAT-------TATTCATATGATAAAAGA-T 1229
                          v  i  i      iii iii i-------  ?i  i   -i      - 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAAT 446

  chrX_133568118_   1230 ACAATTAGATAACTTATTCAAACCCTACATAAAAATCAATTCAAAATGAA 1279
                         iv i  i  ivv  vvi   v   v  i i      i  i        i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_133568118_   1280 TTAAAGATCTAACTGTTAAAAGC-AAAATTTTACAACACTTTGATGCAAA 1328
                          i ?   i    v   -  i   -    i v  v   v   v  v v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_133568118_   1329 TATAGA---ATACCTTTATGACCTCAGAATAG--AAGAATTCATTA---A 1370
                         i    i--- v i   ii      ii iv   --  vii  iv   --- 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_133568118_   1371 TCACACACACAAAACTTACAAATTTTAGTAGAAAAGACTGGTAAATGTGA 1420
                          v    -  -   i --    iivvi iv      i iv i     vv  
  L1M4_orf2#LINE/    596 TGACAC-CA-AAAGC--ACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_133568118_   1421 CCACATTAAACATTATAA-----TGT-CTATAAGAAAAAATGACAGTAT- 1463
                          iv   i   -    v  -----   -  vi  ------ v    v   -
  L1M4_orf2#LINE/    642 CTTCATCAAA-ATTAAAAACTTTTGTGCTTCAA------AGGACACTATC 684

  chrX_133568118_   1464 ---AAAGTTAAA-GATAAGCCATATAGTGGGAGAAGACACTTGCCACACA 1509
                         ---     v   -  i  v   i v i        i i i    v vv  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_133568118_   1510 TGTAATTGAAAAAGAAACAGAGTCAAAAAAGACATAAAATAAATGCTATA 1559
                          i  vi   v  i i viv vi  v i  -v i     i-  v vi  i 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAA-TATATAAAG-AACTCTTACA 782

  chrX_133568118_   1560 AGTCAATTTTAAAAGG-CAATCAACACAATGGAAAAAGGAGCAAAGAATA 1608
                          v     vv     i -   vi   v    v?     v i      i  v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_133568118_   1609 CCAACAGACAACTGGC---AGAAGACACTGGAATGGTCTAGAAATATATG 1655
                         iv  i     vi vv ---      i ivvi     i v v  ii i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_133568118_   1656 CAAAGATACTTAACCTCACTAGTACT 1681
                         v      i  i   v   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (109 / 75)
Gap_init rate = 0.05 (33 / 650), avg. gap size = 2.06 (68 / 33)  


 304 24.07 1.85 16.67  chrX_133614685_133616981.rev      894  1271 (1026)    L1M4_orf2#LINE/L1      378   699 (209)  

  chrX_133614685_    894 TTACTGGGGCAAAGATGGACTTTTTAAATAAATTCTATTGGCACAACTGG 943
                          i v     v  ii  i v     i  -i    vv ii   v        
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAA-CAAATGGTGCTGGGACAACTGG 426

  chrX_133614685_    944 ATAGCCATTTGGACAAAAAGGTAATTTGGTCCCATACTTCACATTGTACC 993
                            ?   iv  v v  i  v -  v    v   v   i     iii  iv
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATG-AAGTTGGACCCCTACCTCACACCATATA 475

  chrX_133614685_    994 CTAGAATAAGCTCCAAATGGAGCTTATTATATAAAATATTTAAAAAATAA 1043
                          v i   v i   v       v ---------- ? v ii    vi-   
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATC----------AWAGACCTAAATG-TAA 514

  chrX_133614685_   1044 AAAATAAAACCATATAGGTACCAGGTGGTCCAAATATTAAAAAAAAAAAC 1093
                         i iv      i   v ---  -------  ------   i  i    ---
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAA---AC-------TC------TTAGAAGAAAA--- 545

  chrX_133614685_   1094 ATATAGGCACTAGAAGAAAACGTCGATTAATTTCTTTATAATCT-GGGTG 1142
                         -i     ?------- v   ------------    ii i i  -    -
  L1M4_orf2#LINE/    546 -CATAGGN-------GTAAA------------TCTTCGTGACCTTGGGT- 574

  chrX_133614685_   1143 TGGGGAAAGCCTTTTAAAATATGACTCCAAATCCAAATGCCATAAAATGA 1192
                          i  v  v vi  i v i       v     vv  v v  v i    vi 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_133614685_   1193 ----TGAGTATTTTCAAGTACATAAAAATCAAAGTAAAAACCTTTTTTTG 1238
                         ---- iii  vv  vi v v   v     -----       --    v  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAAT-----TAAAAAC--TTTTGTG 667

  chrX_133614685_   1239 CATGGCAAAAATCAG-AT-AGGCAAAGTCAAAAGA 1271
                          v --    iiv  v-  - i -     v      
  L1M4_orf2#LINE/    668 CTT--CAAAGGACACTATCAAG-AAAGTGAAAAGA 699

Transitions / transversions = 0.96 (43 / 45)
Gap_init rate = 0.06 (19 / 322), avg. gap size = 3.68 (70 / 19)  

 430 29.28 1.80 0.90  chrX_133614685_133616981.rev     1585  1806 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_133614685_   1585 AGGAAAAAGAAAAGAAAGATGATGAAACTG-AGAAAATACTTATAATGTA 1633
                          i    iv       v iviv iii  iv -        i  ii  vvi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_133614685_   1634 TACATA-AATAAAGGTCCAATATCCCAAACATATAAAGAACTTTT-TAAA 1681
                           i  v-i    i  v ivi     vi  i            i  -i  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_133614685_   1682 TCTAAAGAAAAAAGGCTAAAAAGTCTCAGGAGGAAAATGGGCAAAA-ACA 1730
                           v v iv      i v  v  -- i  ivv?i            i- iv
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAA--CCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_133614685_   1731 TGAATACACAGTTCACAGAAGAAAGTATACAAATGATCCTTAAATATATG 1780
                               v   v   v vi     ii          ii vv   ii i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_133614685_   1781 AAAAGATACTCAACTTCACACATAGT 1806
                                i      v   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (37 / 27)
Gap_init rate = 0.02 (5 / 224), avg. gap size = 1.20 (6 / 5)  


3065 25.17 3.78 0.23  chrX_133617000_133619082      718  1591 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_133617000_    718 AAAAAAAACCCATGCTCATGGGTTGGAAAAATTAATCTAGTTAAAATGAC 767
                            i v v      i      i      i v     v v     i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_133617000_    768 CACATTGCCCAAAGCTATCTATAGATTCGATGCAATCCTTATCAAAATAC 817
                         v i i v      viv     i      i i       i         v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_133617000_    818 CAACATAATTCTTCACAAAATTAGAAAAAACAATCCTAAAATTCATACAG 867
                           i vvvv  i  ii  i  v v  v  ivii               ii 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_133617000_    868 AACAAAAAAAGAGTCCA-AGTAACCAAAACAATCCTGAGCAAAAAGAA-- 914
                           - viv  i iii   - i  i           i   iv  i     --
  L1M4_orf2#LINE/    154 AA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_133617000_    915 -AGCTGGAAGCATCACATTACCTGACTTCAAAATATATTGCAAGGCTATA 963
                         -  i    i vv     i v  ii i       iv  i i   i    i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_133617000_    964 GTAACCAAAACAGCATGGTAATGGTATAAAAACAGACACATATACCAATG 1013
                             i   i    ii     v   i    ii i     i   v i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_133617000_   1014 GAACAGCATAGAGAACTCAGAAATAAAGCCA--CATACACAGCCAACTGA 1061
                            i  v  v    iii          v   --   vi ii i   i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_133617000_   1062 TTTTTGACAAAGCCAGCAAGAACTTTCCCTGGGGAAAGGACACTTTCTTC 1111
                             i     i viiv     v v   vv         i i v i i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_133617000_   1112 AACAAATAGTGCTGGGAAAAATGAATAGCCACATGCA---GAATGAAATT 1158
                                i         v  v  i   ?         ---       i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_133617000_   1159 GGACCCCTATCTCTTACCATATACAAAAATCGACTCAAAATGGAT----- 1203
                                  i   vi               ii             -----
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_133617000_   1204 ---TAAACATAAGACTTGAAACTATAAAAACACTACAAGAAAACCTATGG 1250
                         ---    ii     vi i           vivi  v        v  v ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_133617000_   1251 AAAACTCTCCTGGACATTGATCTAGACAAAGAATTTATGACTAAGACCTC 1300
                         iv  v   i vv   v   ivi   i   v iv  iv iiv  v   vi 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_133617000_   1301 AAAAGCACAGGCAACAAAAACAAAAATAGGCAAAT----------CAAGC 1340
                                  i         iv        ii    ----------   iv
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_133617000_   1341 TAAAAATCTTCTGCACAGTAAAGGAAACAATCAATAGAGTTAAGAAACAA 1390
                          v    v   i  ii vvi      v  v     v i   v  i i    
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_133617000_   1391 CCTGTTGAATATGAGAAAATATTTGTAAACTATTCATCTAAT-GGGGACT 1439
                           iiiv    iv             i   ii  vi    i  -i      
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_133617000_   1440 TAATATCCAGAATATACCAAGAACTC----AAAT-AATAGGAAAACAACA 1484
                          -i             iv        ----  v -    iv    vi   
  L1M4_orf2#LINE/    753 T-GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_133617000_   1485 AATATTCCCACTAAAAAATGGGAAAAGGACATGAATAGACATTTCTTAAA 1534
                             vi  v i ?         v      iv               iv  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_133617000_   1535 AGAAAACATACAAACAGCCAACAGGTATATGAAAAAATACTCTACATCGC 1584
                             i i       ii     i i i i       i  i   v     i?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_133617000_   1585 TAATCAT 1591
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.65 (135 / 82)
Gap_init rate = 0.01 (11 / 905), avg. gap size = 3.18 (35 / 11)  


1305 20.49 3.53 0.35  chrX_133701131_133704527.rev      502   784 (2613)    L1M4_orf2#LINE/L1        3   294 (614)  

  chrX_133701131_    502 GAAAGACATTC-ATGTTCATGGATTGG--GAC--AAT---GTTTAGATGA 543
                               i  i -               --   --   ---   v     i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_133701131_    544 CAATTCCACCCAAAGTGATCAACAGATGCAATGCGCCCCTTACCAAAGTC 593
                             v iv      v     v      v   i  ivi  i  i    i  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_133701131_    594 CCAATCACATTTTTTACAGAAACAGAAAAACCCATCTGAAAATTCATATG 643
                            iiii v      i      iv  v  i iv   iv            
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_133701131_    644 GAATAT-TAAAGGACCCCAAATAGCCAAAGCAGTCTTTGAAAAGATGCAC 692
                            -  -i  i      vi          i  i    vi      v v  
  L1M4_orf2#LINE/    153 GAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_133701131_    693 AAAGCTGGAGGATTCATACTTTCTGATTTCAAAACTTCCTACAAAACTAC 742
                             i       i   i    i ii            v       i    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_133701131_    743 A-TAGTCAAAACAGTGTAGTTCTGGCATAAGAACAGATGCATA 784
                          -  i    i       i  v          i i   iii   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

Transitions / transversions = 2.22 (40 / 18)
Gap_init rate = 0.02 (7 / 292), avg. gap size = 1.57 (11 / 7)  

1692 18.87 0.00 3.10  chrX_133701131_133704527.rev     1416  1770 (1627)    L1M4_orf2#LINE/L1      321   664 (244)  

  chrX_133701131_   1416 AGAAATAAGCCTTTACATAATACATGATCAAATGGTTTTCAACAGTGATG 1465
                                 i  iv     -- -i   i    v  i     i   iv i  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACAT--T-TATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_133701131_   1466 CCAGGACCATTCAATGGGGAAAGGACAATCTTTTCAACAAATGATGTTTA 1515
                            i                   i i i               i  i vi
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_133701131_   1516 GAAAACTGGAGCTCTACATGCAAAAGAATGAAGTTGAACCCCCTTTTTTT 1565
                           v       vv? i                     i     ----- vi
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC-----TAC 462

  chrX_133701131_   1566 TTTTTACCCTATGCAGAAATTCACTCGAAATGAATTAAAGACTTTAACTT 1615
                         i ivi   v   i  i     v    i     i  i ?    i v  iv 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_133701131_   1616 AAAAGATAAAACTCTAAATCTCTTAGAAGATAACATAAGGTTAAATCTTC 1665
                           i  v       v    v           v      i ?v         
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_133701131_   1666 ATGACACTGGATTTCACAATGATTTCTTGGATATGATACCAAAGGCACAG 1715
                         i    vi   i  vvi     i      i       i      i     i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_133701131_   1716 GCAACAAGAGAAAAAAAACAGATAAACTGGTCTTCATCAAAATTAAAAAA 1765
                                i        --i       i   v                  -
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAA--TAGATAAATTGGACTTCATCAAAATTAAAAA- 659

  chrX_133701131_   1766 CTTTT 1770
                              
  L1M4_orf2#LINE/    660 CTTTT 664

Transitions / transversions = 1.91 (42 / 22)
Gap_init rate = 0.01 (5 / 344), avg. gap size = 2.20 (11 / 5)  

1174 15.35 3.15 1.18  chrX_133701131_133704527.rev     2653  2906 (491)    L1M4_orf2#LINE/L1      650   908 (0)  

  chrX_133701131_   2653 AAATTAAAAAAACTTTTGTGCATCAAATGACACTATCAAGAGAGTGAAAA 2702
                                   --         v     v             i        
  L1M4_orf2#LINE/    650 AAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_133701131_   2703 GACAACTGG-ATAATTGGAGAAGATATCTGCAAATCATATATCTGAAAAG 2751
                               ivi- v   v      i    i                  v   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_133701131_   2752 GAATGAATATCCAAAATATATACAGAACTCCTACCACACAGTGACAACAA 2801
                          i ivvi      i        v       i   v  v  i i i  -  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AA 796

  chrX_133701131_   2802 AAAC---CAACCCAATTAAAATATGAGTAAAGAGACTGAATG----TTTC 2844
                          i  ---i         ?   v   i i    iivi     i----    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_133701131_   2845 TCCAAAGAATACATACAAATGACCAAAAAGCACATGAAAAGATGCTCAAC 2894
                                  v i         i    v                       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_133701131_   2895 ATCATTTGTCAT 2906
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (23 / 15)
Gap_init rate = 0.02 (5 / 259), avg. gap size = 2.20 (11 / 5)  


2971 26.56 1.67 0.33  chrX_133839566_133841494.rev      543  1438 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_133839566_    543 TAGGAACATATCCCTTGCTCATGGATGGGAAGAATCAATATTGTGAAAAT 592
                          i i  v       v  i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_133839566_    593 GACCGTACTGCCCAGAGCAATCTACAGATTCAATGCAATTTCCATGAAAA 642
                          i vi    v    i vii              i     ii i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_133839566_    643 TACCATCATCATTCTTCACATAACTAGAAAAAACAATCCTAAAATTTATA 692
                          v   v vv v  i  ii  v  v v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_133839566_    693 TGGAACCAAAAAGGAGCCTGCGTAGCCAAAGCAATACTAAGCAAAACAAA 742
                              viiv  i   v  v vi        i    vi i iv  i vi  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_133839566_    743 TAAATCTGGAGACATCACATTACCAGACTTCAAATTATAGTACAAGGCTA 792
                         i   vi     ivv     i v  vi i      viv  v     i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_133839566_    793 TAATTATCAAAACAAT-----ACTGATATAAAAATAGGGATGTAGACCAA 837
                         i i v     i   i -----    ii    ii    iv  i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_133839566_    838 TGGAACAGAATAGAGAACCCAGAAATAAAGCCAATTAC-TTCA--GCCAA 884
                              i     v    ii           v   --   -  i -- i   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAA 348

  chrX_133839566_    885 CTGATCTTTGACAAAGTATACAAAAAC-AT-AAATGGGGAGAGGGCACCC 932
                         i    i  i     i -i i v  i  -  -v        i  iii vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_133839566_    933 TATTAAATAAATGATGCTGGGA-AACTCACTAGCCATATGTAGAAGAATG 981
                          v  v  i     i        -    viv  ?   i   i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_133839566_    982 AAACTGGTTCCCCATCTCTCACTTTATACGAAAATCAACTCAAGATAGAT 1031
                           ii   vi   i i   v   iv     i     i       i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_133839566_   1032 CAAATGCTGAAATCTAAGACCTGAAACCATAAAAATGTTAGAAGATAACA 1081
                           ? vi iv    v     v  i    i      v v        v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_133839566_   1082 TCAGAAAAACTCTTCTGAACATTGGCTTAGGGAAAGAATTCATGACTAAG 1131
                          vi ?iv  v     vvi  v    v     v  v iv   v iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_133839566_   1132 ACCCCAAAAGCAAATGCAACAAAAACAAAAATAAATACATGGGACCTAAT 1181
                           v         v v         iv       i   v  v    i v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_133839566_   1182 TAAACTAAAAAGCTTCTGCACAACAAAAGAAATAATCAACAGATCAGACA 1231
                         i   v v    i   i  ii vv    i  v iv     v i viii v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_133839566_   1232 GACAACCCACAGAGTGGGAAAAAATATTCACAAACTATGCATCTGAAGAA 1281
                                      i     i        ii    ii  ii      vi i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_133839566_   1282 GAGCTAGTACTCAGAATCTATAAGGTACCCAAGCAAATCAGCAAGAAAAA 1331
                          ii  v   ii      v     i v  i vvi   v   ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_133839566_   1332 AACAA-T--CCCAAC-AAAAAGTGGGCAAATGACATGAATAGACATTTCT 1377
                         i    - --     i-?    i        v  iv               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_133839566_   1378 CAAAAGAAGATACCCAAACAGCCAACAAACATATGAAAATATGCTCAACA 1427
                          v          iv    ii     i  i  i       v          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_133839566_   1428 TCACTAATCAT 1438
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


1941 24.84 2.71 1.75  chrX_133884521_133887499      484  1111 (1868)  C L1M4_orf2#LINE/L1   (0)   908   275  

C chrX_133884521_   1111 GATATAGAGGACCAAC-TGTAGATGAATAGAACTGGATATGCAA-TTCAG 1064
                          ii   -    ivi  - i     v   i   iv i  -  vi - i   
  L1M4_orf2#LINE/    275 GGCATA-AGGATAGACATATAGATCAATGGAATAGAAT-TGAGAGTCCAG 322

C chrX_133884521_   1063 AAATAGACCCACACATATATGGACAGCTGATTTTTG-TAAAGTTGTAAAG 1015
                              i     i    v     v  ii       i -i  i v  iv   
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

C chrX_133884521_   1014 GCAATTCAGTGGAAAAGGGATAATATTTTCAA--AATGATGCAGGAAAAG 967
                         i v     i   ii  i i   i v       --    i   v  i v i
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

C chrX_133884521_    966 TTGAATGTCTATTTACAAAAAAAATTAATTTGATCCATATCTCACACCAT 917
                         i  i  i? i iv i     i  vvv i  v  i  v  i          
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

C chrX_133884521_    916 ATGCAAAAATTAACTAAAAAACGTTAATAGACCTAATGGTAAAACCTAAA 867
                           i            v    vv v v ?        vv    i v     
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

C chrX_133884521_    866 ATTATAAAGCTCCTAGAAGAAAACA--GGAAAAAACAACTTTTGAAACCT 819
                          i      i   i            --  ?iv   i---i  i vi    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCT 569

C chrX_133884521_    818 TGGATTAGACAAAGATTTCTTAGCTATCACAACAAAAGCACAATTCTCAT 769
                            i    i   v i        v   v   v           vivv  v
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

C chrX_133884521_    768 AAGCAAAATTTGGTAAATTGGACTTCAT----ATTAAAAAGCATGTGCTC 723
                            v    v v i               ----        - v v  iv 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGC 668

C chrX_133884521_    722 TTCAAAAGACAATGTTAAGAGAATGAACAGAGAAGGCACAGGCTGGGAGA 673
                               i    v i i    i i    v   v  vv     iv       
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

C chrX_133884521_    672 AAATATTTGTAAGTGGCATATCTAATGAAG-ATTTGAATACAGGATACAT 624
                                  i  i vii      i  i i - i   v  v   i   i  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

C chrX_133884521_    623 ATAGAACTCTCAAAAC--AACAATGTATAGGTCAACAACCTGATTTAAAA 576
                          v        i v   --  i   iv v  iiv  i    ii   ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

C chrX_133884521_    575 -TGGAAAAAAATATCTGAAGAGACATTTCACTAAAAAAGATAAATGTATG 527
                         -   iv   ii-  i    v         v i   i      v iiv   
  L1M4_orf2#LINE/    819 ATGGGCAAAGG-ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

C chrX_133884521_    526 ACAAATAAGCAACA-AAAAAGGTGTTCAGGGACAT-ATGAATTTT 484
                         i v        -  -i     i  i   ---    - ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCA-CATGAAAAGATGCTCA---ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (90 / 62)
Gap_init rate = 0.03 (18 / 634), avg. gap size = 1.56 (28 / 18)  

2416 26.30 6.11 1.38  chrX_133884521_133887499     1620  2486 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_133884521_   1620 TGGAAACACACTCCATGCTCATGGATGGGAAGAATCAATATTGTGAAAAT 1669
                               v i ii     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_133884521_   1670 GACCATACTGCCCAAAGCAATCTACAAATTCTATGCAATTACCATCAAAA 1719
                          i v     v      vii       i    v i     iv i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_133884521_   1720 TACCCTCATCATTCTTCACAGAAGTATAAAAAAC-AATCTTAAAATTCAT 1768
                          v  vv vv v  i  ii     i - i v  i -i   i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_133884521_   1769 ATGGAACCAAAAAAAAAGAGCCCACA-TAGCAAAAGTCATACTAAGCAAA 1817
                               ---- viv  i ii    v -    v   iiv  vi i iv  i
  L1M4_orf2#LINE/    150 ATGGAA----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_133884521_   1818 AAGAACAAATCTGGAGGCATCGCATTTGCTGACTTCAAGTTATACTACAA 1867
                                  vi      vv  i  i  v ii i     iviv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_133884521_   1868 GGCTGTAGTTACCAAAACAGCATGGTACTGGTATAAAAATAGGTATGTA- 1916
                         i   ii   v i   i    ii         i    ii    ii  i  -
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_133884521_   1917 ---------ACAGAATGGAGAACCCAGAAATAAAGTCAAACAC----AAC 1953
                         --------- i     v    ii           vi  v   i----iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_133884521_   1954 CAACATATCTTTAAAAAAGCATACAAAAAC-AT--AATTTGGGGAAAGGA 2000
                            ivv  i  ii v  i -i i v  i  -  --   --        i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAAT--GGGGAAAGAA 392

  chrX_133884521_   2001 CACCCTATGCAATAAATGGTACCGGGAAAACTGTCAAGACACATGTAGAA 2050
                         i vi  v v   i       i i    v     vvv ?v      i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_133884521_   2051 GAATGAAACTGGATCCCCATCTTTCACCTTATAAAAAAATTCAACTCAAG 2100
                                ii    i   i i  iv    v    v       -       i
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AACTCAAA 491

  chrX_133884521_   2101 ATGGAGCAAAGACTTAAACCTTAGACCTGAAACCATAAAAATTCTAGAAG 2150
                              v  ?    i    iv v   v  i    i      v ii      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_133884521_   2151 ATACCAT---CATAAAAACTCTTCTAGACATTGGCTTAGGCAAATAATTC 2197
                          v v   ---?i    ---     vv   v    v        vviv   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_133884521_   2198 ATGACCAAGACCCCAAAAGCAAATGCAACAAAAATAAAAATAAATAAATG 2247
                         v iivi v   v         v v         iv       i      v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_133884521_   2248 GGACCT-A--AAAACTGAAATCTTCTGCACAGCAAAAGAAATAATCAGTA 2294
                             i - --    i i   v   i  ii vv    i  v iv    iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_133884521_   2295 GAGT----AGACAGCT---------------AGTATTAACAAACTATGCA 2325
                         i   ----     i i--------------- i    vi    ii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_133884521_   2326 TTCAACAAAGGACTAATATTCAGAATCTACAAGGAACTAAAAAAAATCAG 2375
                          iii i  i     vi   i      v  i  i     vvv v  v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_133884521_   2376 CAAGAAAAAAA------ACTCA-TCAAAAAGTGGGCAAATGACATGAATA 2418
                         i  v     i ------  i  - i?    i        v  iv      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_133884521_   2419 GACATTTCTCAAAAGAAGACACACAAACAGCCAGTAA--ACATGAAAATA 2466
                                   v        i i     ii    i   --         v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_133884521_   2467 TGCTCAACATCACTAATCAT 2486
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (135 / 89)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.25 (65 / 20)  


1475 29.20 3.87 3.60  chrX_133929138_133930804      459  1208 (459)    L1M4_orf2#LINE/L1      157   908 (0)  

  chrX_133929138_    459 TGCA--GGACTCAATATTGTGAAGAC--TCTTAAAGAAACAGGA----G- 499
                             --    i  iv  v iv  i  --    i  i  iv  i ---- -
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_133929138_    500 -GAAGGATTTGC-TTTAGCAAATGTAAAG-TTATTATAAAGCAATAGTAA 546
                         - i    i ii -i  vv   v vi   i-   i  i     v i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_133929138_    547 TTAGGACACTTTGGTACCAATATAGTGATGTACACATAGATGAGTGGA-T 595
                          i i    v v      iiii   iv   iv   i      v i    - 
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_133929138_    596 AGGCTAGACAGCCCAGAAACTGACTCTGAGCCTGCTTTCATGGCTGCTTG 645
                           iv v  v  i       ivi  i -- --- i v  i    iiiv   
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCC--A---TACATTTATGGTCAATTG 351

  chrX_133929138_    646 ATTCGTGACACTAGTAGCATTGCAGAGCATTTA----GAAAAGAA-AATG 690
                            ivi    vvi  iv  ----   v    i ---- i      - i v
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_133929138_    691 TTTCCAACAAATAGTGTTGAGACAACAGGTTATACACTTGGAAAGAAATA 740
                            i        i   i  i      v  v  ?v   v  v   ii   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_133929138_    741 AAAATAAATCCCCTACTTCACACCAGATATGGGAAAACAATCTCAGG-TG 789
                           iv ii -       i        v   ii--    iv v    ii-  
  L1M4_orf2#LINE/    448 AAGTTGGA-CCCCTACCTCACACCATATACA--AAAATTAACTCAAAATG 494

  chrX_133929138_    790 TATTTTAGAGCAAAATGTCATAGGCAAAATAATAAAGCTTGTAGAAAAAA 839
                         v  iv?   v v      v v  vi    iv     i  iv     i   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_133929138_    840 ATGTAGAAG-AGCTTTTCACACCCTCTGGGT-ATGGAAGGATTTCTCAAA 887
                          ii   i? - iv i   iiiv   -     - v v  v i     i i 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_133929138_    888 CAAGTCA--AAAAATACTAATTATAGTGGGAAATGTTAAAAAAATTATGA 935
                         i v v  --    ii  v iiv i ivi i   vi - i v     -- i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAATT--GG 640

  chrX_133929138_    936 ACCACATTAAGATTAAGACCTTTTGTTCATAAAAAGACAACATTACTAGC 985
                           iv   i  i     i v       v v v   i    vi  i vv iv
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_133929138_    986 AGGAAAAGGCAAGCCACAGAATGTAAGAAGATATTTATCAAAT-ATTTAG 1034
                         iv      i   v          vi    i      i-     -  v  v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG-CAAATCATATAT 739

  chrX_133929138_   1035 GTGACAATAGCTTAGT-TCCAGAGCACATAAACGATTCTTAGAAATCAAA 1083
                         v   i  vi vi v  -      ii i     vi i     v  v    v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_133929138_   1084 GAGAGGAAGACAAATAACACAAT--AGTAATGGCCAAGAGACTTAAACAG 1131
                         i v ii            v    -- iv     v   ii  i  i  i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_133929138_   1132 AACATTG-TCCAAAGAGGAAATCCAAATAGCCAACATTATTAATCAT-TA 1179
                          -    v-        i  v  v     i     ------   v  i- i
  L1M4_orf2#LINE/    840 A-CATTTCTCCAAAGAAGATATACAAATGGCCAA------TAAGCACATG 882

  chrX_133929138_   1180 GAGAAATGCACAGTGAAACCACACTGCAG 1208
                         i i i    v  --- v i  ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCA---ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (128 / 88)
Gap_init rate = 0.04 (30 / 752), avg. gap size = 1.87 (56 / 30)  


2781 26.97 1.78 2.00  chrX_133966050_133970217.rev     2777  3677 (491)    L1M4_orf2#LINE/L1       10   908 (0)  

  chrX_133966050_   2777 ATTCCATGCTAATGGGTAGGAAGAACTAATATAG---AAATGGCCATACT 2823
                           i     i v    i v      vi      v --- i     v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_133966050_   2824 GCCCAAAGCAATTTACAGGTTCAATGCTATTCATATCAAACTGCCAACAT 2873
                         v      vii  i     i     i  v  i v       v v   i vv
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_133966050_   2874 CATTCTTCACAGAATTAGAAAAAAAAACT-ATTCCAAAATTCACATGAAG 2922
                          v  i  ii     v v  v  i----  -  i i        i   i i
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATTCATATGGAA 155

  chrX_133966050_   2923 CCAAAAAGGAGCCTGAATAGCCAATGCAATCCTAGGAAAAAAGTACAAAG 2972
                         viiv  i   v  v          vi     i iii   i   v      
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_133966050_   2973 CTGGAGGCATCATACTACCCAACTTCAAATTATATTATATACCCACAGAA 3022
                         i      vv   i   v     i      viv  i  i v v i    v 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_133966050_   3023 ATCAAAACAGCTTTTTGTACTGGTACAAAAACAGACACATACAGCAATGG 3072
                              i    -- v v       i i  ii i     i   v v      
  L1M4_orf2#LINE/    256 ATCAAGACAG--TGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_133966050_   3073 AACAGAATAGAAAATTTGGAAATAAGGCCACACATCTACAACCATCTGAT 3122
                           i     v  i i iii       iv   i    i  iiii  vi    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_133966050_   3123 CTTCGACAAGG---CCGAGAAAAACCAG-CAATAGGGAAAGGGCTCCCTA 3168
                         i          ---  ----  i    v-    i       iiivvi  v
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCC----AAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_133966050_   3169 TTCAATAAATGGTACTGGGATAGCTGGCTAGTCATATGTAGAAGACTAAA 3218
                              i       i      i i    v  ?i  i   i i    v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_133966050_   3219 GCTGGAACCCTACCTTTCACTATATATAAAATTTCACTCAAAATCAATTA 3268
                          i    v        iv   i     i    v  v         vi  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_133966050_   3269 AAGAGTTAAATGTAAGACCTCAAACTCTAAAAATCCTGGAAGACAGCCTA 3318
                         ?   vi           v  v     v     v  i i     v i v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_133966050_   3319 AAAAATACTCTTCTCAACATCAGCCTTGGCAAAGAATTTTTGACTAAGTC 3368
                         ii?ivv v     vii  v ii vi v     v iv  i  iiv  v v 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_133966050_   3369 CCCAAAAGCAATTGCAACAAAAACAAAAACGGACAAATAAGACCTAATTA 3418
                         v         vvv         iv     ii  i    vi   i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_133966050_   3419 AACTAAAGAGCTTCTACACAGCAAAAGAAACTGTCAATAGAGAAAAAAAA 3468
                           v v  i i   i iii vv    i  v   i    ----    ivi  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA----GAAAGTGAA 695

  chrX_133966050_   3469 AACACAGATAACATGCATAATGGGATAACATATTCACAAACTATGCATCC 3518
                           ----  i   vii  v       v  v     ii    ii  ii   i
  L1M4_orf2#LINE/    696 AA----GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_133966050_   3519 AAGAAAGGCCTAATATCTAGAATCTATAGTGAACTT----AAATTGACAA 3564
                         i v  i  v  vi    i     v    iv     i----  v ii i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_133966050_   3565 GAAAAA-ACAAATAACTCCATT-AAAAATGGGCAAAGGATATGCACAGAC 3612
                         v     -         i v   -                 v  v i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_133966050_   3613 ACTTCTCAAAAGAAGACATACAGGTGGCCAACAA--ATATTATAAAATGC 3660
                          i     v        i     ii       i  -- i  v v  i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_133966050_   3661 TCAATATCACGAATCAT 3677
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (13 / 899), avg. gap size = 2.62 (34 / 13)  


3029 27.64 1.78 1.00  chrX_134023498_134027793     2909  3809 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134023498_   2909 TGGAAATATATCATGTGTTCATGAACAGGAAGAATAAAATATTGTTAAAA 2958
                               v     vii        i iv      v v  -         i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAA-TATTGTTAAGA 49

  chrX_134023498_   2959 TGTCCGTAA--CCTAAAGCAATCTATAGATTCAATGCAACTGCTATGAAA 3006
                           v vi  v--  i   vii     i        i    iiv    v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_134023498_   3007 ATACCAATGACATTCTTCTTGGAAATAGAAGAAATACTCCTAAAATTTGT 3056
                           v   iivi v  i  ivii     v  vi iv iv          ii 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_134023498_   3057 ATGGAACCATG-AAAGATTCCAGA-CAGCTGAAGCAGTCTGGAATACAAG 3104
                               --   -  i ivi     -i   ii  i  i   v   v vi i
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_134023498_   3105 GAACAAAGCTGGAGGCATCACACT--ATGATGTCAAAACATATGACAAAG 3152
                                 i      vv       --vii  v       v  iv      
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_134023498_   3153 CTATAGTAAGCATAACAGCACAGTACCAGTATAAAAACGGACACATCAAC 3202
                            i     v  vi    iiii    ii i    ii ii    i  vi i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_134023498_   3203 CAATGGAGCAGAATACAGAGCCCGGAATTAAATCTGTGCATTTACAGTCA 3252
                                ii     vv    i  i   v    i ii i      ii    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_134023498_   3253 ACTAATTTTTGACAAAAGGCCCGAGAACACACAATGTTGAGAAAGTACAG 3302
                          i i     i     ii vv  i   v  iv     -- i     v i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG--GGGAAAGAATAG 395

  chrX_134023498_   3303 TCTCTTCAATAAATGATGTTGAAAATAACTGGATATTCATCTG-AGAAAA 3351
                            i     i     i  i  ii -i         ?i  iv  - i  i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGA-CAACTGGATAKCCACATGCAAAAGA 444

  chrX_134023498_   3352 ATGAATTTCCACCCTTATCTCTCAGCGTGTATATAAATCAACTCAAAATG 3401
                              v  vv    i  i   v  v i i  i v    i           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_134023498_   3402 ATTTAAAGCTTTAAAATG-AAGACCCAAAGCTGTGAAACTACTAGAAGGA 3450
                         iv i ?  vii    -  -    v i   i  i i     vi      i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_134023498_   3451 GACATAGGGGGAAAGCTCCATGACATTGTTCTGGGCAACGATATTTTAAA 3500
                         i       ? v   v  i i    v   vvi i     i i v i   i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_134023498_   3501 AACAGGACCTCAAAAGCAAAGGCAAGAAAAGGAAAAATACACAAATGGGA 3550
                         --i v   vi        v i    v     i       v i    v   
  L1M4_orf2#LINE/    594 --TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_134023498_   3551 TTACATTGAACTAAAAAGCTTCTGCACCACAGAGGAAACAATCAA-AGAG 3599
                         i v   ii  v v    i   i  ii iv  i    v  v     - i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_134023498_   3600 TGGAGAGACAATCTATGCGATAGGAGAAAACATTGACAATCTATGTATCT 3649
                           i i      i i iivi  i        i   vi   vii  i     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_134023498_   3650 AGTAAGGGGTCAGTTTCCAAAATGTA------ACTCCAACAACACAATAG 3693
                         ii      iiiv  v    i   i  ------    iv     v     i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_134023498_   3694 CAAGAAAACAAATAATCCTATT-AAAAATGAGCAAAAGACCTGAATAGAC 3742
                         i  i  i        i  v   -       i     i  ii         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_134023498_   3743 ATTTCTCAAAAGGAGACATACAAATGGCTAACAGGCATGTGAAAAAACAC 3792
                                v    i   i           i  i i   ii      i ii 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_134023498_   3793 TCACCTTCTCTAATCAT 3809
                            v v  v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (165 / 81)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.67 (25 / 15)  


2794 29.11 1.93 0.91  chrX_134046754_134051048     2912  3794 (501)    L1M4_orf2#LINE/L1        3   894 (14)  

  chrX_134046754_   2912 GAAGTGTATCATGTGTTCGTGGACAGGAAGAATAAATATTGTTAAAATGT 2961
                            ivi    vii     i    iv      v v           i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_134046754_   2962 CCGTAA--CCTAAAGCAATCTATAGATTCAATGCAACTGCTATGAAAATA 3009
                          vi  v--  i   vii     i        i    iiv    v     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_134046754_   3010 CCAATGACATTCTTCTTGGAAATAAAAGAAACACTCCTAAAATGTGTATG 3059
                            iivi v  i  ivii     vi vi iviiv         vii    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_134046754_   3060 GAACCGCAAAAGATTCCAGG-TAGTCGAAGCAGTCTGGAATACAAAGAAC 3108
                            vi    ii  i-    i-   i i  i  i   v   v vi      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_134046754_   3109 AAAGCTGGAGGCATCACACTACTTGATGTCAAAGCATATGACAAAGCTAT 3158
                             i      vv       v iii  v     i v  iv         i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_134046754_   3159 AGTAAGCATAACAGCATAGTACCAG--------TGGGTACATCCACGAAT 3200
                              v  vi    ii i    ii -------- i ii i  vv iv   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_134046754_   3201 GGAGCAGAATACAGAGCCCGGAATGAAATTCGTGCATTTACAGTCAACTG 3250
                            ii     vv    i  i   vv   ii i i      ii     i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_134046754_   3251 ATATTCAACAAAAGGCCCGAAAACACACAATGTTGAGAAAGTACACTCTC 3300
                           v   i    ii vv  i i v  iv     -- i     v i v   i
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATG--GGGAAAGAATAGTCTT 399

  chrX_134046754_   3301 TTCAATAAATGATGTTGAAAATAACTAGATATTCATCTG-AGTAAAATGA 3349
                              i     i  i  ii -i    i    ?i  iv  - iv i     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGA-CAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_134046754_   3350 GTTTCCACCCTTATCTCTCAGCATGTATATAAATCAACTCAAAATGATTT 3399
                         iv  vv    i  i   v  v   i  i v    i           iv i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_134046754_   3400 AAAGCTTTAAAATG-AAGACCCAAAGCTATGAAACTACTAGATAGAGATA 3448
                          ?  vii    -  -    v i   i    i     vi    vii i i 
  L1M4_orf2#LINE/    499 AWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_134046754_   3449 TAGGGGGAAAGCTCCATGACATTGTTTTGGGCAATGACATTTTAAAAATA 3498
                             ? v   v  i i    v   vv  i       iiv i   i --  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA--TA 595

  chrX_134046754_   3499 GGACCTCAAAAGCAAAGGCAACAAAAGGAAAAACAGACAA-TAGGATTAC 3547
                         v   vi        v i          i     i   i  - v   i v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_134046754_   3548 TTTGAACTAAAAAGCTTCTGTACCGCAAAGGAAATGATCAA-AGAGTGGC 3596
                         v ii  v v    i   i   i iv       v iv     - i    iv
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_134046754_   3597 GAGACAATCTACAGGATAGCAGAAAACACTGACAATCTATACATCTAGTA 3646
                         i      i i    i  i v      i i vi   vii   i    ii  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_134046754_   3647 AGGGGTCAGTTTCCAAAATGTATGAGTAACTCCAACAACTCA-TAGCAAG 3695
                             iiiv  v    i   i   i iv     iv        -  ii  i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_134046754_   3696 AAAACAAATAATCCTATT-AAAGATGAGCAAAAGACCTGAATAGACATAT 3744
                           i        i  v   -   i   i     i  ii           v 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_134046754_   3745 TTCAAAAGGAGACATACAAATGGCCAACAGGCATATTAAAAAAATGCTCA 3794
                         i  v    i   i              i i   i  -i    i       
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-GAAAAGATGCTCA 894

Transitions / transversions = 1.92 (167 / 87)
Gap_init rate = 0.02 (15 / 892), avg. gap size = 1.67 (25 / 15)  


2763 28.19 1.89 1.11  chrX_134062612_134067900.rev     3904  4804 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134062612_   3904 TGGAAATATATCATGTGTTCATGGACAGAAAGAATAAATATTGTTAAAGT 3953
                               v     vii          iv i    v v           ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134062612_   3954 GTCCATA--ACCTAAAGCAATCTACAGATCCAATACAACTGCTAAAAAAA 4001
                          v v   --v  i   vii          i   ii   iiv   vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134062612_   4002 TACCAATGACATTCTTCTTGGAAATAGATGAAGC-ACTACTAAAATTTGT 4050
                          v   iivi v  i  ivii     v  i-    -iv v        ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_134062612_   4051 ATGGAACCGTGAAAGATTCCAGA-TACCTGAAGCAGTCTGGAATACAAAG 4099
                               vi ii ii  -i     -  v ii  i  i   v   v vi   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_134062612_   4100 AACAAAGCTGGAGGCACCATACTACTTGATGTCAAAACATATGACAAAGC 4149
                                i      vvi  i   v iii  v       v  iv       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_134062612_   4150 TACAGTAAGCATAACAGCTTGGTACCAGTATAA----AAGCATATACTTC 4195
                                 v  vi    iv      ii i    ---- ii      ----
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA---- 294

  chrX_134062612_   4196 AACCAATGGAGCAGAATACACAGACTGGAATGAAATCCGTGCTTTTACAG 4245
                         i i       ii     vv v  v ii   vv   i  i i v    ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_134062612_   4246 TCAACTGATTTTCGACAAAAGGCCCAGGAACACACAATCTTGAGAAAGTA 4295
                             i             ii vv   i  v  iv    --v i     v 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT--GGGGAAAGAA 392

  chrX_134062612_   4296 CAGCCTCTTCAATAAATGATGTTGAAAATAACTGGATATTCATCTG-AGA 4344
                         i  i  i     i     i  i  ii -i         ?i  iv  - i 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGA-CAACTGGATAKCCACATGCAAA 441

  chrX_134062612_   4345 AAAATGAATTTCCACCCTTATCTCTCAGCATGTATGTAAATCAACTCAAA 4394
                          i      v  vv    i  i   v  v   i  iiv    i        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_134062612_   4395 ATGATTTAAAGCTTTAAAAGGAAGACCCAAAGCTATGAAACTACTAGAAG 4444
                            iv i ?  vii    v v    v i   i    i     vi      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_134062612_   4445 GATACATAGGGAGAAAAGCTCCATGACATTGTTCTGGGCAACAATTTTAA 4494
                         i v       -? v   v  i i    v   vvi i     iii   ivv
  L1M4_orf2#LINE/    542 AAAACATAGG-NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_134062612_   4495 AAATAGGACCTCCAAAGTAAAGACAACAAAAGGAAAAACACACAAATGGG 4544
                          i   v   vi v    i v ii         i     i v i    v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_134062612_   4545 ATTACATTGAACTAAAAAGGTTCTGCACCACAAAGGAAATGATCAA-AGA 4593
                          i v   ii  v v    iv  i  ii iv       v iv     - i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_134062612_   4594 GTGGAGAGACAATCTACAGGATAGGA-AAAACATTGACAATCTATACATC 4642
                            i i      i i    i  i   -    i   vi   vii   i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_134062612_   4643 TAGTAAGGGGTCAGTTTATAAAATGTATGAGTAACTC---CAACTCAATA 4689
                          ii      iiiv  v vi i   i   i iv     ---          
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_134062612_   4690 GCAAGAAAAAAAATAATCCTATT-AAAAATGAGCAAAAGACCTGAATAGA 4738
                         ii  i  i v      i  v   -       i     i  ii        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_134062612_   4739 CATTTCTCAAAATGAGACATACAAATGGACAATGAGCATA--AAAAAATC 4786
                                 v   vi   i          v    i    i --    i  v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_134062612_   4787 CTCACCTTCTCTAATCAT 4804
                             v v  v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (156 / 95)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.69 (27 / 16)  


3361 26.46 0.55 0.44  chrX_134117513_134123914.rev     5005  5911 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134117513_   5005 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5054
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134117513_   5055 GGTCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5104
                           iv     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134117513_   5105 TACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 5154
                          v   iivi i  i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_134117513_   5155 TGGAAGCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAGAGAG 5204
                              iiiv  ii  v  v v  v     i      i i ivv ii   i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_134117513_   5205 CAAAGCTGGAGGCATCACACTACCTGACTTCAAAGTGTACTACAGGGCTA 5254
                              i      vv       v  ii i      iiv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_134117513_   5255 CAGTACCCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5304
                              vi   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_134117513_   5305 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACACATTTACAACCAT 5352
                              i    i--    i  --        vv   i       iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_134117513_   5353 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5402
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_134117513_   5403 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5452
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_134117513_   5453 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGGTT 5502
                          ii    i    v   i     v              i    i    i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_134117513_   5503 AAAGACTTAAATATTAGACCTAAAACCGTAAAAACCCTT-GAAGGAAACC 5551
                          ?    i     i v   v       ii     - i   -    i    v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chrX_134117513_   5552 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 5600
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_134117513_   5601 AACATCGAAAGCAATGGCAACAAAAGCCAAAATATACAAATGGGATTTAA 5650
                         i   i i      vvi          vv      v i    v   i  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_134117513_   5651 TTAAACTAAAGAGCTTCTGTGCAGCAAAGAA-ACTACCATCAGAGTGAAC 5699
                          i   v v  i i   i     vv     i -    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_134117513_   5700 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5749
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_134117513_   5750 AGGGCTAATATCCAGAATCTACAAAGAACTCAAAGAAATTTGCAAGAAAA 5799
                         i  i  vi          v  i         vv v  v ivii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_134117513_   5800 AAACAAACAACCCCATCAAAACGTGGGCAAAGGATATGAATAGACACTTC 5849
                          i     i     v  i?   vi            v          i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_134117513_   5850 TCAAAAGAAGACATCTATGCAGCCAACAGGGACATGAAAAAAAGCTCCTC 5899
                           v        i  vi viii     i i v         i v    vv 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_134117513_   5900 ATCATTGGTCAT 5911
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3189 24.42 1.88 1.55  chrX_134125220_134129473     2857  3761 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134125220_   2857 TAGAAAGATATTCCATGTTCATGGATTGGAAGAAT-AATATCATTAAAAT 2905
                          i         i                     v -     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134125220_   2906 GTCCATACTACCCAAGGCAGCCTACAGATTCAATGCAATCCCTATTAAAA 2955
                          v v     v     iviiii            i           i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134125220_   2956 CACCAATGACATTCTTCACAAAAATAGAAAAAAAAAATCCTAAAATGTTT 3005
                         iv   iivi v  i  ii  i    v  v  ivvi -         viv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_134125220_   3006 ATGGAACCACAAAAGACCCAGAAGAGCCAAAGCTGTCCTGAGCAAAAAGA 3055
                               vii   ii         v       i vi  i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_134125220_   3056 AGAAAACTACAGGAATCACATTACCTGACTTCAGATTATAATACAGAGCT 3105
                          v   ii iv    v     i v  ii i    i viv  v    i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_134125220_   3106 ATAGGAATCAAAACAGCATGGTACCGGCATAAACACAGACACATAGACCA 3155
                          i  v      i    ii      i       iv i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_134125220_   3156 ATGTAACAGAACAGGGAACACAGAAGAAAATCCACAACACCTACAGTGAG 3205
                            v  i    iv i  iiv     iv   i   i -  ii  ii  v i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA-CATTTATGGTCAA 348

  chrX_134125220_   3206 CTCATTTTTGACAAAGGTGCCAAGAACATACACTGGGGAAAAGACAGTCT 3255
                         i v     i     i          v   v  v        ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_134125220_   3256 GTTCAATAAATGGTGCTCGGAAACCTGGATATCCATAAACTGAAGAATGA 3305
                         v     i          v   v v       ?   i vi vi        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_134125220_   3306 AACTAGACCCCCTATCTCTCACCATATACAAAAGTAAAATAAAAATGAAT 3355
                          ii i      -  i   v              i v  v v      i  
  L1M4_orf2#LINE/    449 AGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_134125220_   3356 TAAAGACTTAAACTTAAGACCTCAAACT-TGAAACTACAAACAAGAAAAC 3404
                         i ?    i    iv     v  v     - i     - vv v        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAAC 546

  chrX_134125220_   3405 ATTGGGGGAAATCTCCAGGACGTTGGTCTGGGCAAAAATGTCTTGAGTA- 3453
                           v  ? v      i iv   v    vi i     vii v    iii  -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_134125220_   3454 -ACAACCCACAAGCACAGACAACCAAAGCAAAAATGGACAAATGGGATCA 3502
                         -   --   v       ii    v    v      i  i    v   iiv
  L1M4_orf2#LINE/    597 GACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_134125220_   3503 TATCAAG-TGAAAAACCTTCTGCACAGCAAAAGAAACAACCAACAAAGGG 3551
                         i     i- v      i  -  ii vv    i  v  v i   v    v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_134125220_   3552 AAGAGACAACTCACAGAGTAGGACAAAATTTTTGCAAAGTGCCCATCTGG 3601
                           i       i      i i   v     v        viiivi     i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_134125220_   3602 CAAAGGA--TGAATTAACCAGAACATATAAGGAGC----ACAAAAATCTC 3645
                         i  i   --  v  ---      i      i  i ----    ----   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTAT---CCAGAATATATAAAGAACTCTTACAA----CTC 786

  chrX_134125220_   3646 TACAGGAAAAAATCAAATAATCCAGTT-AAAAATGGACAAAAGATCTGAA 3694
                         v i iv     iv       i   i  -        i    i   i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_134125220_   3695 TAGACATTTCTT-----AAAACATACAAATGACAAAGAGACATATGAAAA 3739
                                    i-----  i i         i v  v ii  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_134125220_   3740 GGTCCTCAACATCATTGATCAT 3761
                          i v          ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (136 / 82)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.94 (31 / 16)  


3014 27.09 0.99 0.99  chrX_134136192_134142893.rev     5304  6211 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134136192_   5304 TGGAAAATCATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5353
                               ivi  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134136192_   5354 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCTCATCAAGC 5403
                            v     v      v i  i  i       ii  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134136192_   5404 TACCATTGACTTTCTTCACAGAATTAGAAAAAAAACT-ACTTTAAATTTT 5452
                          v   vivi i  i  ii     v v  v  i---  - iii    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_134136192_   5453 ATA-AGAAACCAAAAAAAGAGCCCGTTTAGCCAAA-CAATCCTAAGCAAA 5500
                            -i    i--iv  ii  v  v vv        -     i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAAT--GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_134136192_   5501 AAGAACAAAGCTGGAGGCATCATGCTACATGACTTCAAACTATACTACAA 5550
                                   i      vv   ii  v vii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_134136192_   5551 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAG 5600
                         i          i   i    ii         i iv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_134136192_   5601 ACCAATGTAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAAC 5650
                          i     v  i    iv   ivii         vv   i    i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_134136192_   5651 CATCTGATCATTGACAAACATGACAACAACAAGCAATGGGGAAAGGAT-- 5698
                           vi    iv i     ivi  v   v v  vv            i  --
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_134136192_   5699 TCCTTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCACATGCAGAAA 5748
                           i  -- i  i        i     v      v  ?         i  i
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_134136192_   5749 ACTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGAT 5798
                          v    ii    i    v   i     v                   i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_134136192_   5799 GGATTAAAGACTTAAATGTAAGACCTAAAACCATAAATACCCC-AGAGGA 5847
                             i ?    i           v       i     -  i i-   i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGA 542

  chrX_134136192_   5848 AAACCTAGGCA-ATATGATTCAGGACATAGGCATGGGCAAATACTTCATG 5896
                             v    ?i- v  v-   iv   v v  vv i     vvii   v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_134136192_   5897 GCTAAAATGCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGTGA 5946
                          v  vi ii         vvi          vv     v  i    vv  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_134136192_   5947 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAG 5996
                         ii v  i   v v  i i   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_134136192_   5997 TGAACCGGCATCCTATAGAATGGGAGAAAATTTTTACAATCTATCCGTCT 6046
                             vv i  v  i i               v   i   vii  vii   
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_134136192_   6047 GATAAGGGGCTAATATACAGAATCTACAATGTACTTAAACAAATTTACAA 6096
                                 i  vi   v      v  i  v v   ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_134136192_   6097 GAAAAAAAGAAA--ACCTCATCAAAAAGTGGGTGAAGGATATGAACAGAC 6144
                         v     i v   --   iv  i?    i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_134136192_   6145 ACTTCTCAAAAGAAGACATTTATGCGGCCAACAAACTATTAAAAAAAAGT 6194
                          i     v        i  vi vii      i  i vvv i    i v i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_134136192_   6195 TCATCATCACTGGTCAT 6211
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


3998 16.59 3.17 1.59  chrX_134158331_134160074.rev      434  1253 (491)    L1M4_orf2#LINE/L1       76   908 (0)  

  chrX_134158331_    434 AGATTGAACACCGAATACCACATTAATATGGTATTCCTAGATGACTTATT 483
                              v   i --   v  -i  i  v  ------  i  v  v   v  
  L1M4_orf2#LINE/     76 AGATTCAACGC--AATCCC-TATCAAAAT------CCCAGCTGCCTTTTT 116

  chrX_134158331_    484 TGCAGAAACTGACCTGTTTATCCTAAAATTCATATGGAAATTCAAGGGAC 533
                                 i    vv i v                      v        
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_134158331_    534 CCAGAGT--CTAAAACAATTTTGAAAAAGGAGAACAAAGATATAAGATTC 581
                              i -- i        i         i         v iv i  i  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_134158331_    582 ATATTTTGTAATTTCAAAACTTACTACAAAGCAACAGTAATCTAGACAGT 631
                          i i  ivi                       v         v       
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_134158331_    632 GTGGTATTTGCATAAGACTAGACATTTAGATCAATAGAATAGAATTGAAA 681
                               i v       iv       v         i            i 
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_134158331_    682 GTTCAGAAACAAAGCCATACACCTTGAGTTAACTGATTTTCACCAAGGGT 731
                           i      i   v       ii vvi  i  i        iv       
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_134158331_    732 GCCAAAACAATTTAATAGGGAAAGAATAGTCTTT-CAACAAATTATGCTA 780
                              i  v   i   i                 -        vi    i
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_134158331_    781 GGTCAACTGAATATCCATATGCAAAAAAAAGAAGTTGTACCTCTATCTTA 830
                           v      i   ?   i        i  v       v   i   i  i 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_134158331_    831 GATCATACACAAAAATTAACTCAAAATGGATGAAAGATCTAAATAAATTA 880
                         v i    i                       v ?   i      i---  
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG---TA 513

  chrX_134158331_    881 GGGGCTAACATTATAAAACGTCTAAAAGAAAACACAGGTGTAAATGTTTG 930
                         i i     v i        vii  i         i   ?      v  i 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_134158331_    931 TGCCCTTGGATTAGGTGGCTGGTTTTTCAGATGTGACAT---------AA 971
                           v      i     iii-      i i    i     i---------  
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_134158331_    972 GAAACTAAAGAAAAAATAGATAAACTGGCCATTA-CAAAATTAAAATCTT 1020
                          v   v                  i   v v i -           v   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_134158331_   1021 TTGTGCAGCAGAGGACACCATCAAGAATGTTGAAAGTTAATCCACAGAAT 1070
                               vv  i       i        v  vi    vi  i         
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_134158331_   1071 GGAAGAAAA-ATGTGCAAATTATATGTCTGG-------CTTGTGTCTAGA 1112
                           i      -  v       i    i    i-------     i  i   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_134158331_   1113 ATATATAAACAATGATTACAACTCAATAATAAAA-GACAAATAAC---AG 1158
                                  v  ivv                   -          --- v
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_134158331_   1159 TTAAAAATGAGCAAAGGATCTGAA-AAAAGTTTCTCCAAAGAAAATATAC 1207
                          ?       i         i    - i vi             i      
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_134158331_   1208 AAATGCCTAATAAGCACATGAAAATATGCTCAATATCATTAATTAT 1253
                              v i                v        i    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (81 / 51)
Gap_init rate = 0.02 (14 / 833), avg. gap size = 2.79 (39 / 14)  


3071 25.34 3.62 0.90  chrX_134171700_134175895.rev     2822  3705 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134171700_   2822 TGGAAAGACATTCCATGCTCATGGATCAGAAGAATTTGTATTGTTAAAAT 2871
                                 i  i     i        ii     v  vi         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134171700_   2872 AACCATATTGCCCAAAGCAATCTACTGATTCAA---AA-CGCTA-----A 2912
                         ii v   i v      vii      v       ---  - v   ----- 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134171700_   2913 TGCCA----TTTTTTTCACAGAAATAGAAAAAATTATCCTAAAATTCATA 2958
                          v   ----ii     ii       v  v  iv v               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_134171700_   2959 TGGAACAACAACAACAAAAAAAGCCAGAATAGCCAAAGCAAACCTAAACA 3008
                              vvi   -------iii v              i   v i i  v 
  L1M4_orf2#LINE/    151 TGGAAATGCAA-------GGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_134171700_   3009 CAAAGAATAAAGCTGGAAGCAACACACTACTGGACTTCAAAATACATTAC 3058
                         vi     i    i    i vvv      v ivi i       ivi i   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_134171700_   3059 AAGTCTATGGTAACAAATACAATATAGAATTAGTATAAAAATAGCCACTT 3108
                           iv   ii    iv  v   i i i v i i i    ii    v  iv 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_134171700_   3109 AGACCAATGTA-TAGA-----GAACTCTGAGATAAATTCATATATTTACA 3152
                            i     v -    -----  iii v  i     ii    i     ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_134171700_   3153 GCCCACTGATTTTCAACAAAGGCACCAACAACATGCACTGAGGAAATGAC 3202
                          i v i        i    i  ii    v v   v  v  i     vi i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_134171700_   3203 ACCCTCTTTAATAAATGGTGCTGGGAAAGTTGGATATCCATATGTGCAGT 3252
                          vi  i  i  i              v ii      ?   i   iiv iv
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_134171700_   3253 AAGGAAATTAGACCCCTACCTCTAACCATATACAAAAATCAACTCAAGAT 3302
                           v   i  i            vv               i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_134171700_   3303 GGATTAAAGACTTAA------GACCCAAAACTATTAAACTAGTAGAAGAA 3346
                             i ?    i   ------  v i        v     vv        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_134171700_   3347 AACATAGGGAAAAATCTTCAGGACATTGGCATAAGTGAAGATTTTATGGC 3396
                                 ?iv        iv   v    vv  i ii v i   iv i v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_134171700_   3397 TAAGGCTTCAAAAGCACAGACAACTAAAGCAAAAAGAGACAAAAAGGACT 3446
                           v i vi          ii    v    v     v   i   vv     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_134171700_   3447 ATATCAAA-CTAAAAA--TCTGCATAGCAAAGGAAACAATCCATTGAGTG 3493
                         vi      -i      -- i  iiivv       v  v   v vvi    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_134171700_   3494 GAGAGATAACCTGCTGAATGGGTAAAAATGTGTGCAAACTATTCATCTGA 3543
                         i i   i    ii v       vi     i v      ii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_134171700_   3544 TAAGGGATTAATATTCAGAATATACCAGAAACTC----AAGTCAAGAATA 3589
                                i vi   i         iv ii     ----  v    v    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_134171700_   3590 ATAAAACAAATAATCCCATTAAAAAGTGGGCAAATGCCATAAATGGACAA 3639
                          v  i        i  v   ?    i        v viv i   i    v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_134171700_   3640 TTCTCAAAAGAAGACATACAAATGGCCAACAGGTATACGAAAAAAGTACT 3689
                              v        i              i i i i i     i - i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chrX_134171700_   3690 CAACATCACTAAATAT 3705
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (133 / 87)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.33 (40 / 12)  


2349 18.16 0.42 2.09  chrX_134215371_134217439.rev      502   980 (1089)    L1M4_orf2#LINE/L1      299   769 (139)  

  chrX_134215371_    502 AACAGAATAGAAATGAGAATCTAGCAATAAATCCATATACCTGTCCTGTG 551
                           ii        v     i  i  v      i     i ii i ----- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT-----G 343

  chrX_134215371_    552 GTCAACTGATTTT-GAAAAGGGTTTCAAGGATATTCAATATAAAAAGAAT 600
                              i       -  v      vi    ivi       ivii       
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_134215371_    601 AGCCTTTTCAACAAATAATGCTGAGACACCTGGATGTCTCCACGGGAAAA 650
                           i             ii     i    v      i? iv  i vi   i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_134215371_    651 AATTATTATTTGGACCTCTACCTCCCACCCTAT-TAAAAATTAATGAAAA 699
                            v -- v       i       v    v   -i         ivv   
  L1M4_orf2#LINE/    444 AATGA--AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_134215371_    700 ATAGATCAAAGTCTTAGATGTAAGAGCTAAAATTATAAAACTGTTCGATG 749
                           i     ?  v i  i               i         v  v  v 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_134215371_    750 AAAACACAGGAGAAAATTTTTGTGACCTTGGATTAGGCAATTATTTCTTA 799
                               i   ? v    i  i          i         vi       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_134215371_    800 GATAAGACATCAAAAGCACAAACAACAAAAGAAAAAACAATTACATATGA 849
                             v    i           i               i iv  v  vv  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_134215371_    850 CTTCATCAAAATTAAAAAAATATTTTGGGCTACAAAGGACACTATCAAGA 899
                                           v---     v   v                  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAAC---TTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_134215371_    900 AAGTGAAAAGATGGCCTACAGAACGGGAGAAAATACCGGCAAATCATATG 949
                                    iii  i      i           iiv           i
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_134215371_    950 TCTAATAAGGGACTTTTATCTAGAATACACA 980
                            i           v    i      i i 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATA 769

Transitions / transversions = 1.71 (53 / 31)
Gap_init rate = 0.01 (5 / 471), avg. gap size = 2.40 (12 / 5)  

 361 16.67 3.03 0.00  chrX_134215371_134217439.rev     1070  1135 (934)  C L1M4_orf2#LINE/L1   (586)   322   255  

C chrX_134215371_   1135 AACTAAGACAGTGTGGTACTTCCATAAGAATAGACATGTAGATCAACAGA 1086
                           ii                vv      i        i        ii  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

C chrX_134215371_   1085 ATAGAG--GAGAGTTTAG 1070
                              i--      ii  
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAG 322

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.01 (1 / 68), avg. gap size = 2.00 (2 / 1)  

 637 15.33 5.84 0.00  chrX_134215371_134217439.rev     1443  1579 (490)    L1M4_orf2#LINE/L1      764   908 (0)  

  chrX_134215371_   1443 TGTATGAAGAACACATACAATTCAATAATAAAAAGACAAATAATTCAATT 1492
                          i   i      v v     i                      ii     
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_134215371_   1493 -AAAAATGGGCAAGGGGACTAAATAGG----TCT---ATGAAAATATACA 1534
                         -            i  ivi i     i----   --- v   i       
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_134215371_   1535 AATGACCAATAAGCACATGAAAGCATGTTCAGCATCGTTACTCTT 1579
                             i                 iv   i   i    i????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.20 (16 / 5)
Gap_init rate = 0.02 (3 / 145), avg. gap size = 2.67 (8 / 3)  


 218 25.90 14.39 5.76  chrX_134268792_134270472      500   638 (1043)    L1M4_orf2#LINE/L1      121   271 (637)  

  chrX_134268792_    500 GAAATTAAGAAAACAATTCCA---TTTATAATAGCATCACAAAGAA---- 542
                               i v  ivii  i i ---  i   - i v vii   i i ----
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATA-TGGAAATGCAAGGGACCCA 169

  chrX_134268792_    543 GAATATACTTAGGAATAAGTTTAACAGAAATGCAAGAACAAAGTTGAAAT 592
                              -i iv --  i  vi  i ---   v -             i iv
  L1M4_orf2#LINE/    170 GAATA-GCCAA--AACAATCTTGA---AAAAG-AAGAACAAAGTTGGAGG 212

  chrX_134268792_    593 AATTACACTACCTGATTTCAA-------------GCTGCAGCAATCAAGA 629
                          v i     v  ii       -------------   i   i        
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_134268792_    630 TAGTGTAGT 638
                         i     i  
  L1M4_orf2#LINE/    263 CAGTGTGGT 271

Transitions / transversions = 2.60 (26 / 10)
Gap_init rate = 0.05 (8 / 151), avg. gap size = 3.50 (28 / 8)  

1440 25.64 5.45 3.45  chrX_134268792_134270472      639  1188 (493)    L1M4_orf2#LINE/L1      348   908 (0)  

  chrX_134268792_    639 ATTGCTTTAAGACTAGA----CAAAATTGTTCAATAAGGAAAAGAAAGTC 684
                             v   vv   v  i----   i iii      ii     ii v    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_134268792_    685 TTTTCAACAAACGCTGCTGAGATAACTAGATTTTTAAAAATATACATTTA 734
                                    i v     i  i    i   v?ii ----i  i  --- 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA----CATGCA---A 440

  chrX_134268792_    735 AACAATGAAAT-GAACACTGTCTCCTATCTCATGCCATAAACAAGCATTA 783
                           v      i - i  ------i    i    ii     v    iv    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGAC------CCCTACCTCACACCATATACAAAAATTA 484

  chrX_134268792_    784 TTTTGAAATAGGTAACAGACCAGAATACTA-AGCAAAAACTATAAGACTT 832
                         vi ii    i i v ?     vi   iiv -   v          i   i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_134268792_    833 CTAGAATAATACAT-GGGATAAGGTTTTGGTAACTTTGGGACAGGCACAG 881
                         i     v  v    -  ?i   i- i  v  i  i     vi     vv 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_134268792_    882 TTTTATTACATAGGAC--CAAAAG-ACATGAACCATAAAGAAAATACTGA 928
                         v   v   v   v   --      -   v v v  -        v iv  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACA-AAAGAAAAAATAGA 632

  chrX_134268792_    929 TAAA-----CGTCATCAAAGTTAAAATCTTCTCCTCTTTGAAATACAACA 973
                             ----- v        i      v   i viv   ii  iv   vi 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_134268792_    974 TTGCAAAAATTAAAAGGCAAGTCACAGACCGAAA-AAACTATTTGCAAAA 1022
                          iivi   i v     i   vi      vi ii -   v          v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_134268792_   1023 CGTATATCCAACAAAGGCTTTGTATCTTAAACATATAAAGACCTCTTATA 1072
                          i      ii i  i  vi       ivi  i         v      i 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_134268792_   1073 ATTCAATAC-------ACAAACAACCTAATTGTTAAAGGGAATAAAAGAT 1115
                          i      v-------     i    i    -?v   iv iii   i   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATT-WAAAAATGGGCAAAGGAT 831

  chrX_134268792_   1116 TTAAATGGACATTTTAC--AAGAAAATACATGTTGAATGGCAAA-----A 1158
                           i   i       iv --     i   i ii---      v  ----- 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACA---AATGGCCAATAAGCA 878

  chrX_134268792_   1159 TATGTAAAGATACTCAGCATCATTAGTCAT 1188
                         i   v      i    i     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (86 / 51)
Gap_init rate = 0.03 (18 / 561), avg. gap size = 2.72 (49 / 18)  


 458 29.44 6.60 2.03  chrX_134276087_134278586      736   932 (1568)    L1M4_orf2#LINE/L1        1   206 (702)  

  chrX_134276087_    736 TGAAGAAACATACTGTGTTCTTGGATTTGAAGAATCCACACAG--AAACT 783
                           i i i i  v ii     v      v     v iv i iv --  i--
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAG-- 48

  chrX_134276087_    784 ATGTCAATTTTCCCCAAAATTGGTCTTTAAATTGAACACAATTTTCAGCA 833
                            v    vi        -   i   vi i   v   i    iiii v  
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_134276087_    834 A----------GCCTTTTT-GTACCCATAGATCAGCTTATTCTAAATTGT 872
                          ----------        - i vvv  v  iv    v  i     v vi
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_134276087_    873 ATATGGACAGGCACAAGCCCTAGAGTAGCTAAAGAAATGTTCAAAAAAAT 922
                                v v   vii v  i   i    i   iv   v  v     i -
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA- 196

  chrX_134276087_    923 AGAGAAAAGT 932
                            iv     
  L1M4_orf2#LINE/    197 AGAACAAAGT 206

Transitions / transversions = 1.15 (31 / 27)
Gap_init rate = 0.03 (6 / 206), avg. gap size = 2.83 (17 / 6)  

1974 26.35 5.69 1.20  chrX_134276087_134278586     1352  2019 (481)    L1M4_orf2#LINE/L1      211   908 (0)  

  chrX_134276087_   1352 GGACTAATA-TTCCCA-TATTAACACGTACTATATCCAA---ACAGTAAT 1396
                              v i -      - v i  v  v     i ---  ---        
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACA---AAGCTACAGTAAT 257

  chrX_134276087_   1397 AAAGACAGTGTGGTACTGTAGAAAGAATAGACACATAGGCCAATACAACA 1446
                         v                 vviv   i       i    ii    iv  i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_134276087_   1447 GAATAGAGGACATAGAAAGAGACCCA---------AGTC---CGATTTTT 1484
                             v   iiivi     v i     ---------i   ---i      i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_134276087_   1485 GACAAAGATGAAAAAGAAGCTCAGTGGAGGAAGGATACCCTTTCCAACAA 1534
                              i i  vv  iivvii   i   i i   i   vi    i      
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_134276087_   1535 ATTGGGCTCTAACAATTAGACATCCATAAATGAAA-ATTGAACCTGGACC 1583
                           v v   vvi    i i  i ?   i viii   - v    vi      
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_134276087_   1584 TAAACCTCAAATATTATACCAAAGTTAACTCAAAGTGGGGCACAAATTTA 1633
                         ivv      v ivv     v   i          i   iv  ? i ii  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_134276087_   1634 AATGTGAAATATAAAACTACAAAACTTCAAAAAGAAAACGCAGGAGAAAA 1683
                              i i vv        i      iiv i        ii   ? v   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_134276087_   1684 TCTTTAGGACCTAGGGCTTGGTAAAGAGTTCTTACACATGACATCAAAAC 1733
                             iiv     v   i v  i  v iv      v i      i     v
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_134276087_   1734 CATGATCCATAAATAAAAAGGACCAATAAATGGTACTTCATCAAAATTTA 1783
                           ii v v i   - i   ii ivi      v v              v 
  L1M4_orf2#LINE/    608 CACAAGCAACAAA-AGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_134276087_   1784 AGTCTTTTGC---TCAGATAATGCCCTTAATAACAGAATGAAAAGACAAA 1830
                          iv      i---   i vi ii iv i  v  --- i           v
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAA---AGTGAAAAGACAAC 703

  chrX_134276087_   1831 CTACAGAATGGGAGGAAA-ATTTGCAGACCACATATCTGTTAAAGGACTC 1879
                          i            i   -       i i  i       v   i     i
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_134276087_   1880 GTATCTAGAAAATATAAAGAAGTCTCGAGATTTAAGCATAGAAA-----A 1924
                              i    v          v   iivi i i  vv   i   ----- 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_134276087_   1925 CAGTCCAACTAGAAAATGG-CAAA----------AAACATTTTACCAAAA 1963
                         i ii    i ?i       -    ---------- i      iv     i
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_134276087_   1964 AGGATAAACAGATGGAAAATAAGCACATAAAATGATTTTTCACCTTCATT 2013
                          i    v   i    vv           i   v   vi -  v v   ??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT-CAACATCAZZ 902

  chrX_134276087_   2014 ATTGGT 2019
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.57 (105 / 67)
Gap_init rate = 0.02 (15 / 698), avg. gap size = 3.07 (46 / 15)  


4338 16.99 3.15 1.01  chrX_134316517_134318942.rev     1047  1935 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134316517_   1047 TAGAAAGACATCCTGTATGCATGGATTGGGAGAC--AAT---GTTAAGAT 1091
                          i      i    ii i v          i    --   ---        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134316517_   1092 GGCAATATTGCCCAAAAAGATCAACAGA---------------ATCAAAA 1126
                                i v      vv    v     ---------------       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134316517_   1127 TGCCAATGGCCCTTTTTCTTGTAGAAATTGAAAAGCTGATCCTAAATTTT 1176
                          v   iiv   i     --- i         v              v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT---GCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_134316517_   1177 TAAAGGAATTGCAAGAGACTCTACAAATAGCCAAAACAATCTTGACAAAG 1226
                         vv v    v      i   i - -i                    v    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCC-A-GAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_134316517_   1227 AA---CAAATTTTGGGTACTCACACTTCCAGATTTCAGAACTTATTACAA 1273
                           ---    v  v i v            vi      i      i     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_134316517_   1274 AACCATAATAATCAAAACAGTGTGGCATTCATGTATGGATAGACATATAG 1323
                          i i i i       i         i i viii  v              
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_134316517_   1324 ACTAATAGAATAAAATAGAGATTCCAGAAGTAAATCCATACACCTATGGT 1373
                          ii   i     i   v    v       i    i       ii      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_134316517_   1374 CAGTTGCTTCTCAACAAGAGTGCCAAGATAATTCAATAGGCTAAAGAGTA 1423
                           i   v  i  i     i         iv       i  v-     i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATA 394

  chrX_134316517_   1424 GTTTTTTCAAAAAATGGTGCTGGGACAGCTGGATGTGCACATGTAAAACT 1473
                           i       v                i      i?v      i    vv
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_134316517_   1474 ATAAAGTTGGAACTCTGTCTTAAAAACTATGCAACAAACAAATCAAAATT 1523
                           i        v i  ii  i v vvv   i   v  vi  v       v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_134316517_   1524 CATCAAAGACCTAAGTACTAAAGCTAAAACCATAAAACTCTTAGAAGAAA 1573
                         v    ?        i iiv i         i                   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_134316517_   1574 ACATAAGGGTAAATCTTCATGATCTTGGATT-GGCAATGGTTTCTTAGAT 1622
                              i ?          i   i     i  -                  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_134316517_   1623 AGGATAA-AAAAGCACAGGCAACAAAAGAAAAAAATAGATAAATTGGACT 1671
                          v  i v-         i                -               
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACT 643

  chrX_134316517_   1672 TAATCAAAATTTTAAAACTTTTATGCACCAAAGGATGTTATCAA-AAACT 1720
                          v         v-         i   vi       iii      -   v 
  L1M4_orf2#LINE/    644 TCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_134316517_   1721 AAAAAGACAACCCACGGAATAGGAGAAAATATTTACAAAGTGTATATCTG 1770
                         i              i    i             i    vii        
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_134316517_   1771 AGAAGGATCTAGTATCCAGAATATATAAAATACTCTTACCACTCAACAAT 1820
                          v    iv  v                  iv        v      i   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_134316517_   1821 ACAAAAGACAAACAACC-AATTAGAAAATGGGTGAAGGACTTGAATAGAC 1869
                          -          i    -    ?i        ii     i          
  L1M4_orf2#LINE/    793 A-AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_134316517_   1870 ATTTCTCCAAAAAAGATACACAAATGGCAAACAA-TATATGGAAAGATGC 1918
                                    i      i         v  i  -i i   i        
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_134316517_   1919 GCAATGTCATTAGTTAT 1935
                         v   ii   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (93 / 54)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.31 (37 / 16)  


2986 27.80 1.11 0.55  chrX_134519007_134525398.rev     4999  5901 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134519007_   4999 TGGAAGAACATTCCGTGCTCATCGATAGGAAGAATCAATATCATGAAAAT 5048
                              ii i  i  i  i    v   v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134519007_   5049 GGCCATATTGCTCAAGGTCATTTGTAGATTGAATGCCATCCCCATCAAGC 5098
                            v   i v i   iv v  i ii     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134519007_   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAGCT-ACTTTAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v     - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_134519007_   5147 TATGGAAGGAAAAAAGAGCCCACATTTCCGAGACAATCCTAAGCAAAAAG 5196
                                iviv  ii  v  viv  vv  i i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_134519007_   5197 AACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAAGGC 5246
                                i      vv     i v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_134519007_   5247 TACAGTAACCAAAACAGCATGTTACTGGTACCAAAACAGAGATATGGACC 5296
                                 i   i    ii  v      i iv ii i   v    i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_134519007_   5297 AATGGAACAGAAC--AGAGCCCTCAGAAACAATACCACACATCTACAACC 5344
                                i    i--    i  --     i  vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_134519007_   5345 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAAGATTCC 5394
                          vi    i  i     ivv  v   i v  vvv          ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_134519007_   5395 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 5444
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_134519007_   5445 GAAACTGGATCCCTTCCTTACACCTTATATAAACATAAATTCAAGATGGG 5494
                            ii    i    v   i     v    i   v  v  i    i    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_134519007_   5495 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5544
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_134519007_   5545 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTC 5593
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_134519007_   5594 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGGATCTA 5643
                         vi            vvi          vv     v  i   iv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_134519007_   5644 ATTAAA-CTAAAGAGCTCTGCACAGCAA--GAAACTACCAGCAGAGTGAA 5690
                           i   -i    i vi i  ii vv   --  v    i  iv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_134519007_   5691 CAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACTCATCTGACA 5740
                         v  i     i                vv       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_134519007_   5741 AAGGGCTAATATCCATAATCTACAGAGAACTTAAACAAATTTACAAGAAA 5790
                          i  i  vi      v   v  i i      ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_134519007_   5791 AAATCAAACAACCCCAT-AAAAATTGGGCAAAGGATATGAACAGATGCTT 5839
                           iv    i     v  -?    v            v    i   iii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_134519007_   5840 CTCAAAAGAAGACATTTATGCAGCCAACA-GCACATGAAAAAACGCTCAT 5888
                            v        i  vi viii     i -           i i     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_134519007_   5889 CATCACTGGCCAT 5901
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (149 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


 680 24.05 9.91 12.69  chrX_134575162_134578158.rev     1601  2498 (499)    L1M4_orf2#LINE/L1       13   885 (23)  

  chrX_134575162_   1601 CCATG--CCTGG-CTGGAAGACATTATTAAAAGACATTATTAAAA-GACA 1646
                              -- v   -i        ----    ----i   i    i - i  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGAC----TTAA----TATTGTTAAGATGGCA 54

  chrX_134575162_   1647 TTATTGTC-AAGTC--TCT-CAGAATGATCCTAGCAATCATATTTAAAAT 1692
                         v  i vi -  i i--   -    v v v ---      vivv i     
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAAC---GCAATCCCTATCAAAAT 101

  chrX_134575162_   1693 TCCACCATGTTAACAAAAGTTTTTCTGAAAATTCACAAGCAGATCATTTT 1742
                         i   ---- i iv ----v     viii     v      v    ----i
  L1M4_orf2#LINE/    102 CCCA----GCTGCC----TTTTTTGCAGAAATTGACAAGCTGATC----C 139

  chrX_134575162_   1743 TTAAGT--ATATGCAAATTAAAGATTTGGAAAAGCCAAGTTTTTTTTAAG 1790
                          v  i --     v    vv   ----   ----  v  vv ------  
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAG----GGA----CCCAGAAT------AG 175

  chrX_134575162_   1791 CCAAGGAAAATACAAAGTTTTTTTTAAAGAAAAAGAACTAAGTTAGTAGA 1840
                             i------    ------ i  i  i  i      v     i vi  
  L1M4_orf2#LINE/    176 CCAAA------ACAA------TCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_134575162_   1841 TATGCACTACTATATAT-GAAATTTACTATAAAGGTAGAGTAATTAAAAC 1889
                         ivii    v ivv  v -i   i      i    v  v      i  i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_134575162_   1890 AGTGTGGTACTGGAGCAATGACAGGCAAATACACCAAGGGAAGAGGACAC 1939
                                      vii  v  i  i  v   v i   v    v  i ivv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_134575162_   1940 AGAGGCCAGAAACAA-TCTGGAAAT--A----CAA--AAT-----ACAGA 1975
                             v       i  -i iiv v  -- ----   --i  -----   --
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA-- 361

  chrX_134575162_   1976 AGAGTTGTAA-ATCATT----GTGGAAAAGACAGTGCTTTTAATAAATG- 2019
                           i  vvi  - i    ---- v     ii i   vi   i  i     -
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_134575162_   2020 --------CA-CTTGATAA----ATGCAGGGAAAATACAAACCTTGACTC 2056
                         --------  -  v    ?----     ---   iv ii  vi v   i 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCA---AAAGAATGAAGTTGGACCC 458

  chrX_134575162_   2057 TTACTTCTTCCCACTCCACAAAACTTTATTAAAGATGGAT---AGAC--- 2100
                         i   i  viv   - vi      v  v i v  i      ---    ---
  L1M4_orf2#LINE/    459 CTACCTCACACCA-TATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_134575162_   2101 AAT-------------CTAGTAAACACTTA-----AGATACTG------- 2125
                            -------------   vv    v    ----- i i iv -------
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_134575162_   2126 TCTTCACAACTATAGTATAGGCAAAGATGTTTTTA---ATGAGGATAAAC 2172
                              iii  iv i vv       v i -  i   ---    vivi   -
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATATGACACCAAA- 605

  chrX_134575162_   2173 AAGCACTAACCATAAA-GAATGAATTGTTTAATTAGACATAATTAAA-TG 2220
                         -     v i v i   -   vi   v v v    i   v v  i   - v
  L1M4_orf2#LINE/    606 -AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_134575162_   2221 GAAAAGTTCTGTTCCTCAAAG-ACACTATTAAGAG-GTGAAAAACCAAAT 2268
                         i    v  i   v i      -       i    i-       iv   vi
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_134575162_   2269 CATGTTTGTAGATTATACATTATGTAGTATATAGTATAGGTTATATATAA 2318
                           i------   -----------------------  i  ------ v  
  L1M4_orf2#LINE/    705 CAC------AGA-----------------------ATGGG------AGAA 719

  chrX_134575162_   2319 AATATATATTACTTACACACATATATACATATTTATCTGGCAACAAATGA 2368
                              -------  i  v i-------     --     --- i  iv  
  L1M4_orf2#LINE/    720 AATAT-------TTGCAAAT-------CATAT--ATCTG---ATAAGGGA 750

  chrX_134575162_   2369 ATGGAATCCAGAATATATCCAGAACT---ACAAATGAATTTCTAAAAAAC 2415
                         v v v             vv      ---    v v   vviv    i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_134575162_   2416 AAACATCCCA-CTAAAATTTGGGGGGAAAAGCTGAATATGCA---CTTCA 2461
                            i v    -i ?   vv    vii ii vi      vi  ---  i  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_134575162_   2462 TAAGAGTCATACTCTAATGGCTAATAATCACATCAAA 2498
                         v ii  vi    v--      i     v     v   
  L1M4_orf2#LINE/    851 AAGAAGATATACA--AATGGCCAATAAGCACATGAAA 885

Transitions / transversions = 1.10 (112 / 102)
Gap_init rate = 0.06 (55 / 873), avg. gap size = 3.69 (203 / 55)  


3074 28.04 0.33 0.88  chrX_134650038_134652531     1089  2001 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134650038_   1089 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1138
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134650038_   1139 GGCCATATTGCCCAGGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1188
                            v   i v    iiv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134650038_   1189 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1236
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_134650038_   1237 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1286
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_134650038_   1287 AACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTACAAGGC 1336
                                i     ivv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_134650038_   1337 TACAGTAACCAAAACAGCATGGTACTGTTACCAAAACAGAGATACAGACC 1386
                                 i   i    ii        vi iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_134650038_   1387 AATGGAACAGAACAGAACAGAGCCCTCAGAATTAATGCCGCATATCTACA 1436
                                i    iv  ---   i  --    v   vv  ii i  i  ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGA---GAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_134650038_   1437 ACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT 1486
                         iii vi    i  i     ivv  v   i v  vvv           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_134650038_   1487 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAA 1536
                         vvi  v  i  i              v      v  ?   i   v i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_134650038_   1537 GCTGAAATGGGATCCCTTCCTTATACTTTATACAAAAATTAATTCAAGAT 1586
                         iv    i v   i    v   i i  iv              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_134650038_   1587 GGATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGGAGAA 1636
                             i ?    i  v    v   v       i      vi i   i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_134650038_   1637 AACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 1685
                            v    ?i- v i -   iv   v v  vv i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_134650038_   1686 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 1735
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_134650038_   1736 CTAATTAAACTAAAGAGCTTCTGCACGGCAAAAGAAACTACCATCAGAGT 1785
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_134650038_   1786 GAACAGGCAACCTACAGAATGGCAGAAAATTTGTGCAATCTACTCATCTG 1835
                            v  i     i         v       v v     vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_134650038_   1836 AAAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 1885
                          v  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_134650038_   1886 AAAAAAACACACAACCCCATCAACAAGCGGGCGAAGGATATGAACAGATA 1935
                              i   v i     v  i? v  ii    i      v    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_134650038_   1936 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATACT 1985
                         i     v        i  vi viii     i ii          i  i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_134650038_   1986 CATCATCACTGGCCAT 2001
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (149 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3242 26.90 0.66 0.55  chrX_134743786_134750042.rev     4860  5766 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134743786_   4860 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4909
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134743786_   4910 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4959
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134743786_   4960 TACCAA-TGACTTTCTTCCAGAATTGGAGAAAACGACTTTAAAGTTCATA 5008
                          v   i-  v    i  v     v v  v  ivi  iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_134743786_   5009 TGGAACCAAAAAAGATCCCACATTGCCAAGGCAATCCTAAGCCAAAAGAA 5058
                              viiv  ii  i  viv  v     ii     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_134743786_   5059 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGATA 5108
                              i      vv       v  ii i      viv        i v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_134743786_   5109 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 5158
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_134743786_   5159 TGGAACAGAA--GAGAGCCCTCAGAAATAATACCACACATCTACAACCAT 5206
                              i    --     i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_134743786_   5207 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 5256
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_134743786_   5257 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5306
                         v  i  i        i     v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_134743786_   5307 AACTGGATCCCTTCCTTAAACTTTATACAAATATTAATTCAAGATGGATT 5356
                          ii    i    v   i v  iv        v     i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_134743786_   5357 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAAACC 5406
                          ?    i       v   v       i      vi i   i      - v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CA 547

  chrX_134743786_   5407 TAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGACTA 5454
                             ?i- v i -   i- i  v i  i- i     v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chrX_134743786_   5455 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5504
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_134743786_   5505 ATTAAA-CTAAGGGGTTCTGCACAGCAAAAGAAACTGCCAGCAGAGTGAA 5553
                           i   -i   iiiv  i  ii vv    i  v   ii  iv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_134743786_   5554 CAGGCAACCTACAGAATGGGAGAAAATTTTTACCATCTACCCATCTAACA 5603
                         v  i     i                 v   i v vii ivi    i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_134743786_   5604 AAGGGCTAATATCCAGAATCCACAAAGAACTCAAACTAATTTACAAGAAA 5653
                          i  i  vi          vi i         vv  v v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_134743786_   5654 AAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5703
                           iv    i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_134743786_   5704 CTCAAAGGAAGGCATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5753
                            v  i    ii  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_134743786_   5754 CATCACCGGCCAT 5766
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (149 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.22 (11 / 9)  


 586 24.71 10.39 12.36  chrX_134755006_134758030     1659  2524 (501)    L1M4_orf2#LINE/L1       37   885 (23)  

  chrX_134755006_   1659 AACATTATTAAGA-GACATTATTGTC-AAGTC--TCT-CAGAATGATCCT 1703
                           i   i      - i  v  i vi -  i i--   -    v v v --
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC-- 84

  chrX_134755006_   1704 AGCAATCATATTTAAAATTCCACCATGTTAACAAAAGTTTTTCTGAAAAT 1753
                         -      vivv i     i   ---- i iv ----v     viii    
  L1M4_orf2#LINE/     85 -GCAATCCCTATCAAAATCCCA----GCTGCC----TTTTTTGCAGAAAT 125

  chrX_134755006_   1754 TGACACGCAGATCAGTTTTTAAGT--ATATGCAAAT-TAAAG-ATTTGGA 1799
                              v  v    ----i v  i --     v    -i  i - iiii  
  L1M4_orf2#LINE/    126 TGACAAGCTGATC----CTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chrX_134755006_   1800 AAAGCCAAGTTTTTTTAAGCCAAGGGAAAGTCAGTTTTTTTAAGAAAAAG 1849
                          v      --------  --   ------------- i  v  i  i   
  L1M4_orf2#LINE/    172 ATAGCCAA--------AA--CAA-------------TCTTGAAAAAGAAG 198

  chrX_134755006_   1850 AACTAAGTTAGTAGATATGCACTACTATATAT-GAAATTTACTATAAAGG 1898
                            v     i vi  ivii    v ivv  v -i   i      i    v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_134755006_   1899 TAGAGTAATTAAAACAGTGTGGTATTGGAGCAATGACAGGCAAATACACC 1948
                           v      i  i           i   vii  v  i  i  v   v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_134755006_   1949 AAGGGAAGAGGACACAGAGAACAAAAA-GAATCTGGAAAT--A----CAA 1991
                           v    v  i ivv    vv  i   -i  i iiv v  -- ----   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_134755006_   1992 --AAT-----ACAGAAGAGCTGTAAATCATT----GCGGAAAGCACAGTG 2030
                         --i  -----   iii v  ii- i i    ---- v      v i   v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_134755006_   2031 CTTTTAATAAATG---------CA-CTTGATAA----ATGCAGGGAAAAT 2066
                         i   i  i     ---------  -  v    ?----     ---   iv
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA---AAAGA 444

  chrX_134755006_   2067 ACAAACCTTGACTCTTACCTCTTCCCACTCCACAAAACTTTATTAAAGAC 2116
                          ii  vi v   i i      viv   - vi      v  v i v  i i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCA-TATACAAAAATTAACTCAAAAT 493

  chrX_134755006_   2117 GGAT---AGAC---AATC---GAGT----------AAACACTTA-----A 2142
                             ---    ---   v---   i----------    v    ----- 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_134755006_   2143 GATATTG-------TCTTCACAACTATAGAATAGGCAAAGATGTTTTTA- 2184
                         i i  v -------     iii  iv i iv       v i -  i   -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAG 592

  chrX_134755006_   2185 --ATGAGGATAAACAAGCACTAACCATAAA-GAATGAACTGTTTAATTAG 2231
                         --    vivi   --     v i v i   -   vi  iv v v    i 
  L1M4_orf2#LINE/    593 ATATGACACCAAA--AGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_134755006_   2232 ACATAATTAAA-TGGAAAACTTCCGTTCCTCAAAG-ACACTATTAACAGA 2279
                           v v  i   - vi       ii  v i      -       i  v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_134755006_   2280 CTGAAAAACCAAAGCGTGTTTGTAGATTATACATTATGCAGTATATAGTA 2329
                         v      iv   vv ----------------------------- i  v 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCC-----------------------------ACAGAA 711

  chrX_134755006_   2330 TAGGTTATATATAAAAATATATATTAATTACACACATATATGCATATAGA 2379
                          i  -------- i   ---     -----ii  v  -----      --
  L1M4_orf2#LINE/    712 TGGG--------AGAAA---ATATT-----TGCAAAT-----CATATA-- 738

  chrX_134755006_   2380 TCTGGCAACAAATGAGTGGAATCCAGAATATATCCACAACT---ACAAAT 2426
                             --- i  iv  v v v             vv v    ---    v 
  L1M4_orf2#LINE/    739 TCTG---ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_134755006_   2427 GAATTTCTAAAAAACAAACATCCCAAT---AAAATTTGGGGGGAAAAG-- 2471
                         v   vviv    i     i v      ---     ----   v   i --
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAAT----GGGCAAAGGAT 831

  chrX_134755006_   2472 CTGAATATGCA---CTTCATAGGAGTCAAACTTAAATGGCTAATAATCAC 2518
                         i      vi  ---  i  v  i  vi v  --       i     v   
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATAC--AAATGGCCAATAAGCAC 879

  chrX_134755006_   2519 ATCAAA 2524
                           v   
  L1M4_orf2#LINE/    880 ATGAAA 885

Transitions / transversions = 1.20 (116 / 97)
Gap_init rate = 0.06 (52 / 849), avg. gap size = 3.79 (197 / 52)  


3220 25.53 2.58 0.90  chrX_134762323_134764695      988  1880 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_134762323_    988 TGGAAAGCTATTCCACCTTCACAAATTGGAAGATGCAATATTATT----- 1032
                                v   i   iv    iii         ivi      i  -----
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134762323_   1033 GTCAGTCCTTCCCAGCGTGATCTATAGATTCAAAGCAATCAACATGAAAA 1082
                          v  i v  i    ivv       i        v      vvi  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134762323_   1083 TCCCAGCAAACTATCTTGGAGATATTGACAAACAGATTATAAAGCTTCTA 1132
                                viv  v i   v   v        i v   iv    ii iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_134762323_   1133 AGGAAACAGGAAAGACCCTGAATAGCCAACACAATACTGAAAAATAACAA 1182
                         v     iivi ii     v          v     vi       v  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_134762323_   1183 CAAACTTGGAGTACTCATACTACCGAATTTCAAGACATAGTATAAAGGTA 1232
                             v      v     i   v  v        i  v  v  i    v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_134762323_   1233 -AATGATCAAGACACTGTGGGACTGGCA-----ATAGACACATCAACCAA 1276
                         - i i         v     v       -----       i  vi i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_134762323_   1277 TGGAACAAAGTAGACAGCCCAGAAATAGATCCACACATATGCAGTCAATT 1326
                              i i i v  v  i         i i   i    v iii       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_134762323_   1327 GGTTTTTGACAAAGGAACAAAAGCAAAGCAATGAAGAAAGCACAGTCTTC 1376
                          i    i     i  vi v  ii v vv     ii     v i      i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_134762323_   1377 TCAACAAATGGTGCTAGGACAAGCGGATGTCCATATGAAAAAAAAAAAGG 1426
                                        i      vi    i?   i   v    i  ---v 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA---TG 447

  chrX_134762323_   1427 AACCTAGACACAGATCTTATTT-ATACCTTTTGCAAAAATTAATTTCAAA 1475
                           vi i   -----i i  ii - i   v v i          i iv   
  L1M4_orf2#LINE/    448 AAGTTGGAC-----CCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_134762323_   1476 TGGATTATAGATCTAAATGTAAAATGAAAACCTACAAAACCTTTGAATGG 1525
                              i ?   i          i vvv   v   i     ii  ii v i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_134762323_   1526 AAACATAGGAGAATATCTAGATGAGCTTAGGTTTGAAAGTGAACTTTTAA 1575
                                  ? v v    vvi   v   i    v iv i  ivi i   i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_134762323_   1576 ATTCAACACCAAAAGCATGATCCATGAAAGAGAAACCTGATAAGTTGATC 1625
                           vii            ii v v ii     i   viv     i   iv 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_134762323_   1626 TTTACTACAATCAAAA---TTTAT-CTGTGATAGACACTGTTATGAGAAT 1671
                           i ii v   i    ---   i -  vii vi      i i v  i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_134762323_   1672 GAAAAGAGAAGCCACTGACTGGGAGAAAATATTTGCAAAACCCACACGTG 1721
                                v  v    v  v                    v vi i iv  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_134762323_   1722 -TAAAGGACTTGTATTCAAAATATACAAAGAAGTCTTACAACTCAACAAT 1770
                         -   i          i  i      i      v             i   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_134762323_   1771 TAAG---CAAACAAACCAGTTTTAAAATGGGCAAAAGACCTGAACAGATA 1817
                         v  i---    i  v   i  ?v            i  ii    i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_134762323_   1818 CCTCATCACAGGAGAAATGCAGATGGCAGATAAGCACATACAA---TGCT 1864
                         ii  vi  v  i   v  i  i     vi          iv  ---    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_134762323_   1865 TAACATCATTTGTTGT 1880
                         i       ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (133 / 91)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.82 (31 / 11)  


1780 21.12 5.58 0.73  chrX_134915751_134919318.rev      931  1342 (2226)    L1M4_orf2#LINE/L1        1   432 (476)  

  chrX_134915751_    931 TGGAGAGATATATCATGTTGATGGGTTGGAAGAATCAATACTGTTAAGAT 980
                             i      vi      v    i        v i    i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_134915751_    981 GCCAA-ACTCTT-AAATTGATCTCTGGATTTCATGCAGTCCCATTTATAA 1028
                          v   -    ii-          vii    iv i   i    vv i v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_134915751_   1029 TCCCAGTCAATTTCTTTTATAGAAATTGACAAGCTTATTCTAAA-TTTAT 1077
                               iiivi  -    ii               v  i     -  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_134915751_   1078 TTGAAAATGCAAAAGACCTAAA-----CAAAACAAACTTGAAAAAGAAAA 1122
                         v  i        ii    i i -----        v            i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_134915751_   1123 AC---TTTGGGTGATTCACACTGCCTGTATTCAACACTTACTCTAAAGCT 1169
                           ---v    iv  i       v  iivv     v       vi      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_134915751_   1170 AC--T----------GTGTGGTACTGACATAAAGACAGGCAAATAGATTG 1207
                           -- ----------           i     i  i  i  v      ii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_134915751_   1208 ATGGAACAGGATAGAGAGTCCAGTGATAACCCCATACAGGTACTGCCTGT 1257
                               i  i  v          vi    v        vv  iv i vi 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_134915751_   1258 TAATTTTCAACAAAGGTGCAAAGACAATTTAATGGGGGAAACGATAGTCT 1307
                          i      i    i     v     v   i       -   vi       
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCT 398

  chrX_134915751_   1308 GTTCATCAAATGGAGCTGGGAACAGCTAGATATTC 1342
                         v    v       v       -  i  i    ?i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGA-CAACTGGATAKCC 432

Transitions / transversions = 1.53 (52 / 34)
Gap_init rate = 0.02 (10 / 432), avg. gap size = 2.60 (26 / 10)  

 887 24.01 2.15 1.79  chrX_134915751_134919318.rev     2002  2280 (1288)    L1M4_orf2#LINE/L1      419   698 (210)  

  chrX_134915751_   2002 ACAGCTAGATATTCTTATGTAAGAAAAAGGAACTTTGACCCCCTATCTCA 2051
                            i  i    ?i vi   i  -  i  v   v  v      -  i    
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAA-AAGAATGAAGTTGGACCCC-TACCTCA 466

  chrX_134915751_   2052 CCACTTAATTAAAAATTACTTTTAGATGCATCATATGCCTAAAGGCAAAA 2101
                          vv v  vvi        vi iv i   v    ? vi      v i  i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_134915751_   2102 GCTGAAACTCTAAAGCTTCTAAAATAATACATAGGC--AATTATCTTCAT 2149
                            i     v    i  ii  i  v  v       ?--  --      i 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA--ATCTTCGT 564

  chrX_134915751_   2150 GACAT-GGGATAGGCAATGGTTTCTTAGATAAGAC-CCAGAAAGCACTAA 2197
                            v -   v                     v   -   -       v i
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA-AAAGCACAAG 613

  chrX_134915751_   2198 CCTTAAAAGAAAAAATTGATAAATGAAAC--AATTAAAATTTAACATTTC 2245
                          vvi            v       vii  --v  i      v  v i  i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_134915751_   2246 TCCTCATCAAATGACACCATTAAGAAAATGAATAG 2280
                          viv v     v     i  i      i    v  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

Transitions / transversions = 0.94 (31 / 33)
Gap_init rate = 0.03 (8 / 280), avg. gap size = 1.38 (11 / 8)  

 322 23.08 23.63 0.55  chrX_134915751_134919318.rev     2896  3077 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_134915751_   2896 AAGAAAATGAACAGTCAAGCCACAAACTGGGAAAAAAATATTCACAATAC 2945
                               i    v  v   v     i v     i    -    ii   vv 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATC 733

  chrX_134915751_   2946 ATATAACTGACAAAGAAC--------AAAATACA----GAA--------A 2975
                              v    i  i i  -------- i    i ----   -------- 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_134915751_   2976 CTTAATAG-----------------------AAAAATAGACAAAATACTT 3002
                           i    i-----------------------      i i    iv i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_134915751_   3003 GAATAGACACTTTAAAAACGAAGACCTATGAAGGGACAATAAACACATGA 3052
                                  i  ivvv  v     iv  ii  v  v      i       
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_134915751_   3053 AAAGCTCATCAGCATTATTAATTAT 3077
                             v vv   i   i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (24 / 18)
Gap_init rate = 0.02 (5 / 224), avg. gap size = 8.80 (44 / 5)  


1842 26.16 5.78 1.28  chrX_135181966_135187490.rev     1699  2321 (3204)    L1M4_orf2#LINE/L1       15   665 (243)  

  chrX_135181966_   1699 ATGTTCCTAGATTAGAAGACTCAATATTACTAAGAAATAAATTCTCCCAA 1748
                               v i    i       i      ii     vivv   v     v 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_135181966_   1749 AATTGACCAATAACTTCAACTCAATCCAAATCGTAATCTCAGC-AAGTTT 1797
                               i v i iv      v      vv   iv    i    -ivv   
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_135181966_   1798 TTTATACAAATTGATCAGCAGATTTGAAAATTTATATGGACATGCAAAAG 1847
                            ii v       iv   v   iiv      i       v      ii 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_135181966_   1848 GCTTAGAATAACCAAAGCAATCTTGAAAAGCAA---CAATGTTGAAGTAT 1894
                         i ii      i     i            iv  ---   v    i  v i
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_135181966_   1895 TCATATTACCTGACTTCAACACTT------------CAGGAACCAAGACG 1932
                            i i v  ii i     v    ------------   v  i      i
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_135181966_   1933 ACCTGGTAATAACATACGAGTTTAAAAAAAAAAAAAAACAGTATAG---- 1978
                         iiv     v ii    --  vv  i v v v i vv  ii v    ----
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATA--AGGATAGACATATAGATCAATGGAATAGAATT 312

  chrX_135181966_   1979 GAAAGTCCAGAAATAG--CCTTACATTTATA--CAAAATTTGACTTTTTG 2024
                           i            i--  v         i--   ---    -    i 
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAA---TTGA-TTTTCG 358

  chrX_135181966_   2025 TCAAAGGTACCAAAGCAAGCCAATGGGGAAGGAAAAGTCTTTTCAACAAA 2074
                         v   i   i    ii v vi          i   v               
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_135181966_   2075 TGATGCTGGAAATACTGGATATCCACGTAAAACAAAATGATCCTCAACTC 2124
                           i      i vv        ?    i iv  v i     vvi vi  i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_135181966_   2125 CTACCTCATGC-A-ATACATAAATCAATT---AATTGA-----GTTCTAA 2164
                                 ii - -     v    i  i ---   v  ----- vi    
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_135181966_   2165 ACATAAAAGCTAAAATCATAAAGCTTTTAAAGAAAAGCATAAGAGAATGT 2214
                          ii   i        ii     i  i   i ii   i    i ? v vi 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_135181966_   2215 CTTCATGGCTTCCTGATAGACAAAGGTATCATAGACAAGTCAT-ATATGG 2263
                             i  i i ivv v   i   v   v  v    i v v  i- v v v
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_135181966_   2264 TTATTCA-TAAAAGAAAACAGAACTATAAATTAGACTTCACGAAAATTTA 2312
                         vi vv  -i         v v i--       i       iv      v 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAG--ATAAATTGGACTTCATCAAAATTAA 656

  chrX_135181966_   2313 AAACTTTTG 2321
                                  
  L1M4_orf2#LINE/    657 AAACTTTTG 665

Transitions / transversions = 1.30 (91 / 70)
Gap_init rate = 0.02 (16 / 651), avg. gap size = 2.75 (44 / 16)  

 414 26.24 6.44 1.49  chrX_135181966_135187490.rev     2599  2800 (2725)    L1M4_orf2#LINE/L1      587   798 (110)  

  chrX_135181966_   2599 TCTCAAACAACAACAACAACAACAAAAAAAAAAAAAAAAAAAAAAAAGGA 2648
                            i i i -ii   v   v i  v  iv  v    i      v i vi 
  L1M4_orf2#LINE/    587 TCTTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_135181966_   2649 A--AGAAAACAAGAAAGTGAAAAACT-----GCTCATTGAAAGACATTAT 2691
                          --i  vvv  vv   i v       -----   -- ii  i    i   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCT--TCAAAGGACACTAT 683

  chrX_135181966_   2692 TGAGAAAATAGATAGGCAAGTCATA---CGG---AAAACATTTTCAAAAC 2735
                         ii     i ii v  i   vi  i ---i  ---    i    v    v 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_135181966_   2736 ATACATCTGATAAATTGTTTGTATCCAGAATGTGTAAAGAACACTTACAA 2785
                            i         ivvii             i i        v       
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_135181966_   2786 CTCAATAATAAAAGG 2800
                                      i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAG 798

Transitions / transversions = 1.65 (33 / 20)
Gap_init rate = 0.03 (6 / 212), avg. gap size = 2.67 (16 / 6)  

2970 24.75 2.31 2.42  chrX_135181966_135187490.rev     3276  4184 (1341)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_135181966_   3276 TGGAAACACATCCCTTGCTCATG-ATGGAAAGAATCAATACTGTGAAAAT 3324
                               v i     v  i     -  v i    v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_135181966_   3325 GGCCATACTGCCAAAAGCAATCTATAGAT--AATGCAATTCCCACCAAAA 3372
                            v     v  v   vii     i    --  i     i  i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_135181966_   3373 TATCA----TCATTCTTACAGAACTAGAAAAA--AATTCTAAAATTCATA 3416
                          vi  ----i v  i  i     v v  v  i--i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_135181966_   3417 TGGAA-T-CAAAAAAGTCCACATAGCCAAAGCAATTCAAAGCAAAAAGAA 3464
                              - -   iii vi viv         i    iivi iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_135181966_   3465 CAAATCTGGAGGCATCATATTACCCAACTTCAAATTATACTGCAAGGCTA 3514
                             vi      vv   i i v     i      viv    i   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_135181966_   3515 TAGTTACCAAAACAGCATGGTATTGGTATAAAAATAGGTATGTAGACCAA 3564
                         i   v i   i    ii     i   i    ii    ii  i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_135181966_   3565 TAGAACAGAATAGAAAACCCAGAAATAAAGCCAAATACTTACAGCCAACT 3614
                          i   i     v  i ii           v   v i i   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_135181966_   3615 -ATCTTTGACAAAGCAAGTG--AAAAC-ATAAAGTGGAGAAGGGACACCC 3660
                         -  i  i     i ---   --  i  -  vv i   i   i i i vi 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG---GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_135181966_   3661 TGTTCCACAAATGGTGCTGGGATAATTGGTAAGCCACACGGAGAAAAATG 3710
                          v   v                i  i   vv ?     i v i  i    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_135181966_   3711 AAACTGGATCCCCATCCCTCGCAT--TATACAAAAATTAACGCAAGATGG 3758
                           ii    i   i --    i  i--               v   i    
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_135181966_   3759 ATCAAAGTCTTAAATGTAAGAGTCTTAGATATAAGACCTGAAACCATAAA 3808
                             ?  v i            ---------------  i    i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAG---------------CTAAAACTATAAA 530

  chrX_135181966_   3809 AATTCTAGAAGATAACATTGGAAAAAACTCTTCTGAACATTGGCCTAGGC 3858
                          v ii       v     v  ?iv   -     vvi  v    vi     
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGC 579

  chrX_135181966_   3859 AAAGAATTCATGACTAAGACCCCAAAAGCAAATGCA-CAAACAGAAACAA 3907
                           v iv   v iiv  v   v         v v   -    -     v  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA-AGAAAAAA 628

  chrX_135181966_   3908 ---ATAAATGGGATCAAATTAAACTAAAAAGCTTCTGCACAACAAAAGAA 3954
                         ---      v   iivv  i   v v    i   i  ii vv    i  v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_135181966_   3955 ATAATCAGCAGAGTCAACAGGCAATCCAAAGAGTGGGAGAAAACATTTGC 4004
                          iv    iv i   v  v  i   i   v   i          i      
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_135181966_   4005 AAACTATGCATCCAACAAAGGACTAGCATCCAGAATCTACAAGGAATTCA 4054
                            ii  ii   ii i  i     v i         v  i  i   i  v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_135181966_   4055 AACAAATCAGCAAGAAAAAATCAAAGGATCCTATCAAAAAGTGGGCAAAG 4104
                         v    v   ii  v     iv    vi i  v  i?    i         
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_135181966_   4105 GACATGCGTAGACAATTCTCAAAAGAAGATATACAAACACCCAACAAACA 4154
                           iv  vi      v     v                iiv    i  i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_135181966_   4155 TATGAAAAAATGCTCAATATCACTAACCAT 4184
                         i       i        i    ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (138 / 83)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.53 (43 / 17)  

 422 17.83 7.75 0.00  chrX_135181966_135187490.rev     4906  5034 (491)    L1M4_orf2#LINE/L1      770   908 (0)  

  chrX_135181966_   4906 AAAAACTATTGCAA-----TAA-AGAAAGA-AAACTACCCCATTTAAAAA 4948
                           i    v  i   -----   - i     -   iv    v   ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_135181966_   4949 TGGGCAAAAGATTTTAACAGATATTTCACCAAAGA---CATACAAATAAC 4995
                                 i     v  i   i     v       ---i        ii 
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_135181966_   4996 AAATATGAACATGAAAAATTACTCCACATCATTTACCAC 5034
                         v    v v         iv i   v      ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (12 / 10)
Gap_init rate = 0.03 (4 / 139), avg. gap size = 2.50 (10 / 4)  


3328 26.10 0.55 0.55  chrX_135248200_135254480.rev     4883  5790 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_135248200_   4883 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATCGTGAAAAT 4932
                              ii i  i     i      i v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_135248200_   4933 GGCCATACTTCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4982
                            v     i     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_135248200_   4983 TACCAA-TGACTTTCTT-CAGAGAATTGGAAAAAACT-ACTTTAAAGTTC 5029
                          v   i-  v    i  -    -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_135248200_   5030 ATATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAA 5079
                                 viiv  ii  v  v v  vi    iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_135248200_   5080 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5129
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_135248200_   5130 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5179
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_135248200_   5180 CAATGGAACACAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAAC 5227
                                 i v  i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_135248200_   5228 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5277
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_135248200_   5278 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAAAAAGC 5327
                         i  v  i  i              v      v  ?   i   i    iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_135248200_   5328 TGAAACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAGATGG 5377
                             ii    i    v   i     v  i        i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_135248200_   5378 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5427
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_135248200_   5428 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5477
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_135248200_   5478 CAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5527
                         ii            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_135248200_   5528 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5577
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_135248200_   5578 CAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5627
                         v  i     i   i             v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_135248200_   5628 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5677
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_135248200_   5678 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5727
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_135248200_   5728 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5777
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_135248200_   5778 CATCACTGGCCAT 5790
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1278 23.70 2.31 1.16  chrX_135266607_135269650.rev      664  1009 (2035)    L1M4_orf2#LINE/L1        1   350 (558)  

  chrX_135266607_    664 TAGGGAGATATGCCTTGTTCATGGATTGGGAGAATCAATATAGTAAAGAT 713
                          i ii      v  v              i   v i     v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_135266607_    714 GTCAATTCTCCCCAAGTTGATCTACAGGTTTAATGCATTCTCTATCAAAA 763
                          v    v        i           i  i  i   v  i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_135266607_    764 TCTCAGAAAGATGTTTTGTAGATATAGACAAGATTATTTCAAAATATATA 813
                           i   vvivv v     i   v  v      v v  iii     vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_135266607_    814 CGGAAAGGCAAAAGAACTAGAATAGTTAAATCAGT--TGCTAAA-AAGAA 860
                         i     v    ii  v i       ii   v  i --  vv   -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_135266607_    861 TAAATTACAAGGAATCACTCTACCTAATGTTAAGACTTACTATATAGCTA 910
                         i   v vvi    v    v  v  i   v i  i        i v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_135266607_    911 TAGGAACCAAGACAATGTGGTATTGGCAAAGAAATAGATATGTAAATCAA 960
                         i  v  i       i       i     v iii     i  i  i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_135266607_    961 GGTAACAGAAT-GAGAATCCTAGTATAGATGAAC--AGACAT--GTGTTC 1005
                         v v  i     -    i   -  --- i  i   -- v    --i  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC-AG---AAATAAACCCATACATTTATGGTC 346

  chrX_135266607_   1006 AATT 1009
                             
  L1M4_orf2#LINE/    347 AATT 350

Transitions / transversions = 1.22 (45 / 37)
Gap_init rate = 0.02 (7 / 350), avg. gap size = 1.71 (12 / 7)  

1150 21.26 13.79 2.30  chrX_135266607_135269650.rev     1577  1924 (1120)    L1M4_orf2#LINE/L1      345   732 (176)  

  chrX_135266607_   1577 TCACTTCATTTTTGACAAAGGTACAAAAGCAATTCAATGGAGGAAGGATA 1626
                            v  v     i     i   i v  ii v         i i   i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_135266607_   1627 ATGCTTTCAACAAATGGTGTTAGAACAAC--------------------- 1655
                         i vi               i i i     ---------------------
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_135266607_   1656 ------------------CTCACACCATATTTAAAACTTAATTCAAAATG 1687
                         ------------------            vi    v    i        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_135266607_   1688 GATAATAGGTTTAAATG-AAAACATAAAATTATTTTTAAAATT--TAGAA 1734
                            v ?  iii      -  i vv     i   ----    i --     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTAT----AAAACTCTTAGAA 540

  chrX_135266607_   1735 GAAAACATAGAAGAAAATTTTTGTGATCCAGAGCTAAGAAAGGAGTTCTT 1784
                                   i? v    i  i    i iv i i  i v  v iv     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_135266607_   1785 AGACATGACCCTAGAAGCATAATTCATGTAAGAAATAAATGAATAAATTG 1834
                            i     v i i     i  viv iiv      -    ii        
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAA-AAATAGATAAATTG 639

  chrX_135266607_   1835 GACTTCATTAAAATTAAAA-TGTTTCT-CTGGAAAAGTC-CTGTTAAGAG 1881
                                 i          -iv   v -  vv   i v -  i i    i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_135266607_   1882 AATGAAAAGAC---CCACTAGAGACTGGGAGAAAATATTTACAAAT 1924
                          i         ---    ---   v               i     
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCAC---AGAATGGGAGAAAATATTTGCAAAT 732

Transitions / transversions = 1.88 (47 / 25)
Gap_init rate = 0.03 (10 / 388), avg. gap size = 5.60 (56 / 10)  

 538 25.70 1.12 0.56  chrX_135266607_135269650.rev     2375  2553 (491)    L1M4_orf2#LINE/L1      729   908 (0)  

  chrX_135266607_   2375 AAACCATATATTCAACAAAGTCCTTATATCTATAATATA--AAAAACTCT 2422
                            i       iii i  i vv   i    i v      --  i      
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_135266607_   2423 CAAAACTCAACAGTAAAAAGAACAATTAATCCAGTTGTAAAATGGGCAAA 2472
                         i v       i i        -   v   i   i  ?v            
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_135266607_   2473 AGACATCAAAATATATTTTACCATAGAGGAGACATGGATATCACATAAGC 2522
                         i  iv v  v v i    iv   v   i  v i iii  iv vv      
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_135266607_   2523 ACAAGAATAAATATTCAACATCACTAGCCTT 2553
                            v   v i  ii         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (27 / 18)
Gap_init rate = 0.01 (2 / 180), avg. gap size = 1.50 (3 / 2)  


 512 29.00 1.73 3.46  chrX_135643557_135645958.rev      488   718 (1684)    L1M4_orf2#LINE/L1      117   343 (565)  

  chrX_135643557_    488 TGCAGAAAGCATATACAAGATTATTC-AAAATTTTTCATGAAAAGGAACA 536
                                 --- vv     v v  i -      iv -   i   v v vi
  L1M4_orf2#LINE/    117 TGCAGAAA---TTGACAAGCTGATCCTAAAATTCAT-ATGGAAATGCAAG 162

  chrX_135643557_    537 GTCTCTAAAATACTTAAAACAAACTTGAGAAAGAA---TAAAGTAGGAGA 583
                          vvi i i    vii       v     i      ---i     v    i
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_135643557_    584 AATTACTCTACTTGATGTTAAAGGCTAATACATAAATCCTATAATCTGGA 633
                          v i  v  v iii  v i   ivi  v    v iv v vi     vi  
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_135643557_    634 CAATGTGGTATTGGTTGAGGGGTAGCCAGCCATAAAGATTAACAGGACAG 683
                           i       i   ivv i  i   -- --    v    i  ii i i  
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAG--A--CATATAGATCAATGGAATAG 308

  chrX_135643557_    684 AATAGACAACCCAGAAATAGACCCACACAAATATG 718
                            v  v ii         i     i   vv    
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

Transitions / transversions = 1.16 (36 / 31)
Gap_init rate = 0.03 (6 / 227), avg. gap size = 2.00 (12 / 6)  

1503 27.19 1.33 2.66  chrX_135643557_135645958.rev      990  1515 (887)    L1M4_orf2#LINE/L1      312   830 (78)  

  chrX_135643557_    990 TGGGATTACAGACATGAGCCACCACGCCTAGCTGCCTAAAAGATTTTTGA 1039
                           i  v v    v  i i  vvi  iii  --  vii  vv      i  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTA--TGGTCAATTGATTTTCGA 359

  chrX_135643557_   1040 CAATGGCATAAAAGTAACTCAAGGGAGGAAGAATAGCATTTTTAACAAAC 1089
                            v  iiiv  iiiv i    v  i i        iv    i      i
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_135643557_   1090 AGTGCTAGAACAATTGGACATCTAGGTTAAAAATAAAAAAAGCTAATCTT 1139
                         i     i i    i    i ? i vi vv    -i  vi   i iiv i-
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAAGTTGGACC- 457

  chrX_135643557_   1140 AACCTAAACCTCATGACTTATACAAAA-TTAATTCCAAATGGATCTCATA 1188
                         --    --     iiv v         -    i  v         v? v 
  L1M4_orf2#LINE/    458 --CCTA--CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_135643557_   1189 TTTAAATATTAAGTG-TAAAATTATAAAACTTTTGGGAAAAAAAGTATGA 1237
                         ii     i -   v -     i         i  i i i    vi  v ?
  L1M4_orf2#LINE/    504 CCTAAATGT-AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_135643557_   1238 CAAAATCTGTTG-GACCTAAAGACAGGTGAAGAGTTTTTGGATTTGACAC 1286
                         vv      - i -     vii vi   ii v iv  i  i   v      
  L1M4_orf2#LINE/    553 GTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_135643557_   1287 CAAA-GTGCAATCCACAAAGGAAACAAAATGGATAAATTGAACTTCATCA 1335
                             - ii   v v     i    --    i         i         
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAA--AAATAGATAAATTGGACTTCATCA 649

  chrX_135643557_   1336 AAATAAAAAAATTTTGATCTGCAAAAGACCTTGTTAAGAGAATAAAAAGA 1385
                             v     v     vv  v    i   vi i i    i i i      
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_135643557_   1386 CTAGGCCA-AGACTG--AGAAAATATTTGCAAACCACATATCTGACAAAA 1432
                          - iv   -   v  --                i  i        i  ii
  L1M4_orf2#LINE/    700 C-AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_135643557_   1433 GCCCTGGATCTATAATATATAAAGAGCTCTCAAAATTCAACAGTTAAAAA 1482
                          v i  v   i v            i    i v  i    i i -     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAAAA 797

  chrX_135643557_   1483 AACAAGCATTTCAATTAGAAATTGAGCTAAAGA 1515
                         i    ii vii     ?i   v  i  v  i  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.78 (89 / 50)
Gap_init rate = 0.03 (15 / 519), avg. gap size = 1.40 (21 / 15)  

 263 22.41 7.76 0.00  chrX_135643557_135645958.rev     1796  1911 (491)    L1M4_orf2#LINE/L1      784   908 (0)  

  chrX_135643557_   1796 CTCAAAAA-AAAAAAAAAAAGAA---AA---GAAATTGAGCTAAAGATAT 1838
                              v  -     i v   v  ---  ---i   v  i  v  i   v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_135643557_   1839 GAACAGACATT-CACTGAAAAGGACA-ACGGATGGTAAGTAAGCACATAA 1886
                            i       - v ii  i i  i -  ii    iv i         i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_135643557_   1887 TAAGATGGCCAACATCATTAGCCAT 1911
                         v      vi        ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (16 / 10)
Gap_init rate = 0.04 (5 / 125), avg. gap size = 1.80 (9 / 5)  


1038 17.70 10.18 0.44  chrX_135706713_135709262.rev      500   725 (1825)    L1M4_orf2#LINE/L1      259   506 (402)  

  chrX_135706713_    500 AAGACAATGCGGTACTGGCATAAGAATAGACATATAGATCA--------G 541
                               i  i              i                -------- 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_135706713_    542 AATTAAGAGTCCAGAAATAAATCCTTGTATTTAAAGTCAGTTGTTTTTTG 591
                             i                i  v ii     vi    i   v    i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_135706713_    592 ACAAGAGTGCTAAGGCAATTCACTGGGAAAAGGATAGTTT-----ACAAA 636
                              i    i   i v     v    i    i     i -----     
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_135706713_    637 TGGTGCTGCAGA-AA---GAT-GCAACATGCAAAAAGATGA-GCTGGACC 680
                                 -i  -  ---   -? v          ii    - i      
  L1M4_orf2#LINE/    409 TGGTGCTG-GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_135706713_    681 CT--CTTCACAT--TATGAAGAAGTTTACTCAAAATATATCATGGACTT 725
                          i-- i     i--   iv i  i  v         iv    ?i   i 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

Transitions / transversions = 3.22 (29 / 9)
Gap_init rate = 0.04 (9 / 248), avg. gap size = 2.67 (24 / 9)  

 711 25.74 4.64 1.69  chrX_135706713_135709262.rev      992  1228 (1322)    L1M4_orf2#LINE/L1      449   692 (216)  

  chrX_135706713_    992 AGTGAGACTC-TGTCTCAAA----AAACAAAACAAACTAACAAAAAAC-- 1034
                            vi   i - ii    v ---- v      --- i    vv    i--
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAA---ATTAACTCAAAATGG 495

  chrX_135706713_   1035 ----TAGACTTAATTTTTAGAGTTAAAACAATGAAACTTTTAAAAGAAAA 1080
                         ----?    i   v v v    i      v  i     i   i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_135706713_   1081 CATAGGGGAAAATCTTTGAGACCTTGGCTTAGGCAAACATCTCATGGATA 1130
                               ? v       i v        v        vvi i  v i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_135706713_   1131 CAACTCTATAGGCATGTTCCATAAAAGAAAAAATATGGTAAATTTGACCT 1180
                         ii  v i v i   iivv v i             - i      v   i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTT 644

  chrX_135706713_   1181 TACAAAAATTCAAAATGTTTGCACTCCAAAAGACATCATTAAGAAAAT 1228
                         i iv      v    iv    ii  i    i    ii  i      i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

Transitions / transversions = 1.46 (35 / 24)
Gap_init rate = 0.02 (5 / 244), avg. gap size = 3.00 (15 / 5)  

 817 17.15 5.02 4.60  chrX_135706713_135709262.rev     1821  2059 (491)    L1M4_orf2#LINE/L1      669   908 (0)  

  chrX_135706713_   1821 TTCAAAAAATAATAATAATAATAAGGAAAATAAGAAAAAAAAAACCTCAC 1870
                               ii i v  vi  -------    i i ---   i v    -   
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAA-------GAAAGTGA---AAAGACAACC-CAC 707

  chrX_135706713_   1871 AGACTTGGAGGAAATATTTGCAAAAGACATATCAGATAAAGGACTTGTAA 1920
                            v v    i             vv i     v     i         v
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chrX_135706713_   1921 CCTGAATGTATGAAGAACTCTTACAACTCAATAATAAAA-------CAAT 1963
                           v    i   i                           -------i  i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chrX_135706713_   1964 TCAAT-GAAAACTGGCCAAAATATATGAACAGACATTTCATCAAAGAGGA 2012
                         i    -?    v   v    iv  v    i         vi      i  
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chrX_135706713_   2013 CATATAAATG---AA-AAGCACATGAACAGGTGGTCGACATCATTTATCA 2058
                         i   i     ---  -           v  i  v  i      ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chrX_135706713_   2059 G 2059
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.35 (23 / 17)
Gap_init rate = 0.03 (7 / 240), avg. gap size = 3.29 (23 / 7)  


1167 21.15 0.00 0.38  chrX_135775420_135778316.rev     1207  1466 (1431)    L1M4_orf2#LINE/L1        1   259 (649)  

  chrX_135775420_   1207 TGGAGAGAAATACTGTACTCATTGATTGGAAGACTTCATATTATGAAGCT 1256
                             i   v  v ii ii    v             v     i v   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_135775420_   1257 ATCAATAGTCCACAAATTGATCTATAGATTCAATGCAATCATAATCAAAA 1306
                         iv     v   v            i        i      viv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_135775420_   1307 TCCCAGCAGAACTTTTTGTACATATTAATAAGCTGATGCTAAAATTTATA 1356
                                v vvi      i v v   i i        v        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_135775420_   1357 TGGAAAGGAAAATAAACAAGAATAGCCAAAACAATCTTAAAGAAAAATCA 1406
                               v v  ivi v v                    i  i  i  -v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GA 199

  chrX_135775420_   1407 ACAAAGTTAGAGGACTCACACCACCTAATTTCAAATTTTGTTACAAAAAT 1456
                                 i            iv  i         vi  ii      iv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_135775420_   1457 TTAGTAATCA 1466
                         vi        
  L1M4_orf2#LINE/    250 ACAGTAATCA 259

Transitions / transversions = 1.04 (28 / 27)
Gap_init rate = 0.00 (1 / 259), avg. gap size = 1.00 (1 / 1)  

2274 22.17 4.03 0.93  chrX_135775420_135778316.rev     1762  2406 (491)    L1M4_orf2#LINE/L1      244   908 (0)  

  chrX_135775420_   1762 AAAATT-CAGCAATCAAGACAGTCTGATATTTG--TGAGCTGATAGACAC 1808
                            ii -   i            v  i  i v -- i  --        i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG--GATAGACAT 291

  chrX_135775420_   1809 ATAGATCAATGTAACAGAAC--AGAGTGCAGAAACTGGCCAA-ACATACA 1855
                                    v  i    i--     v      ivii  v -    vi 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_135775420_   1856 TGGGCAATTGATTTT-GACAATGTTGCCAAGGTAATTCAATGGAAAAAGA 1904
                            v           -     v v       iiv         ii     
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_135775420_   1905 ACAGTCTTTTCTACAATTAGTACTGAAACCACAGGGCACCCATAAACAAA 1954
                          i         v    v i  i   ii  v  v  ii ?   i vi    
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_135775420_   1955 ATTAAAAAAAACTTTGAGCCACAACTCACAT-ATATCCAATAATTAAGTC 2003
                          ---i  vi  v  v  v  vi v      i-    v   v      v  
  L1M4_orf2#LINE/    442 A---GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_135775420_   2004 AAAATGGATCAGAGGCCTAGACATAAAACATAAAACTATGCATCTTTTAC 2053
                                    ?  i    i ii   i vv         iv v  i   v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_135775420_   2054 AAGAAAACAGAAGA--AAATTTT-GTGATCTTGGATTAGGCAGCG--TTC 2098
                                  v i ?--    i  -    i     i       ii --   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_135775420_   2099 TTAAATACAATACAGAAAGCATACCCA-TAAATGAAAAAAATTGATAAAC 2147
                            i   ii i  vi      i vv  -i   v       - v      i
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAAT 637

  chrX_135775420_   2148 AGGACT-CATCCAAATCAAATCCTTTCATTCTGCAAAAGACCCTGTTAAG 2196
                         v     -    v    i   vv    ii v  v    i   v  i i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_135775420_   2197 ATATTAAGAAGATAAGC-AC----TG--AGAAAATATTT-TAAATCACAT 2238
                          v v i i    i  v -  ----  --           -i      i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_135775420_   2239 ATCTCACAAAGGACTTTTGTCTAGAATATATAAAGAACTCTCAAAACTCA 2288
                             v i  i      v i  i                   i v      
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_135775420_   2289 ATAAGAAAA---CAAACTACCCAATTAAAAAACAAGCAAAAGATTTGAAC 2335
                             v    ---    iv        ?     iii     i        i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_135775420_   2336 AGACACTTCACCAAAGAAGAGACATGGATAGCAAATAAAAACATGCAAAG 2385
                              i   v          v i iii  i  v     iv     v    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_135775420_   2386 ATGTTAAGCATCATTAGTCAT 2406
                            i v i     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (82 / 57)
Gap_init rate = 0.03 (19 / 665), avg. gap size = 1.68 (32 / 19)  


3133 27.10 0.44 1.20  chrX_135785051_135788402.rev     1947  2861 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_135785051_   1947 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 1996
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_135785051_   1997 GGCCATACCGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2046
                            v    iv     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_135785051_   2047 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2094
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_135785051_   2095 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAGTCCTAAGCCAAAAG 2144
                                viiv  ii  v  viv  v     iv  i  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_135785051_   2145 GACAAAGTTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGA 2194
                         i             vv    i  v  ii i      viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_135785051_   2195 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 2244
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_135785051_   2245 AATGGAACAGAACAGAGACCTCAGAAATAAAACCACACATCTACAACTAT 2294
                                i    iv    vii          v   i    i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_135785051_   2295 CTGATCTTTGACAAACCTGACAAAAATAAGAAATGGGGAAAAGATTCCCT 2344
                         i    i  i     ivv  v   i vi vvv          ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_135785051_   2345 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 2394
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_135785051_   2395 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 2444
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_135785051_   2445 AAACACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 2494
                          ? v  i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_135785051_   2495 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 2543
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_135785051_   2544 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 2593
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_135785051_   2594 TCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGTGTGACAG 2643
                         iv  v v  i i   i  ii vv    i  v    i  vv iv    v i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_135785051_   2644 G-CAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCGTCTGACAGA 2692
                          -     i                 v       vii  vii     i ii
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_135785051_   2693 GGGCTAATAGCCAGAATCTACAAAGAATTCAAACAAATTTCAAAAAAAAA 2742
                           i  vi  v       v  i      i  vv    --i    v  v   
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CTCAATAATAAA 795

  chrX_135785051_   2743 AAAAAAAAAAAAAACAACCCCATCAACAAGTGGGCGAAGGATATGAACAG 2792
                           i v   ------i     v  i? v  i     i      v    i  
  L1M4_orf2#LINE/    796 AAGACAAA------TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_135785051_   2793 ACACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAAT 2842
                            i     v        i  vi viii     i ii          i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_135785051_   2843 GCTCATCACCACTGGCCAT 2861
                              v  i  ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


 750 15.25 0.00 0.00  chrX_135792970_135795053.rev      557   674 (1410)    L1M4_orf2#LINE/L1        1   118 (790)  

  chrX_135792970_    557 TGGAAAGATATCCTGTGTGCACGAACTAGAAGACTTAATATTGCTAAGAT 606
                                      ii   v  i i i i               i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_135792970_    607 GGCAATATTCTCCAAATTAATCCACAGATTCCATGCAATACCTATCAAAG 656
                                i  i       i   i        v i     v         i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_135792970_    657 TCACAGCTGGCTTTTTTG 674
                           v      v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG 118

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.00 (0 / 0)  

3622 17.75 5.44 1.17  chrX_135792970_135795053.rev      822  1593 (491)    L1M4_orf2#LINE/L1      104   908 (0)  

  chrX_135792970_    822 CAGTTGACTTTCT-GAAGAAATTGAGAAGTTCTTTCTAAAATACATATGA 870
                            i  v    i - v         v   i vv i       v      i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_135792970_    871 AAATGCAAAAGTC------TAGCCAAAACAATCTTGAAAAAGAAGAAT-- 912
                                 ii v ------                            i--
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_135792970_    913 -GTTGGAGAACTCACACTTCCTAATTTGAAAATTTAATACAAAGCCACAG 961
                         -       i            i     v    i   v        i    
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_135792970_    962 TAATCAAGATGTTGTGGTACTGGCATAAGGATTATCATGTAAGGATAGAC 1011
                                  iiv                    viv   ------     i
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT------ATAGAT 297

  chrX_135792970_   1012 CAATAAAATAGGATTGAGAGTCCAGAAAGAAACCCATAGATTTATGACCA 1061
                             ii     i                v         v       ii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_135792970_   1062 TTTGATTTTCACCAAGGAACTCCAGACAATTAAATAGGGGAAGAACAGTC 1111
                         v         iv     ivvi v    v   v   i   i     i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_135792970_   1112 TTTTCAGCGGATGGTGTCAAGACAAACTGGATATCCACATGCAAA-GAAT 1160
                               i ii      iiii     -       ?           -    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAAT 446

  chrX_135792970_   1161 GAAATTAGACTC--ATCTTGTGCCATATACAAAAGTTAACCTGAAATGGA 1208
                            i  i   i -- i  iiii            i     iii       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_135792970_   1209 TCTAAGACTTAAATTTAAGACATAAAAATATAAAACTGT------AAAAC 1252
                           v?    i     v     vv     v         v ------     
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_135792970_   1253 A--GAAATAAATTTTAGTGACGTTAGATTAGGCAATGGTTTCTTAAATGT 1300
                          -- i?i     i  v     v  i i                  i  i 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_135792970_   1301 GACATGAAATCCACAAGCAACCAATGACA--------------GACTTTG 1336
                             iv   vv          v  v  v --------------     ii
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_135792970_   1337 TCAAAATTTAAA--TTTTGTGCTTCAAAGAATTCAATCAAGAAACTGAGA 1384
                                 v   --               i iv v         v   i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_135792970_   1385 AGACAGTCCATGGGATAGAAGAAAACATTTGCAAGTCACATACCTGATAA 1434
                              ii   ii i  i i      i        i   i   i       
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_135792970_   1435 GGATTTAGTATCCAGAATGTATTTTAAAAACTCTTAAAACGCAACAATAA 1484
                           ivi v           i   v--  i        v   v   i     
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATA--AAGAACTCTTACAACTCAATAATAA 794

  chrX_135792970_   1485 AAAGAAAAATAATCCAGTTTTTAAATGGG-----GATTTTAATAGACATA 1529
                              v      i   i  ?vv       -----     v         v
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_135792970_   1530 CTTCCAAAGAAGACATGCAAATGGTCAATAAGCACATGAAAAGATGCTCA 1579
                         ii           i  i       i                         
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_135792970_   1580 ATATCATTAGTCAT 1593
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (84 / 49)
Gap_init rate = 0.02 (13 / 805), avg. gap size = 3.92 (51 / 13)  


3249 26.93 0.66 0.44  chrX_135882654_135889048.rev     4999  5904 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_135882654_   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5048
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_135882654_   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCATCAAGC 5098
                            v     v     iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_135882654_   5099 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACTAATT-TAAAGTTCA 5146
                          v   iivi i  i  ii     -   -- v  i  i  i-    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_135882654_   5147 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5196
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_135882654_   5197 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5246
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_135882654_   5247 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5296
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_135882654_   5297 AATGGAACACAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5344
                                i v  i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_135882654_   5345 ATCTGATCTTTGACAAACGTGAGAAAAACAAGAAATGGGGAAAGGATTCC 5394
                          vi    i  i     iv   vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_135882654_   5395 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5444
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_135882654_   5445 GAAACTGGGTCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5494
                            ii   ii    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_135882654_   5495 TTAAAGGCTTAAA-GTTGGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5543
                          i ?  i i    -  vi  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_135882654_   5544 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5593
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_135882654_   5594 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTCA 5643
                         i            vvi          vv     v  i    v   ii   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_135882654_   5644 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5693
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_135882654_   5694 AGGCAACCTACAAAATGGGAGAAAATTTTCTCAACCTACTCATCTGACAA 5743
                           i     i   i             v  iv   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_135882654_   5744 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5793
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_135882654_   5794 AAACAAACAACTCCATCAAAAAGTGGGCAAAGAACATGAACAGACACTTC 5843
                          i     i   i v  i?    i         i iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_135882654_   5844 TCAAAAGAAGACATTTATGCAGCCAA-AAACACATGAAAAAATGCTCACC 5892
                           v        i  vi viii     -  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_135882654_   5893 ATCACTGGCCAT 5904
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1847 22.20 6.18 2.17  chrX_135920900_135922490.rev      502  1100 (491)    L1M4_orf2#LINE/L1      286   908 (0)  

  chrX_135920900_    502 AAACATATAGAACACACAGAACAAAATGCAGAGTCCAGAAATAGACTCAC 551
                          i         v  - ii   i i   vv              i  i  i
  L1M4_orf2#LINE/    286 AGACATATAGATCA-ATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_135920900_    552 ACAAATATGACAAATTAATTTT------GGGCCCCAGAAAAACTAAATGG 595
                            vv    iiv    i     ------   iv   ii vv i v     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_135920900_    596 CGAAAGGA----------ACCGTATG---------CA--TG------CAT 618
                         v     i ---------- v iv   ---------  --  ------  i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_135920900_    619 TTGCAAAAAAAAATTAACCTACATCTGAAGCTCACACCTTATACAACAAT 668
                         v       i  -- v  vi iv i ivv v        v       v   
  L1M4_orf2#LINE/    435 ATGCAAAAGAA--TGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_135920900_    669 TAACTCAAAATAGATCATAAACCTAAATATGAAACATAAAGCTATAAAAA 718
                                    i     ? i        i i i vv    i        -
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA- 531

  chrX_135920900_    719 CTTTTAAAATAAAACATAGGAG-AAGTCTTTGTGACCTTGGGTTTAGCAA 767
                           i   i  v          ? -  i    i             vi    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_135920900_    768 TTAGTTTTAAAATACAACAGCAAAAGCATTATCAATACAAGAAAAAAATA 817
                          viv  i v i   ii   v        iv v   i v         vvi
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_135920900_    818 ATAAATAGGACTTCATTAAAATTATAAACTTTTCCTCTGCAAAAGATACC 867
                               v         i       v        viv  v    i  i  i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_135920900_    868 ATTAAGAGACTGAAAACACAAGTCACAGACTGGGAGAAAATATTTGAAAA 917
                           i    i v      v    vi      v                v   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_135920900_    918 CCACACATCTGACAAATAAATTGTTTCTAGAATATACAATAAACTCTTAA 967
                         i  i i      i  ivi v    v  i        i  vi        v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_135920900_    968 AACTCAACAATAATAAAATTAATAAGATAAT--AAGGTTTTTTAAATGGG 1015
                                i     v  i iv     vvi   --  --------       
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAA--------AAATGGG 823

  chrX_135920900_   1016 CAAAATACTTGAATAGACATTTCACCAAAAATTATTTAGAGATGTCTA-T 1064
                             iv i               v     i vv  v  v i   v i - 
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_135920900_   1065 AAGCACATTAAAAACATGCTCAACATCATTAGTCAT 1100
                                 v    i-             ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (69 / 62)
Gap_init rate = 0.02 (13 / 623), avg. gap size = 3.85 (50 / 13)  


3182 26.98 0.77 0.77  chrX_135929598_135935976     4980  5887 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_135929598_   4980 TGGAAGAACATTCCATGTTCATGGATAGGAAGAATCAATATCGTGAAAAT 5029
                              ii i  i              v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_135929598_   5030 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCTCATCAAGC 5079
                            v     v      v i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_135929598_   5080 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5127
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_135929598_   5128 TATGGAACCAAAAAAGAGCGCACATCGCCAAGTCAATCCTAAGCCAAAAG 5177
                                viiv  ii  v vviv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_135929598_   5178 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5227
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_135929598_   5228 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGGGATGTAGACT 5277
                                 i   i    ii         i iv ii i  iv  i    ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_135929598_   5278 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGTATATCTACAACC 5325
                                i    i--    i  --        vv  i  i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_135929598_   5326 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5375
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_135929598_   5376 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGCT 5425
                           v  i  i              v      v  ?       i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_135929598_   5426 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5475
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_135929598_   5476 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAT 5525
                          i ?    i           v       i      vi i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_135929598_   5526 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5574
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_135929598_   5575 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5624
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_135929598_   5625 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 5674
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_135929598_   5675 CAAGCAACCTACAGAATGGGAGAAAACTTTTGCAATCTACTCATCTGACA 5724
                         v ii     i                iv       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_135929598_   5725 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5774
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_135929598_   5775 AAAACAAACAACCCCATCAAGACAAGCGGCTGAAGGATATGAACAGACAC 5824
                           i     i     v  i? i -- ii  vii      v    i     i
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAA--AATGGGCAAAGGATTTGAATAGACAT 843

  chrX_135929598_   5825 CTCTTAAAAGAAGACATTTATGCAGCCAA-AAG-ACATGAAAAAATACTC 5872
                         i   iv        i  vi viii     -   -         i  i   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_135929598_   5873 ATCATCGCTGGCCAT 5887
                          v    i????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


3265 26.71 0.55 0.33  chrX_135937184_135943051     4470  5375 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_135937184_   4470 TGGAAAAATATTCCATGTTCATGGATAGAAAAAATCAATATTATGAAAAT 4519
                               i    i              v i  i v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_135937184_   4520 GGCCATACTTCCCAAAGCAATTTATAGAATCAAAGCCATCCCCATCAAGC 4569
                            v     i      vii  i  i   v    v  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_135937184_   4570 TACCA-CTGACTTTCTTCACAGAATTGGAAAAAAGTACTTTAAACTTCAT 4618
                          v   -   v    i  -i     v v  v  ivvv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_135937184_   4619 ATGGAACCAAAAAAGAGCCCGCATAGCCAAGACAATCCTGGGTAAGAAGA 4668
                               viiv  ii  v  v v        i      i  iiv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_135937184_   4669 ACAAAGTTGGAGGCATCACACTACCTGACTTCAATCTATACTACAAGGCT 4718
                                      vv       v  ii i     vviv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_135937184_   4719 ACGGTAACCAAAACAGCATGGTATTGGTACCAAAGCAGATATATAGACCA 4768
                           i    i   i    ii     i   i iv iiii   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_135937184_   4769 ATAGAACAGAACAGAGGCCTCAGAAACAACATCACACATCTACAACCATC 4818
                           i   i    iv   ivii      i  vvi  i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_135937184_   4819 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGTGAAAGGATTCCCTA 4868
                             i  i     ivv  v   i v  vvv     v     i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_135937184_   4869 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 4918
                           i  i        i     v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_135937184_   4919 ACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGTATTG 4968
                         ii         v   i     v                   i   v  ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_135937184_   4969 AAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5018
                         ?    i    i      v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_135937184_   5019 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTGT--GACTGAA 5065
                           ?i- v i -   iv   v v  vv i     v i   v --  - ivi
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATG 597

  chrX_135937184_   5066 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5115
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_135937184_   5116 TAAACTAAAGAGCCTCTGCACTGCAAAAGAAGCTATCATCAGAGTGAACA 5165
                         i   v v  i i i i  ii  v    i  vi      vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_135937184_   5166 GGCAACCTTCAGAATGGGAGAAAATTTTTGTAATCTATCCATCTGACAAA 5215
                          i     iv                v    i  vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_135937184_   5216 GGGCTGATATCCAGAATCTGCAAGGAACTTAAACAAATTTACAAGAAAAA 5265
                           i  vi          v ii  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_135937184_   5266 -ACAAACAATCCCATCCAAAAGTGAGTGAAGAATATGAATAGACACTTCT 5314
                         -     i  i  v  i?    i  i ii   i  v          i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_135937184_   5315 GAAAAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAATCTCATCA 5364
                         vv        i  vi vii      i  i  i       i vv    v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_135937184_   5365 TCACTGGTCGT 5375
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


2786 26.55 1.04 0.78  chrX_135943942_135947367     1715  2486 (940)    L1M4_orf2#LINE/L1        7   780 (128)  

  chrX_135943942_   1715 GATATTCTATGCTCATAGATAGGAAGACTCAATATTATGAAGATATCAGT 1764
                              i i   i    i   v        i      i v     iv  i 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_135943942_   1765 TCTTCTGATCTTGAGCTAAAGAGTCAATGCAATTCCCATCAGAATCCTAG 1814
                         v  i iv vv    v   v   v    i     i  i    i     i  
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_135943942_   1815 CAAGTCCAATTTTGTGGTTATCAATAAACTGATTTTAACATTTATTTAGA 1864
                          vi--  vv     ii vv  ii i  i     ii   v   i  v i  
  L1M4_orf2#LINE/    107 CTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_135943942_   1865 GAGGCAAAACACCCAGAACAGCCCTCTGAATATTGAAAGATAAGAACAAA 1914
                         i v    iiv        i    vvvvv   v      i v         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_135943942_   1915 ATTAAGGGACTGACACCACCCTACTTCAAGATTTACTATAAAGCTACAGT 1964
                         i  iii     v    iv   v i     i i      i           
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_135943942_   1965 AATCAAGACAGTGTAGTACTGGTAAAGGAATAGACAAATAGATCAGTGGA 2014
                                       i       i v i i       v        i    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_135943942_   2015 ATATAATAGAGAGGCCAGAAATAGACTCATACAT--ATAGTCAACTTATC 2062
                            v   v     v         i  i       --  i     i v  i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_135943942_   2063 TTTAACAAAGGAGCAAAGGCAATGCAATAAAGCAAATACAGTTTTTTCAA 2112
                           ii    i  v  v   i v  v    iii v  iv i   i       
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_135943942_   2113 CAA-TGGTGCTGGAACAACTGGACATGCACATGCAGAAAAATGAACATAG 2161
                            -         i         i ?v        i  i      vv i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_135943942_   2162 ACACAGACTTTATACCCTTCATGAGAATTAACTAAAAATAGATTATGAAT 2211
                           v vv  i i i   v vi ii i        v     i   i ?ii i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_135943942_   2212 CTAAATGTAAAATGC-AAAACTGTGAAGCTCCTAGAAGATATCATAGGAA 2260
                                   i -  -      i i  i   i       v v      ?i
  L1M4_orf2#LINE/    505 CTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_135943942_   2261 AAAACCAAATTGACTTTAGGTATGGTGATGACGTTTTAGATACAACACCA 2310
                         v   i vvvv    i  i   vv  ii   iiv i       ii      
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_135943942_   2311 AAGGCACAATCCATGAAATAAATAGTTGATAAGCTAGATATCATTAAAAT 2360
                           i      v v ii   v   v i v     ii i  iv    i     
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_135943942_   2361 -GAACACTTCTGCTCTACAAAAGACAAGGTCAAGAGAATGAGCAGACAAA 2409
                         -i  v    i  iv  v    i    vvi      i i   iv      v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_135943942_   2410 CCACAGACTGGCAGA---TATTTGCAAAAGACACAAGTGATAAAGGACTG 2456
                                v   v   ---          vv i i vv      i     v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_135943942_   2457 TTACACAAGAGTCCTTAAAAAGAGTCCTTA 2486
                         v  iv  -  i v--  v     iii    
  L1M4_orf2#LINE/    754 GTATCCA-GAATA--TATAAAGAACTCTTA 780

Transitions / transversions = 1.40 (118 / 84)
Gap_init rate = 0.01 (9 / 774), avg. gap size = 1.56 (14 / 9)  

 524 20.14 0.69 3.47  chrX_135943942_135947367     2791  2934 (492)    L1M4_orf2#LINE/L1      769   908 (0)  

  chrX_135943942_   2791 AAAGAGTCCTTAAAACTCAACAGTTAGACAACAAACAACCCAATT-AAAA 2839
                              iii    v       i i v i vi     i         -    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_135943942_   2840 ATGGGCAAAAAAAAAAACTTGAGCAGACATGTCACCAAAGAAAATATACA 2889
                                  ii -----i    ii      v  v        i       
  L1M4_orf2#LINE/    819 ATGGGCAAAGGA-----TTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_135943942_   2890 CATGGCAATTATGCAAATGAAACAATGTCCAACATCGTATGTGTT 2934
                         v     v v  v   v      vi   ii       i????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (18 / 11)
Gap_init rate = 0.01 (2 / 140), avg. gap size = 3.00 (6 / 2)  


2783 25.65 4.65 1.59  chrX_135962547_135965294     1381  2261 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_135962547_   1381 TGGAGAGATATTACACGTTCATGCATC-----ACT----ATTGTTAAGAT 1421
                             i      iv  i       v  i-----   ----           
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_135962547_   1422 ATTAATTCTTCCCAACCTAATCTATAGCTTCAACACAATGCCAAGCAAAA 1471
                         ivi   v  i     vi i     i  v      i    v  v v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_135962547_   1472 TCCCAGCAAACTACTTTTTAGATATCAACAAACTGTTTTTGAAGTTCATA 1521
                                viv  vi   vi   v  ii    i   v ii i  i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_135962547_   1522 TGGGAAGGCAAAAGACACACAATACTGAAGCCAACACAATGT-GAAGAAG 1570
                            i  v    ii   v  v    -----     v     v -   i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATA-----GCCAAAACAATCTTGAAAAAG 195

  chrX_135962547_   1571 AAAAACAAAGTTAGAAGACTCATACTACCTGATTTTAAGAATTACCATAA 1620
                           i         i  i      i   v  ii    i  i v    i i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_135962547_   1621 TGCTACAGTAATCAAGACGGCATAGTATGGGGGAAAGAATAGACAAAGAT 1670
                         v                 i ii i   iv  viv   i       v v v
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_135962547_   1671 ATCAGGGAAACAGAAAACAGAGCCCAGAG-TAGGCTCAAAAAAATACAGT 1719
                             iv i  i    vvv    i     i-  ii i  v v vv  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_135962547_   1720 CAACTGATCTTTGATAAATTAATG--AAGGCAATTCAATGGAGAAAGAAT 1767
                            i    i  i  i  i--ii  --   i v         i        
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAG--GGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_135962547_   1768 AGTTTTTTCAATAAATGGTAATGGAATAATTGTATGTTCATATGTTGAAA 1817
                            i       i       iv   i i  i  v  i?i  i   ivi  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_135962547_   1818 AAAGAACTTAGACACAGATCTTACATC-T---------TTAAC-AAAGAT 1856
                           v   v  i   v vv i  i   i - ---------     -v  i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_135962547_   1857 GGATCATAGACCTAAGTGTAAAA-TTCAAATTGTAACATT-TTATAAAAA 1904
                               ?        i     i -i v   i i   v i -   v  i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_135962547_   1905 ACTATAGGAAAAATATATAGGTGACCTCGCACTTGATAA--GTTT-TTAG 1951
                          vi     ?iv  -  v vv       i vii v ii  --    -    
  L1M4_orf2#LINE/    544 AACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_135962547_   1952 ATACAACACTAAAAGCATGATCCATGAAAGAAACATTATGTAACTTTTAT 2001
                            ii    i       ii v v ii       v v  vi   -----  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA-----AT 637

  chrX_135962547_   2002 T--ATTTTCTTAAAACTTACAACTTCTGCTCTGTAAAAAGACTTTGTTAA 2049
                          -- i  iv i    i v v     i  iv  - v   i   vi i i  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAA 686

  chrX_135962547_   2050 GAGAATAAAAAGACAAGTCACAGAAGGGGAGAAAATATTTGCAAAACACA 2099
                           i i i         vi       v                   v  i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_135962547_   2100 CATGTCATAAAGACCT---ATCTAAAATATACAAAAATCCCTTAAAATTC 2146
                         i  v v    i iv  ---   i i      i   i v i    v  i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_135962547_   2147 GACAATAAGAAAACAAACAATCCAATTTAAAAATGGACAAAACATCTGAA 2196
                         i i     i  i     i  i      ?        i    iv  i    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_135962547_   2197 GAGACACAACATCAAAGAAGATATATAAAT-------AAGCATATGAGAA 2239
                         v     ivv vi             i    -------     i    i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_135962547_   2240 GATGCTCACAATTATTTGTCAT 2261
                                 vv  i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (139 / 83)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.75 (55 / 20)  


 934 25.18 2.88 2.16  chrX_136054754_136057787     1226  1503 (1531)    L1M4_orf2#LINE/L1       21   300 (608)  

  chrX_136054754_   1226 ATGGATTGGAAGACTCAGGGGTGTTATTGTTAGAACATCAGTTCTTCCCA 1275
                                        i i------        ii iiv  i v  i    
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAA------TATTGTTAAGATGGCAATACTCCCCA 64

  chrX_136054754_   1276 AAATGATCTGTAGATTCAGCACACATCCAGTTAGAATCTCAGCATAATTT 1325
                           v      ii       i i  vvi  vi i i    i    vvvv   
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_136054754_   1326 TTTGAGGAAATTGAGAATCTGAC---AAGGT--ATAAAAAAATGCACAGA 1370
                             vi        v  v    i---  ii --   vii       vi i
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_136054754_   1371 ACCTAGGATAGTCAAAGTAATCTTGAAAAAGAAGAACAAAATTAAGCGAC 1420
                            i  i    i    ii                      i  iiiv   
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_136054754_   1421 TTACATTATCGGATTTCAATACTTTTTATAAAGCAATAGTAAT-AAAAGA 1469
                          i   i vi vi       v    vi  i     v i      -  i v 
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_136054754_   1470 GTGTGGTAATG-CAAAAGCAAAGACATGGA-ATCAA 1503
                                 v  -  v   v v      iv -     
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

Transitions / transversions = 1.59 (43 / 27)
Gap_init rate = 0.02 (6 / 280), avg. gap size = 2.33 (14 / 6)  

2010 24.92 4.76 0.95  chrX_136054754_136057787     1912  2541 (493)    L1M4_orf2#LINE/L1      255   908 (0)  

  chrX_136054754_   1912 AGTTAAGAAAAGTGTGGTGCTGGAACAAAGATAGACATATAGA-AAATG- 1959
                          i i    v -       i    v i  i              -v    -
  L1M4_orf2#LINE/    255 AATCAAGACA-GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_136054754_   1960 -ATAGA-------GTTCACAGGTAGCCCCACAAATATATGGTCAATTATC 2001
                         -     -------  i  v ii  iv    i v  v           ivi
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_136054754_   2002 TTTTG-CAAAGGTGCCAAGACACTTCAACTGGGGCAAGGACAGTATTTTC 2050
                            i -   i           vv     -     v   i i   v     
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAA-TGGGGAAAGAATAGTCTTTTC 402

  chrX_136054754_   2051 AACAAATGGTGCTGGAA-AACCAGATATCCATATTTTTAAAAATC---CC 2096
                                        i -   ii    ?   i  vivv  i   v---ii
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_136054754_   2097 TAACCTTTACCTCATTTCATACACAAAAATTAATTCAAG-TGCATTACAT 2145
                         vi   ii       ivi    i           i    i-  v  i ? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_136054754_   2146 ACCAAAAGGTAACAGTTAAAACTGTAAAACC--TATAAGAAGGCACAAGA 2193
                            v   v    v  i       i      i--  v     ii  i i ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_136054754_   2194 GAAAACCTTCACTATTTTGATGTAAGCAAAGTTTTCTTAGATGGAACACA 2243
                          v   i    iiv ii   ivv  i    v v          ivi    v
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_136054754_   2244 AAAAGCATAAATCATAAGGAAAAAGCTTAATAAATTTGACTCCATCAAGA 2293
                                i  iiv i  iii    iv vi       v    i      i 
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_136054754_   2294 TTTAAAACTTCTG-ATTTCTGAAATACA-TATTAAGAAAACGAAATGG-A 2340
                           v       i  -ii   -i  iv   -   i      ii    v i- 
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTC-AAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_136054754_   2341 AGTGACAGAATTGGAGAGAA-ATCTACAATACATAAATCTAACAAAGGAC 2389
                          viv       v     i  -  i i   vv    v    i i  i    
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_136054754_   2390 TTGTGTCCAGAATATATAGTGAACTC--ATAATTCATTAATAA---GACA 2434
                             i             iv      -- i  i   v      ---    
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_136054754_   2435 AGAAACCCAATTAAATGAATAGGCGAAAGAGTTAAAAAGAAACA---CCA 2481
                          iv         ?  -i   i   i  i  v  i  v   --  --- iv
  L1M4_orf2#LINE/    802 AATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGA--CATTTCTC 848

  chrX_136054754_   2482 CAAAAACGATCTAAAAATTGCCAGTAGACACACACAGAGATGTTTATCAT 2531
                             i v   v  v    v    i  ii    iiv i     i i v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_136054754_   2532 CATTAGTCGT 2541
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.68 (96 / 57)
Gap_init rate = 0.03 (20 / 654), avg. gap size = 1.80 (36 / 20)  


4229 17.82 5.17 0.80  chrX_136105883_136107773      529  1398 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136105883_    529 TGAAAGGATATTCTGTGTTCATGGATTGGAAGACTTAATATT---AAGAT 575
                           i  i     i ii                           ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136105883_    576 GGCAATACTAGCCTAAGTGATTAACAGATACAATGCAATCCCTATCAAAA 625
                                  vv  v  v    iv      v   i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136105883_    626 TCCTAACAGCCTTTTTTTTTTACAGAACTAGAAAAGCTAATCCTAAAATT 675
                            i i v         ----i     v v  v     i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT----GCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_136105883_    676 TATATGGTATTGCAAGGAACCCTGAATAACCAAAGAAAAATTCTGGAAAA 725
                         i      v v       i    v     i     -- v   ii  i    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAA--ACAATCTTGAAAAA 194

  chrX_136105883_    726 AAA--------TTGAAAGAATCACACTCGCCAATTTTGAAATGTACTACA 767
                         i  --------   i i  v       iv       ii   iv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_136105883_    768 AAGGTACAATACTCAAGACAATGTGGGACTGGCATAAGCATAGACATACA 817
                            v    i  v        i     v           v         i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_136105883_    818 AATCAATAAAATATAACTGAGAGTCCAGAAATAAACCCATTCATCTACAG 867
                         i      ii    v  i                       v   i  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_136105883_    868 TCAATTGGTTTTTGAAAAGGGTGCCAATGTCTTACAATGGGGGAAATA-A 916
                                i    i  v           vii v v        i  iv - 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_136105883_    917 GTTTCCACAACCAGTGGTGCTGAGACAACTGAAGATCCACATGCAAAAGA 966
                           i iiv    v i        i        i v ?              
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_136105883_    967 ATGAAATTGGGCCTCTGTCTCACAGCATATACAAAAGTTTAGTCAAAATG 1016
                              i    i  i  ii      v           i  v v        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_136105883_   1017 GATCACAGACCTAAACTTAAGGGCTAACACTATAAAACTCTTACAAGAAA 1066
                              ?         iv    i     v               v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_136105883_   1067 ACATAGGAGTAAATCTTCATAACTTTCATTTGCCCAGTGGATTCTTAGAT 1116
                                ?          i i  i  viv  ivv  i   v         
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_136105883_   1117 ATGACAGCAAAAGCACAAGCAATGAAAGAAAAAAACAGATAAGTTGGGCT 1166
                               v               ii          -i      i    i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACT 643

  chrX_136105883_   1167 TTATCAAAATGAAACACTTTT-TGCATCAAAGGACACTAACAAAAGAGTA 1215
                          i        v   v      -   v             v   i i   i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_136105883_   1216 AAAAGATAACCTACAGAATGAGATAAAATATTTGTAAGTTTTATATCTAA 1265
                               i    i        i  v          i  i iv       i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_136105883_   1266 TAAGT--CTAGTATTTAGAATATATAAAGAGC-----------------A 1296
                             v--  v    ii              i ----------------- 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_136105883_   1297 AA------------CCACTATAAAAATGGACAAAGAACTTGAGCAGACAT 1334
                           ------------   v v?        i     i i    ii      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_136105883_   1335 TTTTCTGCAGAAGATATATAAATGGTCAGCAAGTGTATGAGAA-ATACAC 1383
                           i  iiv          i      i  ii   iii    i  -  i v 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_136105883_   1384 AACATCATTAGTCAT 1398
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (96 / 55)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 4.73 (52 / 11)  


3003 13.42 2.16 23.64  chrX_136190198_136192996     1152  2306 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_136190198_   1152 GAAAAGGCATCCCATTTTCGTTGATTGGAAAAATTAATACTGTTAATATA 1201
                          i    ii       v   i v        i v      i      v  i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_136190198_   1202 ACGCAACTCCCTAAATTGATCTACAGACTCAAAGCAATCCCCACCGGAAA 1251
                         i ivv      i               i    v        i i ii  v
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_136190198_   1252 GCTAAGTGGCTTCTTTGTAGAAATTGACAATCCAATCCTAAAATTCATGT 1301
                         v i iv  v   i    i            v ii              i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_136190198_   1302 GGAAATTCAAGGCACCCAGAA-AGTCCAAAACAATCTTGAAAAAGAAGAA 1350
                               v     v        -  -                         
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAG-CCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_136190198_   1351 CAAAGTTGGAGGACTCATACTTTCCCATTTCGAAACTTA-----AAGCAA 1395
                                          i    i  v     i       -----    v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_136190198_   1396 CAGTAATCAAGACAATGTGGTAACTGGAATATGGATAGGCATATAATATA 1445
                                       i       -    v   v      i      -----
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTA-CTGGCATAAGGATAGACATATA----- 294

  chrX_136190198_   1446 GAGCAATGGAATATAATTGAAAGTCTAGAA-TAAAACCATGTATCCACAG 1494
                           v          v      i    i    -    v    ii  ii ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_136190198_   1495 TCAACTGATTTTTTACAAGAGTGCCAAGACCTTTTAATGGGGAAAAAATG 1544
                             i       iv     i           v  i          i   i
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_136190198_   1545 ATCTTTCCGATGAATGGTGCTAAGACAATTGGATAGTCATATGCAAAATA 1594
                         i     i i ii         ii     i      ?i  i        v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_136190198_   1595 ATGAAGTTGTACTTTTACTACACATTATATATAAAAATTTACTCAAAAAT 1644
                                  v  iii   iv    ii     i       v        - 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-T 493

  chrX_136190198_   1645 GGCTCAAATACCTAAATACTCTTTTTTTTTTTTGAGATGGAGTCTTGCTC 1694
                           v   ? v        ---------------------------------
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAAT--------------------------------- 510

  chrX_136190198_   1695 TGTCGCCCAGGCTGGAGTCCAGTGGCGAGATCTTGGCTCACTGCAAGTTC 1744
                         ------------------------------------------ i   ---
  L1M4_orf2#LINE/    511 ------------------------------------------GTAAG--- 515

  chrX_136190198_   1745 TGCCTCCCGGGTTCATGCCATTCTCCTGCCTCAGCCTCCCTAGTAGCTGG 1794
                         --------------------------------------------------
  L1M4_orf2#LINE/    516 -------------------------------------------------- 515

  chrX_136190198_   1795 GACTACAGGCGCCCGCCACCACGCCCAGCTAATTTTTTGTATTTTTAGTA 1844
                         --------------------------      ------------------
  L1M4_orf2#LINE/    516 --------------------------AGCTAA------------------ 521

  chrX_136190198_   1845 GAGACGGGGTTTCACCATGTTAGCCAGGATGGTCTCGATCTCCTGACCTT 1894
                         --- ---------  i  --------------------------------
  L1M4_orf2#LINE/    522 ---A---------ACTAT-------------------------------- 527

  chrX_136190198_   1895 GTGATCTGCCCGCCTCGGCCTCCCAAAGTGAATACTCTTAGCCTATATAT 1944
                         ------------------------   ------        ---------
  L1M4_orf2#LINE/    528 ------------------------AAA------ACTCTTAG--------- 538

  chrX_136190198_   1945 AAAACTCCTCAGAAAAACACAGGGGTAAATTTTTGTGATTTTGGATTTGG 1994
                         ---------- ii      i   ?      i  i    ii    i  v  
  L1M4_orf2#LINE/    539 ----------AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_136190198_   1995 CAACAGATTCTTAGAAATGACACCAAAAACACAAGCAGCAAAAGAAAAA- 2043
                            ii v        v            i        i           -
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_136190198_   2044 TGGATAAATTTGACTCTATCAAAGCTAATAATTTTTGTATT--AAAGGGC 2091
                          i        v    ii      ii   v  i      ii --     i 
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_136190198_   2092 ACTATTAAGAAAGTGTAAAATAAATCCAAAATTTGGTAGAAAATATTTGC 2141
                              i         v   ivv  i   v ivv   v             
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_136190198_   2142 AAATTATGTATATATTAAAGGACTTGTACCTAG--CATATAAAGAACCAT 2189
                             i  i   v iv   i         i i  --i           iv 
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_136190198_   2190 TACAACTCAGTAAGAAAAAGACAA----CCCAATT-AAAATTAGGCAAAG 2234
                                  i   v          ----       -    v i       
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_136190198_   2235 GTTCTGAATAGACATTTCTACAAAGAAGATATGAAACTGGC--------A 2276
                          v i               v            iv  v    -------- 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_136190198_   2277 TATGAAAGGATGCTATGCATCATTAGTCAT 2306
                         i      i      vvi     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (100 / 52)
Gap_init rate = 0.02 (20 / 907), avg. gap size = 14.90 (298 / 20)  


 659 27.00 2.66 3.80  chrX_136199696_136201305       50   312 (1298)    L1M4_orf2#LINE/L1        3   262 (646)  

  chrX_136199696_     50 GAGAGATATATCATGCCTATGCCTCTAAATTGA-TAAAAATTGATCAGTT 98
                           i      vi    iii   vv ivi  --  - v  v    v v  v 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAA--GACTTAATATTGTTAAGAT 50

  chrX_136199696_     99 TAGAGTTCTCCCAAAGTCGATTTATAGATTCAATACGATCCTAATAAAAA 148
                         viv i v     v  i i   i  i        ii i    iv  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136199696_    149 CTCCAGTAGACTTTTTTGTAGAAACTGACAAGCTGAATCTGCAATACATA 198
                         ii    iv v        i     i           vi  iv   v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_136199696_    199 GGGAAATA-AAAAGACATAGACAT-TTCAAAATAAT-TTAAAAATTTAAG 245
                         v      i-  ii   vi   -  -vi     i   -  i    ------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGA-ATAGCCAAAACAATCTTGAAAA------ 193

  chrX_136199696_    246 CAAACAAACAAAA---GAGGACTTAAACTATCTGATTTCAAGACTTACTA 292
                         - i vi      i---       i v   vi ii       i        
  L1M4_orf2#LINE/    194 -AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_136199696_    293 TAAATGTACATTAATTAAAA 312
                         i   vv    v    i  i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGA 262

Transitions / transversions = 1.45 (42 / 29)
Gap_init rate = 0.03 (8 / 260), avg. gap size = 2.12 (17 / 8)  

1877 24.32 3.04 2.40  chrX_136199696_136201305      493  1117 (493)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_136199696_    493 AAGAGCGGGCATTTGGATGAATGGAATAGAAGAGAGAGTCAAAAAATAAA 542
                            iiii i   v i   v            vv       v i       
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_136199696_    543 TCCATACATACTACCTGCTC----GATTTTCAAAAAAACTGCCTTGGAAA 588
                         i        -i  --  v  ----       i v  iiv    vv ivv 
  L1M4_orf2#LINE/    330 CCCATACAT-TTA--TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_136199696_    589 TTCAACTGGGGAAAGGATAGTGTTTTCAACAAATGATGCTGGAACTACCA 638
                              -         i     v             i      i  v  ii
  L1M4_orf2#LINE/    377 TTCAA-TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_136199696_    639 GATATCCATATGCAGAAATACTCAGCATCAACCTTTATCTCATACCATAT 688
                             ?   i     i  iv ivv  i- vi   ii  i    i       
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGT-TGGACCCCTACCTCACACCATAT 474

  chrX_136199696_    689 CCAAAAATTAGCTTAAAATGCATCACATAATTAAATATAAAAAGTAAAAC 738
                         v         i  i      v    ? v vi     i   i iv      
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_136199696_    739 CACAAAACTTCTAGAAGAAAACATAGGAAAAAA-CTGGATTA--TTGAAT 785
                         i i      ii                ?iv   -  vvi v --   ii 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_136199696_    786 TAAGCAAATATTTCTTA--TAAAGCACAAAAAATGTATAAACTGTAAAAG 833
                           i    vvi       --  vii   v    -- i i  i vii     
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAA--GCACAAGCAACAAAAG 622

  chrX_136199696_    834 AAAAAGTTGATAAAATAAACTTGATAATAATTAAAAACTTATTCT-CTTT 882
                              i v      v ii    v  v v            -  v -   i
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT-TTGTGCTTC 671

  chrX_136199696_    883 GAAAGACACAGTTAAGAAAATAGAAAGGCAAACCATACACTGGAAGAAAA 932
                         i  i     vi i      i ii    i   v   i v v   i      
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_136199696_    933 TATGAG-AAATATATATATCTGCCATAGGACTTGTATCAAGAATATATAA 981
                            vv -    -i         vi vi           v           
  L1M4_orf2#LINE/    722 TATTTGCAAAT-CATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_136199696_    982 AGAATTCTTAAAGCTTAGTAATAA---GATAAACACCCTCCCCACCAACA 1028
                             i     v i  i i      ---  i   i v  --- v ii? v 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACC---CAATTWAAA 817

  chrX_136199696_   1029 AATGGCTAAAAAGCATGAACTAAAAGT-----CAAAATGGAGATACAGCA 1073
                              vi   iiiiv    -  i vi -----    ivi  v     -- 
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAA-TAGACATTTCTCCAAAGAAGATATACA--A 864

  chrX_136199696_   1074 ATAGCCATTAAGCAAATGAAAGACTGCTCAACATTATAGAAAGG 1117
                           i    v      v      iiv          i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (89 / 59)
Gap_init rate = 0.03 (18 / 629), avg. gap size = 1.89 (34 / 18)  


2539 27.06 0.90 0.15  chrX_136201394_136206090.rev     2952  3620 (1077)    L1M4_orf2#LINE/L1        1   674 (234)  

  chrX_136201394_   2952 TGAAAATATATTCCACATTCATGGATTGGAAGAATCAATATTGTTAAAAT 3001
                           i   v    i   ii                v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136201394_   3002 GTCTATACTACCCAGAGCAATCTACAGATTTAAAGCAATTCCTATCAAAC 3051
                          v v     v    i vii           i  v     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136201394_   3052 TACCAATGACATTCTTCACAGAAATAGAAAAAACAATCCTAAAATTTATA 3101
                          v   iivi v  i  ii       v  v  ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_136201394_   3102 GGGAACCACAAAAGACTCAGAATACCCAAAGCTATACTAAGCAAAAAGAA 3151
                         v    vii   ii   i       v     i v  vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_136201394_   3152 CAAAACTGTACGAATCACATTACCGGACTCTAAATTATACTACAGAGCTA 3201
                             ii  v v  v     i v  vi i ii   viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_136201394_   3202 TAGTAACCAAAACAACATGGTGCTGGCATAAAAACAGACACAAAGATCAG 3251
                         i     i   i   iii    i         ii i     i v      i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_136201394_   3252 CAGAACAGAATAGAGAATCCAGAGATAAATCCATGCATCTACCATGAACT 3301
                         ii   i     v    i      i     i    i   i  ivi v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_136201394_   3302 TATTTTTTACAAAGTTGCTAAAAACATACATTGGGGAAAGGATGGTTTCT 3351
                         v     iv    i v   i  i v   v  v         i  i  i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_136201394_   3352 TCAAT-----GTGCTGGAAAAACTGAATATCCATAAGCAAAAGAATGAAA 3396
                             i-----       i v     i   ?   i v             i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_136201394_   3397 CTAGATGCCTATTTCTCACCATATACAAAACTCAAAGCAAAATGGACTGA 3446
                         i i  iv    ii  v              v i  vv         iii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_136201394_   3447 AGATTTAAATCTAAGACCTCGAACTATGAAACTACTACAAGGGAACATTG 3496
                            ii     v     v  vi      i     vi  v   ii     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_136201394_   3497 GGGAAACTCTCCAGGACATTGGTTTGGGCAAAGATTTCTTGAGTAATATC 3546
                          ? v  v   i iv   v    v  i     v i      iii  vv iv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_136201394_   3547 CCAGAAGCACAGGCAACCAAAACAAAAATGGACGAATGGTATCACATCAA 3596
                            i       i     v   iv      i  ii   v v iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_136201394_   3597 G-TTAAAAAGCTTCTGCACAGCAAA 3620
                         i-       -   i  ii vv    
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAA 674

Transitions / transversions = 1.70 (112 / 66)
Gap_init rate = 0.00 (3 / 674), avg. gap size = 2.33 (7 / 3)  

 983 16.81 1.77 2.21  chrX_136201394_136206090.rev     3981  4206 (491)    L1M4_orf2#LINE/L1      684   908 (0)  

  chrX_136201394_   3981 CAACAAAGTGAAGAGACAACCCACAGAATGGGAGAAAATATTTGCAAACT 4030
                            v        i                                   ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_136201394_   4031 AACCATGTGACAAGGGATTAACCATGTGACCAGAATATATAAGAAACTCA 4080
                          vvi  v   i      i -----   iv             ii     v
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACT-----TGTATCCAGAATATATAAAGAACTCT 778

  chrX_136201394_   4081 AACAACTCTGTAGGAAAAAATCTAATA---TGATTAAAAAATGGGCAAAA 4127
                         v       vi  iv     iv v    ---ii   ?             i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_136201394_   4128 AATTTGAATAGACATTTCTCAAAAGAAAACATACAAAAGGCAAATGGG-A 4176
                         i                   v      i i       v   v   ii - 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_136201394_   4177 TATGAAAAGGTGCTGAACATCATTGATCAT 4206
                         i        i    v       ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (22 / 15)
Gap_init rate = 0.01 (3 / 225), avg. gap size = 3.00 (9 / 3)  


3420 22.77 1.98 2.09  chrX_136470045_136472873.rev     1432  2340 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136470045_   1432 TGGAGAGATATTCCACATACGTGATTCAGAAGAATTAATATTGTTAAAGT 1481
                             i      i   ii v i  iv ii     v             ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136470045_   1482 TTCCATAGTGCCCAAAGCAACCTACGTATTCAATGCAATCTCCAGCAAAA 1531
                         vv v   v v      vii i    iv      i      i i v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136470045_   1532 TTCAAATAATATTTTTTGAAGAAATAGAAAAAGAAATCCTAAAATTCATA 1581
                          i v iiviiv       v      v  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_136470045_   1582 TGAAACCACACGCACAAAAAAAAAACCC-GAATACCCAAAGCAATTGCAA 1630
                           i  ---- i   ------ iii    -     v     i    ivii 
  L1M4_orf2#LINE/    151 TGGAA----ATGCA------AGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_136470045_   1631 ACAAAAAGAGCAAAGCTAGAGGCATCACACTACCTGATTCCAAAATATAC 1680
                          v  i    i     i i    vv       v  ii   i     iv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_136470045_   1681 TGAAAAGCTATAGTAATCAAAATAGCATGGTACTGGCATAAAAACAGGCA 1730
                          iv       i         i i  ii              ii i  i  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_136470045_   1731 AATAGACCAAAGGAGTAGAATAGATAGCTCAGAAATCAATCCTCACATTT 1780
                         v     i   v   i      v  v  ii       v  i  vi      
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_136470045_   1781 ACAGTCAGTTGATCTTCAACAAAGGTGCCAAGAACACACAATGGGATAGA 1830
                          ii    i     i   i    i          v  iv       iv ii
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_136470045_   1831 GAGAGTCTCTTCAATAAGTGGTGTTGGGAAAGCTGGATATCCACATGCAG 1880
                         i v     i     i  i     i     v i       ?         i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_136470045_   1881 AAGAATGAAATTGGACCCTTATATCTCATCACATACAAAAACCAAGTCAA 1930
                                  i        i  iv  v  i  i         ii  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_136470045_   1931 AATGAATTAAAGACGTAAAGGTTAAGGTCTGAACAC-ATAAAACTACTT- 1978
                             i  i ?    v    v  -   iv  i  -  -        -   -
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGT-AAGAGCTAAA-ACTATAAAACT-CTTA 537

  chrX_136470045_   1979 GAAGAAAACAGAGAA--AAAGCTTCTTGGTGCTGGTTTTGGCGAT--TTT 2024
                                   v  i?--   v    v  iivi   v  v   i  --   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_136470045_   2025 TTTA--TATCACCCAAAAAGCATAGACAACAAAAGCAAAAATAGACAAAT 2072
                         i   --   v  v v       i ii         v         i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_136470045_   2073 GGGATTGCATCAAACTAAAAAGCTTCTGT---TCAGAAAGGAAACAA-CG 2118
                         v   i v       v v    i   i   ---   --     v  v - i
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCA 685

  chrX_136470045_   2119 AGAAGAGTAAAGTGGCAATCTACAAAATGGGAGAAA-CATTTGCAAACCA 2167
                             -   i  iv i   i i   i           -i         i  
  L1M4_orf2#LINE/    686 AGAA-AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_136470045_   2168 TATACCTGATAAGGGGTTTATATCCAAAATTTACAGGAAACTCAAAGAAC 2217
                             i          ii  i      i   v  i iii     vv v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_136470045_   2218 TCAATAGCAAGAAAACAA----CCAAATTGAAAGTAAGGCAAAGGACCCA 2263
                               ii  i  i    ----  v    ?   ivvi         iiii
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_136470045_   2264 AATAGACATTTCTCAAAAGAAGATATAAAAATGGCCAACAGGTATATGAA 2313
                                       v            v          i i i i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_136470045_   2314 AAAAAAAAGCTCAACATAACTAATTAT 2340
                           i v---         v ????????
  L1M4_orf2#LINE/    885 AAGAT---GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (131 / 72)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.06 (37 / 18)  


 794 25.70 4.21 0.00  chrX_136479297_136485689      220   433 (5960)    L1M4_orf2#LINE/L1      309   531 (377)  

  chrX_136479297_    220 AATAGAGATTTCAGAAATAAGACCACACATCTACAACCACCTGATCTTCC 269
                            v    v i         iv   i    i  iiii  vi    i   v
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_136479297_    270 ACAAACCTGACAAAAACAAGCAATGGGGAAAATATTTCCTACTTAATAAA 319
                             ivv  v   i v  vv           iv  vvi  vi i  i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_136479297_    320 TGGTACTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAACTGGACCC 369
                             i      v      v  ?   i     i  i v    ii       
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_136479297_    370 CTGCTT---------TACCGAAATTAACTCAAGATGTATTAAAGACGTAA 410
                           i i ---------   vi            i   v  i ?    v   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_136479297_    411 ATGTAAAACCCAAAACCATAAAA 433
                               i v i     i      
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAA 531

Transitions / transversions = 1.41 (31 / 22)
Gap_init rate = 0.00 (1 / 223), avg. gap size = 9.00 (9 / 1)  

3263 26.43 0.55 0.55  chrX_136479297_136485689     4993  5900 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136479297_   4993 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5042
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136479297_   5043 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGA 5092
                            v     v     iv i  i  i        i  v     i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136479297_   5093 TACCAA-TGACTTTCTT-CAGAGAATTGGAAAAAACT-ACTTTAAAGTTC 5139
                          v   i-  v    i  -    -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_136479297_   5140 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5189
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_136479297_   5190 GAACAAAGCCGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5239
                                 ii     vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_136479297_   5240 CTACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5289
                                  i   ii   ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_136479297_   5290 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAAC 5337
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_136479297_   5338 TATCTGATCTTTGACAAACCTGAGAAAAACAAACAATGGGGAAAGGATTC 5387
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_136479297_   5388 CCTATTTAATAAATGGTGCAGTGAAAACTGGCTAGCCATATGTAGAAAGC 5437
                         i  v  i  i         v v  v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_136479297_   5438 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5487
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_136479297_   5488 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5537
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_136479297_   5538 CCTAGGCATTACCATTCAGGACATAGGCATGAGCAAGGACTTCATGTCTA 5587
                          v    ?i v viv   iv   v v  vv ii    v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_136479297_   5588 AAACACCAAAAGCAATGGCAACAAAAGACGAAATTGACAAATGGGGTCTA 5637
                         vi            vvi           vi    v  i    v  iii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_136479297_   5638 ATTAAACTAAAGAACTTCTGCACAGCAAAACAAACTACCATCAGAGTGAA 5687
                           i   v v  i     i  ii vv    iv v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_136479297_   5688 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5737
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_136479297_   5738 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5787
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_136479297_   5788 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5837
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_136479297_   5838 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAC 5887
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_136479297_   5888 CATCACTGGCCAT 5900
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3199 24.89 1.37 1.94  chrX_136520566_136524191.rev     2260  3135 (491)    L1M4_orf2#LINE/L1       38   908 (0)  

  chrX_136520566_   2260 ATATTGTTATAATAACCACATTCTCTAAAGCAACCTATAGATTCAATGCA 2309
                                  vi  ii v i i  i i   vii i   i        i   
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chrX_136520566_   2310 TTCCCTAAGAAAATACTGAG--ACATTCTTCACAGAAATAGAATAAAAAA 2357
                         v      vv     v i-  --i v  i  ii       v  vv ivvi 
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCC-AGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chrX_136520566_   2358 TCCTAAAATGTATATGGAACCACAAAAGACTCCAAATAGCTCAAGAAATA 2407
                                  vi        vii   ii   i vi      iv  iv   -
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT- 185

  chrX_136520566_   2408 CTTACCAAA-AAGAATAAAGCTGGAAGCATCACACTCACTACCCAACTTC 2456
                            ivv   -     i    i    i vv       i----     i   
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT----CCCAATTTC 231

  chrX_136520566_   2457 AAAATATACTACAAGGCTATAGCAACCAAAACAGCATGGTATTGGTATAA 2506
                             iv        i    i  i  i   i    ii     i   i    
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chrX_136520566_   2507 AAATATACACATCAACCTATGGCACATATTATAGAACCGATAAATAAATT 2556
                         ii   v   i  vi i v    v i v v vv   ii v v       ii
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_136520566_   2557 CATGTGTTTACAACTAA--GATTTTTGACAAAGGCATCAAAATCATATG- 2603
                            iii    iiiii  --      i     i  iii   i i   vii-
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_136520566_   2604 TGGGGAATGGAGACCCTCTTCAATAAATGGTGCTGGGAAAACTGGATATC 2653
                                v i v vi  i     i              v         ? 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_136520566_   2654 TGTGTGCAGAAGAATTAAACTGGACCTCTATCTCTCATTATATACAAAAA 2703
                         iiii    i      v  ii      i   i   v  ii           
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_136520566_   2704 TCAACCCAAGATGGATTAAAGACTTAAACATAAAACCTGAAACTATAAAA 2753
                          i   i   i      i ?    i    ii   i v  i           
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_136520566_   2754 CTACCAAAAGAAAACACAGAAG-AAATACTTCAGGACATTGGTCTAGGCA 2802
                           vii i         i  i? -    -    iv   v    vi      
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCA 580

  chrX_136520566_   2803 AAGATTT--TACGGCTGACTTCAAAAGCACAGGCAACAAAAACAAAAATA 2850
                          v i   --  vivv    vi          i         iv       
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_136520566_   2851 GACAAATGGGACTATACTAAACTAAAAAGCTTCTGTGCAGTAAAGGAAAC 2900
                           i    v     vi ii   v v    i   i     vvi      v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_136520566_   2901 AGTCAACAGAGTGAAGAGACAACCTGTTAAATGGAAGAAAATATTTGCAA 2950
                         vi    v i      i        iiivi     i               
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_136520566_   2951 ACGATTCATCTGACAAGGAACTAATATCTAGAAGATACAGGGAACTCAAA 3000
                          iv  vi      i    i   vi    i    v   i ii      vv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_136520566_   3001 CAACTCAACAGCAAAAAAAAAAAAAAAAACAAATAATTCCATTAAAAAGT 3050
                                 i ---------- v     i        ii v   ?    i 
  L1M4_orf2#LINE/    781 CAACTCAATA----------ATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_136520566_   3051 GGGTAAAGGATCTCAATAGACATTTCTC---AGAAGATATACAAATGGCC 3097
                            i       i v              ---                   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_136520566_   3098 AACACATATATGAAAAAATGCTCAACATCACTAATTAT 3135
                           i vii i       i             ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.01 (143 / 71)
Gap_init rate = 0.01 (12 / 871), avg. gap size = 2.42 (29 / 12)  


3057 26.83 1.33 0.67  chrX_136598921_136605891     5577  6478 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136598921_   5577 TGGAGAAACATTCCATGCTCATGAATAGGAAAAATCAATATTGTGAACAT 5626
                             i i i  i     i     i  v    i v i        v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136598921_   5627 GGCCATACTGCCCAAAGTAATTTAGAGATTCAATGCTATTCTCATCAAGC 5676
                            v     v      v i  i  v        i  v  i ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136598921_   5677 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5724
                          v   vivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_136598921_   5725 TATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAACCCAAAAA 5774
                                viiv  ii  v  v v        i      i i vvv i  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_136598921_   5775 AACAAAGCTGGAGGCATCATGCTACCTGATTTCAAACTATACTA--AGGC 5822
                                i      vv   ii  v  ii        viv     -- i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_136598921_   5823 TACAGTAACCAAAACAGCATGGTACTGGTACCATAACAGAGATATAGACC 5872
                                 i   i    ii         i iv vi i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_136598921_   5873 AATGGGGTAGAACAGAGGCCTCAGAAATAACACCACACATCTACATCCAT 5922
                              ii     iv   ivii         vv   i    i  iivi  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_136598921_   5923 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTGCCT 5972
                         i    i  i     ivv  v   i v  vv            i  v i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_136598921_   5973 ATTTAATAAAGGGTGTTGGGAAAACTGGCTAGCCGTATGCAGAAAACTGA 6022
                         v  i  i   v    i     v      v  ?  ii     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_136598921_   6023 AACTGGAACCCTTCCTTACAACTTATACAAAAATTAACTCAAGATGAATT 6072
                          ii    v    v   i   v v                   i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_136598921_   6073 AAAGACTTAAACGTAATACCTAAAACCGTAAAAGCCCTAAAAGAAAACCT 6122
                          ?    i    i    v v       ii     vi i  i        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_136598921_   6123 AGGCA-ATACCATTCAGGACATAAGCATGGGCACAGACTTCATGACTAAA 6171
                            ?i- v i -   iv   v vi vv i    vv ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_136598921_   6172 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGGATCTAGT 6221
                                     vvi          vv     v  i    v   ii vi 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_136598921_   6222 TAAA-TTAAAGAGCTTCTGCACAGTAAAAGACACTATCATCAGACTGAAC 6270
                         i   -     i -   i  ii vvi   i          vv i v    v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_136598921_   6271 AGGCAACCTACAGAATGGGAGCAAATTTTTGCAA-TC---CATCTGACAA 6316
                           i     i            v    v       -  ---i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_136598921_   6317 AGGGCTAATATCCAGAATCTACAAGGAACTTAAAAAATTTGCAAGAA--A 6364
                         i  i  vi          v  i  i     ivv v  i --   v  -- 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--CAATAATAA 794

  chrX_136598921_   6365 AAAAACAAACAACCTCATCAAAAAGTGGGCAAAGGATATCAACAGTCACT 6414
                            i     i    iv  i?    i            v v  i  v  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_136598921_   6415 TAGCAAAAGAAGACATTTATGTGGCCAGGAAACATATGAAGAAAAGCTCA 6464
                          vv v        i  vi vi      iv  i  i     i i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_136598921_   6465 TCATCACTGGTTAT 6478
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.50 (18 / 12)  


 310 26.98 12.70 0.79  chrX_136639858_136644434.rev     2877  3002 (1575)    L1M4_orf2#LINE/L1        1   141 (767)  

  chrX_136639858_   2877 TAGAAACACATCCCATGCTCACGGATGGGTATAATCAGTATTGTGAAAA- 2925
                          i    v i        i   i    v  v v v i i      v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136639858_   2926 AGCAATA---------------TACAAATTCAATGCAATTCCCATGAAAA 2960
                         i      ---------------    i      i     i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136639858_   2961 CACCACCTTCATTCTTCACAGAACTAGAAAAAAACAATCCTA 3002
                         iv   v  v v  i  ii     v v  v  -ivii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTA 141

Transitions / transversions = 1.27 (19 / 15)
Gap_init rate = 0.02 (3 / 141), avg. gap size = 5.67 (17 / 3)  

2736 26.72 0.26 0.00  chrX_136639858_136644434.rev     3316  4086 (491)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_136639858_   3316 ATCCTAAAATTTATATGGAACCAAAAAAGAGCCTGCATAGCCAAAGCAAG 3365
                                    i        viiv  ii  v  v v         i   v
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_136639858_   3366 ACTAAGCAAAAAGAACAAATCTAGAGGCATCACATTACCTGACTTCAAAC 3415
                         vi i iv  i         vi i    vv     i v  ii i      v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_136639858_   3416 TATACTACAAGTACATAATCATCAAAACAGCATGGTTCTGGTATAAAAAT 3465
                         iv        ivvi i i v     i    ii    v    i    ii  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_136639858_   3466 AGGCACATAGACCAATGGAACAGAATAGAGAACCCAGAAACAAAGCCATA 3515
                           i  i     i        i     v    ii       i   v     
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_136639858_   3516 TACTTACAGCCAACTGTTCTTCAACAAAGCAAACAAAAACATAAACTGGG 3565
                         i i   ii i   i  v i   i    i vviv   i v   vv v    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_136639858_   3566 GAAAGA-TACCATATTCAACTAATGGTGTTGGGATAACTGGCAAGCCACA 3614
                               -  viv v      v       i     i      vv ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_136639858_   3615 TGTAGAAGAATGAAACTGGATCCTCATCTCTCACCTTAAACAAAAATCAA 3664
                           i i         ii    i  ii i   v    v  v        i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_136639858_   3665 CTCAGGATGGATCTGAGACTTAAAGCTAAGACCTGAAACCATAAAGATTC 3714
                             ii       v?    i    vv     v  i    i     iv ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_136639858_   3715 TAGAAGATAACATCAGAAAAACCCTTTTAGACATTGGCTTAGGCAAAGAC 3764
                                v     vi ?iv  vi   ivv   v    v        v ii
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_136639858_   3765 TTTGTGACCAAGAACCCAAAAGCAAATGCAACAAAAACAAAGGTGAATAG 3814
                           iv iivi v  vv         v v         iv   ii ii   i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_136639858_   3815 ATGGGACTTAATTAAACTAAAAAGCTTCTGCATAGCAAAAGAAATAATCA 3864
                           v      v  i   v v    i   i  iiivv    i  v iv    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_136639858_   3865 GCAGAGTTAACAGACAACCCACAGAGTGGGAGAAAGTCTTCACAACCTAT 3914
                         iv i   v  v              i         i v  ii   vii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_136639858_   3915 ACATCCAACAAAGGACTAATGTCCAGAATCTACAAAGAACTCAAACAAAT 3964
                          i   ii i  i     vi i        v  i         vv    v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_136639858_   3965 CAGCAAGAAAAATA-AAACAATCCCATCAAAAAGTGCGCTAAGGACATGA 4013
                           ii  v     v -   i  i  v  i?    i  v  v     iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_136639858_   4014 ATAGACAATTCTCAAAAGAAGATATACAAATGGCCAACAAGCATATGGAA 4063
                                v     v                       i     i   i  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_136639858_   4064 AAATGCTCAGCATCACTAATGAT 4086
                          i       i     ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (117 / 85)
Gap_init rate = 0.00 (2 / 773), avg. gap size = 1.00 (2 / 2)  


2784 25.72 1.07 3.75  chrX_136742772_136745005      809  1741 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136742772_    809 TGGAAA--CATCCCATGCTCAGGGGTGGGTAGAAACAATATTGTGAAAAT 856
                               --i        i   v  i v  v   vvi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136742772_    857 GACCATACTGCCAAAAGCAATTTTCAAATTCAATGCAATTTCCATCAAAA 906
                          i v     v  v   vii  i v  i      i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136742772_    907 TACCACCATCATTCTTCACAGAACTAGAAAAAAACATCCAAAAATTCATA 956
                          v   v vv v  i  ii     v v  v  ivvv    v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_136742772_    957 AGAAACCAAAAAAGAGCCTGCATAGC-AAAGCAAGACTAAGCAAAAAGAA 1005
                         v i  viiv  ii  v  v v     -   i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_136742772_   1006 -AAAATTGAGAGACATCACATTACCTGACTTCAAACTATACTATAAGGCC 1054
                         -   i   iii   -     i v  ii i      viv     i  i  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_136742772_   1055 ATAGTCATCAAAACAACATGGTACTGGTATAAAAATAAGCACATAGACCG 1104
                          i   v     i   iii         i    ii   ii  i     i i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_136742772_   1105 ATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAGCCAAC 1154
                               i     v    ii           v   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_136742772_   1155 TGATCTTTGACAAAGCAGACAAAAACATAAAGTGAGGAAAGGACAGTCTA 1204
                             i  i     i vv v   i v   vv i  i      i i     v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_136742772_   1205 TTCAACATATGGTGCTGGGGTAATTGGCAAACCACATGTAGAATAATGAA 1254
                                v           ii  i   vv ?       i i  v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_136742772_   1255 ACTGGATCCTCATCTCTTACCTTATACAAAAATCAACTCAAGATGGATCA 1304
                         ii    i  ii i   vi   v           i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_136742772_   1305 AAGACTTAAACCTTATACCTGAAATGATAAAGATTCTACAAGATAACATA 1354
                         ?    i    iv v v v  i   iv     iv ii  v    v      
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_136742772_   1355 GGAAGAACCCTTCTAGACATTGGCTTAGGCAAAGACTTTATGACCAAGAA 1404
                           ?iv  vi    vv   v    v        v ii  iv iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_136742772_   1405 CCCAAAAGCAAATGCAACAAAAACAAAGGTAAATAGATGGGACTTAATTA 1454
                         v         v v         iv   ii  i   i  v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_136742772_   1455 AACTAAAAAGCTTCTTCACAGCAAAAGAAACAATCTTAAACTAAAAAGCT 1504
                           v v    i   i vii vv    i  v  v   -------  i  ---
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATC-------AAGAA--- 689

  chrX_136742772_   1505 TCTTCACAGCAAAAGAAACAATCAGCAGTGCTAACAACCCACAGGTAGGG 1554
                         -------  ii   ------------  -----           ivv   
  L1M4_orf2#LINE/    690 -------AGTGAAA------------AG-----ACAACCCACAGAATGGG 715

  chrX_136742772_   1555 AGAAAATCTTTGCAATCTATATATCTGACAAAGGACTAATATCTAGAATC 1604
                                v       vii          i  i     vi    i     v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_136742772_   1605 TACAAGGAACTCAAACAAGTGAGCAAGAAAAAAACAA----CCCCATCAA 1650
                           i  i      vv    v v ii  v     i    ----   v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_136742772_   1651 AAAGTGACCTACGTACACGAATAGACAATTCTCAAAAGAAGATATACAAA 1700
                            i  iv v v v ivi         v     v                
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_136742772_   1701 TGGCCAACAA--ACATGAAAAAATGCTCAATATCACTAATGAC 1741
                                i  --         i        i    ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (133 / 103)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 4.50 (45 / 10)  


3078 25.32 5.46 0.23  chrX_136759195_136763344.rev     1059  1919 (2231)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_136759195_   1059 GAAAGATATTCCATGTTCATGGATTGCAAGATTTAATATTGTTAAAATAT 1108
                                  i                v    i             i  iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_136759195_   1109 CCATACCACCCAAAGCAATCTATAGATGCAATGCAATCCCTATGAAAATG 1158
                          v    iv      vii     i    v   i           v     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_136759195_   1159 CCAA-------TTTCACAGAAATAGAAAAAACAATCCTGAAATTTACATG 1201
                            i-------   ii       v  v  ivii     i     i i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_136759195_   1202 AAACCACAAAAGTCCCAGAATAGCCAAGGCTATCATACACAAGAAGAATA 1251
                         i  vii   ii v              ii v   v iv v        i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_136759195_   1252 AAACTGGAGGAATTACATTACTTGATTTCAAATTATACTACAGAGTGATT 1301
                           ii       v i   i v iii        viv       i  iv iv
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_136759195_   1302 GTAACCAAAAAAGCATGTTACTGGCATAAAAACAGAGACTTAGACCAATG 1351
                             i   i v  ii  v           ii i   v iv    i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_136759195_   1352 GAACGGAATAGAGAACACAGAAACAAATCCGCTCACCTACAGTGAACTCA 1401
                            ii    v    iiv      i   i  iiv  ii  ii  v  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_136759195_   1402 TTTTCGACAAAGGCGCCAA------------------------------- 1420
                                   i  i     -------------------------------
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_136759195_   1421 --TAAATGGTACTGGAAATACTTAATATCCATATGCAGCAGAATAAAACT 1468
                         --i       i    i vv   vi   ?   i     iv     i  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_136759195_   1469 AGACTCCTGTCTCTTGTCATATACAAAAATCAAATCAAAAT-----AAAG 1513
                         i   i   ii   viii             i  v       ----- ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_136759195_   1514 AATTAAATCTAAGATCTCAAAATATAAAACTACTACAA-AAAACACTGGG 1562
                          vi     v     v  v   v         vi  v  -      iv  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_136759195_   1563 GAAGCTCTCCAGGACATCAGTCTGGGCAAAAATTTCTTGAGTAATACCCC 1612
                          v iv   i iv   v ii vi i     vii      iii  vv  v  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_136759195_   1613 ACAAACACAGGCAACCAACGCAAAAATGGACAAATGGGATCATATCAAG- 1661
                          v  i    i     v  v v      i  i    v   iivi     i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_136759195_   1662 TTAAAAAGTTTTAGCACAACAAAGGAAGCAATCAACAAAGTGAAGAGGCA 1711
                                v    - ii vv       vi v     v        i  i  
  L1M4_orf2#LINE/    653 TTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_136759195_   1712 ATCCACAGAACAGAAGAAAATATTTGCAAACTACTCATCTGACAAAGGCT 1761
                          i        ii i                ii ivi      i  i  vi
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_136759195_   1762 TAATAACCAGAATATATAAAGATCTCAAACAACTCTATAGGAAAGAAAAC 1811
                          vi  v                v   vv       v   iv   -  i  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGAC 800

  chrX_136759195_   1812 TAATAATCTGATTAAAAAGTAGGCAAAAGATTTGAATAGACATTTCTCAA 1861
                         v     i ii   ?    i i      i                    v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_136759195_   1862 AAGAAGACATACAAATTGCAAACAGGCATATGAATAGGTGTTCAACATCA 1911
                                i        v  v  i i   i     v  i  i         
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_136759195_   1912 CTGATCAT 1919
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.64 (133 / 81)
Gap_init rate = 0.01 (7 / 906), avg. gap size = 7.00 (49 / 7)  

2904 25.85 0.76 0.25  chrX_136759195_136763344.rev     2872  3664 (486)    L1M4_orf2#LINE/L1      112   908 (0)  

  chrX_136759195_   2872 TTTTTCACAGAAATAGAAAAAC-AATCCTGAAATGTATACAGAACCACAA 2920
                              ii       v  v  i -i     i    vi   ii   vii   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_136759195_   2921 AAGACCCAGGATAGCCAAAGCTTTATTGAGCAAAAAGAATGAAACTGGAG 2970
                         ii       i         i vv v    iv  i     ii  ii     
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_136759195_   2971 AAATCACATTACCTCATTTTAAATTATACCATACAGCTATAGTAACAAAA 3020
                         i v     i v  iv    i   viv   i i v     i     iv  i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_136759195_   3021 ACAACATGAGGCTGGCATAAAAACAGACATATAGGCCAACGGAACAGAAT 3070
                            iii  ivi         ii i          ii   i    i     
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_136759195_   3071 AGAGAACCCAGAACCAAATCCACACATCTACAGTGAACTCATTTTTTACA 3120
                         v    ii      vi   i   i    i  ii  v  i v     iv   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_136759195_   3121 AAAGTGCCAAGAACATACATTGGAAAAAGTATAGTCTCTTCAATGAATTG 3170
                          ii         v   v  v   ii    v       i     ii   v 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_136759195_   3171 TGCTGGGAAAACTGGATATCCATATGCATAAGAATGAACCCTG-CCCCCA 3219
                                 v         ?   i     v         viiv -    i 
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_136759195_   3220 TCTCTTGCCATATAAAAAACTCAAATCAAAATGGATTACAGAATTAAATT 3269
                         i   vii       v    v i  v           i ?   vi     v
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_136759195_   3270 TAAGACCTCAAACTATGAAACTATTACAAGAAAACATTGGGGAAACTCTC 3319
                              v  v       i     v   v          v  ? v  v   i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_136759195_   3320 CAGGACATTGGTCTGGGCAAAAATTTATTGGGTAATAGC-CCACAAGCAC 3368
                          iv   v    vi i     vii   v  i i  - ii -   v      
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGACACCAAAAGCAC 610

  chrX_136759195_   3369 AGGCAACCATAGCAAAAATTGACAAAACAGATCACATCAAGGTAAAAAGC 3418
                          i     v v  v      v  i   vii  iiv      ii v    i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_136759195_   3419 ATCTGCACAGCAAAGGATACAATCAACAAAGTGAAGAGACAACTGACAGA 3468
                         v i  ii vv       i  v     v        i       iv     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_136759195_   3469 ATGGAAGAAGATATTTGCAAACTACCCATCAGACAGGGGATTAATAACCA 3518
                             i    i           ii ivi   v  i i    i vi  v   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_136759195_   3519 GAATATATTAGGAGCTCAAACAGCTCTATAGGAAATAAATCTAATAATCC 3568
                                 v i  i   vv   i   v   iv   -  iv v     i  
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAAATAACCC 809

  chrX_136759195_   3569 AATT-AAAAATGGATAAAAGAACTGAATAGGCATTTTTCAAAAGAAGACA 3617
                             -        ii   i  vi       i     i  v        i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_136759195_   3618 TACAAATGGCAAGCAGGGATACAAAAAAATGCTC--CATCAAAAAGCTA 3664
                                   v ii i v i ii    i      --     ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (125 / 77)
Gap_init rate = 0.01 (7 / 797), avg. gap size = 1.14 (8 / 7)  


3026 27.94 0.55 0.66  chrX_136766866_136773261     4995  5903 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136766866_   4995 TAGAATTACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5044
                          i   vv i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136766866_   5045 GGCCACACTGCCCAAGGTAATTTATAGATTCAATGCCATGCCCATCAAGC 5094
                            v i   v     iv i  i  i        i  v  v  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136766866_   5095 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5142
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_136766866_   5143 TATGGAACCAAAAAAGAGCCCGCATGGCCAAGACAATCCTAAGCCAAAAG 5192
                                viiv  ii  v  v v  i     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_136766866_   5193 AACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTACAAGGC 5242
                                i     ivv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_136766866_   5243 TACAGTAAAGAAAACAGCACAGTACTGGTAACAAAACAGAGGTAGAGACC 5292
                                 vv  i    iiii       i vv ii i   vi  v   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_136766866_   5293 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACATATCTACAACC 5340
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_136766866_   5341 ATCTGATGTTTGACAAGCCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5390
                          vi    v  i      vv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_136766866_   5391 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTATATGTAGAAAGCT 5440
                           v  i  i              v      v  ? i i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_136766866_   5441 GAAACTGCATCCCTTCCTTCCACCTTATACAAAAATTAATTCAAGATAGA 5490
                            ii  v i    v   iv    v              i    i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_136766866_   5491 TTAAAGACTTAAATCTTAGATGTAAAACCATAAAAACCCTAGAAGAAAAC 5540
                          i ?    i     v v   vv      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_136766866_   5541 CGAGGCA-ATACCATTCAGGACACAGGCATGGGAAAGGACTTTATGACTA 5589
                         vv   ?i- v i -   iv   viv  vv i  v  v ii  iv iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_136766866_   5590 AAACACCAAAAGCAATGGCAACAAAATCCAAAATAGACAAATGGGATCTA 5639
                         vi            vvi         vvv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_136766866_   5640 ATTAAACTAAAGAGCTTCTGCGCAGCAAAAGAAAGTACCATCAGAGTGAA 5689
                           i   v v  i i   i  i  vv    i  v v  i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_136766866_   5690 CAGGCAACCTACAGAATGGGTGAAAATTTTTGCAATCTACCCATCTGACA 5739
                         v  i     i          v      v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_136766866_   5740 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5789
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_136766866_   5790 AAAACCAAACAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACGCT 5839
                           i  -   i   i v  i?    i            v    i    ii 
  L1M4_orf2#LINE/    796 AAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_136766866_   5840 TTTCAAAAGAAGACATTTATGCAGCCAACAGACACATGTAAAAATGCTCA 5889
                          i  v        i  vi viii     i ii      v   i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_136766866_   5890 TCATCACTGGTCAT 5903
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (146 / 104)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3359 25.83 0.66 0.44  chrX_136778163_136784557     4997  5902 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136778163_   4997 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAACATTGTGAAAAT 5046
                              ii i  i     i        v      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136778163_   5047 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136778163_   5097 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5143
                          v   -   v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_136778163_   5144 ATATGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAACCAAAAA 5193
                                 viiv  ii  v  v v        i      i i vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_136778163_   5194 CAATAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5243
                         v  i    i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_136778163_   5244 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGGTAGAGAC 5293
                                  i   i    ii         i iv ii i   vi  v   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_136778163_   5294 CAATGGAACATAACAGAGGCCTCAGAAATAACACCACACATCTACAACCA 5343
                                 i v  iv   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_136778163_   5344 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGATTCCC 5393
                         vi    i  i     ivv  v   i v  vv     i      i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_136778163_   5394 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGACATATGTAGAAAGCTG 5443
                          v  i  i              v      v  ?v  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_136778163_   5444 ATACTGGATCCCTTCCTTACACTTTATACAAAAATTAACTCAAGATGGAT 5493
                          vii    i    v   i    iv                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_136778163_   5494 TAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5543
                         i ?    i           v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_136778163_   5544 TAGGCA-ATACCATTCAGGACATAGGCGTAGGCAAAGACTTCATGACTAA 5592
                             ?i- v i -   iv   v v  vv       v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_136778163_   5593 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5642
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_136778163_   5643 TTAAA-CTAAAGACCTTTGCACAGCAAAAGAAACTCTCATCAGAGTGAAC 5691
                          i   -i    i  i    ii vv    i  v   v   vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_136778163_   5692 AGGCAACCTACAGAATGGGAGAACATTTTTGCAATCTATCCATCTGACAA 5741
                           i     i              v  v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_136778163_   5742 AGGGCTAATATCCAGAATCTACAAAGAAGTTAAACAACTTTACAAGAAAA 5791
                         i  i  vi          v  i      v ivv      iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_136778163_   5792 A-ACAAACAACCCCATCAAAAAGTGGGCAAAATATATGAACAGACACTTC 5840
                          -     i     v  i?    i        iv  v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_136778163_   5841 TCTAAAGAAGGTATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5890
                           i       i   vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_136778163_   5891 ATCACTGGCCAT 5902
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (137 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


2364 23.82 3.78 8.50  chrX_136835114_136840055     3497  4449 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136835114_   3497 TGAAAAAATATTCCATGCTTATGGATTAGAAGAATCAATATTATTAAAAT 3546
                           i   i    i     i i       i     v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136835114_   3547 GTCCATACTGCCCAAAGCAATCTACAGATTCAGTGCTATTTCTCTCAAAC 3596
                          v v     v      vii             ii  v  ii  v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136835114_   3597 TACCAAGGTCAGTTTTCATAGAATTAGAAAAAACCATTATAAAATT-ATA 3645
                          v   ivvv vv    iii    v v  v  iviv  iv       -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_136835114_   3646 TGGAACTAAAAAAGAGCCAGCATAGCCAGGGCAATCCTAAGGAAAAAAAA 3695
                              v iv  ii  v    v       iii     i i ------    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA------AAAA 194

  chrX_136835114_   3696 AAAAAAAAAAGCTAGAGA---CACA------GACTTCAAAGTATACTAGA 3736
                         i  i  v    i i   i---    ------i i      iiv     v 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_136835114_   3737 AGGC-AAAGTTAACCAAAACAACATGGTACTAGCACAAAAACAGACACAT 3785
                          i  - v   -  i   i   iii       i   i  ii i     i  
  L1M4_orf2#LINE/    245 AAGCTACAGT-AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_136835114_   3786 AGACCAATGGAACAGAATAGAAA-CCCAGAAATAAAGCTTCACAACTACA 3834
                            i        i     v  i -i           v ivi   vi  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_136835114_   3835 ACCATTTGATCTTTGACAAAGTCGACAAAAATAAGCAATGGAGAAAGGAT 3884
                         ii  v     i  i     i vi v   i vi vv      i     i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_136835114_   3885 ACCCTATTCCATAAATAGTGCTGGGATAAACTGGCTAGCACTATGCGGAA 3934
                          vi  v   v i    i         i  -    v  ? vvi    ii  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAA 442

  chrX_136835114_   3935 GAATAAAACTGGACTCCTACCTTTCACCATATACAAATATTAACTCAATG 3984
                             i  ii     i       iv             v          vi
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_136835114_   3985 TAGATCAAAGACC------------CCAAA-CTATAAAAATCCTGGAAGA 4021
                          i     ?     ------------ i   -        v  i i     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_136835114_   4022 AAACTTAAG---AAATACACTTCTTGGCATTGGGCTTGGCAAAGAATTTA 4068
                             v  i ---    ---    v  i v     i v     v i-   v
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGG-TTTC 588

  chrX_136835114_   4069 TTTTGTAATAAATATTATTACAAAATACAATATTTATATTATATTTTTAA 4118
                           ------- i    v ivv     -------------------------
  L1M4_orf2#LINE/    589 TT-------AGATATGACACCAAAA------------------------- 606

  chrX_136835114_   4119 TATAATATAATTGCATATAATATATATATAATCAAAATTAATTGCAACAA 4168
                         ------------   -----------------   --------       
  L1M4_orf2#LINE/    607 ------------GCA-----------------CAA--------GCAACAA 619

  chrX_136835114_   4169 AAACAAAAATTGACAAGTTGGACCTAATTAAACTAAAGAGCTTCTTCACA 4218
                           iv      v  i  i      i v  i   v v  i i   i vii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_136835114_   4219 GCAAAAGAAACTCCCAACAGAGTAAA----CAACCTACAGAATGGCAGGA 4264
                         v    i  v   vi   v i   i  ----     i         v  i 
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_136835114_   4265 AATATTTACAAACTATGCATCCAACAAAGGTCTAACATCCAGAACCTATA 4314
                                i    ii  ii   ii i  i  v  vii        iv    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_136835114_   4315 ATAAAATTAAACAAATCAAGAAGCAAAAATCAAATAACTCCATTAAAAAT 4364
                          vi  v ivv    v    v  vv    iv        i v   ?    v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_136835114_   4365 TGGGCAAAGGAC----ATGGAAACTTCTCAAAAGAAGACATATGAACAGC 4410
                                    i----  i  v i     v        i   ii  ii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_136835114_   4411 CAATAAACATATCAAAAAATACTCATCATCATGAATCAT 4449
                               i  i  v    i  i    v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (137 / 87)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 6.16 (117 / 19)  


3036 26.87 1.10 1.10  chrX_136880618_136886988     4972  5879 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136880618_   4972 TGGAAGAACATTTCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5021
                              ii i  ii    i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136880618_   5022 GGCCATACTGCCCAAGGTAAC--ATAGGTTCAATGCCATCCCCATCAAGC 5069
                            v     v     iv i i-- i  i     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136880618_   5070 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTGTAAAGTTCA 5117
                          v   iivi i  i  ii     -   -- v  i  - iiv    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_136880618_   5118 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCAAAGCCAAAAG 5167
                                viiv  ii  v  v v  v     i      ivi ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_136880618_   5168 AACAAATCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5217
                               vi      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_136880618_   5218 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5267
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_136880618_   5268 AATGGAACAGAATAGAGCCCCCAGAAATAATACCACACATCTACAA-CGA 5316
                                i     v   vvi          vv   i    i  iii- i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_136880618_   5317 TCTGATCTTCGACAAACCTGACAAAAACAAGAAATGGGGAAACGATTCCC 5366
                          -    i        ivv  v   i v  vvv          vi  vvi 
  L1M4_orf2#LINE/    349 T-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_136880618_   5367 TATTTAATAAATAGTGCTGGGAAAACTGCCTAGCCATATGTAGAAAGCTG 5416
                          v  i  i    i         v     vv  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_136880618_   5417 AAACTGGATCCCTTCCTTACACCTTATGCAAAAATTAATTCAAGATGGAT 5466
                           ii    i    v   i     v   i          i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_136880618_   5467 TAAAGACTTAAATGTTAGACCTAAAACCATTAAAACCCT-AGAAGAAAAC 5515
                         i ?    i       v   v       i  -     i  -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAAC 546

  chrX_136880618_   5516 TTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5564
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_136880618_   5565 AAACACCAAAAGCAATGGCAACAAAATCCAAAATTGACAAATGGGATCTA 5614
                         vi            vvi         vvv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_136880618_   5615 ATTAACCTAAAGAGCTTCTGCACAGCAAAAAAAAAAGTACCGTCAG---A 5661
                           i  vv v  i i   i  ii vv    ii -----i  ii   i--- 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-----CACTATCAAGAAA 690

  chrX_136880618_   5662 GTGAACAGGCAGCCTACAGAATGGGAAAAAATTTTTGCAATCTACCCATC 5711
                              v  i  i  i           i     v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_136880618_   5712 TGACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACA 5761
                            i  i  i  vi          v  i        ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_136880618_   5762 AGAAAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGA 5811
                          v     iv    i     v  i?    i            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_136880618_   5812 CACTTTTCAAAAGAAGACATTTATGCATCCCACAGACACATGAAAAAATG 5861
                           i  i  v        i  vi viiiv  v i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_136880618_   5862 CTCATCATCCCTGGCCAT 5879
                             v    v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


 898 18.45 5.83 0.00  chrX_136892855_136899857      291   496 (6507)    L1M4_orf2#LINE/L1      116   333 (575)  

  chrX_136892855_    291 TTGCAGAAATGGGCAAGCTGATTAAAAAATTTCTATGAAAATTCAAGGAA 340
                                   v i         ivv      iv    i    v     i 
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_136892855_    341 ATTAGAATAGCCAAA-TAATCTTCAAAA-GAA--------TTGGAAGATT 380
                         vii            -i      v    -   --------     i  i 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_136892855_    381 -ACACTTTCCAATTTCAAAACTTACTACAAAAA-ACAAAAATCAAAATAG 428
                         -      i                       iv-   iv      i i  
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_136892855_    429 TGTGGTATTGGCCTAAGGATATATGTATATATCTGTGGAATAGAATAGAT 478
                                i    v        v ii    v   vi           v  v
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_136892855_    479 AGTTCAGACATAAAATCA 496
                            i    v     vi  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCA 333

Transitions / transversions = 1.24 (21 / 17)
Gap_init rate = 0.02 (5 / 218), avg. gap size = 2.40 (12 / 5)  

 694 18.37 4.76 1.36  chrX_136892855_136899857      500   646 (6357)    L1M4_orf2#LINE/L1      250   401 (507)  

  chrX_136892855_    500 ACAAAAATCAAAATAGCGTGGTATTGGCCTAAGGATAAACATATATATCT 549
                            iv      i i  i      i    v        i       v   v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_136892855_    550 GTGGAATAGAATAGATAGTTCAGACATAAACCC-------TATGGTCAAT 592
                         i           v  v   i    v        -------          
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_136892855_    593 TGATTCTTGACAAAGATACCAAGAAAATTTAATAATGAGAGAATGTAGTC 642
                              i i     i i i      vv   i   iiv  i     --    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT--AGTC 397

  chrX_136892855_    643 TTTT 646
                             
  L1M4_orf2#LINE/    398 TTTT 401

Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.01 (2 / 152), avg. gap size = 4.50 (9 / 2)  

1827 19.33 1.86 7.81  chrX_136892855_136899857      975  1512 (5491)    L1M4_orf2#LINE/L1      403   908 (0)  

  chrX_136892855_    975 AAGAAA-GGTGCTGAGACAACTACATAAGCATATGTAAAGGAACGAACTT 1023
                           v   -       i       iv   ?v  i   i   i   i   v  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_136892855_   1024 AATCCTCTACCTCACACCGTATACCAAAATCAACACAAATTAAATCAAAG 1073
                         iiv  i            i     v     i   v    v ii    ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_136892855_   1074 TTTCAAGTGTAAGAACTAATGCTATAAAACTCTTAGGATAAAACATAAGT 1123
                         viii  i       i    vi               i v        i ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_136892855_   1124 GTAAATATTTATGACCTAGAATTAGGCAACAGTTTCACAGACAAGACACC 1173
                               v  ii      v ii        ii     vi   i v      
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_136892855_   1174 TAAAGCAAAAGAAGCTACAGGAAAATAGAATTTTTTCTATTTTTTGATGA 1223
                         v      v   v i ------    -------------------------
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAAC------AAAA------------------------- 621

  chrX_136892855_   1224 ATGAAAAAAATGAATTCAAAAAACTGAATTTCATCAAAATTACAT-TTTT 1272
                         ---i       ii  -----   i  i i             v v-i   
  L1M4_orf2#LINE/    622 ---GAAAAAATAGAT-----AAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_136892855_   1273 TGTGGACCCAAGGATACTATAAACAAAGTGATAAGATATCTTGCAGAATG 1322
                             vvi v     i     v  v       v    i v iii       
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_136892855_   1323 TTAGCAATCATTTCCAAATTATATATCTGACAAGTATCTTTTATCAGGAA 1372
                         vv  v  vi    v     i          i   viv   v    vi   
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_136892855_   1373 TATATAAAGAACTCTTGATAACTGCACAATAAGAGAA-----AACCCAGC 1417
                                         - i    vv i     i ii -----      ii
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTT-ACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_136892855_   1418 TTAAAAATGGGCAAACAATTTGAATAAACATTTCTCCAAAGAAAATATAC 1467
                          ?             vi         i                i      
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_136892855_   1468 AAATGG--AAGCTAAGCACA-GCAAAAATGCTTAACATCATTAGCCAT 1512
                               --  --        - v   i     i       ????????
  L1M4_orf2#LINE/    863 AAATGGCCAA--TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (60 / 40)
Gap_init rate = 0.02 (10 / 506), avg. gap size = 5.20 (52 / 10)  

3152 25.66 1.11 0.66  chrX_136892855_136899857     5607  6510 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136892855_   5607 TAGAAAGACATCC-ATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 5655
                          i      i    -   i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136892855_   5656 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 5705
                          i v     v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136892855_   5706 TAC-AACCATCATTTTTCACAGAATTAGAAATAAC-AATCCTAAAAGTCA 5753
                          v - i iii -     ii     v v  v - i -i         v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chrX_136892855_   5754 -ATCCAAA---AAAGAGCCT-GCAC-GCCAAAGCAAGACTAAATAAGAAG 5797
                         -  vv   ---  i ii  i- v i-      i   vvi i  v      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_136892855_   5798 AACAAATCTGAAGGCATCACATTACCTGATTTCAAACTATACTATAAGGC 5847
                               vi  i   vv     i v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_136892855_   5848 CATAGTCATCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACC 5897
                         i i   v     i    ii         i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_136892855_   5898 AATGGAATGGAGTAGAGAACCCAGAAATAAACCCAAATACTTACAGCTAA 5947
                                 i  i v    ii               v i i   ii ii  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_136892855_   5948 CTTATCTTTGACAAAGCAAACAAAAACATAAAATAGAGAAAGGACACCCT 5997
                         i v  i  i     i vviv   i v   vv   i i     i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_136892855_   5998 ATTCAACAAATGGTGTTGGGATAATTGGCAAGCCACATGTGGGAGAATGA 6047
                         v              i     i  i   vv ?       iiii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_136892855_   6048 AACTGGATCCTCATCTCTCATCCTATATGAAAATCAACTCAAGATGGATC 6097
                          ii    i  ii i   v  i v    ii     i       i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_136892855_   6098 AAGGACTTAAATCTAAGACCTGAAACTATAAAAATTCTGGAAGATAATAT 6147
                          ?i   i     v     v  i           v ii i     v  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_136892855_   6148 TGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCAT-GATCAAG 6196
                         v  ?iv  vi    vv   v    v        v i    v -   - v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATG 597

  chrX_136892855_   6197 AAGCCAAAAGCAAATGCAATAAAAACAAACATAAACAGTTGGGACTTAAT 6246
                          vi         v v    i    iv   v   i i iv v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_136892855_   6247 GAAACTAAAGAGCTTTAGGACAGCAAAAGGAACAGTCAACAGAGTAAACA 6296
                         v   v v  i i    v vi vv    i iv  vi    v i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_136892855_   6297 GACAACTCAAAAAGTGGGAGAAAATCTTCACAATCTATACATCTCACAAA 6346
                               i  v i i           v  ii   vii   i    v i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_136892855_   6347 GGACTAATATCCAGAATCTACAATGAACTCAAACAAATTAGCAAGAAAAA 6396
                              vi          v  i  v      vv    v i ii  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_136892855_   6397 AAAAAACAACAATCCTATCAAAAAGTGGGCTTAGGACATGAATAGACAAT 6446
                         i v   i   ---  v  i?    i     vv    iv          v 
  L1M4_orf2#LINE/    798 GACAAATAAC---CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_136892855_   6447 TCTCAAAAGAAGATATACAAATGTCCAATAAACATATGACAAAATGTTCA 6496
                             v                  v       i  i    v  i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_136892855_   6497 ACATCACTAATTAT 6510
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (134 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.33 (16 / 12)  


1704 26.57 0.61 1.83  chrX_136909332_136918879        2   494 (9054)    L1M4_orf2#LINE/L1       45   531 (377)  

  chrX_136909332_      2 TAAAATGGACATACTGCCGAAAGCAATCTACAGATTCATTGTAATCTCTA 51
                            i    vv     v  v   vii             vi i    i   
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chrX_136909332_     52 TCAAAATACCAA-TGTTATTTTTCACAGAAATAGAAAAA-TAACCATACT 99
                                v   i-  ii-     ii       v  v  i- i i ---  
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATC---CT 140

  chrX_136909332_    100 AAAATTTATTTTGAACCAAAAAAGAGCCCAAAGATCCAAAGTAATTCTGA 149
                               i  v v   viiv  ii  v  vi  v v     ii   ii   
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_136909332_    150 GTAAAAAGAACAAATCTGGAGGCATTTCATTACATGACTTCAAAATATAT 199
                         iv  i         vi      vv iv  i v vii i       iv  i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_136909332_    200 TACAAGACTACAGTAAACAAAACAGCATGGTATTGGTGTATAAAATACAC 249
                              ii         v   i    ii     i   ii  - ii   v  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA-AGGATAGAC 289

  chrX_136909332_    250 ATGTAGAATAATGGTGCAAAATAAAGAACTCATAAATAAATCCACATACA 299
                           i    vi     vii i   vi   iii  v       i   --    
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACA 337

  chrX_136909332_    300 TGTTTATAGCAAACTGAGTTTTGA-AAAGGTGCTATGAACACACACTGGG 348
                          --    i iv  i   v   i  -  i     i v  v  iv  v    
  L1M4_orf2#LINE/    338 T--TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_136909332_    349 GAAAGAATACCCTCTTCACTACATGGTGCTGGGAAAATTAGATATCCATA 398
                                  vi  i    vi v            v  i i    ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_136909332_    399 AGTAGAAGAATGAAACTGGACTCCTACTTTTCACCGTATACAAAAATCAA 448
                         v i i         ii     i     i iv    i           i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_136909332_    449 ATTAAGATAGATTAAAGACCTAAAAATAAGACCTGAGACTATAAAA 494
                         v i  i  i   i ?         vi     v  i i         
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

Transitions / transversions = 1.80 (83 / 46)
Gap_init rate = 0.02 (8 / 487), avg. gap size = 1.50 (12 / 8)  

2964 27.36 1.56 0.56  chrX_136909332_136918879     2667  3565 (5983)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136909332_   2667 TGGAAACACATCCCATGCTCATGGATAAGAAGAATCAATATTTTGAAAAT 2716
                               v i        i        vi     v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136909332_   2717 GACCATACTGTTCAAAGCAATCTACAGATTCAATGCAATTCCTATCAAAA 2766
                          i v     vii    vii              i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136909332_   2767 CACCATCATCATTTTTCACAGAACTAGAAAAAT--ATCCGAAAATTCATA 2814
                         iv   v vv v     ii     v v  v  ii--    v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_136909332_   2815 TGGAA--GCAAAAAATAGCCTGATTAAGCAAAAGAAATCCTAAGCAAAAA 2862
                              --    iii i--  v  v  iv     v  -  i i iv  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAA-TCTTGAAAAAGAA 197

  chrX_136909332_   2863 GAACAAAGCTTGAGGCATCACATTACCTGTCTTTAAATTATACTACAAGT 2912
                                 i v    vv     i v  iivi  i   viv        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_136909332_   2913 CTATGGTAACCAAAAGAGCATGATACTGGTATAAAAATAAACACACAGAT 2962
                            ii    i   i v  ii  i      i    ii   i   i i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_136909332_   2963 AAACGGAACAGAGTAGAGAACCTAGAAATAAAGTCATGTACCTACAACCA 3012
                         v  i    i   i v    ii i         vi   ii ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_136909332_   3013 ACAGATCTCTGACAAAGTCAGCAAAAATATGCATTGGGAAGGTGGCATTC 3062
                          iv   i ii     i viiv   i vi  v  v    i iiviii v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_136909332_   3063 TATTCAATGAATGGTTCTGGGAAAACTGGATAGCCATCTGCAGAAGAATG 3112
                          v     ii      v      v         ?   iv    i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_136909332_   3113 AAACTGGATCCATACCTCTTACTATGCACAAAAATTAACTCAAGATAGAT 3162
                           ii    i  v      vi  i  ii                i  i   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_136909332_   3163 CACAGACCTAAGCATAATATCTGAGACTATTAAAATCCTAGAAGAAAACC 3212
                           ?        iii   v v  i i     v   v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_136909332_   3213 TAGGACAAACTTTTCTAGACATTGGCCCAGTCAAAGAGTTTATGACTAAG 3262
                             ?vv  v i   vv   v    vii  v   v iv  iv iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_136909332_   3263 ATCTCAAAAGCACAGAAAAATAAAACAAAAA-TAGACAAATGAGACTGTT 3311
                          ivi          - iv  i    v     -    i    vi    viv
  L1M4_orf2#LINE/    598 ACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_136909332_   3312 TTCAACTCGAAAGCTTCTGTACAGCAAAAGAAACAATCAACAGAGCAAAC 3361
                          iv  v ii   i   i   i vv    i  v  v     v i  ii  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_136909332_   3362 AGACAATGTACAGAATGGGA-AAAATATTTGCAA-TC-TATGCCCCAACA 3408
                               ivi           -             -  -   ii i-i i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT-GATA 745

  chrX_136909332_   3409 AAGGGCTAATATCCAGCATTTACATGGA--TCTCACAG---AA-GCTAAC 3452
                          i  i  vi       v  v  i vi  --   i   i---  -iv   v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_136909332_   3453 AAGAAAAAAGACCTAATTAAAAAGTGGACAAAGGGTATGAAAAGACATTT 3502
                             v   vi   i    ?    i   i      i v    v        
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_136909332_   3503 TTCAAAAGAAGACATACAAGTGGCCAGGAAACATATGAAAAAATGCTTAA 3552
                         i  v        i      i      iv  i  i       i     i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_136909332_   3553 TATCACTAGTCAT 3565
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (149 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  

3166 27.53 0.33 0.33  chrX_136909332_136918879     8148  9055 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136909332_   8148 TGGAATTACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 8197
                              vv i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_136909332_   8198 GGCCGTACTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 8247
                            vi    vi    iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_136909332_   8248 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTGTAAAGTTCA 8295
                          v   iivi i  i  ii     -   -- v  i  - iiv    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_136909332_   8296 TATGGAACCAAAAAAGAGCCCGCATGGCCAAGACAATCCTAATCCAAAAG 8345
                                viiv  ii  v  v v  i     i      i i vvv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_136909332_   8346 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 8395
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_136909332_   8396 TACAGTAACCAAAGCAGCATGGTACTGGTACCAAAACAGAGATATAGACC 8445
                                 i   ii   ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_136909332_   8446 AATGGAACAGAATAGAGCCCCCAGAAATAATACCACACATCTACAACCAT 8495
                                i     v   vvi          vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_136909332_   8496 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAATGATTCCCT 8545
                         i    i  i     ivv  v   i v  vvv          vi  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_136909332_   8546 ATTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGAAGAAAGTTGA 8595
                         v  i  i     i        v      v  ?   i   v i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_136909332_   8596 AACTGGATCCCTTACTTACACCTTATACCTAAATTAATTCAAGATGGATT 8645
                          ii    i    vv  i     v     vv       i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_136909332_   8646 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 8695
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_136909332_   8696 AGGCA-ATACCATTCAGTACATAGGCATGGGCAAGGACTTCATGACTAAA 8744
                            ?i- v i -   ivv  v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_136909332_   8745 ACACCAAAAGCAATGGCAACACAAGTCAAAACCGACAAATGGGATCTAAT 8794
                                     vvi      v   vv    iv  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_136909332_   8795 TAAACTACAGAGCTTCTGCACAGCAAAAGAAACTCTCATCAGAGTGAACA 8844
                         i   v vv i i   i  ii vv    i  v   v   vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_136909332_   8845 GGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACAAA 8894
                          i     i                 v   i   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_136909332_   8895 GGGCTAATATCCAGAATCTATAAATAACTTAAACAAATTTACAAGAAAAA 8944
                           i  vi          v      v    ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_136909332_   8945 ATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCT 8994
                         iv    i     v  i?    i     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_136909332_   8995 CAAAAGAAGACATTTATGCAGCCAACAGACACATGTAAAAATGCTCATCA 9044
                          v        i  vi viii     i ii      v   i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_136909332_   9045 TCACTGGACAT 9055
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.30 (139 / 107)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


 784 20.00 6.29 0.00  chrX_136927065_136928771.rev       87   261 (1446)    L1M4_orf2#LINE/L1        3   188 (720)  

  chrX_136927065_     87 GAAAGAGATCCTGTGTTCATTGATTGAAAGTCTTAATATTGTTAAAATGT 136
                               v    ii       v     i   v              i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_136927065_    137 CTATACCACACAAAT-AATCTACAGATTCAATGCAATCTCTATCAAAATC 185
                          v    iv v     -i              i      i           
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_136927065_    186 CCAATGACATTTTTCTCAGAAATAGAC---------TTAAAATTCATATG 226
                            iivi v     iv       v   ---------i             
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_136927065_    227 AAACCACAAAAGATTCTGAATAGCCAAAG-AATTTT 261
                         i  vii   ii  ii v           i-   i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.02 (3 / 186), avg. gap size = 3.67 (11 / 3)  

2097 22.12 7.01 6.18  chrX_136927065_136928771.rev      489  1216 (491)    L1M4_orf2#LINE/L1      175   908 (0)  

  chrX_136927065_    489 GCCAAAGCATTTATGAGCAAGAATAACAAAGTTGTAGTCATTGTATTTCC 538
                               i  v iv   iv     v          v  vvv iii i    
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_136927065_    539 TGATTTCAAATTGTATTACAAAACTATAGTAATCAACACAGTATAGTACA 588
                         ii        viv  i      i   i         v     i i    v
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_136927065_    589 GGCAAAAAACAAAAAAAAATCAAAACCAACCAACAAAACAACAGACACAT 638
                             v  ii------------------------------- i     i  
  L1M4_orf2#LINE/    275 GGCATAAGG-------------------------------ATAGACATAT 293

  chrX_136927065_    639 TAACAAATGAAACAGAATTGAGAGTACAGAAGTAAACCCACAAATATAGG 688
                         vi iv    i  i            v     i        i v  v  v 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_136927065_    689 GCCAACT----------------------------------------AAT 698
                          i   i ----------------------------------------   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_136927065_    699 GGTCTCCTTAATAAATGATTTCAGTA-AACAGGATATGCAAATGCTGAA- 746
                         i    ii i  i     i viii v -   v     ?v  v    vi  -
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_136927065_    747 AATGAAATTG-ACCCTTATCTTACACCAGATACAAAAATCAACTCAAAAT 795
                               i   -    i  i  i      v          i          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_136927065_    796 GGATTAAACACTTAAA-ACAAAGGCCCTGAAGCCATAAAACTCTCAGGAA 844
                             i ? v  i    -ii  ii  -- i  i i          i  i i
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGC--TAAAACTATAAAACTCTTAGAAG 541

  chrX_136927065_    845 AAAGTAAATAACAGGGAAAAAAACTCCATGACATTGGTCTTGGCAATAAC 894
                            -- v   ----  ?iv   v  i i    v    vi v      iii
  L1M4_orf2#LINE/    542 AAA--ACATA----GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_136927065_    895 TTTTTTGATATGGCAACAAAAACACAAGCAACAGAAGCAAAAATAAAGAA 944
                           i  v      i  v     i           i   v       i v  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_136927065_    945 GTAGGATTGCATCAAA-CTAAAAAGATT----CTTCACAGCAAGGAAACA 989
                         i v   i v       -i      vv  ----     ----     v  v
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA----AAGGACACT 681

  chrX_136927065_    990 ATCAACAGAGTCAAGAGATAATT-ACAGAATGGGAGGAAATATGCACAAA 1038
                              v i   v  i   i  ii-            i      vii    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_136927065_   1039 CCAAATGCCTGATAAGG-ACTTGATATTCAAAATCTACAAGGGACTCAAA 1087
                         i  v  ii         -     -   i  i   v  i  i i    vv 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTA 780

  chrX_136927065_   1088 CAAATCAACAGTAAGAAAGTAAATAACCCAACTGAAAAATGGCCAAAGTA 1137
                            v    i i   i  iii           i ?        v     v 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_136927065_   1138 CCTGAATAGACATTCTTCAAAAGAAGATATAAAAATGGCCAGCAGGTATA 1187
                         ii            ii  v            v         ii i i i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_136927065_   1188 TGAAAAAATGCTCTAACATCACTAATAGT 1216
                               i      -       ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTC-AACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (102 / 55)
Gap_init rate = 0.02 (16 / 734), avg. gap size = 6.00 (96 / 16)  


2106 26.26 3.75 6.43  chrX_136975947_136977882.rev      513  1445 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_136975947_    513 TGGAAAGACATATTGTGCTCATGGACTGAAAGATTTAACATATGA-AAAA 561
                                 i  viii  i       i  i    i    i  -  v-  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-TGTTAAGA 49

  chrX_136975947_    562 TATAAATTCTCCCCAAACTGATATACAGATTTAATGCAATTTCTATCAAA 611
                          ivv   v         i    v        i  i     ii        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_136975947_    612 ATATGAGCAAGATTTTTTGTAAATATGTAATATGTAAATGTGTAATTACA 661
                           viv   vivv       i i -------------   -  -----   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGA-------------AAT-TG-----ACA 130

  chrX_136975947_    662 TATGTAAATATGTAGTATTATCCCACAATTTATATA-AAAGACAAAGGAG 710
                         -------------  i- v    i v    i    i-   vi   i   v
  L1M4_orf2#LINE/    131 -------------AGC-TGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chrX_136975947_    711 TTATACCAAATAAAATAATTTTGTAAATAAAGA-TAAAGTGGGAAGACAC 759
                         ii v vi ivi    i   i   v   vi    -i     v   i   v 
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chrX_136975947_    760 AGTGTACCCAATGTCAAGACTTGTTATATGGCCAGAGTAATCAAGACTCT 809
                          vvv v      v    i    ii  i vi  i v            vv 
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chrX_136975947_    810 GTGGTGTTA-CAGAGGAATAAACACGTA-----------TAGAAT----- 842
                              ii i-  v i i   i   ii  -----------      -----
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_136975947_    843 --CTACAAACCTAGCCATGCGAATATGTCCAGCTGATTTTTGACAAAGGT 890
                         -- i v   ivv v    i ivv    vi  ii       i     i   
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_136975947_    891 ACAGTAGTAATTCAGTGGTGGAATGA---GTCTTTCCAATAAATTGTGCT 937
                         i viviiiv     i   -    v  ---      i   i    v     
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_136975947_    938 AGAGCAACTAGA-ATCCACATGCAAAAACAAACAAACAAACAAAAAACAA 986
                         i ii     i  - ?            i-----------------  ii 
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAG-----------------AATGA 448

  chrX_136975947_    987 AAA-AGACCTCTTGACATAAGGGTCACACCTTATA-AAAAAGTAATTCAA 1034
                          iv-i    i  --  v ------      v    -     v   i    
  L1M4_orf2#LINE/    449 AGTTGGACCCCT--ACCT------CACACCATATACAAAAATTAACTCAA 490

  chrX_136975947_   1035 ATTATATCAAGGTCTTAAATGTAAAACATAAAAATATTACACTTTTAGAA 1084
                          v iv    ?i v i         i vv     v   v v   i      
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_136975947_   1085 -AAAACAATGGAATG--TGTTCAGGATCTAAAGCTAGTGAAACATTTCTT 1131
                         -      vv  ?i i-- v   iv  i  vii i   vv  vvi      
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_136975947_   1132 AGACTTGACAACAAAAGTACAATCCATAAGAAGAAAAATTGATAAATTGG 1181
                            iv     v      i    v v i  i ii      v          
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_136975947_   1182 ACCTCACCTAAATAAAAGGATTTTCT-CTGTGAAAGACCTTGTTAAGAAG 1230
                           i   i v    v   iiv    v -  vii  i   vi i i     i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_136975947_   1231 ATGAAAAGAAAAGCTACACAGTGTGAGAAACAACGTGCACACCACATATC 1280
                         i        v  v i   v i  v      vv iv    v i  i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_136975947_   1281 CTCCAAAGGAGT-ATATCTAGAACATATGAAGAAACCTCA-AACCCAACA 1328
                         ivvi  i   v -i    i    i    i     vi  i -   i   i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_136975947_   1329 CTTAAA-TCCAAATAATTCAATTAGATAACTGGAAAAATACATCAATAGA 1377
                         v v   -vv       ii     ?i v  iv  v   iv iv v      
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_136975947_   1378 CATTTTACTTAAGAAAATATACAGATGGCAAAGAAGCATACAAAAAGATG 1427
                              iv iv     i       i     v  v     i ii        
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_136975947_   1428 CTCAATATCATTATACAT 1445
                              i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.65 (95 / 26)  


 786 23.50 0.00 0.50  chrX_137002940_137005032.rev        2   201 (1892)    L1M4_orf2#LINE/L1      632   830 (78)  

  chrX_137002940_      2 ACAAATGGGACTACATCAAACTAAAAAGCTTCTGCACAGCAAAGAAAACA 51
                          i    v     v       v v    i   i  ii vv     i v  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_137002940_     52 ATCAACATGGTGAAAAGGCATCCTATGGAATGGAATAAAATATTTGTATG 101
                              v vi        i  v  i ii      i v          i vi
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_137002940_    102 TCATATATCTAATAAGGTGTCAATCTTCAAAATATATAAAGAACTCATAC 151
                                   i      viiivi v i  i                v   
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_137002940_    152 AACTCAATAGTTAAAAAACCTAATAACCTGATTTAAAAATAGGCTAAGGA 201
                                  i v    i  v-       ii   ?      i   v     
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.30 (26 / 20)
Gap_init rate = 0.01 (1 / 199), avg. gap size = 1.00 (1 / 1)  

3003 15.87 2.81 3.31  chrX_137002940_137005032.rev      506  1110 (983)    L1M4_orf2#LINE/L1      122   723 (185)  

  chrX_137002940_    506 AAATGGACAAACTGATTCTAAAATTCCTGGGGAAATTCAAGGGACACTGA 555
                             v     i     i         v iv      v        v v  
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chrX_137002940_    556 ATAAGCAAAACAATTCTGAACAAGAAGGATAAAGTCAGAAGATTCACATT 605
                            iv         ii    v      i i     ii  i  i     i 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_137002940_    606 TCCTGATTTCAAGACTTACTACAAAGCTAGAGCTACAGCTCATTGTAATG 655
                            ii       i                ------   ---------- i
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTA------CAG----------TA 255

  chrX_137002940_    656 ATCAAAATACTGTGGCACTGGCATA------------TAGATCAATGGAG 693
                              i i v     i         ------------            i
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_137002940_    694 TAGAATTCAAAGTCCAGAAATAAACCCATTCATCTACAGTCAATTGATTA 743
                                v i                   v   i  ii           v
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_137002940_    744 T-GACCGGGGTCTGGAGACCACTTAGTGAGGGAAATAATAGTCTTTTCAA 792
                          -   vi    vivi      i i i  -      v              
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTTCAA 404

  chrX_137002940_    793 CAAACGGCTCTGGGACAACTGAATATCCATATGCAAAAGAATGAATTTGG 842
                             i  iv            i   ?   i               v    
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_137002940_    843 ACACCTGCCTTACACCATATATAAAA-TTAACTCAAAATATATCAAAGAC 891
                           v   i   i          i    -            iv    ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_137002940_    892 TCAAATGTAAGAGCTGAAACTATAAATCTTTTAGAAGAAAACATATTAGT 941
                         ii             i          v  i               vv?  
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_137002940_    942 AAATCTTT-TGACCTAAAATTTGGCAACAGTTTCTTAGATATGACAACAA 990
                                i-      viii  v     ii                 v   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_137002940_    991 AAGGGCAAGTAACAAAAGAAAAAATAGGTAAAATGGACTTTCTCAAATTT 1040
                            vi    i                 i    v       iv     v  
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_137002940_   1041 TTCAAAACTT--GCACTTCAAAAGGACACTATTAAGAAAGTAAAAATGCA 1088
                         --v       -- ii       -         i        i    vi  
  L1M4_orf2#LINE/    655 --AAAAACTTTTGTGCTTCAAA-GGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_137002940_   1089 ACCTACAAAATGGGAGAAAACA 1110
                            i   i            i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATA 723

Transitions / transversions = 1.91 (61 / 32)
Gap_init rate = 0.02 (10 / 602), avg. gap size = 3.70 (37 / 10)  

 945 13.21 6.60 0.00  chrX_137002940_137005032.rev     1391  1602 (491)    L1M4_orf2#LINE/L1      683   908 (0)  

  chrX_137002940_   1391 TCAAAAAA---AAAAAAAAA-----AAAA-GGGAGAAAATATTTGCAAAA 1431
                             i   ---    i v  ----- i  -                   v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_137002940_   1432 TATATACCTAACAAGGGTCTAGTATCCAGAATACATAAAGAACTCATACA 1481
                         i     i  i i     v  v            i           v    
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_137002940_   1482 ACTCAACAAGAAAAATATAAACAACCCTATT--AAAATGTACAAAAAATT 1529
                               i  v     v i   i     v   --      vi    ii   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_137002940_   1530 TGAATAGAGATTTTT---AAGAAGATATACAAATAGTCAATAAGCACATG 1576
                                 v    i ---                i i             
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_137002940_   1577 AAGAGATGCTCAACATCAGTAGTCAA 1602
                           i               ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.02 (5 / 226), avg. gap size = 2.80 (14 / 5)  


1076 26.04 1.74 0.00  chrX_137005487_137011864      207   494 (5884)  C L1M4_orf2#LINE/L1   (613)   295     3  

C chrX_137005487_    494 GAAAGTCATCTTATGTTCATGAATTGGAAAACTTAATATTGTTAAAATGT 445
                              vi   ii         i       i               i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

C chrX_137005487_    444 CCATACTACCCAAAGCAATCTACAGATTCAATACAATCCCTAATACA-TC 396
                          v     v      vii              ii         vi v -  
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

C chrX_137005487_    395 TCAAATAAATTTTTCACAGAAATTGAAGAAACAATTCCACAATTCATATT 346
                         i  iv ivv     ii          vi ivii  i i v         v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

C chrX_137005487_    345 GAATCATAAATGACTATGAATAGTTAAA-CAAATTTGAGAAGGAA---CA 300
                            viii  iv   ivv      ii   -   vi    i  i   ---  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

C chrX_137005487_    299 AAGCTAGAAGCATCATACTTCCTGATTTCAAAATAAATTTCAAAGCTACA 250
                            i i  i vv   i      ii         ivv i v          
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

C chrX_137005487_    249 TTAATCAAACCAGTACAGTACTGGAATAAAGACATATATATAG 207
                         v       iv    iii       v    i  i v i      
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 1.68 (47 / 28)
Gap_init rate = 0.01 (3 / 293), avg. gap size = 1.67 (5 / 3)  

3055 26.98 0.77 0.77  chrX_137005487_137011864     4978  5885 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137005487_   4978 TGGAAGAACATTCCATGCTCATGGATAGGAGGAATCAACATTGTGAAAAT 5027
                              ii i  i     i        v   i  v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137005487_   5028 GGCCATACTGCCCAAGGTAATTTATAGATTCAGGGCCATCCCCATCAAGC 5077
                            v     v     iv i  i  i       iv  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137005487_   5078 TACCAATGACTTGCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAAGTCA 5125
                          v   iivi i vi  ii     -   -- v  i  - iii     v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_137005487_   5126 TATGGAACCAAAAAAGAGCCTGCGTTACCAAGACAATCCTAAGCCAAAAG 5175
                                viiv  ii  v  v vi vi    i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_137005487_   5176 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTAAACTACAAGGC 5225
                                i      vv       v  ii i      vivv       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_137005487_   5226 TACAGTAACCAAAACAGCATGGTACTGGGACTAAAACAGAGAGATAGACC 5275
                                 i   i    ii         v iv ii i   v v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_137005487_   5276 AATGGAACAGAAC--AGCGCCCTCAGAAATAATACCACACATCTACAACC 5323
                                i    i--  v i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_137005487_   5324 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATTGGGAAAGGATTCC 5373
                          vi    i  i     ivv  v   i v  vvv   v       i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_137005487_   5374 CTATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5423
                           v  i  i       i      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_137005487_   5424 GAAACTGGATCCCTTCCCTATATCTTATACAAAAATTAATTCAAGATGGA 5473
                            ii    i    v  ii i i v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_137005487_   5474 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5523
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_137005487_   5524 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCAT-GACT 5571
                         v    ?i- v i -   iv   v v  vv i     v ii   v -  iv
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_137005487_   5572 TAAGCACCAAAAGCATTGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5621
                          i -           ivi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    596 TGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_137005487_   5622 AATGAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGTGA 5671
                         v  v   v v  i i   i  ii vv       v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_137005487_   5672 ACAGGCAACCTAAAGAATGGGAGAAAATTTTTACAATCTACCAATCTGAC 5721
                          v  i     i v               v   i   vii ivv      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_137005487_   5722 AAAGGGTTAATATCCAGAATCTACAAAGAGTTTAAACAAATTTATAAGAA 5771
                           i  ii vi          v  i     ii ivv    v iv    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_137005487_   5772 AAACATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGAGTC 5821
                            v -    i     v  i?    i            v    i   vvi
  L1M4_orf2#LINE/    795 AAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_137005487_   5822 TTCTCAAAAGAAGACATTTATGCAGCCAACATTCACATGAAAAAATGCTC 5871
                              v        i  vi viii     i vv          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_137005487_   5872 A-CATCACTGGCCAT 5885
                          -     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3215 26.65 0.44 0.44  chrX_137037922_137044312     4991  5898 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137037922_   4991 TGGAAGAAGAACCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5040
                              ii v v      i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137037922_   5041 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAG- 5089
                            v     v     iv i  i  i        i  v     i     i-
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137037922_   5090 TTACAAATAATTTTATTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCA 5138
                          iv  iv ivi   -  ii     v v  v  i-  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_137037922_   5139 TATGGAACCAAAAAAGAGTCTGCATTGCCAAGACAATCCTAACCAAAAAG 5188
                                viiv  ii  vi v v  v     i      i i vv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_137037922_   5189 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5238
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_137037922_   5239 TACAGTAACCAAAACAGCATGGTACTTGTACCAAAACAGAGATATAGACC 5288
                                 i   i    ii       v i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_137037922_   5289 AATGGAATAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5338
                                     iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_137037922_   5339 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5388
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_137037922_   5389 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5438
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_137037922_   5439 AATTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAGGATAGATT 5488
                          i     i    v   i     v              i   ii  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_137037922_   5489 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5538
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_137037922_   5539 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGCCTTCATGTCTAAA 5587
                            ?i- v i -   iv   v v  vv i     v vi   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_137037922_   5588 ACACCAAAAGCAATGGCAACAAAAGCCAAACTTGACAAAT-GGAGTCTAA 5636
                                     vvi          vv   v v  i    -   v ii v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_137037922_   5637 CTAAACTAAAGAGCTTCTCAATAGCAAAAGAGACTACCATTAGAGTGAAC 5686
                          v   i    i -   i vviivv    i  v    i  vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_137037922_   5687 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5736
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_137037922_   5737 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTCACAAGAAAA 5786
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_137037922_   5787 AATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5836
                          iv    i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_137037922_   5837 TCAAAAGAAGACATTTATGCAGCCAACAGTCACATGAAAAAATGCTCATC 5886
                           v        i  vi viii     i iv          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_137037922_   5887 ATCACTGGTCGT 5898
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.00 (8 / 8)  


2699 27.00 1.84 3.78  chrX_137085020_137089335.rev     2900  3825 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137085020_   2900 TGGAAAGATATCT-ATGCTCACGGACCAGAAGAATTAATATT---AAAAT 2945
                                     i-   i   i   iii     v        ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137085020_   2946 GATCATACTGCCAAAAGCAATCTACAGATTCAATGCAATTCCTATCAAAA 2995
                          iiv     v  v   vii              i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137085020_   2996 TGCTAATATCATTTTCCATAGAAAATGAC--TTTTTTTCTGTTTTCCAAA 3043
                          v i iivv v    iiii     v    --vi vv i  ivvv i  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_137085020_   3044 TAGAAAAAAATTCATTTATAGGGAACCAAAAAAAGAGCCCAAAGAGACAA 3093
                          i    ---------- ii i  i   v i  v  ---     ---    
  L1M4_orf2#LINE/    151 TGGAAA----------TGCAAGGGACCCAGAATAG---CCAAA---ACAA 184

  chrX_137085020_   3094 ATTCACCCATGCAAAAGGAG--CAAAGCTGCAGGCATCATATTGTCTGAC 3141
                         vi ------  v     i  --     i  v   vv   i i vi ii i
  L1M4_orf2#LINE/    185 TCT------TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_137085020_   3142 TTCAAACTATATTACAAGGGTATAGTGAATAAAACAGCATTATATTGGTA 3191
                               viv  i     i v  i   i vi  i    ii vi  i   i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_137085020_   3192 TAAAAAGAAGACACATAGA-CAATTGTAGCAGAATAGATTGCCCAGAAAT 3240
                            ii v -    i     -    v - ii     v  vv i        
  L1M4_orf2#LINE/    279 TAAGGATA-GACATATAGATCAATGG-AATAGAATTGAGAGTCCAGAAAT 326

  chrX_137085020_   3241 AAATCCACACATTTATGGTCAGTTGATTTTCAACAAGA-TGCCAAGA--A 3287
                            i   i             i         i     i-        -- 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_137085020_   3288 GCCAA-GAACACACAATGACTGTCTCTTTAATAAATTATATTGGAGAAAT 3336
                         vi   - iiv v v   i---    i  i  i    vi ii   iiv  i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATA---GTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_137085020_   3337 TGGATGTCCACTTGCAGAAGGATGAAACTGTACCTCTAGCTTTCACCATA 3386
                              i?    v    i   i     ii  v   i   v  iv       
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_137085020_   3387 TACAAAAATCAACTCAAAATCAATTAAAGGCTTAAATGTGAAGCCCGAAA 3436
                                  i          vi  i ?  i i       i iiv ii   
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_137085020_   3437 GTGTGAAACTACTAAGACAAAATATAGGCA-AAATGATTCATTACATTGT 3485
                         v i i     vi  ii v    i     ?i-    v-   i v  v   v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGG 572

  chrX_137085020_   3486 ACTGGGTAAGGATTTTTTGGATAAGACCTCAAACAAAAAAAAAAGGCAAC 3535
                         ii i  i  v i   i  i    v   -----  v    iv v i     
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGAC-----ACCAAAAGCACAAGCAAC 617

  chrX_137085020_   3536 AAAAGCAAAAATCAACAAATGGGGTTACATAAACATAAAAAAGCTCTGCA 3585
                              v      vi i    v  ii v   v  v  v     vi i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_137085020_   3586 CATCAAAGGAAATAATCAATAGAGTGAAGAGCCAACCTACAGAATGGGAG 3635
                          v        v iv     v i      i  v     i            
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_137085020_   3636 AAAATATTTGGAAACTCCACTTTTGTCAAGGGGTTAATATCCAAAATATA 3685
                                   v   iivi iv i  vi     ii vi      i      
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_137085020_   3686 TAAGAAACTCGAACAATTCAACAGCAAAATAAAACATGTGGTCTGACTGA 3735
                            ii     vv    i    i ii    -- i   vi iii ii i ? 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAA--AGACAAATAACCCAATTWA 815

  chrX_137085020_   3736 AAACCTAGCAAAAGACCTGAATAGAAATTTCTC---AAAAGACAGACAAA 3782
                            vivi     i  ii        v       --- i    i v     
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_137085020_   3783 TGACCAACAGATGTGTGAAAAAATGCTCAACACCACTGAACAT 3825
                           i    i iiiiii      i          i  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (162 / 84)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.60 (52 / 20)  


3172 24.92 0.32 2.37  chrX_137124318_137128966.rev     3232  4158 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137124318_   3232 TGGAAGTGCATCCCATGCTCATGGATGGGTAGAATCAATATTGTAAAAAT 3281
                              ivii        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137124318_   3282 GTCCATACTGCCAAAAGCAATTTACAAATTCAAAGCAATTCCCATCAAAA 3331
                          v v     v  v   vii  i    i      v     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137124318_   3332 TACCACCATCATTCTCCGCAGAACTAGAAAAAACAATCCTAAAATTCATA 3381
                          v   v vv v  i ii      v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_137124318_   3382 TGGAACCAAAAAGAGCCC-TCATAGCCAAAGCAAGAGTAAGCAAAAAGAA 3430
                              viiv  i ii   -vv         i   vvv i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_137124318_   3431 CAAACCTGGAGGCATCATATTACTCAACTTCAAATTATATGATTAGGCCA 3480
                             vi      vv   i i v i   i      viv  iv iv i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_137124318_   3481 TAGTTACCAAAACAGCATGGTACTGGTTTAAAAATAGGCATATGGACCAA 3530
                         i   v i   i    ii         iv   ii    i     i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_137124318_   3531 TGAAACAGAATAGTGAACACAGAAATAAAGCCAAATACTTAACAGCCAAC 3580
                           i  i     v v  iiv          v   v i i   -ii i   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAAT 349

  chrX_137124318_   3581 TGATCTTTGATAAAGCAAACAAAAACATAAAGTGGGAAAAGGACAGTCTA 3630
                             i  i  i  i vviv   i v   vv i    i    i i     v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_137124318_   3631 TTCAACTAATGATGCTGGGATACTTGGCAAGCCACATGTAGAAGAATGAA 3680
                               v    i        i vi   vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_137124318_   3681 ACTGGATCCTCATCTCTCACCATATCCAAAAATCAACTCAGGATGGATCA 3730
                         ii    i  ii i   v        v       i      ii        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_137124318_   3731 AAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACATC 3780
                         ?    i     v     v  i    i      v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_137124318_   3781 AGAAAAACCCTTCTAGACATTGGCTTAGGCAAAAACTTCATTACCAAGAA 3830
                         i ?iv  vi    vv   v    v        viii   -   vvv vi 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC-TTAGATATGA 598

  chrX_137124318_   3831 C-CCAAAAGCAAATGCAACAAAAGCAAAGATAAATAGATGGGACTTAATT 3879
                          -         v v          v   i   i   i  v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_137124318_   3880 AAACTAAAAAAAACTTCTGCACAGTAAAAATAAAAAATAATAATCAGCAG 3929
                            v v     --   i  ii -v -----i   ii i v  -   iv i
  L1M4_orf2#LINE/    649 AAAATTAAAAA--CTTTTGTGC-TT-----CAAAGGACACTA-TCAAGAA 689

  chrX_137124318_   3930 AGTTAACAGACAACCCGCAGAGTAGAAGAAAATCTTCA-AAATCTATACA 3978
                            v  v         i    i i i       v  ii-     -   i 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATA 738

  chrX_137124318_   3979 TCTGACAGAGGACTAATATCCAGAATCTACAAAGAACTCAAACAAATCAG 4028
                              i ii     vi          v  i         vv    v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_137124318_   4029 CAAGAAAAAAAAAACAAAAAGCAAACAATCCAATCGAAAAGTGGGCTAAG 4078
                         i  v     i ----------    i  i     i?    i     v   
  L1M4_orf2#LINE/    789 TAATAAAAAGA----------CAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_137124318_   4079 GACATGAATAGACAGTTCTCAAAAGAAGATATACAAATGGCCAACAAGCA 4128
                           iv          v     v                       i     
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_137124318_   4129 TGTGGAAAAATGCTCAACATCACTAATTAT 4158
                         ii  i   i             ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.27 (25 / 11)  


2551 29.52 2.22 1.44  chrX_137191639_137196577     3546  4446 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137191639_   3546 TAGAGAAACATCCCATGCTCATGGATTAGAAGAAACAATATCATTATGAT 3595
                          i  i i i        i         i     vvi     ii   v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137191639_   3596 GGCCATATGCCCCAAAGATATTTAGAGGTTTAATGCTTTTCCTGTGAAAC 3645
                            v   iv       vvv  i  v  i  i  i  vv i   i v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137191639_   3646 TGTCAACATCATTCTTCACAGAATTAGAAAAACTTATTTTAAAATTAATA 3695
                          vi  i vv v  i  ii     v v  v  i  v  ii       v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_137191639_   3696 TGGGATCAAA---AAAAGAGCCTAAATAGCCAAAGCAATCCTAAGCCAAA 3742
                            ----   ---  ii  v  vi          i     i i ivv i 
  L1M4_orf2#LINE/    151 TGG----AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_137191639_   3743 AGAACAAAGCCAGAGGCATCACACTAAATGACTTCAGATTATATTATAAG 3792
                                  iii    vv       vvvii i    i viv  i  i  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_137191639_   3793 GCTACAATGACCAAAACAGCATGGTACTGCTACAAAAACAGACACATAGA 3842
                               i i i   i    ii        vi i  ii i     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_137191639_   3843 CTAATAGAACAGAATAGAAAACTCAGAAATAAAGCCACACACCTACAACC 3892
                         ii   i   i     v  i iii          v   i   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_137191639_   3893 ATCTGATCTTCAACAAGGCTGACAAAAACAAGCAATGGGGAAAGGGCTTT 3942
                          vi    i   i      v  v   i v  vv            iiivv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_137191639_   3943 CTATTCAATAAATGACGCTGGCATAATTGGTTAGCCATAGGCAGAAGAGT 3992
                           v     i     ii     v i  i   v  ?   i v   i    i 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_137191639_   3993 GATATTAGCCACTTAACTTTCACCATATACACAAATTCACTGAAGGTGGA 4042
                           vi  i v v i  v  iv           v     v   v  ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_137191639_   4043 TTAAATATTTAAATGTAGGACCTCAAACTGTAAAAGTCCTAGAAGAAAAT 4092
                          i ? v ii        i  v  v     i     v  i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_137191639_   4093 CTAAG---AAATACCCTTCTCTACATACACCTTGG------CAACAAATT 4133
                         v  i ---    ---    -----i i-       ------   iiiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT---CTTC-----GTG-ACCTTGGGTTAGGCAATGGTTT 587

  chrX_137191639_   4134 TATACCAATTCC-CCAAGAGCAACTGCAAGAAAAACAAAAATTAACAACT 4182
                         iv  vvv  vv -    i    vvv    v    iv      vi i  v 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_137191639_   4183 AGGAACTAATTAACCTAGAGAGCTTCTATACAGCAAAGGAAACCATCGAT 4232
                         v   vi v  i  vv vi i i   i i i vv       v  i   i v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_137191639_   4233 AAAGTAAACAGACAATCTACAGAAGAGAAAAAATTATTCACAAGCTATGC 4282
                              i  v      i i      vi i i   v    ii   iii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_137191639_   4283 GTCCAACAAGGG---CATATCTAGAACCTATGAGGAACTTAAATAAATCA 4329
                         i  ii i     ---ii    i    iv   i i     ivv i  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_137191639_   4330 ACAAGCAAAAAACAA----TCCCATTAAAGTGTGGGCAAAAGACATAAAT 4375
                          i  vv    i    ----i  v   ?  ivi        i  iv i   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_137191639_   4376 ATACACTCCTAAAAAGAAGACATACAAGGGGCCAGCAAACATATGAAAAA 4425
                          v   i i  vv        i      iv     ii  i  i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_137191639_   4426 ATGCTCATCATCACTAATCAT 4446
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (161 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.30 (33 / 10)  


 349 21.43 16.33 0.00  chrX_137244791_137247183.rev      669   766 (1627)    L1M4_orf2#LINE/L1        1   114 (794)  

  chrX_137244791_    669 TGGAAAGATATTTCACATTTATGGATTATAATTCTCAGTAATGATAAGAT 718
                                    ii  ii  i       iv  vv  i i  v  v      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137244791_    719 GG-AA---------AATTGATCCATAGATTCAATGCAACC------AAAT 752
                           -  ---------        i i        i    i ------   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137244791_    753 TCCCAGGTGGCTCT 766
                               v  v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT 114

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.03 (3 / 114), avg. gap size = 5.33 (16 / 3)  

2832 21.50 6.22 2.59  chrX_137244791_137247183.rev     1131  1902 (491)    L1M4_orf2#LINE/L1      109   908 (0)  

  chrX_137244791_   1131 GCTCTTTTTGCAGAAATTGACAAGCTCTTCTTAAAATCCATATGGATATG 1180
                           ii                      vv  i      i        v   
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_137244791_   1181 CAAGGGACCCAGAATAGTCAAAAACAAACTTGAAAAAAAA-----AAGTT 1225
                                          i     -   v         i  -----     
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_137244791_   1226 GGAGGATTCACACTTCCTAGTTTCAAAAATTATTATAAAGATACCTTAGT 1275
                               i          i i        v   i  i    v   vv  i 
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_137244791_   1276 AAAGATAGTATTGTAGTGGTAAACAGATAGGCATATATATTAATGGAATT 1325
                         v    i   i v   v   i v vi     i      v  i        v
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_137244791_   1326 AAACTGAAATTCTCAAAATACATCCTCACCTTTATACTCCATTGATGTTC 1375
                         i  i   i v  ivi     v i  vi  v     iv  v      v   
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_137244791_   1376 AATAAAT-TGCCAAGTCAATTTGATAGAGGAGAGGTAGTCTTT--AACAA 1422
                         i i  iv-       v v   ii  i i i iiii        --     
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_137244791_   1423 ATGGTCCTGAGACATTGAGGTAGC-ATATGCAAAAAGATGAATCTACATT 1471
                              v   i    vivi i  ? - i        ii     vi iv ii
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_137244791_   1472 ATAACCTCACACAGTACCCCAAAATCAATTAAACATCTATCATA--TCAA 1519
                         viv         vi  iv v     i  i v  v  vv    ? --i v 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_137244791_   1520 AATGTAAGAG--------GTAAAACTTTTAGAAGAAAA------------ 1549
                                   --------i       i           ------------
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_137244791_   1550 TCTTTGTAACCTTGGATTAGGCAA--GTT-CTTAAATACAGCACCAAATG 1596
                             i  i       i        --   -    i   iii       v 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chrX_137244791_   1597 CATGATCCATAAAAGAAAATATTGACAAGTTGGACTTTATATGCATAAAA 1646
                           ii v v i         v  v  i  i        i  vviv  v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_137244791_   1647 AGCTTTTGTGTTTCAAAAGACA------AGAAAATGAAATGACAACTCA- 1689
                          i        i      i    ------     i     v      i  -
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_137244791_   1690 -AACCAGGAGAAAAATATGTGCAAGTCATATATCTG-TAAAGGACTGTTA 1737
                         -i vii        -   v     i           -   i     vv  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_137244791_   1738 TCAAGAGTAATTAAACAATTCTCACAACTCAATACAACTCAATTTCTTGT 1787
                           v   i  vv    v  i   i           ----------------
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATA---------------- 790

  chrX_137244791_   1788 CCGTAATAAGACAAATAGCTCAATTAAGAAATGGGCAAAAGATTTGAATA 1837
                         --i   v          i i     ? i           i          
  L1M4_orf2#LINE/    791 --ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_137244791_   1838 GACAGCTC-----AGCAAATATAGGAATAGGAAATAAGCATATGAAGAAA 1882
                             vi  -----  v i     vi   i vv        i     i i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_137244791_   1883 TGGTCAAAATCATTAGTCAT 1902
                           v    v    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (96 / 67)
Gap_init rate = 0.02 (16 / 800), avg. gap size = 4.25 (68 / 16)  


3339 25.94 0.66 0.44  chrX_137263023_137269419     4999  5904 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137263023_   4999 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5048
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137263023_   5049 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5098
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137263023_   5099 TACCAATGACTTTCTTCACAGAATTGGAGAAAACT-ACTTTAAAGTTCAT 5147
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_137263023_   5148 ATGGAACCAAAAAAGAGCCCGCATCACCAAGACAATCCTAACCAAAAAGA 5197
                               viiv  ii  v  v v  vi    i      i i vv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_137263023_   5198 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTGCAAGGCT 5247
                               i      vv       v  ii i      viv    i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_137263023_   5248 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5297
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_137263023_   5298 ATGAAACAGCAC--AGAGCCCTCAGAAACAATACCACACATCTACAACCA 5345
                            i  i  v i--    i  --     i  vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_137263023_   5346 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCTC 5395
                         vi    i  i     ivv  v   i v  vv            i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_137263023_   5396 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCGTAAGTAGAAAGCTG 5445
                          v  i  i              v      v  ?  ii v i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_137263023_   5446 AAGCTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGAT 5495
                            i    i    v   i     v              i    ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_137263023_   5496 CAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5545
                           ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_137263023_   5546 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5594
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_137263023_   5595 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGA-TCAA 5643
                         i            vvi          vv     v  i    v   - iv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_137263023_   5644 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5693
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_137263023_   5694 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAAACTACTCATCTGACAA 5743
                           i     i                 v        ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_137263023_   5744 AGGGCTAATATCCAGAATGTACAGAGAACTCAAACAAATTTAGAAGAAAA 5793
                         i  i  vi          i  i i       vv    v iv v  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_137263023_   5794 AAA-AAACAACCCCATCAAAAAGTGGGCAAAGGATATTAACAGACACTTC 5842
                          i -   i     v  i?    i            v v  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_137263023_   5843 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 5892
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_137263023_   5893 ATCACTGGTCAT 5904
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


2991 27.37 1.55 1.32  chrX_137271383_137276787     4007  4912 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137271383_   4007 TGGAAACACATTCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 4056
                               v i  i     i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137271383_   4057 AACCACACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAA 4106
                         ii v i   v  v   vii       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137271383_   4107 TACCACCATCATTCTTCACAGAATTAGAAAGAAAAAATTCTAAAATTCAT 4156
                          v   v vv v  i  ii     v v  v - ivvi  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_137271383_   4157 ATGGAACCAAAAAAGAGCACACACAGCCAAAGCAAGAGTAAGCAAAAAGA 4206
                               viiv  ii  v vviv i       i   vvv i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_137271383_   4207 ACGAATCTGGAGGCATTATATTACCTGATTTCAAACTATACTATAAGGCT 4256
                           i  vi      vv i i i v  ii        viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_137271383_   4257 GTAGTCACCAAAACAGCGTGGTACTAGTATAAAAATAGGTGCATAGACCA 4306
                         ii   v i   i    i        i i    ii    iiii     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_137271383_   4307 GTAGAACAGAATAGAGAACCCAGAAATGAACCCAAATACTTACAGCCAAC 4356
                         i i   i     v    ii        i      v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_137271383_   4357 TGATCTTTGACAAAGCAAACAAATACATAAAGTGGGGAAAGGACACCCTT 4406
                             i  i     i vviv   ivv   vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_137271383_   4407 TTCAACAAATGGTGCTGGGATAATTGGCTAGTCACATATAGGAGAATGAA 4456
                                             i  i   v  ?i     ii ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_137271383_   4457 ACTGGATCCTCATCTCTCACTGTATACAAAACTCAACTCATGATGGATTA 4506
                         ii    i  ii i   v   ii         v i      vi      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_137271383_   4507 AGGACTTAACTCTAAGACCTGAAAATATAAAAATTCTGATTCTGGAAGAT 4556
                         ?i   i   v v     v  i   v       -i   ----- i     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCT-----TAGAAGAA 543

  chrX_137271383_   4557 AACATTGGAAAAACCCTTCTATACATTGGCTTACGCAAGAATTTCATGAC 4606
                              v  ?iv  vi    vvv  v    v   v    vii    v iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_137271383_   4607 CAAGACCCCCCCAAAAAT----GCAATAAAAACAAAGACAAATTGCTGGA 4652
                         i v   v  ---    ii----    i    iv   i i i  viv v i
  L1M4_orf2#LINE/    594 TATGACACC---AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_137271383_   4653 ACTTAATTAAACTGAAGAACTTTTGCATGACAGAAGGAACATTG------ 4696
                             v  i   v v  i        iiivv  -     -  i i------
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCA-AAGGA-CACTATCAAGA 688

  chrX_137271383_   4697 -AGTAAAGAGACAACCCACAGAGTGGAAGAAAATCTTCACAATCTATACA 4745
                         -   i  i              i   i       v  ii   vii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_137271383_   4746 TCTGACAAAGGACTAATATCCAGAATCCACAAGGTACTCAAATAAATTAG 4795
                              i  i     vi          vi i  i v    vv i  v i i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_137271383_   4796 CAAGAAAAA---AAACAATCCCATCAAAAAGTGAGCTAAGAACACGAATA 4842
                         i  v     ---   i  i  v  i?    i  i  v   i ivi     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_137271383_   4843 GACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAACA 4892
                             v     v                       i  i  i       v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_137271383_   4893 TGCTCAACATCACTATTGAT 4912
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (151 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.89 (26 / 9)  


 638 26.62 1.14 7.98  chrX_137317062_137318971       29   291 (1619)  C L1M4_orf2#LINE/L1   (663)   245     1  

C chrX_137317062_    291 TAAAAAGATATCTTGTGTCCATAAATTGTTAGAATTAATATTATCCTGCA 242
                          ii         iii   i   ii    vv   v        i i---- 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT----A 46

C chrX_137317062_    241 TATTAACAATATTAATCTTGTTAATTATGTTAAAATGGTCTTCAGATTCA 192
                         viv ii     i --i ii------------   v  i   v        
  L1M4_orf2#LINE/     47 AGATGGCAATACT--CCCC------------AAATTGATCTACAGATTCA 82

C chrX_137317062_    191 ATACAATCTGTATCAAATTTCGAAAGACACTTTTCATGGAAATAGAAAGA 142
                          ii     iv       v i v ivvi vi    iiii     v  v - 
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACA-A 131

C chrX_137317062_    141 AACGATCTTAAAATTAACGTGGAACCACAACAGATCCCAAACAGCCAAAG 92
                         ivi    i       v ii     vii   vi  i  vi  i       i
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

C chrX_137317062_     91 CAATCTTGAGAA-GAAGAACAAAGCTGGAGTCATCACACTACCTGATTTT 43
                                  i  -           i     vvv       v  ii    i
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

C chrX_137317062_     42 AAACTACTT--TACAA 29
                            --    --     
  L1M4_orf2#LINE/    232 AAA--ACTTACTACAA 245

Transitions / transversions = 1.92 (46 / 24)
Gap_init rate = 0.03 (7 / 245), avg. gap size = 3.43 (24 / 7)  

1422 26.67 0.77 0.51  chrX_137317062_137318971      480   869 (1041)    L1M4_orf2#LINE/L1      241   631 (277)  

  chrX_137317062_    480 TATAGAATCACAAATGATTTAAACCCTATGGTACTGGCATGAAAACAGAC 529
                           i i iii   i- i  iv i  vv i            i ii i    
  L1M4_orf2#LINE/    241 TACAAAGCTACAG-TAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_137317062_    530 ACAAAGATCAGTGGAACAGAATAGAGAGCCCAGAAGTAAACCCACACATA 579
                          i v      i     i     v     i      i        i    v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_137317062_    580 CAGAGTCAACTAATCTTTTATGACAGTGCAAAGAATACACAATGGGGAAG 629
                         i vi     i i  i  iv ii vi    v    vi iv          i
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_137317062_    630 GGATAGTCTGTTCAATAGATTATATTATAAAAAATAGATATCCACATGAA 679
                          i       v     i i  vi ii ivi v  v i    ?       v 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_137317062_    680 AAAGAATAAAACTGGACCTTTGTCTTAGACCACATACAAAAATTAACTAG 729
                                i  ii      ii ii  i v    i               vi
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_137317062_    730 AAATGAATTAAAGACTTAAATATATATTCTAAAACTATAAAATCCATAGG 779
                              i  i ?    i     i  vivv              ii v   -
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG- 538

  chrX_137317062_    780 AAAAAAACATAGAA--AAAGCTCCTTGACATCAGTTTTGGCAATGAATT- 826
                           i         i?--   v  i v    v ii v  v       iv  -
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_137317062_    827 TTGGATATGACACAAAAAGCATAAGTCAAAAAAGCAAAAATAG 869
                           i          v       i   iv v     v        
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

Transitions / transversions = 1.97 (67 / 34)
Gap_init rate = 0.01 (4 / 391), avg. gap size = 1.25 (5 / 4)  

 769 22.22 14.07 0.37  chrX_137317062_137318971     1150  1419 (491)    L1M4_orf2#LINE/L1      602   908 (0)  

  chrX_137317062_   1150 CAAAAAAAAAA--AAAAAAAGGAAAATTAAATAAGTTGGATTACATCAAA 1197
                              iv v  --  v     i    v  i    i     i v       
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_137317062_   1198 CTAAAAAAGCTTCTGTACAGCAAAGGAAATGATCAAGAGGGTGAAA-GTC 1246
                         v v     -   i   i vv       v iv       ii      - v 
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_137317062_   1247 AACTTATGGAATGGGAGAAAATAATTTCAAACCCCATATCT---AAGGCA 1293
                            ii ii               v  v    i vi      ---    v 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_137317062_   1294 TTAATATCCAAAATATATAAGGAACTCACACAACTTA----TAGGAA--- 1336
                         i vi      i         i      vi      i ----  ii  ---
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_137317062_   1337 ---------------AAAATGAGCAAAG-ACCGGAGTGGACATTTTTTTA 1370
                         ---------------      i      - iiv  i i       i ii 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_137317062_   1371 AA--AGACATACAAACAG-------GTATATGAAAAGGTGTTCAACATTG 1411
                           --   i       ii ------- i i        i  i       ii
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_137317062_   1412 CTAATCAT 1419
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.16 (41 / 19)
Gap_init rate = 0.03 (9 / 307), avg. gap size = 4.33 (39 / 9)  


3025 27.40 0.99 0.66  chrX_137337233_137339299.rev      672  1576 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137337233_    672 TGGAAGAACATTCCATGCTCATGGGTAGAAAAAAATCAGTATCATGAACA 721
                              ii i  i     i      i v i  i v- i i   ii v  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chrX_137337233_    722 TGGCCATACTGCCCAAGGTAATTTATAGAGTCAATGCCATCCTCATCAAG 771
                             v     v     iv i  i  i   v    i  v    ii     i
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_137337233_    772 CTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAAAGTTC 819
                         v v   iivi i  i  ii     -   -- v  i  -  ii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_137337233_    820 ATATGGAAACAAAAAAGAGCCCTCATTGCCAAGTCAATCCTAAGCCAAAA 869
                                  iiv  ii  v  vvv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_137337233_    870 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 919
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_137337233_    920 CTACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAGAC 969
                                  i   i    ii    i    i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_137337233_    970 CAATGGAACACAAC--AGAGCCCTCAGGAATAATGCCACATATCTACAAC 1017
                                 i v  i--    i  --  i     vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_137337233_   1018 TATCTGATCTTTAAGAAACCTGAGAAAAACAAGAAATGGGAAAAGATTC- 1066
                         i vi    i  ii v  ivv  vv  i v  vvv      i     v v-
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_137337233_   1067 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATTTGCAGAAAGC 1116
                         i  v  i  i              v      v  ?   iv    i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_137337233_   1117 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 1166
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_137337233_   1167 ATTAAAGACTTAAATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAA 1216
                           i ?    i       v   v  i    i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_137337233_   1217 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 1265
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_137337233_   1266 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 1315
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_137337233_   1316 AATGAAACTAAAGAGCTTCTGCACAGCTAAAGAGACTACCATCAGAGTGA 1365
                         v  v   v v  i i   i  ii vv v  i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_137337233_   1366 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 1415
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_137337233_   1416 AAAGGGCT-ATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1464
                           i  i  -i          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_137337233_   1465 AAAAA--AACAACCCCATCAACAAGTGGGCGAAGGATATGAACAGACACT 1512
                            i --  i     v  i? v  i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_137337233_   1513 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 1562
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_137337233_   1563 TCATCACTGGCCAT 1576
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


2702 27.50 1.68 1.35  chrX_137342485_137344367      500  1390 (493)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_137342485_    500 ATGTTCATGGATTGGAGAAATTATTATCATTAAAATGACCATATTTCCCA 549
                                         ii v   v   ii    i   i v   i i    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_137342485_    550 AAGCAAACTACAGATTCAATGCAAATGGTAGCAACATACCGACATTATTT 599
                           vii v            i    vivv  v   v  v  ii vviv   
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_137342485_    600 TTCACCGAATTAGACAAAAGC-AATCC-AAAATTCATATGGAACCAAAAA 647
                           ii v   v v     --  -i    -               viiv  i
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAA--GCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_137342485_    648 TTGTTCTAAATAGCCAAAGTAACCACAAGCAAAAAGAACAAAACTGCAGG 697
                         vviii vi          ii  i vii iv  i         ii  v   
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_137342485_    698 CATAACATTACCTGACTTCAAAACATGTTACAAA-CTATAGTAAGCAAAA 746
                         vv v   i v  ii i        v ii      -   i     v   i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_137342485_    747 TAGCATGGTATTGGTGTATAAAATAGACACACCAACCAATGGAACAAAAT 796
                         i  ii     i   ii  - ii       i ivi i        i i   
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATA-AGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_137342485_    797 GGAGAACCCAGAAAGAAAGCCACATATTTAGAGTCAACTGAACTTCAACA 846
                         v    ii       v   v   i i     vi     i   vi   i   
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_137342485_    847 AAACTGACAAGAACTTTCACTGGGAAAAGGATGCCCAATTCAATAAATAG 896
                          iiv  v     v v    v    i    i  ivi vv     i    i 
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_137342485_    897 TGCTTGAGA-ATTTTGATAGCCAGATGCAGAAGATTGAAATTGGACTCAT 945
                             - i  - vi v    ?   v     i    v    i      i v 
  L1M4_orf2#LINE/    412 TGCT-GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chrX_137342485_    946 ATCTTTTATCATATACCAAAAACCAGCTCCAAATTGATTAAAGACTTAAA 995
                          i  ivi i       -     ii i   v    v   i ?    i    
  L1M4_orf2#LINE/    461 ACCTCACACCATATAC-AAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_137342485_    996 TATAAGACCCAAAATTATCAAATTACTAGAAGAAAACCCAGGGAAAACTC 1045
                          i     v i    i   v   i vi           vi   ?iv  v  
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_137342485_   1046 TCCTGT-ATGTTGATATAGGCAAATAATTTATT-GCTAAGATCTTAAAAG 1093
                          i -  - iv   ivv       - ii   v  - v  v  ivii     
  L1M4_orf2#LINE/    560 TTC-GTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAG 607

  chrX_137342485_   1094 CACAGAAAACAAAA------ACAGACAAATGGAACTATATTAAACTGAAA 1137
                             iiv       ------ i   i    v i   vi  i   v v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_137342485_   1138 AGCCTGTACACAGCAAAGGAAATAAGCAACAGAATGAAGAGACAACCCGT 1187
                          i i v iii vv       v iv v   v i i    i         ii
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_137342485_   1188 TGAATGGGAAAAAAAAAATTGGCCAACTATTCATCCAACATGGGACTAAT 1237
                         v        i    --v   v  v  ii  vi   ii i v      vi 
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAA--TATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_137342485_   1238 ATCCAGAATAACCAAGGAACTCAAACACCTCAAGATGATGAAAA--TAAA 1285
                                   vvi  i      vv   v     -- i  i    --i   
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAA--TAATAAAAAGACAAA 803

  chrX_137342485_   1286 TAATCTCATTTAAAAGTAGGCAAAATACAT-AATAGACATTTCTCCAAAG 1334
                            i iv   ?    i i      iv iv -                   
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_137342485_   1335 GAAATACACAAATAGCCAACAGGTATATGAAAAACATGCTCAATATCACT 1384
                         i i   i      i     i i i i       i-        i    ??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAG-ATGCTCAACATCAZZ 902

  chrX_137342485_   1385 ATCATC 1390
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.02 (18 / 894), avg. gap size = 1.50 (27 / 18)  


 474 25.88 3.53 2.94  chrX_137402800_137404394      230   399 (1196)    L1M4_orf2#LINE/L1       87   257 (651)  

  chrX_137402800_    230 AATTCAT-TTAAAA-CCCATTTGGGGCTCTTTTTGAGTAAATATTGACAA 277
                            i v - i    -    vi  --- ii      --i i v        
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTG---CCTTTTTTG--CAGAAATTGACAA 131

  chrX_137402800_    278 GATTATTTTTAAATGCATATGGAAATTCAAAGGACCCAGAATAGCTAACA 327
                          v v  ii v    v           v   i              i  v 
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chrX_137402800_    328 TAGTTTTCAA---TAACAGCAAAATGAGACAACTTAT-CTATTTGATTTC 373
                         i i i  v  ---v  v i    i vi  vi   i i-  viiii     
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_137402800_    374 AAAACTTACTATAATGCTATATCAAT 399
                                    i  v    i vi   
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAAT 257

Transitions / transversions = 1.59 (27 / 17)
Gap_init rate = 0.04 (6 / 171), avg. gap size = 1.83 (11 / 6)  

1764 23.41 8.62 1.79  chrX_137402800_137404394      500  1114 (481)    L1M4_orf2#LINE/L1      252   908 (0)  

  chrX_137402800_    500 AGTAATAAAAACAAAATAGCACTGACGTAAAGGTAGACATATAGATCAAT 549
                               v  i   ivi i i    i i   i i                 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_137402800_    550 AGAACAAAATGGA-AGTTCAGAAATAGACCCATACATACATATATAGCCA 598
                         i   i i   v  -   i        i          --- -   i i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT---T-TATGGTCA 347

  chrX_137402800_    599 AT-GATTTTTGACAAAGGTGCAAAGGCAATCCAGAGTCAAAAAGATAGTC 647
                           -      i     i     v   i v  i  iv vvi   ii      
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_137402800_    648 TTTTAAACAAATTGTGCTTAAACAGTTGAA-A-------GCAGAAACAAT 689
                             v       v     vii   ii  i - -------   -   v   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAAT 446

  chrX_137402800_    690 TAACCTG-ATTTTTTTTTCTGATCATACACAAAA-TTAACTTGAATTGGA 737
                         v  vi  - iiii vii  vv i    i      -      ii  v    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_137402800_    738 TTTTAGACCTAAATCTAAGATCCAAAATTATTAAATTTCTAGAAGA---C 784
                          iv?          v     v i    i   v   i ii       --- 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_137402800_    785 GTAAGAGAATACCATTATGATCTTGGGTTAGGAAAGAATTTCTTAAAGAG 834
                         i  i ? v v i v ii   i           v  vii       i v v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_137402800_    835 CACAC--AAAGTATATGGACCACAAGAAAAATGTTTAG-TAAATTGGACT 881
                         v    --    i i v v v  v        v---   -           
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAA---TAGATAAATTGGACT 643

  chrX_137402800_    882 GCATCAAAATTTAAAAGTATTGTTCTTCAAAATACATGAGTAAGAAAATG 931
                         v          v    v v    v       iv   iv vi      i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_137402800_    932 AAAAGATAAGCCATAGACTTGAAGAAA-TAGTTGCAAAACATG---CTGA 977
                               i  v   i   v v i     -  v       v   i---    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_137402800_    978 TAA---------------AATA-----------CTTACAACCTTACAATA 1001
                            ---------------    -----------        iiv i    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_137402800_   1002 A---GTTAAACAACCCAATT-AAAAATTGGCAAAAGATTTAATCGGCCAC 1047
                          --- vi   i         -      v      i     i vii v  i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_137402800_   1048 TTCACAAAAAAAATGGTATATGAACGGTCAGCAAGCACATGAAATGA-GC 1096
                            v v   i  -- i    ii  i  i  ii            v  -  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAA--GATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_137402800_   1097 AGACACTTCACAAAAGAA 1114
                         vv -  v   ????????
  L1M4_orf2#LINE/    892 TCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (83 / 59)
Gap_init rate = 0.03 (22 / 657), avg. gap size = 2.91 (64 / 22)  


 673 19.05 22.86 1.90  chrX_137412885_137416510.rev      289   498 (3128)    L1M4_orf2#LINE/L1       45   298 (610)  

  chrX_137412885_    289 TAAAACTAACAATCACATTCCACAAATTGATCCACTGACTCACTGCAATT 338
                            i - ii    --- i   v          i  v  i   vi     i
  L1M4_orf2#LINE/     45 TAAGA-TGGCAAT---ACTCCCCAAATTGATCTACAGATTCAACGCAATC 90

  chrX_137412885_    339 CCTATCAAAGTCACAGTTGCTTTTTGTATTAAAATTTAAAAGCTTGTCCT 388
                                  i  v   i   i    v iivi     v v     vi    
  L1M4_orf2#LINE/     91 CCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chrX_137412885_    389 GAAATTCATG-GGAAATGCAAGAGACC-AGAATAACTAAAACAAT----- 431
                         i        i-           i    -      i i        -----
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_137412885_    432 --------AACAAAGGTG-----------------------AAAA----- 445
                         --------       v  -----------------------    -----
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_137412885_    446 ---AAAACTGCAGTAATCAAGAAATTGTGATATTGCTATAAGAATAGA-- 490
                         ---   i  i            v v    i  i  vi     i     --
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_137412885_    491 TACAGATC 498
                           i     
  L1M4_orf2#LINE/    291 TATAGATC 298

Transitions / transversions = 2.08 (27 / 13)
Gap_init rate = 0.03 (8 / 254), avg. gap size = 6.50 (52 / 8)  

3029 26.51 1.10 1.21  chrX_137412885_137416510.rev      744  1652 (1974)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137412885_    744 TAGGAAAATATTCCATGCTCATGGATAGGA-GAATCAGTATCACTAAAAC 792
                          i i  i    i     i        v   -  v i i   iii   i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137412885_    793 GGCCATACTTCTCAAAGCAATTTACTGATTCAATCCTATTCCTATCAAAC 842
                            v     i i    vii  i   v       iv v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137412885_    843 TACCAATAATATTCTTCCCAGAACTAGAAAAAAAACT-ATTTTAAAATTC 891
                          v   iiviiv  i  iv     v v  v  i---  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_137412885_    892 ATATGGAACAACAAAAAAAGAGCCCA-AATAGCCAAGGCAATCCTAAGAA 940
                                 vvi   iii ----    -         ii     i i i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_137412885_    941 AAAAGAACAAAGCTGGAGGCATCATGCTACCCAACTTCAAACTATACTAC 990
                          i          i      vv   ii  v     i      viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_137412885_    991 AGGGCCACAGTAACCAAAACAGCATGGTACTGGTATAAGAACAGACACAT 1040
                          ii  i       i   i    ii         i     i i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_137412885_   1041 AGACCAAGGGAACAGAATAGAGAACCCAGAAATAAGACTGCACACATACA 1090
                            i   v    i     v    ii          iv iii   iv  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_137412885_   1091 ACTATCTGATATTCGCCAAACATGACTAAAACAAGCAATGGGGAAATGAC 1140
                         iii vi    v    v   ivi  v v i v  vv           vi i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_137412885_   1141 TCCCTATTCAATAAATGGTGCTGTGATAACTAGCTAGCCACATGCAGAAG 1190
                         vvi  v     i           v  i    i v  ?         i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_137412885_   1191 ATTGAAACTGGACCCCTTCCTTACACCATATACAGAAATTAACTCAAGAT 1240
                          v    ii         v   i            i            i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_137412885_   1241 GGATTACAGTCTTAAATGTAAAACCTAAAACTATAAAAACCCTGAAAGAC 1290
                             i ?  v i         i v              vi i ii    v
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_137412885_   1291 AACCTAGACAATACTATTCAGGACCTAGGCAAGGGCAAAGATTTCAT-GA 1339
                            v   i?ivv v v   iv     v  vvvi     v i    v -  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_137412885_   1340 TGAAGACAACCAAAGCAATTGCAACAAAAGTGAAAATTGACAAATGGGAT 1389
                          - v    v v      vvv          vi     v  i    v   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_137412885_   1390 CTAATTAAACTAAAGAACTTCTGCACAGCAACGGAAACTATCAACAGAGT 1439
                         i v  i   v v  i     i  ii vv   v   v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_137412885_   1440 AAACAGACACCCCACAGAATGGGAGAAAAATTTTGCAAACTATGCAATTG 1489
                         i  v     v                   vv        ii  ii vi  
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_137412885_   1490 ACAGAAATCTAATATCCAGCTTCTATAAGGAACTTCAACAAATTTACAAG 1539
                          i iiiiv  vi       vv v     i     iiv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_137412885_   1540 AAAAA-----ACAACCCCATTAGAAAGTGAGCAAAGATCATGAGCAGACA 1584
                              ----- i     v   ?i   i  i      iviv   ii     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_137412885_   1585 CTTTTCAAAAGAAGATATACATGCGGCCAGCAAGCCTAAGGAAAAAAAAT 1634
                         i  i  v              vii     ii    vi v ---    i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG---AAAAGAT 889

  chrX_137412885_   1635 -CTCAAAATCACTGATCAT 1652
                         -     v    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.10 (21 / 10)  

2281 20.58 7.65 0.68  chrX_137412885_137416510.rev     2548  3135 (491)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_137412885_   2548 AAGAATAGA--TATAGGTCAATGGAATATAATTAACAGTACAAAAATAAA 2595
                            i     --     i           v    i v   v  i       
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_137412885_   2596 CTCTTACACTTATTGTCAATTGACTTTCATCAAGAGTGCCAAGATAATTT 2645
                          i v    i    v         i    iv    i         iv   i
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_137412885_   2646 AATGGAAAAAGAAGACT-TTTTCAACCAAAGGTTCTGGGATAACTGGATA 2694
                              ii      v v -        v  v   v      i         
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_137412885_   2695 TCTAGACACAAAAGAATACAGTTGGACAACTTGCTCAGATCATGCATAAA 2744
                         ? i v ii         iv        vv  vv    v i   ii i   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_137412885_   2745 AATTAATTCAAAATATAAACA-ATATCTAAATATAAGA--TATAAACTTT 2791
                               i       i-i v  - v i      i     --  -     v 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATG-GATCAWAGACCTAAATGTAAGAGCTA-AAACTAT 527

  chrX_137412885_   2792 AAAACTCTCAGAAGAAAATGTAGGCATAAACATTTACAACTCTAGACTGG 2841
                                 i         ii    ?i    iv  iiii  ii i ii i 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_137412885_   2842 GCAA-ACCTTCTTAGATATGACACAAAAAGCACAAGTAAGAAAAGAAAGA 2890
                             -ivi                v           i  v        i 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_137412885_   2891 ATAACTAAATTTGACTTCATTAAAATTAAATATTTTTGTGCTTCGAAAGT 2940
                            iv      v        i         v i           i  i v
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_137412885_   2941 CA-TATAAAGAAAATGAAAAGGAAACCTACAGAATGAAGGAAAAAA-ATT 2988
                           -   v      i       iv    i        --   i    -   
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATG--GGAGAAAATATT 725

  chrX_137412885_   2989 TACAAATCA---------------------ATCCAGAATATATACATAAC 3017
                          i       ---------------------              v v   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_137412885_   3018 TTTTGTGATCAAATGTTTG---------TGATTCAAT------GTGATCA 3052
                          i  iii iiv   iv vi--------- i ii    ------i  iv  
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_137412885_   3053 AATGATCTGAATAGACATTTCTCCAAAGACTACATCGAAATAGCCAATGA 3102
                           v   i                      vv i  vv    i      i 
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_137412885_   3103 GCACATGAAAAAATGTTCAACACCATTAGTCAT 3135
                                    i   i      i  ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (76 / 43)
Gap_init rate = 0.02 (13 / 629), avg. gap size = 3.77 (49 / 13)  


2193 26.33 4.70 0.16  chrX_137430587_137433277     1053  1690 (1001)    L1M4_orf2#LINE/L1        9   675 (233)  

  chrX_137430587_   1053 TATCCTGTGTTCATAGTTTGGAAGAATTAATTTTGCAAAAATGTTGATAC 1102
                              ii       i v        v     v   iv  i   vii    
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chrX_137430587_   1103 TAACCAAAGTGATCTACAGAGTCAATGCAAGCACTATCAAAATCTTAATA 1152
                          vv     v           v    i    v v           ii iiv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chrX_137430587_   1153 TAATTTTTTACAGAAATAGAAAAAAAATTCTTAAAAC-CTTATGGAACCA 1201
                         vvv      i       v  v  ivviv  i     i- v       vii
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_137430587_   1202 CCTAAGTCCCCAAAGATCTAAAACAATCTTGAGAAAGAAG------TTTA 1245
                          vvii v   vi  v v i             i       ------v  i
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_137430587_   1246 GA------ACATTTCCTGATTTCAAATTATATTGTAAAGCTATAGTAATC 1289
                           ------   i    ii        viv  i ii       i       
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_137430587_   1290 AAAACAGTATGGTATTGGCATAGAAGCAGACACATAGACCAATGGAACAG 1339
                           i     i     i       iiiii     i     i        i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_137430587_   1340 AATAGAAAGCCAAGAAACAAATCCACACATATATGATCAACAAATCTTCA 1389
                            v  i  i v     i   i   i    v    i    ivi  i   i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_137430587_   1390 ACAAAGGCACTAAAAACACATCATGGGGAAATA-TAGTCCATTCAATAAA 1438
                             i  ii i  i v  iviv         v -     iv     i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_137430587_   1439 TCGTATTTTAAACATTGAATATCCAAATACAAAATAATGAAATTGGACCT 1488
                          v  ii vvi vv i  i   ?   v  i     v      i       i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_137430587_   1489 TTATCCTATACCATACACAAAAATCAACTCAAAATCGATTAAAAACTTAA 1538
                         i  i ii i      i        i          v   i ? i  i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_137430587_   1539 ACATAAGACCTAAAATTGTAAAATTACTAGAATAAGAAATA-------AT 1581
                          ii     v      i i     i vi     v  i v   -------  
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_137430587_   1582 GTCTATGGCATTGGTCTTGGCAATAACTTTTTTGGCTGTAACACCAAAAG 1631
                         v iii  i v    vi v      ii-   i  i v i i          
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGG-TTTCTTAGATATGACACCAAAAG 607

  chrX_137430587_   1632 CACATGCAACAAA-GTAAAAATAAACAAGTCAGACTACATTAAA-TTAAA 1679
                             v        - v       i i  i ii    v   i   -     
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_137430587_   1680 AA-------GTTTCAAAG 1690
                           ------- i       
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAG 675

Transitions / transversions = 1.77 (106 / 60)
Gap_init rate = 0.01 (9 / 667), avg. gap size = 3.44 (31 / 9)  

1113 19.62 0.00 1.89  chrX_137430587_137433277     1934  2198 (493)    L1M4_orf2#LINE/L1      649   908 (0)  

  chrX_137430587_   1934 AAAATAAAAAAATTATCTGCCCAGCAAAGGAAATAATCGACAAAACGAAA 1983
                              v     v  v v   ii--       v iv   i v   ii    
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_137430587_   1984 AGGCAACCTGCAGAATAGGAGAAAATATTTGCAAACCATATTTCTCATAA 2033
                           i     ii      i                  i     v   v    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_137430587_   2034 GGGGTTAATATCCAAAATATATAAGGAACTCATACAAGTCAATAGCAAAA 2083
                            ii vi      i         i      v     v      ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_137430587_   2084 ATACAAGTAAACTGTATTTTGAAAAATGGACCAAGGAGCTGAATAGACAT 2133
                          v    i   v ii-   ?--        i v     vi           
  L1M4_orf2#LINE/    797 AGACAAATAACCCA-ATTW--AAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_137430587_   2134 CTCTCCAAGGAAGACATACAAATGGCCAACATATATCTGAAAAGGTACTT 2183
                         i       i     i              i vii iv       i i  i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_137430587_   2184 AACATCATTAATCAT 2198
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (33 / 18)
Gap_init rate = 0.01 (3 / 260), avg. gap size = 1.67 (5 / 3)  


 295 19.12 2.94 0.00  chrX_137585490_137591758      366   433 (5836)    L1M4_orf2#LINE/L1      839   908 (0)  

  chrX_137585490_    366 GGTATTTCTCAAAAGAAAACATACAAATGGC--ACAGATATATGAAAAGG 413
                          ii       v      i i           -- i iii i        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_137585490_    414 TGCTTAACATAATTATCAGA 433
                             i     v ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 5.50 (11 / 2)
Gap_init rate = 0.01 (1 / 70), avg. gap size = 2.00 (2 / 1)  

3290 26.21 0.55 0.55  chrX_137585490_137591758     4869  5776 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137585490_   4869 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4918
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137585490_   4919 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4968
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137585490_   4969 TACCAA-TGCCTTTCTT-CACACAATTGGAAAAAACT-ACTTTAAAGTTC 5015
                          v   i-       i  -  v -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_137585490_   5016 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 5065
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_137585490_   5066 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5115
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_137585490_   5116 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5165
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_137585490_   5166 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5213
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_137585490_   5214 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5263
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_137585490_   5264 CCTATTTAATAAATGGTACTGGGAAAACTGGCTAGCCATATGGAGAAAGC 5313
                         i  v  i  i       i      v      v  ?   i   v i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_137585490_   5314 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5363
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_137585490_   5364 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5413
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_137585490_   5414 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5463
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_137585490_   5464 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5513
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_137585490_   5514 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5563
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_137585490_   5564 CAGGCAACCTACAAAATGGAAGAAAATTTTTGCAACCTACTCATCTGACA 5613
                         v  i     i   i     i       v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_137585490_   5614 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5663
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_137585490_   5664 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5713
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_137585490_   5714 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5763
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_137585490_   5764 CATCACTGGCCAT 5776
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2609 29.55 0.99 0.99  chrX_137603993_137606582.rev     1193  2099 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_137603993_   1193 GAAAAAAAAATCCATGCTCATGGATAGGAAGAGTCAATATCGTGAAAATG 1242
                          i   i v vi     i        v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_137603993_   1243 GCCACACTGGCCAAAGTAATTTATAGATTCAGTGCTATTCC-ATTAAGCT 1291
                           v i   vv     v i  i  i       ii  v  i  -  i  iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_137603993_   1292 ACCATTGACTTTCTTCACAGAAGTAGAAAAAAAAAACT-ACCTTTAGTTT 1340
                         v   vivi i  i  ii     i v  v  i-----  - i i v iv  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAATT 146

  chrX_137603993_   1341 CATATGGAACCAAAAAAGAACCCGTATAGTCAAGACAATCCTAAGCAGAA 1390
                                  viiv  ii  v  v v    i   i      i i iv ii 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_137603993_   1391 AGAACAAAGCTGGAGCCATGATGCTACATGACTTCAAACTATACTACAAG 1440
                                  i     vvv v ii  v vii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_137603993_   1441 GCTACAGTAACCAAATCAGCATGGTACTGATACCAAAATAGATATATAGT 1490
                                   i   iv   ii        ii iv ii     i      v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_137603993_   1491 CCAATGGAACAGAACAGAGGCTTGAGAAATAACAGCACACATCTACAATC 1540
                         i        i    iv   iv iv        vvv  i    i  iii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_137603993_   1541 ATCTGGTCTTCAGTAAACTTTACCCAAAAAAAAGCAATAGGGAAAGGATT 1590
                          vi  i i   iii  ivv v--    i vv vv    i       i  v
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTG--CCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_137603993_   1591 CCCTATTTAATAAATGGCGTTGGGAAAACTGGCTAGCCGTATCCAGAAAA 1640
                         vi  v  i  i      i i     v      v  ?  ii  v  i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_137603993_   1641 CAGAAAGTGGATTCCTTTCTTACACCTTATACAAAAATTGGCTCAAGATG 1690
                         vv   iv    ii   vi  i     v            ii     i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_137603993_   1691 GATTAAAGACATAAACATAAAACGTAATACCATAAAAACCCTAGCAGAAA 1740
                            i ?    v    ii   i vv   v  i      vi i   v     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_137603993_   1741 ACCTAGGCA-ATACCATTCAGGACACAGGCATGGGCAAAGACTTCATGAC 1789
                           v    ?i- v i -   iv   viv  vv i     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_137603993_   1790 TAAAACATCAAAAGCAATTGCAACAAAAGCCAAAATTGACAGATGGGACC 1839
                           vi   i        vvv          vv     v  i i  v    i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_137603993_   1840 TAATTCAACTTAATAGCTTCTGCACAGCAAAATAAACTATCATCAGAGTG 1889
                          v  iv  v    v i   i  ii vv    iv v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_137603993_   1890 AACAGGCAACCTACAGAATGGGAGAACATTTTTG-AAATCTATCCATCTG 1938
                           v  i     i              v  v    -     -  vi     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTG 742

  chrX_137603993_   1939 GCAAAGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAG 1988
                         ii  i  v  vi          v  i  i     ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_137603993_   1989 AAAAAAACAA----CCCCATCATAAAGGGGGCAACGTAAATGAACAGACA 2034
                              i    ----   v  i?v   iv      v v vv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_137603993_   2035 ATTCTCAAAAGAAGACATTTATGCGGCCAACAAACATATGAAAAAA-ACT 2083
                         v     v        i  vi vii      i  i  i       i -i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_137603993_   2084 CATCATCACTGGTCAT 2099
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (146 / 118)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 1.80 (18 / 10)  


3223 27.23 0.44 0.44  chrX_137614520_137619038     3120  4026 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_137614520_   3120 GGAAGAACATCCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAATG 3169
                             ii i        i        v      v i        v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_137614520_   3170 GCCATACTGCCCAAGGTAACTTATAGATTCAATGCCATCCCCATCAAGCT 3219
                           v     v     iv i ii  i        i  v     i     iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_137614520_   3220 ACCAATGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAGTTCATA 3268
                         v   iivi i  i  ii     v v  v  i-  - iii    i      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chrX_137614520_   3269 TGGAGACAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCAAAAGAA 3318
                             i iiv  ii  v  v v  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_137614520_   3319 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 3368
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_137614520_   3369 CAATAACCAAAACAGCATGGTACTGGTGCCAAAACAGAGATATAGACCAA 3418
                           i   i   i    ii         iiiv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_137614520_   3419 TGGAACAAAAC--AGAGCCCTCAGAAATAATACCACACATCTATAAGCAT 3466
                              i i  i--    i  --        vv   i    i   iiv  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_137614520_   3467 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 3516
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_137614520_   3517 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3566
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_137614520_   3567 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 3616
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_137614520_   3617 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3666
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_137614520_   3667 AGGCA-ATACCATTCAGGACATAGGGATGCGCAAAGACTTCATGACTAAA 3715
                            ?i- v i -   iv   v v   v iv    v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_137614520_   3716 ACACCAAAAGTAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 3765
                                   i vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_137614520_   3766 GAAACTAAAGAACTTCTGCACAGCTAAAGAAACTACCATCAGAGTGAACT 3815
                         v   v v  i     i  ii vv v  i  v    i  vv i      vv
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_137614520_   3816 GGCAACCTACAGAATGGGACAAAATGTTTACAATCTACCCATCTGACAAA 3865
                          i     i           v     i   i   vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_137614520_   3866 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAGTTTACAGGAAAAA 3915
                           i  vi          v  i        ivv    v iv i iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_137614520_   3916 ATCAAACAACCCCATCAACAAGTGGATGAAGGATATGAACAGACACTGCT 3965
                         iv    i     v  i? v  i   iii      v    i     i v  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_137614520_   3966 CAGAAGAAGACACTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 4015
                          vi       i ivi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_137614520_   4016 TCACTGGCCAT 4026
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (147 / 96)
Gap_init rate = 0.01 (6 / 907), avg. gap size = 1.33 (8 / 6)  


 250 30.28 9.96 3.19  chrX_137621250_137624427      535   785 (2393)    L1M4_orf2#LINE/L1        1   268 (640)  

  chrX_137621250_    535 TAGAAAGACATTTCTTGTTTTTTGATAGGATGACTCAATAGTATAAATAT 584
                          i      i  ii v    iv v   v   v    i    v i v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137621250_    585 G-----------TAAATTAATTCATAAATTTAATATAATCCCAATAAAAA 623
                          -----------i     i  ii i i   i  iii      v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137621250_    624 TAACAA-TAAGTTATTTTTAGAATTAGACAAGTTG-TCACTGAACCTCAC 671
                          vv  i- ivv  v   vi    v v      i  -  -  i  vi   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-CTAAAATTCAT 149

  chrX_137621250_    672 ATGGAAA---AATTAAC----AATAGCCAGTGAAACA--C---ACAAAAA 709
                                ---  vvi  ----        ---     -- --- v   i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCA---AAACAATCTTGAAAAAGA 196

  chrX_137621250_    710 ATGATAAACTATGAGCAGGTACTAGCCCTACTAGACAGTAAAACATACTA 759
                          vi i   v -  i--   -   vi v  v ivi ivvi     v     
  L1M4_orf2#LINE/    197 AGAACAAAGT-TGG--AGG-ACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_137621250_    760 TAAATCATCTATAATTTAAAGGGTGT 785
                         i   v vv vi    iv i vi    
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGT 268

Transitions / transversions = 1.05 (39 / 37)
Gap_init rate = 0.04 (12 / 268), avg. gap size = 2.75 (33 / 12)  

1007 22.56 1.50 0.00  chrX_137621250_137624427      788  1053 (2125)    L1M4_orf2#LINE/L1      639   908 (0)  

  chrX_137621250_    788 GGATTGCATCAAACTAAATAGCTTCTGCACAGCAAAAGAAACAATGAACA 837
                            i v       v v  v i   i  ii vv    i  v  v  v  v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_137621250_    838 GAGTGAAGAGATAACCTATGGAATGGAAAAAAAAATTT-CAAACCATACA 886
                         i      i   i    i ii      i i    v    -    i    i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_137621250_    887 TTT---AAGGGATTAGTATACAAAATATATAAGGAACTCAAACAACTCAA 933
                          i ---      i v    v  i         i      vv         
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_137621250_    934 TAGCAAGAAAACAAATAACCAAAAGAAAAAATGAGCAAAGCACTTAAGTA 983
                           ii  i  i          v  vv?       i      v i  i i  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_137621250_    984 GACATTTCCCAAAAGAAGGCATACAAATGGCCAACAGGTATAAGAAAAAA 1033
                                 i v       ii              i i i i v     i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_137621250_   1034 TGCTCGACATCCTAATTATC 1053
                              i     v????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (37 / 22)
Gap_init rate = 0.01 (2 / 270), avg. gap size = 2.00 (4 / 2)  

 201 29.41 10.00 4.12  chrX_137621250_137624427     1940  2109 (1069)    L1M4_orf2#LINE/L1      265   444 (464)  

  chrX_137621250_   1940 GTGTGGTACTGACACATCAATAGA------GCCCAGTTAAATAGAGTAGA 1983
                                    i  i vvi     ------ vi  i vi      i v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_137621250_   1984 AAGTTCAGAAATAGACATAAGAAAATATGG--AACTTTAGTATATAATAA 2031
                         i   i        i  vi viv vv     --  --  ii v vii i  
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAA--TTGATTTTCGACAA 362

  chrX_137621250_   2032 AGGTGACATCTCAAATAACTT--TAGAGAAG--ATGGAGTTTTCAA---A 2074
                         i    v  ---- i iv i i-- i i   i--  i vv       --- 
  L1M4_orf2#LINE/    363 GGGTGCCA----AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_137621250_   2075 TGATACTGCAACAA-TGGACA-CCATTTAGGAAAAGA 2109
                           i i   vi    -    i -   iv - v      
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGA 444

Transitions / transversions = 1.63 (31 / 19)
Gap_init rate = 0.06 (10 / 180), avg. gap size = 2.40 (24 / 10)  

 570 25.22 3.26 8.91  chrX_137621250_137624427     2232  2691 (487)    L1M4_orf2#LINE/L1      475   908 (0)  

  chrX_137621250_   2232 ATAAAAATAAATTCCAAATGGATCAGGGATCTAATTGTTCAA--TAAAAC 2279
                          i      v  i  v          ?i  i    v   vvi --      
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_137621250_   2280 CAAACAAACACT-AGGAGAAAACATGGGTG-AATTCTTCTTAAACT-GGG 2326
                         i v -    v  -  i         i  ? -  v     v i v  -   
  L1M4_orf2#LINE/    525 TATA-AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_137621250_   2327 TGTAGA-AAGAGTTCTCCTAATTAGAACTCCAAATCCAGGTACAATAAAA 2375
                          -   i-  vi   -  i  iv  vi  v     vv  vivi   i    
  L1M4_orf2#LINE/    574 T-TAGGCAATGGTT-TCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_137621250_   2376 CAAATGATTGTTAAATCTGACTACATAGCAACAACCAAAAACCTAATGCA 2425
                         v   vi  v v     iv    v   --   -  ii      i v-  --
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCAT--CAA-AATTAAAAACTTT-TG-- 665

  chrX_137621250_   2426 TGCCCAAAATTACCATAAAGAAATCAAAAGATACCATAAAGAAACCATAA 2475
                            i-------------------     i  i  i  v      ------
  L1M4_orf2#LINE/    666 TGCT-------------------TCAAAGGACACTATCAAGAAA------ 690

  chrX_137621250_   2476 AGAAATCAAAAGATAACTGGCAAAAGAGGAGGAA-TAATTGAAACACATA 2524
                         ----i v      i   ivi  i  vi    i  -  v   v  vv    
  L1M4_orf2#LINE/    691 ----GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_137621250_   2525 TAACAGATAAATGGCTAATACCTCTAATATGCAAAGAATTCTTAAAATTC 2574
                           v v     iv i  vi  i ivv     ii      i     v  i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_137621250_   2575 AAGGGGATAAAAAAACAAAT--CTCAGATAGAACAATGATCAAAA-ATAT 2621
                           vi--       i      -- i  iv ?i  -    iv    i-  v 
  L1M4_orf2#LINE/    787 AATA--ATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTT 833

  chrX_137621250_   2622 GAA--AATAAGTCAC--AAGA-GATATTAAAATGGCTTTTACGTTTATGA 2666
                            --i i vv  v --    -     vv       ivv  v ivi    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_137621250_   2667 AAAAATATTCACCCTTACTCATAAA 2691
                            i  ii   v v i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.05 (58 / 55)
Gap_init rate = 0.05 (22 / 434), avg. gap size = 2.55 (56 / 22)  


3060 26.16 1.43 1.32  chrX_137639594_137645205.rev     4216  5121 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_137639594_   4216 GGAGAAACATTCCATGCTCATGGACAGGAAGAATCAATATTGTTAAAATG 4265
                            i i i  i     i       iv      v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_137639594_   4266 GCCTTATTGCCCAAAGCAATTTATAGATTCAGTGCCATTCCTATTAAACT 4315
                           vv  i v      vii  i  i       ii  v  i     i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_137639594_   4316 ACCATTGACATTATTTATAGAACTAGA--AACT-ATTTTAAAATTCATAT 4362
                         v   vivi v  v   ii    v v  -- i  -  ii            
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_137639594_   4363 GGAACCTACAAAG-ATCTTGAATAGCCAAGGCAATCCTAAGCAAAAAGAA 4411
                             v- i   i - i iv          ii     i i iv  i     
  L1M4_orf2#LINE/    152 GGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_137639594_   4412 CAAAGTAGGAGGCATCATGCTACCTGACTTCAAGCTATATACTACAGGAC 4461
                               v     vv   ii  v  ii i     i-- iv       iii 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAGC 248

  chrX_137639594_   4462 TACAGTAACCAAAACCACATGGTACTGGTACAAAAATAGACACGTAGACC 4511
                                 i   i  viii         i i  ii       ii    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_137639594_   4512 AATGGAACAGAATAGAGAGCCCAGTAATAAGTCTGCACACCTATAACTAT 4561
                                i     v     i    v     ii iii   ii   iiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_137639594_   4562 CTGATCATTGACAAACCTGACTAAAACAAGCAATGGAGGAAGGA--GTCA 4609
                         i    iv i     ivv  v v i v  vv      i i   i --   -
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC- 397

  chrX_137639594_   4610 CTATTCAATAAATTGTGCCGGGATAAATGACTAGCCATATGCAGAAGTTT 4659
                         - v     i    v    i    i  v  iv  ?   i     i   vv 
  L1M4_orf2#LINE/    398 -TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_137639594_   4660 GAAACTGGAACCTTTTCTTACACCATATACAAAAATCAACTGAAGAAGGA 4709
                            ii    v  i vi  i                 i    v  i v   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_137639594_   4710 TTAAAGACTTAAATGTAAAATCCAAAACTATAAAAACCCTAGAAGAAAAC 4759
                          i ?    i         i v i            vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_137639594_   4760 CTAGGCA-ATATCATTCAGGATATAGGCATGGGCAAAGATTTTATTATGA 4808
                         v    ?i- v   -   iv  iv v  vv i     v i   i-   -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC-TTA-GA 593

  chrX_137639594_   4809 -A-GATGCCAAAAGCAATAGTGACAGAAGCAAAAATTGACAAATGGAATC 4856
                         - -  ii         vv  ii   i   v      v  i    v i ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_137639594_   4857 TAATTAAACTAAAGAGGTTTTGCACAGCAAAATAAGCTATCAAAAGACTA 4906
                          v  i   v v  i iv     ii vv    iv vi       i i v i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_137639594_   4907 AACAGACAACCTACAGAATGGGAGACAATTTTGGCAAGACATGCATCTGA 4956
                           v        i             v   v  v    iv   ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_137639594_   4957 CAAAGG--TCGACATCCAGCATCTATAAGGTACTTAAACAAATTTACAAG 5004
                         i  i  -- i -i      v  v     i v   ivv    v ---   v
  L1M4_orf2#LINE/    744 TAAGGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACT---CAAT 789

  chrX_137639594_   5005 AATAAAAA--CAAACAACCCTATTAAAAAGTGGGTAAAGGACATCAACAG 5052
                                 --    i     v   ?    i    i      iv v  i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_137639594_   5053 ATACTTTTCCAAAGAAGACATACATGTGACCAATAATCAAATGAAAAAAA 5102
                          i i  i           i     vi  i       v  v       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_137639594_   5103 AATCAACATCACTGGTCAT 5121
                         iv         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (144 / 89)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 1.47 (25 / 17)  


2906 27.83 1.77 1.11  chrX_137658670_137661155     1092  1993 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137658670_   1092 TGGAAAAACATTCCATGCTCATGGATAGAAAAAATAAATATGTTTAAAAT 1141
                               i i  i     i        v i  i v v     vv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137658670_   1142 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCTGTTAAAC 1191
                            v     v      v i  i  i        i  v  i   i i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137658670_   1192 TACCATTTACATTATTCACAGAATTAGAAAAAAACAATTTTACAATTCAT 1241
                          v   vi i v  v  ii     v v  v  iv-ii  ii  v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_137658670_   1242 ATGAGACCA-AAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAAAAGA 1290
                            ii vii-  ii  v  v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_137658670_   1291 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAAGTATACTGTAACGGT 1340
                               i      vv       v  ii i      iiv    ii  v v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_137658670_   1341 ACAGCA------------TGGTACTGGTACAAAAGCAGACACATACAACA 1378
                             i ------------         i i  iiii     i   v v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_137658670_   1379 ATGGAACAGAATAGAGAACTCAGAAATAAGACCGCACACCTACAACCATC 1428
                               i     v    iii         iv  ii   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_137658670_   1429 TGATCTTTGACAAACTTGACAAAAACAAGGAGTTGGGAAAGGATTCCCTA 1478
                             i  i     ivv  v   i v  vvv i v       i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_137658670_   1479 CTTAATAAATGGTGCTGGGTGAACTGGCTAGCCATATGCAGAAAATTGGA 1528
                         i i  i             vv      v  ?   i     i  i v  i 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_137658670_   1529 ACTGGACCTCTTCCTTGTACCTTATACAAAACTTAATTCAAGATGGATTA 1578
                         ii      i  v   iii   v         v    i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_137658670_   1579 AAGACTTAAATATAAAACCCAAAACTACAAAAACCCTAGAAGAAAATCTA 1628
                         ?    i     i   i v i       i    vi i          iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_137658670_   1629 GGC---AATGCCATTCAGGACATAGGCATGGGCAAAGATTCCATAATGAA 1675
                           ?---   -- -   iv   v v  vv i     v i  i v  ivv v
  L1M4_orf2#LINE/    550 GGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_137658670_   1676 AACATCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATTTAA 1725
                         i   i        vvv          v      v  i    v   i  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_137658670_   1726 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAAC 1775
                          i   v v  i i   i  ii vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_137658670_   1776 AAACAGCCTATAAAATGGGAGAAAATGTTTGCAATCTGTCTATCTGGCAA 1825
                          i   i  i i i             i       viii v      ii  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_137658670_   1826 AGGTCTAATATCCAGAGCCTAAAAGGAACTTAAACAAATTTACAAGGGAA 1875
                         i  v  vi        iiv  v  i     ivv    v iv i  vii  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_137658670_   1876 AAACTAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTT 1925
                          i  -   i     v   ?    i           iv    i     i  
  L1M4_orf2#LINE/    797 AGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_137658670_   1926 CTCAAAAGAAGACATTCATGCAGCCAACAAACACATTAGAAAAAAAAAAG 1975
                            v        i  v  viii     i  i     -----i    i v 
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACAT-----GAAAAGATG 890

  chrX_137658670_   1976 CTCATTATCACTGATAAT 1993
                             vi    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.25 (26 / 8)  


3115 26.64 0.77 1.21  chrX_137803246_137809783     5134  6045 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137803246_   5134 TGGAACAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTAAAAAT 5183
                              vi i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137803246_   5184 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCACCATCAAGC 5233
                            v     v     iv i  i           i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137803246_   5234 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACAACTTTAAATTTCA 5282
                          v   iivi i  i  ii     -   -- v  ivii iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_137803246_   5283 TATGGAACCAAAAAGAGCCCACA-TAGCCAAGACAATCCTAAGCCAAAAG 5331
                                viiv  i ii    v -       i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_137803246_   5332 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5381
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_137803246_   5382 TACAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5431
                              i  i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_137803246_   5432 AATGGAACAGAAC--AGAGCCCTCAGAAATAACATCACAAATCTACAACC 5479
                                i    i--    i  --        vvi  i v  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_137803246_   5480 ATCTGATCTTTGACAAATCTGATAAAAACAAGCAATGGGGAAAGGGTTCC 5529
                          vi    i  i     ivv  vi  i v  vv            ii vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_137803246_   5530 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAGCT 5579
                           v  i  i              v      v  ?   i     i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_137803246_   5580 GAAACTGTTTCCCTTCCTTACACCTTATACAAAAATTAACACCAGATGGA 5629
                            ii  vvi    v   i     v               v v i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_137803246_   5630 TTAAAGACTTAACTGTAAGACCTAAAAACCATAAAAACCCTAGAAGAAAA 5679
                          i ?    i   v       v      - i      vi i          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAA 545

  chrX_137803246_   5680 CCTAGGCA-ATACCATTCAGGACTTAGGGATGTGCAAAGACTTCATGACT 5728
                          v    ?i- v i -   iv   i v   v iv    v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_137803246_   5729 AAAACACCAAAAACAATGGCAAGAAAAGCCAAAATTGACAAGTGGGATCT 5778
                          vi         i  vvi    v     vv     v  i  i v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_137803246_   5779 AATTAAACTAAAGAGCTTTTGCATAGCAAAAGAAACTATCATCGGACTGA 5828
                         v  i   v v  i i      iiivv    i  v       vvii v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_137803246_   5829 AAAGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTGTCCATCTGAC 5878
                             i     i       i         v       viii vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_137803246_   5879 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5928
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_137803246_   5929 AAAAACAAACAACCCCTTGAAA--AAAAAATGAGTGAAGGATATGAACAG 5976
                            i     i     -----  --?       i ii      v    i  
  L1M4_orf2#LINE/    795 AAAGACAAATAACCC-----AATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_137803246_   5977 ACTCTTCTCAAAAGAAGACATTTATGTAGCCAACAAAGTTAGGAAAAAAT 6026
                           vi     v        i  vi vi i     i  ivvi v     i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_137803246_   6027 TCTCATCATCACTGGTCAT 6045
                         v    v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


2942 27.21 1.11 0.66  chrX_137816963_137821285     2927  3830 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137816963_   2927 TAGAAACACATCCCATTCTCATAAATGGGTAGAATCAATATTGTTTAAAT 2976
                          i    v i       vi    ii  v  v   v i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137816963_   2977 GACCATACCACCAAAAGCAATCTACAAATTTAATGCAATTCCCATTAAAA 3026
                          i v    iv  v   vii       i   i  i     i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137816963_   3027 TATCA-CCGTCATTCTTCACAGAACTAGAAAATAAAC-AATCCTAAAATT 3074
                          vi  - i i -  i  ii     v v  ---i  i -i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGA---CAAGCTGATCCTAAAATT 146

  chrX_137816963_   3075 CAGATGGGACCAAAAAAAGAGCCCACA-TAGCCAAAGCAAGACTAAGCAA 3123
                           v    i -- viv  i ii    v -        i   vvi i iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_137816963_   3124 ATAGAACAAATCTGGAGGTATCAGATTACCTGACTTCAAACTATACTATA 3173
                         iv        vi      vv   v i v  ii i      viv     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_137816963_   3174 AGGCCATCGTCACCAAAACAGCATGGCACTGGTATAAAAATAGGCATCTA 3223
                          i  i iv  v i   i    ii   i     i    ii    i   v  
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_137816963_   3224 GACCAATTGAACAGAAAAGAGAACCCAGAAATAAACCCAAATACTTACAG 3273
                           i    v   i    vv    ii               v i i   ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_137816963_   3274 CCAACTGATTTTCAACAAAGCAAAGAAAAACATAAAGTGGGGAAAGGACA 3323
                         i   i        i    i vvivv  i v   vv i         i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_137816963_   3324 CCCTGTTCAACAAATGATGCTGGGATTATTGTCAAGCCACATATAGACAA 3373
                         vi  v           i        iv i  vvv ?      ii i vi 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_137816963_   3374 ATGAAACTGGATCCTCATCTCCTACCCTATACAAAAATCAACTCAAGATG 3423
                              ii    i  ii i   vi   v           i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_137816963_   3424 GATCAAAAACTTAAATTTAAGA-CTGAAGCCATAAAGATTTTAGAATATA 3472
                              ? i  i     v     -  i  i i     iv i      v v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_137816963_   3473 ACATTGAAAAAACTCTTCTAGACATTGGCTTAGGCAAAGATTTCATGACC 3522
                             v i?iv  v     vv   v    v        v i    v iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_137816963_   3523 AAGAATGCAAAAGCAAATGCAACAAAAACAAAGATAAACAGATGGAACTT 3572
                          v  vvv        v v         iv   i   i i i  v i    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_137816963_   3573 AATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCAGCAGAGTTA 3622
                         v  i   v v    i   i  ii vv    i  v iv    iv i   v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_137816963_   3623 ACAGACAACCCACAGAGTGGGAGAAAATCTTCACAATTTACACATCCAAC 3672
                          v              i           v  ii   v i i i   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_137816963_   3673 AAACAACTACTATTCAGAATGTACAAA-AACTC----AAATCAGCAAGGA 3717
                           ivi   vv   i      i  i   -     ----  v   ii  vi 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_137816963_   3718 AAAAACAAACAATCCCATCAAAAAGTGGGCTAAGAACATGAAAAGACAGT 3767
                            i     i  i  v  i?    i     v   i iv    v     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_137816963_   3768 TCTCAAAAGAAGATATACAAATGGTCAACAAGCATATGGAAA-ATGCTGA 3816
                             v                   i   i     i   i   -     v 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_137816963_   3817 ACATCACTGATGAT 3830
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


 925 27.48 1.32 2.32  chrX_137860687_137863487.rev     1084  1385 (1416)    L1M4_orf2#LINE/L1        1   299 (609)  

  chrX_137860687_   1084 TGGAAACACATCCCATTCTCATAAATGGGTAGAATCAATATTGTTTAAAT 1133
                               v i       vi    ii  v  v   v i         v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137860687_   1134 GACCACACTGCCAAAAGCAATCTACAAATTTAATGCAATTCCCATTAAAA 1183
                          i v i   v  v   vii       i   i  i     i  i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137860687_   1184 TACCACCATCATTCTTCACAGAACTAGAAAATAAAC-AATCCTAAAATTC 1232
                          v   v vv v  i  ii     v v  ---i  i -i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA---CAAGCTGATCCTAAAATTC 147

  chrX_137860687_   1233 ATATGGGACCAAAAAAAGAGTACACA---TAGCCAAAACAAGACTAAGCA 1279
                               i --- viv   i -  v  ---            vvi i iv 
  L1M4_orf2#LINE/    148 ATATGGAA---ATGCAAGGG-ACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_137860687_   1280 AATAGAACAAATCTGGAGGCATCAGGTTACCTGACTTCAAACTATACCAG 1329
                          iv        vi      vv   vii v  ii i      viv   i v
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_137860687_   1330 AAGGCCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCATGT 1379
                           i  i i   v i   i    ii         i    ii    i   i 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_137860687_   1380 AGACCA 1385
                            i  
  L1M4_orf2#LINE/    294 AGATCA 299

Transitions / transversions = 1.52 (50 / 33)
Gap_init rate = 0.02 (5 / 299), avg. gap size = 2.20 (11 / 5)  

2209 26.43 0.48 0.32  chrX_137860687_137863487.rev     1683  2310 (491)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_137860687_   1683 AAAAAAAGGCACGTAGACCAATCGAACAGAACAGAGAACCCAGAAATAAA 1732
                           ii v  i  ii    i    v   i    iv    ii           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_137860687_   1733 CCCAAATACCTTCAGCCAATTGATCTTTGAAAAGCA-AACAAAAACATAA 1781
                             v i ii vii i        i  i  v   vi-iv   i v   vv
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_137860687_   1782 GGTGTGGAAAGGACACCCTTTTCAACAAATGGTGCTGGGATAATTGGCTG 1831
                         ii  v      i i vi                       i  i   v i
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_137860687_   1832 GCCACATGTAGGAGAATGTAACTGGATTCTCATCTCTCACCTTATACAAA 1881
                         ?       i ii      v ii    ii ii i   v    v        
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_137860687_   1882 AATCAACTCAAAATGGATTAAGGACTTAAACCTAAGACCTGAAACTATAA 1931
                            i              i ?i   i    iv     v  i         
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_137860687_   1932 AAATTCTAGAAGATAGCATTGGAAAAACCCTTCCAGACATTGGCTTAGGC 1981
                           v ii       v i   v  ?iv  vi    vv   v    v      
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_137860687_   1982 AAGGATTTCATGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAGAT 2031
                           v i    v iivi v  vv         v v    i    iv   i  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_137860687_   2032 AAATAGTTGGGACTTACTTAAACTAAAGAGCTTTTTAGACATCAAAAGGA 2081
                          i   iv v      vv i   v v  i i     -ivi v     i iv
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTT-GTGCTTCAAAGGAC 678

  chrX_137860687_   2082 ACAGTCAACAGAGTAAACAGACAACCCACAGAGTGAGAGAAAGTCTTCAC 2131
                           vi    v i   i  v              i  i      i v  ii 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_137860687_   2132 AATCTGTACATCGGACAAAGGACTAATATCCAGAATCTACAAGGAACTCA 2181
                           viii  i   v  i  i     vi          v  i  i      v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_137860687_   2182 AACCAATCAGTAAGAAAATAACCACACAGTCCCATCAAAAAGTGGGCTAA 2231
                         v  v v   i   v    - iv  v i ii  v  i?    i     v  
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_137860687_   2232 AGACATGAATAGACAGTTCTTAAAAGAAGATATACAAATGTCCAACAA-- 2279
                         i  iv          v    iv                  v    i  --
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_137860687_   2280 ACATGAAAAAATGCTCAACATCACTAATGAT 2310
                                  i             ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (95 / 67)
Gap_init rate = 0.01 (4 / 629), avg. gap size = 1.25 (5 / 4)  


3289 24.43 3.62 0.90  chrX_137869003_137870907.rev      533  1416 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137869003_    533 TGGAAAGATACCTAGTGTTCATGGACTAGAAGAATTAATATT---AAAAG 579
                                   i ivi          i i     v        ---  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137869003_    580 GTCCATGCTACCTAAGATGATTTACAGATTCATTGCAATCCCTGTCAGAG 629
                          v v  i  v  i  iv    i          vi         i   i i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137869003_    630 TACCAGTGGCATTCTTCACTGAAGTAGAAATAAC-AATCCTAAAATTTGT 678
                          v    iv  v  i  ii v   i v  v - i -i           ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chrX_137869003_    679 GCGGAATCATAGAAGACCCCAGATAGCCAAAGAAATTTTGAGCAAAAAGA 728
                         ii    viii iii     vii         iv   i    iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_137869003_    729 AGGAAGCTGGAGGTATCACACTACCTTACTTCAAAATATACTATAAAGTT 778
                          vi   i      vv       v  iv i       iv     i    i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_137869003_    779 ACAGTAATCAAAATAGCATTGTCCTG------------ACACACAGACTA 816
                                    i i  ii v  v   ------------   i i   ii 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_137869003_    817 GTGGGACAGAATAGAGAGCCTAGAAATAAATCCATGCATTTACAACCAAT 866
                         i   i i     v     i i         i    i      iiii    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_137869003_    867 TCATTTTTGATAAAGGAGCCAAGAACACACAATGAGGAAGGGACAGTCTT 916
                          v     i  i  i  v       v  iv     i    i i i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_137869003_    917 T--AATAAATGTTGTTGGGAAAACTGGGTATCCACATGCAAAAAAATGAA 964
                          --  i     v  i     v      i  ?            i      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_137869003_    965 ACAAGATCTGTAGCTTACACC-TATACAAAAAC-AACTCAAAATGGATTA 1012
                         iivi  i iv  v  i     -          i-              i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_137869003_   1013 AAGATTTAAATGTAATACTCCAAACCACGAAACTACTAGAGGAAAACATG 1062
                         ?   ii         v viiv    i ii     vi    i        i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_137869003_   1063 GGGG-AAAGCTCCGTGACATTGGCCTGGGAAATGATTTTTTTGGATAAGA 1111
                           ? -   v  i      v    vi i  v    i   i  -i    v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chrX_137869003_   1112 CCAAAAAAGAACAGACAGCAAAAGAAAAACTAGACAAATGGAATTACAT- 1160
                          vvv     v   ii  i           v    i    v i i v   -
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_137869003_   1161 AAAACTAAAAAGCTTCTGCACAGCAAAAGAAAC----AATAGGGTGAAGA 1206
                             i      -   i  ii vv    i  v  ----  v ii     i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_137869003_   1207 GACAAACTATATA-TGGGGGAAA-TATTTTCAAACTATACATTTATTAAG 1254
                              v i i v -    i    -     v    ii   i  i iv    
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_137869003_   1255 G----TGTAAATGTTCAAAATATATAAGGAGCTCAGAGAACGCAATAGCA 1300
                          ----    ---- i  i         i  i   vv v   v     ii 
  L1M4_orf2#LINE/    748 GGACTTGTA----TCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_137869003_   1301 AGAAGACAAGTAACCTGATTTTAAAATGGGCAAGGGACTTGAATAGTCAT 1350
                          i       i     ii   ?v           i   i        v   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_137869003_   1351 TTCTCAAGTGAAGACATACAAACGGCCAACAGGTATATGAAAAAAACACT 1400
                              v iv     i       i      i i i i       i -ii  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chrX_137869003_   1401 CAACATGACTAATCAA 1416
                               v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (143 / 69)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.35 (40 / 17)  


 207 12.20 0.00 0.00  chrX_137874962_137877020.rev      458   498 (1561)  C L1M4_orf2#LINE/L1   (0)   908   868  

C chrX_137874962_    498 GCCAAAGAACACATGAAAAAATGCTCATCATCACTGGCCAT 458
                              vi i          i       v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (3 / 2)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  

3039 26.75 0.70 0.70  chrX_137874962_137877020.rev      705  1560 (499)    L1M4_orf2#LINE/L1        1   856 (52)  

  chrX_137874962_    705 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAACATCGTGAAAAT 754
                              ii i  i     i      i v      v i  i  i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137874962_    755 GGCCATACTGCCCAAGGTAATGTACAGATTCAATGCCATCCCCATCGAGC 804
                            v     v     iv i  v           i  v     i   i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137874962_    805 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 851
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_137874962_    852 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAG 901
                                 viiv  ii  v  v v  v     iv     i i ivv i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_137874962_    902 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 951
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_137874962_    952 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 1001
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_137874962_   1002 CCATGGAACAGAAC--AGAGCCCTCAGAAATAA-CGCAGCATATCTACAA 1048
                          v      i    i--    i  --        - v  -i i  i  iii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCA-TACATTTATGG 344

  chrX_137874962_   1049 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAAGGATT 1098
                         ii vi    i  i     ivv  vv  i v  vv   i        i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_137874962_   1099 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 1148
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_137874962_   1149 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 1198
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_137874962_   1199 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 1248
                            i ?    i    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_137874962_   1249 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 1298
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_137874962_   1299 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 1348
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_137874962_   1349 AATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGA 1398
                         v  i   v v  i i   i  iiivv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_137874962_   1399 ACAGGCAACCTACAAAATGGGAGAAAATTTTCACAGCCTACTCATCTGAC 1448
                          v  i     i   i             v  ii  ivii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_137874962_   1449 AAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAA 1498
                           i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_137874962_   1499 AAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGAAATGAACAGACACT 1548
                            i     i     v  i?    i           vv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_137874962_   1549 TCTCTAAAGTAG 1560
                             i    v  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAG 856

Transitions / transversions = 1.50 (135 / 90)
Gap_init rate = 0.01 (9 / 856), avg. gap size = 1.33 (12 / 9)  

 506 27.56 0.79 0.00  chrX_137874962_137877020.rev     1567  1693 (366)  C L1M4_orf2#LINE/L1   (780)   128     1  

C chrX_137874962_   1693 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCGATATCGTGAAAAT 1644
                               i i  i     i        v      v ii    i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_137874962_   1643 GGCCATATATCCCAAAGTAATTTATAGATTAACTGCTATCCCCATCAAGC 1594
                            v   ivi      v i  i  i     v vi  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_137874962_   1593 TACCATTGACTTTCTTCACAGAA-TTGA 1567
                          v   vivi i  i  ii     -    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA 128

Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.01 (1 / 128), avg. gap size = 1.00 (1 / 1)  


3009 26.42 1.66 0.89  chrX_137968223_137970985     1370  2270 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137968223_   1370 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATACCATGAAAAT 1419
                               i i  i     i        v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137968223_   1420 GGCCATACTGCCCATAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 1469
                            v     v    v v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137968223_   1470 TACCA-TTGACTTTCTT-CACACAATTAGAAAAAACT-ACTTTAAATTTC 1516
                          v   -i  v    i  -  v -    i-- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_137968223_   1517 ATATAGAACCACAAAAAGAGCCTGTATAGGCAAGACAATCCTAAGCAAAA 1566
                             i   vii   ii-  v  v v    v   i      i i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_137968223_   1567 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACACTACAAG 1616
                                  i      vv    i  v  ii i      vivi       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_137968223_   1617 GCTACAGTAAGCAAAACAGCATGGTGCTGGTACAAAAACAGATATAAAGA 1666
                                   v   i    ii    i    i i  ii i   i   v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_137968223_   1667 CCAATGGAACAGAAC--ACAGCCTCAGAAATAAAGCCACACATCTACAAC 1714
                         i        i    i-- v  i -          v   i    i  iiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chrX_137968223_   1715 CTTCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTC 1764
                          vvi    i  i     ivv  v   i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_137968223_   1765 TCTATTCAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAAC 1814
                            v     i        i     v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_137968223_   1815 TGAAACTGGACCCCTTCCTTACATCTTATACAAAAATTAACTCAAGATGG 1864
                             ii         v   i   i v                   i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_137968223_   1865 AT--------TAAACGTTAAGACCTAAAACCATGAACACCCT-AGAAGAA 1905
                           --------    i  -    v       i  i  -  i  -       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAA-ACTCTTAGAAGAA 543

  chrX_137968223_   1906 AACCTAGGCA-ATACCGTTCAGGACATAGGCACGGGCAAAGATGTCACGA 1954
                            v    ?i- v i -   iv   v v  vvii     v i v  viii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_137968223_   1955 CTGAAATACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 2004
                         v ivi i          vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_137968223_   2005 CTAATTCAACTAAAGAGCTTCTGAACAGCAAAAGAAACTATCATCAGAGT 2054
                         i v  iv  v v  i i   i  vi vv    i  v       vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_137968223_   2055 GAACAGGTACCCTACAGAATTGGAGAAAATTTTTGCATTCTATCCATCTG 2104
                            v  ii v  i       v         v      vvii  vi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_137968223_   2105 ACAAAGAGCTAACATCCAGAATCTACAAGGAACTTAAATAAATTTACAAG 2154
                          i  i ii  vii         v  i  i     ivv i  v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_137968223_   2155 ATAAAAACAAACAACTCCATCAAAAAGTGGGCAAAAGATATGAACAGACA 2204
                          v   i     i   i v  i?    i        i   v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_137968223_   2205 CTTCTCAAAAGAAGACATTTATGTGACCAACAAACATATGAAAAAAAGTT 2254
                         i     v        i  vi vi  i    i  i  i       i v i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_137968223_   2255 CATCATCACTGGTCAT 2270
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


3101 26.64 1.33 0.55  chrX_137981335_137985807.rev     3082  3982 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_137981335_   3082 TGGAAAAACATTCCATGCTCCTGGATAGGAAGAAACAATATCATGAATAT 3131
                               i i  i     i  v     v      vvi     ii v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_137981335_   3132 GGCCATACTGCCCATAGTAATTTATAGATTCAATGCTATCCCTATCAAGC 3181
                            v     v    v v i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_137981335_   3182 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 3229
                          v   -   v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_137981335_   3230 TATGGAATCAAAAAAGAGCCTGTATAGCCAAGTCAATCCTAAGCCAAAAG 3279
                                viiv  ii  v  v v        iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_137981335_   3280 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3329
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_137981335_   3330 TACAGTAAGCAAAACAGCATGGTGCTGGTACCAAAACAGAGTTATAGACC 3379
                                 v   i    ii    i    i iv ii i   vv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_137981335_   3380 AATGGAACAGAACAGAGGCCTCAGAAATAAAGCCACACATCTACAACCTT 3429
                                i    iv   ivii          v   i    i  iiii vv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_137981335_   3430 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 3479
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_137981335_   3480 ATTTAATAAATGGTGTTGGGTAAACTGGCTAGCCATATGCAGAAAACTGA 3529
                         v  i  i        i    vv      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_137981335_   3530 AACTGGACCCCTTCCTTACATCTTATACAAAAATTAACTCAAGATGGAT- 3578
                          ii         v   i   i v                   i      -
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_137981335_   3579 -------TAAACGTTAAGACCTAAAACCATGAACACCCT-AGAAGAAAAC 3620
                         -------    i  -    v       i  i  -  i  -          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGT-AAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAAC 546

  chrX_137981335_   3621 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATGTCATGACTA 3669
                         v    ?i- v i -   iv   v v  vv i     v i v  v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_137981335_   3670 AAATACCAAAAGCAATGGCAACAAAAGCGAAAATTGACAAATGGGATCTA 3719
                         vi i          vvi          vi     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_137981335_   3720 ATTCAACTAAAGAGCTTCTGAACAGCAAAAGAAACTATCATCAGGTTGAA 3769
                           iv  v v  i i   i  vi vv    i  v       vv iiv    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_137981335_   3770 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCATTCTATCCATCTGACA 3819
                         v  i     i                 v      vvii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_137981335_   3820 AAGAGCTAACATCCAGAATCTACAAGGAACTTAAATAAATTTACAAGATG 3869
                          i ii  vii         v  i  i     ivv i  v iv i  v vi
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_137981335_   3870 AAAACAAACAACTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 3919
                           i     i   i v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_137981335_   3920 CTCAAGAGAAGACATTTATGTGGCCAACAAACATATGAAAGAAAGTTCAT 3969
                            v i      i  vi vi       i  i  i      ii v i   v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_137981335_   3970 CATCACTGGTCAT 3982
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (133 / 104)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


3252 26.10 0.66 0.66  chrX_138066731_138073107     4977  5884 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138066731_   4977 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5026
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138066731_   5027 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5076
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138066731_   5077 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5124
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_138066731_   5125 ATATAGAACCAAAAAAGAGCCTGCATTGGCAAGACAATCCTAAACCAAAA 5174
                             i   viiv  ii  v  v v  v v   i      i i  vv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_138066731_   5175 GAACAAAGGTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAAG 5224
                                 v      vv       v  ii i      viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_138066731_   5225 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 5274
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_138066731_   5275 TAATGGAACAGAAC--AGAGCCCTCAGAAATAATTCCACACATCTACAAA 5322
                         i       i    i--    i  --        vi   i    i  iiiv
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_138066731_   5323 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5372
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_138066731_   5373 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5422
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_138066731_   5423 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5472
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_138066731_   5473 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5522
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_138066731_   5523 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCT 5571
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_138066731_   5572 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5621
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_138066731_   5622 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5671
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_138066731_   5672 ACAGGCAACCTACAGAATGGAAGAAAATTTTTGCAATCTACTCATCTGAC 5721
                          v  i     i         i       v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_138066731_   5722 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5771
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_138066731_   5772 AAAAACAAACAACCCCATCAACAAGTCAGCAAAG-ATATGAACAGACTCT 5820
                            i     i     v  i? v  i vi      -  v    i    vi 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_138066731_   5821 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5870
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_138066731_   5871 TCATCACTGGCCAT 5884
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3198 23.88 0.31 5.63  chrX_138134693_138139014     2871  3829 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138134693_   2871 TGGAAAGATATTCCATGTTCATATTCTGGAAGAATCAATGTTGTTAAAAA 2920
                                    i          ivvi       v i   i       i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_138134693_   2921 TGTTCAAACTACACAAAGCAATCTACAGATTCAATGTAATCCCTATCAAA 2970
                           viv v   v v    vii              i i             
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_138134693_   2971 ATATCAATGACATTCTTCGTAAAAACACAAAAAACAATCCTAAA-TTTAT 3019
                           vi  iivi v  i  i i i   ivv v  ivii        -  i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_138134693_   3020 ATGGAAACATGAAAGATCAAGAATAGCCAAAGCTATCCTGAGCAAAAAGG 3069
                                iiii ii  i v            i v   i   iv  i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_138134693_   3070 AAAAGACTAGATGAATCACATTACCTGACTTCAAACCATACTACAGAGCT 3119
                          v  iii i  v  v     i v  ii i      ---------------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--------------- 234

  chrX_138134693_   3120 ATGGTAACCAAAGCTGCACATTACCTGACTTCAAATCATACTACAGAGCT 3169
                         ---------------------------    --------      i    
  L1M4_orf2#LINE/    235 ---------------------------ACTT--------ACTACAAAGCT 249

  chrX_138134693_   3170 ATAGTAAACAAAGCAGCATGGTGCTGGTGTAAATACAGACACATAGAACA 3219
                          i     v   ii   ii    i    ii   iv i     i     v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_138134693_   3220 ATGGAACAGAATAGAGAACCCAGAAACAAATCCAAACATCTACAGTGAAC 3269
                               i     v    ii       i   i   v    i  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_138134693_   3270 TGATTTTTGACAAAGATGCCAAGAACATACATTGGAGGAAAAGAGAGTCT 3319
                                i     i i        v   v  v   -     ii v     
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCT 398

  chrX_138134693_   3320 CTTCAATAAATGGTGCTGGGAAAGCTGGTTATCCATATGCAAAGGAATTA 3369
                         i     i              v i    v  ?   i       i    v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_138134693_   3370 AACTAGAACCTTATCTCTCACCATATCCAAAAATCAACTCAAAGTGGATT 3419
                          ii i  v  i  i   v        v       i        i     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_138134693_   3420 TATGACTTAAATCTAAGACCTCACTCTATGAAACTACTGCAAGAAAACAT 3469
                         v?v   i     v     v  v vv    i     vi iv          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_138134693_   3470 TAGGGAAAATCTCCAGGATATTGATCTGGGCAAAAGTTTCTTGAGCGATA 3519
                         vi ? v      i iv  iv   ivi i     vi       -  vv  i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chrX_138134693_   3520 AC-CCATAGGCACAGGCAACCAAAGCAAAAATGGACAAAAGGAATTACAT 3568
                           -   v i     i     v    v      i  i   vv i i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_138134693_   3569 CAAACTAAAAAATCTTCTTTACAGCAAAGAAAATAATTAACAAAATGAAG 3618
                             v v     -   i v i vv     i v iv  i  v   i    i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_138134693_   3619 AGACAAACCCCAGAATAGGATAAAATGTTTGCCAACTACCCATCTGACAA 3668
                               v  v      i   v     i     v  ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_138134693_   3669 GGGATTAATAACAAGAATATATAAGGAGCTCAAACAAATCTATAGGAAAA 3718
                             i vi  v v           i  i   vv    v  v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_138134693_   3719 AATCTGTTAACCCGATTAAAAAATGGGCAAAT-ATTTGAATAGACATTTC 3767
                          iv viv      i   ?             v-                 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_138134693_   3768 TCAAAAGAAGACATACAAATGGCAAGCAGGCATGTTAAAATGTATTCACC 3817
                           v        i           v ii i   ii v    vi ii   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_138134693_   3818 ATCATTGGTCAT 3829
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (133 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 6.33 (57 / 9)  


3421 25.17 1.45 0.11  chrX_138156453_138160692.rev     2856  3749 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_138156453_   2856 GAAAGATATTCCATATATATAGATTGGAAGAATCAATATT---AAAATGT 2902
                                  i    i vi  i          v i      ---  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_138156453_   2903 CCATACTACCCAAAGCACTTTACAGATTCAATGCAATCCCTGTCAAAATA 2952
                          v     v      viiv i           i         i       v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_138156453_   2953 GCAATAACTTTCTTCACAGAAATAGAGAAAC-AATCCTAAAATTTATGTA 3001
                         v  iivi i  i  ii       v  v  i -i           i  i i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_138156453_   3002 GAACCACAAAAGTCACAGAATACCCAAAGCTATACTGAGCACAAAAAGCA 3051
                            vii   ii v v       v     i v  vi   iv vi  i i  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_138156453_   3052 AAAGTGGAGGAATTGCATTACTGGACTTCAAATTATAATACAAAGCTATA 3101
                           iv       v ii  i v ivi i      viv  v          i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_138156453_   3102 GTAACCAAAACAGCATGGTACTGGCATAAATGCAGACACACAGATCAGTG 3151
                             i   i    ii              ivii     i i      i  
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_138156453_   3152 GAACAGAATAGAGAACCTAGAAACAAATCCATACATCTAAAGTGAACTCA 3201
                            i     v    ii i     i   i        i  vi  v  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_138156453_   3202 TTTTCAACAAAGTCACCAAGAACAA-CATTGGGGAAAGGACAGTCTCTTC 3250
                              i    i vii      v  v-  v         i i     i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_138156453_   3251 AATAAATGGTGTAGGGAAAACTGGATATCCATATGCAGAAGAATGAAACT 3300
                           i        iv    v         ?   i     i         ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_138156453_   3301 AGACCCCTATCTCTTGCTGTATACAAAAATCAAATCAAAATGGATTAAAG 3350
                         i        i   vii ii           i  v           i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_138156453_   3351 ACTTAAATGTAAGA-CTCACACTATGAAACTACTACAAGGAAACTTTGGG 3399
                           i           -  v v     i     vi  v   i    v v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_138156453_   3400 GAAAATCTCCAGGATATTGCTCTGGGCAAAGATTTTTTGAGCA--ATAC- 3446
                          v      i iv  iv   vvi i     v i   i  iiii -- i  -
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_138156453_   3447 --AAGCACAGACAACAAAAGTAAATGTGGACAAATGGGATCACATTAAG- 3493
                         --       ii         v   vi i  i    v   iiv   i  i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_138156453_   3494 TTAAAAGCTTCTGCACAGTAAAGGCAACAATCAACCAAGTGGAGAGACAA 3543
                               i   i  ii vvi     vv  v     vv     i i      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_138156453_   3544 CCTACAGAATGGAAGAAAATATTTGCAAAGGA-ATCATCTGACAAAGGAT 3592
                           i         i                vv -  -      i  i   i
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGGGAC 751

  chrX_138156453_   3593 TAATAACAATAATATATAAGGAGATCAAACAACTCTATAGGAAAAAACCT 3642
                          vi  v v v         i  iv  vv       v   iv     iv v
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_138156453_   3643 AATAATTCAATTTAAAAATGATCAAAAGACCTGAATAGACATTTCTGAAA 3692
                              ii     ?       iv    i  ii               vv  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_138156453_   3693 AGAAGACATACAAATTGTAAGCAGGTATATGAAAAGGTGCTAACCATCAA 3742
                               i        v iv ii i i i        i    v v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_138156453_   3743 TGATCAT 3749
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.66 (138 / 83)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 1.56 (14 / 9)  


 792 28.15 2.41 2.95  chrX_138178716_138181088.rev      135   507 (1866)    L1M4_orf2#LINE/L1      432   802 (106)  

  chrX_138178716_    135 CACATGTATACATATGTAACTA-ACCTGCACATTGTGCACATGTACCCTA 183
                               i v viv   v ii i-   ivi  v iiii -   i   --- 
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC-CATATAC---A 477

  chrX_138178716_    184 AAACTTAAAGTATTAAAAAAAAA--AAAGACTTAAACATAAGACCTAACA 231
                            v    ----i v    vii -- ?    i    ii     v    v 
  L1M4_orf2#LINE/    478 AAAATTAA----CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_138178716_    232 CCATAAAAGCTCT-AAAAGAAAACAAAGGCA-ATACCATTCAGGACATAG 279
                          i      -    - i         v   ?i- v i -   iv   v v 
  L1M4_orf2#LINE/    524 CTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chrX_138178716_    280 GCATGGGCAAAGACTTCATGTCTAAAACACCAAAAGCA-ATGTCAACAAA 328
                          vv i     v ii   v ivv  vi            - v -       
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG-CAACAAA 620

  chrX_138178716_    329 AGCCAAAATTGACAAATGGGATCTAATTAAACTAAGGAGCTTCTGCACAG 378
                           vv     v  i    v   ii v  i   v v ii i   i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_138178716_    379 CAAAAAAAACTATCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAC 428
                             ii v       vv i      v  i     i   i          v
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_138178716_    429 ATTTTTGCAATCTATCCATCTGACAAAGGGCTGATATCCAGAATGTACAA 478
                           v       vii  vi      i  i  i  vi          i  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_138178716_    479 GGAACT--TA-AATTTAAAAGAAAAAAGCTAA 507
                         i     --  -  i i  v iv      vi  
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAA 802

Transitions / transversions = 1.29 (58 / 45)
Gap_init rate = 0.04 (13 / 371), avg. gap size = 1.54 (20 / 13)  

2445 23.93 4.91 7.91  chrX_138178716_138181088.rev      947  1882 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138178716_    947 TGGAGACATAGACCACATTCATTGATTGAAAGACCCAACATAATAAAGAT 996
                             i v   vv   ii     v     i     ii  i  vi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138178716_    997 GTCAATTCTCTCCAAATTAATCTGTATGTTTAATATAAATCTCAGCAAA- 1045
                          v    v   i       i    ii vi  i  iii  vi ii v    -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138178716_   1046 ---TGG--GTTTTCTTTGCAT---TT------TTGAT--------TTATA 1073
                         ---ii -- ii  i      v---  ------i    -------- i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_138178716_   1074 TAGGAAGGCATAGGCCCTAGGATAAATAAAATAATCTTGACCAA-----A 1118
                          i i  v   vi  v  i  i   ivi    i        vv  ----- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_138178716_   1119 CAAAGTGGGAGGAATCACTCTACCTAA---CAAGTCTTACTATATAGCTA 1165
                               v      v    v  v  i  ---   iv       i v     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_138178716_   1166 CAATAATCAAGACAATGTGGTATCAGTAGAGGGATAGACAGATTGGTCAA 1215
                           i           i       iii i v i         v  v i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_138178716_   1216 TCAAATAATATAAAGAATCTATTCCAGTCTGGACGACAGAGCGAGACTCC 1265
                          vi    -------    -----------  -------------------
  L1M4_orf2#LINE/    301 TGGAATA-------GAAT-----------TG------------------- 313

  chrX_138178716_   1266 GTCTCAAAAAAAGAAAAAGAATCTAGAAGTAGACCTTCACAAATATGACA 1315
                         -----------------   i  i    i  i   ----  v i  v---
  L1M4_orf2#LINE/    314 -----------------AGAGTCCAGAAATAAACC----CATACATT--- 339

  chrX_138178716_   1316 AATATGCTCAACT-ATTTTTGACAAATGTACAAAAGCAATTCAATAGAGG 1364
                         --    v    i -     i     iv  i v  ii v       i i i
  L1M4_orf2#LINE/    340 --TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_138178716_   1365 AGAGATGGCCTTCTCAGCAAATAGTGCTGGAGCAATTGCATATCCATAGG 1414
                          iii  i i   i   i     i       ii   i  v   ?   i v 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_138178716_   1415 CCAAAAAATTAAGAATT---CTTCTGAACCTCATACTTCATACAAAAATT 1461
                          v   i   v   --  --- ii  --      i  ivi           
  L1M4_orf2#LINE/    438 CAAAAGAATGAAG--TTGGACCCCT--ACCTCACACCATATACAAAAATT 483

  chrX_138178716_   1462 AACTCAAAATGGATCAGAGGCTTAACTGTAAAACATGAAACCATGAAGCT 1511
                                         ?  i i   v     i vv i    i  i  i  
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_138178716_   1512 TTTAGAAAAAAACTTGAGGC---AATCTTTGGAATCTAGGACTAGGCAAA 1558
                         i      i     v -   ?---      i vi i  v  ii       v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACAT-AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_138178716_   1559 GAGTTCTTAGATTTGGCACCAAAAGTATCATCCATAAAAGGAAAAATAGA 1608
                          iv         v  i         i iv v v i     i         
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_138178716_   1609 AAAAT-GAACCTAAACACAATTAAAAGCTTTTGTTCTTTGAAATTCCATG 1657
                         v    - i  i v v  v        i       v   ii  ivv vv i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_138178716_   1658 TGAAAAGGATGAAA-GATAAACAACAGACTTGGAGAAAATATTTGCAAAC 1706
                          v  i iii     -  i  v v     v v                  i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_138178716_   1707 AATACATCTGATATATGTTTTTGAGTAT--AAAAAATATAAAGGTCGCTC 1754
                         v   i        viv vi  ---    -- i  v        iv v  i
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTT---GTATCCAGAATATATAAAGAACTCTT 779

  chrX_138178716_   1755 AAGACTCAGCAGTAAAAACAAAAGCAATTCAATTATAAAATGATCAAGAG 1804
                          vi     ii i      v v  ii  ii     ?v      iv   ii 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_138178716_   1805 ACAT-AATAAGTGACGTTTCACCAAAGTGGGTATAGAGATGGGAAATATG 1853
                          iv -    ---   i    v      vi i    v i    vv    v 
  L1M4_orf2#LINE/    830 ATTTGAATA---GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_138178716_   1854 TACATGA---GATGTTCAACATCATTAGTCAT 1882
                         i      ---    i         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (136 / 84)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 4.80 (120 / 25)  


3272 26.87 0.55 0.55  chrX_138242876_138249267     4992  5899 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138242876_   4992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5041
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138242876_   5042 GGCAATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 5091
                                  v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138242876_   5092 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTCA 5139
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_138242876_   5140 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAA 5189
                                viiv  ii  v  v v  v     iv     i i ivv i  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_138242876_   5190 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5239
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_138242876_   5240 TACAGTAACCAATACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5289
                                 i   v    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_138242876_   5290 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCACACATCTACAACT 5337
                                i    i--    i  --    i   vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_138242876_   5338 ATCTGATCTTTGATAAACTTGACAAAAACAAGAAATGGGGAAAGGATTCC 5387
                          vi    i  i  i  ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_138242876_   5388 CTATTTAATAAGTGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCT 5437
                           v  i  i  i           v  i   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_138242876_   5438 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5487
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_138242876_   5488 TTAAGTACTTAAATGTTAGACCTAAAACCAGAAAAACCCTAGAAGAAAAC 5537
                          i ?iv  i       v   v       i v    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_138242876_   5538 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTG 5586
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_138242876_   5587 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5636
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_138242876_   5637 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5686
                           i   v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_138242876_   5687 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 5736
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_138242876_   5737 AAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTATAAGAAA 5786
                          i  i  vi          v  i  v      iv    v iv    v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_138242876_   5787 AAAACAAACAACCCCATCAAAAAGTGGGCCAAGGATATGAACAGACACTT 5836
                           i     i     v  i?    i     v      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_138242876_   5837 CTTAAAAGAAGACACTTATGCAGCCAAAAGACACATTAAAAAATGCTCAT 5886
                           iv        i ivi viii     v ii     v    i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_138242876_   5887 CATCACTGGTCAT 5899
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3055 27.78 0.66 0.55  chrX_138331858_138337127     3871  4777 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138331858_   3871 TGGAAGAACATTACATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3920
                              ii i  iv    i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138331858_   3921 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3970
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138331858_   3971 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4018
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_138331858_   4019 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 4068
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_138331858_   4069 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4118
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_138331858_   4119 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACC 4168
                                 i   i    ii         i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_138331858_   4169 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 4216
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_138331858_   4217 ATCTGATCTTTGAAAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4266
                          vi    i  i  v  ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_138331858_   4267 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4316
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_138331858_   4317 GAAACTGGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGA 4366
                            ii    i    v   i i   v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_138331858_   4367 TTAAAGACTTCAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4416
                          i ?    i v     v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_138331858_   4417 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 4465
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_138331858_   4466 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCAA 4515
                         vi            vvi          vv     v  i    v   iivv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_138331858_   4516 ATGAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 4565
                           v   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_138331858_   4566 CAGGCAACCTAAAGAATGGGAGAAAAATTTTGCAATCTACTCATCTGTCC 4615
                         v  i     i v              vv       vii ivi     viv
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_138331858_   4616 AAGGGCTAATACCTAGAATCTAAAATGAACTCAAACAAATTTACAG-AAA 4664
                          i  i  vi  i i     v  v  v      vv    v iv i i-   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_138331858_   4665 AAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACACTT 4714
                           i     i     v  i? v  i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_138331858_   4715 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAG 4764
                            v        i  vi viii     i ii          i       i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_138331858_   4765 CATCACCGGCCAT 4777
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2360 28.79 2.90 0.76  chrX_138427583_138431179      824  1615 (1982)    L1M4_orf2#LINE/L1        1   809 (99)  

  chrX_138427583_    824 TGGAGAAAACATTCCATGCTCATAGATTTGAAGAATCACTATCATTCAAA 873
                             -  i i  i     i    i    v     v i v   ii  v i 
  L1M4_orf2#LINE/      1 TGGA-AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_138427583_    874 TGGCCATACTGTCCAAAATAATCTGCCAATTCAATGTTATTCCTATCAAA 923
                             v     vi     v i    i vi      i iv  i         
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_138427583_    924 CTACCAACAGCCTTTTTCACAGAATTAGAAAAACT-ATTCTAAAATTCAT 972
                         v v   i v        ii     v v  v  i  -  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_138427583_    973 ATGGAACCACAAAAGAGCTCAAATAGCCAAAGCAATCATAAGCAAAAAGA 1022
                               vii   ii  v ivi          i     v i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_138427583_   1023 ACAAGG--GCAGAAATAACATATTACCCGACATCAAA-----CTA----- 1060
                             i -- v  i v --  i i v   i iv     -----   -----
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACT--CACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_138427583_   1061 -TAC------CAAAACAACATAGTCCTGGTACAAAAACAGACACTTAGAC 1103
                         -   ------   i   iii i  v    i i  ii i     iv    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_138427583_   1104 CAATGGAACAGAATAGAGAACCCAGAAATAAAGCCACGCATCTACAACCA 1153
                                 i     v    ii           v   ii   i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_138427583_   1154 TCAGATCTTTTACCAAATCAACGAAAATAATCAAAGGGGAAAGGACTCCC 1203
                         viv   i  iv  v iiviiv i i vi v    v        i ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_138427583_   1204 TATTCAACAAATGGTGCTGAGATAGCTGACTAATCATATAAAGAAGAGTG 1253
                          v                 i  i i   iv  ?i  i  iv i    i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_138427583_   1254 AAACTGGACCCCTACCTTTCACCATATATAACAATTAACTAAGGATGGAT 1303
                           ii             iv         i  v        v ii      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_138427583_   1304 TAAAGATCTAAATGCAAGACCTCAATATACAAGAATCTTGGGAGAAAAGC 1353
                         i ?   i       i    v  v  vv  i  i v    i i      vv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_138427583_   1354 TAGGAAACACTAATCT--G-GACATTGGCCTTGGGAAAGAATTTATGACT 1400
                             ?i-i --     -- -   v    vi v  v  v iv  iv iiv 
  L1M4_orf2#LINE/    548 TAGGNG-TA--AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_138427583_   1401 AAAATTTCAAAAGCAATTTCAACAAATACAAAAATTGATACGTGGGACCT 1450
                          vi ivi        vvvv       viv      v    vi v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_138427583_   1451 AATTAAACTAAAGAGCTTCTGCATAACCAAAGAAGCTATCAACAGAGTAA 1500
                         v  i   v v  i i   i  iiivv v  i  vi       v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_138427583_   1501 ACAGACAACCTACAGAATGGGAGAAAATATTCACAAACTATGCATCTGAC 1550
                          v        i                    ii    ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_138427583_   1551 AAAAATCTAATATCCAGAATCTGTAAGGAACTTAAACAATTCAACAAGCA 1600
                           iiiv  vi          v i   i     ivv    i    i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_138427583_   1601 AAAAACTAATAACTC 1615
                            i  v      i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCC 809

Transitions / transversions = 1.56 (137 / 88)
Gap_init rate = 0.01 (11 / 809), avg. gap size = 2.64 (29 / 11)  

2239 26.49 0.16 0.16  chrX_138427583_138431179     1627  2245 (1352)    L1M4_orf2#LINE/L1      290   908 (0)  

  chrX_138427583_   1627 ATATAGATCAATGGAACAGAACAGAGCACTCAGAAATAATGCCGCATATC 1676
                                         i    iv   viii         vv  ii i  i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_138427583_   1677 TACAACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAA 1726
                           iiii  vi    i  i     ivv  v   i v  vvv          
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_138427583_   1727 GGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTA 1776
                          i  vvi  v  i  i              v      v  ?   i   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_138427583_   1777 GAAAGCTGAAACTGGATCCCTTCCTTACATCTTATACAAAAACTAATTCA 1826
                         i  iiv    ii    i    v   i   i v          i   i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_138427583_   1827 AGATGGATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGA 1876
                          i      i ?    i  v    v   v       i      vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_138427583_   1877 AGAAAACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTC 1925
                                v    ?i- v i -   iv   v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_138427583_   1926 ATGTCTAAAACACCGAAAGCAATGGCAACAAAAGCCAAAATTGACAAATG 1975
                         v ivv  vi     i      vvi          vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_138427583_   1976 GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCA 2025
                            ii v  i   v v  i i   i  ii vv    i  v       vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_138427583_   2026 GAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCA 2075
                         i      v  i     i                 v  i    vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_138427583_   2076 TCTGACAAAGGGCTAATATCCAGAATCCACAATGAACTCAAACAAATTTA 2125
                              i  i  i  vi          vi i  v      vv    v iv 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_138427583_   2126 CAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACA 2175
                         i  v     i     i     v  i?    i     i      v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_138427583_   2176 GACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACGCATGAAAAAA 2225
                             i     v        i  vi viii     v  i i        i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_138427583_   2226 TGCTCATCATCACTGGCCAT 2245
                               v     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (91 / 69)
Gap_init rate = 0.00 (2 / 619), avg. gap size = 1.00 (2 / 2)  

 421 21.01 2.52 0.00  chrX_138427583_138431179     2986  3104 (493)    L1M4_orf2#LINE/L1      787   908 (0)  

  chrX_138427583_   2986 AATAA-AAAAAAACTAATAACTCCACTAAAAAGTGAGCAGAGGACATGAA 3034
                              -     i  v      i v i ?    i  i   i    iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_138427583_   3035 CAGATACTTCTCAAAAGAAGACATACAGATTTCCAACAA--AGAGGAGAA 3082
                         i   i i     v        i     i  vv    i  -- v v  i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_138427583_   3083 AATGCTCAATATCACTAATCAT 3104
                         i        i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.02 (2 / 122), avg. gap size = 1.50 (3 / 2)  


3575 24.64 0.88 0.55  chrX_138461571_138464175.rev     1210  2114 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138461571_   1210 TGGAAAGATATTTCATGATCATGGATTGGAAGAATTAATATTGTTAAAAT 1259
                                    ii    v               v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138461571_   1260 GACAATTCTACCCACAGAAATTTACAGATTCGATGCAATCTCTATCAAA- 1308
                          i    v  v    v vvi  i         i i      i        -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138461571_   1309 TTCCAGG-GCATGCTTCAGATAAATAGTAAAA--AATTCTAATAACGTAT 1355
                          i    v-  v vi  iiv v    v vv  i--i  i    -  ivi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA-AATTCAT 149

  chrX_138461571_   1356 ACAGAACCACAAAAGACCTGAAATGGCCAAAGCAGTCCTAACCAAAAAGA 1405
                          ii   vii   ii    iii   i      i  i  i i vv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_138461571_   1406 ACAAAGCTGCAGGCATTGTACTAGGTAACTTCAAAACTTGCTACAAAGCT 1455
                               i  v   vv iii   vvvi  i          i          
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_138461571_   1456 GTATTGACCATAACAGCATGATACTGGCATAAA-ACAGACACATAGACCA 1504
                         ii v i i  vi    ii  i           i- i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_138461571_   1505 ATGGAACAGAATAGAGAACCCAGATGTAAATCCATACATTTACAGCCAAG 1554
                               i     v    ii     vi    i           ii i   v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_138461571_   1555 TCATATTCGACAAAAGTGATAAGAATCTACAATGGGGAAAGGA-AATATT 1603
                          v  v        ii   vi    viv v            i - i v  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_138461571_   1604 TTCAATAAATGATGCTGGAAAAACTGGATAACTGTATGTGGAAGAATGAA 1653
                              i     i      i v         ? iii   iii         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_138461571_   1654 ACTAGATCCCTATCTCTCACCATACACAAAAATCAAATCAAAATGGATTA 1703
                         ii i  i     i   v       i        i  v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_138461571_   1704 AAGAACTTAAATTGAAGACCTGAAACTATGAAACTACTAGATGAAAATGT 1753
                         ?   - i     vv    v  i       i     vi    v     ii 
  L1M4_orf2#LINE/    500 WAGA-CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_138461571_   1754 TGGGGAAACTTTCCAGAACATTGGTCTGGGCAG-AGTTTTTTGTGCAAAA 1802
                         v  ? v  v i i ivi  v    vi i    i-i    i  ivii vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_138461571_   1803 CCTCAAAAGCATAGGCAACCACAGCAAAAATAGACAAATGGGATCACATC 1852
                          vi        i i     v v  v         i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_138461571_   1853 AAGCTAAAAAGCTTCTGCATAGCAAAGGAAACAATCAACAAAGTGAGGAG 1902
                           iv v    i   i  iiivv       v  v     v       ii  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_138461571_   1903 ACAATTCACAGAATGAAAGAAAATATTCGCAAACTATCCATTTGACAAGG 1952
                             ii         ii          i     ii  vi  i   i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_138461571_   1953 GATTAGTAACCAGAAAATATAAGGAGCTCAAACAACTCAATAGCAAAG-G 2001
                           i v   v      v      i  i   vv           ii   i- 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_138461571_   2002 ACCCAAATAATTCAATTTATAAAATGGGCAAAAGATCTGAATAGACATTT 2051
                           --      ii     ? -            i   i             
  L1M4_orf2#LINE/    799 AC--AAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_138461571_   2052 CTCAAAAGAAGACATAACAATGACCAACAGGTATATGAAAAAATGTTCAA 2101
                            v        i   vv    i    i i i i       i   i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_138461571_   2102 CATCACTAATCAT 2114
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (144 / 75)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.18 (13 / 11)  


3189 27.75 0.33 0.33  chrX_138478244_138484634.rev     4994  5901 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138478244_   4994 TGGAAGAACATTCCAAGCTCATGGATAGGAAGAATCAGTATCGCGAAAAT 5043
                              ii i  i   v i        v      v i i   i iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138478244_   5044 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 5093
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138478244_   5094 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5141
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_138478244_   5142 TATGGAACCAAAAAAGAGCCTCCATTGCCTAGACAATCCTAAGCCAAAAG 5191
                                viiv  ii  v  vvv  v   v i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_138478244_   5192 AACAAAGCTGGAGGCGTCATGCTACCTGTCTTCAAACTATATTACAAGGC 5241
                                i      vv   ii  v  iivi      viv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_138478244_   5242 TACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGATATATAGACC 5291
                                 i   i    ii i       i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_138478244_   5292 AATGGAACAGAACAGAGGCCTCAGAAATAACACCAGACATCTACAACCAT 5341
                                i    iv   ivii         vv   v    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_138478244_   5342 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5391
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_138478244_   5392 ATTTAATAAATGGTGCTGGGAAAACTAGCTAGCCATATGTAGAAAGCTGA 5441
                         v  i  i              v    i v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_138478244_   5442 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5491
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_138478244_   5492 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5541
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_138478244_   5542 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGGCTTCATGACTAAA 5590
                            ?i- v i -   iv   v v  vv i     v  i   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_138478244_   5591 ACACCAAAAGCAATGGCAACAAAAGCCAAACTTGACAAATGAGATCTAAT 5640
                                     vvi          vv   v v  i    vi  ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_138478244_   5641 TAAACTAAAGAGCTTCTGCACAGCAGAAGAAACTACCATCAGAGTGAACA 5690
                         i   v v  i i   i  ii vv  i i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_138478244_   5691 GGCAGCCTACAGAATGGGAGAAAATTTTTGCAATCTACCTAACTGACAAA 5740
                          i  i  i                 v       vii iv  v    i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_138478244_   5741 GGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAGGAAAA 5790
                           i  vi          v  i   v    ivv    v iv i  vi    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_138478244_   5791 AACAAAGAACCCCATTAAAAAGTGGGCAAAGGATATGAACAGGCACTTCT 5840
                         i     v     v   ?    i            v    i  i  i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_138478244_   5841 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5890
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_138478244_   5891 TCCCTGGCCAT 5901
                           v????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


4061 19.71 1.45 2.12  chrX_138490530_138492419      500  1397 (493)    L1M4_orf2#LINE/L1       17   908 (0)  

  chrX_138490530_    500 GTCCATAGTTTGGGAAACCTCAATTTGTGCCACTATAAAAATGAGGTTAA 549
                           i   i v    i i  i -   ------- i i v  i   i---i  
  L1M4_orf2#LINE/     17 GTTCATGGATTGGAAGACTT-AAT-------ATTGTTAAGATGG---CAA 55

  chrX_138490530_    550 GGTACTTCCTAAATTCATCTACAGATTCAATGCCATCCCTAGCAACATCC 599
                         --    i  i     v              i  v       v   v    
  L1M4_orf2#LINE/     56 --TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_138490530_    600 CAGATGGCTTTTTGCACAGAAATTTTCAAGCTAGTCTTAAAATTCATATG 649
                            v  v      -ii        vv      ii  i             
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_138490530_    650 GATACGCAAGGGACCTGGAATAACCAAAGCAATCTTGAAAAAGAAAAACA 699
                           v i          ii     i     i                i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_138490530_    700 AATTTGGAAAGTTTATATTTTCTGATTTCAAAA-TTAGTACAAAGCTACA 748
                           v     iiii i i i  i ii         -   v            
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_138490530_    749 GTAATAAAGATAG----GTATT---AT---GATAGACTTATAGATACATC 788
                              v    i  ----   i ---  ---       v       ---- 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT----C 298

  chrX_138490530_    789 AGTGGGAAATAATTGAAAGTCCAGAAATAGATCTTTGTACCGAAGGTTAA 838
                          i   i v v      i            i i iv ii iiv v   i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_138490530_    839 TTTATTTTCATCCAGGGCACCAAGACATTTCAACGGGGAAAGGATATTCT 888
                           v      iv v    ii       vv     i        i   v   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_138490530_    889 TTTTAATAAATGATGTTGGGAAACCTGGAGGTGCACATGGAAAAGAATGA 938
                            i  i     i  i     v v     vi?v      v          
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_138490530_    939 AGCTGAATCTTTGCCGCACACTATACACAAAAATCAACTCAAAATGGATC 988
                           i  i i ii i  v     i   i        i               
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_138490530_    989 AAAGATCTAAGTATAAGAAGTAAAACTATAAAACTCTTAGACAAACACAT 1038
                          ?   i    i i     iv                     vi  v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_138490530_   1039 AGTTGTAATTTATTATGACCTTGGATTAGGCAATGTTTTCTTATATTTGA 1088
                           v?    v iv ii         i          v       v  v   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_138490530_   1089 CATCCAAAGTACAAGCAATAAAAGAAAAAAATAGATACATTCGACCTTCT 1138
                           i v    i        i           -      v   v   i iv 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCAT 647

  chrX_138490530_   1139 CAAAGTTAAAAATATTTGCGATTCAA-GGAAACCATGAAGTACGTAAAAA 1187
                             i       iv    i v     -   v  i  v   v v  i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_138490530_   1188 GACAACCCACAGAGTGGGAGAAAATATTTGCACATTAAATGTCTGATAAA 1237
                                      i                  v  i v  i        i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_138490530_   1238 GATCTCCATTCCAGAGTATATAGAGAACTCTTAAAACTCAACAGTAAAA- 1286
                          iv  ivvv      i      i          v       i i     -
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_138490530_   1287 GAGGAAAAGCCCAATCTTAAATCAGGCAAATAATCCATGTAGACATTTAT 1336
                           vi  v i      i?v   vii      vi  iiivi         v 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_138490530_   1337 CCAAAGAAGATATATAAATGGCCAATAAGCACCTGAAAAGGTGCTCAACA 1386
                                       i                 v       i         
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_138490530_   1387 TCACTAGTCAT 1397
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.62 (107 / 66)
Gap_init rate = 0.01 (13 / 892), avg. gap size = 2.46 (32 / 13)  


 962 25.36 0.36 2.54  chrX_138511187_138514155     1244  1519 (1450)    L1M4_orf2#LINE/L1        1   270 (638)  

  chrX_138511187_   1244 TGGAAAAACATTCCATGTTCATGGATTGGAAGAATCAATATCATAAAAAT 1293
                               i i  i                     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138511187_   1294 GGCCATACTGCCCAAAGCAATCTACAGATTCAGTGCTATTCCTATCAAAC 1343
                            v     v      vii             ii  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138511187_   1344 TGCTAATGGCATTCTTCACACAATTAGAAAAAAAAAAAACT-ATTCTAAA 1392
                          v i iiv  v  i  ii  v  v v  v  i-------  -  i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-------CTGATCCTAAA 143

  chrX_138511187_   1393 ATTCACATGAAACCAAAAAAGAGCCCAAATAACCAAAGCAATCCAAAGCA 1442
                              i   i  viiv  ii  v  vi    i     i     ivi iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_138511187_   1443 AAAAGAACAAAGACGGAGGCATCACACTACCCAACTTCAAACTACACTAT 1492
                          i          vi     vv       v     i      vivi    i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_138511187_   1493 AAAGCCACAGTAAACAAAACAACTTGG 1519
                              i       v   i   iiv   
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGG 270

Transitions / transversions = 1.50 (42 / 28)
Gap_init rate = 0.01 (2 / 270), avg. gap size = 4.00 (8 / 2)  

2469 25.95 1.03 0.44  chrX_138511187_138514155     1795  2476 (493)    L1M4_orf2#LINE/L1      223   908 (0)  

  chrX_138511187_   1795 CTCAGTCTCAAAAACAA--ACAAACAAACA--AATAAAGACAGCTTGGTA 1840
                          i  i i      viv --     vvv   --   v       iv     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_138511187_   1841 GTGGTACAAAAACAGACACATAGACCAATGGAACAGAATAGAGAACTCAG 1890
                         v   i i  ii i     i     i        i     v    iii   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_138511187_   1891 AAATAAAGCTGCACAGCTACAACCATCTGATCTTTGACAAGGCCAACCAA 1940
                                v iii   vi  iiii  vi    i  i       vii-    
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG-CCAA 371

  chrX_138511187_   1941 AACAAG-CAGTGGGAAAACAAT--TCCATATTCAGTAAATGGTGCTGAGA 1987
                         i  v v-  i    i   v   --  -- v    ii           i  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTC--TTTTCAACAAATGGTGCTGGGA 419

  chrX_138511187_   1988 TAACTGGCTAGCCATATGCAGAAGATTGAAGCTGGGCCCATACCTTTCTC 2037
                         i      v  ?   i     i    v     i   i   v     iv v 
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_138511187_   2038 CATATGCAAAAATTAACTAAAAATGGATTAAAGATTTTAATGTAAGATCT 2087
                              i            v         i ?   ii v         v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_138511187_   2088 CAAACTATAGAAATCCTGGAAGAAAACCTAGGAAATACTCTTTTCGACAT 2137
                         v        i  v  i i         v    ?ivv v    ivi   v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_138511187_   2138 TGGCCTTGGTAAAGAATTTTTGGCTAAGTCCCTAAAAGCAATTGCAATAA 2187
                            vi v  i  v iv  i  i v  v v v i       vvv    i  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_138511187_   2188 AACCAGAAATAGACCAGTGGGACCTCATTAAACTAAAGAGCTTCTGTACA 2237
                           vv i       iv i v    i    i   v v  i i   i   i v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_138511187_   2238 GCAAAAGAAACTATCAGCAGAGCAAACAGACAACCTACAGAATGGGAGAA 2287
                         v    i  v       iv i  ii  v        i              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_138511187_   2288 GATATTTGCAAACTATGTATCTGACAAAGGTCTAATACTCAGAATCTATA 2337
                         i           ii  i       i  i  v  vi  ii      v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_138511187_   2338 GGGAACTTGAAAAAATTAACAAGTAAAAACCAAATAACACCATTAAAAAG 2387
                         ii     ivv v  v i  i  vv    iv        v v   ?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_138511187_   2388 TGGGCAAATGACATGAACAGGCACTTTTCGAAAGAAGACATACAAATGGC 2437
                                 v  iv    i  i  i  i  v        i           
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_138511187_   2438 CAACAAATATATGAAACAATACTCAGCATCACTATCATC 2476
                            i  ii i      vi  i    i     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (102 / 71)
Gap_init rate = 0.01 (6 / 686), avg. gap size = 1.67 (10 / 6)  


3026 18.46 0.79 10.53  chrX_138723907_138725781      500  1382 (493)    L1M4_orf2#LINE/L1      112   908 (0)  

  chrX_138723907_    500 TTTTTTGCAGAAATTAAAAAAAATATATATCCACCATAAAATCCATATGG 549
                                        i v  iv--- i-    ----      i       
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGC---TG-ATCC----TAAAATTCATATGG 153

  chrX_138723907_    550 AATCTTAAGGCACCCCAAATAGCCAAAACAATCTTGAAAAAGAG---CAA 596
                           vivi    v    vi                          i---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_138723907_    597 AGTTGGGGGTCTTGCAACTCCTGATTTCAAAACATATTACAAAACAATAT 646
                               i  v  ii  vi   ii          v  i      i --  i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC--TAC 251

  chrX_138723907_    647 GTAATCAAAGTAATCAAAACCACGTGACACTGGCGTAAAGACAGACACAC 696
                         --------         i  vii   ii      i   i  i     i i
  L1M4_orf2#LINE/    252 --------AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_138723907_    697 AGGCAAACAGAATAAAAATAAATATCTCAGAAGTAAACTCTCATGTACAT 746
                           iiv  ii     i  v i ivi  -     i     i vi ii vi  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTAT 342

  chrX_138723907_    747 GGTCAAATGATCTTTAACAAGGGTGCCAAAACCACTCAGTGGGGGAA-AA 795
                               v    i  ii             i    i   i     i  -  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_138723907_    796 GAGTCTTCTCTTTTTTTCTTACCCTGTCCTACGATGCTGGGAGAGTCTTC 845
                         v      i  ----------------------------------------
  L1M4_orf2#LINE/    393 TAGTCTTTTC---------------------------------------- 402

  chrX_138723907_    846 AAATAAATGGTGCCAGGAAAACTGGACATCAACATGCAAAAGAATGAAGT 895
                         -  i         ii   v       i ? v                   
  L1M4_orf2#LINE/    403 -AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_138723907_    896 TGGACCCTTATCTTATACTACATACAAAAATTAACTCAAAGTCGATTGAA 945
                                i  i  i i  i i                   i v   ii? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_138723907_    946 GATCTACATGTAAGACTTATAAACTATCAATTAAACTTAAAAATATGCAA 995
                           i   v        vi  -       ------------    -------
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTA-AAACTAT------------AAAA------- 531

  chrX_138723907_    996 CTCCTAGAAGAAAACAGAGGGGAAAAGACTCATGACATTTGGATTTGACA 1045
                            i            v   ? v   vvi  i    -i    i  v i  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC-CTTGGGTTAGGCA 580

  chrX_138723907_   1046 GTGATTTCATGGATATGACATTAAAAGCACAGGCAACGAAAGCATAAACA 1095
                         i  i    v i         ii         i     i    v v   i 
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_138723907_   1096 GACAAATGATGAGACTACATCAAACTTTAATACTTCTGTTCATCAAAGTA 1145
                           i    --  -    v       v  v  v    i   v v      v 
  L1M4_orf2#LINE/    631 GATAAAT--TG-GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_138723907_   1146 AGTAATCATCACAATGAAAAGGCAACCTATGGAATGTGGGAAAATATTTG 1195
                         viiv    vv v i       i     i ii     v i           
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_138723907_   1196 CAAATCATATATTTCATAAGGAAATATTATCCAGAATATGTAAATAACTC 1245
                                     i v      i v vv            i    v     
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_138723907_   1246 CTACAACTGAGCAACAACAAAAAAGGAAATAACCCCCCCGCAACC--AAA 1293
                         i       ---   i  i     iiv         ------  ii--   
  L1M4_orf2#LINE/    778 TTACAACT---CAATAATAAAAAGACAAATAACCC------AATTWAAAA 818

  chrX_138723907_   1294 ATGGGTAAAGGACTTAGGTAGACATTTCTCAAAAGATGACATACAAATGG 1343
                              i      i  iii            v     v  i          
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_138723907_   1344 CCAAAAAACATAGGAAATGATGCTCA-CATCACTAATCAT 1382
                             v  i  i v    v        -     ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (106 / 54)
Gap_init rate = 0.02 (19 / 797), avg. gap size = 5.26 (100 / 19)  


3158 27.12 0.44 0.33  chrX_138765793_138772503     5312  6218 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138765793_   5312 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5361
                               i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138765793_   5362 GGCCATACTGCCTGAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 5411
                            v     v  ii  v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138765793_   5412 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATCTCA 5459
                          v   -   v    i  -i     v v  v  i-  - iii    vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_138765793_   5460 TATGGAACCAAAAAAGAGTCTGTATAGCAAAGACAATCCTAAGCAAAAAG 5509
                                viiv  ii  vi v v     v  i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_138765793_   5510 AACAAAGCTGGAGGCATCACTCTACCTTACTTCAAACTATACTACAAGGC 5559
                                i      vv    v  v  iv i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_138765793_   5560 TACAGTAACCAAAACAGTATGGTGCTGGTACCAAAACAGATACATAGACC 5609
                                 i   i     i    i    i iv ii i   i i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_138765793_   5610 AAAGGAACAAAACAGAGGCCTCAGAAATGACACCACACATTTAAAGCCAT 5659
                           v    i i  iv   ivii       i vv   i       vi i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_138765793_   5660 CTGATCTTTGACAAACCTGACAAAAACAAGTAATGGGGAAAGGATTCCCT 5709
                         i    i  i     ivv  v   i v  vvi           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_138765793_   5710 ATTTAATAAACGGTGCTGACAAAACTGGCTAGCCATGTGCAGAAAACAGA 5759
                         v  i  i   i       iv v      v  ?   ii    i  i vv  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_138765793_   5760 AACTGGATCCCTTTTTTACACCTTATTCAAAAATTAACTCAAGATGGATT 5809
                          ii    i    vii i     v   v               i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_138765793_   5810 AAAGACTTCAATGTAAAACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5859
                          ?    i v       i v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_138765793_   5860 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGGCTTCATGACTAAA 5908
                            ?i- v i -   iv   v v  vv i     v  i   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_138765793_   5909 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTAAT 5958
                                     vvi          vv     v  i    v i ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_138765793_   5959 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTAAACA 6008
                         i   v v  i i   i  ii vv    i  v       vv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_138765793_   6009 CGCAACCTACAGAATGGGAGAAAATTTTTACAATCTATCCATCTGAGAAA 6058
                         vi     i                 v   i   vii  vi      v  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_138765793_   6059 GGGCTAATATCCAGAATCTATAAGGAACTTAAACAAATTTACAAGAAAAA 6108
                           i  vi          v     i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_138765793_   6109 -ACAAACACCCCCATCAAAAAGTTGGCGAAGGATACGAACAGACACTTCT 6157
                         -     i v   v  i?    i v   i      vi   i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_138765793_   6158 CAAAAGAAGACATTTATGTGGTCAACAAACATATGAAAAAAAGCTCATCA 6207
                          v        i  vi vi   i   i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_138765793_   6208 TCACTGGTCAT 6218
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.00 (7 / 7)  


3308 27.31 0.22 0.22  chrX_138796935_138803342.rev     5010  5917 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138796935_   5010 TGGAAGAACATTCCATGCTCATGGGTAAGAAGAATCAATATCGTGAAAAT 5059
                              ii i  i     i      i vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138796935_   5060 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5109
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138796935_   5110 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5157
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_138796935_   5158 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5207
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_138796935_   5208 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5257
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_138796935_   5258 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5307
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_138796935_   5308 AATGGAATAGAACAGAGCACTCAGAAATAATGCCGCATATCTACAACTAT 5357
                                     iv   viii         vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_138796935_   5358 GTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5407
                         v    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_138796935_   5408 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5457
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_138796935_   5458 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5507
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_138796935_   5508 AAAGAGTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAGCCT 5557
                          ?   vi       v   v       i      vi i         i v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_138796935_   5558 AGGAATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5607
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_138796935_   5608 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5657
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_138796935_   5658 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5707
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_138796935_   5708 GCAACTTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAG 5757
                         i    ii   i             v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_138796935_   5758 GGCTAATATCCAGAATCTACAATGAACCCAAACAAATTTACAAGAAAAAA 5807
                          i  vi          v  i  v    i vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_138796935_   5808 ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTGCTC 5857
                              i     v  i?    i            v    i     i v   
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_138796935_   5858 AAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCAT 5907
                         v        i  vi viii     v ii          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_138796935_   5908 CACTGGCCAT 5917
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (144 / 100)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


2586 28.05 0.26 0.13  chrX_138831975_138833728.rev      502  1264 (490)    L1M4_orf2#LINE/L1      145   908 (0)  

  chrX_138831975_    502 TTTATATGGAATGAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCA 551
                           i        vviv  ii  v  viv  v     i      i i ivv 
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_138831975_    552 AAAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATTACA 601
                         i          i      vv   ii  v  ii i      viv  i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_138831975_    602 AGGCTACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGAGATATA 651
                          i          i   i    ii i       i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_138831975_    652 GACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAA 701
                           i        i    iv   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_138831975_    702 CTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 751
                         ii vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_138831975_    752 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 801
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_138831975_    802 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 851
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_138831975_    852 GATTAAAGAGTTAAATGTTAGACCTAAAACCATTAAAACCCT-AGAAGAA 900
                            i ?   vi       v   v       i  -     i  -       
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAA 543

  chrX_138831975_    901 AACCTAGGCAATACCCATCAGGACATAGGCATGAGCAAGGACTTCATGAC 950
                            v    ?ivv vi v  iv   v v  vv ii    v ii   v iiv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_138831975_    951 TAAAATACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 1000
                           vi i  i       vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_138831975_   1001 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 1050
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_138831975_   1051 AACAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTCTCCATCTGA 1100
                           v  i     i                vv       viiv vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_138831975_   1101 CAAAGGGCTAATATCCAGAATCTACA-GGAAATTAAACAAATTTACAAGA 1149
                         i  i  i  vi          v  i -i   v ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_138831975_   1150 AAAAATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAGCAGACAC 1199
                             iv    i     v  i?    i     i      v   ii     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_138831975_   1200 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 1249
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_138831975_   1250 ATCATCCCTGGCCAT 1264
                          v    v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (120 / 90)
Gap_init rate = 0.00 (3 / 764), avg. gap size = 1.00 (3 / 3)  


3075 25.33 2.11 1.22  chrX_138922151_138924762.rev     1222  2121 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138922151_   1222 TAGAAAAACATTTCATGATCATGGATAGGAAGAATCAATATCATTAAAAT 1271
                          i    i i  ii    v        v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138922151_   1272 TGCCACACTGTCCAAAGCAATTTACAGATTCAATGTTATTCCTATCAAAC 1321
                         v  v i   vi     vii  i           i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138922151_   1322 TACCAAGGACATTTTTCACAAAA---------CT-ATTTTAAAATTCATA 1361
                          v   ivvi v     ii  i  ---------  -  ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_138922151_   1362 TGGAAC--CAAAAAATTGCCCA-AATTGCCAAGGCAATCTTAAGCAAAAA 1408
                              v--   iii ---    -   v     ii       i iv  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_138922151_   1409 GAACAAAGCTGGAGGCATCATGTTACCCAACTTCAAATGATACTACAGGG 1458
                                 i      vv   iii v     i      vvv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_138922151_   1459 TTACAGTAACCAAAATGGGATGGTACACTGGTACAAAAACAGGCACATAG 1508
                         i        i   i ii vi      --   i i  ii i  i  i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTAC--TGGCATAAGGATAGACATATAG 295

  chrX_138922151_   1509 ACCAATGGAACAGAACAGAGAGCCCGGAAGTTAGGTCACACACATACAAC 1558
                          i        i    iv     i  i   i v ivi  i   iv  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_138922151_   1559 CATCTGATCTTCGACAAAGCTGACCAAAACCAG-CAATGGGAAAAGGACT 1607
                           vi    i        i v  -    i    v-       i    i iv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_138922151_   1608 CCCTATTCAATAAATGGTGCTGGG-TAACTGGCTAGCCATGTGCAGAAGA 1656
                         vi  v     i             -i      v  ?   ii    i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_138922151_   1657 TTGAAACTGGACACCTTTCTTACACCACATACAAAAATTAACTCAAGATG 1706
                         v    ii     v   vi  i      i                  i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_138922151_   1707 GATTAAAGACTTACATGCAAAACCCAAAACTATAAAAATCCTAGAAGAAA 1756
                            i ?    i  v   i  i v i            v  i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_138922151_   1757 ACCTTGGCA-ATACCATTCAGAACATAAGCACAGGCAAAGATTTCAT-GA 1804
                           v v  ?i- v i -   ivi  v vi vvi      v i    v -  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_138922151_   1805 TGAAGATGCCAAAAGCAATTTCAACAAAAGCAAAAATTGATAAATGGGAT 1854
                          - v  ii         vvvv         v      v       v   i
  L1M4_orf2#LINE/    594 T-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_138922151_   1855 ATAATTAAA-CTAAAAGCTTCTGCACAACAAAATAAACTGTCAACAGAGT 1903
                         v v  i   -i     i   i  ii vv    iv v   i    v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_138922151_   1904 AAACAGACAACTCAGAGTTTGGGAGAAAATTTTTGCAAACTATGCATCTA 1953
                         i  v       i  v  vv           v        ii  ii    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_138922151_   1954 TCAAAGGTCTAATATCCAGCATCTATAAGGAATT-TAACAAATTTACAAG 2002
                         vi  i  v  vi       v  v     i   i - v    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_138922151_   2003 AAAAAAAACAAACAACCCCATTAAAAAGTAGGCAAAGGACAAGAACAGAC 2052
                              i -    i     v   ?    i i         ivv   i    
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_138922151_   2053 ACTTTTCAAAAGAAGACATACATGCGGCCAACAATCACATGAAAAAAAAA 2102
                          i  i  v        i     vii      i  v          i vi-
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG- 890

  chrX_138922151_   2103 TCTCAACATCACTATCATT 2121
                         -          ????????
  L1M4_orf2#LINE/    891 -CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.76 (30 / 17)  


 617 20.41 2.72 2.72  chrX_138939546_138942951.rev     1687  1833 (1572)    L1M4_orf2#LINE/L1        1   147 (761)  

  chrX_138939546_   1687 TGGAAGCATATCCCACGTCCACAGATTAAAAGACTT--TATTGTTAGGAT 1734
                              iv        i  i  ii    ii       --        i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138939546_   1735 GGTAATACTCCCCCCATATT-ATCTACAGAGTCCAC-CAATCTCTGCCAA 1782
                           i          -- v   -         v  v  -     i  ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCC--AAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_138939546_   1783 AATATCCTAGGTGCCTTTTTTGAATAAATGAATACATTAGTCATAAGATT 1832
                            --  i  v           v v    vi i vii ii  v   i   
  L1M4_orf2#LINE/     99 AAT--CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_138939546_   1833 C 1833
                          
  L1M4_orf2#LINE/    147 C 147

Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.03 (5 / 147), avg. gap size = 1.60 (8 / 5)  

3545 16.38 2.75 1.57  chrX_138939546_138942951.rev     2152  2914 (491)    L1M4_orf2#LINE/L1      137   908 (0)  

  chrX_138939546_   2152 TCCATAACATTCTTATGGAAATGCAAGGGGCCTCTAAGAGCCAAAAAAAT 2201
                            -   v    v                i  ivv  v        v   
  L1M4_orf2#LINE/    137 TCC-TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_138939546_   2202 CTTGAAAAAGGAGAACAAATTCCAAGGACTCACTCACACTTCCCAATTTC 2251
                                   i        v ivi         ----             
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC----ACTTCCCAATTTC 231

  chrX_138939546_   2252 AAAACTTATTACAAAGATACAGTAA--AGCGTATTGTGGAGTACTGGCAT 2299
                                 i       v        -- ivii v     --         
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG--TACTGGCAT 279

  chrX_138939546_   2300 AATAATTAACACATAGATCAGTGGAATAGAATTGACAGTCCAGAAATACA 2349
                           vi  vi   i        i              v            v 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_138939546_   2350 CCCATACATCTATGGTCAATTAATTTTCAACAATTGTATGAAATTCCCTC 2399
                                  i           i      i    vv  iiv  ivi vi  
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_138939546_   2400 AATGGGGAAA-AATAGACTTTTCAACAAAAAGTACTGAGTTAACAAGATA 2448
                                   -     v            vi  i   i vi   vi    
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_138939546_   2449 TCTACATGTAAAAGAATGAATTTGGATCCCTAT-TCACACCATATATAAA 2497
                         ? i     i           v     i     i-            i   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_138939546_   2498 AATTAACCCAAAATAGACTAGAAACCTAAATTTAAGAACTAAATATATTA 2547
                                i      i  ii ? i        v     i     vv   - 
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-A 528

  chrX_138939546_   2548 AAACT-TTAGAAGGAAACATAGGGATATATCTTTATGACCTT-----AAT 2591
                              -       i         ?i  v     ii       ----- iv
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_138939546_   2592 CAATGGTTTTTAAAATATGCCATTCAAA--ACAGGCAACAAATGAAAAAT 2639
                                  i v i     v  iiv   --   i        v      v
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_138939546_   2640 TAGATAAAGTGGACTTCATCATAACTAAAAACTTTTGTGCAACAAAGAAC 2689
                                 v            v  i               vv     i  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_138939546_   2690 ATTATCAAGAGAGTGTAAAGACAACCCACAGAATGGAAGAAAATATTTGC 2739
                          i        i    v                    i             
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_138939546_   2740 ATATCACATATATAATCTTAAAAACTTGTATATAGGCTGTATAAGCAACA 2789
                          v    i    v i  v-- iii        vi  iv i     iv   v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATA--AGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_138939546_   2790 TTTACACCTCAA-AATAAAATGACCAAAAAAA---AAT--AAAAATGGGC 2833
                         i     v     -       v   --   v  ---   --          
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGAC--AAATAACCCAATTWAAAAATGGGC 824

  chrX_138939546_   2834 AAAGGATTTGAGTGGACATTTCTCCATTTA---TATACAAATAGCTAATA 2880
                                    i i            vvv ---         i  i    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_138939546_   2881 AGTACATGAAAATATTCTCAACATCATTAGTCAT 2914
                           i         v  v          ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (67 / 55)
Gap_init rate = 0.02 (16 / 772), avg. gap size = 2.06 (33 / 16)  


2966 26.80 1.11 0.55  chrX_138959397_138961460.rev      671  1573 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_138959397_    671 TGGAAAAACATTCCATGCTCGTGAATAAGAAGAATTAATATCGTGAAAAT 720
                               i i  i     i  i  i  vi     v       i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_138959397_    721 GGCCATACTGCCCAAAGTAATTTTTAGATTCAATGCTATTCCCATTAAAC 770
                            v     v      v i  i vi        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_138959397_    771 TACCA-TTGACTTTCTTGGCAGAATTAGAAAAAACT-ACTTTAAATTTCA 818
                          v   -i  v    i   -     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_138959397_    819 TATGGAACCAAAAAAGGACCC-GTATAGCCAAGAAAATCCTAAGCAAAAA 867
                                viiv  i-      - v        i v    i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_138959397_    868 GAACAACACTGGAGGCATCACGCTACCTGACTTCAA--CTATACTACAAG 915
                               vii      vv    i  v  ii i     --  -        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chrX_138959397_    916 GCTACAGTAACCAAAACAGCACAGTACTGGTACCAC-ACAGATATATAGA 964
                                   i   i    iiii       i iv v- i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_138959397_    965 CCAATGGAACAGAACAGAGAACTCACACATAACACCACACATCTACAACC 1014
                         i        i    iv    iii  v v    vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_138959397_   1015 ATCTGATCTTTGACAAACCTGACAAAAACGAGCAATGGAGAAAGGATTCC 1064
                          vi    i  i     ivv  v   i v ivv      i     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_138959397_   1065 CTATTTAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAAAAACA- 1113
                           v  i ii              v      v  ?   i        iv -
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_138959397_   1114 GAAACTGCACCCTTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 1163
                            ii  v    i v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_138959397_   1164 TTAAAGCCTTAAATGTAAAACCCCAAACCATAAAAACCGCAGAAGAAATG 1213
                          i ?  v i         i v iv    i      vi vi        vv
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_138959397_   1214 CTAGGCA-ATACCATTTAGGACATAGGCATGGGCAAAGACTTCATGACTG 1262
                         v    ?i- v i -  iiv   v v  vv i     v ii   v iiv i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_138959397_   1263 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACACACAGGATCTA 1312
                         vi            vvi          vv        i v iv   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_138959397_   1313 ATCAAACTAAAGAGCTTCTGCACAACAAAAGAAACTATCATCAGAGTGAA 1362
                               v v  i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_138959397_   1363 CAGGCAACCTACAGAATGGGAGAAAATTTTGGCAATCTACCCATCGGACA 1412
                         v  i     i                 v  v    vii ivi   v  i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_138959397_   1413 AAGGTCTAATATCCAGAGTCTACAAGGAACTTAAACAAATTTACAAGAAA 1462
                          i  v  vi        i v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_138959397_   1463 AAAAAAAAAAAAC--ATCAAAAAGTGGGCAAAAGATATGAACCGACACTT 1510
                           i v   v  v --  i?    i        i   v    iv    i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_138959397_   1511 CTCAAAAGAAGACATTTATGTGGCCAATAAACATATGAAAAAAAGCTCAT 1560
                            v        i  vi vi          i  i       i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_138959397_   1561 CATCACTGGTCAT 1573
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (135 / 103)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.15 (15 / 13)  


3219 24.32 3.17 0.45  chrX_139046240_139050440.rev     2827  3710 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_139046240_   2827 TGGCAAAATATTCCATGTTCATGGATTGGAAAAATCAATATTATTAAAAT 2876
                            v  i    i                   i v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139046240_   2877 GTCCACAGTACCCAAAGCAATCTACAGATTCAACACAATCCCTATCTAAG 2926
                          v v i v v      vii               i           -  i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC-AAA 99

  chrX_139046240_   2927 ATT---------TTTCCCACAGAAAA-GAAAAAC-AATCCTCAAAATTTA 2965
                           i---------   iiii      v-  v  i -i     -      i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAATTCA 148

  chrX_139046240_   2966 TATGGAACCAGAAAAGATGCAAAAGAGCCAAAGCCATCCTGAACAAAAAG 3015
                                viiv  ii  iv  i  v       i v   i    v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_139046240_   3016 AAGAAAACGCGAAGAATCACATTGCCTGATTTCAAATTATAATACATAGC 3065
                           v   iivv  i  v     i v  ii        viv  v    v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_139046240_   3066 TATAGTAACCAAAACAGCATGGTACTGGCATAAAAACGGACACATAGACC 3115
                           i     i   i    ii              ii ii    i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_139046240_   3116 AATAAAACAGAATAGAGAACCCAGAAACAAATCCACACACCTACAATTAA 3165
                            ii  i     v    ii       i   i   i   ii  iii i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_139046240_   3166 CTTATTGTTGACAAAGATGCCAAGAACATGCACTGGGGGAAAGAA-AGTC 3214
                         i v   v i     i i        v   v  v     -      -    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTC 397

  chrX_139046240_   3215 TCTTCAATAACTGGTGCTGAA-------GAGA---ATATGCAGAAGAATA 3254
                          i     i  v        ii-------  v --- i     i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_139046240_   3255 AAAGTAGACCCCTATCTACTGGCATATA-AAAAATCAAATCAAGATGGAT 3303
                           iv i        i  vviiv      -      i  v    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_139046240_   3304 TAAAGGCTTAAATCTAAGACCTCAAACTATAAAACTCCTACAAGAAAACA 3353
                         i ?  i i     v     v  v              i  v         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_139046240_   3354 ATGAGAAAAATCTCTAGGACATTGCACTAGGCAAAAGTTTCTTGAGCAAT 3403
                         vv i?iv      iiiv   v   vii       vi       iiii vv
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_139046240_   3404 ACCCCACAAACACAGACAACCAAAGCAAGAATGGACAAATGGGATCACAT 3453
                           v   v  i    ii    v    v  i   i  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_139046240_   3454 CACA-TTAAACAGCTTCTGCACAGCCAAGGATACAATCAACAAAG-GGAA 3501
                           v -     - i   i  ii vv v     i  v     v    - i  
  L1M4_orf2#LINE/    648 CAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_139046240_   3502 AGACAACCCACGGAACAGGAGAAAATATATGCAAACTATCCATCTGACAA 3551
                                    i   ii           v      ii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_139046240_   3552 GGGATTAATAACCAGAATACATAAGGAGCTCAAACAACTCTGTGTGAAAA 3601
                             i vi  v        i    i  i   vv       vi ivv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_139046240_   3602 AATCTAATAATCCAATC--AAAATGGGCACAAGATTTGAATAGACATTTC 3649
                          iv v     i     i--          v i                  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_139046240_   3650 TCAGAAGAAGACATACAA-TGGTAAACAGGCATACAAAAAGGTGATCATC 3698
                           vi       i      -   iv  i i   i ii     i  v   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_139046240_   3699 ATCACTGATCAT 3710
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (135 / 78)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.13 (32 / 15)  


2428 25.50 1.90 6.53  chrX_139074767_139081533.rev     5328  6276 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_139074767_   5328 AAAAAAATTCCTTGCTCATGAATAGGAAGAATCAATAC-GTGAAAATGGC 5376
                            i v  i  v  i     i  v      v i    i-  v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_139074767_   5377 CATACTGCCCAGAGTAATTTATAGATTCAATGCTATTCCCATCAGGCTAC 5426
                         v     v    i v i  i  i        i  v  i  i    iiv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_139074767_   5427 CATTGACTTTCTTCACAGAATTTGAAAAAAAAAACAAAAAACAACAACAA 5476
                           vivi i  i  ii     v    -------------------------
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGA------------------------- 128

  chrX_139074767_   5477 CAACAACAACAACAAA--AAACCTTTAAATTTCATATGGAACCAAAAAAA 5524
                         ------------   i--i v   --   v           viiv  ii-
  L1M4_orf2#LINE/    129 ------------CAAGCTGATCCT--AAAATTCATATGGAAATGCAAGG- 163

  chrX_139074767_   5525 GAGCCTGTATAGCCCAAGACTACTCTAAGCAAAAAGAACAAAGCTGGAGG 5574
                           v  v v      -  i  v iii i iv  i          i      
  L1M4_orf2#LINE/    164 GACCCAGAATAGCC-AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_139074767_   5575 CATCCTGCTATCTGACTT-AAAACTATACTACAAGTCTACAATAACCAAA 5623
                         vv  vii  vi ii i  -      -        iv     i   i   i
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGTAATCAAG 261

  chrX_139074767_   5624 ACAGCATGGTACTTGTACCAAAACAGATATATAGACCAATGGAACAGCAC 5673
                             ii       v i iv ii i   i       i        i  v i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_139074767_   5674 AGAGGCCTCAGAAATAACACCACACATCTACAACCATCTGATCTTTGACA 5723
                         v   ivii         vv   i    i  iiii  vi    i  i    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_139074767_   5724 AACCTGACAAAAACAAGCAATGTTTTTGCTTGTTTTAGAAAGGATTCCCT 5773
                          ivv  v   i v  vv     --------- ----i     i  vvi  
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATG---------G----GGAAAGAATAGTCT 398

  chrX_139074767_   5774 ATTTAATAAATGGTGCTGGGAAAACTGGCCAGCCATATGCAGAAAACTGT 5823
                         v  i  i              v      vi ?   i     i  i v  v
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_139074767_   5824 AACTGGACCCCTTCCT-------TATACACAAATTAACTCAAGATGGATT 5866
                          ii         v   -------      v            i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_139074767_   5867 AAAGACTTAAATGTAAAACCCAAAATCATAAATACTCT-AGAAGAAAACC 5915
                          ?    i         i v i    ii     -     -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACA 547

  chrX_139074767_   5916 TAGGCA-ATACCATTCAAGACATAGGCATGGGCAAAGTCTTCATGACTAA 5964
                             ?i- v i -   iv   v v  vv i     v vi   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_139074767_   5965 AACACCAAAAGTAATTGCAACAAAAGCCAAAATTCAATAA-TGGGATCTA 6013
                         i          i vvv          vv     -vi    - v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAATTGGACTTC 645

  chrX_139074767_   6014 ATTAAA-TTAAAAAGCTCCTGTACAGCAAAAGAAACTATCATGTGAGTGA 6062
                           i   -       -  ii   i vv    i  v       v vi     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_139074767_   6063 ACAGGCAACCCACAGAATAGGAGAGTATTTCTGCAATCTACCCATCTGAC 6112
                          v  i             i     iv  v i     vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_139074767_   6113 AAAGGTCTAATATCCAGAATCTACAAGTAACTTAAACAAATTTACAAGAA 6162
                           i  v  vi          v  i  iv    ivv    v ---   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAA 791

  chrX_139074767_   6163 -AAAAAAACACACAACCACATCAAAAAGTGGGTGAAGGATATGAACAGAC 6211
                         -     i   v i    vv  i?    i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_139074767_   6212 ACTTCTCAAAAGAGGAAATTTATGCAGCCGACAA--ACATGAAAAAAGGC 6259
                          i     v     i  v  vi viii   i i  --         i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_139074767_   6260 TTATCATCACTGGTCAT 6276
                          i v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (138 / 100)
Gap_init rate = 0.02 (22 / 905), avg. gap size = 3.64 (80 / 22)  


3607 23.95 0.44 1.33  chrX_139084871_139089131.rev     2869  3770 (491)    L1M4_orf2#LINE/L1       15   908 (0)  

  chrX_139084871_   2869 ATGTTCATGGATTGGAAGAATCAATATTGTTAAAATGTCCATACTACC-A 2917
                                            v i           i   v v     v  - 
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_139084871_   2918 AAGTAATCTACAGATTCAATGCAATTTCTATTAAAATGCCAATGATATTC 2967
                           v i              i     ii    i     v   iiviiv  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_139084871_   2968 TTCACAGAAATAGAAAAAACGATCCTAAAATTTATATGGAACCACAAAAG 3017
                           ii       v  v  ivi            i        vii   ii 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_139084871_   3018 ACCCAGACTAGTCAAAGCTATCCTGAGAAAAAAGAACAAAATGGGAGGAG 3067
                                v   i    i v   i   i   i         i v      v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_139084871_   3068 TCACATCACCTGACTTCAAATTATGCTACAAAGCTATAGTAACCAAAACA 3117
                              iiv  ii i      viv i           i     i   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_139084871_   3118 CTATGGTAGTAGTATAAAAACAGACACATAGGCCAATGGAACAGTATAGA 3167
                         v i     v i i    ii i     i    ii        i  v  v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_139084871_   3168 GAACCCAGTAACAAATCCACACACCTACAGTGAATGCATTTT-GACAAAG 3216
                           ii    v  i   i   i   ii  ii  v   vv     -     i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chrX_139084871_   3217 GTACCAAGAACATACACTGGGGTAAAGACAGTCTCTTCAATAAATGGTGC 3266
                           i      v   v  v     v  ii i     i     i         
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chrX_139084871_   3267 TGGGAAAACTGGTTATCCATATGCGGAAGAATGAAAC-AGATCCCTATGT 3315
                              v      v  ?   i    ii         ii-i  i     iv 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_139084871_   3316 CTTGCCATATACAAAAATTAAATCAAAACGGATTAAAGGCTTAAATCTAA 3365
                          vii                 v      i    i ?  i i     v   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_139084871_   3366 GACCTCAAACTATGAAACTACTACAAGACGACATTGGGGAAAATCTCTAG 3415
                           v  v       i     vi  v    vi    v  ? v      iiiv
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_139084871_   3416 GACTTTGGACTGGGTGAAAATTTCTTGAGCAATACCCCACAAGCCCACAA 3465
                            i    ii i  ii vii      -  vv  i----   ---   v  
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTT-AGATATG----ACA---CCAAAA 606

  chrX_139084871_   3466 GCACACACAACCAAAACAAAGGTGGACAAATGGGATCACATCAAGTTGTA 3515
                              vi    v   iv   ii i  i    v   iiv      iv vv 
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_139084871_   3516 AAGCTTCTGCACAGCAAAGGATATAATCAACAAAGTGAAGAGGCAACCCA 3565
                           i   i  ii vv       i iv     v        i  i       
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_139084871_   3566 CAGAATGGGAGAAAATGTCTGCAAACTACTCATCTGGGAAGGGATTAACA 3615
                                         i i      ii ivi     iv      i vii 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_139084871_   3616 ACCAGAATATATAAGCAGCTTAAACAACTCTATAGGAAAAAAAAAATCTA 3665
                         v             iv i  ivv       v   iv     i v  ----
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA---- 802

  chrX_139084871_   3666 ATAATCCCATC-AAAAATGGGCAAAAGAGTTGAAGAGACAGTTCTCAAAA 3714
                             i  v  i-             i  v     v     v     v   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_139084871_   3715 GAAGACATACAAACGACAAACAGGCATATGAAAAGGTGATCATCATCAGT 3764
                              i       i i v  i i   i        i  v   v     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_139084871_   3765 GATTAT 3770
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.70 (134 / 79)
Gap_init rate = 0.01 (8 / 894), avg. gap size = 2.00 (16 / 8)  


2775 26.84 1.54 1.65  chrX_139115626_139119701     2677  3585 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_139115626_   2677 TGAAAAAACATTCCTTGCTCATAGATTGGAAGAATCAATGTCATTCAAAT 2726
                           i   i i  i  v  i    i          v i   i ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139115626_   2727 GACAATACTGCCCAAAGCAACCTACAGATTCAACGTTATTCCTATGAAAC 2776
                          i       v      vii i              iv  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_139115626_   2777 TACCGACATCATTCTTCACAAAATTAGAAAAAACAAATCTAAAATTTATG 2826
                          v  ii vv v  i  ii  i  v v  v  ivii vi        i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_139115626_   2827 TGGAACCAAAAAAGAGCCTGAGTAGCCAAAGCAATCCTAAGCAATAAGAT 2876
                              viiv  ii  v  v  i        i     i i iv  v    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_139115626_   2877 CAAAGCCAGAGTCAC-CACATTACCCAACATTAAACTGTACTATAAGGCT 2925
                              iii   v-  -    i v     iv i   viv     i  i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_139115626_   2926 ACAGTAACCAAAACAGCATG-TACTGATACAAAAACAAACACATAGATAA 2974
                                i   i    ii  -     ii i  ii i i   i      v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_139115626_   2975 ATTAATTAGAATAGAGAA-CCAGAAATAAATCTGTACATCTACAGTGAAC 3023
                           vi v      v    i-           i ii     i  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_139115626_   3024 TCACTTTTGGCAAAGGTTCCAAAAACATACACTGGGGAAAGAACAGTCTT 3073
                          v i   i i   i   v    i v   v  v           i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_139115626_   3074 TTCAATGAATGGTGTTGGGATAGCTAGTTACCCTGATGCAGAAGAATGAA 3123
                              ii       i     i i  i v  ?  vv     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_139115626_   3124 ACTGAACCCATACCTGTCACTGTATACAAACATTAACTCACGATATATTA 3173
                         ii  i    v     vv   ii        v         vi  iv  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_139115626_   3174 AAGATTTTAAATTTAAGACATCAGACTATAAGAATCCTAGAAGAAAACCT 3223
                         ?   ii -    v     vv v i       i v  i           v 
  L1M4_orf2#LINE/    500 WAGACCT-AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_139115626_   3224 AGGAA-ACATCATTCTGGACATAGGCCTTGGAAAAGA------ATGTATG 3266
                            ?i- v   -   vv   v v  vi v  v  v i------ vi    
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_139115626_   3267 ACCAAGTCCTGAAAAGCAATTGCGACAACAAAAAAAATGGACAAGTGGGA 3316
                           -- --  --       vvv  i    v i       i  i  i v   
  L1M4_orf2#LINE/    598 AC--A--CC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_139115626_   3317 CCTAACTAAACCAAAGAACTTCTACACAACAAAAGAAACTATCAACAGAG 3366
                          i v ii   viv  i     i iii vv    i  v        v i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_139115626_   3367 TATACAGA-AATGCACAAACTGGGAGAAAATATTTGCAAACAATGTATCC 3415
                          iv v   -  iv    i v                    iv  i    i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_139115626_   3416 AACAAAAGTCTAATATCCAGGATTGATAATGAAAT-TAACAATTCAAGCA 3464
                         i i  ii v  vi       i  vv    v   v - v    i    ---
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA--- 788

  chrX_139115626_   3465 TAATAATAATAATAATAATAACTATATTAAAAAATGGGCAAAAGGCATGA 3514
                               v  -i i  --     ivv   ?             i iiv   
  L1M4_orf2#LINE/    789 TAATAAAAA-GACAA--ATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_139115626_   3515 ACAGAAACTCATCCAAAGGAGATGTACAGGTGGCCAACAA--ACATGAAA 3562
                          i   v i iv       i    i    ii       i  --        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_139115626_   3563 AAATAATCAACATTGCTGATCAT 3585
                          i  iv       ii????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.71 (29 / 17)  


2341 25.64 6.81 1.96  chrX_139173459_139175340      526  1391 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_139173459_    526 TGAAAAGATATACCATATTTATGAATCGGAATACT--ATACTGTTAAGGT 573
                           i        v    i  i   i  i    v   --   i       i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139173459_    574 ATTATTTATTTACAAATTGATTGACAGACTCAATGCAATTCCATTTAAAA 623
                         ivi v vv iiv         iv     i    i     i  vv i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_139173459_    624 ACACTACAGTTAT-TTCTTTGTGGAAGTTGACAAGATGATTCTAAAATTT 672
                         v - --   i ii-  i    ii   i        v    i        i
  L1M4_orf2#LINE/    101 TC-C--CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_139173459_    673 AT-TATAAATGCAAAAGAATC----TAGACAAGAACAACCTTTTATGAAA 717
                           - iv        ii  vi ----   v   -     i   vv --   
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAA-AACAATCTTGAA--AAA 194

  chrX_139173459_    718 GAAGAACAATTTTGGGAGACTTACACTACCCAATTTTAAGACCTATTAC- 766
                                  vv    ii    i     v        i  i  i  i   -
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_139173459_    767 ------CCCTCACTAAGA----ATGAT--TGACCCCTCACTAAGGATAGA 804
                         ------ vv v ii    ----i  i --  i ----- -          
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGC-----A-TAAGGATAGA 288

  chrX_139173459_    805 C-TAACAACTAATGGGAGAAAAC----AGTACAGAAACAGATCCATACAC 849
                          -  vvi ii     i v i  i----   v      i i i       i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_139173459_    850 ATATGGTCAATTGA----------GGACTCCATTGCAATTCAGTGAGGAC 889
                         v             ----------  iiv   vvi v     i  i   v
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_139173459_    890 AGAAAAAACTTTTATGCAAATGGTGCTGGAATGGCTGGATAAATGTATGG 939
                             v iv     vvi             i iii       ?viii   v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_139173459_    940 AAGGAAATGTACACTGACTCCTACCTTACAGCATACACAAATATTAAT-- 987
                           iii    v vviv   i       i   v    i     v     i--
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_139173459_    988 GAGATTAATCATAGACTGAAAAGTATAAACTAAAACTATAAAGATTTTGG 1037
                         i i  vi    ?    iv   v   vi i             iv i  i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_139173459_   1038 AAGAAAACAT-GGTATGGTATCTTTAGGACTTTGGGGTAGACAAGGATTT 1086
                                   -  ?i ii-     iiv   i     v   i   v i   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_139173459_   1087 TTAGGAGATGGCAG-AAAA--ATAACCA-TAAAAGAAAATTT-GATAAAT 1131
                         i vi  v   i  v-    -- i  v  -i         vv -       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_139173459_   1132 TGGACTTCATCAAAA---AATGCT---GTTCTTTTAAATATATGGTTAAG 1175
                                        ---  vi  ---  v   iv  iv i ivi i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_139173459_   1176 AAGATGAAAAAGCAAACCATACACCGGGA-AAAATATTCACAATACATAT 1224
                           ii      ii   v   i v vi    -        ii   vv     
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_139173459_   1225 ATCTGAAAAGGGACTCTTATCAAGAATATGTAAAGATTTCCCACAAATTG 1274
                               v        iv    v       i      vi  ii    v ii
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_139173459_   1275 ATCATAAAGATTTAAA-AAACCAAT-AAAAAATAAGCA---GTCTTGAAC 1319
                           v     i vvi   -  v     -?      ii   --- vi     i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_139173459_   1320 AGTGACTTCACAAAAAAAGATA---AAGGGAACAATAAGCACATACAAAA 1366
                           vv i   v v   i      ---  iv iv            i-    
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAA 886

  chrX_139173459_   1367 TACCGTGTTCAACATTGTTAGTCAG 1391
                         v ---  i       ii????????
  L1M4_orf2#LINE/    887 GA---TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (132 / 86)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 2.38 (76 / 32)  


3671 22.37 1.52 2.93  chrX_139200629_139205040     2999  3919 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_139200629_   2999 TGGAAAAATATTCCATGTTCATGGATTGGAAGAATCAATATTGTTAAAAT 3048
                               i    i                     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139200629_   3049 ATTCATAGTACCCAGAGCAATCTATAGATTCAATGTAATCCCCATGA--- 3095
                         iviv   v v    i vii     i        i i      i  v ---
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_139200629_   3096 ---CA------TTCTTCACAGAAATAAAAAAGAAAATCCTAAAATTTTTA 3136
                         ---  ------  i  ii       vi v   vvi           iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_139200629_   3137 TGGAACCACAAAAGACTCAGAATAGTCAAAGTTATCCTAAGCAAAAAGAA 3186
                              vii   ii   i        i    iiv   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_139200629_   3187 CAAAGCTGGAGGAATCACATTACCTTACTTCAAATTATACTACAGAGCCA 3236
                              i       v     i v  iv i      viv       i   i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_139200629_   3237 CATTAACTATAACAACATGGTACTGGCATAAAAACAGACACATAGACCAA 3286
                           v   ii vi   iii              ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_139200629_   3287 TGGAGCAGAATAGAGAAACTAGAAACAAATCCATACACCTACAGTGAACT 3336
                             ii     v    iv i     i   i       ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_139200629_   3337 CATTTTTGACAAAAGTGTCAAGAACATACACTGGGGAAAAGACAGTCTTT 3386
                         v     i     ii   i     v   v  v        ii i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_139200629_   3387 TCAATAAATGGTGATGGGAAAACTGGATATCCATATGCAGAAGAATGAAA 3436
                             i        v     v         ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_139200629_   3437 CTGGACCCTT-TCTCTTGCCATATACAAAAATAAAATAAACATGGATTAA 3485
                         i       i -i   vii              ---------------   
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAAT---------------TAA 485

  chrX_139200629_   3486 TAAAATAAACATGGATTAAAGACTTCAGTCTGAGACCTTAAACTATGAAA 3535
                         i---- v  v      i ?    i v i v i   v  v       i   
  L1M4_orf2#LINE/    486 C----TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_139200629_   3536 CTAGTACAAGAAAACATTGGGGACAATGTCCTTTTCCCAGGACATTGGTC 3585
                           vv  v          v  ? vv   ---   ---- iv   v    vi
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAAT---CTT----CGTGACCTTGGGT 574

  chrX_139200629_   3586 TGGGCAAAGATTTCTTGAGCAATACCTCACAAGCATAGGCAATCAAAGCA 3635
                          i     v i      iiii vv  vi  v     i i    iv    v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_139200629_   3636 AACATGGACAAATGGGATCACATCAAG-TTAAAAAGCTTCTGCATAGCAA 3684
                           v  i  i    v   iiv      i-       -   i  iiivv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chrX_139200629_   3685 AGGATACAATCAGCAAAGTGAAGAGACAACCCACAAAATGGGAGAAAATA 3734
                             i  v    iv        i            i              
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_139200629_   3735 TTTGCAAACTACCCATCTGACAAGGCATTAGTAACCAGAATATATAAGGA 3784
                                 ii ivi      i    v i v   v             i  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_139200629_   3785 GCTCAAACAAGTCTATAGGAAAAAGTCTAATAATGTTATCAAAAAATGGG 3834
                         i   vv    v  v   iv      v v     iviv  i?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_139200629_   3835 CAAAAGATTTGAATAGACATTTCTCAAAAGAAGATGTACAAATGGCAAAC 3884
                             i                    v         i          v  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_139200629_   3885 AGGCATACGAAAAGGTGCTCAACATCACGATTATC 3919
                          i   i i      i            ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (126 / 76)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 4.56 (41 / 9)  


2967 27.00 1.21 1.54  chrX_139205779_139210110     2929  3839 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_139205779_   2929 TGGAAAAACATTCCATGCTCATGTATAGAATGAATTAATATCATTAAAAT 2978
                               i i  i     i     v  v i v  v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139205779_   2979 GGCCATACTGCCCAAAGCAAATTACAGATTCAATGCTATTCCTATAAAAC 3028
                            v     v      vii vi           i  v  i     v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_139205779_   3029 TACCAATGACATTCTTCACAGAACTAGAAAAAAAACT-ATTGTAAAATTC 3077
                          v   iivi v  i  ii     v v  v  i---  -  iv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_139205779_   3078 ATATGGAACCAAAAAAGAGCCCTAATAGCCAAGGCAGTCCTAAGCAAAAA 3127
                                 viiv  ii  v  vv         ii  i  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_139205779_   3128 TAACAAAGCTGGAGGCATCAAGTTATCCAACCTCAAACTATACCGCAGAG 3177
                         v       i      vv   vii vi    ii     viv   ii  i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_139205779_   3178 CTACAGTAACCAAAACAGCATAGTACTGGTATAAAAACATGCACTTAGAC 3227
                                  i   i    ii i       i    ii i vi  iv    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_139205779_   3228 CAAGGGAACAGAATAGAGAGCCCAGAAATAAGGTGACACATATATGACCA 3277
                            v    i     v     i          iviv i    v    ii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_139205779_   3278 TCTGATTTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAA--ATACTC 3325
                         vi       i     i v  v   i v  vv           --   v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_139205779_   3326 CCCATTCAATAAATGGTGCTGGGATAACTGGCTAACCATATGCAGAAGAT 3375
                         ii--     i              i      v  ?   i     i    v
  L1M4_orf2#LINE/    398 TT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_139205779_   3376 TGAAACTGAGCCCTTTCCTTACACCATATACAAAAATCAACTCAAGATGG 3425
                             ii  ii   i v   i                 i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_139205779_   3426 ATTAAAGACTTAAACATAAAGGCCAAGTTTATAAAAACCTTGGAAGACAA 3475
                           i ?    i    ii   ii  i  ivi       vi   i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_139205779_   3476 CCTAGGCA-ATACCATCCTGGACAGAGGAATGGGCAAAGATTTTTTGACA 3524
                          v    ?i- v i v  v  -  vvv  iv i     v i   i  iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_139205779_   3525 AAGATACCGAAAGCAATTATGACAAAAGCAAAAACTGACAGATGGGATCT 3574
                          v  i   i      vvviii       v     iv  i i  v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_139205779_   3575 AATTAAGCTAAAGAGCTTCTACACAGCAA--GAAACTATCAACAGTGTAA 3622
                         v  i  iv v  i i   i iii vv   --  v        v iv  i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_139205779_   3623 ACAGACAACCTACAGAATGGGAGAAAATATTGGCAAACCATGCATGTGAC 3672
                          v        i                    v     i   ii  v   i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_139205779_   3673 AAAGGTCTAATATCCAGTATCCATGAGGGGCTTAGAATAATTTACAAGAG 3722
                           i  v  vi       v  vi  i i ii  i--------      vvv
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTC--------TTACAACTC 786

  chrX_139205779_   3723 AA-AATCAAAA---AAACAGCCTCATTAAAAATTGGGCAAAGGACATGAA 3768
                           -   v    ---   i i  iv   ?    v           iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_139205779_   3769 CAGACACTTTCATAAAGAAGACATACATAGGAAAAACAAGCACATGCAAA 3818
                         i     i  iivi        i     v v ivv  i         v   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_139205779_   3819 AA-GCTCAATATCACTGATCAT 3839
                         i -      i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.27 (25 / 11)  


3478 24.83 0.88 0.66  chrX_139361806_139364132      929  1834 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_139361806_    929 TAGAAAGACATTCCATGCTCATGGAGCAAAAGAATTAATACCTTTAAAAT 978
                          i      i  i     i       viii    v      iiv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139361806_    979 GACCATACTGCCCAAAGTAATGTACAGATTCAATGTAATCTCTATCAAAA 1028
                          i v     v      v i  v           i i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_139361806_   1029 TACCAATTACATTCTTCACTGAAATAGAAAAAAAAATCCTAAAATTTATA 1078
                          v   ii i v  i  ii v     v  v  ivvi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_139361806_   1079 TGGAACTGCAAAAGACCTCAAATAACCAAAGCAATCCTGGGCGAAAAGAG 1128
                              v     ii    ivi    i     i     i  iivi i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_139361806_   1129 CAAAGTTGGAGTCATCACACTACATGACTTTGAAATATACTACAAAGCTG 1178
                                    vvv       v vii i  ii   iv            i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_139361806_   1179 TAATAACCAAATCAGCGTGGTAGTGTCATAAAGTCAAATACATAAACTTA 1228
                         i i   i   iv   i      v  v     i vi i i i   i iiv 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_139361806_   1229 TGGAACAGAATAGTGAGCCTACATATAAATCTAAACGTTTACAGCCAACC 1278
                              i     v v   i i v v     i i v  i    ii i   ii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_139361806_   1279 CATTTTCGACAAAGGCACCAAGAACATACAATGGGGGAA-AGGAGTATCT 1327
                         v           i  ii      v   v        i  - iv   v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_139361806_   1328 TTAAAAGGATGGTGCTGGAA-AGCTATACAACCATATGCAGAAGAATAAA 1376
                          i  v i-          i - i  iv i ?   i     i      i  
  L1M4_orf2#LINE/    401 TCAACAA-ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_139361806_   1377 ACTG-ACCCC-ACCTCTCACCATATACAAAAATCAAATCAAAGTGGATTA 1424
                         ii  -     -     v                i  v     i     i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_139361806_   1425 AAGACTTAAATCTAAATTGC--AAACTATGAAACTACTAGAAGAAAACAT 1472
                         ?    i     v   iv-  --       i     vi             
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_139361806_   1473 TGGGG-AAATGCTCTAGGATATTGCTCTAGGCAA-ATTTTTTTTGTGTGT 1520
                         v  ? -    -  iiiv  iv   vvi       -iv   i  v ---i 
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG---AT 594

  chrX_139361806_   1521 AAGACCTCAAAAGTCCAGGCAACAAAAGCAAAAGTAGATAAATGGGATCA 1570
                          v   vi      iv  i          v    i         v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_139361806_   1571 CATCAAGCTAAAAAGTTTCTGCACAGCGAAGAAAACAGTCAACACAGTGA 1620
                               iv v    ii  i  ii vv i   i v  vi    v v     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_139361806_   1621 AGAAACAACCCACAGAAAGGGAGAAAATGTTTGCAAATTATCCATCTGGC 1670
                          i i             v          i         i  vi     ii
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_139361806_   1671 AAGAGATTAATAACTAAAATATGTAAAGAGCTCATACAACTCAATAACCA 1720
                            i  i vi  v i i     i      i   v             iv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_139361806_   1721 AAAAACAAATAATCTGATTTAAAAATTGGCAAAAGATATGAATATATATT 1770
                            i        i ii   ?      v      i   v      v i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_139361806_   1771 ATTGAAAAGAAGACATACAAATGGCCAACAGGTATATGAAAAAATGCTCA 1820
                         vi vv        i              i i i i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_139361806_   1821 ACATTACTAATCAT 1834
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (143 / 78)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


1212 25.18 30.65 0.14  chrX_139372872_139377782.rev     1334  2028 (2883)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_139372872_   1334 GGAGATATATACCAAATTCAAAAATTGGATGATCCATTATTATTATGATG 1383
                            i v    v   vi    vii      v  iii v    i   v    
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_139372872_   1384 CCTATTTTCCCAGAATT------TAG--TTAATGAAATCACAAACAAAAT 1425
                         v v  vi    vi    ------i  -- i  i v    v v v      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_139372872_   1426 CCCAGCAGACATTTTGAAAGAAACTGACAAGCTAATTCCAAAAAGTATAT 1475
                               v v v    viv     i         i  i i    vvi    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_139372872_   1476 GAAATTGCAAAGAAGAAAGTATCAACAAAACAATCTTGAAATAAAAGACC 1525
                          i  v     i i vvv  v  viv                v i    v 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_139372872_   1526 AAAGTTAGAGGACATACATAACCAGATTTCAATATTTACTTTAAAACTGT 1575
                               i      vi   ivv  vi       v i     vi   i  ii
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_139372872_   1576 AATAATCAAGACAGTGT---ACT---------------------ATTAAT 1601
                          i               ---   ---------------------  i   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_139372872_   1602 G-----------------CAGGA-----CCTA------------------ 1611
                          -----------------   i -----  i ------------------
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_139372872_   1612 --------CAAG----------------------------------TTTT 1619
                         --------    ----------------------------------    
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_139372872_   1620 TAA--AATAG---------AAC------------------AGAAT----- 1635
                         i  --   i ---------   ------------------     -----
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_139372872_   1636 ---------ACCTGAAACCATA---------------------------- 1648
                         ---------    v v      ----------------------------
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_139372872_   1649 --------------------------AAAACCCT-AGAAGAAAACCTAGG 1671
                         --------------------------     i  -          v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_139372872_   1672 CA-ATACCATTCGGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACA 1720
                         ?i- v i -    v   v v  vv i     v ii   v ivv  vi   
  L1M4_orf2#LINE/    552 NGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_139372872_   1721 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAA 1770
                                  vvi          vv     v  i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_139372872_   1771 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 1820
                          v v  i i   i  ii vv    i  v    i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_139372872_   1821 AACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCAGACAAAGGG 1870
                             i                 v       vii ivi   v  i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_139372872_   1871 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 1920
                           vi          v  i  v      vv    v iv i  v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_139372872_   1921 AAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAA 1970
                            i     v  i?    i     i      v    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_139372872_   1971 AAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCATCA 2020
                                i  vi viii     v ii          i       v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_139372872_   2021 CTGGCCAT 2028
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.04 (88 / 85)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 13.38 (214 / 16)  

 942 24.17 12.72 1.78  chrX_139372872_139377782.rev     4028  4420 (491)    L1M4_orf2#LINE/L1      473   908 (0)  

  chrX_139372872_   4028 ATAAAAAATACTAATTTGAGATCAATCAAAGACCTAAAAGT--------- 4068
                            v    - i   i ii i  vi    ?         v  ---------
  L1M4_orf2#LINE/    473 ATACAAAA-ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_139372872_   4069 --CTATTATGCT-TTAGAA-AAAGT---GGGGCATATTTTTACAACTTTG 4111
                         --    v vi  -      -   ii---  ? i v  i  iiii  i   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chrX_139372872_   4112 ATGTAGATAAAGATTCCT--AATAAGAATACAAAAGGCACTAAAGCAACA 4159
                         ivv   ii  v i  i  --i   v  -i  v   i    --        
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGA-CACCAAAAGCAC--AAGCAACA 618

  chrX_139372872_   4160 AAGGAAAAAATGG-TAAATCAAACATCATTGAAAATATATAAACATCCAT 4208
                           i        i -     iii  v    i-     -  v    v iii 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATC-AAAAT-TAAAAACTTTTGT 666

  chrX_139372872_   4209 TCTTCAATGTACACAGTTAAGATAAT------ACCCTCC-CGAAATGTGA 4251
                         v      v v    vi i    v i ------  vvi  - ii    v  
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_139372872_   4252 GACAATATTCTTACTGCATACAACTGACAA-------------------- 4281
                           v      ivi vvv    i v    i  --------------------
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_139372872_   4282 ---AAGAACTCCAACAAATCAATAATAAAAAGGCAAACAACTCAATTTAA 4328
                         ---        iv    v              i    i   i     ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_139372872_   4329 AAATTAGCAAAAGATTTTGAACAGACACTCC-CCAAGGAAGACATACAAA 4377
                             vi     i     -   i     i i -    i     i       
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTT-GAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_139372872_   4378 TGGCCAATAAGTGCCTGAAAAAGTGTTCAACAGCATTAGTCAT 4420
                                    ii v      ii  i      v  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (59 / 33)
Gap_init rate = 0.04 (16 / 436), avg. gap size = 3.56 (57 / 16)  


1301 25.00 6.53 0.68  chrX_139413537_139415934.rev      124   567 (1831)    L1M4_orf2#LINE/L1      353   822 (86)  

  chrX_139413537_    124 TTTTCCACAAAGGCATCAAGGT-ATTCAATGTAGAAAGTAGAGTCTATTT 172
                              v    i  iii    ii-        vi     v v     v  i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_139413537_    173 AACAAATGGTGCCAGAA-AATTTGATATCCATATGGAAAACTATAAACCC 221
                                     ii i -  i v    ?   i   v    vv  i  vii
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_139413537_    222 CAACCTTTATCTCACATT-CACACAAAAATTAACTCAAAATGGATCACAG 270
                         vi   ii  i      ii-i i                         ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_139413537_    271 AAGTAAATTTAAAAGTTCAAACTGTAAA--TCTTAAAGAAATAACACATG 318
                          vv     v   i  i v     i    --     i ii  -    i v 
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA-AACATAGG 551

  chrX_139413537_    319 A--AAATAT--GTGGTCTTGCGGTAGGCAAAGATTTCTTAG----GGCAT 360
                         ?--    v --   ii    v v       v i        ---- i  i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_139413537_    361 ATAAAACACAAACTATAAACTTAAAAAAGT-GATAAAATTAACT--GTCA 407
                         vv   i     i v i   v--i     i -      v vi   --i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAA--GAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_139413537_    408 AAACTCACATCTTCTGCTCTT--AAAACTACTGTTATGAAAATGAAAAGT 455
                            i v v v   i  iv   --  iivi   i i v    i       v
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_139413537_    456 TAAGCCATATACTGGAAGAAAATATTTTCAGTACATATATCTGATCAAGA 505
                         i  v   i v v   i           v  ivv            v i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_139413537_    506 ACTT-TATCAATAATATATAAAAGACT--TATGACTCAAAGATAAAA-GA 551
                             -    v v          ii   --  ii      vi      -  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_139413537_    552 CAA----CCCA---TAAAGATGG 567
                            ----    ---?   i    
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGG 822

Transitions / transversions = 1.49 (64 / 43)
Gap_init rate = 0.04 (17 / 470), avg. gap size = 1.88 (32 / 17)  

1592 26.10 4.58 2.59  chrX_139413537_139415934.rev      582  1083 (1315)    L1M4_orf2#LINE/L1        1   512 (396)  

  chrX_139413537_    582 TGCAGAGATGAACCATGTTCATGATTTGGAAGACTCTGGATAATAAAGAT 631
                           v i    ivv           iv          iviv  vi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139413537_    632 ATCAATTCTCCTCAAATTAATATATAGGTTGAATGCAATTTCTATAAAAA 681
                         iv    v    i      i  v  i  i  v  i     ii    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_139413537_    682 TTCCAGCACAGGC---TTTTGTAAATGTTGACAAGTATATTCTAAAATTT 728
                          i     ---v  ---     i i vi        ivv  i        i
  L1M4_orf2#LINE/    101 TCCCAGC---TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_139413537_    729 ATATGAAAAGGCATAGTACTAAGAATAACTAAA----TCGTGAAAAGTAA 774
                              i   v   vi v  iv      i i   ----  v      -- i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA--AG 195

  chrX_139413537_    775 AAGAATTGTGAAGAAGGAATCAT--TACCTGATATAAAGACCTACCATGT 822
                              iviv vv i    v   i-- v  ii  v v  i  i   i iiv
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_139413537_    823 AACTACATTAATCAAGATAGTGTGGTATTGGCAGAGGGACAGAAACATTC 872
                          i     v         i         i     v i   i   v i  vv
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_139413537_    873 ATCAATGGAATAGCATAAAGAACTCAGAAACAGACCCACACAAATATGCC 922
                                      v  vi   iii      i i     i   vv    vi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_139413537_    923 CAAATTATTTTTGAGAAAGGTAT-----------AATAGG--AAGAATAG 959
                            v v     i  v  i   ii-----------   i  --        
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_139413537_    960 TCTTTTCCACAAATGGTGCTGGAGCAATTGGACATTTATAGGCAAAAAAT 1009
                                v              ii   i    i ?ii i v      i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_139413537_   1010 TTAAAAAAGATTATTGG-CCTAAATCTCACATCTTATACAGGAATTACCT 1058
                          ----i   ----    -  ivv i      i v      ii     v  
  L1M4_orf2#LINE/    446 T----GAAG----TTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_139413537_   1059 CAAAAGGAATCATGGACTTTGATAT 1083
                              v i    ?i   i vi  i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGT 512

Transitions / transversions = 1.43 (76 / 53)
Gap_init rate = 0.02 (10 / 512), avg. gap size = 3.60 (36 / 10)  

1407 21.27 1.58 5.20  chrX_139413537_139415934.rev     1466  1907 (491)    L1M4_orf2#LINE/L1      483   908 (0)  

  chrX_139413537_   1466 TAATGCAAAAGGACTAATACGGACTTAAATGTAAAATGTAAAATTACACA 1515
                            iv     v iv v ? --   i         i vv     i  i v 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWA--GACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_139413537_   1516 ACTTCTAGAAAAAAAAACATAGAAGAAAATCTTCAAGATCCAGGGCTAGG 1565
                            ii     i    --     i? v        iv  i iv   i    
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAA--CATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_139413537_   1566 TAAGACATTCTTATACTTGACAGCAAAAACATGATACAAAAAAGGCAAAG 1615
                         i  vivv      v iv     v     i  ii -i   v   i v   i
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAA-GCAACAAAAGAAAAA 627

  chrX_139413537_   1616 TTAAATAAATTGGACTTCA---AAATTAAAAACTTTTGTTCAGTGACTGC 1662
                         v  i               ---                 ------i  v 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT------GCTTC 671

  chrX_139413537_   1663 CCAGGTGAACAGAAT---GAAAAGACAAAGACAAGCTACAGAGTGGGAAA 1709
                         vv   ---   vv  ---    iviv        v i     i     i 
  L1M4_orf2#LINE/    672 AAAGG---ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_139413537_   1710 AAATATT-GCAAACCATATCTCCGACAAAGGACTCATATTTAGAACACAT 1758
                                -     i     v  i  i  i     ii   ii    i i  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_139413537_   1759 AAAGAACTCTCAAAACTCAGCAGTTAAGAAAACAAACAAATAAATAGTCC 1808
                                   i v      i----   v    - i        ----i  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAA----TAATAAAA-AGACAAATAA----CCC 809

  chrX_139413537_   1809 AATTTGAAAATTGACAAAAACCATGAAGAGACATTTCACTGAAGAAGATA 1858
                             ?i     v i    iiviv    v         v ii         
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_139413537_   1859 TACAAATGGCAAATAAGCATGTGAAAAGATGTTCAACATTATTAGGCAT 1907
                                   v        ii          i       i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (55 / 36)
Gap_init rate = 0.03 (11 / 426), avg. gap size = 2.73 (30 / 11)  


3217 26.98 0.55 0.55  chrX_139440108_139446520     5014  5921 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_139440108_   5014 TGGAAGAACATTCTATGCTCATGTACAGGAAGAATCAATATCATGAAAAT 5063
                              ii i  i i   i     v iv      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139440108_   5064 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5113
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_139440108_   5114 TACCAATGACTTTCTTCACAGAA-TTGGAATAAACT-ACTTTAAAGTTCA 5161
                          v   iivi i  i  ii     -   -- i  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_139440108_   5162 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5211
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_139440108_   5212 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5261
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_139440108_   5262 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATCGACC 5311
                                 i   i    ii         i iv ii i   v    v  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_139440108_   5312 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5359
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_139440108_   5360 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAACGGGGAAAGGATTCC 5409
                          vi    i  i     ivv  v   i v  vvv  i        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_139440108_   5410 CTATTTAATAAATGGCGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5459
                           v  i  i      i       v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_139440108_   5460 GAAACTGGATCCCTCCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5509
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_139440108_   5510 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAATC 5559
                          i ?    i       v   v       i      vi i         v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_139440108_   5560 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGAATA 5608
                         v    ?i- v i -   iv   v v  vv i     v ii   v ii   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_139440108_   5609 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACTAATGGGACCTA 5658
                         vi            vvi          vv     v  iv   v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_139440108_   5659 ATTAAACTAAAGAACTTCTGCATAGCAAAAGAAACTACCATCAGAGTGAA 5708
                           i   v v  i     i  iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_139440108_   5709 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5758
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_139440108_   5759 AAGGGCTAATATCCAGAATCCACAAAGAACTTAAATAAATGTACAAGAAA 5808
                          i  i  vi          vi i        ivv i  v vv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_139440108_   5809 AAATCAAACAACCTCATCAAAAAGTGGGCCAAGGATATGAACAGACACTT 5858
                           iv    i    iv  i?    i     v      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_139440108_   5859 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5908
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_139440108_   5909 CATCCCTGGCCAT 5921
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 482 23.65 6.71 15.93  chrX_139596889_139599543.rev     1171  2168 (487)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_139596889_   1171 GAGACAGATCCCTCGTTACTAGAT-GCAAAACCCACTATCATAAAGATGG 1219
                           i v v     vi   vv i   - v  i  ii v   ii v       
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_139596889_   1220 CAGTTCTTGACATGTTACTC-AAAGGTCTGAAGCATTTCC----AAGGGA 1264
                           i v  ivv  vi  iv  - v  i iii v   v i  ----  iivv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_139596889_   1265 TTAA-----TTTTTTATGGGCATTCATGAGTTAATTTTAAAATTAATCTG 1309
                         ii i-----      iii iv   v ii  i i  ii       v  v  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_139596889_   1310 GAAA---AATGGGATGCACAAGAATAGCGAAAA--ATTCTGAAAAA-AAT 1353
                             ---  -    iv  ---       v    --  ii       -  v
  L1M4_orf2#LINE/    153 GAAATGCAA-GGGACCCA---GAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_139596889_   1354 AATAATGTAGGGGAA---GCAGTCCCATCATATGTCAAAAC-----ATAA 1395
                           i  v  v  i i ---i  v i  --  -  v       ----- i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCC--CA-ATTTCAAAACTTACTACAA 245

  chrX_139596889_   1396 TGCTACAGTAATTAAAGCAGTGAGGTACTAGC-TCAGTACTAGAGAAATA 1444
                         v           i  ii     v      i  - v  v -    v v   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATA 294

  chrX_139596889_   1445 TTATCAGTTGAACAGAA--AAGAAACAAAAAAATATACCCATATAGTTCA 1492
                         v-    i v   i    --i   iv v i   -  v       i -  i 
  L1M4_orf2#LINE/    295 G-ATCAATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACA-TTTA 341

  chrX_139596889_   1493 TGATAAAAAGAGAATTCCAAATCAGTATG--GAAATAATTCAATTGAATA 1540
                           i v  vv  ---  iivi iv  vi  --i i iv       v ----
  L1M4_orf2#LINE/    342 TGGTCAATTGA---TTTTCGACAAGGGTGCCAAGACCATTCAATGG---- 384

  chrX_139596889_   1541 AGTAAGTTGAAAAAAACTGACTCTCTCTTCTGAAAAAAAATAAGCTTAGA 1590
                         -------- i   i  iv ----   i   ----  v    i--------
  L1M4_orf2#LINE/    385 --------GGAAAGAATAG----TCTTTTC----AACAAATG-------- 410

  chrX_139596889_   1591 TTCCTACTTTGTACCATAGAAACACTTATAAAAGAAAAGCCAATTCTACA 1640
                         ----------  i -- i i vv   ------- i v ?   ------  
  L1M4_orf2#LINE/    411 ----------GTGC--TGGGACAACT-------GGATAKCCA------CA 435

  chrX_139596889_   1641 TAGAGTACTAAGCAATAAGAACGTACAAAATATTGGAAGAACCAGGCACA 1690
                          ----------    -     i ----  i --    ----  --- vi 
  L1M4_orf2#LINE/    436 T----------GCAA-AAGAATG----AAGT--TGGA----CC---CCTA 461

  chrX_139596889_   1691 CTGGCCCACACC-TGTAGTCCCAGCTACTCGGGAGGCTGAGGCAAGAAGA 1739
                          --- i      - i  -------------------------   i  --
  L1M4_orf2#LINE/    462 C---CTCACACCATATA-------------------------CAAAAA-- 481

  chrX_139596889_   1740 TCTCTTTGGCCCAAGA--GTTCA-AGACC--AGTGTGGACAACACAGAAA 1784
                         -----  ii i   i -- v   -     -- i   ------------  
  L1M4_orf2#LINE/    482 -----TTAACTCAAAATGGATCAWAGACCTAAATGT------------AA 514

  chrX_139596889_   1785 GACGATATCTCAAAAAATATATTTTTTGATTAGAAGAATATATAGGAGAA 1834
                           - ----  --    v    vvvi i--         v i     ? v 
  L1M4_orf2#LINE/    515 GA-G----CT--AAAACTATAAAACTC--TTAGAAGAAAACATAGGNGTA 555

  chrX_139596889_   1835 TACTTTTTTAATCTTGGG--AGTGCAGAAGCCTATCTAAATATGAAACAA 1882
                         v ii  iv i i      --  -   ivi ii v -  i      v  v 
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAG-GCAATGGTTTCT-TAGATATGACACCA 603

  chrX_139596889_   1883 AAACAAGAAACTATAAAAGATTAAAATG------TTTGTCTATTTA-CAT 1925
                            vv v  i v i      v-     i------  v v  -- i -  v
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAA-AAAATAGATAAATTGGACT--TCATCAA 650

  chrX_139596889_   1926 AATTAAAT-CTTCTTTATAGTAAATAGCACCATGAATAAATTTAAAAGAC 1974
                                v-   i v iivvi   vii   i  v  v   v v       
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_139596889_   1975 AA--------ATGATA---AACATTTGCAA--TATACACCAGACAAAAGG 2011
                           --------   iv ---  i        --i   i i v  i  ii i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_139596889_   2012 ---ATATC-AGCTCCAATATCCAGAGA--TCT-ACAAATTAATAATAAAA 2054
                         ---i    -  ----     vi i   --   -    v i          
  L1M4_orf2#LINE/    751 CTTGTATCCAG----AATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_139596889_   2055 AAAGACAAATGACACAACAAAAGAATAGGTAAAGGATACAAACAAGCAAT 2104
                          --       i  v   iv?  i   i  i       vii  i ii  - 
  L1M4_orf2#LINE/    797 A--GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA-T 843

  chrX_139596889_   2105 TTCTT-AAAGAAGAAATAAAAATAGCTAGTAAATGTATGAAAAGTTGCTT 2153
                             i-        v   v    i  i i   iiii        v    i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_139596889_   2154 AACTTTACAAATTAT 2168
                            v i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.07 (65 / 906), avg. gap size = 3.48 (226 / 65)  


2383 27.34 3.04 1.09  chrX_139616597_139621203.rev     2832  3654 (953)    L1M4_orf2#LINE/L1        1   839 (69)  

  chrX_139616597_   2832 TGGAACCCTATCCCATGCTTATAGATGGGTAGAATCAATACTGTGAAAAT 2881
                              vvv         i i  i   v  v   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139616597_   2882 GGCCATACTGCCAAAAGCAATCTACAGATTCAATGCAATTCCCATAAAAA 2931
                            v     v  v   vii              i     i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_139616597_   2932 TAGTATCATCATTCTTCACAGAACTAGAAAAAC-AATCCTAAAATTCATA 2980
                          vvi v vv v  i  ii     v v  v  i -i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_139616597_   2981 TGGAACCAAAAAAAAAGCCCACA-TAGCCGAAGCAATACT----AAGAAA 3025
                              viiv  iii --    v -     i  i    vi ----     i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA--CCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_139616597_   3026 AAAAAATCTGGAGGCATAACATTATGTGACTTCAAATTATACTACACGGT 3075
                           v   vi      vv v   i vivii i      viv       vi i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_139616597_   3076 TATAGTAACCAAAAAAGCATTGTACTGCTATAAAAATAGGCATGTAGACC 3125
                           i     i   i v  ii v      vi    ii    i   i    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_139616597_   3126 AATGGAACAGAGTAGAGAACTCAGAAATGAAGCCAAACACTTACATCCAA 3175
                                i   i v    iii       i  v   v   i   iivi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_139616597_   3176 CTGATCTTCAACAAAGCATACAAAAAC-ATGAATTAGGGAATGGAAACCC 3224
                         i    i   i    i -i i v  i  -  vv v i     v i v vi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_139616597_   3225 TATTCAATAAATGGTGCTGGGAAAACAGGAAACTTATATGTAGAAGACAG 3274
                          v     i              v   v   v ?ii i   i i    vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_139616597_   3275 AAACTCGATTCCCATCTCTCACCTTGTACAAAACTCAACTCAACATGGAT 3324
                           ii v  ii  i i   v    v i       v i       v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_139616597_   3325 CAAAGACTTAAATTTAAGGCCTGAAACTATAAAAATTCTA-------ACA 3367
                           ?    i     v    iv  i           v ii  -------   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_139616597_   3368 TTGGAGAAACTTGTCTGGGTATTGGCTTAGGCAAAAAAATTTAT--GACT 3415
                          v  ? v  v iv  vv iiv    v        vii--   v --  - 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG--TTTCTTAGA-T 594

  chrX_139616597_   3416 AAGACCCCAAAAGCAAATGCAA-AAGAACAAAAATAAATAAATGGGACAT 3464
                          v   v         v v    -  i iv       i      v    v 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_139616597_   3465 AATTAAACTAAAAAGCTTCAGCACAGCAAAAGAAATAATCA-----GCAA 3509
                         v  i   v v    i   iv ii vv    i  v iv    ----- ii 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_139616597_   3510 ACAGACAAACCACAGAATGGAAGAAAATATTCACAAACTATGCATCTGAC 3559
                          v      v           i          ii    ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_139616597_   3560 AAAGGACTAGTATCCAGAATCTACAAGGAACTCAAATAAATCAGCCAGAC 3609
                           i     v           v  i  i      vv i  v   iiv v -
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA- 793

  chrX_139616597_   3610 TATAAGA--AATAATCCCATCAAAAAGTGGGCAGAGAACATTGA-TAG 3654
                         - v    --     i  v  i?    i      i  i i-    -   
  L1M4_orf2#LINE/    794 -AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAG 839

Transitions / transversions = 1.23 (122 / 99)
Gap_init rate = 0.02 (16 / 839), avg. gap size = 2.12 (34 / 16)  

 379 19.42 0.00 2.91  chrX_139616597_139621203.rev     4014  4116 (491)    L1M4_orf2#LINE/L1      809   908 (0)  

  chrX_139616597_   4014 CAATGAGAGAATGGACTAATACAAACATGAATAGACATTTCTCAAAAGAA 4063
                             v?i i     i v  ---ii iv                v      
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAA---GGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_139616597_   4064 GATATACAAACAGCCAACAAACATATGAAAAAATGCACATCATTAATCAT 4113
                                   ii     i  i  i       i    v  v   i ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_139616597_   4114 CAA 4116
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.01 (1 / 100), avg. gap size = 3.00 (3 / 1)  


3451 22.41 2.36 0.68  chrX_139681228_139683155      549  1436 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_139681228_    549 AGATATG-CATATGCATGGATAGGAAGACTCAATATTGTCAAGATGTTAG 597
                               v-   i v       v        i        i      vi i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_139681228_    598 TTATTCCTAACTTGATATATAGATTCAATACCATCCCAATCAAAATCCTG 647
                          vv i  i  v     v  i        ii v     v          ii
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_139681228_    648 GGAAGTTATTTTGTGGATATTGACAAACTTATTCTAAAATGTATATGGAA 697
                          vvivi v     ii  v        i  v  i       vi        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_139681228_    698 AGGCAAAAGAC-AAGAATAGATAACACAGTATTGAA------GAACAAAG 740
                          v    ii   -v       vi  v   i v     ------        
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_139681228_    741 TTGGAGAACTGATACTACAAAACTTTA---CTTACTACAAAGCCACAGTA 787
                               i   v i   v vv  i  i ---             i      
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_139681228_    788 ATTAAGA--GTGTGCAATTGATGTTAGAACAGAAA-ATTGATAAATGAAA 834
                           i    --     vv i  iii v  i i   v -  v   v    i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_139681228_    835 CAGAATAGAGAGCCCAGAAATAGACCCACATAAATACACTCAACTGATAT 884
                         i     v     i         i     i i vv  iiv    i    v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_139681228_    885 TTGACAAAGAAGCAAAGGC-ATACAATGGAGAAAAGACAGTCTTTTCAAC 933
                          i     i iv  v   i -  v      i    ii i            
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_139681228_    934 AAATGTTGTAGGAATAACTGGACATCCACATGCAAAAAAATGAACCTAGG 983
                              v  iv  i i       i ?            i      vi i i
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_139681228_    984 TCCAAAACTTACACCCTTCACAAAAATTAACTAGAAATGGATCACAGACC 1033
                         i  vv v  i     v vi             vi          ?     
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_139681228_   1034 TGAAAGTAAAATGC-AAAACTATTAGACTCTTAGAAAATAACATAGGAGA 1082
                          i  v    i -  -        v i          i v        ? v
  L1M4_orf2#LINE/    506 TAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_139681228_   1083 AAATGTAGCTAAACTTGGGTTTGGAGATGACTTTTTTGATATGACACCTA 1132
                             v vvv i v        v  vi   ii  i  v           v 
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_139681228_   1133 CGGCATGATCCATGACAGAAAGAATTGATAAGCTGTACTTCATTAAAATT 1182
                         vi   ii v v ii v     i   v     ii  v       i      
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_139681228_   1183 AAA---TTTTCTGCTTTGTGAGAGACACTGTCAAGAAA-TGAAAATAAAA 1228
                            ---    v     --ii ii      i        -      v v  
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_139681228_   1229 GCCACAGAATAGGAGAAAATATCTGCAAAACA-ATGATCTGCTAAGTGAC 1277
                         v         i           i      v  -  -     v    v   
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATAAGGGAC 751

  chrX_139681228_   1278 TGTTATCCAAAATATACCAAGGCCTCTTAAAACTCAAAAATAAGAAAACA 1327
                          vv      i      iv   iv      v       v     i  i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_139681228_   1328 AACAACCCAATTTAAAAAATTGGCCAATTGAATTTAGCAGATACCTCACC 1377
                           i         ?     --   v   vv  v  v ii   i ii  v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_139681228_   1378 AAGGAAGATCTACAGATGGCAAATAAGCATATGAAAAGATGCTTCACATC 1427
                           i      v    i     v        i             iv     
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_139681228_   1428 TGATATTAT 1436
                         v????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.14 (104 / 91)
Gap_init rate = 0.02 (15 / 903), avg. gap size = 1.80 (27 / 15)  


2257 29.38 1.96 0.73  chrX_139690960_139694671     1897  2713 (999)    L1M4_orf2#LINE/L1        4   830 (78)  

  chrX_139690960_   1897 AGAGACATATTATAATCATGGGTTGGAAGACAACATATTA--AAGGCGCC 1944
                          i   i  vii  iv      i         vvv     i--   ii v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_139690960_   1945 AATTTTCCCCAAATTGATATCTATTTTTAATATAATTACCATAAAAATCT 1994
                            vi             v vi vv  i  iii   iv i  v      i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_139690960_   1995 CACCAGGATTTTTTGTAAATACAGACAAGATGGTTATAAAATTTCAAGTG 2044
                           v v vv       i i v iv      v  i iv       -  vi  
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT-CATATG 152

  chrX_139690960_   2045 GCAAAGCAAAGGACT-AGAATAACCAAAATAATTTTGAAAAA-AAGGATG 2092
                          v  v    i    i-      i      i   i        -   i ii
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_139690960_   2093 AACTGGTAAAAATCAGTCAAC-CTCATTTTCAAGAATTATTTTATAGCTA 2141
                           v v v ii v   --  vi- i  v      i v   i vi v     
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCA--CACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_139690960_   2142 CAGTAATGAACACTGTATGAGACTGTTGGAGGGATAGTAACACAGGTCAA 2191
                                v  v  v  i  iv    viiv i      vv i i  i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_139690960_   2192 TGGAATAGAAATACCTACTCAGAAATAGACCCACACAAATATGTCCAGGT 2241
                                   v ivvviii        i     i   vv    vi  iv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_139690960_   2242 GATTTTTGACAAATGTACAAAAGCAATTTAATAGGGAATGAAGAGCTTTT 2291
                               i     iv  i v  ii v   i   i     v   v  ii   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_139690960_   2292 TCAATAAATAGTACCTGAGTATTTGGACATTCACTGGCAAAAAAGGGAAC 2341
                             i    i  i iv iii vi    i ?i   vv      i iv   -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA- 449

  chrX_139690960_   2342 ACTGG-CCTAAACATTAAAACTTATACAGAAATTAGCT-AAAATGGATCA 2389
                         ii   -  ivv  v i v v v      i      i  -           
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_139690960_   2390 TGAACTTAACTGTAAAATGAAAAATTATAAAACTTTTAGAAAAAATAAGT 2439
                         ?ii  i   v     i vvv    i         i      i   - vi 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA-ACAT 548

  chrX_139690960_   2440 AGGAATAAATCTGTAGGATCTAGGGCTTGGCA--GAGTTCTCACCCTTCA 2487
                            ?i       viiv  i  v   i v    -- iv    i vviv v 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_139690960_   2488 CACCAAA-GTATGATCCATAAGAGAAATGATTTATAAGTTGTGCCTCATG 2536
                                - i ii v v i  i     vi  vv    i   vi i    v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_139690960_   2537 AAAATGAAAA---TTTACTCTGCAAATAACTCTTTTAAGAAGATGACAAG 2583
                              v    ---   iiv  v    vi  v  v i     ii   v   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_139690960_   2584 ACAAGCAACAGACTGGGAGAAAATATTTGCAAAATACATATCTGATAAAG 2633
                             v v     v                    vi i           i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_139690960_   2634 AACTCATATCTAGAATATATAAATAACTG--AAAATTTAATAGCAATAAA 2681
                         i   ii    i            v    v-- v  i i    ii  v  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_139690960_   2682 ACTC-TACATTTAATTAGAAAATGAGTGAATGA 2713
                           vv-  - iii    ?i      i ii  v  
  L1M4_orf2#LINE/    799 ACAAATA-ACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.27 (132 / 104)
Gap_init rate = 0.02 (16 / 827), avg. gap size = 1.38 (22 / 16)  

 265 20.00 3.16 5.26  chrX_139690960_139694671     3125  3219 (493)    L1M4_orf2#LINE/L1      816   908 (0)  

  chrX_139690960_   3125 AAAATAGACTAAGACAGACATAAAGATACATTTTATT---GAGTATATAC 3171
                              i i v   ---  iv i  v v      ivii---  iv      
  L1M4_orf2#LINE/    816 AAAATGGGCAAAG---GATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_139690960_   3172 AGATGGGTAATAAGCACATGAAAAGATGTGCTGAGCATCAGGGAAATT 3219
                          i    vi                    --  v i     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATG--CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (11 / 8)
Gap_init rate = 0.03 (3 / 93), avg. gap size = 2.67 (8 / 3)  


2758 28.57 0.55 1.53  chrX_139863517_139869704     4779  5695 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_139863517_   4779 TGGAAAAACATTACAGGCTCATGGATAGGAAGAATCAACATCGAGAAAAC 4828
                               i i  iv  v i        v      v i  i  i vv  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139863517_   4829 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 4878
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_139863517_   4879 TACCAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4926
                          v   iivi    i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_139863517_   4927 CATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGTCAAAAG 4976
                         i      viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_139863517_   4977 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATATTACAAGAT 5026
                                i      vv    i  v  ii i      viv  i     iii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_139863517_   5027 GACAGTAACCAAAATAGCATGGTACAGGTACCAAAACAGAGATACAGACC 5076
                         v       i   i i  ii      v  i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_139863517_   5077 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5124
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_139863517_   5125 ATCTGATCTTTGACAAACCTGACACAAAACAAGAAATGGGGAAAGGATTC 5174
                          vi    i  i     ivv  v  - i v  vvv           i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAG 395

  chrX_139863517_   5175 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGC 5224
                         i  v  i  i              v      v  ?   i   v i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_139863517_   5225 TGAAACTGCATCCCTTTCTTACACCTAATATGAAAATGAATTCAAGATGG 5274
                             ii  v i    vi  i     vv   ii     v  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_139863517_   5275 ATTAAAGACTTAAATGTTAGACCCAAAAAACCATAAAAACCCTAGAAGAA 5324
                           i ?    i       v   v i    -- i      vi i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAA--CTATAAAACTCTTAGAAGAA 543

  chrX_139863517_   5325 AACCTAGGCA-ATACCATTCAGGACATAGGTATGGGCAAGGACTTCATGA 5373
                            v    ?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_139863517_   5374 CTAAAATACCAAAAGCAATGGCAACAAAAGCCAAACTTGACAAATGGGAT 5423
                         v  vi i          vvi          vv   v v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_139863517_   5424 CTAATTAAACTAAAGAGCTTCTCGTCTGCACAACAGAAGAAACTACCATC 5473
                         i v  i   v v  i i   i ----- ii vv  i i  v    i  vv
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTT-----GTGCTTCAAAGGACACTATCAAG 687

  chrX_139863517_   5474 AGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCC 5523
                          i      v  i     i                 v   i   vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_139863517_   5524 GTCTGACAAAGGCCTAATGTCCAGTATCTACAAAGAACTTAAACAAATTT 5573
                         i     i  i  v  vi i     v  v  i        ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_139863517_   5574 ACAAGAAAAAAATCAAACAACCCCATCAAAAAGGGGGCAATGGAGATGAA 5623
                          i  v     i -    i     v  i?    iv      v   vv    
  L1M4_orf2#LINE/    788 ATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_139863517_   5624 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACACGAAAA 5673
                         i     i     v        i  vi viii     v ii    i     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_139863517_   5674 AATGCTCATCATCACTGGCCGT 5695
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (152 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


1225 29.65 6.63 2.79  chrX_139982428_139986620      596  1455 (2738)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_139982428_    596 TGTTCTTGGAT----AGCCTATGTTAACTTCATAATAATGTCAATACTCC 641
                              v     ----  v  ----   iv ii v vi   v         
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACT----TAATATTGTTAAGATGGCAATACTCC 61

  chrX_139982428_    642 CCAAATTAATATACAAATTTAGGGCTATTTCAAC--AAATATAAGTTATT 689
                                i  v    i   i iv  v  ii v i--    viv  i iii
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chrX_139982428_    690 TTTTCTA---ATGTTAAACATGTGAATTATAACATTCATATAGAAA-ACA 735
                             i i--- vi  i -  v ivi  iv   v        i    -i  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chrX_139982428_    736 AA--AC-----AT-GTAAGAAC--TCT-GAGAAAGAATAACAATAAAAGG 774
                          i--  -----  - iv i   --   -  i      v     - ivv  
  L1M4_orf2#LINE/    161 AGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA-AGTTGG 209

  chrX_139982428_    775 AAGACTAATGCTACCAGATATTAAAACATACTCTAAAGCTTCTATA---- 820
                          i    v ii  v  vi  v i     v    vi      v vi  ----
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_139982428_    821 -GATTGTGAGGTCATGACATAAATA-AGGTCTACAGAACATTTAACT-GA 867
                         -  iv   v   vv  i     iv -  iiv  i   v  v vi v -  
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_139982428_    868 ATAGAAAGTACACAAATAAATACAAGGACTTATGGT-AATTTAGTAT--A 914
                           v  i   v  v       iv  viv i       -    v v v -- 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_139982428_    915 TA----TGATAA--TCATATCACATGGAAGACGTGATGAGTGTTT--AAC 956
                         i ----  vi  --i   -   -    iii v -i  -   v   --   
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCAT-TCA-ATGGGGAAAG-AAT-AGTCTTTTCAAC 405

  chrX_139982428_    957 AAATGGC-TTGGGACACCTCAATAGCCCTTTGGAAAAAAATTAA-TTGAA 1004
                               i-i       v  vi   ?  viv  v    i   v  -   i 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_139982428_   1005 TACTTACTTCACACCATACCCCAGAATAAACTTCAAATAGAAGAGAGATA 1054
                         iv i   i          iv v i   v    iv    i  vv ?   iv
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_139982428_   1055 TAAATGTTAAAAAACTGAGACCACAGAAGTACTGAAAGAAAACATTGGGG 1104
                                --  i i  i i  i i i  v vi ii          v  ? 
  L1M4_orf2#LINE/    506 TAAATGT--AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_139982428_   1105 GCATTCCTTTATAACCTAGATGTGGAGAA-AGTCTTCTAACTATAAC-TC 1152
                         vv v  -  ii i    v ivv i iv  -i  i ii  iv   i  -i 
  L1M4_orf2#LINE/    554 TAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_139982428_   1153 AAAATCTAGAAGCAATAAAAGAGAGCACTGATAAATCTATCTGCATGAAA 1202
                             v - v      i      i iv iv       iviv  v   ----
  L1M4_orf2#LINE/    603 AAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT---- 647

  chrX_139982428_   1203 ACAAAA--AAAAACTTTTGCATTGCAAAATATACATGTCATAAAGAGGAT 1250
                         -     --           iii v    iv i  - i   ---   iii 
  L1M4_orf2#LINE/    648 -CAAAATTAAAAACTTTTGTGCTTCAAAGGACAC-TATCA---AGAAAGT 692

  chrX_139982428_   1251 GAAAC-ACAAATGGCAAACTGGGAGAAAATCTATGTAAGTCGTATCATAG 1299
                             v-    vivi  i v           v v  i  i  i   vviv 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_139982428_   1300 ACAAAAGACTAATTTTCCTGGTAAACAAA-AGCTTTTA-AAT--AATAAT 1345
                          i  ii    vi v i vvii  v i   - i  i   -  i--      
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_139982428_   1346 AAAAAATACAAAAAACAAGAT----AAATGATCAAAAGACATTAACAGAT 1391
                              i-     v   vvi  ----     iv    i  iv v  i   i
  L1M4_orf2#LINE/    793 AAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_139982428_   1392 AATTCATGGAAAAAGAAACACAAATGGCCC-TGAACATATGAAAA-ATAC 1439
                          v   vivi  i    v i          v- i i  i       -  i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_139982428_   1440 TTCAC-TCATAATAAGA 1455
                          iv  -   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (141 / 111)
Gap_init rate = 0.05 (44 / 893), avg. gap size = 1.84 (81 / 44)  

4285 16.32 3.50 4.05  chrX_139982428_139986620     2788  3700 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_139982428_   2788 TGGAAAGACATCC-ATGTTCATCAACTATAAGATTTAATATTGTTAAGAT 2836
                                 i    -        vi i iv    i                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_139982428_   2837 TGCAACACTCCCCAAATTGATCTACAGGTTCTATGCAATCCCAATTAAA- 2885
                         v    i                     i   v i        v  i   -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_139982428_   2886 TTCCAGATGTAGCTTTTGAAGAAACTGAGAATCTGATCATAAGACTCACA 2935
                          i    v  ivvi     v     i   v  v      v   i i   i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_139982428_   2936 TGAAAATGCAAGGGACCCCAAACAACCAAAACAATCTTGAAAAA--AGAA 2983
                           i               vi  i i                   --    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_139982428_   2984 TAAAGTTGGAAGACTCACAATCCCCAATTTCAAAAGCTACTACAAAGCTA 3033
                         i         i        v i             vi             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_139982428_   3034 CTATGAACAAGATAGTTTGATACTGTCATAAAGATAGACATATAGATTAA 3083
                          vi i v     i   v  i     v     i               i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_139982428_   3084 AAGAATAAAATTGAGATTCCAAAAATAAACCTATACATTTGTG---AATT 3130
                         vi     i        v    i         i        i  ---    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_139982428_   3131 GCATTTCAATAAGGGCCCCAAGAGACTTCGAGGAGAAAATAATAGTCTTC 3180
                          vv    i i     iv      vvv   i v i i   v         i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_139982428_   3181 TCAACAAATGGTGTCAGGACAACTAGATCTCCATATACAAAATAATGAAG 3230
                                      iii        i   v?   i  i     v       
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_139982428_   3231 TTGAACTACTACCTCATACTGTATATGAAAATTAGTTCAAAATGGACCAA 3280
                            i  iv        i  ii    ii       ii          i  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_139982428_   3281 AGACCTACATGTAAGAGCTAAAACTGTAAAACTCTATGAACCATGAAAAC 3330
                                v                 i         ---------------
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCT--------------- 535

  chrX_139982428_   3331 ATAAATGTAAAACATGAAATCTGTGAAAACATAGGTGTTAATTGTTGTGA 3380
                         -------  i  ------------           ?  v   iv i    
  L1M4_orf2#LINE/    536 -------TAGAA------------GAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_139982428_   3381 CCCCGGATTAGGCAATGATTTCTTAAACATGACATGAAAAGCACAATCAA 3430
                           ii  i          i       i i      iv          v   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_139982428_   3431 TGAAA---AAAACAGATAAATTGGACTACATCAAAATTAAACATTTTTGT 3477
                         ii   ---    i              v             v i      
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_139982428_   3478 GCATCAAAGGATACTATGAAGAATGTGTAAAGCCAATCGAT-TAATGGGA 3526
                           v        i     v     v   v    v   i v i-v       
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_139982428_   3527 GAAAATATTTGTAAATCATGTATCTGATAATTGTCTAGTATCTAAAATAT 3576
                                    i       i          vv v  v     i i     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_139982428_   3577 ATAAGGAACTCCTATAACTCAACAATGAAAAGACAG----TCCATTT--- 3619
                             i      i  i       i   i        i----i   v  ---
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_139982428_   3620 --------------TTTAAAAGTAGGTATTTCTCCAACAAAAGATATACA 3655
                         --------------   i  --   ii          - i          
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAA--TAGACATTTCTCCAA-AGAAGATATACA 863

  chrX_139982428_   3656 AATGTCCCATAAGCACATGAAAAAATGCTCACCATCATTAAACAT 3700
                             v  v               i       v     ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (92 / 54)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 5.75 (69 / 12)  


1856 27.90 0.91 1.63  chrX_140005164_140011305.rev     4431  4982 (1160)    L1M4_orf2#LINE/L1        1   548 (360)  

  chrX_140005164_   4431 TGGAAAGATATTTTATGATCAGACATTGGAAAAATCAATACTGTCAAAAT 4480
                                    iii   v   viv       i v i    i   i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140005164_   4481 GTCCATACTATTCAAGGCAATCTATAGATTCAATGCAATCTCTATCAAAA 4530
                          v v     vii   ivii     i        i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140005164_   4531 TACCATTGACATTCTTTACAGAAATAGGAAAAATAATCCTAAAATTTATA 4580
                          v   vivi v  i   i       v iv  iv i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_140005164_   4581 TGGAATCATAAAAGACCCAGAACATCCAAAGCCACTGTGAGCAAAAGAAG 4630
                              viii  ii         i v     i v iiv   --        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chrX_140005164_   4631 AA---AACTGCAGGAATCACATGAACATGACTTCAAATTATACTACAGAG 4677
                           --- ii  v    v     ivvv -ii i      viv       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCC-CAATTTCAAAACTTACTACAAAG 247

  chrX_140005164_   4678 TTATAGCAACCAAACCAACATGGTATTAGTATAAAAGCAGATACAAAGAC 4727
                         i  i  i  i   iv  iii     i i i    iiii   i i v   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_140005164_   4728 CAATGAAACAGAATAAAGAACACAGAAACAAATGTACTTATTTACACCCA 4777
                              i  i     vi   iiv      i   ivi ivi     iivi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_140005164_   4778 ACTGATTTTCAACACAGGTGCCAAGTACATATCC--TGGAAAAAGGACAC 4825
                          i        i   vi         -  -i  i --   ii    i i v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAG-AC-CATTCAATGGGGAAAGAATAG 395

  chrX_140005164_   4826 TCTGTTCAATATATAGGGCCAGGAAAATTATATATCCATCCATATGCAGA 4875
                            v     i v  i v  ii   v  i iv   ?   i----     i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC----ATGCAAA 441

  chrX_140005164_   4876 AGACAGAAACTAGACCCCTATCTCTTGCCATATACAAAAATGAAATCAAA 4925
                            vv   ii i        i   vii              v  v     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_140005164_   4926 ATGGATTAAAGACTTAAATCTAAGATCTCAAACCATAAAGTTACTAAAAG 4975
                               i ?    i     v     v  v    i     ii vi  i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_140005164_   4976 AAAACAT 4982
                                
  L1M4_orf2#LINE/    542 AAAACAT 548

Transitions / transversions = 2.10 (103 / 49)
Gap_init rate = 0.01 (7 / 548), avg. gap size = 2.00 (14 / 7)  

1228 24.80 0.81 0.54  chrX_140005164_140011305.rev     5281  5651 (491)    L1M4_orf2#LINE/L1      537   908 (0)  

  chrX_140005164_   5281 AGAAGAAA-CATTGGGGAAAATCTCTAGGACATTGGTCTGGGCAAAAATT 5329
                                 -   v  ? v      iiiv   v    vi i     vii  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_140005164_   5330 TCTTGAGCAGTACCCCACAAACACAAGCAACCAAGGTAATCACAGACAAA 5379
                             iiii vv  v   v  i          v  i v  vv i   i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_140005164_   5380 TGGAATCACATCAAG-TTAAAAAGGTTCTATACAACAAAGAAATGAATCA 5428
                          v i iiv      i-       v-  i i i vv     i vvvv    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCA 685

  chrX_140005164_   5429 ACAAAGTGGAGAGACAACCAACAGAAAGGGAAAGAATATTAGCAAACAAT 5478
                          v      i i        v      v    i i      v     iv  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_140005164_   5479 CCATCTGACAAGGGATTAATAACCACAATATGTAAGGAGCTTAAACAACT 5528
                         vi      i      i vi  v   v     i   i  i  ivv      
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_140005164_   5529 CTATAGGAAAAAATCTAATAGTCCT-TTGAAAAATTGGGCATAAGATCTG 5577
                          v   iv     iv v    ii  v-  ?      -     v i   i  
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAAT-GGGCAAAGGATTTG 834

  chrX_140005164_   5578 AATAGACATTTCTCAGAAGAATACATACAAATGGCAAACAAGCATATGAA 5627
                                       vi     v i           v  i     i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_140005164_   5628 AAGGTGCTCAACATCACTGATCAG 5651
                            i            ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (47 / 43)
Gap_init rate = 0.01 (5 / 372), avg. gap size = 1.00 (5 / 5)  


3223 26.51 0.55 0.66  chrX_140104347_140106582.rev      837  1745 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140104347_    837 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 886
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140104347_    887 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 936
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140104347_    937 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 984
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_140104347_    985 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1034
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_140104347_   1035 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1084
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_140104347_   1085 TACAGTAACCAAAACAGCATGTTACTGGTACCAAAACAGAGATATAGACA 1134
                                 i   i    ii  v      i iv ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_140104347_   1135 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACC 1182
                                i    i--    i  --        vv   i i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_140104347_   1183 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 1232
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_140104347_   1233 CTATTTAATAAATGGTGCTGGGAAAACTGGATAGCCATATGGAGAAAGCT 1282
                           v  i  i              v         ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_140104347_   1283 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCCAGATGGA 1332
                            ii    i    v   i     v              i  v i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_140104347_   1333 TTAAAGACGTAAATGTTAGACCTGAAACCATAAAAACCCTAGAAGAAAAC 1382
                          i ?    v       v   v  i    i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_140104347_   1383 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1431
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_140104347_   1432 AAACACCAAAAGCAATGGCAACAAAAGCCAAACTTGACAAATGGGATCTA 1481
                         vi            vvi          vv   v v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_140104347_   1482 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1531
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_140104347_   1532 CATGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCAACTGACA 1581
                         v vi     i                 v       vii ivi v    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_140104347_   1582 AAGGGCTAATATCCAGAATCTACAATGAACTCGAACAAATTTACAAGAAA 1631
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_140104347_   1632 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGATACT 1681
                           i -    i     v  i?    i     i      v    i   i i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_140104347_   1682 TCTCAAAAGAAGACATTTATGTAGCCAACAGACACATGAAAAAATGCTCA 1731
                             v        i  vi vi i     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_140104347_   1732 TCATCACTGGCCAT 1745
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (137 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2915 25.44 1.86 2.73  chrX_140149009_140151064      648  1563 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140149009_    648 TGGAAAAATATTCCTTGTTCATGAATCAA-----TTAGCATTATTAA-AT 691
                               i    i  v        i  iii-----   ii   i    -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140149009_    692 GTCAATACTACTGAAAACAATTTATAGATCCAATTTATTCCCTGTCAAAA 741
                          v       v iv   vii  i  i    i   ivi v     i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140149009_    742 TTCCAA-TGTCATTTTTACAGAAATAGAAAAAC-AATTCCAAAATTCATA 789
                          i   i-  i v     i       v  v  i -i  i i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_140149009_    790 TGGACCTATAAAAGAACCTGAATAGCCAAGATAATCTTGAGGAAAAAGAA 839
                             vv ii  ii  v  v          i i        ii  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_140149009_    840 GAAAGCCACAGTCATCACACTACTTGACTT-AAAACTACATTACAAGGCT 888
                         v    iiiv  vvv       v iii i  -      -i i     i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCT 249

  chrX_140149009_    889 ATAGTAATCAAAACAGCATAATACTGGCTTAAAATTGGACATGTTGTCCA 938
                          i         i    ii ii       v   iiv i     i v vi  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_140149009_    939 ATCGAACAGAA--AAGAGCCCATAAATGAATCCTCACATTTATGGCCAAT 986
                           v   i    --i    i   v    i  i  vi          i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_140149009_    987 GGATTTTTGACAAAGTTGACAAGAAAATACATTGGTAAAAGGACAATCTC 1036
                         v      i     i v  v     vv  v  v   vi    i i i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_140149009_   1037 TTCAAATAAGGGTGTTGGGAAAACTGGATATCCAAGTGCAGGAGACAAAA 1086
                              vv  v    i     v         ?   vi    ii   vvi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_140149009_   1087 ATTGGACCTTAACCCCACAGCATGTTAAAAAAAGTCAATTCAAAATGGAT 1136
                         i       iiv   i    v   i -- v    i i  i           
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATAT--ACAAAAATTAACTCAAAATGGAT 497

  chrX_140149009_   1137 TAAAGACTTAAATGTAAGA-CAAGAAACTA--AAACTACTAGCAGAAA-C 1182
                         i ?    i           - v -      --     vi   v     - 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_140149009_   1183 ACAGGAAAAAAGCTGCATGTCATTTGTCTGGGCAACTATTTATTTTATTT 1232
                          i   ?iv   v  v i  v v  v vi i     ivi   v  vv  v 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_140149009_   1233 GACTCCTAAAATACAGGCAACTAATATAAAAACAGACAAATAGGATTGTA 1282
                            v  v   ii   i     v  viv     i   i    v   i vi 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_140149009_   1283 TGAAGCTAAAAAGCTTCTGCACAGTAAAGGAAAGAATCAACAGAATGAAA 1332
                          v  iv v    i   i  ii vvi      v vv     v i i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_140149009_   1333 GAGACAATTGGGACAATTTCTCCCAATTAATAGAATTAGGAGGAAATATT 1382
                         -      --------------    -----i     -i    i       
  L1M4_orf2#LINE/    697 -AGACAA--------------CCCA-----CAGAAT-GGGAGAAAATATT 725

  chrX_140149009_   1383 TGCTAACCATATATCTGATAAGGGGTTAATATCCAAAATACAGAAGGAAC 1432
                            v  i                 ii vi      i    i v  i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chrX_140149009_   1433 TCAAACATCTCATTAGCTAGGAAAGAAATAACCCAGTT-AACAATGGGCA 1481
                           vv   v    v  iiv ii i v          i  -  v        
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_140149009_   1482 AAGCACCTAAATGGACATATCTC-AAAAAATACATTCAAATGGCCAACAG 1530
                            v ii i   i     v    -   i  v i  v           i i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_140149009_   1531 ATATATTTAAAAATGCTCAATATCACTAATTAT 1563
                         ii i  vv   i        i    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.33 (42 / 18)  


2937 27.32 1.44 1.00  chrX_140185265_140191208     4548  5451 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140185265_   4548 TGGAAAAACATTCCATCCTCATGGATAGGAAGAGTCAATATCGTGAAAAT 4597
                               i i  i    vi        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140185265_   4598 GGCCATACTGCCCAAATTAATTTATAGATTCAGTACTATTCCCATCAAAC 4647
                            v     v        i  i  i       iii v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140185265_   4648 TACCATTGACATTCTTCACAGAATTATAAAAAACT-ACTTTACATTTCAT 4696
                          v   vivi v  i  ii     v - i v  i  - iii  v v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_140185265_   4697 ATGGAA-T-CAAAGAAGACCCTATATAGCCAAGACAATCCTAAGCAAAAA 4744
                               - -   i --     viv        i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_140185265_   4745 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTGTACTACAAGG 4794
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_140185265_   4795 CTACAGTCACCAAAACAGCATGGTACTGGTAACAAAACAGACATACAGAC 4844
                                v i   i    ii         i vv ii i       i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_140185265_   4845 CAATAGAACAGAAC--AGAGCCCTCAGAAATAACGCCACACATCTACACC 4892
                             i   i    i--    i  --        vv   i    i  iivi
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_140185265_   4893 CATCTGATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATAT 4942
                           vi    i        ivv  v   i v  vv            i   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_140185265_   4943 CCTATTCAATAAATGGTGCTAGGAAAACTGGTTAGCCATATGCGGAAAAC 4992
                         i  v     i          i   v      v  ?   i    ii  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_140185265_   4993 CGAAACTGGACCCCCTTTTTACACCTCATACAAAAATTAACTCAAGATGG 5042
                         i   ii        ivii i     vi                  i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_140185265_   5043 ATTAAAGGCTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAA 5092
                           i ?  i i         i v i     i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_140185265_   5093 CCTAGGCAATAGACATTCAGGACATAGGCATGGGCGACGACTTCATGACG 5142
                          v    ?i-  i iv   iv   v v  vv i   i i ii   v iivv
  L1M4_orf2#LINE/    546 CATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_140185265_   5143 AAAATGCCAAAAGCAATTGCAACAAAATCCAAAACTGATGAGTGGGATCT 5192
                          vi ii         vvv         vvv    iv   i i v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_140185265_   5193 AATGAAACAAAAGAGATTCTGCACAACAAAAGGAACTATCATCAGAGTGA 5242
                         v  v   vvv  i iv  i  ii vv    i iv       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_140185265_   5243 ACAGGCAACCTACAGAATGGGGAAAAGT-TTTGCAATCTACCCATCCGAC 5291
                          v  i     i          ii   i -       vii ivi   i  i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_140185265_   5292 AAAGACCTAATATTCAGGATTTACAAGGAACTTAGACATATTTACAAGAA 5341
                           i iv  vi   i   i  v  i  i     ivv   - i --   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACT--CAATAA 791

  chrX_140185265_   5342 TAAAA-------CAACCCCATCAAAAAGTGGGCAAAGGATATGTACAGAC 5384
                              -------i     v  i?    i            v  v i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_140185265_   5385 ACTTCTCAAAAGAACACATTTACTCAGCCTACAAACATATGCAAAACAGC 5434
                          i     v      v i  vi vvii   v i  i  i   v   ivv  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_140185265_   5435 TCAACATCACTGATCAT 5451
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


 432 19.00 6.00 1.00  chrX_140199269_140204121      401   500 (4353)    L1M4_orf2#LINE/L1        1   105 (803)  

  chrX_140199269_    401 TGGAAAGATATCCCATGTTTATTGAGTAGAAGAAGAAATATTGTTAAAAT 450
                                            i  v  v i     vvv           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140199269_    451 GTTTATACTACCCCA------TCTACAGATGCAGTACAATCCGTATGAAA 494
                          viv     -     ------         v  iii      v   v   
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_140199269_    495 ATTGCA 500
                           iv  
  L1M4_orf2#LINE/    100 ATCCCA 105

Transitions / transversions = 0.73 (8 / 11)
Gap_init rate = 0.02 (2 / 105), avg. gap size = 3.50 (7 / 2)  

2794 26.57 0.65 2.17  chrX_140199269_140204121     1925  2846 (2007)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140199269_   1925 TGGAAGCACATCCCATGTTTATGGATGGTTAGAATCAATATTGCAAAAAT 1974
                              iv i          i      v vv   v i       iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140199269_   1975 GACCATACTGCCCAAAGCAATCTACAGATTCAATGTAATACCCATCAAAA 2024
                          i v     v      vii              i i   v  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140199269_   2025 TACCATCAACATTCTTTACAGAACTAGAAAAA---ATTATAAAATTCATA 2071
                          v   v vi v  i   i     v v  v  i---  iv           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_140199269_   2072 GGAAACTAATAAATAGTCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 2121
                         v i  v ivv iiv vi v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_140199269_   2122 CAAATCTGGAGGCATCACATTACCTGACTTCAAACTATGCTACAAATCAA 2171
                             vi      vv     i v  ii i      viv i       v v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_140199269_   2172 TAGTTACCAACGCAGCATGGTCCTGGTATAAAAACAGGCACATAGACCAG 2221
                         i   v i   vi   ii    v    i    ii i  i  i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_140199269_   2222 TGAAATAGAATAGGGAACCCAGAAATAAAGTCAAATCTAATACTTACAGC 2271
                           i        v i  ii           vi  ----  -i i   ii i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCA----TA-CATTTATGGT 345

  chrX_140199269_   2272 CAACTGATCTTCAACAAAGGAAACAAAAACATAAAGTGGGGAAAGGACAC 2321
                            i    i   i    i  viv   i v   vv i         i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_140199269_   2322 TGTATTCAATAAATGGTCCTGGGAAAACTGGCAAGCCACATGTAGAAGAC 2371
                          v v     i       v      v      vv ?       i i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_140199269_   2372 TGAAACTGGATCCTCATTTCTCACCTTATACAAAA-TTAACTCAAGATGG 2420
                             ii    i  ii ii  v    v         -         i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_140199269_   2421 ATTAAAGATTTAAATCTAAGACCTGAATCCATAAAAATGCAAGAAGATAA 2470
                           i ?   ii     v     v  i  v i      v viv      v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_140199269_   2471 CATCAGAAAAACCCTTCTAGGCATTAGCTTAGGCAAAGATTTCAT-GATC 2519
                            vi ?iv  vi    vv i v  i v        v i    v -   -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chrX_140199269_   2520 AAGAACCCAAAAGCAAATGCAACAAAAATAAAAATAAATGAATGGGACCT 2569
                          v  vv         v v         iv       i  i   v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_140199269_   2570 AATTAAACTAAAAAGTCTTTGAACGGCAAAATAATAATAACAATAAATCA 2619
                         v  i   v v    iii    vi vv    i-------i   v  --   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAG-------GACACTA--TCA 685

  chrX_140199269_   2620 ACAGAGTACAACAGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTT 2669
                          v i   iv  -              i           v  ii   viiv
  L1M4_orf2#LINE/    686 AGAAAGTGAAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_140199269_   2670 TACATTCGACAAAGGACCAATATTCAGAATATACAAGGAACTCAAACAAA 2719
                           i  ii  i  i    ivi   i         i  i      vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_140199269_   2720 TTAGCTAGAAATGAACCAATAATCCCATCAAAAATTGGGCAAAAGATGTG 2769
                          i iiv v   vii  v     i  v  i?    v        i   v  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_140199269_   2770 AATAGAACATT-CTCAATAGAAGATACACAAACATATGAAAACAAACATA 2818
                               -    -   v v        i     ii--- vv  i  i  i 
  L1M4_orf2#LINE/    835 AATAGA-CATTTCTCCAAAGAAGATATACAAATG---GCCAATAAGCACA 880

  chrX_140199269_   2819 AGAAAAAATGCTCAACAACACTAATTAT 2846
                         v     i          v  ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.21 (132 / 109)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.17 (26 / 12)  

2384 25.36 6.44 1.71  chrX_140199269_140204121     3602  4362 (491)    L1M4_orf2#LINE/L1      112   908 (0)  

  chrX_140199269_   3602 TTTTTCATAGAAA--AACAA-----TCCTAAAATTTATATGGAA---CAC 3641
                              iii     --i    -----          i        ---  v
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_140199269_   3642 AAAAATCA-AATATCCAAAGCA-TCCATAAGCAAAAGAAAAAAGCTGAAG 3689
                         iii vi  -    v     i  -  ivv  iv i     v    i  i  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_140199269_   3690 GTATCACATTACCTGATTTCAAACTACACTAAAAAGCTATAGTAATAAAA 3739
                          vv     i v  ii        vivi    v       i      v  i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_140199269_   3740 ACAACATGGTACTGGCAAAAGAAAAAAAAATAGGCACGTCAACCAATGTA 3789
                            iii           v   i -------   i  ii vi i     v 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGA-------TAGACATATAGATCAATGGA 304

  chrX_140199269_   3790 A--------------CAGAAATGAACCCATGCATGTACATTCAACTGATT 3825
                          --------------       i       i   v  iiv    i     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_140199269_   3826 TTCAATAAAGGTGCCAAGAATACGCAATGCAAAAGGAACAGTCTGTTCCA 3875
                            i i  i          vi iv     vii  i   i     v   v 
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_140199269_   3876 TAAGTGGCATTGGGAAAATGAGATATTCATATGCAGAAGAATGAAATTAG 3925
                         i  i   iii     v  ivi    ?i  i     i         i  i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_140199269_   3926 ATTTTTATTCAACACCATATACAAAAATCAACTCAAAATGGATTTAGGAC 3975
                          iiii  iiiv                 i              iv?i   
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_140199269_   3976 TTAAACATAACACCAGAAACTATAAAACTACTT-GAAAAATGTGTAGGGG 4024
                         i    ii   v v vi             -   -   i  viii    ? 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAACATAGGNG 553

  chrX_140199269_   4025 GAATAATACATA---TTTGTCTAGGCAAAGATATTTTTGATTTGACCCCA 4071
                         v  vvv v i i---  v vi       v i v i  v   v    v   
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_140199269_   4072 AAAGTAAAGGCAAGAAAAGCAAAAATAGACAATTGGGATTACATCAAACC 4121
                             i v i    v     v         i  v v   i v       vi
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_140199269_   4122 TAAAA--------GAAGCAAATAACAGT---------GTGCAGAGACAAC 4154
                              -------- vvv    vi   v ---------   v i       
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_140199269_   4155 ATACTTACAGGTAGGAAGGAAATATATGCAAACAATATACCTGATAAAGG 4204
                         ----ii    ivv  i  i      v      iv     i       i  
  L1M4_orf2#LINE/    704 ----CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_140199269_   4205 GTTAATATTCAAAATATACAAGGAATTCAAACAGCTCAATAGCAAGTAAA 4254
                         ii vi   i  i      i  i   i  vv   i       ii  iv i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_140199269_   4255 CAAAATACCCAATTTAAAAATGGGCAAGGGACCTGAATAGACATTTCTCT 4304
                             vv        ?            i   ii                i
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_140199269_   4305 AAAGGAGACATACAAATGGCCAACAG--ATATGAGCAAAATGCTCAATAT 4352
                             i   i              i i-- i    i-  i        i  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGATGCTCAACAT 898

  chrX_140199269_   4353 TGCTAATCAT 4362
                         ii????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.82 (122 / 67)
Gap_init rate = 0.02 (15 / 797), avg. gap size = 4.13 (62 / 15)  


2796 26.80 2.10 1.88  chrX_140204989_140207153.rev      772  1674 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_140204989_    772 AAAAAAATTCCATGCTCATGGATTGGAAGAATCAATATAGTTAAAATGGC 821
                            i v  i     i               v i     v     i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_140204989_    822 CATGCTGCCCAAAGAAAGCTACCAATTCAATGCTATTCCTATCAAACTAC 871
                         v  i  v      vvi v    vi      i  v  i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_140204989_    872 CAACGTCATTATTTGCAGAACTAGAAAAACTGTTTC-AAAATTCATATGG 920
                           i vv v  v         v v  v  i   v i -             
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_140204989_    921 GACAGAAAAACAGCCTGAATAGCTAAAGCAATCCTAAGCAAATAGGACAA 970
                         i vv v  iiv v  v       i   i     i i iv  iv  i    
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_140204989_    971 AGCCTGAGGCAACTCAT--TACCTGACTTCAAACTATACTATAAGACTAC 1018
                           iiv    --     i-- v  ii i      viv     i  ii    
  L1M4_orf2#LINE/    204 AGTTGGAGG--ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_140204989_   1019 TATAACCAAAACAACATACTACTGGTATAAAAACAGAGAAGAACAGACAA 1068
                         vi   i   i   iii iv      i    ---------- i i     v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAA----------GGATAGACAT 291

  chrX_140204989_   1069 AAATAGACCAATGGAACAGAATAGAGAAACCAGAAATCAAGCTGC-CATT 1117
                          --    i        i     v    iv        v  v iii-    
  L1M4_orf2#LINE/    292 A--TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_140204989_   1118 ---AGACATTTTATCTTCAACAAAGTCAACAAAAATA---AGGATAGGGA 1161
                         ---i v  v  v  i   i    i viiv   i vi --- --  i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA--ATGGGGA 387

  chrX_140204989_   1162 AAGGACAGTTTTTTTAATAAACGGTGCTGGGATAATTGGCTAGCCATATT 1211
                            i i   i    i  i   i          i  i   v  ?   i  v
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_140204989_   1212 CGGAAGAATAAAACTGAACCCCTACCAGTCACCATATA-AAAAATTAACT 1260
                          ii      i  ii  i         vvv         -           
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_140204989_   1261 CAAGGTGGATTAAAGATTTAAATGTACGACCTCAAACTATAAGAACCCTA 1310
                            ii     i ?   ii        v  v  v         i vi i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_140204989_   1311 GAAGAAAACCTAGGAA-ACACCATTCTGGACATTGGCTTCGGGAAAGAAT 1359
                                  v    ?i- v i -   vv   v    v  v  v  v iv 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_140204989_   1360 TTATGACTAAGTCCTCAAAGGCAATTGCAACAGAATAATAAATTGACAAG 1409
                          iv iiv  v v vi    i   vvv      i  v  v    v  i  i
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_140204989_   1410 TGGAAACTAATTAAAGTAAAGGGCTTCTGTACAGCAAAAGAAGCTAGCAA 1459
                          v i vi v  i   i v  iii   i   i vv    i  vi   v   
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_140204989_   1460 CAGAGTAAGCTGACACCCTACAGAATGGGAGAAAATATTCACAAACTATG 1509
                         v i   i ivv    v  i                    ii    ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_140204989_   1510 CATTTAACAAAGGCCTAATACCCAGAATCTATGAGGAAC------AACTC 1553
                         i  i i i  i  v  vi  i       v   i i    ------     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_140204989_   1554 AACAAACAAGAAACAAAGAGCCCCATTAAAAAACGAGCAAAGGACATGAA 1603
                           i  vv  i i     v i   v   ?     i i        iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_140204989_   1604 CAGACACTCCTCGAAA-AAGACATACAAGCACCCAATAAACATATGAAAA 1652
                         i     i i   v   -    i      iiiv       i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_140204989_   1653 AATGTTCCACACCACTAATCAT 1674
                         i   i  v   i  ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.02 (14 / 905), avg. gap size = 2.57 (36 / 14)  


2003 28.65 5.39 3.60  chrX_140213072_140215011.rev      562  1451 (489)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_140213072_    562 GAAATAAATCATGTGGCTTTGGATTGGAAGACTCAACATAATAAAAACAG 611
                             v v   vii  viiv              i  i  vi v  i ii 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_140213072_    612 TCAATCTTTTTCAAACTTTATCTGTATGATT-AATGCAATTTCTA-CAAA 659
                         -    vi iii    -  v    ii -    -  i     ii   -    
  L1M4_orf2#LINE/     53 -CAATACTCCCCAAA-TTGATCTACA-GATTCAACGCAATCCCTATCAAA 99

  chrX_140213072_    660 AACACAACAGGATTAATCGTTTATATATATAAT--ACAAGCTTATTTTAA 707
                          v v  i v ------i v   v ii v -   --       v  ii   
  L1M4_orf2#LINE/    100 ATCCCAGCTG------CCTTTTTTGCAGA-AATTGACAAGCTGATCCTAA 142

  chrX_140213072_    708 AATGTATAAGAAAAGGCAGATAAACTAGATAAACTAAAACAATTTTAAAT 757
                            vi   v i   v   iivi v i   vv i i        i  i  v
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_140213072_    758 ATGGAAAATAATGTTGGAGGAACCACACTACCTAATTTTAAAACTTTCTA 807
                          v i i  i  v         vi      v  i     i       v   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_140213072_    808 TATAGCTACCGTTATCAGTATTAAGAC--TGTGGAATTGGTAGAGGGATA 855
                         i v      v  v    ------    --     v i   i v i     
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCA------AGACAGTGTGGTACTGGCATAAGGATA 286

  chrX_140213072_    856 GGCATGTAGGTCAATGGAATAGAAAACAGAGTTCATCAATACACCTACGA 905
                          i   i   i              vvv     i  vv    v   i iiv
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_140213072_    906 AGT-ACTACTGACTGACAGCTGACAAACTTGCAAAGGCAATTTGAAGGAG 954
                          v - iviiii i   ivvii     ivv   v   i v   ii v  i 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_140213072_    955 ATAGGATACTCTTTTCAACAAATA-TATTGCAACAATTGGACAATCATAG 1003
                          v  i   v              i- ii  vi    i    i ?i  i v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_140213072_   1004 ACATAC-AACGAACATTGACTTAAATCTCACATCTTACTCAAAAATGAAC 1052
                         i  v v-  i   vv v   iivv i      i v  iv       v   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_140213072_   1053 CTAAAATAGATGAATCATGGATCTAAATGTAAAATGAC--AAATGATAAA 1100
                         ii     i   ----  ?i  i          i --i --   iv     
  L1M4_orf2#LINE/    487 TCAAAATGGAT----CAWAGACCTAAATGTAAGA--GCTAAAACTATAAA 530

  chrX_140213072_   1101 ATCTTTAAAAGAAAA-----ATGTAAGATTTTTGTTAGTATCTGAGGGTT 1145
                          iii   i       -----i?    -  i  i  -- - i  v-     
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAA-ATCTTCGT--G-ACCTT-GGGTT 575

  chrX_140213072_   1146 TCATGAAAAG----CTTAGAAATGACATTGAAAACAAGATCCATAAAAGA 1191
                         -- v v  v ----      v      iii   i  vi v v i      
  L1M4_orf2#LINE/    576 --AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_140213072_   1192 AAAGTGTTAATA---TGTCCCTCATCAAAATTTAAAAAGCTTCAAT-CTG 1237
                            i-i vi   ---  vv i           --    i   ivi -  v
  L1M4_orf2#LINE/    624 AAAA-ATAGATAAATTGGACTTCATCAAAATT--AAAAACTTTTGTGCTT 670

  chrX_140213072_   1238 TGAAAAACCCTGTTAAGAGAATGTAAAGACAG------------------ 1269
                         ii  ii  v  i i    i i  v       i------------------
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_140213072_   1270 ------GCATACTGTATACCCAAAAAAGGACTGGTATCTAGAGTACATAA 1313
                         ------   v iii    i ii v  i     v     i   i  i    
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_140213072_   1314 AGAACTCTCAAAACTCAGCGGTTAAAAAATAGGCAATCTAATTAGAAAAT 1363
                                 i v      iiii v    i i iii  i i    ?i     
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_140213072_   1364 GGGCAAAAGAGTAGAATTTACACTTCACCAAAGGGGATATGTGAATGGCA 1413
                                i  v v    vv   i   v      ii     iii      v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_140213072_   1414 AACAGACACATGAAGAAATGTTTAAAATTGTTTGCCAT 1451
                           i ii        i i   i i  v  ii????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (159 / 92)
Gap_init rate = 0.03 (28 / 906), avg. gap size = 2.86 (80 / 28)  


3636 22.12 2.71 0.23  chrX_140237838_140241522     2307  3192 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140237838_   2307 TGGAAACACATTCTTCATCGATAGACTGGAAGATTTAAGATTGTTAAAAT 2356
                               v i  i ivii iv  i  i       i    v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140237838_   2357 GGTGATACTACCCAGGC--ATCTACAGAGCCAATGCAATCTCTATGAAAA 2404
                           ii     v    iii--         vi   i      i    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140237838_   2405 TTCCAGTGGCCTTTGTTGCAGAAATGGAAAAGCTGATCCTCAAAATTGTA 2454
                          i    iv      v          v  v           v   v ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_140237838_   2455 TGCAATTTCAATGGTCTCTGAATAACCAAAACAATTTTTAAAAAGGAAAT 2504
                           v  v v   v  v i v     i          i  v      i i v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_140237838_   2505 CAAAGTTGGGTGATTCA-ACTT-------TCAAAGTTTACTACAAAGGAA 2546
                                  iv  i   -    -------     ii           vv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_140237838_   2547 CATTAATCAAGATGAGGTGGGACTGGCATGTGAAAAGACATATAAGTCAA 2596
                           v         iiiv    v        iv i v         ii    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_140237838_   2597 TGGAATAGAACAGATGGTCCAGAA-TAAGCCCTCATATTTATTATTAATT 2645
                                   iv  vi        -   i   vi i      vi i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_140237838_   2646 TATCTTCAACAAGGGTTCCAAAATATTTCAATGGGAAACATATGATCTTT 2695
                         v  i   i        v    i ivv         i  viv  ii     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_140237838_   2696 TGTACAAATCGTGCTAGGACAGTTGAGCTTTTATGTG-AAAAAAATAAAG 2744
                          vv      v     i     ii  iiiv?ii ii  -    i   i   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_140237838_   2745 TGGTATACCTACCTCACACCACATACAAACATTAACTCATAAT----CAA 2790
                          v v iv              i       v         v   ----  ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_140237838_   2791 AAACCTAAATGTAACAGCTAAAGTTTTAGCATACTTAGAATAAAACA--G 2838
                          i            v       ii v  iv iv       v      -- 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_140237838_   2839 GTGTCAACCTTTGTGACCTTAAATTGGGCAATATTTACTTAGATATGACA 2888
                          ?  v  i   i        iii  i      iv  v             
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_140237838_   2889 CAAAAAAACACAAGCAACAGAAATAAAAAATAAATAAATTGGACT-AATC 2937
                          v    i-           -   v        i            -v   
  L1M4_orf2#LINE/    601 CCAAAAG-CACAAGCAACA-AAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_140237838_   2938 TAAATTTAAAACTTTT-TAATCCAAAGGATATTATCAAGAGATTGAAAAA 2986
                         v     v         - iv i       i i        i v      i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_140237838_   2987 ACAACCTACATAATCAGAGTACCTATTTCCAGATCATATATCTGATGAAG 3036
                               i   v   vi   v vv     v  i              i i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_140237838_   3037 GTCCAGTATTTATAATGTACAAAGAACACTTA-AACTCTACAGCAAAAAA 3085
                          v iv    ii v   i  i       v    -     v i ii     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_140237838_   3086 GAATAAAAGTAAAT--AAAAATAGGCAA-GAATTTGAATAGATAAGTCTC 3132
                         iv v v  viv   --      i     - i           i vv    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_140237838_   3133 CAAAGAAGAAAAACAAATGGCCAATAAGTACAAGAAAAGATGCTCGACGT 3182
                                  v v                i   v            i  i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_140237838_   3183 CATTAGTTAT 3192
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.30 (109 / 84)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.86 (26 / 14)  


 504 29.68 7.76 0.91  chrX_140261509_140267336        9   227 (5601)  C L1M4_orf2#LINE/L1   (674)   234     1  

C chrX_140261509_    227 TGGAAAAACATTCCATGTTCA-GG--TAAAGGA---AAT--------GGC 192
                               i i  i         -  -- ii i  ---   -------- ii
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_140261509_    191 CACCACACTGCACAAAGCAGTTTAAAGATTCAATGTTATTCCTGTCTAAC 142
                         vi v i   v v    viii i  v        i iv  i   i  v  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_140261509_    141 TACCAATGACATTCTTCACAGAA-TTAGGAAAAGCT-ATTCAAAATTTTA 94
                          v   iivi v  i  ii     -  --  v     -  i v   v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

C chrX_140261509_     93 TATGGAACAAAAAAGAACCCA-AATATTCAAAGCAATCCTAAACAAAAAG 45
                                vviv  i i     -    vi    i     i i  v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_140261509_     44 AACAAAGCTAGTGGCATCACATTACCTGACTGCAAA 9
                                i i v  vv     i v  ii i v    
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

Transitions / transversions = 1.60 (40 / 25)
Gap_init rate = 0.03 (8 / 234), avg. gap size = 2.38 (19 / 8)  

3069 26.90 1.10 0.99  chrX_140261509_140267336     4429  5335 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140261509_   4429 TAGAAGAACATTTCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 4478
                          i   ii i  ii    i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140261509_   4479 GGCCATACTGCTCCAAGGTAATTTATAGACTCAATGCCATCCTCATCATG 4528
                            v     - i    iv i  i  i   i    i  v    ii    vi
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_140261509_   4529 CTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4576
                         v v   iivi i  i  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_140261509_   4577 ATACAGAACCAAAAAAGAGCCCGCATTGGCAAGACAATCCTAAGCAA-AA 4625
                            ii   viiv  ii  v  v v  v v   i      i i iv  -  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_140261509_   4626 GAACAAAGCTGGAGGCAC-CACGCTACCTGACTT-GAAACTATACTACAG 4673
                                 i      -  -   i  v  ii i  -i     -       i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chrX_140261509_   4674 GGCTACAGTAACCACAACAGCATGGTACTGGTACCAAAACAGAGATATAG 4723
                         i          i  vi    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_140261509_   4724 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACATATCTACA 4771
                          i        i    i--    i  --        vv   i i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_140261509_   4772 ACCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT 4821
                         ii  vi    i  i     ivv  v   i v  vvv           i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_140261509_   4822 TCCCTATTTAATAAATGGTGCTGGGAAAAATGGCTAGCCATATGTAGAAA 4871
                         vvi  v  i  i              v  v   v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_140261509_   4872 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 4921
                         iv    ii    i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_140261509_   4922 GGATTGAAGACTTAAATGTTAGACTTAAAACCATAAAAACCCTAGAAGAA 4971
                             ii?    i       v   vi      i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_140261509_   4972 AACCTAAGCA-ATACCATTGAGGACATAGGCATGGGCAAGGACTTCATGA 5020
                            v  i ?i- v i v i v iv v i  i- i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAG 592

  chrX_140261509_   5021 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGAGAT 5070
                         v  vi            vvi          vv        i    vi  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_140261509_   5071 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5120
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_140261509_   5121 GAACAGGCAACCTACAGAACGGGTGAAAATTTTTGCAATCTACCCATCTG 5170
                            v  i     i      i   v      v       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_140261509_   5171 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAG 5220
                          i  i  i  vi          v  i        ivv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_140261509_   5221 AAAAAAATCAAACAACCCCATCGAAAAGTGGGCCAAGGATGTGAA--GAC 5268
                              i -    i     v  i?    i     v      v    --   
  L1M4_orf2#LINE/    793 AAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_140261509_   5269 ACTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGC 5318
                          i     v        i  vi viii     i ii          i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_140261509_   5319 TCATCATCACTGGCCAT 5335
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (153 / 87)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.27 (19 / 15)  


2766 28.46 0.55 1.53  chrX_140350975_140357162.rev     4781  5697 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140350975_   4781 TGGAAAAACATTACAGGCTCATGGATAGGAAGAATCAACATCGAGAAAAC 4830
                               i i  iv  v i        v      v i  i  i vv  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140350975_   4831 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 4880
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140350975_   4881 TACCAATGACCTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4928
                          v   iivi    i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_140350975_   4929 CATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGTCAAAAG 4978
                         i      viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_140350975_   4979 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGAT 5028
                                i      vv    i  v  ii i      viv        iii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_140350975_   5029 GACAGTAACCAAAATAGCATGGTACAGGTACCAAAACAGAGATACAGACC 5078
                         v       i   i i  ii      v  i iv ii i   v   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_140350975_   5079 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5126
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_140350975_   5127 ATCTGATCTTTGACAAACCTGACACAAAACAAGAAATGGGGAAAGGATTC 5176
                          vi    i  i     ivv  v  - i v  vvv           i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCA-AGACCATTCAATGGGGAAAGAATAG 395

  chrX_140350975_   5177 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGC 5226
                         i  v  i  i              v      v  ?   i   v i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_140350975_   5227 TGAAACTGCATCCCTTTCTTACACCTAATATGAAAATGAATTCAAGATGG 5276
                             ii  v i    vi  i     vv   ii     v  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_140350975_   5277 ATTAAAGACTTAAATGTTAGACCCAAAAAACCATAAAAACCCTAGAAGAA 5326
                           i ?    i       v   v i    -- i      vi i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAA--CTATAAAACTCTTAGAAGAA 543

  chrX_140350975_   5327 AACCTAGGCA-ATACCATTCAGGACATAGGTATGGGCAAGGACTTCATGA 5375
                            v    ?i- v i -   iv   v v  vv i     v ii   v ii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_140350975_   5376 CTAAAATACCAAAAGCAATGGCAACAAAAGCCAAACTTGACAAATGGGAT 5425
                         v  vi i          vvi          vv   v v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_140350975_   5426 CTAATTAAACTAAAGAGCTTCTCGTCTGCACAACAGAAGAAACTACCATC 5475
                         i v  i   v v  i i   i ----- ii vv  i i  v    i  vv
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTT-----GTGCTTCAAAGGACACTATCAAG 687

  chrX_140350975_   5476 AGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCC 5525
                          i      v  i     i                 v   i   vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_140350975_   5526 GTCTGACAAAGGCCTAATGTCCAGTATCTACAAAGAACTTAAACAAATTT 5575
                         i     i  i  v  vi i     v  v  i        ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_140350975_   5576 ACAAGAAAAAAATCAAACAACCCCATCAAAAAGGGGGCAATGGAGATGAA 5625
                          i  v     i -    i     v  i?    iv      v   vv    
  L1M4_orf2#LINE/    788 ATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_140350975_   5626 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACACGAAAA 5675
                         i     i     v        i  vi viii     v ii    i     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_140350975_   5676 AATGCTCATCATCACTGGCCGT 5697
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (151 / 106)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


1761 23.85 5.61 13.15  chrX_140469579_140472077     1026  2006 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_140469579_   1026 GAAAAAAAATTCTATGCTCTTGGATTGGAAAAATCATTATTGTTAAAATG 1075
                          i   i v  i i   i  v          i v i v         i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_140469579_   1076 GCCACACAGCCTAAAGTAATTTACAGATTCAATGTTATCCCTGTCAAAAT 1125
                           v i  vv  i   v i  i           i iv      i       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_140469579_   1126 ACCAACAATATTTTTCATAGAATTAGAAAAATCTATTCTAAAATTCATAT 1175
                         v   i viiv     iii    v v  v  iiiv  i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_140469579_   1176 GTAACCACAAAAGAGCCCAGA-TAGCCAAAGCAATCCTAAGCAAAAAGAA 1224
                          v  vii   ii  -      -        i     i i iv  i     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_140469579_   1225 CAAAGTCAGAGGCATCACATTACATGACTTCAAACTATACTATAAGGCTG 1274
                               ii    vv     i v vii i      viv     i  i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_140469579_   1275 CAGTAAGAAAAACAGCATGGTACTGGTACAAAAAGAGACATATACACTAA 1324
                               vv  i    ii         i i  ii v         v ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_140469579_   1325 CAGAATAGGTTAGAGAACCCAGAAATAAAGCTACAAAGCTACAAGCATCA 1374
                         ii      iv v    ii           v i i v vi  iiiv  viv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_140469579_   1375 GATCTTTGACAAAATCTATCTATCTATCTATATACACACACATGTATATA 1424
                            i  i     ii------------------------------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG------------------------------------ 364

  chrX_140469579_   1425 TATGTATATATATATACACGTGTATATATATATGTGTATATATATACGTG 1474
                         ---------------------------------   i-------i v --
  L1M4_orf2#LINE/    365 ---------------------------------GTGC-------CAAG-- 372

  chrX_140469579_   1475 TGTATATATATATGCATACGTGTGTGTGTATATATATATATATATATATG 1524
                         -----------------  ---------------------------i  v
  L1M4_orf2#LINE/    373 -----------------AC---------------------------CATT 378

  chrX_140469579_   1525 CAATGAGGAAATCACTTCCTATTCAATAAATTGTGCTGAGATAAACTGGT 1574
                              i     vv ivvi  v     i    v      i  i  -    v
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA-CTGGA 427

  chrX_140469579_   1575 GAGCAATATTCAGAAGAGTAAAACTGGATTCCTTTCTTATAC-----ACA 1619
                         v ? v i  v  i    i i  ii    ii   vi  i i  -----   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_140469579_   1620 AAACGTAACTAAAGATGGATTAAAGATTTAAATGTAAGACCTCAAGCTAT 1669
                            vv     v  i      i ?   ii           v  v  i    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_140469579_   1670 AAAAATTCTAGAA---AACCTAGA---AAATACCCTTCTCGACATCAGCT 1713
                             v ii     ---   v   i---    ---    vi   v ii v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGT 574

  chrX_140469579_   1714 TTGGCAAATAATTT-TTGACTAGGTCCCCAAAAGCAATTGCAACAAAACC 1762
                          v     - ii   -  iiv  v v v         vvv         vv
  L1M4_orf2#LINE/    575 TAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_140469579_   1763 AAAAATGGACAAGAGGGACATGATTAAACTAATGAGCCTCTGTACAGCAA 1812
                               i  i  ivv    v v  i   v v vi i i i   i vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_140469579_   1813 AATAAACTGTCAA--------------------TAGCAT------AAACA 1836
                          iv v   i    --------------------i  v  ------   i 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_140469579_   1837 CT--------ATACATCTGAGAAGGGTCTAATATCCAGAAACTA-AAAGA 1877
                         i --------   i      v     v  vi         vv  -     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_140469579_   1878 A-----ACAAGTCAAAAAGTAAAAAAATAAAACATCCAGTT-AAAAATAG 1921
                          -----    v    v  -      i i   vv i   i  -      i 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_140469579_   1922 GCAATAGACATGAACAAACACTTCTC-AAAGGAGACATACAAGTGGCCAA 1970
                             vi  iv    i i   i     -    i   i      i       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_140469579_   1971 CAAACATAAGAAAAAATGCTCAAGATCACTAAGCAT 2006
                         i  i  i v     i        v    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 8.76 (184 / 21)  


 203 25.37 0.00 1.49  chrX_140558776_140561127.rev      304   370 (1982)  C L1M4_orf2#LINE/L1   (0)   908   843  

C chrX_140558776_    370 TTTCTTAAAAGAAGACATTCGTGTGGCCAACAAACATACAAAAAAAACCC 321
                              iv        i  v ivi       i  i  i ii    i vv i
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

C chrX_140558776_    320 CGAGCATCACTGATGAT 304
                          i -     ????????
  L1M4_orf2#LINE/    893 CAA-CATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1)  

3156 27.54 0.77 0.33  chrX_140558776_140561127.rev      958  1861 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140558776_    958 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1007
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140558776_   1008 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCAGCAAGC 1057
                            v     v     iv i  i  i        i  v     i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140558776_   1058 TACCAATGACTTTCTTCACAGAATTGGAAAAAAATACTTTAAAGTTCATA 1107
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_140558776_   1108 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 1157
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_140558776_   1158 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 1207
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_140558776_   1208 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 1257
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_140558776_   1258 TGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACTAT 1305
                              i    i--    i  --        vv  ii i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_140558776_   1306 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAACGGATTCCCT 1355
                         i    i  i     ivv  vv  i v  vv          v i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_140558776_   1356 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1405
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_140558776_   1406 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 1455
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_140558776_   1456 AAAGACTTAAACTTTCGACCTAAAACCATAAAAACTCT-GGAAGAAAACC 1504
                          ?    i    iv vv  v       i      -    -i         v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chrX_140558776_   1505 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 1554
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_140558776_   1555 ACACCAAAAGCAATGGCAACAACAGACAAAATTGACAAATGGGATCTAAT 1604
                                     vvi       v   v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_140558776_   1605 TCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 1654
                         iv  v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_140558776_   1655 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 1704
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_140558776_   1705 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 1754
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_140558776_   1755 AACAA----CCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCT 1800
                         i    ----   v  i?    i    ii     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_140558776_   1801 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 1850
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_140558776_   1851 TCACTGGACAT 1861
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (141 / 104)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 2.00 (10 / 5)  


3094 28.30 0.33 0.33  chrX_140612791_140617777.rev     3589  4496 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140612791_   3589 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3638
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140612791_   3639 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 3688
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140612791_   3689 TACCAATGACTTTCTTCACAGAATTGGAAAAAAATACTTTAAAGTTCATA 3738
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_140612791_   3739 TAGAACCAAAAAAGAGCCCACATCACCAAGTCAGTCCTAAGCCAAAAGAG 3788
                          i   viiv  ii  v  viv  vi    iv  i  i i ivv i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_140612791_   3789 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGATTA 3838
                              i      vv   ii  v  ii i      viv        iii  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_140612791_   3839 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATACAGACCAA 3888
                               i   i    ii         i iv ii i   v   i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_140612791_   3889 TGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACCAT 3936
                              i    i--    i  --        vv   i i  i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_140612791_   3937 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 3986
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_140612791_   3987 ATTTAATAAATGGTGCTGGGAAAAATGGCTAGCCATATGTAGAAAGCTGA 4036
                         v  i  i              v  v   v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_140612791_   4037 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 4086
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_140612791_   4087 AAAGTCTTAAATGTTACACCTAAAACCATAAAAACCCTAGAAGAAAACCT 4136
                          ?  v i       v v v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_140612791_   4137 AGGCA-ATACCATTCAGGACATAGGCATGGGAAAGGACTTCATGTCTAAA 4185
                            ?i- v i -   iv   v v  vv i  v  v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_140612791_   4186 ACACCAAAAGCAATGGCAACAAAAGCCAAACTTGACAAATGGGATCTAAT 4235
                                     vvi          vv   v v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_140612791_   4236 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 4285
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_140612791_   4286 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTGCTCATCTGACAAA 4335
                          i     i                 v       viiiivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_140612791_   4336 GGGCTAATATCTGGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 4385
                           i  vi    ii    v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_140612791_   4386 AACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 4435
                         i     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_140612791_   4436 CAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 4485
                          v        i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_140612791_   4486 TCACTGGCCAT 4496
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (149 / 104)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3049 25.66 1.31 2.18  chrX_140621643_140626181.rev     3133  4048 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140621643_   3133 TGTAAAAGTATTCCATGTTTATGGATTGGAAGAATCAATATTGTTAAAAT 3182
                           v   ii   i       i             v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140621643_   3183 GTCTACAC---CCAAAGCAATCTACAGATTCGATGCAATGCCTATCAAAA 3229
                          v v i  ---     vii            i i     v          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140621643_   3230 TATCAATGATATTCTTCACAGAAATAGAAAAA-TAATCCTAAAATTTGCA 3278
                          vi  iiviiv  i  ii       v  v  i- i           iii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_140621643_   3279 TGGAACAACAAAAGACCCAGAATAGCCAAAGCTATCCAAAGCAAAAAGAA 3328
                              vvi   ii                 i v   ivi iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_140621643_   3329 CATGACTGGATGAATCATATTACCTGACTTTAAATTATGCTACAGAGCTA 3378
                           viii    v  v   i i v  ii i  i   viv i     i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_140621643_   3379 TAGTAACCACAACAGCCTGATACTAACATAAAAACAGACACATAGATTAA 3428
                         i     i  vi    iv  i    ii     ii i     i      i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_140621643_   3429 TGAAACAGAATAAAGAACACAGAAACAAATCCACACACATATAATAAACT 3478
                           i  i     vi   iiv      i   i   i   iv   ii v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_140621643_   3479 CATTTTTGACAAAGATGGCAAGAACATACACTGGAAAAAAAGACAGACTC 3528
                         v     i     i i  v     v   v  v   ii   i - i  v  i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTT 399

  chrX_140621643_   3529 GTCAATAAATAGTGCTGGGAAAACTGGACATGCTTATGCTGAAGAATGAA 3578
                         v    i    i         v       i ?v vi    vi         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_140621643_   3579 ACTGGAGCCCTAT-TCTCACCATATTCAAAAATCAAATTAAAATGGATTA 3627
                         ii    v     i-  v        v       i  v i         i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_140621643_   3628 AGGGCTTTAATATAAGACCTCAAGCTATGAAACTACAACAAGACAACTTT 3677
                         ?i i i v   i     v  v  i    i     viv v    v   v v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_140621643_   3678 GGGGAAAATCTCCAGGACAATGGTCTGGGCAAATATTTCTTGAGTAATG- 3726
                           ? v      i iv   vv   vi i     vvi      iii  -  -
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGA 598

  chrX_140621643_   3727 CAACACAGGCACAGGCAACCAAAGCAAAAATGGACATATGGGATCACATC 3776
                           v  v i     i     v    v      i  i v  v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_140621643_   3777 AAG-TTAAAAAGTTTCTGCACAGCAAAGGA-ACAATCAACAGAGTGAAGA 3824
                           i-       v   -  ii vv       -  v     v i      i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_140621643_   3825 GACAGC----AGAATGGGAGAAAATATTTGCAAACTACCCATCTGACAAG 3870
                             i ----                        ii ivi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_140621643_   3871 GGTTTAATAATCAGAATATATAAGGAGGTTAAACAATTTTATAGGAAAAA 3920
                           vi vi  vi            i  iv ivv    i iv   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_140621643_   3921 ATCTAATAATCCTGTCAAATCTAATAATCCTATTCAAATCCTACCAAATA 3970
                         iv v     i  -----   i?  -----------    vv-i v  iv 
  L1M4_orf2#LINE/    798 GACAAATAACCC-----AATTWAA-----------AAATGG-GCAAAGGA 830

  chrX_140621643_   3971 TTTGAATAGACATTTCTCAAAATAAGACATACACATGAAAAATAGGCATA 4020
                                           v   v    i     v   ivv    i   i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_140621643_   4021 TGAAAAAGTGCTCAAAATCACTGATCAT 4048
                               ii       v    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (139 / 92)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.46 (32 / 13)  


2104 21.41 4.72 15.52  chrX_140661013_140663456      934  1951 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140661013_    934 TGAAAAAAAATTACTTGTTTATGGATTGAAAGAATTAATATTGTTAAGAT 983
                           i   i v  iv v    i        i    v                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140661013_    984 GGTCATACTGCCCAAAGCGATTTATAGATTCAATGTTATCCCTATCAAAC 1033
                           iv     v      vi   i  i        i iv            v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140661013_   1034 TGCCAACATCATTCTTTACAGAAGTAGAAGAAACT-ATTCTAAAATTCAT 1082
                          v   i vv v  i   i     i v  v-  i  -  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_140661013_   1083 ATGGAA-TCCAAAAAGAGCCTGAATAGCCAAAGCAATACTAAGGAAAGGA 1131
                               - v   ii-  v  v           i    -------------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAAT------------- 185

  chrX_140661013_   1132 CAAATACCTGAGGTGATGTATACCCCATTTACTTTGATGTAATTATCATG 1181
                         --------------------------------i    -------------
  L1M4_orf2#LINE/    186 --------------------------------CTTGA------------- 190

  chrX_140661013_   1182 CATTGCATGTCTGTATCGAAATATCTCATGTACCCCATAAATGGATACAC 1231
                         --------------------------------------------------
  L1M4_orf2#LINE/    191 -------------------------------------------------- 190

  chrX_140661013_   1232 CTAATATGTACTCACAAAAATTAAAATAAATACATTTATAGAAAGAACAA 1281
                         ---------------    i----------------------        
  L1M4_orf2#LINE/    191 ---------------AAAAG----------------------AAGAACAA 203

  chrX_140661013_   1282 AGTCAGAGGCCTCACATTACCCAGTTACAAACTATACTATAAGGCTACAA 1331
                            ii    v      i v    i  v    viv     i  i      i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_140661013_   1332 TAACCAAAAAAACATGGTAGTGGTATAAAAACAGACACACAGACCAATGT 1381
                            i   i v iii     v   i    ii i     i i   i     v
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_140661013_   1382 GTCTCTTACAGAAAAGAAAACTCAGAAATAAAGTCACACACCTCCAATCA 1431
                         i------ i    vv  i iii          vi  i   ii viii   
  L1M4_orf2#LINE/    304 A------ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_140661013_   1432 TCTGATATTTGACGAGGCCAACGAAAACAAGCAGTGGGGAAAGGACCCCT 1481
                         vi    v  i   i   viiv i i v  vv  i         i ivvii
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_140661013_   1482 TGTTCAATAAATAGTGCTGGGATACCTGGCTAGCCATATGCGGAAGAATG 1531
                          v     i    i         i v    v  ?   i    ii       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_140661013_   1532 AAACTGAACCACTACCATTCATTAAATATATAGAAATTAACTCAAGATGA 1581
                           ii  i   v     --   ivvv     i i            i   i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACC--TCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_140661013_   1582 ATTAAAAATTTAAATGGAAGACCTCAGACTATAAATATCCTAAAAGAAAA 1631
                           i ? i ii      v    v  v i        vv  i  i       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_140661013_   1632 CCTAGGAAACACTTTTTTTGACATTGACTTTGGCAAATAATTTAT-GGCT 1680
                          v    ?ivv v i  iv    v   iv  v     - ii   v -i v 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT 594

  chrX_140661013_   1681 AAGTCCCCAAAAGCAACAGCAATAAAATCAAAAATTGACAAGTGGGACCT 1730
                          v v v         vv     i    vv      v  i  i v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_140661013_   1731 ------AATTAAA------------TTAAAGAGC-----CAAACAGAGTA 1757
                         ------       ------------ i    ii -----   i- i   i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTG 693

  chrX_140661013_   1758 AA----CAGCCTACAGAATGGGACAACATATTTGTAAACTATGCATCTAA 1803
                           ----  i  i           v  v       i   ii  ii    i 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_140661013_   1804 CAAAGGTCTAATATCCAGAATCTATAAGGAACT------------TAATA 1841
                         i  i  v  vi          v     i     ------------     
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_140661013_   1842 AG--GAAAAATCAACCCTATT--AAAATTAGTAAAGGACATAAGCAGACA 1887
                          i--  v    -     v   --     vi i      iv i ii     
  L1M4_orf2#LINE/    794 AAAAGACAAAT-AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_140661013_   1888 CTTCTCCAAAGGAGACATGAAAGTAGCCAACAAACAC--GAAAAATTGCT 1935
                         i          i   i  iv  i i     i  i   --     iv    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_140661013_   1936 CAGCATCACAAATCAT 1951
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (134 / 81)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 9.81 (206 / 21)  


2721 26.52 2.98 2.65  chrX_140674029_140675999      575  1479 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140674029_    575 TGGAAAGACATCCCATGCTCATGCACCAGAAGAATTAATATAATTAAAAT 624
                                 i        i     v iii     v       vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140674029_    625 AACCATACCTGCCAAAGAAATCTACAGATTCAGTGCAATTTCCATCAAAA 674
                         ii v    iiv     vvi             ii     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140674029_    675 TATCAA-TGCCGTTTTTCACAGAATTAGAAAAAA-AATATGAAAATTTGT 722
                          vi  i-    -     ii     v v  v  iv-i  viv      ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_140674029_    723 ATGGAGCCAAAAAAGAGCCACAATAACCAAAGTAATCCTCAGCAAAAAGA 772
                              iviiv  ii  v   v    i     ii    i v iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_140674029_    773 GAAAAGCTGGAGGCGTAACACTACCTGACTTCAAAA--TATTGTATAAGC 820
                         iv    i      vv v     v  ii i       --  i ii -    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA-AAGC 248

  chrX_140674029_    821 TATAGTAACCAAAACAGCATGGCATTGATATAAAAAGTAGACA------- 863
                           i     i   i    ii   i i  ii    ii -      -------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGAT 297

  chrX_140674029_    864 CAATGGAATGAAATGAAAAACCCAAAAACAAATCCATATATTTACAACCA 913
                                  ii   vi i ii   i   i   i     i     iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_140674029_    914 TCTGATCTTCAACAAAGCCATCAAGAACATACACTGGGGAAAGGGCAGCC 963
                         vi    i   i    i viii     v   v  v         iii  i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_140674029_    964 TCTTCAGTAA-TGGTGCTGGAATATGTGGATAACCAGATGCAGAAGAATG 1012
                          i    ii  -         i i vv      ?   v     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_140674029_   1013 AAACTGGACTCCTACTTTTTACCATATACAAAAATCAACTTGAGATAAGA 1062
                           ii     i     i ivi               i    ii i  iiiv
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_140674029_   1063 CAACTGAAGATTTTACTTAAAGGTAAAACCTGAAAGTATAAAACTACTGG 1112
                           ?----   ----- i    v    i v  i   v         vi i 
  L1M4_orf2#LINE/    498 CAW----AGA-----CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_140674029_   1113 AAGAGAATA-AGGAA-AGCTCTTCAGAACATTGGTCCAGGCAAAGATTGT 1160
                             i  i -   ?i- iv     ivi  v    vii      v i  vi
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_140674029_   1161 ATGGCTAAGATTTCAAAAGCAAATGCAACAAACACAAAAATAGGCAAATG 1210
                         v i v  v  ivi        v v        viv        ii    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_140674029_   1211 GGACTATATTACA-CTAAAAAGTTTC-TGCTCAGCAAAGGAACCAATAAA 1258
                              vi  i v -i      v   i-    i--       vv v  v  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAA 686

  chrX_140674029_   1259 CAAAGTGAAGAGACAATTCCCTTCCTTGAAAGGAAGAAAATATTTGCAAA 1308
                         v        i      ii v v-----   v  i                
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACA-----GAATGGGAGAAAATATTTGCAAA 731

  chrX_140674029_   1309 TGATTTATCCAACCAGGGACTACTACTGAGCATATATCAGGAAGTCAGAC 1358
                          v  v    ii iv       vv  iiv  v      v i   v  vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_140674029_   1359 AACTCAACAATTTTTTAAAA----------TCCCATTAAAAAGTAGACAA 1398
                                i   -----    ----------i  v   ?    i i i   
  L1M4_orf2#LINE/    782 AACTCAATAAT-----AAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_140674029_   1399 ATGACACGAATACACATTTATCCAAAAAAGACATACTAATGGCCAACAAG 1448
                          v  ivi     v      v      i    i    v         i   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_140674029_   1449 TATGGGAAAA-ATGCTTAATATCTCTAAGCAT 1479
                         i iiv     -     i  i   v????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (151 / 85)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.68 (51 / 19)  


 246 22.73 1.52 0.00  chrX_140686468_140688414      434   499 (1448)  C L1M4_orf2#LINE/L1   (666)   242   176  

C chrX_140686468_    499 CTAAAACAATTTTTAAAAAGA-CAGTGAAGTTGGAGGAATCACACAACCC 451
                          i        i  v       -v iii           v      vv   
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

C chrX_140686468_    450 AATTATATTATTTACTA 434
                             vi vv i      
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTA 242

Transitions / transversions = 0.88 (7 / 8)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1)  

2347 24.61 5.59 4.03  chrX_140686468_140688414      562  1455 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140686468_    562 TGAAGGGATATTCAATTTTCAAGGATAGAAAGACTCATTATTGTCAAGAT 611
                           i ii     i v  v    v    v i      i v      i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140686468_    612 GTCAAT----TCTAACTTGATCTATAGATTGCCTAA---AATCCCAGTCA 654
                          v    ----i i  v        i     ---i  ---      vi   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT---CAACGCAATCCCTATCA 97

  chrX_140686468_    655 AAATCCTAGCATGT-TGTTTTGTGGATACCAACAAACTTATTTTAAGGAC 703
                               i   -  i- v     ii  v iii    i  v  i------- 
  L1M4_orf2#LINE/     98 AAATCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATC-------C 139

  chrX_140686468_    704 TAAAATATGTTTTATGTGGAAAGGCAAAAGACTAAGATTAGCCAACACAA 753
                               ----- i  i      v    ii   iv   v       v    
  L1M4_orf2#LINE/    140 TAAAAT-----TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_140686468_    754 TATTAAAGAAGAAGA-CA--GTGGGAAGACTAACACTTCCCAACTTCAGG 800
                          v  i  i       -  --  v   i    v           i    ii
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_140686468_    801 TCTTACTATAAAGTTACGATAATTAAGACAGTGTGATATTAAAGAAATAA 850
                         v       i    i   ii    i           i  i iiviv  vi 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_140686468_    851 TAGACAAAAAAGTCAAAGAAATGCAATAGACATCCCAGAAATAGACCTAC 900
                               v v ii    v i   iv   v  v vi         i   i i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_140686468_    901 AGAAATATAGTCAACCAACTTTTGACAAGGA-ATCAGAGGCATTTAA--- 946
                          v vv   i     iii i   i       i-ii  iiiv    i  ---
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_140686468_    947 ATTAAGAATAATCTTTTCAGCTAATTATACCAGAACAAGTGGACATCCAC 996
                         ivv       i        i v   vi i ii i    v    i ?    
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_140686468_    997 ATGGAGAA-AATGAAGTTAGGCACAGACCTTAAACTCTTCACAAAAGCTC 1045
                            v i  -         i i v vv    i v  iv vi      ii v
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_140686468_   1046 ACATAAATTCAATCACAGACCTAAATGTGAAAATAAAATTTTAAAAAACC 1095
                           vi   v vi    ?            i i ii-------     --- 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-------TAAAA---C 524

  chrX_140686468_   1096 TATGAAACACATAGAAGATACCACAGGGGAAAACCTAAGTAACTATGGTT 1145
                            i    v v       v v  i   ? v   i  vv  i  iv   v 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_140686468_   1146 CGAGAAA--ACTTCTTAGATACAAC-CCAAAA-----AGGAACATCTGTG 1187
                         iii v  --ii          ii  -      -----  v    ------
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA------ 618

  chrX_140686468_   1188 AAAGAAAAAATTGATAAGTTTGGCTTCATAAAAATGAAAAAATTCTGT-- 1235
                                    v     i  v i      v     v     v  i   --
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_140686468_   1236 -TAAGAGAACA------AAAAGGAAAAACGAGAA---AC-GA---GGATA 1271
                         - v i  i   ------ i  i vi   v  v  ---  -  ---   v 
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chrX_140686468_   1272 AAAGTTTTGCAAA--AAAAATCTGACTGAAGATGTGTATCAAAAATATAT 1319
                            vv        -- v v      iviii  iv      v i       
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_140686468_   1320 TCAGAACCCT--CAACTCAATAACAAGAAAGCAA----TCCAAT--AAAA 1361
                         vv     i  --           i  i  ii   ----i     --    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_140686468_   1362 ATGGACAAAAGATCTGAGTAGATACACACTACACCAAAGAATATATACAC 1411
                             i    i   i   i    ----  i v v        v       v
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGA----CATTTCTCCAAAGAAGATATACAA 864

  chrX_140686468_   1412 ATTGCAAATAATCATGTAAAAAGATGATTAGCATCTTATGTCAC 1455
                           v  v     v  ii i        v i i    v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (129 / 88)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 3.07 (86 / 28)  


3394 24.61 1.32 1.10  chrX_140738624_140742867.rev     2853  3758 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140738624_   2853 TGGAAAGGTATTCCATATTCATGGATTGAAAGAATAAATATTGTTGAAAT 2902
                                i   i    i           i    v v         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140738624_   2903 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCACTGTCTTTCAAAA 2952
                          v v     v      vii              i   v vi  v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140738624_   2953 TACCAATGACATTCTTCAAAGAAATAGAAAAAAAAGTATCATAAAATTGA 3002
                          v   iivi v  i  iiv      v  v  ivvi--   v       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCA 148

  chrX_140738624_   3003 TATGAAATCCCACAAGATTCAGAATAGCCAAAGCTATCCCAGAAA----G 3048
                             i  viv  vii  ii             i v   iiii   ---- 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_140738624_   3049 AACAAATCTAGAGGAATCACATTACCTGACTTCCAATTATGCTACAGAGC 3098
                               vi i     v     i v  ii i   v  viv i     i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_140738624_   3099 TATAGTATAATAACCAAAATAATATGGTTCTGGCATAAAAAGAGACACAA 3148
                           i    ----- i   i i i i    v         ii v     i v
  L1M4_orf2#LINE/    249 TACAGTA-----ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_140738624_   3149 AGATCAATGGAACAGAATGAAGACCCCAGAAACAAATCCATGCACCTACA 3198
                                     i     vi   vi       i   i    i  ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_140738624_   3199 GTGAACTCATTTTTAACAACGATTCCAAGAACATACATTGAGGAAAGGGC 3248
                           v  i v     ii    v i v      v   v  v  i      iii
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_140738624_   3249 AGTGTCCTCAATAAATTATGCTGGGAAAACTGGATATTCATATGCAGAAG 3298
                            v ii    i    vi        v         ?i  i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_140738624_   3299 AACGAAATTAGAACCCTATCTCTTGCCACATATAAAAGTGAAATACAAAT 3348
                           i   i  i  v     i   vii   i   i    i v  v vv    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_140738624_   3349 GGATTAAATACTTAAATCTAAGACCTGAAACTATGAAACTACTCAAAGAA 3398
                             i ? v  i     v     v  i       i     vi vi     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_140738624_   3399 AACATGGTGAGAAACTCTCCAGGACATTTGGCTGGGCAAGGACTTCTTGT 3448
                              i - ? v  v   i iv   v  v  i i     v ii     iv
  L1M4_orf2#LINE/    544 AACATAG-GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_140738624_   3449 ATAATACCCCACCTGCACAGGTAACCAAAGCAAAAATGGACAAATGGGAT 3498
                            vv  v   vvv     i i   v    v      i  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_140738624_   3499 CTCATCAAG-TTAAACAGGTTCTGCACAGCAAAGGA-ACCAGTCACCAAA 3546
                         i       i-     - iv  i  ii vv       -  i -   vv   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTA-TCAAGAAA 690

  chrX_140738624_   3547 G-----AGACAATCCACAGAATGGGAGAAAATATTTGCAAACTACATATC 3591
                          -----      i                            ii i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_140738624_   3592 TGACAAGGGATTAATAACCAGAATATATAAGGAGCTCAAACAACTCTACA 3641
                            i      i vi  v             i  i   vv       v i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_140738624_   3642 GGAAAAAATCTAATAATCCAGT-AAAAAATGGGCAGAAGATTTGAATAGA 3690
                         iv     iv v     i   i -?           i i            
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_140738624_   3691 CATTTCTCAAAAGAAGACATACAAATGGCAAACAGGTATATGACTAGGTG 3740
                                 v        i           v  i i i i    vv  i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_140738624_   3741 CTCAAAAACATTGATCAT 3758
                              v v  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (129 / 90)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.20 (22 / 10)  


1388 20.27 1.35 5.41  chrX_140759486_140764029.rev     2790  3159 (1385)    L1M4_orf2#LINE/L1        1   355 (553)  

  chrX_140759486_   2790 TGGAAAGATATCTCATGCTCATGGATTAGAATATTTAATATTGTTAAAAT 2839
                                     i    i         i   v i             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140759486_   2840 GTCCATACTACCCAAAGTGATCTACAGATTCCATGCTATCCCTATCAAAA 2889
                          v v     v      v              v i  v             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140759486_   2890 TTCCA-CTGACATTTTTTCACATAAGTTAAAAAAGAAAAAAAAAATTCTA 2938
                          i   -   v --     ii  v  i  i v  ivvi ------- i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGA-------TCCTA 141

  chrX_140759486_   2939 AAAACCTTATGGAACCACAAAAGACTCAGAATAACCAAAGCAATCTTGGG 2988
                            vi v       vii   ii   i       i     i        ii
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_140759486_   2989 CAA-AACAACAAAGCTGGAGGCCTCAAAGTACCTGACTTCAAAATATACT 3037
                         v  -  v       i      v    v v v  ii i       iv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_140759486_   3038 ATAAAATATAGTAAAGTATAGTAGTACCAG-CAAGGTACTACTGACATAA 3086
                          i   ii---------  i    i - v  -  iv  iv     i     
  L1M4_orf2#LINE/    242 ACAAAGC---------TACAGTAAT-CAAGACAGTGTGGTACTGGCATAA 281

  chrX_140759486_   3087 AAA-AGAGACATACATCAATGGAATAGAATAGAGAACCTAGAAATAAATC 3135
                         ii -   v i   v                v    ii i         i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chrX_140759486_   3136 TGTACATTTACTGG-CAATTTATTT 3159
                         ii        -   -     v    
  L1M4_orf2#LINE/    332 CATACATTTA-TGGTCAATTGATTT 355

Transitions / transversions = 1.59 (46 / 29)
Gap_init rate = 0.03 (10 / 355), avg. gap size = 2.50 (25 / 10)  

2526 21.91 0.18 0.35  chrX_140759486_140764029.rev     3488  4053 (491)    L1M4_orf2#LINE/L1      344   908 (0)  

  chrX_140759486_   3488 GTCAATTTATTTTTGACAAAGGTGCCAAGAATACACAATGGGGAAGGAAC 3537
                                v     i     i          vi iv          i   i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_140759486_   3538 AGTTTCTTCAAAAAATCGTGTAGAGAAAACTAGATATCCATGTATACAGA 3587
                            i i     v    v   iv i  v    i    ?   i--  i  i 
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC--ATGCAAA 441

  chrX_140759486_   3588 AGAATGAAATTAGACCCTTATGTCACACCATATACAAAAATTAACTCAAA 3637
                                 i  i     i  iv                            
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_140759486_   3638 ATAAATCAAACACTTACATGTAAGAACTGAAACTATAAAACTACAAGAAG 3687
                           ii    ? v  i  v        i  i             viv     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_140759486_   3688 AATACATAAGGGAAAATCTCCATAACATTGGTCTGGACAATGAGTTTTTG 3737
                           v     i ? v      i i i  v    vi i i     iv  i  i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_140759486_   3738 GATATGGCCCCAAAAGCACGGGCAACAAAACCATAAATAGACAAATGGGA 3787
                               i v          ii         vv v       i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_140759486_   3788 TTTCATCAAACTAAAAAGCTTCTTTGCAGCAAATGAAACAATCAAGAGAG 3837
                         i         v v    i   i v   vv    v  v  v       i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_140759486_   3838 TGAAGATACTACCTCCAGAATGAGAGAAAATATTTGGAACCTGTATATCT 3887
                             i v  v   iv       i             v  viii       
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_140759486_   3888 TATCAGGGGTTAATATCCCACA-ATATAAGGAACTTGTACAACTTTATAA 3936
                         v  v    ii vi     viv -      i     iv       iv    
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_140759486_   3937 AAAGAAAACAAATCACCACATTAAAAAATGGGCTAAGGGCCTGAATAGAC 3986
                         v  i  i      v   vv   ?          v    iii         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_140759486_   3987 ATTTCTCAACAGAAGACATACAAATGGCCAACAGGGATATAAAAAAGTGT 4036
                                v v      i              i i v i  i    ii  i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_140759486_   4037 TCAATGTCACTAATCAT 4053
                             ii   ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (70 / 50)
Gap_init rate = 0.00 (2 / 565), avg. gap size = 1.50 (3 / 2)  


2832 27.10 1.22 0.77  chrX_140789790_140794070.rev     2887  3790 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140789790_   2887 TGAAAACACATCCCATGCTCATGGGTGGATAGAATCAATACTGTGAAAAT 2936
                           i   v i        i      i v iv   v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140789790_   2937 GACTATACTGCCAAAAGCAATCTACAAATTCCATGTAATTCCCATAAAAA 2986
                          i v     v  v   vii       i    v i i   i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140789790_   2987 TACCACAATTA--TTCTTCACAGAACTAGAAACAGACAATCCTAGAATTC 3034
                          -  -  ii i--  i  ii     v v  v -  vii      i     
  L1M4_orf2#LINE/    101 T-CC-CAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTC 147

  chrX_140789790_   3035 ATATGGATCCGAAAAAGAGCCTACATAGCCAAAGCAAAACTAAGAAA-AA 3083
                                vvi v  ii  v  viv         i   vvi i i   -  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_140789790_   3084 GAACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATGCTATAAGT 3133
                                vi      vv     i v  ii i      viv i   i  iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_140789790_   3134 CTATAGTCACCAAAATAGCATGGTACTGATATAAAAACAGGCACATAGAC 3183
                            i   v i   i i  ii        ii    ii i  i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_140789790_   3184 CAATGGAACAGCATAGAGAACTAAGAAATAAAGCCAAATACTTACAGCCA 3233
                                 i  v  v    iiiv         v   v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_140789790_   3234 ACTCATCTTCCACAAAGCAAACAAAAACATAAAGTGGAGGAAAGGACACC 3283
                          i v  i   v    i vviv   i v   vv i   -      i i vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGT 396

  chrX_140789790_   3284 CTATTCAACAAATGGTGCCGGGATAATTGGCAAGCCATATTCAGAAGAAT 3333
                           v               i    i  i   vv ?   i  v  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_140789790_   3334 GAAACTGGATCCTCATCTCTCACCTTATCAAAAAACCAACTCAAGATGGA 3383
                            ii    i  ii i   v    v   vv     ii       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_140789790_   3384 TCAAAGACTTAAATCTAACACCTGAAACCAAAAAATTCT-AGAAGATAAC 3432
                            ?    i     v   v v  i    i v    i   -      v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_140789790_   3433 ATTGGAAAAACCCTACTAGACATTGGCTTAGCCAAAGACTTCAT-GACCA 3481
                           v  ?iv  vi  v vv   v    v    v   v ii   v -  i--
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-- 594

  chrX_140789790_   3482 AGGAC-CCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGAGACTT 3530
                          v   -         v v         iv   i   i   i  vi     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_140789790_   3531 AATTAAACTAAAAAGCTTCTGCACAGTAAAAGATATAATCAGCAGAGTTA 3580
                         v  i   v v    i   i  ii vvi   i  i iv    iv i   v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_140789790_   3581 ACAGACAACCCACAGAGTGGGAGAAAATCTTTGCAAACTATGCGTCTGAC 3630
                          v              i           v        ii  iii     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_140789790_   3631 AAAGTACTAATATTCAGAATCTACAAGGAACCCAAACAAATCAGCAAGAA 3680
                           i v   vi   i      v  i  i    i vv    v   ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_140789790_   3681 AAAAACAA----TCTCATCAAAAAGTGAGCAAAGGACAAGAATAGACAAT 3726
                            i    ----i iv  i?    i  i        ivv         v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_140789790_   3727 TCTCAAAACAAGATTTAAAAAATGGCAAACAAGTGTATAAAAA-ATGTTC 3775
                             v   v     v  v   -    v  i   iii  i    -   i  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAA-TGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_140789790_   3776 AACATCACTAATTAT 3790
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (141 / 100)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.38 (18 / 13)  


 456 30.56 0.69 1.39  chrX_140821579_140825058.rev     1805  1948 (1532)    L1M4_orf2#LINE/L1        1   143 (765)  

  chrX_140821579_   1805 TGGAAAAACATTTTATGCTCATGGATAGGAAGAATCAAGATTGTTAAAAT 1854
                               i i  iii   i        v      v i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140821579_   1855 GGCCATACTTCCCAAAGCAATTTATACATTCAATGTGGTTTCTATAAAAC 1904
                            v     i      vii  i  i v      i iii ii    v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140821579_   1905 TACTAATGACACTTTTCACAAAGTTAGAAAAATACT-ATCCCAAA 1948
                          v i iivi vi    ii  i iv v  v  i--  -    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAA 143

Transitions / transversions = 2.14 (30 / 14)
Gap_init rate = 0.01 (2 / 143), avg. gap size = 1.50 (3 / 2)  

2199 25.51 2.79 3.05  chrX_140821579_140825058.rev     2213  3000 (480)    L1M4_orf2#LINE/L1      123   908 (0)  

  chrX_140821579_   2213 AATTAA-AAACT-ATGCTAAAATTCATATGGAACCATAAAGGTGGCTTAA 2260
                             i -  i  -  v                 viii  i  vvv vv  
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chrX_140821579_   2261 TAGTCAAAGCAAACTTAAGCAAAAAGAACAAAGCTGAAGGCATCAAATTA 2310
                            i    i   v   i iv  i          i  i   vv   v i v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chrX_140821579_   2311 CCTGATTTCAAACTATAGTACAACGCTGCAATAACCAAAACTACATGGTA 2360
                           ii        viv  v     v   i  i   i   i  viii     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_140821579_   2361 CTGGCACAAAAGCAGACACATAGACCAAGGGAATAGGTTGAAGAACACAG 2410
                               i  iiii     i     i   v       iv vi   iiv   
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_140821579_   2411 AAGTAAAGCCACACACCTACAAACATTTGATATTCGACATAGTTAACAAA 2460
                           i    v   i   ii  iiiv  v     v       vi v iv   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_140821579_   2461 AACAAACAATCCGGAAAAGACT--TCCTATTGAATAAATGGCACTAGAAT 2508
                          v  vv    v-  i     v --  i -  v  i      ii  i i i
  L1M4_orf2#LINE/    373 ACCATTCAATG-GGGAAAGAATAGTCTT-TTCAACAAATGGTGCTGGGAC 420

  chrX_140821579_   2509 AACTGGCTAGCCATGTACAGAAGATTGAAACTGGCTCACTTACTTT-CAA 2557
                               v  ?   ii i  i    v    ii   vi - i   i i-  v
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC-CCTACCTCACAC 469

  chrX_140821579_   2558 CATATACAAAAATTAACTCAAGATGCATTAAAGACTTCAATGTAAAACCT 2607
                                              i   v  i ?    i v       i v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_140821579_   2608 AATACTATAAAAACCTTAGAAGAAAACCTAGG---ACATGCTATTCTGGA 2654
                           v         vi             v    --- v  -  - iv  iv
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CT-TCGTGAC 567

  chrX_140821579_   2655 CACAGGCCCTGCAAAGATTTCATGACAAAGACACCAAAAGCAATTGCAAC 2704
                          vii  iivv    v i    v iivv v             vvv     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_140821579_   2705 AAAAACAAAAATTGACAAGTGGTACCTAATTAAATTCAAGAG----TGT- 2749
                             iv      v  i  i v v  i v  i   v i  i i----   -
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_140821579_   2750 CTCCACAGAAAAACAAAACAAAACAAACAAACTATCAACAGAGCAAACAG 2799
                           i  ---  ii   ----------------       v i  ii  v  
  L1M4_orf2#LINE/    668 CTTCA---AAGGACA----------------CTATCAAGAAAGTGAAAAG 698

  chrX_140821579_   2800 ACAGTCTACAGAATGGAAGAAAATATTTGGAAACTATGCATCTGACAAAG 2849
                            ii i         i            v   ii  ii      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_140821579_   2850 ATCTAATATCCAGAATCTATAA-GAA-TCTTA-AATT-AATAAGCAAAAA 2895
                         iv  vi          v     -   -     -  i -     vv    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_140821579_   2896 AAAAAT---CCA-TTAAAAAATGGGCACAGGATATGAATAGACACTTCTC 2941
                          v    ---   -  ?           v     v          i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_140821579_   2942 AAATGGAGACATGCATGCAGTCATCAAGCATATGAAAAAAATCT-AACAT 2990
                         v  v i   i  i  viii i  vi     i       i vv  -     
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_140821579_   2991 CACTAATCAT 3000
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.41 (116 / 82)
Gap_init rate = 0.03 (21 / 786), avg. gap size = 2.19 (46 / 21)  


 715 24.08 3.66 1.05  chrX_140825597_140829216.rev      133   323 (3297)    L1M4_orf2#LINE/L1        1   196 (712)  

  chrX_140825597_    133 TGAAGAGAAATTCTGTGCTCAAACATTGTAAAACTTAATATAGTTAAGAT 182
                           i i   v  i ii  i   viv    v  i         v        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140825597_    183 GTCAATG-TCCCCAAATTGAT-TATAG-TTTAACACAATC----TCGAAG 225
                          v    i-             -  i  -  i   i     ----  i  i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140825597_    226 TCCCAATAGGATTTTTTTTGTAGATATAGACAAGCTGATTCTGAAATATA 275
                              iiv --ii       i   v  v           i  i    vi 
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_140825597_    276 TACAGAAAGGTAAAGGAACTAGAATAATCAAAACACTTCAGAAAAAAA 323
                           ii    v i  i   v i      ii       v iiv      i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

Transitions / transversions = 2.29 (32 / 14)
Gap_init rate = 0.03 (5 / 196), avg. gap size = 1.80 (9 / 5)  

1842 25.59 4.59 3.25  chrX_140825597_140829216.rev     1978  2653 (967)    L1M4_orf2#LINE/L1       15   699 (209)  

  chrX_140825597_   1978 ATATACATGGATTGGAAGAC--AATCTTCTTAAGATTTCTATTCTTCCCA 2025
                           i v               --   v  v       vv v  v  i    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_140825597_   2026 AATTAATCTGTAGCTTCAATGTATTCCCAGCCAAAGCCTAGGCAGGCATT 2075
                             i    ii  v     i i v    vii    ii ivi  v v v  
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_140825597_   2076 TTTACAGAGATTAACAAACTCACTTTAAAATTCAAATTAAAATTCAAGGG 2125
                            i    i   i    i  v iii         v  vi    v      
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_140825597_   2126 -CCTAGAACAGCCAAACCCATTTTGACAAGGAAGAAGAAAGTTAGAGGAC 2174
                         -  i    i       v v  i    v  i      v      i      
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_140825597_   2175 TTCATCCATCC-ATCTTCAATATATATTTTAAAGGCATAATAATATAGAA 2223
                          -  iv v   - vi     v iv  i vi    vi i i    vv   v
  L1M4_orf2#LINE/    215 T-CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chrX_140825597_   2224 AATGTAGCACTGGCGTAAGGATAAACAAATAGATTAA-AGAAGAGAATAG 2272
                          i   i i      i        i   v      i  -i   v     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_140825597_   2273 ACATTCTTGAAGCAGACCCACACATACACAGTCAATTGATTTCCAACAAT 2322
                          v v  iv   ii i     i    vi ii            i i    v
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_140825597_   2323 AGTCCTAATAAAATTAAATGGGAAGAGGAAAGTGTTTTCAACAAATGGTG 2372
                         i  v i  v vv   v      i i  i v   v                
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_140825597_   2373 CTGGATGAACTGGATATT-A-ATGCTAAAAAATTAA--TGAATCAACAAC 2418
                             ivv         ?i- -    v   i   v  --  i i ------
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC------ 457

  chrX_140825597_   2419 ATCACCTACCTTACACCTTATAGAAAACTTAGTTTAAGATGGATTACAAA 2468
                         ----       i     v    v    v   ii i  i      i ? i 
  L1M4_orf2#LINE/    458 ----CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_140825597_   2469 CTTACATGTAAAAGTTAAAA---TAAAGTTGTTAGAAGAAAA-------- 2507
                          i  v      i  i     ---    ii v           --------
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_140825597_   2508 TACATATT--TGATATTATGATTAGCAAATC-TTTATTAG----GACACA 2550
                           v  v  --   iv  i- i    vv   v-   v    ----     v
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_140825597_   2551 AATGGCATTGTGCTGAAAATAATATAAAAAGAAATA----AATTGGACAC 2596
                           vi   i--------  ii  i v  i  i     ----        vi
  L1M4_orf2#LINE/    603 AAAAGCAC--------AAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_140825597_   2597 AGTAAAAAAAAAAAAAATCCCTGCTTATAGAAGGATGTCATTAAGAAAAA 2646
                         vi v    vv     vv iiv     -i -     iiii  i      iv
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTT-CA-AAGGACACTATCAAGAAAGT 692

  chrX_140825597_   2647 AAAAAAA 2653
                         i    i 
  L1M4_orf2#LINE/    693 GAAAAGA 699

Transitions / transversions = 1.28 (96 / 75)
Gap_init rate = 0.03 (19 / 685), avg. gap size = 2.79 (53 / 19)  

 211 27.46 17.62 1.55  chrX_140825597_140829216.rev     2937  3129 (491)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_140825597_   2937 AGGAAAAGAAAAAGTTAAATCATAAACTAGGC-AAAATATTTGAAATTCT 2985
                          i    ivi     vi  vi  i i v i  v-          v  v  v
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_140825597_   2986 TGCATCTGACAAAG----TGTAT---GAATGTTTAAAAAATTCTTGAAAA 3028
                          ii      i  i ----     ---    i v    i  i    iv  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_140825597_   3029 TTAATAACAA-----CAAA--------------AATGGAAAAAAAGTTTG 3059
                          i     i  -----    --------------     iv   iii    
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_140825597_   3060 AACA-------CTTTAAAAAATAATATAGAAGAATAGCCCATAAGTTTAT 3102
                           i -------  ii   i  -i     v  --  i   v     ivi  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAA-GATATACAA--ATGGCCAATAAGCACAT 881

  chrX_140825597_   3103 CAACAAATATTTAAGATTATATTAATT 3129
                         v  v i  ii i  v  i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (35 / 18)
Gap_init rate = 0.04 (8 / 224), avg. gap size = 4.62 (37 / 8)  


2558 26.32 3.41 2.23  chrX_140873047_140877479.rev     3088  3938 (495)    L1M4_orf2#LINE/L1        1   861 (47)  

  chrX_140873047_   3088 TGGAAATACATCTCATGCTCATGGATGGGAAGAATCAATATTGTGAAAAT 3137
                               v i   i    i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140873047_   3138 GACCACAGTGCCAAAAGCAATCTATAGATTTTATGAAATTTATATCAAAA 3187
                          i v i v v  v   vii     i     iv i v   iiv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140873047_   3188 TACCATCCTCGTTTTTTA-AAAAAT-------------CTAAAATTTATA 3223
                          v   v iv v      i- i    -------------        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_140873047_   3224 TAAAACCACAAAAG-CCTATAA-AGCCTAAGCAATACTAAGCAAAAAGAA 3271
                          ii  vii   ii -  i v  -    v  i    vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_140873047_   3272 CAAATCTGGAGGAATCACATTATCAAACTTCAAATTGTACTACAAGGGTA 3321
                             vi       v     i vi v  i      viv        i v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_140873047_   3322 TAGTTACCAAAGCAGCACTGTAGTGCTATAAAAATAGGCACTTAGACGAA 3371
                         i   v i   ii   iiiv   v  vi    ii    i  iv    iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_140873047_   3372 TAGAACAGAATAGAGAACCCAGAAATATACCCAAATACATATTGCCAACT 3421
                          i   i     v    ii         v     v i iv   v i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_140873047_   3422 GATCTTCAACAAAG---CCTAAAAAAACATAAATTGGAGAAAGGACACCC 3468
                            i   i    i ---  ---  i v   vv v   i     i i vi 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCC---AAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_140873047_   3469 GATTCATTAAATGCTGCTAGGAAAACTGGCTAGCCACATGTCACATGTAG 3518
                         vv    vi     v    i   v      v  ?       i------- i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC-------AA 440

  chrX_140873047_   3519 AAGAATAAAACTGGATCTCCGTCTCTCACTGTACATAAAAATCAACTCCA 3568
                               i  ii    i i iii   v   ii  i i      i     v 
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_140873047_   3569 GGTGGATCAAAGACTTAAATCTAAGACCTTAAACCATAAAAATCTCCGAA 3618
                         ii       ?    i     v     v  v    i      v   iv   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_140873047_   3619 GATAATATTGGA--AAATCTCTTCTGAACATTGGCCTAGGCAAAGAATTC 3666
                           v  i  v  ?--      - iv   v -    vi       v iv   
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCT-TCGTGACC-TTGGGTTAGGCAATGGTTTC 588

  chrX_140873047_   3667 ATGACTAAGACTCCAAAAGCAAAGGCAACAAAA--ACAAATA--TAAATG 3712
                         v iiv  v   v         v i         -- v     --     v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_140873047_   3713 GGACCTCATTAAACCAAAAAGCTTCTGCATAGCAAAATAAATAATCATCA 3762
                             i    i   viv    i   i  iiivv    iv v iv    vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_140873047_   3763 GAATAAACAGACTACCCACAGAGCAGGAGAAAATATTTGCAAATTATGCA 3812
                         i i i  v    v         iii                   i  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_140873047_   3813 TCCAAAAAAAATGACTAGTATCCAGAGTCTACAAGGAACTC----AAATC 3858
                           ii v  ii--    v         i v  i  i      ----  v  
  L1M4_orf2#LINE/    739 TCTGATAAGG--GACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_140873047_   3859 AGCAAGAAAAAAAAAAAGCAAATAATCCCATCAAAAAGCGGCCAAAGGAT 3908
                          ii  v     i -----       i  v  i?    ii  v        
  L1M4_orf2#LINE/    787 AATAATAAAAAGA-----CAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_140873047_   3909 GTGAATAGACATTCCTCAAAAGAAGATTTA 3938
                         v            i   v         v  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATA 861

Transitions / transversions = 1.39 (128 / 92)
Gap_init rate = 0.02 (15 / 861), avg. gap size = 3.20 (48 / 15)  


1997 26.70 7.48 2.99  chrX_140945303_140948096.rev     1437  2305 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140945303_   1437 TGGAGAGACATACCGTGGTAATGGATTGGAC-ACTCAAGATAGTTAAAAA 1485
                             i   i  v  i  v v          v-   i  v  v     i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140945303_   1486 AAAATCAATTCCGCACAAATTGATGAACAGACTTA---TAATTCCAATCA 1532
                         ii---    v iv v         vv     i i ---i   i  v    
  L1M4_orf2#LINE/     51 GG---CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chrX_140945303_   1533 AAATCCTAGC--CCAATGTTTTGCATCTATGGACAAGCTTTATCTAAATT 1580
                               i   --  -- v       vvv  v        vvvi     v 
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCC--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_140945303_   1581 TTATGTGAAAATACAAATAAACTA------CCAAAGTAACTTTTAAAGAG 1624
                          i  i  i    i   ivi v i ------     ii  ii  v   i  
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_140945303_   1625 AAGAATAA-GTTGGAGAAGTTA-ACTACTTCATTATAAAAGTTACTGTAA 1672
                              i  -       i v i -   v iiv   vi    v     ii  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_140945303_   1673 AGCCCCAGTAATCACTGCATTATGGAGTTGAT-----GGTCATCACAGAG 1717
                            iv         vvi  v i   vii  ii----- i viv  i v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_140945303_   1718 ATCAATATAACAGAAT--AGAGTTCAGAAATAGGTCCATTCAAAGGTGAA 1765
                               iv  i     --     i        iii    v  vvvi  iv
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_140945303_   1766 CAATTGATTTT-AACAATGATGTGTAGGTAACTTAGTAGA-----AATAG 1809
                                    -i    v i  ivv  iiv i i i i i-----     
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_140945303_   1810 TCTTTTCAATA--TAGTGTTGGAACAATTGGA----CATATTTAGGGTAA 1853
                                  i -- i   i   i    i    ----  i  ----- i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-----GCAA 440

  chrX_140945303_   1854 ATAAAAACAAAA---AACTCC-ATTTAAACATCATGATAGTTTATGTACA 1899
                          -- i  ii  i---i  i  - ii v -  i   --------  ii v 
  L1M4_orf2#LINE/    441 A--AGAATGAAGTTGGACCCCTACCTCA-CACCAT--------ATACAAA 479

  chrX_140945303_   1900 AGTTAATTCAAAGTGGATGATAAATTTAAAAGTAAAATATAAAAGTATTT 1949
                          i    i     i     v ? i ii    v    i vv     v   vv
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_140945303_   1950 AACTTGTAGAGAAAAACA--GGT-------TTCATGATCTGGGTTTAGGA 1990
                             iv    ii      --  ?-------   i   i  v  v     v
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chrX_140945303_   1991 AAA-------TAGATA-GACACCAAAATCATAATTCATAGAATAAAAA-T 2031
                           v-------      -          v  i  viv i i  v     - 
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_140945303_   2032 ATGATTTAAA--AGATTTAATCTAAATTTTAAAATTTGTTATA--TGAAA 2077
                          -   --   --i  i  v   v     v-    i  -  i i-- v   
  L1M4_orf2#LINE/    630 A-GAT--AAATTGGACTTCATCAAAATTA-AAAACTT-TTGTGCTTCAAA 674

  chrX_140945303_   2078 --ACACAGCTAAGAGAAGGAAAATACAAGGTATAGACTGTGAGAAAATAT 2125
                         --    viii    i iv     v    vvi i   v  v          
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_140945303_   2126 TTGCAAATTACATATTCAACAAAGAACTTGTGTCTAGAACATATGAAGAA 2175
                                 i i    iii i  i i      i  i    i    i     
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_140945303_   2176 CTTTCAAAATTCAATAGTAAGAAAACAACCAACCTGACTTAAAAACGATC 2225
                           i i v  i      i   i  i    vi    ii i ?     i iv 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_140945303_   2226 ACAATATTT-AACAGACAGTTC---AGAGAAGATATATGAGTAATAAATA 2271
                          v iv    -  i     v   --- i          ii i iiiv    
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_140945303_   2272 AGTACATGAAATGATGTTCAACATAATTACCTAT 2305
                           i        v    i       v ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (143 / 86)
Gap_init rate = 0.04 (34 / 908), avg. gap size = 2.68 (91 / 34)  


2874 26.88 1.44 1.00  chrX_140951752_140956344     3203  4106 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140951752_   3203 TGGAAAGATATTCTATGTTTATAGATTGGAATAATCAATATTTTAAAAAT 3252
                                    i i     i  i        v v i      v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140951752_   3253 ATCCATACTACCTGAAGCAATCTACAGTTTCAATATAATCGTTTTCAAAA 3302
                         iv v     v  ii  vii        v     iii    vi v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140951752_   3303 TACCAATGATATTCTCCACA-AAATTAAAAAAGAAAAATCCTAAAATTTC 3351
                          v   iiviiv  i iii  -     i v  ivvi --          iv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA--TCCTAAAATTCA 148

  chrX_140951752_   3352 TATGGAACAAAGCAAAAAATCCAGAAAAGCGAAAGCTATTCTAAGCAAAA 3401
                                -- v    iii i      v   v   i v  ii i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_140951752_   3402 AGAACAAAACTGGAGGACTCACATTACCCGACTTCAAATTATACTACAGA 3451
                                 ii             i v   i i      viv       i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_140951752_   3452 GCTATAGTGATGAA-ATGGCATGGTACTGGCTTAAAAACAGACACACAGA 3500
                             i   i  v  - ii ii          v   ii i     i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_140951752_   3501 CCAGTGGAACAGAATATAGAAACACAAAAATAAATCCATACATTGACAGT 3550
                         i  i     i     vv   iv -  i       i         v ii  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGT 345

  chrX_140951752_   3551 GACCTCATTTTTTACAAAGGTGCCAAGAACATAAACTGGGGAAAGGAAAG 3600
                         v vi v     iv    i          v   vv v         i v  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_140951752_   3601 ATTTAATTTA-TAA---GTGCTAGAAAAACTGG-TATCCATATAAAGAAG 3645
                         vi  --  i -i  ---     i i v      -  ?   i  iv i   
  L1M4_orf2#LINE/    396 TCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_140951752_   3646 AATGAAACTAGACCGTTAACTCTTGCTATATACAAAAATCAAATCAAAAT 3695
                               ii i    vi  v   vii i            i  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_140951752_   3696 TGACTAAAG-CTTAACCTG-AAGACCTCAACCTATGAAACTTGTAAAAAA 3743
                         v  ii ?  - i   v-  -    v  v  v    i     iv  i  i 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_140951752_   3744 AAAAATGGGA--AAATCTGCAAGATATTGGAATTTCCAAGGATTTCTTCA 3791
                            v  i  ?--      v iv  iv    iv vvv   v i      vi
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_140951752_   3792 GTAATACTCCACAAGCACAGGCAGCAAAAGCAAAAATAGACAAATTGGAT 3841
                         i  vv  v   v       i   i      v         i        i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_140951752_   3842 TGCATCATC-TTAAAAAGGTTTTACATAGCAAAGGAAACAATCAGCAAAG 3890
                          v     vv-       v-    iiiivv       v  v    iv    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_140951752_   3891 TGAAGAGGCAACCCACGGAATGGGAGAGCATATTTGCAAACTACTCATCT 3940
                             i  i        i          iv           ii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_140951752_   3941 GACAAGGAAGTAACAACCAGAATATATAAGAAGATCAAACAACTCTGTAG 3990
                           i    i v vii v             ii iv  vv       vi  i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_140951752_   3991 GATAAAATCCAATAATCAAATTGAAAAATGGAGAAAAGATCTGAATAGAC 4040
                         v v   iv v     i v    ?        iv   i   i         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_140951752_   4041 ATTTGTCAAAAAAAGACAGGTAAATG-CAAACAGGTACATGAAATGGGGC 4089
                             v  v   i    i vii     - v  i i i        v iv  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_140951752_   4090 TCAGTACCCTTGATCAT 4106
                            ii i v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.38 (22 / 16)  


2492 27.20 3.19 3.19  chrX_140966276_140969770.rev     2097  3004 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_140966276_   2097 TGGAAAATCATTCAGTGCTCATGGATAGAGAGAATCAATATTGTGAAAAT 2146
                               ivi  i vi  i        v ii   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_140966276_   2147 CGCCATACTGCCCAAAGCAATTTATAAATTCAATGCTATTCCCATTAAAC 2196
                         v  v     v      vii  i  i i      i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_140966276_   2197 TACCA-CTGACATTCTTCATAGAATTAGA-AATCAGTATTTTAAAATTTA 2244
                          v   -   v -  i  iii    v v  -  v v -  ii       i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAATTCA 148

  chrX_140966276_   2245 TATGGAACCAAGAAAGAACCTGAATAGCCCAGACAATCCTAAGCAAAAAG 2294
                                viivi ii  v  v        v i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_140966276_   2295 AACAAAGCTGGAGGAATCATACTC----------AAACTATACTACAAGG 2334
                                i       v   i   i----------     -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_140966276_   2335 CTACAGTAACCCCAAGAGCATAATACTGATAAAAAGAACAACAACAACAA 2384
                                  i vvi v  ii ii     ii v  i  -------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA------------- 284

  chrX_140966276_   2385 CAAAAAAGAAAACAGACACATAGACCAATGGAACAAAATAGAGAACTCTG 2434
                         ------------i     i     i        i i   v    iii v 
  L1M4_orf2#LINE/    285 ------------TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_140966276_   2435 AAATAAGACTGCACACATACGACCATGTGATGTTTGACAAATCTGACAAA 2484
                               iv iii   iv  i ii  vv    v  i     ivv  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_140966276_   2485 GACAAGCAATTCA-AAAGTTTTCCCTATTTGATAAATTGTGCTGGGAGAA 2533
                         iv  vv    vvi-    vv vvi  v  ii i    v         v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_140966276_   2534 CTGGCAAACCATATGCAGAAAATTGAAACTGGACCCCTTCCTTACATCGT 2583
                             vv ?   i     i  i v    ii         v   i   i i 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_140966276_   2584 ATACAAAAATCAGCTCAAGATGGATTAAAGAC-------TAAAACACAAA 2626
                                   i i     i      i ?    -------   i vvi   
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_140966276_   2627 ACTATAAAAACCTTTGAAAAAAATCTAGGCAGTACTATTCAAGACATAGG 2676
                                  vi   v   i    iv    ?ivv v v   iv   v v  
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_140966276_   2677 CATATGCAAAGATTTCAT-GATGATAATGCCAAAAGCAATTGCAACAAAA 2725
                         vv  v    v i    v -   -  i ii         vvv         
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_140966276_   2726 GCAAAAGTTGACAAATGGAATCTAATTAAACTGAAGAGCTCCTGCACAGC 2775
                          v    i v  i    v i ii v  i   v v  i i  ii  ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_140966276_   2776 AAAAGAAACTACCAACAGAGTGTACAGGCAACCTACAGAATGGGAGAATA 2825
                            i  v    i   v i    v v  i     i              v 
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_140966276_   2826 TTTTTGCAATCTATCCATCCAACAAAGGTCTAATATCCAGAATCTACAAG 2875
                          v       vii  vi   ii i  i  v  vi          v  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_140966276_   2876 GAACTT----AAGCAAAT--TTACAAGACAAAAAACC--ATTAAAAAATG 2917
                              i----  viv   -- v v        v    --   ?       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_140966276_   2918 GGCAAAGGTCACGAGCAGACACTTCTCAAAAGAAGACATTCATGCAGCCA 2967
                                 vivi  ii     i     v        i  v  viii    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_140966276_   2968 ACAAACATACGAAAAAAAGCTCAACATCACTGATCAT 3004
                          i  i  i i     i v           ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (139 / 104)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.14 (58 / 14)  


2657 25.80 0.00 1.11  chrX_140983945_140985658      501  1221 (493)    L1M4_orf2#LINE/L1      196   908 (0)  

  chrX_140983945_    501 AAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAA 550
                                   i      vv    i  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_140983945_    551 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 600
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_140983945_    601 ATCAATGGAACAGAACAGAGCCTTCAGAAATAACGCCGCATATCTACAAC 650
                                   i    iv   vv i         vv  ii i  i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_140983945_    651 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 700
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_140983945_    701 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 750
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_140983945_    751 TGAAACTGGATCCCTTCCTTACCCCTTATACAAAAATTAATTCAAGATGG 800
                             ii    i    v   i  v  v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_140983945_    801 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAACCATAAAAACCCTA 850
                           i ?    i       v   v       i       --------i i  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC--------TCTTA 537

  chrX_140983945_    851 GAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTT 900
                                  v    ?i v viv   iv   v v  vv i     v ii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_140983945_    901 CATGTCTAAAACACCCAAAGCAATGGCAACAAAAGCCAAAATTGACAAAT 950
                          v ivv  vi     v      vvi          vv     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_140983945_    951 GGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATC 1000
                         v   ii v  i   v v  i i   i  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_140983945_   1001 AGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTC 1050
                          i      v  i     i   i             v  i    vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_140983945_   1051 ATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTT 1100
                               i  i  i  vi          v  i  v      vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_140983945_   1101 ACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAAC 1150
                          i  v     i     i     v  i?    i            v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_140983945_   1151 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAA 1200
                              i     v        i  vi viii     v ii          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_140983945_   1201 ATGCTCATCATCACTGGCCAT 1221
                                v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (103 / 79)
Gap_init rate = 0.00 (1 / 713), avg. gap size = 8.00 (8 / 1)  


3053 24.75 1.98 2.09  chrX_141059130_141061219      689  1597 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141059130_    689 TAGAATGATATTCTTTACTCATGAATTGAAA----TAATATCGTTAAAAT 734
                          i   v     i iv ii     i    i  ----      i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141059130_    735 CTCCACTGTGCCCAAAGCAATCCACAGGTTTAATGCAATTCCTATCAAAA 784
                         vv v ivv v      vii   i    i  i  i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141059130_    785 TCCCAATGACATTTTTTTCACAGAGATAGAAAAAATAATCTTAAAGTTTG 834
                              iivi v      --i    i  v  v  iv i   i    i  ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_141059130_    835 TATGGAACCACAAAAATACCTGACTAGCCAAAGCAGTCTTGAACAAAAAG 884
                                vii   iiivv  v  v        i  i       v  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_141059130_    885 AATAAAGCTGGAGACATCACAGTACTTGATTGTATCATATACTACAAAGA 934
                           i    i     ivv     v v iii   vi vv iv          v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_141059130_    935 TACAGTAATCAAAACAGCATGATTCTGGTTTAAAAAGAGACACAGACAAC 984
                                     i    ii  i v    iv   ii v     i v v v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_141059130_    985 AATGAAATAGAATAGAGAGCCCAGATATAAATTCACACACTTATAGTATA 1034
                             i        v     i     v     ii  i   i    i  vv 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_141059130_   1035 TTAATTTTCAACAAAGATTGCAAGAATACACAATGGGGAAAGAATAATCT 1084
                           i      i    i i vv     vi iv                i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_141059130_   1085 TTTAAATAAATAATGTTAGGGAAATATTTTATCCACATACAAAATAATGA 1134
                            v  i    ii  i i  iv  ivvvv  ?      i     v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_141059130_   1135 CATTAGACCCTTGTATCACACCACATACAAAAATCAACTCAAAATGGACT 1184
                         vi  i     i iiv        i          i             ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_141059130_   1185 AATGACTTAAATATAAGACCTGAAAATGTAAAATTATAATACTATAAAAA 1234
                          ?v   i     i     v  i   v i     i v -----  v  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-----TAGAAGAA 543

  chrX_141059130_   1235 CGCACAGGGGAAAAGGTCCATGACATGGTCTTAG-CAATGATATTTTGGG 1283
                         vi  i   ? v   vv i i    v v vv    -     i v i  i i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_141059130_   1284 TATGATACCAAAAGCACATGCAACGATAGCAGAAATAAACAAAGGGGGGA 1333
                              i            v     i v  v i     i i   vv  -- 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG--A 641

  chrX_141059130_   1334 CTACATCAAA-CTAAAAACTTCTGTATAGCAAAGAAAACAATTGCCAAGA 1382
                           v       -i         i   iivv     i v  v  ---     
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT---CAAGA 688

  chrX_141059130_   1383 ---TGAAAAGACATTCCATTCTGCAAAATGTGAAAAAGATATTTGCAAAC 1429
                         ---          vi   -----  i    v  i   -           i
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCA-----CAGAATGGGAGAAA-ATATTTGCAAAT 732

  chrX_141059130_   1430 CATATATCTGATAAAAGGTTAATGTTCAAAATATGAAAGAAACAC--AAA 1477
                                       ii ii vi i i  i     iv  ii   v -- v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_141059130_   1478 ATTCAATACCAAAAA---AAATAAA--AATTTAAAA-TGGGCAAAA-ACA 1520
                          i      vi     ---      v--    ?    -        i- iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_141059130_   1521 TGAATAGACATTTTTTCAAAGAAGAGATACAAATGGTCCAACATGTATGT 1570
                                      i i         v          -    i v i ii 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGG-CCAATAAGCACAT 881

  chrX_141059130_   1571 GAAAAGGTGCTCAACATTACTAATCAT 1597
                               i          i ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (134 / 87)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.31 (37 / 16)  


 208 28.00 0.00 0.00  chrX_141150930_141157209      441   490 (5790)    L1M4_orf2#LINE/L1        1    50 (858)  

  chrX_141150930_    441 TGGAAAAACATTCAGTGCTCTTGGATCAGAAGAATCAGTATCGTTAAAAT 490
                               i i  i vi  i  v     ii     v i i   i     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.00 (0 / 0)  

3285 27.20 0.44 0.44  chrX_141150930_141157209     4880  5787 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141150930_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141150930_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141150930_   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_141150930_   5028 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAG 5077
                                viiv  ii  v  v v  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_141150930_   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGAT 5127
                                i      vv       v  ii i      viv        iii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_141150930_   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5177
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_141150930_   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATACCTACAACT 5225
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_141150930_   5226 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5275
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_141150930_   5276 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCT 5325
                           v  i  i              v      v  ?   i   i ii iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_141150930_   5326 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5375
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_141150930_   5376 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5425
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_141150930_   5426 CTAGGCATGACCTTTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5475
                         v    ?i i vii   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_141150930_   5476 AACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAA 5525
                         i            vvi          vv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_141150930_   5526 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5575
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_141150930_   5576 AGGCAGCCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5625
                           i  i  i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_141150930_   5626 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5675
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_141150930_   5676 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5725
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_141150930_   5726 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5775
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_141150930_   5776 ATCACTGGCCAT 5787
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (151 / 92)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3238 26.66 1.11 0.66  chrX_141199150_141205428.rev     4885  5788 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141199150_   4885 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4934
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141199150_   4935 GGCCATACTGCCCGAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4984
                            v     v   i iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141199150_   4985 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCG 5032
                          v   iivi i  i  ii     -   -- v  i  - iii    i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_141199150_   5033 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAGTCCTAAGCCAAAAG 5082
                                viiv  ii  v  v v  v     iv  i  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_141199150_   5083 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5132
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_141199150_   5133 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5182
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_141199150_   5183 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5230
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_141199150_   5231 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT--T 5278
                          vi    i  i     ivv  vv  i v  vv            i  -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_141199150_   5279 CCGTATTTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGTAGAAAG 5328
                          -- v  i  i           i  v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    397 C--TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_141199150_   5329 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5378
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_141199150_   5379 GATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5428
                            i ?   ii    i  v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_141199150_   5429 ACCTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGTCT 5478
                           v    ?i v viv   iv   viv  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_141199150_   5479 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5528
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_141199150_   5529 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5578
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_141199150_   5579 ACAGGCAACCCACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5628
                          v  i         i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_141199150_   5629 AAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAA 5678
                           i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_141199150_   5679 AAAAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACT 5724
                            i    ----   v  i?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_141199150_   5725 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5774
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_141199150_   5775 CCATCACTGGCCAT 5788
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (146 / 91)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


3022 25.75 0.96 0.72  chrX_141223726_141228461     3011  3841 (895)    L1M4_orf2#LINE/L1        1   833 (75)  

  chrX_141223726_   3011 TGAAAAAATATCACATGTTCATGAATTGTAAGAATCAATATTGTTAAAAT 3060
                           i   i     v          i    v    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141223726_   3061 GTCCATATTACACAAAGCAATCTACAGATTCAATTCAATCCCTATCAACA 3110
                          v v   i v v    vii              iv             v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141223726_   3111 TGCCAATGACATTCTTCACAGAAATAGAAAAAAAAATCCCAAAATTTATA 3160
                          v   iivi v  i  ii       v  v  ivvi    i      i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_141223726_   3161 TGGAACTACAAAAGATCCAGAATAACCAAACCCATCCTAAGCAAAAAGAA 3210
                              v i   ii  i        i     v v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_141223726_   3211 CAAAACTAGAGTAGTTACATT-----ACTTCAAATAGTACTACAGAGCTA 3255
                             ii i   v v i   i ----- i      vvv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_141223726_   3256 GAGTAATTAAAACAGCATAGTACTGGCATAAAAACAGACACACACACACC 3305
                         v      i  i    ii i            ii i     i i v i-- 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT--C 298

  chrX_141223726_   3306 AATGAAGCACAATGGAGAACTCAGAAACAAATCCACACACCTGTAGTGAA 3355
                             i ii v   v    iii      i   i   i   ii i i  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_141223726_   3356 CTCATTTTTAACACAGGTTCCAAGAACATACACTGGTGAAAAGACAGTCT 3405
                         i v     ii   vi   v      v   v  v   v    ii i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_141223726_   3406 CTTCAATAAATTTTGCTGTGAAAACTGGATATCCATATGCAGAAGATTAA 3455
                         i     i    vv     v  v         ?   i     i    v i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_141223726_   3456 AACTAGAACCCTATCTCTGGCCATATACAAAAATCAAATGAAAAAGGATT 3505
                          ii i  v     i   vvi              i  v v    v    i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_141223726_   3506 AAATACTTAAATGTACAACTCAAATCT-TGAAACTACTATAAGAAAACTT 3554
                          ? v  i        vi vii   v  - i     vi  v        v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_141223726_   3555 CAGAGAAAATCTCCAGGACATTGTTTTGCGCAAAAATTTCTTGAGTAATA 3604
                         vi ? v      i iv   v   vv  iv    vii      iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_141223726_   3605 CCCCACAAGCACAGGCAACCAAAGCAAAAATGGACAAATGGGATCACATC 3654
                          v   v       i     v    v      i  i    v   iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_141223726_   3655 AAG-TTAAAAGGCTTCTGCGCGGCAAAGGATACAGTCAACAAAGTGAAGA 3703
                           i-      i-   i  i  vv       i  vi    v        i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_141223726_   3704 GACAACCCACAGAATGGGAGAAAATATTTGAAATTTATTTACCTGACAAG 3753
                                                       v  v i  v  i    i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_141223726_   3754 GGATTAATAACCTGAATATATAAGGGGCTCAGCAAACAACTCTAGAA-AA 3802
                            i vi  v  v          i ii   vv---       v v  -  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTT---ACAACTCAATAATAA 794

  chrX_141223726_   3803 AAAATCTAATAATCTGATCAAAAGATAGGCAAAATATTT 3841
                            iv v     i ii  i?   i  i      iv    
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

Transitions / transversions = 1.36 (121 / 89)
Gap_init rate = 0.01 (7 / 833), avg. gap size = 2.00 (14 / 7)  

 387 16.47 0.00 0.00  chrX_141223726_141228461     4159  4243 (493)    L1M4_orf2#LINE/L1      824   908 (0)  

  chrX_141223726_   4159 CAAAAGATGAAAATAGACATTTCTCAACAGAAGAAATGCAAATTGCAAAC 4208
                             i   vvi              v v      v  i     v  v  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_141223726_   4209 AAGCATATGAAAATGTGCTCAACATCATTGATCAT 4243
                              i       vi            ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.75 (6 / 8)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.00 (0 / 0)  


2640 26.20 7.52 0.82  chrX_141247969_141250440     1129  1979 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141247969_   1129 TGGAAAAGTATCTTATGTTCATGGATTGGAAGAATTA-TATTGTTAAAAT 1177
                               ii    ii                   v   -         i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141247969_   1178 GTCCATACTAGTCACAGCAAACTACGGATTCAATGCAATTCTTATCAAAA 1227
                          v v     vvi  v vii v    i       i     i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141247969_   1228 TTACAATGACATTGTTCATAGGAA--GAGTAAAAAAATCA-AAAATTTCT 1274
                          iv  iivi v  v  iii  i  --  -i  ivvi   v-      iv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_141247969_   1275 ATGGCATCACAAAAGACCCCAAATTGCCAAAGCTATCTTGAGAAAGAA-- 1322
                             v vii   ii     vi   v      i v       i      --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_141247969_   1323 -CAAAGCTGAT---TTCACACTTCCTGATTGCAAAGTCTGTTACAAA--- 1365
                         -     i  iv---i          ii   v    iii ii      ---
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_141247969_   1366 --------------AGTGTGTT-----------GAT---CACA---ATCG 1384
                         --------------      v -----------   ---  i ---   i
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_141247969_   1385 A--AAAAAGAATAGAGAGGCCAGAAATAAACCCAATTATATAAGGTCAAC 1432
                          --i  v     v     v               vvi  v  v      i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_141247969_   1433 TAACACTTGACAGTGGCATGAAGAATAGACAATAGGGAAGAGATATCCTT 1482
                          i ivi i    iv  iiiv    vi vv    i     iii   vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_141247969_   1483 TTCAATACACAGTGTTGGGAAAACTGGG------------AAAGAATGAA 1520
                              i v ii   i     v      i------------          
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_141247969_   1521 ATTGAACCCCCTTCTCATACTACTCATTAAA-TTAACTTAACAGGAATTC 1569
                         i   i     ivi    i  i ivi iv   -      i  v v i  iv
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_141247969_   1570 AAGTCTTAAAT-TAAGACCGAAAACTACAAAACTCCTAAGAGAAAACATA 1618
                         ?  v i     -     v v       i       i  ii          
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_141247969_   1619 GGGGGAAAATCTCCATGACTTCAATCTTGGTGATGATTTTTTTGGATAAG 1668
                           ? v   -   i i    i iiivi v  ii   i   i  -i    v 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chrX_141247969_   1669 ACACTGAAAATACAGGCGAAGAAAACAAAAATAAACAAGTGAGGCTACAT 1718
                             ii   ii   i  i vi   iv       i i  i vi i  v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_141247969_   1719 CAAACTAAAAAAAATCTGCACA-CAAAGGTAACAATCAACAAAAGAAAAA 1767
                             v v     vv i  ii v-      vv  v     v   ivi    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_141247969_   1768 GACAACCTATGAAATGTGGTAA--CATTTGCAAACCATATATCTGATAAG 1815
                                i iii    v iv  --i         i               
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_141247969_   1816 GGGTTAATATCCAAAATATATAAAAAACTCATACAACTTGATAGCCAAGG 1865
                           ii vi      i          i     v       ii   iiv  ii
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_141247969_   1866 AGCAGATTACTCCATT-AAAAATGGGCAAAAGACCTGAATAGACATTTTC 1914
                         ii  i  v  i v   -             i  ii             ii
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_141247969_   1915 CCAAAGAAGACAGACACATGGCCAATAGGTTCATGAATGAAAAGTTTCTC 1964
                                   i v   v          i --  i--        v v   
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAG--CAC--ATGAAAAGATGCTC 893

  chrX_141247969_   1965 AACGTCACTAGCAGA 1979
                            i   ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (143 / 78)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.38 (71 / 21)  


2525 27.59 1.62 3.77  chrX_141281144_141283089      526  1453 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141281144_    526 TGTAAACACATCCCATGCTCATGGATGAGTAGAATTAATATTGTGAAAAT 575
                           v   v i        i        vi v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141281144_    576 GACCATATTGCCAAAAGCAATCCACAAATTTAATGCAATTTTCACAAAAA 625
                          i v   i v  v   vii   i   i   i  i     iiii iv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141281144_    626 TACCACCATCACTCTTCACAGGACAAGAAAAAATAATCCGAAATTTCGTA 675
                          v   v vv vi i  ii   i vvv  v  iv i    v   v   i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_141281144_    676 GGAAACCAAAAAAGAGCCCACATAGCCAAAGCAA----GACTAAGAAAAA 721
                         v i  viiv  ii  v  viv         i   ----  vv     i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_141281144_    722 AAAATCTGGAGGCATCACATTATCTAACTTTAAACTATGCCATAAGCCCA 771
                         v   vi      vv     i vi i  i  i   viv i i i  iv i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_141281144_    772 TAGTAACTAAAAGAGCATGGGACTGGTATGGAAATAGGCACATAGACCAA 821
                         i     ii  i v  ii   v     i  iiii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_141281144_    822 TGGAACAGAATAGAAAACTCAGAAATAAAGCAAAACACTTATAGCCAACT 871
                              i     v  i iii          v v v   i    i i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_141281144_    872 GATCTTTGACAAAGCAAACAAAAACATAAGGTGTGGAAAGGACACCGTAT 921
                            i  i     i vviv   i v   vvii  v      i i viv v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_141281144_    922 TCAACAAATGGTGCTGGGGTAATTGGTAAGCCACATG---GAGAATGAAA 968
                                           ii  i   vv ?       ---i        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_141281144_    969 TTGGATGCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATCAA 1018
                              iv ii i   v    v           i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_141281144_   1019 AGACTTAAATTGAAGACCTGAAACCATGAAGATTCTAGAAGATAACATCA 1068
                             i     vv    v  i    i  i  iv ii       v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_141281144_   1069 GA--AAATCC-CATATAGACATTGGCTTAAGCAAAGACTTCATGACCAAG 1115
                          ?--     i- i ---   v    v   i    v ii   v iivi v 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGT---GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_141281144_   1116 -CACCCAAAAGCAAATGAAACTAAAACAAAGATAAATAGATGGTACTTAA 1164
                         -    -       v v v   v   iv   i   i   i  v v    v 
  L1M4_orf2#LINE/    598 ACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_141281144_   1165 TTAAACTAAAAAGCTTCTGCACAGCAAATAATAATAATAATAATAATAAT 1214
                          i   v v    i   i  ii vv    vi i v  vi  v  -------
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA------- 689

  chrX_141281144_   1215 AATAATAATAATAATAATTAGCAGAGTTAACAGACAATCCACAGAGTGGG 1264
                         ------------------------   v  v      i       i    
  L1M4_orf2#LINE/    690 ------------------------AGTGAAAAGACAACCCACAGAATGGG 715

  chrX_141281144_   1265 AGAAAATCTTCACAATCTACACATCCAACAAAGAACTAATATCTAGAATC 1314
                                v  ii   vii i i   ii i  i i   vi    i     v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_141281144_   1315 TACAAAGAACTCAAATAAATCAGCAAGAAAAAAACAA----TCCCATCGA 1360
                           i         vv i  v   ii  v     i    ----i  v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_141281144_   1361 AAAGTGGGCTAAGGAAATTAATAGACAATTCTCAAAAGAAGATATACAAA 1410
                            i     v     vv v        v     v                
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_141281144_   1411 TGTCCAACAAACATATGGAAAAATGCTCAACACCACTAATTAT 1453
                           v    i  i  i   i   i          i  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (146 / 106)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 5.56 (50 / 9)  


3286 26.98 0.44 0.44  chrX_141290656_141296927     4872  5779 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141290656_   4872 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4921
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141290656_   4922 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4971
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141290656_   4972 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5019
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_141290656_   5020 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5069
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_141290656_   5070 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5119
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_141290656_   5120 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATAGAGATC 5169
                                 i   i    ii         i iv ii i   v   v     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_141290656_   5170 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5217
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_141290656_   5218 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5267
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_141290656_   5268 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5317
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_141290656_   5318 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5367
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_141290656_   5368 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5417
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_141290656_   5418 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5467
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_141290656_   5468 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5517
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_141290656_   5518 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5567
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_141290656_   5568 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5617
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_141290656_   5618 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5667
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_141290656_   5668 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5717
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_141290656_   5718 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCACC 5767
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_141290656_   5768 ATCACTGGCCAT 5779
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1594 28.38 6.04 3.38  chrX_141312247_141316320     2754  3581 (493)    L1M4_orf2#LINE/L1       59   908 (0)  

  chrX_141312247_   2754 TTTTCATATTGATTTATA----CAACTGTATTCTCCTTACTTAAAACCAC 2799
                          iii  v      i  i ----    - i --v   i  - i    i v 
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAAC-GCA--ATCCCTA-TCAAAATCCC 104

  chrX_141312247_   2800 AGCAAGATTTCTTCTACAATATTGA-AAGCTGATTCTAAAATTTATATGA 2848
                            vivv   i  vi v  -     -        i        i     i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_141312247_   2849 AAATGTGATATACCTAGAGTAATGAGAATGATATT-AAAAAGAAGACCAA 2897
                              ii viv   i   i  iiv i  ii  v  -          v   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_141312247_   2898 --CTTGAAAACTCACACTTTCTCATTTCAAGATGTAC--CAAATGCTA-- 2941
                         --i v  ii          i iv       i iv   --    -    --
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-GCTACA 252

  chrX_141312247_   2942 GGAATTAAGACTGTATGACATTGTCATACAGATATTAAAGA-AAATTAAT 2990
                          v   i     v  i  ii i  v    vi    v- v v - i  i   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAG-ACATATAGATCAAT 301

  chrX_141312247_   2991 GGATCAGTATAGAGA--CTGGACATATACTCTTATACACATGGTCAATGG 3038
                            vi  v  v    -- ii  v   v  i v  i ivi         v 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_141312247_   3039 ATTTT-GTTAAAATTTTC----CCAT-CAATTGAATTTAAAAAGTAACTT 3082
                              - vi  iiv vi ----    -    v ii---   i i  i-- 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG---AAAGAATAG--T 396

  chrX_141312247_   3083 CTTTTGAACATCCAGTACTAGAAAAACAAGATAACCGTGTGTGTGGAGGG 3132
                              v    vvii  i  i i v   vi    ?  iii  ii--i i i
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA--AAAGA 444

  chrX_141312247_   3133 GTGCATCCAAACACT---CTTGAACTATACATACCACTCTAGACTAATTT 3179
                         i  v viiii  v i---  iiv  i   --   v ---- i i   i i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATA--TACAA----AAATTAACTC 488

  chrX_141312247_   3180 GAAATTAATCATGGACGTAATTCTAAAAGCCAAAACTATAG--TTTTTGA 3227
                         i    vi    ?i   v   v v   i   i         i--i i  ii
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_141312247_   3228 AAGAATATGTGGGAAAGCATCTTCATGA------GTTAAGCAAAGACTTC 3271
                              v ii i  ?iviv      i   ------    i    v ii   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_141312247_   3272 TTAG----GATACACAAATCCTTTGTA-TAAAAGAAAACATTATGATAAA 3316
                             ----  i  vv   v vivv i -i         v  - -      
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT-A-GATAAA 636

  chrX_141312247_   3317 GTGAATCCCATTAAA-TTAAGAAGTTTT-TA--TCACAAATCATTATAAA 3362
                         v  i iii   i   -    i  v    - i--   v iiv  i   v  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_141312247_   3363 TAAAACGAAAAGATAAGCCATAGAAT---AGAAGATATTTTCAG--CATA 3407
                         v   ii       i  v   i     ---    i      v  i--    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_141312247_   3408 TATAACTATCAAAGATCTCACAACTGTAATATATAAAGTATTCTT-CAAT 3456
                            --  ivi  i iv  iii v iiv           v i    -   i
  L1M4_orf2#LINE/    737 TAT--CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_141312247_   3457 TAAATA-CAAAAAGTCATACAACCAAAGATAAAAA--AGAAAATTGAGTT 3503
                          v    -i      v  v i    v  vv?     --i v   -- ii  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA--GGATT 832

  chrX_141312247_   3504 CTTGAACAAACACTTCACCAAAAAAGATGTGCAAATTGGCAATAAGCTTA 3553
                         --    i i   i   v     i     i i     v v        vi 
  L1M4_orf2#LINE/    833 --TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_141312247_   3554 TGAAAAGTTGCTCAATATCATTAGTCAT 3581
                                v       i    ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (146 / 85)
Gap_init rate = 0.05 (40 / 850), avg. gap size = 1.95 (78 / 40)  


2405 25.85 7.60 1.40  chrX_141352865_141354869.rev      660  1514 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141352865_    660 TGAATAGATATTTTGTGTGCATGAATTGGAAGAATTAACATTGTTAAAAC 709
                           i v      iiii   v    i         v    i        i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141352865_    710 ATTCATACTACCCAAAGCAATATACAGATTCA--GCAATCTCTATCAACA 757
                         iviv     v      vii  v          --      i       v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141352865_    758 TTCCAA-TGTCATTCTTCACAAAAATTGAAAAAAATACTTCTAAAATTGT 806
                          i   i-  i -  i  ii  i       v  iv- iv i        vv
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chrX_141352865_    807 TATAGAACCATAAAAGACCCAAAATAATCAAAGCATATTTTTTTAAAAAG 856
                            i   viii  ii      i    ii    i  -  i  v--      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACA-ATCTTG--AAAAAG 195

  chrX_141352865_    857 C----TACGGTCA------TTATATTTCCTGATTTTAAATAATATTTCAT 896
                         v----i vi  ii------ i i i    ii    i   vvv  i v  v
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_141352865_    897 AGCTATAGCAATCAAAAAAGTACAGTATTGGCATAAAAACAGACACACAG 946
                              i  i      i v   iii   i        ii i     i i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_141352865_    947 ACCA------------TGAGTGCTTAGAAATAAACTGGAATATATATGGT 984
                          i  ------------    v iii          iviv i  v      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_141352865_    985 CAACTAATTTTTGACAAGTGCACTATGAAGACACGATAG----AGAATAG 1030
                            i i     i      v ii i v  vv iv i  i ----       
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_141352865_   1031 TATCTTCAATAAATGATGCTGAAACAGCTAAATTTCCACATGCAAAAGAA 1080
                          v i     i     i     ii   i  ii  v?               
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_141352865_   1081 TGAATTTGGACACTTA--TAAAACAA---ACAAAAGTAAACTTAAAATGG 1125
                             v      v i  -- v v  v ---      i v    i       
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_141352865_   1126 ATTTAAAAAAACCTAA-TGGAAAATATGAAACCATAAAATTCCTAGGGGA 1174
                           i--- ? i      -  v  i vv i    i      i  i   ii  
  L1M4_orf2#LINE/    496 ATC---AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_141352865_   1175 AAA------------TCTCCTTGACAGTGGCATTGGCAATGATT----GG 1208
                            ------------   i v    vv   vv v       i  ----i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_141352865_   1209 ATATCACACTAAAAACTCAAGCTAAGGAAGCAAAAGTTAAAAAAAATAGG 1258
                             v    i    i v     v vii   v    i -- i v    v  
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT--AGATAAATTGG 640

  chrX_141352865_   1259 ATTATGTCAAACTTATTAGCATCTGCACAAGAAAGGAAACAATCAACAAT 1308
                          i vii     v   vv i v i  ii vvv      v  v     v  v
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_141352865_   1309 ATGCAAAGGCAGCCTACAGA-TTGGAGAAAA-ATGTGCCAACTCTATATT 1356
                         i  v    i  i  i     - v        -  v   v  iiv     i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_141352865_   1357 TGGTAAGGGATTAATG-CCAAAATATAT--------TTTACAAACTCAAT 1397
                           i       i vi i-   i       --------i      -      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAAT 789

  chrX_141352865_   1398 AGCAAAAAAA-AAA-AATCCAATT-AAAAACGTGTAAAAGGACCTCAATA 1444
                          ii     i -   -  i      -     i v i   -   ii v    
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA-GGATTTGAATA 838

  chrX_141352865_   1445 GACATTTCTTAAAAAAAGATGTAAAAATGGCCAACAGACATATGTAAAGA 1494
                                  iv   i     i  v          i ii  i   v     
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_141352865_   1495 TGCTGAACATCACTAAACAT 1514
                             v       ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (138 / 81)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.96 (77 / 26)  


1027 29.07 1.38 0.69  chrX_141375871_141379304.rev     1570  1858 (1576)    L1M4_orf2#LINE/L1        1   291 (617)  

  chrX_141375871_   1570 TGAGAAGATATTCCACGTTCGTGGATTGGGAGAATCAATGCTGCTAAAAT 1619
                           ii       i   i    i        i   v i   ii  i   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141375871_   1620 GTTTATGCTACCCAAAGAAATCTACAGATTTAATACAATTTTTATCTAAA 1669
                          viv  i  v      vvi           i  ii    iii    v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141375871_   1670 TTCCAATGACATTCTTCACAGAAATTTCTTAAA--AATCCTTAAATTTAT 1717
                          i   iivi v  i  ii        vvi-  i--i     v     i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_141375871_   1718 GTGGAT-CACAAATGACTCAGAATACCCAAAGCTGTCCTCAGCATAAAGA 1766
                         i    v-ii   iv   i       v     i vi  i v iv vi    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_141375871_   1767 ACAAAACTGGAGGGATCACATAACCTGACTT-AAAATTACACTACAGCGC 1815
                              ii      iv     ivv  ii i  -    i -i      iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_141375871_   1816 TATAGTAACCAAAACAGCATGGTGCTGGCATAAAAACAGATAT 1858
                           i     i   i    ii    i         ii i   i  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

Transitions / transversions = 2.65 (61 / 23)
Gap_init rate = 0.02 (5 / 291), avg. gap size = 1.20 (6 / 5)  

2301 23.92 2.55 0.64  chrX_141375871_141379304.rev     2317  2943 (491)    L1M4_orf2#LINE/L1      270   908 (0)  

  chrX_141375871_   2317 GTACTGGCAT-----TAAAAACATAGACCAATGTAACAGAATAGAGAGCT 2361
                                   -----  i v i     i     v  i     v     ii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_141375871_   2362 CAGAAACAAATCCACACACCTACAGTGAACTCATTTTTGATAAAGGTGAC 2411
                               i   i   i   ii  ii  v  i v     i  i  i    v 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_141375871_   2412 AATAACATACACTGAGAAAA--AGAGCCTCTTCAATAAATGGTGCTGGGT 2459
                           v v   v  v  i i   -- v  i  i     i             v
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_141375871_   2460 AAACTAGATTTCCATATGCAGAAGAATAAAACTAGACCCCCATCTCTTAC 2509
                         v    i   v?   i     i      i  ii i      i i   vi  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_141375871_   2510 CACATATGAAAATGAAAT-AAAATGGGTTAAAGACTTAAATCTAAGACCT 2558
                           i   ii     v  v -       i i ?    i     v     v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_141375871_   2559 CAAATTATGAAACTACTACAAGAAAACACCAGCAAAACTCTCCAGGACAT 2608
                         v   i   i     vi  v         ivi ?iv  v   i iv   v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_141375871_   2609 TGGCCTGTGCAAAAACTTCTT-GA-GTGATACCACACAAACATAGGCAAC 2656
                            vi iv    viii     -  -i   i    - -  i  i i     
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCA-A-AAGCACAAGCAAC 617

  chrX_141375871_   2657 CAAAGTAAAA-TGGATAAAT--GAGTTCACATCAAGTTAAAAAACTTCTG 2703
                         v    v    - i       --  v    --    iv v        i  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCA--TCAAAATTAAAAACTTTTG 665

  chrX_141375871_   2704 CACAGCAAAGAAAACAATCAGCAAAATAAAGAGACAACCCACAGAATGGG 2753
                         ii vv     i v  v    iv   i i  i                   
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_141375871_   2754 AGAAAATATTTGCAGACTACCTATCTGACAAGGTATTAGTAACCAGAATA 2803
                                       i ii iv       i    v i v   v        
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_141375871_   2804 TACAAGGAGCTCAAGCAACTCTATAA-AAAATGT--AATAATCCTATCAA 2850
                           i  i  i   vvi      v    -    v v--     i  v  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_141375871_   2851 AAGATGGACAAAAGATTGGAGTAGATGTCTCTCCAAAAAAGAGATACAAA 2900
                           i    i    i    v  i    ii i        i    v       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_141375871_   2901 TGGCAAACAGGTATATAAAAAGACGCTTAACATCACTGATCAT 2943
                             v  i i i i  i      i   i       ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (93 / 53)
Gap_init rate = 0.02 (12 / 639), avg. gap size = 1.67 (20 / 12)  


2435 26.93 4.43 1.25  chrX_141385273_141388074     1435  2314 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141385273_   1435 TGGAAACACCTCCCATGCTCATGGAAGGGTAGAATCAATATTGTAAAAAT 1484
                               v iv       i       vv  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141385273_   1485 GGCCATATTGCCAAAAGCAATCAAATAAATCCAGTTCAATTCCCATCAAA 1534
                            v   i v  v   vii   v -i i  i  iiv    i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTA-CAGATTCAACGCAATCCCTATCAAA 99

  chrX_141385273_   1535 ATATCACCATCATTCTTCATGGAACTAGAGAAAGC---------AATTCA 1575
                           vi  v vv v  i  iiii   v v  v  -  ---------      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_141385273_   1576 TATGGAATTAAAAAAGCCTCAGCATAGCCATAGCAAGAGTAAGCAAAAAG 1625
                                v iv  ii v i   v       v i   vvv i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_141385273_   1626 AACAAATATGGAGGCGTCACATTACCAGACTTCAATCTATACTTACAAAG 1675
                               vv      vv     i v  vi i     vviv    -      
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT-ACAAAG 247

  chrX_141385273_   1676 CTATAGTTACCAAAACAGCATAGTACTAGTATAAAAATAGGTATGTAGAC 1725
                            i   v i   i    ii i     i i    ii    ii  i    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_141385273_   1726 CAACGGAACAGAATAGAGAACCCAGAGATAAAGCCAAATACTTACAGCCA 1775
                            i    i     v    ii     i     v   v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_141385273_   1776 CCTGATCTTTGACAAAGCAAACAAAAACATAAAGTGCGAAAAGGATACAC 1825
                         vi    i  i     i vviv   i v   vv i  v i    i   vv 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_141385273_   1826 AATTCAACAAATGTTGCTGG--CAA-------GCCACATGTAGCAGATTG 1866
                         vv           v      --   -------?       i iv   v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_141385273_   1867 AAACTGAATCCTCATCTCTCACCTTATACAAAAAT-----CAAGATGGAT 1911
                           ii  i i  ii i   v    v           -----   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_141385273_   1912 GAAATACTTAAA-----GAACTGAAACCATAAAAATTCTAGAAGGTAACA 1956
                         v ? v  i    -----  i  i    i      v ii      iv    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_141385273_   1957 TCCAAAAAAACTCTTCTAGACATTGGATTATGCAG-AGTTTAT--GACCA 2003
                          vvi?iv   -     vv   v    i   v   i-i    v --  i- 
  L1M4_orf2#LINE/    548 TAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chrX_141385273_   2004 GGAAACCCAAAACAAATGCAACAAAAACAAAGATAAATATAAATAGATGG 2053
                         v  v   v   i  v v         -----  v   -   i   i  v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAA-----GAAAAA-ATAGATAAATTG 639

  chrX_141385273_   2054 GACTTAATTAAACTAAAAAGCTTCTGCACGGCAACAGAAATAATCAACGG 2103
                              v  i   v v    i   i  ii vv   vi  v iv     vii
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_141385273_   2104 TGTAAATGTACAACCCACAGAGTGGGAGAAAATCTTTGCAAACTATACAA 2153
                         v  i  viv            i           v        ii   i v
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_141385273_   2154 CTGACAAAGGACTAATATCTAGAATCTACAAGAAACTCAAACAAATCAGC 2203
                             i  i     vi    i     v  i  ii     vv    v   ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_141385273_   2204 AAGAAAAA----AATAATCTCATTAAGAAATGGGCTAAGCAAATGAATAG 2249
                           v     ----     i iv   ? i        v   v vv       
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_141385273_   2250 GCAATTCTCAAAAGAAAATATGCAAATGGCCAACAA--ACATAAAAA--T 2295
                         i  v     v      i    i           i  --    i    -- 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_141385273_   2296 TCTCAATTTCCGTAATTAT 2314
                         v     iv  v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.14 (124 / 109)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.94 (50 / 17)  


 475 23.08 0.00 0.77  chrX_141441383_141444443.rev      277   406 (2655)  C L1M4_orf2#LINE/L1   (0)   908   780  

C chrX_141441383_    406 ACAATTTTACAAGAAATAAACAAACTACCCCCATCAAAAAGCGGACAAAG 357
                             i iv i  v   v i     -  v   v  i?    ii  i     
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAAG 828

C chrX_141441383_    356 GATGTGAACAGACACTTCTCAAAAGAAGATATCTATGCAGACAACAGACA 307
                            v    i     i     v           vi viii v   i ii  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

C chrX_141441383_    306 CATGAAAAAATGCTCATCATCACTGGTCAT 277
                                 i       v     ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (18 / 11)
Gap_init rate = 0.01 (1 / 129), avg. gap size = 1.00 (1 / 1)  

2594 28.00 1.54 1.65  chrX_141441383_141444443.rev     1664  2570 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_141441383_   1664 GAAAAACATTCCATCCACATGGACAGGAACAATCAATATTATTAAAATGT 1713
                             i i  i    viv      iv    v v i      i    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_141441383_   1714 CTATACTGCCCAAAGCAATTTACATATTCAGTGCTATTCCTATCAAACTA 1763
                          v     v      vii  i    v     ii  v  i         v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_141441383_   1764 CCAA-TGA-TATTCTGCAAAGAAATAGAATAAACT-ATTTAAAAACTCAC 1810
                            i-  v- v  i    --     v  -i  i  -  iiv    i   i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCA--GAAATTGA-CAAGCTGATCCTAAAATTCAT 149

  chrX_141441383_   1811 ATGGAACCAAAAAGAGCTCA-AATAGCCAAGGCAATTCTAAGCAAAATGA 1859
                               viiv  i ii i  -         ii    ii i iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_141441383_   1860 ACAAAGCAGGAGCCATCATACTACCCAAATTCAAACCATACTACAGGGCT 1909
                               iv    vvv   i   v     v      v v       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_141441383_   1910 ACAGTAACCAA-ACAGCATGGTACTGATACAAAAACAAACACACAGACCA 1958
                                i   -    ii        ii i  ii i i   i i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_141441383_   1959 ATAAAACAAAACAGAAAACTCGGTCTATATG---CTGCACAACTAAAACC 2005
                           ii  i i  iv  i iii i --- v  i--- iii   vi  viii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAG---AAATAAACCCATACATTTATGGTC 346

  chrX_141441383_   2006 ATCTGCTCTTCAATAAGGCTGACAAAAAAAACAAAACAATGGGAAAA--A 2053
                          vi  v i   i i    v  v   i ---- v vv       i   -- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGA----CCATTCAATGGGGAAAGAA 392

  chrX_141441383_   2054 TGACTCCCCATTCAGTAAATGGTGCTGGGATAACTGGTTAGTTATATGCA 2103
                          - v  ii--    ii              i      v  ?ii i     
  L1M4_orf2#LINE/    393 T-AGTCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_141441383_   2104 GAAGATTGAAGCTGGACCCCTTCCTCACACCATACACAAAAACCAACCCA 2153
                         i    v     i         v            i       ii   i  
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_141441383_   2154 GGATGAATCAAAGACTTAGATGTAAAACC--AAACAATGAAAACCATGGA 2201
                         ii   i    ?    i  i      i v --    v  i   vi v i  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_141441383_   2202 TGACAACTTAGGCA-ATACCATTCTGAACACAGGAACT-GGCAAAGATTT 2249
                         v  v   v    ?i- v i v iv   v vii  --i -     v i   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTT 587

  chrX_141441383_   2250 CATCACGAAGATGCCGAAAGTAATTGCCACAAATGCCAAAATTGACAAAT 2299
                          v vivv v  ii  i    i vvv  v     v vv     v  i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_141441383_   2300 GAGATCTAATTAAACTAAAGAACTTCTGCACAGCAAAAGAAACTATCAAC 2349
                         vi  ii v  i   v v  i     i  ii vv    i  v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_141441383_   2350 AGAGCAAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAAACTATGC 2399
                          i  ii  v        i                 v        ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_141441383_   2400 AACTGACAAAGGTCTAATATTCAGCCTTTATAAAGAACTTAAGCAAATTT 2449
                          v    i  i  v  vi   i   vv v           ivvi   v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_141441383_   2450 ACAAGAAAGAAACAACCAACCCCATTAAAAAGTGGGCAAAGGGCATGAAC 2499
                          i  v   i i    vi     v   ?    i          iiv    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_141441383_   2500 AGGCACTTTTCAAAAGAAGACATACATGTAGCCAATAAGCATATGAAAAA 2549
                           i  i  i  v        i     vi i           i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_141441383_   2550 AAGCTCAACACCACTGATCAT 2570
                          v        i  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (153 / 97)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 1.71 (29 / 17)  


1587 26.94 2.74 3.06  chrX_141478003_141479613.rev      501  1120 (491)    L1M4_orf2#LINE/L1      291   908 (0)  

  chrX_141478003_    501 TACAGGCTAATA-AAGAGAATAGAGACCCCAGAAATAAATTAATTCACAT 549
                           i  iii   i-  v     v    vi           ------ v   
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA------CCCAT 334

  chrX_141478003_    550 ACAGTCAACTAATCAACTAATCTTTGACAAGAATGCTGAGAATACACCAT 599
                            v i -- ii    i i  i  i      ii   ii   vi iv v  
  L1M4_orf2#LINE/    335 ACATTTA--TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_141478003_    600 GGGGAAATAATATTTTCTACAATTAATGCTGTTGGGCAAATTGGATACCC 649
                                v    v i i v   iv    v  i    vv  i      ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_141478003_    650 ACATTTAAAAGAATGAAATTGGAGCACTATCTTACATGA-ATCACAAAAA 698
                             vi           i     v v   i  i   iv -  -       
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAA 481

  chrX_141478003_    699 GTAACTAAAAATAGATTATAGATTTTGTCGTGAAACATGAAACCATAAAA 748
                         v     v     i   i ?   ii vivi  i i vv i    i      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_141478003_    749 CTCTCGGTAGAAAAGAGGAAAAAAGATCAAAAAGATCTT---T---GTAA 792
                             ii v      v viii?iv i   vvviv  i   --- --- i  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_141478003_    793 TGATTTTTATGGATATGACACAAAAATTATAGGCAACAAAAGCAGAAGTA 842
                           i   i - i          v    vi i i          v i  i  
  L1M4_orf2#LINE/    582 TGGTTTCT-TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_141478003_    843 AACATGTTAGTCTACAGCAACATAAAAAGCATCTGCAATGCAAAGGAAAA 892
                         i i vi  i v  v  v   v  v    i v i  iiv v       v v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_141478003_    893 AACCAACAAAATAAAAAGGCAACTTATGGGACAAGACAATATATTCGTAA 942
                         v i   v   i i     i    ii ii i iii  v  v     i i  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_141478003_    943 AT-ATATTTTTGATAATGAGTTAATATC-AAAATATATTAA--ACTCAAT 988
                           -    v i      v iii vi    - i       v  --    v- 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT-T 779

  chrX_141478003_    989 ATAAACTCAACCAATCCAACAACAAAACAATATGATCC--T---AAAATG 1033
                          i  -     i------  i  v  i    -  i i  -- ---      
  L1M4_orf2#LINE/    780 ACAA-CTCAAT------AATAAAAAGACAA-ATAACCCAATTWAAAAATG 821

  chrX_141478003_   1034 GGCAAATAACTCAAATAGATATTTTTCAAAAGAAGATATACAAAAGGCCA 1083
                               vi i ii      i    i  v                v     
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_141478003_   1084 GCAGGGATATGAGAAGGTGCTCAACATCAGTAATTAT 1120
                         ii i v i    i   i            ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (103 / 61)
Gap_init rate = 0.03 (17 / 618), avg. gap size = 2.12 (36 / 17)  


2638 27.24 7.67 0.71  chrX_141512159_141514144.rev      649  1496 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_141512159_    649 GGAAAGATATCTCTTGGCCATGGATTAGAAGAATTAATATTGCTAACATT 698
                                    i v  vi        i     v         i   v  v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_141512159_    699 TCCACATTACCCAAAGCAATCTATAGATTTCATCTAATCTCTATTGAAAT 748
                         v v i i v      vii     i     iv ivi    i    ii    
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_141512159_    749 TCCAATAATGTTTCTCACAGAAATAGAAAAAT--ATCCAAAAATTTGAAT 796
                         i   iiviiv   i ii       v  v  ii--    v      iiv  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_141512159_    797 GAAAACACAAAGGATCCCAAATAGCTAAAGCAATCTCGAGAAACAAGAAC 846
                          i   ii   i   i  vi      i   i      i  i   v      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_141512159_    847 AAAGCCATAGAAACTACATTTCTTGATTTCAAACTATATTACAAAGTTAT 896
                             iiiv  i vii   i   iii        viv  i       i  i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_141512159_    897 AGTAATTGAAATAGTATGATACAGGCATTAAAACAGATACATAAGCCAAT 946
                               ii i i   i  i   v     v ii i   i i   iii    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_141512159_    947 GGAACAAAATAGAGAG------------CCCACACATATATGGTAAATGA 984
                             i i   v     ------------    i    v      v   vi
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_141512159_    985 ATGTTCAAAAAGAGTGCCAAAAATACACAATGGGAAA----CAGTCTCTT 1030
                           v   i v   i       i vi iv       i  ----i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_141512159_   1031 CAATAAATGATGTTGGAAAAATGTGATATCCACATACAAAAAAAAAGAAA 1080
                            i     i  i   i v  ivv    ?      i     i  v-   i
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT-GAAG 450

  chrX_141512159_   1081 TTAGATCCTTGGCTTCA-ACCATTTATAAAAATTGACTTGAAATAAATTA 1129
                           i  i  i i- i   -     v  i       i   ii    ii  i 
  L1M4_orf2#LINE/    451 TTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_141512159_   1130 ---------------------------------------AAGAAAATATA 1140
                         ---------------------------------------       i   
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_141512159_   1141 GAGGGAATGCTCCATGACATTGATTTTGTCAATAATTTTTTTTGGATATG 1190
                          i? v  vv  i i    v   iv  v v    ii   i  --i      
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--AGATATG 597

  chrX_141512159_   1191 ACACCAAATGTACAGGCAGCAAAAGCACAAATAAACACAGGGGCATGCAT 1240
                                 v i   i   i      v v     i i v vv  vv v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_141512159_   1241 CAAACTAAAAATCTTCTGCACAGCAAAGAAAACAAGCCATAAAATAAAAA 1290
                             v v    v   i  ii vv     i v  v v v v   i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_141512159_   1291 GGCAATTTATGGAATGGAAGAAGATAATTGGAAGCCATATATTTGATAAG 1340
                          i   iii ii      i    i   v   v  ii       i       
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_141512159_   1341 GGGTTAATATTGAAAATATATATGGAATTCATACAACTCAATGGCAATAA 1390
                           ii vi   iv i        vi   i  v           iii  v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_141512159_   1391 GA---ATAAA--AAT--AAAAATAAGCCAAAGACCTGAGCAGACATTTTT 1433
                           ---    v--   --      ii  v  i  ii   ii        i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_141512159_   1434 TTCCAAAGAAGACATACCAATGACCAAAAGGAATATGAAAATACGCTCAA 1483
                         --          i    v    i    v i v i       v i      
  L1M4_orf2#LINE/    848 --CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_141512159_   1484 CATCGCTAATCAT 1496
                             i????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (152 / 77)
Gap_init rate = 0.01 (12 / 907), avg. gap size = 5.92 (71 / 12)  


 622 25.08 11.29 3.13  chrX_141519973_141521863      500   818 (1073)    L1M4_orf2#LINE/L1      262   606 (302)  

  chrX_141519973_    500 ACAGTGTATTACTAACAAAAGAATATATAAGTAGATCAGTAAAATAAAAC 549
                                iv    ii  v   i   v i vi       i ii    i  i
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_141519973_    550 --AGAGCCTAGAAATAAACACATAAAATTAAATTCCACTGATTTTTGCCA 597
                         --    i i          v    v v   viv  v i       i v  
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_141519973_    598 AAAATGTCAATAC-----AATATAGAAAGTATAGTCTATTCAACAAGTGG 642
                          iii  i   v  -----   ivi     v       v        i   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chrX_141519973_    643 TG---------------ATCTA-----AAAAGTAAATAAATTTGGACATA 672
                           --------------- ? i -----     --   i  v      viv
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAG--AATGAAGTTGGACCCC 459

  chrX_141519973_    673 GGTCTTACAC-ATTTTCACAAAAATTAACTCAAAATATATTATTAAGA-- 719
                         vii  i    -  v --                   iv  i ?--   --
  L1M4_orf2#LINE/    460 TACCTCACACCATAT--ACAAAAATTAACTCAAAATGGATCAW--AGACC 505

  chrX_141519973_    720 TAAATGTAATA--TGAAA--AAGAAACAGCTAAGATGAAGACATAAAA-T 764
                                  v -- i   -- vi    -v  v   v   i     ii?- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACATAGGNGT 554

  chrX_141519973_    765 AATATATTGGTAACCTTGCATT-GGTGATGACATTTTAGATGCAATCCAT 813
                           -  v  v  i      vi  -  ii   iiv i      iii --  i
  L1M4_orf2#LINE/    555 AA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA--CAC 601

  chrX_141519973_    814 CAAAA 818
                              
  L1M4_orf2#LINE/    602 CAAAA 606

Transitions / transversions = 1.57 (47 / 30)
Gap_init rate = 0.05 (16 / 345), avg. gap size = 2.88 (46 / 16)  

 661 23.98 4.07 0.81  chrX_141519973_141521863     1153  1398 (493)    L1M4_orf2#LINE/L1      655   908 (0)  

  chrX_141519973_   1153 AAAAACT---GTTCTGTGAGAAACACTAACAAGAAAATTTAAAGTTAAGC 1199
                                ---  v  vii iii      v       i vv    vi  v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_141519973_   1200 TACAGAGTGTGAGAAAATATTTTCAAAACACACA-------AAGGACTGT 1242
                         i     i  v            v    v  i i ------- i     vv
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_141519973_   1243 TATCCACAATATACAAAAATCACTTAAAACTCAACGATAAGAAACACCAA 1292
                               v      i   i v v    v       ii    -   v  -  
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA-AAAGAC-AA 802

  chrX_141519973_   1293 ACAAGCCAATTAGAAAATAAGCAAAATAAATGAAAAGATACCTCACCATA 1342
                          i  v      ?i     ii     iv vv    v   i ii  v   v 
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_141519973_   1343 AAATAAATACAAATAGCAAATAAACACATGTAAAGATGCTCCATATTATG 1392
                         i  v v        i  v     i      v          v i  i ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_141519973_   1393 TCATTA 1398
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.00 (29 / 29)
Gap_init rate = 0.02 (4 / 254), avg. gap size = 3.00 (12 / 4)  


2739 22.85 5.09 0.78  chrX_141529381_141531134      496  1261 (493)    L1M4_orf2#LINE/L1      110   908 (0)  

  chrX_141529381_    496 CCTATTTT-CAGAAATAAATAAACTGAATTAAATTAAAATGCATGTGAAA 544
                            v    -       vi i  i    - i---i      v   i  i  
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGA-TC---CTAAAATTCATATGGAA 155

  chrX_141529381_    545 ATTCAAAGGATCTCATGTAGCCAAAAGAAGCTTGAA------GAACAAAG 588
                           v   i   i ivivi         v  v      ------        
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_141529381_    589 TTGAAAAACTCATACTTTTCTATTTCAAAATTTACAATCCAGCTATAGTA 638
                            i ii     i    ii v         i    v ivv     i    
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_141529381_    639 AATCAAAACATTGTGGTATTGGCATAAGTTTGGATATTTGGGTCACTTAA 688
                          -    i   v       i         vv i  i  v i i   v vi 
  L1M4_orf2#LINE/    256 A-TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_141529381_    689 GTAGAATTTTGAATCCAAACATAAACCCTCACTTTT-TA--CACCTGATT 735
                         i       vv  i    i v        vi  v   - i--  vi     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_141529381_    736 TTT-ACAAAGATTCTTAGACACTTCAATAGGGAAGGAAATGTTTTTTCAA 784
                           i-    i i v iv    vv      i     i   vv  i       
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_141529381_    785 CACACGACACAGAAATAAATGGATATCTGCATCCAAAATAATTATTTTGG 834
                           v i iii v ii i  v      ? ii   v     v   v vv    
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_141529381_    835 ACTTCTACTTTATACCATATTTAAAAATTATCTCAAAGTGGATCAAAGAC 884
                           ii    i i i       vi        v      i       ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_141529381_    885 ACAAATGTAAGAGCTAAAACTATGAAACTTTTAGAATTCAGCATAAGCAT 934
                         vi                     i     i      vvv i    i ?i 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_141529381_    935 AAATCATTTTGACCATGAATTAGGCAGTGGTTTCTTAGATGTGGCATCAA 984
                              v iv     v  ii       i             i  i  i   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_141529381_    985 ---------CCACATAAGAAATAAACTGATACATTTGATTTCATCAAAAT 1025
                         --------- v   v      -   iv    v   v  i           
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_141529381_   1026 TAAAAACTTACGTGCTTTAAAAGA-A--ATTAGAAAAGTGAAAAGACAAC 1072
                                  vi      i   i  - --  i ii                
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_141529381_   1073 CCATAGAAGGGTGGAAAATGTATTCAATT--TTTATCTGCTAAGAGTTTA 1120
                            i    v  vi      i v v   v -- v      v    i vi v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_141529381_   1121 TTATCTAGAATTTA-AAATAATTCTCACAAATCAGCAGTAAAAAGAAAAA 1169
                         v    i     v  -   v  i   i    v   ii i        v   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_141529381_   1170 -AAC--AATTT-----TT--TAAATGA---GAATAGGTATTTCACTCAAT 1206
                         -   --    ?----- v--i   v  ---      ii     v iv  v
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_141529381_   1207 AAGACATACAAATAGCTAATAAGCACATTAAAAGATACTCAATATCATTA 1256
                             i        i  i           v       i     i    ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_141529381_   1257 TAATT 1261
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.34 (98 / 73)
Gap_init rate = 0.02 (19 / 799), avg. gap size = 2.37 (45 / 19)  


2723 27.26 1.31 2.29  chrX_141570222_141573779.rev     2151  3067 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141570222_   2151 TGGAAACACATCCCATGCTCATGGATTGGAAGAATTACTATTTTGAAAAT 2200
                               v i        i               v   v    v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141570222_   2201 GACCATACTTCCCAAAGCAGTCTACAGATTCAATGCAATTCCCATCAAAA 2250
                          i v     i      viii             i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141570222_   2251 TACCAGCATTATTTTTCACAGAGTTAGAAAAAAAAAT--TAAAATGTGTA 2298
                          v     vviv     ii    iv v  v  ivvi  --      vii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_141570222_   2299 CGGAACCAAAAAAAAAAAAAAAGAGTCCACA-TAGTCAAAGTAATCCTAA 2347
                         i    ---------- viv  i iii   v -   i    ii    i i 
  L1M4_orf2#LINE/    151 TGGAA----------ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chrX_141570222_   2348 GCAAAAAGAACAAATCTGGAGGCATCACATTGCCTGACTTCAAGTTATAC 2397
                         iv  i         vi      vv     i v  ii i     iviv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_141570222_   2398 TACAAAACTA--GTTACCAAAATAGCCTGGTACTGGTATAAACGTATGCA 2445
                               i   --  v i   i i  iv         i    ivi  vi  
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_141570222_   2446 CACAGACCACTGGAACAAAATAGAGAACCCAAAAATAAAGCCAAATTCTT 2495
                         i i   i  v     i i   v    ii   i       v   v ivi  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_141570222_   2496 AAACCCAACTGATCTTTGACAAAGCATACAAAAAC-ATAAATTGGGGAAA 2544
                          vivi   i    i  i     i -i i v  i  -  vv v        
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAA 389

  chrX_141570222_   2545 GGACACCCTATTTAATAAATGGTGCCTAGAAAACTAGCTAGCCATATGTA 2594
                          i i vi  v  i  i         ivi  v    i v  ?   i   i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_141570222_   2595 GAAGAATGAAATTGGATCACTACCTCTCATCTTATACAAAAATCTATTCA 2644
                         i         i     i v       v  i v           iv i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_141570222_   2645 AGACGGATTGAAGATTTAAATCTATTCAAGGTGAATTGAAGATATAAA-- 2692
                          i i    ii?   ii     v  ----  --- ii i  iv      --
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTA----AG---AGCTAAAACTATAAAAC 532

  chrX_141570222_   2693 ---TAGATTATATCCTTGGAAAAACTCTTCTGGACATTACCCTAAGCAAA 2739
                         ---    vv v v v v  ?iv  v     vv   v  ivvi  i    v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_141570222_   2740 GAAATCATGAACAAAACCCGAAAAGCAAATGCAACACAAACAAAAATAAA 2789
                          ivv  v ii i vi  v v       v v      v  iv       i 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_141570222_   2790 TAAATGGGACATGATTAAA-TTAAAAAGCTTCTGGACAACAAAAGAAATA 2838
                              v    v v  i   -       -   i  vi vv    i  v iv
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT 681

  chrX_141570222_   2839 ATCATTCGAGTAAACAGACAACCCACAAAACGGGAGAAAATATTTGCAAA 2888
                             vvvi   i  v            i  i                   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_141570222_   2889 TTATGCATCTGGCAAACGACTAATATCCAGAATCTACAAGGAACTCAAGC 2938
                          i  ii     ii  iv    vi          v  i  i      vvi 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_141570222_   2939 AAATCATCAAGAAAAAAATCCAAATAATCCCATCAAAAAGTGGGAAAATG 2988
                           v   vi  v     i --       i  v  i?    i    v   v 
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_141570222_   2989 ACATGAGTAGACATTTCTCAAAAGGAGATATATGCATGGCCACCAAATGT 3038
                          iv   i            v    i       iiv       vi  iiii
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_141570222_   3039 ATGAAAAAATGTCCAACTTCACTAATCAT 3067
                                i   ii    v   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (141 / 105)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.75 (33 / 12)  


3163 24.67 1.43 1.65  chrX_141577394_141584483.rev     5692  6599 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_141577394_   5692 GAAAAACATTCCATGTTCATGGATAGGAAGAATCAATATTGTGAAAATGG 5741
                             i i  i              v      v i        v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_141577394_   5742 CCATACTACCCAAAGTAATTTACAGATTCAATGCTATCCCCATCAAACTA 5791
                          v     v      v i  i           i  v     i      v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_141577394_   5792 CCA-TTGACTTTCTT-CAGAGAATTAGAAAAATCTACTTTAAATTTCATA 5839
                            -i  v    i  -    -    -  v  iiiv iii    v      
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGA-AATT-GACAAGCTGATCCTAAAATTCATA 150

  chrX_141577394_   5840 TGGAACCAAAAAAGACCCCGTATAGCCAAGAAAATCCTAAGCAAAAAGAA 5889
                              viiv  ii     v v        i v    i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_141577394_   5890 CGAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAGGCTT 5939
                          i   i      vv   vi  v  ii i      viv        i   v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_141577394_   5940 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAAACCAA 5989
                               i   i    ii         i iv ii i   i     i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_141577394_   5990 TGGAAAAGAAC--AGAGCCCTCAGAAATAATGCCACACATTTACAACCAT 6037
                              v    i--    i  --        vv   i       iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_141577394_   6038 CTGATTTTTGACAAACCGGACAAAAACAAGCAATGGGGAAAGGATTCCCT 6087
                         i       i     ivvv v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_141577394_   6088 ATTTAATAAATGGTGTTGGGAAAACAGGCTAGCCATATGCAGAAAACTGA 6137
                         v  i  i        i     v   v  v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_141577394_   6138 AACTGGACCCCTTCCTTACACCTTATATAAAAATTAACTCAAGATGGATT 6187
                          ii         v   i     v    i              i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_141577394_   6188 AAAGACTTAAACGTAAGACGTAAAACCATAAAAACCCTGGAAGAAAACCT 6237
                          ?    i    i      vv      i      vi i i         v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_141577394_   6238 AGACA-ATATCACTCAGGACATAGGCAGGGGCAAACACTT------TATG 6280
                           i?i- v   -i  iv   v v  vvvi     vvii  ------    
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_141577394_   6281 ACTAAAACCTAAAAAGCAATGGCAACCAAAGCCAAAACTGACAAATGGGA 6330
                           ----   --       vvi     v    vv    iv  i    v   
  L1M4_orf2#LINE/    598 AC----ACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_141577394_   6331 TCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAG 6380
                         ii v  i   v v  i i   i  ii vv    i  v       vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_141577394_   6381 TAAACAGGCAATCTACAGAATGGGAGAAAATTTTTGCAGTCTATCCATCT 6430
                          i  v  i   i i                 v      ivii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_141577394_   6431 GACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAAGTTACCA 6480
                           i  i  i  vi          v  i  i     ivv    --i --  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA--CT--CA 787

  chrX_141577394_   6481 AAAAAAAAAAAAAAAAAAACC--ATCAAAAAGTGGGCAAAGGATATGAAC 6528
                          v  v     i v   v    --  i?    i            v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_141577394_   6529 AGACACTTCTCAAAAGAAGACATTTATGCGGCCAACAAACATATGGAAAA 6578
                              i     v        i  vi vii      i  i  i   i   i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_141577394_   6579 AAGCTCATCATCACTGGTCAT 6599
                          v     v     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (127 / 93)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 2.00 (28 / 14)  


1790 24.18 0.66 2.20  chrX_141603831_141609263.rev     1062  1516 (3917)    L1M4_orf2#LINE/L1        2   449 (459)  

  chrX_141603831_   1062 GGAGAGATATTCCACATTTATGGGGTTTATGGCTAGGAAGGCATACTATT 1111
                            i      i   i---------   i    v v     i v  v    
  L1M4_orf2#LINE/      2 GGAAAGATATCCCAT---------GTTCATGGATTGGAAGACTTAATATT 42

  chrX_141603831_   1112 GTCAAGATGTGAGCTCTCCCCAAATTGATCTATGGATTCAATATAAACCC 1161
                           i      vv iiv                 ii       iii  v   
  L1M4_orf2#LINE/     43 GTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chrX_141603831_   1162 AATAAAAATCCCAGCAAGTTATTTTATGTACATCGACAAACTGATTGTAA 1211
                         v  v           vivi v    iiiv v  i     i     iv   
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chrX_141603831_   1212 AGTTTAAATGGAGA-GAAAAAGACCAAGAGTAGCCAACACAATATTAAAG 1260
                          i  i v     i - v  ii    v   i       v     v  i  i
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_141603831_   1261 TTCAAGAACAAAGTTGGAAAACCCACACTACCTGATTTAAAGGCTTTCTA 1310
                         vvv               ii  i      v  ii    v  ii   v   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_141603831_   1311 TAAAGCCACAATAATCGAGACAGTGTGTAATTGGCA-AAGTAATAGACAG 1359
                         i     i   i     i          vv i     -   -i       v
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACAT 291

  chrX_141603831_   1360 ATTGATCAATGGAACAAAATAGAGAGCCCAGAAATAGATGTACACAAATA 1409
                           v           i i   v     i         i ivi i   vv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_141603831_   1410 TAGTCACCTGATCTTTGACAAAGGTGC-AAGGCAATATAATGGAGAAAAG 1458
                          i    vi    i  i     i     -   i v  vi     i    ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_141603831_   1459 ATAATCTTTCCAACAAATAGTGCTGGGATAACTGGAAATACACATTCAGA 1508
                            i     i        i         i       v ?v     v  i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_141603831_   1509 GATATAAA 1516
                         iiv  i  
  L1M4_orf2#LINE/    442 AGAATGAA 449

Transitions / transversions = 1.60 (67 / 42)
Gap_init rate = 0.01 (5 / 448), avg. gap size = 2.60 (13 / 5)  

1125 26.59 3.41 0.91  chrX_141603831_141609263.rev     1865  2304 (3129)    L1M4_orf2#LINE/L1      458   908 (0)  

  chrX_141603831_   1865 CCGACATTAAACCTTTTA-AAAAATAAACT-AAAATTGATTGAAAACCTA 1912
                           v  v i v   v v  -      v    -     v   ii? i     
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_141603831_   1913 AATGTA-GAACTCAGAATTATAAAAGTCTTAGAAGATAACATTGGAGACA 1961
                               -  i  - i  i       v          v     v  ? vv 
  L1M4_orf2#LINE/    508 AATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_141603831_   1962 ATCTAGATATTATTGAGTAGGACAACAACTTTTTATATCTAACGTCAAA- 2010
                             vvi iviv   i  vi i   iiii  i   v  v i  ii    -
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_141603831_   2011 ---CAAATAATTCATAAAAAATAATCTATAAACTGGACTT-----AAACT 2052
                         ---   ii  --  v  i   v   vv     i       -----   i 
  L1M4_orf2#LINE/    607 GCACAAGCAA--CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_141603831_   2053 AAAACCTTCTACTCTGCAAAATTACACTGTCAAGGGAATGAAAAGATATG 2102
                             v   i iiv  v    iv-     i     ii i        i vv
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGG-ACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_141603831_   2103 CCACAGACTGGAATGAAATAATTGGAAAAGACAAATCTCATAAAGGACTG 2152
                                v   i vi     v   v   vv i v    v    i     v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_141603831_   2153 TTATCTAAAATATACAAAGAATACTAAAAGTTCAACAATAAGAAAAAAAA 2202
                         v    i i      i      iv  v v ii    i     i  i v   
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_141603831_   2203 -AACATGATTAAGAAATAGGCCAAAGATATCAACAGACACCTCACCAAAA 2251
                         -   vii   ? i    i   v  i   v v  i     ii  v     i
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_141603831_   2252 AA--TAGGCAGATGGCAAATAAGCATATGAATATACGCTTAACATCATAT 2299
                           --  vi  i     v        i     v v i   i       ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_141603831_   2300 ATCAT 2304
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.19 (62 / 52)
Gap_init rate = 0.02 (10 / 451), avg. gap size = 1.90 (19 / 10)  

3325 26.63 0.66 0.33  chrX_141603831_141609263.rev     4038  4942 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141603831_   4038 TGGGAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4087
                            i ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141603831_   4088 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATTCCCATCAGGC 4137
                            v     v     iv i  i           i  v  i  i    iiv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141603831_   4138 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4185
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_141603831_   4186 TATGGAACCAAAAAAGAGCCTGCCTTGCCAAGTCAATCCTGAGCCAAAAG 4235
                                viiv  ii  v  v vv v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_141603831_   4236 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4285
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_141603831_   4286 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4335
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_141603831_   4336 AATGGAACAGAACAGAGCCTTCAGAAATAATATCACACGTCTACAACCAT 4385
                                i    iv   vv i         vvi  i  i i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_141603831_   4386 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 4435
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_141603831_   4436 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 4485
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_141603831_   4486 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 4535
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_141603831_   4536 AAAGACTTACGTGTTAGACCTAAAACCATAAAAACCCTAGAAGGAAACCT 4585
                          ?    i  vi   v   v       i      vi i      i    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_141603831_   4586 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTTATGTCTAAA 4634
                            ?i- v i -   iv   v v  vv i     v ii  iv ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_141603831_   4635 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 4684
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_141603831_   4685 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACG 4734
                         i   v v  i i   i  ii vv    i  v    i  vv i      vi
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_141603831_   4735 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAA 4784
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_141603831_   4785 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAA 4834
                           i  vi          v  i         vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_141603831_   4835 AACAAACAACCCCATCAACAAGTGGGCGAAGGATGTGAACAGACACTTCT 4884
                         i     i     v  i? v  i     i      v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_141603831_   4885 CAAAAGAAGACATTTATGCGGCCAACAG--ACATGAAAA-ATGCTCATCA 4931
                          v        i  vi vii      i i--         -       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_141603831_   4932 TCACTGGCCAT 4942
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


2612 25.69 3.07 3.40  chrX_141624149_141626515      964  1874 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141624149_    964 TGGAAAACT-TTCCATGTTCATGGACTGAAAGAATCTACATCATTAAAAT 1012
                               iv - i             i  i    v iv i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141624149_   1013 GACCATACTGCCCAAAGTAATCTACAGATTTAATGTTGTTTCCACTAAAA 1062
                          i v     v      v i           i  i ivi ii i ii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141624149_   1063 AACCAAC-ATCATTCTTACCAGAATTAGAAAAAAACT-ATCCTAAAATTC 1110
                         vv   i -ii v  i  i vii    i--- v  i  -            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_141624149_   1111 ATATAGAACCAAAAAATAAAATAAAATAAAATGCCAGAATAGCCAAAGCA 1160
                             i   ------------  iv  -iii i-              i  
  L1M4_orf2#LINE/    148 ATATGGAA------------ATGCAA-GGGAC-CCAGAATAGCCAAAACA 183

  chrX_141624149_   1161 ATCCTGAACAAAAAGAACAAAGCCAAAGGTGTCACATTATCTCACTTCAA 1210
                            i    v  i          iiii   vv     i vi iv i     
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_141624149_   1211 ACTGTACTTCAAAGCTATAGTAACTAAAAGAGCATGGTACTGGTATAAAA 1260
                          viv    v        i     ii  i v  ii         i    ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_141624149_   1261 GTAGACATGTAGACCAATGGAACATAATAGAGAATCTAGAAATAAGGCCA 1310
                         i       i    i        i v   v    i  i        iv   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_141624149_   1311 CACAGCTACATTAAACTGATCTTCAACAAAGTCAACAAAAACAAGCAATG 1360
                         i   vi  iiv v  i    i   i    i viiv   i v  vv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_141624149_   1361 GGGAAAG--TACTCCTTATTCAATAAATAGTGCCGAGATAACAGGGTAGC 1408
                                --  v  i  --    i    i    i i  i   v  i  ? 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_141624149_   1409 CATACACAGGAGAATAAAACTTGACCCTTACCATTCACCATATACAAAAA 1458
                           i ii  ii     i  ii v     i    viv               
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_141624149_   1459 TTAACTCACAATAAATTAAACACTTACATGTAAGGCCTCAAATTATAAAA 1508
                                 v   ii  i ? v  i  v       iv  v   i       
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_141624149_   1509 ATTCTAGAAGAAAACCTAAA---AAATACCTTTCTGGAAATTGTCCTTGG 1555
                         v ii           v  ii---    --   iv  - vv   vvi v  
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTG-ACCTTGGGTTAGG 578

  chrX_141624149_   1556 CAAACAGTTTAT--GATTAAGTCCTCACAA--ACAATTGCAACACAAACA 1601
                            -ii    v --   - v v vi  v  --    --      v  iv 
  L1M4_orf2#LINE/    579 CAA-TGGTTTCTTAGAT-ATGACACCAAAAGCACAA--GCAACAAAAGAA 624

  chrX_141624149_   1602 AAACTTGACAAGTGGGACCTAATTAAACTAAAGAGTTTCTGTACAGCAAA 1651
                            v v  i  i v    i v  i   v v  i ii  i   i vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_141624149_   1652 ATAAAAACTATCAACAGAGTAACCAAACAACCTTCAGAATGGAAGACA-T 1700
                         i--i v        v i   i vv i      iv        i   v - 
  L1M4_orf2#LINE/    675 G--GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_141624149_   1701 ATTCACAAACTATGCATCCAACAAAGGTCTAATATCCAGAATCTATAAGG 1750
                            ii    ii  ii   ii i  i  v  vi          v     i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_141624149_   1751 AACTTAAACTATTTAATAAGAAAAA---AAATA--CCA-TTAA------- 1787
                             ivv  v i i     v     ---     --   -  ? -------
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_141624149_   1788 GCAAAGAACAAGAATAGACATTATTTTTTTAAAGAAGACATATGAGGGGC 1837
                               i ivv           --- i ii        i   ii iv   
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATT---TCTCCAAAGAAGATATACAAATGGC 869

  chrX_141624149_   1838 CAACAA--ACATGAAAAAATGCTCAACATCACTAATCAT 1874
                            i  --         i             ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (149 / 82)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.36 (59 / 25)  


1933 26.68 3.04 1.76  chrX_141653617_141655234.rev      502  1127 (491)    L1M4_orf2#LINE/L1      275   908 (0)  

  chrX_141653617_    502 GGGATAATAACAGAGA-ACAGATAACCAACAGAATAGAATAGAGAGCCCA 550
                           v    vi i   v - i    ---   ii         v     i   
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGAT---CAATGGAATAGAATTGAGAGTCCA 321

  chrX_141653617_    551 GAAACAAATCCACGCACCTACAGTAAACTCACTTTTGACAAAGTGGCCAA 600
                             i   i   ii  ii  ii  v  i v i   i     i vv     
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_141653617_    601 GAGCACACACAGGGAAAAAGACAATCTCTTCAATAAACGATGCTAGGAAA 650
                           v  iv  vv   i   ii i i   i     i   i i    i   v 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_141653617_    651 ACTGGATATCTATTCATATACAGAAAAATAAAACTTGATCCATATCTCCT 700
                                 ? ----  i  i  i  i   i  ii v  i  v  i   vi
  L1M4_orf2#LINE/    422 ACTGGATAKC----CACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_141653617_    701 ACCTCATAGGAAAATGTAA-TCACAGTGGATTAAAGACCT---------- 739
                            vi   vi     -   -   v i     i ?      ----------
  L1M4_orf2#LINE/    468 ACCATATACAAAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_141653617_    740 -C--AAACTATGAACGTACTGCAAAAAATTATTGGGAATACTCTCTAAGA 786
                         - --       i  vv vi iv  i   vi  v  ?ivv v   iiiv  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_141653617_    787 CATTGGGCTGGGCAAACGTTTTCTGAGTGAT-ACCCCACAAGCACAGGCA 835
                          v     i i     -i v     v  vv  -  v   v       i   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_141653617_    836 ACCAAAGCAAAAATA-ACAAATGGGATCACATCAAG-TTAAAAAAACTTC 883
                           v    v       - i    v   iiv      i-       --   i
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA--CTTT 663

  chrX_141653617_    884 TGCACAGTAATGGATACAACCAAGACAGTGAAGAGACAACCCACAGAATG 933
                           ii vvi  v   i  v i     v      i                 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_141653617_    934 G-AGAAAGTATTTGCAAACTACCCATCTAACAAGGGGTTAGTGACCAGAA 982
                          -     i          ii ivi    i i     ii v  iv      
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_141653617_    983 CATGTAAGGAGCTACAACGACTCTATAGGGAAAAACCAAATAATCTGATC 1032
                         i  i   i  i  viv  i    v   ivi    iv       i ii  i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_141653617_   1033 AAAAAATGGGCAAAATATTTGAGTAGATTTTTTTCAAAAAAGGACGTACA 1082
                         ?             iv      i    iv   i  v   i i  ii    
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_141653617_   1083 AATGGCAAACGGTCATATGGAAAGGTGATCAACATCACTGATTAT 1127
                               v  iiiv  i   i    i  v         ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (104 / 59)
Gap_init rate = 0.02 (13 / 634), avg. gap size = 2.31 (30 / 13)  


 437 22.22 3.03 0.00  chrX_141781756_141788985      231   329 (6901)    L1M4_orf2#LINE/L1        1   102 (806)  

  chrX_141781756_    231 TGAAAAGACATCCCGTGTTCATGGATCTGAGCAATTAATATTGTTAAAAT 280
                           i     i     i           iv  iv v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141781756_    281 GTTCATAA---CCAAAGCAATCTGCATATTCAATGAAATCCTTGTCAAAA 327
                          viv   v---     vii    i  v      i v     i i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141781756_    328 TC 329
                           
  L1M4_orf2#LINE/    101 TC 102

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.01 (1 / 102), avg. gap size = 3.00 (3 / 1)  

1026 26.49 1.49 0.37  chrX_141781756_141788985     2344  2611 (4619)    L1M4_orf2#LINE/L1        1   271 (637)  

  chrX_141781756_   2344 TGGGAAAATATTTCATGATCATGGATTGGATGAATTAATATTGTTAAGAT 2393
                            i  i    ii    v            v  v                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141781756_   2394 GACAGTACTACTCAAAGCAATTTATGGACCCAATGAAAGCCCTATCAAAA 2443
                          i  i    v i    vii  i  ii  ii   i v  v           
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141781756_   2444 TACCAATGACATTCCTCACAGAAAT--AAAAAC--ATTCTAAGATTTATA 2489
                          v   iivi v  ii ii       -- v  i --  i    i   i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_141781756_   2490 TGGAACCACAAAAGACCCTGAATTCCCCAAGCAAACCTCAGCAGAAAGAT 2539
                              vii   ii     v    vv  v  i   v i v iv ii    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_141781756_   2540 CAAAGCTGAAGACATCACATTCCCTGACTTCAAAATTTACTACAAAGCTA 2589
                              i  i  ivv     i i  ii i       i              
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_141781756_   2590 TAGAAAACAAAACAGTATTGGT 2611
                         i  v  v   i     i -   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGT-GGT 271

Transitions / transversions = 1.96 (47 / 24)
Gap_init rate = 0.01 (3 / 271), avg. gap size = 1.67 (5 / 3)  

2208 25.65 0.77 2.30  chrX_141781756_141788985     4253  4903 (2327)    L1M4_orf2#LINE/L1      268   908 (0)  

  chrX_141781756_   4253 TGGTACTGGCATAAATACAGACATATAGACCAGGGCAAAAGAATACAGAA 4302
                                       iv i           i  iv v  v     vv   i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_141781756_   4303 CCCAGATATAAATGTATGCACTTACAGCCAATTCATCTTTAGCAAAGGCA 4352
                         i     v     ivi  i  i   ii i     v  i  iii   i  ii
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_141781756_   4353 CCA-GAACATACAATGGGGAAAGGACAGTCTTTTCAACAAACACTGCTGG 4401
                            -  v   v            i i               iiv      
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_141781756_   4402 AAAAACCAGATAACTATATGCAGAAGAATAAAGTTAGACTCCTATTTCTC 4451
                         i v   ii    ? i i     i      i     i   i    ii  v 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_141781756_   4452 AC-ATATACAAAAATAAAATAAAATAAAATAAAATAGATTAAAGACTTAA 4500
                           -            v  v ---------i     i   i ?    i   
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACT---------CAAAATGGATCAWAGACCTAA 508

  chrX_141781756_   4501 ATGTAAGATCTATAACTAAGAAACCTCTAGAAGAAAACACTGGCAAAACA 4550
                                 v   v     vi    iii            iv  ?iv  vv
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_141781756_   4551 CTCCAGGACATTGGTCTGGGTAATGATTTCTTGGGTAAGATCTCAAATGC 4600
                           i iv   v    vi i  i    i      i i  v  ivi    v  
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_141781756_   4601 ACAAGCAAACAAAGCAAAAATAGACAAATGGAATTACATTAG--TTTAAA 4648
                                 vv    v         i    v i i v   i i--  v   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_141781756_   4649 CTGCTTCTTCACAGCAAAGGAAGCAATCAATAAATTGAAGAGTCAACCCA 4698
                         --i   i vii vv       vi v     v   v    i  v       
  L1M4_orf2#LINE/    659 --ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_141781756_   4699 AAGAATGAAAGAAAGGAAT-GCAAACTATGCATTTGAAAAGGGGTTAATA 4747
                         v      ii     iv v -     ii  ii  i   v     ii vi  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_141781756_   4748 TCTTGAATATGTAATGAGTACAAACAACTCTATAAGGAAAAACTTAATGA 4797
                           iv      i   v  iiv vv       v    vi    iviv   i 
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_141781756_   4798 TCCAATTAAAACATGGCGGCAAAATATCTGAGCAGATATTTCTTAAAAAA 4847
                         i      ?   v    --     iv  i   ii   i      iv   i 
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGG--GCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_141781756_   4848 AAAGACATACAGATGGCCAACAATTATATGAAAAAATGCTCAGCATTTGT 4897
                          --  i     i        i  vi i       i       i   iv??
  L1M4_orf2#LINE/    855 A--GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_141781756_   4898 AGTTAT 4903
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.63 (101 / 62)
Gap_init rate = 0.01 (8 / 641), avg. gap size = 2.50 (20 / 8)  

3178 27.24 1.00 0.44  chrX_141781756_141788985     5835  6737 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141781756_   5835 TGGAAAAACATTTCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5884
                               i i  ii    i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141781756_   5885 GACCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCTCCAACAAGC 5934
                          i v     v      v i  i  i        i  v   i i v   iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141781756_   5935 TACCATTGACTTTCTTCACAGAATTAGAAAAAACGACTTTAAATTTCATA 5984
                          v   vivi i  i  ii     v v  v  ivi  iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_141781756_   5985 TGGAAGCAAAAAAGAGCCTGTATAGCCAAGACCATCCTAAGCAAAAAGAA 6034
                              iiiv  ii  v  v v        i  v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_141781756_   6035 CAAAGCTGGAGGCATCATGTTACCTGAATTCAAACTATACTACAAGGCTA 6084
                              i      vv   iii v  ii v      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_141781756_   6085 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAAACCAA 6134
                               i   i    ii         i iv ii i   i     i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_141781756_   6135 TGGAACAGAACAGAGGCCTCAGAAATAACATCACACATCTACAACTGTCT 6184
                              i    iv   ivii         vvi  i    i  iiiiiivi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_141781756_   6185 GATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 6234
                            i  i     ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_141781756_   6235 TTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAA 6284
                          i  i        i     v      v  ?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_141781756_   6285 GTGGACCCCTTCCTTATGCCTTATACAAAAATTAACTCAAGATGGATTAA 6334
                         v         v   i ii  v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_141781756_   6335 AGACTTAAATATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 6384
                             i     i     v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_141781756_   6385 GCA-ATACCATTCAGGACATAGGCATGGGCAAAGACCTC--AGGACTAAA 6431
                          ?i- v i -   iv   v v  vv i     v iii  --  i--  vi
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA--TATG 597

  chrX_141781756_   6432 ACACCAAAAGC-CATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 6480
                                    -  -i          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_141781756_   6481 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTTTCACACTGAAC 6530
                          i   v v  i i   i  ii vv    i  v     ivvv v v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_141781756_   6531 AGGCAACCTACAGAATGGGAGAACATGTTTGCAATCTATCCATCTGACAA 6580
                           i     i              v  i       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_141781756_   6581 ATGGCTAATATCCAGAATCTACAAAGAATTTAAACAATTTTACAATAAAA 6630
                         iv i  vi          v  i      i ivv    i iv i       
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_141781756_   6631 AAA-----AACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAATTC 6675
                          i -----     v  i?    i    ii      v    i     v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_141781756_   6676 TCAAAAGAAGACATTTCTGTGGCCAACAAACATATGAAAAACACCTCATC 6725
                           v        i  vivvi       i  i  i       ivvv    v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_141781756_   6726 ATCACTGGCCAT 6737
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.86 (13 / 7)  


2091 24.58 8.99 1.26  chrX_141795287_141796990      500  1211 (493)    L1M4_orf2#LINE/L1      142   908 (0)  

  chrX_141795287_    500 AAATTTACATGGAAAGACAAGGGAAGTAAACTAGTCAAAATACTTTT-AA 548
                              i i       vi       vvi i v   i     i v i  -  
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_141795287_    549 AGTGAAGACTATCATTGAAGGATGCACACTGTCCTGTTGTAAGATTTACT 598
                          iv     vi vvi   i    iv      vi  vi  vi  i i     
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_141795287_    599 ATAAAACTATAGTAACCAAAACAGTGTAATCTTGGT-TAAGGGAAAGACA 647
                          i   i   i     i   i       ii vi   i-     - v     
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAGACA 290

  chrX_141795287_    648 CAGTGATCAAAAGAGCAGAATTATGCGTTCAGAA-TAGATCCACAGAAAT 696
                         i vv      vi  ii      iv v  i     -  i i   i v vv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_141795287_    697 A-GGCCAATTGATTTTCTACAAAGGTACAAAAACGTTTCAGTGGAGAAAG 745
                          -  i            v    i   i v  i  vv    i   i     
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_141795287_    746 GATG--CTTTCAGATAAATAGTGTTAGGGAAATTAGACATCCCTATGCAA 793
                         i  i--    ivi i    i   i i  iv  i i  i ?  vi      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_141795287_    794 A-TAATGAA------------CCTCACATTGTATCTAAAAATTAACT--- 827
                          -v      ------------       iii   vi           ---
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_141795287_    828 ----GAT---AGACCTAAATATAGAATGTAATACTATGAAACCTTTATTT 870
                         ----   ---          i  ii vv   v     i    ii   ---
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA--- 537

  chrX_141795287_    871 AGAAGCAGAAAT--GAGAAAATC---ATGACTGTGG-TTAGGCAAAGATT 914
                         -    v i v  -- ? v     ---i    iv   -        v i  
  L1M4_orf2#LINE/    538 -GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_141795287_    915 TCTTACACATGACAACACAAGCACAATCCTTAAAAGAAAAAA-AAATACT 963
                              v i      v  v        v vvi           - i   --
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA-- 634

  chrX_141795287_    964 AAATTGGACTTTATCAAAATTAGAGACTTTTGCTCTGAGAAGAACACTGT 1013
                         -          i          i i       iv  vvi   i     i 
  L1M4_orf2#LINE/    635 -AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_141795287_   1014 TAAGAGAATGAAAAGGCAAGCTACAGAA--------AACGT------ATC 1049
                         i    i i       i   v i      --------  ii ------   
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_141795287_   1050 ACATACATGACAAAGAACTTGCATCTAGAATATATAAAGACACT---A-A 1095
                          i   iv   i  i i     i   i              -   --- - 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA-ACTCTTACA 782

  chrX_141795287_   1096 ACTCAGGAATAAGAA-ACAAATAA---------AAAGTGGACAAAATTCT 1135
                              iv     i  -        ---------   i   i    ivvi 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_141795287_   1136 TGAAGCAACAATTCACAAAGGAGAAAATACGGCTGGCATATAAGCACATG 1185
                             vvi   v   v v  i  ii v    iiv    vv           
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_141795287_   1186 AGCATATGGGCAACATCATTGTTCAT 1211
                          iv v   vv        ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (106 / 67)
Gap_init rate = 0.03 (23 / 767), avg. gap size = 3.17 (73 / 23)  


2958 26.82 1.21 0.99  chrX_141831858_141834508     1264  2169 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141831858_   1264 TGGAAAGATATTCCATGTTCCTGTATTGGAAGACACAATATTGTTATAAT 1313
                                    i        v  v          vi          vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141831858_   1314 GTCCATATTACCCAAAGCAATATACAGATTCAATCAAATCCCTGTAAAAG 1363
                          v v   i v      vii  v           ivv       i v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141831858_   1364 TACCAATGACATTCTTCACAGAAATAGAAAAAAGAATTCTAAAACTTATA 1413
                          v   iivi v  i  ii       v  v  ivvi  i      i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_141831858_   1414 TGGAACTACAAACCACCCAGAATAGCCAAAGTTATCCTAAGAAAAATGAG 1463
                              v i   ivv                iiv   i i i   i v  i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_141831858_   1464 CAAAACTGTAGAACTTACAGTACCTGACTTCAAATTATACTA--GAGTTA 1511
                             ii  v  i   i   v v  ii i      viv     --i  i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_141831858_   1512 TAGTAAGCGAAACAGCATGGTATTGGCATAAAAATAGACACATAGACCAG 1561
                         i     v i i    ii     i        ii       i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_141831858_   1562 TGGGAAAGAACATAGAACCCAGAAACAAACCCCAAACACC-ATAGTGAAC 1610
                            i v    ivv   ii       i      - v   ii-  i  v  i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCC-ATACATTTATGGTCAAT 349

  chrX_141831858_   1611 TCATTTTCATCAAGGGTTCCAAGAACATATACTGGGGAAAAGACAGTCCC 1660
                          v      iv       v      v   vi v        ii i    ii
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_141831858_   1661 TTCAATAAATAGTGCTGTGAAAACTTGATACCCATATGCAGAATAATGAA 1710
                              i    i      v  v    v    ?   i     i  v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_141831858_   1711 ACTAGACTC--ATCTCTAGCCATATACTAAACATAAATCAAAATGGATTA 1758
                         ii i   i -- i   vvi        v   vv   v           i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_141831858_   1759 AATATTTAAACGTAAG-GCATCAAACTATGAAAGTACTACAAGAAATCGT 1807
                         ? v ii    i     -  - v       i   v vi  v      v i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_141831858_   1808 TCATGAAACTCTCCAGGACCTTGTTCTGGGCAAAAATGTCTTGAGTAATA 1857
                         vvi? v  v   i iv       vvi i     vii v    iii  vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_141831858_   1858 CCCCATAAGCACATGAAACCAAAACAAAAGTGAACCAATAAAATCACATC 1907
                          v   v       v v   v   iv    i ii iv   vii iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_141831858_   1908 AAGTTTAAAAGTTTCGGCACAGCAAATAAGACAATCAACAACGCGAAGGG 1957
                           iv      ii  iv ii vv    vi v  v     v  v i   ii 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_141831858_   1958 ACAACCCACAGAATGGGAGAAAATATTTTCTAACTACCCATCTGACAAGA 2007
                                                     v v  ii ivi      i   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_141831858_   2008 GATTAATGTAT--AGAATATATAAGTAGCT---GAAACTCTATAGGAAAA 2052
                           i --     --           iv i  ---iv     v   iv    
  L1M4_orf2#LINE/    749 GACT--TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_141831858_   2053 AAATCTAATAATCTTATGCAAAAATAGCCAATAGATTTGAATAAACATTT 2102
                          i - v     i iv  v?      i v   vi          i      
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_141831858_   2103 TTCAAAAGAAGACACACTAATGGCAAACAGGAATATGAAAAGGTGCTCGT 2152
                         i  v        i i  v      v  i i v i        i     i-
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA- 894

  chrX_141831858_   2153 CACTGATCATCAGAGAA 2169
                         -  --    ????????
  L1M4_orf2#LINE/    895 -AC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (137 / 102)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


2915 27.49 1.90 0.45  chrX_141859318_141863503.rev     2801  3695 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141859318_   2801 TAGGAAAATATTCCATGTTCACAGACTGGAAGAATCTGTATTGTTACAAT 2850
                          i i  i    i         ii  i       v ivi        vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141859318_   2851 GTCCATACTACCCAAAGCAATCTGCACATTCAATGAAATATCTATAAAAA 2900
                          v v     v      vii    i  v      i v   vi    v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141859318_   2901 TACCAAGGACAGTCTTCATAGAAATAGAAAACATAATCCTAAAATTTATA 2950
                          v   ivvi vv i  iii      v  v  vv i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_141859318_   2951 TGGAACTGCAAAAGACACAGAATAGCGAAAGCTATCCTAAGCAAAAATAA 3000
                              v     ii   v         v   i v   i i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_141859318_   3001 GATAACAGGAATAATCATGGTACCTTACTTCAAATTATACTACAGAGCTA 3050
                         v v iiv   iv v   iiv v  iv i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_141859318_   3051 TAGTAACCAAAACAGCATGATAATGTCACAAAAACAGATGCATAGACCAA 3100
                         i     i   i    ii  i  v  v  i  ii i   iii     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_141859318_   3101 TAGAACAGAATAAAGAATCCAGAAAAATATCCATACATCTTCAGTGAACT 3150
                          i   i     vi   i        v v i        i vii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_141859318_   3151 CATTTTTGACAAAGGTGCCAAAAACATACACTGGAGAAAAGACAGTCTC- 3199
                         v     i     i        i v   v  v   i    ii i     i-
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_141859318_   3200 -CAGTAAATGCTGCTATGAAAACTAGATTTCCATATGCAGAAGAATGAAA 3248
                         -  ii     v    iv  v    i   v?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_141859318_   3249 CTAGACACCTATATCTTGCCTTATACAAAAATCAAATCAAAGTGGATTAA 3298
                         i i   v    iv  vii  v           i  v     i     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_141859318_   3299 AGACTTAGACCTAATACATGAAACTATGAAACTACTACAACAAAACATTG 3348
                             i  i iv   v vv i       i     vi  v  v       v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_141859318_   3349 GGGAAAATCTCCAGGACATTTGTGTGGGCAAAAATTTATTGAGCAATACC 3398
                          ? v      i iv   v  v vv i     vii   v  iiii vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_141859318_   3399 TCATTAGCACAGGCAATTAAAGCAAAAATGGACAAATGGGG-----TCCA 3443
                         i  vv      i    iv    v      i  i    v  i-----  v 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_141859318_   3444 GTTAAAAAACTTCTGCAC---AAGGGAAACAGTCAAGAAAGTGAATAGAC 3490
                         iv v        i  ii ---  i   v  vi             v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_141859318_   3491 GACCTTCAAAATAAGGAGAAATTATTTGCAAACTACCTACCTGATAGAGG 3540
                         i   iv  i   i-       v          ii iv  i      ii  
  L1M4_orf2#LINE/    701 AACCCACAGAATG-GGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_141859318_   3541 ATTAATAATCAGAA------AATAACTCAAGCAACTCTATAGGGAGAAAA 3584
                          i vi  vi     ------  v     vvi      v   --- v    
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA---ATAAAA 796

  chrX_141859318_   3585 A-ACTAATAATCCAACTAAGAAATGGGTAATTGATTTGAATAGACATTTC 3633
                          -  v     i    i ? i       i  vv                  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_141859318_   3634 TCAAAAGAAGACGTTCAAATGACAAACAGATATATGAAAAGTTTCTCAAC 3683
                           v        ii v      i v  i iii i        v v      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_141859318_   3684 ATCATCAATCAT 3695
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (138 / 104)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.00 (21 / 7)  


 825 28.89 7.29 9.92  chrX_141874103_141876660.rev     1292  2087 (471)    L1M4_orf2#LINE/L1      134   908 (0)  

  chrX_141874103_   1292 TAATTCTACAACTTACATGGAAATTCAATGGGGCAAAATTACTCAAGA-- 1339
                          i  i   v  i i i        v   v  iv v i v  vi   i --
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_141874103_   1340 ATATCGAAATATC-TAACA----TGCAG----TATAATTACTAGACAGCA 1380
                           v i    v vv-v    ----  v  ----i i v  v i - ivv  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTCA 232

  chrX_141874103_   1381 ACA---ATTATAAATCCACTGTAATTTGGACAGAGTAGTATTTGTGTAAT 1427
                          v --- i  i   v i  v     ivi     v  i   i v ii   v
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_141874103_   1428 AATAGAAAAATAACCCAATG--AT--------GAGCCCAGAAAGTAGCCC 1467
                         i     v v   ivi     --  --------   i       vv i   
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_141874103_   1468 ACATATATATGTTAAGGTAACTTATGACAAAGGTGCCCCTACAGTATAGT 1517
                          i i  v    v v iv i i  vi     i      vvv  vi vi i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_141874103_   1518 AGGAAAAGGTTGCTATTTTAAGTAAATGGTGCTTGGA-AATTGGAAATTT 1566
                         i  i    iv iv v    v ii          v   -  i    v ?ii
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_141874103_   1567 TTATATGAAAA---------------CTATCTCATCTGATACGCAAAAAT 1601
                         vi  iii   i---------------   i    iviv   ii       
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_141874103_   1602 TATTTCCAGATGTCTCAAAAATCTGAAAATGAAAGCTAAAACAATAAAGC 1651
                           vi  v i   vv   ? i i  i  vi i i         v     i 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_141874103_   1652 ATTTGAGAGAAGCTATAGGATAATATAATAATAAATAAATAAATAAAATA 1701
                         vi  ---     --------------------------------------
  L1M4_orf2#LINE/    533 TCTT---AGAAG-------------------------------------- 541

  chrX_141874103_   1702 AAAATAAAAATAAAATATAACTAAAATAAAAAAAAAATTAAAAAAAAGTC 1751
                         -----------    i   i---i?i    ------------------  
  L1M4_orf2#LINE/    542 -----------AAAACATAG---GNGTAAA------------------TC 559

  chrX_141874103_   1752 TTTGTGATCTGGAGT-AGGCAAAGATTTCTTCAACAGGACATAAATAGCA 1800
                           i    i  v i  -      v i      vi i v    iv  v    
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_141874103_   1801 TTTTCCATAGAGAAAAAAAAGTTGATTCACTGTATCTTATTAAAGTTAAA 1850
                         ivvv v i i ii      -- v   vv i  v ii i  i   i     
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAA--TAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_141874103_   1851 AATGTATAATCTACAAAATGTATGCTTAAAAGAGTGAAGTAGTAAGTTAC 1900
                           iv v ivv  v    ivii ivv i  i i      iviii  vii  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_141874103_   1901 AAAGTGGGAGAAAAT-TTTATATATATATATATATCT--CAAAGGACCTG 1947
                          i i           -   ii v  ---i        --i  i    i  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAAT---CATATATCTGATAAGGGACTTG 754

  chrX_141874103_   1948 AATCCAAAATATTTCAGGAACT---ACAA----ATAATAAGAAGTCAAAA 1990
                         v     i     v v i     ---    ----       i   v    v
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_141874103_   1991 AATCTAATAGAAAAATGAATACA--ATTTAAAAAGGCAAGTCACCAAAGA 2038
                           i i   v?       iii v --    i  v  i  vv  v       
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_141874103_   2039 GTATAACCAAATAGCCAATAA--AAATGTAA---TGTTTAATCTTGATGC 2083
                         iv   vv     i        -- v   v  ---  i i  iv ii????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_141874103_   2084 CTAA 2087
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.33 (129 / 97)
Gap_init rate = 0.03 (24 / 775), avg. gap size = 5.71 (137 / 24)  


2938 26.91 2.59 0.79  chrX_141956244_141964945      766  1653 (7049)    L1M4_orf2#LINE/L1        5   908 (0)  

  chrX_141956244_    766 AAAATATTCTATGGTAATGAATTGCAAGAATAAATACTGTTAAAATGTTC 815
                           i    i i   v v   i    v    v v    i      i   viv
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_141956244_    816 ATACTACCCAAAGCAATCTGCAGGTTCAAGACAATCCCTATTAAA-TACC 864
                              v      vii    i   i     vi          i   - v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_141956244_    865 AATGACATTTTTCACAAAAAGTGAAAGAATAGTTCTATACTTTATATGGA 914
                          iivi v     ii  i   v   v iiv ii i   v v  i       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_141956244_    915 ACCATTAAAGAGCCAGAATGGTCAAAGCTATCCTGAGCAAAAAGAACAAA 964
                          viiiv ii  v       i i    i v   i   iv  i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_141956244_    965 ATTGTAGGAACCACATTACTTGACTTTAAATTTTACTACAGAGCAACAGT 1014
                         i   v    vi    i v iii i  i   vi        i   v     
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_141956244_   1015 AACCAAAACAAGATGGTAATGGCATGAAAACAGACACATAGACCAATGGA 1064
                           i   i   ivi     v      i ii i     i     i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_141956244_   1065 ACACAATAAAGAATGCAGAACAAAATCCACACAACTACAGTGAACTCATT 1114
                          i v   vi   i v     vv   i   i   vi  ii  v  i v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_141956244_   1115 TTCAACAAAGGTACCAATAACATACACCAGGAAAAAGGCAATCTCTTCAA 1164
                            i    i   i    v v   v  vii  i   iiii i   i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_141956244_   1165 TTAGTGATGCCGGGAAGATAGGATATCCATAGGCA---GAATGAAACTAG 1211
                         iv i  i   i    vi iv     ?   i v   ---       ii i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_141956244_   1212 ACCCCTA------------TGCAAAAATCATATCAAAATAAATTAAAGAC 1249
                                ------------ i       i vv       ii  i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_141956244_   1250 TTACATGTAGGACCTCAAACTATGAAACTACTACAAGAAAACTTTGGTGA 1299
                         i  v     i  v  v       i     vi  v        v v  ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_141956244_   1300 AATTCTTCAAGACATTGGTCTAAGTAATAATTTTTTGAACAATACCCCAC 1349
                           v     iv   v    vi  i i   ii   i  ii i vv  v   v
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_141956244_   1350 GAGCACAAGGCTACCTAAGCAAAAATGGACAAATGGGA--TCACCTAAAG 1397
                         i        - v  vv   v      i  i    v   --   i -   i
  L1M4_orf2#LINE/    605 AAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATC-AAAA 652

  chrX_141956244_   1398 TTAAAAAGCTTCTGAACAGCAATGGATACAATCAACAAAGTGAAGAGGTA 1447
                                -   i  vi vv   v   i  v     v        i  ii 
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_141956244_   1448 ACCCACAGATTAGAAGAAAACATTTGCACAGTACCC-TCTAACAAGGGAC 1496
                                  v i i      i       v vi ivi-   i i       
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_141956244_   1497 TAATAACCAGAATATATAAGGAGCTCAGA-AACT---TTATAGGAAAACA 1542
                          vi  v             i  i   vv -    --- v   ii  i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_141956244_   1543 AATATAAAAATCAAATAAAAAATAAACAGAAGACTTGAGTAGGCATTTCT 1592
                             ---- vi   v ?      iii  i i  i    i   i       
  L1M4_orf2#LINE/    802 AATA----ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_141956244_   1593 GAAAAGAAGACATACAAATGACAAAGAAGCACATGAACAGATGTTTAACA 1642
                         vv        i         i v  v           v     i i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_141956244_   1643 TCATTGTTCAT 1653
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.58 (144 / 91)
Gap_init rate = 0.01 (11 / 904), avg. gap size = 2.73 (30 / 11)  

2606 25.89 3.11 2.22  chrX_141956244_141964945     7311  8210 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_141956244_   7311 TAAAAACACATTTTATGTTCATGGATTGAAAGAATAAATATTTTCAAAAT 7360
                          ii   v i  iii              i    v v      v i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_141956244_   7361 GATCAGACCACTTAAAGCAATCTACAGATTTAATGCAATACCCATCAAAA 7410
                          iiv v  iv ii   vii           i  i     v  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_141956244_   7411 TACCAA-TATCATTTTTTTACAGAA-TTAGGATAAAC-AATCTTAAAATT 7457
                          v   i- ii --      i     -  --  i  i -i   i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATT 146

  chrX_141956244_   7458 CATATGGAA-TCAAAAAGATCCCAAATAGCCAAAGCAATTCTAAGAGGAA 7506
                                  - vv  ii  i  vi          i    ii i i --  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA--AA 194

  chrX_141956244_   7507 AAACAACAAATCTGGAGGCATCACATTACTGGACTTTAAATTATACTACA 7556
                         i  v      vi      vv     i v ivi i  i   viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_141956244_   7557 AGGCTATAGTTACGAAAAAAACATGGTACTGGTATAAAAATAGGGAGACA 7606
                          i    i   v iv  i v iii         i    ii    ----   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG----ACA 290

  chrX_141956244_   7607 TAAAGACCAATGGAACACAATAGGGAACCCATGAATAAAGCCAAACACTA 7656
                           v   i        i v   v i  ii   vi      v   v   i v
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_141956244_   7657 ACAACCAACTAATCTTCAACAACCAATACAAAAAC-ATAAACTGGGGAAA 7705
                          iiii   i i  i   i    v-ii i v  i  -  vv v        
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAG-GGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_141956244_   7706 GGACATCCTATTTAT--AATGGTGCTGGGAAAACAGGGAAGCCACATGTA 7753
                          i i vi  v  i v--             v   v  iv ?       i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_141956244_   7754 GATGAGTGAAATGGGACCAGTTTGTCTCACCTTATACAAAAATCAACTCA 7803
                         i v  i    i v     vv viv  v    v           i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_141956244_   7804 GGATGGATCAAAGACTTAGGTCTAAGACCTGAAACCCTAAACATTCT-AG 7852
                         ii        ?    i  ii v     v  i    iv    - i   -  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAG 538

  chrX_141956244_   7853 AAGATAACATTGGAAAAACTCTTCTGGACATTGACCTAGGCAAAGAATTC 7902
                             v     v  ?iv  v     vv   v   ivi       v iv   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_141956244_   7903 ATGAATAAGACCTCAAAAGTAAATGCATCAAAACCAAAAAATAAATTAAT 7952
                         v ii   v   vi      i v v   v     v-        i  v   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAAT 637

  chrX_141956244_   7953 GAAACCTAATTAAACTGAAAAACTT-----CCTCATAGG-CA-----AAG 7991
                         vii  i v  i   v v        ----- i   v   -  -----   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_141956244_   7992 AAATAATGGAGTAAACAGACAACAGAGAGAATGGGAGAAAATACTTGCAA 8041
                            -------  i  v       vv v                i      
  L1M4_orf2#LINE/    688 AAA-------GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_141956244_   8042 GCAATGCAGCTGAAAAAGGACTAATTTCTGGAATCTACAAGGAACTT--- 8088
                         iiv  ii v    v  i     vi v  ii    v  i  i     i---
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_141956244_   8089 -AAATCAGTAAGAAAAAAA-AAAT--TCCCGTCAAAAACTAGGCAAAGGA 8134
                         -  v   i   v     i -    --i  vi i?    v i         
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_141956244_   8135 TGTAAATAGACATTTCTCAAACTAAGATGTACAAATGACTAACAAGCATA 8184
                          v i              v  vv     i        i i  i     i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_141956244_   8185 --AAAACATACTCAATATCGCTAATCAT 8210
                         --    v  i     i   i????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (134 / 95)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.18 (48 / 22)  


2870 23.76 7.88 1.29  chrX_142011058_142014667.rev     2270  3119 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_142011058_   2270 GAAAAATATTTCATGTTCATGTATTGGAAAGATTGATATTGTTAAAATGT 2319
                             i    ii          v       iiv  i          i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG- 51

  chrX_142011058_   2320 GCCTACCTACTACCCAAGC-AATCTACAGATTCAATTCAATCCCTATCAA 2368
                           -- v-    v     ii-i              iv             
  L1M4_orf2#LINE/     52 GC--AA-TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_142011058_   2369 AATACTAGTGACAATTTTCACATAAATAAGCAAAACAATCCTAAAATTTA 2418
                            v i  ivi vv    ii  v    vii   ivii           i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_142011058_   2419 TACAGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAACTAAAGG 2468
                           ii   vii   ii                 i v   i i  vv i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_142011058_   2469 AACAAATCTCGGGGAATCACATTACCTAACTTCAAATTATACTACAAAGC 2518
                               vi v i   v     i v  i  i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_142011058_   2519 CATAGTAACCAAAACAGCATGGTGCTATCATAATAACAGACATACATACC 2568
                         i i     i   i    ii    i  iv     vi i       i v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_142011058_   2569 AAAGGTACAGAATAGCAAACCCAGAAACAAATCCATACACCTATAGTGAA 2618
                           v  v i     v vi ii       i   i       ii   i  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_142011058_   2619 TTCATTTTTG-CAAAAGTACCAAGAACATACACTGGGGAAAAGACAGTGT 2667
                           v     i -   ii  i      v   v  v        ii i   v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_142011058_   2668 CTTCAATAAATGGTTCTGGGAAAACTGAATATCCATATG---AAGAATTT 2714
                         i     i       v      v     i   ?   i   ---      v-
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG- 447

  chrX_142011058_   2715 ATTTTATTTAGATCCCTGTCTGTCACCATATACAAACGTAAAACCAAAAT 2764
                          ---- v  i  i    ii  vv             vi v  vi      
  L1M4_orf2#LINE/    448 A----AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_142011058_   2765 GGATTAAAGACATAAATATAATAATTCAAAGCATAAAACT---ACAAGAA 2811
                             i ?    v     i   v ii v   vi        --- v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_142011058_   2812 AACTTTGGGGAAAATCTCCAGGACATTGGTCTGCACAAAGGGTTTTTTAG 2861
                            v v  ? v      i iv   v    vi ivi   -v     i    
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAG 592

  chrX_142011058_   2862 -TAATACCCTACAAGCACAGGCAACCACAATAAAAATGGGCAGATGGGAT 2910
                         -  vv  v i v       i     v v iv      i ii i  v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_142011058_   2911 TACATCAAG-TTAAAAAGCTTCTGCACAGCAAAGAAAGCAATCAACAGAG 2959
                          v      i-       -   i  ii vv     i vi v     v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_142011058_   2960 TGAAGAGACAACCCACAGAATGGGAGAAAATATTTGCAAACTGCGTATCT 3009
                             i                                   iiiii     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_142011058_   3010 GACAAAG-ACTT-------------------------------------- 3020
                           i  i -    --------------------------------------
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_142011058_   3021 ----------AATAACC-------AGAATGGGCAAAATGTTTGAATGGAC 3053
                         ----------       ------- i          ivi       i   
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_142011058_   3054 ATTTCTCAAATGAACACATGCAAAATGCAAACAGGCATAT-AAAAGGTGC 3102
                                v  v   v i  i    vv  v  i i   i  -     i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_142011058_   3103 TCAACATCATTAATCAT 3119
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (121 / 78)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 4.59 (78 / 17)  


2696 26.28 2.34 1.56  chrX_142226063_142230338.rev     2888  3785 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_142226063_   2888 AAACATATCACATGTTCATGGACTGGAAATGTCAGTATTGTGAAAATGAC 2937
                            v     v            i     ivv i i      v  i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_142226063_   2938 CATACTGCCAAAAGCAATCTACAGATTCAATGCAATTCCTATCAAAATAC 2987
                         v     v  v   vii              i     i           v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_142226063_   2988 TAACATCATTTTGTTCATAATTAGAATCAGC-AATCCTAAAATTCTTATG 3036
                         i i vv v    v v  v  v v  -iv   -i            v    
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATATG 152

  chrX_142226063_   3037 AAACTAAAACATAACCTGGATAGTCAAAACAATCTTAAGCAAAAAGAACA 3086
                         i  v iv  viv v  v i    i            i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_142226063_   3087 AATTTGAAGGCATCAAATTACTGGATATCAAA--TTATTCTACAAGGGTA 3134
                           v   i   vv   v i v ivi  v     --   --      i v  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGCTA 250

  chrX_142226063_   3135 TAGTTACCAAAAC-GCATGGTACTGATATTTAAGTATG--CATGTAGACC 3181
                         i   v i   i  - ii        ii  --   v  i--   i    i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGATC 298

  chrX_142226063_   3182 AATGGAACAGAATAAAGAACTCAAGAATAAAGCCAAATACTTACAGCCAA 3231
                                i     vi   iii  ii      v   v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_142226063_   3232 CTGATCTTAAACAAAGCATACAAAAAC-ATAAATTGGGGAATGGATGCCC 3280
                         i    i  vi    i -i i v  i  -  vv v       v i  ivi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_142226063_   3281 TATTTAATAAATGGTGCTGGCAAAACTGGATAGCCACATGTAGGAGAAGG 3330
                          v  i  i            v v         ?       i ii    v 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_142226063_   3331 AAACTGGATCCATATCTCT-----TATATGAAAATAAACTTAAGATAGGT 3375
                           ii    i  v  i   v-----    ii     v    i  i  i i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_142226063_   3376 GAAAGACTCAAATCTAAGTCCTGAAACTACAAAAATTCTATAAGATAATC 3425
                         v ?    ii    v    vv  i      i    v ii  v    v  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_142226063_   3426 TAGGAAAAATTCTTCTTGGTATTAGCTGAGGCAAAGAATT------TATG 3469
                             ?iv  v     v  iiv  i v v      v iv  ------    
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_142226063_   3470 ACTAAATCCCAAAAAGCATATGCAACAAAAACAAAAATCAATTAATGAGA 3519
                           --- i ---       i v         iv      vi  v   vi  
  L1M4_orf2#LINE/    598 AC---ACC---AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_142226063_   3520 CAGAATTAAACTAAAAAAACTCTGTACAACAACAAAAATAATT--GCCAG 3567
                          vvv  i   v v     vi i   i vv   vii v iv  i-- vv  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_142226063_   3568 AGAAACCAGACCGTCCTCAGAATGGTAGAAAATATTTGCTAACTATGTAT 3617
                         v    --    vii  v        v             v  ii  i   
  L1M4_orf2#LINE/    692 TGAAA--AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_142226063_   3618 TTGACAAAGGACTAATATCCAGAATCTACAAAGAATTCAAACAACTCAGC 3667
                         i   i  i     vi          v  i      i  vv        ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_142226063_   3668 AAGAAAAA-ACACAGAATCTCATTAAAAAATGGACCAATGACATGAATCA 3716
                           v     -   v v  i iv   ?        i v  v  iv     vi
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_142226063_   3717 ACCTTTCTCAAAAGAAGATACATAAATGGCCAACAAACATAGGAAAACAT 3766
                           v      v          i i          i  i  i v     v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_142226063_   3767 GTTCAACATCATTAATCAT 3785
                          i         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.13 (123 / 109)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 2.19 (35 / 16)  


3123 25.64 2.68 1.45  chrX_142337006_142341250.rev     2858  3754 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_142337006_   2858 TGGAAATATATTCCATTTTAATGGATTGAAAGGATTAATAATTTTAACAT 2907
                               v    i    v  v        i   iv      v v    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_142337006_   2908 GGCCCTACTACCCAAAGCAATCTACAGATTCAATTCCATCTCTATCAAAG 2957
                            vv    v      vii              iv v   i        i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_142337006_   2958 TACCAATGAGATTCTTCACAGGAATAGAAAAACCAATCCTAAAATTTATA 3007
                          v   iivivv  i  ii   i   v  v  i ii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_142337006_   3008 TGGAACCACAATAGATCCAGAATAGCTAACACTATCCTGTGCAAAAAGAA 3057
                              vii   vi  i          i  v  v   i  viv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_142337006_   3058 CAAAACTGAAGGAATCACATTAACTGGCTTCAAACTATACTACAGAGCTG 3107
                             ii  i    v     i vv iiii      viv       i    i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_142337006_   3108 TAGTAACCAAAACAGCATAGTACTGGTATCAAAACAGACTCATAGACCAA 3157
                         i     i   i    ii i       i  v ii i    vi     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_142337006_   3158 TGGAACAAAAT--AGAG------AACATATTTACACATCTAGGGTGAACT 3199
                              i i   --    ------  i v iii i    i  v   v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_142337006_   3200 AATTTTCAACAAAAGTACCAAGAACATACATTGGGACATAGACAGTGTCT 3249
                         i      i    ii  i      v   v  v    iv vii i   v i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_142337006_   3250 TCAATAAATGGTGCTGGGGAAACTGGATATCCATATACAGAAGAATGAAA 3299
                             i             iv         ?   i  i  i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_142337006_   3300 CTAGACCCCTATTTCTCTCCATATACATAATTCAAATCTAAATAGAATAA 3349
                         i i        ii  v v         v  v i  v  v    i  vi ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_142337006_   3350 AAACTTAAATCTAAGACCACAAAC-GTGAAATTGCTACAAGAAAACATTG 3398
                          i  i     v     v vv    -i i   i vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_142337006_   3399 TGGAAAATTTCCAGGACTTTGGTCTGCACAAAAATTCCTTGGGCAATATC 3448
                         v? v    i i iv   i    vi ivi   vii  i   i ---    v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG---ATATG 597

  chrX_142337006_   3449 TTATATCTTACAAGTGCAGGCAACCTAGGCAAACATGGAGAAATGAGATT 3498
                         -- i i -- v   ii  i     vv i v   v  i  v    vi  i 
  L1M4_orf2#LINE/    598 --ACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_142337006_   3499 ATGTCAAG-TTAAAGAGCTTCTGTG--------AACA--GTTAATAAATT 3537
                         vii    i-     i -   i    --------i   --i i  v   v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_142337006_   3538 GAAGAGACAACTCACAGGATGGGAGAAAATATTTGCAAA-CA---AGCTG 3583
                            i       i     i                     -  --- v   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_142337006_   3584 TGGCACAAGGGATTAATAACCAGAATATACAAAAAGCTCAAACAACACTA 3633
                         ---- i      i vi  v          i   i i   vv     v v 
  L1M4_orf2#LINE/    743 ----ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_142337006_   3634 TGAGATACAAATATAATAATCTGATCAAAAAATGGGTAAAAGATTTGAAT 3683
                          i v v v i i -     i ii  i?         i   i         
  L1M4_orf2#LINE/    789 TAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_142337006_   3684 AGACTTTTCTCAAAGGAAGACATACAAATGGCAAACAGGCATATGAAAAG 3733
                             v      v  i     i           v  i i   i        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_142337006_   3734 GTGCTCAACATCATTGATCAT 3754
                         i            ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (140 / 86)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.64 (37 / 14)  


2410 27.97 1.71 2.05  chrX_142351932_142357902     4200  5075 (896)    L1M4_orf2#LINE/L1        1   873 (35)  

  chrX_142351932_   4200 TAGAAACCCATCCTATGCTCATGGATTGAAAAAATCAATATTGCAAAAAT 4249
                          i    vvi    i   i          i  i v i       iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_142351932_   4250 AATCATACTACCCAAAGCAATCTACAGATTCAATGCAATTCCCATCAAAA 4299
                         iiiv     v      vii              i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_142351932_   4300 TACCAACATCATTTTTCACCAAATTAGAAAAACAAATTCTAAAATTCACA 4349
                          v   i vv v     ii vi  v v  v  i vi  i          i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_142351932_   4350 TGGAACCAAAAAAGAGCCTGATTAGTCAGAGCAATCCTAAGCAAAAAGAG 4399
                              viiv  ii  v  v  v   i  i i     i i iv  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_142351932_   4400 CAAATCTGGAGACATCACATTACCAGACTTCAAATTATACTACAAGGCTA 4449
                             vi     ivv     i v  vi i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_142351932_   4450 GAGTTACCCATATTGCATGGTACTGATATAAAAGTAGGCACATAGACCTA 4499
                         v   v i v v iv ii        ii    iii   i  i     i v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_142351932_   4500 GTTTTGAAACAGAAT-AAGAA-ACAGAAATAAAGCCAAATACATACAGCC 4547
                         ----  i  i     -i   i-v          v   v i iv  ii i 
  L1M4_orf2#LINE/    301 ----TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_142351932_   4548 AACTGATCTCTGACAA---TGCATTCAAAAATAT--AAGTTGGGGAATGG 4592
                           i    i ii     ---   ---   i vi  --  --       v i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGC---CAAGACCATTCAA--TGGGGAAAGA 391

  chrX_142351932_   4593 AAAACCTATTTAATAAATGGTGCTGGGAAAGCTGGCAAGCCGCATGTAGA 4642
                          v ii  v  i  i              v i    vv ?  i    i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_142351932_   4643 AGGATGAAACTGGATCCGTACCTCTCACCTTATATAAAAATCAACTCAAA 4692
                           i     ii    i  v      v    v    i      i        
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_142351932_   4693 ATGTTTCAAAACCTTAAATATAAGATTTGAGACCATAAAAATTCTAGAAT 4742
                            vv   ? iv i     i     vi i i  i      v ii     v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_142351932_   4743 ATATCATGGAAAAAACTATTCTAGACATCAGTGTAGAAGAGAATTTAT-- 4790
                          v v   i i?iv  v v   vv   v ii vv   ivi vii   v --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_142351932_   4791 GACTAAGACCCAAAAAGCAAATGGAATAAAAACAAAAATAAATAAATGGA 4840
                           -  v   v v       v v v  i    iv       i      v i
  L1M4_orf2#LINE/    592 GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_142351932_   4841 ACCTAATTAAA-CTAAAAAGGTTTGTACAGCAAAAGAAATAATAATCAGA 4889
                           i v  i   -i      vv     i vv    i  v iv  v vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_142351932_   4890 GTAAATAGCCAACCCACAGAATAGAAGAAAATATTTGCAAACTATGCATC 4939
                           i  v  v             i i                ii  --  -
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT--AT- 737

  chrX_142351932_   4940 TGCATCTGACATAGGACTAGTATCCATGTAATCTATAAGGAACTCAAACA 4989
                         ---      i vi     v       - -   v     i      vv   
  L1M4_orf2#LINE/    738 ---ATCTGATAAGGGACTTGTATCCA-G-AATATATAAAGAACTCTTACA 782

  chrX_142351932_   4990 AATCAGCAAGAAA----TAAACAATTCCATCAAAAAGTGGAAAAATGACA 5035
                          v   ii  v   ----i   i  ii v  i?    i   iv   v  iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_142351932_   5036 GGAATGGACATTTCCCAGAAGAAGAAATATAAATA-CCAGT 5075
                         v    i        i vi       v   i    i-   i 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

Transitions / transversions = 1.36 (139 / 102)
Gap_init rate = 0.02 (16 / 873), avg. gap size = 2.06 (33 / 16)  

 233 17.33 0.00 5.33  chrX_142351932_142357902     5404  5478 (493)    L1M4_orf2#LINE/L1      838   908 (0)  

  chrX_142351932_   5404 AGACTTTATGTCAAAAAATACATATATAGAAATGGCCAACAAACATATCA 5453
                             v  - v  v   i --- v     v          i  i  i  v 
  L1M4_orf2#LINE/    838 AGACATT-TCTCCAAAGA---AGATATACAAATGGCCAATAAGCACATGA 883

  chrX_142351932_   5454 AAAAATGTTCAACCTCACTAATTGT 5478
                            i   i     v   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.86 (6 / 7)
Gap_init rate = 0.03 (2 / 71), avg. gap size = 2.00 (4 / 2)  


2311 28.50 1.88 2.25  chrX_142377314_142380527     1473  2272 (942)    L1M4_orf2#LINE/L1        1   797 (111)  

  chrX_142377314_   1473 TGGAAAAACATTCCATGCTCATGGATAGAAAGAATCAATATCATGAAAAT 1522
                               i i  i     i        v i    v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_142377314_   1523 GGCCATACTGCCTGAAGTAATTTATAGAGTCAATGTTATTGCCATTAAAC 1572
                            v     v  ii  v i  i  i   v    i iv  iv i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_142377314_   1573 TACCATTGACATTTTTCATAGCA--TGAGAAGAAACT-ATTTTAAAATTC 1619
                          v   vivi v     iii  v --   v   ---  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chrX_142377314_   1620 ATGTGAAACCAAAAAATAACTTGTATACCCAAGACAATCCTAAACAAAAG 1669
                           i  i  viiv  iiv v iv v   v    i      i i  v  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_142377314_   1670 GAACAAAGCTGGAGGCAGGCATCTCACTACCCGACTTGATACAA--TACT 1717
                                 i      ---i -  v    v   i i  --i v  --    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG---AC-TCACACTTCCCAATTT--CAAAACTTACT 241

  chrX_142377314_   1718 ACAAGGCTACAATAATCAAAACAGCATGGTACTGGTATAAAAACAGACAC 1767
                             i      i       i    ii         i    ii i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_142377314_   1768 ATAGATTAATGGAACAGAATAGAAAAACTCAGAAATAAAATTGTGCACTT 1817
                               i       i     v  i iv -          viii i  i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTT 340

  chrX_142377314_   1818 ACAACCATCTGATCTTTGGCAAGCCTGACAAAAAACAAGCAATGGGAAAA 1867
                          iiii  vi    i  i i    vv  v   i v-  vv       i   
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAA 389

  chrX_142377314_   1868 TAATTTCCTATTTGATAAATGGTGCTGGGAGAATTGGATAGCCATATGCA 1917
                         v   vvi  v  ii i              v  i      ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_142377314_   1918 GAAAATTGAAACCGGACTCCTTCCTTACACCTTATACAAAAATAAACTCA 1967
                         i  i v    iii    i   v   i     v           v      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_142377314_   1968 AGGTTGGTTAAAGACTTCAATATAAAACTCAACACTATGAAAACCGTAAA 2017
                          ii v i i ?    i v   i   i vii  v     i   vi v  i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_142377314_   2018 AGAAAATCTAGGCG-ATACCATTCAGGGCATAGACACAGGCAAAGATTTC 2066
                               iv    ? - v i -   iv i v v ivvi      v i    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_142377314_   2067 ------ATGACAAAATTGCCAAAAGCAATTGCAACAAAAGCAAAAATTAA 2110
                         ------      ------         vvv          v      vi 
  L1M4_orf2#LINE/    589 TTAGATATGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_142377314_   2111 CAAATACGATCTAATTAAA--TGAAGAGTTCTGCACAGTAAAATAAACTA 2158
                         i    vv  ii v  i   -- i  i v  i  ii vvi   iv v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_142377314_   2159 TCATCAGAGCCAACAGGCAACCTAGAGAGTGGGAGAAAACTTTCGCAATT 2208
                            vv i  iv  v  i     i v   i          iv  i    v 
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_142377314_   2209 TATGCATCTAACAAAGT-CTAATATTCAGAATCTACAAGGAACTTAAACA 2257
                         i  ii    i i  i v-  vi   i      v  i  i     ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_142377314_   2258 AATTTACAGGAAAAA 2272
                          v iv i iv     
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAA 797

Transitions / transversions = 1.56 (137 / 88)
Gap_init rate = 0.02 (15 / 797), avg. gap size = 2.20 (33 / 15)  

 206 22.64 1.89 0.00  chrX_142377314_142380527     2661  2713 (501)    L1M4_orf2#LINE/L1      800   853 (55)  

  chrX_142377314_   2661 CATATCATCC-ATTAAAAAGTGGGCAAAAGACATGACCAGACACTTCTCA 2709
                           v  v i  -   ?    i        i  iv   vi     i     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_142377314_   2710 AAAG 2713
                             
  L1M4_orf2#LINE/    850 AAAG 853

Transitions / transversions = 1.20 (6 / 5)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1)  


3413 20.84 1.57 6.60  chrX_142412104_142415214     1664  2618 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_142412104_   1664 GGGAAAATATTCTGTGTTCACGGTTTAGAAGACTTAATATTGTCAAATTG 1713
                           i  i    i ii      i  v  i                i  iv  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_142412104_   1714 ACCATACTACCTAAAGTGATCTACAGATTCAATTTAATCCCTATGAAAAT 1763
                         i v     v  i   v                ivi         v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_142412104_   1764 CCCAATGGCAATATTTACAGAAATAGAAAAAAAAACAATTCTAAAATTCA 1813
                             iiv  vv v   i       v  v  iv---ii  i          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGC---TGATCCTAAAATTCA 148

  chrX_142412104_   1814 TGCACATATGCAAAGAAATCTGAATAGCCAAAACAGTCTTGAGAAAGCAG 1863
                          iiiv v      i i vi v              i      i    v  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_142412104_   1864 AAAAAAGCTGAAAGCATCACACTTTCTGATTTGCAAATATATTACAAAGC 1913
                           v    i  i i vv        i ii    vv   iv  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_142412104_   1914 TGCTGTAATCAAAACAATATGGTGCTGGCATAATAAAGACAGATATACAA 1963
                          i v        i   i i    i         ---i  i   i   i -
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAA---GGATAGACATATA- 294

  chrX_142412104_   1964 GACCAATGGAGCAAAATAGAAAGTCTGGAAATAAACCCCCACATATATAG 2013
                           i       ii i   v  i    ii           ----   i  --
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC----ATACAT-- 338

  chrX_142412104_   2014 TCAACTTATTTATGTTCGTTTGTTTCACTGCTCCAGTCAAGAGAGAAGTC 2063
                         ---------     ---------------------------------   
  L1M4_orf2#LINE/    339 ---------TTATG---------------------------------GTC 346

  chrX_142412104_   2064 AACTGATTTTTGATAAAGGTACAAATAATAAATT--ATAGGGAAAGGATA 2111
                           i       i  i  i   i v  v vi --  --  i       i   
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCA--TTCAATGGGGAAAGAATA 394

  chrX_142412104_   2112 ATCTCTTTAAAAAATGGTGTTGGAAAAACTGGATATCCACATGCAAAAGA 2161
                         i   i  i  v        i   i v         ?              
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_142412104_   2162 ATGAAATCAGACCCTTATCTTACACCATACACACACAAAAA--AACTCAA 2209
                              i ii     i  i  i        i   ----    --       
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACA----AAAATTAACTCAA 490

  chrX_142412104_   2210 AATGGACTAAAGACTTAAATCCAAGACTTGAAACTGTAAA-CTCCCAGAA 2258
                               ii ?    i     vi    vi i     i    -   ii    
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_142412104_   2259 GACGACATGAGGG-AAAGCTTTGTGACAGTAGTCTCGGCAATGATTTAAG 2307
                           vi    ii ? -   v   i     vv i vi v       i   vvv
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_142412104_   2308 AGACATGACATTAAAAGCACAGGCAACAAAAGAAAAAATGGACAAGTAGG 2357
                            i      ii         i                 i  i  i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_142412104_   2358 ACTACATCACA-CCAAAAACCT----GCTACAAAGCAAAGGAAACAATAT 2402
                            v     v -ii      i ----   v     v v vv v-   v v
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT-CAAGAA 689

  chrX_142412104_   2403 AGTTGAAGAGGCAACCTAT-GAATGGGA-AAAATATTTGCAAACCATATA 2450
                            -   i  i     i i-        -              i      
  L1M4_orf2#LINE/    690 AGT-GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_142412104_   2451 GTTGAAAAGAGGTTAATATCCAAAATATATTAGAAACTCACATAACACAA 2500
                         vi   v   i ii vi      i       v ii     vi i   v   
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_142412104_   2501 CAGCTAAAA--CTGATAGCCCAATTAAAATATGGTCTAAAGACTTGAATA 2548
                         i iiv    -- vi   i       ?   v    v v  i  i       
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_142412104_   2549 GACATTTCCCCAAAGAAGACATACAAATGACCAACAGGTACATTAAAAGA 2598
                                 i          i         i    i i i    v      
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_142412104_   2599 TGCTCAATGTCACTAATAAT 2618
                                ii   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (129 / 66)
Gap_init rate = 0.02 (19 / 907), avg. gap size = 4.11 (78 / 19)  


2705 23.97 3.06 0.80  chrX_142470046_142471791      497  1247 (499)    L1M4_orf2#LINE/L1      109   876 (32)  

  chrX_142470046_    497 GCCCTTTT--CAGAAACAGGAAAAA-AATTCTAAAATTTGTATAGAATCT 543
                            i    --      iv iv  iv-i  i        ii   i   viv
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_142470046_    544 CAAGGGTCCCTGAATTACCAAAACAATCTTGATAAACAAGAATGAA-TTG 592
                               v   v    vi               v   v     ii  -   
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_142470046_    593 GAGACCTCATTCTTGCTGATTTCTATACATATTACAACACTATAGTAATC 642
                            iv    iv   v ii     v v  v  i     vi   i       
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_142470046_    643 AAAACAGTATGGTGCTAGCATAAAGACAGGCATATAGACCAATAGAACAG 692
                           i     i    i  i      i  i  i        i    i   i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_142470046_    693 AATAGAGAGCCCCAAAATAAATTCTCATGTATATGGTCAAATAATAT--A 740
                            v     i  vi       ii vi ii v         v i  v --i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_142470046_    741 ACAAGA-TGCGAAGATCCCACAATGGGGAAAGGATAGTCATTTCAAAACA 789
                              i-   v    i viv            i      v      v v 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_142470046_    790 TGGTGCTGGGATA---GG-----CACATGCAAAA-AATGAAGTTAGACTC 830
                                    i ---  -----           -         i   i 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_142470046_    831 TCACTTTATACTTTATA--AAAATTAACTCAAAATAGATTAAAGATATAA 878
                         ii  i i i  iv    --                i   i ?   iv   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_142470046_    879 ATATAAGCCCTAAA-CTAAAACACTCCTAGAGGGAAACATACGAGAAAAG 927
                           i    vv     -   v  v    i    i i       v ? v   v
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_142470046_    928 CTTCATGACATTAGATTTTGCAGTAATCTATTAGATATGACACCAAAATC 977
                             i    v  i i  vv   i ii i v                  v 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_142470046_    978 ACATGCAACAAAAGCAAAAATACACTAATGAAACAAACATCAAACTTAAA 1027
                            v          v       v iv   vii  vv-       v     
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATCAAAATTAAA 657

  chrX_142470046_   1028 AACTGCTACACATTAAAGAAAAGAATCAACAGAATAAAAAACAGAATCCA 1077
                             vi iii v i    i v vv     v i i i    i- v  i   
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG-ACAACCCA 706

  chrX_142470046_   1078 TGTACAGAATAAGA-AAAATAATTGTAAATTACACATCTGACAAGGGGTT 1126
                         ----      ii  -      v   i    i i i      i     ii 
  L1M4_orf2#LINE/    707 ----CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_142470046_   1127 AATATGCAAACTATATAAGTAACTCCTACAAATAAACAACAAAGGTGT-- 1174
                         vi   v  i v       iv     i     v v  i  i   iivii--
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_142470046_   1175 -TAACCTGATTACAAAATAGGCAAAGAATTTGAATAGACATTTCTCCAAA 1223
                         -     ii   ?v     i       i                       
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_142470046_   1224 AGCGATATAGAAATGGCTATCAAG 1247
                         iiv      v       i vi   
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAG 876

Transitions / transversions = 1.53 (107 / 70)
Gap_init rate = 0.02 (15 / 768), avg. gap size = 1.93 (29 / 15)  


3243 26.43 0.88 0.88  chrX_142571163_142577510.rev     4950  5857 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_142571163_   4950 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4999
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_142571163_   5000 GGCCATACTGTCCAAGGTAATGTATAGATTCAATGCCATCCCCATCAAGC 5049
                            v     vi    iv i  v  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_142571163_   5050 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5097
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_142571163_   5098 TATGGAACGAAT--AAAGAGCCCACATT-GCCAAGTCAATCCTAAGCCAA 5144
                                ---  --  i ii    v v -     iv     i i ivv i
  L1M4_orf2#LINE/    149 TATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_142571163_   5145 AAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAA 5194
                                   i      vv    i  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_142571163_   5195 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 5244
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_142571163_   5245 ACCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACA 5292
                          i        i    i--    i  --        vv   i i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chrX_142571163_   5293 ACTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATCGGGAAAGGAT 5342
                         iii vi    i  i     ivv  v   i v  vvv   v       i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_142571163_   5343 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAA 5392
                         vvi  v  i  i              v      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_142571163_   5393 GCTGAATCTGGACCCCTTCCTTACATCTTATACAAAAATTAATTCAAGAT 5442
                         iv    vi         v   i   i v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_142571163_   5443 GGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5492
                             i ?    i       v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_142571163_   5493 AACCTAGGCA-ATACCATTCAGGACATAGGCCTGGGCAAGGACTTCATGT 5541
                            v    ?i- v i -   iv   v v  vi i     v ii   v iv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_142571163_   5542 CTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAT 5591
                         v  vi            vvi          vv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_142571163_   5592 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5641
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_142571163_   5642 GAACAGGCAACCTACAGAATGGGAGAAAATGTCTGCAATGTACTCATCTG 5691
                            v  i     i                 i i     vvi ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_142571163_   5692 GCAAAGGGCTATTATCCAGAATCTACAATGAACTCAAATAAATTTACAAG 5741
                         ii  i  i  vv          v  i  v      vv i  v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_142571163_   5742 AAAAAAACAAACAACCCCATCAACATGTGGGCAAAGGATATGAACGGACA 5791
                              i     i     v  i? v vi            v    ii    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_142571163_   5792 CTTCTCAAAAGAAGACATTTATGCAGCTAACAGACACATGAAAAAATGCT 5841
                         i     v        i  vi viii  i  i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_142571163_   5842 TATCATCACTGGCCAT 5857
                         i v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (143 / 93)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2125 27.16 3.30 1.15  chrX_142687889_142689574.rev      502  1197 (489)    L1M4_orf2#LINE/L1      198   908 (0)  

  chrX_142687889_    502 GAATGAAGCTGGAGGCATCACACTATCCAACCTCAAACCATACTATAAGG 551
                            ii   i      vv       vi    ii     v v     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_142687889_    552 TTACAGTAATCAAAAAAGCATGGTACAAGTACAAAAACAGATGCATAAAC 601
                         i            i v  ii      vi i i  ii i   iii   i i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_142687889_    602 CGGTGGAACAGAATAGAAAACACAGAAGTAAACCTACACAACTACAACCA 651
                          ii     i     v  i iiv     i      i i   vi  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_142687889_    652 TCCGATTTTCCACAAAATCTACTGAAATAAGCATTGACAAT-----AAGA 696
                         vii       v    iiv- i ii i i---    --    -----    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGG-TGCCAAGAC---CATT--CAATGGGGAAAGA 391

  chrX_142687889_    697 GT-GCCTATTCAATAAATAGTGCTGGGATAACTGGCTAGTCATATGCAGA 745
                         i - i  v     i    i         i      v  ?i  i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_142687889_    746 ATAATGAA-TTGGACCCCTACCTCTTACCATATATGAAAATTAACTCAAA 794
                          v      -               vi        ii              
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_142687889_    795 ATGGATTAAAGACTTAAATGTAAGAGCTCAAATTATAAAAATGCTAAAAC 844
                               i ?    i              v   i       v vi  i  v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_142687889_    845 AAAACCTAAGAA-ACACCTTCTTAACA--AGTTTTGGCAAAGAATTTGTG 891
                              v  i ?i- v i    v i  v--i v  v     v iv  iv i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_142687889_    892 GCTAAGTCCCCAAGAGCAATTACAACAAAAACGAAAAGTA-ATAAGTGGC 940
                          v  v v v    i    vvvi        i-i    i  -    i v v
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGG 640

  chrX_142687889_    941 ACCTAATTCAACTAAAGAGCTTTTGCACAACAAAAGAAGTTACT--GACA 988
                           i v  iv  v v  i i      ii vv    i  vii  ii--  v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_142687889_    989 GTAAACAGACAGGCTACGGAATAGGAGGATATAATCACAAATTATGCATC 1038
                           i  v     iv i  i    i    i v   v ii     i  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_142687889_   1039 TGATAAAGGTCTAATATCAAGAATCTACAGGGAACTT----AAATCAACA 1084
                               i  v  vi    v     v  i ii     i----  v    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_142687889_   1085 AGGAAAGAACAAAAATATCCACTT--AAAATGG-CAGAGAATATGAACAG 1131
                          vi   ii     v - i   v  --       -  i  i  v    i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATA-ACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_142687889_   1132 ACACTTCTTAAAACAAGGTGTACAAGCAGCCAACA-GCATATAAAAA--T 1178
                            i    iv   v   i i     iii     i -   i  i    -- 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_142687889_   1179 GCTCAACATTGGCCAGATG 1197
                                  ii????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (124 / 62)
Gap_init rate = 0.02 (17 / 711), avg. gap size = 1.82 (31 / 17)  


 647 23.79 2.91 1.46  chrX_142704876_142708208.rev     1817  2022 (1311)    L1M4_orf2#LINE/L1        3   211 (697)  

  chrX_142704876_   1817 GAAAGATATAAAATGCCTATGGATTGAAATACTTAATATTATTATGATGT 1866
                                  vvv   iii        i  v          i   v    v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_142704876_   1867 CCATAATATTCAAAGTGATTGATAGTTTAAATTCAATC----TCAAAATC 1912
                          v   v vii    v    iv i  v  v  iv     ----        
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_142704876_   1913 CCAA-TGTCATTTTTTGCCAAAATTAAAAGATTAATCCTAAAATTAACAT 1961
                            i-  i -        vi     i v iii i           v i  
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_142704876_   1962 G-AAATATCAATAAACTCCAATTATCCAAAACAGTTTTGAAAACAAAATA 2010
                          -    i-   vii  i vi v  v        i i       - i  v 
  L1M4_orf2#LINE/    152 GGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA-AGAAGA 199

  chrX_142704876_   2011 ACAAAGTTGGAG 2022
                                     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAG 211

Transitions / transversions = 1.23 (27 / 22)
Gap_init rate = 0.03 (6 / 209), avg. gap size = 1.50 (9 / 6)  

3286 22.58 2.09 1.10  chrX_142704876_142708208.rev     2028  2842 (491)    L1M4_orf2#LINE/L1       86   908 (0)  

  chrX_142704876_   2028 CAATCTCACCTGAAACCCCAATGTCATTTTTTTGGCCAAAATAGA-AAGA 2076
                              i vviii   i    -- iiiii     v  vi    v  -   v
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCA--GCTGCCTTTTTTGCAGAAATTGACAAGC 133

  chrX_142704876_   2077 TGAATCTTAAAATTAACATA-AAATATCAAGTAACTCCAAATATCCAAAA 2125
                            -  i       v i  i-    i-    vi  i vi    v      
  L1M4_orf2#LINE/    134 TGA-TCCTAAAATTCATATGGAAATG-CAAGGGACCCAGAATAGCCAAAA 181

  chrX_142704876_   2126 CAATTTTGAAAAGAGAATAACAAATTTAGAGCCTTCATACTTCCGGATTC 2175
                             i       -    v      v  i   vvi   i      vi   i
  L1M4_orf2#LINE/    182 CAATCTTGAAAA-AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chrX_142704876_   2176 CAGATCATATTACACAGCTACAGTAATTAAAAC--TGTGGTACTGGCATA 2223
                           i v v  i    v            i  i  --               
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chrX_142704876_   2224 A----AGAAATATAAATATTCCAATGGAATAGAATAGAGATCCCAGAAAT 2269
                          ----   v     i  ----              v    vi        
  L1M4_orf2#LINE/    281 AGGATAGACATATAGAT----CAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_142704876_   2270 AAATCCACACATTTGTGATCCACTGATGTTCAGCCAGGTTGCCAAGGCCA 2319
                            i   i      i  i  v i    v   ii v   v       i   
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_142704876_   2320 CTCAATGGAGAAATTACAGTCTTTTTAACAAGTGATGTTAGAAAAGCTGG 2369
                         i       i    vv i        i     i  i  i i i v i    
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_142704876_   2370 GTAAC-ATATGCAAAAAAA--AAGTAGGACTCATAT-TAATCCCATATA- 2414
                         i  ? - i        i  --    v    i v  i- v iv       -
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_142704876_   2415 -AATATGAACTCAAAACAGGTTAAAAACCTAAATGTAAGACTTAAGATTG 2463
                         -  v  v         ii i i ? i              vi   i i i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_142704876_   2464 TACCACTCCGAGAATACAGCACACGTGGAAACCTTTATGACAATGGATTT 2513
                           vv    iv    v v i  i v ? v   i   ii    vv   i  v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_142704876_   2514 GGTAATTATTTCTTGGATATGACACTGAAAGCAGAGGCAACAAAAGCAAA 2563
                           i   vi      i          ii      v i          v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_142704876_   2564 A-CAGATAAATGGGACTGCATCAAACTTAGAAGCCCTTGTGAATCAAGGG 2612
                          -i        v     v       v   i  i ii     vv    i  
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_142704876_   2613 ATTCAATTAGCAGAGTGAAAA-ACAACTTATGAAATGGGAGAAAATATTT 2661
                          iv v  i iv i        -     ii iii                 
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_142704876_   2662 GCAAATCATATATCTGATAAAGAGTGAATACATAGTACATATAAAGAACT 2711
                                             i iiivvi  ivi  v i            
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_142704876_   2712 CCTACAGTTCAACAACAACAAAATAG-TAGCCAGATTTTAAAATGGGCAA 2760
                          i    ii    i  i  v  i i i-  i  vi   ?v           
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_142704876_   2761 AGGACTTGAATAGACATTTCTCCAGAGATGATATATGAATGGCCAACAAG 2810
                             i                   i   v      ii         i   
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_142704876_   2811 CATAAGAAAAGATGCTCAACATCACTAATCAT 2842
                           i v                   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (115 / 65)
Gap_init rate = 0.02 (16 / 823), avg. gap size = 1.62 (26 / 16)  


2062 29.94 3.24 1.90  chrX_142731675_142735992     2931  3825 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_142731675_   2931 GGAGAGATACTCCATGCTTATAGATAGTAAAACTAAATATCATCAAGATA 2980
                            i     ii     i i  i   v v  i   v     ii i     i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_142731675_   2981 CCAATTCCTTGCAACTTGATCTATAAATTTAACACAATTCCAAACAAAAT 3030
                         v    v iiiv   v        i i   i   i    i  v v      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_142731675_   3031 CCAAGTAAGTTATTTCTGTAGATATAGTTGAGCTAATTCAAAAGTTTATA 3080
                           v  ivivi -   i  i   v  v vii    i  i v   i  i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_142731675_   3081 TGGAGAGGCAAATAAC---AAATTTAATTAATTCAGTTTTGAAGGATAAG 3127
                             i v    ivi  ---i   -- iii  vv  i i     ii v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAAT--AGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_142731675_   3128 AA----ATTCAAGTAACTGACA-TTATTAATCTTCAAAAGTCAGTGAAAA 3172
                           ----i  vi  -i   v   -  vii   -       v i v iv   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAG-GACTCACACTTCCCAAT-TTCAAAACTTACTACAAA 246

  chrX_142731675_   3173 TCTGCATTAATCAAGATAGTCTGGTATTAGAATAAACATCTAAAAATAAT 3222
                         v  i  v         i   v     i i v    iv  vv v v   iv
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_142731675_   3223 TCAGTGAAGCAGAATAGAGAATCCAGAAATAGGACCACATAAAAATAGTC 3272
                            i  i ii     v    i          iiv   i i vvv  i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_142731675_   3273 AACTGATCTTTGAGAAAAGCATAAAGGCAATACAAGAGAGCAAAGATTGT 3322
                           i    i  i  v  ii iiiv   i v  v   vi i v  ii  v  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_142731675_   3323 CTTTTTTTTTTAATGTTATCAGAAAAGCTAGACATCCCCATGCAAAAAAA 3372
                              ivviv-    v iiii i v i  i  i ?  v         i  
  L1M4_orf2#LINE/    397 CTTTTCAACA-AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_142731675_   3373 AAAAAATCAATTTACATGTAAACCTCAAACCATTCATAAGGAGAGATGCA 3422
                         vi  iv vi ii-- v ----      v     vi i  ii vvi iv  
  L1M4_orf2#LINE/    446 TGAAGTTGGACC--CCT----ACCTCACACCATATACAAAAATTAACTCA 489

  chrX_142731675_   3423 AAATGCACTGCAGACCTAAATGCTAAATGC-AAAACTATAAAACTCCTAG 3471
                              v iii?           -   iv  -               i   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATG-TAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_142731675_   3472 AAGATAGCAAAGAAA-AAATATAGATGACCTTGGGTATGGTGATGG---- 3516
                             v i  v  i?i-    v vvi           vv  ii    ----
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_142731675_   3517 --AGCCA--ACACCAAAGAAATGATTCATGAAAGAAATAATAGATATGTT 3562
                         --  vi --        iiv ii viv ii       v        vi  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_142731675_   3563 GGGCTCTATTTAAATTAAAAACTTTTGCTTTGTGAAAGATGCTGT--AAA 3610
                           i  ii  iv                ivi vii  i  ii  i -- i 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_142731675_   3611 AAG-AAGAAGACAAACCAAAGACTGAGGGAAAAATATTTGTAAA--AGAC 3657
                            -i i       v   v   v  i i     -      i   -- v i
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATAT 737

  chrX_142731675_   3658 ATAAAATAGTCAACTGTTATCCAAAATATA--AGGAGTTTTTAAAA-TCA 3704
                           vvi   ivvi   vv      i      -- i  ii i   v  -   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_142731675_   3705 CCAATAAATA-ATGAACAACTCGATT-AAAAATGGGCAAAAGACCTGAAC 3752
                         vi      v - ii  i   i i   -             i  ii    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_142731675_   3753 AGACACCTCACAAAAGATGATGTACAGATGATGGCAAATA-GCATATAAA 3801
                              ii  v v     v   i    i   ---  v    -   i  i  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATG---GCCAATAAGCACATGAA 884

  chrX_142731675_   3802 AATATACTCGATATCATGTGTTAT 3825
                           v  i   i i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (165 / 100)
Gap_init rate = 0.03 (25 / 907), avg. gap size = 1.84 (46 / 25)  


 293 29.63 9.12 7.41  chrX_142741567_142743268.rev      502  1203 (499)    L1M4_orf2#LINE/L1      169   882 (26)  

  chrX_142741567_    502 AAAAGAGTTAGGCCAATTTTGAGAAAGA----CGAAGTGGAGGAGAGGAA 547
                          i  v  ii iiv    i    i     ---- i    v ----     v
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG----GAGGAC 214

  chrX_142741567_    548 TACAC-CTTCCCAGGTCTCAAAACATATAATAAACTTAAAGTAAGTAAAA 596
                          -   -       i- i       v  iv i   vi  v     vi  i 
  L1M4_orf2#LINE/    215 T-CACACTTCCCAA-TTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_142741567_    597 CACTGTAGTAATTTTTTAAGAAGAGAAAAACAGAC--ATGGGCAATTGAA 644
                           v   i   v vviv    i v   v v i   i--    --   v   
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG--AATAGAA 310

  chrX_142741567_    645 TTTCACAGAACATTAGATATAAAGTGATTCAGATGTATGTAGGGTT--TT 692
                           v---   ii-ii   v     ----ii  -- ii  v  v   i--  
  L1M4_orf2#LINE/    311 TTG---AGAGT-CCAGAAATAAA----CCCA--TACATTTATGGTCAATT 350

  chrX_142741567_    693 AGTTTAAGATAAAG-T----AG--CATTTAACATTAGCAGAGAAAA---- 731
                         ii   vv  i  i - ----  --    i  -- vi v i    v ----
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAGTCT 398

  chrX_142741567_    732 --TTAGTAAGTAGTAAAATAGTTGAGGCAATTTGTTATCTAT-TTTAAAA 778
                         -- i ii  i i  ------ i  i i   i v v  ? i i- vi    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGT------GCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_142741567_    779 -AATA---TT----TCTTTCTTTACATCATTGATTAATGTTAATTTCAGA 820
                         -   i---  ----i i v i i   i   vv iv  vi    i iv i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_142741567_    821 TGGATAAAATATTTAA-TACAAAAAG-AAAGTTACGTTTTATTAAATAGA 868
                              v ? v ii   - ii  i iv-   ii  --------    - vv
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTA--------TAAA-ACT 533

  chrX_142741567_    869 ATTAGAATTTTGAGAAAATAT-GGAGAATATATTCATAATCTTGGAT--G 915
                         v      ------     i  -  ? v v  v   i i i     i -- 
  L1M4_orf2#LINE/    534 CTTAGAA------GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_142741567_    916 CCGAAGCTTTCTTAAGCGGGACTCAAAAAGCAAAACCTGTGAAAATCAAT 965
                         v i v v       iiiiv   v v       v  v viii   ivv  v
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_142741567_    966 ACTGTTTAATTT--CTTATGTCAAGATTAA--------GTGCATTCTACA 1005
                          iv v v    v--   -ii    i     --------    -   - v 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTT-CATCAAAATTAAAAACTTTTGTGC-TTC-AAA 674

  chrX_142741567_   1006 TGACA-----AAAACAGC-ATAAGCAAATTTTTAAAATCACAAGAAAATA 1049
                         v    -----  i v  i- v   vv  iiivi i   vi-i        
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG-GAGAAAATA 723

  chrX_142741567_   1050 TTTTCAACACATATA---AATATGAGAATTAACATTTACAATGCATAAA- 1095
                            v   vv      ---i   v i  v  i-i  ii v   ii     -
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTG-TATCCAGAATATATAAAG 772

  chrX_142741567_   1096 ---TTTTACAAAAAAAGGATAAGAAAAATTTAAGTA--TTAAATAGAAAA 1140
                         --- i      vvv  vi    i  i ---i  i  --ii  v ?---  
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGA---CAAATAACCCAATTW---AA 816

  chrX_142741567_   1141 AAATGA-CAAAGTATTTGAGTAGACAATTTTCCAAAGCTAATA--CAAAT 1187
                              i-     v      i      v  i       vvi   --     
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_142741567_   1188 GAATAATTAAAACATG 1203
                          ivi   v iv     
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATG 882

Transitions / transversions = 1.34 (117 / 87)
Gap_init rate = 0.06 (45 / 714), avg. gap size = 2.58 (116 / 45)  


1345 27.12 1.65 0.94  chrX_142759009_142760934      499   922 (1004)    L1M4_orf2#LINE/L1      283   709 (199)  

  chrX_142759009_    499 GACAGACATAGCAACTAATGGTACAAAGTAAAGAGCCCAGAAATAAACCC 548
                           i       vvi ii     v i i i vi    i              
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC 332

  chrX_142759009_    549 AAGCATATATGG-CATATTAATCTTTGAAAAGGGCACCAGGAAGACACAA 597
                          vi   v     -  -   i  i  i  v     ii   i  vv iv   
  L1M4_orf2#LINE/    333 ATACATTTATGGTCA-ATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_142759009_    598 TGTGGAAAGAATATTCTCTTCAACCAATAGTAC-AGAAAAACTAAATGTT 646
                           v          v   i      v   i  i -i i v    ii  i?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chrX_142759009_    647 CACATGCAAAAGAATGTAATAGGACACCTATCTTATGCCATACATAAAAA 696
                                         v i v    v    i  i ii     i i     
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_142759009_    697 TCAACCCATAATCGATAAAAAGTTTATGTATAACACCTAAAACTGTAAAA 746
                          i   i  v   v   v ? iiii  vi i   v v        i     
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_142759009_    747 CTTCTTGAAGAAAACGTAGGGGAAAAG-TTCAAGGCATTAGTCTTGGCAA 795
                           ii v         i    ? v   v-   iv i v  i vi v     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_142759009_    796 TGATTTTATGGATACATCACAAGAAGCACAGGCAACAGAAGCAAAAACAG 845
                           i   iv i    iiv   v i       i      i   v     i  
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_142759009_    846 ACAATTGGGACTACATCAAGCTAAAAAGCTTCCGCACCACAAAGTTAACA 895
                          i  v v     v      iv v    i   ii ii iv     --i   
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG--GACA 679

  chrX_142759009_    896 --AACAACAGAGTGAAAAAGGCAGC--ACAG 922
                         -- v   v i        - i  i --    
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAA-GACAACCCACAG 709

Transitions / transversions = 1.67 (70 / 42)
Gap_init rate = 0.02 (8 / 427), avg. gap size = 1.38 (11 / 8)  

 809 19.20 3.12 3.57  chrX_142759009_142760934     1210  1433 (493)    L1M4_orf2#LINE/L1      686   908 (0)  

  chrX_142759009_   1210 AAAAAGAAAAAAGGCAGC--ACAGAATGGGAAAAAAATATTTTCAAACCT 1257
                          i    vi     i  i --           i    -     v    i v
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCA 734

  chrX_142759009_   1258 TATATCTGATAAAGGATTGATATCTAAAATATATAT----CTTCTTTAAC 1303
                                     i   i vi    i i        v----  ii vi   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_142759009_   1304 TCCATAGGAAAAATAAATAAAATAAATAATGGTATT-AAAAATTAGCAAA 1352
                           v   ------     -  i i      ivvv   -      vi     
  L1M4_orf2#LINE/    785 TCAATA------ATAAA-AAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_142759009_   1353 AGATTTAAATAAATATTTCTCCAAAGAAGACGTACAAATGGCCGAGAGAT 1402
                         i     i    i i                ii           i v iii
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_142759009_   1403 ACATGAAAAGGTGCTTAATATCACTAACTAT 1433
                                   i    i  i    ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.58 (31 / 12)
Gap_init rate = 0.03 (6 / 223), avg. gap size = 2.50 (15 / 6)  


2204 28.13 1.38 4.25  chrX_142766470_142774878.rev     4710  5580 (2829)    L1M4_orf2#LINE/L1        2   847 (61)  

  chrX_142766470_   4710 GAAAAAACATTCTATGCTCATGGATAGGAAGAATTAATATTGTTAAAATG 4759
                          i   i i  i i   i        v      v             i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_142766470_   4760 ACCATACTGCCATAAGCAATTTATAGATTCAATGCTATGCCTATTACAGT 4809
                         i v     v  vv  vii  i  i        i  v  v     i v i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_142766470_   4810 ACCATTGACATTCTTCATAGAGCCAGAAAAAGACCATTTTAAAATTCACA 4859
                         v   vivi v  i  iii   iviv  v  - viv  ii         i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATA 150

  chrX_142766470_   4860 TGGAATCAAAATGAGCTTCAATGGCCAAGGAAGTAAGCATAATAAAAAAC 4909
                              ---------------   --     i viv  ---    i---- 
  L1M4_orf2#LINE/    151 TGGAA---------------ATG--CAAGGGACCCAG---AATAG----C 176

  chrX_142766470_   4910 AAAAACAAAC--AAACAAACAAACAAAAACAAAGCTGGAGGCATCACGCT 4957
                         v       v --i  -----   v  i       i      vv    i  
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAA-----AAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_142766470_   4958 ACCTGACTTCAAACGGTACAACAGGGCTACAATAACCAAAACAACATGGT 5007
                         v  ii i      vvv   v   ii      i   i   i   iii    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chrX_142766470_   5008 ACTGGTACAAAAACAGACACATAGACCAATGGAACAGAATAGCAAACCCA 5057
                              i i  ii i     i     i        i     v vi ii   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_142766470_   5058 ----TAAGACTGCACACCTAAAAATATCTGATCTTAGACAAACCTGACAA 5103
                         ----   iv iii   ii  viivi vi    i  v     ivv  v   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_142766470_   5104 AAACATGCAATGGGAAAAGGATTCCCTATTTAATAAATGTTGCTGAGATA 5153
                         i v   v       i    i  vvi  v  i  i     v     i  i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_142766470_   5154 ACCAACTAGCCATATGCAGAAGATTGAAAGTGAACCTCTTCCTAACACCA 5203
                           iiiv  ?   i     i    v    iv  i   i  v   v      
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chrX_142766470_   5204 TATGCTAAAATTAAATCAAGGTGGATTAAAGATTTAAATGTAAAACCCAA 5253
                            i v        v    ii     i ?   ii         i v i  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_142766470_   5254 AACTATAAAAATCCTGGCAGACATCCTAGGC---AATACCACTTAG-GAC 5299
                                   v  i i v   v v v    ?---   ----   v -   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT----CTTCGTGAC 567

  chrX_142766470_   5300 AAAGACACGGGCAAAAATTTCAT-GACACAGATGCTAAAAGCAATTGCAA 5348
                         vvv ivvii     vii    v -  i i-  ii i       vvv    
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATAT-GACACCAAAAGCACAAGCAA 616

  chrX_142766470_   5349 CAAAAGCAGAAATTGACAAATGGGATCTAATTAAACTAAACAAGTTCTGT 5398
                               v i    v  i    v   ii v  i   v v  v  v  i   
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_142766470_   5399 ACAGCAAAAGAAACTATTATCAGAGAGAACAGGCATCCTGCATAACAGGA 5448
                         i vv    i  v     i vv i  v   v  i  v  ii  v  ii   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_142766470_   5449 GAAAACTTTTCCAAGCTATCCATCTGAAAAAGGTCTAATATCCAGAGTCT 5498
                              iv   v   iii  vi      v  i  v  vi        i v 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_142766470_   5499 GCAAGTAACTTAAACAAATTTACAAGAAAATAAGACAA-CAACCCCATTA 5547
                         ii  iv    ivv    v iv i  v    --      -i     v   ?
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAA--AGACAAATAACCCAATTW 814

  chrX_142766470_   5548 AAAAGTGGGCAAAGGACATGAAAAGACACTTCT 5580
                             i           iv    v     i    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

Transitions / transversions = 1.32 (137 / 104)
Gap_init rate = 0.02 (15 / 846), avg. gap size = 3.27 (49 / 15)  

 261 20.29 0.00 0.00  chrX_142766470_142774878.rev     7850  7918 (491)    L1M4_orf2#LINE/L1      840   908 (0)  

  chrX_142766470_   7850 ACGCTCCTCAAAAGAAGACACACATGTGGCCAACAAACAAGTGAAAATAA 7899
                           ii i   v        i i   vi       i  i  vi      v v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_142766470_   7900 GCTCAACATCACTGACCAT 7918
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.00 (0 / 0)  


 861 27.54 0.36 3.26  chrX_142779002_142780623.rev        2   277 (1345)    L1M4_orf2#LINE/L1       10   277 (631)  

  chrX_142779002_      2 ATTCTCTGTTCACGGATTGGAAAAGTCAATATTGTTAAAATGTCCAAGCT 51
                           i iv      i         i v i           i   v v vi  
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chrX_142779002_     52 GCCCAAAGCAATCTACAGAGTCAATGCAATCCCTATCAAAACAACAATGA 101
                         v      vii         v    i                ivv  iivi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_142779002_    102 TATTATCCACATAAATAGAAAAAACAACACTAAAATTTATATAGAACCAA 151
                         iv  v iii  v    v  v  ivii iv        i    i   ----
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA---- 155

  chrX_142779002_    152 AAAAAAAAAAAAAGACGCAGAATAGCAAAAACTATTCTAAGCAAACAGAA 201
                         ----- viv  ii   v         v     v  ii i iv  iv    
  L1M4_orf2#LINE/    156 -----ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_142779002_    202 CAAAACTGGAGGAGTCATATTATCTGAATTCAAATTATACTACAGAGCTA 251
                             ii       v   i i vi ii v      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_142779002_    252 TAGGAACCAA-ACAGCATGGTACTGGC 277
                         i  v  i   -    ii          
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGC 277

Transitions / transversions = 1.45 (45 / 31)
Gap_init rate = 0.01 (2 / 268), avg. gap size = 5.00 (10 / 2)  

1716 26.45 2.82 2.50  chrX_142779002_142780623.rev      493  1131 (491)    L1M4_orf2#LINE/L1      268   908 (0)  

  chrX_142779002_    493 TGAGACTGTCATAAAAACAGATACACAGACCACTGGGACAGAATGAAGAA 542
                           iv    v     ii i   i i i   i  v   i i     vi   i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_142779002_    543 CCCAGAAACAAATCCACACATTTACAGACAGTGAACTCATTTTTGATAAT 592
                         i       i   i   i       ii v  i ---- v     i  i  v
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAAT----TGATTTTCGACAAG 363

  chrX_142779002_    593 GGTACCGAGAACATACACTGAGAAAAAGACAAACTCTTCAACAAATGGTG 642
                            i  i   v   v  v  i i   ii i iv  i              
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_142779002_    643 ATGTGAATACTAGATATCCATATGCAGAAGAATGAAACTAGACCCCTATC 692
                         v  v  vv   i    ?   i     i         ii i        i 
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_142779002_    693 TCTCATCATA---AAAAA--AA-TCAAAACAGATTAAATACTTAAATCTA 736
                           v  i    ---     --  -      ii   i ? v  i     v  
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_142779002_    737 AGA-CAACAAACTATAAAATAACTACAATAAAACTTTTGGGAAAATCTCC 785
                            - v -           ivvi  v  v     v vv ? v      i 
  L1M4_orf2#LINE/    514 AGAGCTA-AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_142779002_    786 AGGACATTGGTCTGGGCAAACATTCCTTAAGCAATACTCCACAAGAACAG 835
                         iv   v    vi i     vvi  i    iii vv  v   v   v   i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_142779002_    836 GCAACCAAAGCAGAAATAA-------GAACA-CATCAAG-TTAAAAAGCT 876
                              v    v i     i------- i  v-      i-       -  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CT 661

  chrX_142779002_    877 TCCACATAGCAAAGGAAACAATCAACAACATAAAGATACAACCTCATATA 926
                          iiiiiivv       v  v     v  vi i  i v      -  i -i
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC-CACA-G 709

  chrX_142779002_    927 AATCAGAGAAATTGTTTGCAAACTACCCCCCTGACAAGACAAGGGATGAA 976
                            vi      v i        ii ivivi    i   -----   ivvi
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAG-----GGACTTG 754

  chrX_142779002_    977 TAACCAAAATATAAAAGAAACTCAAACAGCTCTATT-TAAAAATGCCTAA 1025
                           v   i      v  ii     vv   i   v  v-      - v v  
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA-GACAAA 803

  chrX_142779002_   1026 TAATTTGATCATAAAATGGGCAAAAGATTTGAGTAGTTATTTCTCAAATG 1075
                            iiii  i?v            i       i   vi       v  v 
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_142779002_   1076 AAGACATACCCCAATGGCAAACAGGCATAGGAAAAGGTG-TCAATATCAT 1124
                             i    v--      v  i i   i v      i  -    i    ?
  L1M4_orf2#LINE/    854 AAGATATACA--AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_142779002_   1125 TGATCAT 1131
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.43 (97 / 68)
Gap_init rate = 0.03 (17 / 641), avg. gap size = 2.00 (34 / 17)  


2519 28.86 2.82 0.56  chrX_142803311_142805363      677  1563 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_142803311_    677 GGAAGAACATTCCATGCTCATGGATAAGAAGAACCAATATTTTTAAAATG 726
                             ii i  i     i        vi     vii      v    i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_142803311_    727 GCCATACTACCCAAAGCAATTTACATATGCAATGCTAGTCCTGGCAAACT 776
                           v     v      vii  i    v  v   i  v vi   iv    v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_142803311_    777 AACAGTGACATTTTTTTCACAGAATCAGAAAAAAAATTCTAAAATTCATA 826
                         vv   ivi v      v  v -   iiiv  ivvi  i            
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGA-AATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_142803311_    827 TGGGACCAAAAAAGAGCCTAAATACCCAAAGCAATCCTAAGCATAAAGAA 876
                            i viiv  ii  v  vi    v     i     i i iv vi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_142803311_    877 CAAAGCCAGAGATATTACATTTCCTGACTTCAAA--CTA-TACAATGCTA 923
                              iii   ivv i   i    ii i      --i  -     v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_142803311_    924 CAGTAACCAAAACAGCATGGTCCTGGTACCAAAACAGACATAGAGACCA- 972
                               i   i    ii    v    i iv ii i       v   i  -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_142803311_    973 TCGAACAGAATAGAGAACACAGAAATAAGCC-ACACACTTAACAACCATA 1021
                          v   i     v    iiv         i  - i   i   -iiii  vv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAAT 349

  chrX_142803311_   1022 TCATCTTTGACAAGG---TCAA-------CAATGAGGAAAGGACTCCCTA 1061
                          v  i  i       ---i   -------     i      i ivvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_142803311_   1062 TTTAATAAATCATTCTGAGATAAATGGCTGCCCATATGCAGAAGATTCAA 1111
                           i  i    vi v   i  i  v   v i?   i     i    v v  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_142803311_   1112 CCTGGACCCCTTCCTTTCACCATATGCAAAAATCAACTCAAGATGGATTA 1161
                         vi         v   iv        i       i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_142803311_   1162 AATATTTAAATGTAAAACCTAAAACTATAAAACCCT-GGAAGAAAACCTA 1210
                         ? v ii         i v               i  -i         v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_142803311_   1211 GG---AAATACCATCCTGAGCATTGGCTCTGGCAAAAATTTCATGAGGAA 1257
                           ---    -- v  v   v -    v iv     vii    v iiiv v
  L1M4_orf2#LINE/    550 GGNGTAAAT--CTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_142803311_   1258 GACTCTAAAAGCAATTGCAACAAAAACAAAAATTGACAAGTGGGACCTAA 1307
                            v i       vvv         iv      v  i  i v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_142803311_   1308 TTAAAATAAAGACCTTCTGCATGCCAAAAGAACCTATCCACAGAATAAAC 1357
                          i     v  i v   i  iiivi    i  vv     v v i i i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_142803311_   1358 AGATAACCTATGGAATGGGAGGAAATACTAACAAACTATGCATCCAGTAA 1407
                            i    i ii         i     i vi    ii  ii   iii   
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_142803311_   1408 AGGTCTGATATTCAGAATACATAAGTAACTTAAAGAAATCCACAAGCAGA 1457
                         i  v  vi   i       i    iv    ivv v  v  v i  vv i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_142803311_   1458 AACCAA----CCTCATTATGAAGTAGGAAAAGGACATGAACAGAAACTTA 1503
                          iv   ----  iv   ?vi  i i  v      iv    i   v i  v
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_142803311_   1504 TCAAAAAAAGACAAACG--TAGCAAACAAGCACATGAAAAAATTCTCAGC 1551
                           v   i    i v  i-- i  v  i             i  v    i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_142803311_   1552 AACGCTAACCAT 1563
                          v i????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (150 / 103)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 2.14 (30 / 14)  


2945 26.37 4.57 0.91  chrX_142832229_142834148      553  1428 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_142832229_    553 TGAAAAGGT--CTCATGTTCATGAATTGGAAGAATAAATAGTGTTAAAAT 600
                           i    i -- i          i         v v    v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_142832229_    601 ATCCATACTACCCAAAATGATATACTGATTTAATTGAATTCCTATCCAAA 650
                         iv v     v      v    v   v    i  ivv   i      v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_142832229_    651 TTCTAA-TGCTATTTTTCACAGAAATAGAAAAACT--TTCTAAAATTTGT 697
                          i i i-   i-     ii       v  v  i  -- i        ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_142832229_    698 ATATGACCACAAAATACGCTGAATAGTCAAAGCAATCTTAAGCTGAAAGA 747
                           ivi vii   iiv  v v      i    i       i ivvii    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_142832229_    748 ACAAAACTGGAAGCATCACACCCCCTGATTTTGAAATATATTATAAAGCT 797
                              ii    i vv      ii  ii    ii   iv  i  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_142832229_    798 ATTCCAAACAAGACAGCATGGTATTTGCCTAAAAACAGACATAACAACCT 847
                          ivvi  v        ii     i v  v   ii i       vvi i v
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_142832229_    848 ATGGAACAGAGTTGAAAGCCCAGAAATAAACACACACA---ACCGTCAAT 894
                               i   i    i  i            v  i   --- iv      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_142832229_    895 TGCTTTTTAACAAAAATGTCAAGGACATATATTGGGGAAAATACAGTCTC 944
                           v    ii    iii  i    iv   vi v        iv i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_142832229_    945 TTCAATAAATTATGTTGGGAAAACTGGATATTCACACACAGAAGAATGAA 994
                              i    vi  i     v         ?i    ii  i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_142832229_    995 ATTGGACCGACCTTTATCTCACACAATATACAAATATCAATGGAAAATGG 1044
                         i       --   -- i       v         v  i  ivv       
  L1M4_orf2#LINE/    450 GTTGGACC--CCT--ACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_142832229_   1045 ATTGAATATTTCAACATAAAACAGGAAACTGTAAAACTACCAGAA-AAAA 1093
                           ii? v ii v  ii   i vvvi     i       vii    -    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_142832229_   1094 TATAAGGG--------------------------AATGACTTCTTAGATA 1117
                         i   i ? --------------------------    ii          
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_142832229_   1118 GGAACTCAAAAGTATAGGCTGCAAGAGCAGAAATAGACAAATGGGATTGC 1167
                         v  vvi      i i i  vi   i  v i       i    v   i v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_142832229_   1168 ATCAGT-TTAGAAGTTTCTACACAGAAAAGGGTACATTCAAAAGAGTGAA 1216
                             iv-   i  ii  i iii vvv     ii  vv    i i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_142832229_   1217 AATACAACTTACAGACTGGGAGAAAATATGTGCCAACAATACATCTGATA 1266
                           v     ii     v             v   v  iv   i        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_142832229_   1267 AGTTGCTAATATCCAAAATATATGAGAAACTCAATAAACAACTCAATAAC 1316
                           vvi  vi      i       i ii     -- v -           i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTC--TTA-CAACTCAATAAT 792

  chrX_142832229_   1317 AAGAA----AATGGCCCAGTTATGAATTGAGTAAATGATTTGAAAAGGCA 1362
                           i  ----   ii    i  ?vi  v  i i   v        v  i  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_142832229_   1363 TTTCTCAAAAGGATACATACAAATGGCCCACAGATTCATGAGAAAATGCT 1412
                               v    i v i            v i iiiv     i  i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_142832229_   1413 AAACATCTCTAATTAT 1428
                         v      v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (144 / 83)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.69 (48 / 13)  

 251 16.36 1.82 0.00  chrX_142832229_142834148     1782  1836 (84)    L1M4_orf2#LINE/L1      853   908 (0)  

  chrX_142832229_   1782 GAAGGT-TACTAGTGGCCAATAAGCTCATAAAAGAATGCTCAAAATTATT 1830
                             i -   v i            v   i   ii        v  i ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_142832229_   1831 AGCCAT 1836
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 2.00 (6 / 3)
Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1)  


2531 28.45 1.65 1.54  chrX_142857111_142862236     3738  4644 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_142857111_   3738 TGGAAGAACTTTCCTTGCTCATGG-TAATAAGAATCAATATTGTTAAAAT 3786
                              ii iv i  v  i      - viv    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_142857111_   3787 GATTATATTGCCCCAAAG-AATTTACAGATGCAATGTTATTCCTATTAAA 3835
                          iiv   i -       v-i  i       v   i iv  i     i   
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_142857111_   3836 CTACC-GTTGACATTCTTCACAGAACTAGAGAAAACT-ACTTTGAAATCC 3883
                         v v  - i  v -  i  ii     v v  v  i-  - iii i    i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chrX_142857111_   3884 ATATGGAACCAAAAAGGATATCGAATAGCCAAAGAAATTTTAAGCAAAAG 3933
                                 viiv  i   iviv           iv   i  i iv  i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_142857111_   3934 GAACAAAGCTGGAGTCTTCATGCTACCTGAATTT--AAACTATACTACAG 3981
                                 i     vvi   ii  v  i-     --     -       i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCC-AATTTCAAAACT-TACTACAA 245

  chrX_142857111_   3982 GGCTACAGTATCCAAAACAGCACAGTACTTGTACAAAAACAAACAAATAG 4031
                         i         vi   i    iiii     v i i  ii i i   v    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_142857111_   4032 ACCAATGGAACAGAACAGAGAACCCAGAAATAAGACCACACACCTACAAC 4081
                          i        i    iv    ii          iv   i   ii  ----
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA---- 341

  chrX_142857111_   4082 TATTCAA---AACTTAAACTAACCTGACAAAGACAGGCAATGGGAAAACA 4128
                          iv    --- vi  vi  v ivv  v   iiv  vv       i   v 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_142857111_   4129 ATTCCCTACTTAATAAATGGTGCTATGATAACTGGCTAGCCATATGCAGA 4178
                           vvi  vi i  i          iv  i      v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_142857111_   4179 AGATTGAAACTGGACCACGTCCTTATACCATATACAAAAATCAACTCAAG 4228
                            v    ii      v vv   i i               i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_142857111_   4229 GTGAATTAAAAACTTAAACCTAAAACCAAAAGCTATAAAAAGCCTGGAAG 4278
                         i  i  i ? i  i    iv   i v v   i        vv i i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_142857111_   4279 AAAATTTAGGC-TATATCATTCAGGAAACAGACATGGGCAAATATTTC-- 4325
                             iv    ?-  v   -   iv  vviv ivv i     vvi    --
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_142857111_   4326 ACATTGACGACACCAAAAGCAATTGCAACAAATGCAAAATTAGACAAATG 4375
                          v  -- i             vvv        v v    v    i    v
  L1M4_orf2#LINE/    591 AGAT--ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_142857111_   4376 GGATCTAATTAAACTAAAGAGCTTCCGCACAGCAAAAGGAACTATCAACA 4425
                            ii v  i   v v  i i   ii ii vv    i iv        v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_142857111_   4426 GTGTAAACAGACAACTTACAGAATGGGAGAACACTTTTGCAAACTATACA 4475
                         iv  i  v       ii              v iv        ii   i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_142857111_   4476 TCTTAAAAAGGTCTAATATCCAGCATCTGTAAGGAAGT--TAACCAAATT 4523
                            v v  i  v  vi       v  v i   i   v --  --   v i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA--CAACTC 786

  chrX_142857111_   4524 TACAAGAAAATAACAAACCACCCCATTAAAAAGTGGGCAAATGACATTAG 4573
                         v i  v    vi     iv    v   ?    i        v  iv v i
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_142857111_   4574 CAGATATTTTTCAAAAGAAGACATATATGCAACCAACGGTCATATGAAAA 4623
                         i   i    i  v        i   i viiii    iiiv  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_142857111_   4624 AA-AATCAACATTAGAAAAATG 4644
                         i -iv       i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (151 / 103)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.53 (29 / 19)  


2531 26.96 5.18 0.81  chrX_142869895_142875290     4036  4903 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_142869895_   4036 GAAAGCACATCCCATGCTCATGTATGGGTAGAATAAATATTGTGAAAATG 4085
                              - i        i     v  v  v   v v        v  i   
  L1M4_orf2#LINE/      3 GAAAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_142869895_   4086 AACATACTGCCAAAAGCACTCTACAAATTTGATGCAATTCCCATCAAAAT 4135
                         ivv     v  v   viiv      i   ii i     i  i        
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_142869895_   4136 ACCA-CTATAATTCTTCACAGAACTAGACAAAATAATCCTAAAATTCATA 4184
                         v   -  iiv-  i  ii     v v     iv i               
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_142869895_   4185 TGGAATCAAAAAAGAACCTGCATTGCTAAAGCAAGATTAAGCAAAAAGAA 4234
                              viiv  ii  v  v v  v  i   i   vv  i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_142869895_   4235 CAAATTTGGAGGCATCACGTTACCTGACATCAAACTACACTATAAGGCCA 4284
                             v       vv    ii v  ii iv     vivi    i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_142869895_   4285 TAGTCACGAAAACAACATGATACTAGTATAAAAAATAGTCATACAGA--- 4331
                         i   v iv  i   iii  i    i i    ii -   v    i   ---
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGATCA 299

  chrX_142869895_   4332 -----ATAGA-----GAACCCAGAAATTAAGCCAAATACTTACAGCCAAC 4371
                         -----     -----  ii        v  v   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_142869895_   4372 TGATCTTCAACAAAGCAAACAAAAACATAAGGTGGGGAAGGGACACCGTA 4421
                             i   i    i vviv   i v   vvii       i i i viv v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_142869895_   4422 TTCAACAAATGATGCTGGGATTCATTGGCAAGCCACATGTAGAAGAGTGA 4471
                                    i        i-v i   vv ?       i i    i   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGAC-AACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_142869895_   4472 AGTTGGATCCTCATCTCTTACCTTATACAAAAATCAACTTAACATTGATC 4521
                                i  ii i   vi   v           i    i  v  v    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_142869895_   4522 AAAAACTT-----TAAGACCTGAAATCATAAAAATTCTAGAAAATAACAT 4566
                          ? i  i -----     v  i   ii      v ii     i v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_142869895_   4567 CAAAA-AAACCCTTATAGACATTGGCTTAGGCAAAGACTTCAT-GATAAA 4614
                         vii?i-   i i ii -   v    v        v ii   v -    v-
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATAT- 596

  chrX_142869895_   4615 GAACCCAAAAACAAATGCAACAAAAAACAAAGATAAATAGAT-GGA---- 4659
                           vv      i  v v         i -   i   i   i  -   ----
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTC 645

  chrX_142869895_   4660 ----------AAAACTTCTTCATAGCAAAAGAAA-TAGCAG---AGTTAA 4695
                         ----------       i viiivv    i  v -  v  i---   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_142869895_   4696 CAGATAACCCATAGAGTGGGAGAAGATATTCACAGTCTATACATCTGCCA 4745
                         v   i      i   i        i     ii  ivii   i     vi 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_142869895_   4746 AAACACTAATATCCAGAATCTGCAAAGAACTC----AAATCAACAAGAAA 4791
                          iiv   vi          v ii         ----  v    i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_142869895_   4792 AA-ACAAACAATCCTATCAAAAAGTGGGCTAAGGATACGAATAGGCAATT 4840
                           -     i  i  v  i?    i     v      vi      i  v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_142869895_   4841 CTCAAAAGAAAGTATACAAACAGCCAGCAAACATTTGAAAAAATGCTCAA 4890
                            v      ii        ii    ii  i  iv      i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_142869895_   4891 CATCACCAATGAT 4903
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (142 / 88)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 2.74 (52 / 19)  


1669 25.52 5.46 7.08  chrX_142903257_142904926      500  1177 (493)    L1M4_orf2#LINE/L1      242   908 (0)  

  chrX_142903257_    500 ACAAAGCTATAGTAGCCAAAACACCATGAAATTCGTATTGAAACAGAAAA 549
                                  i    ii   i   vii  iv i v i  viii i   v -
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA- 290

  chrX_142903257_    550 CATAGACCAATTGAATAAAACAGAGAACCCAGAAATAAATCCATGTATTT 599
                         i     i    v     i  iv    ii           i    ii    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_142903257_    600 GAAGCCAACTAACTTTTGG--AGGAGGCTTCAAGATTATATATTAGAAAA 647
                         ivi i   i i i   i i--   iv  --     ii  vi v i ii  
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGC--CAAGACCATTCAATGGGGAA 388

  chrX_142903257_    648 GGAACAACTTACTCAACCAACGATGATGGGAAAACTGGATACTCATATGC 697
                         i   i iii vi     v  i i  v     v         ?i  i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_142903257_    698 AGAAGAATGAA---------------CACA-----------AATCAACTC 721
                          i         ---------------    -----------   i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_142903257_    722 AAAATACATAAAATACTTTAATGTAAGACCTGAAACTGTAAAACTACTAG 771
                              iv  v ? v  i v         v  i     i       vi   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_142903257_    772 AAGAAAACATAGAGGGAAAGCTCCACGACATTATTGTAGGCAAAGATGCT 821
                                     i? v   v  i ii   v  ivvv       v i vii
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_142903257_    822 ATAGGAAAGACTTCAAAAGCTTGGGCAACACAAACAAAAATAGACAAATG 871
                         v   iv v   vi       viii      v  iv         i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_142903257_    872 AGGCTACATTAAGCTTAAAAGCTTCTGCACAGCAAAAGAAACAATCAACA 921
                         i i  v   i  iv      i   i  ii vv    i  v  v     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_142903257_    922 GAGTAAAGAGACAATCTGAAGAATGAGGGACTATATTTACAAACTATATA 971
                         i   i  i      i iiv      i i  vv      i    ii     
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_142903257_    972 TCCAGCAAGGAACTGATATCCAGAGTATACAAGGAACTC----AACTCAA 1017
                           iiii    i   vi        i    i  i      ----       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_142903257_   1018 AAGCAAAACAAACAAACAAACAAAAAACAAAACACAACATTACGGAACAA 1067
                         v ii    --------- i     v   ----------------------
  L1M4_orf2#LINE/    789 TAATAAAA---------AGACAAATAAC---------------------- 807

  chrX_142903257_   1068 AATAAAACAAAATTCTCATTACAAAATAGGCAAAGAATCTGAATAGATAT 1117
                         -------------- iv   ?v     i       i  i        i  
  L1M4_orf2#LINE/    808 --------------CCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_142903257_   1118 TTTTC-AAAAAA---ATACAAGTGGCCAA-AGGTATATGAAAAAATGTAC 1162
                           i  -   i  ---      i       - i i i       i   iv 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_142903257_   1163 AGCAGCACTAATCAT 1177
                          i  v  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (115 / 54)
Gap_init rate = 0.02 (11 / 667), avg. gap size = 7.73 (85 / 11)  


2423 26.38 4.23 5.65  chrX_142913959_142919496     4125  5045 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_142913959_   4125 TGGAAAAATATTCCATGCTCATAGATAGGAGGAATCAATATCATTAAAAT 4174
                               i    i     i    i   v   i  v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_142913959_   4175 GACCATACCATCCAAAGCAATTTATAGATTTAATGACATTCTTGTTAAAC 4224
                          i v    ivi     vii  i  i     i  i vv  i i i i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_142913959_   4225 AGCCATTCATATTCTTCACAGGACTGGAGAAAACT-ATTTTAAATTTCAT 4273
                         vv   viiiiv  i  ii   i v v  v  i-  -  ii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_142913959_   4274 GTGGAACTGAAAAGGAGCCTGAATAGCCAAAGAAGTCCTAAGCAAAACAC 4323
                         i     v  v  i   v  v           iv i  i i --    ---
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAA--- 194

  chrX_142913959_   4324 ACACACACACACACACACACACATACACACACACACAAAAAAAACAAAGC 4373
                         --------------------------------------i  i       i
  L1M4_orf2#LINE/    195 --------------------------------------GAAGAACAAAGT 206

  chrX_142913959_   4374 TGGAGGCATCACACTACCCAACTTCAAACAAC--ACTACAGAGCTACAGT 4421
                               vv       v     i      --  --      i         
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAAGCTACAGT 254

  chrX_142913959_   4422 AACCAAAACAGCACAATACTTGTACAAAAACAGGCAAATAGATCAAAGGA 4471
                           i   i    iiiii    v i i  ii i  i  v         v   
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_142913959_   4472 ACAGAATAGAGAACCCAGAAATAAGACCACACATCCACAGCTATCTGATC 4521
                          i     v    ii          iv   i    ii ii ii vi    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_142913959_   4522 TTTGACAAACTTGACAAAAACAAGCAATGGGGAAAGGATTGT-------- 4563
                           i     ivv  v   i v  vv            i  v  --------
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_142913959_   4564 ------GTGT--------------------ATGCAGAAGACTAAAACTGG 4587
                         ------   i--------------------     i    v i  ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_142913959_   4588 ACCCCTTTCTTACACCTTATACAAAAATTAATTCAAGACGGATTAAAGAC 4637
                               vi  i     v              i    i i    i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_142913959_   4638 TGAAATGTAAAACCCAAAACTATAAAAAAAACCCTGGAAGACAACTTAGG 4687
                         iv        i v i            v---i i i     v   v    
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAAC---TCTTAGAAGAAAACATAGG 551

  chrX_142913959_   4688 CA-ATATCATTCAGGATATAGGCATGGGCAAAGATTTCATGAGGAAGATG 4736
                         ?i- v   -   iv  iv v  vv i     v i    v iiiv v  ii
  L1M4_orf2#LINE/    552 NGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_142913959_   4737 CCAAAACCTATTGCAACAAAAGTAAAAATTGACAAATGGAATCTAATTAA 4786
                               v vvvv          v      v  i    v i ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_142913959_   4787 AATTAAGAGCTTCTCCACAGCCGAGGATACTGTCAATAGAGTAACCCGAC 4836
                               i i   i vii vv vi    i   i    v i   i vvv   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_142913959_   4837 AACCTACAGAATGGGAGAAAATATCTGCAAACTATTCGTCTAGCAAAGGT 4886
                             i                   i      ii  vii   iii  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_142913959_   4887 CTAATATCCTGAATCTATAAGAAAGT-TAATAAATTTACAAGAAAAAAAA 4935
                           vi     v    v     ii  v - v i  v iv i  v     i v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_142913959_   4936 ACCCCACCTCATTAAAAAGTGGGCGATGGACATGAACAGACACTTCTCAA 4985
                          vviv   iv   ?    i     i v   iv    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_142913959_   4986 AAGAAGACATACATGTGACCCACACAATCCTATGAAAAGAAGTTCAACAT 5035
                                i     vi  i  - - i  v vi         v i       
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCC-A-ATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_142913959_   5036 CACTGATCAT 5045
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.55 (146 / 94)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 6.50 (91 / 14)  


2834 25.97 2.55 1.78  chrX_142968229_142973699     4078  4978 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_142968229_   4078 TGGAAAAATATTTCATGCCCATAGATAGAAATAATCAATATCGTAAAAAT 4127
                               i    ii    ii   i   v i  v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_142968229_   4128 GGCCATACTGCCTTAAGTAATTTATAGAGTCAATGCTATTCCCATTAAAC 4177
                            v     v  iv  v i  i  i   v    i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_142968229_   4178 TACCA-CTGACATTCTTCACAGAACTAGAAAAAACT-ATTTCAAAATTCC 4225
                          v   -   v -  i  ii     v v  v  i-  -  iii       v
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_142968229_   4226 TATGGAACCAAAAAAGACCCTGAATAACCATGACAATCCTAAGAAAAACA 4275
                                viiv  ii     v     i   vi      i i i   i vi
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_142968229_   4276 AACAAAGCTGGAGGCATCATATTACCTGACTTCAAATTACACTACACTTC 4325
                                i      vv   i i v  ii i      vivi      ----
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA---- 244

  chrX_142968229_   4326 AAATTAAACTGCAGTAAACCAAACAGCATGGTACTGGTACAAGAACAGAC 4375
                         -----  i  i      v v i    ii         i i   i i    
  L1M4_orf2#LINE/    245 -----AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_142968229_   4376 ACATAGACCAGTGGAACAGAATAGAAAACTAAGAAATAAGACCACACACC 4425
                          i     i  i     i     v  i iiiv        iv   i   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_142968229_   4426 TACGGCCAAGTGATCTTCAACAAATCTGACAAAAACAAACAATGGGGAAA 4475
                           i  i   v    i   i    ivv  v   i v  vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_142968229_   4476 GGATTTCCTATTTAATAAATGGTGCTGGGAGAACTGGCAAACCATATGCA 4525
                          i  vvi  v  i  i              v      vv ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_142968229_   4526 GAAAATTGAAATTGGACCCCTTCCTTACACTATATACAAAAATTAACTCA 4575
                         i  i v    i          v   i    i                   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_142968229_   4576 ACATGGATTAAAGGCTTAAATGTAAAACCCAAAACTATAAAAACCCTAGA 4625
                          v      i ?  i i         i v i            vi i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_142968229_   4626 AGAAAATCTAGGCA-ATACCATTTAGGACATAGGCATGGGCAAAGACTTC 4674
                               iv    ?i- v i -  iiv   v v  vv i     v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_142968229_   4675 AT---CATGAAAATGCCAAAAGCAATTGGAACAAAAGCAAAAATTAACAA 4721
                         v ---i    v ---         vvv v        v      vi i  
  L1M4_orf2#LINE/    589 TTAGATATGACA---CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_142968229_   4722 GTGGTATCTAATTAAA-TTAAAGAGCTTCTGCACAGGAAAATAAACTATT 4770
                         i v v ii v  i   -     i -   i  ii vvv   iv v     i
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chrX_142968229_   4771 ATCAGAGTGAACAGACAACCTAGAGAATGGGGGAAATTTTTTGCAATGTA 4820
                          vv i      v        i v        i    v v       vvi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_142968229_   4821 TCCATCTAACAAAGGTCTAGTATCCAGTGTCTAGGGGAAACTTAAATAAA 4870
                          vi    i i  i  v  v        vi v  viiii    ivv i  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_142968229_   4871 TTTACAAGAAAAA---AAA-AACC----------ATAGGCAAAGGACATG 4906
                          iv i  v     ---   -    ----------  i         iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_142968229_   4907 AACAGACACTTCTCAAAAGAAGACATTCATATGGCCAACAA--ACATGAA 4954
                           i     i     v        i  v  v        i  --       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_142968229_   4955 AAAAAGCTCAACATCACTGATCAT 4978
                           i v           ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (133 / 98)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.60 (39 / 15)  


 240 34.84 1.94 1.29  chrX_143033509_143035344.rev      306   460 (1376)    L1M4_orf2#LINE/L1        1   156 (752)  

  chrX_143033509_    306 TAGAAGAATATACCATGCTTTTAGATTCAGAAAA---AATTTGGTAAAGA 352
                          i   ii    v     i iv i    -i   i ---   v v  v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATT-GGAAGACTTAATATTGTTAAGA 49

  chrX_143033509_    353 CATCAATTATTTAAAAATTAACCTAAGGGTTTATTACAGTTGCAATAAAA 402
                         iiv    vv iivv     i i   vi i  i vii  i iv v  v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_143033509_    403 CTCAGAGCAGATTATTTTGGGGGAAATTGGTAAACTGATGCTGAGATTCT 452
                         v  vv   v vi -    v vi       ii  i     v  i i    v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_143033509_    453 GATGTAAA 460
                         v   v   
  L1M4_orf2#LINE/    149 TATGGAAA 156

Transitions / transversions = 1.08 (28 / 26)
Gap_init rate = 0.02 (3 / 156), avg. gap size = 1.67 (5 / 3)  

1028 28.42 10.76 3.99  chrX_143033509_143035344.rev      532  1358 (478)    L1M4_orf2#LINE/L1       26   908 (0)  

  chrX_143033509_    532 TTGGAAGAGACAATACTGTAAAAATGTCATTTATCTCTAAATTAATTTTT 581
                                 vvi    i   v  i   v  v vv  i i     i  i vi
  L1M4_orf2#LINE/     26 TTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTAC 75

  chrX_143033509_    582 A-AGTCAGTGTGATTACAATAAAACTCCCAA-TATTTTTTAACCTTG--- 626
                          - v   ii ii  iv v  v   v     i- iii    ----   ---
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT----TTGCAG 121

  chrX_143033509_    627 AAATT------CTGATTATAA----CATATTGCAATTCAAATGTCTGCTA 666
                              ------     iv   ----     v v   v   iv v ivvv 
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chrX_143033509_    667 CCACCTAAGACAATCTTAAAGAAGAAAAATAA-GT---AGAACTT---CT 709
                         vi v i  i        i  i     i  i  -  ---  i   i---  
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chrX_143033509_    710 TCT-AGTATAGGCTTGAAGATTTAATA-AAAGCTTATACTAATTAAGAAA 757
                           i- i ------  v  i i   v  -      - i v    i    v 
  L1M4_orf2#LINE/    222 TCCCAAT------TTCAAAACTTACTACAAAGCT-ACAGTAATCAAGACA 264

  chrX_143033509_    758 ATGTAACAT--GTTTACAGAA-------ATAAATCAATGGAA-AGAACAG 797
                         i   iii i-- iv  -  i -------   i          -    iv 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATA-AGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_143033509_    798 ATAGCCCAGAAAAAGACCCATGCATATATGCATATTTGAATTTTAAT--- 844
                          v  i       v i      i   v    vvi v    v   ii i---
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_143033509_    845 --TG--AAGAACCATT-----AGCAAAGA-TGTTCACTTTACTCAA---- 880
                         --  --    -     -----i v     - iv  vi  i viv  ----
  L1M4_orf2#LINE/    364 GGTGCCAAGA-CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_143033509_    881 GCTGAGATAGTTAGATATTCATTTTGAAAAATATGAATGTATATGCCCAC 930
                             i  i ii i    ?i  iv vv    iv     vv iv iv  i  
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chrX_143033509_    931 TTCACTCCACATACAAATATGAA-TCCGGTTGAGTTATAGACCTAAATGT 979
                         i    v   i       v  v  -  viiv  ii i ?            
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_143033509_    980 CAAAGGCAAAACTATAAGGCTTTTAAAAGAAAATGAAAGTTGATATATTC 1029
                         v i  vi          ii  i   i       iiv i ?vv v  v   
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_143033509_   1030 ATGACC----ATTAGGTA---GTTTCTTAAATAAAACAT-AGGAACACAT 1071
                         i     ----i     i ---        i   vi   i- ii i    v
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_143033509_   1072 ACAATAAAA---AAGGGGGAAAAA----AGTCCAC----ATTAAACCAAC 1110
                         i   i    ---  iivi  v   ---- v i  i----      --   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA--AAC 660

  chrX_143033509_   1111 TTACAT-TTACCAAAAATGCCACACAGAGAATAGTTTAAAAAG------C 1153
                           vii -i v v  ii ii i i-  -    -   --i     ------ 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTAT-CA-AGAA-AGT--GAAAAGACAACCC 705

  chrX_143033509_   1154 ACAGAATGAGCGAAA-TACTTCCAGAACCTATAAGCAACAAAGACTTTGT 1202
                                 i v    -  i  v  i v v    vvii i  i ivi    
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_143033509_   1203 ATCCGAAATATTTTTGCAAAAGA-----TACAAATCAGTAAAAAGAAAGA 1247
                             ii     v -----     -----     v   i   v  ----- 
  L1M4_orf2#LINE/    756 ATCCAGAATATAT-----AAAGAACTCTTACAACTCAATAATAA-----A 795

  chrX_143033509_   1248 AAGAAAGAAAACCCAACAGAAAAA-GGATAT-GAATTTTAGTGGCCACTT 1295
                             v i v       iv?     -  ii v- i    v i i v  i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_143033509_   1296 CACAAGCAAGTAAATCCA-AAATAGT-AATGAACACAGGAATAGGC-CTT 1342
                          v v --   v i  vi -    i i-   i i    v   v  ii-  i
  L1M4_orf2#LINE/    846 CTCCA--AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_143033509_   1343 ATGCATCATTAATATT 1358
                          -i     ????????
  L1M4_orf2#LINE/    894 A-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (139 / 92)
Gap_init rate = 0.05 (48 / 883), avg. gap size = 2.54 (122 / 48)  


 952 29.18 1.70 1.98  chrX_143067458_143069138.rev        1   353 (1328)  C L1M4_orf2#LINE/L1   (556)   352     1  

C chrX_143067458_    353 TGAAAACAATATCACATGTACATGGGTTGGAAGATTTAATATTGTTGAAA 304
                           i   -i     v     v     i        i           -  i
  L1M4_orf2#LINE/      1 TGGAAA-GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT-AAG 48

C chrX_143067458_    303 AAAATTATACTGCCCAAAGTAGTCTACAGATTAACTGTGATCCTTATCAA 254
                          viiiv     v      v ii          v vi ii    i      
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

C chrX_143067458_    253 AACACCAA-TACCATTTTTCACATTAATAGGAAAAA-AATGCTACAATTT 206
                           iv   i- i  -     ii  vv   v iv  iv-i  v   v    i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

C chrX_143067458_    205 GTATGG---TACCAAAAAAATGCCCTAATAGCCATAGCAATCTTGAACAA 159
                         i     --- i --  iii i-  vv        v i          v  
  L1M4_orf2#LINE/    148 ATATGGAAATGC--AAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAA 194

C chrX_143067458_    158 CAAGTACAAAGCTAGGGGCATAACACAATCTGACTTCAAAATATCAC-AC 110
                         v   v      i i i  vv v    vvi ii i       i- i  -  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC-TTACTAC 243

C chrX_143067458_    109 AAGGCTATTGCAACCAAAACACCATTGTGCAGGTATAAAAAAATACACGT 60
                           i    iv i  i   i   vii v  i v  i    ii v v   ii 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

C chrX_143067458_     59 AGCCAAAGAGAATAGAACAGAAAATCCAGAAATAAATCCACGTGTTTACA 10
                           viv  vi        iv  i i            i   iiii    ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

C chrX_143067458_      9 GCCAACTGA 1
                          i   i   
  L1M4_orf2#LINE/    344 GTCAATTGA 352

Transitions / transversions = 1.78 (66 / 37)
Gap_init rate = 0.03 (10 / 352), avg. gap size = 1.30 (13 / 10)  

1781 27.87 3.92 1.16  chrX_143067458_143069138.rev      502  1190 (491)    L1M4_orf2#LINE/L1      201   908 (0)  

  chrX_143067458_    502 CAAAGCCAGAGGCATCACACTACCCAACCTCAAACTATACTATAAGGCTA 551
                              iii    vv       v     ii     viv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_143067458_    552 CAGTAACTAAAACAACATGAAACTGGGTACAAAAACAGACACACAGACCA 601
                               ii  i   iii  iv     -i i  ii i     i i   i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGG-CATAAGGATAGACATATAGATCA 299

  chrX_143067458_    602 ATGGAACAAAATAGAGAACACAGAAATAAAGCCACACACTTACAATCATC 651
                               i i   v    iiv          v   i   i   iii   vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_143067458_    652 TGATCTTTGACAAAGTCAACAATAATAAGCAATGGG--AAGAGTACTTCA 699
                             i  i     i viiv   v vi vv       --    i  v i--
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-- 397

  chrX_143067458_    700 TTTTCAATAAATTGTGCTTGGATAATTGGCTAGCCA-------GAGAAAA 742
                                i    v     v   i  i   v  ?   -------i    vi
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_143067458_    743 AAACTGGACCCCTACCTTTCACCCAACAGAAAAATTCACTCGAGATGAAT 792
                           ii             iv    vv i v       v    i i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_143067458_    793 TAAAGACATAAATGTAGGACCTCAAACTA-AAAAATCTTATAAGAAAACC 841
                         i ?    v        i  v  v      -    v     v        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_143067458_    842 TAGG---AAAT------GCCCTTC--TCAGAGAATAATAATTTTGGCTAA 880
                             ---    ------ v    v-- i  iv   ii v- i  i v  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAGATAT 596

  chrX_143067458_    881 GTCCCCCAAATCAGTTGCAAGAAAAACAAAAGTTGAAATATGGGATGTAA 930
                          v v  v   v  vvv    v    iv    i v  v v  v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_143067458_    931 TTCAACTAAAGAGCGCCCACACAGCAAAATAAATTATGAACAGAGTAAAC 980
                          iv  v v  i i viiiiii vv    iv v i   v  v i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_143067458_    981 AGACAACTTACAGAAAGAGAGAACATATTCACAAACTATTCATCTGACCA 1030
                                ii      v i     v     ii    ii  vi      iv 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_143067458_   1031 ---ACTTCTAATATCCAGAATCTACGAAGAATTTAGACTAATCAGAAAGA 1077
                         ---    ---i          v  ii     i ivv  v v   iv  v 
  L1M4_orf2#LINE/    747 GGGACTT---GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_143067458_   1078 AAAA--CAAAGAACCCCATTTAAAA-TGGGCAACAGACATGAATGGAAAT 1124
                             --    v     v   ?    -       vi  iv     i  v  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_143067458_   1125 TTATCAAAAGAAGACATACACACAGCCAACAAACAGGTGAAAAACGTGCC 1174
                           v  v        i     v ii     i  i  vi      i-i   i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG-ATGCT 892

  chrX_143067458_   1175 CATCATCACTAATCCT 1190
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (104 / 85)
Gap_init rate = 0.02 (14 / 708), avg. gap size = 2.50 (35 / 14)  


2680 24.32 7.87 1.18  chrX_143090744_143094828.rev     2744  3594 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_143090744_   2744 TGGAAAGATATGTCATATCCAGGAATTGAAATAATCAACATTCTTGATAT 2793
                                    vi   i i  v i    i  v v i  i   v  i v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143090744_   2794 GTCCATACCACCCAAAGCAATGTATCATTTCAATGCTGTTTTTATTAAAA 2843
                          v v    iv      vii  v  iviv     i  vi iii   i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143090744_   2844 TACCAATGACATTCTTCAAAGAATTAGAAAAA--AATTTTTAAAGCTTAT 2891
                          v   iivi v  i  iiv    v v  v  i--i  ii -   ii i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAATTCAT 149

  chrX_143090744_   2892 ACG---------------------------AACAA-------AAAGATGA 2907
                          i ---------------------------     -------     v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_143090744_   2908 ACA---CTGGCAAGAATCACATTACCTGACTTCAAATTATACTACAGAGC 2954
                            ---i   - i  v     i v  ii i      viv       i   
  L1M4_orf2#LINE/    200 ACAAAGTTGG-AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_143090744_   2955 C---GTAAT--AGA--GTATGGTGCTGGAATAAAAATAAACATATAGACC 2997
                         i---     --   --  i    i    v    ii   i         i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_143090744_   2998 AATGGAACAGAATACAGATATCCCAGAATCAAATCCACAAATCTGCAGTG 3047
                                i     vv   -i   -    vi   i   i v  i iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGA-GTCC-AGAAATAAACCCATACATTTATGGTC 346

  chrX_143090744_   3048 AACTCATTTTCAACAAACTTGCCAAGAACATACACTAGGGAAATCATAGT 3097
                           i v      i    ivv        v   v  v i      vv     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_143090744_   3098 CTATTCAATAAATGGTCCAGAGAAAACTGGATATCCATATGCAGAAGAAT 3147
                           v     i       v v i  v         ?   i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_143090744_   3148 GAAACTAGACCCCTATCTCTCACTGTATACAAAAATAAAATCAAAATGGA 3197
                            ii i        i   v   ii           v  v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_143090744_   3198 TTAAAGTCTTAAATCTAAGACTTCAAAATATGAAACTACTACAAGAAAAC 3247
                          i ?  v i     v     vi v   v   i     vi  v        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_143090744_   3248 TT-TGAGAAAATCTCCAGAACATTGAGCTGGGCAAAAATTTCTT------ 3290
                         v -v ? v      i ivi  v   i i i     vii      ------
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_143090744_   3291 ----------GCACAGACAACCAAAGCAAAAATAAGCAAATGAAA--TCA 3328
                         ----------     ii    v    v       iii    vii --   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_143090744_   3329 TCATATCAAGTTAAAAATCTTCTGCACAGCAAAGGAAACAATCAAAAAAG 3378
                            ----  i       -   i  ii vv       v  v     i    
  L1M4_orf2#LINE/    647 TCA----AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_143090744_   3379 TGAAAACACAACCCACAGAATGGAAGAA--TATTTGCAAACCACCCATCT 3426
                               v                i    --          i  ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_143090744_   3427 GACAAGGGATTAATAACCAGAATATATAAGGAGCTCAAACAACTCTTTAG 3476
                           i      i vi  v             i  i   vv       vv  i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_143090744_   3477 GAAAAAAATCTAATAATTCAATGTTAAAATGGGCAAAAAATCAGAATAAA 3526
                         v     i - v     ii    v?v            ii  iv     i 
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_143090744_   3527 CATTTCTCAAAAGAAGACATACAAATGGCAAACAGGCATATGAAAAGGTG 3576
                                 v        i           v  i i   i        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_143090744_   3577 TTCAATGTCACTGATAAT 3594
                         i    ii   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (121 / 82)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 4.28 (77 / 18)  


1899 15.07 3.50 27.89  chrX_143123395_143126491     1404  2604 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_143123395_   1404 TAGAAAAATATTCCATGTGCATGGTCCAGAAGATTTAATATTATTCACAT 1453
                          i    i    i      v     viii     i        i  v v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143123395_   1454 GGCAATACTCTTCCAGTGGATCTACACATTTAACACAATCCATATCAAAA 1503
                                   ii v i v        v   i   i      v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143123395_   1504 CCCGAGCTGGCTTTTTTTTTTTTTCAGAAAATGATAAGCTGATCTTAAAA 1553
                         i  v     v       v------      v   i         i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG------CAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_143123395_   1554 ATCATATAAACATGTAAGCAATCCATAAAAGCCAAAAGAATCTTCAAAAA 1603
                         v      ii v   i   vi i   v  v        v      v     
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_143123395_   1604 GAGTAACAAACATAGAGGACTCATACTTCCTCATTTCAAAAGTTATTATA 1653
                           iv      vv i         i      iv         v   i  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_143123395_   1654 AAACTACAGTAATCAAGATATTGCAGTACTAGCATAAGAAGTTTCAATAC 1703
                           i               i v  ii     i       ------------
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG------------ 282

  chrX_143123395_   1704 AGATATACATATACATATACATGTATAATCAACTGAATAGAATTTAGTGT 1753
                         -    v       -------------i     iv          v  v  
  L1M4_orf2#LINE/    283 -GATAGACATATA-------------GATCAATGGAATAGAATTGAGAGT 318

  chrX_143123395_   1754 CCAGAAATAAAATCTCACATTTATAGTAAACTGAATTTTAATAAAAATGC 1803
                                    vi vi        i  v  i   v   ii i  iii   
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_143123395_   1804 CAAGATAATTTAATGGGAAAA--ATATTATCTTCAATAAATAGTATTATA 1851
                              iv   i      i   --   v v i     i    i  ii ivi
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chrX_143123395_   1852 GCAAGTGAATATCCAAATGCAAAAGAATGAATTTAGACCTTTACCTCAAA 1901
                         i   v  i   ?   v               v  i    ii       v 
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_143123395_   1902 CCATATAAAAAATAACTCAAGGCCAGGTGCAGTGGCTCATGCCTGTAATC 1951
                                -------------------------------------------
  L1M4_orf2#LINE/    469 CCATATA------------------------------------------- 475

  chrX_143123395_   1952 CCAGCACTTTGGGAGGCTGATGTGGATGGATCACTTGAGGTCGGGAGTTC 2001
                         --------------------------------------------------
  L1M4_orf2#LINE/    476 -------------------------------------------------- 475

  chrX_143123395_   2002 GAGACCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAA 2051
                         -----------------------------------------------   
  L1M4_orf2#LINE/    476 -----------------------------------------------CAA 478

  chrX_143123395_   2052 AAAATTAGTGGGCCATGGTGGCGGGTGCCTGTGATCCCAGCTACTCGGGA 2101
                            -   -------------------------------------------
  L1M4_orf2#LINE/    479 AAA-TTA------------------------------------------- 484

  chrX_143123395_   2102 GGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGTGGAGGTTGCAGGGAG 2151
                         --------------------------------------------------
  L1M4_orf2#LINE/    485 -------------------------------------------------- 484

  chrX_143123395_   2152 CTGAGATTGAGCCACTGCACTCTAGCCTGGGTAACAGAGTGACTCTGCCA 2201
                         --------------------------------------------------
  L1M4_orf2#LINE/    485 -------------------------------------------------- 484

  chrX_143123395_   2202 AAAAAAAAAAAAAAAAACTCAAAATGGATAAGAAACC-GAATGTAAGAAC 2250
                         ----------------             v ? i   -i         i 
  L1M4_orf2#LINE/    485 ----------------ACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_143123395_   2251 TAAAACTATGAAATCCTTAGAAATTAACATAAGTGTAAATCTTCATGACC 2300
                                  i   ii       ivv      i ?          i     
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_143123395_   2301 ATAAATTAGGCAAAGACTTATTAGATATGATCCCAAAAGCACAAGCAA-- 2348
                         v iii        v ii  v          iv                --
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_143123395_   2349 -AATCATAGATGAATTGAATTGGACATTATAAATAGTAAAAACATATTTC 2397
                         -  vv v i  ii  -i        v i  v  v v       v v v v
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGAT-AAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_143123395_   2398 TTTCAGAAAACATCATCAAGAAAATGAGAAGACAACCCACAGAATGAGAG 2447
                         i    i ii   ii         i   i                  i   
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_143123395_   2448 AGTATGCTTGCAAAG-ATATATCTG--------CT--------------- 2473
                          iv  ii       v-         --------  ---------------
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_143123395_   2474 --AAGAACTCTTATAGCTCAATGTTAAATAGACAAAAAATAACCAATTAA 2521
                         --           i i      iv    v       v  i--      ? 
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC--CCAATTWA 815

  chrX_143123395_   2522 AAAATAAGGAATGTATCTGAGTAGACATTTCTGTCAAGAA---------A 2562
                              ii v  v v  i   i           viv     --------- 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_143123395_   2563 TTGTCAATAAGCATATTAAAA-ATGCTTCACGTTATCAGCTGT 2604
                          v i         i  v    -     iv  i i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (105 / 72)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 23.56 (377 / 16)  


2987 26.64 1.90 1.00  chrX_143207871_143210802     1543  2439 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_143207871_   1543 AAAGTACATTCTATGTTCATGGATTGGAAGAATCAGTACTGTTAAAATGT 1592
                             - i  i i                   v i i  i      i   v
  L1M4_orf2#LINE/      4 AAAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_143207871_   1593 CCATACTACCTAAAGCAATCTATAGATTTGATGTAATCCCTATTAAAATA 1642
                          v     v  i   vii     i     ii i i         i     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_143207871_   1643 CAAACAACATTCTTCACAGAAATAGAAAAA-TGCCATCCTAAAGTTAATA 1691
                          v i vi v  i  ii       v  v  i-  --        i  v   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG--ATCCTAAAATTCATA 150

  chrX_143207871_   1692 TGGAATCACAAAAGATCCAAAATAGGCATAGCTATCCTGAGCAAAAAGAA 1741
                              vii   ii  i   i     v  v i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_143207871_   1742 CAAAACTGGAGGAATCACATTACCTGGTTTCAAATTATACTACAGAGGTA 1791
                             ii       v     i v  iii       viv       i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_143207871_   1792 TAGTAACCAAAACAGCATGGTACTGACATAAAAACAGACACATATGCCAA 1841
                         i     i   i    ii        i     ii i     i   vii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_143207871_   1842 TGGAATGAGATAGTGAGCTCAGAAAGAAACCCACACAGCCATAAATGAAC 1891
                               iii  v v   ii      v       i   vii  ii- v  i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG-TCAAT 349

  chrX_143207871_   1892 TCATTTTTGACAAAGTTGCCAAGAACACACAATGAAGAAAGCACAGTCTC 1941
                          v     i     i v        v  iv     ii     v i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_143207871_   1942 TTCAATAAATTGTACTGTGAAAACT----ATTCATACAAAGAACAATGAA 1987
                              i    v  i   v  v    ---- ?i  i iiv i  v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_143207871_   1988 ACTAGACCTCTATCACTTTCCATTTACAAAAATCAAATCAAAATCGATTG 2037
                         ii i    i   i v viv    v         i  v       v   ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_143207871_   2038 AAGGGTTAAATCTAAGATCTCGACCTATGAAACTACTACATGACAACATT 2087
                         ?  ivi     v     v  vi v    i     vi  v v  v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_143207871_   2088 GAGGAAACTCTCCAGGACATTGATCTGGACAAAAATATCTTGAGTA--AT 2135
                          i? v  v   i iv   v   ivi i i   vii v    iii  -- i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_143207871_   2136 ACTGCACAAGCATAGGCAACCAAAGCAAAA-TGAACAAATTAG--TTCAG 2182
                           --  v     i i     v    v    - ii i     i --    -
  L1M4_orf2#LINE/    600 AC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA- 646

  chrX_143207871_   2183 ATCAAG-TTACAAAGCTTCTGCAC---AGAAAAAAAAATCAAAAAAGTGA 2228
                         -    i-   -   i   i  ii --- i ii v vv     i       
  L1M4_orf2#LINE/    647 -TCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_143207871_   2229 AGAGACATTCCACAGAATAGAAGACAATATTAGCAAACTACCCACTTGAT 2278
                          i     vi         i i   v      v     ii ivi ii    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_143207871_   2279 AAAGGATTAATAACCAGAATATATCAGGAGCTCAAACAACCCTGTAGAAA 2328
                           i   i vi  v           v i  i   vv     i vi  iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_143207871_   2329 AAAATCAAATAATTCAATCAAAAAATGGGCAAAATTTTTGAATAGACATT 2378
                            iv       ii    i?             ivv              
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_143207871_   2379 TCTCTAAAGA---CATATAAATGACAAAGATCCACATGAAAGGGTCCTCA 2425
                             i     ---i   i     i v  v vv         i i v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_143207871_   2426 ACATCATTGATCAT 2439
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (149 / 86)
Gap_init rate = 0.02 (14 / 905), avg. gap size = 1.86 (26 / 14)  


2583 25.59 1.68 0.70  chrX_143305907_143309819.rev     2156  2870 (1043)    L1M4_orf2#LINE/L1        1   722 (186)  

  chrX_143305907_   2156 TGGAAAGATATTTTATGTTCACGGACTGGAAGAATCAATATTGTTAAAAT 2205
                                    iii       i   i       v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143305907_   2206 GTACTTACTACCCAAAGCAATTCACAGATTCAATGTTATCCCTATCAAAA 2255
                          vvvv    v      vii  ii          i iv             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143305907_   2256 TACCAAGATAA-TTCTTCACAGATATAGAAAAAAAATTCCCAAAATTTAT 2304
                          v   - v iv-  i  ii    v  v  v  ivviv   i      i  
  L1M4_orf2#LINE/    101 TCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_143305907_   2305 ATGAAACCACAAAAGACTCAGAATAGCCAAAACTATCCTAATCAAAAGGA 2354
                            i  vii   ii   i               v   i i vv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_143305907_   2355 ACAACATTGAGGAAATCACATTACCTGACTT-AAAGTTATACTACATAGC 2403
                             vi   ii i v     i v  ii i  -   ii -       v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chrX_143305907_   2404 TACAGTTACCAGAACAGCCTGGTACTGGCAATACAACAGACACACAGA-C 2452
                               v i  ii    iv           vv vi i     i i   - 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_143305907_   2453 ACATGAAACAGAATGGAGAACACAGAAACAAATTCACACCTTTACAGTAA 2502
                          -   i  i     v    iiv      i   ii  i  v    ii  v 
  L1M4_orf2#LINE/    299 A-ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_143305907_   2503 ACACATTTTTGATAAAGGTGCCAAGAACATACACTGGGGAAAAGACAATC 2552
                          ivv     i  i  i          v   v  v        ii i i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_143305907_   2553 TCTTCAATAAATTGCGCTTGGAAAACTGGATATCCATATGCAGAAGAATG 2602
                          i     i    v i   v   v         ?   i     i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_143305907_   2603 AAACTGGACTCCTATCTCTTGCAAAATACAAAAATCACATCAAAATGGAT 2652
                           ii     i    i   vii v v          i vv           
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_143305907_   2653 TAAAGACTTAACTTTAAGGCCTCAAACTATGAAACTTCTGCAAGAAAAGA 2702
                         i ?    i   v v    iv  v       i     ii iv       v 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_143305907_   2703 TGCAATGTCC-TCTCCAGGACGTTGGTCTGGGCAAAAG------AG-TAA 2744
                          i-ii?  vv-   i iv   v    vi i     vi ------  -  v
  L1M4_orf2#LINE/    548 TA-GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_143305907_   2745 TACTCTACAAGCACAGGCAACCAAAGCAAACATGGACAAACAGGGTCACA 2794
                         v  v i v       i     v    v   v  i  i   iv  iiiv  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_143305907_   2795 TCAAG-TTAAAAATCTTCTGTACAGCAAAGGATACAATCAACAAAGTGAA 2843
                             i-       -   i   i vv       i  v     v        
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_143305907_   2844 GGGACAACCCACAGAATGGGAGAAAAT 2870
                         ii                         
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAAT 722

Transitions / transversions = 1.50 (108 / 72)
Gap_init rate = 0.02 (12 / 722), avg. gap size = 1.42 (17 / 12)  

 579 23.95 2.99 0.00  chrX_143305907_143309819.rev     3256  3422 (491)    L1M4_orf2#LINE/L1      737   908 (0)  

  chrX_143305907_   3256 TATCTGACAATGTATTAATAACCAGAATATATAAGGAA-----AAAAATC 3300
                                i  v v i vi  v             i   ----- v  v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_143305907_   3301 TATAGGAAATAATCTAATAATCTGATCAAAAACTGGACAAATAATGTGAA 3350
                         v   iv   v iv v     i ii  i?    v   i    vi  v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_143305907_   3351 CAGACATTTCTCCAAAGAAGACATACACATGGTAAACAGGCATATAAATA 3400
                         i                    i     v    iv  i i   i  i  v 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_143305907_   3401 GGTGCTTAATATCATTGATCAT 3422
                          i    i  i    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.29 (22 / 17)
Gap_init rate = 0.01 (1 / 172), avg. gap size = 5.00 (5 / 1)  


2589 27.02 2.80 1.01  chrX_143367467_143371712.rev     2865  3756 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_143367467_   2865 TGGAAATACATCCCATGTTCATGGATTGGAAGAATAAA-ATAAA-AAAAT 2912
                               v i                        v v  -  viv-  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143367467_   2913 A-CGACAGTGCCCAAAGCAGACTACAGATTCAGTGCAATTCCTATCAAAA 2961
                         i- i i v v      viiiv           ii     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143367467_   2962 TATAAA-TGTCATTTTTCACAAAATTAGAAAAAACAATCCTAAAATTCTT 3010
                          viv i-  i -     ii  i  v v  v  ivii            v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_143367467_   3011 ATGGAACTAAAAATGAGCCCAAATAGCCAAAGCATTTCTAAGCAAAAGGA 3060
                               v iv  iv  v  vi          i  v ii i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_143367467_   3061 ATAAATCTAGAGGCATTACATCACCTGACTTCAAATTATAGTACAAGGCT 3110
                          i   vi i    vv i   iiv  ii i      viv  v     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_143367467_   3111 ATTGTAACCAAAACAACATGGTACTGGTATAAAAGTAGATACATAGACCA 3160
                          iv    i   i   iii         i    iii    i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_143367467_   3161 ATGAAACTGAATAGAGAAACAAGGAATAAAGCCAAATACTTAAAATTAAT 3210
                            i  iv    v    iv v  i      v   v i i   vii i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_143367467_   3211 GAATCACTGACAAGACATACCTAAAC-ATAAACTGGGGAAAAGACATCCT 3259
                         vi  ivii      i-i i  v i  -  vv v        ii i vi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_143367467_   3260 TTTCAATAAATGGTGCTGGGA-AATTGAATAGCCACATGTGGAAGAATGA 3308
                               i              -  i  i   ?       iii        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_143367467_   3309 AACTGGATCCCTATCTCTCAACATGTACAAAAATTAATTCAAGAT----- 3353
                          ii    i     i   v  v   i            i    i  -----
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_143367467_   3354 AAAGATTTAAATCAAACACCCAAAACCATAAAATTCT-AGAGAAAAACAC 3402
                          ?   ii     vv  v v i     i      i   -   ii      i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_143367467_   3403 AGGGACAACTCTTC-TGGACATGGATCTAGGCAAATAATTAAT--GACTA 3449
                            ?ii  v     -  iv v   i -       - ii  vv --  -  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAA-TGGTTTCTTAGA-TA 595

  chrX_143367467_   3450 AGACCCCCAAAAGCAAATGCAGCAAAA------ATTTAAAAATGGGACCT 3493
                         v   v  -       v v   i     ------  vv v    v    i 
  L1M4_orf2#LINE/    596 TGACACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_143367467_   3494 AATTAAACTAAAAAGCTTCTGCACAGCAAAAGATA-TATCATCAGAGTAA 3542
                         v  i   v v    i   i  ii vv    i  i -     vv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_143367467_   3543 ACAGACAACTTAGAGAATTGGGGAAA-TATTTGCAAATTATGCATCTGAC 3591
                          v       ii v     v  i    -           i  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_143367467_   3592 AAATGACTAACATCCATAATCCACAAGGATCTCAAGGAAATCAGTAAGAA 3641
                           iv    vii     v   vi i  i  v   vviv  v   i   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_143367467_   3642 GAAAACCAAAATACTTCTATT-AAAAGTGGA-AGAAGACATGAATAGACA 3689
                         i  i  --     vii v   -    i   i- i i  iv          
  L1M4_orf2#LINE/    795 AAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_143367467_   3690 TTTCTCAAAAGGAGATACACAATTGGCCGACAAACATATTTTTAAGATGC 3739
                               v    i     i    v     i i  i  i  vvv-       
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA-AAGATGC 891

  chrX_143367467_   3740 TCAAAATCCATAATCAT 3756
                             v   v????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.48 (34 / 23)  


2949 23.51 1.70 5.43  chrX_143429610_143431828      787  1726 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_143429610_    787 AAAAATAGATCTCATGCTCATAGATTTGAAGAAGTAATATTGTGAAAATG 836
                            i   --  i    i    i    v     vv         v  i   
  L1M4_orf2#LINE/      4 AAAGATA--TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_143429610_    837 TCCACAGAACGCACAGTGATCTGCAGATTCAGTGAAATCCCTCTCAAAAT 886
                         v v i vvv v  v v      i        ii v       v       
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_143429610_    887 ACCAA-TATCTTTCTTCTA-AGATATACAAAACAGC-ATTCCTAAAATGC 933
                         v   i- ii    i  vi - i  vv    ----  -iv         v 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAA----GCTGATCCTAAAATTC 147

  chrX_143429610_    934 GTATGGAATCACGAAAAATCCAAAATAGCCAAAGTAGTCTTGACCAAAAA 983
                         i       vii i iii i   i          ii i      vv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_143429610_    984 GATCAAAGCTGCAGGCATCATACCACCAGATTTTAAAATGTAACAAAAAG 1033
                           v     i  v   vv   i  iv  vi    i    iv  vi v    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_143429610_   1034 CTACAGTAACCAA-ACAGCATGGTACTGGCATAAAAACAGATACATAGAC 1082
                                  i   -    ii              ii i   i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_143429610_   1083 TAATGGAAAAGAATGGAGAACCCAGAAATAAATTCATGTTTTTACAGCCA 1132
                         i       v     v    ii           ii   iiv    ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_143429610_   1133 ACTGATTTTTGACAAAAGCACCAAAAATATTCTTTGGGGGAAAAAAAAGT 1182
                          i       i     ii ii    i vi    vv     -   i  v   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGT 396

  chrX_143429610_   1183 TT----AATAAATGGTGCTAGGA-AACTGGATATCTATATGCAGAAGAAT 1227
                         i ----  i          i   -         ? i i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_143429610_   1228 GAAATTAGACCCTTTTTTTTTGACCTTAT-CAAGAATCAACTCAAAATGG 1276
                            i  i     i vii ivi-   v   -   i   i            
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCAC-ACCATATACAAAAATTAACTCAAAATGG 495

  chrX_143429610_   1277 ATTAAACACTTGAAATTATGGAACTACAAGGCTTGAAACTTGAACTACAA 1326
                           i ? v  i i  ---------- ii   ------------------- 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAA----------TGTAAG-------------------A 516

  chrX_143429610_   1327 GCTACAAGACTTGAAACTATGGAACTAGCAGAAGAAAACATTTGGG-AAA 1375
                             ---------       ii    vvi            vv ? -   
  L1M4_orf2#LINE/    517 GCTA---------AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_143429610_   1376 TGCTTCAGGACATTGA-TCAGGGCAATGAGTTTTTGGGTAAAACCTCAAA 1424
                          -    iv   v   i- i   -     iv  i  i i  vi  vi    
  L1M4_orf2#LINE/    558 T-CTTCGTGACCTTGGGTTAGG-CAATGGTTTCTTAGATATGACACCAAA 605

  chrX_143429610_   1425 AGAACAGGCAACAAAAGTGAAAACAGACAAATGGGTTTATATCAAGATAA 1474
                           v   i          vi    i   i    v  vi vi     i  v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_143429610_   1475 AATGCTTATGTGCAGCAAAATAAACTATCAACAGAGTGAACAGACAGCCT 1524
                           vi   v     vv    iv v        v i      v     i  i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_143429610_   1525 ACAGAATGAGAAAAAGCATTTGCAAACTATAGATCTAACAAGGGACTAAT 1574
                                 i  i   ii         ii   v    i i        vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_143429610_   1575 ATTCAGAAGACACAAGACACTC----AACTCAACCACAAAAAAAATACAC 1620
                           i     v i i  iiv    ----       iv i     i -i v i
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAAT 804

  chrX_143429610_   1621 AACCCATTGAAAAAATGTCCAAATGATCTGAATAAACATATCTCAAAAGA 1670
                               v v?       vv    v   i      i    v    v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_143429610_   1671 AGACACACAAAAGACCAACAAGTATAATAAAAACAATGCTCAACATCACT 1720
                            i i     v i    i   i i - i    -i             ??
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACA-TGAAAA-GATGCTCAACATCAZZ 902

  chrX_143429610_   1721 AATCAT 1726
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.71 (137 / 80)
Gap_init rate = 0.02 (22 / 905), avg. gap size = 3.05 (67 / 22)  


2429 28.35 3.37 1.24  chrX_143538163_143544760.rev     5219  6107 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_143538163_   5219 TGGAAAACCATTCCATGCTTATGGATAGGAAGAATGAATATCATGAAAAT 5268
                               ivi  i     i i      v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143538163_   5269 GGCCGTAATGCCCAAAGTAATTTATAGATTTCATGCTATTCCCATTAAAC 5318
                            vi  v v      v i  i  i     iv i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143538163_   5319 TACCA-TTGACATTCTT-CACAAAATAAGAAGAAAATATTTAAAAAATCA 5366
                          v   -i  v v  i  -  v   v i v   vvi  vi --    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chrX_143538163_   5367 TATGGAACCAAGAAAGAGCTTGTATATCCAAGACAATCCTAAGCAAAAAG 5416
                                viivi ii  v iv v   v    i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_143538163_   5417 AACAAAGCTGGAGGCATCACACTAACCAACTTCAAACTATACTACAAGGC 5466
                                i      vv       vv    i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_143538163_   5467 TGCAGTGACCAAAACAGCATTAATCCTGGTACAGAAACAGACACACAGAC 5516
                          i    i i   i    ii -ii v    i i iii i     i i   i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGT-GGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_143538163_   5517 TAATGGAACAGAATAGAGAACTCAGAAATAATACTAAACATCTA----CA 5562
                         i       i     v    iii         vv i v    i  ----  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_143538163_   5563 AC--ATTCT-GACAAAAA---CAAG------CAATAGGGGATAGGATTCC 5600
                          i--   i -     iii---    ------    -     v  i  vvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGAATAGT 396

  chrX_143538163_   5601 CTGTTTAATAAATGATGCTGGAAAAACTGGCTCGCCATATGCAGAAAACT 5650
                           v  i  i     i      i v      v v?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_143538163_   5651 GAAACTGGACCCCTTCCTAACACCTTATACAAAAATTAACTCAAGATGAA 5700
                            ii         v   v     v                   i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_143538163_   5701 TTAAATACCTAAATGTAAAACCCCAAACTATAAAAACCCCAGAAGAAAAT 5750
                          i ? v            i v iv           vi ii         i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_143538163_   5751 CTAGGCA-ATACCATGCAGGACACAGGCATGGACAAAGATTTC------A 5793
                         v    ?i- v i - v iv   viv  vv i i   v i    ------ 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_143538163_   5794 TGACAAAATCTCCAAAAGCAAGTGCAACAAAAGCAATAATTGGAAAATGA 5843
                              ------         viv          v  v   v iv    vi
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_143538163_   5844 GATCTAATTAAACTAAAGGACTTCTGCACAGCAAAAGAAACTATCATCAA 5893
                           ii v  i   v v  ii    i  ii vv    i  v       vv  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_143538163_   5894 AGCGAACAGACAACCTACAGAGTAGTAGAAAATTTTTGTAATCTATCCAT 5943
                           i   v        i     i i v       v    i  vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_143538163_   5944 GTGACAAATGTCTAATATCTAGAATGTATAACTAAGTTAAACAAATTTAT 5993
                         v   i  iv v  vi    i     i     vv  v ivv    v iv  
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_143538163_   5994 AAGAAAAAAA-----AACGCCATTAAAAAGCAGGCAAATGCCATGAACCG 6038
                           v     i -----   v v   ?    iii      v viv    iv 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_143538163_   6039 AGACTTCTCAAAGAAAGAAATTTGTGCGGCCAACAAACATATAAAAGAAA 6088
                          v i     v  ii    v  viivii      i  i  i  i   ii v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_143538163_   6089 GCTCAACATTACTAATTAG 6107
                                  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (140 / 108)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.73 (41 / 15)  


 205 16.67 10.42 0.00  chrX_143592285_143595300.rev      986  1033 (1983)    L1M4_orf2#LINE/L1        1    53 (855)  

  chrX_143592285_    986 TGGAAATATAT-CCATGTTCATGGATGGAAACACT----ATTGACAAAAT 1030
                               v    -              v i  v   ----    vi  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143592285_   1031 GAC 1033
                          i 
  L1M4_orf2#LINE/     51 GGC 53

Transitions / transversions = 1.00 (4 / 4)
Gap_init rate = 0.04 (2 / 53), avg. gap size = 2.50 (5 / 2)  

2683 21.23 1.36 2.26  chrX_143592285_143595300.rev     1399  2062 (954)    L1M4_orf2#LINE/L1       45   702 (206)  

  chrX_143592285_   1399 TACAATGGCAATATTTCTGAAATTGATCCACAGATTCAATGTAATCATTA 1448
                           vi         i i iv         i          i i    vi  
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chrX_143592285_   1449 TCAAAATTCCAACTCCTTTTCTTTTTGCAGAGATTGGAAAACCAATGATA 1498
                                i   i  v i   ---        i    iv  i ii  vv  
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTT---TTTGCAGAAATTGACAAGCTGATCCTA 141

  chrX_143592285_   1499 AAATTAATATGGAAATTCAAGAGACTCAGAATATCCAAAATAATCTTGAA 1548
                              v          v    i   i       v      i         
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_143592285_   1549 AAAGAAAAACATATTTGGAAGTCTCACACTTTGTATTTCCCAAATTTAGC 1598
                               i    v v     i v         ivi v  i v   i   vi
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_143592285_   1599 AGAAAACTACAGTCATCCAAACAGTGTGGTACTGGAATAACAATAGACAT 1648
                          v   i       v   v i               v    vi        
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_143592285_   1649 ATAGACCAATGGAATAGAATTTAGAGTCCAGAAATAAATTCTCATGT-TT 1697
                              i               v                -- i   ii-  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA--CCCATACATT 339

  chrX_143592285_   1698 TAGAGTAAACAGAATTTCAACAAGCATGCCAAAATAAAATAATGAAGAAA 1747
                           vi  v  iv  v    i     vi      i iv vvi    ii    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_143592285_   1748 TAATTGTTTTCTTCAGCAAATAAATGCTGTAATAGCTAGATATTCATATG 1797
                         v   v  i  -    i     ii-     vi i i  i    ?i  i   
  L1M4_orf2#LINE/    390 GAATAGTCTT-TTCAACAAATGG-TGCTGGGACAACTGGATAKCCACATG 437

  chrX_143592285_   1798 CAGAAAAAAATAGATTTGGACACTTATGT-ACACCATAGGCAAAAATAAA 1846
                           --   i   ii v      v i  iv -        vi       v  
  L1M4_orf2#LINE/    438 CA--AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_143592285_   1847 CACAAAATGGATTGATGAACTACATGTAAAAGCTAAGACTATAAAACTAT 1896
                          v          ii?v  v   v      i      i           v 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_143592285_   1897 CATAAGAAAACATAGGTGTGAATCTTTGTGTCCTTGAGCTAGGCAAAGAT 1946
                         i v             ?  i      i   v     i i       v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_143592285_   1947 TTCTTAGCTATCCCACCCCAAGTACAAA-AGCAAAATAAAG--TA-ATGA 1992
                                v   vv    vv   i    i- i     v   i--  -  i 
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_143592285_   1993 ATTGGACTTCATCCAAATTAAAATAAAGTTT---GCTTTAGAGAACCCCA 2039
                                      v         --- v   ---    i i  i  v i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAA---ACTTTTGTGCTTCAAAGGACACTA 682

  chrX_143592285_   2040 TCCACAAAAAATAGAAAAAATAA 2062
                           ---  i   vv     i i  
  L1M4_orf2#LINE/    683 TC---AAGAAAGTGAAAAGACAA 702

Transitions / transversions = 1.38 (80 / 58)
Gap_init rate = 0.02 (13 / 658), avg. gap size = 1.85 (24 / 13)  

 834 21.51 5.58 1.99  chrX_143592285_143595300.rev     2284  2534 (482)    L1M4_orf2#LINE/L1      649   908 (0)  

  chrX_143592285_   2284 AAAATTAAAAA---------TTAAAAAAATACTATTGTAAAAATTAAAAT 2324
                                    ---------  v   ii i     iivi   i v    -
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA- 697

  chrX_143592285_   2325 GA-AACCCACAGAATTGTAGAAAATATTTGCAAATGATATATCTGATAAG 2373
                           -            v v                 v              
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_143592285_   2374 GAATTGTTATTCAGAATATATGA----CTGTTATACCTCAGTCATAAAAA 2419
                          i i vv   i          i ----  v   i v    i v       
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_143592285_   2420 GAAAAATAACTTACTTGGAAAATTGGCAAATAATCTGAACAAATATTTCT 2469
                           v       ii v  ?i     v      vi  i    i i i      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_143592285_   2470 CTAAAGCAGACATGCAGGTATCTAACAAGCATGTGAAAAAATATGCAATG 2519
                          i    v   i  i  ii iv i  i     ii      i  iiv   i-
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC- 896

  chrX_143592285_   2520 CTGATCATTAAGGAA 2534
                         ---    ????????
  L1M4_orf2#LINE/    897 ---ATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (35 / 18)
Gap_init rate = 0.02 (5 / 260), avg. gap size = 3.80 (19 / 5)  


3126 25.78 2.24 0.45  chrX_143599947_143604160     2830  3721 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_143599947_   2830 TGGAAAGATATTCCACGTTCATTGATTGTAAGAATCAATATTGTTAAGGT 2879
                                    i   i      v     v    v i            i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143599947_   2880 TTCCATACTACCCAAAGCAATCTACAGATTAAATGCAATCCCTATCAAAA 2929
                         vv v     v      vii           v  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143599947_   2930 TACCAATGACATTCTTCATAAAAGTAGAAGAAACAATCCTAAAATTTATA 2979
                          v   iivi v  i  iii i  i v  vi ivii           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_143599947_   2980 TGGAACAACAAAAGACCCAGAATACCTAAGGCTATTCCGAGAAAAAACAA 3029
                              vvi   ii           v i  ii v  iii  i   i  -i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA-GA 199

  chrX_143599947_   3030 ACAAACCTGGAGAAATCACATTACCTGACTTCAAATTATACTACAGAGCT 3079
                              vi     i v     i v  ii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_143599947_   3080 ATAGTA-TCCAAACCTTATGGTGCTGGCATAAAAACCGACACATAGACCA 3128
                          i    -  v i  vv i    i         ii iv    i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_143599947_   3129 ATGGAACCAAATGGAGAAACCAGAAACACATCCACAAACCTACAGTGAAA 3178
                               ivi   v    iv       i v i   i v ii  ii  v  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_143599947_   3179 TCATTTTTGACAAAGGTGCCAAGAATATATACTGGGAACAACACAGTCTC 3228
                          v     i     i          vi  vi v    i v iv i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_143599947_   3229 TTCAGTAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAA 3278
                             ii              v         ?   i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_143599947_   3279 ACTAGACCC-TATCTCTCGTCATATACAAAAATCAAAAAAATATGGATTG 3327
                         ii i     -  i   v ii             i  vvv  v      ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_143599947_   3328 AAGACTTAAATATAAGA--------CATGAAACTAATACAATAAAACATT 3369
                         ?    i     i     --------i  i     vv  v  v       v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_143599947_   3370 GGGGAAAATCCCCAGGATTTTCGTCTGGTCAAAAATTTCTTGAGCAATGC 3419
                           ? v     ii iv  ii  v vi i v   vii      -  vv   v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chrX_143599947_   3420 C-CTACAAGTACAGACGACCAAAGCAAAAATGAACAAAT-GGACTCACAT 3467
                          - i v   i   ii i  v    v      ii i    -     i-   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CAT 647

  chrX_143599947_   3468 CAAG-TTAAAAATCTTCTGCACGATGG-GGAAACAATCAACAAATTGAAG 3515
                            i-       -   i  ii vviii-   v  v     v   v    i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_143599947_   3516 AGAGAATTCACATAATGGG-GAATATATTTGCAAATTAGCCAATTTATGA 3564
                            v  ii    v      -   v            i vvi vi v  i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_143599947_   3565 GGGATTAATAACCAGAATATTTAAAGAGCTCAAACAACACTATAGGAACA 3614
                             i vi  v         v      i   vv     v v   iv  v 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_143599947_   3615 AACCTAATAA-----TGAAAAAATGGACAAAAGATTTGAATGAACATTTC 3659
                          iv v     ----- v?        i    i         ii       
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_143599947_   3660 TCAAAAGAAGACATAGAAATAGTAAACAGGCATATGAAAATGTGCTCAAC 3709
                           v        i   v    i iv  i i   i       vi        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_143599947_   3710 ATCACTGATCAT 3721
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (133 / 93)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


2054 20.44 4.28 3.49  chrX_143606233_143607839      484  1114 (493)    L1M4_orf2#LINE/L1      273   908 (0)  

  chrX_143606233_    484 CTGAGATAAGGCTGCTACTGACACATA--T--GTAGAACAGAAT-AATGG 528
                            iv      v i-----    i   -- --i i   i     -i vi 
  L1M4_orf2#LINE/    273 CTGGCATAAGGATA-----GACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_143606233_    529 TTCCAAAATAAACT-ACATATGTATAGTCAAATGAATTTCTACAAGAGTG 577
                          i vi        i- i i  v   i     v   v    v     i   
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG 367

  chrX_143606233_    578 CCAAGACCACTGAATGGGGAAAAGAATAGTCTTTT--ACAAGCTGGTGCT 625
                                  i v          -            --    i-       
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAAA-TGGTGCT 415

  chrX_143606233_    626 GGAAAAACTATATATATCCACATGCAAAA--ATGAATTTAAATCCA-ACT 672
                           i v    iv   ?--            --     v  ii i  v-  i
  L1M4_orf2#LINE/    416 GGGACAACTGGATAK--CCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_143606233_    673 TTGCACCATATACAAAAATTAACTCATAATGGATGAAAGACCTACATGAA 722
                          ii                       v       v ?       v   v 
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_143606233_    723 AAAGCTAAAAGTATAAAACTATTAGAAGAAAACATAAGTGTAAATACGTA 772
                          i        v         v               i ?      vivii
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_143606233_    773 TGACCTTGGATTAGGCAA--GTTTTTAAAGATATGATGCCACAAACAAAG 820
                                  i        --    i v -       ii   v  i  v i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTA-GATATGACACCAAAAGCACAA 612

  chrX_143606233_    821 ACTATAAAACAAAAA-CAGATAAATTTGACTTCCTCAAAATTAAAAAATT 869
                         i v i    v     -i         v      v             v  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_143606233_    870 T-GTGTATCAAAGGATATTATTTAAAAAGTAAAGATACATCCTACAGATA 918
                          -   iv        i i   iv i     i  i v   v  i     --
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA-- 710

  chrX_143606233_    919 ACATTCTGGTATCCAATAT--ACAGAACTTGTATCCAATATACAGAACAA 966
                         --  ---  v vvv     --i  i v v i    ii   - vi  vivi
  L1M4_orf2#LINE/    711 --AT---GGGAGAAAATATTTGCAAATCATATATCTGATA-AGGGACTTG 754

  chrX_143606233_    967 TATACAGTTCCAATATACA--GAACTTATACAAGGCACTGTTAAAAATAT 1014
                            v   ----      i --     iv     vv  v iv      v i
  L1M4_orf2#LINE/    755 TATCCAG----AATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_143606233_   1015 AAA-AA----ATTTAAA--TGGTCACAGAATTCAAATGGACATTTTCCTC 1057
                            -  ----   ?   --   v  v  i   ii   i       ii iv
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_143606233_   1058 AAAATGATACATAAATGGCCTGTAAGCACAT-AAAAGTTGCTCAACATCA 1106
                           i v    i i        vi         -     v            
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_143606233_   1107 TTAGTCAT 1114
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.27 (70 / 55)
Gap_init rate = 0.04 (25 / 636), avg. gap size = 1.96 (49 / 25)  


2207 20.66 5.87 7.40  chrX_143616625_143618372      500  1283 (465)    L1M4_orf2#LINE/L1      137   908 (0)  

  chrX_143616625_    500 TTTTAAAGTTCATATAGAAATGAAAGAGAACAAGAGTACCCAAAACAATG 549
                          ii    i       i      v   i  v v   i  v          v
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_143616625_    550 TTGAAAAACAA---CAAGGT-GGAGGACTCAAGAGTTCCTAATTACAAAA 595
                                 v  ---   i  -          v- v    i    v     
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCAC-ACTTCCCAATTTCAAAA 235

  chrX_143616625_    596 CCTATTACAAAGCTACAGCAATTAAGACAGTATGGTAGTGGAATGAGAGT 645
                          i  i             i   i        i     v   v  i  ii 
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_143616625_    646 AGACATATAAATCAATTTAACATGATTAGAAGTCTAGAAATAAACCATTA 695
                                  i      vv  i vi   iii    i           vv  
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_143616625_    696 CATTCATGGTCAGTTAGTCT-----------GCCAAGACAATTCAATCAA 734
                             i       i  ii i -----------        v       vii
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_143616625_    735 GAAATAATAGATATTTTAAATAAAGAGT-TTGGAATATCTAAATATCCAC 783
                             v     - v    v  i   vi  -i   i i v  ii   ?    
  L1M4_orf2#LINE/    386 GAAAGAATAG-TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_143616625_    784 ATGTAAGTTAATTATGTTAAACCTCTATCTCATAAAAGTCACAAAAATTA 833
                            i  ivv   v v   ii   i   i    i vv vvi          
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_143616625_    834 AATTAAAACAGCTCAAAAACCTAAATACAAGAGCTAAAATGCATAAAGGA 883
                          v i    ii v   ? i        ii           i-i     ---
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC-TATAAA--- 530

  chrX_143616625_    884 AAATTCATAAGGAAAAACTTTTAGA-GAAAAAATAGTT-TAAACATTTGT 931
                         ----------------   i     -     v    v?-    iv  i  
  L1M4_orf2#LINE/    531 ----------------ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_143616625_    932 GACCTTGATTTAGATAATGGTTTCTTAGACATGATATCAAAAGTACAAGT 981
                                iv    ii              i    i i      i     i
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_143616625_    982 GATAGAA--AAAAATAGATAAATTTG----TATCAAAAATAAAAACTTTT 1025
                         i i i  --               v ----i       v           
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_143616625_   1026 ATTCCTCAAAGAATATTATTAAGAAAATAAAA------CCCAGA-AATGG 1068
                         i v i      i i i   i      i i   ------    v -     
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_143616625_   1069 GAGAAAATATTTACCATTTATAAATCCTTTAAGGGATATATATTTGTGTA 1118
                                     i v v i   v   ivv       i------    ---
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGAC------TTGT--- 755

  chrX_143616625_   1119 TGTATGTATATAAATATACATACATGTATAATTAATACTTCTAAGATTCA 1168
                         ---------------  v  v -  i     -- iv   ii  vi i   
  L1M4_orf2#LINE/    756 ---------------ATCCAGA-ATATATAA--AGAACTCTTACAACTCA 787

  chrX_143616625_   1169 ATAATAAGAAGACAAATTACCTCATAAAAATACAGTCAAAAGATTTAAAG 1218
                                i         v   iv  v?   v ii v    i     i  v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_143616625_   1219 AGTCATC------------ATACACCCACGGGCAATAAGCATCATTAGCC 1256
                           v   i------------   i  vv i  v         -------- 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA--------C 879

  chrX_143616625_   1257 ATGAGAGAACTGC--AA-ATCAAAAGTACA 1283
                             i ii -   --  -    ????????
  L1M4_orf2#LINE/    880 ATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (98 / 60)
Gap_init rate = 0.03 (23 / 772), avg. gap size = 4.52 (104 / 23)  


2698 27.70 0.60 0.72  chrX_143641803_143643628      500  1333 (493)    L1M4_orf2#LINE/L1       76   908 (0)  

  chrX_143641803_    500 AGCTTCAATAGCCGATTC-TATCAAACTACCAATGAATTTCTTCACAGAA 548
                           v     ii-- i  i -       v v   iivivi  i  ii     
  L1M4_orf2#LINE/     76 AGATTCAACG--CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAA 123

  chrX_143641803_    549 -TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAAGAGCACAC 596
                         -   -- v  i  - iii    i           viiv  ii  v -  v
  L1M4_orf2#LINE/    124 ATTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC-CAG 170

  chrX_143641803_    597 ACT-GCCAAGACAATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCACGC 645
                          v -     i      i i iv  i          i      vv    i 
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_143641803_    646 TAACTGACTTCAAACTATACTACAAAGCTACAGTAACCAAAACAGCATGG 695
                          vv ii i      viv                   i   i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_143641803_    696 TACTGCTACCAAAACAGATATATAGACCAATGGAACAGAACAGAGGCCTC 745
                              vi iv ii i   i       i        i    iv   ivii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_143641803_    746 AGAAATAACACCACACATCTACAACCATCTGATCTTTGACAAACCTGACA 795
                                 vv   i    i  iiii  vi    i  i     ivv  v  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_143641803_    796 AAAACAAGAAATGGAGAAAGGATTCCCTATTTAATAAATGGTACTGCGAA 845
                          i v  vvv     i     i  vvi  v  i  i       i   v  v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_143641803_    846 AACTGGCTAGCCCTATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACC 895
                               v  ?  vi   i i  iiv    ii    i    v   i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_143641803_    896 TTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAATGTTAGACCTA 945
                         v              i    i      i ?    i       v   v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_143641803_    946 ACACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGACAT 994
                          v  i      vi i           v    ?i- v i -   iv   v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCT 569

  chrX_143641803_    995 AGGCATGGACAAGGACTATATGACTAAAACACCAAAAGCAATGGCAACAA 1044
                         v  vv i i   v ii viv iiv  vi            vvi       
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_143641803_   1045 AAGCCAAAAGAGACAAATGAGATCTAATTAAACTAAAGAGCTTCTGCACA 1094
                            vv    v   i    vi  ii v  i   v v  i i   i  ii v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_143641803_   1095 GCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAA 1144
                         v    i  v    i  vv i      v  i     i              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_143641803_   1145 TATTTTTGCAATCTACCCATCTGACAAAGGGCTAATATCCAGAATCTACA 1194
                         v  v       vii ivi      i  i  i  vi          v  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_143641803_   1195 AAGAACTTAAACAAATTTACAAGAAAAAATCAAACAACCCCATCAAAAAG 1244
                                ivv    v iv i  v     iv    i     v  i?    i
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_143641803_   1245 TGGGCAAAGTATATGAACAGATACTTCTCAAAAGAAGACATTTATGCAGC 1294
                                  v  v    i   i i     v        i  vi viii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_143641803_   1295 CAACAGACACATGAAAAAATGCTCATCATCACTGGTCAT 1333
                            i ii          i       v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (135 / 92)
Gap_init rate = 0.01 (9 / 833), avg. gap size = 1.22 (11 / 9)  


2456 27.34 2.40 3.49  chrX_143655183_143660150.rev     3566  4483 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_143655183_   3566 TGGAAGAACATTCCATGATGATGAATACAAAGAATCAATATTGTTAAAAT 3615
                              ii i  i     v v   i  vvi    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143655183_   3616 GGCCATACTTCCCAAAACAATTTACAGGTTCAA-GCTATTTCTTTCGAAC 3664
                            v     i      vii  i     i     -  v  ii  v  i  v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143655183_   3665 TACCAAAGACATTCTTCACAAAATTAGAAAAA---GTCTTTAAAAATTCA 3711
                          v   ivvi v  i  ii  i  v v  v  i---i  i --        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--AAAATTCA 148

  chrX_143655183_   3712 TATGGAATCAAATAAGAG--CCTGAAACGCCAAGGCAATCCTAAGGAAAA 3759
                                -- vii   i --  v   vv     ii     i i ii  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_143655183_   3760 AGAAGAAAGCTGGAGGAATCACATTATGTGACTTTAAAGTACACTGCAGG 3809
                             v    i       v     i vivii i  i   iivi   i  ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_143655183_   3810 GCTACAGTAACCAAAAGAGAATGCTACTGGTACAGAAACAGACACACAGA 3859
                                   i   i v  vi  v      i i iii i     i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_143655183_   3860 CCAATAGAACAAAATAGAGAGCCGAGAAATAGTGGAACATGCCTATGTCA 3909
                         i    i   i i   v     i v       ----   ---- i  i-  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATA----AAC----CCATA-CA 337

  chrX_143655183_   3910 TGCCTATGACCATTGAACCATTGACAAAG----CAACAAACAAGCAATGG 3955
                          --i    ii  v vi iiv i     i ----   -i v  vv      
  L1M4_orf2#LINE/    338 T--TTATGGTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGG 384

  chrX_143655183_   3956 GGAAAG----GTCTCCCAATTCCATAAATAGTGCTAGGATAACTGGCTAA 4001
                               ----    i----   v i    i     i   i      v  ?
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTT----TTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_143655183_   4002 CCTTATGCGAAAGATTGAATTTGGACCCCTTTCCTACACCACATACAAAA 4051
                           vi    i     v    v          vi ii      i        
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_143655183_   4052 GTCAATTCAAGATGGATTAATTACTTAAATGCAAAACCTAAAACTATTAA 4101
                         i i  i    i      i ?vv  i      i  i v          -  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AA 529

  chrX_143655183_   4102 AAACCCTGGAAGATAATCTAGG---AAATACCCTTCTGGACATAGGACCT 4148
                           vi i i     v  iv    ---    ---    vv   v v  iiiv
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTA 576

  chrX_143655183_   4149 GGCAAAGATTTCATGACAAAGATGCCAAAAAAGCAATTTTAACAAAAAAG 4198
                              v i    v iivv v  ii      ivi   vi--       i i
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC--AACAAAAGAA 624

  chrX_143655183_   4199 AAAATTGCAAAATGGGACCTAATCAT--CTAAAGAGCTTTTGCACTGCAA 4246
                              v vv    v    i v    v--i    i -      ii  v   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chrX_143655183_   4247 AATGA-ACTATGAATAGCTCAAACAGACTTTGTACAGAATGAGAGAAAAT 4295
                          i-  -     v  v ivvii  v    vvivi        i        
  L1M4_orf2#LINE/    674 AG-GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_143655183_   4296 GTTTGCAAACTATGCATCTGACAAAGGTCTAACATCGAGAAACTATCAGA 4345
                         i        ii  ii      i  i  v  vii   v    vv   v ii
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_143655183_   4346 AACTTAAATTTACCAG-CAATAA-ACAAAAACGAATAACCCCATTAAACA 4393
                             i----    v v-      - v   i  i        v   ?  v 
  L1M4_orf2#LINE/    773 AACTC----TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_143655183_   4394 GTGTGCAAATGGCATGAACAGACGCTTTTTGAAAGAAGACATACATGCAG 4443
                         i  v     v iiv    i    ii  i iv        i     viii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_143655183_   4444 CCAACAAGCATATGAAAAAATCCTTAATGTCATTAATCAT 4483
                             i     i       i  v  i  ii   ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (155 / 93)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 2.25 (54 / 24)  


2094 27.32 4.26 5.03  chrX_143671469_143673591      716  1630 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_143671469_    716 TAGAGAGGTAAACTATGATCATGGATTGAAAGATTTGGAGATGTTAAAAT 765
                          i  i  i  vv i   v          i    i  iiviv      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143671469_    766 GCCATTGCTTCCAAAATTGACCCATAAATGTAATAGAATCTCAGTCAAAA 815
                          v  v i  i  v       i i i i  vi  iiv    i vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143671469_    816 TTCCAGCATCCTTTT--AGAAAAATTTTGGAGCTGAATATGAAATTTGTA 863
                          i     vv      --iv i     vvvi      viv i     ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_143671469_    864 TGGAAATTTACAGAGCCTAGACTGGCCAAAATAATTTTAAAATGGGATAA 913
                                vi vi ii  i   v i       i   i  i   vi i v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_143671469_    914 -GAAGTTAAAGAAATAATATTACCTGATATCGATATATAACATAAAGGTA 962
                         -i     ii  i v v i i v  ii  v  i v iv  vi i    v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_143671469_    963 AATTAATCAAGACAATGTAGTACTGATATACACTTTGACATATATA--AA 1010
                         v v           i   i      ii   vivv v        v --  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_143671469_   1011 TAGAACAGAATAATGAGTACAGTGCTGGACCCACATGTACACGATCAATT 1060
                          i   i     viv    v   viv ii     i ii vi i i      
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_143671469_   1061 GACTTTCATCAAAGATGCCAAGACTATTCCGTGGGGAAATATTAATATTT 1110
                           i    iv   i i         i    vi        v v  i v   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_143671469_   1111 TCAAAAAACGATGCTGAGAAAATTGGATTGCTACATGAAAAAATAAATGA 1160
                             v   i i     i  v  i     v? i     v    i--     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG--AATGA 448

  chrX_143671469_   1161 ACCTCAACCATTATATCCCACCATGTACTCAAACTAATT-AAAATGACTC 1209
                          vi vi   vi  iv  v      i   vv   i   i -      iv  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_143671469_   1210 ATAAGTCTA----TAAAAGTTAACAGTATAAAATTTCTAGAAGAAAACA- 1254
                          ? iii   ----   i  i   v v       i ii            -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_143671469_   1255 AGGAGAAAATTTTAGTCACTTTGCATTTGCCACAGATTTTTAAAATACAA 1304
                            ? v    i  v  v  i   vi  v v  vv i   i v i   ii 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_143671469_   1305 CACAAAAAACTTTTTGTCAACTAAAAATGCAAATTTAAAGTTACATAAAA 1354
                            v    i ---------  ----------------   ----------
  L1M4_orf2#LINE/    599 CACCAAAAGC---------AC----------------AAG---------- 613

  chrX_143671469_   1355 TTCAATAAATAACTTTATAAAAATCAATACATTGAAATTCATCAACATAA 1404
                         --   i   vi ------      vi   v    i v        v  v 
  L1M4_orf2#LINE/    614 --CAACAAAAGA------AAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_143671469_   1405 AAAACATTTTTTTCTTTCAAAGATACTGTTATAAAAATCAAAAGGCAAAC 1454
                              -    v v   iv  i  i   i i vi   i v     i   v 
  L1M4_orf2#LINE/    656 AAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_143671469_   1455 CAAATACTGAGAAAAAA-ATTTACA---CAAATATCCAACACAATACTTG 1500
                           v v v  i  i    -    i  ---  v     ii i viiv     
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_143671469_   1501 TATCTATGCTATATAAACA----TTAGAAT--------------ATAAAC 1532
                             i viv        v ----   v  i-------------- i   i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_143671469_   1533 AACCCAATC--AAAATGGGCAAAC-ATTTGAGCAGAAAGTTTAATTAAGA 1579
                                 i--            v-      ii   v v  ivviv    
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_143671469_   1580 A-ATACAGACATGA--AATAAGCACATAGAAAGATATTCAACATCATTAG 1626
                          -   i v v   i--           ii      ii         ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_143671469_   1627 TCAT 1630
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.25 (85 / 20)  


3024 26.87 1.67 0.78  chrX_143717539_143721664.rev     2739  3635 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_143717539_   2739 AAAAATAATTCTATGTTCACATATTGAAAGAATTAATATTTTTTAAATGT 2788
                            i   - i i       iiv    i    v        v  v i   v
  L1M4_orf2#LINE/      4 AAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_143717539_   2789 TCATACTACCCAAAGTAGTCAAAAGATTCA-TACAATTCCTATCAAAATA 2837
                         iv     v      v ii  v v       -ii    i           v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_143717539_   2838 CCAATGACATTCTTCATATAAATTT-TAAAAAGACCCTAAAATGTATACA 2886
                            iivi v  i  iii v     v-i  ivv  i        vi   ii
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_143717539_   2887 GAACCATAAAATATCCAGATTAGATCAAGCTATCCTAAGCAA-AAGAACA 2935
                            viii  iiv i     v   viv  i v   i i iv  -       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_143717539_   2936 AAATTGGAGGAATCACATTACCTTGCTTCAAATTACACTGCAGAGATATA 2985
                           i        v     i v  ivii      vivi   i  i  v  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_143717539_   2986 GTAACCAAAACAGTGTGGCACTGGCCTAAAAACAGATACATAGACTAATG 3035
                             i   i         i      v   ii i   i i     ii    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_143717539_   3036 AAATAGAATAGAAAACCCAGAAATGAATCCACGCACCTACAGTGAACTCA 3085
                         i        v  i ii        i  i   ii  ii  ii  v  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_143717539_   3086 TTTTTGACAATGATGCCAAAAACTTATGCTGGCAAAAAGACAGTTTTTCC 3135
                             i     v i      i v v viiv   vi   ii i   i   i 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_143717539_   3136 AATAAATTGTGCTGGGAAAACTGGATATTCATAGGCAGAAGAATGAAACT 3185
                           i    v         v         ?i  i v   i         ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_143717539_   3186 AGACCCCTATCTCTTGCAACATACAAATATCAAATCAAAATGAATTTAAA 3235
                         i        i   vii v i       v  i  v        i  iv? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_143717539_   3236 ACTTAAATCTAAGACCTCAAACTATGAAACAACGTTAC--GAAAACATTG 3283
                           i     v     v  v       i    --iv   v--        v 
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAAC--TCTTAGAAGAAAACATAG 550

  chrX_143717539_   3284 GGGAAAATCTCCAGGACATTGGTTGGGGCGATAATTTTTTTGATCAATAC 3333
                          ? v      i iv   v    v vi   i  ii   i  v   --  iv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGA 598

  chrX_143717539_   3334 CAC-ACAAGCACAGGCAACCAAAGCAAAA-TAGACAAATTGGATCACATC 3381
                            - v       i     v    v    -    i        iiv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_143717539_   3382 AAG-TTAGAAAGCTTCTGCACAGCAAAGGACACAATCAACAAAGTGAAGT 3430
                           i-   i   -   i  ii vv          v     v        iv
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_143717539_   3431 TACAACCTGCAGAATGGGAAAAAAATGTCTGCAAACTACCCTTTTGACAA 3480
                         v      ii          i    - i i      ii iviv i   i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAA 746

  chrX_143717539_   3481 GGGATTCATA---AGAATATATAAGAATCTCAAATAACTC--TA-TGAAA 3524
                             i ii  ---           ii v   vv i     --  - i   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_143717539_   3525 AATCGAAAAATCTTATC-AAAAATGGGCACCATATTTGAATAGACATTTC 3573
                          iv i  v  i iv  i-           vviv                 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_143717539_   3574 CCAAAAAGAGACATACAAATGGCAAATGGGCCTATTAATAGGTACTCAAC 3623
                         i v   ii   i           v   ii  vi  v  v  i i      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_143717539_   3624 ATCACTGATCAT 3635
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (150 / 88)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 1.38 (22 / 16)  


3006 24.28 1.60 4.49  chrX_143742233_143746784     3125  4059 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_143742233_   3125 TGGAAAGATATTCCATGTTTATGGATTGGAAGAATCAATATTGTTAAGTT 3174
                                    i       i             v i            v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143742233_   3175 GTCCATACTACGCAAGGCAATCTATGAATTCAGTGCAATCCTTATCAAAA 3224
                          v v     v v   ivii     iii     ii       i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143742233_   3225 TACCAATGACGCTTTTCACAGAAATAGAAAATGCC-ATGCTAAAATTTAC 3273
                          v   iivi vi    ii       v  v  -  i-  v        i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_143742233_   3274 GTTGAACCACAAAAGACCCAGAGTAGCCAAAGCTATTCTGAACAATAAGA 3323
                         i v   vii   ii        i        i v  ii    v  v    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_143742233_   3324 ACAAAACTGGAGGAATCACATTACATACCTTCAAGTTATACTATAGAGCA 3373
                              ii       v     i v vi vi     iviv     i i   v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_143742233_   3374 ATAGTAATCCAAACAGCATGATACTGGAATAAAAAGAAACACACAGGCCA 3423
                          i       v i    ii  i      v    ii v i   i i  ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_143742233_   3424 GTGGAACAGAGTGAAAAACCCAGAAACAAATCTATACATATACAGTGAAC 3473
                         i     i   i vi i ii       i   i i      v  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_143742233_   3474 TCATTTTTGACAAAGGTTTTAAGAACAGACATTGGGAAAAGGACAGTCAC 3523
                          v     i     i   vii    v  vv  v    i    i i    vi
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_143742233_   3524 TTCAATAAATGGTGATAGGCAAACTGGATATAGATATACAGAAGAATGAA 3573
                              i        v i  vv         ?vv i  i  i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_143742233_   3574 ACTGGATCCCTATCTCTCACTATGTAAAAAAAAAAATCAAACAAAATGGG 3623
                         ii    i     i   v   i  i  ------------------------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATA------------------------ 475

  chrX_143742233_   3624 CAAAAGAAAGAAAAATAATCAAATCAAAATGGATTAAATAATTAAATCTA 3673
                              ------------  i  v           i ? v vi     v  
  L1M4_orf2#LINE/    476 CAAAA------------ATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_143742233_   3674 ACACCTTAAACTATGAAACTACTAAAAGAGAACATTGGGGAAATTCTCCA 3723
                          v v  v       i     vi  i    i     v  ? v  v   i i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_143742233_   3724 GGACATTGATCTACACAAAAATTTCCT-GA-GTGATACCCTACAAGCACA 3771
                         v   v   ivi  vi   vii    i -  -i   i   -- v       
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC--AAAAGCACA 611

  chrX_143742233_   3772 GGCAACCAAAGTAAAAATGGACAAATAATATTACATCAAG-TTAAAAAGC 3820
                         i     v    v      i  i    viv i v      i-       - 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA-C 660

  chrX_143742233_   3821 TTCTGCACAGCAAAGGAAACAATCAATAATGTTAAGAGACAATCCACAG- 3869
                           i  ii vv       v  v     v  v  v  i      i      -
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_143742233_   3870 ----GAGAAAATATCTGTAAA--ATAACCACGTGACAAGGGATTAATAAC 3913
                         ----          i  i   --   --i iv   i      i vi  v 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATA--TATCTGATAAGGGACTTGTATC 758

  chrX_143742233_   3914 TAGACTATATAAGGAACTCATACAACTCAAAGGGAAAAAATCTAATAATC 3963
                         i   v       i      v          viiv     iv v     i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_143742233_   3964 TGAATTAAAAATGG-CAAAA-ATCTGAGTAGACATTTCTTAAAAGAAGAC 4011
                         ii v ?        -    i-  i   i           iv        i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_143742233_   4012 ATACAAATGGCAAACAGGTATAC-AAAAG-TGCTGAACATTACTGATCAC 4059
                                    v  i i i i i-     -    v     i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (137 / 86)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.56 (57 / 16)  


1512 29.81 2.69 0.96  chrX_143779908_143786843.rev      827  1346 (5590)    L1M4_orf2#LINE/L1        1   529 (379)  

  chrX_143779908_    827 TGCAGAGATATTTTATGTTCATGGATAGAAAGATTCAATATTGTTAATAT 876
                           v i      iii            v i    i i           v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143779908_    877 GTTCATTTTTCTTAACTTGATCTGTAGATTTAGTACAATCTC------AA 920
                          viv  vi i ii  v       ii     i iii     i ------  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143779908_    921 CCCCATCAAGTTATTTTGTGAATATCAACCAAATGATTATAAAATTTATA 970
                         i    v vivi v     iii v  ii  v iv    iv       i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_143779908_    971 TGAAGAGACAAAATACCCAGAATA-CTGACACAGTATTAATAGGGAAGAA 1019
                           i i vi   iiv          - ii v   i v  i v ii      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_143779908_   1020 CAAAGTTGGAGGGCTTCCATTACCTGACATCAAGGCTTACTATAAAGCTA 1069
                                     i  iv  i v  ii iv    ii       i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_143779908_   1070 GGAGATATCAAGACAGTGTGATATTTGTGAAATAACAGACAAATAGATCA 1119
                         v-  vv              i  i v iiv  vi i     v        
  L1M4_orf2#LINE/    251 C-AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_143779908_   1120 ATGAAACAGAATGCAGAGTTTAGAAATAGGTTTATATAAACAT----AAT 1165
                            i  i     vv     ii       iiiii   i vvi  ----   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_143779908_   1166 T---TTTGGGCTAAGGAGCAAAGTCAAATTTATGAAGAAAGATTAGTCTT 1212
                          ---   v i v i  v  v   v v v iv   ii      v       
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_143779908_   1213 TTCAGCAAATGCTACAGAAACAATGGAACATCCACATGCAAAAAAAAAAT 1262
                             i      v i v ii    iv i i ?            i  --- 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA---T 446

  chrX_143779908_   1263 GAATCTAGAGATATACCTTAACACTTTTCACAATAATTACTTCAATATTT 1312
                            vi i  vviv     i -   iv vi    v     vi    v  vv
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTCAAAATGG 495

  chrX_143779908_   1313 ATGATTGCACTAAATGCAAAATATAAAATTATAA 1346
                           v ?v vv       i  i vv     i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

Transitions / transversions = 1.43 (90 / 63)
Gap_init rate = 0.01 (7 / 529), avg. gap size = 2.71 (19 / 7)  

 822 22.49 7.94 3.97  chrX_143779908_143786843.rev     3591  3968 (2968)    L1M4_orf2#LINE/L1      516   908 (0)  

  chrX_143779908_   3591 AGCCAAACCCTATCAAATTGCTTTAGAAGAAAGGTCAGAAAATATATAGG 3640
                            i   v -   v   i --i          --------- i   vi? 
  L1M4_orf2#LINE/    516 AGCTAAAAC-TATAAAACT--CTTAGAAGAAA---------ACATAGGNG 553

  chrX_143779908_   3641 CAAA-CTT---GGCTTTGA---AGGTAA--GTTG--TAG---CAAC-CCA 3675
                         i   -   --- i i   i---   i  --   v--   ---ii  -   
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_143779908_   3676 AAAGGCAAAATTTATAATAGAAAACATA----AATTGTTCTTTATTACAA 3721
                             -  v  viv i  v      v   ----     vv   i  i v  
  L1M4_orf2#LINE/    604 AAAG-CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chrX_143779908_   3722 TTAAAATCTTTTGCTCTACAAATGACACTGTCTAAAAAATTATA-GACAA 3770
                               v      iv  v    v      i  v i   i v v -     
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_143779908_   3771 GCCA-AGACTGAGAGAAAATATTTGGAAGATACATATCTGACAGAGAACA 3819
                         v   -   v  i             v  ivi i        i ii i  v
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_143779908_   3820 TATTTCTATAATATACAAA-AACATTTA-AATTGCAATAATAAG----CA 3863
                          i v  i v      i   -   vi   -  i -         i----  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACT-CAATAATAAAAAGACA 801

  chrX_143779908_   3864 AACAACCCAATTTAAAAAATGGGCAAAT-ATCTGGACATATATGTTACCA 3912
                           i         ?     -        v-  i  i i v i  v iv   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_143779908_   3913 A-GAAGATAAATTGTTGGCAAACAAGCCTGTGAAAAGGTGCTTAACAT-A 3960
                          -       v iviv    v  i    vii       i    i     - 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_143779908_   3961 TTTTTATG 3968
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.31 (47 / 36)
Gap_init rate = 0.06 (22 / 393), avg. gap size = 2.05 (45 / 22)  

1873 27.04 1.49 3.86  chrX_143779908_143786843.rev     5126  5798 (1138)    L1M4_orf2#LINE/L1        3   659 (249)  

  chrX_143779908_   5126 GAAAAATATTCTATGCTCATGCATTGGAAGAATCAATATCATTAAAATGG 5175
                             i    i i   i     v         v i     ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_143779908_   5176 CCATGCTACCTAAAGCAATTTACAAATTCAAAGCAATTCCTAACAATCTA 5225
                          v  i  v  i   vii  i    i      v     i    v   vv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_143779908_   5226 CCAACATCATTTTTTGCAGAATCAGAAAAAAGTCTATTCTAAAATTCATA 5275
                            i vv v            -- vvi v   iiv  i            
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_143779908_   5276 TGGAACCA-AAAAGAGCCTGAATATCCAAAGCAATAGTAAGTAAAAAAAA 5324
                              vii-  ii  v  v     v     i    v- --- i     i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-T---TGAAAAAGA 196

  chrX_143779908_   5325 AAAACAAAGCCAAAGGCATCATGTTACCCTACTTCAAACTATACTACAAG 5374
                          i       iiii   vv   iii v   v i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_143779908_   5375 GCTACAGTAACTAAAACAACATGATATAAAAACATGTATAAAACTGGTAT 5424
                                   ii  i   iii  i  -----------------    i  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTA-----------------CTGGCAT 279

  chrX_143779908_   5425 AAATACAGACAGATAGACCAATGGAACAAAATAGACAGCCCAGAAATAAT 5474
                           iv i     v     i        i i   v  v  i          v
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_143779908_   5475 GCCACACACCTATGACCATCTGATCTTCAAAAAAGACAACAAAAATAAGC 5524
                         v   i   ii    ii  vi    i   i v  i iiiv   i vi vv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_143779908_   5525 AATGAGAAAAAGATTTTCTATTCAACAAATCATGCTGGGTTAACTG-ATG 5573
                             i i   ii  vv   v          vi       vi     -  i
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_143779908_   5574 CTCCATATGCAGAAGAATAAAAATGGACCCCTACCTATCACCATATACAA 5623
                         -?   i     i      i  iv             vv            
  L1M4_orf2#LINE/    430 -KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_143779908_   5624 AAGTCAATTTGAGATAGATTAAAAGATTTAAATTTAAGACCTCAAACTAT 5673
                           i i  i ii i  i   i ? -  ii     v     v  v       
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWA-GACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_143779908_   5674 AAAAATCCTATAAGAAAACCTAGAAA-ATATCTTTCTTGCTATCAGCCTT 5722
                             v  i  v        v   i?i- v     - v  viv ii vi v
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTT-CGTGACCTTGGGTTA 576

  chrX_143779908_   5723 GGCAAAGAATTTATGACTAAATCCTCAAAAGCAATTGCAACAAAA----- 5767
                              v iv  iv iiv  viv vi        vvv         -----
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_143779908_   5768 -ATTGACAAGTGGGACCTGATTAAA-CTAAAGA 5798
                         -  v  i  i v    i v  i   -i    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAA 659

Transitions / transversions = 1.45 (106 / 73)
Gap_init rate = 0.02 (12 / 657), avg. gap size = 3.00 (36 / 12)  

 688 22.49 8.61 0.00  chrX_143779908_143786843.rev     6237  6445 (491)    L1M4_orf2#LINE/L1      682   908 (0)  

  chrX_143779908_   6237 ATCAATGGAGTAAGCAGAAAACCTAGAGAATGGGAGAAAATATTTACAAC 6286
                              vii   i iv   v    i v                   i   v
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_143779908_   6287 T-ATGCAACAGAGAAAGGTCTAATATCCAGAATCTAGAAAGAACT----- 6330
                          -  ii v v  v  i  v  vi          v  v        -----
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_143779908_   6331 -------TAAGAAAAA-ATAAATGACCCTATTGAAAAGTAGGCAAAGGTC 6372
                         -------   v     - i    i    v   ?    i i        vi
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_143779908_   6373 ATGAA----CACTTCTTAGAAGAAGGCATACAGGTGGCCAACACACATAT 6418
                         v    ----  i    ivi      ii     ii       i vi  i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_143779908_   6419 GAAAAAATGCTTATCATCACCAATCAT 6445
                              i     i v     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (27 / 19)
Gap_init rate = 0.02 (4 / 227), avg. gap size = 4.50 (18 / 4)  


3166 24.43 0.65 2.91  chrX_143803202_143806457     1837  2765 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_143803202_   1837 TGGAAAGATTTCCCATGCACATGGATTGGAAGATTCAATATTGTTAAGAT 1886
                                  v       iv              i i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143803202_   1887 AAGCATACTGACCAAACCAATCTACAGAATCAATGCAGTCCCTATCAAAA 1936
                         iivv     vv     iii         v    i   i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143803202_   1937 CACCAATGACATTCTGCACTAAAATAGA-AAATAAATCCTAAAATGTATA 1985
                         iv   iivi v  i vii vi    v  -  iivi          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_143803202_   1986 TGGAACCACAGAAGACCCAGAATAGCCAAAACAATGCTGAGCAAAAAGAA 2035
                              vii  iii                      vi   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_143803202_   2036 CGAAGCTGGAGCCATCACACTACCTGACTTCAAAATTTACCACAAAGCTA 2085
                          i   i     vvv       v  ii i       i    i         
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_143803202_   2086 TAGAAA-CAAATCAGCAAGATACCGGCCTGAAAAGAGACACATAGACCAA 2134
                         i  v  -   iv   iiv i   i   v i ii v     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_143803202_   2135 TGGAAGACATTAGAGAACCCAGATATAAATACACACACTTACACCCAACT 2184
                              v v v v    ii     v     iv  i   i   iivi   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_143803202_   2185 CATCTTCAACAAAGATGCTAAAAATATTCAATGGGGAAAGGATAGTCTTT 2234
                         v  i   i    i i   i  i vi               i         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_143803202_   2235 T-AATAAGTGGTGCTGGGAAAACGATCCAGTTTAGTAAACTTGTATGCAG 2283
                          -  i  i           v   --------- i - v ?iiii     i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAAC---------TGG-ATAKCCACATGCAA 440

  chrX_143803202_   2284 AAGATAGAAACCAGACCTCTATCTCACATCATACAAAAAAATCAAATCAA 2333
                             vv   iiii    i   i      i    i v      i  v    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_143803202_   2334 AACATATTATATACTTAAATGTAAGGCCTGAAATCACAAAAGTACTAGAA 2383
                           iiv  i ? v  i          iv  i   ii i    v vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_143803202_   2384 GAAAATATTGAAAATACACACTAG-GGCATTGGTCTGGGCAAAGAGTTTT 2432
                              i  v i?i-  v ivi v - i v    vi i     v -    i
  L1M4_orf2#LINE/    541 GAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATG-GTTTC 588

  chrX_143803202_   2433 TTGTGTGTAAGACATCAAAAGCATAGGAAACAAAAGCAAAAGCAAACCAA 2482
                           ivi i --    i        i i v        v    ii i iv  
  L1M4_orf2#LINE/    589 TTAGATAT--GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_143803202_   2483 TGGGATCACATCAAGCTAAAAACCTTCTGCAAAGCACAGGAAAGAATCAA 2532
                          v   iiv      iv v    v   i  iivvv  v    v vv     
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_143803202_   2533 AAAAGTGAACAGACAATCCACAGAATGAGAGAAAATATTTCCAAAGTACC 2582
                         i        v      i          i            v    vi iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_143803202_   2583 CATCTGACAAGGGATTAGTAACCAGAAAATATAAGGAGCTCAAACAACTC 2632
                         i      i      i v   v      v      i  i   vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_143803202_   2633 ACCAGCAAAATAAAAATAAAGAGAGAGAATAATTCAATT--AACATGGGC 2680
                          --------    ---    i   v -     ii     --  v      
  L1M4_orf2#LINE/    787 A--------ATAA---TAAAAAGACA-AATAACCCAATTWAAAAATGGGC 824

  chrX_143803202_   2681 AAAATATCTGAATAGACATTTCTCAAAAGAAGACATACAAATGGCCAACA 2730
                            iv  i                v        i              i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_143803202_   2731 GATATAAGAAGAACATGCTCAACATAACTAATCAT 2765
                         iii i v   -  v           v ????????
  L1M4_orf2#LINE/    875 AGCACATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (138 / 86)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.36 (33 / 14)  


3267 24.44 2.11 1.22  chrX_143807823_143810817     1603  2502 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_143807823_   1603 TGCAAAGATATTTTACGTTTATGTATTAGAAGAATAAATATTGTTAAAAT 1652
                           v        iii i   i   v   i     v v           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143807823_   1653 ATCCATACTACCCGAAGT-ATCTAC----TCAATGAAATCTCTGTCAAAA 1697
                         iv v     v   i  v -      ----    i v    i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143807823_   1698 TAGCAATGATCTTCTTCACAGAAATAGAGAAAACGATGCTAAAATATATA 1747
                          vv  iivii   i  ii       v  v  ivi   v       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_143807823_   1748 TGGAGTCACAAAAGACCCAGAATAGCTAAAGCTATCCTAAGCAAAAAGAA 1797
                             ivii   ii             i   i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_143807823_   1798 CCAAACTGGAGAAATTATATTACTTAACTTCAAATTACACTACAGAGGTA 1847
                          v  ii     i v i i i v ii  i      vivi      i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_143807823_   1848 TAGTAACCAAGACAGCATAGCACAGGAATAAAAACAGACACACAGACCGA 1897
                         i     i        ii i i  v  v    ii i     i i   i i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_143807823_   1898 AAGAACAGAATAGACAACCCAGAAATAAATCCATACACTTACAGTGAGCT 1947
                         vi   i     v  v ii           i       i   ii  v ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_143807823_   1948 CATTTTCCACAAGGGGGCCAAGAACATACATGGAGGAAAGGAGGTTCTCT 1997
                         v      v       v       v   v  vv i      i viv   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_143807823_   1998 TCAATAAACGGTGTTGGGAAAACTGGACACCTATATGGAAAAGAATGAAG 2047
                             i   i    i     v       i ? i i   v            
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_143807823_   2048 CTGGACCACTGTCTCTCACCATATACAAAAATAAAATCTACACTGATTAA 2097
                         i      v  ii   v                v  v  v v iv   i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_143807823_   2098 AAAAAACCTTAAATCTAAGACATAACATTATAAAACTAGTACAAGAAAAC 2147
                          i ---- i     v     vv   v i         vv  v        
  L1M4_orf2#LINE/    501 AGA----CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_143807823_   2148 TCCGGGGAAAATCTCCAGGACATTGGTCTGGGCAAAGATTTCTTGAGTAA 2197
                         viv  ? v      i iv   v    vi i     v i      iii  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_143807823_   2198 TACCCCACAAGCACAGGCAACCAAAGCAAACATGGACAAAT-GGA----A 2242
                         v  v   v       i     v    v   v  i  i    -   ---- 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_143807823_   2243 TCACAAGTTAAAAAGCTTCTGCATAGCGAAGAATACGATCAAGAAAGTGA 2292
                            -  i       -   i  iiivv i   i i  v             
  L1M4_orf2#LINE/    647 TCA-AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_143807823_   2293 AGAAGCAACCCACATATTGGAAGAAAATATTTGCAAACTAATCATCTATC 2342
                          i ii         v v   i                ----    v    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA----TCATATATC 740

  chrX_143807823_   2343 --------AACTAATAACCAGAATATATAAGGAGCTCAAACAACTCTATA 2384
                         --------i   vi  v             i  i   vv       v   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_143807823_   2385 GGAAAAAAATCTAATAATCCAATC-AAAAATGGGCTGAAGATCTGAATAG 2433
                         iv     i - v     i     i-          vi i   i       
  L1M4_orf2#LINE/    791 ATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_143807823_   2434 ACATTTCTCAAAAGAAGACATACAAATGGCCAACATATATATGAAAAGCT 2483
                                  v        i              i vii i        v 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_143807823_   2484 GACCAATATCATTGATCAT 2502
                          vi   i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (128 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.73 (30 / 11)  


3027 26.54 0.46 0.80  chrX_143835353_143841668     2023  2900 (3416)    L1M4_orf2#LINE/L1        1   875 (33)  

  chrX_143835353_   2023 TGGAAAGATATTCCAGGTACATGGGCTGGAAGAGTCAATATTGTTAAGG- 2071
                                    i   v  v     ii       v i            i-
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143835353_   2072 GTTCATACTACCCAAAGCAATCTACATATTCAATGCAATCCCTATCAAAA 2121
                          viv     v      vii       v      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143835353_   2122 TACCAATGACACTCTTCACAGAAGTAGAAAAAAACAATCCTAAAAATTAT 2171
                          v   iivi vi i  ii     i v  v  -ivii         v i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_143835353_   2172 ATAAAATCACAGAAGACCCAGAAAAGCCAAAGGTATCCTGAGCATAAAGA 2221
                           ii  vii  iii         v       ivv   i   iv vi    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_143835353_   2222 ACAAAACTGGAAGAATTACATTACCTGATTTCAAATTATACTGCAAAAAT 2271
                              ii    i  v i   i v  ii        viv    i    iv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_143835353_   2272 ATAGTAACCAA-ACTGCATAGTACTGGCATAAAATCAGACTAATAAAGCA 2320
                          i     i   -  v ii i            iivi    vv   i v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_143835353_   2321 ATGGAACAGAATAAAGAATAAAGAAACAAATCCA-ACACCTACAGTTAAG 2369
                               i     vi   i vv     i   i   -   ii  ii  i  v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_143835353_   2370 TCATTTTCCACAAAGATTCTATGAACCTACAGAGGGGAAAAGACAGTCTC 2419
                          v      v    i i v i v  v v v  iv       ii i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_143835353_   2420 TTTAACAAATGGTGCTGGGTAACCTGGATATACATATGTAGAAGAATAAA 2469
                           i                vv v       ?v  i   i i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_143835353_   2470 ACTAAACCCCTATCTACTGCCATATACAGAAATTGAATCAATATGAATTA 2519
                         ii ii       i  vvii         i     i v    v   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_143835353_   2520 AAGACTTAAATCTTAGACCTCAACCTATGAAACTACAAAATGAAAACATT 2569
                         ?    i     v v   v  v  v    i     viv i v        v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_143835353_   2570 GGAGGAATTCTCTAGGACTTTGGGCTGCGCAAAAATTTCTTTGGTAATAC 2619
                           ? v  v   iiiv   i     i iv    vii      v i  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_143835353_   2620 TCCACAAACACAGGCAACCAAAGTAAAAATGGACAAATGGGATCACATCA 2669
                         v   v  i    i     v    v      i  i    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_143835353_   2670 A-GTTAAAAAGCTTCTGCACAGCAAAGGATACAATCAACAAAGTGAAGAG 2718
                          -i       -   i  ii vv       i  v     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_143835353_   2719 ATAACACACGGAGTGGGAAAAAATATTTACAAACTAACTATCTGAAAAGG 2768
                          i   v   i  i     i         i    ii vv       v    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_143835353_   2769 AATTAATAACTAGAATATATAAGGAGCTCAAACAGCTCTATAGAAAAAAA 2818
                         i i vi  v i           i  i   vv   i   v   iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_143835353_   2819 ATCAAATAATCCAATCAAAATACAGGGAAAATATTTGAACATGCAACTTC 2868
                          -       i     i?   v ii  v   iv       i vi - i   
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC-ATTTC 846

  chrX_143835353_   2869 TCAAAAGAAGAAAAACAAATGGCATGCAATAA 2900
                           v        v v         ---      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGC---CAATAA 875

Transitions / transversions = 1.41 (134 / 95)
Gap_init rate = 0.01 (9 / 875), avg. gap size = 1.22 (11 / 9)  

2631 25.22 2.29 3.28  chrX_143835353_143841668     4908  5823 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_143835353_   4908 GGAAAATCATTTCA----CATGCATAGGAAAA----ATACTGTTAGAATG 4949
                              ivi  ii  ----    v  v    i ----   i     ii   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_143835353_   4950 GCCATATTGCCCAATGCAATTTACACATTCAATGTTATTTCTGTCAAACT 4999
                           v   i v     vvii  i    v      i iv  ii  i     v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_143835353_   5000 ACCAATGGCATTTTTCACAGAA--TAAGAAGATAACTATGCTAAAATTCA 5047
                         v   iiv  v     ii     -- i v   v i --- v          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA---TCCTAAAATTCA 148

  chrX_143835353_   5048 TATGGAACCAAAAGGGAGACCAAATAGTCAATGCAATCCTAAGCAAAAGG 5097
                                viiv      vv vi     i   vi     i i iv  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_143835353_   5098 AACAAAGCTGGAGGCATCACATTACCTGGCTT-AAAACTATACTACTAGG 5146
                                i      vv     i v  iiii  -      -      v i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chrX_143835353_   5147 CCATAGTAAACAAAACAGCATGGTACTGGTACAAGAACAGACACATAGAC 5196
                          i i     v   i    ii         i i   i i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_143835353_   5197 CAATGGAACAGAACAGACATTCCACAGATAATGCTACATACCTAAAAGCA 5246
                                 i    iv  v v    v i    --------   i v --  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAA--------ACCCATA--CA 337

  chrX_143835353_   5247 TCTGATG-TCAGATGACATCAGATTTTGATGACAAAGTCAGCAAAAACAA 5295
                          i -   -   ------  i-      --i     i viiv   i v  v
  L1M4_orf2#LINE/    338 TTT-ATGGTCA------ATT-GATTTT--CGACAAGGGTGCCAAGACCAT 377

  chrX_143835353_   5296 GGAATGGGGAAAGGACTGCCAATTCAATAAATGGTTCAGGAGTAACTGGC 5345
                         vv           i iv i vv     i       v v  iii      v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_143835353_   5346 TAGCCATATGCAGAAGATTGAAATTGGACCCCTTCCTTATACCATATACA 5395
                           ?   i     i    v    i          v   i i          
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_143835353_   5396 AA--TTAACTCAAGACGGATTAAAGACTTAAATTTAACATTTAAAACTAT 5443
                           --         i i    i ?    i     v   v vi         
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_143835353_   5444 ATAAACCAT--GACCAATGACCTAGGA--AAACCATTCTAGACATAAGCC 5489
                          -    iv --  vv  -i  v    ?--   i -   vv   v vi vi
  L1M4_orf2#LINE/    528 A-AAACTCTTAGAAGAA-AACATAGGNGTAAATC-TTCGTGACCTTGGGT 574

  chrX_143835353_   5490 CTGGCAAAAATTTTAT-GATGAAGGCTCCAAAAGCAATTGCAACAAAAAC 5538
                         iv     vii   iv -   - v i v         vvv         iv
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_143835353_   5539 AAAAATTGACAA-TTGGAATCTAATTAAAATAAAGAGCTTCTGCACAGCA 5587
                               v  i  -     v - v  i     v  i i   i  ii vv  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACT-TCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_143835353_   5588 AAAGAAACTATCATCAGCGTAACCAGACAACCTAGAAAATGGGAGAAATT 5637
                           i  v       vv iv  i vv        i v i           v 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_143835353_   5638 ATTTGCAAAGTATGCTTCGGACAAAGATCTAATATGAAGAATCTATTAAG 5687
                                  vi  iiv  v  i  i iv  vi   vv     v   v   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_143835353_   5688 AAATTTAAACAAATTAATAAGCAAAAAATAGACAACCCCACTAAAAAGTG 5737
                           v i v -   v i     vv    i i i i     v i ?    i  
  L1M4_orf2#LINE/    773 AACTCTTA-CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chrX_143835353_   5738 GGCAAAATACATGAACAAACATTT-TCAAAAGAGGATTTACACATGGCCA 5786
                               iv iv    i i      -  v     i   v    v       
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_143835353_   5787 ACAAGCATATGAAAAAATGCTCAACATCATTAATCAT 5823
                          i     i       i             ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (125 / 102)
Gap_init rate = 0.03 (25 / 907), avg. gap size = 2.04 (51 / 25)  


1576 24.49 2.65 4.21  chrX_143921841_143923465      498  1138 (487)    L1M4_orf2#LINE/L1      278   908 (0)  

  chrX_143921841_    498 ATAAAATACAGATGCATAGACAAATGGAACAGAACAGAGAATGCAGAAAT 547
                             ii- i   iii     iv       i    iv    i v       
  L1M4_orf2#LINE/    278 ATAAGG-ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_143921841_    548 AATGACACACACCTACCAACATCTGATCTTGGATAAAGTTGATTAAAAAC 597
                           vvv  i   ii  iviv  vi    i  v  i  i v  -ii  i v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTG-CCAAGACC 375

  chrX_143921841_    598 AAGCAACGCTGAAAGGACTTG-CTATTCCATAAATAGTGCTGGGATAACT 646
                          vv   i vv     i - v -  v   v i    i         i    
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAA-TAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_143921841_    647 GGCTAGCCATATGCAGAAGATTGAAACTGGACCCCTACCTCTCACCATAC 696
                           v  ?   i     i    v    ii              v       i
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_143921841_    697 ACAAAAATTAAATCTAGATAGATTAAAGACTTAAATGTAAGACCTAAAAC 746
                                    v  v i  i   i ?    i           v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_143921841_    747 TATAAA--TTCTAGAAGAAAACCTAGG---AAATACACTTCCAGACTT-- 789
                               -- ii           v    ---    ---    vv   i --
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTG 571

  chrX_143921841_    790 GGTCCTAGTCAAGTAATTAAT--GATGAAGACCCGAAAAGCAATTGCA-C 836
                            --   v   - ii  vv --   - v   v v       vvv   - 
  L1M4_orf2#LINE/    572 GGT--TAGGCAA-TGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAAC 617

  chrX_143921841_    837 AAAATCAAAAAATAGACAAATGTGATTTAATTAAACTAAAGAGCTTCTGC 886
                             v-          i    vv  i  v  i   v v  i i   i  i
  L1M4_orf2#LINE/    618 AAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_143921841_    887 ACAGCAAGAAAAATACT--CAACAGATTAAAAAGAGAGCCTAACAGAA-- 932
                         i vv   -- ii i   --   v i v i      v i  i -     --
  L1M4_orf2#LINE/    667 GCTTCAA--AGGACACTATCAAGAAAGTGAAAAGACAACCCA-CAGAATG 713

  chrX_143921841_    933 ACAGAACCACCCATTCAACAGAATTTGCAAACTATGCATCTGAAAAAGGA 982
                         iv    ----------  i ---        ii  ii      v  i   
  L1M4_orf2#LINE/    714 GGAGAA----------AATA---TTTGCAAATCATATATCTGATAAGGGA 750

  chrX_143921841_    983 CCAATACCCACAAC-TCCAAGGAATTTAAACTAATCAATAAGAAAAGCAC 1031
                          ivi  i   v  i- vi  i   i ivv  v v       v    iv  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_143921841_   1032 AAACAACCCTATTAAAAAGAGGGCAAATGACATAAACAAACACTTCCCCA 1081
                            i     v   ?    iv       v  iv i  i i   i   i   
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_143921841_   1082 AA-AAGACATACAAGTGGCCAAGAAACATAAAAAACAATGCTCAATAACA 1130
                           -    i      i       v  i  i vi   vi        i v  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_143921841_   1131 CTAATCAT 1138
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.30 (87 / 67)
Gap_init rate = 0.03 (22 / 631), avg. gap size = 2.00 (44 / 22)  


2085 25.84 1.12 0.19  chrX_143993539_143997985     2755  3292 (1155)    L1M4_orf2#LINE/L1        1   543 (365)  

  chrX_143993539_   2755 TGGAAAGGGATTCCATGTTCATAGACGGGAAGAAATAATATTGTTAAAAT 2804
                                iv  i          i  iv      vv            i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_143993539_   2805 GTTCCTATTCCCCAAAGCAATCTACACATGCAATGCAATCTCTATCAAAA 2854
                          vivv  i        vii       v  v   i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_143993539_   2855 TACCAATGACAATCTTCACAGAAA--GAGAAAAAAATCTTAAAACTTATA 2902
                          v   iivi vv i  ii      --  v  ivvi   i     i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_143993539_   2903 TGGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAGCATAAAGAA 2952
                              vii   ii                 i v   i i iv vi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_143993539_   2953 CAAAACTAGAGGAATCACATTACCTGACTTCAAATTATACTACAGAGCTA 3002
                             ii i     v     i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_143993539_   3003 TAGTAACCAAAACAGCATGGTACTG--AAAAAAATAGA-A-ATAGTCCAA 3048
                         i     i   i    ii        -- v  ii     - -    vi   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_143993539_   3049 TGGAACAGAATAGAAAACCCAGAAACAAATCCAAATGCCTACAGTTAACT 3098
                              i     v  i ii       i   i   v iiii  ii  i  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_143993539_   3099 CATTTTCAACAAAGGTGCCGAGAATGTACACCAGGAAAAAGACAGTCTCT 3148
                         v      i    i      i   vii v  vii  i   ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_143993539_   3149 TCAATAAATGGTGCTGGGAAAACTGGATATCCATAAGCAGAAGAATGAAA 3198
                             i              v         ?   i v   i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_143993539_   3199 CTAGACCTCTATCTCTTGTCAAATACAAAAAACAAATAAAAAATGGATTG 3248
                         i i    i   i   viii  v         vi  v v    -     ii
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA-TGGATCA 499

  chrX_143993539_   3249 AAAACTTAAATCTAAGACCTCAAACTATAAAATTACTACAAGAA 3292
                         ? i  i     v     v  v           i vi  v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

Transitions / transversions = 2.04 (92 / 45)
Gap_init rate = 0.01 (5 / 543), avg. gap size = 1.40 (7 / 5)  

 980 26.19 3.97 1.06  chrX_143993539_143997985     3577  3954 (493)    L1M4_orf2#LINE/L1      520   908 (0)  

  chrX_143993539_   3577 AAAAC---AAAATTACTACATGAAAACTTGGAGGAAACTCTCCAGGACAT 3623
                              ---    i vi  v v      v i i? v  v   i iv   v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_143993539_   3624 TGGAATAGACAAAAATATATTGAGCA--ATACTGTACAAGCACAGGCAAC 3671
                            iv   i   vii v v  iiii -- i  i-- v       i     
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACC--AAAAGCACAAGCAAC 617

  chrX_143993539_   3672 CGAAGCAAAAATGGACAAATGGGA-----TCAAAACTTAAAAAGCTTCTG 3716
                         vi   v      i  i    v   -----      -       -   i  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAA-TTAAAAA-CTTTTG 665

  chrX_143993539_   3717 CACAGAAATGAAAACAATAAAAAATGTGAAGAGACAACC-ATAGGATGGG 3765
                         ii vvv  v i v  v  v  i  v     i        - i  i     
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_143993539_   3766 AGAAAATATTTGCAAACCACTGATCTAAGAAGAGATTAATAGCCAGATTA 3815
                                         i  ivv    i v   i  i vi  v     v  
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_143993539_   3816 TATAAGGGGCTCAAAGAACTCTATAGGAAAA---TAAACAATCTGATCTA 3862
                              i ii   vv v     v   iv    ---i   i  i ii  i? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chrX_143993539_   3863 AAA-TGGGAAAAAGACATAAACACACATTTCTCAAAAGAAGACATACAAA 3911
                            -    v   i  iv i  i v         v        i       
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_143993539_   3912 TGGCTAACAGGCTTATGAAAAGGTACCCAAAATCATGAGAGAA 3954
                             i  i i  vi        i i i   v    ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (56 / 41)
Gap_init rate = 0.02 (9 / 389), avg. gap size = 2.11 (19 / 9)  


2779 28.24 2.12 0.78  chrX_144053604_144058624     3639  4534 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_144053604_   3639 TAAAAAAGCATTCCGTGATCATGGATAGGAGGAATCAATATTGTTAAAAT 3688
                          ii   iii  i  i  v        v   i  v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_144053604_   3689 GGCCATACTGCCCAAAGCAATTTACAGACTCAAGGTTATTCTTATCAAAC 3738
                            v     v      vii  i      i    v iv  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_144053604_   3739 TACCAACTACATTCTCATG-AGATTATTTAAAAACT-ATTTTAAAATTAA 3786
                          v   i  i v  i i-  -   v-   v v  i  -  ii       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAA-ATTGACAAGCTGATCCTAAAATTCA 148

  chrX_144053604_   3787 TATGGGACT-TAAAG--CCTA-AATCACCAAGGCAATTCTAAGCAAAAAG 3832
                              i v -i  i --  i -   vi    ii    ii i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_144053604_   3833 ATAAAAGCTGGAGGCAACACATTACCTGACTTCAAACTATAGTACAAGGC 3882
                          vv    i      vvv    i v  ii i      viv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_144053604_   3883 TACAGTAACCAAAATAGCTTGGTACTGGTACAAAACTAGACACATAGACC 3932
                                 i   i i  iv         i i  iiv      i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_144053604_   3933 ACTGGACCATAATAAAGAGCCCAGAAATAAGGCCACATACTTACAAGCAT 3982
                          v    vi v   vi    i          iv   i i i   iiiv  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_144053604_   3983 CTGATCTTCAACAAAGCTGACAAAAACAAGCAATGAGGAAAAGTTTCCCT 4032
                         i    i   i    i v  v   i v  vv     i     iiv vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_144053604_   4033 ATTCAATAAATGGTGCTGCAATAATTGGCTAGCCACATGCAGAAGATTGA 4082
                         v     i           vi i  i   v  ?         i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_144053604_   4083 AACTATACTTTTTTCCTTGTACCATATATGAAAATCAACTCAAGATGGAT 4132
                          ii iv  iii v-   iii        ii     i       i      
  L1M4_orf2#LINE/    449 AGTTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_144053604_   4133 TAAATATTTAAATGTAAAATTGGGGATTACAAAAATCCTGGAAGATTACC 4182
                         i ? v ii         i viviii i  i    v  i i     vv  v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_144053604_   4183 TAGGG---AGTTTT--TGGCATGGGATCTGGAAAAAAAATTTCAT-GATG 4226
                             ?--- i i  --  i v v  i iv  v  vii--    v -   -
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG--TTTCTTAGAT- 594

  chrX_144053604_   4227 AAGACTCCAAAAGCAATAGCAACAACAGCAAAAATTGACAAATGGGACCT 4276
                          v   v         vv        v  v      v  i    v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_144053604_   4277 AATTAAACTAAAGGGCCTCTGTGTGGCAACAAAAAAGTATCAACAGAGTG 4326
                         v  i   v v  iii i i    ivv   - ii v v      v i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACTATCAAGAAAGTG 693

  chrX_144053604_   4327 AACAGAAAACCTACAGAATGGGAGAAAATATTTGCAAACTATACATCTGA 4376
                           v   v    i                          ii   i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_144053604_   4377 CATAGGTCTAATATTCAGAATCTATAAGGTGCTAA-ACAAATTTACAAGG 4425
                         i vi  v  vi   i      v     i vi  vv-    v iv i  vi
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_144053604_   4426 AAAAAACAA----CCCAGTTATAAGATGGGCAAAGGACATGAACAGATGC 4471
                             i    ----    i  ?v  i            iv    i   iii
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_144053604_   4472 TTTTCAAAAGAAGACATACACGTGTCCAACAAGCATATATAAA--TGCTT 4519
                           i  v        i     vi  v    i     i  iv   --    i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_144053604_   4520 AATAGTACTATCATT 4534
                           i vi ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (151 / 98)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.53 (26 / 17)  


1364 29.89 1.29 1.08  chrX_144087019_144092546.rev     3433  3897 (1631)    L1M4_orf2#LINE/L1        1   466 (442)  

  chrX_144087019_   3433 TGGAAAAACATATCATGCTCATAGATAGGAAGACTAAGTACCATTAAAAT 3482
                               i i  vi    i    i   v        v i  iii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_144087019_   3483 GGTCATACTGCCCAAAG-AATTTTCAGATTCAAAGTTATTCCTATCAAAC 3531
                           iv     v      v-i  i v         v iv  i         -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chrX_144087019_   3532 TATGAAAGTTG--TTATTCACAGAATTAGAAAGAAAACT-ATTGTAAA-T 3577
                         -  vvv  i  --  v  ii     v v  v --- i  -  iv    - 
  L1M4_orf2#LINE/    100 -ATCCCAGCTGCCTTTTTTGCAGAAATTGACA---AGCTGATCCTAAAAT 145

  chrX_144087019_   3578 TTATATGGAACCAAAAAAGACTCTGAATCACAAAAGCAATCCCAAGCAAA 3627
                          i        viiv  ii   i v    vi v   i     iii iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_144087019_   3628 AAGAATAAAGCCAGAGGCATCACACTACCCAACTTCAAACTATACCATAA 3677
                              i    iii    vv       v     i      viv   i i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_144087019_   3678 GGCTATAGTAACCAA-AGAGCATCATACTGGTACAAAGACAGACACATAG 3726
                         i    i     i   - v  ii vi      i i  i  i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_144087019_   3727 ACCAATGAAACAGAATAGAAAACATGGAAATTATACCACACACCTACCAT 3776
                          i     i  i     v  i iivii     v vv   i   ii  ivi 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_144087019_   3777 TGTCTGATGTTCAACAAAGCCAACAATAACAAGAAATGGGGAAACATTAC 3826
                         iivi    v   i    i viiv   v v  vvv          v v  v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_144087019_   3827 CTCATTCCATAAATAGTGCTGGGATAACTGGCTAGCCATATGCAGAAGAA 3876
                         iiiv   v i    i         i      v  ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_144087019_   3877 TAAAACTGGACCCTGACTGCA 3897
                          i  ii       iv  iv  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCA 466

Transitions / transversions = 1.60 (85 / 53)
Gap_init rate = 0.02 (7 / 466), avg. gap size = 1.57 (11 / 7)  

1061 26.91 7.66 0.00  chrX_144087019_144092546.rev     4607  5037 (491)    L1M4_orf2#LINE/L1      445   908 (0)  

  chrX_144087019_   4607 ATGAAAACAGACTTATAC---A-ATCATGTACAAAAACTAACTCAAGCTG 4652
                              ivii   iiv   --- - i   i        i        iv  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_144087019_   4653 CATTAAAGATTTAAAAGTAAGACTTCAAACTGCAAAAATCCTAGAAAGAA 4702
                         v  i ?   ii    v      vi v     ii    v  i     ii  
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_144087019_   4703 ACCTAG----------TCAT-----TGGCTTTGACAAAGAATTTTTGGCA 4737
                           v   ----------  i -----   v  v i   v iv  i  i vv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_144087019_   4738 AAGCCTTCAAAAGAATTTGCAACAAAAACAAAAATAGACAAGTGGCACCT 4787
                          v v vi      v ivv         iv         i  i v v  i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_144087019_   4788 AACTAAGCTAAAGAGCTTCTGCACAGAAAAAGAAACTATCAATAAAGTGA 4837
                         v ii  iv v  i i   i  ii vvv   i  v        v       
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_144087019_   4838 A----CAGTTTACAGAATGAGAGAAAATATTTGCAAACTATGCATCTGAG 4883
                          ----  iiii        i                 ii  ii      v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_144087019_   4884 AAAGGTCTAATATCCAGAAACTATGAGAAACTTAAACAAATGAATAAGCA 4933
                           i  v  vi         vv   i ii    ivv    v v     vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_144087019_   4934 AAAAACAAATAACCCCATT-AAAAATG---ACAGGA-----ACAGACAAT 4974
                            i           v   -       --- v    ----- i     v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_144087019_   4975 TTTCAAAAGAAAACATACAAGTGACAAACAAACATATAAAAA-ATACTCA 5023
                          i  v      i i      i  i v  i  i  i  i    -  i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_144087019_   5024 TGATCACTAATCAT 5037
                         vv    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (65 / 50)
Gap_init rate = 0.02 (9 / 464), avg. gap size = 3.67 (33 / 9)  


1883 26.28 9.63 3.09  chrX_144135613_144137445      500  1340 (493)    L1M4_orf2#LINE/L1       13   908 (0)  

  chrX_144135613_    500 CCATCGTTCATAGATTGGAAAATTCAATATTGTTAAGAGGACAAGTCTCC 549
                             -      i        i i i             v i   vv    
  L1M4_orf2#LINE/     13 CCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chrX_144135613_    550 CCAAATTAATGTATAGATTAAATATGAGCCCAATTGAATTGCCAGCGTGA 599
                                i  v  i     v  iiii v   v  ii  v v     -  v
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGC 110

  chrX_144135613_    600 TTTTT----AAGAATAGATGACAAAGTGAT-----------TATAGAAAT 634
                         i    ---- ii   ---      iv    -----------   i     
  L1M4_orf2#LINE/    111 CTTTTTTGCAGAAAT---TGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_144135613_    635 TC----------------------TAATC----------------AATTT 646
                         v ----------------------i    ----------------  v  
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_144135613_    647 GGAGGAA--ATATTTC--AAT---AAATCTTTCAATAAAATTATAATAAT 689
                               v-- i i   --   ---   v   v v i   ii  i i    
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_144135613_    690 CAAGGTAGTCTGACATTTGCAAATTCATAGGCATATAGAACTATAAAATA 739
                             ii   v  ii i v   v vvv    i        v v  ii    
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_144135613_    740 GACTAGATAGTCCAGAAATATACCTAAACAAATATAGCCAACTAATTTGT 789
                           v v  v            v   i v   vv   i i   i i    vi
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_144135613_    790 GACA-GGGTGAAAAGGCAATTCAATTAAGGCAGGATAGTCTTTACAACAA 838
                             -     vv   i v       vii iv  i         v      
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_144135613_    839 ACAATGCTGGAAGATTCGGTCATCCATA---AATTTTAAAAATGAA---- 881
                          iii      i v vii  vi ?   i ---  ----  i      ----
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAA----AAGAATGAAGTTG 453

  chrX_144135613_    882 ---CTATACTACACACTCTACA-AAAAATTAACTCTAAACAGAACATAGA 927
                         --- iv   iv     iv  i -            v   ii  v  ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_144135613_    928 CCTCATTACAAAATTAAAAACTATCAAACTTCTAGTATAAAACCTAGGAG 977
                            v v ii  i viv        v     ii   v v     v    ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_144135613_    978 AAAATCTTTGTGACCTTAGTTTAGGCAAATAATTAGTAGACATGACAATC 1027
                         v       i        i v        vviv  vv    i      viv
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_144135613_   1028 AAATCATAAGCCACAAAAACAGAAAT-TATAAATTAGACATTCTCAAACA 1076
                            v  i    v      iv i    -v       i   v iv     vv
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_144135613_   1077 TAAAATGTTTCCT-CTCTGAAAAATAACTTTTAAGGGGATAAAATGATGA 1125
                              vv   iv -  iii  ii i -  v i   iiii i   v  ii 
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGAAAGTGAAAAGACAA 702

  chrX_144135613_   1126 ACTACAGACTTGGAGAAAATATTTGTAAATCATGTATTTGTCAAAATATA 1175
                         v i     v v              i       i   i  -------   
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG-------ATA 745

  chrX_144135613_   1176 AAACACCAAAATATATCCATAATATAAAAACACCTCTTAAATCACTTAAA 1225
                          iiv  i---- i      v      v   v v      v --   i  -
  L1M4_orf2#LINE/    746 AGGGACT----TGTATCCAGAATATATAAAGAACTCTTACA--ACTCAA- 788

  chrX_144135613_   1226 TCTCAAAGATAGGAAAATAACCAAATAATACAGTGGG------ATATAAA 1269
                         -- v v i v  iv        v   v?v v i    ------  v i  
  L1M4_orf2#LINE/    789 --TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_144135613_   1270 T-GCCCCGTCACTAGAGAAGATGTACAGATGGCTAATAAGCACATAAAAT 1318
                          - v viv  v i i       i    i     i           i   v
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_144135613_   1319 TTTATCCAACATTATTAGTCAT 1340
                         vv iii      i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.13 (115 / 102)
Gap_init rate = 0.03 (24 / 896), avg. gap size = 4.46 (107 / 24)  


 817 28.63 1.79 8.55  chrX_144139497_144141346       10   512 (1338)    L1M4_orf2#LINE/L1      234   702 (206)  

  chrX_144139497_     10 AACGTTATAAAAAAATGGCATTAAATAAAATGATGT--TACT----CAAG 53
                            -   iv v   iivi  v   vi  i iii   --    ----i   
  L1M4_orf2#LINE/    234 AAC-TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG 282

  chrX_144139497_     54 GATCTGCTGTACACTCATAGATAAATAGGACACGATAGAGAGCCTAGAAA 103
                            ------- v  vi      v   i i i vi  v     i i     
  L1M4_orf2#LINE/    283 GAT-------AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_144139497_    104 GAGACCCACACAAATGTAGTAAACCGATTTTTCACAAAGG--CCAAAAGC 151
                         v i     i   vv i i  v  ii      iv    i  --    i v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_144139497_    152 AATGCAATGAGAAAAGGATAATCTGTTCAACAAATGACCCTAGAAAAATT 201
                          - v     i i    i   i   v           iiv  i i v  i 
  L1M4_orf2#LINE/    376 A-TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_144139497_    202 GGACTTTTACATGTAGATAAATGAATCTAGACAAATAACCTAGATGTTTC 251
                            iv?ii     i i vi      vi i   vvv  v ii v ivv vi
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_144139497_    252 ACAAATACTAACTCACTATGTATGATAGATCATAATGTAAAATGTAAAAT 301
                              v i       vv   v  v ?   i ------    -     i v
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACC------TAAA-TGTAAGAG 517

  chrX_144139497_    302 TTCTAGAAGAAAACATTGTAAAATGCAAAACTGTAAAATTTCTAGAAGAA 351
                         i ------------------------      i     i ii        
  L1M4_orf2#LINE/    518 CT------------------------AAAACTATAAAACTCTTAGAAGAA 543

  chrX_144139497_    352 AACATTGGGAAAAATCTGATTGAGCTGGGATTTGGTGATGAATTAGTAGA 401
                              v  ?iv      vvv   v  v  i  v  ii   iv  vv    
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_144139497_    402 AAAAAAGACCAAAATCATGATCCACAAAGGAAAAAAAATTG-TAAGTTGA 450
                         v vi v-       v  ii v v     -- i       v -   i   i
  L1M4_orf2#LINE/    594 TATGAC-ACCAAAAGCACAAGCAACAAA--AGAAAAAATAGATAAATTGG 640

  chrX_144139497_    451 ACATTACTAAAATAACAAATGTCTGCTCTGTGAAAGATACTGTTAAGAAA 500
                           v i ii     v v   iv i  iv  vii  i  i   i i      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_144139497_    501 ATGAAAATACAA 512
                         i      v    
  L1M4_orf2#LINE/    691 GTGAAAAGACAA 702

Transitions / transversions = 1.27 (79 / 62)
Gap_init rate = 0.03 (12 / 469), avg. gap size = 4.33 (52 / 12)  

2038 29.04 9.88 0.48  chrX_144139497_144141346      528  1357 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_144139497_    528 TGGAAAAACATTCCATGCTCATGGATAGGAAGAGTCAATATCAGGAAAAT 577
                               i i  i     i        v      v i     iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_144139497_    578 GGTCATGCTGTGTAAAGTAAATTATAGATTCGATACTACTCTCATTAAAT 627
                           iv  i  vivi   v i vi  i      i ii v ii ii  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_144139497_    628 TACCATTGACATTCTTCACAGCATTAGAAGAAACT-ATTTTAAAATTAAC 676
                          v   vivi v  i  ii   v v v  v-  i  -  ii       v i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATTCAT 149

  chrX_144139497_    677 ATGGAACCAAAAACAGAGCCTGAATAGCCAAGACAATCCTAAGGAAAAAA 726
                               viiv  i-i  v  v          i      i i ii  i  i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAG-GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_144139497_    727 AAAAAAACTGG----------------------------TAC-------- 740
                           v   ii   ----------------------------   --------
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_144139497_    741 ---------CAAAACAG----------------------ACAAATAAACC 759
                         ---------   i    ----------------------   v   i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_144139497_    760 AATGGAACAGAATACAGAACTCAGAAATAAGACTGTACACCTACAATCAT 809
                                i     vv   iii         iv ii    ii  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_144139497_    810 CTGATCTTCAACAAACCTGACAAAAAGCAAGTAATGGGAAATGGATTCCC 859
                         i    i   i    ivv  v   i v-  vvi      i  v i  vvi 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTC 397

  chrX_144139497_    860 TATTCAATAAATGGTGCTGGGAGAAATGGCTAGCCATATGCAGAAGATTG 909
                          v     i              v  v   v  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_144139497_    910 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAAGTCAAGATGGAT 959
                           ii         v   i     v              v    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_144139497_    960 TAAAGACTTAAATGTAAAACTCAAAACTATGAAAACCCTAGAAGAGAATC 1009
                         i ?    i         i vii        i   vi i       i  iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_144139497_   1010 TAGGCAACACCTTTCAGGACATGGGCACTGGCAAAGATTTCAT-GACAAA 1058
                             ?ivv vii   iv   v v  vviv     v i    v -  i vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_144139497_   1059 CATACCAAAAGTAATTGCGACAAAAGCAAAAATTGACAAGTGGGGTCTAA 1108
                         - i        i vvv  i       v      v  i  i v  iii v 
  L1M4_orf2#LINE/    598 -ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_144139497_   1109 TTAAA-CTAAAGAGCTCTGCACAGCAAATAA-ACTATCAACAGAGCAAAC 1156
                          i   -i    i vi i  ii vv    vi -        v i  ii  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_144139497_   1157 AAACAACCTATGGAATGGGAGAAAAATTTTGCAATCTATCCATCTGACAA 1206
                          i      i ii             vv       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_144139497_   1207 TGGTCTAATATCCAGAGTCTACAAGGAACTTG---AACTTA-CAATAAAA 1252
                         v  v  vi        i v  i  i     iv---    i -i       
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_144139497_   1253 A---AAAAAACC--ATTAAAAAATGAACGAAAGACATGAGCAGACACTTC 1297
                          ---   v    --   ?       ii i  i  iv   ii     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_144139497_   1298 TGAAGAGAAGACATTCATGCAGCCCACAA--ACATGAAAAAAATCTCAAC 1345
                          vv i      i  v  viii   v i  --         i vv      
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_144139497_   1346 GTCACTGATCAT 1357
                         i   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 5.38 (86 / 16)  


3255 23.88 2.18 3.16  chrX_144173841_144180575.rev     3661  4577 (2158)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_144173841_   3661 TAAAAACATATTCCATGCTCATGAATTGGAAGTACC-AATATTGTTAAAA 3709
                          ii   v    i     i     i        -  i-           i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAG-ACTTAATATTGTTAAGA 49

  chrX_144173841_   3710 TGTCCATACTACTTAAAGCAATTTACAGATTTAATGGAATCCCTATCAAA 3759
                           v v     v ii   vii  i        i  i v             
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_144173841_   3760 ATACCAATGACTTTCTTCACAAAAATAGCAAAAATAATCTTAGAATCTAT 3809
                           v   iivi i  i  ii  i    v vv  iv i   i  i   ii  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_144173841_   3810 ATGGAACCACAAAATACCAAGAGTAGCCAAAGCCTTCCTGAAGAAAAAGA 3859
                               vii   iiv   v   i        i vv  i    i  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_144173841_   3860 ACAAAACTGGAGGAGTCATGTTATCTGACTTCAAATTATACTATACAGGT 3909
                              ii       v   iii vi ii i      viv     i v  v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_144173841_   3910 ATAGTAACCAAAACAGCATAGTACTGGCATAAAAACAGACACTTAGGACA 3959
                          i     i   i    ii i            ii i     iv   iv  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_144173841_   3960 ATGGATCAGAAT--AGA------AAATAAATCCATATATCTACAGTGAAC 4001
                              vi     --   ------       i     i  i  ii  v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_144173841_   4002 TCATTTTCAACAAAGGTGTCAAGAACATACATTGGGGAAAAAGACAGTCT 4051
                          v      i    i    i     v   v  v        i - i     
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAGTCT 398

  chrX_144173841_   4052 CTTTAATAAATGGTGCTGGGAAAACTGGATATATCCATATGCAGAAGAAT 4101
                         i  i  i              v         ?--   i     i      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAK--CCACATGCAAAAGAAT 446

  chrX_144173841_   4102 GAAACTAGACCCC-ATCTTTCGCCATATATAAAAAT---CT--AAATGGA 4145
                            ii i      - i  iv i       i      ---  --       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_144173841_   4146 TTAAAGAGTAAAATCTAAGACCTTATATTATGAAACCACTAAAAGGAAAC 4195
                          i ?   viv    v     v  v v i   i    ivi  i   i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_144173841_   4196 ATTGTGGCAACTCTCCAGGACATTGATCTGGGCAAAGATTTCTTGAGTAA 4245
                           v v? i  v   i iv   v   ivi i     v i      iii  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_144173841_   4246 GACCCCAAAAGCACAGACAACCAAAGCAGAAAC-GATCAATTTGGATAAC 4294
                            v           ii    v    v i   i-   v    -   ivv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT-GGACTTC 645

  chrX_144173841_   4295 ATCAAGCTATCAAGTTATAACATTAAGTTAAAAAGCTTCTGCAAG-CAAT 4343
                              -------------------- i       -   i  iivv-   v
  L1M4_orf2#LINE/    646 ATCAA--------------------AATTAAAAA-CTTTTGTGCTTCAAA 674

  chrX_144173841_   4344 GGA-A--ATCAACAAACTGAGAAGACAATCCACAGAAGGGGAGAAAATAT 4390
                            - --     v   v   i       i        v            
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_144173841_   4391 TTGCAAACTAGTCATCTGACAATAGATTAATAACCAGAGTATATAAGGAG 4440
                                ii vvi      i  vi  i vi  v     i       i  i
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_144173841_   4441 CTCAAATGGCTCTATAGGAAAAAAAAATCTAATAACCTGATTTAAAAATG 4490
                            vv iii   v   iv     i v ---       ii   ?       
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACA---AATAACCCAATTWAAAAATG 821

  chrX_144173841_   4491 GGCAAAAGATGTGAATAGACATTTCTCAGAAGAAGACATGCAAATGACAA 4540
                               i   v                vi       i  i      i v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_144173841_   4541 ACAGGTGTATGAAAAGGTGTTCACCATCATTAATCAT 4577
                          i i iii        i  i   v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (141 / 74)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.88 (49 / 17)  

1667 28.92 6.81 2.44  chrX_144173841_144180575.rev     5467  6244 (491)    L1M4_orf2#LINE/L1       97   908 (0)  

  chrX_144173841_   5467 AAAATCCAAGAAAGCTTTTCTTTTGGTAAGGTATGAGTTTTATTCTAAAA 5516
                                v  vv-  i   i  vii v  vvv ii  i v-  i      
  L1M4_orf2#LINE/     97 AAAATCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTG-ATCCTAAAA 144

  chrX_144173841_   5517 TGTGTATGGAAATCAAAAGGACCTAGAGTAGCCAAGATAATATTTAAAA- 5565
                          vii         vv  i     i   i       i i   v  v    -
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_144173841_   5566 GTAGAACAATAATGTAGAATATACATTACCTGTTTTCAAGATTTACTGTA 5615
                          v       viv  v  i ivi   i v  iiv      i i     ii 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_144173841_   5616 AAGTTACACTGATCAAGATAGCCTGACATTGGCATGAGAATAGGTAAGTT 5665
                            i    v i       i  iv  ii i      i  i    ii vi v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_144173841_   5666 CCTCCATGGAATAAAATACTGAGTACAGAAAGAGTCACACTCATACA--- 5712
                         vv  v        i   vvv    v      v i----  i      ---
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAA----ACCCATACATTT 340

  chrX_144173841_   5713 ---GTGAGTTTATGCTTTG-CAAATGTGCCTGAGCAATTCAATGGAGAAA 5758
                         ---  v i  v  -i  i -   iv     viii v         i    
  L1M4_orf2#LINE/    341 ATGGTCAATTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_144173841_   5759 GGGAAGTATTTTTAATAAGTGGTGCTGGGACAACTGGATATCCATATGGA 5808
                          iiv   v    i  i  i                     ?   i   v 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_144173841_   5809 AATATAA-AAACTTCAACTGATATCTTATACTATTCATAAAAGTTAATTT 5857
                           - v  -i  v  vi  ivv  i  i i  i  vi i    i    i i
  L1M4_orf2#LINE/    440 AA-AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_144173841_   5858 GGGAAAAGTCATATAAATCTAAAAATGTAAAA-TAAAAATTATAGA---- 5902
                         iii viii   ? --i i     --     i -iv    i    i ----
  L1M4_orf2#LINE/    489 AAAATGGATCAWA--GACCTAAA--TGTAAGAGCTAAAACTATAAAACTC 534

  chrX_144173841_   5903 ---GAAAAAAACATGAAAATA--TCTTCATAAATTTGGGATAA--AGTA- 5944
                         ---   i       iii?i  --     i i vi     v  i-- i i-
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_144173841_   5945 -TTCT----------ATCAGAATGCAC---TAACAAA-GAAAAATTCGAT 5979
                         -    ---------- i  i  -    ---i      -      v v   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_144173841_   5980 ACAATAAAATTTATCAAAATTAAAACCTCTTTCTCCTCAAAAGTAGTCAT 6029
                          v v ii v  i             v  i  viv i     i vviii  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_144173841_   6030 TGAGGGAATGAATGTTTAAGCTGTTCT--------GGAAAAAATGCTTGT 6071
                         ii  ii i    -----   viivi i--------   i     ii   i
  L1M4_orf2#LINE/    684 CAAGAAAGTGAA-----AAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_144173841_   6072 AAA--ATATAGCTGAGAAAAATCCTTTATCCAGACTATA--AATAATTCC 6117
                            --     v    v  iiiv i v        v    --  v  i  i
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_144173841_   6118 TACTACTCTATGGTAGAAAGACCAACATCACAAT--GACATTGGGCAAAA 6165
                            v    v  ii  i      v  i v v    --i v v        i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_144173841_   6166 TATATGAGCATACATA-CTAGAAAGGAAAATACGCAAATGAACAATAATC 6214
                         v  v   ii v    v-  vv    -  i   ii      iv      v 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAG-AAGATATACAAATGGCCAATAAGC 877

  chrX_144173841_   6215 ACATGAAAA-ATGTTTAATACCATCAGTTAT 6244
                                  -   i i  i i  ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (138 / 84)
Gap_init rate = 0.03 (28 / 812), avg. gap size = 2.57 (72 / 28)  


 267 10.00 0.00 0.00  chrX_144187439_144191136     2537  2576 (1122)    L1M4_orf2#LINE/L1        3    42 (866)  

  chrX_144187439_   2537 GAAAGATATCCCGGGTTCCTGGATTGGAAGCCTTAATATT 2576
                                     iv    v           v         
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT 42

Transitions / transversions = 0.33 (1 / 3)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.00 (0 / 0)  

1984 26.17 3.55 0.81  chrX_144187439_144191136     2579  3197 (501)    L1M4_orf2#LINE/L1      257   892 (16)  

  chrX_144187439_   2579 TTAAACCACTATGCTACTGGCATAAAAACATATATATACACCAATAGAAT 2628
                          i  iv  v i  v           ii i v i     v i    i    
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_144187439_   2629 ATAATAAAGATCCTAGAAATAAATCCACACCTATATAGTCAACAGATCTT 2678
                          v   vi   vi i         i   i  v v   i     iv   i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_144187439_   2679 TGACAAGGATGCCAAGGATACACAATGAAGAAAGGATTGGTTCTTCAACA 2728
                         i       i       ivi iv     ii     i  v vi i       
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_144187439_   2729 AACTGTGCTGGGAAAATTAGATAGCCATATGCCAAAAAAGTTA--CTGGA 2776
                           iv         v  i i    ?   i    -    i i v --i    
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGC-AAAAGAATGAAGTTGGA 455

  chrX_144187439_   2777 GTGTAATATTATATCATACACAAAAGTAAACTCAAAAGGGATTAAAAACT 2826
                         viviv iv i i i    i      i v         v    i ? i  i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_144187439_   2827 TAAGCATAGGACCAGAGATTATTAAACTCCTAGAAGAAAACAAAGGGGAA 2876
                            iii  i  v vi i i   v      i            v   ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_144187439_   2877 AAACTTAGTGCCATTGG--------------TCTTA--CATGATATCAAA 2910
                           v   v   v v    --------------     --i    i i    
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_144187439_   2911 AGCAGAGGTAATAAACATATATATAGACAAGTGGGAATACATCAAACTAA 2960
                             v i i  i   viv v v     i  i v   v v       v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_144187439_   2961 AAAGTTTCTGCACAGCAAAGGAAACAATCATTAGTGATGTGAACAATGTA 3010
                            ii  i  ii vv       v  v    --  vi -     -  vii 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCA--AGAAA-GTGAA-AAGACA 701

  chrX_144187439_   3011 TGCTACAGAATGAAAGAAAATATTTGCAAAT--TATAGTTGATAAGTGGT 3058
                         vv i        ii                 --    vi       v ii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_144187439_   3059 GAATATCCCAAATATATAAGGAACTCCTACAACTCAATAGCAAAAAAAAG 3108
                         vvi     vi         i      i            ii     i vi
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_144187439_   3109 AA-AAAACAATT-AAAAATGAGTGAAGTATTTGAATAGACAATTTTCTGA 3156
                           -  vv     -       i ii   v             v  i  ii 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_144187439_   3157 AAAAGACATACAAATAGACAACAAGTATATTAAAAGATGCT 3197
                          i    i        i v   i   i i  v          
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

Transitions / transversions = 1.52 (96 / 63)
Gap_init rate = 0.02 (10 / 636), avg. gap size = 2.70 (27 / 10)  


 622 24.23 4.62 9.23  chrX_144228660_144230780      436   695 (1426)    L1M4_orf2#LINE/L1       34   281 (627)  

  chrX_144228660_    436 CTTAAAATTGTTAAGGTAACAATTCTCCTTAATTTTAGAGATGTGTGTGT 485
                              v         i ii    v    ii  v  ----   --------
  L1M4_orf2#LINE/     34 CTTAATATTGTTAAGATGGCAATACTCCCCAAATT----GAT-------- 71

  chrX_144228660_    486 GCCTATGTGTGTTTATTCAATGTAATTTCAGTCATAACACCAATGGGCTT 535
                         --   ii--- ---      i i   ii vi   v  iv   iiv v   
  L1M4_orf2#LINE/     72 --CTACA---G---ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chrX_144228660_    536 TTTCATAAAAATTGGCAATCTGATTCTAACATTTATATGAAAA------- 578
                            iii i      i   v     i    v   i     i   -------
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chrX_144228660_    579 GAACTAGAATATCCAAGGCAATCTTGCAAAGGAAAAAACAAAC----AGG 624
                           v i      v    ii        v   i   i  -    v----   
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA-CAAAGTTGGAGG 212

  chrX_144228660_    625 TATCCTTATTTAACTCAACTGTAAGACTTAGTATAATGC-ACAATAATCA 673
                         - ii vi i  -- i   i vi  i     v  i  v  -   i      
  L1M4_orf2#LINE/    213 -ACTCACACTT--CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_144228660_    674 CTACAGTATGATGCTGACTTAA 695
                         vv     i  i i   i v   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAA 281

Transitions / transversions = 2.00 (42 / 21)
Gap_init rate = 0.04 (10 / 248), avg. gap size = 3.60 (36 / 10)  

1263 25.91 5.85 6.48  chrX_144228660_144230780      996  1628 (493)    L1M4_orf2#LINE/L1      280   908 (0)  

  chrX_144228660_    996 AAGAATTAACAACTAGATCAATAGCAAAGAAT-AAATATCACAGTAATAG 1044
                            i  vi   vv         i v v     -i ivi  -   v    i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAA 328

  chrX_144228660_   1045 ACCCCAAAATATATACCCATCTGATTTTCAATAATGACAGTGATGGAGTC 1094
                             vv v  v   ivi  vi        i i  v ---   viiiiii 
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGG---GTGCCAAGACC 375

  chrX_144228660_   1095 ---CAATGGGGGAAAAGCA---TTTTTAATGAATGAAGCTAGAATAATTG 1138
                         ---        i  i ii ---    i  ii    iv   i i i  i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_144228660_   1139 GACAACCATAAAGAAAAACATGAACCTTG-TCCCTGCCTCACAGTATGCA 1187
                           i ?   i viv    iv     vi v -i    i       vi  ii 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_144228660_   1188 TAATAAATAA-TCAGA-TAGATTATAATCTTAAATGTGAAAGCGAAAACC 1235
                         i  v  v   -   i - i   i ? iv i       i i   v     i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_144228660_   1236 ATAAATTTCTTAGAAGAAAACCTAGGAGAATATTTTCATGAT-TTGGACT 1284
                              vi              v    ? v v  i   i   i-    ii 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_144228660_   1285 AGTCA---------TAGA-----------GAGCAATAATCACAAAATATA 1314
                           v  ---------    -----------i    vv iiv      v v 
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_144228660_   1315 ATTTATATA--TTTGATTTAATTGGAATATTAAAATTGTATCTATATATC 1362
                          vv  v   --  v  i  v  iii   - v    i --- i i iiv  
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAAT-TAAAAACT---TTTGTGCTTC 671

  chrX_144228660_   1363 AAAATAATGC-ATTAAGAGAGTGAATAGGCAAGTCCCAAACTAGGAGAAA 1411
                            i-i ii -  i    i      v  i   vi v  i v i       
  L1M4_orf2#LINE/    672 AAAG-GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chrX_144228660_   1412 ATATTTGTAAA-CACATATCTGACAAAGAATGTCACTAATTTTATAATTA 1460
                                i   -  i        i  i i -----  -------------
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGA-----CT------------- 752

  chrX_144228660_   1461 ATGATGTTATACAATTTATTATATAATTATATAATTTGATTACAATTCAA 1510
                         ----   -  v  i--- v       ---- v  i i--      i    
  L1M4_orf2#LINE/    753 ----TGT-ATCCAG---AATATATAA----AGAACTC--TTACAACTCAA 788

  chrX_144228660_   1511 TAATCAAAAGAAAAGCAACCTAAC--AAATACGGGAAGAATATTTGAATA 1558
                             v      v  ii    i  i--   v i   v i iv         
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_144228660_   1559 GACATTTCACAGGAAAAGATATATGAATGGCCAAAAAGCAAATGAAAAGG 1608
                                 v vii i        ii         v     v        i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_144228660_   1609 TGCCCAGTATCATTAATCAT 1628
                            i  ii    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (102 / 59)
Gap_init rate = 0.04 (24 / 629), avg. gap size = 3.25 (78 / 24)  


2442 31.30 1.44 0.78  chrX_144342851_144348164     3921  4821 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_144342851_   3921 GGAAACACGTCCCATGCTCATGGATTGAAAGAATCAATATTGTGGAAGTG 3970
                              v ii       i          i    v i        vi ii  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_144342851_   3971 ACTATACTGCCCAAAGCAGTCTTCAGGTTCAGTGCAATTGCTATCAAAAT 4020
                         i v     v      viii   v   i    ii     iv          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_144342851_   4021 ACCAAACATCATTTTTCACAGAATTAGGAAAAAACAG--TGTAAAATTCA 4068
                         v   iviii -     ii     v v -- v  i v --iv         
  L1M4_orf2#LINE/    102 CCCAGCTGCC-TTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_144342851_   4069 TATGGAACCAAAAAAGATCTCAAATAGCCAAAGCAATCCTAAGCAAATGG 4118
                                viiv  ii  i ivi          i     i i iv  ivi 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_144342851_   4119 AATAAATCTGGAGGAATTATATTGCTGGAGTTCAAATTATACTACAAGCC 4168
                           i   vi       v i i i v ivi v      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_144342851_   4169 TATAATTACCAAAACAGTATAATGCTGG--TGAAAATGGGGACCACATGG 4216
                           i i v i   i     i ii i    -- i ii  i i---  i  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA---CATATAG 295

  chrX_144342851_   4217 ACCAATGGAACGGAGTACAGAACCTGAAAATAAAGCCAAATACTTACAGC 4266
                          i        ii  i vv   ii iii       v   v i i   ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_144342851_   4267 CA---GATCTTCAAAAAAGTATACAAAAA--ATACACTGGGGAGGGGA-A 4310
                           ---   i   i v  i -i i v  i --  v  v      ii i - 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_144342851_   4311 ACCTGTTTTATAAATGGTGCTGGGAAAACTGGCAGGCCACATGTGAAAGA 4360
                         ii  v  iv i              v      vvi?       ii     
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_144342851_   4361 ACGAAACTGGGTCCCTGTATCTCACCTTGTACAGGAGTCATATCAAGGTA 4410
                          i   ii   ii    iiv  v    v i    ii i i vv    ii i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_144342851_   4411 GATGAAAGACTTGAAACTAAAACCTGAAAACATAAAAATTCTACAAGATA 4460
                            v ?    i i  vv   i v  i   vi      v ii  v    v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_144342851_   4461 ATATTGGAAAAACTCTTCTGGACATTGTCCTCCGCAAAGAATTAATGACT 4510
                          i  v  ?iv  v     vv   v   vvi vv    v iv  vv iiv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_144342851_   4511 AAGACCCTGGGAGCAAATGAAACAAAAACAAAAATAAATAAATGGGATCT 4560
                          v   v iiii    v v v       iv       i      v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_144342851_   4561 AATTAAACTAAAATGTTTCTTCACAGCACAGGAGATAATCATCTACGTGA 4610
                         v  i   v v   vii  i vii vv  v    v iv    vvv v    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_144342851_   4611 ACAGACGACCTGCTGAGTAGGAGGAAATATTTGCGAACTATGCATCCACC 4660
                          v    i   ii v  i i    i          i  ii  ii   iivi
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_144342851_   4661 AAAG-ACTAGTACCCATAATCCACAAGGAACTGAAACAAACCAGCAAGAA 4709
                           i -   v   i   v   vi i  i     vvv    vi  ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_144342851_   4710 AAAAACAAATAATCCCATCAAAAGGTGGGCAGAGGACATGAATAAACATT 4759
                            i        i  v  i?   ii      i    iv      i     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_144342851_   4760 TCTCAAAAGACAATCTACAAACGGCCAACAA--ACATGAAGTGATGCTTT 4807
                             v     vi  v      i      i  --       iv      iv
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_144342851_   4808 ACATCACTAAGCAT 4821
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (169 / 109)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 1.82 (20 / 11)  


2835 23.54 2.87 5.08  chrX_144348573_144350532.rev      565  1469 (491)    L1M4_orf2#LINE/L1       24   908 (0)  

  chrX_144348573_    565 GATTGGAAAGCTTAATATTGTTAAAATGTCCACACTCCCTCAAAGCAATC 614
                                 ii              i   v v i      -    vii   
  L1M4_orf2#LINE/     24 GATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC-CAAATTGATC 72

  chrX_144348573_    615 CCAAGATTCATTGCAATCCCCATCAAAATCCCAAAGTAGCATTT---ACA 661
                         ivv       vi        i            -- iv  v   ---i  
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCA--GCTGCCTTTTTTGCA 120

  chrX_144348573_    662 AAAATAG-CATAGACAATACTAAAATTTATATGAAATGGTGATGGACACC 710
                         i    v -  -  vii  v        i     i  vv ii v    v v
  L1M4_orf2#LINE/    121 GAAATTGACA-AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_144348573_    711 GAATAGCCAAAACAATCTTGAAAAGGAAAAACAAAGTTGGAGGCATCACA 760
                                                 i   i              vv     
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_144348573_    761 CCTCCTGATCTCAAAACATATTACAAAACGACAATAATTTAAAAGGTAAT 810
                          i   ii  i       v  i      i v   ------------     
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACA------------GTAAT 257

  chrX_144348573_    811 TAAAACAGTATGGTACTGGACCAAGGACAGATATACAAACCAATGGAGCA 860
                         i  i     i         vvi     i   i   i i i       ii 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_144348573_    861 GACTAGAGAGCCCAGAAACATTGCCATGCATATATGATCAATGGACTTT- 909
                           v v     i       i vvv    i   v    i     v  i   -
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_144348573_    910 GGCAAGGGGTGCCAAGAATACACAATGGCAAAAAGACTGTCCCTTCAACA 959
                          i      -        vi iv      vi   ii iv   ii       
  L1M4_orf2#LINE/    358 GACAAGGG-TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_144348573_    960 AATAGTGCTGGGAAAATCAGATGTTCACATGTGAAAGAATACAACTGGAC 1009
                            i         v  iii   i?i      ii       iv ii     
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_144348573_   1010 TCCCCTATCCCCCTCCTACACCACATACAAAAGTCAACTCAAAATGGAGC 1059
                         --     ----    --      i        i i             v 
  L1M4_orf2#LINE/    457 --CCCTA----CCTC--ACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_144348573_   1060 A-GGACTTAAACATAAAACATGAAACTA--AAATTCCCAGAAAAAAACAC 1106
                          -i   i    ii   i vv i      --   i  ii    i      i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_144348573_   1107 AGGGAGAAAGTTTCATG---------TAAG---TGGT--CCAGAACCTGA 1142
                            ?iv   vi   i  ---------  i ---    -- ivii iv   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_144348573_   1143 TACCAAACATACAAATAATAAATGCAAAGATAGGCAAGTGAGACT--ATT 1190
                         i      vii    ii  i   v v   i    ii  i vi    --  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_144348573_   1191 ACAATCCAAAATATTTCTGGCACCAGAAAGGAGAGAATTAACAAGGCAAA 1240
                          v   iv    iv   v  - vi  --     v vv  i  v  i ii  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTG-CTTCA--AAGGACACTATCAAGAAAGTGAA 695

  chrX_144348573_   1241 GAAACAACTCA--GAGTGAGAGAAAATACTCACCAACCATATATGTAATA 1288
                         i i     i  --  i  i         i ii v  i       v i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_144348573_   1289 AAAGATTAATATCCAAAATATCCAAATATCTAAAATATATAATGTAATCT 1338
                          ii  i vi      i     -----------------    v v v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATAT-----------------ATAAAGAACTCT 778

  chrX_144348573_   1339 TACAACTCAATAGCAAATAAATAAAATAATGTAATTAAGAAATATGCAAA 1388
                                     ii   v i i   -   ivi    ? i    iv     
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAA-TAACCCAATTWAAAAATGGGCAAA 827

  chrX_144348573_   1389 TAATCAGAACAGACATCCCTTCAAAAAAGAAACACAAACGGCCAACAGGT 1438
                         vi  iv   i      ii  i    i    v i     i      i i i
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_144348573_   1439 ATACGTAGAGATGCTCAACTTCATTAATCAT 1469
                          i i v i           v   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.04 (141 / 69)
Gap_init rate = 0.02 (22 / 885), avg. gap size = 3.27 (72 / 22)  


2309 28.90 1.21 0.54  chrX_144421860_144423609.rev      516  1259 (491)    L1M4_orf2#LINE/L1      160   908 (0)  

  chrX_144421860_    516 AAAAGAGCCTGGATAGCCAAGGCAATCCTGTGCAACAA-AACAAAGCTGG 564
                           ii  v  v i        ii     i  viv  v  -       i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chrX_144421860_    565 AGACATCATGCTACCTGACTTCAAGCTATACTACAGGGCTACAGTGACCA 614
                           ivv   ii  v  ii i     iviv       ii        i i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chrX_144421860_    615 AAACAGCATGGTACGGATACAAAAACAGACATACAGACAAACAGAACAGA 664
                          i    ii      v ii i  ii i       i   iv  ii   i   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chrX_144421860_    665 ATAGAGAGTCCAGAAATAAGGCCATATGCCTACAATCATCTGATATTTGA 714
                           v                iv     iiii  iii   vi    v  i  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_144421860_    715 CAAAGCTGACAAAAACAAACAATGTGGAAAGAA-ATTCTTATTCAATAAA 763
                            i v  v   i v  vv     v        - v    -     i   
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT-TTCAACAAA 408

  chrX_144421860_    764 TGGTGCTGGGTTAACTGGTTAGCCATATGCAGAAAATTGAAGCTGGACCC 813
                                   vi      v  ?   i     i  i v     i       
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_144421860_    814 CTTTCTTACACCATATACAAAAATCACCTCAAGATGAATTGAAGACTTAA 863
                           vi  i                 i v     i   i  ii?    i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_144421860_    864 ATGTAAAACCCAAAACTATAAAAACCCTGGAAGACAACCTAGGCAATAAC 913
                               i v i            vi i i     v   v    ?ivv  i
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_144421860_    914 ATTCAGGACACAGGCACGT---GCAAACATTTCATGACAAAGATGCCCAA 960
                         v   iv   viv  ---  ---    vvi    v iivv v  ii  v  
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGG---GTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_144421860_    961 AGCAATTGCGATGAAAGCAAAAATTGACAAATGGGATCTAATTAAACTAA 1010
                             vvv  i ii    v      v  i    v   ii v  i   v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_144421860_   1011 AGAGTTTCTGTACAGCAAAAGAAAATATCAACAGAATAAACAGAAAACTT 1060
                          i ii  i   i vv    i  v v      v i i i  v   v   ii
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_144421860_   1061 ACAGAATAAGATAAAATTTTTGCAAGCTATGCATCCAACAAAAGTCTAAT 1110
                                ii  v     v       iii  ii   ii i  ii v  vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_144421860_   1111 ATCCAGCCTCTATAAGAAACCTAAACAAATTTACAAGTAAAAAACA--T- 1157
                               vv v     ii   iivv    v iv i  vv    i   -- -
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_144421860_   1158 -CTTCATTAAAAAGTGGGCAAAAGACATGAACAGAGACTTTTCAAAAGAA 1206
                         - iiv   ?    i        i  iv    i   v i  i  v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_144421860_   1207 GACATACATGCAGCCAACAATCATATGGAAAAAAGTTCAACACCACTGAT 1256
                           i     viii     i  v  i   i   i v i      i  ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_144421860_   1257 CAT 1259
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.60 (130 / 81)
Gap_init rate = 0.01 (7 / 749), avg. gap size = 1.86 (13 / 7)  


 206 20.00 4.29 4.29  chrX_144427596_144431219      295   364 (3260)    L1M4_orf2#LINE/L1      268   337 (571)  

  chrX_144427596_    295 TGATACTGATACAAAAACAGTCACACATA---CAACCGTAACAGAATAGA 341
                           i     ii i  ii i  --   i   ---   iv -  i     v  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAG--ACATATAGATCAATGG-AATAGAATTGA 314

  chrX_144427596_    342 GAGCCCAGAAATAAAGCCATACA 364
                            i           v       
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACA 337

Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.04 (3 / 70), avg. gap size = 2.00 (6 / 3)  

3047 23.23 1.48 5.81  chrX_144427596_144431219     2185  3131 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_144427596_   2185 GAAAGTCATACCTGGGTCATGGATTGGAAGATTTAATATTGTTAAAATGC 2234
                              vi  v  vv v               i             i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_144427596_   2235 CCATACTACTCAAAGCAATCTACAGATTCAATTCAAAATATATCAAAATC 2284
                          v     v i    vii              iv   vviv          
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_144427596_   2285 TCAATAGCATTTTTCACACACAAAAAGTGAAAAGC-AATCTTAAAATTTA 2333
                         i  iiv  v     ii  ----i   v   v    -i   i       i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCA----GAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_144427596_   2334 TACGGAGTCTTAAAGTACCACACATGTCAAAAACAATCTTGAGAGAGAAT 2383
                           i   ivivi  i v   vviv  iv v             i i    v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_144427596_   2384 AACAAAGCTGAAG-ACACAACCCTTTCTGATTTGAAAATATACTACTTTG 2432
                                i  i  -  v  - v   i ii    v    iv      vvv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_144427596_   2433 CTACAATAATTACAATAGTATGGGAGTGGCATAAGAGAAGACATA--GAC 2480
                              i    i vi i   i   v v         iiv       --  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_144427596_   2481 AAATGTAACCAAATAGAGTGCCCAGAAATAAGCTCATGTGGATATGATCA 2530
                         v    v  ivi   v   v i          i i   iiivv    i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_144427596_   2531 AATGGTCTTCAACAAGGTTGCCATGACTACACAATGGGAAAAGAAATAGT 2580
                          v  i i   i      v     v   i iv       i      -    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGT 396

  chrX_144427596_   2581 CTCTTAAACAATTGATGTTGTGGA-AACTGAATATCCACATACAGAAAAT 2629
                           i  v     v  i  i  -   -     i   ?      i  i  i v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_144427596_   2630 TGGAATTGGACCCTTATCTTACATTAGCCACAAAAATAGACTCAATGTAG 2679
                           i i        i  i  i   ii vvi        vi      vi i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_144427596_   2680 ATTAAAGTCTTAGATATAAGACTTGAAACTATAAAACTCCTAGAAGAAA- 2728
                           i ?  v i  i  i     vi i              i         -
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_144427596_   2729 CATGGGGAAAAACTCTT--TGACATTGGTCTTGACAATGATTTTTTGGAT 2776
                            i  ?iv   -    --    v    vi v i     i   i  i   
  L1M4_orf2#LINE/    546 CATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_144427596_   2777 GTGACCCCAAAAGCACAGGAAACAAAAGCAAAATTAGACAAGTAGGACTA 2826
                         i    v           i v        v    v    i  i v     v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_144427596_   2827 CATCAAACTAAAAAGCTTCTGAACAGCTAAGAAAACAATCAACAGATTGA 2876
                                v v    i   i  vi vv v   i v  v     v i v   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_144427596_   2877 AAAGTCAGCCTACTGAATGTAAGAAGAAATCTTTACAAATCCTACGTCTG 2926
                             v  i  i  v     vi    --   v   i      v  ii    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAA--AATATTTGCAAATCATATATCTG 742

  chrX_144427596_   2927 ATAATGGATTAATATCCAAAACA---AAATGAACTGCTACAACACAAAAG 2973
                             v   i vi      i  i ---   -     vi      v   v -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAA-GAACTCTTACAACTCAATA- 790

  chrX_144427596_   2974 CATGCGCGCGCGCGCGCGCACACACACACACACACACACACACACACACA 3023
                         ------------------------------------------- i v v 
  L1M4_orf2#LINE/    791 -------------------------------------------ATAAAAA 797

  chrX_144427596_   3024 CACACATAACCTGATTAATGAATGGGCTATGGACTTGAATAGACATTGCT 3073
                         v   v      ii   ? vi       v v   i             v  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_144427596_   3074 CCAAAGAAGACACACAAATGGCCAA---GTATGTGGAAATGTGTTCAACA 3120
                                   i i            --- i ii  i   vi  i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_144427596_   3121 TCATTAATTAT 3131
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.25 (120 / 96)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 4.31 (69 / 16)  


2908 25.00 5.07 0.46  chrX_144442388_144444483      736  1603 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_144442388_    736 TGGATAGATATCCAGTGTTCATGGATTAGAATTATTAATAGTGTTAAAAT 785
                             v        vi            i   vvv      v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_144442388_    786 GTTAATACTACCCAAAGTGATCTACAGATTCAAT-CAAT----ATCAAAA 830
                          vi      v      v                i-    ----       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_144442388_    831 TTCCAATCTCATTTTTAACAGAAATAGAAAAGACAATCCTAAAATTTGTA 880
                          i   iiiv v     vi       v  v   vii           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_144442388_    881 TGGAACCCCAAAATATCCGGAATAGCCAAAGCAACCTTGAGCAAAAAGAA 930
                              viv   iiv i  i           i   i     iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_144442388_    931 CAAAGCTGGAGGCATCACACTACCTGACTTCAAAATATACAACAAAACTA 980
                              i      vv       v  ii i       iv   v     i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_144442388_    981 TGCCAATCAAAACATCATGGTACCTGCATAAA-ACAGACACACAGACTAA 1029
                         iivi      i   vii      iv      i- i     i i   ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_144442388_   1030 TGGGACAAAATATAGAAATTAGAAGAAATATCCATGTATATATGGTCAAT 1079
                            i i i   vv   ivii    iv  - i    ii  v          
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCAAT 349

  chrX_144442388_   1080 TGATTTTTGAATAAGGCAATAAGA------AA---AGAAAGAACAGTTCC 1120
                                i  vv i  iivi    ------  ---i       i   iii
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_144442388_   1121 TTCAATAAATGTTGGTGAGAAAACTAGATATCCACACACTTAAGAATTAT 1170
                              i     v  v  i  v    i    ?     ii vv      v v
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_144442388_   1171 ATTAGACCCACATCTC----TATATACAATAATCAACTCAAAATTGATTA 1216
                         i  i     vi i   ----i        v   i          v   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_144442388_   1217 AGGACTTAAATCTAATTACCACAAACTTTAAAACTACTAGCCAAAAACAT 1266
                         ?i   i     v   vvi i -     v       vi   vvi       
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_144442388_   1267 AGGAGAAAAACTTCATGACATTATTCTGGGTAAAGATTGTTTTCAAGATG 1316
                            ? v   v    i    v  ivvi i  i  v i  - i  vi v   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAGATATG 597

  chrX_144442388_   1317 ATGCCAAAAGCACAGGCAACTAAAGCAAAAATATACAAATGGGATTACAT 1366
                          ii           i     v    v       v i    v   i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_144442388_   1367 TAAACCAAAAACCTTCTATGTAGCTAGAGAAACAAT-AAGCAGAGTAAGG 1415
                         i   viv    v   i i  ivv v ii  v  v  -   - i   i ii
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGAAA 696

  chrX_144442388_   1416 AGACAACCTACAGAATGGGAGAATATGTTTGCAAACCATA-ATCTGATAA 1464
                                 i              v  i        i    -         
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_144442388_   1465 AAGGTTAATATTCACAATATATAAGAAATTC----AACCCAGCCA---AA 1507
                         ii ii vi   i  v         ii  i  ----   i  iiv ---  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_144442388_   1508 ACAAAAATAGCCCAATT-AAAAATAGGCCAAAGA---------------C 1541
                          v v     i       -      i   v  i  --------------- 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_144442388_   1542 CTCAAAGAAGACATACAAATAGCAAAAAAGTGTATAAAAACATGCTTAAC 1591
                         ii         i        i  v  v   iii  i    v     i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_144442388_   1592 ATCATTAGTCAT 1603
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (131 / 83)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 3.00 (48 / 16)  


2831 22.89 4.21 6.26  chrX_144456343_144459178.rev     1421  2346 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_144456343_   1421 GGAAAAATTTCTCTTGTTCATGAATCGAAATTATTAATCTTGCTAAAATG 1470
                              i  v  i v        i  i i  vvv     v   i   i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_144456343_   1471 ----T-CTGACAAAAGTGATCTACAGATTAAATGCAATCCTTATCAAAAT 1515
                         ---- -  vv v   v             v  i       i         
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_144456343_   1516 TTCAATGGCATTTTTTACAGAAATAGAAAAAATG---CTGAAATTTAC-T 1561
                         ii  iiv  v      i       v  v  iv  ---  i     i i- 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_144456343_   1562 GGAATTATGAAAGACCTCAAATAGCCAAAACAATCTTGAGCAAGAGGAAC 1611
                             v iii ii    ivi                    iv    i    
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_144456343_   1612 AAAGCTGGAGGCATCACACTACCTGAGTTTAAAATCTACTACAAAGTTTT 1661
                             i      vv       v  ii v  i    ii          i vi
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_144456343_   1662 AGTAATCAAAGCATCATGGTCCTGGCATAAAAACAGGCACATAGACTAAT 1711
                                  ii  vii    v         ii i  i  i     ii   
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_144456343_   1712 GGAAGAGAATAGAAATCCCCTACATAA-CCCACACATGTACGGTCAACTA 1760
                             v     v  i vi  vv v    -    i    v  i      i i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_144456343_   1761 ATCTTTTCCAGGAATTACA----CA--CAATGGGGAAAGGAGAATCTTTT 1804
                           i  ivv  i ii vv  ----  --            i v i      
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_144456343_   1805 TAATATATAGTGTTGGGAAAACTCGATATCCTCATACAAAAGAGTGAAAT 1854
                         i  i v  i   i     v    v    ?  v   i       i    i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_144456343_   1855 TGGAGCCTTGTCTTACACAATACACAAAAATTAACTTGAAATTAATTAAG 1904
                             v  i ii  i    v   i             ii    vi  i ?i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_144456343_   1905 GACTTAAACATAAGATCTAAAACTGTAAAACT---AGTAGGAAA------ 1945
                            i    ii     v        i       ---  v  i   ------
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_144456343_   1946 ----AAGCTCCTTGACATTGGTCTTGGCAATGATTTTTTTCTTTAATATG 1991
                         ----  v  i v    v    vi v       i   ----   vi     
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT----CTTAGATATG 597

  chrX_144456343_   1992 ACTTTAATATGACTGCTAAAGCAAAGGCAACAAAAATAAAAATA------ 2035
                           ---------  -- v      v i         iv       ------
  L1M4_orf2#LINE/    598 AC---------AC--CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chrX_144456343_   2036 TTGAGACTACATCAAACT--GAGACTTTGCTGCACTTCCTGCACAGCGAA 2083
                            -    v       v --i i     --  ii    ---------i  
  L1M4_orf2#LINE/    637 TTG-GACTTCATCAAAATTAAAAACTTT--TGTGCTTC---------AAA 674

  chrX_144456343_   2084 GAAAATAATCAATAAAATAAAAAGGCAACTTGTGAAGCAGGATGAAATAT 2133
                          i v iv     v   i i     i    iiiiii iii   vi      
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_144456343_   2134 TTACATACTGTGTATTATATTCAAATTATA-ATATAATATGAAGAATTAA 2182
                           i  ------------------   i   -  v i   -- i i i vi
  L1M4_orf2#LINE/    725 TTGCA------------------AATCATATATCTGATA--AGGGACTTG 754

  chrX_144456343_   2183 TATGCAAAATGTA-AAAGTAACTTGTATAACTTAATATTTACAAAAAAGA 2231
                            v  i   i  -    -    iv  i    i    v ----       
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAG-AACTCTTACAACTCAATAAT----AAAAAGA 799

  chrX_144456343_   2232 AATCTCAAATGGCCTAATTAAACAGTGGGCAAAGAATCTGAATAGACACT 2281
                         -----     ii  i    ?  v i         i  i          i 
  L1M4_orf2#LINE/    800 -----CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_144456343_   2282 TTTCCAAAAAAAGATATCAAAACGACCAACAGTTATATGAAAAGATATTC 2331
                          i      i  -     vv   i i    i ivi i          ii  
  L1M4_orf2#LINE/    845 TCTCCAAAGAA-GATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_144456343_   2332 AGCATCGCTAATCAT 2346
                          i    i????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (138 / 71)
Gap_init rate = 0.03 (25 / 907), avg. gap size = 3.88 (97 / 25)  


2007 26.00 6.25 3.00  chrX_144489640_144493855     1168  1967 (2249)    L1M4_orf2#LINE/L1        1   826 (82)  

  chrX_144489640_   1168 TGGAGAGATAGTCTGTGTCCTTGGATTGCAGGACTCAATACAGTCAATAT 1217
                             i     vi ii   i v       v i    i    iv  i  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_144489640_   1218 GTCAATTATTCCCAACTTGATTTACATAGATGCAA---AATCA--ATCAA 1262
                          v    vv i     v     i    --   v   ---    v--     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA--GATTCAACGCAATCCCTATCAA 98

  chrX_144489640_   1263 ATGTATGGCAAGCTATTTTGTGGGAATAGACAAACTGATTCTAAAATTTA 1312
                          vvivii  viv  v     ii i   v     i     i        i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_144489640_   1313 TATGGAAAGGAAAAAGACCCAGAAAAGCCAAGAAACACTGCATCT----- 1357
                                 v v  ii         v      --    ----    -----
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAA--AACA----ATCTTGAAA 192

  chrX_144489640_   1358 --GAACAACCAAGTTGGCAGGCTGACACTAACCAACTTCATGACTTATTA 1405
                         --   v   v       vi i  v     vv    i    vi     i  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_144489640_   1406 TAAAGATATAGTAAACAAGGCAAAGTGGTA-TCACCCAAAGA---ATACA 1451
                         i    v  i     v    i  iv      - vi vi  i  --- i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_144489640_   1452 TAGATGAAGAGAACAGAATAAAGAGTGCAGGAATGGACTCACTCAAATAC 1501
                              v  vi   i     vi     v   i   ii  i  iv  vv  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_144489640_   1502 AGCTAACTGATCTTTGACAAAAGAATAAAGGAAAG--AAAAGAGTAAAAA 1549
                         i ii  i    i  i     ii viiv   ivv v--  vi i v  i  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_144489640_   1550 TA-CCCTTTAAATAAATTGTAC--------------ACCCATATGTGAAA 1584
                           -i i   v  i    v  i -------------- ?   i   ii   
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_144489640_   1585 -AATAAA--TAAACAA--ACCTAGACACAGTCTATGAAGCTTTCATAAAA 1629
                         -   i  -- ii  vv--    ---    viv   --------- i    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCT---CACACCATAT---------ACAAAA 480

  chrX_144489640_   1630 ATTGATTCATAATGTATCACTGACGTAGATATAAAA-TGGAAACAATAAA 1678
                            i i   v    v    ?v   v  i  i   i -ivi    v     
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_144489640_   1679 ATTTCTATAAGAAAAC-TAGGGGGAAAATGTAGGTTACCTTAGGTTTGGC 1727
                          i ii  v        -    ? v   - v vv  v     i    v   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGC 579

  chrX_144489640_   1728 AATGAGTTTTTATATTCAACATAAAAAGGACAATCCACAAAAAAAAAAA- 1776
                             iv  i   v  vii   iv     v    v v      i      -
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_144489640_   1777 --GTAAGTTGAGCTTTATGAAAGCTTAAAACCTCTTCT-TTGCAAAAGAT 1823
                         --i   i   ii   i  v   i-      v  i  v -i v    i  i
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAA-TTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_144489640_   1824 GCTTTTAAGAGAATGGAAAGACAAGCCACA-ACTGGTAGAATATATTTGC 1872
                         i  v i    i i  i        v     - v   v    v        
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_144489640_   1873 AAAACACACATTTAATAAACATTTTGAATCCAAAATAGACAAAGAACTCT 1922
                            v  i i  i i    ivivi   v     i    v i          
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_144489640_   1923 TAAAACTCAATAAGTTA----GATAAA-AACCTAATTTAAAAATGAGCAA 1967
                           v          --  ----  i   -    i    ?       i    
  L1M4_orf2#LINE/    779 TACAACTCAATAA--TAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

Transitions / transversions = 1.32 (116 / 88)
Gap_init rate = 0.03 (26 / 826), avg. gap size = 2.85 (74 / 26)  

3178 26.98 0.66 0.66  chrX_144489640_144493855     1997  2904 (1312)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_144489640_   1997 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2046
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_144489640_   2047 GGCCATATTGCCCAAGGTAGTTTATAGATTCAATGCCATCCCCATCAAGC 2096
                            v   i v     iv ii i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_144489640_   2097 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2144
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_144489640_   2145 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 2194
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_144489640_   2195 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 2244
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_144489640_   2245 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATTTATAGACC 2294
                                 i   i    ii         i iv ii i   iv      i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_144489640_   2295 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACC 2342
                                i    i--    i  --        vv  ii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_144489640_   2343 ATCTGATCTTTGACAAACCTGACAAAACAAG-AAATGGGGAAACAATCCC 2391
                          vi    i  i     ivv  v   i  v v-v          v   vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_144489640_   2392 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAGGCT 2441
                           v  i  i              v      v  ?   i   i i   iv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_144489640_   2442 GAAACTGGATCCCTTCCTTACACATTATACAAAAATTAATTCAAGACGGA 2491
                            ii    i    v   i    vv              i    i i   
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_144489640_   2492 TTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2541
                          i ?    i  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_144489640_   2542 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 2590
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_144489640_   2591 AAACACCAGAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 2640
                         vi      i     vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_144489640_   2641 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 2690
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_144489640_   2691 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 2740
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_144489640_   2741 AAGGGCTATTATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 2790
                          i  i  vv          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_144489640_   2791 AAAACAAACAACCCCTTCAAAAAGTGGGTGAAGGATATGAACAGACACTT 2840
                           i     i     vv i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_144489640_   2841 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAAATGCTCA 2890
                            v        i  vi viii     v  i          i -      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCA 894

  chrX_144489640_   2891 TCATCACTGGCCAT 2904
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  

 238 21.18 10.59 0.00  chrX_144489640_144493855     3639  3723 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_144489640_   3639 AAAAATGAGCAAGACTTCTGAACACAAACC-CTC------AGATATACAA 3681
                                i    iivv i    i v v ii-   ------          
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_144489640_   3682 ATAGCAAATAATCATATAAAAA--TGCTCAATGTCATTTTCCAT 3723
                           i  v     v  i  i    --       ii   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.03 (3 / 94), avg. gap size = 3.00 (9 / 3)  


3061 26.68 1.79 1.68  chrX_144549217_144551100      500  1391 (493)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_144549217_    500 TGTTCATGGGTTGGAAGACTTAATATTGTTAAAATGCTCATAGTACCCAA 549
                                  i                      i   viv   v v     
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_144549217_    550 AGTGGTCTGCAGATTCAATGTAATCACT--TAAATTTCCAATGGAATTTT 597
                          v  i   i         i i    v  --i   v i   iiv vv    
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_144549217_    598 T--CAGATA--GAGAAA--AATACTTAAATTTAGATAGAGCCAAAGGAGA 641
                          --    v --  v  i--i  v  v     i v  i  iviiv i i  
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_144549217_    642 ACCTAAATTGTCAAAATGATTATTGGGCCAAGAAAAAAAAAAAAAAAGAA 691
                         v  vi   v i     ii  i-   --------------     i     
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATC-TTG--------------AAAAAGAAGAA 200

  chrX_144549217_    692 CAATGCGGGAGGCATCGCACTCCCTGCTTTCAAAA-----TACAAAGCTA 736
                            v iv     vv  i    i  iiv        -----          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_144549217_    737 TTATAATCAAAACAGTATTGTACTGGCATAAAAAGAGACACATAGACAAA 786
                         ivi       i     i v            ii v     i     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_144549217_    787 TGGAATGGGATAAAAAGCCAAGAAGTAAGCCCATGCATTTATGGTCAGTT 836
                               i i  vi i  i v    i   i     i            i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_144549217_    837 GATTTTT-ACAAAGGTGTTAAGATCACATAATGAGGAAAGGATATTTTCT 885
                               i-    i    ii    i  ivi    i      i   v i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_144549217_    886 TCAACAAATAATGTTGAAAAAACTCGTTACCTGCATGCAGAAGAATAAGA 935
                                  ii  i  ii v    v v  ? ii      i      i ii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_144549217_    936 TTAGATCCTTATCTCAGACCATATACAAAAATTAACTCAAAATGGACTAA 985
                           i  i  i  i    v                             ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_144549217_    986 AGACTTCAACATAAGACCTGAATTTCTAAAACTACT-GTAGAAAACACAA 1034
                             i v  ii     v  i  vi v       vi - v        i i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_144549217_   1035 GAGAAAACTCCCGAAACAGTTGTCTGAACGATGATTT-TTGGATACAACC 1083
                          ? v   iiii  vi  vv v vi iii i   i   -  i    ii  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_144549217_   1084 TCCAAAACACAGGTGACAAAAGCAAAAATAGACAAGTAGAATTTCATCAA 1133
                         i v   i    i ii       v         i  i v i i        
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_144549217_   1134 AATAAAAAGCTTCTACATAGCAAAGAAAACAATCAGCAACATGAAGAGAG 1183
                            v    i   i iiiivv     i v  v    iv  vi    i   v
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_144549217_   1184 AGTCCACACTATGGTAGAAAATATCTGTAAACCATTCATCAGATAAGGAG 1233
                          ii     vv    v         i  i   i   vi   v       ii
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_144549217_   1234 TTAATATGTAAAATACACAAGGAACTAAGGCAGCTAAATATCAAGAAAAC 1283
                         i vi   vi i    i i  i     vvvi  i  v    vi  i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_144549217_   1284 AAATAACTTGATTTAAAAGTGAGCAAAGAACTCAAACAGAAAAATCTCAA 1333
                                iii   ?    i  i      i i ii  i   v vv    v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_144549217_   1334 AAGAAGACATACAAATGGACAGCAGGTACATGAAAAAATCCTCAGTATCA 1383
                                i          v  ii i i         i  v    ii    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_144549217_   1384 CAAATTAT 1391
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.96 (155 / 79)
Gap_init rate = 0.01 (10 / 893), avg. gap size = 3.10 (31 / 10)  


3164 24.45 2.21 1.77  chrX_144570111_144574845     3339  4242 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_144570111_   3339 TGGAAAGATATCCCATGTTTATACATTGGAAGAATTAAAA--ATTAATGT 3386
                                            i  iv         v    v --i    vi 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_144570111_   3387 ATCTACACTAACCAAAGGGATCTACATATTCAGTGCAATCTCTAAGAAAA 3436
                         iv v i   vv     vv        v     ii      i   vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_144570111_   3437 TTCCCG-TGTCATTTTTCACAGAAATAGA-AAATAAACCCTAAAATTCAT 3484
                          i  v -  i -     ii       v  -  iivi i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_144570111_   3485 ATGAAGCCACAAAATACTCTGAATAGCCAAAGCAATCTC---AAGTAAGG 3531
                            i ivii   iiv  i v           i      i---  iv   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_144570111_   3532 ATAAACTTGGAAGCATCAC---TCCTAATGATTTCAAACTATATTACAAA 3578
                          i   v     i vv    ---   i   --  iv     -  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAAT--TTCAAAACT-TACTACAAA 246

  chrX_144570111_   3579 GCTATAGTAATCAAAACAGGCTGATACTGGCATGAAAGCAGACACATAGA 3628
                             i         i    vv  i         i iiii     i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_144570111_   3629 TCAATTAAACAGAATAAAGAGGCCAGAACGAAATCCACATACTTACAGTC 3678
                              vi  i     vi    v      vv   i   i i i   ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_144570111_   3679 AACTGATCTTCAACTAAGGTGCCAAGAACACATAACTGGTAAAGGATACA 3728
                           i    i   i  v i          v  ivi  iv  v    i   vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_144570111_   3729 CTCTTCAATAAATTGTGCTGGGAAAACTGGATATCCACATACAGAAAAAT 3778
                           i     i    v         v         ?      i  i  i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_144570111_   3779 AAAGTAGGACCCTTATCTCCCACTACATGCAAACATTAACTCAAAGTGCA 3828
                         i    v      i  i   v   i i  i    v           i  v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_144570111_   3829 TTGGAGATTTACATATAAGATTTGAAACTGTAAAACTCCTAGAAGAAAAG 3878
                          ii?   ii  v  i     vi i     i        i          v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_144570111_   3879 ATAGAGGATAAA-CTTCTTGACATTGGTCTGAGCGATA-TTTATATATTA 3926
                             i? -    -    v    v    vi ii  i  i-   v ------
  L1M4_orf2#LINE/    547 ATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT------ 589

  chrX_144570111_   3927 TATATATATATGACCCTCAAAGCACAGGTTAAAAAAGCAAAAATAGACAA 3976
                         ----  v       v iv        i iv v     v         i  
  L1M4_orf2#LINE/    590 ----TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_144570111_   3977 ATGAAATTACATCCAACTAAAAAACTTCTGCACAGCAAAGGAAAGAATCA 4026
                           vii i v    v  v v        i  ii vv       v vv    
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_144570111_   4027 ATGCAAA-GAAGAGACAACCTGTGGAATGGGAGAA-----TTACAACT-A 4069
                          - v  i-   i        iiii           -----  i   v - 
  L1M4_orf2#LINE/    686 A-GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_144570111_   4070 CACAACACATAAAGGGTTAATATCCAACCTATGTAAGGAACTAAATCAAC 4119
                         i i v vv    i  ii vi      ivv   i   i     vvvv    
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_144570111_   4120 TCAATAACAAGCAAACAAATAACTGAACTCAAAAATGAGCAA-GGACATG 4168
                                i  iv i         iv  i ?       i    -   iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_144570111_   4169 AGTAGTCATTTCTCAAAAGAAGATATATTAATGACCAACCTATATATGAG 4218
                          i   v        v            iv    i    ivvii i    i
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_144570111_   4219 AAGGTGTGCAACATCACTAATCAT 4242
                            i  iv        ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (129 / 88)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


2900 27.16 2.58 0.67  chrX_144654335_144659708.rev     3993  4883 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_144654335_   3993 TGGAAAAGCATTTCATGCTCGTGGATAGGAAGAATCAATATAGTTAAAAT 4042
                               iii  ii    i  i     v      v i     v     i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_144654335_   4043 GGCCATACTTCCCAAAACAATTTACAGATTCAATGCTATTCCTATTATAT 4092
                            v     i      vii  i           i  v  i     i v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_144654335_   4093 TACCAATGACATTCTTCATAGAACTAGAAAAAAACT-ATTTTAAAATTAA 4141
                          v   iivi v  i  iii    v v  v  i--  -  ii       v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chrX_144654335_   4142 TATGGAA-TGCAAAATGATCCCAAATAGCTAAGGCAATCCTAAGCAAAAA 4190
                                -     ii-  i  vi      i  ii     i i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_144654335_   4191 GAACAAAGCTGGAGGCATCCCATTACCCAACTTCAAATTATATTACAGGG 4240
                                 i      vv  v  i v     i      viv  i    ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_144654335_   4241 CTATAGTAACCAAAACAGCATGGTACAGGCACAAAAACAGACACATAGAC 4290
                            i     i   i    ii      v    i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_144654335_   4291 CAGTGGAACAGAAGAGAGAGCCCAGAAATAAGGCCATACACCTACAACCA 4340
                           i     i    vv     i          iv       ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_144654335_   4341 TCTGATCTTTGACAAAGCTGACAAAAACACGCAATGGGGAAAAGACTCCC 4390
                         vi    i  i     i v  v   i v  iv           ii ivvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_144654335_   4391 TATTCAATAAATAATGCCAGGATAACTGGCTAGCCATATGCAGAAGATTG 4440
                          v     i    ii   ii   i      v  ?   i     i    v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_144654335_   4441 AACCTGGACCCCTTCCTTACGACATACACAAAAATAAACTCGAGATGGAT 4490
                           vi         v   i  iv    i        v     i i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_144654335_   4491 TGAGGACTTAAATGTAAAACCCAAAACTATGAAAACCCTGGAAGACAACC 4540
                         ii?i   i         i v i        i   vi i i     v   v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_144654335_   4541 TAGGCA-ATACCATTCTGAACATAGGAACT-GACAAAGATTTCATGACAA 4588
                             ?i- v i v iv   v v i  --i - i   v i    v iivv 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTTAGATA 595

  chrX_144654335_   4589 AGACAGCAAAAGAAACTGCAAGAAAAGCAAAAATTGACAAATGGGATCTA 4638
                         v    v      v vvv    v     v      v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_144654335_   4639 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTAAA 4688
                           i   v v  i i   i  ii vv    i  v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_144654335_   4689 TAGAAAACCTACAGAATGGGAGAATTGTTTTTCAAACTATTCATCTGACA 4738
                         v   v    i              vvvv   v    ii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_144654335_   4739 AAAGTCGAATATGCAGCAT-TGTAAG--------ATAATTAAACAGATAT 4779
                          ii v vvi   v   v  - i   i-------- i  i v  i -   v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA-ATAA 794

  chrX_144654335_   4780 GCAGAAAAAAAGC---ATTAAAAAGTGGGCAAAGGACATGAA----CACT 4822
                         iv   v   v i ---   ?    i           iv    ----  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_144654335_   4823 TTTCAAAAGAAGACATGTG--TGGCCAAGAAGCATATGAAAAAA-GCTCA 4869
                          i  v        i  iii--       v     i       i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_144654335_   4870 ATATCACTCATTGT 4883
                          i    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (146 / 92)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.07 (29 / 14)  


2447 27.96 2.71 0.99  chrX_144675666_144680381.rev     3030  3841 (875)    L1M4_orf2#LINE/L1        4   829 (79)  

  chrX_144675666_   3030 AAAACCATACTATGCTCATGGACTGGAAGAATCAACATCATAAAAATGAC 3079
                            ivi  v i   i       i       v i  i  ii v  i   i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_144675666_   3080 CATACTCCCCAAAGCAATCTACAGATTGAGCACAACTGCTATCAAATTAC 3129
                         v            vii           v i i   iiv        v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_144675666_   3130 TAATATCATTTTTCACAGTATTAGAAAAACAACAATGTTAAAGTTTACCT 3179
                         i iivv v     ii   v v v  v  i --ii  vi    i  i iv 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGC--TGATCCTAAAATTCATAT 151

  chrX_144675666_   3180 GGAACCAAAAAAGAGCTTGAATAGCCATAGCAATCTTAAGCAAAAAGAAC 3229
                             viiv  ii  v iv         v i       i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_144675666_   3230 AAAGCCAGAGACATAGCATTACCTGA---CATAAATTATATTACAAGACT 3276
                             iii   ivv vi  i v  ii ---  -   i -  i     ii  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCA-AAACT-TACTACAAAGCT 249

  chrX_144675666_   3277 ATAGTAACCAAAACAACATCATACCGGTACAAAAATAGACACATAGGCCA 3326
                          i     i   i   iii vi   i  i i  ii       i    ii  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_144675666_   3327 ATGGAACAGAATAGAGAACACAGAAATAAAGCCAAACACATAAAACCACC 3376
                               i     v    iiv          v   v   iv  viii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_144675666_   3377 TGATCTTTCACAAGGTCGACAAAAATAAACAATGGGGATAGGACACCCTA 3426
                             i  iv      vi v   i vi vv         v  i i vi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_144675666_   3427 TTCAATAGATTGTGCTGGAAAAAATTGGCTAGGCATATGCAGAAGATTGA 3476
                              i i  v       i v  -i   v  ?v  i     i    v   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGA 448

  chrX_144675666_   3477 AACCCGGCCCCTATCACTCACCATATACAAAAATCAAGTCAATATTGATT 3526
                          iiiv i      i v v                i  v    v  v   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_144675666_   3527 AAAGACTTAAATGTAACACCTGAAACTATAAAATTCT-AGAAGAAAATCT 3575
                          ?    i         v v  i           i   -         iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_144675666_   3576 AGAAAAAACTTCTCCTGGACTTGGGCCTAGGCAAATAATATAT-AACTAA 3624
                           i?iv  v ii  v  iv      i-       - ii v v - iv  v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAA-TGGTTTCTTAGATAT 596

  chrX_144675666_   3625 GACCTCAAAAGCAAATGCAGCAAAACAAAAA-TAGGCAAATGAGACTT-- 3671
                            vi        v v   i     v     -   ii    vi     --
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_144675666_   3672 ----AACTAAAAGGATTCTGCACAGCAAAAGAAATAATCAACAGAATAAA 3717
                         ----  i     iv-  i  ii vv    i  v iv     v i i i  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_144675666_   3718 CAGATAATCTACAGAATGGGAGAAAATATTTGCAAATTATATATCTGACC 3767
                         v   i  i i                           i          iv
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_144675666_   3768 AAGGACTAATATTCAGAATATTCAAAGAGCTCACACAACTCAACAGGAAA 3817
                          i     vi   i        vi     i   vi         i iv   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_144675666_   3818 AAAATA----------TTTAAAAATGGGCAAAAG 3841
                           i i ----------  ?             i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.62 (138 / 85)
Gap_init rate = 0.02 (13 / 826), avg. gap size = 2.31 (30 / 13)  

 405 18.09 1.06 1.06  chrX_144675666_144680381.rev     4132  4225 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_144675666_   4132 AAAAGTGGGTACAAGTCATGAAGAGGCATTTCTCCAA-GAAGACATGCAA 4180
                             i    i v i viv    v  i           -     i  i   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_144675666_   4181 GTGGCAAACAAACACGTGAAAAAAATGCTCAACATCACTCATCAT 4225
                         i    v  i  i   i      i -            ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.00 (2 / 2)  


3035 24.56 1.11 1.00  chrX_144681019_144685243.rev     2832  3735 (490)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_144681019_   2832 AAAAATAACTACAAGCTCATGGATAAGTAGAATCAATATTGTTAAAATGG 2881
                            i   v i-  v i        vi v   v i           i    
  L1M4_orf2#LINE/      4 AAAGATATCC-CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_144681019_   2882 CCATACTGCC-AAATGCAAGTTACAGATTCAATGCTATTCTTATCAAAAT 2930
                          v     v  -    -ii vi           i  v  i i         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_144681019_   2931 ACCAACAACATTTTTCACAGAATTAGAATAAACT-ATTCTAAACTTCAGA 2979
                         v   i vi v     ii     v v - i  i  -  i     v    v 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCATA 150

  chrX_144681019_   2980 TGGAACCAAAAAAAGAGCCC-GTATAGCCAAAGCAATTCTAAGCACGAAG 3028
                              -- viv  i ii   - v         i    ii i iv v    
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_144681019_   3029 AACAAAGCTGGAGGAATCATATTTCCCAATTTCAAACTATACTACAAGGC 3078
                                i       v   i i              viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_144681019_   3079 TACAGTAATAAAAACAGCATGGAACTGGTACAA--ATCAGACACATAGAT 3126
                                  v  i    ii   v     i i  --  -     i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGAT 297

  chrX_144681019_   3127 CAATGGAACAGAATAGAGCACCCAGATATAAAGCTATACACCTACAACCA 3176
                                 i     v   vii     v     v i     ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_144681019_   3177 CCTTATTTTTGACACAGTTGACAAAAACAGGCAAAGCTGAAAGAAATTTA 3226
                         vi v     i    vi v  v   i v  vv   v vv       vvv v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_144681019_   3227 TATTCAATAAATGGTGCTGGGATAACTGGTGAGCCATATACATAAGATTT 3276
                          v     i              i      vv ?   i  i  v    v v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_144681019_   3277 AATATGGACCCCTTCTTTACACCATATACAAAAATCAACTCAAGATGGAT 3326
                           vv         v i i                 i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_144681019_   3327 TAAATAATTAAATATCAAACCTAAAACTATAAAAACCCCT-GAAGAAAAC 3375
                         i ? v vi     i v i v              - i i -         
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chrX_144681019_   3376 CTAGGCA-AAACCATTCTGGACATAGTTTTCAGCAAAGACTTCAT-GATG 3423
                         v    ?i-   i -   vv   v v vv  vi    v ii   v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chrX_144681019_   3424 AAGATACTGAAAGCAATTGTAACAAAACGAAAAATCGACAAATAAGACCA 3473
                          v  i  ii      vvv i       vi      v  i    vi   iv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_144681019_   3474 AAGTAAAACAAAGAGCTTCCACACAGCAAAAGAAACTATCAAGAGAGTAA 3523
                         v vi    iv  i i   iiiii vv    i  v          i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_144681019_   3524 ACAGACAACCCAGAGAATGGGAGAAAATATTTGCAAAATATGCATCTGAC 3573
                          v          v                        vi  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_144681019_   3574 AAAGGTCTAATATAAAGAATCTATAAGTAACT-TAAAGACTTAACAAGCA 3622
                           i  v  vi   vv     v     iv    - v vi   i  i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_144681019_   3623 AAA-ACTAACAACCCCATTAAAAATTGGGCAAAGGACATGTACAGACATT 3671
                            -  v  i     v   ?    v           iv  v i       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_144681019_   3672 TCTCAAAAGAAGACATATATGTGGCCAACAAATACATGGAAACATACTCA 3721
                             v        i   i vi       i  ii     i   v  i    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_144681019_   3722 ATATCCCTAATCAT 3735
                          i   v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (114 / 104)
Gap_init rate = 0.02 (17 / 905), avg. gap size = 1.12 (19 / 17)  


1663 28.35 6.47 1.29  chrX_144704656_144706528      686  1380 (493)    L1M4_orf2#LINE/L1      178   908 (0)  

  chrX_144704656_    686 AAAAGAATTTGGAAAA----GAATACAGTTGGAGGAATCTCTTAAT--CC 729
                             v   i v     ----   i v          --   vi v --  
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA--CTCACACTTCCC 225

  chrX_144704656_    730 AATATTGA--CTTATTATATAGCTAGTACAAGTAAGACAGCATAGTATTG 777
                            v ii --    i  i v     vvii  vi       ii i   i  
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chrX_144704656_    778 CTGGATGGTTAGACACATTGGTCAATAGAATGGAATAGAGAACAAAGAAA 827
                         viiv v  v      i  v i     i    i    v    iivv     
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_144704656_    828 TAGACCAA-A-ATTT--GCTCAATT-----TTGACAAAACTGCAAAAGCA 868
                           i   v - -    -- v      ----- i     iiv   v  ii v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_144704656_    869 ATTAAATGGAAGAAAGATAGGTTTTTCAACAAATGCTGTTGAAGAAATTG 918
                            v     iii  ii    vi             v  i  iiiv  i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_144704656_    919 GACATTTATAGGAAAAAAAA-GATTTTGA---CCTAATCCTTACTTCTTA 964
                           i ?ii i v v    i  -  vv   i---    --   i  vi v  
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA--CCTCACACCATA 473

  chrX_144704656_    965 TACACAAAGTCACTCAAAATCTATCACAAAATTATATGTAAAATGTAAAA 1014
                             v   v v         vv    ? i vi  v      i vv     
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_144704656_   1015 GTTTAGGA------AAATAAAACATAGAAGAAAATCTTTGAGATCTAGGA 1058
                         v v  ii ------i  v         i? v       i v  i  v  i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_144704656_   1059 CTAGGCCAGTAATT-CTTAGACTTAACATTGCAAACAAGATCCATAAAA- 1106
                         i     - i ii  -      iv i   iiiv  i  vi v v i    -
  L1M4_orf2#LINE/    574 TTAGGC-AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_144704656_   1107 AGAAAATTGATAAATAAAACCCCATCAAAATTATAAACCTTTGTTCTGTG 1156
                          i     v       vii  ii           v    i     v  - v
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT-TC 671

  chrX_144704656_   1157 AAAGAAT-CTATGAAAAGGGTAAAAAGACAAGCTACAG------------ 1193
                             i i-    v  i ii  i         v i    ------------
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_144704656_   1194 ---TTACAAACCCTATATTCAACAAAGGTCTACTAGTATCTAGAATGTAT 1240
                         ---  i    i v     iii i  i  ---   v     i     i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGG---ACTTGTATCCAGAATATAT 768

  chrX_144704656_   1241 AAAGGACTCTTAAAACTCATCAGTATAAAAATCTACAATCCAATTATAAT 1290
                             i       v      vi i  v   i ivv i  i      ?v  v
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_144704656_   1291 ATAGGCAGAGGACATGAACAGACAATTTACTGAAGAGGATATATAAGTGT 1340
                           i    i    iv    i     v  iv ii    i      i  i  v
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_144704656_   1341 CAAAAATATACATGAAAACACATTTAAAATTATTAGCCAT 1380
                          v  v vii         v iii i  v  i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (115 / 78)
Gap_init rate = 0.03 (19 / 731), avg. gap size = 2.84 (54 / 19)  

 223 21.54 1.54 0.00  chrX_144704656_144706528     1802  1866 (7)    L1M4_orf2#LINE/L1      466   531 (377)  

  chrX_144704656_   1802 ACAACAAATAGAAAAATCAACTCAAAA-AGATTAAAGGTCTAAAGGTAAG 1850
                            v  v   v      i         -i   i ?  ii     v     
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_144704656_   1851 TCCTGAAACTGTAAAA 1866
                         vv  i     i     
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAA 531

Transitions / transversions = 1.17 (7 / 6)
Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1)  


2674 24.35 4.85 1.77  chrX_144742572_144744409      500  1345 (493)    L1M4_orf2#LINE/L1       37   908 (0)  

  chrX_144742572_    500 AATATTGTTAATATGTCCATACTATACAAAGCGATCCACAGATACAATGC 549
                                    v   v v     viv    vi    i      v   i  
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 86

  chrX_144742572_    550 CATCCTTACCAAAATTCCAATGACATTTTTCATAAAAATTAAAAA----A 595
                         v    i  i      i   iivi v     iii i     i v  ---- 
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chrX_144742572_    596 TCCTAAAATTTGTATGGAAACACAAAGG-CCCTGAATAGCCAATGTAATT 644
                                   ii        ii   i  -   v          vii   i
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chrX_144742572_    645 TTGAGTAAGAAGAACAAACCCTTGGTATA-TCACATTTCTTAA------- 686
                             iv            v--    viv -     i   ii  -------
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAG--TTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_144742572_    687 ACTACATTACAATGCTACAGTAATAAAAACAGTATTGTACTATCATAAAA 736
                            -i i     v           v  i     i v     iv     ii
  L1M4_orf2#LINE/    235 ACT-TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_144742572_    737 ATAGACACGTAGACCAATGGAACAGAA--GAGA-TCACAGAAATAAACCC 783
                                ii    i        i    --    -  -             
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAAACCC 332

  chrX_144742572_    784 ACGTATGCAAAGTCAACTAATCATTGACAAGGACACCAAGAATACATAAG 833
                          iii  vi vi     i i  iv i       iii      vi ivi  v
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_144742572_    834 GAGGAGTGAATACACT----AATAA-TGGTGTTGTGAGAACTGAATAGCC 878
                          i   iv     vv  ----  i  -     i  v  v     i   ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_144742572_    879 ACATGCTAAAGAATTAAAATGAACTCTTATCTTATACCACGCACAAACAT 928
                               v       v  iv  i  i i  i  i i    iii     v  
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chrX_144742572_    929 CAATTCAAAATGGATTAAATACTTAAACATAAGA-CAAAATACCTTAAAA 977
                         i  i           i ? v  i    ii     - v   -  iv     
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA-ACTATAAAA 531

  chrX_144742572_    978 CTGCTGCTGGAATAAAACACAGAAAAAAGTTCTTTT-ACATTGTTCTTGG 1026
                           -  -- i   v      i  i?iv  i ii iv -  v   vvi v  
  L1M4_orf2#LINE/    532 CT-CT--TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_144742572_   1027 CAATGATTTTTTTTTTTAGA-ACGACCCTAAAAGCACAAGCAATAAAAGT 1075
                              i   i  -----   - i   v i              i     v
  L1M4_orf2#LINE/    579 CAATGGTTTCTT-----AGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_144742572_   1076 AAAAGTAAA-AAGTGAGATTACGCCAAACTGCAAAGCTTCTGCACAGCAA 1124
                             i  i -  i vi  i v ii    v vv   i   i  ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_144742572_   1125 AGGAGACAATCCACTCATTGAAAAGACAA---AC----TGG-----AATA 1162
                             v  v   v vvv v           ---  ----   -----    
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_144742572_   1163 ATCGCAAACCATATATCTGATAATGAGTTGATATCAAAAATATATAATGA 1212
                         v i     i              v iii vi    v i         v  
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_144742572_   1213 ACTTATATAACACAATAGCACAAAAAACAAACAG----ATTAAACAATGG 1258
                            iv  i   v     ii -    i     i i----   ?  v     
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATA-AAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_144742572_   1259 GCAAAGAATCTGCAGAGACAATTTTCCAAAGGAGGCATTCAGGTGGCTAA 1308
                               i  i  v v     v  i       i  ii  v  ii    i  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_144742572_   1309 AAAGATAAGTGAAAAGATGCTCAACATCATGAATCAT 1345
                         v   -i vi                    ????????
  L1M4_orf2#LINE/    873 TAAG-CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (126 / 76)
Gap_init rate = 0.03 (25 / 872), avg. gap size = 2.24 (56 / 25)  


2867 27.05 3.30 0.34  chrX_144752121_144755989     2497  3376 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_144752121_   2497 GACAAATATTCCATGTTCATGGATTAGAATAATTAATAGTGTTAAAATGT 2546
                           v i    i               i   v v      v      i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_144752121_   2547 TGATACTACTGAAAGCAATCTACAGATTCAATGCAATCTATATCAAAATA 2596
                         ii     v iv   vii              i      iv         v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_144752121_   2597 CCAGTGAAATTCTGCACAACAATTGAAAAACCAATTCTAAAATTTATGTG 2646
                             ivivv  i vii  iv      v  i ii  i        i  i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_144752121_   2647 GAATCACAAAAGCCCCAGAAAGGTCAAAGCTGTCTTAAGCAAAAAGAACA 2696
                            vii   ii v       vi i    i vi    i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_144752121_   2697 AAACTGGAAAAATCATATTACCTCACTTCAAATTATACTACAGAGCTATA 2746
                           ii    ii v   i i v  iv i      viv       i     i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_144752121_   2747 GTAATCAAAACTGCATGGCAGTGGCATAAAAATAGACAAATAGACCAATG 2796
                                 i  v ii   i v        ii       v     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_144752121_   2797 GCA---AATGAACAACCCAGAAACAAATCCACCCACCCTCAGTGAACTCA 2843
                          v ---   vi v ii       i   i   iv  iiivii  v  i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_144752121_   2844 TTTTTAACAAAGTTGCCAAGAACATACCTTGAAGAAAGAACATTGTCTTC 2893
                             ii    i v        v   v vv  ii       i v v i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_144752121_   2894 AATAAATAGTGCTGGGAAAACTGGAT--CTATATGCAGAAAAATGAGGCT 2941
                           i    i         v        -- i i     i  i     i i 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_144752121_   2942 AGAACCA-ATCTCTTACCATATACAAAAATCAAATCAAAATTTATTACAG 2990
                         i  v  v- i   vi               i  v       vv  i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_144752121_   2991 ACTTAAATTTAAGATCTCAAACTATGAGTCTACTAGAAGAAAACATTGGG 3040
                           i     v     v  v       i iv  vi             v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_144752121_   3041 GAAACTCTCTAAGACATTGATCTAGGCAAAAATTTCTTAAGTCATAACTC 3090
                          v  v   iiiv   v   ivi       vii       ii -  i  v 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACAC 601

  chrX_144752121_   3091 CCAA-GCATAGAAAACCAAAGAAAAAACTGGACAAGTGAGATTACAT-AA 3138
                          v  -   i iiv   v          - i  i  i vi  i v   -  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAA 650

  chrX_144752121_   3139 AGTTAGAAAGCTTCTGCACAGTGAAGAAAACATTCAACAAAGTGACGATG 3188
                          i   i   -   i  ii vvii   i v  vv    v       vi vi
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_144752121_   3189 CAACCCTCTGAATCAGGGAAAATATTTATAAACCACCAATTTGACAAGGG 3238
                               v v    vi i          ii   i  ivv  i   i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_144752121_   3239 ATTAATAACCAGAATATATAAGGAGCTCAAACAATTCTATAG-GAAAAGA 3287
                          i vi  v             i  i   vv    i  v   i-i      
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_144752121_   3288 T-------CTAA-------ATGGACAAAAGATTTAAA-----ATT-ATCA 3317
                         i------- i  -------    i    i     i  -----   -v  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_144752121_   3318 AAAGTAGACATACAAATGACAAACAGGTATATGAAAAGGCACTCAAAATC 3367
                             v   i         i v  i i i i        iii     v   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_144752121_   3368 ACTGATCTT 3376
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.59 (145 / 91)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 2.46 (32 / 13)  


2266 25.52 5.86 2.21  chrX_144799202_144800961      500  1267 (493)    L1M4_orf2#LINE/L1      113   908 (0)  

  chrX_144799202_    500 TTTTTACAGAATTAGAAAAAGCT-ATTCTAAAATTCATATGGACCAA--- 545
                              i     v v  v  -   -  i                --  ---
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATGGA--AATGC 159

  chrX_144799202_    546 AAAAGATTCCAATTAAACCAAAGCAATCCTAATAAAAAAGAGCAAAGTTG 595
                           ii  ii vi v  i-     i     i i v   i    i        
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAG-CCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_144799202_    596 GAGGCATCATACTACCAGACTTCAAACTACACAACAAGGCTACAGTAACC 645
                             vv   i   v  vi i      vivi  v    i          i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_144799202_    646 AAAACAGCATGGCACTTGTACAAAAACAGACACACAGACCAATGAAACAG 695
                           i    ii   i   v i i  ii i     i i   i     i  i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_144799202_    696 ATTAGAGAACCCAGACCTAAAGCCACACACCTACAACCATCTGATGTTTG 745
                          v v    ii     vv    v   i   ii  iiii  vi    v  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_144799202_    746 GCAAAGCCAACAATAATAAGCAATGGAGAAAGGAATC-CCTATTCAATAA 794
                         i   i viiv   v vi vv      i     -   v-i  v     i  
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTTTTCAACAA 407

  chrX_144799202_    795 ATAGTGTGAGGATAGCTAGCTAGCCATATGCAGA----TGAAACTGGACC 840
                           i   ivi   i i  i v  ?   i     i ----    ii      
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chrX_144799202_    841 CCAACCTTTCACCATATACAAAAATTGACTCAAGATGGATTAAAGACTTA 890
                           v    iv                 i      i      i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_144799202_    891 AATGTAAGACCTCAAACTGTAAAAATCCTTAAAGAAAACCTAGG---AAA 937
                                  v  v     i     v  i vi        v    ---   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chrX_144799202_    938 TATCCTTCTTTATTTCAGACTTGGCAAAGAGTTTATGGTTAATTCCTCAA 987
                          ---    v v ii ii ii v     v iv  iv i v  vvv vi   
  L1M4_orf2#LINE/    558 T---CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_144799202_    988 AAGCGATTGTAACAAAA----AAATTGACATGTGGAAC--CAT----ATT 1027
                             ivvv i       ----    v  i vi v i  --   ----   
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_144799202_   1028 AAA--CTACAGAGCTTCATCAAGGCAAGAAAAAACTATCAAGGGAATAAG 1075
                            --  viv v      --    ------- v         ii i i i
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCA--AAGG-------ACACTATCAAGAAAGTGAA 695

  chrX_144799202_   1076 CAGACAACTTATAGAATGGCAGAAAATATTCACAAACTATGCATCTTACA 1125
                         v       ii i       v          ii    ii  ii    v i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_144799202_   1126 AAGGTCTAATATTCAGAATCTATGAGGAAC------AAGCCAA------- 1162
                          i  v  vi   i      v   i i    ------  vi   -------
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_144799202_   1163 -AAACAAA---CCCCATTAAAAAGTGGGCAAAG----TACACAAACACTT 1204
                         - i     ---   v   ?    i         ---- iv i i   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_144799202_   1205 CTCAAATGAAGACATACAAGCAGCCAACAAATATATGAAAAAATGCTCAA 1254
                            v  v     i      iii     i  ii i       i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_144799202_   1255 CATCACTTATTCA 1267
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (123 / 70)
Gap_init rate = 0.03 (20 / 796), avg. gap size = 3.10 (62 / 20)  


2616 26.79 4.35 3.01  chrX_144903719_144912157      850  1745 (6694)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_144903719_    850 TGGAAAAACATTTCATGCTCATAGATTGGAAGAATCAATATGATTAAAAT 899
                               i i  ii    i    i          v i     vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_144903719_    900 GGTAATACTGCCCAAAGCAATTTATAGGTGTAGTGCTATTCCTATCAAAC 949
                           i      v      vii  i  i  i vi ii  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_144903719_    950 TACCAATGACATTCTTCACAGAACTAAAATAA-AAACT-ATTTTAAAATT 997
                          v   iivi v  i  ii     v ---- i -  i  -  ii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT----TGACAAGCTGATCCTAAAATT 146

  chrX_144903719_    998 TATGACTGAAAACCAAAGCAAAAAAGAGCTCAACTTAGCCAAAGCAATTC 1047
                         i  i--  i   i----    iii --- i  ivv        i    ii
  L1M4_orf2#LINE/    147 CATA--TGGAAAT----GCAAGGGA---CCCAGAATAGCCAAAACAATCT 187

  chrX_144903719_   1048 TAAGCAAAAAAAA--AGGCTGAAGGCATCACACTATCCAACTTCAAACTA 1095
                          i iv  i  i  -- i i  i   vv       vi    i      viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_144903719_   1096 TACTACAGGACTACAGTAACCAAAAAAAGTATGGTACCGGCACAGAAACA 1145
                                iii         i   i v -  i      i    i iii i 
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACA-GTGTGGTACTGGCATAAGGATA 286

  chrX_144903719_   1146 GATACATAGATCAATGCAACAGAATAGAGAGCTCAGAAATAAAGCCACAA 1195
                           i i           v  i     v     ii          v   i v
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_144903719_   1196 ACCTACAACTGTCTGATCTTTGACAAAGCTGACAAAAACA---------- 1235
                          ii  iiiiiivi    i  i     i v  v   i v  ----------
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_144903719_   1236 -AAGA-CACCCTATTCCATAAATGGTGCTGGGATAACTGGCTAGCCATAC 1283
                         -    -i vi  v   v i              i      v  ?   i i
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_144903719_   1284 ATAGAAGATTGAAACAGGATCCTTTCCTTATACCATATGCAAAAATAAAT 1333
                         ii i    v    iiv   i  i v   i i       i       v  i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_144903719_   1334 TCAAGATGGATTAAAGACTTAAATGTAAAACCCAAACCTATAGAAACCCT 1383
                             i      i ?    i         i v i   v     i  vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_144903719_   1384 GGAAGACAACCTAAGCG-ATACCATTCTGGACTTAGGAATGAGCCAAGAT 1432
                         i     v   v  i ? - v i -   vv   i v  iv ii  v v i 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_144903719_   1433 TTC------ATGACAAAGTTGTCAAAAGCAATCA--CAACAGCA-AAAAA 1473
                            ------      ------i        --  --     iv -     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACA------CCAAAAGCA--CAAGCAACAAAAGAAAAA 627

  chrX_144903719_   1474 AT-GATAAGTTGAATCT------AATTAAAGAGCTTCTG-----CAGAGA 1511
                           -     i   i ii ------       i -   i  -----  --- 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCA---A 673

  chrX_144903719_   1512 AAAAAACTATCAAAAGAGTAAGCTTACAACCTACAGAATGGGAGAAAATA 1561
                          ii v        i i   i ivvv      i                  
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_144903719_   1562 TTTGTAAACTATGCACCTGACAAAGGTTTAATATATACCATCCATAAGTA 1611
                             i   ii  ii i    i  i  vi vi   vi vv  vi    iv 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_144903719_   1612 ACTTAAACATATTTATAA-GAAAAGACATACAATTCCAGTAAAAAGTGGG 1660
                            ivv   vv iv    -i        v i  ii v v ?    i    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_144903719_   1661 CAAAGGACATGAACAGACACTTTTCACAAGAAGACATACATGTGACCAAC 1710
                                iv    i     i  i  vv       i     vi  i    i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_144903719_   1711 AAGCATATGAAGAAAAGCTTAATATCACTGATCAT 1745
                              i     i i v   i  i    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.23 (163 / 73)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.87 (66 / 23)  

1191 27.81 1.69 1.69  chrX_144903719_144912157     6726  7081 (1358)    L1M4_orf2#LINE/L1        1   356 (552)  

  chrX_144903719_   6726 TGGAAGAATGTTCCATGCTCATGCATAGGAAGAACCAATATCGCAAAAAT 6775
                              ii  i i     i     v  v      vii     i iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_144903719_   6776 GGCCATACTGCCCAAGGTAATTTATAGATTTAATGCCATCCCCATCAAGC 6825
                            v     v     iv i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_144903719_   6826 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6873
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_144903719_   6874 TACGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 6923
                           i    viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_144903719_   6924 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTACC--CTACAAG 6971
                                i      vv    i  v  ii i      --  i--      i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAA 246

  chrX_144903719_   6972 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 7021
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_144903719_   7022 CCAATGGAACAGAAC--AGAGCCCTCAGAGATAACACCATGTATCTACAA 7069
                         i        i    i--    i  --   i    vv    ii  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chrX_144903719_   7070 CCATCTGATCTT 7081
                         i  vi    i  
  L1M4_orf2#LINE/    345 TCAATTGATTTT 356

Transitions / transversions = 2.54 (71 / 28)
Gap_init rate = 0.02 (7 / 356), avg. gap size = 1.71 (12 / 7)  

2000 25.45 0.72 0.54  chrX_144903719_144912157     7389  7946 (493)    L1M4_orf2#LINE/L1      350   908 (0)  

  chrX_144903719_   7389 TGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAT--TCCA 7436
                             i  i     ivv  v   i v  vvv           i  --  --
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-- 397

  chrX_144903719_   7437 TATTTAATAAATGGTGTAGGAAAAACTGGCTAGTCATATGTAGAAAGCTG 7486
                          v  i  i        iv  i v      v  ?i  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_144903719_   7487 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 7536
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_144903719_   7537 TAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 7586
                         i ?    i  v    v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_144903719_   7587 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 7635
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_144903719_   7636 AACACCAAA-GCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 7684
                         i        -   vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_144903719_   7685 TTAAACTAAAGAGCTTCTGCACAGCAAAAGGAACTACCATCAAAGTGAAC 7734
                          i   v v  i i   i  ii vv    i iv    i  vv        v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_144903719_   7735 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 7784
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_144903719_   7785 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 7834
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_144903719_   7835 AAACAAACAACCCCATCAAAAAGTCGGCAAAGGATATGAACAGACACTTC 7884
                          i     i     v  i?    i v          v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_144903719_   7885 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCACC 7934
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_144903719_   7935 ATCACTGGCCAT 7946
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (77 / 61)
Gap_init rate = 0.01 (5 / 559), avg. gap size = 1.40 (7 / 5)  


 449 11.03 20.59 11.03  chrX_144919815_144921662.rev      478   613 (1235)    L1M4_orf2#LINE/L1       99   247 (661)  

  chrX_144919815_    478 AAACTCAGCTCACTTT----CAGAAGCTATGGGCAAGCTGATCCTAAAAT 523
                           v i     vv    ----     ---  v i                 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAA---ATTGACAAGCTGATCCTAAAAT 145

  chrX_144919815_    524 TTATAATGAAAATGCAAGAGACCCAGAATAGCCAAAATA----------- 562
                          i   -  i         i                  i -----------
  L1M4_orf2#LINE/    146 TCATA-TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_144919815_    563 -------------GGAGGATTCACACTGTGCAAAGGGTGAGTAAGCTCAA 599
                         -------------      i       viv   -------- ---i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAA--------T---TTCAA 233

  chrX_144919815_    600 AACTTACTACAAAG 613
                                       
  L1M4_orf2#LINE/    234 AACTTACTACAAAG 247

Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.04 (6 / 149), avg. gap size = 7.17 (43 / 6)  

1939 17.79 27.76 0.89  chrX_144919815_144921662.rev      796  1357 (491)    L1M4_orf2#LINE/L1      196   908 (0)  

  chrX_144919815_    796 AAGAACAAAGTTGGATGGA---GGACTTCTCAAGTTAATTCAAAACTTAC 842
                                        -   ---iv     i   -  ---           
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGA-GGACTCACACTTCCCAA-TT---TCAAAACTTAC 240

  chrX_144919815_    843 TACAAAGCTATAGTAATCAAGACAGTGTAGTACTAGTATAAGGATGGACA 892
                                   i                 i     i i        i    
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_144919815_    893 TATAGACCAATG-AACAGAATTGAGAGTACAAAAATAAATCCATACATCT 941
                               i     -  i            v  i       i        i 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_144919815_    942 GTTTGTGATTAATTTTTGACACAGGTGCCAAGACCATCCAATGGTAAATG 991
                         i vvvii   i     i    vi              i      vi  v 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_144919815_    992 TATAGTCTTTTTATAAAATGGCGCTGGGACGGTTGGATACCTATATGCAA 1041
                         v          i vv      i        iii      ? i i      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_144919815_   1042 GAGAATGAATTTGCACCC-------ACACC-------------------- 1064
                         i        v   v    -------     --------------------
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_144919815_   1065 -------------------------------------------------- 1064
                         --------------------------------------------------
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_144919815_   1065 -----TATAGG--------------------------------------- 1070
                         -----i     ---------------------------------------
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_144919815_   1071 -----------------------CAACAAAACAAAAACTAGATGCATTAG 1097
                         -----------------------        v     v     iv   i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_144919815_   1098 ACTTGATTAACATTTAAAACTTTTGTGCATTAAAAG-CACTATCAGGACA 1146
                             v  i  v   v             v i   i -        i  v 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_144919815_   1147 GTGGGAAGACAACTCACAAAATGGTAGAAA-TATTTGCAAATCATAC-TT 1194
                            ii        i    i     v     -               i- i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_144919815_   1195 T-ACAGAGGTTTAATATCTAGAATATATAAATAACTCCTATAACTCAACA 1243
                          - i ii  vi vi    i            v     i  i       i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_144919815_   1244 ACATAAACACAA----TCAAATTAAAACATAGGCAAATAATTTGAATAGG 1289
                          i v   v    ----i v    ?   v  i      vi          i
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_144919815_   1290 TACCACAACAATGAAGATATACAAATAGCTAATAAGCCAATGAAAAGGTG 1339
                         i iiv vv   v              i  i       vv        i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_144919815_   1340 CTCAGCATCATTAGTTAT 1357
                             i     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (62 / 36)
Gap_init rate = 0.02 (13 / 713), avg. gap size = 12.38 (161 / 13)  


2516 26.57 1.09 0.54  chrX_144997104_145000463.rev     1335  2068 (1292)  C L1M4_orf2#LINE/L1   (0)   908   171  

C chrX_144997104_   2068 AATATCCAAGACAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACGC 2019
                             v    i      i i ivv i          i      vv    i 
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

C chrX_144997104_   2018 TACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGG 1969
                          v  ii i      viv        i          i   i    ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

C chrX_144997104_   1968 TACTGCTACCAAAACAGAGATATAGACCAATGGAACAGAAC--AGAGCCC 1921
                              vi iv ii i   v       i        i    i--    i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

C chrX_144997104_   1920 TCAGAAATAATACCACACATCTACAACCATCTGAACTTTGACAAACCTGA 1871
                         --        vv   i    i  iiii  vi   vi  i     ivv  v
  L1M4_orf2#LINE/    321 --AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

C chrX_144997104_   1870 CAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGG 1821
                            i v  vvv           i  vvi  v  i  i             
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

C chrX_144997104_   1820 AAAACTGGCTAGCCATATGTAGATAGCTGAAACTGGATCCCTTCCTTACA 1771
                          v      v  ?   i   i i viiv    ii    i    v   i   
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

C chrX_144997104_   1770 CCTTACACAAAATTTAATTCAAGGTGGATTAAAGACTTAAATGTTAGACC 1721
                           v  i      v    i    ii     i ?    i       v   v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

C chrX_144997104_   1720 TAAAACCGTAAAAACCCTAGAAGAAAACCTAGGCA-ATACCATTCAGGAC 1672
                               ii     vi i           v    ?i- v i -   iv   
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGAC 567

C chrX_144997104_   1671 ATAGGCATGGGGAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAAC 1622
                         v v  vv i  v  v ii   v ivv  vi            vvi     
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

C chrX_144997104_   1621 AAAAGCCAAAATTGACATGTGGGATCTAACTAAACTAAAGAGCTTCCGCA 1572
                              vv     v  i vi v   ii v ii   v v  i i   ii ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

C chrX_144997104_   1571 CGGCAAAAGAATCTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAG 1522
                          vv    i  vv   i  vv i      v  i     i            
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

C chrX_144997104_   1521 AAAAGTTTTACAATCTACGCATCTGACAAAGGGCTTATATCCAAGATCTA 1472
                             vv   i   vii iii      i  i  i   i      ii  v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

C chrX_144997104_   1471 CAAAGAACT--TA-AATTTA-CAAGAAAAAGATCAACCAACCCCATCAAA 1426
                         i        --  -  i i -i  v       -   vi     v  i?  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAA 816

C chrX_144997104_   1425 AAGTGGGCAAAGGATATGAACAGACACTTCTC-AAAGAAGACATTTATGC 1377
                           i            v    i     i     -        i  vi vii
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

C chrX_144997104_   1376 AGCCAACAGACACATGAAAAAATGCTCATCATCACTGGCTAT 1335
                         i     i ii          i       v     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (115 / 76)
Gap_init rate = 0.01 (9 / 738), avg. gap size = 1.33 (12 / 9)  

1922 25.70 9.82 2.30  chrX_144997104_145000463.rev     2045  2869 (491)    L1M4_orf2#LINE/L1       22   908 (0) *

  chrX_144997104_   2045 TGGCTTAGGATTGTCTTGGATATTATTAAAATGGCCATACTGCCCAAAGC 2094
                            v  i i -- v   i-     i    i     v     v      vi
  L1M4_orf2#LINE/     22 TGGATTGGAA--GACTTA-ATATTGTTAAGATGGCAATACTCCCCAAATT 68

  chrX_144997104_   2095 AATTTATAGACTCAATGCTATCCCTATCAAATTTCCAATGACATTCTTCA 2144
                         i  i  i   i    i  v            v i   iivi v  i  ii
  L1M4_orf2#LINE/     69 GATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG 118

  chrX_144997104_   2145 CAGAACTAGAAGAAACT-ATTTTAAAATTTATATGTACCAAAAAAAGAGC 2193
                              v v  v-  i  -  ii       i     v --  viv   i v
  L1M4_orf2#LINE/    119 CAGAAATTGAC-AAGCTGATCCTAAAATTCATATGGA--AATGCAAGGGA 165

  chrX_144997104_   2194 CCCA-AGTAGCCAAGGCAATCCTAAGCAAAAAAAAAAAAA---------- 2232
                             - i       ii     i i iv  i  i  v   i----------
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_144997104_   2233 ----------AA----AAAA--------AAAG-----------AAG---- 2245
                         ----------  ----    --------    -----------   ----
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_144997104_   2246 ----GTACTGGTACAAAAACAGACTAATGAAACAG-AAAACAGAATAGAG 2290
                         ----       i i  ii i    vv  ii v  i-ii  i     v   
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_144997104_   2291 ATCTCAGAAAAAAGACCACACACTTAGAACCATTTGGTCTTCAACAAAGT 2340
                          vii      v  iv   i   i   viii  v   i i   i    i v
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_144997104_   2341 TGACAAAACAAG-CAACGAGGAAAG----GTATTAGCATTCAATAAATGG 2385
                           v   i  v v-   i i      ----  v  ----     i      
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTT----TTCAACAAATGG 411

  chrX_144997104_   2386 TGCTGGGATAATGAGCCTGCCATATGCTGAAGATTCAAACTGGACCCTTT 2435
                                 i  ivi viv?   i    vi    v v  ii       i v
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chrX_144997104_   2436 CTTTACACCACATACAGAAATCGACTCAAGATGAATTAAAGACTTTAATG 2485
                          i i      i     i    ii      i   i  i ?    i v    
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_144997104_   2486 TAAAACCCAAAACTATAAAAAACCCTGA-AAGGCCACTTAGGCA-ATACC 2533
                            i v i            -- i  v -   ivv  v    ?i- v i 
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAA--CTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_144997104_   2534 ATTCTGAACATAGGAACAAGCGAAGATTTCAT-GATGAAGACACCAAAAG 2582
                         -   vvi  v v  ivi i  i v i    v -   - v           
  L1M4_orf2#LINE/    560 -TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAG 607

  chrX_144997104_   2583 CAATCA--CAACAAAAGCAAAATT-GATAAATGGGATCTAAT-AAAGCTA 2628
                           --  --         v    v -       v   ii v  -   ii  
  L1M4_orf2#LINE/    608 CA--CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_144997104_   2629 ACGATATTCTGCAAAACAAAGGAATCTATCAACACAGTTGAACAGAGAAC 2678
                          vi i-  i  iivvv       vv       v v   -   v   v   
  L1M4_orf2#LINE/    656 AAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAGT-GAAAAGACAAC 703

  chrX_144997104_   2679 CTAAAGAATGGGAGAAAATTTTTGCAAACTATGCATCGAACAAAGGTCTA 2728
                          i v               v        ii  ii   vi i  i  v  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_144997104_   2729 ATATTTAGCATCTATAG-GAACT--TA-AATTTA-CAAGAAAAA-----A 2768
                         i   ii  v  v    i-     --  -  i i -i  v     ----- 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_144997104_   2769 TAACCCCATTAAAAAGTGGGCAAGACACATGAA----CACTTTTCAAAAG 2814
                               v   ?    i       iiv iv    ----  i  i  v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_144997104_   2815 AAGACATACATGTGGCCAACAAAGCATATGGAAAAA-GCTCAACATCACT 2863
                             i     vi       i  -   i   i   i -           ??
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAA-GCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_144997104_   2864 GATCAT 2869
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.57 (127 / 81)
Gap_init rate = 0.04 (35 / 887), avg. gap size = 2.86 (100 / 35)  


2964 26.87 0.43 3.21  chrX_145015245_145021657.rev     4989  5922 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145015245_   4989 TGGAAGAACATTCCATGATCATGAATAGGAAAAATCAATATCGTGAAAAT 5038
                              ii i  i     v     i  v    i v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145015245_   5039 GGCCATATGGCCCAAGGTAATTTATACATTCAATGCCATCTCCATCAAGC 5088
                            v   ivv     iv i  i  i v      i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145015245_   5089 TACCAATGACTTTCTTCACAGAATTGGAAAAAAACTACTTTAAGTTCATA 5138
                          v   iivi i  i  ii     v v  ------------i   i v  -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA------------CAAGCTGAT- 137

  chrX_145015245_   5139 TGGAACCAAAAACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCGAATT 5188
                         -----  --------    i           viiv  ii  v  v    v
  L1M4_orf2#LINE/    138 -----CC--------TAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chrX_145015245_   5189 GCCAAGACAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACGCTACC 5238
                              i      i i ivv i          i      vv    i  v  
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chrX_145015245_   5239 TGACTTCAAACTATACTACAAGGCTAAAGTAACCAAAACAGCATGATACT 5288
                         ii i      viv        i    v     i   i    ii  i    
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_145015245_   5289 GCTATCAAAACAGAGATATAGACCAATGGAACAGAAC--AGAGCCCTCAG 5336
                          vi  v ii i   v       i        i    i--    i  --  
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AG 322

  chrX_145015245_   5337 AAATAATACCACACATCTACAACCATCTGATCTTTGACAAACCTGACAAA 5386
                               vv   i    i  iiii  vi    i  i     ivv  v   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_145015245_   5387 AACAAGAAACAGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAA 5436
                          v  vvv  ii       i  vvi  v  i  i              v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_145015245_   5437 CTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTCCCTCACACCTT 5486
                             v  ?   i   i i  iiv    ii    i    v         v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_145015245_   5487 ATACAAAATTTAATTCAAGATGGATTAAAGACTTAAATGTTAGACCTAAA 5536
                                 v    i    i      i ?    i       v   v     
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_145015245_   5537 ACCATAAAAACCCTAGAAGAAAACCTAGGCA-ATACCACTCAGGACATAG 5585
                           i      vi i           v    ?i- v i -i  iv   v v 
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTG 571

  chrX_145015245_   5586 GCATGGGCAAGGACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAA 5635
                          vv i     v ii   v iiv  vi            vvi         
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chrX_145015245_   5636 GCCAAAATTGACATGTGGGATCTAATTAAACTAAAGAGCTTCCGCACGGC 5685
                          vv     v  i vi v   ii v  i   v v  i i   ii ii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_145015245_   5686 AAAAGAATCTACCATCAGAGTGAACAGGCAACCTACAGAATGAGAGAAAA 5735
                            i  vv   i  vv i      v  i     i        i       
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_145015245_   5736 GTTTTACAATCTACCCATCTGACAAAGGGCTTATATCCAAGATCTACAAA 5785
                         vv   i   vii ivi      i  i  i   i      ii  v  i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chrX_145015245_   5786 GAACTTAAACAAATTTACAAGATAAAGATCAACCAACCCCATCAAAAAGT 5835
                              ivv    v iv i  v v     -   vi     v  i?    i 
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAAT 820

  chrX_145015245_   5836 GGGCAAAGGATATGAACAGACACTTCTC-AAAGAAGACGTGTATGCAGCC 5884
                                    v    i     i     -        ii ii viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_145015245_   5885 AACAGACACATGAAAAAATGCACATCATCACTGGCTAT 5922
                           i ii          i    v  v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.78 (34 / 9)  


2201 29.58 2.47 1.80  chrX_145040030_145041932      522  1410 (493)    L1M4_orf2#LINE/L1       14   908 (0)  

  chrX_145040030_    522 CATGTATTTGAATTGAAAGAATATATCAATATAAT-AAAATGGCCATTTT 570
                              viv  i    i    v ----i     vi -  i     v  vi 
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACT----TAATATTGTTAAGATGGCAATACT 59

  chrX_145040030_    571 TCTGAAAGCAATGCACAGATTCAATGCTATTTCTATCAAGCTACCAACGT 620
                         i iv   vii  vi          i  v  ii       iv v   i vv
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chrX_145040030_    621 CATTTTTCACAGAG-TCAAAAATAACT-ATTCCAAAAATCACA-GAAACC 667
                          v     ii    i- ii v  --i  -  i i    v   i - i  vi
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCATATGGAAAT 157

  chrX_145040030_    668 AAAAAAGAGTGTGAATACCCAAAGTAATCCTAAACAAAAAGAATAAAGCT 717
                         iv  ii  vivv     v     ii    i i  v  i     i    i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_145040030_    718 GAACATATCACATTACCTGACTTCAAACTATAGTATAAGGCTACAGTAAC 767
                          i vivv     i v  ii i      viv  v  i  i          i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chrX_145040030_    768 CAAAACAGCATGGTGGTGGTACAAAAACAGATACATACGCCAGTGGAACA 817
                            i    ii    iv   i i  ii i   i i   vii  i     i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chrX_145040030_    818 GAATGGAGAACCTGGAAATAAAGCCACACACATACAGCCACCTATTCTTC 867
                             v    ii ii        v   i   iv  ii i  vi iv i   
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chrX_145040030_    868 GACAAAGTTAACTATAATAAGCAATGGAAAAAGGACTCCCTGTTCCATAA 917
                              i v iv v v vi vv      ii    i ivvi  v   v i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chrX_145040030_    918 ATGGTTCTGTAATAGCTAGCTTAGCCATATGCAGAATAATTAAACTGGAC 967
                              v   vi i i  i v - ?   i     i  v   v  ii     
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGAT-AKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_145040030_    968 CCCCTACCTTTAGCCATATACAAAAATTAA-----GATGGATTAAAGGTT 1012
                            -     ivvi                 -----i      i ?  iii
  L1M4_orf2#LINE/    457 CCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_145040030_   1013 TAAATGTAAGACCCCCAAACTATAGGAATCCTAGAAGAAAACCTTGGAA- 1061
                                    v iv-        ii v  i           v v  ?i-
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTA-AAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_145040030_   1062 ACACCATTCTGGACATTGGCCTTGGGAAATAATGT-TTGACTAAGTCCTG 1110
                          v i -   vv   v    v-  i  v   ii v -  iiv  v v viv
  L1M4_orf2#LINE/    555 AAATC-TTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_145040030_   1111 AAAGGCAATTGCAAAAAA-AAAAAAAAAAATTGAAAACTAGAACCTAATT 1159
                            i   ----   iv  -    i       v  v  v v i  i v  i
  L1M4_orf2#LINE/    603 AAAAGCA----CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_145040030_   1160 AAACTAAAGAGTTTTTGCACACCAACAGAAACTATCAACAGCATCAACAG 1209
                            v v  i ii     ii vi   vi  v        v ivi v  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_145040030_   1210 ACAACCTACAGAATGGGAGAAAGCATTTGCAAACTATGCTTCCAATAAAG 1259
                               i               ii         ii  iiv  ii    i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_145040030_   1260 GTCTAATATCAAAAATCTATAATTAACTTAAACAAC-----AAGCAAAAC 1304
                          v  vi    v i   v     vv    ivv     -----  vv    v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_145040030_   1305 ACAA----CCCA-TTAAAACATGGGCAAAACACATGAATGGACATTTATT 1349
                             ----    -  ?   v         iv iv     i       v i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_145040030_   1350 GAAAGAACACCTACAATTGGCCAAGAAACATGTGAAAAAAATGCTCCACA 1399
                         v      v iv     v       v  i  ii      i -     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACA 897

  chrX_145040030_   1400 TCACTCATCGT 1410
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.35 (149 / 110)
Gap_init rate = 0.02 (20 / 895), avg. gap size = 1.90 (38 / 20)  


2393 30.74 1.44 0.89  chrX_145060711_145065506.rev     3424  4324 (472)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_145060711_   3424 GAAAAACATCCCATACTCAGAGACAGGAAGAATTCATGGCATTAAAATGG 3473
                             i i       ii   vi  iv      v  v  ivii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_145060711_   3474 CCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCTATAAAACTA 3523
                          v     v      vii  i  i        i  v  i     v   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_145060711_   3524 CCAATGACATTATTCACAGAACTACACAAAATG-TTTTAAAATTCATATG 3572
                            iivi v  v  ii     v vv    iv  - ii             
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_145060711_   3573 GAAACCAAAATAACCCA-AATAGCCGAGGCAATCCTAAGCAAAAAGAAAA 3621
                             ivv  ivi     -       i ii     i i iv  i     v 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_145060711_   3622 AAGCTGGAGGCATCACATTATCCAACTTTAAACTATACTACAGGGCTACA 3671
                            i      vv     i vi    i  i   viv       ii      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_145060711_   3672 GTATCCAAAACAACAAGGTACCAATACAAAAACAGGCACATCAACCAATG 3721
                            vi   i   iiiv     iiii i  ii i  i  i  vi i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_145060711_   3722 GAACAGAATAGAGAGCCCAGAAACAAGGCTACACACCTACAACCATCTGT 3771
                            i     v     i       i  iv i i   ii  iiii  vi  v
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_145060711_   3772 TCTTTGGCAAAGCTGACAAAAGCAAGCAATGGGACAAAGACTC-CCTATT 3820
                          i  i i   i v  v   i v  vv       i-     v v-i  v  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTT 401

  chrX_145060711_   3821 TAAAAAATGATACTGGGTTAATTGGCTAGCCATATGCAGAAGATTGAATC 3870
                         i  v     i i     vi  i   v  ?   i     i    v    vi
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_145060711_   3871 TGGACACTTTCCTAACCCCATATAAAAAAATTAAATCAAGATGAATCAAT 3920
                              v i v   v  v       v         v    i   i    ?v
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_145060711_   3921 GACTTAAATGTAAAACACAAAACTATAAATAACCTGGAAGACAACTTGGA 3970
                            i         i vvi           vvv i i     v   v i i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_145060711_   3971 AATACCACCTTG-AACATAGGGACAG-CAAAGATTTCATGACAAAAACAC 4018
                         ?i  vvv i i -i  v v   vi  -   v i    v iivv vi    
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_145060711_   4019 CAATAGCAATTGCAACAAAAGCGAAAGTTGACAAATGTGATCTAATTAAA 4068
                            v    vvv          vi   i v  i    vv  ii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_145060711_   4069 CTGAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGACTGGACA 4118
                         v v  i i   i  ii vv    i  v       vv i     vvi    
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_145060711_   4119 ATCTACAGAATGATTTTAAAAATCTGTAAACTATGCATTCGACAAAGGTC 4168
                          i i        ivvvv   v  i  i   ii  ii  ii  i  i  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_145060711_   4169 TAATATTCAGCATCTATAAGGAACT--TA-AATTTAC-----AAGAGAAA 4210
                          vi   i   v  v     i     --  -  i i v-----  i   v 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_145060711_   4211 AACAACCTCATTAAAAAGTGGACAAATGACATGGACATATGCTTTACAAA 4260
                           i    iv   ?    i   i    v  iv  i i v iii  iv v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_145060711_   4261 AGGAGACATACATGCAGCCAAAAAGCATACGAAAAAAAAAAAAAACCTCA 4310
                           i   i     viii     v     i i     i vi-------    
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG-------CTCA 894

  chrX_145060711_   4311 GTATCACTGATCAT 4324
                         ii    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (161 / 112)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 2.10 (21 / 10)  


3375 25.86 1.00 0.22  chrX_145080185_145082104.rev      529  1429 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145080185_    529 TGAAAAAAAATC--ATGTTCATGGAT-AGAAGAATTAATATTGTTGAAAT 575
                           i   i v   --            -i     v           i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145080185_    576 GTCTATGTTACCCAAACCAATCTACAAATTCAATGCAATCTCTATCAGAA 625
                          v v  ii v      iii       i      i      i      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145080185_    626 TACCAGAGATAATCTTCACAGAAATAGAAAAATGAATCCTAAAATTTATA 675
                          v    vviivv i  ii       v  v  iivi           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_145080185_    676 TGGAAACACAAAAGACCCAGAATAGCCACAGCTATGCT---AAACAAGAA 722
                               ii   ii               v i v  vi ---   v     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_145080185_    723 CAAAACTGGAGGAATCACATTGCCTGACATCCAATTATAATACATAACTA 772
                             ii       v     i v  ii iv  v  viv  v    v i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_145080185_    773 TAATAACCAAAACAACATGGTACTGGCATAAAACCAGACACATGGACCAA 822
                         i i   i   i   iii              iivi     i  i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_145080185_    823 TGGAACAAAATAGAGAACCCAGAAACAAATCCACACACCTACAGTGAATT 872
                              i i   v    ii       i   i   i   ii  ii  v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_145080185_    873 CATTTTCTGCAAAGTTTCCAAGGATATACACTCGGAAAAAGACAGTCTCT 922
                         v      vi   i v v     ivi  v  v v  i   ii i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_145080185_    923 TCAATAAATGGTGTTGGGAAACCTGGATATCCATAGGCAGAAGAATGAAA 972
                             i        i     v v       ?   i v   i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_145080185_    973 GTAGACCCTTATCTCTTACCATATATGAAAATCAAATTAAAATAGGCTAA 1022
                         v i     i  i   vi        ii     i  v i     i iii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_145080185_   1023 ATACTTAAACCTAAGACCTCAAACTATGAAAATTTTACAAGAAAACATCA 1072
                          v  i    iv     v  v       i   v i   v          - 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT-A 549

  chrX_145080185_   1073 GGAG-AAGTATCCAGGTCATTGATCTGGGCAAAAATTTCTTGAGTATTAC 1121
                           ? -  i v i iv v v   ivi i     vii      iii   v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_145080185_   1122 CCCAGAAGCACAAGCAATCAAAGCAATAATTGACAAATAGAATCACATCA 1171
                         v   i            iv    v  v   v  i    v i iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_145080185_   1172 AG-TTAAAAACTTTTGCACAGTAAAGAATACAGTCAACAAAATGAAGAGA 1220
                          i-             ii vvi    i i  vi    v   i    i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_145080185_   1221 CAACCCACATAATGGAAGAAAATATTTGCCAACTACCCATCTGATAAGGG 1270
                                  v     i             v  ii ivi            
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_145080185_   1271 ATTAATAACCAGAACATATGAGGAGCTCAAACAACTTTATGGGAAAAA-A 1319
                          i vi  v      i    i i  i   vv      iv  iiv     - 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_145080185_   1320 TATAATAATCTGATCCAAAAATGGGCAAAAGGTGTGAAAAGAAATGTCTT 1369
                         i -     i ii  i?             i i v    v   v  v   i
  L1M4_orf2#LINE/    800 CA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_145080185_   1370 AGAAGAAGACATACAAATGGCAAACAGGCATATAAAAACATGTGCAACAT 1419
                         vi       i           v  i i   i  i    v   iv      
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_145080185_   1420 CACTGATCAT 1429
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.76 (146 / 83)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2304 25.32 2.49 4.22  chrX_145109096_145111891     1383  2306 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145109096_   1383 TAGAGAAATATGT-AT-TTCTTGTGAGTCAGAGATCCAATACGGTTAAGA 1430
                          i  i i    vi-  -   v  -  v vii   iii    iv       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATG-GATTGGAAGACTTAATATTGTTAAGA 49

  chrX_145109096_   1431 TATCAATACTTCTAAAATTAATCTATAGATTAAGTGTCGTCAAAATCAAA 1480
                          iv       i iv     i     i     v ii ivi  vvv      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_145109096_   1481 ATCTTAGCAGTCTTTTTCTGTACAAAATGTATGAACTAATTTTAAAATTC 1530
                            ii   v i      -  i v   v  - ii i  i  ii        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTT-TGCAGAAATTG-ACAAGCTGATCCTAAAATTC 147

  chrX_145109096_   1531 ATATGGAAATGTGAAAGTACCAGAA-AAATAAAAC---TTTGAAAAAAAA 1576
                                    ii ii vv      - ivi     ---i        i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_145109096_   1577 GACCAAAGTTGGAGAAATAAAAATACCTGATTTTAAGGAGTATTAAAGAG 1626
                           v           i v v v v v  ii    i  iivv  i  v i  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_145109096_   1627 ATATAATAATCAAGACAGTGTATTAGTATTGTCATAAAATTAGACAAATA 1676
                         v  i i               i---   i  v     iiv      v   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTG---GTACTGGCATAAGGATAGACATATA 294

  chrX_145109096_   1677 GCTCA-TGGAACAGAA--GAGAGTTTCCAGA--TAAACCCACACATAGAA 1721
                          v   -     i    --      --     --        i    vv v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGT--CCAGAAATAAACCCATACATTTAT 342

  chrX_145109096_   1722 AGTCTTTGGAATCT-GACAAAGGTGAAAAGGCAATGTAGTGAGTTATGTA 1770
                         i   vv v  v i -     i    vv   i v  vi i  i vv v v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_145109096_   1771 CAATCTTTAAAAAAAAATGGTTCTCGAACAACATTTGGATCTCCATATTC 1820
                         i i     vv  v   -    v  v i     ---     v?   i  v 
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAA-TGGTGCTGGGACAAC---TGGATAKCCACATGC 438

  chrX_145109096_   1821 AAAAATATTGAGCTTTGATTCACAACTGTGAT-TTATATTTAAAAATAAA 1869
                             iv  vi  -  v  ii - v  i- v i-ii    vi      v  
  L1M4_orf2#LINE/    439 AAAAGAATGAAG-TTGGACCC-CTACC-TCACACCATATACAAAAATTAA 485

  chrX_145109096_   1870 CTGAAATTTGAAGATAGATCTAGTTATAAAACTTAACACTCTAAGACTTC 1919
                           v   v v  vv ?   i   iv i   i vi   v   v   i   ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_145109096_   1920 TTGAAAAATATGTAGCCTAAAATCTTTGTGACCTAGGGTTAGGCTATGTT 1969
                          v   i  v ii   v?vv       i       v         v   v 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_145109096_   1970 TTCTCAGATATAACACCAAAAGCATATTCCATAAAATTCAAAATTTATAC 2019
                             i      i            i vv v i    vvv     vv   v
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_145109096_   2020 ATTGGACTTCATCAATATTAAAAGCTTCTTCCCTTCTAAAGATACTGTAA 2069
                                        v       i   i viv    v  i  i   i v 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_145109096_   2070 AAAAAAAGTTAAAAAAGACAAGTCATAAACTGGCAGAAATTCTTTACAAA 2119
                          i   --  --i         vi  i i v   v     v v   i    
  L1M4_orf2#LINE/    686 AGAAA--GT--GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_145109096_   2120 GGGCCCATCTGATAAAGCCTTCTAGAATCCTTTATCATCTAGAATATGTA 2169
                         vviivi         i -------  ----i  i -   i       i  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGG-------GA----CTTGT-ATCCAGAATATATA 769

  chrX_145109096_   2170 AATAA-TCTT-CAGTACTCAATAATAAAATCTAAAC---TAACC-AGTTC 2213
                           v  -    -  --              --- i  ---     - i  -
  L1M4_orf2#LINE/    770 AAGAACTCTTACA--ACTCAATAATAAAA---AGACAAATAACCCAATT- 813

  chrX_145109096_   2214 TTTAAAAATGAGCTAA--ATTTTAACAGACAC--CAGTAAAGAAGATATA 2259
                         --?       i  v  --    v  i     i-- vvi            
  L1M4_orf2#LINE/    814 --WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_145109096_   2260 TGAATGGGAAATAATTCCATGAGAAGATGCTCAACACTATTCGTTAT 2306
                         ii     vv     viv     i             ii ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.11 (121 / 109)
Gap_init rate = 0.04 (33 / 908), avg. gap size = 1.88 (62 / 33)  


2790 27.93 1.69 1.24  chrX_145175679_145180065.rev     3007  3894 (493)    L1M4_orf2#LINE/L1        1   892 (16)  

  chrX_145175679_   3007 TGGAAAGATATTCCATGTTCATCAATTAGAAGAATCAATACC---AAAAT 3053
                                    i          vi   i     v i    ii---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145175679_   3054 GTCTATACTACTCAAATCAATCTACAGATTCAATTCAATTCCTATCAAAA 3103
                          v v     v i     ii              iv    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145175679_   3104 TACCAATGACATTTTTCACAGAGATAGAAAAAACT-ATCCTAAAATGTAT 3152
                          v   iivi v     ii    i  v  v  i-  -          vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_145175679_   3153 GTGGAACCATAAGAGACCCAGAATAACCGAAGTTATTGTAAGAAAAAAGA 3202
                         i     viii   i           i  i  iiv  iv i i   i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_145175679_   3203 A---AACTGGAGGAGTCACATTACCTGACTTGCAATTATACTGCAGAGCT 3249
                          --- ii       v     i v  ii i  vv  viv    i  i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_145175679_   3250 GTAGTAACCAAAATGGTATGATACTGGTGTAACAACTTACGCATAGA-CA 3298
                         ii     i   i ii  i  i      ii   vi ivv  ii     -  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_145175679_   3299 ACTATAACAGAATAGTGAATGCAGAAACACATCCACACAGCTACAGCAAA 3348
                          - iv  i     v v  i v      i v i   i   vi  ii iv  
  L1M4_orf2#LINE/    300 A-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_145175679_   3349 CTTACTTTTAACAAATGGGCCAAATACATACACTGGTAAAAAAAAAAAAT 3398
                         i v i   ii    iv v     ivv   v  v   -----ii   i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-----GGAAAGAAT 393

  chrX_145175679_   3399 AGTTTTTTCAGTCAATGGTTCTGGTAAAACTGAATATTCATATGGTGAAG 3448
                            i      iiv      v    v v     i   ?i  i   vvi   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_145175679_   3449 AATGAA-CTAGACCTCTATCTCTCAACATATACAATAATCAAATCAAAAT 3497
                               -i i    i   i   v  v         v   i  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_145175679_   3498 GAATTAAAGACTTATATCTAAGACCTAAGACTGTGAAACAACTACAGTAA 3547
                          i  i ?    i  v  v     v    i   i i    vvi  v iv  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_145175679_   3548 AACTTTGGGGAAAATCTCCAGGACATTGATCTGGGCAAAAATTTCCTGAG 3597
                            v v  ? v      i iv   v   ivi i     vii    i iii
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_145175679_   3598 TAGTATCCCACAAACACAGGTGTCCAAAGCAAAAGTAGCCAAATGGGATC 3647
                           vv iv   v  i    i iiv v    v    i   vi    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_145175679_   3648 ATATCAAGTTGAAAAGTTTCTGCACAGCAAAGGAAAGAATTAACAAAATG 3697
                         vi     iv v    ii  i  ii vv       v vv  i  v   i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_145175679_   3698 AAGAGACAGCCCACAGAATGAAAGAAAATATTTGCAAACAACCCATCTGA 3747
                           i     i           ii                iv ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_145175679_   3748 CAAGGGATCAATTATA---AGAATATATAAGGAGCACAAACAATTCTATA 3794
                         i      i---  i  ---           i  i v vv    i  v   
  L1M4_orf2#LINE/    744 TAAGGGAC---TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_145175679_   3795 GGAAAAAAA-ATCTAAC--GATTTAAACAATGGACAGAATATATGAATAG 3841
                         iv     i - vv    --i   ?   -     i  i iv  v       
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAA-AATGGGCAAAGGATTTGAATAG 839

  chrX_145175679_   3842 ACATTTCTCAATAGAAAATATACAAATGTCAAAGAGGCATATGAAAACTT 3891
                                  v v    i           v v  v i   i       vv 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_145175679_   3892 GCT 3894
                            
  L1M4_orf2#LINE/    890 GCT 892

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.01 (13 / 892), avg. gap size = 2.00 (26 / 13)  


2873 27.39 0.77 0.99  chrX_145243456_145248422     3566  4474 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_145243456_   3566 GAAAAAATATTCTGTTCTCATGGATTGGAATAATTAATATAGTTATTAAT 3615
                          i   i    i ii vi             v v       v    v-i  
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA-GAT 50

  chrX_145243456_   3616 GGCCATACTTCCCAAAGTAATTTACAGATTCAACACAATTCCTACCAAAC 3665
                            v     i      v i  i            i    i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145243456_   3666 TACCAATATCATTTTTCACAGAATTAGAAAAAAAAAATTCTCAAATTCAT 3715
                          v   iivv v     ii     v v  v  ivvi - i  v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chrX_145243456_   3716 ATGGAATCAACAAAGAGTGAGAACAACCAAAGCAAACCTAAGTAAAAAGC 3765
                               viivv ii  viv    i i     i   v i i iv  i   v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_145243456_   3766 ACAAATCTGAAGGCATCACATAACCCAATTTCAAACTCTACTACAAGGCT 3815
                              vi  i   vv     ivv            vii        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_145243456_   3816 GCAGTAAT-AAAACAGCACAGTACTGGTATAAACACAGACACATAGATCA 3864
                         i       -  i    iiii       i    iv i     i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_145243456_   3865 ATGAAACAGAATAGGGAATCCAGAAATAAACTTGCACACCTACATCTACC 3914
                            i  i     v i  i             iiii   ii  iivii vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_145243456_   3915 TGTTTTTTTACAAAGTCGACAAAAAAAAGCAATGGGGAAAGGAATC-CCT 3963
                           v    iv    i vi v   i vv vv            -   v-i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCT 398

  chrX_145243456_   3964 ATCCAATAATTCGTGCTGGGATAACTGGCTAGTCATATGCAGAAGAATCA 4013
                         v i   i  v v         i      v  ?i  i     i      v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_145243456_   4014 AACTGGACCCCTACCTTTCATTGTATACAAAAATTAACTCAAGATGAATT 4063
                          ii             iv  iii                   i   i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_145243456_   4064 A-AGATTTAAATGTAAGACTTCAAACTATAAAAATCTTAGATGAAAACCC 4112
                          -   ii           vi v           v       v      vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_145243456_   4113 AGGAAATATTAATATAATTCTGAACATTGTTCTTGGCAAAGAATTTATGA 4162
                            ?i-  --   v -- iv   v -   vvi v     v iv  iv ii
  L1M4_orf2#LINE/    549 AGGNG-TA--AATCT--TCGTGACC-TTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_145243456_   4163 CTAAGTCCTCGAA-GCAATTACAACAAAACCAAAAACTGACGAGTGGGAC 4211
                         v  v v vi i  -   vvvi        vv     iv  ii i v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_145243456_   4212 CTAATTAAACTAAAGAGTTTTTGCACAGCGAAATAATCTATCAACAGAAT 4261
                         i v  i   v v  i ii     ii vv i  iv vv       v i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_145243456_   4262 AAACAGACAACCCACAATATGGGAGAAAATATTTGCAAACCATGCATCTG 4311
                         i  v            iv                     i   ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_145243456_   4312 ACGAAGGTCTAATATGCCTAATCTATACGGAACTTAAAGAACTCAA--GC 4359
                          ii i  v  vi   v vv   v    vi     ivv v       --ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_145243456_   4360 AAAAA-ATAAATAACCCTATTAAAAAGTAGGCAAAGGACATGAATAGATA 4408
                              - i         v   ?    i i         iv        i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_145243456_   4409 CTTATCAGAAGAAGACATACAAGCATCCAACAAACATATGAAACAATCTT 4458
                         i  v  vi       i      iiiv    i  i  i      vi  vi 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_145243456_   4459 CATCATCAATAAGCAT 4474
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (141 / 105)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 1.23 (16 / 13)  


1993 27.24 4.16 4.81  chrX_145270343_145272259.rev      513  1426 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145270343_    513 TGGGAAAACATCT-ATGCTCATATATTGCAAGAATTAATGTTATTAAAAT 561
                            i  i i   i-   i    iv    v    v     i  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145270343_    562 GACCACACTGCCCAAAGCAATCTACAGATTCAATGAAATCTCTATCAAAA 611
                          i v i   v      vii              i v    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145270343_    612 TATTAATT-TCATATTTACAGGA-TT-ATAAATATGTATTATTAAATTCA 658
                          vii ii -i v v   i   i -  - i  ii-  -  iv v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TG-ATCCTAAAATTCA 148

  chrX_145270343_    659 TATGGAACCAGAAAAGAGCATGAATAGCCAAAGCAGTCCTGAGCTAAAAG 708
                                viiv  ii  v vv           i  i  i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_145270343_    709 AAAAATGCTGGAAGCATCAAATTACCTGAATTCAAATC------------ 746
                           v  v i    i vv   v i v  ii v      v ------------
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_145270343_    747 -ATATTAACCAAAATAGCATGTTATCTATATAAAAACCTGACAAATA--- 792
                         - i v   i   i i  ii  v  iivii    ii iv-    v   ---
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGAT 297

  chrX_145270343_    793 -AATGGCACATAATAGAGAACACAGAAATAAAGCCACATATTTACAGCTA 841
                         -     v i v   v    iiv          v   i i     ii ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_145270343_    842 ACTGATTTTTGACAAATATTACTAAAAC-ATATATTGGAAAATATAA-AA 889
                          i       i     ivi -i i  i  -  vi v   ii  - v  - i
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGT-GCCAAGACCATTCAATGGGGAA-AGAATAG 395

  chrX_145270343_    890 CCCTTTTAATAAATGATGCTGGGAAAACTAGATTGCCGTATGGAGAAGAA 939
                         i i   i  i     i        v    i   v?  ii   v i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_145270343_    940 TTCAACAGAACTTCTATCTCTCACCAGGTACAAAAATAAACTGAAGATGG 989
                          vv iiv i  ii   i   v     vi         v    v  i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_145270343_    990 ATTAAAAACTGAAACACAAGACCTGACACTATAAAAATATGAGAAGAAAA 1039
                           i ? i  iv   iii    v  i v         v v v         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_145270343_   1040 CCTAGAGAAAACTCTTCTGGGCATTGGTTTTAGGACAGCAATTTAT--GA 1087
                          v   i?iv  v     vv i v    v  -   -  iiii   v --  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTT-AGG-CAATGGTTTCTTAGA 593

  chrX_145270343_   1088 CTAAGACCTTAAAAGCACAGGCAACTAAAATAAAATTTTTTTAATGGGAC 1137
                         -  v   vii         i     v   iv    v vvv v   v    
  L1M4_orf2#LINE/    594 -TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_145270343_   1138 TT-AT----ATTGAAAA---TGGT-CTCCACAGCAAAAACAAAACAAAAC 1178
                           -  ----   i    --- v  -  i  ----  ii   vv i-----
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCA----AAGGACACTAT----- 683

  chrX_145270343_   1179 AAAACAAAAAACAGAGTGAAGTGTCAACCTGCAAAATGGCATAAACAAAA 1228
                         ----   i   ----     iv v     ii  i     ----i v    
  L1M4_orf2#LINE/    684 ----CAAGAAA----GTGAAAAGACAACCCACAGAATGG----GAGAAAA 721

  chrX_145270343_   1229 TGGAATTTACAAGCCATTCATCTGATG-GGGACTAAAATCAAAAATATGC 1277
                          ---    i   ii   vi       i-      viv   v i     ii
  L1M4_orf2#LINE/    722 T---ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_145270343_   1278 AAGGAACTCAAACAACTCGACAACAGTGACAACAAATACAAAACAAATAA 1327
                           i      vv       i i  i --------   ---- i        
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATA--------AAA----AGACAAATAA 806

  chrX_145270343_   1328 TCCCATTAAAAAGTGGGCAATAACCGTAAGGAGACATTTTTCAAAAGAAG 1377
                         i  v   ?    i       viiviv i iv        i  v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_145270343_   1378 ATATACAAATG-TCAACAGGAATACAGAAAA--GCTCAATATTAATAATC 1424
                                    -i   i i v i iii   i--      i  i ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_145270343_   1425 AT 1426
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.61 (151 / 94)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 2.65 (82 / 31)  


3216 26.84 1.22 0.11  chrX_145277788_145284957     5780  6677 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145277788_   5780 TGGAAAAATATTCCATGTTCATAGATTTAAAAAATCAGTATTTTTAAATT 5829
                               i    i          i    vi  i v i i    v    iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145277788_   5830 GTCCATACTATCAAAGGCAGTCTACAGATTCAGTGCAATCTCTATTAAAA 5879
                          v v     vi v  iviii            ii      i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145277788_   5880 TACCAATTACGTTCTTCACAGAAATAGAAAAAACAATTCTAAAATTTATA 5929
                          v   ii i v  i  ii       v  v  ivii  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_145277788_   5930 TGGAATCACAAAAGACCTAGAGTACCCAAAGCTATCCCAAGCAAAATGAA 5979
                              vii   ii    i   i  v     i v   iii iv  i v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_145277788_   5980 CAAAACTAGAAGAATTACATTACCTGGTTTCAAATTATACTACAGAGCAA 6029
                             ii i  i  v i   i v  iii       viv       i   v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_145277788_   6030 TATTTACCAAAACAACATGGTACTGGCATAAAAACAGTCAAATAGACTAA 6079
                         i v v i   i   iii              ii i  v  v     ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_145277788_   6080 TAGAACAGAATTGAGAACCCCGTAATAAATCTATACACCTACAGTGAATT 6129
                          i   i          ii  v v      i i     ii  ii  v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_145277788_   6130 CATTTACAACAAAGGTGCCAAGAACATACATTGGGGAAA-AACAGTCTCT 6178
                         v    v i    i          v   v  v        -  i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_145277788_   6179 TCAGTATATGGTGCTGGAAAAACTCGATATCCATGTGCGGAAGAATAAAA 6228
                            ii v          i v    v    ?   ii   ii      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_145277788_   6229 CTAGACCCCTATCTCTCATCATACACAAAAATCAAGTCAAAATGGATTAA 6278
                         i i        i   v  i    i        i  v           i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_145277788_   6279 AGACTTGAA-----GACCTCAAATTATGAAACTACTGAAAGAAGACTTTG 6323
                             i i  -----  v  v   i   i     vi ii     i  v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_145277788_   6324 GGGAAACTGTCCAGGACAT---GT-GGGCAAATATGTCTTGAGTAAAACA 6369
                          ? v  v v i iv   v ---  -i     vvi v    iii  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_145277788_   6370 CCACAAACACAGGAAATGAAAGCAAAAATGGACAAATGGAATCACATCAA 6419
                            v  i    i v  ii    v      i  i    v i iiv      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_145277788_   6420 G-TTAAAAAGCTTCTGAACCGCAAAGGAAACAATCAACAAAGAGAAGAGA 6468
                         i-       -   i  vi iv       v  v     v    v   i   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_145277788_   6469 AAACCCCCATAATGGGAGAAAATAGTTGCAAAATACCTATCTGACAAGGA 6518
                         v     v  v              v       vi iv       i    i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_145277788_   6519 ATTAATAACAAGAATATATAAGAAGCTCAAAAAACTGTGTAGAAAAAAAT 6568
                          i vi  v v           ii i   vv v    vvi  iv     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_145277788_   6569 CTAATGATCCCATCAAAAAATGGGCAAAAGATTTGAATAGACATTTCTCA 6618
                          v   i i  v  i?             i                    v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_145277788_   6619 CAAGAAGGCATACAGATGACAAACAGGAATATGAAAATGTAATCAACATC 6668
                         v      ii     i   i v  i i v i       vi iv        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_145277788_   6669 ACTGATAAT 6677
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.63 (147 / 90)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


1161 25.00 6.25 0.33  chrX_145301545_145306091.rev     2854  3157 (1390)    L1M4_orf2#LINE/L1        1   322 (586)  

  chrX_145301545_   2854 TGGAAAGATATTTACATGTTCATGGATTGGAAGAATCAACATTGTTAAAA 2903
                                    ii-                    v i  i        i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCC-CATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_145301545_   2904 TTTCCATGCTACCTAAAGCAATCTATAAGTTCAATGCAATCCCTATCAAA 2953
                          vv v  i  v  i   vii     i ii     i               
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_145301545_   2954 ATATCAATTACATTCTTCAAAGAAAT----AAAATAACCC-AAAATTTAT 2998
                           vi  ii i v  i  iiv      ----  iv i i  -      i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_145301545_   2999 ATGGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTAAGCAAAAAGA 3048
                               vii   ii                 i v   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_145301545_   3049 ACAAAA--GGAGGGATTACATTACCTGACTTCAGA------------GCT 3084
                              i--     iv i   i v  ii i    i ------------   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_145301545_   3085 ATAGTAACCCAAACACAATGGTACTGGCATAAAGACAGAAACATAGACCA 3134
                          i     i v i   vvi              i  i   v i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_145301545_   3135 GTGGAAAAGAACAGAGAACCTGG 3157
                         i     v    iv    ii ii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAG 322

Transitions / transversions = 2.62 (55 / 21)
Gap_init rate = 0.02 (5 / 322), avg. gap size = 4.00 (20 / 5)  

2193 25.46 0.93 0.93  chrX_145301545_145306091.rev     3409  4056 (491)    L1M4_orf2#LINE/L1      261   908 (0)  

  chrX_145301545_   3409 GACAGAGCGAGACTCCGTCTCAAAAAAAAATAAAAAAATAAAAAAAA-AG 3457
                              v i iv   -- v vi  ii v i i v v i  v  vii  -  
  L1M4_orf2#LINE/    261 GACAGTGTGGTACT--GGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_145301545_   3458 GACAGAGAACCCAGAAAGAAATCCACACACTTACAGTAAACTCATTTTTA 3507
                         i iv    ii       v   i   i   i   ii  v  i v     ii
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_145301545_   3508 ACAAAGGTACCAAGAACATACACTGAGGAAATGACAGTCTCTTTAATAAA 3557
                             i   i      v   v  v  i     vi i     i  i  i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_145301545_   3558 TGGTACTGGGAAAACTGGATATCCATATACAGGAAAATAAAACTAGACCC 3607
                             i      v         ?   i  i  ii i   i  ii i     
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_145301545_   3608 CTATCTCTCACCATATACAAAAATGAAATCAAAATAGATTTAAGACTCAA 3657
                            i   v                v  v       i   iv?    ii  
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_145301545_   3658 ATCTAAGACCTTAAACTATGAAACTCCTACAAGAAAACTTTTAGGA--AA 3705
                           v     v  v       i      i  v        v --   ?--  
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT--AGGNGTAA 556

  chrX_145301545_   3706 ACCTCCAGGACATTAGTCTGAGCAAAAGTTTATTGAAAAAT-ACTCCATA 3754
                          i  i iv   v  i vi ii    vi    v  - i v  -  v   v 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAA 605

  chrX_145301545_   3755 AGCACAGGCAACCAAACAAAAAGTGGACAAATGGGATTACATTAAG-TTA 3803
                               i     v   v     i i  i    v   i v   i  i-   
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chrX_145301545_   3804 AAAAGCTTCTACACAGCAAAGAATGTAATCGATGAAGTGAAAACAGAATC 3853
                             -   i iii vv     i iiiv   i vi         v v  i 
  L1M4_orf2#LINE/    656 AAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_145301545_   3854 CATAAAATGGGAGAAAATATTTG-AAACTATGCATCTGATAAAGGATTAA 3902
                           i i                  -   ii  ii         i   i vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_145301545_   3903 TAACAAGAATATATAAGGAGCTCAAACAACTGTATAGAAGATAATCTAAT 3952
                           v v           i  i   vv      vv   iv i v iv v   
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_145301545_   3953 AATCCCATCAACAAATAGGCAAAAGATTTGAACAGACATTTCTCAAAAGA 4002
                           i  v  i? v    i      i        i           v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_145301545_   4003 AAACATACAACTGGCAAACAGGCATATGAAAAGGTTCTCAACATCACTGA 4052
                          i i      v    v  i i   i        i v          ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_145301545_   4053 TCAT 4056
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.60 (99 / 62)
Gap_init rate = 0.01 (9 / 648), avg. gap size = 1.33 (12 / 9)  


 980 27.86 9.23 5.32  chrX_145307837_145310168      671  1309 (1023)    L1M4_orf2#LINE/L1        1   664 (244)  

  chrX_145307837_    671 TGGAGACATATTCAGTGTTTATCAACATGGCAAAGATGTAA-ATTATTTA 719
                             i v    i vi    i  vi i-   --    iv   -   i  v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-TGG--AAGACTTAATATTGTTAA 47

  chrX_145307837_    720 AATTGT--------CTATATTGAACTATAGATGAAAATTAAAGTGGCGGT 761
                         i  v i-------- i v     v   i    ------------------
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGAT------------------ 79

  chrX_145307837_    762 TTAATGCAATTT-TATCAAAATTTCAGCAAGTTTTTTATGTAGATAC-AA 809
                          i  i     ii-         ii    vivi     -  i   v i-i 
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTT-TGCAGAAATTGA 128

  chrX_145307837_    810 TAA--T-ATCCTAAAGTTTATGTGGAAAGATGAAGTAAATATAACAGCTG 856
                         i  -- -        i  i  i      viii i v vvi v  i   ii
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chrX_145307837_    857 AAACAATTCT-AAAACTAA--ATAAGTTTGCAGGAAT-ATTCTGCCTAAT 902
                                ii -    vv  -- i  iv   v    v - iv  v  i   
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chrX_145307837_    903 TTCAGGACTTATGATATAGCTACAGTAATCAATAATCTATAGTATTGGTA 952
                             ii     iv i v               v vvv i i   i   i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chrX_145307837_    953 CAGGACTAGGCATATAGATCAATAGAACAAAATACAAAATCTGAAAGTAG 1002
                         i i iv   i             i   i i   vv i i  iii  i  i
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chrX_145307837_   1003 ACCCCTGAAAATATG-CCAACTGGTTTT-GACAAGAGTG--AAAAATAGC 1048
                             v iv vv    -i   i  i    -      i   --  i ---- 
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA----C 374

  chrX_145307837_   1049 AATTTCAT------AGACT-GCCTTTCCAACAA-TGGTGCTGGAATATAT 1090
                         v   iv  ------   v - i    i      -         i i - i
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA-AC 423

  chrX_145307837_   1091 TGTTTTCATCCATAGATTGAAAACAAAATTAACCTCAACCTAAACCTTGC 1140
                           vv -- ?   i ---  v   - i   v  vi vi   ivv    ii 
  L1M4_orf2#LINE/    424 TGGAT--AKCCACA---TGCAAA-AGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_145307837_   1141 AACTTATATAAA--TTAAATAAAAGTAGATCATTGATTTGAATGTAA--- 1185
                          v v    i   --    v v   i i     ?v  ii i       ---
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chrX_145307837_   1186 ----AATTATAAAAC-ATTAGATGACAAAA-------AAAATTTAG-GAT 1222
                         ----  i        -v     v  v  v -------   vi  v -  i
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chrX_145307837_   1223 CTGGAGGTGAGTAAACAGTTCCTAGAGTTGACATAAAATAACATTATTTA 1272
                           v i v ii i  vviv   i    vv     iv   - i  iv viv 
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA-AGCACAAGCAA 616

  chrX_145307837_   1273 TAAAAGAAAG-----------TGCATGTCATCAAAATTAATAACTTTT 1309
                         i        i-----------  v iv             v       
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

Transitions / transversions = 1.44 (104 / 72)
Gap_init rate = 0.05 (31 / 664), avg. gap size = 3.00 (93 / 31)  

 490 29.86 0.95 1.42  chrX_145307837_145310168     1632  1842 (490)    L1M4_orf2#LINE/L1      672   881 (27)  

  chrX_145307837_   1632 AAAAGAC-CTGTGATGGGAATGAAAAGACAAGTTAGAGATTGAATGAAAA 1680
                            i   -  i v v ii i           vii v   v  iiv     
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_145307837_   1681 CATTTGTAATCTACATACCTGACAAAGTACTTGTATCAAGATTATAAGAA 1730
                         i     i  vii i   i    i  i v         v   v    --v 
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA--TA 769

  chrX_145307837_   1731 AAAAACTCTCA-AACTCAACAGAAAAATGACAAACTGTTTAAATAGAAAA 1779
                           i      i -       i iv    v      iviiii  v ?i    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_145307837_   1780 TAGCCAAAAAAACAAGAAGAGGCATTTTACAAAAGAAGTTATAAAGATGG 1829
                          i v    ii -ivv   v  i     iv v       v    v i    
  L1M4_orf2#LINE/    820 TGGGCAAAGGA-TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_145307837_   1830 TCTATTAGTCCAT 1842
                         i v  v  iv   
  L1M4_orf2#LINE/    869 CCAATAAGCACAT 881

Transitions / transversions = 1.38 (36 / 26)
Gap_init rate = 0.02 (4 / 210), avg. gap size = 1.25 (5 / 4)  

 226  8.33 8.33 0.00  chrX_145307837_145310168     2065  2112 (220)    L1M4_orf2#LINE/L1      857   908 (0)  

  chrX_145307837_   2065 ATAT-CAGATGGCAAATAAGCACATGAAAATATGC---ATATCACTAGCT 2110
                             -  i     v                v    --- i    ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_145307837_   2111 TT 2112
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.00 (2 / 2)
Gap_init rate = 0.04 (2 / 52), avg. gap size = 2.00 (4 / 2)  


3213 24.46 0.76 3.25  chrX_145381494_145385818.rev     2911  3834 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_145381494_   2911 ATATTTCATGTTCATCAACTGGAAGAATAAATATTGTTAAAATGTCCATG 2960
                             ii         vi i       v v           i   v v  i
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chrX_145381494_   2961 CTACCCAGAGTAATCTACATATTCAATGCATTCCCTATCAAAATACCAAT 3010
                           v    i v i       v      i   v             v   ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chrX_145381494_   3011 GACATTCTTCACAGAAATAAAAAAAA-AAT--TAAAATTTATGTGGAACT 3057
                         vi v  i  ii       vi v  iv-i  --       i  i     v 
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chrX_145381494_   3058 ACAAAAGGCCCAGAATAGCCAAAGCTATCTTAAGCAAAAAGAACAAACCC 3107
                         i   ii i               i v     i iv  i         vii
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chrX_145381494_   3108 AGAGGAATCGTGTTACCTGACTTCAAA--TTAAACTACGGAGCTAAGGTC 3155
                         i     v  iiii v  ii i      --   --    ii     vi  v
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGCTACAGTA 255

  chrX_145381494_   3156 ATCAAAAGAGCATGGTACTGACAAAAACTAACAAACAAACAAAAAATCCA 3205
                              i v  ii        i  -----   ------------ii  -- 
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCA-----TAA------------GGAT--A 286

  chrX_145381494_   3206 GACACATAGACCAGTGGAAAAGAATAGAAAACCCAGAAACAAACCCAATT 3255
                             i     i  i     v     v  i ii       i       ---
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--- 333

  chrX_145381494_   3256 CCACACACCTAATGTGAACTCATTTTCAACAGAGATCCCAAGAATATACA 3305
                         ---i   ii  vv  v  i v      i   ii i v      vi  v  
  L1M4_orf2#LINE/    334 ---TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_145381494_   3306 CTAGGGAAAGGACAGTCTCTTCAATAAATGGTGCTGAGAAGACTGGGTAT 3355
                         v i       i i     i     i           i  vi     i  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chrX_145381494_   3356 CTATATGCACAAGAATGAAACTAGACCCCTATCTCTTACCCTGCTCAAAA 3405
                          i i     v         ii i        i   vi   v iiv     
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chrX_145381494_   3406 ATCAAATCAAAATAAATTGAAGACTTAAGTCTGAGAACTCAAATTATGAA 3455
                           i  v       ii  ii?    i   i v i   i  v   i   i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chrX_145381494_   3456 ACTACTACAAGAAAACA-ATGTGGAAACCCTCCAGGACATTGGTCTGGGC 3504
                            vi  v         - v ? v   i i  -iv   v    vi i   
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGC 579

  chrX_145381494_   3505 AAAAATTTCTTGAGCAATACCCCACAAGCACAGGAAACCAAAGCAAATAT 3554
                           vii      iiii vv  v   v       i v   v    v   v  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chrX_145381494_   3555 GGATAGATGTGATCACATCAAG-TTAAAAAGCTTCTGCACAGCAAAGAAA 3603
                         i    i  vv  iiv      i-       -   i  ii vv     i v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGAC 678

  chrX_145381494_   3604 ACAATAAACGAAGGGAAGAAACAACCCACAGAGTAGAAGAAAATATTTGC 3653
                           v  v  vi   v   i i            i i i             
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_145381494_   3654 AAAGTACCCATTTGAGAAGGGATTAATAACCAGAATATATAAAGAACTCA 3703
                            vi ivi  i   v      i vi  v                    v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_145381494_   3704 AACAACTCTATAGGAAAAAAATTTAATAATCCAATCAAAAAATGGGCAAA 3753
                         v       v   iv     i iv-     i     i?             
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAA 827

  chrX_145381494_   3754 AGATTTGAGAAGACATTTCTCAAGAGAAAACATAGCAATGGCAAATAGGC 3803
                         i       iv           v i    i i   vv      v    i  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_145381494_   3804 ATGTGAAAAGGTGCTCAACATCACTGATCAT 3834
                          ii       i            ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (139 / 83)
Gap_init rate = 0.01 (13 / 901), avg. gap size = 2.85 (37 / 13)  


2916 25.39 1.19 2.62  chrX_145389908_145391738.rev      502  1340 (491)    L1M4_orf2#LINE/L1       82   908 (0)  

  chrX_145389908_    502 AATGCAATTCTTATCAAAATTCCAATGGCACTTTTCACAGGAATAGATAA 551
                           i     i i         i   iiv  vi    ii   i   v  i  
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

  chrX_145389908_    552 AACAATCCTAAA-TCTGTACGGAACCATAAAAGATGTTAAATAGCTAAAG 600
                         ivii        - iii  i    viii  ii  ivivi      i   i
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chrX_145389908_    601 GAATCTTGAGAAAGAAGAACAAAGCTGGAGGCCTTACACGGGTTGCC--- 647
                         v        i              i      v  i    ---  v  ---
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC---TTCCCAAT 228

  chrX_145389908_    648 TTCAAAATACATTACAAAG-TACTAGTAATGGAAACAGAATGGTACTGGC 696
                                ivi i       -   -      vi i    vi          
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTAC-AGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_145389908_    697 ATAAAAATAGGGAGATTCATCAATGGAAAAGCACAGAGAGCCCAGAAATT 746
                             ii    iv v  vv          v  v iv     i        v
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_145389908_    747 AACTTATACATGTATGGTCAAATAATGTTTGACAAGAGGCCTAAGAACAC 796
                            ii      v         v i  v  i      i vv i    v  i
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_145389908_    797 ACAATGGGGGAAAGGAAAGTCTCTTTAATAAATGTTCCTGGAAAAACTGG 846
                         v        -    i v     i  i  i     v v    i v      
  L1M4_orf2#LINE/    378 TCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_145389908_    847 ACATCTATATGCAAAGGAATGAAATTAGACTATTGTCTTACAACACATAC 896
                          i ? i i       i       i  i   ivi ii  i   v  i    
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_145389908_    897 AAAAGTTAACTTGAAATGATTTAAAAATTTAGATGTAAGAGCTGAATCCA 946
                             i      ii     iv i ? i ii  i           i  v i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_145389908_    947 TAAACCTCCTAGAAGAAAATGTGGTAGAAAATCTCCTTAACATTGGTCTT 996
                             v   i          ii i v? v      i v i  v    vi v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_145389908_    997 GGTAATGATTTTTTGAATATTACATCAAAAACACA-GCAATAAAAGCAAA 1045
                           i    i   i  ii    v   i     i    -    i     v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_145389908_   1046 AAGAAACAAGTAGGACTATGTCAAA-CTAAATACCTCTGCATAACAAAGG 1094
                           v i i  i v     vii     -i    v  i i  iiivv      
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_145389908_   1095 AAACAACCAACAAAATAAAAATGCATCCTACGAAATGGGAGAAAATAGTT 1144
                          v  v i   v   i i    vi  v  i  ii              v  
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_145389908_   1145 GCAAACCTTGTATCTGATGAACGGTTAATGTTTAAAATATATAGGGAACT 1194
                              i v i        i iv ii vi i ii i        ii     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_145389908_   1195 AAAGGGCAAAAGAAACCACCCAA-AATACAAAAAAAGCACTAAATAATCC 1243
                         ------ vv ----- v  i   -    ----     -  -      i  
  L1M4_orf2#LINE/    777 ------CTTA-----CAACTCAATAATA----AAAAG-AC-AAATAACCC 809

  chrX_145389908_   1244 AAGT-AAAAATGAGTAAAAGATTCAGATGGAAATTTTCCCAAAGAAAACA 1292
                           v -       i i   i    iii  i  v    ii        i i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_145389908_   1293 TGCAA-TGGCCAACCGGTATGTGAAAAGATGCTTAACATTATTTGTCAT 1340
                          i   -       ivi i ii            i     i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.18 (144 / 66)
Gap_init rate = 0.02 (16 / 827), avg. gap size = 2.00 (32 / 16)  


 413 20.43 0.00 2.15  chrX_145421585_145423312        1    93 (1635)    L1M4_orf2#LINE/L1       72   162 (746)  

  chrX_145421585_      1 CTACAGATTAAATGCTTTTCCTGCCAAAATCCAAGCTGTCATTTATTTGC 50
                                  v  i  vv i   ii        v     i -   -     
  L1M4_orf2#LINE/     72 CTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC-TTT-TTTGC 119

  chrX_145421585_     51 AGAAATTGATAGGCCAATTATAAAATTTATAATGAAATACAAG 93
                                  i i  ii  iv       i   vv     i    
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.00 (2 / 2)  

3049 18.16 4.61 2.98  chrX_145421585_145423312      500  1237 (491)    L1M4_orf2#LINE/L1      159   908 (0)  

  chrX_145421585_    500 CAAGAGATTCAGAATAGCCAAAAAATGTATTTT-AAAAAG-----CAAAG 543
                             i  ii              v ---  i  -      -----     
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACA---ATCTTGAAAAAGAAGAACAAAG 205

  chrX_145421585_    544 TCTCAGGACGCACATTTCCTGGTTTCAAAACTTATCACAAAGCTCTAATA 593
                          ivv     v    i    iii            ii        vi i  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chrX_145421585_    594 ATTAATACCATATGATACTGGCATAAGGGTAGACATATAAATCAATGAAA 643
                           i  v  vi i  i             i          i       i  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chrX_145421585_    644 TATAATTGAGAGTCCAAAAATAAACCCTTAGTTTTATAGTCAGTTGATTT 693
                           v             i          v  vv     i    i       
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chrX_145421585_    694 TTGTCAGCCGTGCCGAGACAACTCAATAGGGGAA-AATAGTATTTTCATA 742
                          i v  ivv     i    v i     i   i  -      v      vv
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_145421585_    743 AAATGGTGCTGAGACTACTGAA------CATGCAAGAGAATGAAAATGGA 786
                                    i   v    i ------       i        iv    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_145421585_    787 ACTCTGTCTCACAAGATGTA-AAAAATGAACATGAAATA---CATAAAAT 832
                         v i  ii      vv  i  -      v   vii    i---  ? i --
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA-- 503

  chrX_145421585_    833 TCCCTAATTATGAGAGCTAAAACTATAAAACTCTTAGACAAGTGTACTTC 882
                         --     v i i                          ------------
  L1M4_orf2#LINE/    504 --CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA------------ 539

  chrX_145421585_    883 TAGAAGTAAATAGAAGTAAACCTTTATGACCTTGAGTTAGGCAATGATTT 932
                         -    i- v    i?     i   ii        i           i   
  L1M4_orf2#LINE/    540 -AGAAA-ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_145421585_    933 TATAGATATGAAATCAAAAGGAGAAATGACAAAAGAAAAA-TAGGTAAGT 981
                         iv         v i      v v  iii            -   i   i 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_145421585_    982 TGGATTTCATAAAAATTAAAAACTTT-GTCATTCAAAGGATATCATCAAG 1030
                             i     v               -  vv         i ii      
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_145421585_   1031 A---------GACAA---ACAAAATGGGAGAAAACTTTTACAAATTATTT 1068
                          ---------     ---   i            iv   i     i  v 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_145421585_   1069 ATGTGATAAAGAATTTATATCCAGAATATATAAAGAACT---ATAATTCA 1115
                           v      i i i  i                      --- i  i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_145421585_   1116 AAAATGAGAAGATAAATAACATAATTTAAAAATGTGTAAAAGATTCTAAT 1165
                          v   i i    i       vi    ?       v i   i    iv   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_145421585_   1166 AGCTATTTCTTCAAAGAAGATTAAACAAATGACCAATACATGCATGAAAA 1215
                           vi      i          - v       i      viii        
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGAT-ATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_145421585_   1216 GATGATCAAAATAATTAGTCAT 1237
                             v    v  v ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (84 / 47)
Gap_init rate = 0.02 (16 / 750), avg. gap size = 3.50 (56 / 16)  


2933 26.51 2.09 2.31  chrX_145469801_145474084.rev     2885  3793 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_145469801_   2885 GGAAAGATAGTCCATGTTCATGGATTGGAAGTATCAATATTGCTGAAATG 2934
                                  vi                    vv i       i i i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_145469801_   2935 TCCATAGTACCCAAAGCAATCTACAGATTCAGTACATAATACCAAT-AAC 2983
                         v v   v v      vii             --  ii   v  v  -  v
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCA--ACGCAATCCCTATCAAA 99

  chrX_145469801_   2984 ATAC-----------TTCACAGAAATAGAAAAATTAATCCTAATATATTT 3022
                           v -----------  ii       v  v  ii i       v  viv 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_145469801_   3023 ATGGAATAATG--AAAGACCCAGAATAGCCAAAGCTATCCTAAGCAAAAA 3070
                               --   -- ii                 i v   i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_145469801_   3071 GAACAAAACTGGAAGAATCACATTACCTGACTTCAA--CTTATACTACAG 3118
                                ii    i  v     i v  ii i     --    --     i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAA 245

  chrX_145469801_   3119 AGCTATAGTAACCAAAGTAGCATGGTATTGGCATAAAAACAGACACATAA 3168
                              i     i   iii  ii     i        ii i     i   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_145469801_   3169 ATCAGAGGAACAGACTAGAGGTCCCAAAGATAAATTCATACGTCTACAGT 3218
                             iv    i   v v   ivi   i i     ii     i i  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_145469801_   3219 GAACTCATTTTTGACAAAGGTACCAAGAACATACATTGTGAAAAGGGCAG 3268
                         v  i v     i     i   i      v   v  v  v i    iii  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_145469801_   3269 TCCCTTCAATTAATTGTGCTGAGAAAACTGGATATCCATATGCAGAAGAA 3318
                           ii     iv   v      i  v         ?   i     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_145469801_   3319 TGAAACTCTACCCTTATCTGTCATCATATATAAAAATCAAATAAAAATAG 3368
                             ii vv    i  i  vv  i      i      i  v v     i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_145469801_   3369 ATTAAAGACTTAAACCTAAAACCTCAAACTGTGAAACTACTGCAAATAAA 3418
                           i ?    i    iv   i v  v     i i     vi iv  iv   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_145469801_   3419 CTTTGGGGAAACTCTCCAAGACCTTAGTCTCAATAAAGATTTTTTGAGTA 3468
                          v v  ? v  v   i iv      i vi viii  v i   i  iii  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_145469801_   3469 GTAGC-TCACAATCATAGGGAACCAAAGCAAAAGTGGACAAATAGGATCA 3517
                         - ii -i  v  v  i i v   v    v    i i  i    v   iiv
  L1M4_orf2#LINE/    596 -TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_145469801_   3518 CA-CAAAGTTAAATGCTGCTGC-CTAGCAAGGAAACAGTAAATAAAGCAA 3565
                           -    i     vi  vi  i-  vvv     v  vi v  v    ii 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_145469801_   3566 AGAGATAATTCGCAGACTGGGAGACAGTATTTGCAAACTGACCATCTGAC 3615
                          i   i  ii i    v       v i          iiivvi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_145469801_   3616 AAGGGATTAATAATCAGAATATGTAAGAAGCTCAAACCACTCTATAGAAT 3665
                               i vi  vi        i   ii i   vv  v    v   ----
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA---- 790

  chrX_145469801_   3666 ATGTAAGGAGCTCAAACCACTCTATAAATCAATAAAAATTTGGCAAAACA 3715
                           iv  i  ---    iv  i ----   --- ?    v v      iv 
  L1M4_orf2#LINE/    791 ATAAAAAGA---CAAATAACCC----AAT---TWAAAAATGGGCAAAGGA 830

  chrX_145469801_   3716 CCTGAATAGATATTTCTCAAAAGAAGACATACACATGGCAAACGGGCATA 3765
                         ii        i       v        i     v     v  iii   i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_145469801_   3766 TGAAAAAGTGTTCAACATCATTAGTCAT 3793
                               ii  i         ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (149 / 88)
Gap_init rate = 0.02 (15 / 907), avg. gap size = 2.67 (40 / 15)  


3282 22.40 6.18 0.23  chrX_145591734_145593940      861  1717 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145591734_    861 TGGAAAGACATTC-ATGTTCATGAGTTG-AATAATTAATGTTGTTAAGCT 908
                                 i  i -         ii   -  v v     i        v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145591734_    909 GGAAATGCCAGCAAAAGAGATCTACAAATTTAATGTAATTCCTATCAAAT 958
                           v   i ivv v   vv        i   i  i i   i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145591734_    959 TTTCCAATGATTTTTT-----AAAT-ACCAAATTTATTCTAAAATTTATA 1002
                          ii viv  vi     -----    -iv   ii v  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_145591734_   1003 TGGAATCTAAAGGGATCCTTAATAGTCAGACCAATTTTGA----GAAAAA 1048
                              vivv      i  vv     i  i v    i    ----   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_145591734_   1049 CAAAGCTGGAGACGTCACACTTCCTCATGTTAAAACTTATTACAGAGTTA 1098
                              i     ivv          iv  v i        i    i  i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_145591734_   1099 CAGTAATTTA-ACAGTGTGGTATTGGCATAAAGGAAGTCTTATAGACCAG 1147
                                iv -           i        i iv  v v      i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_145591734_   1148 TGAAATGGAATAGAAAGGCCAGAAATAAACTTTCATATATATGGTCAAGT 1197
                           i   i    v  i  v            iivi i  v         v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_145591734_   1198 TATTTTTGACAAGGGTGCTAAGACCTCTTAATGGGGAAAGA-CAGTCTTT 1246
                         v     i           i      vi i            -i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_145591734_   1247 TCAATAAATGATGTTGAGAAAGTTGGATATTCACATGCAAAAGAATGAAG 1296
                             i     i  i  i  v ii      ?i                   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_145591734_   1297 TTGGACCCTTACT-------ATATAAAAAAATCAATTGAAAATTGATGAA 1339
                                 i   i-------     v      i  i v     v   v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_145591734_   1340 AGACTTAAATGTATGTGCTAAAACTGTAAGCCCCTTAGAAGAAAA----G 1385
                             i        v v         i   iv i            ---- 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_145591734_   1386 --------CTTCATG---TTA--TTAGATATGAATTTTTTTGCTATTCCA 1422
                         --------    i  ---  i--    ii vvii   i  v v   vv  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_145591734_   1423 C-AAAAATAAAGGACAACAAAA----AAATAGATAAATTTGAGTGTATGA 1467
                          -    ii v i -        ----             v  v vi  v 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_145591734_   1468 CAATTAAGAACCTTAAGTGCATCAAGGAATGCAATCAACAGAGCCAAA-G 1516
                         v      i   i  v-    v    i i ii v     v i  iv   - 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_145591734_   1517 ACAACCTGCTGTATAGGGGAAAA-ATTTGCAAAGCATATAACTGATGAGG 1565
                               ii v v  i  i     -         v      v     i   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_145591734_   1566 GGTTAATATCCGGAATATGAAAAGAACTC---CAACTTAACGATGAAAT- 1611
                          ii vi     i      iv         ---     i  ii  i   v-
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_145591734_   1612 ----ACAACCTAACTTAAAAACAGGCAAAGGAATTAAATAGACATTTCCG 1657
                         ---- i    i  i ?     ii         v  i            iv
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_145591734_   1658 GAAAGAAAATATACAAACAACCAACAAACACATTAAAAGATTCTGAACAG 1707
                         v      i         iii    i  i     v       v  v    v
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_145591734_   1708 TACCAATTAT 1717
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (114 / 75)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.75 (55 / 20)  


3282 22.40 6.18 0.23  chrX_145604703_145606909.rev      863  1719 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145604703_    863 TGGAAAGACATTC-ATGTTCATGAGTTG-AATAATTAATGTTGTTAAGCT 910
                                 i  i -         ii   -  v v     i        v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145604703_    911 GGAAATGCCAGCAAAAGAGATCTACAAATTTAATGTAATTCCTATCAAAT 960
                           v   i ivv v   vv        i   i  i i   i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145604703_    961 TTTCCAATGATTTTTT-----AAAT-ACCAAATTTATTCTAAAATTTATA 1004
                          ii viv  vi     -----    -iv   ii v  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_145604703_   1005 TGGAATCTAAAGGGATCCTTAATAGTCAGACCAATTTTGA----GAAAAA 1050
                              vivv      i  vv     i  i v    i    ----   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_145604703_   1051 CAAAGCTGGAGACGTCACACTTCCTCATGTTAAAACTTATTACAGAGTTA 1100
                              i     ivv          iv  v i        i    i  i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_145604703_   1101 CAGTAATTTA-ACAGTGTGGTATTGGCATAAAGGAAGTCTTATAGACCAG 1149
                                iv -           i        i iv  v v      i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_145604703_   1150 TGAAATGGAATAGAAAGGCCAGAAATAAACTTTCATATATATGGTCAAGT 1199
                           i   i    v  i  v            iivi i  v         v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_145604703_   1200 TATTTTTGACAAGGGTGCTAAGACCTCTTAATGGGGAAAGA-CAGTCTTT 1248
                         v     i           i      vi i            -i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_145604703_   1249 TCAATAAATGATGTTGAGAAAGTTGGATATTCACATGCAAAAGAATGAAG 1298
                             i     i  i  i  v ii      ?i                   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_145604703_   1299 TTGGACCCTTACT-------ATATAAAAAAATCAATTGAAAATTGATGAA 1341
                                 i   i-------     v      i  i v     v   v ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_145604703_   1342 AGACTTAAATGTATGTGCTAAAACTGTAAGCCCCTTAGAAGAAAA----G 1387
                             i        v v         i   iv i            ---- 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_145604703_   1388 --------CTTCATG---TTA--TTAGATATGAATTTTTTTGCTATTCCA 1424
                         --------    i  ---  i--    ii vvii   i  v v   vv  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_145604703_   1425 C-AAAAATAAAGGACAACAAAA----AAATAGATAAATTTGAGTGTATGA 1469
                          -    ii v i -        ----             v  v vi  v 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_145604703_   1470 CAATTAAGAACCTTAAGTGCATCAAGGAATGCAATCAACAGAGCCAAA-G 1518
                         v      i   i  v-    v    i i ii v     v i  iv   - 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_145604703_   1519 ACAACCTGCTGTATAGGGGAAAA-ATTTGCAAAGCATATAACTGATGAGG 1567
                               ii v v  i  i     -         v      v     i   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_145604703_   1568 GGTTAATATCCGGAATATGAAAAGAACTC---CAACTTAACGATGAAAT- 1613
                          ii vi     i      iv         ---     i  ii  i   v-
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_145604703_   1614 ----ACAACCTAACTTAAAAACAGGCAAAGGAATTAAATAGACATTTCCG 1659
                         ---- i    i  i ?     ii         v  i            iv
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_145604703_   1660 GAAAGAAAATATACAAACAACCAACAAACACATTAAAAGATTCTGAACAG 1709
                         v      i         iii    i  i     v       v  v    v
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_145604703_   1710 TACCAATTAT 1719
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.52 (114 / 75)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.75 (55 / 20)  


2653 27.11 2.16 1.14  chrX_145631467_145633330      500  1377 (487)    L1M4_orf2#LINE/L1       22   908 (0)  

  chrX_145631467_    500 TGGATAGGAAGAATCAATATTGTTAATATGGCCATAATGTCCAAAGCTG- 548
                              v      v i           v     v   v vi     -i  -
  L1M4_orf2#LINE/     22 TGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAA-TTGA 70

  chrX_145631467_    549 TTTACAAATTAAATTTTATTCCTATCAAAATACCAATGACATTTTTCACA 598
                          i    i   v  iviv  i           v   iivi v     ii  
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chrX_145631467_    599 GAATTAGAAAAAAAAATC-TAAAATTTATTTGGAACCCCTCCAAAAAACC 647
                            v v  v  ivvi   -       i  v     v--- v   iii   
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAA---TGCAAGGGACC 167

  chrX_145631467_    648 CATA-CAGCCAAAGCAATTCTAAACAAAAAAAACAAAGCTGGAGTCATCT 696
                           v -i       i    ii i  v  i  i       i     vvv  v
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chrX_145631467_    697 CACCACCTGACTTCAAACTATAGTACAAGGCAACAGTATCTAAAACAGCA 746
                            iv  ii i      viv  v     i  v      vii  i    ii
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_145631467_    747 TGGCAATGGCACAAAAACAGACACATAGATCCATGGGAAT-GATCAGAGA 795
                            i v     i  ii i     i       v    -   -  viv    
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGG-AATAGAATTGAGA 316

  chrX_145631467_    796 ACTCAGGAATAAAGCCATATACCTATAACCATCTGATATTTGACAAAGCT 845
                         iii   i      v     i ii   iii  vi    v  i     i v 
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_145631467_    846 CATAAAAGCAAGCAATGGGGAAA--ATACTCACCACTCAGTAAATGCTGC 893
                         vvi  i v  vv           --   v  vii--   ii     v   
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGC 414

  chrX_145631467_    894 TGGGCTAACTGACTATCCATATGCCAAATATTAAAACTGGACCCCTACCT 943
                             vi     iv  ?   i    v   v v i  ii             
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_145631467_    944 TTCACCATATACAAAAATCAACTCAAGATGGAATAAAGATTTTAATGTAA 993
                         iv                i       i     vi ?   ii v       
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_145631467_    994 AACCTAAAACTATAAAAATTCTAGAAGAAAATCCAGAAA-ATATCATTCT 1042
                         i v              v ii          ivi  i?i- v   -   v
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCG 563

  chrX_145631467_   1043 GAACATCATCCCAGGTAAAGACTTCAT-GATGAAGACTCCAGAAGCATTT 1091
                         vi  v iivvii   i  v ii   v -   - v   v   i     ivv
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAA 612

  chrX_145631467_   1092 GCAACAAAACCAAAACACTGACAAGTGAGACCTAATTAAACTAAAGAACT 1141
                                  vv    - iv  i  i vi   i v  i   v v  i    
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_145631467_   1142 TCCATACAGTATAAGAAATTATCAACAGAGTAAACAGACAACCTAGAGTA 1191
                          iii i vvi v i  v i      v i   i  v        i v  v 
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_145631467_   1192 TGGGAGAAAATGTTTGCAAATTATGCGTCTGACAAAGGCCTAATATCCAG 1241
                                    i         i  iii     i  i  v  vi       
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_145631467_   1242 AATCTATAAGGAACTCAAACAA----ATAATAAAAA-------AATGCAA 1280
                            v     i      vv    ----          -------  iv   
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_145631467_   1281 TTTAAAAATTGGCAAAGGACATAAACAGACACTTTTCAAAAGAAGACATT 1330
                           ?      v         iv i  i     i  i  v        i  v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chrX_145631467_   1331 CACTCAGTCAACAAGCATATGAAAAAATGTTCAATGTTACTAATCAT 1377
                           vvii i   i     i       i   i    ii i ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.02 (16 / 887), avg. gap size = 1.81 (29 / 16)  


3087 26.09 1.45 0.45  chrX_145722676_145727338.rev     3276  4172 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_145722676_   3276 GAAAGAAATTCCACATTCATGGATTGGAAGAAACAATATTGCTGAAATGT 3325
                               v  i   ii                vvi       i i i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_145722676_   3326 CCATACTACCAAAAGCAATCTACAGACAAAATGCTATCTCTATCAAAATA 3375
                          v     v  v   vii         ivv  i  v   i          v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_145722676_   3376 CCAATGACATTTTTCACAGAAATAGAAAAAAC-ATCCTAAAATTTATATT 3424
                            iivi v     ii       v  v  ivi-           i    v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_145722676_   3425 GATCTACAAAAGACCCAGAATAGCCAAAGGTATCCTAAGAAA-AGGAACA 3473
                           vv i   ii                 ivv   i i i   - i     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_145722676_   3474 AAACTGGAAGAATCATATTACCTGACTTCAAATTATACTACAGAGGTATA 3523
                           ii    i  v   i i v  ii i      viv       i  v  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_145722676_   3524 GTAACAAAAACAGCATGGTATTGGCATAAAAACAGACACACAAACCAATG 3573
                             iv  i    ii     i        ii i     i i i i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_145722676_   3574 AAAAAGAATAGAAAACCCAGAAACAA--CTTTACATTTCTACGGTGAAGT 3621
                         i  v     v  i ii       i  -- iv       -- i   v  v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT--ATGGTCAATT 350

  chrX_145722676_   3622 CAGTTTCAATAAAGGTGCTAAGGGCATAAATTGGAGAAAGGACAGTCTCT 3671
                         v v    i i  i     i   iv   vv v   i     i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_145722676_   3672 TCAATAAGTGGTGCTGGGAAAACTGAATATCCATATGCAGAAGAATGAAA 3721
                             i  i           v     i   ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_145722676_   3722 CTT-ACCCATATCTCTCACCATATAGAAAAATCAAATCTAAATGAATTAA 3770
                         i v-    v  i   v         v      i  v  v     i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_145722676_   3771 AGACTTAAATCTAAGTCCTCAAACTATGAAACTAATAAAGGAAAACTTTG 3820
                             i     v    vv  v       i     vv  i i      v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_145722676_   3821 TGGAAACTCTCCAGGACATTGGAGTGGGCAAAGTTTTCTTGAGAGATCTC 3870
                         v? v  v   i iv   v    iv i     v v      -   v  vv 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGAC 599

  chrX_145722676_   3871 -TCACAAGTATAAGCAACCAAAGTAAAAATGGACACATGGGATCACATCA 3919
                         -i  v   i i       v    v      i  i v  v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_145722676_   3920 AG-TGAAAAAGCTTCTGCACAGCAAAGGAAGCAATAAAAAAGGTGAAGTG 3968
                          i- v     -   i  ii vv       vi v  v  i  i     iv 
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_145722676_   3969 ACAACCCACAGAACAGAAGAACATATTTGCAAACTGCCCATCGGAAAAGG 4018
                                      ii i    v           iiiivi   v  v    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_145722676_   4019 GATTAATAACCACAATATGTAAGGAGTTCAAATGACT--ATAGGAAATAT 4066
                           i vi  v   v     i   i  ii  vv ii   --   iv   v v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_145722676_   4067 -CTAATAATCTAACTAAAACATGAGGAAAAGACCTGAAAAGGCATTTCTC 4115
                         - v     i i  i ?   v   i v   i  ii    v  i        
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_145722676_   4116 ---AAAAGACATACAAATGACAAACCAGTATATGAAAAAGTGCTCAACAT 4162
                         --- i    i         i v  iv  i i       ii          
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_145722676_   4163 CATTGACCAT 4172
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (134 / 96)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 1.42 (17 / 12)  


1064 27.79 1.21 2.72  chrX_145790115_145793702.rev     1910  2240 (1348)    L1M4_orf2#LINE/L1        1   326 (582)  

  chrX_145790115_   1910 TGAAAAAACATTCTATTCTTATGGAATGGAAGAATCAATATTGTTAAAAT 1959
                           i   i i  i i  vi i     v       v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145790115_   1960 GGCCATACTGCCCAGAGCAATTTACAGATTTGACACTATTCTTATTAAAC 2009
                            v     v    i vii  i        ii  i v  i i   i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145790115_   2010 TACCTACGTGA-TTCTTCACAGAAATATAAAAATAA-AAACT-ATTCTAA 2056
                          v  vi -  v-  i  ii       ------- i -  i  -  i    
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAAT-------TGACAAGCTGATCCTAA 142

  chrX_145790115_   2057 AATTTACTTGGAACCAAAAAAGAGCCCAAATAGCCAAAGTAATCCTAAGC 2106
                             i iv     viiv  ii  v  vi          ii    i i i-
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA- 191

  chrX_145790115_   2107 AAATAGAAATAAACCTGGAGGCATCACACTACCTAACTTCAAACTATTCT 2156
                            v ii  i   vi      vv       v  i  i      viv v  
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_145790115_   2157 ATAAGGTTACAGTAACCAAAACAGCATGGTACTGATACAAAAA-AGATAC 2205
                          i  i i        i   i    ii        ii i  ii -   i i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_145790115_   2206 ACAGACCAATGGAGCAGAATAGAAAACTCAGAAAT 2240
                          i   i       ii     v  i iii       
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

Transitions / transversions = 2.68 (67 / 25)
Gap_init rate = 0.02 (7 / 326), avg. gap size = 1.86 (13 / 7)  

1571 28.31 2.57 1.47  chrX_145790115_145793702.rev     2546  3089 (499)    L1M4_orf2#LINE/L1      320   869 (39)  

  chrX_145790115_   2546 CAGAATTGAAGCCACATACCTGTAACTATCTGATCTTTGACAAAGCTGAC 2595
                              v i  v   i i ii i iiii vi    i  i     i v  v 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_145790115_   2596 AAAATCAAGCAATGGGGAAAGGACTCTGTATGCAATACATGGTGCTGGGA 2645
                           i i  vv            i ivv v v v   i v            
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_145790115_   2646 TAACTAGCGAGTCATATTCAGTGGAATAAAACTAGACCCTTACCTTTCAT 2695
                         i    i vv ?i  i  v  ivi    i  ii i     i     iv  i
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_145790115_   2696 CATATACAAAAATTAACTCAAA---GACTAAAATTTTTAAATGTAACACC 2742
                                               ---  ii ? ivii -        v v 
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCT-AAATGTAAGAGC 518

  chrX_145790115_   2743 TCAAACTGTAAAAATCCTAGAAGAAAACCTAGGAAATAACCTTCCCAGCA 2792
                          v     i     v  i           v    ?ivv  i    viii v
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_145790115_   2793 TTGGCCTTAGCAACTGATTT-TTGGCTATCTCCTTAAAA--ACAATTGCA 2839
                             vi vi    -  i   -  i v   vv vii    --    --   
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAA-TGGTTTCTTAGATATGACACCAAAAGCACAA--GCA 615

  chrX_145790115_   2840 ACAACAACAACAAATGGACAACTGGAACCTAGTTAAACTAAAGACCTTCT 2889
                             -  v  v    i  i  v v i  i vi i   v v  i v   i 
  L1M4_orf2#LINE/    616 ACAA-AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_145790115_   2890 GCACAGCAAAAGAAACTATCGACAAAGTGAACAGATAACCTACAGAATGG 2939
                          ii vv    i  v      i v        v   i    i         
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_145790115_   2940 GAGAGAATACTCACAAACCATGCCATCTGACAAAG-ATTTACTATTCACA 2988
                             i    i ii    i   ii-      i  i - i  i-   i  v 
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATAT-ATCTGATAAGGGACTTG-TATCCAGA 762

  chrX_145790115_   2989 ATATCTAAGAAACTTAAGCAAATCAA--GTAAGAA-----ACAACCCTGT 3031
                             v   ii    ivvi   v    --i   i  ----- i     vi 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chrX_145790115_   3032 TAAAAAATGAGTGAAGAACATGAACAGACACTCCTCAAAAAAAAGACATA 3081
                          ?       i ii   i iv    i     i i   v   i  -  i   
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-GATATA 861

  chrX_145790115_   3082 CAAGTGGC 3089
                            i    
  L1M4_orf2#LINE/    862 CAAATGGC 869

Transitions / transversions = 1.73 (95 / 55)
Gap_init rate = 0.02 (13 / 550), avg. gap size = 1.69 (22 / 13)  


2539 27.95 4.09 0.91  chrX_145795357_145799173.rev     2447  3326 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145795357_   2447 TGGAAAAATATTTTGTGTTCTTGGATTAGAAGAATCAATATTATTAAAAT 2496
                               i    iiii     v      i     v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145795357_   2497 G---------TTCAA-----TCTACAGATTCCTTGCAATCCCTATCAACA 2532
                          ---------ii   -----           vvi              v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145795357_   2533 CATCAATGAAATTATTCACAGCAAAAGAAAAAC-AATTCTAAAATTGATA 2581
                         ivi  iivivv  v  ii   v  vv  v  i -i  i        v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_145795357_   2582 TAGAACCACAAAACACCAGGAATAGCCAAATTC-TCCTGAGCAAAAA-AC 2629
                          i   vii   iiv   vi           viv-  i   iv  i  - v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_145795357_   2630 CAAAACTGGAAAAAAATCACATTACCTGACCTCAAA--TTAAATGGCAGA 2677
                             ii    ii v--     i v  ii ii     --   --ivi  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGAC--TCACACTTCCCAATTTCAAAACTTA--CTACAAA 246

  chrX_145795357_   2678 GCTATAGTAACCAAAAAAGCATGACACTTGCATAAAGTCAGAAACACAGT 2727
                             i     i   i v  ii  ii   v      i vi   v i i  v
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_145795357_   2728 CCAATGGAAAAGAATAGAAAACTCAGAAATAAATTCATACATCAGCACTG 2777
                         i        v     v  i iii          ii       iviiiv v
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_145795357_   2778 AATTCATTTTTAACAAAGTTGCCAA-AGCATTCACTGAGGAAAAGAGTGT 2826
                             v     ii    i v      - v      v  i     ii vv  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_145795357_   2827 TTCTTCAATAAATGGTGCTGAGAGAACTGAATATTCATATGCAAAAGAAT 2876
                         i i     i           i  v     i   ?i  i            
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_145795357_   2877 GAAACTAGACCTCTCTCTCTCACCATACATAAAAATCAAAT-GAAATGCA 2925
                            ii i    i  vi   v       i i      i  v -i     v 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_145795357_   2926 GTAAAGACTTAAGTCTAAGTTCTTACACGATGAAACTACTAAAAAGAATC 2975
                         vi ?    i   i v    vv  v v  v  i     -  v i     vv
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAAA 545

  chrX_145795357_   2976 CAT-------------TGTGGAATTGGACTATGCAAAGATTTCTTGTGTA 3012
                            -------------i   ivv    ii  v    v i      ivi  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_145795357_   3013 ATACCCCACATGCACAGGCAACCAAAACAAAAATTGACAAATGGGATCCC 3062
                         vv  v   v v     i     v   iv      v  i    v   iii 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_145795357_   3063 ATCAAGTGGAAAAGTTTCTGCACAGAAAAGGAAACAATCAATAATGTGAC 3112
                              ivvv    ii  i  ii vvv      v  v     v  v    v
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_145795357_   3113 AGGACAACCCAGACAATGAGAAAAAAACATTTGCAAACCACCCATCTCCC 3162
                          i         v v    i  i    -i         i  ivi    vvi
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGAT 744

  chrX_145795357_   3163 ATGGGATAAATAACCAGAACATGTAAAGAGCTCAAATAACTCTATAGGAA 3212
                          v    ivvi  v      i  i      i   vv i     v   iv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_145795357_   3213 ACAATCTAATAATCTCATTTAAAAATGGAGTAAAAAGAT--GAATAGACA 3260
                          v iv v     i iv   ?        - i   i-   --         
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGG-GCAAAG-GATTTGAATAGACA 842

  chrX_145795357_   3261 TTTCTGAAAGGAAGACATACAAATGGCAAACAGGTATATGAAAAGGCACT 3310
                              vv  i     i           v  i i i i        iii  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_145795357_   3311 CAAGATCACTGAACAT 3326
                            v    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.75 (44 / 16)  


2321 27.81 2.98 2.76  chrX_145799891_145802755     1467  2372 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145799891_   1467 TGAGAAAACATTCCATGCTCATGGACTGGAAGACTCAGTATCATTTAAAT 1516
                           ii  i i  i     i       i         i i   ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145799891_   1517 GACCATTTTATCCAAATAAATCTGCACATTTAATACAATTTCTATCATAT 1566
                          i v  vi vi      vi    i  v   i  ii    ii      v v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145799891_   1567 TATCAG-TGTCATTTTCACAGAAATATTATAAAA-AATTCTAAAGTTCAT 1614
                          vi   -  i v    ii       - v i  iv-i  i     i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_145799891_   1615 ATGGAA---CAAAAAAAGCCTGAATATTCAAAGAAATCCTAAGCAAAAAA 1661
                               ---   iii v-  v     vi    iv    i i ------  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGA------AA 192

  chrX_145799891_   1662 AAAAAAAACAA---TGCA----TCAGATTGCATGACTTCAAATTATACTA 1704
                           i  i     ---  v ----   v i v vii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_145799891_   1705 TTAGGCTGCAATAACTAAAACAGCATGATACTGGTGCAAAAATAGTCACA 1754
                         iv i   i  i   ii  i    ii  i      iii  ii    v  i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_145799891_   1755 TAATTCAATGGTACA-AATAGAGAACACAGAAATAAAGCCACATACCTAC 1803
                           iv       v i -   v    iiv          v   i i ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_145799891_   1804 AACAAACTGATCTTCAATAAAGTCAACAAAAATAAACAACTGGGATAAGA 1853
                         iiiv  i    i   i i  i viiv   i vi vv   iv    v ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_145799891_   1854 CGCCCTATGTCATAAATAGTACTGGGAAAACTGGCTAGACATATGCAGAA 1903
                         iivi  v viv i    i  i      v      v  ?v  i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_145799891_   1904 GAAAGAAATTGGACCTCTGTCCTTCAACATATAAAAAAAAATTATCTCAA 1953
                            v   i       i  ii iiv  v      v     --   v     
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAA 490

  chrX_145799891_   1954 GATGAATTAAAGACCTAAATTTAAAACCTGAAACTATAATAATACTAGAA 2003
                         i   i  i ?          v   i v  i         v v vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_145799891_   2004 AAAATTATTTTAGGG----ATCTT-GTGGATATTGGGCTAGGCAACAAAT 2048
                         i   vi  ---   ?----     -   - iv     i       iiiv 
  L1M4_orf2#LINE/    541 GAAAACAT---AGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTT 586

  chrX_145799891_   2049 TTAT-GATGAAGA-ATCAAAA-TACAAATGCAACAGAAACAAAAATAAAT 2095
                          iv -   - v  - i     -i    --      i  iv       i  
  L1M4_orf2#LINE/    587 TCTTAGAT-ATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGAT 633

  chrX_145799891_   2096 GA----GACTTAAT-AAAACTAAAAAGTTTC-TGCTCAGCAAAAGAAGTA 2139
                         i ----     v  -    i      v   i-    i--    i  viiv
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACT 681

  chrX_145799891_   2140 ATCAATAGGATAAACAGACAGCCTACAGAATGGAAGAAAACATTTATAAA 2189
                              v iii i  v     i  i         i      i    ii   
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_145799891_   2190 TTATGCCTCCAACAAAGAATTATTATATAGTATCTACAAGGAACTCAAAA 2239
                          i  iiv  ii i  i i i vv   vi  v  v  i  i      vv -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA- 780

  chrX_145799891_   2240 CAACTCAATGACAATGAATGAACACTAATAATCTCATTAAAAAGTGGGTG 2289
                                  ---   i  --  v  v     i iv   ?    i    ii
  L1M4_orf2#LINE/    781 CAACTCAAT---AATAAA--AAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_145799891_   2290 AAGATTATTAACAGACATTTCTCAAGAGAAGAAATACAGGTAGTCAACAA 2339
                            iv v v  i           v i      v     ii i i   i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_145799891_   2340 ACACATGAAAAAATGTTCAACATTACTAATAAT 2372
                         i          i   i       i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (166 / 82)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.00 (52 / 26)  


1291 25.71 11.04 3.47  chrX_145812519_145814143.rev      503  1136 (489)    L1M4_orf2#LINE/L1      227   908 (0)  

  chrX_145812519_    503 ATTTTAAGACATAATATA--GCTACAGTAATCAAGAGTGTGTGGTTATCT 550
                             i  i  v  v  i --                vv       - iiv
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT-ACTG 275

  chrX_145812519_    551 GTGGAGAAATGAGCACATAGATCAATGGAAAATAATTAAGAACTCAAAAA 600
                          iiv iii  iii  i              v v    i   iii  i   
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chrX_145812519_    601 TACATGTACACAAATATGTCCAACTAATTTTT--TAAAGGTATAAAAGTA 648
                           v ivi i   vv    vi   i i     i--i  i   iiv  iiiv
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_145812519_    649 ATTCATTGGAGGGAAATATAGCCTTT-CAACAAATAGTGTTGAAATAATT 697
                              v   -  i  iv    i    -        i   i  ii i  i 
  L1M4_orf2#LINE/    376 ATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_145812519_    698 GGACACCCACAGGCAAATAAAAGAAAAACAATCTAGGCCTAAGTCTTAGG 747
                            i ?     v     vi  v   i------i i i  ivvii  i vi
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAG------TTGGACCCCTACCTCACA 468

  chrX_145812519_    748 CCTTCAACAAAA-TTAATTCAAACTGAATAACAGGCTTAAATGCAA---C 793
                           v vv      -    i     v  i  v ?  i i      i  --- 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_145812519_    794 -----------AACTTTTAGAAGAAA---CAGGAGAAAATCTTTGGTACC 829
                         -----------    i          ---i   ? v       i vv   
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_145812519_    830 TAGGATTAGCCAGAATG--TTTTTAGATTTGACACCAAAATTATAATTTA 877
                          v  i    v  --   --  i      v           vi i  viv 
  L1M4_orf2#LINE/    569 TTGGGTTAGGCA--ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_145812519_    878 TAAAATTTTTAAAAAT-GATAAATTTGACTTTGTCAAAATCTAAAAA--- 923
                         i    vv---      -        v     ii       -      ---
  L1M4_orf2#LINE/    617 CAAAAGA---AAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTT 662

  chrX_145812519_    924 TTGTGCTCTGAGAAAGAC-CTGTCAA---------AAGACTA-------A 956
                                iii -- i   -  i    ---------     v ------- 
  L1M4_orf2#LINE/    663 TTGTGCTTCAA--AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_145812519_    957 ATG--------TAT----AAGCTATATAT-----AAAG---CTATATATA 986
                            --------   ----  iii      -----  i ---i i   vi 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_145812519_    987 AGCTGTATAAAGAACT-TCAAAATTCAACACTAGGAAAAAAGGAGCAGA- 1034
                         iiv i           - i v  i    i v  --    i ----  i -
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATA--AAAAGA----CAAAT 804

  chrX_145812519_   1035 AACAC--TTAGAACAAAGGCAAAAGATATGTGGAAATATTTCACAGAAGA 1082
                            v --  ?i  v vi      i   v  viv i i     v vi    
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_145812519_   1083 AGATATATAAATGGCATATAAGCACATGTAAAGGTGTTTGATATAATTAT 1132
                                i       vv           v    i  i ii i  v ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_145812519_   1133 AAGG 1136
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.79 (102 / 57)
Gap_init rate = 0.04 (29 / 682), avg. gap size = 3.17 (92 / 29)  


2531 27.65 2.65 2.30  chrX_145823885_145825739.rev      502  1369 (486)    L1M4_orf2#LINE/L1       38   908 (0)  

  chrX_145823885_    502 ATATTGTTGAAATGTTCATACTACCCCCAGTAATCTACAGATTCAATGCA 551
                                 i i   viv     v   vv v i              i   
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chrX_145823885_    552 ATCCTTATTAAAATACGTATGACATTCTTCACAGAAATATTAAAAA---- 597
                             i   i     v vviivi v  i  ii       -- i v  ----
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTG 135

  chrX_145823885_    598 ATCCTAACATTTATATGGAATTACAGCAGACCCAAAATAACCAAAGCTAT 647
                                v   i        v i  ivi      i    i     i v  
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_145823885_    648 TCTGGGAATAATAAACAAAAATGAAAACAAATAAACTGTCAGAATCACAT 697
                         ii  ------------     vi i      ---ii  vvi  v     i
  L1M4_orf2#LINE/    186 CTTG------------AAAAAGAAGAACAAA---GTTGGAGGACTCACAC 220

  chrX_145823885_    698 TACTTGATTTCAAATTATACTACAGAACTATTGTAAACACAACAACACGG 747
                          v iii        viv       i i   iv    v  vi   iiii  
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_145823885_    748 TA-TGGTAC-----------TATAGGCCAATGGAACAGAACAGACAACCC 785
                           -   i i-----------     ii        i    iv  v ii  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_145823885_    786 TGAAACAAATTCATATGCCTGCAGAGAACTAATTTGCAACAAATATGCCA 835
                         v    i   ii    iiii iii vv  i i    v i    ivi     
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_145823885_    836 AAGACATATACTGGGAAATAGGCAATTTCTTCAATAAATGCTGTTGGGAA 885
                          iiv   vi v    i  viiii i i i     i     v  i     v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_145823885_    886 AACTGTATATCCACATGCAGAAGAAATGAAACTAGACTCACACCTCTCAC 935
                              v   ?         i     -    ii i   i vi     v   
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACAC 469

  chrX_145823885_    936 CATATACAAAAATCAAAACAAAATGTATTAAAGGCTTAAATATAAGACTT 985
                                      i  vv       v  i ?  i i     i     vi 
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_145823885_    986 AAAACCATGAAACTACTGCACGAAAACATTGGGGAAAATCTCCAGGACAT 1035
                              i  i     vi iv v        v  ? v      i iv   v 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_145823885_   1036 TGGTCTGGGCAAAAATTTCTT-GAC-TGATATCCCAGACGAACAGGCAAC 1083
                            vi i     vii      -  i-   i --   i v v   i     
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACA--CCAAAAGCACAAGCAAC 617

  chrX_145823885_   1084 TAAAGCAAAAATGAACAAGTAGAATCACATCAAGTTAAAAAACTTCTCCA 1133
                         v    v      ii i  i v i iiv      iv v        i vii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_145823885_   1134 CAGCAAAGGGAACTATCA-GCTAGTGATGAGACAATCCACAGAACTGGAG 1182
                          vv      iv       - vv     vi      i        iv    
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_145823885_   1183 AAAATATTTACAAAGTACCCATCAAACAAAGGAGTAATAACCAAGATCTA 1232
                                  i    vi ivi   vi i  i   v vi  v   ii  v  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_145823885_   1233 TAACAAGCTCAAACCACTC--TA-TAAAAAATCTAATAATCTGAT-GAAA 1278
                            vi i   vv  v    --  -      iv v     i ii  -?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_145823885_   1279 AATGGGCAAAAGATGTTCATAGACATTTCTCAAAAGAAGACATTCCTGTG 1328
                                   i   v vv             v        i  v vvi  
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_145823885_   1329 GCAAACAGGCATATGAAAAGGTGCTTAAATTCATGGATCAT 1369
                           v  i i   i        i    i  vv   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.02 (14 / 871), avg. gap size = 3.07 (43 / 14)  


1761 25.64 2.00 3.27  chrX_145833468_145835989      683  1232 (1290)    L1M4_orf2#LINE/L1        1   543 (365)  

  chrX_145833468_    683 TGAAATGATATTCCGTGTCCATGGTTTGGAAGAATCAATATTTTTAAAAT 732
                           i  v     i  i   i     v        v i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145833468_    733 GACCATACTACCCAAAGGCATCTACCTATTCAATGTAATCCTTATCAAAA 782
                          i v     v      vvv      vv      i i     i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145833468_    783 TACAAATGACATTCTTCACAGAAAT-AAAAAATAAATCCTAGAATTTGCT 831
                          v v iivi v  i  ii       -i v  iivi      i    iiiv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_145833468_    832 TAGAATCACAAAAAGGG--TGAGAATAGCCATAGCTACCCTAAGGAAAAA 879
                          i   vii   ---   --iv          v i v i i ---      
  L1M4_orf2#LINE/    151 TGGAAATGCAA---GGGACCCAGAATAGCCAAAACAATCTT---GAAAAA 194

  chrX_145833468_    880 AAAAAAAAGCAAACAAAAAACATACAGGAATCACATTATCTGACTTCAGA 929
                         i  i  -------    iv--- iv    v     i vi ii i    i 
  L1M4_orf2#LINE/    195 GAAGAA-------CAAAGT---TGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_145833468_    930 TTATACTACCAAGCTATGGTAACCAAAAACAACATGGTACTGGCATTAA- 978
                         viv      v      ii    i   i -  iii            v i-
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGG 283

  chrX_145833468_    979 ACAGACACATATACCAATGGAAAAGAATAAAGAACCCAGAAACAAATCCA 1028
                          i     i   v i        v     vi   ii       i   i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_145833468_   1029 CACACGTACAGCAAACTCATTTTTGACAAAGGTACCAAAAATATACACTG 1078
                         i   iv  ii iv  i v     i     i   i    i vi  v  v  
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_145833468_   1079 GGTAAAAGACAGTCTCGTCTATCAATGGTGCTGGGAAAACTGGATATCCA 1128
                           v   ii i     iv  v iv             v         ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_145833468_   1129 TATGCACAAGAATGAAACTACACTGCTATCTCTCACCATATATAAAAAT- 1177
                         i     v         ii iv  iv   i   v         i      -
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_145833468_   1178 -----AAAATGGATTAAAGACTTAAATCTAAGA-CAACAAACTGTGAAAT 1221
                         -----         i ?    i     v     - v -     i i   i
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA-AAACTATAAAAC 532

  chrX_145833468_   1222 TCACACAAGAA 1232
                           vi v     
  L1M4_orf2#LINE/    533 TCTTAGAAGAA 543

Transitions / transversions = 1.67 (87 / 52)
Gap_init rate = 0.02 (11 / 543), avg. gap size = 2.64 (29 / 11)  

1063 25.71 1.30 2.60  chrX_145833468_145835989     1662  2046 (476)    L1M4_orf2#LINE/L1      529   908 (0)  

  chrX_145833468_   1662 AAATTCACACAAGAAAACATTGGGG-AAA-CTCCAGGACATTGATCTAGG 1709
                            i  vi v          v  ? -   -  i iv   v   ivi    
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chrX_145833468_   1710 CCAAAAGTTCTT-GAT-TGATAACCCACAAGCATAGGCAACCAAAGAAAT 1757
                          v viiv     -   -   i --   v     i i     v       v
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACA--CCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_145833468_   1758 AATGGACAGATAAAATCATATCATA-TTAAAAGCTTCTGCACAGCATTGA 1806
                            i  i i  vii iivi    v -      i   i  ii vv  vv i
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_145833468_   1807 AAATAATCAATAAAGCAAAGAGGCCGTCCACATCATGGGAAAAAATATTT 1856
                          v iv     v    ii  i  i vii     vv      i         
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_145833468_   1857 TCAAAGTAACCATCTGACAAGACACTAATAACCAGAATATACAAGAAGCT 1906
                         v    vi vvi      i   iv   vi  v          i  ii i  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_145833468_   1907 CAAACAGCTCTATAGAAAAAAATCCAATAATTCAATTCAAAAAATGGGCA 1956
                          vv   i   v   iv     iv v     ii     -?           
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATT-WAAAAATGGGCA 825

  chrX_145833468_   1957 AAACATTTGAATAGACATTTCTCAAAAGAAGATATACAAATGGCAAGCAG 2006
                           iv                   v                    v ii i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_145833468_   2007 GCATTTGTAAAGGTGATAAATAATGACCATCAGAGAAATG 2046
                            iv  v    i  v v  -------     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAA-------CATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (52 / 45)
Gap_init rate = 0.02 (8 / 380), avg. gap size = 1.88 (15 / 8)  


2715 26.58 2.33 1.77  chrX_145898730_145901708     1584  2486 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145898730_   1584 TGGAAAAACCTCCCATGCTCATGCATACGATGAATCAATATCTTTAAAAT 1633
                               i iv       i     v  vv  v  v i     iv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145898730_   1634 GGCTATACTTCCCAAAGCAATGAATAGATTCAAGGCTATTCCCATTAAGC 1683
                            v     i      vii  vv i        v  v  i  i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145898730_   1684 TTCCA-CTGATATTCTTCCCAGAACAAGAAAAAACT-ATTTAAAAATTCA 1731
                          i   -   vi-  i  iv     - vvi v  i  -  iiv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCA 148

  chrX_145898730_   1732 TATGGAACAATATAAAAG-CCCA-AATAGCCAAGGCAATCCTGAGCAAAA 1779
                                --  ii  ii -    -         ii     i   iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_145898730_   1780 AGAACAAAGCTGGAAG-CTTGT--TGCCTGACTTTAAAATATATTACAGG 1826
                                  i    i -  iii-- v  ii i  i    iv  i    ii
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_145898730_   1827 GCTACAGTAACCAAAACAGGATGGCACTGGTACAAAAACAGTCACATAGA 1876
                                   i   i    vi   i     i i  ii i  v  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_145898730_   1877 CCAAAGGAACACAATTGAGAACCCAGAAATAAGATCC-CACATCT----T 1921
                         i   v    i v        ii          - i  -i    i ---- 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGT 345

  chrX_145898730_   1922 CAAATATCTGATGTTCCACAAACCTGACAAAAAAACAAACAATGGGGAAA 1971
                            ----i    v   v    ivv  v   i v--  vv           
  L1M4_orf2#LINE/    346 CAA----TTGATTTTCGACAAGGGTGCCAAGAC--CATTCAATGGGGAAA 389

  chrX_145898730_   1972 GGATTCCCCATTTAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCA 2021
                          i  vvi iv  i  i              i      v  ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_145898730_   2022 GAAGATTAAATCTAGACTCCTTCCTTACAACATGTACAAAAATGAACTCA 2071
                         i    v i  vi i   i   v   i   v   i         v      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_145898730_   2072 AGATGAGTTAAGGACTTAAATGTAAAACCCAAAACTGTAAAAGCCCTGGA 2121
                          i   ii i ?i   i         i v i      i     vi i i  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_145898730_   2122 AGACAACCTAGGCAATACTATTCAGGACATAGACATGGGCAAACATTTTA 2171
                            v   v    ?ivv v v   iv   v v ivv i     vvi   iv
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_145898730_   2172 T-GATAAAGATACCTAAAGCAATTATGACAAAAGCAAAAATTGATAAATC 2220
                          -    v-  i   v      vvviii       v      v       i
  L1M4_orf2#LINE/    590 TAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_145898730_   2221 AGATCTAATTAAA--CAAAAGAGACTCT-GTACAGGCAAGGACGCTATCA 2267
                         i  ii v  i   --i    ---   i -  i vvvv      i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAA---ACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_145898730_   2268 ACAAAGTAAACAGACAGTCTACAGAATGGGAGAACAAT-TTTGAAAACTA 2316
                          v     i  v     ii i              -   -    v   ii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCA 734

  chrX_145898730_   2317 TGCATTTAACAAAGGTCTAATATCCATCACCTATAAGGAACT--TA-AAT 2363
                          ii  i i i  i  v  vi      vv iv     i     --  -  i
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_145898730_   2364 TTA-CAAGAAGAAAAAAAACAATCCTATTAAAATGTGGGCAAAGAACATG 2412
                          i -i  v  i  i v   i  i  v   ?   vi         i iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_145898730_   2413 AACAGGCACTTTTCAAAAGAAGACATACATGCAGCCAACAATCAGTTGAC 2462
                           i  i  i  i  v        i     viii     i  v  vv   v
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_145898730_   2463 AAAATGCTGAACATCACTGATCAC 2486
                           i     v       ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.54 (37 / 24)  


2844 26.00 2.90 1.56  chrX_145921703_145924243     1153  2048 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145921703_   1153 TGGGAAAAAATTCCATGTTCATGGATAGGAAGAATCAATATTGTGAAAAT 1202
                            i  i v  i              v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145921703_   1203 GGCCATACTGCCCAAGGTAATTCATAGATTCAATGCTGTTCCCATCAAAC 1252
                            v     v     iv i  ii i        i  vi i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145921703_   1253 TGCCA-CTGACATTCTTCACAGAATTAGAAAGATCTACTTTAAATTTCAT 1301
                          v   -   v -  i  ii     v v  v iiiiv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_145921703_   1302 ATGGAA-T-CAAAGAAGACCCTATATAGCCATGACAATCCTAAGCAAAAA 1349
                               - -   i --     viv       vi      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_145921703_   1350 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 1399
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_145921703_   1400 CTACAGTAACCAAAACAGCATGGTACTGCTACCAAAACAGACAC------ 1443
                                  i   i    ii        vi iv ii i     i------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_145921703_   1444 CAATGGAACAGAACAGAGACCTCAGAAATAACACCACAAATCTACAACCG 1493
                                 i    iv    vii         vv   i v  i  iiii i
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_145921703_   1494 TCTGATCTTTGACAGACCTGACAAAAACAAACAATGGGAAAATGATCTCC 1543
                         vi    i  i    iivv  v   i v  vv       i   vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_145921703_   1544 TATTTGATAAATGGTGCCAGGAAAACTGGCTAGCCATATGCAGAAAACTG 1593
                          v  ii i         ii   v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_145921703_   1594 AAGCTGTACCCCTTCCTTATACCTTATACATAAATTAACTTTAGATGGAT 1643
                            i  v      v   i i   v      v         iv i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_145921703_   1644 TAAATACTTGAATGTAAG-TCCCAAACCATAAAAAGCCCTAGAAGAAAAC 1692
                         i ? v  i i        -v iv    i      v-i i           
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAAC 546

  chrX_145921703_   1693 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTC------A 1735
                         v    ?i- v i -   iv   v v  vv i     v ii   ------ 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_145921703_   1736 TGACAAAAACTCCAAAAGCA-ATTCAACAAAAGACAAAATTGACAAATGT 1784
                              ------         - vv          v     v  i    vv
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_145921703_   1785 GATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAG 1834
                           ii v  i   v v  i i   i  ii vv    i  v    v  vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_145921703_   1835 AGTGAACAGGCAACCTACAGAATGGGAGAAAATATTTGCAGTCTACCCAT 1884
                               v  i     i                        ivii ivi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_145921703_   1885 CTGACAGAGGTCTAATATCCAGAATTTACAAGGAATTT----AAATAAAT 1930
                             i ii  v  vi          v  i  i   i i----  v v   
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_145921703_   1931 --TTACAAGA-AAA-AACGCCATCAAAAAGTGGGCAAAGGATATGCACAG 1976
                         -- v v    -   -   v v  i?    i            v  v i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_145921703_   1977 ACACTTTTCAAAAGAAGACATTTACATGGCCAAGAAATATATTTTTAAAA 2026
                            i  i  v        i  vi v        v  ii i  v---    
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG---AAAA 886

  chrX_145921703_   2027 AAAGCTCAACCTCACTGATCAT 2048
                         i v       v   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (130 / 99)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.22 (40 / 18)  


3328 26.65 0.33 0.33  chrX_145929330_145935725.rev     4998  5905 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145929330_   4998 TGGAAGAACATTCCAAGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5047
                              ii i  i   v i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145929330_   5048 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5097
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145929330_   5098 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5145
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_145929330_   5146 TATGGAACCAAAAGAGAGCCCGCATCGCCAAGTCAATCCTAAGTCAAAAG 5195
                                viiv   i  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_145929330_   5196 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5245
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_145929330_   5246 TACAGTAACCAAAACAGCATGGTTCTGGTACCAAAACAGAGATATAGATC 5295
                                 i   i    ii    v    i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_145929330_   5296 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCACATATCTACAACTAT 5345
                                i    iv   ivii         vv   i i  i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_145929330_   5346 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5395
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_145929330_   5396 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5445
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_145929330_   5446 AACTGGATCCCTTCCTTACACCTTCTACAAAAATTAATTCAAGATGGATT 5495
                          ii    i    v   i     v v            i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_145929330_   5496 AAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5545
                          ?    i  v    v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_145929330_   5546 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5594
                            ?i- v i -   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_145929330_   5595 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 5644
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_145929330_   5645 TCAAGTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5694
                         iv  i v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_145929330_   5695 GGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5744
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_145929330_   5745 GGGCTAATATCCAGAATCTACAATGAACCCAAACAAATTTACAAGAAAAA 5794
                           i  vi          v  i  v    i vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_145929330_   5795 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 5844
                         i     i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_145929330_   5845 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5894
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_145929330_   5895 TCACTGGCCAT 5905
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (139 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


2790 28.13 1.55 1.00  chrX_145946806_145951071.rev     2873  3775 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145946806_   2873 TGAAAAAATATCCCACACTCATGGATTGGAAGA----ATACTGTTAAAAT 2918
                           i   i        iii               ----   i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145946806_   2919 ATTTATACTGCACAAACTGATTGACAGATTAAATGTAATATCTATTAAAA 2968
                         iviv     v v    i    iv       v  i i   vi    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145946806_   2969 TACCAGTGACATTCTTCAAAAAAATTT-TAAA---ATCCTAAAATTCATA 3014
                          v    ivi v  i  iiv i     v-i  i---               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_145946806_   3015 TAGAACCAAAAAAGACCCTTAATAGCTAAAGCAATCCTTATCAAAAAGAA 3064
                          i   viiv  ii     vv      i   i     i v vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_145946806_   3065 CACGTCTGGAGACATCACACTAACTGGATTTAAATTGTACTATGAAGCTG 3114
                           vivi     ivv       vv iiiv  i   viv     ii     i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_145946806_   3115 TAGTAACCAAAACAGGATGGCACTGGCATTAAAACAGACATATAGACCAA 3164
                         i     i   i    vi   i        v ii i           i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_145946806_   3165 TGGAACACAATAGAGAACCCAGAAATAAATCCACACACATACAGCCAATT 3214
                              i v   v    ii           i   i   iv  ii i     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_145946806_   3215 GGTTTTCAACACAGGCACCAAGAACATATAATGGGAAATGAA--GTCCCC 3262
                          i     i   vi  ii      v   vi      i  v   --   iii
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_145946806_   3263 TTAGGAAGTGACACAGAAAAAAAAACTAGATATTCATATACAGAAGAATA 3312
                          i iv  i  iii v ii v  ---  i    ?i  i  i  i      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAA---CTGGATAKCCACATGCAAAAGAATG 447

  chrX_145946806_   3313 AAACTAGATCTTCACCTTTCACCCTA-AAAAAAATTAAACTCAAAATGAA 3361
                           ii i  i iii    iv    v  - v         -         i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAA-CTCAAAATGGA 496

  chrX_145946806_   3362 TTAAGCACTTACACGAAAGATCCTAAAACTATTATATGATTAAAAGAAAA 3411
                          i ?iv  i  v i v    v -         v v ivv   i       
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_145946806_   3412 CGCTGGAA-AAATGCTCCAGGACATTGG-TCAGAGCAAATATTTTATGAC 3459
                          iiv  ?i-    -  i iv   v    - i  -    vvi   iv iiv
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAG-GCAATGGTTTCTTAGA 593

  chrX_145946806_   3460 TAAGACCTCAAAAGCCCAGGCAACAAAATCAAAAGTAGACAAAGGGGATT 3509
                           v   vi       v  i         vv    i    i   vv   i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_145946806_   3510 ATATCAAGCTAAAAAGCTTCTGCACAGCAAAGAAAACAATTAACAAAGTG 3559
                         vi     iv v    i   i  ii vv     i v  v  i  v      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_145946806_   3560 AAGAGACAACCTACAAAATGGGA-AAATTATTTGCAGACTATCCATCTGA 3608
                           i        i   i       -   v        i ii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_145946806_   3609 CAGGAGATTAATAACTATGTTATATGAGGATGTCAAATAACTCAATAGCA 3658
                         i i i  i vi  v i viv     i i  vv  vv i         ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_145946806_   3659 AAAAGCCCCAAATAATTTAACAACAAAATGGGCAAAAGACCTGAATAGAC 3708
                              v --      iii  iv?v            i  ii         
  L1M4_orf2#LINE/    794 AAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_145946806_   3709 ATTTATCAAATGAAGACATATGAATAGACAACAAGTATATGAACAAATGC 3758
                             v  v  v     i   ii   i v   i   i i     v i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_145946806_   3759 TCAATATTAGTAATCAT 3775
                             i  i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (159 / 91)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.64 (23 / 14)  


3071 27.39 1.78 0.67  chrX_145989642_145993255     2224  3121 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_145989642_   2224 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 2273
                              ii    i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_145989642_   2274 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAGC 2323
                            v     v     iv i  i  i        i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_145989642_   2324 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTCA 2371
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_145989642_   2372 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 2421
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_145989642_   2422 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 2471
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_145989642_   2472 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 2521
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_145989642_   2522 AATGGAACAGAGCAGAGGCCTCAGAAATAACGCCACACACCTAAAACCAT 2571
                                i   iiv   ivii         vv   i   ii  viii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_145989642_   2572 CTGATCTTTGACAAACCTGACAAAAACCAG-AAATGGGGAAAG--TATTC 2618
                         i    i  i     ivv  v   i -   v-v           --  v  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGA-CCATTCAATGGGGAAAGAATAGTC 397

  chrX_145989642_   2619 CGTATTTAATAA-TGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGC 2667
                         -- v  i  i  -           v      v  ?   i  ii i  iiv
  L1M4_orf2#LINE/    398 --TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_145989642_   2668 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 2717
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_145989642_   2718 ATTAAAGACTTAAGTTTTAGACCTAAAACCATGAAAACCCTAGAAGAACA 2767
                           i ?    i   i v v   v       i  i   vi i        v 
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_145989642_   2768 CCTAGGCA-ATACCATTCAGGATATAGGCATGGGCAAGGACTTTGTGACT 2816
                          v    ?i- v i -   iv  iv v  vv i     v ii  iv iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_145989642_   2817 AAAGCACTAAAAGCAATGGCAACAAAAGCCACAATAGACAAACGGGATCT 2866
                          vii   i       vvi          vv v      i   iv   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_145989642_   2867 AATTAAACTAAAGAGTTTCTGCATGGCAAAAGAAACTACCATCAGAGTGA 2916
                         v  i   v v  i ii  i  iiivv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_145989642_   2917 ACAGGCAACCTACAGAGTGGGAGAAAATTTCTGCAATCTACTCATCTGAC 2966
                          v  i     i     i           v i     vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_145989642_   2967 AAAGGGCTAATATCCAGAATCTACAAAGAA-----ACAAGTTTACAAGAA 3011
                           i  i  vi          v  i      -----    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_145989642_   3012 AAAAACAACCCCCCCAA----AAAGTGGGCAAAGGATATGAACAGACACT 3057
                            i    vivv     ----   i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_145989642_   3058 TCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCA 3107
                             v        i  vi viii     i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_145989642_   3108 TCATCACTGTTCAT 3121
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (152 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.83 (22 / 12)  


2595 27.85 1.99 1.66  chrX_146142337_146144439      712  1616 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146142337_    712 TGAAAAAATGTTTCATATGTATGGATTGGAAGAATTAAAACTGTTAAAAT 761
                           i   i  i ii   i vi             v    v i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146142337_    762 GATCATATTGTCCAAAGCAACAAAGAGATTCTTTGTAATCCCTGTTAATA 811
                          iiv   i vi     vii ivv v      vvi i       i i  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146142337_    812 TACCAACATTATTTTTCACA-AGATTAGAAAAAAAAAATCCTAAAATTAG 860
                          v   i vviv     ii  - i   i-- v  ivvi           vi
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_146142337_    861 TATGAAATTGTGTAAAAGAGCCTGAACAGCCAAAGTGATTCTAAGCATAA 910
                             i  --i  i  ii  v  v   i       iii  ii i iv vi 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_146142337_    911 AGAACAAAGCTGGTGGCATCACATTACCTGATTTCAAATTATATTACAAA 960
                                  i   v  vv     i v  ii        viv  i      
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_146142337_    961 GCTATGGTAACCAAAAGAACATGGTACTTGGATAAAAACAGTCATATAGA 1010
                             ii    i   i v iii       v v    ii i  v        
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_146142337_   1011 TCAATGGACGAGAGTAGAGAAGAAAAAAAACAAAGCCACATATCTACAAT 1060
                                 vv   i v    - vvv i   i   v   i i  i  iii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGA-GTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_146142337_   1061 CACATGATCTTTGCCAAAGTTGACAAAAAAAAAATACACTAGGGAAAGGA 1110
                           vv    i  i v   i v  v   i vv --- v  v i       i 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCA---TTCAATGGGGAAAGAA 392

  chrX_146142337_   1111 TACCCTTTTGAATAAAAGGTTCTAGGAAAATTGGATAGCCATATGTACAG 1160
                           vi     v  i   v   v  i   v  i      ?   i   i v i
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chrX_146142337_   1161 GAATGGAGCTGGACTCCTCTCTCCCACTACATACAAAAATCTACTCAAGA 1210
                              i  i     i   vi   v   i i          iv      i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_146142337_   1211 TGGATCCAAAGACTTAAATGTAAGA--TAAGAAACTATAAAAATACTAGA 1258
                               - ?    i           --   --          v vi    
  L1M4_orf2#LINE/    493 TGGATC-AWAGACCTAAATGTAAGAGCTAA--AACTATAAAACTCTTAGA 539

  chrX_146142337_   1259 AGAAAATGTAGAGAAAGCTCTTCCAGACATTGGTATGGGTAAATAATTAA 1308
                               ii   i?iv iv     vv   v    vv i  i  vviv  vv
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_146142337_   1309 TAACTAAGACCTCAAAAGCACAAGGAACAAAAATAACAATGGACAAATAG 1358
                           iv  v   vi            v       iv  v   i  i    v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_146142337_   1359 TACTT-----AAACTAAAAATTTT----CTGCAAAGCAAAAAAAATCAAC 1399
                         v    -----   i      i   ----  v     --i v vv     v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG--GACACTATCAAG 687

  chrX_146142337_   1400 AGAGTAAACAGACAGCTGGCAGAATGAGA-AAAATATCTGCAAACTATGC 1448
                          i   i  v     i ivi       i  -       i      ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_146142337_   1449 ATCTGACTGGGTATTGATATACACAATTTACAGGGAAATCAAACAACTCA 1498
                               ivi  v i vi   v  v   v  i ii   v  vv        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_146142337_   1499 ACAG--AAAAACCCAATAGTTCCATTAAAAAGTGGGTAAAAGGACATGAA 1546
                          i i--    iv v    iii v   ?    i    i   -   iv    
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA-GGATTTGAA 836

  chrX_146142337_   1547 TGGACACTTTTTCAAAAGAAGATATACAAACACCCAAAAAGCATGTGAGA 1596
                          i    -   i  v                iiv    v     ii   i 
  L1M4_orf2#LINE/    837 TAGACA-TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_146142337_   1597 AAATGC---ACGCCAGTGATGAT 1616
                          i    ---  ii  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (144 / 104)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.06 (33 / 16)  


2469 28.49 1.86 2.73  chrX_146157881_146163147.rev     3861  4776 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146157881_   3861 TGAAAAAACATTCCATGCTCATGGAATAAATATGTAAGAATACATATCAT 3910
                           i   i i  i     i       ----- -  v    v vv    ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGA-----T-TGGAAGACTTAATATTGT 44

  chrX_146157881_   3911 TAAAATGGCCTTACCGCCCAAAGCAATCTATGGATTCAAAAGCATTCCTA 3960
                            i     vv   iv      vii     ii       vivv  i    
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chrX_146157881_   3961 TCAAACTCTGAACATCAATTTTCACAGAATTAGAAAAAAAACT-ATTTCA 4009
                              v  iv i vv vv    ii     v v  v  i---  -  iii 
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTA 141

  chrX_146157881_   4010 AAATTCATGTGGAATCAAAAAAGACCCCAAATAGCAAAAGCAACCCTAAG 4059
                                 i     viiv  ii     vi      v   i   i i i -
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA- 190

  chrX_146157881_   4060 CAAAAAGAGAA-AAAGCTGGAGGCATCACACTACCCGATTTCAAACTATA 4108
                         -    ii    -    i      vv       v   i        viv  
  L1M4_orf2#LINE/    191 -AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_146157881_   4109 CCGTAAGATTATAGTAACCAAAATAGCATGGGACTGTGTGCAAAAACAGA 4158
                          iii  iii  i     i   i i  ii   v    - iii  ii i   
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG-GCATAAGGATAGA 288

  chrX_146157881_   4159 CACATACGCCAGTAGAACAAAATAGAAAACTCAGACATAAACCCATGCAT 4208
                           i   vii  i i   i i   v  i iii    v          i   
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_146157881_   4209 CTATAACCATCTGATCTTTGAAAAGGCCAACAAAA--A--CAATGCAGAA 4254
                         i   iii  vi    i  i  v    viiv   i -- --     vi   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_146157881_   4255 ATGGCGCCCTATTCAACAAATGGTGCTGGGATAACTGGCTAGCCATATCC 4304
                          viiiivi  v                    i      v  ?   i  v 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_146157881_   4305 AGAAAAATAAAACTAGACCTTTGCCTTTGGCTATATATAAAAATTAACTC 4354
                          i  i   i  ii i    ii i   ivvi i     i            
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_146157881_   4355 AAAGTGAATTAAAAGTTTAAATATAAGACCTCAAAGTATAAAAGCCCTAG 4404
                            i  i  i ? iiii     i     v  v   v       vi i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_146157881_   4405 AACAAAACCCAGG---AAATACCCTTCTAGATATTGGCTGTGGCAAAGAA 4451
                           v     vi   ---    ---    vv  iv    v vv     v iv
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_146157881_   4452 TTTTTGGCTGAGTCCCCAAAAGCAATTGCAACCAAAACTAAAATTGACAA 4501
                           i  i v iv v v         vvv     v   ivv     v  i  
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_146157881_   4502 GTGGTATCTAATTAAA-CTAGAA----TAGTTCGGCAAAGCAAAATAATC 4546
                         i v v ii v  i   -i  i  ---- v  v vv     ---i i -- 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG---GACA--C 680

  chrX_146157881_   4547 TATCAACAGAGTAAGGGGACAGATAAGCTATTCAATGGGAGAAAATTTTC 4596
                               v i   i ---- v   i  v i ivv             v  i
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGA----AAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_146157881_   4597 ACAAACTCTGTATCCGACAAAGGGCTAATATCCAGAATCTATAAGGAACT 4646
                         i    iiv i    i  i  i  i  vi          v     i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_146157881_   4647 TAAACAAATTAAGAAGCAAAAAATAAA-AACCCA--TTAAAAATAGGCAA 4693
                         ivv    v i  v  vv    i i   -      -- ?      i     
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_146157881_   4694 AAGACATGAACAGATACTTCTTAAGGGAAGACACACAAGTGTCCAACAAA 4743
                          i  iv    i   i i    iv ii     i i    i  v    i  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_146157881_   4744 CATATGAAAAACATGGTCCACATCAATAATCAT 4776
                           i       i-   v  v      ????????
  L1M4_orf2#LINE/    877 CACATGAAAAG-ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.66 (161 / 97)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.21 (42 / 19)  


2676 25.95 1.16 5.78  chrX_146193064_146196392     1890  2841 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146193064_   1890 TGGAAAAACATTCCATCCTCATAGACAAGAAGAATCAATATTGTGAAAAT 1939
                               i i  i    vi    i  ivi     v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146193064_   1940 GGCCATACTGCCCAAAGTAGTTTATAGACTCAAAGTTATTCCCATCAAAC 1989
                            v     v      v ii i  i   i    v iv  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146193064_   1990 TACCATTGACATTCTTCACAGAATTAGAAAAAAGAACTTTACATTTCATA 2039
                          v   vivi v  i  ii     v v  v  ivvi iii  v v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_146193064_   2040 ----AATGTTTTTCTTTCAAAAAAGCCTGTATAGTCAAGACAATCCTAAG 2085
                         ----    ---------   iii v  v v    i   i      i i i
  L1M4_orf2#LINE/    151 TGGAAATG---------CAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chrX_146193064_   2086 CATAAAGAACAAAGCTAGAGGCATCACACTGTCTGACTTCAAACTATACT 2135
                         v vi          i i    vv       vi ii i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_146193064_   2136 ACAAGGCTACAATAACCCAAACAGCATGGTACTGCTACCAAAACAGACAT 2185
                             i      i   i v i    ii        vi iv ii i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_146193064_   2186 ATAGACCAATGAAACAGAGCAGAGACCTCAGAAATAACTCCACACATCTA 2235
                              i     i  i   iiv    vii         vi   i    i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_146193064_   2236 CAACCATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGA 2285
                         iiii  vi    i  i     ivv  vv  i v  vv             
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_146193064_   2286 -----CTTCTCTAATAAATAGTGCTGGGAAAACTGGCTAGCCATATGCAG 2330
                         -----   i  -  i    i         v      v  ?   i     i
  L1M4_orf2#LINE/    392 ATAGTCTTTTC-AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_146193064_   2331 AAAACTGAAACTGGACTCCTTCCTTATACCTTATACAAAAGCTAACTCAA 2380
                           i v    ii     i   v   i i   v         ii        
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_146193064_   2381 GACGGATTAAAGACTTAAATGTAAAACCCCAAACCATAAAAACCTTGCAA 2430
                         i i    i ?    i         i v iv    i      vi   iv  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_146193064_   2431 GAAAACCTAGGCAATACAAT--TCAGGACATAGGCATGGGCAAAGACCTC 2478
                               v    ?i-  -   --  iv   v v  vv i     v iii  
  L1M4_orf2#LINE/    541 GAAAACATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_146193064_   2479 ATAACGAAAAAACCAAAAGCAATTGCAACAGAAGCCAAAATTGACAAATG 2528
                         v  ivv vi v          vvv      i   vv     v  i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_146193064_   2529 GGATCTAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAGCTAGCATCA 2578
                            ii v  i   v v  i i   i  iiivv    i  vi   v  vv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_146193064_   2579 GAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCA 2628
                         i      v  i     i                 v       vii ivi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_146193064_   2629 TCTGACAAAGGTCTTATATCCAGAATCTACAAGGAACTTAAACAAATTTA 2678
                              i  i  v   i          v  i  i     i--------   
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC--------TTA 780

  chrX_146193064_   2679 CAAAAAAAAAAAACCAAAAAAACAAACAAACAAACAAAAAACAAAAAAAA 2728
                            ----------- vv  v  i   -----------  i     -----
  L1M4_orf2#LINE/    781 CAA-----------CTCAATAATAAA-----------AAGACAAA----- 803

  chrX_146193064_   2729 AAAACACAACCCCATCAAAAAGTGAGCAAAGGATATGAACAGACACTTCT 2778
                         ------i     v  i?    i  i         v    i     i    
  L1M4_orf2#LINE/    804 ------TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_146193064_   2779 CAAAAGAAGACATTTACACGGTCAACAAACACATGAAGAAAAGCTCATCA 2828
                          v        i  vi v i  i   i  i        i i v     -- 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA--A 895

  chrX_146193064_   2829 CATCCCTTGTAAG 2841
                             v????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 5.50 (66 / 12)  


 216 12.20 0.00 0.00  chrX_146247840_146249501       74   114 (1547)  C L1M4_orf2#LINE/L1   (0)   908   868  

C chrX_146247840_    114 GCCAACAGACACATGAAAAAATGCTCATCATCACTGGCCAT 74
                              i ii          i       v     ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 4.00 (4 / 1)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.00 (0 / 0)  

1286 26.11 1.31 0.26  chrX_146247840_146249501      115   497 (1164)    L1M4_orf2#LINE/L1      474   860 (48)  

  chrX_146247840_    115 TGCATAAATTAATTCAAGATGGATTACAGACTTAAACGTTAGACCTAAAA 164
                          i  v       i    i      i ?    i    i  v   v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_146247840_    165 CCATAAAAACCTTAGAAGAAAACCTAGGCA-ATACCATTCAGGACATAGG 213
                          i      vi             v    ?i- v i -   iv   v v  
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGG 572

  chrX_146247840_    214 CACGGGCAAGGACTTCATGCCTAAAACACCAAAAGCAATGGCAACAAAAG 263
                         vvii     v ii   v ivv  vi            vvi          
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_146247840_    264 CCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA 313
                         vv     v  i    v   ii v  i   v v  i i   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_146247840_    314 AAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAAT 363
                           i  v    i  vv i      v  i     i                 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_146247840_    364 TTTTGCAATCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATG 413
                         v       vii ivi      i  i  i  vi          v  i  v 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_146247840_    414 AACTCCAACAAATTTACAAGAAAAAAACGA----CCCCATCAACAAGTGG 459
                              iv    v iv i  v     i  i ----   v  i? v  i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_146247840_    460 GCGAAGGATATGAACAGACACTTCTCAAAAGAAGACAT 497
                           i      v    i     i     v        i  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

Transitions / transversions = 1.16 (52 / 45)
Gap_init rate = 0.01 (3 / 387), avg. gap size = 2.00 (6 / 3)  

2094 27.01 3.28 1.49  chrX_146247840_146249501      500  1169 (492)    L1M4_orf2#LINE/L1      227   908 (0)  

  chrX_146247840_    500 ATTTCAAAGCTTATTCTTAAGCTACAGTAATCAACACAGTATGTTACTGG 549
                                 i    i viv                v     i  v      
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_146247840_    550 TATATAGGTAGACTAATATTA--CAATGGACCAGAAGAGAAAATTCAAAA 597
                         i   vi i     --    vi--       vi    vv  i i i  i  
  L1M4_orf2#LINE/    277 CATAAGGATAGAC--ATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_146247840_    598 ATAGACCCACGCATAGATGACCAAATGATTTTCAGCAGAGGCACAAAGAC 647
                            i     ii   vv   ii   v        ii  ii  ii v     
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chrX_146247840_    648 AATTCAGTAGAGAAAAGATAGTTTATTAAGCAAACAGTGCTCAAATAATT 697
                         v     i i i    ii     i v  v i    ii     vii i  i 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_146247840_    698 AGATAT--ACATAAAAATGAAAGAAATAATTTAGATTTATATTATACATC 745
                         i    ?--    iv   v   v   i ---- i  iiiv  iivi   i 
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGT----TGGACCCCTACCTCACACC 470

  chrX_146247840_    746 CTACATAAAATTTAATTCAGAATGAATTATAGACCTAAATGCAAAACTTA 795
                         v  i i    v    i   i    i  i ?           i  i vi  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_146247840_    796 AAACTATAGAATATCTAGGAGAAAATA----AGTA--------TGACCTT 833
                                 i  ivii   i      i ----?   --------       
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_146247840_    834 GGCTTAGGCAAATATTTTTTAGTTATGACATCAAAAGGA-AAGTTCAGT- 881
                           v        vvi   i    v       i      v -   --  ii-
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG--CAACA 618

  chrX_146247840_    882 ---TTAAAAATTG-TCAGTTGAACGTATTCAAAACTAAAAACTTATGTAC 927
                         ---vv      v - v i   i  v vv      i         v   i 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chrX_146247840_    928 TTCAAAATATATTGCTAAGTGAATTCAAAGATAAACAATAGGCTGAGAGG 977
                               iv i i iii   vi i vv     i  v v i  iv  i   -
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG- 717

  chrX_146247840_    978 AAAATATTTACAAAACATATATCTAATAAGGAACTTACATTTGAAACATA 1027
                                  i    v         i      i    ii  iiii  i   
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_146247840_   1028 GAAAGAATCCCCAAAACTTATCAGTAAGAAAACCAACAGCCCTATGAAAA 1077
                         v      ii ii v    i vi i   i  i  v  i i   v  v?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_146247840_   1078 AAATGAGCAAAAGATTTGAATAGGTATGTCAGCAGAGAGGATATAGGGAT 1127
                           -  i     i           ii  v  vv  i   i      vii  
  L1M4_orf2#LINE/    818 AA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_146247840_   1128 GGGAAATAAGCATATCGAAAGATGTTCAGCATCATTAGTCAT 1169
                           vv        i  vi       i   i     ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (117 / 60)
Gap_init rate = 0.02 (12 / 682), avg. gap size = 2.67 (32 / 12)  


2225 29.37 5.24 0.23  chrX_146267330_146271468.rev     2791  3648 (491)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_146267330_   2791 ACATTTCATGCTCCTTGATGGGTAGAATCAATATTTTTTTAAACGGCCAT 2840
                          i  ii    i  v v   v  v   v i      v  v- i i   v  
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGATGGCAAT 56

  chrX_146267330_   2841 ACTACCCAAAGCAAT-------TTGAACACTATTCCTATCCAACTGGCAA 2883
                            v      vii  -------  v   i v  i      v  v vv  i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_146267330_   2884 CAATATTTTTTACAGAATTAGAAAAATGTATTCTAAAATTCATTTGGAAC 2933
                          viiv      i     v v  v  iivv  i           v     v
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_146267330_   2934 CTAAAAAGAGCCTGAATGGCCAAAGCTATCCTAAGCAAAAAGAACAAAGC 2983
                         ivv  ii  v  v    i      i v   i i iv  i          i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_146267330_   2984 CAGAGGCATCATACTACCTAACTTCAAACTATAATACGGGGCTAAATTAA 3033
                         ii    vv   i   v  i  i      viv  v   iii    v v   
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_146267330_   3034 CCAAAACAG-------CTGGTACAAAAACA--CACATAGACCAATGGAAC 3074
                         i   i    -------    i i  ii i --  i     i        i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_146267330_   3075 TGCTTAGAAAACCCCAAAATAAAACCACACACCTAAAACCATCTGACTTT 3124
                         v vv v  i ii  vi       v   i   ii  viii  vi   i   
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_146267330_   3125 TGACAAAGTAGATAATAACAAGCAATAGG-AAAGGATTCCCTATGCAATA 3173
                         i     i vv vi  v v  vv    i  -    i  vvi  v v   i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_146267330_   3174 TATGGTGCTTGAATAACTGGCTAGCC-TATGCAGAAGAATGAAACTGGAT 3222
                         v        v i i      v  ?  -i     i         ii    i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_146267330_   3223 CCCTTCCTTTCACCGTACACAAAAATCAACTCAAGATGGATTAAATACTT 3272
                             v   iv    i  i        i       i      i ? v  i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chrX_146267330_   3273 AAAGGCAAAACCTAAAACTATAAAAACCT----AGGAAACACCATTCTGG 3318
                            v i  i v              vi  ----  i     iviv?v ii
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chrX_146267330_   3319 ATATCAG---CCTTGGG--A---AATAATTTATCAC-CAAGTCCTCAAAA 3359
                           v iv ---       -- ---   ii   v i v-i v v vi     
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_146267330_   3360 GCAATGGTAAGAATAACAAAAATTGATGCCTGACACCTTATTAAA-TTAA 3408
                            vvi i  v  v iv      v   ivv viv  i i  i   -    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_146267330_   3409 AGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTAAGCAGACAACCT 3458
                          i -   i  ii vv    i  v        v i   i iv        i
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_146267330_   3459 ACAGAATAGGAGCAAATAATCACAATCTGTACATAT-ACAAAGGTCTAAC 3507
                                i    v     v ii   viii  i  v - i  i  v  vii
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_146267330_   3508 -TTCAGAATCCATAAGGAACTTAAACAACTTAA-----------CAAATA 3545
                         - i      vi    i     ivv      i  -----------      
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_146267330_   3546 ACCCCATTAAAAAATGGGCAACTGACACGAACAGATACTTCTCAAAAGAA 3595
                             v   ?            vv  ivi   i   i i     v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_146267330_   3596 GATATACAAGTGGCAAACAGACATATTAAAAAACGCTCGACATCACTAAT 3645
                                  i    v  i ii  i  v    i i    i      ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_146267330_   3646 CAT 3648
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.30 (140 / 108)
Gap_init rate = 0.02 (16 / 901), avg. gap size = 2.94 (47 / 16)  


 286 23.81 1.19 0.00  chrX_146303249_146304962.rev       21   104 (1610)    L1M4_orf2#LINE/L1      477   561 (347)  

  chrX_146303249_     21 AAAAATCTAATCAAAATCAGTCAAAGTCCCGAATATAAGAGCTTAAACTA 70
                               iv v       vii   ?  v  ii   i        v      
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_146303249_     71 TAAAACTCTTAGTTG-ACACATAAACCTAAACCTT 104
                                     vv - v     ii?v    i   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

Transitions / transversions = 1.00 (9 / 9)
Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1)  

 410 15.07 1.37 0.00  chrX_146303249_146304962.rev      400   472 (1242)    L1M4_orf2#LINE/L1      554   627 (281)  

  chrX_146303249_    400 TGAATCTTTATGA-CTTAGATTAGGCATTGTTTTCTTAGATGAGACACCA 448
                          i      ii   -   i i       v  v          iv       
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_146303249_    449 AAAGCACAAGCAGCAAAATAAAAA 472
                                     i     v     
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAA 627

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1)  

1987 27.51 4.17 3.39  chrX_146303249_146304962.rev      505  1271 (443)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_146303249_    505 ATCCTAAAATTCATAGGAAACCATAAAAACCCCTGAGTACCTAAGGCAAT 554
                                        v i  viii  iiiv   v  i  v i  ii    
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_146303249_    555 TTTTAGCAAAAGGAACAAAGCTATATGCATCACATGAACTGATTTCAAAC 604
                         i  v iv  i i        i iv v vv     ivvv ii        v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_146303249_    605 TATATTATAAAACTACAATAAT-ATGAGCAAAATGGCACTGGTGCTAAAA 653
                         iv  i  i   i     i    - v  -  ivi   i     iiiv ii 
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGA-CAGTGTGGTACTGGCATAAGGA 284

  chrX_146303249_    654 TAGATA-----ACCAATGGAACAGAATAGAGAACCCAGAAACACACCCAT 698
                             i ----- i        i     v    ii       i v      
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_146303249_    699 TCATTTACAGCCAACTGATTTTTGATGAAGCTGTCAAGAACACATGATGG 748
                         v      ii i   i       i  ii i v  i     v  ivii    
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_146303249_    749 GAAAAAGACAGTCT---CAATAAAAGATGTTGTGAGAACTGGTTATAGAC 795
                          i   ii i     ---   i   v i  i  v  v      v  ?vv  
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_146303249_    796 ATGCCTAAGAATGAATTGAGACTCTTATTTCACACTATATGTGAAAATC- 844
                             vv         v vi   i i  ii      i    iii     i-
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_146303249_    845 -CTTAATGAATGGATTAAAGACTTAAACATGAGACCTAAAACTGTGAAAC 893
                         -  i  --       i ?    i    ii i   v        i i    
  L1M4_orf2#LINE/    485 ACTCAA--AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_146303249_    894 TACTAGAAGAAATCCTAGGAAAAAAGCTATGCAACATTGGTCTGGGCAAT 943
                          vi         v v    ?iv   v  vi ii  v    vi i      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_146303249_    944 AAGTTTAAGTTTTTT---TATTAGACCCCAAAAGCTTAGGCAAAAAAAGT 990
                         i-------    i  ---   --   v        vi i    v     v
  L1M4_orf2#LINE/    583 G-------GTTTCTTAGATAT--GACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_146303249_    991 AT---TCTTTAGTTTGG----TAT-AAACCCACAAAGCA---AGATTCCA 1029
                          v--- vvv  iv    ----i  -   vii -   i v---ivii i  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCA 672

  chrX_146303249_   1030 CAGAACAAACAAACCATTTAATGGAGTGAAGAGCCAACCTACAGAATGGA 1079
                         v  i   ------ i  i-  vii      i  v     i         i
  L1M4_orf2#LINE/    673 AAGGACA------CTATC-AAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_146303249_   1080 AGAAAATGAATTGTCAGCCACACATCTGATAAGTGGTGAGTATCCAAAAT 1129
                                - v   iv ii  i i          v iivv       i   
  L1M4_orf2#LINE/    716 AGAAAAT-ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_146303249_   1130 ATATAAAGAATTC----AATGCAATAGCAAGGAAACAAATAACATGATTA 1175
                                   i  ----  iv     ii  ii i         vii   ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_146303249_   1176 AAAAATGGGCAAAGGACCTGAAAACACATTTTTC---AACAGATGTGAAA 1222
                                         ii    v v      i  --- iv    i iv  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_146303249_   1223 AGGAATGGTAATCATCCATGAAAAGGAATGATGCAACCACATGAATGAA 1271
                          v iviii   v  --         --   v -    vv  ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCA--CATGAAAAG--ATGCT-CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (131 / 76)
Gap_init rate = 0.03 (22 / 773), avg. gap size = 2.64 (58 / 22)  


2743 27.51 3.04 0.68  chrX_146307820_146310535     1343  2229 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146307820_   1343 TGTAAAAATATTCCATGCTCATTAATAGGAATAATCAATATGATTAAAAT 1392
                           v   i    i     i    vi  v    v v i     vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146307820_   1393 GGCCATACTGCCCAAGGCAATTTACAGATTCAATGCTATTCCTATCAATC 1442
                            v     v     ivii  i           i  v  i        vv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146307820_   1443 TACCAATGACATTCTTCACAGAACTAGATACAAAT--ATTTTAAAATTTG 1490
                          v   iivi v  i  ii     v v  --   ii--  ii       ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGA--CAAGCTGATCCTAAAATTCA 148

  chrX_146307820_   1491 TATGGAACCCGAAAAGAGCCTGAATAGCCAAGGCAATCCTAAGCAAAAAG 1540
                                vivv  ii  v  v          ii     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_146307820_   1541 AACGAAGTAGGAGGCATCACACTACCTGACTTCAAA--TTAT-----AG- 1582
                            i    v     vv       v  ii i      --   i-----  -
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_146307820_   1583 TACAATAATAAAAACAACATGATATTGGTACAAAAACACACATATAGACC 1632
                             i    v  i   iii  i  i   i i  ii i v         i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_146307820_   1633 AATGGAACAGAATAGAGCGCCCAGAAATAAGGCCACACACTTATGACCAT 1682
                                i     v   v i          iv   i   i     ii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_146307820_   1683 CTGATATTTGACCAAGCTGACAAAAACAAGCAATGGGGAAAAGACTCACT 1732
                         i    v  i   v i v  v   i v  vv           ii ivvv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_146307820_   1733 ATTCAATAAATGGTGCTGGGATAACTGGCTAGCCACATGCAGAAGATTGA 1782
                         v     i              i      v  ?         i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_146307820_   1783 AACTGGACCACTTCCTTACACCATACAAAAAAATCAACTCAAAATGTATT 1832
                          ii      v  v   i        i v      i           v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_146307820_   1833 AAAGGCCTAAATC------CTCAAACTTTGAAAACCCTGGAAGACAATCT 1876
                          ?  i       v------  v     v i   vi i i     v  iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_146307820_   1877 AGAC---AATACCACTCTG-GACATAGGAACTGGCAAAGATTTTATGACA 1922
                           i?---   ----  ii -   v v  iviv     v i   iv iivv
  L1M4_orf2#LINE/    549 AGGNGTAAAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_146307820_   1923 AAGGCACTAAAAGCAATCGCAACAAAAGAAAAAATTGACAAATGGGATAT 1972
                          v i   i       vvv                 v  i    v   iv 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_146307820_   1973 AATTAAACTAAACAGTTTCTGCAAAGCAAAATAAACTATCAATAGAGTAA 2022
                         v  i   v v  v ii  i  iivvv    iv v        v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_146307820_   2023 ACACACAACCTATGGAATGGCAGAACATATTTGCAAACTATGCATCCAAC 2072
                          v v      i ii      v    v           ii  ii   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_146307820_   2073 AAAAGTCTAGCATCCAGCATCTAAAAGGAACT--TAAAAATTTACAAGCA 2120
                           ii v  v i      v  v  v  i     --  v  v iv i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_146307820_   2121 AAAACCAAACAGCCCCATTAAAAAGTGGGCAAAGAAC----ATGCACAAT 2166
                            iv    i i   v   ?    i         i i----  iv   v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_146307820_   2167 TTTCAAAAGATGACATATATGTCACCAACAAGCATGTGAAAAAA-GCTCA 2215
                          i  v     v  i   i vi vi    i     ii      i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_146307820_   2216 ATGTCAATGATCAT 2229
                          ii   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (137 / 103)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.75 (33 / 12)  


2431 27.87 1.71 4.39  chrX_146364723_146367846     1699  2631 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146364723_   1699 TGGAAACACATTCCATGTTTATAGGTTAGAAAAATCAATAGTGTTATAGT 1748
                               v i  i       i  i i  i   i v i    v     vii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146364723_   1749 GGCCATGCTGCCCAAAGCTATCTGCAGATTCATCACCAAGCCTATAGAGC 1798
                            v  i  v      viv    i        v i v vv     vi iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146364723_   1799 TACCAACATCATTTATTACACAACTATAAAAATCTG-TTTTAAAATTCAT 1847
                          v   i vv v   v  i  v  v - i v  v   - ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_146364723_   1848 ATGGAACCAAAAAAGTGCCTGAACAGCCAAAGCTATCCTAAGTAAAAAGA 1897
                               viiv  ii vv  v   i       i v   i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_146364723_   1898 ACGAAGCCATAGGCATAATGTTATCTGATTTCAAACTATACTATAAGGCT 1947
                           i   iiiv   vv v iii vi ii        viv     i  i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_146364723_   1948 ACAGCAACCAAAATAGCATGGTACTGGTGCAAAAACAGATGTGTAGACCA 1997
                             i  i   i i  ii         iii  ii i   ii i    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_146364723_   1998 GTGGAACACATCTACAGAGAACCCAGAAATAAAGCCATATACCTACAGCC 2047
                         i     i v vi ---    ii           v     i ii  ii i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATT---GAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_146364723_   2048 ATCTGATCTTCAACGAAGTCAACAAAAATGAGCAATGGGGAAACAACTCC 2097
                          vi    i   i  i i viiv   i viivv           v  ivvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_146364723_   2098 CTATTCAATAAATGGTGCCAGAATAACTGGCTAGCCGTATGCAGAAGAAT 2147
                           v     i         ii i i      v  ?  ii     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_146364723_   2148 GAAATTGGATCCCTACATTTTACCATATA-AAAAATTAACTCAGGATGGA 2196
                            i     i      v ivi        -             ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_146364723_   2197 TTAAAGACTTAAATTTAAGAACTCAAACTGTAAGAATCCCAGAAAAAACC 2246
                          i ?    i     v     i  v     i   i v  ii    i   v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_146364723_   2247 CTAGGAG-ACACCATTCTGGACATTAGCCTTGGAAAATAATTTAGGACTA 2295
                         v    ? - v i -   vv   ------     i-------     ----
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGAC------CTTGGG-------TTAGG---- 578

  chrX_146364723_   2296 AATCCTCAAAAGCAATTCACACACACACACACACACACACACACACACAC 2345
                         ------   vi i--   vi v i ii---    -  v vi    vi  -
  L1M4_orf2#LINE/    579 ------CAATGGT--TTCTTAGATATG---ACAC-CAAAAGCACAAGCA- 615

  chrX_146364723_   2346 ACACACACACACACACCTTGACCAGTGGGACCTAATTAAACCAAAGAGCT 2395
                            v viv v v i ----  iv i v    i v  i   viv  i i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATA----GATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_146364723_   2396 TCTGCACAGCGAAAGAAACTACTGACAGAGTAAACACACAACCTACAGAA 2445
                          i  ii vv i  i  v    iii v i   i  v v      i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_146364723_   2446 TGGGAGAATATATTCACAAAT-ATCACATCTGACAAAGGTCTAATATGAA 2494
                                 v     ii     -  - i      i  i  v  vi   vv 
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCAT-ATATCTGATAAGGGACTTGTATCCA 760

  chrX_146364723_   2495 GAATCTATAAGGAACTTATATAATTGCAAAAACAAAAA-----------C 2533
                             v     i     iv  i  i -   v  i     ----------- 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACT-CAATAATAAAAAGACAAATAACCC 809

  chrX_146364723_   2534 AATTCAAAA-TGGGCAAAAGACATGAACAGACACTTCTCAAATGAAGACA 2582
                             ?    -        i  iv    i     i     v  v     i 
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_146364723_   2583 TACATGCTTCCAACAAAGATATGAAAAAATGCTCAATATCAATAATCAT 2631
                             viivv    i  iv i       i        i    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (158 / 98)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.00 (57 / 19)  


2419 26.01 5.09 0.94  chrX_146374794_146377357      876  1621 (943)    L1M4_orf2#LINE/L1        1   777 (131)  

  chrX_146374794_    876 TAGAAAGTTATTCCATGCTCATGCTTTGAAAAAATTA---TTATTAAAAT 922
                          i     v   i     i     vv   i  i v   ---  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146374794_    923 GACAATACTACCCAAAGCAACCTACAGATTCAATGCATTCCCTATCAAAA 972
                          i       v      vii i            i   v            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146374794_    973 TACCAATGACAGTTTTCATAGAAATAGAAAAAACAAAACCATACAGAACC 1022
                          v   iivi vv    iii      v  v  i- vi v  -  - i vi 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCC-TA-AAATTC 147

  chrX_146374794_   1023 ATATAGAAC--CAGAAGACTCCAAATAGCTAAAGCAATCCTGAGCAAAAA 1070
                             i   v--  iii   i vi      i   i     i   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_146374794_   1071 GAACAATGCTGAAGGCATCACGTTACCTGACTTCAAATTCTACTACAAAG 1120
                               v i  i   vv    ii v  ii i      vii          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_146374794_   1121 CTGTAGTAACCAAAATAGTGTGGTACTTCCATAAAAACAGACACATAGAA 1170
                           ii     i   i i           vv     ii i     i     v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_146374794_   1171 CTATCAAACAGAATGGGGAACTCAGAAATAAATTCATGCACTTACAGCTA 1220
                          v  vi  i     v i  iii          ii   i  i   ii ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_146374794_   1221 AGTCATTTTCAACAGAGATGCCAAGA--ATACA-TGG------------C 1255
                          v v      i   ii i        --  v  -   ------------ 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_146374794_   1256 ATTTAAA-ATATGATGCTGGGAAAACTGGATATCCATATGCAAAAGAATG 1304
                         v   v  - v   i        v         ?   i             
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_146374794_   1305 TAATTAGATCCTCATCTTTCACTATATGTAAGAAT-----CAAAATGAAA 1349
                         v i  i  i  ii i  iv   i    ii  i   -----       i v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_146374794_   1350 TAAAGACTTAAATCTAATACCCAAAACTATAAAACTACTAGAAGATAAAT 1399
                         i ?    i     v   v v i              vi       -   i
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA-AAAC 546

  chrX_146374794_   1400 ATTAGGA--AAATGCGATAGGACATTGGTCTGGGCAAAGCTTTTTTGGGT 1447
                           -   ?--    - vviiv   v    vi i     v v   i  i i 
  L1M4_orf2#LINE/    547 AT-AGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_146374794_   1448 AAGACCTCAAAAGCATAGGCAACCAAAGCAAAAACAGACTAAAG-GGATT 1496
                          v   vi        i i     v    v     i   -    v-   i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA-TAAATTGGACT 643

  chrX_146374794_   1497 AAATCAAGCTAAAAAGCTGTTGCACAGCAAAGGAAAC-------AAAGTG 1539
                         vv     iv v    i  v   ii vv       v  -------      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_146374794_   1540 AAGAGACAATTCA--GAATGGAAGAAGATACTTGCAAACTATCCATCCAA 1587
                           i      ii  --      i    i   i       ii  vi   ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_146374794_   1588 CGAGGGATTAATAACAATAGTATATATGGAACTC 1621
                         ii     i vi  v v v i      vi      
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

Transitions / transversions = 1.73 (121 / 70)
Gap_init rate = 0.02 (18 / 777), avg. gap size = 2.50 (45 / 18)  

 492 17.97 1.56 2.34  chrX_146374794_146377357     1946  2073 (491)    L1M4_orf2#LINE/L1      782   908 (0)  

  chrX_146374794_   1946 AACTAAATGAAAATAAAAAGT--AATAATCTTATTTTAAAATGGGCAAAA 1993
                             v   ---         v--     i iv   ?v            i
  L1M4_orf2#LINE/    782 AACTCAAT---AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_146374794_   1994 GATCTGAATAGACAATTCTCAAGAGAAAACATACAAATGGCCAACAGATG 2043
                            i          v     v i    i i              i iiii
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_146374794_   2044 TATGAAAACATGCTTAACATAACTAATTAT 2073
                         i       v     i     v ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (14 / 8)
Gap_init rate = 0.02 (2 / 127), avg. gap size = 2.50 (5 / 2)  


2693 24.80 3.70 3.37  chrX_146378833_146380786      563  1453 (501)    L1M4_orf2#LINE/L1        1   894 (14)  

  chrX_146378833_    563 TAGAAAGATAATCTATGTTCATGGAT---AAGACTCAATATTTTTAAAAT 609
                          i        vi i            ---      i      v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146378833_    610 AGCAGTTTTCCC--AATCGATCTATAAATTTA-TGCAATCTTAATCAAAA 656
                         i   i vi    --   i      i i   i -i      iiv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146378833_    657 TCCTAGAATG---TTTTTGTGGATACCAGGAAACTGATTCTAAAGTTTAT 703
                            i  v-  ---      ii  v iiiiv  i     i     i  i  
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_146378833_    704 CTGAAAAGGCAAAAGACTCAGAGAAGTCAACAGAATTTTTTAGAAAAAAA 753
                         v  i   v    ii   i    iv  i   v v   i  ----i     i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTT----GAAAAAG 195

  chrX_146378833_    754 AAAAACAGAGCCAGAAGAC----ATTACCTGACTTCAAAACTTACCACAA 799
                           i    i  iii  i   ---- i v  ii i            i    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_146378833_    800 AGCTATAATAATCAAGAAAGTGTCATAGAGGCAAAAGAATTGACACATAG 849
                              i i         v     vi  vv    v   i  v    i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_146378833_    850 ATCAATAGAACAGATCAGATTGATAAAACAGAATAGATAACACAAAAGTA 899
                               i   i   ----     -------  i ------ -  i  i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGA----ATTGA-------GAGT------C-CAGAAATA 327

  chrX_146378833_    900 AACACATGCAAATATAGTCCAATGATCTTTAAGAAG----CAAAAGTAAT 945
                            v   i  vv   i   v v    i  ii v   ---- v  iiiv  
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_146378833_    946 TCAATGGAAGAAAGGATAGTCTTTTCAGCAAATGGTGCTGGACCAGCTAG 995
                                i-     i            i             iv  i  i 
  L1M4_orf2#LINE/    378 TCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_146378833_    996 ACGCCCACAAGCAAAAATAGTTTAATATAGACACAGATCTTATATCTTTC 1045
                          ii?     v      i- i vv i - i   v vv i  i i i v vi
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAG-AATGAAGT-TGGACCCCTACCTCACACCATAT 474

  chrX_146378833_   1046 ACAAAA-TTAACTAAAAATGAATCTTAAACCTAAATTCAAAACACAAATC 1094
                               -      v      i   v? i        vi  i vvi   v 
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_146378833_   1095 TATACTATTCATAGAAAATAACACATAAA-AAGTCCAAATGACCTGGGGT 1143
                             vv i  v     i v    i vi?i-  i  ivvi      v    
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_146378833_   1144 TTGGCATTGAGTATTCAGATATGGCACTAAAAGTATAATCCATTAGAGAA 1193
                          v    v  iv vi i       i   i     i i  v v iv i    
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_146378833_   1194 ATGATGGATAGGTGAGACTTCATTAAAAT-AAAAATTTTCCATTCTACAA 1242
                          vi  i    ii vi        i     -     i   i-i v  v   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT-GTGCTTCAA 673

  chrX_146378833_   1243 ATGACACCATAACGAGAAGT-AAATGACAAGCCATAGACTAAAGGAAAAA 1291
                          v     i  v v  -    -   v     v   i   v i--   i   
  L1M4_orf2#LINE/    674 AGGACACTATCAAGA-AAGTGAAAAGACAACCCACAGAATG--GGAGAAA 720

  chrX_146378833_   1292 AAATTCACAA--CACATATTTGATACAGGACTTGTATCCAAAATATACTA 1339
                          v   ii   --  i    i     vi             i      iv 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_146378833_   1340 A-AACTCCTAAAGCTCAAAAATAAGAAAGCAAACAA---------AAAGT 1379
                          -     i  v i     v     i  ii    i  ---------   i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chrX_146378833_   1380 CGGCAAAAGATCTAAACAGACACCTCAGCAAAGAAGTTATTCAGATGGCA 1429
                         v      i   i i  i     ii  vv        v   v  i     v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chrX_146378833_   1430 AATAAGCATACGAAAAAATGCTCA 1453
                                 i i     i       
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCA 894

Transitions / transversions = 1.79 (140 / 78)
Gap_init rate = 0.03 (25 / 894), avg. gap size = 2.52 (63 / 25)  


3312 26.32 0.66 0.66  chrX_146444185_146446578      994  1901 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146444185_    994 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1043
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146444185_   1044 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1093
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146444185_   1094 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1141
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_146444185_   1142 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1191
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_146444185_   1192 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1241
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_146444185_   1242 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1291
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_146444185_   1292 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1339
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_146444185_   1340 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1389
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_146444185_   1390 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1439
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_146444185_   1440 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 1489
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_146444185_   1490 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 1539
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_146444185_   1540 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 1589
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_146444185_   1590 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 1639
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_146444185_   1640 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 1689
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_146444185_   1690 AGGCAACCTACAAAATGGGAGAAAATTTTCGCA--TCCTACTCATCTGAC 1737
                           i     i   i             v  i   --  v  i--      i
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGAT 744

  chrX_146444185_   1738 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 1787
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_146444185_   1788 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 1837
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_146444185_   1838 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCA 1887
                             v        i  vi viii     v  i        i i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_146444185_   1888 TCATCACTGGCCAT 1901
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (142 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2297 24.76 4.48 4.72  chrX_146449833_146451667.rev      502  1349 (486)    L1M4_orf2#LINE/L1       63   908 (0)  

  chrX_146449833_    502 CAAAGCAACCTGTAGATTCAATGCAATC---A--AAAATACCAA-TGTCA 545
                             vii i  ii        i      --- --     v   i-  i v
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chrX_146449833_    546 TTTTC-CAGAGTTAGAAAAAATAATTCTAAAATTCATACAGTACCAAAAA 594
                             i-    iv v  v  iv i  i            ii v viiv  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chrX_146449833_    595 AGAGCGTGAATAGCCAAAACAATCCTAAGCAAAAAGAAGAAAGCTGGAAA 644
                         i  v vv                 i i iv  i     v    i    ii
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chrX_146449833_    645 CATCACAACACCTGACCACAAATTATACTACAGGGCTGCAGTAATGAAAA 694
                         vv     viv  ii iiv    viv       ii   i       v  i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chrX_146449833_    695 TATCATGGTACTGGTTCTAAAAATACTGGCTCTAAACATGGTATTAAAAA 744
                         i vii         i-v   ii   ---------i    -----------
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGC-ATAAGGATA---------GACAT----------- 291

  chrX_146449833_    745 CAGACATAGATCAATGGAATAGAATCCAGAATCCAGAAACAAAGCTACGT 794
                         -----                    iv   i        i   v i iii
  L1M4_orf2#LINE/    292 -----ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chrX_146449833_    795 ATCTACAGCCAACTAATCTTTGACAAAATCAACAAAAACACACATTGGGA 844
                           i  ii i   i i  i  i     iiviiv   i v  iv  v    i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_146449833_    845 AAAGAATACCCTCTTCAATAAATGGTGCTGAGAAAACTGGATAGCTATAA 894
                                 vi  i     i           i  v         ? i i -
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA- 435

  chrX_146449833_    895 CACAGAAAAATGAA--TCAATCCTTAAATCTCAC-GTATACAAAAATCAA 941
                         ii  i  i      -- vi i  i  vv  v   -i           i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_146449833_    942 CTGATGATGGATCAGAGACATAAATGTAAGACCTGAAACTATAAAAAAAA 991
                           v vi        ?    v           v  i           v---
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC--- 532

  chrX_146449833_    992 AAAAATCCTAGGAGAAAACCTAGGGAAAAACTCCTC-TGGAATTGGTCTA 1040
                         -----  i   i       v    ?iv   -  i  -  ivv    vi  
  L1M4_orf2#LINE/    533 -----TCTTAGAAGAAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTA 576

  chrX_146449833_   1041 GGCAAAGAATTTATGACTGAGACTTCAAAA--ACAAGCACAATGAAAACA 1088
                              v iv  iv iiv iv   vi     --       -- ii   iv 
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA--ACAAAAGAA 624

  chrX_146449833_   1089 AAAATAGACACGTTGGGATTAACTTAAACTAAAAAGCTTCTGCATGTCAA 1138
                                 i vi    iv  v iiv   i      -   i  iiiv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chrX_146449833_   1139 AAGAAAT----AACAGACTGAACAGACAACCAGCAGAACGGGAGAAAATA 1184
                          i  v i----  v i v    v        vi     i           
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_146449833_   1185 TTTT----TCA---ATCTGACAGGGGACTGATACCCAGAATGTACAAGAA 1227
                            v----   ---      i i      vi  i       i  i  ii 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_146449833_   1228 ACCC--A-AACTCAAC--------GACAAACAACTCCATTAAAAAGTGGG 1266
                           i -- -       i--------      i   i v   ?    i    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_146449833_   1267 CAAAGGACATGAACAGACATTTTTC---AAAAGACATGTAAATGGCCAAC 1313
                                iv    i        i  --- i    i  ii          i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_146449833_   1314 AAGCACATGAAGAAAATGTTCAAAAGCACTAATTGT 1349
                                    -  i   i    v v  ????????
  L1M4_orf2#LINE/    874 AAGCACATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.90 (135 / 71)
Gap_init rate = 0.03 (24 / 846), avg. gap size = 3.25 (78 / 24)  


 796 28.25 13.98 5.65  chrX_146459823_146461500      500  1207 (471)    L1M4_orf2#LINE/L1      121   887 (21)  

  chrX_146459823_    500 GAATTTAACAAAGCTGA--CTCAAAGTTATATAGAAATTTACTGGGTCAA 547
                            v  i    -     --  v   v i    i     vi vv  ii v 
  L1M4_orf2#LINE/    121 GAAATTGACAA-GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_146459823_    548 TAATAGCCATGACACTTT-----AAGAAGAAAGAGGTGAAAAGTCTTGCT 592
                         v        vi   v i -----        vi i  vii i v  ii v
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_146459823_    593 CTGCTAAATATGAAGA-TTA----AAAGCATTAC--TAATTAC-ATAATG 634
                           v iv   v v  i -   ----     --   --    i v- i i  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGC--TACAGTAATCAAGACAGTG 267

  chrX_146459823_    635 TAATATTGGTGCTAGAACAGACAAGTAGAGAAACAGGGAAAAAAAAAAAA 684
                          ii  i   iiiv  i i     vi    vv  ii --------  v i 
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGG--------AATAGA 309

  chrX_146459823_    685 AAAAAGAGTCCACAAACAGACCCACGCATGGAGAGACATTTGAATTACAG 734
                          vvi        v   i i     ii   vv vi v  v    v  v ii
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chrX_146459823_    735 CAAAGG---------------ATGGG-AAAGGATAATCTTTTTAGTAAGA 768
                            i  ---------------     -    i   i      i ii  iv
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chrX_146459823_    769 GATGCTGGGATAATTGAGTAACGATATG--AAAAAATGTTAAACTGAACC 816
                          i        i  i  ii  ? v i   --   i    --  ii  i   
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG--AAGTTGGACC 457

  chrX_146459823_    817 TCCAACTCGCTCT-TCTATTA---CCAACTCCAGGTGGATTTTAGACTAA 862
                         i i v   i v i- v  iv ---ii     v ii     iv?    iv 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chrX_146459823_    863 AATGTGAAAACGTGAAAGTATAAAGCATCTTC----ATAATATAGAAG-- 906
                              i i i - i   v      i -    v---- v  i    i? --
  L1M4_orf2#LINE/    508 AATGTAAGAGC-TAAAACTATAAAAC-TCTTAGAAGAAAACATAGGNGTA 555

  chrX_146459823_    907 AAT----GTCACATATGG-------AATTATTTTTAAGAT--GAGATGAA 943
                            ----  v  v -   -------   vi   i v    --  v iv  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_146459823_    944 AGGCATAAAGCATAAATGA-----TTGATATAAACTTGAACAAATTTATC 988
                          i   i  ivv i   v  ----- v    --  -   i  ---  i   
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATA--AA-TTGGAC---TTCATC 648

  chrX_146459823_    989 AAAGTTATATATGATTTTCTCAAAATTATCTTGAAATTAAAAATGT-CCA 1037
                            i   --------------    i --i   viv  v   ivii- i 
  L1M4_orf2#LINE/    649 AAAATTA--------------AAAACT--TTTGTGCTTCAAAGGACACTA 682

  chrX_146459823_   1038 TCAAAAGACACAATAGACAAGCTATAGAATATAAGAAGATATTTGCAG-- 1085
                             i i vvv  v      v i i     ivi    i         i--
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_146459823_   1086 ----TATC----AGTGGGCTCATTTCTAGAATATATAAAGAGCT---GCA 1124
                         ----    ---- iv  i  ii v  i              i  ---i  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_146459823_   1125 AC--------------ATAAATG------TGAAAAAATGGGCAAAAGATG 1154
                           -------------- i    i------ v?             i   v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_146459823_   1155 TGAGCAGGCCTGTC-ACAAAGAAGTCA---AAATGATGAGTGTATATACA 1200
                            ii  i v v  -v        vi ---     iiv i -- vii   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT--AAGCACA 880

  chrX_146459823_   1201 TGGAAAG 1207
                           i    
  L1M4_orf2#LINE/    881 TGAAAAG 887

Transitions / transversions = 1.58 (120 / 76)
Gap_init rate = 0.05 (38 / 767), avg. gap size = 3.66 (139 / 38)  


2544 25.20 7.35 1.40  chrX_146463894_146465793      551  1407 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146463894_    551 TGGGAAAACATCCCATGCACTTGGAAGGGAAGA----ATATTATTAACAT 596
                            i  i i        iv v    vv      ----     i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146463894_    597 GACCATACTAACCAAA--GAATTCTACAGATTCAATGAAATTCTTGTCAA 644
                          i v     vv     --  --             i v   i i i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGA--TCTACAGATTCAACGCAATCCCTATCAA 98

  chrX_146463894_    645 ATTACCAA-TGTCATTTTTTACAGAATTAGAAAAAAAAAATCCTAAAGGT 693
                          v v   i-  i -      i     v v  v  ivvi -       iv 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATT 146

  chrX_146463894_    694 CATATGAAATCAAAAAAGATTTA--ATAGC-AAAGCAATCCTAAGCAAAA 740
                               i  viiv  ii  iii --     -   i     i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_146463894_    741 AGAGCAAAACTGGAGGCATAACATTACCTGACTTGAAATTATACTATAAT 790
                            i    ii      vv v   i v  ii i  v   viv     i  -
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA- 245

  chrX_146463894_    791 TCTATCTATAGTAACCAGAACAACATGGTACTGGTATAAAAATAGACATA 840
                         --- v   i     i  ii   iii         i    ii         
  L1M4_orf2#LINE/    246 ---AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_146463894_    841 TACCTCAATGGAACAGAATAGAGAACCCAGAAATAAAGCCACCTACAT-- 888
                           vv         i     v    ii           v   --     --
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTT 340

  chrX_146463894_    889 ACAACCAAGTGATCTTCAACAAAGTCAATGAAAATATATGCTGGAGAA-G 937
                          iiii   v    i   i    i viivii i vi  viiv   i   - 
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_146463894_    938 TATACCTTATTTAATAAATAGTGCTGAAAAAATTGGGTAGTCATATGTAG 987
                         v   vii v  i  i    i      ii v  i   i  ?i  i   i i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_146463894_    988 AAAAATGAAACTGGATCCGTACCTCTCACCATATACAAGAATTAACTCAA 1037
                           i      ii    i  v      v            i           
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_146463894_   1038 GAT-----AAAGACATAAATGTAAAACCTGAAACTATAAAAATACTAGAA 1082
                         i  ----- ?    v         i v  i           v vi     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_146463894_   1083 GAAAACCTAGGA--AATTCTTCTGGACATTGGCCTAGGAAAATAATTAAT 1130
                               v    ?--  v     vv   v    vi    v  - ii  vv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCT 589

  chrX_146463894_   1131 --GACTAAGTCATCAAAAGCAAATGTAATGAAACCAAAAATAGACAAATG 1178
                         --  -  v v  i        v v i  ii   vv         i    v
  L1M4_orf2#LINE/    590 TAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_146463894_   1179 GGACTT-----------AAAGCGTCTGT-----AAAGAA----------- 1201
                               -----------   i v i   -----    i -----------
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_146463894_   1202 AAACAAAAA---AACCTACAGA-----------TGTTTGCAAGTGTTGCA 1237
                           iii    ---    i     ----------- i       i vv ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_146463894_   1238 TCTGACAAAGGGCTAACATCCAGAATCTACAATAAATTCAAACAACTCAA 1287
                              i  i  i  vii         v  i  vi  i  vv         
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_146463894_   1288 TAACAAAAAAGCAAACAGTCCCATTAAAAAGTGGGCCAAGGATAAGAATA 1337
                            i     ii    i ii  v   ?    i     v      vv     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_146463894_   1338 AACATTTTTCAAAAGAAGACATGCAAATGGTCAATACATTTATGAAAAAA 1387
                         i      i  v        i  i       i     viivi       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_146463894_   1388 TGCTCAATATCACAAATCAG 1407
                                i    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (133 / 79)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.41 (75 / 22)  


2631 25.69 4.82 1.49  chrX_146470285_146475140     3493  4364 (492)    L1M4_orf2#LINE/L1        8   908 (0)  

  chrX_146470285_   3493 ACATCCCATGCTCATGGATGGGTAGAATCAATATTGCAAAAACGACCAAT 3542
                          i        i        v  v   v i       iv  i i i -   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC-AAT 56

  chrX_146470285_   3543 ACTTCCAAAAGCAATCCACAGATT-AATGCAATTCCTGTCAAAG---CAG 3588
                            i  v   vii   i       -  i     i   i     i---   
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_146470285_   3589 CATCATTCCTCACAGAACTAGAAAAAAAAAATCCTAAAATACATATAGAA 3638
                          vv v  ii ii     v v  v  ivvi -         v     i   
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATATGGAA 155

  chrX_146470285_   3639 CCAAAAAAGAGCCCACATAGCCAAAGCAAGATTAAGCAAAAAGAACAAAT 3688
                         viiv  ii  v  viv         i   vv  i iv  i         v
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_146470285_   3689 CTGGAGGCATCACATTACCTGACTTTGAACTGTGCTACAAAGGCTATAGT 3738
                         i      vv     i v  ii i  ii  viv i        -   i   
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG-CTACAGT 254

  chrX_146470285_   3739 TATCAAAACAGCATGGTGTTGGTATAAAAATAGGCACATAGACCAACAGA 3788
                         v     i    ii    ii   i    ii    i  i     i   ii  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_146470285_   3789 ACAGAATAGAGAATCCAGAAATAAAGCCAAATACTTACAGTCAACTGACC 3838
                          i     v    i            v   v i i   ii     i   ii
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_146470285_   3839 TTCAACAAAGCAAACAAAAACA--AAGTGGAGAAAGGACAACCTTTTCAA 3886
                            i    i vviv   i v  --v i   i     i i ii        
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_146470285_   3887 GAAATGGTGCTGGAATAATTGGCAAGCCATGTGTAGAAGAATGAAACTGG 3936
                         v            i i  i   vv ?   ii  i i         ii   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_146470285_   3937 ATCCTCATCTCTCACCCTATACAAAAATTAACTCAAGATGGATCAAAGAC 3986
                          i  ii i   v    v                   i        ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_146470285_   3987 TTAAATCTAAGACCTGAAACCATAAAAATTCTAGAA-----CATTGGAA- 4030
                         i     v     v  i    i      v ii     -----   v  ?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_146470285_   4031 AAACCCTC----CCTT---CTAGACATTGG---CAAAGACTTCGTCACCA 4070
                            i i  ----    ---i   i  v   --- vv   iv - v     
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-GACACCA 603

  chrX_146470285_   4071 AGAACCCAACAGCAAATCCATCAATAACAAAGATAAATAGACAGAACCTA 4120
                          i i v   --    ------   v iv   i   i   i iv i  i v
  L1M4_orf2#LINE/    604 AAAGCACAA--GCAA------CAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_146470285_   4121 ATTGAA-CTAAAAGCTTATGCACAGCAAAATAAGTTATCAGCAGAGTTAA 4169
                           ii  -i     i   v  ii vv    iv vii     iv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_146470285_   4170 ACCAACAACTTACAGAATGGGAGAAAATATTCTCAAACTAAGTATCCAAC 4219
                          v-i     ii                    iv    ii vi    ii i
  L1M4_orf2#LINE/    696 AA-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_146470285_   4220 AAAGAA----TATCCAGAATCTACAAGGAACTC----AAATCAGCAAGAG 4261
                           i i ----          v  i  i      ----  v   ii  v i
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_146470285_   4262 AAAAA--AATAATCACATCAAAAAGTGGACAAAGGACATTAGTAGACAAT 4309
                            i --     i vv  i?    i   i       iv v i      v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_146470285_   4310 TCTC--AAGA-GATATACAAATGGCCAA-----ACGTGAAAA-ATGCTCA 4350
                             --    -                 -----  i      -       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_146470285_   4351 AGATCTCTAGTTAT 4364
                          v   v????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (143 / 77)
Gap_init rate = 0.03 (23 / 901), avg. gap size = 2.39 (55 / 23)  


2135 27.46 2.91 0.97  chrX_146481701_146483485      572  1292 (493)    L1M4_orf2#LINE/L1      174   908 (0)  

  chrX_146481701_    572 AACCAAAA-AA-CTTGAAAGCCAA-AGCAAATCTGGAGGCATCACATTAC 618
                          i      -  -       ivv  - i    vi      vv     i v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_146481701_    619 CTGATTTCAAATTATACTATAAGGATATAGTAAACAAAAAAGCATAGTAC 668
                          ii        viv     i  i v  i     v   i v  ii i    
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_146481701_    669 TGGTATAAAAATAGACACATAGATAAATGGAACAGAGTAGAGAACCCAGA 718
                            i    ii       i      v       i   i v    ii     
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chrX_146481701_    719 AATAAAGCCACCTATCCACAATGAACTGATCTTTGAAAAAGTGGACAAAG 768
                               v   ivi  ii iii v  i    i  i  v  i vv v   ii
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chrX_146481701_    769 CCAAACATTTGAGAGAGGACATCCTATTTGAAAAATGATGCTGAAAACAT 818
                            vv  v v i  i  i i vi  v  ii v     i     ii vv i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_146481701_    819 TGAGTAGCCATATGCAAA-GAATGAAACTAGATCCATATTTCTCATCATA 867
                           ii  ?   i       -       ii i  i  v  ii  v  i    
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chrX_146481701_    868 TGTATAAATGAACTCAAGATAGATTAAAGAATTAAATATAAGATGTAAAA 917
                          ii v    v       i  i   i ?   vi     i     vv     
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chrX_146481701_    918 TTATAAAAACCCTAAAATAAAACATAGGAAAAAATATTCTGGACATTGGC 967
                         i       vi i  i  v          ?iv    v   vv   v    v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_146481701_    968 CTAGGCAAAGAATTTATGAGTAAGTCTTCAAGACCACAAACAACAAGAAA 1017
                         i       v iv  iv iii  v v vi   i v     i      i i 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_146481701_   1018 AAAATTAGACAAATGGGA----AT-GAAACTAAAATGCTGCTGCACAGCA 1062
                             v    i    v   ----  -i   i     -i  vi  ii vv  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCA 672

  chrX_146481701_   1063 AAGGAAACTATCAACAGCATCACCAAAGAACATACGGAGTGGGAAAAAGT 1112
                              v        v ivi v vv i v   vi  i  i     i   i 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_146481701_   1113 ATTTGCCAACTATTAATATGTATCTGACAAAGGACTAATATTCAGAACCT 1162
                               v  ii  ------i       i  i     vi   i     iv 
  L1M4_orf2#LINE/    723 ATTTGCAAATCAT------ATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_146481701_   1163 ATAAGGAATTCTAACAACTCAACAAGAAAATGACAA----CCTCATCAGG 1208
                             i   i   v         i  v    v     ----  iv  i?ii
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_146481701_   1209 AAGTGGGCAAAAGACATAAACAGACATTTTTCAAAAGAAGATACACAATT 1258
                           i        i  iv i  i        i  v          i    v 
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_146481701_   1259 GGCCAA-----ACA---AAAAATGCTCATCATTAATCAGAAA 1292
                               -----   ---   i       v   i ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (119 / 75)
Gap_init rate = 0.01 (11 / 735), avg. gap size = 2.55 (28 / 11)  


2522 24.74 6.79 2.30  chrX_146486099_146488397      941  1809 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146486099_    941 TGGAAACACATCCCATGCTCGTGGATGGGTAGCATCAATATTGTGAGAAT 990
                               v i        i  i     v  v  vv i        v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146486099_    991 AACCATATTGCCAAAAGCAATCTACAAATTCAATGCAATCCCCATCAAAA 1040
                         ii v   i v  v   vii       i      i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146486099_   1041 TACCACTTTCATTCTTCACAGAA-TTAGGAAAAAC-AATTCTAAAATTCA 1088
                          v   vi v v  i  ii     -  --  v  i -i  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTCA 148

  chrX_146486099_   1089 CATGGAACCAAAAAAGAGCCCACATAACCAAAGCAAGAT-AAGCAAAAAG 1137
                         i      viiv  ii  v  viv   i     i   vv -i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_146486099_   1138 AACAAA-TTGA--GACATCACACTACCTGATTTCAAACTGTATTTTAAGG 1184
                               -   i--   -       v  ii        viv  i vi  i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_146486099_   1185 CCATAGTCACCAAAACAGCGTGAAACTGGTATAAAAATAGGGACATAGAC 1234
                          i i   v i   i    i   iv     i    ii    iv i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_146486099_   1235 AAATGGAACAGAATAGACAACCAAGAAATAAGCCCAAATACTTACAACCA 1284
                         v       i     v  v ii v        i    v i i   iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_146486099_   1285 ACTGATCTTTGACAAAG----TAA-ACGA---AGTGGGGAAAGGA----- 1321
                          i    i  i     i ----i  -  v --- i         i -----
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_146486099_   1322 -------CAAATGGTGCTGGGATAATTGGGTATCCACATGTAGGAGAATA 1364
                         -------               i  i   i  ?       i ii     i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_146486099_   1365 AAACTGGATCCTCATCTGTCACCCTATACAAAAATCAACTCAACATGGAT 1414
                           ii    i  ii i  vv    v           i       v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_146486099_   1415 TAAGGACTTAAATCTAAGACCTGAAACTA-AAAATTCT-AGAAGATAACA 1462
                         i ?i   i     v     v  i      -    i   -      v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_146486099_   1463 TCGGAAAAACTTGTCTAGACATTGGCTTAGGCAAGGATTTC------ATG 1506
                          v  ?iv  v iv  vv   v    v        v i    ------   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_146486099_   1507 AC--CAAGAATGCAAATGCAATAAAAACAAAGATAAATAGCTAGGACTT- 1553
                           --   i iii   --    i    iv   i   i   iv v      -
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_146486099_   1554 ----AAACTAAAGAGCTTTTGCACAGCAAAAGGAAAAGTCAGCAGAGTAA 1599
                         ----   i    i -      ii vv    i iv vvi   iv i   i 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_146486099_   1600 ACAGACAACCCAGAGAATGGGAGAAAATCTTCACAATCTATAAATCTGAC 1649
                          v          v               v  ii   vii   v      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_146486099_   1650 AAAGGACTAATACCAAGTACCTACAAGGAACTCAAATTAGCAAAAAAAAA 1699
                           i     vi  i v  v iv  i  i      ---   -   vvv  v 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTC---TTA-CAACTCAATA 790

  chrX_146486099_   1700 AAAAAAAAAAAAAAAAAAAAAAAAAATCCCATCAAAAAGTGGGC------ 1743
                          v     i v   v  ----------i  v  i?    i     ------
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAA----------CCCAATTWAAAAATGGGCAAAGGA 830

  chrX_146486099_   1744 T---AATCGACAATTCTC---AAAAGATATACAAATGACCAA------CA 1781
                          ---   v    v     --- i              i    ------  
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_146486099_   1782 TGAAAAAATGTTCATCACTAATGATCAG 1809
                               i   i   v  ii ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (130 / 81)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 3.16 (79 / 25)  


1634 16.62 3.53 27.29  chrX_146498764_146500970.rev      526  1716 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146498764_    526 TGGAGAGAT--CCCATGTTTATGGATTGAAAGAGTTAATACTGTCAAAAT 573
                             i    --        i        i    v      i   i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146498764_    574 GTTTATGCTTCCCAAAACAGTCAACAGATTCAATGAAATGC-TAACAAAA 622
                          viv  i  i      viii  v          i v   v -  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146498764_    623 TTCCAATGAGATTTTTCACAGAAATAGACAAA--AAGCCTAAAATTCATA 670
                          i   iivivv     ii       v     i--i v             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_146498764_    671 TGGGACCACAAAAGACCCTAAATACCCCAAACAACCTTGAACAAAAAGAA 720
                            i vii   ii     vi    v  v      i      v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_146498764_    721 CAAAGCTGGAGGCAC-CATACTACCTGATCTAAAAATTTACTACAAAGCT 769
                              i      -  -  i   v  ii  i v    i             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_146498764_    770 ATAGTAATCAATACAGCATGGTACTGGCATAGAAACAGACATATAGACCA 819
                          i         v    ii             iii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_146498764_    820 ATGGAATGGAATAGAGAA---AGCAGTAAATGTGTGTACTTATGGTCAAC 866
                                i    v    i---  v i    ivii ii i          i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_146498764_    867 TGATCTCTGACAAAGTT-TCAAAAACA--CAAGGGGGAAATGAATA-TTT 912
                             i ii     i v -i   i v  --   v       -     - i 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCT 398

  chrX_146498764_    913 TGCATAAATCATGCTAGGAAAGCTAGAGTTTGACATGAAGAATGAAATTG 962
                          ---------------------------  ii   -----    ------
  L1M4_orf2#LINE/    399 T---------------------------TTCAACA-----AATG------ 410

  chrX_146498764_    963 GGCCGGGTGTGGGGTGGCTCAGGCCTGTAATCCCAGCACTTTGGGAGGCT 1012
                         -------------   --------------------------------  
  L1M4_orf2#LINE/    411 -------------GTG--------------------------------CT 415

  chrX_146498764_   1013 GAGGCAGGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGGTAAC 1062
                          i i  iv     ------------------------- ?  ------  
  L1M4_orf2#LINE/    416 GGGACAACTGGAT-------------------------AKCC------AC 434

  chrX_146498764_   1063 ATGGTGAAACCCTGTCTCTACTAAAAATACAAAAATTAGTCAGGCATGGT 1112
                            --------------------------     ----------------
  L1M4_orf2#LINE/    435 ATG--------------------------CAAAA---------------- 442

  chrX_146498764_   1113 AGCACACTCCTGTAATCCCAGCTACTTTGGAGGCTGAGACAGGAGAATCG 1162
                         --------------------------------------------    --
  L1M4_orf2#LINE/    443 --------------------------------------------GAAT-- 446

  chrX_146498764_   1163 CTTGAACCCGGGAGATGGAGGTTGCAGTGAGCTGAGGAGGTACCACTGTA 1212
                         --------------------------------------------------
  L1M4_orf2#LINE/    447 -------------------------------------------------- 446

  chrX_146498764_   1213 CTTCAACTGGGGTGACAGAGTGAGACTCCATTTCCCACCCCACCCCTCCT 1262
                         --------------------------------------------------
  L1M4_orf2#LINE/    447 -------------------------------------------------- 446

  chrX_146498764_   1263 CAAACAAAAATTGGACCCTTATCTCATACCATATACAAAATTCAACTTGA 1312
                         ------i  i        i  i    i             v i    ii 
  L1M4_orf2#LINE/    447 ------GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_146498764_   1313 AGCGAA----AGACTCGAACGTAAGACTGGAAATGGTAAAG-----AGAC 1353
                          ii i ----    iii  i      vivi   ivi    i-----   v
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_146498764_   1354 AAAAACATAGGGGAAAAGCAACATAATATTGGTCTAGGCAAAGGTATTTT 1403
                         i          ? v   v vv i i iv    vi       v   v i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_146498764_   1404 TAATATGACCCCAAAAGCACAGACAATAAAAACAA------------TGG 1441
                         vi       v           ii   i    iv  ------------   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chrX_146498764_   1442 ATTTCATCAAA-CTAGAAAGCTATGTACGGCAAAGGAAACAATCAACAGA 1490
                          i         -i  i   vi v   i vv       v  v     v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_146498764_   1491 GT--AAAGAATACCTATGGAATAGGAGAAAATATTTGAAAACCATATATC 1538
                           --     vv   i ii    i              v   i        
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_146498764_   1539 TGATAAGGGGTTAGTATCCTTTAGCATGTAAGTATATGTATATAAGGGGC 1588
                                  ii v      ---  -----  -------       i ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCC---AG-----AA-------TATATAAAGAAC 775

  chrX_146498764_   1589 TC----AATTCAATTGCAAAAAAGCAAATAACCTAGCTAAAAAGTCAGCA 1634
                           ----  i     vii     ii         i ii ?    i vi   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chrX_146498764_   1635 AAGGCCCTGAATAGACATTTCTCAAAAGAAGACGTACAAATTGCCAACAT 1684
                             vii                v        ii       v     i v
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chrX_146498764_   1685 GTATA-AAAAAAATTTTCAGCATCACTAATCAT 1716
                          i i -i    i  vi   i     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (133 / 62)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 12.66 (367 / 29)  


2155 25.50 3.31 4.75  chrX_146555065_146557394.rev      940  1845 (485)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_146555065_    940 TGTTAATTAGTTAAAAGACTCAATGTAATTAAAGCTGTTAATTCTTTCCA 989
                             v  vii  ii      i   i vi    - v  vi   v  ii   
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAA-GATGGCAATACTCCCCA 64

  chrX_146555065_    990 AATAGATATACATATTTAACCCAAGTCTTAATCAAAATCCTAGCATTATT 1039
                            v   v    v   i   v   vi i  -         i   vviv  
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTA-TCAAAATCCCAGCTGCCTT 113

  chrX_146555065_   1040 TTTTGTGGGCAGAGAAAACCTTATA-TAAAATTTATATGGAGAGGCACAG 1088
                              ii iv vv  v  v  v  v-       i       i v   vi 
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 163

  chrX_146555065_   1089 GCTTTAAAATTGCTAAAACTATCTTGACCA----GAATAATGTGGGAGAA 1134
                          viii i   v  i     v       vv ----   i  v  v    i 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chrX_146555065_   1135 ATCAC---TCCCTGGATAGTAAGGCTTAATACATAGCTATAGTAATGAAG 1181
                         v    ---    --i  vvi  ii    v    v     i      v   
  L1M4_orf2#LINE/    214 CTCACACTTCCC--AATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_146555065_   1182 ACAATCTAGTATTGGCA-AAGCAATATACACACAGATCAATGAAACAGAA 1230
                            i v i   i     -   -i   v   i i         i  i    
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAG-GATAGACATATAGATCAATGGAATAGAA 310

  chrX_146555065_   1231 TGGAGAACCCGGAAATAGTCCCACACCAATATTCTATGTT---TTAACT- 1276
                          v    ii  i      iv    i  ----   -    v ---  i i -
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATAC----ATT-TATGGTCAATTGATTT 355

  chrX_146555065_   1277 --GGAAAAGGTGCAAAAGCAATTCAATGGACAAGCCATGGCCTTTACAAC 1324
                         -- iv  i     v  ii v         iv  ivv  i i    v    
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chrX_146555065_   1325 AAATAGTCTCAAAGCAATTAGGCATCCATAGGCAAATAAATAAATAAATA 1374
                             i  viiiiii   i i ii ?   i v     vi   i  ------
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA------ 449

  chrX_146555065_   1375 TACAAAACTTTAGCCTAAATTTCACACTTTTTACAAAAATTAA-----AA 1419
                         -iivii  i----    --ii      iv v            -----  
  L1M4_orf2#LINE/    450 -GTTGGACC----CCTA--CCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_146555065_   1420 TAGATCACTAATTAAACATAAAATGTAAACTGTGAAAATAAAACACTTTT 1469
                          i     -----? i  v    -     ivvv i   v  v  v   i  
  L1M4_orf2#LINE/    493 TGGATCA-----WAGACCTAAA-TGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_146555065_   1470 TCAA--AAACA--GGAGAAAATCTTCAGGATCTAGGGCTAGAAAAAATG- 1514
                         vv  --     --  ? v        iv  i  v   i   iv  --  -
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA--TGG 584

  chrX_146555065_   1515 -TTCTTAGACA--ACACCAAAACCAGAATCCATAAAA--AAAAATTGATA 1559
                         -        i --         v  v  v v i    --      v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_146555065_   1560 AAATGAACTTAATCAAAATTTAAAAACTTTTATTCTGAGAAAGACCCAGT 1609
                           v  i    v         -          i v  vvi  i   v vi 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_146555065_   1610 GAAAAAGATGAAAAGACAATCTAAAGACTTTAAGAAAATATTTGCAAACC 1659
                         v  i  ii           i i v   v vvi                i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_146555065_   1660 TCATATGGAACAAAGGACTATTATCTAGAATATATAAAGAACTCAAAACA 1709
                         vi    vvi i  i     vv    i                  v---i 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT---TA 780

  chrX_146555065_   1710 CAACAGGTAAAAAACAAAAACAAAAACAACTCAATCTAATTATAAACAGG 1759
                             --- v  v  i     v v   i   i    i?  ----   ii  
  L1M4_orf2#LINE/    781 CAAC---TCAATAATAAAAAGACAAATAACCCAATTWAA----AAATGGG 823

  chrX_146555065_   1760 CAAAAGACATTAAGAGGCATTTCACCAAAAAGAATATACAGATGGCAAAT 1809
                             i  iv v  v  i      v     i ii       i     v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_146555065_   1810 AATCACACGAAAATGTGTTAAAAAATTATTAGCCAT 1845
                           v    i     vi  i v  v - i ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.20 (124 / 103)
Gap_init rate = 0.03 (29 / 893), avg. gap size = 2.52 (73 / 29)  


3153 27.36 0.44 0.66  chrX_146605642_146612378     5335  6244 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146605642_   5335 TGAAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATGGTGAAAAT 5384
                           i   i i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146605642_   5385 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCTCATCAAGC 5434
                            v     v      v i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146605642_   5435 TACCATTGACTTTCTTCACAGAATTAGAAAAACT-ACTTTAAATTTCATA 5483
                          v   vivi i  i  ii     v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_146605642_   5484 CGGAACCAAGAAAGAGCACGTGTAGCCAAGACAATCCTAAGCAAAAAGAA 5533
                         i    viivi ii  v vv vi       i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_146605642_   5534 CAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5583
                              i     ivv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_146605642_   5584 CAGTAAGCAAAACAGCATGGTACTGTTACCAAAACAGAGATACAGACCAA 5633
                               v   i    ii        vi iv ii i   v   i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_146605642_   5634 CAGAACAGAACACAGGCCTCAGAAATAATGCCACACATCTGCAACCATCC 5683
                         ii   i    ivv  ivii         vv   i    i iiiii  vii
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_146605642_   5684 GATCTCTGACAAACCTGACAAAAACAAGCAATGGGGGAAGGATTCTCTAT 5733
                            i ii     ivv  v   i v  vv        i   i  vv   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_146605642_   5734 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCACATGCAGAAAACTGAAA 5783
                          i  i              v      v  ?         i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_146605642_   5784 CTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGAATTAA 5833
                         i         v   i     v                   i   i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_146605642_   5834 AGACTTAAATGTAAGACCTAAAATCATAAAAACCCTAGAAGAAAACCTAG 5883
                             i           v      ii      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_146605642_   5884 GCAGTG--CCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTATAA 5931
                          ?-  i--i -   iv   v v  vv i     v ii   v iiv   i 
  L1M4_orf2#LINE/    551 GN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_146605642_   5932 CACCAAAAGCAATGGCAACAAAAGCTAAAATTGACAAATGGGATCTAATT 5981
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_146605642_   5982 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTTATCATCTGAGTGAACA 6031
                            v v  i i   i  ii vv    i  v   -    vvvi      v 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACT-ATCAAGAAAGTGAAAA 697

  chrX_146605642_   6032 GGCAATCTACAGAATGGGAGAAAATTTTTGCAATCTATCTATCTGACAAT 6081
                          i   i i                 v       vii  v       i  v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_146605642_   6082 GGGGTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAA-AA 6130
                           iv vi          v  i  i     ivv    v ---   v  -  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAA 794

  chrX_146605642_   6131 AAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 6180
                            i     i     v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_146605642_   6181 TCTCAAAAAAAGACATTTATGCAGCTGACAAACATATTTTAAAAAGCTCA 6230
                             v   i    i  vi viii  ii i  i  i  vvv  i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_146605642_   6231 TCATCACTGGTCAT 6244
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (145 / 100)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2865 25.80 2.55 0.38  chrX_146639554_146641330.rev      504  1286 (491)    L1M4_orf2#LINE/L1      109   908 (0)  

  chrX_146639554_    504 GCGTTCTTCAAAGAAATAGAAAAAATAATCCTAAAATTTATATGGAACCA 553
                           v  i  iiv      v  v  iv i           i        vii
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chrX_146639554_    554 CAAAAGACCCAAAATAGCCAAAACTAGCTTAAGCAGAAAGAACAAAACTG 603
                            ii      i            v v   i iv ii         ii  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_146639554_    604 CAGGTATCATTTTACCTGACTTCAAGTTATACTACAGAGGTATAGTAACC 653
                         v   vv   ivi v  ii i     iviv       i  v  i     i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_146639554_    654 AAAATAACATGGTACCAGCATAAAATCAGGCACATAGACCAATGGAATGG 703
                           i i iii      ii      iivi  i  i     i         i 
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_146639554_    704 AATAGAGAAACTAGAAACAAATCCACACACTTACAGTGAACTCATTTGCA 753
                            v    iv i     i   i   i   i   ii  v  i v    v i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_146639554_    754 ACAAAGGTGCCAAGAACACATACTGGGGAAGAGGGAGTTTCTTCAATAAA 803
                             i          v  ivi v       iiiiv   i i     i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_146639554_    804 TGGTGCTGGGAAAACTGGATATCCATCTGCAGAAGAATGAAACTAGACCT 853
                                    v         ?   iv    i         ii i    i
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_146639554_    854 CTATCTCTTGCCATATTAAAAAATCAAATCAAAATTGATTAAAGATTTAC 903
                            i   vii      vv      i  v       v   i ?   ii  v
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_146639554_    904 ATCTAAGGCCTCAAACAATGAAACTAT-AGCAAGAAAACTTTGGGGAAAA 952
                           v    iv  v    v  i     v -  -        v v  ? v   
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAG-AAGAAAACATAGGNGTAAA 557

  chrX_146639554_    953 TCTTTAGGACACTGCTCTAGGCAAAAATTTCCTGAGCAGTAAC-CCATAA 1001
                             iiv   vi  vvi       vii    i iiii - i  -   v  
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGACACCAAAA 606

  chrX_146639554_   1002 GCACAGGCAACCAAAGCAAAA-TGAACTAATGGGATCTCATCAAA-TTAT 1049
                              i     v    v    - ii iv   v   ii        -   -
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA- 655

  chrX_146639554_   1050 AAAGCTTCTG------------CAC----AACAAAGTGAAGAGATGACTC 1083
                            i   i  ------------   ----  v        i   ii  i 
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chrX_146639554_   1084 ACAGAATGGGAGAAAATATTTGCAAACTACTCATCTGACAAGGGATTCAA 1133
                                                   ii ivi      i      i iiv
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chrX_146639554_   1134 AACCAGAATGTATAAGGAACACAAACAGCTCTATAGGAAGAAATCTAATA 1183
                          v       i     i    v vv   i   v   iv  i  iv v    
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chrX_146639554_   1184 ATCTGATCAAAAGATGAGCAAAAGATTTCAACAGACATTTCCCAAAAGAA 1233
                          i ii  i?   i   i     i     v  i         i v      
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_146639554_   1234 GACATACAAATGACAAACAGGAACACAAAAAGGTGCTCAACATCACTGGT 1283
                           i         i v  i i v   ii     i            ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_146639554_   1284 CAT 1286
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.91 (130 / 68)
Gap_init rate = 0.01 (9 / 800), avg. gap size = 2.56 (23 / 9)  


3258 24.71 0.53 4.45  chrX_146656603_146660892     2855  3797 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_146656603_   2855 GAAAAATTTTCCACGTTCATGTATTGGAAGAATCAATATTGTTAAAATGC 2904
                             i  v i   i       v         v i           i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_146656603_   2905 CCATACTACCCAAGGCAATTTACAGATTCAATGAAATCCCTATCAAAACA 2954
                          v     v     ivii  i           i v              iv
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_146656603_   2955 CCAATGACATTCTTCCCAGAGATAGAAAAAAATGATCTTAAGATTTATAT 3004
                            iivi v  i  iv    i  v  v  iv-     i   i   i    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATAT 151

  chrX_146656603_   3005 GGAACCACAAAAGACCCAGAATAGCCAAAACTATCCTAAGCAGAAAGAAC 3054
                             vii   ii                   v   i i iv ii      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_146656603_   3055 AAAACTGCAGGTATCATTTTATTTAACTT-AAAATTATATTGCAGAGCTG 3103
                            ii  v   vv   ivi viii  i  -    i -  i i  i    i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTA 250

  chrX_146656603_   3104 TAGTAACCAAAACAGCATGGTATCAGCATAAAATCAAACACACAGAACAA 3153
                         i     i   i    ii     iii      iivi i   i i   v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_146656603_   3154 TGGAACAGACTAGAGAACCTAGAAACAAATCCACAGACTTCCAGTGAACT 3203
                              i   v v    ii i     i   i   i v i  vii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_146656603_   3204 CATTTGCAACAAAGGTGCCAAGAACATACACTGGGGAAGAGACAGTTTCT 3253
                         v    v i    i          v   v  v       iii i   i i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_146656603_   3254 TCAATAAATGGTGCTGGGAAAACTGGATATCCATCTGCAGAAGAATGAAT 3303
                             i              v         ?   iv    i         -
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA- 449

  chrX_146656603_   3304 ATCCTTCATTCTTCTAGATAGATAGATAGTCTATCTCTTGTCACATTCTA 3353
                         -------------------- v i  iv-i   i   -----   -----
  L1M4_orf2#LINE/    450 --------------------GTTGGACC-CCTACCTC-----ACA----- 468

  chrX_146656603_   3354 TCACTTGCCACATTCAAAAATCAAATCAAAATGGATTAAACACTTAAATC 3403
                         -------   i  v       i  v           i ? v  i     v
  L1M4_orf2#LINE/    469 -------CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chrX_146656603_   3404 TAACACCTCAAACAATGGAACTATTGCAAGAAAACATTGGGGAAAATCTC 3453
                            v v  v    v  ii    v  iv          v  ? v      i
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_146656603_   3454 CAAGACATTGGTCTGATCAAAAATTTCTTGAGCAGTACCCCATAAGCACA 3503
                          iv   v    vi iiv   vii      iiii vv  v   v       
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_146656603_   3504 GGCAGCCAAAGCAAAAATGAACAAATGGGATCTCA----AGTTATAAAGC 3549
                         i   i v    v      ii i    v   ii   ---- i   -   i 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA-AAAAC 660

  chrX_146656603_   3550 TTCTACACAGCAAAGGATACAATCAACAAAGTGAAGAGATGACCCACAGA 3599
                           i iii vv       i  v     v        i   ii         
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_146656603_   3600 ACAAGAGAAAATATTTGCAAACTACTCATCTGACAAGGGATTCATAACCA 3649
                          iii                 ii ivi      i      i ii  v   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_146656603_   3650 GAATGTATAAGGAACACAAACAGCTCTATAGGAAGAAATCTAATAATCAA 3699
                             i     i    v vv   i   v   iv  i  iv v     i v 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_146656603_   3700 ATTAAAAGATGGGCAAAAGATTTGAACAGACATTTCTCGAAAGAAGACAT 3749
                            ?   i         i        i           v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_146656603_   3750 ATGAGTGGCAAACAGGAATATTAAAAGGTGTTCAACATCATTGATCAT 3797
                          ii i    v  i i v i  v     i  i         ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (148 / 81)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 5.22 (47 / 9)  


1177 25.69 1.39 0.00  chrX_146692070_146694719      654   941 (1709)    L1M4_orf2#LINE/L1        3   294 (614)  

  chrX_146692070_    654 GAGAAATATCCCATGTTCATAAATAGCAAGACT-AATGTTGTTAAACTGT 702
                           i i               ii  v v      -   i       iv  v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_146692070_    703 CACTTCTTCCCTACTTGATCTATAGATTCAATGCTGTCTGAATCAAAATC 752
                           v v  i   v v        i        i  vi  ivv         
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_146692070_    753 CTAGCAAGTTATTTTGTGAATATTGACAAACTGACTGTAAAGTCTATATG 802
                          i   vivi v     iii v        i    iiv    i ii     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_146692070_    803 GAAAGACAGAAGATCCAGAATAGGCAGTATAATATTGA---GGAAGAACA 849
                             vi  iii  i         v  iv i   v    ---i        
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_146692070_    850 AAGTTGGAAGACAGACACTATCTTACTTCAAAGCTTATTACAAAGTTACA 899
                                 i   vv     vi iv i      i    i       i    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_146692070_    900 GTAGTCAAGACAGTAGGGTATTGATGAAAGAAAAGAGAAATA 941
                            i          iv    i  iiiv   i v   v v   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

Transitions / transversions = 1.55 (45 / 29)
Gap_init rate = 0.01 (2 / 292), avg. gap size = 2.00 (4 / 2)  

1983 26.40 5.08 0.51  chrX_146692070_146694719     1572  2162 (488)    L1M4_orf2#LINE/L1      291   908 (0)  

  chrX_146692070_   1572 TGTAGATAAATGGAACAAAATAAAGATGCCAGAATTAGATCCATACAAAT 1621
                          i     v       i i   vi   vv      v  i i       vv 
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chrX_146692070_   1622 ACAGTCAACTGATCATTGACAAAGGAGC--AAATAATTCAATGGAGAAAC 1669
                          ii     i    iv i     i  v  -- i iv         i    v
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG 390

  chrX_146692070_   1670 AATGGTCTTTTCAACAAACGGTGCTGGAATAACTGGACATTCATATGCAA 1719
                            i              i        i i       i ?i  i      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_146692070_   1720 AAAAC--AATCTAGACACAGACCTTATATCTTTCACAAAAATTTACTCAA 1767
                           i v--  vi i   v vv    i i i v vi         v      
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_146692070_   1768 AATGGATCATAGACCTAAATGCAAAACACAAAACTGTAAAACTTCTGGAA 1817
                                  ?           i  i vvi      i       ii i   
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_146692070_   1818 GATAACATAGGAGAAAATCTAGGTGAACTTGTGTTTGGTGATGACTTTTT 1867
                           v        ? v      vv    v    v   v  ii   ii  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_146692070_   1868 GGGTACAATGCTAAAAGCACGATCCCTGAAAAAAACTGAACAGTCGAA-- 1915
                         i i  ii ii i        i v vvii   i   --i  i  vii  --
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAA--AAATAGATAAATT 638

  chrX_146692070_   1916 --ATTTTTTCA---TTACAAATGTCTGCTCAATGAAAGACATTGTTAAAT 1960
                         -- i  iv   ---   v   iv i  iv vvii  i    i i i  iv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_146692070_   1961 GAATGAAAAGACAAGCCACTGTCTGGGAGAAAATATCTGCAAAATACATA 2010
                         i i           v    v vv             i      vi i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_146692070_   2011 ATCTGATAAAGGGCTGATATCTAAAATATATAAAGAACACTGAAAAATCA 2060
                         -        i  i  vi    i i              v  v v  v   
  L1M4_orf2#LINE/    739 -TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_146692070_   2061 TCAATAAAAAAA------ACCCAAT--------GGGTAACAGATCTGAGC 2096
                         vi        i ------       --------   i  vi   i   ii
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chrX_146692070_   2097 AGACACCTTATCAAAGAAGATACATACGTGACAAACAAGCATA-----AG 2141
                              ii ivi           i i vi  i v  i     i -----  
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_146692070_   2142 ATGCCCAATGCCATATGTCAT 2162
                             i   iii  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (99 / 54)
Gap_init rate = 0.01 (9 / 618), avg. gap size = 3.67 (33 / 9)  


1223 26.71 2.48 0.31  chrX_146754414_146762046      180   501 (7132)    L1M4_orf2#LINE/L1        1   329 (579)  

  chrX_146754414_    180 TGGAAAGATATGCTATGCTTATGAATC-----AC--AATATTATTAAAAT 222
                                    v i   i i   i  i-----  --      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146754414_    223 TACAGTACCCTCCCAAAGCAACTTACAGATTCAATGCAATCCTTATCAAA 272
                         vi  i   i -      vii ii           i       i       
  L1M4_orf2#LINE/     51 GGCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_146754414_    273 ATACCAATGATATTCTCCATAGAAATAGGAAAAAAATTCCTAAAAATTAT 322
                           v   iiviiv  i iiii      v iv  ivviv        v i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_146754414_    323 GTGGAAACACAAAAGACTCA-AATAGCTAAAGCAATCCTGAGTAAAAAGA 371
                         i      ii   ii   i  -      i   i     i   iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_146754414_    372 ACAAAGCTGAAGGCATTACATTATTGGACTTCAAAATTTACTACAAAGTT 421
                               i  i   vv i   i viivi i       i           i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_146754414_    422 ATAATAACCAAGACAGCATGGTACTAGCATAAAAACAGACACATAGACCA 471
                          i i   i        ii       i      ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_146754414_    472 ATGGAGCATAATAGAGAACCCAGATATAGA 501
                              ii v   v    ii     v   i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAA 329

Transitions / transversions = 3.30 (66 / 20)
Gap_init rate = 0.01 (4 / 329), avg. gap size = 2.25 (9 / 4)  

3021 27.83 0.88 0.99  chrX_146754414_146762046     4584  5492 (2141)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146754414_   4584 TGGAAGAACATTCCATGCTCATGGAAAGGAGGAATCAGTATAGTGAAAAT 4633
                              ii i  i     i       vv   i  v i i   v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146754414_   4634 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4683
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146754414_   4684 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 4731
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_146754414_   4732 ATATGGAAC--CAAAAAACAGCCCGCATTGCCAAGACAATCCTAAGCCCA 4779
                                 v--   iii  --  v v  v     i      i i ivv- 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAA-A 194

  chrX_146754414_   4780 AAAGGACAAAGCTGGAGGCATCACGCTTCCTGACTTCAAACTATACTATA 4829
                         i   i      i      vv    i     ii i      viv     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_146754414_   4830 AGGCTACAGCAACCCAAACAGCATGGTACTGGTACCCAATCAGAGATATA 4879
                          i       i  i v i    ii         i ivviivi   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_146754414_   4880 GACTGATGGGACAGAACAGAGGCCTCAGAAATAACACCCA--CATCTACA 4927
                           iii    i i    iv   ivii         -     --   i  ii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATG 343

  chrX_146754414_   4928 ACCATCTGATCTTTGATGAACCTGACAAAAATAAGCAATGAGGAAAGGAT 4977
                         ii  vi    i  i  ii ivv  v   i vi vv     i      i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_146754414_   4978 TCCCTACTTAATAAATGCTGCTGGGAAAACTGGCTAGCCATATGTAGGAA 5027
                         vvi  vi i  i     v        v      v  ?   i   i ii i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_146754414_   5028 GCTGAAACTGGACCCCTTCCTTACACCTTATACAAAA-TTAATTCAAGAT 5076
                         iv    ii         v   i     v         -    i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_146754414_   5077 GTATTGAAGACTTCAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 5126
                          v  ii?    i v     v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_146754414_   5127 AACTTAGGCA-ATACCATTCAGGACATAACGCATGGGCAAGGACTTCATG 5175
                            v    ?i- v i -   iv   v viv i- i     v ii   v i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTA 591

  chrX_146754414_   5176 ACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGA 5225
                         iv  vi            vvi          vv        i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_146754414_   5226 TCTAATTAAACTAAAGAGCTTCTGCCCAGCAAAAGAAACTACCATCAGAG 5275
                         ii v  i   v v  i i   i  iv vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_146754414_   5276 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCT 5325
                             v  i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_146754414_   5326 GACAAAGGGCTAATATCCAGAATCTACAAAGAATTTAAACAAATTTACAA 5375
                           i  i  i  vi          v  i      i ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_146754414_   5376 GAAAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGAC 5425
                         v     iv    i     v  i?    i            v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_146754414_   5426 ACTTTTCAAAAGAAGACATTTATGCAGCCGACAGACACAAGAAAAAATGC 5475
                          i  i  v        i  vi viii   i i ii    v     i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_146754414_   5476 TCATCATCACTGCTCAT 5492
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (155 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.42 (17 / 12)  

1944 24.53 0.94 1.12  chrX_146754414_146762046     6220  6753 (880)    L1M4_orf2#LINE/L1      298   830 (78)  

  chrX_146754414_   6220 CAATAAAAAAAAATAGAGAACCCAGATATAAATCCATTCATTTATAGCCC 6269
                             ii  v i   v    ii     v     i    v       i i v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_146754414_   6270 ACTCATCTTCAACAAAAGCATGAAGAACATCCAGTGGGGAAAGGACAGTC 6319
                          i v  i   i    ii iiiv    v   i  i         i i    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_146754414_   6320 TTTTCAATAAGTGGTGCTG-TACAGGCTGGATAACTATATGCAGAAGAAT 6368
                                i  i        -v   -i       ? i i     i      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACA-ACTGGATAKCCACATGCAAAAGAAT 446

  chrX_146754414_   6369 GAATCTATACCCCTATCTCTCACCCTACACAAAAATAAAATCAAAGTGGA 6418
                            vi iv       i   v    v  i        v  v     i    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_146754414_   6419 TAAAAGACTTGAATCTAAGACCTCGAACGATGAAACTACTAGAAGGAAAC 6468
                          v ?    i i   v     v  vi   v  i     vi      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_146754414_   6469 ACTGGGG-AAATGTCCCATGACATTGGTGTGGGCAAATATTTTTTTGTGT 6517
                          iv  ? -    v -i i    v    vv i     - iv   i  ivi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGAT 594

  chrX_146754414_   6518 AAGACCTCAAAAGCACAGGCAACAAA-GTAAATGTAGATAAATCGGATCA 6566
                          v   vi          i        - v   vi         i   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_146754414_   6567 CATC-TGATTAAAAAGCTTCTGCACAGTAAAGAAAACCTATCAACAAATT 6615
                             -vi        -   i  ii vvi    i v  -      v   v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACAC-TATCAAGAAAGT 692

  chrX_146754414_   6616 GAAGAGACAATCCACAGA-TGGAAGAAAATATGTGCAAACTATCCATCTA 6664
                            i      i       -   i         v      ii  vi    i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_146754414_   6665 ACAAGGGATTGAAAACCAGAATACATAAGGAGTTCAAAATACTCAATAGC 6714
                          i      i viv v        i    i  ii  vv vv        ii
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_146754414_   6715 AAAAAAGACCCATAATCTGATTTAAAAATGGGCAAAAGA 6753
                              -   vv    i ii   ?             i  
  L1M4_orf2#LINE/    793 AAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.54 (77 / 50)
Gap_init rate = 0.02 (11 / 533), avg. gap size = 1.00 (11 / 11)  

 367 21.05 0.00 1.05  chrX_146754414_146762046     7046  7140 (493)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_146754414_   7046 AAAAAAAGGCAAAAGATCTATATAGACATTTCTCAAAATAATACATACAA 7095
                              vi      i   i iv             v   v  v i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_146754414_   7096 ATGGTCAACAGGTATATGAAAAAAAGGTTCGACATTACCAATGAT 7140
                             i   i i i i       i -v i  i    i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


3020 27.45 0.66 0.66  chrX_146770054_146778008.rev     3976  4882 (3073)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_146770054_   3976 GAAAAAAAATTCCATGTTCATTGATAAGAAGAATCAGTATCGTGAAAATG 4025
                          i   i v  i          v   vi     v i i   i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_146770054_   4026 GCCATACTGCCCAAAGTAATTTATAGACTCGTTGCTATTCCCATCAAGAT 4075
                           v     v      v i  i  i   i  ivi  v  i  i     i  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_146770054_   4076 ACCATTGGCTTTCTTCACAGAACTAGAAAATACT-ACTTTAAATTTCATA 4124
                         v   viv  i  i  ii     v v  v  -i  - iii    v      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATA 150

  chrX_146770054_   4125 TGGAACCAAAAAAGAGCCCGTGTAACCAAGACAATCCTAAGCAAAAAGAA 4174
                              viiv  ii  v  v vi  i    i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_146770054_   4175 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGACTA 4224
                              i      vv       v  ii i      viv        ii   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_146770054_   4225 CAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGATATATAGAAAAA 4274
                               i   i    ii i       i iv ii i   i       vv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_146770054_   4275 TGGAACAGAACAGAGGCCTCAGAATTAACACCC-CACCTCTACAACCATC 4323
                              i    iv   ivii     v   -    -i  v i  iiii  vi
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACATTTATGGTCAAT 349

  chrX_146770054_   4324 TGATCATTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 4373
                             iv i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_146770054_   4374 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGGAAGCA-GA 4422
                           i  i        i     v      v  ?   i     i-   v -  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA-AAGAATGA 448

  chrX_146770054_   4423 AACTGGACCCCTTCCTTACACCTTATGCAAAAGTAAACTCAAGATGGATT 4472
                          ii         v   i     v   i     i v       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_146770054_   4473 AAAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAATCT 4522
                          ?    i    ii     v       i      vi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_146770054_   4523 AGGCA-ATACCATTCAGGACAGAGGCATGGGCAAAGGCTTCATGACTAAA 4571
                            ?i- v i -   iv   vvv  vv i     v  i   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_146770054_   4572 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 4621
                                     vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_146770054_   4622 TAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATCATCAGAGTGAACA 4671
                         i   v v  i i   i  iv vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_146770054_   4672 GGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 4721
                          i     i i               v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_146770054_   4722 GGTCTAATAACCAGAATCTACAAGGAGCTTAAACAAATTTACAAGAAATA 4771
                           v  vi  v       v  i  i  i  ivv    v iv i  v   v 
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_146770054_   4772 AATAAACAACCCCATTAAAAAGTGGGTGTAGGATAGGAACAGACACTTCT 4821
                         i i   i     v   ?    i    iiv     vv   i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_146770054_   4822 GTAAAGAAGCCATTTATGA--GGCCCCCAAACATATGAAAAGAAGCTCAT 4869
                         vi       --  v  ii --    vvi  i  i         v     v
  L1M4_orf2#LINE/    848 CCAAAGAAG--ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_146770054_   4870 CATCACTGGTCAT 4882
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (140 / 105)
Gap_init rate = 0.01 (10 / 907), avg. gap size = 1.20 (12 / 10)  

4286 18.89 2.71 0.00  chrX_146770054_146778008.rev     6581  7464 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146770054_   6581 TGGAAAGACATGGGGTGGTCACAGATTGGAATCCCTAATATTGTTAAGAT 6630
                                 i  vvvi  v   ii        vv i               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146770054_   6631 GGCAGCACTTCC-AAAGTGATCTACAGATTCAATGCCAACTCTATCAACA 6679
                             ii   i  -   v                i  v v i       v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146770054_   6680 TTCCAATGGGCTTGGG-GCAGAAACGGAAAAGCTGACTCTCAAATTTATA 6728
                          i   iiv v   vvv-       iv  v       ii  v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_146770054_   6729 TAGAGTCGTTAGTGGCCATGAATACGCAAAACAGTATGGATAAAGAAGAA 6778
                          i  ivi iv  v i  vv     vv       i v v  v         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_146770054_   6779 CGAAAATGATGGACTCACACATTCCAATTTCTAAACTTGCTATAAAGCTG 6828
                          i  iv  iv          v i        v      i   i      i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_146770054_   6829 CAGTAATCCAAAGAATGTGGTACCAGCATAGAGATAGACACGTAGACCA- 6877
                                 v i v i        ii     ii        ii    i  -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_146770054_   6878 --GAATAAAATTCAGAGTCCAGAACTAAACCTATAAATCTATAATCAACT 6925
                         --     i    v           v      i   v  i   ii    i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_146770054_   6926 GATTTTTCAGAAGGCTGCCAAGA-----------GGAAAAAATCGTCTCT 6964
                               iv v    v        -----------     i   v    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_146770054_   6965 TCAACAAGTGGTGCTGGAACGAGGGGCTATCCACACGCCAAAGAATGAAG 7014
                                i         i  i vv  v  ?     i  v           
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_146770054_   7015 TTGGACCCTTAACATACACCATATGCCAAAATCAACTCCAAATGGATCAA 7064
                                 i  v vi         i v     i     v          ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_146770054_   7065 CAATCTGAATATGAGAGTTAAAACCGTAAAACTCTTAGAAGCAAACATGG 7114
                         vi i  i   i i    i      ii               v      i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_146770054_   7115 GAGTAA-TCGTCATGACCTTGGATCTGGCAACGGATTCTTAGATATGACT 7163
                          ?    -  v  i         i iv     i  v              v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_146770054_   7164 CCAAAA-CACAAGCAACCAAAGACAAAATAGATAAATTGAACTTTCTCAA 7212
                               -          v     v               i    iv    
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_146770054_   7213 AATTAAAAACATTTTTACATCAAAGGACATTATCAAGAAAGTGAAAAGAC 7262
                                   v   v i v          i                    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_146770054_   7263 TACCCACAGAATGGGAGGAAACATTTGCAAATCAGGTATCTGATAAGGAT 7312
                         v                i   i            vi            iv
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_146770054_   7313 CCAGTATCCAGAATATATAAAGAATTCTTAAAGCTCAACAGCAAAACCAC 7362
                          iv                     i     v i     i ii    vv  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_146770054_   7363 AAACGATCCAATT-AAAAATGGTCAAATAATT-GAAAAGACATTTCTCCA 7410
                            ii i      -        v    vi   -   v             
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_146770054_   7411 AAGA---TGTACGAATGGCCAACAAGCATAT-AAAACATGCTCAACGTCA 7456
                             --- i   i         i     i  -    v         i   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_146770054_   7457 TTAGGCAT 7464
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.28 (92 / 72)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.40 (24 / 10)  


3092 26.00 1.42 0.47  chrX_146845032_146846865.rev      499  1344 (490)    L1M4_orf2#LINE/L1       55   908 (0)  

  chrX_146845032_    499 ACACTACCCAAAGCAATTTACAGATACAATGCAATCTTTATCAAAATACC 548
                          i   v      vii  i       v   i      ii         v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_146845032_    549 AGG-ACATTTTTCACAGAAAGAGAGTAAAC-AATTCTAAGATGTATATGT 596
                           v-i v     ii      vv  -i  i -i  i    i  vi     v
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATATGG 153

  chrX_146845032_    597 AACTACAAAAGACCCCAAATAGGTAAAGCATTCCTGACCAAAAAAAGCAG 646
                           v i   ii     vi     vi   i  v  i   vv  i  i i  i
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_146845032_    647 AGCTGGAAACATCACACCACCTGACTTGAAAATATATTACAAAGCTATAG 696
                           i    iivv      iv  ii i  v    iv  i          i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_146845032_    697 TAGGCAAAACAGCATGGTACTGCCAGAAAAACAGACATATAAACCAACAG 746
                           iv   i    ii        v  v  ii i         i i   ii 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_146845032_    747 AACAGAGTAAAGAACCCAGATATAAATCTATGCATTTACAGCCAACTCAT 796
                           i   i vi   ii     v     i i  i      ii i   i v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chrX_146845032_    797 TTTTTTATAAAGGTGCCAAGAACCTACAATGAAGAAAGGACAGTGTCTTC 846
                            iv- i  i          v v v     ii     i i   v i   
  L1M4_orf2#LINE/    354 TTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_146845032_    847 AATAAATGGTGTTGGAAAATTTGAATAATCATGTGTAGAAGAATGAAAGT 896
                           i        i   i v vi  i   ?i  ii  i i         iv 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_146845032_    897 AGACCTCTAGCTCTCACCATATACAAACATCAATTCAAAATGTATTAATG 946
                         i    i   v   v             v  i  i        v  i ?v 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_146845032_    947 ACTCCAATCTAAGACCTCAAACTGTGAAACCACTAGAAAGAAACATTGGG 996
                           iiv   v     v  v     i i    ivi     ii      v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_146845032_    997 AAAGCACTTCTGGACATTGGGCTGGGCAA-AGTTT-TTGTGTAAGACCTC 1044
                         iv ivv    vv   v     i i     -i    -  ivi  v   vi 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_146845032_   1045 AAAAGCACG-GTAACAAAAGTAAAAATAGGCAAATGGGA--TCACTTTAA 1091
                                 i- i        v        ii    v   --   - iv  
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA-TCAAA 651

  chrX_146845032_   1092 GCTAAAAATCTTCTGCACAACAAAGGAAACAATCAACAAAGTGAAGAGAT 1141
                         ii      -   i  ii vv       v  v     v        i   i
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_146845032_   1142 AGCCCACTGAATGGGAGAAAATGTTTGCAAACTATACATTTGGCAAGGGA 1191
                          i     v              i        ii   i  i  ii      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_146845032_   1192 TTAATAACCAGAATATATGAGAAACTC----AACTCAATAGCAGGGAAAC 1237
                         i vi  v           i ii     ----         ii iii i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_146845032_   1238 AAATAATATGATTAAAAAATGGGCAAAAGATCTGAATAGACATTAATCAA 1287
                               ivii   ?             i   i            vv  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_146845032_   1288 AAGAAGACATACAAATAGCAAACAGGTATATAAAAA-ATTCTCAACATCG 1336
                                i        i  v  i i i i  i    -  v         i
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_146845032_   1337 CTAATCAT 1344
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 2.00 (144 / 72)
Gap_init rate = 0.01 (12 / 854), avg. gap size = 1.33 (16 / 12)  


3300 26.32 0.55 0.55  chrX_146910784_146917041.rev     4860  5767 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146910784_   4860 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4909
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146910784_   4910 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4959
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146910784_   4960 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5006
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_146910784_   5007 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5056
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_146910784_   5057 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5106
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_146910784_   5107 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5156
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_146910784_   5157 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAAC 5204
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_146910784_   5205 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5254
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_146910784_   5255 CCTATTTAATGAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5304
                         i  v  i  ii             v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_146910784_   5305 TGAAACTGGATCCCTTCCTTACACCTTACACAAAAATCAATTCAAGATGG 5354
                             ii    i    v   i     v  i        i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_146910784_   5355 ATTAAAGACTTAAACGTTAGACCTAACACCATAAAAACCCTAGAAGAAAA 5404
                           i ?    i    i  v   v    v  i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_146910784_   5405 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5454
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_146910784_   5455 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5504
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_146910784_   5505 ATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5554
                           iv  v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_146910784_   5555 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5604
                         v  i     i                 v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_146910784_   5605 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGACA 5654
                          i  i  vi          v  i  v      vv    v iv i  v v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_146910784_   5655 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5704
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_146910784_   5705 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5754
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_146910784_   5755 CATCACTGGCCAT 5767
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1891 26.50 1.74 2.21  chrX_146925348_146926974      501  1134 (493)    L1M4_orf2#LINE/L1      278   908 (0)  

  chrX_146925348_    501 ACAAAAACAGACATATAGACCAATAGAACAGAATAGAGAAGTCAGAAATA 550
                          i  ii i           i    i   i     v    ivi        
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_146925348_    551 AGATCAAACACCTACAACCATCTGATCTTTGACAAGCCTGACAAAAACAA 600
                          ivi  v   ii  iiii  vi    i  i      vv  v   i v  v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_146925348_    601 GCAATAGGGAAAGGATTCCCTATGTAATTAATGTTGCTGGGATAACTGGC 650
                         v    i       i  vvi  v vi  iv    v        i      v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chrX_146925348_    651 TAGCTATATGCAGAACATTGAAATTAAACCCCTTCCTTACAACTTACACA 700
                           ? i i     i  v v    i  ii      v   i   v v  i   
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_146925348_    701 AAAATTAACTCAAGTTAGATTAAAGGCTTAAATGTAAAACCCAAAACTAT 750
                                      iv i   i ?  i i         i v i        
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_146925348_    751 AAAA-----AAAAAAAAAACCCTAGGAGAAAATCAAGGCAATACCATTCA 795
                             ----- i  i    -- v    ? v     ------------   i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAA--CATAGGNGTAAATC------------TTCG 563

  chrX_146925348_    796 GAACACAGGCACGGGCAAATATGTCATGACAAAAACACCTAAAGCAATTG 845
                         vi  viv  vvii     vvi v  v iivv vi     v      vvv 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_146925348_    846 CAACACAAGCAAAAATTGACAAATGGGATGAAATTAAACTAAAGAGCTCT 895
                              v   v      v  i    v   ivvv  i   v v  i i  i 
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_146925348_    896 TGCACAGCAAAAGAAACTATCATCAGAGTAAACAGACAACCTACAGAATG 945
                           ii vv    i  v       vv i   i  v        i        
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_146925348_    946 GGAGAAAATGTTTGCAATCTATCCACCTGACAAAGGTCTAATATCCAGGG 995
                                  i       vii  vi i    i  i  v  vi       ii
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_146925348_    996 TCTAAAAGGAGCTTAAACAAATTTACAAGAAAAAAACAA----CCCAATT 1041
                          v  v  i  i  ivv    v iv i  v     i    ----       
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_146925348_   1042 AAAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACACATA 1091
                         ?    i           iv    i     i     v        i i i 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chrX_146925348_   1092 TGTGGCCAACAA--ACATGAAAAAAAGCTCAACATCAGTGATCAT 1134
                         vi       i  --         i v           ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (91 / 73)
Gap_init rate = 0.01 (5 / 631), avg. gap size = 5.00 (25 / 5)  

1435 25.78 0.48 0.95  chrX_146925348_146926974     1208  1626 (1)  C L1M4_orf2#LINE/L1   (61)   847   431  

C chrX_146925348_   1626 CCATATGCAGAAAACTGAAACTGGACCCCTTCTTTACACCTTATACAAAA 1577
                            i     i  i v    ii         v i i     v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

C chrX_146925348_   1576 ATTAACTCAAGATAGATTAAAGACTTAAACATTAAGACCTAAAACCATAA 1527
                                   i  i   i ?    i    ii-     v       i    
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATG-TAAGAGCTAAAACTATAA 529

C chrX_146925348_   1526 AAATCCTAGAAGAAAACCTAGG--TAATACCATTCAGGACATACGCATGT 1479
                           v  i           v    --   - i -   iv   v vv vv iv
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAA-ATC-TTCGTGACCTTGGGTTAG 577

C chrX_146925348_   1478 GCAAAGACTTCATGAGTAAAACACCAAAAGCAATGGTAACAAAAGCCAAA 1429
                             v ii   v iii  vi            vvi i        vv   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

C chrX_146925348_   1428 ATTGACAAATGGGATCTAATTAAACTAAGGGGCTTCTGCACAGCAAAAGA 1379
                           v  i    v   ii v  i   v v iiii   i  ii vv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

C chrX_146925348_   1378 AACTATCATCCGAGTGAACAGGCAACCTATGGAATGGGAGAAAATTTTTG 1329
                         v       vvvi      v  i     i ii              v    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

C chrX_146925348_   1328 CAATCTATCCATCTGACAAAGGACTAATGTCCAGAATCTACAAGGAACTT 1279
                            vii  vi      i  i     vi i        v  i  i     i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

C chrX_146925348_   1278 AAAGAAATTTACAAGAAAAAAAACAAACAACCCCATCAAAAAGTGGGCAA 1229
                         vv v  v iv i  v     i -    i     v  i?    i       
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAA 826

C chrX_146925348_   1228 AGGATATGAACAGACACTTCT 1208
                              v    i     i    
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCT 847

Transitions / transversions = 1.36 (61 / 45)
Gap_init rate = 0.01 (5 / 417), avg. gap size = 1.20 (6 / 5)  


3254 26.58 0.89 0.33  chrX_146963462_146970068.rev     5214  6116 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_146963462_   5214 TGGAAAAACATTCCATACTCATGGATAGAAAGAATCAGTATCGTGAAAAT 5263
                               i i  i    ii        v i    v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_146963462_   5264 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATTAAGC 5313
                            v     v      v i  i  i        i  v     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_146963462_   5314 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 5361
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_146963462_   5362 TATGAAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAG 5411
                             i  viiv  ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_146963462_   5412 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5461
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_146963462_   5462 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGAGATATAGATC 5511
                                 i   i    ii  i      i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_146963462_   5512 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTATAACCAT 5561
                                i    iv   ivii         vv   i    i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_146963462_   5562 CTGATCTTTGACAAACCTGAAAAAACAAG-AAATGGGGAAAGGATTCCCT 5610
                         i    i  i     ivv  vv  i  v v-v           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_146963462_   5611 ATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGGAAACTGA 5660
                         v  i  i        i     v      v  ?   i     ii i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_146963462_   5661 AACTGGACCCCTTCCTTATACCTTATACAAAAGTTAACTCAAGATGGGTT 5710
                          ii         v   i i   v         i         i    i i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_146963462_   5711 AAAGACTTAAACATGAAACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5760
                          ?    i    ii i i v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_146963462_   5761 AGGCA-ATACCATTCAGGACATAAGCATGGGCAAAGATTTCATGAGTAAA 5809
                            ?i- v i -   iv   v vi vv i     v i    v iii  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_146963462_   5810 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTAAT 5859
                                     vvi          vv     v  i    v i ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_146963462_   5860 TAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTATCATCAGAGTGAATA 5909
                         i   v v  i i   i  iv vv    i  v       vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_146963462_   5910 GGCAACCTACAGAATGGGAGAAAATTTTTGTAATCTATCCATCTGACAAA 5959
                          i     i                 v    i  vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_146963462_   5960 GGACTAATATCCAGAATCTACAAGGAAGTTAAACAAATTTACAAGAAAAA 6009
                              vi          v  i  i   v ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_146963462_   6010 AACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 6055
                         i    ----   v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_146963462_   6056 CAAAAGAAGACAATCATGTGGCTAACAAACATATGAAAAAAAGCTCATCA 6105
                          v        i vv  vi    i  i  i  i       i v     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_146963462_   6106 ACACTGGTCAT 6116
                         v  ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (142 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


2660 26.35 2.65 2.54  chrX_147060948_147066686     4340  5246 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147060948_   4340 TGTAAAAACTTTCCATGCTCATGGATAGGAAGAATCAATATTGCGAAAAT 4389
                           v   i iv i     i        v      v i       iv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147060948_   4390 GGCCCTACTGCCCTAAGCAACCTATAGATTCAATGCTATTCCCATTAAAC 4439
                            vv    v   v  vii i   i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_147060948_   4440 TACCATTGGCATTCTTCACAGAACTAGAAAAAATTATTTTAGAATTCATA 4489
                          v   viv  v  i  ii     v v  v  iv v  ii  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_147060948_   4490 TGGAACCAAAAAAAAAAAAAGCCCA-AATAGCCACGGCAATCCTAAGCAA 4538
                              viiv  iii ------    -        vii     i i iv  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA------CCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_147060948_   4539 TAAGAACAAAGCTGGAGGTATCACGCTACCTGACTTCAGA-CTGTATACT 4587
                         v          i      vv    i  v  ii i    i -  ---    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT---TACT 241

  chrX_147060948_   4588 ACAGGGCTACAGTAACCAAAAGAGCATAGTACTGGTACAAGAACAGATAC 4637
                            ii          i   i v  ii i       i i   i i   i i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_147060948_   4638 ATAGACAAATGGAACAGAATAGAGAACCCAGAAATAAGACTGCACACCTA 4687
                              iv       i     v    ii          iv iii   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_147060948_   4688 CACCTATCTGATCTTTGACAAACCTGAAAAGAGCAGGTTT----GTCAAA 4733
                         iivii vi    i  i     ivv  vv    v  --  i---- vv   
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA--TTCAATGGGGAAA 389

  chrX_147060948_   4734 GGATTCCCTATTCAATAAATAGTACTAGGATAACTGGCTAGCCATATGCA 4783
                          i  vvi  v     i    i  i  i   i      v  ?   i     
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_147060948_   4784 GAAGATTGAAACTGGACCCCTTCCTTACAACTTATACAAAAATCAACTGA 4833
                         i    v    ii         v   i   v v           i    v 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_147060948_   4834 AGATGGAATAAGGACTTAAATACAAAACCCAAAACTATAACAACCCT-GG 4882
                          i     vi ?i   i     ii  i v i          -   i  -i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAG 538

  chrX_147060948_   4883 AATACAACCTAGG---AAATACCATTCAGAATATATAAGCACTGGCAAAG 4929
                           v v   v    ---    -- -   ivi iv - ii i-iv     v 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAAT--C-TTCGTGACCT-TGGGT-TAGGCAATG 583

  chrX_147060948_   4930 ATTTCAT-GATGAAGACAGCAAAAGCAATTGCAACAATAGAACAAATTGA 4978
                         i    v -   - v    v        vvv       v    v    v  
  L1M4_orf2#LINE/    584 GTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_147060948_   4979 CAAATGCAATCTAATTAAACTAAACAGCCCCTGCACTGCAAAAATAAACT 5028
                         i    vvi ii v  i   v v  v i iii  ii  v    ii- v   
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG-ACACT 681

  chrX_147060948_   5029 ATCAACAGAGTAAACAGACAACCTACAGAATGGGAGAACATTTTTGCAAA 5078
                              v i   i  v        i              v  v        
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_147060948_   5079 CTATGCATCTGACAAAGGTCTAATATCCAGCATTTATAAGGAACT--TA- 5125
                         ii  ii      i  i  v  vi       v  v     i     --  -
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_147060948_   5126 AATTTG-CAAGAGAAAAACCAACAGCCTCATTAAAAAGTGGGCAAAGGAC 5174
                           i ii-i  v i   i  v  i i  iv   ?    i           i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_147060948_   5175 ATGAA----CACTTCT--AAAGAAGACATACACGTGGC---TAAGTCATA 5215
                         v    ----  i    --        i     vi    ---    -  i 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACA 880

  chrX_147060948_   5216 TAAAAAAAAAAAGCTTAGCATCACTTATCAT 5246
                          i    i v---   i i     ????????
  L1M4_orf2#LINE/    881 TGAAAAGAT---GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (145 / 91)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.96 (47 / 24)  


3215 27.34 0.55 0.44  chrX_147087068_147093430.rev     4966  5872 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147087068_   4966 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCATGAAAAT 5015
                              ii i  i     i      i v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147087068_   5016 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATTCCCATCAAGC 5065
                            v     v     iv i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_147087068_   5066 TACCAATGACTTTCCTCACAGAATAGGAAAAAACT-ACTTTAAAGTTCAT 5114
                          v   iivi i  ii ii     - vvi v  i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_147087068_   5115 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5164
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_147087068_   5165 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5214
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_147087068_   5215 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5264
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_147087068_   5265 CTGGAACAGAAC--AGAGCCCTCAGAAATACGCC-ACATATCTACAACTA 5311
                         v     i    i--    i  --       vi  - i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_147087068_   5312 TCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCC 5361
                         vi    i  i     ivv  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_147087068_   5362 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATATGTAGAAAGCTG 5411
                          v  i  i              v      v  ?i  i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_147087068_   5412 AAACTGGATCCCATCCTTACACCTTACACAAAAATTAATTCAAGGTGGAT 5461
                           ii    i   vv   i     v  i           i    ii     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_147087068_   5462 TGAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5511
                         ii?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_147087068_   5512 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAT 5560
                             ?i- v i -   iv   v v  vv i     v ii   v ivv   
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_147087068_   5561 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAGTGGGATCTAA 5610
                         i            vvi          vv     v  i  i v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_147087068_   5611 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAAAGTGAAC 5660
                          i   v v  i i   i  ii vv    i  v    i  vv        v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_147087068_   5661 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAGAA 5710
                           i     i                 v       vii ivi      v  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_147087068_   5711 AGGGCTAATATCCAGAATCTACAATGAAGTCAAACAAATTTACAAGAAAA 5760
                         i  i  vi          v  i  v   v  vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_147087068_   5761 AAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTTC 5810
                          i     i     v  i? v  i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_147087068_   5811 TCAAAAGAAGACATTTAGGCAGCCAACAGACACATGAAAAAATGCTCATC 5860
                           v        i  vi iiii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_147087068_   5861 ATCACTGGCCAT 5872
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (149 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


 526 22.06 0.00 0.00  chrX_147112818_147119169.rev      179   314 (6038)  C L1M4_orf2#LINE/L1   (0)   908   773  

C chrX_147112818_    314 AACTTGAACAAATTTATAAGAAAACAACAAACAACTCCATTAAAAAGTTG 265
                             ivv    v iv    v    vi     i   i v   ?    i v 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

C chrX_147112818_    264 GCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATACACATGGTCAA 215
                                 iv    i     i     v        i     v    i   
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

C chrX_147112818_    214 CAAGTATATGAAAAATAGCTTAACATCACTGATCAT 179
                         i   i i       ivv   i       ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.00 (0 / 136), avg. gap size = 0.00 (0 / 0)  

3238 27.17 0.44 0.55  chrX_147112818_147119169.rev     4953  5861 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147112818_   4953 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCGTGAAAAT 5002
                              ii i  i     i      i v      v i    ii  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147112818_   5003 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATTCCCATCAAGC 5052
                            v     v     iv i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_147112818_   5053 TACCAATGACTTTCTCCACACAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5100
                          v   iivi i  i iii  v  -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_147112818_   5101 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5150
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_147112818_   5151 GAACAAAGCTGGAGGCATCACCCTACCTGACTTCAAACTATACTACAAGG 5200
                                 i      vv    v  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_147112818_   5201 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGTTATAGAC 5250
                                  i   i    ii         i iv ii i   vv      i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_147112818_   5251 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5298
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_147112818_   5299 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5348
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_147112818_   5349 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5398
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_147112818_   5399 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTCATTCAAGATGG 5448
                             ii    i    v   i     v            v i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_147112818_   5449 ATTAAAGAATTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5498
                           i ?   vi  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_147112818_   5499 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5548
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_147112818_   5549 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5598
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_147112818_   5599 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAGAGTGAA 5648
                           i   v v  i i   i  ii vv    i  v    v  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_147112818_   5649 CAGGCAACCTACAGAATGGGAGACAATTTTTGCAATTTACTCATCTGACA 5698
                         v  i     i             v   v       v i ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_147112818_   5699 AAGGGCTAATATCCAGAATCTACAAAGAGCTCAAACAAATTTACAAGAAA 5748
                          i  i  vi          v  i     i   vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_147112818_   5749 AAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGAGACTT 5798
                           i     i     v  i? v  i            v    i   v i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_147112818_   5799 CTCAAAAGAAGACATTTAGGCAGCCAACAGACACATGAAAAAATGCTCAT 5848
                            v        i  vi iiii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_147112818_   5849 CATCACTGGCCAT 5861
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (142 / 101)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.80 (9 / 5)  


2984 25.44 2.40 3.28  chrX_147127767_147132104     2930  3845 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147127767_   2930 TGAAAAGATATACCATGTTCATGTATTGGAAGACTCAATATTGTTAAAAA 2979
                           i        v           v           i           i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147127767_   2980 GACTGTACCACCCAAAGCAGTCTACGGATTCAATTCAGTGCTGTCCCTAT 3029
                          i vi   iv      viii     i       iv  i -----      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT-----CCCTAT 95

  chrX_147127767_   3030 CAAAATACAAATGACATTCTTCACAGA--TTTAAAAGAAACC-ATCCTAA 3076
                               v v iivi v  i  ii    --  v v   --- i-       
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAA 142

  chrX_147127767_   3077 AATTTACATGGAATCACGAAAGACCAAGAAAAGCCAAAGCTATCCTAAGC 3126
                             i i      vii i ii    v    v       i v   i i iv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chrX_147127767_   3127 ATAAAGAACAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACTA 3176
                          vi         ii       v     i v  ii i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chrX_147127767_   3177 GAGAACTATAGTAACCAAAACAATGTGGTACTGGTATAAAAACAGACACA 3226
                         v i i   i     i   i   i           i    ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chrX_147127767_   3227 TAGACCAATGGAGTAGAAGGCAGAACCCGGAAAGAAATCCACTGC--CTA 3274
                             i       i     vvv   ii  i    v   i   - i --i  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA-TACATTTA 341

  chrX_147127767_   3275 CAGTTAACTCATTTTTGAGAAATGTGTGAAGAACAAACATTAGGGAAAAT 3324
                         ii  i  i v     i  v  iv   iv    v  vv  v i      iv
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_147127767_   3325 ACATTAGGGTCTCTTCAATAAATGGTGGTGCTGTGAAAACTGGATATCCA 3374
                          i -----    i     i        ---   v  v         ?   
  L1M4_orf2#LINE/    392 ATA-----GTCTTTTCAACAAATGGTG---CTGGGACAACTGGATAKCCA 433

  chrX_147127767_   3375 TATGTAGGAGAATGAAACTAGACCCCTATATTTCACCACATACAAAAGTC 3424
                         i   i ii        ii i        iv iv     i        i i
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_147127767_   3425 GAATCAAGATGTGTTAAAGACTTCACTCTAAAATCTAAAATTATGTGACT 3474
                         i v    i   vi i ?    i v v v   i v      i   ivi   
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_147127767_   3475 ACTACAGGAAAACATTGGGGAACATCTCCAGGTTATTGGTCTAGCCAAAA 3524
                         vi  v i        v  ? v v    i iv viv    vi   v   vi
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chrX_147127767_   3525 ATTTCTTGAGCGAT-ACCCTACAAGCACAGGCAACCAGGGCAAAAATGCA 3573
                         i      -  vv  -  v i v       i     v ii v      iv 
  L1M4_orf2#LINE/    584 GTTTCTT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_147127767_   3574 CAAATGGAATCACATCAAG-TTACAAAGCTTTTGC--------------- 3607
                         i    v i iiv      i-   -   i      i---------------
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTA-AAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_147127767_   3608 ATCAACAAAATGAAGAGACAACCCATAAAATCAGAGAAAATATTTGCCAG 3657
                              v   i    i          i i   vi              v i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_147127767_   3658 CTACCCATCTAACAAGGGATTAATAACCAGAATGTATAAGAAACACAAAC 3707
                         ii ivi    i i      i vi  v       i     ii   v vv  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_147127767_   3708 AACTCTATAGGAAAAAAAAGTAATATTCTGATCAAAAGATGAGCAACAGA 3757
                              v   iv     i vi-    vi ii  i?   i   i    vi  
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_147127767_   3758 TTTGAATGGACATTTCTCAAAAAAAAAAAAAAAAAGACATACAAATGGCA 3807
                                i          v   i  ----------  i           v
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAA----------GATATACAAATGGCC 870

  chrX_147127767_   3808 AACAGGCATAGGAAAAGGTGCTCAACATCACTGATCAT 3845
                           i i   i v      i            ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (144 / 85)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.47 (52 / 15)  


 582 28.29 5.71 4.29  chrX_147134227_147140602.rev      140   489 (5887)    L1M4_orf2#LINE/L1      376   730 (178)  

  chrX_147134227_    140 ATTTAATGAATAAAG-------TTTTCAA-AAATCTTGTTATAATAATTG 181
                            i    iiv    -------       -    vv  i ivi i  i  
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_147134227_    182 GATAGTTATAT-TAAAA--ATGAAACAATGTATCTCAATTACTATTTTGG 228
                             ?ii i  -i    --     ii--  v i i ------  ii iiv
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGT--TGGACCCC------TACCTCAC 467

  chrX_147134227_    229 TCCATTCACAAAAAATTAAACTCAATATGGTCTATATAAATGAATATAAA 278
                         v    vi       -    -     v    vii ? v vv i   i   i
  L1M4_orf2#LINE/    468 ACCATATACAAAAA-TTAA-CTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_147134227_    279 AGGTAAAGG---AAAACTTT---AAGAAAAGTTGTAAGAGAATATCTTT- 321
                           v    iv---      i ---       --ii  i ? v v     i-
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATCTTCG 563

  chrX_147134227_    322 CAACCTTGGAGGTAGACAATGATTTCTTAGAGAGAACACACATAAAATAT 371
                         ii       - v   i     i         v vi    -  -   ii i
  L1M4_orf2#LINE/    564 TGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACAC-CA-AAAGCAC 610

  chrX_147134227_    372 TGTTAATCATTTTAAAAATTGGTAAATTTGACTTCAACAGAATTCAAACT 421
                         vivi  iv vvvv      v i      v       v  i    v   vi
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_147134227_    422 TTCTCTTCCTCAAAG-ACATTCTTAAGAAAGTAAAAAGTCAAGCTATAGA 470
                           i v v i      -   i v i        i     v   v i i   
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_147134227_    471 CTGG-AGTAAAGAATCACAA 489
                         v   -  v   v v ii   
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAA 730

Transitions / transversions = 1.34 (55 / 41)
Gap_init rate = 0.05 (17 / 355), avg. gap size = 2.06 (35 / 17)  

3025 27.54 1.22 0.77  chrX_147134227_147140602.rev     4982  5885 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147134227_   4982 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATACCATGAAAAT 5031
                              ii i  i     i      i v      v i    iii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147134227_   5032 GGCCATACTGCCCAAGGTAATTTATACATTCAATGCCATTCCCATCAAGC 5081
                            v     v     iv i  i  i v      i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_147134227_   5082 TACCAATGACTTTCCTCACAGAATAGGAAAAAACT-ACTTTAAAGTTCAT 5130
                          v   iivi i  ii ii     - vvi v  i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_147134227_   5131 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5180
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_147134227_   5181 ACAAAGCTGGAGGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5230
                               i      i -    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_147134227_   5231 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATGGAGC 5280
                                 i   i    ii         i iv ii i   v    i  v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_147134227_   5281 ACTGGAACAGAAC--AGAGCCCTCAGAAATAATACCGCACATCTACAACT 5328
                          v     i    i--    i  --        vv  ii    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_147134227_   5329 ATCCGATCTTTGACAAACCTGACAAAAACAAGAAATGGCGAAAGGATTCC 5378
                          vii   i  i     ivv  v   i v  vvv     v     i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_147134227_   5379 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5428
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_147134227_   5429 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTCATTCAAGATGGA 5478
                            ii    i    v   i     v            v i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_147134227_   5479 TTAAAGAATTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5528
                          i ?   vi  v    v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_147134227_   5529 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5577
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_147134227_   5578 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGGCAAATGGGATCT- 5626
                         vi            vvi          vv     v ii    v   ii -
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_147134227_   5627 -----AACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5671
                         -----  i    i -   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_147134227_   5672 ACAGGCAACCTACAGAATGGGAGAAAATTTTTG-AAATCTACCCATCTGA 5720
                          v  i     i                 v    -     - ivi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGA 743

  chrX_147134227_   5721 CAAAGGGCTCATATCCAGAATCTACAAAGAACTTAAATAAATTTACAAGA 5770
                         i  i  i  ii          v  i        ivv i  v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_147134227_   5771 AAAAGTCAAACAACCCTATGAAAAAGTGGGCAAAGGATATGAACAAACCC 5820
                              v    i     v  v?    i            v    i i  vi
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_147134227_   5821 TTTTCAAAAGAAGACATTTATGCAGCCAACAGACGCATGAAAAAGTGCTC 5870
                           i  v        i  vi viii     i ii i        ii     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_147134227_   5871 ATCATCACTGGTAAT 5885
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (149 / 96)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.64 (18 / 11)  


2961 24.84 2.25 5.03  chrX_147176502_147180780     2856  3789 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147176502_   2856 TGGAAAGACATCCCAAATTCATGAATCAGAAGAATTAATATGATTAAAAT 2905
                                 i      vi      i  ii     v       vi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147176502_   2906 GACCAAAATGCCCAAGGCAATCTAAAGATTCAATGTAATTCCTATCCAAA 2955
                          i v v v v     ivii     v        i i   i      -   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC-AAA 99

  chrX_147176502_   2956 ATACTAA-TGTCATTTTTCACAGAAATAGAAAAAACACTCCAAAAATTTG 3004
                           v i i-  i -     ii       v  v  iviiv   v      ii
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_147176502_   3005 TACAGAAACCAAAAAAAAAAAAAAAAAAAAAAAAGAGCCAGAATATCCAA 3054
                           ii    i-------------------iv  ii  v        v    
  L1M4_orf2#LINE/    149 TATGGAAAT-------------------GCAAGGGACCCAGAATAGCCAA 179

  chrX_147176502_   3055 AGCAATCCTGAACAAAAATATCAAAGCTGGAGGCATTATACCATCTGACT 3104
                          i     i    v  i  v v     i      vv i i  ivi ii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_147176502_   3105 TCAAAATATATTACAAGGCTGTACTAACCAAAACAGCATGGTATTTGTAG 3154
                               iv  i     i   ii v   i   i    ii     i v i v
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_147176502_   3155 AAAAACAGATGCATAGACCAATGGAATAGAATAGAGAACCCAGAAATAAA 3204
                           ii i   iii     i              v    ii           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_147176502_   3205 TCCATTTATTTACAGCCAATTAATTTTCAACAAAGGCATAGAGAGCATAC 3254
                         i    vi     ii i     i      i    i  iiivi   v   v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chrX_147176502_   3255 ATTGGAGAAAGAATACTCTCTTCAATAAATGGTTCTGAGAAAATTGAGTG 3304
                          v   i         v   i     i       v   i  v  i  ii i
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chrX_147176502_   3305 CCCATATGCAGAAAAATGAAACTGGACCCCTATC-------------AAA 3341
                         ?   i     i  i      ii          i -------------   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chrX_147176502_   3342 AATACACTCAAGACAGACTAAAGACTTGAATGTAAGAACTGAAATTGTAA 3391
                            vv      i ii  ii ?    i i         i  i   i i   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chrX_147176502_   3392 AACTACTAAAAGAAAACA---GGGAAAACACTTCAGAACATTGGTCTAGG 3438
                             vi  i         --- ? v   i-    ivi  v    vi    
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGG 578

  chrX_147176502_   3439 CAAAAATTTTATGTCTAAAACTCCAAAAGCACAAACAGCCAAGACAAAAA 3488
                            vii   iv ivv  vi  v            i  i v  iiv     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_147176502_   3489 TGGACAAATGGGACTATATTAAACTAAAAAGCTTCTACACACCAGAGGAA 3538
                          i  i    v     vi  i   v v    i   i iii vi  i    v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chrX_147176502_   3539 ACAATCAATAGAGTGCAGATACAACCTGTAGAATGGGA-AAAATAACTTC 3587
                           v     v i    v i v      iii         -      vi v 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_147176502_   3588 AAATTATTCATCTGACAAAGGACTAATATCCAGAATATACAAGGAACTCA 3637
                             i  vi      i  i     vi             i  i      v
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_147176502_   3638 AACTACTCAATGGTAGAAAACAACAACAACAACAACAACAAAACTCAAAT 3687
                         v  v       ----------------------  i  v  i  --    
  L1M4_orf2#LINE/    779 TACAACTCAAT----------------------AATAAAAAGAC--AAAT 804

  chrX_147176502_   3688 AATCCTATTAAAAAGTGGGCAAAGGACATGAACGGACATTTCTC---AGA 3734
                           i  v   ?    i           iv    ii          ---   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_147176502_   3735 AGGTATACAAATGGCCAGAAGGTATGTGAAAAAAATGTTCAGCAGTACTA 3784
                           i              iv i i ii      i -  i   i  vi ???
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZ 903

  chrX_147176502_   3785 ACCAA 3789
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.08 (154 / 74)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 5.67 (68 / 12)  


3067 23.59 3.10 2.55  chrX_147182753_147184715.rev      570  1472 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147182753_    570 TGGAGGGACATACTATGTTCATGGATAAAAAGATTCTACATAGCAAATAT 619
                             ii  i  v i            vii    i iv i  v iv  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147182753_    620 GTCAATGCTCCCCAAATTGATATACAGGTTTAACACAATCCCTATCAAAA 669
                          v    i              v     i  i   i               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_147182753_    670 TCCTAGCAGGATCATTTTGCAGATATAGACAGTTTGGTTCTAAAATATAT 719
                            i   v vv i-         v  v    ivi  i i       vi  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_147182753_    720 ATTGAAAGGTAAAGGAATTAGAATAGAAAAAAAAAACTT---AAAGAAGA 766
                           v    v i  i   vii       vv    v  v   ---        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_147182753_    767 CTAAACTTGGAAAAATTATTTTGCCTGATTTTAAGACTTATTATAATGCT 816
                         vi   v     ii v i ivi v  ii    i  i     i  i  v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_147182753_    817 ACAGTATTTGAGACAGTTTACTGTTGGCTGAGGGCTAAACACACAGATGA 866
                               v ii       v iv ii    vv i  v  i   i i    v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_147182753_    867 ATGGAACAGAATAAGAAACCCAGAAATAGACCCAAACAACTATTACCAAT 916
                               i     viii ii         i     v   vi   vii    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_147182753_    917 TGACTTTTAACAAGG-TACAAAAAGAATTCAATGGAGAAAGAATAGTCTT 965
                            i   ii      - i v  i vv         i              
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_147182753_    966 --CAACTAATGACGCTGGAACAATTGGATATCCCTAAACAACAACAACAA 1013
                         --    v    ii     i    i      ?  vi vi   -------  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA-------AA 442

  chrX_147182753_   1014 CAACAAAAT--GACTCTTTATCTAAACTTCACACCTTATATAAAA-TTAA 1060
                         v  ii  i --   i i -------  i       v    i    -    
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCT-------ACCTCACACCATATACAAAAATTAA 485

  chrX_147182753_   1061 CTCAAAATGGATGATAGATTTAAATGTAAGACATACAATTGTAAGATATT 1110
                                     v ?   ii           vv  v  i i   i ivi 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chrX_147182753_   1111 AAGTAGATAAGATAGGAGAAAATCATCATGACATGGGGTTAGGATATAGG 1160
                         v  v   v  v     ? v     v  i    v v        vv  i v
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_147182753_   1161 TTCTCAGATGTGGCATCCAAAGCATAATTCTGCAAAAGAA------GATA 1204
                             i    i  i  i v      i  v- vi        ------    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATA 634

  chrX_147182753_   1205 AATGAGTCCTTA--AAAAAGTTTTTAAAA--TGTTGTTCTGTTAAAGACA 1250
                            vi v i i --    -----      -- v    v  viv  i    
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAA-----TTAAAAACTTTTGTGCTTCAAAGGACA 679

  chrX_147182753_   1251 TTGTCAAATAAATAAAAAGACAAATCACAGATTAAGAGAAAATATTTGTA 1300
                         i i    iv  i i         vi      v ii             i 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chrX_147182753_   1301 AACCACATATCTGACAAATGGCTTGTATCTAGAATATATAAA-ATCTCTC 1349
                           i  i        i  iv i        i            - v    i
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chrX_147182753_   1350 AAAACTCCATAGTAAGAAAACAA-TAGCCCAATATTAAAAA-GAGCAACA 1397
                          v     v   i   i  i    -  i      - ?     - i    vi
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAAT-TWAAAAATGGGCAAAG 828

  chrX_147182753_   1398 AACTCAAACTAAA-ACTTCACCAAAGAAGATATA-AA----CAAATATGT 1441
                         i i ii  -  i - i   v              -  ---- v    v i
  L1M4_orf2#LINE/    829 GATTTGAA-TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_147182753_   1442 GCATGAAAAGATGTTCAACATCACTAGCCAT 1472
                         i            i         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (126 / 83)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.43 (51 / 21)  


3117 26.96 0.55 0.22  chrX_147522939_147527235.rev     2902  3806 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147522939_   2902 TGAAAACACATTCCATGCTTATGGATGGGTAGAATCAATATTATAAAAAT 2951
                           i   v i  i     i i      v  v   v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147522939_   2952 GAGCATACTGCCGAAAGCAATCTACAAATTCAACACAATCTCCATTAAAA 3001
                          ivv     v  v   vii       i       i     i i  i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_147522939_   3002 TACCACCATCATGCTTCACAGAATTAGAAAAAAACAATTCTAAAATTCAT 3051
                          v   v vv v vi  ii     v v  v  iv-ii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_147522939_   3052 ATGGAACCAAAAAGGAGCCTGCACAGCCAACGCAAGACTAAGCAAAAAGA 3101
                               viiv  i   v  v v i      vi   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_147522939_   3102 ACAAATCTGGAGGCATCACACTACCTGATTTCAAGCTATATTATAAGGCC 3151
                              vi      vv       v  ii       iviv  i  i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_147522939_   3152 ATAGTCACCAAAACAGTGTGGTACTGCTATAAAAATAGGCACAGAGACCA 3201
                          i   v i   i              vi    ii    i  i v   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_147522939_   3202 ATGGAATAAAATAGAGAACCTAGAAATTAACCCAAATACTTACACCCAAC 3251
                                 i   v    ii i      v      v i i   iivi   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_147522939_   3252 TGATCTTCTACAGAGCAAACAAAATCACAAAGTGGGGAAAAGACACCCTT 3301
                             i   v   ii vviv   i i  ivv i        ii i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_147522939_   3302 TTCAACAAATGGTGCTGGGATAATTAGCTAGCCATATGTAGGATAATGAA 3351
                                             i  i i v  ?   i   i ii v      
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_147522939_   3352 ACTGGAGCCTCATCTGTCACGTTATACAAAAATCAACACAAGATGGATTA 3401
                         ii    v  ii i  vv   vv           i   v   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_147522939_   3402 AGAACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATT 3451
                         ?ii  i     v     v  i           v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_147522939_   3452 GGAAAAACCCTTCTAGACATTAGCTTAGGCAAAGATTTAATGACCAAGA- 3500
                           ?iv  vi    vv   v  i v        v i   vv iivi v  -
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_147522939_   3501 ACCCAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTAATTA 3550
                            v      v v    i    iv   i   i   iv v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_147522939_   3551 AACTAGAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAACAGA 3600
                           v vi i i      iiivv    i iv  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_147522939_   3601 CAACCCACAGAGTGGGAGAAAATCTTCACAATGTATACATCTAACAAAGG 3650
                                    i           v  ii   vvi   i    i i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_147522939_   3651 ACTAATATCCAGAATCTACAACGAACTCAAACAAATCATTAAGAAAAAAA 3700
                            vi          v  i  v      vv    v   v   v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chrX_147522939_   3701 -AAAT--CCCA-TCAAAAAATGGGCTAAGGACATGAATAGACAATTCTCA 3746
                         -    --    - i?          v     iv          v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_147522939_   3747 AAAGAAGATATACAAATGACCAACAAACATATGAAAAAAATGCTCAACAT 3796
                                           i    i  i  i       i -          
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACAT 898

  chrX_147522939_   3797 CACTAGTGAT 3806
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.33 (137 / 103)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.17 (7 / 6)  


2582 25.56 6.42 1.55  chrX_147606001_147607852.rev      513  1353 (499)    L1M4_orf2#LINE/L1        1   882 (26)  

  chrX_147606001_    513 TGGAGAGGCACATTGACCACATCCATGAGATGAAAGA-TGCACACAGTAA 561
                             i  -- i  i--   ii i    iiv  i    - vv i iv  v 
  L1M4_orf2#LINE/      1 TGGAAAG--ATATC--CCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chrX_147606001_    562 AGGTGTTAATTCCCTCAAAATTGATTTATAGATGTAATGCAATACTAGCC 611
                           i  vi   v i i v        i  i    vi  i     v ivii 
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_147606001_    612 AACATTTAAGCAGAATTCTTTGTAAATATAAATAATAT-ATC-TAAAATT 659
                           v  iiv   v vv  i    i i v  vi i  vv -   -       
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_147606001_    660 CATATGGAAAGGAAAAGGAACTAGGATAGCTAAACCATTTTAGGAAAAGA 709
                                   v v  i   v i  i     i   v  v i v i      
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_147606001_    710 A---CAAAGTTGGAAGATTCACATTATGCTATTTTCAGACTTACAATA-- 754
                          ---          i  i     i viv v    iv i      v i --
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_147606001_    755 TCTACAGAAATTAAGACATTATGGTATTAGTGAAAGGTCAAGGACACAGA 804
                         v      v   i      v i     i i iiv    vi iiv i i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_147606001_    805 CAAGTAGAAGAGACTGGAGAGTCAAGAAGTAGACCCACACAAATATGGTC 854
                         iv i i   v   v v       v    i  i     i   vv       
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_147606001_    855 AATTGACTTTTTACAAAAATGCAAAAGCAATTCAATGGAGAAAGATTAAA 904
                               i   iv    iii   v  ii v         i      -----
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA----- 391

  chrX_147606001_    905 TACAATCTTTTCAATAAATCGTGCTGGAACA------TA-----ATGTAA 943
                         - i i         i    v       i   ------  -----   i  
  L1M4_orf2#LINE/    392 -ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chrX_147606001_    944 A----T----CTCAACCTATACCTCACATCACACATAAAAATTAATCCAA 985
                          ---- ----i vi   iv         i  i i i         ii   
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_147606001_    986 AATGAA-----GACTTAAAT-----------------AAAACTCTTAGAA 1013
                             i -----   i     -----------------             
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_147606001_   1014 TAAAACATGGGAG--AATTTTTTTGACCTTGAATTAACCCAAAAGTTCTT 1061
                         v       i  ? --   i  iv        ii   iv v viiv     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_147606001_   1062 CGACTTGACAGCAAAATAATAATCCATAACATGAAACAA-AGATAAATTG 1110
                         v  iv     v     vv i  v v i  v -    v  -          
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTG 639

  chrX_147606001_   1111 GATTTTATCAAAATTAAGAAATTTTTCT-CTTAGAAGGATATCACCAAGA 1159
                           i  i           -   i    v -   vi     i ii i     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAA-AAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_147606001_   1160 GAATGAAAAGACAAGCCACAGCCCGAGAGAAAATATTTGCAAATCACATA 1209
                         i i           v      vvi i                    i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_147606001_   1210 TCTGACAAATGACTTATGTCCAGAAACAATAAA-AGCTCTCAAGATTCAT 1258
                              i  iv     i i       vvv     - i    i vi i   v
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_147606001_   1259 TTATAAGGTAATAGACAACCTGATTTAGTAAATGAGTAAATGATTTGAAC 1308
                          v    iivi i i i    ii   ? i-     i i   v        i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAAT 837

  chrX_147606001_   1309 AGACACTTCATCAAAAAAGATATACAAATGGGAAATAAGTACATG 1353
                              i   vi    i               vv      i     
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

Transitions / transversions = 1.60 (131 / 82)
Gap_init rate = 0.02 (21 / 882), avg. gap size = 3.19 (67 / 21)  


2518 24.69 1.46 6.88  chrX_147808832_147810945      668  1627 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147808832_    668 TGGAAAAACACTCCATGAACATGTATAGGAAGAATCAATGTTGTTAAAAT 717
                               i i ii     vv    v  v      v i   i       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147808832_    718 GGCCATACTGCCCAAAGCAACTTACAGATTCAATGCTATTCCTCTCAAAA 767
                            v     v      vii ii           i  v  i   v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_147808832_    768 TACT-GCTGACATTCTTTACAGAATTAGAAAAAAACT-ATCTTAAAATAC 815
                          v i-    v -  i   i     v v  v  i--  -   i      v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chrX_147808832_    816 ACATGGAACAAATAAAAGAG-CCCA-AATTGCCAAGGCAATCCTAAGCTA 863
                          i      ---  iv   i -    -   v     ii     i i ivv 
  L1M4_orf2#LINE/    148 ATATGGAA---ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_147808832_    864 AAAGAATAAAACTGGGGGCAC-CATATAACCCGACTTTAAACTATATTAC 912
                         i     i   ii   i  -  -  i ivv   i i  i   viv  i   
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_147808832_    913 AAAGCTACAGTAATCAAAACAGTACGGTACTGGCACAGAAACAGACACAT 962
                                          i     ii          i iii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_147808832_    963 AGACCAATGGAACAAGCTAGAGAGCCCAGAAACAATGCTGCACATGTAAA 1012
                            i        i iiv v     i       i  vv iii    v  vi
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_147808832_   1013 ACCATCTGATCTTCAACAAAATTGACAAAAACAAGCAATGGAGAAAAGAC 1062
                         ii  vi    i   i    iiv  v   i v  vv      i    i---
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG--- 390

  chrX_147808832_   1063 TCCTTATTCAATAAATGGGAATGAAATAGTTATGGTTATGGTTATAATAG 1112
                         ------------------------      i----  ----  -i  i -
  L1M4_orf2#LINE/    391 ------------------------AATAGTC----TT----TT-CAACA- 406

  chrX_147808832_   1113 AATGGTTATGGTCATAATAGAAAGGCTATGAAATAACTGGCTAGGCATAT 1162
                               ------------------   -- ii i      v  ?v  i  
  L1M4_orf2#LINE/    407 AATGGT------------------GCT--GGGACAACTGGATAKCCACAT 436

  chrX_147808832_   1163 GCAGAAGATTAAAACCGGACACCTTCCTTACACCATATACTAAAATAAGT 1212
                            i    v i  iii    v   v   i           v     v ii
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_147808832_   1213 TCAAGATGCATCAAAGACTTAAATGTAAGCTCAAAAACTATAAAAACCAT 1262
                             i   v    ?    i          vv v            vi v 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_147808832_   1263 GGAAAATAACCTAGGAAATATTATTCTGGACATAGGACCTGGCAAGGATT 1312
                         i   i v   v    ?ivv v v   vv   v v  iiiv     v i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chrX_147808832_   1313 TCAT-GACGCAGATGCCAAAACCAATTGCAGCAAAACCAAAAATCGACAA 1361
                           v -  iii-  ii      v  vvv   i     vv      v  i  
  L1M4_orf2#LINE/    587 TCTTAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_147808832_   1362 ATAGGACCTAATTAAACTAAACATCTTCTGCACAGCCAAAGAAGCTGTCA 1411
                           v    i v  i   v v  v v   i  ii vv v  i  vi  i   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_147808832_   1412 GAAGAGTAAATAGACAATGTACA-AATGGGAGAAAGTATTTGCAAGCTAT 1460
                         ii i   i  v      ivi   -           i         iii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_147808832_   1461 GCATCCAAAAATGGTCTAGTATCCAGTATCTACAAAGAACTT----AAAT 1506
                         ii   ii v  v  v  v        v  v  i        i----  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_147808832_   1507 CAACAAGCAAACAACAAATAACCCTATGAGAAAA-GGGTAAGGGACATGA 1555
                            i  vv   vi           v  v?i    -   i  i   iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_147808832_   1556 ACAGACACTTCTCAAAAGAAGATATACAAGCAGCCAAGAA--ACATGAAA 1603
                          i     i     v               iii     v  --        
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_147808832_   1604 AAAATGCTCAATATAACTAATCAT 1627
                          i -       i  v ????????
  L1M4_orf2#LINE/    886 AGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.48 (80 / 23)  


 720 25.96 4.68 0.43  chrX_147870559_147873608     1854  2088 (962)    L1M4_orf2#LINE/L1        1   245 (663)  

  chrX_147870559_   1854 TGGAAACACTTCCCAATATCATGGATGGGTAGAATCAATATTGTGAAAAT 1903
                               v iv     vvv        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147870559_   1904 GACCATACTGCCAAAAGCAATCTACAAATTCAATGCAGTTCCCATCAAAA 1953
                          i v     v  v   vii       i      i   i i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_147870559_   1954 TACCA-TTACCATTCT--CAGAACTAGAAAAAAAAATCCTGAAATTCATA 2000
                          v   -i i  v  i --     v v  v  ivvi     i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_147870559_   2001 TAAAAAATGC--------CTGCATAGCCAAAGCAAGACTAAGCAAAAAGA 2042
                          ii   -   -------- v v         i   vvi i iv  i    
  L1M4_orf2#LINE/    151 TGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_147870559_   2043 ACAAATCTGGAGGCATCACGTTACCTGACTTCAAACCATACTACAA 2088
                              vi      vv    ii v  ii i      v v        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

Transitions / transversions = 0.97 (30 / 31)
Gap_init rate = 0.02 (4 / 245), avg. gap size = 3.00 (12 / 4)  

1511 24.52 0.43 3.41  chrX_147870559_147873608     2089  2557 (493)    L1M4_orf2#LINE/L1      454   908 (0)  

  chrX_147870559_   2089 GGTCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATCAAAGA 2138
                          ii  ii i   v    v           i       i        ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chrX_147870559_   2139 CTGAAATCTAAGACCTGAAACCCTAAAGATTCTAGAAAATAGCATCGGAA 2188
                          iv    v     v  i    iv    iv ii     i v i   v  ?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chrX_147870559_   2189 AAAGCTCTTC-TAGCCATTGGCCTAGGCAAAGGCTTCATGACCAAGAACC 2237
                         v  i-     - ii  -    vi       v  i   v iivi v  vv 
  L1M4_orf2#LINE/    554 TAAA-TCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_147870559_   2238 CAAAACCAAATGCAACAGAAACAAAGATAAATAGATGGGACTTAATTAAA 2287
                              v  v v      i  iv   i   i   i  v      v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_147870559_   2288 CTCAAAAGCCTTTGCACAGCAAAAGAAATAATCAGCAGAGTTAACAGACA 2337
                         v i    i i    ii vv    i  v iv    iv i   v  v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_147870559_   2338 ACCCGCAGAGTAGGAGAAAATCTTTGCAAACTATGCATCTGACAAAGGGC 2387
                             i    i i         v        ii  ii      i  i  i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_147870559_   2388 TAATATCCAGAATCTATGAGGAACTCAAACAAATCAGTAAGAGAAAAAAC 2437
                          vi          v   i i      vv    v   i   v i   i --
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-- 799

  chrX_147870559_   2438 CAAACAGTCCTATC-AAAATTGGGATAAGGAAATGAATAGACACTTTCCA 2486
                             i ii  v  i-    v    vv     vv          i  ii v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_147870559_   2487 AAAGAAGACATACACATGGCCAACAAACATATGGAAAAACATATGAAAAA 2536
                                 i     v        i  i  i   ------------    i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATG------------AAAAG 887

  chrX_147870559_   2537 ATGCTCAACATCACTAATGAT 2557
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (67 / 46)
Gap_init rate = 0.01 (6 / 455), avg. gap size = 3.00 (18 / 6)  


2949 27.07 2.72 0.11  chrX_147899037_147903457     3046  3928 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_147899037_   3046 GAAAAACATTCTAGGCGCATGGATTGGAAAAATCAATATTGTTAAAACGG 3095
                             i i  i i v iv            i v i           i i  
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_147899037_   3096 CCATACTGCTCAAAGCAATTTAGAGATTCACTGCTGTTCCCATCAAGCTA 3145
                          v     v i    vii  i  v       vi  vi i  i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_147899037_   3146 CTGACGTCATTCTTCACAGAATTAGAAAAAACT-ATTCTAAAATTCATAT 3194
                          iii vv v  i  ii     v v  v  i-  -  i             
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chrX_147899037_   3195 GGAGCCAAAAAAGAGCCTGAATAGCCAAA-CAGTCCTAAGCAAAAAGAAC 3243
                            iviiv  ii  v  v           -  i  i i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_147899037_   3244 AAAGCTGGAGGCATCACACTACCCAATTTCAAACTGTACTATAAGGTTAC 3293
                             i      vv       v            viv     i  i i   
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_147899037_   3294 AGTAAGCAAAACAGCAAGGTGCTGATACAAAAACAGACACAAAGACAAAC 3343
                              v   i    iiv   i   ii i  ii i     i v   iv  i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_147899037_   3344 AGAACAGAATAGAAACCTCAGAAATAAAGACACACACCCACAACCATCTG 3393
                         i   i     v  i vii          vv  i   iii iiii  vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_147899037_   3394 ATCTTTGGCAAGGCTGACAAAAC-A---AATGGGGAAAGGACTCCCTATT 3439
                           i  i i     v  v   i  - ---           i ivvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_147899037_   3440 CAATAAGTGGTGCTGGAATAATTGGCTAGCCATATGCAGAAGAAGGAAAC 3489
                            i  i         i i  i   v  ?   i     i     v   ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_147899037_   3490 TGGACTGTTACCTTTAACCATATACACAAATTAACTCAACATGAATTAAA 3539
                              ivi     ivv          v            v   i  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_147899037_   3540 GATTTAAATGTAAGACCTCAAACAATAAAAATCCTAGAAGAAAAC----- 3584
                           ii           v  v    v      v  i           -----
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_147899037_   3585 -------CTTCTCAACATCAGCCTTGGCAAAGAATCTTTGGCTAAGTCCG 3627
                         -------    vii  v ii vi v     v iv ii  i v  v v vv
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_147899037_   3628 CAAATCCAATAGTAACAAAAACAAAAATTGACAGGTGGTACCTAATTAAA 3677
                             vv  vv  i       iv      v  i ii v v  i v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_147899037_   3678 CTAAATAACTTCTGCATGGCAAAAGAAACTATCAACAGAGTAAACAGACA 3727
                         v v  v     i  iiivv    i  v        v i   i  v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_147899037_   3728 ATCTACAGAATGGGAGAAAATATTTGCAAATTAAGCACCCAAAAATGGTC 3777
                          i i                           i vii i ii v  v  v 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_147899037_   3778 TAGTATCCAGAATCTACAAGGAACTT----AAATCAACAAGCAAAAAACA 3823
                          v           v  i  i     i----  v    i  vv    i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_147899037_   3824 AATAACCCCATGAAAACATTGGCGAAGGACACAAACAGACACTTCTCAAA 3873
                                 v  v?   v  v   i     ivii  i     i     v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_147899037_   3874 AGAAGATATACAAGAAACCAAGAA--ACATGAAAAAATGCTCAATATCAC 3921
                                      ivii    v  --         i        i    ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_147899037_   3922 TAATCAT 3928
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.43 (139 / 97)
Gap_init rate = 0.01 (8 / 906), avg. gap size = 3.12 (25 / 8)  


2579 23.10 6.18 4.78  chrX_147939718_147944411.rev     3347  4203 (491)    L1M4_orf2#LINE/L1       40   908 (0)  

  chrX_147939718_   3347 ATTGTTAATGTGTCAATGCTCCCCAAATTAATGTACAGAGTCAACATAGT 3396
                                 vi  v    i           i  v      v     ii i 
  L1M4_orf2#LINE/     40 ATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAAT 89

  chrX_147939718_   3397 CCCATTTAAAAGTCCAGCAGT-TCTTTTA-AGAAATTGACAAACTGGTCT 3444
                            vv i    vi     v i- i    i-            i   i  i
  L1M4_orf2#LINE/     90 CCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC 139

  chrX_147939718_   3445 TATAATTCGTATGGAAATTCAAAGAACCTACAATAACCAGAAC---TTTG 3491
                           v     i         v   i i   i v    i   i   ---i   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chrX_147939718_   3492 AAAAAGGAGAAAAAAGTTAAAGGATTTTCACCACCTGAATTCAAGACTTA 3541
                               i    v      ii    i iv   iv  ii v     i     
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_147939718_   3542 TTATAAAGCTACAGAAAGCAAG--------GTAGTGACATAAATATAGAA 3583
                         i  i          v  v    --------   v  i     iv     v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_147939718_   3584 AAATAGATCAATGAA--------------CCAGAAG-------ATA---- 3608
                          v           i --------------      i-------   ----
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_147939718_   3609 --TGATCAATTTAATGTAGATGAAAGAACAAAGGCAATAAAATAAATAAT 3656
                         --  i      v v v v  ii ii vi v   i v  ---- v   ---
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT----TCAAT--- 382

  chrX_147939718_   3657 GTAGATGAAAGTACAGTACATTGCAATAAATGATGCTGGAGCAATTGGAT 3706
                         --- iv     v i   - v  v   i     i      ii   i     
  L1M4_orf2#LINE/    383 ---GGGGAAAGAATAGT-CTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_147939718_   3707 ATCTATATGGAAAAACACACAAAAAATAAAACATAACCTTGGTTCCATAC 3756
                          ? i i   --------  -   i   i  i-------    vi  v   
  L1M4_orf2#LINE/    429 AKCCACATG--------CA-AAAGAATGAAG-------TTGGACCCCTAC 462

  chrX_147939718_   3757 TTTACACCATTTAAGAAAATTAACTC-----GAATCACAGACATAAATAT 3801
                         i i       v  vi           ----- i    ?    v     i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_147939718_   3802 AAAACCTAAAATTGTGAAACTTCTGGAAGTAAGCATAGGAGAAAATT--- 3848
                           i v      i i i     ii i    v  i      ? v    i---
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_147939718_   3849 GTGACCTTCAGTTAAGCAAAGATTTCTTTGCTACAACACCAAAGTCATGA 3898
                                 vi    i    v i      v v  ii        iv  ii 
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_147939718_   3899 TTAATAGAAGAGAAATAAAAAT-GATAAATTGAACTTTATCAAAAT-AAA 3946
                         vi  i i    -----      -         i    i        -   
  L1M4_orf2#LINE/    613 GCAACAAAAGA-----AAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_147939718_   3947 CATTTCTGTTCTTTGAAAGACACTGTCA-GAGAATGCA--TACAAGGTGT 3993
                         v i  i   v   ii  i      i   -  i i  v --v    vviii
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_147939718_   3994 AGACTGAGAGAACATATTTGCAAAGCATATAAATAATATAGCTAATAAAG 4043
                            v  i     v           v      ------- --  i    i 
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATA-------T--CTGATAAGG 748

  chrX_147939718_   4044 GATTTAATTCTAGAATATATAAACAACTTTCAAAACTCAATAATAAGAAA 4093
                           i  ivv  i            v    i i v             i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_147939718_   4094 ATGAACACCTAAATGAACAAATGAACAAAGGATTTAAATAAACTTTAAAC 4143
                          ii  i v iv   v? v     ii          i    i  v  vvv 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_147939718_   4144 CTATGAAGATACATAGACAGCAAATAAACACATGAGAAGATTCTTGGCAT 4193
                          v v       i i i ii  v     i       i     v  iii   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_147939718_   4194 CATTAGTCAT 4203
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.69 (122 / 72)
Gap_init rate = 0.03 (22 / 869), avg. gap size = 4.27 (94 / 22)  


2568 28.97 2.57 1.01  chrX_147949291_147954148     3472  4365 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147949291_   3472 TGAAAAAATGCTCCATGTTCATGGATGGGAACAATCAATATCATTAAAAT 3521
                           i   i  iii              v    v v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147949291_   3522 GGCCATACTGCCCAAAGCAAGTTACCAATTCAATGTTATTTCTATCAAAT 3571
                            v     v      vii vi   vi      i iv  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_147949291_   3572 TACCAATAACATTCTTCACAAAACTAGAAAAACT-ATTTTAATATTCACA 3620
                          v   iivi v  i  ii  i  v v  v  i  -  ii   v     i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_147949291_   3621 TAGAAATGAAAAAGAGTCAGAATAACCAAGGCGATCCTAAGCAA-AAGAA 3669
                          i      v  ii  vi       i    ii i   i i iv  -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_147949291_   3670 CAA-GACAGAGGCATCACATTACCAGACTTCAAATAATACTACAGGGTTA 3718
                            - vii    vv     i v  vi i      vvv       ii i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_147949291_   3719 CAGTAATCAAAACACCATGGCACTGATACAAAACTAGACACATAGACCGA 3768
                                   i   vii   i    ii i  iiv      i     i i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_147949291_   3769 TGGAACAGAGTAGAGAGCCTAGAAATAAGGCTGCACACCTACAACTATCT 3818
                              i   i v     i i        iv iii   ii  iii---  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG---TCA 347

  chrX_147949291_   3819 ATCTGATCTTCAACAATGCTAGCAAAAACAAGTAATGGGGAAAGGACACG 3868
                           -    i   i    v v iv   i v  vvi           i i vv
  L1M4_orf2#LINE/    348 AT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_147949291_   3869 CTTTTTAATAAATGGTGCTGGGATAACTGGCTAACCTTATGCAGGAGATT 3918
                              i  i              i      v  ?  vi     ii   v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_147949291_   3919 GAAACTGAACCCCTTCTTTAAACTATACTCAAAAATCAACTCGAGATGAA 3968
                            ii  i      v i i v  i   iv       i     i i   i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_147949291_   3969 TTAAAGACTTAAA------ACTCAAAATCCATAAAAACCCTAGAAGGAAA 4012
                          i ?    i    ------ vii    - i      vi i      i   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAA 545

  chrX_147949291_   4013 TCTAGGCA-ATACCATTCAGGACATAGGCACAGGAAAAGATTTCAT-GAT 4060
                         iv    ?i- v i -   iv   v v  vvi   v  v i    v -   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_147949291_   4061 GAAGACACCAAAAGCGATTGCAACCAAAGCAAATATCGACAACTGGGATC 4110
                         - v            ivvv     v    v   v  v  i  v v   ii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_147949291_   4111 TAATTAAACTCTAGGGTTTCCGTACAGCAAAAGATACTATCAACAGACTA 4160
                          v  i   v iv iiii  ii  i vv    i  i        v i v i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_147949291_   4161 AACAGACAACCTACAGATTGGGAGAAGCTATTTACAAACTATGCACCTGA 4210
                           v        i     v        iv     i    ii  ii i    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_147949291_   4211 CAAAAGTCTAATATTTTTCATCTATAAGGAACT--TA-AATTTA-CAAGA 4256
                         i  ii v  vi   iivvv  v     i     --  -  i i -i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_147949291_   4257 AAAAAACAAACA--CCA-TTAAAGAGAAGGTGAAGGACATGAA----CAA 4299
                             i     i --   -  ?  i ivi  ii     iv    ----  v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_147949291_   4300 TTTTCAAACGAAGACATACCA-TGCAACCAAAAGGCATATGAAAAAAGGC 4348
                           i  v  v     i    v -  --i    v i   i       i v  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGC 891

  chrX_147949291_   4349 TCAGTATCACTGATTAT 4365
                            ii    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (161 / 94)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.68 (32 / 19)  


3295 26.98 0.44 0.44  chrX_147965446_147972732      492  1399 (5888)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_147965446_   1399 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 1350
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_147965446_   1349 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1300
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_147965446_   1299 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1252
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_147965446_   1251 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1202
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_147965446_   1201 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTGTACTACAAGGC 1152
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chrX_147965446_   1151 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1102
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chrX_147965446_   1101 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 1054
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chrX_147965446_   1053 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1004
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chrX_147965446_   1003 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 954
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chrX_147965446_    953 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 904
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chrX_147965446_    903 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 854
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chrX_147965446_    853 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 804
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chrX_147965446_    803 AACACCGAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 754
                         i     i      vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chrX_147965446_    753 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 704
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chrX_147965446_    703 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 654
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chrX_147965446_    653 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 604
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

C chrX_147965446_    603 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 554
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

C chrX_147965446_    553 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 504
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

C chrX_147965446_    503 ATCACTGGCCAT 492
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  

1950 28.33 4.78 3.19  chrX_147965446_147972732     5922  6800 (487)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_147965446_   5922 TGTTCTCGGGTAAGAAGACTTAGCATTGTAAAGATG-TAATTCTCTCTAA 5970
                              vi  i vi         ii     v      -i   v   i i  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chrX_147965446_   5971 ATTGATCTATAGATTCAAAGCAATTTCAATAAAAATTGCAA-----TTTT 6015
                                  i        v     ii v  v     iv  i-----    
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chrX_147965446_   6016 TTCCAGGGGAAGTT-ACA--CTTATTCTAAATTTTACATGGAAAGAGCAA 6062
                           v   ---  i  -   --  v  i     v  i i       v-    
  L1M4_orf2#LINE/    116 TTGCAG---AAATTGACAAGCTGATCCTAAAATTCATATGGAAAT-GCAA 161

  chrX_147965446_   6063 ATGTCTTAAAACCGTCAATACCCTCCTAAAAAA--AGAGCAAGGTAGGGA 6110
                         iv v ii i  iv i   v  vv  i i     --   i   i  v  ii
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_147965446_   6111 GAATTAGCCTACTTAATATCAAGACATAATTTTAAGCTACAGTAAATAAG 6160
                           v i vv  v ii   v    i  v  v viv            vi   
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_147965446_   6161 ACGGTGCAAGATTGTCCCTGGGATAAACA----GGTTAGTGTAAAAGCTT 6206
                           i   iiiv i  v vivi     i   ---- i i i  v  v  vv 
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_147965446_   6207 AGAGAGCCCAGAAAACAACCTACACATATATGG--AAATGCTGTATGACA 6254
                         v     i       vv    i i    v     --  v  v v vi    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chrX_147965446_   6255 GAATAACATTGCC--GACCAT------GGGTAGAAACA--CCATTCAAAA 6294
                         ----- viv    --      ------   v ii  i -- iv     v 
  L1M4_orf2#LINE/    362 -----AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_147965446_   6295 TATAGTACTGAGACAATTGGCTATTCACATAAAGAAAAATATAAAATTGA 6344
                         v  i  i   i     i   v  ?i     iv i  i   i--  i   i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG--AAGTTGG 454

  chrX_147965446_   6345 ATCCCTATCTCATAGCATA-ATATAAATTCAATTCTAAGTGGAGTAAACA 6393
                          i     i    i v    - i v     -  i  v  i    vi ? v 
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATT-AACTCAAAATGGATCAWAGA 503

  chrX_147965446_   6394 CTTGAATGTGAACTTTAAAAGTATTCAAACTTTTACAAAAA----TAA-- 6437
                          i i     i ivvi     v   -v     i   v  i  ----  i--
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATAGGN 552

  chrX_147965446_   6438 -TACATTTCCAATATAACCTTAGAGTGGGAAA--ATTT-TAAAACAAGTC 6483
                         -  v  i i i--- i     i iv i  v  --i   - v i i v v 
  L1M4_orf2#LINE/    553 GTAAATCTTCG---TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_147965446_   6484 ACAAAAGGCACGAATTATAAAGGGAATGACTAATAAATTCAAATACGTCA 6533
                           v   i    i iiv i   i i  vi ivi       vi v v i   
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_147965446_   6534 AAATTTAGAACTTTGGTTCATCAAAAGACACAATGAAGGGAATAGAAAAA 6583
                              v i      v  v v     i     v  v   ii i ii   i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_147965446_   6584 CAAGCTACAAGCTGGGTAAAAATTTTTGTAA--CATATATCACCTACAAA 6631
                            v i   iiv    vi     v    i  --        --iv i  i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC--TGATAAG 747

  chrX_147965446_   6632 TAATTAGCATCCAAAATATATAAACGACTCTTATAAACCACTTAGAAAAA 6681
                         vi i v i     i          vi       i  vi  v v v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_147965446_   6682 TACACATAGCCCAACAGAAAAAAATATATATATAGCACAAAAACTGAATA 6731
                         v   v   i     iv--?      i-------i   v ii vi      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATT--WAAAAATG-------GGCAAAGGATTTGAATA 838

  chrX_147965446_   6732 GGCATTTCCCAGAAGATGAAATACAAATGGCCCATA--CACTATGGATAG 6779
                          i      i vi    v  v            v   --   -   i v  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC-ATGAAAAG 887

  chrX_147965446_   6780 ATGCCCATTCTCGTTAGTAAT 6800
                             i  viv  i????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (140 / 106)
Gap_init rate = 0.03 (28 / 893), avg. gap size = 2.50 (70 / 28)  


3282 26.62 0.44 0.55  chrX_147979411_147983862     3051  3959 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_147979411_   3051 TGGAAGAATATTCCATGCTCATGGATAGGAAGAATCAATAATGTGAAAAT 3100
                              ii    i     i        v      v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_147979411_   3101 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3150
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_147979411_   3151 TACCAATGACTTTCTTCACAGAATTGGAAAATACT-ACTTTAAAGTTCAT 3199
                          v   iivi i  i  ii     v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chrX_147979411_   3200 ATGGAACCAAAAAAGAGCCTGCATTTCCAAGACAATCCTAAGCCAAAAGA 3249
                               viiv  ii  v  v v  vv    i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_147979411_   3250 ACAAAGCTGGAGGCATCATGCTGCCTGACTTCAAACTATAGTACAAGGCT 3299
                               i      vv   ii  v  ii i      viv  v     i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_147979411_   3300 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGACCA 3349
                                i   i    ii         i iv ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_147979411_   3350 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACGTCTACAACCATA 3399
                               i    iv   ivii         vv   i  i i  iiii  vv
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_147979411_   3400 TGATCTTTGATAAACCTGACAAAAACAGGCAATGGGGAAAGGATTCCCTA 3449
                             i  i  i  ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_147979411_   3450 TTTAATAAATGGTGCTGGGA-AACTGGCTAGCCATATGTAGAAAGCTGAA 3498
                           i  i              -      v  ?   i   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_147979411_   3499 ACTGGATCCCTTCCTTACACCTTATACAAAAAATAATTCAAGATGGATTA 3548
                         ii    i    v   i     v          v   i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_147979411_   3549 AAGACTTACATGTTACACCTAAAACCATAAAAACCCTAGAAGAAAACTTA 3598
                         ?    i  v    v v v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_147979411_   3599 AGCA-ATACCATTCAGGACAGAGGCATGGGCAAGGACTTCATGACTAAAA 3647
                         i ?i- v i -   iv   vvv  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_147979411_   3648 TACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATG 3697
                         i          vvi          vv     v  i    v   ii v  v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_147979411_   3698 AAAAAACTAAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGTGAA 3747
                             --i    i -   i  ii vv       v    i  vv i      
  L1M4_orf2#LINE/    649 AAAA--TTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_147979411_   3748 CAGGTAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCTATCTGACA 3797
                         v  ii    i                 v       vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_147979411_   3798 AAGGGCTAATATCCAGAATCTACAAAGAACTGAAACATTTTTACAAGAAA 3847
                          i  i  vi          v  i        vvv   vi iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_147979411_   3848 AAATCAAACAACCCCATCAAAAAGTGGGCAAAG-ATTTGAACAGACACTT 3896
                           iv    i     v  i?    i         -       i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_147979411_   3897 CTCAAAAGAAGACATTTAGGCAGCCAACAGACACATGAAAAAATGCTCAT 3946
                            v        i  vi iiii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_147979411_   3947 CATCACTGGCCAT 3959
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


2377 24.27 8.56 2.11  chrX_148022619_148025761     1799  2651 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_148022619_   1799 TGGAGAGACAAACTATGTTTACAGATTGGAAGACTCAACAT-ATTAA--- 1844
                             i   i vv i     i ii            i  i  -i    ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_148022619_   1845 --CAATATTTCCCAAAATTTTTCTATATATTTAATAAAATTCTAACTAAA 1892
                         --     i i      -  vv    i v   i  iiv   i iv ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_148022619_   1893 ATCCCAGCAGGATTTTTAATAGATACAGACAAGGTAACTCTAAAATTTAT 1942
                                 v vv     vii   v iv      v i ii        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_148022619_   1943 GTGGAAAAGAAAAGGAACCCAAATAGTGAAAACAATTT------AAAAGA 1986
                         i      v v  i   v  vi     iv        i ------ i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_148022619_   1987 ATAATGTTGAAAGAC--ACACTATGCAGTTTTACAACCTATTATCTGCAT 2034
                          i  v    i i   --     viv  i   i v   i  i  i------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC------ 243

  chrX_148022619_   2035 ATAGCTACAGTAATAAATACAGTGTGATATTGG--------TAGACATAC 2076
                          v            v  v        i  i   --------        i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_148022619_   2077 AGATCGATGGAACAGAATTATG--TCCAGAAAATGATCCACACAAATAAG 2124
                              i      i      iv --        vvi i   i   vv  v 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_148022619_   2125 TTCAATTGATTTTTGACA---------------------GAGGAAAGA-T 2152
                         v            i    --------------------- i       - 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_148022619_   2153 AGTCTTTTCAAAAAATGGTTTTACAAAATTTGAACATGTATAGGAAAAAC 2202
                                    v       vi ivi v vi  i i ?vi i v v    v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_148022619_   2203 AAACATCTTATTTTACCTAACTTCACACCTTATA--AAAATTAA------ 2244
                           vv vv  ivvii-    - i       v    --        ------
  L1M4_orf2#LINE/    444 AATGAAGTTGGACC-CCTA-CCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_148022619_   2245 ATGGATCATCAATCTAAATGTAAAACATGATATTGTGAAAGATTTACAAG 2294
                                 ?vi i          i vv i v i i i   vvi   v   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_148022619_   2295 AAAACACAGGAGAAAAATTCTGTAAGCTTAAGTTATGCAATGATTTCTTA 2344
                               i   ? v   vi ii  i v   ii    v      i       
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_148022619_   2345 GACATGAC--CAATGG-ACTGATGCA-TAGAAGAAAAATT-GATAAATTG 2389
                           i     --   vi -  -- v   -i i        v -         
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCAC--AAGCAACAAAAGAAAAAATAGATAAATTG 639

  chrX_148022619_   2390 GACTTCAGCAAAATGAAAAATTTTGCTGTGC-----GATACACTGT-AAG 2433
                                v      v     i   --     -----iiv     i -   
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTT--TGTGCTTCAAAGGACACTATCAAG 687

  chrX_148022619_   2434 AAAATGCAAATACAATCTAAAGACTTGT-GAAAATATGTTTCAAATTATA 2482
                            i  v   v    i i v   v v v-        -  v     i   
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT-TTGCAAATCATA 736

  chrX_148022619_   2483 TATCTGATAAAGGACTTGTA--CTGAACATGTAAAGAGACTCA-ACAATA 2529
                                   i         -- v   i  i      -    v-    i-
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGA-ACTCTTACAAC- 784

  chrX_148022619_   2530 GTTCAACAATAAGAAAACAA----TGCAATTAGAAAATGGGTTAGAGACC 2575
                         --    i     i  i    ----iv     ?i        iv ii  ii
  L1M4_orf2#LINE/    785 --TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_148022619_   2576 TGAAGAGAAACTTTACCAAAGAGGATATATGAAAGATGAATGTGCATATG 2625
                             v   v i  iv       i      ii  v iiv   iv   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_148022619_   2626 AAAACATGTTCAGCGTCGCTAGCTAT 2651
                             v   i   i i  i????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (119 / 84)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 3.14 (91 / 29)  


3715 23.37 1.22 1.00  chrX_148027372_148029272      506  1408 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_148027372_    506 AAAGATATATTCCATGTTCACAAGTGGGAATAATTAATATTGTTCAAATG 555
                                 --i         iiii v    v v           v i   
  L1M4_orf2#LINE/      4 AAAGATAT--CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_148027372_    556 TCCATACTGTCAAAAATAATCTACAGATTCAATGCAATCTCTATCAAAAT 605
                         v v     vi v   v i              i      i          
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_148027372_    606 TCTAGTTACATTTTTCACAGAAAT-AAAAAAC--GTCCTAAAACTCATAT 652
                         i i  i i v     ii       -i v  i --i        i      
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_148027372_    653 GGTAGCCCAAAAGATCCCAAATAACCAAAGCAATCTTGAGAAGAAAGAAC 702
                           v iiv   ii  i  vi    i     i         i  ii      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_148027372_    703 AAAGCCA------TCGGACTGCCTGATTTCAAAATCTACTACCAAGCTAT 746
                             iii------  iv   v  ii         ii      v      i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_148027372_    747 AACAACCAAAACAGCGTGCTACTGGTATAAGAATAGAAACATAGACCAAG 796
                          ii  i   i    i   v      i     i     v i     i   v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_148027372_    797 GGAACAGACTAGAGAACCCAGAAATAAATCAACCCATTTACGGTCAATTG 846
                             i   v v    ii           i v iv      i         
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_148027372_    847 ATTTTCAATGAGGATGCCAAGAACACACAATAGAGAAAGGACAGCCTCTT 896
                               i ii   i        v  iv    i i     i i  i  i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chrX_148027372_    897 CAATAAATAGTGCTGGAAAAACTGGATATTCACATGCTGAAGAATAAAAT 946
                            i    i       i v         ?i       vi      i  i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chrX_148027372_    947 TAGACTCTCATCCTATCCCATATACAAAATTAAACTCAAAATGTATTAAA 996
                          i   i ii i ii iv            v v           v  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_148027372_    997 GACTTAAACACAAGATATGAAACTGTAAAACTACTAGAAGAAAACATAGG 1046
                            i    iii    vv i     i       vi                
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_148027372_   1047 GA-AAAGCTTCATGACATTGTTCTGGGCAACGATATTATGGCTAAGGACA 1095
                         ?i-   v    i    v   vvi i     i i v iv i v  -v    
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGACA 600

  chrX_148027372_   1096 G-AAAAGCACAGACAACCAAAGCGAAAACTGGCAAATGAGTTTACATCAA 1144
                         v-         ii    v    vi    iv ii    vi ---  v   -
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG---ACTTCA- 646

  chrX_148027372_   1145 GTTAAAATAAAAAGCTTCTGCACAGCAAAGGAAATAATCAACAGACTGAA 1194
                         - i     v    i   i  ii vv       v iv     v i v    
  L1M4_orf2#LINE/    647 -TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_148027372_   1195 GAGACAACCTACAGAATGGGAGAAAATATTTGCAAACCATGCATCTGATA 1244
                         i        i                          i   ii        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_148027372_   1245 CAGAGTTAATATCCAAAATATATAAGGAACTCAAACAACTCAATAGTAAG 1294
                         vi iii vi      i         i      vv           i   i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_148027372_   1295 AAAGTAAGTAGCCAGATTAAAAAAATGGGCAAAGAACCCAAATAGACATT 1344
                           iii  i  i  vi   ?     -         i iiii          
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATT 844

  chrX_148027372_   1345 TCTCAAAAGAATACATACAAATGGCCAGCAGACATATGAAAAAATGCTCA 1394
                             v      v i             ii ii  i       i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_148027372_   1395 ACATTATTAATCAT 1408
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 2.29 (144 / 63)
Gap_init rate = 0.01 (10 / 905), avg. gap size = 2.00 (20 / 10)  


2898 27.13 1.64 2.30  chrX_148029852_148032457.rev     1255  2168 (438)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_148029852_   1255 TGGAATGATATTTCATTTTCATAGATTGGAAGAATTAATATTGTCAAAAT 1304
                              v     ii   v     i          v          i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_148029852_   1305 GTTCATACTATCCAGAATAGTGTACAGATTCAATGCAATCTCTATCAGAA 1354
                          viv     vi   i v ii v           i      i      i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_148029852_   1355 TACCAATGACATTCATCCCAGAAATAGACAAA-TAATTCTAAAATTTATA 1403
                          v   iivi v  iv iv       v     i- i  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_148029852_   1404 TCAAACCACAAAAT-CCCTGAATAGCCAAAGTCGTACTGAGCAAAAATAA 1452
                          vi  vii   iiv-   v           iivi vi   iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_148029852_   1453 CAAAATTAAAGGCATCACATTACCTGAATTCAAATAATATTACAGAGGTA 1502
                             i  ii   vv     i v  ii v      vvv  i    i  v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_148029852_   1503 TAGTAATCAAAACAGCATGGTACTGTCATAAAAACAGACACACAGACCAA 1552
                         i         i    ii        v     ii i     i i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_148029852_   1553 CGGAACATAACAGAGAACCCAGAAATAAATCTGTACATCCATAGTGACTT 1602
                         i    i v  iv    ii           i ii     ii  i  v v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_148029852_   1603 C-TTTTTGACAAAGGCTCCAAGAACACACATTGCAGAAAGGACAGTCTCT 1651
                         v-    i     i  iv      v  iv  v  vi     i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_148029852_   1652 TCATTAAATGATGCTGAGAAAACTGGATAGCCATATGCAAAAGAATGAGA 1701
                            vi     i     i  v         ?   i              ii
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_148029852_   1702 TTATACTCCTATCTCTTACCATATTCCACAATGAAATCAAGATGGACTAC 1751
                           iv  i    i   vi       v v v   v  v    i     ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_148029852_   1752 ATGCTTAAATCTGAAACTTTAAACTATGAAACTACTACAAGAAAACATCG 1801
                          vi i     v i i vi v       i     vi  v          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_148029852_   1802 AGAACACTCTCCAGGACATGTGGAATGATCAAAGACTTCTTGAGTAATAC 1851
                         i?ivv v   i iv   v -   iv iiv   v ii     iii  vv  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_148029852_   1852 CCCAAAAGCACAGGGAACCAAAGCAAAAATGGACAAACAGGATAATATCA 1901
                         v           i v   v    v      i  i   iv   ivvi    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_148029852_   1902 AGCTAAAAACCTTCTGCACAGCAAAATAAATAATTAACGAAGTGAAAAGA 1951
                          iv v    v   i  ii vv    iv v iv  i  vi           
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_148029852_   1952 CAACATACAGAATGGGAGAAAATATTTACAAGCTACCCACCTGACAAGTC 2001
                             vi                     i   iii ivi i    i   vv
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_148029852_   2002 ATTAATAACTGGAATATAT------------TAACTCGATCAGAAAAAAA 2039
                          i vi  v ii        ------------i     i  - iv     i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT-AATAAAAAG 798

  chrX_148029852_   2040 ACTAATAATCTGGTTTAAAAATGAACAAAAGATCTAAATAGACATTACTC 2089
                           v     i iii  ?       ii    i   i i          v   
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_148029852_   2090 AAAAGAAGACATACAAATATTCTATGCCTGTTTCCTATGAAAAGAGGCAT 2139
                         v        i        i------   -------------  v i   i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATG------GCC-------------AATAAGCAC 879

  chrX_148029852_   2140 AGGAAAATGTACTCAACATCATTGATAAT 2168
                          v     vi i          ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 4.50 (36 / 8)  


3280 26.24 0.66 0.55  chrX_148120616_148126881     4867  5773 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_148120616_   4867 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4916
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_148120616_   4917 GGCCATGCTGCCCAAGGTAATTTACAGATTCAACGCCATCCCCATCAAGC 4966
                            v  i  v     iv i  i              v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_148120616_   4967 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5014
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_148120616_   5015 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTGAATCCTAAGCCAAAAG 5064
                                viiv  ii  v  v v  v     ivv    i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_148120616_   5065 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5114
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_148120616_   5115 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5164
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_148120616_   5165 AATGTAACAGAAT--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5212
                             v  i     --    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_148120616_   5213 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5262
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_148120616_   5263 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5312
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_148120616_   5313 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5362
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_148120616_   5363 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5412
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_148120616_   5413 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5461
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_148120616_   5462 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5511
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_148120616_   5512 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5561
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_148120616_   5562 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5611
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_148120616_   5612 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5661
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_148120616_   5662 AA-ACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5710
                           -     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_148120616_   5711 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5760
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_148120616_   5761 CATCACTGGCCAT 5773
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1122 20.23 1.91 1.53  chrX_148178721_148180363       18   279 (1364)    L1M4_orf2#LINE/L1        5   267 (641)  

  chrX_148178721_     18 AAAAAATCTCTTGTTCATGGATTAGAAGACT-AATATTGTTAAAATATTC 66
                           i v   i v            i       -           i  iviv
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chrX_148178721_     67 ATACTGTCCAAAGCAATCTACAGATTCAATGCAAACCTTAT-AAAATCCC 115
                              vi     vii              i    v  i   -        
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_148178721_    116 AACAACACTTTTTGCAGAAATAGAAAAATCCACCATAAAATGCCTATGGA 165
                          i vi vi             v  v  iiiv i v      v v      
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chrX_148178721_    166 ATAGGAAGGAACCAAGAATAGCCACAGTAGTCTTGAAAAAGAA---CAGA 212
                          vv v    i   v          v ii i             ---  i 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_148178721_    213 ATTGAAGGTCTCACACTTCCAGATTTCAAAACTTAGTATAAAACTACAGT 262
                         i   i   v           vi             v  i   i       
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_148178721_    263 AATTGCCAGGCACAATG 279
                            ---  i -   i  
  L1M4_orf2#LINE/    255 AAT---CAAG-ACAGTG 267

Transitions / transversions = 1.30 (30 / 23)
Gap_init rate = 0.02 (5 / 263), avg. gap size = 1.80 (9 / 5)  

2833 17.58 4.89 3.21  chrX_148178721_148180363      497  1150 (493)    L1M4_orf2#LINE/L1      244   908 (0)  

  chrX_148178721_    497 AAAGCTACAATAATCAAAGCAATGTAGTACTGGTACAAAGACAGACATAT 546
                                  i       ii  i   i       i i  i  i        
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_148178721_    547 AGACCAATGGAATAGAATAGAAATCCCAGAAACAATTCCTCACATACATA 596
                            i              v  i vi       i  vi  vi    vi  i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_148178721_    597 GTCAAATGATTTTCAACAAGGATGCCAAGACCATTGGATGGGGAAGGA-C 645
                              v        i      i             vi        i  -i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_148178721_    646 GATCTTTTCAACACATGGTACTGGGAAACCTGAG------------AAAA 683
                         ii           v     i      v v   ii------------   i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_148178721_    684 AATTAAGTTGAACCCATACCTTACAACATATACAAAAATTACCTCAAAAT 733
                            v      i    v     i   v               v        
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_148178721_    734 GGATCAAAGGCC-AAA----AGAGCTAAAA-------ACCTTTAGGAGTA 771
                               ?  i  -   ----          -------  ii    i  v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_148178721_    772 AACATAATGGGAAAATTTCATGACATTGGATTTAACAATAATTCCTTGGA 821
                               iv? v   vi   i    v    i  vii    ii  i   i  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_148178721_    822 TATGACACCAAAGGCACAGGAAACTAAAGGAAAAATAGGCAAATTGAACT 871
                                     i     i v   v    i        ii      i   
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_148178721_    872 ACATTAAATTGTAAAGACTTTTGTGCATCAAAGGACGCTATCATCAGAGA 921
                         v   i   v -    i          v         i      vv i  v
  L1M4_orf2#LINE/    644 TCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_148178721_    922 GAAAATATAACCCACAGAATGGGAGGAAATATTTGCAAGCTATATATC-- 969
                              v i                 i            iii       --
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_148178721_    970 ----GGAGTTAATATCCAGAATATATAAAGAACACTTATAACTCAACAAC 1015
                         ----  iii vi                     v    i       i  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_148178721_   1016 AAAAAATACATAAATAAATAGTAAACACTTTTGCCAAT-AAAAAATGGGC 1064
                              i--- i      ---------- -----     -?          
  L1M4_orf2#LINE/    793 AAAAAG---ACAAATAA----------C-----CCAATTWAAAAATGGGC 824

  chrX_148178721_   1065 AAAATATTTGAATAAACATTTCTCCATAGGATATATACAAGTGGCCAGCA 1114
                            iv         i           v  i v        i      ii 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_148178721_   1115 AGAATATAAAAAGATCCTCAAATCATCAATTATTAA 1150
                           v i  i       v     --     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAA--CATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (76 / 36)
Gap_init rate = 0.02 (12 / 665), avg. gap size = 4.42 (53 / 12)  


2598 19.38 4.06 1.25  chrX_148202716_148204347      500  1139 (493)    L1M4_orf2#LINE/L1      251   908 (0)  

  chrX_148202716_    500 CAGTCATGAAAATATTGTGATACTGGCATAAGGACAGACATATAGACTAA 549
                             v  v  i i v    i              i           ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_148202716_    550 GAGAATAGAAGTAAGAGGCCAGAAATAATCCCACATATCTATGAAAAATT 599
                         vi        v i    v          v    i i  i    ivv    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_148202716_    600 GATTTCTAACAAGGGTTCAAAGACAAGTCAGTGGAGAAAGAATAGTTATT 649
                              iii        v v     v v   i   i           iv  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_148202716_    650 TCAACAAATGATATTGTGGCAACTGGATATTCACATGCAAAATAGTGAAT 699
                                   i ii  v i          ?i           v i    v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_148202716_    700 TTGGACCC-TAAATCACATCATACACACAAATTAATTTAAACTGGATCAA 748
                                 -  vv     i    i   v       i i   v       ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_148202716_    749 AGAGCTTAATATAAGACCTAAAACTATAAAATTATTTGAAGAAAACATAG 798
                            v  v   i     v              i v  v             
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_148202716_    799 GC-TAAATTCTTCATGACCCTTCATTCAGCAATAGTGTCTTATAGTATAA 847
                          ?-     -    i     i vvi  vi     i  v     v -   i 
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGA 598

  chrX_148202716_    848 CACCAAAGGCACAAGTAACAAAAGAAAAATTTGATAAGTTG-ACATCATC 896
                                i       i             v v     i   -  v     
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_148202716_    897 AAAATCAAAACCTT--GTGATTCAACAGTTAAAATTAAGAAAGTGATA-G 943
                              i    v   --   v     vi vi vv  i          v - 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_148202716_    944 ACAATGCACAGAATGGGAAAAAAATTTTGCAGATCATACATCAG-TAAGT 992
                             iv            i    vv      i      i   v -    v
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_148202716_    993 GAAATTCATGTAAAATATATAATATAAAGAACTCTTACAACTCAATAATA 1042
                           vv vi  vi i         -----                       
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAA-----AGAACTCTTACAACTCAATAATA 793

  chrX_148202716_   1043 ATAATG----TTACCCAACTTAAAAAGTGGACAAGGGGTAGGAA-AAACA 1087
                          v  vi---- v      i ?     -   i   i  i vv   - i   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chrX_148202716_   1088 TATCTC--------------AAATGGCCAATAAGCAGATAACGATATAGT 1123
                          v    --------------                v  i vi v  iv 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_148202716_   1124 CAGCATCAGTAGCCAT 1139
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (60 / 60)
Gap_init rate = 0.02 (13 / 658), avg. gap size = 2.62 (34 / 13)  


2772 27.56 1.56 0.67  chrX_148212366_148216657     2900  3799 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_148212366_   2900 TGAAAACACATCCTATGCTCATGGATAAATAGAATCAATATTGTGAAAAT 2949
                           i   v i    i   i        viiv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_148212366_   2950 GACCATATTACCTAAAGTAATGTATAAATTTAATGCAATTCTCATCAAAA 2999
                          i v   i v  i   v i  v  i i   i  i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_148212366_   3000 TGCTA-TTATCAATCTTCACAGAACTATAAAAAAC-AATCCTAAAATTCA 3047
                          v i -i ii v- i  ii     v - i v  i -i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chrX_148212366_   3048 TATGGAACAAAGAAAGAG-CCCACA-TATTCA---CAAGACTAAGCAAAA 3092
                                -- v v   i -    v -  vi  ---   vvi i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_148212366_   3093 AGAACAAATCTGGAAGCATCACATTACCTGACTTCAA--CCTA-TACATG 3139
                                 vi    i vv     i v  ii i     -- i  -    vi
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_148212366_   3140 GCTATAGTTACCAAAACATCATGGCACTGTTATAAAAACAGGCAAGTAGA 3189
                             i   v i   i   vii   i    vi    ii i  i  vi    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_148212366_   3190 CCAATGGAACAGAATAGAGAAACCAGAAATAAAGCCAAATACTTATAGTC 3239
                         i        i     v    iv           v   v i i    i   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_148212366_   3240 AACTGATCTTTGACAAAGCAAACAAAAC-ATAAAGTGGGAAAAGGACACC 3288
                           i    i  i     i vviv   i  -  vv i    i    i i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_148212366_   3289 CTATTAAGCAA-TGGTGCTGGGATAATTGGCAAGCCACACGTAATAGAAT 3337
                           v  v i   -           i  i   vv ?     i i  v     
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_148212366_   3338 AAAGCTGTATCCTCATCTCTCACCTTATACAAAAAGCAACTCAAGATTGA 3387
                         i   i  v i  ii i   v    v          vi       i  v  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_148212366_   3388 TCAAAGACTTAAATCTAAGACATGAAAACATAAAAATTCTAAAAGACAAC 3437
                            ?    i     v     vv i   vi      v ii  i    v   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_148212366_   3438 ATCAGAAAAACTCTTGCAGACATTGGCTTAGGCAAAGAGTTCATGACCAA 3487
                           vi ?iv  v    vvv   v    v        v iv   v iivi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_148212366_   3488 AAAACCAAAAGCATATGCAACAGAAACAAAGATTTAAAAAGGGGAGACTT 3537
                         i v          i v      i  iv   i  vv v   vv   --   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA--CTT 644

  chrX_148212366_   3538 AATTAAACTCAAAAGCTTCTGCACAGCAAAAGAAATTATCAGTAGAGTAA 3587
                         v  i   v i    i   i  ii vv    i  v i     iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_148212366_   3588 ACAGACAACCCACAGGGTGGGAGAAAATCTTCACAAGCTATGCATCCAAC 3637
                          v             ii           v  ii   iii  ii   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_148212366_   3638 AAAGGAATAATATCCAGAATCCACAAGGAACTCAAATAAATTAGCAAGAA 3687
                           i   v vi          vi i  i      vv i  v i ii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_148212366_   3688 ATAAACAAATAATTTTATCAAAAAGTGGACTAAGGACATGAATACACAAT 3737
                          v i        iiiv  i?    i   i v     iv      v   v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_148212366_   3738 TCTCAAAAGAAGGTATACAAATGGTCAACAA--ACATGAAAAAATGCTCA 3785
                             v       i           i   i  --         i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_148212366_   3786 ACATCAGTAATGAT 3799
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (146 / 98)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.43 (20 / 14)  


2235 25.04 0.64 0.96  chrX_148216832_148218458      500  1126 (501)    L1M4_orf2#LINE/L1      245   869 (39)  

  chrX_148216832_    500 AAGCTACAGTGATCAAAACAGCATGCTACTTGCATAAAAGCAGACACATA 549
                                   i     i    ii  v    v      iiii     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_148216832_    550 GACCAATGGAACAAAATAGAGTAACCCAGAAACAAATCCACACACCTACA 599
                           i        i i   v   - ii       i   i   i   ii  ii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAG-AGTCCAGAAATAAACCCATACATTTATG 343

  chrX_148216832_    600 GTGAACTCATTTTCAACAAAGGTGACAAGGACATACATTGGGGAAAAGAC 649
                           v  i v      i    i    v    iv   v  v        ii i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_148216832_    650 AATCTCTTCAATAAATAGTGCTGGCAAAATTAGATATCCATATGCAGAAA 699
                          i   i     i    i       v v  i i    ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_148216832_    700 AAGGGATCTAGACCCTTATCTCTTACCGTATACAAAAATCAAATCAAAAT 749
                           v i vi i     i  i   vi   i           i  v       
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_148216832_    750 GCATTAAATACTTAAATCTAAGACCTCAAACCAAGAAGCTCCCACAAGAA 799
                          v  i ? v  i     v     v  v    i vi  i   ii v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_148216832_    800 AACATTGGGGAAAATCTCTAGGACATTGGTCTGGGCAAAAAATAGTTGAA 849
                              v  ? v      iiiv   v    vi i     viiv vv  ii 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_148216832_    850 TAATACCCCACAAGCACAGACAACCAAACCAAAAATGGATAAATGTGG-- 897
                           vv  v   v       ii    v   vv      i       -   --
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT-TGGAC 642

  chrX_148216832_    898 -TCATAACAAGTTAAAAAGACTCTGCACAGCAAAAGAAACAATCAACAAA 946
                         -    v -  i       -vi i  ii vv    i  v  v     v   
  L1M4_orf2#LINE/    643 TTCATCA-AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_148216832_    947 GTGAAGAAGCAAACCACAGAATGGAACAAAATATTTGCAAAGTACCCATC 996
                              i ii   v           i v              vi ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_148216832_    997 TGACAAGAGATTAATAACTAGAATATTTATGGAGCTAAAACAACTATATA 1046
                            i   i  i vi  v i       v  vi  i  vvv      vv   
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_148216832_   1047 GGAAAAAAAACCTACTAATCCAATC-AAAAATGGGCAGAAGATTTGAATA 1095
                         iv     i -- v v   i     i-           i i          
  L1M4_orf2#LINE/    791 ATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_148216832_   1096 GACATTTCTCAAAAGAAGACGTACAAATGGC 1126
                                   v        ii          
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGC 869

Transitions / transversions = 1.48 (92 / 62)
Gap_init rate = 0.01 (7 / 625), avg. gap size = 1.43 (10 / 7)  

1084 24.68 1.28 0.00  chrX_148216832_148218458     1128  1439 (188)    L1M4_orf2#LINE/L1      512   827 (81)  

  chrX_148216832_   1128 TATGACCTAAAACCATAAAACTCCAAAAAGAAAATAAAGGGGAAAATATT 1177
                           v  v       i         iv i       i v   ? v    v  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chrX_148216832_   1178 -GAGA--TTGGCCTTGGCAATGATTTCTTGAGTATCACAACTTAAGCTCA 1224
                         - v  --    vi v       i      iii   v   v vv    v  
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chrX_148216832_   1225 GGCTACAAAAGAAAAAATAAATAAATGAGACCACATCAAACTAAAAAGCT 1274
                         i  v               i      vi   iv       v v    i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_148216832_   1275 TCTTCACAGCAAAGAAAACAATTACCAAAATAAAAAGGCAACCTACAGAC 1324
                          i vii vv     i v  v  i vv   i i     i     i     v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_148216832_   1325 TGGGA-AAAATATTCACAAACCATGTATCAGGTAAGAGGTTAATATCCAA 1373
                              -        ii    i   i    v i    i ii vi      i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_148216832_   1374 GCTATATAAGGAAGTCATACAACTCAATAAGAAGAAAATATATTACCTGA 1423
                         iv       i   v  v             v  i  i i v  v   ii 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chrX_148216832_   1424 TTTAAAAATGGGCAAA 1439
                           ?             
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAA 827

Transitions / transversions = 1.14 (40 / 35)
Gap_init rate = 0.01 (3 / 316), avg. gap size = 1.33 (4 / 3)  


3064 27.44 1.33 0.44  chrX_148222645_148228892     4856  5755 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_148222645_   4856 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4905
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_148222645_   4906 GGCCATACTGCCCAAGGT-ATTTACACATTCAATGCCATCCCCATCAAGC 4954
                            v     v     iv -  i    v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_148222645_   4955 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5002
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_148222645_   5003 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCA-TCCTAAGCCAAAAG 5051
                                viiv  ii  v  v v  v     iv  -  i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_148222645_   5052 GACAAAGCTGGAGGCATCACGCTACCTAACTTCAAACTATACTACAAGGC 5101
                         i      i      vv    i  v  i  i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_148222645_   5102 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5151
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_148222645_   5152 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAACT 5199
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_148222645_   5200 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5249
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_148222645_   5250 CTATTTAATAAATGG------GAAAACTGGCTAGCCATATGTAGAAAGCT 5293
                           v  i  i      ------  v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_148222645_   5294 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5343
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_148222645_   5344 TTAAAGACTTAAACGTTTGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5393
                          i ?    i    i  vv  v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_148222645_   5394 CTAGGCATTACCATTCAGGACACAGGCATGGGGAAGGACTTCATGTCTAA 5443
                         v    ?i v viv   iv   viv  vv i  v  v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_148222645_   5444 AACACCAAAAGCAATGACAACAAAAGACAAAATTGACAAATGGGATCTAA 5493
                         i            vvii          v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_148222645_   5494 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATGAGAGTGAAC 5543
                          i   v v  i i   i  ii vv    i  v    i  v  i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_148222645_   5544 GGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5593
                         i i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_148222645_   5594 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5643
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_148222645_   5644 AAACATACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5693
                          i   v i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_148222645_   5694 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5743
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_148222645_   5744 ATCACTGGCCAT 5755
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


2461 25.43 5.11 2.27  chrX_148303831_148308882     3679  4559 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_148303831_   3679 GAAAAATCATTCCATGCTCATAGATTGGAAGAATCAGTATTATTAAAATA 3728
                             i  -  i     i    i          v i i    i    i  i
  L1M4_orf2#LINE/      3 GAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_148303831_   3729 TGCATATAT---CCACATT---CTACAGATTCAAAATTATTCCTATCAAA 3772
                         -   -   i---   v   ---            viiv  i         
  L1M4_orf2#LINE/     52 -GCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_148303831_   3773 ATACCAA-TGTCATTTTTCACAGAATTAGATAAAACT-AGCCTAAAATTT 3820
                           v   i-  i -     ii     v v  i  i-  - v         i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chrX_148303831_   3821 GTATGGAACCAAAAGAAAAAAAAAAGTCCA-AATAGCCAAAAGAATCCTA 3869
                         i       viiv   ii --------i   -           v    i i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA--------CCCAGAATAGCCAAAACAATCTTG 189

  chrX_148303831_   3870 AGCAAAAAGAATAAAGCCAGAAGCAACACATTATCCAACTTCACGCGATA 3919
                          iv  i     i    iii  i vvv    i vi    i    vivvv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_148303831_   3920 CTACAAGCCTACAGTAACCAAAACAGCATAGTACGAGTACAAAAACAGAC 3969
                               iv         i   i    ii i    vi i i  ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_148303831_   3970 ACACACACCAATAGAACAGAATAGAGAGCCCAGGAATAATGAAGC---AC 4016
                          i i v i    i   i     v     i    i     --- v ---  
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA---ACCCATAC 336

  chrX_148303831_   4017 ACCTACAA-CAA--AGTCTTCGACAAAGTCAACAAAAATAAGCAATAATG 4063
                          ii  iii-   --ii i        i viiv   i vi vv    iiv 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_148303831_   4064 AAAGGAATTA--CTACTCAATAAATGGTTCTGGGAAAACTGGCTAACCAT 4111
                             i --  --  vi    i       v      v      v  ?   i
  L1M4_orf2#LINE/    387 AAAGAA--TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_148303831_   4112 ATGCAGAAGAATGAAACTGGACCCTTACCTATCACCTTATACAAAAATTA 4161
                              i         ii       i     vv    v             
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chrX_148303831_   4162 ACTCAAGATGGATTAAAGATTTAAATGTAAGACCTAAAACTACAAAAATC 4211
                               i      i ?   ii           v         i    v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chrX_148303831_   4212 CTAGAAGAAAA--------------TTCTGGACATCAGCATTGGCAGAGA 4247
                         i          --------------   vv   v ii vv v    iv i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_148303831_   4248 ATTCATGACTAAGTCCTCAAAAGCAATTGCAACACAAACAAAAATTGGCA 4297
                         v   v iiv  v v vi        vvv      v  iv      v ii 
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chrX_148303831_   4298 AGTGGGACCTAGTTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTGTC 4347
                          i v    i vi i   v v  i ii  i  ii vv    i  v   i  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chrX_148303831_   4348 AACAGAGTAAGCAGACAACCTACAGAACAAGAGAAAATACTTACAAAGTA 4397
                           v i   i iv        i      iii         i  i    vi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_148303831_   4398 TGCATCCAA-AAATGTCTAATATCCAGAATCTACAAGGAACT---AAAA- 4442
                          ii   ii -  iv v  vi          v  i  i     --- v  -
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_148303831_   4443 TCAACAAGCTAAAAA------CAACCCCATTAAAAACCAGGCAAAGGACA 4486
                             i  --      ------i     v   ?    vii         iv
  L1M4_orf2#LINE/    785 TCAATAA--TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_148303831_   4487 TGAACAGACGCTTCTCAAAAGACGACATACAAGCG-CCAACAA--ACATG 4533
                             i    ii     v     v  i      ii -    i  --     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_148303831_   4534 ATAAAATGCGCAACATCACATCTGAG 4559
                          v  i    v        ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (140 / 81)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 2.60 (65 / 25)  


1434 28.65 3.42 1.33  chrX_148361855_148364660      642  1168 (1638)    L1M4_orf2#LINE/L1        6   543 (365)  

  chrX_148361855_    642 AGACATAGCATGTACATTCACTGGAAGACTCA-----GTGAAGATATGTG 686
                            i  vv     v   vv i         i -----  v     i- ii
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG-GCA 54

  chrX_148361855_    687 ATCTGTAACAAAGCGATCCATAGATCCAATGTAACTCC-AGTAAAATACC 735
                           vivivv    vi    i i    i   i i  ii  - vi     v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_148361855_    736 AGCAAGCTTTTTTGTAC---TTGTACACAAGCTGATTCAAAAAG-CATAC 781
                            viv        i v---   ---          i v    v-    i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCATAT 151

  chrX_148361855_    782 GGAAAGGTAAAGGTTTTGAAATAATTAAAACAATTTTCAAAACACAGAGT 831
                              v i  i  viiiii    iii        i  v    viv   ii
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_148361855_    832 AA--TTGCACAAATCGTACCACTCAATTTTAAGATTTAGCATAAGCCTAA 879
                           --   v vi v  ii  iv i      i  i i   vi i  iv   v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_148361855_    880 AACAATCAAGTCATTATGG-ACTTTTCTAAGGGATACACGTATAGATTAA 928
                          ii       v  v i   -   vviv     -   v  i       i  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAGACATATAGATCAA 300

  chrX_148361855_    929 TGGATTAAAACAGAGAATCCATAAATAGATCCACGCGAATATAG-CAATG 977
                             v  i  iv    i    v     i i   ii ivv   i -    v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_148361855_    978 GAGGTTTTAGAAAGGGGTA--AAGACAATTTATTGGAAAAATATTAGTCT 1025
                           --    v  v i    i--     v   i v   ii   v v      
  L1M4_orf2#LINE/    351 GA--TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_148361855_   1026 TTTCAATTAGTGGTATTGGAACAACTGAACATCCATGTGTTATAAAAAAG 1075
                               iv i    ii   i       i i ?   ii  iv v i  vii
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_148361855_   1076 ACTTG-ACCAAAACCTCACATGTTATACAAAAATTAACTCAAAGTGGATT 1124
                          v   -   vvv        ivv                    i     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_148361855_   1125 ACAGATCCAAATGTTACATGAAATACTATAAAACTTTTA-AAGAA 1168
                          ?   i i      v v vvv  v           i   -     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

Transitions / transversions = 1.33 (85 / 64)
Gap_init rate = 0.03 (14 / 538), avg. gap size = 1.79 (25 / 14)  

 557 31.97 2.23 0.37  chrX_148361855_148364660     1492  1760 (1046)    L1M4_orf2#LINE/L1      528   801 (107)  

  chrX_148361855_   1492 AAAAAACTTA-AAGAAAACACAGGGTGAAATATTAGTAGCCTGATGTGAG 1540
                             vv    -         i   ?vv    v  v  ii   viv  v  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_148361855_   1541 GCAAAGAGGTCTTAAACATGACACCAGCAGTGTGATTCATAAAGAAAAGA 1590
                             v ivv     i i         iv  iiii viv i   ii   i 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_148361855_   1591 AACAATAAATTAGACTTCCTCAGAGTTAAAA-CTTTTGCTCTGAGAAAGA 1639
                          vvi       i      v   i i      -      iv  vvi  i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_148361855_   1640 CACTGAAGAGACACTAAAAAGCCAA---ACGAAGTATTCACAAGTATTTG 1686
                             ivvi   v v i     v   ---  ii i ivvviv  i      
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_148361855_   1687 CAAATCATATATACACCAAAGGCCTTTTATGAAAATTGTATAAAGA-TTC 1735
                                     viivi  i  v   v   vv i v i        -i  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_148361855_   1736 CCAAAATCTCAAAACTTAGAACACA 1760
                         ii v  -     v v v i  v   
  L1M4_orf2#LINE/    778 TTACAA-CTCAATAATAAAAAGACA 801

Transitions / transversions = 1.02 (43 / 42)
Gap_init rate = 0.02 (5 / 274), avg. gap size = 1.40 (7 / 5)  

 347 23.68 0.00 0.88  chrX_148361855_148364660     2200  2313 (493)    L1M4_orf2#LINE/L1      796   908 (0)  

  chrX_148361855_   2200 AACACAAACAACCACATTTTTTAGAAGGGCAAAACATATCAATAGACATT 2249
                           v     i    -  v  ?vv i v       iv  v v          
  L1M4_orf2#LINE/    796 AAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_148361855_   2250 TCACCCAAAAGGACATACGCATGACAAATAAGCCCATGAAAAACTATTCT 2299
                           v  v  i i  i    iv   i v       v        iv ii  v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_148361855_   2300 ACATCACAGCTATT 2313
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 0.73 (11 / 15)
Gap_init rate = 0.01 (1 / 113), avg. gap size = 1.00 (1 / 1)  


2550 23.03 8.01 2.00  chrX_148403545_148405333      500  1298 (491)    L1M4_orf2#LINE/L1       62   908 (0)  

  chrX_148403545_    500 CCAAATTATTTTAAAGAATCAATGCAATCCCAGCGAAAATTGGGAGCCAG 549
                                iv i  v   v    i        viiv     i-----    
  L1M4_orf2#LINE/     62 CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC-----CCAG 106

  chrX_148403545_    550 CAGGTTCTTCTGTAGAAATTGACATACTGACTTTAAAAGTCATATGACAG 599
                          v vi i  i  i           vi    iii     v       iv i
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chrX_148403545_    600 TGCAAAGGACCTAGAATGGGCAAAACAATTCTGAAAAAGAA---CAAAGT 646
                              i     i     i v         ii          ---      
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_148403545_    647 TGGACAATTTATACTACATGCTTTCAAAGCTTACTATAAAGCTACAGTAA 696
                             vi i i i   v viiv       i       i             
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_148403545_    697 TAAACACAATGTAGTACTGGCATAAGAATAGATATATAGA---ACGTACT 743
                          v  v   i   i             i     i       --- i v v 
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_148403545_    744 AGA-----GAGTTGGAAAACAGACCCATACATATAGAGTCAGTTAATTTT 788
                            -----    ivii   i i          v  vi    i  i     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_148403545_    789 CCACAAAGGTGCCAAAACAACTCAATGGAGAAATAATTATGTTT-CAATA 837
                          v    i        i  v i       i    v   vi v   -   i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_148403545_    838 AATGGTG---GTACAACTGGATAA----ATG-AGGAAAGTACACCTTGAC 879
                                --- v           ?----   - ii i i iv vi v   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chrX_148403545_    880 TCTTAACCTTATAACATATACAAAAATTTATGTGACATGGATCATAGACC 929
                         i i  -   i i v              v ivii v        ?     
  L1M4_orf2#LINE/    457 CCCTA-CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_148403545_    930 TAAATGTCATACACAAAACTATAAAATGTCC----AAAACACATATGAAA 975
                                v v vvi            i-  i---- i  v     v ?iv
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACATAGGNGT 554

  chrX_148403545_    976 AAAAAATACTTGCAACCTACGGTTAGGCAAACATTTCTTAGATGGGATAT 1025
                            --- vi i ii    vv          vvi          iv  i i
  L1M4_orf2#LINE/    555 AAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_148403545_   1026 --------------------GAAA-----------TTGGACTTCTCCAAA 1044
                         --------------------    -----------         vi    
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_148403545_   1045 ATGAAAAACTCTTACTCTCCAAAAGATACCTATCATTAACAAAATGACA- 1093
                           v       i  iiv  i    i  i  -     --- v   i   v -
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACAC-TATCA---AGAAAGTGAAAA 697

  chrX_148403545_   1094 GCCAAGCCACAAACTGGGAGACCATACTCTGAAAA-CACGTATCTGACAA 1142
                          v   v     i v       vv   i -  v   -  ii       i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATT-TGCAAATCATATATCTGATAA 746

  chrX_148403545_   1143 AGTAACCTGTATCCAGTATATAAAAAGGACTTTTACAACTAAA-AA-AAT 1190
                         i -i  i         v     v    i   i        v  -  -  v
  L1M4_orf2#LINE/    747 GG-GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_148403545_   1191 AAG-TGAACAACCCGATTTAAAA-TGGCCAAAAAATTC--AGAGACATCC 1236
                            -ii  i     i   ?    -   v    ii   i-- v      ii
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_148403545_   1237 CATCAAAGAAGGCATACAAAAAGCAAATAAGCACACAAAAA-ATACTCAG 1285
                          vi        ii       vi  v          ii    -  i    i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_148403545_   1286 TATTTTCAGATGT 1298
                         i  iv????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (111 / 69)
Gap_init rate = 0.03 (26 / 847), avg. gap size = 3.08 (80 / 26)  


1426 28.65 3.42 1.33  chrX_148579359_148582164.rev      644  1170 (1636)    L1M4_orf2#LINE/L1        6   543 (365)  

  chrX_148579359_    644 AGACATAGCATGTACATTCACTGGAAGACTCA-----GTGAAGATATGTG 688
                            i  vv     v   vv i         i -----  v     i- ii
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG-GCA 54

  chrX_148579359_    689 ATCTGTAACAAAGCGATCCATAGATCCAATGTAACTCC-AGTAAAATACC 737
                           vivivv    vi    i i    i   i i  ii  - vi     v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chrX_148579359_    738 AGCAAGCTTTTTTGTAC---TTGTACACAAGCTGATTCAAAAAG-CATAC 783
                            viv        i v---   ---          i v    v-    i
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCATAT 151

  chrX_148579359_    784 GGAAAGGTAAAGGTTTTGAAATAATTAAAACAATTTTCAAAACACAGAGT 833
                              v i  i  viiiii    iii        i  v    viv   ii
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_148579359_    834 AA--TTGCACAAATCGTACCACTCAATTTTAAGATTTAGCATAAGCCTAA 881
                           --   v vi v  ii  iv i      i  i i   vi i  iv   v
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_148579359_    882 AACAATCAAGTCATTATGGAATTTTC-TAAGGGATACACGTATAGATTAA 930
                          ii       v  v i   v i vv -     -   v  i       i  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAGACATATAGATCAA 300

  chrX_148579359_    931 TGGATTAAAACAGAGAATCCATAAATAGATCCACGCGAATATAG-CAATG 979
                             v  i  iv    i    v     i i   ii ivv   i -    v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_148579359_    980 GAGGTTTTAGAAAGGGGTA--AAGACAATTTATTGGAAAAATATTAGTCT 1027
                           --    v  v i    i--     v   i v   ii   v v      
  L1M4_orf2#LINE/    351 GA--TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_148579359_   1028 TTTCAATTAGTGGTATTGGAACAACTGAACATCCATGTGTTATAAAAAAG 1077
                               iv i    ii   i       i i ?   ii  iv v i  vii
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_148579359_   1078 ACTTG-ACCAAAACCTCACATGTTATACAAAAATTAACTCAAAGTGGATT 1126
                          v   -   vvv        ivv                    i     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_148579359_   1127 ACAGATCCAAATGTTACATGAAATACTATAAAACTTTTA-AAGAA 1170
                          ?   i i      v v vvv  v           i   -     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

Transitions / transversions = 1.33 (85 / 64)
Gap_init rate = 0.03 (14 / 538), avg. gap size = 1.79 (25 / 14)  

 557 31.97 2.23 0.37  chrX_148579359_148582164.rev     1494  1762 (1044)    L1M4_orf2#LINE/L1      528   801 (107)  

  chrX_148579359_   1494 AAAAAACTTA-AAGAAAACACAGGGTGAAATATTAGTAGCCTGATGTGAG 1542
                             vv    -         i   ?vv    v  v  ii   viv  v  
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chrX_148579359_   1543 GCAAAGAGGTCTTAAACATGACACCAGCAGTGTGATTCATAAAGAAAAGA 1592
                             v ivv     i i         iv  iiii viv i   ii   i 
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chrX_148579359_   1593 AACAATAAATTAGACTTCCTCAGAGTTAAAA-CTTTTGCTCTGAGAAAGA 1641
                          vvi       i      v   i i      -      iv  vvi  i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chrX_148579359_   1642 CACTGAAGAGACACTAAAAAGCCAA---ACGAAGTATTCACAAGTATTTG 1688
                             ivvi   v v i     v   ---  ii i ivvviv  i      
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chrX_148579359_   1689 CAAATCATATATACACCAAAGGCCTTTTATGAAAATTGTATAAAGA-TTC 1737
                                     viivi  i  v   v   vv i v i        -i  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_148579359_   1738 CCAAAATCTCAAAACTTAGAACACA 1762
                         ii v  -     v v v i  v   
  L1M4_orf2#LINE/    778 TTACAA-CTCAATAATAAAAAGACA 801

Transitions / transversions = 1.02 (43 / 42)
Gap_init rate = 0.02 (5 / 274), avg. gap size = 1.40 (7 / 5)  

 347 23.68 0.00 0.88  chrX_148579359_148582164.rev     2202  2315 (491)    L1M4_orf2#LINE/L1      796   908 (0)  

  chrX_148579359_   2202 AACACAAACAACCACATTTTTTAGAAGGGCAAAACATATCAATAGACATT 2251
                           v     i    -  v  ?vv i v       iv  v v          
  L1M4_orf2#LINE/    796 AAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_148579359_   2252 TCACCCAAAAGGACATACGCATGACAAATAAGCCCATGAAAAACTATTCT 2301
                           v  v  i i  i    iv   i v       v        iv ii  v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_148579359_   2302 ACATCACAGCTATT 2315
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 0.73 (11 / 15)
Gap_init rate = 0.01 (1 / 113), avg. gap size = 1.00 (1 / 1)  


2096 26.82 4.92 3.46  chrX_148601265_148603691     1040  1934 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_148601265_   1040 TGGGAAAACATTACATGCTCATGCTTAGGAAAAATCAATAATATTTAAAT 1089
                            i  i i  iv    i     vv v    i v i    v i  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_148601265_   1090 GGCCATAATGCCTAAAGCAATTTACCGATTTAATGCTATTCCTAACAAAC 1139
                            v   v v  i   vii  i   v    i  i  v  i    v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_148601265_   1140 TACCAATGACATTTTTCACAGA--TTAGAAAAAAAACT-ATTCTAAATTC 1186
                          v   iivi v     ii    --  i---- v  i  -  i     v i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chrX_148601265_   1187 CATATGGAACCAGAAATAAACCTGAATAGTCAAAAGCAATCATAAGCAAA 1236
                                  viiv  ivi v  v      i     -     v i iv  i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGAAAAAG 195

  chrX_148601265_   1237 AAGAGCATAGCCAGAGGCATCACAGGACCTGACT-CTAAACTATACTATA 1285
                             i  v  iii    vv     vvv  ii i - v     -     i 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACA 244

  chrX_148601265_   1286 ATGCTACAGTAACCAAAACA-TG----------------ATAGTCTTCTC 1318
                          v          i   i   -  ----------------    v v v v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_148601265_   1319 TAACA-CGGGTTAGA-----GAACCCAGAAATAAAGCCACACAGCTATAA 1362
                         v v  -i  iv    -----  ii           v   i   vi   ii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_148601265_   1363 CCATCTGATCTTCAACAAAATTGACAAAAACAAGCAATGAGGAAATGAGT 1412
                         i  vi    i   i    iiv  v   i v  vv     i     -  i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAAT 393

  chrX_148601265_   1413 --TCCTATCAATAAATGGTGCTGGCATAACTGGCTAGCCATACGCAGAAG 1460
                         --  i v    i            v i      v  ?   i i   i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_148601265_   1461 ATTGAAACTGAGCCCCTTCCAGTTTCAACTCAAGATGAATTCATCTTTAA 1510
                          v    ii  ii     v  ----   ---  vv  --  v  -----  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACC----TCA---CACCAT--ATACA-----AA 479

  chrX_148601265_   1511 TCCATCAACTCAAGATGGATTAAAGACATAAATGAAAAACCTAAAACGAT 1560
                         --v  i       i      i ?    v      v  i v       v  
  L1M4_orf2#LINE/    480 --AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_148601265_   1561 AAAAGTCCTAGAAGAAAACCAAGG---AAATACCATTCTGGATGTGGGCC 1607
                             v  i           vv   ---    -- -   vv  iv v  vi
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGT 574

  chrX_148601265_   1608 TTGACAAAGATTTCAT-GATGAGGATTCCAAAAGC-----TATTGTAAAA 1651
                          v i   v i    v -   - v  iv        -----i viiv  i 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_148601265_   1652 ACCCCCAAATTGA-GAATAAGACCTAAGTAAACTAAAGAACTTCTTCACG 1700
                          v----    v  -i   vi   i v vi   v v  i     i vii v
  L1M4_orf2#LINE/    624 AA----AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_148601265_   1701 TGAAAAGAAACTATCAACCCAGCAAACAGAAAGGCTACAGAATGGGAGAA 1750
                          v   i  v        vvv  ii  v   v iv i              
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_148601265_   1751 AG-ATTTGCAGACTACACATCCAACAGAGGTCTAATATCCAGAATCTATA 1799
                          i-       i ii i i   ii i ii  v  vi          v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_148601265_   1800 AGGAACTTTAACAAATTAATAAGGAAAAAACAA----CCCCATTAAAAAA 1845
                          i     i v    v i     vi    i    ----   v   ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_148601265_   1846 TGGGCCAAGAACATGAGCAGACACTTCTCAAAAGATGACATACACACAGC 1895
                              v   i iv   ii     i     v     v  i     v ii  
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_148601265_   1896 CAACAAGCATAGGAAAAAGTGTCCAACGTCACTAACATA 1934
                            i     i v     ii  ii    i   ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.19 (129 / 108)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.78 (75 / 27)  


2633 28.33 1.09 0.73  chrX_148646373_148652019     3934  4759 (888)    L1M4_orf2#LINE/L1        1   829 (79)  

  chrX_148646373_   3934 TGGAAA-ATATTCCACGTTCAAGGAGAGTAAGAATCAATATTGTTGAAAT 3982
                               -    i   i     v   vv v    v i         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_148646373_   3983 GACCATACTGCCCAAAGTAATTTAGAGACTCAATGCTATTCCTATCAAAC 4032
                          i v     v      v i  i  v   i    i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_148646373_   4033 TGCCAATGACATTTCTCTCACAATTAGAAAAAAAATCTATTTTTAAAATT 4082
                          v   iivi v   i iv  v  v v  v  i----  iv ii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG----CTGATCCTAAAATT 146

  chrX_148646373_   4083 CATATGGAACCAAAAACAGCCCA-AATAGCCAGGGCAATCTGAAGCAAAA 4131
                                  viiv  ivii    -        iii      vi iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_148646373_   4132 AGAGCAAAGTTTGAAGCGTCACACTGCCTGAATTCAAACTGCACTACAAG 4181
                            i       v  i vv       v  ii v      vivi       i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_148646373_   4182 GCTACAATAACCAAGAAACCATGGTACTGGTACAAAAAACAGACATATAA 4231
                               i   i     v vii         i i  ii -i         i
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAG 295

  chrX_148646373_   4232 ACCAATGGAACAGGTTAGAGAACCCATAAATAAAACCACACACCTACAAT 4281
                          i        i  iv v    ii   v       v   i   ii  iii 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_148646373_   4282 CACCTGATCTTTGACAAAGTCAACAAAAATAAGCAGGGGGGAAAGGACTA 4331
                           vi    i  i     i viiv   i vi vv  iv        i ivi
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_148646373_   4332 CCCATTCAACAAATGGTGCTGGGATTACTGGCTAGCCATATGTAGAAGAT 4381
                         i iv                    iv     v  ?   i   i i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_148646373_   4382 TGAAACTGGACCACTTCATTACATCATATTCAAAAAACAACTCAAGATGG 4431
                             ii      v  v v i   i     v      vi       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_148646373_   4432 ATTAGAAACTTAAACCTAAAACCTAAAACTATAAAAACCCTGGAAGAGAA 4481
                           i ? i  i    iv   i v              vi i i     i  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_148646373_   4482 C-CAAGAAAATACCATTTTAGACCTAGGCCCTGGCAAGGATTTCACA--- 4527
                          -i i ?iv v i v iv -     v  viiv     v i    vi ---
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_148646373_   4528 ATGATGCCAAAAGCAATTGCAACACAAACAAAAATTGACAAATAGGACCT 4577
                             ii         vvv      v  iv      v  i    v    i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_148646373_   4578 AATTAAACTGAAGAGCATCTGCACAGCAAAAGAAACTATTAAGAGAATAA 4627
                         v  i   v v  i i v i  ii vv    i  v     i    i i i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_148646373_   4628 ACAGACAATCTACAGAATGGGATAAAATATTTGCAAACTATGCATTTCAC 4677
                          v      i i           v              ii  ii  i v i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_148646373_   4678 AAAGGTCTAATATTCAGAATCTATAAGGAACTTAAACAAATTTACAAGCA 4727
                           i  v  vi   i      v     i     ivv    v iv i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_148646373_   4728 AAA--CAA-CAACTCAATTAAAACATGAGCAGAGG 4759
                            --   -i   i     ?   v   i   i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.45 (136 / 94)
Gap_init rate = 0.01 (9 / 829), avg. gap size = 1.67 (15 / 9)  

 420 20.59 0.00 0.00  chrX_148646373_148652019     5053  5154 (493)    L1M4_orf2#LINE/L1      807   908 (0)  

  chrX_148646373_   5053 CCCAAAAAAAAAGTGAGCAAAGGACATGAACAGACACTTTTCAAAAGAAG 5102
                              vv?    i  i        iv    i     i  i  v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chrX_148646373_   5103 ACATACACGTGGCCAACAAACATATGAAAAAATTTTCCACATCACCAACT 5152
                          i     vi       i  i  i       i  vi  v      ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chrX_148646373_   5153 AT 5154
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.00 (0 / 0)  


 273 17.57 4.05 0.00  chrX_148676787_148679673      438   511 (2376)  C L1M4_orf2#LINE/L1   (0)   908   832  

C chrX_148676787_    511 TTGAA-AG-CATTT-TCCAATGTGGACATATACATGACAAATAAGCACAT 465
                              -  -     -     v vi  i   i v   i v           
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

C chrX_148676787_    464 GAAAAATTATTCTACATCACAGCTATT 438
                              iv ii  v      ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (7 / 6)
Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3)  

 423 20.00 0.00 0.00  chrX_148676787_148679673     1052  1131 (1756)    L1M4_orf2#LINE/L1        1    80 (828)  

  chrX_148676787_   1052 TGGAAAAATACTCCATGCTCATGGATAGGAAGAATCAATATTGTTAAAAT 1101
                               i   ii     i        v      v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_148676787_   1102 GGCCATACTGCCTAAAGCAATTTACTGATT 1131
                            v     v  i   vii  i   v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT 80

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.00 (0 / 0)  

2125 28.55 2.51 2.75  chrX_148676787_148679673     1564  2400 (487)    L1M4_orf2#LINE/L1       74   908 (0)  

  chrX_148676787_   1564 ACTGATTTAATGCTATTTCTATCAAACTACCAATGACATCTTTCATATAA 1613
                           v    i  i  v  ii        v v   iivi v i   iii v  
  L1M4_orf2#LINE/     74 ACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAA 123

  chrX_148676787_   1614 TTAGAAAAAAAATATTCTACAGTTCATACAGAACCAAAAAAAGAATGTA- 1662
                         v v  v  ivvi-  i   v i      ii   -- viv  i i ivi -
  L1M4_orf2#LINE/    124 ATTGACAAGCTG-ATCCTAAAATTCATATGGAA--ATGCAAGGGACCCAG 170

  chrX_148676787_   1663 AATAGCCACAGCAATCCTAAGGAAAAAGAGCACAGCCACAGGCATCACAC 1712
                                 v i     i i ii  i    i  v  iiiv   vv      
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_148676787_   1713 TAGTCAACTCTAAACTGTATTATAAAGCTACACTAACCAAAACAGCATGA 1762
                          vvi   i ii   viv  i  i         v   i   i    ii  i
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_148676787_   1763 TATTGGTAGAAAAACAGACACATAGACCAATGAAACAGGTTAGAGAACCC 1812
                           i   i v  ii i     i     i     i  i  iv v    ii  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_148676787_   1813 AGAAATAAAGCCACACACATACAACCATCTGACATTCAACAAAATTGATA 1862
                                  v   i   iv  iiii  vi   iv   i    iiv  vi 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_148676787_   1863 AAAACAAGCAATGAGGAAATGACTCCCTATTTAATAAATGGTGCTGGAAT 1912
                          i v  vv     i     vi ivvi  v  i  i            i i
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_148676787_   1913 AAGTGGCTAGCCATAGGCAGAAGATTTAAATTGGACCCCTTCCAGTTTCA 1962
                           v   v  ?   i v   i    v v  i          v  ----   
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC----TCA 466

  chrX_148676787_   1963 ACTCAAGATGGATTAATCTTTAATTTGTCAACTAAAACTAGATTGAAGAT 2012
                         ---  vv  iv iv  -----    ----    v   v i   ii?   i
  L1M4_orf2#LINE/    467 ---CACCATATACAAA-----AATT----AACTCAAAATGGATCAWAGAC 504

  chrX_148676787_   2013 TTAATTCAAAAACCTAAAACTATAAAAATCCTAGAAGGAAACCTAAG--- 2059
                         i   v vv  i v              v  i      i    v  i ---
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_148676787_   2060 AAATACCATTCTGGAACTAGGCCTTGGCAGAGATTTCAT-GATGCAGATT 2108
                             -- -   vv  v  v  vi v    iv i    v -   ii-  iv
  L1M4_orf2#LINE/    555 AAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT-GACA 600

  chrX_148676787_   2109 CCAAAAGCAATTGCAACAAAAACAAAAATTGACAAATGAGACCT------ 2152
                                  vvv         iv      v  i    vi   i ------
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_148676787_   2153 AATT---------TGCATATCAAAAGAAACTATAAACAGAGTAAACAGAC 2193
                             ---------  iiiv     i  v     v  v i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_148676787_   2194 AAGCTACAGAATGGGAGAAAATATTTGCGAACTATGCATCCAACAAAAGT 2243
                           v i                       i  ii  ii   ii i  ii v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_148676787_   2244 CTAATATCCACAATCTCTAAGGAAGATTAACAAATTAACAAGCAAAAAAC 2293
                           vi      v   v v   i   vvi v    v i  i  vv    i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_148676787_   2294 AAACAACCCCATT-GAAATTGGGCAAAGGACAAGAGTAGGCATTTCTCAA 2342
                            i     v   -i   v           ivv  i   i        v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_148676787_   2343 AAGAAGACATACAAGTGGCCAACAAGCATATGAAAAAGTGTCCAACCTTG 2392
                                i      i       i     i       ii  ii    v ii
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_148676787_   2393 CTAATATT 2400
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.42 (139 / 98)
Gap_init rate = 0.02 (15 / 835), avg. gap size = 2.93 (44 / 15)  


2589 26.84 1.93 1.45  chrX_148857616_148859420.rev      502  1328 (477)    L1M4_orf2#LINE/L1       78   908 (0)  

  chrX_148857616_    502 ATTTAATGCAATTCTAATCAATATCCCA-TAGAACTTTTTGTATTTACAG 550
                            i  i     i iv     v      -iv vvi      i vvv iv 
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTG 127

  chrX_148857616_    551 ATAAGTGGAATGTAGAATTTATATAAAAA-GCAAAGGAACTAAAAGAGCT 599
                          i   iv  viv  i    i    ii   -    i   v i i  v   i
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chrX_148857616_    600 AAAACAATTTTAAAGAAAAAGAATAAAACTGTAGAAATAACATTAACTGA 649
                                 i  i  i  i     i   ii  v  i v v   i vv ii 
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_148857616_    650 TTTTAAGACCTACTGTATATACACAGTAATCAAGACGGTGTGGTATTGTC 699
                            i  i  i    ii v vvi              i        i  v 
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_148857616_    700 AAAGGGAAGGACACACAGATCAATAAAACAGAAAACAGAGTCTAAAAATT 749
                          v i   vi    i i        ii  i    vvv      i i    v
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_148857616_    750 GGCTCACATAAACATAGCCAACTCATTGTTGACAAAAATGC-AAAAGCAT 798
                         ii i  i i vvi  i i   i v   v i     iii   -  i v   
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chrX_148857616_    799 TTCAATGGAGAAATGATATGTTTTTTCAACAAATGGTGCTGAAATCATTG 848
                          -      i    vi   -  i                   ii iv i  
  L1M4_orf2#LINE/    378 T-CAATGGGGAAAGAATA-GTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_148857616_    849 TATAACAGTATGAAAAAAAATAACATTAA--CCTAACCTTACACCTTAAA 896
                         v   ? vii   v    i   i vi  ii--  iv    i     v  v 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_148857616_    897 CAAAAATTTACTCAAGGTGGATTATAGATCTAAACATATAACATAAAACA 946
                                 v      ii     i ?   i     ii  vi vv      v
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_148857616_    947 ATAAAATGCTTAGAAAAAAA--TAGGAGAAAATTTTCCTGACCTTGAGTT 994
                               iv       i    --    ? v    i   v        i   
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_148857616_    995 ACTTGAAGAGTACTTGGATATGACATCAAAAGCATGATCCATAAAAACAG 1044
                          vvii v iv v   i         i        ii v v i    iv i
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_148857616_   1045 AAGTTGATAAATTGGATTTTATCAAAATTAAAAAGTTTTGTTCAGTGAAA 1094
                           i v           i  i              v      v vvii  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_148857616_   1095 TACACTGTTAAGAGAATGAAAAGACTAGCTACAGACTAGAAGAAAATATT 1144
                         v     i i    i i         v v i     v i i          
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chrX_148857616_   1145 TTCAAATCACATATCTTACAAAGGCCTTTTATCTAGAATATAATAAAGAA 1194
                          v       i      v i  i  v   v    i        -       
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA-TAAAGAA 774

  chrX_148857616_   1195 CTCTCAAAACTCAGTAGTAAGAAAA-AAGT---CCACTTAGAAAATGGGG 1240
                             i v      i  i   i  i -  i ---   v  ?i        v
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_148857616_   1241 AAAATACATCAAACATTTCAACATTACATTTCAACATAGATGTGTAGATA 1290
                            iv i- ii  i ----i     v -- i   viv    i ii i  i
  L1M4_orf2#LINE/    825 AAAGGAT-TTGAATA----GACATTTC--TCCAAAGAAGATATACAAATG 867

  chrX_148857616_   1291 GCAAATAAGCACATGA-----TACTTTCAACATTGTTAACTAT 1328
                           v             ----- i  --      ii????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCT--CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (138 / 80)
Gap_init rate = 0.02 (15 / 831), avg. gap size = 1.87 (28 / 15)  


2450 23.44 4.17 3.52  chrX_148867942_148869692      500  1267 (484)    L1M4_orf2#LINE/L1      136   908 (0)  

  chrX_148867942_    500 ATTCCAAAATTTATATGAAAAGACACAGGTCCTAGAATAACTAGAACAAT 549
                           i i      i     i   vi  vi  v  i      i i i      
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_148867942_    550 TTTGAAAAAGAGTAATAAAGTTGGAGGAATCGGTCTACCTAACATTAAGG 599
                         i          iv  i            v  ivv  v  i  iv i  ii
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_148867942_    600 CTAACTACATAGCTGTGGTAACCAAGACCATGCAGTATTGCCAGATGAGT 649
                           v      v    iii    i      vi  ii   i  v  v v - v
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GA 284

  chrX_148867942_    650 TAGATATATAGGTCAATGGAACAGAATAGAGAACCCAGAAATAGACCCAC 699
                             i      i         i     v    ii         i     i
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chrX_148867942_    700 ATAAATATTCCCAACTGAATTTTAACAAAGATGCAAAGGTGATTCAATGA 749
                          i vv   vvi   i   v   ii    i i   v   iiv        i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chrX_148867942_    750 AGGAAGGATAGACTTTTCAACAAATGGTGCTGTGTTGGAACAACTGGATA 799
                         i i   i    v                    ----- i           
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTG-----GGACAACTGGATA 429

  chrX_148867942_    800 TTCATAGGCAACACAAACAAAGTTCAACTTAAGCCTTACACCTTATGTAG 849
                         ?i  i v    v -i  ii     vi  iivvi   i     v   ii i
  L1M4_orf2#LINE/    430 KCCACATGCAAAA-GAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chrX_148867942_    850 ACATTTACTCAAAATGGATCATG----TAAGTTTTTAAAACATAAAACTA 895
                          v   v               ?i----   i v --  i vv        
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGT--AAGAGCTAAAACTA 526

  chrX_148867942_    896 AACATATTTTAGAA---AAC-T-GGAAAAAATCTTCCAGCTCTAAGGCTA 940
                         v v vv i      ---   - -  ?iv        vv vi  vi  i  
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_148867942_    941 GGCAACAGATTCTTAGACTTGACACCAAAAGCATGATCCATAAAAGGAAA 990
                              ii v        iv              ii v v i     i   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_148867942_    991 AAGTAATTGGTAAATTGGAACTCATCAAAGTTAAAAACTTTCTGTGGAAG 1040
                           -  --- i         vi        i           -    ----
  L1M4_orf2#LINE/    627 AA-TA---GATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTG---- 667

  chrX_148867942_   1041 TTTTTATGAAACATCCTTTTAAATA--TGAAAATACAAGCTATAAACTGG 1088
                         -i  i viii   --  v i  iv --      v    v i i i v   
  L1M4_orf2#LINE/    668 -CTTCAAAGGACA--CTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_148867942_   1089 AAGAAAGTATTTGTAAATCATAT--CCAACAA-------------AGAAT 1123
                         i     i      i         -- ii i  -------------     
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_148867942_   1124 ATATAAATAACTCTCAAAACTCAATAGAGTAAAAA---AAAT---CCTAT 1167
                                v      i v         i--      ---    ---  v  
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAA--TAAAAAGACAAATAACCCAAT 812

  chrX_148867942_   1168 TAGAAAATAAGCAACAAACAGCAACAGACATTTCACTGAAGAAGATATAC 1217
                          ?i     ii    vii ivvv  i         v ii            
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_148867942_   1218 AGATGACAAATAGGCACATGAAAAGTTGTTCAATCAACATCACCATTAAA 1267
                          i   i v    i            v  i    ----     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAA----CATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (110 / 66)
Gap_init rate = 0.03 (20 / 773), avg. gap size = 2.95 (59 / 20)  


3090 26.37 2.36 0.56  chrX_148905172_148910923.rev     4371  5261 (491)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_148905172_   4371 GGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATG 4420
                             ii i  i     i      i v      v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_148905172_   4421 GCCATAGTGTCCAAGGTAATTTATAGATTCAATGCCATCCCCATAAAGCT 4470
                           v   v vi    iv i  i  i        i  v     i  v  iv 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_148905172_   4471 ACCAATGACTTCCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCAT 4518
                         v   iivi i ii  ii     -   -- v  i  - iii    i     
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chrX_148905172_   4519 ATGGAACCCAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAATA 4568
                               vivv  ii  v  viv  v     iv     i i ivv i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_148905172_   4569 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 4618
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_148905172_   4619 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 4668
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_148905172_   4669 ATTGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACTA 4716
                           v   i    i--    i  --        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_148905172_   4717 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 4766
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_148905172_   4767 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 4816
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_148905172_   4817 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 4866
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_148905172_   4867 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 4916
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_148905172_   4917 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 4965
                             ?i- v i -   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_148905172_   4966 AACACCAAAAGCAATGGCAACAAA-GCCAAAATTGACAAATGGGATCTAA 5014
                         i            vvi        - vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_148905172_   5015 TTAAACTAAAGAGCTTCTG-----CACAG--------CAA--AAGTGAAC 5049
                          i   v v  i i   i  -----  v  --------   --       v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_148905172_   5050 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5099
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_148905172_   5100 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTGCAAGAAAA 5149
                         i  i  vi          v  i  v      vv    v ivii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_148905172_   5150 AAACAAATAACCCCATCAACAAGTGGGCAAAAGATATGAACAGACACTTC 5199
                          i           v  i? v  i        i   v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_148905172_   5200 TCAAAAGAAGATATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATC 5249
                           v           vi viii     v ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_148905172_   5250 ATCACTGGCCAT 5261
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (136 / 95)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 2.36 (26 / 11)  


3073 24.78 1.98 1.98  chrX_148960450_148965557     3708  4615 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_148960450_   3708 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 3757
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_148960450_   3758 GACCATACCGCCAAAAGGAATCTACAAATTCAATGCAATTCCCATCAAAA 3807
                          i v    iv  v   vvi       i      i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_148960450_   3808 TACCACCATCATTCTTCACAGAATTATAAAAAA--AATTCTAAAATTCAT 3855
                          v   v vv v  i  ii     v - i v  i--i  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_148960450_   3856 ATGGAACCAAAAAATAGCCTGCATAGCCAAAGCAAGACTAAACAAACAAA 3905
                               viiv  iiv v  v v         i   vvi i  -----   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-----AAA 194

  chrX_148960450_   3906 CAAACAAAACAAATCTGGAGGCATCACACTACCTGATTTCAAA-----CT 3950
                         v  i---      vi      vv       v  ii        -----  
  L1M4_orf2#LINE/    195 GAAG---AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_148960450_   3951 ATAAGGCCATAGTCACCAAAACAGCGTGATACTGGTATAAAAATAGGCAC 4000
                          i  i  i i   v i   i    i   i      i    ii    i  i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_148960450_   4001 ATACACCCATGAAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTA 4050
                            v i v   i  i     v    ii               v i i   
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_148960450_   4051 GAGCCAACTGATCTTTCACAAAGGAAACAAAAACATACAGTGGGGAAAGG 4100
                         vi i   i    i  iv    i  viv   i v   v  i         i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_148960450_   4101 ACACCCTTTTCAACAAATGGTGCTGGGATAACTGGCTAGCCACAGGTAGG 4150
                          i vi                       i      v  ?     v i ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_148960450_   4151 AGAATGAAACTGGATCCTCATCTCTCACCATATACAAAA-TCAACTCAAG 4199
                                 ii    i  ii i   v              - i       i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_148960450_   4200 ATGGTTTAAGCACTTAAACCTAAGACCTGAAACTACAAAAATTTTTGAAG 4249
                             v i ?iv  i    iv     v  i      i    v i  v    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_148960450_   4250 ACAACATTGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGAATTTCATG 4299
                          v     v  ?iv  vi    vv   v    v        vii    v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_148960450_   4300 ACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGTA 4349
                         ivi v  vv         v v    i    iv   i   i   iv v v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_148960450_   4350 CCT------AGTTAAAGAGCTTTTGCACGGCAAAAGGAACAGTTGGCAGA 4393
                          i ------ i     i -      ii vv    i iv  vi iiiv i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_148960450_   4394 GTAAACAGACAACCCACAGAATGGGAGAAAAACTTCACAGTCTATACATC 4443
                           i  v                         vv  ii  ivii   i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_148960450_   4444 ----AAAGGACTAATATCCAGAATCTACAACGAACCCAAACAATTCAGTA 4489
                         ----  i     vi          v  i  v    i vv    i   i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_148960450_   4490 AGAAAAACAAACAAACAAACAAATGCCATCAAAAAGTGGGCTAAAGACAT 4539
                          v     --i     i  v ----- v  i?    i     v  i  iv 
  L1M4_orf2#LINE/    791 ATAAAAA--GACAAATAACC-----CAATTWAAAAATGGGCAAAGGATTT 833

  chrX_148960450_   4540 GAGTAGACAATTCTCAAAAGAAGATATACAAATGGCCAAAAAAACGTATG 4589
                           i      v     v                       v  i- ii   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACATG 882

  chrX_148960450_   4590 AAAAAATGCTCAACATCACGAATGAT 4615
                             i             ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (128 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.00 (36 / 12)  


1977 25.92 6.51 1.22  chrX_148967759_148969428.rev      449  1185 (485)    L1M4_orf2#LINE/L1      133   908 (0)  

  chrX_148967759_    449 CTTATGCTAAAATTCATA--GAACTATATAAAAACGGCAGTTTA--CAAA 494
                           v  v            --   v ii - iii  v-   vv  --    
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCA-AGGGACC-CAGAATAGCCAAA 180

  chrX_148967759_    495 TAAAAGTTTTTAAAAAAGAAGAGCAAAGTTGTAGGAGTTACATTGACTGG 544
                         - v  -- i  i          i        v    v i   i vv iii
  L1M4_orf2#LINE/    181 -ACAA--TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chrX_148967759_    545 CTTAAATAATTGTTATAAAGATTAAACAACTGGGGAAGTAGAGTATTGGT 594
                         i  v  v v  ii  i    v vv ii  iiii iv   ivi   i   i
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chrX_148967759_    595 ATAAGGATAGACAAATGTATCA-TGGGAAAAAATTAGAAAGTCCAGAAAT 643
                                      v  iv    -   i v i    -  i           
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATT-GAGAGTCCAGAAAT 326

  chrX_148967759_    644 AGCCTCACACATGTATGACCAATTGATTTTCAGCAAAGATGTCAAAGTGA 693
                          iv i  i    v    ii            ii   i i  i   iiiv 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_148967759_    694 TTTAATGGGTGATAACATAGACTTAAAAAAAAAAAGGTGCAATTACAACT 743
                           i      -  v iv    v   vvv  v   v-     vivv      
  L1M4_orf2#LINE/    377 TTCAATGGG-GAAAGAATAGTCTTTTCAACAAAT-GGTGCTGGGACAACT 424

  chrX_148967759_    744 GAATATTCATTTGGGGAAGA-TGAACCTCAACCCTTATTACATACCATAT 792
                          i   ?i  iv  vii    -    vi vi    i  iiv  i       
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_148967759_    793 ACATATATTAACTTGAGATGGTTCATAAATCTAAACATAAAAGTTAAAAC 842
                            v v       ii i    v   ? i i     ii   i  i      
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_148967759_    843 TATAAAAAT-TCAGAAGAAAAAAATAGGAA-AAATAATTGCAAATTTGGA 890
                                v - i         v -    ?i-    vv i ii vi    i
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACA-TAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_148967759_    891 AGAGGCAAAAAT--CTT-GATAGGACACAAAAAGTATAAACTATATAAGA 937
                         vv      vii --   -    v     v     i i  i v i v    
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chrX_148967759_    938 AAAAAT-GATACAATGGATTTCATTAAA---------TTTTGCTCTTTGA 977
                               -    v v    i     i   ---------     iv   ii 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chrX_148967759_    978 AT--CACTA--AAAAAAATGAAATGGTAA--------------------A 1003
                          v--     --  i   i     v ii  -------------------- 
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_148967759_   1004 TTTGCAAACCATAGATCTGAGAAAGGACTTACATCAAGAATATAGAAATC 1053
                                 i    v      v  i      ii   v        v   vv
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_148967759_   1054 ACAATTATAATT---TAATAACAAGACCAGGAACCCAATTTAAAAATGGG 1100
                           vv   i  i ---      v     v iv         ?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_148967759_   1101 CAAATGATTAAAACAGACACTTCACAAAAGAAAATATATGAATGGCCAAC 1150
                             v    vi  i     i   v v      i     ii         i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_148967759_   1151 AAGCACATGACAATATATTCACTGTCACTTGTTAT 1185
                                   v  v  ii   vii   ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (108 / 79)
Gap_init rate = 0.03 (22 / 776), avg. gap size = 2.59 (57 / 22)  


1636 26.66 3.94 2.84  chrX_149047909_149049532.rev      502  1135 (489)    L1M4_orf2#LINE/L1      268   908 (0)  

  chrX_149047909_    502 TGGTATTGGTATAAGGCAAGACAAATAGAATGATGGAGTAGAAGAGTGAG 551
                              i   i      vv     v     vii     i     vv v   
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_149047909_    552 CCCAGAGATACAGCCATGCATACGTAAAGT---TTAATTTATAACAGAGG 598
                         i     i   v v    i   --v  vi  ---  i    vii   ii  
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACAT--TTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_149047909_    599 -----AGACACTGCACAGGAGTGGAGAAGGGATAGTCTTCTCAATCAATT 643
                         -----    vv v  -----i   i   i i        i    iv   v
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCA-----ATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chrX_149047909_    644 GTGCAGGGATA-CTGAGGTATCCACAGGATAGAAAATGAAATAGGACTCT 692
                             v    i -   - i  ?     v vv i i      i v    i i
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTG-GATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chrX_149047909_    693 TATTTCGCATCA-ACACAAAAATCAAGTCCAGATGGATTAAGGACTTATA 741
                           ii  i  i  - i        i  v  v i      i ?i   i  v 
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chrX_149047909_    742 TGTTAAAGGTAAAACTATAAAGCTTTCAGAAGATCATATAGGAGAATATC 791
                            v i  v            i  i i      vv i     ? v v   
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chrX_149047909_    792 TTCATGACCTAAAGGTAGGGAAAAATTTCTTAAACATGACATGAAAAACA 841
                            i      vii v    v  vii       i i      iv    i  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_149047909_    842 CTAAGCAT--AAGGAAAAGATGGGCAAGCTGTACTATATAAAAATGAAGA 889
                          -     v--  i     i  i ii  ii  v   vi  v     v  i 
  L1M4_orf2#LINE/    610 C-AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_149047909_    890 ATTCCTAGTTTTTGAAAGG-TAGCATGAAAAGAGTGAAAAAGCAAGCCAC 938
                          i ii -  vi  v     -i vi  v  i i        ii   v    
  L1M4_orf2#LINE/    659 ACTTTT-GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_149047909_    939 AGACTGAGAGAAGTTATCTGCAA--CATGTAAAACTGACAAAGGGCTTAT 986
                            v  i     iv   i     --   i  v--    i  i  i   i 
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATAT--CTGATAAGGGACTTGT 755

  chrX_149047909_    987 ATCTAGAATATATTTTTAAAATGCT---ACAAATTATTTTGAAAAAGAGA 1033
                            i         ----   ivi  ---    v i v vvv       v 
  L1M4_orf2#LINE/    756 ATCCAGAATATAT----AAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chrX_149047909_   1034 GAGAACTCAACAGAAAAACTGTCAAAAGGCTTAACCAG-TAATTCAC--A 1080
                         i v   i   iv?     iv v    i ii  i vi  -i v   v -- 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chrX_149047909_   1081 AGCCAGGAAATCCAAATAGCTAATAA-C-CGTGAAATGGTGCT--ACATT 1126
                           -- i  v  v     i  i     - - i     v i    --    i
  L1M4_orf2#LINE/    852 AG--AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_149047909_   1127 TCCTAGTAA 1135
                         v????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.46 (98 / 67)
Gap_init rate = 0.03 (21 / 641), avg. gap size = 2.05 (43 / 21)  


2908 26.61 1.81 2.15  chrX_149125941_149128314      991  1873 (501)    L1M4_orf2#LINE/L1        1   880 (28)  

  chrX_149125941_    991 TGGAGAGACATACCATATTCAGGGATTAAAAGATGCAACATAGTAAAGAT 1040
                             i   i  v    i    v     ii    ivi  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_149125941_   1041 GTCAATTCTCCCCATATTGAAATACAGTTTTAATGCCATTCCTATCAAAA 1090
                          v    v       v     vv     v  i  i  v  i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_149125941_   1091 TTCCAGCAGGATTTGTTTGTAAATATAGACAATATTATCCTTAAATTTAT 1140
                          i     v vv   -    i i v  v     vv v     v     i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_149125941_   1141 ATGAAAAAGCAAAGGAACTCGAATAGTTAAAACAACTTTGAAAAATAAAA 1190
                            i   v    i   v iv      ii       ii        v  i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_149125941_   1191 ATAAACTAAGAAGAATTTCTCTGCTTGGTGTTAAGGCCTATTGCATAACC 1240
                          i   v vi  i  v iv v  v iiii v i  ii i  i i  v i i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_149125941_   1241 AAAGTAAGCAGTATAGTGTGTTTAGGGCAGAGGAACAGACACTGATATAG 1290
                          v     v  iv i      v vvv    v i i i     ----     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA----TATAG 295

  chrX_149125941_   1291 ATCAGTGAGACAGAACAGAGAATTCATAAATAGACCCACACAAATACGCC 1340
                             i  ii i    iv    i i  v     i     i   vv  i vi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_149125941_   1341 CAACAGATTTTTGACAAAGTTGCAAAAGCAATTTAATGGAGGAAGGATAG 1390
                            iv      i     i v   v  ii v   i     i i   i    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_149125941_   1391 TCTTTTTAACAAATGGTACTGGAGCAAGTGGACACCCACA-GTAAAAAAA 1439
                               i          i    ii   v    i ?     - i    i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_149125941_   1440 AAAAAAAAAAAATTTGACCTA-ACCGTCACACTTTTTA--------AACT 1480
                         vi  i-------  v    iv-   -      iv v  --------    
  L1M4_orf2#LINE/    446 TGAAG-------TTGGACCCCTACC-TCACACCATATACAAAAATTAACT 487

  chrX_149125941_   1481 CAAAATGGATCACAGACTTAAATATAACATGTCAAAGTATAAAGTTTTCA 1530
                                     ?    i     i   v vv v   v      ii i i 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_149125941_   1531 GAAGAAAACATAAGCAAAAATCTTTGGAACCTATGGCTGAGTGAAGAATT 1580
                                     i ?iv       i vi    vv  i ii ii v iv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_149125941_   1581 CTTAGACTTGACACCAAAATCATAATCTATTAAAAAAAAAATAGATTAAC 1630
                               iv           v  i  v v iv   i           v  i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_149125941_   1631 TGGGTCACACCGAAACTA-----CTTTGCTCCTGAAAGG-CACTGTTAAG 1674
                            iiiv  i i   i  -----i    iv i v     -    i i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_149125941_   1675 AGGGTGAAAAGACAAGCTACAGACTGGGAGAAAATATTTACAAACCATAT 1724
                          ii            v i     v               i    i     
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_149125941_   1725 ATTCAACAAAAGACTTGTATCTAGGATATATAAAGAGCTCTCAAAAATCA 1774
                           iii i  ii          i  i           i    i v  v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chrX_149125941_   1775 AGAGTATAATAATAATAATAAAAACTCCTGTCAGAAAATAGGCAAAACAC 1824
                          -----      v  -i i   v vi  vi i?i     i      iv i
  L1M4_orf2#LINE/    788 A-----TAATAAAAA-GACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_149125941_   1825 ACGAAGAAACATTTTGTGGAAGATAATCCACAGATGGCAAATAAGCACA 1873
                         vi   v i      ivivi    vi  vi   i     v          
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

Transitions / transversions = 1.51 (139 / 92)
Gap_init rate = 0.01 (11 / 880), avg. gap size = 3.18 (35 / 11)  


2416 27.67 3.53 3.42  chrX_149130151_149132511      964  1870 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_149130151_    964 TGGAGAGATAAATCATCCC-TATTCTTGGGTTAAAAGACTCAAGATAATA 1012
                             i     -----    - i   v   i  ii      i  v  vi v
  L1M4_orf2#LINE/      1 TGGAAAGATA-----TCCCATGTTCATGGATTGGAAGACTTAATATTGTT 45

  chrX_149130151_   1013 AAGATTTCAATTCTTATGTAATTGATACACAGATTTAGCATAATTCCTAT 1062
                              vv    v  ivivv       vi       i i ii   i     
  L1M4_orf2#LINE/     46 AAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chrX_149130151_   1063 CAAAATACCAGCAAGGTTTACTTGTAGATCTATACAAGCTTATTTTACAA 1112
                               v     vivv   -i   i   vv vv       v  ii  v  
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTT-TTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chrX_149130151_   1113 TTTACATGGAATGGCACAGG-TTTAAATTAGCTAAAACAATCTTGTCAAA 1161
                           i i      vv   vi  -iii i v    i            vv   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_149130151_   1162 AAAGAATAAAGTTGAAGGTATCACTCTACCCAATATTAAGGTTGAGTTTA 1211
                         i     i       i   vv    v  v      v i  iii v v vi 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_149130151_   1212 TAGCTCCAGTAATTAAGACAACTCAGGATTAGTGGAGGGACAGATACATA 1261
                         v    v       i      iivii v i i iiv i   i   i i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_149130151_   1262 GACCAGTGGAACAGAATGAAGAACTGAGAAATAGAAAGAACCATA-AT-- 1308
                           i  i     i     vi   iiiv       i v----     -  --
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC----CCATACATTT 340

  chrX_149130151_   1309 AGAACCACCCTTTGATTTTTGACAAAATTGCAAAAGCAATTCAACAGAGG 1358
                          viii  v---        i     iiv   v  ii v      ii i i
  L1M4_orf2#LINE/    341 ATGGTCAA---TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_149130151_   1359 AAGGTTTGTCTTT-CAGCAAGTGATGCTGAAGCAATTCAATATCCATAAG 1407
                            iv v      -  i   i  i     iii   i vi   ?   i v 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_149130151_   1408 CCAAAAAAAAAAAAAAACCCACGTTG-ACCTAAATCTCACAGGTAATGTA 1456
                          -----    i  vi  -----    -   ivv i      vvvv  ii 
  L1M4_orf2#LINE/    438 C-----AAAAGAATGAA-----GTTGGACCCCTACCTCACACCATATACA 477

  chrX_149130151_   1457 AAAATTAACTCAAAATGGATCATAAAATTAATTGTGAAATGTAAAACTAT 1506
                                               ? i vi   v   i i vv         
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_149130151_   1507 AAAACTC--AGAAAAAAACAACACAAGAAAAAATCTTCAAGATTTAGGAC 1554
                                --    i      ---i i ?iv        iv  ii v  ii
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACA---TAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_149130151_   1555 TAGGCAGGGAGTTCTTAGCCATTACTCCAAAAGCATGTCCCATAAAAAGA 1604
                               iv iv       vi  v  v         iivv v i    ii 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_149130151_   1605 AAACTAGATAAATTAGACTACATCAAAATGAAAAAATCTTGCTCTGAGAA 1654
                            v          i    v         v     v i   iv  vvi  
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_149130151_   1655 AGACCCTAT---GAAAATGATCAAACAAGTTACAGACAGGGAGAAATTCT 1701
                         i   v    ---    i   vv i    vii     vv        v v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_149130151_   1702 TTGAAAACTACAGTTTTGA----GAACTCCTTATATATTCTAGATACA-- 1745
                            v   ii i vv i   ---- i   ----- i   i vii   i --
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACT-----TGTATCCAGAATATATA 769

  chrX_149130151_   1746 ---AGTTCTT------TGACAGTAAAAA-----ACAATTCAATTAGAAAA 1781
                         --- ii    ------ii i i      ----- i  ii     ?i    
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chrX_149130151_   1782 TGGGCAAAAGACATAAAGATGTATTTCACTGAAGAAAATCCACAGATGGC 1831
                                 i  iv i  v vii     v ii     i  vi   i     
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_149130151_   1832 AAATAAACACATGAAAAGATGCTCAACATTGTTAGTTAT 1870
                         v     i                      ii????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (148 / 99)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.15 (63 / 20)  


2427 27.25 7.84 2.22  chrX_149218620_149221973.rev      521  1375 (1979)    L1M4_orf2#LINE/L1        6   908 (0)  

  chrX_149218620_    521 AGACATACTATGTTTACTGCCTAGAAGACTCAACATAGTAAAGATGTCAA 570
                            i  v i     i iv vi i       i  i  v  v      v   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chrX_149218620_    571 T---TCTTGAATTGACCTGTAGGTTTAATGCAGTTCTCATCAAAATCTCA 617
                          ---i iii      i  ii  i  i  i   i i ii         i  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chrX_149218620_    618 GCAAAGTTTTTTGTAGACGTAGACAAGGTTATTCTAAAAT--ATATGGAA 665
                           vivv       i   vi v      v v  i       --        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chrX_149218620_    666 AGGCACAAGTCCTAG----GTTAAAACAATTTTGAGAAACAATTATACAA 711
                          v   vii v  i  ---- ii        i    i   v  vv i v i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chrX_149218620_    712 TGGGAGGAGT-ACTTTTACCCAGTATTAACATTT-TTATATGGCTACATT 759
                          v      v -  vi  -    i v i  v i  -i  i vi      v 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTT-CCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_149218620_    760 AGTCAAGACTGTGTGGTATTGGCAGAGGGATAGACACATAGATCAGTGGA 809
                          i       v        i     v i         i        i    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_149218620_    810 GCAGAATAAGGAGCCCAGAAATAGACCCATAAAAATATTTCCCACGAATT 859
                         ii     vii   i         i       v vv   vvi v ivi   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_149218620_    860 TTTGACAAAGGTGTAAAAGCAGTTCAGTGAGGTGGGGATAGCCTTTTCAA 909
                           i     i    iv  ii vi    i  i  vii i    i        
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_149218620_    910 CAAATGCTACTAGAGCCATTGAGCATCCATAGGCAAAAAAATAATAAACA 959
                               v i  i ii v i  iii ?   i v      i   i -- ii-
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA--AGT- 451

  chrX_149218620_    960 TCAACCTAAACCTCACACCTTATACAAAAATCAACTCAAAATCGATTATG 1009
                          vi   ivv          v           i          v   i ?i
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_149218620_   1010 GCCTTAAATGT----GT---AACCATCAAACTT-----AAAAAATATTAG 1047
                          v i       ---- i---   i  v     i----- i    i  vi 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_149218620_   1048 AGAAAATTTTCAGGACCTAAGACTTGGGGTA--GAGTTCTTAGACTCAAC 1095
                         ? v    i   iv     vi ii --i  i -- iv        ivii  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTT--AGGCAATGGTTTCTTAGATATGAC 599

  chrX_149218620_   1096 --------CACAA---------------------AAATCTGACCCC--CA 1114
                         --------     ---------------------    iv   ii --  
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_149218620_   1115 AAAT--AGTCTTTTTGTG----AAAGAAC-CTATTAAAAGGAGGGAAAGA 1157
                             -- ivvi       ----    i  -    i  i iiiv i     
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chrX_149218620_   1158 TAAGATACAGACTGAGAGAAAGTATTTTCAAATTACATATTGGACAAAAT 1207
                         i  vvi     v  i      i     v     i i    iv  i  iiv
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_149218620_   1208 ACAAGTATCTAGAATATATAAAGAACTTGCAAAACTCAACAGTGAAAAAA 1257
                           vv     i                 ivi v       i i ----   
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT----AAA 795

  chrX_149218620_   1258 AAGAGAAAAAATGCAAATAATCCAACTAGAAAATGGGCCAAAGTCATGAA 1307
                             ---------       i    i ?i         v  i viv    
  L1M4_orf2#LINE/    796 AAGA---------CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_149218620_   1308 CAGACATTCCGT----GAAGTTATATGGATGAAAAATAAACTCCAGAAAA 1353
                         i       i vi----    v    iii   ivv     i v vv     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chrX_149218620_   1354 TATGTTCAATCTCATTAGGCGT 1375
                         v   i    iv   ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (147 / 82)
Gap_init rate = 0.02 (22 / 903), avg. gap size = 3.91 (86 / 22)  

 472 29.03 4.61 2.76  chrX_149218620_149221973.rev     1920  2136 (1218)    L1M4_orf2#LINE/L1      230   450 (458)  

  chrX_149218620_   1920 TTAAAAATCACAATAAAGCCTCTATAATTAAAACAGTGTGGTACTGGAAG 1969
                          i    v i  v i     iv vi    i  i               v v
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_149218620_   1970 AAGAATAGGCAAATTGACCAGTGGAATAAAATATGCATGT--AGAAATAG 2017
                            i    i  v  v  i  i       i   -  viv  --       i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAAT-TGAGAGTCCAGAAATAA 328

  chrX_149218620_   2018 ACCCAAGTATATGTGGAGACTGAATATATAATAATGGTG-----ACTTTT 2062
                              vii  v i   vv v vi  v vii i  v    -----  iv  
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chrX_149218620_   2063 CAAATCACTGGAGCAAGATGAACATTTGTAA--AATGGGGCTGCGATAGC 2110
                            -----   i v    vv iiv   vi  --     v    v  i i 
  L1M4_orf2#LINE/    379 CAA-----TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chrX_149218620_   2111 TGGGTAGTCTCTTG-AAAAAAGGGAAG 2136
                            i  ?i v v  -    i iv    
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAG 450

Transitions / transversions = 1.07 (32 / 30)
Gap_init rate = 0.03 (6 / 221), avg. gap size = 2.67 (16 / 6)  

 611 28.57 4.76 3.25  chrX_149218620_149221973.rev     2409  2870 (484)    L1M4_orf2#LINE/L1      440   908 (0)  

  chrX_149218620_   2409 AAAGAGGTAAAGTAAGATCCCTCCCATATACCATTCATAAGAATAAACTC 2458
                              i- i    vi  i    v  vi i     vi i  i   v     
  L1M4_orf2#LINE/    440 AAAGAA-TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_149218620_   2459 CAAATGGATTAGGAATCTAAATGTAAAACATGAAACCATACAAATACTGG 2508
                         v        i ?ii i          i vv i    i   v  v vi i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_149218620_   2509 AAGAAAATTT-GGTGAATTTCTCTTTAAACTGGATGTGAGGAAA-GGCTT 2556
                                iv -  ? v vv   iiv i v  v i-  v   v  -  i  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTT 587

  chrX_149218620_   2557 TCTAACTGTGAT-TCAAATCCGGATATGATAAAAGAAAAGACTGATA--- 2602
                         ii  iv i   i-i    vv iv viii i         i iv    ---
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_149218620_   2603 ----CTTGA-CGACATAAAAAAATTTTTTGCATGGCAAA--ACAAAA-CA 2644
                         ----   v - i v  v     v    v   v --    --   vv -  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCA 685

  chrX_149218620_   2645 A-ACATTGAAAA---AAACCACAAACCAATTAAGTGAAATTACTTGCAA- 2689
                          - v v      ---  v     i ---  -ii v    v  i      -
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGA---AT-GGGAGAAAATATTTGCAAA 731

  chrX_149218620_   2690 -CATATATCACAAATAAAAAAAGCTAATATACCTAACACAGAAAAATACT 2738
                         -        v--i    iii --  vi   v vv  i i v   i -   
  L1M4_orf2#LINE/    732 TCATATATCT--GATAAGGGA--CTTGTATCCAGAATATATAAAGA-ACT 776

  chrX_149218620_   2739 CTTAAAATTGAG-GGTAAAA-GACTAAAAACCCAATAGAAAAAGGGAGAA 2786
                             v  i v i-ii     -   v  v        v?     v  iv  
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_149218620_   2787 AAGACATGAACAGATAATTCACACACATAAAAATATCAAAAGGGCTCTTA 2836
                          i  iv    i   i v   v -  v -i  i    vv   v   ivv  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTC-CAAA-GAAGATATACAAATGGCCAATA 874

  chrX_149218620_   2837 AGCATATGAAAAGATGTTCCAAGCCACTCCTAAT 2870
                             i           i  v vii  ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.05 (66 / 63)
Gap_init rate = 0.05 (22 / 469), avg. gap size = 1.68 (37 / 22)  


3543 23.28 1.53 2.30  chrX_149232024_149236007.rev     2580  3494 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_149232024_   2580 TGGAAAGAGATTCCATGTTCATGAATAGGAAGACTCAATATTGTTAAGAT 2629
                                 v  i           i  v        i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_149232024_   2630 GCCAGTTTTTCCCAATTTGATCTATAGATTCAGTGCAATCCCAATCAATA 2679
                          v  i vi i     v        i       ii        v     v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_149232024_   2680 CTCCAGC-ACATTCTTTTGTGGACACCAACAAACTTATTTTAAAGTTTAT 2728
                         ii     -i v  -     ii  v iii    i  v  ii    i  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_149232024_   2729 GTGGAGAGGCAAAAGATCCAGAATAGTTAGTAAAATATTGACAGAGAAGA 2778
                         i    i v    ii  i         ii iv v   v    v i      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_149232024_   2779 ACAAAGTCAAAGGACTGACACTACCTGACCTCAAGACTTACTATAAAGAT 2828
                                iii      v     v  ii ii    i        i    v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_149232024_   2829 AGAATAATCAAGACAGTGTGCTACTGGTAAAAGAATATACAAATAGATCA 2878
                          v i                v      i v   i   v   v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_149232024_   2879 ATGCAGCAGAATGGAGAACCCAGAAATAGACCCACAGGAATATACTCAAC 2928
                            v ii     v    ii         i     i vivv   iv    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_149232024_   2929 TGTTCTTTGACAAAGGAGCAAAGGCAGTAAAATGGAGCAAAGATAGTCTG 2978
                           v i  i     i  v  v   i vi vv     i v  ii       v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_149232024_   2979 TTCAACAAATAGTGCTAGAACAACTGGACATTGATAAGCAAAAAAAAAAA 3028
                                   i     i i         i ?iv i v      i  vi  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_149232024_   3029 AAAAAAAAAAAAAAAGGATGTAGATATAGACCTTACACCCCTCACAAAAA 3078
                         ---------------- v  --  ivivv    i     vivi       
  L1M4_orf2#LINE/    450 ----------------GTTG--GACCCCTACCTCACACCATATACAAAAA 481

  chrX_149232024_   3079 TTAACTCAAAATGAATCATAGACATAAATGCAAAAGAAAAAATTATAAAA 3128
                                      i    ?    v      i  i  vv    i       
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_149232024_   3129 CTCCTGGAGCATAACATAAGAAAAAACTTAAATCACCCCGGATGTGGCAA 3178
                            i i  iv v      i ?iv   ii vvi v   ii  i vv     
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_149232024_   3179 TGACTT-TTAGATACAACACTAACGGCACAAACCATGAAAGAAAGAATTA 3227
                           ii  -       ii    i  vi      i v ii       i   vi
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_149232024_   3228 ATAACCTGGACTTCATTAAAATGGAAAACTTCAGCTCTGCAAAG------ 3271
                             vi          i     vi       iv iv  v     ------
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_149232024_   3272 ----AGAA--TGAAAAGACAAGCCATAGAGTGGGAGAAAACATTTACAAA 3315
                         ----    --           v   i   i          i    i    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_149232024_   3316 AGACACATCAGATAAGGGACTGCTGTCCAAAATAGACAAAGAACTCTTAA 3365
                         vv i i   v           vv i    i    v i            v
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chrX_149232024_   3366 AACTCAACAATATAAGAAAACAAACAACCTGATTAAACAATGGGCCAAAG 3415
                                i    -- i  i     i    ii   ?  v       v  i 
  L1M4_orf2#LINE/    782 AACTCAATAATA--AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chrX_149232024_   3416 GCTTGAACAGACATCTCATCAAAGAAGATACACAAATGGCAAATAAGAAT 3465
                         ii     i      i  vi           i         v      v i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_149232024_   3466 GTGAGAAGATGCTCCACATCTTATTTCTT 3494
                         i   i         v     v????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (129 / 80)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 4.38 (35 / 8)  


2796 27.10 2.91 1.23  chrX_149268237_149276208.rev     4319  5211 (2761)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_149268237_   4319 TGGAAAAACATTCCATGCTGATGGATAGAAAGAATCAATATTGTTAAAAT 4368
                               i i  i     i v      v i    v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_149268237_   4369 GGCCATACTGCCTGAAACAATCTACAGATTCAATATTATTCCTATCAAAC 4418
                            v     v  ii  vii              iiiv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_149268237_   4419 TAACAATGACATTCTTCAGAGAATTAGAAAAAAAAAT---AAAATTCATA 4465
                          vv  iivi v  i  iiv    v v  v  ivvi  ---          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_149268237_   4466 TGGAACCTAAAAGAAACTGAAATAGTCAAGGCAATCCTAAGGAAAAAGAG 4515
                              vivv  i i v iii     i   ii     i i ii  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_149268237_   4516 CAAAGCTGGAGGCATCATGTTACCAAACTTCAAACTGTACTACAATGCTA 4565
                              i      vv   iii v  v  i      viv        v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_149268237_   4566 CAGTACCCAAAACAGCATGATGCTGGTACAATAACAGGCACATAGACCAG 4615
                              vi   i    ii  i i    i i  vi i  i  i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_149268237_   4616 TGAAACATAATAGAGAGCCCGGAAATAATGTTGCACACTTACAACCATCT 4665
                           i  i v   v     i  i       vviiii   i   iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_149268237_   4666 GATCTTCAACAAAGTTGACAA---CAAGTAATGAAGAAAGAAC--TCCAT 4710
                            i   i    i v  v   ---  vvi    ii       i--  -- 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC--T 398

  chrX_149268237_   4711 ATTCAGTACATGGTGCTGGGATAAGTGGCTAGCCATATGCAGAAGATTGA 4760
                         v    ii v            i  v   v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_149268237_   4761 AACTTGACCCCTTCCTTACACCATATAGAAAAATCAACTCCAGGAGGTTT 4810
                          ii v       v   i          v      i     v iiv  v i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_149268237_   4811 AAAGACTTAAATGTAATACTTCAAACTATAAAAATCCTGGAAGATAACTT 4860
                          ?    i         v vi v           v  i i     v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_149268237_   4861 AGGAA-ATATCATTCTGCATATAGGCTCTGGCAAAGATTT------TATG 4903
                            ?i- v   v iv  - iv v  v iv     v i   ------    
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_149268237_   4904 ACAAAGATGCCAAAAGCAATTGCAAAAAAACCCAAAAATTGACAAATAAG 4953
                            ------         vvv    v    vv-      v  i    vi 
  L1M4_orf2#LINE/    598 ACA------CCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGG 640

  chrX_149268237_   4954 ACCT-ATTTAAACTAAGGAACTTCTGCACAGCAAAAGAAACTATCAACAG 5002
                           i -  iv   i   i-     i  ii vv    i  v        v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chrX_149268237_   5003 TGTGAACAGATAACCTACGAAATGGGACAAAATATTCTCAAACTATGCAT 5052
                         v     v   i    i  ii       v        iv    ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chrX_149268237_   5053 CCAACAAAGGTCTAATATCTAGAATCTATAAGGAACTT----AAATCAAC 5098
                          ii i  i  v  vi    i     v     i     i----  v    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chrX_149268237_   5099 AAGCAAAA-----ATAACCCCATTAAAAAGTGG-CAGAGCACACGAATAG 5142
                           vv    -----       v   ?    i   -  i  v ivi      
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chrX_149268237_   5143 ATACTTTTTAAAAGAAGTCATACATGTGGCAAACAAGCATATGAGAAAAT 5192
                          i i  i iv       vi     vi    v  i     i    i  i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_149268237_   5193 GCTCAACATCACTAATCAT 5211
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.64 (37 / 14)  

2683 24.57 4.79 2.46  chrX_149268237_149276208.rev     6289  7102 (870)    L1M4_orf2#LINE/L1        1   833 (75)  

  chrX_149268237_   6289 TGGAGTAATATACCATGTTCATAGATTGGAAAACTCAACATAGTAAAGAC 6338
                             ivi    v          i        i   i  i  v  v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_149268237_   6339 ATTGACTTCTCCCAAATAGACATCCAGGTTTAAC-CAATTCTTATCAAAA 6387
                         ivii iviii       v  iv v   i  i   -    i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_149268237_   6388 TTCAAGTAAGATTTTTTGTAGATATAAAAAAGATTTTTCCAAAATTT-TA 6436
                          i v  ivivv       i   v  vi v   v vv i i      i-  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_149268237_   6437 TGGAAAGG-AAG-----TAGAGGGGCTGAAACAATTGTGAAAAAGAAGAA 6480
                               v -   -----i   ivi  ii       iv             
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_149268237_   6481 TAACCAGT----GTAC---------CTGATTTAAAGACTTATTATAGGGC 6517
                         i  --   ---- v  --------- ii    v  i     i  i ii  
  L1M4_orf2#LINE/    201 CAA--AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_149268237_   6518 TACATTAATCAAGACTGTGCAGTAATGGCAGAGGGACAGACAGATA-AT- 6565
                             v          v   ii   v     v i   i     v   -  -
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_149268237_   6566 --TGGAACTGGACAGAGAACCTAGAAATAGACTCACGTAGATACGCCAAA 6613
                         --     iv i iv    ii i       i  i  iii vv  i viv  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_149268237_   6614 CTGATTTTTGACAAAAGTGCAAAAGCAATTCAGTGGAGGAATAATAGCCT 6663
                         i       i     ii    v  ii v     i   i i  v     i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_149268237_   6664 TTTCAACACATGGTTCTGGAA--------TATCTATAGGCAAAACA-TGA 6704
                                 v     v    i --------  ? i i v      v -   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_149268237_   6705 ACTTCAATCTATACCTTATACCTTACACAAAAATTCACTCAAAGTG-ATC 6753
                          v  vi i iv     i i   v  i         v       i  -   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_149268237_   6754 ACTGAGCTAAATTTAAAATATAAAACTATAAAAGTTTTAG--GAAAA-AT 6800
                          ?v  v      v   i vv             v i    --     -  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_149268237_   6801 AGGAGAAAATCTTCTGGATTTAGAGCTAGGCAAAGAGTTCTTTCTTAGAC 6850
                            ? v        vv  ii v i i       v i----         i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG----TTTCTTAGAT 594

  chrX_149268237_   6851 GTGACACCAAAAGCATAACCCATAAAAGGAAAAATTCATAAACTAGACTT 6900
                         i              i  v v i     i      vv     i i     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_149268237_   6901 CATCAAAAATAAAATCTTTCGCTCTGTGAAAGACCCTGTGAAAGACCCTG 6950
                                 v     v    -----    -------  vii  i   v  i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTT-----TGTG-------CTTCAAAGGACACTA 682

  chrX_149268237_   6951 TGAATAGAATGAAAAGTCAAGCTGTAGACTGGGAGAAAATATTTGCAAAC 7000
                          v  v i i       v   v iii   v                    i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_149268237_   7001 CTTATGTTTAACAAAGGACTTGTATCTAGAGTGTATAAAGAA-TATCAAA 7049
                          v   i i i i  i           i   i i         - v i v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_149268237_   7050 ACTTAACAGTAAGAAGACAAACCATCCAATTAGAAAACGGGCAGAAGCCA 7099
                            i  i i   i        iv i      ?i    i     i i -- 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG--A 830

  chrX_149268237_   7100 TTT 7102
                            
  L1M4_orf2#LINE/    831 TTT 833

Transitions / transversions = 1.61 (121 / 75)
Gap_init rate = 0.02 (19 / 833), avg. gap size = 3.11 (59 / 19)  

 431 12.62 0.00 9.71  chrX_149268237_149276208.rev     7379  7481 (491)    L1M4_orf2#LINE/L1      816   908 (0)  

  chrX_149268237_   7379 AAAATGGGCAAAAGATATGAAGAGGCATTTCACTGAATTTCACTGAAGAG 7428
                                     i   v    v  i      ------- i  ---    i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTC-------TCCA---AAGAA 855

  chrX_149268237_   7429 GATATACAGATGGCAAGTAAACACATGCAAAGACGTTCAACATCATTAGC 7478
                                 i     v i   i      v     i i         ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_149268237_   7479 TAT 7481
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.02 (2 / 93), avg. gap size = 5.00 (10 / 2)  


 721 16.55 8.97 0.00  chrX_149277425_149279398.rev      469   613 (1361)    L1M4_orf2#LINE/L1      177   334 (574)  

  chrX_149277425_    469 CAAAACATTATTGAAAAACAAGAA-----------GACTCACG--TCCTG 505
                                v v        v     -----------       i--   ii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_149277425_    506 ATTTTAAGACTTACCACAAAGCAATAGTAATCAAAACAATGTAGCACTGG 555
                             i  i      i       v i         i   i   i i     
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_149277425_    556 TATAAGTATAGACATATAGACCAATGAAATAGGCTTGAGAATTCAGAAAT 605
                         i     v             i     i     iv      i i       
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chrX_149277425_    606 AAATCCAT 613
                            i    
  L1M4_orf2#LINE/    327 AAACCCAT 334

Transitions / transversions = 3.00 (18 / 6)
Gap_init rate = 0.01 (2 / 158), avg. gap size = 6.50 (13 / 2)  

2695 17.94 3.73 0.18  chrX_149277425_149279398.rev      921  1483 (491)    L1M4_orf2#LINE/L1      326   908 (0)  

  chrX_149277425_    921 TAAACCCATTAATCTATGGCCAATTGATTTTCAACCAGGGTGCCAACACC 970
                                  vv  i     i            i  v          v   
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_149277425_    971 ACTCAATGAGGCAAAGATTAGTCTT--CAACAAATGGTAGTGTGACAACT 1018
                          i      i  -     v       --           iv  v       
  L1M4_orf2#LINE/    376 ATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_149277425_   1019 GGATATCCACAGAGAAAAGAATGAAGTTGGACTCCTACCTTATATCATAT 1068
                              ?     viv                  i       i i i     
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_149277425_   1069 ACAAAATTCAGCTCAAAACTGATCAACAACCTAAACATAGGAGTTAAAAC 1118
                               v i i       iv     ?vi       ii  i   i      
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_149277425_   1119 TGTAAAACTCTTAAAAGAAAACATAGAAGTAAATCTTCATGACCTTGAAT 1168
                          i           i            i?          i        ii 
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_149277425_   1169 TTCGCAATGGAA-CTT---TATGACCCTAAGAACATGAACAACAACA-AC 1213
                          vv       vv-   ---      v i  i i  ii i      v - v
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_149277425_   1214 AAAATAGATAAATTGGACTTCAT-------AAAAACTTTTGGGCATCAAA 1256
                                                -------           v  v     
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chrX_149277425_   1257 GGACGTTATCAAGAAAATGAAAAGAC---CTACGGAATGGGAGAAAACAT 1303
                             ii          i         --- i  i             i  
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_149277425_   1304 TTGCAAATCATATGGCTAATTAAAACCTAGTCTCTAGAATATACACATAA 1353
                                      iv  i  v iiiv  v  v  i        i v v  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_149277425_   1354 CACCTAAAATGCAACAATAAAAA---AGACAACACAAT-AAAAAACAGGC 1399
                          v i  v  iv   i        --- i i   v    -?     ii   
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_149277425_   1400 AAAGGACTTAAATAGATTTATTCCCAAAGAAGATATATAAATGGCCAACA 1449
                               i  i      iv v ii              i          i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_149277425_   1450 AGCATATGTAATGATGTTCAACATTATTAGTCAT 1483
                             i   v  v    i       i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (61 / 36)
Gap_init rate = 0.02 (9 / 583), avg. gap size = 2.44 (22 / 9)  


 286 20.98 0.70 9.09  chrX_149545084_149547035      342   484 (1468)  C L1M4_orf2#LINE/L1   (82)   826   696  

C chrX_149545084_    484 AATACATCCC-CAAAATTTCATAAGAAAATATTTGCAAATCACATCTCTG 436
                           v   v   -  i   ---ivi                   i  v    
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAAT---GGGAGAAAATATTTGCAAATCATATATCTG 742

C chrX_149545084_    435 GCAAGGTATTAATACCCAGAACATATTAAAAAACTCCTACGTCTCAACAG 386
                         ii    v i vi  i      i    -   i     i   iv     i -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATAT-AAAGAACTCTTACAACTCAATA- 790

C chrX_149545084_    385 CAACAACAAAAACCACAAACATCACAAATAACAACTGTTGGCAA 342
                         ----- i     v-     i v v   v ? v  v  --     
  L1M4_orf2#LINE/    791 -----ATAAAAAG-ACAAATAACCCAATTWAAAAATG--GGCAA 826

Transitions / transversions = 1.23 (16 / 13)
Gap_init rate = 0.05 (6 / 131), avg. gap size = 2.33 (14 / 6)  

2704 22.33 7.56 3.72  chrX_149545084_149547035      600  1459 (493)    L1M4_orf2#LINE/L1       16   908 (0)  

  chrX_149545084_    600 TGTTCATGTATTTGGATGATTCAATATAGGGAAGATGTCACTTCTCCCCT 649
                                 v   -   v  i i     v vv      v  v v      v
  L1M4_orf2#LINE/     16 TGTTCATGGATT-GGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chrX_149545084_    650 AATTGATATACACATTTAGCACAATTCCTATCAAAATCCCAGAAAGATTT 699
                                v    v   i i i    i                vvivv   
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chrX_149545084_    700 TTTGTAGA--T--ACA----GATT-TAAAACTTATATGGAAAGGCAAAGG 740
                             i   -- --   ----   i-     i i         v    i  
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chrX_149545084_    741 AACTGAAGTAGCTGAAACAATTTTGAA------GAATAAAGTGGGAAGAA 784
                          v iii i    ii       i     ------   i     v   i  v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chrX_149545084_    785 TCAG---TCTAAATGACTTCAAGACATGCTGCATAGCTACAGTAATCAAG 831
                            v---  iv   ---     i  v i  i  v                
  L1M4_orf2#LINE/    215 TCACACTTCCCAAT---TTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chrX_149545084_    832 AC-------TA-TGGCAGAGGTACAGACACATAGATCAGTGGAACAGAGC 873
                           -------  -     v i v i     i        i     i   ii
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAAT 311

  chrX_149545084_    874 AGAGAACCTAGAAGTCATCCCACAGAAATATGCTCAGCCGATTTTTTTTT 923
                         v    ii i    i v v    i v vv    v   iii      -----
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT----- 356

  chrX_149545084_    924 TCCACCAAGACATGAAAACAATTTAATGGTTGAAAGA-TAGGCTTTTCAA 972
                         - v  v i iiiiv  i  v   i     v-      -   v        
  L1M4_orf2#LINE/    357 -CGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTCTTTTCAA 404

  chrX_149545084_    973 CAAATACTGCTGGAGTAATTGGACATCTATAGACAAAAAAACAAAACAAA 1022
                              iv      iii  i    i ? i i vi     i  ii  iivii
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_149545084_   1023 ACAAAACAAAACCTTGATCTAAGTCTCACATCTTATACAAAAATTAACTC 1072
                           ---------  -----   --i      i v                 
  L1M4_orf2#LINE/    455 AC---------CC-----CTA--CCTCACACCATATACAAAAATTAACTC 488

  chrX_149545084_   1073 AAAATGAATCACAAACTTAAA---AA----------TATAAAACTTTTAC 1109
                               i    ? i  i    ---  ----------         i   v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_149545084_   1110 AGAAAAA---AGA---AAATCTTAAGGATCTGGGGCTAGGTAAATCATTC 1153
                          ii    ---  i---       viv  i  v   i    i  - vi  -
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTT- 586

  chrX_149545084_   1154 TTCTTAAACTTTACACCAAAAGCACAATCCATAAAAGGAAAAA------- 1196
                         -     i iv v               v v i     i     -------
  L1M4_orf2#LINE/    587 -TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_149545084_   1197 ATTG------ATCAAAATTTAAAATCTTTTGCTCTGTGAAAGACTCTG-- 1238
                             ------         v    -      iv  vii  i   v  i--
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATC 684

  chrX_149545084_   1239 -AGAAGATGAAAAGACAAGCTACAAAGTGGAAGAAAATATTTGCACACCT 1287
                         -    ii           v i   i i   i              v i v
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_149545084_   1288 CATATCTGACAGATGACTAGTATTTAGAATATATAAGGAATATTTGAAAC 1337
                         i        i iiv    v    ii           i   ivi  iv   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_149545084_   1338 TCGACAGTAAAAACATCAAACCATCCAATTAGAAAATGAGCAAAAAACAT 1387
                           i i i      v -    iv i      ?i      i     ii iv 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_149545084_   1388 GA---GGCATCTCAACAAAGAAGATATACACATGGCAGGTAAGCACGTGA 1434
                           --- i   i  vv               v     vii       i   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_149545084_   1435 AAAGACGTTCAACATCATTTCTCAA 1459
                              i i         ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (120 / 69)
Gap_init rate = 0.03 (28 / 893), avg. gap size = 3.46 (97 / 28)  


4191 13.72 1.19 1.58  chrX_149592107_149593856.rev      502  1259 (491)    L1M4_orf2#LINE/L1      154   908 (0)  

  chrX_149592107_    502 AAATTCAAAGGATCTGGAATAGCTAAAATAATCCTGAAAAAGAA---CAA 548
                             v   i   i ii       i    i    i          ---   
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_149592107_    549 AGTAGGAGGACTCATACTTCCCATTTTCAAAACTTACCACAAAGCTACAG 598
                            v          i        v             i            
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_149592107_    599 TAATCAATGCCAGCA--GTGCTGGCGTAAGGACAGACATGCAGATCAATG 646
                                - v   ii--  i     i      i      ii         
  L1M4_orf2#LINE/    254 TAATCAA-GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_149592107_    647 GAACAGAATAGAAAGCACAGAAATGAACTCTCTGACATTTACGGTCAACT 696
                            i     v  i  iv       i   i vi--       i      i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCAT--ACATTTATGGTCAATT 350

  chrX_149592107_    697 GATCTTCAACAAGGTTGGCAAGAAAATTGAATGAGGGAAAGAA-AATCTT 745
                            i   i      v  v     vv   v    -         - i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTT 399

  chrX_149592107_    746 TCCAACAAATGGTGCTGGGACAGCTAGATAGCCAACACACAAAAGAATGA 795
                          i                    i  i    ?   -  ii           
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCA-CATGCAAAAGAATGA 448

  chrX_149592107_    796 AGTTGGATCCTTAATTCACACCGTATACAAACGTTACCTCAGAACAGATC 845
                                i  i  vi       i        vi   v    i  ii    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_149592107_    846 ACAGACCTAAATGTAAGACCTAAAAGTATAAAGCTCTTAGAAGAAAACA- 894
                          ?                v      v      i                -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_149592107_    895 -GGAGCAAATCTTCATGACTTTGGGTTAAGCAATGGTTTCTTAGATATGA 943
                         -  ? i        i    i        i                     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_149592107_    944 TACCAAAAGTGTAAGCAGCAAGAGAAAAAATAGATAAATTGCAGTTCATC 993
                         i        iii     i   i                   v v      
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_149592107_    994 AAAATTAAAAACTTTTGTGCTTCAAAGAACACCATGAAGAAAGTAAAAAA 1043
                                                    i    i  v        i    i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_149592107_   1044 AAACAACCCCTAGAGTGGGAGAAAATTTTTGCAAATCATGTATCTTATAA 1093
                          --      vi   i           v            i     v    
  L1M4_orf2#LINE/    699 A--CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_149592107_   1094 GGGACTTGAATATATAAAGAATGTATAAGGAACTCTTACAACTCCATAAT 1143
                                 ----   vv     i     i               v     
  L1M4_orf2#LINE/    747 GGGACTTG----TATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_149592107_   1144 AAAAAGGACAAACACCACAATTTTAAAATGAACTAAGGAGCTGAATACAC 1193
                               -     i v v     ?v      ii v     vi      v  
  L1M4_orf2#LINE/    793 AAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_149592107_   1194 ATT-CTCCACAGAAGATATGCAAATGGCCAATAAGCACATGGAAATATGC 1242
                            -     v         i                     i   v    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_149592107_   1243 TCAACATCATTAGTCGT 1259
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (66 / 34)
Gap_init rate = 0.02 (12 / 755), avg. gap size = 1.75 (21 / 12)  


1089 14.98 8.37 2.64  chrX_149829893_149832924      996  1222 (1810)    L1M4_orf2#LINE/L1        2   241 (667)  

  chrX_149829893_    996 GGAAATAGACATTCCACGTTCATGAATGGGAAGGTTTAATATTGTTAAGA 1045
                              --  i  i   i       i  v     ii               
  L1M4_orf2#LINE/      2 GGAAA--GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_149829893_   1046 TGGCAATACTCCTGAAATTGATCTA--GA----ACGCAATCTCTATTAGA 1089
                                     iv           --  ----        i    i i 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_149829893_   1090 ATCCCAGCTGGCTTCCTCTAGTAGAAAT---CAGGCTGATTCTAAATGTC 1136
                                   v   -- i v i      ---  i      i     vv  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_149829893_   1137 ATATAGAAATTCAAGAGATGCAGGAGATACCCAGATCAATCTTGAAAA-- 1184
                             i     v    i  iv   i --  v   i v            --
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAA--TAGCCAAAACAATCTTGAAAAAG 195

  chrX_149829893_   1185 -----CA--GTTGGAGGATTCACATTTCTTGATTTCAAAACT-ACT 1222
                         -----  --         i     i   iii           -   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

Transitions / transversions = 2.40 (24 / 10)
Gap_init rate = 0.04 (9 / 240), avg. gap size = 2.78 (25 / 9)  

3400 16.50 5.59 1.96  chrX_149829893_149832924     1825  2539 (493)    L1M4_orf2#LINE/L1      168   908 (0)  

  chrX_149829893_   1825 CAGAGTGACTGAGACTCCGTCTCAAAAAAACAAAAACAAA--CAAAAAAC 1872
                             i ii ii i  --vi   ii     i-  i      --iii ii  
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAAC--AATCTTGAAAAAG-AAGAACAAAGTTGGAGGAC 214

  chrX_149829893_   1873 CCA--------------AAAACTTA-----AAGCTACAATAATCAAGACG 1903
                         i  --------------        -----        i          i
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chrX_149829893_   1904 GTGTAGTACCAGCATAAGGACAGACATATAGGCCAAT-----ACAATTGT 1948
                             i    ii         i          ii    ----- v     v
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chrX_149829893_   1949 GAGTCCAGAAATGAACCCAGACATTTGTGGCCAACTGATTTTTCAATGGG 1998
                                     i      v      i   i   i       - i iii 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT-CGACAAG 363

  chrX_149829893_   1999 GATAAAAATAACATTCAATGGGGGAA--ATAAT--TTTCAACAAATGATG 2044
                          i ivv  v v            i  --   i --            i  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_149829893_   2045 TTGGGACAACTGGATATCCATGTGCAAAGGAATGAATTTTGACCCTTCCC 2094
                         i               ?   ii      i       v  v     i v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_149829893_   2095 TCACAGCACATTCAAAAATCAATTCAAAATAGATGAAAGACCCAAATGTA 2144
                              v  i  v       i  i       i   v ?     i       
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_149829893_   2145 AGAGCTACAACTATAAAATTCTTAGTAGGAAACATAAGTGTGAAT-TTCA 2193
                                v          i      v  i       i ?  i   -   i
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_149829893_   2194 TGACCTTGGATTTGGCAATAGTTTCTTAG----GACACCAAAAGCATGTG 2239
                                  i  v      i         ----             iiv 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_149829893_   2240 CAACTAAAGAAAACAATAGATAAGTTGAACTTCATTAAAATTAAAACAAA 2289
                             v        -         i   i       i          ----
  L1M4_orf2#LINE/    614 CAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAA---- 658

  chrX_149829893_   2290 CAAAACATTTGTGCTTCAAACAGTACCACCAGGAAAGTGAAAAGACAACC 2339
                         ----  v             viii  i i  i                  
  L1M4_orf2#LINE/    659 ----ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_149829893_   2340 TACAGAATGGGGGAAAATATTTGCACAACGTATATCCTATAGGGATCTAG 2389
                         i          i             v v i      iv   i  iv  v 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_149829893_   2390 TATTCAAAATATATAAAGGACTATTACAACTCAGCAATAAAAAGACAA-- 2437
                            i  i           i   v          ii             --
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_149829893_   2438 --CCCAATTTAAAAAATGAGCAAAAGATCTTAACAGACATTTCTCCAAAG 2485
                         --       ?     -  i     i   i v  i                
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_149829893_   2486 AAGATGTATAAATGGCCAATAAACACATGAAAA-ATCCTCAGCATCATTA 2534
                              i  i             i          -  v    i     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_149829893_   2535 GTCAT 2539
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.93 (85 / 29)
Gap_init rate = 0.02 (16 / 741), avg. gap size = 3.38 (54 / 16)  


 453 26.47 4.41 5.39  chrX_149901807_149904121.rev        5   208 (2107)    L1M4_orf2#LINE/L1       37   238 (670)  

  chrX_149901807_      5 AATATTATAACGATTTCAATTCTTCCAAAATTGATCTACAGATCCAATGA 54
                               i v v   vv    v  i  v                i   i -
  L1M4_orf2#LINE/     37 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACG- 85

  chrX_149901807_     55 CAATGCTAATCGAAATTCTA----CATTTTCCATGGAGCCTGA-AAACTG 99
                             v iv   i    i i ---- v    iiiii  ivi   -  i   
  L1M4_orf2#LINE/     86 CAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTG 135

  chrX_149901807_    100 GCTCTAAAATGTATATGAAAGAGCAAATCGCACAAAAAA---AAATTATA 146
                         iii       vi     i  iv    ivvi v  i  v ---   ---- 
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA----A 181

  chrX_149901807_    147 CATTTCTGAATAAAAAGAATAAGAGCTGGGCACAGTGGTTCACACTTGC- 195
                           v ii    v  i     i  -  i   ----  - ii        v -
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAA-AGTTGG----AG-GACTCACACTTCCC 225

  chrX_149901807_    196 AATTCTAACACTT 208
                             ii  v    
  L1M4_orf2#LINE/    226 AATTTCAAAACTT 238

Transitions / transversions = 1.70 (34 / 20)
Gap_init rate = 0.04 (9 / 202), avg. gap size = 2.22 (20 / 9)  

 854 26.02 0.81 2.44  chrX_149901807_149904121.rev      600   845 (1470)    L1M4_orf2#LINE/L1        3   244 (664)  

  chrX_149901807_    600 GAAAGGTATCTTGTATTCATGGACTGGCAGAATTAATATTGTTAAAATAT 649
                              i    iii i        i   v   v             i  iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_149901807_    650 CCATAGTGTCCAAAGTAATTTATAGATTCACCGCAATCCCTCTCAAAATT 699
                          v   v vi     v i  i  i       v          v       i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_149901807_    700 CCAA-TGCCACTGTCCACAGAAATAGAAAAAACT-ATTTTGAAATTAATA 747
                            i-    -i v iii       v  v  i-  -  ii i     v   
  L1M4_orf2#LINE/    103 CCAGCTGCC-TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATA 150

  chrX_149901807_    748 TGGAACAACAACAACAAAAACTTGAATAGCCAAGGCAGTCTTAAGCAAAA 797
                              vvi   ----iii v iv          ii  i    i iv  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAA----GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_149901807_    798 AGAACAAAGCTGAAGGCATTACACAACCTGACTTTAAAATATACTACA 845
                                  i  i   vv i    vv  ii i  i    iv       
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

Transitions / transversions = 1.78 (41 / 23)
Gap_init rate = 0.02 (5 / 242), avg. gap size = 1.60 (8 / 5)  

2586 23.05 1.80 1.35  chrX_149901807_149904121.rev     1158  1825 (490)    L1M4_orf2#LINE/L1      238   908 (0)  

  chrX_149901807_   1158 TACTACAAAGATATAGTAGTCAAAACAGCATGGTACTGGCATAAAAACAG 1207
                                   v  i    i    i    ii              ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_149901807_   1208 ACACGTAGACCAATTGAATCGTATAGAGAGCCCAGAAATAAACCCATACA 1257
                            ii    i    v    v v  v     i                   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_149901807_   1258 TCTACAATTAATTGCTTTATG-CAAATGTGCCAAGAACGCACATTGGGGG 1306
                          i  iii i     v   vi -   iv         v iiv  v     i
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_149901807_   1307 AAGGACAGTCTCTTCAATAAATGGGGTTGGGGAAGCTGGATATCCACATG 1356
                            i i     i     i      v i    iv i       ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_149901807_   1357 CAGAAGAATGAAAATGAACTCTTATTTCACCACTTGTACAAAA-TCAACT 1405
                           i         iv  i  i i  ii    vv v i       - i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_149901807_   1406 CAAAATGGATTAAAAACTTAAACATAAGACTTTCAACTATAAAACTACTA 1455
                                   i ? i  i    ii     vi vv            vi  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_149901807_   1456 GAAAAAAACATAGG-GTGAGGCTCCATGACATCAATCTGGGCAGAAATGT 1504
                            i          -  i iv  i i    v iiivi i    ivii v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_149901807_   1505 ATTAGATGTGAACCTAAAAACAAAAGTAACTAAAGCAAAAATAGACAAAT 1554
                         v      i   vv i    i  v   i   v    v         i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_149901807_   1555 GGGATTGCATCAAACTAAAAAGCTTCTACACAGCAAATGAAACAATTTAA 1604
                         v   i v       v v    i   i iii vv    v  v  v  i-- 
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC--A 685

  chrX_149901807_   1605 ATAGAATGAAGAAACAACCCACAGATTGGGACAAAATATTTGCAAATCAC 1654
                          v i i    i i            v     v                 i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_149901807_   1655 ACATC----AAGGGGCTAATATCCAAAATATACAAGGAACTCAAACTACT 1700
                          i   ----     i  vi      i      i  i      vv  v   
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_149901807_   1701 CAATAACAAGAA-----ATAACCCAATCTAAAAATGGGTAAAGGGCTTGA 1745
                               i  i  -----          i?         i     ii    
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_149901807_   1746 ATAGAAATTACTCAAAAAAAGAAAAACCACACAAAATAGCCAACAGATAT 1795
                              v   v   v   i    v v  ------    i     i iii i
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATAC------AAATGGCCAATAAGCAC 879

  chrX_149901807_   1796 TTTGAAACAATGCTCAACATCTCTAATCAT 1825
                         v -    vi            v????????
  L1M4_orf2#LINE/    880 AT-GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (95 / 56)
Gap_init rate = 0.01 (8 / 671), avg. gap size = 2.62 (21 / 8)  


2837 27.27 1.31 1.86  chrX_149945226_149950983.rev     4355  5267 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_149945226_   4355 TGGAAAAACATTC-ATGCTCATGGATAGGAACAATCAATATTGTCAAAAT 4403
                               i i  i -   i        v    v v i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_149945226_   4404 GGCCATACTGCCCAAAGCAATGTATAGATTCAATTTGCTATTCCTATCAA 4453
                            v     v      vii  v  i        i--  v  i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAAC--GCAATCCCTATCAA 98

  chrX_149945226_   4454 ACTACCAATGACATTCTTCACAGAA-TTGGAAAAAAAACAATTTTAAAAT 4502
                          v v   iivi v  i  ii     -   --- v  ivii  ii      
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAAT 145

  chrX_149945226_   4503 TCATATGGAACCAAAAAAGAGCTCAAGAGCTCAAATAGCCAAGGCAATCC 4552
                                   viiv  ii  - i  i-------         ii     i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGA-CCCAG-------AATAGCCAAAACAATCT 187

  chrX_149945226_   4553 TAAGCAAATAGAAAAAAGCTGGAGGCATCCCGTTACCTGACTGCAAACTA 4602
                          i iv  iv    v    i      vv  v ii v  ii i v    viv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_149945226_   4603 TACTACAAGGCTACAGTAACCAAAATAGCATGGTACGGGTACAAAAGCAG 4652
                                 i          i   i i  ii      v  i i  iiii  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_149945226_   4653 ACACATAGACCAATAGAACAGAAT--AGATGCACAGAAATAATGCCACAC 4700
                            i     i    i   i     --   - iv         vv   i  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGA-GTCCAGAAATAAACCCATAC 336

  chrX_149945226_   4701 ACCTACAACCATCTGATCTTTGATAAACCTGACAAAAGCAAGCAATGAGA 4750
                          ii  iiii  vi    i  i  i  ivv  v   i v  vv     i i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chrX_149945226_   4751 AAAGGACTCCCTATTCAATAAATGATACTGGGATAACTGGCTAGCCATAA 4800
                             i ivvi  v     i     i i      i      v  ?   i v
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chrX_149945226_   4801 GCAGAAGATTGAAACTGGACCCCTTCCTGACACCATATACAAAAATCAAC 4850
                            i    v    ii         v   v                 i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chrX_149945226_   4851 TCAAGAGGGATTAAGGACTTAAATATAAAACCTCAAACTATAAAACCCCT 4900
                             i v    i ?i   i     i   i v  v            i i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chrX_149945226_   4901 GGAGGATAATGCAGG---AAATACCATTCTGAACATAGGGCCCAGCAAAG 4947
                         i  i  v  iii   ---    -- -   vvi  v v   iivi    v 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATG 583

  chrX_149945226_   4948 ATTTCATGACGAAGATGCCAAAGGCAATTGCAACAAAAATTAAAATGAAC 4997
                         i    v iivv v  ii     i   vvv         ivv     ii i
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_149945226_   4998 AAATGAGACCTAAGGAAACTAAAGAGATTCTGCACAGCAAAAGAAACTAT 5047
                             vi   i v vv   v v  i iv  i  ii vv    i  v     
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_149945226_   5048 CAACGGAGTAAA----CAACCGACAGAATGGGAGAAAA-ATTTTCAAACT 5092
                            vii   i  ----     v                -    v    ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_149945226_   5093 ATGAATTCAACAAAAGTCTAATATCCATAATCTATCAGGAGCTTAAACAA 5142
                           iv  iii i  ii v  vi      v   v   v i  i  ivv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_149945226_   5143 ATTAACAAGAAAAAAATGAACAACCTAATAAAAAAGTGGGCAAATGACAT 5192
                         v i  i  v     i ii  i    i   v?    i        v  iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_149945226_   5193 GAATAGACACTTTTCAAAAGGAGACATGCATATGGCCAACAAGCATATGA 5242
                                  i  i  v    i   i  i  v        i     i    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_149945226_   5243 AAAAATGCTCAACATCACTAATCAT 5267
                            i             ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (154 / 92)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.23 (29 / 13)  


2416 21.85 7.33 2.85  chrX_149988258_149989941.rev      457  1193 (491)    L1M4_orf2#LINE/L1      139   908 (0)  

  chrX_149988258_    457 CTAAA---CATGTAGAAAACCACAAGGCAC-----ATA---AAAATTAAA 495
                              ---   i i    --ii     v  -----   ---    i--  
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAA--TGCAAGGGACCCAGAATAGCCAAAAC--AA 184

  chrX_149988258_    496 TTGTTGAAAAGGAA---TAAAGCTGGAGACATCACACT--ATGACTTCAA 540
                          i-       i   ---i    i     ivv       --vii i     
  L1M4_orf2#LINE/    185 TC-TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_149988258_    541 AATACACTACAAAGCTATAGTAACAAAAACTGCATAGTACTGGCATAAAA 590
                           ivi            i     iv  i  v ii i            ii
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_149988258_    591 ACAGACACATAGACCAATAGAACAGAAC-------CCAGAAATAAATTCA 633
                          i     i     i    i   i    i-------           ii  
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chrX_149988258_    634 TGTACTTACATCCAACTGATTTTCAACAAAGATGCCAAGAACATTCAATA 683
                          ii i   iivi   i        i    i i        v        i
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chrX_149988258_    684 GGAAAATGAT-GTCTCTTCAATGAATGGTGCTGAGAAAACTGGCTATCTG 732
                           i   vi  -    i     ii          i  v      v  ? ii
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chrX_149988258_    733 TATGCAGAAAAATGAAACTAGACCCCTATATCTCACCACATAAAAAAAT- 781
                         i     i  i      ii i        iv  v     i   v      -
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chrX_149988258_    782 ----CAAAATAGATTAAATACTTAAATGTAAAGCCTGAAACTATGAAACT 827
                         ----      i   i ? v  i         iiv  i       i     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chrX_149988258_    828 ACCAGAAGAAAACATTGGAG-AAATACTTCAGGACATTGGTCTGGGCAAA 876
                         vii            v  ? -    -    iv   v    vi i     v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_149988258_    877 GATTT-TGGGGTAAGACCTCAAAAACACAGGTAACAAAAACAAAAATAAA 925
                          i   - vi i  v   vi     i    i i       iv       i 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_149988258_    926 CAAATGGGGCTT----AAACTAAAAAAGTTCTGAACAGCAAA------T- 964
                         i    v  i   ----   v v     v  i  vi vv    ------ -
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_149988258_    965 ----GAAAGT--AGAGACAACCTGTTGAATGGGATAAAATATTTTCAAAA 1008
                         ----      -- i        iiiv        v         v    v
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_149988258_   1009 TATGCACCTGATATGGGAATAATAATGTCCAGAAAGTACAAGGAACTC-- 1056
                         i  ii i      v    v vi  ---       vi  i  i      --
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTA---TCCAGAATATATAAAGAACTCTT 779

  chrX_149988258_   1057 --AAATCAACAGGAAACAAACAAACAAACAAACAAGTAATCCA-TTAAAA 1103
                         --  v    i ------------ i   v i    i   i   -  ?   
  L1M4_orf2#LINE/    780 ACAACTCAATA------------ATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_149988258_   1104 AGTGGTCAAAGGACATGAATAGATATTTCTCAGAAGAAGATATACAAATG 1153
                          i   v       iv        i       vi                 
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_149988258_   1154 GACAACAGATATATGAAAA-ATGCTCAACATCACTAATCAT 1193
                          v   i iii i       -             ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.27 (109 / 48)
Gap_init rate = 0.03 (23 / 770), avg. gap size = 3.26 (75 / 23)  


1324 27.33 7.42 4.74  chrX_150025113_150026737.rev      502  1134 (491)    L1M4_orf2#LINE/L1      259   908 (0)  

  chrX_150025113_    502 AAAACGATGTGGTATTGGTGCAAGGATAGAC--------TAATGTAACAG 543
                           i  ii       i   iii          --------i    v  i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_150025113_    544 AATAAACAGTCCAGAAACAAAGAGATAAAAAGAGAGACATGTTTATATAT 593
                            vi v          i   vvv   ----------------i  v   
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATA----------------CATTTAT 342

  chrX_150025113_    594 GATTACCTAAATGGCAACAAAGTCTTTACTGCAGTTCAGTGGGGTAAAGT 643
                          i i vi i v vv i    i vivii vvi vi    i     -    v
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGA 391

  chrX_150025113_    644 ATGGTCTTTTCAATAAATGGTGATAAAATGA--AAATATGAACCCTGGCT 691
                           i          i        v iii ii --ii   ?vv  -------
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC------- 434

  chrX_150025113_    692 ATACAAAAACATGGACTTTGATTCCTAACCCACACCATACACAAACAAAT 741
                           i     iv   i v  v  ii    v i         i     --   
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA--AAT 482

  chrX_150025113_    742 TAACTTGAGATGGAACATAGACTTAAACGTGAAAGGCAAAACTATAAGGT 791
                              ii i     v  ?    i    i  i i  vi          iii
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chrX_150025113_    792 TTCTAAAATAAAAATTAGGAGAATACATTAATTATATTAGAATAATCAGA 841
                          ii  i  v    vv    ? v v iv  vi v iv  i iv  iv  iv
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chrX_150025113_    842 AATTTCTTAAA-----CAC--AAAGCACAGTCA------GAAAAACT-GA 877
                         ii       i -----   --        iv  ------      v -  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chrX_150025113_    878 TAAATTGAACTTTAT-AATATTAAAGATTTTTGTTCATCAAAAGATACAA 926
                                i    i  -  v      i i      v v     i  i  v 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_150025113_    927 TTAAGAGAGCAAAAAGGCAAACCACCAACTGAGAGAAGATATTCATGAAA 976
                          i    i  ii     i   v    vi v  i     i     iii-   
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC-AAA 731

  chrX_150025113_    977 TTGGCATATAT----------AC--ACATGCA---TATC-------CTGT 1004
                          ---       ----------  --ii  v  ---   v-------  v 
  L1M4_orf2#LINE/    732 T---CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_150025113_   1005 TACAAGTCTATAAGAAAAAGACAGAAACTTCCATTTTAAAATAGTCAAAA 1054
                              v  v    v         i v vii v   ?v     i v    i
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

  chrX_150025113_   1055 TATTTGTTCAGGGCCTTCAATAAAGAAAATATTTAAATGGTCAATAATCA 1104
                         v     vvi  ivvi   vvi      i    vi      i      v  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chrX_150025113_   1105 TGTAAAAAGACGATTAACATCATTGCTCAT 1134
                         ii i      i v i       ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (101 / 68)
Gap_init rate = 0.03 (17 / 650), avg. gap size = 4.53 (77 / 17)  


3223 26.80 0.78 0.22  chrX_150038373_150044784     5017  5919 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_150038373_   5017 TGGAAGAAAATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 5066
                              ii v  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150038373_   5067 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5116
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150038373_   5117 TACCAATGACTTTCTTCACAGAATTGGAAAAACT-ATGTTAAAGTTCATA 5165
                          v   iivi i  i  ii     v v  v  i  -  vi    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_150038373_   5166 TGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCT-AAGCAAAAAGAA 5214
                              viiv  ii  v  viv        i       -i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_150038373_   5215 CAAAGCTGGAGGCATCACGCTACCTCACTTCAAACTACACGACAAGGCTA 5264
                              i      vv    i  v  iv i      vivi  v    i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_150038373_   5265 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACAAA 5314
                               i   i    ii         i iv ii i   v       iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_150038373_   5315 TGGAACAGAACAGAGCTCTCAGATATAACACCACACATCTACAACCATCT 5364
                              i    iv   vvii    v    vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_150038373_   5365 GATCTTTGACAAACCTGTCAAAAACAAGAAATGGGGAAATGATTCCCTAT 5414
                            i  i     ivv  i   i v  vvv          vi  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_150038373_   5415 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGACAGCTGAAA 5464
                          i  i              v      v  ?   i   i i viiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_150038373_   5465 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 5514
                         i    i    v   i     v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_150038373_   5515 AGACTTAAATGTTAGACCTAAAAACCATAAAAACCCTAGAAGAAAACCTA 5564
                             i       v   v      - i      vi i           v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAACATA 549

  chrX_150038373_   5565 GGCA-ACACCATTCAGGACATAGGCATGTGAAAGGACTTCATGACTAATA 5613
                           ?i- v i -   iv   v v  vv iv v  v ii   v iiv  vv 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_150038373_   5614 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5663
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_150038373_   5664 AAACTAAAGAGCTTCTGCACATCAAAAGAAAGTACCATCAGAGTGAACAG 5713
                            v v  i i   i  ii v     i  v v  i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_150038373_   5714 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAG 5763
                         i     i                 v       vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_150038373_   5764 GGCTAATATCCAGAATCTACAAAGAACTTGAATAAATTTACAAGAAAAAA 5813
                          i  vi          v  i        ivv i  v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_150038373_   5814 ACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 5859
                             ----   v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_150038373_   5860 AAAAGAAGACATTTATGCAGCCAAGAGACAGATGAAAAAATGCTCATCAT 5909
                         v        i  vi viii     v ii  v       i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_150038373_   5910 CACTGGTCAT 5919
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.29 (134 / 104)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


1894 25.39 6.05 5.80  chrX_150045660_150048723.rev     1359  2185 (879)    L1M4_orf2#LINE/L1        1   829 (79)  

  chrX_150045660_   1359 TGGAAAAACATCTCACGCTCATGGATTGGAAGAATCAACATCATTAAAAT 1408
                               i i   i  i i               v i  i  ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150045660_   1409 GGCCATACTGCT-AAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 1457
                            v     v i-   vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150045660_   1458 TACCAA-TGTCATTTTTCTAAGAATAAGAACAAATT-ATTCTAAAATTCC 1505
                          v   i-  i v     vi ii   --vi    ii -  i         v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT--TGACAAGCTGATCCTAAAATTCA 148

  chrX_150045660_   1506 TGTGGAACATA-AAACAACCCA-AATAGCCAAAGCAATCCTAAGCAAAAA 1553
                          i     -  i-  ivi     -          i     i i ----   
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA----AAA 193

  chrX_150045660_   1554 AAAACAACAAAGCCAGAGGCATCACTTCTCCTAACTTTAAACTATACTAC 1603
                          i  v       iii    vv    vii   i  i  i   viv      
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_150045660_   1604 AAGGCTACAGAGTAACAGAAACAGCATGGTACTGGTACAGAAACAGACAT 1653
                           i       --   ivi i    ii         i i iii i      
  L1M4_orf2#LINE/    244 AAAGCTACAG--TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_150045660_   1654 GTAGACCAACGGAAGAAAATAGAAAAAAAAATAGAGAAACCAGCAATAAA 1703
                         i    i   i    -----     ------- v    iv    v      
  L1M4_orf2#LINE/    292 ATAGATCAATGGAA-----TAGAA-------TTGAGAGTCCAGAAATAAA 329

  chrX_150045660_   1704 GCTGCACACCTACAACCTCCTGATCTTCGACAAAG---CCAACAGACATA 1750
                         v iii   ii  iiii vvi    i        i ---    --   -i 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA--GAC-CA 376

  chrX_150045660_   1751 AGAAATTGGGAAAAGATTCCCTATGCAATAAATGGTCCT----------- 1789
                         vvv   v      ii  vvi  v v   i       v  -----------
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_150045660_   1790 ------------------ATGAAACTTGACCCCTACCTATCACCATATAT 1821
                         ------------------     ii v           vv         i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_150045660_   1822 AAATATTAACTCAAGATGGATTA-AGTCTTTACTCCATCTTGAATTAATG 1870
                            v          i      i -  ---------- i  --  ---   
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAG----------ACCT--AA---ATG 511

  chrX_150045660_   1871 TAAGACCTCAAACTACAAAAATCCTAAAAGAAAACCTAGAA--AACTCCC 1918
                              v  v      i    v  i  i        v   i?--  v  --
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-- 559

  chrX_150045660_   1919 TTCCTAATATCAGCCTTGGAAAAGAATTTATGGCTAAGTCCTCAAAAGCA 1968
                            v i iv ii vi v  v  v iv  iv i v  v v vi        
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chrX_150045660_   1969 ATTGCAACAAAACAAAAATT-GACAAATGAAACCTAATTAAACTAAAGAG 2017
                         vvv         v     v -  i    vii  i v  i   v v  i i
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chrX_150045660_   2018 CTTCTGCACAGCAAAAGAAACTACCAAG----T-AACAGACCACCTATAA 2062
                            i  ii vv    i  v    i    ---- -  v    v   i i i
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chrX_150045660_   2063 AATAAGAGAAAATATTCACAAACTATGCATCTAATAAATGTCTAATATAC 2112
                            ii           ii    ii  ii    i    iv v  vi   v 
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chrX_150045660_   2113 AACATTTATAAGGAACTT----AAATCAACAAACAAAAAAGCAAAAGCAA 2158
                          iv  v     i     i----  v    i  vv    i -------   
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-------CAA 802

  chrX_150045660_   2159 ACAACCCCATTAAAAAGTAGACAAAGG 2185
                          i     v   ?    i i i      
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.63 (129 / 79)
Gap_init rate = 0.03 (26 / 829), avg. gap size = 3.77 (98 / 26)  

 378 17.02 2.13 2.13  chrX_150045660_150048723.rev     2480  2573 (491)    L1M4_orf2#LINE/L1      815   908 (0)  

  chrX_150045660_   2480 AAAAGTGGTCATAGGACATGAACAGACACACTTCTCAAAAGAAGACGTAC 2529
                             i   v  v    iv    i     --i     v        ii   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACA--TTTCTCCAAAGAAGATATAC 862

  chrX_150045660_   2530 AAGTGGCCAAGAA--ACATGAAAAAATGCTTGTCATCACCAATCAT 2573
                           i       v  --         i     iiv     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 2.00 (4 / 2)  


2242 21.79 4.33 7.04  chrX_150054332_150056059.rev      499  1237 (491)    L1M4_orf2#LINE/L1      190   908 (0)  

  chrX_150054332_    499 AAGAAGAAGAACAAAGTCAGAAGATTTACACTATCACACTTCAAGACATA 548
                           i              ii  i  i i     vi vv i     i  v  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_150054332_    549 CCATAAAGCTACAGTGATCAAGGTAGTGTGGTATTGATGAAAGAACAGAC 598
                          i i           i      ii         i  iiiv   i i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_150054332_    599 AAATAAATGAATGAAAGAGAATGGAGAGCCCAGAAAGAGTTCCACACAAA 648
                          v   i  v    i  v     v     i       v ivi   i   vv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_150054332_    649 TATAGTCAACTTATTTTTGACAAAGGAGCAAAGGTAATTCAACGGAAAAA 698
                            i     i v     i     i  v  v   iiv      i  ii   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_150054332_    699 -AGCATTCTTTTTAACAAATGGTGCCGGAACAACTGTACAACCACATGTA 747
                         - ii v      i            i  i       v i ?       i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_150054332_    748 AAAAGATTTTTTAAAGCCCAAAAACAAATAAACAAAGAGCCCCACAAGAA 797
                            ii  -----i   i----------- ii  ------   i  -----
  L1M4_orf2#LINE/    440 AAAGAAT-----GAAGT-----------TGGAC------CCCTAC----- 462

  chrX_150054332_    798 TCTAGAGACAGAATTTACACCTTTTCCCCAAATTAAATAGATATAATTAA 847
                         -------------i i     v v v vv       v ---------i  
  L1M4_orf2#LINE/    463 -------------CTCACACCATATACAAAAATTAACT---------CAA 490

  chrX_150054332_    848 AATAGACTATAAGTGTTAAATGTAAAATGC-AAGGCTATAAAACTTCTAG 896
                            i  ii ? iii-i         i -  -  ii          ii   
  L1M4_orf2#LINE/    491 AATGGATCAWAGAC-CTAAATGTAAGA-GCTAAAACTATAAAACTCTTAG 538

  chrX_150054332_    897 AAGATAGCAAAGGAGAAAATCTGAGTGACCTTCACTTTGGTAATGACTT- 945
                             v i  v   ? v      vv        viv  v  i    ii  -
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_150054332_    946 -------TAACA--AAAGGT-CAATCTATAAAAGAAAAAAATGATAAATT 985
                         ------- i   --   i i-   v v i           vv        
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_150054332_    986 AAACTTCATTAAA-TTCAAAACT---------------ACTCTGTTAAGT 1019
                         ii       i   -  v      ---------------  v  i i   v
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_150054332_   1020 GAACGAAAAGACAAACAACAGAGTAGGAGAAAATATTTGCAAAACATATA 1069
                         i ii          v v     i i                  v      
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_150054332_   1070 TCTGATTAAGGACT-GTATCCAAAATGTACAAAGAACTC--AAAACTCAA 1116
                               v i     -       i   i  i         -- v       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_150054332_   1117 CAACAAGAAAACATACAAACCAATTTAAAAATGGGCCATAGATTTGAACA 1166
                         i  i  i  i   v i  v      ?          v vi        i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_150054332_   1167 GATGCCTCATCAAAGAAGAGGTACAGATAGCAAAATAAACATATTAAAAG 1216
                           iiii  vi         vi    i  i  v  -   i  i  v     
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAA-TAAGCACATGAAAAG 887

  chrX_150054332_   1217 ATGCTCAACATCATATGCCAT 1237
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (104 / 53)
Gap_init rate = 0.02 (17 / 719), avg. gap size = 4.94 (84 / 17)  


2395 23.25 1.60 10.62  chrX_150090969_150097758     5300  6297 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_150090969_   5300 TGGAAAATCATTCCATGCACATGGATAGGAAGAATCAATATTGTGAAAAT 5349
                               ivi  i     iv       v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150090969_   5350 GGCCATACTGCCTAAAGTAATTTATAGATTCAATGGCATTCCCATCAAGC 5399
                            v     v  i   v i  i  i        i vv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150090969_   5400 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 5447
                          v   -   v    i  -i     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chrX_150090969_   5448 TATGGAACCAAAAAATAGCCCGTATAGCCAAGACAATCCTAAGCAAAAAG 5497
                                viiv  iiv v  v v        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_150090969_   5498 AACAAAGCTGGAGGCAGCACACTACCTGACTTCAAACTATACTATAAGGA 5547
                                i      vvv      v  ii i      viv     i  i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_150090969_   5548 TACAGTAACCAAAACAGCATGGTACTGGTACCAAACCTGATATATCTATA 5597
                                 i   i    ii         i i-  i---    v i-----
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCAT-AAG---GATAGAC----- 289

  chrX_150090969_   5598 TCTATATCTATATCTATATATCTATATCTATATCTATATCTATATCTATA 5647
                         --------------------------------------------------
  L1M4_orf2#LINE/    290 -------------------------------------------------- 289

  chrX_150090969_   5648 TCTATATCTATATATCTATATCTATATATCTATATCTATATCTATACCAA 5697
                         -----------------------     v---------------- i   
  L1M4_orf2#LINE/    290 -----------------------ATATAG----------------ATCAA 300

  chrX_150090969_   5698 TGGAACAGAACAGAGACCTCAGAAATAACACCACATATCTACAACCAGCT 5747
                              i    iv    vii         vv   i i  i  iiii  ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_150090969_   5748 GATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 5797
                            i   i    ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_150090969_   5798 TTAATAAATGGTGCTGGGAAAACTGGCTGGCCATATGCAGAAAACTGAAA 5847
                          i  i              v      v i?   i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_150090969_   5848 CAGGACCCCTTCCTTACACCTTATACAAAAATTAA-----GATAGATTTA 5892
                         iv        v   i     v              -----i  i   iv?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_150090969_   5893 AGACTTAAATGTAAAACCCAAAACCATAAAAACTCT-AGAAGAAAACCTA 5941
                             i         i v i     i      -    -          v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACATA 549

  chrX_150090969_   5942 GGCA-ATACCATTCAGGACATAAGCATAGGCAAAGACTTCATGACTAAAA 5990
                           ?i- v i -   iv   v vi vv       v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_150090969_   5991 CACCAACAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTAATT 6040
                               v    vvi      i   vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_150090969_   6041 AAACTAAAGAGCTTCTGCAGAGCAAAAGAAAACTATCACCAGAGTGAACA 6090
                            v v  i i   i  iivvv    i  v -      vv i      v 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACA-CTATCAAGAAAGTGAAAA 697

  chrX_150090969_   6091 GGCAACCCTACAGAATGAGAGAACAAT-TTTGCCATCTACTTATCTGACA 6139
                          i      -        i     -   -     v vii iv       i 
  L1M4_orf2#LINE/    698 GACAACCC-ACAGAATGGGAGAA-AATATTTGCAAATCATATATCTGATA 745

  chrX_150090969_   6140 AAGGTCTAATATCCAGAATCTACAACGAACT--TAAAAA--AAT--TTAC 6183
                          i  v  vi          v  i  v     --  v  v--   -- v v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_150090969_   6184 AAGAGTAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 6233
                             -i   i     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_150090969_   6234 TCTCAAAAGAAGACATTTATGCAGCCAACAAATATATGAAGAAAAGCTCA 6283
                             v        i  vi viii     i  ii i     i i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_150090969_   6284 TCATCACTGATCAT 6297
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.28 (128 / 100)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 5.81 (122 / 21)  


1931 25.28 2.60 1.86  chrX_150124152_150127323.rev     1227  1764 (1408)    L1M4_orf2#LINE/L1        1   542 (366)  

  chrX_150124152_   1227 TGGAAAAACATTCCATGCTCATAGATTGGAAGAATCAATATCATTAAAAT 1276
                               i i  i     i    i          v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150124152_   1277 GGCCATACTGCCCAAAGCAATTTACAAGCTCAACATTATTCCTATCAAAC 1326
                            v     v      vii  i    iii     iiv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150124152_   1327 TATCAACATCATTTTTCACAGAACTAGAAAAACTT-TTCTAAAATTCAT- 1374
                          vi  i vv v     ii     v v  v  i  v- i           -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_150124152_   1375 --GAAAC-CAAAGAAGAGCCCA-AATAACTAACATGATCCTAACCAAAAA 1420
                         --    i-   i i ---    -    i i  v ii   i i vv  i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_150124152_   1421 GAACAAAGCCAAAGGAATCACATTACCTGATATTGAACTACACTATAAGG 1470
                                 iiii    v     i v  ii  v ii  vivi    i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_150124152_   1471 TTGCAGTAACCAAAACAGCATGGTACTGATACAAAAACAGACACGTAGAC 1520
                         i i      i   i    ii        ii i  ii i     ii    i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_150124152_   1521 TAATGAAACAGAATAGAGAGCCCAGAAATAAAGCCACACACCTACAGCCA 1570
                         i    i  i     v     i           v   i   ii  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_150124152_   1571 ACTGATCTTCAACAAAGTCAACAAA--CATAAGCAATGGGGAAAGGAATC 1618
                          i    i   i    i viiv   i--   --v            -   v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAG-AATA 394

  chrX_150124152_   1619 -CCTATTCAATAAATGGTGCTGGGATAGCTGTCTAGCCATATGCAGAAGA 1667
                         -i  v     i              i i   vv  ?   i     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_150124152_   1668 ATACATATGGCCATCTATCTATCTATCACCATTTACAAAAATTAA----- 1712
                           iv vv   v vi   i  ---i -      v            -----
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCT---CA-CACCATATACAAAAATTAACTCAA 490

  chrX_150124152_   1713 GATGGATTAAAGATTTAAATGTAAGAGCTCAAACTATAAGAATCCTAGAA 1762
                         i      i ?   ii              v         i v  i     
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chrX_150124152_   1763 GA 1764
                           
  L1M4_orf2#LINE/    541 GA 542

Transitions / transversions = 2.44 (95 / 39)
Gap_init rate = 0.02 (12 / 542), avg. gap size = 2.00 (24 / 12)  

 925 25.41 6.35 1.10  chrX_150124152_150127323.rev     2321  2682 (490)    L1M4_orf2#LINE/L1      528   908 (0)  

  chrX_150124152_   2321 AAGAATCCTAGAAGAAAATCTAGGAAATAACATTTTG-GACATCAGCCTT 2369
                           i v  i          iv    ?i-   vvi  i -   v ii vi v
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTA 576

  chrX_150124152_   2370 GGGAAGGATTTAT--GAC-TAACTACTCAAAAGCAATTGCAGCAAAATCA 2416
                           v  v i   v --  i- i  -  -        vvv   i     vv 
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGAC-AC-CAAAAGCACAAGCAACAAAAGAA 624

  chrX_150124152_   2417 AAAATTGACAAGTGAGACCT------AATTAAAAAGCTTCTGCACAGCAA 2460
                              v  i  i vi   i ------         -   i  ii vv   
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAA 673

  chrX_150124152_   2461 AAGCAATTATCAACAGAGTAAA-------CCTACAGAATGGGAAATAATA 2503
                          i vv i      v i   i  -------  i           i v    
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_150124152_   2504 TTTGTAAACTATGCATCTGACAAAGGTCTAATATCCAGAGTCTATAAGAA 2553
                             i   ii  ii      i  i  v  vi        i v     ii 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_150124152_   2554 ACTGAAACAATTGAATAAGCAAAAAACAA----CCCTATTTAAAAATGGG 2599
                            vvv    i v     vv    i    ----   v   ?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_150124152_   2600 GAATAGACAAGAACAAACACTTCTCAAAAGAAGACATACACACAGCCAAC 2649
                         v  vi  ivv   i i   i     v        i     v ii     i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_150124152_   2650 AA--ACATGAAAAAATGCTCATCATCCCTAATCAT 2682
                           --         i       v    v????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (49 / 41)
Gap_init rate = 0.03 (11 / 381), avg. gap size = 2.45 (27 / 11)  


 287 24.17 9.58 6.67  chrX_150129808_150133005.rev      381   620 (2578)    L1M4_orf2#LINE/L1      400   646 (262)  

  chrX_150129808_    381 TTCAATAACTGGAGCTAAAAAAAAATTGGTTACCAATATGGAAAAAA--- 427
                              i  v   v   iii v  --i   v  ? v i   v    i ---
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAA--CTGGATAKCCACATGCAAAAGAATG 447

  chrX_150129808_    428 ---TTGGGTCCC-ACCTCACACCATACAGTAAAAA--AAATCTAGATGGA 471
                         ---    ii   -             i -i     --  v  v i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATA-CAAAAATTAACTCAAAATGGA 496

  chrX_150129808_    472 TTTAAGACTTTAATGTCAAAAAC-AAAACT-TAAGGCATTCATATTGTAA 519
                          iv?    i v     -  i i -      -   i-- i  ---  iv  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGT-AAGAGCTAAAACTATAAA--ACTC---TTAGAA 540

  chrX_150129808_    520 GAGAAGA--GGT-TAAGTTGTCTCTGTTTATAGATTA--CA-TGAT--CT 561
                           i  v --  ?-   i iv  v-  viiv i i   --  -  i --  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGGCAATGGTTTCT 589

  chrX_150129808_    562 TATATATAGAAAACCCTAAAGACTCCACCAA-AAAATATTAAAAGTA-AT 609
                           v    i----  v i   ii v v v   -    v --    i  -  
  L1M4_orf2#LINE/    590 TAGATATG----ACACCAAAAGCACAAGCAACAAAAGA--AAAAATAGAT 633

  chrX_150129808_    610 AAATGGG--TTCA 620
                             v  --    
  L1M4_orf2#LINE/    634 AAATTGGACTTCA 646

Transitions / transversions = 1.39 (32 / 23)
Gap_init rate = 0.09 (21 / 247), avg. gap size = 1.86 (39 / 21)  

2909 23.20 3.48 3.48  chrX_150129808_150133005.rev     1146  1921 (1277)    L1M4_orf2#LINE/L1        1   776 (132)  

  chrX_150129808_   1146 TGGAAAGATCTCCTGTGCTCATGGATTGGAAGAATTAATATTGTTAAAAT 1195
                                  v   ii  i               v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150129808_   1196 GCCCACACTACCCAAAACTG-TCTATAGATTCAAAGCAATTTCAATCAAA 1244
                          v v i   v      -i  -    i        v     ii v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_150129808_   1245 ATTCAAGTGACATTTTTCAAAGAAACAGAAAAACCAATCCTAAAATTCAC 1294
                           i v  ivi v     iiv     iv  v  i ii             i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_150129808_   1295 ATGGAAATATGAAAGATCTTGAATAGTCAAAGCAATCTTGAGAAAGAAAA 1344
                                 iii ii  i iv      i    i         i      i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_150129808_   1345 ACAAAGCTAGAGGCAC-CACACTCCCTGATTTCAAATTATATTACAAAGC 1393
                               i i    -  -      i  ii        viv  i        
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_150129808_   1394 TATGGTAACCAA-ATAGCATGGTACTGGCATAAAAACAGACACATAGAAC 1442
                           ii    i   - i  ii              ii i     i     v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_150129808_   1443 AACTGAGCAGAATACAGAGCTCAGAAATAAATCCGTGCATATATATCGTT 1492
                           iv  ii     vv    ii          i  i i   v   i--  i
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG--GTC 346

  chrX_150129808_   1493 AGCTAATCTGTGACAAAGGTGCTAAGAATACACAATGGG----------- 1531
                          ii i  i vi     i     i    vi iv       -----------
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_150129808_   1532 CTATCATCAATAAGTGACTTTGGGAAAACTGGATATATACATGCAAAAGT 1581
                           v --    i  i  iivi     v         ?vi           v
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_150129808_   1582 ATGAAATTGGACCCTTGTCTTTAATCACATATAAAAATTAACTCAAAATA 1631
                              i        i ii  ivv i  i   i                 i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_150129808_   1632 GATTAAAGACTTAAATGTAAGAACCTGAAACTGTAAAAATCCTGGAAGA- 1680
                            i ?    i           i - i     i     v  i i     -
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAA 543

  chrX_150129808_   1681 --CATAGGGAAAAAGCTCTTTGATGTTAGTCTTGACAATGATTTTTTTGG 1728
                         --      ?iv   v  iiv   iv  i vi v i     i   i  v i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chrX_150129808_   1729 TGTAACACAAAAATCATAAACAACAAAAGCAAAAG-AAATGGGTGGGACT 1777
                          i i    v    v  i  i         v    i- i  iii v     
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chrX_150129808_   1778 TCATCATACTATAAAGCTTCCGCACAACAAAGGAAACAATCATCAACAAA 1827
                               v v vv   i   ii ii vv       v  v    --------
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA-------- 685

  chrX_150129808_   1828 ACAAAACAAGCAATGAAATGAAAAGATAACCTACAGAATGGGAGAAAATA 1877
                         -- i  ---------- i        i    i                  
  L1M4_orf2#LINE/    686 --AGAA----------AGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chrX_150129808_   1878 TTTGCAAACTATACCTCTGATA---------TATTCAAAACATATAAGGG 1918
                                 ii   iv       ---------   i  i  i      i i
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chrX_150129808_   1919 GCT 1921
                         i  
  L1M4_orf2#LINE/    774 ACT 776

Transitions / transversions = 2.40 (125 / 52)
Gap_init rate = 0.02 (14 / 776), avg. gap size = 3.86 (54 / 14)  

 573 19.34 2.76 5.52  chrX_150129808_150133005.rev     2527  2707 (491)    L1M4_orf2#LINE/L1      733   908 (0)  

  chrX_150129808_   2527 CATATATATAATATGGAA-----ATAAAGAGGGAGAGAGAAAGAATTCAC 2571
                                v i   v  i -----  vv   --- v v v      i  vi
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGA---ATATATAAAGAACTCTT 779

  chrX_150129808_   2572 ACAATTCAATAGCAAAAATAAATAAATAAATAATCTGATTTTAAAAAGGA 2621
                             i      ------     v i i      i ii   ?v    v  i
  L1M4_orf2#LINE/    780 ACAACTCAATA------ATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_150129808_   2622 CAAAAGATCTGAATAGACATTTCTCAAAGAAAGATGTACAAATGGCTAAC 2671
                             i   i                v  ii     i          i  i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_150129808_   2672 AGGTACATGAAAAAAATGCTCGACATCACTAATCAT 2707
                          i i         i -     i      ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (22 / 12)
Gap_init rate = 0.02 (4 / 176), avg. gap size = 3.75 (15 / 4)  


 911 30.75 3.28 0.60  chrX_150158775_150161082.rev      623   957 (1351)    L1M4_orf2#LINE/L1        1   344 (564)  

  chrX_150158775_    623 TGGTAAGATATACTATGCTTATGGATGCAAAAAACTAAATATCATAAAGA 672
                            v       v i   i i      -iii  i   v     ii v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT-TGGAAGACTTAATATTGTTAAGA 49

  chrX_150158775_    673 TGTCAAT--TCTCCAGATTATTCTACATGTGCGACGTACTTTCAGTCAAA 720
                           v    --  i   i   iv      vi v i   i v ii vi     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_150158775_    721 ATCTTAACT-----TTTTGTGGTACTTGATGAGCTGATTTAAAAAATTTA 765
                            ii i  -----     ii v v    ii       iiv-      i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT-AAAATTCA 148

  chrX_150158775_    766 TACAGAAAATCAAAGGGCCAAAAATAACCAGCAAAATCTT-AACAAGTAA 814
                           ii    vv   i  i  v i    i   iv v      -  v   v i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_150158775_    815 AACAAGGTAAGGGG-TTTTCTCTACTACATATCAAGTCTTATTCTAAAAC 863
                              i  vi i  -i iv v  v ivv  v    iv    i vi   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_150158775_    864 AATGAACATTATGACAATGTGGTATTG-CATAGGGATAGGCAAACAGATC 912
                         v iiivv  i v    i       i  -    i      i  v i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_150158775_    913 AATGAAACAGTACAATGAACTCAGACACATACC-ACACATTTATGG 957
                             i  i  v iviv  iii    v i v   - i          
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

Transitions / transversions = 1.64 (64 / 39)
Gap_init rate = 0.02 (8 / 344), avg. gap size = 1.62 (13 / 8)  

 932 28.35 5.36 3.83  chrX_150158775_150161082.rev     1296  1817 (491)    L1M4_orf2#LINE/L1      379   908 (0)  

  chrX_150158775_   1296 CAGTGAGGAAAAGAAAAACTGTTCAATAAATGGCAA-GGGAAAATTAGGT 1344
                           i  i     ii v iv  v     i      iiv-    v  i i i 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chrX_150158775_   1345 ATTCACATAATGACAAATAAAAATATAAATAATAGGTATTTATTCTTACC 1394
                          ?i     i----    -- i   i-  i -- i ------ ii i    
  L1M4_orf2#LINE/    429 AKCCACATG----CAAA--AGAATG-AAGT--TGG------ACCCCTACC 463

  chrX_150158775_   1395 TTAAACCATATGCAAGAAGTAATCCCAAGTGGGCTACAGTGCTAAA-GTG 1443
                          i v       i   i  v   ii v  i   iii ?  vv     -  i
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chrX_150158775_   1444 AAAATCAAA--TTTTAAACTTTTACAAGAAAGTATAGGGAAATGTCATTA 1491
                          i iii   -- v v     i   v      ii     ?iv vi  v ii
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chrX_150158775_   1492 TGGCCTTAGATTAAGGAAGGGATTCTTAACCAAGTCACAAAAAACACAAA 1541
                           i    i i   i v  v  v      ivi v v   v    i     i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_150158775_   1542 CCATTAAA---AAGACTGATAAATTTTGCCTTTCTAAAATGTAAAA---T 1585
                          v iv   ---  i iv        vvi i ivii     -     --- 
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTT 662

  chrX_150158775_   1586 ATCTACTCAATAAAAGACACCATAAAAAGAGTGAAAAGAAAAGCCACAAA 1635
                         v v i  i--i   i     i  v  i i          v  v     i 
  L1M4_orf2#LINE/    663 TTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_150158775_   1636 C---AAGAAGATACATATAATGCATATAACTTATAAAATATTAATATCCA 1682
                         v---i    i   iv ii  vv      v  v    iiv i vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_150158775_   1683 GAATTAACAAAGAATTC--ATAATATCAACAAGAAAAAGACAAAACAATG 1730
                             vv i      i  -- i  i-    i  v           -i  iv
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAAC-TCAATAATAAAAAGACAAA-TAACC 808

  chrX_150158775_   1731 CAA----AAAATGGGCAATTAATGTTAACAGGCAAT-------AGTAGAA 1769
                            ----           vvi  v v  i  i  v -------  v   v
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_150158775_   1770 AT-CTAATAGCCA-TAAGCGTATAAAAATATGTTCAACGTCACTAGCAAT 1817
                           - v   i    -     ii  i    v   i     i   ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (90 / 55)
Gap_init rate = 0.04 (20 / 530), avg. gap size = 2.40 (48 / 20)  


3296 26.76 0.44 0.44  chrX_150168861_150175139     4879  5786 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_150168861_   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150168861_   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150168861_   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_150168861_   5027 TATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_150168861_   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_150168861_   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_150168861_   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_150168861_   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_150168861_   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_150168861_   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_150168861_   5375 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_150168861_   5425 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCCAA 5474
                         v    ?i v viv   iv   v v  vvii     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_150168861_   5475 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5524
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_150168861_   5525 TTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5574
                          i   v i  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_150168861_   5575 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5624
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_150168861_   5625 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5674
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_150168861_   5675 AAACAAACAACCCCATCAAAAACTGGGCAAAGGACATGAACAGACACTTC 5724
                          i     i     v  i?    v           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_150168861_   5725 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5774
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_150168861_   5775 ATCACTGGCCAT 5786
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3125 23.42 5.28 1.03  chrX_150239338_150241640.rev      942  1812 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_150239338_    942 TGTAAAGATATCCTGTGTTCATGGATTGGAAGAATTAATACTGTTGAAAT 991
                           v          ii                  v      i    i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150239338_    992 GTCTACAGCACCCAAAGCAACATACAGATATAACACAATCTCTATCAAAA 1041
                          v v i viv      vii iv       vi   i     i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150239338_   1042 TTACAGTAGCATTCTTCATTAAAATAGAAAAAC-AATCCTAAAATTCATC 1090
                          iv   iv  v  i  iiivi    v  v  i -i              -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT- 149

  chrX_150239338_   1091 ATACAGAACCACAAAAAGCCCCAAATAGCCAAAGCAACATTGAAAAAG-- 1138
                         -- ii   vii   iiii   vi          i   iv         --
  L1M4_orf2#LINE/    150 --ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_150239338_   1139 --------TTGTAAGCATCACACTTTCTGATTT-AAAA--TATTACA--G 1175
                         --------   v i vv        i ii    -    --  i    -- 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_150239338_   1176 TTATAGTAATCAAAACAATATGGTATTGGCATAAAAACAGAAACATATAA 1225
                         i  i         i   i i     i        ii i   v i   v v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_150239338_   1226 CAATGAAACAGAAT--AGAGCCCAGAAATAAATCCAAACATATATGGCCA 1273
                              i  i     --    i           i   v    v     i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_150239338_   1274 ACTAATCTTCGACAGGGGTGTTAAGAGGAACA--CAATGGGGAAAGGACA 1321
                          i i  i       i     ii    v---  --            i i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGAC---CATTCAATGGGGAAAGAATA 394

  chrX_150239338_   1322 GTCCCTTCAATAAGTGGTACTGGGAAAACAGGATTTCTACATGCAAA-GA 1370
                            ii     i  i    i      v   v    v? i         -  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_150239338_   1371 AAAAAACTGGACTCTTAC-----ACCATAAACAAAAATCAACCCAAAATG 1415
                          vi  ii     i i   -----      v        i   i       
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_150239338_   1416 GATAAAATAACTAAAACATAAAGATATAAAGTTTTAAGAC----ATAAAA 1461
                            v ? v v     -ii   -  vv    ii v   i  ---- v  i 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAA-TGTAA-GAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_150239338_   1462 GAACACAGAGGGAAAGGTCCTTAACATTGGCCTCAGTAATGATTTTTTGG 1511
                         i    i  i? v   vv i v i  v    vi vi i    i   i  i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_150239338_   1512 ATATCACACCAAAAGCTCAGGCTACAAAAGAAAAAATA----AAGCGGCT 1557
                             v           v  i  v               ----  vi  vi
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_150239338_   1558 TGCATCAAACTAAAAAGCTTCTGTACTGCAAAGGAAACAATCAACAAAAT 1607
                          v       v v    i   i   i  v       v  v     v   i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_150239338_   1608 GAAAAGGCAGCTTACAGACTAGGAAAACATATTTGCGAACCACCTATCTT 1657
                               i  i ii     v i   i  v        i  i  iv     v
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_150239338_   1658 GTAAGGGGTTAATACCCCAAAATTTATAAAGAACTCTTACAACTCAGCA- 1706
                         i      ii vi  i  - i   v                      ii -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCC-AGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_150239338_   1707 ------GAAAAACCACCTGATTAAAATATGGACAACAG--CTGGACAGAC 1748
                         ------  v   iv   ii   ?   v    i   vi --i  i i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chrX_150239338_   1749 ATTTCTCCAAAGA---CATAAAAATGGCCAAGAGATAAATGAAAATGTGC 1795
                                      ---i   v          v iii v       vi   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chrX_150239338_   1796 TCAACATCACTAAATCA 1812
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (128 / 72)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.89 (55 / 19)  


3381 25.06 1.67 0.56  chrX_150289188_150292816.rev     2241  3138 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_150289188_   2241 TGGAAACACATGCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2290
                               v i  v     i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150289188_   2291 GACCACACTGCCAAAAGCAATCTACAAATTCAATGCAATCTCCATCAAAC 2340
                          i v i   v  v   vii       i      i      i i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150289188_   2341 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 2390
                          v   v vv v  i  ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_150289188_   2391 TGGAACCAAG-AAAGAACT--GCATAGCCAAAGCAA----GACTAAGCGA 2433
                              -- v -  i i  i-- v         i   ----  vv   ---
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG--- 195

  chrX_150289188_   2434 AAGAACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAA 2483
                                  vi      vv       v  ii        viv     i  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_150289188_   2484 GGCCACAGTCACCAAAACAGTATGGTACTGGTATAAAAATAGGCACATAG 2533
                         i  i     v i   i     i         i    ii    i  i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_150289188_   2534 ACCAGTGGAACAGAATAGAGAACCTAGAAATAAGCCCAAATACTTATAGC 2583
                          i  i     i     v    ii i        i    v i i    i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_150289188_   2584 CAACTGACCT-CAACAAAGTAAACAAAAACATAAAGTGGGGAAAGGACAC 2632
                            i   ii - i    i vviv   i v   vv i         i i v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_150289188_   2633 CCTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAAGAGAA 2682
                         i                       i  i   v  ?       i  i    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_150289188_   2683 TGAAACTGGATCCTCATCTCTCACCGTATACAAAAATCAACTCAAGATGG 2732
                             ii    i  ii i   v    i           i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_150289188_   2733 ATTAAGGACTTAAAC-------CTGAAACTATAAAAATTCTAGAAAATAA 2775
                           i ?i   i    i-------  i           v ii     i v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_150289188_   2776 CATTGGAAAAACCCTTCTTGACATTGGCTTAGGCAAGGATTTCATGACCA 2825
                            v  ?iv  vi    v    v    v        v i    v iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_150289188_   2826 AGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGTTGGGACCTA 2875
                         v  vv         v v    i    iv   i   i   iv v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_150289188_   2876 ATTAAACTAAAGAGCTTTTGCGTGTCAAAAGGAACAGTCAGCAGAGTAAA 2925
                           i   v v  i i      i iv     i iv  vi   iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_150289188_   2926 CAGGCAACCCAGAGAGTGAAAGAAAGTCCTCATAATCTATACATCTGACA 2975
                         v  i       v   i  ii     i vi iii  vii   i      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_150289188_   2976 GAGGACTAATATCCAGAATCTACAACAAACTCAAACAAATCAGTAAGAAA 3025
                         ii     vi          v  i  vi     vv    v   i   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_150289188_   3026 AAAACCAACAATCCCATCAAAAAGTGGGCTAAAGACATGAATAGACAATT 3075
                           i  v  i  i  v  i?    i     v  i  iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_150289188_   3076 CTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATATTCAA 3125
                            v                       i  i  i       i  ii    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_150289188_   3126 CATCACTAGTGAT 3138
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (136 / 85)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.86 (20 / 7)  


4094 15.14 3.24 5.73  chrX_150294111_150297059.rev     1535  2459 (490)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_150294111_   1535 GATATCTCATTTTTAAGGATTAAAAGAATTAATATTTTTAGGATGGCAAT 1584
                               i   v  i v     ii    v        v   i         
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_150294111_   1585 ATTCCGCTAATTGAAATACAGATTCAGTAGAATCCCTATCAAAATTCCAG 1634
                          i   v v      vv          iiiv               i    
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_150294111_   1635 CCTCACTTTTTTTGTTTTTTGCAAAAAT-GACAAGCTGACCCTAAA-TTC 1682
                          iv -       --------   i    -          i      -   
  L1M4_orf2#LINE/    107 CTGC-CTTTTTT--------GCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_150294111_   1683 ATATGGAAGTGTTAGGGGACCCAAAATAGTCAAAACAATCTTGAAATAGA 1732
                                 i  i- i        i     i                v   
  L1M4_orf2#LINE/    148 ATATGGAAATGC-AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_150294111_   1733 AAAACAAATTTGGAGGACTCACATTTTCCA-CTTCTAAACTTACTACAAA 1781
                          i      v              i  i   -i   v              
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_150294111_   1782 GTTACC-TATT---GACA-TAAGGTACTGACATAAGGACAGACATATAGA 1826
                          i   v-  v ---    - iv       i        i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_150294111_   1827 TCAACGGACTA----------------AATAAGCCCATACATCTATGATC 1860
                             i   v  ----------------     i         i    i  
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_150294111_   1861 AACTTATTTTTGACAAAGGTGACAATGTCAGACAATAAGAGAGGAGTAGT 1910
                           i v     i     i    v   vii  vv    ii ii i  i    
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_150294111_   1911 GTCTTCAGCAGTGGTGCTGGAAAAACTGGATAAATGGTGCTGGAAAAACT 1960
                         v i    ---------------------- i            i v    
  L1M4_orf2#LINE/    397 CTTTTCA----------------------ACAAATGGTGCTGGGACAACT 424

  chrX_150294111_   1961 GGATATCCACATGGAAAAGAATAGAGTTGGATCCCTATCACATACAATAT 2010
                              ?       v        ii       i     i v  i  v    
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_150294111_   2011 -TAAAAAAAAACTCAAAATGGATCAAAGACTTATACTGTAAGAGCAAAAG 2059
                         -i     vv                ?    i  - v         v   i
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTA-AATGTAAGAGCTAAAA 523

  chrX_150294111_   2060 CTATAAA-CTCTCAGAAGAAAACATAAGTATAAATCTTTGTAATCCTGGA 2108
                                -    i             i ?i        i  i i i   i
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chrX_150294111_   2109 TTAGGCAATGGCCTTTTAGGCAATGGTCTCTTAGACATGATACCTAAACT 2158
                                    --------------- i       i    i   v   vi
  L1M4_orf2#LINE/    574 TTAGGCAATGG---------------TTTCTTAGATATGACACCAAAAGC 608

  chrX_150294111_   2159 ATAAGCAACCAAAGAAAAAAATAGATAAATTGGACTTCATCAAAATTTAA 2208
                          i       v          -                          v  
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAA 657

  chrX_150294111_   2209 AACTTTTATG-TTCAAAAGACACTATCAAAAAGGCGAGAAGACAACCAAC 2257
                                i  -      i           i  i i  i         v  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chrX_150294111_   2258 AGAATGGGAAAACAACATTTGCCTGTCATATATCTGTTAAGTCTCTAGCA 2307
                                  i  -  i      vvi           v    vvv  v i 
  L1M4_orf2#LINE/    708 AGAATGGGAGAA-AATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chrX_150294111_   2308 TCCAGAATATATAAAGAACTCCTACAACTCAA-AATTAAAAGACAAATAA 2356
                                              i          -   v             
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chrX_150294111_   2357 TCCAAT-AAAAATTGGGCAAAGAATTTAAATAGACATAGAATTTTAAAAG 2405
                         i     -?    v         i    i         v--- i iv    
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT---TCTCCAAAG 853

  chrX_150294111_   2406 AAAGTACACAAATAGCCAAGAAGAACATGAAAAGATGATCTACAT-AGTT 2454
                           ii  i      i     v   v             v  v    - ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_150294111_   2455 AGCCA 2459
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.67 (85 / 51)
Gap_init rate = 0.02 (22 / 902), avg. gap size = 3.77 (83 / 22)  


2955 17.44 2.16 2.16  chrX_150308618_150313212.rev      968  1569 (3026)    L1M4_orf2#LINE/L1        1   602 (306)  

  chrX_150308618_    968 TGGGAAAACATTCCATGTTCATGAATCAGAAGA--TAACATTGTTAAGCA 1015
                            i  i i  i           i  ii     --   i         vv
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150308618_   1016 GGCAGTGCTCTCTAT-TTGAGCTACAGATTCAAAGCAATCCTTATCAGAA 1064
                             i i   i i v-    v            v       i     i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150308618_   1065 TCCCAGTTGACTTATTTGTGGAAATTGACAAACTGATTTTAAAAT-CATA 1113
                               i  v   v    ii           i     ii      -    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_150308618_   1114 TGGAATTGCAAGAAATCCAGAATAGTCAAAACAATTTTGAAAAGAAACAA 1163
                              v      ii i         i         i       ii  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_150308618_   1164 CCAAGT---AAAATGCACA--TCTTAATT-AAAAATATACTACAAAGCAA 1207
                          v    --- ii iv    --  ii    -v    iv           v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_150308618_   1208 TGGTAATCAATACAGTATGGTAGTGGCACAAGGATAGACATACAGGTCAA 1257
                         ii        v     i     v     i             i  i    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_150308618_   1258 TGCAATAGAATTGACAGTCATGAAATAAGCCTATATATCTATCTATGGTC 1307
                           v           v    vv       i  i   i  i   ----    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT----GGTC 346

  chrX_150308618_   1308 AACTGATTTTCAACAATGGTGCCAAAATTATCCAGTAGGGAAACAATAGT 1357
                           i        i    v        i ii  i  i i      v      
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_150308618_   1358 ATTTTCAACAAATGTTGCTCAGACAACTGGATAGCCACGTGCAAAAGAAT 1407
                         v             v    vi            ?    i           
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_150308618_   1408 GAAGTTGTATACTTACTTCATACCATATA-AAACGTGTTTAATTCAAAAT 1456
                                v iv i   i   i        -   vi ---   i       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAAT---TAACTCAAAAT 493

  chrX_150308618_   1457 GGATCAAAAGCCTAAATGTAAGAGCTAAAAATATAAAATATGTACAAGAA 1506
                               ? ii                    v       iviv  v     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_150308618_   1507 AACATACAGGTAAATCTTCATGATCTTGGATTTATTTGGCAAAGCAGTTT 1556
                               vi?          i   i     i  - ---     v --    
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTT-A---GGCAATG--GTTT 587

  chrX_150308618_   1557 --TAGGTATGACACC 1569
                         --   i         
  L1M4_orf2#LINE/    588 CTTAGATATGACACC 602

Transitions / transversions = 2.00 (68 / 34)
Gap_init rate = 0.02 (13 / 602), avg. gap size = 2.00 (26 / 13)  

1394 18.67 5.33 0.00  chrX_150308618_150313212.rev     3805  4104 (491)    L1M4_orf2#LINE/L1      593   908 (0)  

  chrX_150308618_   3805 ATACAACAACAAAAGCATTAACAACAAAA--ATATATAGATTAATTGGAT 3852
                            ii   v        iv i        -- v v      v       i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_150308618_   3853 TTCATTACAATTAAAAACTTTTTTGCTTCAAAAAATACAATCAAGAAAAT 3902
                              i v              v         ii i  v         i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chrX_150308618_   3903 GGAAGGGTAACTCACAGAATGGGAGCAAATATTTGTAAATTATATA-CTG 3951
                          i  i ii   i             v         i    i     -   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chrX_150308618_   3952 GTAAAGGACTTATATCTAGAACACATAAATAACTTTTACAA--------- 3992
                         i   i      i    i    i i     v    i      ---------
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chrX_150308618_   3993 ----AGACATACAGCACAATTTAAAACTAGACAAATGATCTGAATAGACA 4038
                         ----     v i i v     ?    v i i    v   i          
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_150308618_   4039 TTTCTCCAAGGAAGATATGCAAATGACTAATAATCACATAAAAGGATGTT 4088
                                  i        i      i i     v     i   i    i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_150308618_   4089 TGGCGTCATTGGTCAT 4104
                         iii i   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.67 (40 / 15)
Gap_init rate = 0.01 (3 / 316), avg. gap size = 5.33 (16 / 3)  


1586 26.07 4.10 2.42  chrX_150319466_150321914      709  1245 (1204)    L1M4_orf2#LINE/L1        1   546 (362)  

  chrX_150319466_    709 TGAAGACACATGCTTTGTTCATGAATTGGAAGACTCAATATTGTTAAGAT 758
                           i i v i  v iv        i           i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150319466_    759 GTTAATTCTACCTCAATTTATATATAGATTCAACACAATCCCGATAAAAA 808
                          vi   v  v  iv    v  v  i         i       v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150319466_    809 TCTCAGAAGGATTTTGTCTTTTTTTAAAAAAAAGGAATAACCAAACTGAT 858
                           i   -------i  i       ------iv  i   viv   i     
  L1M4_orf2#LINE/    101 TCCCAG-------CTGCCTTTTTT------GCAGAAATTGACAAGCTGAT 137

  chrX_150319466_    859 ACTAAAATGTATATGAAAAGGCAAAGACTCTAGAACAGTCACA-CATTTT 907
                         v       vi     i   v    i ivi i    i  i  v -  v i 
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chrX_150319466_    908 TTGAGAA--AGAACTAATTTGGTAGAATCACACTAACTGGCTTTAAGACT 955
                          vi i  --     v  v    vi  v       vv iiii  i  i   
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chrX_150319466_    956 TACAATAAAGCTGCAATAATCAAGACGATATAGCATTGGTA-AAAGATAG 1004
                            v i      i  i          ii i i i i   i -  i     
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_150319466_   1005 ---CATTGATCAGTGGAACAAGAT--ATAGTC-ACTAATGGAC--ACACA 1046
                         ---i  v     i     i ii  -- v    - vv   ii  -- i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_150319466_   1047 T--ATAACCA-TTCATTTTCAAAAATGGTTCAAAGATAATGTAATGGA-A 1092
                          --  iii  -  v      i v  v   v v    iv  vi     i- 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_150319466_   1093 AATCATAGTGTATTTAACACTTGGTGCTGAAACCACTGAATATTCATGTA 1142
                           vv     v v  i    vv        ii  v    i   ?i  ii i
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_150319466_   1143 CATAAATAT----TC--ACTTCAACCTCAAAACATATACAAAAAATAAGA 1186
                           v  iv  ---- i--  ii v      v v            v   vv
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_150319466_   1187 CAAAATGGATTATAGACCTAAATGTAACAGCTATAAGAAAGAAATTTCTA 1236
                                   i ?              v     v  vv vi   i ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_150319466_   1237 GAAGAGAAC 1245
                              i   
  L1M4_orf2#LINE/    538 GAAGAAAAC 546

Transitions / transversions = 1.34 (79 / 59)
Gap_init rate = 0.03 (14 / 546), avg. gap size = 2.50 (35 / 14)  

1178 20.22 4.10 3.83  chrX_150319466_150321914     1591  1956 (493)    L1M4_orf2#LINE/L1      542   908 (0)  

  chrX_150319466_   1591 AGAACCTAAGC-TAAAGTCTTTGTAACCCTGAGTTAGGCAAAAATGTCTT 1639
                          i   v  i ?-    -    i  i   i  i         vii v    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chrX_150319466_   1640 ATATATGACACCAAAATCATAA-TACTTTTACAGAA-AAAAAATTGATAC 1687
                          v              v  i  -i -----   i  -       v    v
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCA-----ACAAAAGAAAAAATAGATAA 635

  chrX_150319466_   1688 ATTAGACCTCATCAAAATTTAAAACTCT-ATG-----AAACACACTATTA 1731
                            i   i           v      i -i  -----  iv       i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_150319466_   1732 AGAGAATGAAAAGACAAACTATGGACTTGGAGAAAATATTT-CAAGACAC 1780
                            i i           v i ii  v v             -   iv  i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_150319466_   1781 TTTCCTGATAAAGGATTTGTAATCATAATATATTTTTTAAA--ACTCTCA 1828
                         v vi       i   i     vi  v       -----   --     i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATAT-----AAAGAACTCTTA 780

  chrX_150319466_   1829 AAGCCGAATAATAAGAAAACAAATACGCCAAT---AAAATATTCAAAAAT 1875
                         v i iv        i  i       vv     ---     ivv    ii-
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG- 829

  chrX_150319466_   1876 ATTTGCAGAGACACTTCATCAAAGAAGATATTTGGATGGCAAATTAGCAC 1925
                              v v     i   vi            viii     v   v     
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chrX_150319466_   1926 ATGAAGTGATGTGCTCAGCATCATTACTCAT 1956
                              iv    --    i     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATG--CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (43 / 30)
Gap_init rate = 0.04 (13 / 367), avg. gap size = 2.23 (29 / 13)  


1111 24.69 8.64 1.85  chrX_150332560_150335215.rev      724  1047 (1609)    L1M4_orf2#LINE/L1        6   351 (557)  

  chrX_150332560_    724 AGATATCGCCCTCATTCATAGGTCAGAAGACTCAATATTGTTAAGATGCC 773
                                --  vii     i i ii       i               v 
  L1M4_orf2#LINE/      6 AGATATC--CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_150332560_    774 AAGTCTTCTTAACTTGGTCTACAGATTCAACACCATCTCAATCATTATCC 823
                           vv  i ii  v   i              i v   i v    vv    
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_150332560_    824 CATCAGTGTTTTT-GTAAAAATTGGCAATATGATCCTAAAATTCAAATGA 872
                           v v iv     - i i      i   vv               v   i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_150332560_    873 AAATACAAAAGACC----------AGAACAACTTTAGAAAAAAA---TAA 909
                             i   ii    ---------- i     ii  ii    i  ---i  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chrX_150332560_    910 ATTTACAGGATGAACAGGGCCTCATTTGAGG--TTATTATAAAGCTACAA 957
                          v  iv    ivv   vvv  iv    v ii--   i  i         i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chrX_150332560_    958 CAGTCAAAGCAATGCGGTACCAGCATAA------------AGGTCAGTGG 995
                         i i    ii  i  i     ii      ------------  i   i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chrX_150332560_    996 AACCGAATGGAGAGTACAGAAATACACTGATGCATACTGTGATGGTTAAT 1045
                           iv    v      v        v  iv  i   ---- v     i   
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACAT----TTATGGTCAAT 349

  chrX_150332560_   1046 TG 1047
                           
  L1M4_orf2#LINE/    350 TG 351

Transitions / transversions = 1.67 (50 / 30)
Gap_init rate = 0.02 (7 / 346), avg. gap size = 4.86 (34 / 7)  

1661 21.79 5.98 4.75  chrX_150332560_150335215.rev     1597  2165 (491)    L1M4_orf2#LINE/L1      333   908 (0)  

  chrX_150332560_   1597 ACACATATATAGACAAATGAATTTTTTA-AAAAGTGCAAAGAAAATTCAG 1645
                          i    v   i v   v   -    iv -  ii    v    vv     i
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGA-TTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chrX_150332560_   1646 TAGAGCAAGAG--GTACTTTCAACAAATGGTACTAGAA-AACTCAGATAT 1692
                          i i v    i--  vi              i  i i -    -i    ?
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT-GGATAK 430

  chrX_150332560_   1693 AGATACGCAAAA-AATCCCCCAAACCTCTTATT--ACCCATACCTCACAT 1739
                         vv i i      -   -----i  ------i  --    v         i
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAAT-----GAA------GTTGGACCCCTACCTCACAC 469

  chrX_150332560_   1740 TACATACAAATATTAA------AGAGATCACAGACCTAAATGTAAAACCT 1783
                         i i       v     ------ vi     ?              i v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_150332560_   1784 AAAAATATAAAACTTCTAGAAGAAACTAAAGGAGAAAACCACTGGGACCT 1833
                             v         ii         vi v   ? v   i vii v     
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_150332560_   1834 CAGTTTAGACAAAGATTTGTTAGATGTGACATCAAAACC-CAATTCATAA 1882
                         ii v    i   v i   v      i     i     v -   viv i  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_150332560_   1883 -----------------CTGGGCTTCATCTAAGTTAAAAACATTTACTCT 1915
                         -----------------i   i       v  i        v   iiv  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_150332560_   1916 TTGAAAGACACTGTTAAAGGAATTAAAGGACAAGCAGCAGATAGGAAGAA 1965
                          ii  i      i i  iii i v   i     v vi    vv  i    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_150332560_   1966 AACCATATATAGGAAGAAAACCGTATATATGGTA-GAGACATTGTATCTA 2014
                           ---   v ----- v   i i     v  i  - i   -       i 
  L1M4_orf2#LINE/    720 AA---TATTT-----GCAAATCATATATCTGATAAGGGAC-TTGTATCCA 760

  chrX_150332560_   2015 AACATAT-TGAAGAGCCCTGAAAACTCAATAACAAAAAC-CAAACAGCCC 2062
                         i -    - i    i i  v v          i     v-    i i   
  L1M4_orf2#LINE/    761 GA-ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCC 809

  chrX_150332560_   2063 AATTTTTAAAAACTTGGGCAAAAGATTTGAACAGACACTTCACCGAGGAA 2112
                             ?--     --        i        i     i   v  i i   
  L1M4_orf2#LINE/    810 AATTW--AAAAA--TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chrX_150332560_   2113 GATATACGAATGGTTAATAAGCACATGAAGAGATGCCCAAGACCATTGGG 2162
                                i     ii              i      i   v i  ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_150332560_   2163 GAA 2165
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.79 (77 / 43)
Gap_init rate = 0.04 (21 / 576), avg. gap size = 2.90 (61 / 21)  


2769 24.03 3.14 4.87  chrX_150337627_150341428     2448  3371 (431)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_150337627_   2448 TGGAAATACATACTCTAGTTATGAATTGGAAGACTCACTATCATTAAAAT 2497
                               v i  v iv iv i   i           i v   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150337627_   2498 GTCAATTATCTGCAAACTGATCTATGGATACAGC------CCCAACAAAA 2541
                          v    vv  iv    i       ii   v  i ------  i v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150337627_   2542 TCACAGGTTTTTTTTTTGTAGTTATCAACACATTGATTTTATGATTCATA 2591
                           v   v vii       i  vv  ii   vii    ii  vi       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_150337627_   2592 TAGAAAGACATAGGAAATAGAATA---AAAATGAAATTTTGGAAAAGAAG 2638
                          i    vi  vi   vvi      ---    i--   i   i        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAAC--AATCTTGAAAAAGAAG 198

  chrX_150337627_   2639 AACAAAGTTGGAAAAGTCATACTACCTGCTTGTAAGACTTAATATAAAGC 2688
                                     ii v   i   v  iiv  vi  i     v  i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_150337627_   2689 TAAAGTAAACAAACCAGTGTGATGTTGGTGGAGGAACTGACCCATAGATC 2738
                           v     v   iv       i ii   iiv i i iv   vi       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_150337627_   2739 AACAGGAAAAAAAAATAGGGAACCTATAAATAGACCCACACACATACGAA 2788
                           ii ---  v i   v i  ii i v     i     i   iv  i iv
  L1M4_orf2#LINE/    299 AATGG---AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_150337627_   2789 TAATTGATTTTTGACAAAACTTCAATGGCAATTCAATGGGGAAA---TAG 2835
                         i          i     iiv v v v i v              ---   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_150337627_   2836 TTTTTTCAACAAATAGTACTTAAACAATCAGACATCCATATGCAAAAAAA 2885
                          i            i  i  vii    iii  i ?   i        i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_150337627_   2886 -GAACTTTGACTTATACCTCAAATCTCAT-CACAAGTTAGCTCAAAATGG 2933
                         -   v  v   iiv       v i vi  -  v  i   i          
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_150337627_   2934 ATCATAGACATAAATG-AAAAGCATAAAATCATAAAATTCT-AAATTAAA 2981
                             ?    v      -  i   -     ii      i   - i vv   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_150337627_   2982 ACATAGGGGAAAAATCCATTTGGCCTTTGGTTAGGCAAAAAGGTTT--TA 3029
                                ? v   -  iviv  i    v          v--     --  
  L1M4_orf2#LINE/    545 ACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAAT--GGTTTCTTA 591

  chrX_150337627_   3030 GATATG---CCAAAAGCATGATCCATAAAAGAAAAA-TATATA--TCAG- 3072
                               ---         ii v v i          -  v   -- ii -
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_150337627_   3073 CTTTATATAAATTAAAAACATTTCCTTTGCAAAAAATACTATTAAAAGAA 3122
                            i  vv           v   vivi v    ii i     i  i i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_150337627_   3123 TAAAAGTATAAGCTATAGACTGGGAGAAATTATTTGTAA-TCAGATATTT 3171
                          i   iv i  v i i   v         v      i  -   v    i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_150337627_   3172 GAAAAAGGAACTGTATTTAGAATACACAAGGCAATCTCAAAACTCAACAA 3221
                           v  i   vi     ii      i i  i v v   i v       i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_150337627_   3222 CAA---GATCAAACAATCCAATTAAGAAAATGGATAAAATATTTGAACAG 3268
                         i  ---  -    i  i      ? -       ii   iv       i  
  L1M4_orf2#LINE/    792 TAAAAAGA-CAAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAG 839

  chrX_150337627_   3269 ATACTTCACCAAAGAAGATACATGATGGACCAAAGAGGATATACAGAATA 3318
                          i i   v            ---------------------    -   -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATA---------------------TACA-AAT- 866

  chrX_150337627_   3319 TATATACATAAGACAAATAAGCACATGAAAAAATACTTGGCATCATTAGT 3368
                         ----------- i v                i  i  iii     ?????
  L1M4_orf2#LINE/    867 -----------GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chrX_150337627_   3369 TGT 3371
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.73 (138 / 80)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.08 (74 / 24)  


1318 18.30 2.61 2.29  chrX_150381069_150383317.rev      568   873 (1376)    L1M4_orf2#LINE/L1        2   308 (600)  

  chrX_150381069_    568 GGAAAGGCATCCCCATGTTCATGGATTGGAAGATTTAATGTTGTTAATAT 617
                               ii     -                   i     i       v  
  L1M4_orf2#LINE/      2 GGAAAGATATCCC-ATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150381069_    618 GTCAGTACTACCCAGCGCAATCTACAGATTCATCCCAATCCTTATCAAAA 667
                          v  i    v    ivvii             v v      i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150381069_    668 TCCTGATGGCAATTT--GCAGAAATAGAAAAATCTG-TCCTAAAATATAT 714
                            iiiiv  vv   --        v  v  i-   -         --- 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAAT---T 146

  chrX_150381069_    715 GTATATGGAATCTCAAGAGACATTGAATAACCAAAATAATCTTTAAAAAG 764
                         -i        viv    i   viv     i      i      v      
  L1M4_orf2#LINE/    147 -CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_150381069_    765 AA---CAAAGTTGAAGGTCTCACACTTCCTGATTCCAAAACTTACAACAA 811
                           ---        i   v           ii   i          v    
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_150381069_    812 AGCTACACGAATCAAAAGAATGTAGCTA-TGGCATAAAGACAGACATATA 860
                                vv      i v i   i -  -        i  i         
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGG-TACTGGCATAAGGATAGACATATA 294

  chrX_150381069_    861 AAG-AATAAACTAG 873
                         i v-   ii v   
  L1M4_orf2#LINE/    295 GATCAATGGAATAG 308

Transitions / transversions = 1.33 (32 / 24)
Gap_init rate = 0.03 (10 / 307), avg. gap size = 1.50 (15 / 10)  

2835 16.78 3.77 1.71  chrX_150381069_150383317.rev     1175  1758 (491)    L1M4_orf2#LINE/L1      313   908 (0)  

  chrX_150381069_   1175 GACAGCCCAGAAATAAAAGTTCACATATATAGTCAAATGATTTTCAACAA 1224
                           v  i           vvivi    v   i     v        i    
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chrX_150381069_   1225 ATGTACCAAGACCATTCAATGAGGAAAGGGCAGTCTTTTCAACAAATGAT 1274
                         iv  i                i      iii                 i 
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chrX_150381069_   1275 GCTGGGAAAACTCAGTATCCACATGCAAAAAAATTTAAAAAGAAGTTGGA 1324
                                v    vii  ?            i   -------         
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAAT-------GAAGTTGGA 455

  chrX_150381069_   1325 ACCTTACCTTATACCATATTCAAAAATTAACTCAAAGTTAATCAAAGACA 1374
                         v  i     i i       v                i vi    ?    v
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_150381069_   1375 TAAATGCAAGTGCTAAAACTACAGAACTCTTAGAAGAAAACATAAGAGAA 1424
                               i   v          i i                    i ? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_150381069_   1425 AAGCCTCATGATATTAGATTTAGCAATGATTTCTTAAATATGGCACTAAA 1474
                           v i  i   iv  i i  vi      i       i     i   i   
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chrX_150381069_   1475 AGCATACACAACAAAAGAAAAAATGAATAAATTGGCTTTCATCAAAATTT 1524
                             i vi                ii         vi            -
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT- 654

  chrX_150381069_   1525 TTAAAA---TTTATGCATTAAAGGACACTGTCAG---AGTGAAAGG-CAG 1567
                         --    ---   i   v i          i   i---       i -  i
  L1M4_orf2#LINE/    655 --AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chrX_150381069_   1568 CTCATGGAATGGTAGAAAATATTTGTAAATCATATACCTGATAAGGGATT 1617
                          i  ii      v            i          i           i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chrX_150381069_   1618 AAAATCTAGATTATATAGAGAACTTCTACAACTCAACAA---------AA 1658
                         viv   i   v      i      ii          i  ---------  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_150381069_   1659 ATAA---AACTCAAAA---GGAAAAGGACTGGAATAAACATTTCTCTAGA 1702
                             ---  i ?    ---  v      i v     i         i i 
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_150381069_   1703 GAAGCTATACAAATGGCCGATAAACATATGAAAAGATGCTCACCATCACT 1752
                             v             i    i  i               v     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_150381069_   1753 AATCAT 1758
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 2.24 (65 / 29)
Gap_init rate = 0.01 (8 / 596), avg. gap size = 4.00 (32 / 8)  


2654 24.23 4.06 4.50  chrX_150624739_150626645      503  1414 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_150624739_    503 TGGAAAAATATACCATATACATGAACTGGAAGAC--ACTATTTGTGGAG- 549
                               i    v    i v    i i        -- v    -  vi  -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-GTTAAGA 49

  chrX_150624739_    550 TGTCAA--CTCACAAATAGATTTACAAATTTATAGATTTTATTTAATAGA 597
                           v   --   v -----------      ------------------  
  L1M4_orf2#LINE/     50 TGGCAATACTCCC-----------CAAATT------------------GA 70

  chrX_150624739_    598 TTTATAGATTTAACACAAGCA-TGTCATCATCATGACAATTTGTTTTGGT 646
                          i  i     i   i   v v- i   vv   viii viii v     -i
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG-C 119

  chrX_150624739_    647 AGAAATTAACAAGCTGGCTCTAAGAGCTATATGGAAATGCTAAGGACCTA 696
                                i        iii    i vii            v i     i 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chrX_150624739_    697 GAA-ACCTAGAGTAATTTTGAAAAATATGAGCAAAATTACAGGA-TGAAA 744
                            - v i i ii   i        v v  i    i  iv    - v v 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chrX_150624739_    745 CTTAACCTGACTTCAAGATTTGCTCTAAAGCTATGTTAATAAAGATAGTG 794
                            --  ii i     i i  i  vi       iiv    v    i    
  L1M4_orf2#LINE/    220 CTT--CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chrX_150624739_    795 TATTACTGGCATAAGTCTTGACCAATATATTG-TGTGACA-AATACAGAG 842
                          iv            vv v   vv   v  ii-  vi i -   vv    
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_150624739_    843 TCCAGAAATAGATTCACATTTATATAGTCATATT-ATGTTTGACAAAGGT 891
                                   i ii  i iv v   i    -   -  v  i     i   
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCA-ATTGATTTTCGACAAGGGT 366

  chrX_150624739_    892 GCCAAAGCAATCTAATAAGAAAGGGAAAGTCTTTTCAATAAATGGCACTG 941
                              ii v  ii   ii i  i i v           i      ii   
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_150624739_    942 GAAGAACCAGCTATCCATATG--AATAAATGAACCTTGAACCTTACTTCA 989
                          i v   ii v  ?   i   --  vi      vi v  v  i   i   
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_150624739_    990 CACCCACCATACATAAAATGTAACTGGGGAGAGATCCAGGGACCTAGACA 1039
                             ----   i i    vv     viii vi    - ?i      i ii
  L1M4_orf2#LINE/    467 CACC----ATATACAAAAATTAACTCAAAATGGATC-AWAGACCTAAATG 511

  chrX_150624739_   1040 TAA-AGTAAAAGACCACAAACCTTTTAGAA--AAGCATTG--------CT 1078
                            -  iv   -  i i   v  i      --  i   v --------  
  L1M4_orf2#LINE/    512 TAAGAGCTAAA-ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chrX_150624739_   1079 TCATC-CCTTAGGCTAGTCAAATGTTTCTGAG----GATACAGAAAACAG 1123
                           i v-    i  i   v   vv      v  ----  i  vi   i  v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_150624739_   1124 AATTAACAAGG---ACAATTGATCAATTAAACTTCATAAAAATTAAAAAC 1170
                           vi     ii--- v   v   v    ii       v            
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_150624739_   1171 TTCTGCTCATCAAAAAAC--TGCCAAGAAAATGAATAGTTAAGTTACATA 1218
                           i  iv v     ii  -- ii       i    v  vi  vii   v 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_150624739_   1219 TTGTGAAATATTATTTACAAAACATATATTTGACAAGGGACTGGTATTCA 1268
                         v  v  i v v     i    v       i   i        v    i  
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_150624739_   1269 GGATATGTAAAGATCTTCTACAATCCAATAATTAAAAGACAAACAACC-A 1317
                          i    i      v  ii     ii       v          i    - 
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_150624739_   1318 ATT-AAATGTGGGCAAAAATTATTGAATGAACACTTCACAAAAGAAGATA 1366
                            -   vi        iiv -      ii   i   v v          
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGAT-TTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_150624739_   1367 TACAAATGGTCAATAAGCACAAGAAAGATTGCTCA-CATTATTTGTCAT 1414
                                  i           v    iiv      -   i ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (135 / 84)
Gap_init rate = 0.03 (30 / 908), avg. gap size = 2.60 (78 / 30)  


2807 27.82 2.01 0.78  chrX_150671694_150674645     1565  2459 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_150671694_   1565 GGAGGAGATTTTATGTTCATGGATAACATAACTCAATATTGTCAAGATGT 1614
                          i i  v  iii            viv vi   i        i      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_150671694_   1615 CAGTTGTTCACAACTTAATCTATAATTTCGATGCAATCCCAATAAAAATC 1664
                           i vv i v   v  i     i iv   i i        v  v      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_150671694_   1665 CCAGCATCTTATTTTGTTG---CTCACAAAAACTGATTCTAAAGTTTATA 1711
                              vv i v     iv ---i v    i--     i     i  i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chrX_150671694_   1712 TGGAGAGGCAAAAAACACAGAATAGTCAACTCAATATTCAGGGAGATGAA 1761
                             i v    iii  v        i   vv    v  v iii   v   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_150671694_   1762 CAAAGTCAGAGGACTGACACTACCTGACTTCAAGACTTACCATAAATCTA 1811
                               ii       v     v  ii i     i      i i   v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_150671694_   1812 CAGTAATCAAGGCAGCATAGTA-TGATAAAAGAGTAGACAAATGGATCAG 1860
                                    i   ii i   -  ii v   ii      v  i     i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_150671694_   1861 CGGAAAAGAACAGAGGGTC-AATAATAGACCCACATAACTCTACTCAGCT 1909
                         i    v    iv   i   - iv    i     i i vi v iv   ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_150671694_   1910 GATTTTTGACAGAAAAACAAAGGCAATACAATGGAGAAA--AGAGTCTTT 1957
                               i    iiiivi v   i v  v      i    -- v       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_150671694_   1958 TCAATAAATATTGGTAGAAGAACTGGACATCTACAAGGAGAAAAAAATGA 2007
                             i    iv  v i i v       i ? i   v v --   i     
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA--AAAGAATGA 448

  chrX_150671694_   2008 ATCTCGACACAGAAATTACATCCAT-CACAAAATTCAA-TCAAGATTAAT 2055
                          vi v   v vv vv i   -    -i      v i  -    i  vi  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACA-CCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_150671694_   2056 CACAGAC--A---GTAAAATTCAAAACTATAAAATTCCTAGAAGATAACA 2100
                           ?    -- ---    i vii            i  i       v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_150671694_   2101 --GGGGAAAACCTAGATGACCTCAGATATGGAGATGATATTTTAGACACA 2148
                         --  ? v   i  vvi      ii i vv  vi   i v i     i ii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_150671694_   2149 ACGCCAAAGGCATGATACATGAAAAACCTAGTTGATAAGCTGAACTTCAT 2198
                           i     i   ii vvv ii   i vvv i v     ii  i       
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_150671694_   2199 GAAAATGAAAAACTTCTGCTCTGTGAAAGACAATGCTGAAAGAATAAGAA 2248
                         v     v        i  iv  vii  i    v iiii i i i i i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_150671694_   2249 GACAAAGCACAGATTGAGTGACAATATTTGCAAAAGATATATATGATAAA 2298
                              vv      v  i v  v            vv      v      i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_150671694_   2299 GTATTGTTATTCAAAATATAATAAGATTTCATAAAATTCAACAATATGAA 2348
                          v i vv   i  i      vv    vi  v  v  i    i    vi  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_150671694_   2349 AATGAACAACCCAATTTTTTAAAATGGGCAAAAGACCCAAACAGACACTT 2398
                         i ii  i         ?v--            i  iiii  i     i  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWA--AAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_150671694_   2399 TACCAAAAAA--TATATGAATGACAAGTAAGCATATGAAAAGACGCTCAA 2446
                         iv     i  --    ii    i v i      i         i      
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_150671694_   2447 CATCATATGTCAT 2459
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (150 / 95)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 1.79 (25 / 14)  


1573 26.95 1.85 1.65  chrX_150675222_150681343     1995  2480 (3642)    L1M4_orf2#LINE/L1       13   499 (409)  

  chrX_150675222_   1995 CCAT-TTTATGGAATAGAATACTCAATATTGTTAAAATATCAATTTTACC 2043
                             -  i     v i   v   i           i  iv    vi v  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chrX_150675222_   2044 CAAATTGATTTATAAACTCAGTGCAATCCCAGTCAAAATTCCATCATAAT 2093
                                  i  i i i   ii        vi       i   v - ivi
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCC 111

  chrX_150675222_   2094 TTTTGTATAGAAAT-GACAAGCTGATTCTAAAATACGTATGAAAAGACAA 2142
                             v ii      -           i       v i    i   vi   
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chrX_150675222_   2143 AAACTGTTGCATGTATATAGGAATCTTGATAAA----AACAAATTTGGAG 2188
                         iiiviviv v  ivvi v iv        v   ----      v      
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chrX_150675222_   2189 TAGTTACATGACCTGACCTATAGAATTACTAAAATGGCTATAATGATCAT 2238
                         v v i   ivv  ii ii vv i v      v  -i    i i i    v
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAA-AGCTACAGTAATCAA 260

  chrX_150675222_   2239 AAAAGTGTGATACTGGCATAAAGATTAACAAACAAACTAATGGAACAGAA 2288
                         i v      i           i   vi   v i i ii       i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chrX_150675222_   2289 TTAAGAGTACAGAAATAAGCCCATAC-TACATGGTCATTTGATTTTATTC 2337
                           i     v         i       - vi       v        --- 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT---C 357

  chrX_150675222_   2338 TATATCATTCTCAAAGCAATTTAGTGCAGGAAAAGAAT--TTTTTTCGAC 2385
                         v i vviv vi   ii v   i i  --  i       -- i     i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATG--GGGAAAGAATAGTCTTTTCAAC 405

  chrX_150675222_   2386 AAATAATGCTAACACAACTGGATAGCTATATAGATAAAAATGAACTTCAG 2435
                             ii    iiv           ? i i  iv v  i      v  -i 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT-GG 454

  chrX_150675222_   2436 TCACCTCCTTCACACTCTACACAAAACTGAATTTAAAATGGATTA 2480
                         v v   v i      iv  i      v v  i i         i 
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

Transitions / transversions = 1.50 (78 / 52)
Gap_init rate = 0.02 (10 / 487), avg. gap size = 1.70 (17 / 10)  

3041 25.49 1.65 1.87  chrX_150675222_150681343     3541  4450 (1672)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_150675222_   3541 TGGAAATATATCCTATGCTTGTGGATTGGAAGAATCAGTATAATGAAAAT 3590
                               v      i   i ii            v i i   vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150675222_   3591 GACCATACTGCCTAAAGCAATCTACAGATTCAATGCAATTCTCATCAAAA 3640
                          i v     v  i   vii              i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150675222_   3641 TACTAACATAACTTTTC-ACAGAA-TTAGGAAAAAC-AATTCTAAAATTC 3687
                          v i i - iv     i-i     -  --  v  i -i  i         
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTC 147

  chrX_150675222_   3688 GTCTGGAACCAGAAAAGAGCCCAAATATTCAAGGTAATCCTAAGCAAAAA 3737
                         i v     viiv  ii  v  vi    vi   iii    i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_150675222_   3738 GAACAAATCCAGAGGTATCACATTGCCTGACTTCAAATTATGCTACAAGG 3787
                                viii    vv     i v  ii i      viv i      i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_150675222_   3788 CTGTTGTTACCAAAACAGCATGGTACTGGTATAAAAGTAGATACATAGAC 3837
                           iiv  v i   i    ii         i    iii    i i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_150675222_   3838 CAATGGAACAGAATAGAGAATCCAGAAATAAAGCCAAACACTTACAACCA 3887
                                 i     v    i            v   v   i   iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_150675222_   3888 ACTGATCTTTAACAAAGCATACAAAAAATAATT--TGGGGAAAGGAGGCC 3935
                          i    i  ii    i -i i v  i vi v i--         i vivi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_150675222_   3936 CTGTTCAATAAATAATTCAATAAATACAATAGGAAATTTGGATAGTCACA 3985
                           v     i    ii v ----------- i   v vi      ?i    
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGC-----------TGGGACAACTGGATAKCCACA 435

  chrX_150675222_   3986 TGTAGAAGAATGAAATTGGTTCCCTAATACTCAGCATATA-AAAAATCAA 4034
                           i i         i    vi     viv v  v      -      i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_150675222_   4035 CTCAAGATAGATCAAAGACTTAAATCTAAGACATGAAACGATACAAATTC 4084
                              i  i     ?    i     v     vv i    v   -   i  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTC 534

  chrX_150675222_   4085 T-AGAGGAAAACTTAGGAAAACCTCTTC-TGCACACTGGCCTAGGTAAAG 4132
                          -   i      v    ?iv vv     -  -  vi   vi    i  v 
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATG 583

  chrX_150675222_   4133 AATTTACAACTAAGACCCCAAAAGCAAATGCAACAAAAATAAAAATAAAT 4182
                         iv  ivi iv  v   v         v v         iv       i  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chrX_150675222_   4183 AAATGAGACATAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAAT 4232
                             vi   v v  i   v v    i   i  ii vv    i  v iv  
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chrX_150675222_   4233 CAG---AGTAAACTGACAATTCATAGAATGGGAGAAAATATTTGCAAACT 4279
                           i---   i  vv     ii  i                        ii
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chrX_150675222_   4280 ATGCATCTGACAAAGGACTAATATCCAGAATCTACAAGGAACTCAAACAA 4329
                           ii      i  i     vi          v  i  i      vv    
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chrX_150675222_   4330 ACCAGTAAGAAAAATA---ATAATCCCATCAAAAAGTGGGCAAAAGACAT 4376
                         vi  i   v     v ---    i  v  i?    i        i  iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chrX_150675222_   4377 GAATTGACATTTATCAAAAGCAGATATA-AAATGGCCAACAAATAGATGA 4425
                             v       v  v    v       -          i  ii v    
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chrX_150675222_   4426 AAAAATGCTCAACATCACTAGTCAT 4450
                            i             ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (142 / 86)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.00 (32 / 16)  

 600 29.12 7.16 2.63  chrX_150675222_150681343     5217  5635 (487)    L1M4_orf2#LINE/L1      471   908 (0)  

  chrX_150675222_   5217 ATATAATAAAAAT------AAAATGAATAATTAGCCAAGATAAAAAAGTT 5260
                              -i      ------      i  v ?vii  v i  iv  i  i 
  L1M4_orf2#LINE/    471 ATATA-CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_150675222_   5261 AAAACCATAATTCATTTACGAGAAAACAAA-----AAAACTTTGTAATTT 5305
                              i    vv vi   vi        v -----   v   i  i ii 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_150675222_   5306 GGTATTATGCAAATATTTCTTATGCACATCACAGAAAACAATAACAATAA 5355
                         v vi   v    vvi       vii iiv   vi   i  vv i   i  
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_150675222_   5356 AAAGAGAAATC-ATGAATTAGATTTTATCTACATTAAAAATTTCTAATTA 5404
                           ii i    v-  i    i  i  i   v v        i  i ivviv
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_150675222_   5405 TCAAAAGAAA--A-CAAGAGACAATAAGTATGCAAGCCACCTACAG---- 5447
                              i  v -- -     ------    iviv ii v   i    ----
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGA------AAGTGAAAAGACAACCCACAGAATG 713

  chrX_150675222_   5448 GGAAAATATATTTTAAAAACAACTATATGG-AAAGGTCTGATAGCCAGTA 5496
                            i  v      vv   v  vv   v  i-  i  v  vi  v    v 
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_150675222_   5497 CATATTTAGAAATCTTAAAACT-AA-GATAA---GACAAGTAACCCAATT 5541
                         i    vv    v     v    -  -i    ---     i          
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chrX_150675222_   5542 TTATGATAAACAAAATATTTCAGCACTCACTTT-----AGAAGAGAGTAT 5586
                         ?v vi  iii    iv    v ii vv  i  i-----      v -  i
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA-TAC 862

  chrX_150675222_   5587 GACTGGCCAATAGGCACATCAACAAGTGTTCAACAAATTTAAACCATGG 5635
                         i v         i      v  v ii  i      --- i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACA---TCAZZZZZZZZ 908

Transitions / transversions = 1.18 (65 / 55)
Gap_init rate = 0.03 (15 / 438), avg. gap size = 2.73 (41 / 15)  


2372 26.83 5.78 1.16  chrX_150684218_150685962      480  1258 (487)    L1M4_orf2#LINE/L1       94   908 (0)  

  chrX_150684218_    480 ATTAAAACTCTAGCAAAACCTTTTTAATAAAATCTAACAAGCTTAATC-- 527
                           i    ii i   vi--       vii i  vi i       -i   --
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCT-GATCCT 140

  chrX_150684218_    528 -ACATATATATATATGTTCAAAAGATTTTTAATATGTTAA-----TCTTG 571
                         - v  vi    iv vi v   ii  iiivv    - ii  -----     
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATA-GCCAAAACAATCTTG 189

  chrX_150684218_    572 AACAAGAAGAACACAGTTGGAGGACTTACACCATCTAATTTTAAGACTTA 621
                           v          v            i    ivi i     i  i     
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chrX_150684218_    622 CCATAAAGCTACAGTAATCAAGTTATTGTGG-ACTGGTGAAAGGATAGAT 670
                          i i                  vi v     -     iiv         i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_150684218_    671 GCATAGATCAATGGAACAGAATAGAGAACTCAAAAATA------------ 708
                         ii              i     v    iii  i     ------------
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_150684218_    709 ---GATAAGCTGATGTTTGACTAAGATGCCAATGTAACTCAATTGGGAAA 755
                         --- i v ii    v  i   v i i      viiv i     v      
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_150684218_    756 --ATATTTTCTTTCAAGAAATGGTGTCAGAACAACTGGATATCCA----- 798
                         --   v i -      v        iii i           ?   -----
  L1M4_orf2#LINE/    390 GAATAGTCT-TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_150684218_    799 ---AAAATAAATCTTGATTCTTTTCTCATGCAAGTCACAGATATTAACTC 845
                         --- i   i  vi v  ii i vi    ii v vvi   i v        
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_150684218_    846 GATGTGGATAATAGACCTAAACATAAAAGCTGAAATCATGAAACTTTTG- 894
                         i vi     v ?         ii   i    i   ii  i     i  i-
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_150684218_    895 -AGGAAACATAGGAGAAAAATTTTTTAACACTAAGT-AGGCAAAGCTTTC 942
                         -  i         ? v   vi  iv i  vi ii  -      v v    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_150684218_    943 TTAACTAAGACACAGAAAACCTAAAC--CATACGAAAACA---ATAATTT 987
                            iv  v     vi   i vi  i --  v v     v ---    v  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_150684218_    988 GTACTTCACCGGAATTAAAACCTTCTGCTTTTCAGAAGACATTTATGTTT 1037
                          v      i ii        v   i  ivi    i i    i ---i iv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT---ATCA 685

  chrX_150684218_   1038 AGAAAATAAAAGGACAGGCCA--GAGTCAGGGGTTATATTCACAAATCAT 1085
                              i i   i    iv   --  i vi i ivv     ii        
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_150684218_   1086 ATATTTGATGCAGGACCTGTATGTTGAGTCTATAAAGAACTCTTAAAATT 1135
                             i    ivi    i     viv  i v               v  i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chrX_150684218_   1136 CTGTAATATGAAGAAAAACAAATAAATT-ATAAATGGGCAAAAGATTTGA 1184
                          vi     vi    v   i  viv    - v           i       
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_150684218_   1185 ATAATAAACTTCACAAAAGAAGATATATGAATAATCTATAAGTACTTGAA 1234
                            i- v i   v v            ii   iii v     i  v    
  L1M4_orf2#LINE/    836 ATAG-ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_150684218_   1235 AAGATTTTCATTGTCATTAGTCAT 1258
                              vi   vii   ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (132 / 74)
Gap_init rate = 0.02 (18 / 815), avg. gap size = 3.00 (54 / 18)  


2189 23.79 4.55 6.02  chrX_150688114_150689789      503  1183 (493)    L1M4_orf2#LINE/L1      238   908 (0)  

  chrX_150688114_    503 TATTGCAAATCCACCATAATAAAAACAGTATGGTACTGGCATAAAAACTG 552
                           i i    v i  vi    v  i     i              ii iv 
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chrX_150688114_    553 ACATGTAGACCAATGAAGCAGAATAGACAGCCCAGGAATAAACTTACATA 602
                             i    i     i ii     v  v  i    i       ii i i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chrX_150688114_    603 TGTATTATCAACTAAACTTTGACAAGGGTGCCAAGAGTACGCAATGGGGA 652
                          v   vi    i i vi  i                vi iv         
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chrX_150688114_    653 AAGAATAGGCTCTTCAATAAATAGTGCTGGAAAAACAGTACATCCACATG 702
                                 v  i     i    i       i v   v v i ?       
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_150688114_    703 CAAAAAAGGAAAATTGAACCCTTGTCTTACGCCATATATAAAAATTTATT 752
                              i ivi  i   i    i ii  i  i       i       v i 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_150688114_    753 TGAAATGGCTTAAAGATTTAAAAGTAAGGCCTGAAG-TGTAAAACTTCTA 801
                         ii      v i ?   ii    v     iv  i  i- i       ii  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_150688114_    802 GAAGCAAACATAGGGGAAAAGCTCCTTGCTATTGGTCTTGGTAATGATTG 851
                             v         ? v   v  i v  viv    vi v  i    i  -
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT- 586

  chrX_150688114_    852 TTTTGGGGTATGATATCAGAAGCACAGGCAAAAAAAGCAAAAATGAACAA 901
                          i  i i-     i i  i       i    v     v      ii i  
  L1M4_orf2#LINE/    587 TCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_150688114_    902 GTGGGACTACAT-GAAATTACAAG-------GCTCCCA----CAC----- 934
                         i v     v   -i      v  i-------   i v ----   -----
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_150688114_    935 ----AGCAAAGAAACCATCAGCAAAATG-----AAATA----CAAGATAC 971
                         ----  ii  i i  v i vi  i    -----     ----   ivi i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_150688114_    972 GTATCTGATAAGAGGTCAATACCTATTCATGAAACATGTAAGGAACTTAC 1021
                         i           i iiivi  i i ------i  i  i   i     ivi
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCA------GAATATATAAAGAACTCTT 779

  chrX_150688114_   1022 ACAACCCAATAACAAACAAACATAAAGAAAATCACAAAACAACATCAAAC 1071
                              i      i   v i   ---------------  i   -------
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACA---------------AATAAC------- 807

  chrX_150688114_   1072 TCCAAATACATTAATTTTAAAAATGGGCAAATGACCTGAATGGACATTTT 1121
                         -    ----------  ?             v  ii     i       i
  L1M4_orf2#LINE/    808 -CCAA----------TTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_150688114_   1122 TCTGAAGAAGACATACAAATGGCCAATGGATATGTGATAAAATGCTCAAC 1171
                           ii       i               iiii ii   v  i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_150688114_   1172 ATCACCAATCAT 1183
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.76 (116 / 42)
Gap_init rate = 0.02 (13 / 671), avg. gap size = 5.54 (72 / 13)  


1746 26.51 5.40 0.82  chrX_150746326_150747910      483  1093 (492)    L1M4_orf2#LINE/L1      270   908 (0)  

  chrX_150746326_    483 GCATTAGCA-AAGAATAGACACATAGATTAATAAAACAGGAT--AGGGCT 529
                          i i i   -   i       i      i   ii  i  i  --  i ii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_150746326_    530 CAGAAATAGACCTGCACACATAAAGTCAGGTGATTTACAACAAAGG---C 576
                                 i   iii   iv  vi    iv      v i    i  --- 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_150746326_    577 AA-------TAATGGTAAAAGTATAGTTTTTCCAACAAATGCTGCCTGAA 619
                           -------i     vi    v     i   i         v   iv i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_150746326_    620 CA-TTGGACATCTATACACACATAATAAT-AACCTAGACATAT-CCTTAC 666
                           -i    i ? i --  ii  v  v   -  vi i   viv -   i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCA--CATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_150746326_    667 AT-ATTTCAAAAAAAATTAACTCAAAACACATCATAGACCTAA-TGCAAA 714
                          i-  v -- v                iiv    ?        -  i  i
  L1M4_orf2#LINE/    468 ACCATAT--ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chrX_150746326_    715 ATGCAAAATCCATACAACTTCTATACGAAAACATAAGAGTAAATCTACAT 764
                          -  v   v i   v    ii  v v         i ?        v i 
  L1M4_orf2#LINE/    516 A-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chrX_150746326_    765 AATTTTCAGTTTGGTGGTGAGTTTTTAAATTCAACACCAAAAGCATCATC 814
                         i ii  vi   v  iii  iv  i   i  vii            iv v 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chrX_150746326_    815 AATGAAAGAAAAATTTGCCAAGTTGGACTTTATTAAAATAAAAATAGTAT 864
                           ii         v v vi  i        i  i     v    vvv v 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chrX_150746326_    865 GCTCTTCAAAAGACAGTGTGAATAGAATAAAAACAGAAGCTACAGACTAG 914
                          iv       i    v i v  v i i i    v v  v i     v i 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chrX_150746326_    915 GAGAAAACATCTGTAGTATACATAAGTGATAAACAACTTGTCTCTACAAT 964
                                i  i  i ivvi i   vv      ivi      v  i v   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chrX_150746326_    965 ATACACA-AATTCTTAAAACTCGATGATAGAAA--TAAATGA-------- 1003
                            i v -  i     v     i  i   i   --i    i --------
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_150746326_   1004 --AAATAGTCAAAG-ATCTGGACAGACACTACACCAAAGAAGATATACAG 1050
                         --    i v     -  i  i i     i v v                i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_150746326_   1051 ATGGCAAATAAGCATAATAAAAG-TGCTGAACGTCCTTTGTCAT 1093
                              v        i vv     -    v   i  v????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (98 / 61)
Gap_init rate = 0.03 (17 / 639), avg. gap size = 2.24 (38 / 17)  

 337 30.07 9.79 0.00  chrX_150746326_150747910     1439  1581 (4)    L1M4_orf2#LINE/L1      286   442 (466)  

  chrX_150746326_   1439 AAACACGTAGATTAAAAAAACAGAAT--AGAGCCCCAACATAGACCTGCA 1486
                          i   ii     i  vii  i     --    i  vi v   i   iii 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_150746326_   1487 CACATACAATCAAGTGATTTATAACAAAAG---CAA-------TAAAGGT 1526
                           iv  iii    v      vii    ii ---   -------i  v  v
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_150746326_   1527 GAAAGTATAGTTGTTCCAACAATTGGTACATGAACAACTGGGTATCTAAA 1576
                              v     iv  i      v    i vv i        i  ? i v 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_150746326_   1577 --CAAAA 1581
                         --     
  L1M4_orf2#LINE/    436 TGCAAAA 442

Transitions / transversions = 2.00 (28 / 14)
Gap_init rate = 0.03 (4 / 157), avg. gap size = 3.50 (14 / 4)  


1515 26.28 5.75 0.41  chrX_150777103_150779051.rev      501   987 (961)    L1M4_orf2#LINE/L1      241   753 (155)  

  chrX_150777103_    501 TACAAAGCTATAGTGATCAAGATGGTGTGGTTTTAGC-TAAGAGACAGAG 549
                                   i   i       ii       vi i  -    -  i   v
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGAC 289

  chrX_150777103_    550 ACATAGATTAATAAAACCAGAT--AGAGTTCAGAACCAGACTCACATAAA 597
                          i      i   ii  ivii  --     i     vi i  i  i i vv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_150777103_    598 TACAGCCCAGCAATTTTT-ACAAAAG-ACTAAGGCTATTCAATTGAGAAA 645
                           ii i v vii     i-    ii -i i   i i       v i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_150777103_    646 TATTGG-CTTTTCAATAAGTGCTATTGGAACGATTAGACATGTTT-TGTT 693
                         v v i -        i  i  v ii   i  i i i  i ?vivi-  iv
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_150777103_    694 AAAAATTGAAACTCTACCTAAACCTCACACTTTAAACAAAAACTAACTCA 743
                            i v    ii vv   ivv         iv  v       i       
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_150777103_    744 AAATGCATTA----TCTAGATGTTAAATGAAAAACTATAAAAGTTTTAAA 789
                              v  i ----i   i    v i vvv            v i   i 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chrX_150777103_    790 AGAAAACAT-GGAGTCAAGTCTTCATGACCTAGAGTTAGGCAAAAAGGTC 838
                                  -  ?  -  i     i      v i         viivv  
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGT-AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_150777103_    839 TTAAACATGACACCAAAAGAATGACTCATAAAAGAAAAAA-AGATAAATT 887
                            i i             v ii viv i           -         
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_150777103_    888 AAACTTCCTCGAAACGAAAAACGTTTG--CTTTGA--GA-------AAGA 926
                         ii     v  i   iv      v    --   ii --  -------    
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_150777103_    927 A--TAAAAAGTCAAGCTACAAACTGGAA--ACATTTTTGCCAATCATATA 972
                          -- i     v   v i   i v   i -- v  v     v         
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_150777103_    973 TCTAATAATGGTCTT 987
                            i    v  v   
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTT 753

Transitions / transversions = 1.74 (80 / 46)
Gap_init rate = 0.03 (16 / 513), avg. gap size = 1.88 (30 / 16)  

 354 24.67 3.33 3.33  chrX_150777103_150779051.rev     1309  1458 (490)    L1M4_orf2#LINE/L1      759   908 (0)  

  chrX_150777103_   1309 CAAATTACATGAAGAGCTCTCAAAACTCCAATATGATAAAATAACAACAC 1358
                           i v  i  i    i    i v     -    --      vi    - i
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTC-AATA--ATAAAAAGACAA-AT 804

  chrX_150777103_   1359 AAT--ATTTTAA---TTGCCAAAAGATAACGATACATACTTCACCCAAAG 1403
                           i-- v  ?  --- v v    i   vvvi   v i i   -i      
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC-TCCAAAG 853

  chrX_150777103_   1404 CAGACATGTGGATGGCCAGTAAGCACATGGAAAATTGTTCTACATCTTTA 1453
                         v   i  iiii       i          i   iv  i  v     v???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_150777103_   1454 GCAAT 1458
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.57 (22 / 14)
Gap_init rate = 0.04 (6 / 150), avg. gap size = 1.67 (10 / 6)  


 903 27.06 1.98 2.31  chrX_150838990_150840983.rev      193   495 (1499)    L1M4_orf2#LINE/L1      359   660 (248)  

  chrX_150838990_    193 ACAAGG-TGTAAAGTCAATTCAATGATGAAAGAA-AGTCTTTTTAATAAA 240
                               -  iv   v v        iv       -        i  i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_150838990_    241 TGGTACTATGAAAACTGGATATCTGTGGGGGGTGGGGAAATGAATCCTAA 290
                             i  iv  v         ? iiiiv ---iiiiii      viivi 
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATG---CAAAAGAATGAAGTTGGA 455

  chrX_150838990_    291 TCCTTACTTCACACCATATACAACATTTTAATTTAAAATTGAGCATAAAC 340
                         i  i   i               v v  -  i i     v  v  ? i  
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATT-AACTCAAAATGGATCAWAGAC 504

  chrX_150838990_    341 CTAAATGTAGAAGCTAAAACTAAAAAAATTTTTAGATAGAAA---T-GGA 386
                                  ii           v    -i i     -     --- -  ?
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGA-AGAAAACATAGGN 552

  chrX_150838990_    387 GAAAATTCCCATAATCTTGGGGTAGACAAATATTTATTCACCAGGGCATA 436
                          v    iii i i i      v   i   vvi   v  vivi v i  iv
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chrX_150838990_    437 AAAATCACTAACCATAAAAGGAGAAAAATGATAAATTGTGCTTTCTTAAA 486
                             v   v i v i     i i   v -         vi   iv i   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTCATCAAA 651

  chrX_150838990_    487 ATCAAAAGC 495
                           i    i 
  L1M4_orf2#LINE/    652 ATTAAAAAC 660

Transitions / transversions = 1.72 (50 / 29)
Gap_init rate = 0.03 (9 / 302), avg. gap size = 1.44 (13 / 9)  

1664 24.38 6.99 3.73  chrX_150838990_150840983.rev      502  1145 (849)    L1M4_orf2#LINE/L1      192   856 (52)  

  chrX_150838990_    502 AAAGAAGAATAAAGTTGGAGGTCCTATACTACTAGATTTCAAGATCTACT 551
                                  i           v ii i   v ivi       i ii    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_150838990_    552 -----TTT----TAATCAAGACAGTGTAGAAATGCCATAAGGATAGACAC 592
                         -----vi ----               i v v  v              i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chrX_150838990_    593 ACAGATCAGTGAAACAGAATTGAGAAGCCAGAAATAGACACATGCAC--- 639
                          i      i  i  i          iv         i  v   i  i---
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_150838990_    640 -AGTCATTTGATTTTCGCAAAGGTTTCCAAG-CAATACAAGGGGCAACAA 687
                         -i    v          vv    v v     - v  v   v   v  vi 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_150838990_    688 AAAAACGTTTGAACATATGGTGCTGGAACAACTGGTTAGCTATATTGAAA 737
                          v iv v   v    v          i        v  ? i i  vv   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_150838990_    738 AACACACACCT---CCAATCTACCACACACCATA----AAGATTAATTCA 780
                          iv iiv vi ---  --i     v         ----  i     i   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACC--CCTACCTCACACCATATACAAAAATTAACTCA 489

  chrX_150838990_    781 AGATAAATCACATACCTAAATGTAAAAACTTACAATCCTAAATCTTTT-T 829
                          i  ii    ? v            i i  - v  iiv    v  i  -v
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAG 538

  chrX_150838990_    830 AAGAAAA-AT-GAAGAATGTCTTTGAGAACTGGAGGTAAGCAAAGGTTTC 877
                                -  - i? v vi    i v  v  v i v  i    v      
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_150838990_    878 TTAA----GCCACAGAAAGCACTAATCATAAATAAAAAA-----CAAAGT 918
                            i---- v   vi       v iiv i   vi     -----i   v 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_150838990_    919 GAACTT----AAAATCAAAA---TTTCTGTTTCATAAGACACTTATTTCT 961
                          i    ----     i    ---   v  i    v i      -------
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT------- 681

  chrX_150838990_    962 GCTCATAATTAATAAAATGAATGG-CAAATCATAGGTTGGAAGAAAGTAT 1010
                         -------  i  v   i    vi -   vi  i  iv   i     i   
  L1M4_orf2#LINE/    682 -------ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_150838990_   1011 TCCCAA--CACATATCTTACAAAATACTGTTTTTCAGAATATATATATAT 1058
                          iv   --  i      v i  iiv   vv v i           v ---
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA--- 771

  chrX_150838990_   1059 GCGCTCTCCTGCAGCTCAGTAAGAAAAAGACAAAATAAAAACACTTTAAA 1108
                          vi    -- i  i    i   v           -   vv-  v  ?   
  L1M4_orf2#LINE/    772 GAACTCT--TACAACTCAATAATAAAAAGACAAA-TAACC-CAATTWAAA 817

  chrX_150838990_   1109 AGTTGGCAAAATATGTGAACAAACCATTCAC--AAGAGG 1145
                          i v      iv  v    i i  vv   v --    i 
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

Transitions / transversions = 1.10 (80 / 73)
Gap_init rate = 0.03 (23 / 665), avg. gap size = 3.00 (69 / 23)  

 247 17.46 3.17 0.00  chrX_150838990_150840983.rev     1441  1503 (491)    L1M4_orf2#LINE/L1      844   908 (0)  

  chrX_150838990_   1441 TTCACAAGAGAA-ATATATAAATGGCTAA-AAACATATGAAAAAGTATTC 1488
                            v v i    -     i       i  -  i  i       ii ii  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_150838990_   1489 AACATCAGTAGCTAT 1503
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 4.50 (9 / 2)
Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2)  


1276 25.44 1.48 1.48  chrX_150850142_150851868      162   499 (1228)    L1M4_orf2#LINE/L1        1   338 (570)  

  chrX_150850142_    162 TGGAAGAACATTCCATGCTCATGGGTAGGAATAATCAATATCGTGAAAAT 211
                              ii i  i     i      i v    v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150850142_    212 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 261
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150850142_    262 TACCAATGACTTTCTTCACAGAA-TTGGAAACAA-CT-ACTTTAAAGTTC 308
                          v   iivi i  i  ii     -   ---    -  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_150850142_    309 ATATGGAACCAAAAGAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 358
                                 viiv   i  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_150850142_    359 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 408
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_150850142_    409 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 458
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_150850142_    459 CAATGGAACAGAAT--AGAGCCCTCAGAAATAATGCCGCATAT 499
                                 i     --    i  --        vv  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACAT 338

Transitions / transversions = 1.97 (57 / 29)
Gap_init rate = 0.02 (6 / 338), avg. gap size = 1.67 (10 / 6)  

2303 27.79 3.00 0.54  chrX_150850142_150851868      501  1234 (493)    L1M4_orf2#LINE/L1      157   908 (0)  

  chrX_150850142_    501 TACAAAAAAGTCCAAATAGCCAAAGCAACTCTAAACAAAATGAACAAACC 550
                          i   iii vi vi          i   iii i  v  i v       vi
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chrX_150850142_    551 TGGAGGCATCACATTACCTGACTTTAAAATATATTACAAGGATATAGTAA 600
                               vv     i v  ii i  i    iv  i     i v  i     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chrX_150850142_    601 CCTAAATAGCATGGCATTGGTATAAA---------ATAGATCAACAAAAC 641
                         i v i i  ii   i i   i    i---------         iii  i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chrX_150850142_    642 AAAATAGAGAATCCAGAAGTAAAGACACATATTTATAGCAAAATGATCTT 691
                          i   v    i       i    vv  i i      i iv  v    i  
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chrX_150850142_    692 CAGCAAAGCTGACAAGAACTTACACTGGGGAAAGGACACTTTTTTTAGTA 741
                          ii   i v  v     v v v  v         i i v i    i ii 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chrX_150850142_    742 AATGGTGCTGGGAAAAATTTGATAGTCACAAGCA---GATTGAAACAGGG 788
                                      v  -i v    ?i    v   ---  v    iiv  i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chrX_150850142_    789 CTCTCATCTCTCACTATATATAAAAATCAACACAAAAGGGCTTAAAGACC 838
                          i ii i   v   i     i      i   v     v  v i ?     
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chrX_150850142_    839 TAAACATAAGACCTGAAACTATAAAAATACTAGAAAAAAACTTAGGAA-A 887
                             ii     v  i           v vi     i     v    ?i- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chrX_150850142_    888 AGCTTTCCTGGACATTGGTCTAGGCAATGAATTTGTGACTAAGACCTCAA 937
                          iii   v  -  v    vi         iv  iv iiv  v   vi   
  L1M4_orf2#LINE/    556 AATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_150850142_    938 AAGCACAGGCAACAAAACAAAAA-TAGACAAATGTGACTTAAATAAACTA 986
                                i         v     -    i    vv     v vi   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_150850142_    987 AATAGCTTCTGTACCAAAAAAGAAATAGTCAATAAAG-----AGACAACT 1031
                           v i   i   i ivv   i  v ivi    v    -----       i
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_150850142_   1032 TGTTGAATGAAAGAAAACATTTGCAAACTATTCATCTCGCAAAAGACTCA 1081
                         iiiv     ii      i         ii  vi    vii  ii    ii
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_150850142_   1082 TATCCTGAATATACAAGGAACTCAAATACTTAAATGGAATAAAAA--CAA 1129
                              v       i  i      vv i vi v   --        --   
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAAT--AATAAAAAGACAA 802

  chrX_150850142_   1130 ATAATTCCAATAAGTAGTGGACAAAGGACATGAATAGGCATTTCTTAAAA 1179
                             ii v v ? iv i   i       iv       i       iv   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chrX_150850142_   1180 GAATACATGTAA-TGATCAACAAGTATATTAAAAAGTGCTCAACATCACT 1228
                            v i  ii  -  ii   i   i i  v    ii            ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chrX_150850142_   1229 AATCAT 1234
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.78 (128 / 72)
Gap_init rate = 0.01 (10 / 752), avg. gap size = 2.60 (26 / 10)  


2698 27.62 3.72 1.35  chrX_150889543_150894558      492  1378 (3638)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_150889543_   1378 TGGAAAAATATTCCATGCTCATTGACTGGAAGAACCAAAATCATAAAAA- 1330
                               i    i     i    v  i       vii  v  ii v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_150889543_   1329 -GCAAT---------------TTACAGATTCAGTGCTATTCTTTTCAAAC 1296
                         -     ---------------i          ii  v  i i v     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_150889543_   1295 TACCAAAGCTA--TTCTGTGAAGAATTAGAAAAATACT-ACTTTACAATT 1249
                          v   --   i--  i v  v    v v  v  i--  - iii  v    
  L1M4_orf2#LINE/    101 TCCCA--GCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT 146

C chrX_150889543_   1248 CATATGGGAC--CAAAAAACGGGCCTGAATAGCCAAGGCAATCCTGAATA 1201
                                i v--   iii  ---  v          ii     i    v 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGAC---CCAGAATAGCCAAAACAATCTTGAAAA 193

C chrX_150889543_   1200 AAAAGAACAAAGCTGGAGGTATCACACTACTCAGATTCAAACTATACTAT 1151
                          i          i      vv       v i  iv      viv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

C chrX_150889543_   1150 AAAGCCACAGTAACCACAACAACTTGGTACTGGTACAAAAATGGACACAT 1101
                              i       i  vi   iiv         i i  ii  i    i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

C chrX_150889543_   1100 AGACCAATGGAACGGAATAGAAGACTCAGTAATAAAGCTACACACCTACA 1051
                            i        ii    v  iiiii   v      v i i   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

C chrX_150889543_   1050 ACCATTTGATCTTCAACAAGG---CCAAGGAAACCAAGAAATGGAGAAAG 1004
                         ii  v     i   i      ---     ---    vvv     i     
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAG---ACCATTCAATGGGGAAAG 390

C chrX_150889543_   1003 GACTCCCTATTCAATGAATGGTGCTGGGATAACTGGCTAGCCATATGCAG 954
                         i ivvi  v     ii             i      v  ?   i     i
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

C chrX_150889543_    953 AAGGTTGAAGCTGGGCCCCTACCTTTTTATCACAGGTAGAAATTAACTTC 904
                            iv     i   i         ivi- i  i vii i         iv
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCAC-ACCATATACAAAAATTAACTCA 489

C chrX_150889543_    903 AAATGGATTAAAGATTTAAATGTAAGACCTCAAACTATAAAATTCCTGCA 854
                                 i ?   ii           v  v           i  i iv 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

C chrX_150889543_    853 AGACAACTTAAGAAATACTCTTCTCAATATCAACCTTGGCAAAGAATTTT 804
                            v   v  i ?ivv v     vii iv iiivi v     v iv  i 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

C chrX_150889543_    803 TGGCTAAATCCCCACAAGCAATTGTAACAAAAACAAAAATTGACAAGTGG 754
                          i v  viv v   v     vvv i       iv      v  i  i v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

C chrX_150889543_    753 GACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTAACAG 704
                            i v  i   v v  i i   i  ii vv    i  v     i  v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

C chrX_150889543_    703 ATTAAA----CAGTCTACAGAGT---ACAAGATATTCACAAACTATGTAT 661
                          v i  ----  ii i     i --- v  i     ii    ii  i   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

C chrX_150889543_    660 CTGACCAAGGCCTAATATCCAGAATTCATAGGGAACTTAAACAAATGAAC 611
                             iv i  v  vi          vi   ii     ivv    v v  i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

C chrX_150889543_    610 AAGCAAAAACCAAGTAACTCCATTTACAAATGGTCAATGGACATGAAGAG 561
                           vv    iv   i    i v   ? v      v   v   iv    v  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

C chrX_150889543_    560 ATATGTCTCAAAAGAAAACTA-ACAAGTGGCCAACAAACACATGAAAAAC 512
                          i  v    v      i -  -    i       i  i          iv
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGA-TATACAAATGGCCAATAAGCACATGAAAAGA 888

C chrX_150889543_    511 TTCTTAGCATCACTAATCAT 492
                          v  i i     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 3.00 (45 / 15)  

4063 18.99 2.81 0.90  chrX_150889543_150894558     3638  4527 (489)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_150889543_   3638 GGAAAGTCATTTCGTGTTCATGGATTGTAAGACTTAATATTGCTAAGATG 3687
                               vi  ii i             v              i       
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_150889543_   3688 TCTATACTTTCTAAAGTGATAAGTAGATTAATTGCAAATCCCATAAAAAT 3737
                         v v     ii i   v    vvii     v vi    vi  i  v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_150889543_   3738 CTCAATGGCCTATTTTACAGAAATGGAAAAGTTGATCCTGAAATTCATAT 3787
                          i  iiv    v    i       v  v   i       i          
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_150889543_   3788 GGAATTACAAGGGGCCTTGAATTGCCAAAACAATACTGAAAAAGAAGAGT 3837
                             v i      i  iv    v           vi            ii
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_150889543_   3838 GAATTTGGAGGACTCACACTTCCTGATTCCAAAACATATTAAAAAGCTAC 3887
                         i  v                   ii   i      v  i  v        
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chrX_150889543_   3888 AGTAATCAAAATGGTCAAGTATGGGTATAAGGATAAACATATAAATCAAT 3937
                                  i ii  vvi   iv  i         i       i      
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chrX_150889543_   3938 GGAATATAATTGAGAATCCAAACAAAAATAGATACATGTATGGTCAACTG 3987
                               v        i    i v v   ivv      v         i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chrX_150889543_   3988 ATTTGTGACAAGGTTTCCAAGACCATTCAAAGGAGGAAATAATAATCTCT 4037
                             vi       v v              v  -     v    i   i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTT 400

  chrX_150889543_   4038 TCAACAAATGATGCTAGGACAATTGTATAACCACATACAAAAGAATGAAG 4087
                                   i    i      i  v   ?      i             
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_150889543_   4088 TAGAATTCTTACCTTACACAATATACAAAGATTAACTCAAAATGGATCAA 4137
                          v i ii i     i    v         i                   ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_150889543_   4138 AGATATAAATGCAAGATGTGAAACTATAAAATTCTTAGAAGAGAACATAA 4187
                            iv      i    vv i           i          i      i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_150889543_   4188 GGGTACATATTCATTACCTTGAAATTGGCAACAGATTTTTAAAATATGAC 4237
                          ?   v  v   i v      iiv v     ii v  i   i -      
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGAC 599

  chrX_150889543_   4238 G----------AAGCAACA---GAATAAATAAGTAAATTGGAATTCATCA 4274
                         i----------        ---   v     ii         v       
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_150889543_   4275 AAATTTTGAAAA---TTGT----CAATGGGAAGGCACTATCAAGAAACTG 4317
                              --i    ---    ----   ---- i i             v  
  L1M4_orf2#LINE/    650 AAATT--AAAAACTTTTGTGCTTCAA----AGGACACTATCAAGAAAGTG 693

  chrX_150889543_   4318 AA--GGCAAACTATTGAGTGGTA-AAAATACTTAAAGATCATATATGTGA 4364
                           -- i   v i iv  i   v -      i  iv i         v   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_150889543_   4365 TAAGTGTCTAATATCCAAAATATGTAAAGAAAAGCTAAAACTCAACAACA 4414
                             v v  vi      i     i       vvvi  v       i  i 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_150889543_   4415 AAATGACAAGCAACCCAATT--AAAATAAGCAAAGGATTTGAAGAGACAT 4462
                            v     ii         --     ii              v      
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_150889543_   4463 TTCTCCAAAGAAGGTATACAAATGGACAACAGGCACATTAAAAAATGTTC 4512
                                      i           v   i i      v    i   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_150889543_   4513 AACGTTTGTCATTAG 4527
                            i iv????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (98 / 68)
Gap_init rate = 0.01 (11 / 907), avg. gap size = 3.00 (33 / 11)  


3267 26.71 0.56 0.56  chrX_150896898_150899562     1274  2164 (501)    L1M4_orf2#LINE/L1        1   891 (17)  

  chrX_150896898_   1274 TGGAAGAACATTCCATGCTCGTGGGTAGGAAGAATCAATATCGTGAAAAT 1323
                              ii i  i     i  i   i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150896898_   1324 GGCCATACTACCCAAGGTAATTTATACATTCAATGCCATCCCCATCAAGC 1373
                            v     v     iv i  i  i v      i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150896898_   1374 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1421
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_150896898_   1422 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 1471
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_150896898_   1472 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 1521
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_150896898_   1522 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1571
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_150896898_   1572 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCACATCTACAACT 1619
                                i    i--    i  --        vv iii    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_150896898_   1620 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1669
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_150896898_   1670 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGTAGAAAGCT 1719
                           v  i  i              v      v  ?   ii  i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_150896898_   1720 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1769
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_150896898_   1770 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAAC 1819
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_150896898_   1820 CTAGGC-CATACCATTCAGGACATAGGTATGAGCAAGGATTTCATGTCTA 1868
                         v    ?-i v i -   iv   v v  vv ii    v i    v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_150896898_   1869 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1918
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_150896898_   1919 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1968
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_150896898_   1969 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACA 2018
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_150896898_   2019 AAGGGCTAATATCCAGAATTTACAGTGAACTCAAACAAATTTACAAGAAA 2068
                          i  i  vi          v  i iv      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_150896898_   2069 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 2118
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_150896898_   2119 CTCAAAAGAAGACATTTATGTAGCCAAAAAACACATGAAAAAATGC 2164
                            v        i  vi vi i     v  i          i    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (7 / 891), avg. gap size = 1.43 (10 / 7)  

1589 26.82 2.17 0.79  chrX_150896898_150899562     2159  2665 (0)  C L1M4_orf2#LINE/L1   (75)   833   320 *

C chrX_150896898_   2665 CAGAAATAAGGTCATACACCTACAACTATCTGATCTTCAACAAAG-TCAA 2617
                                  ivi      ii  iiiii vi    i   i    i - vvv
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

C chrX_150896898_   2616 AAAACACAAGCAAAGGGGAAAAGATTTCCTTGTCAATAAATG-TGCTGGG 2568
                           i  -  vv   v       ii  vvi   v    i     -       
  L1M4_orf2#LINE/    370 AAGAC-CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

C chrX_150896898_   2567 ATAACTGGCTAGCCATATACATAAGATTAAAACTGGACCTCTTCCTTATA 2518
                          i      v  ?   i  i  v    v i  ii      i  v   i i 
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

C chrX_150896898_   2517 CCATATACAAAAATAAACTCAAGATGGATGAAAGACTTAAATATAAAACC 2468
                                       v       i      v ?    i     i   i v 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

C chrX_150896898_   2467 CAAAACTATAAAAACCCTGGAAGACAACTTAGGCAGTACCACTCTG-GAC 2419
                         i            vi i i     v   v    ?-   vvv  ii -   
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGN-GTAAATCTTCGTGAC 567

C chrX_150896898_   2418 ATAGGAATGGGCAAAGATTTTATGACGAAGACACCAAAA--ACAATTGCA 2371
                         v v  iv i     v i   iv iivv v          --    --   
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GCA 615

C chrX_150896898_   2370 ACAAAAGAAAAATT-GAGAAATGGGATCTAATTAAACTAAAGAGCTTCCG 2322
                                     v -  v    v   ii v  i   v v  i i   ii 
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

C chrX_150896898_   2321 CACAGCAAAAGAAACTAACAACAGAGTAAACAGACATCCTACAGAATGGG 2272
                         ii vv    i  v    v   v i   i  v     v  i          
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

C chrX_150896898_   2271 AGAAAATATTTGCGAACTATGCATCCAACAATGGTCTAATATCCAGCATC 2222
                                      i  ii  ii   ii i  v  v  vi       v  v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

C chrX_150896898_   2221 TATTAGGAACTTAGACAAATT-----TACAAAAACACACAACTGCATTAA 2177
                            v i     ivv    v i-----  v   i   v i   ivv   ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

C chrX_150896898_   2176 AAAGTGGGCAAGGCATTT 2159
                            i       i v    
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTT 833

Transitions / transversions = 1.24 (73 / 59)
Gap_init rate = 0.02 (9 / 514), avg. gap size = 1.67 (15 / 9)  


1437 27.67 6.06 6.62  chrX_150900354_150902278      528  1434 (491)    L1M4_orf2#LINE/L1        7   908 (0)  

  chrX_150900354_    528 GATTTACCATATTTATGACTTGGTAACC--AATATTGGAAAAATGTCAAC 575
                            v v    i  i   iv    v iv --       vv  i   v   i
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chrX_150900354_    576 TGTCTCAAAATTAAGCCATAG--TTAGTACATGTAGAATCAAAATCTTAG 623
                         vv  i v     i v i i  -- i iii  vvivvv         ii  
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chrX_150900354_    624 TATTATTTTTTGTTGTTGGAGAACTTAATAACCTGACTCTAAAATATATG 673
                         i-- iii    ----   v    v  i i  v    ii       vi  i
  L1M4_orf2#LINE/    107 C--TGCCTTTT----TTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_150900354_    674 TGGAAAT-CAAAGTGCCAAAAGTAGC-AAAGTGTATCTTGAAGGGAAAGA 721
                                -   i vi  v i i    -   iii-        iiii    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACA-ATCTTGAAAAAGAAGA 199

  chrX_150900354_    722 ACAAAATAGGAAGGCTTACAATGATAAATAGCAAGACATGTTAAAAAAAA 771
                              i v   i i  i   v vviv   vv   i  v ii  v   ---
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA--- 246

  chrX_150900354_    772 AGGTATAGTAATTAAAACAATGTGGCATTGACACAGAGACA--CAAATAG 819
                         - v  i      i  i   i     i i  i  i ii  i --  v    
  L1M4_orf2#LINE/    247 -GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_150900354_    820 AT----GAAACAAAAT--AGAGTCC-GTAATCA-TCCATATATAGATCTT 861
                           ---- i  i i   --       - v   v -i     i  -----  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT-----TT 340

  chrX_150900354_    862 ATAAGATCTTCTGATTTATGACAAAGATG-----ACTCTTTAATCCAGAG 906
                           -- i  vvi      vi     i i  -----  iv  i   ----- 
  L1M4_orf2#LINE/    341 AT--GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-----G 383

  chrX_150900354_    907 GGGAATAGATGATTTTTAAAACAAATGGT-CTGAATGTATAAGT---TAC 952
                              vii  ii i   vv          -   --- v i  v ---  ?
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTG---GGACAACTGGATAK 430

  chrX_150900354_    953 CCATGCATTGGGGAAAAAA--AAATCAAATCCTAACGAGTATATCACACC 1000
                            --   -- vi   i  --  i iii i  i------  iv       
  L1M4_orf2#LINE/    431 CCA--CAT--GCAAAAGAATGAAGTTGGACCCC------TACCTCACACC 470

  chrX_150900354_   1001 ATACACAAAGATCAATTCCATATGGATAGTAAGCATAAATGCAAAAATTA 1050
                            i     i  i  i  v v      vi? ii v      i  i ii  
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_150900354_   1051 AAACAATTAAACTTTTTAAGGATAATATAGA---ATATCTTCATGACTTT 1097
                             v  v     i  vi i  v  i    i--- v      i    i  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_150900354_   1098 GGAGTAAGCAATACTTTCTTAAATTAGAAA--AAAGGCATAA----TAAA 1141
                           iv  i     iv       i  vv  v --   i   i  ----i   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chrX_150900354_   1142 A----ATATTGATAATTTAGACCTCATTGAAATTATGAACACTGAT-CAT 1186
                          ---- v  v     v  i   i    ii      vi   vi vi - v 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chrX_150900354_   1187 CAAAAGATACCATTAAAAGA-TAAAAACTTGCAAGCCATAAAGTGGACTA 1235
                             i  i  i  i  i i - i    v--i   v   i i i   ivv 
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAG--ACAACCCACAGAATGGGAGA 718

  chrX_150900354_   1236 ATATACTGGCAA--TATATATTAGACAA------TGCATCCAGAATGTAT 1277
                          v   i v    --i      iv  i  ------  i         i   
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chrX_150900354_   1278 TTGTGTGTGCTTTTATACACAAATACTCCAGAAAATCATTAAGAAAAAGA 1327
                         ------------------ v i -    iviv  v   v   v       
  L1M4_orf2#LINE/    769 ------------------AAAGA-ACTCTTACAACTCAATAATAAAAAGA 799

  chrX_150900354_   1328 CAGAAATCCTCCCCTCACCAAAATGGTCAAAATACTTCA-CAGGGACTTC 1376
                           i v v  - vvi ? --       v    iv i  v -i  iv i   
  L1M4_orf2#LINE/    800 CAAATAACC-CAATTWA--AAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_150900354_   1377 AGCAAGAAGAATAAACAAATAACTAATA----TATGAAAAGATACTGAAA 1422
                         vv   ii ii   v      ii i    ----i          i  v  v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_150900354_   1423 ATAATTAGTCAT 1434
                           v ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (153 / 95)
Gap_init rate = 0.04 (39 / 902), avg. gap size = 2.95 (115 / 39)  


2528 27.24 2.77 2.21  chrX_150902849_150905358.rev     1119  2021 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_150902849_   1119 TGGAAAGCTATGCCAAATTCATGTATTTGAAGTTTCAATGTTATTAAGAT 1168
                                v   v   vi      v   v    vi i   i  i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150902849_   1169 ATCAATTCTCCC-AAATT----TATAGATTTGACATAATCCCAGTCAAAA 1213
                         iv    v     -     ----  i     ii  ii      vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150902849_   1214 TACCAGCAGGGCTTTGGATTTTTTAATAGAAAACTATAAGCTGATTTTGG 1263
                          v     -------  vv      i-i     viv i        ii --
  L1M4_orf2#LINE/    101 TCCCAGC-------TGCCTTTTTTG-CAGAAATTGACAAGCTGATCCT-- 140

  chrX_150902849_   1264 AAAAGCAAAACAAAGCAAATAAGCAATAAGT--AGAAAAGCCAAAGAAAT 1311
                             viv v i--- v    --    viiii--    v       iv   
  L1M4_orf2#LINE/    141 AAAATTCATAT---GGAAAT--GCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_150902849_   1312 TTTAGAAATGAAGAACACAGTTGGAGGATTCA-ACTACTTGATTTCAACA 1360
                         i  ii   v        v          i   -   v iii       v 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_150902849_   1361 CTCACTATAAAGCTGAATTAACCAAGACTTTGTGGGATTGGCCATAAT-A 1409
                           i    i      iv v   i      vv     v i    -    v- 
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGA 284

  chrX_150902849_   1410 CAGACAAACAGATCAATGGGACAAAAT--AGAGTTAGCAGAAGAAGATGC 1457
                         i     v i          i i i   --     i--     iv i iv 
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTC--CAGAAATAAACCC 332

  chrX_150902849_   1458 ACACATATACAGTAAATTTATTTTCAACGGAGATGTAAAGGAAATTTAGT 1507
                          i    v  ii  v    v      i  iii i  iv   ivv   i i 
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chrX_150902849_   1508 GAAGAAAGCATAGTGCTTTTAGTAAATGATGCTGGAAGAATTG-ACATTT 1556
                          ii     v     vi   i ii     i      i v  i  - i ?ii
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chrX_150902849_   1557 ATAAGAAAAATAAAAGAATCTTGACCTTTATTTTATGCCATATACAAAA- 1605
                          i v v    -i  v   vi v    ii  ii i ii            -
  L1M4_orf2#LINE/    433 ACATGCAAAA-GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_150902849_   1606 TGAATTTGCATTGTATCATAGACTTAAATATATAAACAAGAACTATAAAG 1655
                          v  i iiv v  v    ?    i     i  vi i v i         i
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_150902849_   1656 CCTCTACATGAAA-CATAAGAGAAAATATTTGAAACCTTAGGTTAGACAA 1704
                          iii  v v    -    i ? v    v  i vi     i      i   
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_150902849_   1705 ATATTTTTTTAGATAGGACACAAAAAGCAAGAGCCATAAGAGAAAAACT- 1753
                         - iv   i       v     v       vi   v i  i       v -
  L1M4_orf2#LINE/    582 -TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chrX_150902849_   1754 GATGAATTAGAGTTTATCAAAATTTAGAATTTCTATTATTCGAATGACAT 1803
                            i    i  v  i         v i  i  i i vv   i  v    i
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chrX_150902849_   1804 TA---AAAGAATGAAAAGACAAGCCACAAGCTTGGAAAAATTGTTTGCAC 1850
                           --- i i i           v     iiv v   i   v i      v
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chrX_150902849_   1851 ATCACATATTTCATAAAGAATGTATATATGGAATATATAAGGAAACCCCA 1900
                             i    i v    i i iv i   vii          i   vi ii 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chrX_150902849_   1901 -GACTCAATAATAAGAAAACACACTATTGAATATATTAATTGACAAAATA 1949
                         -i            i  i   v iv iiv   v? vv   v i    iv 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chrX_150902849_   1950 TTTGT-TATATGCTTCATCAGAGA-----TATAGATGGCAAATAGGCACA 1993
                             v-  v iii   vi  i   -----  i i     v    i     
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chrX_150902849_   1994 TACAAACATGTTCAACATAATTATGAGG 2021
                          iv   v   i       v ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.96 (45 / 23)  


2355 24.67 7.10 2.29  chrX_150915734_150917767.rev      722  1552 (482)    L1M4_orf2#LINE/L1       38   908 (0)  

  chrX_150915734_    722 ATACAGTGAAAACATCAATTCTCCCCAAATTTTTCTATAAATTGACTTCA 771
                            iv  v  i iiv    v           vv    i i   v viv  
  L1M4_orf2#LINE/     38 ATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCA 87

  chrX_150915734_    772 ATCCCAA-CAAAA--CTAACAGCCTTTTCTTTGCAGAC-TTCACAAGTTA 817
                              v -     -- i i v       --       v-  v     i i
  L1M4_orf2#LINE/     88 ATCCCTATCAAAATCCCAGCTGCCTTTT--TTGCAGAAATTGACAAGCTG 135

  chrX_150915734_    818 ATTATAAAGTACATATGGAAATACAAATTACCTGGAATCGCCAAAATAAA 867
                           iv    i v           i   ivv   ii    v       i  v
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chrX_150915734_    868 TTTGATAAGAAAGAACAAGTTTGGAAGACTTACATTTTCTAATCCCAAGA 917
                         i    v  ii        iv     i    i   i  i i   ii   i 
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_150915734_    918 CTTATTACAAAGCTACGGCAATCAAGATTGTGTTATATCAGCATCAAGAT 967
                             i           i i        iv    vi  iii    v i   
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_150915734_    968 AGACAAATAGGTCAATGGAACAGAAT--AAAATCCAGAAATAGACCCTTA 1015
                              v    i         i     -- i i          i    v  
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_150915734_   1016 CATACATGAACAACTGATTTGCAATAAAGCTACAGAGGC-ATAGGAGTGG 1064
                            vi   iv   i      v i i  i v i vi  i -  -vv i   
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT-TCAATGG 384

  chrX_150915734_   1065 AGGAAATATAGCCTTTTCAACAAATTTTGCTTTTAAAATTGGCTATCTAT 1114
                         i i  iv    i             vv    vvv v  i   v  ? i i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chrX_150915734_   1115 ATACCAATCATATCCATATGAGTTATGAACTTTGATCTATACCTCATACT 1164
                           i v  ---------- -  ---     v  v  i iv       i  i
  L1M4_orf2#LINE/    435 ATGCAAA----------A-GA---ATGAAGTTGGACCCCTACCTCACACC 470

  chrX_150915734_   1165 ACATATAAAGATTATCTTTAAATAGATAAGAGACCAAAATGTAAAACCCC 1214
                          i   i   i    v  iv    i   v ?     v        i v iv
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chrX_150915734_   1215 AAACTATAATATTTCTAAAATAAAACAAAAGA--AAATGTTTACAACCT- 1261
                                  v i ii  i  v      v i ?--    v  iiii    -
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chrX_150915734_   1262 ----------ATAGATTTCTTAGACATGACAATAAAACCATGA----TAA 1297
                         ----------  i -         i      vi    v  ii ----i  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_150915734_   1298 AA----AAATAGGT---------TTTATGAAAATTAAAATCTCT-GCTCT 1333
                           ----      i ---------  i  v          v  i - iv  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_150915734_   1334 TCAAAATACATTGTTAAGAGAATGAAA-TACAGGGCATATGCCAGAAGAA 1382
                              iv   i i i    i i     -v   ivv  i vivii i    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_150915734_   1383 AATAATTGCAAATCAT--------TAAGGACTTTATA---AGGATCATAT 1421
                             v           --------     ivi  i  ---  i  -    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT-ATAT 768

  chrX_150915734_   1422 AAATAAATCATAAAACTCCATAATGAGAAGGCAAACA-TTCAATT-AAGA 1469
                            v  v  v  v     v     i i   i    i -ii     -  i 
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chrX_150915734_   1470 ATAGGCAAAATATTTGAAGAGACACTTCGCCAAAGAAGATATACAAATCA 1519
                           i      iv       v     i   v                   vi
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_150915734_   1520 C----AAACAAATATAAAAATG---AATATCATTACTCAT 1552
                          ----  i  v  iv   i   ---  i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (123 / 79)
Gap_init rate = 0.03 (25 / 871), avg. gap size = 3.12 (78 / 25)  


1027 25.64 2.56 1.42  chrX_150929752_150931408      159   509 (1148)  C L1M4_orf2#LINE/L1   (0)   908   554 *

C chrX_150929752_    509 TAAATTTTGAGGTGACTTTGGCTTTGTCAATGAGTTATTAAAT-T--CAG 463
                              i  v--     i    v  v v     iv  v   i  - --  v
  L1M4_orf2#LINE/    554 TAAATCTTC--GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

C chrX_150929752_    462 TAACAATACCAAGATCCATGAAAAAAGTTGATGATACTGGACTTGATTAA 413
                         i  v ii  v iv v v vii     i v   i - i       v  i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAA-ATTGGACTTCATCAA 650

C chrX_150929752_    412 AATTAAAATATTCTACTCTCTGAAATACACTGTTAAGAGAATGAAAATAC 363
                                 vv  i iiv  iii  iv     i i    i i      v  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

C chrX_150929752_    362 AAGCCACAGACCAGAAGAAAATATTTTCAAAGCACATATATGACAAAGAA 313
                           v       vii i           v    v  i    v   i  i i 
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

C chrX_150929752_    312 CTTGTATCTAAAATATTAAAAAGAATATTTAAACCTTAGATA-TAAGAAA 264
                                 i i     - v      ivi   v v  i -   -   i  i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATAT-ATAAAGAACTCTTACAACTCA-ATAATAAAAAG 798

C chrX_150929752_    263 ACATACAACCTAATC-AAAAACAGACAAAATATTC----AGACGCTTCAC 219
                            v i    i   i-     ii i    iv   i----    ii   v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

C chrX_150929752_    218 CAAAGAAGACATACAGATGTGAAATAAGCATATGAAAAGATGTTCAATGT 169
                                  i     i   vvv        i           i    ii 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

C chrX_150929752_    168 CATTTGTCAT 159
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.57 (55 / 35)
Gap_init rate = 0.03 (9 / 355), avg. gap size = 1.56 (14 / 9)  

1198 30.54 4.64 2.99  chrX_150929752_150931408      500  1167 (490)    L1M4_orf2#LINE/L1      230   908 (0)  

  chrX_150929752_    500 TCAAAATTTATCATACAATTACA--AATTAAGAAGGCATGGTGTTGTTTC 547
                               i   ii i v ii    --   i    vi ii    ii  vivi
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_150929752_    548 AAG--TAAA---ATAAACCAATGGAACCCAATGGAGA-TCACAGAAACAG 591
                            --  i ---   i i        ivv   v    -  -      i i
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC-CAGAAATAA 328

  chrX_150929752_    592 ACCCATATATATGTGAATATATGCTTTAAGGCTTTAAGACAAAGGTAGTA 641
                                i  v i  ivi -  ---- i ---   vv     i   ivi 
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCA-AT----TGA---TTTTCGACAAGGGTGCCA 370

  chrX_150929752_    642 TTGCTGAGCAGTAGTGAACGGATGATTCGTTCAACAAAACTTACTGGGGC 691
                         vvi iivv  i i v   v i  ii iiv         vvv i     i 
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chrX_150929752_    692 AAATGAAAACATTTATGTAAAAAGA-GAA-TTA------TACCTCAAAAG 733
                           v  i v ?vivi   i    ii -   -  i------       v vv
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chrX_150929752_    734 CTACATAGTAATCATTTCCAATATGGATCATAAGTCTTAATGAGAAAAGA 783
                         v  i i iv   i vi  v  -        ? iii  v    vi i ivv
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAA-ATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_150929752_    784 AAATCAATAAAACTTCTAGAAGGTAATATACATGAATATTTTTGTTGCTC 833
                            v v        ii      iv  i   vi? v v  i  i  vi ii
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_150929752_    834 TAGAGTAGATAATGATA----AAGCAAAACTAACCACAAAGCACTAATAG 879
                          i iv   ii    i v---- iii vi  --    -       v ii i
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGAC--ACCA-AAAGCACAAGCAA 616

  chrX_150929752_    880 TAAATGAAAAGACCGATAAATTGGACTACATTAAAATTAAGAGCTTTGGT 929
                         i   v     i iv             v   i        i i    ---
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT--- 663

  chrX_150929752_    930 TATTATTTAAAAAGCATTA---AAACAACGAAAAGACAAGCCACAC--TT 974
                          i vv  i   iii  i  --- i v ii          v     v-- v
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_150929752_    975 GTAGAAGACATTTGCAACACATAAAATAAACCAGGTTATTTATACATCTA 1024
                          v    i i        vv    v vivi iv   v- i  i  --  i 
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGG-ACTTGTA--TCCA 760

  chrX_150929752_   1025 CAGTGTATAAATAACTTCTGCAAGTCAATAATAAAGTGACAGAATGA--- 1071
                         v i i      v    ii i   v           iv    -   i ---
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA-AATAACCC 809

  chrX_150929752_   1072 --TGTAAAAATGTGTGAGAGACTGAAACAGACACTTCACAAAAGAAGATA 1119
                         -- v?       v ii ii  i vi  i     i   v v          
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chrX_150929752_   1120 TACAAATAGCCAACAAGCATATAAAATGGTGATCAACCT-ATTTGCCTA 1167
                                i     i     i  i   v i  v     v - ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (123 / 77)
Gap_init rate = 0.03 (23 / 679), avg. gap size = 2.22 (51 / 23)  


1546 27.36 4.64 2.72  chrX_150962758_150964355.rev      495  1119 (479)    L1M4_orf2#LINE/L1      272   908 (0)  

  chrX_150962758_    495 ATTAGCA-AAGAATAAACACATAGATTAATAAAACAGAAT--AGAGCTCA 541
                          i i   -   i   i   i      i   ii  i     --    ii  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chrX_150962758_    542 GAAACAGACTGGCACACATATAGTCAGGTGAATTGCAACAAAGG---CAA 588
                             i i  ivii   iv   i    iv   v  v i    i  ---   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_150962758_    589 -------TAATGGTAAAAGTATAGTTTTTTCCAACAAGTGGTGCCTGAAC 631
                         -------i     vi    v     i     -     i      iv i  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTC-AACAAATGGTGCTGGGAC 420

  chrX_150962758_    632 AATTGGACATCTAGACACAAATAATAATAATAATAATAATAATAACCTAG 681
                           i    i ? i v ii    -- v   i - i viv vivv  v ii v
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAA--AGAATGA-AGTTGGACCCCTACCTCAC 467

  chrX_150962758_    682 AC-ATATCCTTAAAAATTTCACAAGATCAACTCAAAATACGTCATAGATC 730
                           -    v --       ----------          ivi   ?   i 
  L1M4_orf2#LINE/    468 ACCATATAC--AAAAATT----------AACTCAAAATGGATCAWAGACC 505

  chrX_150962758_    731 TAA-TGCAAAATGCAAAAACCATACAACTTCTAGAAGAAAGCGTAAGAGA 779
                            -  i  i -  v     i   v    ii         i i  i ? v
  L1M4_orf2#LINE/    506 TAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_150962758_    780 AAATCTACACAAATTTGAGTTTGATGATGAGTTTTAAAATTCAGCACCAA 829
                               v iii vi   i   v iii   iv  i v i  viii      
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chrX_150962758_    830 AAGTATCATCAATGAAGGAAAAATTAGCCAAGTTGGATTTTATTAAAATA 879
                            i iv v   ii  i      v   vi  i     i  i  i     v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chrX_150962758_    880 AAAATCTTATGCTCTTCAAAAAACAGAGTTAACAGAATAAAAACAGAAGC 929
                             v   v  iv       ii   vvi i  v i i i    v v  v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chrX_150962758_    930 TACAGACTAGCAGAAAACATCTGTAGCACACATATGTGATAAAGAACTTG 979
                         i     v i v      i  i  i ivv  i    v      i i     
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chrX_150962758_    980 TCTCTACAATATACACA-ACTTCTTAAAACTCAACAATAGAAA-----AT 1023
                          v  i v      i v - vi     v       i    i   -----  
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chrX_150962758_   1024 AAAC------GAAAATAGTTGAAG-ATCTGAACAGACAGTACACCAAAGA 1066
                           v ------i     i vii   -  i    i     v v v       
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_150962758_   1067 AGATATACAGATGGCAAATAAGCATAGTAAAAG-TCCTGGACGTCTTTTG 1115
                                  i     v        i vv     - v  vi  i  v????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chrX_150962758_   1116 TCAT 1119
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.67 (105 / 63)
Gap_init rate = 0.03 (17 / 637), avg. gap size = 2.71 (46 / 17)  

 346 25.00 13.19 0.69  chrX_150962758_150964355.rev     1455  1598 (0)    L1M4_orf2#LINE/L1      268   429 (479)  

  chrX_150962758_   1455 TGGTGAATGG-ATAAAGA---ACATATA--TTAAAAAAACAGAAT--ACA 1496
                             - v   -    i  ---       -- i  vii  i     -- v 
  L1M4_orf2#LINE/    268 TGGT-ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chrX_150962758_   1497 GCCCAGAAATAGACCTGCACACATATATTCAGGTGATTTATAACAAAG-- 1544
                          i         i   iii   iv   iv   iv      vii    i --
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chrX_150962758_   1545 --CAA-------TAATGCTGAAAGTATAGTTGTTCCAACAAATGGTGCAT 1585
                         --   -------i    vv     v     iv  i             vv
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_150962758_   1586 GAAAAATTGGACA 1598
                          i v  i    i 
  L1M4_orf2#LINE/    417 GGACAACTGGATA 429

Transitions / transversions = 1.57 (22 / 14)
Gap_init rate = 0.04 (7 / 162), avg. gap size = 2.86 (20 / 7)  


1967 26.78 10.86 1.33  chrX_150982216_150985439.rev     1905  2733 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_150982216_   1905 TGGAAAGTCATTCTGCATTCATGGGTTGGA-GACAGAAAATTGTTAGTAT 1953
                                vi  i iiii       i     -   vv  v       iv  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_150982216_   1954 GTCAGTTTTTCCCAATATGTTCTGTACATACAATATGATTCCAATCAAAT 2003
                          v  i vi i     vv  v   ii v  v   iiii  i  v      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_150982216_   2004 TCTCATCAAGGTATTTTCTAGATATCAACAAACT-ACTGTATATTTTATA 2052
                           i  v vivv v    vi   v  ii    i  - iiv  v v  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_150982216_   2053 TGGA----TAAGAGTAGCTGAGCATAGGCAATACAATAT---AGAAGAAC 2095
                             ----i   i --i iv  v    v   v     v --- i     v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGG--ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_150982216_   2096 AACAAAGTCAGAGGACTCACATTACTTAATTTCAAGACTTACTATAAAGT 2145
                                 ii           i v ii        i        i    i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_150982216_   2146 TATAGTAATCAAGACAATGTGGAATTGGTGAAAGAATAAAAACATAGATA 2195
                           i             i     v i   iiv   i   i v i      v
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_150982216_   2196 AATAGAATAG---TG----TCCAGAAATAGAACCACACCCATAGAGTCAA 2238
                            i      ---  ----          i v   i  viv  vi     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_150982216_   2239 TTTATTTCTGACAAAGGCGCAAATGCAATTTCATGAAGAAAGT-TAATTT 2287
                           v    ii     i  i  v  vi v   iv   ii     v-  i i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_150982216_   2288 TTAAAATAAAATATA-------AAATGAAT--CCAGA--CAAAACC---- 2322
                           vv  i   vvi i-------  v  i  --   v --     vv----
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_150982216_   2323 --TTAGACCTTT------CACTA------AAAACTAATCCAAAATAGCTT 2358
                         --  i    ii ------   i ------    i   ii      i v i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_150982216_   2359 GTAGACCTAAGCGTAAAATGCAGAAACTATATAAAATCTCTAGGAGAAAG 2408
                         i?        ii    i -  vi        -   v   -   i     i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGA-GCTAAAACTATA-AAACTCT-TAGAAGAAAA 545

  chrX_150982216_   2409 CA--GGAGAAAATCTATATAACCTTGGATTTAGTGATGAGTTTTCAGATT 2456
                           --  ? v      vii i       i  vi ii   iv  i i    -
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chrX_150982216_   2457 CATGA------AAG--------ACAAA--------TTGGTAAAGTTAAGT 2484
                         -    ------   --------     -------- v i    -  iiii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA-TTGGAC 642

  chrX_150982216_   2485 ATCGTT----TTAAAAATGTGTGCACTCTGTGAAAAACATTGTAAAGAGA 2530
                         v  i i----       iv v  ii  iii--  ii   i i v    i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAAA 690

  chrX_150982216_   2531 ATGAAAAGAAAATCCACAGA----GAGAAAATAGTTGCAAAACACCTACC 2576
                         i        v  i       ----         v       v  iv  i 
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_150982216_   2577 AAATAAGGCACTTGTATGCAAAATACA--AAAAACT--TAAAACTCAACA 2622
                         vi      v        v  i    i --  i    --  v       i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_150982216_   2623 ATTGAAAACCAGAAAACTCATTT---AACTGGGCAAAGG-TTTGAAGCAG 2668
                           vi   iv  i v   i  v  ---  v          -      -i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA-TAG 839

  chrX_150982216_   2669 ATGCATCACCAAAGAAGACAGGTAAA----AAATGAGCATAGGAAAAGAT 2714
                          iiiv  v          i vii   ----v   i    i v        
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chrX_150982216_   2715 ACTGAATATTATTTGTTAT 2733
                         i  v  i  i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (136 / 84)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 3.16 (101 / 32)  


3203 26.76 0.55 0.55  chrX_151075286_151077589.rev      906  1813 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151075286_    906 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 955
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151075286_    956 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1005
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151075286_   1006 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1053
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_151075286_   1054 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 1103
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_151075286_   1104 AACAAAGCTGGAGGCATGACACTACCTGACTTCAAACTATACTACAAGGC 1153
                                i      vv v     v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_151075286_   1154 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1203
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_151075286_   1204 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAACT 1251
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_151075286_   1252 ATCTGATCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCC 1301
                          vi    i  i     ivv  vv  i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_151075286_   1302 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 1351
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_151075286_   1352 GAAACTGGATCCCTTCCTTACACCTTAGACAAAAATCAATTCAAGATGGA 1401
                            ii    i    v   i     v  v        i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_151075286_   1402 TTAGAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1451
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_151075286_   1452 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 1500
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_151075286_   1501 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1550
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_151075286_   1551 ATTAAACTAAAGAGCTTCTGCACAACTAAAGAAACTACCATCAGAGTGAA 1600
                           i   v v  i i   i  ii vv v  i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_151075286_   1601 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 1650
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_151075286_   1651 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1700
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_151075286_   1701 AAAACAAACAACCCCATCAAAAAGTGGGCGAAAGACATGAACAGACACTT 1750
                           i     i     v  i?    i     i  i  iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_151075286_   1751 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1800
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_151075286_   1801 CATCACTGGCCAT 1813
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3135 28.49 0.33 0.44  chrX_151128804_151135368.rev     5166  6074 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151128804_   5166 TGGAAGAACATTCTACCCTCATGGATGGGAAGAATCAATATTGTGAAAAT 5215
                              ii i  i i ivi        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151128804_   5216 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGT 5265
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151128804_   5266 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5313
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_151128804_   5314 ATATGGAACCAAAAAAGAGCCCACATTGCCAAGATAATCCTAAGCCAAAA 5363
                                 viiv  ii  v  viv  v     i i    i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_151128804_   5364 GAACAAAGCTGGAGACGTCATGCTACCTGACTTCAAACTATACTACAAAG 5413
                                 i     ivv   ii  v  ii i      viv          
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_151128804_   5414 CTATAGTAACCAAAACAGCATGTTACTGGTACCAAAACAGATATATAGAC 5463
                            i     i   i    ii  v      i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_151128804_   5464 CAATGGAACAGAACAGAGGCCTTAGAAATAACACCACATATCTACAACTA 5513
                                 i    iv   iviii        vv   i i  i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_151128804_   5514 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5563
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_151128804_   5564 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTTG 5613
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_151128804_   5614 AAATTGGATCCCTCCTTTAACCCTTATACAAAAATTAATTCAAGATTGAA 5663
                           i     i    v i i vv  v              i    i  v  v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_151128804_   5664 TAAAGAATTAAATGTTAGACCTGAAACCGTAAAAGCCCTAAAAGAAAACC 5713
                         i ?   vi       v   v  i    ii     vi i  i        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_151128804_   5714 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTGATGACTAA 5762
                             ?i- v i -   iv   v v  vv i     v ii  vv iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_151128804_   5763 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5812
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_151128804_   5813 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGGGTGAAC 5862
                          i   v v  i i   i  ii vv    i  v       vv ii     v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_151128804_   5863 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAA 5912
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_151128804_   5913 AGGGCTGATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 5962
                         i  i  vi          v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_151128804_   5963 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACATACACTTC 6012
                          i     i     v  i?    i    ii     iv    i v   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_151128804_   6013 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 6062
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_151128804_   6063 ATCACTGGTCAT 6074
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (156 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.40 (7 / 5)  


2770 25.77 2.75 2.75  chrX_151142604_151144524.rev      529  1436 (485)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151142604_    529 TGGAATAATATTTCTTGCTCATTGGTTGGAAGAATCAATATTACTGAAAT 578
                              vi    ii v  i    v i        v i      ii i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151142604_    579 GGCCATACTGCCCAAAGCAATCTACAGATTCAACACTATTCCTATATCAA 628
                            v     v      vii               i v  i     --   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT--CAA 98

  chrX_151142604_    629 GCTACCAA-TGTCATTTTTCACAGAACTTGAAAAATT-ATTCTAAAATTC 676
                         iv v   i-  i -     ii     v    v  ii -  i         
  L1M4_orf2#LINE/     99 AATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_151142604_    677 ATACAGAACAACAACAACAACAAAAAAACAGTCTGAGGAGCCAAAGCAAT 726
                            ii   vvi   ----------iii  --i v  iv       i    
  L1M4_orf2#LINE/    148 ATATGGAAATGCAA----------GGGAC--CCAGAATAGCCAAAACAAT 185

  chrX_151142604_    727 TATATGCAAAAAGAATAAAGCTGGAGGCATCACATTAGCCTATTTCAAAC 776
                         iv iviv  i     i    i      vv     i vv  v        v
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAA 235

  chrX_151142604_    777 TATACTAGAAAGCCACAGTAACCAAAACAGCATGGTACTGGTACAAAAAC 826
                         iv     v     i       i   i    ii         i i  ii i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chrX_151142604_    827 AGACACATAGACCAATGGAACAGAATGGAGA--CCAGAAATAAAGCCTCA 874
                              i     i        i     v    --           v  vi 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chrX_151142604_    875 CACCTACAACCATCTGATCTTCAACAAAGTGGATAAAAATGAGCAATGGG 924
                           ii  iiii  vi    i   i    i vv vi  i viivv       
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chrX_151142604_    925 GAAAGGACACCCTATTCAATAAATGGTGCTGGAATAAGTGGCTATCCACG 974
                              i i vi  v     i            i i  v   v  ?    i
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chrX_151142604_    975 TGTAGAAGAATGAAACTGGAAAC-TACCTATCACCATATA-GAAAATCAA 1022
                           i i         ii    vv -     vv         -i     i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chrX_151142604_   1023 CTCCAGATGGATTAAAGATTCAAATATAAGACGCCAAA-CTACAAAAATC 1071
                            v i      i ?   iii    i     -  i   -   i    v  
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTC 534

  chrX_151142604_   1072 CTAAAAGAAAATCTAGG---AAATACCCTTCTCAAC-----ATCAGCCA- 1112
                         i  i       iv    ---    ---    vii  -----i i  v  -
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA 581

  chrX_151142604_   1113 TGGTAAATACATGGCTAAGTCCTCAAAAGCAATTGCAACAAAAATAAAGA 1162
                             --- v v i v  v v vi        vvv         iv   i 
  L1M4_orf2#LINE/    582 TGGT---TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chrX_151142604_   1163 TTGACAAGTGGGATCTAATTAAT-CTAAGGTAACTTCTGCACAGAAGAAA 1211
                          v  i  i v   ii v  i  v-i   i--     i  ii vvv i ii
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAA--AACTTTTGTGCTTCAAAGG 676

  chrX_151142604_   1212 AAATTATCAACAGAGTTAACAGACAACCTACAGAATGAGAGAAAATATTT 1261
                          v i      v i   v  v        i        i            
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chrX_151142604_   1262 GTAAATTATGCATCTGATCAAGGTTTAATATCCATATGCTATAAGGAACT 1311
                          i    i  ii       v i  vi vi      v vvv     i     
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chrX_151142604_   1312 TAAATAAATCAAGAAGCAAAAAACAA----CTCCATTAAAAAGTGGGCAA 1357
                         ivv i  v    v  vv    i    ---- i v   ?    i       
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chrX_151142604_   1358 ATAAC----ATGGACACTTCTCTAAAGGAGATATACAAACATCCAAAAAA 1403
                          vi i----  i    i     i    i           iiv    v  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chrX_151142604_   1404 CAAATGAAAAAAATGCTCAATATTGCTAATCAT 1436
                           v       i -       i  ii????????
  L1M4_orf2#LINE/    877 CACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (142 / 89)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.38 (50 / 21)  


2231 27.56 2.31 1.41  chrX_151147631_151152432     3530  4309 (493)    L1M4_orf2#LINE/L1      122   908 (0)  

  chrX_151147631_   3530 AAATGGCCATACTGACC---AAAGCAATGTACAGATTCAATGAGAAGCCC 3576
                             v v  vi    i ---   viv  i iv i  v   - i  --   
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA-GGGA--CCC 168

  chrX_151147631_   3577 A-AATAGCCAAAGAAGTCCTAAGCAAAAAGAACAAAGCCGGAGGCATCAT 3625
                          -          iv i  i i iv  i          ii     vv   i
  L1M4_orf2#LINE/    169 AGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCAC 218

  chrX_151147631_   3626 ACTGTTCTACTTCAAACTGTACTATAAGGCTACAATAACCAAAACAGTAT 3675
                            vii v i      viv     i  i      i   i   i     i 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chrX_151147631_   3676 GGCACTAGAACAAAAACAGACACATAGACCAATAGAACATGCTACAGAAC 3725
                           i   i v i  ii i     i     i    i   i viv vv   ii
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chrX_151147631_   3726 CCAGAAATAAAGCTACACACCTACAACCATGTGATATTTGACAAAGTTGA 3775
                                    v i i   ii  iiii  vv    v  i     i v  v
  L1M4_orf2#LINE/    319 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chrX_151147631_   3776 CAATAACAAGCAATGGCGAAA----AGTCTCCTTATTTAATAAATTGTGC 3821
                            v v  vv      v    ----     i----  i  i    v    
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTT----TTCAACAAATGGTGC 414

  chrX_151147631_   3822 TGGGATAACTGGCTAGCCATATGCAGAAGATCGAAACTATACGTTTTCTT 3871
                              i      v  ?   i     i    vi   ii iv  vii v i 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chrX_151147631_   3872 TTCACCATATACAAAA-TCAACTCAAGGTAGATTAAAGACTTAAATTTAA 3920
                         iv              - i       ii i   i ?    i     v   
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_151147631_   3921 AACCTAAAACTATAAAGACCCTT-GAAGAAAACCTGGG---AAATACCAT 3966
                         i v             -  i   -         v i  ---    -- - 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAAAT--C-T 560

  chrX_151147631_   3967 TCTGGACATAGGACCTGGCAAATATTTCATGACAAAGAAATTAAAAGCAA 4016
                           vv   v v  iiiv     vvi    v iivv v  v ii       v
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chrX_151147631_   4017 TTGCAACAAGAACAAAAATTGACAAATAATACCTAATTAAACTGATGAGC 4066
                         vv       i iv      v  i    viv  i v  i   v v vi i 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chrX_151147631_   4067 TTCTGCACAGCAAAAGA----ATCAAAAATGTAAATGGACAGCCTACAGA 4112
                           i  ii vv    i  ----     i  v  i  vi    i  i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chrX_151147631_   4113 ATGGGA-AAAATAATCACAAACTACACATCTGACAAAGATCTAATTTCCA 4161
                               -      v ii    ii i i      i  i iv  vi v    
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chrX_151147631_   4162 TAATCTATACAGAATTCAAACAAATCAACAAGCAAGAATCAAACAACTCC 4211
                         v   v    v    i  vv    v    i  vv  i iv    i   i v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chrX_151147631_   4212 ATTAAAAAATGGGAAAAGGACATGAACAGACACTTCTTCAAAGAAAACAT 4261
                            ?         v      iv    i     i    i       i i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chrX_151147631_   4262 ACATGCAACCAACAGGCATATGAAAAAATGCTCAACATCACTAATCAT 4309
                            viiii    i i   i       i             ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (127 / 85)
Gap_init rate = 0.02 (14 / 787), avg. gap size = 2.07 (29 / 14)  


3108 27.39 0.55 0.66  chrX_151166500_151169650     1750  2658 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151166500_   1750 TGGAGGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCGTGAAAAT 1799
                             iii i  i     i        v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151166500_   1800 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1849
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151166500_   1850 TACCAATGGCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1897
                          v   iiv  i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_151166500_   1898 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCCAAAAG 1947
                                viiv  ii  v  viv        i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_151166500_   1948 AACAAAGCTGGAGGCATCATGCTACCCGACTTCAAATTATACTACAAAGC 1997
                                i      vv   ii  v   i i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_151166500_   1998 TACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGACC 2047
                                 i   i    ii         i  v ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_151166500_   2048 AACGGATCAGAAC--ACAGCCCTCAGAAATAATACCACACATCTTCAACC 2095
                           i   vi    i-- v  i  --        vv   i    i viiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_151166500_   2096 ATCTGATCTTTGATAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 2145
                          vi    i  i  i  ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_151166500_   2146 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCAATAAGTAGAAAGCT 2195
                           v  i  i              v      v  ? v i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_151166500_   2196 GAAACTGGATCCCTTTCTTACACCTTACACAAAAATTAATTCAGGATGGA 2245
                            ii    i    vi  i     v  i           i   ii     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_151166500_   2246 TTAAAGACTTAAATGTTAGACCTAGAACCATAAAAACCCTAGAAGAAAAC 2295
                          i ?    i       v   v   i   i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_151166500_   2296 CTAGGTG-AAACCATTCAGGACACAGGCATGGGCAAGGACTTGATGACTA 2344
                         v    ? -   i -   iv   viv  vv i     v ii  vv iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_151166500_   2345 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATCGAAAAATGGGATCTA 2394
                         vi            vvi          vv     v  v    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_151166500_   2395 ATTAAACTAACGAGCTTCTGCACAGCAAAAGTAACTACCATCAGAGTGAA 2444
                           i   v v vi i   i  ii vv    i vv    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_151166500_   2445 CAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCATCTGACA 2494
                         v  i     i                 v   i   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_151166500_   2495 AAAGGCTGATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAA 2544
                          ii i  vi          v  i  i     ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_151166500_   2545 AAAATCAAACAACCTCATCAAAAAGTGGGCAAAGGATATGAACATACACT 2594
                           i -    i    iv  i?    i            v    i v   i 
  L1M4_orf2#LINE/    796 AAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_151166500_   2595 TCTCAAAAGAATACATTAATACAACCAACAGACACATGAAAAAATGCTCA 2644
                             v      v i  vv v iii    i ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_151166500_   2645 TCATCACTGGCCAT 2658
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


2217 27.80 9.87 0.84  chrX_151195918_151199367.rev     2129  2959 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_151195918_   2129 GAAAAAAATTCCATGCACATGGATAGGAAGAATCAATATTGTTAAAATGG 2178
                             i v  i     iv       v      v i           i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_151195918_   2179 CCATACTTCCAAAAGCAATTTACAGATTCAATGCTATTCTTATCAAACTA 2228
                          v     i  v   vii  i           i  v  i i       v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_151195918_   2229 CCAATGACATTCTTTACTGAACTAGAAAAAAACT-ATTTTAAAATGTATA 2277
                            iivi v  i   i v   v v  v  i--  -  ii      vi   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chrX_151195918_   2278 TGGAACCCCAAAAGAGCCCAAATAGCCAAGGTAATCCTAAGCAAAAAGAA 2327
                              viv   ii  v  vi         iii    i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_151195918_   2328 CAAAGCTAGAGACATCACACTACCTGACTTCAAACTATACTATGGGGCTG 2377
                              i i   ivv       v  ii i      viv     iiii   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_151195918_   2378 TAGTAACCAAAACAGCATGGTACCGGTACAGAAATAGACACCTAGACCAA 2427
                         i     i   i    ii      i  i i iii       iv    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_151195918_   2428 GGGAACCGAATAGAGAGCCCAGAAATAATGCCACAGATCTACAAACATCT 2477
                         v    iv    v     i          vv   i v  i  iiiv  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_151195918_   2478 GATCTTTCACAGCATTGACAAAAACAAGCAATGGGGACAGAAATCCCTAT 2527
                            i  iv   iviv  v   i v  vv         v    vvvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_151195918_   2528 TCAATAAATGGTGCTGGGA------------------------------- 2546
                             i              -------------------------------
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_151195918_   2547 ---------------------------------------AGGTGGATTAA 2557
                         --------------------------------------- ii     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_151195918_   2558 AAACTTACATGTCAAACCTAAAACTACAAAAACCCTGGAAGATAATCTAG 2607
                          i  i  v    v i v         i    vi i i     v  iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_151195918_   2608 AAA-ATATCATTCTAGACATAGGACCTGGCAAAGATTTCAT-GATGAAGA 2655
                         i?i- v   -   vv   v v  iiiv     v i    v -   - v  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGA 598

  chrX_151195918_   2656 CATGAAAAGCAATTGCAACAAAACCAAAAATTGACAAATGAGACCTAAT- 2704
                           iv       vvv         vv      v  i    vi   i v  -
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_151195918_   2705 AAAATGAAAGAGCTTCTGCACAGCAAAAGAAACTATCAAGGGAGTAAA-- 2752
                              v   i -   i  ii vv    i  v         ii   i  --
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_151195918_   2753 --CAGTCTACAGAATGGAAGAAAATATTTGTAAGGTGTGCATCCAACAAG 2800
                         --  ii i         i            i  ivii ii   ii i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_151195918_   2801 GGTCTAATATCCAGCATCTATAAGGAACCTAAACAAATTCACAAGCAAAA 2850
                           v  vi       v  v     i    iivv    v iv i  vv    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_151195918_   2851 AACAA----CCCAATTAAAAAATAGGCAACAGACATGAACAGACACTCCT 2896
                         i    ----       ?      i     vi  iv    i     i i  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_151195918_   2897 CAAAAGAAGACATTTTTTTGTGGCAAACAAGCATATGAAAAAATGCTGAA 2946
                          v        i  vivv--i    v  i     i       i     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAA--ATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_151195918_   2947 CATCACTGATCAT 2959
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (133 / 95)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 7.42 (89 / 12)  


 664 28.70 7.83 0.00  chrX_151212599_151214565.rev      279   508 (1459)  C L1M4_orf2#LINE/L1   (648)   260    13 *

C chrX_151212599_    508 CCATGTTCATGGATAGGAAGAATCAATACCATGAAAATGGCCATACCGCC 459
                                       v      v i    iii v  i     v    iv  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

C chrX_151212599_    458 CAAAGTAATTTATA------------TTCCCATTAAACTACCATCGACAT 421
                             v i  i  i ------------ i  i  i   v v   v vi v 
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

C chrX_151212599_    420 TCTTCACAGAATCAGAAAAAACTACTTTAAAATTAATATGGAACCAAAAA 371
                          i  ii     viv  v  iviv iii       v        viiv  i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

C chrX_151212599_    370 AGAGCCCAAATAGTTAA-----TCCTAAGCAAAAAGAACAAAGTTGGAGG 326
                         i  v  vi     ii  -----  i i iv  i                 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

C chrX_151212599_    325 CATCACACTCCCC-GCTTCAAACTATACTACAAGGCTACAATAACCAA 279
                         vv       i   -ii      viv        i      i   i   
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

Transitions / transversions = 1.54 (40 / 26)
Gap_init rate = 0.01 (3 / 248), avg. gap size = 6.00 (18 / 3)  

1239 24.32 0.81 2.97  chrX_151212599_151214565.rev      506   875 (1092)    L1M4_orf2#LINE/L1      268   629 (279)  

  chrX_151212599_    506 TGGTCCTGGCACAAGAACAGACACATCGACCAATGGAACAGAAAAGAGAA 555
                             v      i   i i     i  v  i        i    vv    i
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chrX_151212599_    556 CTCAGGAAAAAGACCACACACCTACAAT-AATCTGATCTTTGACAAACTT 604
                         ii   i  v  iv   i   ii  iii -   -    i  i     ivv 
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAAT-TGATTTTCGACAAGGGT 366

  chrX_151212599_    605 GACAAAAACAAGCAATGTGGAAAGGATTTCCTATTTAATAAATAGTGCTG 654
                          v   i v  vv     v      i  vvi  v  i  i    i      
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chrX_151212599_    655 GGAGAACTGGCTAGCCATATGCAGAAAATTGGAACTGGACCCCTTCCTTA 704
                            v      v  ?   i     i  i v  i ii         v   i 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chrX_151212599_    705 TACCTTATACAAAAATTAACTCAAGATGGATAAAAGACTTAAATGTAAAA 754
                         i   v                   i      v ?    i         i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_151212599_    755 CCAAAAACTATAAAATGAAGAAAATCCTAGAAGAAAATCTAGG--TAATA 802
                         v v            i--------  i          iv    --   - 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAAC--------TCTTAGAAGAAAACATAGGNGTAA-A 557

  chrX_151212599_    803 CCATTCAGGATATAGGCATAGGCAAACATTTCATGACAAAAACATCAAAA 852
                         i -   iv  iv v  vv       vvi    v iivv vi   i     
  L1M4_orf2#LINE/    558 TC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chrX_151212599_    853 GCAATTGCAACAAAAGCAAAAAT 875
                            vvv          v      
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAAT 629

Transitions / transversions = 1.20 (48 / 40)
Gap_init rate = 0.02 (6 / 362), avg. gap size = 2.33 (14 / 6)  

 874 22.90 3.70 0.67  chrX_151212599_151214565.rev     1180  1476 (491)    L1M4_orf2#LINE/L1      603   908 (0)  

  chrX_151212599_   1180 AAAAAAAAAAGAAAAGAAAAGAAAAAATTGACGAATGGTATCTAATTAAA 1229
                             iv v   v  v-            v  ii   v v ii v  i   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_151212599_   1230 CTAAAGAGCTCCTCCACAACAAAAGAAACTATCATCAGAGTGAACAGACA 1279
                         v v  i i  ii vii vv    i  v       vv i      v     
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chrX_151212599_   1280 ACCTACAGAATGGGAGAAAATGTTTGCAATCTATCCATCTGACAAAGG-T 1328
                            i                 i       vii  vi      i  i  -i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chrX_151212599_   1329 TTGCTATATAGAGTCTACAAGGAA-TCT-A-AAC--AA-ACTTACAAG-C 1371
                            -   vi   i v  i  i   -   - -   --  - v v v   - 
  L1M4_orf2#LINE/    752 TTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_151212599_   1372 AAAAAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTCCTC-- 1419
                            v     v   ?    i           iv    i     i i   --
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_151212599_   1420 -ACAAGACATTCATGTGGCCAACAAACATATGAAAAAATGCTCAACATCA 1468
                         - v    i  v  vi       i  i  i       i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_151212599_   1469 TTGATCAT 1476
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.23 (37 / 30)
Gap_init rate = 0.03 (10 / 306), avg. gap size = 1.30 (13 / 10)  


1124 25.64 19.97 2.96  chrX_151222927_151224538      351  1126 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151222927_    351 TGGAAAGATAGCTCATGTTCATAAATTGAAAGAATTAATGTTTTTCA-AT 399
                                   v i         ii    i    v     i  v  v -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151222927_    400 CTCCATACTACCCAAAGTGATCTACAGATTTAATGAAAACCTTACCAAAA 449
                         vv v     v      v             i  i v  v  i  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151222927_    450 TACCAATGACATTTTT--CAGA---------------------------- 469
                          v   iivi v     --    ----------------------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_151222927_    470 --GAAAT-----------AGAA------------------AAAAGA---- 484
                         --     -----------    ------------------      ----
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_151222927_    485 -------------CT-----------ATTT-AAAA--------AAAATTA 501
                         -------------  -----------    -    --------   ii  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_151222927_    502 -----ATTAGCACAGAG-GGTATTGGTGCCAGAAGAGA----TAAACAAA 541
                         -----  i iv    v -    i   iiiv  i v   ----  i iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_151222927_    542 TGGCATTGAATAGAGAGTTCAGAAATAGAT--ATAGGTTTATAAGACAAT 589
                            v  v    v      i        i i--   vi     i- v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG-GTCAAT 349

  chrX_151222927_    590 TGATTTGTGACTAAAGTAGCACCAAAGACT-TTC--TGGCAAAT--ACAG 634
                               vi   -  i -- ii    -   i-   --   vi  v-- i  
  L1M4_orf2#LINE/    350 TGATTTTCGAC-AAGG--GTGCCAA-GACCATTCAATGGGGAAAGAATAG 395

  chrX_151222927_    635 GCTTTTCAATAAATGGTTGTAGGACAATTTGCTATTTTCAAAATTTATAC 684
                         v        i       vv i      i v v  ?i--  -----i  i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC--CA-----CATGC 438

  chrX_151222927_    685 AAAA---TTAAATTGTAACCTTACC-CATA--GTATACAAAAATGTATTA 728
                             --- v  i   v v  i    -  i --i           vv i v
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_151222927_    729 CAGGTGGATTGAAGATCTAAATATGAAAGGCAGAATGATAAAGCCTGTAC 778
                         v ii     ii?   i      i i i  vi i  iv     i iiv  v
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_151222927_    779 AA-------TAGAAATGAA-CTTCTTCACA--GAGTAAGAGAATA-TTAC 817
                           -------   i?i i  -    v v  v-- i  v  iv   i-  v 
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_151222927_    818 TTAAAC-TTACAC--AAAGTGATAACCTATAAAGGAAGCAACTGTTAAAA 864
                            i i- v    --    i- i  v v i   i   iv  iv v    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGC-ACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_151222927_    865 CAGACTACATTAAAATTCAGATCTCT-GTTCATTAAAAGATGC----AAG 909
                         ii    v   i      v i v  i -  v v i   i  ii ----   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_151222927_    910 AAAGTGAGTAAACAACAAATACCGAATGGTAGA---CGTTTGTCACACAT 956
                                iv i     v--i  v      v   ---ii    ---  v  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACC--CACAGAATGGGAGAAAATATTTG---CAAAT 732

  chrX_151222927_    957 CATACGTATATCTGATAAAGAAACAT-TATCCA---------AAGAATTC 996
                             ----          i i - v -      ---------     i  
  L1M4_orf2#LINE/    733 CATA----TATCTGATAAGGGA-CTTGTATCCAGAATATATAAAGAACTC 777

  chrX_151222927_    997 CTACAACATCATAAGAAAAAGAGAGAAAATCCAATAGAAAAATGGACAAA 1046
                         i      viv    v       v i v  i     v?        i    
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_151222927_   1047 AGACTTAAAAAGGCACTTCACAAAAAAGGAAGGTCAAATTGTCATTAACC 1096
                         i  i  i  v  i  i   v v   i i  vivv     v i  v   v 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chrX_151222927_   1097 ATAAGAAAAAGTGTTTGCC-TCATTAATAAT 1126
                          i v     ii  i iiv -   ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (111 / 84)
Gap_init rate = 0.05 (42 / 908), avg. gap size = 4.24 (178 / 42)  


 741 20.49 1.41 11.66  chrX_151273001_151277755     2071  2353 (2402)    L1M4_orf2#LINE/L1        1   254 (654)  

  chrX_151273001_   2071 TAAAACGTTATACCATCTTAATGTATCAGGAGACTCAAGGTAGTTAAGAT 2120
                          ii  v v   v    v  v   v  ii i     i  vi v        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151273001_   2121 GTCATTTCTTCCCAAATTGACCTAAAGATTTAACTCAATCCCAAT--AAA 2168
                          v  v v  i          i   v     i   v       v  --   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151273001_   2169 TCTTTCAGTAGCATTTTTGGAGGAGAAAGGGAAAAGCTGG--CTGATCAA 2216
                           i--   iv  v     v v--     vv  v      i--  i --  
  L1M4_orf2#LINE/    101 TCC--CAGCTGCCTTTTTTGC--AGAAATTGACAAGCTGATCCTAA--AA 144

  chrX_151273001_   2217 TTTATCTGGAAATACAAAGGACCTAGGATAGCCAAAGACAGTTTTTAATT 2266
                           i  v       i   i     i  i         -   i i  -----
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTT----- 188

  chrX_151273001_   2267 GTTTTTCAAAAATAATTTTTAAATGAAGAACAAAGTTAAAGGATCCACAA 2316
                          ------     ------------             ii    ii    v
  L1M4_orf2#LINE/    189 G------AAAAA------------GAAGAACAAAGTTGGAGGACTCACAC 220

  chrX_151273001_   2317 TGCTTTACTTCAAGATTTACGAAAATGCTATTGCAGT 2353
                          v iiv i     i i    v v  v    ---    
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTA---CAGT 254

Transitions / transversions = 1.07 (30 / 28)
Gap_init rate = 0.04 (10 / 254), avg. gap size = 3.70 (37 / 10)  

1782 23.63 10.13 2.41  chrX_151273001_151277755     2526  3147 (1608)    L1M4_orf2#LINE/L1      239   908 (0)  

  chrX_151273001_   2526 ACCACTGAATTATAATAATTGATGCAGCATGTTAGTTTCA--AGGTTACA 2573
                           i  vi ii  i i    ii vi   ii  v  v vv  --   v  v 
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_151273001_   2574 CAAACAGATCAAATAAACAGAAT--AGAGTCCAGAAGTAGATCCATCCAT 2621
                           v i       vvi  i     --           i  i i    v   
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_151273001_   2622 ACACAGTCAGTTGATTTTGGACAAGGGTGCCAAGGTAATTCAATGGGCAA 2671
                         vi ii    i        v               iiv          v  
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_151273001_   2672 AACATACTCTTGTCAACAAATGGGGCTGGAAAAACTGGACATACATAAGG 2721
                          iv   v    v           v     i v       i ?v  i v v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_151273001_   2722 AAAAATATATTGTATATGCCTGGAACATTACCTTGCTCCAAAGGCAAAAG 2771
                             iv  ivv  -------    v vi     ii v   v vi     i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGT-------TGGACCCCTACCTCACACCATATACAAAAA 481

  chrX_151273001_   2772 TCATCTAAACATGCACCAAAGACATAAATCAAAGAACAGAAACTACAAAA 2821
                          i v  v  v   v i  ?    v     vv    i vi      i    
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_151273001_   2822 CTCT-AGAACAAAACAAGAGAG--AATTATTTTGAACTTAATTAATGCAA 2868
                             -    v      vii ? --   iv iv   v   iiv v v    
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA 581

  chrX_151273001_   2869 AGACTTCTTAGA-ATG-CA--AAAGGTACAAG------------------ 2896
                         v ii        -   -  --   i i     ------------------
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chrX_151273001_   2897 ------------TCAT---AATAGAAAAC-------------------CC 2912
                         ------------    ---   vi     ------------------- i
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chrX_151273001_   2913 ATTAAGAAAATGAAAAGACAAGCCACAGAAGGGCAGAAAATATTTCCAAA 2962
                           i      i           v        v  v           v    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chrX_151273001_   2963 ACACATATCTTCTAAAGAATTTGTATTATATTTAATATTATATATTGTAT 3012
                         v  i      vv   i i i      i-----i iv  -     vv v i
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATC-----CAGAAT-ATATAAAGAAC 775

  chrX_151273001_   3013 TATAGAATGACCCAATAATAAGAACACAAATATCCCAATTTTAAAATGGG 3062
                          v v-- ii  i         i  v       v       ?v        
  L1M4_orf2#LINE/    776 TCTT--ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chrX_151273001_   3063 CAAACGATTTGAATGGACATTTCTCCAAATGAGATACACAGATGGCTAAT 3112
                             v         i              vi     i   i     i   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_151273001_   3113 AAGCACATGAGAAAATGTTCAGTATCATTAGTCAT 3147
                                   i  i   i   ii    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.10 (75 / 68)
Gap_init rate = 0.02 (14 / 670), avg. gap size = 5.57 (78 / 14)  

2451 24.53 9.86 3.29  chrX_151273001_151277755     3414  4265 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151273001_   3414 TGGAGAAATATTCCATGGTCATGAATAGGAAGACTCAGTATTGTTGGATA 3463
                             i i    i     v     i  v        i i       -----
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTT----- 45

  chrX_151273001_   3464 GGAAGATTCATTATTGGTAAGGTCAGTTCTTCTCAA-CTGATATATACAT 3512
                         --     --------  i  ------ v  i i   -i    v  i v  
  L1M4_orf2#LINE/     46 --AAGAT--------GGCAA------TACTCCCCAAATTGATCTACAGAT 79

  chrX_151273001_   3513 TCAATGCAGTCCCAACCAAAATCCCAACAATTTATTTTCTAGATATCAAT 3562
                             i   i    v i          i viii v    vi   v  ii i
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chrX_151273001_   3563 AAACAGATGCTGAAGTTTATATAGGAAGACAAAAGACCCAGAATAGTAAA 3612
                           i v   v  i  i  i    i i  vi   ii            iv  
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chrX_151273001_   3613 CACAATACTAAAGAATAGGAATAAAGTTAGAGGACTGACACTACCTGA-- 3660
                         v     vi i  i  v i   i      i       v     v  ii --
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chrX_151273001_   3661 ---------------------CAGGAAACAAGGCAGTGTAGTGCTGGTAA 3689
                         ---------------------   v  v    i      i  i    i v
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chrX_151273001_   3690 AAGAATAGATGAATACGTCAGTGGAACAGAATAGAGACCCCAGAAATAGA 3739
                            i     iiv   vi   i     i     v    vi         i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chrX_151273001_   3740 TAGACCCACATGAATATAGTCAACTGATCCTTGACAAAGAAGCAAAGATA 3789
                         ----    i iivv   i     i    ii i     i iv  v    iv
  L1M4_orf2#LINE/    330 ----CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_151273001_   3790 ATATAAGGGATAAATGATAGTCTTTTCAACAAATGGTGCTGGAATAACTG 3839
                           vi  v  iv   vi                          i i     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_151273001_   3840 GTCATCCACTTGCAGAAAAAAGATGAATCTTGACAAAGACCTTACATTCT 3889
                          vi ?    v    i  i  ---    vi v   vvvv    i   iiv 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAA---TGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_151273001_   3890 TAACAAAAATTAGCTCAACATGGGTCATAG--CCA---GTAAAATACAAA 3934
                         vv          i     v    i   ?  -- i ---    i vvi   
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chrX_151273001_   3935 ACCAAAAAAGTCCTAGAAGACAAAATAGGGGAAAA-------GA------ 3971
                           i v    v  i       v  v     ? v   -------  ------
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chrX_151273001_   3972 ---AAG-AATGAT---------------CCA-------------TGAAAG 3989
                         --- i -    i ---------------   -------------ii    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chrX_151273001_   3990 TAAAAACTGATAAATTGACCTTCATTAAAATTTAAGATCTTTGCTCTGTG 4039
                         v     iv         iv      i      v  i ii    iv  vii
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_151273001_   4040 AAACGCACTGTTAAGAGTATGAAAATACATGCCATAGACTAGGAGAAAAT 4089
                           ivi    i i    ivi      v   vv   i   v i         
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chrX_151273001_   4090 ATTTGCAAAACATATATCTAGTACAGAACTTATATTGAAAATATATAAAG 4139
                                  v         ii  vi i    i   iv i           
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chrX_151273001_   4140 GACTCTTACA-CTGAACAATAAGAAAACAG----CCCCGTT-AAAAATGA 4183
                         i         -  v  i     i  i   i----   vi  -       i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chrX_151273001_   4184 GCAAAAGAACTGAAGAGACAGCTCAGCAAAACAGATA---AGATTGCAAA 4230
                              i  vi    v     vi  vv    iv     --- i  v  v  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chrX_151273001_   4231 TAAGCATGCAAAAAGATGCTCAAC-TCGTATGTCGC 4265
                               iiii              -  i????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (127 / 79)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 5.89 (112 / 19)  


3018 26.03 2.74 1.14  chrX_151300994_151303402     1033  1908 (501)    L1M4_orf2#LINE/L1        1   890 (18)  

  chrX_151300994_   1033 TGTAAAGACATGTTGAGTTCATCATTTGGAATAATTAATATTGATAATAT 1082
                           v     i  viiiv      viv      v v         v   v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151300994_   1083 GTCCATAC-CACCAAAGCAATCTACAGATTCAATACTATCCCCATGAAAA 1131
                          v v    - v     vii              ii v     i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151300994_   1132 TTTCA-----TTTTTTTTCAGAAATAGAAAAAACACTTCTAAAACTTACA 1176
                          ii  -----i      v       v  v  iviiv i      i i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_151300994_   1177 CGGCACCATAAAGACCCCA-AGTAGACAAAATACTCATGAGCAAGAAGAA 1225
                         i  v viii  i iv    - i   v     i v  v   iv        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_151300994_   1226 CAAAACAAAAGTCATCACACTTCATTATTTCAAGCTGTAATACAAAGCTG 1275
                             iivii  vvv         viv       iviv  v         i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_151300994_   1276 CATTAATTAAAACAGTACGGTATTAGCATAAATGCAGGCATGTAGACCAA 1325
                           v    i  i     ii    i i      ivii  i   i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_151300994_   1326 TGGAACAAAATAGAGCACCTA-ACCTTAACCCACACATATATGCTCAAGT 1374
                              i i   v   vii i - vv v      i    v    v    v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_151300994_   1375 GATCTTCTACAATAGTGGCAAAAATACACAATGGGGAAA-AATAGTCCCT 1423
                            i   v    vi   v   i vi iv           -       ii 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_151300994_   1424 TTAACAACTAGCATTGGAAAAAGTGGATATCCACATGCAACAAGATAAAA 1473
                          i     v i iii   i v  v      ?          v ii  i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_151300994_   1474 TTGGACTCTTAT-----ACCATACACAAAAATTAACTCAAACTGGATTAA 1518
                               i i  i-----      i                 v     i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_151300994_   1519 AGTTTTAATCATAATATCGGAAACTGCAAAACTCCTAAAAGAAAACATGG 1568
                           vii   vii   v v vi     ii       i  i          i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_151300994_   1569 AGGAAAAGCTTT-TGACTTTGTTCTTGGCAATGATTTCTTGGATATGACA 1617
                         i? v   v   i-    i   vvi v       i      i         
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_151300994_   1618 CCAAAAGTATAGGTAACTGAAGCAAAAATACATAGGTGGGACTACATAAA 1667
                                i i i i   vi   v       v   ii v     v   v  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_151300994_   1668 ACTGAAAAGCTT-----CTTCACAGAAAGGAAAACAATTAACAGAGTAAA 1712
                          v v    i   -----     ----     v - v  i  v i   i  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCA----AAGGACA-CTATCAAGAAAGTGAA 695

  chrX_151300994_   1713 GAGACAACTTACAGAATGGAAATAGGAAATACAGTTGCAAACCATACATT 1762
                         i       ii         i --- i     i--       i    i  i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGA---GAAAATAT--TTGCAAATCATATATC 740

  chrX_151300994_   1763 GGATAAAGGGTTAATATCTGAAATATATAAGGAACTCAAACAACTGAGTA 1812
                         v     i  ii vi    iii         i      vv      v i  
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_151300994_   1813 GCAAGAA----AATGACCCAATTTAAAAATGGGCAAAAAACCTGAATAGA 1858
                         ii  i  ----   i        ?             ii ii        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_151300994_   1859 CATTTCTCAAAAGAAGATATACAAATGTATAACAGGTGTATTTAAAAATG 1908
                                 v                  vvi  i i iii  vv   i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

Transitions / transversions = 1.57 (137 / 87)
Gap_init rate = 0.01 (13 / 890), avg. gap size = 2.62 (34 / 13)  


3540 22.76 2.58 0.78  chrX_151304348_151306459      728  1619 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151304348_    728 TGGAAATATATCACATGCTCATTATTTGGAAGAATTAATATT-TTAAAAT 776
                               v     v    i    viv        v        -    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151304348_    777 TTTCCATAC-ATTCAAAGTGATCTACAGATTCAATGCAATTCCTATCAAA 825
                         vv- v    -vii    v                i     i         
  L1M4_orf2#LINE/     51 GG-CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_151304348_    826 ATTCCAA-TGCCTTTTTTTTAAAGAAATAGAAAAA--AATCCTAAAATTT 872
                           i   i-          vi --     v  v  i--i           i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCA--GAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_151304348_    873 GTATAAAAGCACAAAAGACCCTGAATAGCCAAAGCAATCTTGAGGAAGAA 922
                         i   ii  iii   ii     v           i         ii     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_151304348_    923 GAACAAAACTGGAGTCATCACACTACCTGATTTCAAAACATACCAAAAAG 972
                                ii     vvv       v  ii          v   i v    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_151304348_    973 CTATAGTAATCAAAACAGAATGGTACTGGCCTAAAAGTAGACAAATAGAC 1022
                            i         i    vi          v   iii      v     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_151304348_   1023 CAAAGGAACAGAATAGAGAGATCAGCGATAAATCTGCACATTTATAGTCA 1072
                            v    i     v     vi   vi     i iii        i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_151304348_   1073 ATTGATCTTTGACAAAGCAGCCAAGAACACACAATGGGGAAAGGATATTC 1122
                               i  i     i vv       v  iv            i   v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_151304348_   1123 TCTTCAATAAATGGTGCTTGGAAAACTGGACCTCCACTTGTAGAAGAATA 1172
                          i     i          v   v       iv?    v  i i      i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_151304348_   1173 AAATTGGACACTTATCTTACACCATATGCAAAAATAGACTCAAAATAGAA 1222
                           i      v i  i  i         i       vi         i  v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_151304348_   1223 TATAGACTTAAATGTAATACCCGAAACTGTAATATTCCTAGAAGAAAACA 1272
                         i ?    i         v v ii     i   v i  i            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_151304348_   1273 TAGGAAAAAATTTTCTTGACAGTGTTCCAGGCAATACTCTCTTGGATATT 1322
                             ?iv    i   v    vv  vvii       iv i    i     v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_151304348_   1323 ACCTCAAAAGGACACAACC--CAAAAGCGAAAATAGACAAATGAGGCTAC 1370
                           vi      --     v --      vi        i    vi i  v 
  L1M4_orf2#LINE/    598 ACACCAAAAG--CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_151304348_   1371 AT-GAAATAAAAAAAGCTTCTGCATAGCAAATCAAATTATCAGCAGAATA 1419
                           -i    v     --   i  iiivv    vv v i     iv i i i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_151304348_   1420 AAAAGAC----TATGGAATGGAAGAAAATGTTTTTAAACCACATTTCTGA 1465
                                ----i ii      i       i   vi   i  i  v     
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_151304348_   1466 GATGGGGTTAATATTTAAAATGTATTAGGAATTTAAACAACTCAATAGCA 1515
                         v v   ii vi   ii i   i   v i   i ivv           ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_151304348_   1516 AGAAAACAAATAACATAATT-AAAAATGGGCAAAGGA----------CAT 1554
                          i  i         vi    -                ----------   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chrX_151304348_   1555 TTCTCAAAAAAACACATACAAATTGCCAATAGGTGTAATAAAGTATGTTC 1604
                              v   i  v i        v       i iii vv   iv   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chrX_151304348_   1605 AACACCACCAATTAT 1619
                             i  ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (123 / 77)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.31 (30 / 13)  


1936 26.20 7.87 1.72  chrX_151308626_151314891      757  1569 (4697)    L1M4_orf2#LINE/L1        1   863 (45)  

  chrX_151308626_    757 TAAAAAGATAATACCATGTTTGTG-ATTGTAAGACTTAAT---GTTAAGA 802
                          ii       - v       ii  -    v          ---       
  L1M4_orf2#LINE/      1 TGGAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chrX_151308626_    803 TATCAATTTTCCCCAAATTTGATG-ATAAATTCAACACAATTACCTAGCA 851
                          iv    vi          -   v- i i       i    i-    v  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATT-GATCTACAGATTCAACGCAATC-CCTATCA 97

  chrX_151308626_    852 GGATTTTTATAGAAAAATTTTTTTTCA-AAATTATGATGCTGAG--TAAA 898
                         ii  iiiviiv v----i      v  -     ivv v     v--    
  L1M4_orf2#LINE/     98 AAATCCCAGCTGC----CTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chrX_151308626_    899 ATTTTTATATAAAT-TGATAAATT-----TATTCTAAAC--TCC--ATAA 938
                            iv   iv    -ii vii ii-----  vi v    --  i-- v  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chrX_151308626_    939 GGCAACACAAAATT------------CTT---AATT--AA-------TGT 964
                         i v iv     i  ------------   ---    --  ------- ii
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_151308626_    965 AAAGATACATTAACTAAGACAGTGTGGTATTAGCATAA---TAGAAAAAT 1011
                             v    v   ii              i i      ---    v v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_151308626_   1012 AAATAAGTTGAACAAAATATAGAGTCCAGAAATAAACTGACACATATACC 1061
                          i  v i v   i i   vv                 iv i    v  iv
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_151308626_   1062 ATCAATTGATTCTCAATAAAGTCCTCAAAGCAATTCAATTGGAGATAAGA 1111
                         i          i  i i  i vivi   ii v       -  i  -    
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGA-AAGA 391

  chrX_151308626_   1112 AT-GTCTG--CAATAAATGGTGCTGAAACAACTGGATATTCCTGTGGAGG 1158
                           -    v--   i           ii           ?i vii  v --
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA-- 439

  chrX_151308626_   1159 AAAAAATGAAACTTAACCT-TCCCTCACACCATACTCCCAAATTATGTTG 1207
                            i      ii vi   i- v            iv vv      -ii v
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA-ACTC 488

  chrX_151308626_   1208 AGAATG-ATTATAGATATCAGTGTGGAAGCTGGAATTATAAAGCTTCTGA 1256
                          i    -  i ?   iv v i   iii    ii  i      i  ii ii
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_151308626_   1257 AAGAAAA--TAGGAAAATGTCTTCAAGGCTTTGAGGTAGGCTAAGGTTTC 1304
                                --    ?iv vi     iv i i   i v     v v      
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_151308626_   1305 TTAGATACG-CAT-AAGGGCAATATCCATAAAACAAAACAAAT-GATAAA 1351
                                i -  i-  ii   vv v v i    v    --   -      
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA--AATAGATAAA 636

  chrX_151308626_   1352 TTAGGTCTCAACAAATTTTAAAACCTTTGTTCAACAAAACACACCATTAA 1401
                           i iii   v    v  v     i     v vv    iv    i  i  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chrX_151308626_   1402 GAACGTGCAATAGCAGTC-ACAGGATGGAAGAAAATATTTTAATAT-ATA 1449
                            v   v  vii  ii -    i    i           vv v  -   
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_151308626_   1450 TATGTGACAAAGACCTCATATCTGGAAAATATAAAGAATTCT-ACAA--- 1495
                            v   i  i iv  ii    ii   v          i   -    ---
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_151308626_   1496 AACAATAATAAGGTTAATAAAC-AAC--AAAAATTGGCAAAATATTTCAA 1542
                           i     v   iiv     v -  i--      v      iv    v  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chrX_151308626_   1543 TATACACTGCACTAAAGAATATAGATA 1569
                           v   i v v i      v   v i 
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.47 (125 / 85)
Gap_init rate = 0.04 (37 / 863), avg. gap size = 2.11 (78 / 37)  

3135 25.51 0.21 2.89  chrX_151308626_151314891     4841  5773 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151308626_   4841 TGGAAACAGATCCCAGGCTCATGGACGGGTAGAATCAATATTGTGAAAAT 4890
                               v v      v i       iv  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151308626_   4891 GACCACACTGCCAAAAGCAACCTATAAATTCAGCACAATCCCCATCAAAA 4940
                          i v i   v  v   vii i   i i     i i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151308626_   4941 TACCACCATCATTCTTCACGGAGTTAGAAAAACACAATTCTAAAATTCAT 4990
                          v   v vv v  i  ii i  iv v  v  i -ii  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_151308626_   4991 ATGGAACCAAAAAAGAGCCCTCATAGCCAAAGCAAGACTAAGCAAAAAGA 5040
                               viiv  ii  v  vvv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_151308626_   5041 ACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATAGTATAAGGCC 5090
                              vi      vv       v  ii        viv  v  i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_151308626_   5091 ATAGTCACCAAAACAGTGTGGTACTGATATAAAAATAGGCACATAGATCA 5140
                          i   v i   i              ii    ii    i  i        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_151308626_   5141 ATGAAACAGAATAGAGAACCCAGAAATAAACCCCAAATTCTTA-AGCCAA 5189
                            i  i     v    ii              - v ivi   -i i   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCC-ATACATTTATGGTCAA 348

  chrX_151308626_   5190 CTGATCTTCCACAAAGCAAACAAAAACACAAAGTGGGGAAAGGACACCGT 5239
                         i    i   v    i vviv   i v  ivv i         i i viv 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_151308626_   5240 ATTCAACAAATGGTCCTGGGATAATTGGCTAGCCAAATGTAGGAGAATTA 5289
                         v             v      i  i   v  ?   v   i ii     v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_151308626_   5290 AACTGGATCCTCATCTCTCACCTTATACAAAAATCAGCTCAAGATGGATT 5339
                          ii    i  ii i   v    v           i i     i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_151308626_   5340 AAGGACTTAAACCTAAGACCTGAAACTATAAAAATTCCAGAAGACAACAT 5389
                          ?i   i    iv     v  i           v iii      v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_151308626_   5390 TGGAA-AAACCCTTATAGACATTGGCTTAGGCAAGGATTTCATGAACAAA 5438
                         v  ?i-   i i ii -   v    v        v i    v ii i vi
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGT-GACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_151308626_   5439 AACTCAAAAGCAATTGCAATAAAAACAAAGATAAATAGCTGGGACTTAAT 5488
                          vvi        vvv    i    iv   i   i   iv v      v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_151308626_   5489 TAAACTAAAGAGCTTTTGCACGGCAAAAGGAACAGTCAGCAGAGTAAACA 5538
                         i   v v  i i      ii vv    i iv  vi   iv i   i  v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_151308626_   5539 GACAATCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAA 5588
                              i       i           v  ii   vii   i      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_151308626_   5589 GGACTAATATCCAGAATCTACAATGAACTCAAACAAATCAGTAAGAAAAG 5638
                              vi          v  i  v      vv    v   i   v    -
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA- 796

  chrX_151308626_   5639 AAAAACACACAAAACAAAACAAAACAAAATCAATCCCATAAAAAAGTGGG 5688
                         --------------------- i     --i  i  v  v?    i    
  L1M4_orf2#LINE/    797 ---------------------AGACAAA--TAACCCAATTWAAAAATGGG 823

  chrX_151308626_   5689 CTAAGGACGTGAATAGAAAATTCTCAAAAGAAGATATACGAATGGCCAAC 5738
                          v     iv        v v     v             i         i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chrX_151308626_   5739 AAGCATATGAAAAAATGCTCAACATCACTAATGAG 5773
                              i       i             ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 4.14 (29 / 7)  


1378 26.53 6.48 5.99  chrX_151320943_151322750      498  1315 (493)    L1M4_orf2#LINE/L1       87   908 (0)  

  chrX_151320943_    498 AGTCTCAATCAAGATAACAGCAGAGATTTTTGTGGAAACTGACAAGCTGA 547
                          i  i v     i  vv    v vvv      ii    i           
  L1M4_orf2#LINE/     87 AATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA 136

  chrX_151320943_    548 TTCTAAAATCCATGTAGAAAAGCAAAA-AGCTAAAATAGTCAGAGGCAAT 596
                          i       i   i i    v    ii- v i i     i  i i-    
  L1M4_orf2#LINE/    137 TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAAT 185

  chrX_151320943_    597 CTTGAAAAAAAAAGAACACATCTGGAAGACCTACACTACCATATATCAA- 645
                                  i  -     v vi    i   ii     v  vv  v    -
  L1M4_orf2#LINE/    186 CTTGAAAAAGAA-GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chrX_151320943_    646 ------------GCTATGGTAAATAAGA-ACTGTGGTATTAGTGCAAGGA 682
                         ------------    ii    vi    - v       i i iii     
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chrX_151320943_    683 TATACTAACTGGAATGGTTATAGATATAATGGAATAAA-----GAATTCA 727
                           v  --------  ----      -i         i -----  i i  
  L1M4_orf2#LINE/    285 TAGAC--------AT----ATAGAT-CAATGGAATAGAATTGAGAGTCCA 321

  chrX_151320943_    728 GGCAAATA-----------TTATCACCCAATTTTTTTTTCATAAAGGTGA 766
                          --     -----------    vii -    vv    iv i  i    v
  L1M4_orf2#LINE/    322 G--AAATAAACCCATACATTTATGGTC-AATTGATTTTCGACAAGGGTGC 368

  chrX_151320943_    767 CATTGCAGTGCAGAGGTGAAAGTGTAGTCTTTCAAATAAATAGTGCCATA 816
                           vvi vi v  iv  v     vi        iv  i    i    iivi
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chrX_151320943_    817 TTAAATGCACACTTATATGGAAAAAACTGCAATTATATCACAAAGTCACA 866
                         vi  v  v i ?ii i   v    i v  v i  iv i v v vv     
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chrX_151320943_    867 CCATACG----AATTG---CAAA-TGAGTTGAAAAATTTTATGTCAGAAG 908
                              ii----    i---    -  ii ii? i vi vv    v   iv
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_151320943_    909 TAAAATAATAAATATTTTATA-GAAAATATCTTTAAGGATAACCTCTTTG 957
                              iv     vv i   v -     i  ---- i ?i   v-    i 
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACAT----AGGNGTAAA-TCTTCG 563

  chrX_151320943_    958 TGACTTTGGTATAGGCAAAGTTTTTTTAAAAAAAAATAGGACACAAAAAA 1007
                             i    vv       v v   i   i ------  v     v    i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGA------TATGACACCAAAAG 607

  chrX_151320943_   1008 CACTAACCATTAAAGAAAGAAATGG-TAACTTAGACCACACTAAAATTAA 1056
                            v i v iv       -    i -   v  i   iv  ii        
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAA-AAATAGATAAATTGGACTTCATCAAAATTAA 656

  chrX_151320943_   1057 GA---TCTGTTCATCAAAA-ACACCAATAAAAAA-TGAAAAGGTAATCCA 1101
                         i --- i   v v     i-    i vi  i   -       ii  i   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_151320943_   1102 CAGGATAGGAGATGACATTAG-AAATACACATATCTGGCAAAGAACTTCT 1150
                            i  i     vi i   v -    -  i       ii  i i    v 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAAT-CATATATCTGATAAGGGACTTGT 755

  chrX_151320943_   1151 A-CCATGAATATATAAACA-----TACATACATATATAGATAGATAGATA 1194
                          -   -           v -----    -  vi -   -   i v   i 
  L1M4_orf2#LINE/    756 ATCCA-GAATATATAAAGAACTCTTACA-ACTCA-ATA-ATAAAAAGACA 801

  chrX_151320943_   1195 GATAGAACATAGATAGAGATAAAAAGACAACCTATCTAAAAAACTAGACA 1244
                         i   --  vi iv ?i ---   vi i   vvv  i i  ----      
  L1M4_orf2#LINE/    802 AATA--ACCCAATTWAA---AAATGGGCAAAGGATTTGAA----TAGACA 842

  chrX_151320943_   1245 AATGAACATAATGAAAAGGATATTAAAATATCCAACAAATATTTGAAAAG 1294
                         vv vvv  -----  i i     vv    iv    i  ii iv       
  L1M4_orf2#LINE/    843 TTTCTCCA-----AAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_151320943_   1295 CTGTTTAACTTCATTCTCATC 1315
                         v  i i   v   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (123 / 90)
Gap_init rate = 0.04 (36 / 822), avg. gap size = 2.83 (102 / 36)  


1730 27.45 6.64 0.90  chrX_151356694_151359258      944  1606 (959)    L1M4_orf2#LINE/L1        1   701 (207)  

  chrX_151356694_    944 TGCAAAGATATACTGTACTGACAGATCGGAAGTTTTATTATTGTTAATAT 993
                           v        v ii ii v ii   i     vi   v         v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151356694_    994 --TCAT-TTCTACA----GATCGACA--TTCAATATGAAGTCAATGAAAA 1034
                         --iv  -i  iv  ----    v   --     iiii vvi v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151356694_   1035 CTCTTGCAGACTTTT--GTAAAAGTTGACAAGCTAATTCTAAAATTGATG 1082
                         ii iv  v v     -- i i  i          i  i        v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_151356694_   1083 TGGAAATGCAAGAAACCTAAAACAGTCAAAACAAT-TTAAAAAAATAAAA 1131
                                     ii   i i  i  i         -  i     iv i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_151356694_   1132 TAAGAATTGTAGGACTCACACTACTAAATTTAAAGA--TAATATAAAACT 1179
                         i  - i   v            v iv     v  i --  v  i   i  
  L1M4_orf2#LINE/    201 CAA-AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_151356694_   1180 ACAATAA---AGACAGTATAGTATTGGTGTAAATATAGATATATAGATCA 1226
                            i   ---       i i   i   ii   iv     i          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_151356694_   1227 ACGAAACATAGTAAAGCATGTAGATATAGAACCATTCAAACATGGTCAAT 1276
                          i i  i v i vi  vi vi   v   i v    v  vvi         
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_151356694_   1277 TGGT-----ATA-------CAGAACCA----ATG---AAACGGCAATTAT 1307
                           i ----- i -------  ii    ----   ---   viii i iv 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_151356694_   1308 TTCAAAAAATTGTACTGGAACAATAAGATATCTGTATGCAAAAAAAAAGA 1357
                              v    v  i    i    ivi    ? iii        i  v-  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT-GA 448

  chrX_151356694_   1358 ACACTGACCATTACCACACACC-T-TACAAAAGTATTAACTTGAAATTGA 1405
                          vviv    vi    v      - -       --       ii    v  
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAA--ATTAACTCAAAATGGA 496

  chrX_151356694_   1406 TTGTAGACCTAAATGTAAGGGCTAAAACTTTTAATGTTCTAGAAAAAAA- 1454
                          ii?               i         v v  vv ii     i    -
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_151356694_   1455 --AAGAAAAAATTTGAGTGACTTTAGAATAGAAAAATATTGTTTTAAATA 1502
                         -- i ?iv    i vv     i  i iv   iv  - iv v i   i   
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATA 595

  chrX_151356694_   1503 GAACACAATAACCATGA-CATGTAAAAGAAAGG-T-GATAAATTTGTCTT 1549
                         vi    v v  v  ii -  -ii        ii- -        v v   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCA-ACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_151356694_   1550 CACTAAAATTAGAGGCTTTGGCTCTTCCAAAGACACTGTTAAGAAAATTA 1599
                           ii       i ii    v iv    v  i      i i      i v 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_151356694_   1600 ACAGGCA 1606
                          v  i  
  L1M4_orf2#LINE/    695 AAAGACA 701

Transitions / transversions = 1.67 (112 / 67)
Gap_init rate = 0.03 (23 / 701), avg. gap size = 2.17 (50 / 23)  

 474 26.06 2.42 0.61  chrX_151356694_151359258     1900  2064 (501)    L1M4_orf2#LINE/L1      685   852 (56)  

  chrX_151356694_   1900 AAGGAAATTAAAAGGTAAGCCACAGACTGATAGAAA-TATTTATAAGATA 1948
                            i  i v     ii  v       v  iv     -     ii  ivi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_151356694_   1949 TATATCTGACAAAAAA-TTGTATAGAGACTATATTAAG--CATGTACACC 1995
                                  i  iii -      vv   v     v   -- viv    v 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_151356694_   1996 TCAATAATAAAAAGGCAAACAGCCTAATTTTTTTAATGGGCAAAATATAT 2045
                                       i    i i  i    -?vvv          iv  v 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATT-WAAAAATGGGCAAAGGATTT 833

  chrX_151356694_   2046 GAACTGTCACTTTACCAAA 2064
                            iv v  i  iv     
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAA 852

Transitions / transversions = 1.10 (22 / 20)
Gap_init rate = 0.02 (4 / 168), avg. gap size = 1.25 (5 / 4)  


3121 17.20 1.92 14.79  chrX_151361867_151364424     1030  2070 (488)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_151361867_   1030 GGAAAGGCGTGCCATGTTCATGGATTGGAAAATTCAATATTGTTAAGACA 1079
                               iii v                   i i i             ii
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_151361867_   1080 CCAGTATTACTCAAAGAAATCTACATATTCAATTGAATCCCTATGAAAAT 1129
                         v  i  i v i    vvi       v      ivv         v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_151361867_   1130 CTTAAAGGACTTCTTTTTTTGCAAAAAT-GAAAAACTGATCCTAAAATTC 1178
                          ii i----  v i         i    -  v  i               
  L1M4_orf2#LINE/    102 CCCAG----CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chrX_151361867_   1179 ATATGGAATTGTATTGGACTCTGAATAGCCAGAATAATAGGGGAAAAGAA 1228
                                 v  i vv    i v         i  i   vvv i       
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_151361867_   1229 AAACAAAGTTTGAGGACTTACACTTCCTTCTTTCAAACCTTACTACA--- 1275
                         i         v       i        ivv       v         ---
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_151361867_   1276 CCA-----ATCAAAATAGTGTGGTACTAGCATGATGACAGACATATATAT 1320
                          i -----     i i           i    i v  i         ---
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA--- 294

  chrX_151361867_   1321 ATATATATATATATATATATATATATATATATATAGATAGATAGATAGAT 1370
                         ---------------------------------------   vi  i  -
  L1M4_orf2#LINE/    295 ---------------------------------------GATCAATGGA- 304

  chrX_151361867_   1371 ATATAGATATATAGATATAGATATAGATATAGATATATATGATATATATC 1420
                         --     ---  v  v ---i vi   v   i ivi   -----------
  L1M4_orf2#LINE/    305 --ATAGA---ATTGAGA---GTCCAGAAATAAACCCATA----------- 335

  chrX_151361867_   1421 TGTATGTATAGCTGTATATGTACATATATCATTTATATACCTAGGTTCAA 1470
                         -----------------------------       -------   -   
  L1M4_orf2#LINE/    336 -----------------------------CATTTAT-------GGT-CAA 348

  chrX_151361867_   1471 TTGATTTTGAAATTGATTTTAATCCATTGATTTCGAATGGCACAAATATC 1520
                                 -------------------i  i----  v  ii v  v i 
  L1M4_orf2#LINE/    349 TTGATTTT-------------------CGAC----AAGGGTGCCAAGACC 375

  chrX_151361867_   1521 ATTCAATATGAAAATAATAGTCT---CAA-AAATGGTGCTGGAACAACTG 1566
                                iv i   v        ---   -            i       
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_151361867_   1567 GGTATCCATACGCAAAAGAATTAAGTTGGGCCCATTTATCATACCATAGG 1616
                          i  ?   i i          v       i   v viv   i      vi
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_151361867_   1617 CAAACAGTGACCCAAAATGGGTCAATAATCTAAATATAAAAGCTAAAACC 1666
                             v v i  i        i   ?vi i      i   i         i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_151361867_   1667 ATAAAACTGCTAAAATAAAATATAGG-GTAAATCTTCATGACCTTGGATT 1715
                                 vi  i  v    i     -          i         i  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_151361867_   1716 TGGCAATGGGTTTCTTA--TATGAAACCAAAAGCATGAGCTACAAAATAA 1763
                         v        -       --     v          ii   v      ---
  L1M4_orf2#LINE/    576 AGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA--- 621

  chrX_151361867_   1764 AAATAGACACATTGGATTTCAAAATTAAAAATGGATAAATTTGACTACAT 1813
                         --------------  ----------      i        v    v   
  L1M4_orf2#LINE/    622 --------------GA----------AAAAATAGATAAATTGGACTTCAT 647

  chrX_151361867_   1814 CAAAATTAAAAATTTTTCTCTTTCAAAT-ACACCATCAAGAAAGTGAGAA 1862
                                     i    v vi      v-    i             i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_151361867_   1863 GACAACCCACACAATGGGAGAAACTAATTGCGAATCATATATATAACAAG 1912
                                    v           v  v    i          v i i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_151361867_   1913 GGCCTATTACTCAAAATATACAAGGAAATTTTACAAATTGACAACAAAAT 1962
                           v  vv  ii  i      i  i   v i      v ii i  i    v
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_151361867_   1963 GACAAACAACCTAACTAAAAATTGAGCAGATTATTTGAACAGATATTGCT 2012
                               i    i  i ?    v  i   i vv       i   i   v  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_151361867_   2013 CTAAAGA---TATTCAAACAGCCAGCAAGCACATGGAAGTACATTCAATG 2059
                          i     ---   v    ii    ii         i  iv iii    ii
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_151361867_   2060 TTATTAGTCAC 2070
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.59 (108 / 68)
Gap_init rate = 0.02 (22 / 907), avg. gap size = 7.91 (174 / 22)  


3321 26.35 0.55 0.44  chrX_151383066_151389338     4874  5780 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151383066_   4874 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4923
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151383066_   4924 GGCCATACTGCCCAAGGTAATTTACAGAT-CAATGCCATCCCCATCAAGC 4972
                            v     v     iv i  i       -   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151383066_   4973 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5020
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_151383066_   5021 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5070
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_151383066_   5071 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5120
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_151383066_   5121 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5170
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_151383066_   5171 AATGGAACAGAAC--AGAGCCCTCAGAAAGAACGCCGCATATCTACAACT 5218
                                i    i--    i  --     v  vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_151383066_   5219 ATCTGATCTTTGACAAACGTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5268
                          vi    i  i     iv   vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_151383066_   5269 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5318
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_151383066_   5319 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5368
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_151383066_   5369 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5418
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_151383066_   5419 CTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATATCTAA 5468
                         v    ?v v viv   iv   v v  vv i     v ii   v  vv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_151383066_   5469 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5518
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_151383066_   5519 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5568
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_151383066_   5569 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5618
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_151383066_   5619 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5668
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_151383066_   5669 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5718
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_151383066_   5719 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5768
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_151383066_   5769 ATCACTGGCCAT 5780
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


3263 26.56 0.55 0.88  chrX_151420455_151426845     4988  5898 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151420455_   4988 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5037
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151420455_   5038 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCGTCTCCATCAAGC 5087
                            v     v     iv i  i  i        i ivi  i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151420455_   5088 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5135
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_151420455_   5136 TATGGAACCAAAAAAGAGCCCGTGTTGCCAAGTCAATCCTAAGCCAAAAG 5185
                                viiv  ii  v  v vi v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_151420455_   5186 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5235
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_151420455_   5236 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5285
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_151420455_   5286 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATATACAGCT 5333
                                i    i--    i  --        vv  ii i  v  ii ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_151420455_   5334 ATCTGATCTTTGACAAATCTGACAAAAACGAGCAATGGGGAAAGGATTCC 5383
                          vi    i  i     ivv  v   i v ivv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_151420455_   5384 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5433
                           v  i  i              v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_151420455_   5434 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5483
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_151420455_   5484 TTAAAGACTTACGTGTTAGACCTAAAACCATAAAAACCCTAGAAGAAGAC 5533
                          i ?    i  vi   v   v       i      vi i        i  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_151420455_   5534 CTAGGCA-ATACCATTCAGCACATAGGCATGGGCAAGGACTTCATGTCTA 5582
                         v    ?i- v i -   ivv  v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_151420455_   5583 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5632
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_151420455_   5633 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 5682
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_151420455_   5683 CAGGCAACCTACAGAATGGGAGAAAATTCTTGCAATCTATCCATCTGACA 5732
                         v  i     i                 vi      vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_151420455_   5733 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5782
                          i  i  vi          v  i  v      vv    v ---   v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAAT 792

  chrX_151420455_   5783 AAAAAAACAAACAATCCCATCAAAAAGTGGGCGAAGGATATGAACAGACA 5832
                              i     i  i  v  i?    i     i      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_151420455_   5833 CTTCTCAAAAGAAGACACTTATGCAGCCAAAAAACACATGAAAAAATGCT 5882
                         i     v        i ivi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_151420455_   5883 CAGCATCACTGGCCAT 5898
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (144 / 94)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3106 21.99 4.92 5.58  chrX_151431719_151434125.rev     1003  1916 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151431719_   1003 TGTAGATATATGTCTTGTTCATGGACTGAA---CTCAATATT---AAGAT 1046
                           v i v    vi v          i  i ---  i      ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151431719_   1047 GTCAGTTCTCCCCAGATTGATCTGTAGATTCAGTACAATCTCAATCAAAG 1096
                          v  i v       i        ii       iii     i v      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151431719_   1097 TTCTAGCAGGCATTTTTTGTAGACATGGACAAACTAATTTTAAAGTTCCC 1146
                          i i   -v  v       i   v  v     i  i  ii    i   vi
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_151431719_   1147 ATGGAAATGCAGATGACCCAGAATAACCAAAAGAACTTTCAAAAACAA-- 1194
                                    iiv           i      v  ii  v     v  --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_151431719_   1195 -CAAATTTGGAAGACTTACTCTAGCTTATTTAAAGAGGTACTATATAGCC 1243
                         -    v     i    i  v  vv iv    v  i vv     i v   i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_151431719_   1244 ATAGTA-----------------TTGGCATAAAGATAGACA--------A 1268
                          i    -----------------i        i        -------- 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_151431719_   1269 GTAGAACAGAACAGAGAGTCCAGAAATAGACGCCTATGTGTGTGGTCAAT 1318
                         i i   i    iv               i  v v  ii v i        
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_151431719_   1319 TGATTTTTGACAAAAGTGCAAAGTCAAGTCAGTGGAGAAAATATGATCTT 1368
                                i     ii    v   v v v   i   i    iv  ii    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_151431719_   1369 TTTAACCTAACAATGCTAAAACAATTTGGATAGTTATATGCAAAAACAAT 1418
                           i   v-  iii    iii    i -     ?ii i        i----
  L1M4_orf2#LINE/    400 TTCAACA-AATGGTGCTGGGACAACT-GGATAKCCACATGCAAAAG---- 443

  chrX_151431719_   1419 AGCAACAATATCAATAAACAAAACCCAAAACCAACCAAATAAACAAAACT 1468
                         -------------------------------------   i  v----- 
  L1M4_orf2#LINE/    444 -------------------------------------AATGAAG-----T 451

  chrX_151431719_   1469 TTGATCCATACCTTGCAC---ATATAAAAATTCTGTAAAAGTGGATCATA 1515
                          v  i  v     ii   ---   i       vvv v   i       ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chrX_151431719_   1516 GACCTAAACATAGAAATGAAAACTATATAATTTCTAGAAAAAAA--TCGG 1563
                                 ii  ii iiv         v  i ii     i    -- v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chrX_151431719_   1564 AGAAAGTCTT-GAGACCTTGGGTTAAGCAAAGATTTCTTTGAGAGGGCAG 1612
                         ? v  i    - v            i    v i      v  v v i  v
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chrX_151431719_   1613 AAAAAAGCAAGATCCATAAAAGAAAAATTTGATAAATTAGACATAATCAA 1662
                         v    -   vi v v i          v v        i   v v     
  L1M4_orf2#LINE/    602 CAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_151431719_   1663 AATTGGAAACTTTTGCAGTTTGAAAAACAGTGCTAAGAGAA-GAAAAAAC 1711
                             ii         iiv  ii  ii   v iii    i i-     i  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_151431719_   1712 AAGCCATAGGCTTAGAAAAAATTTTTGCAAATTACATATCTGATAAGGGA 1761
                           v   i  iv vi  i     v         i i               
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_151431719_   1762 CTAGTATCCAGCATATGTAAAGTAATTTTCTAATTCAATGATAAGAAGAC 1811
                           v        v    i     v v i  vi  i     i    i     
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_151431719_   1812 AA----CCCAATACATAAAATGGGCAGAGGATTTGAACAGACACTTCACC 1857
                           ----      v? -          i          i     i   v  
  L1M4_orf2#LINE/    801 AAATAACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_151431719_   1858 AGAGAAGATATATTGATGGCAAATAAGCACATGAAAAGACGCTCAATATC 1907
                          i          ivi     v                  i      i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_151431719_   1908 ATTATTTAT 1916
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.63 (122 / 75)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 5.65 (96 / 17)  


2035 24.57 2.29 1.33  chrX_151502252_151504815.rev      797  1321 (1243)    L1M4_orf2#LINE/L1        1   530 (378)  

  chrX_151502252_    797 TGGAAAAATATTTCATGCTCATAGATTGGAAGAATCAATATTGTTAAAAT 846
                               i    ii    i    i          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151502252_    847 GACTATATTGCCTGAAACAATCTACAGATTCAATGCTATTCTTATCAAAC 896
                          i v   i v  ii  vii              i  v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151502252_    897 TACCAA-TGTTATTTTTTCACAGAA-TTGGAAAAAACT-ATTCTAAAATT 943
                          v   i-  ii--     ii     -   -- v  i  -  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCC--TTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATT 146

  chrX_151502252_    944 CACATAGAA--GCAAAAAATAGCCTGAATTGCCAAAGTCATCATAAGCAA 991
                           i  i   --    iii i--  v    v      iiv   v i iv  
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_151502252_    992 AAGGAACAAAGATGGAGGCATCACATTACCTGACTTCAAACTATAGTATA 1041
                         i i        v      vv     i v  ii i      viv  v  i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_151502252_   1042 AAGCTACAGTAACTGAAACAGCATGGTACTGGTAGAAAAACAGACACATA 1091
                                     iii i    ii         i v  ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_151502252_   1092 GACCAATGGAACATAATAGAGAACCCAGAAATAAAGCCATACACCTACTG 1141
                           i        i v   v    ii           v       ii  iv 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_151502252_   1142 CCATCTAATCCTTGACAAAGTCAACAAAAATAAGCAATGAGGAAAGTACT 1191
                         i  vi i  ii i     i viiv   i vi vv     i      v iv
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_151502252_   1192 CCCTATTTAATAAATGGTGCTGGGATAGCTGGCTAACCATATGCAAAAGA 1241
                         vi  v  i  i              i i    v  ?   i          
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_151502252_   1242 ATGAAACTGGACCCCT--TTCACCACCACATGCTGAAATTAACTCAAGAT 1289
                              ii         --i    -    i  i vi            i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCAC-ACCATATACAAAAATTAACTCAAAAT 493

  chrX_151502252_   1290 -----AAAGATTTAAATGTAAGACCTCAAACTGTAAA 1321
                         ----- ?   ii           v  v     i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

Transitions / transversions = 2.26 (88 / 39)
Gap_init rate = 0.02 (10 / 530), avg. gap size = 1.90 (19 / 10)  

 773 24.34 8.73 4.23  chrX_151502252_151504815.rev     1696  2073 (491)    L1M4_orf2#LINE/L1      514   908 (0)  

  chrX_151502252_   1696 AGACCCAAATCATATCAGAATCCTAGAAGAAAATATCAGAAAACACTATT 1745
                            v i   v -   v i v  i          i  vi ?iv v - v  
  L1M4_orf2#LINE/    514 AGAGCTAAAAC-TATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTT 561

  chrX_151502252_   1746 C-TGGACATGGGTCCTGGGAAATAATTT-------ATGACAAAGTCCTCA 1787
                          -  iv v     -- i  v   ii   -------      ------i  
  L1M4_orf2#LINE/    562 CGTGACCTTGGGT--TAGGCAATGGTTTCTTAGATATGACA------CCA 603

  chrX_151502252_   1788 AAAGCAATTGCAGCAAAAATAAAAATTGATAAGTCAGATCTAATTAAACT 1837
                               vvv   i     iv      v     i ii  ii v  i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_151502252_   1838 AAAAAAATTCTGCACAGCAAGGTA-AGTATCAAGA--------------- 1871
                         v     v  i  ii vv   i v - v        ---------------
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_151502252_   1872 ---CAGAATGGG-GAAAA-ATTTGCAAAAGTATGCATCTGACAAAGGTCT 1916
                         ---         -     -         -vi  ii      i  i  v  
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAA-TCATATATCTGATAAGGGACT 752

  chrX_151502252_   1917 AATATCCAGAATCTATAAGGAACTTAAACAGTTCAACAAGGAAAA-ATAA 1965
                         vi          v     i     ivv   ii    i  vi    - i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chrX_151502252_   1966 CCCACAACCCCATTTAAAAACTGAGCAAAAGACACAAAGAGACACTTCTC 2015
                         --- i     v   ?     -  i     i  ivii  v     i     
  L1M4_orf2#LINE/    803 ---ATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_151502252_   2016 AAAAGATTGCATACAAGCAGCCAAC---CATCGTGAAAAAATGTTCAGCA 2062
                         v     vvii      iii     i---  - i      i   i   i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCA-CATGAAAAGATGCTCAACA 897

  chrX_151502252_   2063 TCACTAATCAT 2073
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.43 (53 / 37)
Gap_init rate = 0.04 (16 / 395), avg. gap size = 3.06 (49 / 16)  


3182 26.79 0.77 0.66  chrX_151513763_151518107.rev     2948  3854 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151513763_   2948 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATAGTGAAAAT 2997
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151513763_   2998 GGTCATAGTGCCCAAGGTAATTTATAGATCCAATGCCATCCGCATCAAGC 3047
                           iv   v v     iv i  i  i    i   i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151513763_   3048 TACCAATGACTTTCTTCACAGAA-TTGGAAACAA-CT-ACTTTAAAGTTC 3094
                          v   iivi i  i  ii     -   ---    -  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chrX_151513763_   3095 ATATGGAACCAAAAATAACCT-GCATTGCCAAGACAATCCTAAGCCAAAA 3143
                                 viiv  ivi   i- v  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_151513763_   3144 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 3193
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_151513763_   3194 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAC 3243
                                  i   i    ii         i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_151513763_   3244 CAATGGAACAGAA--GAGAGCCCTCAGAAATAATACCACACACCTACAAC 3291
                                 i    --     i  --        vv   i   ii  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_151513763_   3292 CATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 3341
                           vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_151513763_   3342 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCAATAAGTAGAAAGC 3391
                         i  v  i  i              v      v  ? v i v i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_151513763_   3392 TGAAACTGGATCCCTTCCTTACACTTTAGACAAAAATTAATTCAAGATGG 3441
                             ii    i    v   i    iv  v           i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_151513763_   3442 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 3491
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_151513763_   3492 CCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 3540
                          v    ?i- v   -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_151513763_   3541 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 3590
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_151513763_   3591 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGGAACTACCATCAGAGTGA 3640
                         v  i   v v  i i   i  ii vv    i iv    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_151513763_   3641 ACAGGCAACCTACAGGATGGGAGAAAATTTTTGCAATCTACTCATCTGAG 3690
                          v  i     i    i            v       vii ivi      v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_151513763_   3691 AAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACACGAA 3740
                           i  i  vi          v  i         vv    v iv i vv  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_151513763_   3741 AAAAACAAACAACCCCATCAAAAAGTGGTCGAAGGATATGGACAGATACT 3790
                            i     i     v  i?    i   v i      v  i i   i i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_151513763_   3791 TCTCAAAAGAAGACATTTATGCAGCCAAGAGACACATGAAAAAATGCTCA 3840
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_151513763_   3841 TCATCACTGGCCAT 3854
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.44 (13 / 9)  


1639 27.29 5.56 1.14  chrX_151532739_151534330      500  1111 (481)    L1M4_orf2#LINE/L1      270   908 (0)  

  chrX_151532739_    500 GCATTAGCA-AAGAATGCACACATAGATTAATAAAACAGAAT--AGAGCT 546
                          i i i   -   i  iv   i      i   ii  i     --    ii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_151532739_    547 CAGAAATAGACCTGCACACTTATAGTCAGGTGATTCACAACAAAGG---C 593
                                 i   iii   i    i    iv     iv i    i  --- 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_151532739_    594 AA-------TAATGGTGAAAGTACAGTTTTTCCAGCAAAAGGTGCCTGAA 636
                           -------i     v     v i   i   i  i    v     iv i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_151532739_    637 CAATTAGACATCTACAGGCAAATTATAAT-AACCTAGAAACAT-CCTTAC 684
                            i i  i ? i   v     -- v   -  vi i  vv v -   i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAA--AGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_151532739_    685 ATATTCCAGAAAAATTAACTCGATATAAATCACAGACCTAA-TGCAAAAT 733
                          ivv vi v            i v  ii    ?        -  i  i -
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA- 516

  chrX_151532739_    734 GCAAAAACTATACAACCCTCTATAAGAAAACATAAGAGAAAATTCACATA 783
                           v         v   i  -  v           i ? v    iiv i i
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCT-TAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_151532739_    784 ACTTTGAGTTCAGTGGTGAGTTTTTAAATTCAACACCAAAAGCATGATCA 833
                           i   i   vi iii  iv  i   i  vii            ii v  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_151532739_    834 ATGAAAGAAAAATT---TACCAAGTAGATTTTATTAAAATAAACATCATG 880
                          ii         v ---  --  v i  i  i  i     v  v v v v
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATA--AATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_151532739_    881 TGCTCTTCAAAGGACAATGTTAAGAGAATGAAAACAGAAGCCACAGACTA 930
                           iv            v i i    i i      v v  v       v i
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_151532739_    931 GCAGAAAACATCGGTGGTACACATATGTGATAAAGAACATATCTCTACAA 980
                          v      i  iv iiivv  i    v      i i  v i v  i v  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_151532739_    981 CATACAC-GAATTCTTAAAGTTCAACGACAGAAAAAACA----------- 1018
                         i   i v-   i     v ii    ii i -    i   -----------
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATA-AAAAGACAAATAACCCAAT 812

  chrX_151532739_   1019 -TGAAAATAGGCAAAG-ATCTGAACACACTCCTCACAAAAGAAGATATAC 1066
                         -?i     i       -  i    i v  vii  v v             
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_151532739_   1067 ACATGGCAAATAAGCATAATAAAAG-TACTGAGAATCCGTTCTCAT 1111
                          v     v        i vv     - i  v iv   v????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (102 / 61)
Gap_init rate = 0.03 (17 / 639), avg. gap size = 2.41 (41 / 17)  


1797 26.77 5.42 0.49  chrX_151548404_151550003      500  1108 (492)    L1M4_orf2#LINE/L1      270   908 (0)  

  chrX_151548404_    500 GCATTAGCA-AAGAATAGACACACAGATTAATAAAACAGAAT--AGAGCT 546
                          i i i   -   i       i i    i   ii  i     --    ii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_151548404_    547 CAGAAATAGACCTGCACGCATATAGTCAGGTGATTCACAACAAAGG---C 593
                                 i   iii  iiv   i    iv     iv i    i  --- 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_151548404_    594 AA-------TAATGGTGAAAGTACAGGTTTTCCAACAAAAGGTGTCGGAA 636
                           -------i     v     v i  vi   i       v    ii  i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_151548404_    637 CAATTAGACACCTATACACAAATTATAAT-AACCTGGACATAT-CCTTAC 684
                            i i  i ? i i ii    -- v   -  vi     viv -   i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAA--AGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_151548404_    685 ATATTCCATGAAAACTAACTCAAGATACATCATAGGTCTAA-TGAAAAAT 733
                          ivv vi ii    i        i  iv    ?  ii    -  v  i -
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA- 516

  chrX_151548404_    734 GCAAAAACAATACAACCTCTATAAGAAAACATAAGAGAAAATCCACATAA 783
                           v     v   v   iii  v           i ? v     iv i i 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_151548404_    784 CTTTGAGTTTGGTGATGAGTTTTTAAATTCAACACCAAAAGCATGATCAA 833
                          i   i   v  ii   iv  i   i  vii            ii v   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_151548404_    834 GGAAAGAAAAATTTGCCAAGTTG-ATTTTATTAAAATAAAAATCTTATGC 882
                         vi         v v vi  i   - i  i  i     v    v   v  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_151548404_    883 TCTTCAAAGGACAATGTTAAGAGAATGAAAACAGAAGCCACAGACTAGCA 932
                         v            v i i    i i      v v  v       v i v 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_151548404_    933 GAAAACATCTGCGGTACACATATGTGATAAAGAACTTGTCTCTACAATAT 982
                              i  i   iivv  i    v      i i      v  i v     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_151548404_    983 ATGC-GAATTCTTAAAGCTCAATGATAGAAA---AAATGA---------- 1018
                           iv-   i     v i      i   i   ---    i ----------
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_151548404_   1019 AAATAGTCAAAG-ATCTGAACACACACTACACAAAAGAAGATATACACAT 1067
                             i v     -  i    i v   i v v v              v  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_151548404_   1068 GGCAAATAAGCATAATAAAAG-TACTGAGCACCCTTTGGCAT 1108
                            v        i vv     - i  v i  i v????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (102 / 58)
Gap_init rate = 0.02 (15 / 639), avg. gap size = 2.40 (36 / 15)  


1640 27.84 5.50 0.52  chrX_151577473_151579054.rev      502  1083 (499)    L1M4_orf2#LINE/L1      270   880 (28)  

  chrX_151577473_    502 GCATTAGCA-AAGAATAGACACACAGATTAATAAAACAGAAT--AGAGCT 548
                          i i i   -   i       i i    i   ii  i     --    ii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_151577473_    549 CAGAAATAGACCTGCACACATATAGTCAGGTGATTCACAACAAAGG---C 595
                                 i   iii   iv   i    iv     iv i    i  --- 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_151577473_    596 AA-------TAATGGTGAAAGTACAGGTTTTCCAACAAAAGGTGTCGGAA 638
                           -------i     v     v i  vi   i       v    ii  i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_151577473_    639 CAATTAGACACCTATACACAAATTATAAT-AACCTGGACATAT-CCTTAC 686
                            i i  i ? i i ii    -- v   -  vi     viv -   i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAA--AGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_151577473_    687 ATATTCCATGAAAACTAACTCAAGATACATCATAGGTCTAA-TGAAAAAT 735
                          ivv vi ii    i        i  iv    ?  ii    -  v  i -
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA- 516

  chrX_151577473_    736 GCAAAAACAATACAACCTCTATAAGAAAACATGAGAG-AAATCCACATAA 784
                           v     v   v   iii  v          ii ? -     iv i i 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_151577473_    785 CTTTGAGTTTGGAGATGAGTTTTTAAATTCAACACCAAAAGCATGATCAA 834
                          i   i   v  vi   iv  i   i  vii            ii v   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_151577473_    835 GGAAAGAAAAATTTGCCAAGTTG-ATTTTATTAAAATAAACATCATGTGC 883
                         vi         v v vi  i   - i  i  i     v  v v v v  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_151577473_    884 TCTTCAAAAGACAATGTTAAGAGAATGAAAACAGAAGCCACAGACTAGCA 933
                         v       i    v i i    i i      v v  v       v i v 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_151577473_    934 GAAAACATCTGCGGTACACATATGTGATAAAGAACTTGTCTCTACAATAT 983
                              i  i   iivv  i    v      i i      v  i v     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_151577473_    984 ATGC-GAATTCTTAAAGCTCAGCGATAGAAAAA--AATGA---------- 1020
                           iv-   i     v i    iii   i   i --   i ----------
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_151577473_   1021 AAATAGTCAAAG-ATCTGAACACACACTACACAAAAGAAGATACACACAT 1069
                             i v     -  i    i v   i v v v          i   v  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_151577473_   1070 GGCAAATAAGCATA 1083
                            v        i 
  L1M4_orf2#LINE/    867 GGCCAATAAGCACA 880

Transitions / transversions = 1.84 (103 / 56)
Gap_init rate = 0.02 (15 / 611), avg. gap size = 2.33 (35 / 15)  


1797 26.77 5.42 0.49  chrX_151596614_151598213.rev      502  1110 (490)    L1M4_orf2#LINE/L1      270   908 (0)  

  chrX_151596614_    502 GCATTAGCA-AAGAATAGACACACAGATTAATAAAACAGAAT--AGAGCT 548
                          i i i   -   i       i i    i   ii  i     --    ii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_151596614_    549 CAGAAATAGACCTGCACGCATATAGTCAGGTGATTCACAACAAAGG---C 595
                                 i   iii  iiv   i    iv     iv i    i  --- 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_151596614_    596 AA-------TAATGGTGAAAGTACAGGTTTTCCAACAAAAGGTGTCGGAA 638
                           -------i     v     v i  vi   i       v    ii  i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_151596614_    639 CAATTAGACACCTATACACAAATTATAAT-AACCTGGACATAT-CCTTAC 686
                            i i  i ? i i ii    -- v   -  vi     viv -   i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAA--AGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_151596614_    687 ATATTCCATGAAAACTAACTCAAGATACATCATAGGTCTAA-TGAAAAAT 735
                          ivv vi ii    i        i  iv    ?  ii    -  v  i -
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA- 516

  chrX_151596614_    736 GCAAAAACAATACAACCTCTATAAGAAAACATAAGAGAAAATCCACATAA 785
                           v     v   v   iii  v           i ? v     iv i i 
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_151596614_    786 CTTTGAGTTTGGTGATGAGTTTTTAAATTCAACACCAAAAGCATGATCAA 835
                          i   i   v  ii   iv  i   i  vii            ii v   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_151596614_    836 GGAAAGAAAAATTTGCCAAGTTG-ATTTTATTAAAATAAAAATCTTATGC 884
                         vi         v v vi  i   - i  i  i     v    v   v  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_151596614_    885 TCTTCAAAGGACAATGTTAAGAGAATGAAAACAGAAGCCACAGACTAGCA 934
                         v            v i i    i i      v v  v       v i v 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_151596614_    935 GAAAACATCTGCGGTACACATATGTGATAAAGAACTTGTCTCTACAATAT 984
                              i  i   iivv  i    v      i i      v  i v     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chrX_151596614_    985 ATGC-GAATTCTTAAAGCTCAATGATAGAAA---AAATGA---------- 1020
                           iv-   i     v i      i   i   ---    i ----------
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chrX_151596614_   1021 AAATAGTCAAAG-ATCTGAACACACACTACACAAAAGAAGATATACACAT 1069
                             i v     -  i    i v   i v v v              v  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chrX_151596614_   1070 GGCAAATAAGCATAATAAAAG-TACTGAGCACCCTTTGGCAT 1110
                            v        i vv     - i  v i  i v????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (102 / 58)
Gap_init rate = 0.02 (15 / 639), avg. gap size = 2.40 (36 / 15)  


1642 27.33 5.73 1.15  chrX_151612270_151613864.rev      502  1112 (483)    L1M4_orf2#LINE/L1      270   908 (0)  

  chrX_151612270_    502 GCATTAGCA-AAGAATGCACACATAGATTAATAAAACAGAAT--AGAGCT 548
                          i i i   -   i  iv   i      i   ii  i     --    ii
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chrX_151612270_    549 CAGAAATAGACCTGCACACTTATAGTCAGGTGATTCACAACAAAGG---C 595
                                 i   iii   i    i    iv     iv i    i  --- 
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chrX_151612270_    596 AA-------TAATGGTGAAAGTACAGTTTTTCCAGCAAAAGGTGCCTGAA 638
                           -------i     v     v i   i   i  i    v     iv i 
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_151612270_    639 CAATTAGACATCTACAGGCAAATTATAAT-AACCTAGAAACAT-CCTTAC 686
                            i i  i ? i   v     -- v   -  vi i  vv v -   i  
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAA--AGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_151612270_    687 ATATTCCAGAAAAATTAACTCGATATAAATCACAGACCTAA-TGCAAAAT 735
                          ivv vi v            i v  ii    ?        -  i  i -
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA- 516

  chrX_151612270_    736 GCAAAAACTATACAACCCTCTATAAGAAAACATAAGAGAAAATTCACATA 785
                           v         v   i  -  v           i ? v    iiv i i
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCT-TAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chrX_151612270_    786 ACTTTGAGTTCAGTGGTGAGTTTTTAAATTCAACACCAAAAGCATGATCA 835
                           i   i   vi iii  iv  i   i  vii            ii v  
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chrX_151612270_    836 ATGAAAGAAAAATT---TACCAAGTAGATTTTATTAAAATAAACATCATG 882
                          ii         v ---  --  v i  i  i  i     v  v v v v
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATA--AATTGGACTTCATCAAAATTAAAAACTTT 663

  chrX_151612270_    883 TGCTCTTCAAAGGACAATGTTAAGAGAATGAAAACAGAAGCCACAGACTA 932
                           iv            v i i    i i      v v  v       v i
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chrX_151612270_    933 GCAGAAAACATCGGTGGTACACATATGTGATAAAGAACATATCTCTACAA 982
                          v      i  iv iiivv  i    v      i i  v i v  i v  
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chrX_151612270_    983 CATACAC-GAATTCTTAAAGTTCAACGACAGAAAAAACA----------- 1020
                         i   i v-   i     v ii    ii i -    i   -----------
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATA-AAAAGACAAATAACCCAAT 812

  chrX_151612270_   1021 -TGAAAATAGGCAAAG-ATCTGAACACACTCCTCACAAAAGAAGATATAC 1068
                         -?i     i       -  i    i v  vii  v v             
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chrX_151612270_   1069 ACATGGCAAATAAGCATA--AAAAAGTACTGAGAATCCGTTCTCAT 1112
                          v     v        i --    ii i  v iv   v????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (104 / 59)
Gap_init rate = 0.03 (17 / 639), avg. gap size = 2.47 (42 / 17)  


2003 26.20 2.84 2.69  chrX_151631508_151633167.rev      502  1169 (491)    L1M4_orf2#LINE/L1      240   908 (0)  

  chrX_151631508_    502 CTGTAAAGGTACAGCAATCTACAAAGTATGATATTGCCAAAAGAATGGAC 551
                           ii    v     i    v v v   i  i  i  v  v   i  i   
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chrX_151631508_    552 ACACA--TCAATGGAACAAAAT---------AGAAATAGATCCATAAAAA 590
                          i i --         i i   ---------       i i     v vv
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_151631508_    591 TATAGTTTACTGATTTTTTGACAAAGATGCAAAGATAATCCTATAGAGAA 640
                            i  iv i       i-     i i   v    iv  i v  i i   
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTC-GACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_151631508_    641 ATGATAGTCTTTTCAACAAAGGGCACCTGAACAAATGGATCTCAATATGC 690
                          vi                 v  ii iv i    v     v? v i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_151631508_    691 AAAGAAATGAACCTAGATAAA-ACTTTATATCTTTCACAAAAAATAACCT 739
                            ii      vi i  ivvv-  i i i i v vi       v    - 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC-T 487

  chrX_151631508_    740 CAAAGTATATTATAGACTCAAATTTAAAATGC-AATATTATAAAACTTCT 788
                             i iv  i ?    ii    v   i -  -  v i         ii 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTT 536

  chrX_151631508_    789 TGAAGAAAA--TAGGGGAAGATCTACATGACCTGGGTTTTGGTGATAAAT 836
                         v        --    ? v i    v i      v  v  v  ii  ii- 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG-T 585

  chrX_151631508_    837 TTTTTAGATACAACATCAAAAGGGTGGTCTATGAAAGGCAAAATTGATAA 886
                           i       ii   i      viiiiv v ii    iv     v     
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_151631508_    887 GTTAGACTTTCTAAAAATAAAAAAGAAACCTCGAAAGCTCTTTGAAAGAC 936
                         i  i     iv v     v     ---- i iv--- iv   ii  i   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAA----CTTTT---GTGCTTCAAAGGAC 678

  chrX_151631508_    937 ATTGTTAGGAAAAAGAAAAGAGAAGCCACAGACTATGACCAAGTGTTTGC 986
                          i i i i    iv       v  v       v iv  vv  i i     
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chrX_151631508_    987 AAAACATATATCGGATAGAAGATCTGTATCCAAAATCTACAAAGGAGGCT 1036
                            v        v    iii  ii        i   v  i    i vv  
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCT 778

  chrX_151631508_   1037 TACAACTGAACAATAAGAAAACAAATTTATAAAAACTCAATC----AATG 1082
                                v  i     i  i      -------   i    i----    
  L1M4_orf2#LINE/    779 TACAACTCAATAATAAAAAGACAAAT-------AACCCAATTWAAAAATG 821

  chrX_151631508_   1083 GGCAGAAACTCTGAACAGACACATCGCCAAAGAAGATATACAGATGGGAA 1132
                             i iiv i    i     iv  v                i    vv 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_151631508_   1133 ATAAGCATAAGACAAGACCATCAACATCATTCTTCGT 1169
                                i v  v    ivv         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (105 / 67)
Gap_init rate = 0.02 (13 / 669), avg. gap size = 2.85 (37 / 13)  


3262 27.31 0.33 0.33  chrX_151674665_151681050.rev     4988  5895 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_151674665_   4988 TGGAAGAACATTCCATGCTCATGAATAGGAAAAATCAATATTGTGAAACT 5037
                              ii i  i     i     i  v    i v i        v  iv 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_151674665_   5038 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCACCATCAAGC 5087
                            v     vi    iv i  i  i        i  v   v i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_151674665_   5088 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5135
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_151674665_   5136 TATGGAACCAAAAAAGAGCCCACATAGCCAAGAGAATCCTAAGCAAAAAG 5185
                                viiv  ii  v  viv        i v    i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_151674665_   5186 AACGAAGCTGGAGGCATCATACTACTTGACTTCGAACTATACTACAAGGC 5235
                            i   i      vv   i   v iii i   i  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_151674665_   5236 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5285
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_151674665_   5286 AATGGAACAAAACAGAGCGCTCAGAAATAACACCACACATCTACAACCAT 5335
                                i i  iv   v ii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_151674665_   5336 CTGATCTTTAACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5385
                         i    i  ii    ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_151674665_   5386 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTGA 5435
                         v  i  i              v      v  ?   i   v i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_151674665_   5436 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5485
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_151674665_   5486 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5535
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_151674665_   5536 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 5584
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_151674665_   5585 ACACCAGAAGCAATGGCAACAAAAGCCAAAATAAACAAATGGGATGTAAT 5634
                               i     vvi          vv      i i    v   iv v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_151674665_   5635 TAAACTAAAGAGTTTCTGCACATCAAAAGAAACTACCATCATAGTGAACA 5684
                         i   v v  i ii  i  ii v     i  v    i  vv v      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_151674665_   5685 GGCAACCTACAGGATGGGAGAAAATGTTTGCAATCTACCCATCTGACAAA 5734
                          i     i    i            i       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_151674665_   5735 GGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 5784
                           i  vi          v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_151674665_   5785 CACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5834
                         v     i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_151674665_   5835 CATAAGAAGACATTTATGCAGCCAACAGACACACGAAAAAATGCTGATCA 5884
                          vv       i  vi viii     i ii    i     i     v v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_151674665_   5885 TCACTGGCCAT 5895
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (149 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


 606 30.11 7.13 4.12  chrX_152116408_152118018.rev      482  1112 (499)    L1M4_orf2#LINE/L1      227   876 (32)  

  chrX_152116408_    482 ATATTAAAAC-----ATAAATTGAGAGTAATTTAAAAGAACTGTGTAGTA 526
                           v i     ----- i   viv v      i---    - v    i   
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATC---AAGA-CAGTGTGGTA 272

  chrX_152116408_    527 CTAATATATGAATAGA-AGACAGAACAATAGAA-AAAACAGAAAGTCTA- 573
                           iii   v i     - v i   v    i   - i  iv  i    i -
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_152116408_    574 AAATACATCCAAATACAAACGAGGATTTAGAATAT-GATAGAAATGTTAT 622
                              v i   v i ivv i ivv v  -  v v -  i iiii  ii v
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATT-GATTTTCGACAAGGGTGCCAA 371

  chrX_152116408_    623 TTCAGTTCCTTGGGGAAAGA-TGGGTTATTCAATAAATGGTGTAGGGATA 671
                         vv vi   vv          - i vi v     i        iv    i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_152116408_    672 AGTAGGTGGCCATCTGGGAAAAATGTGAAGTTGAATCCC-ACATCATA-- 718
                          v i i i?   iv  vi   i -i        i i   -  v   i --
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGA-ATGAAGTTGGACCCCTACCTCACACC 470

  chrX_152116408_    719 ATGTGCAACCAACTAAATTCTGGATGGATCA--GATTTAAAGATTAAAAA 766
                           i i   --  v v  i  vii        --  ii    vi --  i 
  L1M4_orf2#LINE/    471 ATATACAA--AAATTAACTCAAAATGGATCAWAGACCTAAATGT--AAGA 516

  chrX_152116408_    767 AATAAAGCTATAAAAATATTGGAAGAAAATATGGGACATTTAAAAT---- 812
                         iv    i        v v  i        i  i  ?-i ---    ----
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN-GT---AAATCTTC 562

  chrX_152116408_    813 ATG---TTGGAAGAGAGAA-GGCCTTTTAAAGTATGACA---GAAGC-CA 854
                         i  ---    ivv  iv  -  ii i   i -       ---i    -  
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACA 611

  chrX_152116408_    855 A--AACA---GAGAAGCTTGATTAATTC-AGTACATAAAAACGAAAAGTT 898
                          --    ---  i  iv v   v    v- v v   v    iv    ii 
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chrX_152116408_    899 T-----CTTCAACACAAAACTTCCTGCCAGCAAAGTCCAGGG-CAAATGT 942
                          -----      --- ii  --v  ii  iv     vv ii -   vivv
  L1M4_orf2#LINE/    662 TTTGTGCTTCAA---AGGAC--ACTATCAAGAAAGTGAAAAGACAACCCA 706

  chrX_152116408_    943 TAAACCGGGA-AAATTATTTGCAATTCCTGTTGGAGACAAGGAGGCTAGT 991
                         i i vi    -   v         v  v i vvvv  i    - i  v  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG-GACTTGT 755

  chrX_152116408_    992 TTTCCTATTATTTAA-TAGTTCCTACAAAATAGTAAGAAAAATGACAG-C 1039
                         v i vv v   v   -v ii  i     vvi i   v     -    i-i
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA-GACAAAT 804

  chrX_152116408_   1040 AACACAATAGCAAAACAGGCATAAACTAGGAATA--CGGTTCACGGGAGA 1087
                            v    v?v    ii    v iiv vv     -- iv   v vii   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chrX_152116408_   1088 -GAAATACAAATGACTTCCAAATAAG 1112
                         -  v         i i----      
  L1M4_orf2#LINE/    855 AGATATACAAATGGCC----AATAAG 876

Transitions / transversions = 1.20 (102 / 85)
Gap_init rate = 0.06 (38 / 650), avg. gap size = 1.87 (71 / 38)  


3560 18.12 0.43 0.72  chrX_152403236_152404894.rev      479  1168 (491)    L1M4_orf2#LINE/L1      221   908 (0)  

  chrX_152403236_    479 TTATCAAATACAAACTTTAGGAT-AACCTACGGGAATCAAGACTGCATGG 527
                           vi   v v    vi   vv i-  v    i v         v ii   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chrX_152403236_    528 TATTGACATAAGAAAAGGCTCATAGATCCATGGAATAGAATTGAGAAGCC 577
                           i  i      i v  i vi       v                 iv  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chrX_152403236_    578 AGAAATAAACCCACACATCAATGGTCAATTGATTTTTGCCAAGTGCACCA 627
                                      i    iv                i v    v ii   
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chrX_152403236_    628 AGACCATTCAATGGGAGAAAGAATCATCTCTTTAACAAACGGTGCTGGGG 677
                                        -        vi   i  i      i         i
  L1M4_orf2#LINE/    371 AGACCATTCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chrX_152403236_    678 TAACTAAACATCCACATGCCAAAGAATGAAGCTGAACTCCAGCTTCACAC 727
                         i    ii i ?        v           i  i  i  vi i      
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chrX_152403236_    728 CATACAGAAAAAGTCACTCAAAATGGATTAAAGACTCACATGCAAGCCCC 777
                             i v     v v             i ?    ii v   i   vv i
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_152403236_    778 AAAACTATGAAACTCTTAGAAGAAAACGTAGGTGTAAGTCTTCATGACCT 827
                                 i                  i    ?    i     i      
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chrX_152403236_    828 TAGATCAGGCAATAGTTTCTTAAACGTGATACACAAAGCCCAAGTGACAA 877
                          i i i       i        i ii   i  vv     v    ii    
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chrX_152403236_    878 AAGATAAAATAGATACATTGGACTTCATCAAAATTGAACAGTTCTGTGCT 927
                             v          v                   i  v v  i      
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chrX_152403236_    928 GCAAATGTTACTATCAAGAAAGTGAAAAGACAACTCGCAGAATGAAATAG 977
                         v    v vi                         i i       ii v i
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chrX_152403236_    978 AAGATTTGCAAATTATATATCAGATAAGGGACTTGTATCTAGAATATATC 1027
                           v          i       v                 i         v
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chrX_152403236_   1028 AAGAAC-CTCACAAAAACCC-ACAATAAAAAGACAAATGACCCAATTTTT 1075
                               -  i    --- i - i               i        -?v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAA---CTCAATAATAAAAAGACAAATAACCCAATT-WA 815

  chrX_152403236_   1076 AAAGTGAGTGGAGGATTTGAATAGATATTTCTCCAAATAAGATGTGCGAG 1125
                            i  i iii              i           v     i i i i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chrX_152403236_   1126 AGGCGAATGAGCACAGGAAAAGATGCTCGACATCACCAGTCAT 1168
                         v   v   i      v            i      ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (77 / 44)
Gap_init rate = 0.01 (6 / 688), avg. gap size = 1.33 (8 / 6)  


3445 22.29 0.51 8.51  chrX_152540401_152543875     1997  2983 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_152540401_   1997 TGGAAAGATACCCTGTGTTCATGGATTGGGATAGTTAATATTGTTAAAAT 2046
                                   i  ii              i v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_152540401_   2047 GTCTATACTACCCAAAGTGATCTACACATTCAATGTAATCCCTATCAATA 2096
                          v v     v      v         v      i i            v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_152540401_   2097 TTCCCATGAGATTTTTCACAGAAATAGAGAAAGCAATTCTAAAATGTATG 2146
                          i  viivivv     ii       v  v  ivii  i       vi  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_152540401_   2147 TTAAACCACAAAAGACCCCAAATAGCCAAAGCAATCTTGAACAAAAAGAA 2196
                          vi  vii   ii     vi          i          v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_152540401_   2197 CAAAACTGGAAGACTCATGCTATCTGATCTCAAAATATGTTACAAAGCTA 2246
                             ii    i      ii  vi ii  i      iv ii          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_152540401_   2247 TAGTAACCAAAACAGCATGGTTCTGGCATAAAAACAGACACATACACCAA 2296
                         i     i   i    ii    v         ii i     i   v i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_152540401_   2297 CGTAACAGAATAGTGAACCCAGAAATAAATCTATGCATTTACAGTTGATT 2346
                         i v  i     v v  ii           i i  i      ii  ii   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_152540401_   2347 GATCTTCGACAAAGGTGCCAATAATACATGATAGACAAAAGACAGTCTTG 2396
                            i        i        v vi ivii  i iv   ii i      v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_152540401_   2397 TCAATAAATGGTGTTGGGAAAATTGGATATTCACTTGCAGTAGAATGAAA 2446
                             i        i     v  i      ?i   v    iv        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_152540401_   2447 TTAGACCCTTATCTCACACAATGCACAAAGATCAACTCAAAACGGACTGA 2496
                           i     i  i       v  ii     i  i         i   iii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_152540401_   2497 AGATTCAAATGTGAGACCTGAAATTAGAAAACTACTAGAAGAAA-CTTAC 2545
                            iii      i   v  i   i  v      vi         - v  v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_152540401_   2546 GTGAAAAGCTGCTTGGCACTGGTCTGGGCAATAAGTTTTTCAATATGACA 2595
                          ? v   v  v v  i vi   vi i      iiv  i  vi        
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_152540401_   2596 CCAAAAGCACAGGCAACAAAACAAAAA-CAGACAAATGAGTTTGCATCAA 2644
                                    i         v     -i   i    vi vi v      
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_152540401_   2645 ACTAAAAAGCTTCTGCACAGCAGAGGAAGCAATCAACAGAGTGAAGGAGA 2694
                          v v    i   i  ii vv  i    vi v     v i      i-   
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA-AGA 699

  chrX_152540401_   2695 CAGCCTATGGAATGGAAGAACATAGTTGTAAACCATCCATCTGATACAAG 2744
                           i  i ii      i    v   v   i   i   vi        vii 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chrX_152540401_   2745 GTTAATACACAGAACACACAAGGAACTCATACAACTCAATAGCAAGCAAA 2794
                         ii vi  iv     i i i  i      v            ---------
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA--------- 790

  chrX_152540401_   2795 TGTATTTTCTAACCCAGTTAAAATAACCCAGTTACACCTACTATGTACTC 2844
                         ----------------------    ------------------------
  L1M4_orf2#LINE/    791 ----------------------ATAA------------------------ 794

  chrX_152540401_   2845 CTAAAAATTAAAAATTGAAAATTGAAAAAATAAATAACCCAATTTAAA-- 2892
                         -------------------------   i i             ?   --
  L1M4_orf2#LINE/    795 -------------------------AAAGACAAATAACCCAATTWAAAAA 819

  chrX_152540401_   2893 TGGGCAA-GGACCTGAACAGGCATTTCTCAAAAGAAGACATACAAACGGC 2941
                                -   ii    i  i        v        i       i   
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chrX_152540401_   2942 CAATAGGTCTATTAAAAAAAAATGCTCAACATCAGCCGGGTG 2983
                              i ivi  ---i    i             ????????
  L1M4_orf2#LINE/    870 CAATAAGCACAT---GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (147 / 69)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 11.12 (89 / 8)  


3184 26.56 1.44 0.56  chrX_153457362_153462830.rev     4079  4978 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153457362_   4079 TGGAAGAATGTTCCATGGTTATGGATAGGAAGAATCAATATCGTGAAAAT 4128
                              ii  i i     v i      v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153457362_   4129 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 4178
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153457362_   4179 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4226
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_153457362_   4227 CATGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCATAAGCAAAAAG 4276
                         i      viiv  ii  v  v v  v     i      v i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_153457362_   4277 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4326
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_153457362_   4327 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 4376
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_153457362_   4377 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACC 4424
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_153457362_   4425 ATCTGATCTTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCC 4474
                          vi    i  i     ivv  v   i vv vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_153457362_   4475 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4524
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_153457362_   4525 GAAATTGGATCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 4574
                            i     i    v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_153457362_   4575 TTAAAGACTTAAATGTTAGACCTAAAACCAAAAAATCTCTAGAAGAAATC 4624
                          i ?    i       v   v       i v    iiii         v 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_153457362_   4625 CTAGGCAGTACCACT-CAGGACATAGGCATGGGCAAGGACTTCATGACTA 4673
                         v    ?-   vvv  - iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_153457362_   4674 AAACACCAAAAGCAATAGCAACCAAAGCCAAAATTGACAAATGGGATCTA 4723
                         vi            vv      v    vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_153457362_   4724 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACAACCATCAGTGTGAA 4773
                           i   v v  i i   i  ii vv    i  v  v i  vv iv     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_153457362_   4774 CAGGCAACCTACAGAATGGGAGAAAATGTTTGCAATCTACCCATCTGACA 4823
                         v  i     i                 i       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_153457362_   4824 AAGGGCTAATATCCAAAATCTACAAAGAACTTAAACAAATTTACAA---- 4869
                          i  i  vi      i   v  i        ivv    v iv i  ----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_153457362_   4870 ----CAAACAACCCCATCAAAAAGTAAGCAAAGGATATGAACAGACATAT 4915
                         ----    i     v  i?    i ii         v    i      v 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_153457362_   4916 CTGAAAAGAAGACATCTATGCAGCCAACAGACACATGAAAAAATGCTCAT 4965
                           vv        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_153457362_   4966 CATCACTGGTCAT 4978
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.25 (18 / 8)  


 292 28.12 4.17 0.00  chrX_153478212_153481216     1010  1105 (1900)    L1M4_orf2#LINE/L1        1   100 (808)  

  chrX_153478212_   1010 TGGAAAGATATACTGTGCTCAGTAATTGGAAGATTCAGAATAGTAAAGAC 1059
                                    v ii  i   vvi         i i iv  v  v    i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153478212_   1060 T-CAAT---TCTCAAATGTATGTATAGATTTAATGCAATTCCAACTAAAA 1105
                         v-    ---i i     vv  v  i     i  i     i  v ii    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

Transitions / transversions = 1.45 (16 / 11)
Gap_init rate = 0.02 (2 / 100), avg. gap size = 2.00 (4 / 2)  

1883 24.30 9.03 0.99  chrX_153478212_153481216     1422  2030 (975)    L1M4_orf2#LINE/L1       97   754 (154)  

  chrX_153478212_   1422 AAAGTCTTAGCAGGATATTTTTGTAGATAAAGAACATCTGACTCTAA--T 1469
                            i  ii   v vv -      i   v vv  vv v    ii    -- 
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chrX_153478212_   1470 TATACATGGAAAGGCAAAGGAAGTAGAATAACAAAAACAAGTTTTAAAAA 1519
                          -i i       v    i   vvi      i v       vi  v     
  L1M4_orf2#LINE/    146 T-CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chrX_153478212_   1520 CAAGAATGATGTTAGAGAAAATAAACTTCCTGATTTTAAAATTTACTCCA 1569
                         v     ii v   i   i vvi v      ii    i    i     v  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chrX_153478212_   1570 AAGCTACAATAATCAAGACTGTATGGCATAGGCA-AAG---AGACA---- 1611
                                 i          v  i   i iv    -   ---     ----
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chrX_153478212_   1612 -----ATGGAACAGAAT---------AGAAA---ATCTACACAAATATGT 1644
                         -----      i     ---------     --- i i i   vv    v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_153478212_   1645 CCAACTGATTTATTACAGAGGTGCAAAGAAAATTCAATGAAGAAAGGATT 1694
                         i   i      viv   ii     v    vv        ii     i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_153478212_   1695 ATATTTTCCATAAATGGTACTGAAACATTTGGACATCCATATGCAAAA-- 1742
                         i v     v i       i   ii   vi    i ?   i        --
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_153478212_   1743 -TGTCAGCTTCGACTTC-ACCTCACATCTCATACAAAAATAAACTTAAAA 1790
                         -  -- iv  v   ii -        i vi          v    i    
  L1M4_orf2#LINE/    445 ATG--AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chrX_153478212_   1791 TGGATCATAGACCTAAATGTAA-------AACCATAATTCTTTTAGAAGG 1833
                                ?              -------   i    vv  i       i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_153478212_   1834 AAATAAAGGAGAAAATTCTAATGAACTAAGGTTAGGCA--GAGTTCTTAG 1881
                            i v   ? v    ii vi   v  vi         -- iv       
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_153478212_   1882 ACATAACA-----------ATCCATTAAGGAAACAAAATCAATAAATTGG 1920
                          i  i   ----------- v v iv  i    --    vi         
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAA--AAATAGATAAATTGG 640

  chrX_153478212_   1921 ACTTAATTAAATTTTTAAATGTTTGCTCTGCAAAAGACAG----AAGAGA 1966
                             v  i   v  vv   iv    iv  v    i    v----    i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chrX_153478212_   1967 ATGGAAAGACAAGCTCCAGATACGGAGAAAATATTTGCAAACTATATATC 2016
                         i  i        v iv    vvv                  ii       
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_153478212_   2017 CATTGGAGGACTTG 2030
                         iiv iii       
  L1M4_orf2#LINE/    741 TGATAAGGGACTTG 754

Transitions / transversions = 1.23 (80 / 65)
Gap_init rate = 0.02 (16 / 658), avg. gap size = 3.81 (61 / 16)  

 667 21.25 0.62 0.00  chrX_153478212_153481216     2355  2514 (491)    L1M4_orf2#LINE/L1      748   908 (0)  

  chrX_153478212_   2355 GGACTTGTACACAGAATATATAAAGAACTCTCAAAACTCAAT-GTAAGAA 2403
                                  iv                    i v        -i   i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_153478212_   2404 AACAAACAACCTGATTTAAAAATTGGCAAAAAGATTGAACAGATACTCCA 2453
                         i     i    ii   ?      v      iiiv     i   i i i v
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_153478212_   2454 CCAAAGAAAATATATGGATGGCAAGTAAACACACCAAAATATGTCCAACA 2503
                                 i     iii     v i   i    iv    v   ii     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_153478212_   2504 TAATTTACCAT 2514
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.67 (24 / 9)
Gap_init rate = 0.01 (1 / 161), avg. gap size = 1.00 (1 / 1)  


4427 16.74 3.12 1.79  chrX_153482922_153484898      596  1491 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153482922_    596 TGAAAAGATATCT-GTGTTCATGAATTGAAAGACTTAATATTGTTAACAT 644
                           i         i-i        i    i                  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153482922_    645 GATAATATTATGCAAAACGGTTTGCAGATTCAAAGCATTCCCCATCAGAA 694
                          ii    i viv    vi i i i         v   v    i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153482922_    695 TTCCAATGGTCTTTTTTTGCAGAAATAAAAAACCCTGTCCTTAAAGTTCA 744
                          i   iiv i       -        vi v  v -  vi i    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGC-TGATCCTAAAATTCA 148

  chrX_153482922_    745 CGTGTAATAT-TAAGTGACCCTTAAATGACAAATCAATCATAAAAAAGAA 793
                         ii  v  -  -i   v     vv  vv v    v     v i        
  L1M4_orf2#LINE/    149 TATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_153482922_    794 GAACAAAGTTGGAAGACTCATACTTTCTGATTTCAAAGCTTACTACAAAG 843
                                      i      i    i ii        i            
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_153482922_    844 CTACACTAATCAAAACATTGTGGTACTGGCATAAGGATAGACATATAGAC 893
                              v       i   v                               i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_153482922_    894 CAA---------------------GAAATAAACCCTTGCATATATTGATT 922
                            ---------------------           ----   i   v  v
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCC----ATACATTTATG 343

  chrX_153482922_    923 TTCAACGAGATTTTCAATGAGAGCGCCAGGACCATTCGACATGGAAAGGA 972
                         v    iv-       i ii  i i    i        i iiv      i 
  L1M4_orf2#LINE/    344 GTCAATT-GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chrX_153482922_    973 TAGTCTAGACTTTCCAACAAATGGTGCTGGGAAAACTGAATGTCCACAAG 1022
                               -----  i                  v     i  i?     v 
  L1M4_orf2#LINE/    393 TAGTCT-----TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chrX_153482922_   1023 CAAAAGAATGACGTTGGCCTCTAACTTTATACCACATACAAAAATTAACT 1072
                                    v     v i iv  i i i    i               
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_153482922_   1073 CAAAAAAGATCAAAGATCTAAACATAAGAGCTAAAACTATAAAACTTTTA 1122
                              vi     ?   i     ii                      i   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chrX_153482922_   1123 GAAGAAAACATAGGAGAGAATCTTCATGACATTGGATTTGGCAATGATTT 1172
                                       ? vi       i    v    i  v       i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_153482922_   1173 CATGGATATGACGCCAAAAGCA-AGGCAATAAAAGGAAAGA-AAAT---T 1217
                          v i        i         - i    i     i   i - i  --- 
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chrX_153482922_   1218 TTGACTTCATCAAAATAAAAAACTTCTGCGCATCAAAGGACACTATCAAG 1267
                          v              v        i  i  v                  
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chrX_153482922_   1268 AGAATGAAAAGACAACCCACAGAATGAGAGAAAATATTTGGAAATCATGT 1317
                          i i                      i             v       i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chrX_153482922_   1318 ATCTGATAAGGGGTTAACATCCAGAATATATTTTAAAAATTCCTATAACT 1367
                                     ii vii             v--  i  i  i  i    
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATA--AAGAACTCTTACAACT 785

  chrX_153482922_   1368 CAACAACAAAAAAAGAAACAACCTAACTTAAAAATATGCAAAGGACTTGA 1417
                            i  i     i v   i    i  i ?      iv        i    
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chrX_153482922_   1418 ATAGACAGTTCTCCAAAGAAGATATATAAATGGCCAATAAGTACATAAAA 1467
                                v                  i              i    i   
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chrX_153482922_   1468 AGATGTTCATTAATCATTAGGGAA 1491
                              i   vi -   ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 2.11 (99 / 47)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 3.14 (44 / 14)  


3274 23.44 0.21 5.62  chrX_153493120_153495300      735  1694 (487)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153493120_    735 TAGAAAAATATTCCATGTTCATGTACTGGAAGAATCAACATTATTTAAAT 784
                          i    i    i           v i       v i  i   i  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153493120_    785 GTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTACCAAAA 834
                          v v     v      vii              i          i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153493120_    835 TACCTATTAAAGTCTTCACAGAAATAGAAAAAA-AATCCTAAAATTTGTA 883
                          v  vii ivvv i  ii       v  v  iv-i           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_153493120_    884 TGGAACCATGAAAGACCCAGAATAGCCAAAGCTATCCTAAGCAAAAAGAA 933
                              viiii ii                 i v   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_153493120_    934 CAAAACTGGAAGAATCACATTACCTGACTTCAAATTATACTACAGAGCTA 983
                             ii    i  v     i v  ii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_153493120_    984 TGGTAACCAA-ACAGCATGGTGCTGGCATAAAAACAGACACATAGACCAA 1032
                         ii    i   -    ii    i         ii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_153493120_   1033 TGGAACAGAATAGGGAACTCAGAAACAAATCCACACACCTACAGTGAACT 1082
                              i     v i  iii      i   i   i   ii  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_153493120_   1083 CATTTTTGACAAAGGTGCCAAGAACATACACTGGGAAAAAGATAGGCACA 1132
                         v     i     i          v   v  v    i   ii    v viv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_153493120_   1133 TAAATAAATGGTGTTGGGAAAACTGGATATCCATACACAGAATAATTAAA 1182
                          v  i        i     v         ?   i ii  i  v   v  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_153493120_   1183 CTAAGACCCCTATCTCTCACCATATACAAAAATCAAATCTAAATGGATTA 1232
                         i i-        i   v                i  v  v        i 
  L1M4_orf2#LINE/    451 TTG-GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_153493120_   1233 AACACTTAAATCTAAGACATCGAACTATAAAACTACTACAAGAAAACATT 1282
                         ? v  i     v     ---------------------------------
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGA--------------------------------- 516

  chrX_153493120_   1283 AGGGAAAAAACGCTAAGGCATCAAACTATAAAACTACTACAAGAAAACAT 1332
                         -----------     -------            vi  v          
  L1M4_orf2#LINE/    517 -----------GCTAA-------AACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_153493120_   1333 TAGGGAAAATCTCGAAGACATTTGCCTGGACAAAAAAATTCTTCAGCAGT 1382
                         vi ? v      iviv   v  v vi i i   viiv-     viii vv
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGATATG 597

  chrX_153493120_   1383 ACACCAAAAGTACAGACAACCAAAGCAAAAATGGACAAATGGGATCACAT 1432
                                   i   ii    v    v      i  i    v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_153493120_   1433 GAACTTGAAAAACTTCTGCACAGCAAAGAATACAATCAACAGAGTGAAGA 1482
                         v  vv v        i  ii vv     i i  v     v i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_153493120_   1483 GACAACCCACAGAATGGGAGAAAATATTTGCAAACTACCCATCTGACAAG 1532
                                                           ii ivi      i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_153493120_   1533 GGATTAATAAACAGAATATTTAAGAAGCTCAAACAACTCTATAGGAAAAA 1582
                            i vi  vv        v   ii i   vv       v   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_153493120_   1583 AGTCTAATAATCTGATTAAAAGATGGAACAAAGATTTGAATACACATTTC 1632
                         - v v     i ii   ?   i    ivv  i          v       
  L1M4_orf2#LINE/    798 -GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_153493120_   1633 TCAAAAGAAGACAAACATATGACAAACAGGCATATGAAAAGGTGCTCAAT 1682
                           v        i v   v   i v  i i   i        i       i
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_153493120_   1683 GTTACTGATCAT 1694
                         i i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (137 / 84)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 8.00 (56 / 7)  

 201 19.67 4.92 0.00  chrX_153493120_153495300     1718  1778 (403)    L1M4_orf2#LINE/L1      845   908 (0)  

  chrX_153493120_   1718 TCTCAAAAGA-GACATACATGCAGCCAACAAGGATACAAAAAA--GCTCA 1764
                             v     -  i     viii     i   v i ii    i--     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chrX_153493120_   1765 ACATCATTGATCAC 1778
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.50 (3 / 2)  


2471 22.31 3.89 1.65  chrX_153499485_153501101      457  1124 (492)    L1M4_orf2#LINE/L1      226   908 (0)  

  chrX_153499485_    457 AACTATAAAACATTATATACACAAATTA----AATAAAATCTACGTTGTA 502
                           i vi     -   i-    -  ii  ----   v  iv vii  v   
  L1M4_orf2#LINE/    226 AATTTCAAAAC-TTAC-TACA-AAGCTACAGTAATCAAGACAGTGTGGTA 272

  chrX_153499485_    503 CTGGCATAAAAACAGATACATAAACCAAAAGAACAGAATAGAGAGGCCAG 552
                                  ii i   i i   i i   vi   i     v     v    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chrX_153499485_    553 AAATACACCCACATGTACATGGTCAACTATGCTTTGACAAGAGAGCAAAG 602
                              v     i ii vi        i ivvi  i      i v  v   
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_153499485_    603 AATACACAATGGAGAAAGGAGAGTCTCTTCAATAAATTGTGTTGGGAAAA 652
                          vi iv      i     i v     i     i    v   i     v  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_153499485_    653 CTGGATATCCACACGCAAAAGAATGAACTTGGGCCCTTTTCTTATACCAT 702
                                ?     i             v    i   i vi  i i     
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chrX_153499485_    703 ATACAAAAAATTAACTTGAAATGGATTATAGACTTCAATCTAAAATCTAA 752
                                  -      ii        i ?    i v   v   i v    
  L1M4_orf2#LINE/    473 ATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chrX_153499485_    753 AACCATTTAGCCCCTAGAAGAAAATATAGGGGGAAAGCTCATTGACATTG 802
                            i  vv i i i          i     ? v   v  ivv    v   
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chrX_153499485_    803 GTATTGATTGACAATGATATTTTGGATATGATTCCAAATGCACAGGCAAA 852
                          -i  i--- i     i v i  i       iv     v     i    v
  L1M4_orf2#LINE/    572 G-GTTA---GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_153499485_    853 AATAGCAAAAATAAACAAGCGGAGCTACATCAAA-CTAACAAGTGTC-TG 900
                           v  v       i i  iiv ii  v       -i   v  v v i-  
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_153499485_    901 CTCAGCAAAGGAAACAATCAACAAAATGAAAAGGCAACCTAGAGAATGAG 950
                           i--       v  v     v   i       i     i v      i 
  L1M4_orf2#LINE/    668 CTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chrX_153499485_    951 AGAAAATATTTGCAAATCATATA----A-AAGGGGTTAACAGTAAAAATA 995
                                                ---- -     ii vii viv i    
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chrX_153499485_    996 TATAAGGAACTCACATAACTGAGTAGCAAAAAAACTAAATGACCCAATTT 1045
                              i      vi i    v i  ii     i  -    i        ?
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTW 814

  chrX_153499485_   1046 TAAAATGGGCAAAG-ATCCGAATAGACATTTCTC--------------AA 1080
                         v             -  ii               --------------  
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_153499485_   1081 ATGGCCAACAGGTATATGAAAAAATGCTCGACATCACTAACCAT 1124
                                 i i i i       i      i      ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (93 / 52)
Gap_init rate = 0.02 (15 / 683), avg. gap size = 2.47 (37 / 15)  


1567 24.21 1.96 1.96  chrX_153546743_153549032      499   907 (1383)    L1M4_orf2#LINE/L1      225   633 (275)  

  chrX_153546743_    499 CGATTTCAAGGCTTATTATAAAGCTACAGTAATCAAAAC-TTTTTGTATT 547
                          i       ii    i  i                 i  -v v v   i 
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACT 274

  chrX_153546743_    548 GGTGAAAGGATAGACATATAGATAAATGGTACGGAATAGAGAGCCTGGAG 597
                           iiv                  v     v ii    v     i ii  i
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chrX_153546743_    598 ATAGGCTCACATAAATTCGT--CCAACTGGTTTTTGACAAAGGTGCAAAA 645
                            ii i  --  v   ii --i   i  i    i     i     v  i
  L1M4_orf2#LINE/    325 ATAAACCCA--TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chrX_153546743_    646 GCAATTCGATGGAGGAAGGATAGTCTTTTCAACAAA-----CTGTAGCAA 690
                         i v    i    i i   i                 -----   vii   
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chrX_153546743_    691 CTGGACGTCCATAGGCCGAAACCAAACAAAAAACCTCAACCCAATCCTCA 740
                              ii?   i v  --   ---- v  vi  vi vi    vvv     
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGC--AAA----AGAATGAAGTTGGACCCCTACCTCA 466

  chrX_153546743_    741 CACCTTATACAAAAATGAACTCAAAATGGATCCTAGATTTACATATAAAA 790
                             v           v               v?   ii  v  i   i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chrX_153546743_    791 TGTAAAACTACAAAACTTTTAGAAGATAAAATAGGAGAAAATCTTTGGGA 840
                         vv        i      i        v  v     ? v       i v  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chrX_153546743_    841 CCTACGACCTGGTGATAAGTTCTTAGACATGGCACCAAAAATGCAATCCA 890
                            vv iiiv  ii  iiv        i   i        iii   v v 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chrX_153546743_    891 TAAAAGAAAAACTTGAT 907
                         i          v v   
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGAT 633

Transitions / transversions = 1.59 (59 / 37)
Gap_init rate = 0.01 (6 / 409), avg. gap size = 2.67 (16 / 6)  

 310 20.39 0.97 1.94  chrX_153546743_153549032     1171  1273 (1017)    L1M4_orf2#LINE/L1      603   704 (204)  

  chrX_153546743_   1171 AAAAACAAAAAAAAAAAAAAGAAAAAAGTGATAAATTGGACTTCATCAAA 1220
                             i  v  iv  v    -       vv                     
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCAAA 651

  chrX_153546743_   1221 ATTAAAA-CTTGTGCTCTACAAAATACCTTGTTAAGAAGTATAAAAAGAC 1269
                                -   v  iv  v    iv  vi i i     i-i i       
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA-GTGAAAAGAC 700

  chrX_153546743_   1270 AGCC 1273
                          i  
  L1M4_orf2#LINE/    701 AACC 704

Transitions / transversions = 1.10 (11 / 10)
Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.00 (3 / 3)  

 786 20.00 3.18 1.36  chrX_153546743_153549032     1578  1797 (493)    L1M4_orf2#LINE/L1      685   908 (0)  

  chrX_153546743_   1578 AAAAAAGTATAAAAAGACAAGCTACAGACTGGGAGAAAATATTTACAAAT 1627
                           i     i--         v i     v               i     
  L1M4_orf2#LINE/    685 AAGAAAGTG--AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_153546743_   1628 CATGGATCTAACAAAGGACTCATATCAAGAATATATAAAGAA---TTAC- 1673
                            iv    i i  i     ii    v               ---    -
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_153546743_   1674 ---CAAAAATAAACAGTAAAAAAAATCCAAATAGAAAATAAACAAAAGAT 1720
                         ---   v      v  - v   v  i    v ?i     iii    i   
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAG-ACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_153546743_   1721 ATGAAGAGATATTTCACTGAAGAGGATATACAGGTATCAAATAAGCCCAT 1770
                         v    v   i     v ii    i        ii iv v       v   
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_153546743_   1771 AGAAAGAGGTTCAGCATCATTAGCTAT 1797
                         ii     v i   i     ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (27 / 16)
Gap_init rate = 0.02 (4 / 224), avg. gap size = 2.50 (10 / 4)  


1989 23.62 10.04 1.84  chrX_153588818_153590509      493  1199 (493)    L1M4_orf2#LINE/L1      144   908 (0)  

  chrX_153588818_    493 ATACATGATGGAAAGGTACAG-ACCCATGAAAAGCTAAAATAATTTTGAA 541
                           v   -       v i vi -     -   v   i    i   i     
  L1M4_orf2#LINE/    144 ATTCAT-ATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAA 191

  chrX_153588818_    542 AAACAAGAG---AGTAGGAAGACTCAGTCTGCACAGTTTCAAAACTTACT 588
                            v    i---   v   i      vv  v v  i              
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chrX_153588818_    589 GTAGTATAGTCTCAGTAA---AGACTATGTGGTA------------TAGA 623
                         ii i---  iiv      ---    vi       ------------    
  L1M4_orf2#LINE/    242 ACAA---AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_153588818_    624 CATGCAGATCAAGGGAACAGGATAGGGAACCCAGAAACAGACCCACAGAG 673
                            ii       v    i  i  v i  ii       i i     i v v
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_153588818_    674 ATATGCCCAGTTGATTTTTAACAAAGATGCAAAAGCAACTCAATGG---- 719
                         v    vi  i        ii    i i   v  ii v i       ----
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_153588818_    720 -----------------------TGCTGCAGCAATTGGAAACTCAT-CAC 745
                         -----------------------     vii   i    v ?i  i-ii 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_153588818_    746 CAAAAAGGGAAATGCTGACCTGAACCTTAC-C------------TT--CT 780
                         v   i iv   i -iv    ivv    i  - ------------  --  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chrX_153588818_    781 -AAAATGGAT-ATGGACTTACATGTAAAGTGC-AAAACTAGAAAATATAT 827
                         -         - ?i   i  v      - v  -       v    i- v 
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAA-GAGCTAAAACTATAAAAC-TCT 535

  chrX_153588818_    828 TTGAAAAAAA--TAGAAGAAACTTGTCAGGATCTAGAGCTAGGCAAAAAG 875
                          v   i    --   i? v  v iv  iv  i  v i i       viiv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chrX_153588818_    876 TTCCTATACATGACATCAAAAGCAGAATCCATTAAAGGAAAAATTGGTAA 925
                            i  v i      i        v  v v iv    i      v i   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chrX_153588818_    926 ATTGGACCTCATCAAAATGAAAAACTCTTGTTCTGTGAAAGCCCAC-ATG 974
                                i          v       i    v  - v    vv   -  v
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATC 684

  chrX_153588818_    975 AAGATTGTGAAAATACAAGCTACAGACCGGGAGAAA-CATTTACAAACCA 1023
                             vv       v    v i     vi        -i    i    i  
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_153588818_   1024 CATATCCAATAAAAGACTGGTATATAGAATATAAAAAGAGAGTGCTCAAT 1073
                         i     ii    ii    v    vi        v     - v -  i vv
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA-ACT-CTTACA 782

  chrX_153588818_   1074 ACTCAACAGTAAAAA--CGAACAATCTAATTAGAAAATGGGCAAAAAACA 1121
                               i i      -- i  i  i i    ?i            ii iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_153588818_   1122 TGAACAGATATTTCACCAAAGAGGATATATAAAGATGGCAAATGAGGATA 1171
                             i   i     v       i      i   --    v   i  v i 
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAA--TGGCCAATAAGCACA 880

  chrX_153588818_   1172 TAAAAAGATATTCAACATCATTAGCCAT 1199
                          i       ii         ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (97 / 66)
Gap_init rate = 0.03 (26 / 765), avg. gap size = 3.23 (84 / 26)  


1070 28.32 7.28 3.80  chrX_153597951_153599574      500  1131 (493)    L1M4_orf2#LINE/L1      255   908 (0)  

  chrX_153597951_    500 AATTAAGAC--TGTGATATTGAGGCAT--GGATAGATTAATTGAGCAATG 545
                            i     --    i  i  --    --       ivv  v  v     
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTG--GCATAAGGATAGACATATAGATCAATG 302

  chrX_153597951_    546 GCATAGAATAGAGAACCCCGAAACGCAACCATGCAAGTATAG-AAATGTG 594
                          v       v    ii  v    iiv v    i  vv   i -v   -  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT-TG 351

  chrX_153597951_    595 GTATATGATAGAAGTGGCATGTTAGGTAAGTAAACAGGGACA------TT 638
                         i v vi  i iii   v  ----  iiv v v  ii    v ------ i
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_153597951_    639 TTATTAAC---TGACGCTGGAA-AA-TGGTTATTTATATTGGAAAAGA-T 682
                           v i   ---  ii     i -  -   v  ?ii i  - v      - 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-GCAAAAGAAT 446

  chrX_153597951_    683 GAAATTGGAATCCTCATTCATGTGATATGGAAAATAATAATAATCTATTC 732
                            i     vi   vvi   iiiv    -------- i  v   iv i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATAT--------ACAAAAATTAACTC 488

  chrX_153597951_    733 CAGATGGATTAAGGAATTAAATGTCAAAAAC-ATACCCTTAAAGCTCTTG 781
                         v i      i ?i  vi       -  i i - v v iv    i     i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGT-AAGAGCTAAAACTATAAAACTCTTA 537

  chrX_153597951_    782 ACAGGAAACATAGGCAAGGAACTTTTAGACTTTGGGATA--CA--GATTT 827
                         iv  i         ?ivii v   ivv   i     v  --  -- i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chrX_153597951_    828 CTAAACAATGTAGAC--AAACCATTGACCATAGAATGGAATAGTGG-TAA 874
                           v ivv   - v  --   v  ivii v i i  - i  v i i -   
  L1M4_orf2#LINE/    588 CTTAGATATG-ACACCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAA 635

  chrX_153597951_    875 CTTTGACTTTA--AGAATTTTAA---TTTATG------AAGACACCATAA 913
                         v  v     i -- i    vv  ---   i  ------ i     i  v 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_153597951_    914 AGA--GCAAAAA-ACACAGCTGTGCATTGGGAGAAAATATTTTCAATACA 960
                            -- ii    -   - v iiiiv v               v   vv  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACA-ACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_153597951_    961 GATAAGTGGCAAGGAATTCCAATTGCGAATATATAAAGGACT---ACAAA 1007
                         v   vv  ii    i i ivv  ivv            i   ---    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_153597951_   1008 TTATTAAGAAAAACACAA----TCCAGTAAAGAAGTGGGCAAAACACATG 1053
                          i v   v     v    ----i   i v? i  i        iv iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_153597951_   1054 AATAGGCATTTCACCAACAGAGAGACGCATATGGCCAATAAACATACATA 1103
                              i      v    vii   v ii  v           i  i ----
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA---- 880

  chrX_153597951_   1104 TAAAGAGATGTTCGACATCATTAGTGAT 1131
                          i  i     i  i      ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (99 / 76)
Gap_init rate = 0.05 (30 / 654), avg. gap size = 2.33 (70 / 30)  


3139 27.13 1.11 0.55  chrX_153635025_153641412.rev     4995  5897 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153635025_   4995 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5044
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153635025_   5045 GGCCATACTGCCCAAGGTATTTTATAGATTCAATGCCATCCCCATCATGC 5094
                            v     v     iv iv i  i        i  v     i    viv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153635025_   5095 TACCAATGACTTTCTTTACAGAATTCTAAAAAACT-ATTTTAAAGTTCAT 5143
                          v   iivi i  i   i     v - i v  i  -  ii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chrX_153635025_   5144 TTGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5193
                         v     viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_153635025_   5194 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACACGGCT 5243
                               i      vv    i  v  ii i      viv       vi   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_153635025_   5244 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 5293
                                i   i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_153635025_   5294 ATGGAACAGAAC--AGAGCCCTCAGAAGTAATACCACACATCTACAACCA 5341
                               i    i--    i  --    i   vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_153635025_   5342 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCC 5391
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_153635025_   5392 TATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5441
                          v  v  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_153635025_   5442 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5491
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_153635025_   5492 TAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5541
                         i ?    i       v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_153635025_   5542 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGAACTTCATGTCTAA 5590
                             ?i- v i -   iv   v v  vv i     viii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_153635025_   5591 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5640
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_153635025_   5641 TGAAACTAAAGAGCTTCCGCACAGCAAAAGAAACTACCATCCCAGTGAAC 5690
                          v   v v  i i   ii ii vv    i  v    i  vvvv      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_153635025_   5691 AGGCGAGCTACAAATTGGGAGAAAATGTTTGCAATCTATTCATCTGACAA 5740
                           i i v i   i v           i       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_153635025_   5741 AGGGCTAATATCCAGAATCTACGAAGAACTCAAACAAACTTA-CAAGAAA 5789
                         i  i  vi          v  ii        vv    -  i -i  v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAA 795

  chrX_153635025_   5790 AAAA-----GACCCCATCAAAAAGTGGGTGAAGGATATAAACAGACACTT 5834
                           i -----i    v  i?    i    ii      v i  i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_153635025_   5835 CTCAAAAGAAGACATTTATGCAGCCAACAGATACATGAAAAAATGCTCAT 5884
                            v        i  vi viii     i iii         i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_153635025_   5885 CATCACTGGCCAT 5897
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (142 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


 348 23.86 1.14 1.14  chrX_153643139_153645249.rev      270   357 (1754)    L1M4_orf2#LINE/L1        1    88 (820)  

  chrX_153643139_    270 TGAAAAGGCATCCTGGATTTATGGATTTGAAGACATAATATTCTTAAGAT 319
                           i    ii    iivi  i       v      v       v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153643139_    320 AAGAATATTACCACAAACC-ATTTGCAGATTCAAAGCAA 357
                         iiv    i v  -    ii-  i i         v    
  L1M4_orf2#LINE/     51 GGCAATACTCCC-CAAATTGATCTACAGATTCAACGCAA 88

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.02 (2 / 88), avg. gap size = 1.00 (2 / 2)  

2835 11.73 0.88 26.98  chrX_153643139_153645249.rev      487  1620 (491)    L1M4_orf2#LINE/L1       71   908 (0)  

  chrX_153643139_    487 TCTCCGGCCTCAAAGCATTCTCTATCAGAATCCCAAAGACATTTTTTTTT 536
                            v i vi    v   v  i      i       i-----i vii    
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAG-----CTGCCTTTT 115

  chrX_153643139_    537 TTG-AGGAATAGAAAAATCTATCCTAAAATTCAGATGGAATTTCAAGGGA 585
                            -  i   v  v  iiiv             v      v v       
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGA 165

  chrX_153643139_    586 CCCTGAATAGCCAAAACAATCTTGAAAAAGAACAAC---GTTGGAGGAGT 632
                            v                            v   ---         v 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chrX_153643139_    633 CATACTTCCCAATTTCAGAACTTACTACAAAGCTACAAGAATCAAAACAG 682
                           i              i                   iv      i    
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chrX_153643139_    683 GGCAGTACTTACATAAATATAGACACATAGATCAATGGAATAGAATTGAG 732
                         v ii     vi     iv       i                        
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chrX_153643139_    733 AGTCCAGAAATAAGCCTATACATCTATGGTCAATTGATTTTCAATAAAAG 782
                                      i  i      i                  i i  ii 
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chrX_153643139_    783 TGCCAAGACCATTTTGTGGGAAAAGAATAGTCTCTTCAACAAATGGTGCT 832
                                      ivi    i            i                
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chrX_153643139_    833 GGGACAATTGGATATCCACATGCAAAAGAATGAAGTTGGATCTTTACCAT 882
                                i      ?                         i ii    --
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC-- 463

  chrX_153643139_    883 ATACAAAATTTAACTCAAGGCTGGATGTGGTGGCTCACATCTGTAATCCC 932
                         ----------------------------------     i ---------
  L1M4_orf2#LINE/    464 ----------------------------------TCACACC--------- 470

  chrX_153643139_    933 AGCACTTTGGGAGGCTAAGGCTGGTGGATCACTTGAGCTCAGGAGTTTGA 982
                         --------------------------------------------------
  L1M4_orf2#LINE/    471 -------------------------------------------------- 470

  chrX_153643139_    983 GACCAGCCTGGGCAACACAGTGAGACTCTGTATCTACAAAACAAGAAAAA 1032
                         -------------------------------  v       ---------
  L1M4_orf2#LINE/    471 -------------------------------ATATACAAAA--------- 480

  chrX_153643139_   1033 AAAATTAGCTGGCATGATGGTACACACCTGTAGTCCCAGCTACTAGGGAA 1082
                         ---    -------------------------------------------
  L1M4_orf2#LINE/    481 ---ATTA------------------------------------------- 484

  chrX_153643139_   1083 GCTGGGATAGGAGGATCGCTTGAGCCCAGGAGGTGGAGGCTGCAGTGAGC 1132
                         --------------------------------------------------
  L1M4_orf2#LINE/    485 -------------------------------------------------- 484

  chrX_153643139_   1133 CATGATCGCACCACTGCACTCCAGCCTGGGTGTCAGAGCAAGACCCTGTC 1182
                         -----------------    -----------------------------
  L1M4_orf2#LINE/    485 -----------------ACTC----------------------------- 488

  chrX_153643139_   1183 TGTAAAAAATCATTTAACTAAAAATGTATCAAAAAACTAAATATAAAAGC 1232
                         --------------------      v    ? i v      i   i   
  L1M4_orf2#LINE/    489 --------------------AAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chrX_153643139_   1233 TAAAACCATAAAACTGTAAGAA-AAAACAAAGAGGTAAATTGTTATGATA 1281
                               i        v v    -      v  i?      iv ii   iv
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 568

  chrX_153643139_   1282 CTGGATTTGGCAATGGTTTCTTAGATGTGACACCACAATCACAAGCAACA 1331
                         i   i  v                  i        v  v           
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chrX_153643139_   1332 ACTCTATAAAAATATATATAGTAGGCATCTTTAAAGTTAAAAGCTTTTGT 1381
                          vv--iv       v   v v i i v  v i   i      i       
  L1M4_orf2#LINE/    619 AAA--GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chrX_153643139_   1382 ACATCAAAGAACACTATCAAGAAAGTAAAAAGATGATCTACAGTATAGGA 1431
                         i v      i                i      ii i i    v  i   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chrX_153643139_   1432 GAAAAAAATTGCAAATCATATATCTGATAAAGGGCCTAGTATCCCAGAAT 1481
                              v v                      i  i i -      -     
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTT-GTATCC-AGAAT 764

  chrX_153643139_   1482 ATAAAAAGAACTCTTACAACTCAACAACAGAAAGACAA----CCAAATTT 1527
                            v                    i  i i        ----  v    ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chrX_153643139_   1528 TAAAATGGGTAAAGGACTTCAATGGA-ACTTCTCCAAAGAAGATATACAA 1576
                         v        i      i  v   i  - i                     
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chrX_153643139_   1577 GGATCCAACAAACTCATGAAAAGATAGACAACATCATTAGTTAT 1620
                         iviv    i  i v           ivv        ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (78 / 51)
Gap_init rate = 0.02 (14 / 838), avg. gap size = 22.57 (316 / 14)  


3238 26.24 0.66 0.55  chrX_153659925_153666701     3115  4021 (2755)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153659925_   3115 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCATTATCATGAAAAT 3164
                               i i  i     i        v      v i v   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153659925_   3165 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCTCCATCAAGC 3214
                            v     v      v i  i  i        i  v   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153659925_   3215 TACCA-CTGACTTTCTTCACAGAATTGGAAAACACT-ACTTTAAACTTCA 3262
                          v   -   v    i  -i     v v  v  -i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAA-GCTGATCCTAAAATTCA 148

  chrX_153659925_   3263 TATGGAACCAACAAAGAGCCC-TCATAGCCAAGACAATCCTGGACAAGAA 3311
                                vii-   i ii   -vv        i      i  i v     
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_153659925_   3312 GGACAAAGCTGGAGGCATCATGCTACCTGACTT-GAAACTATACTACAAG 3360
                          i      i      vv   ii  v  ii i  -i     -        i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAA 246

  chrX_153659925_   3361 GCTACAGTAACCAAAACAGCATGGTACTGGGGCCAA-ACAGATATGCAGA 3409
                                   i   i    ii         viiv i- i   i  ii   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chrX_153659925_   3410 CCAATGGAACAGAATGGAGGCCTCAGAAATAACACCACACAGTTACAACC 3459
                         i        i     v   ivii         vv   i   v   iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chrX_153659925_   3460 ATATGATCTTTGACAAACCTGACACAAACAAGCAATGGGGAAAAGATTCC 3509
                          vv    i  i     ivv  v  vi v  vv           ii  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_153659925_   3510 CTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACT 3559
                           v  i  i        i     v      v  ?   i     i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_153659925_   3560 GAAACTGGATCCCTTCCTTACACCTTTTACAAAAATCAACTCAAGATGGA 3609
                            ii    i    v   i     v v         i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_153659925_   3610 TCAAATACTTAAACGTAAGACCTAGGACCATAAAAATCCTAGAAGAAAAC 3659
                            ? v  i    i      v   ii  i      v  i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_153659925_   3660 CTGGGCA-ATACCATTCAGGAGATAGGCATGGGCAAAGACTTCATGTCTA 3708
                         v i  ?i- v i -   iv  vv v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_153659925_   3709 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAGGAGATCTA 3758
                         vi            vvi          vv     v  i   vvi  ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_153659925_   3759 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGGGTGAG 3808
                           i   v v  i i   i  ii vv    i  v       vv ii    i
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_153659925_   3809 CAGGCAACCTACAGGATGGGAGAAAATTTTTGCAATCTATCCATCTGAGA 3858
                         v  i     i    i            v       vii  vi      v 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_153659925_   3859 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 3908
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_153659925_   3909 AAAACAAACAACCCCATCAAAAAATGGGCAAAGGATATGAACAGACACTT 3958
                           i     i     v  i?                 v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_153659925_   3959 CTCAAAAGAAGACATTTATGCAGCCAACAGACATTTGAAAAAATGCTGAT 4008
                            v        i  vi viii     i ii  iv      i     v v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_153659925_   4009 CATCACTGGTCAT 4021
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (136 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.00 (11 / 11)  

 708 26.92 1.65 0.00  chrX_153659925_153666701     5103  5284 (1492)    L1M4_orf2#LINE/L1        4   188 (720)  

  chrX_153659925_   5103 AAAGATATTCCATATTCCTAGATTGGAAGAATTAGTATTGTTAAAATGTC 5152
                                 i    i   v i          v   i         i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_153659925_   5153 CACACTACCCAAAGTAATCTATAGATTTGATGTGATCCCTATCAAAATCT 5202
                         v i   v      v i     i     ii i ii               i
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_153659925_   5203 CAATGGTGTTCTTCACAGAAATAAAAAAAA-AATTTTAA--TTAATATGA 5249
                           iiv iv  i  ii       vi v  iv-i  ii   --  v     i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_153659925_   5250 AATCACAAAAGACCCCAAGGAGGCAAAGCAATCTT 5284
                           vii   ii     vi iv  v    i       
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTT 188

Transitions / transversions = 2.06 (33 / 16)
Gap_init rate = 0.01 (2 / 185), avg. gap size = 1.50 (3 / 2)  

3006 19.86 4.86 0.29  chrX_153659925_153666701     5585  6284 (492)    L1M4_orf2#LINE/L1      177   908 (0)  

  chrX_153659925_   5585 CAAAGCAATCTTAAGCAAGAAGAACAAAGCTAGAGGCATCATACTTCCTG 5634
                             i       i iv             i i    vv   i      ii
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chrX_153659925_   5635 ATTTCAAAATATACTACAAGTCTCCAGTAATCAAAATAGTATGGTACTGG 5684
                                  iv        iv  v          i i   i         
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chrX_153659925_   5685 CATAAAAATAGACACATCAACCAAGGGAACAGAATAGAAAAGCCCAGAAA 5734
                              ii       i  vi i   v    i     v  i - i       
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA-GTCCAGAAA 325

  chrX_153659925_   5735 TAAGTTCACACATTTACAGTCAACAGATTTTTGACAAGGGTGCCAAGAAC 5784
                            iii  i       ii     iv      i                v 
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chrX_153659925_   5785 ACACAACGGGGAAAAGAGAGTCTCTTCAATAAATGATATTGGGAAAACTG 5834
                          iv   i       ii v     i     i     i ii     v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chrX_153659925_   5835 AATATCCACATGCAGAAGAAAGAAATTGGGCCCTTTTCTCACACTATACA 5884
                         i   ?         i     v   i    i   i vi       i   i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chrX_153659925_   5885 TAAAATTCAACTCAAAATTGATTAAACACTTGTATATAAGACCTGAAACT 5934
                         i    v i          v   i ? v  i iv  i     v  i     
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chrX_153659925_   5935 ATAAAACTCCTAGAAGAAAACA--GGAAAAAAGCTACCTGATATTGATTT 5982
                                  i            --  ?iv   v  v v   iv   iv  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chrX_153659925_   5983 GGGCAATAATTTTTT-TATATGACACCAAAAGCACAGGCAACAAAAACAA 6031
                         i      ii   i  -v                   i         iv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_153659925_   6032 AAATAGA-AACTGGGATTGCATTAAA-CTAAAAACTTTCTGCACAGCAAA 6079
                                -  v v   i v   i   -i          -  ii vv    
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAA 674

  chrX_153659925_   6080 AGAAATAATCAACAGAGTGAAAAGACAACCTATGGAATGGATGAAAATAT 6129
                         i  v iv     v i               i ii      iv        
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chrX_153659925_   6130 TTGCAAACTGTATATCTGATAATGG----GTA---AGAA----------A 6162
                                iii            v  ----   ---    ---------- 
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_153659925_   6163 CTCAAACAACTCATTAGTAAGAA-----ACAACCCAATT-AAAAATGGGC 6206
                            vv        v  i   i  ----- i         -          
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_153659925_   6207 AAAGAACCCAAATAGA-ATTTTTCAAAAGAAGAAATATAAAAGGCCAA-- 6253
                             i iiii      -    i  v        v   i   v      --
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_153659925_   6254 --CAGAT-AAATGATGCTCAGCATCACTAACCCA 6284
                         --  v  -   v        i     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (89 / 47)
Gap_init rate = 0.02 (14 / 732), avg. gap size = 2.57 (36 / 14)  


3979 19.57 3.20 1.60  chrX_153672963_153675988     1654  2527 (499)    L1M4_orf2#LINE/L1        3   890 (18)  

  chrX_153672963_   1654 GAAAGGCATTTTGTGTTAACGGATTGGGACACTTAATATTGTTAAGATGC 1703
                              ii  iiii    v i       i v                   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_153672963_   1704 CCATAATCTCCAAGGCAATATACAGATTCATCGTGATGCCTGTCAGAATC 1753
                          v   v  i    ivii  v          v  ii  v   i   i    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_153672963_   1754 CAACCTGCCTTCTTTGTAAAAACTGACAAGCTGATCCTAAAATTCATAAG 1803
                          v v       i    i i   i                         v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_153672963_   1804 AAAATGTAAGGGGCTCAGA-TAGCCAAAACAATCTCAGAAAAGAAAAA-- 1850
                         i     i     i i    -               iii       i  --
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_153672963_   1851 -AGTTGAAGGACTCACACTTCCCAATTTCAAAACGTACTACAAAACCGCA 1899
                         -     i                           v         i ii  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_153672963_   1900 GTAATCCGAAAAGGGTGGTACTGCCATCGTGATCGATACATTAGGTCAAT 1949
                               vii v  v         v   viv   v  i i  -  i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT-AGATCAAT 301

  chrX_153672963_   1950 GTTACAGAACTCAGAGTC-AGGAATAAACCCATATATTTATG-TAAAGTT 1997
                          vv i    i v      -  i            i       - v  -  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA-TT 350

  chrX_153672963_   1998 TATTTTCAGTAAGAGTTCCGGCACCCCTCAATGGGTGGAGGGGAAGAATA 2047
                         v      iii   i  v  iiv   vi        ------ i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGG------GAAAGAATA 394

  chrX_153672963_   2048 ATCCCCTCAACAAACTGCGCTGGGACAACTGGATAGCCACATGCAAAAGA 2097
                         i  iii        iv i                 ?              
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_153672963_   2098 AGGCCCCTGGACCCCTACCTCACATCATGTA-AAGAATTAATTCAAAATG 2146
                          v vvvi                 i   i  -  i      i        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_153672963_   2147 GATCACAGATCTAAATGTAAGGGCTGAAACTATAAAACTCTAAGAAGAAA 2196
                              ?   i           i   i               v        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_153672963_   2197 ACGGAGATGTAACTTTGCACGACCTTGGATTAGGCAACAGCTCCTTCAGT 2246
                           iv  i?    v i v ii        i        ii i i   vii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_153672963_   2247 ATGACACCAAAGGCA-AAGCCACA---GATATCTTTTCATTTGGCAAGTT 2292
                                    i   -    v   ---  v ------v v v ii  i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAA------AAATAGATAAATT 638

  chrX_153672963_   2293 GGACTACATCCAAATGTAAATCTTTTGGGCAACAAAGGGCTCTATCCAGA 2342
                              v    v    vv   v      v  vv      i v     v   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_153672963_   2343 AAGTGAA----------------TGGGAGAAA-CATTTGCAAGTCACATA 2375
                                ----------------         -i        i   i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_153672963_   2376 TCTGATAAGAGTCTATTTTCCAGAATATATGAATAAGTTTTAGAAGCCCA 2425
                                  i v  vv v            i  v  v i   v  vi v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_153672963_   2426 CAGCCAAAATACAATCAACCGAATTAAAAAATGGGCAAAGGGCTTGAATA 2475
                         i iiv    v    vi    v    ?               ii       
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_153672963_   2476 GACATTCCTCCAAAGCAGAGGTACAGAGGGCCAAGAAGCACATGAAAAGA 2525
                               i        v   vi    i v      v               
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_153672963_   2526 TG 2527
                           
  L1M4_orf2#LINE/    889 TG 890

Transitions / transversions = 1.39 (97 / 70)
Gap_init rate = 0.01 (13 / 888), avg. gap size = 3.23 (42 / 13)  


3009 23.60 1.33 0.80  chrX_153703431_153705166.rev      496  1245 (491)    L1M4_orf2#LINE/L1      155   908 (0)  

  chrX_153703431_    496 AATACA---GACCCTAAATATCCAAAGCAGTCCTGAGCAAAGAGAACAAA 542
                            i  ---     vi    v     i  i  i   iv  ii        
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chrX_153703431_    543 GCTGGAGGCATGATGCTACTTTATTTCAAACTATACTACAAAGCTGTAGT 592
                          i      vv v ii  v iiv        viv            ii   
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_153703431_    593 AACCAAAACAGCATGGTACTGGCATAAAGACAGAAACATATGCCAGTGGA 642
                           i   i    ii              i  i   v i   vii  i    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_153703431_    643 ACACAACAGAGAACCCAGAAATGAATCCACACATTTAGAGCCAACTCATT 692
                          i v  iv    ii        i  i   i       vi i   i v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_153703431_    693 TTTGACAAAG-TGCCAAGAATATGCATTGGTGAAAGAATAGTCTCTTCAA 741
                           i     i -        vi  v  v   v             i     
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_153703431_    742 TAAATGATGTTGGGAAAACTGGATATCCACATGCAGAAGAATTAAACTAA 791
                         i     i  i     v         ?         i      v  ii ii
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_153703431_    792 ACCCCTATCTCTCACTGTATACAAAAATTAAATCAAAATGGATTAGAGAC 841
                                i   v   ii              v           i ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_153703431_    842 TTAAATATACAACCTGAAAGTATGAAGCTACTGGAAGAAAACATTGGGG- 890
                         i     i  vi v  i   v   i  i  vi i           v  ? -
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_153703431_    891 AAATGCTCCAGGACATTGGTCTGGGAAATATTTTATGGCCTGGGA---AA 937
                             -  i iv   v    vi i  v   iv   -----  vi  ---i 
  L1M4_orf2#LINE/    555 AAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTT-----CTTAGATATGA 598

  chrX_153703431_    938 TATCAAAAGCACAGACAACTAAAGCAAAAGTAGACAAACGGGATTATATC 987
                         i i          ii    v    v    i    i   iv   i vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_153703431_    988 AAGCTATAAAGCTTCCGCACAACAAAGGAATCAATTAACAAAGTGAAGGG 1037
                           iv vv   i   ii ii vv       vv v  i  v        ii 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_153703431_   1038 ACAACCTACAGGATGGGATGAAATATTTGCAAACTATACAACTGAGAGGG 1087
                               i    i      vi             ii   i v    v i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_153703431_   1088 TATTAATAACCAGAATATATAAGGAACTCAAACAAGTCAATGGCAAAAAA 1137
                         v i vi  v             i      vv    v     iii     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_153703431_   1138 GCAAAGGATCCTATT-AAAAATGAACAAAG-ATCTGAATAAACATTTCTC 1185
                         i    vi i  v   -       ii     -  i      i         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_153703431_   1186 AAAAGAAAACATACAAATGGCCAACAGGTATATGAAAAACTGCTCAACAT 1235
                         v      i i              i i i i       iv          
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_153703431_   1236 CACTAATTAC 1245
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.85 (113 / 61)
Gap_init rate = 0.01 (8 / 754), avg. gap size = 2.00 (16 / 8)  


3138 27.31 0.55 0.55  chrX_153733556_153739776     1955  2862 (3359)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153733556_   1955 TGGAAGACTATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 2004
                              iiv   i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153733556_   2005 GGCCATACTGCCCAATGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2054
                            v     v     vv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153733556_   2055 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2102
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_153733556_   2103 TATGAAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCTAATG 2152
                             i  viiv  ii  v  v v  v     iv     i i ivvvi v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_153733556_   2153 AACAAAGCTGGAGGCATCACGCTCCCTGACTTCAAACTATGCTACAAGGC 2202
                                i      vv    i  i  ii i      viv i      i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_153733556_   2203 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 2252
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_153733556_   2253 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACGCATCTACAACT 2300
                                i    i--    i  --        vv   ii   i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_153733556_   2301 ACCTGATCTTTGACAAGCCTGAGAAAAATAAGCAGTGGGGAAAGGATTCC 2350
                          vi    i  i      vv  vv  i vi vv  i         i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_153733556_   2351 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2400
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_153733556_   2401 GAAACTGGAACCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGA 2450
                            ii    v    v   i     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_153733556_   2451 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 2500
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_153733556_   2501 CTAGGCA-ATACCATTCAGGACATAGGCATGTGCAAGGACTTCATGTCTA 2549
                         v    ?i- v i -   iv   v v  vv iv    v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_153733556_   2550 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAACTA 2599
                         vi            vvi          vv     v  i    v   vi v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_153733556_   2600 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 2649
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_153733556_   2650 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 2699
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_153733556_   2700 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 2749
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_153733556_   2750 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 2799
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_153733556_   2800 CACAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 2849
                          v v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_153733556_   2850 CATCACTGGCCAT 2862
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  

3106 24.50 3.08 0.95  chrX_153733556_153739776     4522  5366 (855)    L1M4_orf2#LINE/L1        1   863 (45)  

  chrX_153733556_   4522 TGAAAAGGTATCTATCCCATTTTAATGGGCTGGAAAAACTAATATTGTTA 4571
                           i    i    ----    v  v    ii     i vi           
  L1M4_orf2#LINE/      1 TGGAAAGATATC----CCATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chrX_153733556_   4572 AAATATCAATGCTACC-------------AGATTTAATGTAATACCTATC 4608
                          i  iv    i  v  -------------     i  i i   v      
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_153733556_   4609 CAAATGCCAGTGAAGTTTTTCACAGAAATAGAAAAAAGAATCTTAAAATT 4658
                         v    v    ivivv     ii       v  v  ivvi   i       
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_153733556_   4659 TGTGTGGAACCACAAAAGACTCCAAACAGCTAAA-TAATCTGGAGCAAAA 4707
                         ii i     vii   ii   i vi  i   i   -i     v  iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_153733556_   4708 TGAACAAAGCTGGAGGCATGACACTACTTGACTT-GAAACTATACTACAA 4756
                         v        i      vv v     v iii i  -i     -        
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chrX_153733556_   4757 AGCTGTAGTAACAAAAACAGCACGGTACTGGCATAAAACCAGAAATATAT 4806
                             ii     iv  i    iii             iivi   v     v
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_153733556_   4807 GCCAGTGGAACACGACAGAAAACCCAGAAATAAATCCACACATTTATAGC 4856
                         ii  i     i vi iv  i ii           i   i        i i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_153733556_   4857 CAACTCACCTTTGACAAAG-TGCCAAGAACACGCACTGGTGAAAGAATAG 4905
                            i v ii  i     i -        v  iv  v   v          
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_153733556_   4906 TCTCTTCAATAAATGGTG-TGGGAAAACTGGATATCCACATGCAGAAGAA 4954
                            i     i        -     v         ?         i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_153733556_   4955 TGAAACTATACCCCTATCTCTCACTATATACAAAAATCAAATCAAAATGG 5004
                             ii iv       i   v   i            i  v         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_153733556_   5005 ATTAGAGACTAAAATATACAACCTGAAAGTATGAAACTACTGGAAGAAAA 5054
                           i ?    iv    i  vi v  i   v   i     vi i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_153733556_   5055 CATTGGGGGAATGCGCCAGGACATTGGTCTGGGAAA-GATTTTGCAGGTA 5103
                            v  ? v  vv vi iv   v    vi i  v  - i   ivi  i  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_153733556_   5104 AGACCTCAAAAGCACAGGGGACTAAAGCAAAAGTAGACAAATGGGATTAT 5153
                         v   vi          i vi  v    v    i    i    v   i vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_153733556_   5154 ATCAAGCCAT--AAAGCTTCTGGACAGCAAAGGAAACAATTAACAAAGTG 5201
                              i--  --   i   i  vi vv       v  v  i  v      
  L1M4_orf2#LINE/    646 ATCAAA--ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_153733556_   5202 AAGAGACAATTTATAGGATGGGATGAAATATTTGCAAACTATACAACTGA 5251
                           i      iii i  i      vi             ii   i v    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_153733556_   5252 GAGGGCATTAATAACCAGAATATATAAGAAACTCT----AGTCAATAGCA 5297
                         v i  v i vi  v             ii      ---- v      ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_153733556_   5298 AAAAAAACAAAGAACCCTATT-AAAAATGGACAAAG-ATCTGAATAGACA 5345
                             i -    v     v   -        i     -  i          
  L1M4_orf2#LINE/    794 AAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_153733556_   5346 TTTCTCAAAAGAAGACATTCA 5366
                               v        i  v  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 1.62 (126 / 78)
Gap_init rate = 0.02 (14 / 863), avg. gap size = 2.43 (34 / 14)  

 334 10.17 0.00 0.00  chrX_153733556_153739776     5670  5728 (493)    L1M4_orf2#LINE/L1      850   908 (0)  

  chrX_153733556_   5670 AAAGAAGACATACAAATGGCCAACAAGTATATGAAAAACTGCTCAACATC 5719
                                 i              i   i i       iv           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chrX_153733556_   5720 ACTAATTAC 5728
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 5.00 (5 / 1)
Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.00 (0 / 0)  


2313 15.14 1.55 27.25  chrX_153763753_153768890.rev     3426  4647 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153763753_   3426 TGGAAAGATATTTCATGTTCATGGATTG-AAGAATTAATATTATTAAAG- 3473
                                    ii               -    v        i    ii-
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153763753_   3474 -----------CCAAAGCAATCTACAGATTCAATGCAATTCCTATCAAAA 3512
                         -----------     vii              i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153763753_   3513 TTCCAA-TGTCATTCTTCACAGAAATAGAAAAAC-AATCCTAAGATTTGT 3560
                          i   i-  i -  i  ii       v  v  i -i       i   ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_153763753_   3561 GTGGAACCACAAAAAATCCCAAAGAGCCAAAGAAGTCTTGAGCAAAAAGA 3610
                         i     vii   iii i  vi  v       iv i      iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_153763753_   3611 ATAAACCTGGAGGCATCACACTACCTGATTTCAAATTATACTACAAAGTT 3660
                          i   vi      vv       v  ii        viv          i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_153763753_   3661 ATAGTAACCAAAACAGCATTGTGTTGACATAAAAACAGACATATAGACCA 3710
                          i     i   i    ii v  ii  i     ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_153763753_   3711 ATAGAACAAAATAGAGAGCCCAGAAATACACCCAAACATTTAAAGCCAAC 3760
                           i   i i   v     i         v     v       vi i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_153763753_   3761 TGATTTTCTACGAAGTTGGCAAGAATACATGATGGGTAAAGAACAGTCTT 3810
                                 v  i i v  v     vi ivii     v      i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_153763753_   3811 TTCAATAAATGGTGCTGGGAAAACTGGATATCCATATGCAAAAGAATGAA 3860
                              i              v         ?   i               
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_153763753_   3861 CCTAGACCCCCTATCTCTCACCACGTATGAAAGTCAAATAGGCCAGGCAC 3910
                         vi i      -  i   v     i--------------------------
  L1M4_orf2#LINE/    450 GTTGGACCCC-TACCTCACACCAT-------------------------- 472

  chrX_153763753_   3911 AGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCAGA 3960
                         --------------------------------------------------
  L1M4_orf2#LINE/    473 -------------------------------------------------- 472

  chrX_153763753_   3961 TCACTTGGGGTCAGGAGTTTGAGACCGGCCTGGCCAACATGGTGAAACCC 4010
                         --------------------------------------------------
  L1M4_orf2#LINE/    473 -------------------------------------------------- 472

  chrX_153763753_   4011 CGTCTTTACTAAAAATACAAAATTAGCCAGGTGTGGTGGCACACCTGTAG 4060
                         --------------        ----------------------------
  L1M4_orf2#LINE/    473 --------------ATACAAAA---------------------------- 480

  chrX_153763753_   4061 TCCCAGCAACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCCCAGAGG 4110
                         --------------------------------------------------
  L1M4_orf2#LINE/    481 -------------------------------------------------- 480

  chrX_153763753_   4111 TGGAGGCTGCAGTGAGCCTAGATCGTGCTATTGCACTCCAGCCTGGGCAA 4160
                         -----------------------------   ----------------  
  L1M4_orf2#LINE/    481 -----------------------------ATT----------------AA 485

  chrX_153763753_   4161 CAGAGTGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAG 4210
                          ----------------      ---------------------------
  L1M4_orf2#LINE/    486 C----------------TCAAAA--------------------------- 492

  chrX_153763753_   4211 ACAGAAAGAAAAGAAAAGAACAATAGATTAAGGAATTAAATTTAAGACCT 4260
                         ----------------------- i   i ?i  vi     v     v  
  L1M4_orf2#LINE/    493 -----------------------TGGATCAWAGACCTAAATGTAAGAGCT 519

  chrX_153763753_   4261 GAAACTCTGAAATTATTAGAAGAAAACATAG-TGTAAGCAT-TTCATGAC 4308
                         i     v i   i v                -?    --  -   i    
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA--ATCTTCGTGAC 567

  chrX_153763753_   4309 ATCAATTTGGGCAAGAATTTGTTAGACAAGACCTCAAAATCATGAGTAAC 4358
                         v iiiv  i     vii   v     i v   vi     v  ii  i   
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chrX_153763753_   4359 AAAAGCAAAAATAAAGAAATTGGATTACATCAAACTAGAAAGCTTCTGCA 4408
                              v       i v        i v       v vi   i   i  ii
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chrX_153763753_   4409 CAGCAAAGGAAACAATCAACAGAGTGAAGAGACAACCTATAGAATGGGAG 4458
                          vv       v  v     v i      i        i i          
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chrX_153763753_   4459 AAAATATTTGCAGATTATACATCTGACAAGGGATTGATATCTAGAATATA 4508
                                     i  i   i      i      i vi    i        
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chrX_153763753_   4509 TAAGGAACTCAAACAACTCAATAGCAAAAGTCCAAATAATCCTATT-AAA 4557
                            i      vv           ii    ivv       i  v   -   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chrX_153763753_   4558 AATGAACAAAAGACCTGAATAGACATTTCTCCAAAAGAGACCTACAAATG 4607
                             ii    i  ii                    ii   iv        
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chrX_153763753_   4608 GCCAACAGGTATATGAAAA-ATGCTCAACATCACTAACCAT 4647
                              i i i i       -             ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (124 / 58)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 22.00 (352 / 16)  


2254 25.67 11.42 0.67  chrX_153803729_153808401     3042  3785 (887)    L1M4_orf2#LINE/L1        4   827 (81)  

  chrX_153803729_   3042 AAAGCCATACCATGTTGTTGTATTGAAAGATTCAGTATTGTTTAAATGTC 3091
                             vi  v       vv  v    i    i i i       v i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chrX_153803729_   3092 AATTCTCCCCAAATTGATCTACAGATTCAATTCAATTCCAGTCAAAATCC 3141
                            v                          iv    i  vi         
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chrX_153803729_   3142 CAGTTGGCTATTTGGTGGAG-TTGGCTAGTTGACTATAAAATTAATACAG 3190
                            i  v  v   v ii  i-   i v  i   iiv       v   ii 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chrX_153803729_   3191 AAATATAAAAG-CCTAAATATATCAAAAGCAATTTCAATAAAAAAGTA-- 3237
                             ii  ii -  i i -   v v   i    i ii v   i   v --
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGA-ATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_153803729_   3238 -AGTTGGAGGTTTTAGACTGCCTGATATTAAGACTTACTATAAAGTTACA 3286
                         -         vi i v   v  ii  v i  i        i    i    
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_153803729_   3287 ACAATCAAAACAATCTGGTACTGGCATAAGCACAGATATACACATCTATG 3336
                         ii      i   i v               v i   i   i v   v   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_153803729_   3337 GAAC----TAGAGAATCCATAAACAGATTTGCCTATATACAGTCATTTAA 3382
                            i---- v    i    v   i i iiiiivi  v  ii    v  i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chrX_153803729_   3383 TTTTCTACAAAGGCACCAAGGGAATTCAATAGAGAAAGAA---------- 3422
                              v    i  ii     ivv       i i       ----------
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chrX_153803729_   3423 ---------------------------------------------AAGT- 3426
                         ---------------------------------------------    -
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chrX_153803729_   3427 ------------CACACCATACAGAAAATTTAACTCAAAATGTATTATAA 3464
                         ------------         i v    v             v  i ? i
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chrX_153803729_   3465 ACCTAAATACTAATGCTAAAATGATAAAAGTTCTAGAAGAAAACAGAAGA 3514
                                 iiv iv       iv      v ii            v i ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chrX_153803729_   3515 --AAGGCTTTGTGAACTTGAGGTGGGCAAAGATTTCCTAGGACAGGGGAA 3562
                         --  iv   i    v    i v i     v i    i   - i v iv v
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG-ATATGACAC 601

  chrX_153803729_   3563 AAAAAAGCATGAATCATAGAAGAAGAAA-AGCTAAATTGGACTTAACTAC 3611
                         v    -   ii iiv i i     i   -  v            v ii v
  L1M4_orf2#LINE/    602 CAAAA-GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_153803729_   3612 AACTATAAATTTCCACTATTTGAAAGACACCATTTGGAAAATGAAAATGC 3661
                           i  v   i  iiiivv  ii  i     i  ivi    i      vi 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_153803729_   3662 AAGCCATAGATTGGAAAAAAACATT--CAAAACAGGTACCTCTGA--ATA 3707
                           v   i   v   i i    i   --    v  vi  --     -- vi
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATA--TCTGATAAGG 748

  chrX_153803729_   3708 GTCTTGTACCCAGAATATATAAAAAATTATCAAAACTCAACAATAACAAG 3757
                          v      i              i  i v i v       i     v   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_153803729_   3758 ACAAACAACCCAATTAAAAACTGG-CAAA 3785
                              i         ?    v   -    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAA 827

Transitions / transversions = 1.65 (117 / 71)
Gap_init rate = 0.02 (15 / 824), avg. gap size = 6.00 (90 / 15)  

 454 13.40 3.09 3.09  chrX_153803729_153808401     4085  4181 (491)    L1M4_orf2#LINE/L1      812   908 (0)  

  chrX_153803729_   4085 TTTAAAAACAAAGGACCAATGATTTGAATAGACACTTCC---AAGAAGAT 4131
                           ?     i---  i v  v              i   i---        
  L1M4_orf2#LINE/    812 TTWAAAAAT---GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_153803729_   4132 ATAGGAATGGCTAATTAGCACATGCAAAGATGCTCAACATCTTTAGTCAT 4181
                            vi      i   v        v                v????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.00 (6 / 6)
Gap_init rate = 0.02 (2 / 97), avg. gap size = 3.00 (6 / 2)  


 657 28.68 11.22 5.86  chrX_153811441_153813228      500  1301 (487)    L1M4_orf2#LINE/L1       64   908 (0)  

  chrX_153811441_    500 AAATTAAGGTCTG-AG-TTTAATGAAATTGCAGTTAGAATCACAACAGGG 547
                              i --   i-  -  i  i v   iv vi i i    v  i ----
  L1M4_orf2#LINE/     64 AAATTGA--TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC---- 107

  chrX_153811441_    548 CTTGGATCTTTTT-----AATTTGAAAAAT--ATCTTAACAGTTTTATGT 590
                         --  --i      -----  v    v  ii--   i   v --  i  i 
  L1M4_orf2#LINE/    108 --TG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA--TTCATAT 151

  chrX_153811441_    591 GGAAGAATAAAGTGTCTAAGAATAGCTAAGAAAG----GTACAAAAAGAA 636
                             ivii  i - v iv        i  i v i---- v v  i     
  L1M4_orf2#LINE/    152 GGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_153811441_    637 TA--GT--GAGGATTGCTTTCACCCACCAGATATCAGAAGATATCATAG- 681
                         i --  --     ---  iv   iiv   -  v   i  vv  ii i i-
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGA---CTCACACTTCCCA-ATTTCAAAACTTACTACAAA 246

  chrX_153811441_    682 GCTCACTGTAATCAAATCACTATGGTACTGGCATAGCAAGATA---ATAG 728
                            -  v        iv  v i             -- i    ---   -
  L1M4_orf2#LINE/    247 GCT-ACAGTAATCAAGACAGTGTGGTACTGGCATA--AGGATAGACATA- 292

  chrX_153811441_    729 TAGATTAGTGAAACAGCCTAAT---GAATCCAGAAATATATGCTAATATA 775
                              i i  i  i  ---   ---  i          v iv vv i  v
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAG---AATTGAGAGTCCAGAAATAAACCCATACATT 339

  chrX_153811441_    776 TATGAGAACTTTATAT--GATGAATGTGTTGATTCAAATCAGTGG----- 818
                             ivv v  v  v --  ii iv   iii vv v v   i   -----
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chrX_153811441_    819 ---------------CAAAAGGTGCCATCACAATAGGCTATTGATCTGGA 853
                         ---------------    v     iivv    iv  v  ?iv iv  v 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_153811441_    854 TGGAAATAAAACTAGACAAATCCCTCTCTCATGCCATATGACAAAAGTAA 903
                         viii   i  ii i   ----    vi    ii      -      --- 
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGAC----CCCTACCTCACACCATAT-ACAAAA---A 481

  chrX_153811441_    904 TTAGC---AGATA-ATTGAAGCAATGCATATAAAAAGCGAAACAGTAAAC 949
                            i --- i  i-  ii?  vvv iv  i   i ivii    vi    v
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chrX_153811441_    950 ATCTTGCAAGAAAATCTGGGAGATTACA----CGTACAATCTTGAGGTGT 995
                         v    iv       iv i  ? --  v ----   i-- i    -   - 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAACATAGGNG--TAAATCTTCGTG--ACCTTG-GGT-T 575

  chrX_153811441_    996 GGGAAACA--TTTTTA--------ACCAACCTTGCCGACTCTGAAGATAT 1035
                         i  v  ii--  i   --------     vvvii vii ----  v v v
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC----AACAAAA 621

  chrX_153811441_   1036 GAAAGAAAAGATATCTCTGATT--ATAAAAATTAAAAACTGTTTTGGT-- 1081
                             i  v     vv iv  i --  v             v  v  v --
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chrX_153811441_   1082 AAAAG---TTAT-AAGAAAGTCAACAGACAAACAATAGATCTTGGGGAAA 1127
                            i ---i   -        v  v      v v i   -v v  i    
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA-ATGGGAGAAA 720

  chrX_153811441_   1128 AC---TGCAA----TATACATGACAAAGAGTTAATATTTGTAATA-ATAA 1169
                          i---     ----    iv   i  i iii vi   iiiv    -    
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chrX_153811441_   1170 AAGGGTTCTCATAATT---TTTTTAAATGA--AAGAGTCCAA--AGAATA 1212
                          - iii   i i  i --- vv v   v  --  v ii    --?i  - 
  L1M4_orf2#LINE/    771 A-GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA-A 818

  chrX_153811441_   1213 ATGGGCAAATCATATGACTAATTAAATCCCCCAAATAAAT---CCAATAG 1259
                                  vv  v   v  ivi vv  i  v  iv i  --- v   i 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_153811441_   1260 CCAACAAGCATTTAAAAAGATGCTCAACTTATTAGAAATAAA 1301
                             i     iv i              --  i ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAAC--ATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (128 / 98)
Gap_init rate = 0.06 (51 / 845), avg. gap size = 2.69 (137 / 51)  


2253 20.15 12.09 6.55  chrX_153827742_153829760.rev      735  1528 (491)    L1M4_orf2#LINE/L1       71   908 (0)  

  chrX_153827742_    735 TTTATGGAT-CAATGCAATCCCAGTCAAAATCTCATCGGG-TGTCTGGCA 782
                          i  ii   -   i        vi        i  v v v- v i v   
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chrX_153827742_    783 GAAACTGGCAGCAACCTAATTCTAAAATTCATATGGAGGAGTGTATAAAA 832
                             i  i  --- v  i  i                -------------
  L1M4_orf2#LINE/    121 GAAATTGACA---AGCTGATCCTAAAATTCATATGGA------------- 154

  chrX_153827742_    833 ACAAGATAAAATTCAGATGGAAATGCTAAATACCTAGAATACTCAAAATA 882
                         ---------------------     v iiv   i      vi     i 
  L1M4_orf2#LINE/    155 ---------------------AATGCAAGGGACCCAGAATAGCCAAAACA 183

  chrX_153827742_    883 GCTTTGAT---GAAAAACAAAATTTCAAGACTTGCATTACCTAA------ 923
                         iii    v---   i      i  vv i    ii  i v  i  ------
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chrX_153827742_    924 -------------GTTACAGTAATCAAAACAGCATGATAATGGCAC---- 956
                         ------------- i            i    ii  i  v     i----
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chrX_153827742_    957 -----C---TAGATCAATTTGGCAGTACAA---AGAGCTCAAAAACA--- 992
                         ----- ---         --  - i  v  ---    ii  i   i ---
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAAT--GG-AATAGAATTGAGAGTCCAGAAATAAAC 330

  chrX_153827742_    993 ---------TATAGTCAACTGATTTTCAACATAGGTGTAAAGACAATTCA 1033
                         ---------   i     i        i   vi    iv     v     
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chrX_153827742_   1034 GTGGAGAAAAAGACAGTCTTTTTTTTACAAATG-TG--GGGACAACTAGA 1080
                         i   i    i - i        iv--       -  --         i  
  L1M4_orf2#LINE/    381 ATGGGGAAAGA-ATAGTCTTTTCA--ACAAATGGTGCTGGGACAACTGGA 427

  chrX_153827742_   1081 TACCCATACGCAAAAAAA---ACTTGGATTCCTACCTTATACTATATACA 1127
                           ?   i i      i  --- v     ii       i i  i       
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chrX_153827742_   1128 AAAAGTAAATCAAAATGGATCACAGAACTAAATATAAAATCCGAACCTAT 1177
                             v   v             ?   v      i   i v ii  v    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chrX_153827742_   1178 ATACAATCT----AGAAAAAGCGAGAGAAAATCTTGGTGACCCTGGATTA 1223
                          - v v   ----      viiii ? v       v      i   i   
  L1M4_orf2#LINE/    528 A-AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_153827742_   1224 GGCAA--ATATTCTCAGACATGACACCAAAAGCTGGAGCTACAAAAGAG- 1270
                              --i -    i   i              vvi   v        i-
  L1M4_orf2#LINE/    577 GGCAATGGT-TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chrX_153827742_   1271 -----------CTGCACTTCA---AGATTAAGAACTTCTGCTCTTTGAAA 1306
                         -----------i  v      --- i     i     i  iv   ii  i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chrX_153827742_   1307 GGTACAGTTCAGATAATGAAAAG-----CTACAGA---GAAGTAATATAT 1348
                          ii  vi iv   v i       ----- i     --- i  v  -    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA-ATAT 724

  chrX_153827742_   1349 TTGCAAATCACATATCTAA-----GACTTCTATCCAGAATATTTAAAGAA 1393
                                   i      i -----     v            v       
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_153827742_   1394 CTCTCACGATTCAGCAGTGAAAGAAAACCAACAACCCAATAAAAATATGT 1443
                             i  i i   ii i i   -- i  v  i        v?   v   -
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAA--AGACAAATAACCCAATTWAAAAATG- 821

  chrX_153827742_   1444 GGAAAAAGATTTGAACAAATAAGTCATCAAAGA---TATATGAATGGCAA 1490
                           v   i        i i i vv  vi      ---    ii      v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chrX_153827742_   1491 AAAATAAGCCCGTGAAAA--TGCTCAACATCATTAGTCAT 1528
                          ---     v i      --            ????????
  L1M4_orf2#LINE/    872 A---TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (105 / 51)
Gap_init rate = 0.04 (32 / 838), avg. gap size = 4.62 (148 / 32)  


3809 20.35 2.32 2.10  chrX_153830576_153832596.rev      627  1530 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_153830576_    627 GAAAGATATTCCATGTTCATGAATGGGAAGAATTAAAATTGCTAAAATCT 676
                                  i           i  v      v    v    i   i  vv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_153830576_    677 CCATACCTCCCAAAGCAATCTACAGATTCAATGCAATCCACATCAAAATT 726
                          v    ii      vii              i       vi        i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_153830576_    727 CCAATGACATTTTTCACAGAAAGAGGAAAAAAAATCCTAAAATTCACATG 776
                            iivi v     ii      vv iv  ivvi             i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_153830576_    777 GAAGTACAAAAGACCCCTAATAGCCAAAGCAATCTTCAGCAAAAAGAACA 826
                            i i   ii     vv          i       v iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_153830576_    827 AAGTTGGAGGCATCATCATACTACCTGATCTCAAAATATACTACAAAGCT 876
                                   - i--   i   v  ii  i      iv            
  L1M4_orf2#LINE/    203 AAGTTGGAGG-AC--TCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_153830576_    877 ATAGTAACCAAAACAACATGGTCCTGGCATTAAAAACAAACACATAGACC 926
                          i     i   i   iii    v       -  ii i i   i     i 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGATC 298

  chrX_153830576_    927 AACGGATCAGAATAGAGAGCCCAGAAATAAATCCACGTATTTACAGTCAA 976
                           i   vi     v     i           i   iii     ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_153830576_    977 CTGATTTTTGACAAAGATGCCAAGAACACACAACAGGGAAAGGATAGTCT 1026
                         i       i     i i        v  iv   ii       i       
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_153830576_   1027 CTTCAAAAAATGGTCCTAAGCAAACTGTTTATCCACATGCAAAAGA---- 1072
                         i     v       v  ii vv     vv  ?              ----
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_153830576_   1073 -----GACCCTCATCTCAAACCAT-TGCAAAAATCAACTGGAAACAGATT 1116
                         -----     ii i    v     - i       i    vi   ii   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_153830576_   1117 AAATACTTAAATATAAGACCTGAAACTGTAAAACTGTTAGAAGAAAACA- 1165
                          ? v  i     i     v  i     i       v             -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_153830576_   1166 -GGGAGAAAGCTCCATGACACTGGTCTGCACAAATATTTTTTGGATATGA 1214
                         -  ?iv   v  i i    vi   vi ivi   vvi   i  i       
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_153830576_   1215 CCCGAAAAGCAGAGGCAACAAAAGGCAAAAATAGACAAATGGGATTACAT 1264
                          v v       v i          i-         i    v   i v   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAAATTGGACTTCAT 647

  chrX_153830576_   1265 CAAACTAAAAAGCTTCTGTACAGCAAAGGA----ATCAACAGAGTGAAGA 1310
                             v v    i   i   i vv       ----     v i      i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_153830576_   1311 GACAACCTAAAGAATGGGAGAAAATATTTGCAAAGCATATATCTGATAAG 1360
                                i v                        v               
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_153830576_   1361 AGATTAATATAAAAGATATACAAGGGATTAA-ACAACTCAATTGTAAAAA 1409
                         i  i vi   vv ii     i  i i i vv-          vi      
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_153830576_   1410 TACAA----CCTGATTTAAAAATGGGCAAAGGACCTGAATAGACATTTCT 1455
                         v    ----  ii   ?                ii               
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_153830576_   1456 CAAAAGAAGACATACAAACATACAAATGGCCAATAAATAAGGTATATGAA 1505
                          v        i       --------          ----- i i     
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAA--------TGGCCAATAA-----GCACATGAA 884

  chrX_153830576_   1506 AAAAATGCTCAACATCACTAATCAT 1530
                           i -            ????????
  L1M4_orf2#LINE/    885 AAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (116 / 64)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 3.08 (40 / 13)  


 483 16.82 0.00 3.74  chrX_153888057_153889894      345   451 (1387)    L1M4_orf2#LINE/L1      806   908 (0)  

  chrX_153888057_    345 ACCTAAATTTTAAAAAATGTGTAAAAGGATTTTAATGGACGTTTTTCCAA 394
                            i  ---  ?       v i   -      v   i   i   i     
  L1M4_orf2#LINE/    806 ACCCAA---TTWAAAAATGGGCAAA-GGATTTGAATAGACATTTCTCCAA 851

  chrX_153888057_    395 GGAAGATATACAAGTGGTCAATAAACACGTGAAAAATTGCCCCAAATCAT 444
                         i            i   i      i   i      iv   i v v    ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chrX_153888057_    445 TAGTCTT 451
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.02 (2 / 103), avg. gap size = 2.00 (4 / 2)  

3598 22.14 1.65 0.82  chrX_153888057_153889894      497  1345 (493)    L1M4_orf2#LINE/L1       53   908 (0)  

  chrX_153888057_    497 CACTACTACCCAATGTCATCTACAGATCCAGTGTAATCCCTATCAAAATT 546
                           v    v     vv v          i  ii i               i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_153888057_    547 CCAATAACATTTTTCACAGAGATAGA-AATAAAATCATAAAATTCATATG 595
                            iivi v     ii    i  v  -  vvvi   v             
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_153888057_    596 AAACTACAAAAGTTCCTGAATAGCCAAAGCAATCTTGAGAAAGAAGAACA 645
                         i  v i   ii vi  v           i         i           
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_153888057_    646 AAGCTGGAGAAATCACACTATGTGATTTCACAGTATATTATAAAGCTATA 695
                            i     i v       vivii      v iiv  i  i       i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_153888057_    696 ATAATCAATGCAATATGGTACTGGCATAAAAATAGACACATAGACTAATA 745
                         i       vi  i i              ii       i     ii   i
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chrX_153888057_    746 GGACA--ATAGAGAGCCCAGAAATAAACCCATGC--TTATGCAGTCAACT 791
                          i i --  v     i                i --     --     i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG--GTCAATT 350

  chrX_153888057_    792 AACCGTCAACAAAGATGTCAGGAATATTCAATGGGAAAAGGATAGTCTCT 841
                         i iiv  i    i i  i  i  vi          i    i       i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_153888057_    842 TCAATAAATGATGTTGGGGAAACAAGATACCCACATGCGAAAGAATGGAA 891
                             i     i  i    iv   vi    ?        i        i i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_153888057_    892 GTGGATCCTTA--TCACACGTATATACAAAAATCAAGTTAAAATGAATTA 939
                         v    i  i  --      -i            i  v i      i  i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACAC-CATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_153888057_    940 AAGACTTAAACATAAGACCTGAAAGTGTAAAACTACTAGTGGAAAGCAGA 989
                         ?    i    ii     v  i   v i       vi   vi    i  v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_153888057_    990 GG---AAACACTGCTTGACATTGGTCTTGGCAAAGATTTTATGAATACGA 1036
                           ---   i-  v v    v    vi v     v i   iv ii   i  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_153888057_   1037 CTCCAAAAGCACAGGCAACAAAGGAAAAAAGAAACGGGTGGGACTATATC 1086
                          v           i        i       v i iiii v     vi   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_153888057_   1087 AAACT--AAAACGCCTGCACAGCAAAAGAAACTG--AACAAAATGAGAAG 1132
                            v --     vii  ii vv    i  v   i--  v   i   i   
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_153888057_   1133 GCAACCTACAGAAGGGGAGAAAAATATTTGCAACCCATATATCTGATAAA 1182
                         i     i      v         -         vi              -
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAA- 746

  chrX_153888057_   1183 GGGGCTGATATCCAAAATATATAAAGAACTCATATAGCTCAATAGCGAAA 1232
                            i  vi      i                v  i i       ii-   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT-AAA 795

  chrX_153888057_   1233 AACCCAAATAATATAATTTATAAATGGGCAAAGATCCTGAATAGACATTT 1282
                           vv       ivi    ? v            ivii             
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_153888057_   1283 TTCCAAAGAAGACATATAAATGGCCAATAAGTACACGTAAAGGTACTCAG 1332
                         i           i   i              i   i v    i i    i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_153888057_   1333 CATCACTAATCCG 1345
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (125 / 60)
Gap_init rate = 0.02 (13 / 856), avg. gap size = 1.62 (21 / 13)  


1585 24.45 13.64 4.76  chrX_153900127_153903101.rev     1711  2487 (487)    L1M4_orf2#LINE/L1       63   908 (0)  

  chrX_153900127_   1711 CAAATTGATGAATGGATTCAATTCTATCCCAGTCAAA-TTTCAGCTGACA 1759
                                  vv ii       iv v     vi     - ii      v -
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC- 111

  chrX_153900127_   1760 TGTTTCAGCAAGTTTTCTTGTGGAAATCAACAAACCGATTTTAAAATTTA 1809
                         -------------   i   ii     ii    i i   ii       i 
  L1M4_orf2#LINE/    112 -------------TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chrX_153900127_   1810 TATGGGGCTACAAAGGGCGAAGAATAGCCAAGACAGTCTTGAAGAATAAC 1859
                              iiv i   i  i vv           i   i       i  v  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_153900127_   1860 AACAAAGG-GGAGAACTAATGTTACCGCATATCATCAAGACTTATTATAA 1908
                                v-    i   v iii v  -  -  i-    i     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCC-CA-ATT-TCAAAACTTACTACAA 245

  chrX_153900127_   1909 AGCTACAGCAACTAAG----TGTGTTACTGACACAAGGATAGACACATAG 1954
                                 i  ii   ----    v     i  i           i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_153900127_   1955 A-CAA---AACAGAATTCGCCTAGAGTCCAGAAACATAATCATATATATA 2000
                          -   ---  i      - ---            i v vi    i  v  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATT-G---AGAGTCCAGAAATAAACCCATACATTTA 341

  chrX_153900127_   2001 GGGACGACTGATTTAAGGCAAAG-TGGCAAGGC--------------AG- 2034
                         v  v i i      vv i   i -  v    i --------------  -
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chrX_153900127_   2035 ----------CAATAAATGGTGCCAGGTCAATTGGATACACACGTGGGAA 2074
                         ----------   i         ii  v   i      ?v   i  vi  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chrX_153900127_   2075 AAAGGGAATGTCAACTCACATCCCACATCATATCCTAAAGTTAACACTAA 2124
                          i iv   vv vi  i vi i i    i     v v   i     v v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chrX_153900127_   2125 GTAGATTGTAGATTTAAGCACGAATGGTGAAATAATAAAGC--------- 2165
                         i i   ii?   ii   iiiii iv v i   iv     i ---------
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chrX_153900127_   2166 ---------------ATCT------CTTCCAGATAGGGAAAGATGTCTTA 2194
                         ---------------    ------ i ivi v    v  v i v     
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_153900127_   2195 AATAGTGTAGGACACTAAAAAGCACTAG-ATCGAAAAGATAAAA-AGATA 2242
                         i   -  ----    i    -    v  - v -      v    -     
  L1M4_orf2#LINE/    592 GATA-TG----ACACCAAAA-GCACAAGCAAC-AAAAGAAAAAATAGATA 634

  chrX_153900127_   2243 ATTTGGACTATTATATTAAATAAACAACTTAGGCTCATCAAATGATACCA 2292
                          v       - i  -iv    v  v     vv iv v     v  i  i 
  L1M4_orf2#LINE/    635 AATTGGACT-TCAT-CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_153900127_   2293 TTAAGATAGTGAAAA------CCAGGTCAGGGTGAGAGAGTAGATACTTG 2336
                          i    v        ------   ---   ii  i    -- i   i   
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCA---CAGAATGGGAGA--AAATATTTG 727

  chrX_153900127_   2337 GAATAGGTATAGCTGACAG----CTTGTATCCAGAACATACTG-GAATTC 2381
                         v  vvvi    v    i i----             i   ivi-   i  
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chrX_153900127_   2382 TTTTGA---AGTACTAAGAA------------AGTTAAAGAA-----AAA 2411
                           vii --- i  v   i  ------------ i  ?  i  -----   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chrX_153900127_   2412 -----TGAATATGAC--TTATACATGAGGGGATATCCAAAAAGCCTATAA 2454
                         -----      -   --  v v  -i  ii     v    vi   v    
  L1M4_orf2#LINE/    828 GGATTTGAATA-GACATTTCTCCA-AAGAAGATATACAAATGGCCAATAA 875

  chrX_153900127_   2455 ACATTTGAAAAGGTGTTCAACCTAATTAGTCAC 2487
                         i  iv       i  i     v v ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (115 / 72)
Gap_init rate = 0.04 (36 / 846), avg. gap size = 3.97 (143 / 36)  


 366 24.62 8.46 1.54  chrX_153904113_153906358      371   500 (1746)    L1M4_orf2#LINE/L1      687   825 (83)  

  chrX_153904113_    371 GAAACCATGGAAAGTAAAACCA-AGGATAAGAGAGGAC----------TA 409
                             --i  i    vv  v   -  i  ii    ii i----------i 
  L1M4_orf2#LINE/    687 GAAA--GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chrX_153904113_    410 CATATTTGATAATGGTATAGCATCCAGAATAGGTAAAGAATTCTTACAAC 459
                         i    i      v  vv v i          vi       i         
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chrX_153904113_    460 TCAAAAATAAAAGGACATACACTTCAATTTAAAAATAAGCA 500
                             v       i    v i vii     ?      ii   
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 1.82 (20 / 11)
Gap_init rate = 0.02 (3 / 139), avg. gap size = 4.33 (13 / 3)  

3380 20.11 7.34 4.75  chrX_153904113_153906358      869  1753 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153904113_    869 TGGAAAGACATCTCATGTTCATGGATTGGATAAATTAATATTGTTAAGAT 918
                                 i   i                 vi v                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153904113_    919 ATCA-TACTACTCAAAGTGATCTGTAGATTTAATGCAATCACTGTAAACA 967
                         iv  -    v i    v      ii     i  i      v  i v  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153904113_    968 TCCCAATGGCTTGCTTGCTTTTTTTTTTTTTTTTTTTTTTTTTTTGATGG 1017
                              -------   -  i      ---------------------iii 
  L1M4_orf2#LINE/    101 TCCCA-------GCT-GCCTTTTTT---------------------GCAG 121

  chrX_153904113_   1018 AGTCTCACTCTGTCACCCAGGCTGGCCATTTTAAG-TTGATACGGAATCT 1066
                          ivi v  ---------- i    ---  ii   i-  v   i    viv
  L1M4_orf2#LINE/    122 AAATTGAC----------AAGCTG---ATCCTAAAATTCATATGGAAATG 158

  chrX_153904113_   1067 CGGGGGACCTTGAATAGCCAAAACAAGTTCGAAAAAGAA---CCAATTTG 1113
                          ii      iv               vi i         --- v  v   
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chrX_153904113_   1114 GGCAATTCACACTGCCTGGTTTCAAAAGTAACTACAAAGCTACAGTCATC 1163
                          ivi i       v  iii        v v                v   
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chrX_153904113_   1164 AAAACAGTGTGGTA------------------------TCAATGAAACAG 1189
                           i           ------------------------      i  i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chrX_153904113_   1190 AATGGTCAGCCCAGATTTAAACCCTTGCAT--ATGGTCAAGCAAACTTCA 1237
                            v vv  i     vv       v i   --        vii vi   i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chrX_153904113_   1238 ACAAGGATACCAACACCACTAAATGGGAAAAAGACAGTCTCTTTAATAAA 1287
                               i i    v    i v      i   ii i     i  i  i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chrX_153904113_   1288 TGATACTGGGAAAACTGAATATTCACATGCAAAAGAAAGAAGCTGGACCC 1337
                           i i      v     i   ?i              v    i       
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chrX_153904113_   1338 TTATCTTACACCGTATATAAAACTTAA------ATGAATTAAAGACCAAA 1381
                         i  i  i     i    i    v    ------   i  i ?     v  
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chrX_153904113_   1382 ATATAAGACCCCGAACTACAAAACT---AGCAGAAAACATAGGGAAAAAG 1428
                           i     v ivi     i      ---  v            ?iv   v
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chrX_153904113_   1429 CTTCATGACATTGGATTTGACAATAATTTCTTGAATATGACACCAAAAGC 1478
                             i    v    i  v i    ii      ii                
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chrX_153904113_   1479 ACAGCTAACAAAAGCAAAA-TAGACAAATGAGACTACATCCAGCTTTAAA 1527
                            ivi        v    -    i    vi    v    v iv  v   
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chrX_153904113_   1528 ACTTATGTGCACGAAAGGAAGCAATGAACTGAGTGAAAAGGCAACCTATG 1577
                             v     viv      vi v  v  vvi         i     i ii
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chrX_153904113_   1578 GAATGGGAGAAAATATTTGCAAATCATATATTTAATAAGGGGTCAATATC 1627
                                                        i i       iiivi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chrX_153904113_   1628 CAGAATATATAAAGAACTCCTACA-CTCAACAACAAAAA-------AATC 1669
                                            i    -     i  i     -------  i 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chrX_153904113_   1670 TGATTTTAAAATGGGCAAAGGACTTAAAGTGATATTTCTCT--------- 1710
                         ii   ?v               i  i  vv  i       i---------
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chrX_153904113_   1711 -------TGGTCAACAAGCATATGAAAGAGTGTTCAATATCACTAATTGT 1753
                         -------   i   i     i      iii  i    i    ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (112 / 62)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 6.69 (107 / 16)  


2000 22.74 7.18 2.05  chrX_153912735_153914739      500  1084 (921)    L1M4_orf2#LINE/L1      174   788 (120)  

  chrX_153912735_    500 AGCTAAATCAATTTCAAAGAAGAAAAAC----TTGGAGGACTCATTTTAC 545
                            i   v    i ii  i     i   ----            ivi v 
  L1M4_orf2#LINE/    174 AGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTC 223

  chrX_153912735_    546 CTGACTTCAAGACTTACTATAAAGCTATAGTAATCAAGATAG-ATGGTAT 594
                          ii i     i        i       i           i  -i     i
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chrX_153912735_    595 TGGCAGAGGAACAGACACATACGTCAATGGAACAGA--TGAGAGAACCCA 642
                              v i i i     i   vi         i   --      --i   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG--TCCA 321

  chrX_153912735_    643 GAAATAAACCCATATAAATATGCTCAGCTGATTTT-GA-AAAAGTGAAAA 690
                                       i vv    v   ii       -  -  ii   vv  
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chrX_153912735_    691 AGCAATTCAATGGAGGAAGAATAGCCTTTCTGACAAATTATGCTAGAGCA 740
                         ii v         i i        i    iii      vi    i ii  
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chrX_153912735_    741 ATTAGACACCCATG-GCGAGGAGAAAAAAG---AACCTCTACTTAAACCT 786
                          i i  i ?   ii-  i i-    vi   ---i   i    ------  
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAA-AGAATGAAGTTGGACCCCTAC------CT 464

  chrX_153912735_    787 CACATCTTATATAAAATTTAACTCAAAATGTATAACGGACTTAAATGTGA 836
                             i v    i    v             v  v ?i   i       i 
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chrX_153912735_    837 TACATAAAACTAGATAACT-TTGAAAAAAGCCACAGGAGAAAAATCTTCA 885
                         v vv        v v    -  ii  i  iv  i   ? v   -     i
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-TCTTCG 563

  chrX_153912735_    886 GGATCTTGGGCTAGGTGACAAGTTCTTGGACTTTGCCCCGAAAGCACA-T 934
                         v  i      i    ii iiiv     i  iv vi v  i        -v
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chrX_153912735_    935 CCATAAAAGACAAAATCTGATATATTGGACTTCTTCAAAATTTAAAAACT 984
                          v i      v     v-    v          v        -       
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATA-GATAAATTGGACTTCATCAAAATT-AAAAACT 661

  chrX_153912735_    985 T--GTGATTTAA-------------GAAGAGGAAAAGATAAGCTACAGAT 1019
                          --   v  i  -------------   iiv       i  v i     v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chrX_153912735_   1020 TGAGATGAA---TTTGCAAACCATATATCTGATCA---ATTTG------G 1057
                           i  vi  ---        i            v --- i   ------ 
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chrX_153912735_   1058 AATATATAAAGTGTACTAAAAACTCAA 1084
                                    viiv  v v       
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAA 788

Transitions / transversions = 1.89 (85 / 45)
Gap_init rate = 0.03 (20 / 615), avg. gap size = 2.70 (54 / 20)  

 535 20.80 1.60 0.00  chrX_153912735_153914739     1392  1516 (489)    L1M4_orf2#LINE/L1      782   908 (0)  

  chrX_153912735_   1392 AACTCAACAATAAAAA--CAAACAGTCCAATTAGAAAATGGGCAAAAGAC 1439
                                i        --    i ii      ?i            i  i
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chrX_153912735_   1440 ATGAATAGATGTTTCACTGAAGAGGATCTATAGATGGCAAGTAAGCATAT 1489
                         v        ii    v ii    i   v  i i     v i      i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chrX_153912735_   1490 GAAAAGCTGTTAAACTCCATAAGTCAT 1516
                               v  i v   vi  ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.01 (1 / 127), avg. gap size = 2.00 (2 / 1)  


2571 17.84 4.80 0.17  chrX_153916959_153918533      500  1082 (493)    L1M4_orf2#LINE/L1      299   908 (0)  

  chrX_153916959_    500 AATGGAATTGAATTGACAGTCCAGAAATAAGCCCACACATCTACAGTCAA 549
                                 v       v             i    i    i  ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_153916959_    550 CTGATTTTCAACAAGGGTGCCAAGACTAT------GGGAGAGAATAGTCT 593
                         i        i                i  ------    i          
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_153916959_    594 T--CAACAACTGGCGAATGGACAAGTGGATATCCACGTGCAAAATAATGA 641
                          --      v   i vvv      v      ?    i       v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_153916959_    642 AGTTGGACTGAGATCCCACACGATAAATGAATATTAACTCCAAACGTATT 691
                                 ivvv i i     v   v ii  v        v   i v  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_153916959_    692 GAAGACTTAAATTCAAGAGCTTAAACAATAAAAACTTTATAAGAAAACA- 740
                         i?    i     vi       v    v      vii   v         -
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_153916959_    741 -GTAGTAAATCTTTACGATCTTGGTTTTTACAATGGATTCTTAGATATGA 789
                         - v?         iii  i     v  vvi      v             
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_153916959_    790 CACCAAA-GTACAAGCAACAAA-TAAAAAATAGATAAATTGGAATTTATG 837
                                - i            -v                   v  i  v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_153916959_    838 GAAGTTAGAAAATTTTGTGCATCCAAAGACATGATCAA-AAAGTGAAAA- 885
                         i  i   i   v        v  v  i    iv     -          -
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_153916959_    886 ----CTCAGGACAATGGCAGAAAATATTTGCAAATCCTATGT---ATAAG 928
                         ---- i  v- v     v                  v   i ---     
  L1M4_orf2#LINE/    699 ACAACCCAC-AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_153916959_    929 AGTCTAGTATGCAAAATATATAAAGAACACTGAAAAC-----AACAAAAA 973
                         i v  v    v  i              v  v v   -----  i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_153916959_    974 C-CAAACAGCACAATTCAAAAATGGGCAAAGGACCTAAATAGAAATTT-T 1021
                         v-    i i v     ?                ii i      v    - 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_153916959_   1022 CCAAAGAAGACCTACAAATTGCGAAGAAGCACATGAAAAGATGCTTGACG 1071
                                   iv       v  v  v                   ii  i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_153916959_   1072 TTACTAGTCAC 1082
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.00 (50 / 50)
Gap_init rate = 0.02 (12 / 610), avg. gap size = 2.42 (29 / 12)  


3079 27.16 1.11 0.44  chrX_153942057_153946341.rev     2893  3794 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153942057_   2893 TGGAAACACATCCCATGCTTATGGATGGGTAGAATCAATGTTGTGAAAAT 2942
                               v i        i i      v  v   v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153942057_   2943 GACCATACTGCCAAAAGCAATCTGCAAGTTCAATGCAATTCCCATCAAAA 2992
                          i v     v  v   vii    i  ii     i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153942057_   2993 TGCTACCATCATTCTTCACAGAACCAGAAAAAA-AATCCAAAAATTCATA 3041
                          v i v vv v  i  ii     viv  v  iv-i    v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_153942057_   3042 TGGAACCAAAAAAAGAGCCTGCATACCCAAAACAAGACCAAGCAAAAAGA 3091
                              viiv  ii-  v  v v   v         vviii iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_153942057_   3092 ACAAATCTGGAAGCATCACATTACCTGACTTCAAACTATACTATAAGGCC 3141
                              vi    i vv     i v  ii i      viv     i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_153942057_   3142 ATAGTCACCAAAACAGCATGGTACTGGTATAAAAATACATGCATAGACCA 3191
                          i   v i   i    ii         i    ii   v iii     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_153942057_   3192 ATGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATGCTTACAGCCAAC 3241
                               i     v    ii           v   v iii   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_153942057_   3242 TGATCTTTGACAAAGCAAATAAAAACATCAAGTGGGGAAAGGACAACCTT 3291
                             i  i     i vvivi  i v   iv i         i i ii   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_153942057_   3292 TTCAACAAATGGTGCTGGGATAACTGGCTAGCCACATGTAGGAGAATGAA 3341
                                             i      v  ?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_153942057_   3342 ACTGGATCCTCCTCTCTCATCTTATATAAAAATCAACGCAAGATGGATCA 3391
                         ii    i  iivi   v  i v    i      i   v   i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_153942057_   3392 AAGACTTACACCTAGGACCTGAGTCTATAAAACCTCTAGAAGATAATGTC 3441
                         ?    i  v iv  i  v  i iv         iii       v  ii v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_153942057_   3442 AGAAAAACCCTTCTAGACCTCAGCTTAAGGAAGGATTTCATGACCAAGAG 3491
                         i ?iv  vi    vv     ii v   i v  v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chrX_153942057_   3492 CCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATCA 3541
                         v         v v    i    iv   i   i   iv v      v    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chrX_153942057_   3542 AA-TGAAAGAGCTTTCCAATGG--CAAAAGGAACAGTCAGTAGAGTAAAC 3588
                           - v   i -    i--i  v--    i iv  vi   iv i   i  v
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTT--GTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_153942057_   3589 AGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAA 3638
                                       i           v  ii   vii   i      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_153942057_   3639 AGGACTAACATCCAGAATCTACAATGAACTCAAACGAATTATCAAGAAAA 3688
                         i     vii         v  i  v      vv  i v i vi  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_153942057_   3689 A---AAAT--CCCA-TCAAAAAGTGGTCTAGGGACATGAATAGACAATTC 3732
                          ---    --    - i?    i   v v i   iv          v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_153942057_   3733 TCAAAAGAAGATATACAAATGGACAACAAACATATGGAAAAATGCTCAAC 3782
                           v                   v   i  i  i   i   i         
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_153942057_   3783 ATCACTAATTAT 3794
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (146 / 95)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3118 27.75 0.55 0.55  chrX_153949648_153955812.rev     4767  5674 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153949648_   4767 TGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATTGTGAAAAC 4816
                              ii i  i     i     i  v      v i        v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153949648_   4817 GGCCATACTGCCCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 4866
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153949648_   4867 TACCAATGACTTTCTCCACAGAA-TTGGAAAAAACTACTTC-AAAGTTCA 4914
                          v   iivi i  i iii     -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_153949648_   4915 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4964
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_153949648_   4965 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 5014
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_153949648_   5015 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5064
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_153949648_   5065 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACACATCTGCAACT 5112
                                i    i--    i  --        vv   i    i iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_153949648_   5113 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGGTTCC 5162
                          vi    i  i     ivv  v   i v  vvv           ii vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_153949648_   5163 CTATCTAATAAATGGTGTGGGGAAAACTGGCTAGCCACATGGAGAAAGCT 5212
                           v ii  i        iv    v      v  ?       v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_153949648_   5213 GAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTAAAGATGGA 5262
                            ii    i    v   i     v     v        i v  i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_153949648_   5263 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5312
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_153949648_   5313 CTAGGCA-ATACCATTCAGGACATAGGCATGGGTAAGGACTTCATGTCTA 5361
                         v    ?i- v i -   iv   v v  vv i  i  v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_153949648_   5362 AAACACCAAAAGCAATGGCAACAGAAGCCTAAATTGACAAATGGGATCTA 5411
                         vi            vvi      i   vvv    v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_153949648_   5412 ATTAAACCAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGAA 5461
                           i   viv  i i   i   i vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_153949648_   5462 CAGGCAACCTACAGAATGGGAGAAAATTTTTGTAATCTACTCATCTGACA 5511
                         v  i     i                 v    i  vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_153949648_   5512 AAGGGCTAATATCCAGAATCTAGAATGAACTCAAACAAATTTACAAGACA 5561
                          i  i  vi          v  v  v      vv    v iv i  v v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_153949648_   5562 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5611
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_153949648_   5612 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAGAAAATGCTCAT 5661
                            v        i  vi viii     v ii       i  i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_153949648_   5662 CATTACTGGTCAT 5674
                            i ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (147 / 101)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2816 26.10 1.86 2.30  chrX_153981949_153987323.rev     4029  4940 (435)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153981949_   4029 TGGAAAAACATTCCATGCTCATGGATAGGAGGAATCAATATCGTGAAAAT 4078
                               i i  i     i        v   i  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153981949_   4079 GGCCATACTGCCCAAAGTAATTTATAGATTTGATGCTATTCCCATTAAGC 4128
                            v     v      v i  i  i     ii i  v  i  i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153981949_   4129 TACCATTGACATTCTTCACA-AAATTAGAAAAAACT-ATTTTAAAATTCA 4176
                          v   vivi v  i  ii  -     i-- v  i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_153981949_   4177 TATCGAATCAAAAAAGAGCCCATATAGCCAAGAAAATCCTAAGCAAAGAA 4226
                            v   viiv  ii  v  viv        i v    i i i-      
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAA 197

  chrX_153981949_   4227 --ACAAAGCTGGAGGCATCATACTACCTGACTTCAAA--CTACAGTACAA 4272
                         --      i      vv   i   v  ii i      --i   --     
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAA 245

  chrX_153981949_   4273 GGTTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATACATAG 4322
                         i i        i   i    ii         i iv ii i   i i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_153981949_   4323 ACCAATGGAACAGAATAAAGATCTCAGAAATAAAACTGCACACCTACAAC 4372
                          i        i     vi   vii          v iii   ii  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_153981949_   4373 CATCTGATCTTTTACAAACCTGACAAAAACAAGCAATGGGGAAAGGGTTC 4422
                           vi    i  iv    ivv  v   i v  vv            ii vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_153981949_   4423 CCCATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAAT 4472
                         i iv  i  i              v      v  ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_153981949_   4473 TGAAACTGGACCCTT-CCTTACACTTTTTACAAAAATTAACTCAAAATGG 4521
                             ii       i -   i    iv v                      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_153981949_   4522 ATAAAAGACTTAAATATAAAACCCAAAACTATAAAAACCCTAGAAGGAAA 4571
                           v ?    i     i   i v i            vi i      i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_153981949_   4572 TCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTCATGACG 4620
                         iv    ?i- v i -   iv   v v  vv i     v i    v iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_153981949_   4621 AAAATGTCAAAAGCAATCGCAACAAAAGCAAACATTGATAAATGGGGTCT 4670
                          vi iii        vvv          v   v  v       v  iii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_153981949_   4671 AATTAAACTAAAGACCTTCTGCACAGCAAAAGAAACTATCATCAGAATGA 4720
                         v  i   v v  i v   i  ii vv    i  v       vv i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_153981949_   4721 ACAGTCCACCTACAAAATGGGAGAAAATTTTTGCAAGCTATCCATCTGAC 4770
                          v  v v   i   i             v       iii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_153981949_   4771 AAAGGTCTAATATCCAGAATCTACAAGGAACT--TA-AATTTA-CAAGAA 4816
                           i  v  vi          v  i  i     --  -  i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_153981949_   4817 AAA-AGAAACAACCCCATAAAAAATTGGGCAAAGGACATGAACAGACACT 4865
                            - v   i     v  v?    v           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_153981949_   4866 TCTCAAAAGAA--TGT-CAAA-AGCAATTTTATATGTTGTGGACAACATA 4911
                             v      -- i -    -i  v ----   ---------- i  i 
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCA----ATA----------AGCACA 880

  chrX_153981949_   4912 TAAAAAAAAAGCTCACCATCACTGATTGT 4940
                          i    i v-     v     ????????
  L1M4_orf2#LINE/    881 TGAAAAGAT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (142 / 92)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.90 (38 / 20)  


3268 27.92 0.33 0.11  chrX_153989108_153995502     4997  5902 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_153989108_   4997 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATTGTGAAAAT 5046
                              ii i  i     i      i v      v i i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_153989108_   5047 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5096
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_153989108_   5097 TACCAATGACTTTCTTCACAGAATTGGAAAAA---ATTTTAAAGTTCATA 5143
                          v   iivi i  i  ii     v v  v  i---  ii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_153989108_   5144 TGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAA 5193
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_153989108_   5194 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 5243
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_153989108_   5244 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5293
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_153989108_   5294 TGGAATGGAACAGAGCTCTCAGAAATAACGCCGCATATCTACAACTATCT 5343
                               i   iv   vvii         vv  ii i  i  iiiii vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_153989108_   5344 GATCTTTGACAAACCTGAGAAAAACAAGCAGTGGGGAAAGGATTACCTAT 5393
                            i  i     ivv  vv  i v  vv  i         i  vii  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_153989108_   5394 TTAATAAATGGTGCCGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5443
                          i  i         i    v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_153989108_   5444 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAGTAA 5493
                         i    i    v   i     v              i    i     vi ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_153989108_   5494 AGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 5543
                             i    i  v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_153989108_   5544 GCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACA 5593
                          ?i v viv   iv   v v  vv i     v ii   v ivv  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_153989108_   5594 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAA 5643
                                  vvi          vv     v  i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_153989108_   5644 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 5693
                          v v  i i   i  ii vv    i  v    i  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_153989108_   5694 AACCTACAAAATGGGAGAAAATTCTCACAACCTACTCATCTGACAAAGGG 5743
                             i   i             vi ii   vii ivi      i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_153989108_   5744 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAATAAAAAATC 5793
                           vi          v  i  v      vv    v iv i        iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_153989108_   5794 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 5843
                            i     v  i?    i     i     iv    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_153989108_   5844 AAGAAGACATTTATGCAGCCAACAGACACATGAAAAAAATGCTCACCATC 5893
                                i  vi viii     i ii          i -      v    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATC 899

  chrX_153989108_   5894 ACTAGCCAT 5902
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.52 (150 / 99)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


4090 15.09 0.97 12.56  chrX_154059118_154063536.rev     2913  3939 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154059118_   2913 TGGAATGATATCCATCTTGTGCTCATGGATTGAAAGACTTAATTTTAATA 2962
                              v       ----ii  i          i          v  iv  
  L1M4_orf2#LINE/      1 TGGAAAGATATCC----CATGTTCATGGATTGGAAGACTTAATATTGTTA 46

  chrX_154059118_   2963 AGACAGCAACACTCTCCAAATTGATCTACAGAGTCAAATCAATACCTATT 3012
                            ii    i    i                 v    vv    v     i
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chrX_154059118_   3013 AGCATTCCAACTGCCTTATTTGCAGAAACTGATAAGCTGTTCTTAAAATT 3062
                          iv  i   i       v          i   i      v  i       
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_154059118_   3063 CATATGAAATTGCAAAGGGCTCCAAATAACCAAAACAATCTTTGAAAAGA 3112
                               i  v     i  i i vi    i             vi      
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_154059118_   3113 TTGGATCCTCCACAGTAGGAGGACTCACACTTTCTGATTTCAGAACTTTC 3162
                         --i  ----v  v   v               i ii      i     v 
  L1M4_orf2#LINE/    197 --AGA----ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chrX_154059118_   3163 TACAAAGCTACAACAGTCAAGAGAGTGTCATACCAGCATAAGGGCAGACA 3212
                                     ii i      v     vi   ii        ii     
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chrX_154059118_   3213 TATAGACCAATGTGTATTGACCATTTCATTTCCTCTTCTGGGAATTGTCT 3262
                               i     -----------------------------    -----
  L1M4_orf2#LINE/    291 TATAGATCAATG-----------------------------GAAT----- 306

  chrX_154059118_   3263 CTTTATATACTTTGTATTTTTTATGTGTAATCTTTTATCATTGCCTTACT 3312
                         --------------------------------------------------
  L1M4_orf2#LINE/    307 -------------------------------------------------- 306

  chrX_154059118_   3313 GTTTTAAAACAAATCAGCTTTATTAACATAGAAATAGAAAGTCCAAAAAT 3362
                         -----------------------------    v -  i      i    
  L1M4_orf2#LINE/    307 -----------------------------AGAATT-GAGAGTCCAGAAAT 326

  chrX_154059118_   3363 ACATCCATACATCCATGGTCAATTGATTTTC--CA-GAGTGTCAAAATCA 3409
                          v i        ii                 --  - i   i   i i  
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chrX_154059118_   3410 TTCCATAGAGAAAGAATAGTATCCTCAATAGA--GTGCTGGGATAGCTGG 3457
                            v  i i           v ii    i i --         i i    
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chrX_154059118_   3458 ATATCCACATGCAAAGGAATGAATTTGAACCCCTTCCTCACACCATGCAT 3507
                            ?           i       v   i      v           ii i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chrX_154059118_   3508 AAAAACGAACACAAAATGGATCATAGACCTAAATGAATGAACTACAACTA 3557
                              iv   v            ?           v v  i   v     
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chrX_154059118_   3558 TAAAACTCTTAGAAGAAAGAAT--GAGTAAACCTTCATGACCTTGGATTG 3605
                                           iv  -- ?     i    i         i  i
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chrX_154059118_   3606 GGCAAAGTATTCTTAGACATGACACCAGAAGCATGAGCAACAAAATAGAA 3655
                              v vv        i         i     ii          v i  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chrX_154059118_   3656 ACTCGATAAATTATACTTCTTAAAAATCTAA---CTTTGTTTTTCAAAGG 3702
                          v v        iv     v v     iv  ---i     vi        
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chrX_154059118_   3703 ACACCCTCAAGAAAGTGAAAAAAAAGAACACACTGAATTGGAGAAAATAT 3752
                             iv               i v --  v   v    v           
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACA--ACCCACAGAATGGGAGAAAATAT 724

  chrX_154059118_   3753 TTGCAAATCATATATGTGATAAAGGACTTGTGTCTAGCATATATAAAGAA 3802
                                        v      i        i  i  v            
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chrX_154059118_   3803 CTCTTATAACTCAATAATACAAAGACTAGTAATCCAGTTTAAAAATGGGC 3852
                               i            v      v i   i   i  ?          
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chrX_154059118_   3853 AAAAGATCTAAGTCAATATTTTTCCAAGGAAGATACACAAATGGCCAATA 3902
                            i   i i i vi i    i     i       i              
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chrX_154059118_   3903 AGAACGTAAAAATATGCTTGAAGTCATCAGTCGTTAG 3939
                           v  i i    v     ii ---     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAA---CATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (97 / 54)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 10.69 (139 / 13)  


3290 26.32 0.55 0.55  chrX_154092845_154099118.rev     4876  5783 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154092845_   4876 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154092845_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154092845_   4976 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5022
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chrX_154092845_   5023 ATATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAA 5072
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_154092845_   5073 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5122
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_154092845_   5123 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5172
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_154092845_   5173 CAATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATCTACAAC 5220
                                 i    i-- v  i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chrX_154092845_   5221 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5270
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_154092845_   5271 CCTATTTATTAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5320
                         i  v  i vi              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_154092845_   5321 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5370
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_154092845_   5371 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5420
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_154092845_   5421 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCGTGTCTA 5470
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_154092845_   5471 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5520
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_154092845_   5521 ATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTCAA 5570
                           iv  v v  i i   i  ii vv    i  v    i  vv i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_154092845_   5571 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5620
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_154092845_   5621 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAGG 5670
                          i  i  vi          v  i  v      vv    v iv i  v ii
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_154092845_   5671 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5720
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_154092845_   5721 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5770
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_154092845_   5771 CATCACTGGCCAT 5783
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1682 26.71 0.83 0.62  chrX_154111782_154118539        1   483 (6275)    L1M4_orf2#LINE/L1      194   677 (231)  

  chrX_154111782_      1 AAAAGAACAAATCTGGAGGCATCTCATTACCCGACTTCAAACTAGACTAT 50
                          i         vi      vv  v  i v   i i      vivv    i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chrX_154111782_     51 AAGGCTATAGTCACCAAAACAGCATGGTACTGGTATAAAAATGGACACAT 100
                           i    i   v i   i    ii         i    ii  i    i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_154111782_    101 AGACCAATGGAACTGAATACAGAACCCAGAAATATAGCCAAATACTTATA 150
                            i        iv    vv   ii         v v   v i i    i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chrX_154111782_    151 GCCAACTGATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGAC 200
                          i   i    i   i    i vviv   i v   vv i         i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chrX_154111782_    201 ACCCTATTCAACAAATAATGTCGGGATAATTGGCAAGCCACATGTAGAAG 250
                          vi  v          ii  ii    i  i   vv ?       i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chrX_154111782_    251 AATGAAACTGGATCCTCATCTCTCACCTTATACAGAAAT-AATTCAAGAT 299
                               ii    i  ii i   v    v      i    -  i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chrX_154111782_    300 GAATCAAAGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGAA 349
                          i    ?    i     v     v  i    i      v ii        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chrX_154111782_    350 AACATTGGA--AAATCTCTTCTAGACATTGGTTTAGGCAAAGACTTCATG 397
                              v  ?--      --  vv   v    v        v ii   v i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chrX_154111782_    398 ACCAAGAACCCAAAAGCAAATGCAATACAAACAAAGCTAAATAGATGGGA 447
                         ivi v  vv         v v    i v  iv   iv  i   i  v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_154111782_    448 ATTAATTAAA-TGAAAAAGCTTCTGTATAGCAAAAGA 483
                         v  v  i   - v     -   i   iivv    i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

Transitions / transversions = 1.42 (74 / 52)
Gap_init rate = 0.01 (5 / 484), avg. gap size = 1.40 (7 / 5)  

2562 24.12 1.01 9.75  chrX_154111782_154118539     5271  6265 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154111782_   5271 TGGAAAAACATTCCATGCTCATGGATAGGAATAATCAATATCATGAAAAT 5320
                               i i  i     i        v    v v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154111782_   5321 GGCCATGCTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAGC 5370
                            v  i  v      v i  i  i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154111782_   5371 TAC-AATTGCCTTTCTTCACAGAATTGGAATATGTAACAAACCTGCACGT 5419
                          v - ii       i  -i     -------  - i    i --------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAA-------AT-TGACAAGC-------- 133

  chrX_154111782_   5420 TGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATTTTTAAAAACC 5469
                         --------  - i       ------------------------------
  L1M4_orf2#LINE/    134 --------TG-ATCCTAAAA------------------------------ 144

  chrX_154111782_   5470 TACTTTAAATTTCATATGGAACCAATAAAGAGCCTGTATAGCCAAAACAA 5519
                         ----------           viivv ii  v  v v             
  L1M4_orf2#LINE/    145 ----------TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chrX_154111782_   5520 TCCAAAGCAAAAACAAAAAACAAAAACAAACAAACAAACAAAAAACCAAA 5569
                           i----------ii     v  i      --------------------
  L1M4_orf2#LINE/    185 TCT----------TGAAAAAGAAGAACAAA-------------------- 204

  chrX_154111782_   5570 GCTGGAGACATCATGCTACCTGACTTCAAACTATACTACAAGGCTACAGT 5619
                          i     ivv   ii  v  ii i      viv        i        
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chrX_154111782_   5620 AACCAAAACAGCATGGTACTAGTACCAAAACACATATATAGACCAATGGA 5669
                           i   i    ii       i i iv ii i v i       i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chrX_154111782_   5670 ACATAACAGAGACCTCAGATATAACACCACACATCTACAACCATCTGATC 5719
                          i v  iv    vii    v    vv   i    i  iiii  vi    i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chrX_154111782_   5720 TTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGATTC-CCTATTTAA 5768
                           i     ivv  v   i v  vvv            v v-i  v  i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chrX_154111782_   5769 TAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACGGAATCTGG 5818
                         i              v      v  ?   i     i  i vv   vi   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chrX_154111782_   5819 ACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAAAAAC 5868
                               v   i     v                   i      i ? i  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chrX_154111782_   5869 TTAAACATAAGACCTAAAACCATAAAAACCCTAGAAAAAAACCTAGGCA- 5917
                         i    ii     v       i      vi i     i     v    ?i-
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chrX_154111782_   5918 ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAACAACA 5967
                          v i -   iv   v v  vv i     v ii   v iiv  vi   v  
  L1M4_orf2#LINE/    555 AAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chrX_154111782_   5968 AAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACT 6017
                               vvi          vv     v  i    v   ii v  i   v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chrX_154111782_   6018 AAAGAGCTTCTGCATGGCAAAAGAAACTGTCATCAGAGTGATCAGGCAAC 6067
                         v  i i   i  iiivv    i  v   i   vv i     vv  i    
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chrX_154111782_   6068 CTACAGAATGG-AGAAAATTTTTGCAATCTATCCATCTGACAAGGGGCTA 6116
                          i         -       v       vii  vi      i     i  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chrX_154111782_   6117 ATATCCAGAATCTACAAGGAACTTAAATAAATTTACAAGAAAAAACCAAA 6166
                         i          v  i  i     ivv i  v iv i  v     iv    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chrX_154111782_   6167 CAACCCCATCAAAAAGTGGGTGAAGGATATGAGCG------TCTCAAAAG 6210
                         i     v  i?    i    ii      v   iii------    v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_154111782_   6211 AAGACATTTATGTGGCCAACAATCATATGAATAAAAGCTAATCATCACTG 6260
                             i  vi vi       i  v  i     v i v   v v     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_154111782_   6261 ATCAT 6265
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 7.64 (107 / 14)  


2829 26.04 2.84 3.50  chrX_154130075_154133081.rev     1603  2516 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154130075_   1603 TGAAAACACATCCCATGCTCATGGATCAAAAGAACCAATATTATTAAAAA 1652
                           i   v i        i        iii    vii      i    i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_154130075_   1653 TGACCACACTGCTCAAAGCAATTTACAGATTCAGTGCAGTCTCTATCAAA 1702
                           i v i   v i    vii  i          ii   i  i        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_154130075_   1703 TTACCAACACAATTTTTCACATAA-TTAAAAA----AACTTAAAATTCAT 1747
                         v v   i vvvv     ii  v  -  i v  ---- v i          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_154130075_   1748 ATGAAACCGAAAGAAGAGTCTGAATAGCCAAACCAATCCTAAGCAAAAAG 1797
                            i  vi v   i-  vi v           v     i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_154130075_   1798 AACAAAGCTTGAAGTATT-ACATT--CTGACTTTGAATTATACTACAAGG 1844
                                -   i  v i -   i -- ii i  ii  viv        i 
  L1M4_orf2#LINE/    199 AACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_154130075_   1845 CTATAGTAACCAAAACGTCATGATATTGGTATAAAAATAGACATATAGAC 1894
                            i     i   i  ivii  i  i   i    ii             i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_154130075_   1895 CAACGGAACAGAATAGTGAACCCAGAAATAAA---GTAC--CTATTAACA 1939
                            i    i     v v  ii           ---i   --i   viv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_154130075_   1940 ACTGATCTTCTGCAATATTGACAAAATTAAACAATAGAGAAAGAACACCC 1989
                          i    i   vi   viv  v   i ii vv    i i       i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_154130075_   1990 TCTTCAATATACGGTGCTAGGAAAACTGGCTAGCCATATGCGGAAGAATG 2039
                          i     i v i      i   v      v  ?   i    ii       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_154130075_   2040 AAACTGGACCCCTGTCTCTCACCATATACATGAATTAACTCGAGATGGAT 2089
                           ii         ii   v           vi         i i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_154130075_   2090 TAAAGATTTATACTTTAGACATGAAACTGTAAAAATCCTGTGAGAAAATG 2139
                         i ?   ii  v iv v   vv i     i     v  i ivi      ii
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_154130075_   2140 TAGGAAAAATTCTTCTGGACATTGGCCTGGCTTAGGCAAAGAATTTTTGA 2189
                             ?iv  v     vv   ----- i   v        v iv  i  ii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGAC-----CTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_154130075_   2190 CCAGGTCCTCAAAAGCAAATGCAACACAAACAAAAATAAACAGACGGGAC 2239
                         vi v v vi        v v      v  iv       i i i iv    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_154130075_   2240 T-CAGTTAAGCTAAAAACCTTCCACACAGCAAAAGAAACAATCAACAGAG 2288
                          -  viv  ii       i  i-iii vv    i  v  v     v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_154130075_   2289 TAAA-------CCTACCTAATGAGAAAAAATATTTGCAAATTATGTATCT 2331
                          i  -------  i  vv    i  i               i  i     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_154130075_   2332 AACAAAGG-CTAATATCCAGAATCTACAAGAAACTCCAACAACTCAACAA 2380
                         i i  i  -  vi          v  i  ii     iv         i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_154130075_   2381 CAACAACAACGACAAAAACAAAAACAAAAAACAAGTAACGCCATTAAAAA 2430
                         i  -----------------------   i    i    v v   ?    
  L1M4_orf2#LINE/    792 TAA-----------------------AAAGACAAATAACCCAATTWAAAA 818

  chrX_154130075_   2431 GTAGGCAAAGGGCATGAATGGGTGTTTTTTGAAAGA---CATACAAGTGG 2477
                         i i        iiv     i iii   i iv     ---i      i   
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_154130075_   2478 CCAACAAACATATGAAA-GATGCTCAATATCACTAATTAT 2516
                             i  i  i      -         i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (155 / 79)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.41 (58 / 17)  


3227 27.09 0.55 0.55  chrX_154133365_154135412.rev      650  1557 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154133365_    650 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 699
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154133365_    700 GGCCATACTGCCCAAGGTAATTTATAGACTCAATGCCATCCCCATCAAGC 749
                            v     v     iv i  i  i   i    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154133365_    750 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 797
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_154133365_    798 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 847
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_154133365_    848 AACAAACCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 897
                               vi      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_154133365_    898 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 947
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_154133365_    948 AATGGAACAGAAC--AGAGCCCTCAGAAACAATGCCGCATATCTACAACT 995
                                i    i--    i  --     i  vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_154133365_    996 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 1045
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_154133365_   1046 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1095
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_154133365_   1096 GAAACTGGATCCCTTCCTTACAGCTTATACAAAAATTAATTCAAGATGGA 1145
                            ii    i    v   i   v v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_154133365_   1146 TTAAAGACTTAAATATTAGACCTAAAACCATAAAAATCCTGGAAGAAAAC 1195
                          i ?    i     i v   v       i      v  i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_154133365_   1196 CTAGGCA-ATACCATTCAGGACATAGGCATGAGCAAGGACTTCATGTCTA 1244
                         v    ?i- v i -   iv   v v  vv ii    v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_154133365_   1245 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1294
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_154133365_   1295 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACCACCATCAGAGTGAA 1344
                           i   v v  i i   i  ii vv    i  v  i i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_154133365_   1345 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTTGTCTGACA 1394
                         v  i     i                 v       vii iv i     i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_154133365_   1395 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 1444
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_154133365_   1445 AAAACGAACAACCCCATCAAAAAGTGGGCGAAAGATATGAACAGACACTT 1494
                           i  i  i     v  i?    i     i  i   v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_154133365_   1495 CCCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1544
                          i v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_154133365_   1545 CATCACTGGCCAT 1557
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2909 25.93 1.53 2.19  chrX_154146867_154152633     4375  5288 (479)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154146867_   4375 TGGAAAAACATTCCAAGCTCATGGATAGGAAGAATCAGTATT---AAAAT 4421
                               i i  i   v i        v      v i i    ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154146867_   4422 GGGCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCCATTAAAC 4471
                           vv     v      vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154146867_   4472 TACCATTGACAGTCTTCACAGAACGAGAAAAAAAAAACT-ATTTTAAAAT 4520
                          v   vivi vv i  ii     ----- vvi v  i  -  ii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-----ATTGACAAGCTGATCCTAAAAT 145

  chrX_154146867_   4521 TCATATGGAACCAAAAAACAAAAAAAGCCC-GAATACCGAAGGCAATCCT 4569
                                   ----- vi   iii --   -     v v  ii     i 
  L1M4_orf2#LINE/    146 TCATATGGAA-----ATGCAAGGGA--CCCAGAATAGCCAAAACAATCTT 188

  chrX_154146867_   4570 AAGCAAAAAGGACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTAT 4619
                         i iv  i   i      i      vv   ii  v  ii i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_154146867_   4620 GCTACAAGGCTACAGTAACCCAAACAGCATGGTGCTGGTACAAGAACAGA 4669
                         i      i          i v i    ii    i    i i   i i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_154146867_   4670 CACATAGACAAATGGAACAGAACAGAGAACCGAGAAATGAGACCACACAC 4719
                           i     iv       i    iv    ii v      i iv   i   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_154146867_   4720 CTACAACTAACTGATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAA 4769
                         i  iiiii  i    i        ivv  v   i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_154146867_   4770 AGGATTCCCGGTTCAATAAATGGTGCTGGGATAACTGGCTAGCCATGTGC 4819
                           i  vvi vv     i              i      v  ?   ii   
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_154146867_   4820 AGAAGATGAAAACCGGCTCCCTTGCTTACACTATATACAAAGATTAACTC 4869
                          i    vvi  iii  vi    vv  i    i         i        
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_154146867_   4870 AAGATGGATTAAAGACTGACATGTAAAACCCCCAACTATGAAAACTCTGA 4919
                           i      i ?    iv v      i v ivv      -        v 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTA 537

  chrX_154146867_   4920 -AAGACAACTTAGGC---AATGCCATTCAGGGCATAGGCATGGGCAAAGA 4965
                         -    v   v    ?---   -- -   iv i v v  vv i     v i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_154146867_   4966 TTTCAT-GATGAAGACGCCAAAAGCAATTGCAACAAAAGCAAAAAATTGA 5014
                             v -   - v   i         vvv          -       v  
  L1M4_orf2#LINE/    585 TTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGA 632

  chrX_154146867_   5015 CAAATGGGGTCTAAT-AAAATTAAAGAGCTGTGCACAGTGAAAGAAACTA 5063
                         i    v  iii v  -         i vi v  ii vvii  i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_154146867_   5064 TCAACAGAGTAAACAGACAACCTACAGAATGGGAGAAAATATTTGCAAAC 5113
                             v i   i  v        i                          i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_154146867_   5114 TATGCATCTGACAAAGGTCTAATATCCAGCATCTATAAAGAACTTAAACA 5163
                         i  ii      i  i  v  vi       v  v           ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_154146867_   5164 AAT---TTACAGGAAAACAAACAATCCCATAAAAAAGTGGGAAAAGGACA 5210
                          v --- v i ii  i     i  i  v  v?    i    v      iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_154146867_   5211 TGAACAGACACTTTTCAAGAGGAGACATACATGCAGCCAACAATCATATG 5260
                             i     i  i  v i  i   i     viii     i  v  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_154146867_   5261 AAAAAAAAAGGTCAACATCACTGATCAT 5288
                             i v-- v         ????????
  L1M4_orf2#LINE/    883 AAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (140 / 93)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


3979 19.57 3.20 1.60  chrX_154170117_154173099     1611  2484 (499)    L1M4_orf2#LINE/L1        3   890 (18)  

  chrX_154170117_   1611 GAAAGGCATTTTGTGTTAACGGATTGGGACACTTAATATTGTTAAGATGC 1660
                              ii  iiii    v i       i v                   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_154170117_   1661 CCATAATCTCCAAGGCAATATACAGATTCATCGTGATGCCTGTCAGAATC 1710
                          v   v  i    ivii  v          v  ii  v   i   i    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_154170117_   1711 CAACCTGCCTTCTTTGTAAAAACTGACAAGCTGATCCTAAAATTCATAAG 1760
                          v v       i    i i   i                         v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_154170117_   1761 AAAATGTAAGGGGCTCAGA-TAGCCAAAACAATCTCAGAAAAGAAAAA-- 1807
                         i     i     i i    -               iii       i  --
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_154170117_   1808 -AGTTGAAGGACTCACACTTCCCAATTTCAAAACGTACTACAAAACCGCA 1856
                         -     i                           v         i ii  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_154170117_   1857 GTAATCCGAAAAGGGTGGTACTGCCATCGTGATCGATACATTAGGTCAAT 1906
                               vii v  v         v   viv   v  i i  -  i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT-AGATCAAT 301

  chrX_154170117_   1907 GTTACAGAACTCAGAGTC-AGGAATAAACCCATATATTTATG-TAAAGTT 1954
                          vv i    i v      -  i            i       - v  -  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA-TT 350

  chrX_154170117_   1955 TATTTTCAGTAAGAGTTCCGGCACCCCTCAATGGGTGGAGGGGAAGAATA 2004
                         v      iii   i  v  iiv   vi        ------ i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGG------GAAAGAATA 394

  chrX_154170117_   2005 ATCCCCTCAACAAACTGCGCTGGGACAACTGGATAGCCACATGCAAAAGA 2054
                         i  iii        iv i                 ?              
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_154170117_   2055 AGGCCCCTGGACCCCTACCTCACATCATGTA-AAGAATTAATTCAAAATG 2103
                          v vvvi                 i   i  -  i      i        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_154170117_   2104 GATCACAGATCTAAATGTAAGGGCTGAAACTATAAAACTCTAAGAAGAAA 2153
                              ?   i           i   i               v        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_154170117_   2154 ACGGAGATGTAACTTTGCACGACCTTGGATTAGGCAACAGCTCCTTCAGT 2203
                           iv  i?    v i v ii        i        ii i i   vii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_154170117_   2204 ATGACACCAAAGGCA-AAGCCACA---GATATCTTTTCATTTGGCAAGTT 2249
                                    i   -    v   ---  v ------v v v ii  i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAA------AAATAGATAAATT 638

  chrX_154170117_   2250 GGACTACATCCAAATGTAAATCTTTTGGGCAACAAAGGGCTCTATCCAGA 2299
                              v    v    vv   v      v  vv      i v     v   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_154170117_   2300 AAGTGAA----------------TGGGAGAAA-CATTTGCAAGTCACATA 2332
                                ----------------         -i        i   i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_154170117_   2333 TCTGATAAGAGTCTATTTTCCAGAATATATGAATAAGTTTTAGAAGCCCA 2382
                                  i v  vv v            i  v  v i   v  vi v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_154170117_   2383 CAGCCAAAATACAATCAACCGAATTAAAAAATGGGCAAAGGGCTTGAATA 2432
                         i iiv    v    vi    v    ?               ii       
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_154170117_   2433 GACATTCCTCCAAAGCAGAGGTACAGAGGGCCAAGAAGCACATGAAAAGA 2482
                               i        v   vi    i v      v               
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_154170117_   2483 TG 2484
                           
  L1M4_orf2#LINE/    889 TG 890

Transitions / transversions = 1.39 (97 / 70)
Gap_init rate = 0.01 (13 / 888), avg. gap size = 3.23 (42 / 13)  


2799 26.83 1.88 1.44  chrX_154185683_154188788     1752  2653 (453)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_154185683_   1752 GAAAAACATTCCATGCTCATAGATAAGAGGAATCAATATCATTAAAATGG 1801
                             i i  i     i    i   vi  i  v i     ii    i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_154185683_   1802 CCATACTGCTCAAAACAATTTATAAATTCAATGCTATTCTTATCAAACTA 1851
                          v     v i    vii  i  i i      i  v  i i       v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_154185683_   1852 CCAATGACATTCTCCACAGAACTAGAAAAAACTG-TTTTAAAATTCACAT 1900
                            iivi v  i iii     v v  v  i-   - ii         i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATAT 151

  chrX_154185683_   1901 GGAATAAAAAAGGAGCCCA-AATAGCCAAGGCAATCCTAAGCAAAAATAA 1949
                             - viv    ii    -         ii     i i iv  i  v  
  L1M4_orf2#LINE/    152 GGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_154185683_   1950 CAAAGCTAGAGGCATCAGGTGACCTGACTTCAAACTATACTGTAGGGCTA 1999
                              i i    vv   viivv  ii i      viv    ii ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_154185683_   2000 CAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACAAA 2049
                               i   i    ii         i i  ii i     i     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_154185683_   2050 TGGAACAGAATAGAGAGCCCAGAAATAAGGTCACACACCTACAATCATCT 2099
                              i     v     i          ivi  i   ii  iii   vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_154185683_   2100 GATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTTCCTAT 2149
                            i  i     ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_154185683_   2150 TCAATAAATGGTGTTAAGATAACTGGCTAACCATATGCAAAAGATTGAAA 2199
                             i        i ii  i      v  ?   i          v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_154185683_   2200 CTGAACCCCTTCCTTGCATCATACACAAAAAATAACTCAAGATGGATTAA 2249
                         i  i      v   ii  i    i       v        i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_154185683_   2250 AGACATAAATGTAAAACCCCAAACTATGAAAACCCTGGAAGACAACCTAG 2299
                             v         i v iv       i   vi i i     v   v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chrX_154185683_   2300 GCA-ATATCATCCTGGACGTAGGAACTGGCAA-GATTTCAT-GATGAAGA 2346
                          ?i- v   v  v  -  v v  iviv     - i    v -   - v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGA 598

  chrX_154185683_   2347 CAGCCAAAGCAATGGTGAAAAAAAAGCAGAAAATTGACAAATGGGATCTA 2396
                           v v      vvi i--  v     - i     v  i    v   ii v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGC--AACAAAAG-AAAAAATAGATAAATTGGACTTC 645

  chrX_154185683_   2397 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTAAA 2446
                           i   v v  i i   i  ii vv    i  v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_154185683_   2447 CAGACAACTTAAAGAATGGGAGAAAATATTTGTAAACTATGCATCTGACA 2496
                         v       ii v                    i   ii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_154185683_   2497 AAGGTCTAATATCCAACATCTATAAGGAACTTAAGCAGATTTACAAGAAA 2546
                          i  v  vi      iv  v     i     ivvi  - i --   v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACA-ACT--CAATAAT 792

  chrX_154185683_   2547 AAAAAGGC------CATAAT--AAAGA-GGGCAAAGGACATGAATGGACA 2587
                               i ------ vi   --   i -          iv     i    
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_154185683_   2588 CTTTTCAAAAGATGATATATGCAGGGAGCCGA-AGGCCCCGTGGGACG-T 2635
                         i  i  v     v      --  iivi   i - i  v -i  ii v - 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATA--CAAATGGCCAATAAGCAC-ATGAAAAGAT 889

  chrX_154185683_   2636 GACCAAC-TCAGCATTCCA 2653
                          vi    -   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (151 / 88)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 1.43 (30 / 21)  


3042 24.59 1.65 1.98  chrX_154199442_154205098      492  1402 (4255)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chrX_154199442_   1402 TGGTAAAACACCCCATGCTTATGAATTGAAATAATTAATATTGTTAAAAT 1353
                            v  i i i      i i   i    i  v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_154199442_   1352 GGCCATACTGACCAAAGAAATTTATAGATTCAATGCTATTCCTAGCAAAT 1303
                            v     vv     vvi  i  i        i  v  i    v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_154199442_   1302 GGCCAACATCATTTTTCACAGAATTAGGAAAAAACT-ATTCTAAAATTCA 1254
                         vv   i vv v     ii     v v -- v  i  -  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chrX_154199442_   1253 TATGCAACCAAAAAAGAGCATGAATCACCAAAGTAACCCTAAGCAAAAAG 1204
                             v  viiv  ii  v vv    vi     ii  i i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chrX_154199442_   1203 AACAAAGCTGGAGGCATCACACTACCTGACCT-GAAACTATACTACAAGG 1155
                                i      vv       v  ii ii -i     -        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

C chrX_154199442_   1154 CTACAGTAACCAAAACAGCATGGTACTGGCACAAAAACAGACACATAGAC 1105
                                  i   i    ii           i  ii i     i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chrX_154199442_   1104 CAATGAAACAGGATAGAGAACTTAGAAATAAGGTCACACACCTACAA-CA 1056
                              i  i  i  v    iiii        ivi  i   ii  iii-  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

C chrX_154199442_   1055 ACTTGATCTTTGACAAACTCAACAATGA--A---AATGGGAAAAGGA--G 1013
                          -     i  i     ivviiv   -  -- ---      i    i -- 
  L1M4_orf2#LINE/    348 A-TTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAG 395

C chrX_154199442_   1012 TCCTTATTTAATAAATGGTGC-AGGATAACAGGCTATCCATATACAGAAG 964
                           i  -- i  i         -i   i   v  v  ?   i  i  i   
  L1M4_orf2#LINE/    396 TCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

C chrX_154199442_    963 ATTGAAACTGGACCCCTTCCTGTCACCATATACAAAATTCAACTCAAGAT 914
                          v    ii         v   vv              v i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

C chrX_154199442_    913 GGATTAAAGACTTAAATGTAAGACCCAAAACAACAAAAACCCTAGAAGAA 864
                             i ?    i           v i     v i    vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

C chrX_154199442_    863 AAGCTAGGAA-ACATCATTCTGAACATTGGCCTTGGCAAACAATTTAT-- 817
                           vv    ?i- v   -   vvi  v    vi v     -iii   v --
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA 591

C chrX_154199442_    816 GACTAAGTCCCCAAAAGTATTTGCAACAAAAACAAAAATTGACAAGTGGG 767
                           -  v v v       i ivv         iv      v  i  i v  
  L1M4_orf2#LINE/    592 GA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

C chrX_154199442_    766 ACCTAATTAAACTAAAGAGCTTGTGTACAGCAAAAGAAACTATCAACAGA 717
                           i v  i   v v  i i   v   i vv    i  v        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

C chrX_154199442_    716 ATACACAGACAAACTACAAAATGGGAGAAAATATTCTCAAACTGTACATC 667
                         i iv v      v i   i                iv    iii  i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

C chrX_154199442_    666 TGACAAAGGTCTTATATCCAGAATCCATAATGAACTTAAACAAATCATCA 617
                            i  i  v   i          vi    v     ivv    v   vi 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

C chrX_154199442_    616 AGTAAAAAACAAATAACCTCATT-AAAAATGGGCAAAGAACATGAACAGA 568
                          vv    i          iv   -              i iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

C chrX_154199442_    567 CATTTCTCAAAAGAAGACATATGGCTGACATGTGGCTGACAAGCATATGA 518
                                 v        i   -------  vi    ii i     i    
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATA-------CAAATGGCCAATAAGCACATGA 883

C chrX_154199442_    517 AAAAAATGCTCATTATCACTAATGAT 492
                            i -      vi    ????????
  L1M4_orf2#LINE/    884 AAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.65 (33 / 20)  

2160 23.18 7.46 2.92  chrX_154199442_154205098     4548  5164 (493)    L1M4_orf2#LINE/L1      264   908 (0)  

  chrX_154199442_   4548 AGTATGGTAAAAGCATGAAAATAGACACATGGACCAATGAAA-AAAATGG 4596
                            i     vvi    i ii       i  i  i     i  - i   v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chrX_154199442_   4597 AAAGCCCAAAAATAAACCCATGCATATATGGTCAACTAATCTTTGACAAA 4646
                          i  i   i            i   v         i i  i  i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chrX_154199442_   4647 ATCTCTAAGAACACATATTGGAGAAAAGATAGTCTTTTCAATAAATGGTA 4696
                         iviv i    v  ivi v   i    ii             i       i
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chrX_154199442_   4697 TTGGAAACACTAGATATCCACTTGCAAAAGG-TGAAGTTGGATCCCTA-- 4743
                         i   i vv   i    ?    v        i-          i     --
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chrX_154199442_   4744 TTGTATTACCTACAAAAAATCAATTCAAA---GATC-------------- 4776
                          iii ii iv        - i  i     ---    --------------
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chrX_154199442_   4777 --------------TGAAACTCCTAGAAGAAAACAC-GGAGGAAAGCTCT 4811
                         -------------- i      i            i-  ? v   v  ii
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chrX_154199442_   4812 ATAACATTGGTCTCAGCAATTATTTTTTGGATTTGGTGCCAAAAACATAG 4861
                         i i  v    vi vi     vi   i  i   v  iii      i  i i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chrX_154199442_   4862 ACAACAAAGGCAAAAATAAATGACTGGTACTATATTAAA-CTAAAAAGTT 4910
                         i       i v       i  i v v v   vi  i   -i      v  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chrX_154199442_   4911 T----CTGCAAAGCAAACAATCAAA----TGAAAAGGCCACATATGGAAT 4952
                          ----  v     v v  v     i----       i v  vi ii    
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chrX_154199442_   4953 GGGAGAAAATATTTGTAAGCCACATGTCCAATAAGGGGGTAATATCCA-A 5001
                                        i  ii  i  i  ii       iv vi      - 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chrX_154199442_   5002 ATATATAAGGAACTCATACAACTCAACAGCAAATAAGTAAATAAATAATA 5051
                                 i      v          i ii   -   -------------
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAA-AAG------------- 798

  chrX_154199442_   5052 ATAACAAATAACCTGATTAAACAATGGGCAAAGGGCCTGAATGGATGTGT 5101
                         ---          ii   ?  v            iii     i  ii v 
  L1M4_orf2#LINE/    799 ---ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_154199442_   5102 TTCCATAGAAGACCTGCAAATTGCCAATAGGTATATGAAAAGATGCTCAA 5151
                         i    v      iv i     v       i i i                
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_154199442_   5152 TATCACTAATTAT 5164
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (100 / 40)
Gap_init rate = 0.02 (13 / 645), avg. gap size = 4.92 (64 / 13)  


3197 27.09 0.55 0.55  chrX_154214840_154221241     5002  5909 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154214840_   5002 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5051
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154214840_   5052 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5101
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154214840_   5102 TAACAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5149
                          vv  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_154214840_   5150 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5199
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_154214840_   5200 AACAAACCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5249
                               vi      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_154214840_   5250 TACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5299
                                 iv  i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_154214840_   5300 AATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATCTACAACT 5347
                                i    i-- v  i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_154214840_   5348 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCC 5397
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_154214840_   5398 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5447
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_154214840_   5448 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5497
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_154214840_   5498 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5547
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_154214840_   5548 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5597
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_154214840_   5598 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5647
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_154214840_   5648 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAACATCAGAGTGAAC 5697
                          iv  v v  i i   i  ii vv    i  v    v  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_154214840_   5698 AGGCAACCTACAGA-TGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5746
                           i     i     -           v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_154214840_   5747 AGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAA 5796
                         i  i  vi          v  i         vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_154214840_   5797 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5846
                          i -    i     v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    797 AGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_154214840_   5847 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCTT 5896
                            v        i  vi viii     i ii          i      vv
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_154214840_   5897 CATCACTGGTCAT 5909
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3979 19.57 3.20 1.60  chrX_154254333_154257315.rev     1613  2486 (497)    L1M4_orf2#LINE/L1        3   890 (18)  

  chrX_154254333_   1613 GAAAGGCATTTTGTGTTAACGGATTGGGACACTTAATATTGTTAAGATGC 1662
                              ii  iiii    v i       i v                   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chrX_154254333_   1663 CCATAATCTCCAAGGCAATATACAGATTCATCGTGATGCCTGTCAGAATC 1712
                          v   v  i    ivii  v          v  ii  v   i   i    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chrX_154254333_   1713 CAACCTGCCTTCTTTGTAAAAACTGACAAGCTGATCCTAAAATTCATAAG 1762
                          v v       i    i i   i                         v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chrX_154254333_   1763 AAAATGTAAGGGGCTCAGA-TAGCCAAAACAATCTCAGAAAAGAAAAA-- 1809
                         i     i     i i    -               iii       i  --
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chrX_154254333_   1810 -AGTTGAAGGACTCACACTTCCCAATTTCAAAACGTACTACAAAACCGCA 1858
                         -     i                           v         i ii  
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chrX_154254333_   1859 GTAATCCGAAAAGGGTGGTACTGCCATCGTGATCGATACATTAGGTCAAT 1908
                               vii v  v         v   viv   v  i i  -  i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT-AGATCAAT 301

  chrX_154254333_   1909 GTTACAGAACTCAGAGTC-AGGAATAAACCCATATATTTATG-TAAAGTT 1956
                          vv i    i v      -  i            i       - v  -  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA-TT 350

  chrX_154254333_   1957 TATTTTCAGTAAGAGTTCCGGCACCCCTCAATGGGTGGAGGGGAAGAATA 2006
                         v      iii   i  v  iiv   vi        ------ i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGG------GAAAGAATA 394

  chrX_154254333_   2007 ATCCCCTCAACAAACTGCGCTGGGACAACTGGATAGCCACATGCAAAAGA 2056
                         i  iii        iv i                 ?              
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_154254333_   2057 AGGCCCCTGGACCCCTACCTCACATCATGTA-AAGAATTAATTCAAAATG 2105
                          v vvvi                 i   i  -  i      i        
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_154254333_   2106 GATCACAGATCTAAATGTAAGGGCTGAAACTATAAAACTCTAAGAAGAAA 2155
                              ?   i           i   i               v        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_154254333_   2156 ACGGAGATGTAACTTTGCACGACCTTGGATTAGGCAACAGCTCCTTCAGT 2205
                           iv  i?    v i v ii        i        ii i i   vii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_154254333_   2206 ATGACACCAAAGGCA-AAGCCACA---GATATCTTTTCATTTGGCAAGTT 2251
                                    i   -    v   ---  v ------v v v ii  i  
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAA------AAATAGATAAATT 638

  chrX_154254333_   2252 GGACTACATCCAAATGTAAATCTTTTGGGCAACAAAGGGCTCTATCCAGA 2301
                              v    v    vv   v      v  vv      i v     v   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_154254333_   2302 AAGTGAA----------------TGGGAGAAA-CATTTGCAAGTCACATA 2334
                                ----------------         -i        i   i   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_154254333_   2335 TCTGATAAGAGTCTATTTTCCAGAATATATGAATAAGTTTTAGAAGCCCA 2384
                                  i v  vv v            i  v  v i   v  vi v 
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_154254333_   2385 CAGCCAAAATACAATCAACCGAATTAAAAAATGGGCAAAGGGCTTGAATA 2434
                         i iiv    v    vi    v    ?               ii       
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_154254333_   2435 GACATTCCTCCAAAGCAGAGGTACAGAGGGCCAAGAAGCACATGAAAAGA 2484
                               i        v   vi    i v      v               
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_154254333_   2485 TG 2486
                           
  L1M4_orf2#LINE/    889 TG 890

Transitions / transversions = 1.39 (97 / 70)
Gap_init rate = 0.01 (13 / 888), avg. gap size = 3.23 (42 / 13)  


2899 26.04 1.53 2.19  chrX_154274985_154280765.rev     4377  5290 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154274985_   4377 TGGAAAAACATTCCAAGCTCATGGATAGGAAGAATCAGTATT---AAAAT 4423
                               i i  i   v i        v      v i i    ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154274985_   4424 GGGCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCCATTAAAC 4473
                           vv     v      vii  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154274985_   4474 TACCATTGACAGTCTTCACAGAACGAGAAAAAAAAAACT-ATTTTAAAAT 4522
                          v   vivi vv i  ii     ----- vvi v  i  -  ii      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-----ATTGACAAGCTGATCCTAAAAT 145

  chrX_154274985_   4523 TCATATGGAACCAAAAAACAAAAAAAGCCC-GAATACCGAAGGCAATCCT 4571
                                   ----- vi   iii --   -     v v  ii     i 
  L1M4_orf2#LINE/    146 TCATATGGAA-----ATGCAAGGGA--CCCAGAATAGCCAAAACAATCTT 188

  chrX_154274985_   4572 AAGCAAAAAGGACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTAT 4621
                         i iv  i   i      i      vv   ii  v  ii i      viv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chrX_154274985_   4622 GCTACAAGGCTACAGTAACCCAAACAGCATGGTGCTGGTACAAGAACAGA 4671
                         i      i          i v i    ii    i    i i   i i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chrX_154274985_   4672 CACATAGACAAATGGAACAGAACAGAGAACCGAGAAATGAGACCACACAC 4721
                           i     iv       i    iv    ii v      i iv   i   i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_154274985_   4722 CTACAACTAACTGATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAA 4771
                         i  iiiii  i    i        ivv  v   i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_154274985_   4772 AGGATTCCCGGTTCAATAAATGGTGCTGGGATAACTGGCTAGCCATGTGC 4821
                           i  vvi vv     i              i      v  ?   ii   
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_154274985_   4822 AGAAGATGAAAACCGGCTCCCTTGCTTACACTATATACAAAGATTGACTC 4871
                          i    vvi  iii  vi    vv  i    i         i   i    
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_154274985_   4872 AAGATGGATTAAAGACTGACATGTAAAACCCCCAACTATGAAAACTCTGA 4921
                           i      i ?    iv v      i v ivv      -        v 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTA 537

  chrX_154274985_   4922 -AAGACAACTTAGGC---AATGCCATTCAGGGCATAGGCATGGGCAAAGA 4967
                         -    v   v    ?---   -- -   iv i v v  vv i     v i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGG 584

  chrX_154274985_   4968 TTTCAT-GATGAAGACGCCAAAAGCAATTGCAACAAAAGCAAAAAATTGA 5016
                             v -   - v   i         vvv          -       v  
  L1M4_orf2#LINE/    585 TTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGA 632

  chrX_154274985_   5017 CAAATGGGGTCTAAT-AAAATTAAAGAGCTGTGCACAGTGAAAGAAACTA 5065
                         i    v  iii v  -         i vi v  ii vvii  i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chrX_154274985_   5066 TCAACAGAGTAAACAGACAACCTACAGAATGGGAGAAAATATTTGCAAAC 5115
                             v i   i  v        i                          i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chrX_154274985_   5116 TATGCATCTGACAAAGGTCTAATATCCAGCATCTATAAAGAACTTAAACA 5165
                         i  ii      i  i  v  vi       v  v           ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chrX_154274985_   5166 AAT---TTACAGGAAAACAAACAATCCCATAAAAAAGTGGGAAAAGGACA 5212
                          v --- v i ii  i     i  i  v  v?    i    v      iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chrX_154274985_   5213 TGAACAGACACTTTTCAAGAGGAGACATACATGCAGCCAACAATCATATG 5262
                             i     i  i  v i  i   i     viii     i  v  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chrX_154274985_   5263 AAAAAAAAAGGTCAACATCACTGATCAT 5290
                             i v-- v         ????????
  L1M4_orf2#LINE/    883 AAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


2829 26.04 2.84 3.50  chrX_154294540_154297546     1601  2514 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154294540_   1601 TGAAAACACATCCCATGCTCATGGATCAAAAGAACCAATATTATTAAAAA 1650
                           i   v i        i        iii    vii      i    i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chrX_154294540_   1651 TGACCACACTGCTCAAAGCAATTTACAGATTCAGTGCAGTCTCTATCAAA 1700
                           i v i   v i    vii  i          ii   i  i        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chrX_154294540_   1701 TTACCAACACAATTTTTCACATAA-TTAAAAA----AACTTAAAATTCAT 1745
                         v v   i vvvv     ii  v  -  i v  ---- v i          
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_154294540_   1746 ATGAAACCGAAAGAAGAGTCTGAATAGCCAAACCAATCCTAAGCAAAAAG 1795
                            i  vi v   i-  vi v           v     i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_154294540_   1796 AACAAAGCTTGAAGTATT-ACATT--CTGACTTTGAATTATACTACAAGG 1842
                                -   i  v i -   i -- ii i  ii  viv        i 
  L1M4_orf2#LINE/    199 AACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_154294540_   1843 CTATAGTAACCAAAACGTCATGATATTGGTATAAAAATAGACATATAGAC 1892
                            i     i   i  ivii  i  i   i    ii             i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chrX_154294540_   1893 CAACGGAACAGAATAGTGAACCCAGAAATAAA---GTAC--CTATTAACA 1937
                            i    i     v v  ii           ---i   --i   viv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chrX_154294540_   1938 ACTGATCTTCTGCAATATTGACAAAATTAAACAATAGAGAAAGAACACCC 1987
                          i    i   vi   viv  v   i ii vv    i i       i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_154294540_   1988 TCTTCAATATACGGTGCTAGGAAAACTGGCTAGCCATATGCGGAAGAATG 2037
                          i     i v i      i   v      v  ?   i    ii       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_154294540_   2038 AAACTGGACCCCTGTCTCTCACCATATACATGAATTAACTCGAGATGGAT 2087
                           ii         ii   v           vi         i i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_154294540_   2088 TAAAGATTTATACTTTAGACATGAAACTGTAAAAATCCTGTGAGAAAATG 2137
                         i ?   ii  v iv v   vv i     i     v  i ivi      ii
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_154294540_   2138 TAGGAAAAATTCTTCTGGACATTGGCCTGGCTTAGGCAAAGAATTTTTGA 2187
                             ?iv  v     vv   ----- i   v        v iv  i  ii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGAC-----CTTGGGTTAGGCAATGGTTTCTTAG 592

  chrX_154294540_   2188 CCAGGTCCTCAAAAGCAAATGCAACACAAACAAAAATAAACAGACGGGAC 2237
                         vi v v vi        v v      v  iv       i i i iv    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chrX_154294540_   2238 T-CAGTTAAGCTAAAAACCTTCCACACAGCAAAAGAAACAATCAACAGAG 2286
                          -  viv  ii       i  i-iii vv    i  v  v     v i  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTT-GTGCTTCAAAGGACACTATCAAGAAAG 691

  chrX_154294540_   2287 TAAA-------CCTACCTAATGAGAAAAAATATTTGCAAATTATGTATCT 2329
                          i  -------  i  vv    i  i               i  i     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chrX_154294540_   2330 AACAAAGG-CTAATATCCAGAATCTACAAGAAACTCCAACAACTCAACAA 2378
                         i i  i  -  vi          v  i  ii     iv         i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chrX_154294540_   2379 CAACAACAACGACAAAAACAAAAACAAAAAACAAGTAACGCCATTAAAAA 2428
                         i  -----------------------   i    i    v v   ?    
  L1M4_orf2#LINE/    792 TAA-----------------------AAAGACAAATAACCCAATTWAAAA 818

  chrX_154294540_   2429 GTAGGCAAAGGGCATGAATGGGTGTTTTTTGAAAGA---CATACAAGTGG 2475
                         i i        iiv     i iii   i iv     ---i      i   
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chrX_154294540_   2476 CCAACAAACATATGAAA-GATGCTCAATATCACTAATTAT 2514
                             i  i  i      -         i    ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.96 (155 / 79)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.41 (58 / 17)  


3295 26.87 0.44 0.44  chrX_154309634_154315913.rev     4882  5789 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154309634_   4882 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4931
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154309634_   4932 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4981
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154309634_   4982 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5029
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_154309634_   5030 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5079
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_154309634_   5080 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5129
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_154309634_   5130 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5179
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_154309634_   5180 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5227
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_154309634_   5228 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5277
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_154309634_   5278 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5327
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_154309634_   5328 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5377
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_154309634_   5378 TTAAAGATTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5427
                          i ?   ii       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_154309634_   5428 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 5477
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_154309634_   5478 AACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAA 5527
                         i            vvi     v    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_154309634_   5528 TTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5577
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_154309634_   5578 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5627
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_154309634_   5628 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5677
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_154309634_   5678 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTC 5727
                          i     i     v  i?    i           iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_154309634_   5728 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5777
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_154309634_   5778 ATCACTGGCCAT 5789
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3216 26.99 0.88 0.44  chrX_154360719_154367109     4995  5898 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154360719_   4995 TGGAAGAACATTCCGTGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5044
                              ii i  i  i  i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154360719_   5045 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5094
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154360719_   5095 TACCAATGACTTTCTTCATAGAATTAGAAAAAACT-ACTTTAAAGTTCAT 5143
                          v   iivi i  i  iii    v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chrX_154360719_   5144 ATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGA 5193
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_154360719_   5194 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACCGCAAGGCT 5243
                               i      vv    i  v  ii i      viv   ii   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_154360719_   5244 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5293
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_154360719_   5294 ATGGAACAGAAC--ACAGCCCTCAGAAATAACGCCGCATATCTATAACTA 5341
                               i    i-- v  i  --        vv  ii i  i   iiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chrX_154360719_   5342 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5391
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chrX_154360719_   5392 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5441
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_154360719_   5442 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5491
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chrX_154360719_   5492 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTATAAGAAAACC 5541
                         i ?    i    i  v   v       i      vi i  v        v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chrX_154360719_   5542 TAGGCATTACCATTCAGGACATAGGCATGGGCACGGACTTCATGTCTAAA 5591
                             ?i v viv   iv   v v  vv i    vv ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_154360719_   5592 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGA-----T 5636
                                     vvi           v     v  i    v   ----- 
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_154360719_   5637 CTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5686
                          v   i    i -   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_154360719_   5687 AGACAACCTACAAAATGGGAGAAAATTCTCACAACCTACTCATCTGACAA 5736
                                 i   i             vi ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_154360719_   5737 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5786
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_154360719_   5787 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTC 5836
                          i     i     v  i?    i     i      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_154360719_   5837 TCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCACC 5886
                           v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_154360719_   5887 ATCACTAGCCAT 5898
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


3183 26.61 1.22 0.55  chrX_154368469_154371131     1269  2170 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154368469_   1269 TGGGAAAACATTCCATGTTCATGGATAAGAAGAGTCAATATTGTTAAAAT 1318
                            i  i i  i              vi     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154368469_   1319 GGCCATACTACCCAAAGCATTTTACAGATTCAATGCTATTCCTATCAAAC 1368
                            v     v      viiv i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154368469_   1369 TACCAATGACATTCTTCACATAATTAGAAAAA--AAATCTAAAATTCATA 1416
                          v   iivi v  i  ii  v  v v  v  i--i vi            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_154368469_   1417 TGAAACCAAAAAGTAGCCTGACTAGCCAAAACAATCGTAAGGAAAAAGAT 1466
                           i  viiv  i v v  v  v              v i ii  i    v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_154368469_   1467 CAAAGCTGGAGGAATCACATTACTTGACTTTAAACTACACTACAAGGCTA 1516
                              i       v     i v iii i  i   vivi       i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_154368469_   1517 CTGTAAGCAAAGGAGCATGGTACTGGTACAAAAACAAAGATATAGACCAA 1566
                          v    v   iiv  ii         i i  ii i i v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_154368469_   1567 TGGAACAGAATGGAGAGCCCAGAAATAAAGTTGTGCACCTATAACCATCT 1616
                              i     v     i           viii i  ii   iii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_154368469_   1617 GATCTTCAATGAAGTTGACAAAAGCAAGCAATGAAGAAAGGATTCCCTAT 1666
                            i   i ii i v  v   i v  vv     ii     i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chrX_154368469_   1667 TCAATAAATGGTGCTGGGATAACTGC-TAGCCATATGCAGAAGATTAAAA 1715
                             i              i     v-  ?   i     i    v i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chrX_154368469_   1716 CTGGACCCCTTCCTTATACCATATACAAAAATCAACTCAAGATGGTTTCA 1765
                         i         v   i i               i       i    v iv?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chrX_154368469_   1766 AGACTTATAAATGTAAAGCCTAAAACTACAAAACCCCTGGAAGATAACCT 1815
                             i  --       iiv         i     i i i     v   v 
  L1M4_orf2#LINE/    501 AGACCTA--AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_154368469_   1816 AAG---AAATACCATTCTGGACACAGGCCCAGTGAAAGATTTCATAACGA 1862
                          i ---    -- -   vv   viv  vii  vv  v i    v  ivv 
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_154368469_   1863 AGATATCAAAAGCAATTGCAATGACAACAAAAATTGACAAATGAGACCTA 1912
                         v  i i        vvv    ii v iv      v  i    vi   i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_154368469_   1913 ATTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTATCAACAGAGTAAA 1962
                           i   v v  i i      ii vv    i  v        v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_154368469_   1963 TAGACAACACACAGAATGGG-GCAAATATTTGCAAGCTATGCATCTGACA 2011
                         v       v           - v            iii  ii      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_154368469_   2012 AAGGTCTAATATCTGGAAGCTATAAGGCACTT----AAATTAACAAGCAA 2057
                          i  v  vi    ii   vv     i v   i----  v i  i  vv  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_154368469_   2058 AAACCAAACAACCCCATTAAAGAGTGGGCAAAACACATGAACAGATACTT 2107
                           iv    i     v   ?  i i        iv iv    i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_154368469_   2108 TTCAAAAGAAGACATACACATGGCCAACAAGCACATAAAAAAGTGCTAAA 2157
                         i  v        i     v        i        i    ii    v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_154368469_   2158 CATCACCAAATCA 2170
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (142 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


2002 19.42 1.05 21.70  chrX_154371728_154374116      754  1896 (493)    L1M4_orf2#LINE/L1        2   908 (0)  

  chrX_154371728_    754 GGAAAAACATCCCATACTCATGGGTCAAAAGAATCAATATTGTTAAAATG 803
                              i i       ii      i iii    v i           i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_154371728_    804 ACCATACTGCTCAAAGTAACCTACAGATTAAATTGCAATCCCTATCAAGG 853
                         i v     v i    v i i         v  i-              ii
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAAC-GCAATCCCTATCAAAA 100

  chrX_154371728_    854 TACCCACATCATTTTTCACAGAATTAGAAAAA--AATTATAAAATTCATA 901
                          v  vi vv v     ii     v v  v  i--i  iv           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_154371728_    902 TGTAAACAAAAAAGAGCCTGAATAGCCAAAGGAATCCTAAGCAAAAAGAA 951
                           v   iiv  ii  v  v           iv    i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_154371728_    952 CAAAGACGGAGGTATCTCATTACCTGACTTCAAATTATACTACAAAGCTA 1001
                              vi     vv  v  i v  ii i      viv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_154371728_   1002 TAGGAACCAA-ACAGCATGGTACTGGTATAAAAACAGGCACACAAATCAA 1050
                         i  v  i   -    ii         i    ii i  i  i i i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_154371728_   1051 TGGAACAGAATAGAGAACACAGAAATAAAACCACATATCTACAACCAACT 1100
                              i     v    iiv          v   i i  i  iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_154371728_   1101 GGTCTTTGACAAAGGTGACAAAAACACACAATGGGGAAAAGACACCCTTT 1150
                          i i  i     i    v   i v  iv           -----------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA----------- 389

  chrX_154371728_   1151 ATTTTTCTTTTTCAACTTTTGTTTTAGAATTAGAGGTTACACGTGCAGGT 1200
                         --------------------------    --------------------
  L1M4_orf2#LINE/    390 --------------------------GAAT-------------------- 393

  chrX_154371728_   1201 TTGTTACAAAGGTATATTACATAATGCTGAAGTTTGGGGTATGACTAAAT 1250
                         --------------------------------------------------
  L1M4_orf2#LINE/    394 -------------------------------------------------- 393

  chrX_154371728_   1251 CTGTCACTCTGGTAGTGAACATAGTACCCAATAGGTAGTTTCTCAGCCTT 1300
                         --------------------------------------------------
  L1M4_orf2#LINE/    394 -------------------------------------------------- 393

  chrX_154371728_   1301 TAGCCCCCTCTTTCTCTCCCACCTCTAGCAGTCCCCAGTGTCTGTCTATT 1350
                         -----------------------------    -----------------
  L1M4_orf2#LINE/    394 -----------------------------AGTC----------------- 397

  chrX_154371728_   1351 GTTCCCATCTTTATAGGACATCATTTTCAATAAATGGTCTTGGGAAAATT 1400
                         -----------------------       i       vi     v  i 
  L1M4_orf2#LINE/    398 -----------------------TTTTCAACAAATGGTGCTGGGACAACT 424

  chrX_154371728_   1401 GGATTGCCACATGCAGAGGAATGAAACTGGACTCCTATCTCTCACCACAT 1450
                             v?         i i       ii     i    i   v     i  
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chrX_154371728_   1451 AAAAAAATCAACTTAAGATGGAGTAAATACTTCAATATAAAACCAGAAAC 1500
                          v      i    i  i     vi ? v  i v   i   i v vi    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chrX_154371728_   1501 TATACAAATACTGGCAGAAAACCCAGGG--AAA-CTGCTGGATATTGGTC 1547
                             v  v vi i v       vi   ?--   -  v vv  iv    vi
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chrX_154371728_   1548 TAGGCAAAGAATTCACAACTAAGACCTCAAAATCGCAAGCAACAAAAAAA 1597
                                v iv   vi iv  v   vi     v i            i  
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chrX_154371728_   1598 AAAAAATAGAAAAATGGGACTTCATTAAAA-----AGCTCTTATACAGCA 1642
                             --    v    v         i    ----- i  i  i i vv  
  L1M4_orf2#LINE/    625 AAAA--TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chrX_154371728_   1643 AAATA-ATTAATCAACCAGGTGCACAGACAACCTGGAGAATGGGAGAAAA 1691
                           iv - i  -    vv i   v v        iiv              
  L1M4_orf2#LINE/    673 AAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chrX_154371728_   1692 ATATTTGCAAACGATGCATCCAACATGAACCTAGTTCTCAGCAGCCAGCA 1741
                         -          iv  ii   ii i v iiv  v  ------- v    --
  L1M4_orf2#LINE/    722 -TATTTGCAAATCATATATCTGATAAGGGACTTGT-------ATCCAG-- 761

  chrX_154371728_   1742 CTCAAATTCACAAGGAACATGAACAACTCAACAACAACAAAGAAAACAAA 1791
                         ----   vi i  i    vivv         i  i  -     ---    
  L1M4_orf2#LINE/    762 ----AATATATAAAGAACTCTTACAACTCAATAATAA-AAAGA---CAAA 803

  chrX_154371728_   1792 TAACTCCATTAAAAAGTGGGTGAAGAACATAAATAGACATTTTTCAAAAG 1841
                             i v   ?    i    ii   i iv i           i  v    
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chrX_154371728_   1842 AAGACATACAAATGACCAATAGACATATGAAAAAATGCTCAGCATCACTA 1891
                             i         i      ii  i       i       i     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chrX_154371728_   1892 ATCAC 1896
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.63 (135 / 83)
Gap_init rate = 0.02 (17 / 907), avg. gap size = 15.29 (260 / 17)  


3001 25.28 2.92 0.90  chrX_154377156_154382608     4072  4961 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154377156_   4072 TGGAAA-ACATCCCATGCTTAAGTATTGGAATAATTAATATTATTAAAAT 4120
                               - i        i i v v       v v        i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154377156_   4121 GACCAAATTACCCAAACCAATCTACAGATTCAATGTGATCCCTATCTAAG 4170
                          i v v i v      iii              i ii         v  i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154377156_   4171 AACCAA-TGTTATTTTACACAGAATTAGTGA-AAAC-AATCTTAAAATTT 4217
                         vv   i-  iiv    -ii     -- v   -  i -i   i       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chrX_154377156_   4218 GTATGGAACTAAAACAGAGCCCGAGTAGCCAAAGCAATACTAAGCAAAAA 4267
                         i       v iv  vi  v  v  i        i    vi i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chrX_154377156_   4268 GAACAAAGATGGAGGCATCACATTACCTGACTTCAAATTATATTACAAGG 4317
                                 v      vv     i v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chrX_154377156_   4318 CTATAGTGTCTAAAACAGCATGGCATTGGTATAAAAACAGATGACACATA 4367
                            i   ivii  i    ii   i i   i    ii i   ---  i   
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA---CATATA 294

  chrX_154377156_   4368 GACAAATGGAACAGAATAGAGAGTCTAGAAATAAATCCATGTACTTATAT 4417
                           iv       i     v       i         i    ii i    iv
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chrX_154377156_   4418 CCAACTGATTTTTGACAAAGATACCAAGAACATATACTGGTGAAAGGAAA 4467
                         i   i       i     i i i      v   vi v   v     i v 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chrX_154377156_   4468 CCCTCTTCAATAGATGATTCTGAGAAAATGGGAGACCTGTATGCAGAAGA 4517
                         vi  i     i i   i v   i  v  iv   v ? iii     i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chrX_154377156_   4518 ATAAAACTGGACCTCTTTCTCTCTCCATATA-AAAAATTAAGTCAAGAAG 4566
                           i  ii      i  vi   v v       -         v    i v 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chrX_154377156_   4567 GATTAAAGTCTTAA--GCATGACCCAAACCGTTTAAGC-AGTAGAACAAA 4613
                            i ?  v i   -- i v  v i   v vv v  i -vv     v   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chrX_154377156_   4614 ACACAGAG--AAA--------ACATTGGTCTAGGTAAAGATTTCATGGCT 4653
                            i  i?--   --------  v    vi    i  v i    v i v 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chrX_154377156_   4654 AAGACATCAAAGGCACAATTA-TAATA---AAAACATACAAATGAGACTT 4699
                          v    i    i      vi -i  v ---    i v i    vi     
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_154377156_   4700 TATTAAACTAAAGAGCTTTTGTACAGCAAAAGAAACAATCAACAGAGTGA 4749
                         i  i   v v  i i       i vv    i  v  v     v i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chrX_154377156_   4750 AGAGACAACCCATTGAATGGGAGAAAATATTTGCAAATTATTCATCCAAC 4799
                          i          iv                        i  vi   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chrX_154377156_   4800 AAGGGACTAATATCCAGAATCTAGAAGGAACTCAAAGAACTCAACAATAA 4849
                                 vi          v  v  i      vv v       i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chrX_154377156_   4850 AAAAAAAAAT--CCCG-TTAAAAAGTGAACAAAGGATATGAATAGACATT 4896
                            i v    --   i-  ?    i  ii        v            
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chrX_154377156_   4897 TCTTTTTAAAATACATACAAATTGCCA-TCAGCTGTAGGAAAAAAATGCT 4945
                            iivv i  v i        v    - v   -ii v     i -    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGC-ACATGAAAAGA-TGCT 892

  chrX_154377156_   4946 CAACATCCCTAATCAT 4961
                                v????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (133 / 88)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.79 (34 / 19)  


2876 26.22 2.22 1.56  chrX_154398099_154402680     3190  4089 (493)    L1M4_orf2#LINE/L1        3   908 (0)  

  chrX_154398099_   3190 GAAAAATCATTCCATGCTCACGGATAGGAAGAATCAATATTGTTAAAATA 3239
                             i  -  i     i   i    v      v i           i  i
  L1M4_orf2#LINE/      3 GAAAGAT-ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chrX_154398099_   3240 GCCATACTGCTCAAAGCATTTTATAGATTCAATGCTATTCTTATCAAACT 3289
                           v     v i    viiv i  i        i  v  i i       v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chrX_154398099_   3290 ACCAATGGCATTCTTCACATAATTAAAAAAAATTATTCTAAAATTCTTAT 3339
                         v   iiv  v  i  ii  v  v vi v  iv v  i         v   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chrX_154398099_   3340 GGAACCAAAAAGGAGCCCAAATAGCCAAAGAAATCTTAAGCAAAAATA-C 3388
                             viiv  i   v  vi          iv      i iv  i  v - 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chrX_154398099_   3389 AAACTTGGAAGCATCACATTACTTGATATCAAA-----CTATAGAAGTCT 3433
                            v     i vv     i v iii  v     -----   i -   -  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA-AAG-CT 249

  chrX_154398099_   3434 ACAGTAACCAAAAGAGCATGGTACTGGTACAAAAACAGACATATAGACCA 3483
                                i   i v  ii         i i  ii i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_154398099_   3484 ATGGAACAAAATGGAGAGCCCAGAAATAAGGTTGTGTGCCTACAGCCATC 3533
                               i i   v     i          iviii iiiii  ii i  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_154398099_   3534 TGATCTTTGACGCTGATG--AAAACAAGT-AATGGG-ATAGA-TACTCCC 3578
                             i  i   ivv i  --  i  v v -      - v   -  v  --
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-- 397

  chrX_154398099_   3579 TATTCAATAAATGGTGCTAGGATTGCTGGTT-GCTGTGTGCAGAAGATAG 3627
                          v     i          i   ivi    v -? iiii    i    vv 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chrX_154398099_   3628 AAACCAGAAGGCGTCTGCCTTCTTTACACCATATACAAAAATCAACCCAA 3677
                           iiii  ------ i-   v i i                 i   i   
  L1M4_orf2#LINE/    448 AAGTTGGA------CC-CCTACCTCACACCATATACAAAAATTAACTCAA 490

  chrX_154398099_   3678 AATGGATTA--GACTTAAATGTAACAACTAAAACCATAAAAACCCTT-GA 3724
                                i --   i         v i       i      - i   -  
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGA 539

  chrX_154398099_   3725 AGAAGACCTAGGCA-ATACCATTCTAGACATGGGCCCTGTCAAATATTTC 3773
                             i  v    ?i- v i -   vv   v v  viiv v   vvi    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_154398099_   3774 ATGACAAAGACATCAAAAGCAATGGCAATAATAATAAAAACTGATAAATA 3823
                         v iivv v    i        vvi    i  v iv     iv       v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_154398099_   3824 GCACCTAGTTAAACTGAAGAGCTTCTGTACAGCAAAATAACCTATCAATA 3873
                          v  i vi i   v v  i i   i   i vv    iv vv       v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chrX_154398099_   3874 GAGTAAATAGACAACACACAGAATGGGAGAAAATATTTGCAAACTAGGCA 3923
                         i   i  v       v                           ii vii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chrX_154398099_   3924 TCTGACAAAGTTCTAATATCTAGAATCTATAAGGCACTT----AAATTAA 3969
                              i  i vv  vi    i     v     i v   i----  v i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chrX_154398099_   3970 CAAGCAAAAACCAAACAACCTCATTAAAAAGTGGGCAAAGGATATGAACA 4019
                         i  vv    iv    i    iv   ?    i            v    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chrX_154398099_   4020 GACACTTTTCAAAAGAAGACATACATGTGGTCAACAAGCATATGAAAAAA 4069
                             i  i  v        i     vi   i   i     i       i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chrX_154398099_   4070 TGCTCAACATCACTAATCAA 4089
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 1.79 (34 / 19)  


1310 26.13 2.25 0.45  chrX_154411660_154413302.rev        1   444 (1199)  C L1M4_orf2#LINE/L1   (18)   890   439  

C chrX_154411660_    444 AAGAAAATGAACCTCAAACTCTACCTCATACCATAAAAAAAACTCAACTT 395
                           i i      vi vi v i        i      v v    v i    i
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

C chrX_154411660_    394 AGAATTAATCATAGACCTAAACGTAAATGCTGAAATTGTTAAGCATAAGG 345
                          i   vi    ?         i    iv   i   i i v  i vivvi 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

C chrX_154411660_    344 AAGAAAACATGGGAGAATATCTTCATGATCTTGTGTTAGGCAATTGTTTC 295
                                   i  ? v v      i   i    v          v     
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

C chrX_154411660_    294 TCAAA-ATAGAAAAAAAATCATTAACCATAAAAGTTTAAAGTGATAAA-- 248
                          i i -  iiv vv    v  iv i v i     vvv   vv      --
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

C chrX_154411660_    247 ---CTTCATTAACATTAAAAACTTCTGCATGCCAAAG-ACATTGTTATGA 202
                         ---      i  v           i  iiivi     -   i i i v  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

C chrX_154411660_    201 AAATGAAAATATAAGCCATGGACTAAATACAAAATATTTATAATACCTAT 152
                           i      v i  v   ii  v iii- v         ii  vv v   
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGG-AGAAAATATTTGCAAATCATAT 737

C chrX_154411660_    151 ATCTTACAAAAGTAAGGTATCTATAATACATATAGAACTCTTAAAA-TCA 103
                             v i  ii vvvv     i v    i   v          v  -   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

C chrX_154411660_    102 AACATAAAAACACAAACAAACCCAATT-AGAAATGGGAAAAAGATTTAAA 54
                          vv       v     i  -       - i       v   i     i  
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAA 836

C chrX_154411660_     53 CATATACTTA-CAAAAGAAGATGTACGAATGGCCAATAAACATATGAAAA 5
                         i v i i  v- v         i   i            i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

C chrX_154411660_      4 GATG 1
                             
  L1M4_orf2#LINE/    887 GATG 890

Transitions / transversions = 1.19 (62 / 52)
Gap_init rate = 0.02 (8 / 452), avg. gap size = 1.50 (12 / 8)  

1912 26.11 3.53 1.38  chrX_154411660_154413302.rev      502  1152 (491)    L1M4_orf2#LINE/L1      244   908 (0)  

  chrX_154411660_    502 AAAATTAAAGTAAT-AAGACAGCATTGTATTGGCTGAAGGATAGACACTT 550
                            ii  v      -       ii v   i    vv           iv 
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chrX_154411660_    551 AGATCAATGGAACCAAATACAAAAAAACAGAAACAGACCCTCACAAATTT 600
                                     ivi   -ii i ivv      i i    vi   vv v 
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chrX_154411660_    601 GCCCAACTGACTTTTGACAAATGTGCAAAAGCAAGTTAAAAAAAAAGTAA 650
                          vi   i   i   i     iv    v  ii v v i  viiii  --- 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA---A 389

  chrX_154411660_    651 GGATAGCCTTT-CAAGCAATAGTCCTGGAGCAACTGAACATCTATAGGCA 699
                          i    i    -   vv   i  v    ii      i i ? i i v   
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chrX_154411660_    700 AAAGTATGAACTTCAACCTAAATTTCATACTTTACCAAAAAAAGTCACTG 749
                             v     v  vi   ivv ii   i  iv  i- v     v v   v
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATAT-ACAAAAATTAACTC 488

  chrX_154411660_    750 AAAATGGATAATGGACTTAAATGTAAGCCACAAAACTATAAAACTTTTTT 799
                                  v ?i   i          vvvi              i  vv
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_154411660_    800 TA-AAAACAT-GATA-AAATCTTTG-GATATAGGTTTCAGTAA------- 838
                         v -       - i?i-       i -  iv v  v  vi i  -------
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_154411660_    839 --AGACTTGACATCTAAAGCGCAATCCATAAAA---AAACTTGGTAGATT 883
                         --   iv     i v     i   v v i    ---   v v i  i   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chrX_154411660_    884 GGA-TTCCTCAAAATTCAAAACTTTTACTCTGCA--GAATATTGTCTTAA 930
                            -   v        v         iiv  v  -- i i i i  --  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC--AA 686

  chrX_154411660_    931 GAGGATGAAAAGACAAGCAACAGAGTGGGAGAAAATACTTGTAAACCACA 980
                           iii           v v     i            i   i   i  i 
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chrX_154411660_    981 TATCTAACAAAGAATTAGTATGTTAAATATATAAAG--TTCTCAAAACTC 1028
                              i i  i i i v    vivi           --i   i v     
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chrX_154411660_   1029 AACCATAAAAAATGCTGAACAATCCAAGTAGAAAATGGGCAAAAGACATG 1078
                           iv       -- vii  i  i    v ?i            i  iv  
  L1M4_orf2#LINE/    787 AATAATAAAAA--GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chrX_154411660_   1079 AAGAAACCTTTCACCAAAGATTATATACAGATAGAAAATAAGCACATGAA 1128
                           v i  v    v       vv       i  i vv              
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chrX_154411660_   1129 AATATGTTCAATATCATTCATCAT 1152
                           v   i    i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (95 / 71)
Gap_init rate = 0.02 (16 / 665), avg. gap size = 2.00 (32 / 16)  


4072 14.93 1.66 5.45  chrX_154445833_154447668.rev      502  1345 (491)    L1M4_orf2#LINE/L1       97   908 (0)  

  chrX_154445833_    502 AAAGTCCCAATAACCTTTTCTATAGATATGGAAATGACAATACTAAAATT 551
                            i     iivi      i ii   v  v  v v vii  v        
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chrX_154445833_    552 CATATGGAATTGCAATGAGTCCA-AGTAGCCAAATCAATTTAGAAAACAA 600
                                  v     v iii   - i        v    i v     vi 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chrX_154445833_    601 AATAAAAAGTTGGAAGACTCACACTTTCCAATTTCAAAACTTATTATAAC 650
                          iv v         i           i                i  i  v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chrX_154445833_    651 ACTACAGTAATCCAAACAATGTGGCACTAGCATAAGGATAGACAATGGCA 700
                         i           v i   i     i   i               ------
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA------ 290

  chrX_154445833_    701 TCTATAAATCACTGAAATGGAATTGAGAATCCAGAAATAAACCCAAACAT 750
                         --    i    v  i   i         i                v    
  L1M4_orf2#LINE/    291 --TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chrX_154445833_    751 CTATGTATAATTGATTTTCAACCAGGATGCCAAGACCATACAATGGGGAA 800
                         i    vvi           i  v   i            v          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chrX_154445833_    801 AGAACAGTCTCTTCAACAAATGGTTCTGGGAAAACTGGATATCCACATGC 850
                             i     i             v      v         ?        
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chrX_154445833_    851 AAAAGAATGAAGTTGGACCTTTACCTAACATTATGTATAAAAATTAACTC 900
                                            ii     v   ii  i  i            
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chrX_154445833_    901 AAAATAGTTCAAAGACCTAAATATAAGAGCTAAAACTGTACCAATATTAG 950
                              i v   ?          i              i  vv v v    
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chrX_154445833_    951 AAGAAAACTTGGGAATAAATC---ATGATGTTGAATCAGGCAATGGTTTC 997
                                 v i  ?i      ---i   iv   ii i             
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chrX_154445833_    998 TTAGATATGGCACCAAAAGCACAAGTAACAAAATTTTAAAAACCA--TAA 1045
                                  i               i       v---     vi --   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAG---AAAAAATAGATAA 635

  chrX_154445833_   1046 AATGGACTTCATCAAAATTCAAAACCTTAGTGCATCAAAAGACATTATTA 1095
                          v                 v     i  v    v     i    i   i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chrX_154445833_   1096 AGAG-GTGAAAAGACA-------GAATGAGAGAACATATTTGCAAATCAT 1137
                            i-           -------     i     v               
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chrX_154445833_   1138 ATATCTGATAACTAGATAAGGGTCCATATATCTGATAACTAGATAAGGAT 1187
                                    ----------------------------------i   -
  L1M4_orf2#LINE/    736 ATATCTGATAA----------------------------------GGGA- 750

  chrX_154445833_   1188 CTAGTGTTCAGAATATATGAGTAACTCCTACAACTCAATAATAATGAGAA 1237
                           v  i i          i iv     i                vi   v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_154445833_   1238 AAGCAACCCAATTTAAAAATGAGCAAATGACTTGAATAGACATTTCTCTA 1287
                           ii         ?       i     v  i                 i 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chrX_154445833_   1288 AAGGAGATATGCAAATGGCCAGTAAGCACATGAAAAGAGGCTCAATATTA 1337
                            i      i          i                v      i  i 
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chrX_154445833_   1338 ATCACTGG 1345
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.71 (77 / 45)
Gap_init rate = 0.01 (9 / 812), avg. gap size = 6.67 (60 / 9)  


 691 28.36 6.88 11.11  chrX_154457070_154459023      517  1461 (493)    L1M4_orf2#LINE/L1        4   908 (0)  

  chrX_154457070_    517 AGAGTTATACTATGTTCCTG-AGGGAAAGATTTGTGAACAT-----AAAT 560
                          i  v   v i      v  - vv i    i  ---  i  ----- i  
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTT---AATATTGTTAAGAT 50

  chrX_154457070_    561 GAT--TATTCTC-AAGTTATTCCATACATTAAATGAAAGTTTAATCAAGA 607
                          ii--  i  i -  i  iv  i i v   v  i v  viiiv     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154457070_    608 TATCAACAATAAATATGGATTAAGGATATTATTCTTACAGAACTTGACAT 657
                          vi  i ------------------- iiiv  i  i     v      v
  L1M4_orf2#LINE/    101 TCCCAGC-------------------TGCCTTTTTTGCAGAAATTGACAA 131

  chrX_154457070_    658 ACTGATACTAAAATTCATATAAAATTGAAAATAGGTAATAATGATCATGA 707
                         i     v             ii  v  v  iviiviv v   iii  vi 
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chrX_154457070_    708 CTATTTTGAGGAATAAG--CA----TGAAGAACTGACATTACTAGATAGT 751
                          v  i    ii  v   --  ----  i  i   v   i v ivi  vvi
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chrX_154457070_    752 GAAACTTACCATAAAGCCATAATATTTTTAAAA-AGTGTAATATTATAGC 800
                         i        i i     i i i  v i--  i -     ii  i i--  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATC--AAGACAGTGTGGTACTG--GC 277

  chrX_154457070_    801 ATAA--ATAGACAAATA----AATGG-------TGGAGAATC--ACAATG 835
                             --       v   ----     ------- v    i  --iv   i
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chrX_154457070_    836 AACTTACAAATATACAAGAATAAATGATTAGTATATGACATATAGAGTAT 885
                            ii i v  v  i-- ivi  v     ---- vi    ---  i  ii
  L1M4_orf2#LINE/    328 AACCCATACATTTAT--GGTCAATTGATT----TTCGACA---AGGGTGC 368

  chrX_154457070_    886 -ATAATAAATCAGTGTATGAAATGATGGACTTTCCAATAAATGGTGTTAG 934
                         - vi iv v   i  vi-    vi  i v    i   i        i i 
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chrX_154457070_    935 GATATTTGGTTACCCTTATGGAAACAGATAAAATTAGATCAATACTTTAC 984
                           i vi   v  ?  vi   v   vii  i  i  i  i vv   i i  
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chrX_154457070_    985 ACAATTTATAAAAATTTAATAATTTAATTTCTGGCAGGTTTAAACCCTAA 1034
                           v  v  i       ----  i i  -----iiii i iv? iv     
  L1M4_orf2#LINE/    468 ACCATATACAAAAATT----AACTCAA-----AATGGATCAWAGACCTAA 508

  chrX_154457070_   1035 --GTAAAAATAATAAGAAGAGTAGAATACATATGTTTGTGGGGTGCGTGT 1082
                         --    i ii--   i v---  v  v  ---------------------
  L1M4_orf2#LINE/    509 ATGTAAGAGC--TAAAAC---TATAAAAC--------------------- 532

  chrX_154457070_   1083 GTGTGTGTGTTTGTGTATTAGTAAGAAGAAAGTAAGAAAAAAGAGAACAG 1132
                         --------------- v    ------------       v v  i?-- 
  L1M4_orf2#LINE/    533 ---------------TCTTAG------------AAGAAAACATAGGN--G 553

  chrX_154457070_   1133 TAGGAAGTCTTTATGATATCTAGATGGG--AGGAGTTCTTTAATAAAACA 1180
                           --- i    ii   iv ivi v i  -- v iv     vi   vi   
  L1M4_orf2#LINE/    554 TA---AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chrX_154457070_   1181 T-AAAAACACAAGCCATAAAGGGAAA----GATAAATTTAAATATATTAA 1225
                         i-    i       v i   i i   ----        vi v vi  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chrX_154457070_   1226 AATTTAAAA------TATTTCAG-------TAT-AAGCAAAGGTAAAGGC 1261
                             v    ------ ii    i-------   -   v  iv v    i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chrX_154457070_   1262 AAGTTACAGACTGACAGAAGATATTTACAACTCACAAAT--GACAAACGT 1309
                           vii     v  iv    i      i   v   i v  --  i  iv v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chrX_154457070_   1310 TTAAAATTCTGAATATATAAAGAATTTCTATAA----ACAA-AAAAAGAC 1354
                         i viv  i v              i ii  i  ---- i  -        
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chrX_154457070_   1355 AAATAACCAAATCAAAAATATAGATATA--ATATGAATCAGCAGTTACTA 1402
                                 v   i?    -  i ii v --  v     vii  v  viiv
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chrX_154457070_   1403 GAGGAAGGATCT-TGAATGACTAGTAAACATGTTAAAAGAAAATCAACCT 1451
                         i i    -  v -ii    i i i   i  ii v      viv     v 
  L1M4_orf2#LINE/    850 AAAGAAG-ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chrX_154457070_   1452 CACAGAGGTT 1461
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.67 (165 / 99)
Gap_init rate = 0.05 (42 / 905), avg. gap size = 4.05 (170 / 42)  


3437 24.58 1.11 0.55  chrX_154502282_154506564.rev     2890  3792 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154502282_   2890 TGGAAAGATATTCTATGTTTATGGATTGGAAGAATCAATGTTGTCAAAAT 2939
                                    i i     i             v i   i    i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154502282_   2940 GTTCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCGTATCAAAA 2989
                          viv     v      vii              i       v        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154502282_   2990 TACCAGTGATATTCTTCACAGAAATAAAAAAAAGC-AATTCTAAAATTTA 3038
                          v    iviiv  i  ii       vi v  --  -i  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chrX_154502282_   3039 TATAGAACCACAAAAGACCCAAAGTAGCCCAATCTATTTTGAGCAAAAAG 3088
                            i   vii   ii      i i     v  v v  i    iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_154502282_   3089 AAGAAAACTGGAGGAATTATATTACCTGACTTCAAATTATATTACAGAGC 3138
                           v   ii       v i i i v  ii i      viv  i    i   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_154502282_   3139 TATGGTAATCAAAACAGCATGGTACTCGCATAAGAATATACACATAGGCC 3188
                           ii        i    ii       v       i   v   i    ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_154502282_   3189 AATGGAACAGAATAGAGAACCCAGAAACAAATCCACATACCTACAGTGAA 3238
                                i     v    ii       i   i   i i ii  ii  v  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_154502282_   3239 CTCACTTTCTGTAAAAGTGCCAAGAACATACATTGGGGAAAAGGAAGTCT 3288
                         i v i    vii  ii         v   v  v        iiiv     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_154502282_   3289 CTTCAATAAATGCTGAGGGGAATAGTGGATATACATAAGCAGAAGAATGA 3338
                         i     i     v  vv    vv v      ?v  i v   i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_154502282_   3339 ACCTAGAACCC-ATCTCTCACCTTATACAAAA-CCAAATCCAAATGGATT 3386
                          vi i  v   - i   v    v         -ii  v  v        i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_154502282_   3387 AAATACTTAAATCTAAGA-CTAAACTTATGAAACTACTACAAGAAAACAT 3435
                          ? v  i     v     -     vi   i     vi  v          
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chrX_154502282_   3436 TGGGAGAACTCTCCAGGACATTGGTCTGGGCAAAAATTTCTTGAGA-ATT 3484
                         v  ?iv  v   i iv   v    vi i     vii      -   -  v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATG 597

  chrX_154502282_   3485 ACCTTGCAAGCACAGGCAACCAAAGCAAAAATGGAAAACTGGGATCACAT 3534
                           viiiv       i     v    v      i  v  v v   iiv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_154502282_   3535 CAAG-TTAAAGAGCTACTGCACAGCAAAGAATACAATCAACAAAGTGAAG 3583
                            i-     i -  vi  ii vv     i i  v     v        i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_154502282_   3584 AGACAACCCACAGAATGGAAGAAAATATTTGCAAACTACTCATCTGACAA 3633
                                           i                ii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_154502282_   3634 GGAATTGATAATCAGAATAAATAAGGAGCTCAAACAACTCTATAGAAGAA 3683
                           i i vi  vi       v    i  i   vv       v   iv -  
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA-AA 795

  chrX_154502282_   3684 AATATAAA-AATCTGATTTAAAAATGGGCAAAAGACTTGAA--GACATTT 3730
                           v i   -  i ii   ?             i  i     --       
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chrX_154502282_   3731 CTCAAAAGAAGGCATACAAATG-CAAACAGGAATATGAAAAAGGGCTCAG 3779
                            v       ii         - v  i i v i       iiv     i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chrX_154502282_   3780 CATCATTGCTCAT 3792
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (134 / 84)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.15 (15 / 13)  


3140 28.05 0.22 0.33  chrX_154516400_154522689.rev     4891  5799 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154516400_   4891 TGGAAAAACATTCCATGCTCATGGGTAGGAAGAATGAATATCATGAAAAT 4940
                               i i  i     i      i v      v v     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154516400_   4941 AGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCGAGC 4990
                         i  v     v     iv i  i  i        i  v     i   i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154516400_   4991 TACCAATGACTTTCTTCACAGAATTGGAAAAAAATACTTTAAAGTTCATA 5040
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_154516400_   5041 TGGAACCAAAAAGGAGCCCGCATAGCCAAGCCAATCCTAAGCCAAAAGAA 5090
                              viiv  i   v  v v        iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_154516400_   5091 CAAAGCTGGAGGCATCACGCTACCTGATTTCAAACTGTACTGCAAGACTG 5140
                              i      vv    i  v  ii        viv    i   ii  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_154516400_   5141 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGGTATAGACCAA 5190
                               i   i    ii         i iv ii i   vi      i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_154516400_   5191 TGGAACAGAACAGAGGCCTCAGAAATAAAACCACACATCTACAACCATCT 5240
                              i    iv   ivii          v   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chrX_154516400_   5241 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGAATC-CCTA 5289
                            i  i     ivv  v   i v  vvv           -   v-i  v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG-AATAGTCTT 399

  chrX_154516400_   5290 TCTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGGAGAAAGCTGAA 5339
                          ii  i        i     v      v  ?   i   v i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_154516400_   5340 ACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGATTA 5389
                         ii    i    v   i     v  i           i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_154516400_   5390 AAGACTTAAATGTTAGACCTAAAACCATTAAAAACCCTGGAAGAAAACCT 5439
                         ?    i       v   v       i  -    vi i i         v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACAT 548

  chrX_154516400_   5440 AGGCA-ATACCATTCAGGACATAGGCATGTGCAAGGACTTCATAACCAAA 5488
                            ?i- v i -   iv   v v  vv iv    v ii   v  ivi vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chrX_154516400_   5489 ACATCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAAT 5538
                            i        vvi          vv        i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chrX_154516400_   5539 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACTATTAGAGTGAACA 5588
                         i   v v  i i   i  ii vv    i  v    ii vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chrX_154516400_   5589 GGCAACCTAGAGAATGGGAGAAAATTTTTACCATCTACCCATCTGACAAA 5638
                          i     i v               v   i v vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chrX_154516400_   5639 GGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 5688
                           i  vi          v  i  i     ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chrX_154516400_   5689 AACAAACAACAACATCAAAAAGTGGGCAAAGGATATGAACAGATACTTCT 5738
                         i     i   vvv  i?    i            v    i   i i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chrX_154516400_   5739 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 5788
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chrX_154516400_   5789 TCACTGGTCAT 5799
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (151 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


4579 16.52 1.77 1.11  chrX_154546712_154548827.rev      724  1625 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154546712_    724 TGGAAAGACACTCCATATTCGTAGATTGAAAGATTTAATATTGTTAAGAT 773
                                 i ii    i   i i     i    i                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154546712_    774 AGAAATACTCTCCAAAGTGATCTACAGA--AAACATAATCCCTATCAAAG 821
                         i v       i     v           --v   ii             i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154546712_    822 TCCCAGCCAGATTTTTTTGCAAAAATTCATGAATGAACCCTAAAATTCAT 871
                                i- vi         i     v ii iivi i            
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chrX_154546712_    872 ATGGAAATGCAAGGGGTACAGAATAGTCAAAACAATCTTGAAAAGGAAGA 921
                                        iiv        i                 i     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_154546712_    922 ACAAAATAAAAGTATTAAATCTTTCTGACTTCAAAGCTTACTACAATACT 971
                              i vii  v i v vv   i ii i      i          vi  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_154546712_    972 ACAGTAATCAAGATGGTATAGTACTGGAATAAGGATATACATATAG-TCA 1020
                                      ii  i i       v         v        -   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_154546712_   1021 AATGTAATATAATTGAGAGTCCAGAAATAAAACCTTACGTTTATGATCCA 1070
                          -  v    v                     v  v   i      i  v 
  L1M4_orf2#LINE/    300 A-TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chrX_154546712_   1071 TTGATTTTCTACAAGGGAGTCAGCACAATTTAATGGAGAAAGAATAATCT 1120
                                  v       v i  iv  v   i     i         i   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_154546712_   1121 CTTCAACAAATGGTGCTGCAACAACTGAATAGCCACATGCAAAAGAATGA 1170
                         i                 vi       i   ?                  
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_154546712_   1171 AGTTGGACTCCTACTTCAAATCATATGCTGTACAAAAAATTAACTCAAAA 1220
                                 i     i   v i     i ------                
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATAC------AAAAATTAACTCAAAA 492

  chrX_154546712_   1221 T----CATAGACATAAATGTATGAGCCAAAACTACAAAACTCTTAGAATA 1266
                          ----  ?    v        v    i       i             v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chrX_154546712_   1267 AAACATAGGAGTAAATATTTGTGACCTTGGATTAGGCA-TAGTATTCCTA 1315
                                  ?      v  i          i       - i  -   i  
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTA 591

  chrX_154546712_   1316 GACGCAACAAGAAAAGCACAAGTGACAAAAGAAGAAATAGATAAATTACG 1365
                           iiii   vv           ii         i             ivi
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chrX_154546712_   1366 TTTCTTCAAAATCAAAACCTTTTTTTCCTGCCAAAAATATAATCAATAAT 1415
                         i   v       i    v     v v i - v  ii i iv     v  v
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTT-CAAAGGACACTATCAAGAAA 690

  chrX_154546712_   1416 GTGAAAATGCAACCCACAGAATAGGAGAAAATGTTTACCAGTCATATATC 1465
                                vi             i         i   i v i         
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chrX_154546712_   1466 TGATAAGGAACTTGTATCCACAATAGATAAAGA--TCTT-CAACTCAACA 1512
                                 i           v    v       --    -        i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chrX_154546712_   1513 ACTAAAA--CAAAGAAACAAATGGAAAAATGCGCAAAGGATTTGAATAGA 1560
                          iv    --    v  v v   v?       v                  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chrX_154546712_   1561 CATCTCTTCAAAGA---CACACAAATGGCCAATATGTGCATGAAAACATG 1607
                            i   i      ---i i              v ii        v   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chrX_154546712_   1608 CTCAATAACATCAGTCAT 1625
                              i v  ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (91 / 54)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.00 (26 / 13)  


2322 29.30 1.53 0.38  chrX_154600844_154608090      492  1276 (5971)  C L1M4_orf2#LINE/L1   (0)   908   115  

C chrX_154600844_   1276 TTCACAGAACTAGAAAAAACT-ATTTTAAAATTCACATGAAACCAAAAAT 1228
                           ii     v v  v  i-  -  ii         i   i  viiv  iv
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGGAAATGCAAGG 163

C chrX_154600844_   1227 AGCCC-GATTAGTCAAGGCAATCCTAAGCAAAAGGAACAAAGCTGGAGAC 1179
                         ii   -  v   i   ii     i i iv  i i        i     iv
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

C chrX_154600844_   1178 ATCATGCTATCCATCTTCAAATTATACCACAGGGATAGAGTAACCAACAC 1129
                         v   ii  vi   vi      viv   i   ii v  v     i   v  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

C chrX_154600844_   1128 AGCATGGTACTGGTACAAAAACAGACACATAGACCAACAGAACCGAAGAC 1079
                           ii         i i  ii i     i     i   ii   iv   vvv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

C chrX_154600844_   1078 AGAACTCAGAAATAAGACAAGATACCTACAATTATCTGATCTTTGACAAA 1029
                            iii         iv v v i ii  iii i vi    i  i     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

C chrX_154600844_   1028 GCTGACAAAAACAAGCAATGGAGAAAGGATGCCCTATTCAATAAATGGCG 979
                          v  v   i v  vv      i     i  ivi  v     i      i 
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

C chrX_154600844_    978 CTGGAATAACTGTCTAGCTATATGAAGAAGATTAAAACTGCACCCCTTCC 929
                             i i     vv  ? i i   v i    v i  ii  v      v  
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

C chrX_154600844_    928 TTATGCTATATACACAAATTGACTCGAGATGGATTAAAGACTTAAATGTA 879
                          i ii i       v     i    i i      i ?    i        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

C chrX_154600844_    878 AAACCCCAGACTATAAAAACCCTGGAAGACAACCTAGGCA-ATACCATTC 830
                          i v iv i         vi i i     v   v    ?i- v i -   
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTC 562

C chrX_154600844_    829 AGGGCATAGGCATGGGCAAAGATTTTATGACGAAAACACCAAAAGCAATT 780
                         iv i v v  vv i     v i   iv iivv vi            vvv
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

C chrX_154600844_    779 GCAACAACAACAAAAATTGACAAATGGGATATAATTAAACTAAAGAGCTT 730
                                v iv      v  i    v   iv v  i   v v  i i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

C chrX_154600844_    729 CTGCACAGCAAAAGAAACTATCAACAGAGTAAACAGACAACCTACAGAAA 680
                         i  ii vv    i  v        v i   i  v        i      v
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

C chrX_154600844_    679 GGGAGAACATTTTTGCAAACTATGCATCTGACAAAGGTCTAATATCCAGC 630
                                v  v        ii  ii      i  i  v  vi       v
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

C chrX_154600844_    629 ATCTATAAGGAACTTAAGCAAATTTACAAGAAAAAAACAACT---TCA-- 585
                           v     i     ivvi   v iv i  v     i    v ---i  --
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

C chrX_154600844_    584 TAAAAAGTGGGCAAAGGAC---ACTA-ACACTTTTCAAAAGAAGACATGC 539
                          ?    i           i--- v  -   i  i  v        i  i 
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

C chrX_154600844_    538 ATGTGGCCAGCAATCACATTAAAAAAAAGCTCAATATCACTGATCAT 492
                          vi      ii  v     -i    i v      i    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACAT-GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (137 / 89)
Gap_init rate = 0.01 (10 / 794), avg. gap size = 1.50 (15 / 10)  

3129 27.64 0.44 0.44  chrX_154600844_154608090     5847  6754 (493)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154600844_   5847 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5896
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154600844_   5897 GGCCATACTGCCCAAGGTAGTTTAGAGATTCAATGCCATCCCCATCAAGC 5946
                            v     v     iv ii i  v        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154600844_   5947 TACCAATGACTTTCTTCACAGAATTGGAAAAAAATACTTTAAAGTTCATA 5996
                          v   iivi i  i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chrX_154600844_   5997 TGGAACCAAAAAAGAGCGCACATTGTCAACACAATCCTAAGCCAAAAGAA 6046
                              viiv  ii  v vviv  v i   v      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chrX_154600844_   6047 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTGTACTACAAGGCCA 6096
                              i      vv   ii  v  ii i      viv        i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chrX_154600844_   6097 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCAA 6146
                               i   i    ii         i iv ii i   v       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chrX_154600844_   6147 TGGAACAGAAC--AGAGCCCTCAGAAATAACACCACACATCTACAACCAT 6194
                              i    i--    i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chrX_154600844_   6195 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 6244
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chrX_154600844_   6245 GTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTGA 6294
                         v  i  i              v      v  ?   i   v i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chrX_154600844_   6295 AACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGATT 6344
                          ii    i    v   i     v     v        i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chrX_154600844_   6345 AAAGACTTAAATGTTAGACCTAAAACCATAACAACCCT-AGAAGAAAACC 6393
                          ?    i       v   v       i    -   i  -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACA 547

  chrX_154600844_   6394 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 6442
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chrX_154600844_   6443 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 6492
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chrX_154600844_   6493 TTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGAAC 6542
                          i   v v  i i   i  iiivv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chrX_154600844_   6543 AGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACCCCTCTGACAA 6592
                           i     i                 v   i   vii iviv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chrX_154600844_   6593 AGGGCTAATATCCAGAATCTTCAAGGAACTTAAACAAATTTACAAGAAAA 6642
                         i  i  vi          v vi  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chrX_154600844_   6643 ATTCAAACAACCCCATCAAAAAGAGGGTGAAGGATATGAACAGACACTTC 6692
                          vv    i     v  i?    iv   ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chrX_154600844_   6693 ACAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATC 6742
                         v v        i  vi viii     i ii          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chrX_154600844_   6743 ATCACTGGTCAT 6754
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (143 / 104)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


4459 15.28 5.02 1.48  chrX_154698034_154703458.rev     4058  4934 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154698034_   4058 TAGAAAGAAAGCCCATGTTCATGGATCAGAAG-TTTAATATTGTTAAAAT 4106
                          i      v v               ii    -i             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154698034_   4107 GGC-----TCCCTAA-TTGATCTACAGATTCAACACAATCCCTATCAAAA 4150
                            -----    i  -                  i               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154698034_   4151 TCCCAGATAGCTTTTTTTGCTATCTGAAATTGACAAGCTCATCCTAAAGT 4200
                               v -  i        - ---              v        i 
  L1M4_orf2#LINE/    101 TCCCAGCT-GCCTTTTTTGC-A---GAAATTGACAAGCTGATCCTAAAAT 145

  chrX_154698034_   4201 TCAT--GAAAATGAAAGGTACCCAGAATAGTCAAAGCAATTTTGAGAAAG 4248
                             -- i     v    v           i    i    i    i    
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chrX_154698034_   4249 AA---TAAAGTTGGAAGATGAATATTTCCTGATTTTAAAACCTACTACAA 4295
                           ---i         i  ivv i i    ii    i     i        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chrX_154698034_   4296 AGCTATAATAATCATGACAGCCTGGTACTGGCATAAAGATAAAC------ 4339
                              i i      v     iv              i    i  ------
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chrX_154698034_   4340 -----TG-AACAGAACTGAAGGTCCAGAAACAAAGCTATACATCCATTGA 4383
                         -----  -  i    i   ii         i   v i      ii  v v
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chrX_154698034_   4384 TAACTAATTTTTGATAAGAATGCTAAGATCATTCAACAGGGAAAGAAAAG 4433
                         i  i i     i  i   ii   i    i       ii         v  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chrX_154698034_   4434 CCTTTTCAGCAAATGGTTCTGGAACAACTGTATATACATATTCAACAGAA 4483
                         i       i        v    i       v   ?v  i  v   v    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chrX_154698034_   4484 TTAAGTTGGATCTCTTCTTTATTCCATACATAAACATTAACTCAAAATAG 4533
                          v        i i  v i i iv     i i   v             i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chrX_154698034_   4534 ATCATAGATAGAAATGTAAGAGCTAAAACTAG-----TCTTAGAAGAAAA 4578
                             ?   ivv                    v-----             
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chrX_154698034_   4579 CAAAGTAGTAAATCTTCATGATCTTGGCTTAGGCGACAGTTTCTTAGATA 4628
                           v  v?          i   i     v      i ii            
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chrX_154698034_   4629 TGTTATTCAAAGCACAA---ACTAAAGAAAAAA---ATAAATTGGACTTC 4672
                           vi iiv         ---  v          ---              
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chrX_154698034_   4673 AT-------AAAAACTGTTGTGCTTCAAAGAACACCATCAAGAAAATGAA 4715
                           -------       v             i    i         i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chrX_154698034_   4716 AAGACAACTCACAGAATAGAGCAAAATATTTGAAAATCATGTATCTGATA 4765
                                 i        i iiv          v       i         
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chrX_154698034_   4766 AGGGTCTAGTATCCAGAATATATAAAGTACTGTTATAGCTCAACCATAAA 4815
                             v  v                   v   v   i i     iv     
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chrX_154698034_   4816 AAGACAAATAACCCACTTAAAAAC--AATAAAGTATTTTTAAATAGACAT 4863
                                        v  ?    v--iii    v    --i         
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT--GAATAGACAT 843

  chrX_154698034_   4864 TTCTCCAAAGGTAAAGAAAATATACGAATGGCCTATAAGCACATGAAAAA 4913
                                   ------  i      i       v               i
  L1M4_orf2#LINE/    844 TTCTCCAAAG------AAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chrX_154698034_   4914 ATGCTCAACATCATTAGTCAT 4934
                                      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (86 / 44)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.35 (57 / 17)  


3166 26.76 2.02 0.34  chrX_154705994_154712630.rev     5254  6146 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154705994_   5254 TGGAAAAACATTCCATGCTCATGGATAGGAAGA----ATAT--------- 5290
                               i i  i     i        v      ----    ---------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154705994_   5291 GGCCAAACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCCAGC 5340
                            v v   v      v i  i  i        i  v     i   v iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154705994_   5341 TACCATTGACTTTCTTCACAGAATTAGAAAAACACTACTTTAAATTTCAT 5390
                          v   vivi i  i  ii     v v  v  i -iv iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chrX_154705994_   5391 TTGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAGAAGA 5440
                         v     viiv  ii  v  viv        i      i i iv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chrX_154705994_   5441 ACAAAGCTGGAGACATCACGCTACCTGACTTCAAATTATACTACAAGGCT 5490
                               i     ivv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chrX_154705994_   5491 ACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGATACATAGACCA 5540
                                i   i    ii     i   i iv ii i   i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chrX_154705994_   5541 ATGGAACAGAACAGAGGCCTCAGAAATAACGCTACACATCTACAACCATC 5590
                               i    iv   ivii         vv i i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chrX_154705994_   5591 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 5640
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chrX_154705994_   5641 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATTCAGAAAACTGAA 5690
                           i  i        i     v      v  ?   i  v  i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chrX_154705994_   5691 ACTGGCCCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTA 5740
                         ii   v     v   i     v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chrX_154705994_   5741 AAGACTTAAACATAAGACTTAAAACCATAAAATCCCTAGAAGAAAACCTG 5790
                         ?    i    ii     vi      i      ii i           v i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chrX_154705994_   5791 GGCA-ATACCATTCAGGACATAGGTATGGGCAAAGATTTCATGACTAAAA 5839
                           ?i- v i -   iv   v v  vv i     v i    v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chrX_154705994_   5840 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5889
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chrX_154705994_   5890 AAAGCAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 5939
                            iiv  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chrX_154705994_   5940 GCAACCTACAGAATGGGAAAAAATTTTTGCAATCTATCCATCTGACAAAG 5989
                         i     i           i     v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chrX_154705994_   5990 GGCTAATATCCGGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAA 6039
                          i  vi     i    v  i  i     ivv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chrX_154705994_   6040 ACAA----CCCCATCAAAAAGTGTGTGAAGGATATGAAAAGACACTTCTC 6085
                             ----   v  i?    i  v ii      v    v     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chrX_154705994_   6086 AAAAGAAGACATTTATGTGGCCAATAAACATATGAAAAAAAAGCTCATCA 6135
                         v        i  vi vi          i  i       i v-     v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACA 897

  chrX_154705994_   6136 TCACGGGTCAT 6146
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 3.00 (21 / 7)  


 624 27.33 0.62 0.00  chrX_154724330_154730691.rev      188   348 (6014)  C L1M4_orf2#LINE/L1   (746)   162     1  

C chrX_154724330_    348 TGGAAAGATACCTTATGTTTATGGATTGGAAGAATCAATATTATTAAAAT 299
                                   i ii     i             v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chrX_154724330_    298 GTTCATACTGCCTGAAGCAATACACAGATTCAACACAATCCCTATTGAAA 249
                          viv     v  ii  vii  vi           i          ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chrX_154724330_    248 TTCCAATGGCATTTTTCACAGAA-TAGAAAAAAAAATTCTAAAATGTGGA 200
                          i   iiv  v     ii     - v  v  ivvi  i       viiv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chrX_154724330_    199 TGAAACTAGAAG 188
                           i  v iv   
  L1M4_orf2#LINE/    151 TGGAAATGCAAG 162

Transitions / transversions = 1.75 (28 / 16)
Gap_init rate = 0.01 (1 / 162), avg. gap size = 1.00 (1 / 1)  

3044 27.10 1.33 0.88  chrX_154724330_154730691.rev     4968  5871 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chrX_154724330_   4968 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5017
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chrX_154724330_   5018 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCTATCAAGC 5067
                            v     v     iv i  i  i        i  v           iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chrX_154724330_   5068 TACCAATGACTTTCTTCACTGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5115
                          v   iivi i  i  ii v   -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chrX_154724330_   5116 TGTGGAGCCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAG 5165
                          i    iviiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chrX_154724330_   5166 AACAAAACTGTAGGCATCATGCTACCTGACTTCAAACTATACTGCAAGGC 5215
                               ii  v   vv   ii  v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chrX_154724330_   5216 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5265
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chrX_154724330_   5266 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATACCACACATCTACAACC 5313
                                i    i--    i  --    i   vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chrX_154724330_   5314 ATGTCATCTTTGACAAACCTGACAAAAAGAAGAAATGGGGAAAGGATTCC 5363
                          vv v  i  i     ivv  v   i vv vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chrX_154724330_   5364 CTATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCT 5413
                           v  i                 v      v  ?   i   v i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chrX_154724330_   5414 GAAACTGGATCCCTTCCTTACACCTTATACTAAAATTAATTCAAGATGGA 5463
                            ii    i    v   i     v     v        i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chrX_154724330_   5464 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5513
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chrX_154724330_   5514 CTAGG--TAATACCATTGAGGACATAGGCATGGGCATGGACTTCATATCT 5561
                         v    --   - i v i v iv v i  i- i    vv ii   v  vv 
  L1M4_orf2#LINE/    547 ATAGGNGTAA-ATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chrX_154724330_   5562 AAAACACCAAAAACAATGGAAACAAAAGCCAAAATTGACAAATGGGATCT 5611
                          vi         i  vvi v        vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chrX_154724330_   5612 ------AATTAAGGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5655
                         ------      ii -   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chrX_154724330_   5656 AACAGGCAACCTACAGAGTGGGAGAAAAGTTTTGCAATCTACTCATCTGA 5705
                           v  i     i     i          vv       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chrX_154724330_   5706 CAAAGGGCTAATATCCAGATTCTACAAAGAACTCAAACAAATTTATAAGA 5755
                         i  i  i  vi        v v  i         vv    v iv    v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chrX_154724330_   5756 AAAGAAACAAACAACCCCATCAACAAGTGGGTGAAGGATATGAACAGACA 5805
                            - i     i     v  i? v  i    ii      v    i     
  L1M4_orf2#LINE/    794 AAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chrX_154724330_   5806 CTTCTCAAAAGATGGCATTTATGCAGCCAACAGACACATGAAAAAATGCT 5855
                         i     v     v ii  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chrX_154724330_   5856 CATCATCACTGGCCAT 5871
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (143 / 99)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


2749 26.79 2.84 0.79  chr20_32931_38007     3705  4585 (492)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr20_32931_380   3705 ATTCCATACTCATATATCAAAAAGATCAATGTCATTTAAATGGCTATACA 3754
                           i    ii    iv  iii  iiv i   i ii  v i     v    v
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr20_32931_380   3755 TTCCAAAGCAATCTACAGATTCAATGCTATTTCTATCAAACTACAAAAAC 3804
                         ii     vii              i  v  ii        v v v i-- 
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG--C 107

  chr20_32931_380   3805 TGC--TTTTCACAGAATTATAAAAAAACT-ATTCTACAATTCATATGGAA 3851
                            --    ii     --  vi v  i  -  i   v             
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr20_32931_380   3852 -TCCAAAAAGTACCCA-AATCACCAAAGCAATCCTAAGCAAAAGGAACAA 3899
                         - v   i-- v     -   vi     i     i i iv  i i      
  L1M4_orf2#LINE/    156 ATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr20_32931_380   3900 AGCCAGAGGCATCACATTATCTGACTTCAAACTATATTATAAACCCACAG 3949
                           iii    vv     i vi ii i      viv  i  i   v i    
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr20_32931_380   3950 TAACCAAAACAGC-TGATACTGGTACAAAAATAAACATATC-ACTAATGG 3997
                            i   i    i-  i      i i  ii   i      v- ii     
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr20_32931_380   3998 AACAGAATAGACAACCCAGAAATGAAGCCACACACCTACAGACATCTGAT 4047
                           i     v  v ii        i  v   i   ii  ii v  vi    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr20_32931_380   4048 CTTTGATAAAGACAACAAAAATAAGCA-CAGGGAAAAGACCCCCTATTCA 4096
                         i  i  i  i iiiv   i vi vv  -ii      ii ivvi  v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr20_32931_380   4097 ATAAACGGTGCTTGGGTAGCTGGCTAACCATATGCAGAAGAATGAAAGTG 4146
                          i   i      v  ii i    v  ?   i     i         iv  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr20_32931_380   4147 GACCCCTGCCCTTCACCATATATAAAAATTAACTCCACAAGGATTAAATA 4196
                                i  iiv         i            v v v    i ? v 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr20_32931_380   4197 TTTAAATGTAAGATCTTAAACTATAAGAATCCTGGAAGAAAACCTGGAAA 4246
                         ii           v  v         i v  i i         v i i?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr20_32931_380   4247 TAC-CCTTCTCAACATCCACGTT-GGTAAAGAATTCTTGGCTAAGTCTCC 4294
                           v-i    vii  v ivi-   -  i  v iv     i v  v v v  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr20_32931_380   4295 AAAAGCAATTGCAACAAAAACAAAAATTGGCAAGTGGGACCTAATTAAAC 4344
                                vvv         iv      v ii  i v    i v  i   v
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr20_32931_380   4345 TAAAGAGCTTCTACACAGCAAAAGAAACTCTCAACAGAGTAAACAGACAA 4394
                          v  i i   i iii vv    i  v   v    v i   i  v      
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr20_32931_380   4395 CCTACAGAATGGGAGAAAATATTCGCAAACTATACATCCAATAAAGGTCT 4444
                           i                    i     ii   i   ii    i  v  
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr20_32931_380   4445 AATATCCAGAATCTATAAGGAAATT----AATTCAATAAGCAAAAAA-AA 4489
                         vi          v     i   v i----  i       vv    i -  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr20_32931_380   4490 AT--CCCA--TTAAAAATGGGCAAAAGTTATAAACAGACACTTCTC---A 4532
                           --    -- ?             i v v i  i     i     --- 
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr20_32931_380   4533 AAAGACATACAAGTGGCCAAAAA--ACATGAAGA-ATTCTCATCATCACT 4579
                         i    i      i       v  --       i -  v    v     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr20_32931_380   4580 AATCAT 4585
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.76 (148 / 84)
Gap_init rate = 0.02 (20 / 899), avg. gap size = 1.60 (32 / 20)  


 991 25.06 7.29 3.19  chr20_40777_43316.rev        4   442 (2098)    L1M4_orf2#LINE/L1      353   809 (99)  

  chr20_40777_433      4 TTTTTTACAAAGATAT-AAAACCAATTAAATGAAGGAAGAATAATCTTTT 52
                             iv    i i ii-  i    -  v    ii i       i      
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_40777_433     53 TAA-ATATAGGTGATGGAACAGTTGCATATCCACAGGTTAAAAAA---AA 98
                         i  - v  -    v   i   ii  v   ?     v iv   i  --- i
  L1M4_orf2#LINE/    402 CAACAAAT-GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_40777_433     99 TTAA---CTTACCTAAACACCCCACATACATGAAAAAAAAGCCCTCAAAA 145
                           ii--- i     ---   v   i     --    vv  ---       
  L1M4_orf2#LINE/    451 TTGGACCCCTACCT---CACACCATATACA--AAAATTAA---CTCAAAA 492

  chr20_40777_433    146 TTGGTCATAGAATCACATGTAAGATGTAAAACCATAAAGCTTTTAAAAGA 195
                          v i   ?   vii v        vv      i     i  i   i    
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_40777_433    196 AAACATAGGAGAAAATCTATG-GAGCTTAATGCTTGGTTATGAGGTTTTA 244
                                  ? v      vi -  v   ii- i v  iv   ivv i   
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGG-GTTAGGCAATGGTTTCTTA 591

  chr20_40777_433    245 GACATGACACAAAAAGCCCAATCCATAAAA--AGTAATTGACAAATTTAA 292
                           i       v      v   v v i    -- iv   v  i     vi 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_40777_433    293 CTTCATCAAAGTCTTAAAA---TTTGCTCTGCAAAAGACCCTGTTAAGAA 339
                                   i --     ---    iv  v    i   v  i i     
  L1M4_orf2#LINE/    642 CTTCATCAAAAT--TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_40777_433    340 AATAAAAAGACAAGCAATAACCTTACAGAATGTATTTGCAGACTACACAT 389
                          i i         v v i ivv viv    vi        i ii i i  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_40777_433    390 --AATAA---------AT--AAAATATA----AAACTCTGAAAATT-AAC 421
                         --i    ---------  -- i      ----i      v v  i -  i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_40777_433    422 AGTAAAAGAAAAAAATTATCC 442
                          i     - i v    v i  
  L1M4_orf2#LINE/    790 AATAAAA-AGACAAATAACCC 809

Transitions / transversions = 1.49 (64 / 43)
Gap_init rate = 0.04 (20 / 457), avg. gap size = 2.30 (46 / 20)  

1941 24.73 1.81 3.97  chr20_40777_43316.rev      814  1367 (1173)    L1M4_orf2#LINE/L1        1   542 (366)  

  chr20_40777_433    814 TGAAAAAATATCCCATGCTCATGGATTGGAAGAATCAATATCATTTAAAT 863
                           i   i          i               v i     ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_40777_433    864 GGCCAAACTGCCCAATGCAGTCTATAGATTCAACACTATTTCTATCAAAC 913
                            v v   v     vviii    i         i v  ii        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_40777_433    914 TGCCA-TTATCATTTTTCACAGAATTAGAAAATCT-ATTCTACAATTCAT 961
                          v   -i ii -     ii     v v  v  v  -  i   v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_40777_433    962 ATGAAACCAAAAAAGAGCCCCAATAGTCAAAGCAAACTTAAGCAAAAGGA 1011
                            i  viiv  ii  v  vv     i    i   v   i iv  i i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_40777_433   1012 ACAAAGCTGGAGGCATCACATGACCTAACTTCAAA-----CTATAAGCCA 1056
                               i      vv     ivv  i  i      -----   i  iv v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_40777_433   1057 ACAGTAACCAAAACAGCATGATACTGGTACAAAAACAGACTCATAAACCA 1106
                                i   i    ii  i      i i  ii i    vi   i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_40777_433   1107 ATGGAACAGAATGGAGAACCTGGAAATAAAGCCACAAACCTGCAGCCATT 1156
                               i     v    ii ii        v   i v ii iii i  v 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_40777_433   1157 TGATCTTCAACAAAGACAACAAAA--ATTATCATGGAGAAAGGACTCCCT 1204
                             i   i    i iiiv   i --   -iv    i     --------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAG-------- 390

  chr20_40777_433   1205 ATTCAATAATTCTATTCAATAATTCAGTAATGGTGCTTGGATAGCTGGCT 1254
                         ----    i -  v     i  -------        v   i i    v 
  L1M4_orf2#LINE/    391 ----AATAGT-CTTTTCAACAA-------ATGGTGCTGGGACAACTGGAT 428

  chr20_40777_433   1255 AGCCATATGCAGAAGAATGAAAT-GGACCCCTGCCCTTCACCATGTATAA 1303
                          ?   i     i         i -        i  iiv      i  i  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr20_40777_433   1304 AAATTGACTCAAGTTCGATTAGAGATTTAAATGTAAGATCCAAAACTTTA 1353
                              i      iv v   i ?   ii           v i      v  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr20_40777_433   1354 AGAATCCTAGAAGA 1367
                          i v  i       
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGA 542

Transitions / transversions = 2.07 (91 / 44)
Gap_init rate = 0.02 (10 / 542), avg. gap size = 3.20 (32 / 10)  

 833 26.29 5.69 2.44  chr20_40777_43316.rev     1680  2048 (492)    L1M4_orf2#LINE/L1      528   908 (0)  

  chr20_40777_433   1680 AAGAATCCTAGAAGAAAACCTAGAAA-ACACCATTCTCAACATCACCTTG 1728
                           i v  i           v   i?i- v i -   vii  v iivv  i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTA 576

  chr20_40777_433   1729 GAAAATAATTTAT--GACTAAGTTCTCAAAAGCAATTGAAAAAAACAAAA 1776
                          iv   ii   v --  -  v vivi        v----  iv       
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGA-TATGACACCAAAAGCAC----AAGCAACAAAA 621

  chr20_40777_433   1777 ACCAAAAATTGGA-AAGTGGGACTT------AATTAAA--CTTCTGCACC 1817
                         i--     v i  -  i v      ------       --   i  ii i
  L1M4_orf2#LINE/    622 G--AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr20_40777_433   1818 ACAAA----ACTCTCAACAGAGTAAACAGATAACCTATAGAATGGAAGAA 1863
                         v    ----   v    v i   i  v   i    i i       i    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_40777_433   1864 AATATTTACAGACTATGCATCCAACAAAGATCTAATATCCAGAATCTATA 1913
                                i  i ii  ii   ii i  i iv  vi          v    
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr20_40777_433   1914 AGGCAATTAAACAATTCAATAAGAAAAAAA-----AACTCATGGAAAAAA 1958
                          i v v ivv    i       v     i -----   i  vvv?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_40777_433   1959 TGGGCAAAGGACACAAACAGACACTTCTCAAAGGAAGACATATAAGTGCT 2008
                                    ivii  i     i     v  i     i   i  i  vi
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr20_40777_433   2009 CAACAAACATATGAAAAAAATGCTCATCATCACTAATCAT 2048
                            i  i  i       i -      v     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (60 / 35)
Gap_init rate = 0.03 (12 / 381), avg. gap size = 2.50 (30 / 12)  


 205 26.42 0.00 0.00  chr20_58106_64382        3    55 (6222)  C L1M4_orf2#LINE/L1   (855)    53     1  

C chr20_58106_643     55 TGGAAATGCCTCCCATGCTCATGAAAAGGAACAATCAATTTTGTTAAAAT 6
                               viiv       i     i vv    v v i   v       i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr20_58106_643      5 GAC 3
                          i 
  L1M4_orf2#LINE/     51 GGC 53

Transitions / transversions = 1.00 (7 / 7)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.00 (0 / 0)  

3317 26.16 0.77 0.55  chr20_58106_64382     4880  5785 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_58106_643   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_58106_643   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_58106_643   4980 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5027
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_58106_643   5028 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCTTAAGCCAAAAG 5077
                                viiv  ii  v  v v  v     iv       i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_58106_643   5078 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5127
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_58106_643   5128 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATGTAGATC 5177
                                 i   i    ii         i iv ii i   v  i      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_58106_643   5178 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCCATAC--CTACAAC 5223
                                i    i--    i  --        -i       --i  iiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAA-ACCCATACATTTATGGT 345

  chr20_58106_643   5224 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5273
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_58106_643   5274 CCTATTTAATAAATGGTGCTGGGAAAACTGG-TAGCCATATGTAGAAAGC 5322
                         i  v  i  i              v      -  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_58106_643   5323 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5372
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_58106_643   5373 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5422
                           i ?   ii    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_58106_643   5423 CCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCA 5472
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_58106_643   5473 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5522
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_58106_643   5523 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5572
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_58106_643   5573 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5622
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_58106_643   5623 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5672
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_58106_643   5673 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5722
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_58106_643   5723 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5772
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_58106_643   5773 CATCACTGGCCAT 5785
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


2689 27.12 2.90 1.56  chr20_111361_115972     3225  4120 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_111361_11   3225 TGGAAAAACATTCCATGCCCATGGGTTGGAAAAATCAATATCATTTCAAC 3274
                               i i  i     ii     i      i v i     ii  vvi i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_111361_11   3275 AGTCATTCTGCCCAAAGCAATCTACAGATTCAATGTTATTCCTATCAAAC 3324
                         i iv  v  v      vii              i iv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_111361_11   3325 TACCAAA-GCCATTTTTCACAGAATTAGAAACAACT-ATCCTGAG-TTCT 3371
                          v   iv-   -     ii     v v  v - i  -     i i-   v
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chr20_111361_11   3372 TATGGA---GCCAAAAAAAGAGCCTGAATAGGCAAAACAATTCTAAGCAA 3418
                               ---  ----  ii  v  v      v         ii i iv  
  L1M4_orf2#LINE/    149 TATGGAAATGC----AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_111361_11   3419 AAAGAACAAAGCCAGAGGCATC-TAATTACCCATCTCAAACTACACGATA 3467
                         i          iii    vv  -i v  v  v  i     vivi  v i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_111361_11   3468 AGGTTACAGTAACTGAAACAGCATAATACTGATACAAAAACAGACATATA 3517
                          i i        iii i    ii ii     ii i  ii i         
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_111361_11   3518 GACCACTGGAACAGAATAAAGAATCCAAAAATAAAGCTGCATGCCTACAG 3567
                           i  v     i     vi   i    i       v iii iiii  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_111361_11   3568 CCATCTGATCTTTGACAAAGTCAACAAAAATACGCAATGGGAAAAGGGC- 3616
                         i  vi    i  i     i viiv   i vi iv       i    iii-
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_111361_11   3617 -TCCTTATTCAATAAATGGTGCTGGGATAGCTGGCAAGCCACATATAGAA 3665
                         -  i  --    i              i i    vv ?      ii i  
  L1M4_orf2#LINE/    395 GTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_111361_11   3666 GAATAAAACTGGACCCCT-CCTCTCACCATATA-AAAAATTAACTCAAGC 3713
                             i  ii         -    v         -              iv
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_111361_11   3714 TGGATTAAAGATAGAAATGTAAGAACTCAAATTACAAGAATCCTAGAAGA 3763
                              i ?   ivv          i  v   i  i  i v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_111361_11   3764 CAACCTAGAA--ACACCATTCTGGACATAGGTCTTGGGAAATAATTTAT- 3810
                         v   v   i?-- v i v iv  iv v i   -- i  v   ii   v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGT--TAGGCAATGGTTTCTT 590

  chr20_111361_11   3811 -GACTAAGTCCTCAAAT---CAATTGCAACAAAAACAAAAATTGACAAGT 3856
                         -  -  v v vi    v---   --         iv      v  i  i 
  L1M4_orf2#LINE/    591 AGA-TATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAAT 637

  chr20_111361_11   3857 GGGACCTAGTTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAAC 3906
                         v    i vi i   v v  i i   i  ii vv    i  v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_111361_11   3907 AGAGTAAAAAGACAACATACA--ATGGTAGAAAATATC-ACAAACTATGC 3953
                          i   i          vi   --    v         i-i    ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_111361_11   3954 CTCTGACAAAGGTCTAATATCAAGCATCTATAAGGAACTT----AATTCA 3999
                         v     i  i  v  vi    v  v  v     i     i----  i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_111361_11   4000 ACAAGCAAAAAGA-AAATAGCCCCATTAAAAAGTGCGCACAAGACATGAA 4048
                          i  -i       -     i   v   ?    i  v   v i  iv    
  L1M4_orf2#LINE/    788 ATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_111361_11   4049 CAGACACCTCTAAAAAGAACACGTACAAGTGGGCAACAAATATATGAAAA 4098
                         i     ii   vv      v ii     i   v   i  ii i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_111361_11   4099 AATGTTCAGCATCACTGAACAC 4120
                         i   i   i     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.91 (157 / 82)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.74 (40 / 23)  


3842 15.23 3.37 3.87  chr20_340385_342510.rev      449  1249 (877)    L1M4_orf2#LINE/L1       14   810 (98)  

  chr20_340385_34    449 CAT-TTCAAGAAGTAGATATCTCAATATTTTGTTTAAAAT--CAAG--TG 493
                            -    v i v i  viv  i      --   -  i  --   v-- v
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATT--GTT-AAGATGGCAATACTC 60

  chr20_340385_34    494 GCCAA--TGATCTACAGATTCAATGAAATCCCTACCAAAATTCCCAGTTG 541
                         v    --                i v        i      -     i  
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT-CCCAGCTG 109

  chr20_340385_34    542 TTGTTGTTTTTTTTTTGCAGAAACAGACAAGCTGATCGTAAAATTTATAT 591
                         ii--------             iv            v       i    
  L1M4_orf2#LINE/    110 CC--------TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr20_340385_34    592 GGAAATTCAAGAGACTTGCAATAACCAAAACAATATTGAAAAAGAACAA- 640
                               v    i   iiiv    i          v           v  -
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_340385_34    641 -AAGTTGGAGAACTTGTATTTCCTGATTTCAAA---TACTATGAAGCTAT 686
                         -         i   iii i    ii        ---     ii      i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr20_340385_34    687 AGTAATTA-----GTGTGGTACTGGCGTAAGGGCAGATATATATTATAGT 731
                               i -----             i     ii   i     ----- v
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA-----GA 296

  chr20_340385_34    732 TCAATGGTATAGAAATGAGAGTCCAGAAATAAGCACTCACATTTATGGTC 781
                                v      v                 i v vi            
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_340385_34    782 AATTAATTTCCAAAAAGGGT--TAAGATGATTAAACAGAGGAA-AACAGC 828
                             i    i i v      --i    iv   v  ii i i  -  i  i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_340385_34    829 CTT---AACAAATAGTGCCGGCACAACTCAATATCCACGTGCAAAAGAAT 875
                            ---       i    i  v      vi   ?    i           
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_340385_34    876 GAAGCTGGACCCTTACCTCACACCTTATATAAAAATTAAATCAAAATGGA 925
                             i       i           v    i         v          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_340385_34    926 CCAAAGACCTAAATGTAAGAGCTAAAACCATAAAATCTTTAGAAGAAAAT 975
                         i  ?                        i      iii           i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_340385_34    976 ATAGAGGTAAATCTTCATGACCTTGGATGAGGCAACGATTTCTTAGATAT 1025
                             i?          i         i v      i i            
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_340385_34   1026 GACACCAAAAGCACAAACAACAAAATAAAACATAGACTAACTGGACATCA 1075
                                         i        v    v     iv  i     v   
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_340385_34   1076 TCAAAATTTAAAACTTTTGTGGTTCAAAGGATACCATCAACAAAGTGAGA 1125
                                 v            v         i  i     v       i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_340385_34   1126 AGACAATCCACAGAATGAGAGAAAATTTTTGCAAATCATGTAGCTGATAA 1175
                               i          i        v            i  v       
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_340385_34   1176 GCTAAAATGAATAAAGTACTTCTAGCTAAAATGAATAAAGTACTCCTACA 1225
                          -------------- v    v  v i i   iv      v    i    
  L1M4_orf2#LINE/    747 G--------------GGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr20_340385_34   1226 ACTCAATA-TAAAAACATAAA---CCCA 1249
                                 -      v i   ---    
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCA 810

Transitions / transversions = 1.83 (77 / 42)
Gap_init rate = 0.02 (18 / 797), avg. gap size = 3.22 (58 / 18)  

 406 16.38 16.38 0.00  chr20_340385_342510.rev     1519  1634 (492)    L1M4_orf2#LINE/L1      774   908 (0)  

  chr20_340385_34   1519 ACTC---CATCTCAAAAAAAAAAAAAGATA-AACCCAATTTTAAAATGGG 1564
                             ---  v     v  v     i v v -         ?v        
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr20_340385_34   1565 CAAAAGACCTGAATAGGCAAACCTCCAAAGAAAATAT------------- 1601
                             i  ii       i  vvi          i    -------------
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr20_340385_34   1602 --GTGCATGAAAAGATGCTTAACATCATTTGTCAT 1634
                         -- ii              i       ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (10 / 8)
Gap_init rate = 0.02 (3 / 135), avg. gap size = 6.33 (19 / 3)  


 905 23.50 3.42 0.00  chr20_448389_450460      501   734 (1338)    L1M4_orf2#LINE/L1      153   394 (514)  

  chr20_448389_45    501 GAAATCCAAATGAACCAGAATAATCCAAACAATTCTGAAAAATAA---TA 547
                              v   iv  v        ii v       ii       v  ---i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_448389_45    548 AAGCTGGAAGAATTATACTAACTGATCTTAAA-CTTATTACAAAGCTATA 596
                            i    i  v i i   vv ii  i i   -    i          i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_448389_45    597 GTTGTCAAAACAGTGT---ATTGGCAAAAGGATA-ATACATAGATCAAGG 642
                           vi    i       --- i     v       - i i         v 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr20_448389_45    643 GAACAGAATAAAGAGTACAGAAATACACTCACACAAACAAGGCCAATTAA 692
                            i     vi     v        v  i  i   vvi v  i     i 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_448389_45    693 TTTTTGACAAAGGTACAAAGGCAGTTCAATGGAGAAAGGACA 734
                             i     i   i v   i vi        i     i i 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

Transitions / transversions = 1.89 (36 / 19)
Gap_init rate = 0.02 (4 / 242), avg. gap size = 2.00 (8 / 4)  

1015 21.98 7.69 12.82  chr20_448389_450460     1038  1583 (489)    L1M4_orf2#LINE/L1      391   908 (0)  

  chr20_448389_45   1038 AATAATCTTTTCTATAAATTGTTTTGGAAGACTTGGAGATCAATATGCAA 1087
                             i       v i    v  vi   i v vi    v ? v i      
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr20_448389_45   1088 AATCATAAACTTTAATCTAAATCTCACACTTTATATAAAGAT-AATTCAT 1136
                           vv  i  v  vi i ivv i       iv    i   i  -  i   v
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr20_448389_45   1137 AATGAATCACAGATATCAATGTAAAACTTGGGTCAGATGCGGTGGCTCAT 1186
                             i    ?   iv v       i ------------------   v -
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGA------------------GCTAA- 521

  chr20_448389_45   1187 GACTGTATAATCCCAGGCTGGGTGACAAGGCAAGACTCTACCTCTGGGGG 1236
                         i   i  ------------------------- i     ----- -----
  L1M4_orf2#LINE/    522 AACTATA-------------------------AAACTCT-----T----- 536

  chr20_448389_45   1237 GGAAAAAAAAAGATATAAATGTAAAATTATCAAACCTTCTTGCAACCAGG 1286
                         ---- i  i  i i   ii?     ---------i    v  --   vv 
  L1M4_orf2#LINE/    537 ----AGAAGAAAACATAGGNGTAAA---------TCTTCGTG--ACCTTG 571

  chr20_448389_45   1287 GGTTAGGCA--GAGTTTGAAGACATGACACTAAAAGCATGGGCTGTAAAA 1334
                                  -- iv  ivv   i       i       iii  vii    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr20_448389_45   1335 -------CTGATAAACTGAACTTCATCAACGTTAAAATATTTCTGCTCTG 1377
                         -------iv      i  i          vi      - i  i  iv  v
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTT 670

  chr20_448389_45   1378 TGAAAGACACTATTAAGAAAAT---AAGCCAG---ACACAA--GAAGAAT 1419
                         ii  i        i      i ---   v  i---   v  -- i    v
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr20_448389_45   1420 GTATTTGCAAATCACAAATCGAATAAAGAACTTGTATCTGTAACAT-TAA 1468
                         i             i v   vi    i i         iiv  i  -   
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr20_448389_45   1469 AAAACTC------------AATAAGAAAACAG----CTCAATTTAAAAAT 1502
                          i     ------------     i  i   i---- i     ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr20_448389_45   1503 GGGCAAAAGACGTGAACATACACACCACAAAAGAAGATATACA------C 1546
                                i  iv    i v   ivi v v              ------ 
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr20_448389_45   1547 A-TAAGTATATGAAAAGATACACAACACTGCCAGACAG 1583
                          -    i i          i v     iii????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (75 / 41)
Gap_init rate = 0.04 (19 / 518), avg. gap size = 5.89 (112 / 19)  


 748 27.68 10.98 5.25  chr20_1025365_1027494.rev      370   788 (1342)    L1M4_orf2#LINE/L1        7   449 (459)  

  chr20_1025365_1    370 GGTATCATCTATGTTCATGT-TTG-----TTCAAC-TTGCAGTGATGTCA 412
                          i    -- i         v-   -----i i  i-   iviv    v  
  L1M4_orf2#LINE/      7 GATATC--CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr20_1025365_1    413 CCTTTTCCTGATTGGGCCTACAAATTTAATGCAGTCTTGATTAAG-CCTC 461
                         vivi i  ii v v ii     i   i  i   i  iiv  i  i-i i 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr20_1025365_1    462 AGGAAATTTTTCTTTCTTTCTTTGAAAAAAAAAAAAAGTCAATCTTATTC 511
                           ---------  vi    -    v i   vvi v   -----  v  i 
  L1M4_orf2#LINE/    105 AG---------CTGCCTTT-TTTGCAGAAATTGACAAG-----CTGATCC 139

  chr20_1025365_1    512 TAAAATTTACATGAAAACCCAGAG--CCAAGAATAGCCAAATAAAATCTT 559
                                i i   i   iv  ii --  v            - v      
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA-ACAATCTT 188

  chr20_1025365_1    560 GAAGAAGAAA-------TT--AGGATTT-CACT--CTAG---CAGAGATG 594
                            i     i-------  --    i i-    -- i i---  i - iv
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-ACT 237

  chr20_1025365_1    595 TAAATTATAAAAT--CAGTAATTGAGGTAAGGTAGTATTGGCACAAAGA- 641
                           --i  i   ii--       ii  ii iv  i   i     i  i  -
  L1M4_orf2#LINE/    238 TA--CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr20_1025365_1    642 ---------GACCAATGGAAT-GCAC--AGAATCTAGAAACAGCCCCA-- 677
                         ---------  i         - v i--   i  i     i iv    --
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr20_1025365_1    678 CCTGTATG-TGA--TGATTTAGGACAAAAATGACCATG-TAGTACAGTGA 723
                          v v    - v --      vv     iii  -   v -ivi v  i  i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGG 384

  chr20_1025365_1    724 GGAAAAAGCAGACTTTTCAATAAATGGTGATAGGGCAATAGGATGTCCAT 773
                              i ii  v        i        v i  i   iv    i?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr20_1025365_1    774 TTGGGAAAAAATAAA 788
                         v  vi   i   i  
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAA 449

Transitions / transversions = 2.29 (80 / 35)
Gap_init rate = 0.06 (26 / 443), avg. gap size = 2.62 (68 / 26)  

 950 29.07 6.51 1.40  chr20_1025365_1027494.rev     1209  1638 (492)    L1M4_orf2#LINE/L1      457   908 (0)  

  chr20_1025365_1   1209 CCCTACCTCACACCAT-TA----AATTAAT---AAATAAAT--AAATCCC 1248
                                         -  ----      i---    ii  --? iv  i
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr20_1025365_1   1249 AGGTGATTTGTGAATCTAAATT-TGAAAATC-------AAAACAATAGGT 1290
                          ii  --- iv  iiiv   i - i   v  -------      -    ?
  L1M4_orf2#LINE/    507 AAATG---TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA-TAGGN 552

  chr20_1025365_1   1291 AAATATATTCTTGTCCTTAGGTTAGGCAAAGATTCCTTAAATGGTTCAG- 1339
                         iv v  v   v  v    i          v i  i    i  ivvv  v-
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr20_1025365_1   1340 AGAAATGCTAATCATAAAGGAAGA--TTGATAAACTGGACTTTATTGAAA 1387
                          i  iii v iiv i   i   i -- v      i       i  ii   
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr20_1025365_1   1388 TTAGGAATGTCTGTTCATCCAAAGACATTATCAAAAAAGC-AAAAGGTAA 1436
                            ii  iv i   v v  v  i    i      i    i-     ii  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr20_1025365_1   1437 ACTACAGAGTAAAAGAACACATTTGCTGTATGA-ACAACCAAAAAAGGAC 1485
                         v i     i iii    v i      vi-  v - i v ii v  i    
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATAAGGGAC 751

  chr20_1025365_1   1486 TTGTCAAATAGAACATATAAAAAGTGCCTTCAG-TCGTTAAGAAAAAGGC 1534
                             - vvi    i       i iiv i v  i-  iv   v      i 
  L1M4_orf2#LINE/    752 TTGT-ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_1025365_1   1535 AA----TTCAATTTAAAAAGGGACAACACACCCAAACAAGCTCTTCACAA 1580
                           ----ii     ?     v  i   viv iiii  i ii vi   v v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_1025365_1   1581 AAGAGAATATCCAAATGGCCAATAAGCAATTGAAAATGTGCTCAGCTTCA 1630
                             ii    v                 vv      vi      i v   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr20_1025365_1   1631 CTGGTTAT 1638
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.77 (78 / 44)
Gap_init rate = 0.04 (16 / 452), avg. gap size = 2.12 (34 / 16)  


2243 11.62 4.54 29.31  chr20_1028149_1030958.rev      862  1963 (847)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr20_1028149_1    862 TGGGAAGAAATCT-GTGTTCATA-ATTGAAAGAGATAATATTG------- 902
                            i    v   i-i       i-    i    vv        -------
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_1028149_1    903 -GCAATATTCTCCAAATTGATTTATAGAT-CATAGTAATTCCTATCAAAA 950
                         -      i  i          i  i    -  vv i   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_1028149_1    951 TCCCAGCTGACTATTTGGCAGATATTGATAAGTTGGTCCTAAAATTCATG 1000
                                  v  v   v     v     i   i  i             i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_1028149_1   1001 TGGAAATGCAAGGGACCTAGAAAGGTCAAAATAATCTTAAGAAGGAA--A 1048
                                          i    vi i     i      i i  i   -- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_1028149_1   1049 CA---TTGGCAGACTCATACCTTCCTATTTTGAAATCTTTTACAAAGCTC 1095
                           ---    vi      i  i i  v    ii   ii vi         v
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_1028149_1   1096 TAGCAATCAAGACTATGTGGTACTGGCATAAGGATAGACATATAGATCAC 1145
                         i  i         vi                                  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_1028149_1   1146 TGGAACAGAATTGAGAGTCCAGAAATAAGTAAATTCATACATTTATGGGC 1195
                              i                      ---- ii             v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAA----ACCCATACATTTATGGTC 346

  chr20_1028149_1   1196 AATTGATTTTTGATAAAGATACTAAGATAATTCAATGGGGAAAAGAATAG 1245
                                   i  i  i i i i    iv              -      
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAG 395

  chr20_1028149_1   1246 TCTTTTATTTCTCTTTCTTTTTTTTTTTTTTTGAAACGAAGTCTTGCTCT 1295
                               ---------- -----------------   i  ----------
  L1M4_orf2#LINE/    396 TCTTTT----------C-----------------AACAAA---------- 408

  chr20_1028149_1   1296 GTCACCCGGGCTGGAGTGAAGTGGCATGATCTCAGCTCACTGCAACCTCC 1345
                         --------------------------  i --------------------
  L1M4_orf2#LINE/    409 --------------------------TGGT-------------------- 412

  chr20_1028149_1   1346 ACCTCCTGGGTTCATGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGG 1395
                         --------------------------------------------      
  L1M4_orf2#LINE/    413 --------------------------------------------GCTGGG 418

  chr20_1028149_1   1396 ACTACAGGTGTGTGCCACCATGCCTGGCTAATTTTTTTTGTATTTTTAAT 1445
                           ------------------------------------------------
  L1M4_orf2#LINE/    419 AC------------------------------------------------ 420

  chr20_1028149_1   1446 AGAGATGGAGTTTCACCATGTTGGCCAGGCTAATCTCAAACTCCTTACCA 1495
                         --------------------------------------    --------
  L1M4_orf2#LINE/    421 --------------------------------------AACT-------- 424

  chr20_1028149_1   1496 CGTGATCTGCCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAG 1545
                         ----------------------------------    ---------- ?
  L1M4_orf2#LINE/    425 ----------------------------------GGAT----------AK 430

  chr20_1028149_1   1546 CCACCATGCCTGGCCAAAGAATAGTCTTTTCAACAGATGGTCCTGGAATG 1595
                             ----------------------------------------------
  L1M4_orf2#LINE/    431 CCAC---------------------------------------------- 434

  chr20_1028149_1   1596 ACAGAATACAAAAGACTAAAGGTGGATTCTTATCTTAATCCATATATGTA 1645
                         -----  i       v i   v    ii i  i  i vv       iiv 
  L1M4_orf2#LINE/    435 -----ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr20_1028149_1   1646 AATTGACTAAAAATGGATCAAAGTCTTAAATGTAAGAGCTAACACTATAA 1695
                             i   v           ?  v i                v       
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr20_1028149_1   1696 AACTCTTAGAATAAAATTTAGGAGTAAGTCTTCATTGCCTTGGATTAGGC 1745
                                    v    iv    ?    i     i vi      i      
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr20_1028149_1   1746 AATGTTTTTTTCAATATAACATCTAAAGCACAAGCAACCAAAAGAAAAA- 1794
                             v   i  vi    i   i v              -          -
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC-AAAAGAAAAAA 628

  chr20_1028149_1   1795 ------------------------TTGAAGATGTTTGTA-TTCAAATAAC 1819
                         ------------------------  i  i iv     i-      vi  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr20_1028149_1   1820 ACTATCAAGAAAATTAAAAGACAACCCACAGAATTGGAGAA--TATTTCC 1867
                                     i v                   v      --     v 
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr20_1028149_1   1868 AAAACACATATCTGATAAGGGTCTAAATATCCAGAATATATA-----CTC 1912
                            v  i              v  vi-               -----   
  L1M4_orf2#LINE/    729 AAATCATATATCTGATAAGGGACTTG-TATCCAGAATATATAAAGAACTC 777

  chr20_1028149_1   1913 CTACAGCTCAGGAATTAAAAAACCA-CAACCCAATTTAAAAATGGACCAA 1961
                         i    i    iv   v    i  v -i         ?        i v  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr20_1028149_1   1962 GG 1963
                           
  L1M4_orf2#LINE/    828 GG 829

Transitions / transversions = 1.82 (80 / 44)
Gap_init rate = 0.03 (23 / 829), avg. gap size = 16.22 (373 / 23)  

 476 17.02 0.00 0.00  chr20_1028149_1030958.rev     2225  2318 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr20_1028149_1   2225 AAAAAAAGACAAAGGATTTGTGTAGACGTTTTTCCAAGGAAGATACACAA 2274
                              vi i           vi     i   i     i       i    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr20_1028149_1   2275 ATGGGTGATATACACATGAAAAGATGATCAACATTATTAGTCTT 2318
                             vii   vi              v       i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.20 (11 / 5)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


3557 17.61 1.31 0.15  chr20_1039640_1041317      501  1187 (491)    L1M4_orf2#LINE/L1      214   908 (0)  

  chr20_1039640_1    501 CTCATACTTCCTGATTTCAAAACTTACTACAAAGCTACA-TAATCAAAAC 549
                             i      ii                          -       i  
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr20_1039640_1    550 ATTATGGTACTGGCATAAAGACAGACATATAGACCAATGGAACAGAATAG 599
                          v i              i  i           i        i     v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr20_1039640_1    600 AGAGCCCAGAAATGAACCTTCACATGTATGGCCAAATGATTTTCAACAAA 649
                             i        i    ivi    v     i   v        i    i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr20_1039640_1    650 GACACCAAGACCATTCAATAGGGAAAGAACAGCCTTTTCAACCAATGATG 699
                          iii               i         i  i         v    i  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr20_1039640_1    700 CTGGGGAAACTGGATATTCATATA-AAAAGAATGAAGCTGGACCTCTCCT 748
                              iv         ?i  i  i-            i      i  v i
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr20_1039640_1    749 TCACACCACACATAAAAATGAACTCAAGATGGATCAAAGACCTGAATGTA 798
                                 i i i      v       i        ?      i      
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr20_1039640_1    799 AGACGTAAAAATATAAAACTCTTGGAAGAAAATGTAGG-GCAAATTCTTC 847
                            vv     v            i        ii    - i    -    
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTC 562

  chr20_1039640_1    848 ACAACACTGGATTTGGCAGTGATTTCTTGGATGTGACATCAAAGGCACAG 897
                         iii  vi   i  v    i  i      i   i     i    i     i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr20_1039640_1    898 GCAACAAAAGGAAAATCAGGCAAATTGAACTTTATGAAAATTAAAAGCTT 947
                                   i    vi  ii      i    i  v          i   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr20_1039640_1    948 TTGTGCATCAATAGACACTATCAACAGAGT-AAAAGGCAATTCACAAAAA 996
                               v    vi           v i   -     i   ii    i  v
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr20_1039640_1    997 GGCAGAAAATATTTACAAATCGTATATCTGATAAGGGAATAATATCCAAA 1046
                           v           i      i                v vi      i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr20_1039640_1   1047 ATATACAGAGAACACCTAAAATTGAACAACAAAAA-CCCAACAACTCAGT 1095
                              i i     v i  v  i v  i  i     -v v  i   i  i 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr20_1039640_1   1096 TAAAAAATGGGTAAAGGACTTGAACAAACATT-CTCC---TAAGTCATAC 1141
                          ?         i      i     i i     -    ---v   vi    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr20_1039640_1   1142 AAAAGGCCAATAAGTACATCAAAAGTTGCTCAGCATCCCTAATCAT 1187
                            v          i    v     v      i    v????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.47 (84 / 34)
Gap_init rate = 0.01 (8 / 695), avg. gap size = 1.25 (10 / 8)  


4223 16.28 4.21 3.77  chr20_1067343_1073327     1270  2172 (3813)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr20_1067343_1   1270 GGAAAGACATTCTGTGCTCACGGCTAGGAAGAATTAATATTA-------- 1311
                                i  i ii  i   i  v v      v        i--------
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_1067343_1   1312 GCCATACTCCCCAC-TTGATCTACCTATTCAGTGCGATCCCAGTGAAAAT 1360
                           v          v-         vv     ii  i     vi v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_1067343_1   1361 CCCAGCAGGTTTTGGGTTTTTCCCCCCCAGAAATTGGCAAGCTGATCCTA 1410
                               v vi   -----   v -----        i             
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTT-----TTTGC-----AGAAATTGACAAGCTGATCCTA 141

  chr20_1067343_1   1411 AAATTCAGGTAGAAATGCAAGGGAACCAGAATGGCTAAAACAATCTC--- 1457
                                vi i             v       i  i          i---
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr20_1067343_1   1458 AAAGAAAAACAAAGTTGAAAGACTTCCAGATCCCTATTTCAAAACTTATT 1507
                               i          i i    iv  vv    v             i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr20_1067343_1   1508 ACAAAGCTTCAATCATCAGGACCGTGTGGCACTGGCATTAGGATAAACAT 1557
                                 v  i v    i   v      i        v      i    
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_1067343_1   1558 ATAGAGCAAGGAAATAGAATTGAGAGTCTAGAAATTAACCCATACATTCA 1607
                              v   v i                i      v            i 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_1067343_1   1608 TAGGGAATTGATTT-CAGCAAGGTTGCCAAGACAATTTAGTAGAGAAACC 1656
                          i vv         - ii     v         v   i i i i    vv
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_1067343_1   1657 ATAGTCTTTTCAA---ATGGTGCTGGGACAATTGGATATCTACATGCAAA 1703
                                      ---               i      ? i         
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_1067343_1   1704 AGAATGAAGTTGGGTCCCTTCCTCG--------------ATTACCTCTAA 1739
                                      ii    v    i--------------    v   v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_1067343_1   1740 ATGAATCACACACCTGAGTGTAAGAGCTTGAACTATAAAATTTCTAGACC 1789
                            i    ? v    i i          vi          i ii    --
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA-- 539

  chr20_1067343_1   1790 TAGAAATAAGTCTACCTTGG-GTAG-TCTTATTCCCTGACCTTCAGTTAG 1837
                         -     -------  v v  -   i-    ---- v       vi     
  L1M4_orf2#LINE/    540 -AGAAA-------ACATAGGNGTAAATCTT----CGTGACCTTGGGTTAG 577

  chr20_1067343_1   1838 ACTGTGGTTTCTTAGACACAATACCTGGGAGGTTAAAAGCACAAGCAGCG 1887
                         i vi            i ii i   ---------             i i
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACC---------AAAAGCACAAGCAACA 618

  chr20_1067343_1   1888 A--GAAAAAATAGACAAATCAAACTTTGTCAAAATTAAAATATTTTGTGC 1935
                          --           i    iii    ii            vv        
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr20_1067343_1   1936 ATAAAAGGATAGTATCAAGAAACTGAAAAGATAACCCAAAGAATGGGAGA 1985
                         v v      i v          v        i      v           
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr20_1067343_1   1986 GAATATTTGCAAATCAGATATCTGACAAGAAGCTTGTATCCAGAATATAT 2035
                         i               v        i   iii                  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr20_1067343_1   2036 AAAGAGCTCTTACGACTGAACAATACAAAAGA-AAA---CTCAATTTTAA 2081
                              i       i   v  i    -      -   --- i     ?v  
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATA-AAAAGACAAATAACCCAATTWAAA 817

  chr20_1067343_1   2082 AATGTTCAAAGGATTTGAGTAGATATTTCTCCAAGGAGGATGTACAGATA 2131
                             vv            i    i          i  i   i    i  i
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr20_1067343_1   2132 GTCCATGAGCACAAGAAAAGGTGTGCAACAACATTGGTCAT 2172
                          i v  i      v      i  iv     v  ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (87 / 57)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 4.00 (72 / 18)  

2430 25.76 6.19 1.39  chr20_1067343_1073327     4317  5108 (877)    L1M4_orf2#LINE/L1        1   830 (78)  

  chr20_1067343_1   4317 TGGAGAGACATAACATATTCATGGATTAAAAAA-TCAGCATAGTAAAAAT 4365
                             i   i  vv   i          ii  i - i ii  v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_1067343_1   4366 GTCAGATACTCCACAAATTGATACACTATTTTAATGCAATTCCTATCAAA 4415
                          v  -       v         vi  viv  i  i     i         
  L1M4_orf2#LINE/     51 GGCA-ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_1067343_1   4416 AATCCCAACAAGAATTTCTGCAGATATAGCAAGATACAGCAGAT---AAT 4462
                          -     i vivvv   i      v  v ---- i -   v   ---  v
  L1M4_orf2#LINE/    100 A-TCCCAGCTGCCTTTTTTGCAGAAATTG----ACA-AGCTGATCCTAAA 143

  chr20_1067343_1   4463 ATTTATATGGAAAGGCAAAGAATCTAAGATAGCTATAACAATTTTTTAAA 4512
                            i         v    i i i i ii     i v      i  vv   
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr20_1067343_1   4513 AGAA---TAAAGTAGAAGAAATCATTCTACCCAATATTAGGGCTAATTAT 4559
                             ---i     v i  i v   iv  v      v i iii  v i  i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr20_1067343_1   4560 ATAGCTAAAGTAATCAAGATGGTG--GAATTGGCAGAGGGACAGACATAT 4607
                          v     v           ii   -- v i     v i   i        
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr20_1067343_1   4608 AGATAAGTAGAACAGAATAGTGAACACAGAACTAAGACCA---------- 4647
                             v i i   i     v v  iiv     v   iv   ----------
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr20_1067343_1   4648 GCCAACT----TTTGACAAGGGTGCAAAAACAAGTCAATGGAGGAAAGAA 4693
                          i   i ----  i           v  i  v v       -        
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAA 392

  chr20_1067343_1   4694 T-GTCTTT-CAGTAGATGATGCTGGAGCAATTGGATAATCACAAGCAAAA 4741
                          -      -  ii i   i      ii   i      ?i    v      
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_1067343_1   4742 ATATGA-------CCCTTGACCTTA-ACCTTCTATAAAAATGACCTCAAA 4783
                         iv    -------   i -    i -   v v  i      v v      
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCT-ACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_1067343_1   4784 GTGGATCATTGATTTAAATGTAACATACAATACCACAGCACTCCTAGAAG 4833
                         i       ?v  ii         v vvi  v  i i iv    i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_1067343_1   4834 AAAACACAAGAGGAAATCTTCAGTG-TCTCAGGCTTGGTGAAGAGTTCTT 4882
                               i i ? v        -   -i  ii  i v  ii v iv     
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_1067343_1   4883 AGATACAGCACTAAATGCACA-GTGTTTAAA---AAGAT-GCTAAATTGG 4927
                              iii   i   v     - iiviv   ---  i  - v        
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_1067343_1   4928 ACTTCATTGAAATTTAAAACTTTTGCTCTGTGAAAGACCCTGTTAAGAGG 4977
                                ii     v          iv  vii  i   v  i i    ii
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_1067343_1   4978 ATAGAAGCATAACCTACAGTTTGGGAGGCAATGCTTGGAAACCATATATT 5027
                         i ii  iv i    i    vv      iv   ii   v   i       i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_1067343_1   5028 CAACAAAGGATTCATATCTAGA-----TAAAGAACTCTCAAAA-TCAACA 5071
                         ii i  i   i ii    i   -----           i v  -    i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_1067343_1   5072 GCTTAAGAAAC---TA-TCCAATTAGAAAATGGAAAAATGA 5108
                         i- v  i i  ---  -i      ?i       iv   v  
  L1M4_orf2#LINE/    791 A-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.74 (127 / 73)
Gap_init rate = 0.03 (26 / 830), avg. gap size = 2.31 (60 / 26)  

 298 23.66 1.08 0.00  chr20_1067343_1073327     5403  5495 (490)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr20_1067343_1   5403 AAAAATGGAAAAATGATATGAAGAGGTAGTACACTGAGAAGGATGTACAG 5452
                                 iv   v   v    v  ii v v v ii ii i   i    i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr20_1067343_1   5453 ATGGCAAAGAAGCA-ATGAAAAGATGCTCAGCATTGTTAGCCAT 5495
                              v  v     -               i   ii????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)  


 474 27.68 0.00 0.00  chr20_1144919_1151713     4966  5077 (1718)    L1M4_orf2#LINE/L1        6   117 (791)  

  chr20_1144919_1   4966 AAACATTCCATGCTTATGGATAGGAAGAATCAATATTGTGAAAATGGCCA 5015
                          i i  i     i i      v      v i        v  i     v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr20_1144919_1   5016 CACTGCCCAAGGTAATTTATAGATTCAATGCCTTCCCCATCAAGCTACCA 5065
                         i   v     iv i  i  i        i  vv    i     iv v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr20_1144919_1   5066 ATGACTTTCTTT 5077
                         iivi i  i   
  L1M4_orf2#LINE/    106 GCTGCCTTTTTT 117

Transitions / transversions = 1.82 (20 / 11)
Gap_init rate = 0.00 (0 / 112), avg. gap size = 0.00 (0 / 0)  

2730 26.58 0.74 0.99  chr20_1144919_1151713     5495  6303 (492)    L1M4_orf2#LINE/L1      102   908 (0)  

  chr20_1144919_1   5495 CCCAGCCTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5542
                               -  v    i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    102 CCCAGC-TGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_1144919_1   5543 ACATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAA 5592
                          i      viiv  ii  v  viv  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_1144919_1   5593 GAACAAAGCTGGAGGCGTCACGCTACCTAACTTCAAACTATACTACAAGG 5642
                                 i      vv    i  v  i  i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_1144919_1   5643 CTACAGTAACCAAAACAGCATGGTACTGGTACCGAAACAGAGATATAGAC 5692
                                  i   i    ii         i iviii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_1144919_1   5693 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAAC 5740
                                 i    i--    i  --        vv   i    i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr20_1144919_1   5741 CATCTCATCTTTGACAAACCTGACAAAAACAAGAAATGAGGAAAGGATTC 5790
                           vi v  i  i     ivv  v   i v  vvv    i      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_1144919_1   5791 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5840
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_1144919_1   5841 TGAAACTGCATCCCTTCCTTACACTTTATACAAAAATCAGTTCAAGATGG 5890
                             ii  v i    v   i    iv           i ii    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_1144919_1   5891 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5940
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_1144919_1   5941 CCTAGGCA-ATACCATTCAGGACATAGGCATGGACAAGGACTTCATGACT 5989
                          v    ?i- v i -   iv   v v  vv i i   v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_1144919_1   5990 AAAACACCAAAAGC-CATGGCAACAAAAGCCAAAATTGACAAATGGGATC 6038
                          vi           -  -i          vv     v  i    v   ii
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_1144919_1   6039 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 6088
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_1144919_1   6089 AACAGGCAACCTACAGAATGAGAAAAAATTTTTACAATCTACCCATTTGA 6138
                           v  i     i        i  i     v   i   vii ivi  i   
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_1144919_1   6139 CAAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 6188
                         i  i  i  vi          v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_1144919_1   6189 AAAAATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACAC 6238
                             iv    i     v  i?    i     i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_1144919_1   6239 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 6288
                              v        i  vi viii     i ii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_1144919_1   6289 ATCATCACTGGCCAT 6303
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (130 / 81)
Gap_init rate = 0.01 (11 / 807), avg. gap size = 1.27 (14 / 11)  


3313 23.69 3.87 0.80  chr20_1274334_1281831.rev     3588  4465 (3033)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr20_1274334_1   3588 AGAGATATTCCATGTTCATGGGTTGGAAGAATCAATATTGTTAAAATGTC 3637
                          i      i            i        v i           i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr20_1274334_1   3638 CATATTATCCAAAGCAATCTACAGAGTCAATGCAATTCCTATCAAAATAC 3687
                         v   i vi     vii         v    i     i           v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_1274334_1   3688 CAGTGACATTCTTAATAGAAATAGAAAAA---ATTCTATAATTTATATAG 3734
                            ivi v  i  vii      v  v  i---  i   v    i    i 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr20_1274334_1   3735 AACCACAAAAGACCCAGAATACCCAAAGCTATTGTGAGCAAAAGGAACAA 3784
                           vii   ii           v     i v  iv   iv  i i      
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr20_1274334_1   3785 AACTTGAGGAATCACATTACCTGGCTTCAAATTATACTACAGAGCTATAA 3834
                          ii v     v     i v  iiii      viv       i     i i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr20_1274334_1   3835 TAACCAAAACAGTATGTTAATGGCATAAAAACAGACA----GACTAATGG 3880
                            i   i     i  v  v        ii i     ----  ii     
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr20_1274334_1   3881 AACAGAATAGAGAACCCAGAAACGAATCCAT-C-----TGATCTATTTA- 3923
                           i     v    ii       ii  i    - -----  i  v   v -
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr20_1274334_1   3924 ----AACAAAGATGCCAAGAATATAAATTGGGAAAAGGACAGTCTCTTCA 3969
                         ----i    i i        vi  vv v    i    i i     i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr20_1274334_1   3970 ATAAATGGTGCTGGAGAAACTGGATATCCATATGCAGAAGCATGAAACTA 4019
                          i            iiv         ?   i     i   v     ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr20_1274334_1   4020 GAC---TATCTCCTGCAATATATACAAAAATCAAATTAAAATGGATTAAA 4066
                            ---  i   --i  vi            i  v i         i ? 
  L1M4_orf2#LINE/    454 GACCCCTACCTC--ACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_1274334_1   4067 GATTGAAATCTAAGACCACAAACGATGAAACTACTAAAAGAAAACATTGG 4116
                           iiv    v     v vv    v  i     vi  i          v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_1274334_1   4117 AGAAACTCTCCTGGACATTGGACTGGGCAA---------AG---TAATAC 4154
                         ? v  v   i vv   v    ii i     ---------  --- i i  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_1274334_1   4155 CTTACAAGCACAGTCGGCCAAAGCAAAAATGAACAAATGGGATCACAT-G 4203
                          -- v       iv ii v    v      ii i    v   iiv   -i
  L1M4_orf2#LINE/    602 C--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_1274334_1   4204 AAGTTAAAAACCTTCTTCACAGCAAAAGAAACAATCAACAAAGTAAAGAG 4253
                           i        i  iv -i vv    i  v  v     v     i  i  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGT-GCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_1274334_1   4254 ACAACCCACAGAATGGGAGAAAATATCTGCAAACTATCCATTTGATAGGA 4303
                                                   i      ii  vi  i     i i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_1274334_1   4304 GATTAATAACCAAAATATATAAGGAGCTCAAACAACTCAATAGGAAAAAA 4353
                           i vi  v   i         i  i   vv           iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_1274334_1   4354 AATCTAATAATCTGAGTTTAAAATGGGCAAAACATCTGAATAGACATTTC 4403
                          -- v     i ii v ?v            iv  i              
  L1M4_orf2#LINE/    799 A--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_1274334_1   4404 TCAAAAGAAGACATACAAATGGCAAACAGGCGTAGGAAAAGGTGCTTAAC 4453
                           v        i           v  i i  ii v      i    i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_1274334_1   4454 ATCATTATCATC 4465
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (130 / 74)
Gap_init rate = 0.01 (13 / 905), avg. gap size = 3.15 (41 / 13)  

2662 25.26 6.72 1.51  chr20_1274334_1281831.rev     6144  7006 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_1274334_1   6144 TGGAGAGATATTCCATGTACATGAATAGCAAAACTCAATAATTTTAAGAC 6193
                             i      i      v    i  v v  i   i    v v      i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_1274334_1   6194 GAGAATTCTCCCCAACCCTATCTATAGATTCAACACAATTCCAAT-AAAA 6242
                          iv   v        viiv     i         i    i  v  -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_1274334_1   6243 TTCGAATAAGTTATTTTGTGAATATTGACA----GATTCTAAAGTTAATA 6288
                          i v iivivi v     iii v       ----   i     i  v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_1274334_1   6289 TGGGAAGTCAAATGACCTAGAATGACCAACACAATCCTGAAAAGGAA--- 6335
                            i  vv   iv    i     ii    v      i      i   ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_1274334_1   6336 CAAAGTCAGAGGATTAACACTACCTGACTTTATGACTTACTATAAATCTA 6385
                               ii     i v     v  ii i  i vi        i   v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_1274334_1   6386 CATTAGGCAAGACTGTGTGGTATTGGTGAAAAAACAGACAAACTGATCAA 6435
                           v  iv      v        i   iiv  ii i     v iv      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_1274334_1   6436 CAGCACAGAATAGAGAGCCCAGAAATACACCCACATAAATATAGTCAAAT 6485
                         ii v i     v     i         v     i i vv   i     v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_1274334_1   6486 TATATTTGTCAAAGAAGCAAAGGCAATTCAGTGCAGGAAGAGGGAAGAGG 6535
                         v  v  i v   i iv  v   i v     i  --------     -  i
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATG--------GGGAA-AGA 391

  chr20_1274334_1   6536 AGAATCTTTTTAACAAATGG-------------GAAAATCCAGAC----- 6567
                          v i      i         ------------- i v ?   v i-----
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_1274334_1   6568 -------AGT----------CCTTCCACCTTTTATAAAAGTTAGATCAAA 6600
                         -------   ----------   iv    v v  i    i   iv     
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_1274334_1   6601 ATGGATCTTAGACTTAAATGTGAAACATAAAACTACAAAACTTACAGAAG 6650
                                v?    i       i i vv        i      ivi     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_1274334_1   6651 CTAATATAGGAACCAATCTATGTGGTTTGTGGTTTGGCGATGAGTTTTTA 6700
                         vv  i     ?iiv     vi   iii vv    v   i   iv  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_1274334_1   6701 AATTCAACACCAAAAGCACAACCCATGGAACAAAAAATTCTTAAACTGAA 6750
                         i  vii               v v iii  v       vvv    i  i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_1274334_1   6751 CTTTATTAAAATTAAAAACTTCTGCTCTGTGAAAGAA---TGTTAAGAGA 6797
                            i  i              i  iv  - v    i --- i i    i 
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACTATCAAGAAA 690

  chr20_1274334_1   6798 ATGAAAAGGTAAGCCAAAGATT---AGAAGTTATTTGCAAAACACATTAA 6844
                         i       ii  v   v   v ---    iv          v  i  - v
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-AT 739

  chr20_1274334_1   6845 CTGATAAAGGACTGGTATTCAAAAT-TATAAACA---CTTAAAACTCAAC 6890
                                i     v    i  i   -      v ---    v       i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_1274334_1   6891 AATAAGAA----AAGAACCTAATTTTTTACATGGGCAAAAGGTCTGAAAA 6936
                              i  ----  v    i    ?vv- v         i i i    v 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAGGATTTGAATA 838

  chr20_1274334_1   6937 TTACACCTCACTAAAGAAAATATGCAGGTGACAAATAAGCATA-GAGATG 6985
                         v-   ii  v i      i    i  ii  i v        i -  i v 
  L1M4_orf2#LINE/    839 G-ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_1274334_1   6986 AAGATCCACATCATATGTCAT 7006
                          v v  v      ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (123 / 91)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.94 (71 / 18)  


 247 26.25 1.25 0.00  chr20_1359524_1362240.rev      366   445 (2272)  C L1M4_orf2#LINE/L1   (76)   832   752  

C chr20_1359524_1    445 TTGTAATCACAATTTGTAAAGAATTCTCAAAATCCAACAGTAAGAAAACA 396
                              vi  v   v i       i   i v  ii   i i   i  i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

C chr20_1359524_1    395 AATAATCCAATAAACAAAAAGGCAA-GGACT 366
                              i     v? v   vi     -   i 
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATT 832

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.01 (1 / 81), avg. gap size = 1.00 (1 / 1)  

3752 17.71 5.27 3.70  chr20_1359524_1362240.rev     1334  2225 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_1359524_1   1334 GGAAGACAACACATGTTGATGTATTGGAATA-TTAAT--TG--------- 1371
                          i    i v v      v   v       v -     --  ---------
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_1359524_1   1372 ----------CAAAT-GATCCACAGATTCAATGCAACCCCTATCAAAATT 1410
                         ----------     -    i          i    i            i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_1359524_1   1411 CCAATGGCATTTCCTAAGGAAATAGAAAAACTAATCCTCAAATTTATGTG 1460
                            iiv  v   ii ivi     v  v  i  i     v     i  i  
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_1359524_1   1461 GAACTGGAATGAACCCCAAGTAGTCAAAATACTATTGAAAAAGAAACACA 1510
                            v  v  v i    vi i   i     i v v           -----
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA----- 197

  chr20_1359524_1   1511 CCAAAAAAGAAAGAAAAAGAAACACAAAGTTTCAGGGCTCATGCTTCCAG 1560
                         ------------------   ---       vv   i    ii     vi
  L1M4_orf2#LINE/    198 ------------------GAA---CAAAGTTGGAGGACTCACACTTCCCA 226

  chr20_1359524_1   1561 ATTTCCAAACATGCTCCAAA-CTTCTATAATCAAACCAGTGTGGTACTGA 1609
                              v    v i  v    -  v vi       iv             i
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr20_1359524_1   1610 CATAAGGACAGACATATACACCAGTGGAATATAATTGACAGCCTAGAAAT 1659
                                 i         v i  i       v      v  i i      
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr20_1359524_1   1660 AAAT------ATCTATGGCTAATTGATTTTCAATAAGTGT-TCAGCACAA 1702
                            i------  i     ii           i i   v  -i  iv  v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr20_1359524_1   1703 CTCAATGGGGAAAGAATAGTCTCTTCAACAAACAGTGCCGGGGCAACTGC 1752
                         i                     i         ii    i   i      v
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr20_1359524_1   1753 ATAATCACAGGCAAAAGAATGAAGCTGGACCCGTACCTCACTCCATACAC 1802
                            ?i    v              i       v        v     i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr20_1359524_1   1803 AAAAATTAACTCAAAATGGATCAATGACCCAAATACAAGAGG-AAAAC-A 1850
                                                ?v    i    ii     v-     - 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr20_1359524_1   1851 TAGGGGTAAACTATTTAGAGAAAAACATAGGAGTAAATATTTATAACCTC 1900
                           -----     -i     ii          ?      v  ii i    i
  L1M4_orf2#LINE/    527 TA-----AAACT-CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr20_1359524_1   1901 AGACTTGGCAATGGATTCTTAGATTTGACACCAAAAGCATGAGCAACAAA 1950
                         i ii v        v         v              ii         
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr20_1359524_1   1951 AGGAAGAAATGGATAAATTAGACTTCATAAAAAGTAAAACCATTTGCACA 2000
                           i  -    i        i        v    v     v v    ii v
  L1M4_orf2#LINE/    621 AGAAA-AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr20_1359524_1   2001 ATAAAATATATTATCTAGAAAGTAGAAACACAGCCCACAAAATGAGAGAA 2050
                         vi   iv i i    v       ii   v   i      i    i     
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_1359524_1   2051 AGTATTTGCAAATAAT------------GGACTTGTATCCAGAATATATA 2088
                          i           v  ------------                      
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr20_1359524_1   2089 AAGAACACTTAAAACTCAACCACAAAAAAAAAAAAAAA--AATTAAGAAA 2136
                               v    v       iv i     i v   v  v--    ? i   
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_1359524_1   2137 TAGGCAAAGAACCTGAATAGACATATCTCCAGAGAAGACATACAAATGGC 2186
                          i       i ii           v      i      i           
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr20_1359524_1   2187 CAATAAGCACATGAAAGCATGTTCAGCATCATTTGTTAC 2225
                                         iv   i   i     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (94 / 60)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 5.00 (80 / 16)  


 964 21.90 2.92 7.30  chr20_1412165_1417469        6   416 (4889)  C L1M4_orf2#LINE/L1   (38)   870   478  

C chr20_1412165_1    416 AAAAAGAACACAAAAT--ATC---GATACTAA--GGAAGATCAGTAAGA- 375
                             vv   v      --   ---  i-    -- v    v --   i -
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGAC-CTAAATGTAAGAGC--TAAAAC 524

C chr20_1412165_1    374 TACAAGATAATTCTGAAAAACAATACAAAGAAATCAGAAAACACTCCAAG 325
                           i  ---  i   v i  iv  -   v  i?i ----   i-  i iv 
  L1M4_orf2#LINE/    525 TATAA---AACTCTTAGAAGAAA-ACATAGGNGT----AAAT-CTTCGTG 565

C chr20_1412165_1    324 ACATTGCTCTAGGCAAAGGTTTTGTGGCTAAGACTTCGAAAG-ACAGGCA 276
                           v   vvi       v     iv i v  v   vi i    -   i   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

C chr20_1412165_1    275 ACAAAGGCAAAAAAAAGACAAATGGGACTATATTAAACTAAAAAGCTTCT 226
                              i -      v   i    v     vi  i   v v    i   i 
  L1M4_orf2#LINE/    616 ACAAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

C chr20_1412165_1    225 GCACTGCAGAAAA-ATAATCAAAAGAGTGAAGAGACAACCTCCTGAATGA 177
                          ii  v  i ii - iv     i i      i        iv v     i
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

C chr20_1412165_1    176 GAGATAATATTCACAAAGTACCCATTTGACAAGGGACTAATATCTGGAAT 127
                             v      ii    vi ivi  i   i        vi    ii    
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

C chr20_1412165_1    126 ATACAAGGAACTCAAACAATTCAACAGTTAAAAAAGCAAACAAACAAATA 77
                            i  i      vv    i    i i --      ----------- i 
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAAT--AAAAAG-----------ACA 801

C chr20_1412165_1     76 AATAATCTAATT-AAAAATGAGCAAAGGAAAGGAATGAATAAACATTTC- 29
                              i i    -       i        vv----      i       -
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATT----TGAATAGACATTTCT 847

C chr20_1412165_1     28 CCAAAGAAGACATACAAATGGCC 6
                                   i            
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCC 870

Transitions / transversions = 1.62 (55 / 34)
Gap_init rate = 0.05 (18 / 393), avg. gap size = 2.33 (42 / 18)  

2166 24.25 4.35 1.17  chr20_1412165_1417469      501  1098 (4207)    L1M4_orf2#LINE/L1      292   908 (0)  

  chr20_1412165_1    501 ATAGACCAATGGCACAGAATAGAAAACACAGAAATAAATCCATGTATTTA 550
                              i      v i     v  i iiv          i    ii     
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_1412165_1    551 CAGCCAATTGATTTTTGGCAAAGGTATCAAGAATACACA----------- 589
                         ii i           i i   i   ii     vi iv  -----------
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_1412165_1    590 --------TTCAATAAATGGTGCTGGAAAAACTGGATATCCATATGCAGA 631
                         --------     i            i v         ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_1412165_1    632 AGAATAAAGGTAGACTGCTATTTCTCACCATATACCAAAATCAACTAAAG 681
                              i   v i   iv   ii  v          v     i    v  i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_1412165_1    682 ATGAATTAAAGATCTAACTGTAGGACCTAAAACTATAAAAACTACTAGGA 731
                            i  i ?   i    v    i  v              -  vi   i 
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAA 540

  chr20_1412165_1    732 GAAAACAGGGAAGGGA--CTCCAGGACACTGGTATAGGTAAAGATTTTAT 779
                                vi i? vi --  i iv   vi   vv    i  v i   iv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_1412165_1    780 GACTAAGACCTCAAAAGGGTCAGGCAACTAAGACAAAAATAGACAAATGG 829
                         iiv  v   vi      vi-  i     v  iiv         i    v 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_1412165_1    830 GACTATATTAAACTAAAAAGCTTCTTCATAACAAAAGCAACTATCAACAC 879
                             vi  i   v v    i   i viiivv    i vv        v v
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_1412165_1    880 AGTGAAGAGACAAACTCTTGAATGAGAGAAAATATTTGCAAAGTACTCAC 929
                               i      v iviv     i                 vi ivi i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_1412165_1    930 CTGACAGGGGACTAATCTAATATCCAAAATATACAGGAAACTCAAACAAC 979
                             i i      ---- i-      i      i iii     vv     
  L1M4_orf2#LINE/    740 CTGATAAGGGACT----TG-TATCCAGAATATATAAAGAACTCTTACAAC 784

  chr20_1412165_1    980 TCAACAGTTAAAAAA-----AATCTCATTAAAAAGTGGGCAAAGGACATG 1024
                             i i v    i -----  i iv   ?    i           iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr20_1412165_1   1025 AATCAACATCTCTCAAAAGAAGACATACAAATGGCCAACAGGCACATGAA 1074
                            vi    i    v        i              i i         
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr20_1412165_1   1075 AAAATGCTCAACATTACTAATCAT 1098
                           i           i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (90 / 51)
Gap_init rate = 0.01 (7 / 617), avg. gap size = 4.71 (33 / 7)  

2220 18.09 6.69 17.40  chr20_1412165_1417469     3797  4813 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_1412165_1   3797 TAGAGAGGTA-CACACTGTTCATATGTTGGAAGATTCAATATTGCTTAGA 3845
                          i  i  i  - v  -       ivi        i i       i v   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCA-TGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr20_1412165_1   3846 TGTCAATTCTTCTCAAGTTGATATATAAACTCAATGCCATTCCCATTCAA 3895
                           v    v  i i   i     v  i i i    i  v  i  i  iv  
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_1412165_1   3896 ATCCTAGCAGGCTTCACTTTAGCA----TTGATAAACTAAATCTAAAATT 3941
                             i   v v   ---   v   ----    i  i  i vi        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTT---TTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr20_1412165_1   3942 TATA-------------------GAATAGCCAAAACCAT-TTGAAAAAGA 3971
                         i   -------------------             v  -          
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_1412165_1   3972 A---TAAAGTTAGAAAACTAATACCACCTGCTTTCAAGACTTAG-ATAAT 4017
                          ---i      i  ii   v i  iv  iiv      i     v- i  v
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_1412165_1   4018 GTTACAGTAATCAAGACAATGTGGTATTG-CACAAAGATAGATAAACATA 4066
                          i                i       i  -  i  i      i v i v 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_1412165_1   4067 TCAGTGGAACTGAATAGAGAGTCTAGAAATAG-TCCATGCAAATAGAGGC 4115
                            i     iv    v       i       i-i    i  ---------
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA--------- 337

  chr20_1412165_1   4116 AACTGATTTTTTAAAAAGAGATGAGGTCTCGCTATGTTTTCCAGGCTGGA 4165
                         ---------    -------------------------------------
  L1M4_orf2#LINE/    338 ---------TTTA------------------------------------- 341

  chr20_1412165_1   4166 GTGCAGTGCTATTTTGGGTGTGATCGTCATAGCACACTGCAGCCTCAAAC 4215
                         --------------   ---------------------------------
  L1M4_orf2#LINE/    342 --------------TGG--------------------------------- 344

  chr20_1412165_1   4216 TGCTAGTCTCAAGCAATCCTCCTGAGTAGCTAGGAGTACAGGTGCATGCC 4265
                         --------    --------------------------------------
  L1M4_orf2#LINE/    345 --------TCAA-------------------------------------- 348

  chr20_1412165_1   4266 ATGGCTCCTAACTATAATTATTTGATATTTGACAAAGGTGCAAAGACAAT 4315
                         ---------------------     v  i     i     v     v  
  L1M4_orf2#LINE/    349 ---------------------TTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr20_1412165_1   4316 TCAATGGAGAATGGGGAGTTTTTTCAACAA-TGGTGCAAGAACCATTGGA 4364
                                i   v iiv   i          -      vi i  v i    
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr20_1412165_1   4365 AATACATGTGCAAACAAATGAACTTTGGTTTATATCTCAAACTATATA-- 4412
                         v ?v  ii      vi      v  v iiiiv  i    v  i     --
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr20_1412165_1   4413 AAAATTAACTCAAAATAGATCATATAACTAAACATAAAATGTTAAACGAT 4462
                                         i     ? v v     ii   i vv v    v  
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr20_1412165_1   4463 ACAACTTCTAGCTGCAAACAT-GGAAAAAAACTTTGTAACTTTGGGTTAG 4511
                          v    ii   vv v      -  ?iv   v   i  i  i         
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr20_1412165_1   4512 GCAAAGATTTCTTAGATGTAACACCAAAATCATGATCCATTAAAGACAAA 4561
                             v i          i i         v  ii v v iv     v   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr20_1412165_1   4562 TT-GATGAATTGGACTTCATAAAAATTAAGAACTCCTGCTG-TTCGGAAA 4609
                         v -   i             v        i    ii  -  -   ii ii
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTTCAAAGG 676

  chr20_1412165_1   4610 ACACTTGTAAAAGAATAAAAAGACAAGTCACAGAGTAGGAGAAAAATCTT 4659
                              vvi  i i i i         vi      i i        - v  
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATT 725

  chr20_1412165_1   4660 TGCAAAGCATATATCTGGCAAAATATTTGTATCCATAATATATAACGAAC 4709
                               v          ii  iiv i         v         v    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr20_1412165_1   4710 TCTCAAAACTCAATAATAAGAA-ACA-------CACTTAAAAAATGAG-- 4749
                            i v             i  -   -------  v  ?       i --
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr20_1412165_1   4750 -AG---TCGAATAGACACTTCACCAAAAAGGAT----------------- 4778
                         -  --- i         i   v     i i   -----------------
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr20_1412165_1   4779 GCATGATGTAAAAAATGTTCAGCATCATTACATAT 4813
                            i-   -    i   i   i     ????????
  L1M4_orf2#LINE/    876 GCAC-ATG-AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (113 / 67)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 8.75 (245 / 28)  


3033 27.89 0.44 0.66  chr20_1469535_1475356.rev     4424  5330 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr20_1469535_1   4424 AAAAACATTCCACTCTCATGGATAGGAATAATCAATATCGTGAAAATGGC 4473
                            i i  i   ivi        v    v v i     i  v  i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr20_1469535_1   4474 CACACTGCCCAAAGTAATTTATAGAATCAATGCTATTCCCATCGAGCTAC 4523
                         v i   v      v i  i  i   v    i  v  i  i   i iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_1469535_1   4524 CATTGACTTTTTTCACAGAATTAGAAAAAAATGACTTTAAATTTCATATG 4573
                           vivi i     ii     v v  v  iv-   iii    v        
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATG 152

  chr20_1469535_1   4574 GAAC--CAAAAAACAGCTCGTATAGCCAAGACAATCCTAAGCAAAAAAGA 4621
                            v--   iii  -- iv v        i      i i i-   i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAA-AAAGAAGA 199

  chr20_1469535_1   4622 GCAAAGCTAGAGGCATCATGCTACCTGACTTCAAACTGTACTACAGTGCT 4671
                         i     i i    vv   ii  v  ii i      viv       iv   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_1469535_1   4672 ACAGTAACCAAAACAGCATGGTACTGATATGAAAACAGATATATAGACCA 4721
                                i   i    ii        ii  i ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_1469535_1   4722 ATGGAACAGAACTGAGGCCTCAGAAATAACACCACACATCTACAACCATC 4771
                               i    i    ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_1469535_1   4772 TGATCTTTGAGAAACCTGACAAAAATAAGCAATGGGGAAAGGATTCCCTA 4821
                             i  i  v  ivv  v   i vi vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_1469535_1   4822 TTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTAAA 4871
                           i  i        i     v      v  ?   i     i  i v i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_1469535_1   4872 ACTGGACCCCTTCCTTACCCCTTATACAAAAATTAACTCAATATGAATTA 4921
                         ii         v   i  v  v                   v   i  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_1469535_1   4922 AAGATGTAAATGTAAGACCTAAAACCATAACAACCCT-AGAAGAAAACCT 4970
                         ?   iv           v       i    -   i  -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAACAT 548

  chr20_1469535_1   4971 AGACA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTTATGACTAAA 5019
                           i?i- v i -   iv   v v  vv i     v ii  iv iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_1469535_1   5020 ACACCAAAAGCAATTGCAACAAATGCCAAAATTGACAAATGGGATCTAAG 5069
                                     vvv        v vv     v  i    v   ii v v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_1469535_1   5070 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTATCAGAGTGAACA 5119
                         i   v v  i i   i  ii vv    i  v     i vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_1469535_1   5120 GGCAAGCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGGCAAA 5169
                          i   v i                 v       vii  vi     ii  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_1469535_1   5170 GGGCTAACATCCAGAATCTACAAGGAACATGAACAAATGTACAAGAAAAA 5219
                           i  vii         v  i  i    vivv    v vv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_1469535_1   5220 AACAAGCAACCCCATCAAAAAGTGGGCGAAGGATATGAGCAGACACTTTT 5269
                         i    ii     v  i?    i     i      v   ii     i  i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_1469535_1   5270 CAAAAGAAGACATTTATGCAGCCAACAAACAAATGAAAAACAGCTCATCA 5319
                          v        i  vi viii     i  i  v       ivv     v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_1469535_1   5320 TCACTGGTCAT 5330
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.44 (147 / 102)
Gap_init rate = 0.01 (8 / 905), avg. gap size = 1.25 (10 / 8)  


3169 25.06 3.89 0.23  chr20_1512067_1514638     1207  2080 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_1512067_1   1207 GAAAGATA-CCTATGTTTGTGGATTGGA-GAATTACTATTGT-AAAATGT 1253
                                 -  i     ii         -  v   v      -  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_1512067_1   1254 ACATACTACCCAAAGAGATCTACAGATTCAATTCAATGTC-AGTAAAATT 1302
                         vv     v      vv               iv    vi - vi     i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_1512067_1   1303 TCAATGAAATTCC--ACAGAAATGGACAAAACAATCCTTAAGTTCATATT 1350
                         i  iivivv  ii--i       v     ivii     v  i       -
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT- 151

  chr20_1512067_1   1351 AGCCAT---AGAAAACCATGAATAGCTAAGGCAAGCTTTAGCAAAAAGAA 1397
                         i vv  ---  ii v   -       i  ii   v   v iv  i     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_1512067_1   1398 CAAAGCTGGAGGTATCACACTGCTTGATTTAAAAATCTTCTACAGTGCCA 1447
                              i      vv       v iii    v    ii v     iv  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_1512067_1   1448 CAGTAATCAAAACAGCATGGCACTGGCACAAAAAGAGACACATAGACCAA 1497
                                   i    ii   i       i  ii v     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_1512067_1   1498 TGGATCAGACCAGAGAGCCCAGCAATAAACTCACACATTTGCACTCAATT 1547
                             vi   viv     i    v       i  i      iiiv      
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_1512067_1   1548 GACCTTTGACAAAAGGGTCAAGAAGACACAATGGGGAAATGTCAGTCTCT 1597
                           ii  i     ii v i     vv iv           vivi     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_1512067_1   1598 TGAAAAAGGGGTGTTGGGAAACCTGAATATCCATGTGTAGAGAAATGAAA 1647
                          v  v  iv    i     v v   i   ?   ii  i i ii      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_1512067_1   1648 TTAGACCTCTGTCTCATACCACATACAAAAATCAACTCCAAATGTATTAA 1697
                           i    i  ii    i    i          i     v     v  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_1512067_1   1698 AGACTTAAATGTAAGATCTGAAACTGTAAAAGTACTAGAAGAAAA----- 1742
                             i           v  i     i     v vi          -----
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_1512067_1   1743 --GT-----TCCATGACATTGGTCCGGGCAATGAATTTTTGGATATGAGC 1785
                         --  ----- i i    v    viii       iv  i  i       vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_1512067_1   1786 CCCAAAGCACAGGCAACAAAAGCAGAAATAAATAAATGGCACTACAACAA 1835
                           v        i          v i     i      v v   v  v   
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_1512067_1   1836 ACTAAAAAGTTTCTACACAGCCAAGGAAACAATCAACAGAGTGAAGAGAC 1885
                          v v    ii  i iii vv v     v  v     v i      i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_1512067_1   1886 AGCCTACAAAATGGGAGAAGATATTTTCAAACCATACATCTGATGAAGAG 1935
                          i  i   i          i      v    i    i       i i ii
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_1512067_1   1936 TTAATATGCAAAATATATAAGGAAGTCAAACAACTCACTCATAAGAAAAC 1985
                         i vi   v  i         i   v  vv        v v    i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_1512067_1   1986 AA----CCCAAGTAAAATATGAGCCAA--------ATAGCCATTTCTCAA 2023
                           ----     v ?   v   i  v  --------    v        v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_1512067_1   2024 AAGAAGACATCAAAATGGCCAGTCAACATATAAATA-ATATCCAACCTCA 2072
                                i  vv         i v i  i  i  v -  iii    v   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr20_1512067_1   2073 TCATTCTT 2080
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.45 (128 / 88)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 2.77 (36 / 13)  


2932 27.66 2.13 0.45  chr20_1567518_1573239.rev     4338  5230 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_1567518_1   4338 TGGAAAAACATTCCATGCTCATGGATAGGAAGGATGAATGTCATGAA--- 4384
                               i i  i     i        v     iv v   i ii v  ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_1567518_1   4385 -------------AAAGTAATTTATAGATTCAGTGCTATTCCCATCAAAT 4421
                         -------------   v i  i  i       ii  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_1567518_1   4422 TACCATTGACATTCTTCACAGAATTAGAAAAAAAACT-ACATTAAATTTT 4470
                          v   vivi v  i  ii     v v  v  i---  - ivi    v  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr20_1567518_1   4471 ATATTGAACCAAAAAAAAGCCCGTATAGCCAAGACAATCCTAAGCAAAAA 4520
                             v   viiv  iii v  v v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_1567518_1   4521 GAACAAAATTGGAGGCATCACGCTACCTGACTTCAAACTATATTACAAGG 4570
                                i       vv    i  v  ii i      viv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_1567518_1   4571 CTACAGTAACCAAAACAGCATGGTACTTGTACCAAGACAGACATATAGAC 4620
                                  i   i    ii       v i iv i  i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_1567518_1   4621 CAATGGAACAGAACGGAGACCTCAGAAATAATGCTGTACATTTACAACCA 4670
                                 i    iv    vii         vv ii        iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_1567518_1   4671 TCTGATCTTCAACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 4720
                         vi    i   i    ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_1567518_1   4721 TATTTAATAAATGGGACTGGGAAAACTGGTTAGCCATATGCAGAAAACTG 4770
                          v  i  i      vi      v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_1567518_1   4771 AAACCAGACCCCTTCCTTACACCTTATACAAAAATTAACTGAAGATGGGT 4820
                           iiii       v   i     v                v  i    i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_1567518_1   4821 TAAAGACTTAAATGTAAAACCCAAAACCATAAAAACCCTAGAAGAAAACC 4870
                         i ?    i         i v i     i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_1567518_1   4871 TAGGCA-ATACCATTCA-GGCATAGGCATGGGCAAAGACTTCATGACGAA 4918
                             ?i- v i -   i- i v v  vv i     v ii   v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_1567518_1   4919 AATGCCAAAAGCAATTGCAACAAAAGTGAAAGTTGACAAATGGTATCTAA 4968
                         i ii         vvv          vi   i v  i    v v ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_1567518_1   4969 TTAAACTAAAGAGATTCTGCACAGGAATAGAAACTATCATGAGAGTGAAC 5018
                          i   v v  i iv  i  ii vvv  vi  v       v  i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_1567518_1   5019 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATTTACCCATCTGACAA 5068
                           i     i                 v       v i ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_1567518_1   5069 AGGTCTAATATCCAGAATCTACAAGGAACTTAAACAAATTCACAAGAAAA 5118
                         i  v  vi          v  i  i     ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_1567518_1   5119 AAACAAACAACCCCATCAAAAAGTATGCAAAGTATATGAACACACACTTC 5168
                          i     i     v  i?    i iv      v  v    i v   i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_1567518_1   5169 TCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGCTCAAC 5218
                           v        i  vi vi       i  i  i       i v       
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_1567518_1   5219 ATCACTGATCAT 5230
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 3.83 (23 / 6)  


2943 24.37 5.15 1.26  chr20_1631333_1633896     1199  2072 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_1631333_1   1199 TGACAAGATATGT-GTGTTTAGGGATTGGA-GAATTAATACTGTTTA--- 1243
                           iv       vi-i    i v        -  v      i    v ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_1631333_1   1244 ---AATATTTCCTGAGGAGATCTACAAATTCAGTTCAATCC-TAAAAAAA 1289
                         ---    i i  ii ivv        i     iiv      -  vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_1631333_1   1290 TTCCAATGATATTTTCCACAGAAATTGACAGAACAATC-TGAAATTAATA 1338
                          i   iiviiv    iii            iivii   - i     v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_1631333_1   1339 TT-AACTACAGAAAACCATGAATAGGTGAAGCCATCTTGAGCAAAAGAAG 1387
                          v-  v i  iiii   vv      vii  i v       --        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAAGAAG 198

  chr20_1631333_1   1388 AA---AGCTGGAGGCAC-CAGACTGCCTTATTTCAAAATCTGGTACAATG 1433
                           ---  i      -  -  v   v  iv         ii iv     v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_1631333_1   1434 CTATAATAATCAAAATAGCATGGCATTGGCATAAGAAGAGACACATAGAT 1483
                            i i       i i  ii   i i         i v     i      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_1631333_1   1484 CGATGGTACAGAATAGAGAGTCCAGAAACAAACTTACATATTTTTGCTTA 1533
                          i    v i     v             i    ii i i    v  v i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_1631333_1   1534 ATTGACTTTTGACAAAACTGTTA-GAC-ATACAATGAGGAAAGACCAGTC 1581
                              i   i     iiv  ii -   -  v     i       vi    
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_1631333_1   1582 TT--CAAAAACTGGTGTTGGCAAAACTGGATGTCCACATGTAAAGGAATA 1629
                           --   v  v     i   v v        i?       i   i    i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_1631333_1   1630 AAATTGGACCTTCATCTTATATCACATAAAAAAATCAACT-AAAATGGAT 1678
                           i       iii i  i i i  i   v      i    -         
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_1631333_1   1679 TAAAGACATAAATGTAAGATCCAAAACTGTAAAAGTACTAGAAGAAAA-- 1726
                         i ?    v           v i      i     v vi          --
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_1631333_1   1727 ---GTGC-------CATGACATTGGTCTGGGCAGTTAATTTTGGGATATA 1766
                         --- ? i------- i    v    vi i    i viv  i vi     i
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_1631333_1   1767 AACCCAGAAGGACAGACAACAAAAGCAAAAATAGACACATGAGATTCCAA 1816
                          vv   i   v   ii         v         i v  vi  i i  v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_1631333_1   1817 CAAA-CTAAACACT---GT-CTACACAGGCAAGAAAACAATCAACAGAGT 1861
                             -i    v   ---  -  v  -----   i v  v     v i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCA-----AAGGACACTATCAAGAAAGT 692

  chr20_1631333_1   1862 GAAGAGACAACCTGTAGAATGGGAGAA--TATTTGCAAACCATACATCTG 1909
                            i        iii            --          i    i     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_1631333_1   1910 ATAAAAAGTCAATATATAAAATATAGAAGGAAGTCAAACAACTCCATAGT 1959
                             iiiiiivi   vi i      v  i   v  vv       v   i 
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_1631333_1   1960 GAGAAAACAA----CCCAAAATATAAAATACAGGCCAAATATCTGAACAG 2005
                         i i  i    ----     -- v?    - ii   v  iv  i    i  
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAA--TTWAAAA-ATGGGCAAAGGATTTGAATAG 839

  chr20_1631333_1   2006 ACATTTCTCAAAAGAAGACATTCAAATGGCTG-TAGGCATATGAAAAAA- 2053
                                  v        i  v        ii-  i   i       i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_1631333_1   2054 ATCCAACATTACTATTCTC 2072
                         iii      i ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (138 / 71)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.15 (56 / 26)  


3124 17.29 6.20 2.59  chr20_1720716_1722401      501  1194 (491)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr20_1720716_1    501 AGAAAGAAGTACAAAGTAGGAGGACTCACACT-CTCAATTTCAAAACTTA 549
                          i       v       v              - i               
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_1720716_1    550 GGATAAAGCTATAGTAATTAACACAGTATGATAATGACATAAGGTTATAT 599
                         vv i       i      i  v     i  i  v  i       ------
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG------ 283

  chr20_1720716_1    600 AAACCAATATATAGACATATAGACCAGTGCAATAGAATTGAAAGTCCAGA 649
                         ----------             i  i  v           i        
  L1M4_orf2#LINE/    284 ----------ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr20_1720716_1    650 AATAACCCCATAAAGT-ATAG-------------GGCCAGGGTGTTAAGT 685
                              v      v v -  i ------------- i v      ii   v
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr20_1720716_1    686 CCAGTCAGTGTGGAAAGAATAGCCTCTTCAACAGGTTGTGCTGAGACAAC 735
                            v   i  v           i  i       ii v      i      
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr20_1720716_1    736 AGGATGTCCATGAACAAAAGAAATGAAGTTGGATTCCTACATCACTCCAT 785
                         v    i?   iivi        -          ii     v    v    
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACACCAT 472

  chr20_1720716_1    786 ATGTAAAAATTGACCCAAAATCCATCAGAG-CCTGAATGTAAAAGCTAAA 834
                           ii       i  i      vv    ?  -   i       i       
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr20_1720716_1    835 ATCATAAAATTATTAGAAGAAAGCATAGTTGTAAACCTTCACAACCTTGG 884
                          ii      i v          i     v?     i    iii       
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr20_1720716_1    885 ATTTGGCAGGGGTT-----G---------CAAAAGCATGAGCAATAAAAG 920
                         i  v    iv    ----- ---------        ii     i     
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_1720716_1    921 AACAAATAAATTAATT----------AAAATTAAAAACTTTGGTGCATCC 960
                           v     i  v    ----------               v    v  v
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_1720716_1    961 AATGTTATCATCAAGAGAGTGAAAAGACAACCTATGCGATGGGAGAAAAT 1010
                           v vi ii       i               i iivi            
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_1720716_1   1011 ACTTGCAAATTATATATCTAATAATATAATTAT---TAGAATATATTAAG 1057
                          i        i        i    viv v  i ---i         v   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_1720716_1   1058 AGCTCCTACAACTCAACAATTAAAGAGACAAACAACCCAATTAAAAAATG 1107
                          i   i          i   -   i       i         ?       
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAAT-AAAAAGACAAATAACCCAATTWAAAAATG 821

  chr20_1720716_1   1108 GGAAGAGGACTTGAATAAGCATTTTCCCGGAGAAGATACACAAATGTCCA 1157
                           v i    i       ii     ii  ii        i       v   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr20_1720716_1   1158 ATAAGCACAAGAAAATATGCTCAACATCATTAGTAAT 1194
                                  v     v             ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (75 / 41)
Gap_init rate = 0.02 (11 / 719), avg. gap size = 5.55 (61 / 11)  


2540 23.28 10.86 1.57  chr20_1945226_1947736     1191  2019 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_1945226_1   1191 GAGAGACATACCATACTCATTGATTGAAAGACTCAACATAGTTAAGATGT 1240
                           i   i  v    ii    v     i      i  i  v         v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_1945226_1   1241 CAATTCTCCC-AAACTAAT-------------GCAATTCTAATCATAATC 1276
                             v     -   i i  -------------     i iv    v    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_1945226_1   1277 ACAGCAGGAATTTTTCAGTAGATGTAGACAAACTGATTCTAAAATTTATA 1326
                         v    v vvv     -- i   vi v     i     i        i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_1945226_1   1327 TGTATAGGCAAAGGAATTAGAAGAGCCTAAATAATTTTGATGATTAA-AA 1375
                           v v v    i   vii    v    v   i   i    vi vv  -  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_1945226_1   1376 TAATGTTAGAGGGCCTACACCACCCAATTTTAACATTTGCTATAAAGGTA 1425
                         i  v   i    i ii    iv        i  v i  i   i    v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_1945226_1   1426 CAGTAATAAAATCAATGAGGTATTAACAAAAAGACAGACCCATAA--CAG 1473
                                v  iv  i  v    i ii  v  i  i    vi   i--  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_1945226_1   1474 TGGGACAGAACAGAGAGTACAGAAAGAGACACATAAAC--ATGGTCAATT 1521
                            i i    iv      v      v i  v    v i--          
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_1945226_1   1522 GCTTTTTGACAAAGTTGCAAAAGCAATTCAATGGAAAAA----AGTCTCT 1567
                          v    i     i v   v  ii v         ii   ----     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_1945226_1   1568 TCAACAAATAGTGTTGGAACAATTGAACACCTATGTG-AAAAAAA---AG 1613
                                  i   i   i    i  i i ? i ii  -    i  ---  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_1945226_1   1614 CTGAACCTCAACTTATACATCATGCCTTACATAAAATTAACTCAAAATT- 1662
                         i  i   i v  i -i   i   i---    -                v-
  L1M4_orf2#LINE/    451 TTGGACCCCTACCT-CACACCATA---TACA-AAAATTAACTCAAAATGG 495

  chr20_1945226_1   1663 ATCA------CAAATGGAACATTTGAGAC---AAAATCTCT-----AAAA 1698
                             ------i     v  v vi i i  ---    -    -----i   
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAA 544

  chr20_1945226_1   1699 ACA--GGAG-AAATCTTCATGTCCTTTGGTTAGGCACAGAATTCATAGAT 1745
                            --  ? -        i  v    v         vv iv   v     
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_1945226_1   1746 ATGACACCAAAAGCATAATCCACTAAA------ATTTTTTTATAAATTGG 1789
                                        i  v v  v   ------  vv----         
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG----ATAAATTGG 640

  chr20_1945226_1   1790 GCTTTATCAAAATTTAAAATGTTTG--CT----------CTGCTAACAGA 1827
                         i   i         v    iv    --  ----------  iii  v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_1945226_1   1828 GTGAGAACACAAGCTACCTGTGGGGACAAAATATTTGCAAGAAATATATT 1877
                             i  v    v i  vvivv    v             ivv      i
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_1945226_1   1878 TTACAAAGGACTTGTCTTCAGAATATTCAAAGAACTCTCAAAAATCAAGA 1927
                          v i  i        v i        vi          i v  v    v 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_1945226_1   1928 AGAA---------------------------GGCAAAAAATTTAAACAGC 1950
                          v  ---------------------------      ii    i  i  v
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_1945226_1   1951 CACTTTACCAAAGAAGATACATGAGTTAACAAATAAGCACATGAAGAAAT 2000
                           i  iv            i ii i -ii v              i i  
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAAT-GGCCAATAAGCACATGAAAAGAT 889

  chr20_1945226_1   2001 GTTCGACATCATTAGCCCT 2019
                          i  i      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (112 / 79)
Gap_init rate = 0.03 (25 / 906), avg. gap size = 4.12 (103 / 25)  


2007 24.85 3.25 4.29  chr20_2004082_2005749      501  1176 (492)    L1M4_orf2#LINE/L1      240   908 (0)  

  chr20_2004082_2    501 CTACAGTAATTACAGTAATCAAGAC--TGTAATATGGGTGAATGAATAGA 548
                              i- ii               --   ii  iv  iiv v i     
  L1M4_orf2#LINE/    240 CTACAA-AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr20_2004082_2    549 CA----AATCAATGGACCAGAATAAACATCCTAGAAATAGACCCACATAA 594
                           ----i         vi     vi v vi i       i     i i v
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr20_2004082_2    595 AAATAGT----TGATCTTTGACAGAGGAAGAAAGGTAGTACAATAGAGAA 640
                         vv  i  ----    i  i    ii  vivv   iivi v    i i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr20_2004082_2    641 AAGATAGTCTTT-CAAAAAATAATAATGGAACAACTGGTCATTCACATGC 689
                          ii         -   v    ii iv   i        vi ?i       
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr20_2004082_2    690 AAAGAAAATGAATCTAGACACAGATCTCACACTCTTCACAAAAATTAACT 739
                            - i      vi i   v vv i       iv vi             
  L1M4_orf2#LINE/    439 AAA-AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr20_2004082_2    740 CAAAATGGACCATAAACCTAAATGTAAAACACAAAATTATAAGACTCTTA 789
                                  i  ? i            i vvi    i     i       
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr20_2004082_2    790 GAAGATAACATAAAATAAAATCTAAATGACCTTGTGTATGGTGATAACTT 839
                              v      ii?vv      vvi        v  vv  ii  iii  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_2004082_2    840 TTTAGATACTATTTACATTATTACACCAAAAGCATGA--AACATGAAAGA 887
                         i       ------------ v            ii --    --     
  L1M4_orf2#LINE/    588 CTTAGATA------------TGACACCAAAAGCACAAGCAACA--AAAGA 623

  chr20_2004082_2    888 AAGAACTGATAAGCTAGACTTCATTAAAATTAAAAGCT---GTTCTTGAG 934
                           i  iv     ii i        i          i  ---  v   v i
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr20_2004082_2    935 AAGACAATGTCAAGAGAATGAAAAGACAAGCCACAGACCAACAGAAAATA 984
                          i    v i      i i           v       viiiv        
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr20_2004082_2    985 TTTGTAAAAGACACATCTGATATAGGACTGTTACCTAAAATATACAAAGA 1034
                             i   vv i i        vi     vv  i i i      i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr20_2004082_2   1035 ACTGTTAAAAACTCAACAGAAACAAAAAAAC------CCTGATTTTAAAA 1078
                            v   v  -     i --- i     i  ------  ii   ?v    
  L1M4_orf2#LINE/    774 ACTCTTACAA-CTCAATA---ATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_2004082_2   1079 TGGGCAAAGGACCTGTACACACACCTTTGTGTGTTGTGTTGTGAAGATAT 1128
                                    ii  v i v   ii i viivi---------        
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAA---------GAAGATAT 860

  chr20_2004082_2   1129 ATGGATAACAAATAAACATCTAAGCAGATGCTTCACATCATATGTCAC 1176
                          iii  ii v     i  iv i iv       iv      ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (106 / 58)
Gap_init rate = 0.02 (14 / 669), avg. gap size = 3.64 (51 / 14)  


2466 26.06 3.45 0.47  chr20_2084379_2087952     1908  2544 (1030)    L1M4_orf2#LINE/L1       16   671 (237)  

  chr20_2084379_2   1908 TGTTCGTGGGCCGGAAAACTCAAAGTCATTAAGATGGCAATTCTCTCTGA 1957
                              i   iii    i   i  vi ii             v   i ii 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr20_2084379_2   1958 ACTCACCTATAGATTCACTGGAATCCCCACCAAAATCTCAGCAGGCTCTT 2007
                          i v i   i       vi v      i i       i    v v  -  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT-TT 114

  chr20_2084379_2   2008 TTTGTAGGAGTCGACAAGCTGATTTTAAAACTCATATAAAAAAGTAAAGG 2057
                             i  i i i           ii     i      ii   v i  -  
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA-GG 163

  chr20_2084379_2   2058 GGCCTAAAATGGTCAAAACAACTCT----AAAAAAGAACA--GTTAGAGG 2101
                          i  i i   i i        -   ----   i       --   i    
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr20_2084379_2   2102 GCTAACACTATCTGATTTGAAGAAGTATTATGAAGCTACATTAATCAGAA 2151
                         i  v     vi ii    v  i vv  i  ii        v      ii 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr20_2084379_2   2152 CAGCATGGTATTGGCATAAAGATAGGCATATAGATCAACAGACAAGAATA 2201
                            ii     i        i     i            ii  vv     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr20_2084379_2   2202 GTGAGTCCAAAATTAGATCCACATGTATTTAGACAACTGATTTTTGACAA 2251
                          v       i  v  i i   i ii v v i v   i       i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr20_2084379_2   2252 AGTTACAAAGGCAGTGCTGTGGAAAAAGGCTAGCGTTTTTAACAAATGGT 2301
                         i v i v   i vi v vi   ii    iv   iv    i          
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr20_2084379_2   2302 GCTAGAATAACCAGATAACTATATTTAAAAAAATAAACTCA-ATATATGC 2350
                            i i i   ii    ? i i  vi    i   i  v ii- iviv i 
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr20_2084379_2   2351 CTCACACTGTATACAAAAGTTAAATCGAAGTGGATCAAAGATTTAAATAT 2400
                                ii         i    v  i  i       ?   ii     i 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr20_2084379_2   2401 AA-------AATGACAAAACTTCTAGGAGAAAACATACAAGAAAATCCCG 2443
                           -------  iv i      ii   i          vi? v     iiv
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr20_2084379_2   2444 ATGGCACTGG--CAGATA----TCTCTTAGAT--GACAGCAAAAGCACAA 2485
                         i  i vi   --i  ii ---- i        --    v           
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr20_2084379_2   2486 TTTATAAAAGAACAAATGGATAAATTGAACCACATCAAAATTTAAAACTT 2535
                         viv i       v    i         i  iv          v       
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr20_2084379_2   2536 CTGTATTTC 2544
                         i   ii   
  L1M4_orf2#LINE/    663 TTGTGCTTC 671

Transitions / transversions = 2.62 (118 / 45)
Gap_init rate = 0.02 (10 / 656), avg. gap size = 2.50 (25 / 10)  

 903 21.22 6.12 0.00  chr20_2084379_2087952     2838  3082 (492)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr20_2084379_2   2838 AAACCTAAAAACTTCTGCATTTCAAGGGACACTGTTAAAAGAATAAACAG 2887
                            vi         i  iii     i       i i  i i i i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_2084379_2   2888 ACAAA--ACAGACTGGGAGAAAATCTTTACAAAGCATGTATTTAATAAAG 2935
                             v--     v           v   i    v   i   i i    i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_2084379_2   2936 AATTTGTATCAAGAATATA--AAGAACTGTCAAAATTGAATAATAATAAA 2983
                         i i       v        --       v i v  i v        v  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_2084379_2   2984 ACA-----CCC---CCGCAAGCTGGCAAAAGATTTGAATAGACATGTCAC 3025
                            -----   ---i?iv  iiv      i               v  v 
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_2084379_2   3026 CAGAGACCATAAGCA--TGGCAAACT-GCACATAAAAAGATGCTCAACAT 3072
                           i   vv   vi  --    v  iv-      i                
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_2084379_2   3073 CATTTGCCAT 3082
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.55 (31 / 20)
Gap_init rate = 0.02 (6 / 260), avg. gap size = 2.50 (15 / 6)  


2998 28.27 1.11 0.44  chr20_2192596_2199006     5018  5919 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_2192596_2   5018 TGGAAGAACATTCCGTGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5067
                              ii i  i  i  i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_2192596_2   5068 GGCCATACTGCCCAAAGTAATTTATAGATTAAATGCCATCCCCATCAAGC 5117
                            v     v      v i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_2192596_2   5118 TACCAGTGACTTTCTTCACAGGA-CTGATAAAAACT-ACTTTAAAGTTCA 5165
                          v    ivi i  i  ii   i -i   i  i--  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr20_2192596_2   5166 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAAG 5215
                                viiv  ii  v  viv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_2192596_2   5216 AACAAATCTGGAGGCATCATGCTACCTGACTTCAAACTATACTAAAAGGC 5265
                               vi      vv   ii  v  ii i      viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_2192596_2   5266 TGCACTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACC 5315
                          i  v   i   i    ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_2192596_2   5316 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACCAC 5365
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_2192596_2   5366 CTAATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5415
                         i i  i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_2192596_2   5416 GTTTAATAAATGATGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5465
                         v  i  i     i        v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_2192596_2   5466 AACTGGATCCCTTTCTTACACCTTG---AAAAATTAATTCAAGATGGATT 5512
                          ii    i    vi  i     v i---         i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_2192596_2   5513 AAAGACTTAAATTTTAGACGTAAAACCACAAAAACCCTAGAAGAAAACCT 5562
                          ?    i     v v   vv      i i    vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_2192596_2   5563 AGGCA-ATACCATTCAAGACATAGGCATGGGCAAGGACTTCATGACTAAA 5611
                            ?i- v i -   iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_2192596_2   5612 AACACCAAAACCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCCAA 5661
                          -        v  vvi          vv        i    v   iiiv 
  L1M4_orf2#LINE/    598 A-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_2192596_2   5662 TCAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGAGTGAAC 5711
                              v v  i i   i  iiivv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_2192596_2   5712 AGGCAACCTACAAAATGGGAGAACATTTTTGCAATCTACCTATCGGACAA 5761
                           i     i   i          v  v       vii iv    v  i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_2192596_2   5762 AGGGCTAATATCCAGAATCCTCAAAGAACTCAAAAAAATTTACAAGAAA- 5810
                         i  i  vi          vivi         vv v  v iv i  v   -
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_2192596_2   5811 ---CAAACAACCTCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 5857
                         ---    i    iv  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_2192596_2   5858 TCAAAAGAAGACATCTATGCAGCCAACAGACATATGAAAAAATGCTCATC 5907
                           v        i  vi viii     i ii  i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_2192596_2   5908 ATCACTGGTCAT 5919
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (153 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3287 14.18 4.88 1.07  chr20_2283236_2284890      510  1165 (490)    L1M4_orf2#LINE/L1      228   908 (0)  

  chr20_2283236_2    510 TTTTGAAACTTACTACAAAGCAACAGTAATCATAATAGTGTGGTACTGGC 559
                            ii                v          vi i              
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr20_2283236_2    560 ATTAAAGACAGACATATGGACTCAAAGGAATAGAATAGAGAGCCCAGAAA 609
                           -  i  i        i  -    v          v     i       
  L1M4_orf2#LINE/    278 AT-AAGGATAGACATATAGA-TCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr20_2283236_2    610 TAAATCTTCACATATATAGCCAAATGATTTTTTGCAAGGGTGCCCAAACC 659
                             i ivi    v   i i   v       ivi          v i   
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr20_2283236_2    660 ATTCTGTAGGGGGAAAAGACAGTCTTTTCAACAATTGGTGCTGAGAAAAC 709
                             vi --       ii i              v        i  v   
  L1M4_orf2#LINE/    376 ATTCAAT--GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr20_2283236_2    710 T--ATATCCAAATGCAAAAGAATGAAGTTGGACTCTTACCTAATAACATA 757
                          --   ?   v                      i i     v i v    
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr20_2283236_2    758 TACAAAA-CAAATTCAAAATGGACCAAAGAACTAAATCTAAGAGCTAAAA 806
                                -iv  i          i  ?   v      v            
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr20_2283236_2    807 CTATAAAATCCTTAGACGAAAACAGAGG-GCAAATATTTCATGACATTGG 855
                                 ii      v       v   - i    -i   i    v    
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGG 572

  chr20_2283236_2    856 ATTTGGTAATG----C----------CACCAAAAGCACAAGCAATAAAAG 891
                         i  v  i    ---- ----------                  i     
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_2283236_2    892 AAAAAATAGACAAATTGGACTTCATCAAAATTAAAAACTTT-GT-----A 935
                                   i                              -  ----- 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_2283236_2    936 AA---CACTATCAATAGAGTAAAAAGGCAACTCAAAGAATGGGAGAAAAT 982
                           ---         v i   i     i    i  v               
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_2283236_2    983 ATTTGCAAATCACATTTCTGATAAGGGATTAATATACAGAATGTATGGAG 1032
                                     i  v            i vi   v      i   ii  
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_2283236_2   1033 AATCCTTAAAACTCAAGAACAAAAA-----ACAATCCAAAATTTTAAAAT 1077
                           ii    v       v  i     ----- i  i    --  ?v     
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA--TTWAAAAAT 820

  chr20_2283236_2   1078 GAGCAAAAGACTTGAAGAGAGATTTATCCAAAGAAGATATGCAAATGGCC 1127
                          i     i  i     v   v    v              i         
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr20_2283236_2   1128 AATAAGCACATAAAAAGATGCTCAACATGACTAACAAT 1165
                                    i                v ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (56 / 34)
Gap_init rate = 0.02 (14 / 681), avg. gap size = 2.79 (39 / 14)  


 623 21.43 8.57 0.00  chr20_2349681_2354824.rev       27   166 (4978)    L1M4_orf2#LINE/L1        1   152 (756)  

  chr20_2349681_2     27 TGGAGAGATATTCCATGTTCATGGATAGAAAGGCTCAATATTGTCAAAAT 76
                             i      i              v i   i  i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_2349681_2     77 GTCAATTTTTCCTAGCTTGATCTATAGATTCAATGCAATC----TGAAGA 122
                          v    vi i  i iv        i        i      ---- v  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_2349681_2    123 ----AGTTA----TTTTGTGGATATTGACAAACTGATTCCAAACTTTATG 164
                         ----  i i----     ii  v        i     i i   v  i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_2349681_2    165 TG 166
                           
  L1M4_orf2#LINE/    151 TG 152

Transitions / transversions = 3.29 (23 / 7)
Gap_init rate = 0.02 (3 / 152), avg. gap size = 4.00 (12 / 3)  

 553 20.45 0.00 14.77  chr20_2349681_2354824.rev      483   658 (4486)    L1M4_orf2#LINE/L1      141   290 (618)  

  chr20_2349681_2    483 AAAGTTTATGTCAAGAGGCAAAAGACCCAGAGTAGTCAGTACAATTGTAC 532
                            i  i  i vi i v    ii        i   i  iv     i----
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC---- 186

  chr20_2349681_2    533 AATTGTACATTATTGAAGGAGAGGAACAAAGTTAGAGGACTGGCACTACC 582
                         ------------     ii   i          i       vi    v  
  L1M4_orf2#LINE/    187 ------------TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr20_2349681_2    583 TGACTTCAGGTACCTTTAAGATTTACTATAAAGGTACAGTCATCAAGACA 632
                         ii i    ---------- i i      i    v      v         
  L1M4_orf2#LINE/    225 CAATTTCA----------AAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr20_2349681_2    633 GTGTGGTATTAGTGAAAGAATGGACA 658
                                 i i iiv   i  i    
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACA 290

Transitions / transversions = 3.50 (28 / 8)
Gap_init rate = 0.01 (2 / 150), avg. gap size = 13.00 (26 / 2)  

1007 23.38 4.68 0.36  chr20_2349681_2354824.rev     3754  4031 (1113)    L1M4_orf2#LINE/L1      293   582 (326)  

  chr20_2349681_2   3754 TAGATCAATGGAATAGAA--GAGAGTTCAGAAATAGACCTGCACAAACAT 3801
                                           --      i        i   iii   vvi  
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr20_2349681_2   3802 AGTCAGTTGATCTTTGACAAAGTAGCAAAGGAAATACAATGGAGAAAAGA 3851
                         i    i     i  i     i vv  v   ivv  v      i    ii 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr20_2349681_2   3852 TAGTC-----AACAAATGGTGCTGAAGCAACTGGATATCCACACGGGGAA 3896
                              -----              iii          ?     i vii  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_2349681_2   3897 AAAC-AATCTAGACACAGGCCTTACATTCTTTACAAAATGTA-CT-AAAC 3943
                         i  i-  vi i   v vvi   i   iiv v       vv  -  -   v
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_2349681_2   3944 TGAATCATTGACCTAAATGTAAAATGC-AAAACTACAGAACTCTTA-AAG 3991
                           i    ?v             i -  -       i i        -   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAG 541

  chr20_2349681_2   3992 ATAACATGGGAGAAAATCTAGATGACCTGAGATT-GGTAAT 4031
                          v     i  ? v      vvi      vi i  -  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

Transitions / transversions = 1.58 (38 / 24)
Gap_init rate = 0.03 (9 / 290), avg. gap size = 1.56 (14 / 9)  

1235 24.46 2.79 0.00  chr20_2349681_2354824.rev     4330  4652 (492)    L1M4_orf2#LINE/L1      577   908 (0)  

  chr20_2349681_2   4330 GGTAAT--TTTTTTTGATACAATACCAAAGGCATGATCCATGAAAGAAAA 4377
                           i   --   i  v    ii i      i   ii v v ii        
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr20_2349681_2   4378 AATTGATAAGTTGGACTTTATTAAAACTAAAAACTCT-GCACTGCAGAAA 4426
                            v     i        i  i    i        i - ii  v  i ii
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr20_2349681_2   4427 ACACTGTGAAGAGACTGGGAAGAGAGGACACAGCCTGGGAGAAAATGTTT 4476
                              i v    i v  ii    v ivv     vv           i   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr20_2349681_2   4477 GCAAA--AGACATCCGATAAAAGACTGTTATCCAAAATACACAAAGACCT 4524
                              -- v i   i     ii    vv      i    i i     v  
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr20_2349681_2   4525 TTTAAAAACCAGCAATGAGAAAATGAACAACCCGATTAAAATATGGGCAA 4574
                         i   v  vi  ii   i i  i ii  i     i   ?   v        
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr20_2349681_2   4575 AAGACCTG----GACACCTCACCAAAGAAGAGATAGAGATGTCAAATAAG 4620
                          i  ii  ----    ii  v          v   v i   v v      
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr20_2349681_2   4621 TATATGAAAAGATGCTCAATGTCATATGTCAT 4652
                         i i                ii   ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (54 / 24)
Gap_init rate = 0.01 (4 / 332), avg. gap size = 2.25 (9 / 4)  


2810 18.05 14.46 2.35  chr20_2387797_2390271.rev     1175  1983 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr20_2387797_2   1175 GGAAAG----CCAACATGTTCATGGATCC--AGACTTACTATT---AAAG 1215
                               ----  --             iv--       v    ---  ii
  L1M4_orf2#LINE/      2 GGAAAGATATCC--CATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr20_2387797_2   1216 TAACAAATAATAGTCTCCAAAC----------ATTCAATGTAATCCCTAT 1255
                          ii   ----  v  i     i----------      i i         
  L1M4_orf2#LINE/     50 TGGCAA----TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT 95

  chr20_2387797_2   1256 AATAATTCCAGTGGTCATT---GCAGAAATGGAGAAGCTAATCCTCATAT 1302
                         v v   i    iv i v  ---        v  v     i     v v  
  L1M4_orf2#LINE/     96 CAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr20_2387797_2   1303 --ATATGAAGCTACAAAAGGCCCCAAATAGCCAAAACAATCTTGA----- 1345
                         --     i iv i   ii i   vi                    -----
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_2387797_2   1346 --TCACA---TTAGAAGTCTCACA-------------AAAC---CTACAA 1374
                         --vv   ---  i  i v      -------------    ---      
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_2387797_2   1375 AATT---GTAATAAACACTGCAT----CTGGCATAAAGATAGACA----- 1412
                          ii ---     v  v  v ii ----         i        -----
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_2387797_2   1413 ----ATGGA-TAGA--TGAGAGTACAGAAATAAACCCTTACATAAATGGT 1455
                         ----     -    --       v             v     vv     
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_2387797_2   1456 CAATTGATTTTCTGCAGTGGTACCAAAACCATCTATTGGGAAAAGAGTAG 1505
                                     vi  iv   i    i     ii v    i     i   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_2387797_2   1506 TCTTTTCAG---ATGGTGCTGGGACAACTGGATAACCACATGTAAAAGAA 1552
                                 i---                      ?       i       
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_2387797_2   1553 TGAAGTTGGAACTCTACCTCATATGCCTTCATTTATCACTCATTAACTCA 1602
                                   v i        i i-----   v  -  vvv         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACAC-----CATATA-CAAAAATTAACTCA 489

  chr20_2387797_2   1603 AAATTGGTAAACAATCT----GTAAGAGCTAGA----------TCT-AGA 1637
                             v i v ?vi i  ----          i ----------   -   
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_2387797_2   1638 AGAAAAT----GAGTAAGTCCTCATCACCTTGGATTTGGCAATGGATTAT 1683
                               i---- ?    i  i  i v       i  v        v  v 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr20_2387797_2   1684 TGCATTGGACATTGAAA--ACAAGCAACAGAAGAAAAAATATGTAAATGG 1731
                          iv  vv    iii   --          i           vi     v 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_2387797_2   1732 GACTTCATCAAAATTAAAAACTT--GTACATCCAAGAATGGTG--AAGAA 1777
                                                --  i v  v   i iiv i--     
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_2387797_2   1778 --TGAAAAAAAAACTTATGGAAGGGGAGAATATTTTTGCAAACGATATGA 1825
                         --      i v   ii ii   v       v  v        iv    i-
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA- 738

  chr20_2387797_2   1826 TAGTCTGATATCTGTAGTTTGCTATTT-GAAC-TATAAAAAATTCTTA-- 1871
                         ---       v-- viii   -   ii-   i-      i  i     --
  L1M4_orf2#LINE/    739 ---TCTGATAA--GGGACTTG-TATCCAGAATATATAAAGAACTCTTACA 782

  chr20_2387797_2   1872 --------ATAAAAA---AGATAACCTTTTTCAAAAATGAG---AGGAAT 1907
                         --------       --- i      ivv  ?       i ---    v 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_2387797_2   1908 TGAACAGATATTTCTCCAAAGAAGATACACAAATGGCCAAAAAGCACATG 1957
                             i   i                  i            v         
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_2387797_2   1958 AAAACTGGTTCAACATCATTGGTTAT 1983
                             vvv i         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (82 / 60)
Gap_init rate = 0.04 (36 / 907), avg. gap size = 3.78 (136 / 36)  


2125 16.73 16.34 1.36  chr20_2401998_2403994.rev      491  1004 (993)    L1M4_orf2#LINE/L1      110   700 (208)  

  chr20_2401998_2    491 CCTTATTTGTAGA--TTGGCAAACTAATT--------------GAGTTGC 524
                             v    i   --   i   i  i  i--------------  iv   
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr20_2401998_2    525 AAGGCATCTAGAATAGCCAAAACAACCTTGAAAAAGAA----AAAGGAGG 570
                             v i i                i            ----    vv  
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr20_2401998_2    571 AGGATTCACACTT-----TTTC---------------------------- 587
                             i        -----    ----------------------------
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr20_2401998_2    588 --------------TGACTT---------CATATAGATCAAAGGAATAGA 614
                         --------------  i v ---------            v        
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr20_2401998_2    615 ATTGGAAGTCCAGAAATAAAACCATGTGTCAATGGTCAAATGATTTTCCA 664
                             ii              v    iii iv        v        v 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr20_2401998_2    665 CTAGGGTGCCAAGATTATTCAGTGGGGGAAAGAAGAGTCTTTTTAACAAA 714
                          v            ii     i     -      v        i      
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAA 408

  chr20_2401998_2    715 TGATGCTGAGCTAACTGTATATCTACTTAGAAAAGAATACAGTTTGACCC 764
                           i     i vi     v   ? i  v iv        iv    v     
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr20_2401998_2    765 -TACCTTATACCATATATAAAATATGAACTAAAAATATATCAAAAATCTA 813
                         -     i i        i    -  v    v     iv    ? i i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAA-ATTAACTCAAAATGGATCAWAGACCTA 507

  chr20_2401998_2    814 AATGTAAGAGCTAAAACTATAAAACTATTAGAAGAAAACAAAGGGGTAAA 863
                                                   v             v   ?     
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr20_2401998_2    864 TCTTCATAATCTTAGATTTGGCAGAAAAGATTTTTCT--TATTGCACCAA 911
                              i i i   i i  v    --- v i   i iv--   vi      
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCA---ATGGTTTCTTAGATATGACACCAA 604

  chr20_2401998_2    912 AAACATGAGCAACAACAACAACAAAAAGATAAATTAGACTTCATCCAAAT 961
                           i  ii        -  v  v   v         i         v    
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAA-AAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr20_2401998_2    962 TAAAAAACTTTTGTAC-----AGGATATTACCAAGAAAGTGAAAAGGC 1004
                               -       i -----    i i  i               i 
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

Transitions / transversions = 1.59 (51 / 32)
Gap_init rate = 0.02 (14 / 591), avg. gap size = 6.50 (91 / 14)  

1194 15.70 0.45 0.00  chr20_2401998_2403994.rev     1283  1505 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr20_2401998_2   1283 AAAAAAAAAAAAAAAAAACTCACAGAATGGGAGAAAACCTGTATAAATCA 1332
                           i   ivi    i v   i                 iv v ii      
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr20_2401998_2   1333 TATATCTGACAAGGAACTTGTATCTGTAATGTAGAAAGAATTCTTACAAC 1382
                                  i    i         iiv   i  v      i         
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr20_2401998_2   1383 TCAATAATAAAA-GTCAAATGGTCCAATTAAAAAATGAGAAAAGGATCTG 1431
                                     - v     iii      ?       i v       i  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr20_2401998_2   1432 AATGGGCATTTCTCCAAGGATGATATATAAATGGCCAACAAGCACATGAA 1481
                            i i           i  v      i          i           
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr20_2401998_2   1482 AAGATGTTCAACATCATTAGTCAT 1505
                               i         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.78 (25 / 9)
Gap_init rate = 0.00 (1 / 224), avg. gap size = 1.00 (1 / 1)  


 962 28.07 11.30 3.32  chr20_2416053_2417646.rev      501  1102 (492)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr20_2416053_2    501 AAAACATTGTGGTGCTGGCCCATGACTAGACAAATAGACCAGTGGAAT-- 548
                           i   v      i     vi v iv      v     i  i      --
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr20_2416053_2    549 ----------CAAGAAGTCAACCCAAGTACTTATGG--AACTTTGGTATG 586
                         ---------- v    i v      vii i      --  --   i v v
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA--TTGATTTT 356

  chr20_2416053_2    587 TGATGAAGGTGGCA---TC--TCAAATTCCTGGAGTAAAGATGGACATTT 631
                         i  ii i    v  ---i --    -----   i v  ii  i v v   
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAA-----TGGGGAAAGAATAGTCTTTT 401

  chr20_2416053_2    632 TAATAAATGGTGTTGGG-CAACTAGATATCCATTTGGAAAAACATAACAT 680
                         i  i        i    -     i    ?   iv  v    iv  i vi 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_2416053_2    681 TGGACCATATACCACACACCATACACAAGAAA-AATCCCAAATG-ACTAG 728
                               vi-    v         i    i  v-  ii v     - ii ?
  L1M4_orf2#LINE/    452 TGGACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_2416053_2    729 AGATCTAAATGTAAAAAATTAAACCGTAAACACACT---AGGATAGGATG 775
                            i          i iv v    ii    -  v  --- i  v iv  i
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATA 549

  chr20_2416053_2    776 GGGGTAAATATTCTATCACCTGGACACAGGAAAAGGTTTTCTAAATTTGG 825
                           ?      v   -i v    v ivvi   v  v     ii  i  v  i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTC-GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_2416053_2    826 C--TAAAAATCCAGATGCCTAGAAGGGAAGAGTGATAAGTTTGACGCTGT 873
                          --i    iiv  iiiiv - i   ii  i vv     i  v   viii 
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAAC-AAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_2416053_2    874 ---------AAGC-----------AAAG-------TCAAAA----GAAAG 892
                         ---------  i -----------    -------    i ----    i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_2416053_2    893 GACTAATTTCCAGGA--------AATATTTGCCACATACAGTATATCACA 934
                            -  iiiv   i --------         v -  -  -      vv 
  L1M4_orf2#LINE/    698 GAC-AACCCACAGAATGGGAGAAAATATTTGCAA-AT-CA-TATATCTGA 743

  chr20_2416053_2    935 TATAAAGAGTTATTTTCCATAACATAGAATGAA-TCTTAAAATTCAAAGA 983
                           - ii  v  i v -   v  i   v  v   -     v  i    vi 
  L1M4_orf2#LINE/    744 TA-AGGGACTTGTAT-CCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_2416053_2    984 GAAGAACCCTAA-AACCAGATAGGAAGAAAATAGGCAAAATACCTAAATA 1032
                         v  i  vv v  -    vi  v---?i     i      iv ii i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATT---WAAAAATGGGCAAAGGATTTGAATA 838

  chr20_2416053_2   1033 GACGATTCACAAAATAAAATATAACATTGTCCCTTAAATGTTTGAAAAGG 1082
                            iv   v v   v  i     vv v  v  vv   iiiiv       i
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr20_2416053_2   1083 TGTTCAACTTCACTTCTAAT 1102
                           i     v   ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (94 / 71)
Gap_init rate = 0.04 (29 / 650), avg. gap size = 3.03 (88 / 29)  


3119 26.36 1.55 1.00  chr20_2428972_2435352     4987  5889 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_2428972_2   4987 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5036
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_2428972_2   5037 GGCCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5086
                            v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_2428972_2   5087 TACCAATGACATTCTTCACTGAA-TTGGAAAAAACTACTTC-AAAGTTCA 5134
                          v   iivi v  i  ii v   -   -- v  i  iv i -   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_2428972_2   5135 TATGGAAC--CAA-------AAAACAGCCCTAAGTCAATCCTAAGCAAAA 5175
                                v--   ------- i  i    --  iv     i i iv  i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCC--AAAACAATCTTGAAAAAGA 196

  chr20_2428972_2   5176 AGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACGAG 5225
                                  i      vv    i  v  ii i      viv      i i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_2428972_2   5226 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5275
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_2428972_2   5276 TCAATGGAACAAAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 5323
                                  i i  i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr20_2428972_2   5324 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 5373
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_2428972_2   5374 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5423
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_2428972_2   5424 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATG 5473
                         v    ii    i    v   i     v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_2428972_2   5474 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5523
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_2428972_2   5524 AACTAGACA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5572
                          vv   i?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_2428972_2   5573 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAACGGGATC 5622
                           vi            vvi          vv     v  i   iv   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_2428972_2   5623 TAATTAAACTAAAGAGCTTTTGCACAGCAAAAGAAACTACCATCAGAGTG 5672
                          v  i   v v  i i      ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_2428972_2   5673 AACAGGCAACCTATACAGAATGGGAGAAAATTTTTCCAATCTACTCATCT 5722
                           v  i     i --                v   v   vii ivi    
  L1M4_orf2#LINE/    694 AAAAGACAACCCA--CAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_2428972_2   5723 GACAAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAA 5772
                           i  i  i  vi          v  i  v      iv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_2428972_2   5773 GAAAAAAACAAACAACCCCATCAGCAAGTGGGTGAAGGATATGAACAGAC 5822
                         v     i     i     v  i?iv  i    ii      v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_2428972_2   5823 ACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACAGGAAAAAATGC 5872
                          i     v        i  vi viii     v ii    v     i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_2428972_2   5873 CCATCATCACTGGCCAT 5889
                         i  v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (141 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.09 (23 / 11)  


3418 15.64 3.75 0.33  chr20_2439929_2442524      911  1524 (1072)    L1M4_orf2#LINE/L1        8   642 (266)  

  chr20_2439929_2    911 ATACTCC--GTTCATGGGTTGGAAGGCTTAATATTGTTAAAATGGCATTA 958
                            ii  --        i       i              i      v  
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr20_2439929_2    959 TTCCTCAAAGCAATCTACAGATGCAATGCTATCCTTGTCAAAATTCCAAT 1008
                         i   i    vii          v   i  v    i i       i   ii
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr20_2439929_2   1009 GGCCTTTTT-GCAGAAATGGAAAAGTTGATCCTAAAGTTCGTATGGAATT 1057
                         v        -        v  v   i          i   i       v 
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr20_2439929_2   1058 TTAAGGGACCCAGAGTAGCCAAAACAATTTTGAAAAAGAA---TAAGGTT 1104
                         vi            i             i           ---i  i   
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr20_2439929_2   1105 GGAGGACTCACTCTTCTTAATTTTAAAACTTAATACAAAGCTTCAGTAAT 1154
                                    v    ii     i        v         v       
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr20_2439929_2   1155 TAAAACAGTGTGGTACTGCCATAAGGGTAGACATA--GACCAATGGA-TA 1201
                         i  i              v       i        --  i       -  
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr20_2439929_2   1202 GGATTGAAAGTCCAGAAATGAAACTGTAGAGAAATGGTCAATTGCTTTTC 1251
                          i     i           i  v ii  v vvv           v     
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr20_2439929_2   1252 AACAAGGATGCCGAGACCATTTAATGGGGAAAGAATAGCCTTTTCAATAA 1301
                         i      i    i        i                i        i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr20_2439929_2   1302 ATCATGCTGGAACAACTGGATAACCACAAGTAAAAGAATGAAGTTGGACC 1351
                           vi      i           ?     v i                   
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr20_2439929_2   1352 TCTACCTCCCACTGTATACAAAAATTAACTCAAA--GACTATAAAGATCT 1399
                         i       v   ii                    -- iv -i ?   i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT-CAWAGACCT 506

  chr20_2439929_2   1400 AAATATAAAAGCTAAAACT--------CTTAGAAGAAAGCATAAGGGTTA 1441
                             i   i          --------           i    i ?  v 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_2439929_2   1442 ATTTTCATTACCTTGCATCTGAAAAATTGTTTCTTAGATGTGACACCAAA 1491
                           i   i v      vi - iiiv   v           i          
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr20_2439929_2   1492 AGCAGAAGCAACAAATGGAAAAATA----AATTGGGC 1524
                             v          v i       ----      i 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

Transitions / transversions = 2.10 (63 / 30)
Gap_init rate = 0.02 (10 / 635), avg. gap size = 2.50 (25 / 10)  

1135 17.07 2.79 3.83  chr20_2439929_2442524     1818  2104 (492)    L1M4_orf2#LINE/L1      625   908 (0)  

  chr20_2439929_2   1818 AAAAAAGA--AATTGGAATTTATCAAAATTTAAAACTTT-GTGCGCCAAA 1864
                             v   --       v  i         v        -    vi    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr20_2439929_2   1865 GGACACTACTGGAAGAGTGACAAGGCAACCCATAAGAATGAGAGAAAATA 1914
                                 iiiii i     v   i       i -     i         
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACA-GAATGGGAGAAAATA 723

  chr20_2439929_2   1915 TTTGCAAATCATATATCTGATAATGGTCTAATGTCCAGAATATATTAAGA 1964
                                                v  v  vi i            v    
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr20_2439929_2   1965 TTTCT-ATGACTCAATAACAAAAAGACTAACAACCCAATTTTAAAATGAG 2013
                         vi   - ii         i        v  i         ?v      i 
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr20_2439929_2   2014 CAAAGGACTCAAATAAACATTTT---GAAGAA-ATAACTGCATACAAAAC 2059
                                i ii    i      i---i     -   ------      -i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA------TACAAA-T 866

  chr20_2439929_2   2060 AGCCAGCAAGAACACACCAAAAAAATGCTTACTGTCACTAATAAT 2104
                         i    ii   --    i-i    i     i vii   ????????
  L1M4_orf2#LINE/    867 GGCCAATAAG--CACAT-GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.69 (35 / 13)
Gap_init rate = 0.04 (10 / 284), avg. gap size = 1.90 (19 / 10)  


 438 30.25 0.00 0.00  chr20_2479363_2484817.rev     3779  3897 (1558)    L1M4_orf2#LINE/L1       27   145 (763)  

  chr20_2479363_2   3779 TGGAACATTCAACATTATTAAAATGTAAGTTCTTCCCAGCTTTGTCTATA 3828
                              v i i  i   i    i   vv i v  i    iv  vi    i 
  L1M4_orf2#LINE/     27 TGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACA 76

  chr20_2479363_2   3829 GAGTTAATGCGATTTCAATCAAAATCCCAGCAAATTATTCTGTGGATATT 3878
                           v i  i  i  ii v              vivi v  i  ii  v   
  L1M4_orf2#LINE/     77 GATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATT 126

  chr20_2479363_2   3879 GATAAACTGATTCTAAAGT 3897
                           i  i     i     i 
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAAT 145

Transitions / transversions = 2.00 (24 / 12)
Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.00 (0 / 0)  

2210 20.91 7.27 6.49  chr20_2479363_2484817.rev     4196  4965 (490)    L1M4_orf2#LINE/L1      133   908 (0)  

  chr20_2479363_2   4196 CTGATTCTAAAGTTTATATGGAAAGGCAAAAGACCCAGAATATCCAGCAC 4245
                              i     i  i         v    ii           v   iv  
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr20_2479363_2   4246 AATCC---------ACATCAAGACTCTAAAGCTC-TACTTCATACACATC 4285
                             i--------- v v   iii vv iii   -i     vi - iv  
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTC 231

  chr20_2479363_2   4286 AA----CACTATAAAGGTACAGTAATCAAGATGGTGTGATACTGGTGAAA 4331
                           ----i    i    v              ii     i      iiv  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr20_2479363_2   4332 G---AGA-AT-TAGATCAATGGGATGGAATAGAGAGCTCAGAAATAGACC 4376
                          ---   -  -           i  i    v     ii        i   
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr20_2479363_2   4377 CACACAAATATAGCCAACC----TTTGACGA------------------- 4403
                           i   vv   i i   ii----  i   i -------------------
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr20_2479363_2   4404 TGGAGAAAGGATAGTTTTTTTCAACAAATTGTGCTGGAACAACTGGGCAC 4453
                            i     i     i    -        v       i        ii ?
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAK 430

  chr20_2479363_2   4454 CCATAGGCCAAAACCAAAAATCTAGATACAGACCTTATGCCTTTCACAAA 4503
                            i v  -    vv vi  vi i  iv vv    i ii  v vi     
  L1M4_orf2#LINE/    431 CCACATGC-AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr20_2479363_2   4504 AATTAACTCCAAATGGATCATAAACCTAAATGTAAAACACAAAGCTATAA 4553
                                  v          ? i            i vvi   i      
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr20_2479363_2   4554 AACTGT-AAAAGATAACAAAGGAGAAAA-CTGCAATGGCCTTCAATTTAG 4601
                             v - i    v    v   ? v   -  v i-  i    vii  vi 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCG-TGACCTTGGGTTAGG 578

  chr20_2479363_2   4602 CAATGACTTTTAAAATACCACAGCATAAATGAAAACAAAAATAAAAACAA 4651
                              ii  i v i   iv   v  ------   i  v  ii  v  -- 
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCA------AAAGCACAAGCAACAA--A 620

  chr20_2479363_2   4652 AGAATAAAATACGATACCAAAAGCATGATCCATTAAAGAGAAAAATTGAT 4701
                             -      -    ---------------------------     i-
  L1M4_orf2#LINE/    621 AGAA-AAAATA-GATA---------------------------AATTGG- 640

  chr20_2479363_2   4702 GTTTTAATTCATTAAAACTAAAAACTTCTGCTCTGCAAAAGACACTGTGA 4751
                         ----- v     i    i         i  iv  v    i      i v 
  L1M4_orf2#LINE/    641 -----ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr20_2479363_2   4752 AGAGAATTAAAAAAAAAAACCCACAAACTAGTAGAAAATATTTGCAAAAC 4801
                            i i --i    i v        i v i v                v 
  L1M4_orf2#LINE/    686 AGAAAGT--GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr20_2479363_2   4802 ATGTATCTGACAAAGGACGTGTATCCAAAATACACACATGAA-------A 4844
                           i       i  i    v        i    i i v -   ------- 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAA-GAACTCTTACA 782

  chr20_2479363_2   4845 ACTCAAGAATAAGAAAACAAA-----CAATTAAAAAATGGAAAAAAGATC 4889
                               v     i  i     -----     ?        iv   i   i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_2479363_2   4890 TGAGCAGACATCTCACCAAAGAAAGTATACAGATGGTAAATAGGCATATG 4939
                            ii      i  v        ii      i    iv    i   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_2479363_2   4940 AAAAGATGCTCAACATGGTATGTCAT 4965
                                         vi????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.85 (102 / 55)
Gap_init rate = 0.03 (24 / 776), avg. gap size = 4.42 (106 / 24)  


3022 27.35 0.55 0.33  chr20_2498059_2500557     1105  2007 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr20_2498059_2   1105 AAAAAAAATCCATGCTCATGGATTGGAAGAATCAATATCATTAAAATGCC 1154
                            i v vi     i               v i     ii    i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr20_2498059_2   1155 CATACTACTGAAAGCAATCTACAGATTCAATGCTATTTCTACCAAACTAC 1204
                         v     v iv   vii              i  v  ii   i    v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_2498059_2   1205 CAA-TGTCATTTTTCACAGAAATAGAAAAAAAGATTCTAAAATTCACA-G 1252
                           i-  i -     ii       v  v  ivv   i          i - 
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_2498059_2   1253 GAACCAAAAATGAGCCCAAACAGCCAAAGCTATCCTAAACAAAAAGAATA 1302
                            viiv  iv  v  vi  i       i v   i i  v  i     i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_2498059_2   1303 AAGCCAGAGGCATCACATTACTCAACTTCAAACTATACTATGAGGCTACA 1352
                            iii    vv     i v i   i      viv     ii i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_2498059_2   1353 GTAACGAAAACAGCACAGTACTGGTACAAAAACAGACACATAGACCAATG 1402
                             iv  i    iiii       i i  ii i     i     i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr20_2498059_2   1403 GAACTGAATAGAGAATGCAGAAATAAAGCTGCCCACCTACAACCATCTGA 1452
                            iv    v    i v          v iiiv  ii  iiii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_2498059_2   1453 TCTTCAATAAAATCAACAAAAAACAAGCAATGGGGAAGGACT-CCCTATT 1501
                          i   i i  iiviiv -  i v  vv          i  v -vi  v  
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCC-AAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_2498059_2   1502 CAATAAATGGTGCTGGGATAACTGGCTAGACATATGCAGAAGAGTGAAAC 1551
                            i              i      v  ?v  i     i    i    ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_2498059_2   1552 TGGACCCCCGCCTCTCACCATACACAAAAATCAGCACAAGATGGATTAAA 1601
                                 ii    v       i        i i v   i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_2498059_2   1602 TACTTGAATGTAAGACCTAAAATTATTAAAATCCTAGAAGAAAACCTAGG 1651
                         v  i i         v      i   v   v  i           v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_2498059_2   1652 AA-ATATCATTCTGGATATTGGCCTTGGGAAAGAATTTACGACTAAGTCC 1700
                         ?i- v   -   vv  iv    vi v  v  v iv  iviiiv  v v v
  L1M4_orf2#LINE/    552 NGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_2498059_2   1701 TCAATAGCAACTGCAACAAAAACAAAAATTGACACATGGGACCTAATCAA 1750
                         i   v    vvv         iv      v  i v  v    i v     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_2498059_2   1751 ACTACAAAGCTGCTGCACAACAAAAGAAACTATCAGCAGAGTAAACAGAC 1800
                          v vv   i  vi  ii vv    i  v       iv i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_2498059_2   1801 AACCTACAGAATGG-AGAAAATATTCTCAAACTATGCATCTGACAAAAGT 1849
                             i         -          iv    ii  ii      i  ii v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_2498059_2   1850 CTAATATCCAAAATCTGTAAAGAACTTACACAATTCAACAAGCAAAAAAC 1899
                           vi      i   v i         ivi    i    i  vv    i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_2498059_2   1900 AAATAACTCCATTAAAAAGTGGACAAAGAATATGAACAAACACTTCTCAA 1949
                                i v   ?    i   i     i  v    i i   i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_2498059_2   1950 AAGAAGACATACAAGCCTCCAACAAACATATGAGAAAATTCTCATCATCA 1999
                                i      iivv    i  i  i    i  i  v    v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr20_2498059_2   2000 CTAATTAT 2007
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (8 / 905), avg. gap size = 1.00 (8 / 8)  


 909 16.27 4.78 4.31  chr20_2755219_2758122     1218  1426 (1478)    L1M4_orf2#LINE/L1        3   212 (696)  

  chr20_2755219_2   1218 GAGAGATATACTTTGTGCATGGGGTCAGATATAGGTCAGAC---ATATTG 1264
                           i      v iv   v     i- ii  --------    ---      
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGA-TTGGA--------AGACTTAATATTG 43

  chr20_2755219_2   1265 TTAAGATGTCAAT-TTCCCCCAATTTATCTATATATTCAATACAATCGCA 1313
                                 v    -i     v    v     i v      ii     v v
  L1M4_orf2#LINE/     44 TTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr20_2755219_2   1314 ATCAAAATCCCAGCAGCATTTTT-ATAGGAAT-AACAAGCTGATTTTAAA 1361
                                       v  v     -ii  i   -i          ii    
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr20_2755219_2   1362 ACTCATATGGAAATGTAAAGGACCTAGAATAGCCAAAATAACTTTGATAA 1411
                          i             i  i     i             i  ii    v  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr20_2755219_2   1412 AGAA---CAAAGTTG-AGG 1426
                             ---        -   
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGG 212

Transitions / transversions = 1.83 (22 / 12)
Gap_init rate = 0.04 (8 / 210), avg. gap size = 2.38 (19 / 8)  

2639 22.67 3.59 0.43  chr20_2755219_2758122     1718  2414 (490)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr20_2755219_2   1718 AAAAAAAAGAACCAAGTTGAAGGACTAACACTTCCCAATGTCAAGATTT- 1766
                              i      v      i      v            v    i i  -
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_2755219_2   1767 -CATCAAGGTACA---ATCAAAAGAGTGTGGTATTGGTATAAGGACAGAC 1812
                         -i iv   v    ---     i v         i   i       i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr20_2755219_2   1813 AAATAGACCAGTGGAACACAGT--AGAGTCCAGAATTAGATCCACACATA 1860
                          v     i  i     i v i --           v  i i   i    v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr20_2755219_2   1861 TATGAACAAGTGAGTCTCAATGCAAGTGCAAATGTAATTTAGCGGAGAAA 1910
                             iv   v   v i  i iivii    v  viiv   i ii  i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr20_2755219_2   1911 GAATAGTCTT--CAACCAATGGTGCTGA-ACCATTGTATATTCACAT--- 1954
                                   --    v          i-  v i  v   ?i     ---
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr20_2755219_2   1955 -AAAAATGAATTTCAATTTATACTTCACACCATAAACAAAAAATTAACTC 2003
                         -  i      v  vi iiiv   i          v       -       
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTC 488

  chr20_2755219_2   2004 AAATTTGATCATAGACCTAAATGTAAAACCAAAAACTATAACCCTTCTAA 2053
                            v v     ?              i v v          vv  ii  i
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr20_2755219_2   2054 GAGAAAACATAGAAAACAAATAGTTGTAACCTTGCATTAGGAAAATATTT 2103
                         i           i?i-i    vv i  i      vi     v  vvi   
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_2755219_2   2104 CTTAGATATGACACCAAAAGCACAATCCATAAAAGAAAAACTTGATTAAC 2153
                                                  v v i          v v   v  i
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr20_2755219_2   2154 TGTACTTTATCAAAATTAAAAACTTCTGTTCTTGAAAAGACACTGTTAAG 2203
                           v    i                 i   v   v   i      i i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_2755219_2   2204 AAAAAAAGAAGACAAGCCACAGATTGGAAGAAAGTATTTTCAGATCATAT 2253
                            ivi i       v       v   i     i     v  i       
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_2755219_2   2254 --CTGATAAAATACTTGTATCCAGAATA----AAGAACTCTCAAAGTCCA 2297
                         --       iiv                ----         i v iii  
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_2755219_2   2298 ATATGTAAAAAGGGGGATAG----AGGGAAAGA-GAGAGAAAAATGTGAA 2342
                            -i       ivii   i---- vv?   i - i vi  ii  v    
  L1M4_orf2#LINE/    788 ATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_2755219_2   2343 AACCTACTTAACAGAAGAAGATATATAGGTGAAAAATAAGCATATGAAAA 2392
                         v vvi i  vv vi           i ii  ivv        i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_2755219_2   2393 GGTGTTCAACATAATTGGTTAT 2414
                          i  i       v ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (90 / 64)
Gap_init rate = 0.02 (13 / 719), avg. gap size = 2.15 (28 / 13)  


1356 15.90 0.00 0.84  chr20_2843513_2846413.rev      808  1046 (1855)    L1M4_orf2#LINE/L1      120   356 (552)  

  chr20_2843513_2    808 AGAAATAAAAAAACTGATCCTAAAATTTATATGGAATTGCAAGGGACTCC 857
                               vi v  i              i        v          i v
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr20_2843513_2    858 GAATGGCCAAAACAATCTTGAAAAGGAAGAACAAAGTTGGAGAACTCATA 907
                             i                   i                 i     i 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr20_2843513_2    908 CTTCCTGATTTCAAAACTTATTGCAAAGCACCGGTAACCAAAGCTGTGTG 957
                              ii             i i      vv i    i   ii v     
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr20_2843513_2    958 GTAATGGTATAAGGAGTGATATATAGATCAATGGAATAGTTTTAAATGAG 1007
                            v   i       vv  i                   vv  i --   
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA--GAG 317

  chr20_2843513_2   1008 TTCAGAAATAAATCCACAAATCTATAGTCAACTGATTTT 1046
                          i          i   i v  i   i     i       
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 1.92 (25 / 13)
Gap_init rate = 0.00 (1 / 237), avg. gap size = 2.00 (2 / 1)  

 908 13.82 4.61 1.32  chr20_2843513_2846413.rev     1271  1422 (1479)    L1M4_orf2#LINE/L1      331   487 (421)  

  chr20_2843513_2   1271 CCATGC-CCTATGGTCAACTAATTTTTGGAAAGAGTGCTAAGACAACATT 1319
                             i -ii         i i     i iv   i    i     --    
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC--CATT 378

  chr20_2843513_2   1320 CAATGGGGAAAGAACAGGCTCTTCAACAAATGGCACTGGGACAACTGGAT 1369
                                       i  v  i            ii               
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr20_2843513_2   1370 ATTCACATGCAAAAGAATGAA------TCCTTACCTCATACCATATATAA 1413
                          ?i                  ------i  i       i        i  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr20_2843513_2   1414 AAATTAACT 1422
                                  
  L1M4_orf2#LINE/    479 AAATTAACT 487

Transitions / transversions = 9.00 (18 / 2)
Gap_init rate = 0.02 (3 / 157), avg. gap size = 3.00 (9 / 3)  

1312 14.12 15.00 3.82  chr20_2843513_2846413.rev     2062  2401 (500)    L1M4_orf2#LINE/L1      518   895 (13)  

  chr20_2843513_2   2062 CTAAAACTATAAAATTCTTAGAAGAAAACATAGG--TAAATCTTCATGAC 2109
                                       i                   --         i    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr20_2843513_2   2110 ACTGAATTTGAAAATGGATTCTTAGATATGACACTAAAAATCATAAGCAA 2159
                         vi  ii  v iv     v                i    i-  i      
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG-CACAAGCAA 616

  chr20_2843513_2   2160 CAAAA-------CTGACAAATTGGAATTCGTCAAAATT--------TTG- 2193
                              -------iv  i        v   i        --------   -
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr20_2843513_2   2194 ----------------------------AAAGACAACCTATGGGATGCAA 2215
                         ----------------------------          i ii i   vi 
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr20_2843513_2   2216 GAAACTATGTGTTAATCAGATATCATGTATCTGATAAGGGTCTAGTTATC 2265
                             v   v  i-  ------     i             v  v  vvi 
  L1M4_orf2#LINE/    717 GAAAATATTTGC-AA------ATCATATATCTGATAAGGGACTTGTATCC 759

  chr20_2843513_2   2266 AGAATA----AAGAACTCTTACAATTCAGTAACAAAAAAAGACAACTTCC 2311
                               ----              i   i   i     --     v --v
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAAA--GACAAAT--A 805

  chr20_2843513_2   2312 CCCCAATTTAAAAAATAGGCAAAGAATTT-AAGAGACATTTCTCCAAAGA 2360
                         v       ?     - i       i    -  v                 
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr20_2843513_2   2361 ATATATACTAATGGCCAACAAGCACATGAAAAGATTTTCAA 2401
                          v      v         i                vi    
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

Transitions / transversions = 1.35 (27 / 20)
Gap_init rate = 0.03 (12 / 378), avg. gap size = 5.33 (64 / 12)  


 272 28.10 12.86 4.76  chr20_2889532_2891371.rev      234   443 (1397)    L1M4_orf2#LINE/L1      406   632 (276)  

  chr20_2889532_2    234 AAATGGTTTTGGGAAAA----ATAACTACATATTTGAGAGGAGGGAGTTA 279
                                vi     v  ----   ? i    ii--i i  i v i    i
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGC--AAAAGAATGAAGTTG 453

  chr20_2889532_2    280 GACCACCACCTCATTCCATATACCAAAATAAATTCCACATAGGTTTAAAA 329
                             v i      iv        v     v  i  v v  i i iv? i 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr20_2889532_2    330 ATTAAATG------CTTGAAAAC-ACA----TTTTAAAAGAAAATAAATG 368
                         vi      ------  --     - i ---- i   i       i v v 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCT--AAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_2889532_2    369 AATA------TGTGAGCTCAGGATGAGGAAAAACTTTCTAAG------CA 406
                         ?i  ------i    v  ii  - v   v  viv     v  ------  
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_2889532_2    407 TAAAAGGCAATTAAGAAATCATAAAGGTAGAAGTGGA 443
                         iv   i   --i   v  i---   i v i  i i  
  L1M4_orf2#LINE/    601 CCAAAAGCA--CAAGCAAC---AAAAGAAAAAATAGA 632

Transitions / transversions = 1.55 (34 / 22)
Gap_init rate = 0.05 (11 / 227), avg. gap size = 3.36 (37 / 11)  

2520 25.12 6.96 1.53  chr20_2889532_2891371.rev      501  1348 (492)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr20_2889532_2    501 ATGTTTATGGACAGGAAGACTCAATATTGTCAAGATGTCAGTTATTCCCA 550
                              i     iv        i        i      v  i vv i    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr20_2889532_2    551 AATAAGCCTATAGATTCAATGCAATCTCAATCATAATCTCAGCAAGTTAT 600
                            viii   i        i      i v    v    i    vivi v 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr20_2889532_2    601 TTTGTGAATATAAAAATGCTGATTCTAAAGTTTACATGGAGAGACATTAA 650
                             iii v  vi v v      i     i  i i     i vi  v-ii
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA-GG 163

  chr20_2889532_2    651 GATTCTGAAGGGGCAACTCAATATT---AAAGAAGAGTCAAAG------- 690
                           ii v   vi v   vv    v  ---        i-     -------
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA-CAAAGTTGGAGG 212

  chr20_2889532_2    691 ATTAATGCTATTGGACTTCAAGACTTACTTTAAAGCTATGGTAATTAAGA 740
                          i v ii  viivi i     i       vi       ii     i    
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr20_2889532_2    741 C--TGTGGTATTAGCAAAAGAAAAGGCAAACAGATCAATGGAACGGAACA 788
                          --       i i   v   i v  i  v i            ii   iv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr20_2889532_2    789 GAGA--TCATAAACAGACCCACATAAATATAGTCAACTGA-------CAA 829
                             --i  v   i i     i i vv   i     i   -------   
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr20_2889532_2    830 AGGAGCAAAGGCAATAAAATGGAGCAAGA-TAGTCTTTTCAACAAATGAT 878
                         i  v  v   i v  vv     i v    -                  i 
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr20_2889532_2    879 ACTGG---AAAGGGACAGCTACATATAGAAAAATTAA------TCCATA- 918
                         i    ---  vv   i ? i    ii i  i   v  ------i  v  -
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr20_2889532_2    919 -TCAGACCTTATTATCTTTCACAAAAATTTAACTAAAAATGAATCATAGA 967
                         -   v   v   --------         -    v      i    ?   
  L1M4_orf2#LINE/    463 CTCACACCATAT--------ACAAAAATT-AACTCAAAATGGATCAWAGA 503

  chr20_2889532_2    968 CCTAAATATCAATCATAAGACTATAAAATGCCAAGAAGATAACA--GGAG 1015
                                i v ivvv   i         iv iv      v    --  ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr20_2889532_2   1016 AAAATCTAGATGACTTTGGGTATGGCGAGAACTTTTTAGATATAACATCA 1065
                         v      vvi    i      vv   i viii  i        i   i  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr20_2889532_2   1066 AAGGCATGATC--CATGAGAACATAATTGATAGTCTGGACTTCATTAAAA 1113
                           i   ii v --  vi    v -   v    ivi          i    
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAA 652

  chr20_2889532_2   1114 TATAAAATGTCTACTCTGTGAAAGACAATGCCAAGAGAATCAGAGGATAA 1163
                          vv    iv i iiv  vii  i    v ii     i i v i i  i  
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr20_2889532_2   1164 GCCACAGACTAGGAGAAAATATTTGCAAAAGATAGATCTGACAAAGGAC- 1212
                         v       v i                  vv   v      i  i    -
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr20_2889532_2   1213 ----------------AGAGAATTCTTA-AACTCAACAAGAAAAATA--- 1242
                         ---------------- i    i     -       i  v     v ---
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr20_2889532_2   1243 ACAACCAGATT-AAAAATGGGCAAAAGACCTGAAGAGACACCTCACCAAA 1291
                          i    vi   -             i  ii    v     ii  v     
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr20_2889532_2   1292 GAAGATAAACAGTACGGCAAATAAGCATCTGAAAAGACACAGAACATCAA 1341
                                v   i- i   v        iv        ii vv       ?
  L1M4_orf2#LINE/    853 GAAGATATACAA-ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr20_2889532_2   1342 GTCATTA 1348
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.44 (124 / 86)
Gap_init rate = 0.02 (21 / 894), avg. gap size = 3.43 (72 / 21)  


 675 29.21 12.84 6.12  chr20_2898604_2900482.rev      539  1387 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_2898604_2    539 GGAATATATTGCAT--TCTTGGATAGTTAGACTCAACATCTGT-AAGATG 585
                          i  v    iv   --  v     v vv     i  i  -   -      
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATAT-TGTTAAGATG 51

  chr20_2898604_2    586 CCATT-TTCTCTG--TTAATCTACGTATTTAACATGATC--------AAT 624
                         v  v -i  i ii--  i      iv   i   iii   --------   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_2898604_2    625 ACAAACTTTTTTTCCTGC-----TAGACAAGTTAATTCTAATGTTTATA- 668
                         v v i  vii   ii   ----- v      i i  i    vi  i   -
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr20_2898604_2    669 ----ATA----------AGAATTGCTAACAAAATTCTGAAAAATAAAATT 704
                         ----  i----------     v  i  v v   ii       v  i --
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA-- 199

  chr20_2898604_2    705 AACAAGG---AATGACTCATTTTACTGGATATTAAATACTT--TACAAAG 749
                         -    i ---i v      ivi v ivi  v i   -    --       
  L1M4_orf2#LINE/    200 -ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-ACTTACTACAAAG 247

  chr20_2898604_2    750 TTACAATTATTGAGACAGTGAGGC-TTTGCACATGGACAGAGAAAAAGAT 798
                         i    i v  ii        v  i-i v   i v   i   v v v    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_2898604_2    799 TAATAGAAAATAAAAT-GAATGTTCCCAAATA--CTCAAATACATATGAA 845
                         i   i   --  i   -  iv  i vv     -- i  v i iv    --
  L1M4_orf2#LINE/    298 CAATGGAA--TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG-- 343

  chr20_2898604_2    846 GAGGTAAATAAATATCTGAATTCAATATATAAGATAGGTGGCATTTCAAA 895
                         ---  v   vi  v ii  ----------i   ---    v  vvv v v
  L1M4_orf2#LINE/    344 ---GTCAATTGATTTTCGA----------CAAG---GGTGCCAAGACCAT 377

  chr20_2898604_2    896 TCAATGAGGAAA-AATAAATTATT----AAGGGGTATTGGGACAAGTTAG 940
                               i     -    ivi v  ----  iv   ii        -i i 
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA-CTGG 426

  chr20_2898604_2    941 ATATT----TGGGGAAAAACA------GATCCATAGCTCACTCTGCAT-C 979
                            ?i----  vii  i  ii------  i  v  v     v iii  - 
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr20_2898604_2    980 AGAA-TAAATTCGAGACAGACTTAAGTGCGTGTACACACACACACACACA 1028
                          i  - v  i  i i ii  iiv?  ---------  vi v iii vivi
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAG---------ACCTAAATGTAAGAG 517

  chr20_2898604_2   1029 CACGAAACCATAGAAGTCC-AGAAGAAAAT-TA--------TTTTTATAA 1068
                          -ii    i   i  v  i-         i-  -------- i  ii i 
  L1M4_orf2#LINE/    518 C-TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr20_2898604_2   1069 TCTTGGAGTAAGGAAAGCCTTCCTAGATATGAC-CCAAT-TCCTAGAAAA 1116
                         i     iv  i v  v vi   i          -    v-v vi iiv  
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr20_2898604_2   1117 CCTAAACTGAGAAATATTTAAATTAAA-------AAAATTAAAAA----T 1155
                          --   vvi i     vv      ii -------           ---- 
  L1M4_orf2#LINE/    617 C--AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr20_2898604_2   1156 A-GCT---AATGATATCTTCTGCAATGCAGAAAATCTAGATGACCACCTA 1201
                         i-   ---  v  i ----  ---  vv     i vv i -   v   i 
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACA----CT---ATCAAGAAAGTGAAAA-GACAACCCA 706

  chr20_2898604_2   1202 ------GGGA-ACAACATTTGCAGTTTTACCATA-----GGCAAAGGACT 1239
                         ------    - v  i       i---- i    ----- ii  i     
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAA----ATCATATATCTGATAAGGGACT 752

  chr20_2898604_2   1240 CATTTCCCAAACGTACAAAGAACATCTACAAACGAGTCAGGAAAACCTTG 1289
                         ii v   vi  ii  i       vii     viv i v vi    vvivi
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr20_2898604_2   1290 ACACTCTAAT--AAAAATGGGTAAAGAATATCAACAGAGAATGCTC---A 1334
                          i vi i   --         i    i  v v  i   v v v   --- 
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr20_2898604_2   1335 GAAAA---ATAAATGATCTTTTAAATTACACAAAAT--TGCTCAATCTCA 1379
                            i --- i     ii vv --  vi   ii   v--       iv   
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAAT--AAGCACATGAAAAGATGCTCAACATCA 900

  chr20_2898604_2   1380 GCAAAATG 1387
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.51 (148 / 98)
Gap_init rate = 0.06 (51 / 906), avg. gap size = 3.16 (161 / 51)  


1958 29.18 4.38 1.46  chr20_2927171_2929537      720  1473 (894)    L1M4_orf2#LINE/L1       21   796 (112)  

  chr20_2927171_2    720 ATGGATTAGGAGGCTCAATTTTGTAAAGATGTCAATTCTCCCCCAA--GA 767
                                i i  i  i   v    v      v    v      v  --  
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr20_2927171_2    768 TATATAGATTCAATGCAATTCCAATAAAAATCCCAACAGGTTTTTTTGTG 817
                          v  i        i     i  v  v         i v vi       ii
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr20_2927171_2    818 GAACTTGACAAGCTGATTCTAAAATTTATATGGAGGAGAAAAGATTCAAG 867
                            v             i        i       iiv v  i ivi v  
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr20_2927171_2    868 AATAGCCAAGACATTCCTGAAGAAGAAGAACAAGGTGAGGAGACCTGC-C 916
                                  i   v  i    i           i  vi ii   iii - 
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr20_2927171_2    917 TTACCAGATATAAAGAG--ATTATAAAATTTTAGTAATTAAGACAGTTTT 964
                           v   -  v v  i v-- i  i   ii vi      i        v v
  L1M4_orf2#LINE/    221 TTCCCA-ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr20_2927171_2    965 GTATTGGCACTGGGATAGACAGATCGACCAGTGGAATGAAATAAAGAGCC 1014
                            i     ivi         v  v  i  i      ii   vi    i 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr20_2927171_2   1015 CAGAAGCAGATCCATTTGTAAGTGG-AAACCTATTTATGACAGAAATGCT 1063
                              ii i i    vii vvi   -v  iiv    vi    iiii   i
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr20_2927171_2   1064 CTTGCAGTTTGGGTGGGGAAAAGATGGTCTTCACAATAAATAGTGCCTGG 1113
                         vvvi vi  iii-        ii  i     iv   i    i    -   
  L1M4_orf2#LINE/    370 AAGACCATTCAA-TGGGGAAAGAATAGTCTTTTCAACAAATGGTGC-TGG 417

  chr20_2927171_2   1114 GACCATTGG-TAACCCTGTGGGAATAAATGAAATTGAATGCTTGTCACAT 1162
                            v i   -  ?  vii  vi  vi      i   i iv i ii v  i
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr20_2927171_2   1163 ATCAAACACAAAAACCAATTCCAGTTGCTGTAAACACTGAAATTTAAAGG 1212
                          i  v i       ii  i  v iv  vvvi ? v  iv    v   ii 
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr20_2927171_2   1213 ACAAAAATGATAAAAT-----GTAGAGATCATAATGTAGTAAAATATACT 1257
                         - v    iv      i----- v   i v    -- v?     --- -  
  L1M4_orf2#LINE/    518 -CTAAAACTATAAAACTCTTAGAAGAAAACATA--GGNGTAAA---T-CT 560

  chr20_2927171_2   1258 TC-TGATCTCACAGTAGGAAAGGATTTCTTAA----GACTTAAAATGT-- 1300
                           -   i  iiviv    v  v i       i----   viv   v i--
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr20_2927171_2   1301 ---TGATAAAAGGGAAGATTGATGAATT----TACATGAAAATGCAAAAC 1343
                         ---ii i     ii  i  v   i    ---- v   v     vv     
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr20_2927171_2   1344 CTCTGTTCAT-AAATGATACCATAAAGAAGATGAAAGGGAAGGCCACAAC 1392
                         i i   v v -   v  i  i  v     ii     i iv iv     iv
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr20_2927171_2   1393 CTTGGTAAAAGATA---ACA---CAGGTAACTGATAAAGGAAGAGTATCC 1436
                         v v  - i  i   ---i  ---  vi  v       i   vvv      
  L1M4_orf2#LINE/    711 ATGGG-AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCC 759

  chr20_2927171_2   1437 AGAATATATAAAGAACTTCTACAAATTGTTAAGAAAA 1473
                                          ii     v iiv   v    
  L1M4_orf2#LINE/    760 AGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

Transitions / transversions = 1.47 (129 / 88)
Gap_init rate = 0.03 (21 / 776), avg. gap size = 2.10 (44 / 21)  

 242 30.33 3.28 0.00  chr20_2927171_2929537     1754  1875 (492)    L1M4_orf2#LINE/L1      783   908 (0)  

  chr20_2927171_2   1754 ACTCCATTTTGAAAA---AAATAATCCAGTAGGACAACGGGGAAACCACT 1800
                             v  vv i    ---      i   i v?i v  i   v   vv i 
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_2927171_2   1801 TGACTAGGTACTTCACGGAAGAGGAAACTCTTTTGACCAGTATGC-TATG 1849
                            v   ii i   v vi    i  v iv vvv  i   i  v  -i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_2927171_2   1850 GAAAGATGATGAACCTCATTAATAAT 1875
                         i       v v   v   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.80 (16 / 20)
Gap_init rate = 0.02 (2 / 126), avg. gap size = 2.00 (4 / 2)  


3068 23.84 2.31 1.46  chr20_2989495_2992043      883  1704 (845)    L1M4_orf2#LINE/L1        1   829 (79)  

  chr20_2989495_2    883 TGGAAAGGCATCCCATGCTCATGGATTGGAAGA----GTATTGTTAA-AT 927
                                ii        i               ----i         -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_2989495_2    928 GACTGTACTACTCAAAGCAATCCACAGATTCAGTGCAATCCCTATCAAAA 977
                          i vi    v i    vii   i         ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_2989495_2    978 TACCAATGACATTCTTCACAGAAATAGAAAAAACAATCTGAAAATTTGTA 1027
                          v   iivi v  i  ii       v  v  ivii   iv      ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_2989495_2   1028 TGGAACCACAAAAGATACTTAATAGCCAAAGCAATAATGAGCAAAAAGAA 1077
                              vii   ii  iv vv          i    vv   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_2989495_2   1078 CAAAGCTTAGAGGTAC-CACACCACCTGACTTCAAAATTTACTACAAAGG 1126
                              -  i    -  -     iv  ii i       i           v
  L1M4_orf2#LINE/    201 CAAAG-TTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_2989495_2   1127 TGTAGTAATCAAAACAGCAGGCTATTGGTATAAAAATAGACACA--GACC 1174
                          ii         i    iiv v  i   i    ii       i --  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_2989495_2   1175 AATAGAACAGACTGGAGAATCCAGAAATAAATCCATGTGTTTACAGTCAA 1224
                            i   i   v v    i            i    iii    ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_2989495_2   1225 CTGATTTTTGACAAAGGCATCATGAACAAACACTGGGGAAAGAACATCCT 1274
                         i       i     i  iii  v  v  vv  v           i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_2989495_2   1275 CTTTAATAAATGATGCTGGGAAAACAGGATATCCATAGGTAGAAGAATAA 1324
                         i  i  i     i        v   v     ?   i v i i      i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_2989495_2   1325 AACTAGACCCCTATCTCTCACAATGTACAAAACTCAACTCAAAATGGCTT 1374
                          ii i        i   v   v  i       v i            v i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_2989495_2   1375 AAAGAC--AAACATAAGACCTGAAACTATAAATCTACTAGAAGAAAACAT 1422
                          ?    --   ii     v  i          v  vi             
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_2989495_2   1423 AGGGAAAACACTTCAGGACGTTGGTCCAGGTAAAGATTTTATGGCTAAGA 1472
                            ?iv  vv    iv   v    vii   i  v i   iv i v  v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_2989495_2   1473 CTTCAAAAGCACAGTCAACAACAACAACAACAACAAAATAGACAAATGGG 1522
                          vi          ------ i      -  v  -        i    v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACA------AGCAACAA-AAGAA-AAAATAGATAAATTGG 640

  chr20_2989495_2   1523 AATACAGTCAA--CTAAAAAGCTTCTGAACAGCAAAGGAAGCAATCAACA 1570
                          v v  -    --i      -   i  vi vv       vi v     v 
  L1M4_orf2#LINE/    641 ACTTCA-TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr20_2989495_2   1571 ----GAAA---CAACCTGTAGAACAGGAGGAAATCTTTACAAACCATTCA 1613
                         ----    ---     iii    ii    i    v   i    i   vi 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_2989495_2   1614 TCTGACAAGGGGCTAATATTCAGAATATACAAGGAATTCAAACAACTCAG 1663
                              i     i  vi   i         i  i   i  vv        i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_2989495_2   1664 CAGCAAAAACATAAACAATCCCAGTAAAAAGTGGGCAAAGG 1704
                         i ii     v i   i  i  v v ?    i          
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

Transitions / transversions = 1.82 (124 / 68)
Gap_init rate = 0.02 (15 / 829), avg. gap size = 2.07 (31 / 15)  


 391 28.76 8.50 0.00  chr20_3312838_3316019     1674  1826 (1356)    L1M4_orf2#LINE/L1        1   166 (742)  

  chr20_3312838_3   1674 TAGTAAGACATACCATGTTCATGGATTAGGAACCTCAACATAGTACTGAT 1723
                          i v    i  v               i i iv  i  i  v  vvv   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_3312838_3   1724 ATCAATTTTCCCTAATGTGGT----AAGTTTAACACA-TCCCTATGAAAA 1768
                         iv    vi    i  vv  i ---- ii  i   i  -       v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_3312838_3   1769 TCC-AG-TA--TTTTTTATAGATGTAGAAGAGATTATTCTAAAATTTACA 1814
                            -  - i--      ii   vi v  vi  v v  i        i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_3312838_3   1815 TAA----GCCAGGAAC 1826
                          ii----  v   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGAC 166

Transitions / transversions = 1.44 (26 / 18)
Gap_init rate = 0.04 (6 / 166), avg. gap size = 2.17 (13 / 6)  

2567 24.06 4.30 0.94  chr20_3312838_3316019     1947  2690 (492)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr20_3312838_3   1947 TAAAACTCATAAGGAAAAGCAAAGGAACTACAATAGCTTAAAACTGTTTT 1996
                              i     v     v    i   v i v      i-     vi i  
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC-AAAACAATCTT 188

  chr20_3312838_3   1997 GAAAAAGAA----AAAGTGGGAGGAATCACTCTACCCAATGTCAAGACTT 2042
                                  ----     v      v    v  v      v    i    
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr20_3312838_3   2043 ACTGCATAGCTAAAGTAATCAAGACTGAGTGGTACTGGC-TAAGGGACAG 2091
                            i  v     v            v v           -     - i  
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG-ATAG 287

  chr20_3312838_3   2092 ACACATAAGTCAATGGAACAGA-T--AGAGTAACCAGAAGCAGACCCACA 2138
                            i   ii         i   - --     --      ii i     i 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGT--CCAGAAATAAACCCATA 335

  chr20_3312838_3   2139 CAAGTACAACTAACTAATTTTTAACAAAGGCACAAAAGCAATTCAATGTT 2188
                           vv  iiiii  i i     ii    i  ii v  ii v        vv
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr20_3312838_3   2189 GGATGGATAGTCTTTTCAATAAGTAGGGCTAGAATAACTGGATATCTACG 2238
                          i v i             i  i i v   i i i         ? i  i
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr20_3312838_3   2239 GGCAAAA--ATG----TAAACCTCAACCTTACACATTATATACAAATTAA 2282
                         v      --   ---- ii   i v    i    vv    i v       
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr20_3312838_3   2283 ----------AGCATAGATCTAAATGGAAAATGTAAAATCATAAAATCTT 2322
                         ---------- v  ?   i       v  i vv     ii      iii 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr20_3312838_3   2323 TGGAAGAAAACAGAAGA--AAATATTCTGGACCTAGGATTTGGTGAAGAG 2370
                          i          v i ?--    v   vv     v  i  v  ii v iv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr20_3312838_3   2371 TTCTTACACTTGACACCAAAAAGTGTGATCCATAGGGAAAAAAAAT-GAT 2419
                               v iv           - iiii v v i ii- i       -   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAA-GCACAAGCAACAAA-AGAAAAAATAGAT 633

  chr20_3312838_3   2420 AATGTGGACTTCATTACAATTTTAG--TTTTGCTCTATGAAAGACTCTGT 2467
                           vv          i v    vv i--     iv  vii  i   v  i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr20_3312838_3   2468 TGAGAGAATGAAAAGACAAGCTACTGACTGGGAGAAAATATCTGCAAACC 2517
                         ii   i i           v i  v  v             i      i 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr20_3312838_3   2518 ACATATCTGAAAAAGAACC-ATATGTGGA-TACATAAAGAACTCTCAAAA 2565
                          i        v  i i  i-i   vii  -  i            i v  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr20_3312838_3   2566 CTCAATGGTAAAAAAAAAAA-AATCCAATTAGAAAATGGGCAAAAGGTAT 2614
                               ii      i v   -  i      ?i            i i v 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr20_3312838_3   2615 AAAGAAACAATTTGTCAAAGAGGATACAGAAATGGCAGAGAAGCCCTATG 2664
                         i  v i   v  ivi      i    i v       vi v    v -   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC-ATG 882

  chr20_3312838_3   2665 ACAACATGTTCGACATCATTATCCAT 2690
                          v  v   i  i      ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (107 / 68)
Gap_init rate = 0.02 (19 / 769), avg. gap size = 2.05 (39 / 19)  

1551 21.68 2.60 0.00  chr20_3312838_3316019     2837  3182 (0)    L1M4_orf2#LINE/L1        1   355 (553)  

  chr20_3312838_3   2837 TGAAAAGATACCCTCTGTTCATGCATTGGTAGAC--AATATCGTTAAGCT 2884
                           i       i  iv        v     v    --     i      v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_3312838_3   2885 GTCAATGTTACCCAAAGCAATCTACACATTCAGTGTAATCCCTTCTCAAA 2934
                          v    ii v      vii       v     ii i       viiv   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_3312838_3   2935 TCCCAATGATGTTTTTTACAGAAGTAGAAAAATCCATTCTAAAATTTATA 2984
                              iiviiv      i     i v  v  iiiv  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_3312838_3   2985 TGGAATCTCAAGAGACTCTGAATATCCAAAACAATCTTGATAAAGA---T 3031
                              viv    i   i v     v               v     ---v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_3312838_3   3032 TAAAGCTGTAGAACTCACACT-CCTGATTTTAAAACTTATTACAAAGCTA 3080
                         i    i  v  i         -  ii    i        i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_3312838_3   3081 CAGTCATCAA--CAGTGGGATACTGGCATAAG-ACAGATATACAGACCAA 3127
                             v     --     v i            - i   i   i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_3312838_3   3128 TGAAACAGAATAAAGAGACCAGAAACAAACCCTCACATACCTGGTCAAAT 3177
                           i  i     vi    v       i      vi    viv       v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_3312838_3   3178 GATTT 3182
                              
  L1M4_orf2#LINE/    351 GATTT 355

Transitions / transversions = 1.50 (45 / 30)
Gap_init rate = 0.01 (5 / 355), avg. gap size = 1.80 (9 / 5)  


3013 27.07 1.90 0.34  chr20_3450635_3456482     4463  5356 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_3450635_3   4463 TGGAAA-ACATTCCATGCTCATGGATAGGAAGAGTCAATATAGTGAAAAT 4511
                               - i  i     i        v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_3450635_3   4512 GGCCATATTGCTGAAAGTAATTTATAGATTCAATACTATCCCCATCAAGC 4561
                            v   i v iv   v i  i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_3450635_3   4562 TACCATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 4610
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_3450635_3   4611 ATGGAGCCAAAAAAGAGCCCATATAACCAAGACAGCCCCAAGCAAAAAGA 4660
                              iviiv  ii  v  viv   i    i   ii iii iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_3450635_3   4661 ACAAAGCTGGAGGCATCTTGCTACCTGACTTCAAACTATACTACAAGGCT 4710
                               i      vv  vii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_3450635_3   4711 ACAGTAACCAAAACAGCATGATACC------AAAACAGATATATAGACCA 4754
                                i   i    ii  i   i------ ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_3450635_3   4755 ATGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTGCAACCATC 4804
                               i    iv   ivii         vv   i    i iiiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_3450635_3   4805 TGATCTTTGAGAAACCTGACAAAAACAAACAATGGGGAAAGGATTCCCTA 4854
                             i  i  v  ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_3450635_3   4855 TTTAATAAATGGTGTCGGGAAAACTGGCTAGCCATATGCAGAAAACTGAA 4904
                           i  i        ii    v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_3450635_3   4905 ACTGGACCCCTTCCTTATACCTTATACAAAAATTAATTGAAGATGGATTA 4954
                         ii         v   i i   v              i v  i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_3450635_3   4955 AAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5004
                         ?    i    i      v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_3450635_3   5005 GGCA-ATACCATTCAGGAGATAGGTATGGGCAAAGACTTCATGACTAAAA 5053
                           ?i- v i -   iv  vv v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_3450635_3   5054 CACCAAAGGCAAAGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5103
                                i   v i          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_3450635_3   5104 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAG 5153
                            v v  i i   i  ii vv    i  v       vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_3450635_3   5154 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAG 5203
                         i     i                 v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_3450635_3   5204 GACTAATACCCAGAATCTACAAAGA-C-----CAAATTTACAAGAAAAAA 5247
                             vi  i       v  i     - -----   v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_3450635_3   5248 AGCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCT 5297
                          -    i     v  i?    i            v    i     i    
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_3450635_3   5298 CAAAAGAAGACATTTATGCAGCCAAAAA--ACATGAAAAAAAGTTAATCA 5345
                          v        i  vi viii     v  --         i v i v v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_3450635_3   5346 TCACTGGTCAT 5356
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.51 (143 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


 285 20.00 0.00 0.00  chr20_3515137_3517399.rev      555   604 (1659)    L1M4_orf2#LINE/L1        6    55 (853)  

  chr20_3515137_3    555 AGACATTCCAGGTTCATAGGCTAGAAGATTTAACCTTGTTAAGATGGCAA 604
                            i  i   v      i ii i     i    iv               
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

Transitions / transversions = 4.00 (8 / 2)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.00 (0 / 0)  

3820 16.78 3.78 2.36  chr20_3515137_3517399.rev      926  1771 (492)    L1M4_orf2#LINE/L1       51   908 (0)  

  chr20_3515137_3    926 GGCAATACACCCCAAATTGGTCAGTAGATTCAATGCAAACCTTATCAAA- 974
                                 v          i  vii        i    v  i       -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_3515137_3    975 --CCAGTTGGCTTTTTGTTGTTGCAGAAAATGGCAAGCTCATCCTAAAAT 1022
                         --    i  v      -----        v  i      v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-----TGCAGAAATTGACAAGCTGATCCTAAAAT 145

  chr20_3515137_3   1023 TAATATGAACATGCAAGAAACCCAGAATAGCTGTAACAGTCTTGCAAAAT 1072
                          v     i v       ii            iiv    i     v    v
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_3515137_3   1073 AAGAACAAAGGTGGAGGACTTAGCCTTCCCAATTTTAAAACTTA-TACAA 1121
                                   v         i vv           i        -     
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_3515137_3   1122 AGCCACAGTAATCAAAACAGTGTAATATTGGCAAAAGGAGAAACAT-TGG 1170
                            i           i       ii  i     v     v i    - i 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_3515137_3   1171 -TCAACTGCACAAAAATGAGAGCTTAGAAAAAAGTTCCTAGATTCACAGT 1219
                         -    iv v i i  v      iii     v  iii v  v   i ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_3515137_3   1220 CAACTGATCTGCAACAAATGTGCCATGAAAATTCAATGGTTAAAAAAAAA 1269
                            i    i v i    iv      v  vv         ------ii   
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG------GGAAA 389

  chr20_3515137_3   1270 AAAAAATCTTTTCAACAAATGGTGC-AGGACCAC-----ATCCACAGGCA 1313
                         i  v i                   -i    v  ----- ?     v   
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr20_3515137_3   1314 AGAAGA--GAGTTTGGACCCCTACCTCACACCATACACAAAAATTAACTC 1361
                          -    --  iv                       i              
  L1M4_orf2#LINE/    440 A-AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr20_3515137_3   1362 AAAATGGATCAAGGACCTAA-TGTAACACACAAATCTATGAAACTTTTCA 1410
                                    ?i       -     v vvi   v    i     i  vi
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr20_3515137_3   1411 AAGAAAACTTAGGAGCAAATCTATGTGATCCTGGGTTACTTGGGCACTGA 1460
                                 v    ? i      vi    i i       ----    v  i
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA----GGCAATGG 584

  chr20_3515137_3   1461 TTTTCTAGATACAATACCAAAAAGCACATGGGATAAAATAAAACATTGAT 1510
                            ii      ii i       -     v vi i    v    v  v   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAA-GCACAAGCAACAAAAGAAAAAATAGAT 633

  chr20_3515137_3   1511 ACATGGAACTTAATCAAAACTGAAAACTTTTG-ATTTCAAAAGGCA-TAT 1558
                          v  v i    v       i i          -ii      i i  -   
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr20_3515137_3   1559 TAAGAAAGTGAAAAGA-AACCCATATAATGGGAGAAAGTATTTGCAAATA 1607
                         i               -      i v           i           v
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr20_3515137_3   1608 ATATATCCAATAAGGGACTT-----CAGAATTCATAAAGAACTCTTACAA 1652
                                ii           -----      vi                 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr20_3515137_3   1653 CTCAATAATAAAAAAGACAACATAAC-----TGAAAAATGGGCAAAGAAT 1697
                                       -     -     ----- ?              i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAA-GACAA-ATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr20_3515137_3   1698 TTGACTAAATATTTCTCCAAAGAAGATATACAAAAGGCTAACTA----AT 1743
                             v  i i                        v   i  iv ----  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr20_3515137_3   1744 GAAGTTGATGTTCAATTTCATTAGTTAT 1771
                            iv-    i    iv   ????????
  L1M4_orf2#LINE/    882 GAAAA-GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (83 / 55)
Gap_init rate = 0.03 (22 / 858), avg. gap size = 2.36 (52 / 22)  


 387 18.06 1.39 0.00  chr20_3757768_3760758.rev      501   572 (2419)    L1M4_orf2#LINE/L1      195   267 (641)  

  chr20_3757768_3    501 GAAGAAAAAAGTTAAA-GATTGACACTGCCTGACTTCAAGACTTACTATA 549
                               v      ii -  i v     v  ii i     i        i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_3757768_3    550 AAGTTACAGTAATCAAGATAGTG 572
                            i              i    
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTG 267

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1)  

1321 24.51 1.41 2.54  chr20_3757768_3760758.rev     1205  1559 (1432)    L1M4_orf2#LINE/L1      259   609 (299)  

  chr20_3757768_3   1205 AAAATAGTGTAGTATTGGCAAAAGAATAGACAAACAGATTAATGGAACAG 1254
                           i i     i   i     v   i       v i    i       i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr20_3757768_3   1255 AATAAAGAACCCAGGAG-AGACCCA--CATTAATACAGTCAACTGGTCTC 1301
                            vi   ii    i i- i     --    --  ii     i  i i i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATT--TATGGTCAATTGATTTT 356

  chr20_3757768_3   1302 TGACAAAGGAGTAAAAGCAATACAATGGAACAAAGATAGAAAGACTCTTT 1351
                         i     i  v iv  ii v  v      iiv  ii    ------     
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG------TCTTT 400

  chr20_3757768_3   1352 TCAAGAGATTATGTTGGAACAACTGAACATCCACATGCAAAAACATGAAT 1401
                             v i  vi  i   i       i i ?            iv     v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_3757768_3   1402 CTACACATAGACCTTACACCCTTCACAAAAATGAACTCAAAATGGATCAT 1451
                         i iv  vivv    i     v vi        v                ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_3757768_3   1452 AGACCTAAATGTAAAATGC-AAAACTGTAAAACTTCTAGTAGATAACATA 1500
                                       i -  -      i       ii   v   v      
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_3757768_3   1501 GGAGAAAATCTAGATGATATTGGATT-GGTGATGACTTTTTAAATACAAC 1549
                           ? v      vvi   iv    i  -  ii   ii  i   i   ii  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_3757768_3   1550 AGTAAAGGCA 1559
                          vi   i   
  L1M4_orf2#LINE/    600 ACCAAAAGCA 609

Transitions / transversions = 2.23 (58 / 26)
Gap_init rate = 0.02 (7 / 351), avg. gap size = 2.00 (14 / 7)  

1115 18.40 3.12 4.51  chr20_3757768_3760758.rev     2212  2499 (492)    L1M4_orf2#LINE/L1      625   908 (0)  

  chr20_3757768_3   2212 AAATTATATGAAACTGGACTTCATTAAATTTAAAAAGCTCTGCTTTGTGA 2261
                            v  v  -   i          i   v       vi i  ivi vii 
  L1M4_orf2#LINE/    625 AAAATAGAT-AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr20_3757768_3   2262 AAGACACTGTCAAGAGAATGAGAAGACAAGCCACAGACTGGGAGAAAATA 2311
                          i      i      i i   i       v       v            
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr20_3757768_3   2312 TTTGCAAAAGGTATATCTGATAAAGAGCTGTTATCCAAAATACACAAAGA 2361
                                 vvi            i ii  vv      i    i i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr20_3757768_3   2362 ACTCTTAAAACTCAACAA---AAAGA--AATCACCCAAACAAGTTGCCTG 2406
                                v       i  ---     --   v      ------------
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA------------ 811

  chr20_3757768_3   2407 TTTTAAAATGGGCAAAAGACTTGAACAGACACCTCACTAAAGA---TTTA 2453
                           ?v            i  i     i     ii  v i     --- v  
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr20_3757768_3   2454 CAGATGGCAAGTAAGCATA-GGAAAGATACTCTACGTCATGTTATTA 2499
                           i     v i      i - i      i   v  i   ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (33 / 19)
Gap_init rate = 0.02 (6 / 284), avg. gap size = 3.67 (22 / 6)  


2588 15.87 5.75 1.59  chr20_3843058_3845416.rev      672  1175 (1184)    L1M4_orf2#LINE/L1        1   525 (383)  

  chr20_3843058_3    672 TGGGAAGACATTCCATCTTTTTGGATCAGAAGACTTTGTATT---AGGAT 718
                            i    i  i    v  iv     ii        vi    --- i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_3843058_3    719 GGC---------CAAA---------AGATTCAATGTAATCTCTATTAAAA 750
                            ---------    ---------        i i    i    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_3843058_3    751 TCCCAGTTGTCTTATTTACAGACCTTGCCAAGTTAACCCTACAATTCATA 800
                               i  i   v   i    vv   v    i i i    v        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_3843058_3    801 TT----CTCAAGGTACCCAGAATAGCCAAAATAATCTCGAAAAA--AGAA 844
                          v----iv     v                 i     i      --    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_3843058_3    845 CAA-GTTGGATGACTCACACTTTCTTACTTCAGAACTTAATACAACGCTA 893
                            -      v           i iv i    i      v     v    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_3843058_3    894 CAGTA-TCAAGGCAGTATGGTACTGGTATAAAAACAGACATATATATCAA 942
                              -     i    i         i    ii i         v     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_3843058_3    943 TGGAACATAACTTAAGAGTCCAGGAGTAAACCCAAACATCTATGGTCAAC 992
                              i v  -  i         i i        v    i         i
  L1M4_orf2#LINE/    301 TGGAATAGAA-TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_3843058_3    993 TAATTTTTGACAAAGGGGCCAAGAGAATTTAACAGGGAAAGAATCATCTT 1042
                          i     i     i  v       vv   i  ii          vi    
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_3843058_3   1043 TTCAACAAATGGTACTAGGACAACTGGATATCCACACGCAAAAAGAAATG 1092
                                      i  i             ?     i      i--    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG--AATG 447

  chr20_3843058_3   1093 AACTTGGAGCTCTACCTCACACCATACACAAAAACTTACTCAAAATGGAT 1142
                           v     v i               i       i v             
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_3843058_3   1143 CAAATATAAGAGCTAAATATAAGAGCTAAAACT 1175
                           ? -----  v      i              
  L1M4_orf2#LINE/    498 CAWA-----GACCTAAATGTAAGAGCTAAAACT 525

Transitions / transversions = 2.00 (52 / 26)
Gap_init rate = 0.02 (10 / 525), avg. gap size = 3.70 (37 / 10)  

1582 17.07 8.94 3.79  chr20_3843058_3845416.rev     1491  1859 (500)    L1M4_orf2#LINE/L1      506   893 (15)  

  chr20_3843058_3   1491 TATATATATGAGCTAAAACTATAAAACTCTTAAAAGAAAATA----AACA 1536
                           v  i  v                       i       i ----?ii 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr20_3843058_3   1537 ATTCTTCATGATCTTAAATTAGGCAATTCTTCATGATCTTAGATTTCTTA 1586
                          v     i   i   iii         -------------- i       
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAAT--------------GGTTTCTTA 591

  chr20_3843058_3   1587 CACATAACACCAAAAGCACAAGTGACAGAAGA-----TAGATAAGATTAA 1631
                         v i  i                ii   i    -----       iv vi 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_3843058_3   1632 CTTCATCAAAATTTAAAATTTCCATGCTGCAAAGGACACCATCAAGGAAG 1681
                                      v    i  iii    v          i      i   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_3843058_3   1682 TGAAAAGACAACTAACAAAATGGGACAAAACATTTGCGAATTATGTATCT 1731
                                     iv   i       v    i      i   i  i     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_3843058_3   1732 AATAAGGGACTTGTATCCAGAA--------------------CTCAATAA 1761
                         i                     --------------------        
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_3843058_3   1762 TAAAAAGACAA----TCCAACTAAAAACTTAGCAATAGACTTCAGCAGAC 1807
                                    ----i    i ?    v vi    vi  i  v ii    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_3843058_3   1808 ATTTATCCAAAGACTACAGACAGATGGCCAGTAAACACATGAAAAGATGT 1857
                             v        vv i v   i       i   i              i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_3843058_3   1858 TC 1859
                           
  L1M4_orf2#LINE/    892 TC 893

Transitions / transversions = 2.39 (43 / 18)
Gap_init rate = 0.01 (5 / 388), avg. gap size = 9.40 (47 / 5)  


1094 28.11 4.14 0.30  chr20_3958270_3961008.rev     1049  1386 (1353)    L1M4_orf2#LINE/L1        6   356 (552)  

  chr20_3958270_3   1049 AAACATACCTTGTTTACATTTTGGAAGAGTCAACATAATAAAGATATAAG 1098
                          i i  v  v    i iivv        v i  i  vi v     ivv i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr20_3958270_3   1099 TTTTCCCAAGATTTATCTCCAAGTTTAATACAATTCCTATCAAAACCCCC 1148
                          vi    v i   v    v  ii  i  ii    i          i   -
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC- 104

  chr20_3958270_3   1149 AGAAAGGGTTTTTATAGACACAGGCTAATTTATTCTAAAATTTATATTAA 1198
                           vvivvv     ii   v iv i v ii v  i        i    vi 
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr20_3958270_3   1199 AAGGCATGGACCCTAGAATAGATATAGCAATTACGTAAAATAAGAATAAA 1248
                           v   v  iv  i       vi v i    ivi v    v     i   
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr20_3958270_3   1249 GTAAGAGGA-------------ATTTCAAGAGTTATTATATAGCTACAGT 1285
                           vi     -------------       i v   i  i v         
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr20_3958270_3   1286 AATCAAGACTGTGCAATATTGGCAAAGGGATAGACACACAGATCAATGGA 1335
                                  v   iii  i     v i         i i           
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr20_3958270_3   1336 ACGGAATAGAGAATCCAGAAATAGATCCACACAAATA-AGCCAACTGATT 1384
                          ii    v    i          i i   i   vv  -i i   i     
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr20_3958270_3   1385 TT 1386
                           
  L1M4_orf2#LINE/    355 TT 356

Transitions / transversions = 1.44 (56 / 39)
Gap_init rate = 0.01 (3 / 351), avg. gap size = 5.00 (15 / 3)  

1842 24.42 3.57 2.85  chr20_3958270_3961008.rev     1687  2247 (492)    L1M4_orf2#LINE/L1      344   908 (0)  

  chr20_3958270_3   1687 GCCAACGGATTTTTGACAAAGGTGCAAAAGCAATCCAGTGAAGGAAGGAT 1736
                          i   iv      i     i     v  ii v  i  i  ii i   i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_3958270_3   1737 AGCCTTTTCAACAAATTGTACTGTAACAATTGGACATCCAAGGGCAAAAC 1786
                           i             v  i   vi    i    i ?   viv      v
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_3958270_3   1787 AAAACAGT-GAACTCCAACCAAAACGTGACAACTTATACAAAAATTAACT 1835
                           viv   - i  i  v   ------ v   v v                
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACC------TCACACCATATACAAAAATTAACT 487

  chr20_3958270_3   1836 CAAAATGAAACATGAACTTAAATATAAATGC----------AAACATTTT 1875
                                i v  ?ii  i     i   iv  ----------    - i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTT 536

  chr20_3958270_3   1876 AGGAAACAACTTAGGGGAAAATCTTCAGGATCTAGGGCTAAGCAAAGAGT 1925
                           i i v   v    ? v        iv  i  v   i  i    v iv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_3958270_3   1926 TCTTAGGAT-TAACAGCAAAAGTGCAATCCACAAAAGGAAAATTGGATAA 1974
                               -  - i   v      ii   v v       i    v i     
  L1M4_orf2#LINE/    587 TCTTAG-ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr20_3958270_3   1975 TTTAAACTTCATCAAAA-------CTTTTACTCTGTGAAAGACCCT-TTA 2016
                         v  ii            -------     iiv  vii  i   v  - i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr20_3958270_3   2017 AGCTGATGAAAAGACAAGCCACAGACTGAAAGAAAATATTTGCAAACCAC 2066
                           vvii           v       v  ii                i  i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr20_3958270_3   2067 ATGTTTAACAAAGAACTATTATCTAGAATACATACAGAGCTCTCAAAACT 2116
                           i i i i  i i   vv    i      i   v   i    i v    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr20_3958270_3   2117 CAAGGGGAAAAAAAATCCCACAAATAATCCACTTAGAAAATAGGCAAAAG 2166
                            viiv     i ------       i   v  ?i     i      i 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGA------CAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr20_3958270_3   2167 ATATGACCAGCCATTTCACTAAATAGAATATACAGATGGCAAATAGAGAT 2216
                           v   vi  v      v i   v ii       i     v    iiv i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr20_3958270_3   2217 AAGAAAAAAAAAGTTCACCATCAGTAATTAC 2247
                          v     i v-- i   v     ????????
  L1M4_orf2#LINE/    880 ATGAAAAGAT--GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (81 / 52)
Gap_init rate = 0.02 (10 / 565), avg. gap size = 3.60 (36 / 10)  


3167 27.86 0.22 0.22  chr20_4212622_4219028.rev     5008  5915 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_4212622_4   5008 TGGAAGAACATTCCATGCTCCTAGGTAGGAAGAATCAATATCATGAAAAT 5057
                              ii i  i     i  v i i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_4212622_4   5058 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5107
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_4212622_4   5108 TACCAATGACTTTCTTCATAGAATTGGAAAAAAGTATTTTAAAGTTCATA 5157
                          v   iivi i  i  iii    v v  v  ivvv  ii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_4212622_4   5158 TGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 5207
                              viiv  ii  v  v v  v     iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_4212622_4   5208 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 5257
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_4212622_4   5258 CAGTGACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5307
                             i i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_4212622_4   5308 TGGAACAGAAC--AGAGCCCTCACAAATAACACCACATATCTACAACTAT 5355
                              i    i--    i  -- v      vv   i i  i  iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr20_4212622_4   5356 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 5405
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_4212622_4   5406 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTGA 5455
                         v  i  i              v      v  ?   i   v i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_4212622_4   5456 AACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGGATT 5505
                          ii    i    v   i     v  i           i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_4212622_4   5506 AAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5555
                          ?    i    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_4212622_4   5556 AGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAA 5605
                            ?i v viv   iv   v v  vv i     v ii   v ivv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_4212622_4   5606 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATATAATT 5655
                                    vvi          vv     v  i    v   iv v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_4212622_4   5656 AAACTAAAGCACTTCCGCACAGCAAAAGAAACTACTATCAGAGTGAACAG 5705
                            v v  iv    ii ii vv    i  v    ii vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_4212622_4   5706 ACACCCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAG 5755
                            v  i   i             v  i    vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_4212622_4   5756 GGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAA 5805
                          i  vi          v  i         vv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_4212622_4   5806 ACAAACAACCCCATCAAAAAGTGGGCAAAGGACATAAACAGACACTTCTC 5855
                              i     v  i?    i           iv i  i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_4212622_4   5856 AAAAGAAGACACTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCAT 5905
                         v        i ivi viii     v  i          i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_4212622_4   5906 CACTGGCCAT 5915
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.37 (144 / 105)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 2.00 (4 / 2)  


 700 27.37 1.05 1.05  chr20_4316641_4320199        1   190 (3369)  C L1M4_orf2#LINE/L1   (718)   190     1  

C chr20_4316641_4    190 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 141
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr20_4316641_4    140 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 91
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr20_4316641_4     90 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 43
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chr20_4316641_4     42 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAA 1
                                viiv  ii  v  v v  v     iv     i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

Transitions / transversions = 1.89 (34 / 18)
Gap_init rate = 0.02 (3 / 190), avg. gap size = 1.33 (4 / 3)  

2647 25.62 4.16 2.13  chr20_4316641_4320199     2184  3073 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_4316641_4   2184 TAGAGAGATATTTTGTGGTCTTGGATTAGAAGAATCAACATAGTAAAGAT 2233
                          i  i      iiii  v  v      i     v i  i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_4316641_4   2234 GTAAATTCTTCTCAAATTGATAAACAAGTTTTAAGCAATTTCTATCAAAA 2283
                          vv   v  i i         vv   ii  iv v     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_4316641_4   2284 TCCTAG-TAATTTTTTTGTATATATAGATAAGCTTATTCTAAAACTTATA 2332
                            i  - ivi       i v v  v  i     v  i      i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_4316641_4   2333 TAGAAAAGCAAAAGAAG-AAAATACCTAAT----TCTTAAATAGGAAGTA 2377
                          i    v    ii  vv- i    v i  v----    i  v i    v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_4316641_4   2378 ---AGTCAGGAGGAATCACTTTACTTGATTTCAAGACTTATTATAGCATA 2424
                         ---   i-      v    vi v iii       i     i  i i----
  L1M4_orf2#LINE/    201 CAAAGTT-GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA---- 245

  chr20_4316641_4   2425 TAGCTACAGCAATCAAAACTGTTTGGAATTGGCAGA--GATAGGCACAAA 2472
                         -        i      i  v  v   v i     v --     i  i v 
  L1M4_orf2#LINE/    246 -AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_4316641_4   2473 AGTCAATAAGATTTTATACAGAACCCAGAAATAACCCCACATAAGTATGT 2522
                         ii     iii  vvv  vv   ii          v    i i vv    v
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_4316641_4   2523 CCAACTGATTTTTGACAAAGAAGCAAAAACAATTCAAGGGAGGAAAGACC 2572
                         i   i       i     i iv  v  i  v      v  -       vi
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAAT 393

  chr20_4316641_4   2573 A-TTTTTTCAACAAATGATGCTGGAGCAACTCTATATCCATAGGTATAAA 2621
                          - i             i      ii     vv   ?   i v i v  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_4316641_4   2622 AATGAGCCTTGACCTAAACCTCAAACTGTATA--AAAATGAACTCAAA-T 2668
                              ivi v    ivv      v  ii    --     v        - 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_4316641_4   2669 GGATCATAGATTTAAGTGTAA-AGCATACATTTATAAA-CTTTTAGAATA 2716
                               ?   ii   i     -   -  v vi      -  i      v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGA 542

  chr20_4316641_4   2717 AAA-----------ATCTTCAGGACCTAGAGCTTGGCGAAGAGTTCTTAG 2755
                            -----------      iv     v i i v   i v iv       
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr20_4316641_4   2756 ACATTGCACCAAAAGCATAATCCATAAAAGAAAAAAATCTATAAAGTGGA 2805
                          i  vi           i  v v i           - vv     v    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGA 641

  chr20_4316641_4   2806 CTTAATTAAAATTAAAATTAAAATCTTCTGCTCTGCAAAAGATTGCGTT- 2854
                            v  i          ----- -   i  iv  v    i  --- ii -
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAA-----A-CTTTTGTGCTTCAAAGGA---CACTA 682

  chr20_4316641_4   2855 TGGAGAATGT---AATACAAATTATAGAC--AGAGAAAATATTTATGAAC 2899
                          vi    v  ---  v    vii i   v--i            iii  i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr20_4316641_4   2900 CACGTAGCTGACAAAAAACTCTTATCTAGAATACATAAAGAACTTTCAAA 2949
                           ii  v    i  iii   iv    i      i          i i v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr20_4316641_4   2950 ACTCAACAGTACAAAAACCAAAAAATCCTATTAGAAAATGTATAAGAGAC 2999
                               i i  v   i  -   v  i  v   ?i      vii  ii  i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr20_4316641_4   3000 ATGAACACACATTTCACCAAAGGTGACAT-TGCATGTC--ATAAGCACAC 3046
                         v    i v       v      iv  i  -iiv   v --         i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr20_4316641_4   3047 AAGAAGATGTTCAATGTCACTAACCAT 3073
                         i i      i    ii   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (134 / 91)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.24 (56 / 25)  


3659 22.32 1.14 2.51  chr20_4324862_4327537     1299  2176 (500)    L1M4_orf2#LINE/L1        1   866 (42)  

  chr20_4324862_4   1299 TGAAAAGATATACCATGTTCATGTATTGAAATAATTAATATTGTTAAAAT 1348
                           i        v           v    i  v v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_4324862_4   1349 GTTGATACTATCCAAAGTGATCTACAGATTCAATGCAATTCCTATCAAAA 1398
                          vii     vi     v                i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_4324862_4   1399 TTCCAA-TGTCATTTTTCACAGAAATAGAAAAAAAAATCCTAAAATT-GT 1446
                          i   i-  i -     ii       v  v  ivvi           -i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_4324862_4   1447 ATAGAACCACAAGAGACTCTAAATAACCAAGA-AATCATGAGCAA-AAGA 1494
                           i   vii    i   i vi    i    i -    v   iv  -    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_4324862_4   1495 ACACAGCTGGAGGCATCATACTCCCTGATTTCAAAATGCATTATAAAGCT 1544
                            v  i      vv   i   i  ii         ivi i  i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_4324862_4   1545 ATTGTAATCAAAACAGCATGGTATCGGCATTAAAACAGACACATTGACTG 1594
                          iv        i    ii     ii     v ii i     i  v  iii
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_4324862_4   1595 ATGGAACAGTTTAGGAAGCCAAGAAATAAACCCAAGTATTTGCAGTCAAT 1644
                               i  vv v ii  i v             vii    iii      
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_4324862_4   1645 TGATCTTTAACAAAGTTGCCAAGAAGATGCAATGGGGAAAGAACAGTCTC 1694
                             i  ii    i v        vv  v              i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_4324862_4   1695 TTCAATAAACGGTGTTGGGAAAACTGGATAGCCACATGCGGAAGAATGAA 1744
                              i   i    i     v         ?        ii         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_4324862_4   1745 ATTGGACTCTTATCTCACACCATATACAAAAATAAACTCAAAACAGATAA 1794
                         i      i i  i                    v         ii   v 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_4324862_4   1795 AATAGTTAAATGTAAGAACTGAAGTTTTAAAATATCTAGAAGAAAACATA 1844
                         ? v vi           i  i  ii v     ivii              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_4324862_4   1845 GGGGAAAATCTCTACAACATTGGTCTGGGCAATAATTTTTTGGATAGAAC 1894
                           ? v      iiiii  v    vi i      ii   i  i    vi  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_4324862_4   1895 TCCATAAACACAGACAACAGAAGCAAAAATAGACAAATGGGATAACATCA 1944
                         v   v  i    ii     i   v         i    v   ivv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_4324862_4   1945 AACTAAAAAGCTTCTGCACTGCAAAGGAAAC------AACAGTGAGGAGA 1988
                           v v    i   i  ii  v       v  ------i v     ii   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_4324862_4   1989 CAACTTATGGATTGGTAGAACATATTTGCAAACCATACATCTGATAAAGG 2038
                             ii ii  v   v    v           i    i         i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_4324862_4   2039 GCTAATATCCAAAATCTATAAGGAACTCAAACAACTCAACAGCAAAACAA 2088
                         i  vi      i   v     i      vv         i ii    - i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA-AG 798

  chr20_4324862_4   2089 ACAAACAACAACAACAACAACAACAAAACCTGATTAAAAAGTGGGCAAAC 2138
                              i   -------------------- ii   ?    i        v
  L1M4_orf2#LINE/    799 ACAAATAAC--------------------CCAATTWAAAAATGGGCAAAG 828

  chr20_4324862_4   2139 GACATGAACAGACATTTCTCAAAATAAGACATACAAAT 2176
                           iv    i           v   v    i        
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

Transitions / transversions = 2.00 (128 / 64)
Gap_init rate = 0.01 (8 / 866), avg. gap size = 4.00 (32 / 8)  


 500 27.16 13.28 6.58  chr20_4388210_4389929.rev      413  1233 (487)    L1M4_orf2#LINE/L1       33   908 (0)  

  chr20_4388210_4    413 ATTTAATTTTATTAATTT---AATTATTTTAGAATTAATTTA-ATATTTA 458
                          i     v  i    vv ---   vv iiivi    i  i  - v   i 
  L1M4_orf2#LINE/     33 ACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCA 82

  chr20_4388210_4    459 ATTAATATGATTCTTTTAAAAATACTAACAGCTTACCGGGTATTTTTTCC 508
                          i----iii  i i v v     v ---     -i  -----      v 
  L1M4_orf2#LINE/     83 AC----GCAATCCCTATCAAAATCC---CAGCT-GCC-----TTTTTTGC 119

  chr20_4388210_4    509 CTAGAACTAGACAAACTAGTTCTAAAGTTGATTTGGAAAAATAAG----C 554
                         --    v v     i  ii i     i  v  v      vii   ---- 
  L1M4_orf2#LINE/    120 --AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 167

  chr20_4388210_4    555 AAAAGGAGCCAAGAAGATTCTGAAAAGGTCTGGCTCTACCAGGAATTAAA 604
                         v i iv      i vi  ii      i ------------ i   i--  
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAG------------AAGAAC--AA 203

  chr20_4388210_4    605 AGTATGG-----TCAAACTTC--AATT----------------AACTACA 631
                            -   -----   v     --    ---------------- i     
  L1M4_orf2#LINE/    204 AGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_4388210_4    632 ATGAT---------GTGCTACTGGTTCATGGATAGAAAGATGGATACATG 672
                         i i  ---------   v      ivi v       v v  i   vv   
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr20_4388210_4    673 GAATAGAAATATAAGCCTTGAAATGAATCCAGATACACATGGGAATTTAG 722
                                 v ivi  i iv     i  i   v i ivi    vv v  ii
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_4388210_4    723 TATATGATAAAGGTGGCA---TC-TCAAATATATAAAGATTTTTTTTTCC 768
                          v vi  i  i    v  ---i - iv   iviv     v vv i   i 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr20_4388210_4    769 AA-AAGTG-TATTGGAACAATTGAGGAACCATGTGATGAAAGA-TAAAGC 815
                           -  i  - ii   i    i  iiv ?   ii  -ii     - i   i
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATG-CAAAAGAATGAAGT 451

  chr20_4388210_4    816 TGGATCCATATCTC-TAC--TACACG----TT---CCAAAATA----ATA 851
                             i  v  i   -i  --  i  i----  ---i      i---- ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_4388210_4    852 ----TAAATGTAAAAAATAAAA---TAAAATAATTAAGAAGAAAAGATAG 894
                         ----         i iv     ---     ivv   -        v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA-GAAGAAAACATAG 550

  chr20_4388210_4    895 GT-TA--TTTT----ACATTAGAGTAGGAAA-GATTGTCTAAAAATAATG 936
                          ?-  -- i  ----  v  i iv    v  - i  vii  i v  i ii
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_4388210_4    937 C-AAAAGTTCACAGTTATAAAATAAAGCTTTGATAAATTGTGTTAAATTA 985
                          -     iv  -  iv i    v   ivv v         vii vv  i 
  L1M4_orf2#LINE/    601 CCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_4388210_4    986 ATAATACAAA-------GCTGTCACATGACCAAAATACCACATAAAAAGT 1028
                          v v  v   -------   -   v v   --- v  i  --- i     
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCT-TCAAAGGAC---ACTATCA---AGAAAGT 692

  chr20_4388210_4   1029 CAAAAGACAA--------ATG--AAAAAATGCTCCCCAAATTGCAACTCA 1068
                         v         --------   -- i     -------- v      v   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAAT--------ATTTGCAAATCA 734

  chr20_4388210_4   1069 TA-----GAGAAATGCCTAATCTT---AATATAGAAAAAGCTACTGGAAA 1110
                           -----  v  iv v  vi v i---      v   i i  vi iv  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr20_4388210_4   1111 TTAAGAAAGAATAATGCAA-CAAGCCAAT--AAAAATTTGATTTCAAAAA 1157
                          i  v  vi  -  vi   -i  v     --      vv ----    ii
  L1M4_orf2#LINE/    785 TCAATAATAAA-AAGACAAATAACCCAATTWAAAAATGGG----CAAAGG 829

  chr20_4388210_4   1158 AT--GAA--GACAATTTACAGATTAAGAAATAAAAGGTGGCCTATTAAAA 1203
                           --   --    v  iv vi vv    v   v  i-     v  v iv 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAA-TGGCCAATAAGCA 878

  chr20_4388210_4   1204 TATGAAAAGATGCTCAATGTCTACAAAAAA 1233
                         i                ii  v????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (121 / 99)
Gap_init rate = 0.06 (51 / 876), avg. gap size = 3.20 (163 / 51)  


3259 27.77 0.00 0.33  chr20_4424702_4431106.rev     5003  5913 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_4424702_4   5003 TGTAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATTGTGAAAAT 5052
                           v  ii i  i     i     i  v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_4424702_4   5053 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5102
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_4424702_4   5103 TACCAATGACTTTCTTCATAGAATTGGAAAAAATTACTTCAAAGTTCATT 5152
                          v   iivi i  i  iii    v v  v  iv v iiii   i     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_4424702_4   5153 TGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCCCAAAGAA 5202
                              viiv  ii  v  v v  v     i      i i ivvvi     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_4424702_4   5203 CAAAGCTGGAGGCATCACGCTACCTGACTTCGAACTATACTACAAGGCTA 5252
                              i      vv    i  v  ii i   i  viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_4424702_4   5253 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGACCAA 5302
                               i   i    ii         i iv ii i   v v     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_4424702_4   5303 TGGAACAGAATAGAGGCCTCAGAAACAACACCACACATCTACAACCCCAT 5352
                              i     v   ivii      i  vv   i    i  iiii -- v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC--AA 348

  chr20_4424702_4   5353 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 5402
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_4424702_4   5403 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5452
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_4424702_4   5453 AACTGGATCCCTTCCTTACACCTTATACGAAAATTAATTCAAGATAGATA 5502
                          ii    i    v   i     v     i        i    i  i   v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_4424702_4   5503 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 5552
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_4424702_4   5553 AGGCACTACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 5602
                            ?iiv viv   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_4424702_4   5603 CACCAAAAGCAATGGCAATGAAAGTCAAAATTGACAAATGGGATCTAATT 5652
                                    vvi    ii    vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_4424702_4   5653 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 5702
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_4424702_4   5703 GCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAG 5752
                         i     i                 v       vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_4424702_4   5753 GGCTAATATCCAGAATCTACAAAGAACTTCAACAAATTTACAAGAAAAAA 5802
                          i  vi          v  i        iiv    v iv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_4424702_4   5803 ATCAAACAACCCCATTGAAAAGTGGGCAAAGGATATGAACAGACACTTTT 5852
                          -    i     v   ?    i            v    i     i  i 
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_4424702_4   5853 CAAAAGAAGACATTTATGCAACCAACAGACACATGAAAAAATGCTCATCA 5902
                          v        i  vi viiii    i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_4424702_4   5903 TCACTGGTCAT 5913
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (148 / 101)
Gap_init rate = 0.00 (2 / 908), avg. gap size = 1.50 (3 / 2)  


2673 23.85 10.77 1.09  chr20_4456405_4459536     1825  2650 (482)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_4456405_4   1825 GGAAGATAGCCCATATTCATGAACTGGAAGAATTAATAGTGTTAAAATGT 1874
                          i      v     i      i i       v      v      i   -
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG- 51

  chr20_4456405_4   1875 GCA-TACTTACCCAAAGCATTCTGAAGATTTATTGCAATCTCTATCAAAA 1923
                            -    i-      viiv   iv     i vi      i         
  L1M4_orf2#LINE/     52 GCAATACTC-CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_4456405_4   1924 TTTCAA-TGCTATTTTTTATTAAAATAGAAAAAACAATTCTAAAATTTGT 1972
                          ii  i-   i-      iivi    v  v  ivii  i        ii 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_4456405_4   1973 ATGGGACCACAAAAAAAACTTGAAAAGCCAAAGCAATCTTGAGCAAGAA- 2021
                             i vii   iii v- iv   v       i         iv     -
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_4456405_4   2022 --CAAAGCTGGAGGCATCAGAC-----------AAAATGTCCTATAAAGT 2058
                         --     i      vv   v  -----------    iv v   i    i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_4456405_4   2059 TATGGTAGCCAAAACAGCATAGTATTGTAATAAAAGCATACATACAGATC 2108
                           ii   ii   i    ii i   i  vv    iiii v     i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_4456405_4   2109 AATGGAACAGAATAGAGAGCCCAGAAATAAATCCATGAATTTACAGTCAA 2158
                                i     v     i           i    iv     ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_4456405_4   2159 TTAATCTTTGACAAAAGTGCCGGGAATATACAGTGGGGAAAAGAAAGTCT 2208
                           i  i  i     ii     ii  vi  v  i        ii v     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_4456405_4   2209 CTTTAACAAATGGTGTTGGAAAAACTGGATATC-ATAATCAGAAATACTA 2257
                         i  i           i   i v         ? - i vv  i  iv iv 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_4456405_4   2258 ATTTGCACCC-TATCTTATACCATATACAAAAAATCACTCAAAAT----- 2301
                          v   v    -  i  i i              v v         -----
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_4456405_4   2302 --------AAGTTTAATACCTGAAACTATAAGATTCCTAGAAGAAAACAA 2343
                         --------  i v   v v  i         i i  i            v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_4456405_4   2344 AAGA--AAA-------GACATTGGTCTGG---ATGGTGACTT-----TGA 2376
                          i ?--   -------   v    vi i ---     vv   -----   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_4456405_4   2377 --------GCACAGGCAACAAAAGTAAAAATAAACTAATGAAATGACATC 2418
                         --------     i          v       i iv   vii ivv    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_4456405_4   2419 AAACTGAAAAGCTTCTGTGCAGCAAAGAAAACAATTCCTAAAGTAAAGAG 2468
                            v v    i   i     vv     i v  v  ivvv     i  i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_4456405_4   2469 ACAACTTGTGGAATGGGACAAAATATTTGCAAATCATATATCTGATAAGG 2518
                              iiiii        v                               
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_4456405_4   2519 GGTTAATATAAAAAATATATAAGGAACTCAAACAACTCAATAGCAAGAAA 2568
                          ii vi   vv i         i      vv           ii  i  i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_4456405_4   2569 ACAAACA---------------------------------GACATTTCTC 2585
                              i ---------------------------------          
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_4456405_4   2586 TGAAGAAAACATACAAATAACCAACAGGTATATCAAAAAATGCTAAATTG 2635
                         ii     i i        ii    i i i i  v    i     v  i--
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC-- 896

  chr20_4456405_4   2636 CTGATCACCAGGGAA 2650
                         ---    ????????
  L1M4_orf2#LINE/    897 ---ATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (127 / 68)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 5.44 (98 / 18)  


3593 22.76 1.33 1.10  chr20_4464236_4467171     1540  2444 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr20_4464236_4   1540 GGAATAGTTATCCCATGTTCATGAATTGGAAGAATTAATATTGTCAAAAT 1589
                             -  v               i         v          i  i  
  L1M4_orf2#LINE/      2 GGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_4464236_4   1590 CTTCTTACTACCCAAAGTGATATACAGATTTAATGCAATCCCTATCAAAA 1639
                         vvivv    v      v    v        i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_4464236_4   1640 TCCCAATGGTATGTTTTACAGAAATAAAAAAA--AATCTTAAAATTAATA 1687
                              iiv iv v    i       vi v  i--i   i       v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_4464236_4   1688 TGATACCACAAAAAGCCCTAAATAGTCAAAGCAATCTTGAGTAAGAAAAA 1737
                           iv vii   iiii   vi     i    i         iv     i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_4464236_4   1738 TAAAATTGAAGGCATCACACCACCTAATTACAAAATATACTACAAAGCTA 1787
                         i   i   i   vv      iv  i    v     iv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_4464236_4   1788 TAGTAATCAAAAGAGTTTAGTACTGGCATAA----AAACACATAGACCAA 1833
                         i         i v   v i            ---- i   i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_4464236_4   1834 TGGAACAGAATAGAGAACCCAGAAATAAACCCACATATATATGATTAATT 1883
                              i     v    ii               i i  v    i i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_4464236_4   1884 GGCCTTTGTCAGGAGTGTCAGTAACACAAAATGGA-AAAGAACAGTCTCT 1932
                          iii  i v  i i   i  iv v  ivv     i-      i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_4464236_4   1933 TCAACAAATGGTGATTTTTAAAAATCTGGATATCCACATGCAAGAAAAAA 1982
                                      ---i vii v v       ?          ---  i 
  L1M4_orf2#LINE/    401 TCAACAAATGGTG---CTGGGACAACTGGATAKCCACATGCAA---AAGA 444

  chr20_4464236_4   1983 ATTTAATTAGACCCCTATTTCACACCATATACAAAAATTAACTCAAAATG 2032
                           vv i  i        ii                               
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_4464236_4   2033 GATTAAAGACTTAAATGTAA-ACTTGAAACTGTAAACCTCCTAGAAGAAA 2081
                            i ?    i         - vi i     i    v   i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_4464236_4   2082 ACATAGGAA-AAACCAATCTTGACATTGGTCTTGGCAATAATTT-TTGGT 2129
                                ?i-   i v-  v    v    vi v      ii   -  i v
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_4464236_4   2130 TATGACCCCAAAAGTTCAGGCAACAAAAGCAAAAATAGACAAGTGGGATA 2179
                               v       iv  i          v         i  i v   iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_4464236_4   2180 ACATGAAACCCAAAAACTTCTGCATAGCAAGAGAAACAATCAACAAAATG 2229
                         v   v   vii        i  iiivv   ii  v  v     v   i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_4464236_4   2230 AAAAGACAACATATGATATAAGA-AAAGTATTTGCAAACC-TACATCCAA 2277
                                   vi iiiv  ii  -   i          i -  i   ii 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_4464236_4   2278 TAAGGGATTAGTATCCAAAATATAGAAGGAGCCACTACAACTCAATAGCA 2327
                                i v       i      v  i  i ivi            ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_4464236_4   2328 AAAATAAGCAAAAAGCATGATTTTAAAATGGGCAAAGGACCTCAATAGAC 2377
                             v --    v i vii   ?v               ii v       
  L1M4_orf2#LINE/    794 AAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_4464236_4   2378 ACTCCATGAAAGAACAAATTTAAATGGCCAGCAGGCGTATGAAAATGTGT 2427
                          i i viv      v v  vi         ii i  ii       vi  i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_4464236_4   2428 CCAACATCAATTATCAG 2444
                         i        ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (127 / 75)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 1.69 (22 / 13)  


3297 23.83 2.78 1.67  chr20_4485860_4488201      953  1850 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_4485860_4    953 TGGAGAGATATTCCATGTTCATGGATTGGAAGATTCAATATAGTTAAGAT 1002
                             i      i                     i i     v        
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_4485860_4   1003 GTCAATTCTTGATAACACCTGACTTGATCTATAGATCCAATACAGTCCCA 1052
                          v    v  i-------  ii v        i    i   ii  i    v
  L1M4_orf2#LINE/     51 GGCAATACTC-------CCCAAATTGATCTACAGATTCAACGCAATCCCT 93

  chr20_4485860_4   1053 ATCAAAATTCCAGCAACTTATTTGGTATATATTGTCAGACTAATTCTACA 1102
                                 i     vi i v   v i v v    v  ii  i  i   v 
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr20_4485860_4   1103 GTTTATAGAGAAAGACAAAAGACCCAGAATAGACACCATGATACT---AA 1149
                         i  i   vi    vi   ii            v  vv ii  vi ---  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr20_4485860_4   1150 AGAAGAACAAAGTTGGAAGACTGACACTACCAGAATTCAAAACTTACTAT 1199
                                          i    v     v  vi v              i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr20_4485860_4   1200 AAATCCACAGTAATCAAGACAGCGTGGTATTGGTTAAAGAACAGACCCAT 1249
                            v i                i      i   ivv   i i    vi  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr20_4485860_4   1250 AGATCAATGGAACAAAATAGAGACCCCTAAAATAGATTCACACAAATTTA 1299
                                     i i   v    vi  vi     i ii  i   --    
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA--TTTA 341

  chr20_4485860_4   1300 --GTCAACTAATCTTTGAAAAAGGAGCAAAGGCAATTCAATGGAAAAAGG 1347
                         --     i i  i  i  v  i  v  v   i v         ii    i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_4485860_4   1348 ATAATTTTTTCAACAAATTGTTTTGCAACAATTGAACTTCTAAATGGAAA 1397
                            i i            v  vi  vi    i  i iv? i v   v   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_4485860_4   1398 AAACAAAAAAAGTCTAAGCACTGATT-ATACCTTTTACAACAATTAACCC 1446
                          i --- vi    ivi v v  ivi - i   v v     v       i 
  L1M4_orf2#LINE/    442 AGA---ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr20_4485860_4   1447 AAAATGAATGATAGAACTAAATATGAAATGTAATACTTTAAAACATCTAG 1496
                               i  v ?   v      i i i vv   v   v      vii   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr20_4485860_4   1497 AAGAAAACATAGGACAAAAATCTATGTGGCCTTGAGTTTGCTAATGAGTT 1546
                                      ?-iv      vi   i     i   v vi    iv  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_4485860_4   1547 TTTAGAC-T--CACTAAAAGCATAATTCATTGAAAGAAAGAGTT--TAAA 1591
                         i     i- --   i       i  v-  vii       i i v--    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAA 636

  chr20_4485860_4   1592 TTAGACTTTATTAAAATTAAAGGCTTTTACTCTAAAAACGACACTGTGAA 1641
                           i     i  i         ii     iiv  vv   v      i v  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr20_4485860_4   1642 GAGATC--AAAGATAAGCCATAGACTGGAAGGACTTATTTTTAAGCCATA 1689
                           i vi--     i  v   i   v   i  i vv     vi  ii    
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr20_4485860_4   1690 TACCTAATATGGGATTTGTATCCAAAATACATTAAAAACTCTTAAAATTC 1739
                           i  i   v    i         i    i  v  i        v  i  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr20_4485860_4   1740 AACAGTAAGAAAACAA-T--CCCATATTTAAAA-TGGGCAAAAGATCTGA 1785
                           i i   i  i    - --    -   ?    -        i   i   
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGA 835

  chr20_4485860_4   1786 ACAGACATCTCACCAAAAAAGAT--------GGCAAATAAACATATGAAA 1827
                          i      i  v     i     --------   v     i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr20_4485860_4   1828 AGGTGTTTAATATTATTTGTCAT 1850
                           i  i i  i  i ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (132 / 78)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.35 (40 / 17)  


3070 26.13 3.17 0.45  chr20_4547906_4554919.rev     5639  6522 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_4547906_4   5639 TGGAAAAACATTCCATGCTCATAGATAGGAAGAATCAATATTGTGAAAAT 5688
                               i i  i     i    i   v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_4547906_4   5689 GGCCATACTGCCCAAAGTAATGCTATAAG-------------CTACCA-- 5723
                            v     v      v i  -   i ii-------------   i  --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT-CTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_4547906_4   5724 -------TTGACTTTCTTCACAGAATTAGAAAAAACTACTTC-AAATTTC 5765
                         -------i  v    i  -i     v v  v  i-  iv i -   v   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTC 147

  chr20_4547906_4   5766 ATATGAAACCAAGAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAA 5815
                              i  viivi ii  v  v v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_4547906_4   5816 GGACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5865
                          i      i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_4547906_4   5866 TTACAGTAACCAAAAAAGCACGGTACTGGTACCAAAACAGAGATATAGAC 5915
                         i        i   i v  iii        i iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_4547906_4   5916 CAACGGAACAGAACAGAGGCCTCAGAAATAACGCCACACATCTACAAGCA 5965
                            i    i    iv   ivii         vv   i    i  iiiv  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_4547906_4   5966 TCTGATCTTTGACAAACCTGACAAAAACAAGCCATGGGGAAAGAATTCCC 6015
                         vi    i  i     ivv  v   i v  vv v             vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_4547906_4   6016 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 6065
                          v  i  i        i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_4547906_4   6066 GAACTAGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGAT 6115
                         i ii i       v   i     v                   i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_4547906_4   6116 TAAAGACTTAAATGTAAGACCTAAAATCATAAAAACCCTAGAAGAAAACC 6165
                         i ?    i           v      ii      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_4547906_4   6166 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 6214
                             ?i- v i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_4547906_4   6215 AACACCAAAAGCAATGGCAACAAAAGTCAAAATTGACAGATGGGATCTAA 6264
                         i            vvi          vv     v  i i  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_4547906_4   6265 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGGGTGAAA 6314
                          i   v v  i i   i  ii vv    i  v       vv ii      
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_4547906_4   6315 AGGCAACCTACAGAATAGGAGAAAATTTTTGCAATCTCTCCTTCTGACAA 6364
                           i     i       i         v       viiv viv     i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_4547906_4   6365 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAA 6414
                         i  i  vi          v  i        ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_4547906_4   6415 AAACAA----CCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 6460
                          i    ----   v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_4547906_4   6461 TCGAAAGAAGTCATTTATGTGGCCAGCAAACATATGAAAAAAAGCTCATC 6510
                           v       vi  vi vi      ii  i  i       i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_4547906_4   6511 ATCACTGGTCAT 6522
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (133 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.56 (32 / 9)  


3165 16.85 2.03 1.40  chr20_4587262_4588880      487  1127 (492)    L1M4_orf2#LINE/L1      264   908 (0)  

  chr20_4587262_4    487 AATGTACTGCTAACATAAGGATAAATACATAGGTCAATGGAATAGAATTG 536
                          i   iv i  ii          i i i    i                 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr20_4587262_4    537 AGAGTCCAGAAATAAACCCTCATATTTATGGTCAATCGGTTTTCAAAAAG 586
                                            vi i             i i     i v   
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr20_4587262_4    587 AGCGT-AAGACAATTCAGTGGGGAAA--ATTGGCTTTTTAATAAGTGGTA 633
                         i i i-     v     i        --  v v     i  i  i    i
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr20_4587262_4    634 CGTACTTGGGCAACTGGATATACACATGCTAAAGAATGA-TTTGGACCCC 682
                          ---- v  i          ?v       v         -v         
  L1M4_orf2#LINE/    414 C----TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr20_4587262_4    683 TACTTCAAATTATACACACACAAAAA--AACTGAAAATGGATCATAGACC 730
                            i   v ii   i   ----    --    v           ?     
  L1M4_orf2#LINE/    460 TACCTCACACCATATACA----AAAATTAACTCAAAATGGATCAWAGACC 505

  chr20_4587262_4    731 TAACTTCAAGAGCTAAATTGCATAAAATTTCTAGAAGAACATACTGGAG- 779
                            v vi          vi-i      i ii        v i iv  ? -
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAAC-TATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr20_4587262_4    780 AAATCTTTGTGACATCAGGTTAGGCATTGGTTGTCTGGATACAACACAAA 829
                                i     v ii         v     vii i    ii    v  
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr20_4587262_4    830 ATACGCACACA-CA---GAAAAAATAGGTAAGTTG-ACTGCATCAAAATG 874
                          vi i  vi  -  ---          i   i   -   v         v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr20_4587262_4    875 TAAAACTTTTGTGCTTTAAAGGACATCATCAAAAAAGTAAAAAGACAACC 924
                         v               i        ii     i     i           
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr20_4587262_4    925 CACAGAGTGTGAGAAAATATTTGAAAATCATATATCTGATAAGGGGCTGG 974
                               i  v             v                     i  v 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr20_4587262_4    975 TATTCAGAATATATAAATAAATCTTACAACTCAACAACAAAAAGATAAAT 1024
                            i             v  v             i  i       i    
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr20_4587262_4   1025 AACTCAATC-AAAAGTGGGCAAAGCCTTTGAATAGACACTTCTCCAAAGA 1073
                            i    i-    i         vv            i           
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr20_4587262_4   1074 AGAAATACAAATGGCCGACAAACAAAGGAAAAGACGTTCAACGTCATAAG 1123
                            v            i i  i  v v       i i     i   ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr20_4587262_4   1124 TCAC 1127
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.92 (69 / 36)
Gap_init rate = 0.02 (12 / 645), avg. gap size = 1.83 (22 / 12)  


3070 26.33 3.06 0.00  chr20_4682063_4686994.rev     3560  4440 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_4682063_4   3560 TGGAAACACATTCCATGCTCATAGATGGGTAGAATCAATATTGTGAAAAT 3609
                               v i  i     i    i   v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_4682063_4   3610 GACCATACTACCAGAAGTAATCTACAAATTCAACTCAATCGGCATCAAA- 3658
                          i v     v  vi  v i       i       v     vvi      -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_4682063_4   3659 TAGCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 3708
                          vv  v vv v  i  ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_4682063_4   3709 TGGAACCAAAAAAGAGCACACATAGCCAAAGTAAGACTAAGCAAAAAGAA 3758
                              viiv  ii  v vviv         ii  vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_4682063_4   3759 CAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTCTAAGGCCA 3808
                             vi      vv       v  ii        viv    vi  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_4682063_4   3809 TAGTCACCAAAACAGCGTGGTACTGGCATAAAAATAGGCACATAGACCAA 3858
                         i   v i   i    i               ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_4682063_4   3859 TAGAATAGAATAAAGAACCCAGAAATAAACCCAAATACTTAC-ACCAACT 3907
                          i         vi   ii               v i i   i-ii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_4682063_4   3908 GGTTGTCGACAAAGCAAACAAAAACATGCAGTGGGGAAAGGACACCCTTT 3957
                          i  v       i vviv   i v   v  i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_4682063_4   3958 TCAACAAATGGTGTTGGGATAATTGGCAAGCCATTTGTAGGAGAATGAAA 4007
                                      i     i  i   vv ?   iv  i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_4682063_4   4008 CTGGATCCCTATCTCTCACTTTATACAAAAATCAACTCAAGATGGATTAA 4057
                         i    i     i   v   iv           i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_4682063_4   4058 GGACTTAAACCTAAGATCTGAAACTATAAAAATTCTAGAAGATAACATTG 4107
                         i   i    iv     v  i           v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_4682063_4   4108 GAAAAACCCTTCTAGACACTGGCTTAGGCAAGTATTTCATGACCAAGAAC 4157
                          ?iv  vi    vv   vi   v        vvi    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_4682063_4   4158 CCAAAAGCAAATGCAATAAAAACAGAGATAAATAGCTGGGACCTAACTAA 4207
                                  v v    i    iv i i   i   iv v    i v ii  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_4682063_4   4208 ACTAAAGAGCGTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAGAC 4257
                          v v  i i v    ii vv    i iv  vi   iv i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_4682063_4   4258 AACCCACAGAGTGGGAAAAAA------CAATCTATACATCTGACAAAGGA 4301
                                   i     i    ------   vii   i      i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_4682063_4   4302 CTAATATCCAGAATCTACAATGAACTCAAACAAATCAGTAAGAAAAAAAC 4351
                           vi          v  i  v      vv    v   i   v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_4682063_4   4352 A------------------TGGCC-AAGGACATGAATAGACAATTCTCAA 4382
                          ------------------   v -     iv          v     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_4682063_4   4383 AAGAAGATATACAACTGGCCAGCAAACATGTAAAAAAATGCTCAATATCA 4432
                                       v      ii  i  ii i    i        i    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr20_4682063_4   4433 CTAATGAT 4440
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.31 (130 / 99)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 5.40 (27 / 5)  


 591 18.58 0.00 0.00  chr20_4770929_4772821.rev      501   613 (1280)    L1M4_orf2#LINE/L1      242   354 (554)  

  chr20_4770929_4    501 ACAAAGCTACAGTAATCAAAACAGTGTGGTGCTATCATAGAGACAGATAG 550
                                            i          i  iv    ii  i   i v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_4770929_4    551 ATAGACCAATGTTATAGAATAGAGAACCCAGAAATAAACCCTCACACATA 600
                              i     vv       v    ii              vi   iv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_4770929_4    601 TGGTCAAATGGTT 613
                                v  i  
  L1M4_orf2#LINE/    342 TGGTCAATTGATT 354

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.00 (0 / 113), avg. gap size = 0.00 (0 / 0)  

1743 16.14 16.14 2.12  chr20_4770929_4772821.rev      931  1401 (492)    L1M4_orf2#LINE/L1      372   908 (0)  

  chr20_4770929_4    931 GACCATTTATTAGGAGAAAAGACCGTCTTTTCATCAAATGATGCCGAAA- 979
                                i v i  -    ii iv         v      i   i ii -
  L1M4_orf2#LINE/    372 GACCATTCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr20_4770929_4    980 AACTAGATATCCATAGAGAAAAGAAT-AAGTTGAACCCTTACCAAACACC 1028
                             i    ?   i viv        -      i    i    vv     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr20_4770929_4   1029 ATATACAAAAATTAACTCATTAGGGACCAAAGACCTACATGTAAGATCTG 1078
                                            vv v   i  ?       v        v  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr20_4770929_4   1079 AAACTATAAAACTCGTAAAAGAAAGCATAGGGCAAAATCTTCATGACA-- 1126
                                       v  i      i      ?vv        i    v--
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr20_4770929_4   1127 AAATTGGAC----------TA--TAT-ACAC------------------- 1144
                         iii  i i ----------  --   -    -------------------
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr20_4770929_4   1145 ---------------ATT----TT--------TTAAA-----TTGTGCAT 1162
                         ---------------   ----  --------     -----      v 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr20_4770929_4   1163 CAAAAGATAATATCAG---AGTAAACAGCCAACCCACAGAATGGGAGAAA 1209
                             i  i v     i---   i  v  v                     
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr20_4770929_4   1210 ATATTTGCAAATCATATATCTGATAAGGGATTACTATCCAGAACATTTAG 1259
                                                       i vv         i  v  i
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr20_4770929_4   1260 AAAACCCCTAATAAC--AACAACAAAAA--CAAACAATGCAATTCAAAAA 1305
                          i   i i  -i   --  i  i     --    i  iv     ?     
  L1M4_orf2#LINE/    771 AGAACTCTTA-CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_4770929_4   1306 TGAGCAAAGGACTTGAATAGACATTTCTTCAAAGAATACAATACAATATA 1355
                           i        i                i       --------i     
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA--------GATATA 861

  chr20_4770929_4   1356 CAATTGACCAATAAGCA-ATGAAAAGATGTCCAACCTCAGTAATCAT 1401
                            v  i          -           ii    v   ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (46 / 26)
Gap_init rate = 0.03 (17 / 537), avg. gap size = 5.06 (86 / 17)  


3049 27.41 1.11 0.33  chr20_5164659_5171316.rev     5266  6166 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_5164659_5   5266 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5315
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_5164659_5   5316 GGCCAAGCTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5365
                            v vi  v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_5164659_5   5366 TACCATTAACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5414
                          v   vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_5164659_5   5415 ATGAAACCAAAAAAGAGCCTGTATAGCCAAGACAATCCTAAGCAAAAAGA 5464
                            i  viiv  ii  v  v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_5164659_5   5465 ACAATGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5514
                             v i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_5164659_5   5515 ACAATAACCAAAACAGCATGGTAGTAGTACCAAAACAGAGATATAGACCA 5564
                            i   i   i    ii     v i i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_5164659_5   5565 ATGGAACAGAACAGAGGCCTCAGAAGTAATGCCACACATCTACAACCATC 5614
                               i    iv   ivii     i   vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_5164659_5   5615 TGATTTTTGACAAACCTGACAAAAACAAGCAATGGGGGAAGGATTCCCTA 5664
                                i     ivv  v   i v  vv        i   i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_5164659_5   5665 TTTAATAAATGGTGTTGGGAAAACTGGTTAGCCATATTCAGAAAACTGAA 5714
                           i  i        i     v      v  ?   i  v  i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_5164659_5   5715 ACTGGACCCTTTCCTTACACCTTATACAAAAATTAACTCAATATGGATTA 5764
                         ii       i v   i     v                   v      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_5164659_5   5765 AAGACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5814
                         ?    i    ii     v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_5164659_5   5815 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAA 5863
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_5164659_5   5864 CACCAAAAGCAATGGCAACAAAAGCCAGAATTGACAAATGGCATCTAATC 5913
                                    vvi          vv i   v  i    v v ii v   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_5164659_5   5914 AATCTAAAGAGCTTCTGCACAACAAGAGAAACTATCATCAGAGTGAAAAG 5963
                           vv v  i i   i  ii vv   ii  v       vv i         
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_5164659_5   5964 GCATCCTACATAATGTGAGAAAAT-TTTTCAATCTATCCATCTGACAAAG 6012
                         i  v  i   v    v        -   v   vii  vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_5164659_5   6013 GGCTAATATCCAGAATCTACAAAGAATTTAAACAAATT-----TACAAGA 6057
                          i  vi          v  i      i ivv    v i-----  v  ii
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_5164659_5   6058 ACAAACCACCGCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTCTC 6107
                              iv   vv  i?    i    ii      v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_5164659_5   6108 AAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAAAGCTCATCA 6155
                         v        i  vi viii     i  --         i v-     v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT-GCTCAACA 897

  chr20_5164659_5   6156 TCACTGGTCAT 6166
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2948 27.01 0.43 1.95  chr20_5174190_5179179.rev     3577  4498 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_5174190_5   3577 TGGAAACACATCCTATGTTCATGGATATGTAGACTCAATATTGTCAAAAT 3626
                               v i    i            vv v     i        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_5174190_5   3627 GACCATACTGTCAAAAGCAATGTACAGATTCGATGGAATTTCCATCAAAG 3676
                          i v     vi v   vii  v         i i v   ii i      i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_5174190_5   3677 TACTATCATAATTCTTCAC-GAACTAGAAAAAACAATCTTAAAATTCATA 3725
                          v i v vvvv  i  ii -   v v  v  ivii   i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_5174190_5   3726 TGGAACCAAAAAAAAAAAAAAAAAAAAGGCTCAC-ATAGCCAAAGCAAGA 3774
                              -------------- viv  ii i i  v-         i   vv
  L1M4_orf2#LINE/    151 TGGAA--------------ATGCAAGGGACCCAGAATAGCCAAAACAATC 186

  chr20_5174190_5   3775 CTAAGCAAAAA-AACAAATCTAGAGGCATCACATTACTTGACTTCAAACT 3823
                         i i iv  i  -      vi i    vv     i v iii i      vi
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr20_5174190_5   3824 ATACTACAAGGCTATGGTTACCAAAACAGCATAGTACTTGTATAAAAATA 3873
                         v        i    ii  v i   i    ii i     v i    ii   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr20_5174190_5   3874 AGCACATAGGCCAAGGAAACAGAATAAAGAAACCAAAAATAAAGCCAAAT 3923
                         ii  i    ii   v i  i     vi   iv   i       v   v i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr20_5174190_5   3924 ACTTACAGCCAACTGGTCTTTGACAAAAGCAAACAAAAACATAAAGTGGG 3973
                          i   ii i   i  i i  i     ii iiv-   i v   vv i    
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGG 385

  chr20_5174190_5   3974 GGAGGGACACCCTATTCAACAAATGATCCTGGGATAATTGGCAAACCACA 4023
                          i i i i vi  v           i v      i  i   vv ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr20_5174190_5   4024 TGTAGAAGAATGAAACTGGACCCTCATCTCTCACCCTGTACAACAATTAA 4073
                           i i         ii       ii i   v    v i     v      
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr20_5174190_5   4074 CTAAAGAGGGATCAAAGACTTAAATCTTAGACCTGAAACTATAAAAATTC 4123
                           v  i v      ?    i     v v   v  i           v ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr20_5174190_5   4124 TAGAAGATAACATTAGAAAAACTCTTCCAGACATTGACTTAGGAAAAGAG 4173
                                v     vi ?iv  v     vv   v   iv     v  v iv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr20_5174190_5   4174 TTTATGGTGAAGAACCCAAAAGCAAATGCAACAAAAATAAAAATAAATAG 4223
                           iv i vv v  vv         v v         iv       i   i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr20_5174190_5   4224 ATGGGACCTACTTAAACTAAAAGGCTTCTGCACAGCAAAAGAAATAGTCA 4273
                           v    i vv i   v v   ii   i  ii vv    i  v ivi   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr20_5174190_5   4274 GTAGAGTAAACAGACAATCCACAGAATGGAAGAAAATATTCACAAACTAT 4323
                         iv i   i  v      i           i          ii    ii  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr20_5174190_5   4324 GCATCATTGACAAAGGACTAATATCCAGAATCTACAAGGAACTC-AACAA 4372
                         ii   --   i  i     vi          v  i  i      -v    
  L1M4_orf2#LINE/    736 ATATC--TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr20_5174190_5   4373 ATCAGCAAGAAAAAAACAAATAATCCCATTGAAAAGTGGGCAAAGGACAT 4422
                         v   ii  v     i        i  v   ?    i           iv 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr20_5174190_5   4423 GAATAGACAGTTATCAAAAGAAGATATACAAATGGCCAACAAACATGTGA 4472
                                  v  v  v                       i  i  ii   
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr20_5174190_5   4473 AAAAAATGCTCGATGTCACTAATTAT 4498
                            i -     i ii   ????????
  L1M4_orf2#LINE/    884 AAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.75 (22 / 8)  


 236 35.09 0.00 0.00  chr20_5186003_5187615       24   137 (1476)    L1M4_orf2#LINE/L1      120   233 (675)  

  chr20_5186003_5     24 AGATATAGATAAGTTTATTCTAAATTTTATATAAAAGGACAAAAGAACTA 73
                            v  v  i   i v  i     v  i    ii  ivi   ii  v i 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr20_5186003_5     74 AAATATCTCAAACAGTTCTGAAAATGAAAAATAAAACAGTAAGAAACAGT 123
                         i    v iv     i ii      v   i  i   iiv v i  vv  vv
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr20_5186003_5    124 CTACCTGATTCCAA 137
                           v  ii   i   
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAA 233

Transitions / transversions = 1.50 (24 / 16)
Gap_init rate = 0.00 (0 / 114), avg. gap size = 0.00 (0 / 0)  

1753 25.77 5.06 1.47  chr20_5186003_5187615      501  1113 (500)    L1M4_orf2#LINE/L1      232   866 (42)  

  chr20_5186003_5    501 AAAGCTTACTGTGTAATTACAGTTAATTAAGACTATGTCATATTGGTAGA 550
                            i      iiiv ii      -   i     vi   vi  i   i v 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGT-AATCAAGACAGTGTGGTACTGGCATA 280

  chr20_5186003_5    551 GAGATAAACATATAGATCAATGGAGCAGAATAGGGAACTCAGAAATAACC 600
                         ii    i                 ii     v i  iii         v 
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr20_5186003_5    601 CCAAACAGTTAGAGTCAAGTGATTTTTAACAATGAT-CCAAAAGCAATTT 649
                            v   v   vi     v       ii    v i -    i v  -  i
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTC 379

  chr20_5186003_5    650 AACAGAGGAAGGAAAGCCTTTTTAATAAATAGTGCTGGAGTAATTGGACG 699
                           ii i i   i v  i     i  i    i       iii  i    ii
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr20_5186003_5    700 TCCATAGGCACAA-AATAAGCCTTGACCAAAGTCTTACATCTAACACAAA 748
                         ?   i v   v  -   i ivi v    vvvii  i   i vv i     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr20_5186003_5    749 AATGAACTCAAA-TAGATCATG----TAAATGTAAAATGC-AAAACTATA 792
                            v        - i     ?i----         i -  -         
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATA 528

  chr20_5186003_5    793 TAATT-TTAGA-GAAAA---AGGAGAAAATATT-GTGAATTCAGA----G 832
                         v  i -     -     ---   ? v    v  -    vi ii i---- 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr20_5186003_5    833 C----------TAGACTTGATACCAAAAATACAATCTATAAAGTTAAAAA 872
                          ----------    iv   i       ii    v v i   ivv     
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr20_5186003_5    873 TTGATAAATTTTACCTCTTTGAAATTAATAACTTTTGCTCTGCAAAAGAC 922
                          v        vv  i  v ii       v        iv  v    i   
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr20_5186003_5    923 -CTGTTAAGAGTATGAAAAGACAAACTAGAAACTAGAAGAAAATAATTGC 971
                         -  i i    ivi           v i v i v i i        v    
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr20_5186003_5    972 AAAACAACATACCTAGCAAAGGATTAATATCTAGAAAATATAAAGAACTA 1021
                            v  -i   i  iii  i   i vi    i    v            v
  L1M4_orf2#LINE/    729 AAATCA-TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr20_5186003_5   1022 T--CAATCACAACAGTAAAACAAAACCCAAAAAATCCTATTAGAAAATAG 1069
                          --   - v   i i     -- i  --   v  i  v   ?i     i 
  L1M4_orf2#LINE/    778 TTACAA-CTCAATAATAAAA--AGAC--AAATAACCCAATTWAAAAATGG 822

  chr20_5186003_5   1070 GAAAAAGACATGAAGGAACATTTCACCAAAGAGGACCTACAAAT 1113
                          v   i  iv    vii       v       i  iv       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

Transitions / transversions = 1.75 (98 / 56)
Gap_init rate = 0.03 (20 / 635), avg. gap size = 2.00 (40 / 20)  


3267 26.53 0.78 0.00  chr20_5212786_5217358     3181  4081 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_5212786_5   3181 TGGAAACACATCCCAGGCTCATGGGTGGGTAGAATCAATATTGTGAAAAT 3230
                               v i      v i      i v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_5212786_5   3231 GACCATGCTGCAAAAAGCAATCTATAAATTCAACACAATCCCCATAAAAA 3280
                          i v  i  v vv   vii     i i       i       i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_5212786_5   3281 TACCACCATCATTCTTCACAGAATTAGA-AAAC-AATTCTAAAATTCATA 3328
                          v   v vv v  i  ii     v v  -  i -i  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_5212786_5   3329 TGGAGCCAAAAAATAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 3378
                             iviiv  iiv v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_5212786_5   3379 CGAATTTGGAGGCATCACACTACCTGATTTCAAACTATATTGTAAGGCCA 3428
                          i  v       vv       v  ii        viv  i ii  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_5212786_5   3429 TAGTCACCAAAACAGCATGGTATTGGTATAAAAATAGGCACATAGACCAA 3478
                         i   v i   i    ii     i   i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_5212786_5   3479 TGAAACAGAATAGAGAACCCAGAAATAAACCCAGATACATACAGCCAACT 3528
                           i  i     v    ii               v i iv  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_5212786_5   3529 GATCTTCAACAAAGCAAACAAAAACATAAAGAGGGGAAAGGACACCCTTT 3578
                            i   i    i vviv   i v   vv iv        i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_5212786_5   3579 TCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATGACA 3628
                                            i  i   v  ?       i ii       vi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_5212786_5   3629 CTGGATTCTTATCTCTCACCTTATACAAAAATCTACTCAAGATGGATTAA 3678
                         i    ii i  i   v    v           iv      i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_5212786_5   3679 GGACTTAAACCTAAGACCTGAAACTGTAAAAATTCTAGAAGATAACATTG 3728
                         i   i    iv     v  i     i     v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_5212786_5   3729 GAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAAC 3778
                          ?iv  vi    vv   v    v        v i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_5212786_5   3779 CCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACTTAATTAA 3828
                                  v v    i    iv   i   i   iv v      v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_5212786_5   3829 ACTAAAGAGCTTTTGCACAGCAAAAGGAGCAGTCAGCAGAGTAAACAGAC 3878
                          v v  i i      ii vv    i ivi vi   iv i   i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_5212786_5   3879 AACCCACAGAGTGGGAGAAAATCTTCACAATCTCTACATCTGACAAAGGA 3928
                                   i           v  ii   viiv  i      i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_5212786_5   3929 CTAATATCCAGAATCTACAATGAACTCAAACAA----ATAAGCAAGAGA- 3973
                           vi          v  i  v      vv    ----    vv  i   -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_5212786_5   3974 AAACAATCACATCAAAAAGTAGACTAAGGACATGAATATACAGTTCTCAA 4023
                            i  i vv  i?    i i i v     iv      v   v     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_5212786_5   4024 AAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCA 4073
                                               i  i  i       i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr20_5212786_5   4074 CTAATGAT 4081
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.37 (136 / 99)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.75 (7 / 4)  


2619 12.90 1.76 25.71  chr20_5267739_5272230     2807  4000 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_5267739_5   2807 TAGAAAGATGTCCTATGTTCATCGATTGGAGAAA--AATATTGTTCAGAT 2854
                          i       i   i        v       ii v--         v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_5267739_5   2855 GTCAGTACTACCCAAGGTGGTCTGGAGATTTAATGCAATACCTGTCAAAC 2904
                          v  i    v     iv  i   iv     i  i     v   i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_5267739_5   2905 TGCCAATAATTTTTTTTTGCAGAAATAGAAAAATCCATTCCAAAATTCAT 2954
                          v   iiviii      -        v  v  iiiv  i i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_5267739_5   2955 ATGGAATCTCAAGGAATCCAGGATAGCTAAAACAATCTTGAAAAAGAAGA 3004
                               viv     i i    i     i                      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_5267739_5   3005 GCAAAGTTTGAGGACTCACACTTCCTGATTTCAAAACTTACTATAAATCT 3054
                         i       v                ii                i   v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_5267739_5   3055 ACAGTAATCAAAACAGTGTGCTATTGACGTAAATACAGACATAGAGAGTT 3104
                                    i        v  i  i i   iv i       v   ---
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA--- 296

  chr20_5267739_5   3105 CAGAAATAAACCTCAGACATATGGTCAAACGAGTTTTGAAAAGAATGCCT 3154
                         ------------   -----    -------------------   ----
  L1M4_orf2#LINE/    297 ------------TCA-----ATGG-------------------AAT---- 306

  chr20_5267739_5   3155 ACCATTCACTGGGGGAGAAGACAGTCTGTTCTTTTGTTTTTGTTTTTGTG 3204
                         ---------------    -------------------------------
  L1M4_orf2#LINE/    307 ---------------AGAA------------------------------- 310

  chr20_5267739_5   3205 TTTTTCTTTTTGAGACAGGATCTCTCTCTGTTGCCTAGGCTGGAGTGCAG 3254
                         ---------      -----------------------------  v   
  L1M4_orf2#LINE/    311 ---------TTGAGA-----------------------------GTCCAG 322

  chr20_5267739_5   3255 TGGCAAAATCACAGCTCACTGCAGCCTCAACCTCCTGGGCTCGAGTTATT 3304
                         -----    - - i i  - i  --i i ------   --  i v v   
  L1M4_orf2#LINE/    323 -----AAAT-A-AACCCA-TACA--TTTA------TGG--TCAATTGATT 354

  chr20_5267739_5   3305 CTCCCACCTCAGCCTCTCGAGTAGCTTGGACTACAGGCATGTGCCAACAT 3354
                         i  -------------------------   - -   ---       v -
  L1M4_orf2#LINE/    355 TTC-------------------------GAC-A-AGG---GTGCCAAGA- 373

  chr20_5267739_5   3355 ACCCAGCTTTTGTGTCTGTGTGTGTGTAGAGATGGGTCTCAGTATGTTGC 3404
                         --   ---  ii-------------------     --------------
  L1M4_orf2#LINE/    374 --CCA---TTCA-------------------ATGGG-------------- 385

  chr20_5267739_5   3405 CCAGGCTGGTCTTGAACTCCTGGGCTTAAGTGATCTTCCTGCCTCAGCCT 3454
                         -------------   ------------  -i  -----------  i  
  L1M4_orf2#LINE/    386 -------------GAA------------AG-AAT-----------AGTCT 398

  chr20_5267739_5   3455 CCCAAATTGCTGAGATTTCAGGCATGAGCCACCATGCCTGGCCAAGGCAG 3504
                         ---------------     ------------------------------
  L1M4_orf2#LINE/    399 ---------------TTTCA------------------------------ 403

  chr20_5267739_5   3505 TCTGAAAAATAAATAGTGCTGGGAAAATTGGATATTCAAATGCAAAAGAA 3554
                         -------- i    i         v  i      ?i  v           
  L1M4_orf2#LINE/    404 --------ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_5267739_5   3555 TAAAGTTGTTCCATTACCTAACACTGTATA-AAAAATTAGTTCAAAATGG 3603
                          i      vv  vi     v    ii    -        ii         
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_5267739_5   3604 ATCCATGATCTAAATGTAAGACCCAAAACTATAGAACCTTTGGGAGAAAG 3653
                            v?v  i            v i         i   ii  i i     i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_5267739_5   3654 CATAGGA-CAAACACTTCATAACATTGGATTTGGCAATGATTTCTTGGTT 3702
                               ?-i   i-    i i  v    i  v       i      i v 
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_5267739_5   3703 GTGACACAAAAGGCACAGGCAACAAAAGAAAAAATAGACAAATTGGACTT 3752
                         i      v   i     i                    i           
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_5267739_5   3753 CATGAAAGTTAAAAACTTTTGTGTATCAAAAGACAATATCAACAGAGTAA 3802
                            v   i               iv     i    v      v i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_5267739_5   3803 AAAAAGCAACCCACAGAATTGGAGAAAATATTTGCAAATCATAAGTCTGA 3852
                            i -             v                       vi     
  L1M4_orf2#LINE/    695 AAAGA-CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_5267739_5   3853 TAAGGTATTAATACCCAGAATATGTACAGAACTCCTGAAACTCAACAATA 3902
                              v i vi  i         i  v       i iv       i    
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_5267739_5   3903 AAA---CAACTAA----ATTAAAAA---GGCA-------TGAATAGATAC 3935
                            ---   v   ----   ?    ---    -------        i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_5267739_5   3936 TTCTCCAAAGAAGATGTACGAATGGCCAACAAACATATGAAAAGGTGTTC 3985
                                        i   i         i  i  i        i  i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_5267739_5   3986 AATATCACTGATCAC 4000
                           i    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (101 / 49)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 9.11 (328 / 36)  


2987 25.34 4.05 2.14  chr20_5313040_5317685     3273  4160 (486)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr20_5313040_5   3273 AAAGAAGTCTCATGCTTATGGATTGAAAGAATTAATATTGTTAAAAATGA 3322
                              vi  i    i i        i    v             i -  i
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-TGG 52

  chr20_5313040_5   3323 CAG-----CCCAAAGCAATCTGCAGGTTCAATGTAATCACTATCAAAATA 3367
                           i-----      vii    i   i     i i    v          v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_5313040_5   3368 CCAA-----TTTTTCACTGAAATAGAAAAAACAATCCTAAAATTTGTTTT 3412
                            i-----     ii v     v  v  ivii           ii v v
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_5313040_5   3413 GAAGCAAAAAAGAGCCCAAATAGCCAAAGCAGTCCTGAGCAAAAGGAATA 3462
                            iiiv  ii  v  vi          i  i  i   iv  i i   i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_5313040_5   3463 AAGCTCTAGGCATCACACTACCTAACTTCAAAATATA-TGCAAATGTTGT 3511
                            i vv   vv       v  i  i       iv  - i    - i ii
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-GCTAC 251

  chr20_5313040_5   3512 AGTAACCAGAACAGCATGGTATTGATGTAAAAACAGACACA--GACCAAT 3559
                              i  ii    ii     i  iii   ii i     i --  i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_5313040_5   3560 GGAAAAGAATAGAGGACTCAGAAATAAGCCTGCATATTTACAGCTAACTG 3609
                             v     v   iiii         i  iii i     ii ii  i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_5313040_5   3610 ATTTTCAACAAAGGTGCTAAGAACATGCATTGGGGAAAGGATACCCTCTT 3659
                               i    i     i    v   v  v         i   vi  i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_5313040_5   3660 TAGTTATGGGTGCTGGCAAAATTAGGTTTCCATATGCAGAAGAATGAAAC 3709
                         i iiv vv        v v  i i i v?   i     i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_5313040_5   3710 TGTACTCCTGTATCTCACCATATACAAAAATTGACTCAAGATGAATTAAA 3759
                           v  i   iiv  v                 i      i   i  i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_5313040_5   3760 GACT--AACATAAGAGCCCAAACTACAAAACTACTAGAAGAAAACATAGG 3807
                            i--  ii       iv      i      vi                
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_5313040_5   3808 GG-AAACACTCAGGACATTGGTGTAGGCAA-----------ATATGACCA 3845
                         ? -   ivi  iv   v    vv       -----------       --
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC-- 599

  chr20_5313040_5   3846 AGACCTCAAAAGCATAGACAACAAAAACAAAAATAGACAAATTAGACTAC 3895
                         --   --       i ii        iv         i     i    v 
  L1M4_orf2#LINE/    600 --ACC--AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_5313040_5   3896 ATTAAACTAAAAGGCTTCCACACAGCAAAAGA-ACAATCAACAGAGTAAA 3944
                           i   v v   ii   iiiii vv    i  -  v     v i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_5313040_5   3945 GAGACAACCTATTGAATAGAATAAAATATTTGCAAACTTTTCATCTGACA 3994
                         i        i iv    i i v              iiv vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_5313040_5   3995 AGAGACTAATATCCAGAGTATACAAGGAACTT----AACAC--TAAAACA 4038
                           i    vi        i    i  i     i----   v --   v v 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_5313040_5   4039 ACAACAATCATCATCAGCAGCATCTCATTAAAAAGTAGGTGAAGGACACG 4088
                          vi    --  v i -----  ----   ?    i i  ii     ivi 
  L1M4_orf2#LINE/    796 AAGACAA--ATAACC-----CA----ATTWAAAAATGGGCAAAGGATTTG 834

  chr20_5313040_5   4089 AATAGGCATTTCT--AAAGAGAAGACACAAATGGCCAAAAGGTATATGAA 4136
                              i       --     ii v i            v i i i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr20_5313040_5   4137 AAAATACTTATCGCTAATTATCAA 4160
                           i  i  i v iii ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (156 / 65)
Gap_init rate = 0.02 (18 / 905), avg. gap size = 3.06 (55 / 18)  


3351 25.77 0.77 0.77  chr20_5322791_5324979      790  1697 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_5322791_5    790 TGAAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 839
                           i   i i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_5322791_5    840 GGCCATACTGCCCAAAGTAATTTATAGATTTAATGCTATCCCCATCAAGC 889
                            v     v      v i  i  i     i  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_5322791_5    890 TACTATTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 938
                          v i vivi i  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_5322791_5    939 ATGGAACCAATAAAGAGCCCATA-TAGCCAAGACAATCCTAAGCAAAAAG 987
                               vii-i  i ii    v -       i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_5322791_5    988 AAGAAAGCTGGAGGCATCACACTACCTGATTTCAAACTGTACTAGAAGGC 1037
                           v    i      vv       v  ii        viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_5322791_5   1038 TACAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGATATATAGACC 1087
                                 i   i i  ii         i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_5322791_5   1088 AATGGAAAAGAATAGAGGCCTCAGAAATAATGCCACACATCTACAACCAT 1137
                                v     v   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_5322791_5   1138 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 1187
                         i    i  i     ivv  v   i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_5322791_5   1188 GTTTAATGAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTGA 1237
                         v  i  ii       i     v      v  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_5322791_5   1238 AGCTGGACCTATTCCTTACACCTTATACAAAAATCAACTCAAGGTGGATT 1287
                           i      iv v   i     v           i       ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_5322791_5   1288 AAAGACTTAAATATAAGACCTAAAACCATACAAACCCT-AGAAGAAAACC 1336
                          ?    i     i     v       i   -    i  -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACA 547

  chr20_5322791_5   1337 TAGGCAATACAATTT--GGGACATAGGCATGGGCAAAGACTTCATGACTA 1384
                             ?i-  -   i -- v   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_5322791_5   1385 AAACATCAAAAGCAACGGCAACAAAAGGCAAAATAGACAAATGGGATCTA 1434
                         vi   i        vvi          iv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_5322791_5   1435 ATTAAACTAAAGAGCTTTCTGCACAACAAAAGAAACTATCATCAGAGTGA 1484
                           i   v v  i i    -  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_5322791_5   1485 ACAGGCAACCTAGAGAACGGGAGAAAATTTTTGCCATCTATTCATCTGAC 1534
                          v  i     i v    i          v     v vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_5322791_5   1535 AAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACGAGAA 1584
                           i  i  vi          v  i  i     ivv    -i i vv iv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATA 793

  chr20_5322791_5   1585 AAAAAACAAATAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGATAC 1634
                             i           v  i?    i            v    i   i i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_5322791_5   1635 TTCTCAGAAGAAGACATTTATGTGGCCAACAAATGTATGAAAAG--GCTT 1682
                              vi       i  vi vi       i  iiii        --   i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_5322791_5   1683 ATCATCATTGGTCAT 1697
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (141 / 89)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.17 (14 / 12)  


 271 21.90 5.71 4.76  chr20_5348987_5350915      501   605 (1324)    L1M4_orf2#LINE/L1      290   395 (513)  

  chr20_5348987_5    501 ATACAGACCAATGCAATAGAATAGAGAATCCAGAAATAAAGCCAAAATAC 550
                            i   i     v        v    i            v   ---   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA---TAC 336

  chr20_5348987_5    551 GT--ACAGCCAACCAGTCTTCAACAAAGCATGCAAAAACACA---AATTG 595
                         i -- ii i   iiii i   i    i -i   v  i  -  ---   v 
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGAC-CATTCAATGG 384

  chr20_5348987_5    596 AGAG-GAATAG 605
                         i  i-      
  L1M4_orf2#LINE/    385 GGAAAGAATAG 395

Transitions / transversions = 3.60 (18 / 5)
Gap_init rate = 0.06 (6 / 106), avg. gap size = 1.83 (11 / 6)  

1821 24.20 2.40 0.00  chr20_5348987_5350915      938  1437 (492)    L1M4_orf2#LINE/L1      397   908 (0)  

  chr20_5348987_5    938 CTATTTAGTAAATGGTG-TGGAAAAATTGGCAAGCCACATGTAGAAGAAT 986
                           v  i ii        -   i v  i   vv ?       i i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_5348987_5    987 AAAACTGAGTCCTTATCTGTCACCTTATACAAAAATCAACTCAAGATGGA 1036
                         i  ii  iii  i  i  vv    v           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_5348987_5   1037 TCAAAGACTTAAATACAAGACCTGACACTA-AAAATTCT-AGAAGAGAAC 1084
                            ?    i     ii    v  i v    -    i   -      i   
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_5348987_5   1085 ATTGGGAAAACTTTTCCAGACATCAACCTAGGCAAAGAATTCATGACTAA 1134
                           v  ?iv  v i   vv   v iiivi       v iv   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_5348987_5   1135 GACCCCAAAAGCAAATGCAACAAGAAGAAAAATAAACAGATGGGACCTGA 1184
                            v         v v       i ii       i i i  v    i v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_5348987_5   1185 TTAAACTAAAAAGTATCTGCACAGCAAAAGAAATAATCAGCAGAGTAAAC 1234
                          i   v v    iiv i  ii vv    i  v iv    iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_5348987_5   1235 AGACAACCCATAGAATGGGAGAAAATATTGACAAACTATGCATCTGACAA 1284
                                   i                  vi    ii  ii      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_5348987_5   1285 AGGACTAGTATCCAGAATCTACAAGGAACTC----AAATCAGCAAGAAAA 1330
                         i     v           v  i  i      ----  v   ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_5348987_5   1331 AAAAAAAT--CCCA-TTAAAAAATAGACAAAGGCCATGAATAGACATTTC 1377
                          i v    --    -  ?      i i      viv              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_5348987_5   1378 TCAAAAGAAGATACACAGATGGTCAACCA--ACATGAAAAAATGCTCAGC 1425
                           v          i   i    i   iv --         i       i 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_5348987_5   1426 ATCACTAATCAT 1437
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (72 / 45)
Gap_init rate = 0.01 (7 / 512), avg. gap size = 1.71 (12 / 7)  


2132 26.67 0.19 0.19  chr20_5386009_5392973.rev     5257  5796 (1169)    L1M4_orf2#LINE/L1        3   542 (366)  

  chr20_5386009_5   5257 GAAAAACATTCCATGCTCATGGATAGGAAGAATCGATATCATGAAAATGG 5306
                             i i  i     i        v      v ii    ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_5386009_5   5307 CCATACTGTCCCAAAT-AATTTATAGATTCAATGCTATTCCCATCAAGCT 5355
                          v     -i       -i  i  i        i  v  i  i     iv 
  L1M4_orf2#LINE/     53 CAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_5386009_5   5356 ATCATTGACTTTCTTTGCAGAACTAGAAAAAACTACTTTAAACTTCATAT 5405
                         vi  vivi i  i         v v  v  iviv iii    v       
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr20_5386009_5   5406 GGAACCAAAAAAGAGCCCACATAGCCAAGATAATCCTAAGCAAAAAGAAC 5455
                             viiv  ii  v  viv        i i    i i iv  i      
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_5386009_5   5456 AAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTATAAGGCTAC 5505
                             i      vv       v  ii i      viv     i  i     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr20_5386009_5   5506 AGTAACCAAAACAGTATGGTACTGGTACTAAAACAGATAAATAGACCAAC 5555
                              i   i     i         i iv ii i   i v     i   i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_5386009_5   5556 AGAACAGAACAGAGACCTCAGAAATAGCGCCACACATCTACAACCATCTG 5605
                         i   i    iv    vii        ivv   i    i  iiii  vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_5386009_5   5606 ATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTTCCTATT 5655
                           i  i     ivv  v   i v  vv            i  vvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_5386009_5   5656 TAATAAATGATGCTGGGAAAACTGGCTAGCCATATGCAGAAAACAGAAAT 5705
                         i  i     i        v      v  ?   i     i  i vv   i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_5386009_5   5706 TGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAAA 5755
                                  v   i     v                   i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_5386009_5   5756 GACTTAAATGTAAAACCCCAAACCATAAAAACCCTAGAAGA 5796
                            i         i v iv    i      vi i       
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

Transitions / transversions = 1.78 (91 / 51)
Gap_init rate = 0.00 (2 / 540), avg. gap size = 1.00 (2 / 2)  

1216 26.25 0.52 0.52  chr20_5386009_5392973.rev     6093  6473 (492)    L1M4_orf2#LINE/L1      528   908 (0)  

  chr20_5386009_5   6093 AAAAC-CTTAGAAGATAACCTAGGCA-ATACCATTCAGGACATAGGCATG 6140
                              -         v   v    ?i- v i -   iv   v v  vv i
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTA 576

  chr20_5386009_5   6141 GGCAAAGACTTCATGACTAAAACACCAAAAGTAATTGCAACAAAAGCCAA 6190
                              v ii   v iiv  vi          i vvv          vv  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr20_5386009_5   6191 AATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAG 6240
                            v  i    v   ii v  i   v v  i i   i  ii vv    i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr20_5386009_5   6241 AAACTATCATCAGAGTGAACAGGAGACCTACAGAATGGGAGAAAATTTTT 6290
                          v       vv i      v  ivi   i                 v   
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr20_5386009_5   6291 GCAAGCTACCCATCTGACAAAGGGCTAATATCCAGAATCTACAAAGAACT 6340
                             iii ivi      i  i  i  vi          v  i        
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr20_5386009_5   6341 TAAACAAATTTACAAGAAAAAAATTAAACAACCCCATCAATAAGTGGGCA 6390
                         ivv    v iv i  v     i i-   i     v  i? v  i      
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCA 825

  chr20_5386009_5   6391 AAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAACAG 6440
                               v    i     i     v        i  vi viii     i i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr20_5386009_5   6441 ACACATGAAAAAATGCTCATCATCACTGGCCAT 6473
                         i          i       v     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (53 / 45)
Gap_init rate = 0.01 (4 / 381), avg. gap size = 1.00 (4 / 4)  


 969 20.00 7.78 3.33  chr20_5468985_5471706.rev      501   770 (1952)    L1M4_orf2#LINE/L1      139   420 (488)  

  chr20_5468985_5    501 CTAAAATTTGTTTGGAGAGGCAAAGGAACTAGAATAGCTAAAAACAATTT 550
                                 ii v    i v    i   v i        i    -    i 
  L1M4_orf2#LINE/    139 CTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCT 187

  chr20_5468985_5    551 TGAGCAAGAAG--CAA-GTGGGAGGAATCACTCTACCTGATTTTAAAACT 597
                            iv      --   -  v      v    v  v  ii    i      
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr20_5468985_5    598 TAC-GTAA--CTACAGGAATCAAAAC----TGGTACCGGCGGAAGGATAG 640
                            -ii  --      v      i  ----      i   iv        
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr20_5468985_5    641 ATACATAGATCAGTGGCCTAGAAT---------AGAAA--AATCCACACA 679
                          i i        i   vv      ---------     --  i   i   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr20_5468985_5    680 AGCACAGCCAAATGCTTTTTGACAAACATGCAAAGGCAATTCAATGAAGG 729
                         vvi ii i   v  v    i     ivi   v   i v        --  
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG--GG 385

  chr20_5468985_5    730 ATTGAAAGAAGGATGGTCTTTTTAAGAAATGATGCTGGAGC 770
                         ---       --- i       i  v     i      ii 
  L1M4_orf2#LINE/    386 ---GAAAGAA---TAGTCTTTTCAACAAATGGTGCTGGGAC 420

Transitions / transversions = 1.70 (34 / 20)
Gap_init rate = 0.04 (11 / 282), avg. gap size = 2.73 (30 / 11)  

 272 24.22 19.53 3.12  chr20_5468985_5471706.rev     1059  1186 (1536)    L1M4_orf2#LINE/L1      406   554 (354)  

  chr20_5468985_5   1059 AAAAAATGCTGGAGCAATGGGACATCCA-ATGCCACGAGAGTGAA----- 1102
                            vii      ii   iv   i ?   -    - vi   i    -----
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGC-AAAAGAATGAAGTTGG 454

  chr20_5468985_5   1103 -------CGTTACACC-TATACAAGAAGTAACTCA----GAATCATAGAT 1140
                         ------- v i     -       i  v       ---- i    ?   i
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr20_5468985_5   1141 TAAAATATAA-------AACCCCAAATCTTTTAGCAGATAACAGGCTGGG 1183
                         iv    i   -------   ivi   v  i    v   v    --- i  
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA---TAGG 551

  chr20_5468985_5   1184 TGT 1186
                         ?  
  L1M4_orf2#LINE/    552 NGT 554

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.05 (7 / 149), avg. gap size = 4.14 (29 / 7)  

 453 27.78 1.85 1.85  chr20_5468985_5471706.rev     1432  1593 (1129)    L1M4_orf2#LINE/L1      537   698 (210)  

  chr20_5468985_5   1432 AAAAGATAATGTAGGAGAAAATCTTCAGGACCTAGGGCTTGGTAAAGAAC 1481
                          i    v  ii    ? v        iv     v   i v  i  v ivi
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_5468985_5   1482 TCTCAGACATGACACCAAAAGTACCATTCATAAAATTTAAAAATCAATAA 1531
                            i   i             i  v viv i    vv-      vi    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA-AAAAATAGATAA 635

  chr20_5468985_5   1532 ACTGGACTTTGTAAAAATGTAAAACTGTTG--CTCCATGAAAGAC-CCAT 1578
                          i       ii v     vv      v   --  i  --  i   - i  
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTAT 683

  chr20_5468985_5   1579 TAAAAGGACAAAAAG 1593
                         i  i iiiii     
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAG 698

Transitions / transversions = 1.59 (27 / 17)
Gap_init rate = 0.02 (4 / 162), avg. gap size = 1.50 (6 / 4)  

 200 25.00 1.47 1.47  chr20_5468985_5471706.rev     1880  1947 (775)    L1M4_orf2#LINE/L1      685   752 (156)  

  chr20_5468985_5   1880 AAAAGAATAAAAAGACAAGTTTACAAAGTGAGAGATAA-ATTTGCAAAAC 1928
                           i i i i         -iii   i i  i    v  -         v 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAA-CCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr20_5468985_5   1929 AAATCTCTGACAACGAACT 1947
                          v  v     i  v i   
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACT 752

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2)  

 289 22.13 7.38 1.64  chr20_5468985_5471706.rev     2109  2230 (492)    L1M4_orf2#LINE/L1      780   908 (0)  

  chr20_5468985_5   2109 ACAAC-CAAGAA-AAAAAAATGAA-AATTCAGTTTAAAAATGAGCAAAAG 2155
                              -   v  -     i ii  -  ii  i  ?       i     i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr20_5468985_5   2156 ATATGAG--GATATGTCATATTAAAGATGATATAAGAATATC----AAAC 2199
                           v   i--  i  v  - -ii     v      vi   iv ----  i 
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTC-T-CCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr20_5468985_5   2200 ACATGATAAGACATTTAACATCATTAGCCAT 2230
                               v    iii i       ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.71 (19 / 7)
Gap_init rate = 0.05 (7 / 129), avg. gap size = 1.57 (11 / 7)  


 209 33.20 15.02 3.95  chr20_5720101_5722401.rev       54   306 (1994)    L1M4_orf2#LINE/L1      400   680 (228)  

  chr20_5720101_5     54 TTAAATAAATAACATTGAGACAACTGGCT-TCCATTTGGAAAACAATAGA 102
                           v  i    iiiii  i         v -?   iv  v    v   ii 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_5720101_5    103 GCTATCATCTTGTTTCATACT-----------TTACCCTAAAAT-----A 136
                          i ivvvi i iii   i  i-----------   v ii     ----- 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_5720101_5    137 AAGACTTCAA------AGTTGAAA--ATTAAACTTTTAAAAATACTAAGA 178
                         ?    i v  ------  i i   --  v     i   i  i----  i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG----AAAA 545

  chr20_5720101_5    179 AATGGAGGTGCCTATTTATATAATCTTGGA--AAGCAAGAATGGTTTTCC 226
                         v  --   ? ivv  i vii i i     i-- i    ---      - i
  L1M4_orf2#LINE/    546 CAT--AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA---TGGTTT-CT 589

  chr20_5720101_5    227 TA-ATTTTATGCTAAA-GCAGAAGCATTGA---------TTGATAAGCTT 265
                           -  v v ii i   -   v     vii --------- v     ii v
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_5720101_5    266 GACTATATAGGAATCTAAAATCTCTATACATCAAAAAAAAC 306
                             vi  vii   iv    ii i i i v     ii v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

Transitions / transversions = 2.12 (55 / 26)
Gap_init rate = 0.05 (13 / 281), avg. gap size = 3.69 (48 / 13)  

1297 19.03 4.15 0.69  chr20_5720101_5722401.rev      491   779 (1521)    L1M4_orf2#LINE/L1      155   453 (455)  

  chr20_5720101_5    491 AATACATACAGACCTCCAAATAGCAAAAACAATTCCGAG---GAAAAAAA 537
                            i  - vi    - vi      v        iii  i---   i  v 
  L1M4_orf2#LINE/    155 AATGCA-AGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_5720101_5    538 AAGTTGGAGGACCCACACTTCCTGATT-CAAAACATA-------GCTACA 579
                                     i         ii   -      v  -------      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_5720101_5    580 GTAATCAAAACAGTGTGGCACTGTCATAAAGACAGACATACGGACCAATG 629
                                 i         i    v     i  i       ii  i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr20_5720101_5    630 GAACAGGACAAAGA-CCCAGAAATAAACCCTTACGTATATGCTCAAATGA 678
                            i  i ivi   -i              v   i v    v    v   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_5720101_5    679 TCTTTGACAAGGGTGCCAAGACTACTCAATAGGGAAAAGAAGGTCTCTCC 728
                          i  i                 i i     i      ii vi    i i 
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr20_5720101_5    729 AACAAATGGTGAGGGGAAAACAGCATATCCACATGCAAAAGAACAAAGTC 778
                                    vv    v   v v   ?               ii    i
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr20_5720101_5    779 G 779
                          
  L1M4_orf2#LINE/    453 G 453

Transitions / transversions = 2.18 (37 / 17)
Gap_init rate = 0.02 (6 / 299), avg. gap size = 2.33 (14 / 6)  

2106 17.98 3.95 0.88  chr20_5720101_5722401.rev     1353  1808 (492)    L1M4_orf2#LINE/L1      439   908 (0)  

  chr20_5720101_5   1353 AAAAGAACAAACTCAAAACCTTATCTTACACAATATACAAAAATTAATTC 1402
                                ii  v iii v  i  i  i    v               i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr20_5720101_5   1403 AAAAATGGATTAAAGACCTAAACATAAGCCCTAAAACTATAAAACTCCTA 1452
                             -     i ?         ii    vv                 i  
  L1M4_orf2#LINE/    489 AAAA-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr20_5720101_5   1453 GAAGAAAGCACAGAGGAAAAGCTTCATGACATTAGACTTGGCAATGATTT 1502
                                i  i  i? v   v    i    v  i ii v       i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_5720101_5   1503 CTTAGACATGACACCGAAAGTACAGGAAACAAAAGCAAAAATGGA----- 1547
                               i        i    i   i v        v      i  -----
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr20_5720101_5   1548 ----------CAAACTCAAAAACTTTTGCACATCAAAGGACATAATCAAC 1587
                         ----------    v i           ii v          iv     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_5720101_5   1588 AGAGTGAAAAGGCCATCTATAAAAAGGAAGAAAATATTTGCAAATCACAT 1637
                          i         i v i i i i  v  i                   i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_5720101_5   1638 ATCTGATAAGAAGTTAGTATCTAGAATACATAAAGAACTCCTACAACTCA 1687
                                   iiii v     i      i           i         
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_5720101_5   1688 ATAACAAAAA---AAATCAACCCAATTTTAAAAATAGGCAAAGGATTTCA 1734
                             i     ---    -         ?-      i            v 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAAT-AACCCAATTW-AAAAATGGGCAAAGGATTTGA 835

  chr20_5720101_5   1735 ATAGATGTTTCTTCAAAGATGGTATGCAAATGGCCAATAAACATGTGGAA 1784
                              ii     i      v i   i              i  ii  -  
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG-AA 884

  chr20_5720101_5   1785 AATATGTTCAACGTTACCAATCAT 1808
                           v   i     i i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.76 (58 / 21)
Gap_init rate = 0.01 (6 / 470), avg. gap size = 3.67 (22 / 6)  

 732 22.78 0.56 0.00  chr20_5720101_5722401.rev     1953  2132 (168)  C L1M4_orf2#LINE/L1   (104)   804   624  

C chr20_5720101_5   2132 AAACATTGATAAATTGGACCTCATAAAAATTAAAAACCTTTGCTTTGTGA 2083
                            v  v            i    v            i    ivi vii 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

C chr20_5720101_5   2082 AAGCCCATGTGAAGAGAATGAAAAGACAGGCCACAGACTGGGAGAAAATA 2033
                          i v vv i v    i i          iv       v            
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

C chr20_5720101_5   2032 TTTGCAAATCCCATACCTGACAAAGAACTAGTTTCTACAATATGTAAAGA 1983
                                   vi   i    i  i i   v  v  i v     i      
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

C chr20_5720101_5   1982 ACTCTCAAAACTCGACTCTCAAAAAA-AAAT 1953
                              i v     i ivv v    i -    
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAAT 804

Transitions / transversions = 1.16 (22 / 19)
Gap_init rate = 0.01 (1 / 181), avg. gap size = 1.00 (1 / 1)  


4334 15.99 3.97 1.02  chr20_5825885_5829256     2007  2888 (484)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_5825885_5   2007 TGGAAAGGCATCCTGTGTTAATGGATCATATGACTTAATATTGCTTAGAT 2056
                                ii    ii    v      iiv v            i v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_5825885_5   2057 TGCAGTGTTCCCCAAACTGATCTACAGTTACAATGCAATCACTATTAAAA 2106
                         v   i ii        i          v v   i      v    i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_5825885_5   2107 TCCC-GTT--TTTTTTTTCAGTAATAGGCAAACTGATCCTAAAATTTGTA 2153
                             - i --i      v   v   v i   i              ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_5825885_5   2154 TGGAGATTCAAGGGGTCCAGAATAGCCAAAATAGTCTTGGAAAAAAAAAA 2203
                             i  v      ii               i i     -------    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG-------AAAA 193

  chr20_5825885_5   2204 AAAAGAACAAAGTTGAATGACTCACACTT----------------ACTAC 2237
                          i             i v           ----------------     
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr20_5825885_5   2238 AAAGCTACTGTAAATAAGATTGTGTGGTACTGGCATAAGAATAGACATAT 2287
                                 v    vi    iv                  i          
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr20_5825885_5   2288 AGGTCAACAGAATAGAATTG-GAATACAAAAATAAAAACATACATTTATG 2336
                           i    ii           -  i v  i       vv            
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr20_5825885_5   2337 TAAAATTGGT-----ACAAGGGTGACAAGACAATTCAAGGGGGAAAGAAT 2381
                         vvv     i -----         v      v      v           
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_5825885_5   2382 ATTCTTTTCAACAA-TAATGCTGACTCATCTGGATATCCATATGCAAAAG 2430
                          v            - ii     ivv  v       ?   i         
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_5825885_5   2431 AATGAAGTTGTATCCCTACCTTACATCACATACAAAA-TGAACTCAAAAT 2479
                                   v i        i   i  i        - v          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_5825885_5   2480 GGATCATAGACATAAACATAAGACCTCAAAGTATAAAACTCTTAGAAGAA 2529
                               ?    v    ii     v  v   v                   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_5825885_5   2530 AACATAGGAGAAAATCT-CGAG-CCTTAGACTAAGCAATGATTTCTTAGA 2577
                                 ? v      -  v -    i ii  i      i         
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_5825885_5   2578 TATAAAACCTAAAGCAAAAGCAACCAAGGAAAAAGTAGATAAATCGGGTG 2627
                            i v   v      v       v  i      i         i  iiv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_5825885_5   2628 GCATCAAAAGTTAAAACTTTTGTGCTTCAAAGTACACCATGAAAAAATTG 2677
                         v        v v                    v    i  v  i   v  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_5825885_5   2678 AAAAGACAACC-AGAAAGTGGGAGAAAATATTTGCAAATCGTATATCAGA 2726
                                    - v i i                      i      v  
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_5825885_5   2727 TTAGAGAC--ATATACAAAAGATATAAAACAATTC--ACAACTTAGCAAT 2772
                          v  i   --i   v  i  v       i-  i  --      i ii   
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAG-AACTCTTACAACTCAATAAT 792

  chr20_5825885_5   2773 AAAAAGACAAATAACTCAATTTAAAAATGACAAAAGGATTTGAATATATA 2822
                                        i     ?       ivv              v i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_5825885_5   2823 TTTTTTTCAGAGAAGATATACTAATGGCCAATAAGCATGTGAAAAGATGC 2872
                            i i-  i           v               ii           
  L1M4_orf2#LINE/    843 TTTCTC-CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_5825885_5   2873 -AAATATTATTAGCTAT 2888
                         -v  i  i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (79 / 58)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.75 (44 / 16)  


 910 29.17 2.27 0.00  chr20_6080411_6085357.rev     3174  3437 (1510)    L1M4_orf2#LINE/L1        1   270 (638)  

  chr20_6080411_6   3174 TGGAAAAATGCTCCATGCTCATGGATTGGAAAAATCAGTATTATTAAAAT 3223
                               i  iii     i             i v i i    i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_6080411_6   3224 GGCCATACTGCCTAAAGCAATTTACAGTTTTAATGCTATTTGTATCAAAC 3273
                            v     v  i   vii  i     v  i  i  v  iiv       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_6080411_6   3274 TACCAACATTATTTTTCACTGAATTAGAAAAAGCCATTCTAAAATTTATA 3323
                          v   i vviv     ii v   v v  v  iviv  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_6080411_6   3324 TGAAACCAAAAAGGAGCCCGAATAGCCAAAGGAATTCTAAGCAAAAAGAA 3373
                           i  viiv  i   v  v           iv   ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_6080411_6   3374 CAAAGCCAGAGGCATCACATTACCTGACTTCAAACTATACTATAAGGCTA 3423
                              iii    vv     i v  ii i      viv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_6080411_6   3424 C--TAAT----ACGGTTTGG 3437
                          --    ----  i  v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGG 270

Transitions / transversions = 1.57 (47 / 30)
Gap_init rate = 0.01 (2 / 270), avg. gap size = 3.00 (6 / 2)  

2055 26.92 1.78 1.63  chr20_6080411_6085357.rev     3780  4455 (492)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr20_6080411_6   3780 AAAATGGACTAACACAGCTATAGTAACCAAAACAACATGGTACTGGTATA 3829
                             ivv    -  v     i     i   i   iii         i   
  L1M4_orf2#LINE/    232 AAAACTTACTA-CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr20_6080411_6   3830 AAAACAGACACATAGACCAATGAAACAGAACAGAGAACCCAGAAATAAAG 3879
                          ii i     i     i     i  i    iv    ii           v
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr20_6080411_6   3880 CTGCACACTTACAACCACAAGATCTTCAATGAACTGGACAAAAATAAGCA 3929
                          iii   i   iiii  vvv   i   i ii ivvv v   i vi vv  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr20_6080411_6   3930 ATGGGGAAATGAC--TCTTTATTCAGTAAATTGTGCTGGGATAACTGGCT 3977
                                  vi i--     --   ii    v         i      v 
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGAT 428

  chr20_6080411_6   3978 AGCCATATACAGAAGAATAAAACTGGACCTCTACTTATCACCACATAGAA 4027
                          ?   i  i  i      i  ii      i    i vv     i   v  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr20_6080411_6   4028 AAATTAACTCAAGATAAATTAAAGATTTAAATGTAAGACCTAAAACTATA 4077
                                     i  ii  i ?   ii           v           
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr20_6080411_6   4078 AAAAACCCTAGAGGAAAATCTAGG---AAATACCCTTCTCAATATTAGCC 4124
                            v-i i    i     iv    ---    ---    vii iv  i v-
  L1M4_orf2#LINE/    529 AAAC-TCTTAGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGG- 573

  chr20_6080411_6   4125 TTGGGAAATAATTTAT-GGCTAAGTCCTCAAAAGTGATCA--CAACAAAA 4171
                           i  v   ii   v -i v  v v vi      ii--  --        
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA--CAAGCAACAAAA 621

  chr20_6080411_6   4172 ACAAAAATTGATAATTGGGACCTAACTAAACAAAAGAACGTCCTCACAGC 4221
                         iv      v     v v    i v ii   vvv  i   v iivii vv 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr20_6080411_6   4222 AACAGAAATTATCAAGGAATTAAACAGATAATCCACAAAATAGGAGAAAA 4271
                           vi  v i       i  v i  v   i  i     i   i        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr20_6080411_6   4272 TATTCACAAATTATGCATCCAACAAAGGTCTAATATCAAGAATCTATACG 4321
                             ii     i  ii   ii i  i  v  vi    v     v    vi
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr20_6080411_6   4322 GAATTT----AAATCAATAAACAAAAAACAAATAACCCCATTAAAAAGTG 4367
                            i i----  v       vv    i           v   ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr20_6080411_6   4368 GTCAAAAGACACGAGCAGACACTTCTTAAAAGAAGACATACAAGCAGCCA 4417
                          v    i  ivi  ii     i    iv        i      iii    
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr20_6080411_6   4418 ACAAATATATGAAACAAATGCTCATCAGCACAAATTGT 4455
                          i  ii i      - i       v  v  ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAA-AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (116 / 63)
Gap_init rate = 0.02 (12 / 677), avg. gap size = 1.92 (23 / 12)  


 950 29.28 10.80 3.37  chr20_6123064_6124790.rev      501  1241 (486)    L1M4_orf2#LINE/L1      113   908 (0)  

  chr20_6123064_6    501 TTTTTGTCATACTTGATACACTGATTCTAAATTTCATA-GAAAAGGCAAA 549
                               iviv v    i vi     i     v      - i   v    i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr20_6123064_6    550 ------AAAAT---CGAGA-AATATTTAAATATAAG--TAAAG-----AA 582
                         ------ i   --- i i -   v  v   v v   --i    -----ii
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr20_6123064_6    583 ACTTGC-CTTACCAAATATAAAG---ATTTTAAAGCTACAGAAATCTAGA 628
                            ii -   v    v vi   i--- i vi          v    v   
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr20_6123064_6    629 AAGTAT----TTGATACAAAGATGGATAAACTGATTA-TTGCTCAAAACA 673
                         v   i ----i  ii i  i   i  i v iv   i - v vvi i  iv
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr20_6123064_6    674 GAGAACCCAAAAATGGACCCAAACATACATAGACACTTAATATTTGATAG 723
                             ii   i    ii     v    vi  i v  v  i  v  i  i -
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA- 361

  chr20_6123064_6    724 AAAGGGCATTGC--AGACCTAT----------AAAAATAGGCTATTTGAT 761
                         --    ---   --     -  ----------  i     v  v  ii i
  L1M4_orf2#LINE/    362 --AGGG---TGCCAAGACC-ATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr20_6123064_6    762 AA-T--TCCTGGGATAATTAGTTGTCCAAATTTTTTAAGCACA---TTAG 805
                           - -- v      i  i i v i?   v  vivv-   v ii---  i 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAA-AAGAATGAAGTTGG 454

  chr20_6123064_6    806 ATTTTCACCTCATAC--------AAAATGAATTCCAGCTGAGCTAAAGAC 847
                          iiiii      i  --------     v  i  v iv  iiii ?    
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr20_6123064_6    848 ATAAATACAAAACTCAAAACTTTTTAAAAA---TTAGAATAAAATGTGTA 894
                         v     ii  i vii      v ---    ---      v    ii -- 
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTAT---AAAACTCTTAGAAGAAAACAT--A 549

  chr20_6123064_6    895 GGAG--AATGTCTATGACCTTGAAGTAGGGAAGGATCTCTTTAAATAAGA 942
                           ? --   v iii        iiv    v  v i i    - i   v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGA 598

  chr20_6123064_6    943 CATGCAAAAGCA-AAATACAGATAACAAAAGATTGAAAAATTT-ACTGCA 990
                           i-        -  ii - v v  v    i  v  v     v-   v  
  L1M4_orf2#LINE/    599 CAC-CAAAAGCACAAGCA-ACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_6123064_6    991 CTAATTTATTTAA-----TTCATCTCTCATGAAAATCAACAT-AGGAAAA 1034
                         ii  --- v    -----  ii vii   --  iiv  vi  - i    i
  L1M4_orf2#LINE/    647 TCAA---AATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAAAG 691

  chr20_6123064_6   1035 -GAAATGACAAGCCACAATCTAGAAAAAGTTCTTTTC----CATATATAA 1079
                         -    v     v     ivv i i i  iv v   v ----       --
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT-- 739

  chr20_6123064_6   1080 CACCAACAAAGGATTAGTACTCAGAATATATGTAGCACTTTTAC------ 1123
                         -- ii i  i   i v   ii          iv  v   i    ------
  L1M4_orf2#LINE/    740 --CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_6123064_6   1124 -TGA-AAAAAGAGAAGCAATCCAAT-GGAAAATGGGCAAAAGGTATTAAT 1170
                         - i -       v  ii  i     -?i            i i v v   
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_6123064_6   1171 AGGCAATTCACAGAAGGAAAAAAATAAATATACAATAAATATATGAAGGT 1220
                           i  v   v vi   i i v v i    ivv      ii i     iiv
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_6123064_6   1221 ATTCTCAGTCTCACTGAGAAT 1241
                           v    iiv   ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (130 / 83)
Gap_init rate = 0.05 (39 / 796), avg. gap size = 2.69 (105 / 39)  


3878 22.82 1.10 0.99  chr20_6215722_6218122     1006  1912 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_6215722_6   1006 TGGAAGGACATTCTGTATTCATGTATTGCAAGATTTAAAATTGTTAAAAT 1055
                              i  i  i ii i      v    v    i    v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_6215722_6   1056 GTCCATACTACCTAAAGCATTCTACAAATGTAATGCAATCCCCATCAAAA 1105
                          v v     v  i   viiv      i  vi  i        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_6215722_6   1106 TCCCAATGGCATTTTTTTTTACA-AAAGTAAAAAAAAAATCTGAAAATTC 1154
                              iiv  ---i      i  -   v i v  ivvi   iv       
  L1M4_orf2#LINE/    101 TCCCAGCTGC---CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr20_6215722_6   1155 ATATGGAACCACAAAGGACCCCAAATACCCAAAACAGTCTTGAGAAAGAG 1204
                                 vii   i      vi    v        i      i     i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_6215722_6   1205 ---CAAAGCTAGTGGTGTCACACGTCTTGATTTCAAAACATATTACAAAG 1251
                         ---     i i v  vv      v  iii          v  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_6215722_6   1252 CTACAACAATAAAAACAGTATGACATGGATGTAAAGACAGGCACATAGAC 1301
                              ii   v  i     i  ii iv iii   i  i  i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_6215722_6   1302 CAAGGGAACAGAATAGAAAGCCCAGAGAATAAACCCATGTATATACGGTC 1351
                            v    i     v  i  i     -           ii  v  i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGA-AATAAACCCATACATTTATGGTC 346

  chr20_6215722_6   1352 AAATCATCTTCAATGAGGGTGCCAAGACTGCACAATGGGGGAAAGGATAA 1401
                           v v  i   i ii             iiiv        -    i   i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAG 395

  chr20_6215722_6   1402 TCTGTGTGACAAATGGTGCTGGGAAAACTGAATATCCACATTCAAAAGAA 1451
                            v vii                v     i   ?      v        
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_6215722_6   1452 TGAAATTAGACTCTTACCTTACACCATACACAAACATCAGCTCGAAATGG 1501
                             i  i   i i     i        i     v  i i   i      
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_6215722_6   1502 ATTAGAGACTTAAATGTAAGACCTGAAACTATAAAACTCTTAGAAAAAAA 1551
                           i ?    i           v  i                    i    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_6215722_6   1552 CATAGGGA-AAAGATTCATAACATTTGGCTTGGCAATGATTTCTTGGATA 1600
                               ?i-   vv   i i  v  v  i v       i      i    
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_6215722_6   1601 TTATATCAAAAATACAGGTAACAAAAGCAAAAATAGGCAGATGCTAATAC 1650
                          v i i     ii   i i        v        ii i  vvv v v 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_6215722_6   1651 ATCAAACTACAAATCTTCTGTACAGCAAAGGAAACAATCAA---AGTGAA 1697
                               v vv   v   i   i vv       v  v     ---      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_6215722_6   1698 AAGGCAATTTATGGAATGGAAGAAAATATTTGCTAGTCATATTTCTGATA 1747
                            i   iii ii      i             v i      v       
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_6215722_6   1748 AGTGTTTAGTGTCCAAAATATGTAAGAAACT--TACAATTCAATAGCAAA 1795
                           v vi v  i    i     i   ii    --     i      ii   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_6215722_6   1796 ACACCCCTGAGTAGCCTGAATAATAAGTGGGCAAATGATTTGAATAGATA 1845
                          viv ---i i  i  ii v ? v  i        v            i 
  L1M4_orf2#LINE/    796 AAGAC---AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_6215722_6   1846 TTTCTTCAAAGAAGACATATCAGTTACCAAGAGGTATATGAAAAGATGCT 1895
                              i         i   iv i vi    v i i i             
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_6215722_6   1896 CAATATGCAAATGCAAA 1912
                            i  -  ????????
  L1M4_orf2#LINE/    893 CAACAT-CAZZZZZZZZ 908

Transitions / transversions = 1.90 (133 / 70)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


3241 26.95 0.44 0.55  chr20_6244721_6250991.rev     4871  5779 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_6244721_6   4871 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATGGTGAAAAT 4920
                              ii i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_6244721_6   4921 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4970
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_6244721_6   4971 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5018
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_6244721_6   5019 TATGGAACCAAAAAAGAACCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5068
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_6244721_6   5069 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5118
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_6244721_6   5119 TACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGAGATATAGATC 5168
                                 i   i   iii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_6244721_6   5169 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5216
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_6244721_6   5217 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5266
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_6244721_6   5267 CTATTTAATAAATGGTGCTGGGAAAATTGGCTAGCCATATGTAGAAAGCT 5316
                           v  i  i              v  i   v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_6244721_6   5317 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5366
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_6244721_6   5367 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5416
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_6244721_6   5417 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5466
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_6244721_6   5467 AACACCAAAAGCAATGGCAACAAAAGACAAAACTGACAAATGGGATGTAA 5516
                         i            vvi           v    iv  i    v   iv v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_6244721_6   5517 CTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5566
                         ii   v v  i i   i  ii vv    i  v    i  vv i      -
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA- 695

  chr20_6244721_6   5567 AGGGCAACCTACAAAATGGGAGAAAATTTTCACCACCTACTCATCTGACA 5616
                          i i     i   i             v  ii v vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_6244721_6   5617 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5666
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_6244721_6   5667 AAAACAAACAACCCCATCAGAAAGTGGGCAAAGGACATGAACAGACACTT 5716
                           i     i     v  i?i   i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_6244721_6   5717 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5766
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_6244721_6   5767 CATCACTGGCCAT 5779
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2423 25.73 4.77 3.03  chr20_6252941_6254793      503  1361 (492)    L1M4_orf2#LINE/L1       35   908 (0)  

  chr20_6252941_6    503 TTAATATCATTAAAATGGCCATACTGCTCAAAGCAATCTGTGGATTCAAT 552
                                ii    i     v     v i    vii    iii       i
  L1M4_orf2#LINE/     35 TTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAAC 84

  chr20_6252941_6    553 ACTATTTCTATCAA----TCAA-TGCTATTTTTCACAGAATTAGAAAAAG 597
                         i v  ii       ----i  i-   i-     ii     v v  v  - 
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAA-G 132

  chr20_6252941_6    598 CT-ATTCTAAAATTTATATAGAACCAAAAAAAAAGCCCA-AATAGACAAA 645
                           -  i        i    i   viiv  iii --    -     v    
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGA--CCCAGAATAGCCAAA 180

  chr20_6252941_6    646 GCAATCCAAAGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGCAAAC 695
                         i     ivi ----------------    i  i  v   iv   vii  
  L1M4_orf2#LINE/    181 ACAATCTTGA----------------AAAAGAAGAACAAAGTTGGAGGAC 214

  chr20_6252941_6    696 ATCACATCATCCAACTTCAAACTATACTATAAGGTTACAGTAACCAAAAC 745
                         -     iivi    i      viv     i  i i        i   i  
  L1M4_orf2#LINE/    215 -TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr20_6252941_6    746 AGCATGATACTGGTACAGAAACAGA-ATATAGGCCAATGGAACAGAAGAG 794
                           ii  i      i i iii i   -      ii        i    vv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr20_6252941_6    795 AGAACCCAGAAATGAAGCCACACACCTACAGCCATCTTATCTTCAACAAA 844
                            ii        i  v   i   ii  ii i  vi v  i   i    i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr20_6252941_6    845 GTCAACAAAAATAAGCAATGGGGAAATGACTCCCTATTCAAT-------- 886
                          viiv   i vi vv           vi ivvi  v     i--------
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr20_6252941_6    887 ------CAG-TGGATAGC-ATATGTAGAAGAATGAAACTATATCCCTACC 928
                         ------  i-      ? - i   i i         ii iv i       
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr20_6252941_6    929 TTTTACCATATACAAAAATTAACTCAAGATGTATTAAAGATTTAAATGTA 978
                          ivi                       i   v  i ?   ii        
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr20_6252941_6    979 AGACCTCAATCTATAAGAATCCTAGAAGAAAACCTAGA---AAATACCGT 1025
                            v  v  v      i v  i           v   i---    -- v 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTT 561

  chr20_6252941_6   1026 TCTGAAAATAGGCCTTGGGAAAGAATTTAT--GACTAAGTCCTCAAAAGC 1073
                         iv   vvv i  --  i  v  vii   v --  -  v v vi       
  L1M4_orf2#LINE/    562 CGTGACCTTGGG--TTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGC 608

  chr20_6252941_6   1074 AATTACAACAAAACCAAAAATTGATAAGTGGGGCCTAGTTAAACTAAAGA 1123
                          vvvi        vv      v     i v  i i vi i   v v  i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr20_6252941_6   1124 GCTCCTGCACAACAAAAGAAACTATCAATGA-GTAAACAGACAACCTACA 1172
                         i  ii  ii vv    i  v        vi -  i  v        i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr20_6252941_6   1173 GAATGGCAGAAAGTATTTACAAACTATGTGTCCAACAAAGGTCTAATATC 1222
                               v     i     i    ii  i i  ii i  i  v  vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr20_6252941_6   1223 CAGAATCTATAAAGAACTT---------AACAATCAAAAACCAAATAAGC 1263
                               v           i---------  i   v    iv       v 
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr20_6252941_6   1264 CCATTAAAAAATGGGCAAACGACATGAACAGACACTTCTCAACAGAAAAC 1313
                          v   ?             v  iv    i     i     v v    i i
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr20_6252941_6   1314 ATGCAAGTGGCTAACAA--ACATGAAAAAATGCTCATCATCAGTAATCCT 1361
                           i   i    i  i  --         i       v     ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.79 (140 / 78)
Gap_init rate = 0.02 (21 / 874), avg. gap size = 3.19 (67 / 21)  


3320 25.06 0.88 0.66  chr20_6256253_6260539.rev     2890  3795 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_6256253_6   2890 TGGAAATATATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2939
                               v          i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_6256253_6   2940 GACCATACTGCCAAAAGCAATCTACAAATTCATTGCAATCCCCATCAGAA 2989
                          i v     v  v   vii       i     vi        i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_6256253_6   2990 TACCACCATCATTCTTCACAGAATTAGAAAAAGC--ATTCTAAAATTTAC 3037
                          v   v vv v  i  ii     v v  v  -  --  i        i i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr20_6256253_6   3038 ATGGAACCAAAAAAGAGCCCACATAGCCAAAGCAAGACTGAGCAAAAAAG 3087
                               viiv  ii  v  viv         i   vvi   i-   i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA-AAAGAAG 198

  chr20_6256253_6   3088 AACAAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTATAAGGC 3137
                               vi      vv       v  ii        viv     i  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_6256253_6   3138 -ATAGTCACCAAAACAACATGGTACTGGTATAAAAATAGGCACATAGACC 3186
                         - i   v i   i   iii         i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_6256253_6   3187 AATGGAACAGAATAGAGAACCCAGAAATAAATGCAGATACTTACAGCCAC 3236
                                i     v    ii           iv  v i i   ii i  -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA- 347

  chr20_6256253_6   3237 ACCCAAATACTTTGACAAAGCAAACAAAAGCATATAGTGGGGAAAGGACA 3286
                          ii--i  -i  i     i vviv   i v   vi i         i i 
  L1M4_orf2#LINE/    348 ATT--GAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_6256253_6   3287 CCCTTTTCAACAAATGGTGCTGGGACAATTGGTAAGCCATATGTAGGAGA 3336
                         vi                          i   vv ?   i   i ii   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_6256253_6   3337 ATGAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATG 3386
                              ii    i  ii i   v    v           i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_6256253_6   3387 GATTAAGGACTTAAACCTCAGACCTAAAACTATAAAAATTCTAGAAGATA 3436
                            i ?i   i    iv v   v              v ii       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_6256253_6   3437 ACATTGGAAAAACCCTTCTAGACATTGGCTGAGGCAAGGATTTCATGACC 3486
                             v  ?iv  vi    vv   v    v v      v i    v iivi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_6256253_6   3487 AAGAACCCAAAAGCAAACCCAATAAAAACAAAGATAAATAACTGAGACCT 3536
                          v  vv         v vv   i    iv   i   i    v vi   i 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_6256253_6   3537 AATTAAACTAAAGAGCTTTTGCATGGAAAAGGA-ACAGTCAGCAGAGTAA 3585
                         v  i   v v  i i      iiivvv      -  vi   iv i   i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_6256253_6   3586 ACAGACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGAC 3635
                          v              i           v  ii   vii   i      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_6256253_6   3636 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATCCGTAAGAA 3685
                           i  i  vi          v  i  v      vv    v  vi   v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_6256253_6   3686 AAAAACAA----TCCTATCAAAAAATGGGCTAAGGACATGAATAGACAAT 3731
                            i    ----i  v  i?          v     iv          v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_6256253_6   3732 TCTCAAAAGAAGATATACATATGGCCAACAAATATATGAAAAAATTCTCA 3781
                             v              v        i  ii i       i  v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_6256253_6   3782 ACATCACTAATGAT 3795
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (127 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


 376 24.39 0.00 0.00  chr20_6440855_6442838      491   572 (1412)    L1M4_orf2#LINE/L1      213   294 (614)  

  chr20_6440855_6    491 ACCCAGCCTTCCTGTTTTCTAATCATATTGCAAAACTATATTAATTAAAA 540
                           i  vv     iiv    v  v v  i i    i   i v    i  i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr20_6440855_6    541 CAGTATGGTACTGGCATAAGAATAGATATGTA 572
                             i               i     i  i  
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATA 294

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.00 (0 / 0)  

2766 20.93 0.64 1.28  chr20_6440855_6442838      867  1492 (492)    L1M4_orf2#LINE/L1      287   908 (0)  

  chr20_6440855_6    867 GATACATAGACCAATGAAACAGAATGAAGAGCCCAGAAATAAACCTGAAC 916
                           i i     i     i  i     vi    i             iiv  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr20_6440855_6    917 ATTTATGATCAATTGATTTTTGACAAAGCTGCCAAGAATATATAATGGGG 966
                                i            i     i v        vi  vi       
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr20_6440855_6    967 AAAGGAGAGTCTCTTCAATAAATGGTGCTGGGGAAACTGGATATACACAT 1016
                             i v     i     i             iv         ?v     
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr20_6440855_6   1017 GTAAAGGAATGAAACTGGATCTTTATCTTATAACACACACAAAAGACAAA 1066
                          i   i       ii    i ii  i  -------     v v v     
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCT-------CACACCATATACAAA 479

  chr20_6440855_6   1067 AGTCAATTCAAAATGGATTAATGACCTAAACGTAAGATCTGGAAATGTAA 1116
                          i i  i           i ?v        i      v  ii  v i   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr20_6440855_6   1117 AATT-TTATAAGAAAACATAGGAGAAAAACTCCTTGATATTGGCCTTGGT 1165
                           i -   v             ? v   v  i v   iv    vi v  i
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr20_6440855_6   1166 GATAATTTTTCAGATATGACACCAAAAGCTCAGGCAACAAAAGCAAAAAT 1215
                         i  ii   i i                  v  i          v      
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr20_6440855_6   1216 AAACATGTGGGACTACATCAAACTAAAAATCTTCTGCATAGCAAAAGAAA 1265
                          i i vi v     v       v v    v   i  iiivv    i  v 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr20_6440855_6   1266 TAATTAATAAAATAAAAAGACACCCTACAGATTGGGAGAAAATATTTTCA 1315
                         iv  i  v   i i        v  i     v               v  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr20_6440855_6   1316 AACCATCTATCTGATAAGGAA-TTATATCCAAAATACGTAAAGAACTCAC 1364
                           i   v            i -  i      i    ii          vi
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr20_6440855_6   1365 ACAACTCAGTAGAAAAAAGAAACA-AACCTGATTTAATAAATAGGCAAAG 1413
                                 i  iv       v v -    ii   ?  -    i       
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAA-AAATGGGCAAAG 828

  chr20_6440855_6   1414 AATCTGAATAGACGTTTCTCAAAAGGAGA-ACACAAGTGACCAGCAAGTA 1462
                         i  i         i      v    i   - i    i  i   ii   i 
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr20_6440855_6   1463 CATGAAAAAATATTCGACATCATTAATCTT 1492
                                 i  ii  i      ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (84 / 43)
Gap_init rate = 0.01 (6 / 622), avg. gap size = 2.00 (12 / 6)  


3029 17.39 2.90 0.16  chr20_6463948_6465553.rev      494  1114 (492)    L1M4_orf2#LINE/L1      271   908 (0)  

  chr20_6463948_6    494 TACTGGCA---GTATAGACATATAAATCAATGGAATGGAATGAAAAGTTC 540
                                 --- v           i           i    vi i   i 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr20_6463948_6    541 AGGAA-AAACTCATATAACTG-GGTGAAATGATTTTTGGCAAGTGAGCTA 588
                           i  -    i    i vi i-   v  v       i i    v v  i 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr20_6463948_6    589 AGGTCAGTCAATGGAGAAAGAACAGTCTCTTCCACA----GTGCTGGGAC 634
                           ii  v       i       i     i   v   ----          
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr20_6463948_6    635 AA-TGGATATCCACATGCAAAAGAGTGAAGTCAGATCCTTACCTCACATT 683
                           -      ?              i      ii  i  i         ii
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr20_6463948_6    684 ATATGCACAAATTAACTTCAAATGAATCAAAGACTGAAATATAAGAGCTA 733
                             i  v         iv     i    ?    iv    i         
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr20_6463948_6    734 AAACCATAAAACACTTAGCAAAAAAACATAGAGATAAATCTTTAAGCCCT 783
                             i       v     -  i         i?i        iiv v   
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAG-AAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr20_6463948_6    784 TGGATCTAGCAATGGTTTCTTAGATATCACACCAAAGGCACAAGCAACAA 833
                            i ivi                   v        i             
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr20_6463948_6    834 CAGAAAAAA-AAATAAATTGAACTTCAT-AAAATTAAAAATTATTTTGCA 881
                         v        - i        i       -           i v  v   v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr20_6463948_6    882 TTATAAAACATTATCAAAAGAGTAAAAA-ACAATCCACAGAATGGGATAA 930
                          i v ii   i      i i   i    -    i             v  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_6463948_6    931 AATATTTGCAAATCATATATCTGGAAAGGATCTAGTATCCAAAAAATATA 980
                                                iv    iv  v       i  v     
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr20_6463948_6    981 AGGAAGTCTTACAACTCAACAACAAAGA---AAACAACTCCATTAAAAAA 1027
                          i   v             i  i   i ---   i   i v   ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_6463948_6   1028 TGGGCAAATGATT-GAAT-GACATTTCTCTAAAGAATATATAGAGATGAT 1075
                                 v    -    -          i      v     v i   ii
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr20_6463948_6   1076 AAACATGTACGTGGAAAGATACGCAACATCACTAGTCAC 1114
                         v  i v i  i  i      i v        ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.97 (69 / 35)
Gap_init rate = 0.02 (12 / 638), avg. gap size = 1.58 (19 / 12)  


3288 19.48 3.25 8.17  chr20_6474689_6479322     3188  4142 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_6474689_6   3188 TGTAAAGACATCTTGTGTTCACATATTAGAAGACTTAATATTTTTAAGAT 3237
                           v     i   iii      iiv   i              v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_6474689_6   3238 GGCAATATTCATTAAAGTAATTGAGAGACTGAATACAACAATCCTAATAG 3287
                                i  vii   v i  iv v   i v  ii   ------------
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAA------------ 88

  chr20_6474689_6   3288 GCTTTCTTATAAAAGAGAGAATCCCAGTTTGCTTTTCC-CAAAAATTGAC 3336
                         --- i i   v   ------       i vv     ii-  i        
  L1M4_orf2#LINE/     89 ---TCCCTATCAAA------ATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chr20_6474689_6   3337 AAACTGATTGTAAAATTCAAATGGAAATGCAAGAAATCTAGAATAGCCAA 3386
                           i     iv         v             ii i i           
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr20_6474689_6   3387 ACTAATCCT-----AGAAAAACAAAATTGAAGGTCTCAAAATTCCAAATT 3431
                          vi    i -----    i      i   i   v    v v    v    
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr20_6474689_6   3432 TCAAAAC-------AAAGCCATAGCAATTGAGACAGCATG-TACTAGCTT 3473
                                -------     i i  i   ii      ii  -    i  v 
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr20_6474689_6   3474 AAGGATATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCATCTATC 3523
                                -------------------------------------------
  L1M4_orf2#LINE/    280 AAGGATA------------------------------------------- 286

  chr20_6474689_6   3524 TGTCTGTCTGTCTTATCTATCTAAATGGAATAGAATCGAGGGTTTACAAA 3573
                         --------- v v   vv   --             i   i  ii v   
  L1M4_orf2#LINE/    287 ---------GACATATAGATC--AATGGAATAGAATTGAGAGTCCAGAAA 325

  chr20_6474689_6   3574 TAAACCCTTATTATTTGTGCTCAACTGACTTTTAAACAAAGATAGCAAGG 3623
                                v  i-    i  v    i   -    vi    i i iv    i
  L1M4_orf2#LINE/    326 TAAACCCATAC-ATTTATGGTCAATTGA-TTTTCGACAAGGGTGCCAAGA 373

  chr20_6474689_6   3624 CAATTCAATGAAAAAAGAACAGT-TTTTCAACGAGCAGTCATGGGAGAAT 3672
                          v        iii      i   -        i iii  vv     v  i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr20_6474689_6   3673 TGTATATCCACATGTAAAAATCATGAGGCTGTGTTCCTACCTCACAAAAT 3722
                           v   ?       i    i-v    i i  viii           vv  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAG-AATGAAGTTGGACCCCTACCTCACACCAT 472

  chr20_6474689_6   3723 ATG-AAAATTTAACTCAAAATCAATCATAGACCTAA-TCTGAGAGTGTGA 3770
                           i-    v            vi    ?        - v i    ivvi 
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr20_6474689_6   3771 ACTATAAA-TTCTTAGAAGAAGGCTT-GGAATAAATATTTGTGGCCTTGA 3818
                                 -i           ii v -  ?i     v  i   i     i
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr20_6474689_6   3819 TTCAGGCAATGATTTTTTAGATGTAACACCAAAAACACAAATGACAAAAT 3868
                         v i        i   i      i i         i     iii      v
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_6474689_6   3869 AAAAAATAGGTTAATTGTACTTTATCATAATTAAAATCTTTTGTGCTGCA 3918
                                  i v     v    i    v        v          v  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_6474689_6   3919 AATAATACAATCAAGAAAGTGAAAAGACCACC-ACTGAATGGAAAAAAA- 3966
                           vi i  v                   v   -  v      i i    -
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_6474689_6   3967 ATTTGCAAGTCAAATTTGTAAAAAGAGACATGTACCTAGCATATATGGAG 4016
                                 i   v  v v i v   i   v    i i  v      ii  
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_6474689_6   4017 AGCTCTTACAATTCAATAATGAAAAG----------TAAGTTAAAAATAG 4056
                          i         i        i     ----------i  v ?      i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_6474689_6   4057 GTAAACAATTTGAATAGGCATTACTAAAAATAAGATATACAAATGACTAA 4106
                          i   vi          i    v  vv   v              i i  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_6474689_6   4107 TAAAAACATAAAAAGATGCTCAACATCATTAGTCAT 4142
                            iv    i                  ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (114 / 68)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 5.74 (109 / 19)  


2550 25.06 2.47 0.91  chr20_6482555_6485286.rev     1471  2240 (492)    L1M4_orf2#LINE/L1      127   908 (0)  

  chr20_6482555_6   1471 GAAAACCTCAATCTAAAGTTTATACAGACAGGCAAAAGACCCAGAATAGC 1520
                           v  v  v vi     i  i   ii  v v    ii             
  L1M4_orf2#LINE/    127 GACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGC 176

  chr20_6482555_6   1521 CAACACAATACTGAA---GAAGAGCAAAGCTGGAGGACTGACATTACCCA 1567
                            v     vi    ---     i     i         v   i v    
  L1M4_orf2#LINE/    177 CAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr20_6482555_6   1568 ACTTCAAGACTTACTAGAAAGCTGCAGTAATCAAGACAGTGAGATATTGT 1617
                          i     i        v      i                 v i  i  v
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr20_6482555_6   1618 TGAAAGAATAGCCAAATAGATCAGTAGAACACAATAGAGA-TCCAAGAAA 1666
                         iiv   i    v  v        i i   i v   v    -    -    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA-GAAA 325

  chr20_6482555_6   1667 TAGACCCACATAAATATAGTCAATTGATCTTTGACAAAGGGGCAGAGACA 1716
                           i     i i vv   i          i  i     i  v  vi    v
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr20_6482555_6   1717 ATAAGATGGAGGAAAGACAGTCTTTTCAACAAATGCTGCTGACATAACTA 1766
                           vvi    i i  ii i                 v     iv i    i
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr20_6482555_6   1767 GACATCCATGTGCAAAACACATATGAATCTATATACAGGCCTTACACCCT 1816
                           i ?   ii       v ---     vi iv iv vvi   i     v 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGA---ATGAAGTTGGACCCCTACCTCACACCAT 472

  chr20_6482555_6   1817 TCACAAAA-TTAACTCAAAATGCATCATAGACCTCAATGCAAAACACAAA 1865
                         vi      -             v    ?      v    i  i vvi   
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr20_6482555_6   1866 AATATAAAAGT---AGAAGATAACATAGGATAAAATCTAAATGATCTTGC 1912
                          v       v ---      v        ?vv      vvi   i    v
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr20_6482555_6   1913 ATATGGAGATGACCTTTT-GATAGAACATCAAAGGCATGATCCATGAAGG 1961
                         i vv  vi   iii i  -    vi   i    i   ii v v ii  i 
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_6482555_6   1962 AATAATT-GATAAGCTAAATTTAATTAAAATGGATACCTACTGCTCTG-A 2009
                           v  v -     ii ii i  v  i     vi v v  vi  iv  v- 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_6482555_6   2010 AAAGACAATGTTAGAAGAATGAGAAAACAAGCCACAAACTGGGAGGAAAT 2059
                           i    v i i ii i i   i  i    v     i v      i    
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_6482555_6   2060 ATTTGTAAAAGACACATATGATAAATGACA-GTAGACCAAAATATACAAA 2108
                              i   vv i i  v      iv   v-   v-   i      i   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTAT-CCAGAATATATAAA 771

  chr20_6482555_6   2109 GAACTCCTTA-AACTCAACAATAAGAAAACAA------CAATTAAAAAAT 2151
                               -   -       i     i  i    ------     ?      
  L1M4_orf2#LINE/    772 GAACTC-TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr20_6482555_6   2152 GAGCCAAAGACCTTACCAAACACCTCACCAAAGAAGATATACAGATGGCA 2201
                          i  v  i  ii v vi i   ii  v                i     v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr20_6482555_6   2202 AATAGGAATATGAAAAAAATCCTCTGTATCATATGTCAT 2240
                             i v i       i - v   vii    ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (110 / 79)
Gap_init rate = 0.02 (15 / 782), avg. gap size = 1.73 (26 / 15)  


 717 29.76 3.17 0.40  chr20_6723562_6725173.rev      100   351 (1261)    L1M4_orf2#LINE/L1       16   274 (634)  

  chr20_6723562_6    100 TGTTCATGTATTCAAACACTCAATGGAGTAAAAATATCAGTTCTCCCCAG 149
                                 v   vi  v   i   ivv  v  i  iv  i v       i
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr20_6723562_6    150 ACTGATATGCAGGTTTAACAGAATTCC-AACAAAAACCTAGTATGGTATT 198
                          i    v i   i  i   iv   i  - v     v  i  i-  viv  
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC-TGCCTTT 114

  chr20_6723562_6    199 TTTGTAGATACAGGTAAGATTATTCTGAAATGTATATGGAAAAGCAAAAG 248
                             i   v iv ii   v v  i  i    vi         v    ii 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr20_6723562_6    249 AACTGGAATAACTAAAACTATTCTATAAAAGAAGAA---AGTGAGGGGAA 295
                          v ii     i i     v  ii iv          ---   vi i   v
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr20_6723562_6    296 TCACTGTACCTTATTTCAAGACTTAC---ATAGCTATAATTGTGAAAAT- 341
                             vv v  iv       i      --- v     i i vi v  i i-
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr20_6723562_6    342 GTATGATACT 351
                           i  i    
  L1M4_orf2#LINE/    265 GTGTGGTACT 274

Transitions / transversions = 1.34 (43 / 32)
Gap_init rate = 0.02 (5 / 259), avg. gap size = 1.80 (9 / 5)  

1744 22.42 8.23 4.35  chr20_6723562_6725173.rev      501  1120 (492)    L1M4_orf2#LINE/L1      265   908 (0)  

  chr20_6723562_6    501 GTATAGTATTAGCAAACAGATTGACATATAGATCAATAGAAGAGAATAAA 550
                           i i   i i   v vi   v               i   v     vi 
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr20_6723562_6    551 GAACCCCAAAACAGCCCCAC---TTCGATATGAAAAACTGATTTTTGACG 597
                           ii  vi   i iv    i---  ---    ivv  i       i   i
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATT---TATGGTCAATTGATTTTCGACA 361

  chr20_6723562_6    598 ATGGT---AAAA---TTCAATGAAGGAAGAACCTGTTTTTTCCAACCAAT 641
                          v   ---  i ---       ii i     -- iv i   i    v   
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAA--TAGTCTTTTCAACAAAT 409

  chr20_6723562_6    642 GGTGCTGGAGTAATTGGATATCCATAGGCAAAAA----------GACCCC 681
                                 iii  i      ?   i v      i----------      
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr20_6723562_6    682 TAAACCTTACATGTTATATAGATATTAACTCAAAATGGATCAGGATCATA 731
                           --   i   ivv    i i v                   ------? 
  L1M4_orf2#LINE/    460 TA--CCTCACACCATATACAAAAATTAACTCAAAATGGATCA------WA 501

  chr20_6723562_6    732 GATTTAAATGTAAA--TTAA-----TAAAATTTTTAGGA-AAAACATAGA 773
                           ii         i--i   -----     i i    i -         i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_6723562_6    774 AAAAAGCCTTCAAGACCTAGAACCTGGCAAAGAGTTGTTAGACATGACAC 823
                         ?iv  ii    iv     v iiiiv     v iv  v     i       
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_6723562_6    824 CAAAAGCAGAATCCATAAATGAAAAATT-GATAA-TTTGATCTCATCAAA 871
                                 v  v v i   v      v -     -  v  ii        
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_6723562_6    872 AATAAAAAAAATGAAAAAGATTTGT-----AAAAGATCCTATTAAGA--- 913
                          v      v-- --------     -----   i  iv    i    ---
  L1M4_orf2#LINE/    652 ATTAAAAAC--T--------TTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_6723562_6    914 TGAAAAAAGACAAGCTACAGACTGAGAGAGAAAATATTTGCAAATCACAT 963
                               --     v i     v  i    --                i  
  L1M4_orf2#LINE/    692 TGAAAA--GACAACCCACAGAATGGGAGA--AAATATTTGCAAATCATAT 737

  chr20_6723562_6    964 ATCTGAGAATAGATTCATATCTAGATTATATAAAGAAGTCTTAAAACTCG 1013
                               v  vi  i ii    i   v           v     v     i
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_6723562_6   1014 TTAA-----AAATAAGCAATCCAATTAGAACATGA-CAAAAAAAATGAGG 1057
                         v   ----- i i  ii  i      ?i  v   i-    ii vv   iv
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_6723562_6   1058 AGA---TTTTTTATTGAAGG-----AAGTGGCAAAAAAGCACAAGGAAAT 1099
                            ---  i ii vv    i-----  i    v  v       v i   v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_6723562_6   1100 ATGTTCAATATCATCAGGCAT 1120
                            i    i    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (85 / 50)
Gap_init rate = 0.04 (23 / 644), avg. gap size = 3.39 (78 / 23)  


2783 24.90 2.62 1.05  chr20_6735341_6737452      495  1257 (855)    L1M4_orf2#LINE/L1       52   826 (82)  

  chr20_6735341_6    495 GCTATTCTCTCCAAATTGATCTATAGGTTCAACACAATCCCTATTAGAAT 544
                           v  v   i             i  i      i          i i   
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_6735341_6    545 CCCAGCAGACTTTTTTTTTAAAAATGACAAGCT-------AAATTATATA 587
                               v v       vivi   v         -------     -i   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT-CATA 150

  chr20_6735341_6    588 TGAAAATGCAAAGGACCCAAAATAGCCAGAACAACTTTG-----GGGGAA 632
                           i        i       i        i     ii   ----- ii   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_6735341_6    633 AAAGGTTGAGAGATATATATTTTTCAATTATAAA-CTTACGGTAA--CTG 679
                         v  i    iii  ivi i i  ii     vi   -     vii  --  i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_6735341_6    680 CAGTAATCAGGACAGCATGGCAGTGTAATAAGGGTAGACATA--GATTAA 727
                                  i     ii   i v  vv      i        --   i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_6735341_6    728 AGGAGTGGCATTGAAAGTAAAAAAATTAAGTCTCATATTTATGGTAAGTT 777
                         v   i i v     i   vv i    v  vi vi i         v i  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_6735341_6    778 TATTTTTAACAAAGTTACTCTAATAATTCAATGGGGGAAAGGATTGAGTT 827
                         v     ii    i v i ivvi iv           -    i  v vv  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTCTT 399

  chr20_6735341_6    828 TTCAACAAATGGTACTGGGAGAATTGTCTATCCATTTGCAAAAAGAAT-A 876
                                      i      v  i  vv  ?   iv       -    - 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGA 448

  chr20_6735341_6    877 ATTCAGACTCCTACCTCATATCATGCATAAAA-TTAACTTAAAGTTTATC 925
                          v ii   i         i i   ii i    -      i   i vv   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_6735341_6    926 ATCTGCCTAAAAGAAAAATACAAAACTCTAAAACTTCTGGGAGAAGAAAC 975
                          ?vvi      v v  i vvi      v       ii i i    --   
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA--AAC 546

  chr20_6735341_6    976 ATAGTAGGAACTCTTTATGGCATTGTGATAAGCAAAGAGTTCTTAGATAT 1025
                             v? v  v    ii  i v   v v  i    v iv           
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_6735341_6   1026 GGCGCTAAAAGTAAGATCCATAAAACAAAAATTTTGTGCAGTGGGCTTCA 1075
                          i i i     i vi v v i    v     v vvi iv v   i     
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_6735341_6   1076 TTTAAATTAAAACCTTTAGTACTTCAAAAAAAAACACCATTAAGAAA-TG 1124
                          iv         v    v  i       ii ---   i  i      -  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGA---CACTATCAAGAAAGTG 693

  chr20_6735341_6   1125 AAAAGATAAACCACAAGCTGGGTAAAAATATTTGCAATTCATATATCTGA 1174
                               i  v     iiv    vi             v            
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_6735341_6   1175 TAGGGGACTAACATCCATAATATCAAAAAAACTTTTACAAGTCAATATCA 1224
                           i      vii     v     vv   i    i      v      vi 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_6735341_6   1225 AGAAAAGCAACAACCTAATTAAATAATGAACAA 1257
                          i  i vv  i    i    ?  v    ii   
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

Transitions / transversions = 1.42 (109 / 77)
Gap_init rate = 0.02 (13 / 775), avg. gap size = 2.15 (28 / 13)  

 454 10.81 12.61 0.00  chr20_6735341_6737452     1510  1620 (492)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr20_6735341_6   1510 CTCAAAAA-AGAAAGA--AATAAT--AATTAA--------CAAATTATCT 1546
                              v  - i     --     i--    ? --------    vv  i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr20_6735341_6   1547 GAATAGATATTTTACCAA-GAAGATATACAAATGGCCAATAAGCACATGA 1595
                                i    iv    -                               
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr20_6735341_6   1596 ATAGATGCTCACCATCATTAGTTAT 1620
                          v         v     ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.83 (5 / 6)
Gap_init rate = 0.04 (5 / 125), avg. gap size = 2.80 (14 / 5)  


1061 32.07 5.78 1.39  chr20_6933373_6935711        1   502 (1837)  C L1M4_orf2#LINE/L1   (284)   624   101  

C chr20_6933373_6    502 TTCCAG-TAACTTATTTAGAGACATGGACAAGATTTTTCTAAGATGCATA 454
                          i    - iv   v   iv   v  v      v vv i    i  v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr20_6933373_6    453 GAGAAAAATGCA---GATCATAGAACAGTTAAAAAATAATCTTGACAAAG 407
                         vi    --    ---  i -i    i  ii    --i        v    
  L1M4_orf2#LINE/    151 TGGAAA--TGCAAGGGACC-CAGAATAGCCAAAA--CAATCTTGAAAAAG 195

C chr20_6933373_6    406 GAGAGTAAAGTGGGAAGAATCACAGGGCCTGGTGTTTACTCTTACTCTGT 357
                         i   ii     v   i  v     vvv  iii v iv vv      viiv
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

C chr20_6933373_6    356 AGCCACAA----CAAGACAATGTGG------CAGAGGGATAGATACCTAG 317
                            i   i----       i     ------  v i       i iv   
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

C chr20_6933373_6    316 TTTAACATGACAAAACAGAAAACCCAGAA-TAGACTCACATACATAAATG 268
                         v i  iivi i i  iv  i ii      -  i  i  --     vv   
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTATG 343

C chr20_6933373_6    267 -TAACTTAATTTT-GATGAACGTACAAAAGCAATTCAATGCGAGATGGAT 220
                         - v v  i     -  ii iv  i v  ii v        v ii v i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

C chr20_6933373_6    219 AGCTTTTTTAACATATGGTAATGGACCAACTGAACATCTGTTGGCCACA- 171
                           ii    i    v     iv   iv      i i ? iiivv  v v -
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

C chr20_6933373_6    170 AATGAACTTCAACTTCAACTCCAAAATTTACATAAAAATTAACT-AAAGT 122
                               v  vi  ii v  ii  v viv  i i           -   i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

C chr20_6933373_6    121 GAATCGTGAACTTAAATGCCAAACATATAACTATAAAGCTTTGAGAAAAA 72
                          i   i?ii  i      iv i vv  v         i  i v    i  
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

C chr20_6933373_6     71 GA---AGAAAT---TTTTCAGGATTTAGGACTAAGCA--GAGTACTTAGG 30
                         i ---  i?i --- i   iv  ii v  ii  i   -- iv v     i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

C chr20_6933373_6     29 CA--GCACCAAAACCACAGTCTGTCAAAGAA 1
                         i --i        v    iv viiv      
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAA 624

Transitions / transversions = 1.55 (96 / 62)
Gap_init rate = 0.03 (17 / 524), avg. gap size = 2.12 (36 / 17)  

3222 23.28 4.54 0.81  chr20_6933373_6935711      981  1839 (500)    L1M4_orf2#LINE/L1        1   891 (17)  

  chr20_6933373_6    981 TAGAAAGATATTTCATGTTCATAGATT---AAAC-----------AAAAT 1016
                          i         ii         i    --- i  -----------  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_6933373_6   1017 -----TACTACCTGAAGTGATTTAAAAATTTCAATGAAAACCCTAT-AAA 1060
                         -----    v  ii  v    i  v i   -   i v  v      -   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT-CAACGCAATCCCTATCAAA 99

  chr20_6933373_6   1061 ATTCCAA-TGTCCTTTTTATAGAAATAGACAAAATAATCTCAAAAATTCA 1109
                           i   i-  i i     ii      v     iv i   - v        
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC-CTAAAATTCA 148

  chr20_6933373_6   1110 CATAAAACCACAAAAAAAAAACCCA-AAT-GCCAAAGAAATCTTTAGCCA 1157
                         i  ii  vii   iii ----    -   -      iv      v ivv 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA----CCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_6933373_6   1158 AAAGAACAGAGTTGGGGGCAGTACATTACCTGATCTCAAAAAT-ATTACA 1206
                         i       i      i  vvvi   i v  ii  i      v - i    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_6933373_6   1207 AAGCTATATTAATGTAAAAAA---TGATACTGACATAAAAATAGACATAT 1253
                               i v    -i  i v ---  i     i     ii          
  L1M4_orf2#LINE/    245 AAGCTACAGTAAT-CAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr20_6933373_6   1254 TGATAAATGTAAGTGGAGAGACAGCCCAGAAATAAATTTACACATTTACT 1303
                         v   v    v  vv i vv  v  i           iii i       iv
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr20_6933373_6   1304 CTCAATCGATTTTTGACAAAGGTGCCAACAATACACAATGGGGAAAGGGA 1353
                         v     i      i     i        v vi iv            iiv
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_6933373_6   1354 AATCTCTTCAATAAATGGTGTTGGAAAAACTGGATATCCACATGCAGAAG 1403
                          i   i     i        i   i v         ?         i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_6933373_6   1404 AATGAAACTGGACCCTTTTTT---ACCATATACAAAAATTAACTCAAAAT 1450
                               ii       i vii ---                          
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_6933373_6   1451 GGATTAAAGACTTAAATGTAAGATGTGAATCTCTAAAACTAT---AAGAA 1497
                             i ?    i           vv i  v  v       v ---     
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_6933373_6   1498 AACATGGAGGAAAATCTCCAAGACATTGGCCTGAGCAATAATTTCTTTGA 1547
                              i i? v      i iv   v    vi ii     ii      v  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_6933373_6   1548 TATGACCCCAAAAACATAGGCAACAA--GCAAAAATGGACAAATGAGATT 1595
                               v      i  i i       -- v      i  i    vi  i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_6933373_6   1596 ACATCAAACTAAAAAGCTTCTCCACAGCAAAGGAAAT----AATAGAGTG 1641
                         v       v v    i   i vii vv       v i----  v i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_6933373_6   1642 AAGACAGAAGCCATGGATTGAGAGAACATATTTGCAAATCATACATCTGA 1691
                           i v v  v   ii  v  i     v                i      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_6933373_6   1692 TAAGGGAATAATATCCAAAATATGTAAGGAACTCAAACAACTTAACAGCA 1741
                                v vi      i     i   i      vv      i  i ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_6933373_6   1742 AGAAAACCAATAATCCTATCTAAAAATGGGCAAAGGACCTGAGTAGATAT 1791
                          i  i  v     i  v  i?                ii   i    i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_6933373_6   1792 TTCTCAAAAGAAGACATATAAATAGCCAATAGATATATGTGAAAATAC 1839
                              v        i   i    i       iii i   vi  i  i 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

Transitions / transversions = 1.80 (126 / 70)
Gap_init rate = 0.02 (17 / 891), avg. gap size = 2.71 (46 / 17)  

 698 28.93 1.65 0.83  chr20_6933373_6935711     1843  2084 (255)    L1M4_orf2#LINE/L1      166   409 (499)  

  chr20_6933373_6   1843 CCTAGACTAGCTAAAACAATCTTGACAAAGGAAAGTAAAGTGGAAGGAAT 1892
                           i   v    i             v    i i ii     v i    v 
  L1M4_orf2#LINE/    166 CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACT 215

  chr20_6933373_6   1893 CACTGAACCCAGTGTTTAGGCTTACCCTATAGCCACAGTAATGAAGATGA 1942
                            vvvv    i v iv ii     ivi v   i        v    iii
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAG 265

  chr20_6933373_6   1943 TGTGGTATCAGCAGAGGGATAGATACATAATTCAAAGAAATAAAATGAAA 1992
                                iii   v i       i i   iv    v i    i   vi i
  L1M4_orf2#LINE/    266 TGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAG 315

  chr20_6933373_6   1993 CACCCAGAAATAGACACAAACAAATA-AGTCTAACTTAATTTT-GACAAA 2040
                         vii         i  v  v   vv  -i   -  -  i     -     i
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTC-AA-TTGATTTTCGACAAG 363

  chr20_6933373_6   2041 CATGGAAAAGCAATGCAATGGGGGAAAAA--ATCTATTTAACAGAT 2084
                         vi  vv  ii v  v        i  i  --i   v  i    i  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

Transitions / transversions = 1.50 (42 / 28)
Gap_init rate = 0.02 (5 / 244), avg. gap size = 1.20 (6 / 5)  


1390 29.16 8.73 4.48  chr20_6979489_6981559.rev      709  1579 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_6979489_6    709 TGGAGAAATATGCCATACTTAT--------------AATAT-ATTAGGAT 743
                             i i    v    ii i  --------------     -i   i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_6979489_6    744 ------ACTC---AAATTATTCTGCAGGTTTAATTCAATTCTAATCAAAA 784
                         ------    ---     iv   i   i  i  iv    i iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_6979489_6    785 TTTCCTCATATTATTTGATTGTATGTATTTGTGTGTATATTCAGAGACTA 834
                          --- i  ---------ii  iv ---   v  iiv v   v v ii  i
  L1M4_orf2#LINE/    101 T---CCCA---------GCTGCCT---TTTTTGCAGAAATTGACAAGCTG 135

  chr20_6979489_6    835 ATTCTAAAATGCATATTCAAATGTAAAAGTTCAAGGATATATAAAAAAA- 883
                           i       v     vv     i  ii vi v  i   vvi    v  -
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr20_6979489_6    884 ---GGAAATTTGTAGAAGAGCATATTTGAAACCCTTACACTACTAGATTT 930
                         --- i   -----      i  v v   i ivv  i     v ivi    
  L1M4_orf2#LINE/    186 CTTGAAAA-----AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr20_6979489_6    931 AAGGA--TATTATTCAGCTACAATACATAAAATGGTGCGGTAGTGGCACA 978
                         v ii --  i  ivv       i  vvi  i ii   i    v     i 
  L1M4_orf2#LINE/    231 CAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr20_6979489_6    979 ACCATATACAAATAGGATAATATAACAGA-----GCACCCAGAAACAGAC 1023
                          vv   v   v    ivi   iv  i   ----- vii       i i  
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr20_6979489_6   1024 ACACATCTACATGGACACTTGAGTA-AGACAAAGG---CAGTACTGCATA 1069
                         v  i iv vi    v  v    v v-v     i  ---  iv  --   -
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC--CAT- 377

  chr20_6979489_6   1070 GTAGTGGGGAGAGGATAGTCTTTTCAATTAGTTGTGTTGGATTAACTGGA 1119
                         vi i      i  i             iv i v   i   ivi       
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr20_6979489_6   1120 TATTTACATGAAAGAAAATGAATTTTGACCTTCATACCACACTA-ATTAA 1168
                           ?ii     v  i i      v  v    iii ivi     i -  -- 
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT--A 475

  chr20_6979489_6   1169 CAAA---TAACT--GAGTG-ATTTTACATCCAAATGT--GAACTATAAAA 1210
                             ---     --i i  -  iv? v i i      --  i   --   
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA--AAA 523

  chr20_6979489_6   1211 CAGTAACACTTTTAAAAGAAAACATGAGACTATA-CTT-GTGATCTTAAA 1258
                          vi   v   i   i          ii ?v  v -   -    i   iii
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr20_6979489_6   1259 GTACACAA-ACTATCCTAAACAAGAT-------GCATTAACCATAAACGG 1300
                         v  vi   -iv v  i  i i v  i-------   iv i v i   -i 
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA-AG 622

  chr20_6979489_6   1301 AAAAACATAAATACATTTTAGACTACATTAAAATTTAGAAGTTCCCATAA 1350
                              -   i   v   --i    v   i      - i  ii iiii iv
  L1M4_orf2#LINE/    623 AAAAA-ATAGATAAATT--GGACTTCATCAAAATT-AAAAACTTTTGTGC 668

  chr20_6979489_6   1351 TT-AAAACACACCATTAGGAGCATGAATAAGA-AAGCTGTAGAGTAGGAA 1398
                           -   iv    i  i i  ivi    -    -  v iii   i i   i
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAA-AAGACAACCCACAGAATGGGAG 717

  chr20_6979489_6   1399 AAGACA----CATACCATATGTATAATTGACAAAGGACTTGTATACAGAA 1444
                           i i ----  v i     i ----i   i  i          v     
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATAT----CTGATAAGGGACTTGTATCCAGAA 763

  chr20_6979489_6   1445 TGTATACA-AGTTCCCACCAATCTATAAGAAAAAGA-GACTAGCT-AATA 1491
                          i    v - ii  ii  v v  v    v       -i v  i i-   v
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr20_6979489_6   1492 CAAAATTGATGAGAG---------AGGTATTTCACAAAAGAGGATATCCA 1532
                         ?    v  ivv i  ---------  ii     v v     i     v  
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr20_6979489_6   1533 AATAATCAAAATGGATATATAATAATACGTTCAACTTCATTAGTTAT 1579
                            iii   -- iiii i  i v  v i i     v   ????????
  L1M4_orf2#LINE/    864 AATGGCCAA--TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (159 / 91)
Gap_init rate = 0.04 (40 / 908), avg. gap size = 2.88 (115 / 40)  


3530 24.22 1.00 0.44  chr20_7027196_7031376     2796  3695 (486)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr20_7027196_7   2796 AAAAAAATTTCATGTTCGTGGATTGAAAGAATCAATCTTGTTAAAATGTC 2845
                            i v  ii       i       i    v i   v       i   v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr20_7027196_7   2846 CATACCACCCAAAGCAATCTACAGATTCAATGCAATCCCTGTCAAGGTAC 2895
                         v    iv      vii              i         i    ii v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_7027196_7   2896 CAATGACATTCTTCACAGAA-TAGAAAAAACAATCCTAAAATACATATGG 2944
                           iivi v  i  ii     - v  v  ivii          v       
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr20_7027196_7   2945 AACCACAAAAGGCCCAGAATAACCAAAACTATTCTAAGAAAAAAGAACAA 2994
                           vii   ii i         i       v  ii i i   i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr20_7027196_7   2995 AACTGAAGGAATTACAGTTCCTGACTTCAAATTTTACTACCGAGCAATAG 3044
                          ii  i    v i   v    ii i      vi       vi   v i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr20_7027196_7   3045 TAACCAAAGCAGTATGGTACTAGCATAAAAACAAAAACATAGACCAATGG 3094
                            i   ii    i       i      ii i i v i     i      
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr20_7027196_7   3095 AACAGAATAGAGAACCCAGAAAGAAATCCACACACCTACAATGAACTCAT 3144
                           i     v    ii       v   i   i   ii  iii v  i v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr20_7027196_7   3145 TTTTGACAAAGGTACCAAGAACATACACTGGAGGAAAGATAGTCTTGTCA 3194
                            i     i   i      v   v  v   i i  ii        v   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr20_7027196_7   3195 ATAAATGGTGCTGGGAAAACTGGATATCCACAT-CATAAGAATGAAACTA 3243
                          i              v         ?      -  v         ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr20_7027196_7   3244 GACCCCTATTTCTCACCATATACAAAAATAAAATCAAAATGCATTAAAGG 3293
                                 ii  v                v  v        v  i ?  i
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr20_7027196_7   3294 CTTAAATCTAAGACCTTGAACTATGAAACTACTACAATAATACATTGGGG 3343
                          i     v     v  vi      i     vi  v  v  v    v  ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr20_7027196_7   3344 AAGATCTTCAGGACATTGGTCTGGGCAAAAATTTCTTGAGCAATACTCTA 3393
                         v i      iv   v    vi i     vii      iiii vv  v i 
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr20_7027196_7   3394 CAAGCACAGGCAAGTAAAGGAAAAATGGATGAATGGGATT--ATCAAAGT 3441
                         v       i    vv    i      i   i   v   i --      i 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr20_7027196_7   3442 TAAAAAGTTTTCT-CTCAGCAAAGGATACAATCAACAAGGGGAAGATAAA 3490
                               v    v -  i--       i  v     v  i v   i v v 
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr20_7027196_7   3491 ATCCATACAATGGGAGAAAATATTTGTAAACTACTCATCTGAGAAGAGAT 3540
                          i   i v                  i   ii ivi      v   i  i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr20_7027196_7   3541 TAATAACCAGAATATATAAGGAGCTCAAACAACTCTATAG-AAAAAATTC 3589
                          vi  v             i  i   vv       v   i-     iviv
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr20_7027196_7   3590 AGTAATCTGATC-GAAAATAGGCAAAAGATTTGAATAGACATT-CTCAAA 3637
                          i   i ii  i-i     i      i                -   v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr20_7027196_7   3638 AGAAGACATAAAAATGGTAAACAGGCATATGATCAGAGAAATGCAA-ATC 3686
                               i   v      iv  i i   i    -- i   viiv   -   
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGA--AAAGATGCTCAACATC 899

  chr20_7027196_7   3687 AAAACTACA 3695
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.76 (137 / 78)
Gap_init rate = 0.01 (10 / 905), avg. gap size = 1.30 (13 / 10)  


3275 26.87 0.44 0.44  chr20_7045081_7051346.rev     4867  5774 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_7045081_7   4867 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4916
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7045081_7   4917 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4966
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_7045081_7   4967 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5014
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_7045081_7   5015 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5064
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_7045081_7   5065 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5114
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_7045081_7   5115 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5164
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_7045081_7   5165 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5212
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_7045081_7   5213 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5262
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_7045081_7   5263 CTATTGAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5312
                           v  v  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_7045081_7   5313 GAAACTCGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5362
                            ii v  i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_7045081_7   5363 TTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAAC 5412
                          i ?   ii    i  v i v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_7045081_7   5413 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5462
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_7045081_7   5463 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5512
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_7045081_7   5513 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5562
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_7045081_7   5563 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5612
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_7045081_7   5613 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5662
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_7045081_7   5663 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5712
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_7045081_7   5713 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5762
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_7045081_7   5763 ATCACTGGCCAT 5774
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2277 27.27 3.61 4.16  chr20_7151735_7154257.rev     1121  2033 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_7151735_7   1121 TGGAAAGACTTCCTTTGCTCATGGATTGGAAAAATTAATATGCTTAAAAT 1170
                                 iv   iv  i             i v       vv    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7151735_7   1171 GAGCATATTATCCAAAGCAATACATAGATTAACTGCAATTCTTAGCAAAA 1220
                          ivv   i vi     vii  vi i     v vi     i i  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_7151735_7   1221 TACCAATGACATTTTTCACAGAAATAAAAAAA--AATTCTGAAATT-GTA 1267
                          v   iivi v     ii       vi v  i--i  i  i     -i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_7151735_7   1268 TGGAACAATACAGGAAAAAAAAAAAGATCCTAAGCATCCGAAGGAATCCT 1317
                              --  i  ---------- ii  i  vi ii v  i  iv    i 
  L1M4_orf2#LINE/    151 TGGAA--ATGCA----------AGGGACCCAGAATAGCCAAAACAATCTT 188

  chr20_7151735_7   1318 GAGCCAAAAGAGCAAAGTTGGAGGA---ACAGTTT--------AAAATAT 1356
                           ivv i    i             ---   v  i--------    iv 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr20_7151735_7   1357 ATTGCAAGGCTATATTAA------CAGCATGATATTGGTAGAAA-ACAGA 1399
                          i i   i    i v   ------   ii  i  i   i v  i- i   
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr20_7151735_7   1400 TACATAGACTAAGGGAACA-AGTAAAGAACTCAAGAATATATCTACGTAT 1448
                         i i     ii  v    i - i vi   iii  ii    v i i iii  
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr20_7151735_7   1449 TTATAGCCTAGTGATTTAAAACCAAAGCACCAAGAACATACATTGGAGAA 1498
                             i i v v      vvi  v ii ii      v   v  v   i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr20_7151735_7   1499 AGGATACCCTCTTCAATAAATGCTGTTGGGAAACCTGGATATCCATCTGC 1548
                           i   vi  i     i     v  i     v v       ?   iv   
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr20_7151735_7   1549 AGAGGAATGAAACTAAAGCCCTAACTCCTGACATATACAAAAAAAAAAAA 1598
                          i i       ii ii v     v   viiv            vv  ---
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA--- 485

  chr20_7151735_7   1599 AAAAAAAAAACTTCAAAAATGGATTCAAGACTTAAATGTAAGACCTGAAA 1648
                         -----------i      -     iv?    i           v  i   
  L1M4_orf2#LINE/    486 -----------CTCAAAA-TGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr20_7151735_7   1649 TTATGCAATTACTAGAAGAAAACACAGGGG-AAGGCCTCCCAACCATCAG 1697
                         i   iv  i vi            i   ? -  iv i  vii   v vi 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr20_7151735_7   1698 TATAAGCAAGTATTTTATGGCAAAAATCTCAAAAATCACAGACAACAAAA 1747
                          -  i    vvi   iv i vv vi ivi     i-    ii        
  L1M4_orf2#LINE/    574 T-TAGGCAATGGTTTCTTAGATATGACACCAAAAG-CACAAGCAACAAAA 621

  chr20_7151735_7   1748 CTGAAAATAGACAAATGGAATAATATCAAA-CTAAAAACCT--GCACAAT 1794
                         vvi        i    v i ivvi      -i       i -- ii vvi
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr20_7151735_7   1795 AAAGGAAAC-----AAAAAGTGAAGAGACAAAATATTTAATGGAAGAAAA 1839
                               v  ----- i        i      vvi ivv     i      
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr20_7151735_7   1840 CACTTGCAAACTATTCATCCAACAAGGGACTAATAACCAGAAGATACAAA 1889
                         i i       ii  vi   ii i        vi  v      v   i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr20_7151735_7   1890 GAACTCAACCCACTCAACAGCTAACTGAATAAATAG-CAAATAGTCTTAT 1938
                               vvv v      i ---------     v  -      ii iv  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATA---------ATAAAAAGACAAATAACCCAAT 812

  chr20_7151735_7   1939 TAAAAAGTGTGCAAATGCTTTGAATAGACTTTTCAACAAAGAAGATATAC 1988
                          ?    i  v     v v           v    vv              
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr20_7151735_7   1989 AAATAGGCAACAGGAATATGAAAA-ATGATCAACATAACTAAACAT 2033
                             i v   i i v i       -   v       v ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (149 / 96)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.55 (71 / 20)  


1217 22.43 4.05 2.18  chr20_7226651_7230326.rev     1666  1986 (1690)    L1M4_orf2#LINE/L1        1   327 (581)  

  chr20_7226651_7   1666 TGAAAAGACATGCTGTATTTATGAATTG-AATACTTACTACTGTTAAGCT 1714
                           i     i  v ii i  i   i    -  v     v  i       v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7226651_7   1715 ATCAATACTACCTAAAGCTACCTACAAATTCATTGCAATCCCTATCAAAA 1764
                         iv       v  i   viv i     i     vi                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_7226651_7   1765 TACCAATT----TTTTTGTAGAAATAGAAAAA--AATCCATTTGAAAATA 1808
                          v   ii ----      i      v  v  i--i    --- -     v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCC---T-AAAATT 146

  chr20_7226651_7   1809 TGTATGGAATCTCAAGAGATCCTAAATAGCCAAAACTATGCTGAAAAAGA 1858
                         ii       viv    i  i  vi            v  vi         
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_7226651_7   1859 A---CAAAGTTAGAGGACTCGTGCTTTCTGATTTCAAAATTTACTATATA 1905
                          ---       i        iii   i ii         i      i v 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_7226651_7   1906 GCTACAGTAATCAAAACAGCGCAGCACTTGCATAAATACAGAGATTT--- 1952
                                       i    i ii i   v      iv i   v  v ---
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_7226651_7   1953 TCACAGATAGGAGAGAATAGAGAACTCAGAAATA 1986
                            ---  i i v     v    iii        
  L1M4_orf2#LINE/    297 TCA---ATGGAATAGAATTGAGAGTCCAGAAATA 327

Transitions / transversions = 1.88 (47 / 25)
Gap_init rate = 0.02 (8 / 327), avg. gap size = 2.50 (20 / 8)  

2467 19.76 1.87 1.70  chr20_7226651_7230326.rev     2599  3185 (491)    L1M4_orf2#LINE/L1      321   908 (0)  

  chr20_7226651_7   2599 AGAAATAAACCCTTGAAGATGTGGTCAAATAATTCTTAACAAGAATACCA 2648
                                     v iv vv i       v i   i ii     ii i   
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr20_7226651_7   2649 AATTCATTTAAAAAGGAA-GACCATA---TTTTTAACAA-TGGCACTGGG 2693
                          ivi    i  vii    -  --   ---    i     -   ii     
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGA--ATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr20_7226651_7   2694 AAAACTGGACGTCCACATACAAAAGAATGAAGTTGGTCTCTTCCCTTAAG 2743
                          v       ii?      i                 v i i v   i vi
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr20_7226651_7   2744 TCCAATAACAAAATTAACTAAAAATAGACCAAAGACCTAAACAGAAGAGT 2793
                         i vv   vv          v     i  i  ?         iiv     i
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr20_7226651_7   2794 TAAAG-TATAAAACTCTTATATGAAAAAAAAATAGGAGGGAAATTCCATG 2842
                             i-             ---   i    v     ? vi  vi i i  
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTA---GAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr20_7226651_7   2843 ACACTGGATTTAGCAATTATTCCTTGGATAAGACAC-AAAAGCACAGGCA 2891
                           vi   i  vi     vi  i   i    v     -         i   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr20_7226651_7   2892 ATGAAAGGAAAATAATATTAATAAATTGGACTTCATCAAAATTAGAAACG 2941
                          ii    i    --   --i                        i    v
  L1M4_orf2#LINE/    616 ACAAAAGAAAAA--ATA--GATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr20_7226651_7   2942 TTT-TGCATCAAAACACACTAATTAACAGATTGAAAAGGCAACTCACAGA 2990
                            -   v     iv      - i  v i v       i    i      
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr20_7226651_7   2991 ATGAGAGAAAATATTTGCAAATCACATATCTGATAAGGGATTGATATCCA 3040
                            i                    i               i vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr20_7226651_7   3041 GAATATATAGAGAATAATTAATATTCAACAACAAAAA-ACAAA--ACCCA 3087
                                  i    ivv   vv i    i  i     -     --     
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr20_7226651_7   3088 TTTGAAAAATGACCAAGGGTCTTGAATAGACATTTCTTTAAAGAAGACAT 3137
                         v  ?       iv   i  vi                ii        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr20_7226651_7   3138 ACAGGTGGCCAATAGGCATGTGAAAAGATGCTCAATATCCCTAATCAT 3185
                            ii         i   ii               i   v????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.95 (74 / 38)
Gap_init rate = 0.02 (13 / 588), avg. gap size = 1.62 (21 / 13)  


2683 25.85 3.74 1.52  chr20_7269853_7272114      908  1762 (500)    L1M4_orf2#LINE/L1        1   874 (34)  

  chr20_7269853_7    908 TGGAAAGGCATTCCATGCACAAGGATCAGAAGAAACCTAATGTTGTTAAA 957
                                ii  i     iv  v    ii     -- i    i       i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGA--CTTAATATTGTTAAG 48

  chr20_7269853_7    958 ATGACTATGCTGCCCAAAGCAGTCTGCAAATTCAAGGTAATTCCTATCAA 1007
                            i v  i  v      viii   i  i      v i   i        
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr20_7269853_7   1008 AACACCAA-TGTCATTTTTAACAGAAATAGAT---TTAAA---AAAATTT 1050
                           iv   i-  i v     i-       v  i---i i v---      i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr20_7269853_7   1051 GTATGGAACCCAAAAGGAGACTGAATAGCCAAAGAGATCCTAAGCAAAAA 1100
                         i       vivv  i   vv v           ivi   i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_7269853_7   1101 GAACAAAGCTGGAGGCATCATACTACCTAACTACAAAATATATTACAAGG 1150
                                 i      vv   i   v  i  i v     iv  i     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_7269853_7   1151 TTGTAGTAAGCAGAACATCATGATAGTGGTATTAAAAACAGACA-A-AAA 1198
                         i ii     v  ii   vii  i  v   i  -  ii i     - - i 
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAGA 296

  chr20_7269853_7   1199 CCAATGGAACAAAATTGAGAATCCAGAAATAAATCTGCCTGTTTATAGAC 1248
                         i        i i        i            i iiivii     i v 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_7269853_7   1249 AATGTATTTTTGACAAAAATGCCAAAAACATACATTGGGGAAAAGATGCT 1298
                            vv     i     iii      i v   v  v        ii  iv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_7269853_7   1299 TTCTTCAATAAATGATCCTGGGAAAATTGGATATTTATATACAGAAGAAT 1348
                         i i     i     i v      v  i      ?ii i  i  i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_7269853_7   1349 GAAATTATAAACCTATCTGTAACTATA---AAAAATTAACTCACAATAGA 1395
                            i  iv vv    i  vvv  i   ---             v   i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_7269853_7   1396 TTACAGAATTAAATGAAAAACCCAAAACTATAAAACTAGTAGAAGAAAAC 1445
                          i ?   vi      v  i v i              vv           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_7269853_7   1446 ATAG-TGAAAACACTTCAGGATGTTGGTCTAGGCAA---------AAA-- 1483
                             -? v   i-    iv  iv    vi       --------- i --
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_7269853_7   1484 -------AAAAAAAAAAAAAAAAAAACTTCAAAAAATAGACAAATGGGAT 1526
                         -------    iv v  iv  v    v---          i    v   i
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAG---AAAAAATAGATAAATTGGAC 642

  chr20_7269853_7   1527 TGCATTAAACTGAAAAGCTTCCACACAGCAAGAGAAACAGTCAACAGAGT 1576
                          v   i   v v    i   iiiii vv   ii  v  vi    v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr20_7269853_7   1577 GAAGAGACAACCTGATGAATGGGATAAAATATTTACAAACTATTTATCTG 1626
                            i        iivv        v         i    ii  v      
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_7269853_7   1627 ACAAAGGGCTAATATCCAGAGTGTACAAGGAACTCA-ACAACAATAACAA 1675
                          i  i  i  vi        i i  i  i      v-     -- --   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC--T--CAA 788

  chr20_7269853_7   1676 CAACAAAATATACAAATAGTCCCATTAAAATGTGGGCAAAATACATGAAT 1725
                         i  i    - v       ii  v   ?   vi        iv iv     
  L1M4_orf2#LINE/    789 TAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_7269853_7   1726 AGACATTTCTCAAAATAATACATACAAATGGCCGACA 1762
                                    v   v  v i            i i 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.71 (137 / 80)
Gap_init rate = 0.02 (18 / 874), avg. gap size = 2.50 (45 / 18)  


2497 28.29 2.56 1.45  chr20_7340588_7342911.rev      936  1833 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_7340588_7    936 TGGAAAAACGTTCCATGCTCAGGGATTAGAAGAATAAAAATTATTAACAT 985
                               i ii i     i   v     i     v v  v   i    v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7340588_7    986 GGCCATAAGGCTGAAAGCAATCTGCAATTTCAATGCTATTTGTATCAAAC 1035
                            v   vvv iv   vii    i  iv     i  v  iiv       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_7340588_7   1036 TATCAAA-GTCATTTTTGACAGAACTAGGAAAAAACT-ATTCTAAAAT-- 1081
                          vi  iv- i v      -     v v -- v  i  -  i       --
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_7340588_7   1082 --ATGAGTCAAA---AAAGAGCACGGA-TAGCCAAAGCAATCGTAAGCAA 1125
                         --   i---   ---  i ii v i  -        i     v i iv  
  L1M4_orf2#LINE/    148 ATATGG---AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_7340588_7   1126 AAAGAGCAAAGCTGAAGGGATCACATTTAACCAACTT-AAAACTCTACTA 1174
                         i    i     i  i   iv     i  v-    i  -      -     
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTC-CCAATTTCAAAACT-TACTA 242

  chr20_7340588_7   1175 TAAGGCTACAGAAACCAAAATAGCATAGTACTGGTACAAAAACAGACACA 1224
                         i  i       v  i   i i  ii i       i i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr20_7340588_7   1225 CAGACCAATGGATCAGAACAGAGAACCCAGAAATAAAGCTGCACACTGAC 1274
                         i   i       vi    iv    ii           v iii   i v i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr20_7340588_7   1275 AGTCATCTGATCTTTGACAAAGTGGACAAAAA-A---AATGGGGAAAGTA 1320
                         i    vi    i  i     i vv v   i v- ---           v 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr20_7340588_7   1321 CTGCCTATTTAATAAGTGATACTGGAATAGCTGATTAGCCATATGCAGAA 1370
                         iv i  v  i  i  i  i i    i i i   iv  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_7340588_7   1371 GAATAAAATTGTACTCTTACTTTTCGCCATATTCAAAAATTAACTCGAG- 1419
                             i  i   v  i i   i iv i      v             i i-
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_7340588_7   1420 -GGATTAAAGATTCAAATGTAAATCCTCAAA-TAAAAGAATCCTAGAAGA 1467
                         -    i ?   iii        ivv  v   -  v  i v  i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_7340588_7   1468 AAACCTAGGAAACATAATTCT--G-GACATCAGCCTTGGGAAAGAATTTA 1514
                             v    ?i---   v   -- -   v ii vi v  v  v iv  iv
  L1M4_orf2#LINE/    543 AAACATAGGNG---TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr20_7340588_7   1515 TGACTAAGTCCTCAAA--CTCAATTGCAACAAAAACAAAAATTGACAGGT 1562
                          iiv  v v vi    -- v   --         iv      v  i ii 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAA--GCAACAAAAGAAAAAATAGATAAAT 637

  chr20_7340588_7   1563 GGGTCCTAATTAAGCTAAAGAGTTTCTGCACAGCAGAAGAAACTATCAAC 1612
                         v  v i v  i  iv v  i ii  i  ii vv  i i  v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_7340588_7   1613 AGAGAAAACAGGCAACTTTCAGAATGGGAGAAAATATTTTAAAACTATGC 1662
                          i  vi  v  i    iiv                    vv   ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_7340588_7   1663 ATCTGACAAAGGTCTAATATCCAGAATCTATAAGGAACTAAAACAATTCA 1712
                               i  i  v  vi          v     i     vvv    i   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_7340588_7   1713 ACAAGCAAAAAACAAATTACCCCATTAAAAAATGAGGAAAAGGCAGGAAC 1762
                          i  vv    i      v    v   ?       i v   i iivv   i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_7340588_7   1763 AGATAACTTTCAAAAGAATATATATAAGTAGACAAGAAACATATTTAAAA 1812
                            i vi i  v      v     i  i i v   v  i  i  vv   i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_7340588_7   1813 ATGTTCCACATCGCTAAACAT 1833
                            i  v     i????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (151 / 99)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 1.80 (36 / 20)  


2835 26.78 4.60 0.23  chr20_7375238_7377836.rev     1238  2107 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_7375238_7   1238 TAGAAACACTTCCCATGCTCATGGGTGGGAAGAATAAATATTGTGAAAAT 1287
                          i    v iv       i      i v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7375238_7   1288 GATCGTACTGCCCAAAGCAATCTACAGATTCAATGGAATTCCCATCAAAA 1337
                          iivi    v      vii              i v   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_7375238_7   1338 TACCATCATCATTCTTCACAGAACTAGAAAACACAATCCTAAAATTCATA 1387
                          v   v vv v  i  ii     v v  v  vvii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_7375238_7   1388 TGGAACCAGAAAACAGCCCACATAGCTAAAGCTATGCTAAGCAAAAATAA 1437
                              viiv  iiv v  viv     i   i v  vi i iv  i  v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_7375238_7   1438 CAAATCTGGAGGGATCACATTACTTGACTTCAAA--TTATTCTACAAGGC 1485
                             vi      iv     i v iii i      --   --      i  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGC 248

  chr20_7375238_7   1486 TATAGTTACCAAAACAGCATGGTAGTGGTATAAAAATACACACATAGATC 1535
                           i   v i   i    ii     v   i    ii   v   i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_7375238_7   1536 CATGTAACAGAATAGAGAATCCAGAAATAAAGCCAAATACTTATAGCCAA 1585
                         v   v  i     v    i            v   v i i    i i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_7375238_7   1586 CTGATCTTTGATGAGGCATCCAAAAACATAAATTGGGGAAGAGACACCCT 1635
                         i    i  i  ii   vvv    i v   vv v       iii i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_7375238_7   1636 ATTCAATAAATGGTGCTAGGAAAACTGGCAAGCCACATGTAGAAGAATGA 1685
                         v     i          i   v      vv ?       i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_7375238_7   1686 AACTGGATCCC-ATCTCTCACCTTACACAAAACTCACCTCAACATGGATC 1734
                          ii    i   - i   v    v  i      v i v     v       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_7375238_7   1735 A--------------------AAAACTA-----------GAAGATAACAT 1753
                          --------------------       -----------     v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_7375238_7   1754 CAGGAAAACTTTTCTGGACATCAGCTTAGGCAAAGAATTTATAACTAGGT 1803
                         vi ?iv  v i   vv   v ii v        v iv  iv  iv  v v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_7375238_7   1804 CCCTAAAGGCAAATGCAACACAA------ATAAATAAATGGGACCTAATT 1847
                          v i   i   v v      v  ------   i      v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_7375238_7   1848 AAACTAAAAAGCTTCTGTACAGCAAAAGAAATAATCAGCAGAGTAATCAG 1897
                            v v    i   i   i vv    i  v iv    iv i   i vv  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_7375238_7   1898 ACAACCCAAAGAGTGGTAGCAAATATTCACAATCTATGCATTGGGCAACA 1947
                                 v   i   v  v       ii   vii  ii  iv ii  vi
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_7375238_7   1948 GACTAGTATCCAGAATCTACAAGTAACTCAAACAAATCAGCAAAGAAAAA 1997
                             v           v  i  iv     vv    v   ii  vi    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_7375238_7   1998 ACAAATAATCCCATCAAAAAGTGGACAAAGGGCATGAATACACTTTTCTC 2047
                                 i  v  i?    i   i      iiv      v  v      
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_7375238_7   2048 TAAAGAAGATATATAAACAGCCAACAAACACATGAAAAAATGCTTAGCAT 2097
                         i            i   ii     i  i          i     i i   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_7375238_7   2098 CACTAACCAC 2107
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.21 (126 / 104)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 7.00 (42 / 6)  


3117 26.10 2.36 0.45  chr20_7393705_7397890.rev     2806  3694 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_7393705_7   2806 GAAAGATATTCCATGTGCATGGATTGGAAGAAA-AATATTGTTATAATGT 2854
                                  i      v              vv-          vi   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_7393705_7   2855 CCATACTACCCAAAGCAATCTAGAGCTTTAATGCAATTCCTGTCAAAATC 2904
                          v     v      vii     v  v  i  i     i   i        
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_7393705_7   2905 CCAATGACATTCTTCACAGAAATAGAAAAAACAATCTTAAAATTTACATG 2954
                            iivi v  i  ii       v  v  ivii   i       i i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_7393705_7   2955 GAACCATAAAAGACCCAGAAAAACCAAAGCTATCTTAAGCAA-AAGAACA 3003
                            viii  ii         v i     i v     i iv  -       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_7393705_7   3004 AAACTG-AGGAATCTCATTACCTGACTTCAAA--TTATTCTAGAGGGCTC 3050
                           ii  -    v  v  i v  ii i      --   --   v ii   v
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAAAGCTA 250

  chr20_7393705_7   3051 TAGTAACTAAAACAGCATGGTACTGGCATAAAAGCAGATATTTAAATCAA 3100
                         i     ii  i    ii              iiii   i  v  i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_7393705_7   3101 CAGAGCATAACAGAGAGCTCAAAAACAA-TCCACACACCTAAAGTGAACT 3149
                         ii  ii v  iv     ii  i   i  -i   i   ii  vi  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_7393705_7   3150 CATTTTTGACATAGGCGCCAAGAACACCTACTGGCAAAAAGACAGTCTTT 3199
                         v     i    vi  i       v  iii v   vi   ii i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_7393705_7   3200 TCAATAAATGATGCTGG-ATA--TAGATATCCATATGCAGAAGAATAAAA 3246
                             i     i      - i -- i    ?   i     i      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_7393705_7   3247 CTATACTCCTATTTCATGCCATATACACA---TGCC-----ATATAT-AC 3287
                         i iv  i    ii   ii         v --- iv -----  iv  - ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_7393705_7   3288 AGATC-AAATCTAAGATATCAAAATGCAAAACTACACAAAGAAAACGTTG 3336
                            i -    v     vv v   v ii      vivvi        i v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_7393705_7   3337 GAAAAAATCTTCAAGACATTGGTCTGGGCAAAAATTTCTTAAATAATCTT 3386
                          ?iv        iv   v    vi i     vii       i   vvviv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_7393705_7   3387 CCAAAAGCATAGGCAACAAA-GCAAATATGGACAAATGGGATCATATCAA 3435
                                  i i        - v   v  i  i    v   iivi     
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_7393705_7   3436 A-TTAAAAGCTTCTTCATGGCAAAGGAAACAATCAACAAAGTGAAAAGAC 3484
                          -      i   i viiivv       v  v     v             
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_7393705_7   3485 AGTCCACAGAATGGGAGAAAATATATGCAAACTACCCATTTGACAAGGGA 3534
                          ii                     v      ii ivi  i   i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_7393705_7   3535 TTAATATCCAAAATACATAAGGAGCTTTAACAACTCTGTGGGAAAAAAAG 3584
                         i vi      i    i    i  i  i v       vi iiv     i -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA- 799

  chr20_7393705_7   3585 CATAATAATCTAATCAAAAAATTAACAAAGTATTTGAATAAACATTTTTG 3634
                           -     i i   i?      vii     v         i      i v
  L1M4_orf2#LINE/    800 CA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_7393705_7   3635 TAAAGAAGACATACAAATGGCAAACAGGCATTAGAAAAGGTGCTCAACAT 3684
                         i        i           v  i i   ivv      i          
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_7393705_7   3685 TATTGATCAT 3694
                         i ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.92 (150 / 78)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 1.56 (25 / 16)  


2622 27.12 2.90 1.56  chr20_7421038_7423904     1482  2377 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_7421038_7   1482 TGGTAATACATTCCATGCTCATGGATTGGAAGAATCAATATTGTTAAAAT 1531
                            v  v i  i     i               v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7421038_7   1532 GTTCACATTGCCCAAGGCAATCTACAGATTCAACACTATTCTTATCAAAT 1581
                          viv i i v     ivii               i v  i i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_7421038_7   1582 TACCAA-TGTCATTTTTGACAGAATTAGAAAAAAAAGAT-ATTCTAAAAT 1629
                          v   i-  i v      -     v v  v  ---- v -  i       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAA----GCTGATCCTAAAAT 145

  chr20_7421038_7   1630 ACATAGGGAACCAAAAAGAGCACA-AAGAGCTAAAGCAATCCTAAGCAAA 1678
                         v    v    viiv  i ii v  -  v   i   i     i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_7421038_7   1679 AAGAACAAAGCTGAAGGCAGGCAC-CACATT----GACTTCAAACTATAC 1723
                                   i  i   -----  -    i ----i i      viv   
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGG-----ACTCACACTTCCCAATTTCAAAACTTAC 240

  chr20_7421038_7   1724 TATAAAGCTACAGTAACCAAAACAGCATGGTACTGGTTAAAAAAATACAG 1773
                           i             i   i    ii         i- v  ii   v v
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC-ATAAGGATAGAC 289

  chr20_7421038_7   1774 ACATAGATTAATA-AACAGAATAGAGAACCTAGAAATAAAGCCAGACACC 1822
                          i      i   i-  i     v    ii i         v   v   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr20_7421038_7   1823 TACAAGCTACTGATCTTCGACAAAGTTGACAAAAATAAGCAATAGAGAAA 1872
                           iiiv v i    i        i v  v   i vi vv    i i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr20_7421038_7   1873 GGACTGCCTATTCAACAGTTGGTGCTAGAAAACCTGGCTAACTATACACA 1922
                          i iv i  v       iv       i i v v    v  ? i i ii  
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr20_7421038_7   1923 GAAGAATGAAACTGGACTCCTGCTTATCACTGTATACAAAACTTAACTCA 1972
                         i         ii     i   i i vv   ii         v        
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr20_7421038_7   1973 AGAGGGATCAAATACTTAAATGTAAAACCTCAAACTATCAAAATCCTAGA 2022
                          i v      ? v  i         i v  v       v   v  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_7421038_7   2023 AGAAAGCCTAGG---AAATACCCTTCTGGACAGCGACCTAGGTGAAGAAT 2069
                              i v    ---    ---    vv   vvi ivi    ii v iv 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_7421038_7   2070 TTGTAACTAAATCCCTGAAAGCAATTGCAACAAAAACAAAAATTGACAAA 2119
                          iv  iv  viv v ii      vvv         iv      v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr20_7421038_7   2120 TGGGACCTAATTAAACTAAAGAGCTTCTACACGGCAAAATAAACTATCAA 2169
                          v    i v  i   v v  i i   i iii vv    iv v        
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr20_7421038_7   2170 CAGAGTAAACATACAACATACTGAATGGGAGAAAATATCTGCAAACTATG 2219
                         v i   i  v v     vi  v                i      ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr20_7421038_7   2220 CATCTGACAAAGCATTAATATTCAGAACTTAGAGGAAACAA--ACAAATC 2267
                         i      i  i v i vi   i     iv  v iii   vv--    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr20_7421038_7   2268 AACAAGGAAAAAA-----------ATTAAAAAGTGGTCAAAGGTCATAAA 2306
                           i  vi    i -----------   ?    i   v      viv i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_7421038_7   2307 CACACACTTCTCAAAAGAAGACATA-AAACAGCCAAGAAACATGTTTAAA 2355
                         i v   i     v        i   -   ii     v  i  ii vv   
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_7421038_7   2356 AATGTTCCACATAACTAATCAT 2377
                         i   i  v    v ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (139 / 101)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.67 (40 / 15)  


1230 30.25 8.17 1.74  chr20_7462055_7465619     1826  2572 (993)    L1M4_orf2#LINE/L1       32   826 (82)  

  chr20_7462055_7   1826 GACTTAGTATCACAAAGATGTCAGTTCTCTTCAAATT---TTGTA----- 1867
                               i   iiiv      v  i v   ii      ---i ii -----
  L1M4_orf2#LINE/     32 GACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTC 81

  chr20_7462055_7   1868 ----TAATTCCAATAAAAATAT-AGAT---TTTTTTGATGGAAATTAAAA 1909
                         ----i   i  v  v     vi-  v ---       -ii      i v 
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG-CAGAAATTGACA 130

  chr20_7462055_7   1910 AGATGATTATAAAACTTATATGGAAATAACAAATGAATTGGCATATTCAA 1959
                           v    iv     i i          i-   iv  viii v   vi   
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATG-CAAGGGACCCAGAATAGCCAA 179

  chr20_7462055_7   1960 GACAATATTGAG---GAAGAAAAAAGC--ATGGATTTATACTATCAGATA 2004
                         i     v    i---      v    i--iv   i i i   vi vi  v
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr20_7462055_7   2005 TCTATACTTACTATAAAGCTATAGTAATTAAGACAGTGTAGTTACTCCAA 2054
                           v v        i       i      i          i  -   --ii
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT-ACT--GG 276

  chr20_7462055_7   2055 CAAAAAGAAAAAAAAATAG-TGGGAGAAACAAA---GAGAGTCTAGAAAT 2100
                           v  i  v i v v    - viiv i  i i ---       i      
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr20_7462055_7   2101 AGAACCACATGTTTATAGTCACTCAATCAT-GTCAAAGACAGCATTGCAG 2149
                          i v   i ii     i    v ii  iv - v   i iiiv  vvi vi
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr20_7462055_7   2150 TACAGTTGGTAAAGAA-GGACTTTTCAGTAAATTGTTCTGAGTAAATAAT 2198
                          v  i v  v      -i v       ii    v  v   i --- i  -
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG---ACAA- 422

  chr20_7462055_7   2199 CT--ATA-CAATATG-AGAAACATAAGACTGGACTCCTACCTCACAGCAT 2244
                           --   - v i   - i  iv  i iii     i           v   
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr20_7462055_7   2245 GTGCAAAAATTT-TTCCAGATTCATTATAGAACTAAACATAA------AA 2287
                         i i        v-i  v i  vv  i ?   v     ii   ------  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr20_7462055_7   2288 ATAATAATACTTTTAGAATAAAACACAGGATAAGAAATCT--GTAATTTT 2335
                          iv    v   i      v      i   ?--iv      --  i ii  
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGN--GTAAATCTTCGTGACCTT 570

  chr20_7462055_7   2336 AG---AAACA-----TTTTTA--TAGGACAATAAA-GCACTAACCATAAT 2374
                         i --- ii  -----  i   --  v    vi   -    v i v i  v
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr20_7462055_7   2375 GGAGATTGTTGATGAATTGGAGTCTATCAAAAGGAAGATCCATT---CAT 2421
                         i  i vvi v   i       v ii       vv  i v iv  --- v 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr20_7462055_7   2422 CGAA--ACAGAATTGACAGACTAAAAATATAAGCTAGATACAAGGAGAAT 2469
                          i  --   vv  ii v i v i    v i  v i v v vvi      v
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr20_7462055_7   2470 ATATGT-CAATGAATACGCTTTATAAAAGGTTTAGATCCAAAATCTATTA 2518
                             v -   vvv   iiii v    ii ii  iv     i   v   v 
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr20_7462055_7   2519 AATACTTCTACAAGTCAACAA--AGAAG-CAGGCGACACA-TTAAAAAAC 2564
                          iv   ii     v    i  -- i   -  iiii  v  -  ?     i
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr20_7462055_7   2565 AAGGGCAA 2572
                         --      
  L1M4_orf2#LINE/    821 --GGGCAA 826

Transitions / transversions = 1.48 (133 / 90)
Gap_init rate = 0.04 (34 / 795), avg. gap size = 2.18 (74 / 34)  

 256 20.00 2.73 3.64  chr20_7462055_7465619     2964  3073 (492)    L1M4_orf2#LINE/L1      800   908 (0)  

  chr20_7462055_7   2964 CAAA-AATACAATTTAAAAAACTGGGCAAAA-ATATGTAATATATACTT- 3010
                             -  iv     ?     --        i-  v  -    v i i  -
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAA--TGGGCAAAGGATTTG-AATAGACATTTC 846

  chr20_7462055_7   3011 TATAAAATAAATCATCCAAATGGCCAATAAACATAATAAAAGGTGTCCAA 3060
                          vi   iv i  -  v              i  i vv     i  ii   
  L1M4_orf2#LINE/    847 TCCAAAGAAGAT-ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_7462055_7   3061 TATCATTAGTCAT 3073
                         i    ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.06 (6 / 109), avg. gap size = 1.17 (7 / 6)  


3367 25.03 2.14 0.11  chr20_7471513_7475775     2885  3771 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr20_7471513_7   2885 AAAGATATTCCATGTTCATGGATTGAAAGAATCAATATTGTTAA-ATGTA 2933
                                 i                i    v i           -   vv
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr20_7471513_7   2934 CATACTGCTCAAAACAATCTACAAATTCAACACAATACCTATCAAAATGC 2983
                         v     v i    vii       i       i    v           v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_7471513_7   2984 CAACAATATTCTTCACAGAAATAGAAAAAGCAATCTTAAAATTCATGTGG 3033
                           i viiv  i  ii       v  v  ivii   i          i   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr20_7471513_7   3034 AACCATAAAAAGCCCAGAATATCTAAAGCCATCCTTAGCAAAAAGAACAA 3083
                           viii  iiii         v i   i v   i v iv  i        
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr20_7471513_7   3084 AACTGGAGGAATCACATTACCTGACTTCAAACTATATTACAGAATTTTAA 3133
                          ii       v     i v  ii i      viv  i    i ii vi i
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr20_7471513_7   3134 TAACCAAAACTGCATGGTAGTAACATAAAAACAGACACACAGACCAATAG 3183
                            i   i  v ii     v ii     ii i     i i   i    i 
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr20_7471513_7   3184 AACAGAATAGACATCTCAGAAAT-----CATACATCTTCAGTGAAGACAT 3228
                           i     v  v vii       -----       i vii  v  vvv  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr20_7471513_7   3229 TTTTGACAAAGGTGCCAAGAATATATATTGGGGAAAAAACAGTTTCTTCA 3278
                            i     i          vi  vi v        i  i   i i    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr20_7471513_7   3279 ATACATGGTGCTGGGAAAACTAGATATCCATAGGCAGAACAATGAATCTA 3328
                          i v            v    i    ?   i v   i  v      vi i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr20_7471513_7   3329 GACCCCTATCTCTTGCTGTATACAAAAATCAAACCAATATGGCTTAAAGA 3378
                                 i   vii ii           i  vi   v    v i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr20_7471513_7   3379 CTTAAATTTAAGACCTCAAACTATAAAACTACTAAAAAA-----TTGAGG 3423
                          i     v     v  v             vi  i  i ----- v i? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr20_7471513_7   3424 AAACTCTCCAGGTCATTGGTCTAGTCAAAGATTTCTTGAGTAATATCCCA 3473
                         v  v   i iv v v    vi   v   v i      iii  vv iv   
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr20_7471513_7   3474 AAAGCACAGGCAATCAAAGCAAAAATGGACAAATGGGATCATATCAAGTT 3523
                                 i    iv    v      i  i    v   iivi     iv 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr20_7471513_7   3524 TAAAAGCTTCTGCACATCAAAGAAAACTATCAACAAAATGAAGAGGCAAC 3573
                              i   i  ii v      i v        v   i    i  i    
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr20_7471513_7   3574 CCATAGCATGGAAGAAAATATTTGCAACCTAATTATCTGACAAGGGGTTA 3623
                            i  v    i               vii vv       i     ii v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr20_7471513_7   3624 ATAACCAGAATATATTAAAAGCTCAAAC-ACTCAATAGGAAAAAAAGGTA 3672
                         i  v           v  i i   vv  -        iv     i vi- 
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA-A 802

  chr20_7471513_7   3673 ATAATCCAATT-AAAAATGGGCAAA-CATCTGAATAGACATTTCTC-AAA 3719
                             i      -             -v  i                -   
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr20_7471513_7   3720 AAATACATACAAATGAC----AAGTGTATGAAAAAGTGCTCAACATCACT 3765
                         i  v i         i ----   iii       ii            ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr20_7471513_7   3766 GATCAT 3771
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.67 (137 / 82)
Gap_init rate = 0.01 (9 / 905), avg. gap size = 2.22 (20 / 9)  


2730 25.40 6.09 1.72  chr20_7486766_7488674.rev      548  1417 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_7486766_7    548 TGGAAAAACAACCCATGCTCATGAACAGGAAGAATTACTATCATTTAAAT 597
                               i i v      i     i iv      v   v   ii  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7486766_7    598 GACCATATTGCACAAAACAATATACAAATTTAATGCATTCTATATCAAAA 647
                          i v   i v v    vii  v    i   i  i   v  iv        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_7486766_7    648 TACCAG-TGTCATTCTTCACAGAAATAGAAAAA--AATTCCTAAAATTCA 694
                          v    -  i -  i  ii       v  v  i--i  -           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGAT-CCTAAAATTCA 148

  chr20_7486766_7    695 TAAGGAATCAAAAAGGAGCCTGAATAGCCAAAGCAATCCTGAGGAAAAAG 744
                           v    viiv  i   v  v           i     i   ii  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_7486766_7    745 GACAATGCTGTAGGAATCACATTACT--GCTTCAACATATATTACAAGGC 792
                         i    v i  v    v     i v i--ii     v iv  i     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_7486766_7    793 TACAGTCACCAAAATAGCTTAGTATTGCTACAAAAATTGACACATAGACC 842
                               v i   i i  iv i   i  vi i  ii  v    i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_7486766_7    843 AATGGAATGGAATAGAGA-CCCAGAAATAAACC-ACACATTTACAGTCAA 890
                                 i    v    -i             - i       ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_7486766_7    891 CTGATTTTTGACAAAACCAACAAGA--ATTTACCTTGGAGAAAGGACACC 938
                         i       i     iiviiv     --   i v--   i     i i v-
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAA--TGGGGAAAGAATAG- 395

  chr20_7486766_7    939 TTTTTTCAATATAGGGTGCTGGGAAAATTGTACAGCCACATGCTGAAGAA 988
                          i       i v v          v  i  v i ?        vi     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_7486766_7    989 TAAAACTGGACCCTTGTCTC-TATCATATA-AAAAATCAGCTCAAAGTGG 1036
                          i  ii       i ii   -i i      -      i i      i   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_7486766_7   1037 ATTAAAGACTTAATCATAAGACCTGAAATTATAACACTAATAGAAGAAAA 1086
                           i ?    i   vii     v  i   i     v   vv          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_7486766_7   1087 TCTGCAGAATAC-TCTTCTGGGTATTGGTCTAGGCAATAAATTT------ 1129
                         iv i-i ?i  v-     vv iiv    vi        iiv  i------
  L1M4_orf2#LINE/    546 CATA-GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_7486766_7   1130 -----------AGTGCAAG-------AGAAACAACAAATAAACGGGCCTT 1161
                         -----------  ii    -------     v  i i     iv  v   
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_7486766_7   1162 ----------AAAAGCTTCTGTACAGCAGGAAGAAATT--CAACAGAGTG 1199
                         ----------    i   i   i vv  i- i  v i --   v i    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACTATCAAGAAAGTG 693

  chr20_7486766_7   1200 AAGAGACAACCTGCTGAATGGAAGAAAATATTTGCAAATTATTCATCCTT 1249
                           i        ii v      i                 i  vi   ivv
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_7486766_7   1250 CAATAAACCAATATCCAGAATATACAAGGAATTCAAACAACTCAACAGGA 1299
                         i  vii  ivi             i  i   i  vv         i iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_7486766_7   1300 AAAAAACACACACACAAATAATCCCATTAAAAAGTGGGCAAAGGAGATGA 1349
                             i   --------     i  v   ?    i           vv   
  L1M4_orf2#LINE/    794 AAAAGACA--------AATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr20_7486766_7   1350 ATAGACATTTCTC---AAAAGACTTAAAAATGGCTGACAGTGACACAACA 1396
                                      --- i    iv  v       ii i ivv   ii v 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr20_7486766_7   1397 A--CGCTTAACACCACTAATCTT 1417
                          --i   i    i  ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (141 / 76)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 3.09 (68 / 22)  


3552 26.15 0.11 0.55  chr20_7531297_7535610     2913  3822 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_7531297_7   2913 GAAAAATATTCCATGTTCATGGACTGGAAGAATTAACATTATTAAAATGT 2962
                             i    i             i       v    i   i    i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_7531297_7   2963 TCATACTACCCAAAGCAATCTACAGACTCAATGCAATCGCTATCAAAATA 3012
                         iv     v      vii         i    i      v          v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_7531297_7   3013 CCATTAACATTCTTCACAGAAATAGAAAACATAATCCTAAAAGTTATATG 3062
                            vivi v  i  ii       v  v  vv i         v i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_7531297_7   3063 GAACCACGAAAGACTTAGAATAGCCAACGCTATCCTAAGCAAAAAGAACA 3112
                            vii i ii   ii           vi v   i i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_7531297_7   3113 CAACTGAAGAAATCACATTACCTGACTTCAAATTATACTAACAGAGCTAT 3162
                         v ii  i  i v     i v  ii i      viv     -  i     i
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA-CAAAGCTAC 251

  chr20_7531297_7   3163 GGTAACTAAACCAGCATGGTACTGGCATAGAAACAGACACATAGGTCAAT 3212
                         i    ii  iv   ii             iii i     i    i     
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_7531297_7   3213 GGAACAGAATAGAGAACTCAGAGACAAATTCATCTGCCTACAGTGAACTC 3262
                             i     v    iii    i i   ii   viiii  ii  v  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_7531297_7   3263 ATTTTTGACAAAGTTTCCAAGAGCATGTGGTAGGGAAAGAATAGTATCTT 3312
                              i     i v v      v   viii i             v i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_7531297_7   3313 CAATAAATTGTGATGGGGAAATTGAATATCTGTATGCAGAATGATGAAAC 3362
                            i    v   v    iv  i  i   ? iii     i  vi     ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_7531297_7   3363 TAGACCCCTATCTCTTGCTCTACACAAAAAAGTCAATTCAAAATGGATCA 3412
                          i        i   vii iv  i       -- i  i             
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAATGGATCA 499

  chr20_7531297_7   3413 AAGACTTAAATTTGAGGCCTCAACCTATGAAACTACTATGAATAAACATT 3462
                         ?    i     v i  iv  v  v    i     vi  vi iv      v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_7531297_7   3463 GGGAAAACTCTACAGGACATTGGTCTGGGCAAAAATTTCTTGAGTAACAC 3512
                           ?iv  v   v iv   v    vi i     vii      iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_7531297_7   3513 CCCACAAGCACAGGCAGCCAAAGTAAAAATGGACAAATGGGATCACATCA 3562
                         v   v       i   i v    v      i  i    v   iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_7531297_7   3563 A-GTTAAAAAGCTTCTGCACAACAAAGGATACAATCAACAAAGTAAAGAG 3611
                          -i       -   i  ii vv       i  v     v     i  i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_7531297_7   3612 ACAAGCCACAGAATAGGAGAAAATAATTGCAACCTACTCATCTGACAAGG 3661
                             v         i          v      vii ivi      i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_7531297_7   3662 GATTAATAACCAGAATACATCAGGAGCTCAAACAACTCTACAAGGAAAAA 3711
                           i vi  v        i  v i  i   vv       v i  vi    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_7531297_7   3712 ATCTAATAATCCAATTTGAAAATGGGCAAAATATCTAAATAGATATTTCT 3761
                          - v     i      ?i            iv  i i      i      
  L1M4_orf2#LINE/    799 A-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_7531297_7   3762 CCAAAGAAGACATATAAATGGCAAGCAGGCCTATGAAAAGGTGCTCAACG 3811
                                   i   i       v ii i  vi        i        i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_7531297_7   3812 TTATTAATCAT 3822
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.85 (152 / 82)
Gap_init rate = 0.01 (5 / 906), avg. gap size = 1.20 (6 / 5)  


 754 20.10 0.52 2.06  chr20_7541430_7546027     2772  2965 (1633)    L1M4_orf2#LINE/L1      718   908 (0)  

  chr20_7541430_7   2772 AAAATTAATTTGCAAATCACATATCTGATAATGGACCTATATTCACAATA 2821
                              --            i           v    i i   i  v    
  L1M4_orf2#LINE/    718 AAAAT--ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr20_7541430_7   2822 TATAAATAACTCATAAAACTTGATACTAAAGAGAGGAATATATCAATTTT 2871
                               v     v  v    ii   v    i   vi    vvi     ?-
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW- 814

  chr20_7541430_7   2872 TCAAAATGGGCAAAAACTATGAATAGGTATCTTTCTAAAGAGGATACACA 2921
                         -v            iiv v       ii  i i  i     i    i   
  L1M4_orf2#LINE/    815 -AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr20_7541430_7   2922 AATGTCTAAAATGGGCATGAAAAG-TGCTCAGCATTATTAATCAT 2965
                             v i  v v vi         -      i   i ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (22 / 16)
Gap_init rate = 0.02 (3 / 191), avg. gap size = 1.67 (5 / 3)  

1341 25.17 7.09 1.14  chr20_7541430_7546027     3038  3474 (1124)    L1M4_orf2#LINE/L1      130   592 (316)  

  chr20_7541430_7   3038 AAACTGATTCTAATATTTATTTGGAAAAACAAAGGATTTAAACTAGTCTA 3087
                           i     i    v   i  v      vi   i   iii i v   i v 
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr20_7541430_7   3088 CAGAATACTGA-------GAACAAAGTTGGAGGACTCACAGTACCCAACA 3130
                         v v   vi   -------                      v v     iv
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr20_7541430_7   3131 TCAAGACTTACTATAAAGCTCTACTTAATC----CAGTGTCATATTGGCA 3176
                             i        i      vi v -    ----      vi  i     
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGT-AATCAAGACAGTGTGGTACTGGCA 278

  chr20_7541430_7   3177 AAAGAATGAAGATATTGATTAATGAAATAGAATACAGAAACCAAAAACAG 3226
                         v   i  ii v    v   i    i        vv   iv   i   i i
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr20_7541430_7   3227 ACCTGTGCATATATAGCCAACTAATGTTTGACAAAG---TCCAGACAATT 3273
                            ii i   v   i i   i i  v  i     i ---i v    v   
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr20_7541430_7   3274 CAATGGATAAAGAATAGTACT--CAA-AAATTGTGCTAA---AATT---- 3313
                               iv          vi --   -    v     ii---  i ----
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr20_7541430_7   3314 -----TATGTCATAAAATGAACCTAGATACAGACCTCACATTTTAGAAAA 3358
                         -----i   iv v i      vi i  iv vv        iiv  v v  
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr20_7541430_7   3359 AAATTAAATCAAATTGAATCAAAGACATTCATGTAAAATACAAAATGATA 3408
                                v     v  i    ?    v vv      i vvi    iv   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr20_7541430_7   3409 AAACTTCTGGAAGGAAAACATAGTAGTAAATCT--GTGACTTTGTGTTTG 3456
                              ii i    -         v?        --     i   v   v 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAG-AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr20_7541430_7   3457 GTGATAAGTTTTGTTTAG 3474
                          ii  i-    i--    
  L1M4_orf2#LINE/    578 GCAATG-GTTTC--TTAG 592

Transitions / transversions = 1.30 (61 / 47)
Gap_init rate = 0.03 (12 / 463), avg. gap size = 3.00 (36 / 12)  

 921 24.20 4.78 1.91  chr20_7541430_7546027     3793  4106 (492)    L1M4_orf2#LINE/L1      586   908 (0)  

  chr20_7541430_7   3793 TTTTTATATATAACA----AAACACAATCCATAAAC-----AAT-GATG- 3831
                           i   v    i   ----  i     v v i   v-----   -   i-
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr20_7541430_7   3832 -TTAGACTTTTTTAAAAGTAAAA-CTCTTGATCTATGAAAGATGCTGTTA 3879
                         -  i     iv i    v     -  i   vv  vii  i  ii  i i 
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr20_7541430_7   3880 AGATATTGAAAAGAGGAGCCACAGTATGTGAAAAAAATATTTGCAAAGCA 3929
                            v v        vi v      v   - i i              v  
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATG-GGAGAAAATATTTGCAAATCA 734

  chr20_7541430_7   3930 CTTATCTGATAAAAGATTTGT-TCCAGAATATACAAAATAACACTGAAAA 3978
                         iv          ii  i    -           i   i-   v  v v  
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAG-AACTCTTACAA 783

  chr20_7541430_7   3979 TTCAGCAATGAGAAAACAAACAACTCAATTTTTTAAAAATTGGGCAAAAG 4028
                         i   ii   i i  i     i   i     ?---      -       i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTW---AAAAAT-GGGCAAAGG 829

  chr20_7541430_7   4029 ATCTGAACAGCTACCTTGCTGAAAAAGATATATAGACGGTAAATAA-TAT 4077
                           i    i  vi ii iv ii  i        i i i  iv     -i i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr20_7541430_7   4078 ACGAAACTATGTTCAACATCAAATATCAT 4106
                          i    vv   i         ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.12 (51 / 24)
Gap_init rate = 0.03 (11 / 323), avg. gap size = 1.91 (21 / 11)  


 450 28.98 3.27 4.90  chr20_7559786_7563719.rev     2243  2487 (1447)    L1M4_orf2#LINE/L1        3   243 (665)  

  chr20_7559786_7   2243 GAGAGACATACCATGTTCACATATTTGAGGACTCAACAAAGTAAAGATGT 2292
                           i   i  v         iiv   v  i    i  i vv  v      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_7559786_7   2293 CAATTATCTCCAAATT-ATTTATAGGCTTAATACAATTCCCCAAAAAATC 2341
                             vv  i       -  i  i  ii i  ii    i  ivvv      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_7559786_7   2342 CTACCAGGGTCTTTTGTTGTTGCTGGCATGTA-AAACTTACTTTAAAACT 2390
                          i v --v i     ----    v iv  vv -  i  v iii     i 
  L1M4_orf2#LINE/    103 CCAGC--TGCCTTTT----TTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr20_7559786_7   2391 TATATAGAAAGATGCTGG----TCAAATCATAGCTAAA-CTTTCTTGAAA 2435
                         i    i    --   vi ----i  i --     i   - vv        
  L1M4_orf2#LINE/    147 CATATGGAAA--TGCAAGGGACCCAGA--ATAGCCAAAACAATCTTGAAA 192

  chr20_7559786_7   2436 A-TAAAAACATATTCTGGGAGACACCACTCTATTAAATGTTAAATTCCAC 2484
                          -v  i    v v -   ii   -i   v  viiv   v i   viii  
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGT-TGGAGGAC-TCACACTTCCCAATTTCAAAACTTAC 240

  chr20_7559786_7   2485 TAC 2487
                            
  L1M4_orf2#LINE/    241 TAC 243

Transitions / transversions = 1.37 (41 / 30)
Gap_init rate = 0.05 (11 / 241), avg. gap size = 1.82 (20 / 11)  

1393 27.27 8.15 2.04  chr20_7559786_7563719.rev     2805  3442 (492)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr20_7559786_7   2805 AAAAATCACTATATAGGTATAGTAATCAATACAATATGCTATTGGTAAAG 2854
                             v i    i v  v  i         v   i i  v  i   i v i
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr20_7559786_7   2855 AGATACACACATAGA-CAA-GTAAAAG----GAGATTCCAGAAATATAAC 2898
                         i    v   i     -   - v  v  ----    v          v v 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr20_7559786_7   2899 CACATAAATATGACAGACTGATTTTTGACAGAGGAGGAAAAGAA-ATTCT 2947
                           i i vv    iivi i       i    -   iv vv    v-    v
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACA-AGGGTGCCAAGACCATTCA 380

  chr20_7559786_7   2948 TTGGAGAAAAGAGT--TTTTTTCAATAAAATGTACTGTAGCAATTGAACA 2995
                         v   i    -  i -- i       i   vv  i   vii   i  i i 
  L1M4_orf2#LINE/    381 ATGGGGAAA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr20_7559786_7   2996 CGCATAAGCATTTAAAAAAAAATCTCAATTTAAACCTCACACTTTATACA 3045
                         ?v  i v   ------   i   v--  v  ii   i -i  i i i  v
  L1M4_orf2#LINE/    430 KCCACATGCA------AAAGAATG--AAGTTGGACCCC-TACCTCACACC 470

  chr20_7559786_7   3046 ACAATCAAAAATAAACTAAAAGTGTGTTAAACACTTAAATTTAAAACCAA 3095
                          i vv       v    v   i  vi i ? v  i     v   i v v 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr20_7559786_7   3096 AAACTATAAATCTTCTGGGAAAAAACCCAGGAGAAAATCTTCA-GATTTA 3144
                                   v  ii i i i     vi   ? v        i-  ii v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr20_7559786_7   3145 GGACTGGG--ATAGAGTTCTTAGAATTGACATAAAAATAATGACTTATAA 3192
                           ii i  --  i -v        vv     iv    vv ii viv i  
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr20_7559786_7   3193 AAGGAAAAATTAATAAATTGGATCTCATCAAA-TTCAAGATTTTTCTTCT 3241
                            i      vi          ii        -  v  i i    v v  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr20_7559786_7   3242 GTGAAAGACTGTCTT-------TGAAAAA-----CTAGAGATGAAGAGAA 3279
                         vii  i   vv v i-------      i----- i v   vvii     
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_7559786_7   3280 CATATTTGCAAATTACGTATTCAACAAAGGGCTACTATCTGGAATATATA 3329
                         v            i ii   iii i  i  i  vv    ii         
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr20_7559786_7   3330 ATGAAT-------GCTCAA-------------AATCAGCC---TCAAAAA 3356
                          v   i-------i     -------------   v v  --- ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_7559786_7   3357 ----CAGAATATCTTGAACTGACATTTCACCAAAAAGAATATACAGATGT 3402
                         ----  i iv  -     iv        v     i ii       i   v
  L1M4_orf2#LINE/    820 TGGGCAAAGGAT-TTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr20_7559786_7   3403 CAAATAAGCACATGAAAAGATGTGGAACATCATTAGCCAT 3442
                          v                    ivv       ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.30 (96 / 74)
Gap_init rate = 0.03 (21 / 677), avg. gap size = 3.10 (65 / 21)  


 828 21.64 1.12 10.07  chr20_7706099_7707831      215   482 (1251)    L1M4_orf2#LINE/L1        1   244 (664)  

  chr20_7706099_7    215 TGGAAAGGTTTCCTTTGTTAATGG-TTGAAAGAGTTAATACCATTAGGAT 263
                                i v   iv    v    -   i    v      iii   i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7706099_7    264 GGCAATATTACCCATAGCAATCTATAGATTCAACTCAATGCGATTTCTCT 313
                                i v    v vii     i         -----  i  ii  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAAC-----GCAATCCCTAT 95

  chr20_7706099_7    314 CAAATTTCTAATAAGCTTTTTGTTTTTTGCATAAATGTAAAAGTCAATCT 363
                             v i i ----   vii --        v    vv v   iii   i
  L1M4_orf2#LINE/     96 CAAAATCCCA----GCTGCCT--TTTTTGCAGAAATTGACAAGCTGATCC 139

  chr20_7706099_7    364 TCAGATTTATATAGAATTTCTAGGGGCACAAAATAGCTAGAACAACATTG 413
                          v i   i    i   v v v    i v  i      i i     iv   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr20_7706099_7    414 AAAAAGTTTGTAAGAACTTTTTTCTTGCAAAGTTGGAAGATTTATGCTTC 463
                               -----      -----------         i  i i ii    
  L1M4_orf2#LINE/    190 AAAAAG-----AAGAAC-----------AAAGTTGGAGGACTCACACTTC 223

  chr20_7706099_7    464 TCAATTTTAAAA--TATTACA 482
                         i      i    --  i    
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACA 244

Transitions / transversions = 1.90 (38 / 20)
Gap_init rate = 0.03 (7 / 244), avg. gap size = 4.29 (30 / 7)  

2746 21.07 7.65 3.09  chr20_7706099_7707831      497  1241 (492)    L1M4_orf2#LINE/L1      130   908 (0)  

  chr20_7706099_7    497 AATTTAATTCTCAAATTTACATGGAATTTCTAAGGCCCCCAAAAAACTAA 546
                           vi i  i  v     i i      v v v i  v   vi  v i i  
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr20_7706099_7    547 AACAATGTTTAAAAGTTTGTAAGAACTTTGTTCCTACAAAGTTGGAAGAT 596
                               v  v    i--- -      -----------         i  i
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAA---G-AAGAAC-----------AAAGTTGGAGGAC 214

  chr20_7706099_7    597 ATATGCTTCCCAATTGTAAAACATTCTATAAAACTCCAGTAGCCTAAACA 646
                         vi ii          vi     v v   i   i  v     ii v i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr20_7706099_7    647 TTGAATTGTTCTACTGGCATAAAGATCGATATTTAGACAAGTGGAATAGA 696
                         v  ---  v --          i   v  i  v    iv i         
  L1M4_orf2#LINE/    265 GTG---TGGT--ACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr20_7706099_7    697 ATTGACAGTTCAGAAATAAATCTGTGCATTTATAGCTAATTGAATTCTGA 746
                              v   i          i ii i       i ii      v  ii  
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr20_7706099_7    747 CAAGGGTGACAAGACCGTTCAATGGGGAGAAAA-AGTCTCTTCCACAAAT 795
                                 v       i           i i  -     i   v      
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr20_7706099_7    796 GATGATGAGACAACTGGGTATCCACAAAAACTAAAACAA-AAAATTGGAC 844
                          i  v  i         i  ?     vi---i    v  -i  i      
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATG---CAAAAGAATGAAGTTGGAC 456

  chr20_7706099_7    845 CCCTACTTCGCGTTATATATAAAATTTAACTCAGAATGTATCAGGGACCT 894
                               i  i iii     i    v        i    v    ?i     
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr20_7706099_7    895 AAATGTAA-----------------TTCTTAGAAGAAATCCTACAGGTAA 927
                                 -----------------i            v v  vi?    
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_7706099_7    928 GTGTTCATGACCTTGAATTTGGGGATGAGTTCCTACATGTGACACCAAAT 977
                         i v   i        ii  v  vi   iv   i  v  i          v
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr20_7706099_7    978 CTACAAGAAACAAAAGA---------TAAACCAGACTTCA---AAGTTAA 1015
                         vi     v         ---------    iii       ---  i    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr20_7706099_7   1016 A--CTTTTGTATGGCCAAGAACATTATCTAGACA-TGAAAAGGCAACCTA 1062
                          --       iivv v   i   i    v   v -       i     i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr20_7706099_7   1063 TGAAATGAAAGAAAATATTTTTAAATCACAAATCTTATAAGGGTCTACTA 1112
                         iii    ii           vi      i v    v       v  vv  
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr20_7706099_7   1113 TCCAGGATATATAAAGAACT---A-AACT-----GCAGCAAGACACACAA 1153
                              i              --- -    -----ii iv      v i  
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr20_7706099_7   1154 TCTAATTAAAAAATGAGCAATGTACTTGAATAGATATTTCTCCAG----- 1198
                         i i    ?       i    v v i         i         i-----
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr20_7706099_7   1199 ---------TGGCCAACAAGCACATTAAAAGATCCACAACATCATTACTC 1239
                         ---------       i        v       v v        ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr20_7706099_7   1240 AT 1241
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.59 (94 / 59)
Gap_init rate = 0.02 (17 / 779), avg. gap size = 4.71 (80 / 17)  


1206 29.25 5.19 2.49  chr20_7709686_7714256.rev     2914  3395 (1176)    L1M4_orf2#LINE/L1       10   504 (404)  

  chr20_7709686_7   2914 ATACTATGTTCACTAGTGGGAATACGCAACATAATATAGACATAAATTCT 2963
                           v i       ivii v    v  vi  i  vi vv   iivv   v  
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr20_7709686_7   2964 CTCCAAACTGATATGCAGGGTTCATGCAATACTTATCTGATTTCCAGAAA 3013
                          i     i    v i   iv iv i     v i    vi v i    vvi
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr20_7709686_7   3014 GTTTTTTTCTAGCTAGAGACAAGATTATTCTAAAATTGATATGGAAATGT 3063
                         vi      vi  vv vv      v v  i        v           i
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr20_7709686_7   3064 AAAAGATGTAGAATAGCTAAAACAATTTTGAAAAATAAAAACAAAGTAGG 3113
                           ii  ivi        i        i        v  i        v  
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr20_7709686_7   3114 AAGAATCAGTATATCTGATTTCAAGACTTATTATATAGTTACAGTAGTCA 3163
                          i  v   vvv vi ii       i     i  i v  i       i   
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr20_7709686_7   3164 AAACTGTGTAGTATTTG---AAGGATGGA-ATATGAATCAATGGAACACA 3209
                          i  v    i   i v ---      i  -    ii          i v 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr20_7709686_7   3210 A--AGGAATCCAGAAATAGGCCTACATAAATACG--CAGTAGGCACATGT 3255
                          --ii  i          ii  i i i vv  i --  i v -- iv vi
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG--ATTTTC 357

  chr20_7709686_7   3256 GACAAAGGTGCAAAAGTAACTGAAAGGAGGAAAGATAA------------ 3293
                              i     v  iiiv i v  v  i i  ii   i------------
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr20_7709686_7   3294 --GGT--TGGAGCGATCAGACATCCAAAGGCCAAAGGAAGAAAAAAAAAA 3339
                         --   --   ii i iii  i ?   v v  -   ---    vi  ivvi
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGC-AAA---AGAATGAAGTTG 453

  chr20_7709686_7   3340 GACCTTGACCCAAGTGTTGCACCTTGTACAAAA-TTAACTCAAAATGGAT 3388
                             iiv   ------ ii    v i       -                
  L1M4_orf2#LINE/    454 GACCCCTACC------TCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_7709686_7   3389 CATAGAC 3395
                           ?    
  L1M4_orf2#LINE/    498 CAWAGAC 504

Transitions / transversions = 1.48 (83 / 56)
Gap_init rate = 0.02 (11 / 495), avg. gap size = 3.36 (37 / 11)  

 943 25.06 6.52 2.26  chr20_7709686_7714256.rev     3681  4079 (492)    L1M4_orf2#LINE/L1      493   908 (0)  

  chr20_7709686_7   3681 TGAATTGTAGACTTAAATGTAAATCAG--AAAATTATAAAACTTTTTT-- 3726
                           i  ii?    i         i--  --    i         i  vv--
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAG--AGCTAAAACTATAAAACTCTTAGAA 540

  chr20_7709686_7   3727 TTAAACA-------AAATCTTCAGGATTTAGGGCT-GGAAAT---TTCTT 3765
                         vv     -------        iv  ii v   i -  v   ---     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_7709686_7   3766 AAGCTTGTCACCAAAAGTAGGATGCAGTAAAGGAAAAAGTA-ATACACTG 3814
                          iiiv  v         i vi -   ii   i      i  -   v i  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_7709686_7   3815 AACTTAATCAAAAATTAAAATATTTGCTCTATGAAGGATCTTGCAAACAG 3864
                         i    v       v v    iv    iv  vii     ivi iiv  v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_7709686_7   3865 AATAAAAGGGAAAGTTACAGACTGGGAGAAAACATTTTTAAGCCACATAT 3914
                          i i   i iv  vii     v          i    vi  ii  i    
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_7709686_7   3915 TGAACAAAGGACTAGTATCTAGAATATATAAAGAATTC--AAAATCTCAA 3962
                         ivi i  i     v     i               i  -- v  -     
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAA 788

  chr20_7709686_7   3963 TA-TAAAAGCAAAAAT--TCCTACTAAAACATAGGCAAAATATATAAGGG 4009
                           -     iv v    --i  v i ?   v  i      iv  v i ivi
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr20_7709686_7   4010 GACATTTCACCAAAGAAGATAAACTTTTCATATG-CAAATAA----ATAA 4054
                                 v            v  ----- v   - v     ----  i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATAC-----AAATGGCCAATAAGCACATGA 883

  chr20_7709686_7   4055 AAAGATGTTCATAATCATGAACCAT 4079
                                i   vv    ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (58 / 40)
Gap_init rate = 0.04 (15 / 416), avg. gap size = 2.33 (35 / 15)  


 246 22.99 4.60 2.30  chr20_7735753_7741893.rev      183   269 (5872)    L1M4_orf2#LINE/L1      820   908 (0)  

  chr20_7735753_7    183 TGGATAAA---TTTGAAACTACA-ACTCCACCATAGAAAATATACAAATG 228
                            ii   ---      --  v - i i v   v    i           
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAA--TAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr20_7735753_7    229 AAAAGCATGTATATGAAAAGGTGCTCTGCCTCACTAGTTGT 269
                         ivv ii v i i        i     vi v   ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (12 / 8)
Gap_init rate = 0.03 (3 / 89), avg. gap size = 2.00 (6 / 3)  

3237 25.88 0.77 0.77  chr20_7735753_7741893.rev     4742  5649 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_7735753_7   4742 TGGAAAAACATTCCATGCTCATGGGTAGGAACAATCAATATCGTGAAAAT 4791
                               i i  i     i      i v    v v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7735753_7   4792 GGCCATACTGCCCAAAGTAATTTACAGATTCAATGCTATCCCTATCAAAC 4841
                            v     v      v i  i           i  v            v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_7735753_7   4842 TACCA-TTGACTTTCTT-CACATAATTAGAAAAAAACTGCTT-TAAATTT 4888
                          v   -i  v    i  -  v -    i--- v  i   v i-    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG---ACAAGCTGATCCTAAAATT 146

  chr20_7735753_7   4889 CATATGGAGCCAAAAAAGAGCCCATATAGCCAAGATAATCCTAAGCAAAG 4938
                                 iviiv  ii  v  viv        i i    i i iv  ii
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_7735753_7   4939 AGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATATTACAAG 4988
                                  i      vv       v  ii i      viv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_7735753_7   4989 GCTACAGTAACCAAAACAACATGGTACTGGTACTAAAACAGATATATAGA 5038
                                   i   i   iii         i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_7735753_7   5039 CCAATGGAAAAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAACC 5088
                         i        v    iv   ivii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_7735753_7   5089 ATCTGATCTTTGGCAAGCCTGAGAAAAACAAGCAATGGGTAAAGGATTCC 5138
                          vi    i  i i    vv  vv  i v  vv       v    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_7735753_7   5139 CTAGTTAATAAGTGGTGTTGGGAAAACTGG-CAGCCATATGTAGAAAACT 5187
                           vv i  i  i     i     v      -i ?   i   i i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_7735753_7   5188 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGA 5237
                            ii         v   i     v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_7735753_7   5238 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5287
                          i ?    i           v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_7735753_7   5288 CTAGGCA-ATACCATTTAGGACATAGGCATGGGCAAAGACCTCATGACTA 5336
                         v    ?i- v i -  iiv   v v  vv i     v iii  v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_7735753_7   5337 AAACACCAAAAGCAATGGCAACAAATGCCAAAATTGACAAATGGGATCTA 5386
                         vi            vvi        v vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_7735753_7   5387 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGGAACTATCATCAGAGTGAA 5436
                           i   v v  i i   i  ii vv    i iv       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_7735753_7   5437 CAGGCAACCTACAGAATGGGAGATAATTTTTGCTATCTATCCATCTGACA 5486
                         v  i     i             v   v     v vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_7735753_7   5487 ATGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5536
                          v  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_7735753_7   5537 AAAAAGCAAACAACCCCATC-AAAAATGGGCAAAGTATATGAACAGACAC 5585
                           i --    i     v  i-              v  v    i     i
  L1M4_orf2#LINE/    796 AAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_7735753_7   5586 TTCTCAAAAGAAGACATTTATGTGGTTAACAAATATATGAAAAAA-GCTC 5634
                              v        i  vi vi   ii  i  ii i       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_7735753_7   5635 ATCATCACTGGTCAT 5649
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (134 / 98)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3010 25.65 1.08 3.23  chr20_7873865_7878836.rev     3554  4481 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_7873865_7   3554 TGGAAAAACATTCCATGCTCATGGATTGGAAGAATTAATATCAT-AAAAC 3602
                               i i  i     i               v       ii -  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7873865_7   3603 AGCCATACTGCCAAAAGCAATCTACAAATTAAACACTATTCCTATCAAAC 3652
                         i  v     v  v   vii       i   v   i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_7873865_7   3653 TACCAA-TGTCATGCTTCACAGAATTAGAAAAAACAACAGCAACAACAAC 3701
                          v   i-  i - vi  ii     v v  v  ivii -------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA------------- 136

  chr20_7873865_7   3702 AACAAAAACAAAAACTTCTAAAATTCACATGGAACCAAGAAAGAGCCCGA 3751
                         --------------- i          i      viivi ii  v  v  
  L1M4_orf2#LINE/    137 ---------------TCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr20_7873865_7   3752 ATAGCCAAAGCAATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCACACC 3801
                                  i     i i iv  i          i      vv      i
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr20_7873865_7   3802 ACCCAACTTCAAACTATACTATAAAGCTACAGTAACCAAAATAATATAGT 3851
                         v     i      viv     i             i   i i i i i  
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr20_7873865_7   3852 ACTAGTACAAAAACAGACACATAGACTAATGGAACAGAAAAGAAAACTCA 3901
                            i i i  ii i     i     ii       i    vv  i iii  
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr20_7873865_7   3902 GAAATATGCCACATAC--CTACAACCATTTGACTCTTGCCAAGGCTGACA 3949
                               vi  -     --i  iiii  v    i i i v     v  v  
  L1M4_orf2#LINE/    322 GAAATAAACC-CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr20_7873865_7   3950 AAAACAAGCAATGGGGAAAGGACTCTCTATTCAATAAATTGTCCTGGGAT 3999
                          i v  vv            i ivv   v     i    v  v      i
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr20_7873865_7   4000 AGCTGGCCAGCCATATGCCAAAGACTGAAGCTGGACCCCT--TTCAC--C 4045
                          i    vi ?   i    v     v     i         --i    -- 
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr20_7873865_7   4046 ATATACAAAAATTAACTAAACATGGATCACAGATTTAAATGTAAGACTTC 4095
                                          v  v        ?   ii           vi v
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr20_7873865_7   4096 AAACTATAAAATTACTAGAAGACAACCTAGGAAACACTCTTCTTGACATT 4145
                                    i vi       v   v    ?ivv v     v    v  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr20_7873865_7   4146 GGCCCTGGCAAGAAATTTTTGGCTAAGTTCCCAAAAGCAATTTCAATAAA 4195
                           viiv     viiv  i  i v  v viv         vvvv   i   
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr20_7873865_7   4196 AACAAAAATGGAAAAGTGGGACATAATTAAACTAAAAAGGTTCTGCACAG 4245
                          iv      i  v  i v    v v  i   v v    iv  i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr20_7873865_7   4246 CAAAAGAAGCTATTAACAGGGTAAATAGACAACCTACAGAATGGGAGAAG 4295
                             i  vi    i  v ii  i  v        i              i
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr20_7873865_7   4296 ATATTTGCAAATTATGCGTCCAATAAAGGCTTAATATCTAGAATCTATAG 4345
                                     i  iii  ii    i  vi vi    i     v    i
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr20_7873865_7   4346 GGAACATAAAGAAATCAACAAGCAAGAAACAAATAACCTCATTAAAAAAT 4395
                         i    vivv v  v    i  vv  i i          iv   ?      
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr20_7873865_7   4396 GGGCAAAGTATATGAGCAGATACTCCTCAAAAGAAGACAGACAAGCAGCC 4445
                                 v  v   ii   i i i   v        i v    iii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr20_7873865_7   4446 AAGAA--ACATAAAAAAATTCTCAGCATCTCTAATCAT 4481
                           v  --    i    i  v    i    v????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (137 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 4.44 (40 / 9)  


3195 26.90 0.88 0.77  chr20_7880434_7887813.rev     5982  6888 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_7880434_7   5982 TGGAAGAACATTCCATGCTCATTGATAGGAAGAATCAATAACATGAAAAT 6031
                              ii i  i     i    v   v      v i    vii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_7880434_7   6032 GGCCATACTGCCTAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 6081
                            v     v  i  iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_7880434_7   6082 TACCAATGACTTTCTCCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6129
                          v   iivi i  i iii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_7880434_7   6130 TATGGAACCAAGAAAGAGCCCTC--ATTGCCAAGACAATCCTAAGCCAAA 6177
                                -- v v   i v  iv--  v     i      i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_7880434_7   6178 AGAACAAAGCTGGAGGCATCGCACTACCTGGCTTCAAACTATATTACAAG 6227
                                  i      vv  i    v  iiii      viv  i     i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_7880434_7   6228 GCTGCAGTAAGCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 6277
                            i      v   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_7880434_7   6278 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAG 6325
                         i        i    i--    i  --        vv   i    i  ii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr20_7880434_7   6326 CCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 6375
                         i  vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_7880434_7   6376 CCCTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 6425
                         vi  v  i  i   i          v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_7880434_7   6426 CTGAAATTGGATCCCTTCCTTACACCTTATACAAAAACTAATTCAAGATG 6475
                         v    i     i    v   i     v          i   i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_7880434_7   6476 GATTAAAGACTTAAATGTTAGACCTATAACCATAAAAACCCTAGAAGAAA 6525
                            i ?    i       v   v   v   i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_7880434_7   6526 ACCTAGGC-CATACCATTCAGGTCCTAGGCATGGGCAAGGGCTTGATGAG 6574
                           v    ?-i v i -   iv v   v  vv i     v  i  vv iii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_7880434_7   6575 TAAAACACCAAAAGCAATGGCAACAAAAGCTGAAATAGACAAATGGGATC 6624
                           vi            vvi          vvi       i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_7880434_7   6625 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 6674
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_7880434_7   6675 AACAGGCAACCTACAGAATGGGAGAAAAT-TTCACAATCTACCCATCTGA 6723
                           v  i     i                 -  ii   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_7880434_7   6724 CAAAGGGCTAATATTCAGAATCTACAAAGAACTTAAACAAATTTACAAGA 6773
                         i  i  i  vi   i      v  i        ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_7880434_7   6774 AAGAATCAAACAACCTCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 6823
                           i iv    i    iv  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_7880434_7   6824 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGTTC 6873
                              v        i  vi viii     i ii          i   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_7880434_7   6874 ATCATCACTGGCCAT 6888
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (149 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.50 (15 / 10)  


2931 22.55 4.78 1.37  chr20_8013102_8017327.rev     2857  3734 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_8013102_8   2857 TAGAAAGACATCTCATGCTCATGAATCTAAAGA-TTCATATTGTTAATAT 2905
                          i      i   i    i     i  ivi    -  v          v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_8013102_8   2906 GGCAATTTTCTCCAATTTGATGAATAGATTCAACGCAATCTCAATCAAAA 2955
                               vi  i    v     vv i               i v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_8013102_8   2956 CCAGAGTAGGCATTTTATTGT-GAAATTGACAAG---ATTCTAAAATTCA 3001
                         i vv  i-v  v    -   i-            ---  i          
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_8013102_8   3002 AAGGAAAGTGCAAAGGACCTGAAATAGCCAAAATAA-CT--AAAAAGAAA 3048
                         v v i  i     i     iii           i  -  --        i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_8013102_8   3049 AGCAAATTTGGAGGAGTAACTCTACTGGATTTCAATACTTAT---AAAGC 3095
                          i    v        v v  v  v ivi       v     i---     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_8013102_8   3096 TATAATAATTAAGACAGTGTCGTGTTTGTGTGACGGTAGACAACGATA-A 3144
                           i i    i          v  ii v ii i v i      --v   - 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA--TATAGA 296

  chr20_8013102_8   3145 T-AATAGATCAGAATAGAAATTCCATAAATAGACCTACATATTCATTGAC 3193
                          -   i  vi     v  i v    v     i   i i i   i  v v 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_8013102_8   3194 CATTGATTTTAGGAACAGGCGCAAAGGAAAATCAATGGAGAATGAATAGT 3243
                         v         v iv vi  i  v   ivv v       i   v       
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_8013102_8   3244 CTTTTAAACAAGTAGTACTGG-ATATATTGAATAA------ACAAAA-AA 3285
                              v     i i  i    - i - i  i   ?------i     -  
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACA-ACTGGATAKCCACATGCAAAAGAA 445

  chr20_8013102_8   3286 TAAATTTTGATCCATATCTCTTAGTATATATACAGATTAATTCAAAATAA 3335
                          i  v  v  i  v  i   vi vi     i v i     i       ii
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_8013102_8   3336 ATCGTAGATTTCAATATTAAACTTAAAACTTTAAAACATCTT-GAAGAAA 3384
                            i?   ii v   i v i vi       v      -    -       
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAA 544

  chr20_8013102_8   3385 ACAAAGGAAAAAGCCTTTATGACCTTTGGTTAGGCA--GAGTTCTTAGAT 3432
                            v   ?iv  ii   ii       v         -- iv         
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_8013102_8   3433 AAGATGCCTAAAGCATAGTTCATACAAGAAAACATTGACAAATTGGACTT 3482
                          v  ii  v      i iviv i v       v  v  i           
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_8013102_8   3483 CATCAAAATTAAAAATTATT----TTCAAAAAACGGTATTTACAGAATGA 3528
                                        i v  ----      ii  iv   iv v i i   
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_8013102_8   3529 AAAAAATGAACCTCAGAATGTGAGAAA-TATTTGACAAA-CATATATTGG 3576
                            i -ii v  v       v      -      -    -       iv 
  L1M4_orf2#LINE/    695 AAAGA-CAACCCACAGAATGGGAGAAAATATTTG-CAAATCATATATCTG 742

  chr20_8013102_8   3577 ATAAAGGATTTGTGTGAAGAATAAGTAAATAACCCTCA-AATCCAA--AT 3623
                             i   i    i vv      vi    v   i  i -  ii   --  
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_8013102_8   3624 AATAATACAAAAAACTCCAAATCAATAAAAATTGGCAAATTACTTGAACA 3673
                           v  v     v   -    v ---?      v      vv i     i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAAC-CCAATT---WAAAAATGGGCAAAGGATTTGAATA 838

  chr20_8013102_8   3674 ---------CCAAAGAAGATATGCAGAGGACAAATAAGCAGATGAAAAGA 3714
                         ---------             i  i v i v        v         
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr20_8013102_8   3715 TGTTCAACATCAATCAATAG 3734
                           i         ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.31 (110 / 84)
Gap_init rate = 0.03 (28 / 908), avg. gap size = 1.93 (54 / 28)  


1975 23.30 5.96 11.39  chr20_8028393_8030570      730  1686 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr20_8028393_8    730 AAAGATGCATACTACATTCATAGATTGAATGAATCAACACAGGAAAGATG 779
                               --  v i ii     i     i v  v i  i iv vv      
  L1M4_orf2#LINE/      4 AAAGAT--ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_8028393_8    780 TCAATTATCCCCAAAATTACATACAGTTTTAATGCAATTCCTGTCAAAAG 829
                         v    vv        v v iv     v  i  i     i   i      -
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA- 100

  chr20_8028393_8    830 CCCCCCCAGCAATTTCTTTAGTAGATATGGAAGAAACT-ATTCTAAAATT 878
                         ---i      viii i   v i   v  v  v-  i  -  i        
  L1M4_orf2#LINE/    101 ---TCCCAGCTGCCTTTTTTGCAGAAATTGAC-AAGCTGATCCTAAAATT 146

  chr20_8028393_8    879 TGTATGGGGA-----GGGA------------------------------- 892
                         ii     ii -----    -------------------------------
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_8028393_8    893 --GACAAACTGAGAGGGATCAGTCTTCTTGATTCTAGGAATTTTTAAAGA 940
                         --i     v vi    iv   vv    iii   ii ii v  vi  v i 
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_8028393_8    941 GCTATAGTAATCAGACCCGTGTAGCACTGACAAGAGGAATAGACACACCA 990
                             i        iiv v    i i    i  vi    -      i ivi
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAG 295

  chr20_8028393_8    991 ATCAATGGAACAGAATAGAGAATCCAGAAATAGATTCATACAAGTATGCC 1040
                                   i     v    i          i ii      vv    vi
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_8028393_8   1041 CAATTGGTATTTTGACAAATTTACCAAAGCAATTCAATGGAGGAAAAATA 1090
                               i -   i     ivv i    ii v         i i  i    
  L1M4_orf2#LINE/    346 CAATTGAT-TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_8028393_8   1091 GCCTTTCCAATAAGTGGCAAGTGGTGTTGAAGCAATTGGAAATCCAGAAA 1140
                          i    i   -------   i     i  iii   i    v ?   ----
  L1M4_orf2#LINE/    395 GTCTTTTCAA-------CAAATGGTGCTGGGACAACTGGATAKCCA---- 433

  chr20_8028393_8   1141 GAAAGAGAGAAAGAGGAAGAGAGAGAGAGAGACAGAGACAGAGAGATAGA 1190
                         --------------------------------------  ------ i--
  L1M4_orf2#LINE/    434 --------------------------------------CA------TG-- 437

  chr20_8028393_8   1191 GAGAGAGAGAAAGAGAAAGGAAGAAAGACAAAGGGAAGAAAAAGAAAAAG 1240
                         ----------------------------    ------ i  v   ivv 
  L1M4_orf2#LINE/    438 ----------------------------CAAA------AGAATGAAGTTG 453

  chr20_8028393_8   1241 AACCTCAACCTAAACCTCACAATTTATTCAGAAATTA-CTCAAAATTGAT 1289
                         i   ----    --       viv   v  i      -        v   
  L1M4_orf2#LINE/    454 GACC----CCTA--CCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_8028393_8   1290 CACAGATTTAAATACAGTATACAAATCTATAAAATT-TTAGAA----ACC 1334
                           ?   ii     ii iv vvi   v        i -      ----  v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_8028393_8   1335 TAAGAGAAAATCTTTGGCATATAAGACTAGGCAAAGCATTCTTAGACTTG 1384
                           i ? v       i vv iv vi ii       v vv        iv  
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_8028393_8   1385 ACACCAAAAACATGATCCAAAAAAGGAAAAAAT-TATAAATGAAACTTCA 1433
                                  i  ii v -  v   i        -v      vii      
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGC-AACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_8028393_8   1434 ----AATTTAAAAGTTTTACTCTGCAAAA-ACCCTGTTGAAAGGATGAAA 1478
                         ----    v    v    iiv  v    i-  v  i ii i iii     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_8028393_8   1479 AGAGAAGATACAGAGTGAGAGAAAATATTTGCAAACCACATATGCAAAGA 1528
                            v  vvi     i  i                 i  i    vii vi 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_8028393_8   1529 AGGACTAGTTTCTAGAATATACAAAAAGAACTGCCAAAACTCAACAA--- 1575
                         i     v  v  i        i   --     vii v       i  ---
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAA--GAACTCTTACAACTCAATAATAA 794

  chr20_8028393_8   1576 ---AACAAGCAATCAAATTAGAACATGGTCAAAAGACATGAAGAGACATT 1622
                         ---i    ii  i v    ?i  v    v    i  iv    v       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_8028393_8   1623 TCACGAAAGAAGATACACAGATGGCAAATAAATACATAAAAAGTTGTTCA 1672
                           v v          i   i     v     ii    i     v  i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_8028393_8   1673 ACATCATTAACTAT 1686
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (133 / 86)
Gap_init rate = 0.03 (24 / 905), avg. gap size = 6.92 (166 / 24)  


3040 26.38 1.19 3.03  chr20_8037765_8044064.rev     4884  5808 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_8037765_8   4884 TGGAA---CATTCCATGCTCATGGGTAGGAAGAATCAATATGGTGAAAAT 4930
                              ---i  i     i      i v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_8037765_8   4931 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGC 4980
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_8037765_8   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_8037765_8   5029 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATGCTAAGTCAAAAG 5078
                                viiv  ii  v  v v  v     iv    vi i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_8037765_8   5079 AACAAAGCTGGAGACATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i     ivv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_8037765_8   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_8037765_8   5179 AATGGAACAGAAT--AGAGCCCTCAGGAATAACGTTGCATATCTACAACT 5226
                                i     --    i  --  i     vviiii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_8037765_8   5227 ATCTGATCTTTGACAAACCTGAGAAAAGCA----ATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vv  i v  ----          i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_8037765_8   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGGCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?v  i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_8037765_8   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_8037765_8   5373 TTAAAGACTTAAACATTAGACCTAAAACTATAAAAACCCTGGAAGAAAAC 5422
                          i ?    i    ii v   v              vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_8037765_8   5423 CTGGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5472
                         v i  ?v v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_8037765_8   5473 AACACCAAAAGCAATGGCAACAAGAGCCAAAATTGACAAATGGGATCTAA 5522
                         i            vvi       i  vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_8037765_8   5523 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTGCCATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv    i  v   ---    i---   -
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT---ATCAA---GAA- 689

  chr20_8037765_8   5573 AGGCAACCTACCATCAGAGTGAACAGGCGACCTACAAAATGGGAGAAAAT 5622
                         -----------------      v  i i   i   i             
  L1M4_orf2#LINE/    690 -----------------AGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_8037765_8   5623 TTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCGGAATCTACAATG 5672
                         v  i    vii ivi      i  i  i  vi     i    v  i  v 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_8037765_8   5673 AACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGG 5722
                              vv    v iv i  v     i     i     v  i?    i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_8037765_8   5723 GCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAA 5772
                           i     iv    i     i     v        i  vi viii     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_8037765_8   5773 AAAACACATGAAAAAATGCTCACCATCACTGGCCAT 5808
                         v  i          i       v     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.90 (39 / 10)  


2988 25.68 2.36 0.79  chr20_8278044_8280899     1477  2364 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr20_8278044_8   1477 GATATTTCATGTTCATGGATGGAAAGATTTAACATTGTAAAGATATTAAT 1526
                              ii             v i    i    i     v     ivi   
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr20_8278044_8   1527 TTTTTTCACATTGAACCACGGATTCAATGTAATCCCAGTCACAATCCCAG 1576
                         vi iii  v     v i  i       i i      vi   v        
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr20_8278044_8   1577 CAAACTTTTTT-TATATGTTGGCATAATTGTTGC-AAAATTTATATGGTA 1624
                          viv       -i v vi   i  - ii  v v -      i      v 
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATATGGAA 155

  chr20_8278044_8   1625 ATGCAAAGAACTGAGATTAGCTAATACAAAACTAAAATGGAAGAATAAAG 1674
                               i i  iv   v    i  v    vvi i   vi      i    
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr20_8278044_8   1675 TTAGAGAACTCATAT-----GATTT-AAGACTTACTATAAAGCTACAATA 1718
                           i   i     i i-----i    -  i        i         i  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr20_8278044_8   1719 ATCAAGAAAGCATGGTGTTGGCA-AAT--TAGATACATAGATCAATGGAA 1765
                                v  ii    ii     -  v--    i i              
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr20_8278044_8   1766 AATAATAGCAAGCCCCCATATAGACCCAGATAAGTATAGTAAACTGACTT 1815
                         v v   v vi  i  vv v   i     v i vv   i  v  i   -  
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA-TT 354

  chr20_8278044_8   1816 TTTTATGAAAGTGCAAGAATAATTCAATAAAGAAAGGATAGTCTTTTCAA 1865
                           iv ii ii    v ii iv       iii     i             
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr20_8278044_8   1866 AAAATAGTGCTGGAGCAATTGGGTGTCCATATGCAAAAATATGAACTTAG 1915
                         v    i       ii   i   i i?   i        iv     v  i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr20_8278044_8   1916 AGTTCATACTTTACA------AAAAAAATTAACTCAAAATGAGTCATAGA 1959
                          vii -   i i   ------ v                  ii   ?   
  L1M4_orf2#LINE/    455 ACCCC-TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr20_8278044_8   1960 CATATATGTAAAATGC-AAACCAATTAAACTTCTAGTAGAAAA-ATAGAA 2007
                          v  v      i -  -   v v  v     ii   v      -    i?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr20_8278044_8   2008 -TAAATTTTGTACAATCTTGGATTTGTGGATGAGTTTTTAGATACAACAC 2056
                         -     i  -iiii i     i  v vvi   iv  i       ii    
  L1M4_orf2#LINE/    553 GTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_8278044_8   2057 CAAAAGCATAATCCATGAAAGAAAATTTTGATAAACTATAATTTGCTTAA 2106
                                 i  v v ii        vv v      i iv v  iiiiv  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_8278044_8   2107 ATTTAAAACTTTTGCTATGCAGAAGACAGTATTAAAAGAATGAAAGGAAA 2156
                            v          ivv v  i i    v   i  i i i     i  v 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr20_8278044_8   2157 AGACATAGACTGGGAGAAAGTATATGGAAATCACAT-TGTGATAAAAGAA 2205
                          vv  i   v         i   v  v      i  - v      ii  v
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr20_8278044_8   2206 TAGTATTCTGAATATATAGAGAACCCTTAAAACCCGACAAGAAGAAAATA 2255
                          v    i v         i     i    v   i i i  v  i  i i 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr20_8278044_8   2256 AATAATGTAAATTAATATTTGGCAAAACATATGAACAGATATCTCACCAA 2305
                              ivi  v ?  v v v      iv  v    i   i  i  v    
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr20_8278044_8   2306 AGAAAACATACAAACATAACAAATACCCATATGAAAAGATGCTCAACATC 2355
                             i i       -- ii v    vv  i                    
  L1M4_orf2#LINE/    852 AGAAGATATACAAA--TGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr20_8278044_8   2356 ATTTGTCAT 2364
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.55 (136 / 88)
Gap_init rate = 0.02 (17 / 902), avg. gap size = 1.65 (28 / 17)  


2822 24.39 3.33 2.66  chr20_8307850_8314197.rev     4955  5856 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_8307850_8   4955 TGGAAAAAGATTCCATCATCATGGATAGGAAGAATCAATATCATGAAAAT 5004
                               i v  i    vv        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_8307850_8   5005 GTCCGTACTGCCCAAAATAATTTATAGATTCAATACTATACCCATGAAAC 5054
                          v vi    v      v i  i  i        ii v  v  i  v   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_8307850_8   5055 TACCATTGACATTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCAT 5103
                          v   vivi v  i  ii     v v  v  i-  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_8307850_8   5104 ATGGGA-T-CAAAGAAGACCTTGTATAGCCAAGACAATCCTGAGCAAAAA 5151
                             i - -   i --    iv v        i      i   iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_8307850_8   5152 GAACAAAGCTGGAGGCATCACACTAGCTGACTTCAAACTATACTACAATA 5201
                                 i      vv       vv ii i      viv        vi
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_8307850_8   5202 CTACAGTAACCGAAACAG-GTGGTACTGGTACCAAAACAGACATACAGAA 5250
                                  i i i    -          i iv ii i       i   -
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA- 296

  chr20_8307850_8   5251 CCAATGGAATAGAA---------CA---------CCACACACCTACAACC 5282
                         i             ---------  ---------   i   ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_8307850_8   5283 ATCTGATCTTCAACAAACCTGACAAAAACAAACAATGGGGAAAGGATCTC 5332
                          vi    i   i    ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_8307850_8   5333 CTATTAAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGCAGGAAACT 5382
                           v  v  i              v      v  ?   ii    ii i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_8307850_8   5383 GAAACTTGATCCCTTCCTCCTACCTTATACAAAAATTAACTCAAGATGGA 5432
                            ii v  i    v    vi   v                   i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_8307850_8   5433 TTAAAGACTTAAATGTAAAACCCAAAACCATAAAAATCCCTGGAAGAAAA 5482
                          i ?    i         i v i     i      v  i- i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT-TAGAAGAAAA 545

  chr20_8307850_8   5483 TCTAGGC---AATGCCATTCAGGACATAGGTATGTGCAAAGACTTCATGA 5529
                         iv    ?---   -- -   iv   v v  vv iv    v ii   v --
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT-- 590

  chr20_8307850_8   5530 CAAATATG---CCAAAAGCAATTGCAACAAAAGCCAAGCTTGACAAATGG 5576
                         - i     ---         vvv          vv  iv v  i    v 
  L1M4_orf2#LINE/    591 -AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_8307850_8   5577 GATCTAACTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTATCATCAG 5626
                           ii v ii   v v  i i   i   i vv    i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_8307850_8   5627 AGTGAACAGGCAACCTACAGAATGGGAGAAAATGTTTGCAA-TCA-ACCG 5674
                               v  i     i                 i       -   - i--
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-- 737

  chr20_8307850_8   5675 ATCTGACAAAGGTCTAATATCCAGAATTTACAAGGAACTTAAACAAATTT 5724
                               i  i  v  vi          v  i  i     ivv    v --
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT-- 785

  chr20_8307850_8   5725 ACAAGAAAAAAAACAAAACAAAACAAATACCACCATCAAAAAGTGGGCAA 5774
                         -   v  v     --------i       v v v  i?    i       
  L1M4_orf2#LINE/    786 -CAATAATAAAAA--------GACAAATAACCCAATTWAAAAATGGGCAA 826

  chr20_8307850_8   5775 AGGATATGAACAGACACTTTCCAAAAGAAGACATTTATGCAGCCAAGAAA 5824
                              v    i     i  ii v        i  vi viii     v  i
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr20_8307850_8   5825 CATATGAAAAAAAGCTCAACATCACTGATCAT 5856
                           i       i v           ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (120 / 96)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.70 (54 / 20)  


3251 26.65 0.66 0.66  chr20_8523999_8530274.rev     4877  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_8523999_8   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4926
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_8523999_8   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATAAAGC 4976
                            v     v     iv i  i           i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_8523999_8   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_8523999_8   5025 TATGGAACCAAAAAAAGAGCCC-GCATCGCCAAGGCAATCCTAAGCCAAA 5073
                                -- viv  i ii   - v  v     ii     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_8523999_8   5074 AGAACGAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAG 5123
                              i   i      vv       v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_8523999_8   5124 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5173
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_8523999_8   5174 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAA 5221
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr20_8523999_8   5222 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5271
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_8523999_8   5272 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5321
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_8523999_8   5322 CTGAAACTGGATCCCTTTCTTACACCTTATACAAAAATCAATTCAAGATG 5371
                         v    ii    i    vi  i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_8523999_8   5372 GATTAAAGACTTAAACGTTAGACCTAAAACCATAAAACCCT-AGAAGAAA 5420
                            i ?    i    i  v   v       i       i  -        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_8523999_8   5421 ACCTAGGCATTACCATTCGGGATATAGGCATGGGCAAGGACTTCATGTCC 5470
                           v    ?i v viv    v  iv v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_8523999_8   5471 AAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCT 5520
                          vi            vvi           v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_8523999_8   5521 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGTGTGA 5570
                         v  i   v v  i i   i  ii vv    i  v    i  vv iv    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_8523999_8   5571 ACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5620
                          v  i     i   i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_8523999_8   5621 ACAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5670
                          vi  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_8523999_8   5671 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5720
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_8523999_8   5721 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5770
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_8523999_8   5771 TCATCACTGGCCAT 5784
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (145 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3304 26.45 0.68 0.46  chr20_8814517_8816951.rev     1058  1934 (500)    L1M4_orf2#LINE/L1        2   880 (28)  

  chr20_8814517_8   1058 GGAACGATATTGCATGTTCATGGATTGGAAGAATCAATACTGTTAAAATG 1107
                             v     iv                    v i    i      i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_8814517_8   1108 TCCATATCACCCAAAGCAATCTACAGATTCAGTGCAATCCCTATCAAAAT 1157
                         v v   iiv      vii             ii                 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_8814517_8   1158 ACCAATGACATTCTTCACAGAAATAGAAAAAAAAAATCCTAAAATTTATG 1207
                         v   iivi v  i  ii       v  v  ivvi -          i  i
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATA 150

  chr20_8814517_8   1208 TGGAACCACAAAAGGCCCAGAATAGCCAAAGCTGTCATGAGCAAAAAGAA 1257
                              vii   ii i               i vi  v   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_8814517_8   1258 CAAAACTGGGGAGGCCACATTATTTGACTTCAAATTATACTACAGAGCTA 1307
                             ii   i iivi    i viiii i      viv       i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_8814517_8   1308 TAGTAACCCAAACAGCATGGTGCTGGCATAGAAACAGACACATTGACCAA 1357
                         i     i v i    ii    i        iii i     i  v  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_8814517_8   1358 TGGAACAGAGTAGAGAACCCAGAAATAAATCACTACATCTACAGTGAGCT 1407
                              i   i v    ii           i vv     i  ii  v ii 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_8814517_8   1408 CATTTTGAACAAAGGTGCCAAGGACATATGTTGGAGAAAGGACAGTCTCT 1457
                         v     vi    i         iv   viiv   i     i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_8814517_8   1458 TCAATAAATGGTGCTGGGAAAACTGTATATCCATATACAGAACAATAAAA 1507
                             i              v     v   ?   i  i  i  v   i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_8814517_8   1508 CTTGACCTCTATCTCTCACCATATACAAACATCAAATCAAAATGGACTAA 1557
                         i v    i   i   v             v  i  v          ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_8814517_8   1558 AGACTTAAATCTAAGACCTGAAACTATGAAACTACTAAGATAAAATATTG 1607
                             i     v     v  i       i     vi  ii v    i  v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_8814517_8   1608 GGGAAACTCTCCAGGACATTGAAGTGGACAAAGATTTCTTAAGGAATACC 1657
                          ? v  v   i iv   v   iiv i i   v i       iiv vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_8814517_8   1658 CCACAAGTGCAGGCAACTGGGGGGAAAATAGACAAGTGGGA--TCA-CAC 1704
                            v   ii  i     viii ii        i  i v   --   -  -
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA- 649

  chr20_8814517_8   1705 AGATTAAAAATCTTCTACACAGAAAAGGAAACAATCAACAAAGTGAAGAG 1754
                          i        -   i iii vvv      v  v     v        i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_8814517_8   1755 ACAATCCACAGAATGGGAGAAAACATTTTAAGACTTCCCAGCTCCCAAGG 1804
                             i                  i    vv i iivivi v  vvi    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_8814517_8   1805 GATTAATAAGCAGAATATATAAGTAGCTCAAACAATTCTTTAG--AAAAG 1852
                           i vi  vv            iv i   vv    i  vv  i--     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_8814517_8   1853 A-AATCCATCCAATTTAAAAATGAGCAAAAGATCTGAATAGACATTTTTT 1901
                          -  viv i      ?       i     i   i             i i
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_8814517_8   1902 CAAAAGATGACATACAAATGGCAAACGGGTATA 1934
                             -  v  i           v  iii i i 
  L1M4_orf2#LINE/    849 CAAA-GAAGATATACAAATGGCCAATAAGCACA 880

Transitions / transversions = 1.75 (145 / 83)
Gap_init rate = 0.01 (8 / 879), avg. gap size = 1.25 (10 / 8)  


2697 18.27 5.12 6.57  chr20_9155210_9156950.rev      489  1249 (492)    L1M4_orf2#LINE/L1      159   908 (0)  

  chr20_9155210_9    489 CAAGAGGAGCCCCCCAAGTAGCCAAAATAATAATGGGAAAGAA---CAAA 535
                             -   ---   vi i         i   vv  ii      ---    
  L1M4_orf2#LINE/    159 CAAG-GGA---CCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr20_9155210_9    536 GCTAGAGGACTCACATTTCCTGAATTCAAAACTTACTACAAAAGACACAG 585
                          i i           i    ii v                  - vi    
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA-GCTACAG 253

  chr20_9155210_9    586 TAATAAAAACAGTGTGTCAGTGACATAAGTATAGGCATACAGAACAATGC 635
                             v  i        vi v  i      v    i    i   v     v
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr20_9155210_9    636 AATGGAATTTAGAATCAAGAAATAAACCCACAAATCTACAGCCAATAGAC 685
                            i     v   i  v             i v  i  ii i    v  i
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr20_9155210_9    686 TCCTGACAAGGGTGCCAAGATGATTCAATCTTGGAAAGAATAGTTTCTTC 735
                          iii                iv       vv-            i i   
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTC 402

  chr20_9155210_9    736 AATAAATGGTGCTGGGGCAACTGGATATCTACATGCGAATTAATGAAATT 785
                           i             i          ? i      i  vv      i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr20_9155210_9    786 AGACCCCTACCTCACATCATAT------------TCAGGATGGCTCTATG 823
                         i               i     ------------   ii    v  v?v 
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr20_9155210_9    824 ACTTAAATATAAGGGCTAAAAATCATAAAACTGATAGAAGAAAACACAGG 873
                           i     i    i       v -        vv            i   
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACT-ATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_9155210_9    874 GTGTAAATCTTAGGGTAATTCTTCA--TAAACT-TGGATTCTTAAATATA 920
                         ?-         v -- i i-   vi--  ii v-   v      i    i
  L1M4_orf2#LINE/    552 N-GTAAATCTTCG--TGAC-CTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_9155210_9    921 ACAACAAAATATGAAGGGATCTAACATATGACAAGAAAAGTGGGAAAAAA 970
                            v     --------------i  -----    v  v--------   
  L1M4_orf2#LINE/    598 ACACCAAAA--------------GCA-----CAAGCAAC--------AAA 620

  chr20_9155210_9    971 AGAAAAAATAGATACATTTGACT--GTCAAA-TTAAAAACTTTTGTGTAT 1017
                                       v   v    --i     -               iv 
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr20_9155210_9   1018 CAAAAGATGTTATCAAGAAAATGAAAAGACAGTCTACAGAATGGGAGAAA 1067
                             i  iii          i          ii i               
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr20_9155210_9   1068 ATATCTTCAAGTCATATATCTGAAAAGGATCAAGTGCCCAGTACATATAA 1117
                             i v   i            v    iv vv  ii    v i      
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr20_9155210_9   1118 AAAAAAAAAGTCTTACAATGAATTCAACAACATCAAAAAAGCAGACAACC 1167
                          i  v-----        i----    i  i ---    ii  i i    
  L1M4_orf2#LINE/    771 AGAAC-----TCTTACAAC----TCAATAATA---AAAAGACAAATAACC 808

  chr20_9155210_9   1168 CACTTAAAAAATGGGCAAAGGG------------------CAGAGAAGAG 1199
                           v  ?               i------------------  i      v
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr20_9155210_9   1200 GTATAAATGATCAGCAAGCAAGTGAAAAGGTGAACAATAGCATCAGTCAT 1249
                         i  i     ii  ii     vi       i  vv   i v  ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (86 / 49)
Gap_init rate = 0.03 (21 / 750), avg. gap size = 4.24 (89 / 21)  


3923 18.97 6.44 2.07  chr20_9346101_9348330.rev      869  1738 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_9346101_9    869 TGGGAAGACATCTTGCCTTCATGGGTTGGAAGACC--ATATTGTTAAGCT 916
                            i    i   iiiiv       i         i--           v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_9346101_9    917 GGAAGTATTTCTCAAATTGATGTGTGAATTCAGTGTAATCTCTATCAAAA 966
                           v i  i i i         v iiii     ii i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_9346101_9    967 TCCCAGCTGACTTTTTGGTAGAAACTGACAAGCTAATCCTAAAATTCATA 1016
                                  v      v i     i         i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_9346101_9   1017 TAGAAACTCAAGGGATCAAGAATAGCCAAAACAATGTTAAAAGAGA-GAA 1065
                          i    iv       i v                 v  i   i   -   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_9346101_9   1066 CAAAATTGGGTGTCTCACACTTCTTGATTTCAAAACTTATTACTAAGCTA 1115
                             i    iv v          iii             i   v      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_9346101_9   1116 CAAGATTTAATCAAGACAGTCTGGTACTGACATAAAGAAAAACACATAAC 1165
                           i----             v        i     i  v i   i   iv
  L1M4_orf2#LINE/    251 CAG----TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_9346101_9   1166 TCATTGAGACAGAATCAA-AGTCTATAAATAAATCCACGTTATCTATGGC 1214
                            v  ii i     ii -    i v       i   iii-  i     i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC-ATTTATGGT 345

  chr20_9346101_9   1215 CAATTGATTTTTGACAAGGATGCCAAGACCAATCAATGGGTGAAAGAATA 1264
                                    i       i           v        -         
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATA 394

  chr20_9346101_9   1265 GTCTTTTAAATAAATAGTGACAGGATAATAGGATAGTTCCATGCAAATAA 1314
                                v  i    i   vii   i  iv     ?iiv        ---
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA--- 441

  chr20_9346101_9   1315 ATAGATAAATAAATAAAACTGGATCTTTACCTTATACCATATACAAAAAT 1364
                         --   -------  i  ii    i ii     i i               
  L1M4_orf2#LINE/    442 --AGA-------ATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr20_9346101_9   1365 TAGCTCAAAGAGGATAAAATAACTAAATGCAAGAGCCAAA-CTACAAAAT 1413
                           i      iv    v ? v v       i      i   -   i    i
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr20_9346101_9   1414 TCCTAAAAGAAGCCATAAGGACAAATCTTTATGACCT-GAATTTGGCAAT 1462
                           i  i     iv    i ?ii       ii      - ii  v      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr20_9346101_9   1463 GGATTCT-AAACATGATACCAAAAGCACATGCAAT-------------GA 1498
                           v    - i i    i            v    i-------------  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr20_9346101_9   1499 TACACTGGATTTTCT----GTTGAAAACTTTTATGCTTCAAAAGACACTA 1544
                           v i    i  iv ----i  i         i         i       
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr20_9346101_9   1545 TGAAGAAAGTAAAAAGACTAGTCACAAAA-AGGAAAAAAT--TTGCAATT 1591
                          v        i       v vi    i  -i   i     --      v 
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr20_9346101_9   1592 CATATATCTGATTAGAGGCCTGTATCTAGAATACATAAAGAA-------- 1633
                                     v  i i i      i      i        --------
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr20_9346101_9   1634 ---------------------TAACTCATCTAAATAATGGTCAAATGATC 1662
                         ---------------------    i  vi ?  v     v    v   i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_9346101_9   1663 TGAACAGACATTTCTCCAAATAAGATATACAAAAAACCAAGAAGCACATA 1712
                             i               v            vii    v        i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_9346101_9   1713 AAAAGATGTCTAACATCATTAGTCAT 1738
                                 iii       ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.66 (117 / 44)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.62 (74 / 16)  


3201 26.61 1.22 0.55  chr20_9389437_9395838     5009  5910 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_9389437_9   5009 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTATCGTGAAAAT 5058
                              ii i  i     i        v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_9389437_9   5059 GCCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5108
                          v v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_9389437_9   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ATTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  -  ii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_9389437_9   5157 TATGGAACCAAAAAAGAGCCCTCATTGCCAAGACAATCCTAAGCAAAAAG 5206
                                viiv  ii  v  vvv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_9389437_9   5207 AACAAAGCTGGAGGCATCATGCTACCCAACTTTAAACTATACTACAAGGC 5256
                                i      vv   ii  v     i  i   viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_9389437_9   5257 TACAGTAACCAAACCAGCATGGTACTAGTACGAAAACAGAGATATAGACC 5306
                                 i   iv   ii       i i ii ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_9389437_9   5307 AATGGAACAGAAC--AGAGCCCTTAGAAATAACACCACACATCTACAACC 5354
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_9389437_9   5355 ATCTGATCTTTGACAAACCTGACAAAAACAAAAAATGGGGAGAGGATTCC 5404
                          vi    i  i     ivv  v   i v  vvv        i  i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_9389437_9   5405 CTATTTAATAAATGGTGCTGGGAAAACTGTCTAACCATATGTAGAAAGCT 5454
                           v  i  i              v     vv  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_9389437_9   5455 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5504
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_9389437_9   5505 TTAAAGACTTAAATGTCAGACCTAAAACCATAAAAGCCCTAGAAGAAAAC 5554
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_9389437_9   5555 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5603
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_9389437_9   5604 AAACA--AAAAGCAATGGCCACCAAAGCCAAAACAGACAAATGGGATCTA 5651
                         vi   --       vvi  v  v    vv    i   i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_9389437_9   5652 ATTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATTAGAGTGAA 5701
                           i   v v  i i   i  iiivv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_9389437_9   5702 CAGGCAACTCACAGAATGGGAGAAAATTTTTGCAGTCTACCCATCTGACA 5751
                         v  i    i                  v      ivii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_9389437_9   5752 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5801
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_9389437_9   5802 AAAACAA----CCCCATCAAAAAGTAGGCAAAGGATATGAACAGACACTT 5847
                           i    ----   v  i?    i i          v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_9389437_9   5848 CTCAAAAGGAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5897
                            v    i   i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_9389437_9   5898 CATCACTGGTCAT 5910
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (144 / 92)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


3749 21.63 2.12 0.89  chr20_9527755_9529683.rev      542  1438 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_9527755_9    542 TGAAAAGACATCCTCTGTTCATACATTGGAAGACATAATATTGTTAAGGT 591
                           i     i    iv       iv          v             i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_9527755_9    592 GAAAATGCT-ACGAAAGTCATCCATAGGTTCAATCCAATCCCTATCTAAA 640
                          iv   i  -v v   v v   i i  i     iv           v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_9527755_9    641 TGTCAACAGTGTTTTTTACAGAAATAGGAAAACC-ATCCTAAAATTCATA 689
                          vi  i v iv      i       v iv  i i-               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_9527755_9    690 TGGAATCCCAAAGGGCCCA-AATAGCCAAAACTCTCTTGAAAAAGAA--- 735
                              viv   i  i    -            vv             ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_9527755_9    736 CAATGTTAGAGGATTCACACCTCCTGATCTCAAAACTTACTACAAAACTA 785
                            v   i     i      i   ii  i                 i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_9527755_9    786 CAATTAAAACCAAAATAATATTATAATGGTATAAGAACGGACATCTAGGC 835
                           i ---  i   i i i i vi  v   i     i ii     v   ii
  L1M4_orf2#LINE/    251 CAGT---AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_9527755_9    836 CAATGGAATAGAATATAGCACTCAGAAACAAACCCTCACATATGAGGTCA 885
                                       vv  viii      i      vi    v iv     
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_9527755_9    886 GATGCTTTTCCACAAGGCAACCAAGACTATTTAATGGAGAAAGGATAATC 935
                         iv  v     v      vvi       i   i     i     i   i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_9527755_9    936 TTTTCAACAAATAACGCCGGGAGAACTGGATACCCAACAGCCTAAAAAAT 985
                                     iii  i    v         ?   -  vv v   i   
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA-CATGCAAAAGAAT 446

  chr20_9527755_9    986 GAAGGTGGCCCCTTATCTTATACCATATACATAAATTAACTCAAAATGGG 1035
                             v   v   i  i  i i          v                 i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_9527755_9   1036 TCA-AAATGTAACCACAGAAGTTAAAACTATAAAACTTTTAGAAGGAAAC 1084
                            - i iv   viii ii  i               i       i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_9527755_9   1085 AT-GGCGGAAG-CTTCATGACATTGGATTTAGTAATAATTCCTTGAAAAT 1132
                           -  ? v  i-    i    v    i  vi i   ii  i   ii v  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_9527755_9   1133 TACACCAAAAGCGCAAGCACCGAAAGAAAAAAAATGATAAATTAGACTT- 1181
                         v           i      v i          v -        i     -
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATA-GATAAATTGGACTTC 645

  chr20_9527755_9   1182 ATCAAAATGCAAAACTTTT-TGCACTGAATTACACTGTTAAGAGAGTGAA 1230
                                 vv         -   viii  vv     i i    i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_9527755_9   1231 AA-----TCCGTAGAATATGAGAAAATAGTTGCAAATAATATATCTGATA 1275
                           -----i  ii     iv         v        v            
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_9527755_9   1276 AGGGATTAATACCCAGAATATAGAAAAATCTGTAACAACTCAGCAACAAT 1325
                              i vi  i          v   i v  v v        --- i   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA---ATAAT 792

  chr20_9527755_9   1326 AAAAAGA--AACAGCCCAACTCAAATACAAGCAAAAGACATAGCTAGATA 1373
                                --  i i     i ?   v iii     i  iv iiv    i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_9527755_9   1374 CTGCTCCAGAGAAGATATATAGATGGCTAATAAGTGCAGGAAAAGAAAAT 1423
                         i v     i          i i     i      ii  v       viv 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_9527755_9   1424 CAACAT-AGTCTGAGA 1438
                               - ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (121 / 70)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.69 (27 / 16)  


3204 26.95 0.77 0.88  chr20_9598671_9600410.rev      340  1248 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_9598671_9    340 TGGAAGAACATTCTATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 389
                              ii i  i i   i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_9598671_9    390 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCTCATCAAGC 439
                            v     v     iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_9598671_9    440 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 487
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_9598671_9    488 TATGGAA-TGAAAAAAGAGCCCACATT-GCTAAGTCAATCCTAAGCCAAA 535
                                -  v  i-- ii    v v -  i  iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAG--GGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_9598671_9    536 AGAACAAAGCTGGAGGCGTCATGCTACCTGACTTCAAACTATACTACAAG 585
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_9598671_9    586 GCTACAGTAACCCAAACAGCATGCTACTGGTACCAAAACAGACATATAGA 635
                                   i v i    ii  v      i iv ii i           
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_9598671_9    636 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 683
                         i        i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr20_9598671_9    684 CTATCTGATCTTCGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 733
                         ii vi    i        ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_9598671_9    734 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 783
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_9598671_9    784 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATA 833
                         v    ii    i    v   i     v              i    i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_9598671_9    834 GATTAAAGACTTACATGTTAGACCTAATACCATAAAAACCCTAGAAGAAA 883
                            i ?    i  v    v   v    v  i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_9598671_9    884 ACCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 932
                           v    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_9598671_9    933 TAAAACACCAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATC 982
                           vi            vvi     i    vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_9598671_9    983 TAATTAAACTAAAGAGCTTCTGCACAGTGAAAGAAACTACCATCAGAGTG 1032
                          v  i   v v  i i   i  ii vvii  i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_9598671_9   1033 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGA 1082
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_9598671_9   1083 CAAAGGGCTAATATCCAGAATCTACAATGAACGCAAACAAATTTACAAGA 1132
                         i  i  i  vi          v  i  v    v vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_9598671_9   1133 GAAAATCAAACAACCCCATTTAAAAAGTGGGTGGAGGATATGAACAGACA 1182
                         i   iv    i     v   ?     -    iii     v    i     
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAA-TGGGCAAAGGATTTGAATAGACA 842

  chr20_9598671_9   1183 CTTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCT 1232
                         i     v        i  vi viii     i ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_9598671_9   1233 CATCATCACTGGCCAT 1248
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (148 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


 986 22.65 1.05 5.23  chr20_9690063_9691675        1   287 (1326)    L1M4_orf2#LINE/L1       20   294 (614)  

  chr20_9690063_9      1 CATGGATTGAAATAATTCATATTGGTAAAATGTTCATTCTACCCTGCACA 50
                                  i  v v  v      v   i   viv  v  v   vivvii
  L1M4_orf2#LINE/     20 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 69

  chr20_9690063_9     51 ATCTATAGATTCAAAATTTTGCATCAAAATTCTATCAAAATTCCAATGGC 100
                              i        -----i   ---- vii          i   iiv  
  L1M4_orf2#LINE/     70 ATCTACAGATTCAA-----CGCA----ATCCCTATCAAAATCCCAGCTGC 110

  chr20_9690063_9    101 AATTTTTAACATCAGAAGTAGAAAAAGCAGTGTTAAAATTCATATGAAAC 150
                         vv     i----     i v  v  iviii vi             i  v
  L1M4_orf2#LINE/    111 CTTTTTTG----CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr20_9690063_9    151 CACAAAG-ACCCTGAATAGCCAAACCGATTTTGAGCAAGAACAAGAAGGC 199
                         ii   i -    v           v i  i    iv     v  v  i i
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr20_9690063_9    200 TGGAGGCAC-CATACTTCCCAATTT-AAAATTATATTACAAAGCTATAGT 247
                               -  -  i            -    i -  i          i   
  L1M4_orf2#LINE/    207 TGGAGG-ACTCACACTTCCCAATTTCAAAACT-TACTACAAAGCTACAGT 254

  chr20_9690063_9    248 AATCAAAACAGCATGGCACTGGCATAAAAATAGACACATA 287
                               i    ii   i          ii       i   
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

Transitions / transversions = 1.60 (40 / 25)
Gap_init rate = 0.03 (8 / 275), avg. gap size = 2.25 (18 / 8)  

2282 22.98 1.90 1.90  chr20_9690063_9691675      492  1122 (491)    L1M4_orf2#LINE/L1      278   908 (0)  

  chr20_9690063_9    492 ATAAA-ATAAACATA--GACCAATTGAACAGAATAAAAAACCAAGACATA 538
                             i-   i     --  i    v   i     vi i ii v   v   
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr20_9690063_9    539 AACCCCACACATATACAGTCAAATAATTGTTGACAAGGGCAGCAAGAATA 588
                              - i    v  ii     v i   v i        iiv     vi 
  L1M4_orf2#LINE/    328 AACCC-ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr20_9690063_9    589 CAAAAAGGGGAATGAACAGCCTCTTCAATAAACAGTGATGGGAAAACTGA 638
                         ivv  v      v   i  i  i     i   ii   v     v     i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr20_9690063_9    639 ATATTCACATGTAAAATAATAAAATTGGGCCCTTCTCTTACACCACACAC 688
                            ?i      i    v   i  i    i   i vi  i      i i  
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr20_9690063_9    689 AAAAATCAACTTAAAATGGATTAAAGACTTAAATGTAACACTTGAAGATG 738
                               i    i         i ?    i         v vi i  iv i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr20_9690063_9    739 TAAAACTCCTAGAAGAACACAGAGAAAAAATTCTT--TGACATTGGTCTT 786
                                 i        v   v  i?iv  v    --    v    vi v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr20_9690063_9    787 GGCAGTAAATTTTTGGATATAGCACCCAAAGCATAGGAAACAGAAGCAAA 836
                             i iiv  i  i     ii    v      i i v    i   v   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr20_9690063_9    837 AATAAACAAATGGGACTACATCAAA-TTAAAATGCTTCTGCATAGCAAAG 885
                             i i    v     v       -      -i   i  iiivv     
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCAAAG 675

  chr20_9690063_9    886 GAAACAATTAACAAAATGAAAAGACAACCTATGGAATAGTAGAACATATT 935
                           v  v  i  v   i             i ii    i v    v     
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr20_9690063_9    936 TGCAAATCTTGTATCTGATAAGGTGTTAATATCCAAAATCTATAACAAAC 985
                                 v i            vii vi      i   v     vi   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr20_9690063_9    986 TCATACAACTCAATAGCAAATAAAATAAAACAAATA-CCTAATTTAAA-- 1032
                           v            ----      -- i       -  i    ?   --
  L1M4_orf2#LINE/    776 TCTTACAACTCAATA----ATAAAA--AGACAAATAACCCAATTWAAAAA 819

  chr20_9690063_9   1033 TGGGCACAGGAAGGATCTGAACAGATATATCTCCACAGAAGACAAACAAA 1082
                               ----      i    i   i  v      v      i v     
  L1M4_orf2#LINE/    820 TGGGCA----AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr20_9690063_9   1083 TGGCCAAC---TATATTAAAAGGCACCTGACATCTCTAATCAT 1122
                                i---i i  v     iii iii     v????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (90 / 51)
Gap_init rate = 0.02 (12 / 631), avg. gap size = 2.00 (24 / 12)  


2240 12.17 2.03 21.67  chr20_9732509_9734282      494  1282 (492)    L1M4_orf2#LINE/L1      275   908 (0)  

  chr20_9732509_9    494 GGCACAGAGGATAGACATATACATCAATGGAATAAAACTAAGAGTTCAAG 543
                             i -              v            i  i i     i  ii
  L1M4_orf2#LINE/    275 GGCATA-AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr20_9732509_9    544 AA-AAATTCATACATCTATGGTCAGTTGATTTATGACAAAGGTGCCAGGA 592
                           -   ii       i        i       vi     i       i  
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr20_9732509_9    593 CAATACA-TGGGAAAA-AATCATATTTTCAACAAATGGTGCTGAGACAAT 640
                          v  v  -    i   -   vi v                   i     i
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr20_9732509_9    641 TAAATATCCACATACAAAAGAATAAATTTG-ACCATACCACCTCATACAA 689
                          ii   ?      i         i  v   -   v-- i      i  v 
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCC--CTACCTCACACCA 471

  chr20_9732509_9    690 TATACAAAATTTAACTAAAAATAGATCAAAGACCTAAATGTAAAAGCTAA 739
                                  v      v     i     ?              i      
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr20_9732509_9    740 AGCTATATAACTCTTAGAAGAAAACATAAGGGTAAATCTGCATGACATCA 789
                          i     v                    i ?        v i    v ii
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr20_9732509_9    790 AATTTGGCAGTGGTTCCTCAGTTATAACACCTAAAGCGCAAGCAACCGAA 839
                         ii  v    i     i  i  v   i     v     i        vi  
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr20_9732509_9    840 GAAAAA-T-GATAACTTTGGCTTCATCAAAATTTAAAACTTTCATGC--- 884
                               - -     v  v i             v        ii   ---
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr20_9732509_9    885 AAAGGACACTATCCAGAGTGTGGGCCAGGTGTGATGGCTCATGTCTGTAA 934
                                      -------------------------------------
  L1M4_orf2#LINE/    672 AAAGGACACTATC------------------------------------- 684

  chr20_9732509_9    935 TCCCAGCACTTTGGGAGGCTGAGGTGGAAGGATTGCTTGAGGCCAGGAGT 984
                         --------------------------------------------------
  L1M4_orf2#LINE/    685 -------------------------------------------------- 684

  chr20_9732509_9    985 TTAGGACCAGCCTGGGCAACACAGTGCGACCTTGTCTCTATTAAAAGAAA 1034
                         --------------------------------------------      
  L1M4_orf2#LINE/    685 --------------------------------------------AAGAAA 690

  chr20_9732509_9   1035 ACAACAAACAAACAAAAACAGCAATCAAAAAACAGTGTGAAAAGGTGACC 1084
                         ------------------------------------        iii   
  L1M4_orf2#LINE/    691 ------------------------------------GTGAAAAGACAACC 704

  chr20_9732509_9   1085 CACAAAATGGGATAAAATAAT-GCTAATATTATATCTGATAATGGTCTAG 1133
                             i       v      v -  v   vv            v  v  v 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr20_9732509_9   1134 TATCCAGAATATA--AAAAACTCTTACAACTCAACAATAAAAC-ACAATT 1180
                                      --  i                i       v-    v 
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr20_9732509_9   1181 AACTCAATTTAAAAATGGACACAGAATGTGAATAGACATATTTCCCAAAA 1230
                            i     ?        i  v  i  v           -  ii     i
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT-TTCTCCAAAG 853

  chr20_9732509_9   1231 AA---ATACAAATGGCCAATAAGCACATAAAAAGATGTTTCGCATCATTA 1277
                           ---                       i        i ivi     ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr20_9732509_9   1278 GTCAT 1282
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.71 (58 / 34)
Gap_init rate = 0.03 (16 / 634), avg. gap size = 11.69 (187 / 16)  


1527 26.77 1.60 0.46  chr20_9774316_9777450       22   458 (2677)    L1M4_orf2#LINE/L1        1   442 (466)  

  chr20_9774316_9     22 TGGAGAGGCATACTATATTCATAGATTAGAAGACTCAGCATAGCAAAGGT 71
                             i  ii  v i  i     i    i       i ii  v iv   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_9774316_9     72 ATCAATTTTCCCTAAATTGATCTATATAATCACTGAAATTTCTAT-AAAA 120
                         iv    vi    i           i v v   vi v   ii    -    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_9774316_9    121 TAGTCAG-TATATTTTTTATAGATATAGACAAGTTTATTCTAAAATTTAT 169
                          -vi   - iiv      ii   v  v      i v  i        i  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_9774316_9    170 ATGGAAAGGTATGGG-TCTAGAATAGCTAAA-CAAT-TTGTTCAAGAAGA 216
                                v i v   -i i        i   -    -   vvv       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_9774316_9    217 ATAAGGTGGGAGGAATTGCCCTATCCAAACATTAAGATTTACTCTATAGC 266
                          i  i  v      v ii v  -   v  iv i  i i     vi v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACT-TCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_9774316_9    267 TGCAGTAATCATGACAGCATAGTATTAGCAGAGTGCTAGACACATAGATC 316
                          i         v     ii i   i i   v iv v      i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_9774316_9    317 AATGGAATTGAATAGAGAACCCAGAAATAGACCAATATAAATATGAACAA 366
                                 v    v    ii         i   v   i vv    iv   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_9774316_9    367 CCAATTTTTGACAAAAGTGAAAAAACAATTTCTTGGAGTAAGA-TAG-AT 414
                         iii     i     ii   vv  i  v   ivv   i v    -   -v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_9774316_9    415 TTTCAGCAAATGGTGCTACAACAATTGAACATATATAGGCAAAA 458
                              i           ivi    i  i i ?vi i v      
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

Transitions / transversions = 1.52 (70 / 46)
Gap_init rate = 0.02 (9 / 442), avg. gap size = 1.00 (9 / 9)  

3630 19.78 4.16 2.13  chr20_9774316_9777450     1754  2643 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_9774316_9   1754 TAGAAAGACATCCCATGTTCATAGATTGGAAGACCTAATATTGTTAAGAT 1803
                          i      i             i           i               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_9774316_9   1804 ATCAATACTACCTAAAGCAGTCCACAGATTCCATGCAATCCCTAGCAAAA 1853
                         iv       v  i   viii  i        v i          v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_9774316_9   1854 TCCAAA-TGTTTTTGCAGCAGAA---GAAAGATCTATCCTAAAATTTATA 1899
                            v i-  ii   viv      ---  v iiiiv           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_9774316_9   1900 TGGAATCTCAAGCGACTTGGAATAGCCAAAACAACCTTGAAAAAGAAGAA 1949
                              viv    v   iii               i               
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_9774316_9   1950 CAAAGTTAAAG-ACT-A-ACTTTTTTATTTCGAAGCTCTCTACAAAGCAA 1996
                                ii  -   - -    iiiv     i  i  iv         v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_9774316_9   1997 CAATAATCAAAAGAGTATGGTATTGGCAT-----TAAAT-CACAGACTGA 2040
                           i       i v   i     i      -----  i i-i i   iii 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_9774316_9   2041 TGAAATAGAATAGAGATCCCAGAAATAAACCCTTGCAT--ATTGTCAAAT 2088
                           i        v    vi              v i   --  v     v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_9774316_9   2089 GATTCTTGACAAAGTTGCCAAGACCATTCAGGATGGGGAAAGAACAGTCT 2138
                             i i     i v               --            i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAGAATAGTCT 398

  chr20_9774316_9   2139 TTTTAACAAATGGCACTGGGAAAACTGAGCATCCACTTGCAAAA-AGTGA 2187
                            i         ii      v     iii ?    v       - i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_9774316_9   2188 AGATGGGCCCTTTGTTACCTAACATCATATACAGAAATTAGCTACATTTT 2237
                           v   i   i ----    v   i        i      i  vv vv v
  L1M4_orf2#LINE/    449 AGTTGGACCCCT----ACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_9774316_9   2238 TACCAAAGATGTAAACATAAGTGCCAAAACCATTAAACTCTTAGAAGAAA 2287
                         v i  ?   iv    ii    v  i     i  v                
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_9774316_9   2288 ACATAAAGGAAAACCTACACAACATTGGATTTAGCAGTAATTTCT--AAC 2335
                              ii? v   i  v iii  v    i  vi   i ii     --i i
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_9774316_9   2336 ATGACACCAAAAGTATAGGATAAAAAAGAAAAATTAGATAAGTTGGACTA 2385
                                      i i i vv v          v       i       v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_9774316_9   2386 CAT-AAGATTTAAAACTTCTGTGC--AAAAGACACAATCAGACACAATCA 2432
                            -  i   v       i     --v    ---------     v    
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAG---------GACACTATCA 685

  chr20_9774316_9   2433 ACAGACTGAAAAGGCATCCCATAGTATGGAAAAAAATATTTGTAAATCAT 2482
                          v i v       i  v    i  v    i i          i       
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr20_9774316_9   2483 ATATCTGGTAAGGAATCAATATCCAGAAGATAGAAAGAACTCCTAAAACT 2532
                                i     i iivi         v   v         i  v    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr20_9774316_9   2533 CAACAACAAT----TAAA-AACTC--TTTAACATAAAATAGGCAAATAAC 2575
                            i  i  v----i   -   i --  ?  ----    i      vi i
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAA----AAATGGGCAAAGGAT 831

  chr20_9774316_9   2576 TTGTAT-GACATTTCTCCAAAGAAGACATA-AAAT-------AAGCACAT 2616
                            v  -                   i   -    -------        
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr20_9774316_9   2617 GATATGAAGCTTAACGTCACTAATCAG 2643
                           v v  v   i   i   ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (110 / 62)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.55 (56 / 22)  


1945 22.82 4.22 7.12  chr20_9838927_9840581.rev      476  1163 (492)    L1M4_orf2#LINE/L1      241   908 (0)  

  chr20_9838927_9    476 TACATGAAGCTTCAAAAGTGAACAGACAGCATGGCATTGGTTCAAAAACA 525
                             --     v  iv i v  --     ii   i i   ivi  ii i 
  L1M4_orf2#LINE/    241 TACA--AAGCTACAGTAATCAA--GACAGTGTGGTACTGGCATAAGGATA 286

  chr20_9838927_9    526 GACACATAGACCAATAGAACAGA--TAA---CCCAGGAATAAAGCCACAT 570
                             i     i    i   i   -- i ---i    i      v   i i
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr20_9838927_9    571 ACCTACAGCCATCTGGTCTTCAACAAAGTTGACAAAAATAAGCAATGGGG 620
                          ii  ii i  vi  i i   i    i v  v   i vi vv        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr20_9838927_9    621 AAAAGACTGTCTATTCAATAGATGGTGCTGGGATAACTGG---------- 660
                            ii iv    v     i i            i      ----------
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr20_9838927_9    661 -CAGAAGAATGAAACTGGACTCCGACCTATCACCATATACAAAAATTAAC 709
                         -  i         ii     i  v    vv                    
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr20_9838927_9    710 TCAAGATGGATTGAAGACTTAACTGTAAGACCTCAAACTATAAAAATCCT 759
                             i      ii?    i   v       v  v           v  i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr20_9838927_9    760 AGAAGGAAACCTAGG---AAATACCCTTCTCAATGTCAGCCTTGGCAAAT 806
                              i    v    ---    ---    vii iv ii vi v     - 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAAT---CTTCGTGACCTTGGGTTAGGCAA-T 582

  chr20_9838927_9    807 AATTTAT-GGCTACATCCTCAAAAGCACTTGCAACAAAACTAAAAGTTGA 855
                         ii   v -i v  iiv vi         vv         vv    i v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr20_9838927_9    856 CAAATGGGAC---AT---AATTAAAGAGCTTCTGCACAGCATGAGAAACC 899
                         i    v    ---  ---       i -   i  ii vv  vii  v  i
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACT 681

  chr20_9838927_9    900 ATCAAGGGAGT-AACAGACAACACACAGAGTGGGAGAAAATATTCACAAA 948
                               ii   -  v       v      i              ii    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr20_9838927_9    949 CCACACATCTGACAAAGGTCTAATATCCAGAATCTATAAGGAACTTCAGC 998
                         i  i i      i  i  v  vi          v     i     iivi 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr20_9838927_9    999 AAATCAACAAGCAAAAAAAAAAAAAAAAAACCAAAAACCAAAAACCAAAA 1048
                           v    i  v------------     i  -------------------
  L1M4_orf2#LINE/    782 AACTCAATAAT------------AAAAAGAC------------------- 800

  chr20_9838927_9   1049 AAAAAAAAAAAACAACTCCATAGAAAAGTGGGCAAAGGACATGGGCAGAA 1098
                         ---------   i   i v  v?    i           iv  iii   v
  L1M4_orf2#LINE/    801 ---------AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_9838927_9   1099 ACTTCTCAAAAGAAGACATACATGTAGCTAACAA--ACATGAAAAAATGC 1146
                          i     v        i     vi i  i  i  --         i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_9838927_9   1147 TCGTCATCACTAATCAT 1163
                           iv     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.87 (101 / 54)
Gap_init rate = 0.02 (16 / 668), avg. gap size = 4.88 (78 / 16)  


4338 15.59 3.84 1.24  chr20_9946880_9948912.rev      657  1541 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_9946880_9    657 TGGTAAGCTATTGCACGTGCATGGATGGGAAGAC--GAT---GTTAACAT 701
                            v   v   iv  i  v       v       --i  ---     v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_9946880_9    702 GGTAGTATTCCCAAAATTGGACTACAGATTCAACACAATCCTTATCAAAA 751
                           i i  i    v      iv             i      i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_9946880_9    752 TCCTAGCTGTCTTTCTTGCAGAAGTTGACATGGCTGATTATAAAGTCCAT 801
                            i     i    i        i      -i      iv    i i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

  chr20_9946880_9    802 ATGGAAATGCAAGGGATGCAGTAAGAAGAGTCAAAACACTCTTGAAAAAC 851
                                         iv   ----  v  i       v          v
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAG----AATAGCCAAAACAATCTTGAAAAAG 195

  chr20_9946880_9    852 AA--ACAAAGTTAGAGAACTAACACTTTAGAGTT-CAAAATTTACTACAA 898
                           --        i   i   v      ivv i  -     i         
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_9946880_9    899 AGCTGTAGTAAACAAAAC--TGTGGTACTGGCATAAGGATAGAGATATAG 946
                             ii     v   i  --                       v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_9946880_9    947 GTCAATGGAATCTA-CTAAGAGTACAGAAATAAACCAATACACCTATGGT 995
                         i          vv -i i     v            v     ii      
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_9946880_9    996 CAGTTGAATTTTAACAACGTT-TCAAGACCATCTAATGGGGAAAAGAAGA 1044
                           i    v   ii    v v -i         ii          -   v 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATA 394

  chr20_9946880_9   1045 GTCTTTTCAGTAAATGATACAGGGACAACTGGATATCTACATGCAAAATA 1094
                                  ii     i i v              ? i          v 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_9946880_9   1095 ATAAAGTGGGACCTCTACCTCACATCTTATACAAAAAAATTAACTCAAAA 1144
                           i    v     i          i v          --           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAA 492

  chr20_9946880_9   1145 TGGACCAAAGACCTAAATATAAAAGGTAAAATTATAAAATTCTTAGCCAA 1194
                             i  ?          i   i  v     i       i      vvi 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_9946880_9   1195 AAACATAGCAGTAAGTCTTTGTGACCTTGGATTAGGCA-TAATACCTCTT 1243
                                 v?    i    i          i       - ii --i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT--TTCTT 590

  chr20_9946880_9   1244 AAATGTAAAACCTAAA-TACAAGTAACCAAAGAGAAAATAGATAAATAGG 1292
                          i  i i v   v   -i     i   v     i             v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_9946880_9   1293 ACATCATTAAAA---AAAACTTTTGTGTTATAAAGAATACTATCAAGAA- 1338
                           v    i    ---            i vi    i i           -
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_9946880_9   1339 GTAAAAA-----CCCACAGATTGGGAGAAAATATTCGCAAATCATATATC 1383
                           i    -----        v              i              
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_9946880_9   1384 TGATAAAGTTATAGTATCCAGAATATATAAAGGACTCTTACAACTCATCA 1433
                               i vvv v                   i              vi 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_9946880_9   1434 ATAAAA-GACAAGTGACTCAATTAAAAAAT----AAAAGAGTTGAATA-- 1476
                               -     i i  i     ?      ----   i  v       --
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_9946880_9   1477 --CTTATCCAAAGAA-ACATATAAATGACCAATAA-CACATGAAAAAAAA 1522
                         --i  v         - i   i     i       -          i vi
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr20_9946880_9   1523 TCTCAACATTATTAGTCAT 1541
                         -        i ????????
  L1M4_orf2#LINE/    891 -CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (85 / 49)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 1.96 (45 / 23)  


4142 17.43 7.42 0.71  chr20_10048080_10049964      545  1393 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_10048080_    545 GAAAGTCATTTTATGTTCATGGATTGGAAGAC--AATATTGTTAAGCTAG 592
                              vi  iii                    --            v i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_10048080_    593 CAACACTCCCTACATTAATTTACAGATTAAACCCAAGTCTTATCAAAATC 642
                            i      i v   i  i        v   v   vi i          
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_10048080_    643 TCAACTGCCTTGCTTACAGAATTTGACAAACCTATCCTCAAATTCACATG 692
                         i  i       vi  i     v       i iv     v       i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_10048080_    693 GAAATGTAGTAAACTCAGAATAGCCAAAATAGTCCTGAAAAAGAGGAATA 742
                               i ivii  i              i i  i         i   i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_10048080_    743 AAGTTGGAAGACTTACACTCCCTGATTTCAAAACTTACTACGTAGCTACA 792
                                 i    i     i  ii                 iv       
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_10048080_    793 GGAATCATCCTGAATACTTTG-TACTGGCATAAGGATAGTTATATAGATC 841
                          v     ----ii i v v  -                 vi         
  L1M4_orf2#LINE/    253 GTAATCA----AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_10048080_    842 TATAGAACAAAATTGAGAGTCTAGAAATAAACCCTTACATTTATAATCAA 891
                         v  i   i i           i            v         ii    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_10048080_    892 TTGATTTTGGACAAAGATGTCAACAAAATTCAGTGAGGAAAGAATAGTCT 941
                                 v     i i  i   v vv     i  i              
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_10048080_    942 -----------GGTGCTGGGGTGACTGGATATCCTCATGCAAAAGAATAA 980
                         -----------         iii        ?  v             i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_10048080_    981 AGTTGGACCC-TACCTCATATCATATACAAAAATTAACTCAAAATGTAGG 1029
                                   -       i i                         v vv
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_10048080_   1030 AGAGATCTGAATGTAAGAACTAAAA-TATAAAAATCTTAGCAGAAAACCT 1078
                          ?   i  i         i      -       v      v       v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_10048080_   1079 AGGTATAAATATTCGTGATCTCATATTAAGTGATACTTTCATATGTATGA 1128
                            ?i     v       i  iivi   i ii  iv    v  vi     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_10048080_   1129 CACCAAAAGCACAA------------------------------------ 1142
                                       ------------------------------------
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_10048080_   1143 ---ATCAAAAACTTTTGTGTGTCAGAGAACATCATGAAATAAGTGAAAAT 1189
                         ---  i             iv   i  i   ii  v  iv         -
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA- 697

  chr20_10048080_   1190 AAAAAAACCACAGAATGGGAGAAAATACTTGCAAGCCATATATCTGATAA 1239
                         -i v  v                    i      ii              
  L1M4_orf2#LINE/    698 -GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_10048080_   1240 AACACTTG---CCG-----TATAAAGAACTCTTCAAAGTCAACAAGAAAA 1281
                         iiv     ---  i-----              vv  v    i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_10048080_   1282 TGACAAACAACTCAATTAACAAATGGGGAAATGATCTGAATGAACATTTT 1331
                         v      i   i     ? v       v   v   i     ii      i
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_10048080_   1332 TCCAAAGAAGATATTCAGATGGCTAATAAGCACATGTAAATATCTTCAAC 1381
                                       v  i     i            v   v  vi     
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_10048080_   1382 ATCATTAGCCAC 1393
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (92 / 52)
Gap_init rate = 0.01 (10 / 906), avg. gap size = 6.90 (69 / 10)  


3267 26.46 0.66 0.55  chr20_10087218_10093952     5337  6243 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_10087218_   5337 TGGAAGAACACTCCATGCTCATGGATGGGAAGAATCAGTATCGTGAAAAT 5386
                              ii i ii     i        v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_10087218_   5387 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCTCATCAAGC 5436
                            v     v     iv i  i  i        i  v    ii     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_10087218_   5437 TACCA-CTGACTTTCTCCACAGAAATGGAAAAAAACT-ACTTTAAGGTTC 5484
                          v   -   v    i i-i       v  v  i--  - iii   ii   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr20_10087218_   5485 ATATGGAGCCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAA 5534
                                iviiv  ii  v  viv        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_10087218_   5535 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACAATACTACAAGG 5584
                                 i      vv   ii  v  ii i      vvv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_10087218_   5585 CTACAGTAACCAAAACAGCGTGGTACTGGTACCAAAACAAATATATAGAC 5634
                                  i   i    i          i iv ii i i i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_10087218_   5635 CAATGGAATAGAACAGAGGCCTCAGAAATAACACCACACATCTAAAACCA 5684
                                      iv   ivii         vv   i    i  viii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_10087218_   5685 TCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAATGATTCCC 5734
                         vi    i  i     ivv  v   i v  vv           vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_10087218_   5735 TATTTAGTAAATGGTGCTGGGAAAGCTGGCTAGCCGTACATAGAAAGCTG 5784
                          v  i ii              v i    v  ?  ii iii i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_10087218_   5785 AAACTGGATCCCTTCCTTACACCATATACAAAAATTAACTCAAGATGGAG 5834
                           ii    i    v   i                         i     v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_10087218_   5835 TAAAGACTTAAATGTAAGACCTAACACCATAAAAACCCTAGAAGAAAACC 5884
                         i ?    i           v    v  i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_10087218_   5885 TAGG--TAATACCATTTAGGACATAGGCATGGGCAAAGACTTCATGACTA 5932
                             --   - i -  iiv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_10087218_   5933 AAACACCAAAAGCAATGGCAACAAAAGTCAAAATAGACAAATGGGATCTA 5982
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_10087218_   5983 ATTAAACTAAATAACTTCTGCACAGCAAAAGAAACTATCATCAGGGTGAA 6032
                           i   v v  v     i  ii vv    i  v       vv ii     
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_10087218_   6033 CAGGCAACCTACAGAATGGGAGAAAATCTTTGCAATCTACCCATCTGACA 6082
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_10087218_   6083 AAGGGCTAATATCCACAATCTACAAAGAACTTAAACAAATTTACCAGAAA 6132
                          i  i  vi      v   v  i        ivv    v iv iv v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_10087218_   6133 AAAATAAACAACCTCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 6182
                           i i   i    iv  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_10087218_   6183 CTCAAAAGAAGACATCTATGCAGCCAACAG--ACAGGAAAAAATGCTCAT 6230
                            v        i  vi viii     i i--   v     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_10087218_   6231 CATCACTGGTCAT 6243
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (144 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


1557 20.91 4.03 1.26  chr20_10134201_10136013.rev      104   500 (1313)    L1M4_orf2#LINE/L1       82   489 (419)  

  chr20_10134201_    104 AACAAAAACTTTACTGAAAAACCCAGAAATG---TTTTTGGGAAAATAAA 150
                            iv  v ii  - v    v     v--  ---      vii    vi 
  L1M4_orf2#LINE/     82 AACGCAATCCCTA-TCAAAATCCCAGC--TGCCTTTTTTGCAGAAATTGA 128

  chr20_10134201_    151 CAGTATGGTTCTAAAATTTATATAGCAATGCAAGTAACCCAGAATAGCCA 200
                           ivv  i i        i    i v        vi              
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr20_10134201_    201 AAA-AATCTTGAAAAAGAAGAACAAAGTTGGAAGAGTCACACTTCCGCAT 249
                            -                            i  v          vv  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr20_10134201_    250 TTCCATACTTAATACAAAGGTATAGTAATAAAGACTTTACGACACCAACA 299
                            v v     v       v  i      v     vv ii ii  iii  
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr20_10134201_    300 TAA----AAACAAATA----ACTGGGATCAGATTAAATGTCCAGAAGTAA 341
                            ---- i   v   ---- v   i  vii   i iv        i   
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr20_10134201_    342 -CCCTTTCATTTATGATTAATTTATTTTTTGACAAGGGTGACAACAGAAT 390
                         -   v v        i i    v     i-          v   v vv  
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTC-GACAAGGGTGCCAAGACCAT 377

  chr20_10134201_    391 TCAATGTGGAAAAAAATAGTATTTTTAACAAATGGTGCTGCAAGAATTGG 440
                               -  i   i      v    i              vi v  i   
  L1M4_orf2#LINE/    378 TCAATG-GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr20_10134201_    441 ATATCCACATGCAAAAAAATGGCGT---ATCTGTTTCTCACACCATATAG 487
                            ?            i    iv  --- i iv vi             v
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr20_10134201_    488 AAAAACTAACTTA 500
                              i     i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCA 489

Transitions / transversions = 1.10 (43 / 39)
Gap_init rate = 0.02 (10 / 408), avg. gap size = 2.10 (21 / 10)  

3087 18.10 6.93 3.89  chr20_10134201_10136013.rev      501  1323 (490)    L1M4_orf2#LINE/L1       61   908 (0)  

  chr20_10134201_    501 CCCGAAGTGATCTATAGGTTCAATGCAATTCCTATCAAAATCTCA-TTGA 549
                            i  v       i  i     i     i            i  -i  v
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGC 110

  chr20_10134201_    550 CATTTTTTTTCAGAAATAGAAAA----ATCCCTCTAAAATTCATATAGAA 595
                          --      v       v  v  ----    ---            i   
  L1M4_orf2#LINE/    111 C--TTTTTTGCAGAAATTGACAAGCTGATCC---TAAAATTCATATGGAA 155

  chr20_10134201_    596 TCTCAAGGGATTCTAAATAACCAAAATGATATTGAAAAAGAAGAATAAAG 645
                         viv       ii vi    i      ii  v              i    
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr20_10134201_    646 TTGCAGT-TTCAGATTTCCTGATTTCAAAACTTACAATGAAGCTTCA-TA 693
                            v  v-i   v i    ii              v ii     v  -  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr20_10134201_    694 ATCAAGGCAGTGTAGTATTGGCATAAAGTCAGAC--------CAATGGAA 735
                               i      i   i        i vi    --------        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr20_10134201_    736 TAGAATAGAGGGTCCAGAAATAAATGCTTGCATATAGTATGGTCAAATCA 785
                               v   i             iv v i   - --         v v 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACAT-T--TATGGTCAATTGA 352

  chr20_10134201_    786 TTTTTGACAAAGGCTCCAAGACCA----ATGGGGAAAGGGCAGTATTTTC 831
                             i     i  iv         ----          iii   v     
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr20_10134201_    832 AACAAATGATGCTCAGAAAACTGCAAAATATGCAAAAGAATGAGGTTCAT 881
                                 i    vi  v     ---i   ?v  -------------   
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTG---GATAKCCA-------------CAT 436

  chr20_10134201_    882 TTGCAAAAGAATGAGGTTGGCCCAGTTCCTCATATCATAGAAAAAAATTA 931
                         --            i     v  vv v     i i    v v        
  L1M4_orf2#LINE/    437 --GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr20_10134201_    932 ACTCAAAATTGATCA-AAACCT-----TAAGAGCTAAAACTATAAAAATC 975
                                  v     - i    -----                    v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr20_10134201_    976 TTAGCATAAAACATATGTGCACATTTTTATGACCCTGGATCAGGCATTGA 1025
                             v v        v ? i v  i  ii     i   i i     v  i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr20_10134201_   1026 -------------ACACCAAAA-TACAAATGACAGCA-----AAT-TATA 1055
                         -------------         -i    iii   iv -----   -v   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr20_10134201_   1056 AATTTGACTTCCTCAAAATAAAAAAAAGTTAAATGTGTTTCTAAAGATAC 1105
                             v      v       v     v-v  ---    i   v  i  i  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAAC-TTT---TGTGCTTCAAAGGACAC 680

  chr20_10134201_   1106 AATTTTACAAATGAAAAGGCAAAAAGCAAAAAGGAAAATAATATTTGCAG 1155
                         v  ivviv  i       i   vvvi  i  v  i i v          i
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr20_10134201_   1156 ATCATATATCTGATAAAGGACTTCTATGCAGAGTATTTAAAGGACCTTTA 1205
                                         i      v   v    i   v     i  ii   
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr20_10134201_   1206 CAACTCAATAA---AAAGACAA----CACAACTTAAAAATGAGAAAAAAA 1248
                                    ---        ---- v   i ?       i v   ii 
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr20_10134201_   1249 TTTAAGAAT---TATTTTTCTAAAGCAGAT-TACAAATGGCTAATAAACA 1294
                            --    ---i    i  i    v    -          i     i  
  L1M4_orf2#LINE/    831 TTT--GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr20_10134201_   1295 CATGAAAA-ATGCTTGACATGATCAGTCAT 1323
                                 -     ii    v ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (84 / 62)
Gap_init rate = 0.03 (27 / 848), avg. gap size = 3.30 (89 / 27)  

 740 18.18 0.61 0.00  chr20_10134201_10136013.rev     1649  1813 (0)    L1M4_orf2#LINE/L1      598   763 (145)  

  chr20_10134201_   1649 ATACCAAAGGCACAGGCAACAAAAGAAAAAAAAG-TAAGTTGGACTACAT 1697
                          i      i     i                v  -   i       v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_10134201_   1698 CAAAAATAAAAATCTCTAGGCATCAAAGGAAATAATTAATAGAGTGAAAA 1747
                              v      ii i iv  v        v iv  i  v i        
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_10134201_   1748 GACAACCCACAAAATGGAAGAAAATATTTGCAAATAGCATATCTGATAAA 1797
                                    i     i                 vii           i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_10134201_   1798 GAATTAATATACAGAA 1813
                          i i vi   v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAA 763

Transitions / transversions = 1.73 (19 / 11)
Gap_init rate = 0.01 (1 / 166), avg. gap size = 1.00 (1 / 1)  


1314 17.77 0.83 0.00  chr20_10383144_10386985.rev     1457  1698 (2144)    L1M4_orf2#LINE/L1        1   244 (664)  

  chr20_10383144_   1457 TGGAAAGATAACCCGTGTTCATGGATTGTAAGACTTAAAGCGGTTAATAT 1506
                                   v   i             v         viiv     v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_10383144_   1507 AGCAATATTCCC-AAATTGTTCT-CAGATTCAACATAATCCCTATCAAAA 1554
                         i      i    -      v   -          ii              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_10383144_   1555 TCCCAGCTGACTTCTTTATAGAAATTAACAAGTTTATCCTAAAACGTATA 1604
                                  v   i   ii       i     i v         ivi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_10383144_   1605 TGAAAATGCAAGAGATCTGGAGTAACAAAAACAATACTGAAAAAGAAGAA 1654
                           i         i  i ii  i  i v        vi             
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_10383144_   1655 TCAAATTGGAGAACTCAGCCTTCTCAATTTAAAAGCTTATTACA 1698
                         iv  i      i     vv    i      v   i    i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

Transitions / transversions = 1.87 (28 / 15)
Gap_init rate = 0.01 (2 / 244), avg. gap size = 1.00 (2 / 2)  

 227 21.74 0.00 0.00  chr20_10383144_10386985.rev     2011  2056 (1786)    L1M4_orf2#LINE/L1      232   277 (631)  

  chr20_10383144_   2011 AAAGCTTACTACAACATCACAACAATCAAAACAGTATGGTACAGGC 2056
                            i          viii   ii      i     i      v   
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

Transitions / transversions = 4.00 (8 / 2)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.00 (0 / 0)  

3041 14.70 5.57 0.34  chr20_10383144_10386985.rev     2759  3350 (492)    L1M4_orf2#LINE/L1      286   908 (0)  

  chr20_10383144_   2759 AGACATACAGGTCAATTGGAATAAAATTGA-----TAGAAATAGATCCTT 2803
                                i  i     -      i      -----i       i i  v 
  L1M4_orf2#LINE/    286 AGACATATAGATCAAT-GGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr20_10383144_   2804 AAATTTATGTTCAATTGATTTTCAACAAGGGTACTAAGATAACTTGATGG 2853
                          v       v             i        i i    iv i ii    
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr20_10383144_   2854 GAAAA---TAGTTTTTTCAACAAATGGTTCTAGAACAACTGAGTATCCAT 2900
                          i   ---    i               v  i i       ii  ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr20_10383144_   2901 ATGCCAAATAATAAAGTTAGACTGCTACATCACACTATATACAAAAAGTT 2950
                             v   v   i     i   iv    v      i           -  
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA-TT 483

  chr20_10383144_   2951 AAATCAAAATGGATCATAGACCTAAATATAAGAGCTAAAACTATAAAAAT 3000
                           v             ?          i                    v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr20_10383144_   3001 CTTAGGAAAAAACAAAGGCATAAATTTTTGTGACCTTTCATTAGGCAACA 3050
                              i i      v   ?i     i  i        vvi        ii
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr20_10383144_   3051 GTTTCTTAGATATGATACCAAAA-CAGAAGTGACAAAC--ACAATTAG-T 3096
                                        i       -  v   ii     v-- v  v   - 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr20_10383144_   3097 AAATTAGATTTTATCAAAATTAAAAACTTTTATACTTCAAA--------C 3138
                              i  i  i                   i i       --------i
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr20_10383144_   3139 CAAGAAAGTAAAAAGATAATACACAGAATAGAAAAAAA-ATCTGCAAATC 3187
                                  i      i  iv        i i i    -  i        
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr20_10383144_   3188 ATACATCTGATGAAGGACTCATGTCCAGAATATATAAAGAACTC----AA 3233
                            i       i i     ii i                     ----  
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr20_10383144_   3234 CTCAATAA---GAGGACAAATAA-----TTTAAAAATAAGCAAAGAATTT 3275
                                 ---i i         -----  ?      ii      i    
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr20_10383144_   3276 GAATAGACATTCCTTCAAAGAAGATATACAAATGACCAATAAGCACATGA 3325
                                    i  i                   i               
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr20_10383144_   3326 AAAGATGCTTAACATCATTAGCCAT 3350
                                  i       ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.37 (64 / 19)
Gap_init rate = 0.02 (12 / 623), avg. gap size = 2.92 (35 / 12)  


3273 23.87 1.46 0.49  chr20_10491310_10493117.rev      496  1316 (492)    L1M4_orf2#LINE/L1       80   908 (0)  

  chr20_10491310_    496 TTAAC-CAATCCCTACCAAAATACCAATGACATTCTTCACAGAAATAGAA 544
                          i   -         i      v   iivi v  i  ii       v  v
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chr20_10491310_    545 GAAAGTAACACTATAATTTGTATGGAACCACAAAAGACCCA-AATAGCCA 593
                         -  iv i iv   v    ii       vii   ii      -        
  L1M4_orf2#LINE/    130 -AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr20_10491310_    594 AAGCAACTGTGAGCAA-AAGAACAAAGCTGGAAACATCATACTACCTGAT 642
                           i   iiv   iv  -          i    iivv   i   v  ii  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr20_10491310_    643 TTCAAAATATACTACAAAGCTATAGTAACCACAACAGCATGGTATGGTTA 692
                                iv             i     i  vi    ii     iv vi 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr20_10491310_    693 TAAAAACAGACACATAGAGCAATGGAACAGAATAGAGAACCCAGAAATAA 742
                            ii i     i     v        i     v    ii          
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr20_10491310_    743 GTTCACTTATTTAGAGCCAACTGATTTTTAACAAAGGTGCCAAGAACCAT 792
                         iii  ivi     vi i   i       ii    i          -    
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA-CCAT 377

  chr20_10491310_    793 ATTA--GGGGAAAGGACACTTTCTTTAATAAATGCTGCTGGGAAAACCGG 840
                         - i --        i i v i i  i  i     v        v   i  
  L1M4_orf2#LINE/    378 -TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr20_10491310_    841 ATATCCATATGCAGAAGAATGAAACTGGGCCCCTATCTCTCACTGGATAC 890
                            ?   i     i         ii   i      i   v   iiv    
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr20_10491310_    891 AAAAATCAACTCAAAATGAATTAAAGACTTGAATTTAAGACCCAAAAACT 940
                               i           i  i ?    i i   v     v i    -  
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CT 525

  chr20_10491310_    941 AAAAAACTACTAGAAGAAAACCCAGAGGAAACTCTTCAAGACATTGGTCT 990
                          v      vi           vi  i? v  v     iv   v    vi 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr20_10491310_    991 AGGCAAGGATTTTATGAATCAGACTTCAAAAGCACAAGCAATAAAAACAA 1040
                               v i   iv ii  vv   vi               i    iv  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr20_10491310_   1041 AAATAGAAAAATGGGACTATATCAAACTAAAAATCTTCTATACAGCAAAG 1090
                                v    v     vi      v v    v   i i i vv     
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr20_10491310_   1091 GAAACAATCAACAGCATGAAGAGACAACCTGTAGAATGGAAGACAGTATT 1140
                           v  v     v ivi    i        iii       i   v i    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr20_10491310_   1141 TGCAAACTATTAATCTGACAAGGGACTAATGTCCATAATATACAAAGAAC 1190
                               ii  vv      i        vi i    v      i       
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr20_10491310_   1191 TCAAATAACTCAATAGCAAATAAGCGAAT---CTGATTTTAAAATGTGCA 1237
                           vv i         ii   v ii i   --- ii   ?v      v   
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr20_10491310_   1238 AAGGATTTGAATA----TTTCTCAAAGGAAGACATACCCATGGCCAACAA 1283
                                      ----      v  i     i    vv        i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr20_10491310_   1284 GTATATGAAACATTGCTTAACGTTATTAATCAT 1316
                          i i      viv    i   i i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (122 / 70)
Gap_init rate = 0.01 (10 / 829), avg. gap size = 1.60 (16 / 10)  


2362 20.89 4.86 5.87  chr20_10515742_10517417      486  1184 (492)    L1M4_orf2#LINE/L1      217   908 (0)  

  chr20_10515742_    486 ATACATACAAATTACTCAAA--TTAAAACAAAGCTATAGCAAGCAAAACA 533
                          i  v v v    --     --   vv         i  i  v   i   
  L1M4_orf2#LINE/    217 ACACTTCCCAATT--TCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr20_10515742_    534 GAATAGCACTGGCGTAAAAATGGGCCC-TAGACCAACAGAACAAAATAGA 582
                          vi i i      i   ii  i i vi-    i   ii   i i   v  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr20_10515742_    583 GAGCCCAGAAATAAACTCATGTGTATATGGCCAAATATTCTTTGACAAGA 632
                            i            i   iii v     i   v iv i  i      i
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr20_10515742_    633 GCACCAAAA--ATGCAAAATGGGGAAAGAATAGTCTCTTCAATAAATGGT 680
                          ii    i --  v   --                 i     i       
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAA--TGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr20_10515742_    681 TCTGGGTAAACTGGATATCCAAATGCAAAAGAATGAACTTGGATCTTTAT 730
                         v     vv         ?   v               v     i ii  i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr20_10515742_    731 CTTATACCATACACAAAAATTAA-----AATATATTAAAGTCTTAAATGT 775
                           i i      i           -----   iv  i ?  v i       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr20_10515742_    776 GAGACCTGAAACCATAAAACTTCTAGTAGAAGAAGTTGGG--AAATGGCT 823
                         i   v  i    i        ii   v    i vi v  ?--    --  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CT 560

  chr20_10515742_    824 CCTTGACATTGGTCCTGACAATGATTTTTTTGGATGTGACCCCAAAAG-A 872
                         i v    v    viiv i     i   i  -i   i    v       - 
  L1M4_orf2#LINE/    561 TCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCA 609

  chr20_10515742_    873 CAGGTAACAAAAGCAA----------------CTATATCAAA-CTAAAAA 905
                           i i        v  ----------------  vi      -i      
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr20_10515742_    906 CTTCTGTGCAGCAAAGGAAACAATCAACAAAATGAAAAGGTAACCTATAG 955
                            i     vv       v  v     v   i       ii    i i  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAG 709

  chr20_10515742_    956 AATGGAATAAA-TATTTTCAAGCCCATATATCTAATAAGGGATTAATATC 1004
                              i v   -     v   ii -        i        i vi    
  L1M4_orf2#LINE/    710 AATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGGGACTTGTATC 758

  chr20_10515742_   1005 CAAAATATATAAGGAACTCATACAACTCAATAGCAAAGAAAAAAAAGGAA 1054
                           i         i      v            ii   -------------
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAA------------- 795

  chr20_10515742_   1055 AAGGAAGAAAGAAAACAACTAAATTAAATACCCCAATT-AAAAATGGG-G 1102
                         -----------  i    v   ---------       -         -i
  L1M4_orf2#LINE/    796 -----------AAGACAAATAA---------CCCAATTWAAAAATGGGCA 825

  chr20_10515742_   1103 AAGGACCTAAGTAGATATTTTCCCAAAGAAAACATATAA-TTGTAAACAG 1151
                              ii i i    i    ii        i i   i  - v iv  i i
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr20_10515742_   1152 GTATATGGAAAGGTGCTTAACGTTATTTACCAT 1184
                          i i   i    i    i   i i ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (100 / 43)
Gap_init rate = 0.03 (19 / 692), avg. gap size = 3.95 (75 / 19)  


3061 27.23 0.88 0.77  chr20_11075605_11082365.rev     5363  6269 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_11075605_   5363 TGGAAAAACATTCCATGCTCATTGATAGAAAGAATCAATATCGTGAAAAT 5412
                               i i  i     i    v   v i    v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_11075605_   5413 GGCCATACTGCCCAAGGTAATTT-TAGATTCAATGCTATTCCCATCAAGC 5461
                            v     v     iv i  i -i        i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_11075605_   5462 TACCATTGACCTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTCA 5510
                          v   vivi    i  ii     v v  v  i--  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr20_11075605_   5511 TATGGAACCAAAAAAGAGCCTACATAGCCAAGACAATCCTAAGCAAAAAG 5560
                                viiv  ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_11075605_   5561 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATGCTACAAGTC 5610
                                i      vv   ii  v  ii i      viv i      iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_11075605_   5611 TACAGTAACCAAAACAGCATGATACTGTTACCAAAACAGATATATAGACC 5660
                                 i   i    ii  i     vi iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_11075605_   5661 AATGGAACAGAACAGAGGCCTCAGAAATAATGCCACAGATCTACAACCAT 5710
                                i    iv   ivii         vv   i v  i  iiii  -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA- 347

  chr20_11075605_   5711 CAT--ATCTTTGACAAACCTGGCAAAAATAAGCAATGGGGAAAGGTTTCC 5758
                         -  --  i  i     ivv  v   i vi vv            iv vvi
  L1M4_orf2#LINE/    348 -ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_11075605_   5759 CTATTTAATAAGTGATGTTGGGAAAACTGGCTTGCCATATGCAGAAAACA 5808
                           v  i  i  i  i  i     v      v v?   i     i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_11075605_   5809 GAAACCGGACCCCTTCCTTACACCTTATACAAACATTAACTCAAGATGGA 5858
                            iii        v   i     v        v          i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_11075605_   5859 TTAAAGACTTAAACGTAAGACCTGAAACCATAAAAACTCT-AGAAGATAA 5907
                          i ?    i    i      v  i    i      -    -      v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr20_11075605_   5908 CCTAGGCAGTA--CCATTCAGGACATAGGCATGGGTGAAGGCTTCATGAC 5955
                          v    ?-   --i -   iv   v v  vv i  ii v  i   v iiv
  L1M4_orf2#LINE/    546 CATAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_11075605_   5956 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATC 6005
                           vi            vvi          vv     v  i    vi  ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_11075605_   6006 TAATTAAACTAAAGAGCTTCTGCACAGGAAAAGAAACTATCATCAGAGTG 6055
                          v  i   v v  i i   i  ii vvv   i  v       vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_11075605_   6056 AACAGGCAACCTAAAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGA 6105
                           v  i     i v               v       vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_11075605_   6106 CAAAGGGCTAATATCCAGAATCTACAAGGAACTTTAACAAATTTACAAGA 6155
                         i  i  i  vi          v  i  i     i v    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_11075605_   6156 AAAA-ACAAACAACCCCATCAAAAAGTGGGCAAAGGATGTGAACAGACAC 6204
                             -     i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_11075605_   6205 TTTTCAACAGAAGACATTTATGCAGCCAAAAAACATATGAAAAAAAGCTT 6254
                           i  v v      i  vi viii     v  i  i       i v   i
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_11075605_   6255 ATCATCACTGGCTAT 6269
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


3405 21.49 5.23 0.23  chr20_11225691_11229713     2671  3531 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr20_11225691_   2671 AAGACACCCTAAGTTCAAGGATTGAAAGAC--AATATTGTTAATACAGCA 2718
                             i i  i v     v      i     --           v ii   
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr20_11225691_   2719 ATGCTCCCCAAATTGATCCAAAGCTTCAATGCAAACTCTATCAGAACACT 2768
                           i               i v  v     i    v i      i  iv i
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr20_11225691_   2769 AGTTGGCTTTTAAGAATAATTTGACAAGCTGGCCCTAAAATTCATACGGA 2818
                           i  v     vv v v  v           ii             i   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr20_11225691_   2819 AATGCAAAGTATCTGGAATAGGAGAAACAATCTTGAAAAAGAAGAAAAAG 2868
                                i v i ii      vvi                      v  i
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr20_11225691_   2869 ATTGGAAGACTCACACTTCATAATTCCAAGTCTTCCTACAAAGCTGCAGT 2918
                         i     i            vi    i   iv   v          i    
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr20_11225691_   2919 AATAAAGACCAAGTAATACTAACATAATGATAGACATATAGATTAATAGA 2968
                            v     viv  ii    ii     v               i   i  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr20_11225691_   2969 GTAAAATTAGTGGTCCAAAAATAAACTCTCAAATTTATGGTCAACTAATT 3018
                         i  i    iivi     i        i vi v            i i   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr20_11225691_   3019 TTCAACAACATTGTCCAGAAAATTTAAT-------------TCTTTTAAT 3055
                            i    viv  i v   vv   i   -------------      v v
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr20_11225691_   3056 TAAATTGAGCTGGGGCA---------CCA--TGCAAAATAATTATTTTAG 3094
                         i    v v      i  ---------   --       v   v vv  i 
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr20_11225691_   3095 ACCCCGACCTCACATCATACTCAAAAATTAA-----AGTAGATCATAGAA 3139
                              v        i    iv          ----- i i     ?   v
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr20_11225691_   3140 TTAAGTTTAAGAATTAAAATGTTAAAACTCTTAGAATAAAACA--GAAGT 3187
                         i   i v     ii     ivv              v      -- i?  
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr20_11225691_   3188 AAATTTTTGTCACTCTGAATTAAGCAATGGTTTCTTAAATATGACACCAA 3237
                             i  i  v  ii  ii   i              i            
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr20_11225691_   3238 AATCAGAA--AATAAAAAAAAA----GATGTATTAGACTTGATCAAAATT 3281
                           v  v  --  i    i    ----   iv   i     v         
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr20_11225691_   3282 TAAAATATTCATCCTT-AAACCACATCATCAAGACAACAAAGCAACAATC 3330
                         v    iv  ii v   -   vv   ii       v iii  ivi    i 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr20_11225691_   3331 CA--GTCTTGGAGAAAATATTTGACAATAATATATTTGAGAAGGAGACTA 3378
                           -- vv v              vv   v      i   v    -    v
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG-GACTT 753

  chr20_11225691_   3379 CT-TACAAAATACATTTAAAAACTCTTACATTTCA-TAATGAAAATACAA 3426
                         v - v  i    i  v-  i          vi   -    i    v    
  L1M4_orf2#LINE/    754 GTATCCAGAATATATA-AAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr20_11225691_   3427 GTAATCCAACTTAAAAATGAACAAAGTATTTGAATAGGCATTTCTTCAAA 3476
                         i   i    i ?       ii     v          i       i    
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr20_11225691_   3477 GAAGATATCAAAACAGACAATAAGGACATGACA-GATACTTAGCATCATT 3525
                                 vv   ii v       v      v -   i  i i     ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr20_11225691_   3526 AACTGT 3531
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.33 (104 / 78)
Gap_init rate = 0.02 (15 / 904), avg. gap size = 3.13 (47 / 15)  


3859 19.32 1.75 2.44  chr20_11236307_11238154      498  1356 (492)    L1M4_orf2#LINE/L1       56   908 (0)  

  chr20_11236307_    498 TAATCTTCATATTGATCTACAGATTCAACACAATTCCTATTGAAATCTCA 547
                           v  ii  v                   i    i     ii     i  
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr20_11236307_    548 ACTGGCTTTTTCTTTTTTTATTTTTATTTTTTTTAGAAATTGACAAACTG 597
                         i   ------- i      ii-------------            i   
  L1M4_orf2#LINE/    106 GCTG-------CCTTTTTTGC-------------AGAAATTGACAAGCTG 135

  chr20_11236307_    598 ACCCTAAAATTCATATGGAAATGTAGAGGACTCCAAATACACAAAACAAC 647
                          i                     i ii    i vi    vv        i
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr20_11236307_    648 CTTCCAAAACACGAAAGAAATTTGAAAGACATACATTTTCCAATTTCAAA 697
                            vv    v v   v-   v   i i   vi   i  i           
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAAC-AAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr20_11236307_    698 GCTTACTACAAAGCTATAGTAACTAAGACTCTATGGTATTGACATGAGGA 747
                         i               i     ii     vv i     i  i   i    
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr20_11236307_    748 TAGACATATGAATCAATAGAACAGAATTGACAGACCAGAAATAAACT-A- 795
                                  ii      i   i        v  v            i- -
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr20_11236307_    796 ACATTTATAGTCAATCGATTATCAACAAAGTGAGCAAG-CAATTTGTTGG 844
                                 i      i    v  i    i vviv    - v   iiv   
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr20_11236307_    845 AGAAATAAGAGCCTTTTCAACAAATTATGCTGGTACAACTGGATATCTAC 894
                         i    v  v  i             vi      v           ? i  
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr20_11236307_    895 ATGCAAAATAATGAATTTGGGTGCCTATCTTACACTATATGCACAAAT-A 943
                                 v      v    iiv    i  i    i    i  v    - 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr20_11236307_    944 ACTCAAAGTGAATCACAGACCTAACTATAAGAGCTAAAACTATAAAACTA 993
                                i  i    ?        v i                      v
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr20_11236307_    994 TGAGAATAACACATAGGTGTAAATT---GTGAAGTTAGATCAGACAGTGC 1040
                          v    v  v       ?      i---    vv  i i i  i  i  v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr20_11236307_   1041 TTTCTTATATATGACACCAAA-------GTGTCAATAGAAAAAATAGGTA 1083
                                v             ------- iiv   v           i  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr20_11236307_   1084 AACTAGACTTCATCAAAATTAAAAACGTTTGTGTTTCAAACTACGCAATT 1133
                           i i                     v      i      vv  i v  i
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr20_11236307_   1134 AATAAAGTGAAA-GATAGTATCTAGTCTTGGAGAACATACTGACCAATCA 1182
                           v         -  i iivivi  vv v      v   i vi v     
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr20_11236307_   1183 CGTATCTGATTAAGAACTTGTACCTAGAATATATAAATAACTCTTAAAAC 1232
                         ii        v i i       i i            v        v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr20_11236307_   1233 TAAATAACAAAAAGCCAAATAATTCAATTACAAAATGGGCAAAGGATTCA 1282
                          v     i      v       ii     ?v                 ii
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr20_11236307_   1283 AATAGATAGTTCTCTGAAGAAGATATGCAAACAGACATTAAGCATATAAA 1332
                               i v     ii          i    ii v  v      i  i  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr20_11236307_   1333 AGGATGCTCAATATCATTAGTCAT 1356
                          i         i    ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (99 / 63)
Gap_init rate = 0.01 (10 / 853), avg. gap size = 3.60 (36 / 10)  


2825 21.60 4.27 2.20  chr20_11245214_11246939.rev      467  1239 (487)    L1M4_orf2#LINE/L1      120   908 (0)  

  chr20_11245214_    467 AGAAA---ACAACCC-ATCCCAAA---CA-GTGAGAATAAAAAAAAGACT 508
                              ---    v i-    i   ---  -i  ii   iv  ii--   i
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG--GACC 167

  chr20_11245214_    509 CTGAACAGCCAAACTAATCTTGGGCAAGAAAAATAAAGCTGGAGGCCTCA 558
                          v   i       vi       iiv     i  i    i      v    
  L1M4_orf2#LINE/    168 CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCA 217

  chr20_11245214_    559 CACTTTCTAATTTCAAAATATATTACAAAGCTACAGTAATTAAAACAGTA 608
                              i i          iv  i                 i  i     i
  L1M4_orf2#LINE/    218 CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG 267

  chr20_11245214_    609 CAGTACTGACATAAAGACAGACATACAGACCAATTAAAT-GAATAGAAAG 657
                         ii      i     i  i       i   i    vi   -    v  i  
  L1M4_orf2#LINE/    268 TGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAG 317

  chr20_11245214_    658 CCCAGAAATAAACCCA--CATTAATATGGTCAACTGATCTTCAACAAGAG 705
                         i               --    --         i    i   i     i 
  L1M4_orf2#LINE/    318 TCCAGAAATAAACCCATACATT--TATGGTCAATTGATTTTCGACAAGGG 365

  chr20_11245214_    706 TGCCAAACATACACAATGAGGAAAAGATAGTCTCTTTAGAAAATTGTGCT 755
                               ivvi iv     i     ii       i  i iv    v     
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCT 415

  chr20_11245214_    756 GAGAAAACTGGATATTCACAAGCAAAAGAATAAAACTTAGACCCATATAC 805
                          i  v         ?i    v          i  i-  i     v  -- 
  L1M4_orf2#LINE/    416 GGGACAACTGGATAKCCACATGCAAAAGAATGAAG-TTGGACCCCTA--C 462

  chr20_11245214_    806 TTTACA--------GAAAATCAGCTAAAAATGGATTAAAGACTCAAATGT 847
                         i i   --------i     i i  v         i ?    ii      
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr20_11245214_    848 AAGACCTGTAATTTTAAAACTCCTAGAAAAAAAATGTAGGGGAAAATCTT 897
                             v  iv  i v        i     i    -ii    ? v       
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGTAAATCTT 561

  chr20_11245214_    898 CTTAGTATTGGTCTTGGCAATGATTTCTTTGATATGGCATCAAAAGCACA 947
                          v iiiv    vi v       i      v      i  i          
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr20_11245214_    948 GGCAACAAAAGCAAAAATAGACAAGTGGGACAACAGTAAACTAAAAAGCT 997
                         i          v         i  i v    vv  vi   v v    i  
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr20_11245214_    998 TCTGCACAACAAAGGAAACAATCAACAGAGTGAAAAAGCAGCT-ATGGAA 1046
                          i  ii vv       v  v     v i        ii  i i- ii   
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr20_11245214_   1047 AAGAACTGCGAAAAGAACTGCAAACCATATATGTGAGAAGAGCTTAATAT 1096
                         vi i ----     v vi      i       v   v   i vi vi   
  L1M4_orf2#LINE/    712 TGGGA----GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr20_11245214_   1097 CCAAAATACATAAGGAACTACTAACA-CT-AATTTGAAAAAGACACAAAT 1144
                            i    i    i     -  v   -  -   vvv         --   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACT-CTTACAACTCAATAATAAAAAGACA--AAT 804

  chr20_11245214_   1145 AACC-------AAAATGAACGAAGGACTTGAACAGATATTTCTTCAAAGA 1187
                             -------      ii i     i     i   i      i      
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr20_11245214_   1188 AGATGCACAATTGGCCACGAGGTTTATGCAAAAGTATTCTC----TCATC 1233
                             ii    v      vv i ivi   -     -  v   ----   ??
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATG-AAAAG-ATGCTCAACATCAZZ 902

  chr20_11245214_   1234 TAGGTT 1239
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.98 (109 / 55)
Gap_init rate = 0.03 (22 / 789), avg. gap size = 2.27 (50 / 22)  


3047 28.00 0.55 0.44  chr20_11287148_11293375.rev     4830  5736 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_11287148_   4830 TAGAAAAACATTTCATCCTCATGGATAGGAAGAATCAACATCATGAAAAT 4879
                          i    i i  ii   vi        v      v i  i  ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_11287148_   4880 GGTCATACTGCCCCAAGTAATTCATAGATTCAATGTTATTCCCATCAAAC 4929
                           iv     v   v  v i  ii i        i iv  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_11287148_   4930 AACCATTGACATTCTTCACAGAATTAGAAAAAACT-ATTTTAAATTTTAT 4978
                         vv   vivi v  i  ii     v v  v  i-  -  ii    v  i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_11287148_   4979 ATAGAG-T-CAAAGAAGACCCTACATAGCCAAGACAATCCTAAGCAAAAA 5026
                           i  i- -   i --     viv        i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_11287148_   5027 GAACAAAGCTGGAGACATCATGCTACCTGACTTCAAACTATACTACAGGG 5076
                                 i     ivv   ii  v  ii i      viv       ii 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_11287148_   5077 TTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAGAC 5126
                         i        i   i    ii         i iv ii i           i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_11287148_   5127 CAATGGAGCAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCA 5176
                                ii    iv    vii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_11287148_   5177 TCTGATCTTCGACCGACCTGACAAAAACAAGCAATGGGGAAAGAATCTCC 5226
                         vi    i      viivv  v   i v  vv               vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_11287148_   5227 TATTCAGTAAATGGTGCTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5276
                          v    ii              v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_11287148_   5277 AAACTGGACCCCTTCCTTATACCTTTTACAAAAATTAACTCAAGATGGAT 5326
                           ii         v   i i   v v                 i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_11287148_   5327 TAAAGACTTAAATATAAAACCCAAAACCATAGAAACCCTAGAAAAAAACC 5376
                         i ?    i     i   i v i     i   i  vi i     i     v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_11287148_   5377 TAGGCA-ATACCATTCAGGACATAGGCATGGGCAGAGACTTCATGACAAA 5425
                             ?i- v i -   iv   v v  vv i    iv ii   v iivv v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_11287148_   5426 AACACCAAAAACAATAGCAACAAA-GTCAAAATTGGCAAATGAGATTCTA 5474
                         i         i  vv         - vv     v ii    vi  i ii 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_11287148_   5475 TTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTATCATCAGAGTGAAC 5524
                          i   v v  i i   i   i vv    i  v       vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_11287148_   5525 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATTTGACAA 5574
                           i     i                 v       vii ivi  i   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_11287148_   5575 AGGTCTAACATCCAGAATTTACAAGGGACTTAAACAAATTTACAAGAAAA 5624
                         i  v  vii         v  i  i i   ivv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_11287148_   5625 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATAAACAGACACTTC 5674
                          i     i     v  i?    i            v i  i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_11287148_   5675 TTAAAATAAGACATTTATGTGGGCAACAAACATATGCAAAAAAGCTCATC 5724
                          iv   v    i  vi vi   v   i  i  i   v   i v     v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_11287148_   5725 ATCACTGATCAT 5736
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (152 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.12 (9 / 8)  


3265 26.75 0.33 0.77  chr20_11392438_11396696.rev     2856  3767 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_11392438_   2856 TGAGAAAACATCTCATGCTCATAGGTTAGAATAATTAGTATCATTAAAAT 2905
                           ii  i i   i    i    i i  i   v v   i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_11392438_   2906 GACCATGGTGCCCAAAGCAATTTAGAGATTCAATGCAATTTCTATCAAAA 2955
                          i v  iv v      vii  i  v        i     ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_11392438_   2956 TACCAA-TGTCATTTTTGTATAAATTTAAAAAAATATTCTAAAATTCATA 3004
                          v   i-  i v      i v     v v  ivvv  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_11392438_   3005 TGGAACCAAAGGAGAGCCTGAATAGTCAAAGCCCTCCTGAGCAAAAAGAA 3054
                              viiv i i  v  v      i    i vv  i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_11392438_   3055 CAAAGCTGGAGGCATGACATTCCCTGACTTCATATTATACTACAAGGCTG 3104
                              i      vv v   i i  ii i    v viv        i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_11392438_   3105 TAGTAATCAAAACAGCATGATAGTGGTATAAAAACAGAAACATAGATCAC 3154
                         i         i    ii  i  v   i    ii i   v i        v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_11392438_   3155 TGAAACAGAATAGATAACCCAGAAATAAAGCCACACAATTACAGCCAACT 3204
                           i  i     v  v ii           v   i   v   ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_11392438_   3205 GATCTTTGACAAAATTGACAAGAACATACTCTGGGGAAAAACT-CTCTTT 3253
                            i  i     iiv  v     v   v vv        i v -v     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_11392438_   3254 CCAATAAAAGGTGACGGGAAAATTGGATTGCCAAAGGCAGAAGAATGAAA 3303
                         i   i   v    vi    v  i     v?   v v   i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_11392438_   3304 CTGGACTCTTATTTCTCACTATATAAAAAAATCAACTCAAGATGAATTAA 3353
                         i     i i  ii  v   i     v      i       i   i  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_11392438_   3354 AGACTTAAACGTAAGATATAAAACTATAAAATTTTTAGAAGAAAACCTAG 3403
                             i    i      vv             i i            v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_11392438_   3404 GAA-AACTCTTCCAGATATTGGTCTAGGCAAAGAATTTATGACTAAGATC 3452
                          ?i-  v     vv  iv    vi       v iv  iv iiv  v  iv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_11392438_   3453 TTAATGGCTCAGACAACAAAACCAAAAAGAGACAAATGGGTGTTAATTAA 3502
                         ii  vi  v  ii        vv     v   i    v  vv  v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_11392438_   3503 ACTCAAAAAGCTTTTACACAGCAAAAGAAATAACTGATAGAGTAAACAGA 3552
                          v i     -     iii vv    i  v iv iii v i   i  v   
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_11392438_   3553 CAACCTGCAGAATACAGGAAAATATTTGCAAACTATACATCTGACAGGGA 3602
                              ii      ivii               ii   i      i i  i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_11392438_   3603 ATTAATATCCACAATTTAGAAGGAACTCAAACAATTTAACAACATAACAA 3652
                          i vi      v   v  v  i      vv    i i  -----   i  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA-----TAATAA 794

  chr20_11392438_   3653 AATGACAAATAATCTCATTAAAGAGTGGGCAAGTGACATGAATAGACATT 3702
                           v         i iv   ?  i i       iv  iv            
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_11392438_   3703 TTTTAAAAGAAGACATACCAATGGCCAGCAAACATATGAAAACAATGCTC 3752
                          i iv        i    v        ii  i  i       -i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCTC 893

  chr20_11392438_   3753 ATCATCACTAACTTA 3767
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.67 (10 / 6)  


3299 24.49 2.48 0.45  chr20_11405815_11410036     2845  3730 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr20_11405815_   2845 AAGCTAGCTCATGTTCATGAATTGGAAGAATCAATATTGTTA-------- 2886
                            v  v i          i         v i          --------
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr20_11405815_   2887 ------TCCAAAGTAATTTACAGATTCAGTGCAATCCCTATCAAAATATC 2930
                         ------i     v i  i          ii                 vi 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr20_11405815_   2931 AATGACATGCTTTACAGAAATTGAAATAATAATCCTAAAATCTATATGGA 2980
                          iivi v vi   i          v viv i          ii       
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr20_11405815_   2981 ACCACAAAAGATCCAGAACAGCCAAAGACA-TCCTGAGCAAAAATAACAA 3029
                          vii   ii  i      i       -   -  i   iv  i  v     
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAA-ACAATCTTGAAAAAGAAGAACAA 203

  chr20_11405815_   3030 AACTGGAAAAATTACAATACCTGGCTTCAAATTATACTAAAGACCTATAG 3079
                          ii    ii v i   v v  iiii      viv     v i v   i  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr20_11405815_   3080 TAACTAAG-CAGCATGGTACTGGAATAAAAACAGACACATAGACCAGTGG 3128
                            ii   -   ii         v    ii i     i     i  i   
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr20_11405815_   3129 AA-AAAATAGAGAATCCATAAAGAAGTCCACACACTAACAGTGAACTCAT 3177
                           - i   v    i    v   v  ii   i   i v ii  v  i v  
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr20_11405815_   3178 TTTCAACAAAGGTGTCAAGAACATACACTGTGGAAA-AACAGTCTCTTTA 3226
                             i    i    i     v   v  v  v     -  i     i  i 
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr20_11405815_   3227 ATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATAAAACTA 3276
                          i              v         ?   i     i      i  ii i
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr20_11405815_   3277 GACCCCTATATCTTGCCATGTACAAAAATCAAATTAAAATAAATTAAAAA 3326
                                 iv  vii    i         i  v i     ii  i ? i 
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr20_11405815_   3327 CTGAAATCTAAGAGCTCAAACTATGAAATTACTAAAACAAAGCATTTGGG 3376
                          iv    v        v       i   i vi  i  v   i   vv ? 
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr20_11405815_   3377 GAAACTCTCCAGCACATTGGCCTGGGAAAATAATTTTTAAGAAAT-ACCC 3425
                         v   -   i ivv  v    vi i  v  - ii   i v   v  -  v 
  L1M4_orf2#LINE/    554 TAAA-TCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGACAC 601

  chr20_11405815_   3426 TAAAAGCATAGGCAATGAAAACAAAAATGTACAAATTGGATTACTTTA-- 3473
                         i       i i    ii   iv      iv i        i v v i --
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_11405815_   3474 -TTAAAAAGCTTCTGCACAACAGAAGAAATCATGAACAAATTTAAAAAAC 3522
                         -       -   i  ii vv  i i  v ii  v  v   v v    i  
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_11405815_   3523 AACCCACAGAATGGGAGAAAATATTTGCAAACTATCCATCTGACAAGAGA 3572
                                                        ii  vi      i   i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_11405815_   3573 CCAATAACCAGAATATATAAGGTGGTCAAACAACTCAATAGGAAAAAATC 3622
                          ivi  v             i viv  vv           iv     iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_11405815_   3623 TTATAATCTAATTTAAAAATGAGTAAAAGAAATGAATAGAAATTTCTCAA 3672
                         vv    i i    ?       i i   i  vv        v       v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_11405815_   3673 AAGAAGACATACAAATGGCAAATAGGCATATGAAATGGTGCTCACCATCA 3722
                                i           v    i   i      v i      v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr20_11405815_   3723 CTGATCAT 3730
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.63 (132 / 81)
Gap_init rate = 0.01 (11 / 904), avg. gap size = 2.36 (26 / 11)  


 615 27.03 0.00 0.00  chr20_11431943_11436647     2940  3124 (1581)    L1M4_orf2#LINE/L1        1   185 (723)  

  chr20_11431943_   2940 TAGAAACACATCCCATGCTCATAGATAGGAAGAATCAATACTTTGAAAAT 2989
                          i    v i        i    i   v      v i    i v v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_11431943_   2990 TACTATACTACCCAAAGAAACCTACAGATTCAATGCAATTTCCATCAAAA 3039
                         vi v     v      vvi i            i     ii i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_11431943_   3040 TACCATCATCATTTTTCACAGAACTAGAAAAAATAATCCTAAATTTCACA 3089
                          v   v vv v     ii     v v  v  iv i        v    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_11431943_   3090 TGGAACCAAAAAAGACCCCTAATATCCAAAGCAGT 3124
                              viiv  ii     vv    v     i  i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

Transitions / transversions = 1.00 (25 / 25)
Gap_init rate = 0.00 (0 / 185), avg. gap size = 0.00 (0 / 0)  

2102 24.58 3.51 2.95  chr20_11431943_11436647     3502  4213 (492)    L1M4_orf2#LINE/L1      193   908 (0)  

  chr20_11431943_   3502 AAAAAGAACAAATCTGAAGGCATCACATTACTAGACTTCAAATTATACTA 3551
                           i         vi  i   vv     i v ivi i      viv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr20_11431943_   3552 TAAGGTTATAGTTACCAAAACAGCAAGCAGTACTGGTATGAAAATAGGTA 3601
                         i  i i  i   v i   i    i-- ii       i  i ii    ii 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGT--GTGGTACTGGCATAAGGATAGACA 290

  chr20_11431943_   3602 CTTAGACCAATGGAACAGAATAGAGAACCGAGCAATAAAGCCAAATATTT 3651
                         iv    i        i     v    ii v  v      v   v i    
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr20_11431943_   3652 ACAGCCAACTGATTGTCAACAAAGTATACAAAAAT-ATAAACTAGGGAAA 3700
                          ii i   i     v  i    i -i i v  i i-  vv v i      
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAA 389

  chr20_11431943_   3701 GAA-AACCATAATTCAATAAATGGTGCTGGGACA--------------TG 3735
                            - ii v --     i                --------------  
  L1M4_orf2#LINE/    390 GAATAGTCTT--TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr20_11431943_   3736 TAGAAGAATGAAACTGGATCCCCATCTCTCACATTATACAAAAATCAACT 3785
                         i i         ii    i   i i   v   vv           i    
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr20_11431943_   3786 CAAGATGGATCACAAGACTTAAATCTAAGATCTGAAACCATAACAATTCT 3835
                            i        -?    i     v     v  i    i    -  i   
  L1M4_orf2#LINE/    488 CAAAATGGATCA-WAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCT 535

  chr20_11431943_   3836 CA-AGGATAAGATTGACA-AATTCTTCTGAACATTGACCCAGATAAAGAA 3883
                         i - i  v  v  v i?i-  v     vvi  v   ivii  ii  v iv
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr20_11431943_   3884 TTCATGATTAAGACCCCAAAAGCAAATGCATCAGAAACAAAAATAAATAA 3933
                            v iiv  v   v         v v   v  i  iv       i    
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr20_11431943_   3934 ATGAGACTAAATTAAACTAAGAAACTTCTGCACAGCAAAATAATAATAAT 3983
                           vi    vv  i   v v i      i  ii vv    i----------
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG---------- 675

  chr20_11431943_   3984 AATAATAATAATCAGCAGAGTAAACAGACAAACCACAGAATGGGAGGAAA 4033
                         ---i i v  -   iv i   i  v      v              i   
  L1M4_orf2#LINE/    676 ---GACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr20_11431943_   4034 TATTTGCAAACGATGTATCTGACAAAAAACTAGCATCCAGAATCTATAAG 4083
                                   iv  i       i  iii   v i         v     i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr20_11431943_   4084 GAACTCAAACAAATCAGCAAGAAAAAGA-AAACAATACCATCAAAAAGTG 4132
                               vv    v   ii  v       -   i  iv v  i?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr20_11431943_   4133 GGCAAAGGAC----ATAGACATTTCTCAAAAGA-TATATACAAA-GACCA 4176
                                  i----             v     -v         - i   
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr20_11431943_   4177 ACAAACATATGAAAAAATGCCCTACATCACTAATCAT 4213
                          i  i  i       i    i v      ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (106 / 66)
Gap_init rate = 0.02 (16 / 716), avg. gap size = 2.88 (46 / 16)  


2883 25.73 2.57 1.01  chr20_11458260_11461776     2132  3025 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_11458260_   2132 TGGAAAAATATTTCCTGCTCATAAATTGGAAGAATAAAAAATTATTAAAA 2181
                               i    ii v  i    ii         v v  v -  i    i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA-TTGTTAAGA 49

  chr20_11458260_   2182 TGTCTATACTGTTCAAAAGTGATCTATATTCTCAATGCAATTC-TATCAA 2230
                           v v     vii    -v       i vvi    i     i -      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr20_11458260_   2231 ATTACCAACATCTTTCTTCACAGAATTAGAAAAAAACT-ATTCTAAAATT 2279
                          v v   i vv i  i  ii     v v  v  i--  -  i        
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT 146

  chr20_11458260_   2280 TGTATGAAACTGAAAGGAGCCCA-AATTGCCAAAACAAACCTAAGCAAAA 2328
                         ii    i  v  v    ii    -   v          v i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_11458260_   2329 CGAACAAAGCCAG-GGACACCACATTACCTGACTTCAAGCTGTACTATAA 2377
                         v        iii -    -i    i v  ii i     iviv     i  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_11458260_   2378 GGCTACAGTAACCAAAACAGCATAGTACTTGTACAAAAATAAACAAAAAG 2427
                         i          i   i    ii i     v i i  ii   i   v v  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_11458260_   2428 ACGAATGAAACAGAAAAGAGAACCCAGAAATAAAGCCACATATTTACAAC 2477
                          iv    i  i    vv    ii           v   i i     iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_11458260_   2478 CAACTGACTTTTGACAAAGTCAACAAAAGTAAACAATGGG-AAAGGATAC 2526
                            i   i   i     i viiv   i vi vv       -    i   v
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_11458260_   2527 CCTATTCAAAAAATGGTGCTGCTGAAC--CTGGCTAACCATATGCAGAAG 2574
                         i  v     v           -- i  --    v  ?   i     i   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTG--GGACAACTGGATAKCCACATGCAAAAG 443

  chr20_11458260_   2575 AATGAAACTCTATCCCTACCTCTTGTCATATACAAATATTAACTCAAGAT 2624
                               ii vv i         viii          v          i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_11458260_   2625 AGATTAAAGACTTAAATCTAAGACCTGAAACAATCAAACTTCTAGGAGAA 2674
                         i   i ?    i     v     v  i    v  v     ii   i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_11458260_   2675 AAACTAGAAAACATTCTTCTGGACATTGGCCTAGGCAAATAATTT---AA 2721
                           vv   i?ivv v     vv   v    vi       - ii   --- i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAG 592

  chr20_11458260_   2722 GTCT----TTAAAAGCAAATGCAACAAAAGCAAAAATTGGCAATTGAGAC 2767
                         i v ----ii       v v          v      v ii  v vi   
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr20_11458260_   2768 CTAATTAAACTAAAAAGCTTCTGCACATCAAAATAAACTATCAACATAGT 2817
                         i v  i   v v    i   i  ii v     iv v        v v   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr20_11458260_   2818 AGACAGACAACCTACAGAATGGGAGAAAACATTTCCAGACTATGAATCTG 2867
                         ii v        i                i    v  i ii  iv     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_11458260_   2868 ACAAAGGACTAATATCCAGAATCTGCAAGAAACTTAAACAAATCAACAAG 2917
                          i  i     vi          v ii  ii    ivv    v    i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_11458260_   2918 AAAAA---AAAT---CCA-TTAAAAAGTGGGCAAAGGACATGAACAGACA 2960
                              ---    ---   -  ?    i           iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_11458260_   2961 CTTCTTAAAAAGAAGACATATAAGCAGCCAACAAACACA--AAAAAATGC 3008
                         i    iv   -     i   i  iii     i  i    --    i    
  L1M4_orf2#LINE/    843 TTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_11458260_   3009 TTATCATCATGAATCAT 3025
                          i v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (140 / 86)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.68 (32 / 19)  


3629 21.54 1.76 1.98  chr20_11522913_11530127     5814  6723 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_11522913_   5814 TGGAAAGAAATCCCATGTACATGAACTAGGTGATTTACTACTATTGTTAT 5863
                                 v         v    i i i iv  i   -- -        v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTA--A-TATTGTTAA 47

  chr20_11522913_   5864 GATATTCATACTATCCAAACTAATCTACAGATTCAATGCAATCCCTTTTA 5913
                            iviv     vi     i i              i         v i 
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr20_11522913_   5914 AAATTTCAATGATGTCTTTTGCAAAAATTAAAAAAAAAATCACTCCTAAC 5963
                             ii  iiviiv i       i     i v  ivvi   ----    v
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATC----CTAAA 143

  chr20_11522913_   5964 ATTCATA-ATAAATCTCAAGGAATTCCCAACTGCCAAAACAATCCTGTAA 6012
                                -iv    v-     i ii vv  iv            i  v  
  L1M4_orf2#LINE/    144 ATTCATATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr20_11522913_   6013 AGGAAAAACAAAGTTAGAGGTCTTATATTTTCTGCTTTTGAAACTTACTA 6062
                          i   i         i    v  i i i  i iiv   ii          
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr20_11522913_   6063 CAAAGCTATGGCAATCAAAACAGTGTAGTAGTAACATAAAGACAGACATA 6112
                                 ii i      i       i   v ii     i  i       
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr20_11522913_   6113 TAGACCAATGGAATAGAATAGAGAGCACAGAAATAAATCTTTACATTTAT 6162
                             i              v     iv          i iv         
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr20_11522913_   6163 GATCAAATAA------ACAATGGTGCCAAGATGGCTTAATGGGGGAAAAG 6206
                          i    v i ------    v          ivii i       i  i -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA- 391

  chr20_11522913_   6207 ACAGTCTTTTCAACAAGTGGTACATAGAAAAATACATATTCACATGCAAA 6256
                          i              i    i vvi  v  v iv   ?i          
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_11522913_   6257 AGAGCAAAGTTGAACATTTTATTGTCTAATATTATTGAAAAAACTTAACT 6306
                            iii      i  -iii  i---  v i ii  vv v    v      
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGAC-CCCTAC---CTCACACCATATACAAAAATTAACT 487

  chr20_11522913_   6307 GAAAATGTATCAAATATCTAAACCTAAGAGCTAGAGCTATAAAACTTTTG 6356
                         v      v    ? v i     iv         i i          i  i
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr20_11522913_   6357 GGAGAAAACATAGGGGAAAAGCTTCATGACATTGGATTTGGTAGTAATTT 6406
                          i            ? v   v    i    v    i  v  i i ii   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_11522913_   6407 GTTGGCTATGACACCAAAAGCACAGACAACAAAAGAAAAAAAATACACAA 6456
                         v  i v                  ii               --  v i  
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAA 635

  chr20_11522913_   6457 ATTGGACTCCATCAAAATTTAAAAGATTTGTTCATCAAAGGATGTTATCA 6506
                                 i          v    vv     v v        iii     
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr20_11522913_   6507 ACAAAGTAAAACAAGTAACACAAAAAATGAGAGAAAAAAT--GCAAATCA 6554
                          v     i   - iii   v  v i    i       v  --        
  L1M4_orf2#LINE/    686 AGAAAGTGAAA-AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr20_11522913_   6555 CCTATCTGATAAAGGAATAATATATAGAATATAAAAAGAGCCCCTACAAC 6604
                         iv          i   v vi   vi        v     i i i      
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr20_11522913_   6605 TCAACACCATAAAA---CAAACAGTTCAATTCAAAAATGAGCCAAGGATT 6651
                             i --      ---    i iii     ?       i  v       
  L1M4_orf2#LINE/    785 TCAATA--ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_11522913_   6652 T--ATAGACATTGGTCCAAA-AATATATACAAATGGTCAATAAACATATA 6698
                          --         vv      -  v            i      i  i  i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_11522913_   6699 ACAA-ATACTCAACATCACCAGGAAT 6723
                          v  -  i          ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (123 / 69)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


3304 26.32 0.66 0.66  chr20_11560928_11567202     4876  5783 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_11560928_   4876 TGGAAGAACACTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4925
                              ii i ii     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_11560928_   4926 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4975
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_11560928_   4976 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5023
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_11560928_   5024 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5073
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_11560928_   5074 AACAAAGTTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5123
                                       vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_11560928_   5124 TACAGTAACCAAAACAGCATGGTACTGGTACTTAA--ACAGAGATATAGA 5171
                                 i   i    ii         i --   -- i   v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCA--TAAGGATAGACATATAGA 296

  chr20_11560928_   5172 TCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 5219
                                  i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr20_11560928_   5220 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5269
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_11560928_   5270 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5319
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_11560928_   5320 CTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATG 5369
                         v    ii    i    v   i     v           i  i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_11560928_   5370 GATTAAAGATTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAA 5419
                            i ?   ii    ii v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_11560928_   5420 ACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCC 5469
                           v    ?i v viv   iv   v v  vv i     v ii   v ivvi
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_11560928_   5470 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5519
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_11560928_   5520 AATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGA 5569
                         v  i   v v  i i   i   i vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_11560928_   5570 ACAGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 5619
                          v  i     i   iv            v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_11560928_   5620 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5669
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_11560928_   5670 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5719
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_11560928_   5720 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCA 5769
                             v        i  vi viii     v  i        i i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_11560928_   5770 TCATCACTGGCCAT 5783
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (140 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.71 (12 / 7)  


2980 26.94 1.55 0.89  chr20_11656727_11662592     4473  5374 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_11656727_   4473 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATTAAAAT 4522
                               i i  i     i        v      v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_11656727_   4523 GGCAATAATGTCCAAAGTAATTTATAGATTCAATGCTATTACCATGAAAG 4572
                                v vi     v i  i  i        i  v  iv i  v   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_11656727_   4573 TACCATTGACATTCTTCATAGAATTAGAAGAAAACT-ATTTTAAAATTCA 4621
                          v   vivi v  i  iii    v v  v--  i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chr20_11656727_   4622 TATGGAACCAAAATTGGCC--ATATAGCCAAGACAATCCTAAGCTAAAAG 4669
                                viiv  vv i  --iv        i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_11656727_   4670 AACAGGGCTGAAGGCATCACATTACCCGACTTCAAACTATACTACAAGGC 4719
                             ii i  i   vv     i v   i i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_11656727_   4720 TACAATAACCAAAGCAGTATAGTACTAGTACAAAAACAGACAAATAGACC 4769
                             i   i   ii    i i     i i i  ii i     v     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_11656727_   4770 AAAGGAACAGAATAGAGAACTCAGAAATAAGACCACACATCTACAATCAT 4819
                           v    i     v    iii         iv   i    i  iii   v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_11656727_   4820 CTGATCTTTGA--AACCTAGCAAAAACAAGCAATGCGAAAAGAATTTGCT 4867
                         i    i  i  -- ivv iv   i v  vv     v i       vvv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_11656727_   4868 ATTTAATAAATGGCTCTGGAAGAACTGGCTAGCCATGTGCAGAAAATTCA 4917
                         v  i  i      iv    i v      v  ?   ii    i  i v v 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_11656727_   4918 AACTGGACCCGTTCTTCACACCTTTTACAAAAATTAACTCAAGATGGATT 4967
                          ii       v v i       v v                 i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_11656727_   4968 AAAGACTTGAATGTAAAACCCAAAACTATAAAAATCCTAGATGAAAATCT 5017
                          ?    i i       i v i            v  i    v     iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_11656727_   5018 AGGCAGTA--CCATTCA-GGTCATAGGCACGGGCAAAGATTTCATGGTGA 5064
                            ?-   --i -   i- ii v i  i-ii     v i    v i vv 
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr20_11656727_   5065 AAACACCAAAAGCAATTGCAACAAAAGCAAACATTGACAAATGGGATCTA 5114
                         vi            vvv          v   v  v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_11656727_   5115 ATTAAACTAAAGAGCTTCTTCACAGCAAAAGAAACGATCATCAGAGTGAA 5164
                           i   v v  i i   i vii vv    i  v  v    vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_11656727_   5165 CAGACAACCTACAAAATGGGAGAAAAT-TTTGCAATCTATCCGTCTGTCA 5213
                         v        i   i             -       vii  vii    vi 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_11656727_   5214 AAGATCTAATATCCAGAGTCTATGAAGAACTT----AACTTTACAAGAAA 5259
                          i iv  vi        i v   i       i----    ---   v  v
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAAT 792

  chr20_11656727_   5260 AAAAAAACAAACAACCCCATTAAAAAGTGGACAAAAAACATGAACAGAAA 5309
                              i     i     v   ?    i   i    ii iv    i   v 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_11656727_   5310 TTTCTCAAAAGAAGACATACATGCGGCCAACAGACATGTGATAAAA-GCT 5358
                               v        i     vii      i ii  ii   v  i -   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_11656727_   5359 CAATATCACTGATCAT 5374
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.69 (22 / 13)  


3463 24.43 0.98 1.96  chr20_11687638_11690932.rev     1887  2803 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_11687638_   1887 TGGAAAGATATTACATTTTCACAGATCAGAAGGATCAGCATTATTAAAAT 1936
                                    iv   v    ii   ii    iv i ii   i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_11687638_   1937 GTCCATATTATCCAAAATGATCTATAGATTCAACACAATCCTTGACAAAA 1986
                          v v   i vi     v       i         i      i iv     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_11687638_   1987 TTTCAATGACATTTTTCACAGAAATACAAAAAATAATTCTAAAATTCA-A 2035
                          ii  iivi v     ii       vv v  iv i  i          - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_11687638_   2036 TGGAACCATAAAAGACCCAGAACAACCAAAACAATTCTGAGAAAGAA--- 2082
                              viii  ii         i i          ii   i      ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_11687638_   2083 CAAAGCTGAAGGCTTCATATTTTCTGATTTCAAACTATATTACAGAAATA 2132
                              i  i   vi   i i  i ii        viv  i    i iv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_11687638_   2133 TAGTAATCAAAGGAGTATGGTACTGTCATAAAAACAGACACATTAATTAA 2182
                         i         iiv   i        v     ii i     i  vi  i  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_11687638_   2183 TGGAACAGAATAATGAGCACAGAAATAAATAAACCCATGCATACATAGTT 2232
                              i     viv   iv          ----     i   vi  i  -
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAA----CCCATACATTTATGGT- 345

  chr20_11687638_   2233 ATCAACTAATATTTGACAAGGGTGCCAAGAATACACAATGGAGAAAGAAT 2282
                         --   i i  v  i                vi iv      i        
  L1M4_orf2#LINE/    346 --CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_11687638_   2283 AGTTTCTTCAATAAACCATACTGAAAC--CTGGATATCCACATGTAGAAG 2330
                            i i     i   ivi i   ii  --       ?       i i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_11687638_   2331 AATGAAATCGGACTCTTATCTTACACTACACAAAATAATCAATGCAAAGT 2380
                               i i    i i  i  i    i i i v  v   i  iv    i 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_11687638_   2381 GTATTAAAAACTTTAACGTAAGACCTGAAACTCCAAAACTCTTAGAAGGA 2430
                          v  i ? i  i v  i      v  i     vi              i 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_11687638_   2431 AACA--GGAGAAAGACTGCTTGACAGAAGTCTCGGTAATAATTATTTTTG 2478
                             --  ? v  iv  v v    vvvi vi v  i   ii  -- i  i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT--TCTTA 591

  chr20_11687638_   2479 GATATGACACCCAAAGTACAAGCAACAAAAGCAAAAATAAACAAGTCCAA 2528
                                    v    i              v       i i  i ivi 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_11687638_   2529 CTACATCAAAGTAAAAAGCTTCTGTAAAACAAAGGAAACATTCAATAAAA 2578
                           v       i v    i   i   ivvv       v  vv    v   i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_11687638_   2579 TGAAAAGACGACCTACAGAATGGGAGAAAATATTTGCAAACCATCTATCT 2628
                                  i   i                          i   v     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_11687638_   2629 TATAAGGAACTAATACCCAAAATGTATAAAAAAACTCATATATCTTAATA 2678
                         v      i   vi  i   i   i      i  -   v  i v  i    
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAA-CTCTTACAACTCAATA 790

  chr20_11687638_   2679 GTGAAGAAAACCCCCACAAATAACCCAATTTTAAAAATGGGCAAAGAGTC 2728
                         i i  i i -------              ?-              ii i
  L1M4_orf2#LINE/    791 ATAAAAAGA-------CAAATAACCCAATTW-AAAAATGGGCAAAGGATT 832

  chr20_11687638_   2729 TGAATAAAAATTTTTCAAAAGAAGACAGACTG-TGACAAACAGGTAATTG 2777
                               i v    i  v        i v  vi-  i v  i i i vv  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_11687638_   2778 GAAGGGTGCCCAGCATCACTAATCAT 2803
                         i  i i   i  i     ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (150 / 70)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.45 (27 / 11)  


3161 23.71 6.43 0.35  chr20_12032281_12036930     3303  4158 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12032281_   3303 TGGAAAGACATCCTGTGTTTATACA--GAAAGATTTAATGTTATTAAAAT 3350
                                 i    ii    i  iv -- i    i     i  i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12032281_   3351 GTCTATACTATCCAAAGCAATCTACAAGTACAGTAAGATCCTTATCAAAA 3400
                          v v     vi     vii       ii v  iiivi    i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12032281_   3401 TTTCAGTGGTGTTTTTTAAACATAAGTAGAAATAATAATTCTAAAATTCA 3450
                          ii   iv iv      i--  v  i v  v viv i  i          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG--CAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_12032281_   3451 TTTCAAACAACAAAGGATCCC-AATAGCCAAAACAGT--TGAGAAAGAAG 3497
                          v vi  vvi   i   i  v-             i --   i       
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_12032281_   3498 AACAAAGTTGGCAACATCGTACTTCCTCAATTCAAAATACATTACAAAGC 3547
                                    viivv  ii      iv v       ivi i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_12032281_   3548 TATGGTAATTAAAACAATATGGTAGTGGCATAA--ATACATATTTAGATC 3595
                           ii     i  i   i i     v        --   v i  v      
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_12032281_   3596 AATGGAACAGAAAAGAGAGCTCAGAAATAAAACCACACATGTGTGGTTAA 3645
                                i    vv     ii          v   i    v i    i  
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_12032281_   3646 CTGATCTTCAGTAAGGATGACAAGAATATGGAATGGGGAGAGGACAGTTT 3695
                         i    i   iii    i  v     vi  vv        i  i i   i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_12032281_   3696 CTTAAACAAATGGTG-TAGGAAAACTACATATCCACATGCAAAATAATAA 3744
                         i  v           - i   v    iv   ?            v   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_12032281_   3745 AATTGAACCCTTATCTCACACTAGACACAACCATCAATTCAAGATGGATT 3794
                          i   i    i  i       i v i    vv  i  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_12032281_   3795 AAAGAC----------------AAAC-ATAA--------GAAGAAAACTT 3819
                          ?    ----------------    -    --------         v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_12032281_   3820 AGGGCAAAAGCTTTATGACATTGGTCTTGGCAATTATTTCTTGAATATGA 3869
                            ?vv   v   ii    v    vi v      vi      ii      
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_12032281_   3870 CACCAAAAGCACTGGCAACAAATGCAGAA-TAAACTAGTGGAACTACAGT 3918
                                     vi        v v i  -  i iv i v i   v  vi
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_12032281_   3919 AAACTAAAAAGCTTCTGCAGAGCAAAGAAAACAATTAAAAGAGTGAAAAA 3968
                            v v    i   i  iivvv     i v  v  i  i i        i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_12032281_   3969 GCAATCTAATGAGTGGGAGAAAATATTTGCAAACCATATATTTGATAAGG 4018
                         i   i i vv  i                    i       i        
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_12032281_   4019 GGGTAAATATTCAAAATATATAAGGAACTCTTTGAACCAAATAGCAAAAA 4068
                          iv vi-   i  i         i        vv   iv    ii     
  L1M4_orf2#LINE/    749 GACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_12032281_   4069 AAAAAAAAA-------AAAAAATGGGCAAAGAACTTGAATAGACATTTCT 4111
                         i v   v  -------?              i i                
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_12032281_   4112 -------------ACAA-TGGCTAACAGGTATATGAAAAGATGCTCAACA 4147
                         -------------    -    i  i i i i                  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_12032281_   4148 TCATTAATCAT 4158
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.69 (125 / 74)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 4.14 (58 / 14)  


3201 26.87 0.55 0.55  chr20_12052612_12054955.rev      945  1852 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12052612_    945 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 994
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12052612_    995 GGCCATACTGGCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 1044
                            v     vv    iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12052612_   1045 TATCAA-TGCCTTTCTTCACAGAACTGGAAAAAACT-ACTTTAAAGTTCA 1092
                          vi  i-       i  -i     v v  v  i-  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr20_12052612_   1093 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAAG 1142
                                viiv  ii  v  v v  v     ii     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_12052612_   1143 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATAATACAAGGC 1192
                                i      vv       v  ii i      viv  v     i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_12052612_   1193 TACAGTAGCCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 1242
                                ii   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_12052612_   1243 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAACT 1290
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_12052612_   1291 ATCTGATCTTTGACAAACCTGAGCAAAACGAG-CAATGGGGAAAGGATTC 1339
                          vi    i  i     ivv  v-   i  v v-            i  vv
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_12052612_   1340 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 1389
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_12052612_   1390 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 1439
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_12052612_   1440 ATTAAAGACTTAAATATTAGACCTATAACCATAAAAACCCTAGAAGAAAA 1489
                           i ?    i     i v   v   v   i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_12052612_   1490 CCTAGGCATTACCATTCAGGACACAGGCATGGGCGAGGACTTCATGTCTA 1539
                          v    ?i v viv   iv   viv  vv i   i v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_12052612_   1540 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 1589
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_12052612_   1590 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1639
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_12052612_   1640 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 1689
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_12052612_   1690 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGGAA 1739
                          i  i  vi          v  i  v      vv    v iv i  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_12052612_   1740 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 1789
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_12052612_   1790 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACAGGAAAAAATGCTCAC 1839
                            v        i  vi viii     v  i    v     i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_12052612_   1840 CATCACTGGCCAT 1852
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.25 (10 / 8)  


1094 26.21 10.54 0.28  chr20_12065149_12069551.rev     2800  3150 (1252)    L1M4_orf2#LINE/L1       15   401 (507)  

  chr20_12065149_   2800 ATGTGCATGGATTGGAAGATTTAATATTGTTAAAATG------------- 2836
                             v              i             i   -------------
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr20_12065149_   2837 ---------------------CAATCTCTATGAAAACAACAATGACATTC 2865
                         ---------------------     i    v    ivv  iivi v  i
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr20_12065149_   2866 TTCACAGGAATAGAAAATACAATTCTAAAATTCATATGGAACAACAAAAG 2915
                           ii   i   v  v  vvii  i                 vvi   ii 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr20_12065149_   2916 ACCCAGAATAGCTAAATAAATCCTTAGAAAAAAGAACAAAGCTAAAGACA 2965
                                     i   vv    i v i   i          i ii  ivv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr20_12065149_   2966 TCACAATATCTGGTTTTAAATTATACTACAAAGCTATAGTAGCCAAAACA 3015
                              v vi iii   i   viv             i    ii   i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr20_12065149_   3016 GAATGGTACTGGTAGAAAAAACAAATACATAGAACAGTGGAATAAAAC-- 3063
                          vi         i v  ii -i i i i     v  i       i  i--
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAATTG 313

  chr20_12065149_   3064 ATAACCCAGAAACAAATCCAAAAATTTACTGCCAACTCATTT-AGACAAA 3112
                          v ii       i   i   v v     iv i   i v    -v     i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr20_12065149_   3113 GGTGCCAAGAATGTACATTGGGAAAAGGAAAGTCTTTT 3150
                                   vii v  v    i    i v        
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

Transitions / transversions = 1.71 (58 / 34)
Gap_init rate = 0.01 (4 / 387), avg. gap size = 9.50 (38 / 4)  

1772 22.75 4.10 1.02  chr20_12065149_12069551.rev     3423  3910 (492)    L1M4_orf2#LINE/L1      406   908 (0)  

  chr20_12065149_   3423 AAATGGTGCTAGGA--ACTGGATATCCAAATGCAGGAGAAT----CTAGA 3466
                                   i   --        ?   v     ii     ----i i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr20_12065149_   3467 TTTCCATCTTTCACCATATAAGAAAATCAACTCAAAATGGATTAAAGACT 3516
                         iii i i  iv         vi     i              i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr20_12065149_   3517 TAAATATAAAATCTGAAATTATGAAACTACTA----AAAACATTTGGG-A 3561
                              i   i v  i   i   i     vi  ----       vv ? - 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr20_12065149_   3562 AATGCTTCAGGACTTTGGTCTGGGCAAAGATTTTTTTGGATAAGACCTCA 3611
                            -    iv   i    vi i     v i   i  -i    v   vi  
  L1M4_orf2#LINE/    556 AAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTT-AGATATGACACCA 603

  chr20_12065149_   3612 AAAGCCCTGTCAACAAAAACAAAAATG---AGATT--ACCTCA----AGT 3652
                              v viv        iv      i--- i   --  i   ---- i 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr20_12065149_   3653 TAAAAAGCTTTCACACAGCAAAGGTAACAATTAACAAAGTGAAGAGACAA 3702
                               -    iiii vv      vv  v  i  v        i      
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr20_12065149_   3703 TGTAAAAAAAATGGGAGAAAATATGTGCAAACTACTTATCCAATAAGAGA 3752
                         ivi v i  --             v      ii iv    ii     i  
  L1M4_orf2#LINE/    703 CCCACAGAA--TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_12065149_   3753 TTCATAACCAGAATATATAAGGAACTCAAACAACTCAACAGGAAATAAAC 3802
                         i ii  v             i      vv         i iv   v i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_12065149_   3803 AAATAACCCATTTTAAAAATGGTCAAAATATCTGAATAGACATTGTTCAA 3852
                                   v  ?        v    iv  i            vi  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_12065149_   3853 AACAAGACATACAACTGGTCAACAGGTATATGAAAAACTGCTCAACACCA 3902
                           v    i      v   i   i i i i       iv         i  
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr20_12065149_   3903 CTAACCAT 3910
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.74 (68 / 39)
Gap_init rate = 0.02 (11 / 503), avg. gap size = 2.27 (25 / 11)  


2530 26.16 1.27 5.91  chr20_12115221_12117800.rev     1148  2095 (485)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr20_12115221_   1148 AAAATATTCCATGCTCATGGATTAGAAGAATTAATATTGCAAAAAATGGC 1197
                           i    i     i         i     v         iv  i -    
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA-TGGC 53

  chr20_12115221_   1198 CATACTGCCCAAAACAATTTACAGATTCAATGCCATTCTTATCAAGCTAC 1247
                         v     v      vii  i           i  v  i i      iv v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_12115221_   1248 CAA-TGTCATTCTTCACAGAATTAGGAAAATTAGAATTAGAAAAATAGCA 1296
                           i-  i -  i  ii     --------------   -  v  ---  v
  L1M4_orf2#LINE/    104 CAGCTGCC-TTTTTTGCAGAA--------------ATT-GACAA---GCT 134

  chr20_12115221_   1297 TATTCTACAATTTATATGGAACCAAAAAAGAGCCTGAATAGCCAAAGAAA 1346
                         v  i   v    i        viiv  ii  v  v           iv  
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr20_12115221_   1347 TCTTAAGCCAAAAGGACAAATCCAGAGACATCTTACTATGCAACTTCAAA 1396
                             i ivv i   i     viii   ivv  vi   viv   i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr20_12115221_   1397 CTATACTATAAAGACACAGTAATCAAAACAGTTCAGTATTGGAAAAAAAA 1446
                         viv     i    vi           i     vii   i   v v  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr20_12115221_   1447 AAAGACACGTGGACCAATAAAACAAAATAGAAAACCCAGAAATAAAGCCA 1496
                         v -    ii i  i    ii  i i   v  i ii           v   
  L1M4_orf2#LINE/    285 TA-GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr20_12115221_   1497 CACGCCTAGAACCATCTGTCCCTCAACAAGGCTGACAAAAACAAGCAATG 1546
                         i  iii  viii  vi  viii  i      v  v   i v  vv     
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr20_12115221_   1547 GGGAATGGACTTCCTATTCAACAAATGGTGCTAGGATAATGGGCCAGCCA 1596
                              v i ivvi  v                i   i  iv  vi ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr20_12115221_   1597 TATTCAGAAGATTAAAGCAGTACACCTACAAAAATTACAAAAAACATATG 1646
                         i  v  i    v i   iv v  v     ---------------------
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTAC--------------------- 462

  chr20_12115221_   1647 CCATATTTTCACTATATACAAAAATTAACTCAAAATAGGTTAAAGATTTA 1696
                         -----i iv   i                       i i i ?   ii  
  L1M4_orf2#LINE/    463 -----CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr20_12115221_   1697 AATGTAAGACCTTGAACTCTAAAAATCCTGGTAGACAACCTAGG---AAA 1743
                                  v  vi    v     v  i i v   v   v    ---   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr20_12115221_   1744 TATT-ATTTTCTTAG--TACTGGCCATGGCAAACAATTTTTGGCTAAAGC 1790
                          v  -i vvi   i --  --   v    i------  i  i v  vii 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTA--GGCAATGGT------TTCTTAGATATGAC 599

  chr20_12115221_   1791 CGCAAAAGTAATTGCAACAAAAACAAAAATAGACAAGTGAAACCTAATTA 1840
                         vv      i vvv         iv         i  i vii  i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_12115221_   1841 TTCTAAAGAATTTCTGCAAAGCAAAAGAAACTATCAACAGAGTGAACATA 1890
                         vvv v  i  i  i  iivvv    i  v        v i      v v 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_12115221_   1891 CAACCTACAGAATAGG-GTAGATATTTGCAACCTATACATCCAACAAAGG 1939
                              i       i  - v i          vii   i   ii i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_12115221_   1940 CCTAATATCCAGAATCTATAGGGAAC----ATAAATCAACAAGCAAAAAG 1985
                         v  vi          v    ii    ---- i  v    i  vv    ii
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_12115221_   1986 CAAATAGCTCCATTAAAAAATAAGCAAAGGACATGAACAGACAATTCTCA 2035
                               i i v   ?      ii        iv    i     v     v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr20_12115221_   2036 AAAGAAAACATACAAGTGACCAACAAACATATGAAAAAATGCTCATAAAT 2085
                               i i      i  i    i  i  i       i       - v  
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA-ACAT 898

  chr20_12115221_   2086 CGATCGTCAG 2095
                          i????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.02 (16 / 904), avg. gap size = 4.25 (68 / 16)  


3199 20.70 9.39 0.12  chr20_12132949_12135071.rev      801  1631 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12132949_    801 TGTAAAGTCATAGTATGTTCATGGGTTGGAAAAC--AATACTGTTAAGAT 848
                           v    vi  vvi          i      i  --    i         
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12132949_    849 GTTCATACGACCCAAAGCAATCTACAGATACAATG-AATCTTTATCAAAA 897
                          viv    vv      vii          v   i -    ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12132949_    898 CCCCACAAGCATTTTTTACAGAAATATATAAATTCTTCCTAAAATTCATA 947
                         i    vvv  v      i       vv i  ii vv              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_12132949_    948 TAAAATCTG-AAGGGATACTGTGTACTCAAAACAATTTTGAAAAA----- 991
                          ii  -v  -      iv v vi  vi         i        -----
  L1M4_orf2#LINE/    151 TGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_12132949_    992 ----AGCTGGAGGCCTCACATTTCCTGATTTCAAAATATATTATGAAGCT 1037
                         ----  i      v      i    ii         iv  i  ii     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_12132949_   1038 ATGGTAATCAAAGCAGTGTGGTACTGGCATAA----AGACAAATAGATCA 1083
                          ii        ii                   ----     v        
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_12132949_   1084 ATGGAATACAATACAGAGCCAAAAAGTAAACC---ACCGT----GT---- 1122
                                 v   vv    i v i  i      ---  vv ----  ----
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_12132949_   1123 --ATTTTTGACAAACAGACCGAGACTACTTAATGTACAATGAACA----- 1165
                         --     i     ivivi  i    i i i    viv  v   i -----
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_12132949_   1166 -----CAAATAGTATTGGGAAAACTGGATATCCACATGCAAAAGAACAAA 1210
                         -----     i  ii     v         ?               ii  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_12132949_   1211 GTTGGATTTTTATTTTACAACATATATAGAAATTAACTCAAAATGTATTA 1260
                               iiii  ii i   v      i i                v  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_12132949_   1261 AAGACCTAAA-------------ACTATAAAACTCCTAGAAAAAAA--TA 1295
                         ?         -------------            i     i    --  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_12132949_   1296 GGCAAAAATCTTCACGGCATTGTACTTAGCAGTGACTTTT-----ATGAC 1340
                           ?iv        ii i v   vii vi   i  ii  i -----     
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_12132949_   1341 ACCAAAAGCACAGACAACAAAAGCAAAAATAGACAAATGGAGCTATATCA 1390
                                     ii         v         i    v ii  vi    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_12132949_   1391 AACTTAAAAG-TTTTATGCATCAAAGGACACAATCATCAGAGTATAAAGG 1439
                           v      i-    i   v           v    vv i   iv    i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_12132949_   1440 AAACCTATAGAACAGGAGAAAGTATTTAC------TATATCTGA-AAAGG 1482
                         v    i i    ii       i     i ------         -  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_12132949_   1483 AGTAATAATCAGAATATATAAAGAACTCTTACAGCTCAACAACAAAAAT- 1531
                          v vi  vi                        i     i  i     v-
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_12132949_   1532 CAAATAA-----TTTAAAAATGTACAAAGGACTTAAATAGATATTTCTCC 1576
                                -----  ?       vi       i  i      i        
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr20_12132949_   1577 AAAAAA--TATACAAATTGCCAAAAA--AAATGAAAATATTTTCAACATC 1622
                            i  --         v     v  -- v       v  vi        
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr20_12132949_   1623 ACTAATCAT 1631
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.62 (104 / 64)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.95 (79 / 20)  


3066 23.57 0.51 8.06  chr20_12206860_12211227     2897  3876 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_12206860_   2897 GAAAAATATTTCATGTTAATGGGTTAGAAGAATCAATATTGTGTAAATGC 2946
                             i    ii      v    i  i     v i        vv i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_12206860_   2947 CCATACTACTCAAAGCAATCTATAGATTCAATGCAATTCCTATCAAAATA 2996
                          v     v i    vii     i        i     i           v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_12206860_   2997 CCAATTACATTCTTCACAGAAATAGAAAAAATAATCCTAGAATGTACATG 3046
                            ii i v  i  ii       v  v  iv i      i   vi i   
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_12206860_   3047 AAACCACAAAAGACCTAGACTAGCCAAAATCATCCTGAGGAAAAGGAACA 3096
                         i  vii   ii    i   v         iv   i   ii  i i     
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_12206860_   3097 AAACCAGAAGAATCAGGTTACCTGACATCAAATTATGCTACAGCACTATA 3146
                           iiii  i  v   vii v  ii iv     viv i     ivi   i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_12206860_   3147 GTAACCAAAGCAGCATGTGTACTGGCAAACAAACAGACACACAGACCAAT 3196
                             i   ii   ii  -         v vii i     i i   i    
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTG-GTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_12206860_   3197 AGAACAAGGTGGAGAATGCAGAAATAGATCCATACATCTACAGTTAACTC 3246
                         i   i iii v    i v        i i        i  ii  i  i v
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_12206860_   3247 ATTTGTGTCAAAGTTGCTAAGAACATACACTGGGGAAAAGACAGTCTCTT 3296
                             vi v   i v   i    v   v  v        ii i     i  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_12206860_   3297 CAATAAGTGGTGCTGGGAAAACTGAATATTCATATGCAGAAGAATGAAAC 3346
                            i  i           v     i   ?i  i     i         ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_12206860_   3347 TAGACCCCTATCTGTCACCATACACAAAAGTCAAATCAAAATGGATTAAA 3396
                          i        i  vv       i      i i  v           i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_12206860_   3397 GACTTAAATCTAAGACTTCAAGCTATGAAACTACTAAAAGAAAACATTGG 3446
                            i     v     vi v  i    i     vi  i          v  
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_12206860_   3447 GGAAACCCTCCAGGGCATTGGTCTAGGGAAAAATTCCTTGAGTAATGCCC 3496
                         ? v  vi  i iv i v    vi    v  vii  i   iii  -  v v
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA-TGACA 600

  chr20_12206860_   3497 CCCAAAA---AAGTCAACCAAATAAAAAATGGACAAATGAGA-TTAATCA 3542
                           v   i---   -    v   v       i  i    vi  -  v    
  L1M4_orf2#LINE/    601 CCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_12206860_   3543 TATCAAATTAAAAAGCTTCTGCACAGTAAAAAACAAACAAAACAAAACAA 3592
                         ----          -   i  ii --------------------------
  L1M4_orf2#LINE/    650 ----AAATTAAAAA-CTTTTGTGC-------------------------- 668

  chr20_12206860_   3593 AACAAAACAAAAAACCCACCAAAAATCCAAAAAACACAAAAGAAAACCGT 3642
                         ------------------------- i    ii    ------------ 
  L1M4_orf2#LINE/    669 -------------------------TTCAAAGGACAC------------T 681

  chr20_12206860_   3643 AAAACAGTCAACAAAATGAAGAGACAACTCACAGAATGAGAGACAACAGT 3692
                          ------    v   i    i       i         i    v  i v 
  L1M4_orf2#LINE/    682 A------TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr20_12206860_   3693 TGCAAGCTATCCATCTGACAAGGGATTAAAAACCGGAATATGTAAGGAGT 3742
                              iii  vi      i      i viv v  i      i   i  ii
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr20_12206860_   3743 TCACACAACTCAACAGGAAAAAAGATCTAATAATTCAATTTAAAAATGGG 3792
                           vi         i iv     -  - v     ii     ?         
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAA-GA-CAAATAACCCAATTWAAAAATGGG 823

  chr20_12206860_   3793 CAAAAGATATAAATCGGCATTTCTCGAAAGAAGACAGACAAATTGCAAAA 3842
                             i   v i   v i        v        i v      v  v  v
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr20_12206860_   3843 AAGTATGTGAAAAG-TGCTCAACATCACTGATCAG 3876
                            i ii       -            ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (152 / 75)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 6.46 (84 / 13)  


1303 28.38 12.34 3.59  chr20_12265985_12267928.rev      618  1452 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12265985_    618 TGGAGAGATCTACTATTTTCTTGTATTGAA---CTCAACATTTATTAAGA 664
                             i    v v i  v   v  v    i ---  i  i   -i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-GTTAAGA 49

  chr20_12265985_    665 TGTTAATGCTCCTCAAATTTATCTAAAGGTCTAGTGAAGTCCCTTTAGGG 714
                           vi   i    i      v     v  i ii ii v i     v viii
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_12265985_    715 ATT---GCCACATTTTCTTGTCTATATGTGAAGAG--GAGC----AAGTG 755
                           i---  ii v    -   ivv v  -   vi  --  v ----  v v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTT-TTGCAGAAAT-TGACAAGCTGATCCTAAAATTC 147

  chr20_12265985_    756 AT-T---------AGGGATA-AAAATAAACAAAGCAATTT---AAAAGAC 791
                           - ---------     iv- i    iv    i    i ---      v
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_12265985_    792 CAGCCTTCTGAATATGAAGGCTTTACACTATTTGTTATCAAGATT----- 836
                         v i -----i  vv  i   vi i     viiiiv v    i i -----
  L1M4_orf2#LINE/    198 GAAC-----AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr20_12265985_    837 -AAACCT-CAGTAAGTAAATCAGAGTAGGATTGTCTGAAGAATACATAAA 884
                         -   v  -      vi  iv   v  i v i  v vv   i   v i v 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr20_12265985_    885 TAGACTGATGAAACAGAATATAGAGTTCAAAAACAGACTCATGCATG-AC 933
                             iii   i  i     vv     i  i   i i  i   i   v- i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr20_12265985_    934 AGCCGGT-GATTTATGACAAAGGTGACACTATAGACTA----GTAAGTAA 978
                         i i ii -     vi     i    v  ----    i ----i ii v  
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCA----AGACCATTCAATGGGGAA 388

  chr20_12265985_    979 ACAATTTTTTTTTTTTTTTACAATTACTGGTGTTTGGCCAATTGAATATC 1028
                          v   vv i    -------   iv v     i v  v   i  i   ? 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTT-------CAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr20_12265985_   1029 CATATGGAAAAATACAAATTT-------TCCCTCACCATCATCTATAGAA 1071
                           i   v    iv ii  v  ------- v      - i   v  i -  
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC-ACCATATACA-AA 479

  chr20_12265985_   1072 AATCAATTCCAGGCTGATCAT-GATC---AT---AGAAC-AAAACAACAA 1113
                            i  i  v iiiv     ?-  i ---  ---   i -     v i  
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr20_12265985_   1114 GCCTTCTAGGACAAAATGTAGGAG--AAT-------GCCTTG-------- 1146
                         iv  ii   i v    ii    ? --   -------i     --------
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr20_12265985_   1147 -----TTTCT-------AACA--AAAAGCCCCAACCATAAAGAAATAGAT 1182
                         -----     -------i   --      v v i v i   ii  v i  
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr20_12265985_   1183 GAATAAATGTGA----ATTAAAATTAGAAACTT--ATGCATCAAAACACA 1226
                         ii      vv  ----  i       i      --i   v     iv   
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr20_12265985_   1227 CAATTAAAATAACGAAAAGGCAAGGAAGAGAGTGAGTAAAGCCATTTGCT 1276
                          v  i  i v ii      i   vvv v   i  i vi  ivi      v
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr20_12265985_   1277 AATCAAGTATCTTGTATATGCAAAGGTCATATATTCAGAGAATAGAAATA 1326
                              vi     vi  ------ i  v v i   i    iv   v   v 
  L1M4_orf2#LINE/    730 AATCATATATCTGATA------AGGGACTTGTATCCAGAATATATAAAGA 773

  chr20_12265985_   1327 -TTCTTACAA------AGCAAAAAG-CAAATAATCCAATGGAAAAATGAA 1368
                         -i        ------ ii      -       i     v?       ii
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr20_12265985_   1369 CAAA--ATTCCTGAATG--TTTTTTTCACAAAGAGGTTATCCAAAGAGCC 1414
                             --   --     i--iv   i  -      i v   v    vi   
  L1M4_orf2#LINE/    824 CAAAGGATT--TGAATAGACATTTCTC-CAAAGAAGATATACAAATGGCC 870

  chr20_12265985_   1415 ACTTGACATATGAAAAAGTGCATGACATCATTAGTTAC 1452
                          v vii  i       ii   vii      ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.05 (41 / 908), avg. gap size = 3.24 (133 / 41)  


2237 24.44 1.63 9.16  chr20_12292283_12295134     1379  2360 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12292283_   1379 TAGAAAAGCATTCCATGCTCATGGATTGGAAGAATCAATATTGTCCAAA- 1427
                          i    iii  i     i               v i        iv i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12292283_   1428 -GCGATGTTC---AAAGCAATCTACAAATTCACCTCTATTTCTGTCAAAC 1473
                         -  i  ii  ---   vii       i     v v v  ii  i     v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12292283_   1474 TACCAACTTCATATTGCACATAATTAGAAAATACTAGTC-TAAACTTCAT 1522
                          v   i  v v v  vii  v  v v  v  -i  ii  -    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr20_12292283_   1523 ATAGTATCAGAAAAAGATCCTGCATAGCCAAGGCAATGTAGAGCAAAAAG 1572
                           i v vi- v  ii  i  v v        ii    v v  iv  i   
  L1M4_orf2#LINE/    150 ATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_12292283_   1573 AACAGACCTAGAGAAATCACATTATTGC---TTCACACTATATCTCAAGG 1619
                             i vi i   i v     i - iv ---    v viv  iiv   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACT-TCCCAATTTCAAAACTTACTACAAAG 247

  chr20_12292283_   1620 CTACAGTAACCAAAACAGCATGGTACTGGCACAAAAATAGACACACAGAC 1669
                                  i   i    ii           i  ii       i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_12292283_   1670 CAATGGAAGAGAATAGAGACCCTTGAAAGAAAGCCACACATCCA----CA 1715
                                 v     v    vi iv    v   v   i    ii ----  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_12292283_   1716 ACCAATCTTCAACAAAGTCGACAACAACAACAAAAAACCACAGGGAAAGA 1765
                          iii  i   i    i vi v   v v  vi------ v ii        
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATT------CAATGGGGAAAGA 391

  chr20_12292283_   1766 ACACCCTATTCAATAAATGGTGCTGGGAAAATTGGCTAACCAATATGCGG 1815
                          i vi  v     i              v  i   v  ?   -i    ii
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA-CATGCAA 440

  chr20_12292283_   1816 AAGAATGAAACTGGACTGTTACCTCTCACCA-ATACAAAATTTAGCTCAA 1864
                                  ii     ivi      v     -        ----------
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA---------- 480

  chr20_12292283_   1865 AATTAACTCAAAAATGTATTAAACACTCAAACATCGGGTGTCAAATTGTA 1914
                         -            -  v  i ? v  ii   -------   v i vi-  
  L1M4_orf2#LINE/    481 -ATTAACTCAAAA-TGGATCAWAGACCTAAA-------TGTAAGAGC-TA 520

  chr20_12292283_   1915 ATAATTATAAAAACTCAACATTAACTCAAAATGATTAAAAACTCAAATGT 1964
                          -  i       -   --------- i i  -----i     ----  --
  L1M4_orf2#LINE/    521 A-AACTATAAAA-CTC---------TTAGAA-----GAAAAC----AT-- 548

  chr20_12292283_   1965 CAGATGCCAAATTATAAAATTTCTAGTAGAAATCCTGGGAAATTATTATA 2014
                         -  i? --------    vi   --  i--- i i    ------   --
  L1M4_orf2#LINE/    549 -AGGNG--------TAAATCTTC--GTG---ACCTTGGG------TTA-- 576

  chr20_12292283_   2015 GGTATTGGTATAGGCAAAGAATTTAGGATGAAGACTCCAAAAGCAAATGC 2064
                           i v    v ----------i    -  - v   v         v v  
  L1M4_orf2#LINE/    577 GGCAATGGTTT----------CTTAG-AT-ATGACACCAAAAGCACAAGC 614

  chr20_12292283_   2065 AACAA--GTTTTTTAAATAGGCAAATGGGACTTAATTTAACCAAAGAGTT 2112
                              -- vvv---      ii    v      v  iv  viv  i ii 
  L1M4_orf2#LINE/    615 AACAAAAGAAA---AAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr20_12292283_   2113 TCTGCACAGCCAAAGAAACTCTCCAAAAGAGCAAGCAGACAACCTACAGA 2162
                          i  ii vv v  i  v   v  -  i i  ii iv        i     
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATC-AAGAAAGTGAAAAGACAACCCACAGA 710

  chr20_12292283_   2163 ATGAGAGAAAATATTCACAAACTATGCAGCCAACCAAAGACTAATATCCA 2212
                            i           ii    ii  ii v ii iv ii    vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr20_12292283_   2213 GAATCTATAAGGAACTTAAGTGAATCAACAAGAAGAAAACAAACACCTCC 2262
                             v     i     ivviii v    i  v  i  i     i v i v
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr20_12292283_   2263 ATCAACAGGTGGGCAAAGGACATGAAGAGACATTTCTCAAAAGAAGACAT 2312
                           i? v ii           iv    v           v        i  
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATAT 860

  chr20_12292283_   2313 AGAAGTGGCCAACAAACATATGAAAAAATGCTCAACATTACTCTCATC 2360
                          v  i       i  i  i       i           i ????????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (146 / 90)
Gap_init rate = 0.04 (32 / 908), avg. gap size = 3.31 (106 / 32)  

 662 24.88 2.87 0.96  chr20_12292283_12295134     2644  2852 (0)  C L1M4_orf2#LINE/L1   (0)   908   696  

C chr20_12292283_   2852 AAGACAAGGCATACATTTAGATAAATTATTTTCAAATTACATATTTGACA 2803
                                vv  i v v vi  v   v     v     i i    i   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chr20_12292283_   2802 AAAGACTTGAATCCAGAATATATAAATAATTTTTTTAACTCAACAGTAAG 2753
                          ii      v                v  i i  vi       i i   -
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA- 794

C chr20_12292283_   2752 GGAAAAAAAACAGTTTGATTACAAAAAGGGCAAAAG-TTTGAA----CAT 2708
                         -i  i v   i iiiii   ?v    v       i -      ----   
  L1M4_orf2#LINE/    795 -AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

C chr20_12292283_   2707 TTTTCCACACAGGATATAGGAATGACAGACATGC-CACAAAAAGATGTTG 2659
                           i    v v i      vi    i vi i v  -  ii        i v
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

C chr20_12292283_   2658 AACATCACTAGCCTT 2644
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (31 / 20)
Gap_init rate = 0.02 (4 / 213), avg. gap size = 2.00 (8 / 4)  


3237 26.39 1.11 0.44  chr20_12351576_12356392.rev     3424  4325 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12351576_   3424 TGGAAGAACAGTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 3473
                              ii i vi     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12351576_   3474 GGCTATACTGCTCAAAGTAATGTACAGATTCAATGCTATCCGCATCAAGC 3523
                            v     v i    v i  v           i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12351576_   3524 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTCA 3571
                          v   vivi i  i  ii     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_12351576_   3572 TATAGAACCAAAAAAGAGCCCGCATAGCCAAGACAATCCTAAGACAAAAG 3621
                            i   viiv  ii  v  v v        i      i i i v i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_12351576_   3622 AACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATACTACAAGGC 3671
                                i      vv   vi  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_12351576_   3672 TACAGTAACCAAAACAGCATGATACTGGTACCAAAACAGATATATAGACC 3721
                                 i   i    ii  i      i iv ii i   i       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_12351576_   3722 GATGGAACAGAACAGAGGCCTCAGAAATAACACCACACGTCTACAACCAT 3771
                         i      i    iv   ivii         vv   i  i i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_12351576_   3772 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAAGATTCCCT 3821
                         i    i  i     ivv  v   i v  vv           ii  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_12351576_   3822 ATTTAATAAATGATGTTGGGAAAACTGGCTAGCCATATGCAGAAAGCTGA 3871
                         v  i  i     i  i     v      v  ?   i     i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_12351576_   3872 AACTGGATCCCTTCCTTACACCTTATACAAAAACTAACTCAAGATGGACG 3921
                          ii    i    v   i     v          i        i     iv
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_12351576_   3922 AAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3971
                          ?    i           v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_12351576_   3972 AGGCA-ATACCATTCA-GGTCACAGGCATGTGCAAAGACTTCATGACTAA 4019
                            ?i- v i -   i- ii vii  i- iv    v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATAT 596

  chr20_12351576_   4020 AACACCAAAAGCAAAGGCAACAAAACCCAAAATAGACAAATGGGATCTAA 4069
                         i            v i         vvv        i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_12351576_   4070 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAAAGTGAAC 4119
                          i   v v  i i   i  ii vv    i  v       vv        v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_12351576_   4120 AGACAACCTACAGAATGGGAGAAAATTTTTGCAATCTATGCATGTGACAA 4169
                                 i                 v       vii  ii  v   i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_12351576_   4170 AGGGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTA-CAAGAAAA 4215
                         i  i  vi          v  i        --  -  i i -i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_12351576_   4216 AAACAAACAATCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTTC 4265
                          i     i  i  v  i?    i    ii      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_12351576_   4266 TCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAATGCTTATC 4313
                           v        i  vi viii     i  --         i     i v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_12351576_   4314 ATCACTAGTCAT 4325
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (149 / 85)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3213 26.87 0.55 0.55  chr20_12372020_12378288.rev     4870  5777 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12372020_   4870 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4919
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12372020_   4920 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4969
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12372020_   4970 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5016
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_12372020_   5017 ATATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAA 5066
                                 viiv  ii  v  viv  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_12372020_   5067 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5116
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_12372020_   5117 CTACAGTAACCAAAACAGCATGGTACGGGTACCAAAACAGAGATATAGAT 5166
                                  i   i    ii      v  i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_12372020_   5167 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCGTATCTACAAC 5214
                                 i    i--    i  --        vv  iiii  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr20_12372020_   5215 TATCTGATCTTTGACAAACCTGAGAAAAACGAGCAATGGGGAAAGGATTC 5264
                         i vi    i  i     ivv  vv  i v ivv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_12372020_   5265 CCTATTTAATAAATGGTGCTGGCAAAACTGGCTAGCCATATGTAGAAAGC 5314
                         i  v  i  i            v v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_12372020_   5315 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5364
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_12372020_   5365 ATTAAACACTTAAACGTTAGACCCAAAACCATAAAAACCCTAGAAGAAAA 5414
                           i ? v  i    i  v   v i     i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_12372020_   5415 CCTAGGCATTACCATTCAGGACATATGCATGGGCAAGGACTTCATGTCTA 5464
                          v    ?i v viv   iv   v vv vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_12372020_   5465 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5514
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_12372020_   5515 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5564
                           i   v i  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_12372020_   5565 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5614
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_12372020_   5615 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5664
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_12372020_   5665 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5714
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_12372020_   5715 CTCAAAAGAAGACATTTTTGTAGCCAAAAAACACATGGAAAAATGCTCAT 5764
                            v        i  vivvi i     v  i      i   i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_12372020_   5765 CATCACTGGCCAT 5777
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (142 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1177 28.70 5.16 2.24  chr20_12403235_12404957.rev       16   461 (1262)    L1M4_orf2#LINE/L1        2   460 (448)  

  chr20_12403235_     16 GAAGAGATACTCCATGTTCATGAATTAGAAGATTCCCGATGGTTAAGATG 65
                          i i     ii           i   i     i ivvv  v         
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_12403235_     66 TCAGTCTTTTCTAACGTGATCTATAGATTCAATACATAGCCAATCAAAAG 115
                         v  i vi ii i  vv       i        ii  vvv  v       v
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_12403235_    116 TT--ATTGTGTATTT-------ATCAGTAAACTGATTCTAAAGTTTATAT 156
                         ii--ii  iv v   -------  iiii  i     i     i  i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr20_12403235_    157 GGAAAAGTAAA--ATTCTAATTATAGCCAACACAATACTGAAGAAGAAAA 204
                              v i  i-- ii vi --        v     vi    i     i 
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGA--ATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_12403235_    205 ACAAAGTTGAAG-ACTCCCACTATTTATTTTTATTTAAAGC--AATATAA 251
                                  i  -    v    viii v   i ----  i -- v  i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCA----AAACTTACTACAA 245

  chr20_12403235_    252 AGTTACAGTAATTAATACTTTTAGCAAGATAAGGGCAAAAGAATAGACAC 301
                           i         i  v  ----  iiv i  vv    v   i       i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGAC----AGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_12403235_    302 A--G--CAATGCAACAGAACAAAGAACCTACAAATAGATTCACAAAT--A 345
                          -- --     v  i    ivi   ii i v     i ii  i v  -- 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_12403235_    346 TACTGAGCTGATCTTTGATAAAAGAGC-AAGGCACTTAAATCAAGAAAAG 394
                          iv v ii    i  i  i  ii v  -   i vv  v   vii    ii
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_12403235_    395 ATAACCTTT-CAACAAATGATGCTGGGAAAATTGGACATTCTTATGCAAA 443
                            ii    -         i        v  i    i ?i vi       
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_12403235_    444 A-AATGAACATAAACACCT 461
                          -      vv ii  v   
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCT 460

Transitions / transversions = 1.89 (83 / 44)
Gap_init rate = 0.03 (14 / 459), avg. gap size = 2.36 (33 / 14)  

3024 20.39 5.71 1.69  chr20_12403235_12404957.rev      462  1231 (492)    L1M4_orf2#LINE/L1      108   908 (0)  

  chr20_12403235_    462 TGCACCTTTCACATAAATTAACTCAAAATGGCTCATACACTACAATTTAT 511
                            vii   ii  v     i  ----  --   v  - -   v    i  
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGAC----AA--GCTGAT-C-CTAAAATTCAT 149

  chr20_12403235_    512 ATGGGAACAAAAGGAACCCAGAATCGCAAAAGTAATCTT-------AAGA 554
                             i  iiv    i         v  v   ii      -------    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_12403235_    555 ATAAATTCAAAAGCCTTAAAATTTCCAATTTCAAAATTTACTAGACAACA 604
                          i   v iii i v  i v v  i            i      v v i v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_12403235_    605 AAAATAATTAAGACAGTGTGGTATTGGCGTATGGATAGGCATATAAATCA 654
                          v i    i              i    i  v      i      i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_12403235_    655 GT----T-GAATTGAGAGTTCAGAGATAAACCCATATATCTATGGCTAAC 699
                         i ---- -           i    i           i  i     ii  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_12403235_    700 TGATTTTAG-CAAGGATGTCAAGACCATTCAATGGGGAAA--ATAGTCTT 746
                                v -     i  i                     --        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_12403235_    747 TTCAACAAATAATTATAAAACACTTAGATATATACATGCAAAA-AATAAA 795
                                   ii vv iii   vi i    ?vi          -   i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_12403235_    796 GATGGACCCCTACTTTACACC-TACACAAAAATTAATGCAAAATGGATCC 844
                          v           i i     -  i           iv           v
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_12403235_    845 AAGACC-AAG-----GAGTTAGCACTGTAAAACTCTTAGAAAAAACACAC 888
                         ?     -  i-----   i  iv   i              i   -   i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA-ACAT 548

  chr20_12403235_    889 AGATGTAA-TCTTCCTGTGACCTTGGATATGGCAATAAGTTTTCGTATAT 937
                           i?    -     --          i vv      iiv  i iiv    
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTC--GTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_12403235_    938 AAAATCCAAAGCACAAGCAAGAAAGGAAAAAGAGTAGACAAACTGGATTT 987
                         i v i v             v   i      i--    i   i    i  
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAAATTGGACTT 644

  chr20_12403235_    988 CATCACATTTAAAAACTCTTGTTCTTCAAAAACAAATATAAAGAAAGTAA 1037
                              v v         i    v       iivv v   v        i 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_12403235_   1038 AAACATAACAGATAAAATGGAAGAA----TTCTTAAATTGTATACCTAAT 1083
                            v i   vv i i     i    ----  ivi    ii    i  i  
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_12403235_   1084 ATGGGGTTTATATTTCGAATTTATAAAGAATACTTGTAACTCAATAATA- 1132
                          v   ii  i   iiv    v         iv   ii            -
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_12403235_   1133 ---GACAAATAATGGAAATAAAAATTAGG----------GAA-AGACATT 1168
                         ---         ivv  v ?    v i  ----------   -       
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_12403235_   1169 TCTCCAAA-AATATGTACAAATGGCCAGTAGACACATGAAAAGATGCTCA 1217
                                 -  v  i            i  ii                  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_12403235_   1218 GTGTCATTAGTAAT 1231
                         iii   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (101 / 52)
Gap_init rate = 0.03 (22 / 801), avg. gap size = 2.59 (57 / 22)  


3190 26.76 0.66 0.66  chr20_12419773_12426152     4981  5888 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12419773_   4981 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5030
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12419773_   5031 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5080
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12419773_   5081 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5128
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_12419773_   5129 CATGGAACCAAAAAAGAGCCCGCATTGCCATGTCAATCCTAACCCAAAAG 5178
                         i      viiv  ii  v  v v  v    viv     i i vvv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_12419773_   5179 AACAAAATTGGAGGCATCATGCTACCTGACTTCAAACTATACTAAAAGGC 5228
                               i       vv   ii  v  ii i      viv     v  i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_12419773_   5229 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5278
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_12419773_   5279 AATGGAACAGAAC--AGACCCCTCAGAAATAATGCCACATATCTACAACT 5326
                                i    i--   vi  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_12419773_   5327 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCT 5376
                          vi    i  i     ivv  v   i v  vvv           i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_12419773_   5377 CTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5426
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_12419773_   5427 GAAAGTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCCAGATGGA 5476
                            iv    i    v   i   i v              i  v i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_12419773_   5477 TTAAAGACTTACATGTTAGACCTAAAACCATCAAAACCCT-GGAAGAAAA 5525
                          i ?    i  v    v   v       i  -     i  -i        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAA 545

  chr20_12419773_   5526 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5574
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_12419773_   5575 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAACTGACAAATGGGATCT 5624
                          vi            vvi          vv    iv  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_12419773_   5625 AATTAAACTAAAGAGCTTGTGCACAGCAAAAGAAACTACCATCAGAGTGA 5674
                         v  i   v v  i i   v  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_12419773_   5675 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGAC 5724
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_12419773_   5725 AAAGGGCTAATATCCAGAATCTACAAAGAACCCAAACAAATTTACAAGAA 5774
                           i  i  vi          v  i       i vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_12419773_   5775 AAAAACAAAGAACCCCATCAAAAAGTAGGCAAAGGATATGAACAGATATT 5824
                            i     v     v  i?    i i          v    i   i   
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_12419773_   5825 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5874
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_12419773_   5875 TCATCACTGGCCAT 5888
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (139 / 100)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.33 (12 / 9)  


1156 24.71 15.19 3.34  chr20_12455865_12457454      501  1099 (491)    L1M4_orf2#LINE/L1      239   908 (0)  

  chr20_12455865_    501 ACTTCAAA-CTACGGTGATCAATACTAAT-TGGCATTAGTGAAAAGTTAA 548
                            v    -    i  i     v  - i -   i i i iiv  i v  i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGAC-AGTGTGGTACTGGCATAAGGATAG 287

  chr20_12455865_    549 ACATGTAGATTAATGAAACAGAATAGAAAG--------------CATACA 584
                             i     i    i  i     v  i  --------------      
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr20_12455865_    585 TATACAGTCAATTAGTTCATAACAAAATTACTAAGGGAATAGAGAAGGCA 634
                          v  ii       ii  ivii    iiv i i   ivv  vv ivi  v 
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr20_12455865_    635 AAGGAAAATCTCTGCAATGAATGGTGCTGGATCAGCTGGAAATTCATTTG 684
                            i v i   i v   ii           iv  i     v ?i  iv  
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr20_12455865_    685 AAATGGGAAAAAAATTGATCTTGATAATTACTTGACAATATATACAAAAA 734
                         v  -ii   vi  i   -----  ivvi   i v   vi           
  L1M4_orf2#LINE/    438 CAA-AAGAATGAAGTTG-----GACCCCTACCTCACACCATATACAAAAA 481

  chr20_12455865_    735 C-A--TCAACATTATTCATTATCATAAGTATAA-AGCATAAAACTATAAA 780
                         i- --    v  viv   ?viv v   i i   -   -            
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC-TAAAACTATAAA 530

  chr20_12455865_    781 ACTTCTAAAATAAAACA--GGAA-AACTATTTGTGACCATTGGGT-AAGC 826
                            ii  i  v      --  ?i-  v v  i      -      - i  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGC 579

  chr20_12455865_    827 TTAATTGTTT-----ATAT--CATAAAAAGGATA----------GAAAAA 859
                         --   v    -----    --  iv     v i ----------      
  L1M4_orf2#LINE/    580 --AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr20_12455865_    860 AGCTGGGTAAAATGGACTGCATTTTTTTTAAAA--AAAAACCT-----CT 902
                          -- i i    v      v   i------    --      i -----  
  L1M4_orf2#LINE/    628 A--TAGATAAATTGGACTTCATC------AAAATTAAAAACTTTTGTGCT 669

  chr20_12455865_    903 TTAAAATATATTAT---GAAAACAAAAAGGCAAGTCGCAGAGTG--AGAA 947
                          i   iv i i   ---    iii     i   vi i    i  --    
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_12455865_    948 AATAT---------------------------------CCGGGATGTACA 964
                              ---------------------------------  i i  i  i 
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr20_12455865_    965 AAACAACTCTTATAAATCAATAA---GAAGACACCTAACCTAAT-ACAAT 1010
                           i-        i  v       ---i      vv     i   -?v  v
  L1M4_orf2#LINE/    770 AAG-AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr20_12455865_   1011 ATGGGCAAAC-ATTTGAATAGAGGCTTCACTGAAGAAGATATGCAAATGA 1059
                                  v-           vii   v ii          i      i
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr20_12455865_   1060 CAAGTACACACATAAAAAGATGCTCAATATCTTTAGTCAT 1099
                          v i  vi     i             i   v????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (92 / 52)
Gap_init rate = 0.04 (29 / 670), avg. gap size = 3.83 (111 / 29)  


1792 26.09 3.59 7.17  chr20_12484365_12487225.rev     1442  2361 (500)    L1M4_orf2#LINE/L1        1   887 (21)  

  chr20_12484365_   1442 TGGAGAAATATAACAGGTCCATGGATTGCAAGATTTAACA--GTACAGAT 1489
                             i i    vv  v  i         v    i    i --  vv    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12484365_   1490 ATCAGTTCTCCCAAAATTCACTTACAGATTTAACAC---TTCAATAAATA 1536
                         iv  i v     v     v ii        i   i ---ii v  v  v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12484365_   1537 TCCT--CTACACAATATTGTGCAGACCTAGACAAAGTGATGCTAATATTT 1584
                            i--  i - -- v  v      vv v     iv    v    v   i
  L1M4_orf2#LINE/    101 TCCCAGCTGC-C--TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr20_12484365_   1585 ATATTCAAAGGTAAAGGACCTAGAATAGTGGGGAAAATATTTTTTAAAAA 1634
                             vv   v i  i     i       iv---    i v i  v     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCC---AAAACAATCTTGAAAAA 194

  chr20_12484365_   1635 ------TAAACTGGGATAATT-ATGCCAGCTGGTTTTTAAGGTTATTATG 1677
                         ------i   v v   vi i - ii ivv iii   iv  iv   i  ii
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_12484365_   1678 AAGCTATAGTAATCAAAACTATAAAGTATTGGAA-AGGGATAGAAAAAGG 1726
                               i         i  vi ivi   i   v - i       v v vi
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_12484365_   1727 AATCAATGTAACCATAT--AGAGTCCAGAAATAGACTCACACAAATATGG 1774
                         i       v  iviv  --              i  i  i   vv     
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_12484365_   1775 CCAATTGATTTTTGAAAAAAAGTACATAAAGA--ATTTAATAAATTAAAA 1822
                         i           i  v  ii-  i v--    --   i   iiivv  i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGG-GTGCC--AAGACCATTCAATGGGGAAAGA 391

  chr20_12484365_   1823 ATAGTTATTTCAACAAATAATGTTTTAAAAAATTGTAAATCCAGATTCCA 1872
                              iv           ii  i v-ii v  i  v v ?   v  v --
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTG-GGACAACTGGATAKCCACATGC-- 438

  chr20_12484365_   1873 AAACCAAAAAAAAAAATAAACACACACACACACACACACACACACACACA 1922
                         ---------    i   i  vviiv  v vi  ----------- v    
  L1M4_orf2#LINE/    439 ---------AAAAGAATGAAGTTGGACCCCTAC-----------CTCACA 468

  chr20_12484365_   1923 CACACACACACCAAAAACCTTGACCTAAACTTCATGACTTATACAAAAAT 1972
                          -  i i   ---    --  i  ii   ----   iv i ? -------
  L1M4_orf2#LINE/    469 C-CATATACA---AAAA--TTAACTCAAA----ATGGATCAWA------- 501

  chr20_12484365_   1973 TTACCTCAAAGTAGACCTAAATATAAAATTTAAAACTATAAAATCTTTGG 2022
                         -------------         i   i vi             iii  i 
  L1M4_orf2#LINE/    502 -------------GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr20_12484365_   2023 GAGTAAATAAA-----AAATATTTGCCACCTGGTATTAGACAAAGAGCTC 2067
                         i  v   i v -----    v  i iv    v vi    i   v ivi  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_12484365_   2068 TTATATGTGACACCAAAAGAATAATCAATGAAGGAAAAAAATTATAAACT 2117
                            v  i            v i  v   ii  i       vvv     i 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_12484365_   2118 GAATTTTTATTAACTTTTAAAAA---TTGCTCTGAAAAAGACACTG--AT 2162
                          i i  i-  i  vv  -     ---   iv  vv   i      i-- v
  L1M4_orf2#LINE/    639 GGACTTC-ATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr20_12484365_   2163 GACAATAAAAAGACAAATTACAGAAATGGGAGTGAAGATTTTCAAGTCAC 2212
                           v i i         vii      -      vi  v    v   i   i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAA-TGGGAGAAAATATTTGCAAATCAT 735

  chr20_12484365_   2213 ACATTTAATAAAG-ACTATTTTCCAAAATATATAAAGACTTCTAAAAACT 2261
                          i  i i    i -   vv v    i            vi   v v    
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr20_12484365_   2262 CAAAATGTAGAAAG-CAAA-AGTCTA-TTAAAAAATGGGTGAAATATTTG 2308
                            v -i  i    -    - ii i -  ?         ii  iv     
  L1M4_orf2#LINE/    786 CAATA-ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr20_12484365_   2309 AATGGACATTTCACCAGTGAGAATATACAGAAGACAAATAAGTACATGAA 2358
                            i        v   iv  ii       i v i v      i       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr20_12484365_   2359 AAG 2361
                            
  L1M4_orf2#LINE/    885 AAG 887

Transitions / transversions = 1.35 (136 / 101)
Gap_init rate = 0.04 (32 / 887), avg. gap size = 3.09 (99 / 32)  


3271 26.65 0.55 0.55  chr20_12510655_12516928     4875  5782 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12510655_   4875 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4924
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12510655_   4925 GGCCATACTGCCCAAGGTAATTTGCAGATTCAATGACATCCCCATTAAGC 4974
                            v     v     iv i  i i         i vv     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12510655_   4975 TACCAA-TGCCTTTCTTCACAGAA-TTGCAAAAAACT-ACTTTAAAGTTC 5021
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_12510655_   5022 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5071
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_12510655_   5072 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTAAAAGG 5121
                                 i      vv       v  ii i      viv     v  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_12510655_   5122 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5171
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_12510655_   5172 CAATGAAACAGAAC--AGAGCCATCAGAAATAAAGCCGCATATCTACAAC 5219
                              i  i    i--    i --          v  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC--CAGAAATAAACCCATACATTTATGGT 345

  chr20_12510655_   5220 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAACGGGGAAAGGATTC 5269
                         i vi    i  i     ivv  vv  i v  vv   i        i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_12510655_   5270 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5319
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_12510655_   5320 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5369
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_12510655_   5370 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5419
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_12510655_   5420 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5469
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_12510655_   5470 AAACACTAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5519
                         vi    i       vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_12510655_   5520 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5569
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_12510655_   5570 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5619
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_12510655_   5620 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5669
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_12510655_   5670 AAAACAAACAACCCCATCAGAAAGTGGGCGAAGGATGTGAACAGACACTT 5719
                           i     i     v  i?i   i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_12510655_   5720 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCAT 5769
                            v        i  vi viii     v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_12510655_   5770 CATCACTGGCCAT 5782
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3102 26.91 1.33 0.78  chr20_12590910_12596654     4351  5253 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12590910_   4351 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4400
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12590910_   4401 GGCCATACTGCTCAAGGTAACTTATAGATTCAATGCCATCCCCATCAAGC 4450
                            v     v i   iv i ii  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12590910_   4451 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 4497
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_12590910_   4498 ATATGGAAC--CAAAAAACAGCCTGCATCGCCAAGTCAATCCTAAGCCAA 4545
                                 v--   iii  --  v v  v     iv     i i ivv i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_12590910_   4546 AAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAA 4595
                                   i      vv       v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_12590910_   4596 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 4645
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_12590910_   4646 ATCAATGGAACGGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACA 4693
                                   ii   i--    i  --        vv  ii i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr20_12590910_   4694 ACTATCTGATCTTTGACAAACCTGAGAAAAACGAGCAATGGGGAAAGGAT 4743
                         iii vi    i  i     ivv  vv  i v ivv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_12590910_   4744 TCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGGCATATGTAGAAA 4793
                         vvi  v  i  i              v      v  ?v  i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_12590910_   4794 GCTGAAACTGGATCCCTTCCTTACGCTTTATACAAAAATCAATTCAAGAT 4843
                         iv    ii    i    v   i  i iv           i  i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_12590910_   4844 G-ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 4892
                          -  i ?    i    i  v   v       i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_12590910_   4893 AACCTAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTC 4942
                            v    ?i v viv   iv   v v  vv i i   v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_12590910_   4943 TAAAACACTAAAAGCAATGGCAACGAAAGCCAAAATTGACAAATGGGATC 4992
                           vi    i       vvi     i    vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_12590910_   4993 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5042
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_12590910_   5043 AACAGGCAACCCACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGA 5092
                           v  i         i             v  ii   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_12590910_   5093 CAAAGGGCTAATATCCAGCATCTACAATGAACTCAAACAAATTTACAAGA 5142
                         i  i  i  vi       v  v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_12590910_   5143 AAAAAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAGACAC 5188
                             i    ----   v  i?    i           iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_12590910_   5189 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGGAAAAATGCTC 5238
                              v        i  vi viii     v  i      i   i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_12590910_   5239 ACCATCACTGGCCAT 5253
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (145 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


1848 24.25 4.79 4.34  chr20_12632620_12634278.rev      501  1168 (491)    L1M4_orf2#LINE/L1      238   908 (0)  

  chr20_12632620_    501 TATTCCAAAGCTACAATAA-AAAGTTAGTACAGTATTAGCAAAAGAACAG 549
                           i v          i   -v   vi   iii   i i   v   i i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr20_12632620_    550 ACACATAGAATGATGAAACAGTAC--AGAGTCCAGAAATAGGCCC---CC 594
                            i     vii   i  i  v i--              ii   --- v
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr20_12632620_    595 TGTATACAGTTAGCTAATCTTTGACAAAGGAGTAAAAGCAATAAAATAGA 644
                          v   i--  i ii i  i  i     i  v iv  ii v  vv   i i
  L1M4_orf2#LINE/    338 TTTATG--GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr20_12632620_    645 CAAAGAATAGTCATTTCACCATATAATTCTGGATCAATTGGACATCCATG 694
                         v           v     v  v  ii v    iv   i    i ?   ii
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr20_12632620_    695 TGCAAATAATAATAAAAATTTTTTAAAAACTACACAGAAATCTTAAACAC 744
                               -- v   i  i----  vi vvv    --------  i v  - 
  L1M4_orf2#LINE/    436 TGCAAA--AGAATGAAG----TTGGACCCCTAC--------CTCACAC-C 470

  chr20_12632620_    745 AGATCTTATGCAAAAATTAACTCAAA-----TAATATACCTAAATATAAC 789
                          -----   i                ----- v ? v        i   v
  L1M4_orf2#LINE/    471 A-----TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr20_12632620_    790 ATGC-AAAATTATGGAACATCTAGAAGAAAACATAAAAGAAAATATTTAT 838
                          -  -    i   ii   vii              ii? v    v  ii 
  L1M4_orf2#LINE/    516 A-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr20_12632620_    839 GACCACTGGGATTTGTGATGGGTTTTTAAATAAAATATCAACATCACAAC 888
                             -i    v vv ii    v  i   i   vi i i   v v     v
  L1M4_orf2#LINE/    565 GACC-TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr20_12632620_    889 CCTT----GGAAAAATATTAATGCATTGAACTTTGTTAAAATTAAAA-CT 933
                          vvi---- i       --i  iv    i    ii i          -  
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATA--GATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr20_12632620_    934 GCTCTGC----AGAGACACTGTCAAGAGAAACAAAAGGCAAGCAACAAAC 979
                         vi v   ---- ii      i      i ivv     i   v v   i v
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr20_12632620_    980 TAGAAGAAGATATTTGCAAAAACATATGTCTGGTAGAGAACTTGTATCCA 1029
                          i i    i           v-     i    i  ii i           
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAAT-CATATATCTGATAAGGGACTTGTATCCA 760

  chr20_12632620_   1030 ACATCTATAATGAACTCTTAAAACTCAATAATTGGAAAAAACA------- 1072
                         iv  v     v         v           --i    i   -------
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAAT--AAAAAGACAAATAACC 808

  chr20_12632620_   1073 ----TTAAAAATGAGTGAAAGATCTGAATAGATCCTTCACCAAAGAAGAT 1118
                         ---- ?       i ii  i   i        ivi   v           
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr20_12632620_   1119 ATTCAAATGGAAAATAAGCATATGAAAACATGCTCAATATCGTTTGCAAT 1168
                           v       vv        i       v        i   i????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (98 / 60)
Gap_init rate = 0.03 (20 / 671), avg. gap size = 3.05 (61 / 20)  


2184 25.28 3.84 1.42  chr20_12639655_12641331.rev      484  1187 (490)    L1M4_orf2#LINE/L1      188   908 (0)  

  chr20_12639655_    484 TGAAAAATTTGGAGTTAAAAAA--TAGATGACTGATTTTTCCTACTTT-A 530
                                --- i  --  v   -- i  v    v ivi    i v   - 
  L1M4_orf2#LINE/    188 TGAAAAA---GAAG--AACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr20_12639655_    531 AATCTTACTATAAAAGCTACAATAAATAAGACAGTCTCAGATTAGTG-AA 579
                           v       i   -      i   vi        v viv i i ii-  
  L1M4_orf2#LINE/    233 AAACTTACTACAAA-GCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr20_12639655_    580 AAATAGATAAACAGATCAATGAAACAGAAGAAAGGACTTAGAAACAGACC 629
                         ii     i v i         i  i    vvi  iiiii     i i   
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr20_12639655_    630 CACACAA--ACAGCCAACTGATATTTGAAAAAGAAGCAAAGGCAATTCAA 677
                           i   v-- ii i   i    v  i  v  i iv  v   i v      
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr20_12639655_    678 TGAAGAAAGAATAATCCTTTCAGCAACTGGTGCTGGAACAACTGGACATT 727
                           ii         i  i     i   v         i         i ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr20_12639655_    728 CACAAG-AAAAAAA--AA--TAGATCTTATATCTTTCAC--------AAA 764
                             v -    i  --  -- i  i ii-  i  iv   --------   
  L1M4_orf2#LINE/    432 CACATGCAAAAGAATGAAGTTGGACCCC-TACCTCACACCATATACAAAA 480

  chr20_12639655_    765 ATTAACTTAAAATGGATCATAGACCTAAGTGTAAAACACAAAACTATAAG 814
                                i           ?        i     i vvi          i
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr20_12639655_    815 ACTCCTCGAAGATAACATTGGAG-AAACCTAGGTCACCATGGTTTTGCCA 863
                             i v     v     v  ? -   i  vv  v   v   v  v v  
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr20_12639655_    864 ATCACTTTTCAGATATAATAACAAAAGCCTTATCTATGAGAGAAAAACAT 913
                           vii  i i      i i v       viv v v ii i       -  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-AT 629

  chr20_12639655_    914 TGACAAATTGGACTTCATTAAAATGGAACATTTCTGCTCTATATAAAACC 963
                         v  i              i     vi  v i  i  iv  vi v ii  v
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr20_12639655_    964 CTGTTCAGAGAATGAAATAACATGCCATAGACTGGGAGAAAATATTTACA 1013
                           i iv   i i     vi   vv   i   v               i  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr20_12639655_   1014 AAACACATATTTGATAAAGGACTGGTATCCAAAATACACAAAGAGCTCTT 1063
                           v  i    i      i     v       i    i i     i     
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr20_12639655_   1064 AAAACTCAAGAATAAGAAAACCAATTATCTGATT-AAAAATGAGTGAAAC 1112
                          v       v     i  i  v   v i ii   -       i ii  iv
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr20_12639655_   1113 ATCTTAATAGAAACTTGCT-----AAAAATATATAGATGGGAAAAAATGT 1157
                           i v      v i  -  -----i  i     i i    vv  v  - i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTT-CTCCAAAGAAGATATACAAATGGCCAATAA-GC 877

  chr20_12639655_   1158 ATATGAAATAATGCTCAATA-CAATATGCCA 1187
                          i      vi        i -  ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (110 / 65)
Gap_init rate = 0.03 (19 / 721), avg. gap size = 1.95 (37 / 19)  


3252 27.20 0.44 0.44  chr20_12729916_12736192.rev     4878  5785 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12729916_   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12729916_   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4977
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_12729916_   4978 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5025
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_12729916_   5026 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5075
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_12729916_   5076 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5125
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_12729916_   5126 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5175
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_12729916_   5176 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5223
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_12729916_   5224 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5273
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_12729916_   5274 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5323
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_12729916_   5324 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5373
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_12729916_   5374 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5423
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_12729916_   5424 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5473
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_12729916_   5474 AACACCAAAAACAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5523
                         i         i  vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_12729916_   5524 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5573
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_12729916_   5574 AGGCAACGTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5623
                           i    vi   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_12729916_   5624 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5673
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_12729916_   5674 AAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5723
                          i     i     v  i?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_12729916_   5724 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5773
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_12729916_   5774 ATCACTGGCCAT 5785
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2761 27.57 1.67 1.34  chr20_12739116_12742900     2398  3293 (492)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr20_12739116_   2398 ATCCTATGTTAATGGATTGTAAGAATTAACATTGCCAAAATAACCATACT 2447
                             i     v        v    v    i    ii  i  ii v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr20_12739116_   2448 GCCCAAAGCAATTTACAGATTCAGTGCAATCCTTATCAAAACACCAG-TG 2496
                         v      vii  i          ii       i        iv    -  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr20_12739116_   2497 TCATTTATCACAGAAATAGAAAAAACAATCCGAAAATTCATATGGAACCA 2546
                         i v   - ii       v  v  ivii    v               vii
  L1M4_orf2#LINE/    110 CCTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr20_12739116_   2547 AAAACAATTCA-AGCAGCCAAAGCAACCTTAAGTAAAAAGAACAAAGCTA 2595
                         v  ivi ii  - ii       i   i   i iv  i          i i
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr20_12739116_   2596 GAGACATCAGACCACCCAACTTCAAAATATCTTATAAAGCTATAGTAACC 2645
                            ivv   v  iv     i       iv vi  i       i     i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr20_12739116_   2646 AAAACAGCATGGTATTGATATAAAAACACACATCTAAACCAGAGGAATAC 2695
                           i    ii     i  ii    ii i v    v  i i  iv      v
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr20_12739116_   2696 AATAGAGAACCCAGAAATAAATTCACATATTTATAGCCAACTGATTTTTG 2745
                            v    ii           ii  i i      i i   i       i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr20_12739116_   2746 AGTAAGGTACCAAGATCATACATTGGAAAAAGAACACCCTCTCTAATAAA 2795
                          vv i   i      i   v  v   ii      i vi  i ii  i   
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr20_12739116_   2796 TGGTACTGGAAAAACTGGATATCCATACACAGAAGAATGAAACTAGATCC 2845
                             i    i v         ?   i ii  i         ii i  i  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr20_12739116_   2846 CTATTTCTCAGTGTAT-TAAAAATGTCCACTCAAAATTAATTAAAGACTT 2894
                            ii  v  vii   -i      --iv         vi  i ?    i 
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAAT--TAACTCAAAATGGATCAWAGACCT 506

  chr20_12739116_   2895 AAGTGCAAGACCCAAAATTATAAAGCTACTAGAAGGAAACATAGAAGAAA 2944
                           i  i    v i    i      i  vi      i        i? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_12739116_   2945 CACAGCAGAACATTGGTCTAGGCAAAGATTTTATGGCTAAGACCTCAAAA 2994
                         vv vv ivi  v    vi       v i   iv i v  v   vi     
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr20_12739116_   2995 GCATGGACAACAAAAACAAAAGTAGACAAATGGGACTATATTAAACTAAA 3044
                            iiii        iv    i    i    v     vi  i   v v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr20_12739116_   3045 AAGTTTCAACACCACAAAGGAAACAATTG-GTAAG-GAAAA--CA-CCTG 3089
                           ii  iviii iv       v  v  ii- v   -     --  -  ii
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr20_12739116_   3090 TTGAATGGGAGAAAATATTTGCAAACAATTAAACCCACAAGGCAGTAACA 3139
                         iv                       iv  vv v iv i    v v vii 
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTA 756

  chr20_12739116_   3140 TTCAGGATATA-AAAGCAACTC--A-AACTCAATAGAAAAGCAATGAAAT 3185
                          i   i     -    -     -- -         iv   ivi i-    
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAG-AACTCTTACAACTCAATAATAAAAAGAC-AAAT 804

  chr20_12739116_   3186 ATTCTCATTAAAGAGTTAAGAAAAGTATCTAAATAAAAAATTTCACTAAA 3235
                          vi iv   ?  i i -ii v    v  i i    i v -    v i   
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAAT-GGGCAAAGGATTTGAATAGACA-TTTCTCCAAA 852

  chr20_12739116_   3236 ACAGACATATAAATGACCAACAGGTGTATTTTTTAAAAAG---CTCAACA 3282
                         iv   i   i     i    i i iii  -----i     ---       
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACAT-----GAAAAGATGCTCAACA 897

  chr20_12739116_   3283 TTATCTTTTGC 3293
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.04 (163 / 80)
Gap_init rate = 0.02 (18 / 899), avg. gap size = 1.50 (27 / 18)  


2950 26.41 1.10 0.77  chr20_12871141_12873608     1072  1976 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_12871141_   1072 TGGAAAAACATCCCATGCTTATGTATGGGCAGAATCAATATTGAGAAAAT 1121
                               i i        i i   v  v  v   v i       vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_12871141_   1122 GACCATACTGGC--AATGCAATCTACAAACTCAGTGCAATTCCCATCAAA 1169
                          i v     vv --   -ii       i i   ii     i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAAT-TGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_12871141_   1170 ATACCACCATCATTCCTCACAGAACTAGAAAAAACT-ATCCTAAATTTTA 1218
                           v   v vv v  ii ii     v v  v  i-  -        v  i 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr20_12871141_   1219 TATGGAAACAATAAAGAGCTCACA-TAGCCAAAGCAAGATTAAGTAAAAA 1267
                                 ii-i  i ii i  v -        i   vv  i iv  i  
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_12871141_   1268 GAACAAATCTGGAGGCATCACATTACCTGATATCAAACTATACTATAAGG 1317
                                vi      vv     i v  ii  v     viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_12871141_   1318 CCATAGTCACCAACATACCATGGTACTGATATAAAACTAGGCACATAGAC 1367
                          i i   v i   v i vii        ii    iiv   i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_12871141_   1368 CAATGGAACAGAATAGAGAACCCAGAATTAAACCCAAATACTTACAGCCA 1417
                                 i     v    ii      v        v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_12871141_   1418 ACTGATTTT-AACAAGGCAAACAAAGAC-ATAAAGTGGGGAAAGGACATC 1465
                          i       -i      -ivi v     -  vv i         i i vi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGG-GTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_12871141_   1466 CTATTCAACAAATGATGCTGGGATAATTGGCAAGCCACACGTAGGAGAAA 1515
                           v           i        i  i   vv ?     i i ii    v
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_12871141_   1516 GAAACTGGATCATCAGCTCTTGCCTTATACAAAAATCAACTCAAGATGGA 1565
                            ii    i vii v   vii  v           i       i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_12871141_   1566 TCAAGAACTTAAATCTAAGACCTGAAACTATAATAATTCT-AGCAGACAA 1614
                            ?ii  i     v     v  i         -  i   -  v   v  
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTTAGAAGAAAA 545

  chr20_12871141_   1615 TATCAAAAAAACTCTTCTAGACATTGGCTTAGTCAAGGATTTCATGACCA 1664
                         i  vii?iv  v     vv   v    v    v   v i    v iivi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_12871141_   1665 AGA-ACCAAAAACAAATGCAATATAAACAAAAATAAATAGCTGGAACTTA 1713
                         v  -       i  v v    i v  iv       i   iv v i    v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_12871141_   1714 ATTAAACTAAAGAGCTTTTGCACAGCCAAAGGTACAGTCAGCAGAGTGAA 1763
                           i   v v  i i      ii vv v  i ii  vi   iv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_12871141_   1764 CAGAAAACTGACAGAGTAGGA-AAAATATTCACAA-TCAATACATCTGAC 1811
                         v   v   iv     i i   -        ii   -   -  i      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA-TATATCTGAT 744

  chr20_12871141_   1812 AAAGGACTAATATCCAGAATCTAAAATGAACTCAAACAAATTGGCAAGAA 1861
                           i     vi          v  v  v      vv    v iiii  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_12871141_   1862 AAAAACAAACAATCCCATCAAAAAGTGGGCTAAGGATAGGGATAGATAAT 1911
                            i     i  i  v  i?    i     v      vv i     i v 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_12871141_   1912 TCTCAAAAGAAGATATTCAAATGGCCAACAAACATATGAAAAAAATGCTC 1961
                             v           v           i  i  i       i -     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCTC 893

  chr20_12871141_   1962 AACATCACTAATGAT 1976
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (138 / 97)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 1.06 (17 / 16)  


3158 22.74 2.44 6.16  chr20_13244159_13247393     1803  2743 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_13244159_   1803 GAGAGATACTCCATGTT-A------GGGAGGCTCAATTTTGTCAAGATGT 1845
                           i     ii       - ------  i  i  i   v    i      v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_13244159_   1846 CAGTTCTTCCCAACTTGATCTATAGATTCAAGGCAATCTTATTCAAAATC 1895
                           i v  i     v        i        v      iivv        
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_13244159_   1896 CCAACAAGTTATTTCATAGATATCAATAAATTGGTTCTAAAGTGTATAGG 1945
                            i vivi v   iii   v  ii i  ii  i i     i vi   v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_13244159_   1946 GAGAGATAAAAGACCCAGAATAGCCAACAAAATATTGAAGGAGAAGAACA 1995
                           i vii  ii                v v   v     ii         
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_13244159_   1996 AAGGTAAACGACTCATACTACCTGACTCTAAGACATAATATAAAGCTACA 2045
                            v ii v      i   v  ii i ii  i  v  v  i         
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_13244159_   2046 GTAATCAAGACAGTGTAGTACTGACAAAAGAATAGGCAAATAGATCAATG 2095
                                         i      i  v   i    i  v           
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr20_13244159_   2096 GAACAGACTAGAGAG-CCAGAGAATAGACCTACACCAATAGAGTCAGTTG 2144
                            i   v v     -     -    i   i i  vvv  vi    i   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGA-AATAAACCCATACATTTATGGTCAATTG 351

  chr20_13244159_   2145 ACCTTTGACAAGGGATGA-AAGACAACACAGTGGAGAAAGGA--GTTTCT 2191
                          ii  i        -  v-     v iv  i   i     i --  i i 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_13244159_   2192 TTAATAAGTGTTATTGGAAAAAGTGAGCATTCACATGCAAAACAAATGAA 2241
                          i  i  i  v ii   i v  v  iii ?i           -i      
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA-GAATGAA 449

  chr20_13244159_   2242 TCTAGTCACAGACTTTATACCCTTCACAAAAATTAACTCAAAATGAATCA 2291
                         vi i v v vv  i i i   v vi                    i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_13244159_   2292 TAGACCTAAATGTGAAACATAAGATTATCTAAAAGTCCTAGAAGATAACA 2341
                         ?            i i vv   i i   --    v  i       v    
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTAT--AAAACTCTTAGAAGAAAACA 547

  chr20_13244159_   2342 TAGGAGAAAATCTAGATGACCTTGTGTTAGGCAATGACTTTTTAGGTACA 2391
                             ? v      vvi        v           ii  i    i  ii
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_13244159_   2392 ATACCAAAGGCACTATCCGTGGAAAAAAAAGTGTTGGTAAGCTGGACTTC 2441
                          i      i    v v viiii  i     i i-- i   ii        
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTC 645

  chr20_13244159_   2442 ATTAAAATTAAACTTTTTTGTTCTGTGAAAGACACTGTCTGCA---TGAA 2488
                           i         vvi      v  vii  i      i  viv ---    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_13244159_   2489 AAAACAAGCCAAAGACTGGGAGAAAATATTTTCAAAAGACCTAACAGATA 2538
                           i    v   v   v               v    vv iv  v v    
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_13244159_   2539 AA-------TATCCA-AATATACAGAGAACCCT-AAAACTCAACAATAAG 2579
                          i-------      -      i i     i  - v       i     i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_13244159_   2580 AACACAAACAACCCGATTCTTTAAATGTTTCTGAGGACACTTGAAAAAAT 2629
                           v     i     i   --------------------------------
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATT-------------------------------- 813

  chr20_13244159_   2630 AAATAAATAAATAAATAAATAAAAATGAGCCAAAGACTCTAACAGACACT 2679
                         -------------------?       i  v  i  i iv  i     i 
  L1M4_orf2#LINE/    814 -------------------WAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_13244159_   2680 TCACCAAAGAAGATATACAGATGGCAAATAAGCATATAAAAAGATATTTC 2729
                           v                i     v        i  i       ii iv
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_13244159_   2730 ACATCATATGTCAT 2743
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (134 / 76)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 5.40 (81 / 15)  


3154 25.64 1.55 0.78  chr20_13303982_13310674.rev     5301  6201 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_13303982_   5301 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAAAATTGTGAAAAT 5350
                               i i  i     i        v      v i  v     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_13303982_   5351 GGTCATACTGCCCAAAGTAATTTATAGATTCTATGCTATCCCCATCAAGC 5400
                           iv     v      v i  i  i      v i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_13303982_   5401 TACCA-TTGACTTTATTCACAGAATTAGAAAAAAAACT-ATTTTAAATTT 5448
                          v   -i  v    -  ii     v v  v  i---  -  ii    v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTT-TTTGCAGAAATTGACAAG---CTGATCCTAAAATT 146

  chr20_13303982_   5449 CATATGGAACCAGAAAAAGAGCCCATA-TAGCCAAGACAATCATAAGCAA 5497
                                  -- viv  i ii    v -       i      v i iv  
  L1M4_orf2#LINE/    147 CATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_13303982_   5498 AAAGAACAAAGCTGGAGGCATCACGCTTCCTGACTTCAAACTATACTACA 5547
                         i          i      vv    i     ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_13303982_   5548 AGGCTACAGTAGCCAAAACAGCATGGTACTGGTACCAAAACAGATATATA 5597
                          i         ii   i    ii         i iv ii i   i     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_13303982_   5598 GACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAA 5647
                           i        i    iv   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_13303982_   5648 CCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 5697
                         i  vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_13303982_   5698 CCCTATTTAATAAATGGTGTTGGGAAAACTGGCTGGTCATATACAGAAAA 5747
                         vi  v  i  i        i     v      v i?i  i  i  i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_13303982_   5748 CTGAAACTGGACCCCTTCCTTACACCTTATA-AAAAATTAACTCAAGATG 5796
                         v    ii         v   i     v    -              i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_13303982_   5797 GATTATACACTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAGAAA 5846
                            i ? v  i    ii     v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_13303982_   5847 ACCTAGGCAATACTATTCAGGACACAGGCATGGGCAAAGAGTTCAT-GAT 5895
                           v    ?ivv v v   iv   viv  vv i     v iv   v -   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_13303982_   5896 GAAAACACCAAAAGCAAAGACAACAAAAGCCAAAATTGACAAATGGGATC 5945
                         - vi            v ii         vv     v  i    v   ii
  L1M4_orf2#LINE/    595 -ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_13303982_   5946 TAATTAAACTAAAGAGCTTTTGCGCAGCAAAATAAATGATCATCAGAGTG 5995
                          v  i   v v  i i      i  vv    iv v iv    vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_13303982_   5996 AACAGGCAACCTACAGAATGGGAGAAAATTTTTTCAATCTACCCATCTGA 6045
                           v  i     i                 v   v   vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_13303982_   6046 CAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAAA 6095
                         i  i  i  vi          v  i  i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_13303982_   6096 AAAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAC 6141
                             i    ----   v  i?    i    ii      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_13303982_   6142 TTCTTAAAAGAAGACATTTATGCAGCCAGCAA--ACATGAAAA-AT--TC 6186
                             iv        i  vi viii    ii  --         -  --  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_13303982_   6187 ATCATCACTAGTTAC 6201
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (132 / 95)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.62 (21 / 13)  


4160 18.37 4.20 1.25  chr20_13390862_13392907      673  1554 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_13390862_    673 TGGAAAGGCATCTTGTGTTTATGGAGTACAA---TTAATATTGTTAAGAT 719
                                ii   iii    i     v iv  ---                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_13390862_    720 GTCAATACTACCCAGAATGATCTACAGATTTAATGCCATCTCTATCAAAT 769
                          v       v    i v             i  i  v   i        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_13390862_    770 TCCCAGTGGCAATTTTGGCAGAAATAAAAACACCCATCCAAAAATTTACA 819
                               iv  vv    v        vi v vi iv    v      i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_13390862_    820 TGGAATCTCAGGAGACCCCAAATAACCAAAACTATCCTAAAAAAGAA--- 866
                              viv  i i     vi    i       v   i i        ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_13390862_    867 CAAAATTGGAGGCTTCACACTTCCTGATTTCAAAACTTAGTATGATGCCA 916
                             i       vi          ii             v  ii v  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_13390862_    917 CAGTAACCAAAAGAGTATGGTAATGGCATAAAGACAGACATATAGATCGA 966
                               i   i v   i     v        i  i             i 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_13390862_    967 TGGAATAGAATAGAGAGCCCAGAAATAAAC--ACTCATATGTGTTTAATG 1014
                                    v     i            -- iv   v i  v i   v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_13390862_   1015 ATTTTTCAAGACGGGTGTCAAGACCATTCGATGGGGAAAGGATAGTCTTT 1064
                         iv     i v v     i           i          i         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_13390862_   1065 TTCGATAA-TGATGCTAGGAAAAGTGGATATCCACATGCAAAGGAATTAA 1113
                          - i i  -  i    i   v  v      ?           i    v  
  L1M4_orf2#LINE/    401 T-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_13390862_   1114 GTTGGACCCTTGCTTTACAACATATGCAAAAATAAACTCATAATGAATCA 1163
                                  i i i i   v     i       v      v    i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_13390862_   1164 AAGATCTAAATGTAAGAGTAAAAACTATAAAACTCCTATAAGAAAACACA 1213
                         ?   i             iv               i  v         i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_13390862_   1214 GGGGGCAAGCTTCATGACATTGGATTTGGCAATGACTTTTTGTATATGAC 1263
                           ? vv  v    i    v    i  v       ii  i  iv       
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_13390862_   1264 ACCAAAAGCACAGGCAACAAATAAAAAAACAGGCAAATTAGATCACATCA 1313
                                     i        vi      i  ii     i  iiv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_13390862_   1314 AAATTAAAATTAAAAAGTTATTCTGTGCATCAAAGGACA----------- 1352
                                  vi---------  i     v          -----------
  L1M4_orf2#LINE/    650 AAATTAAAAAC---------TTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_13390862_   1353 -TGA--------TCTATGGAATAACAGAAAATATCTGTAAATCACATATC 1393
                         -   --------i i ii    iiv         i  i      i     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_13390862_   1394 TAATAAGAGGTTAATATCCAGAATATACAAAGAACTTTTACAACTCAATA 1443
                          i     i ii vi             i        i             
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_13390862_   1444 ACAAAT---CAAAGAACT-AATCAAAAAGTGGGCAAAGGACTTCA-TACA 1488
                          i   v---    v   i-   i?    i           i  v -  v 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_13390862_   1489 CATCTTCTCCAAAGA---TATACAAATGGCCAATAAGCACATGAAAAGAT 1535
                            -           ---                                
  L1M4_orf2#LINE/    841 CAT-TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_13390862_   1536 GCTTAATGTCACTAATTAA 1554
                            i  ii   ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.77 (101 / 57)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 3.69 (48 / 13)  


2604 24.23 2.29 4.04  chr20_13433073_13437899     3180  3922 (905)    L1M4_orf2#LINE/L1        9   738 (170)  

  chr20_13433073_   3180 TGTTCTGTGTTCACGGACTGAAAGA----ATACTGTCAAAACATCCATAC 3225
                          i i ii      i   i  i    ----   i   i  i iiv v    
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr20_13433073_   3226 TACCCAAAGTGATCCACAGATTGAATGTAATCCTTATCAAAATTTCAATG 3275
                          v      v     i       v  i i     i         ii  iiv
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr20_13433073_   3276 ATGTTTTTCACAGAAATAGAAAGAACAATGCTAAAATTCATACAGAACCA 3325
                         iiv     ii       v  v iivii  v            ii   vii
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr20_13433073_   3326 CAAAACACCCTAATTAGCTAATGCAATCTTGTGCAAGAAAAACAAGGGTG 3375
                            iiv    vi v    i  vi        viv     i     i v  
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr20_13433073_   3376 GAAGCATCATGTGTCCTAACTTCAAATTATATTACAAAGCTATAGTAACC 3425
                           i vv   iiiv   i  i      viv  i          i     i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr20_13433073_   3426 AAAATAGTGTGGCACTGGCATAAAAACAGAAACACAGATCAATGGAACAG 3475
                           i i       i          ii i   v i i            i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr20_13433073_   3476 AATAGAAAGCCTAGAAATAAACCCACACATACGCAGTCAACTAATCTTTG 3525
                            v  i  i i             i    viiii     i i  i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr20_13433073_   3526 ACAAAGGCAATAAAACACA--CAATGGAGAAGGGATGTTCTCTTCAA-AA 3572
                             i  iivi  i  -  --      i   i i  iv   i     -  
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr20_13433073_   3573 ATCGGGTTGAAAAAACTGAATATCTACGTGCAAAA-AATAAAATTGGATC 3621
                           v v i  ii v     i   ? i  i       -   i  i     i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr20_13433073_   3622 CTTAT-----ACCATACACAAAAACCAACTCAAAATAGATTAAAGATTTA 3666
                          i  i-----      i       ii          i   i ?   ii  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr20_13433073_   3667 AACATAATACCTAGACTCCTGGAAGAG-TAAAACTAAAGGAGTAAAACTC 3715
                           -----------------  v     -        ------        
  L1M4_orf2#LINE/    508 AA-----------------TGTAAGAGCTAAAACTA------TAAAACTC 534

  chr20_13433073_   3716 CTAGAAGAAAACATAGGGAAGAAGCTCCATGACAAATGTGTT-GGAAATG 3764
                         i                ?ivi  v  i i    vv-  v   -  v    
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT-TGGGTTAGGCAATG 583

  chr20_13433073_   3765 ATTTTTTTTTTTTGATATGACAACAAAAGCACAGGCAACAAAAGCAAAAA 3814
                         i   i  v-----         v          i          v     
  L1M4_orf2#LINE/    584 GTTTCTTA-----GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr20_13433073_   3815 TAAGCAAGTAGGACTACATCAAACTGAAAGGTTTCTGCACAGCAAAGGAG 3864
                           iii  i v     v       v v   iii  i  ii vv       v
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr20_13433073_   3865 ACAATCAACAAAATGAAAG--CAATCCATTGAATGGGAAAAAATATTTGC 3912
                           v     v   i     i--   i   iv        i           
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGC 728

  chr20_13433073_   3913 AAACTAAATA 3922
                            ii v   
  L1M4_orf2#LINE/    729 AAATCATATA 738

Transitions / transversions = 2.34 (124 / 53)
Gap_init rate = 0.02 (13 / 730), avg. gap size = 3.62 (47 / 13)  

 520 19.67 3.28 5.46  chr20_13433073_13437899     4153  4335 (492)    L1M4_orf2#LINE/L1      730   908 (0)  

  chr20_13433073_   4153 AATC-TGTAGCCAATAAGGGATTAAAATCCAAAATATATAAGGACCTC-- 4199
                             - i  v ii        i viv     i         i  v   --
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr20_13433073_   4200 ACTAGCAAAAAATAAAATAAACTAAAATAACTTTATTTTTTATAATGGAC 4249
                           v viv  v       - i  --       iiv   ?v-- v     i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAA-AGAC--AAATAACCCAATTWA--AAAATGGGC 824

  chr20_13433073_   4250 AAAGGACATGAATAGGACATTCTCCCAAAGA---TACACAAATAGCCAAT 4296
                               iv       -     iii       ---  i      i      
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAG-ACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr20_13433073_   4297 AGGTAGTTATATGAAAAGTTGTTCAACATCACTATCAGG 4335
                          i i ----i        v  i         ????????
  L1M4_orf2#LINE/    874 AAGCA----CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.04 (8 / 179), avg. gap size = 2.00 (16 / 8)  


1249 19.49 1.47 2.21  chr20_13490083_13494749     3012  3283 (1384)    L1M4_orf2#LINE/L1        1   270 (638)  

  chr20_13490083_   3012 TGAAAAGACA-CCCAGGTTCATGAATTGGAAGCTTTAATATTGTTAAGAT 3060
                           i     i -    v       i        vi                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_13490083_   3061 GTCAGTACTACTAAAAGCAATCTACAGATTCAGTGTAATCCCTAACAAAA 3110
                          v  i    v iv   vii             ii i        v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_13490083_   3111 TCCCAATAGTGTTTTTTTTTTTTTAAGAAATAGAAATATCAATCCTAAAA 3160
                              ii--  ii      vi----      v  v viiii         
  L1M4_orf2#LINE/    101 TCCCAGC--TGCCTTTTTTGC----AGAAATTGACAAGCTGATCCTAAAA 144

  chr20_13490083_   3161 TTCATGTACAATCTAAAGGGACCCTAAATAATCAAAACAATCTTGGAAAC 3210
                              i iv  vivv         vi    ii             i   v
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_13490083_   3211 AAAAAA-AAAGTTGGAAGTCTCAC--TTCCTAATTTCAAAACTTACTGCA 3257
                         i  i  -         i v     --    i                i  
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_13490083_   3258 AAGCTACAGCAATCAAAACAGTATGG 3283
                                  i      i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGG 270

Transitions / transversions = 1.94 (35 / 18)
Gap_init rate = 0.02 (5 / 270), avg. gap size = 2.00 (10 / 5)  

2173 20.61 10.14 0.34  chr20_13490083_13494749     3584  4175 (492)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr20_13490083_   3584 AAAAAAATATGGAAATGGCATAAAGGCCATTACACAGAAAAATGCAATAG 3633
                           i v i i   v v        i iivivi i i   vv    v     
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr20_13490083_   3634 ATTAAAGAGTTCAAAAATAAACTCTCACATATATGGTCAAC-GATTT--G 3680
                          v vi     i  i        i vi    v         i-     -- 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr20_13490083_   3681 ACGAGGGTACTAGCACCATTCAATAGGGAAACAACAGTCTT--CAACAAA 3728
                           i     i i iv          i      v  i      --       
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr20_13490083_   3729 CTGTGTTTGAAAGATTAGACAACCACATGCAAAGGAATGTAGTTAGACCC 3778
                         iv   i v i vi i i  i ?           i     v    i     
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr20_13490083_   3779 CCACTTTATACCATATAAAAAAATTAATTCAAAATGGATCAAAGACCTAA 3828
                          i  i i i        v         i             ?        
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr20_13490083_   3829 GTGTAAGAGCTAAAACTATAAATCTCTTAGAAAACAACATAGGGG-AAA- 3876
                         i                     v         i v        ? -   -
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr20_13490083_   3877 -------------GGTTGG---------------ATATAACACCAAAA-C 3897
                         -------------    i ---------------    i         - 
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr20_13490083_   3898 ACAGACAATAAAAGAAAAAAATAGATAAA---AATTT----AAAA---GA 3937
                            ii   i           -        ---i i  ----    ---i 
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAATTAAA 657

  chr20_13490083_   3938 CACAATGGAGT---GAAAGACACAATCAATGGAGTGAAAAGGCAACTCGT 3984
                         v  vv v v i---i  i     v     vii         i    i ii
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr20_13490083_   3985 GGAATGGGATAAGATATTTGCAAGTCATAT--CGGATAAGTG-TTAACAT 4031
                         i        v  i          i      -- v      v -i vii  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr20_13490083_   4032 CCAGAACATATGAAGAATTCCTATATCTCAACAAGAAAAA--C------C 4073
                               i    i     i  i  i v     i  v     -- ------ 
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr20_13490083_   4074 CTGATTGAAAAATAGGCAAAGGACTAGGATATATATTTCTCTAAGAAAGA 4123
                          ii   ?      i         i v i   v i       i  ii    
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr20_13490083_   4124 TATAAAAATGGCCAATAAGCACATAAAAAGACACTTTAACAGCATAATCA 4173
                             v                   i      ii  i-    v  ??????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTC-AACATCAZZZZZZ 906

  chr20_13490083_   4174 TT 4175
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 2.11 (80 / 38)
Gap_init rate = 0.03 (17 / 650), avg. gap size = 3.65 (62 / 17)  


2525 11.87 3.43 27.51  chr20_13516237_13519000     1089  2284 (480)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_13516237_   1089 TGGAAA-ACATTCTATGTACGTGGACCAGAAGGCTTAATGTTGTTACAAT 1137
                               - i  i i    v i    iii    i      i      vi  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_13516237_   1138 GGCAATACTCCCCAAATCAATCTA---ATTCAAAATAATCCTTTATCAAA 1184
                                          ii     ---      vii     i -      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT-ATCAAA 99

  chr20_13516237_   1185 -TCCTAGCTACTTTTTTTGGCAGAAACTGACAGGCTGATCCTAAAATTCA 1233
                         -   i    i i       -      i     i                 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_13516237_   1234 TATGGAAATGCAAGAGACGCAGAATAACCAAAACAATCTTGAAAA----G 1279
                                       i   v       i                  ---- 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_13516237_   1280 AACAGAACTGAAGGACTCATACTT----------------ACTACAAAAC 1313
                             i ii  i        i    ----------------        i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_13516237_   1314 TACAGTAATCAAGACAGTGTAATATAGACATATAGCTAAGGATAGATATA 1363
                                             ii  iv i    ------        i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATA------AGGATAGACATA 292

  chr20_13516237_   1364 TAAATTGATATAATAGAAATGAGAATCCAGAAATAATACACCCTTATAAT 1413
                           i  ii  iv       v     i           ---    v  i --
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA---ACCCATACA-- 337

  chr20_13516237_   1414 CAATTCAACAAGGTTGCCACAACAATTCAATAAAGAAGGTATAGTCTTTC 1463
                         -------------------------  ------------   i   ----
  L1M4_orf2#LINE/    338 -------------------------TT------------TATGGTC---- 346

  chr20_13516237_   1464 GTGGGTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTGCGCAG 1513
                         --------------------------------------------------
  L1M4_orf2#LINE/    347 -------------------------------------------------- 346

  chr20_13516237_   1514 GCTGGAGTGCAGTGGTGTGATCTCGGCTCACTGCGAGCTCTGCCTCCTGG 1563
                         --------------------------------------------------
  L1M4_orf2#LINE/    347 -------------------------------------------------- 346

  chr20_13516237_   1564 GTTCACGCCATTCTCCTGCCTCAGCCTCTTGAGTAGGTGGGACTACAGCC 1613
                         --------------------------------------------------
  L1M4_orf2#LINE/    347 -------------------------------------------------- 346

  chr20_13516237_   1614 ACCCACTACCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAGACAGGGT 1663
                         --------------------    ---- -     i------    i  -
  L1M4_orf2#LINE/    347 --------------------AATT----G-ATTTTC------GACAAGG- 364

  chr20_13516237_   1664 TTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCAC 1713
                         -------   ----   i  --------------------------   i
  L1M4_orf2#LINE/    365 -------GTG----CCAAGA--------------------------CCAT 377

  chr20_13516237_   1714 CCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCGCC 1763
                         -----   ---------------------------   i ----------
  L1M4_orf2#LINE/    378 -----TCA---------------------------ATGGG---------- 385

  chr20_13516237_   1764 TGGCCAGAAGGTATAGTCTTTTCAATAAATGGTACTGGGACAATTAGATA 1813
                         ------   i v             i       i         i i    
  L1M4_orf2#LINE/    386 ------GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr20_13516237_   1814 GCCACATGTAAGAAAATGAAGTTGGACCCCTATCTCACACCATGTATAAA 1863
                         ?       i  i i                  i          i  i   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr20_13516237_   1864 AATTAACTCAAAGTGGACCAAAGCCCTGTATGTAAGAGCTAAAACTACCT 1913
                                     i    i  ?  v   iv                  ivv
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr20_13516237_   1914 AACTCTTCAAAGAAAACATAACAACAAATGTTCATAACCTTGGATAACAA 1963
                                vi           iv?ii    v   i i       i v viv
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr20_13516237_   1964 AATAGTTTC--AGATTTGACACCAAAAATACAACCAA----AGAAAAAAC 2007
                            i     --    v           ii    v   ----        -
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA- 628

  chr20_13516237_   2008 TAGGTAAATAGGACTTCATCAAAATTTAAAACTTTTAT--TTCAAAGGAC 2055
                            i     v                v         i --          
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC 678

  chr20_13516237_   2056 ACCATAAAGAAAATAGGGGGAAAAAAAC--ACAAAATGGAAGAAAAAATT 2103
                           i  v      i --- ii  i v   --   i     i      v   
  L1M4_orf2#LINE/    679 ACTATCAAGAAAGT---GAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr20_13516237_   2104 T-CAAGCCATGTATCTAATAAGGGATTTATATCCAGAATATATATTTAAA 2152
                          -   ii   i     i        i  i               ----  
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA----AA 771

  chr20_13516237_   2153 AAAATTCTACAGCTCTAAAACAAAAAGA----TGACACAATTTAAAAATG 2198
                         i  v ii    i   v v  i       ---- i  v     ?       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr20_13516237_   2199 GGAAAAGAATATGAATTAACATTTCTCCAAATAAGATATATAAATCAACA 2248
                           v    i  v     vi             v        i    viv  
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr20_13516237_   2249 GCAAGCACATGAAAAGATGTTCA-TGCCATTGTACTC 2284
                         ii                 i   -iii  ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.83 (102 / 36)
Gap_init rate = 0.03 (31 / 908), avg. gap size = 11.94 (370 / 31)  


3187 27.49 1.00 0.33  chr20_13521387_13528086     5307  6208 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_13521387_   5307 TGGAAGAACAGTCCATGCTCATGGGTAGGAAGAATCAATGTCATGAAAAT 5356
                              ii i vi     i      i v      v i   i ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_13521387_   5357 GGCCATAGTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5406
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_13521387_   5407 TACCAATGACTTTCTTTACAGAATTGGAAAAACT-ACTTTAAAGTTCATA 5455
                          v   iivi i  i   i     v v  v  i  - iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_13521387_   5456 TGGAACCAAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAAGA 5505
                              viiv  ii-  v  v v  v     i      i i iv  i    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_13521387_   5506 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 5555
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_13521387_   5556 ACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGATATATAGACCA 5605
                                i   i    ii i       i iv ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_13521387_   5606 ATGGAACAGAACAGAGGCCTCAGAAATAACACTACACATCTACAACCATC 5655
                               i    iv   ivii         vv i i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_13521387_   5656 TGATCTTTGACAAAACTGACAAAAACAAGAAATGGGGAAATGATTCCCTA 5705
                             i  i     iiv  v   i v  vvv          vi  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_13521387_   5706 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCTTATGTAGAAAGCTGAA 5755
                           i  i              v      v  ?  vi   i i  iiv    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_13521387_   5756 ACTGGATCCCTTCCTTACACCTTATATAAAAATTAATTCAAGATGGATTA 5805
                         ii    i    v   i     v    i         i    i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_13521387_   5806 AAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5855
                         ?    i       v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_13521387_   5856 GGCA-ATACCATTCAGGACACAGGCAGGGGCAAAGACTTCATAACTAAAA 5904
                           ?i- v i -   iv   viv  vvvi     v ii   v  iv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_13521387_   5905 CACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAATT 5954
                                    vvi          vv        i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_13521387_   5955 AAACTAAAGAGCTTCTGCACAGCAAAAAGAAACTACCATCAGAGTGAACA 6004
                            v v  i i   i  ii vv    i-  v    i  vv i      v 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAG-GACACTATCAAGAAAGTGAAAA 697

  chr20_13521387_   6005 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAA 6054
                          i     i                 v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_13521387_   6055 GGGCTAATATCCAGAATCTGCAAAGAACTTAAATAAATTTACAAGAAAAA 6104
                           i  vi          v ii        ivv i  v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_13521387_   6105 -------AACCCCATCAAAAAGTAGGCAAAGGATATGAACAGACACTTCT 6147
                         -------     v  i?    i i          v    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_13521387_   6148 CAATAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 6197
                          v v      i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_13521387_   6198 TCACTGCTCAT 6208
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.57 (149 / 95)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


 668 29.88 9.84 2.64  chr20_13669576_13671144      501  1069 (500)    L1M4_orf2#LINE/L1      264   873 (35)  

  chr20_13669576_    501 AGTGTGGTACTGGTCTAGGGATAGGCAGACGAACTGACC-AGTAAAACAC 549
                                      iv  i      i  v iii iii iv- i  i  ivv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr20_13669576_    550 AGAGCCAAGCAACAAACCCA--CAGTTCTG---AA---ACTCTGGTACAT 591
                             i v  v  i       --  v  v  ---  --- i i v -   -
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG-ACA- 361

  chr20_13669576_    592 GAGAGGTGACATGTCACATT-ACTAGAGGAAAGGAGAGATTATTCAACAA 640
                         -  -    v  v v -    - v i -      i v  vi v        
  L1M4_orf2#LINE/    362 -AG-GGTGCCAAGAC-CATTCAATGG-GGAAAGAATAGTCTTTTCAACAA 407

  chr20_13669576_    641 ATGGAACAAGATAAAAAAGATTTTCTATATGGCACAAGA-TAAAATCAGG 689
                             vi vi ivv  vvi   v?i - i   -  v    - i  i ii i
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCC-ACATG-CAAAAGAATGAAGTTGGA 455

  chr20_13669576_    690 TCCCTACCTCATAT----TAAAAAAAACAACTCAAG----------GACT 725
                         i          i i----  v     vi       i----------   i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr20_13669576_    726 TAAATGT-----CCCAAACCTTACATCTTTTAGTAAAAAATCAAAGGGAA 770
                                ----- iv    iv  v v  i    v i    -  v   ?iv
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CATAGGNGT 554

  chr20_13669576_    771 CATTCTTC-TCATCT--GGACAAAAAAGAGTTTCTTAGATAAAACAGCAA 817
                         v v     - v i  --  vi iiv  vi            vi   v   
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr20_13669576_    818 A--TATTAACTATAAAAGA---------TAAATCTGACAATATTAAAATC 856
                          --i iv i v i      ---------     iv   vvi  i     i
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr20_13669576_    857 AAGTATTCTTGTTCATTAGATGACAG----AAGAAAGTGGGAGAAGAGAG 902
                           iv i i    v v i i v    v----         ----  i   v
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG----AAAAGAC 700

  chr20_13669576_    903 GAATTACAAATT---AGAAGATATTAGCTG-TCTTATACAAGACAAAGGA 948
                         i vii   i v ---    i     v  vi-  v    ivv  i  i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_13669576_    949 TCAGTATC-AGAAGTAAATAAAGAGCTGCTAAAAGCCAACAGGAAAAGCA 997
                         iiv     -    -  v       i  vi  v  vi   i iv    iv 
  L1M4_orf2#LINE/    751 CTTGTATCCAGAA-TATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_13669576_    998 CAAACAGTACAACAGAAAAATGGCCAAAAAACATCTATTAG-TATTTC-A 1045
                             i iiv   iv?        v    ii i- iv v   -i     -v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGAT-TTGAATAGACATTTCTC 848

  chr20_13669576_   1046 CAGAGAAGGAA-ACACATGTTCAAT 1069
                           i     iv -   v   vi    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAAT 873

Transitions / transversions = 1.20 (91 / 76)
Gap_init rate = 0.05 (31 / 610), avg. gap size = 2.29 (71 / 31)  


3997 20.36 1.69 0.90  chr20_13821477_13826810     3954  4842 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr20_13821477_   3954 CTGTGTTGATGGATTGTGAGACTTAAGATTGTTAAAATCCTCATACTACT 4003
                          ii    v        vi        v        i  vviv     v i
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr20_13821477_   4004 CAAAACAAT-TACAGATTTAATGCAATCCCTATTAAAATATCAA-TGTTA 4051
                             vii  -        i  i           i     vi  i-  ii-
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC- 111

  chr20_13821477_   4052 TTTTTTGCAGAAATAGAAAAACCCATCCTAAAATTTATACGGAATTGCAA 4101
                                       v  v  i iv           i   i    v     
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr20_13821477_   4102 AAGAACCATGCATAGCCAAAACAATCTTGAGAAAGAAAAACAAAATGGGA 4151
                         ii  v   - v                   i      i      i v   
  L1M4_orf2#LINE/    162 GGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr20_13821477_   4152 GGCCTCATATTTCCTGATCTCAAAACATTCTACAAACCTACAGTAGTCAA 4201
                           v    i i    ii  i       v v       v        i    
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr20_13821477_   4202 AATCGTGTAGTACTGGTATAAAGACAGACATTTAGACCAATGGAACAGAA 4251
                         i iv    i       i    i  i      v    i        i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr20_13821477_   4252 TGCATAAAA---CACAAACAAAACCTCACATACAAGGTCAAATGATCTTT 4298
                          --- i i ---  v   i   v  vi    vi v      v    i  i
  L1M4_orf2#LINE/    311 T---TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr20_13821477_   4299 GACAAGGATGACAAGGCTGCACAATGGGGAAAGGATAGTCTCTTCAACAA 4348
                                i  v    i iiiv            i       i        
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr20_13821477_   4349 ATGGGGCTGGGAAAACTGGATATCCACATGCAAAAGAATGTAGTTGGACC 4398
                             v       v         ?                 v         
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr20_13821477_   4399 CTTACTCTAGATCATATACAAAAGTTAGCTAAAAATGGA--ATAGACCAA 4446
                          i   iii v i           i   i  v        -- ?     v 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr20_13821477_   4447 AA-GTAAGTCCTGAAACTATAAAACTCCTCAAAGAAACTATAGAGGAAAA 4495
                           -     vv  i              i vi      vi    i? v   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr20_13821477_   4496 GCTTCATGACATTGGATTTGGCAGTGATTTCTTGGATATCACAACAAATG 4545
                         v    i    v    i  v    i  i      i     v   v    v 
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr20_13821477_   4546 TGCAGACAACCAAAGCAAAAATGGACAAGTGGGACTATACCAAACTTTAA 4595
                         ii  ii    v    v      i  i  i v     vi i    v  v  
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr20_13821477_   4596 AAAGTAGG------AAAGGAAACAATTGATACAGTAAAACAGCAATCTAT 4639
                           vv vv ------      v  v  ii v v   i   vii   i i i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr20_13821477_   4640 GGAAGTGGAGAAAATATTTGCAAACCATATATCTGTTAAGGGATTAACAT 4689
                         i   vv                  i          v       i vii  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr20_13821477_   4690 CCAGAATGTATAAA-AATTCTTACAACTCAATAACAAAAACCCCCAAGTA 4738
                                i      -  i                i     vv --  i  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC--AAATA 805

  chr20_13821477_   4739 CCCCAATTTTTAAAATGGGTAAAGAACTTGAATACATATTTCTCCAAAGA 4788
                         v       ?v-        i    i i       v i             
  L1M4_orf2#LINE/    806 ACCCAATTWA-AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr20_13821477_   4789 AGATATACAAATGGCCAACAGGTATATGAAAATGTGCTCAATATCAAGGT 4838
                                           i i i i       vi       i    ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr20_13821477_   4839 GCTC 4842
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.46 (105 / 72)
Gap_init rate = 0.01 (12 / 896), avg. gap size = 1.92 (23 / 12)  


 367 28.45 5.98 11.13  chr20_13899185_13901339.rev      476   960 (1195)    L1M4_orf2#LINE/L1       54   513 (395)  

  chr20_13899185_    476 AACATTTCC--AATCAAT-TGTAAATT-AAC--AATTCCAGTCAAAATAT 519
                           i i i  --   ii  - ii i   -   --   i  vi       vi
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_13899185_    520 CAACAGA--TTTCTAAATGAATCTGACAAGCTTATTCTAAAATTTATCTA 567
                           i v v--   i iv vi   -         v  i        i  v i
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCATATG 152

  chr20_13899185_    568 GAAAAG-AAATTACGCCGGAATTCCCAAGATAAGTTTCACAAAGAGGAAC 616
                             v -  ivv  -  i    vv    i i  vi  v v     i    
  L1M4_orf2#LINE/    153 GAAATGCAAGGGAC-CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_13899185_    617 A----TAGAGGGCGTGTGTGTGTGTGTCCTCACACACACAGAGAAGTTCC 662
                          ---- i    i ----------------      -----------    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGAC----------------TCACAC-----------TTCC 224

  chr20_13899185_    663 TGCTCAACCAGATAGTAAAATATGCAATTATAAATATACAGTAATTAGAT 712
                         ----   ----- vvi    iv --- i  i   vv         i ---
  L1M4_orf2#LINE/    225 ----CAA-----TTTCAAAACTT---ACTACAAAGCTACAGTAATCA--- 259

  chr20_13899185_    713 ATACAGTAATTAGGGTATTGCCAGAAGAATAGAGGAGTAGATCAGGAAAA 762
                          v     i-- --    i  v  v   i     vivi       ivii  
  L1M4_orf2#LINE/    260 AGACAGTG--T--GGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr20_13899185_    763 CAGAACAGAGAGTTAAAAAATGGACCAGTGTATGAATAAGAATTTAGTAC 812
                         i    iv      iv i    ii   vi ii  vv  iivv v  ii vi
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr20_13899185_    813 CTGAAAGAAGGTTTTAAAA---TGTAATAGGAAAGAGATGGATTGT---- 855
                         ii  v - i   vii  i --- vi   i  i  iii  i vi v ----
  L1M4_orf2#LINE/    356 TCGACA-AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr20_13899185_    856 --AATGATTGCTAGTGACAAATTGTCCATTTATTTAGGACAAAATGG--- 900
                         --    i -   i -     -i  vvi ?ii iv ivi v i    i---
  L1M4_orf2#LINE/    405 CAAATGGT-GCTGG-GACAA-CTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_13899185_    901 TAGATCCC-ACTTCATACGA-ATCACAAAAATGA--TCCAGATGGATTAA 946
                          i  i   -  i   i  v -  -        v --  v i      i ?
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGATCAW 500

  chr20_13899185_    947 AAATGTAAATTGTA 960
                          i iv     -   
  L1M4_orf2#LINE/    501 AGACCTAAAT-GTA 513

Transitions / transversions = 1.72 (86 / 50)
Gap_init rate = 0.06 (29 / 460), avg. gap size = 2.86 (83 / 29)  

 429 26.07 11.01 6.29  chr20_13899185_13901339.rev     1226  1670 (485)    L1M4_orf2#LINE/L1      443   908 (0)  

  chr20_13899185_   1226 GGATGACAGAGTGAGACCCC-ATCTCA--------ACAAAA--CAAAACA 1264
                          i    ---   vi      - i    --------      --i  vv  
  L1M4_orf2#LINE/    443 GAATGA---AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr20_13899185_   1265 AAACAAAACAAAAG--TACATTGTAAAAAC-AAAACTATAAAAATAGTTT 1311
                            iii v  ? ii--  v  -    i i -            v --i  
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACT--CTT 536

  chr20_13899185_   1312 A-AGGAAATACATTAAAATATAGATTCAAATG--CTTGG--TAAGAAA-A 1355
                          - i    -    -- ii?i  i  iivvi  --     --  i v  -i
  L1M4_orf2#LINE/    537 AGAAGAAA-ACAT--AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr20_13899185_   1356 CCTTCTTGAACAAAACACAAACAAAAAGGTTATAAGTGA----GGAAGGA 1401
                         vi     ii i vi    ---     i---i i   ii ----i   ii 
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACAC---CAAAAG---CACAAGCAACAAAAGAAAAA 627

  chr20_13899185_   1402 ATGGATAATTTTCACTGCTTCAGGATTTAAGACCTCTATGGTGAAAAGGA 1451
                           i     v  vv   v v   ii   v  i  i i i  v vv      
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr20_13899185_   1452 TACAAT--AAACAGTTAAAAGGCTGAAA---ACAGACTGA-AGAATATAT 1495
                         i  v  -- i v   v     i ---  ---     v  i-    v    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGAC---AACCCACAGAATGGGAGAAAATAT 724

  chr20_13899185_   1496 TTACAACATACACACCATATCAAATAA--------CATCTAGAACATATA 1537
                           i   -  -  i ---    vi    --------i   i    i     
  L1M4_orf2#LINE/    725 TTGCAA-AT-CATA---TATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr20_13899185_   1538 AGGAATTCCTAAAGATTTTTTTTAAAAA-----AGAGCCTGATAGAAAAA 1582
                          i   i  i  v iv ivv vv      ----- v i  ii  v?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_13899185_   1583 TGGGCAAATGACCT-AACAGTCAGTTCCTTAGAGAGGAAATATAAATGCT 1631
                                 v  ii -  i  v  v   iii i   i  v   i     v-
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG- 868

  chr20_13899185_   1632 CCCAA-----ATGTGAAAAGATGGTTAACTGTACCAGTAATCAT 1670
                         -    ----- ii          v i   --- i  ????????
  L1M4_orf2#LINE/    869 -CCAATAAGCACATGAAAAGATGCTCAAC---ATCAZZZZZZZZ 908

Transitions / transversions = 1.82 (73 / 40)
Gap_init rate = 0.06 (30 / 466), avg. gap size = 2.57 (77 / 30)  


3285 18.17 11.46 0.73  chr20_13944329_13947709.rev     2070  2889 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_13944329_   2070 TAGAAAGACATCGCATGTTCATGGATTGGAACTCTAAATATTGTGAAGAT 2119
                          i      i   v                  vv  v        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_13944329_   2120 GACAACACTACCCAAAATGATCTACAGATTCAATATAATC------GGCA 2163
                          i   i   v      v                iii    ------iiv 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_13944329_   2164 TCCCAACAGTATTTTTTGTGGGGA--AAAAAA---ATCCTAAAATTCATT 2208
                              i v iv       ii ii --i v  i---              v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_13944329_   2209 TGGAATCTCAAGGGACACCAAACAGCTATG-CAATCTTCAAAAAGAA--- 2254
                              viv        v vi  i   i vi-       v        ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_13944329_   2255 -AAAGTTGGAAGACTCACACTTCCTGATTTCAAAACTTACTACAAAGCTA 2303
                         -         i             ii                        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_13944329_   2304 CATTAATCAAAATAATGTGGTTCTGG-ATTACAAGAGATTTACAAATCAA 2352
                           v       i i i      v    -  v vi v   iv  i i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_13944329_   2353 TAGAAT----------GTTT-----------------TTT----TCAAAT 2371
                          i    ----------  ii-----------------   ----    - 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA-T 349

  chr20_13944329_   2372 TGATTTTCAACACGAGTGCCAAGACCATTCAAATGTCTTGAAAAGACAAG 2421
                                 i   v i                 -  v--- i     vv  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAA-TGG---GGAAAGAATAG 395

  chr20_13944329_   2422 TCTTTTCAACAGCAAATACTGGAA-AACTGGGTATCAACATGCAAAAA-- 2468
                                    ivvii i    i -      i  ? v          i--
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_13944329_   2469 -------GGATCTTTAT-----ACCATATACAAAACTTAATACAAAATGG 2506
                         -------   i ii  i-----             v    iv        
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_13944329_   2507 ATCAAAGACC-AA--GCAAAAGCTAAATCAATGAGACCCTTAGAAGAAAA 2553
                             ?     -  -- i  i       v v  i i  i            
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_13944329_   2554 CA--AGAGAAAATTTATGAAACATTGGATTTAACAATGTCTTCTAGAATA 2601
                           --i ? v    i vi vi  v    i  vii     vi    vii   
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_13944329_   2602 T-ACACCAAAAGCA--ATCAACCAGAGAAAAAACAGATAAACTGGACTTC 2648
                          -            -- v    v i        i       i        
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_13944329_   2649 ATCAAAATTAAAAACTTTTCAA--TCAAAGGACACTATTAAGAGAGTGAA 2696
                                            vvi--              i    i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_13944329_   2697 AAGACGACCCACAAAGTGTGAGAAAACACCTGCAAATAATATATCTGATA 2746
                              i       i i  v       i ii       v            
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_13944329_   2747 AGGAATTAATATCCAGAACATACAAAGGAATTCCTACAAC---------- 2786
                            i i vi         i   i    -  i  i      ----------
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAG-AACTCTTACAACTCAATAATAA 794

  chr20_13944329_   2787 AAGGA-----AATCCAACTCAACAATGGACAAAGGATTTGAATAGATACT 2831
                           i  -----  i    i ?  v     i                 i i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_13944329_   2832 TCTCCAAAGAA---ATACACATGGCCAATAAGCATCTATAAAGATGCTCA 2878
                                    ---     v              iv iv           
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_13944329_   2879 ---TCAAAAGCACA 2889
                         ---   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (92 / 53)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 3.85 (100 / 26)  


3138 25.83 1.44 0.78  chr20_13951302_13958003.rev     5309  6210 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_13951302_   5309 TGGAAAAACATTCCACGCTCATGGATAGGAAGAATCAGTATCGTGAAAAT 5358
                               i i  i   i i        v      v i i   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_13951302_   5359 GGCCATACTACCCAAAGTAATTTATAGATTCAATACCATCCCCATCAAGC 5408
                            v     v      v i  i  i        ii v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_13951302_   5409 TACCA-CTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAATTTC 5455
                          v   -   v    i  -i     -   -- v  i  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_13951302_   5456 ATATGGAA-T-CAAAAAACAGCCCGCATAGCCAAGACAATCCTAAGCAAA 5503
                                 - -   iii  --  v v        i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_13951302_   5504 AAGAACAAAGCTGGAGGCATCATACTACCTGACTTCAAACTATACTAGAA 5553
                                   i      vv   i   v  ii i      viv     v  
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_13951302_   5554 GGCTACAGTAACCAAAACAGCATGATACTGGTGCTAAAACAGATATATAG 5603
                         i          i   i    ii  i      iiiv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_13951302_   5604 ACCAATAATACAGAACAGAGGGCTCAGAAATAATGCCACACATCTACAGC 5653
                          i    iiv i    iv   i ii         vv   i    i  ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_13951302_   5654 CATCTGATCTTTGACAAACCTGACTAAACAAG-CAATGGGGAAAGGATTC 5702
                           vi    i  i     ivv  v v i  v v-            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_13951302_   5703 CCTATTTAATAAACAGTGTTGGGAAAACTGGCAAGCCATATGCAGAAAAC 5752
                         i  v  i  i   ii   i     v      vv ?   i     i  i v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_13951302_   5753 TGAAACTGGACCCCTTCCTTACACCTTATACAGAAATTAACTCAAGATAG 5802
                             ii         v   i     v      i            i  i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_13951302_   5803 ATTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAATAAAA 5852
                           i ?    i           v       i      vi i     v    
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_13951302_   5853 CCTAGAAGAATACCATTCAGGACATAGGCATGGGCAAAGGCTTCATAACT 5902
                          v   i? v v i -   iv   v v  vv i     v  i   v  iv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_13951302_   5903 AAAACATAAAAAGCAATGGCAACAAAAGCCAAAATTGACAGATGGGATCT 5952
                          vi   iv       vvi          vv     v  i i  v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_13951302_   5953 AATTAAACTAAAGAACTTCTGCACAGTAAAAGCAACTATCATCAGAGTGA 6002
                         v  i   v v  i     i  ii vvi   i vv       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_13951302_   6003 ACAGACAACCTACAGAATGGGAAACAATTATTT-CAATCTATCCATCTGA 6051
                          v        i           i v   -    -   vii  vi      
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAAT-ATTTGCAAATCATATATCTGA 743

  chr20_13951302_   6052 CAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGA 6101
                         i  i  i  vi          v  i  i     ivv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_13951302_   6102 AAGAAACAA----CCCCATCAAAAA--GGGCGAAGGATATGAACAGACAC 6145
                           i i    ----   v  i?    --    i      v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_13951302_   6146 TTCTCCAAAGAAGACATTTATGCAGCCAACATACATATGAAAAAAAGCTC 6195
                                       i  vi viii     i vi  i       i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_13951302_   6196 ATCATCACTGGTCAC 6210
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.43 (20 / 14)  


3553 23.34 2.81 0.90  chr20_14036545_14040766     2840  3730 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_14036545_   2840 TGGAAAGATATTCCACATTCATGGATTGGAAGAATCAATAATGTTAAAAT 2889
                                    i   ii                v i    v      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_14036545_   2890 ATTCA-ACTACCCAAAGCAATCTATAGATTCAGTGCAGTCCCTATCAAAA 2938
                         iviv -   v      vii     i       ii   i            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_14036545_   2939 TACCAATGGCATTCTTCTTTACAGAAATAGAAAAATCAATCCTAAAATGT 2988
                          v   iiv  ---   i   i       v  v  iiii          vi
  L1M4_orf2#LINE/    101 TCCCAGCTGC---CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr20_14036545_   2989 ATATGGAACCACAAAAGACCCACAATAGCCAAAGCTATCCTGAACAACAG 3038
                                 vii   ii      v          i v   i    v  v i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_14036545_   3039 GAGCAAAAACTGGAAGAATCACTTTACCTGACTT--AAATTATACTGCAG 3086
                           i    i-i    i  v    vi v  ii i  --   i -    i  i
  L1M4_orf2#LINE/    198 GAACAAAG-TTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAA 245

  chr20_14036545_   3087 AGCTATAGTAACCAAAACAGCATGGTGCTGGCATAAAAACAGACACATAG 3136
                              i     i   i    ii    i         ii i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_14036545_   3137 ACTAATGGAACAGA-----GAGTCTGGAAACAAATCCATACACCTACAGT 3181
                          ii       i   -----     ii    i   i       ii  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_14036545_   3182 GAACTAATTTTCAACAAAGGTGCCAAGAACATACATTGGGGAAAAGACAA 3231
                         v  i i      i    i          v   v  v        ii i i
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_14036545_   3232 TCTCTTCAAAAATTGATGCTGGGAAAAACTGGATATCCATATGCAGAAGA 3281
                            i     v  v  i        v  -       ?   i     i    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGA 444

  chr20_14036545_   3282 ATGAAACTAAACCTATATCTCAT--CATATACAAAAGTCAAACCAAAATG 3329
                              ii ii   iv  i    i--           i i  vi       
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_14036545_   3330 GATTAAAGACTTAAAT-------CTGA--CTATGAAACTACTACAAGAAA 3370
                            i ?    i     -------  i --    i     vi  v      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_14036545_   3371 ACATTGGGGAAACTCTCCAGGATATTGGTCTGGGCAAAATTTTCCTGAGT 3420
                             v  ? v  v   i iv  iv    vi i     viv    i iii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_14036545_   3421 AATACTTCACAAGCATAGGCAACCAAAGCAAACATGGACAAATGGGATCA 3470
                          vv  vi  v     i i     v    v   v  i  i    v   iiv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_14036545_   3471 CATCAAG-TTAAAAAGCTTCTGCACAGTAAATGAAAC----AACAAAGTG 3515
                               i-       -   i  ii vvi   v  v  ----  v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_14036545_   3516 AAGAGACAGCCCACAGAATGGGTGAAGATATTTGCAAACTACCCATCTGA 3565
                           i     i             v   i           ii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_14036545_   3566 CAAGGAATTAATAACCAGAATATGTAAGGAGCTCAAACAACTTTATAGGA 3615
                         i    i i vi  v         i   i  i   vv      iv   iv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_14036545_   3616 AAAAAATATAATAATCCCATT-AAAAATGGGCCAAAGATGTGAATAGACA 3664
                             i i -     i  v   -          v  i   v          
  L1M4_orf2#LINE/    794 AAAAGACA-AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_14036545_   3665 TTTCTCAAAAGAGGACACACAAATGTCAAACAGGCATATGAAAAGGTGTT 3714
                               v     i  i i       v v  i i   i        i  i 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_14036545_   3715 CAGCATCACTGATCAT 3730
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (139 / 66)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.20 (33 / 15)  


2923 25.81 2.22 1.22  chr20_14111935_14114099.rev      775  1673 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_14111935_    775 TAGAAAAATATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 824
                          i    i    i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_14111935_    825 GGCCCTACTGCCCAAAGCAATTTGTAGATTCAATGCTATTCCTATTAAAC 874
                            vv    v      vii  i ii        i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_14111935_    875 TACCATGGACATTCTTCACAGAACTAGAAAAAAAACT-ATTTTAAAATTC 923
                          v   vvvi v  i  ii     v v  v  i---  -  ii        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr20_14111935_    924 ATATGGAACCAAAAAAAAAAACCA-AATAGCCTACGCAATCCTAAGCAAA 972
                                 -- viv  iii v   -       v vi     i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_14111935_    973 AAGAACAAAGCCGAGGGCATGACACTACCTGACTTCAAACTATACTACAG 1022
                                   ii ii  vv v     v  ii i      viv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_14111935_   1023 GGCTACAATAACCAAAACAGCATGGTACTGGCACAAAAACAGACACATTG 1072
                         i      i   i   i    ii           i  ii i     i  v 
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_14111935_   1073 ACCAATGCAACAGAATAGAGAAACCAGAAATAAGACCACACACCTACAGT 1122
                          i     v  i     v    iv          iv   i   ii  ii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_14111935_   1123 TACCTGATCTTCAACCC---TGACAAAAACAAGCAATGGGGAAAGAATTC 1169
                         i vi    i   i  vv---  v   i v  vv               vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_14111935_   1170 CCTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGAT 1219
                         i  v     i              i      v  ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_14111935_   1220 TGAAACTAGACCCCTTACTTACACCACATACAAAT-TCAACTCAAGATGG 1268
                             ii i       vv  i      i       v- i       i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_14111935_   1269 ATTAAAGACTTAAATGCAAAGCCCAAAACTACAAAACCCT-GGAAGAAAA 1317
                           i ?    i      i  iiv i       i     i  -i        
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_14111935_   1318 CATATGCAATACAAT--TCAGGACACAGGCACAAGCAAAGATTTC----- 1360
                             v ?i-  -   --  iv   viv  vvi i    v i    -----
  L1M4_orf2#LINE/    546 CATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_14111935_   1361 -ATGACG--AAGATGC-CAAATTGTAACAAAAGTAAAAATTGACAAATGA 1406
                         -     i--  i -  -   --- i        v      v  i    vi
  L1M4_orf2#LINE/    594 TATGACACCAAAA-GCACAA---GCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_14111935_   1407 GATCTAATTAAACTAAAGAACTCCTGCACAGCAAAGGAAACTATCAAAAA 1456
                           ii v  i   v v  i    ii  ii vv       v        i  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_14111935_   1457 AGTAAACAGACAACCTAGAGAATGAAAGAAAATTTTTGCAAACTATGCAT 1506
                            i  v        i v      ii       v        ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_14111935_   1507 CTGACAAAGGTCTAATATCCAGCATCTCTAAGGAACTTAAACAAATTTAC 1556
                             i  i  v  vi       v  v v   i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_14111935_   1557 AAGGAAAAAGTAAACAACCCCATTACAAAGAGGGCAAAGGAAATGAACAG 1606
                           vi    iii   i     v   ?v   iv          vv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr20_14111935_   1607 G-ACTTTTCAGAAGAAGACATATATGCAGCCAACAATCATATGAAAAAA- 1654
                         i- i  i  vi       i   i viii     i  v  i       i -
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_14111935_   1655 GCTCCACATCACTGATCAC 1673
                             v      ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (140 / 88)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 1.82 (31 / 17)  


3212 25.81 1.56 0.56  chr20_14143910_14145864.rev      565  1463 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_14143910_    565 TGGAAACACATCCCATGCTCATGGATGGGTGAAATCAATATTGTGAAAAT 614
                               v i        i        v  vii v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_14143910_    615 GACCATACTGCCAAAAGCAATCTACAAATTTAGTGCAATCCCCATCAAAA 664
                          i v     v  v   vii       i   i ii        i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_14143910_    665 TACCACCATCATTCTTCACAGAATTAAAAAAAACAATTCTAAAATTCTTA 714
                          v   v vv v  i  ii     v vi v  ivii  i         v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_14143910_    715 TGAAACCAAAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 764
                           i  viiv  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_14143910_    765 CAAATCTGAAGGCATCACACAACCTGATTTCAAACTATACTATAAGGCCA 814
                             vi  i   vv      vv  ii        viv     i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_14143910_    815 TAGTCACCAA-ACAGTGTGGTACTGGTACAAATGCAGGCACATAGACCAA 863
                         i   v i   -               i i  ivii  i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_14143910_    864 TGAAACAGAATAGAGAGCCCAGAAATAAACCCAAATACTTACAGCCAAGT 913
                           i  i     v     i               v i i   ii i   v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_14143910_    914 GATCTTCAAGAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTTT 963
                            i   i v  i vviv   i v   vv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_14143910_    964 TCAACAAATGGTGGTGGAATAATTGGCTAGCCACCTGTAGGAGAATGAAA 1013
                                      v   i i  i   v  ?    v  i ii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_14143910_   1014 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGAATTGA 1063
                         i    i  ii i   v    v           i       i   i  ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_14143910_   1064 GGACTTAAACCTAAGACCTGAAACTATTAACATTCT-AGAAAAGAACACT 1112
                         i   i    iv     v  i       -  v i   -    i i    iv
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAACATA 549

  chr20_14143910_   1113 GGAA-AAACCTGTCTAGACATTGGCTTA-----CGATTTCATGACCAAGA 1156
                           ?i-   i  -  vv   v    v   -----i i    v iivi v  
  L1M4_orf2#LINE/    550 GGNGTAAATCT-TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_14143910_   1157 ACCCAAAAGCAAATGCAATAAAAAAAAAGATAAATAGCTGGGACTTAATT 1206
                         vv         v v    i    i    i   i   iv v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_14143910_   1207 AAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAACAG 1256
                            v v  i i      ii vv    i iv  vi   iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_14143910_   1257 ACAACTCA--GGGTGGGAGAAAATCTTTACAGTCTATACATCTGACAAAG 1304
                              i  -- ii           v   i  ivii   i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_14143910_   1305 GACTGATATCCAGTCTAATATCCAATGAACTC----AAATCAGTAAGAAA 1350
                             vi       ---     vi  v      ----  v   i   v   
  L1M4_orf2#LINE/    749 GACTTGTATCCAG---AATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_14143910_   1351 AAAACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATT 1400
                           i     i  i  v  i?    i     v     iv          v  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_14143910_   1401 CTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAA 1450
                            v                       i  i  i       i        
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_14143910_   1451 CATCACTAATGAT 1463
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (138 / 90)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


2539 26.81 6.33 1.84  chr20_14166331_14169243     1553  2421 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_14166331_   1553 TGGAAAAACATTTCATACTCATGGATAGGAAGAATCAATATTGTTAACAT 1602
                               i i  ii   ii        v      v i           v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_14166331_   1603 GGCTGTACTGCCCAAAGCAATTTACAGATTCAATGCTATTAATATCAAGT 1652
                            vi    v      vii  i           i  v  ivv      iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_14166331_   1653 TACCAATGACATTCTTCAACGAATTAGAGAAACTG-TTTTAAAATTCATA 1701
                          v   iivi v  i  iivv   v v  v  i   - ii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_14166331_   1702 TGGAACAACAACAAAAAGCTTCAATAACCAAGGCAATCCTAAGCAAAAAG 1751
                              vvi   --iii v ivv    i    ii     i i iv  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAA--GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_14166331_   1752 AA--ATGCTGGAG-----ACATTTTCTACCTATCTTTAAACTATTCTACA 1794
                           -- v i     -----   i  i i ---  i iv     - v     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCA---ATTTCAAAACT-TACTACA 244

  chr20_14166331_   1795 AGGCTGGAGTAACTGAAACGGCATGATACTGTCACA------GACACACA 1838
                          i   iv     iii i  i ii  i     v  i ------    i i 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_14166331_   1839 GACAAATGGAGCAGAATAGAGAGACCTGAAATAATGCCATATACCTACAA 1888
                           iv      ii     v     v  v       vv     i ii  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_14166331_   1889 CCATCTGATCATCAAAAATGTTGACAAAAACAACCAATGGAGAAAGGA-- 1936
                         i  vi    iv  i v  v v  v   i v  vi      i     i --
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_14166331_   1937 --CTCATTCAATAAATGGTG------------GATATGCAC--------- 1963
                         --  i-     i        ------------    ?v   ---------
  L1M4_orf2#LINE/    395 GTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_14166331_   1964 --------TAGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGAT 2005
                         -------- i       v   i                 i       i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_14166331_   2006 GGATTAAAGTCTTAAATGTAAAACCTGAAACTATAAAAACCATGGAAGGT 2055
                             i ?  v i         i v  i           vi v i    iv
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_14166331_   2056 AATCTAGG---AAAT----ACCATTCTGGACACAGGCCCTAAAGATTTCA 2098
                           iv    ---    ----iiv iii   ii-i    ---  v i    v
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGC---AATGGTTTCT 589

  chr20_14166331_   2099 T-GACGTAGATGCCAAAAGCGGTTGCAATAAAAACAAAAATTGACAAATG 2147
                          -  ii -  ii        ivvv    i    iv      v  i    v
  L1M4_orf2#LINE/    590 TAGATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_14166331_   2148 GGACCTAATTAAACTAAAGAGCTTCTGCAGAGCAAAAGAAACTATTAGCA 2197
                             i v  i   v v  i i   i  iivvv    i  v     i iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr20_14166331_   2198 CAGTAAAGAGACTACCTACAGAATGGGAGAAAATATTTGTAAGCTGCACA 2247
                         v   i  i    v   i                      i  iiiii i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_14166331_   2248 TCTGACAAGGCTCTTATATCCGGAATCTATAAAGAACTTAAACAAATTAA 2297
                              i    vv   i     i    v           ivv    v i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_14166331_   2298 CAAGCAAATGAACCCCAAACAACTTCATGAAAAAGTGGGCAATGGACGTG 2347
                         i  vv   v  ----    i   iiv  v?    i       v   iv  
  L1M4_orf2#LINE/    789 TAATAAAAAGA----CAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr20_14166331_   2348 AATAAATACTTTTCTAAAGAAGACTTACATGTGGTTAAGAAGAACATGAA 2397
                             i i i  i  i        iv    vi   ii  v   v       
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr20_14166331_   2398 AAAATGCTCAACATCACGAATCAT 2421
                           i             ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (143 / 87)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.94 (71 / 18)  


2987 27.40 2.82 0.45  chr20_14198939_14205035     4719  5605 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_14198939_   4719 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAA-- 4766
                              ii i  i     i        v      v i     i  v  i--
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_14198939_   4767 GGTAAT---------------TTATAGATTCAATGCCATCCCCATCAAGC 4801
                           i   ---------------i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_14198939_   4802 TACCAATGACTTTCTTTACAGAA-TTGGAAAAAACT-ACTTTAAACTTCA 4849
                          v   iivi i  i   i     -   -- v  i  - iii    v    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_14198939_   4850 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAACG 4899
                                viiv  ii  v  v v  v     iv     i i ivv i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_14198939_   4900 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGC 4949
                                i      vv   ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_14198939_   4950 TACAGTAACCCAAACGGCATGGTACTGGTACCCAAACAGAGATATAGACC 4999
                                 i v i  i ii         i ivvii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_14198939_   5000 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGTCGCATATCTGCAAGT 5047
                                i    i--    i  --        vvi ii i  i iiiivi
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_14198939_   5048 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5097
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_14198939_   5098 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5147
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_14198939_   5148 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5197
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_14198939_   5198 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5247
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_14198939_   5248 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5297
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_14198939_   5298 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5347
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_14198939_   5348 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5397
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_14198939_   5398 AGACAGCCTACAGAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5447
                              i  i                 v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_14198939_   5448 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5497
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_14198939_   5498 AAACAA----CCCCATCAACAAGTGGGCGAAGGACATGAACAGACACTTC 5543
                          i    ----   v  i? v  i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_14198939_   5544 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5593
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_14198939_   5594 ATCACTGGCCAT 5605
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 3.62 (29 / 8)  


3277 24.58 2.46 1.01  chr20_14278655_14281351.rev     1310  2204 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_14278655_   1310 TGGAAAGATATTCCATGTTCATGGAGTGAAATAATCAATATTATTAAAAT 1359
                                    i             v  i  v v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_14278655_   1360 ATCCATACCACCCAGAGCAATCTACAGATTCAATGCAATCTCTATCAAAA 1409
                         iv v    iv    i vii              i      i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_14278655_   1410 CACCAATGACAATCTTCACAGAAATTTAAAA---------AAAATT-ATG 1449
                         iv   iivi vv i  ii        v v  ---------      -  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_14278655_   1450 TGGAACAACAACAACAAAAAAACCAGAATAGCCAAAGCCACCCTGAACAA 1499
                              ----- ii-   iii v              i v i i    v  
  L1M4_orf2#LINE/    151 TGGAA-----ATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_14278655_   1500 AAAGAAAAGTAGTTGAAGGAACCACATTACCTGACGTCAGATTGTACTAC 1549
                         i     v i-     i    vi    i v  ii iv   i viv      
  L1M4_orf2#LINE/    195 GAAGAACAA-AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr20_14278655_   1550 AGGGCTATAACAACCAAAACAGCATGGTACTGGCATAAAAACAGACACAT 1599
                          ii    i ii  i   i    ii              ii i     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr20_14278655_   1600 AGCTCAATGGAACAGAATAGAGAACCCAGAAAGAAATCCACACACCTACA 1649
                           v         i     v    ii       v   i   i   ii  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr20_14278655_   1650 GTGAACTCATTTTTGACAAAGGTGCCAAGAACACACCTTGGGGAAAAGAC 1699
                           v  i v     i     i          v  iv vv        ii i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_14278655_   1700 AGTCTCTTCAATAATTTGTCCTGGGAAAACTGAATATCCATATGCAAAAG 1749
                              i     i  v v  v      v     i   ?   i         
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_14278655_   1750 AATTAAACTTGATCCCTATCTCTCACCTTACACAAAAATCAAATCGAAAT 1799
                            v  ii v  i     i   v    v  i        i  v  i    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_14278655_   1800 GGATTGAAGATTGAAATCTGAGACCTCAAGCTAT----------GAGGAA 1839
                             ii?   iiv    v i   v  v  i    ----------  i   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_14278655_   1840 ACTCATAAGGGAAACTCTTCAGGACATAGGTCTGGGCAAAGATTTCTTGA 1889
                          v-    i ? v  v     iv   v v  vi i     v i      ii
  L1M4_orf2#LINE/    544 AA-CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr20_14278655_   1890 GTAATACCCCACAAGCACAGGCAACCAAAGCAAAAATGGGCAAATGGGAT 1939
                         i  vv  v   v       i     v    v      i ii    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr20_14278655_   1940 CACATCAAG-TTAAAAAGTTTCTGCACAGCAAAGGAAACAATCAACAAAG 1988
                         iv      i-       v   -  ii vv       v  v     v    
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_14278655_   1989 TGAAGAGACAACCCACAGAAAAGGAGAAAATATCTGTAAACTACCCATCT 2038
                             i               vi           i  i   ii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_14278655_   2039 GACAAGGGATTAATAACCAGAATATACAAGGAGCTCA-AGAACTCTATAG 2087
                           i      i vi  v          i  i  i   v- v     v   i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_14278655_   2088 GAAAAAAAATATTAATCCAATCAAAAAATGGACAAAATAGTTGAATAGAC 2137
                         v     i vv v   i     i?        i    iv v          
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_14278655_   2138 ATTTCTCAAAAGAAGACACACAAATAGCAAACAGGCATAGGAAAAAGTGA 2187
                                v        i i      i  v  i i   i v     ii  v
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_14278655_   2188 TTGACACCACTAATCAT 2204
                          ii   i  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (133 / 83)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.10 (31 / 10)  


3147 18.77 7.42 0.70  chr20_14308348_14310039.rev      487  1200 (492)    L1M4_orf2#LINE/L1      147   908 (0)  

  chr20_14308348_    487 CATA-GTAAATTCTAAAAGAGCCCTGAATAGGAAAAACAGTTTTGAAAAA 535
                             - v    v --  i ii   v      vv      i i        
  L1M4_orf2#LINE/    147 CATATGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_14308348_    536 GAA---CAAGGTTGGAGTACTCACACTTCCTGATTTCAATAGTCACTATA 582
                            ---   i       v            ii       v v i    i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_14308348_    583 AAGGTACAATAATTAAAGCAGTATAATGGAGGCATAAGGACAGACATATA 632
                            v    i    i  ii    i ii ivv          i         
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_14308348_    633 AGCAAATGAAACAGA-TTGAGAGTCTGGAAAATAAACCTACACATCTATG 681
                         iiiv    i  i   -         ii    -      i i    i    
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATG 343

  chr20_14308348_    682 GTCAATGGGATTTTGGCAAGGGTATGAAGAGACCAGTCAATAGAGAAAGA 731
                               v iv   i i       iiv    --   v     i i      
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGA--CCATTCAATGGGGAAAGA 391

  chr20_14308348_    732 ATAATCTCTTCCACCAGTGGCACTGGGACAACTAAATTTCCACAAGTAAA 781
                            i   i   v  v i   ii           ii  v?     v i   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_14308348_    782 AGAATTAAGTTGGACTCCCACTTCATACTA-ATA------TTAACTCCAA 824
                              v         i  i  i   i  i -   ------       v  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_14308348_    825 ATGGATCAACAACTTAAATATAAGACCTTAAACTACAAAACTCTTAGAAG 874
                                 ?vi  i     i     v  v      i              
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_14308348_    875 AAAACATAAGGGCAAATCTTCTTGATCTTGGATTTGGCAATTGAGTACCA 924
                                 i ? i        v   i     i  v      v vv vii 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_14308348_    925 GATAGGATAACAAAAGCACACACAA-AAAAGAAAAAATAGACAAGTTGGA 973
                             v  i v          vi   -               i  i     
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_14308348_    974 TATCATCAAAATTAAAAACTCT-GTGTACCGAAGGACACTCTCAAGAGAG 1022
                         iv                  i -   ivi i         v      i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_14308348_   1023 TGAAAAGACAACCTATTAAATGGGA-AAAATGTTTACAAATCATATATCA 1071
                                      i ivi       -     i   i             v
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_14308348_   1072 CATGAG-----TGT---TAAA---TATCCAGAACTCT------------- 1097
                         v  i  -----   ---i i ---   vv        -------------
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_14308348_   1098 --------------ACCCAACTAAAAAATGGGCAAAGGGCTTGAACACAC 1133
                         --------------      i ?               ii     i v  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_14308348_   1134 TTTTCTCCAAAGAAGACATACAAATAGCAAATAAGCACATGAAATGATGC 1183
                         v               i        i  v               v     
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_14308348_   1184 TCAATATCATTAATCAT 1200
                             i    ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (84 / 46)
Gap_init rate = 0.02 (15 / 762), avg. gap size = 3.87 (58 / 15)  


2362 26.32 3.90 1.39  chr20_14366815_14368536.rev      443  1236 (486)    L1M4_orf2#LINE/L1       95   908 (0)  

  chr20_14366815_    443 TCAATAACTCAG-TGTGGTTTTT--AGAAAATGAAAACTTAATAGGATAT 489
                             v v i   -  ivv     --     v   v  vi i  vvv v v
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr20_14366815_    490 TTTTTAAATGGGGAACCACAAAATACTATGAATAGCCAAAGCAATTCTGA 539
                           i----  iv    vii   iiv  ivv           i    ii   
  L1M4_orf2#LINE/    145 TTC----ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr20_14366815_    540 ----GAAAAATACGGTTAGAGGCATCACACTGCCCGATTT-AAAATTATA 584
                         ----   i  i vi   i    vv       v   i    -    i -  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TA 239

  chr20_14366815_    585 TTACAAAGCTACAGTAATCAAAACAGTATGGTACTAGCATAAAAAAAGAG 634
                         i                    i     i       i      ii v   v
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr20_14366815_    635 ACACAGA------GAACAGAGTAGAGAGCTCAAAAGTAAACCCGAACTTA 678
                          i i   ------   i   i v     ii  i  i       iv  v v
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr20_14366815_    679 CACAGTCAACAAATTTTTGACAAGATCACCAACTGGACG---CAAAGAGG 725
                         i ii     ivi     i      ivii    ---   v---   v i  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAA---GACCATTCAATGGGG 386

  chr20_14366815_    726 AAAAAATAGTCTCCTCAACAAATAGTGCTACAAAAACTTGATTTCCACAT 775
                            i        ii         i     ivi v    v   v?      
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr20_14366815_    776 GCGAAATAATAAAATTG-ACTCTTATCTTACATCATGTACAAAAATCAAA 824
                           i   v   i  i   -  i i  i  i   i   i         i  v
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr20_14366815_    825 TCAAAACAAATAAAAGACCTACACTTAAGACCTGAAACCGCAAAAGTCTT 874
                               iii  v ?       v iv     v  i    iii    v    
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr20_14366815_    875 AGGAGAAA---TACGGAAAAACCTCCTTGGCATTAGCCCTGACAATTATT 921
                           i     ---  v ?iv   i  i v  i v  i viiv i    vi  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_14366815_    922 TCTTGTGTATTATGCCAAAATT-CAGCCTACAAAATCAAAAATAAATAAA 970
                             ivi   v ii      vi-  iv v      vv       i     
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr20_14366815_    971 TGGGACTACATCAAACTTAAAAGCTTCTGCACAGCAAAGGAAAC----AA 1016
                          v     v       v      i   i  ii vv       v  ----  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr20_14366815_   1017 TAAAATAAAAAGACAACCTACAAATTATTTTTTAAAAC---TGTAAACCC 1063
                         v   i i           i   i --  vvvvv    i---  i   i v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGA--ATGGGAGAAAATATTTGCAAATCA 734

  chr20_14366815_   1064 TGCAACAGATAACGGGTTAATATCCATGACTTATAAAGAACTCATGACA- 1112
                          ii v v     v  ii vi      vi iv            - v   -
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC-TTACAA 783

  chr20_14366815_   1113 CTGAATAGCAAGAAAACATATAATCCAATTTTAAAATGGGCGAAGAACTT 1162
                           v    ii  i  i   v    i      ?v         i   i i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr20_14366815_   1163 GAATATGCATTTCTCCAAAGATGACATAAAAATGGCTAACTGGTACATGA 1212
                              vi              v  i   v       i  ivi i      
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr20_14366815_   1213 AAAGGTGCCCTA-ATCTTTAATCAT 1236
                             i   i v -   v????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (120 / 85)
Gap_init rate = 0.02 (18 / 814), avg. gap size = 2.33 (42 / 18)  


3212 26.54 0.77 0.77  chr20_14390431_14396821.rev     4992  5899 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_14390431_   4992 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATAGCGTGAAAAT 5041
                              ii i  i     i      i v      v i    vi  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_14390431_   5042 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5091
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_14390431_   5092 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5139
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_14390431_   5140 TATGGAAC--CAAAATACAGCCCGCATTGCCAAGTCAATCCTAAGCCAAA 5187
                                v--   iiv  --  v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_14390431_   5188 AGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAG 5237
                                  i      vv   ii  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_14390431_   5238 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 5287
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_14390431_   5288 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAA 5335
                         i        i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr20_14390431_   5336 CTATCTGATCTTTGACAAACCTAACAAAAACAAGAAATGGGGAAAGGATT 5385
                         ii vi    i  i     ivv iv   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_14390431_   5386 CCCTGTTTAACAACTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 5435
                         vi  v  i     v           v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_14390431_   5436 CTGAAACTGGATCCCTTCCTTACAACTTATACAAAAATTAATTCAAGATG 5485
                         v    ii    i    v   i   v v              i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_14390431_   5486 GATTAAAGACTTACATGTTAGATCTAAAATGATAAAAACCCTAGAAGAAA 5535
                            i ?    i  v    v   v      iv      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_14390431_   5536 AGCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5584
                          vv    ?i- v i -   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_14390431_   5585 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATC 5634
                           vi            vvi          vv     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_14390431_   5635 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5684
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_14390431_   5685 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTCAACTGA 5734
                           v  i     i                 v       vii ivi v    
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_14390431_   5735 CAAAGGGCTTATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5784
                         i  i  i   i          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_14390431_   5785 AAAAAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACAA 5834
                             i     i     v  i?    i    ii      v    i     v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_14390431_   5835 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5884
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_14390431_   5885 ATCATCACTGGTCAT 5899
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.39 (138 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.56 (14 / 9)  


3899 17.22 1.59 0.93  chr20_14485035_14486781      501  1255 (492)    L1M4_orf2#LINE/L1      149   908 (0)  

  chr20_14485035_    501 TATGGAAATGCAAGGGACCCAGGATAGTTTAAACAGTTTTGAAATGAAAG 550
                                               i    iiv     i i      vii   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_14485035_    551 AACCAAGTTTGAATACTTAGATTTTCTGATTTTAAAACT----GTAAAAC 596
                            v     v  iv   i v i  i ii    i      ----ii   i 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_14485035_    597 TATGGTAATGAAGACAACATGGGGCTGGCCTAAGGATAAACAGATAGATT 646
                           ii     v      iii   vi     v        i   v      i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_14485035_    647 GATGGAATAGAATTAAGAGTCCAGAAATAAAGCCTTCCATTGATGTCCAA 696
                         i             i                v  v v    v   vi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_14485035_    697 TTGATTTGCAACCAGAGTGCCAAGACAATTCAATGGGAGAAAGAATAGTG 746
                                v i  v  i          v          -           v
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGTC 397

  chr20_14485035_    747 TTTTTGACAAATGGTACTGGGTTAACTGGATATCCACATGCAAAAGAATG 796
                             ii         i     vi         ?                 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_14485035_    797 AAGTTAGATCCCTTCCTTACACCATATATAAAAATTAACTCCGAATGGAT 846
                              i  i    v   i          i            vi       
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_14485035_    847 CATAGATCTAAGTGGAAGAACTAAAGCTATAAAACTCTCAGAAGAAAGCA 896
                           ?   i    i  v    i     i            i        i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_14485035_    897 TAGGTGTAAA-ATTCATGACCTTG-----CGCAATGAATTCTTAGATATG 940
                             ?     -v   i        -----v      iv            
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_14485035_    941 ATACCAAAAGTACAAGCACTGACAACAAAAAGAAAGATACATACACTGGA 990
                          i        i       ------      ii   i   v   v i    
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCA------ACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_14485035_    991 CTTTATCTAAATTGAAA-CTTTTGTGTTTCAAATCACACCACAAAGAAAG 1039
                            i   v     i   -        i      vv    i iv       
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_14485035_   1040 T-AAAATACAGGTCACAAAATGGGAGAAAATATTTGTAAAGCATACATCT 1088
                          -    v   ivi    i                  i   v    i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_14485035_   1089 GATAAGAAACTTGTATCCAAAATACATAAAGTACTCATATACCTCATTAA 1138
                               ii           i    i      v    v  i v    v   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_14485035_   1139 TTAAAAGACAGATAACACAATTTTGGATTAGGCAAGGGTTCTGAATAGAT 1188
                          v        i     v     ?vii v i     i  v i        i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_14485035_   1189 ATTTCTCCATATAAGTTATTCAAATTGCTAATAAGCACATGAAAAGATGC 1238
                                  v v   v   v     v  i                     
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_14485035_   1239 TGAACATCATTAGCTCT 1255
                          v       ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (76 / 50)
Gap_init rate = 0.01 (7 / 760), avg. gap size = 2.71 (19 / 7)  


3416 18.70 2.27 1.27  chr20_14662818_14664523      501  1206 (500)    L1M4_orf2#LINE/L1      172   884 (24)  

  chr20_14662818_    501 ATAGCCAAAATGACTTTGATAAAGAAGGAGAAAGTTGGAGGGTTCACATT 550
                                   ii ii    v       i v           ii     i 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr20_14662818_    551 TCCCAATGTTAAAACATATTACAAAAATACAGTAGTCAAAACAGCTTGGT 600
                                v i     v  i      iv       i    i    iv    
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr20_14662818_    601 ACTGGCATGAATATAGGCATATAGACCAATGAAATAGAATTTATCATCCA 650
                                 i iv    i        i     i         v vvi    
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr20_14662818_    651 GAAATAAATCCATGCATCTATGGGCCACTGATTTTCAACAAGACTATCAA 700
                                 i    i   i     v v i        i     iv ii   
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAA 371

  chr20_14662818_    701 GACCATTGCATGGACAAAGAATAATATCTTCAACAAATAGTACTGGGATG 750
                                vv    iv        i v i          i  i      ii
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr20_14662818_    751 ACTGAATATTCATATGCAAAAGGATGACATTGAGCCCTTACCTCATACCA 800
                             i   ?i  i         i    vi   ii   i       i    
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr20_14662818_    801 TTTACAAAAATTAACTCATGATAGATTAATGATATAAATAT--GAGCTAA 848
                          v                vi  i   i ?v  iv     i --       
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr20_14662818_    849 AACTATAAAACCCTTAGAAAAAAA-ATAGGAGTAAGTCTTCATGACTTAG 897
                                    i       i    -     ?    i     i    i v 
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr20_14662818_    898 AGTT-GGTGATGGATTCTTACATATGACACCAA-----CAAGTAATAAAA 941
                         i   -  ii    v      v            -----    i  i    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr20_14662818_    942 GAAAAATATTAATAGATAAATTAGACGTTATTAAAACAAAAAAAGCCCTT 991
                               -----           i   v i  i    iv     ----   
  L1M4_orf2#LINE/    622 GAAAAA-----ATAGATAAATTGGACTTCATCAAAATTAAAAA----CTT 662

  chr20_14662818_    992 TTGTGCCTCAAACGACACTATGAAGAAAGTGAAAGGACAGCCCACTGAAT 1041
                               i     v        v            i    i     v    
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr20_14662818_   1042 GAGAGAAAATATTTGCCTGTCATAT--CTGATGAG-----TCTATCTAGA 1084
                          i              vvi      --     i  ----- v    i   
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr20_14662818_   1085 ATATATAAAGGACACTTACAACTAAACAACTGAAAGAGAAACAATGTAAG 1134
                                   i  v         v  i  ivi     v   i  ivi  v
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr20_14662818_   1135 TAAAAATTAGACAATGAACTTGAAAAGACATTTGTCTAAAGAAGGTATAC 1184
                          ?    v i i   v i i     v        v  i       i     
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr20_14662818_   1185 GAATGGCCAACAAGCACATGAA 1206
                         i         i           
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAA 884

Transitions / transversions = 1.98 (85 / 43)
Gap_init rate = 0.01 (8 / 713), avg. gap size = 3.12 (25 / 8)  


3115 27.57 1.56 0.22  chr20_14734845_14740985     4754  5649 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_14734845_   4754 TGGAAAAACATTTCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 4803
                               i i  ii    i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_14734845_   4804 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATGAAGC 4853
                            v     v      v i  i  i        i  v  i  i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_14734845_   4854 TACCATTGGCTTTCTTCACAGAATTAGAAAAACT-ACTTTAAATTTCATA 4902
                          v   viv  i  i  ii     v v  v  i  - iii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_14734845_   4903 TGGAAACAAAAAAGAGCCCATATAGCCAAGTCAATCCTAAGCAAAAAGAA 4952
                               iiv  ii  v  viv        iv     i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_14734845_   4953 CGAAGCTGGTGGCATCACATTACCTGACTTCAAAGTATACTACAAGGCTA 5002
                          i   i   v  vv     i v  ii i      iiv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_14734845_   5003 CCGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAA 5052
                          v    i   i    ii         i iv ii i   i       i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_14734845_   5053 TGAAACAGAACATAGGCCTCAGAAATAACACCACACATCTACAACCACCT 5102
                           i  i    ivv  ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_14734845_   5103 GATCTTTCACAAACCTCACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 5152
                            i  iv    ivv vv   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_14734845_   5153 TTAATAAATGGTGTTGGGAAAACTGGCTAGCTGTATGCAGAAAACTGAAA 5202
                          i  i        i     v      v  ? iii     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_14734845_   5203 CTGGACCCCTTCCTTACACCTTTTACAAAA-TCAACTCAAGATGGATTAA 5251
                         i         v   i     v v       - i       i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_14734845_   5252 AGATTTAAATGTAA--------ACCATAAAAAGCCCTAGAGGAAAACCTA 5293
                            ii         --------  i      v-i i    i      v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAAC-TCTTAGAAGAAAACATA 549

  chr20_14734845_   5294 GGCA-ATATCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAG 5342
                           ?i- v   -   iv   v v  vv i     v ii   v iiv  vii
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_14734845_   5343 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5392
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_14734845_   5393 GAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTATCAGAGTGACCAG 5442
                         i  v v  i i   i  ii vv    i  v     i vv i     vv  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_14734845_   5443 GCAACCTACAGAATAGGAGAAAAGTTTTGCAATCCATCCATCTGACAAAG 5492
                         i     i       i        vv       vi   vi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_14734845_   5493 GGCTAATATCCAGAGTCTACAAGGAACTTAAACAAATTTACAAGAAAAA- 5541
                          i  vi        i v  i  i     ivv    v iv i  v     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_14734845_   5542 --AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAATGGACACTTCTC 5589
                         --   i     v  i?    i            v     i    i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_14734845_   5590 AAAAGAAGACATTTGTGTGGCCAACGAGCATATGAAAAAAAGCTCATCAT 5639
                         v        i  viivi       ii    i       i v     v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_14734845_   5640 CACTGGTCAT 5649
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (145 / 98)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.29 (16 / 7)  


2994 25.93 2.21 1.28  chr20_14867022_14870421.rev     2041  2900 (500)    L1M4_orf2#LINE/L1        4   871 (37)  

  chr20_14867022_   2041 AAAAATAATTAATGCTCATGGATTGGAAGAATTAATATAGCTAAAATGAT 2090
                            i   viiv   i               v       v i   i   ii
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr20_14867022_   2091 AATATTATCCAAAGCAATTTTACAGATTCAATGCAATCCCTATCAAAATA 2140
                             i vi     vii  i -          i                 v
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCT-ACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_14867022_   2141 CCA--TGGCATTTTCACAGATATAGAAAAAGCAATCCTAAAATTGATATG 2188
                            --  v v    ii    v  v  v  ivii           v     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_14867022_   2189 GAACCACAAAACACCCCAAATAGCCAAAGTAATCCTGAGCAAAAAGAACA 2238
                            vii   iiv    vi          ii    i   iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_14867022_   2239 ATGCTGGAAGCATCACACTACCCAACTTTAAAATATACTGCAGAGCTATA 2288
                          v i    i vv       v     i  i    iv    i  i     i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_14867022_   2289 GTAACCAAATCAGCATGATGCTGGGACAAAAAGAGACACATAGTACAATG 2338
                             i   iv   ii  i i    v i  ii v     i    vv     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr20_14867022_   2339 GAACAGAATAGAAAGCCCAGATATGAATCTGCACATTTATAGCCAACTCA 2388
                            i     v  i  i     v  i  i iii        i i   i v 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_14867022_   2389 TTTTTGACAAAGCCACCAAGAACATACAATGAGGAAAGGA--GTCTCTTC 2436
                             i     i vii      v   v     i      i --    i   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr20_14867022_   2437 AATGAA-GGTGCTAGGAAAATTGGGTAACCATTTGTAGAAAAATGAAACT 2485
                           ii  -      i   v  i   i  ?   iv  i i  i      ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr20_14867022_   2486 AGATCCCTATCTCTCACCATATATAAAAATCAAATCAAA-TGGATTACAG 2534
                         i  i     i   v         i      i  v     -     i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr20_14867022_   2535 ACTTAAATATAAGACCTGAAACTATAAAAGTACTAGAAGAAAACTTTGGG 2584
                           i     i     v  i           v vi           v v  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr20_14867022_   2585 G-AGATGCTCCAGGCCA------AAGCAAAGACTTTTTGCATAAGATTTC 2627
                          - i  vi  vv i  v------ i    v ii  i  iv   v  ivi 
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr20_14867022_   2628 AAAAGCAGAGGCAGCAAAAGCAAAACTTGGTAAATGAGATTACGTCAAG- 2676
                                v i   i      v    v v i     vi  i v i    i-
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr20_14867022_   2677 CTAAAGA-TTCTGCACAGCAAAGGAAACAACCCCAAA---GAGAAGTTGG 2722
                         i    i -  i  ii vv       v  v i vvi  ---  i   vi--
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC-- 700

  chr20_14867022_   2723 AGTCCATAGCATGGGAGAAA-TATGTGCAGAGTATCCCTTTGACAAGGGA 2771
                          ii   i  v          -   v    i vi  viv i   i      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_14867022_   2772 TTGATAACCAGAGTATGTAAGAAGCTCAAACAACTCAATAGTAAAAAAAA 2821
                         i vi  v     i   i   ii i   vv           i      i v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_14867022_   2822 AAAAAAAAAAAAAATCTGATTTAACAATGAAAAAAATATCTGAATAGACA 2871
                            v  --------i ii   ?  v    iiv   iv  i          
  L1M4_orf2#LINE/    801 AAATAA--------CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_14867022_   2872 CTTCTCAAAAGAAGACACATAAATGGCCA 2900
                         i     v        i i i         
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCA 871

Transitions / transversions = 1.77 (140 / 79)
Gap_init rate = 0.01 (13 / 868), avg. gap size = 2.31 (30 / 13)  


2613 29.30 1.54 1.65  chr20_15288951_15291739.rev     1390  2297 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr20_15288951_   1390 GAAGAAGCATACTGTGCTCATAGATTAAAAGAATCGACATAATAAGGATA 1439
                          i i iii  v ii  i    i    ii    v ii i  vi v i   i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_15288951_   1440 TCAATTTCCTTCTAAATGACATAGAAGTTTAACACAATTCCAATAAAAAT 1489
                         v    vii ii v  v   iv  v ii  i   i    i  v  v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_15288951_   1490 TCTGGCAAGATTATTTGTAGCTACAGAAAACGTTATTCCAAAATTTCTAT 1539
                         i ii  vivv  v    i  vv iv  v  vv v  i i      iv   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr20_15288951_   1540 GA-----CAAAGGAACTAGAATAG-----ACAATGATGAAAGAGAAGAAT 1579
                          i-----   i   v i       -----     vv     i       i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_15288951_   1580 AAAGTGGGAAGAATCACTCTACTTGATTTTAAATCTTATTATATAGCAAC 1629
                              v   i  v    v  v iii    i   v    i  i v   v  
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr20_15288951_   1630 ATCAATCAAAACTCTGTGGTATTGACAGAGGGGCTGACACA-AGATCAAT 1678
                          vi      i  vv       i  i  v i  iiv    i -        
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_15288951_   1679 ACATCGTAATAGTGAACCCAAAAGTAGATCCATACATGTATGGCCAACCG 1728
                         iv viiv   v v  ii   i  i  i i        v     i   ii 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_15288951_   1729 ATTTCTTGACAGAAGTACAAAAGCAATTCAATAGAGTAAGGATAACCTTT 1778
                             - i    iii  i v  ii v       i i v   i   ii    
  L1M4_orf2#LINE/    352 ATTT-TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_15288951_   1779 TCAACAAATGTTGCTATAGCAGTTGGCTATCCATAGATAAAGTAAATAAA 1828
                                   v    ivii  ii   v  ?   i -- --- i   vi  
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACA--T---GCAAAAGAA 445

  chr20_15288951_   1829 TAAATCATCTCAACCTCAACTTCACATCCTATACAAAAGTGAACTCAAA- 1877
                          i  --i - vi   i v  i     i v         i v        -
  L1M4_orf2#LINE/    446 TGAA--GT-TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_15288951_   1878 TAGATTGTAGATTTAAGTATAAAATATAAAACTATGAAATTTTTAGTAGA 1927
                          i   ii?   ii   i i   i vv         i   i i    v   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_15288951_   1928 AAATGTAGAAGAAAAGTATCAAGGTATAGAGCTTGTGAAAAGTT-CTTAG 1976
                            ii   i? v   viv  iv iiv v i i v vv  vi   -     
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr20_15288951_   1977 ACATGACAGCAAAAGCATGATCTGTAAAAGAAAAAAATCTATAAATTAAA 2026
                          i      v        ii v vii           - vv       ii 
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGA 641

  chr20_15288951_   2027 CTTTATCAAAATGTAAAATTTTTGCTCTGTGAAAGACCCTATTAAAAGA- 2075
                            i        vv    i     iv  vii  i   v    i  i i -
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_15288951_   2076 TGAGGAGAAAACACACAGACTGAGAGAAAATATTTGCAAACCATATATAT 2125
                            ii   v   v      v  i                 i       v 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_15288951_   2126 GACAAAGGTCCGATATCTAGTATCCAAAAAGAACTCTTGAAACTCAACAG 2175
                           i  i  v ivi    i  v  vi v           iv       i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_15288951_   2176 TAAAAATACAAATGGTCCAACTAGAAAATGGGCAAAGGACATAAAGAGAT 2225
                               v      iii    i ?i               iv i  v   i
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_15288951_   2226 ATCTCACTGAAGAGTATATTTGGATGGTAAATTAAACACACGAAAAAAAA 2275
                           i  v ii    iv    viii    iv   -  i    i     i --
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAAT-AAGCACATGAAAAGA-- 888

  chr20_15288951_   2276 ACTGTGCAACATCACTAGTTAT 2297
                         --  iv        ????????
  L1M4_orf2#LINE/    889 --TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (165 / 97)
Gap_init rate = 0.02 (14 / 907), avg. gap size = 2.07 (29 / 14)  


3107 23.53 3.44 2.66  chr20_15410964_15413273.rev      918  1818 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_15410964_    918 TGAAGAGATAGTCTATGTGCATGGATAGAAATACTCAATATTGTCAAGAT 967
                           i i     vi i    v       v i  v   i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_15410964_    968 GTCAGTTCTTCCCAACTTTTCAGTTGGAAAGAAGAATCTATATTTTCAAT 1017
                          v  i v  i     v  ----------------i     i vv     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATT----------------GATCTACAGATTCAAC 84

  chr20_15410964_   1018 GCAATCCCAACCCAGATTCCAGCAAGTTATTTTGTGGATATAAACAAACT 1067
                                 v i v i  i     vivi v     ii  v  vi    i  
  L1M4_orf2#LINE/     85 GCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT 134

  chr20_15410964_   1068 GATTCTAAAGTTTATGTGGAGAGATAAAAGCCCCAGAATAGCCAACACAA 1117
                            i     i  i  i    i vii  ii v              v    
  L1M4_orf2#LINE/    135 GATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr20_15410964_   1118 TATTGGAAAA------CA--GTCAGAGGACTGATATTACCTGACTTCAAG 1159
                          v   i    ------  --  ii       v i i v  ii i     i
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr20_15410964_   1160 ACTTACCATAAAGCTTCAGTAATCAAGACAGTGTGGTATTGGCAAAAGGA 1209
                               i i      v                      i     v     
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr20_15410964_   1210 TGGAGAAATAGATCAATGGAAAACAATACAGAGTCCATAAATAGACCCTC 1259
                          i  v v              v v   vv        v     i    vi
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr20_15410964_   1260 GTAAATATAGTCAACTAATCTTTAACAAAGAAGCAAAGACACTACAATGA 1309
                         ii vv   i     i i  i  ii    i iv  v     vv v     i
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr20_15410964_   1310 AGCAAG-----TCTTTTCAACAAACTGG-GCTGGAACAACTGGACAATCA 1353
                         i v   -----             -   -     i         i ?i  
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCA 433

  chr20_15410964_   1354 CATGCAAGA-AATGGA-TCGTGACACAGATTTTACACACTTCACAAAAAA 1401
                                i -    i - i -   v vv ii i    vv vi       v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTG-GACCCCTACCTCACACCATATACAAAAAT 482

  chr20_15410964_   1402 TAATTCAAAGTTAATAATAGTCCTAAATTTAAAA--CAAGGAACTATAAA 1449
                            i     i vi  v ?  v       v   i --i  --         
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA--AACTATAAA 530

  chr20_15410964_   1450 ACTCCTAGGGGATAACA--GGATAAAACCTAGGCAACTTTGGAT---ATA 1494
                             i   ii  v    --  ?vv   i  vv ii  i    i ---ii 
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr20_15410964_   1495 CTGGTGACATTTTAGATATGACACCAAA--TACATGCTTTAT--GAAAAA 1540
                         v    v--- i                 --i   v  vvi v--      
  L1M4_orf2#LINE/    581 ATGGTT---TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr20_15410964_   1541 A---ATAAGCTAAATTTCATTAAAATTAAAAAACATCTGCTCTGTGAAAG 1587
                          ---    ii ii i     i           - v i  iv  vii  i 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGG 676

  chr20_15410964_   1588 ACAACATCAATAGAATGAGAAGGCAAGCCACAGATAGAGTGAAAATATTT 1637
                            vi     v i i   i   i   v       vv i v          
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr20_15410964_   1638 GCAAAAGACATACTTGATAAAGGATTTTTATCCTAAATATACAAGAAACT 1687
                              vv i   ii      i   i  v     vi      i  ii    
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr20_15410964_   1688 CTTAAAACTCACTAATAAATAAATGAACAACCCAATT-AAAAATTGGCAA 1736
                             v      v       v i ii  i         -      v     
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr20_15410964_   1737 AAGACTTCAACAAACACCCCACCAAAGAAGATACACAGATGGCAAATAGG 1786
                          i  i  v  i i   iii v            i   i     v    i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr20_15410964_   1787 CATATGTAAAGATGCTCAACATCATATGTCAT 1818
                           i   v                 ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (126 / 83)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.89 (55 / 19)  


3344 26.10 0.33 0.33  chr20_15622612_15627238.rev     3228  4135 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_15622612_   3228 TGGAAAAACATCCCATGCTCGTGGATGGGTAGAATTAATATTGTAAAAAT 3277
                               i i        i  i     v  v   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_15622612_   3278 GACCATACTGCCAAAAGCAATGTACAAATTCAATGCAATCCCCATCAGAA 3327
                          i v     v  v   vii  v    i      i        i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_15622612_   3328 TACCA-CTGTTATTCTTCACAGAATTAGAAAAAA-AATTCTAAAATTCAT 3375
                          v   -   ii-  i  ii     v v  v  iv-i  i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_15622612_   3376 ATGGAACCAAAAATGAGCCTGCATAGCCAAAGTAAGACTAAGAAAAAAGA 3425
                               viiv  iv  v  v v         ii  vvi i i   i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_15622612_   3426 ACAAATCTGGAGACATCACACTACCTGATTTCAAACTACACTATAAGGCC 3475
                              vi     ivv       v  ii        vivi    i  i  i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_15622612_   3476 ATAGTCACCAAAACAGCATGGTATTGGTATAAAAATGGGCACATAGACCA 3525
                          i   v i   i    ii     i   i    ii  i i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_15622612_   3526 ATGGAACGGAATAGAGAACCCATAAATAAACCTAAGTAGTTACAGACAAC 3575
                               ii    v    ii   v         i vii v   ii v   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_15622612_   3576 TGAACTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTT 3625
                            vi   i    i vviv   i v   vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_15622612_   3626 TTCAACAAATTGTGCTGGGATAATTGGCTAGCCACTTGTAAAAGAATGAA 3675
                                   v         i  i   v  ?    v  i           
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_15622612_   3676 ACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATTA 3725
                         ii    i  ii i   v    v           i       i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_15622612_   3726 AGAACTTAAACCTAAGACCTGAAACTATAAAAATTCTAGAAGGTAACATT 3775
                         ?ii  i    iv     v  i           v ii      iv     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_15622612_   3776 GGAAAAACTCTTCTAGACATTAGCTTAGGCAAGGATTTCATGACCAAGAA 3825
                           ?iv  v     vv   v  i v        v i    v iivi v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_15622612_   3826 CCCAAAAGCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTAATTA 3875
                         v         v v    i    iv   i   i   iv v    i v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_15622612_   3876 TACTAAAGAGCTTTTGCATGGCAAAAGGAACAGTCAGCAGAGTAAACAGA 3925
                         v v v  i i      iiivv    i iv  vi   iv i   i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_15622612_   3926 CAATCCACAGAGTGGGAGAAAAACTTCACAGTCTATACATCTGGCAAAGG 3975
                            i       i          vv  ii  ivii   i     ii  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_15622612_   3976 ACTAATATCCAGAATCTACAATGAACTCAAACAGATCAATAAGAAAAAAA 4025
                            vi          v  i  v      vv   iv       v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_15622612_   4026 AACAAACATCACA-TCCAAAAGTGGGCTAAGAATATGAATAGACAATTCT 4074
                         --    i v v  - i?    i     v   i  v          v    
  L1M4_orf2#LINE/    800 --CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_15622612_   4075 CAAAAGAAGATATACAAATGGCCAACAAATATATGAAAAAATGCTCAACA 4124
                          v                       i  ii i       i          
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_15622612_   4125 TCACTAATGAT 4135
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.45 (138 / 95)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.20 (6 / 5)  


2853 25.60 2.41 3.06  chr20_15652178_15660052.rev     3821  4734 (3141)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_15652178_   3821 TGGAAAAACATTCCATGCTCATGGATAGGAAGAAGCAACGTTGTTAAAAC 3870
                               i i  i     i        v      vvi  ii       i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_15652178_   3871 AACCACACTTCCCAAAGCAAGCTACCAACTCAATGCTATTCCTATCAAAC 3920
                         ii v i   i      vii v    vi i    i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_15652178_   3921 TACCAATGATATTCTTCACAGAATCAGAAAAAAACT-ATTTTATAATTTA 3969
                          v   iiviiv  i  ii     -- vvi v  i  -  ii  v    i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTCA 148

  chr20_15652178_   3970 TATGAAACCAAAAAAGGGGCCCA-AATAG---AGGCAATCTTAAGCAAAA 4015
                             i  -- viv     i    -     --- ii       i iv  i 
  L1M4_orf2#LINE/    149 TATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_15652178_   4016 AGAACAAAGCTGGAGCCATCACATTACTTGATGTAAAAGTATACTACAAA 4065
                                  i     vvv     i v iii  v v   iiv         
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_15652178_   4066 GATACAGTAACCAAAACAGCATGGTACTGGAACCAAAATAGAAACATAGA 4115
                          v        i   i    ii         v iv ii     v i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_15652178_   4116 CCAATGGAACAGAATAGAAAACCTAGAAATAAAGCTGCCTATCTACAGCC 4165
                         i        i     v  i ii i         v iiivi  i  ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_15652178_   4166 ATCTG-TTTTTGTTAAG----TTAAAAACAAGCAATGGGGAAAGGAC--T 4208
                          vi  -    i vi   ----ii  i v  vv            i i-- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_15652178_   4209 CCTTATTCAACAAATTATGCTGGGATAACTGGCTAGCCACATGCAGAAGA 4258
                          i  --         vi        i      v  ?         i    
  L1M4_orf2#LINE/    397 CTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_15652178_   4259 TTGAAACTGAACTCCTTCCTTATAGCATATACAAAAATCAGCTCAA---- 4304
                         v    ii  i  i   v   i i v             i i     ----
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_15652178_   4305 GATTAAAGACTTAAATATGGATTATGGATTAAGACTTAAATCCTAAAACT 4354
                            i ?    i     i ------------    v-------        
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGT------------AAGAG-------CTAAAACT 525

  chr20_15652178_   4355 ATAAAAATCCCAGAAGATAACCTAGG---AAATACCATTTG-GACATAGG 4400
                               v  ii      v   v    ---    -- -  i -   v v  
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--C-TTCGTGACCTTGG 572

  chr20_15652178_   4401 CCCTGACAAAGGTTTCATGACAAAGATGCCAAAAGCAATTGCAACAAAAA 4450
                         viiv i   v      v iivv v  ii         vvv         i
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_15652178_   4451 CAAAAGTTGACAAATGGGACCTAATTAAAATAAAGAGCTTTTGCATGGCA 4500
                         v    i v  i    v    i v  i     v  i i      iiivv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_15652178_   4501 AAAGAAACTATCAACAGAGTAAGCAGACAACCTACAGAAACAGAAAAAAT 4550
                           i  v        v i   i iv        i      vvi  i     
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_15652178_   4551 ATTTGTAAACTATGCATCTGACAAGGGTCTAACATCCAGAATGTATAAGG 4600
                              i   ii  ii      i     v  vii         i     i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_15652178_   4601 AATTTAAACAAATTAACAAGCAAAAAACAAATAACTCTATTAAAAAGTAG 4650
                           i ivv    v i  i  vv    i         i v   ?    i i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_15652178_   4651 GCAAAGGACATGAATAGATGCTTTTA-AAAGAAGACACCCAC-TGGCCAA 4698
                                 iv        iii  i v-        i iv  v-       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_15652178_   4699 CAAACATATGAAAAAATGCTCAACATCTCTGATCAT 4734
                         i  i  i       i            v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (147 / 84)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.78 (50 / 18)  

 433 26.52 11.36 0.76  chr20_15652178_15660052.rev     6167  6298 (1577)    L1M4_orf2#LINE/L1        1   146 (762)  

  chr20_15652178_   6167 TAAAGAGATATTTCATATTATTTGACAGAAAAACTCAATATTGTCAAGAT 6216
                          ii i      ii   i  vv v  iv i  i   i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_15652178_   6217 GTCAGTTCTTCCCAACTTGATCTATAGATTCAA---------------AA 6251
                          v  i v  i     v        i        ---------------  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_15652178_   6252 TCTCAGCAAGCTATTCTGTGGATATCAACAAGCTAATTCTATAGATT 6298
                           i    viv  v  i  ii  v  ii       i  i   - i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA-AAATT 146

Transitions / transversions = 2.18 (24 / 11)
Gap_init rate = 0.01 (2 / 146), avg. gap size = 8.00 (16 / 2)  

2713 25.16 1.67 1.93  chr20_15652178_15660052.rev     6605  7383 (492)    L1M4_orf2#LINE/L1      132   908 (0)  

  chr20_15652178_   6605 GCCAATTCTATAGTTTATATGGAGATGCAGAAGACCCAGAACAGCTAACA 6654
                           ii  i   v i  i       i     iii         i   i  v 
  L1M4_orf2#LINE/    132 GCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr20_15652178_   6655 CAATATTAAAGGACAAGAACAAAGCTGGAAGACAGACACTACTCAACTTC 6704
                             v  i  ii v          i    i   vv     v i   i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr20_15652178_   6705 AAGACCTATTGTAAATCTACAGTAATCAAGACAGTATGTTATTGGTGAAA 6754
                           i  i  i ii   v                   i  v  i   iiv  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr20_15652178_   6755 AAATATACAAATAGATCAATGGAAGAGAATAGACAGGCCAGAAATAGATG 6804
                         ii   v   v              v     v  v  v         i iv
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr20_15652178_   6805 CACATAAATATAATCAACTGATCTTTGACAAAGGAGCAAAGGAAATACAA 6854
                           i i vv   ii    i    i  i     i  v  v   ivv  v   
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr20_15652178_   6855 TAGAACAAAGATAGTCTTTTAAGCAAATGGTTCTGGAGCAACTGGACATT 6904
                          i iiv  ii          v i        v    ii        i ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr20_15652178_   6905 CACATGCAAAACAAAAAAACAAAAAAAATGAATTTAGACAAAGACCTTAC 6954
                                    --------------i      v  i   vvvv    i  
  L1M4_orf2#LINE/    432 CACATGCAAAA--------------GAATGAAGTTGGACCCCTACCTCAC 467

  chr20_15652178_   6955 ACCTTCCCCAAAAATTTACTCCAAATGGATCAAAGACATAAATGTAAAAT 7004
                            v viv        v    v          ?    v         i v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr20_15652178_   7005 GTGAAACTATAAGACTCTTAGAGAATAGCATACAAGAAAACATAGATGAC 7054
                         v i         i         ii v i    vi? v   iv vvi    
  L1M4_orf2#LINE/    518 CTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGAC 567

  chr20_15652178_   7055 CTTGGGTATGACAATGACTCATCAGATACAACACCAAAGGCATAATCCAT 7104
                                vv i     ii iv i     ii        i   i  v v i
  L1M4_orf2#LINE/    568 CTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAAC 617

  chr20_15652178_   7105 GAAATAAGTAATTGATAAGCTAAACTTCAT-AAAACTCAAAACTTCTGC- 7152
                         i   v  iv   v     ii ii       -    i v       i  i-
  L1M4_orf2#LINE/    618 AAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr20_15652178_   7153 TTTGAAAAGATAATGTCAAGAAAATGAAAAGATAAGATGCAGACTGGGAG 7202
                         i  v   i  i v i        i        i  vvii    v      
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr20_15652178_   7203 AATATATTTGCAAAAGACACATCTGATAAAGGACTATCATCCAAAATATA 7252
                           v           vv i i         i     vvi     i      
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr20_15652178_   7253 CACAGAACTCTTGAAACTCAATAATAATAAAATTAGCCATTCAATTAAAA 7302
                         i v         iv             v  i iv iiv ii     ?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

  chr20_15652178_   7303 AATGGACCAAAAATCT---T-GATACCTCACCAACAAAGA-------ATG 7341
                              i v  ii  i --- -  i ii  v    vi    -------   
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

  chr20_15652178_   7342 GCAAATAGACATATGAGAAAAATGTACTACATCATGTGGCAT 7383
                           v    ii  i    -   i   iv v      ????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGA-AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (116 / 76)
Gap_init rate = 0.01 (7 / 777), avg. gap size = 4.00 (28 / 7)  


2937 27.40 0.47 0.82  chr20_15737994_15740494     1156  2009 (492)    L1M4_orf2#LINE/L1       58   908 (0)  

  chr20_15737994_   1156 CTCCACATCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACC 1205
                             ---i   iv i  i  i        i  v     i     iv v  
  L1M4_orf2#LINE/     58 CTCC---CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr20_15737994_   1206 AATGACTGTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATG 1253
                          iivi iv i  ii     -   -- v  i  - iii    i        
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATG 152

  chr20_15737994_   1254 GCACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAGAACG 1303
                          v viiv  ii  v  v v  v     iv     i i ivv i      i
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_15737994_   1304 AAGCTGGAGGCATCACGCTACCTGACTTCAAACTGTACTACAAGGCTACA 1353
                            i      vv    i  v  ii i      viv        i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_15737994_   1354 GTAACCAAAACAGCATGGTACTGGTACCAAAACAGTGATATAGACCAATG 1403
                             i   i    ii         i iv ii i  vv       i     
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr20_15737994_   1404 GAACAGAAC--AGTGCCCTCAGAAATAATGCCGCATATCTACAACTATCT 1451
                            i    i--  v i  --        vv  ii i  i  iiiii vi 
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_15737994_   1452 GATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 1501
                            i  i     ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_15737994_   1502 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 1551
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_15737994_   1552 CTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAA 1601
                         i    i    v   i     v           i  i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_15737994_   1602 AGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 1651
                             i    i  v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_15737994_   1652 GCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACA 1701
                          ?i v viv   iv   v v  vv i     v ii   v ivv  vi   
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_15737994_   1702 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAA 1751
                                  vvi          vv     v  i    v   ii v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_15737994_   1752 ACTAAAGAGCTTCTACACAGCAAAAGAAACTGCCATCAGAGTGAACAGGC 1801
                          v v  i i   i iii vv    i  v   ii  vv i      v  i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_15737994_   1802 AACCCACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAGGG 1851
                                 i             v  ii   vii ivi      i  i  i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_15737994_   1852 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 1901
                           vi          v  i  v      vv    v iv i  v     i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_15737994_   1902 AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAA 1951
                            i     v  i?    i            v    i     i     v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_15737994_   1952 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCA 2001
                                i  vi viii     v  i          i       v     
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr20_15737994_   2002 CTGGCCAT 2009
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.47 (137 / 93)
Gap_init rate = 0.01 (6 / 851), avg. gap size = 1.83 (11 / 6)  


2703 27.12 3.95 1.36  chr20_15998939_16001227.rev      913  1797 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_15998939_    913 TGGAAAAGTATTCCATGCTCATGGATTGGAAGAATCAATAGAATTAAAAT 962
                               ii   i     i               v i    vvi    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_15998939_    963 GAGCACACTGCCCAAAGCAATCTACAGATTTAATGCTATTCCCATCAAAC 1012
                          ivv i   v      vii           i  i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_15998939_   1013 TACC-GATGTCATTTTTCACAGAACTATAAAGAACT--TTCTAACATTCA 1059
                          v  - v  i -     ii     v - i vi i  -- i    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCA 148

  chr20_15998939_   1060 TGTGGAACCAAGAAAGAGCCTGAATAGCCAATGCAATCCTAAGCAAAAAG 1109
                          i     viivi ii  v  v          vi     i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_15998939_   1110 AACAAAGCCAGAGGCATCACATTATCTGACTTCAAACTATACCACAAGGC 1159
                                iii    vv     i vi ii i      viv   i    i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_15998939_   1160 TACAGTAACCAAAATAGCATGGTACTGGTACAAAAACAGACACATAGACC 1209
                                 i   i i  ii         i i  ii i     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_15998939_   1210 AGTGGAACAGAATAGAGAACCCAGAAATAAAGCTGCACACTTACAGCCAT 1259
                          i     i     v    ii           v iii   i   ii i  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_15998939_   1260 CTGATCTTTAACAAAGTCAATGAAAATGATAATAACCAATGGAGA----- 1304
                         i    i  ii    i ---i  vv  -  iv  --i      i  -----
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGG---GTGCCAA-GACCAT--TCAATGGGGAAAGAA 392

  chr20_15998939_   1305 TA-----TTCAATAAATGGTGTCGGGACAACTGGCTAGCCACATGCAGAA 1349
                           -----     i        ii           v  ?         i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_15998939_   1350 GAATAAAACTGCACACCTACCTTTTGCCACATACAAAAATTAACTCAAGA 1399
                             i  ii  v  v       ivii   i                  i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_15998939_   1400 TGGAATAAAGATTTAAATTTAAGACCTTAAACTATAGGAATACTAGTAGA 1449
                             vi ?   ii     v     v  v        ii v vi   v   
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_15998939_   1450 AAACCTGGGAA-ACACCATTCTGAACATCAGCCTTGGGAAAGAATTTAT- 1497
                             v i  ?i- v i v iv   v v vi --  i  v  vii   v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGG--TTAGGCAATGGTTTCTT 590

  chr20_15998939_   1498 -GACTAAGTCCCCAAAACCAACTGCAACAAAAACAAAAACTGACAAGTGG 1546
                         -  -  v v v      v  vvv         iv     iv  i  i v 
  L1M4_orf2#LINE/    591 AGA-TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_15998939_   1547 GACCTAATTAAGATAAAGAGCTTCTGCATGGCAAAAGAAACTATCAACAG 1596
                            i v  i  i  v  i i   i  iiivv    i  v        v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_15998939_   1597 AGTAAACAGACAACCTACAGAATGAGAGAAAATATTCACCAACTGTGCAT 1646
                            i  v        i        i           ii v  iii ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_15998939_   1647 CTCACAAAGGTCTAATATGCAGTATCTATAGGGAATTG---------AGC 1687
                           v i  i  v  vi   v   v  v    ii   i v--------- ii
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_15998939_   1688 AGGTGAAAAACAAATAACCCCATTAAAAATTA--CA-------TGAATGA 1728
                          ivvi   i           v   ?    v i--  -------     ii
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr20_15998939_   1729 ACACTTCTCAAAATAAAACAAATAAGTGTCCA-TAAGCATATGAAAAAAA 1777
                            i     v   v  i i v i  i  v   -      i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_15998939_   1778 AACCCAACATCACTAATCAT 1797
                         i- i        ????????
  L1M4_orf2#LINE/    890 G-CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.74 (150 / 86)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.61 (47 / 18)  


3260 26.30 0.99 0.66  chr20_16012101_16016323     2827  3731 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_16012101_   2827 TGGAAAGACATTCCATGCTTGTAGATCAGAAATATTAATATTTTTAAAAT 2876
                                 i  i     i ii i   ii   ivv        v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_16012101_   2877 GACCATGCTGTCCAAAGCCATACACAGATTCAATGCAATCCCCAATAAAA 2926
                          i v  i  vi     viv  vi          i        i vi    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_16012101_   2927 TACCATTGACATTCTTCACAGAAATTGAAAAAAAAATACTAAAATTCATA 2976
                          v   vivi v  i  ii          v  ivvi  v            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_16012101_   2977 TGGAACCACAGAAGACCCTGAATGGCCAAAGTCATCCTAAGCAAAAAGAA 3026
                              vii  iii     v    i      iiv   i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_16012101_   3027 CAAAGCTAGAGGCATGATAGTGTCAGCCTTCAAAATATGCTACAAAAGTA 3076
                              i i    vv v i v vi vivi       iv i       iv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_16012101_   3077 TAGTAACCAAAACAGCATTGTTCTGGCATAAAGACAGATGCATAGACCAA 3126
                         i     i   i    ii v  v         i  i   iii     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_16012101_   3127 TAGAACAGAATACAGAACCCAAAAATTAATCCATATATCTACAGCCAACT 3176
                          i   i     vv   ii   i    v  i     i  i  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_16012101_   3177 AGTTTT-GGCAAAAGCACCAAGAACATTCATTAGAGAAAGGACACTCTCT 3225
                         ii    - i   ii ii      v      v i i     i i v   i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_16012101_   3226 TCAATACATGGTGCTGGGAAAACTGTATATTCATATGTGGAAGAATAAAA 3275
                             i v            v     v   ?i  i   iii      i  i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_16012101_   3276 CTAGACTCCTATTTCTCACCCAATGTAAAAATCAACTCAAAATTGATTGA 3325
                         i i   i    ii  v    vv  ii      i          v   ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_16012101_   3326 AGGCCTAAATGTATGACCTGAAACTATAAAAATACCACAAGAAAAGATTC 3375
                           i          v  v  i           v vii v       v  vv
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_16012101_   3376 GAG-AAATGCTTCAGGACATTGGTCTAGGGAAAGATTTTATGAATAAGAC 3424
                          ? -    -    iv   v    vi    v  v i   iv ii   v   
  L1M4_orf2#LINE/    551 GNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_16012101_   3425 TGCAAATGCACAGTCAACAGAAGCAAAAACAAATGA----GATTATATTA 3470
                         vv    v     iv     i   v     i i  i ----  i vi  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_16012101_   3471 AA--CAAAAAATCTTCTGTACAGCAAAGGAAACAATCAACAAAGTGAAAA 3518
                           --i     --   i   i vv       v  v     v          
  L1M4_orf2#LINE/    650 AAATTAAAAA--CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_16012101_   3519 GACAACCTATTGAATGGGAGAAAATATTTCCAAAGTATTCACCTAACAGG 3568
                                i iv                  v    vi  vi i  i i i 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_16012101_   3569 AGATTAATATTCAGAATATAAAAGGAACCCAAACATCTCCACAGCAAAAA 3618
                         i  i vi   i         v  i    i vv   v   v i ii     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_16012101_   3619 CCACACAAACAATCCAATTTAAAAATGGGCAAATGATCTGGACAGACATT 3668
                         v---     i  i      ?             v   i  i i       
  L1M4_orf2#LINE/    798 G---ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_16012101_   3669 GC-CAAAAGAAGACATACAAATGGCCAACAAACATATGAAATAATTCTCA 3717
                         v - v        i              i  i  i      vi  v    
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_16012101_   3718 ACATCATTGTTTTA 3731
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (147 / 87)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.88 (15 / 8)  


4353 16.29 4.16 2.13  chr20_16017263_16020359     1716  2605 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_16017263_   1716 TAGAAGAACATCCTATGTTCATGAAT-GGAAAA--TGATATTGTTAAGGT 1762
                          i   ii i    i         i  -    i -- i           i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_16017263_   1763 AACACTATACCCCAAATTGATCTACAAATTCAACTCAATCCCTATCAAAA 1812
                         ii  v  iv                 i       v               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_16017263_   1813 TCACAGCAGGCTCTTTTGAAGAAATTGACAAGCTGTTCCTAAAATTTATG 1862
                           v    v v  i     v                v          i  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_16017263_   1863 TGGGAATTCAAGATTTCCATATAAAAATTGTTTTTGTAGCCAAAACAATC 1912
                            i   v    ivvi   -----i   ---------             
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCA-----GAAT---------AGCCAAAACAATC 186

  chr20_16017263_   1913 TTGGAAAAGAAGAACAAAGTTGAAATATTCACATTTCTTGATTTTCAAAA 1962
                            i                  i iv i     i   iii    -     
  L1M4_orf2#LINE/    187 TTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTT-CAAAA 235

  chr20_16017263_   1963 GTTATTACAAAGCTATAGTAATCAAAACAGTATGGTACTGCCATA-GGAC 2011
                         v   i          i         i     i        v    -   i
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr20_16017263_   2012 AGACATATAGATAAACGGAATATAATTGAAAGTTGAGAAGTAAACCTACA 2061
                                     v  i      v      i   iv    i      i i 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr20_16017263_   2062 CATCTATAGTCAATTGACTTTT--TAAGGGTATCTTGACAATTCAGTGGG 2109
                            i   i         i   i--i      ii vv   v     i    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr20_16017263_   2110 GAAAATAATAGTTTTTTCAACAAATGGTGCTAGAGCAACTAAATATCCAC 2159
                             i-      i                  i ii     ii   ?    
  L1M4_orf2#LINE/    386 GAAAG-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr20_16017263_   2160 ATGCAAAAGAATGAAATTGGACTCCTACCTCATAGGAGGTA--AATATTA 2207
                                        i      i         i vv vi  --  v    
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr20_16017263_   2208 ACTCAAAAT--ATTCAAG---TAAATATG-------------------TC 2233
                                  --  iv?  ---     i i-------------------  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr20_16017263_   2234 TTAAAAGAAAACATATGTATAAATCTTCATGACCTTGGTTTAGGCAATGT 2283
                            i           v ?i         i         v          v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr20_16017263_   2284 GTTTTTGGATGTGAACTCAAAAGCAAAATCAATAAAAGAAAAAATAAATA 2333
                         v  i  i   i   vvi        v  v   i             i   
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr20_16017263_   2334 CATTGGGCTTCATCAGAATTAAAAATATTTGTGCTTCAGGGGAACACTAT 2383
                         v     i        i         iv           ii   -      
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA-CACTAT 683

  chr20_16017263_   2384 GAAAAAAATGAAAAGATAACTTATAAAATGGGAGAAA-TATTTACAAATC 2432
                         v  i   i        i   ii i i           -     i      
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr20_16017263_   2433 ACACATCTGATAGGGAAATTGCATCCAGAATATATTTAAAGA---CTTAT 2479
                          i i        i  i v   i             --     ---    i
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATAT--AAAGAACTCTTAC 781

  chr20_16017263_   2480 AACTCAATGATAAAAATACAAATTATCCCATTAAAAGATGGGCAAAAGAT 2529
                                 i       v      v i  v   ?   i         i   
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr20_16017263_   2530 TTGAACAAACATTCTTCCAAA-AAGATATACAACAGGTCTATAAGCACAT 2578
                              i i     ii      -           vv  i v          
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr20_16017263_   2579 GAAAAGATGCTCAACATCATTAGGCAT 2605
                                            ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.28 (98 / 43)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 3.29 (56 / 17)  


3881 17.38 4.07 4.40  chr20_16068016_16070120      705  1613 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_16068016_    705 GAAAAGTATCCTGTGTTCATGGATTGAAAGATTTATGTTTCCTAAGATGG 754
                             ii     ii             i    i   vvv  vi        
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_16068016_    755 CAGTACTCTCCAAATTGGTCTACAAATTCAATGCAATCTCTATCAAAAGC 804
                           i     i        i      i      i      i         v 
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_16068016_    805 AAAGCTGGCTTTTTTTTTTTTTTTATAAAATATTAACAAACGAATCCTAA 854
                         vv     v       ---------ii i  -   i    i vi       
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTT---------GCAGAA-ATTGACAAGCTGATCCTAA 142

  chr20_16068016_    855 AACTCTTATGAGATTGCAGAGGACCCAGAATAATCAAATCAATCAATAAT 904
                           i  v    ii v    ii            ii    ------------
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA------------ 180

  chr20_16068016_    905 CAAAACAATCTTGAAAAAAAAAAACAAAGTTGAAGGATTCACATTTCTTA 954
                         ----              i  i          i    i     i   ii 
  L1M4_orf2#LINE/    181 ----ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA 226

  chr20_16068016_    955 ATTTCAAAACTTACTATAAAGCTACAGTAATCAAGAC--TGCAGTACTAG 1002
                                         i                    --  ii     i 
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr20_16068016_   1003 TACAAGAATAGACATATATATATATGGAATAGAACTGAGACACAAAGAAT 1052
                         i i   i           v  vv           i     vv v ii   
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr20_16068016_   1053 AA--CTATAGGT--ATAGTCGAA-AATTTTTCACAAGGATACCAAGACAA 1097
                           -- i   vi --  i   i v-i     iv      i i       v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA 376

  chr20_16068016_   1098 TT-AATGGGGCAAGGATCATCTTTTCAACAAATGGTATTGAAACAACTGA 1146
                           -       v   i  vi                 ii  ii       i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr20_16068016_   1147 ATATCCATGTGGAAAAGAATGAAATTGGATCCCTACCTCACATCATACAT 1196
                            ?   ii  v           i     i            i    i i
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr20_16068016_   1197 AAAAATTAACTCAAAATGGATCAGACACCTAAATATATGAGCTGAAACT- 1245
                                                ? v        i  v     i     -
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr20_16068016_   1246 -------CATAGAAGAAACCTTAAATATAAATCTT-ATGACTGTGGATTA 1287
                         ------- v         v v  ii?i        -i    iv   i   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr20_16068016_   1288 GATTTAGATGTAGATTTGTTT-TTAGATATGACAACAAACATACAAACAA 1336
                          ii---i   -------    -            v    vii    i   
  L1M4_orf2#LINE/    577 GGC---AATG-------GTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr20_16068016_   1337 CAAAAGATAAAAATAGATAAATTTGGCTCTGAAGCACAAACCAAAATTGT 1386
                                -               v i  ii-- v  -   ii    viv 
  L1M4_orf2#LINE/    617 CAAAAGA-AAAAATAGATAAATTGGACTTC--ATCA-AAATTAAAAACTT 662

  chr20_16068016_   1387 TTGTGCTTCAAAGGATACTATAAAGAA-GTGAGAAAGGAATACACAGAAT 1435
                                        i     v     -    i  iiv  iv        
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr20_16068016_   1436 GGGAGAAAATATT-GCAAAATATATATCAGG-AAGGGACTTTTATCCAGA 1483
                                      -     vi       v i-         v        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr20_16068016_   1484 ATATATAGATAATTATTACAATTCAATGATAAAA-GACACCTCATTT--T 1530
                                i v  i v      i     i      -    vv v iii-- 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr20_16068016_   1531 TTAAAACACGGCAAAGAATTTGAATAGATAT-------------ATATAC 1567
                          ?    vvv       i           i  -------------      
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr20_16068016_   1568 AAATGGCTAATAAGCACCTGAAAAGATGTTCAACATCATTAGTCAT 1613
                                i         v          i         ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (103 / 51)
Gap_init rate = 0.02 (22 / 906), avg. gap size = 3.50 (77 / 22)  


 457 23.08 0.00 0.00  chr20_16229722_16232168.rev      869   959 (1488)    L1M4_orf2#LINE/L1        1    91 (817)  

  chr20_16229722_    869 TGAAGAGGTATTCCATGTTCATGGGTAGGAAGACTCAACACTGTTAGGAT 918
                           i i  i   i            i v        i  i i     i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_16229722_    919 GTCAGTTCTTTGCAAGTTGGTCTATAGATTCAACTCACTCC 959
                          v  i v  iiv   i   i    i         v  v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCC 91

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.00 (0 / 0)  

2094 24.71 5.07 1.96  chr20_16229722_16232168.rev      964  1574 (873)    L1M4_orf2#LINE/L1      201   830 (78)  

  chr20_16229722_    964 CAAATTAGGAAGACTGACACTACCAAACTCCAATACTTAATACAAAGCTG 1013
                             v v   i    v     v  v  i i   v     v         i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_16229722_   1014 CAGTAATCAAGACAGCGTTGTACTGGTGAAAGAATAGACA----GAT-AA 1058
                                        i  v       iiv   i       ----   -  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_16229722_   1059 TGGAACAGAACAGAGAGCCCAGAAATAGA----------TATAATTAATT 1098
                              i    iv     i         i ----------   ii i    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_16229722_   1099 ATCTTTTG-CAAAGGAGCAAAGGCAATAAAATGAAGTAAAGATAGTCTTT 1147
                         ivi   i -   i  v  v   i v  vv    ii v  ii         
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_16229722_   1148 TCAACAAATAGTCTTTTCAATAAATGGAACAATTGGATATCCACATGCAA 1197
                                  i  vi ----------  i    i      ?          
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCT----------GGGACAACTGGATAKCCACATGCAA 440

  chr20_16229722_   1198 AAAAACCAATCTAGACACAGACCTTATGCCATTCACAAAAACTAA----- 1242
                           i  iv  vi i   v vv    i ii    vi       i   -----
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr20_16229722_   1243 ACTGGATTATAGGCCTAGAAGTAAAACACAAAGCTATAAAATTCCTAGGA 1292
                          v     i ?  i    i v    i vvi   i        i  i   i 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr20_16229722_   1293 GATGACATAGGAGAAAACCTAGATGACTTTGGATGTGGAAATAACTTTTT 1342
                           vi       ? v   i  vvi    i    i vv  v   iii  i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_16229722_   1343 AGATACAACACCAGTGACATGATTCATAAAA-------TAAATAAGATAG 1385
                              ii      ivii  ii viv i    -------  i    iv i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_16229722_   1386 ACTTCACTAAAGTTTAAAACTTCTGCTCTGCAAAAGACACCGTCAGGAGG 1435
                               ii   i  v       i  iv  v    i     ii   i  ii
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_16229722_   1436 ATGAGAAGGGAATCTACAGACTGAGAAAAAATATTTGCAAAAGGCATGTC 1485
                         i   i   iv  i i     v  i  i              vvii  i  
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_16229722_   1486 TGATAAAGGGGT-GTAATTCCA-AGTATACAAAGAACTCTTAAAACTCAA 1533
                               i  iv -   --    - i    i            v       
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTA--TCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_16229722_   1534 CAATAAGAACACAAACAACCTCATT-AAAAATAGGCAAAAGA 1574
                         i     i  v     i    iv   -      i      i  
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

Transitions / transversions = 1.96 (98 / 50)
Gap_init rate = 0.02 (11 / 630), avg. gap size = 3.91 (43 / 11)  

 487 13.83 0.00 0.00  chr20_16229722_16232168.rev     1862  1955 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr20_16229722_   1862 AAAAATGGGCAAAAGACTTGGACAGACATCTCACCAAAGAAGATATACAG 1911
                                      i  i   i i      i  v                i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr20_16229722_   1912 AAGGCAAATAAGCATATGAAAAGAGGCTCAATAACATATGTCAT 1955
                          v   v        i         v      i v  ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


2457 26.69 0.29 0.29  chr20_16477730_16479404      502  1183 (492)    L1M4_orf2#LINE/L1      227   908 (0)  

  chr20_16477730_    502 ACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGG 551
                          i      viv        i          i   i    ii         
  L1M4_orf2#LINE/    227 ATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGG 276

  chr20_16477730_    552 TACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTCAGAA 599
                         i iv ii i   v                i    i--    i  --    
  L1M4_orf2#LINE/    277 CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGAA 324

  chr20_16477730_    600 ATAACGCCGCATACCTACAACTATCTGATCTTTGACAAACCTGAGAAAAA 649
                             vv  ii i ii  iiiii vi    i  i     ivv  vv  i v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr20_16477730_    650 CAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACT 699
                           vv            i  vvi  v  i  i              v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr20_16477730_    700 GGCTAGCCATATGTAGGAAGCTGAAACTGGATCCCTTCCTTACACCTTAT 749
                           v  ?   i   i ii iiv    ii    i    v   i     v   
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr20_16477730_    750 ACAAAAATCAATTCAAGATGGATTAAAGATTTAAACGTTAGACCTAAAAC 799
                                 i  i    i      i ?   ii    i  v   v       
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr20_16477730_    800 CATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCA 849
                         i      vi i           v    ?i v viv   iv   v v  vv
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr20_16477730_    850 TGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAAAAGAC 899
                          i     v ii   v ivvi vi            vvi           v
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr20_16477730_    900 AAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 949
                              v  i    v   ii v  i   v v  i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr20_16477730_    950 AGAAACTACCATCAGAGTAAACAGGCAACCTACAAAATGGGAGAAAATTT 999
                         i  v    i  vv i   i  v  i     i   i             v 
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr20_16477730_   1000 TCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAA 1049
                          i    vii ivi      i  i  i  vi          v  i  v   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr20_16477730_   1050 CTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGC 1099
                            vv    v iv i  v     i     i     v  i?    i     
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr20_16477730_   1100 GAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAA 1149
                         i     iv    i     i     v        i  vi viii     v 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr20_16477730_   1150 AACACATGAAAAAATGCTCATCATCACTGGCCAT 1183
                          i          i       v     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (107 / 71)
Gap_init rate = 0.00 (2 / 682), avg. gap size = 2.00 (4 / 2)  


3959 16.88 3.33 4.13  chr20_16521492_16524250     1401  2271 (488)    L1M4_orf2#LINE/L1       45   908 (0)  

  chr20_16521492_   1401 TAAGATGGCAATATTCCCCAAACTGATCTACAGATTCAACACAATCCTGA 1450
                                      i        i                 i      iv 
  L1M4_orf2#LINE/     45 TAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA 94

  chr20_16521492_   1451 TCAAAATTCTAGCTGGTTTATTTGTAGAAATGGCCACACTGATCCTAGGA 1500
                                i i     vi  v    i      v v  vi         ii 
  L1M4_orf2#LINE/     95 TCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr20_16521492_   1501 TTCATATGAAAATTCAAAGGACCCAGAATAGCCAAAA-AATCTTGAAAAA 1549
                                 i    v   i                   -            
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_16521492_   1550 GAACAAAAAA--TAGGGGATTCACACTTCACAATTTCAAAACTTACTACA 1597
                            v  v   -- i i   i         v                    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_16521492_   1598 AAGCTACAATAATT----CAGTGTGGTACCAGCATAAGGATAGCCATATC 1643
                                 i    i----           ii            v     v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_16521492_   1644 AATCCATGGCATAGAATTGAGAGTCCAGAAAATAAACCCGTATATTTATG 1693
                         i   v    v                     -       i  i       
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAA-TAAACCCATACATTTATG 343

  chr20_16521492_   1694 GTTAATTGGTTTTTAACAAGGGTGCCAAGACAGCTTAATGGGAAAAAGAA 1743
                           i     i    ii                vii i      i   -   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAA 392

  chr20_16521492_   1744 GAGTCTTTTCAACAAATGGTTTCAGGAAAGCGGATTGTCCACGTGCAAAA 1793
                         v                   viii   v i v iv i?    i       
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_16521492_   1794 GAATGAAGCTGGACTCCCTCCTTATACCACATGCAAACATCAACTCAGAA 1843
                                 i     i  iv   i i    i  i    v  i      i  
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_16521492_   1844 TGAATCATGTATGTACATGTTAGAGCTCAAAATTAGAAATTTGTTAGAAG 1893
                           i    ?iv iv  v    v      -    i  v   vi v       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAG 541

  chr20_16521492_   1894 AAAACAAACAAGTAAATCATTGTTGCCTTAGGTTAGGTAATAGTATTTTG 1943
                               v vi?       v i  vi    i       i   ---------
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT--------- 582

  chr20_16521492_   1944 TTGTTGTTGTTTGTTTTTTGGTTTTTAAGTTATGACACCAAAAGCGCAAG 1993
                         -------------------     i v  v               i    
  L1M4_orf2#LINE/    583 -------------------GGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr20_16521492_   1994 TGACAAAAGAAAACAA-----AAATTGTATTTTAACAAAATTTAAAACTT 2038
                         ii           -  -----      v i  i v       v       
  L1M4_orf2#LINE/    614 CAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr20_16521492_   2039 CTCTGCTTTAAAAGATACCATCATGAAAGTGAAAAGACAACCCACAAAAT 2088
                         i v     i   i  i  i    v                      i   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr20_16521492_   2089 GGGAGAAAATATTTTCAAAT-----ATTTGCAAA-----TTGTATGCT-- 2126
                                       v     -----  i  vv  -----      v v--
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr20_16521492_   2127 -TGT-TAAGGGAATCAGACAACAAGTTCAGAAATAAAAAGACA--TAACC 2172
                         - i -   i i v  vv     ----   iv            --     
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAAC----TCAATAATAAAAAGACAAATAACC 808

  chr20_16521492_   2173 CAATTTAAATATAGGAAAAGGGTCGAAATAGTCATTTCTCTAA-GAAGAT 2221
                              ?   v  i  v     i ivi     v        i  -      
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr20_16521492_   2222 ATACAAACATCCGACATGTACATGAAAATATACTCAACCTTACTGGTCAT 2271
                                iiv  i i v i         v  i      v i ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (86 / 57)
Gap_init rate = 0.02 (16 / 864), avg. gap size = 4.06 (65 / 16)  


 878 24.24 0.43 2.60  chr20_16699750_16705559.rev     4133  4363 (1447)    L1M4_orf2#LINE/L1        1   226 (682)  

  chr20_16699750_   4133 TGGAGAAAAGCCTCATAATCCTGGATTGAAAGACTTAATATTCTTAAAAT 4182
                             i i vii i   iv  v       i             v    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_16699750_   4183 GGCAATACTTCCCAAGCTTATCTATATTTTCAATTCAATTCCTATCAAAA 4232
                                  i     ii v     i vv     iv    i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_16699750_   4233 TTCCAGGTTTCTTTTGTATAGAAATGGACAAGCTAATCCTAAGTATTATA 4282
                          i    v vi     v ii      v        i       ivv i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_16699750_   4283 TGAAATCATAGGATAATACA-AATAGCTAAAATAATGTTTGAAAATAGGA 4331
                           i  viii i i-i iv  -      i    i   v  vi    v i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_16699750_   4332 ATAAAGTTGGAAGGGCTGGGCACAGTTGCTCA 4363
                          i         -  i  ---    v  - i  
  L1M4_orf2#LINE/    200 ACAAAGTTGGA-GGACT---CACACTT-CCCA 226

Transitions / transversions = 1.80 (36 / 20)
Gap_init rate = 0.02 (5 / 226), avg. gap size = 1.40 (7 / 5)  

3348 16.74 4.95 0.29  chr20_16699750_16705559.rev     4634  5320 (490)    L1M4_orf2#LINE/L1      190   908 (0)  

  chr20_16699750_   4634 AAAAAAAAGAATAAAGTTGGAGGACTCATACTTTCTGGCTTCAAAACTTA 4683
                              i     i                i    i iiii           
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_16699750_   4684 CTACAAAGATACGGTAAACAAAA--ATGTGTTACTGGCATGAGGATAAAC 4731
                                 v   i    v   i --i    v         i      i  
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr20_16699750_   4732 ATATGTATCAATGGGATAAAATCAAGAATCCAGAAATAAACCCATACATC 4781
                             iv        i   i   ii   i                     i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr20_16699750_   4782 -ATG------TGATTTCCAACAAGGATACAAAAGTCATTTCATGAGGAAA 4824
                         -   ------      i i      i i v  iii    iv   i     
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr20_16699750_   4825 GACTATTCTTTTCAACAA-TGGTTCTAGGACAACTGAATATCCACATAGA 4873
                           v  v            -    v  i         i   ?      iv 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr20_16699750_   4874 AAAGAATGAATTTGAGCCCCTTCCTCAACATCATATAAAAAAAT-AACT- 4921
                                   v   ii     v     -  i      v      -    -
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCA-CACCATATACAAAAATTAACTC 488

  chr20_16699750_   4922 AAAATGAATCAAAGACCTCAATGAAAGTG--------ATAAAACTCTTCG 4963
                               i    ?      v    v   v --------           v 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr20_16699750_   4964 AAGGAAAAAATAGATGCAAATCTTTATGACCTTGGATTAGGCCATGGTTT 5013
                            -    v    i? i       ii         i      v       
  L1M4_orf2#LINE/    539 AAG-AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_16699750_   5014 CTTAACTACAACACCAAA-GCACAAGCAATAACAAAGAAAAGAGATAAAT 5062
                             iv  ii        -          i  v i i    v        
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr20_16699750_   5063 TTGACT-CATTAAAACTAAAATGTCTTGTGCATCAAAGAACACTACTAAG 5111
                          v    -   i    i     vv i      v      i      ii   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_16699750_   5112 AG-GTCTAAAGACAATCCACATAAAGGGAGAAAATATTTGCAAACCGTGT 5160
                          i-  vv        i     v  v                   i i i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_16699750_   5161 ATCTGATAAGGGTCTAGTAACCAGAATGTATAAAGAACTCTTACAA---- 5206
                                     v  v   v       i                  ----
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_16699750_   5207 -------AAAGACAAACAACTTCATTAAAACATGAGAATGGGACTTGAAT 5249
                         -------         i   iiv   ?   v   i v vi   i      
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_16699750_   5250 AAACATTTCTCCAAAGAAGATGTACAAATGAGCAATAAGCACATGAAAAT 5299
                          i                   i        iv                 v
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_16699750_   5300 ATTCTGAACATTGTTAGTCAG 5320
                           v  v     ii????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (70 / 41)
Gap_init rate = 0.02 (13 / 719), avg. gap size = 2.77 (36 / 13)  


3251 26.15 0.88 1.10  chr20_16716726_16723130.rev     5004  5913 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_16716726_   5004 TGGAAGAACATTCCATGCCCATGGATAGAAAGAATCAATATTGTGAAAAT 5053
                              ii i  i     ii       v i    v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_16716726_   5054 GGCCATACTGCCCAAGGTAATTTATAGATTGAATGCCATCCCCATCAAGC 5103
                            v     v     iv i  i  i     v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_16716726_   5104 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAAACT-ACTTTAAAGTT 5151
                          v   iivi i  i  ii     -   ---- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr20_16716726_   5152 CATATGGAACTAAAAAAGAGCCCGCATTGCCAAGACAATCCTGAGCCAAA 5201
                                  v iv  ii  v  v v  v     i      i   ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_16716726_   5202 AGAACAAGGCTGGAGGCATCATGCTACCTAACTTCAAACTATACTACAAG 5251
                                i i      vv   ii  v  i  i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_16716726_   5252 GCTACAGTAACCAAAACAGCATAGTACTGGTACCAAAACAGATATATAGA 5301
                                   i   i    ii i       i iv ii i   i       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_16716726_   5302 CCAATGGAATAGAACAGAGGCCTCAGAGATAACCTCACACATCTACAACT 5351
                         i             iv   ivii    i    v i  i    i  iiiii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_16716726_   5352 ATCTGATCTTTGACAAACCTGACGAAAACAAGAAATGGGGAAAGATC--T 5399
                          vi    i  i     ivv  v i i v  vvv            vi-- 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_16716726_   5400 CCTGTTAATAAATGGTGCTGGGAAAACCGGCTAGCCATGTGTAGAAAACT 5449
                          i v i  i              v   i  v  ?   ii  i i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_16716726_   5450 GAAACTACATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATAGA 5499
                            ii iv i    v   i     v              i    i  i  
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_16716726_   5500 TTAAATACTTAGATGTTAGACCTACAACCATAAAAACCCTAGAAGGAAAC 5549
                          i ? v  i  i    v   v   v   i      vi i      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_16716726_   5550 CTAG---TCAATACCATTCAGAACATAGGCATGGGCAAGGACTTCATGAC 5596
                         v   --- v   -- -   ivi  v v  vv i     v ii   v iiv
  L1M4_orf2#LINE/    547 ATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_16716726_   5597 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATC 5646
                           vi            vvi          vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_16716726_   5647 TAATTAAACAAAAGAGCTTCTGTACGGCAAAGTAAACTACCATCAGAGTG 5696
                          v  i   vvv  i i   i   i vv     v v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_16716726_   5697 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 5746
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_16716726_   5747 CAAAGGACTAATATCCAGAATCTACAAAGAAATCGAACAAATTTACAAGA 5796
                         i  i     vi          v  i      v  vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_16716726_   5797 AAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5846
                             i     i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_16716726_   5847 TTCTTCAAAGAAGACATTTGAAATGCAGCCAACAGACACGTGAAAA-ATG 5895
                             i         i  vi-     --     i ii   i      -   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATAC-AAATG--GCCAATAAGCACATGAAAAGATG 890

  chr20_16716726_   5896 CTCATCATCACTGGTCAT 5913
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


2422 27.88 3.36 1.68  chr20_16780671_16784929.rev     2875  3767 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_16780671_   2875 TGGAAACACATCTTATACCCACAGATGGGTAGAATCAACATTGTCTAAAT 2924
                               v i   ii  iii  ii   v  v   v i  i     iv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_16780671_   2925 GACCATACTGACATATTGCCAAAAGCAATCTATAAATTCAATGCAATTTC 2974
                          i v     -- ------  v   vii     i i      i     ii 
  L1M4_orf2#LINE/     51 GGCAATACT--C------CCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chr20_16780671_   2975 CATCAAAATACTATCATCATTCTTCACAGAACTAGAAAAAC--ACCCTAA 3022
                         i        v i v vv v  i  ii     v v  v  i -- i     
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA 142

  chr20_16780671_   3023 AATATATACAGAA-T-CAAGGAGGAGCCCACATACCCAAAGCAA----GA 3066
                            vi   ii   - -     --  v  viv   v     i   ----  
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGA 190

  chr20_16780671_   3067 CTAAGAA----AAAG-----------ATAC---CTGACTTCAAA--CTAC 3096
                         vv     ----    ----------- i  --- ii i      --i   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr20_16780671_   3097 AGTATAAGGCTAAAGTCACCAAAACAGCATGGTACTGGCATAAAAACAGG 3146
                         --  i  i    v   v i   i    ii              ii i  i
  L1M4_orf2#LINE/    241 --TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA 288

  chr20_16780671_   3147 CACATAGACCAAGGGAACTGAATAGAGAACCCAGAAATAAACCCAAATAC 3196
                           i     i   v    iv    v    ii               v i i
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr20_16780671_   3197 TTAACAGCCAACTGATCTTCAACAAAGCAAACAAAAACAGAGAGTGGGGA 3246
                            -ii i   i    i   i    i vviv   i v  vvv i      
  L1M4_orf2#LINE/    339 TTA-TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr20_16780671_   3247 AAGGGCACCCTATTCAACAAATGATGCCAAGATAATTGGCAAGCCATATG 3296
                            iii vi  v           i   iii  i  i   vv ?   i   
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG 437

  chr20_16780671_   3297 TAGAAGAATGAAACTGGATCCTCCACTCCCACCATACACAAAAATCAAGT 3346
                         i i         ii    i  iivv   v       i        i  v 
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr20_16780671_   3347 AAAGATGGATCGAAGACTTAATCCTGAGACCTGAAACCATAACAATTCT- 3395
                         v  i       i?    i   viv i   v  i    i    -  i   -
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-AACTCTT 536

  chr20_16780671_   3396 AGAACATAACATTGGAAAAACCCTTCTAGACATTGGCTTGGGCAAAGACT 3445
                             v v     v  ?iv  vi    vv   v    v  i     v ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_16780671_   3446 TCATGACCAAGAACCCAAAAGCAAATGCAACAAAAACAAAGCTAAATAGA 3495
                           v iivi v  vv         v v         iv   iv  i   i 
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr20_16780671_   3496 TGGGACTTAATTAAA-CTACTAGTTCCTGGTCAGTAAAATAAATAAACAG 3544
                          v      v  i   -i  vv ii ii  vv vvi   iv v iv v  i
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr20_16780671_   3545 CAGAGTAAACAGACAACCCACAGAGTGGTAAAAAGTCCTCACAAACTATG 3594
                         v i   i  v              i   v i   i vi ii    ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr20_16780671_   3595 TATCCAACAAAGGACTAATATCCAGAATCTACAAGGAACTCAAACAAATC 3644
                             ii i  i     vi          v  i  i      vv    v  
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr20_16780671_   3645 AGCAAGAAAAAAACCAAATAATCCCATCAAAAAGTTGGCTAAGGACATGA 3694
                          ii  v     i  -      i  v  i?    i v   v     iv   
  L1M4_orf2#LINE/    787 AATAATAAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr20_16780671_   3695 ATAGACAATTTTCAAAGGAAGATACGCAAATAACCAACAAACATATGAAA 3744
                                v  i  v  i       ii     ii    i  i  i      
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr20_16780671_   3745 AAATGCTTAACATCAGTAATTGT 3767
                          i     i       ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (150 / 95)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.65 (45 / 17)  


2816 28.81 0.55 0.33  chr20_16800162_16802359.rev      801  1706 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_16800162_    801 TGGAAAAACATTCCATGCTCGTGGATAGGAAGAATCAATATAGTGAAAAT 850
                               i i  i     i  i     v      v i     v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_16800162_    851 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATTTCCCTTAAAC 900
                            v     v      v i  i  i        i  v  ii iv i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_16800162_    901 TACCATTGACATTGTTTACAGTATTAGAAAAAAAAACTTTAAAATTCATA 950
                          v   vivi v  v   i   v v v  v  ivvi iii           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_16800162_    951 TGGCACCAAAAAAGAGCCTGTATAGCCAATAGAAGCCTAAGCAAAAAGAA 1000
                            v viiv  ii  v  v v        v v  v i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_16800162_   1001 CATAGCTGGAGACATCACACTACTTGACTTCAAGCTATACTGCAAGGCTA 1050
                           v  i     ivv       v iii i     iviv    i   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_16800162_   1051 TAGTAACCAAAATAGCATGGTACTGGTACCAAAACAGAGACATA--CCAA 1098
                         i     i   i i  ii         i iv ii i   v i   --i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_16800162_   1099 TGGAACAGAATAGATATCTCAGAAATAATACAACAAATCTACAATCATCT 1148
                              i     v  v vii         vv v i v  i  iii   vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_16800162_   1149 GATTTTTAACAAACCTGACAAAAACAAGCAATGGAGAAAGGATCCCCTAT 1198
                               ii    ivv  v   i v  vv      i     i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_16800162_   1199 TTAATAAATGGTGCTGAGAAAACTGGCTAGCTATATGCAGAAAATTGAAA 1248
                          i  i           i  v      v  ? i i     i  i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_16800162_   1249 CTAGACTCCTTCCTTATACATTATAGAAAAATTAACTCAAGGTGGAGTAA 1298
                         i i   i   v   i i  vv    v              ii    vi ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_16800162_   1299 AGACTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGAAAATCTAG 1348
                             i         i v i            vi i          iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_16800162_   1349 GCA-ATACCATTCAGGACATAGGCACGGGCAAAGATTTCATGACAAAAAC 1397
                          ?i- v i -   iv   v v  vvii     v i    v iivv vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_16800162_   1398 ATCAAAAGC-CATTGCAACAAAAGCCAAAATTGACAAATGGGATCTAACT 1446
                          i       -  v-          vv     v  i    v   ii v ii
  L1M4_orf2#LINE/    600 ACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_16800162_   1447 GAACTAAAGAACTTCTGCGCAGCAAAAGGAAATATCATCAGAGTGAACTG 1496
                         i  v v  i     i  i  vv    i iv v     vv i      vv 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_16800162_   1497 ACAACCTACAGAATAGGAGAAAATTTTTGCAGTCTATCCATCTGAGAAAG 1546
                               i       i         v      ivii  vi      v  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_16800162_   1547 GCCTAACATCCAGAATCTACAAGGAACTTAAAAAAATGTACAAGAAAAAA 1596
                          v  vii         v  i  i     ivv v  v vv i  v     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_16800162_   1597 GCAAAGAACCCCATCAAAAACTGGGCCAAGTAATATGAACAGACACTTCT 1646
                         i    v     v  i?    v     v   -i  v    i     i    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAG-GATTTGAATAGACATTTCT 847

  chr20_16800162_   1647 CAAAAGAAGACATATATGCATCCAACAAGCATATGAAAAAA-GCTCAACA 1695
                          v        i   i viiiv    i     i       i -        
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_16800162_   1696 TCACGGATCAT 1706
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.22 (141 / 116)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


3140 25.22 1.55 1.11  chr20_16817768_16823161     3999  4902 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_16817768_   3999 TGGAAAAACATTCCATGTCCATGGATAGAAAGAATCAATATTGTTAACAT 4048
                               i i  i      i       v i    v i           v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_16817768_   4049 GGCCATACTGCCCAAAGCAATTTATAAATTCAATGCTATTCCCATTAAAC 4098
                            v     v      vii  i  i i      i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_16817768_   4099 TACCATTGACATTCTTCATAGAATTAGAGAAAAAACT-ATTTTAAAATTT 4147
                          v   vivi v  i  iii    v v  v  i---  -  ii       i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr20_16817768_   4148 ATGTGGAACTGAGAAAGAGCCCAGA-TAGCCAAGACAATCCTAAGCAAAA 4196
                           i     v  vi ii  -      -       i      i i i-   i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAA-AAAG 195

  chr20_16817768_   4197 AAGAACAAAGCCGGAGGCATCACCCTACCCAACTTCAAACTATACTACAG 4246
                                   ii     vv    v  v     i      viv       i
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_16817768_   4247 GGCTACAGTAACCAAAACAGCATGATACTGGTTAAAGAACAGACACATAG 4296
                         i          i   i    ii  i      ivv   i i     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_16817768_   4297 ACCAATGGAACAGAAT--AGAGTTCTCAGAAATAATACCACACACATACA 4344
                          i        i     --     i --        vv   i   iv  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr20_16817768_   4345 ACTATTTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGAC 4394
                         iii v     i   i    ivv  v   i v  vv            i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_16817768_   4395 TCCCTATTCAGTACATGGTGTTGGAAGAATGGGCTAGCCATATGCAGAAA 4444
                         vvi  v    ii v      i   i v  iv  v  ?   i     i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_16817768_   4445 ATTGAAACTGGACCCTTTCCTTACACCATATA-AAAAATTACCTCAAGAT 4493
                          v    ii       i v   i          -        v     i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_16817768_   4494 GAATTAATGACTTAAATTTTAAACCCAAAACTATAGAAACCCTAGAGGAA 4543
                          i  i ?v   i     v v i v i         i  vi i    i   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_16817768_   4544 AACCTAGGCA-ATATCATTCAGGACATAGGCATGGGCAA--GTATTTTAT 4590
                            v    ?i- v   -   iv   v v  vv i     --  v i   -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA- 591

  chr20_16817768_   4591 GACAAAGATGCCAAAAGCAATTGCAACAAA-GCAAAAATTGACAAATGGT 4639
                           i v-  ii         vvv        - v      v  i    v v
  L1M4_orf2#LINE/    592 GATAT-GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_16817768_   4640 ATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAGGA-ACTATCAACAGA 4688
                          ii v  i   v v  i i   i  ii vv       -        v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_16817768_   4689 GTAAGCACACAACCTACAGAATGGGAGGACATTTTTGCAAACTATGCATC 4738
                           i iv v      i            i v  v        ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_16817768_   4739 TGACAAAGGTCTAATATTCAGGATCTATAAGGAACT--TA-AACACATTT 4785
                            i  i  v  vi   i   i  v     i     --  -   v  v v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_16817768_   4786 AGAAGAAAA-AAACAACTTCATTAAAAGGTGGGCAAAGGACATGAACAGA 4834
                          v  i  i -   i   iiv   ?   ii           iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_16817768_   4835 CACTTCTCAAAAGAAGATATACATGCGGCCAAAAATCATATGAAAGGAAG 4884
                           i     v              vii      v  v  i      i  v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr20_16817768_   4885 CTAAACATCACTGATTAT 4902
                           v       ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (133 / 91)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 1.33 (24 / 18)  


3192 25.89 1.23 0.67  chr20_16836331_16842722.rev     5005  5900 (492)    L1M4_orf2#LINE/L1        8   908 (0)  

  chr20_16836331_   5005 ACATTCCATGTTCATGGATAAGAAGAATCAATATCATGAAAATGGCCATA 5054
                          i  i              vi     v i     ii v  i     v   
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr20_16836331_   5055 CTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATCAAG---CTA-- 5099
                           v     iv i  i  i        i iv     i     i--- i --
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr20_16836331_   5100 TGACTTTCGTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCACATGGA 5147
                           v    i- ii     -   -- v  i  - iii    i    i     
  L1M4_orf2#LINE/    108 TGCCTTTT-TTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGA 154

  chr20_16836331_   5148 ACCAAAAAAGAGCCTGTGTTGCCAAGACAATCCTAAGCCAAAAGAACAAA 5197
                          viiv  ii  v  v vi v     i      i i ivv i         
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr20_16836331_   5198 GCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGT 5247
                          i      vv       v  ii i      viv        i        
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr20_16836331_   5248 AACCAAAACAGCATGGTACTGGTACCAAAACAAAGATATAGACCAATGGA 5297
                           i   i    ii         i iv ii i i v       i       
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr20_16836331_   5298 ACAGAAC--AGAACCCTCAGAAATAATACCACACATCTACAACCATCTGA 5345
                          i    i--   ii  --        vv   i    i  iiii  vi   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_16836331_   5346 TCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTC 5395
                          i  i     ivv  v   i v  vvv           i  vvi  v   
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr20_16836331_   5396 AATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACTGAAACT 5445
                           i              v      v  ?   i   i i  i v    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr20_16836331_   5446 GGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTA-AG 5494
                            i    v   i     v              i    i      i -  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr20_16836331_   5495 ACTTAAATGTTAGACTTAAAACCATAAAAACCCTAGAAGAAAACCTAGAC 5544
                           i       v   vi      i      vi i           v   i?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr20_16836331_   5545 A-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACAC 5593
                         i- v i -   iv   v v  vv i     v ii   v ivv  vi    
  L1M4_orf2#LINE/    553 GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_16836331_   5594 CAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAATTAAA 5643
                                 vvi          vv     v  i    vi  ii v  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_16836331_   5644 CTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCA 5693
                         v v  i i   i  ii vv    i  v    i  vv i      v  i  
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr20_16836331_   5694 ACCTACAGAATGGGAGAAAATTTTTGCAATCTGCTCATCTGACAAAGGGC 5743
                            i                 v       viiiivi      i  i  i 
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr20_16836331_   5744 TAATATCCAGAACATACAAAGAACTCAAACAAATTTATGAGAAAAAAACA 5793
                          vi         i   i         vv    v iv  i v     i   
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr20_16836331_   5794 AACAACCCCATCAAAAAGTGGGCGGAGGATATGAACAGACACTTCACAAA 5843
                           i     v  i?    i     ii     v    i     i   v v  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr20_16836331_   5844 AGAAGACATTTATGCAGGCAACAAACACATGAAAAAATGCTCATCATCAC 5893
                               i  vi viii v   i  i          i       v     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr20_16836331_   5894 TGGCCAT 5900
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.57 (140 / 89)
Gap_init rate = 0.01 (11 / 901), avg. gap size = 1.55 (17 / 11)  


2874 24.10 3.61 4.16  chr20_16944014_16946078.rev      661  1573 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_16944014_    661 TGGAAATACATGCCTTGTTCATGGATCAGAAAAATCAATATTATTGAAAT 710
                               v i  v  v           ii   i v i      i  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_16944014_    711 GTCCATAGTAC--AAAGTGATCTATGGAATCAATGCAATCCCTAAGAAAA 758
                          v v   v v --   v       ii  v    i          vv    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_16944014_    759 TTCAAATAACATTTTTCATAGAAATTAAATAAAAAAAATCCTAAAATTTG 808
                          i v iivi v     iii       i v--  ivvi           ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGAC--AAGCTGATCCTAAAATTCA 148

  chr20_16944014_    809 TTTGGAACCAGAAACAATCCATAATAGCTGAAGCAATCTGTAGGAATAAG 858
                          v     viiv  ivi i   v      ii  i      vv ii  v   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_16944014_    859 AACAAAGCTGGAGGCCTCACACTATTTGACTTCAAAATGCACTACAAAGC 908
                                i      v        viiii i       ivi          
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_16944014_    909 TATACTAATCAAAGCAGCATGGTACTGGAACAAAG-CAGACATATAGGCC 957
                           i v       ii   ii         v i  i -i          ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_16944014_    958 AATAGAATAGAATAGAAGGCCCA-AAATAAGGCCATGCCTTTACAGTCAA 1006
                            i         v  ii i   -      iv    i v    ii     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_16944014_   1007 TTGATCATTGGTAAAGGTGCCAAGAATATACAATGAGGGAAAGAGT---- 1052
                              iv i ii  i          vi  v     -        i ----
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTC 397

  chr20_16944014_   1053 --TTTAATAAATGGTGTTGGGCAAACTAGGACATCCACATGCGGAAGAAT 1100
                         --  i  i        i    vv    -   i ?        ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACT-GGATAKCCACATGCAAAAGAAT 446

  chr20_16944014_   1101 GGAATTTAAACTTCATGTCACCCCATATA-AAAAATCAACTTAAAA---- 1145
                          i i  vi v iii iv    v       -      i    i    ----
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_16944014_   1146 ----AGATTTAAATGTAAGACCTGAAACTACTATAAAACTACTAGAAGAA 1191
                         ----   ii           v  i      ---       vi        
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTA---TAAAACTCTTAGAAGAA 543

  chr20_16944014_   1192 AAAACATGAA-AAACTTTCTTAGCATTGGTCTCAGCAATGATGATTTTGG 1240
                           v i v ?i-   ii   v ii v    vi vi      i v- i  i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT-TCTTAG 592

  chr20_16944014_   1241 ACGTGACCCCAAA-GCCCAGGAAA-AAAAGCAAAAATATACAAATTAGAT 1288
                          ii    v     -  v  i v  -     v       v i     i  i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr20_16944014_   1289 TGCATCAAACTAAAAAGCTTCTGCACAGCAAAAGAAACAATCAACAGAGT 1338
                          v       v v    i   i  ii vv    i  v  v     v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr20_16944014_   1339 GAAGAGACAACCTACAGAGTAAGAGAAAATATTGGCAAACCATACATACA 1388
                            i        i     i ii           v     i    i  ---
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT--- 739

  chr20_16944014_   1389 TCTGATAAAGGTTTAATATCCACAATATGTCAGGGACT---ATAAC---- 1431
                         -       i  vi vi      v     i v i i   --- i   ----
  L1M4_orf2#LINE/    740 -CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_16944014_   1432 -AATAGAACAGCACAAAA---AATTTTTAAATTGGCAAAGTTCCTAAATA 1477
                         -    i  vii  v v  ---    ?vv    v       vvii i    
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr20_16944014_   1478 GACATTCCTCAAAATGTCTATTTTGGGACATTGGGGTGGGAGAGACATAG 1527
                               i   v   -------------------------  -   i   v
  L1M4_orf2#LINE/    839 GACATTTCTCCAAA-------------------------GA-AGATATAC 862

  chr20_16944014_   1528 AAATGTCCAGTAGGCATATGGAAAAATGCTCAACACCACTAACCAT 1573
                              v   i  i   i   i   i          i  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (136 / 81)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.55 (71 / 20)  


2996 26.06 1.53 1.65  chr20_17038426_17040821.rev      688  1535 (861)    L1M4_orf2#LINE/L1        1   847 (61)  

  chr20_17038426_    688 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATTATTAAAAT 737
                               i i  i     i        v      v i      i    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_17038426_    738 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTGTTTCTATTAAGC 787
                            v     v      vii  i           i  vi ii    i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_17038426_    788 TATCA-TTGACAGACATTCTTCACAGAACTAGAAAAAACT-ATTTTAATA 835
                          vi  -i  v -----  i  ii     v v  v  i-  -  ii   v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-----TTTTTTGCAGAAATTGACAAG-CTGATCCTAAAA 144

  chr20_17038426_    836 TTCATATGGAACTAGCAAAG-ACCCTGAATAATGAAGACAATCCTAAGCA 884
                                    v -    i -    v     iiv  i      i i iv 
  L1M4_orf2#LINE/    145 TTCATATGGAAAT-GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr20_17038426_    885 AAAAGAAAAAAAGCTAAAGGCGTCATGCTACCTGACTTCAAACTATATTA 934
                          i     v   - i ii   vv   ii  v  ii i      viv  i  
  L1M4_orf2#LINE/    194 AGAAGAACAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr20_17038426_    935 CAGGGTCATAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACA 984
                           ii ii i     i   i    ii         i i  ii i     i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr20_17038426_    985 TAGACCAATGGAACAGAATAGAAAACCCAGAAATAAGACCGCACACCTAC 1034
                             i        i     v  i ii          iv  ii   ii  i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr20_17038426_   1035 AACTATCTGATTTTTGACAAGCCTGACAAAAACAAGCAATAGGGGAAAGG 1084
                         iiii vi       i      vv  v   i v  vv    -        i
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGA 391

  chr20_17038426_   1085 ATTCTCTATTCAATAAATGGTGCTGGGGTAACTGGCTAGCCATATGCAGA 1134
                           vv   v     i             ii      v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_17038426_   1135 AGATAGAAACTAGACCCCTTCCTTACACCACATACAAAAATTAACTCAAG 1184
                            vv   ii i       v   i      i                  i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_17038426_   1185 ATGAGTTAAAGACTTAA-TGTGAAATACAAAACTATGAAAACCCTGGAAG 1233
                            ii i ?    i   -   i i vvi        i   vi i i    
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_17038426_   1234 ACAACCTAGGCATTACCATTCTGGATATAGGAATGGGCAAAGATTTCAT- 1282
                          v   v    ?i v viv   vv  iv v  iv i     v i    v -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_17038426_   1283 GATGAAGATGCCAAAAGCTATTGCAACAAAAGCAAAAATTGACAAGTGGG 1332
                            - v  ii        vvvv          v      v  i  i v  
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_17038426_   1333 ATCTAATTAAACCAAAAAGCTTCTGCACATCAAAAGAAGCTATTAACAAA 1382
                          ii v  i   viv    i   i  ii v     i  vi    i  v   
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_17038426_   1383 GTAAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAAATTATGCATC 1432
                           i  v        i                 v         i  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_17038426_   1433 CAACAAAAGTCTAATATCCAGCATCTATAAGGAAGTTAAGTTTACAACT- 1481
                         ii i  ii v  vi       v  v     i   v i----        -
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTC----TTACAACTC 786

  chr20_17038426_   1482 ----ATAAAA---CAAGCAACCCCATTAAAAAGTGGGCCAAGGATATGAA 1524
                         ----      ---   ii     v   ?    i     v      v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_17038426_   1525 CGGACACTTTT 1535
                         ii    i  i 
  L1M4_orf2#LINE/    837 TAGACATTTCT 847

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.02 (14 / 847), avg. gap size = 1.93 (27 / 14)  

 311 22.37 0.00 0.00  chr20_17038426_17040821.rev     1830  1905 (491)    L1M4_orf2#LINE/L1      833   908 (0)  

  chr20_17038426_   1830 TGAATGGACACTTTTCAAAAGAAGACATACATGCAGCCAACAATCATATG 1879
                              i    i  i  v        i     viii     i  v  i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_17038426_   1880 AAGAAAAGCTCAATATCTCTCAATAT 1905
                           i i v      i   v????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.00 (0 / 0)  


1107 25.23 1.20 0.30  chr20_17043688_17050063.rev      170   502 (5874)    L1M4_orf2#LINE/L1      466   801 (107)  

  chr20_17043688_    170 ATACCCCACAAAAAAATTAACTCAAAATGGACAATAAATGTAATTGTACA 219
                          i   vi i v                    iv ? i iv   v    vi
  L1M4_orf2#LINE/    466 ACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr20_17043688_    220 ATGC-AAAATTGTAAAACTTCTTGAATAAAACATAAGAAAAAATCTACAT 268
                          -  -    i i       ii v   v        i ?iv      v i 
  L1M4_orf2#LINE/    516 A-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr20_17043688_    269 GACCTTAGGTTTGGAGATGAGGTTTTAAATGCAATACTAATAGCATAATC 318
                               i    v  vi   ivv i   i  iii i  i  v    i  v 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr20_17043688_    319 CACACAC-AAAAAAT-GATACTTTGGACTTCATTAAAATTAAAAACTTAT 366
                         v   v v-       -    vv           i              v 
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr20_17043688_    367 TTTCTGTGAAAAAGACTATTTTGAGAGAAAAAATACAAGCCACAGACTGG 416
                         v v  vii  ii v     ivv  i  vi    v    v       v   
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr20_17043688_    417 GAGAAAATGTTTATAAAACACTTATCTGATAAATAACTTGTGTCCAAAAT 466
                                 i   ii   v  iv          ivi      i    i   
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr20_17043688_    467 ATACAAAGACCTCTTAAAATTTAACAATAAAAA-ACA 502
                            i     v      v  i i  i        -   
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

Transitions / transversions = 1.22 (45 / 37)
Gap_init rate = 0.01 (5 / 336), avg. gap size = 1.00 (5 / 5)  

3169 27.35 1.11 0.55  chr20_17043688_17050063.rev     4982  5884 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_17043688_   4982 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5031
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_17043688_   5032 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 5081
                            v     v     iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_17043688_   5082 TACCAATGACTTTCTTCACAGAG-TTGGAAAAAACT-ACTTTAAAGTTCA 5129
                          v   iivi i  i  ii    i-   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_17043688_   5130 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAGTCCTGAGCCAAAAG 5179
                                viiv  ii  v  v v  v     iv  i  i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_17043688_   5180 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAAGC 5229
                                i      vv    i  v  ii i      viv           
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_17043688_   5230 TACAGTAACCAAAACGGCATGATACTGGTACCAAAACAGAGATATAGATC 5279
                                 i   i  i ii  i      i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_17043688_   5280 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGGATATCTGCAACT 5327
                                i    i--    i  --        vv  iv i  i iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_17043688_   5328 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5377
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_17043688_   5378 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5427
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_17043688_   5428 GAAACTGGATCCCTTCCTTACACT-TATACAAAAATTAATTCAAGGTGGA 5476
                            ii    i    v   i    i-              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_17043688_   5477 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5526
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_17043688_   5527 CTAGGCA-ATACCATTCAGGACATAAGCATGGGCAAGGATTTCATGTCTA 5575
                         v    ?i- v i -   iv   v vi vv i     v i    v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_17043688_   5576 AAACACCAAAAGCAATGGCAACAGAAGCCAAAATTGACAAATGGGATCTA 5625
                         vi            vvi      i   vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_17043688_   5626 ACTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5675
                          ii   v i  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_17043688_   5676 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5725
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_17043688_   5726 AAGGGCTAATATCCAGAATCTACAATGAACTCCAATAAATTTACAAGAAA 5775
                          i  i  vi          v  i  v      iv i  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_17043688_   5776 AAAACAA----CCCCATCAAAAAGTGGGCAAAGGACATGAACAAACACTT 5821
                           i    ----   v  i?    i           iv    i i   i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_17043688_   5822 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5871
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_17043688_   5872 CATCACTGGCCAT 5884
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (152 / 91)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.67 (15 / 9)  


3178 26.27 1.44 0.78  chr20_17084332_17087087.rev     1363  2264 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_17084332_   1363 TGGAAAAACATCTTATGCTCATGGATTGGAAGAATTAATCTAGTCAAAAT 1412
                               i i   ii   i               v     v v  i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_17084332_   1413 GACCACACTGCTCAAAGCAATCTACATATTCAGTGTAATTCCTATCAAAA 1462
                          i v i   v i    vii       v     ii i   i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_17084332_   1463 TATCAGTATCATTTTTCACAGAAGTAGAAAAAAAAATCCTAAAATTTGTA 1512
                          vi   ivv v     ii     i v  v  ivvi           ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_17084332_   1513 TGGAACCAAAAAAAGCCCA-AATAACCAAAGCTACCTGGAGCAAAAAGAA 1561
                              viiv  iiii    -    i     i v i  v  iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_17084332_   1562 CAAAGCTGGAAGGATTACACTGTCTGATTTCAAAACATATCACCAGGCTG 1611
                              i    i iv i     vi ii          v  ii  v i   i
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_17084332_   1612 TAGTAACGAAAACCATAT----TT---ATAAAAATAGATATGTAAACCAA 1654
                         i     iv  i  vi i ----i ---    ii     i  i  i i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_17084332_   1655 TGGAATAGGATAGAGAACATATAAATAAATCCGTGTATTTACAGCCAACT 1704
                                 i  v    iivi v       i  i ii     ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_17084332_   1705 GAGATTTGCCAAAGCTGCCAAGAATATAAACTGGGGAATGGATACCCTCT 1754
                           vv  i v   i v        vi  vv v       v i   vi  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_17084332_   1755 TAAATAAGTGGCGCTGGGCAAACTGGATAACCATATGCAAAAGAATGAAA 1804
                          v  i  i   i      vv         ?   i               i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_17084332_   1805 CTGGGTCCCTATGTCTCATCATGCACAAAAATCAACTCAAGATGGACTAA 1854
                         i   ii     iv  v  i   ii        i       i     ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_17084332_   1855 AGACTTACATGTAAGACCCAAAACTATAAAACTATTAGAAGAAAGCATAG 1904
                             i  v        v i              v          i     
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_17084332_   1905 GA--AAAACTTCA-AAAATCACTCTAGGCAAAGATTTTATGGATAAGACT 1951
                          ?--   v    i-i vv iivvi       v i   iv i    v   v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_17084332_   1952 GCAAAAGCACAGAAAACAAAAATAAAAGTAGATAAATGGAACTATATTAA 2001
                         v          iiv       iv    i         v i   vi  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_17084332_   2002 ACCAGAAACCTTCTGTACAGCAGAAGAAACAATTAACAGAGTGAAGAGAC 2051
                          vivi   v   i   i vv  i i  v  v  i  v i      i    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_17084332_   2052 AACCTATTAAATGGGAGAAAATATTTTCAAATTACTCATCAGACAGGCGA 2101
                             i ivi                 v     i ivi   v  i i v  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_17084332_   2102 CTGATATCCAAAAAATACAAGGAACTCAAACAACTAAACAGTGAAAACAA 2151
                           vi      i  v   i  i      vv      v  i i i    v v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_17084332_   2152 AAAAAGTC--ACTAAAATATGGGCACAGGACATATTTTGAGAATAGACAT 2199
                            v ii -- i ?   v       v    -----     --        
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGA-----TTTGA--ATAGACAT 843

  chr20_17084332_   2200 TTCTCAAAAGACCACATACACATGGCCAACAGGTTTATGAAAAAATGCTC 2249
                              v     vv i     v        i i ivi       i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_17084332_   2250 AACATCACTAACCAT 2264
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (144 / 89)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.50 (20 / 8)  


2634 27.22 2.84 2.01  chr20_17109324_17114757     4090  4934 (500)    L1M4_orf2#LINE/L1        4   855 (53)  

  chr20_17109324_   4090 AAAAAAATTTCATGCTCATAGATAGGAAGAATCAAGATTTTTAAAATGGC 4139
                            i v  ii    i    i   v      v i  v   v    i     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr20_17109324_   4140 CACATTACCCAAAGCAATTTACAGATTTAGTGCTATTCCTATCAAACTAC 4189
                         v i i v      vii  i        i ii  v  i         v v 
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_17109324_   4190 CAATGACATTCCTCACAGAATTAGAAAAAAAAAACT-ATTTTAAAAATCA 4238
                           iivi v  ii ii     v v  v  i-----  -  ii     v   
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG-----CTGATCCTAAAATTCA 148

  chr20_17109324_   4239 CATGGAACCAAAAAAGGCTT-GAATAGTTAAGGTAATTCTAAGCCAAAAA 4287
                         i      viiv  ii i ii-      ii  iii   ii i --------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-------- 190

  chr20_17109324_   4288 AAAAAAAAAAACAAAGCTGGAAGAATCATGTTACCCAACTTCAAACTATC 4337
                         -    i  i       i    i  v   iii v     i      viv v
  L1M4_orf2#LINE/    191 -AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_17109324_   4338 TTACAAGGCTATAGTAATCAAAACAGCATGGTACTGGTGCAAAAACACTC 4387
                         i     i    i         i    ii         iii  ii i vv 
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr20_17109324_   4388 ACATAGACCAATGGAAAAGAATAGAGAACCCAGAAATAAACCTGCACACC 4437
                          i     i        v     v    ii             iii   ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr20_17109324_   4438 TACAATCTTCTGATCTTTGTCAAAGTTGACCAAAAAGAA-CAATGGGGAA 4486
                           iii  vvi    i  i v   i v  -    i vv v-          
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAA 388

  chr20_17109324_   4487 ATGATTTTCTATTCAACAAATGGTGCTGGAGTAACTGGCTAGCCATATGC 4536
                          vi  vv   v                  iii      v  ?   i    
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr20_17109324_   4537 AGAAGACTGAAGCTAGACCTCTTCCTTACACCATAAACAAAAACTAACTC 4586
                          i    v     i i    i  v   i        v       i      
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr20_17109324_   4587 AAGATCAATTAAAGACTTAAATGTAAAACCTGAAACTATAAAACCCT-GG 4635
                           i  vi  i ?    i         i v  i            i  -i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr20_17109324_   4636 AAGATAACCTAGGAG-----CCTAGCAA----AGATT---TAATGAC--- 4670
                             v   v    ? ----- i v ii ----i i  ---i    ii---
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_17109324_   4671 --AAATA---CACCAAAAGCAATTATGACAAAGACAAAAATTGACAAAGA 4715
                         -- i   ---           vvviii     iiv      v  i   vv
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_17109324_   4716 GGACCTAATTAAACTAAAGAGCTTCTGCACAGTTTAAAAGAAACTACCAA 4765
                             i v  i   v v  i i   i  ii --  i   i  v    i   
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGC--TTCAAAGGACACTATCAA 686

  chr20_17109324_   4766 GAAAATAAACAGACAACATACAGAATGGGAGAAAACATTCACAAACTATG 4815
                             i i  v       vi                i   ii    ii  i
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr20_17109324_   4816 CATCTGACAAAGGTCTAATATCCAGTATCTATACGGAACTTAAACAAATT 4865
                         i      i  i  v  vi       v  v    vi     ivv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr20_17109324_   4866 AACAAGCAAAAATCAAACAACCCCATTAAAAAGTGGGCAAAGCACATGAA 4915
                           i  vv    iv    i     v   ?    i         v iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_17109324_   4916 CACACAATTTTCAAAAAAA 4934
                         i v   v  i  v   i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAA 855

Transitions / transversions = 1.90 (148 / 78)
Gap_init rate = 0.02 (13 / 852), avg. gap size = 3.15 (41 / 13)  

 598 25.60 0.00 0.00  chr20_17109324_17114757     5267  5434 (0)    L1M4_orf2#LINE/L1      673   840 (68)  

  chr20_17109324_   5267 AAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGAAGAAAAT 5316
                           i  v    i  vv i      v  i     i         i       
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_17109324_   5317 GTTTGCAATCTACCCATCTGACAAAGGGCTAATATCCAGAATCTACAAAG 5366
                         i       vii ivi      i  i  i  vi          v  i    
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_17109324_   5367 AACTTAAATAAATATACAAGAAAAAATCAAACAACCCCATCAAAAAGTGG 5416
                             ivv i  v vv i  v     iv    i     v  i?    i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_17109324_   5417 GCAAAGGATATAAACAGA 5434
                                  v i  i   
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGA 840

Transitions / transversions = 1.47 (25 / 17)
Gap_init rate = 0.00 (0 / 168), avg. gap size = 0.00 (0 / 0)  


2350 24.51 2.92 0.00  chr20_17148756_17150363.rev      501  1116 (492)    L1M4_orf2#LINE/L1      275   908 (0)  

  chr20_17148756_    501 GACATAAA-ACATACACATAGACCAATGGAACAGAATACAGAACCCAGAA 549
                          i     i- i v   i     i        i     vv   ii      
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr20_17148756_    550 ATAAATTCATGCATTTATAGCCAAATCATTTTTTATGAAGGTGCCAAGAA 599
                              ii   i       i i   v v     iv ii i          v
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr20_17148756_    600 CACACGTTGGGGAAACGATAGTTTCTTCAATAAACGATGCTGGGAAAACT 649
                           iv iv        vi     i i     i   i i        v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr20_17148756_    650 GGATATCCACATACAGAAGAATGAAACTAGTCTCCAATCTCTCAGCATCT 699
                              ?      i  i         ii i v i  v i   v  v   v 
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr20_17148756_    700 AAAAAAATCAACTCTACATGTATTAAAGATGTAATTGTAAGACCTGAAAC 749
                          v      i     v v   v  i ?   iv   v       v  i    
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr20_17148756_    750 TAC--------TAGAAGAAAATATAGGTGGAATGCATCTTGAAATTGGGC 791
                           i--------          i     ? v  vv v  v   vv     i
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr20_17148756_    792 TAGACAAGAAGTTTTTAAATAAAAACTCAGAAGCACAGGCAACAAAAGCA 841
                            i   viiv  i   i   vi vvi  i       i          v 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr20_17148756_    842 AAAACAGACAAAA-AAATTACATTGAACTAAAAAGCTTCTGCCCAGCAAA 890
                             i   i   v-ii i v   ii  v v    i   i  iv vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr20_17148756_    891 AGAAAC----AATAGAGTGAAGAAACAACCTACAGAATGGGAGAAAATAT 936
                         i  v  ----  v i      i i      i                   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr20_17148756_    937 TTTCAAACTATGTGTCTGACAAAGGGTTAATATTCTGAATATATAAGGAA 986
                           v    ii  i i     i  i  ii vi   i v          i   
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr20_17148756_    987 CTC----AACTCAATAGCAAAAAATCAAATAAACTAATTTAAAAATGGAC 1032
                            ----         ii     iv       v i    ?        i 
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr20_17148756_   1033 AAAAGGACTGAACAGACATTTCTCAAAAGAAGACATATATATGGCCAACA 1082
                            i ivi    i           v        i   i v        i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr20_17148756_   1083 GATGTATGAAAAACTGCTCAACAACATGAACATC 1116
                         iiiii       iv         v  ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (92 / 55)
Gap_init rate = 0.01 (5 / 634), avg. gap size = 3.60 (18 / 5)  


3612 17.87 7.42 2.09  chr20_17182113_17185280.rev     1815  2676 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_17182113_   1815 TGGAAAAGCATCTCATGTTCACGGATT-------TT-------TTAAAAT 1850
                               iii   i        i     -------  -------    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_17182113_   1851 GGCAATGCTCCCTAACTT-ATCTGTAAATTCTATACAATTACTTTCAAAA 1899
                               i     i  v  -    ii i    v ii    iv  v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_17182113_   1900 TCTCAGCTGTCATTTTTGC-----TT---------ATCCTAAAGTTCAAA 1935
                           i      i v       -----  ---------        i    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_17182113_   1936 TGTAAACTCAAGAGACCAAGAATAGCCAAAATAATCTTAATAAAGAAGAA 1985
                           v   iv    i    v             i      i v         
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_17182113_   1986 CAAAGTTGGAAGACTCACATTTTTCAATTTCAACACTT-CTTCAAAGCTA 2034
                                   i        i  ii         v    -  v        
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_17182113_   2035 AAGTAATCAAAGTAGTATGGTACTGGCATA-GGAGAGACATATAGTAGTT 2083
                         v         iii   i             -   v          - -- 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG-A--T 297

  chr20_17182113_   2084 TAATGGAATAAAACTGAA--TCCAGAAATAA-TTTATGATAATCAACTTA 2130
                         i         i  i   i--           -iii  - i -----i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT-ACA-----TTTA 341

  chr20_17182113_   2131 TGGTCAATTGATTTTCAACATGGATGCTAGAACAATTCAATGAG-AATGA 2179
                                         i   v  i   i ii  v        i -  v  
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_17182113_   2180 ATAGTCTGTTCAAGCACAGTTTTGTGCTTGGACAATTAGATATTCACATG 2229
                                v     -  v --- v     v      i i    ?i      
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAA-CAAA---TGGTGCTGGGACAACTGGATAKCCACATG 437

  chr20_17182113_   2230 -AAAAAAATGAATTTGGATTCCTATCTCATACCACATGCAAAATTTAACT 2278
                         -    i      v     ii    i    i    i  i     v      
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr20_17182113_   2279 CAAAATG-ATTAGTAGTCCCAAATGTAAGAGCTAATATTGTACAACTCTT 2327
                                -  i -?  v  i               v i i  v       
  L1M4_orf2#LINE/    488 CAAAATGGATCA-WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr20_17182113_   2328 AGAATAGAACATATAAATAAATCTTCATGGCTTTAGGTTAGGCAATGTTT 2377
                             v i      vi?i         i  i i  i            v  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_17182113_   2378 TCTTAGATACAACACCAAAAGTGTAAG-AACA--------------TAAA 2412
                                  ii          iii   -    --------------    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr20_17182113_   2413 TTGTACTTCATTAAAATTAAGAATATTTGTACTTCAAAAGAAA-TAGCGA 2461
                            v       i        i  iv     i       i  v -  v - 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC-A 685

  chr20_17182113_   2462 AGGAAACGAAAAGACAACCCACAGATTGGAGAAAAAT-TTTGAAAATCAT 2510
                           i  ii                  v   iii     -    v       
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr20_17182113_   2511 ATCTCTGATAAGGATCTCGCA-CAGGAATGTTTTAAAAATGTTTACAATT 2559
                           v          iv  i i - vi    i v v  i  ivi      i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr20_17182113_   2560 CAACAATAAATTCAAGA-----AATCCAATT-AAAAATGTGCAAA---TT 2600
                            i      ---    -----  i      -       v     ---  
  L1M4_orf2#LINE/    786 CAATAATAAA---AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_17182113_   2601 AGAGGAATCATTTCTTCAAAGAAGAAGTAAAAATGGCCTATAAACATACA 2650
                         v  iv iv       i         vi  v        v    i  i ii
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_17182113_   2651 GAAAGATGTTCAACATTATTAGACAT 2676
                         i       i       i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.15 (103 / 48)
Gap_init rate = 0.03 (29 / 908), avg. gap size = 2.83 (82 / 29)  


2818 26.88 3.04 0.90  chr20_17279415_17282239     1445  2333 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_17279415_   1445 TGGGAAAGCAGTCTATGCTCATGGATTGGAAGAATCAGTATCATTAAAAT 1494
                            i  iii vi i   i               v i i   ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_17279415_   1495 GGTCATACTGCCCAAAGCAATCTACAGATTCAACGCTTTTCCTACCAAAC 1544
                           iv     v      vii                 vv i    i    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_17279415_   1545 TACCAA-TGTTATTTTTCATAGAATTAGAAGAAACAATTCTAAAATTC-T 1592
                          v   i-  ii-     iii    v v  vi ivii  i         - 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_17279415_   1593 ATAAAACCAAAAAGAGCCC-GAATAGCCAAAGCAATCCTAAGCAAAAAGA 1641
                           ii  viiv  i ii   -           i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_17279415_   1642 ACAAAGCTGGAGGCATTGCATTACCCAATGTCATATTATATTGTAAGCCT 1691
                               i      vv ii  i v      v   v viv  i ii  iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_17279415_   1692 ACAGTAATCAAAGCAGCATGGTAGTGGTACAAAAACAGACACATAGAACA 1741
                                    ii   ii     v   i i  ii i     i     v  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_17279415_   1742 ATGGAACAGAAAAGAGAACTCAGAAATAAAGCCACACACCTACAACCATC 1791
                               i    vv    iii          v   i   ii  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_17279415_   1792 TGATCTTCAAGAAAGTCTACAAAAGTAAGCAATGGGAAAAGGGCTTTTTA 1841
                             i   i v  i vivv   i vi vv       i    iiivv i v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_17279415_   1842 TTCAATAAATGATGCTAGGATAACTGTCTAGCCGTATGCAGAAGAATAAA 1891
                              i     i    i   i     vv  ?  ii     i      i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_17279415_   1892 ACTGCACCCCTTTCTTTCACCATATGCAAGAATGAACTCAATATAGATTG 1941
                         ii  v      vi  iv        i   i   v       v  i   ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_17279415_   1942 AAGATTTGAAAGTAAGACATCAAACAATAAAAACTCT-AGAAGAAAACCT 1990
                         ?   ii i  v      vv v    v      -    -          v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr20_17279415_   1991 AGG---AAATGCCATTCCAGACATAGGTCTTGGTAAAGATTTCAT-GATG 2036
                            ---    -- -   vv   v v  vi v  i  v i    v -   -
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr20_17279415_   2037 AAGACTCCAAAAGCAATCA--CAACAGAACAAGAATT-GACAGGC-GGAC 2082
                          v   v         --  --     i  v  i  v -  i iii-    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr20_17279415_   2083 CTAATTAAGGT-----GCTTCTGCACAGCAAAAGAAACTATCAACAGAGT 2127
                         i v  i  ii -----i   i  ii vv    i  v        v i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr20_17279415_   2128 AAACAGGCAACCTAGAGAATGGGAGAAAATATTTGCAAACTATGCATCTG 2177
                         i  v  i     i v                        ii  ii     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_17279415_   2178 ACAAAAATCTAATACCTAGAATCTATAAGAAACTTAAACAAATCAACAA- 2226
                          i  iiiv  vi  i i     v     ii    ivv    v    i  -
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_17279415_   2227 AAAAA---AAAT--CCCTATTTTAAAATGGGCAAAGGACATCAACAGATA 2271
                              ---    --   v   ?v               iv v  i   i 
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_17279415_   2272 CTTCTC---AAAAAACACACAGGTGGCCAACAAACATATGAAAA-ATACT 2317
                         i     --- i  i i i   ii       i  i  i       -  i  
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_17279415_   2318 CAATATCACTAATCAT 2333
                            i    ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (154 / 82)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.67 (35 / 21)  


3113 27.20 1.78 0.56  chr20_17339262_17345578     4929  5825 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_17339262_   4929 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATGAATATCATGGAAAT 4978
                              ii i  i     i        v      v v     ii vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_17339262_   4979 GGCCATACTGCCCAAGGTAATTTGTAGATTCAATGCCATCCCCATCAAGC 5028
                            v     v     iv i  i ii        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_17339262_   5029 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5076
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr20_17339262_   5077 ATATTGAACCAAAAAAGAGCCCGCATTGCCAAAACAATCCTATGCCAAAA 5126
                             v   viiv  ii  v  v v  v            i ivivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_17339262_   5127 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACCATAATACAAGG 5176
                                 i      vv    i  v  ii i      v v  v     i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_17339262_   5177 CTACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGATATATAGA- 5225
                                  i   i    ii   i     i iv ii i   i       -
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_17339262_   5226 -------ACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACTG 5268
                         ------- i    iv   ivii         vv   i    i  iiiiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_17339262_   5269 CCTGATCTTTGACAAACCTGACAAACACAATAAATGGGGAAAGGATTCCC 5318
                         vi    i  i     ivv  v   ivv  v v           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_17339262_   5319 TATTTAATAAATGGTGCTGGCAAAACTGGCTAGCCACATGTAGAAAGCTG 5368
                          v  i  i            v v      v  ?       i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_17339262_   5369 AAACTCGATCCCTTCCTTATACCTTATACAAAAATTAATTCAAGATGGAT 5418
                           ii v  i    v   i i   v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_17339262_   5419 TAAAGACTTAAATGTTAGACCTAAAACCATCAAAACCCT-AGAAGAAAAC 5467
                         i ?    i       v   v       i  -     i  -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAAC 546

  chr20_17339262_   5468 CTAGGCA-ATACCACTCAGGACATAGGCATGGACAAGGACTTCATGACTA 5516
                         v    ?i- v i -i  iv   v v  vv i i   v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_17339262_   5517 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTA 5566
                         vi            vvi          vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_17339262_   5567 ATTAAACTTAAGAGCTTCTGCACGGCAGAAGAAACTACCATCAGAGTGAA 5616
                           i   v    i i   i  ii vv  i i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_17339262_   5617 CAGGCAGCCTGCAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5666
                         v  i  i  ii                v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_17339262_   5667 AAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAA 5716
                          i  i  vi          v  i        ivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_17339262_   5717 AAGACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACTT 5762
                                ----   v  i?    i    ii      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_17339262_   5763 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5812
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_17339262_   5813 CATCATTGGTCAT 5825
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (147 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.33 (21 / 9)  


3451 25.11 0.88 0.44  chr20_17819627_17821772      751  1654 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_17819627_    751 TGAAAAGATATTACATGTTCATGAATTGAAATAACCAATATTGTCAAAAT 800
                           i        iv          i    i  v vii        i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_17819627_    801 GTTCATACTATCCCAAGCAATCTATAGATTCAATACAATCCCTATCAAAA 850
                          viv     vi  v  vii     i        ii               
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_17819627_    851 TAACAATGACATTCTTCACAGAAATAGAAAAAAAAATCCTAAAATATATA 900
                          vv  iivi v  i  ii       v  v  ivvi          vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_17819627_    901 TGGAACCACAAAG-ACCCAGAGTATCCAAAGATATCCTCAGCAAAAAGAA 949
                              vii   i -       i  v     ivv   i v iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_17819627_    950 CAAAACTGGAGGAATCACATAACCTGACTTCCAGTTATATTACAGAGCTA 999
                             ii       v     ivv  ii i   v iviv  i    i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_17819627_   1000 TAGTAACCAAAACAGCACAGCACTGGCATAAAAACTGACACGTAGACCAA 1049
                         i     i   i    iiii i          ii iv    ii    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_17819627_   1050 CAGAAAACAATGGAGAACCCAGGAAAAAACCCATACATCTACAGTGAACT 1099
                         ii   v v   v    ii    i  v            i  ii  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_17819627_   1100 CATTTTTTACAAAGGTACCAAGAACATACATTGAGGAAAGGACAGTCTCT 1149
                         v     iv    i   i      v   v  v  i      i i     i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_17819627_   1150 TCAATAAATAGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAAA 1199
                             i    i         v         ?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_17819627_   1200 CTAGACCCCTATCTCTTGCCATATACAACAATCAAATCAAAACGTATTAA 1249
                         i i        i   vii          v   i  v      i v  i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_17819627_   1250 AGACTTAAATCTAAGACCTGAAACTATGACACTATTAAAAGAAAACATTG 1299
                             i     v     v  i       i v   v   i          v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_17819627_   1300 GGAAAAAATCTCTCCAGGACTTTGGACTGAGCAAAGATTTCTTGAATAAT 1349
                          ?iv   ---   i iv   i    ii ii    v i      ii   vv
  L1M4_orf2#LINE/    551 GNGTAAA---TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_17819627_   1350 ACCCCACAAGCACAGACAACTAAAGCAAACATGGACAAA-----CCACAT 1394
                           v   v       ii    v    v   v  i  i   ----- iv   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_17819627_   1395 C-AAGTTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAAAATAAAG 1443
                          -  i       -   i  ii vv       v  v     v   i i  i
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_17819627_   1444 AAACAACCCACAGAATAGGAGAAAATATCTGCAAACTATCCATCTGGCAA 1493
                          i              i           i      ii  vi     ii  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_17819627_   1494 AGAATTAATAGCCAGGACATATAAGGAGCTCAAACCAGTCTATAGAAAAA 1543
                         i i i vi  v    i i      i  i   vv  v v  v   iv    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_17819627_   1544 AATCTAATAATCCAACC-AAAAATGGGCAAAAGATCTGAATAGACATTTC 1592
                          iv v     i    ii-             i   i              
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_17819627_   1593 TCAAAAGAAAACATACAGATGGCAAACAGGCATATTGAAAGGTGCTCAAC 1642
                           v      i i     i     v  i i   i  vi    i        
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_17819627_   1643 ATTATCGGTCAT 1654
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (144 / 80)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.00 (12 / 6)  


1346 27.39 2.26 0.50  chr20_17847572_17850169      561   958 (1640)    L1M4_orf2#LINE/L1        1   405 (503)  

  chr20_17847572_    561 TGGAGAGGCATCACATGTTCATGAATTGGAAGACTCATCACAGAAAAGAT 610
                             i  ii   v          i           i vi iv vv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_17847572_    611 GTCAGTTCTCCATAAAAATTG---CATAGGTTTAAAAAAATACCCATCAA 657
                          v  i v    vi   --   ---i i  i  i  viv   v  i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr20_17847572_    658 AACCCCAGCAGAGTTTTTTGTAGATATAGACAACATTAGTTTAAAATGTA 707
                           i      v vv       i   v  v     vv v vii      vi 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_17847572_    708 TCCAGAAAGGCAAA------AGAATAGCTAATACAATTTTGAGAAAGAGA 751
                          vii    v    i------        i  v     i    i     ii
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_17847572_    752 AATAAAATGGGAGTAATCAGCCTACCCAATTTCAAGACTTACAATACAGC 801
                           i   i v    v v   vv  v           i      v i v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_17847572_    802 TACAGTAATCAAGACTGTGTTGTGCTAGTGGAGGAAGAGACACATAGATC 851
                                        v    v  i  i iiv i i v     i       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_17847572_    852 AATGGAACAGAGCAGAGTATCCAGAATTAGATGCACAAAAATATGCACGA 901
                                i   iiv   vi       v  i iv  i v vv    vv i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_17847572_    902 CTGATATTTGACAAAGGCACAAACACAATTCAATGAAGAAAAGTTGGCCT 951
                         i    v  i     i  ii v  v  v        ii    iiv i i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_17847572_    952 TTTCAGC 958
                              i 
  L1M4_orf2#LINE/    399 TTTCAAC 405

Transitions / transversions = 1.18 (59 / 50)
Gap_init rate = 0.01 (3 / 405), avg. gap size = 3.67 (11 / 3)  

 837 18.35 10.11 3.37  chr20_17847572_17850169     1257  1523 (1075)    L1M4_orf2#LINE/L1      385   669 (239)  

  chr20_17847572_   1257 GAAAAGAAAAGTTGGCCTTTTCATCAAGTGATACTGGGACAACTGGATAG 1306
                          i      v   ----       v   i  i i                ?
  L1M4_orf2#LINE/    385 GGAAAGAATAGT----CTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr20_17847572_   1307 CCAGAGGCAAAA-AATGA-------CCCACCTAAACCCCACACCTTCTAC 1348
                            v v      -     -------   --   --  i      v v   
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCC--CTA--CCTCACACCATATAC 476

  chr20_17847572_   1349 AAAAATTAACTCAAAATGGATTGCAGACTTAAATGAAAAATGTAAAACCA 1398
                                              ii?    i      v  i vv      i 
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr20_17847572_   1399 TAATACTTTTATAAATAAACAAAGA---ACATCTCCA-GA-----GTTTA 1439
                            v   i   v  iv     v  i--- v    i i-  ----- v   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr20_17847572_   1440 GG----G----CTTACACTTGATAGCAAAAGCACTATCTGTAAAAGGAAA 1481
                           ---- ----    v iv   i v         v v vii     i   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr20_17847572_   1482 AAAACTGTATATTGAACTTTATCAAAATTAAAA-CTTTT-TGCT 1523
                           v v-i  v    i    i             -     -    
  L1M4_orf2#LINE/    627 AATAG-ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

Transitions / transversions = 0.96 (23 / 24)
Gap_init rate = 0.05 (13 / 285), avg. gap size = 2.77 (36 / 13)  

 810 27.89 1.20 2.39  chr20_17847572_17850169     1862  2112 (486)    L1M4_orf2#LINE/L1      661   908 (0)  

  chr20_17847572_   1862 TTTTGCTCTGTGAAAGAC--TGTTGAGAGGGTGAAAGG-CAAGCTATAAA 1908
                              iv  vii  i   -- i ii   ii      i -   v i i i 
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr20_17847572_   1909 CTAGGAGATAATATTTGTGAGTCACTTATTCAACAAAGGACAAGTATTTA 1958
                         v i     v        ii i   iv   iii i  i    vv    ii 
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr20_17847572_   1959 GAAAACATAAGGAATCCCTAAAACTCAACGGTATGAAAATACGCCATCCA 2008
                            v i    i   ii i  v       iii  vi  i i viiv i   
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr20_17847572_   2009 GTTAGAATAAAATGGGCAAAAAATATGAAGAGATATTTCTCTGAAGAGGA 2058
                         i  ?i  ---          ii  v    v   i       ii    i  
  L1M4_orf2#LINE/    811 ATTWAAA---AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr20_17847572_   2059 TGTACAGATAACAAATAAATACATGAAAAGATGCTCAACAATGTCAGCCA 2108
                          i    i  ii v     ii                    ---   ????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA---TCAZZZZ 904

  chr20_17847572_   2109 TCAG 2112
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 3.31 (53 / 16)
Gap_init rate = 0.02 (4 / 248), avg. gap size = 2.25 (9 / 4)  


 715 31.14 13.70 2.14  chr20_17992176_17994384      530  1091 (1118)    L1M4_orf2#LINE/L1        1   627 (281)  

  chr20_17992176_    530 TGGAAAGTTTTACTATATTAATGGATTGGAAGATTCAGAATCA--AAGAG 577
                                v v v i  i  v             i i iv  ii--    v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_17992176_    578 GCCAAAAATCTCCAAATTCATCTATAGATATAATACAATTTTTA--AAAA 625
                          v   v v  i       v     i    vi  ii    iii  --    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_17992176_    626 TACTTGACAGTCTTTTT-GTGGGACATGATAAATTTCTTTCAAAATTTAT 674
                          - iiii v i      - ii i vv   i  ii vv iii      i  
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_17992176_    675 GTGAAA--------------GAAGAGTCGAAACACTCCTGAA------GG 704
                         i  i  --------------   v  i i     v  i    ------ i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_17992176_    705 ACAAGGTGTGTAGGCTTGAT------CAAT--CAGA---TATCA------ 737
                             i  -  v   vi v i------    --  i ---  ii ------
  L1M4_orf2#LINE/    200 ACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_17992176_    738 -ATAGTAATTAAAATGATGTGG--CTTTCAT-----TC-ACAGAGGGACC 778
                         - i      i  i iii     --  vv   ----- v-   v vi  i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_17992176_    779 ACTGGTACCTGAGA---GAGAGCCTGGAAACAGCCCCACACATATGTGTG 825
                          v   v i---   ---     i ii    i iv    i    v i  vv
  L1M4_orf2#LINE/    299 AATGGAAT---AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_17992176_    826 CA-TTGATTTATGAGAGAGGGTATGCAG----TGCAGCAGGGAAAGA-T- 868
                           -       vi  v -     iivv  ---- v  iii        - -
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACA-AGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_17992176_    869 GTCATATTCAATACATGGAATTGGAACAAGTGCTTATCCGTTTGGGAAA- 917
                            v -     i v    vii   i    v  vv  ?  iiv  vi   -
  L1M4_orf2#LINE/    395 GTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_17992176_    918 AATAAAG--GAA-----ACTGAATA----ACACACATATCAGTTTCTGGT 956
                            i   -- i -----  ivv i ---- i   v v  i ii ivvii 
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_17992176_    957 GGATTAAACATTTAGATGT--GTGTGAATACATATACATGTATATGTATA 1004
                             i ? v ii  i    -- v iv  v  -    v --- iviv  v 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAAC-TATAAA---ACTCTTAGA 539

  chr20_17992176_   1005 TAGACAATGTAGAGGAATATGTTTATGACCACAGGATAAGAAAGAATTTC 1054
                         -   v  ii   i? v v  v  ii     vii  v  i v  vii    
  L1M4_orf2#LINE/    540 -AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_17992176_   1055 TTAAATAAGAC-CCAAAAA-ATAAACCACAAAAGAAAAA 1091
                            i   v   -      i- i  i v            
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

Transitions / transversions = 1.49 (103 / 69)
Gap_init rate = 0.05 (32 / 627), avg. gap size = 2.78 (89 / 32)  

 451 26.96 7.17 2.39  chr20_17992176_17994384     1425  1717 (492)    L1M4_orf2#LINE/L1      602   908 (0)  

  chr20_17992176_   1425 CAAAAGAA-AAG----AAAAGAAAAAGTTGATAAATTTAATTGTAGACAA 1469
                               v -   ----          i v        vi i vi vvv  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_17992176_   1470 ATTAAGAATGTCTTTA--TCAAAACACACAATAAGGAGAATGATATGCTA 1517
                              i  iv i v i--     iv    v  v i  i i   v v vi 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr20_17992176_   1518 AACAATAAGCTG--AGAAAACTTTTTCAACACATTTCTCTTACAAATGAT 1565
                          v v i iiv  --      iv   v   vv   v v   v i  iv  i
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr20_17992176_   1566 TAGAATCCAGAATATGTAAAGAACTGTTATGAATCAATTTTTAAAAAAAA 1615
                          v v           i         v   ii v     ----  v     
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT----AATAAAAA 797

  chr20_17992176_   1616 GATAAA---CTCAATAGAAAAATGA-CAAAAGACATGAACGGGCATT--- 1658
                           i   --- i    v?       i-    i  iv    ii i    ---
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_17992176_   1659 CCCAGGAAAACATGAATAT-----ATAAACATATATATAAAAGATGCACG 1703
                           v i   i i  iv v  -----    i  i  i---         v i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATG---AAAAGATGCTCA 894

  chr20_17992176_   1704 ATCTCATTCATAAA 1717
                          iv   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.05 (40 / 38)
Gap_init rate = 0.03 (10 / 307), avg. gap size = 2.80 (28 / 10)  


 427 30.88 0.74 1.47  chr20_18036740_18041074.rev     2182  2317 (2018)    L1M4_orf2#LINE/L1        1   135 (773)  

  chr20_18036740_   2182 TAAAGAGAAATTCCATGTTCATTACTAGAAAGACTCAATATCACCAGGAT 2231
                          ii i   v  i          viv v i      i     iiii i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_18036740_   2232 GCCACTTCTTCCCTGTTTGGCTTATAGATTCAATGCCATCCCAGTCAAGC 2281
                          v  v v  i   viv   iii  i        i  v     vi    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_18036740_   2282 TCCCAGCAAGTTCTATTTTATAGATATTGATG-GCTG 2317
                                vi--i  v    ii   v     ii-    
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTG 135

Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.01 (2 / 135), avg. gap size = 1.50 (3 / 2)  

2454 17.68 3.15 16.70  chr20_18036740_18041074.rev     2923  3844 (491)    L1M4_orf2#LINE/L1      112   908 (0)  

  chr20_18036740_   2923 TTTTTTACAAAAAGATATTGACAAACTGATTCTAAAGTTTACATGGAGAG 2972
                               i  i   ----       i     i     i  i i     i v
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAA----TTGACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr20_18036740_   2973 GCAAAAGACCCAGGAGAGCCAGCTTAATATTGAAGGAGAA-AATGAAGTT 3021
                             ii       i v     ivvi   v     ii    -  ii     
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr20_18036740_   3022 GGAAGACTGACA-TGCCTAACTTCAAGACTTACTAAAAGGCTATAGAGTA 3070
                            i    v   - v  i  i     i        v  i    i  --  
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG--TA 255

  chr20_18036740_   3071 ATCAAGACAGTGTGATACTGGTGAAAGAATGAACAAATAGATCAATTGGA 3120
                                       i      iiv   i  ii   v          v i 
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr20_18036740_   3121 CAGAATAGTAAGCCCAGAAATAGACCCACATAAACACAGTCAACTGAGCT 3170
                         i     v vi  i         i     i i vvi ii     i   vi 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr20_18036740_   3171 TTGACAAAGGAGC-------------------AAAAATAGTCTCTACAGC 3201
                          i     i  v  -------------------  i        i v  i 
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr20_18036740_   3202 AAATGGTGCTGGAACAATTGGACATCCACATGAAAAATAATAAGAAGAAT 3251
                                     i    i    i ?       v    v   --    ---
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT--GAAG--- 450

  chr20_18036740_   3252 CTGGACAG--ACATTACTCCCTTTACAAAAACTAACTAAAAATGCATCAT 3299
                         i     vv--  v i  v  v v        i     v      ------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG------ 494

  chr20_18036740_   3300 AGACCTGCCAGGTAGGATGGCACCCACCTATTGTCCCAGCTGCTTAGGAG 3349
                         --------------------------------------------------
  L1M4_orf2#LINE/    495 -------------------------------------------------- 494

  chr20_18036740_   3350 GCTGAGGTGGGAGGATCCCTTGAACCCAGGAGTTCAAGGTCAGCCTGGAT 3399
                         --------------------------------------------------
  L1M4_orf2#LINE/    495 -------------------------------------------------- 494

  chr20_18036740_   3400 AACATAGCAAGACCCTATCTCTTAAGAAAAGAAAAATCACAGACCTAAAT 3449
                         ----------------------------------i    ?          
  L1M4_orf2#LINE/    495 ----------------------------------GATCAWAGACCTAAAT 510

  chr20_18036740_   3450 GTAAAATGC-AAAACTATAAAATTGCTAGACAATAATATGGAAAAAAAAT 3498
                             i -  -            i vi    vi v  i  i i?iv   - 
  L1M4_orf2#LINE/    511 GTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA-T 558

  chr20_18036740_   3499 CTAGATGACCTTGGGTTTGGCAATGACTTTTTAGATACAACACTGAAGGT 3548
                           vvi            v       ii  i       ii    ii  i i
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr20_18036740_   3549 ACAATCCATAAAA-AAAGAATTGATAAGCTGGACTTCATTAAAATTAAAA 3597
                             v v i    -   i   v     ii          i          
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr20_18036740_   3598 ACTTCTGCTCTGCAAAAGACACTA-CAAGAGAATAAAAAGCCAAGTCACA 3646
                             i  iv  v    i       -     i i i     v   vi    
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr20_18036740_   3647 GACTGGGAGAAAATATGTGCTAGA--ACATGCCTGGTAGAAGACTGGTAT 3694
                           v             v   - i -- i  ii   i  iii    v    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGC-AAATCATATATCTGATAAGGGACTTGTAT 757

  chr20_18036740_   3695 CCAAAATAGACAAAGAATTCTTAAAACTCAACAGTAAGAAAACAAACAAT 3744
                            i    v i      i     v       i i   i  i     i  i
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr20_18036740_   3745 CCAATTTAAAAATGAGCAAAAGACCTTAACAGACACCTCACCAAAGAAGA 3794
                               ?       i     i  ii v  i     ii  v          
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr20_18036740_   3795 TATACAGATGGCAAATAAGCATATGAAAAGATGCTCCACAT-ATGTCATA 3843
                               i     v        i              v    - ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr20_18036740_   3844 A 3844
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.18 (109 / 50)
Gap_init rate = 0.02 (17 / 797), avg. gap size = 10.76 (183 / 17)  


 351 30.22 2.16 0.72  chr20_18168167_18173650     4241  4379 (1105)    L1M4_orf2#LINE/L1        1   141 (767)  

  chr20_18168167_   4241 TGGAAACACATCCCGTGCTCACAGATGGGTACAATCAAT---GTGAAAAT 4287
                               v i     i  i   ii   v  v v v i   ---  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_18168167_   4288 GACCATACTGCCAAAAACAATCAACAAATTCAATGCAATTCCCATAGAAA 4337
                          i v     v  v   vii   v   i      i     i  i  vi   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_18168167_   4338 TTACACCAGCATTCTTCACAGAACTAGAAAAAAATAATTCTA 4379
                          iv  v v  v  i  ii     v v  v  iv- i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTA 141

Transitions / transversions = 1.10 (22 / 20)
Gap_init rate = 0.01 (2 / 141), avg. gap size = 2.00 (4 / 2)  

2029 26.26 1.31 0.33  chr20_18168167_18173650     4380  4992 (492)    L1M4_orf2#LINE/L1      290   908 (0)  

  chr20_18168167_   4380 ATGTAGACCAATG-AACAGAAGAGAAAACTCAGAAATAAAACCAAGTACC 4428
                           i    i     -  i    vv  i iii          v   vii ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr20_18168167_   4429 TACAGCCAACTGATCTTTGACAAAG----CAAACACAAACAGTCGAGAAA 4474
                           ii i   i    i  i     i ----   ivv  vv  i v i    
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr20_18168167_   4475 GGACACCCTAGTCAACAAGTGGTGCTGGGATAATTGACTAGCCACAGGTA 4524
                          i i vi  vv       i           i  i  iv  ?     v i 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr20_18168167_   4525 GAAGAGTGAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCA 4574
                         i    i    ii    i  ii i   v    v           i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr20_18168167_   4575 AGATAGATCAAAGATTTAAATCTAAGACCTGAAACCTTAAAAATTCTAGA 4624
                          i  i     ?   ii     v     v  i    iv     v ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_18168167_   4625 AGATAATATCAGAA-AAATCCTTCTAGATATTGGCTTAGGCAAAGACTTC 4673
                            v  i  vi ?i-     -   vv  iv    v        v ii   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_18168167_   4674 ATGACCAAGAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATG 4723
                         v iivi v  vv         v v         iv   i   i   i  v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_18168167_   4724 GGACTTAATTAAACTAAAAAGCTTCTGCACAGCAAAAGAAACAATTAGCA 4773
                               v  i   v v    i   i  ii vv    i  v  v  i iv 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr20_18168167_   4774 GAGTAAATAGTCAACACACAGAATGGGAGAAAATCTTCACAATCCATACA 4823
                         i   i  v  v    v                  v  ii   vi    i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_18168167_   4824 TCCAGCAAAGGACTAATACCCAGAATCTACAAGAAACTCAAACAAATCAG 4873
                           iiii  i     vi  i       v  i  ii     vv    v   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_18168167_   4874 CAAGAAAAAGA-AAACAATCCATATCAAAAAGTGGGCTAATGACATGAAT 4922
                         i  v       -   i  i   -  i?    i     v  v  iv     
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCA-ATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_18168167_   4923 AGATAATTCTCAAAAGAAGATAAACAAATGGCTAACAAGCATATAAAAA- 4971
                            i v     v          v         i  i     i  i    -
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_18168167_   4972 ATGCTCAGCATCACTAATGAT 4992
                                i     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (96 / 61)
Gap_init rate = 0.01 (7 / 619), avg. gap size = 1.43 (10 / 7)  


 201 20.00 0.00 0.00  chr20_18228603_18233308     3056  3090 (1616)    L1M4_orf2#LINE/L1        1    35 (873)  

  chr20_18228603_   3056 TGGAAAGACATCACATGTTTGTAGACTGGAAAACT 3090
                                 i   v      ii i  i     i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACT 35

Transitions / transversions = 6.00 (6 / 1)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.00 (0 / 0)  

3527 20.24 6.91 0.24  chr20_18228603_18233308     3390  4214 (492)    L1M4_orf2#LINE/L1       29   908 (0)  

  chr20_18228603_   3390 GAAAACTTAAT---GTTAAAATAATAATACTACTCAAACCAATCTACAGA 3436
                            i       ---     i  iii      v i    iii         
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chr20_18228603_   3437 GTCAATGTAATCCCTATAAAAATAACAATT----TTTTTA-ATAAATAGA 3481
                         v    i i         v     vv  ii ----     i- v    v  
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chr20_18228603_   3482 AAAATTCATATTAAACTTGATATGGAATCTCAAGGGACACTGAATACCTA 3531
                         v  ii v  vi    v  v        viv        v v     v i 
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr20_18228603_   3532 AAACAATCATGAAAGAGAA---CCAAGTTGGAGGACTTACAGTTCCTTAT 3578
                                 v     i    --- v             i   v    iv  
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr20_18228603_   3579 TTCAGAATTTACTACAAAGCAACAGTAACCCAAAC--TGTGGTACTAGCA 3626
                             i  i            v       i v i  --         i   
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr20_18228603_   3627 TAAAAACAGACTTACAGACTAATAGAACAGAATAGAGATCCCAGAAATAA 3676
                            ii i    v  i   ii   i   i     v    vi          
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr20_18228603_   3677 ACCCTTGCATATATGGTCAAATGATTTTTGACAAGAGTGGCAAGACCATT 3726
                             v i   v         v       i      i   v          
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr20_18228603_   3727 CAATATGAAAAAGACTA---TACTCAACAAACGCTATTGGGCAAACTGTA 3773
                             i- ii     v  --- vi        i v ii    vv     v 
  L1M4_orf2#LINE/    379 CAATG-GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr20_18228603_   3774 TATTTATATGCTGAAGAATGAAGTTGAACCCTTACCTAACACCATATACG 3823
                           ?ii i    vi             i    i     v           i
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr20_18228603_   3824 CAAATTAACTGAAAATGGATCGAAGACCTAAACATAAATGTGAAAACTAT 3873
                         v         v          i?         ii   iv iv        
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr20_18228603_   3874 AAAAATTGTAGATGAAAACCTAGGCAAACATCTTTATAACTTTGGATTTG 3923
                             v iv    v      v    ?iv v     ii i  i    i  v 
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr20_18228603_   3924 GTGATGATTTCTTGGAAATGACACCAAAA-CATAGGCAATAAAAGAAAAG 3972
                          ii   i      i  v            -  i i    i         -
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA- 626

  chr20_18228603_   3973 AATAGTGAACTTGGACTTCATCAAAATTTAAAACTTTCATTCATCAAAGG 4022
                              vv  v                  v        ii v v       
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr20_18228603_   4023 A------------------------------------AGGGAATATATTT 4036
                          ------------------------------------i i   v      
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr20_18228603_   4037 GCAAGTCACATATCTGATAAGGGATTAATATTTAGAATATATAAAGAACT 4086
                             i   i               i vi   ii                 
  L1M4_orf2#LINE/    727 GCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr20_18228603_   4087 CCTACAGCTTAACAACAATA-GAAGAACGCCCCAGCTTAAAAATGGACAA 4135
                          i    i  i  i  i  v -  vi  iiv    ii ?        i   
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr20_18228603_   4136 AGGATTTGAATAGTCATTTTTGCAAAGA---TATACATGTGGCCAATAAG 4182
                                      v     i v      ---      vi           
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr20_18228603_   4183 CACCTGAAAAGATGTTCACTATCATTCACATT 4214
                            v          i   vi    ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (97 / 66)
Gap_init rate = 0.01 (12 / 880), avg. gap size = 4.92 (59 / 12)  


3229 26.62 0.55 0.66  chr20_18261057_18267482     5026  5934 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_18261057_   5026 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5075
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_18261057_   5076 GGCCATACTGCCCAAGGTAATTTATAGATTCAACACCATCCCCATCAAGC 5125
                            v     v     iv i  i  i         i v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_18261057_   5126 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5173
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_18261057_   5174 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5223
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_18261057_   5224 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5273
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_18261057_   5274 TACAGTAACCAAAACAGCATGGTACTGGTACCGAAACAGAGATATAGATC 5323
                                 i   i    ii         i iviii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_18261057_   5324 AATGGAACAGAAC--AGAGCCCTCAGAAGTAATGCCATGTATCTACAACC 5371
                                i    i--    i  --    i   vv    ii  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_18261057_   5372 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5421
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_18261057_   5422 CTATTTAATAAATGGTTCTGGGAAAACTGGCTGGCCATATGTAGAAAGCT 5471
                           v  i  i       v      v      v i?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_18261057_   5472 GAAACTGGATCCCTTCCTTACACCCTATACAAAAATTAATTCAAGATGGA 5521
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_18261057_   5522 TTAAAGACTTACATGTTAGACCAAAAACCATAAAAACCCTAGAAGAAAAC 5571
                          i ?    i  v    v   v v     i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_18261057_   5572 CTAGGCA-ATACCATTCAGGACAGAGGCATGGGCAACGACTTCATGTCTA 5620
                         v    ?i- v i -   iv   vvv  vv i     i ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_18261057_   5621 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5670
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_18261057_   5671 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTAAA 5720
                           i   v v  i i   i  ii vv    i  v    i  vv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_18261057_   5721 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCACCTGACA 5770
                         v  i     i                 v       vii ivi i    i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_18261057_   5771 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5820
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_18261057_   5821 AAAACAAAAAAACCCCATCAAAAAGTGGGCAAAGGATGTGAACAGACACT 5870
                           i     v  -   v  i?    i            v    i     i 
  L1M4_orf2#LINE/    796 AAGACAAATAA-CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_18261057_   5871 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5920
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_18261057_   5921 TCATCACTGGCCAT 5934
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3026 21.37 1.81 10.28  chr20_18527911_18535333      493  1484 (5939)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr20_18527911_   1484 TGGAGAGATATTCCATGTTCATAGACAGGGAGATTCAATATAGTCAAGGT 1435
                             i      i          i  iv  i   i i     v  i   i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr20_18527911_   1434 GTCAGTTCTTCCCAACTTCATCTACAGACTCAATGCAATCCCAATCTAAA 1385
                          v  i v  i     v  v         i    i        v   v   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr20_18527911_   1384 TCC-AGCAAGTTATTTTGCAGATATCAACAAACTGATTCTAAAGTTTACA 1336
                            -   vivi v         v  ii    i     i     i  i i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

C chr20_18527911_   1335 TGGGGAAGCAAAAGACCCAGAATGGTCAAAAAAATATTAAAAGAGAAGAA 1286
                            ii v    ii          i i     v   v  i   i       
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

C chr20_18527911_   1285 CAAAGTTAACGGGCTGACACTATACGACTTCAATACTTATAATAAAGCTA 1236
                                iiv  i  v     viv i i     v     iv i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

C chr20_18527911_   1235 CAATAAATAAGACAGTGTGGTATCAATGAAAGAAGAGAGAAACAGACCAA 1186
                           i   vi              iiiiiiv   i v   v v i   i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

C chr20_18527911_   1185 TGGAACAGAACAGAGAGCCCAGAATTCGACCCTGATAAAT--ACAGTGAA 1138
                              i    iv     i      v vi    --   v  -- ii  v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCC--ATACATTTATGGTCAA 348

C chr20_18527911_   1137 TTGATCTTTGACAAAGGAGCAAAGGCAATACAATGGAGCAAGGG--GTCT 1090
                              i  i     i  v  v   i v  v      i v   ii--    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

C chr20_18527911_   1089 TTTCAACAAATGATGTTGGAATAACTGGATATCCACATACAAAAAAGCGC 1040
                                     i  i   i i         ?      i     i ii v
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

C chr20_18527911_   1039 CTCTAGACAAAGACCACAGACCCTTCACAAAAATTATCT-GAAATGAATC 991
                         vvi i   vvvv   v  v   v vi          v  -i     i   
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

C chr20_18527911_    990 ATAGGCCTAAATGTAAAATGC-AAACCTATAAAGCTCCTAGAAGATAACA 942
                          ?  i           i -  -   v       i   i       v    
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACA 547

C chr20_18527911_    941 --GGAAAAAATCTAGATTATGTTGGGTAGGATGATGACTTTTTAGATATA 894
                         --  ?iv      vvi v iv      vi iii   ii  i        i
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

C chr20_18527911_    893 ATACCAAAGGCACAATCTATGAAAATAAGAATTGATAAGCTAAGCTTTAT 844
                          i      i      v v ii   iv  i   v     ii iii   i  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

C chr20_18527911_    843 TAAAATTAAAA--TTTTCCTCTCCATGAAAGGCACTGTCAAGAGAATGAA 796
                         i          --    viv  i  --  i i    i      i i    
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCA--AAGGACACTATCAAGAAAGTGAA 695

C chr20_18527911_    795 AAGACAAGCCACAGATTGAGAAAAAATATTTACAAAAGAAATATCCTATA 746
                                v       v  i  i         i    --------------
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAA-------------- 731

C chr20_18527911_    745 AGGATAAATATTTGTAAATTGAATATTCACAGAAGACATATCTGATAAAG 696
                         --------------------------   i -------------------
  L1M4_orf2#LINE/    732 --------------------------TCATA------------------- 736

C chr20_18527911_    695 GATAAATATTTGCAAGTTGAATATTTGCAAAAGACATATCTGATAAAGGA 646
                         ------------------------------------          i   
  L1M4_orf2#LINE/    737 ------------------------------------TATCTGATAAGGGA 750

C chr20_18527911_    645 CTAGTATCCAAAATATAAAAAGAACTCTTAAAACACAGTAA------GA- 603
                           v       i      v            v   v  i   ------  -
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

C chr20_18527911_    602 AAACAATCCAATTTTTTAAAATGGGCCAAAGACCTTAACAGATACCTCAC 553
                            i  i      ?v--         v  i  ii v  i   i ii  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWA--AAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

C chr20_18527911_    552 CAAAGATGATATACAGATAGTAAATAAGCATATGAAAAAATGTTCCATAT 503
                               v        i  i iv        i       i   i  v i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

C chr20_18527911_    502 CATATGTCAT 493
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.77 (133 / 75)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 8.00 (120 / 15)  

3252 26.98 0.44 0.44  chr20_18527911_18535333     6024  6931 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_18527911_   6024 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 6073
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_18527911_   6074 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 6123
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_18527911_   6124 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 6171
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_18527911_   6172 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 6221
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_18527911_   6222 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 6271
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_18527911_   6272 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 6321
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_18527911_   6322 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCCTACCTACAACT 6369
                                i    i--    i  --        vv  iivi ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_18527911_   6370 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 6419
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_18527911_   6420 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 6469
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_18527911_   6470 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 6519
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_18527911_   6520 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 6569
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_18527911_   6570 CTAGGCATTACCATTCAGGACATAGGCATGGACAAGGACTTCATGTCCAA 6619
                         v    ?i v viv   iv   v v  vv i i   v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_18527911_   6620 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 6669
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_18527911_   6670 TTAAACTAAAGTGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 6719
                          i   v v  ivi   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_18527911_   6720 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 6769
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_18527911_   6770 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 6819
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_18527911_   6820 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAATTC 6869
                          i     i     v  i?    i     i     iv    i     v   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_18527911_   6870 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 6919
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_18527911_   6920 ATCACTAGCCAT 6931
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3202 26.49 0.88 0.66  chr20_18684166_18690514.rev     4952  5857 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_18684166_   4952 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5001
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_18684166_   5002 GGCCATACTGCCCAAGGTTATTTATAGATGCAATGCCATCCCCATCAAGC 5051
                            v     v     iv v  i  i    v   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_18684166_   5052 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5099
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_18684166_   5100 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 5149
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_18684166_   5150 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5199
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_18684166_   5200 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5249
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_18684166_   5250 AATGGAACAGAGC--AGAGTCCTCAGAAATAATTCCACACATCTACAACT 5297
                                i   ii--       --        vi   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_18684166_   5298 ATCTGATCTTTGACAAAACTGACAAAAACAAGAAATGGGGAAAGGATTTC 5347
                          vi    i  i     iiv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_18684166_   5348 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5397
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_18684166_   5398 GAAACTGGATCCCTTCCTTATACCTTATACAAAA-TTAATTCAAGATGGA 5446
                            ii    i    v   i i   v         -    i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_18684166_   5447 TTAAAGACTTAAATGTTAGCCATAAAACCATAAAAACCCTAGAAGAAAAC 5496
                          i ?    i       v  vvv      i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_18684166_   5497 CTAGGCAATACAAT--TCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5544
                         v    ?i-  -   --  iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNG-TA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_18684166_   5545 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5594
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_18684166_   5595 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5644
                         v  i   v v  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_18684166_   5645 ACAGGCAACCTACAAAGTGGGAGAAAATTTTTGCAGTGTACTCAACTGAG 5694
                          v  i     i   i i           v      ivvi ivi v    v
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_18684166_   5695 AAACGGCTAATATCCAGAATCTACAATGAACTTAAACAAATTTACAAGAA 5744
                           iv i  vi          v  i  v     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_18684166_   5745 AAA-ACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACT 5793
                            -     i     v  i?    i     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_18684166_   5794 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCA 5843
                             v        i  vi viii     v ii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_18684166_   5844 TCATCACTGGCCAT 5857
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (138 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.40 (14 / 10)  


3129 25.60 0.65 1.96  chr20_18790106_18806773.rev     2790  3707 (12961)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_18790106_   2790 GAAATACATCCCATGATCATGGAAGGGTAGAATCAATATTGTGAAAACAA 2839
                             v i        v       vv  v   v i        v  i iii
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_18790106_   2840 CCATACTGTCAACAGCAATCTACAAATTCAATGCAATCCCCATGAAAATA 2889
                          v     vi v v vii       i      i        i  v     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_18790106_   2890 CCA--T-CATTCTTCACTGAATTAGAAAAAACAATTCTAAAATTCATATG 2936
                            -- - v  i  ii v   v v  v  ivii  i              
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_18790106_   2937 GAACCAAAAAAGAGCCCGCATAGCCAAAGCAAGGCAAGCAAAAAAAAAAA 2986
                            viiv  ii  v  v v         i   v- vv ----------  
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAAT-CTTG----------AA 191

  chr20_18790106_   2987 AAAAAAAAAAAAAATCAAATATGGAGGCATCACATTACCTAATTTCACAC 3036
                            i  i  v   i ------      vv     i v  i       v v
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGT------TGGAGGACTCACACTTCCCAATTTCAAAA 235

  chr20_18790106_   3037 TATACCATAAGGCCATAGTCACCAAAACAGCATGGTATTGGTATAAAAAT 3086
                         iv   i i  i  i i   v i   i    ii     i   i    ii  
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr20_18790106_   3087 AGACACATAGGCCAGTGGAACAGGATAGAGAACCCAGAAATAAACCCAAA 3136
                              i    ii  i     i  i  v    ii               v 
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr20_18790106_   3137 TGCTTACAGCCAAA-GATCTTCGACAAAGCAAACAAAAACATCAAGCAGG 3185
                         iii   ii i   v-   i        i vviv   i v   iv iii  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr20_18790106_   3186 GAAAGGACACCTTTTTCAACAAATGGTGCTGGGATAATTGGCTAGCCACA 3235
                              i i vii                      i  i   v  ?     
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr20_18790106_   3236 TGTAGGAGAATAAAACTGGATCCTCATCTCTCACCTTATATAAAAATAAA 3285
                           i ii     i  ii    i  ii i   v    v    i      v  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr20_18790106_   3286 CTCAAGATGGATTAAGGACTTAAATCTAAGACTGGAAACTATAAAAATTC 3335
                              i      i ?i   i     v     vivi           v ii
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr20_18790106_   3336 T-GAAGATAACACTGGAAAAACCCTTTTAGATATTGGCTTAGGCAAGGAT 3384
                          -     v    iv  ?iv  vi   ivv  iv    v        v i 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr20_18790106_   3385 TTCATGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAGATAAATAG 3434
                            v iivi v  vv         v v    i    iv   i   i   i
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAA 635

  chr20_18790106_   3435 TTTGGACTTAATTAAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCA 3484
                         v        v  i   v v  i i      ii vv    i iv  vi   
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr20_18790106_   3485 GCAGAGTAAACAGACAACCCATAGGGTGGGAGAAAATCTTCA-AAATCTA 3533
                         iv i   i  v          i  ii           v  ii-     - 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-A 734

  chr20_18790106_   3534 TACATCTGACAAAGGACTAATATCCAGAATCTATAATGAACTCAAACAAA 3583
                           i      i  i     vi          v     v      vv    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr20_18790106_   3584 TCAGTAATAAAAAAACAAACAATTTCATCAAAAAATGGGCTAAAGACATG 3633
                            i         i     i  iiiv  i?          v  i  iv  
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr20_18790106_   3634 AATAGAGAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAA 3683
                               v v     v                       i  i  i     
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr20_18790106_   3684 AAAATACTCAACATCACTAATGAT 3707
                           i  i          ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (138 / 93)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 2.67 (24 / 9)  

2974 27.01 1.10 0.99  chr20_18790106_18806773.rev     9056  9962 (6706)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_18790106_   9056 TGGAAAAACATTCCATGATCATGGATAGGAAGAATCAATATCGTGAAAAT 9105
                               i i  i     v        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_18790106_   9106 AGCCACACTGACCAAAGTAATTTACAGATTCAATGCTATTCCCATCAAGC 9155
                         i  v i   vv     v i  i           i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_18790106_   9156 CACCATTAATTTTCTTCACAGAATAAGAAAAAACT-ACTTTAAATTTCAC 9204
                         iv   viviii  i  ii     - vvi v  i  - iii    v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_18790106_   9205 AGGGAACCAGATAAGAG-CTCATA-TAGCAAAGACAATCCTAAGCAAAAA 9252
                          v    -- vii   i - i  v -    v  i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_18790106_   9253 GAACAAA-CTGGAGGCATCGCACTACCTGACTTCAAACTATACTACAAGG 9301
                                -i      vv  i    v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_18790106_   9302 CTACAGGAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 9351
                               v  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_18790106_   9352 CAATGAAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACAACCA 9401
                              i  i     v   ivii         vv   i    i  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_18790106_   9402 TCTGATCTTTGACAAACCTGTCAAAAACAAGCAATGGAGAAAGGATTCCC 9451
                         vi    i  i     ivv  i   i v  vv      i     i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_18790106_   9452 TATTTAATAAATGGTGTTGGGAAAACTGGCTGGCCATATGCAGGAAACTG 9501
                          v  i  i        i     v      v i?   i     ii i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_18790106_   9502 AAACTGGACCACT-TCTTACACCTCATACAAAAAATTAACTCAAGATGGA 9550
                           ii      v  -i  i     vi         -         i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGA 496

  chr20_18790106_   9551 TTAAAGACTTAAACATAAGACCTAAAATCATAAAAACCCTAGAAGAAAAC 9600
                          i ?    i    ii     v      ii      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_18790106_   9601 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTG 9649
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_18790106_   9650 TAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 9699
                          i            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_18790106_   9700 ATTAAACTAAAGACCTTCTGCACAGCAAATGAAACTATCATCAGAGTGAT 9749
                           i   v v  i v   i  ii vv    v  v       --   iv - 
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--AGAAAG-T 692

  chr20_18790106_   9750 GAACAGGCAACTTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCAG 9799
                            v  i    ii                 v       vii  vi   v 
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_18790106_   9800 ACAAAGGGCTAATATCCAGAATCTACAAGAAACAA--ACAAATT--TAAG 9845
                          i  i  i  vi          v  i  ii   vv--    v i--   v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_18790106_   9846 GAAAAAACCAAACAACCCCATCAAAAAGTGGGCAAAGGGTATAAACAGAC 9895
                         i    i  -   i     v  i?    i          i v i  i    
  L1M4_orf2#LINE/    793 AAAAAGAC-AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_18790106_   9896 ACTTCCCAAAAGAAGACATTTATGTGGCCAACAAACATATGAAAAAAAGT 9945
                          i   i v        i  vi vi       i  i  i       i v i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_18790106_   9946 TCATCATCACTGGTCAT 9962
                            v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (149 / 92)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.27 (19 / 15)  

3051 27.44 0.55 0.88  chr20_18790106_18806773.rev    15266 16176 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_18790106_  15266 TGGAAGAACATTCCATGCTCATGGAAAAGAAGAATCAATATCGTGAAAAT 15315
                              ii i  i     i       vvi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_18790106_  15316 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 15365
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_18790106_  15366 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAATTCA 15413
                          v   iivi i  i  ii     -   -- v  i  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_18790106_  15414 TACGGAACCAAAAAAGAGCCTGCATTGCCAAGACAAACCTAAGCCAAAAG 15463
                           i    viiv  ii  v  v v  v     i    v i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_18790106_  15464 AACAAAGCTGGAGGAATCACACTACCTGACTTCAAACTATACTGCAAGGC 15513
                                i       v       v  ii i      viv    i   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_18790106_  15514 TACAGAAACCAAAATAGCATAGTACTGGTACCAAAACAGAGATATAGACC 15563
                              v  i   i i  ii i       i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_18790106_  15564 AATGGAACAGAAC--AGAGCCCTCAGAAACAATACCACACATCTACAACT 15611
                                i    i--    i  --     i  vv   i    i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_18790106_  15612 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 15661
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_18790106_  15662 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 15711
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_18790106_  15712 GAAACTTGATCCCTTCCTTACACCTTATACAAAAATTTATTCGAGATGGC 15761
                            ii v  i    v   i     v            v i  i i    v
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_18790106_  15762 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 15811
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_18790106_  15812 CTAGGCA-ATACCATTCAGGACATAGGCATGGGTAAGGACTTCATGTCTA 15860
                         v    ?i- v i -   iv   v v  vv i  i  v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_18790106_  15861 ACACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 15910
                         vv    v       vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_18790106_  15911 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCGTCAGAGCAAC 15960
                           i   v v  i i   i  ii vv    i  v    ---   iiiv ii
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA---TCAAGAAAGT 692

  chr20_18790106_  15961 CATCAGGCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACTCATCTG 16010
                         v vv  i     i                vv       vii ivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_18790106_  16011 ACAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAAGAAATTTACAAT 16060
                          i  i  i  vi          v  i         vv v  v iv i   
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_18790106_  16061 AAAAGAACAAACAACCCCATCAAAAAGTGGGTGAAGGATATGAACAGACA 16110
                             ii     i     v  i?    i    ii      v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_18790106_  16111 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCT 16160
                         i     v        i  vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_18790106_  16161 CATCATCACTGGCCAT 16176
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (146 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


3035 22.56 2.20 0.55  chr20_18812271_18813991.rev      503  1229 (492)    L1M4_orf2#LINE/L1      170   908 (0)  

  chr20_18812271_    503 GGATAGCCAAAACAATCTTGAGAAAAAA---CAAAGCCATAGGCATTTCA 549
                          i                   i   i  ---     iiiv   vv iv  
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACA 219

  chr20_18812271_    550 CTTACTGATTTCAAAATATATTACAAAGCTAAAGTAATCAAAACAGCATG 599
                            v ii         iv  i          v         i    ii  
  L1M4_orf2#LINE/    220 CTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTG 269

  chr20_18812271_    600 AGACTGGCATAAACCCCAACATATAGACCAATGGAACAAAAT--AGA--C 645
                         iv          ivvivi         i        i i   --   -- 
  L1M4_orf2#LINE/    270 GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr20_18812271_    646 TAGAAATAAATCCATGCGTCTATGGTCAGATGATCTTTGACAAGAGTGCC 695
                         i         i    i i i        iv    i  i      i     
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCC 369

  chr20_18812271_    696 AAGA--ACT--ATGGGGATAGGATGGTCTCTTCAATAAATGGTGCTGGGA 741
                             -- i --       v  i  i    i     i              
  L1M4_orf2#LINE/    370 AAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr20_18812271_    742 AAACTATATATCCACATGCAGAATAATGATATTAGACCCTTCTCTCACAC 791
                         v    iv   ?         i  v     vi  i     i vi       
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr20_18812271_    792 CATATACAAAACTCAACTCAAAATTAAT-AAAGACTTAACTGTAAAACCT 840
                                    v i          vi  - ?    i   v     i v  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr20_18812271_    841 GAAGCCTTAAAACTACTGGAAGAAAATGTAAGGGAAAATCTTCCTGACAC 890
                         i  i iv       vi i        ii  i ? v        v    vi
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr20_18812271_    891 TAGCCTGGGGAATAATTTTTTTGATATGACAACAAAAGCAGAGACAACAA 940
                          i vi i  v   ii   i  v         v        v ii      
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr20_18812271_    941 AAGCAAAAATAGACAGGTGAGGCTGCATCAAACTAAAAGGCTTCTGCACT 990
                            v         i ii vi i  v       v v   ii   i  ii  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr20_18812271_    991 ACAAAGGAAATAATCAACAGGGCAAAAAGGCAATCTACAGGATGAGAGAA 1040
                         v       v iv     v ii ii     i   i i    i   i     
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_18812271_   1041 AATATTTGCAAATCACATATATAATAAAGTCCTAATATTCAAAATATATA 1090
                                        i    v i    i vv  vi   i  i        
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr20_18812271_   1091 AAGAACTCAAAAAACTCAGTAGCAAAAAG-CAAATAACCTGATTTAAAAA 1139
                                 vv v      i  ii      -         ii   ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_18812271_   1140 TAAATGAGCTAAAGACCTGAGTAGACATGTCT---AAGAAGACATACAAA 1186
                          ---- i  v  i  ii   i       v   ---       i       
  L1M4_orf2#LINE/    820 T----GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr20_18812271_   1187 TACCCAACAGATGTAGGAAGAGATGGTCAACATCACTAATCAT 1229
                          iv    i iiiii v   i     v         ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (107 / 53)
Gap_init rate = 0.01 (9 / 739), avg. gap size = 2.22 (20 / 9)  


2873 23.98 4.18 4.40  chr20_18819713_18824187     3077  3985 (490)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr20_18819713_   3077 GGAGAGATATGCCATGTTGATGGATGGGAAAACTCAATAT-GT------- 3118
                            i      v       v      v    i   i     -  -------
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_18819713_   3119 -CAGTTCCTTCCAATTTCATCTATAAAGTCTATGTAATCCCAATAAAAAT 3167
                         -  i v iii    v  v     i i v  v i i      v  v     
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_18819713_   3168 TCTATCAAGTTATTTTGTGGATATGAACAAGCTCATTCTAAAGTTTGTAT 3217
                         i i v vivi v     ii  v  vi       v  i     i  ii   
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr20_18819713_   3218 GGAGAGATAAAAGACTCAGAATAGCCAACACAATAGTGAAGGAGAAAAAG 3267
                            i vii  ii   i            v     vv    ii    i  v
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_18819713_   3268 AAAGTCAGGGAACTGACACTACTTGACTTTAAGACTTACTATAAAGCTAT 3317
                              ii i i   v     v iii i  i  i        i       i
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr20_18819713_   3318 AGTAGCAAAGACAGTGAGGCACTGTTGAAAGAACAGACAAATAGATTAGT 3367
                             iiv         v  i    viiv   i i     v      i i 
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_18819713_   3368 GGAATAGAATAGAGAGCCCAGAAATAGACCCACATACATATAATGGTCAG 3417
                                   v     i         i     --     v  -      i
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTA-TGGTCAA 348

  chr20_18819713_   3418 TTACTGTTTGACAAAGAAGC------------------AAAGA-TAGTCT 3448
                           iv v  i     i iv  ------------------     -      
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_18819713_   3449 TTACAACGGAGGATGCTGGAATAACTAGACATCCACATGGGCCCTCCCCC 3498
                           v    ii v i      i i    i  i ?       -----------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATG----------- 437

  chr20_18819713_   3499 ACCCTCACCAATAAAAAGAATCTAGACACAGACCTCAACAAAACTAATTC 3548
                         --------   v i  v   vi i   v vv      ------------ 
  L1M4_orf2#LINE/    438 --------CAAAAGAATGAAGTTGGACCCCTACCTCA------------C 467

  chr20_18819713_   3549 AACCGCA-ACAAAAACTAATTCAAATGGGATCACAGTACTAAATATAAAA 3597
                          -  ii -       i   i     vv      ?  vv      i   i 
  L1M4_orf2#LINE/    468 A-CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr20_18819713_   3598 CGC-AAAACTGTAAAACGACTAGAATACAACATAGGAGAAAATCTATATG 3646
                         -  -      i      vvi     v v        ? v      vii  
  L1M4_orf2#LINE/    517 -GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr20_18819713_   3647 GCCTTGGCATATGGTCTTGACTTTTTAGATATAACACCAAAAGTATAATC 3696
                         i      vv  -  ivv  ii  i        i          i i  v 
  L1M4_orf2#LINE/    566 ACCTTGGGTTA-GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr20_18819713_   3697 CATGAAAGAAAAAACTGATATGCTGGACATCATTAATATCAAA---TTTT 3743
                         v ii          iv    vii     v    i  v  i   ---    
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr20_18819713_   3744 CTGCTCTGTCAAAG-ACATTGTTAAGAGAATGAGAAGACAAGCCACAGAC 3792
                         v    ---      -   i i i    i i   i       v       v
  L1M4_orf2#LINE/    665 GTGCT---TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA 711

  chr20_18819713_   3793 TAGGAGAAAATATTTGCAAAAGATATATCTGATGAAGGACTGTTATCCAA 3842
                          i                  vv           i i     vv      i
  L1M4_orf2#LINE/    712 TGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAG 761

  chr20_18819713_   3843 AACATACAAAAAGCTTTCAAAACTCAACAAGAAAATGA---ACAACTTGA 3889
                           i   i   i i  i i v       i  v    v  --- i   iii 
  L1M4_orf2#LINE/    762 AATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr20_18819713_   3890 TGGAAAAACAGGCTTAGGACCTGACAAAATATCTCACCAAA-AATATATA 3938
                          v?     ii   vv    ii   vv i i  i  v     -  v     
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr20_18819713_   3939 CATATAACACATAAACATCTAAAAAGGTGCTCGACATTGTAAGTTAA 3985
                           v  ii vv    i  iv i     i     i    ii????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (131 / 83)
Gap_init rate = 0.02 (18 / 907), avg. gap size = 4.33 (78 / 18)  


 606 22.73 0.65 1.30  chr20_18860051_18864639.rev     2871  3024 (1565)    L1M4_orf2#LINE/L1        1   153 (755)  

  chr20_18860051_   2871 TGGAAACACATCCCATGTTCATGGATGGATAGAATCAATACTGTGAAAAA 2920
                               v i                 v iv   v i    i   v  i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr20_18860051_   2921 TGACCATACTCCCCAAAGCAATCTACAAATTCAATGCAATTCCCATCAAA 2970
                           i v            vii       i      i     i  i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_18860051_   2971 ATACCA-CAATCATTCTTCACAGAACTAGAAAAAACAATCTTAAAATTAA 3019
                           v   - vii -  i  ii     v v  v  ivii   i       v 
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_18860051_   3020 TATGG 3024
                              
  L1M4_orf2#LINE/    149 TATGG 153

Transitions / transversions = 1.50 (21 / 14)
Gap_init rate = 0.02 (3 / 153), avg. gap size = 1.00 (3 / 3)  

2514 26.24 1.17 1.17  chr20_18860051_18864639.rev     3332  4097 (492)    L1M4_orf2#LINE/L1      143   908 (0)  

  chr20_18860051_   3332 AATTAATATGGAACCACAAAAGAGCCCACATAGCCAAAGCAAGACTAATC 3381
                             v        vii   ii  v  viv         i   vvi i vv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr20_18860051_   3382 AAAAAGAACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATACCA 3431
                           i         vi      vv     i v  ii i      viv   i 
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr20_18860051_   3432 TAAGGCCACAGTCACCAAAACAGCATAGTATTGGTGTAAAAATAGGCACA 3481
                         i  i  i     v i   i    ii i   i   ii   ii    i  i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr20_18860051_   3482 TAGACCAATGGTACAGAAT--AGAG-----AAATAAAGCCAAATAGTTAC 3524
                             i      v i     --    -----       v   v i v   i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr20_18860051_   3525 AGCCAACTGATGTTTGACAAAGCAAACAAAAACATAAAGTTGGGAAAGGA 3574
                         i i   i    v  i     i vviv   i v   vv i v       i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr20_18860051_   3575 CACCCTATTCAACAAATGGTGCTGGGATAATTGGCTAGCCACATGTAGAA 3624
                         i vi  v                    i  i   v  ?       i i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_18860051_   3625 GAATGAAACCATATCCCCATCTCTCACCTTATACAAAAATCAACTCAAAA 3674
                                iiiiv i   i i   v    v           i         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_18860051_   3675 TAGATCAAAGACTTACATCTAAGACCTGAAACCACAAATATTCT-AGAAG 3723
                          i     ?    i  v  v     v  i    i i   - i   -     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAG 541

  chr20_18860051_   3724 ATAACATCTAAA-AAATCCTTTTAGTTATTGGCTTAGGCAAAGACTTCAT 3772
                          v     vvi?i-     i iv iiii-    v        v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTT 590

  chr20_18860051_   3773 GAACAAAAACCCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATAGG 3822
                         ii i vi vv         v v         iv   i   i   i  v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_18860051_   3823 ACTTAATTAAACTAAAAACCTTCTGCACAGCAAAATAAATAATCAGCAGA 3872
                             v  i   v v    v   i  ii vv    iv v iv    iv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_18860051_   3873 GTTAACAGACAACCCACAGAGTGGGAGAAAGTCTTGACAATCTATACATC 3922
                           v  v              i         i v  vi   vii   i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_18860051_   3923 TGGCAAAGGACTAATATCCAGAATCTACAAGAGACTCAAACAAATAAACA 3972
                           ii  i     vi          v  i  iii    vv    v v  i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_18860051_   3973 AGTAAAAATCAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAAA 4022
                          vv    iv    i  i  v  i?    i     v     iv      i 
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_18860051_   4023 TCATTAACCATTCTCAAAAGAAGATATGCAAATGTCCAAAAAGCATATGG 4072
                         -    ------    v           i      v    v     i   i
  L1M4_orf2#LINE/    841 -CATT------TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr20_18860051_   4073 AAAAATGCTCAACATCACTAATTAT 4097
                            i             ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (116 / 81)
Gap_init rate = 0.01 (8 / 766), avg. gap size = 2.25 (18 / 8)  


2914 26.61 0.64 3.22  chr20_18864724_18870893.rev     4747  5678 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_18864724_   4747 TGAAAAAACATTCTATGCTAATGGAAATTGAAAGAATCAGTATCATGAAA 4796
                           i   i i  i i   i v     --   i    v i i   ii v  i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGA--TTGGAAGACTTAATATTGTTAAG 48

  chr20_18864724_   4797 ATAGCCATAATACCCAAAGTAATTTATAGATTCAGTGCTATTCCTCTCAA 4846
                           i  v   v v      v i  i  i       ii  v  i   v    
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr20_18864724_   4847 GCTACCATTGACTTTCCTTGCAGAATTAGAAAAAAACGACTTTAAATTTT 4896
                         iv v   vivi i  ii        v v  v  iv-i  iii    v  i
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTC 147

  chr20_18864724_   4897 ATATGGAACCAAACAAGAG-CCC-GTATACCCAAGACAATCCTAAGCAAA 4944
                                 -- vi    i -   - v   v    i      i i iv  i
  L1M4_orf2#LINE/    148 ATATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_18864724_   4945 AAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAATTATACTACAA 4994
                                   i      vv       v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_18864724_   4995 GACCACAGTAATCAAAGCACCATGGTACTGGTAACAAAACAGATATATAG 5044
                         ii i           ii  vii         i vv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_18864724_   5045 ACCAATGGAACAGACCAGAGGCCTCAGAAATAACACCACATGTCTACAAC 5094
                          i        i   viv   ivii         vv   i ii i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_18864724_   5095 CATCTGACCTTTGACAAACCTGACAAAAACAAGCAATGAGGAAAGGATTC 5144
                           vi   ii  i     ivv  v   i v  vv     i      i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_18864724_   5145 CCTATTTAATAAATGGTGTTGGGGAAACTGGCTAGCCATATGCGGGAAAC 5194
                         i  v  i  i        i    ---  -------------------   
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGG---AC-------------------AAC 423

  chr20_18864724_   5195 TGGCTAGCCATATGCAGAAAACTGAAACTGGACCCCTTCTTT-TACCTTA 5243
                            v  ?   i     i  i v    ii         v i i-i   v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr20_18864724_   5244 TACAAAAAATAACTCAAGGTGGATTAAAGATGTAAACATAAGACCTAAAA 5293
                                 v        ii     i ?   iv    ii     v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr20_18864724_   5294 CCATAAAAACCCTAGAAGAAAACCTAGGCAGTA--CCATTCAGGATATAG 5341
                          i      vi i           v    ?-   --i -   iv  iv v 
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGN-GTAAATC-TTCGTGACCTTG 571

  chr20_18864724_   5342 GCATGGGCAAAGACTTCATGACTAAAACACCAAAAGCAATAGGAACAAAA 5391
                          vv i     v ii   v iiv  vi            vv  v       
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr20_18864724_   5392 GCCAAAAAT-GACAAATGGGATCTAATTAAACTAAAGAGCTTTGGCACAG 5440
                          v-      -  i    v   ii v  i   v v  i i    v ii vv
  L1M4_orf2#LINE/    622 GA-AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr20_18864724_   5441 CAAAAGAAACTATCGTCAGAGTGAACAGGCAACCTACAGAATGGGAGAAA 5490
                             i  v      ivv i      v  i     i               
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr20_18864724_   5491 AATTTTACAATCTATCCATCTGACAAAGGGCTAATATCCGGAATCTACAA 5540
                          vv   i   vii  vi      i  i  i  vi     i    v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr20_18864724_   5541 AGAACTTAAACAAATTGACAAGAAAAAAACAAACAACCCTATCAAAAAGT 5590
                               ivv    v ii i  v     i     i     v  i?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr20_18864724_   5591 GGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGTGGCC 5640
                                    v    i     i     v        i  vi vi     
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr20_18864724_   5641 AACAAACATATGAAACAAAGTTCATCATCACTGGTCAT 5678
                           i  i  i      vi v i   v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (148 / 96)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.77 (36 / 13)  


3275 26.98 0.44 0.44  chr20_18878862_18883535.rev     3275  4182 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_18878862_   3275 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3324
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_18878862_   3325 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3374
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_18878862_   3375 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 3422
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_18878862_   3423 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 3472
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_18878862_   3473 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 3522
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_18878862_   3523 TACAGTAACCAAAACAGCATGGCACTGGTACCAAAACAGAGATATAGATC 3572
                                 i   i    ii   i     i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_18878862_   3573 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 3620
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_18878862_   3621 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 3670
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_18878862_   3671 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 3720
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_18878862_   3721 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 3770
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_18878862_   3771 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 3820
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_18878862_   3821 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAA 3870
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_18878862_   3871 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3920
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_18878862_   3921 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3970
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_18878862_   3971 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4020
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_18878862_   4021 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4070
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_18878862_   4071 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 4120
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_18878862_   4121 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 4170
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_18878862_   4171 ATCACTGGCCAT 4182
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (145 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3062 22.20 0.81 9.18  chr20_18983306_18985421      634  1624 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_18983306_    634 TGGAAGGATGTTCTGTGTTCAGGTATTACAAGATTCAGTATTGTTAAGAT 683
                              i   i i ii      v v   iv    i i i            
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_18983306_    684 GTGTGCT-TTTCTCAACTTGATCTACAGGTTTAATGCAATTCCAACGAAA 732
                          - iiv -i i i   v           i  i  i     i  v iv   
  L1M4_orf2#LINE/     51 G-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_18983306_    733 ATCCCAGTAAGGTATTTTGTGGGTGTTGACAAATTGATTCTAAAGTTTAC 782
                                ivivv v     ii ivi       ii    i     i  i i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_18983306_    783 ATGGAAAGGCAAAGGAACCAATACAGCCAATACGATAATGAACAAGAAGA 832
                                v    i   v   iv i      v  i  vv    v       
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_18983306_    833 ACAAAGTTGGAGGACTGACATTACCCAACTTCAAGGCTTACTATAGTAAT 882
                                         v   i v     i     ii       i -----
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA----- 244

  chr20_18983306_    883 CAAGACAGAAATTA-AATGATCAAGACGGTGTAGTATTGGTGAAGGAATA 931
                         --------  ii  - i i        i    i   i   iiv i i   
  L1M4_orf2#LINE/    245 --------AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr20_18983306_    932 GATACATAGGCCAATGGAACATAATAGAAAGCCCAGAAATAGACCCACAC 981
                           i i    ii        i v   v  i  i         i     i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr20_18983306_    982 AAATATACTCAACTAATATTTGACAATGGAGC-AAGAGCAATTCAATTGA 1030
                          vv   iv    i i  v  i     v  v  -    v  -      v i
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGG 385

  chr20_18983306_   1031 GCAAAGATAGTCTTTTTCATAAATGATGCTGGAACAATTGAGGGTCCAGA 1080
                          v  ii          iv i     i      i    i  iivi?   v 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr20_18983306_   1081 AGCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1130
                         v  -------------------------------------    i  vi 
  L1M4_orf2#LINE/    436 TGC-------------------------------------AAAAGAATGA 448

  chr20_18983306_   1131 AATCTGGGCACAGATCTTA-ACCCTTTCATAAAAATTAACTCAAAATGGA 1179
                          i -   i v vv i  i -   v v - i                    
  L1M4_orf2#LINE/    449 AGT-TGGACCCCTACCTCACACCATAT-ACAAAAATTAACTCAAAATGGA 496

  chr20_18983306_   1180 TCATAGACCTCAATGTAA-AGCACAAACCTGCAAA-CATGCAGGACAAAC 1227
                            ?      v       -   -i   v  ii   - vivi  i v   v
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_18983306_   1228 CACAGGAG-AAATCAAAGTGACCTTGGGTGGAGTGATGAGCTTTTAGACA 1276
                           i   ? -     vvv            vii ii   ivi i     i 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_18983306_   1277 AAATACTAAAAGCATGAATCTATGAAAGAAAACGCTTATTTAAATTTGAC 1326
                         vi i  i       i-  v v ii        vi--  vv      v   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCAC-AAGCAACAAAAGAAAAAA--TAGATAAATTGGAC 642

  chr20_18983306_   1327 TTTATTAAAATAAAAAACTTTTGCACTGCAGAAGACATTGTTAAGAGAAT 1376
                           i  i     v           ii  v  i i    i i i    i i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr20_18983306_   1377 GAAAAGACAAGTCACAGACTGGGAGAAAATATTTGCCAGACAAATATCTG 1426
                                   vi      v                 v iv  v       
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_18983306_   1427 GTAATGGACTTATATCTGAAATATAAAAAGAACTCTTAAAACTCAACAAC 1476
                         i   v      i    iii      v            v       i  i
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_18983306_   1477 GACAACAACAAA-AACTCATGTGGGTCCATCTGGAAATTGGGATTTTTGT 1525
                         i v  -i     -   i  -----------------------   ?----
  L1M4_orf2#LINE/    793 AAAAA-GACAAATAACCCA-----------------------ATTW---- 814

  chr20_18983306_   1526 CCAATTTAAATAAGCAAAAGATCTGAATAGATCCCTCATCAAAGAAGATG 1575
                         --  ---    ii     i   i        ivii  vi          i
  L1M4_orf2#LINE/    815 --AA---AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 859

  chr20_18983306_   1576 TACAGATGGCAAATAAGCATATGAAAAAATATTCAACATCATATGCCAT 1624
                             i     v        i       i  ii         ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (141 / 75)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 4.71 (99 / 21)  


3020 24.28 0.64 3.94  chr20_18986699_18991039     2911  3849 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_18986699_   2911 TGGAAACATATCCCATGCTCATGGATAGGTAGAATCAATATTGTGGAAAT 2960
                               v          i        v  v   v i        vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_18986699_   2961 GACTGTACTGCCAAAAGCAATCTATAAATTCAATGCAATTCCCACCAAAA 3010
                          i vi    v  v   vii     i i      i     i  i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_18986699_   3011 TACCACCATCATTCTTCACAGAACTAGAAAAAAACT-ATCCTAAAATTCA 3059
                          v   v vv v  i  ii     v v  v  i--  -             
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr20_18986699_   3060 TAAATTTTGTGAATTTATTTATGAATTTACAAATCAAAAAAAGAGCCTGC 3109
                           -----  -   -------   -----------   ii---  v  v v
  L1M4_orf2#LINE/    149 TA-----TG-GAA-------ATG-----------CAAGG---GACCCAGA 171

  chr20_18986699_   3110 ATA-CCAAAAGCAAGACTAAGCAAAAAGAACAAATCTAGTGGCATCACAT 3158
                            -      -   vvi i iv  i         vi i v  vv     i
  L1M4_orf2#LINE/    172 ATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr20_18986699_   3159 TACCCAATTTCAAACTATACTATAAAGCCATAGTCACCAAAACAGTATGG 3208
                          v            viv     i     i i   v i   i     i   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr20_18986699_   3209 TACTGGTATAAAAAATAGGCACATAGATCAATGGAACAGAAAAGAGAACC 3258
                               i    ii -   i  i              i    vv    ii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAATTGAGAGTC 319

  chr20_18986699_   3259 CAGAAATAAAGCCAAATGCTTACAGCCAACTGATATTTGAAACAAAGCAA 3308
                                   v   v iii   ii i   i    v  i  --   i vvi
  L1M4_orf2#LINE/    320 CAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA--CAAGGGTG 367

  chr20_18986699_   3309 CCAAAAACATAAAGTGGGGAAAGGACACCCTATTCAACAAGTGGTGCTGG 3358
                             i v   vv i         i i vi  v        i         
  L1M4_orf2#LINE/    368 CCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGG 417

  chr20_18986699_   3359 GATAATTGGCAAGCAACATGTAGAAGA-TGAAACTGGATCCTCATCTCTC 3407
                           i  i   vv ? v     i i    -    ii    i  ii i   v 
  L1M4_orf2#LINE/    418 GACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCAC 467

  chr20_18986699_   3408 ACCTCACACAAAAATCAACTCAAGATGGATCAAAGACTTAAATGTAAGAC 3457
                            vi i        i       i        ?    i           v
  L1M4_orf2#LINE/    468 ACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAG 517

  chr20_18986699_   3458 CTGAAACCATAACGATTCT-AGAATATAACATCTGG--AAACCCTTCTAC 3504
                           i    i    -i i   -    v v     vv ?--   i i iv iv
  L1M4_orf2#LINE/    518 CTAAAACTATAA-AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr20_18986699_   3505 TCATTGGCTTAGGCAAAGACTTCATGACCAAAAATCCAAAAGCAAATGCA 3554
                         i -    v        v ii   v iivi vi vv         v v   
  L1M4_orf2#LINE/    567 CC-TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr20_18986699_   3555 GTAAAAAAACAAAAATAAATAGTTGGGACTTAATTAAACTAAAAAGCTCC 3604
                         ii    i  --      i   iv v      v  i   v v    i  ii
  L1M4_orf2#LINE/    616 ACAAAAGAA--AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr20_18986699_   3605 TGCACAGCAAAAGAAATAATTAGTGGAGTAAACAAACAACCCACAGAGTG 3654
                           ii vv    i  v iv  i ivii   i  v i            i  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr20_18986699_   3655 GGAGAAAATCTTCACAATCTGTACATCTGACAGAGGACTAATATCCAGAA 3704
                                  v  ii   viii  i      i ii     vi         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr20_18986699_   3705 TCTACAAAGAACTCAAACAAATAAGCAAGGAAAAAACAAATAATCCCATC 3754
                          v  i         vv    v v ii  vi    i        i  v  i
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr20_18986699_   3755 AAAAAGTGGGCTAAGGACATGAATAGAAAATTCTCAAAAGAAGATATGCA 3804
                         ?    i     v     iv        v v     v           i  
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr20_18986699_   3805 AATGGCCAACAAACATATGGAAGAATGCTCAACATCACTAATTAT 3849
                                  i  i  i   i  ii             ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (134 / 90)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.53 (43 / 17)  


3615 23.84 1.43 1.21  chr20_19054604_19056534.rev      534  1439 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_19054604_    534 TGGAAAGATATCTCACACTCATGGGTTGGAAGAGTTAATATTGTCAAAAT 583
                                     i  iii      i        v          i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_19054604_    584 GTTCATACTACCCACAGCAATCTGCAAACTCAATGCAATCCCTATAAAAA 633
                          viv     v    v vii    i  i i    i           v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_19054604_    634 TTCCAA-TGCTATTTTTCCCAGAAACAGAATAAAC-AACTGTCAGATTCA 681
                          i   i-   i-     iv      iv  -i  i -i iiv v i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chr20_19054604_    682 TATTGAACCAGAGAAGACCTTGAATAGCCAAAGCAATCTTGAGCAAGAA- 730
                            v   viiv iii    iv           i         iv     -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_19054604_    731 --CAAAACTGAAGGTATCAGACTTCCTGATTTCATACTATAAAACAAAGC 778
                         --    ii  i   vv   v      ii      v viv  vv       
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_19054604_    779 TATAGTAACCAAGACAGCATGGCATT----TAAAAA-AGACATATAGGCC 823
                           i     i        ii   i i ----   ii -          ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_19054604_    824 ATTGGAACACAATAGAGAGCCCAGAAATAAGCCCATACATTTAGGGCCAA 873
                          v     i v   v     i          i            v  i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_19054604_    874 TTGATCTTCAACAAAGGTGCCAAGAATAAACAATGGAGAAAGGACAGTCT 923
                              i   i    i          vi vv      i     i i     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_19054604_    924 CTTCAATAAATAGTGTTAGGAAAACTGGATATCTTCGTGGAGAGGAATAA 973
                         i     i    i   i i   v         ? iv i  v i i    i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_19054604_    974 AATTTGACTCTTACATAATGCCATATATGAAAATCAACTCAAAATTGATT 1023
                          i  v   i i   v v ii       ii     i          v   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_19054604_   1024 AAATATTTAAATATAAGACACGGTCCTGTAAAACTTCTAGAAGGACACAC 1073
                          ? v ii     i     vviiivv  i       ii      i v   i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_19054604_   1074 AGGGAAGAAGTTTCTTGACATTGGTCTGGGCAATGATTTTTTAGATATGA 1123
                            ?ivi  vi   v    v    vi i       i   i          
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_19054604_   1124 CCCCAAAAGCACAGGCAACAAAAACAAAAGTAGACAAATGATATTACAT- 1172
                          v           i         iv    i    i    viv i v   -
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_19054604_   1173 AAAACTAAAAATTTCTGCACAGCAAAGGAAACAATCAACAAAGTGAAGAG 1222
                             i      i  i  ii vv       v  v     v        i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_19054604_   1223 ATGATCTATGAAACTGAATAATATATTTGCAAATCATATATCTGATAAGG 1272
                          ii i i iii  iv i v  v                            
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_19054604_   1273 GGTTAATATCCAAAATATATAAGGAAATCATACAACCCAATAGCAAAACA 1322
                          ii vi      i         i   v  v      i     ii    --
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA-- 796

  chr20_19054604_   1323 AAAACAAAAACATAACCTGATTGAGAACTAG--AAAAGACTTAAATTGTC 1370
                         - i     ----     ii   ? i  v i --   i  i  i   v v 
  L1M4_orf2#LINE/    797 -AGACAAA----TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_19054604_   1371 ATTTCTCCACAAAAGACATTCAAATGGCTACATGAGGTATATGAAAAGGT 1420
                                  v i    i  v        i -  i  -i i        i 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCA-ATAAG-CACATGAAAAGAT 889

  chr20_19054604_   1421 ACTCAACATCATTAGTCAT 1439
                         i          ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (142 / 70)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.85 (24 / 13)  


3133 25.58 1.33 1.66  chr20_19077594_19082221     3234  4136 (492)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr20_19077594_   3234 TATTCCATGTTCATGGATAGGAGAACGCAATACTATCTTAGATGTAGGTT 3283
                            i              v   ii  vi    i i - v     vvii v
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGT-TAAGATGGCAATA 57

  chr20_19077594_   3284 CTTCACAACTTGATCTATAGATTCAATGCAATTCCAATAAAAACCCCAGT 3333
                           i v   v        i        i     i  v  v    i     i
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC 107

  chr20_19077594_   3334 AAATTATTCTGTGGATATCAGAAAAAACTGATTCTAAAGATTATATGGAA 3383
                         vivi v  i  ii  v  ii-- v  i     i     iv i        
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAA 155

  chr20_19077594_   3384 AGACAAAAGACCCAGAATACCCAACACGGTGTTAAGGGAGAAAAATAGTG 3433
                          vi   ii           v    v  ii v  i iii    i  i iv 
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr20_19077594_   3434 TTGAAAGACTGACACTTCCCAACTTCAACACTAAATATAAAGCCACAGTA 3483
                            i i    v           i     v   v v  i     i      
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr20_19077594_   3484 ATGAAGACAGTTTGGTTTTGACAAAAGAATGGACAAATAGATCATTGGAA 3533
                           v        v    vi  i  v   i  i    v        v     
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr20_19077594_   3534 CGTACTAGGGAGCCCAGGGAAAGACACCCACAGTTAGTTAGAATCAATTG 3583
                         iiv v v i   i    --   v v     i --i v   vii       
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAG--AAATAAACCCATA--CATTTATGGTCAATTG 351

  chr20_19077594_   3584 ATGTTTTATGAAGGAGTAAAGGGAATTCTGTGGAGAATAAATAGTCTTTT 3633
                           v  iv ii i  v iv   ivv    vi   i   vi           
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_19077594_   3634 CAACAAATAATGCTGGAACAATTGGAAATTGACATGCAAATAAGTAAAAA 3683
                                 ii      i    i    v ?iv         vi i i  iv
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_19077594_   3684 TAGGCATAGACCTTATGCTTTTTACAAAACTTAACTCAAAATGGACCATT 3733
                          i i vivv    i ii iv v       v               i  ?v
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_19077594_   3734 AATTTAAATGTAAGATATAAAACTACATACCCCC----AGGTAACATAGG 3779
                         i ii           vv        i v v i i----  iv        
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_19077594_   3780 TAAAAATCTAGGTGACCTTGGGTTTGGTGACGACTTTTTGGATACTACAT 3829
                         ?iv      vv             v  ii i ii  i  i    iv   i
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_19077594_   3830 CAGAAGAACAATCCATGAAA---AAAATTGATAAGTTGGACTTCATTAAA 3876
                           i   v    v v ii   ---     v     i           i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_19077594_   3877 ATTAAGAAAAACAATTGCTCTGAAAAAGACACTGT-AAGAGACTGAGAGG 3925
                              ---    vv   iv  vv   i      i -    i v   i i 
  L1M4_orf2#LINE/    652 ATTAA---AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_19077594_   3926 ACAAGTCA--GACTGAGGAAAAAATCTTTGTAAAACACTTATCTGTTAAA 3973
                             vi  --  v  -   i     v    i   v  iv      v   i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATG-GGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_19077594_   3974 GGACTGGTATTCAAAATATAGGAGAAAAAACATCTTAAAACTCACAAATA 4023
                              v    i  i      v---   i   -     v      vv    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATAT---AAAGAAC-TCTTACAACTCAATAATA 793

  chr20_19077594_   4024 AGAAAACCAATAAGCCAACTAAGAAATTGGTAAAAGGTCTGACTAGATAT 4073
                          i  i  v     v    i ? i    v  i   i i i   v    i  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_19077594_   4074 CTCACTCAGTAAGATATATAGATGGCAAATAA--ACATGAAAATATGCTC 4121
                         i  v iv iv        i i     v     --         v      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_19077594_   4122 AACATCATATTTCAG 4136
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (130 / 97)
Gap_init rate = 0.01 (13 / 900), avg. gap size = 2.08 (27 / 13)  


2967 27.12 1.10 0.99  chr20_19090533_19096960.rev     5030  5936 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_19090533_   5030 TGGAAGAATACTCCATGCTCGTGGAAAGGAAGAATCAATATCGTGAAAAC 5079
                              ii   ii     i  i    vv      v i     i  v  i i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_19090533_   5080 GGCCATACTGGCCAAGGGAATTTATAGATTCAATGCCATCCCCATCAAGC 5129
                            v     vv    ivvi  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_19090533_   5130 TTCCAA-TGACTTTCTT-CAGAGAATTGGAAAAAACT-ACTTTAAAGTTC 5176
                          i   i-  v    i  -    -     -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_19090533_   5177 ATGTGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAAAA 5226
                           i     viiv  ii  v  v v  v     i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_19090533_   5227 GAACAAAGCTGGAGGCATCATTCTACCTGACTTCAAACTATACTACAAGG 5276
                                 i      vv   iv  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_19090533_   5277 CTATAGTAACCAAAACAGCATGGGACTGGTACC-GAACAGAGATACAGAA 5325
                            i     i   i    ii   v     i iv- i i   v   i   v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_19090533_   5326 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACATATCTACAAC 5373
                                 i    i--    i  --        vv   i i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr20_19090533_   5374 TATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTC 5423
                         i vi    i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_19090533_   5424 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5473
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_19090533_   5474 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5523
                             ii    i    v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_19090533_   5524 ATTAAAGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5573
                           i ?    i  v    v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_19090533_   5574 CCAAGGC---AATGCCATTCAGGACATAGGCATGGACAAGGACTTCATGA 5620
                          vv   ?---   -- -   iv   v v  vv i i   v ii   v ii
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr20_19090533_   5621 CTAAAACACCAAAAGCAATAGCAACTAAAGCCAAAATAGACAAATGGGAT 5670
                         v  vi            vv      v    vv        i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr20_19090533_   5671 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5720
                         i v  i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr20_19090533_   5721 GAACAGGCAACCTACAGAATGGGAGAACAAT-TTTGCAATCTACCCATCT 5769
                            v  i     i              -   -       vii ivi    
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAA-AATATTTGCAAATCATATATCT 741

  chr20_19090533_   5770 CACAAATGGCTAATATCCACAATCTACAAAGAACTTAAACAAATTTACAA 5819
                         v i  iv i  vi      v   v  i        ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_19090533_   5820 GAAAAAATCAAACAACCCCATCAAAAAGGGGGCGAAGAATATAAACACAC 5869
                         v     iv    i     v  i?    iv    i   i  v i  i v  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_19090533_   5870 ACTTCTTAAAAAAAGACATTTATGCAGCCAACAGACACGTGAAAAAATGC 5919
                          i    iv   i    i  vi viii     i ii   i      i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_19090533_   5920 TCAGCATCACTGGCCAT 5936
                            i     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (144 / 98)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.46 (19 / 13)  


3276 18.98 2.34 0.69  chr20_19111425_19113144.rev      501  1227 (493)    L1M4_orf2#LINE/L1      143   881 (27)  

  chr20_19111425_    501 AATTTACTTGGTAATGAAAGAGATA-AAAATAGTGAAAATAAACTTTAAA 549
                             i iv   v    v   i  iv- i     iv    i  v   v   
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr20_19111425_    550 AA--AGAATAAAGTTAGAGAATTCACACTTCC-AGTTTCAAAACTTACTA 596
                           --    i      i   i i          - i               
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr20_19111425_    597 CAAAGCTCCAGGAATCAATACTGTGTGGTATGGATGTAACAGTAGACACA 646
                                v   v      v  v        iv iii   vii      i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr20_19111425_    647 TAGATCAATGCAATATAATTGAAAGTCCAGAAATAAATTGATACTTTTAT 696
                                   v    v      i              iiv    v     
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr20_19111425_    697 GATGAATTAATTTTTGACAGGGGTGCTAAAAAAATTTAATGGGGGAAAAT 746
                          i v    i     i    i      i  i vv   i       i  i -
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA- 391

  chr20_19111425_    747 ATAGCTTTTGCAGCAAATGGTATCGGAACAACTATGTATCTACCTGAAAA 796
                             ii   v  i        iii  i      ivi  ? i  v  v   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_19111425_    797 AAGAATGAATTTGGAGTCAAATCTCAGA--ATATACAAGAATTAAGTCAA 844
                          -       v     vi vv i    v --        i      v    
  L1M4_orf2#LINE/    442 A-GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr20_19111425_    845 AATGAATCAAAGACCTAAATGTAAGAGTGAAAATGATAAAACTCTTAGAA 894
                             i    ?                 iv    iv               
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr20_19111425_    895 GAAATCATAGTCATAAGTCTTTGTGACCATGTATTAGCCAATGGTTTTTT 944
                             v     v?i   i    i      v  vi    v         i  
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_19111425_    945 TAGATATGATACCAAAAACACAAGCAATAAAATA-----TTGATTAATTG 989
                         -        i       i         i    v ----- v   v     
  L1M4_orf2#LINE/    591 -AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_19111425_    990 GACTTCATAAAAATCAAAAGTAACTATGCTTCAAAGGACACTATTAATAA 1039
                                 v     i    iivvi i                  i  v  
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_19111425_   1040 AGT-AAAATACACCCTACATAATGGGAAAAAA-ATATGCAAATCATATAG 1087
                            -    v   v  i   v       i    -  v             v
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_19111425_   1088 CTGATAAGAGACTAATGTTTATAATATATAAGGAACT--TGTAATTCTAC 1135
                                 i    vi i ii v         i     -- ii  i  v i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_19111425_   1136 ACTAAAAAGACAAATAACCCAACTTAAAAATGGGCAAA--ATTTGAACAG 1183
                          v                    i ?             --       i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr20_19111425_   1184 ACATTACTCCAAAGAAAGTATACTGATGGCCAATAAGATCATAT 1227
                              v          ii     vi            --  i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG--CACAT 881

Transitions / transversions = 1.44 (79 / 55)
Gap_init rate = 0.02 (13 / 739), avg. gap size = 1.69 (22 / 13)  


1824 25.14 10.86 7.09  chr20_19126100_19129753.rev     2288  3162 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_19126100_   2288 TGGAAAAACATTCCATGCTCATAAATTGGAAGAAGAAATATCATCAAAAT 2337
                               i i  i     i    ii         vvv     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_19126100_   2338 GTCCATGCTACCCAACATGATCTGCAGATTTAGTGCAATTCCTATCAAAT 2387
                          v v  i  v     vv      i      i ii     i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_19126100_   2388 TATCAACATCATTTTTCACATAATTAATTTTAGAAAATTAATTTATAAAT 2437
                          vi  i vv v     ii  -------------i     i i--------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCA-------------GAAATTGAC-------- 129

  chr20_19126100_   2438 TTAATTTTTCTAAAATTAAAATCATAAGTTTAGAAAAAACTATTCTAAAA 2487
                         -------------------------   i --  -------- i      
  L1M4_orf2#LINE/    130 -------------------------AAGCT--GA--------TCCTAAAA 144

  chr20_19126100_   2488 TTCATATGGAACCAAAAAAGAGCCCAAATAGCCAAAGCAATCCTAAGAAA 2537
                                    viiv  ii  v  vi          i     i i i   
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_19126100_   2538 -AAGAACAAAAACAGAAGCTAGATTACATTACCTGACTTCAAACTGTACT 2586
                         -         ivii  i vi--- i   i v  ii i      viv    
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGAC---TCACACTTCCCAATTTCAAAACTTACT 241

  chr20_19126100_   2587 ACAAAGCCACAGTAACCAAAACAGCTTGGTACTGG--------TAGA--- 2625
                                i       i   i    iv         --------    ---
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_19126100_   2626 -------AA---AATAGAAC-------CCAAATATAAAGCTATATACCTA 2658
                         -------  ---       i-------   i v     v i   i ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_19126100_   2659 CAACCAACTAATCTTTGACAGAGTTGACAAAAAGAAACTGTGGGAAAAGG 2708
                         iiii   i i  i  i    ii v  v   i vv vv vi    i    i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_19126100_   2709 ATACCTTATTGAATAAATGGTGCTAGGAAAACTGGCTAGCTATATGCAGA 2758
                            vii v  v  i          i   v      v  ? i i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_19126100_   2759 AGAGTGAAACTGAACCTCTATCTCTTACCATAAGCAAAAA---------- 2798
                            i    ii  i   i   i   vi      vi      ----------
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_19126100_   2799 ------------CCTAG------GA---AATACT------CTTCTGGA-- 2819
                         ------------    i------  ---  v   ------  ii i  --
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_19126100_   2820 ----CATTGGC------CTT---GACAAAGAATTAAG-AATTAAGTCTT- 2854
                         ----   v  ?------   ---   vvv ii   i -   vivv    -
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_19126100_   2855 ----------CAAAAGCAATTGCAACAAAAACAAAAAGTGA-AAATTGGT 2893
                         ----------        vvv         iv     vv  -       -
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG- 640

  chr20_19126100_   2894 AACTAATTAAA-CTAAAGACCTACTGCACAGCAAAAGAAACTATCAACAG 2942
                          vi v  i   -i    i  i -i  ii vv    i  v        v i
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTT-TTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_19126100_   2943 AGCAAACAGACAACCTACGGAATGGGAGAAAATATTTGCAAACTATGCAT 2992
                           ii  v        i  i                       ii  ii  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_19126100_   2993 CCAACAAGGTACAAATATCCTGAATTTATAAGAAGCTCAAACAATTCAAC 3042
                          ii i    v  vvi     v    v     ii i   vv    i    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_19126100_   3043 AAGAAAAAAAACAAGCAGCCCCATTAAAAAGTATGCAAAGGACATAAATA 3092
                           v     i -   ii i   v   ?    i iv        iv i    
  L1M4_orf2#LINE/    790 AATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr20_19126100_   3093 TACACTTCTCAAAAAAACACATACAAGTGGCCAACAAACATAAAAAAAAG 3142
                         v   i     v   i  v i      i       i  i  i vi    ii
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr20_19126100_   3143 TGTTCGGTATCACTAAACAT 3162
                           i  iii    ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (142 / 75)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 6.54 (157 / 24)  


1882 23.83 8.12 0.69  chr20_19233709_19235279      501  1079 (492)    L1M4_orf2#LINE/L1      287   908 (0)  

  chr20_19233709_    501 GACACATAGACCAATGGAACAGGATAGAGAACCCAGAAATAAAGCCA--C 548
                             i     i        i  i  v    ii           v   -- 
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATAC 336

  chr20_19233709_    549 ATCT--GGTC--------TTCAAAAAAGTCAACATTAACAAGCAATGGGG 588
                           i --    --------   i v  i viiv  vv v  vv        
  L1M4_orf2#LINE/    337 ATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG 386

  chr20_19233709_    589 AAAGGAC--TCCTTACGCGATAAACGGTGCTGGGATAAGTGGCCAGCCAC 636
                             i i--  i  --v i i   i          i  v   vi ?    
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr20_19233709_    637 ATGCAGAAGAATGAAACTAGACCCCATTCTTTCACCATATACAAAAATTA 686
                              i         ii i      vvi  iv                  
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr20_19233709_    687 AC-CAA-----------GACCT-----------C--AAACAATAAAAATC 711
                           -   -----------     ----------- --    v      v  
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr20_19233709_    712 CTAGAAGAAAACCTAGGAA-ATATCATTCTGAACATTGACGTT-GGCAAA 759
                         i           v    ?i- v   -   vvi  v   i-   -     v
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGG-GTTAGGCAAT 582

  chr20_19233709_    760 GAATTTATGACTAAGTCCTTAAAAGCAGTGGCAACAAAAACAAAAATTGA 809
                          iv  iv iiv  v v vii       vvi         iv      v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr20_19233709_    810 CAAGTGAGATCTAATTAAACTAAAGAGCTTCTGCATAGCAAAATAAACTA 859
                         i  i vi  ii v  i   v v  i i   i  iiivv    iv v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr20_19233709_    860 TCAACAGAGTAAAAAGACAACCTACAGAATGGGAGAAAATATTTGCAAAC 909
                             v i   i           i                          i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr20_19233709_    910 TATGCATCTGACAGAAGTCTAATGTCTAGAATCTATAAGGAACTT----A 955
                         i  ii      i iii v  vi i  i     v     i     i---- 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr20_19233709_    956 ATTCAATAAGCACAAAACAAATAACCCA--TTAAAAATGGGTAAAGGACA 1003
                          i       vv v  i            -- ?         i      iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_19233709_   1004 TAAACGGACATTTCTCAAAAGAAGACATACGTGTGGCCAACAAATATATG 1053
                          i  ii          v        i    ivi       i  ii i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_19233709_   1054 AAAAAGTGTTCAACATCACTAATGAT 1079
                             ii  i         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (83 / 52)
Gap_init rate = 0.02 (15 / 622), avg. gap size = 3.40 (51 / 15)  


 695 19.08 0.00 0.00  chr20_19313057_19317086.rev     2375  2505 (1525)    L1M4_orf2#LINE/L1        1   131 (777)  

  chr20_19313057_   2375 TGGAAAGATATCCTGTGTTCATGCATTGGAAGAATGAATACTGTTAAAAT 2424
                                      ii        v         v v    i      i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_19313057_   2425 GTCCATGCTAGCCAAAGTGATCTACAGATTCAATGTAATCCCTATCAAAA 2474
                          v v  i  vv     v                i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_19313057_   2475 TTCCAATGGTATTTTTCACAGAAATAGAAAA 2505
                          i   iiv iv     ii       v  v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA 131

Transitions / transversions = 1.08 (13 / 12)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.00 (0 / 0)  

2543 24.56 6.75 1.62  chr20_19313057_19317086.rev     2798  3538 (492)    L1M4_orf2#LINE/L1      130   908 (0)  

  chr20_19313057_   2798 AAGCCAATTTTAAAATTCATATGAAACCACAAGG-ACTTTGAATAGCCAA 2846
                             ii  ii             i  vii     -  iiv          
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr20_19313057_   2847 AGCAATCTTGAGCAAAAAGAACAAAGCTGGAGGCATCACGCCACCTGACT 2896
                          i         iv  i          i      vv    i iv  ii i 
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr20_19313057_   2897 TCAAA------------GCTCCAATAAGCAAAAGAGCAAGGCACTGGCAT 2934
                              ------------   v  i   v   i v  iiv  i        
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr20_19313057_   2935 AAAAACAGACACACAGGTCAATGGAACAGAACAAAAAGCCCAGAAATTAA 2984
                           ii i     i i  i         i    ivi i  i        v  
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr20_19313057_   2985 TTCATGCATTTACAGTTGATTGATCTTCAACAAAG-TACCAAGAACACAC 3033
                         ii   i      ii  ii      i   i    i - i      v  iv 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr20_19313057_   3034 AACGGGGAAAGAACAGTCTCTTCAATAAATGGCATTAGG------GAA-- 3075
                           i          i     i     i      iii i  ------ i --
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr20_19313057_   3076 ---ACATGCTTAATAATGAAATTGGACCATTATCTCACACCATATACAAA 3122
                         ---      vv  v      i       vi  i                 
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr20_19313057_   3123 AATCAATTCTAAATTAATTAAAAACTTAC-CATAAGGGCTGAAACTGTTT 3171
                            i  i  v    vi  i ? i  i  v-ii    i   i     i --
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT-- 527

  chr20_19313057_   3172 TAAAACTACTAGAAGAAAATATAGAGTGAAAGCTTCTTGACATAGGTCTG 3221
                         -      vi          i    i?vv   v    v    v v  vi i
  L1M4_orf2#LINE/    528 -AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr20_19313057_   3222 GACAATGATTTTGGTTTTTTGGGTATGACCCCAAAATTATAGGCAACAAT 3271
                          i     ------    i  i i      v      vi i i       v
  L1M4_orf2#LINE/    577 GGCAATG------GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr20_19313057_   3272 AGTAAATACAGACAAATGGGATTGCATCATAACTAAAACCCTTCTGCCCA 3321
                           v   v i   i    v   i v     v  i     v i  -  iv v
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT-TGTGCT 669

  chr20_19313057_   3322 GTAAAGGAAACAATCAACAGAGTGAAGAGGCAACCTAAGAAATGAGAAAA 3371
                         vi      v  v     v i      i  i     i vii    i  i  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_19313057_   3372 AATATTTGCAAGCCATACATCTGATAAGGCATTAATATCTAGAATGGATA 3421
                                    ii    i           v i vi    i     iv   
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr20_19313057_   3422 AGGAACTCAAACAATTTCACAGCAAGAAAACAAATAACCTGATTAAAAAA 3471
                          i      vv    i iv i ii  i  i          ii   ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_19313057_   3472 TGATCAAGGG--------------TCCT--------GATA-A-AAATGGC 3497
                           iv   i  -------------- i  --------    - -       
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr20_19313057_   3498 CAGCAGGTATACAAGAAAAATGTCTAATCATCAGAGAAACG 3538
                           ii i i i ii -   i   iii  -     ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGA-AAAGATGCTCAA-CATCAZZZZZZZZ 908

Transitions / transversions = 2.44 (127 / 52)
Gap_init rate = 0.02 (15 / 779), avg. gap size = 4.13 (62 / 15)  


4204 20.42 0.88 0.66  chr20_19321466_19323765      903  1808 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_19321466_    903 TGAAAAGACATCACATATTTATGTAATTGGAATAGTTAATATTGTTAAGA 952
                           i     i   v   i  i   -i       v v               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATG-GATTGGAAGACTTAATATTGTTAAGA 49

  chr20_19321466_    953 TGTCAAGATTACACAAAATGATCTACGTATTTAATATAATACCCATCAAA 1002
                           v   v i v v    v        iv   i  iii   v  i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_19321466_   1003 ATTGTAATAGTGTTTTTTGAAGAATTAGAAAAATCCACCCTAAAATTCAT 1052
                           ivi iiv iv       v    v v  v  iiiv i            
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_19321466_   1053 ATAGAATCTTAAGGGACCCCAAATAGCCAAAACAATCTTGAAAAAGAA-- 1100
                           i   vivi         vi                           --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_19321466_   1101 -TGAAGTTGGAAGTCTCACACTTACTGATTACAAAATATATTACAAAGCT 1149
                         -ii        i v         v ii   v     iv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_19321466_   1150 ACAGTGATCAAAACAGTGTAGTACTTGTGTAAAGACAGACATA--GATCA 1197
                              i     i       i     v ii   i  i       --     
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_19321466_   1198 ATGGAATAGAATAGGTAGCCCATATATTAACCCTCACATATGTGGTCAAA 1247
                                     v iv  i   v v  v     vi    v i       v
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_19321466_   1248 TTATTTTCAACAAGAGTTCCAAGACTATTCAATGGGGAAAGGACAGTCTC 1297
                          v      i     i  v       i               i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_19321466_   1298 TTCAACAAATGTTTCTGGGTAAACTTGATATCTACATGCAAAAGGATGAA 1347
                                    v v     vv    v    ? i           i     
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_19321466_   1348 GTTGAGCTCTTACCTTACACCATAGACAAAAATTAAGTCAAAATGAATCA 1397
                             ii i i     i        v           v        i    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_19321466_   1398 AAGACCTAAATATAATATCTAAAAATATAAAATTCTTAGAAGAAAACATA 1447
                         ?          i   v v      v       i                 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_19321466_   1448 GGAGTAAAGCTTCCTGCTGTTGGATTTTGCAGGGATTTCTCAGATATGAC 1497
                           ?     v    v  viv    i  vv   iv i     i         
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_19321466_   1498 ACCAAAACCATAGGCAACAAAAGTAGAAATATCTAAATTGGACTGCATCC 1547
                                v  i i          v i     vv           v    v
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_19321466_   1548 AAATGAAAAACTTTCACCAATTAAAAAACACTATCAACACAATGAAAAGG 1597
                             v         iiivvv i   ii          v v i       i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_19321466_   1598 CAACCTACAGAGTGGGAGAAAATACTTGCAAATTATATATCTGATCATAA 1647
                              i     i            i        i           v vii
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_19321466_   1648 GTTAATATCCAGGATATATAAGGAAGTCCTACATCTAAAAGCAAATGAGA 1697
                         ii vi       i        i   v  i    v  v  ---v   i i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA---TAATAAAA 796

  chr20_19321466_   1698 AAACCCAAATAACCCAA---AAAACTCAATAAAGGACTTGAATAGACATT 1744
                          i  --           ---    v viii      i             
  L1M4_orf2#LINE/    797 AGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_19321466_   1745 CCTTCAAAAAAGATGTACAAGTGGCCGACAAGTGTATGAAAAAATGCTCC 1794
                         i  i    i     i     i     i i   iii       i      v
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_19321466_   1795 ATGTCACCAGTCAC 1808
                          ii   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (107 / 75)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 2.33 (14 / 6)  


3113 26.02 0.43 3.21  chr20_19348691_19350600      485  1418 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_19348691_    485 TGAGATGATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 534
                           ii v     i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_19348691_    535 GGCCATACTGCCATTTTCATAATTTCATAATTTCATAATTTCATAATTTA 584
                            v     v  ---------------------  -    ----i  i  
  L1M4_orf2#LINE/     51 GGCAATACTCCC---------------------CA-AATT----GATCTA 74

  chr20_19348691_    585 CAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTCACAGAA- 633
                                  i  v     i     iv v   iivi i  i  ii     -
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAA 124

  chr20_19348691_    634 TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCGCA 682
                            -- v  i  - iii    i           viiv  ii  v  v v 
  L1M4_orf2#LINE/    125 TTG--ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr20_19348691_    683 TCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACACTA 732
                          v     iv     i i ivv i          i      vv       v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr20_19348691_    733 CCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTA 782
                           ii i      viv        i          i   i    ii     
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr20_19348691_    783 CTGGTACCAAAACAGAGATATAGATCAATGGAACAGAAC--AGAGCCCTC 830
                             i iv ii i   v                i    i--    i  --
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC-- 320

  chr20_19348691_    831 AGAAATAATGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGAGA 880
                                 vv  ii i  i  iiiii vi    i  i     ivv  vv 
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr20_19348691_    881 AAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAA 930
                          i v  vv            i  vvi  v  i  i              v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr20_19348691_    931 AACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACC 980
                               v  ?   i   i i  iiv    ii    i    v   i     
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr20_19348691_    981 TTATACAAAAATCAATTCAAGATGGATTAAAGATTTAAACGTTAGACCTA 1030
                         v           i  i    i      i ?   ii    i  v   v   
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr20_19348691_   1031 AAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATA 1080
                             i      vi i           v    ?i v viv   iv   v v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr20_19348691_   1081 GGCGTGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAAA 1130
                           vv i     v ii   v ivvi vi            vvi        
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAA 620

  chr20_19348691_   1131 AGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAG 1180
                           vv     v  i    v   ii v  i   v v  i i   i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr20_19348691_   1181 CAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAACATGGGAGAAA 1230
                             i  v    i  vv i      v  i     i   iv          
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr20_19348691_   1231 ATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAA 1280
                           v  i    vii ivi      i  i  i  vi          v  i  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr20_19348691_   1281 TGAACACAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGT 1330
                         v    v vv    v iv i  v     i     i     v  i?    i 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr20_19348691_   1331 GGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCC 1380
                             i     iv    i     i     v        i  vi viii   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr20_19348691_   1381 AAAAAACACATGAAGAAATGCTCATCATCACTGGCCAT 1418
                           v  i        i i       v     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 4.25 (34 / 8)  


3088 24.54 4.34 0.80  chr20_19370615_19372932.rev      960  1835 (483)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr20_19370615_    960 GGAGAGACATTCCATGTTAATGGATAGCAAGACTCAATATTGTTAGGATA 1009
                            i   i  i       v      v v      i          i   i
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_19370615_   1010 TCAGTTTTTCCTGACTTGCTCTATGGGTTCAATGCAATCTAAAATCAATA 1059
                         v  i vi i  ii v   v    ii i     i      ivv -    v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAAAA 100

  chr20_19370615_   1060 TCATAGCAAGTAATTTTGTGGATATGAACAAGCTGATTCCAGAGTTTATA 1109
                           vi   vivivv     ii  v  vi          i i i i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_19370615_   1110 CAGTAAGGCAAAAGACCCAGAAGAGCCAACACACTATTGGA---GAAAAA 1156
                         ii v  v    ii         v      v   v v   i ---   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_19370615_   1157 TAA-GTCAGAGGACTAAAACTACCTGACTTCA---TCTCTTACAAGGCTA 1202
                         i  -  ii       v v   v  ii i    ---ii vi     i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_19370615_   1203 TGGTAATCAAGATAATGTGATATTTCTGAAAGCAAAGACA----GACTAA 1248
                         ii          i i    i  i vviiv   v v     ----  ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_19370615_   1249 TGGAACACAATAGAAAGCTTAGAAATAGACCCATGCAAACATAGTCAATT 1298
                              i v   v  i  iii       i      i  vvi  i       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_19370615_   1299 GATCTCTGACAAGG-TATCAAAGGCAATGCAATAGAGAAAAGACAGTATT 1347
                            i ii       - ii   - i v  v    i i    ii i   v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_19370615_   1348 T--AATAAATGGTGCTGGGAAAGTTAGAT--CCATATGCAAAAGAAAATG 1393
                          --  i              v ii i   --   i           --  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--TG 447

  chr20_19370615_   1394 AACATAGATGCTGACATTACACCTTTCCCAAAAATTAACTCAAAATGGAT 1443
                           vv i  iv iv  v i     v viv                      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_19370615_   1444 CATAGACCAAAA-GTAAAATGC-AAAACTGTAAAACCTCTGGAAGATAAC 1491
                           ?     v   -    i -  -      i      iii i     v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_19370615_   1492 ATAAGAGAAAATATAGGTGACCTTGGGTTTGGTGATGATTTTTCAGATGC 1541
                            i ? v    v vv             v  ii   i   i i    ii
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_19370615_   1542 AACATACAAAATAAAAG-----AAATAAAAAATAGATAAATTGAACTTCA 1586
                         i   ivv   ii v   -----   v                 i      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_19370615_   1587 TTAAA-TTAA---CTGTTTTGTG-----AAAGACACTGCTCAGAGAGTGA 1627
                          i   -    ---  --      -----  i      iiiv   i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACT--TTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_19370615_   1628 AAAGACAAGCCACAGACTGGGTGAATATATTTGCAAAACAGATATTTGAT 1677
                                 v       v    v   v           v  v    i    
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_19370615_   1678 AAAGAACTAGTAAGCAATCTACACAAATAATTCTTTAAATTCAACAATAC 1727
                           i i   v   vv  ivv  i i   v  i    vv  i    i    v
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_19370615_   1728 G----CAAACAACCCAATTAAAAAGTGAGCAAAAGATCTGAACAGACACT 1773
                         i----    i         ?    i  i     i   i    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_19370615_   1774 CTGACAAAGAAGATGTACAGATGACAAATGAGCATACGAAAAGATTC-CA 1822
                         iivv          i    i   i v   i    i i        v -  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_19370615_   1823 A-ATCATATGTCAT 1835
                          -    ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (133 / 79)
Gap_init rate = 0.02 (21 / 907), avg. gap size = 2.14 (45 / 21)  


2845 25.81 4.84 0.23  chr20_20051166_20054954.rev     2430  3297 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_20051166_   2430 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTTGTGAAAA 2479
                               v i        i        v  v   v i      -  v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT-GTTAAGA 49

  chr20_20051166_   2480 TGACCATGCTGCCAAAAGCAATCTACAGATTCAATGCAATCCCCATCAAA 2529
                           i v  i  v  v   vii              i        i      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_20051166_   2530 ATACCACCATCATTCTTCACAGAATTAGAAAATACAATTCTAAAATTCAT 2579
                           v   v vv v  i  ii     v v  v  vvii  i           
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_20051166_   2580 ATGGAACCAAAAAAGAGCCCGCATAGCCAAAGCAAGACTAAGCAAAAAGA 2629
                               viiv  ii  v  v v         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_20051166_   2630 ACAAGTCTGGAGGCATCACAC----CA---CCAAAAC--AGCATGAG--- 2667
                             ivi      vv      ----  ---i      -- vi ii i---
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_20051166_   2668 --AGTCACCAAAACAGCATGATACTGGTATAAAAATCGGCACATAGACCA 2715
                         --   v i   i    ii  i      i    ii  v i  i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_20051166_   2716 ATGGAACAGAATAGAGAACCCAGAAATAAACCCAAA----TACAGCCAAC 2761
                               i     v    ii               v ----  ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_20051166_   2762 TGATCTTTGACAAAA----CAAAAACATAAAGTGGGGAAAGGACACCCTT 2807
                             i  i     ii----   i v   vv i         i i vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_20051166_   2808 ATCAACAAATGGTGCTGGGATAATTGCCTGGCCACATGTAGGAGAATGAA 2857
                         v                   i  i  vv i?       i ii        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_20051166_   2858 ACTGGATCCTCATCTCTCACC-T-TGGAAAAACCAACTC----------- 2894
                         ii    i  ii i   v    - - iv     ii     -----------
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_20051166_   2895 -----TTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACACT 2939
                         -----i     v     v  i    i      v ii       v    iv
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_20051166_   2940 GGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATCACCAAAAA 2989
                           ?iv  vi    vv   v    v        v i    v vivi vi v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_20051166_   2990 CCCAAAAACAAATGCAATAAAAACAAAGATAAATAGTTGGGACTTAATTA 3039
                         v      i  v v    i    iv   i   i   iv v      v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_20051166_   3040 AACTAAAGAGCTTTTGCATGGCAAAAGGAACGGTTAGCAGAATAAACAGA 3089
                           v v  i i      iiivv    i iv  vi i iv i i i  v   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_20051166_   3090 CAACCTACAGAGAGGGAGAAAGTCTTTACAATCTGTACATCTGACAAAGG 3139
                              i     iv        i v   i   viii  i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_20051166_   3140 ACTAATATCCAGAATCTACAACGAACTCAAACAAATCAGTAAGAAAAAAA 3189
                            vi          v  i  v      vv    v   i   v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_20051166_   3190 ACAAACAATCCCATCAAAAAGTGAGCTAAGGACATGAATAGATAATTCTC 3239
                         -    i  i  v  i?    i  i  v     iv        i v     
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_20051166_   3240 AAAAGAAGATATACAATTGGCCAACAA--ACATGAAAAAATGCTCAACAT 3287
                         v               v       i  --         i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_20051166_   3288 CACTAATGAT 3297
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.40 (129 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.67 (44 / 12)  


3262 25.64 1.00 0.22  chr20_20080492_20084824     2941  3841 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_20080492_   2941 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2990
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_20080492_   2991 GACTATACTGCCAAAAGCAATCTACAGATTCAATGCACTTCCCATAAAAA 3040
                          i v     v  v   vii              i   v i  i  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_20080492_   3041 TACCATCATCATTCTTCACAGAACTAGAAAAAACAATCCAAAAATTCATA 3090
                          v   v vv v  i  ii     v v  v  ivii    v          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_20080492_   3091 TGGAGCCATAAAAGAGCCTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 3140
                             iviii  ii  v  v v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_20080492_   3141 GAAATCTGGAGGCATCACATTACGTGACTTCAAGCTGTACTATAAGGCTA 3190
                         v   vi      vv     i v vii i     iviv     i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_20080492_   3191 TAGTTACCAAAAAAGCATGGTACTGGTATAAA-ATAGGCATGTAGACCAA 3239
                         i   v i   i v  ii         i    i-    i   i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_20080492_   3240 CAGAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTAAGAGCCAAC 3289
                         ii   i     v    ii           v   v i i   v - i   i
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG-GTCAAT 349

  chr20_20080492_   3290 TAATCTTCAACAAAGCAAACAAAAACATAAAGTAGGAAAAGGACACCGTA 3339
                          i  i   i    i vviv   i v   vv i i  i    i i viv v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_20080492_   3340 TTCAACAAATAGTGCTGGGAAAACTGGCGAGCCACATGTAGAAGAATGAA 3389
                                   i         v      vv ?       i i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_20080492_   3390 GCTGGATCCTCATCTCTCACCTTATACAAAGATCAACTCAAGATGGATCA 3439
                          i    i  ii i   v    v        i  i       i        
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_20080492_   3440 AAGACTTAAATCTAAGAGGTAAAGCCGTAAAAATTCTAGAAGATAACATT 3489
                         ?    i     v      v    i ii     v ii       v     v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_20080492_   3490 GGAAAAAACTCTTCTAGACATTGGCTTAGGCAAAGA---CCAAGA----A 3532
                           ?iv   -     vv   v    v        v i--- iv   ---- 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_20080492_   3533 C-CCAAAAGCAAATGCAACAAAAACAAAGATAAATAGATGGGACCTAATT 3581
                          -         v v         iv   i   i   i  v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_20080492_   3582 AAACTAAAAAGCTTCTGCACAGCAGAAGAAATAACCAGCAGAGTAAACAG 3631
                            v v    i   i  ii vv  i i  v iv i  iv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_20080492_   3632 ACAGCCCACAGAGTGGGAGGAAATATTTGCAAACTGTGTATCTGACAAAG 3681
                            i        i      i             iii i       i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_20080492_   3682 AACTAGTATCCAGAATCTACAAAGAACTCAAATGAATCAGCAAGAAAGAA 3731
                         i   v           v  i         vv ii v   ii  v   i i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_20080492_   3732 ACAAATAATCCCATCAAAAAGTGGGCAAAGGACATGAATAGAGAATCCTC 3781
                                 i  v  i?    i           iv        v v i   
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_20080492_   3782 AAAAGAAGATTTACAAACAGCCAACAAACATACGAAAAAATGCTCAACAC 3831
                         v         v      ii     i  i  i i     i          i
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_20080492_   3832 CACTAATTAT 3841
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.44 (134 / 93)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


 676 29.01 10.32 9.29  chr20_20254239_20256488.rev      879  1750 (500)    L1M4_orf2#LINE/L1        3   883 (25)  

  chr20_20254239_    879 GAAAAAAAACCTATCAGAGTTCATGGA--AGAAAATTTAAAAAGACCTGA 926
                             i v v  i  ----         --i   i i    v vviiivii
  L1M4_orf2#LINE/      3 GAAAGATATCCCAT----GTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr20_20254239_    927 ATGGTAATATTCCATTTTATAAATGTACCCCAAATTAACCTGTAACTTCA 976
                             i    i   ----------------       i i  ii iv    
  L1M4_orf2#LINE/     49 ATGGCAATACTCC----------------CCAAATTGATCTACAGATTCA 82

  chr20_20254239_    977 ATTCAGACTCAGTTAAAATTCCAAAAATAATTTTTATAAAGTTGGACA-- 1024
                          iv  iv i vi i     i   ivviivv     ii i iv v    --
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG 132

  chr20_20254239_   1025 -TGAT-----AATACATTCGGAAA-------------GAATAGCTAA--- 1052
                         -    -----   v   vi     -------------       i  ---
  L1M4_orf2#LINE/    133 CTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAAC 182

  chr20_20254239_   1053 ------------GAAGACTACACA-TTAAAG---------------ATAT 1074
                         ------------     --   v -  ii  ---------------  v 
  L1M4_orf2#LINE/    183 AATCTTGAAAAAGAAGA--ACAAAGTTGGAGGACTCACACTTCCCAATTT 230

  chr20_20254239_   1075 CAAGCCAACTTAT---AATGTCTCAATCATTACAACAGCATGG-AAGAGT 1120
                            ---      i---  v iiv  i v  i vi    ii   - vvi i
  L1M4_orf2#LINE/    231 CAA---AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr20_20254239_   1121 ACAGAAACAGACAAAATGGAGCAAAGAAACAGGGTAGGAAATTCAGAAAC 1170
                          i iii i     v - i  v   v i  i  ii v ii i i      -
  L1M4_orf2#LINE/    278 ATAAGGATAGACATA-TAGATCAATGGAATAGAATTGAGAGTCCAGAAA- 325

  chr20_20254239_   1171 TGAATTCTCTGTAGAAAAAGATTT-TGGCTCAGTGTAT----GATAATGG 1215
                          i  ii --------- v v    -   -   i vv  ----  i  v  
  L1M4_orf2#LINE/    326 TAAACCC---------ATACATTTATGG-TCAATTGATTTTCGACAAGGG 365

  chr20_20254239_   1216 TAGTATTTCAATTACATAGGAAAAAACATGAATTATTTAGAAAGAGTTGT 1265
                          ivi vvv v   vv  i  i   i -  iivi v  i iv  iv v  i
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGGGGAAAGA-ATAGTCTTTTCAACAAATGGTGC 414

  chr20_20254239_   1266 TGGGAAAATT--ATCTCTACACTTG-GAAACAGTAAAATTAAATTCTTAT 1312
                              v  i --  v? i   --  -i   v i i  i  ii ii i  i
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACA--TGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr20_20254239_   1313 ATTACACCACACACAATCACACACACAGTTTTCCAGATGAATTAAAGATG 1362
                         v i      i i    -- v ivv  -----  v i   i  i ?   iv
  L1M4_orf2#LINE/    463 CTCACACCATATACAA--AAATTAAC-----TCAAAATGGATCAWAGACC 505

  chr20_20254239_   1363 TCAATGTAAAA--CAAAGCTACGAAAGTGATAGAAGAAAA--TAGGAGCA 1408
                          v       i --i   i   ii   v vv          --    ? i 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr20_20254239_   1409 TATTTT-ACAATTTCCAGGTGGAGAA-AATTTCCTAAGTAGGAGAC--AG 1454
                         v  i  -iii ii ivi v i iv  -ii    i  ii  v  v  -- i
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr20_20254239_   1455 AATTCAA------AAAGAAGAATTTTGTTATTCTTCTTTGTTAGAGACGG 1498
                          iiv   ------      i  -------  -----------   v -ii
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAA-------AT-----------AGATA-AA 636

  chr20_20254239_   1499 TTTGATTATGTAAAAATTCCAA-CCTTTATA----AAAAAAGA-TATCAA 1542
                           v  i vii v      vv  - i   i i----   ii v -      
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr20_20254239_   1543 AAACAAATAATAAAAGTGAATAAAAAGACAAGCCACAAACTGGGAGAAAA 1592
                         i  -----------      ----       v     i v          
  L1M4_orf2#LINE/    687 GAA-----------AGTGAA----AAGACAACCCACAGAATGGGAGAAAA 721

  chr20_20254239_   1593 TCTTTGCAAAACACATATCCAATAAAGGAATAGTAAACCAAATACACAAA 1642
                          v        v  i     ii    i   v v   vv vi    i i   
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr20_20254239_   1643 GAGCTCTTAAAATTCAACAGTAGGAAAACAGACATCCAAATTTAAAAATG 1692
                           i      v  i    i i  ii  i   i i v  v    ?       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr20_20254239_   1693 GGCAAAAGAGCTG----GACACGTCACCAAAGAAGACATAGAGATAGCAA 1738
                               i  vi  ----    iv  v          i   v i  i  v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr20_20254239_   1739 GCAAGCATTTGA 1750
                         ii     iv   
  L1M4_orf2#LINE/    872 ATAAGCACATGA 883

Transitions / transversions = 1.71 (157 / 92)
Gap_init rate = 0.05 (40 / 881), avg. gap size = 4.28 (171 / 40)  


 252 24.59 0.00 1.64  chr20_20280608_20282891        6    66 (2218)    L1M4_orf2#LINE/L1      217   276 (632)  

  chr20_20280608_      6 ACACTACCTGATTTCAAAATATATTTCAAAACCATAGTAATCAAAACAGC 55
                              v  ii         iv  i v    i i i         i    i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr20_20280608_     56 ATGTGTATTAG 66
                         i  -   i i 
  L1M4_orf2#LINE/    267 GTG-GTACTGG 276

Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1)  

2336 20.81 1.51 7.69  chr20_20280608_20282891      482  1144 (1140)    L1M4_orf2#LINE/L1      242   863 (45)  

  chr20_20280608_    482 ACAGAGCCA----AACCATATCAGCATGGTACTGCCATAAAAACAGATAA 527
                            i   i ----  i  viv   ii        v     ii i   i v
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_20280608_    528 ATGTACCAGTGGGACAGGATAGAGAGTC-ATAAATAAACCTACACATTTA 576
                           iv i  i   i i  i  v       - v         i i       
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_20280608_    577 CAGGCAATTGATTTTTGACAAAAGTGCCAAGAACACACAATGGGGAAAGG 626
                         ii v           i     ii         v  iv            i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_20280608_    627 ACAGTCCCTCCAATAAATGGTATTGGGAAAATGGGAACATTCCACATGCA 676
                          i    ii i   i       ii     v  iv   -i ?-         
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA-TAK-CCACATGCA 439

  chr20_20280608_    677 GAAGAATGAAATTGGACTCTTCTCTCAGCCCATACACAAAAATCAATTCA 726
                         i         i      i i vi    vv     i        i  i   
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr20_20280608_    727 AAATGGAGTGAAGACTTAAACATAAGACCGGAAACTGTAAAACTTCTAGA 776
                                vii?    i    ii     v vi     i       ii    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_20280608_    777 AGAGAACATAGGAG-AAATAGTTCTTGACGTTGGTCTCAGAAAGGATTTT 825
                            i        ? -    v-   v    v    vi vi v  v i   i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_20280608_    826 TTTGGATGTGACACCAAAAGCACAGGCAACAAAAGCAAAAACAGACAAGT 875
                           -i   i                i          v     i   i  i 
  L1M4_orf2#LINE/    589 TT-AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr20_20280608_    876 GGGTCTACATCAAATTTAAAAGCTTCTGCACAGCAAAGAAAAC----AAC 921
                         v  v  v       v      i   i  ii vv     i v  ----  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_20280608_    922 AGAGTGAAGAGACAGCCCACAGACTGGGAGAAAATATTTGCAAATCATAC 971
                          i      i     i        v                         i
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_20280608_    972 ATCTGATTTGATGTATGATATCCAATTTTGGCTAATATCCAAAATATACA 1021
                                ------- v i----------- i  vi      i      i 
  L1M4_orf2#LINE/    738 ATCTGAT-------AAGG-----------GACTTGTATCCAGAATATATA 769

  chr20_20280608_   1022 GGCAACTATATAACTCACTAACTCACTAACTAACAGGAAACAACTCACTA 1071
                         iiv    --------------  i  ---------------      v  
  L1M4_orf2#LINE/    770 AAGAACT--------------CTTAC---------------AACTCAATA 790

  chr20_20280608_   1072 ACAGGAAAACAAATGACCTGATATAAACATAAGCAAAGGACCTGAATAGA 1121
                          i ii  i      i   ii  v?   v  ii        ii        
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_20280608_   1122 CACTTCTCAAAAGAAGACATACA 1144
                           i     v        i     
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACA 863

Transitions / transversions = 2.19 (92 / 42)
Gap_init rate = 0.02 (12 / 622), avg. gap size = 5.08 (61 / 12)  


2568 28.37 0.91 0.39  chr20_20470037_20473198      881  1652 (1510)    L1M4_orf2#LINE/L1        1   776 (132)  

  chr20_20470037_    881 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 930
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_20470037_    931 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCGTCAAGC 980
                            v     v      v i  i  i        i  v  i  ii    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_20470037_    981 TACCATTGACTTTCCTCACAGAATTAGAAAAGACT-ACTTTAAATTTCAT 1029
                          v   vivi i  ii ii     v v  v   -  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_20470037_   1030 ATGGAACCAAAAAAGAGCCCATATAGCCAAGACAATCCTAAGCAAAAAGA 1079
                               viiv  ii  v  viv        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_20470037_   1080 ACAAAGCTGGAGGCATCACGATACCTGACTTCAAACTCTACTACAAGGAT 1129
                               i      vv    iv v  ii i      vii        i v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_20470037_   1130 ATAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACACATAGACCA 1179
                          i     i   i    ii         i iv ii i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_20470037_   1180 ATGGAACAAAACAGAGGCCTCAGAAATAACATCACACATCAACAACCATC 1229
                               i i  iv   ivii         vvi  i    iv iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_20470037_   1230 TGATCTTTGACAAATCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTA 1279
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_20470037_   1280 TTTAGTAAATGGTGATGTGAAAACTGGCTAGCCATATGCAGAAAACTGAA 1329
                           i ii        v  v  v      v  ?   i     i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_20470037_   1330 ACTGGACCCCTTCTTTACACCTTATACAAAAATTAACTCAAGACATATTA 1379
                         ii         v i i     v                   i iiv  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_20470037_   1380 AAGATTTAAACATAAGACCTAAAACCATAAAAACCCTAGAAAAAAACCTA 1429
                         ?   ii    ii     v       i      vi i     i     v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_20470037_   1430 GGCA-ACACCATTCAGGACATAGGCATGGGCAAAAACTTCAT-GACCTAA 1477
                           ?i- v i -   iv   v v  vv i     viii   v -  iv i 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_20470037_   1478 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAAT 1527
                         -           vvi          vv     v  i    v   ii v  
  L1M4_orf2#LINE/    599 -CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_20470037_   1528 TAAACTAAAGAGTTTCTGCACACCAAAAGAAACTATCATTGGAGTGAACA 1577
                         i   v v  i ii  i  ii vi    i  v       vvii      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_20470037_   1578 GGCAACCTACAGAAAGGGAGAAAAATTTTGCAA-TC---TAACCATCAAA 1623
                          i     i      v         vv       -  ---  v iivi  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_20470037_   1624 GGGCTAATATCCAGAATCTACAAGGAACT 1652
                           i  vi          v  i  i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACT 776

Transitions / transversions = 1.57 (132 / 84)
Gap_init rate = 0.01 (8 / 776), avg. gap size = 1.25 (10 / 8)  

 416 24.17 1.67 0.00  chr20_20470037_20473198     2551  2670 (492)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr20_20470037_   2551 AAAAACAAACAAACAAACAACCCCATATGAAAGTGGGTGAAGGTTATAAA 2600
                           v  i   v i     i     v  v?i   i    ii    v v i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_20470037_   2601 CAGATACTTCTCAAAAGAAGACTTATG--TGGCCAACAAACATATGAAAA 2648
                         i   i i     v        iv  ii--       i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_20470037_   2649 AAAGCTCATCATCACTGGTCAT 2670
                         i v     v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 2.00 (2 / 1)  


1660 16.88 1.52 26.70  chr20_20915656_20917767      501  1620 (492)    L1M4_orf2#LINE/L1       71   908 (0)  

  chr20_20915656_    501 TCTATGGATTCAAAGCAATTCCAATCAAAATCT-AGCAAGTTATTTTGTG 549
                             ii       v     i  v         i-   vivi v     ii
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr20_20915656_    550 GATATTAACAAACTGATTCTCAAGTTTATGTGGAAAAGCAAAAGACCCAG 599
                           v   i    i     i  v  i  i  i      v    ii       
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr20_20915656_    600 AATAGCCAAAAAAATTATGAA---GAAGAACAGGGTTGGAGGAGTGATGC 646
                                    v   iv    ---        ii         v v ii 
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr20_20915656_    647 TACTAGATTTCAACACATACCGTAAAAT--CAGTGATCAAGACAGTGTGG 694
                          v ivi       v  v   iii   ii--    i               
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGG 270

  chr20_20915656_    695 TATTGTTGAAGGGAAAGATAAATAGATCCAAGGAACCAAATAAAGAGCCC 744
                           i  viiv i   v   i v       v v    ivi   vi    i  
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

  chr20_20915656_    745 AGAAACAGACCTCCACAAACAGAACCAACTGATCTCTGACAAAGGAGCAT 794
                              i i   ivi   vvi viii   i    i ii     i  v  vv
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

  chr20_20915656_    795 AGACAATTCAATGGAGAAAGA-TAATCTTTTCAACAAATGGTGCTAGAAC 843
                             v         i      -  i                    i i  
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr20_20915656_    844 AACTGGACAGCTGTATGACAAAAAAAAAAAAAAAAACCTAACGTACACCT 893
                                i ? iii   -     i  vi  ivvii   --- v   --  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATG-CAAAAGAATGAAGTTGGACC---CCTAC--CT 464

  chr20_20915656_    894 TACATCTTTCACAAAAATTAATGCAGAATGGATC-CAATCCTCAATGTAA 942
                         i   i v vi           iv  i        -? iv   v       
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr20_20915656_    943 AAG--AAAACTTCTAGAAGATAACATGAGAGAACACGTGGGTAACCTTGG 990
                         i  --      --------    -------------------   -----
  L1M4_orf2#LINE/    515 GAGCTAAAACT--------ATAA-------------------AAC----- 532

  chr20_20915656_    991 ATTTGGTGATGAGTTTTTCTTTAATGAGACAGAGTCTTGCTCTGTCACCC 1040
                         -----------------    -----   -   -----------------
  L1M4_orf2#LINE/    533 -----------------TCTT-----AGA-AGA----------------- 542

  chr20_20915656_   1041 AGGCTGGAGTGCAGTGGTGTGATCATAGCTCACTGCAACCTCAAACTCCT 1090
                         ------------------------------------------    ----
  L1M4_orf2#LINE/    543 ------------------------------------------AAAC---- 546

  chr20_20915656_   1091 GGGCTCAAGCAATCCTCTTGCCTCAGCCTCCCTAGCTAGGACTACAGGTG 1140
                         ------------------------------------------- i   ? 
  L1M4_orf2#LINE/    547 -------------------------------------------ATAGGNG 553

  chr20_20915656_   1141 CATGTCACCACTCCCAGCTAATGTGAAAATTTTTTGTAGAGACAGAGTCT 1190
                         i -------------------------   i  i----------------
  L1M4_orf2#LINE/    554 TA-------------------------AATCTTC---------------- 562

  chr20_20915656_   1191 CACTATGTTGTGCAGGCTGGTTTCAAACTCCTGGCCTCAAGCCATCCTCT 1240
                         ---------   --------------------------------------
  L1M4_orf2#LINE/    563 ---------GTG-------------------------------------- 565

  chr20_20915656_   1241 TGCCTTGGCCTCCTAAACTGTTGGGACTACAGGTGTGAGCCACCACGCCT 1290
                         -i      -----------   i  ----  i------------------
  L1M4_orf2#LINE/    566 -ACCTTGG-----------GTTAGG----CAA------------------ 581

  chr20_20915656_   1291 GGCCTGGCGACTTTTTAGATACCACACCAAAAGCATAATCTCTGAAAGAA 1340
                         ----   i---  i       iv            i  v vvii      
  L1M4_orf2#LINE/    582 ----TGGT---TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr20_20915656_   1341 AAAATTGGTAAGTGGGACTTCATTAAAATTAAATACTTCTA--CTCCACA 1388
                              v i   i v         i         v    i i--  i  --
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA-- 672

  chr20_20915656_   1389 AAAAAATACCATAAAGAGAATAAAAAG-----CCACAGACCAGAACAAAA 1433
                         -  ii i  i  v    i i i     -----       vii i v    
  L1M4_orf2#LINE/    673 -AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr20_20915656_   1434 TATTTGCAAAATACGTATCTGAAAAAGGACTTGTATCTAACACATATAAA 1483
                                   vi ii       v  i           i iv i       
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr20_20915656_   1484 GAACTCTTAAAACTCAACAATAAGAAAGCAAATAACCCAATTTAAAAATG 1533
                                  v       i     i  ii              ?       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr20_20915656_   1534 GGAAGAAAACCTGAATGGACACCTCACCAAAGAAAATATACAGATGGCAA 1583
                           v i ii ii     i    ii  v        i       i     v 
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr20_20915656_   1584 ATAAGTATATGAAAATATCCTTCACATCATATGTCAT 1620
                              i i       v  v  iv      ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (124 / 61)
Gap_init rate = 0.03 (26 / 838), avg. gap size = 12.15 (316 / 26)  


 966 21.47 6.52 9.78  chr20_21007647_21010344      836  1203 (1495)    L1M4_orf2#LINE/L1        1   356 (552)  

  chr20_21007647_    836 TGGAGAGATATACTATTTTCATGGAGTGGCAAACTCAATATTGT--AGAT 883
                             i      v i  v        v   v i   i        --    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21007647_    884 AGCAATTCACCCCCAAACTGAGCTATTAAATCACCATGATTCTAATCAAA 933
                         i     v -i       i   v   ivi v   v iii  i iv      
  L1M4_orf2#LINE/     51 GGCAATAC-TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_21007647_    934 ACCCTAGCAAGCCTTATTT-TAGAAATCAACAAGTTGAT----------- 971
                          i  i   v-     v   -i      ii     i    -----------
  L1M4_orf2#LINE/    100 ATCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_21007647_    972 -GTGGAAATGCAAAGGCACTAGATTAGCAAAGACAATCATGAGAAAAAA- 1019
                         -i           i  vv i   v    v  i      v   i   i  -
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_21007647_   1020 AACAAAGCAGGAGGACTTATACTACTAGCAGAGTTTAAGACTTATTACAA 1069
                                iv        i i   v i--  - v  i  i     i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCC--CA-ATTTCAAAACTTACTACAA 245

  chr20_21007647_   1070 AGCTGCATGAATTAAAACAGCACATCTATGCCAAGAAAAAACAAAACAAA 1119
                             i  vv   i  i    ------ i  --------------------
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAG------TGTG-------------------- 269

  chr20_21007647_   1120 GCAGTGTATCTGTGCAAAGACATATAGATAGATCAAAGTAATAGACT--A 1167
                         -----   iiv iii  i  i v i v         v v      v -- 
  L1M4_orf2#LINE/    270 -----GTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr20_21007647_   1168 GAGGCAAAAAATAGACCCATAAA------GTCAATTAATTTT 1203
                            v v i     i       v ------       i     
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

Transitions / transversions = 1.55 (48 / 31)
Gap_init rate = 0.03 (12 / 356), avg. gap size = 5.00 (60 / 12)  

 757 20.86 2.43 21.86  chr20_21007647_21010344     1509  2208 (490)    L1M4_orf2#LINE/L1      345   908 (0)  

  chr20_21007647_   1509 TCAATTGATTTTCAATGAAGATGCTCA-ACAACTCAAAGGGAAAAGAAAA 1557
                                      i ii i i   iv -  v i    v   i      v 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_21007647_   1558 ACATTTTCAATAAATAGTATGGAGA-AATTTGA-ATTTATATCTTAAA-A 1604
                         iiv       i    i  iiv i  -  i v  - ?ii i  viv   - 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_21007647_   1605 ATGAAACTTGACCTCCTACCTCACACCATTCACACAAAAA--AAATTAAG 1652
                              ii v    -               -- i       --  v i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACC-CCTACCTCACACCAT--ATACAAAAATTAACTCAAA 491

  chr20_21007647_   1653 ATAAATCATAAACCTAAATGTGAAAGTTAACA-TATAAAGTTCCTAAAA- 1700
                           ii    ? i          i i  i   v -      ii  i  i  -
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_21007647_   1701 -ATATATAGGAGACTATCTTCATGATCTTAGAGTAGAGAAATATTTTTTA 1749
                         - v i     ? vvv      i   i   i iv   iv  vvi   i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_21007647_   1750 A----GGCAC-AAAACTTTAAAGACCATTAGAGAAAACATCTAATAAATT 1794
                         i---- i   -    vivi  iv v  vv   i    i ---i       
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA---GATAAATT 638

  chr20_21007647_   1795 AGACTTCATGAAAATGTAAAATTTTACTCATAAAAAAAAAAAAACACCAT 1844
                         i        -------i      ----------------      ---- 
  L1M4_orf2#LINE/    639 GGACTTCAT-------CAAAATT----------------AAAAAC----T 661

  chr20_21007647_   1845 TAGCCAGGTGCAGTGGTGCACACCAGTAGTTTCAACTACTCAGGAGACTG 1894
                          ------------ v    -----------     ---------------
  L1M4_orf2#LINE/    662 T------------TTGTGC-----------TTCAA--------------- 673

  chr20_21007647_   1895 AGGTGGGAGGATCTCTAGAGCCCAGGAGTTTGAGGCCAGACTGGAAAACA 1944
                         -----------------------    -----------------------
  L1M4_orf2#LINE/    674 -----------------------AGGA----------------------- 677

  chr20_21007647_   1945 GTGAGACTCTGCCTGGAGAGAAAAAAAAAACAAAACACTATTAATATAGT 1994
                         -----------------------------------      i  v v   
  L1M4_orf2#LINE/    678 -----------------------------------CACTATCAAGAAAGT 692

  chr20_21007647_   1995 GAAAAGGCAAGCCACTCACTGGGAAAAAATACTCTCAACCTGTGTTTCTA 2044
                               i   v    vv v     i      i iv   viii i v   i
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_21007647_   2045 ACAAAAGATTCACATACGTAATTTACAAA-AACTCCTGTAAATCAAGAAG 2093
                          i  ii  i iii  v iv   v  i   -     i ii  v    v  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_21007647_   2094 AGAAAGTCAAACAACCCAATTCTTAAAATGGACAAAAGACTTGAACAGGT 2143
                          i    v    i         -?v       i    i  i     i  ii
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_21007647_   2144 ACTTG-CAAAATAATATATCCAAATGGATAATAAATATATGAATAGGTGT 2192
                          i  v- v   v  v    v       vi     ii i     v  i  i
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_21007647_   2193 TCAATA-CAATTACTCA 2208
                             i -  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (91 / 51)
Gap_init rate = 0.04 (23 / 564), avg. gap size = 7.39 (170 / 23)  


3185 26.91 1.22 0.66  chr20_21096503_21098480      584  1486 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21096503_    584 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 633
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21096503_    634 GGCCATACTGCCCAGGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 683
                            v     v    iiv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21096503_    684 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 731
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_21096503_    732 TATAGAACCAAAAGAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 781
                            i   viiv   i  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_21096503_    782 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 831
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_21096503_    832 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 881
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_21096503_    882 AATGGAACAGAA--AAGAGCCCTCAGAAATGATGCTGCATATCTACAACC 929
                                i    --i    i  --      i vv iii i  i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_21096503_    930 ATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATCCC 979
                          vi    i  i     ivv  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_21096503_    980 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGTCATAGGTAGAAAGCT 1029
                           v  i  i              v      v  ?i  i v i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_21096503_   1030 GAAACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1079
                            ii    iv   v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_21096503_   1080 TTAAAGACTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1129
                          i ?    i    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_21096503_   1130 CTAGGCA-ATACCATTCA-GGCCATAGGCATGGGCAAGGACTTCATGTCT 1177
                         v    ?i- v i -   i- i  v i  i- i     v ii   v ivv 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr20_21096503_   1178 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 1227
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_21096503_   1228 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACAACCATCAGAGTGA 1277
                         v  i   v v  i i   i  ii vv    i  v  v i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_21096503_   1278 ACAGGCAACCTACAGCATGGGAGAAAATTTTTGCAACCTACTCATCTGAC 1327
                          v  i     i    v            v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_21096503_   1328 AAAGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAA 1377
                           i  i  vi          v  i  v      iv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_21096503_   1378 AAAAA-----AACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 1422
                            i -----     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_21096503_   1423 TCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGTTCA 1472
                             v        i  vi viii     v ii          i   i   
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_21096503_   1473 TCATCACTGGCCAT 1486
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (148 / 91)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


3894 21.85 1.66 1.43  chr20_21105471_21109329.rev     2465  3370 (489)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21105471_   2465 TGGAAAGA-ATTCCATGTTCATGGATTATAAGATTTAATATTGTTAAAGT 2513
                                 -  i               iv    i             ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21105471_   2514 GTCCATACTACC-AAAGCAATCTCCAGATTCTATGAAATTGCTATCAAAA 2562
                          v v     v  -   vii    v       v i v   iv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21105471_   2563 TTTCAATGGCATTTTTTTTCAGAAATAAAAAAAC-AAGACTAAAATTCAT 2611
                          ii  iiv  -i      v       vi v  i -i vv           
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_21105471_   2612 GTGGAATCACAAAAGACCCTGAACAGCCAAGACAATCTTGAGAAAGAAGA 2661
                         i     vii   ii     v   i      i          i        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_21105471_   2662 A-AAAGCTGGAGGCATCACACGTCCTGATTTCAAAATATATTACAAAGCT 2710
                          -    i      vv      v   ii         iv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_21105471_   2711 ACCATAATCAAAACAGTATGGTATTGGCATAAAGACAGACATATAGACCA 2760
                           vi       i     i     i        i  i           i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_21105471_   2761 ATGGAACATTCAGAATAGAGAGCCCATAAATCAATCCATGCATATGCAGT 2810
                               i ----    v     i   v    v  i    i   v iii  
  L1M4_orf2#LINE/    300 ATGGAATA----GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_21105471_   2811 CAACTGATCTTTGACAAGGGTATCAAGAATATATGATGAGGAAAGGACAG 2860
                            i    i  i         ii     vi  vii   i      i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_21105471_   2861 TCTTTT-AACATACGGTATTGGGAGAAACTGGAAATCCATATGCAAAAGA 2909
                               -    v i   ii     v  -     v ?   i          
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGA 444

  chr20_21105471_   2910 ATGAAACTGGACTC-----TCATACCACACAGAAAAATCAACTCAAAATG 2954
                              ii     i -----   i    i i v      i           
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_21105471_   2955 AATTAAGGATTTAAATATAAGACCTGAAGTTTTAAAACTCCTAGAAGAAA 3004
                         i  i ?i  ii     i     v  i  ii v        i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_21105471_   3005 ACATAGGGGAAAAGCTTCATAACATTGGCCTTGGCAAAGATTTCATGGAT 3054
                                ? v   v    i i  v    vi v     v i    v i   
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_21105471_   3055 ACGACACCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAGTGGGACTA 3104
                          i               i          v         i  i v     v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_21105471_   3105 CATCAAACTAAAAAGTTTCTGCATAGCAAAGGAAACAACTAACAGAGCAA 3154
                                v v    ii  i  iiivv       v  v ii  v i  ii 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_21105471_   3155 AAAGGCAATCTACTGAATGAGAGAAAATATTTGCAAAACACATAT----- 3199
                             i   i i  v     i                 v  i    -----
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_21105471_   3200 AAGGGGTTAATTTCCCAAACATGTAAGGAACTCCAACAGTTCAACAGCAA 3249
                              ii vi v   vi  i  i   i      iv   ii    i ii  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_21105471_   3250 AAAAACTAATAACCTGATTAAAATACGGGCTAAAGACCTGAATAAACATT 3299
                            i  v       ii   ?   v i    v  i  ii      i     
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_21105471_   3300 TCTTCAACGTCTCCATAAAACATATAAATGGCCAAGAGGTATATGAAAAG 3349
                            i   v -------  i i   i          v i i i        
  L1M4_orf2#LINE/    845 TCTCCAAAG-------AAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_21105471_   3350 ATGCTCATCACTAATCATCAG 3370
                                v  ii ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.08 (131 / 63)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.55 (28 / 11)  


 648 18.32 2.29 0.76  chr20_21174921_21177621      501   631 (2070)    L1M4_orf2#LINE/L1       82   214 (694)  

  chr20_21174921_    501 AATGCAATGCCCATCAAAATTCAAGGTGGTTTCTATGTTAGAAATTAGCC 550
                           i     v  i        i v  v  vi  i v  -i       ii v
  L1M4_orf2#LINE/     82 AACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG-CAGAAATTGACA 130

  chr20_21174921_    551 AGCTGATCTTAAA-TTCATATGGAAATTCAAGAGGCCCAGAATAGCCAAA 599
                                 i    -             v    i i               
  L1M4_orf2#LINE/    131 AGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAA 180

  chr20_21174921_    600 ACAATCTTGCAAAAGAAATACA--GTTGGGAGGC 631
                                  v       iv   --     ii i 
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

Transitions / transversions = 1.67 (15 / 9)
Gap_init rate = 0.02 (3 / 133), avg. gap size = 1.33 (4 / 3)  

1617 14.81 2.08 7.53  chr20_21174921_21177621      882  1266 (1435)    L1M4_orf2#LINE/L1      190   553 (355)  

  chr20_21174921_    882 AAAAAAAAAAATAGAGTTAGATTTCTCACATTTCCTTATTTCAAAACTTA 931
                              i  i  i i    i  vvv      i    iv             
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_21174921_    932 CTGAAAAGCTACAGTAATTGAGATACTGTGGTACTAG-ATAAACAGAAAT 980
                           iv              ii   i v         i -    i-------
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAG------- 282

  chr20_21174921_    981 CAATGGA-ATATTGACTCTGTTGATTCATATGTATCTAGAATTGAGAATA 1029
                         -i  i  -    v  ----------   -   v -v           i v
  L1M4_orf2#LINE/    283 -GATAGACATATAGA----------TCA-ATGGA-ATAGAATTGAGAGTC 319

  chr20_21174921_   1030 CAAAAACA---CTGTCACATTTA--GTCAATTAATTTTTGACAAGGGTAA 1074
                           i   i --- ii -       --       i     i         iv
  L1M4_orf2#LINE/    320 CAGAAATAAACCCAT-ACATTTATGGTCAATTGATTTTCGACAAGGGTGC 368

  chr20_21174921_   1075 CAATTTCTGCTACTCAATGGGATAAAGAATAGCCATTTCAACAAATGATG 1124
                            v----i i i        i-         i v            i  
  L1M4_orf2#LINE/    369 CAAG----ACCATTCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTG 413

  chr20_21174921_   1125 CTGGGACAAATGGATAGCCACATGGCCAAAGAATGATCTTGGATCCCTAC 1174
                                  v      ?       - v         vv     i      
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATG-CAAAAGAATGAAGTTGGACCCCTAC 462

  chr20_21174921_   1175 CTCACACTGTATACAAAAATTAAC-CAAAATGGATCAAGAACCTAAATGT 1223
                                ii               -            ?ii          
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr20_21174921_   1224 AAGAGCTAAAACTACAAAACTGTGTTAGAAGTAAACATAGGTG 1266
                                       i      v --      v         ? 
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCT--TAGAAGAAAACATAGGNG 553

Transitions / transversions = 1.84 (35 / 19)
Gap_init rate = 0.04 (14 / 364), avg. gap size = 2.64 (37 / 14)  

 376 20.29 0.00 0.00  chr20_21174921_21177621     1613  1681 (1020)    L1M4_orf2#LINE/L1      537   605 (303)  

  chr20_21174921_   1613 AAAAGTAAACATAGGTGTAAGTTTCTCTCACCTTGGATTAGGCAACAGTT 1662
                          i   v         ?    i i iiv v       i        ii   
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_21174921_   1663 TCTTAGATATGACCGCAAA 1681
                                      vv    
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAA 605

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.00 (0 / 0)  

1027 12.82 3.59 2.05  chr20_21174921_21177621     2014  2208 (493)    L1M4_orf2#LINE/L1      685   882 (26)  

  chr20_21174921_   2014 AAAAGAGTGAAAAGACAATCTATAGAATGAG-GAAAGTATTTGCAAATTA 2062
                           i i             i i i      i -    i           i 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr20_21174921_   2063 TACATCTAAAAATGGACTTGTATCCAGAAATACATAAATAACTCTTATGA 2112
                           i    i v  v                -  i     v        ii 
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAA-TATATAAAGAACTCTTACAA 783

  chr20_21174921_   2113 CTCAATAATTTAAAAAAC------CCCGATTTTGAAAATGGGCAAAGGAT 2156
                                  v-    i  ------   i   ?-i                
  L1M4_orf2#LINE/    784 CTCAATAATA-AAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGAT 831

  chr20_21174921_   2157 CTGAATAGATATTTCTCCAAAGAAGATATACAAATGGCCAATAAGATGCA 2206
                         i        i                                   -ii  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG-CACA 880

  chr20_21174921_   2207 TG 2208
                           
  L1M4_orf2#LINE/    881 TG 882

Transitions / transversions = 5.00 (20 / 4)
Gap_init rate = 0.03 (6 / 198), avg. gap size = 1.83 (11 / 6)  


 372 18.67 4.00 0.00  chr20_21243554_21245823.rev      413   487 (1783)    L1M4_orf2#LINE/L1        8    85 (823)  

  chr20_21243554_    413 ACATCCCATATTTATGGAACACAAGACTCAACATT---AAGATGACAATA 459
                          i       i  i     viiv      i  i   ---      i     
  L1M4_orf2#LINE/      8 ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATA 57

  chr20_21243554_    460 CTCCCCAAACTGATTGACAAATTCAACG 487
                                  i    iv   i        
  L1M4_orf2#LINE/     58 CTCCCCAAATTGATCTACAGATTCAACG 85

Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.01 (1 / 78), avg. gap size = 3.00 (3 / 1)  

2066 15.71 2.62 2.38  chr20_21243554_21245823.rev      501   920 (1350)    L1M4_orf2#LINE/L1      250   670 (238)  

  chr20_21243554_    501 ACAGTAATCAAGACAGTGCGGTACTGGGACAAGGATAAACATTTAGATCA 550
                                           i        v i       i    v       
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_21243554_    551 ATGGAATGGAATTGAG--TCCAGAAATAAATGCACACAGCTATTATTAGC 598
                                i        --            iv  i   vi   vi i ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_21243554_    599 TGATTTTTGATAAGG-TGTCAAGATCATTTAATGGGGAAAAGAACAGTCT 647
                                i  i    -  i     i    i          -   i     
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCT 398

  chr20_21243554_    648 T--CAACAAATGGTG-TAGGACAACTAGATAGCCA-ATGCAAGAAAGTGA 693
                          --            - i        i    ?   -      i i i   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_21243554_    694 AGCTGGACTATTACTTCACACCTTAACTCAACCCAAAC-AACTCAAAATG 742
                           i     ivi   i       v  -iv   ---   i-           
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATA-TACAA---AAATTAACTCAAAATG 494

  chr20_21243554_    743 GATCATGAACCTACATTTAAGAGCTAAAGCTATAAAACTCTTCCGA-AAA 791
                              ?ii     v  v           i             vvi -   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_21243554_    792 ACA--GGTGTAAATATTTGTGACCTTGAATTTGGCAATGGAATTCTTAGA 839
                            --  ?      v  i         ii  v        v-        
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT-TTCTTAGA 593

  chr20_21243554_    840 TATGCCATCAAAAGCACAAACGATAAAAGAAAAAAGCAGATGAACTGCAC 889
                             v  i           i i i           -i    i  i  v  
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGAC 642

  chr20_21243554_    890 TTCATCATCAAAATTTTAAACTTTTTTGTTT 920
                                ---     vv        v  i  
  L1M4_orf2#LINE/    643 TTCATCA---AAATTAAAAACTTTTGTGCTT 670

Transitions / transversions = 2.15 (43 / 20)
Gap_init rate = 0.03 (14 / 421), avg. gap size = 1.50 (21 / 14)  

 885 12.72 6.36 1.73  chr20_21243554_21245823.rev     1215  1387 (883)    L1M4_orf2#LINE/L1      648   828 (80)  

  chr20_21243554_   1215 CAAAATTTTAAACTTTTATTCTTCAAAGGACACCATCAAGAAAGTGGAAA 1264
                                vv        i v             i            i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_21243554_   1265 GACAATCCACAGAATGTGGGAAAATATTTGCAAATCATTTATCTTATAAG 1314
                              i          v i                   v     v     
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_21243554_   1315 GGACTTATATTCAGAATACATTCTTTAAAACTCTTACACTTCAATAG--- 1361
                               i   i       i  vv--- i          vi      i---
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAA---AGAACTCTTACAACTCAATAATAA 794

  chr20_21243554_   1362 ---GACAA----CCCAATTTTAAAA-GGGCAAAG 1387
                         ---     ----       ?v    -        
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 1.10 (11 / 10)
Gap_init rate = 0.02 (4 / 181), avg. gap size = 3.50 (14 / 4)  

 479 11.76 2.35 0.00  chr20_21243554_21245823.rev     1697  1781 (489)    L1M4_orf2#LINE/L1      822   908 (0)  

  chr20_21243554_   1697 GACAAAGAACCTAAATAGACATTTCTCCAAA--AGATACACAGATGGCCA 1744
                          i     i ii i                  --     i   i       
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr20_21243554_   1745 GTAAGCACATGAAAAGATGCTCAACACGACTAGTCAT 1781
                         i                         iv ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 9.00 (9 / 1)
Gap_init rate = 0.01 (1 / 87), avg. gap size = 2.00 (2 / 1)  


3241 18.06 9.58 0.28  chr20_21279489_21281148.rev      449  1168 (492)    L1M4_orf2#LINE/L1      122   908 (0)  

  chr20_21279489_    449 AAATT--TAAACCCATCCTAAAATTCATGTGAAATCTCAACGGACCTTGA 496
                              --i  i iv              i  i  viv   v     iv  
  L1M4_orf2#LINE/    122 AAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGA 171

  chr20_21279489_    497 ATA-------------TGAA---------TAAAGTTGGAAGAC--ACAAT 522
                            -------------    ---------i         i   --   v 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACT 221

  chr20_21279489_    523 TTCTGACTTCAAAACTCACTACAAAGCGACAGTAATTACAACAGTATAGC 572
                          i ii i         i          v        i vi     i i i
  L1M4_orf2#LINE/    222 TCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGT 271

  chr20_21279489_    573 ATTGGCATAAGGAAAAACACATAGCTCAATGGACTAGAATAGACAGCCCA 622
                          i           v i   i    v        v      v  v  i   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr20_21279489_    623 GAA---------------TAT-----------TTTCAACAAAGAGTGCCA 646
                            ---------------   -----------    i    i -      
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCA 370

  chr20_21279489_    647 AC-TTATTCAATGGGGGGAAGAATGGTCTTTTCAACAAGTGGTGCCGGGA 695
                          v-ii           i-      i             i      i    
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGA-AAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr20_21279489_    696 AAATTTGATATGCACATGCAAAAGAATGAAGTTGGACCATTACTTTACAC 745
                         v  i v    ?v                          vi   i i    
  L1M4_orf2#LINE/    420 CAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACAC 469

  chr20_21279489_    746 CATATACAAAAATTAATTCAAAATGGATCA--GATTTAAATGTAAGAACT 793
                                         i             --  ii           i  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

  chr20_21279489_    794 AAAACTGTGTAACTTTTAGAAGCAGACATAGGAAAAAAGATTCATGATGT 843
                               i iv    i       v i       ?iv   vv   i   iv 
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCT 569

  chr20_21279489_    844 CGGATTTGGTAAAGATTTCTTGGATATGACACCAAAAGCACAGGAAACAA 893
                         i  i  v  i  v i      i                    i v     
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr20_21279489_    894 CAAAAAA----GATAAACTTGATTTCATCAAAATTAAAAACTTGTGTGCA 939
                         v i    ----      i v  i                    v     v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr20_21279489_    940 TCAAAGGACATCATCAC-AGGGTGAAAAGATAATCCACAGAATAAGAGAA 988
                                   ii    v- ii         i  i         ii     
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_21279489_    989 AATACATGCAAATCATATATCCAATAAAAGATTAATGTCTAGAATATATA 1038
                             iv               ii    ii  i vi i  i          
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr20_21279489_   1039 AAAAACTTCTATAATGCAACAACAAAAT------CAACCCAATTCAAAAT 1082
                           i    ii  i  iv   i  i    v------i         ?    v
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_21279489_   1083 TGAGCAAAGGATTTGAACAGACATTTCTCCAAAGA---TTTAGAAATGGC 1129
                           i              i                 --- v  v       
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr20_21279489_   1130 CAAAAAGGACATGAAACGATGTTCAGTATCACTAATCAT 1168
                            v   v        v    i   ii    ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (85 / 42)
Gap_init rate = 0.02 (14 / 787), avg. gap size = 5.07 (71 / 14)  


2281 25.64 7.04 2.19  chr20_21384334_21386173.rev      513  1378 (462)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21384334_    513 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATAATGAAAAA 562
                               i i  i     i        v      v i     vi v  i v
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21384334_    563 G------------AAATT----TACAGATTCAATGCTACTCCCATTAAAC 596
                          ------------     ----           i  v ii  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21384334_    597 TACCA-TTGACATTCTCACGGAATTAGAAAAAACT-ATTTTAAAATTCAC 644
                          v   -i  v v  i ii i   v v  v  i-  -  ii         i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_21384334_    645 ATGGAATCAAAAAAGAGACC--AAATAGCCAAGACAAGCCTAAGCAAAAA 692
                               -- viv   i    --i         i    v i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_21384334_    693 GAACAAAGCTGGATGCATCATGCTGCCCAACTTCAAATTATACTACAAGG 742
                                 i    v vv   ii  v     i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_21384334_    743 CTACAGTAACCAGAACAACATGGTACTAGTATAAAAATAGACACATAGAC 792
                                  i  ii   iii       i i    ii       i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_21384334_    793 CAA-GGAACAGAATAGAGAACTCAGAAACAAAACCACACACCTACAACCA 841
                            -    i     v    iii      i   v   i   ii  iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_21384334_    842 CCTGATCTTTGACAAACCTAAAAAAAACAAGCAATGAGGAAAGGATTGCC 891
                         vi    i  i     ivv ivv  i v  vv     i      i  v i 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_21384334_    892 TATTCAATACATGGTGCTAGGAGAACTGGCTAGCAATACGCAGAAAATTG 941
                          v     i v        i   v      v  ? v i i   i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_21384334_    942 AAAGTGGACCCCTTGATTATACCATATACAAAAATTAACTCAAGATGAAT 991
                           iv         vvv i i                       i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_21384334_    992 TAAAGACTTAAAT-TAAAACCCAAAAACTATAAAAACCCTAAAAGGCAAC 1040
                         i ?    i     -   i v i    -        vi i  i   iv   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTAGAAGAAAAC 546

  chr20_21384334_   1041 CTAGGCAATACCCTTCTAGACATAGGAATGGGCAAAGATTTCAT-GATGA 1089
                         v    ?ivv vi    vv   v v  iv i     v i    v -   - 
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-A 595

  chr20_21384334_   1090 AAACACCAAAAGCAATTGCAACAAAAGCAAAAATTGATGAGT-GGGCTCT 1138
                         vi            vvv          v      v   i i -  i  ii
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_21384334_   1139 AAATCAA--CTAAAAAGCTTATGCACAGCAAAAGAAAACTACCATCAGAG 1186
                          --    --i      -   v  ii vv    i  v -   i  vv i  
  L1M4_orf2#LINE/    646 A--TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACA-CTATCAAGAAAG 691

  chr20_21384334_   1187 TGAACAGACA-CCTATAAAATGGGAGAAAATTTGTGCAATCTATCCATCT 1235
                             v     -  i i i             v v     vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_21384334_   1236 GACAAAGGTCTAATATCCAG--TCTATAAGAAACTTAAACAAATTTACAA 1283
                           i  i  v  vi       -- v     ii    ivv    v iv i  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_21384334_   1284 GAAAAAAA-----AACCCA--------------------------CAGAC 1302
                         v     i -----      --------------------------i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_21384334_   1303 ACATCTCAAAAGAAGACATTCGTGTGGCCTACAAACAC-TGATCATTAGA 1351
                          iv    v        i  v ivi     v i  i   -   ------- 
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-------A 884

  chr20_21384334_   1352 GAAATGCAAATCGAAACCACAATAAGA 1378
                         i i    ---  i v i  ????????
  L1M4_orf2#LINE/    885 AAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (130 / 89)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 3.33 (80 / 24)  


1463 27.14 16.36 1.56  chr20_21494132_21496829.rev     1429  2198 (500)    L1M4_orf2#LINE/L1       13   896 (12)  

  chr20_21494132_   1429 CCATATTCATGCACTGAAGGGCTCAATGTCATAAAAATACCAATCCTACA 1478
                             i      v i  i i i  i   i ii v  i  iv    v  v v
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr20_21494132_   1479 TGAACTTGGTGTATAGATTTACTG--ATCCCAACTGAAATCCCA------ 1520
                         ii  -   i v  i     i vi --     v iii        ------
  L1M4_orf2#LINE/     63 CAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCC 111

  chr20_21494132_   1521 ----------------ACAAGCAGATTCTAAAATGTATATGGAAATG-AA 1553
                         ----------------      v   i       vi           -  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr20_21494132_   1554 AAGACCAAAAGTGGTTAAGCTATTCCTGAAGAACAAAGAAGAGAGT---- 1599
                         ii    v i i i ii  ivi v  i    i  -i     v i   ----
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAA-GAAGAACAAAGTTGGA 210

  chr20_21494132_   1600 GGATTTGCTCTGCCCAGTATCAA--CTTAAAATAACACTACATTAATTAA 1647
                            i ii v  v    i v    --    vv i  vi     v    i  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr20_21494132_   1648 AGCAGCCTAGTGTTTGTACAAGGACAGATA-ATAGATTAATGGAATAGGA 1696
                         ii   iv i  ii v i i     i   i -      i          i 
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr20_21494132_   1697 TAGAGTGTTCTTAAAGAGATCCAGATATATATGGACACTTGATTTATGGC 1746
                          v   v  i vv   v i i   v i  v     v  v       vi i 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr20_21494132_   1747 AAAGAT---AAAA---TTGAAGGAGGATAGAGAAAAAACTATTTTAA-AA 1789
                           i i ---  i ---  v  v i   --i    v iv  -   i  -  
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGA--AAGAATAGTCT-TTTCAACAA 407

  chr20_21494132_   1790 ATGTATGTGGCTGGGACAATTGAGTATCCACAAGGAAAACA-TGAAATGA 1838
                            ---   -         i  ii  ?     v v    v -    i vi
  L1M4_orf2#LINE/    408 ATG---GTG-CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr20_21494132_   1839 GGCCCCTACCTCAAACCATATACAAAATTCAATTCCAGGTGGA-----G- 1882
                          i           v             v i  i  v ii    ----- -
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr20_21494132_   1883 --TATATGTGAAAACCAAGTTGAAAAGACC-----AAGAAAA-A------ 1918
                         --  v    i i i i  iviv v  i  i-----       - ------
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr20_21494132_   1919 -AAAGCTT------------TTAG--AA-GGTT----------------- 1935
                         -   v   ------------    --  -    -----------------
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr20_21494132_   1936 ---------------AAAGAAAA--CTGATAAATTCGAGTACATTAAATA 1968
                         ---------------        --iv        v  v v   i   vv
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr20_21494132_   1969 TAAGAA-TTTTGTTAATCGAAAGACAACATTAAGAGAGCGAGAAGGCAAG 2017
                            i  -      vvv  i  i    vi  i    i  i  i   i   v
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr20_21494132_   2018 CCACAGAGTGGGAGAAAATATTAGGGGAACATAAAACTGACAGAGAGCT- 2066
                                i              v vii v    v v    i ii ii  -
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr20_21494132_   2067 -----CAAACTACATAAAGAATGTCTATAAATCAGTAAGGAATAAACAAA 2111
                         -----  i v  i        ivii  i  v   i   vi  v i     
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr20_21494132_   2112 --AC---ATAGAAAAATGGGCCCCCAAAACCCTGA-TATGCGTTTC--AA 2153
                         --  ---  v?          v---  iivii   -  vi i    --v 
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCA---AAGGATTTGAATAGACATTTCTCCA 850

  chr20_21494132_   2154 AAAAGGGAATCCAAATAGCCAACAGACATATGAAG-GATGCCCAAC 2198
                           i i iv  v     i     i ii  i     i-     i    
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

Transitions / transversions = 1.65 (129 / 78)
Gap_init rate = 0.04 (34 / 884), avg. gap size = 4.06 (138 / 34)  


2876 26.41 1.88 1.55  chr20_21585715_21588449     1339  2243 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21585715_   1339 TGGAAACACATCCCACGCTCATGGATGGGGAGAATCAATTTTGTGAAAAT 1388
                               v i      i i        v  i   v i   v    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21585715_   1389 GACCATATTGCC-AAAGCAGTCTACAAATTCAACACAATTCCCATCAAAA 1437
                          i v   i v  -   viii      i       i    i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21585715_   1438 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCATG 1487
                          v   v vv v  i  ii     v v  v  ivii  i           i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_21585715_   1488 TGGAACCAAAAAAGAGCCCATATAGCAAAAGCAA----GACTAAGAAAAA 1533
                              viiv  ii  v  viv     v   i   ----  vv     i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_21585715_   1534 -AAATCTGGAGGCATCACACTACCTGATTTCAAACTATACTACATAAGAC 1582
                         -   vi      vv       v  ii        viv       -   - 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA-AAG-C 248

  chr20_21585715_   1583 CATAGTCACCAAAACAGCATGGTGCC--TATACAAATAGGCACATAGACC 1630
                         i i   v i   i    ii    i i--i   vii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_21585715_   1631 AATGGAACAGAACAGAGAATCCAGAAATAAACCCAAATGCTTACAGCCAA 1680
                                i    iv    i                v iii   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_21585715_   1681 CTGATCTTCGACAAAGCAAACAAAAACATAAAGCGGGGAAAGGACACTGT 1730
                         i    i        i vviv   i v   vv ii        i i v v 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_21585715_   1731 TTTCAACAAACAGTGCTGGGGTAATTGGCTAGCCACATGTAGGAGAATAA 1780
                                   ii        ii  i   v  ?       i ii     i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_21585715_   1781 AACTGGATCCTCATTTCTCATCTTATACAAAAATCAACTCAAGATGGATT 1830
                          ii    i  ii ii  v  i v           i       i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_21585715_   1831 AAGGACTTCAATCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACAT 1880
                          ?i   i v   v     v  i           v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_21585715_   1881 TGGAAAAACTCTTCTAAACATTGGTTTAGGTAAGGATTTCATTCATGACT 1930
                         v  ?iv  v     vvi  v    v     i  v i    -- i -  - 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC--TTA-GA-T 594

  chr20_21585715_   1931 AAGAACCCAAAAGCAAATGCAATAAAAACAAA----GAAAAATTGCAGGG 1976
                          v  vv         v v    i    iv   ----  v      ---- 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG----G 640

  chr20_21585715_   1977 ACT-----AAAACTAAAGAGCTTTTGCATGGCAAAAGGAATAGTCAGTTG 2021
                            -----    i    i -      iiivv    i iv ivi   ivvi
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_21585715_   2022 AGTAATTACAGATAACCTACAGAGTGGGAAAGAATCTTCACAATCTATCC 2071
                            i -- v   i    i     i     i i   v  ii   vii  vi
  L1M4_orf2#LINE/    690 AGTGA--AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_21585715_   2072 ATCTGACAATGGACTAATATCTAGAATCTACAATGAACTCAAACAAATCA 2121
                               i  v     vi    i     v  i  v      vv    v   
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_21585715_   2122 ACAAGGAAAAAAACAAAAAATCCCATCAAAACGTGGGCTAAGGGCAAGAA 2171
                          i  v-     i     v  i  v  i?   vi     v    iivv   
  L1M4_orf2#LINE/    788 ATAAT-AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_21585715_   2172 TAGACAGTTCTCAAAAGAATACATACCAATAGCCAACAAACATATAAGAA 2221
                               v     v      v i    v   i     i  i  i  i i  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_21585715_   2222 AACACTCAACATCATTAATGAT 2243
                         i ii          ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.07 (31 / 15)  


3063 26.41 1.33 0.99  chr20_21662823_21667100.rev     2882  3786 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21662823_   2882 TGGAAACACATCCCATTCTCATGGATGGGTAAAATCAATATTGTGAAAAT 2931
                               v i       vi        v  v i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21662823_   2932 GACCATACTGCCAAAAGCAATCTATAAATTCAGTGTAATTCCCATCAAAA 2981
                          i v     v  v   vii     i i     ii i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21662823_   2982 TATTATACCACCATCATTCTTCACAGAATAGAGAAAAAACAATCCTAAAA 3031
                          vii -i ii  ----  i  ii     - vv  v  ivii         
  L1M4_orf2#LINE/    101 TCCCA-GCTGCC----TTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAA 144

  chr20_21662823_   3032 TTCATATGGAACCAAAAAAGAGCCTGCATAGCCAAAACAAGACTAAGCAA 3081
                                    viiv  ii  v  v v             vvi i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_21662823_   3082 AAAGAACAAATCAGGAAGCATTACATTACCTGTTTTCAAACTACGCTATA 3131
                         i         viv   i vv i   i v  iiv       vivii   i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_21662823_   3132 AGGCCATAGTCACCAAAATGGCATGGTACTGGTATAAAAACAGGCATATC 3181
                          i  i i   v i   i ii ii         i    ii i  i     v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_21662823_   3182 GACCAGTGGAACAGAATAGAGAACCAAGAAATAAGCCCAAATACTTACAG 3231
                           i  i     i     v    ii v        i    v i i   ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_21662823_   3232 TCAATTGATCTTAAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACA 3281
                                  i  vi    i vviv   i v   vv i         i i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_21662823_   3282 CCCTATTCAACAAATGGTGCTGGGATAATTGGCAAGCCACATGTAGAAGA 3331
                         vi  v                    i  i   vv ?       i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_21662823_   3332 ATGAAACTGAATCTTCATCTCTCACCTTATATAAAAATCAACTCAAGATG 3381
                              ii  i i iii i   v    v    i      i       i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_21662823_   3382 GATCAAAGACATA--TCTGAGACCTGAAACCATAAAAAAAATCT-AGAAG 3428
                              ?    v  -- v i   v  i    i      v---   -     
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC---TCTTAGAAG 541

  chr20_21662823_   3429 ATAACATTGGAAAACCCCTTCTAGACATTGGCTTAGGCAAAGACTTCATG 3478
                          v     v  ?iv vvi    vv   v    v        v ii   v i
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_21662823_   3479 CCCAAGAACCCAAAAGCAAATGCAACACAAAGATTAATAGATG----GGA 3524
                         vvi v  vv         v v      v  ii vv       i----   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_21662823_   3525 CTTAATTAAGCTAAAAAGCTTTTGCACAGCAAAAGAAATAATCAGCAGAG 3574
                            v  i  iv v    i      ii vv    i  v iv    iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_21662823_   3575 TAAACATACAACCCACAGAGTGGGAGAAAATCTTTGCAATCTATACATCT 3624
                          i  v v            i           v       vii   i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_21662823_   3625 GACAAAGGACAAATATCCAGAATCTACAAAGAA-----ACAAATCAGCAA 3669
                           i  i    vvi          v  i      -----    v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_21662823_   3670 GAAAAAAACAAACAATCCCGTCAAAGAGCAGGCTAAGGACATGAATAGAC 3719
                         v     i     i  i  vi i?  i iii   v     iv         
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_21662823_   3720 AATTCTCAAAAGAAGATATACAAATGGCCGACAAACATATGAAAAAATGC 3769
                          v     v                     i i  i  i       i    
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_21662823_   3770 TCAACATCACTAATTAT 3786
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (139 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.62 (21 / 8)  


3325 25.30 0.99 1.10  chr20_21674555_21680229.rev     4275  5183 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21674555_   4275 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4324
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21674555_   4325 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAAC 4374
                            v     v     iv i  i           i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21674555_   4375 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4422
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_21674555_   4423 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 4472
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_21674555_   4473 AACAAATCTGGAGGAATCACACTACCTGACTTCAAACTATACTACAAGGC 4522
                               vi       v       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_21674555_   4523 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 4572
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_21674555_   4573 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 4620
                                i    i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_21674555_   4621 ATCTGATATTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 4670
                          vi    v  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_21674555_   4671 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAACT 4720
                           v  i  i              v      v  ?   i   i i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_21674555_   4721 GAAACTGGCTTCCTTCCTTACTTACCCCTTATACAAAAATTAATTCAAGA 4770
                            ii   vii   v   i  --   v--              i    i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCAC--ACCA--TATACAAAAATTAACTCAAAA 492

  chr20_21674555_   4771 TGGATTACAGACTTAAATGTTAGACCTAAAACCGTAAAAACTCT-AGAAG 4819
                              i ?    i       v   v       ii     -    -     
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAG 541

  chr20_21674555_   4820 AAAACCTAGGCAATACCTTTCAGGACATAGGCATGGGCAAGGACTTCACG 4869
                              v    ?ivv vii   iv   v v  vv i     v ii   vii
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_21674555_   4870 ACTAAAACACCAAAAGTAATGGCAACAAAAGTCAAAATAGACAAATGGGA 4919
                         iv  vi          i vvi          vv        i    v   
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_21674555_   4920 TCTAATTAAACTAAAGAGTTTCTGCACAGCAAAAGAAACTACCATCAGAG 4969
                         ii v  i   v v  i ii  i  ii vv    i  v    i  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_21674555_   4970 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCT 5019
                             v  i     i                 v       vii  vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_21674555_   5020 GACAAAGGGCTAATATCCCAGAATCTATAAAGAACTTAAACAAATTTACA 5069
                           i  i  i  vi     -     v           ivv    v iv i 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCC-AGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_21674555_   5070 AGAAAAAGACAA----TCCCATCGAAAAGTGGGCAAAGGATATGAACAGA 5115
                          v          ----i  v  i?    i            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_21674555_   5116 CACTTCTCAAAAGAAGGCATTTATGCAGCCAACAGACACATGAAAAAATG 5165
                           i     v       ii  vi viii     i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr20_21674555_   5166 CTCATCATCACTGCTCAT 5183
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.73 (19 / 11)  


4337 19.36 1.11 0.66  chr20_21772906_21777075     2775  3678 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21772906_   2775 TGGAAAAATACCCTGTGTTCATAGAATTGAAGACTTAATATTGTTAAGAT 2824
                               i   i  ii       i  v v                      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21772906_   2825 GTTAATACCACCCAAATTGATGTACACATTTAATGCAATCTCTACCAAAA 2874
                          vi     iv           v    v   i  i      i   i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21772906_   2875 TCTTAA-TGATTTTTTTGTAGCTATAGAAAAATCTCTCCTAAAATT--TG 2921
                           ii i-  vi       i  vv  v  v  iiivv          -- i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_21772906_   2922 TGTAATCTCAAGGAACCCTGA-TAGCCAAAACAATCTTGAAAAGGAAGAA 2970
                           v  viv     i    v  -                     i      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_21772906_   2971 CAAAGCCAGAGGACTCACAACATTTCCTGATTTCAAAATTTACTACAAAG 3020
                              iii           ---i    ii         i           
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACA---CTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_21772906_   3021 CAACAGTAACCAGAACAGTCTGGTACTGGTATAAAGACAGATATATAGA- 3069
                          v       i  ii     v         i    i  i   i       -
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_21772906_   3070 CAATGGAAAATAATAAAAAGCTCACACATAAACACTCACGTATGTGGTCA 3119
                                 v v   vi i  ii  v v      v vi  i v i      
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_21772906_   3120 AGTGATTTTTGACAAGGGTGCCAAGACCATTTAGTGGGGAAAAGAAATTC 3169
                          v       i                     i i        ii v v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_21772906_   3170 TT--CAACAAACAGTCCTAGGAAAACTGGATATCCAGATGGAAAAGAGTG 3217
                           --       ii  v  i   v         ?   v   v      i  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_21772906_   3218 AAGTTGGATCCTTACCCTACACTGCATACAAAAATTAACTCAAAATGAAT 3267
                                 i  i    ii    iii                      i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_21772906_   3268 TCATGACCTAAATGTAAGACCTAAAACTATAAAGCTTTTAGAAGAAAACA 3317
                         iv?v               v             i  i             
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_21772906_   3318 TAAAGGAAAAGCATCACAACACTGGATTTTGCAATGATTTCTTGGATATG 3367
                           ii? v   v v  iii  vi   i  vv      i      i      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_21772906_   3368 ACACTAAAGGCAGAGGCAACAAAGGAAAAAAATAGACAATTTGACCTTCA 3417
                             i   i   v i        i       -    i  v   iv     
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCA 646

  chr20_21772906_   3418 TGGAAATGAAAAA-TTTTGTGCATCAAAAGACACTATGTATATGGTAAAA 3466
                          vi    v     -        v     i        vv v vi  i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_21772906_   3467 AAGGCAACCTAAAGAATAAGAGAAAATACTTGCAAATCATATATCTGATA 3516
                          - i     i v     ii         i                     
  L1M4_orf2#LINE/    697 A-GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_21772906_   3517 AGGGATTAATATCCAGACTACGTAAACAATGTCTACAATTTAACAAGAAA 3566
                              i vi        v  ii    v  ivii     i i  i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_21772906_   3567 AA--CAAACAACCTGATTAAAAAATGGACAATGAACTTGAACGGACATTT 3614
                           --    i    ii   ?        i   v i i     ii       
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_21772906_   3615 CTCCAAAGAAGATATAAAAATGGCCGATAAGCACATAAAAAAGACGCTCA 3664
                                         v        i          i    -  i     
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCTCA 894

  chr20_21772906_   3665 ACATTACTAATCAT 3678
                             i ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.80 (110 / 61)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.45 (16 / 11)  


3336 26.49 0.55 0.33  chr20_21781584_21788306     5326  6231 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21781584_   5326 TGGAAGAACATTCCATGCTCATGTATAGGAAGAATCAATATCATGAACAT 5375
                              ii i  i     i     v  v      v i     ii v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21781584_   5376 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5425
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21781584_   5426 TACTAATGACTTTTTTCACAGAATTGGAGAAAGCT-ACTTTAAAGTTCAT 5474
                          v i iivi i     ii     v v  v  -   - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr20_21781584_   5475 ATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGGAAAAAGA 5524
                               viiv  ii  v  viv  v     i      i i ii  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_21781584_   5525 ACAAATCTGGAGGCATCACACTACCTGACTC--AAACTATACCACAAGTC 5572
                              vi      vv       v  ii i i--     -   i    iv 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT-TACTACAAAGC 248

  chr20_21781584_   5573 TACAGTAACCCAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5622
                                 i v i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_21781584_   5623 AATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCAT 5672
                                i    iv   ivii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_21781584_   5673 CTGATTTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCTCT 5722
                         i       i     ivv  v   i v  vvv           i  vv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_21781584_   5723 ATTTAATAAGTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 5772
                         v  i  i  i           v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_21781584_   5773 AACTGGATCCCTTCTTTATACCTTATATAAAAATTAATTCAAGATGGATT 5822
                          ii    i    v i i i   v    i         i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_21781584_   5823 AAAGACTTAAATGTTAGACCTAAAACCATAAAACCCT-AGAAGAAAACCT 5871
                          ?    i       v   v       i       i  -          v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_21781584_   5872 AGGCA-ATACCACTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAA 5920
                            ?i- v i -i  iv   v v  vv i     v ii   v iiv  vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_21781584_   5921 ACACCAAAAGCAATGGCAACAAAAGCTAAAATAGAAAAATGGAATCTAAT 5970
                                     vvi          vv        v    v i ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_21781584_   5971 TAAACTAAAGAGCTTCTGTACAGCAAAGGAAACTATGATCAGAGTGAACA 6020
                         i   v v  i i   i   i vv       v     v vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_21781584_   6021 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 6070
                          i     i                 v       vii  vi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_21781584_   6071 GGGCTAACATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAAAAA 6120
                           i  vii         v  i        ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_21781584_   6121 ATCAAACAATCCCATTAAAAAGTGGGCAAAGGATATGAACAGACACCTCT 6170
                         iv    i  i  v   ?    i            v    i     ii   
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_21781584_   6171 CAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCA 6220
                          v        i  vi viii     i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_21781584_   6221 TCACTGGTCAT 6231
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.48 (141 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.14 (8 / 7)  


2872 27.67 2.00 1.11  chr20_21806198_21811552.rev     3964  4863 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21806198_   3964 TGGAAAAACATTCCATGCTCATGGATAATGACAAGC--AATATCTTTATA 4011
                               i i  i     i        --  iv ii --     iv   vi
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGAT--TGGAAGACTTAATATTGTTAAG 48

  chr20_21806198_   4012 ATGGCCATACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCTATCAA 4061
                              v     v      vii  i  i        i  v  i        
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr20_21806198_   4062 ACTACCATTATTGATATTTCTCCACAAAACTAGAAAAAACT-ATTTTAAA 4110
                          v v   --ii  viv   i v  -i   i i-- v  i  -  ii    
  L1M4_orf2#LINE/     99 AATCCCA--GCTGCCTTTTTTGCA-GAAATTG--ACAAGCTGATCCTAAA 143

  chr20_21806198_   4111 ATTCATATGGAACCAAAAAAGAGCCCGAATAGTCAAGACAATCCTAAGCA 4160
                                     viiv  ii  v  v      i   i      i i iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr20_21806198_   4161 A-AAGAACAAAGCTGGAGGCATCATACTACTCAACGTTGAAGTATGCTAT 4209
                          -          i      vv   i   v i   iv ii  iiv i   i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr20_21806198_   4210 AGGGCTATAGTAACCAAAACAGCATGGTATTGATACAGAAACAGACAGAT 4259
                          ii    i     i   i    ii     i  ii i iii i     v  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr20_21806198_   4260 AGACTGATGGAACAGAATAGAGAGCCCAGAAATAAGGCTGCACACATACA 4309
                            iii      i     v     i          iv iii   iv  ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr20_21806198_   4310 ACTATCTGATCCTTGAAAAACCTGACAAAAAACAAGCAATGAGGAATGGA 4359
                         iii vi    ii i  v  ivv  v   i v-  vv     i    v i 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAAGAA 392

  chr20_21806198_   4360 TTCCCTATTCAATAAATTGTGCTAGGATAACTGGCTAGCCATATGCAGAA 4409
                          vvi  v     i    v     i   i      v  ?   i     i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_21806198_   4410 GATTGAAACAGGACACTTTCCTTATGCTATATATAAAAATTAACTCAGTA 4459
                           v    iiv    v i v   i ii i     i             iv 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_21806198_   4460 TGGATTACAGACTTAAATGTAAAACCCAAATCTATAAAACTCCTAGAAGG 4509
                              i ?    i         i v i   v           i      i
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_21806198_   4510 CAACCTAGGCA-ATACCATTCTGGACCTAGAAACAGGCAAAGATTTCAT- 4557
                         v   v    ?i- v i -   vv     v iivi      v i    v -
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_21806198_   4558 GATGAAGATACCAAAAGCAATTGCAACAAAGACAAAAATTAACAAATAGA 4607
                            - v  i          vvv        iiv      vi i    v i
  L1M4_orf2#LINE/    592 GAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_21806198_   4608 ATCTCATTAAACCAAAGAGCTTCTGCACAGCAAAAGAAACTAC----AGA 4653
                          ii    i   viv  i i   i  ii vv    i  v    i---- i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_21806198_   4654 CTGAACAGACAACCTACAGAATGGGAGAAAATTTTTGCAAACTGTTCATC 4703
                         v    v        i                 v        iii vi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_21806198_   4704 TGACAAAGATCTAATATCCAGACTCTACAAGGAACTTAAACAAATTTACA 4753
                            i  i iv  vi        v v  i  i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_21806198_   4754 AGAAAAA-----ATAAC---ATTAAAAAGTGGGCAAAGGACATGAACAGA 4795
                          v     -----     ---   ?    i           iv    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_21806198_   4796 CGTTTTTCAAAAGAAAGCATACATGCAGGCAACAATCTTATGAAAAAAAG 4845
                          i   i  v      iii     viii v   i  v vi       i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr20_21806198_   4846 TTCAACATCACTGATTAT 4863
                         i         ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (156 / 89)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 1.87 (28 / 15)  


3254 27.09 0.33 0.33  chr20_21815794_21822071     4879  5786 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21815794_   4879 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii    i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21815794_   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAAC 4978
                            v     v     iv i  i           i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21815794_   4979 TACCAATGACTTTCTTCACAGAATTGGAAAACACT-ACTTTAAAGTTCAT 5027
                          v   iivi i  i  ii     v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr20_21815794_   5028 ATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAGA 5077
                               viiv  ii  v  viv  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_21815794_   5078 ACAAATCTGGAGGAATCACACTACCTGACTTCAAACTATACTACAAGGCT 5127
                              vi       v       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_21815794_   5128 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5177
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_21815794_   5178 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGGCGCATAACTACAACTA 5225
                               i    i--    i  --        vvv ii i vi  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr20_21815794_   5226 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5275
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_21815794_   5276 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGGAAGCTG 5325
                          v  i  i              v      v  ?   i   i ii iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_21815794_   5326 AAACTGGATCCCTCCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5375
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_21815794_   5376 TAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5425
                         i ?   ii    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_21815794_   5426 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5475
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_21815794_   5476 ACACCAAAAGCAATGGCAATAAAAGACAAAATTGACAAATGGGATCTAAT 5525
                                     vvi    i      v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_21815794_   5526 GAAACTAAAGAGCCTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5575
                         v   v v  i i i i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_21815794_   5576 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5625
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_21815794_   5626 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5675
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_21815794_   5676 ATCAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 5725
                         iv    i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_21815794_   5726 CAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5775
                          v        i  vi viii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_21815794_   5776 TCACTGGCCAT 5786
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


1694 23.04 11.52 2.27  chr20_21834947_21836511.rev      501  1073 (492)    L1M4_orf2#LINE/L1      283   908 (0)  

  chr20_21834947_    501 GATAGAT-TCTAAATCTTGGGAACAGAATCAAGAATCCAGAAATGGATGG 549
                               i- v  i   vvv    i     ii   i         ii i--
  L1M4_orf2#LINE/    283 GATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC-- 330

  chr20_21834947_    550 AACCACACGTATATGAACAACTGATTTTCAACAAAGATAAAAAGGTAATT 599
                         --   i  i v    iv   i        i    i i ivv   iiv   
  L1M4_orf2#LINE/    331 --CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr20_21834947_    600 CAGTAAAGAAAAAACAGCCTTTTCAACAAATG-TACTGTTTTAAAAAAAT 648
                           i iii    i  i  i              - i   ----ii v  v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG----GGACAACT 424

  chr20_21834947_    649 GGATATATATGTGTAAAGGAAAATTAACTTATTTTCACACCTTATACCAT 698
                              ?vi ii  i   -- i   v  v  ivvii vi    i i     
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAA--AGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr20_21834947_    699 ATTAAAAAGAGCAATGCAAA-TAGATAATAGATTTAAATGTTAAACCTAT 747
                           - v   i vi  iv    - i   v ?   ii       v i v   v
  L1M4_orf2#LINE/    473 AT-ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr20_21834947_    748 CACTGTAAAATT-TTACAAGAAAACATAGA--TAAATTTT----A--TTA 788
                         v   i     i -   v            i--     i  ---- --  i
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr20_21834947_    789 GGTTA------------TTAGATATGACCCTGAAAACATGATTCATAAAA 826
                              ------------           v ii   i  ii viv i    
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr20_21834947_    827 GAAAAAGTTAATAAATTGGACTTCATTAAAATT-----TTTCTGTTCTTC 871
                               i vi                i      -----i  i   v    
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr20_21834947_    872 AAAGTGCAGTGTTAAGAGAATGAAAA--------AGAGACGTGGAGAAAA 913
                             vi  v i i    i i      -------- v   vvv        
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr20_21834947_    914 TATTTGCAAATTATATATCTGATAAAGGACTTGTATCCA----------- 952
                                    i             i             -----------
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr20_21834947_    953 -----------------TAATAGAAA-ATAAACCACCCAATTTAAAAATG 984
                         -----------------     i   - i   iv        ?       
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr20_21834947_    985 GGCAAAAGATTTGAACAGACATTTTCTTGGAAAAAAAATACTTGTATGGC 1034
                               i        i        iiii--   i  i   iviiv     
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCC--AAAGAAGATATACAAATGGC 869

  chr20_21834947_   1035 AAATAAGCACATGAATAGATGCTTGACATCATTAGTCAT 1073
                         v              v       ii      ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (87 / 42)
Gap_init rate = 0.03 (17 / 626), avg. gap size = 4.65 (79 / 17)  


3266 27.09 0.33 0.33  chr20_21839740_21846019.rev     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21839740_   4881 TGGAAGAATATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 4930
                              ii    i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21839740_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21839740_   4981 TACCAATGACTTTCTTCACAGAATTGGAAAACACT-ACTTTAAAGTTCAT 5029
                          v   iivi i  i  ii     v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr20_21839740_   5030 ATGGAACCAAAAAAGAGCCCGCATCTCCAAGGCAGTCCTAAGCCAAAAGA 5079
                               viiv  ii  v  v v  vv    ii  i  i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_21839740_   5080 ACAAAGCTGGAGGCGTCACACTACCTGACTTCAAACTATACTACAAGGCT 5129
                               i      vv       v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_21839740_   5130 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5179
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_21839740_   5180 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGGCACATAACTACAACTA 5227
                               i    i--    i  --        vvv  i i vi  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr20_21839740_   5228 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 5277
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_21839740_   5278 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5327
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_21839740_   5328 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGAT 5377
                           ii    i    v   i     v           i  i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_21839740_   5378 TAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5427
                         i ?   ii    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_21839740_   5428 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5477
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_21839740_   5478 ACACCAAAAGCAATGGCAACAAAAGCCAACATTGACAAATGGGATCTAAT 5527
                                     vvi          vv  v  v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_21839740_   5528 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACA 5577
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_21839740_   5578 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5627
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_21839740_   5628 GGGCTAATATCCAGAATCTATAATGAACTCAAACAAATTTACAAGAAAAA 5677
                           i  vi          v     v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_21839740_   5678 AACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 5727
                         i     i     v  i?    i           iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_21839740_   5728 CAAAAGAAGACATTTTTGCAGCCAAAAAACACATGAAAAAATGCTCATCA 5777
                          v        i  vivviii     v  i          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_21839740_   5778 TCACTGGCCAT 5788
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.40 (141 / 101)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3152 26.20 0.66 1.53  chr20_21857127_21861503     2970  3885 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21857127_   2970 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCAAGAAAAT 3019
                              ii i  i     i      i v      v i     iivv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21857127_   3020 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3069
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21857127_   3070 TACCAAGCTACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTT 3117
                          v   -   i  -------  i  ii     -   -- v  i  - iii 
  L1M4_orf2#LINE/    101 TCCCA-GCTGCC-------TTTTTTGCAGAAATTG--ACAAGCTGATCCT 140

  chr20_21857127_   3118 AAAGTTCATATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAA 3167
                            i           viiv  ii  v  viv  v     iv     i i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr20_21857127_   3168 GCCAAAAGAACAAAGCTGGAGACATCACACTACCTGACTTCAAACTATAC 3217
                         ivv i          i     ivv       v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr20_21857127_   3218 TACAAGTCTACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGA 3267
                              iv         i   i    ii    i    i iv ii i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr20_21857127_   3268 TATAGATCAATGGAACAGAAC--AGAGCCCTCAGAAATAAAGCGCATA-- 3313
                                        i    i--    i  --         v -    --
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACC-CATACA 337

  chr20_21857127_   3314 TCTACAACTATCTGATCTTTGAAAAAACCTGAGAAAAACAAGCAATGGGG 3363
                          i  iiiii vi    i  i  v  iiv-  vv  i v  vv        
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGG-TGCCAAGACCATTCAATGGGG 386

  chr20_21857127_   3364 AAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATAT 3413
                             i  vvi  v  i  i              v      v  ?   i  
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr20_21857127_   3414 GTAGGAAGCTGAAACTGGATCCCTTTCTTACACCTTATACAAAAATTAAT 3463
                          i ii iiv    ii    i    vi  i     v              i
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr20_21857127_   3464 TCAAGATGGATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCT 3513
                             i      i ?    i       v   v       i      vi i 
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT 536

  chr20_21857127_   3514 AGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACT 3563
                                   v    ?i v viv   iv   v v  vv i     v ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_21857127_   3564 TCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAA 3613
                           v ivv  vi            vvi          vv     v  i   
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr20_21857127_   3614 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAT 3663
                          v   ii v  i   v v  i i   i  ii vv    i  v    i  v
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr20_21857127_   3664 CAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACT 3713
                         v i      v  i     i   i             v       vii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr20_21857127_   3714 CATCTGACAAAAGGCTAGTATCCAGAATCCACAATGAACTGAAACAAATT 3763
                         i      i  ii i  v           vi i  v     vvv    v i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr20_21857127_   3764 TACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAA 3813
                         v i  v     i     i     v  i?    i           iv    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_21857127_   3814 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAA 3863
                         i     i     v        i  vi viii     v  i          
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_21857127_   3864 AATGCTCACCATCACTGGCCAT 3885
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (140 / 96)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2887 24.46 4.17 1.80  chr20_21879947_21884209.rev     2885  3771 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21879947_   2885 TGGAAAGACATCCCATGCTCATGGATGGAAAGAATTAATATCATTAAAAT 2934
                                 i        i        v i    v       ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21879947_   2935 GATCATATTGCTCAAGT-AATCTCCAGATTCAATGCAATCTTTATCAAAA 2983
                          iiv   i v i   i -i    v         i      ii        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21879947_   2984 TATGTATGTGA-TTTCTTATAGGATTATTAAAAA--TAATCCTGAAATTC 3030
                          vi-i vv  v-   i  ii  i --   i v  -- i     i      
  L1M4_orf2#LINE/    101 TCC-CAGCTGCCTTTTTTGCAGAA--ATTGACAAGCTGATCCTAAAATTC 147

  chr20_21879947_   3031 ATATAAAACCAAAAAAGAGCCCAAATAGCCAAAGCAATCCTTGTCTAA-A 3079
                             ii  viiv  ii  v  vi          i     -   vvv  - 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAAGA 196

  chr20_21879947_   3080 AGAACAAAACTGGAGGTATTATACCACCTGACTTCAAAA-----TAAAAG 3124
                                 ii      vv i i  iv  ii i       -----  v  i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_21879947_   3125 GCTATAGCAATCAAAACAGAATGCTATTGGTATAAAAAATGACACATCGA 3174
                             i  i      i    vi  v  i   i    ii vv    i  v  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_21879947_   3175 CCAGTGGAATAGAATAGAGAAGCCAGAAATAAGCCTACATATTTACAGCC 3224
                         i  i           v    iv          i  i i i     ii i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_21879947_   3225 AACTGATTTTCAACAAAGGC-TCAAGAACACGCACTGGGGAAGGACACA- 3272
                           i        i    i  i-i     v  iv  v       i  - i -
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA-ATAG 395

  chr20_21879947_   3273 -CTCTTAAATAAGTGGTCCTAGGAAAATTGGATATCTAGATGCAGAAGAA 3321
                         -  i  v  i  i    v  i   v  i      ? i v     i     
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_21879947_   3322 TGAAATTTCACCC-TCCCTCTCACCACCTACAAAAATCAATTCAAGATGG 3370
                             i  vv    - v    v     iv         i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_21879947_   3371 ATTAAAGACCTAAACATAAGACCTGAAATCACAAATCTTCTAGAAGAAAA 3420
                           i ?         ii     v  i   ii i   v  ii          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_21879947_   3421 CATAGAGG-AAATACTTCAGGATATTGATCTAGGCAAAGATTTTATGTAT 3469
                              i? -    -    iv  iv   ivi       v i   iv iv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_21879947_   3470 AGGACCTCAAAAGCACA-----TAAAACAAAAA-TAGGCAAATAGTGCTA 3513
                          v   vi          -----i    v     -   ii    v vi  v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_21879947_   3514 TATTAAA-CTAAAAGCTTCTACACAGCAAAGGAAATGATTAACAAAGAGG 3562
                         i  i   -i     i   i iii vv       v iv  i  v    v i
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_21879947_   3563 AAA--CATGTCA---AATAGTAAAACATATTTGCAAGCTAT---CCTG-C 3603
                            --  vvi  ---   i v i  v          iii  ---i   -i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_21879947_   3604 AAGGGACTAATATCCAGAATATAATAGGAACTC----AACTAAACAGTAA 3649
                                 vi             vv i      ----    v  i i   
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_21879947_   3650 AAGAAAAAAATTAAACAAATAATCCA-TTAAAAAGTGGACAAAGGACATA 3698
                           ---------- i        i   -  ?    i   i       iv i
  L1M4_orf2#LINE/    795 AA----------AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr20_21879947_   3699 AATAGACCTGTCTCAAAAGAAGTTATACAAATATCCAACAGACAAACAAA 3748
                                v v    v       v         iv    i ii  v ii  
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr20_21879947_   3749 AA-ATGTTCAACATCACTAGTCAT 3771
                           -   i         ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (138 / 75)
Gap_init rate = 0.03 (25 / 908), avg. gap size = 2.12 (53 / 25)  


3593 19.61 5.88 1.15  chr20_21886373_21891675.rev     3945  4811 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21886373_   3945 TGAAAAGACATCC-ATATACATGGATTGGAAGACTCAATATTGTTAAGAT 3993
                           i     i    -  i v                i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21886373_   3994 GACAATATTCCCAAAACTGATATAAAGATTCAATACAAGCCCTATAAAAA 4043
                          i     i    v   i    v  v        ii   v      v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21886373_   4044 TCTCAGTTTTTGTTTTTTCAGAAATT-----------CC--AAATTT-TA 4079
                           i   i viiv     v        -----------  --     i-  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_21886373_   4080 TG----TGCAA---ACTCAAGAATAACCAAAATTATTTTTAAAAAGGTGA 4122
                           ----     ---  i  -     i      iv  i  v      iv  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_21886373_   4123 ACAAAATTGAAAGAC----ACCTATTGATTTCAAAACTCTCTAAAAAGCT 4168
                              i   i i   ----  i viii           iv   v      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_21886373_   4169 ACAAAAATGAAAACAGTGTGCTCCTGGTGTAAGCATAGACATAAAAATCA 4218
                            iv   v  i        v v    ii    v         v i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_21886373_   4219 ATGGATTAGAATTAAGATTCCAGAAATAAACCCACATATTATTAGCCAAT 4268
                              v       i   v                i i   vv i i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_21886373_   4269 TGATTATCAATAATAGAGTCAA-----TTCAATTTGGAAAAGAATCATCT 4313
                              v  i i  vi v i   -----      v-  i       vi   
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCT 398

  chr20_21886373_   4314 TTTCAACAAATAATGCTGGGATAACTGGATATCCACATGCAAAAAAATAA 4363
                                    ii        i         ?            i   i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_21886373_   4364 ATTTGAACCC-TACCTAATACCACATACAAAAATGAATACAAAGTTGATC 4412
                          v   i    -     v i    i          v  iv    i v    
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_21886373_   4413 TAGGATCTAAATATAAGAGCAATATGTACAGAAGCCTCAGAAGAAA-CTT 4461
                         v?i  i      i       v v vv  i i  vi  i        - v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_21886373_   4462 AGATGTAAATCTTTATGATCTTGTATTAGGCAATGGTTTCTTAGATATAA 4511
                           i?         ii   i    vi                       i 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_21886373_   4512 CACCAAAAGTACAAGCAATGAAA-----AACAGATAAATTGAATTGTA-- 4554
                                  i        ii   -----  i          i i vi --
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_21886373_   4555 AAAATTTGAAATTCTTGTGTGTCACAGAATACTATCACAAGTATGAAAAC 4604
                               vi   i i     iv   v  i i       vi ivi      v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_21886373_   4605 ACAACCAACACAAACACAAAATTGGAGAAAATATTTGCAAGTCATGTGTC 4654
                               --------    i   v                 i    i i  
  L1M4_orf2#LINE/    699 ACAACC--------CACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_21886373_   4655 TGACAAGTATCTGGTATCCAGAGTATCCA--GAATTCTTATAATTCACCA 4702
                            i   viv  v         i   vi --   i     i  i   vi 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_21886373_   4703 ATTAAAATA-AAA-----CAAT--AAAAATGGGCAAAAAATTTCAAAAGA 4744
                           v    v -   -----    --             ii    v  v   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_21886373_   4745 TGGTTCTCCAAAGAAGATACATAAATAGCCAATG-GCCTATGAAAAGATG 4793
                         iiv                i i    i      i-  vi           
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr20_21886373_   4794 CTAAATATCAGTATTCAT 4811
                           v  i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (104 / 63)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 3.05 (61 / 20)  


2582 26.49 3.09 3.20  chr20_21925395_21928651     1860  2765 (491)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr20_21925395_   1860 AAAGTCACCGCATGCTCATGGATCAGAAGTATTCATATCATTAATGTTTC 1909
                             vi i v    i        ii    vv  v    ii    ------
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA------ 47

  chr20_21925395_   1910 TATACTGGAACCATAATGCCCAAAGCAGTCTGTAGATTGGATACAATCAC 1959
                         ---iv   -- v   v v      viii   ii     vi ii     v 
  L1M4_orf2#LINE/     48 ---GATGG--CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCC 92

  chr20_21925395_   1960 TA-CTAAATACCAA-TGCTATTTTTTACAAAAATAGAAAAA--AATTATA 2005
                           - v    v   i-   i-      i  i    v  v  i--i  iv  
  L1M4_orf2#LINE/     93 TATCAAAATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr20_21925395_   2006 AAATTTGTATAGGA-T-CAAAAAGCCCA-AATAGCCTGAGCAATCCTGAG 2052
                              ii   i i - -   iiii    -       vi i     i   -
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA- 190

  chr20_21925395_   2053 CAAAATCAGAA---AGCTGGAGGCATTACACTACCTGTTTTCAAAATGTA 2099
                         -    vv    ---  i      vv i     v  iiv        iv  
  L1M4_orf2#LINE/    191 -AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_21925395_   2100 TTACAAGGCTATAGGAATCCAAACAGCATGATATTGTTATAAAAACAGAC 2149
                         i     i    i  v    v i    ii  i  i  vi    ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr20_21925395_   2150 ACAAGGATCAA---AGTAGA-----GAATCCGGAAATAAATTAACATATT 2191
                          i vi      --- i    -----  i   i        iiv i i   
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr20_21925395_   2192 TAAAATCAACTGATTTTTGACAAAAGTGCCAAGAACAT---ATGTTATGG 2238
                           vii    i       i     ii         v   ---   ----  
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG----GG 385

  chr20_21925395_   2239 GACAGA-CACCCTCTTCAATAAATGGAGCTGTAAAAATTGGATATCTATA 2287
                           v   -i vi  i     i      v    vi v  i      ? i i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr20_21925395_   2288 AGTAGAAGAATGAAACTGGATCCCCATCTTTTATGACACATGAAAATCAA 2337
                         v i i         ii    i   i i  ivi iv i i ii     i  
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr20_21925395_   2338 CTCAAGATGAATTAAAGACTTTAACACAAGACCCCAAACTATAAAACTAC 2387
                              i   i  i ?    i v  iii    v iv             vi
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr20_21925395_   2388 AGGAAGAAAACATAGGA-TAAAACACTCAGGACATTCGTCTAGGCAA--A 2434
                         vi              ?-    v -i  iv   v  v vi       --i
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGG 584

  chr20_21925395_   2435 TATTTTATGTCTAAGACCTTAAAAGCACATACAACAAAAATAAAGATAGA 2484
                          v i   vi v i v   --         vi        iv   i     
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACC--AAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr20_21925395_   2485 CAAAAGGGACTATATTAAACTAATAAGATTCTTCACAGAAAAGGAAACAG 2534
                         i   vv     vi  i   v v v  iv  i vii vvv      v  vi
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr20_21925395_   2535 TCAATAGAGTGGA--GACAACCTGTTGAATGG-AGAAAATATTTACAACT 2581
                             v i    i --       iiiv      -           i   v 
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr20_21925395_   2582 TATTCATCTGACAAAAGACTAATATTGAGAATATACTAGAAATTTGAAAA 2631
                         i  vi      i  ii    vi   iv        iv ii  i ivv v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr20_21925395_   2632 ACTCAACAGTAAAAAAAAACAACAACAAATAATTCCATTAAAAAGTGGGC 2681
                               i i      i --------       ii v   ?    i     
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGA--------CAAATAACCCAATTWAAAAATGGGC 824

  chr20_21925395_   2682 AAAGGACATGAGTAGATACTTCTCAGAAGAAGACACACAAATGGCCAATA 2731
                               iv   i    i i     vi       i i              
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr20_21925395_   2732 AGTACATGAAAAACTACTTAACATTACTAATCAA 2765
                           i         iv i  i     i ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.84 (153 / 83)
Gap_init rate = 0.03 (23 / 905), avg. gap size = 2.48 (57 / 23)  


3182 27.12 0.66 0.55  chr20_21937571_21943982     5014  5920 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21937571_   5014 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAGTATCATGAAAAT 5063
                              ii i  i     i      i v      v i i   ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21937571_   5064 GGCCATACTGCCCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 5113
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21937571_   5114 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5160
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_21937571_   5161 ATATGGAAC--CAAAGATGAGCCTACATCCTCAAGTCAACCCTAAGCCAA 5208
                                 v--   i --  v  viv  vvi   iv   i i i ivv i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_21937571_   5209 AAGAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAA 5258
                                   i      vv   ii  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_21937571_   5259 GCCTACAGTAACCAAAACAGCATGGTGCTGGTACCAAAACAGAGATATAG 5308
                         iv         i   i    ii    i    i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_21937571_   5309 ATCAATGGAACAGAACTGAGCCCTCAGAAATAACTCTGCATATCTACAAC 5358
                                   i    i    vvii         vi iii i  i  iiii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_21937571_   5359 TATCTGATCTTTGACAAACCTGAGAAAAGCAAGCAATGGGGAAAGGATTC 5408
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_21937571_   5409 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5458
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_21937571_   5459 TGAAACTGGATCCGTTCCTTACACCTTATACAAAAATTAATTCAAGATGG 5508
                             ii    i  v v   i     v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_21937571_   5509 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5558
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_21937571_   5559 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5608
                          v    ?i v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_21937571_   5609 AAACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5658
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_21937571_   5659 ATTAAACTTAAGAGCTTCTGCAAAGCAAAAGAAACTACCATCAGAGTGAA 5708
                           i   v    i i   i  iivvv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_21937571_   5709 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCCACTCATCTGACC 5758
                         v  i     i   i             v  i    vi  ivi      iv
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_21937571_   5759 ATGG-CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5807
                          v  -  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_21937571_   5808 AAAACAAACAACCCTACTAAAAAGTGGGCGAAGGACATGATCAGACACTT 5857
                           i     i     v i ?    i     i     iv   vi     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_21937571_   5858 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAC 5907
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_21937571_   5908 CATCACTGGCCAT 5920
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.38 (11 / 8)  


3226 26.79 0.66 0.55  chr20_21969352_21975752.rev     5003  5909 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_21969352_   5003 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5052
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_21969352_   5053 GGCCACACTGCCCAAGATAATTTATAGATTCAATGCCATCCCCATCAAGC 5102
                            v i   v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_21969352_   5103 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGGTCA 5150
                          v   iivi i  i  ii     -   -- v  i  - iii    iv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_21969352_   5151 TATGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAGAG 5200
                                viiv  ii  v  v v  v     iv     i i ivv ii  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_21969352_   5201 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5250
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_21969352_   5251 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5300
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_21969352_   5301 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTTCAACT 5348
                                i    i--    i  --        vv  ii i  i viiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_21969352_   5349 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5398
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_21969352_   5399 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5448
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_21969352_   5449 GAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5498
                            ii         v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_21969352_   5499 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5548
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_21969352_   5549 CTAGGCATTACCATTCAGGACATAGGCACGGGCAAGGACTTCATGTCTAA 5598
                         v    ?i v viv   iv   v v  vvii     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_21969352_   5599 AACACCAAAAGCAGTGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5648
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_21969352_   5649 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5698
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_21969352_   5699 AGGCAACCTACAAAATGGGAGAAAATTTTCTCAA--CCTCTCATCTGACA 5746
                           i     i   i             v  iv   -- v v -      i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT-ATCTGATA 745

  chr20_21969352_   5747 AAGGGCTAATATCCAGCATCTACAATGAACTCAAACAAATTTACAAGAAA 5796
                          i  i  vi       v  v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_21969352_   5797 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGACATGAACAGACACTT 5846
                           i     i     v  i?    i           iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_21969352_   5847 CTCAAAAGAAGACATTTATGCAGCCAGAAAACACATGAAAAAATGCTCAT 5896
                            v        i  vi viii    iv  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_21969352_   5897 CATCACTGGCCAT 5909
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (140 / 99)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3445 21.37 5.26 1.49  chr20_22003729_22007363.rev      508  1382 (2253)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22003729_    508 TGGAAAG-TACCCCATGTTCATGAATTAGAA-ACTTA---TTTTTTAAAT 552
                                -  i            i   i   -     ---  v  v i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22003729_    553 AGATATTTTTAAACTTCATAAATTGATCTATATATCCAACACAAAAATTG 602
                         i vv  ------   i vi           i v  i    i   --- iv
  L1M4_orf2#LINE/     51 GGCAAT------ACTCCCCAAATTGATCTACAGATTCAACGCAA---TCC 91

  chr20_22003729_    603 ATATCAAAATTTAAATGGTCTTTACTAGAGAAATGAAAAAGCTTACCTTT 652
                         v         iiv iiv i    vi iv      vi v     v i i v
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr20_22003729_    653 AAATATGTACGGAATTGTAAAGTGTCCTAAATAGTGAAAACAATCTTAGT 702
                             vii  i    v  i  i vii  vi     iv           iiv
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr20_22003729_    703 AAAGGAGAACAAAGTTGGAAGACTCACACTTCCTAATGTCTAAAGTTATT 752
                             i              i             i   v  v   v   i 
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr20_22003729_    753 GCAAAACAACAGAAATCAGAACAATG--ACACTAGCATGAGGATAGACAT 800
                         i    i v    v     ii   i  --ii   i    i           
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_22003729_    801 ATAGACCAATGGAATAAAATAGAGAGTCCA-AAGTAA-TCCATATGTCTA 848
                              i          i   v         -  i   -i     ii i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_22003729_    849 TGGCCAATTCATTTTTGACAAGAGTTCCATGACTAATAAGTGGGGAAATA 898
                            i     v     i      i  v   v   i v v i        v 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_22003729_    899 ATAGTTTCTTCAACAAATAATGATGAAACAACTGGACAGCCACCTACAAA 948
                              i i          ii  v  ii         i ?    v i    
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_22003729_    949 AAAGTAAAGTTGGATCCTTACCTCACACCAGGGA--AAAATTCACTCAAA 996
                          i i i        i  i            viv --      v       
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_22003729_    997 AATAGATCAAAAATCTAAAT----------AGAC------------AGAG 1024
                          - i     ? i i      ---------- i  ------------   i
  L1M4_orf2#LINE/    492 A-TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr20_22003729_   1025 AAAAACATAGGGGTAAATTTCCATGACTTTGATTTGAG-AATAGATTCTT 1073
                         i          ?      i i i    i   iv  ii -   i v     
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_22003729_   1074 AGATAAAATGCTGAAAGCCAAAGCAACAAAAGTAAAATAAATAAATTAAT 1123
                              vi ii ii     vv            -    --    i  v   
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAG-AAAA--AATAGATAAAT 637

  chr20_22003729_   1124 TAAACTATATCAAAATTTAAAACTTTTTTGGGTCAAAGGAAATTAATAAG 1173
                          ii   vi         v         v  vv        v i  vi   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_22003729_   1174 AAAGTGAAAATATAGCCTACAGAATGGGAGAAA-TATCTTCAAATTATAT 1222
                                   v i i  i               -   i v     i    
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_22003729_   1223 ATCTGGTAAGGGTCTAGTATTTAGACTGTATAAA-AACTTTTACATTTTG 1271
                              i      v  v    ii   v i      -    i     vi ii
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_22003729_   1272 ATAACCAAAATACAAACAATCCAATTTTAAAATGGACAAAGGATT--GAC 1319
                             iv    v     i  i      ?v       i         --i i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_22003729_   1320 AGACA--------AAGTAGATACACAAATGGGCAATAGGCACATGAGAAG 1361
                              --------   v     i        v     i        i   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_22003729_   1362 ATGTTCAACAGCATAAGTCAC 1382
                            i      v  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (119 / 64)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.11 (59 / 19)  

2898 22.43 4.76 2.63  chr20_22003729_22007363.rev     2348  3145 (490)    L1M4_orf2#LINE/L1       94   908 (0)  

  chr20_22003729_   2348 ATCAAAATCCCAGC-ATTTTTATTTTGGAAATTGACAAACTGATTCTAAA 2396
                                       -iii   v  vii           i     i     
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr20_22003729_   2397 ATTAATATGGAAGTGCAAGGGACCTAGAATAGCCAAAATAACTTTTTTTG 2446
                            v        i           i             i  --- i  vi
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA---TCTTGA 190

  chr20_22003729_   2447 GAAGGAAGAAAATAGTTGAAAGACCAAAACTCACTAATCTTAAGACTTAT 2496
                         i  i      v v     i i   iv v   iv i   i i  i     i
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr20_22003729_   2497 TATAAAGCTACTGTAATCAAGACAGGTGTGAT--TGGTACAAAACACAGA 2544
                           i        v             -    i --   i i  ii- i   
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAG-TGTGGTACTGGCATAAGG-ATAGA 288

  chr20_22003729_   2545 CAAATAAATCAATGGGAAAAAATAGAGAATACAGAAATAGACCCA--CAT 2592
                           v   i        i v i   v    i v        i     --   
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr20_22003729_   2593 TTATGTAAATAACTGATTTTCTACAAAGGTGCATAAG-TAATTCCATGGG 2641
                              --ivi  i        v    i     -i   -iv    v     
  L1M4_orf2#LINE/    339 TTATG--GTCAATTGATTTTCGACAAGGGTGC-CAAGACCATTCAATGGG 385

  chr20_22003729_   2642 GGAAAGGGTAGTCTTTTCAACAACTAATGCTGGAACAATTAGATATTCAT 2691
                          -    ii               v ii      i    i i    ?i  i
  L1M4_orf2#LINE/    386 G-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr20_22003729_   2692 ATACAAAA-AATGAACTTCAATCCACACCTTGTACCATATACAAAAATTA 2740
                           i     -      v  vi i  vi    iii                 
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr20_22003729_   2741 ACTCAAA-TGGATTGTAGAATGAAATGTAAAATCTAAGACTATAAAACTT 2789
                                -     ii?   viv        i v    i           i
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr20_22003729_   2790 GTAGAAGGAAACA--GGACAAAATCTTTGTGGCCTTGAGTTAGGCAAAAC 2837
                         v      i     --  ?vv       i   i     i         viv
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr20_22003729_   2838 CTTCTTTGCTATGACAGCAAAGTCATGGTCCATTAA-GAACAAATTGGTA 2886
                         i     v v       v    iv  iiiv v iv  -   v    v i  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr20_22003729_   2887 AACTGTATTTC--CACAAATTAGAAACCTTTGTTTTTGGACCAACATTGT 2934
                           i  v i   --  -      i    i     vi  vi vvi   i i 
  L1M4_orf2#LINE/    635 AATTGGACTTCATCA-AAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr20_22003729_   2935 TTCATTCATAAAAGAATGAAAAGGCAAGTTACAGCCTGGAAAGGTATATT 2984
                         i--------  i i i       i   vii    vv   i iiiv     
  L1M4_orf2#LINE/    684 C--------AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr20_22003729_   2985 TGCAAAGCATAAGTCTAATAAAGGACTTACATTCTGAATACA----GAGC 3030
                               v    vi   i    i      ii  i v     i ----  i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr20_22003729_   3031 CCCCAAAACTCAATAACTTTAAAAA-----ATATTTTAAT--------AG 3067
                         i ii v          ---      -----   viii   --------i 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAA---TAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_22003729_   3068 GCAAA--------ACAGACACTTCACCAGAGAAGATATATGAATGATAAA 3109
                              -------- i     i   v   i          ii    iiv  
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_22003729_   3110 TAAGCACATGAAAAGATAATCAACATTGTTAGTCAC 3145
                                          iv       ii????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (120 / 56)
Gap_init rate = 0.03 (22 / 815), avg. gap size = 2.68 (59 / 22)  


2857 26.25 0.98 2.60  chr20_22040747_22049474      992  1913 (6815)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr20_22040747_    992 GGTAAAATATTCCATGTACATAAATAAGAAGAATCAATATCGTGAAAATG 1041
                           v  i    i      v   ii  vi     v i     i  v  i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_22040747_   1042 GCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATTAAACT 1091
                           v     v      v i  i  i        i  v  i  i  i   v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_22040747_   1092 ACCA-CTGACATTATTCACAGAATTAGAAAAAAACT-ATTTTAAATTTTA 1139
                         v   -   v v  -  ii     v v  v  i--  -  ii    v  i 
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTT-TTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr20_22040747_   1140 TATGGAATTCAGACTCTGAAAACAGAGCCGAAATAGCCAAGACAATCCTA 1189
                                ----- ---  v  i-i  v  ii         i      i i
  L1M4_orf2#LINE/    149 TATGGAA-----A---TGCAAG-GGACCCAGAATAGCCAAAACAATCTTG 189

  chr20_22040747_   1190 AGCAAAAAGAACAAAGCTGGAGGTATCACACTACCCAACTTCAAACTATA 1239
                          iv  i          i      vv       v     i      viv  
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_22040747_   1240 CTACAAGGCTATGATAACCAAAACAACATAGTACTGGTACAAGAACAGAC 1289
                               i    iii   i   i   iii i       i i   i i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr20_22040747_   1290 ACATAAACCAATGTAACAGACTAGAGAACTCTAGAAACAAGACCACTTGC 1339
                          i   i i     v  i   v v    i-  i     i  iv   iviii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAG-TCCAGAAATAAACCCATACAT 338

  chr20_22040747_   1340 CTACAACCATCTGATCTTCAATAAACCTGACAAAAACAAGCAATGGGGAA 1389
                         i  iiii  vi    i   i i  ivv  v   i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr20_22040747_   1390 AGGATTTCCTATTTAATAAATGTTGTTGGGAGAACTGGCTGGCCACATGA 1439
                           i  vvi  v  i  i     v  i     v      v i?       v
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr20_22040747_   1440 AGACAATTGAAACTGGACTCCTTCCTTACACCATGTACAAAAGTTAACCC 1489
                          i vi v    ii     i   v   i       i       i     i 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr20_22040747_   1490 AAGATGGATTAAAGACTTAAATGTAAAACACCGAACTATATAAAAAAAAA 1539
                           i      i ?    i         ------  i   ----   vv v 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAA------GAGCTA----AAACTATA 528

  chr20_22040747_   1540 AAAACCCTAAAAGAAAATCTAGGCACTACCATTCAGGACACAGGCACAGG 1589
                            vi i  i       iv    ?iiv viv   iv   viv  vvi   
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr20_22040747_   1590 CAAGGATTTCAT-GATGAAAATGCCAAAAGCAATTGCAACAAAAGCAAAA 1638
                            v i    v -   - vi ii         vvv          v    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr20_22040747_   1639 ATTGACAAATGGGATCTGATTAAACTAAAGAGCTTCTGCACAGCAAAAGA 1688
                           v  i    v   ii v  i   v v  i i   i  ii vv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr20_22040747_   1689 AACTATCATCACAGTGAACAGACAACCTGCAGAATGGGGGAAATT-TCTA 1737
                         v       vv v      v        ii         i    v - i i
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr20_22040747_   1738 CAATCTATCCATCTGATGAAGGTCTAATATCCAGAGTTTACTAGGAACTT 1787
                            vii  vi       i i  v  vi        i v  iv i     i
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr20_22040747_   1788 AAACAAATTTACAAGAAAAA---AAA-AACCCTATTAAAAAGTGGGCAAA 1833
                         vv    v iv i  v     ---   -     v   ?    i        
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr20_22040747_   1834 GGACATGAACAGACCCTTCTCAAAAAGAGACATACATGTGGCCAACAAAC 1883
                            iv    i    vi     v   ii   i     vi       i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr20_22040747_   1884 ATAAGAAAA-ATGCTCAACATCACTAATCAT 1913
                          i v     -             ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.02 (16 / 907), avg. gap size = 2.06 (33 / 16)  

 625 25.81 1.29 1.29  chr20_22040747_22049474     7017  7171 (1557)    L1M4_orf2#LINE/L1        1   155 (753)  

  chr20_22040747_   7017 TGGAAGAACATTCCATGCTCACGGGTAGGAAGAATCAATATCGTGAAAAT 7066
                              ii i  i     i   i  i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22040747_   7067 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 7116
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22040747_   7117 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 7164
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_22040747_   7165 TATGGAA 7171
                                
  L1M4_orf2#LINE/    149 TATGGAA 155

Transitions / transversions = 2.64 (29 / 11)
Gap_init rate = 0.02 (3 / 155), avg. gap size = 1.33 (4 / 3)  

2641 27.09 0.92 0.39  chr20_22040747_22049474     7473  8236 (492)    L1M4_orf2#LINE/L1      141   908 (0)  

  chr20_22040747_   7473 AAAGTTCATATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAA 7522
                            i           viiv  ii  v  viv  v     iv     i i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA 190

  chr20_22040747_   7523 GCCAAGAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATAC 7572
                         ivv ii         i      vv    i  v  ii i      viv   
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr20_22040747_   7573 TACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGA 7622
                              i          i   i    ii         i iv ii i   v 
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr20_22040747_   7623 TATAGACCCATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATAT 7670
                               i v      i    i--    i  --        vv   i i  
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACAT 338

  chr20_22040747_   7671 CTACAACTATCTGATTTTTGACAAACCTGAGAAAAACAAGCAATGGGGAA 7720
                         i  iiiii vi       i     ivv  vv  i v  vv          
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr20_22040747_   7721 AGGATTCCCTATTTAATAAGTGGTGCTGAGAAAACTGGCTAGCCATATGT 7770
                           i  vvi  v  i  i  i        i  v      v  ?   i   i
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr20_22040747_   7771 AGAAAGCTGAAACTGGATCTCTTCTTTACACCTTATACAAAAATTAATTC 7820
                          i  iiv    ii    i i  v i i     v              i  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr20_22040747_   7821 AAGATGGATTAAAGACTTAAATGTTAGACCTAAAATCATAAAAACCCTAG 7870
                           i      i ?    i       v   v      ii      vi i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr20_22040747_   7871 AAGAAAACCTAGGCA-ATACCATTCAGGACATGGGCATGTGCAAGGACTT 7919
                                 v    ?i- v i -   iv   v v  vv iv    v ii  
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_22040747_   7920 CATGTCTAAAACACCAAAATCAATGGCAACAAAAGCCAAAATTGATAAAT 7969
                          v ivv  vi         v  vvi          vv     v       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr20_22040747_   7970 GGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATC 8019
                         v   ii v  i   v v  i i   i  ii vv    i  v    i  vv
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_22040747_   8020 AGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACTC 8069
                          i      v  i     i                 v       vii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_22040747_   8070 ATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTT 8119
                               i  i  i  vi          v  i  v      vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_22040747_   8120 ACAAGAAAAAAGCAAA---CCCA-TCAACAAGTGGGCAAAGGATATGAAC 8165
                          i  v     ii    ---    - i? v  i            v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_22040747_   8166 GGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAA 8215
                         i    i     v        i  vi viii     v ii          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_22040747_   8216 ATGCTCCTCATCACTGGCCAT 8236
                               vv     ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (117 / 86)
Gap_init rate = 0.01 (6 / 768), avg. gap size = 1.67 (10 / 6)  


2816 27.11 0.25 0.12  chr20_22113827_22118441.rev     2915  3718 (897)    L1M4_orf2#LINE/L1        1   805 (103)  

  chr20_22113827_   2915 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 2964
                               v i        i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22113827_   2965 GACTATACTGCCAAAAGTAATCTACAGATTCAATGCAATCGCCATCAAAA 3014
                          i v     v  v   v i              i      v i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22113827_   3015 TACCACCATTATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTCATA 3064
                          v   v vviv  i  ii     v v  v  ivii  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_22113827_   3065 TGGAACCAAAAAAGAGGGTGCATAGCCAAAGCAAGACTAAGCAAAAAGAA 3114
                              viiv  ii  vvvv v         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_22113827_   3115 CAAACCTGGAGGCATCACACTACCTGATTTCAAACAATACGATAAGGCCA 3164
                             vi      vv       v  ii        vvv   v i  i  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_22113827_   3165 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCAA 3214
                         i   v i   i    ii         i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_22113827_   3215 TGGAACAAAATGGAGCACCCAGAAATAATCCCAAACACTAACAGCCAACT 3264
                              i i   v   vii          v    v   i v ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_22113827_   3265 GATCTTCAACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTTT 3314
                            i   i    i vviv   i v   vv i         i i vi    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_22113827_   3315 CCAACCAATGGTGCTGGGATAATTGGCTAGCCACATGTGGGAGAATGAAA 3364
                         i    v             i  i   v  ?       iiii        i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_22113827_   3365 CTGGATCCTCATCTCTCACCTTATATAAAAATCATCTCAAGATGGATTAA 3414
                         i    i  ii i   v    v    i      i v     i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_22113827_   3415 TGACTTAAATCTAAGACGTGAAACTATAAAAATTCTAGAAGATAACATTG 3464
                         v   i     v     vv i           v ii       v     v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_22113827_   3465 GAAAAACCCTTCTAGACATTGGCTTAGTCAAGGATTTCATGACCAAGAAC 3514
                          ?iv  vi    vv   v    v    v   v i    v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_22113827_   3515 CCAAAAGCAAATGCAATAAAAACAAAGATAAGTAGCTGGGACTTAATTAA 3564
                                  v v    i    iv   i   ii  iv v      v  i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_22113827_   3565 ACTAAAGAGGTTTTGCATAGCAAAAGGAACAGTCAGCAGAGTAAACATAC 3614
                          v v  i iv     iiivv    i iv  vi   iv i   i  v v  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_22113827_   3615 AACCCACAGAGTGGGAGAAAATCTTTG-AAATCTATACATC-GACAAAGG 3662
                                   i           v    -     -   i   -  i  i  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATAAGGG 749

  chr20_22113827_   3663 ACTAATATCCAGAATCTACAACAAACTCAAACAAATCAACAAGAAAAAAA 3712
                            vi          v  i  vi     vv    v    i  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_22113827_   3713 TAAACA 3718
                         i   i 
  L1M4_orf2#LINE/    800 CAAATA 805

Transitions / transversions = 1.17 (116 / 99)
Gap_init rate = 0.00 (3 / 805), avg. gap size = 1.00 (3 / 3)  

 432 15.33 3.65 4.38  chr20_22113827_22118441.rev     3987  4123 (492)    L1M4_orf2#LINE/L1      773   908 (0)  

  chr20_22113827_   3987 AACTC---CATCTCAAAAAAAAAAAAAAAACCAAAAAAATTTACATCAAA 4033
                              ---  v     v  v     i ----    v  -iii -  i?  
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGA----CAAATAA-CCCA-ATTWAA 816

  chr20_22113827_   4034 AAGTGGGCTAAGGACGTAAATAGACAATTCTCAAAAAAAGATATACAAAT 4083
                           i     v     iv i        v     v   i             
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr20_22113827_   4084 GGCCAAGAA--ATATGAAAAAATGCTCAACATCACTAATGAT 4123
                               v  -- i       i             ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.04 (5 / 136), avg. gap size = 2.20 (11 / 5)  


2952 24.89 1.99 2.10  chr20_22118553_22120656      709  1612 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr20_22118553_    709 AAACATTCTGTGCTCATGGATAGGAAGAATCAATATCATTAAAATGTCTA 758
                          i i  i ii  i        v      v i     ii    i   v v 
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr20_22118553_    759 TACTGCCCACAGTAATCTACAGATTCAATGCTATTCCTATCAAAGTACCA 808
                             v    v v i              i  v  i         i v   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr20_22118553_    809 ACATCATTTTTCACAGAATTAGAAAAAAAACT-ATTATAAAATTCATATG 857
                         i vv v     ii     v v  v  i---  -  iv             
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTCATATG 152

  chr20_22118553_    858 GAATAAAAAAAGAGTCCA-AATAGCCAAGGCAATCCTTAGCAA-AACAAT 905
                            - viv  i iii   -         ii     i v iv  -  v  i
  L1M4_orf2#LINE/    153 GAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_22118553_    906 GAAGCATGCAGTA-TCACATTACCTGTCTTCAGATTATGCTACAGGACTG 954
                         i   i-  v  v -     i v  iivi    i viv i     iii  i
  L1M4_orf2#LINE/    202 AAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_22118553_    955 TGGTAACCAAAACAGGATGGTACTGGGACAAAAACAGAAACATAGACCAG 1004
                         ii    i   i    vi         v i  ii i   v i     i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_22118553_   1005 TGGAACAGAATAGAGCACTCACATATAAAGCTGCAAACAT--ACAATCAA 1052
                              i     v   viii  v v     v --  v    -- iii    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCAA 348

  chr20_22118553_   1053 TTGGTCTTTGACAAAGGTGACTAAACTAAGTAATGGGGAAAGGAT-GTCC 1101
                            i i  i     i    v v i  i vvi           i  -   i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_22118553_   1102 TATTCAATAAATAATGCTGGGA-AACTGGCTAACCATATGCAGAAGAATG 1150
                          -     i    ii        -      v  ?   i     i       
  L1M4_orf2#LINE/    399 T-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_22118553_   1151 AAACTGGACCTTTACCTATCACCCTATACAAAAACTAACTCAAGATGGAT 1200
                           ii      ii     vv    v          i        i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_22118553_   1201 TAAATACTTAAATGTAAGACCTAAAACTTTTGAAATTCT-AGAAGAAAAC 1249
                         i ? v  i           v        v -i   i   -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAAAC 546

  chr20_22118553_   1250 CAAGG---AAATATTCTTTTAGGCATTGGCCTAGGCAAAGACCTCAT-GA 1295
                         vv   ---    v   v --- i v    vi       v iii  v -  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGT---GACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_22118553_   1296 C-TAACTCCTCAAAAACAAATGCAACAACAACAAAAAAAATGGATGTAGG 1344
                         i- i  v  --    i  v --- i      v i       i   iv vv
  L1M4_orf2#LINE/    594 TATGACACC--AAAAGCACA---AGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_22118553_   1345 AGACCTAATTAAA--CAAAAGCTTTTGCATGGCAAAAGAAACTGTCAAGG 1392
                         i   i v  i   --i    i      iiivv    i  v   i     i
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr20_22118553_   1393 AGGGAAACAGATAACCTACAGATTATAAGAAAATATTTGCAAAATATGCA 1442
                          i vi  v   i    i     v ivi                vi  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_22118553_   1443 TCTGACAAAAGTCTAATGTCCAGAATATGTAAGGAACTTAAACAAATCAA 1492
                              i  ii v  vi i          i   i     ivv    v    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_22118553_   1493 TGAGAAAAAAA-AAA-AACTCCATTAAAAAGTGGGCAAAGGACATGAACA 1540
                          i v     i -   -   i v   ?    i           iv    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr20_22118553_   1541 GACACTTCTCAAAAGGAGACATGCATGTGGCCAAAAAATACATGGAAAAA 1590
                             i     v    i   i  i  vi       v  ii     --    
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG--AAAA 886

  chr20_22118553_   1591 AATGCTCATCATTACTAGTCAT 1612
                         i       v   i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (140 / 82)
Gap_init rate = 0.03 (24 / 903), avg. gap size = 1.54 (37 / 24)  


3096 25.91 1.10 1.43  chr20_22122276_22131533     4992  5902 (3356)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22122276_   4992 TGGAAGAACATTCCACGCTCATGTTTAGGAAGAAACAATATTGTGAAAAT 5041
                              ii i  i   i i     vv v      vvi        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22122276_   5042 GACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5091
                          i v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22122276_   5092 TACCATTGACTTTCTTCACAGAA-TTGGAAAAAAAAACT-ACTTTAAACT 5139
                          v   vivi i  i  ii     -   ----- v  i  - iii    v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-----ACAAGCTGATCCTAAAAT 145

  chr20_22122276_   5140 TCATATGGAACCAAGAAAGAGCCCGCATTGCCAAGACAATCCTAAGCAAA 5189
                                   viivi ii  v  v v  v     i      i i iv  i
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_22122276_   5190 AAGAACAAAGCTGGAGGTATCACGCTACCTGACTTCAAACTATACTACAA 5239
                                   i      vv    i  v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_22122276_   5240 GGCTACAGTAACCAAAACAGCACGGTACTGGAAACAAAACAGATATATAG 5289
                         i          i   i    iii        v vv ii i   i      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_22122276_   5290 ACCAATGGAACAGAAC--AGAGTCCTCAGAAATAATACAATACATCTACA 5337
                          i        i    i--       --        vv v      i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr20_22122276_   5338 ACCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATAGGGAAAGGAT 5387
                         ii  vi    i  i     ivv  v   i v  vv    i       i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_22122276_   5388 --TCCCTAATTAATAAATGGTGCTGAGAAAACTGGCTAGCCATATGAAGA 5435
                         --  ii -- i  i           i  v      v  ?   i   v i 
  L1M4_orf2#LINE/    394 AGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_22122276_   5436 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAAGTGATTCGAG 5485
                          iiv    ii    i    v   i     v          v i i  i i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_22122276_   5486 GTGGATTAAAGACTTAAATGTCAGACCTAAAACTATAAAAGCCCTAGAAG 5535
                         i     i ?    i       v   v              vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_22122276_   5536 AAAACCTAGG---AAATACCATTCAGGACATAGGCATGGGCAAGGACTTC 5582
                              v    ---    -- -   iv   v v  vv i     v ii   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_22122276_   5583 ATGACTAAAACACCAAAAGCAATGGCAACAAAAACTAAAATAGAAAAATG 5632
                         v iiv  vi            vvi         ivv        v    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_22122276_   5633 AGATCTAATTAAA-TTAAAGAGTTTCTGCAGAGCAAAAGAAACTACCATC 5681
                         i  ii v  i   -     i v   -  iivvv    i  v    i  vv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAG 687

  chr20_22122276_   5682 AGAGTGAACAGGCAACCTACAGAATGGTAGAAAATTTTTGCAATCTCTTC 5731
                          i      v  i     i         v       v       viiv vi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_22122276_   5732 ATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTT 5781
                               i  i  i  vi          v  i  v      vv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_22122276_   5782 ACAAGAAAAAATCAAGTAGCCCCATCAAAAAGTGGGGAAAGGATATGAAC 5831
                          i  v     iv   i  i   v  i?    i    v       v    i
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_22122276_   5832 AGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAA 5881
                              i     v        i  vi viii     v  i          i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_22122276_   5882 ATGCTCATCAACACTGGCCAT 5902
                                v  v  ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (134 / 99)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.92 (23 / 12)  

2882 26.42 2.90 1.67  chr20_22122276_22131533     7870  8766 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22122276_   7870 TAGATAAACATTACATGCTCATGAATAGGAAGAATTGATATCATTAAAAT 7919
                          i  v i i  iv    i     i  v      v  i    ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22122276_   7920 GGC---------CAAAGCAATTTATATATTCAGTGCTGTTCCTATCAA-- 7958
                            ---------    vii  i  i v     ii  vi i        --
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22122276_   7959 -TCTA-CTGAGGACATTCTTCACAGAACTAGACAAAAAATCT-ATTTTAA 8005
                         -i i -   ---- v  i  ii     v v     i----  -  ii   
  L1M4_orf2#LINE/    101 TCCCAGCTG----CCTTTTTTGCAGAAATTGACAAG----CTGATCCTAA 142

  chr20_22122276_   8006 AATTCCTATGGAACCAAAAAAGAGCCCACAA-AGCCAAGGCAATCCTAAG 8054
                              v       viiv  ii  -    v  -      ii     i i i
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAA 191

  chr20_22122276_   8055 CAAAAAGAGCAAAGCTGGAGGCATCACACTATCCAACTTCAAACTATACT 8104
                         v  i    i     i      vv       vi    i      viv    
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr20_22122276_   8105 ATAGGGCTGCAGTAGCCAAAACAGCATGACACTGGTGCAAAAACAGACAC 8154
                          i ii   i     ii   i    ii  ii     iii  ii i     i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_22122276_   8155 ATAGACCAATGGAACAGAATAGAGAG-CTAGAAATAAGGCTGCACACCTA 8203
                              i        i     v     - i        iv iii   ii  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_22122276_   8204 CAACTACCTAATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAGGA 8253
                         iiiii vi i  i  i     ivv  v   i v  vv          i  
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_22122276_   8254 TTC-TCTATTCAATAAATGGTGCTGAGATAACTGGCTAGCCATATGCAGA 8302
                         v v-   v     i           i  i      v  ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_22122276_   8303 GGATTGAAACTGGACCCCTTCTTTATACCACATA-AAAAATTAAGGCAAA 8351
                         i  v    ii         v i i i    i   -         vv    
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_22122276_   8352 ATGGATTAAAGGCTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAA 8401
                               i ?  i i         i v i            vi i i   i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_22122276_   8402 ACAAAC-TAGGCAGTACCCTTCTAGATGCAGGAACAGACAAAGATTTCAT 8450
                          -    -    ?ivv vi    vv  iviv  ivi  i   v i    v 
  L1M4_orf2#LINE/    542 A-AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_22122276_   8451 -GATGAAGATGCCAAGAGCAATTGCAACAAAAGCAAAAATTGACAAATGA 8499
                         -   - v  ii    i    vvv          v      v  i    vi
  L1M4_orf2#LINE/    591 AGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_22122276_   8500 GATCT------AATTAAAGAGCTTCTGCACAGAAAAATAAACTATCAACA 8543
                           ii ------       i -   i  ii vvv   iv v        v 
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr20_22122276_   8544 GAATAAACAGACAACCTACAGAATGGGAGGAAATTTTTGCAAACTATATA 8593
                         i i i  v        i            i    v        ii     
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_22122276_   8594 GTTGATGAAGGTCTAATATCCAGCATCTATAAGGAACTTAAGCAAATTTA 8643
                         vi    i i  v  vi       v  v     i     ivvi   v ---
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT--- 785

  chr20_22122276_   8644 CAAGAAGAAACAACCAACCAACCCTATTAAAAAGTGAGAAAAGGACATGA 8693
                            v  v   v iv   vi     v   ?    i  i v      iv   
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr20_22122276_   8694 ACAAACATTTTTCTAAAGAAGACATACATATGACCAACAATCATATGAGA 8743
                          i i      i  i        i     v   i    i  v  i    i 
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr20_22122276_   8744 AAAAGCTCAACATCACTGATTTA 8766
                          i v           ????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (150 / 83)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.28 (41 / 18)  


 260 32.99 5.08 7.11  chr20_22235938_22237952.rev      501   697 (1318)    L1M4_orf2#LINE/L1      244   436 (472)  

  chr20_22235938_    501 AAAGCTAAAGTAACTAAGATAATGTTGTATTAATGTAGGGATAGACTCCC 550
                                v     ii    i i   v   i iiii  i        vi--
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT-- 291

  chr20_22235938_    551 CCTAAAAAATCC-CAGAACTGAATAGTGGTTCTAGAAACATATCTATG-A 598
                         ---- v i   v-ii   iv    v v iv  i     i v i i  i- 
  L1M4_orf2#LINE/    292 ----ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr20_22235938_    599 TTATATAAGCAACCCTGACTTGAGGCAGAGCTTGTACTGCAGA----TTA 644
                           -   iiv   i--   i  vv i  ii ---  i ii-   ---- i 
  L1M4_orf2#LINE/    338 TT-TATGGTCAAT--TGATTTTCGACAAGG---GTGCCA-AGACCATTCA 380

  chr20_22235938_    645 GTGGAGAGAAAGCA----CTTCAACCAATGATGTAAAGGTGATTGGGCAT 690
                         i   i  i i ii ----i      v    i  ivii iii i   ii ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr20_22235938_    691 CCATCAT 697
                            -   
  L1M4_orf2#LINE/    431 CCA-CAT 436

Transitions / transversions = 3.27 (49 / 15)
Gap_init rate = 0.05 (10 / 193), avg. gap size = 2.40 (24 / 10)  

 449 30.43 7.83 4.78  chr20_22235938_22237952.rev     1068  1527 (488)    L1M4_orf2#LINE/L1      435   908 (0)  

  chr20_22235938_   1068 ATGTAGAAAGAGCATGAGGTTAACACTGTACTTCACACCATA-ACAA--- 1113
                            i -     --    i   iivv iv   i          -    ---
  L1M4_orf2#LINE/    435 ATGCA-AAAGA--ATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr20_22235938_   1114 -CAAC---AAATGG-TGATGCACACTTATATATGAAAATGTAAAA---TG 1155
                         -i   ---      - v ?-- v  i  v  i i i ii-     --- i
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAW--AGACCTAAATGTAAGAGC-TAAAACTATA 528

  chr20_22235938_   1156 AATACTTTCAGCAGATAATATGAG-----ATCATTATAACGTTGCAATAG 1200
                           -   i i  v   v  i  ii -----   v ii i  v   viv   
  L1M4_orf2#LINE/    529 AA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAG 577

  chr20_22235938_   1201 G-AAGGAGTTTTTAAACAATTCATAAGAAACACAAACTGTAAGAAAAGAG 1249
                          -  v iv  i   i i vvv  iv i  i     i vii  i i  i i
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr20_22235938_   1250 ATAAATTAATTTAATTAGATTTTAATTAATAACTAATGTG----AAAAAA 1295
                            i  v    vi i vv  ivv      v    vv    ----   ii 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr20_22235938_   1296 ----ATCAAAA---TAAAAAGACAGACTAGACAGACTAGGAAGAGATCCT 1338
                         ----     i --- i        iv i --    v i   ii i  vi 
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCA--CAGAATGGGAGAAAATATT 725

  chr20_22235938_   1339 TGTAGTGCATGTAACTGACAAAGGGTTAGTATATTGGATATTTAAATTAT 1388
                           i ivv   i  v    i  i  ii v    viv i    v    ----
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA---- 771

  chr20_22235938_   1389 GCCAAGAATGTCCACAAA--AATAAAAAAAAAGAAAACAACCCAAC---- 1432
                         -----   iviii    v--     v     iiv   i       i----
  L1M4_orf2#LINE/    772 -----GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr20_22235938_   1433 AGATGAATAAAAAGAACATTTGAAGAGGAACTTTATAGAAGAGAAAATTT 1482
                          i   iii   ii----       v  iv i  ivivi    ii v  vi
  L1M4_orf2#LINE/    817 AAATGGGCAAAGG----ATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr20_22235938_   1483 GGATGGCTAATAAGCATATGAAA-GAAGTTCAACCTGATTAGGAAA 1527
                         ii     i        i      -  v i     v v ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (88 / 51)
Gap_init rate = 0.04 (21 / 474), avg. gap size = 2.76 (58 / 21)  


2617 26.48 2.26 3.21  chr20_22283783_22292389     2508  3349 (5258)    L1M4_orf2#LINE/L1        1   834 (74)  

  chr20_22283783_   2508 TGAAAAAAAATCC-ATGCTCATGGATTGGAAGAATCAATATCATTAAAAT 2556
                           i   i v    -   i               v i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22283783_   2557 TACCATGCTGCCCAAAGCGATTTATATATTCAATGCTGTTGCTATCAAAC 2606
                         vi v  i  v      vi   i  i v      i  vi iv        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22283783_   2607 AACCAAC-ATCATTTTT-CAAAGA-----AAACT-ATTCTAAAATTCATA 2648
                         vv   i -ii v     -  i i -----  i  -  i            
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_22283783_   2649 TGGAGATGAAAAAGAGCCCAAACAGCCAAAGCAATCCTAAACAAAAGGAA 2698
                             i   v  ii  v  vi  i       i     i i  v  i i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_22283783_   2699 CAAAGCTAG-GGTCATCATACTACCCAACTTCAAACTACACTATAAGGCT 2747
                              i i -  v -   i   v     i      vivi    i  i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_22283783_   2748 ACAGTGACTAAAACAGCATGATACTGGTCCAAAAATTAAAAAAAAAAAAA 2797
                              i ii  i    ii  i      i------  ------------- 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGC------AT-------------A 280

  chr20_22283783_   2798 AAAACAGACACATAGACCAATGGAATAGAATAGAAAACTCTCAGGAAAAA 2847
                          ii i     i     i              v  i i---  vi    v 
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAG---TCCAGAAATA 327

  chr20_22283783_   2848 AAGTTGCACATCTGTAAGCATCTGATCTTCAACAGAGCCAACAAAAACAA 2897
                           viiii    i i iiv  vi    i   i   ii viiv   i v  v
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCAT 377

  chr20_22283783_   2898 GCAATGGGGAAAGGACATCCTAATTAATAAATGGTGCTGGGATGGCTGGC 2947
                         v            i i vi  vv i  i              iii    v
  L1M4_orf2#LINE/    378 TCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr20_22283783_   2948 TAGCCACATGCAGAAGAGTGAAATTGGACCCTTACCTTTTGCCATATACA 2997
                           ?         i    i    i        i     ivii         
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr20_22283783_   2998 ATAATCAACCTGAGTTGAATTAAATATTTAAATATAAGAATTCAAGCTAT 3047
                          v   i   iii iv  i  i ? v ii     i     ii v  i    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr20_22283783_   3048 AAAAATTCTATAAGAAAACCTAGG---AAATACCTTTGTCAACACTGGCC 3094
                             v ii  v        v    ---    --   i  -i  vi   vi
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGT-GACCTTGGGT 574

  chr20_22283783_   3095 TTGGCAAAGAATTCTTGACTATGTCACCAAAAGCAGTTGCAACAAAAACA 3144
                          v     v iv     iiv    v           vvv         iv 
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAA 624

  chr20_22283783_   3145 AAAATTGACAAGTGAGACCTAATTAAACTAGAGAGCTTCTGCACAGCAAA 3194
                              v  i  i vi   i v  i   v vi i i   i  ii vv    
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

  chr20_22283783_   3195 AGAAACTATCAATAGACTAAACAGATAACCTACAGAATGGGAGAAG-TAT 3243
                         i  v        v i v i  v   i    i              i-   
  L1M4_orf2#LINE/    675 GGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATAT 724

  chr20_22283783_   3244 TTACAAACTA-ATATCTGTCAAAGGTCTAATATCCAGTATCTATAAGAAA 3292
                           i    ii -       vi  i  v  vi       v  v     ii  
  L1M4_orf2#LINE/    725 TTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAA 774

  chr20_22283783_   3293 CTT----AAATCAACAAGCAAAACACAAACAACCCCGCTCAAATATGAGC 3338
                           i----  v    i  vv    v     i     vii ?   v   i  
  L1M4_orf2#LINE/    775 CTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGC 824

  chr20_22283783_   3339 AAAGATATCTG 3349
                             i-  i  
  L1M4_orf2#LINE/    825 AAAGG-ATTTG 834

Transitions / transversions = 1.86 (143 / 77)
Gap_init rate = 0.02 (17 / 834), avg. gap size = 2.71 (46 / 17)  

 362 22.34 0.00 0.00  chr20_22283783_22292389     3634  3727 (4880)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr20_22283783_   3634 AAAAAAAAGCAAAGACTATGAACAGACACTTCTCAAAAGAAGACATACAA 3683
                              vii      iv v    i     i     v        i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr20_22283783_   3684 GCAGCTAACAAACATGTGAAAATATGCTCATTATCACTAATCAT 3727
                         iii  i  i  i  ii      v       vi    ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  

3302 22.48 5.73 1.83  chr20_22283783_22292389     7246  8117 (490)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_22283783_   7246 GGAAGACATCCCATGTTCATGGATTAGAAGATGTAATATTGTTAAAATGT 7295
                          i    i                  i     iv            i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_22283783_   7296 CAATATTATTTAAAGTAATTTA--AAT--AATGTCATGTCTTTCAAATTT 7341
                              i viii   v i  i  --i  --  i iv  vi  v     v i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_22283783_   7342 CCAACACTGC--TTTTTGCACAGGTTAAAAAAAATTCACCCTAAAACCCA 7389
                            i --   --        v ii  i v  i--i v i       ii  
  L1M4_orf2#LINE/    103 CCAGC--TGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr20_22283783_   7390 TATGAAATCTCAAGGACTCCCAAGTAGCCACAACAATTTTGAAAAAGCAG 7439
                             i  viv     ivi  vi i      v      i         v  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_22283783_   7440 AA--------GAGGGCTCACACTTCCTGATT--AA-------TACAAAGC 7472
                           --------    i           ii   --  -------        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_22283783_   7473 TAAGGTAATTAAAATAG-GCTGTGTTGACAAAAAGACAAGACATATAGAC 7521
                           vi     i  i i  - iv  ii  i  v  i  i -          i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGAT 297

  chr20_22283783_   7522 TAATAGAATAGAATAAAGATCTCAAAAATAAATCTTTGCATATATGGTC- 7570
                         i   i         vi   vii  i       i iv i   v       -
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_22283783_   7571 ------TTTAAATAAGGGTGTCAAGGCTATGTAATAGAAAAAAAATAGGC 7614
                         ------   vi i       i    i i  vi   i ii   i     v 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_22283783_   7615 TTTTCAAAAGGTGGTATTGAAAAAACTGGATATCTATGTGCAAAAAAATT 7664
                                v ii    ii  ii v         ? i ii       i   v
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_22283783_   7665 AACTGGGACCCTTACC-------ATATACAAAAATTCACTTAAGATGGGT 7707
                           v v      i    -------             v   i  i    i 
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_22283783_   7708 GAAAAACCTAAATGGTTTTTGGTAAG---TAAGACCA--AAACTTTTAAC 7752
                         v ? i         --------    ---   i  i --     i   iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATG--------TAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_22283783_   7753 AAAAAATGTAGGAGAAATTTTTCATGACATGGGATTTGGCAGTGGTTATT 7802
                          i    ii    ? v  v i   i    v v  i  v    i     vi 
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr20_22283783_   7803 TAGATACAACACCAAAAGCATCAGTAACAAAATTAAAAATAGATAAATTG 7852
                               ii            iv  i       vv                
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_22283783_   7853 GATTGACTTAAAATTAGAAACTTTTGTGCATGAAAAGACGCCATCAACAG 7902
                           i vvv i       i            v v   i   i i     v i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_22283783_   7903 AGTGAAAAGGCAATT-ATAAAATAATGCAAAATGCTTGCAAGTTGTATAC 7951
                                  i   ii- i i   iiviv     ii      i ii    i
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_22283783_   7952 CTGATAAAAAATTAATATCCAGAATATATAAAGAATTCCTACAACTCAAC 8001
                                iii i vi                    i  i          i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_22283783_   8002 AATATCAACAAAACAAACAA----ATTAAAAAATTGGCAAAGAACTTGAG 8047
                             --  -  i     i  ----   ?      v       i i    i
  L1M4_orf2#LINE/    790 AATA--AA-AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_22283783_   8048 TAGATATTTC--CAAAGAAGATATACAGATGGCCAACAAGCAGTTGAAAA 8095
                             i     --               i        i     vv      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_22283783_   8096 GATGTTCAACATTGCTTATCAT 8117
                             i       ii????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.43 (136 / 56)
Gap_init rate = 0.02 (20 / 906), avg. gap size = 3.30 (66 / 20)  

1395 25.37 6.40 1.23  chr20_22283783_22292389     8121  8526 (81)    L1M4_orf2#LINE/L1      189   615 (293)  

  chr20_22283783_   8121 GAAAATGCAAATCAAAATTATGAGATTT-CATTTCCTGATTTCAAG-CTT 8168
                              v v i v    i  ivii  i i-  i    ii       i-   
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT 238

  chr20_22283783_   8169 AGTACAAAACTACAGTAA--AAGAAAACAGTGCTACATTGACATAAAGAC 8216
                          v      i         --    ---     ivii i  i     i  i
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGA---CAGTGTGGTACTGGCATAAGGAT 285

  chr20_22283783_   8217 AGACATGTAGACTAATGAAATAGAGTACAGACTTTAGAAATAAATCCTTG 8266
                               i    ii    i      i vv   v ii         i  v i
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr20_22283783_   8267 TATATATGGTC-------TTTCAATA-TGGTATCAAGACTATTCAATAGG 8308
                         i  v       -------    i i -v   ii      i       i  
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr20_22283783_   8309 AAAA-AATAGTCTTTTCAAAAGGTGGTATTGGGAAAACTGGATATCTTTG 8357
                         i   -              v ii    ii     v         ? ivii
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr20_22283783_   8358 TGCAAAAGAATAAAATTGGACCCTTATC-------ATATACAAAACTTCA 8400
                                    i  i        i  i -------          v  v 
  L1M4_orf2#LINE/    436 TGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr20_22283783_   8401 CTTAAAATGGATTGAAAACC-ATATATAAGACTCAAAGCTACCAAACTTT 8449
                           i         ii? i   - v  i     vii   i   iv     i 
  L1M4_orf2#LINE/    486 CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr20_22283783_   8450 TAGAAGAAAGTGTAAGGAAAATTTTTCATGACATTGGACTTCACA----T 8495
                                  iii  i ?iv  v i   i    v    ii vvi  ---- 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr20_22283783_   8496 TCATTAG-CATGGCCAGCATAAAACACACACA 8526
                          iv    -i   i - v  -   i    vi  
  L1M4_orf2#LINE/    586 TTCTTAGATATGAC-ACCA-AAAGCACAAGCA 615

Transitions / transversions = 2.57 (72 / 28)
Gap_init rate = 0.03 (13 / 427), avg. gap size = 2.38 (31 / 13)  


1850 27.05 0.38 2.29  chr20_22598411_22601590     1439  1963 (1217)    L1M4_orf2#LINE/L1        1   515 (393)  

  chr20_22598411_   1439 TGAAAAGGAGGTTCCATGTTCATGGATTAGAAGAATTAATATTGTTGAAA 1488
                           i    - vi i               i     v           i i 
  L1M4_orf2#LINE/      1 TGGAAAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr20_22598411_   1489 TGTCTATACTACT-AAACATATTTATAGATTTAATGCCATCTGTATCAAA 1537
                           v v     v i-   ivv  i  i     i  i  v   iv       
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_22598411_   1538 GTATCAATGATATTCTTCACAGAAATACAAAAAACAATTATAAAATTAAT 1587
                         i vi  iiviiv  i  ii       vv v  ivii  iv       v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_22598411_   1588 ATGAAATCACAAAAGACCCCCAATAGCCAAAGCAATCTTAAGCAAAAAGA 1637
                            i  vii   ii     vv          i       i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_22598411_   1638 ACAAAACTGTAAGGCATCACACTACCTAACTTCAAAGTACACTATAAAGC 1687
                              ii  v i i -       v  i  i      iivi    i     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGAC-TCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_22598411_   1688 TGTAATAACCAAATCAGCATGGTACTGGCACAAAATCAGACAGATGGACT 1737
                          ii i   i   iv   ii           i  iivi     v  i  ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_22598411_   1738 AATGGAACACAAAAGAGAACACAGCAATAAATCTATACACTTACAGCCAA 1787
                                i v  vv    iiv   v      i i     i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_22598411_   1788 CTAATTTTAGACAAAGATGCCCAAGAACACACAATGGGAAAAGGACAGTC 1837
                         i i     v     i i    -    v  iv       i    i i    
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCC-AAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_22598411_   1838 TGTTCAATAAATAGTGTTGGTAAAACTGGGTGTCCAAA-GAAGAAGAATG 1886
                          v     i    i   i   v v      i i?   v - v i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_22598411_   1887 AAACTAGATTTGTATCTGTCATCATATATAAAACCAACAGAAATTAACTC 1936
                           ii i  iiiv  i  vv  i      i    ---------        
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAA---------ATTAACTC 488

  chr20_22598411_   1937 AAGATGGATTAAAAACTTAAATGTAGG 1963
                           i      i ? i  i        i 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAG 515

Transitions / transversions = 2.18 (96 / 44)
Gap_init rate = 0.01 (6 / 515), avg. gap size = 2.33 (14 / 6)  

1397 22.48 1.61 5.50  chr20_22598411_22601590     2253  2688 (492)    L1M4_orf2#LINE/L1      490   908 (0)  

  chr20_22598411_   2253 AAACAAAT-AAAAACTTAAATGTAAGACCTAGAACTATAACATTCCTAGA 2301
                            iii  - ? i  i           v   i        v i  i    
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_22598411_   2302 AGAAAGCATAGAGG-AAATACTTTATGACACTGATCTGAGCAAAGATTTT 2350
                              i     i? -    -   ii    vi  ivi ii    v i   i
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_22598411_   2351 TTGGG-AGAAGACCAA---CACAGACAATAAAAGCAAATGTAGACAAATG 2396
                           i i- vi v     ---    ii   i     v   vi    i    v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_22598411_   2397 AGATCACATCAAAATAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACA 2446
                         i  iiv         v    i   i  ii vv       v  v     v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr20_22598411_   2447 GAGTGAAGATACAACCTACAGAATGGGAGAAAATACTGGCAAACTCTATA 2496
                         i      i v      i                  i v     iiv    
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_22598411_   2497 TCTGACAAGAGGAC-AATATCTAAACTATATAAGAAACTCAAACAACTCA 2545
                              i   -    -vi    i i v       ii     vv        
  L1M4_orf2#LINE/    739 TCTGATAAG-GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_22598411_   2546 ATAGCAAAAAGAAAAGAAAACAAATTAAAAAACCTAAATAACCCAATTTA 2595
                            ii       ----------------------i             ? 
  L1M4_orf2#LINE/    788 ATAATAAAAAGA----------------------CAAATAACCCAATTWA 815

  chr20_22598411_   2596 AAGTAGAGCAAAATACCTGAATAAGCATTTCTCAAAGGAAGACATACACA 2645
                           ivv i     iv ii      ii        v  i     i     v 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr20_22598411_   2646 TGACCAACTGGTATATGAAAAAATGCTCAGCATCACTAATCAT 2688
                           i    ivi i i       i       i     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (65 / 30)
Gap_init rate = 0.02 (8 / 419), avg. gap size = 3.88 (31 / 8)  


2192 26.83 5.90 0.70  chr20_22632319_22634085.rev      564  1275 (492)    L1M4_orf2#LINE/L1      160   908 (0)  

  chr20_22632319_    564 AAAAGACTCTAAATACCCAAAGCAATCTTGAGCAGAAAGAACAAAACTGG 613
                           ii   i vi    v     i         iv ii         ii   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr20_22632319_    614 AGGCAATTAC-TTTACCAGACTACAAGATATACCACAAAGCTATAGTAAC 662
                            - v i  -i  v   - i v   i iv   i         i     i
  L1M4_orf2#LINE/    210 AGG-ACTCACACTTCCCA-ATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr20_22632319_    663 CAAAACAGTGTGGTACTGGCATAAAAACAGACACAAATACCAATTGTACA 712
                            i                    ii i     i v v i    v v i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr20_22632319_    713 GTACAGTGGACCCAGAAGTTAATTCACATATCTATAGCCAACTGATTTTT 762
                          v iv v iii      i v  ii  i i  i   i i   i       i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr20_22632319_    763 AACAGAGTTGCCTAGGTCGCTCACTGAGGGAGAGGACTGTCTCTTCAATA 812
                         i   ii v    v  ii ii   v  -    i  i iv    i     i 
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATG-GGGAAAGAATAGTCTTTTCAACA 406

  chr20_22632319_    813 AGTGGTCTTTAGAAAACTGAATATTCATATGCAGATGAATAAAACT---- 858
                          i    vi vi  v     i   ?i  i     i v    i  ii ----
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr20_22632319_    859 ------CTCACTC----TACAAAAATAAACTTAAAATGGATCCCAGACCT 898
                         ------     v ----         v    i          v?      
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr20_22632319_    899 AATTGTAAGACCTGAAACTATAAAATTACTAGAAGAAAACA---GGGAAA 945
                           v       v  i           i vi            --- ? v  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_22632319_    946 ATGCTTCATTACTTTGGTCTGGGAAAATATTTTATGAATAAGACCTCAAA 995
                           -    i v  i    vi i  v  vvi   iv ii   v   vi    
  L1M4_orf2#LINE/    557 AT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr20_22632319_    996 AGCACAGGTAACAAAAGCAAAAATAAACAAATGGGATTACATCAAACTAA 1045
                               i i        v       i i    v   i v       v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr20_22632319_   1046 AGAGCTTCTGCACAGCAAAGGAAGCCATTAGCTGAGTAAAACAACAGCCT 1095
                          i i   i  ii vv       vi i  i ivvi   i   vi   i  i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr20_22632319_   1096 GCAGAACGGGAAAACATATTTGCAAACTATTCATCCCAAAGGGGATT--- 1142
                         i     i    i  v           ii  vi   iv v i    i ---
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr20_22632319_   1143 ------AATATGCAAGAAACTCAAACATTTCAACAGCAAAATATATATAT 1186
                         ------     ii  ii     vv   vi    i ii    - v i v  
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA-AGACAAAT 804

  chr20_22632319_   1187 A------TATACATATATCTAAA-------AACAGACATT-CTCAAAAGA 1222
                          ------ v? v v  ivvi   -------  i       -   v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr20_22632319_   1223 AGACATACAAATAGCCAGCAAATATATGAAAA-ATGCTGAATATCACTAA 1271
                            i        i    ii  ii i       -     v  i    ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr20_22632319_   1272 TCAA 1275
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.88 (122 / 65)
Gap_init rate = 0.02 (14 / 749), avg. gap size = 3.36 (47 / 14)  


1434 26.20 7.51 1.35  chr20_22662808_22669172        2   520 (5845)    L1M4_orf2#LINE/L1      164   714 (194)  

  chr20_22662808_      2 GACCGAGAATAGCCAACTCAACATTGAAAGAGAAGAA---AGTCAGAATA 48
                             v           vv   iv      i       ---   ii  iv 
  L1M4_orf2#LINE/    164 GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGA 213

  chr20_22662808_     49 CTTACACTAACCAACTTCAGGGCTTACTG-AAAGCTACAGTAATCAAGAT 97
                           i     vv    i    iii      i-                   i
  L1M4_orf2#LINE/    214 CTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGAC 263

  chr20_22662808_     98 GGTGAGGTATTGATGAAAGAATAAACAAATAGTTCAAAGTAATAGAACAG 147
                         i   v    i  iiiv   i   i   v    v    v v       iv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr20_22662808_    148 AGAGCTAAGGTATAGACCCA--CATTAATATAGTCAATTACTCTTTGATA 195
                             iiv  iv   i     --    --   i       iv i  i  i 
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATT--TATGGTCAATTGATTTTCGACA 361

  chr20_22662808_    196 TAGGAT-CAAAGGGGATGCAATGGAGAAATGTT-GTCTTTTCCATAAATG 243
                         -   i - v   ivv  v      i    viv -        v i     
  L1M4_orf2#LINE/    362 -AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr20_22662808_    244 GTGCTGAAACAACTGGACATTTCTGTGTAAAAAAAATGAATCTAGATCAA 293
                               ii         i ?iivii  i    i  -    vi i  i vv
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCC 459

  chr20_22662808_    294 -ATCTTACATCCTTCACAAAAATTAATCCAA--TAGAGCATAGACCTAAA 340
                         - i  i   i v vi           ii   -- i  v  ?         
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr20_22662808_    341 TATAAAATGC-AGAACTATTAACCTCCCAGCAAATAACA--GGAGAAAAT 387
                          i   i -  - i      v  v   ii  v i v    --  ? v    
  L1M4_orf2#LINE/    510 TGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr20_22662808_    388 C--AATGAC-TTGGATATGGCAAT------------ATAACGCCAGAGGC 422
                          --vi    -    i vv      ------------  i  i   i i  
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr20_22662808_    423 AAAACCCATAAAA-----AATA-ATAAGCTTGA-TTAATTAAAATTAAAA 465
                          v  v v i    -----    -    ii v  -  v  i          
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr20_22662808_    466 G--TTTCTGCTTGGTAAAACACACAGTTAAGAAAATCGGGGGGCAGTTC- 512
                         i--   v     --i   iv    vi i      i viiii i  iii -
  L1M4_orf2#LINE/    659 ACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr20_22662808_    513 CAAGATGG 520
                           ii    
  L1M4_orf2#LINE/    707 CAGAATGG 714

Transitions / transversions = 1.77 (85 / 48)
Gap_init rate = 0.04 (22 / 551), avg. gap size = 2.09 (46 / 22)  

3239 27.42 0.44 0.44  chr20_22662808_22669172     4966  5873 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22662808_   4966 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAGTGTTGTGAAAAT 5015
                              ii i  i     i        v      v i i i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22662808_   5016 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCACTATCAAGC 5065
                            v     v     iv i  i  i        i  v   v       iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22662808_   5066 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5113
                          vi  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_22662808_   5114 TATGGAACCAAAAAAGAGCCCACATAGCCAAGACAATCCTAAGCAAAAAG 5163
                                viiv  ii  v  viv        i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_22662808_   5164 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5213
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_22662808_   5214 TACAGTAACCGAAACAGCATGGTACTGGTACCAAAATAGAGATATAGACC 5263
                                 i i i    ii         i iv ii     v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_22662808_   5264 AATGGAACAGAAC--AGAGCCCTCAGAAATAATACCGCACATCTACAACC 5311
                                i    i--    i  --        vv  ii    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_22662808_   5312 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5361
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_22662808_   5362 CTATTTAAAAAATGGTGCTGGGAAAACTGGCTAGCCATACGTAGAAAGCT 5411
                           v  i  v              v      v  ?   i i i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_22662808_   5412 GAAACTAGATTCCTTCCTTACACCTTATACAAAAATTAATTCAAGGTGGA 5461
                            ii i  ii   v   i     v              i    ii    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_22662808_   5462 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5511
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_22662808_   5512 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAA 5561
                         v    ?i v viv   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_22662808_   5562 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5611
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_22662808_   5612 TTAAACTAAAGAGCTTCTGCACAGCAGAAGAAACTACCATCAGAGTGAAC 5661
                          i   v v  i i   i  ii vv  i i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_22662808_   5662 AAGCAACCTATAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAA 5711
                          ii     i i               v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_22662808_   5712 AGGGGTAATATCCAGCATCTACAATGAACTCAAGCAAATTTACAAGAAAA 5761
                         i  iv vi       v  v  i  v      vvi   v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_22662808_   5762 GAACAAACAACCCCATCACAAAGTGGGCCAAGGATATGAACAGACACTTC 5811
                         ii     i     v  i?v   i     v      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_22662808_   5812 TCAAAAGAAGACATTTATGTAGCCAAGAGACCCGTGAAAAAATGCTCATC 5861
                           v        i  vi vi i     v ii v i      i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_22662808_   5862 ATCACTGGCCAT 5873
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (147 / 98)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2927 26.29 0.97 3.12  chr20_22758191_22762463     1786  2713 (1560)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr20_22758191_   2713 TGGAAAAACATTCTATGCTCATGGATAGGAAGAGTGAATATTGTGAAAAT 2664
                               i i  i i   i        v      v v        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr20_22758191_   2663 AGTCATACTGCCCAAAGTAATTTATAGATTCAATAGTATCCCCATCAAGC 2614
                         i iv     v      v i  i  i        iivv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr20_22758191_   2613 TACCA-CTGACTTTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTTC 2566
                          v   -   v    i  -i     v v  v  i--  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG--CTGATCCTAAAATTC 147

C chr20_22758191_   2565 ATATGGAACCAAAAAAGAGCCCATATAGCCAAGACATTCCTAAGCAAAAA 2516
                                 viiv  ii  v  viv        i   v  i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

C chr20_22758191_   2515 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTACACTACAAGT 2466
                                 i      vv   ii  v  ii i      vivi       iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

C chr20_22758191_   2465 CTACAGTAACCAAAACAACATGGTACTGGTACCAAAACAGATATATAGAC 2416
                                  i   i   iii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

C chr20_22758191_   2415 CAATGGAACAGAC------GCCTCAGAAGTAACACCACACATCTACAACC 2372
                                 i   v------ i -     i   vv   i    i  iiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTC-CAGAAATAAACCCATACATTTATGGTC 346

C chr20_22758191_   2371 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 2322
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chr20_22758191_   2321 CTATTTAATAAATGGTATTGGGAAAACTGGCTAACCATATGTGGAAAACT 2272
                           v  i  i       ii     v      v  ?   i   iii  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chr20_22758191_   2271 GAAACTGGACCCCTTCCTTACACCTTACACGTAAATTAACTCAAGATGGA 2222
                            ii         v   i     v  i  iv            i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chr20_22758191_   2221 TTAAAGACTTAAACGTAAGACCTAAAACAAGAAAAACCCTAGAAGAAAAC 2172
                          i ?    i    i      v       v v    vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chr20_22758191_   2171 CTAGGCAATACTATTCAGGACATAGGAATGGGCAAAGACTTCATGACTAA 2122
                         v    ?ivv v v   iv   v v  iv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

C chr20_22758191_   2121 AACACCAAAAGCAATGGCAGCAAAAGCCAAAATGCACAAATGGGATCGAA 2072
                         i            vvi   i      vv     iv i    v   iivv 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

C chr20_22758191_   2071 TTAAGCTAAAGAGCTACTGCACAGCAAAAGAAACCACCATCAGAGTGAAA 2022
                          i  iv v  i i  vi  ii vv    i  v  i i  vv i       
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

C chr20_22758191_   2021 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATTCATCTGACAA 1972
                           i     i                 v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

C chr20_22758191_   1971 AGGACTAATATCCAGAATCTACATAGGACTAATATCCAGAATCTACAAAG 1922
                         i     vi          v  i v  i   -----------ii     --
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACT-----------CTTACAA-- 783

C chr20_22758191_   1921 AACTTAAGCAAATTTACAAGAAAAAAAACAAACAACCCA-TCAATAAGTG 1873
                         --  i  v--   --------     i     i      - i? v  i  
  L1M4_orf2#LINE/    784 --CTCAAT--AAT--------AAAAAGACAAATAACCCAATTWAAAAATG 821

C chr20_22758191_   1872 GGTAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGGGGCCA 1823
                           i       v    i     i     v        i  vi viv     
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

C chr20_22758191_   1822 AAAAACTTATGAAAAAAAGCTCATCATCACTGGTCAT 1786
                          v  i vi       i v     v     ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (140 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 3.45 (38 / 11)  

2835 23.94 6.46 1.53  chr20_22758191_22762463     2931  3782 (491)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr20_22758191_   2931 ATGTTCATAAAT----AGACT-AA-ATTGTCAATATTTCAGTTCTTCTCA 2974
                                 ii  ----     -  -     i  v  vv  i v  i i  
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr20_22758191_   2975 ATTTAAACTATATATCCAATGCAATCCTAATCAAAATCC-AGCAAATTAT 3023
                          v  i v   i v  i   i       iv          -   vivi v 
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr20_22758191_   3024 TTTATAAATATTGGAAAACTAATTATAAAGTTTATATGGAGAGGCAAGAG 3073
                            ii i v    iv  i  i  iv    i  i       i v     i 
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr20_22758191_   3074 ACACAGAATAGCCAATACA-TATTGAAGGATAAGAACAACACTGGGGAAT 3122
                           v            v   - v     ii v        vii   i i i
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr20_22758191_   3123 TGATACTACTTTCC---TTCAAGTCC-ACTATAAAGCCACAGTAATAAAG 3168
                          --i  -    i  ---     iv i-    i     i        v   
  L1M4_orf2#LINE/    215 T--CAC-ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr20_22758191_   3169 ATAGTGTGGTATTGTTGAAAGAATAGTCAAATAATAGATTAATGGAACCA 3218
                          i         i  viiv   i    v  --  -     i       ivi
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACA--TA-TAGATCAATGGAATAG 308

  chr20_22758191_   3219 AATACAGAGCCTAGAAATAGACCCA--CATACATGCTGTCAACTGACCTT 3266
                            vv    i i       i     --   vi   --     i   ii  
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATG--GTCAATTGATTTT 356

  chr20_22758191_   3267 TGACAAAGAAGCAAAAGCAATACAATGGAGCAAAAACAGTCTTTTCCACA 3316
                         i     i iv  v  ii v  v      i v  i  i         v   
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr20_22758191_   3317 AGTGGTGCTGAAACAACTGGACATCCACACGCAAAACCATGAATCTAGAT 3366
                          i        ii         i ?     i      vv     vi i  i
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr20_22758191_   3367 ACAGACTTTACACCATTTACAAAAAGTAACTCAAAATGGATTATTGACAT 3416
                         v vv  i i       v        v               i ?v   v 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr20_22758191_   3417 AAATGTAAAATGC-AAAGCTATAAAACTCCTAGAAGACAGCATATGAGAA 3465
                                 i -  -   i           i       v i    v ? v 
  L1M4_orf2#LINE/    507 AAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr20_22758191_   3466 CATCTCGATGAGCTTGGATATGGCAATTACTTTTTAGATATAACAC--AA 3513
                         v    ivi   v     i vv      vii  i        i    --  
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr20_22758191_   3514 AG-----------AAAGAAAAAA-------GTTGAACCCCATTAAAATTA 3545
                           -----------          -------i   i  ii   i       
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr20_22758191_   3546 AAAACGTCTGCTCTGTGAAACACACAGTTAAGAGAATGTGAAGACATGCC 3595
                              v i  iv  vii  iv    vi i    i i  vi      vv  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr20_22758191_   3596 ACAGACTGGGAGAAA-TATTT------------------AAAGAACTGCT 3626
                              v         -     ------------------  i i   vv 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr20_22758191_   3627 ATTCAAAATATACAAAGAACTCTTAAAAGTCAATAG-AAAAAAACGAACA 3675
                           i  i      i            v  v      i-     i  i  i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr20_22758191_   3676 ACCCAAATAAAAAGTAGGCTGAAGACCTGAATGAACACTTCACCAAATAA 3725
                               v ?    i i   vi i  ii     ii   i   v     v  
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr20_22758191_   3726 GGTACAAAGATGATACACAAATGGGCATATGAAAAGGTTTTCAACACCCT 3775
                          i  i v i   i---- v   ii   i        i vi      i v?
  L1M4_orf2#LINE/    856 GATATACAAATGG----CCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr20_22758191_   3776 ATGTCAG 3782
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.67 (125 / 75)
Gap_init rate = 0.02 (22 / 894), avg. gap size = 3.09 (68 / 22)  


3478 24.78 2.24 0.45  chr20_22778165_22785941     1011  1902 (5875)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22778165_   1011 TGGAAAGATATTCT-TGTTTATGGATAGGAAAAATTAATATTGTTAAAAT 1059
                                    i i-    i      v    i v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22778165_   1060 GTCCATGTTACCCTAAGCAATCTACAGATTCAATGCCATCCCTATCAAAA 1109
                          v v  ii v   v  vii              i  v             
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22778165_   1110 GGCCAATGACATTTTTCACAGAAATAGG-AAAC-AATTATAAAATGTGTA 1157
                         vv   iivi v     ii       v i-  i -i  iv      vii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_22778165_   1158 TAAAACCACAAAAGACCCCAAATAGCCAAAGTAACTATGAGCAAGAA--- 1204
                          ii  vii   ii     vi          ii  iiv   iv     ---
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_22778165_   1205 TGAAGCTGAAGGTATTACACTTTCTAATTTCAAATTATATAACAAAGCAA 1254
                         ii   i  i   vv i      i i         viv  iv       v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_22778165_   1255 TAGTAATCAAAAAGGCATAGTACTGGCATAAAAACAGACACATAGACTAA 1304
                         i         i vi ii i            ii i     i     ii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_22778165_   1305 CAGAACAGAATAGAGAGCTGAGAAATAAACCCACACATTCATGGTCAACT 1354
                         ii   i     v     iiv             i     i        i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_22778165_   1355 AATCTTTGACAAGAATGGCAAGAATACACAATGGGGAATGGCTGATCTCA 1404
                         i  i  i      ii  v     vi iv          v iv ii   iv
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_22778165_   1405 TTAATAAATGATTTTAGGACAAGAAGATGTCCACATGCAGATTAATGACA 1454
                          i  i     i vi i      vvi   i?         i vv     vi
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_22778165_   1455 TTAGACCCTTATCTGACACCATGCACAAAAATCAACTCAAAATGTATTGA 1504
                           i     i  i  v       ii        i           v  ii?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_22778165_   1505 AGAATTAAACATAAAGCCTAAGATTCTAAAACTCATAGAAGAAAACAAAG 1554
                            vi    ii   iiv    i i v        v            v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_22778165_   1555 GGAAAAGATCCTCA--ACATTGGTTTGAGCAATAATTTTTTAGATTTGAC 1602
                          ?iv  -   i  i--  v    v  ii     ii   i      v    
  L1M4_orf2#LINE/    551 GNGTAA-ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_22778165_   1603 ACAAAAAGCACAGACAGAATAAGCAAAAATAGACCACTGGGACCACATCA 1652
                           v         ii  iv v   v         iv v v    iv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_22778165_   1653 CACTAAAAAGCTTCTGCACAGCAGAGGAAACAATCGACAAAACGAAAGGA 1702
                         v v v    i   i  ii vv  i    v  v   i v   ii    i  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_22778165_   1703 CAACCTATGTAATGGCAGAAAATATTTGCAAACCAGATATCTGATAAGGG 1752
                              i iiv     v                i  v              
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_22778165_   1753 ATTAATATCCAAAATATATAAGGAATTCATACAACTTAGTAACAAAAAAG 1802
                          i vi      i         i   i  v       i i   i     ii
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_22778165_   1803 -----------ATTTAAAAGTGGGCAAAGGACCTGAATAGACATTTTTTT 1841
                         -----------   ?    i           ii             i --
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT-- 847

  chr20_22778165_   1842 CCCAAAGAAGA-ATACAAATGTTCAACATATATATGAAAAGATGCTCTAC 1890
                         -          -         vi   i vii i              v  
  L1M4_orf2#LINE/    848 -CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_22778165_   1891 ATCACTATCATC 1902
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (142 / 75)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  

2923 28.51 0.66 1.10  chr20_22778165_22785941     6374  7285 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22778165_   6374 TGAAAGAACATTCCATGCTCATGGATAAAAGGAATCATTATCGTGAAAAT 6423
                           i  ii i  i     i        vii i  v i v   i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22778165_   6424 GGCCATACTGCCCAAGGTAATTTATAGATGCAATGCCATCCCCATCAAGC 6473
                            v     v     iv i  i  i    v   i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22778165_   6474 TACCAATGACTTTCTTCATAAAACTGGAAAAAACT-ACTTTAAAGTTCAT 6522
                          v   iivi i  i  iii i  v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_22778165_   6523 ATGGAAC--CAAAAAACAGCCCACGTTGCCAAGACAATCCTAAGCAAAAA 6570
                               v--   iii  --  vivi v     i      i i -----  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGA-----AA 192

  chr20_22778165_   6571 AAGAAAAAAAAAAGCTGGAGGCATTGTGCTACCTGACTTCAAACTATACT 6620
                              i  v   - i      vv iiii  v  ii i      viv    
  L1M4_orf2#LINE/    193 AAGAAGAACAAA-GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr20_22778165_   6621 AAAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAT 6670
                          v  i          i   i    ii         i iv ii i   v  
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_22778165_   6671 ATAGATCAATGGAACAGAACAGAGGCCTCAGAAATAATACCACACATCTA 6720
                                       i    iv   ivii         vv   i    i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_22778165_   6721 CAGCCATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGG 6770
                         ii i  vi    i  i     ivv  v   i v  vvv           i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_22778165_   6771 ATGCCCTATTTAATAAATTGTGCTGGGAAAACTGGCTAGCTATATGTAGA 6820
                           ivi  v  i  i    v         v      v  ? i i   i i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_22778165_   6821 AAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAG 6870
                          iiv    ii    i    v   i     v              i    i
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_22778165_   6871 ATGGATTAAAGACTTAAATGTTAGACCTAAAATCATAAAAACCCTAGAAG 6920
                               i ?    i       v   v      ii      vi i      
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_22778165_   6921 AAAACCTAGGCA-ATACCATTCAGCACACAGGCATGGGCAAGGACTTCAT 6969
                              v    ?i- v i -   ivv  viv  vv i     v ii   v 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_22778165_   6970 GACTAAAACACCAAAAGCAACGGCAACAAAAGCCAAAATTGACAAGTGGG 7019
                         iiv  vi            vvi          vv     v  i  i v  
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_22778165_   7020 ATCTAATTAAACTAAAGAGCTTCTGCATGGCAAAAGAAACTACCATCAGA 7069
                          ii v  i   v v  i i   i  iiivv    i  v    i  vv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_22778165_   7070 ATGAACAGGCAACCTACAGAATGGGAGAGCATTTTTGCAATCTACCCATC 7119
                         i    v  i     i             iv  v       vii ivi   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_22778165_   7120 TGACAAACGGCTAATATCAATAATCTACAAAGAACTTAAACAAATTTACA 7169
                            i  iv i  vi    v v   v  i        ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_22778165_   7170 AGAAAAA-ACAAACGACCCCATCAAAAAGTGGGCAAAGGATATGAACAGA 7218
                          v     -     ii    v  i?    i            v    i   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_22778165_   7219 CACTTCCCAAAAGAAGACAT-TATGCAGTGAACAGACACATGAAAAAATG 7267
                           i   i v        i  -i viii iv  i ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr20_22778165_   7268 CTTATCATCACTGGTCAT 7285
                           i v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (158 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3155 26.84 0.44 0.55  chr20_22798477_22802926.rev     3050  3958 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22798477_   3050 TGAAAGAACATCCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 3099
                           i  ii i        i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22798477_   3100 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 3149
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22798477_   3150 TACCAATGACTTTCTTCACAGAATTGGAAAACACT-ACTTTAAAGTTCAT 3198
                          v   iivi i  i  ii     v v  v  -i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCAT 149

  chr20_22798477_   3199 ATGGAACCAAAAAAGAGCCTGCATTGACAAGTCAATCCTAAGCCAAAAGA 3248
                               viiv  ii  v  v v  v v   iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_22798477_   3249 ACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCT 3298
                               i      vv   ii  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_22798477_   3299 ACAGTAACCGAAACAGCATGGTACTGGTACCAGAATAGAGATATAGATCA 3348
                                i i i    ii         i iv  i     v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_22798477_   3349 AAGGAAAAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAAACA 3396
                          v    v    i--    i  --        vv   i i  i  iiiv  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr20_22798477_   3397 TCTGATCTTTGACAAATCTGACAAAAACAAGAAATGGGGAAAGGATTTCC 3446
                         vi    i  i     ivv  v   i v  vvv           i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_22798477_   3447 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCTATATGTAGAAAGCTG 3496
                          v  i  i              v      v  ? i i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_22798477_   3497 AAACTGGATCCCTTCCTTACACCTTATACACAAATTAATTCAAGATGGAT 3546
                           ii    i    v   i     v      v       i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_22798477_   3547 TAAAGACTTAAATGTTAGACCAAAAACCATAAAAACTCT-AGAAGAAAAC 3595
                         i ?    i       v   v v     i      -    -          
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAAC 546

  chr20_22798477_   3596 CTAGGCATTACCATTCAGGACATACGCATGGGCAAGGACTTCATGTCTAA 3645
                         v    ?i v viv   iv   v vv vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_22798477_   3646 AACACAAACAGAAATGGCAACAAAAGCCAAAATTGACATATGGGATCTAA 3695
                         i    v  v  v vvi          vv     v  i v  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_22798477_   3696 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3745
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_22798477_   3746 AGACAACCTACAGAATGGGAGAAAATTTTTTCAATCTACTCATCTGACAA 3795
                                 i                 v   v   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_22798477_   3796 AGGTCTAAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAA 3845
                         i  v  vi-          v  i  v      iv    v iv i  v   
  L1M4_orf2#LINE/    747 GGGACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_22798477_   3846 AAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 3895
                           i     i     v  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_22798477_   3896 CTCAAAAGAAGACATTTATGCAACCAAAAGACACATGAAAAAATGCTCAT 3945
                            v        i  vi viiii    v ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_22798477_   3946 CATCACTGGCCAT 3958
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.22 (132 / 108)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.29 (9 / 7)  


3027 26.72 1.22 1.00  chr20_22811652_22816356.rev     3312  4213 (492)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr20_22811652_   3312 AAAATATTCTATGTTCATGGATAGGAAGAAACAATATTGTTTAAATGGCC 3361
                           i    i i            v      vvi         v i     v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr20_22811652_   3362 ATAACTGCCCAAAGCAATTTATAGATTCAATGCTATTCCTATTACACTGC 3411
                            -  v      vii  i  i        i  v  i     i v v v 
  L1M4_orf2#LINE/     55 ATA-CTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_22811652_   3412 CATTGACATTCTTCACAGAACTAGAAAAAACTAAT-TTGAAATTCATATG 3460
                           vivi v  i  ii     v v  v  -i  i  -i i           
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATG 152

  chr20_22811652_   3461 GAACAAAAAATGAGTCCA-AATAGCTAAGGCAATCCTAAGCAAAAAGAAT 3509
                            - viv  v iii   -      i  ii     i i iv  i     i
  L1M4_orf2#LINE/    153 GAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_22811652_   3510 GAAACTGGAGGCATCATGCTACCCAACTTCAAACTATACCACAGGGCTAC 3559
                         i  ii      vv   ii  v     i      viv   i   ii     
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr20_22811652_   3560 AGTAACCAA--CAGCATAGTACTGGTACAAGAACAGACACATAGATTAAC 3607
                              i   --   ii i       i i   i i     i      i  i
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_22811652_   3608 AGAACAGAATACATAACCCAGAAATAAGACTGCATGCCTACAACTATCTG 3657
                         i   i     vv v ii          iv iii iiii  iiiii vi  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_22811652_   3658 ATCTTCAACAAACCTGACAAAAACAAGCAATGGGGACAGAATTCCCTATT 3707
                           i   i    ivv  v   i v  vv         v     vvi  v  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_22811652_   3708 CGACAAATGGTGCTGGGATAACTGTCTAGCCATATGCAGAAGATTGGAAT 3757
                          i                i     vv  ?   i     i    v  i i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_22811652_   3758 TGGAACCCTTTCTTATGCCATATACAAAAATTAACTCAAGATGGATTAAA 3807
                             v    vi  i ii                      i      i ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_22811652_   3808 GACTTAAATATAAAACCCAAAACTATAAAAACCCTGGAAGACAGCCTAGG 3857
                            i     i   i v i            vi i i     v i v    
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_22811652_   3858 CAATACTGTTCAGGACATAGATATGAGTAAAGGTTTTAT-GATGAAGAAG 3906
                         ?ivv v v   iv   v v ivv ii i  v     iv -   - v  vi
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACA 600

  chr20_22811652_   3907 CCAAAAGCAATTGCAATAAAAGCAAAACTTGATAAATGGGACCTAACTAA 3956
                                  vvv    i     v    v v       v    i v ii  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_22811652_   3957 GCTAAAGAGCTTCTGCACAGCAAAGGAAACTATCAACAGGGTAAACAGAC 4006
                         iv v  i i   i  ii vv       v        v ii  i  v    
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_22811652_   4007 AACCTACAGAATGGCAGAAAATTTTTACAAGTTATCCATCTAACAAAGGT 4056
                             i         v       v   i   i i  vi    i i  i  v
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_22811652_   4057 CTAATATCCAGCATCTATAA-GAA---TTA-AACT-AATTTGCAAGAGAA 4100
                           vi       v  v     -   ---   -    -   vvvv  i   v
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_22811652_   4101 AAACAACCTTATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAA 4150
                            i    iv   ?    i           iv    i     i  i  v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_22811652_   4151 AAGAAGACATACATGTAGCCAACAATCATATGAAAAAAAAAAAAGCTCAA 4200
                                i     vi i     i  v  i       i -----v      
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-----TGCTCAA 895

  chr20_22811652_   4201 CATCACTAATCAT 4213
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (13 / 904), avg. gap size = 1.54 (20 / 13)  


1537 19.32 0.73 26.73  chr20_22841107_22845297.rev     2473  3699 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22841107_   2473 TGGAAACACATCCCATGCACATGGATGGGTAGAATCAATATTGTGAAAAT 2522
                               v i        iv       v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22841107_   2523 GACCATTTTCACATGGTCAATCCCCA--TTTCACAGTGCAATCCCCATCA 2570
                          i v  vi  v vvii ii   iv  --  ---  ii        i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATT---CAACGCAATCCCTATCA 97

  chr20_22841107_   2571 AAATACTACCATCATTCTTCACAGAATTAGAAAAAA-AACACTAAAATTC 2619
                             v i v vv v  i  ii     v v  v  iv-i iv         
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr20_22841107_   2620 ATATGGAACCAAAAAAGAGCCCACATAGTCGAAGAGAGACTAAGTGAAAA 2669
                                 viiv  ii  v  viv    i i  ivi vvi i ivi i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_22841107_   2670 GAACAAATCTGGAGGCATCACACTACCTGATTTCAAATTGTACTATAAGG 2719
                                vi      vv       v  ii        viv     i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_22841107_   2720 CCATAGTCACCAAAACAGCATGGTACTGGTAGAAAAATAGGCATATAGAC 2769
                          i i   v i   i    ii         i v  ii    i        i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_22841107_   2770 CAATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCA 2819
                                 i     v    ii               v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_22841107_   2820 ACAGATCTTCAATAAAGCAAATAGAAACATAAAGTGGGGAAAGGACACCC 2869
                          iv   i   i i  i vvivi ii v   vv i         i i vi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_22841107_   2870 TTTTCAACTAATGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATG 2919
                                 v             i  i   v  ?       i ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_22841107_   2920 AAACTGGAACCTCATCTCTCACCTTATACAAAAATTAACTCAGGGTGGGC 2969
                           ii    v  ii i   v    v                  --------
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA-------- 489

  chr20_22841107_   2970 ACCGTAGCTCACACCTGTAATCCCAGGATTTTGGGAGGCCGAGGCGGGTG 3019
                         --------------------------------------------------
  L1M4_orf2#LINE/    490 -------------------------------------------------- 489

  chr20_22841107_   3020 GATCACCTCGGCCAGATTGATACCATCCTGGGTAACATGGTGAAACCCCA 3069
                         --------------------------------------------------
  L1M4_orf2#LINE/    490 -------------------------------------------------- 489

  chr20_22841107_   3070 TCTCTACTAAAAAAAAAAAAGAAAAAAAAATTAGCCAGGCATGGTGGCAC 3119
                         --------------------------------------------------
  L1M4_orf2#LINE/    490 -------------------------------------------------- 489

  chr20_22841107_   3120 GTACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAAAAGAATTGCTTGA 3169
                         --------------------------------------------------
  L1M4_orf2#LINE/    490 -------------------------------------------------- 489

  chr20_22841107_   3170 ACCCAGGAGGCGGAGGTTGCAGTAAGCCAAGACCATGCCACTGCACTCCA 3219
                         --------------------------------------------------
  L1M4_orf2#LINE/    490 -------------------------------------------------- 489

  chr20_22841107_   3220 GCCTGCGTGACAGAGCGAGACTCAATCTCAAAAAAAAAAAAAAAAAAAAA 3269
                         --------------------------------------------------
  L1M4_orf2#LINE/    490 -------------------------------------------------- 489

  chr20_22841107_   3270 AAAAAAATTCAACTGAAGATGGATTAAAGACTTAAATCTAAGACTTGAAA 3319
                         ---------------- i      i ?    i     v     vi i   
  L1M4_orf2#LINE/    490 ----------------AAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr20_22841107_   3320 CTATAAAAATTCTAGAAGATAACATTGGAAAAACCCTTCTAGTCATTGGC 3369
                                 v ii       v     v  ?iv  vi    vv v v    v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr20_22841107_   3370 TTAGGCAAGGATTTCATGACCAAGAACCCAAAAGCAAATGCAATAAAAAC 3419
                                 v i    v iivi v  vv         v v    i    iv
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr20_22841107_   3420 AAAGATAAATAGCAGGGACTTAATTAAACTAAGGAGCTTTTGCACAACAA 3469
                            i   i   ivvv      v  i   v v ii i      ii vv   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr20_22841107_   3470 TAGGA-ACAGTCAGCAGAGTAAACAGACAACCCACAGAATGGGAGAAAAT 3518
                         -    -  vi   iv i   i  v                          
  L1M4_orf2#LINE/    674 -AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_22841107_   3519 ATTCACAATCTATTCATCTGACAA----CTAATATCCAGAATCTACAATG 3564
                            ii   vii  vi      i  ----  vi          v  i  v 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_22841107_   3565 AACTCAAATAAATCAGTAAGAAAAAAGCAAACCATCCCATC-AAAAGTGG 3613
                              vv i  v   i   v     ii    iv i  v  i-    i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_22841107_   3614 GCTAAAGACTTGTATAGACAATTCTCAAAAGAAGATATACAAATGGCCAA 3663
                           v  i  i   v       v     v                       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_22841107_   3664 CAAACATATGAAAAAATGCTCAACATCACTAATGAT 3699
                         i  i  i       i             ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (133 / 101)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 42.12 (337 / 8)  


1426 25.86 4.75 6.06  chr20_22881695_22883305      501  1111 (500)    L1M4_orf2#LINE/L1      272   874 (34)  

  chr20_22881695_    501 ACTGGCAAAGGGGTAGATGCATAGATCAATGGAACAGAATAGAGAACCCA 550
                                v i  i    iii              i     v    ii   
  L1M4_orf2#LINE/    272 ACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr20_22881695_    551 GAACAAGACCCACAAAT--ATGCCCAAATGATTTTTTTTTACAAGG-TAC 597
                            vv i     i v  --   vi   v       iv---      - i 
  L1M4_orf2#LINE/    322 GAAATAAACCCATACATTTATGGTCAATTGATTTTCG---ACAAGGGTGC 368

  chr20_22881695_    598 AAAAGCAATTCAATGGAGGAAAGACAGCCCTTTCAACAAACAGTGCTAAA 647
                         v  ii v         i i  ii i  i i          ii     iii
  L1M4_orf2#LINE/    369 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr20_22881695_    648 GCTACTGGACACCCACAGGCAAACAAACAAACAAACAAACAAACAAACAA 697
                         i v      i ?     v     vi  ii  ----------iviii  --
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAA----------GTTGGAC-- 456

  chr20_22881695_    698 AGAATATCAACCTAAGACTCACACCTTTGAACATAAATAAACTCAAAATG 747
                         ------- --    v--        v -iv   v    v           
  L1M4_orf2#LINE/    457 -------C--CCTAC--CTCACACCAT-ATACAAAAATTAACTCAAAATG 494

  chr20_22881695_    748 GAGCATGGATTTAAATGTAAAAGGTAAAACTATAACCCATTTAGAAAAAA 797
                           v  ?i  ii         i  v           vv vi      i   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_22881695_    798 AAAAAAAAACAGAAGAATATTTGTAGGATCTGGGACCAGGCAAAGAGTTC 847
                          v v ii?ii ----   v  i  --  i  v  iii      v iv   
  L1M4_orf2#LINE/    545 ACATAGGNGTA----AATCTTCGT--GACCTTGGGTTAGGCAATGGTTTC 588

  chr20_22881695_    848 TTAGAATTGACATCAAAAGTT------------GGAACATTTGATAAATA 885
                              vv     i      iv------------ i  v v v       v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_22881695_    886 GAACTTCATCAAAATTTAAAACTTTTGCTCTGTGAAAGACCCTGTCAAGA 935
                          i              v          iv  vii  i   v  i      
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr20_22881695_    936 GAACAACAACAAAAA-AAGCTACAGACAGGGAGAATGTATTTGAAAACGA 984
                         i iii ----   i -  v i     vv       vi      v   iv 
  L1M4_orf2#LINE/    689 AAGTGA----AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr20_22881695_    985 CATATCTAACAAAGGACTACTATCTAGAATATA---------CGTAGAAC 1025
                         i      i i  i     vv    i        --------- v  v   
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr20_22881695_   1026 TCAACAGTAAAAAACCAA----CCTAATCAGGAAACAAGCAAAACACATA 1071
                             i i      iv   ----  i   i?ii   iii     iv iv i
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTG 834

  chr20_22881695_   1072 AACACACATTTCTCTAAATGGATTAAACAGATGGAAAATA 1111
                           i v         i   viiiv  v   i    vv    
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

Transitions / transversions = 1.57 (94 / 60)
Gap_init rate = 0.02 (15 / 603), avg. gap size = 4.40 (66 / 15)  


3122 26.11 1.00 0.55  chr20_22896643_22901604     3567  4470 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22896643_   3567 TGGAAACACATCCCATGCTCATGGATGGTTAGAATCAATATTATGAAAAT 3616
                               v i        i        v vv   v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22896643_   3617 G-CA-TATTGCCAAAAGCAATCTACAAATTCAACGTAATCCCCATCAGAA 3664
                          -  -  i v  v   vii       i        i      i    i  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22896643_   3665 TACCACCATCACTCTTCACAGAATTAGAAAAAAATAATTCTAAATTTCAT 3714
                          v   v vv vi i  ii     v v  v  iv- i  i     v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATTCAT 149

  chr20_22896643_   3715 ATGGAACCAAAAAGGAGCCTGCACAGTCAAAGCAAGACTAAGTGAAAAGA 3764
                               viiv  i   v  v v i  i    i   vvi i ivi i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_22896643_   3765 ACAAATCTAGAGGTAC-CACACTACCTGATTTCAAAACTATGCTATAAGG 3813
                              vi i    -  -      v  ii           - i   i  i 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACT-TACTACAAAG 247

  chr20_22896643_   3814 CCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGAC 3863
                          i i   v i   i    ii         i    ii    i  i     i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_22896643_   3864 CAATGAAACAGAACAGAGAACCTAGAAATAAACCCAAATACTTACAGCCA 3913
                              i  i    iv    ii i             v i i   ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_22896643_   3914 ATTGATCTTCAGCAAAGCAAACAAAAACACAAAGTGGGGAAAAGGCACTC 3963
                               i   ii   i vviv   i v  ivv i        iiii v  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_22896643_   3964 TTTTCCACAAGTGGTGCTGGGATAATTGGCTAGCCACATGTAGGAGAATG 4013
                              v    i           i  i   v  ?       i ii      
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_22896643_   4014 AAACTGGATCCACATCTCTCACCTTATACAAAACTCAACTCAAGATGGAT 4063
                           ii    i  vi i   v    v         v i       i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_22896643_   4064 TAAAGACTTAAACCTAAGACCTGAAACTATAAAAATTCTGGAAGACAACA 4113
                         i ?    i    iv     v  i           v ii i     v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_22896643_   4114 TTGGA--AAATCCCTTCTAGACACTGGCTTAGGCAAGGATTTCATGACCA 4161
                          v  ?--     --   vv   vi   v        v i    v iivi 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_22896643_   4162 AGAACCCAAAAGCAAATGCAATAAAAACAAAGGTAAATAGCTGGAACCTA 4211
                         v  vv         v v    i    iv   ii  i   iv v i  i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_22896643_   4212 ATTAAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAGAGTAAA 4261
                           i   v v  i i      ii vv    i iv  vi   iv i   i  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_22896643_   4262 CAGACAACCAAGAGAGTGGGAAAAAATCTTCACAATCTATACATCTGATA 4311
                         v        v v   i     i     v  ii   vii   i        
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_22896643_   4312 AAGAACTAATATCCAGAAACTGTAACAAACTCAAATAAATCAGTAAGAAA 4361
                          i i   vi         vv i   vi     vv i  v   i   v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_22896643_   4362 AAAACAAACAATCCCATCAAAAAGTGAGCTAAGGACATGA-TAGAAAAT- 4409
                           i     i  i  v  i?    i  i  v     iv   -    v v -
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_22896643_   4410 CTCAAAAGAAGATATACAAATGGCCAAAAA--ACATGAAAAAATGCTCAG 4457
                            v                       v  --         i       i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_22896643_   4458 CATCACTAATGAT 4470
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (139 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.27 (14 / 11)  


3259 26.96 0.77 0.44  chr20_22916480_22918595.rev      720  1624 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22916480_    720 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 769
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22916480_    770 GGCCATACTGCCCAAGGTAACTTATAGATTCAATGCCATCCCCATCAAGC 819
                            v     v     iv i ii  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_22916480_    820 TACCAGTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 867
                          v    ivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_22916480_    868 TATGGAACCAAAAAAGAGCCTGCACTGCCAAGTCAATCCTAAGCCAAAAG 917
                                viiv  ii  v  v v iv     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_22916480_    918 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTGTACTACAAGGC 967
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_22916480_    968 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 1017
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_22916480_   1018 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 1065
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_22916480_   1066 ATCTGATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGATTCC 1115
                          vi    i  i     i v  v   i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_22916480_   1116 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1165
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_22916480_   1166 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1215
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_22916480_   1216 TTAAAGACTTAAATGTTAGACCTAAAATCATGAAAACCCTAGAAGAAAAC 1265
                          i ?    i       v   v      ii  i   vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_22916480_   1266 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAAGACTTCATGTCTAA 1315
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_22916480_   1316 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 1365
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_22916480_   1366 TTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACCACCATCAGATTGAAC 1415
                          i   v v  i i   i  iiivv    i  v  i i  vv i v    v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_22916480_   1416 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 1465
                           i     i                 v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_22916480_   1466 AGGGCTAATATTCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 1515
                         i  i  vi   i      v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_22916480_   1516 A-ACAAAGAACCCCATCAAAAAGTGGGAGAAGGATATGAACAGACACTTC 1564
                          -     v     v  i?    i    vi      v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_22916480_   1565 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATAAAAA--TGCTCATC 1612
                           v        i  vi viii     v  i     i    --      v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_22916480_   1613 ATCACTGGCCAT 1624
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (145 / 95)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3939 16.87 4.85 4.74  chr20_22983692_22986024      994  1900 (433)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_22983692_    994 TGGAAAGACACCCTACGTTCATGGATTGGAAGACTTAATATGATTAAGGT 1043
                                 i i  i i                         vi     i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_22983692_   1044 GGAAATA-TCCCCACAATTTATCTACAAATTAGATGCAATCTCTATCAAA 1092
                           v    -      -    v       i   vi i      i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCA-AATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_22983692_   1093 ATCTCCGCTTTTTTCTTTGCAGAAATTTACATATTGATCCTAGCATTCAC 1142
                            i v   vii  i            v   vii        iv     i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_22983692_   1143 ATGGAAGTTCAAGGGATTCCAAAGAGCCAAAGAAATCTTGGAAAAGAAAA 1192
                               i v       ii vi  v       iv       i       i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_22983692_   1193 A-AATAT--GAACACTTAC--TTCCTGATTTCAAAACTTACCGCAAAGCA 1237
                          -  vi --  iv   i  --    ii              ii      v
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_22983692_   1238 CCAG-AACCAAAACAATATAGTGCTGGGATAAAGACAGACACG--AATCA 1284
                         v   -  i   i   i i i  i    v    i  i     ii--i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_22983692_   1285 ATGGAATAGAATTGAGAATCTAAAAATAA-CCCTCACATTTGTGGTCAAT 1333
                                          i  i i      -   vi      i        
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_22983692_   1334 TGATTTCC-ACAAGGGTGCCAAGGCAATT-------GAAAGAATAGTCTC 1375
                               i -              i v   -------             i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_22983692_   1376 TTCCACAAATGATTCTGGAACAACTGCATATCTACATGTGGTAGGGTG-- 1423
                            v       i v    i       v   ? i     iiiv  ii  --
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_22983692_   1424 ---GGACCTCTACCTCACATCAAATA-AAAAATTAAAGAAAAATGG-TCA 1468
                         ---     i          i  v   -         vvv       -   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_22983692_   1469 AAACACTTAAATGTAAGA-TTAAAACTAGAAAATCCTTAGAAGAAAATAT 1517
                         ? i-  i           -i        v    ii            i  
  L1M4_orf2#LINE/    500 WAG-ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_22983692_   1518 AGGTGTAAATCTTTGTGGCCTTCAATAAGGCACTGGTTTCTTAAATATGG 1567
                            ?         i   i    vii v     v          i     i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_22983692_   1568 TACAAAAAACACAAGCAATCCAAGAAAATGTAGATAAGTTAGACATTATC 1617
                         i  v    i         ivv       vi       i  i   v i   
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_22983692_   1618 AAAATTTAAAACTTTTATGCTTCAAAAAA--------AAAAGGTGGA--G 1657
                               v         i         ii -------- i  i   i -- 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_22983692_   1658 ACAAGCCACAGAATGGGAGAATGGTAGGAGACATTTACAAATTATGTACC 1707
                             v                --------i i    i     i  i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAA--------AATATTTGCAAATCATATATC 740

  chr20_22983692_   1708 TGATAAGG----TCTCTCTAGAATATATAAGGAACT---ACAAGTCAATA 1750
                                 ---- v v  i           i     ---    v      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_22983692_   1751 ATTAAA-GACAACAAACCCAATTAAAATGTGGGCAAAAGATCTGGATAGA 1799
                           v   -     vv         ?   vi        i   i  i     
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_22983692_   1800 TATTTCTCAAAAGAAGGTATATAAATGGCCAATATATCAGGACACCTGAG 1849
                         i       v       i    i            ----------------
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATA---------------- 874

  chr20_22983692_   1850 TGAGAAGACAGATCCTGTGCACATGGAAAGATGCTCAACATCATTAGCCA 1899
                         ---------  --------      i                 ???????
  L1M4_orf2#LINE/    875 ---------AG--------CACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr20_22983692_   1900 T 1900
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.17 (102 / 47)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 3.78 (87 / 23)  


3844 17.78 3.67 3.11  chr20_23062089_23064439      960  1859 (492)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr20_23062089_    960 AAAGATTTCCTTTGTTCATGAATTGGAAGACTTAATATTGATAATGTGTC 1009
                               v   iv        i                   v   vi  v 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr20_23062089_   1010 AAAACTAACAAGAGTGATCTACAGATGCAATGCAATCTCTATCAAAATCC 1059
                           v   vv v i v            v   i      i            
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_23062089_   1060 CAAAGGGATTTGCTGCAGAAATAG-CAGGATTCATCCTAAAATTCATATG 1108
                           ivv vv   vi         v -  i -i v                 
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATG 152

  chr20_23062089_   1109 GAATTTTAAGGGGCCCTGGAGAGCCAAA-CAATCTTGAGAAAAAAAGAAC 1157
                            v vi     i   v i v       -         -    i      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAAGAAC 201

  chr20_23062089_   1158 AAAGTTGGAGGACTCAAACCTCCTGATTTCAAATCATATTACAAAGCTAC 1207
                                         v  i   ii        v v  i           
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr20_23062089_   1208 AGTAGGCAAAACATTGTGGTACTGGAATAAAGACAGATATATAGACCAAT 1257
                             iv   i   v           v    i  i   i       i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_23062089_   1258 GGAATGAAATAGGGGGCCCAGAAATACACCC----------------TTG 1291
                              ii   v i i i         v    ----------------   
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_23062089_   1292 ATTTTCAGCAAGGATGTCAAGACCATTTAATGAAGGAAGGGTAAAATTTT 1341
                               ii     i  i          i    ii i   ii  ivv    
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_23062089_   1342 CAACAGATGGT-TTGGGAAAATTGGAAATACATATGCAAAAGCAAGAAGT 1390
                              i     -i     v  i    v ?v  i         v v     
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_23062089_   1391 TAGACCT-TACCTCATATCATATAAAAAAATTAATTCAAA-TTGATCAGA 1438
                          i    i-       i i      v         i     - v     ? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_23062089_   1439 TGCCTAAACATAAGACATAAAACTATAAAGCTCCTAGAAAAAAACATAGA 1488
                         vi      ii     vv            i   i     i         i
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_23062089_   1489 AGAAAATCTTTATAACATTAGATTTGGCAATG---------ATATAACAC 1529
                         ? v       ii i  v  i i  v       ---------    i    
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_23062089_   1530 CAAAACCAGGTGCTGCAAGAGTAAAAATACTAATAGATAAATTGGACTAT 1579
                              v  viv  vi   i  -     -----                vi
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAG-AAAAA-----ATAGATAAATTGGACTTC 645

  chr20_23062089_   1580 ATCAAAATTGAAATGTTTTGTGCATCAAAGGACAAAAAATGATAATAAAC 1629
                                  i   vv        v          ----------------
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA---------------- 679

  chr20_23062089_   1630 AATAATAAACAGAGTGAAAAGGCAACCCATTGAATGGGAGAAAATATT-A 1678
                         --iv  v  v i         i       iv                 -i
  L1M4_orf2#LINE/    680 --CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr20_23062089_   1679 CAAATCATATATAGAATAAGGGGTTAATGTCCAGATTATATAAAGAACTC 1728
                                     vvi       ii vi i      v              
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr20_23062089_   1729 CTGCAACTAAACAACAACAA-ACAACAACAAAACAATTAAAAAATGT-CA 1776
                         i i     v  i  i  v  -    -- i  vv     ?       v-  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAA--ATAACCCAATTWAAAAATGGGCA 825

  chr20_23062089_   1777 AAGGACACGAATAGACATTTCTACAAAGAAGATATACAAAGGGTCAATAA 1826
                              ivi              v                 v  i      
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr20_23062089_   1827 GCACATGAAAAGATGTTCAGCATCACTAATCAT 1859
                                        i   i     ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.26 (87 / 69)
Gap_init rate = 0.02 (16 / 905), avg. gap size = 3.81 (61 / 16)  


1291 25.96 30.67 1.43  chr20_23123054_23125418     1173  1873 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_23123054_   1173 GAAAGAAAAGTTCTGTGTTCATGAATTGGAAAACTTAATATTGCTAAGAA 1222
                               v -- i ii        i       i           i     v
  L1M4_orf2#LINE/      3 GAAAGATA--TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23123054_   1223 GTCAGTACTACCCAAAATGATCTACCAATTCAATAAAATCCCTGTAAAGA 1272
                          v  i    v      v        vi      iiv       i v  i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23123054_   1273 TCCTAGTGACTTTTTGTGCACAAGT--ACAAAAATCT-ATTCTAAAATT- 1318
                            i  ivi i    v    v  i --    i---  -  i        -
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr20_23123054_   1319 ATATGAATCT-CAAAGGACCTCAAATAACCAGAGCAATCTTTAAAAAGAG 1367
                              i vv -   i     ivi    i   i i       v       i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_23123054_   1368 GAACAAAACTGAAAGTCTTTCACTTCTTGATTTCAAAACTTACTACAAAA 1417
                                ii  i i v  iv      iii                    i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_23123054_   1418 CTGCAGTAATCA-------------------------------------- 1429
                           i         --------------------------------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_23123054_   1430 -------------------------------------------------- 1429
                         --------------------------------------------------
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_23123054_   1430 -------------------------------------------------- 1429
                         --------------------------------------------------
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_23123054_   1430 -------------------------------------------------- 1429
                         --------------------------------------------------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_23123054_   1430 -----GGACCTCTACCTTTCACCATATACAGTCACCAACTCAAGATGGAG 1474
                         -----     i      iv           ivv ii       i     v
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_23123054_   1475 AGAAGATGTACATGTAAGACCTCAAACTAGAAGAATCCTAGAAGAAAACC 1524
                         vi?   iv  v        v  v      v  i v  i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_23123054_   1525 TAGGAA-ACACCATTTTG-GACATCGGCCTTGGGAAAGAATTTGTGACTA 1572
                             ?i- v i --  i -   v i  vi v  v  v iv  iv iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAAATC--TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_23123054_   1573 AGTCCTCAAAAGCAATTGCAACAAAAACAAAAAAT-GACAAGTGGGACCT 1621
                         v v vi        vvv         i-       -  i  i v    i 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTT 644

  chr20_23123054_   1622 AATTAAACTAAAGAACTTCTGCATAGCAAAAGAAACTGTCAACA------ 1665
                         v  i   v v  i     i  iiivv    i  v   i    v ------
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_23123054_   1666 ---GACAGCCTCCACAGTGGGAGGATATATTCACAAACTATGCATCTGAC 1712
                         ---    i  iv  v i      i v     ii    ii  ii      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_23123054_   1713 AAAGGTCTAGTATCTAGAATCTATAAAGAATTTAAGCAATTGAACAAGCA 1762
                           i  v  v     i     v         i ivvi   i v  i  -i 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TA 793

  chr20_23123054_   1763 AAAAAA-----GACCCCATTAAGAGGTGGGCAAAAAACATGAACAGGCAA 1807
                             i -----i    v   ? i ii        ii iv    i  i  v
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_23123054_   1808 ATTTTAAACAAAGACATATAAGCAGCCAATAAACATATGAAAAAGATGGT 1857
                         v i iv  vi    i   i  iii        i  i       -    v 
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA-GATGCT 892

  chr20_23123054_   1858 CATTGTCACTAATAAT 1873
                           vii   ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (110 / 69)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 14.06 (225 / 16)  


2760 19.26 1.78 0.65  chr20_23125500_23127117      501  1118 (500)    L1M4_orf2#LINE/L1      242   866 (42)  

  chr20_23125500_    501 ACAAA-CTACAGTAATCAAAACATTGT---ACTTACATAAAGACAGACAT 546
                              -             i   v   ---   vi     i  i      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_23125500_    547 ACAGAATAATGGGATAGAATACAGAGTTCAGGTTTAAATTCTCACATATA 596
                          i   vi     i       vv     i   ivv    ii vi    v  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_23125500_    597 TGGTCAAATAATTTTGAATGAGGGTACCAAAACCATTCAACAAGGGTAAG 646
                                v i     vi ii     i    i         ii-   v   
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG-GGGAAAG 390

  chr20_23125500_    647 GACAGTCTTTTTAACAAATGGCACTGGAAAAACACAATATTCACATGTAA 696
                         i i        i         ii    i v   vvi   ?i      i  
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr20_23125500_    697 AAGAACGAAGTTGAACCCCTACCTTA-ACTATATACAAAAATTAACTCAA 745
                              i       i          i -  i                    
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAA 490

  chr20_23125500_    746 AATGGATTAAAGACCTAAATGTAATTACTAAAACTATAAAACTCTTAGAA 795
                                i ?              vvi                       
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr20_23125500_    796 GAAAACATAGAGG-AAACCTTCACATCATTGGATTTGGCAATGATTTAT- 843
                                   i? -   i    iiiv v    i  v       i   v -
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_23125500_    844 GGATATAGCAGTAAAAGCACAAACGACAAAAGAAAAAATCGATAAATTGG 893
                         i     ii  vi          i i              v          
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_23125500_    894 AATACTTCAAAATTTAAAAATGTTGTGCACCAAAGGACACTGTCAACAGA 943
                          v v v        v    v v      vi           i    v i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_23125500_    944 GT-AAAAG-CAATCCACAAAATGGAAGAAAATATTTGCAAATCCATATAT 991
                           -     -   i     i     i                  -      
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATAT 739

  chr20_23125500_    992 CCAATAAGAGATTAATAGCCAGAATTTCTACAGA--TTTCACAACTGAAA 1039
                          ii     i  i vi  v       v v  v   -- i i      v  v
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_23125500_   1040 AAAATGAAAACGAAAACAACCGGATTAAAACATTAGCAAAGGACTTGAGC 1089
                           v vi  i  --   i    vi   ?   v  vi        i    ii
  L1M4_orf2#LINE/    790 AATAAAAAGAC--AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_23125500_   1090 AGACATTTCTCCAAAAAATATATACCAAT 1118
                                        i  v      v   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAAT 866

Transitions / transversions = 1.56 (70 / 45)
Gap_init rate = 0.02 (11 / 625), avg. gap size = 1.36 (15 / 11)  


2834 27.24 2.24 0.45  chr20_23146027_23150280.rev     2871  3762 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23146027_   2871 TGGAAACACATCCCATGCTCATGGACAGGTAGAATCAACATTGTGAAAAT 2920
                               v i        i       iv  v   v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23146027_   2921 GACCATACTGCCAAAAGCAATGTATAAATTTAATGCAATTCCCATCAAAA 2970
                          i v     v  v   vii  v  i i   i  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23146027_   2971 TACTATCATAATTCTTCACAGAACTAGAAAAA--AATCCTAATATTCATA 3018
                          v i v vvvv  i  ii     v v  v  i--i       v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_23146027_   3019 TGGAAACAAAAAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAA 3068
                               iiv  ii  v  viv         i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_23146027_   3069 CAAATCTGGAGGTATCACATTACTTGACTTCAGACTATACTACAAGGCTA 3118
                             vi      vv     i v iii i    i viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_23146027_   3119 TAGTTATCAAAGCAGCATGGTACTGGTATGAAAACAAGCATGTAGACCAA 3168
                         i   v     ii   ii         i  i ii i ii   i    i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_23146027_   3169 TAGAACAGAATAGAGAACCCAGAAATAAAGCCCAGTAC--TTACAGTCAA 3216
                          i   i     v    ii           -    -   --   ii     
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAA-CCCA-TACATTTATGGTCAA 348

  chr20_23146027_   3217 CTGATCTTTGACAAAGCAAACAAAAACATCAAGTGGGGAAAGGACACCCT 3266
                         i    i  i     i vviv   i v   iv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_23146027_   3267 ATTCAACAAATGTTTGTGGGATAATTAGCAAGCCACATGTAGAAGAATGA 3316
                         v           v vv     i  i i vv ?       i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_23146027_   3317 AACTGGATTCTTATCTCTCATCTTACACAAAAATCAAATCAAGATGGATC 3366
                          ii    ii i  i   v  i v  i        i  v    i       
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_23146027_   3367 AAAAACTTAAAACTAAGTCCTGAAACCATAAAAATTCTAGAAGATAACAT 3416
                          ? i  i    vv    vv  i    i      v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_23146027_   3417 CAGAA-AAAT--TCAT--CTATTGGCTTAGGCAA---------AGACCAG 3452
                         vi ?i-    --  i -- i-    v        ---------   i- v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACC-TTGGGTTAGGCAATGGTTTCTTAGAT-AT 596

  chr20_23146027_   3453 GAACCCAAAAGCAAATGCAACAAAAACAAAGAGAAATAGATGGAAATTAA 3502
                           vv         v v         iv   i v i   i  v i v  v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_23146027_   3503 TTAAACTAAAAAACTTCTACACAGCAAAATAAATAATCAGCAGAGTAAAT 3552
                          i   v v        i iii vv    iv v iv    iv i   i  v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_23146027_   3553 AGACAATCCACAGAGTGGGAGAAAATATTCCCAAACTACGCATCCAACAA 3602
                               i       i              iv    ii iii   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_23146027_   3603 AGGACTAATATCTGGAATCTACAAAGAACTTAAAAAATTCAGCAAGAAGA 3652
                         i     vi    ii    v  i        ivv v  i   ii  v  i 
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_23146027_   3653 AAACAAATAATCCCACCAAAAAGTGGGCTAAGAACA-GAATAGACTACTC 3701
                          i        i  v ii?    i     v   i iv-        vvi  
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_23146027_   3702 TCAAAAGAAGTTATACAAATGGC-AACAAACATGTGAAATAATGCTAAAC 3750
                           v       v            -  i  i  ii     vi     v   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_23146027_   3751 ATCACTTTTATC 3762
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.00 (24 / 12)  


2871 26.16 0.63 0.63  chr20_23234519_23236314      506  1304 (492)    L1M4_orf2#LINE/L1      110   908 (0)  

  chr20_23234519_    506 CTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCATATGGAACC 553
                          i  i  ii     -   -- v  i  - iii    i           vi
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCATATGGAAAT 157

  chr20_23234519_    554 AAAAAAGAGCCTGCATTGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCT 603
                         iv  ii  v  v v  v     iv     i i ivv i          i 
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr20_23234519_    604 GGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAAC 653
                              vv    i  v  ii i      viv        i          i
  L1M4_orf2#LINE/    208 GGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr20_23234519_    654 CAAAACAACATGGTACTGGTACCAAAACAGAGATATAGACCAATGGAACA 703
                            i   iii         i iv ii i   v       i        i 
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr20_23234519_    704 GAAC--AGAGCCCTCAGAAATAATGCCACACATCTACAACTATCTGATCT 751
                            i--    i  --        vv   i    i  iiiii vi    i 
  L1M4_orf2#LINE/    308 GAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr20_23234519_    752 TTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAAT 801
                          i     ivv  v   i v  vvv           i  vvi  v  i  i
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr20_23234519_    802 AAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGA 851
                                       v      v  ?   i   i i  iiv    ii    
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr20_23234519_    852 TCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACT 901
                         i    v   i     v              i    i      i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr20_23234519_    902 TAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAGCCTAGGCA-A 950
                             i  v   v       i      vi i         i v    ?i- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr20_23234519_    951 TACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTGAAACACCAA 1000
                         v i -   iv   v v  vv i     v ii   v ivv ivi       
  L1M4_orf2#LINE/    556 AATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr20_23234519_   1001 AAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTA 1050
                              vvi          vv     v  i    v   ii v  i   v v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr20_23234519_   1051 AAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGACAACC 1100
                           i i   i  ii vv    i  v    i  vv i      v        
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr20_23234519_   1101 TACAGAATGGGAGAAAATTTTTGCAATCTACTCATCTGACAAAGGGCTAA 1150
                         i                 v       vii ivi      i  i  i  vi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr20_23234519_   1151 TATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAAACAAAC 1200
                                   v  i         vv    v iv i  v     i     i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr20_23234519_   1201 AACCCCATCAAAAAGTGGGTGAAGGATATGAATGGACACTTCTCAAAAGA 1250
                              v  i?    i    ii      v     i    i     v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr20_23234519_   1251 AGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCATCACTGG 1300
                            i  vi viii     v ii          i       v     ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr20_23234519_   1301 CCAT 1304
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.50 (123 / 82)
Gap_init rate = 0.01 (7 / 799), avg. gap size = 1.43 (10 / 7)  


 299 17.65 0.00 0.00  chr20_23315255_23318295     1146  1196 (1845)    L1M4_orf2#LINE/L1       12    62 (846)  

  chr20_23315255_   1146 CCTGTATTCATCGACTGTCAGACTTAGTATTGTTAAGATGGCAATACTCT 1195
                           ii i     v  i  vv       i                      i
  L1M4_orf2#LINE/     12 CCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCC 61

  chr20_23315255_   1196 C 1196
                          
  L1M4_orf2#LINE/     62 C 62

Transitions / transversions = 2.00 (6 / 3)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.00 (0 / 0)  

3901 18.73 2.40 0.48  chr20_23315255_23318295     1717  2549 (492)    L1M4_orf2#LINE/L1       60   908 (0)  

  chr20_23315255_   1717 CTCCAAATTGGTATGCACATTCCATACAATCCCTATCAAAATCCAAGCTG 1766
                          i        i v i  v    v ii                  v     
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr20_23315255_   1767 GCTACTTTGCAGAGATTGACAAGCTGATCCTAATATTCGGATGAAAATGC 1816
                         v  vi        i                   v    iv   i      
  L1M4_orf2#LINE/    110 CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGC 159

  chr20_23315255_   1817 AAGGGATCTGGAATAGCCAAAACAATTCTGAAAAAGAACAA-AAAGCTGG 1865
                               i ii                ii          v  -    i   
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr20_23315255_   1866 AGGACTCACACTTACTGACTTCAAAACTTACTGCAAAGTTACAG--ATAT 1913
                                      v ii i             i     i     --  vv
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr20_23315255_   1914 AAACAGTGTAATACTGGCACAAAGATGGATAAATAGATCAATGGAATAGA 1963
                          i       ii        i  i   i  i v                  
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr20_23315255_   1964 -----GAGCCCAGAAGTAAGCCCTCATATTTCATATGGTGAAATAATTTT 2008
                         -----   i      i   i   vi i    ---     v  v i     
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTT---ATGGTCAATTGATTTT 356

  chr20_23315255_   2009 CAATAAGGGTCTTAATACCATTCAATAGTTAAAATATAGTTCTATTCAAC 2058
                          i i      vii  v          i vv   iv     -  v      
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT-CTTTTCAAC 405

  chr20_23315255_   2059 AATTAGTGCTAGAAAAACTGGATATCCACATATAAAAGAATAAAGTTGGA 2108
                           v i     i i v         ?      ii        i        
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr20_23315255_   2109 CCCTTACCTCATACTATATACAAAAATTAACTCAAAATGGATAAAAGACC 2158
                            i       i  i                           v ?     
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr20_23315255_   2159 TAAACCTAACAGCCAAAACTATACAATTCCTATAACAAAACAGAAAGGAA 2208
                             iv   v   i         v  i  i  v  v      v ii? v 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr20_23315255_   2209 AAGCCTCATA---TCAGATTTAGCGATGATTTCTTCTATATAACAACAAA 2255
                           v i  i i--- ii i  vi  i   i      vv    i   v    
  L1M4_orf2#LINE/    556 AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr20_23315255_   2256 AGC-CAGACAA----AGAAAAAATAGACAAACTGGACTTCAAAAATATGA 2300
                            -  ii   ----            i   i         vv  v  v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr20_23315255_   2301 AAGACTTCAGTGAATCAAAGGACATTAATAACAGAGTCCAGAGACAACCC 2350
                           i    iv   vv          i  vi  v i   vv i         
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr20_23315255_   2351 ACAGAATGAGAGTAAATACTTGCAAATCACATATCTAATAGGGGATTAAT 2400
                                 i   v     i          i      i   i    i vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr20_23315255_   2401 ATCCAGAATATATAAAGAACACCTAAAACTCACCACCAAAAA-ACAAACA 2449
                                             v i  v      vi vi     -     i 
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATA 805

  chr20_23315255_   2450 GCCAAATTAAAATCCGGAGAAAGTACTGGAATAGACATTTCTCCAAAGA- 2498
                         i  v    ?   vvi  iv    v i v                     -
  L1M4_orf2#LINE/    806 ACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA 855

  chr20_23315255_   2499 --TATACAAATAGCCAATAAGCAAATAAAAAGATGCTCAACATCACTAGT 2546
                         --         i           v  i                  ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr20_23315255_   2547 CAT 2549
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.49 (91 / 61)
Gap_init rate = 0.01 (10 / 849), avg. gap size = 2.40 (24 / 10)  


3317 26.76 0.44 0.44  chr20_23354246_23360525     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23354246_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23354246_   4931 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23354246_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_23354246_   5029 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_23354246_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_23354246_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_23354246_   5179 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5226
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_23354246_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_23354246_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_23354246_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_23354246_   5377 TTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?   ii    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_23354246_   5427 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_23354246_   5477 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5526
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_23354246_   5527 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_23354246_   5577 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_23354246_   5627 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_23354246_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_23354246_   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5776
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_23354246_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3062 26.83 0.44 1.42  chr20_23483668_23487955.rev     2881  3797 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23483668_   2881 TGGAAAAATATTCCATGCTCATGAATAGGAAGAATCAATATTAATAAAAT 2930
                               i    i     i     i  v      v i      iv   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23483668_   2931 GGCCGAACTGCCCAAAGTAATTTACAGATTTAATGCTATTCCCGACAAAC 2980
                            viv   v      v i  i        i  i  v  i  iiv    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23483668_   2981 TACCAAAGACATAATTCTCAGCACTAGAAAAAACT-ATTTTAAAATTAAT 3029
                          v   ivvi v vv  iv   v v v  v  i-  -  ii       v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_23483668_   3030 ATGAAACCAAAACAGAGCCTGAATAGCCAAGGCAATTTTAAGCAAAAAGA 3079
                            i  viiv  vi  v  v          ii    i  i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_23483668_   3080 ACAAAGCTGGAGTCATCATGTTACCCAATGTTAAACTATGCTACAGGGCT 3129
                               i     vvv   iii v      v i   viv i     ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_23483668_   3130 ACAGTAATCAAAACAGCATAGTACTAGTACAAGGACAGACACATAGACCA 3179
                                    i    ii i     i i i     i     i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_23483668_   3180 TTGGAACAGAATAGAGAGCGCAGAAATAGGGTCACACAGGTGTGTGACCT 3229
                         v     i     v     iv        iivi  i   -- v i  ----
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA--TTTATG---- 343

  chr20_23483668_   3230 CCAGTCATCTGATCTTCAACAAACCTGAAAAAAAACAAGTAATGGAAAAA 3279
                         ---    vi    i   i    ivv  vv  i v-  vvi     ii   
  L1M4_orf2#LINE/    344 ---GTCAATTGATTTTCGACAAGGGTGCCAAGAC-CATTCAATGGGGAAA 389

  chr20_23483668_   3280 GGACCCCCTATTCAATAAAAGGTGTTGGGATAACTAGTTAGCCATATGCG 3329
                          i ivvi  v     i   v    i     i    i v  ?   i    i
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr20_23483668_   3330 GAAGATTGAATCTGGACCCCTTCCTTACACCATATACAAAAATCAACTCA 3379
                         i    v    vi         v   i                 i      
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr20_23483668_   3380 AGATGTATTAAAGACTTACATGTAAAACTCAAAACTATAAAAACCCTGAA 3429
                          i   v  i ?    i  v      i vii            vi i ii 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_23483668_   3430 AGACAATGTCGGCA-ATACCATTCTGGACATAGGAACTAGCAAAGATTTC 3478
                            v  ii v  ?i- v i -   vv   v v  ivivi    v i    
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_23483668_   3479 AT-GATGAAGACAC-AAAAGCATAGGCAACAAAAGCAAAAATTGACAAAT 3526
                         v -   - v     -       i i          v      v  i    
  L1M4_orf2#LINE/    589 TTAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr20_23483668_   3527 CGGATCTAATTAAACTGAAGGGCTTCTGCCCCACAAAAGAAACTATCAAC 3576
                         i   ii v  i   v v  iii   i  iv iv    i  v        v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_23483668_   3577 AGAGTAAACACACAGCCTACAGAATGGGAGAAAATTTTTGCAAACTATGC 3626
                          i   i  v v   i  i                 v        ii  ii
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_23483668_   3627 ATTGGACAAAGGTCTAATAGCCAAAATCTATAAGGAACTTAAACAAATTT 3676
                           iv  i  i  v  vi  v   i   v     i     ivv    v iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_23483668_   3677 ACAAGAAAAAAATGCATAACCCCATTAAAAAGTGGGCAAAGGCCATGAAG 3726
                          i  v     i iiv       v   ?    i          viv    v
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_23483668_   3727 AGACACTTATCTAAAGAAGACATACATGTGGCCAACAAGCATATGAAAAA 3776
                              i  v  i        i     vi       i     i       i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_23483668_   3777 ATGCTCAGCATCTCTAATCAT 3797
                                i    v????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (140 / 102)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.70 (17 / 10)  


2785 27.49 0.21 3.10  chr20_23504383_23508497.rev     2689  3623 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23504383_   2689 TGGAAACACATCCCATGCTCATGGAAGGGTAGAATCAATATTATGAAAAT 2738
                               v i        i       vv  v   v i      i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23504383_   2739 GATCATACTGTTAAAAGCAATCTACGGATTCAATGTAGTTCCCACCAAAA 2788
                          iiv     viiv   vii      i       i i i i  i i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23504383_   2789 CACCATCATCATTCTTCATAGAACT--ACAAAAAAAATTGTAACATGCAT 2836
                         iv   v vv v  i  iii    v --    ivvi - iv   v  v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCAT 149

  chr20_23504383_   2837 ATGGAACCAAAAAAGAGGCCACATAGCCAAAGCAAGACTAAGCAAAAAGA 2886
                               viiv  ii  vv viv         i   vvi i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_23504383_   2887 AAGAATCTGGCAGCATCACATTACCCAACTTCAAGTTATACTACAAGGCT 2936
                          vi  vi   vi vv     i v     i     iviv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_23504383_   2937 ATAGTTACCAAAATGGCATGGTACTCATATAAAAATAGGCACGTAGACCA 2986
                          i   v i   i ii ii       vii    ii    i  ii    i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_23504383_   2987 ATGGAAGTGAATAGTGAACTCAGAAATAAAGCCAAATACTTACAGCCAAC 3036
                               vv    v v  iii          v   v i i   ii i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_23504383_   3037 TAATTTTTGACAAAGGTTTTTACTTTATATACACAAAATATATATAAAGT 3086
                          i     i     i   -------------i -   i i-i  vi  -- 
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGT-------------GC-CAAGAC-CATTCAA--T 382

  chr20_23504383_   3087 AGATAAAGTACACCCTATTCAGGAAATGGTGCTGGGATAATTGGCAAGCC 3136
                         i iv    v i vi  v    iv              i  i   vv ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr20_23504383_   3137 ACATGTAGAAGAATGAAACAGGATCCTCATCTCTCACCTTATACAAAAAT 3186
                              i i         iiv   i  ii i   v    v           
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr20_23504383_   3187 CAACTCTAGATAGTTCAAAGACTGAAATCTAAGACTTGAAACCATAAAAA 3236
                         i     v i  i v   ?    iv    v     vi i    i      v
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr20_23504383_   3237 TTCCAGAAGATAACACTGGAAAAATTCTTCTAGACATTGGCTTAGGCAAA 3286
                          iii      v    iv  ?iv  v     vv   v    v        v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr20_23504383_   3287 GAGTTCATGACCAAGAACCTAAATGCAAATGCAACAGAAACAAAAATAAA 3336
                          iv   v iivi v  vv i   v   v v      i  iv       i 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr20_23504383_   3337 TAGATGGGACCTAATTAAACTAAATTAAACTAACAAGCTTCTGCACAGCA 3386
                           i  v    i v  i   ----      ------ i   i  ii vv  
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAA----ATTAAA------AACTTTTGTGCTTCA 672

  chr20_23504383_   3387 AAAGAAATAATTAGCAGAATAAATAGAAAACCCACAGACTGGGAGAAAAT 3436
                           i  v iv  i iv i i i  v   v          v           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_23504383_   3437 GTTCACAAACTGTGCATCTGATAAAGAACTAATATCCAGAATCTATGAAG 3486
                         i  ii    iii ii         i i   vi          v   i   
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_23504383_   3487 AACTCAAACAAATCAGCAAGACAAAAGCAAAAAACCCCATCAAAAAGTGG 3536
                              vv    v   ii  v v   ii    v     v  i?    i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_23504383_   3537 TCAAAGGACATGAATAGACAATTCTCAAAAGAAGATATACAAATGGCCAA 3586
                         v       iv          v     v                       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_23504383_   3587 TAAACATATGAAAAAAATGCTCAATATCACTAATTAT 3623
                            i  i       i -       i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.41 (148 / 105)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.44 (31 / 9)  


3190 26.98 0.55 0.55  chr20_23517446_23523712     4868  5775 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23517446_   4868 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4917
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23517446_   4918 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4967
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23517446_   4968 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5015
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_23517446_   5016 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAACCCTAAGCCAAAAG 5065
                                viiv  ii  v  v v  v     iv   i i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_23517446_   5066 AACAAAGCTGGAGGCATCACAATACCTGACTTCAAACTATACTACAAGGC 5115
                                i      vv     v v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_23517446_   5116 TACAGTAACCAAAACAGCATGGTACTGGTACCAA-ACAGAGATATAGATC 5164
                                 i   i    ii         i iv i- i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_23517446_   5165 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATACCTACAACT 5212
                                i    i--    i  --        vv  ii i ii  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_23517446_   5213 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5262
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_23517446_   5263 CTATTTAATAAACGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5312
                           v  i  i   i          v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_23517446_   5313 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5362
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_23517446_   5363 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5412
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_23517446_   5413 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAA 5462
                         v    ?i v viv   iv   v v  vv i     v ii   v ivvi v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_23517446_   5463 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAATGGGATCTA 5512
                         i            vvi          vv     v  i   - v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA-TTGGACTTC 645

  chr20_23517446_   5513 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5562
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_23517446_   5563 CAGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5612
                         v  i     i   iv            v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_23517446_   5613 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5662
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_23517446_   5663 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5712
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_23517446_   5713 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5762
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_23517446_   5763 CATCACTGGCCAT 5775
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (144 / 97)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


 971 20.43 0.43 2.13  chr20_23544238_23550604.rev       84   318 (6049)    L1M4_orf2#LINE/L1      678   908 (0)  

  chr20_23544238_     84 CACTATCAGCAGAATGAAAAGGCAACCCACAGAAAAGGAGAAAATATCTG 133
                                 iv i i       i            vi           i  
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr20_23544238_    134 CAAAATTACATATCTGACAAGTGGTTAGTATCCAAAATATATAAGGAACT 183
                             - i i        i   v ii v       i         i     
  L1M4_orf2#LINE/    728 CAAA-TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACT 776

  chr20_23544238_    184 CCTACAACTTGACAACAAAAACAGAGCAAACAACATGACC-AAAGATGGG 232
                          i       ii i  i     --  -    i   vii ii-   i     
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAA--GA-CAAATAACCCAATTWAAAAATGGG 823

  chr20_23544238_    233 CAATAGGCTTGAATCGATATTTCTGCAAAGATACATGCATGCATGGCCAG 282
                            vi ii      v  i      v      - v  ii iiv       i
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGA-AGATATACAAATGGCCAA 872

  chr20_23544238_    283 TACACACATGAAAAGCTACTCGACATCACTCATCAT 318
                           vi           v i   i      ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (36 / 12)
Gap_init rate = 0.02 (5 / 231), avg. gap size = 1.20 (6 / 5)  

3155 28.18 0.55 0.22  chr20_23544238_23550604.rev     4971  5875 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23544238_   4971 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5020
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23544238_   5021 GGCCTTACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5070
                            vv    v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23544238_   5071 TACCAATGACTTTCTTCACAGAATTGGAAAAAACCACTTTAAAGTTTATA 5120
                          v   iivi i  i  ii     v v  v  iviv iii    i  i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_23544238_   5121 TGGAACCAAAAAAGAGCCTGCATTGCCAAGACAATCCTAAGCAAAAACAT 5170
                              viiv  ii  v  v v  v     i      i i iv  i  v v
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_23544238_   5171 CAAAGCTGGAAGCATTGTGTTACCTGATGTCAAACTATACTACAAGGCTA 5220
                              i    i vv iiiii v  ii  v     viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_23544238_   5221 CAGTAACCTAAACAGCATGGTACTGATACCA----AAACATATAGACCAG 5266
                               i v i    ii        ii iv ---- i         i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_23544238_   5267 GGGAACAGAATAGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 5316
                         v    i     v   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_23544238_   5317 GATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTAT 5366
                            i  i     ivv  v   i v  vv            i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_23544238_   5367 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATATAGAAAGCTGAAA 5416
                          i  i              v      v  ?   i  ii i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_23544238_   5417 CTGGATCCCTTCCTTATACCTTATACAAAAATTAACTCAAGATGGATTAA 5466
                         i    i    v   i i   v                   i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_23544238_   5467 AGACTTAAATGTTAGACCTAAAACCATAAAAGCCCTAGAAGAAAACCTAG 5516
                             i       v   v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_23544238_   5517 GCA-ATACCATTCAGGACTTAGGCATGGGAAAAGACTTCATGACTAAAAC 5565
                          ?i- v i -   iv   i v  vv i  v  v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_23544238_   5566 ACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCTAATTA 5615
                                   vvi          vv        i    v   ii v  i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_23544238_   5616 AACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAACAGG 5665
                           v v  i i   i  ii vv    i  v       vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_23544238_   5666 CAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACAAATG 5715
                              i                 v       vii ivi      i  iv 
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_23544238_   5716 GCTAAAGTCCAGAATCTGCAAAGAACTTAAACAAATTTACAAGCAAAAAA 5765
                         i  vivi        v ii        ivv    v iv i  -i     i
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA-TAAAAAG 798

  chr20_23544238_   5766 ACAAAGAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACACTTCTC 5815
                              v     v  i? v  i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_23544238_   5816 AAAAGAAGACATTTATGCATCCAACAGACACATGGAAAAATGCTCATCAT 5865
                         v        i  vi viiiv    i ii      i   i       v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_23544238_   5866 CACTGGTCAT 5875
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.49 (150 / 101)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.75 (7 / 4)  


2542 26.29 6.69 1.17  chr20_23603549_23607532.rev     2643  3494 (490)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr20_23603549_   2643 ATCCCATGCTTATAGATTGGGAGAATCAATATCATTAAAATGACCATACT 2692
                                 i i  i      i   v i     ii    i   i v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr20_23603549_   2693 GCCCAAGCT-ATCTACAGATTCAGTTAAATTACTATCATACTACCAA-TG 2740
                         v     ii -             iivv   iv      v v v   i-  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr20_23603549_   2741 TCATTCTTCATAGAATTAGAAAAAAAAATCCTAAAATTCATATGAAACCA 2790
                         i -  i  iii    v v  v  ivvi                 i  -- 
  L1M4_orf2#LINE/    110 CC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA--A 156

  chr20_23603549_   2791 AG-AAAAGATCATGAATACCCAAAGTAATGCTAAGCAAAGAGAATAAAAT 2839
                         v -  ii  i vv     v     ii   vi i iv  ii    i   i 
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr20_23603549_   2840 TGGAGATATCATATT-----AT----------ATTGCAAGGCTGTAGTAA 2874
                              ivv   i i -----  ---------- i i   i   ii     
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr20_23603549_   2875 CCAAAACAGCACGGTCATGTTATAGAAATAGACACATA------------ 2912
                         i   i    iii   vv  vi   iii       i   ------------
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr20_23603549_   2913 ----CTGAAA-------AATAAAGCCACACAGCTACAGTCAACTGATTTC 2951
                         ----i   i -------      v   i   vi  ii     i      i
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr20_23603549_   2952 TGACAAACTTGACAAAATTATATAA-AGGGAAATCACATTCTATTCAATA 3000
                         i     ivv  v   i ii  vi  -i      vv i v   v     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr20_23603549_   3001 AATGGTGCTGGGATAATTGCTGAGCCATATGTAGATTCATGAAACTGGCC 3050
                                      i  i  vvv ?   i   i i vvv     ii   v 
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr20_23603549_   3051 TCTTACCTTCCATCACATACAAAAATTAACTCAAGGTGGATTAAAGACTT 3100
                         i i     iv  i  i                  ii     i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr20_23603549_   3101 AAATGTAAGAACTGAAACTATAAAAATCTTAGAAGACAACCTAGGAAAAA 3150
                                   i  i           v          v   v    ?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_23603549_   3151 CTCTTC-TAACTATTGATCTAGGCAAAGAATTTCT--GATGAAGTCCTCA 3197
                         v     - i  i-   ivi       v i-     --   iviiiv iv 
  L1M4_orf2#LINE/    557 ATCTTCGTGACC-TTGGGTTAGGCAATGG-TTTCTTAGATATGACACCAA 604

  chr20_23603549_   3198 AAGTAAAATACAACAAAAACCAAAACAGAGAAATGGGATTTAAT-AAAAC 3246
                            i v  -i        ivv    i   v    v   i  v  -    i
  L1M4_orf2#LINE/    605 AAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr20_23603549_   3247 TAAAAAGCTTCTGCACAGCGAAAGAAATAATTATCA-----GTAAACAAA 3291
                               -   i  ii vv i  i  v i---     -----  i  v i 
  L1M4_orf2#LINE/    654 TAAAAA-CTTTTGTGCTTCAAAGGACAC---TATCAAGAAAGTGAAAAGA 699

  chr20_23603549_   3292 CAACCTACAGAATGGGAGAAAAGATTTGCCAACGGTGTGTCTGACAAAGA 3341
                              i                v      v  ivi i i     i  i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_23603549_   3342 GCTAATTTCCAGACTCTACAAGGAACTCAAACAACTCAACGAGAAAAACA 3391
                         i  vi v      v v  i  i      vv         ii v     v 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_23603549_   3392 AGAATAACCCCATTAAAAAGTGGGCATAGGGTATGAACAGACATTTTTAA 3441
                         vi        v   ?    i      v   i v    i        i vv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr20_23603549_   3442 ATAAAAGACATACAAATGGC----AAACTTATGAAAA--TGCTTAACATA 3485
                          v i    i           ----  i vi       --    i     v
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr20_23603549_   3486 ATTAAATAT 3494
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.65 (137 / 83)
Gap_init rate = 0.02 (21 / 899), avg. gap size = 3.19 (67 / 21)  


3177 27.64 0.44 0.44  chr20_23643991_23645865.rev      476  1383 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23643991_    476 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 525
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23643991_    526 GACCATACTGCCCAAGGTAATTGACAGATTCAATGCCATCCCCATCAAGC 575
                          i v     v     iv i  iv          i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23643991_    576 TGCCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 623
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_23643991_    624 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCAAAAG 673
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_23643991_    674 AACAAAGCTGGAGGCATCACATTACCTGACTTCAAACTATACTACAAGGC 723
                                i      vv     i v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_23643991_    724 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGGGATATAGATC 773
                                 i   i    ii         i iv ii i  iv         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_23643991_    774 AGTGGAACAGAAC--AGAGCCCTCAGAAATAACACCACATATCTACAACT 821
                          i     i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_23643991_    822 GTCTGATCTTTGACAAACCTGAGAAAAACAAGCAAAGGGGAAAGGATTCC 871
                         ivi    i  i     ivv  vv  i v  vv   v        i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_23643991_    872 CTATTTAATAAATGGTGCTGGGAAAACTGGGTAGCCATATGTAGAAAGCT 921
                           v  i  i              v      i  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_23643991_    922 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 971
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_23643991_    972 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 1021
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_23643991_   1022 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 1071
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_23643991_   1072 AACACCAAAAGCAATGGCAAACAAAGCCACAATAGACATATGGGATCTAA 1121
                         i            vvi    vv    vv v      i v  v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_23643991_   1122 TTAAACTAAAGAGCTTCTGCACAGTAAAAGAAACTACCACCAGAGTGAAC 1171
                          i   v v  i i   i  ii vvi   i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_23643991_   1172 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 1221
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_23643991_   1222 AGGGCTAATATCCAGAATCTGCAATGAACTCAAACAAATTTACAAGAAAA 1271
                         i  i  vi          v ii  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_23643991_   1272 AAACAAACAACCCCATCAAAAACTGGGTGAAGGACATGAACAGACACTTC 1321
                          i     i     v  i?    v    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_23643991_   1322 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 1371
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_23643991_   1372 ATCACTGGCCAT 1383
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (147 / 100)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2311 27.93 6.81 1.29  chr20_23658811_23662797.rev     2646  3497 (490)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr20_23658811_   2646 ATCCCATGCTTATAGACTGGGGGAATCAATATCATTAAAATGACCATACT 2695
                                 i i  i  i   ii  v i     ii    i   i v     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr20_23658811_   2696 GCCCAAGCT-ATCTACAGATTCAATTAAATTACTATCAAACTACCAA-TG 2743
                         v     ii -              ivv   iv        v v   i-  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr20_23658811_   2744 TCATTCTTCATAGAATCAGAAAAAAAAAATCGTAAAGTTCACATGGAACC 2793
                         i -  i  iii    viv  v  ivvi -  v    i    i      vi
  L1M4_orf2#LINE/    110 CC-TTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCATATGGAAAT 157

  chr20_23658811_   2794 AAAAAAGATCCTGAATACCCAAAGCAATGCTAAGCAAAGAGAATAAAATT 2843
                         iv  ii  i  v     v     i    vi i iv  ii    i   i  
  L1M4_orf2#LINE/    158 GCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTT 207

  chr20_23658811_   2844 GGACAGA-TCACATT-----AT----------ATTGTATGGCTCTAGTAG 2877
                            -i  -     i -----  ---------- i ii vi   vi    i
  L1M4_orf2#LINE/    208 GGA-GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr20_23658811_   2878 CCAAAACAGCATGGTCTTGTTGTAGAAAGAGACACATA------TGGAA- 2920
                         i   i    ii    vi  vii  iii v     i   ------     -
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr20_23658811_   2921 ----------------AAATAAAGCCACATAGCTACAACCAACTGATCGC 2954
                         ----------------       v   i i vi  iiii   i    ivi
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr20_23658811_   2955 TGACAAAGTTGACAAAATTTTATAA-AGAGAAATCACATTCTATTCAATA 3003
                         i     i v  v   i iiv vi  -i i    vv i v   v     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr20_23658811_   3004 AATGGTGCTGGGATAATTGGTGAGCCATATGTAGATTCATGAAATTGGCC 3053
                                      i  i   vv ?   i   i i vvv     i    v 
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr20_23658811_   3054 TCTTACCTTCCATCACATACAAAAATTAACTCAAGGTGGATTAAAGACTT 3103
                         i i     iv  i  i                  ii     i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr20_23658811_   3104 AAATGTAAGAACAGAAACTAAAAAAATCTTAGAAGACAACTTAGGAAAAA 3153
                                   i vi      v    v          v   v    ?iv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_23658811_   3154 CTCTTCTAAATATTGGTCTAGGCAAATAATTTATCA----TGAAGTCCTC 3199
                         v     vvi iv    vi       - ii   v i ----   --- vi 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTAGATATGA---CACC 602

  chr20_23658811_   3200 AAAATAAAATACGACAAAAACCAAAACAGAGAAATGGGACTTAAT-AAAA 3248
                             vv v vi i      ivv    i   v    v      v  -    
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAA 652

  chr20_23658811_   3249 CTAAAAAGCTTCTGCACATCAAAAGAAATAATTCTCA-----GTAAACAA 3293
                         i      -   i  ii v     i  v i--- v   -----  i  v i
  L1M4_orf2#LINE/    653 TTAAAAA-CTTTTGTGCTTCAAAGGACAC---TATCAAGAAAGTGAAAAG 698

  chr20_23658811_   3294 ACAACCTGCAGAATGGGCGGAAAGATTTGCCAGCAGTGTATCTGACAAAG 3343
                               ii         v i   v      v iivi i       i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_23658811_   3344 AGCTAATATCCAGGCTCTACAAGGAACTTAAACAACTCAACAAGAAAAAC 3393
                         ii  vi       iv v  i  i     ivv         i  v     v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_23658811_   3394 AAGAATAACCCCATTAAAAAGTGGCCACAGGGTATGAACAGACATTTTTA 3443
                          vi        v   ?    i   v  v   i v    i        i v
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_23658811_   3444 AATAAAAGACATATAAACGGC----AAACATATGAAAA--TACTTAACAT 3487
                         v v i    i   i   i   ----  i  i       -- i  i     
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_23658811_   3488 AATTAAATGT 3497
                         v ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.63 (145 / 89)
Gap_init rate = 0.02 (20 / 899), avg. gap size = 3.45 (69 / 20)  


2256 28.94 6.47 0.71  chr20_23734672_23736775.rev      765  1614 (490)    L1M4_orf2#LINE/L1       10   908 (0)  

  chr20_23734672_    765 ATCCCATGCTTATAGACTGGG-GAATCAATATCATTAAAATGATCATACT 813
                                 i i  i  i   i-  v i     ii    i   iiv     
  L1M4_orf2#LINE/     10 ATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACT 59

  chr20_23734672_    814 GCCCAAGTT-ATCTACAGATTCAATTAAATTACTATCAAACTACCAA-TG 861
                         v     i  -              ivv   iv        v v   i-  
  L1M4_orf2#LINE/     60 CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTG 109

  chr20_23734672_    862 TCATTCTTCATAGAATCAGAAAAAAAAATTGTAAAATTCACACGGATCCA 911
                         i -  i  iii    viv  v  ivvi  iv         i i   vvii
  L1M4_orf2#LINE/    110 CC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr20_23734672_    912 AAAAAGATCCTGAATGCCCAAAGTAATGCTAAGCAAAGAGAATAAAATTG 961
                         v  ii  i  v    iv     ii   vi i iv  ii    i   i   
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr20_23734672_    962 GACAGA-TCACATT-----AT----------ATTGTATGGCTGTAGTAAC 995
                           -i  -     i -----  ---------- i ii vi   ii     i
  L1M4_orf2#LINE/    209 GA-GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAAT 257

  chr20_23734672_    996 CAAAACAGCATGGTCATGTTATAGAAAGAGACACATA------CGGAA-- 1037
                            i    ii    vv  vi   iii v     i   ------i    --
  L1M4_orf2#LINE/    258 CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATA 307

  chr20_23734672_   1038 ---------------AAATATAGCCACATAGCTACAACCAACTGATCTCT 1072
                         ---------------     v v   i i vi  iiii   i    i ii
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr20_23734672_   1073 GACAAAGTTGACAAAATTATATAA-AGGGAAATCACATTCTATTCAATAA 1121
                              i v  v   i ii  vi  -i      vv i v   v     i  
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr20_23734672_   1122 ATGGTGCTGGGATAATTGGTGTGCCATATGTCGATTCATGAAACTGGCCT 1171
                                     i  i   vvv?   i   ivi vvv     ii   v i
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr20_23734672_   1172 CTTACCTTCCATCATGTACAAAAATTAACTCAAGGTGGATTAAAGACTTA 1221
                          i     iv  i   i                 ii     i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr20_23734672_   1222 AATGTAAGAACTGAAACTATAAAAATCTTAGAAGACAACCTAGGAAAAAC 1271
                                  i  i           v          v   v    ?iv  v
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr20_23734672_   1272 TCTTCTAAATATTGGTCTAGACAAAGAATTTAT-GATGAAGTCCTCAAAA 1320
                              vvi iv    vi   i   v iv  iv -   - v v vi     
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT-ATGACACCAAAA 606

  chr20_23734672_   1321 TAAAATACAACAAAAACCAAAACAGAGAAATGGGACTTAATAAAAGTAAA 1370
                         vv v vi        ivv    i   v    v      v  v   i v  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr20_23734672_   1371 AAGCTTCTGCACAGCAAAAGAAATAATTCTCA-----GTAAACAAACAAA 1415
                           i   i  ii vv    i  v i--- v   -----  i  v i    v
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACAC---TATCAAGAAAGTGAAAAGACAAC 703

  chr20_23734672_   1416 CTGTAGAATGGGCGAAAAGATTTGCCAGCAGTGTATCTGACAAAGAGCTA 1465
                          iii        v     v      v iivi i       i  i ii  v
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr20_23734672_   1466 ATATTCAGACTCTACAAGGAACTTAAACAACTCAACAAGAAAAACAAGAA 1515
                         i   i    v v  i  i     ivv         i  v     v vi  
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr20_23734672_   1516 TAACCCCATTAAAAAGTGGCCACAGGGTATGAACAGACATTTTTAAATAA 1565
                               v   ?    i   v  v   i v    i        i vv v i
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr20_23734672_   1566 AAGACATACAAACGGC----AAACATATGAAAA--TACTTAACATAATTA 1609
                             i       i   ----  i  i       -- i  i     v ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr20_23734672_   1610 AGTAT 1614
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.49 (145 / 97)
Gap_init rate = 0.02 (17 / 899), avg. gap size = 3.59 (61 / 17)  


2992 27.26 0.99 0.77  chr20_23763600_23770014     5018  5923 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23763600_   5018 TGGAAGAATATTCCACGCTCATGGATAGGAAGAATCAATATCCTGAAAAT 5067
                              ii    i   i i        v      v i     iv v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23763600_   5068 GGCCATAATGCCCAAGGTAAATCATAGATTCA-TGACATCCCCTTCAAGC 5116
                            v   v v     iv i vii i       -i vv     iv    iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23763600_   5117 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5164
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_23763600_   5165 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5214
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_23763600_   5215 AACAAAGCTGGAGGCATAATGCTACCTGACTTCAAACTATACTACAAGGC 5264
                                i      vv v ii  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_23763600_   5265 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGTGATATAAACC 5314
                                 i   i    ii         i iv ii i  vv     i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_23763600_   5315 AATGGAACAGAA--GAGAGCCCTCAGAAATAACTCCACACATCTACAA-C 5361
                                i    --     i  --        vi   i    i  iii- 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_23763600_   5362 AATCTGATCTTTGACAAACCTGACAAAAACAA-AAATGGGGAAAGGATTC 5410
                            -    i  i     ivv  v   i v  v-v           i  vv
  L1M4_orf2#LINE/    347 AAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_23763600_   5411 TCTATTTAATAAATTGTGCTGGGAAAACTGGCTAACTATATGTAGGGAGC 5460
                            v  i  i    v         v      v  ? i i   i iiiiiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_23763600_   5461 TGAAACTGGATCCCTTCCTTATATCTTATACAAAAATTAATTCAAGATGG 5510
                             ii    i    v   i i i v              i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_23763600_   5511 ATTAAAGACTTAAATGTTAGACCTAAAACCCTTAAAACACT-ACAAGAAA 5559
                           i ?    i       v   v       iv -     v  - v      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTAT-AAAACTCTTAGAAGAAA 544

  chr20_23763600_   5560 ACCTAGGCA-ATACCATTCAGGACATAGGCACGGGCAAGGACTTCATGAC 5608
                           v    ?i- v i -   iv   v v  vvii     v ii   v iiv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_23763600_   5609 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATC 5658
                           vi            vvi          vv        i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_23763600_   5659 TAATTAAACCAAAGAGCTTCTGCGCAGCAAAAGAAACTACCATCAGAGTG 5708
                          v  i   viv  i i   i  i  vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_23763600_   5709 AACAGGCAACCTAGAGAATGGGAGAAAATTCTTGCAATCTATCCATCTGA 5758
                           v  i     i v               vi      vii  vi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_23763600_   5759 CAAAGGGCTAATATCCAAAATCTACAAAGAACTTAAACAAATTTAGAAGA 5808
                         i  i  i  vi      i   v  i        ivv    v iv v  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_23763600_   5809 AAAAATCAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACAC 5858
                             iv    i     v  i?    i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_23763600_   5859 TTGTTAAAAGAAGACATTTATGTAGCCAACGGACACATGAAAAAATGCTC 5908
                           v iv        i  vi vi i     iiii          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_23763600_   5909 ACCATCACTGGTCAT 5923
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (143 / 100)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 1.23 (16 / 13)  


2246 26.76 6.27 0.64  chr20_23789814_23794817.rev     1600  2380 (2624)    L1M4_orf2#LINE/L1        1   825 (83)  

  chr20_23789814_   1600 TGAAAAAACATCCCTTGCTCATAGATTTGAATAATCAATATTGTTAAAAT 1649
                           i   i i     v  i    i    v   v v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23789814_   1650 GACCATACTGACAAAAGCTT--TCTAGAGATTCAGTGCACTTCCTATCAA 1697
                          i v     vv v   --  --    v       ii   v i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA--TTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr20_23789814_   1698 ATTATCAATATCATTCTTCATAGAATTAGAAAAAA-AATCCTAAAATTCA 1746
                          v vi  iivv v  i  iii    v v  v  iv-i             
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_23789814_   1747 -------ATCCTAAAATCCTAAAA---CCAAACCAATCTTAAACAAAAAT 1786
                         -------  v v iiiv  i i  ---     v       i  v  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_23789814_   1787 AATAGAATTGGAGGTATCACATT-----AT----------ACTACAAGGC 1821
                           i i i       vv     i -----  ----------       i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_23789814_   1822 TATAGTAAGCAAGACAGCAGGGGCCTGATATAAAAAACGACACATAGATT 1871
                           i     v        iiv  vv   ii    ii vv    i      i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_23789814_   1872 AATGGAACAAAATAGACA-CCTAGAAATAAAGAAAGATACCT-CAATCAA 1919
                                i i   v  v -i i         vvv v i ii -iii    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_23789814_   1920 CTTGTCTTTGACAAAGTTAAGAA-ATCATACACTGGGGAAAGA-TACCCT 1967
                         i vi i  i     i v ivv  - i   v  v          -  vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_23789814_   1968 ATTCAATAAATGGTGCTGGGGCAATTGGAGAGCCACATGCAGACACATGA 2017
                         v     i             i   i    v ?         i viv    
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_23789814_   2018 AACTGGACCCTTGTCTCTCACCATATACAAAAATTAACTCAAGGTG-ATT 2066
                          ii       i ii   v                        ii  -  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_23789814_   2067 AAAGACTTAAATGCAAGAACTGAAACAATAATA-TCACAGAAGAAAACCT 2115
                          ?    i      i    i  i    v    v -  vi          v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_23789814_   2116 AAGAGAAACTCTTCTGGATATTGATCTAGGCAAAGAATTTATGACTAAGT 2165
                          i ? v  v     vv  iv   ivi       v iv  iv iiv  v v
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_23789814_   2166 CCTCAAAATG---AAGCCCAACATCAACTACCTTAGACAAATGGGACTTA 2212
                          vi     - ---    --    vv ivv vvv    i    v      v
  L1M4_orf2#LINE/    599 CACCAAAA-GCACAAGC--AACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_23789814_   2213 ATTAAACTGAAAAGCTTCTGCACAGCAAAAGAAATAATCAACAGAGTCAA 2262
                           i   v v    i   i  ii vv    i  v iv     v i   v  
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_23789814_   2263 CAGATAACCTACAGAATGAAAGAAAATATTTGCAG----TGTATCTGATA 2308
                         v   i    i        ii              i---- i         
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_23789814_   2309 AAAGACTAATATTGAGAATCCACTAGGAACTCAAATAACTCAAT--TAAA 2356
                          ii    vi   iv     vi iv i      vv i        --    
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_23789814_   2357 AA------TAATCCCATTAAAAAGTGGGCA 2380
                           ------   i  v   ?    i      
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 1.20 (112 / 93)
Gap_init rate = 0.02 (19 / 825), avg. gap size = 2.84 (54 / 19)  

2768 27.36 2.22 1.22  chr20_23789814_23794817.rev     2783  3681 (1323)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23789814_   2783 TGGAAAAAAATTC-ATGCTCATGAATAGGAAGAATCAATATCATGAAAAT 2831
                               i v  i -   i     i  v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23789814_   2832 GGCCATATTGCCCAAAGTAATTTATTGATTCAATGCTATTCCCATCAAGC 2881
                            v   i v      v i  i  iv       i  v  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23789814_   2882 TATCATTGATTTTCTCTGCAGAATTAGAAAAAAAACT-ACTTTAAATTTC 2930
                          vi  viviii  i i       v v  v  i---  - iii    v   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG---CTGATCCTAAAATTC 147

  chr20_23789814_   2931 ATATGAAACCAAAAAAAGATCCCATATAGCCAAGCCAATACTAAGCAAAA 2980
                              i  viiv  ii-  i  viv        iv    vi i iv  i 
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_23789814_   2981 AGAACAAAGCTGCAGACATCAGGCTACCTGACTTCAAACTATACTACAAG 3030
                                  i  v  ivv   vi  v  ii i      viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_23789814_   3031 GCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 3080
                                   i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_23789814_   3081 CCAATGGAACAGAACAGAGGCCTCAGAAGTAACATCACACATCTGCAACC 3130
                         i        i    iv   ivii     i   vvi  i    i iiiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_23789814_   3131 ATCTGATCTTTGACAAATCTGACAAAAACAAGCAATGGG-AAAGGATTCT 3179
                          vi    i  i     ivv  v   i v  vv       -    i  vv 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_23789814_   3180 CTAGTTAATAAATGGTGCTGGGAAAACTGGCAAGCCTTATGCAGAAAACA 3229
                           vv i  i              v      vv ?  vi     i  i vv
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_23789814_   3230 GAAACTGGGCCCCTTCCTTATATCTTATACAAAAATTAACTCAAAATGGA 3279
                            ii   i     v   i i i v                         
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_23789814_   3280 TTAAAGACTTAAATGTAAAACCTATAACCATAAAAACCCTAGAAGAAAAC 3329
                          i ?    i         i v   v   i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_23789814_   3330 CTAGGCA-ATACCATTGAGGACATAGGCATGGGCAAAAACTTCATGACTA 3378
                         v    ?i- v i v i v iv v i  i- i     viii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr20_23789814_   3379 AAACACCAAAAGCAATTGCAACAAAAGTCAAAATTGACAAATGGGATCTA 3428
                         vi            vvv          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_23789814_   3429 ATTAAACTAAAGAGCTTCTGCACACCAAAAGAAACTATCATTGGAGTGAA 3478
                           i   v v  i i   i  ii vi    i  v       vvii      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_23789814_   3479 CAGGCAATCTAGAGAAAGGGAGAAAATTTTTGGAATCTATCCATCTGACA 3528
                         v  i   i i v    v          v    v  vii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_23789814_   3529 AAGGGTTAATATCCAGAATCTTCAAGGAACT---ACAAGGAACTGCAATA 3575
                          i  ii vi          v vi  i     ---    ----  -     
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA----CT-CAATA 790

  chr20_23789814_   3576 -TAAAAA------CAACCCCAGCAAAAAGTGGGCAAAGGATATGAAGAGA 3618
                         -      ------i     v vi?    i            v    v   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_23789814_   3619 CATGTGTC--AAGACATTTATGCAA----CCAATAAACACATGAAAAAAA 3662
                            v v  --    - vv   i   ----       i          i v
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGA-AGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_23789814_   3663 GCTCACCATCATTGGTCAT 3681
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (139 / 103)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.07 (31 / 15)  

 436 14.58 2.08 1.04  chr20_23789814_23794817.rev     4417  4512 (492)    L1M4_orf2#LINE/L1      812   908 (0)  

  chr20_23789814_   4417 TTAAAAAGTGGGCATAGGACATGAACAGATATTTTTCAAAAGAAGACATA 4466
                           ?    i      v    iv    i   i    i  v        i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr20_23789814_   4467 CAAGTGGCAAACAA--ACATGAAAAAAATGCTCAACATCACTAAATAT 4512
                            i    v  i  --         i -            ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGA-TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.02 (2 / 97), avg. gap size = 1.50 (3 / 2)  


2869 27.26 1.79 0.34  chr20_23821770_23825100     1945  2839 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23821770_   1945 TGTAAACACATCCCATGCTCATGGGTGGGTAGAATCAATATTGTGAAAAT 1994
                           v   v i        i      i v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23821770_   1995 GACCATACTGCCAAAAGCAATCTACAAATTCCATGCAATTCCCATCAAAA 2044
                          i v     v  v   vii       i    v i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23821770_   2045 TACCA-CTATTATTCTTCACAAAACTAGAACAAA--AATCCTAAAATTCA 2091
                          v   -  iii-  i  ii  i  v v  -   i--i             
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCA 148

  chr20_23821770_   2092 TGTGGAATCAAAAAATAGCCTGCATA-TCAAAGTAAGACTAAGCAAAAGG 2140
                          i     viiv  iiv v  v v   -i    ii  vvi i iv  i i 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_23821770_   2141 AACAAATCTGGAGGCATTACATTTCCTGACTTCAAACTATACTATAAGGT 2190
                               vi      vv i   i    ii i      viv     i  i i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_23821770_   2191 CACAGTCACAAAAACAGCATGGTACTGATATAAAAGTAGGCATATAGACC 2240
                         i     v iv  i    ii        ii    iii   i        i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_23821770_   2241 AATGGAACAGATTGAAGAATCCAGACATAAAGCCAAAGAATTATAGTCAA 2290
                                i   v vi   i      v     v   v v v    i     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_23821770_   2291 CTGATCTTAGACAAAGCAAACACAAACATAAAGTGGGGAAAGGACACCCT 2340
                         i    i  v     i vviv  vi v   vv i         i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_23821770_   2341 ATTAAACCTATGGTGCTAAGATAACTGGCAAGTCACATGTAGAAGAATGA 2390
                         v  v   vv        ii  i      vv ?i      i i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_23821770_   2391 AACTGGAGCCTCATCTCTCACCCTATACAAAAATCTACTCAAGATGGATT 2440
                          ii    v  ii i   v    v           iv      i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_23821770_   2441 AAAGACTTAAATCTAAGACATGAAACCATAAAAATTCTAGAAGATAATAT 2490
                          ?    i     v     vv i    i      v ii       v  i  
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_23821770_   2491 TGGAAAAACCCTTCTGGACATTGGCTTAGGCAAAGACTTCATGACCAAGA 2540
                         v  ?iv  vi    vv   v    v        v ii   v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_23821770_   2541 CCTCAAAAGGAAATGCAACAAAAACAAAGATAAATAGATGGGATT----- 2585
                          vi      v v v         iv   i   i   i  v   i -----
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_23821770_   2586 -AAACTAAAAAGCTTCTGCACAGCAAAAGAAATAATCATGAGAGTAAACA 2634
                         -   i      -   i  ii vv    i  v iv    v  i   i  v 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_23821770_   2635 CACAACTCACAGAGTGGGAGAAAATCTTCACAATCTATACACACAACAAA 2684
                         v     i      i           v  ii   vii   i ivii i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_23821770_   2685 GGACTAATATCCAGAATCTGCAAAGAACTCAAAAAAATCAGCAAGAACAA 2734
                              vi          v ii         vv v  v   ii  v  v  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_23821770_   2735 AACAAACAATCCCATT-AAAAGTGGGCTATGCACATGAATAGACAATTCT 2783
                         i     i  i  v   -    i     v v v iv          v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_23821770_   2784 C---AAAAGATATAAAAATGGTCAAGAA--ACATGAAGAAATGATCAACA 2828
                          --- i        v      i   v  --       i i   v      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_23821770_   2829 TCACTAATTAT 2839
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.30 (136 / 105)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.90 (19 / 10)  


3168 28.19 0.33 0.33  chr20_23825737_23827685.rev      550  1457 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23825737_    550 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAGT 599
                              ii i  i     i      i v      v i     i  v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23825737_    600 GGCCATACTGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 649
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23825737_    650 TACCAATGACTTTCTTCACAGAATTGGAGAAAACT-ACTTTAAAGTTCAT 698
                          v   iivi i  i  ii     v v  v  i-  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_23825737_    699 ATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCCTAAGCCAAAAGA 748
                               viiv  ii  v  v v  vi    iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_23825737_    749 ACAAAGCTGGAGGCATCACGCTAGCTGACTTCAAAGTATACTACGAGGCT 798
                               i      vv    i  vv ii i      iiv      i i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_23825737_    799 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 848
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_23825737_    849 ATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCTTATCTACAACTA 896
                               i    i--    i  --        vv iiivi  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr20_23825737_    897 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 946
                         vi    i  i     ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_23825737_    947 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTGGAAAGCTG 996
                          v  i  i              v      v  ?   i   iii  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_23825737_    997 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTTGGGATGGAT 1046
                           ii    i    v   i     v           i  i iiii      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_23825737_   1047 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 1096
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_23825737_   1097 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAA 1146
                             ?i v viv   iv   v v  vv i     v ii   v ivvi vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_23825737_   1147 ACACCAAAAGCAATGGCAACAAAAGCCATAATTGACAAATGGGATCTAAT 1196
                                     vvi          vv v   v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_23825737_   1197 GAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCTTCAGAGTGAACA 1246
                         v   v v  i i   i  ii vv    i  v    i vvv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_23825737_   1247 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 1296
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_23825737_   1297 GGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAA 1346
                           i  vi          v  i         vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_23825737_   1347 AACAAACAACCCCATCAGAAAGTGGGCGAAGGATATGAACAGACAGTTCT 1396
                         i     i     v  i?i   i     i      v    i     v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_23825737_   1397 CAACAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCA 1446
                          v v      i  vi viii     v ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_23825737_   1447 TCACTGGCCAT 1457
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.47 (150 / 102)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3078 26.27 1.77 1.22  chr20_23832687_23837707.rev     3628  4529 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr20_23832687_   3628 GAAAAAATGTCATATGCTCATGGATAGGAAGAATCAATATTATTCAAATG 3677
                          i   i  i  vi   i        v      v i      i  v i   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_23832687_   3678 GCTATAGTGCTCTAGGCAATTTACAGATTCAATGCTATTTCTATCAAACT 3727
                           v   v v i v ivii  i           i  v  ii        v 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_23832687_   3728 ATCAATGAAATTATTCACAGAACACGAAAAAATTATTTTAAAATTTATAT 3777
                         vi  iivivv  v  ii     vvi  v  iv v  ii       i    
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr20_23832687_   3778 GGAACCAAAAAAGAGCCTGAATAGCCAAGGTAAATCT--AAGCAAAAGAA 3825
                             viiv  ii  v  v          iii  -   --  iv i     
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAAGAA 200

  chr20_23832687_   3826 CGAAGCTAAGAGAATCACATTACCTGACTTCAAACTATACTACAAGGCTA 3875
                          i   i iiii  v     i v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_23832687_   3876 CAGTGAACAAAACAGCATGGTACTGGTGCAAAAACAGGTACATAGACCAA 3925
                             i v   i    ii         iii  ii i  ii i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_23832687_   3926 TGGAGTAGAATAGACAGCCCAGAAA-AAGGCGACACGTCCAGGACCATCT 3974
                             i      v  v  i       -  iv v i  i ii v ii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_23832687_   3975 GATCTTTGACAAAGCTGACAAAAACAAGCAATGGGGAAAAGAC--TCCTT 4022
                            i  i     i v  v   i v  vv           ii i--  i  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_23832687_   4023 ATTCAACAAATGGTGCTGAAA-AACTGGCTAGCCATAT-CTGAAGATTTA 4070
                         --                ii -      v  ?   i  - vi    v v 
  L1M4_orf2#LINE/    401 --TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_23832687_   4071 AGCTGGACCCCTTCTTTACACCATATACAAAAATTAACT-AAGATGGACT 4119
                           i         v i i                      -  i     ii
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_23832687_   4120 AAAGACTCAAATGTAAAACCTAAAACTATAAAAACCT-GGAAGACAGCCC 4168
                          ?    ii        i v              vi  -i     v i vi
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_23832687_   4169 AGGC---AATATGATCCTGGACTTGGAATGGGAAAAGATTTCACAACAAA 4215
                            ?---   v --  v  iv     iv i  v  v i    vi ivv v
  L1M4_orf2#LINE/    549 AGGNGTAAATCT--TCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_23832687_   4216 AACACCAAAAGCAACTGCAACAAAAGCAAAAATTGACAAATGGGATCTAA 4265
                         i            vvv          v      v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_23832687_   4266 TTAAAGTTAAGAGCTAGAGCTTCTGTACAGCAAAAGAAACTATCAACAGA 4315
                          i   i    i i  ------ i   i vv    i  v        v i 
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACT------TTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_23832687_   4316 GTAAACAGACAACCCACAGAATGGGAGAAAATATTTGCAAACTATGCATC 4365
                           i  v                                   ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_23832687_   4366 TGACAAAGGTCTTATATCTAGCATTTATAAGGAACTTAAACAAATTTACA 4415
                            i  i  v   i    i  v  v     i     ivv    v iv i 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_23832687_   4416 AGAGAAAAACAA----CTCCATTAAAAAGTGGGCAAAGGACATAAATGGA 4461
                          v i   i    ---- i v   ?    i           iv i   i  
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_23832687_   4462 CACTTCTCAAAAGAAGACATACATGCAGCCAACAAGCATGTGAGAAAAAG 4511
                           i     v        i     viii     i     ii   i  i v 
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr20_23832687_   4512 GTCAATATCACTGATCAC 4529
                         v    i    ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (146 / 87)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 2.08 (27 / 13)  


2068 28.15 1.61 1.32  chr20_23867742_23870486     1047  1728 (1017)    L1M4_orf2#LINE/L1        3   686 (222)  

  chr20_23867742_   1047 GAAAACCATTATATGCTAATTGATTGGAATAATCATTATAGTTAGAATGA 1096
                             ivi  ivi   i v  v        v v i v   v    ii   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_23867742_   1097 CCTCAGTGCCCAGAGCAATCTACAGATTCAATGCAATTCCTATCAAA--- 1143
                          vvi v v    i vii              i     i         ---
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_23867742_   1144 TCAGCAGTATTATTTTCCACAAAATTAGAAGAAAACAATTCTAAAATTTA 1193
                         i    v iv  -    v  -i     i-- v  ivii  i        i 
  L1M4_orf2#LINE/    103 CCAGCTGCCTT-TTTTGCA-GAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_23867742_   1194 CATGGAACCAAAAAAGAACTCGAATAGCCAGAGCAAGTCT--AAGCAAAA 1241
                         i      viiv  ii  v iv         i i   -   --  iv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAA-TCTTGAAAAAGAA 197

  chr20_23867742_   1242 GAGCAAAGCTGGAGATAC-CACATCACCTCATTTCAAATTATACTACAAT 1290
                           i     i     i-  -    iiv  iv        viv        v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_23867742_   1291 GCTACAGTAATCAAAACAGCATGGTACTGGTATAAAAATAGACATATGAA 1340
                                       i    ii         i    ii          ii 
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_23867742_   1341 TCAGTGAAACAGAGTAGAGAATGTAGAAATGAAGCCACATACCTACAACC 1390
                            i  i  i   i v    i vi      i  v   i i ii  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_23867742_   1391 AACTTATCTTAGACAAAGTCAGTAAAAATGTACACTGGGGAAATGACACC 1440
                           i v  i  v     i viivi  i vii v  v        vi i vi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_23867742_   1441 CTCTTCAATAAATGGCACTGGGAAAATTGGACAGCCATATGCAGAAGAAT 1490
                           i     i      ii      v  i    i ?   i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_23867742_   1491 GAAACTAGACCCAAGCCTCTCACCATATACAAAAATTAGCTTAACATGGG 1540
                            ii i     vvi    v                  i  i  v    i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_23867742_   1541 TTAAAGACATCAACATAAGAGACAAAACTATTAAAAAATCCTACAAGAAA 1590
                          i ?    v v  ii      vi        --    v  i  v      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTAT--AAAACTCTTAGAAGAAA 544

  chr20_23867742_   1591 ACTTAGGA--ACATCTTTTGGACATTGGACTAGGAAAAGAATTTATGAGC 1638
                           v    ?-- v     ivv   v    ii    v  v iv  iv iiii
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_23867742_   1639 AAGTCCTCAAAAGGACA--TAACAAAAACAAAAATAGGCAAATGAAACTT 1686
                          v v vi      v   --i       iv        ii    vii    
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_23867742_   1687 AAT-AAAACTAAAGAGCTTCTGCACAGCAAAAGAAATAATCAA 1728
                         v  -    i    i -   i  ii vv    i  v iv     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAA 686

Transitions / transversions = 1.70 (119 / 70)
Gap_init rate = 0.02 (13 / 684), avg. gap size = 1.54 (20 / 13)  

 221 20.92 29.29 1.26  chr20_23867742_23870486     2015  2253 (492)    L1M4_orf2#LINE/L1      603   908 (0)  

  chr20_23867742_   2015 AAAAAAAAAAGAAAGAAAGAAAAAAAAGAAACAAA--------CAACAA- 2055
                             iv v   v  v   - i      v i i   --------  v   -
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAA-AGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_23867742_   2056 --TAACAACTATTACTACAGCAAA-------ATCAATAGAGTAAATGGAC 2096
                         --   v    v  i- i vv    -------     v i   i  vi   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTG-TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_23867742_   2097 AACCTA-AGATTGGGGAAAAAATATTTGCAAACTATGCATCTGACAATGG 2145
                             i -   v    - i              ii  ii      i  v  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGG-AGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_23867742_   2146 GCTAATATCCAGCATCTACAAGGA-CTCT---GTCTCAA-AATAAAAAAA 2190
                         i  vi       v  v  i  i  -    ---iv     -        i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_23867742_   2191 -------------------------AAAG-------------------CC 2196
                         -------------------------    -------------------  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr20_23867742_   2197 ATACAA-ACATACAAACAGCCAACAAA-ATATGAAAAAATACTCAACATC 2244
                          v v  - i       ii     i  i- i       i  i         
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr20_23867742_   2245 AGTAATCAT 2253
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.50 (30 / 20)
Gap_init rate = 0.05 (14 / 306), avg. gap size = 5.21 (73 / 14)  


3214 25.64 0.99 0.66  chr20_23876111_23878768.rev     1262  2166 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_23876111_   1262 TGGGAAAACATTCTGTGCTCATAGACAAGAAGAATCAATATCATAAAAAT 1311
                            i  i i  i ii  i    i  ivi     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_23876111_   1312 GGCCATATTGCCCAAAACAATTTATAGATT--ATGCTATTCCTATTAAAC 1359
                            v   i v      vii  i  i     -- i  v  i     i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_23876111_   1360 TACCA-CTGACATTCTTCACAGAACTAGAAACAACT-ATTTTAAAATTCA 1407
                          v   -   v -  i  ii     v v  v - i  -  ii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCA 148

  chr20_23876111_   1408 CATAGAACCAAAAAAGAGCCTGAATAGCCAAGGCAATCCTAAACAAAAAT 1457
                         i  i   viiv  ii  v  v          ii     i i  v  i  v
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_23876111_   1458 AACAAAGCTGAAGGCATCACACTACCCTACTTCAAACTATACTATAGGTC 1507
                                i  i   vv       v   v i      viv     i iiv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_23876111_   1508 TACAGTAATCAAAATACCATGGTACTGGTACAAAAGCAGACACATAGACC 1557
                                     i i vii         i i  iiii     i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_23876111_   1558 AATGGAAAAGAATAGAGAACCCAGAAATAAGGCTGCATACCTCCAATGAT 1607
                                v     v    ii          iv --     v ii -  i 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTA-TGGT 345

  chr20_23876111_   1608 C---TGATTTTTTACAAATCTGACAAATAAAAGCAATAGGGACAGGATTC 1654
                          ---       iv    ivv  v   ivvv vv    i    v  i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_23876111_   1655 CCTGTTCAATACATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGAT 1704
                         i  v     i v            i      v  ?   i     i    v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_23876111_   1705 TGAAATTGGACCCCTTCCTTACACCATATACAAAAATTAACTCAAGATGG 1754
                             i          v   i                         i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_23876111_   1755 ATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAATCCTGGAAGACAA 1804
                           i ?    i         i v i            v  i i     v  
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_23876111_   1805 CCTAAGCA-ATACCATTCAGAACATAGGAACAGGCAAAAATTTCATGACG 1853
                          v  i ?i- v i -   ivi  v v  ivi      vii    v iivv
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_23876111_   1854 AAGAATCCAAAAGCAATTGCAACAAAAGCAAAAATTGGGAAATGGGATCT 1903
                          v  vv         vvv          v      v iv    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_23876111_   1904 AATTGAACTAAGGAGCTTCTGCACAACAAAGGAAACTATCAACAAAGCAA 1953
                         v  ii  v v ii i   i  ii vv       v        v    ii 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_23876111_   1954 ACAGACAACCTACAGAATGGGAGAAGATTTTTGCAAATTATGCACCTGAC 2003
                          v        i              i  v         i  ii i    i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_23876111_   2004 AAAGGACTAATAGCCAGCATCTATAAGAAACTTAAACAAATTTACAATAA 2053
                           i     vi  v    v  v     ii    ivv    v iv i     
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_23876111_   2054 AA-TACAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACT 2102
                           -v     i     v   ?    i           iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_23876111_   2103 TTTCTAAAGAAGACATACATGTAGCCAACAATCACATGAAAAAAAGCTCA 2152
                          i  i        i     vi i     i  v          i v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_23876111_   2153 ACACCACTGATCAC 2166
                            i  ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (134 / 94)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


3033 21.67 3.84 0.27  chr20_23984909_23986605      481  1209 (488)    L1M4_orf2#LINE/L1      154   908 (0)  

  chr20_23984909_    481 AAATG-AATGAACAGCCA-AGCAGTCAAAACAATCTTGAAAAAGAAGAAC 528
                              -  v i  --   - ii  i                         
  L1M4_orf2#LINE/    154 AAATGCAAGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_23984909_    529 AAAGTTGGAGGTCTCACACC-CCTGATTTCAAAACTTACTATAAAACTAC 577
                                    v       i-  ii                i   i    
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr20_23984909_    578 AGTAACCAAAACAG-----------CATAAAGACAGACTTACAGA-CTAT 615
                              i   i    -----------     i  i    v  i   - v  
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_23984909_    616 GAAATAGATATG-GAGCCCAGAATTAG-CCCTCACATGGAGGGTCAAATG 663
                          i      vv  -   i      v  i-   vi    vv v      v  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_23984909_    664 ATTTTGCACAAGGGCGTCAGGTTCATTCAATGAGAAGAGGAGCACATCAT 713
                              vv       i i  i vi         i i i  i vviiv iv 
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_23984909_    714 TAACAAACGGTGCTGGGAAAACTGAATATCCACCCAAAAAATAGCGAAAT 763
                         i      i          v     i   ?    viiv    v ii   i 
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_23984909_    764 TGGACCATTGCTTTATATCATCTACAAAAATTAACTAAAAATGGATTGAA 813
                               vi i i i i i   v              v         ii? 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_23984909_    814 GGTCTAAACAGAAGAGATAAAACTCTATAACTCTTAGAACAAAACATACG 863
                          ii     iiv     v       v  v           v        v 
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_23984909_    864 AAGAAACTGTCATGATATTAGATTTGGCAGTTATTTCTTGGATATGACAC 913
                         ?iv   iiv  i   iv  i i  v    i vi      i          
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_23984909_    914 CTAAACCA-AGGCAACAAAG--AAAAATAGATAAATTGGACTTATTCAAA 960
                          v   v  - i        i--                     vv     
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_23984909_    961 ATTAAAGACTTTTGTGCATCTAAGTACACTACCAAGAAAGCAATATAATG 1010
                               i          v  v   v      i        ii v vi ii
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr20_23984909_   1011 GCCTACAGAAGGGGAAAAAACATTTGCAAATTACACATGTGATAAGGAGT 1060
                         i  i      v    i    i          i i i  v        iii
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGAC 751

  chr20_23984909_   1061 TAATACCCAGAACACATAAAAGACTCCTAAAATCCAACAA----ATGCAA 1106
                          vi  i      i i     ii    i  v  ii   i  ---- v vv 
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr20_23984909_   1107 AACAACTCAATT--AAAATTGACAAAGGCCTTGAATAGACATTTCTTCAA 1154
                           i   i     --     v i      vi                i   
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr20_23984909_   1155 GGAAGATGTACAGACAGCCAATAAGCACATGACAAGATGCTCAG--TCAA 1202
                         i      i    i ii                v          i--   ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr20_23984909_   1203 TATCTTT 1209
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 1.77 (99 / 56)
Gap_init rate = 0.02 (13 / 755), avg. gap size = 2.31 (30 / 13)  


2167 23.73 5.10 0.64  chr20_24015782_24017401.rev      500  1127 (492)    L1M4_orf2#LINE/L1      253   908 (0)  

  chr20_24015782_    500 GTAATCAAGA--------TACTG---TATGAATAGACAAATAGATCAATG 538
                                   --------     ---  v i       v           
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr20_24015782_    539 AAACAGAATACACAGCCCAGAAATAGACCCACATAAATATAGTCAATAGA 588
                         i  i     vv v  i         i     i i vv   i      v  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_24015782_    589 CTTT-GACAAAGGGGCAAAGGCAATACGATGGAGAAA----AGTC----- 628
                         i   -     i  v  v   i v  v i    i    ----    -----
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr20_24015782_    629 AACAAATGGTCCTCGAATGACTGGGCCTATACATGCAAAAAAGTGA-GTC 677
                                   v  v i ii     iiv?vi          i i   -  i
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr20_24015782_    678 AACACACAGACCTTACACCCTCTGCAAAAATTAACTCAAAATGCATCATA 727
                         ii-  v vv    i     v v i                   v    ? 
  L1M4_orf2#LINE/    453 GG-ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_24015782_    728 GCCCTAAATGTAAAACACAAAATCATAAAACCCCTAGAAGATAACATAGT 777
                          v           i vvi    ii       i i       v       v
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_24015782_    778 AGAAAATCTAGATACCCT--GATTATGGCAAAGACTTTTTAGATATAACA 825
                         ? v      vvi iv   -- i   -     v ii  i        i   
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATATGACA 600

  chr20_24015782_    826 T-AAAGGCACAATTTATAAAAGAAAAGTT-GATAAGCTGGATGGCATTAA 873
                         i-   i      viv i         iv -     ii    ivv   i  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_24015782_    874 AATTAA---CTTCTGCTCTGGAAAAGATAATCTCAAGAGAATGAGAAAAC 920
                               ---   i  iv  vv   i  i v v      i i   i  i  
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_24015782_    921 TAGCCCCAGACTAGGATAAAATATTTGCAAAAGACACATCTGCTAAAGGA 970
                         v v  v    v i   v              vv i i     v   i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_24015782_    971 CTGTTATTCAAAATGTACCAAGAATTCTCACAACTCAACGATAA---GAT 1017
                           vv   i  i   i  iv     i   i         ii    ---  i
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_24015782_   1018 TAACAGTCCAATTAAAAAAAATGGGTAAAAGACCTGAACATACAGTTCAC 1067
                         v  i ii      ?     --    i   i  ii    i v   v   v 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAA--TGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_24015782_   1068 CAAAGAAGACGAGCACATAGCAAGTAAACATATGAAAAGATGCTCAGCAT 1117
                                  iivi  v  i  v i   i  i               i   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_24015782_   1118 CATTTGTCGT 1127
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.42 (85 / 60)
Gap_init rate = 0.02 (14 / 656), avg. gap size = 2.57 (36 / 14)  


2225 26.89 1.21 0.76  chr20_24114281_24115934.rev      501  1162 (492)    L1M4_orf2#LINE/L1      244   908 (0)  

  chr20_24114281_    501 AATGCTATAGTAACCAAAACAGCATGGTACTGGCACAAAAACAGACATAT 550
                           v    i     i   i    ii           i  ii i        
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr20_24114281_    551 AGACAAGTGGAAAAGAATAAAGAACCCAGAAGTAAAGCAGCACGCCTATA 600
                            iv i     v     vi   ii      i    v vii  iii   i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr20_24114281_    601 GCCACCTGGTCTTCAACAAAGTTGACAAAAAGAAGCAATAGGGAAAGGAC 650
                          i  vi  i i   i    i v  v   i vv vv    i       i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_24114281_    651 TTCCTGTTCAATAAATGGTGCTGGTATAACTAACTAGCTATATGCAGAAG 700
                         vvi  v     i            v i    iiv  ? i i     i   
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_24114281_    701 AATGAAACTAGGCCCCTAATTT-CACCATATACAAAAATTAACTCAGGGC 749
                               ii i i      vi i-                       iiii
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_24114281_    750 AGATTAAAGATTTAAATGTAAAGTCTCAAATTAGAAAAATCCTAGAAGAA 799
                         i   i ?   ii         iiv  v   i  v    v  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_24114281_    800 AACCTAGG---AAATACCGTTCTGGACATCAGCCTTTCGAAAGAATTTTT 846
                            v    ---    -- -   vv   v ii v-  vv v  vii   i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT--C-TTCGTGACCTTGGG-TTAGGCAATGGTTTCT 589

  chr20_24114281_    847 --GACCAAATTCTCAAAAGCAATTGCAA-AATAACAAAAATTGCCAAGTG 893
                         --  ivvi iv -        vvv    -  v iv      v vi  i v
  L1M4_orf2#LINE/    590 TAGATATGACAC-CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_24114281_    894 GGATCTGATTAAACTGAAGAGCTTCTGCACAGCAAAAGAAATTATCAACA 943
                            ii v  i   v v  i i   i  ii vv    i  v i      v 
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr20_24114281_    944 AAGTAAACAGACAACCTACAGAATGGGAGCAAATATTCACAAGCTATGCA 993
                             i  v        i            v       ii   iii  ii 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_24114281_    994 TCTGACAAAGGTCTAACATCCAGAATCTATGAGGAACTTAAACAATTTAA 1043
                              i  i  v  vii         v   i i     ivv    i i  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_24114281_   1044 CAAGCAAAAAGCAAATAACCCCGTTAAAAAGTGGGCAAAAGAGAAGAACA 1093
                         i  vv    ii          vi  ?    i        i  vvv   i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr20_24114281_   1094 GATACTTCTCAAAAGAAGACATACAGGTGGCCAACAAGCATATAAAAA-A 1142
                           i i     v        i     ii       i     i  i    - 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr20_24114281_   1143 TGCTCAACATCACTAATCAC 1162
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (111 / 64)
Gap_init rate = 0.01 (9 / 665), avg. gap size = 1.44 (13 / 9)  


2702 20.78 18.44 0.52  chr20_24158021_24160493     1222  1991 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24158021_   1222 TGAAAAGACATTCCGTGTTCAAGAATTAGAAGACTCAATATTGTTAAAAT 1271
                           i     i  i  i      v i   i       i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24158021_   1272 GTTAATACTACCCAA-----TCTACAGATTCAATGCAATTCCTATCAAAA 1316
                          vi      v     -----             i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_24158021_   1317 TTCCAGGGACATCTTTTGCAGAAA-------------------------- 1340
                          i    vvi v i           --------------------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_24158021_   1341 ----AATAC----------------------------------------- 1345
                         ----   i -----------------------------------------
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_24158021_   1346 ---------------------TCCCAA----------------------- 1351
                         ---------------------      -----------------------
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_24158021_   1352 -------------GGGGTAGTACTAGTATGAAAACAGACCTATAGATGAA 1388
                         -------------i v  i     i i  i ii i    v       v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_24158021_   1389 TGGAATCGACTAGAGAGCTCAAAAATAAACCCTTGAATGTATGGTCAAAT 1438
                               v  v v     ii  i          v iv  v         v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_24158021_   1439 GATTTTTTACGAGGTTGC-ACAACTATTCAATGGAGAAAGGACAGTCTTT 1487
                               iv  i   v   - vi  i         i     i i       
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_24158021_   1488 TCAACAAAAATTGCTAAAATAAATGGGATATCCACCTGCAAAGGAAAGAA 1537
                                 viv    iii i  v   -   ?    v      i   v   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGG-ATAKCCACATGCAAAAGAATGAA 449

  chr20_24158021_   1538 GTTGGAGCCTTAATTTATGACATACACAAAAGTTAGCT-GAAATGGATCA 1586
                               v  i  vi i iiv    i      i   i  -i          
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_24158021_   1587 AAGACTTAAATGTAGGAGATGAATCTATAAAACTCTTAGAATGAAAACTT 1636
                         ?    i        i   v i  v                 -      v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA-GAAAACAT 548

  chr20_24158021_   1637 AGGAGAAAATCTTTATGACATTAAATTCAACAATGATTTATTTGGTGTGA 1686
                            ? v       ii    v  iii  vii     i   v  v i i   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_24158021_   1687 CACCAAAAGCACAATCAATGAAATAAAAAATTGATAAACTGGACTTCATC 1736
                                       v   ii   v       v      i           
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_24158021_   1737 AAATGTTAAATA-TTTCATGCATCAATACACACTATTAACAGAGTAAAAA 1785
                            -i     v -   ii   v    viv       i  v i   i    
  L1M4_orf2#LINE/    649 AAA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_24158021_   1786 AGCAGCACACGGAATGGGAGATGTTATTTGTAAATCCTATATCTGTTAAG 1835
                         ii  i v   i          viv      i     v        v    
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_24158021_   1836 GTATTAATGTCCAGAATAAATGAAAATACTCT-ACGTATCAACAACAAAA 1884
                          v i vi i         v  i  i -     -  ivv    i  i    
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGA-ACTCTTACAACTCAATAATAAAA 796

  chr20_24158021_   1885 A--CAAACAACACAATTTAAAAATTGGCAAAGGAATTAAATA-ATATTTC 1931
                          --    i   v     ?      v         v  i    - i     
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_24158021_   1932 TCCAAAGAT--TATACAGATGATCAATAAGTACATGAAAAGATGGCTACT 1979
                                 v--      i   ii       i             vii vi
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_24158021_   1980 ATCTCTAATCAT 1991
                            v????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (96 / 60)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 9.73 (146 / 15)  


2959 25.20 3.23 2.01  chr20_24234765_24236700.rev      548  1444 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24234765_    548 TGGAGAGGTATTCAACATTAATAGGTTGGAAGACTTGAAATTGTCAAGAT 597
                             i  i   i v ii  v  i i           i v     i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24234765_    598 GCAAATTCTTTCCAACTTGATCTATAGATTCAACATAACCCCAATCAAAA 647
                          vv   v  ii    v        i         ii  i   v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_24234765_    648 TCTCAGAAAGCTATTGTATAGATATTGACAAATTGATTCTAAAATGTATG 697
                           i   vviv  v  v ii   v        ii    i       vi  i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_24234765_    698 TGGAAAGTG-AAAAGACTCCGAATGGCCA------TACTGAAGAAGAATA 740
                               -  -  ii   i v    i    ------ vi    i     v 
  L1M4_orf2#LINE/    151 TGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_24234765_    741 ACAAAATCAGGGCCAATTCCCATTACCATTACCTAATTCCAAGACTCACT 790
                              i ii i --i i  v  i ----- -  i    i   i   i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAG--GACTCACACT-----T-CCCAATTTCAAAACTTACT 241

  chr20_24234765_    791 ATAGAGCTACAGTACTCAAGATAGCATGGTGTTGGTGAAAGTATAGACAT 840
                          i i          v      i  ii    ii   iiv   v        
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_24234765_    841 GTAGATCAATGGAACAGAGTAGACAACCCAGAAATAGATCCACACAAATA 890
                         i             i   i v  v ii         i i   i   vv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_24234765_    891 CTTTCAACTGATCGTTAGCAAAAGAGCAAAGGCAATTCAATGAAGAAAGA 940
                         ivv    i    iv iii   ii v  v   i v        ii      
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_24234765_    941 AGAATTTTTTTAAAAAAATAGTGCTGGAAAATTTGAATATCCATATTAAA 990
                          v i i    i  v   - i       i v vi  i   ?   i  vv  
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr20_24234765_    991 AAATAATTGAGCCTAGACACAGACCTTACACTTTTCACAAACATTAACTC 1040
                           i-   vi  i- i   v vv    i    iv vi     v        
  L1M4_orf2#LINE/    441 AAG-AATGAAGT-TGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr20_24234765_   1041 AAAATCAACTGTAGACCTAAATGTAAAGTGC-AAAGATATAAAACTTCCA 1089
                              vi iii?              - v  -   iv         iii 
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAA-GAGCTAAAACTATAAAACTCTTA 537

  chr20_24234765_   1090 GAAGAAACCATAGCAGAAAGTCTATGTGATAT---ATTGGGTGATGAATT 1136
                                v     v? v  i   vi    iv ---i  i  ii   iv  
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_24234765_   1137 TTTAGATACAAAACGAAAA-CATAATGCA-TGAAAGAAAAATT-GATAAA 1183
                         i       ii v  v    -  i  -   -ii         v -      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAA 636

  chr20_24234765_   1184 TTGGACTTGATTAAAATTTAAAAGTCTCTGCTCTGTGAAAGAAACAATTA 1233
                                 v  i      -    iii i  iv  vii  i  v  v  i 
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATT-AAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr20_24234765_   1234 AAAGAATGAAAATACAAACCACAGACTGGGAGAAAATATTTGCAAAAAAC 1283
                          i i i      v    v       v                    vv i
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr20_24234765_   1284 ACATCTGATAAAGAATTTATATCCA-AATATAAAAAGAGCTTGTAAAATT 1332
                          i         i i i  i      -      v     i  iv  v  i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr20_24234765_   1333 CATCAATAA---GAC------CCCGATTTTTAAAAATGGGCAAAAGACCT 1373
                           vi     ---   ------   i   ?--             i  ii 
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTW--AAAAATGGGCAAAGGATTT 833

  chr20_24234765_   1374 GA-TGGAGTACCTTATCAAATATGATATACAGATGAC----AAACACACA 1418
                           - i  -i ii ivi    v v        i   i ----  i    ii
  L1M4_orf2#LINE/    834 GAATAGA-CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_24234765_   1419 GAAAGATGCCCAGCATTATTTGTCAC 1444
                         i        i  i   i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (148 / 74)
Gap_init rate = 0.03 (24 / 908), avg. gap size = 1.96 (47 / 24)  


2974 26.87 0.87 2.49  chr20_24325375_24327685.rev      897  1819 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24325375_    897 TGGAAGAACATCCCATGCTCATGAATAGGAAGAATCAATATTGTGAAAAT 946
                              ii i        i     i  v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24325375_    947 GGCCATAGTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 996
                            v   v v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_24325375_    997 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1044
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_24325375_   1045 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCAAAAAA 1094
                                viiv  ii  v  viv  v     i      i i --------
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-------- 190

  chr20_24325375_   1095 AAAAAAAAAAAGAAAAAAAAAACAAAACTGGAGGCATCACACTACCTGAC 1144
                         ------------    i  i      ii      vv       v  ii i
  L1M4_orf2#LINE/    191 ------------AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT 228

  chr20_24325375_   1145 TTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACCGGTA 1194
                               viv        i          i   i    ii      i  i 
  L1M4_orf2#LINE/    229 TTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCA 278

  chr20_24325375_   1195 CCAAAACAGATATATAGACCAAAGGAACAGAACAGAGGCCTCAGAAATAA 1244
                         iv ii i   i       i   v    i    iv   ivii         
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr20_24325375_   1245 CACCACACATCTACAACCATCTGATCTTTGAAAAACTTGACAAAAACAAG 1294
                         vv   i    i  iiii  vi    i  i  v  ivv  v   i v  vv
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr20_24325375_   1295 AAATGGGGAAAGGATTCCCTATTTAATACATGGTTCTGGGAAAACTGGCT 1344
                         v           i  vvi  v  i  i v     v      v      v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr20_24325375_   1345 AGCCATATGCTGAAAGCTGAAACTGGATCCCTTCATTACACCTTATGCAA 1394
                          ?   i    vi  iiv    ii    i    v v i     v   i   
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr20_24325375_   1395 AAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACTATA 1444
                                i    i      i ?    i    i  v   v           
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr20_24325375_   1445 AAAACCCTGGAAGAAAACCTAGGCA-ATACCGTTCAGGACATAGGCATGG 1493
                            vi i i         v    ?i- v i -   iv   v v  vv i 
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAG 577

  chr20_24325375_   1494 GGAAAGACTTCATGACTAAACCACCAAAAGCAATGGCAACGGAAGCCAAA 1543
                          v  v ii   v iiv  viv           vvi     ii   vv   
  L1M4_orf2#LINE/    578 GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr20_24325375_   1544 ATAGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGA 1593
                              i    v   ii v  i   v v  i i   i  ii vv    i  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr20_24325375_   1594 AACTACCATCAGAGTGAACAGGCAACCTACA-AATGGGAGAAAATTTTTG 1642
                         v    i  vv i      v  i     i   -             v    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr20_24325375_   1643 CAATCTACCAGTCTGACAAAGAGCTAATATCCAGAATCTACAAATAACT- 1691
                            vii ivvi     i  i ii  vi          v  i   v    -
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr20_24325375_   1692 -TA-AATTTA-TAAGAAAAAATCAAACAACCCCATCAAAACGTGGGCAAA 1738
                         -  -  i i -   v     iv    i     v  i?   vi        
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr20_24325375_   1739 GGCTATGAACAGACACTTCTCAAAAGAAGACATTTATGCAACCAACAGAC 1788
                           v v    i     i     v        i  vi viiii    i ii 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr20_24325375_   1789 ACATGAAAAAATGTTCATCATCACTGGTCGT 1819
                                  i   i   v     ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.10 (31 / 10)  


3556 21.71 4.23 0.69  chr20_24331773_24334223.rev     1085  1959 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_24331773_   1085 GAGATACATTCCAAGTTTGTGTGTGGGGTGACTCAATATTGTTAAGATGA 1134
                           i v i  i   v   ii  vi v  iv    i               i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_24331773_   1135 CAATTTTTATCTAACTGAGCTATAGATTGAATGCAATTACTTTAAAAATC 1184
                             vi ivi v  i   v   i     v  i     iv  v v      
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_24331773_   1185 CTGGCAGG--TTTTTGCAGAAATTGACAAGATGATCCTAAAATGTATAAA 1232
                          ii  v v--                    v            vi   vi
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_24331773_   1233 GAAATGCAGAGGACCCAACATAGCCAAAACAATTTT--AAAAGATAAATA 1280
                                 ii       iv              i  --      vi  i 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_24331773_   1281 AAATTGGAGGACTTAAATTTCTCTATTTCAAAACTTATTATAAAGCTAAA 1330
                           i          i v i   i v             i  i       v 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_24331773_   1331 ATAATCAAGACAGTGTGAAGCTGGTATAAGGATAGACATATAGATCAATG 1380
                         i                ivi    i                         
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr20_24331773_   1381 GAACATATTTGAGAATCCAAAACTAAATCCCTACATTCATGGTCTACGGA 1430
                            i v v      i    i  v    i  v      i      v iv  
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_24331773_   1431 TTTTTGACAA---TG---------------GAGAAAAGAATAGTCTTGTT 1462
                             i     ---  --------------- i i             v i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr20_24331773_   1463 AACAAACTGTGTTGGGAAAATTAAAAATCCACATGTTAAAAAATGAGTTT 1512
                               iv   i     v  i ii v ?       iv   i     iv  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr20_24331773_   1513 AGATCCTTACATCACAATATGGATTCATAAAACAACCCAAAATGAGTCAT 1562
                         i  i  i   v     vi  --  v  v   vi   i       ii   ?
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCAT--ATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_24331773_   1563 AGACA-AAATGTAAGAGTTAAAAGTATAAAACTTTTAGAAGAAAACAGAC 1611
                             v-           i     v         i             v v
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_24331773_   1612 GAGAAAATCTTCATGACAGTTTGTTTGGCAAAAAGTTTTTACCTATGATG 1661
                          ? v        i    vv vv   v     viiv  i   vv     ii
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_24331773_   1662 CCAAAAGACTGATCCA-GAAATAGAAGTTTGATGAATTGGACTTCTGCAA 1710
                                vvii v v -i   v i  iv v   i           vv   
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_24331773_   1711 AATTAAGAACTATTTTCCTTCAAAAGACACCATTAGGGAAATGAAAAGAC 1760
                               i    v  v v       i     i  i i i  i         
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_24331773_   1761 AAGAC-CAGACTG--------TCTTTTTGGCAAATCATATATCTTATGAA 1801
                           vv -    v  -------- v   ---               v  i i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTT---GCAAATCATATATCTGATAAG 747

  chr20_24331773_   1802 GGATTTTATATCCAGTATATATAAGGAACTCTTACAACTCATTTCTAAGA 1851
                            i  -i       v        i                v vv   i 
  L1M4_orf2#LINE/    748 GGACTT-GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_24331773_   1852 GAACAAACAACCCAAT--AAAAATGGACAAAATGTTTCAACAGAC--TTC 1897
                         ii     i        --        i    ivi   v  i    --   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_24331773_   1898 ACCAGAGAAGATGCAGGAATGGCCAAGAAGCACAAGGAAAGATTCCTACC 1947
                         v   i       ii vi         v       v i      v ii v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_24331773_   1948 ATCATTAGTCAC 1959
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (103 / 84)
Gap_init rate = 0.01 (13 / 906), avg. gap size = 3.31 (43 / 13)  


4119 19.66 3.41 0.23  chr20_24466992_24470148.rev     1786  2665 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24466992_   1786 TGGGAAGACATTCCATATTCATGCACTGGGAACCTTAACATTGCTAGGAT 1835
                            i    i  i    i      v i   i iv     i    i  i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24466992_   1836 GTCAGTACTACCCAAAGTTATCTATAGATTCAGTGCGATCAGTAGCAAAA 1885
                          v  i    v      v v     i       ii  i   vv  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_24466992_   1886 TCCCAGTAATGTTGTCTGCAGAAACAGAAAAACCCATTCTAACATTCATA 1935
                               iviiv  v i        iv  v  i iv  i    v       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_24466992_   1936 TGGAATCTCAAGGAGCTCAG----GCTGGA-----CTT--------AGAA 1968
                              viv     ii i   ----  iii -----   --------    
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_24466992_   1969 CAAAGTAGGAGTACTCACACCTCCTGATTTTAAGACTTACTACAATGGCA 2018
                               v    v        i   ii    i  i           v vi 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_24466992_   2019 CTAGAATCAAAACAGTGTGATA-TGGCATAAATACACACATATAGACCAA 2067
                          viv      i        i  -        iv i v         i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_24466992_   2068 GTGAATAAAATAGAGAGCCCAGAAATAAACCCTTGCTTATACAATCAAAT 2117
                         vv     i   v     i              v i v v  iii    v 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_24466992_   2118 GATTTTTAACAAGGGTGCCAACACCATTCAATAGGGAAAGGACATTTTTT 2167
                               ii             v          i       i i v i   
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_24466992_   2168 TTCAACAAATGGTGCTAAAA-AATTGGATATCCACATGCAAAAGAATGAA 2216
                          -              iii -  i      ?                   
  L1M4_orf2#LINE/    401 T-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_24466992_   2217 GTTGAACCCTTACCTAACACCATATTCAAAAACCAATCCCAAATAAATCA 2266
                             i    i     v         v      ii  ii v    ii    
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_24466992_   2267 ATCACCTAAATGTAAAATCTAAAACCATAAAACTCTTAGAAGAAAACA-G 2315
                         ?vv            i v       i                      -i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_24466992_   2316 GGCA-AAAGCTTCATGACATTGGATTTGTCAATGATTTCTTGGATGTGAC 2364
                           ?i-   v    i    v    i  v v     i      i   i    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_24466992_   2365 ACCAAAGGCAGAGGCAACAAAAGAAAAAACA----AGTTGGACTTCATAA 2410
                               i   v i                i ---- i           v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_24466992_   2411 CAATTTAGATATTTTTGTGCATCAATAGACAATATCAACAGAGTAAGAAA 2460
                         v    v i - i        v    vi    v      v i   i i  i
  L1M4_orf2#LINE/    650 AAATTAAAA-ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_24466992_   2461 GTAAGCCACAGAATGGGAGAAAACATTTGCAAATCATATATCTAATAAGG 2510
                         ii  v                  i                   i      
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_24466992_   2511 AATTAATACCCAAGATATATAGAGAATGGTTAAAACTCAACAACAAAAA- 2559
                         i i vi  i   ii       i    ivv   v       i  i     -
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_24466992_   2560 ----ATAATCTGATTCAAAAACTGGCAAAGGTCTTGAATAGAAATTTCTC 2605
                         ----    i ii   ?     iv        vi         v       
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_24466992_   2606 CAAAGAAGATATACAGATGGCCAATAAGCCCAGGAAAAGATGCTCAACAT 2655
                                        i             v  v                 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_24466992_   2656 CACTAATAAT 2665
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.68 (106 / 63)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.91 (32 / 11)  


3119 26.82 1.10 0.88  chr20_24481197_24487006.rev     4413  5318 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24481197_   4413 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAAACAATATCGTGAAAAT 4462
                              ii i  i     i      i v      vvi     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24481197_   4463 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGGCATCTCCATCAAGC 4512
                            v     v     iv i  i  i        i vv   i i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_24481197_   4513 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 4560
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr20_24481197_   4561 ATATGAACCAA---AAAAGAGCCCGCATTGCCAAGTCAATCCTAAGCCA- 4606
                              i --  ---  ii  v  v v  v     iv     i i ivv -
  L1M4_orf2#LINE/    148 ATATGGA--AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_24481197_   4607 AAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAA 4656
                                   i      vv       v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_24481197_   4657 GGCTACAGTAACCAAAACAGCATGGTCCTGGTACCAAATCAGAGATATAG 4706
                         i          i   i    ii    v    i iv iivi   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_24481197_   4707 ATGAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACA 4754
                           v       i    i--    i  --        vv   i i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr20_24481197_   4755 ACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAGGATT 4804
                         iii vi    i  i     ivv  vv  i v  vv          i  v 
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_24481197_   4805 --TCCTATTTAATAACTGGTGCTGGGAAAACTGGCTAGCCATATGTAGAA 4852
                         --  i -  i  i  v           v      v  ?   i   i i  
  L1M4_orf2#LINE/    394 AGTCTT-TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_24481197_   4853 AGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGA 4902
                         iiv    ii    i    v   i     v              i    i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_24481197_   4903 TGGATTAAGGACTTACATGTTAGACCTAAAACCATAAAAACCCTAGAAGA 4952
                              i ?i   i  v    v   v       i      vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_24481197_   4953 AAACCTAGGCATTACCATTCAGGACACAGGCATGGGCAAGGACTTCATGT 5002
                             v    ?i v viv   iv   viv  vv i     v ii   v iv
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr20_24481197_   5003 CTAAAACACCAAAAGCAATGGCAACAAAATCCAAAATTGACAAATGGGAT 5052
                         v  vi            vvi         vvv     v  i    v   i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr20_24481197_   5053 CTCATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGT 5102
                         i    i   v v  i i   i  ii vv    i  v    i  vv i   
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr20_24481197_   5103 GAACAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTGCTCATCTG 5152
                            v  i     i   i             v  i    viiiivi     
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_24481197_   5153 ACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAG 5202
                          i  i  i  vi          v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_24481197_   5203 AAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACA 5252
                              i     i     v  i?    i     i     iv    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_24481197_   5253 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCT 5302
                         i     v        i  vi viii     v  i          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_24481197_   5303 CACCATCACTGGCCAT 5318
                           v     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (141 / 98)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


2731 25.85 1.85 2.84  chr20_24773315_24779102.rev     4380  5296 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24773315_   4380 TGGAAAAGCATCCCATCCTCATGAGTAGGAAGAATCAACATTGTGAAAAT 4429
                               iii       vi     ii v      v i  i     v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24773315_   4430 GGTCATATCGCCCAAAGTAATTTATAGATTCAATGCTAGTCC--ATCAAA 4477
                           iv   iiv      v i  i  i        i  - i   --      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGC-AATCCCTATCAAA 99

  chr20_24773315_   4478 CTACTA-CTGACATTCTTCACAGAATTAGAAAAAAACT-ACTTTAAATTT 4525
                         v v i -   v -  i  ii     v v  v  i--  - iii    v  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATT 146

  chr20_24773315_   4526 CATATGGAACCAAAAAAAGAGCTTGTATAACCAAGACAATCCTAAACAAA 4575
                                  viiv  ii-  v iv v   i    i      i i  v  i
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_24773315_   4576 AAGAACAAAGATGGAGGCATCACAGTATCTGACTTCAAACTATGCTACAA 4625
                                   v      vv     v vi ii i      viv i      
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_24773315_   4626 GTCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGACATATAT 4675
                         iv         i   i    ii         i iv ii i         v
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_24773315_   4676 ACCAATGGAACAGAACAAAGA-CCTATGAAATAATACCACACATCTACAA 4724
                          i        i    ivi   -i i -       vv   i    i  iii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCA-GAAATAAACCCATACATTTATGG 344

  chr20_24773315_   4725 CCATCTGATCTTCAACAAACCTGACAAAAACAAGCAACGGGGAAAGGATT 4774
                         i  vi    i   i    ivv  v   i v  vv   i        i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_24773315_   4775 CCCTATTTAATAAATGATGCTGGGAAAACTGGATAGTCATATGCAGGAAA 4824
                         vi  v  i  i     i        v         ?i  i     ii i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_24773315_   4825 CTGAAACTGGACCCGTTCCTTACACTTTATACAAAAATTAACTCAAGATA 4874
                         v    ii       v v   i    iv                   i  i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_24773315_   4875 GATTAAAGACTTAAATGTAAAACCTAAAACCATAAAAACCCTAGAATAAA 4924
                            i ?    i         i v       i      vi i     v   
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_24773315_   4925 ACCTGGGCAATACCACTCAGGATGCCCATTCAGGATGTAGGCATGGGCAA 4974
                           v i  ?i-  -- v  ----------   iv  iv v  vv i     
  L1M4_orf2#LINE/    545 ACATAGGNG-TA--AATC----------TTCGTGACCTTGGGTTAGGCAA 581

  chr20_24773315_   4975 AGACTTCATCACAAA-AACACCAAAAGCAACTGCAACAAAAGCCAAAATT 5023
                         v ii   - i v v -i            vvv          vv     v
  L1M4_orf2#LINE/    582 TGGTTTC-TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATA 630

  chr20_24773315_   5024 AACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAAC 5073
                         i i    v   ii v  i   v v  i i   i  iiivv    i  v  
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr20_24773315_   5074 TGTCATCAGAGTGAACAGACAACCTACAGAATGGGAGAAAAGTTTTGCAA 5123
                          i   vv i      v        i                vv       
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr20_24773315_   5124 TCTACCCATCTGACAAAGGTCTAATATTCAGAATCTACAAGGAACTTAAA 5173
                         vii ivi      i  i  v  vi   i      v  i  i     ivv 
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr20_24773315_   5174 CAAATTTACAAGAAAAAACCAG----CCCCATCAAAAAATGGGCAATGGA 5219
                            v iv i  v     iv  i----   v  i?            v   
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr20_24773315_   5220 TATGAACAGACACT-CTCAAAAGAAGACATTTTATGCA----GCCAAAAA 5264
                          v    i     i -   v        -----   i  ----     v  
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGA-----TATACAAATGGCCAATAA 875

  chr20_24773315_   5265 --ACATGAACAAAGACTCCAACATCACTGATCAT 5296
                         --       v i vi   -       ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTC-AACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (136 / 97)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.15 (43 / 20)  


3460 20.86 1.72 4.30  chr20_24815013_24817484     1051  1980 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_24815013_   1051 GGAAGACACTCC-TGATTATAGATTGGGATACCTAATATTGCTGAAATGT 1099
                          i    i ii  -  v i  i      i v  i        i i i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_24815013_   1100 CAATATTAGGCAAAGAAAATCTACATATTTAATGCAGTCCCTATCAAAAT 1149
                              i vvv    vvi -      v   i  i   i             
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGA-TCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_24815013_   1150 TTCAATGATGTGTTTTAGAGAAATTTTTAAAAACCCATTCTGAAATTTAT 1199
                         ii  iiviiv v    iv       v-- v  i iv  i  i     i  
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCAT 149

  chr20_24815013_   1200 ACTGAATAT-CATGAAACCCTAAATTGTCAAGAAAATTCTGAAGTTGGAG 1248
                          -  i v  -  v ii    vi   v i   i v   ii    ivv i  
  L1M4_orf2#LINE/    150 A-TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_24815013_   1249 AATCAAATTATATCTATCTGATAAGGAATTGTTATCCAGAATACATAGAG 1298
                           iv  i  i------------i    v -------  v v v vi ---
  L1M4_orf2#LINE/    199 AACAAAGTTG------------GAGGACT-------CACACTTCCCA--- 226

  chr20_24815013_   1299 AATTCCTAAAACTCAATGACAAAA----AACAAACAACCCAATTTAAAAA 1344
                         -   i -      i v -     i---- ii  v   vv  i v iiv v
  L1M4_orf2#LINE/    227 -ATTTC-AAAACTTACT-ACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr20_24815013_   1345 TGGGCA----GACAGACATCTAGACCAATGAAATAGACTAGGCAGGCCAA 1390
                            -  ----  i      v    i     i      v v iv  v   i
  L1M4_orf2#LINE/    274 TGG-CATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr20_24815013_   1391 AAATAAACCCTCACAATAATGTCCAAATAATTCTCAACAAAGGTGCCAAG 1440
                                   vi   v v   vi   v i   i  i    i         
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr20_24815013_   1441 ACCATTCAGTAGAAAAAGATC--TCTTTTCAACAAATGG-GCTGAGCAAA 1487
                                 i i ii     vi--                -    i vv  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr20_24815013_   1488 CTGGATTTCCACATGCAAAATGATAAAGTTAGACTCTTACCTAATACCAT 1537
                               v?            vi  i     i   i i     v i     
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr20_24815013_   1538 ATACAAAGATTAACTCAACAGGGATCAAAGATCTAAATGTAAGAGGTAAA 1587
                                i          v v      ?   i             v    
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr20_24815013_   1588 ACTATGAAACTCTTACAAGAAAA-ATAGGGG-GAATCTTCATGAAAGTGG 1635
                              i         v       -     ? -i       i   vvv   
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr20_24815013_   1636 ATTTGGCAGTGTTTTCTTAGATATGACACCAAAGGTGCAGGCAACAAAAG 1685
                         i  v    i  v                     i ii  i          
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_24815013_   1686 AAAAAAAAGTAGACAAATTAGACTTTATTTTGTAAAAATTTAAAAATTTT 1735
                               ---    i     i     i  i-----      v    v    
  L1M4_orf2#LINE/    623 AAAAAA---TAGATAAATTGGACTTCATC-----AAAATTAAAAACTTTT 664

  chr20_24815013_   1736 GTGCATTAAAAGACACTATCAACAAAGTAAGAGGGCAATCCATAGAATGG 1785
                             v i   i           v     i i i i   i   i       
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr20_24815013_   1786 GAGAAATTATTTGCAAATTATATCTATCTGATAAGGGATTGTTATCCAGA 1835
                               v           i    --             i vv        
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATAT--ATCTGATAAGGGACTTGTATCCAGA 762

  chr20_24815013_   1836 ATACATAGAGAATTCCTAAAACTCAATGACGAAAA-ACAAACAACCCAAT 1884
                            i   i    i  i  v        i ii    -     i        
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr20_24815013_   1885 TTAAAAATGGGCAAAGAACTTTAATAGACATTTATCTAAAGAAGATGTAA 1934
                          ?              i i  v           v  i         i  v
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr20_24815013_   1935 AAATGATCAATAAGCAGACGGAAAGATGTTCAATATCACTATTAGG 1980
                              ii         v i i       i    i    ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (117 / 73)
Gap_init rate = 0.02 (21 / 906), avg. gap size = 2.67 (56 / 21)  


 937 29.96 13.36 2.50  chr20_24817621_24820065     1153  1953 (492)    L1M4_orf2#LINE/L1       21   908 (0)  

  chr20_24817621_   1153 ATGGATAGGAGGACTTGATATC---ACAATGTTAGTCCTTCACAACC--A 1197
                               v   i     i    i--- vi   vi i v  i v   vi-- 
  L1M4_orf2#LINE/     21 ATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGA 70

  chr20_24817621_   1198 TCAGTGGATTTAATGTAATCCC-ATCAAAATCTTCATAAGATTTTTTTTT 1246
                           viii    i  i i      -         i-  vvv vi      vi
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCC-CAGCTGCCTTTTTTGC 119

  chr20_24817621_   1247 GGAAATTGACACGTTGGTTCTAAAATGCACGTGGAGAGTCAAAGGCCTTA 1296
                         i          v i  i i       v  ii    i vv   i  v ii 
  L1M4_orf2#LINE/    120 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 169

  chr20_24817621_   1297 GCAAAGCCCACACCTACCTGAGGAGGGAAAGTCCAGG--GGAAGACTTGC 1344
                          v v    v v  vvv i   ii i i i i- v i --   i    ii 
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGAAAAAGAAGAA-CAAAGTTGGAGGACTCAC 218

  chr20_24817621_   1345 ----CCTACTT--GAGACTTGCCCTACAACTCAATATAA-AACCAA-ATA 1386
                         ----  i v  --i i    i --     vv --  i i-  i   - i 
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTAC--TACAAAGC--TACAGTAATCAAGACA 264

  chr20_24817621_   1387 AT-TCACACTGAGATAAAGAGTGGGCA---AGAACA---GAACAGAATGC 1429
                         i - vii    iv    i  - i i  ---   v  ---   i     vv
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGA-TAGACATATAGATCAATGGAATAGAATTG 313

  chr20_24817621_   1430 AGAGTCCAGAAACAGACCC------------------------CGA---- 1451
                                     i i    ------------------------   ----
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr20_24817621_   1452 -GTGCACGCAACCTAGTGTAA-GGCAAAGGCAGAGC---TTCAGACCAGT 1496
                         -    - ivi   --i vi  -  vi  i v v  i---    -  v i 
  L1M4_orf2#LINE/    364 GGTGC-CAAGACC--ATTCAATGGGGAAAGAATAGTCTTTTCA-ACAAAT 409

  chr20_24817621_   1497 GGAGA-GGGACA--TGCATGAGTGCCGTGGAAGAGAGTGAAAATGGGTCG 1543
                           v v-      --  v  - ?ivv i  v  i   i    iv   ii v
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGAT-AKCCACATGCAAAAGAATGAAGTTGGACCC 458

  chr20_24817621_   1544 CCAGCTC-TGCCATACACACAA-CCGATTCCGGCTGGAT-GGAGAC-TAA 1589
                          i v   -ii     i   v  -iii i  viiv     -i?    -   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr20_24817621_   1590 ATGCACATG-TAGCACCATGAAGACT-TTAGGAGCTAACACAAGAAAATA 1637
                            i viv -  iv  i  i  -   -    i  vv    i i ?iv v 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAA-ACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr20_24817621_   1638 TCGTCAGGACTCTATAGAAGAAAACGGTTCATT-----------CAA--- 1673
                           v  iv   ii ivivv  iv  i    iv  -----------   ---
  L1M4_orf2#LINE/    558 TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAG 607

  chr20_24817621_   1674 --CAAG--ACATGAGATTCGATACTGGTACATTTGCTTTTGTTAT--TTA 1717
                         --    --   vi   vvvi   -- i  v   v vi  ii i v--   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTCATCAAAATTA 655

  chr20_24817621_   1718 AAAA----TGT---TCAACAGATGCCAGTCTACAGAGATTGGAAAGATAA 1760
                             ----   ---    vi  ii i -  - -   i v  i     i  
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTA-TC-A-AGAAAGTGAAAAGACAA 702

  chr20_24817621_   1761 GTCAAACACTAGGAGAA--TATTTGCAAGGTATGTTTCTTAAAAGAGATT 1808
                         vi  v v v i      --         ivi  i v   v v   i  i 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr20_24817621_   1809 TTGAAGCCACAATATATGCAGATCTCTTTAAA---AATA-TAAAAATTAC 1854
                          - v v   v       iv   v     vv  ---    -      v-  
  L1M4_orf2#LINE/    753 T-GTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG-AC 800

  chr20_24817621_   1855 AAACAATCTAATGGGAAAACA--CATAG-ATTTG------CATTTCACTG 1895
                            i  i i   v?i    ii--  v  -     ------      v ii
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_24817621_   1896 AAGACAAACCCCAAATGGTCAGTAAACAGATGAAAAGGTGCTTAACTTCA 1945
                             vi vviv       i  i   i  v        i    i   v   
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr20_24817621_   1946 TTTCTAAT 1953
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.36 (136 / 100)
Gap_init rate = 0.06 (51 / 888), avg. gap size = 2.49 (127 / 51)  


3205 27.42 0.33 0.33  chr20_24828742_24835008     4868  5775 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24828742_   4868 TGGAAGAACATTCTATGCTCATGGGTACGAAGAATCAATATCATGAAAAT 4917
                              ii i  i i   i      i vv     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24828742_   4918 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGA 4967
                            v     v     iv i  i           i  v     i     i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_24828742_   4968 TACCAAA-GCCTTTCTTCACAGAATTGGAAAAAACGACTTTAAAGTTCAT 5016
                          v   iv-      i  -i     v v  v  ivi  iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_24828742_   5017 ATGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAGA 5066
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_24828742_   5067 ACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATGCTACAAGGCT 5116
                               i      vv       v  ii i      viv i      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_24828742_   5117 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCA 5166
                                i   i    ii         i iv ii i   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_24828742_   5167 ATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACTA 5214
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr20_24828742_   5215 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAACGATTCCC 5264
                         vi    i  i     ivv  vv  i v  vv           vi  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_24828742_   5265 TATTTAATAAATGGTTTTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 5314
                          v  i  i       vi     v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_24828742_   5315 AAACTGGATCCCTTCCTTACACCTTATACAAAAATCAGTTCAAGATGGAT 5364
                           ii    i    v   i     v           i ii    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_24828742_   5365 TGAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5414
                         ii?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_24828742_   5415 TAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5464
                             ?v v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_24828742_   5465 ACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAAT 5514
                                     vvi           v     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_24828742_   5515 TAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAATA 5564
                         i   v v  i i   i  ii vv    i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_24828742_   5565 GGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAA 5614
                          i     i   i             v  i    vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_24828742_   5615 GGTCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5664
                           v  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_24828742_   5665 AACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACCCTTCT 5714
                         i     i     v  i?    i     i     iv    i    vi    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_24828742_   5715 CAAAAGAAGACATTTATGCAGCCAAAAAACACCTGAAAAAATGCTCATCA 5764
                          v        i  vi viii     v  i   v      i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_24828742_   5765 TCACTGGCCAT 5775
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.38 (142 / 103)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.50 (6 / 4)  


3086 28.27 0.22 0.33  chr20_24849860_24856292     5033  5941 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24849860_   5033 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATGAATATCGTGAAAAT 5082
                              ii i  i     i      i v      v v     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24849860_   5083 GGCCATACTGCCCAAGGAAATTTATAGATTCAATGCCATCCCCATGAAGC 5132
                            v     v     ivvi  i  i        i  v     i  v  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_24849860_   5133 TAGCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAGAGTTCATA 5182
                          vv  iivi i  i  ii     v v  v  iv v iii  i i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_24849860_   5183 TTGAACCAGAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAGAA 5232
                          v   viiv  ii  v  viv  vi    iv     i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_24849860_   5233 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACGAGGCTA 5282
                              i      vv    i  v  ii i      viv      i i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_24849860_   5283 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5332
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_24849860_   5333 TGGAACAGAACGGAGCCCTCAGAAATAATGCCGCATATCTACAACCATCT 5382
                              i    iv   vvii         vv  ii i  i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_24849860_   5383 GATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAACGATTCCCTAT 5432
                            i  i     ivv  vv  i v  vv           vi  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_24849860_   5433 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAGGCTGAAA 5482
                          i  i              v      v  ?   i   i i   iv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_24849860_   5483 CTGGATCCCTTCCTTACATCTTATACAAAAATTAATTCAAGATGGATTAA 5532
                         i    i    v   i   i v              i    i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_24849860_   5533 AGACTTAAATTTTAGACCAAAAACCATAAAAACCCTAGAAGAAAACCTGG 5582
                             i     v v   v v     i      vi i           v i 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_24849860_   5583 GCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAAC 5631
                          ?i- v i -   iv   v v  vv i     v ii   v ivv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_24849860_   5632 ACCAAAAGC-CATGGCAACAGAAGCCAAAATTGACAAATGGGATGTAATT 5680
                                  -  -i      i   vv     v  i    v   iv v  i
  L1M4_orf2#LINE/    600 ACCAAAAGCACA-AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_24849860_   5681 AAACTAAAGAGCTTCTGGACAGCAAAAGAAACTACCATCAGAGTGAAAAG 5730
                            v v  i i   i  vi vv    i  v    i  vv i         
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_24849860_   5731 GCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 5780
                         i     i   i             v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_24849860_   5781 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAGGAAAAAA 5830
                          i  vi          v  i  v      vv    v iv i iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_24849860_   5831 ACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTC 5880
                              i     v  i?    i            v    i     i     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_24849860_   5881 AAAAGAAGACATTTATGCAGCCAAAAAACACGTGGAAAAAACGCTCATCA 5930
                         v        i  vi viii     v  i   i  -    i i     v  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATG-AAAAGATGCTCAACA 897

  chr20_24849860_   5931 TCACTGGCCAT 5941
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.36 (146 / 107)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.00 (5 / 5)  


3062 25.95 2.35 0.78  chr20_24872226_24877307     3697  4590 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24872226_   3697 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATGTTGTGAAAAT 3746
                               i i  i     i        v      v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24872226_   3747 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGATATCCCCCATCAAG 3796
                            v     v      v i  i  i       ii vv     i-     i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCT-ATCAAA 99

  chr20_24872226_   3797 CTATCATTGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 3844
                         v vi  vivi i  i  ii     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_24872226_   3845 ATAGGGAACCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAAAA 3894
                            v    viiv  ii  v  v v        i      i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_24872226_   3895 GAACAAAGCTGGAGGCATCATGCTATCTGACTTCAAACCATACTACAAGC 3944
                                 i      vv   ii  vi ii i      v v        iv
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_24872226_   3945 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 3994
                                  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_24872226_   3995 CAATGGAACAGAACAGA-AGCCCAGAAATAACACCACACATCAACAACCA 4043
                                 i    iv  -  i          vv   i    iv iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_24872226_   4044 CCTGATCTTTGACAAACCTGACTAAAACAACCAATGGGGAAAGGATTCCC 4093
                         vi    i  i     ivv  v v i v  vi            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_24872226_   4094 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATTTGCAGAAAACTG 4143
                          v  i  i        i     v      v  ?   iv    i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_24872226_   4144 AAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACTCAACATGGAT 4193
                           ii         v   i     v                   v      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_24872226_   4194 TAAGGACTTAA------GACCTAAAACCATAAAAACCCTAGAAGAAAACC 4237
                         i ?i   i   ------  v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_24872226_   4238 TAGGCAGTA--CCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 4285
                             ?-   --i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_24872226_   4286 AAACACCAAAAGGAATAGCAACAAAAGCCAAAATTGATAAATGGGACCTA 4335
                         vi          v vv           vv     v       v    i v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_24872226_   4336 ATTAAACTAATGAACTTCCACACAGCAAAAGAAACTGTCATCAGAGTGAA 4385
                           i   v v vi     iiiii vv    i  v   i   vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_24872226_   4386 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAA--TATATCCATTTGA 4433
                         v  i     i                 v       --i    --  i   
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chr20_24872226_   4434 CAAAGAGCTAATGTCGAGAATCTACAAGGAACTTAAACAATT-GACAAGA 4482
                         i  i ii  vi i  v     v  i  i     ivv    i -i i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_24872226_   4483 AAAAAACAA----CCCCATCAAAAATTGGGTGAAGGATATGAACAGACA- 4527
                             i    ----   v  i?    v    ii      v    i     -
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_24872226_   4528 --CTAAAAAGAAGACATTTATGCAGCCAAGAAACATATGAAAAAACGCTC 4575
                         --  vv        i  vi viii     v  i  i       i i    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_24872226_   4576 ATCATCACTGGTCAT 4590
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (135 / 93)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.00 (28 / 14)  


3298 23.00 1.73 3.67  chr20_24903038_24905589     1135  2060 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24903038_   1135 TGGAGAGATATTCCATGTTCATGGACAGGAATACTCAATATTGTCAAGAT 1184
                             i      i             iv    v   i        i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24903038_   1185 GTCAGTTTTTCCCAACCTTAATCTATAGATTCAATGCAATCCCAATCAAA 1234
                          v  i vi i     v-  i     i        i        v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_24903038_   1235 ATCCCAGCAAGTTATTTTGTAGATACAGACAAATGAATCCTAAAGTTCAT 1284
                                 vivi v     i   v iv     iivi        i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_24903038_   1285 ATGGAGAGGGCGAAGACTCAAAATATCCAATACAATATTGAAGGAAAAGA 1334
                              i v vviii   i  i    v    v     v     ii i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_24903038_   1335 ATAAAGTCAGAGGACTGAAACTACTCAACTTCAAGATTCTCTATAAAGCT 1384
                          i     ii       v v   v i   i     i i iv   i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_24903038_   1385 ACAGTAATCAAGACAATGTGGTATTAGCAAAAGAATAGAAAAATAAATCA 1434
                                        i       i i   v   i     v v   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_24903038_   1435 ATAGAACAGATAAAATTTTTAGCCCAGAGACAGACCCACATAAATACAAT 1484
                           i   ----  i    vvv  i     i i i     i i vv  iii 
  L1M4_orf2#LINE/    300 ATGGAA----TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_24903038_   1485 CAACTGATCTTTTGACAAAGGAGTAAAGGCAATGCATAATGGAGAAAAGA 1534
                            i    -   i     i  v iv   i v  v  --    i    ii 
  L1M4_orf2#LINE/    346 CAATTGAT-TTTCGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAGAA 392

  chr20_24903038_   1535 CAGTGTTTTCCACAAATGGTGCTGGAACAAATTTGTTTGCATCCACATGC 1584
                         i   v     v              i    --i  vv -- ?        
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAA--CTGGAT--AKCCACATGC 438

  chr20_24903038_   1585 AAACAAATAAATCTAGACACAAACCTTATACCCTTCACAAAAATGGAATT 1634
                            vi   i  vi i   v vv    i i   v vi        v-  i 
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT-AACT 487

  chr20_24903038_   1635 CAAAATGGATCATAGACCTAAATATAAAATACAAAAC----AAATTCCTA 1680
                                     ?          i   i vvi     ----   i  i  
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr20_24903038_   1681 GAACATAGGAGAAAATCTAGGTATGATGATGAATTTTTAGATATAACACC 1730
                            -------     iv    ?i i ------  i  ii---- i  - i
  L1M4_orf2#LINE/    538 GAA-------GAAAACATAGGNGTAA------ATCTTCG----TGAC-CT 569

  chr20_24903038_   1731 TAGGGTATGATGATGAATTTTTAGATATAAAACCAAGG---TGAGATACA 1777
                          i  v  - iii   iv  i        i v     ii---ii  vv   
  L1M4_orf2#LINE/    570 TGGGTTA-GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

  chr20_24903038_   1778 TGAAGAAATAATTAATAAGTGAAACTTCATTAAAATTAAAAACTCTTGCT 1827
                         -i      v   vi    i vii       i             i   iv
  L1M4_orf2#LINE/    619 -AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

  chr20_24903038_   1828 CTACAGAAGATACTGTCAAAAGAATGAGAAG-----CCACAGACTGG-AG 1871
                           v  i i  i   i    i i i   i   -----       v   -  
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr20_24903038_   1872 AAAATATTGGCAAACAACATGTCTGATAAAGAACTATTATCCAAAATACA 1921
                                 v     iv i  i        i i   vv      i    i 
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

  chr20_24903038_   1922 CAAACAACTCTTAAAACTCAACAATAAGAAAATGAACAACCCAATTACAA 1971
                         i   v        v       i     i  i ii  i         ?-  
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-AA 816

  chr20_24903038_   1972 AAATGGGCAAAAGGCCTGAACAGACACATCACCAA-GAAGATATACAGAT 2020
                                    i iii    i     iv  v    -           i  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr20_24903038_   2021 GGCAGGTAGGCATATGAA--GATATTCCACATCAAATATCAT 2060
                            vii  i   i     --   ii  v      ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.99 (139 / 70)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 2.50 (50 / 20)  


2941 12.75 2.33 24.12  chr20_24955309_24958424     1464  2624 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_24955309_   1464 TGGAAAGATATCCCATGTTTGTGGATT---------AATATTGTCAATAT 1504
                                            ii      ---------        i  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_24955309_   1505 GGCAATACCTTCCAATTTT-TCTACAGATTGAATGCAATC------AAAA 1547
                                 iii    v  v-          v  i      ------    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_24955309_   1548 TCCCAACATCTTTTTTTGCAGAAATGGAAAAGCTAATCCTAAAATTCCTA 1597
                              i vv i              v  v     i            v  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_24955309_   1598 TGAAAATACAAGAAAGCAAGAAGAGCCAAAACAATCTTGAAAAAAGAAGA 1647
                           i    i    ii v v    v                     -     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA-GAAGA 199

  chr20_24955309_   1648 ACAAAGTTGGGAGACTCACGCTTCCTGGTTTTAAAACTTAC---AAAGCT 1694
                                   ii       i     iii   i         ---      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_24955309_   1695 ACAGTG-TCAAAACAGTTTGATACTGAGATAATAATAGATACATAGGTAA 1743
                              i-    i     v  i     iv    vi     -----------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA----------- 288

  chr20_24955309_   1744 TCATATGGATAAATGGAATAGGATAGAGAGCCCAGAAATAATCCCTCACA 1793
                         -     i   v          i  v     i          v   vi   
  L1M4_orf2#LINE/    289 -CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr20_24955309_   1794 TATATGGTCAAATTATTTTCAACAAGAGTACCAAGTCCATTTAACAGGGA 1843
                          v         v v      i     i  i     v     i  ii    
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr20_24955309_   1844 AAAGAACAGCCTCTTTAGCAAATGGCGCTGGGACCACTGGATAGCCATAG 1893
                           -   i  i  i  i i       i        v        ?   i v
  L1M4_orf2#LINE/    388 AA-GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr20_24955309_   1894 GACAAAGAATGAAACTGGACCCTTACCTCACACCCTGTACAAAAATCAAC 1943
                          vv          ii       i           v i         i   
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr20_24955309_   1944 TCAAAATTAAAGATCTAAATGTAAAAAGGTAAAACTTAAATTCTTTGAAG 1993
                                ---i    --------- ?  -----  i     ---------
  L1M4_orf2#LINE/    487 TCAAAAT---GGATC---------AWAG-----ACCTAAAT--------- 510

  chr20_24955309_   1994 AAAACATACGAACAGGGAGGCCGAGGCGGGCGGATCACGAGGTCAAGAGA 2043
                         -----------------------------------------  -     -
  L1M4_orf2#LINE/    511 -----------------------------------------GT-AAGAG- 517

  chr20_24955309_   2044 TCGAGACCATCCTGGTCAACATGGTGAAATCCTGTTTCTACTAAAACTAC 2093
                         ----------------------------------------         i
  L1M4_orf2#LINE/    518 ----------------------------------------CTAAAACTAT 527

  chr20_24955309_   2094 AAAAATTAGCTCGATGCAGTGGCACGTGCCTGTAATCCCAGCTACTCGGG 2143
                             ----------------------------------------   ---
  L1M4_orf2#LINE/    528 AAAA----------------------------------------CTC--- 534

  chr20_24955309_   2144 AGGCTGAGGTAGGAGAATCACTTGAACCCAGGAGGCGGAGGTTGCAGTGA 2193
                         -----------------------------------------  -------
  L1M4_orf2#LINE/    535 -----------------------------------------TT------- 536

  chr20_24955309_   2194 GCTGAGATCATGCCCCTGCACTCCAGCCTGGCAACAGAGCGAGAATCCAT 2243
                         --------------------------------------------------
  L1M4_orf2#LINE/    537 -------------------------------------------------- 536

  chr20_24955309_   2244 CTCAAAAAGAAAAAAAAAAGAAAACATAGGAAAAAATCTTCACAGCATTA 2293
                         --------------- i             ?iv        iiii v  i
  L1M4_orf2#LINE/    537 ---------------AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTG 571

  chr20_24955309_   2294 GATTTGGCAATGTTTTCTCAAATAATACAGCAAAGACACAAGCAACAAAA 2343
                          i  v       v     i i   vv   v    ii              
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr20_24955309_   2344 TAAAAAATAGATAAATTAGACTCCATTAAAATTTAAAACTTTTATACACC 2393
                         v                i    i   i      v         i i vi 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr20_24955309_   2394 AAAGTTTACTACTGAGAAAGTGAAAAGACCACCCACAGAATGGGAGAA-- 2441
                             vvi    iii               v                  --
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr20_24955309_   2442 TATTTGCAAATCATATATCTGATAGAGGTCTAATATTCAGAATATATAAG 2491
                                                 ii  v  vi   i            i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr20_24955309_   2492 TAACT--TACATACTCAACAACAAAAAGACAAGCAAGC-AATTAAAATAT 2538
                         v    --    -      i  i          ii  v -    ?   v  
  L1M4_orf2#LINE/    772 GAACTCTTACA-ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr20_24955309_   2539 GGGCAAACAGCTTAAGTAGAC-TTTGTCCAGTGAAAACATACAAATGGCC 2587
                                viii  i i     -   v    iv   i i            
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr20_24955309_   2588 AACAAGTACAT-AAAAGATGTTCAATATTATTAGTCAT 2624
                           i   i    -        i    i  i ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.94 (95 / 49)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 13.35 (307 / 23)  


3220 23.72 4.43 1.36  chr20_25024195_25026557      991  1871 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_25024195_    991 TGGAGAGATATCC-ATGTTCATGAATATGAAGACTAAATATTGTTAAGAT 1039
                             i        -         i  vv       v              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25024195_   1040 GTCAATTCTTCCTAACTTAATCTATAGATTCAAAACTATCCCAATCAAAA 1089
                          v    v  i  i  v  i     i        vi v     v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25024195_   1090 TCCCAGCAAGTTGCTTTGTGGATATCAACGAAGTAATTCTAAAGTTTGTG 1139
                                vivi vi    ii  v  ii  i iv i  i     i  ii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_25024195_   1140 TGGGAAGGTAAAAGACTCATAAAAGCCAACACAGTTGCATTGGCTGAAAT 1189
                            i  v i  ii   i  v  v      v   i i---   ivvi i -
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATC---TTGAAAAAGA- 196

  chr20_25024195_   1190 AGAACAAGGCCAGAGGACTGACACTACCTAATTTCCAGCCTTGCTATAAA 1239
                                i iii       v     v  i      v iv   i   i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_25024195_   1240 GCTACAGTAATAAAGCCAAAATGGTATT--CATGAAAGAAGAGACACATA 1287
                                    v   v  ivi     i --   --   i v     i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATA 294

  chr20_25024195_   1288 GGTTAATGGAACAGAACAGAAAGCCTAGGAGTGGACCTACCTAAATATAT 1337
                          i i       i    iv  i  i i  i i ii   i --  v  v   
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA--TACATTTAT 342

  chr20_25024195_   1338 --TCAACTGATCTT-AACAA--------AGACAATTTACTGGAGACAGGA 1376
                         --    i    i  -i    --------    v   i v   i  v  i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr20_25024195_   1377 TAAGTTTTTCAGCAAATGATGTGGGAATAATTA-ACACCCACAGTCAAAA 1425
                           ivi      i      i  iv  i i  i i- i ?     vv     
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_25024195_   1426 AAATAACGTT-------------ACACCTTATCCAAAAAATAACTCAAGA 1462
                         i   i v   -------------     v   v      v        i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_25024195_   1463 TGAATCATAGACCTAAATGTAAAATGC-AAAACTATAAAACTCCTAGATG 1511
                           i    ?              i -  -               i    v 
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAG 541

  chr20_25024195_   1512 ATAATTTAGGAAGAAATCTAAATGATCTTGGATTTGGTGATGACTTTTTA 1561
                          v  iv    ?iv      vvi   i     i  v  ii   ii  i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_25024195_   1562 GATACAACCCCAAAAGTACAATCCATGGCAAAAATAATTGACG--TTAGA 1609
                             ii  v       i    v v iiiv i   v   v  ii--  i  
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_25024195_   1610 CTTTATTAAAATTAAAAATATCTGC---TCAGTGATACACATTGTTAAGA 1656
                            i  i           iv i  i---   iv i---   i i i    
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG---ACACTATCAAGA 688

  chr20_25024195_   1657 TAATGAAAAGACAAGACACAGACTGGGAAAAAATATTTGCAAATCACAGA 1706
                         v i           vv      v     i                 i v 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_25024195_   1707 TCTGTTAAAGGTCTTGTATTCAATATATAGAAAGAACTCTTAAAATTCAA 1756
                             v   i  v       i  iv     v            v  i    
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_25024195_   1757 CAAGAAAA---CAAGCGACCCAGTTTTTAAGTGGGCAAAAGATCTGAACA 1803
                         i  v    ---   iii     i  ?vv  i        i   i    i 
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr20_25024195_   1804 GACACTTATG-AAAGAAGATATCCAGATGGC-AACAATTATATGAAATGA 1851
                             i  v v-           v  i     -  i  vi i      v  
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr20_25024195_   1852 TGCTCAACATCATATGTCAT 1871
                                     ????????
  L1M4_orf2#LINE/    889 TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (130 / 75)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 2.68 (51 / 19)  


3248 26.11 0.88 0.66  chr20_25033383_25039792     5015  5918 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_25033383_   5015 GAAAAACATTTCATGCTCATGGATAGGAAGAATCAATATCGTGAAAATGA 5064
                             i i  ii    i        v      v i     i  v  i   i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_25033383_   5065 CCATACTGCCCAAGGTAATTTATAGATTCAATGCTATCCCCATCAAGCTA 5114
                          v     v     iv i  i  i        i  v     i     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_25033383_   5115 CCAATGACTTTCTTCACAGAA-TTGGAAAAAAGCT-ACTTTAAAGTTCAT 5162
                            iivi i  i  ii     -   --- v     - iii    i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCAT 149

  chr20_25033383_   5163 ATGGAACCAAAGAAGAGCCCGCATTGACAAGACAATCCTAAGCCAAAAGA 5212
                               viiv iii  v  v v  v v   i      i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_25033383_   5213 ACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCT 5262
                               i      vv    i  v  ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_25033383_   5263 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAAAGATATAGACCA 5312
                                i   i    ii         i iv ii i i v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_25033383_   5313 ATGGAACAGAAC--AGAGCCCTCAGAAATAA-TACATACATCCACAACCA 5359
                               i    i--    i  --        -iv       ii iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

  chr20_25033383_   5360 TCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCTC 5409
                         vi    i  i     ivv  v   i v  vvv           i  vv  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_25033383_   5410 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAAAATCCTG 5459
                          v  i  i              v      v  ?   i   i    vvv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_25033383_   5460 AAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGAT 5509
                           ii    i    v   i     v              i    i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_25033383_   5510 TAAAGACTTAAATGTTAGACCTAAAACTATAAAAACCCTAGAAGAAAACC 5559
                         i ?    i       v   v              vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_25033383_   5560 TAGGCA-ATACCATTCAGGACATAAGCATGGGCAAGGACTTCATGTCTAA 5608
                             ?i- v i -   iv   v vi vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_25033383_   5609 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGAGATCTAA 5658
                         i            vvi          vv     v  i    vi  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_25033383_   5659 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5708
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_25033383_   5709 AGGCAACCTACAGAATGGGAGAAAATTTTTGTAATCTACCCATCTGACAA 5758
                           i     i                 v    i  vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_25033383_   5759 AGGGCTAATATCCAGAATCTACAAAGAACTTAAACTAATTTACAAGAAAA 5808
                         i  i  vi          v  i        ivv  v v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_25033383_   5809 AATCAAACAACCCCATCAAAAAGTGGGCAAAGGCTATGAACAGACACTTC 5858
                          iv    i     v  i?    i          v v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_25033383_   5859 TCAAAAGAAGACATTTATGCAGCCAACAG--ACATGAAAAAATGCTCATC 5906
                           v        i  vi viii     i i--         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_25033383_   5907 ATCACTGGCCAT 5918
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (137 / 95)
Gap_init rate = 0.01 (9 / 906), avg. gap size = 1.56 (14 / 9)  

 549 21.10 0.00 0.00  chr20_25033383_25039792     6302  6410 (0)  C L1M4_orf2#LINE/L1   (354)   554   446  

C chr20_25033383_   6410 TGAAACTGGATCCCTTCCTTACACCTTACACAAAAATTAATTCAAGATGG 6361
                             ii    i    v   i     v  i           i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

C chr20_25033383_   6360 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 6311
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

C chr20_25033383_   6310 CCTGGGCAT 6302
                          v i  ?i 
  L1M4_orf2#LINE/    546 CATAGGNGT 554

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.00 (0 / 0)  


3941 19.08 2.90 1.56  chr20_25050777_25053204     1041  1936 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_25050777_   1041 TAGAAAGACACCCAGTGTTTATGGCTTGAAAGACTTAATATTGTCAGGAT 1090
                          i      i i  vi    i    v   i               i i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25050777_   1091 TTCCATACTACCCAAAGTGATTGACAAATTAAATGCAATCCCTATCAAAA 1140
                         vv v     v      v    iv   i   v  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25050777_   1141 TTCCAATGACATTTATGGCAGAAATTTTAAAAATTCATCCTAAAATTTAT 1190
                          i   iivi v   v v         v- v  ii v           i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCAT 149

  chr20_25050777_   1191 AATGGAATCTCAAGGGACCTGGAATAGCCAAGACAATCTTGAAAAAGAA- 1239
                          -     viv         ii          i                 -
  L1M4_orf2#LINE/    150 A-TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_25050777_   1240 --TAAAGTTGGAGG--CCACA--TCCCAATTTCAAA-CTTACTGCAAAGC 1282
                         --i           --i    --             -      i      
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_25050777_   1283 TACACTAATCAAAACAATGTGAAACTGGTGTAAAGACAGACATAGAAACC 1332
                             v       i   i    iv     ii   i  i       v i i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_25050777_   1333 AATGTAATAGAATAGAGAATCCAGAAATAATTTCTTGTACACATGGTGGA 1382
                             v        v    i           vii v ii ivi     vi 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_25050777_   1383 ATGATTTTTGACAAGTGTGCCAAGAACATTCAATGGGGAAAAGACAAACT 1432
                         v       i      v         v               ii i iv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_25050777_   1433 TTTCAACAAATGGTGTTGAGAAAACTGAATATCCACAAGCAAAAGATATG 1482
                                        i  i  v     i   ?     v        -   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA-ATG 447

  chr20_25050777_   1483 CAA------CATTACCTTACACCATACGTAAAAATTAACTTGAAATGGAT 1526
                         v i------ vi     i        iii           ii        
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_25050777_   1527 CAAAGACCTACATATAAGACCTAAAAC-ATAAAACTCTTAGAAGAAGATA 1575
                           ?       v  i     v       -                  i i 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_25050777_   1576 -AAGAGAAAGCCTTCATGACATCGGACTTAGCAACAATTTATTGGATATG 1624
                         - i ? v  ii    i    v i  ii vi    iii   v  i      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_25050777_   1625 ACATCAAAAGCACAGG----GAAAAGAAAAATAGGGAGATTGGATTACAT 1670
                            i          i ----i   ii        iv i      i v   
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_25050777_   1671 CAAACTGTAAAAA-TTTTAT-CCCCAAAGGACTCTGTCTAAACAGAGTGA 1718
                             v -      -    i - ii        v  i  --  v i     
  L1M4_orf2#LINE/    648 CAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATC--AAGAAAGTGA 694

  chr20_25050777_   1719 AAAGATAACCCATTGAATGGGAGAAAATATTTCTAAATTACATATCTGAT 1768
                              i      iv                  vi    i i         
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_25050777_   1769 AAGGGGTTAATGTCAAGATTATATTTTTTAAA--ACTCCTATATCTCAGC 1816
                              ii vi i  v   v     -----   --    i  i v    ii
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATAT-----AAAGAACTCTTACAACTCAAT 789

  chr20_25050777_   1817 AACAACAACAACAAATGCAAACCAGTTCAAAAGTGA-CAAAGGACTTGAA 1865
                           i  v  -i      --  v   i  ?    i  i-       i     
  L1M4_orf2#LINE/    790 AATAAAAA-GACAAAT--AACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_25050777_   1866 CAGACATTTCTCCAAAGA-GATATACAAATGGTCCATAAGCATCTGAAAA 1914
                         i                 -             i v       iv      
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_25050777_   1915 GATGCCAAAAATCACTAATCAT 1936
                              iv  v    ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.88 (109 / 58)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 1.90 (40 / 21)  


3956 19.60 6.30 0.35  chr20_25083566_25087541.rev     2628  3484 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_25083566_   2628 TGGGAAGCCACTTTGTGTTTGTGGATTGGGAGACGTAGAGTTGTTAGAAT 2677
                            i   vi iiiii    ii        i    v  ivi      ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25083566_   2678 GGCAGTGCTCCTGAAAGTGACCTACAGATGCATGGCAATGTCTTTCAAAA 2727
                             i i    iv   v   i        v  vv     vi  v      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25083566_   2728 TACCAATGGTCTTTTTTGCAGAAATGAAAAAGCTGATTCTAAAATTCATC 2777
                          v   iiv i               vi v        i           v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_25083566_   2778 TGGAATTAT--GAGACCCCAAACAGCCAAAACGATGTTGAAAAAAAA--A 2823
                              v ii-- i     vi  i         i  v        i  -- 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_25083566_   2824 TAAAGTTTGAAGACACACACTTTCCAATTTCAAAGCTTGACTACAAAGCT 2873
                         i      v  i   v       i           i   -           
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT-ACTACAAAGCT 249

  chr20_25083566_   2874 ACAGTAATCAAAGAATCATGGTTGTGGCATAAGGATGGAC--------CA 2915
                                    iiv vii    vv            i   --------  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_25083566_   2916 GTGAAATGGAACTGAGAGTCCAGAAATAAACCAATACATCTATGATCAAT 2965
                         i  i   i   i                    v      i    i     
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_25083566_   2966 TAATTTTCAACAAGGGTGCCAAGTTTATTAATTGGACAAA----AGTCTC 3011
                          i      i              vii   v v   iv   ----     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_25083566_   3012 TTCGACAAATAATTCTGGGGCAACTGTATATCCACATGTAAAAGAATGA- 3060
                            i      ii v     i      v   ?       i          -
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_25083566_   3061 -------CTATGCTGCATACTGTATACAAAGATTAACTCAAAGTGGATCA 3103
                         ------- iv i iv  i  ii        i           i       
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_25083566_   3104 AAGACCTAAACACAAGAGCTAAGACTGTAAAACTTTTAAGAGAAAAATGT 3153
                         ?         iii         i   i       i   ii      -ii 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA-CAT 548

  chr20_25083566_   3154 AGGGATAAATCTTCATAACTTTGAATTTGGCAATATAATCTTAGCTATGA 3203
                            ?i         i i  i   ii  v      ivvv      v     
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_25083566_   3204 CAT---------AGATGACAAAAGAAAAGCTAGATAAACTGCAACCCATC 3244
                           i--------- iiii           iv        i  v vii    
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_25083566_   3245 AAAATTAAAAACTTTTGTGCATCAAAGAACACTTTCAAGAA-GCGAAAAG 3293
                                             v      i     v       - i      
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_25083566_   3294 AAAATCTGCAGGATGAGAGAAAATATTTGCAAATTATATATGTAAGAAGG 3343
                          v  i ii   i   i                  i      v i v    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_25083566_   3344 G-CTTACTTTCCAGAACATAGAAATAACTCTCAGAACT------------ 3380
                          -   i- v       i   v   v      i v    ------------
  L1M4_orf2#LINE/    749 GACTTG-TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_25083566_   3381 ------TAACCCAATT-AAAAATGGTGAAAGGCCTTGAATAGACTTTTCT 3423
                         ------          -        vv     vi          v     
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_25083566_   3424 CCAAAGAAAACATACAAAGGTCCAACAAGGATATGAAAAGATGCTCAACA 3473
                                 i i       v v    i   v i                  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_25083566_   3474 TCATTAGACAT 3484
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.89 (108 / 57)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 4.38 (57 / 13)  


3125 26.05 1.44 0.78  chr20_25098643_25100807      772  1673 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_25098643_    772 TGGAAGAACATTCCACGCTCATGGATAGGAAGAAACAATATCATGAAAAT 821
                              ii i  i   i i        v      vvi     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25098643_    822 GGCCATACTGTCTGTCCAAAGTAATTTATAGACTCAATGATATCCCCATC 871
                            v     -- i--     v i  i  i   i    i vv     i   
  L1M4_orf2#LINE/     51 GGCAATACT--CC--CCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr20_25098643_    872 AAACTACCA-CTGACTTTCTTCACAGAATTAGAAAAAACT-ACTTTAAAT 919
                            v v   -   v    i  -i     v v  v  i-  - iii    v
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTT-GCAGAAATTGACAAG-CTGATCCTAAAA 144

  chr20_25098643_    920 TTCATATGGAACCAAAAAAGAGCCCTTATAGCCAAGAAAATCCTAAGCAA 969
                                    viiv  ii  v  vvv        i v    i i iv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_25098643_    970 AAAGAGCAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTGTACTACA 1019
                         i    i     i      vv    i  v  ii i      viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_25098643_   1020 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 1069
                          i          i   i    ii         i iv ii i   v     
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_25098643_   1070 AACCAATGGAACAGAACAGAGGCCTCAGAAATAATGCCACACATCTACAA 1119
                         i i        i    iv   ivii         vv   i    i  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_25098643_   1120 TCATCTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATT 1169
                            vi    i  i     ivv  v   i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_25098643_   1170 CCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAA 1219
                         vi  v  i  i        i     v      v  ?   i     i  i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_25098643_   1220 CTGAAACTGGACCCCTTCCTTATACCATATACAAAAATTAACTCAAGGTA 1269
                         v    ii         v   i i                       ii i
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_25098643_   1270 AATTAAAGACTTGAACATAAAACCTAAAACCATAAAAACCATAAAAGAAA 1319
                         i  i ?    i i  ii   i v       i      vi v  i      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_25098643_   1320 ACCTAGGTG-ATACCATTCAGGGCACAGGCATGGGCAAAGACTTC----- 1363
                           v    ? - v i -   iv i viv  vv i     v ii   -----
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_25098643_   1364 -ATGACACAAAAAGCATA-GCAACAAAAGCCAAAATTGATAAATGGCATC 1411
                         -       v       i -          vv     v       v v ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_25098643_   1412 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAATG 1461
                          v  i   v v  i i   i  ii vv    i  v       vv i i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_25098643_   1462 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGG 1511
                           v  i     i                 v       vii  vi     i
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_25098643_   1512 CAAAGGGCTAATATCCAGAATCTA-AAGGAACTTAAATAAATTGACAAGA 1560
                         i  i  i  vi          v  -  i     ivv i  v ii i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_25098643_   1561 AAAAAACAAACAACCTCATCAAAAAGTGGGAAAAGGATATGAACAGACAC 1610
                             i     i    iv  i?    i    v       v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_25098643_   1611 TTCTCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAAAAAGCTC 1658
                              v        i  vi viii     i  --         i v    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_25098643_   1659 ATCATCACTGGTCAT 1673
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (140 / 91)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


3138 26.64 1.33 0.55  chr20_25109725_25116120.rev     5004  5904 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_25109725_   5004 TGGAAGAACTTTCCATGCTCATGGATAGAAATAATCAATATAATGAAAAT 5053
                              ii iv i     i        v i  v v i     vi v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25109725_   5054 GGCTATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5103
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25109725_   5104 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 5148
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_25109725_   5149 TGGAACCAAAAAAGAGCCTGCATAGCCAAGAGAATACTAAGCAAAAAGAA 5198
                              viiv  ii  v  v v        i v   vi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_25109725_   5199 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAGGGCTA 5248
                              i      vv       v  ii i      viv       ii    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_25109725_   5249 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 5298
                               i   i    ii         i iv ii i   v           
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_25109725_   5299 TGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAGCCATAT 5348
                              i    iv   ivii         vv   i    i  ii i  vv 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_25109725_   5349 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAAGATTCTCTAT 5398
                            i  i     ivv  v   i v  vvv          ii  vv   v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_25109725_   5399 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 5448
                          i  i              v      v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_25109725_   5449 CTGGGTCCCTTCCTTACACCTTATACAAAAAATTAATTCAAGATGGATTA 5498
                         i   ii    v   i     v          -    i    i      i 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCA 499

  chr20_25109725_   5499 AAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTA 5548
                         ?    i       v   v       i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_25109725_   5549 GGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAAAA 5597
                           ?i- v i -   iv   v v  vv i     v ii   v iiv  vi 
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_25109725_   5598 CACCAAAAGCAATGACAACAAAAGCCAAAATTGACAAATGGGATCTAATT 5647
                                    vvii         vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_25109725_   5648 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATTATCAGAGTGAACAG 5697
                            v v  i i   i  ii vv    i  v     i vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_25109725_   5698 GCAACCTACAAAATGGGAGAAAATTTTTGTAATCTACCCATCTGACATAT 5747
                         i     i   i             v    i  vii ivi      i viv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_25109725_   5748 GGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAGAATAAA 5797
                          i  vi          v  i   v    ivv    v ---   v      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAAA 795

  chr20_25109725_   5798 AA--CAAA----CTTATCAAAAAGTGGGCAAAGGATATGAACAGACACTT 5841
                           --    ---- iv  i?    i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_25109725_   5842 CTCAAAAGAAGACATTTATGCAACCAACAGACACATGAAAAAATGCTCAT 5891
                            v        i  vi viiii    i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_25109725_   5892 CATCACTGGTCAT 5904
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (137 / 99)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.12 (17 / 8)  


3260 26.84 0.44 0.55  chr20_25258086_25264354     4869  5777 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_25258086_   4869 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4918
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25258086_   4919 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4968
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25258086_   4969 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5016
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_25258086_   5017 TACGGAACCAAAAAAGAGCCTGCATCGCCAAGTCAATCCTAAGCCAAAAG 5066
                           i    viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_25258086_   5067 AACAAAGCTGGAGGCATCACACTACCTGGTTTCAAACTATACTACAAGGC 5116
                                i      vv       v  iii       viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_25258086_   5117 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5166
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_25258086_   5167 AATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTGCAACT 5214
                                i    i--    i  --        vv  ii i  i iiiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_25258086_   5215 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5264
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_25258086_   5265 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5314
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_25258086_   5315 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5364
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_25258086_   5365 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5414
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_25258086_   5415 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5464
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_25258086_   5465 AACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5514
                         i            vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_25258086_   5515 TTTAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAT 5564
                          iv  v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_25258086_   5565 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5614
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_25258086_   5615 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5664
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_25258086_   5665 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5714
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_25258086_   5715 TCAAAAGAAGACAGTTATGTAGCCAAAAAAACACATGAAAAAATGCTCAC 5764
                           v        i vvi vi i     v  i-          i       v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAG-CACATGAAAAGATGCTCAA 895

  chr20_25258086_   5765 CATCACTGGCCAT 5777
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.50 (9 / 6)  


2035 24.91 5.96 0.36  chr20_25271279_25274836     1896  2449 (1109)    L1M4_orf2#LINE/L1        6   590 (318)  

  chr20_25271279_   1896 AGATATTCCATCTTCATGGACAGGAAGGCCCAATATTGTCAATATGTCAG 1945
                               i    v        iv     i ii        i  v   v  i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr20_25271279_   1946 TTCTTCCCAACTT----TATAGATTCAATATAATCCCAATCAGA-TCCCA 1990
                          v  i     v  ----  i        iii      v    i -     
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr20_25271279_   1991 GCAAGTTATTTCCCGGATATTGACAAACTGATCCTAAAGTTTATATGGAA 2040
                           vivi v   iv i  v        i           i  i        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr20_25271279_   2041 AGGCAAAAGACTCAGGATAG-----ACAGCATTAAAGGAGAAGAACAAAC 2085
                          v    ii   i   i    -----   iiv  i  ii           v
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr20_25271279_   2086 TTGGAGGACTGACACAAGCTGGCTTGAATACTTACAATAAAGCCACAGTA 2135
                                   v    vvv iiii  v  v      v i     i      
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr20_25271279_   2136 ATCAAGACAGTGGTGTACTGTCA--AAAATAC-CA-ACAGACCAA----- 2176
                                     vv      v  -- ii   v-  - i   i   -----
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr20_25271279_   2177 --------AGAGCCTAGAAATAGACCCACATAACTATAGTCGACTCATCT 2218
                         --------    i i       i     i i vi   i   i i v  i 
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr20_25271279_   2219 GTGACAAAGGAGCAAGGGCAATACAATGGAGCAAAGATGATCTTTTCCAC 2268
                         vi     i  v  v i i v  v      i v  ii  ii       v  
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAAC 405

  chr20_25271279_   2269 AAATGGTGCTGTAACAACTGTACATTCGTATGGAAAAAAATGAAAGTAGA 2318
                                    vi       v i ?i ii   v    i      iv i  
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGA 455

  chr20_25271279_   2319 CC------TGATACCCTTCACAAAAATAAAACTCAAAATGAGTCATAGAC 2362
                           ------ v i   v vi        v  -         ii   ?    
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAA-CTCAAAATGGATCAWAGAC 504

  chr20_25271279_   2363 CTAAATGTAAAAACAGAAAACTATAAAACTCCTAGGAGATAACAGAGAAA 2412
                                   i i -v               i   i   v    v  i?i
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGC-TAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr20_25271279_   2413 AAAATTTAGGTGAACTTGGGTATGACGAAGACTTTTT 2449
                         v    i vv    v       vv i i v ii  i  
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

Transitions / transversions = 1.55 (82 / 53)
Gap_init rate = 0.02 (10 / 585), avg. gap size = 3.50 (35 / 10)  

1111 24.22 2.17 0.93  chr20_25271279_25274836     2749  3070 (488)    L1M4_orf2#LINE/L1      583   908 (0)  

  chr20_25271279_   2749 GACTTCTTAGATACAAAACCACCAAGGTATGATCCATGAAAGAAATATTA 2798
                          ii          ii v    --  i i ii v v ii       v v  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCA--AAAGCACAAGCAACAAAAGAAAAAATA 630

  chr20_25271279_   2799 -ACAAGCTAGGTTTCATTAAAATTGAAATCTTCTGCTCTGTAAAAGACAA 2847
                         - i  ii i ii     i      i   v   i  iv  vi   i    v
  L1M4_orf2#LINE/    631 GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr20_25271279_   2848 TGTCAACAGAATGAGAAGATAAGCCACAGACTCGGAAAAACATATTAACA 2897
                          i    v i i   i    i  v       v v   i   -     vi  
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA-ATATTTGCA 729

  chr20_25271279_   2898 AA-AGTATATCTGATGAAAGACAGTTATACAAAATATACAAAGAACTCTT 2946
                           -vi          i ii   vvv   v  i      i           
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr20_25271279_   2947 AAAACT---TGATAAGAAAATAAATAACTGGATTTTAAAAGGAGCAAAGG 2993
                          v    --- i    i  i i       ivi   ?v    v i       
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr20_25271279_   2994 ACCTGAACAGACACCTCTCCAAAGAAGATACACAGATGGCAAGTAAGCAT 3043
                          ii    i     ii               i   i     v i      i
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr20_25271279_   3044 ATGAAAAGGTGTTCA-CAT-ATGTAATCA 3070
                                 i  i   -   - ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.21 (53 / 24)
Gap_init rate = 0.02 (7 / 326), avg. gap size = 1.43 (10 / 7)  


 651 19.77 12.99 0.00  chr20_25355695_25361434.rev     3331  3507 (2233)    L1M4_orf2#LINE/L1        1   200 (708)  

  chr20_25355695_   3331 TGGAAACACATCCCATGTTCATGGATTGGAAGATTTAATATT---AAGAT 3377
                               v i                        i        ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25355695_   3378 GTCAATGCACCCTAAGT-GACCTACA---------CAATCCCTACTATAA 3417
                          v    i v   i  i -  i     ---------         ii v  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25355695_   3418 TCCCAAAAGTGTCTTTTGGAGAAACAGAAAAACCCATCCCACAATCCATA 3467
                              ivv iv i     v     iv  v  i iv    i v   i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_25355695_   3468 TA-AAAT--------CTCA-AATAGTGAAAACAACCTTTAAAAAGAGGAA 3507
                          i-    -------- i  -     iv       i   v       i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

Transitions / transversions = 1.50 (21 / 14)
Gap_init rate = 0.03 (6 / 200), avg. gap size = 3.83 (23 / 6)  

 798 19.85 0.75 14.61  chr20_25355695_25361434.rev     3829  4095 (1645)    L1M4_orf2#LINE/L1      190   419 (489)  

  chr20_25355695_   3829 AGAGAGAGGAATGAAGGTGGAGGACCCAAAATCCCTAATTT--AAACTTA 3876
                          i i   i   ii   v        i  v v i  i     --       
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_25355695_   3877 CTGCAAAGCTACAACAATCGAAATACTACAGTTCTGGCATAAAGACAGAT 3926
                           i          ii    i i i v iii  v         i  i   i
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr20_25355695_   3927 GTATATATATATTAAAAAAACTTTTTTTACGACAGATGTACAGAACAATG 3976
                         i    -----------------------------   --------     
  L1M4_orf2#LINE/    290 ATATA-----------------------------GAT--------CAATG 302

  chr20_25355695_   3977 GAATAGGATAAAGAGATAAAAAATAAACCCTTGCCTACATAGTCAAATGA 4026
                               i  vi    viv i          v i v vi  i     v   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_25355695_   4027 TTTTTGACAAGAGTGTCAAAACCATTCACAATGGGGAAAGGGCAGTCTTA 4076
                             i      i   i   i        --          iii      v
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCA--ATGGGGAAAGAATAGTCTTT 400

  chr20_25355695_   4077 TTAAGAAATTATGCTTGGA 4095
                          i  v    vi    v   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGA 419

Transitions / transversions = 2.31 (37 / 16)
Gap_init rate = 0.02 (4 / 230), avg. gap size = 10.25 (41 / 4)  

 928 21.83 3.93 0.00  chr20_25355695_25361434.rev     4400  4628 (1112)    L1M4_orf2#LINE/L1      403   640 (268)  

  chr20_25355695_   4400 AAGAAATTATGCTTGGAAAGCTAGATTTCCACATGCAAAAAAATAAAGTT 4449
                           v    vi    v   v i  i   v?            i   i     
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr20_25355695_   4450 GGACCATCACCTAACACCATA--CAAAAATTAACTTGAAATGGATCAAAG 4497
                              vii    v        --            ii          ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr20_25355695_   4498 ACCGAAATGCAAATG-TAAAACAACATAATACTTAGAAGGAAATACAGGT 4546
                            v     i  iv -      v i v  iv        i   i i   ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr20_25355695_   4547 CAAAAGTTTTATGACATTGTATTTAGCAATGATTTCTGGGATATGACTCC 4596
                         vv   vi  ii    v   vi  vi      i     vi        v  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr20_25355695_   4597 TAAGGCACAACCAACAAAACAAAAAA------AATTGG 4628
                         v  i      v        v      ------      
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

Transitions / transversions = 1.04 (24 / 23)
Gap_init rate = 0.01 (3 / 238), avg. gap size = 3.00 (9 / 3)  

1019 15.57 2.87 5.74  chr20_25355695_25361434.rev     5005  5248 (492)    L1M4_orf2#LINE/L1      672   908 (0)  

  chr20_25355695_   5005 AAAAGACACTATCAACAGCATAAAAAGGCAACCCAGAGAATGGGAGAAAA 5054
                            i           v ivi i     i       v              
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr20_25355695_   5055 TATTTGCAAATCATATATCTGATAACAAATTAACATACTGAATACATAAA 5104
                                                  vii i vii  v v     i     
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr20_25355695_   5105 GGATTTCTAAATCTCCACAACAA-----CAAA--ACCCTATTTGAAAATG 5147
                          i i ii  v v   v i  i  -----    --    v   ?i      
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr20_25355695_   5148 GGCCCCATAAAGGGGGCCAATTATTTGAATAAACATTTCTCCAAAGAAGA 5197
                            -----     ---------         i                  
  L1M4_orf2#LINE/    822 GGC-----AAAGG---------ATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr20_25355695_   5198 CACAGGAATAGCTAATAAGCATATGAAAAGATGCTCAACATCACTAATCA 5247
                         i i vi   i  i        i                     ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr20_25355695_   5248 T 5248
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 2.08 (25 / 12)
Gap_init rate = 0.02 (4 / 237), avg. gap size = 5.25 (21 / 4)  


2378 26.91 9.33 0.96  chr20_25593651_25596484.rev     1507  2342 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_25593651_   1507 GAAAGACATGCCACGCTTAAGGAGCAAAAGAATTAATGTTGTTAAGATGA 1556
                               i  v   i i i v   viii    v     i           i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_25593651_   1557 CCATACTACCCAGAGCAATCTACAAATTTAATGCAATCCTTATCAAACTA 1606
                          v     v    i vii       i   i  i       i       v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_25593651_   1607 CCAATGACATTCTTCACAAAAATAGAAAAAATACTCCTAAAGTTTGTAAG 1656
                            iivi v  i  ii  i    v  v  iv iv       i  ii  v 
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_25593651_   1657 GAACCACAAAAAATCTCAAAATAGCCAAAGCAATGT-AAGCATAAAGAAC 1705
                            vii   iii i -  i          i    v -i iv vi      
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_25593651_   1706 AAAGTGGGAGG---CATCCTTTCTA--------------TATA------- 1731
                              v     ---  iv   i i --------------  i -------
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr20_25593651_   1732 -------------------TACT-------------------AAACCAAT 1743
                         -------------------    ------------------- i i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_25593651_   1744 G-AAGAGAATAAATAGCACAGAAAAACATTCATGTATTTACAGCCAACTG 1792
                          -  v     vi v  iv      v v ii   ii     ii i   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_25593651_   1793 ATTTTTAACA--GTCACCAGGAATATACATTGGGTAAAGGACA--CTGTC 1838
                              ii   -- vii   i  vi  v  v    v    i i --  v i
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_25593651_   1839 TAATAAATGGTACTAGGAAAACTGGACAGCCATATGCAGAAGAATAAAAC 1888
                         i  i       i  i   v       i ?   i     i      i  ii
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_25593651_   1889 TATACCCCTATCTTTTACCATATGCAAAAAAATCTGCTAAAAACAGATTA 1938
                          iv       i  ivi       i      -- ivi  v    ii   i 
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAA--TTAACTCAAAATGGATCA 499

  chr20_25593651_   1939 AAGACTTAG-TGTAGGACCTGAAATCATAAAACTGCTAGAAGCAAACATA 1987
                         ?    i  i-    i  v  i   ii        vi      v       
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_25593651_   1988 GGGA-AAATGCTTCAGGAA-TTGGTCTAGGCTAAGATTTTGTGACGGAGA 2035
                           ?i-    -    iv  v-    vi     v v i   iv iivviv  
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_25593651_   2036 CCTCAAAATCACAGCCAACAAAACCAAAAATTGACAAATGGGATTATATG 2085
                          vi     v    iv        vv      v  i    v   i vi  v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_25593651_   2086 AAACTAGAAAGCTTCTGCATAGCAAGTAAAAC----AACAGAGTGAAGAG 2131
                            v vi   i   i  iiivv   ivi v  ----  v i      i  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_25593651_   2132 ACAACATATAGAATAGAAGAAAATATTTGCAAACTATTCATCTTGTAAGG 2181
                              vi i     i i                ii  vi    vi     
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_25593651_   2182 GACTAATATACAGAATATACAAGGAACTCAAACAACTCGACAC--AAAAC 2229
                             vi   v         i  i      vv       i i v--    v
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_25593651_   2230 CCAAATAATCTAATTAAAAAGTGG-CAAGGGATCTGAATAGGCATGTCTC 2278
                         v       i i    ?    i   -   i    i       i   v    
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_25593651_   2279 AAAAGAAGACAGACATACAAATAGGCAACAAGTATATGGAAAAATGCTCA 2328
                         v        i ----       i v   i   i i   i   i       
  L1M4_orf2#LINE/    849 CAAAGAAGATA----TACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_25593651_   2329 ACCTCACTAATCAT 2342
                           v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.73 (140 / 81)
Gap_init rate = 0.02 (18 / 906), avg. gap size = 4.78 (86 / 18)  


1006 26.43 3.57 0.00  chr20_25605179_25608711     1840  2119 (1414)    L1M4_orf2#LINE/L1        1   290 (618)  

  chr20_25605179_   1840 TGAAAAGACATCTTATGTTCATGGA--GCAAAA--TAATACTGTTGAGAT 1885
                           i     i   ii           -- v  i --     i    i    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25605179_   1886 GACCATACTGCCCAAAGCAATCTACAGATTCACTGCAATACCTATTAAAA 1935
                          i v     v      vii             vi     v     i    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25605179_   1936 TACCAGTGATATTCTTTATAAAAATAGACAAAATACTCCTAGAATTCATA 1985
                          v    iviiv  i   ii i    v     iv iv     i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_25605179_   1986 AGGAACCA-AAAAGACCTCCAATAG-----GCAATAGTGAGCATAAAGTA 2029
                         v    vii-  ii    ivv     -----i    vv   iv vi   v 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_25605179_   2030 CAAAGTGGGAGGCATCATACTACCTCACTTCAAAATATAATACAAAGCTA 2079
                               v     vv   i   v  iv i       iv  v          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_25605179_   2080 GTGTCATCAAAGCAGCATGGTATTGGTCTAAAAATAGACA 2119
                         vv  v     ii   ii     i   iv   ii       
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

Transitions / transversions = 1.31 (42 / 32)
Gap_init rate = 0.01 (4 / 290), avg. gap size = 2.50 (10 / 4)  

1886 23.84 3.04 2.40  chr20_25605179_25608711     2417  3041 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr20_25605179_   2417 AATGAAATACACATAGACCAATAAAAGAGAATAGATAATCTACAAATAAA 2466
                           v  v v   i     i    ii  v     v  v i  i v       
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr20_25605179_   2467 TCCATATATTTATAGCCAACTGATTTTTGACAAAGGCACTAAAAACATAC 2516
                         i     i      i i   i       i     i  ii i  i v   v 
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTC 379

  chr20_25605179_   2517 CTTAGGGTAAGGACAGAATCTTCAATAAATGGTATTAGAAAAAGTGAATT 2566
                         vv i   v   i i  vv i     i       ii i i v  v  i  v
  L1M4_orf2#LINE/    380 AATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr20_25605179_   2567 CCAAAATGAGTAAGAATGAAGTTAGATGTTTGTTTCTCATAC--TATACA 2614
                         ? v v   viv            i  ivii ii--    i  --      
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTAC--CTCACACCATATACA 477

  chr20_25605179_   2615 AAAATAAACTCAAAATAGATTAAAGACTTAAACATGAGTTCCACAATTAT 2664
                              v          i   i ?    i    ii i  vv i v  i   
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr20_25605179_   2665 AAAACAACTT-GAAGAAA-CACAGGAG-AAATGCTTTAGGACACTGGCCT 2711
                              v-   -       -  i   ? -    -   iiv   vi   vi 
  L1M4_orf2#LINE/    528 AAAACT-CTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTT 575

  chr20_25605179_   2712 AAACTAGCCATA-TTTTATGGCTAAGACTTCAAAATCACAAGCAACAAAA 2760
                          i----  v  i-   iv i v  v   vi     v              
  L1M4_orf2#LINE/    576 AG----GCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr20_25605179_   2761 GCAAAAATACACACATGAGACTACATTAAACTAAAAACTAAAAAGCTTCT 2810
                          v       v i v  vi    v   i   ------ i      -   i 
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAA------ATTAAAAA-CTTTT 664

  chr20_25605179_   2811 GTACAGCAAAGGAAAGTATCAACA--GTGAAGATACAAAATGTAGAATGG 2858
                           i vv       v v      v --     i v    vviii       
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr20_25605179_   2859 GAGGAAATATCTGCAAAGTATTCATCTTACAAGGGACTAATATACAGAAT 2908
                            i      i      vi  vi    v i        vi   v      
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr20_25605179_   2909 ATACAA-GAAGTC--AAAA---AACAACAA-----CAAAAAATCCAACTA 2947
                            i  -   v  -- v  ---  i  i  -----    v  i    i ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr20_25605179_   2948 AAAAGTGGGAAAAGGATCTGAATAGACATTTCTCAAAATAAGACATACAA 2997
                             i    v       i                v   v    i      
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr20_25605179_   2998 ATGGGCAACAGGTATACGAAAAAATGCTCATCATCACCAATCAT 3041
                             v   i i i i i     i       v     ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.34 (83 / 62)
Gap_init rate = 0.03 (16 / 629), avg. gap size = 2.12 (34 / 16)  


2837 26.91 2.35 0.78  chr20_25629599_25636288.rev     5307  6198 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_25629599_   5307 GAAAAACATTCCATGCTTATGGATAGGAAGGATCAGTATCATGAAAATGG 5356
                             i i  i     i i      v     iv i i   ii v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_25629599_   5357 CCACACTGCCCAAAGTAATTTATAGATTCAATGCTATCCACATCAAGCTA 5406
                          v i   v      v i  i  i        i  v    vi     iv v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_25629599_   5407 CCA-CTGATTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAATTTCAT 5453
                            -   vi  i  ii     -   --- v  i  - iii    v     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTCAT 149

  chr20_25629599_   5454 ATGGAACCAAAAAAGAGCCCGTATAGCCAAGACAATCCTAAGAAAAAAGG 5503
                               viiv  ii  v  v v        i      i i i   i   i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_25629599_   5504 ACAAAG--GCA----TCACCCTATCTGACTTCAAAGTATACTACAATGCT 5547
                               -- v ----    v  vi ii i      iiv        v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_25629599_   5548 GCGGTAACAAAAACAGCATGGTACTGATACCAAAACAGAGAGATAGACCA 5597
                         i i    iv  i    ii        ii iv ii i   v v     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_25629599_   5598 ATGGAACAGAACAGAGGCCTCAGAAATAACACCACACATCTACAACCATC 5647
                               i    iv   ivii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_25629599_   5648 TGATCTTTGATAATCCTGACAAAAACAAGCAATGTAGAAAGAAT--TCCA 5695
                             i  i  i  vvv  v   i v  vv     vi        --  --
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-- 397

  chr20_25629599_   5696 TATTTAATAAATGGTGTTGGGAAAACTGGCTATCCATATGCAGAAAGCTA 5745
                          v  i  i        i     v      v  ?   i     i  iiv i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_25629599_   5746 AAACTGAATCCCTTCCTTACACCTTATACAAAAATTAACTCAGGTTGAAT 5795
                           ii  i i    v   i     v                  iiv  i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_25629599_   5796 TAAAGACTTAAACGTAAGACATAAAACCATAAAAACCCTAGAAGGAAACC 5845
                         i ?    i    i      vv      i      vi i      i    v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_25629599_   5846 TAGG--TAATACCATTCGGGACATAGGCATGGGCAAAGACTTCATGACTA 5893
                             --   - i -    v   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    548 TAGGNGTAA-ATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_25629599_   5894 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATAGGATCTA 5943
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_25629599_   5944 ATTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTATCATTAGAGTGAA 5993
                           i   v v  i i   i  ii vv    iv v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_25629599_   5994 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATATGACA 6043
                         v  i     i                 v       vii  vi  v   i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_25629599_   6044 AAGGGCTAATATGCAGAATCTACAAAGAAGGTAAACAAATTTACAA--AA 6091
                          i  i  vi   v      v  i      vvivv    v iv i  --  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_25629599_   6092 AATAAAAATAA---AA---AAAATTGGGTGAAGGATATGAACAGAAACTT 6135
                           v v      ---  ---    v    ii      v    i   v i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_25629599_   6136 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 6185
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_25629599_   6186 CATCACTGGTTAT 6198
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (140 / 98)
Gap_init rate = 0.02 (14 / 906), avg. gap size = 2.00 (28 / 14)  


3202 27.03 0.55 0.77  chr20_25637384_25645865.rev     1924  2833 (5649)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_25637384_   1924 TGGAAGAACATTCCATGCTCACGGGTAGGAAGAATCAATATCGTGAAAAT 1973
                              ii i  i     i   i  i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25637384_   1974 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 2023
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25637384_   2024 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 2071
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_25637384_   2072 TATGGAACCAAAAAAGAGCCCGCAAC-GCCAAGTCAGTCCTAAGCCAAAA 2120
                                viiv  ii  -   iv  i-     iv  i  i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA-CCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_25637384_   2121 GAACAAAGCTGGAGGCATCACACTACCTGACTTCACACTATACTACAAGG 2170
                                 i      vv       v  ii i    v viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_25637384_   2171 CTACAGTAACCAAAACAACATGGTACTGGGGTATCAAAACAGAGATATAG 2220
                                  i   i   iii         --i  v ii i   v      
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGG--CATAAGGATAGACATATAG 295

  chr20_25637384_   2221 ATCAATGGAACAGAAC--AGAGCCCTCAGAAATGACGCCGCATATCTACA 2268
                                   i    i--    i  --      i vv  ii i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr20_25637384_   2269 ACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCCATGGGGAAAGGAT 2318
                         iii vi    i  i     ivv  vv  i v  vv v          i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_25637384_   2319 TCCCTATTTAATAAATGGTGCTGGGGAAACTGGCTAGCCATATGTAGAAA 2368
                         vvi  v  i  i             iv      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_25637384_   2369 GCCGAAATTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 2418
                         ivi   i     i    v   i     v              i    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_25637384_   2419 GGATTAAAGACTTAAATGTTAGACTTAAAACCATAAAAACCCTAGAAGAA 2468
                             i ?    i       v   vi      i      vi i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_25637384_   2469 AACCTAGGCATTACCATTCAGGACATAGGCTTGGGAAAGGACTTCATGTC 2518
                            v    ?i v viv   iv   v v  v  i  v  v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_25637384_   2519 TAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATA 2568
                           vi            vvi           v     v  i    v   iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_25637384_   2569 TAATTAAACTAAAGAGCTTCTGCACAGCAACAGAAACTACCATCAGAGTG 2618
                          v  i   v v  i i   i  ii vv   vi  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_25637384_   2619 AACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAGCCTACTCATCTGA 2668
                           v  i     i   i             v      ivii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_25637384_   2669 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAATCAAATTTACAAGA 2718
                         i  i  i  vi          v  i  v      vvv   v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_25637384_   2719 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAC 2768
                             i     i     v  i?    i     i     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_25637384_   2769 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 2818
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_25637384_   2819 ACCATCACTGGCCAT 2833
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (146 / 96)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  

3077 28.13 0.89 0.33  chr20_25637384_25645865.rev     7088  7990 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_25637384_   7088 TGGAAAAACATTCCATGCTCATGGATAGGAGGAAC-AGTATTGTGAAAAT 7136
                               i i  i     i        v   i  vi- i      v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25637384_   7137 AACCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 7186
                         ii v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25637384_   7187 TACCAATGACTTCCTTCATAGAATTGAAAAAACCTACTTTAAAGTTCATA 7236
                          v   iivi i ii  iii    v vi v  i iv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_25637384_   7237 TGGAACCAAAAAAGAGCCCAAATTGCCAAGACAATCCTAAGCAAAAAGAA 7286
                              viiv  ii  v  vi   v     i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_25637384_   7287 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 7336
                              i      vv   ii  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_25637384_   7337 CAGTAACCAAAACAGCATGTTACTGGTACCAAAACAGAGAGATAGACCAA 7386
                               i   i    ii  v      i iv ii i   v v     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_25637384_   7387 TGGAGCAGAACGGAGGCCTCAGAAATAACACCACACATCTACAACCATCT 7436
                             ii    iv   ivii         vv   i    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_25637384_   7437 GATCTTTGATAATCCTGACAAAAACAAGAAATGGGGAAAGAATTCCCTAT 7486
                            i  i  i  vvv  v   i v  vvv              vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_25637384_   7487 TTAATAAATGCTGCTGGGAAAGCTGGCTAGCCATATGTAGAAAGCTGAAA 7536
                          i  i     v        v i    v  ?   i   i i  iiv    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_25637384_   7537 CTGGATCCCTTCCTTACACCGTATACAAAAATTAATTCAAGATGCACTAA 7586
                         i    i    v   i     i              i    i   v ii ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_25637384_   7587 AGATGTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 7636
                            iv           v       i      vi i           v   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_25637384_   7637 GCA-ATACCATTCAGGACACAGGCATGGGCAAGGACTTCATGACTAAAAC 7685
                          ?i- v i -   iv   viv  vv i     v ii   v iiv  vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_25637384_   7686 ACCAAAAGCAATGGCAATAAAAGCCAAAATTGACAAATGGGATCTAATGA 7735
                                   vvi    i     vv     v  i    v   ii v  v 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_25637384_   7736 AACTTAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGG 7785
                           v    i i   i  ii vv    i  v    i  vv i      v  i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_25637384_   7786 CAGCCTACAGAATTGGAGAAAAATTTTGCAA--TATAGCCATCTGACAAA 7833
                           i  i       v        vv       --i   --i      i  i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATA--TATCTGATAAG 747

  chr20_25637384_   7834 GGGCTAATATCCAGAATCTACAAATAACTTAAACAAATTTACAAGAAAAA 7883
                           i  vi          v  i   v    ivv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_25637384_   7884 ACCAA----CCCCATCAAAAAGTGGGCAAAGGATACGAACAGACACTTCT 7929
                         iv   ----   v  i?    i            vi   i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_25637384_   7930 CAAAAGAAGACATTTATGCAGTCAACAGACACATGAAAAAATGCTCATCA 7979
                          v        i  vi viii i   i ii          i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_25637384_   7980 TCACTGGTCAT 7990
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.55 (152 / 98)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


 242 24.32 4.05 0.00  chr20_25664725_25667120.rev      738   811 (1585)    L1M4_orf2#LINE/L1       16    92 (816)  

  chr20_25664725_    738 TGTTCATGGATTGGATAAATTAATATT---AAAACATTCATACTACTAAA 784
                                        vi v        ---  i iiviv     v iv  
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr20_25664725_    785 AGTGATATAAAGATTTAAAGCAATCTC 811
                          v    v  v     i  v      i 
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCC 92

Transitions / transversions = 0.80 (8 / 10)
Gap_init rate = 0.01 (1 / 77), avg. gap size = 3.00 (3 / 1)  

1991 27.00 4.13 3.23  chr20_25664725_25667120.rev     1119  1892 (504)    L1M4_orf2#LINE/L1       76   856 (52)  

  chr20_25664725_   1119 AAATTTAAAGCAATCTCCATCAAAATTAAAA-TATCATTTTC-CAGAAA- 1165
                          i   i  v      i i        ivv i- ii v    i-      -
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr20_25664725_   1166 -AATAAAAAATTTCTAAAGTTTGTAAGGAATTAGAAAAGACCCAAAATAA 1214
                         -i i  ivviv i     i  ii  v    v iv  ii      i    i
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr20_25664725_   1215 CCAAAG-AATTTTGAGCAAGAA---CAAAGCTGAAGGCATCAAACTTCTT 1260
                              i-   i    iv     ---     i  i   vv   v     ii
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr20_25664725_   1261 AATTTCAAATGATATAACAAAGCTACAGTCATCAAAACAGCATGATGCTG 1310
                                  vvv  iv             v     i    ii  i i   
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr20_25664725_   1311 GCATTAACACAGACACATAGACCAATGAAACTGAATAGAGAGCTCAGAAA 1360
                             v iv i     i     i     i  iv    v     ii      
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAA 325

  chr20_25664725_   1361 TA--TCCATCTGAACACAGTCAACTAATTTTCAACAAAGATATATAAAT- 1407
                           --i    viivvi ii     i i      i    i i iivv i i-
  L1M4_orf2#LINE/    326 TAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC 375

  chr20_25664725_   1408 ATACAGTGAAGAAAGAATACACTGTTCAATAAATGGTGATGGGAAAACTG 1457
                           v  i  ii         vv  v     i        v     v     
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr20_25664725_   1458 GATATACACATGCAAAAAAA----ATTTAACCCATCTTTTACAGAATACA 1503
                             ?v           i  ----i  vi    v vii i   vv   i 
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr20_25664725_   1504 CAAAAATTAACTTAAGA--GATTAAAGACTTCAATATTGGACCTGAAACC 1551
                                     i  i --   i ?    i v   i vi  v  i    i
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr20_25664725_   1552 ATAAAACTTTTAGAAAACAACATTGGGGAAAATTCTT-TGGCATTGTTTG 1600
                                 i      i v     v  ? v    ii i-  i v   vv v
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr20_25664725_   1601 CGGCAATAATTATTTTTTGTATTTGACACTAAAAGCCCAGG------GAG 1644
                         v      ii  --- i  iv  v      i      v  i ------i  
  L1M4_orf2#LINE/    576 AGGCAATGGTT---TCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_25664725_   1645 AAAAAA------AATGAAACGACATCAAACTAAAAAGTTTCTACTGCATA 1688
                               ------   vii  vv       v v    ii  i i-   v -
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG-TGCTT- 670

  chr20_25664725_   1689 GCAAAAGACA--GTCAATCAATTTAAAAGGCAATCCACAGAACCGAAGAA 1736
                         -    i    --i    vv  v v     i   i        iv i    
  L1M4_orf2#LINE/    671 -CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_25664725_   1737 AAATACTTGTAAGCCAAATATCAGATAAAGGGTTAGCATTCAAAATCTGT 1786
                           -  i   i  ii  v     v     i  ii v i  i  i   v i 
  L1M4_orf2#LINE/    720 AA-TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr20_25664725_   1787 AAGAAATTCATAAAATATAACCCCCTCTGAATAAAAATAACAATAAAAAT 1836
                           ii  i  v  v  ---------   --     ---   v  v v    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAA---------CTC--AATAA---TAAAAAGACAAAT 804

  chr20_25664725_   1837 AACACATTCTTTTTAAAAGTAGCCAAATAATCTAAATGGATCCTTTTTCA 1886
                            v  v ---- ?    i i v    vi  i i   i  ivi  i i  
  L1M4_orf2#LINE/    805 AACCCAAT----TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_25664725_   1887 AAGAAG 1892
                               
  L1M4_orf2#LINE/    851 AAGAAG 856

Transitions / transversions = 1.59 (126 / 79)
Gap_init rate = 0.03 (21 / 781), avg. gap size = 2.71 (57 / 21)  


 942 23.93 16.03 3.42  chr20_25732342_25734320.rev      505   972 (1007)    L1M4_orf2#LINE/L1      148   674 (234)  

  chr20_25732342_    505 ATATGGAAAAGAGAAGGTCCAAGAATATCAAAGACA---TTGAAGAAGAG 551
                                  v vi i  v  v      v v  i   ---     i    i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_25732342_    552 GAA-AGATTTG------TC---CTGCCAAATATCAGAACTT-TTATAAAG 590
                            - i v   ------  ---  v  v   v   i     -i  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_25732342_    591 CTACAGCAATTAAGACAGTGTGGTCCTCAC-T---GATAAAC-T---GAC 632
                               i   i             v  vi - ---    i  - ---  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_25732342_    633 TAATGAAACAGAATAGAGAGCTCCCAAGCAAATCTCTACA---------A 673
                         i    i  i     v     ii vv  ii   i iv    --------- 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_25732342_    674 ATTTAATCTTCGATACGTGATGTAGGTGACATGGCAGATCAGTAAGGAAA 723
                            -i  i     i v -------    v  v i viv   i ii     
  L1M4_orf2#LINE/    348 ATT-GATTTTCGACAAG-------GGTGCCAAGACCATTCAATGGGGAAA 389

  chr20_25732342_    724 GAAAGGACTTTTCAATAAATAG-AATAGAAAAATAATGGTTATTGATATA 772
                            vi v        i    i -iv i i v  i--   v  ?iv i  -
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAAC--TGGATAKCCACAT- 436

  chr20_25732342_    773 AGAAACAAAATGAAATTATATTCCTACTTCACTCTATATACAAACATTAA 822
                         - v  v i      i  iv ii     i    v i         v     
  L1M4_orf2#LINE/    437 -GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr20_25732342_    823 ATTCCAGA-GGACCAAAGACTTACATGTCAGAAACAAAACTTTAAAACTT 871
                         -i  v i -   i  ?    i  v    v   ivi      v       i
  L1M4_orf2#LINE/    486 -CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr20_25732342_    872 TTAGTAGAAAATGTAAGTG--------------------------AATGG 895
                             v      ii  i ? --------------------------     
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr20_25732342_    896 ------------GACACAAAAAGC-CATTTAACCATTAAAAAAGATTAGA 932
                         ------------     v      -  vvi   v --  i   i v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAA--AAGAAAAAATAGA 632

  chr20_25732342_    933 CAT-TTTGACTATCA-CAAAATTAAGAACTTTT-TACATCAAA 972
                         i v-  v    -   -         i       - i v     
  L1M4_orf2#LINE/    633 TAAATTGGACT-TCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

Transitions / transversions = 1.37 (63 / 46)
Gap_init rate = 0.05 (25 / 527), avg. gap size = 3.64 (91 / 25)  

 245 29.69 6.99 2.62  chr20_25732342_25734320.rev     1259  1487 (492)    L1M4_orf2#LINE/L1      670   908 (0)  

  chr20_25732342_   1259 TTAAAAAATAAAAGTAAAAAAGTCAAAAGATAAACTATA-AATTAGAGAA 1307
                          i   ii i vv vi  i     v      i  v i i -   vi     
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_25732342_   1308 GATATTTGCAGTACCTAAAACCTATGAAAGATTAATATCATATCA-ACTA 1356
                         i         ivv v  v v iv  i ii  i vi    ----  - v  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATC----CAGAATA 765

  chr20_25732342_   1357 AGCATAAGGAGCTCCTATGAATTAATTTTAAAAATA---GCAACCCAACA 1403
                         --i    i  i   i  ii v i   vv      v ---ii       iv
  L1M4_orf2#LINE/    766 --TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr20_25732342_   1404 GAAAATTGGG-AAAAGACATTAATAGGGATTTCACAAAAGAGAA-----A 1447
                         ?    v    -   i  iv v     iv     v v     ii ----- 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr20_25732342_   1448 GCTTGCAAA-----ACATAAAAATTTTCTCAACCTCATTAGTAAT 1487
                         iv v  v  -----    i    vv v      v   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (35 / 32)
Gap_init rate = 0.03 (8 / 239), avg. gap size = 2.75 (22 / 8)  


 930 28.50 6.99 1.81  chr20_25801995_25804004.rev      505   890 (1120)    L1M4_orf2#LINE/L1      148   553 (355)  

  chr20_25801995_    505 ATATGGAAAAGGGAAGGGCCAAGAATATCAAAGACA---TTGAGGAAGAG 551
                                  v vi i  i  v      v v  i   ---    ii    i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_25801995_    552 GAA----------AGATTTGTGCTGGCAAATATCAGAACTT-TTATAAAG 590
                            ----------i  i iiii  vv v   v   i     -i  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_25801995_    591 CTACAGCAATTAAGACAGTGTGGTCCTCAC-T---GATAAAC-T---GAC 632
                               i   i             v  vi - ---    i  - ---  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_25801995_    633 TAATGAAACAGAATAGAGAGCTCCCAAGCAAATCTCCACAAATTTA--AT 680
                         i    i  i     v     ii vv  ii   i --  i v     --i 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGGT 345

  chr20_25801995_    681 CT-TTGATATGTGATGTAGGTGACATGGCAGATCAGCAAGCAAAGAAAGG 729
                          v-     v vi  iivi    v  v i viv   iiii v      vi 
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_25801995_    730 ACTTTTCAATAAATAG-AATAGAAAAATAATGGTTATTGATATAAGAAAC 778
                         v        i    i -iv i i v  i--   v  ?iv i  -- v  v
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAAC--TGGATAKCCACAT--GCAAA 441

  chr20_25801995_    779 AAAATGAAATTATATTCCTGCCTCACTCTATATACAAACATTAAATTCCA 828
                          i      i  iv ii   i      v i         v     -i  v 
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA-CTCAA 490

  chr20_25801995_    829 GATGGA-CAAAGACTTACATGTCAGAAACAAAACTTTAAAACTTTTAGTA 877
                         i     -  ?    i  v    v   ivi      v       i    v 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr20_25801995_    878 GAAAATGTAAGTG 890
                              ii  i ? 
  L1M4_orf2#LINE/    541 GAAAACATAGGNG 553

Transitions / transversions = 1.61 (66 / 41)
Gap_init rate = 0.04 (15 / 406), avg. gap size = 2.27 (34 / 15)  

 283 27.70 7.51 2.82  chr20_25801995_25804004.rev     1306  1518 (492)    L1M4_orf2#LINE/L1      686   908 (0)  

  chr20_25801995_   1306 AAAAAGTCAAAAGATAAACTATA-AATTAGAGAAGATATTTGCAGTACCT 1354
                          i     v      i  v i i -   vi     i         ivv v 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr20_25801995_   1355 AAAACCTACGAAAGATTAATATCATATCA-AATAAGTATAAGGAGCTCCT 1403
                          v v iv ii ii  i vi    ----  -    --     i  i   i 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATC----CAGAATA--TATAAAGAACTCTT 779

  chr20_25801995_   1404 ATGAATTAATTTTAAAAATA---GCAACCCAACAGAAAATTGGG-AAAAG 1449
                          ii v i   vv      v ---ii       iv?    v    -   i 
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

  chr20_25801995_   1450 ACATTAATAGGGATTTCACAAAAGGG-------AAA--GCCTGCAAA-AC 1489
                          iv v     iv     v v    ii-------   --   vii  i-  
  L1M4_orf2#LINE/    830 ATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCAC 879

  chr20_25801995_   1490 ATAAAAATTTTCTCAACCTCATTACTAAT 1518
                           i    vv v      v   ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (32 / 26)
Gap_init rate = 0.04 (9 / 223), avg. gap size = 2.44 (22 / 9)  


 918 25.18 12.95 0.00  chr20_25831739_25835610.rev     2227  2504 (1368)    L1M4_orf2#LINE/L1        1   314 (594)  

  chr20_25831739_   2227 TGGAAAGCCATCTCATTTTCATGAATTGAAAGA----ATATTTATAA-AT 2271
                                vi   i   v      i    i    ----     vv   -  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25831739_   2272 TCTAATACTAGCCAAA------------------GCAATTCC------AA 2297
                         vvi      vv     ------------------     i  ------  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25831739_   2298 TGCTAATTA-------TAGAGAAATAGAAAGGACAATTCTAAAATCCATA 2340
                          v i ii i------- iv      v  v i vii  i       i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_25831739_   2341 TGGAAACACAACAGACCCTGAATATCCAAAACAATCCTAAGAAAGAAAAA 2390
                               ii   vi     v     v           i i i      i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_25831739_   2391 CAAAATTAGAGGCCTCACATTTTCTGACTTTGAAATGTACTACAAAGCTA 2440
                             i  i    v      i  i ii i  ii   iv             
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_25831739_   2441 CAGCAATCCCAATAGTGTGATATTAATGTAAAACTAATCATATAGATGAA 2490
                            i    vvi i      i  i iiii   iiv  iv         v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_25831739_   2491 TGGAAGAGAATGGA 2504
                              v     v  
  L1M4_orf2#LINE/    301 TGGAATAGAATTGA 314

Transitions / transversions = 1.80 (45 / 25)
Gap_init rate = 0.02 (5 / 314), avg. gap size = 7.20 (36 / 5)  

2417 23.13 2.04 0.68  chr20_25831739_25835610.rev     2793  3380 (492)    L1M4_orf2#LINE/L1      313   908 (0)  

  chr20_25831739_   2793 GAAAACCCAGAAATAAACCCACATGCATATAGTCAAATGATCTTTGACGA 2842
                           i ii               i iiiv   i     v    i  i   i 
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr20_25831739_   2843 GGGTGACAAAACTATACAATGGAGAAAGGATAATTTCTTCAACAAATATT 2892
                              v   i  i  v      i     i   i i i          iv 
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr20_25831739_   2893 TTTGGGAAAACTGGATATCCATATGCAAAAGAATGAAAGTGAACCCTTAT 2942
                         vi     v         ?   i               iv  i    i  i
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr20_25831739_   2943 CTTACACTGTTCACAAATGTTAACTCCAAACGGATTGAAGACTTAAATGT 2992
                           i    ii vi     vi       v   i    ii?    i       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr20_25831739_   2993 AAGAACTAAAGCTGTAAAACTCCTACAAGAAAGCATAAAGA-AAGGCTTT 3041
                             i     i  i        i  v      i    ii?i-  iv   i
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr20_25831739_   3042 ATCACATTGGTCGT--GGCAATAGTTCCTTGGATTTGACACCAAAAGCAC 3089
                         i v  v    --  --      i   i   i   v               
  L1M4_orf2#LINE/    563 GTGACCTTGG--GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr20_25831739_   3090 AGGCAACCAAAGCAAAAATAGGTTAGGGTGATTACATCAAGATAAAATGC 3139
                          i     v    v        i v ivvv  i v      i  v   vi 
  L1M4_orf2#LINE/    611 AAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAAC 660

  chr20_25831739_   3140 TTCTGTGCAAAAAAAGAAACCAC----AGAGTGAACAGGCAGCCTACAGA 3185
                           i     vvv   i  v  i i---- i      v  i  i  i     
  L1M4_orf2#LINE/    661 TTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGA 710

  chr20_25831739_   3186 ATTGGAGAAAATATTTGAAAACTGTATATGTGCTAAGGGCTTAATATCCA 3235
                           v              v   iii     v  v      vi vi      
  L1M4_orf2#LINE/    711 ATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCA 760

  chr20_25831739_   3236 AAATATATAAGAAACAACTATAACTCAAAAGCAAATAAACACATAACCCA 3285
                         i         ii   vvi  i       v ii   v i   v        
  L1M4_orf2#LINE/    761 GAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA 810

  chr20_25831739_   3286 ATTTAAAAATGGCTAAA---TTCTTAAATAGATATTTTTC--AGGAAGAC 3330
                            ?        vi   ---  -- i      i    i  -- i     i
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATT--TGAATAGACATTTCTCCAAAGAAGAT 858

  chr20_25831739_   3331 ATGCAAATGACCAACAGGGATATAAAAATATACTCAACATCATTAATCAT 3380
                           i      i    i i v i  i    v  i          ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (88 / 44)
Gap_init rate = 0.01 (7 / 596), avg. gap size = 2.29 (16 / 7)  


3135 26.67 0.77 1.10  chr20_25863670_25866143.rev     1072  1982 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_25863670_   1072 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 1121
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_25863670_   1122 GGCCATACTGCCCAAGGTAACTCATAGATTCAATGCCATCCCCATCAAGC 1171
                            v     v     iv i iii i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_25863670_   1172 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1219
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_25863670_   1220 TATGGAACCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 1269
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_25863670_   1270 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1319
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_25863670_   1320 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGAGATATAGACC 1369
                                 i   i    ii         i i  ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_25863670_   1370 AACGGAACAGAAC--AGAGCCCTCAGAAATATTGCCGCATATCTACAACT 1417
                           i    i    i--    i  --       vvv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_25863670_   1418 ATCTGATCTTTGACAAATCTGACAAAAACAAGAAATGGGGAAAGGATTCC 1467
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_25863670_   1468 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 1517
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_25863670_   1518 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 1567
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_25863670_   1568 TTAAAGACTTAAATGTTAGA-CTAAAACCATAAAAACCCTAGAAGAAAAC 1616
                          i ?    i       v   -       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_25863670_   1617 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 1665
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_25863670_   1666 AAACACCAAAAGCAATGGCAACAAAAGGCAAAATTGACAAATGGGATCTA 1715
                         vi            vvi          iv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_25863670_   1716 ATTGAACAAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 1765
                           ii  vvv  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_25863670_   1766 CAGGCAACCTACAGAATGGGAAAAAA-ATTTTGGAATCTACTCATCTGAC 1814
                         v  i     i           i    -    vvi    - ivi      i
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGAT 744

  chr20_25863670_   1815 AAAGGGCTTATATCCAGAATCTACAAAGAACTCATACAAATTTACAAGGA 1864
                           i  i   i          v  i         v     v iv i  vi 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_25863670_   1865 AAAAAAAAACTATCAACCCCATCAACAAGTGGACAAAGGATATGAAATGA 1914
                            i v   i----     v  i? v  i   i        v    vv  
  L1M4_orf2#LINE/    795 AAAGACAAAT----AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_25863670_   1915 CACTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATG 1964
                           i     v        i  vi viii     v ii          i   
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr20_25863670_   1965 CTCATCATCACTGGCCAT 1982
                             v     ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.55 (17 / 11)  


 942 23.93 16.03 3.42  chr20_25978858_25980836      505   972 (1007)    L1M4_orf2#LINE/L1      148   674 (234)  

  chr20_25978858_    505 ATATGGAAAAGAGAAGGTCCAAGAATATCAAAGACA---TTGAAGAAGAG 551
                                  v vi i  v  v      v v  i   ---     i    i
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_25978858_    552 GAA-AGATTTG------TC---CTGCCAAATATCAGAACTT-TTATAAAG 590
                            - i v   ------  ---  v  v   v   i     -i  i    
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_25978858_    591 CTACAGCAATTAAGACAGTGTGGTCCTCAC-T---GATAAAC-T---GAC 632
                               i   i             v  vi - ---    i  - ---  i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_25978858_    633 TAATGAAACAGAATAGAGAGCTCCCAAGCAAATCTCTACA---------A 673
                         i    i  i     v     ii vv  ii   i iv    --------- 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_25978858_    674 ATTTAATCTTCGATACGTGATGTAGGTGACATGGCAGATCAGTAAGGAAA 723
                            -i  i     i v -------    v  v i viv   i ii     
  L1M4_orf2#LINE/    348 ATT-GATTTTCGACAAG-------GGTGCCAAGACCATTCAATGGGGAAA 389

  chr20_25978858_    724 GAAAGGACTTTTCAATAAATAG-AATAGAAAAATAATGGTTATTGATATA 772
                            vi v        i    i -iv i i v  i--   v  ?iv i  -
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAAC--TGGATAKCCACAT- 436

  chr20_25978858_    773 AGAAACAAAATGAAATTATATTCCTACTTCACTCTATATACAAACATTAA 822
                         - v  v i      i  iv ii     i    v i         v     
  L1M4_orf2#LINE/    437 -GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

  chr20_25978858_    823 ATTCCAGA-GGACCAAAGACTTACATGTCAGAAACAAAACTTTAAAACTT 871
                         -i  v i -   i  ?    i  v    v   ivi      v       i
  L1M4_orf2#LINE/    486 -CTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr20_25978858_    872 TTAGTAGAAAATGTAAGTG--------------------------AATGG 895
                             v      ii  i ? --------------------------     
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr20_25978858_    896 ------------GACACAAAAAGC-CATTTAACCATTAAAAAAGATTAGA 932
                         ------------     v      -  vvi   v --  i   i v    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAA--AAGAAAAAATAGA 632

  chr20_25978858_    933 CAT-TTTGACTATCA-CAAAATTAAGAACTTTT-TACATCAAA 972
                         i v-  v    -   -         i       - i v     
  L1M4_orf2#LINE/    633 TAAATTGGACT-TCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

Transitions / transversions = 1.37 (63 / 46)
Gap_init rate = 0.05 (25 / 527), avg. gap size = 3.64 (91 / 25)  

 245 29.69 6.99 2.62  chr20_25978858_25980836     1259  1487 (492)    L1M4_orf2#LINE/L1      670   908 (0)  

  chr20_25978858_   1259 TTAAAAAATAAAAGTAAAAAAGTCAAAAGATAAACTATA-AATTAGAGAA 1307
                          i   ii i vv vi  i     v      i  v i i -   vi     
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_25978858_   1308 GATATTTGCAGTACCTAAAACCTATGAAAGATTAATATCATATCA-ACTA 1356
                         i         ivv v  v v iv  i ii  i vi    ----  - v  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATC----CAGAATA 765

  chr20_25978858_   1357 AGCATAAGGAGCTCCTATGAATTAATTTTAAAAATA---GCAACCCAACA 1403
                         --i    i  i   i  ii v i   vv      v ---ii       iv
  L1M4_orf2#LINE/    766 --TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr20_25978858_   1404 GAAAATTGGG-AAAAGACATTAATAGGGATTTCACAAAAGAGAA-----A 1447
                         ?    v    -   i  iv v     iv     v v     ii ----- 
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr20_25978858_   1448 GCTTGCAAA-----ACATAAAAATTTTCTCAACCTCATTAGTAAT 1487
                         iv v  v  -----    i    vv v      v   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.09 (35 / 32)
Gap_init rate = 0.03 (8 / 239), avg. gap size = 2.75 (22 / 8)  


3282 26.76 0.44 0.44  chr20_26161814_26168093     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_26161814_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4930
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_26161814_   4931 GGCCATACTGCCCAAGGTAATTTACAGACTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i      i    i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_26161814_   4981 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5028
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_26161814_   5029 TATGGAACCAAAAAAGAGCCCACATCACCAAGTCAATCCTAAGCCAAAAG 5078
                                viiv  ii  v  viv  vi    iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_26161814_   5079 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5128
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_26161814_   5129 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5178
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_26161814_   5179 AATGGAACAGA--CCAGAGCCCTCAGAAATAACGCCACATATCTACAACT 5226
                                i   --iv    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_26161814_   5227 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5276
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_26161814_   5277 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGTT 5326
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_26161814_   5327 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5376
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_26161814_   5377 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5426
                          i ?    i    i  v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_26161814_   5427 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5476
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_26161814_   5477 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 5526
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_26161814_   5527 TTAAACTAAAGAGCTTCTGCTCAGCAAAAGAAACTACCATCAGAGTGAAC 5576
                          i   v v  i i   i  iv vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_26161814_   5577 AGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 5626
                           i     i   iv            v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_26161814_   5627 AGGGCTAACATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5676
                         i  i  vii         v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_26161814_   5677 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5726
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_26161814_   5727 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC 5776
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_26161814_   5777 ATCACTGGCCAT 5788
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (142 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


1153 25.65 2.27 0.32  chr20_28046741_28050650.rev     2235  2542 (1368)    L1M4_orf2#LINE/L1        1   314 (594)  

  chr20_28046741_   2235 TGGAAAGCCATCTAATTTTCATGAATTGAAAGA----ATATT--TACAAA 2278
                                vi   iv  v      i    i    ----     --  - i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGA 49

  chr20_28046741_   2279 TTCTAATACTAGCCAAAGCAATTTACAGATTTGATGTAATCCCTATAAAA 2328
                          vvi      vv     vii  i        ii i i         v   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_28046741_   2329 ATTCCAA-TGCTAATTTTAGAGAAATAGAAAGGACAATTTTAAAATCCAT 2377
                           i   i-   ivv    iv      v  v i vii  ii      i   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_28046741_   2378 ATGGAACCACAACGGACCCTGAATATCCAAAACAATCATAAGAAAGAAAA 2427
                               vii   v      v     v           v i i      i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_28046741_   2428 ACAAAGTTAGAGGCCTCACATTTTCTGACTTTGAAATATACTACAAAGCT 2477
                                 i    v      i  i ii i  ii   iv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_28046741_   2478 ACAGCAATCCCAATAGTGTGATATTAATGTAAAACTAATCATATAGATGA 2527
                             i    vvi i      i  i iiii   iiv  iv         v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_28046741_   2528 ATGGAAGATAATGGA 2542
                               v v   v  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGA 314

Transitions / transversions = 1.63 (49 / 30)
Gap_init rate = 0.01 (4 / 314), avg. gap size = 2.00 (8 / 4)  

2482 21.94 2.38 1.02  chr20_28046741_28050650.rev     2831  3418 (492)    L1M4_orf2#LINE/L1      313   908 (0)  

  chr20_28046741_   2831 GAAAGCCCAGAAATAAACCCACTTGCAT--ATAGTCAAATGATCTTTGAC 2878
                           i  i               -- i   --  i     v    i  i   
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCA--TACATTTATGGTCAATTGATTTTCGAC 360

  chr20_28046741_   2879 GAGGGTGCCAAAACTTTACAATGCAGAAAGGATAATTTCTTCAACAAATA 2928
                         i          i  iv v     vi     i   i i i          i
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr20_28046741_   2929 TTGTTGGGAAAACTGGATATCCATATGCAAAAGAATGAAAGTGAACCCTT 2978
                         v  i     v         ?   i               iv  i    i 
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr20_28046741_   2979 ATCTTACACTGTTCACAAATGTTAACTCCAAATGGATTGAACACTTAAAT 3028
                          i  i    ii vi     vi       v        ii? v  i     
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr20_28046741_   3029 GTAAGAACTAAAGCTGTAAAGCTCCTACAAGAAAACATAAAGA-AAGGCT 3077
                               i     i  i    i   i  v           ii?i-  iv  
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCT 560

  chr20_28046741_   3078 TTATCACTTTGGTCGT--GGCAATAATTCCTTGGATTTGACACCAAAAGC 3125
                          ii v  i    --  --      ii  i   i   v             
  L1M4_orf2#LINE/    561 TCGTGACCTTGG--GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr20_28046741_   3126 ACAGGCAACCAAAGCAAAAATAGGTTAGGGTGATTACATCAAGATAAAAT 3175
                            i     v    v        i v ivvv  i v      i  v   v
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr20_28046741_   3176 GCTTCTGTGCAAAAAAGGAAAC----AATGGAGTGAACAGGCAGCCTACA 3221
                         i   i     vvv      v  ----  vii      v  i  i  i   
  L1M4_orf2#LINE/    659 ACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACA 708

  chr20_28046741_   3222 GAATTGGAGAAAATATTTGAAAACTGTATATGTGCTAAGGGCTTAATATC 3271
                             v              v   iii     v  v      vi vi    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr20_28046741_   3272 CAAAATATATAAGAAACACCTATAACTCAAAAGCAAATAAACACATAACC 3321
                           i         ii   v i  i       v ii   v i   v      
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr20_28046741_   3322 CAATTTAAAAATGGCTAAA---TTCTTAAATAGATATTTTTC--AGGAAG 3366
                              ?        vi   ---  -- i      i    i  -- i    
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATT--TGAATAGACATTTCTCCAAAGAAG 856

  chr20_28046741_   3367 ACATGCAAATGACCAACAGGGATATAAAAAGATACTCAACATCATTAATC 3416
                          i  i      i    i i v i  i       i          ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr20_28046741_   3417 AT 3418
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.98 (83 / 42)
Gap_init rate = 0.02 (9 / 596), avg. gap size = 2.22 (20 / 9)  


 840 25.91 15.20 2.36  chr20_28189298_28191235.rev      502   968 (970)    L1M4_orf2#LINE/L1      148   674 (234)  

  chr20_28189298_    502 ATATGGAAAAGGGAAGGGGCCAATAATATCAAAGACA---TTGAAGAAAA 548
                                  -v v     i  v v    v v  i   ---     i  i 
  L1M4_orf2#LINE/    148 ATATGGAAA-TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_28189298_    549 GGAA-AGATTTG------TC---CTGCCAAATATCAGGACTT-TTATAAA 587
                         i   - i v   ------  ---  v  v   v   ii    -i  i   
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_28189298_    588 GCTACAGCAATTAAGACAGTGTGGTCCTCAC-T---GATACAC-T---GA 629
                                i   i             v  vi - ---    v  - ---  
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_28189298_    630 CTAGTGAAACAGAAT--AGAGTTCCCAAGCAAATCTCCACAAATTTA--A 675
                         ii i  i  i     --     i vv  ii   i --  i v     --i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACC--CATACATTTATGG 344

  chr20_28189298_    676 TCT-TCGATATGTGATGTAGGTGACATGGCAGATCAGCAAGGAAAGAAAG 724
                           v- i   v vi  iivi    v  v i viv   iiii        vi
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_28189298_    725 GACTTTTCAATAAATAG-AATAGAAAAATAATGGTTATTGATATAAGAAA 773
                          v        i    i -iv i i v  i--   v  ?iv i  -- v  
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAAC--TGGATAKCCACAT--GCAA 440

  chr20_28189298_    774 CAAAATGAAATTATATTCCTACTTCATTCTATATACAAACATTAAATTCC 823
                         v i      i  iv ii     i   iv i         v     -i  v
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA-CTCA 489

  chr20_28189298_    824 AGATGGACAAAAGACTTACATGTCAGAAA-AAAACTTTAAAACTTTTAGT 872
                          i     iv ?    i  v    v   iv-      v       i    v
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_28189298_    873 AGAAAATGTAAGTG--------------------------AATGA----- 891
                               ii  i ? --------------------------    i-----
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr20_28189298_    892 -------GACACAAAAAGC-CATTTAACCATTAAAAAAGAGTAGACAT-T 932
                         -------     v      -  vvi   v --  i   i i    i v- 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAA--AAGAAAAAATAGATAAAT 637

  chr20_28189298_    933 TTGACTATCA-CAAAATTAAGAACTTTT-TACATCAAA 968
                          v    -   -         i       - i v     
  L1M4_orf2#LINE/    638 TGGACT-TCATCAAAATTAAAAACTTTTGTGCTTCAAA 674

Transitions / transversions = 1.41 (69 / 49)
Gap_init rate = 0.05 (27 / 527), avg. gap size = 3.04 (82 / 27)  

 269 27.07 7.86 3.49  chr20_28189298_28191235.rev     1254  1482 (456)    L1M4_orf2#LINE/L1      670   908 (0)  

  chr20_28189298_   1254 TTAAAAAATAAAAGTAAAAAAGTGAAAAGATAAACTATA-AATTAGAGAA 1302
                          i   ii i vv vi  i            i  v i i -   vi     
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_28189298_   1303 GATATTTGCAGTAACTGAA-ACCT-ACAAAAGATTAATATCATATCA-AC 1349
                         i         --  iiiv - i  - i  ii  i vi    ----  - v
  L1M4_orf2#LINE/    720 AATATTTGCA--AATCATATATCTGATAAGGGACTTGTATC----CAGAA 763

  chr20_28189298_   1350 TAAGTATAAGGAGCTCCTATGAATTAATTTTAAAAATA---GCAACCCAA 1396
                           --     i  i   i  ii v i   vv      v ---ii       
  L1M4_orf2#LINE/    764 TA--TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr20_28189298_   1397 CAGAAAATTGGG-AAAAGACATTAATAGGGATTTCACAAAAGAG------ 1439
                         iv?    v    -   i  iv v     iv     v v     i------
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr20_28189298_   1440 -AAA--GCCTGCAAA-ACATAAAAATTTTCTCAACCTCATTAGTAAT 1482
                         -   --   vii  i-    i    vv v      v   ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.54 (37 / 24)
Gap_init rate = 0.05 (12 / 239), avg. gap size = 2.17 (26 / 12)  


2878 26.71 3.14 1.46  chr20_28199890_28201976.rev      706  1596 (491)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_28199890_    706 GAAAGACAACCCATG------GATTGAAAGAGTTAGTACTGTATTATTAA 749
                               i v      ------     i    v   i  -----  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATA-----TTGTTAA 47

  chr20_28199890_    750 AGTGTCCATATTACTCAAAGCAATCTACACATTTAATGTAATCCATATCA 799
                         ii  v v   i v i    vii       v   i  i i     v     
  L1M4_orf2#LINE/     48 GATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr20_28199890_    800 AAATCCCAA-TGGTACTCTCACAGAAATAGAAAAAAATGATCCTAAAATT 848
                                 i-  vivi i ii       v  v  iv-             
  L1M4_orf2#LINE/     98 AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGC-TGATCCTAAAATT 146

  chr20_28199890_    849 CATATAGAATCACAAAAATCCCTGAGTGGCTGAAGCTATTTTGAGCAAGA 898
                              i   vii   iiiv   v  i i  ii  i v  i    iv    
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_28199890_    899 A---CAGAGCTACAGGTATCACAGTTCCTGATTTCAAA--TTAAATTACA 943
                          ---  i  i iv   vv     v    ii        --   --i    
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACA 244

  chr20_28199890_    944 AAGCTGTAGAAAGAAAAACACTGTGGTACTGGCATAAAAACAGACACATA 993
                              ii  v  vv  i   v                ii i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_28199890_    994 AACCAGTGAAACAAAATAGAGAACCTAGGCATAA-CCCACACATTTGCAA 1042
                         i i  i  i  i i   v    ii i  iv    -    i      iiii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_28199890_   1043 CCA-TTGATCACCCTGGAAGGTGACAAGGAGACACTATAGGCAGAGGATA 1091
                         i  -     ivi vvvi i    v    ivv iv v  i  v i  i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_28199890_   1092 TGCTCTTGACCAAATGGTGTTAGGAAAGCTGGATGTCTACATGTAACAGA 1141
                         vv  i  v v         i i   v i      i? i     i  v   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_28199890_   1142 ATGAAATCGGATCCCTAGCTCACGCCTTATGTAAAAATTAACTCAAAGTG 1191
                              i i   i     v     i  v   ii               i  
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_28199890_   1192 GATCAAACGTTTAAATGTAATCACTGAAACCACAAAACTCCTGGAAGAAG 1241
                              ? viii         vvi  i    i i       i i      i
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_28199890_   1242 ACA--GGAGAAAACATTCTTGACATTGGTCTTGGCAATAATTTGTTTAGA 1289
                            --  ? v   iv   v    v    vi v      ii   -i     
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT-CTTAGA 593

  chr20_28199890_   1290 TATGATTCCAAAAGCACAGGCAACAAAGGCAAAA-TAGATAAAT-GAATT 1337
                              iv           i        i v    -         - i i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_28199890_   1338 ACATCGAACTAAAAAGCTTCTGCACAGCAAGGAAAACAACTAGTGAAATG 1387
                         v    i  v v    i   i  ii vv   i i v  v ii ivi  i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_28199890_   1388 ATAAGGCCACCTATGAAATGGG-GAAAATGTTTGTAAACCATATCTCTTA 1436
                          v   i v   i iii      -      i    i   i     v   v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_28199890_   1437 TAAGGAGTT------CAAAAAATAAGAAGGACACACACACATCAATTCCA 1480
                              iii ------  i  v   vi   i  v vi   vv     vvi 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_28199890_   1481 AAATTATAAATAACCTAATTTTATTTTAA---GGCAAAGAACCTAAATAA 1527
                            vv i        i    ?v ----  ---       i ii i    i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAA----AAATGGGCAAAGGATTTGAATAG 839

  chr20_28199890_   1528 ATACATCTCCAAAGAAGAAATTCAAATGGCTAACAGGTATAAGAAAATGT 1577
                          i iv             v  v        i  i i i i v     vi 
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_28199890_   1578 GCTCAACATCTCTAAACTT 1596
                                   v????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.72 (148 / 86)
Gap_init rate = 0.02 (17 / 906), avg. gap size = 2.41 (41 / 17)  


3666 23.33 1.33 0.44  chr20_28212406_28216896     3100  3999 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_28212406_   3100 TAGAAAGATATCCCATGTTCATGGACTAGAAGAATTAATATTGTTGAAAT 3149
                          i                       i i     v           i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_28212406_   3150 TACCATACTACTCAAATCAATCTATAAATCCAATATAATCTCTATCAAAT 3199
                         vi v     v i     ii     i i  i   iii    i        v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_28212406_   3200 TTCCAATTTCATTCTTCACAGATATTAAAAAAT--ATCTTAAAATCCATG 3247
                          i   ii v v  i  ii    v   i v  ii--   i      i   i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_28212406_   3248 TGAAACTACAAAACACCCCAAATAGCCAAATAAATCTTAAGCAAAAAGAG 3297
                           i  v i   iiv    vi          vv      i iv  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_28212406_   3298 CAATGCTAGAGGTATTACACTATCTAATTTCAAAATATATTACAAAGCTA 3347
                            v i i    vv i     vi i          iv  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_28212406_   3348 CCCTAACTAAAACAGCATGGTATTGGCATAAAAACAGGCATGTAGACCAG 3397
                          vv   ii  i    ii     i        ii i  i   i    i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_28212406_   3398 TGGAACAAAAATAGAGAGCCCAGGCATAAATCCACATATTTACATGCAAC 3447
                              i i  v -     i    iv     i   i i     iivv   i
  L1M4_orf2#LINE/    301 TGGAATAGAATT-GAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_28212406_   3448 TTATTTTTGACAAAGGTGCAAA---CATTCAATTGGGAAAGA-CAGTCTT 3493
                          v     i     i     v  ---        v        -i      
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_28212406_   3494 TTCAACAAATGGTGCTGGGAAATGTGCATACCCACATACAAAAGAATGAA 3543
                                             v vv  v   ?      i            
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_28212406_   3544 AGTAGACCCCTATCTCTCATCATATACAAAAATCAACTCAAAATAAATTA 3593
                         iv i        i   v  i             i          ii  i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_28212406_   3594 AATATTTAAATGTAAGACCCCAAACTATGAAACTAGTAGAAGAAAACATA 3643
                         ? v ii           v iv       i     vv              
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_28212406_   3644 AGTG-AAATGTTATATGTCATTGATCTGGGCAACGACTTTTTAGAAAAGA 3692
                         i ? -    v  -ii  v v   ivi i     i ii  i     v v  
  L1M4_orf2#LINE/    550 GGNGTAAATCTT-CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_28212406_   3693 CATCAAAAG-ACAGGCACAACAAAAGCAAAAATAAACAAATGAGATTACA 3741
                           i      -   i   --       v       i i    vi  i v  
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCA--ACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_28212406_   3742 CCAAA--TAAAAACTTCTGCACTGCATAGGAAACAATCATGACAGTGAAG 3789
                         i    --         i  ii  v  v    v  v    v  v      i
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_28212406_   3790 AGACAACCTACAAAACAGGAGAAAATATCTGCAAACTATTCACTTCATAA 3839
                                 i   i  ii           i      ii  vi ii v    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_28212406_   3840 GGGGTTAATATCCCAAATTTATAGAAAACTCAAACAACTCAATAGCAAAA 3889
                            ii vi     vi   v    i i     vv           ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_28212406_   3890 ATACAAATAATTGGATTAGAAAA--GTCAAGACAGTTGAATAGACATTTC 3937
                          v        iivi   ?i    -- v   iiv v               
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_28212406_   3938 TCCAAATAAGACAAAAAAATCGCCAACAGGTATATGAAAAAATGCTCACC 3987
                               v    i v v    v     i i i i       i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_28212406_   3988 ATCACTAATAAT 3999
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (134 / 72)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


2521 25.65 2.59 4.74  chr20_28263007_28265599.rev     1176  2103 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_28263007_   1176 TGGAAACATATCCCATGCTCACGGATGGGTAAAATCAATATTGTGAAAAT 1225
                               v          i   i    v  v i v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_28263007_   1226 ACCA-TACTGCCAAAAGCAATCTACAAACTCAATGCAATCCCCATTAAAG 1274
                         iv  -    v  v   vii       i i    i        i  i   i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_28263007_   1275 TGCTAACATCAGTCTTCACAGAACTACAAAAATTCACATGGAACTAA--- 1321
                          v i i - -- i   ivi----- i  i     v   --- i  i ---
  L1M4_orf2#LINE/    101 TCCCAGC-T--GCCTTTTT-----TGCAGAAATTGACA---AGCTGATCC 139

  chr20_28263007_   1322 -AAAAGACATAGAAGGGACATACCTTAAGGTAATAAAAGCCTAGAACCAA 1370
                         -    vv    v---   v  i ---    -------------  v   i
  L1M4_orf2#LINE/    140 TAAAATTCATAT---GGAAATGC---AAGG-------------GACCCAG 170

  chr20_28263007_   1371 AAAAGAGTTTGTATAGCCAAAGCAAGACTAAGCAAAAAGAACAAATCTAG 1420
                           -----------        i   vvi i iv  i         vi i 
  L1M4_orf2#LINE/    171 AA-----------TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr20_28263007_   1421 AAG-----------CCGACTTCAAACTATACTAGAAGGCCATAGTCACCA 1459
                          i -----------  i i      viv     v  i  i i   v i  
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr20_28263007_   1460 AAACAGCATGGCACTGGTATAAAAATAGCCATATAGATCAATGGAACATA 1509
                          i    ii   i     i    ii    v                 i v 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr20_28263007_   1510 ATAGAGAACACAGAAATAAAGCCAAATACTTACAGTCATCTAATCTTCAA 1559
                           v    iiv          v   v i i   ii    vi i  i   i 
  L1M4_orf2#LINE/    310 ATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr20_28263007_   1560 CAAAACAAACAAAAACATAAAGCAGAGAAAGAATACCCTATTCAACAAAT 1609
                            iivviv   i v   vv iii i         vi  v          
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr20_28263007_   1610 GGTGCTGAGATAAATGGCAAGCCACACATAGAAGAATGAAAGTGGATGCT 1659
                                i  i  v   vv ?     iii i         iv    iv i
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr20_28263007_   1660 CATTTCTCACCCTATTCAAAAATCAACTCAAGATGGATCAAGGACTTAAA 1709
                         i ii  v    v   v       i       i        ?i   i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr20_28263007_   1710 TCTAATACCTGAAACCATAAAAATTCTAGAAGACGACATTGGAAAAACCC 1759
                          v   v v  i    i      v ii       vi    v  ?iv  vi 
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr20_28263007_   1760 TTCTAGACATTGGCTTAGGCAAAGACTTCAT-GACCAATAACCCAAAAAG 1808
                            vv   v    v        v ii   v -  i--  i  v v     
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT--ATGACACCAAAAG 607

  chr20_28263007_   1809 CAAATGCAACTAAAACAAAGATAAATAGATGAGACTTAATTAAACTAAAA 1858
                           v v     v   iv   i   i   i  vi     v  i   v v   
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr20_28263007_   1859 GGCTCCTGAGCAGTAAGAGAAATAATCAGCAGAGTAAACAGATAACCTAC 1908
                         ii  ii  v  vvi  ii  v iv    iv i   i  v   i    i  
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr20_28263007_   1909 AGAGTGGGAGAAAATCTTCGCAATCTGTACTTCTGATTAAAGGACTAATA 1958
                            i           v  i    viii  iv      -  i     vi  
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGAT-AAGGGACTTGTA 756

  chr20_28263007_   1959 CCCAGAATCTGCAAGGAACTCAAACAAACCAGCAAGAAAAACAT------ 2002
                         i       v ii  i      vv    vi  ii  v     v i------
  L1M4_orf2#LINE/    757 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 806

  chr20_28263007_   2003 CCCA-TCAAAAAGTGGGCTAAGGACATGAACAGACAATTCTCAAAAGAAG 2051
                             - i?    i     v     iv    i     v     v       
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr20_28263007_   2052 ATAAGCAACTGGCCAACAAACACATGAAAAAATGTTCAACATAACTAATT 2101
                            vi   v       i  i          i   i       v ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr20_28263007_   2102 AT 2103
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.44 (138 / 96)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 4.25 (68 / 16)  


2397 22.72 2.05 9.02  chr20_29302950_29304817      501  1376 (492)    L1M4_orf2#LINE/L1       94   908 (0)  

  chr20_29302950_    501 ATCAACATATTAATGACATTCTTTACAGAAATAGAAAAAACAATCCTTG- 549
                              v  vii iivi v  i   i       v  v  ivii     vi-
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr20_29302950_    550 -TTTCTATTGAACTGCAAAAGACTTTTAATAACCAAAGCAATCTAGAGCA 598
                         -  iv   v   v     ii   iivv    i     i      v  iv 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr20_29302950_    599 AAAACAGCAAATCTAAAGGTATCACACTACCTTACTTTAAAATATACTAT 648
                          i  v i    vi ii   vv       v  iv i  i    iv     i
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr20_29302950_    649 AAAGATCTAGTGACCAAAATAGGTTGATATTGGCATAAAATCAGACACAT 698
                             v vi   i i   i i  vv  i  i        iivi     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr20_29302950_    699 AGACCAATGGAACAGAATAGAAAGACCAGAAACAAATCTGCACATCTATA 748
                            i        i     v  i  v       i   i iii    i   i
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr20_29302950_    749 GCCAACTGACTTTAAAAAAAATTTCCAAGGACACACATTGGGAATAGGAC 798
                          i   i   i   vi v  iiv v     iv  iv  v    i v  i i
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_29302950_    799 AGTCTCTTCGATAAATGGTACTAGGG-AACTGGATAGCCACATGAACAAA 847
                              i   i i       i  i  i-         ?       v v  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_29302950_    848 AATGAAACTAGATCCTTATCTTTCACCATATTCAAAAATCAACTAAAAAT 897
                               ii i  i  i  i  iv        v       i    v     
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_29302950_    898 GATTGAAAGACTTGAATGTAAGACTTGAAACTAAGGAATTAGTAGGAGAA 947
                          iv v ?    i i         vi i      vii  i vv   i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_29302950_    948 AACATTGGAG-AAATACTTCATGACATTAGACTGAGGCAAAGATTTTTTG 996
                              v  ? -    -    i    v  i ii -      v i   i  -
  L1M4_orf2#LINE/    544 AACATAGGNGTAAAT-CTTCGTGACCTTGGGTT-AGGCAATGGTTTCTT- 590

  chr20_29302950_    997 TTACTTTTTTTATTTTTCAAAAGTACTATTTTCACAAGAGGATGGGTGTC 1046
                         --------------------------------------------------
  L1M4_orf2#LINE/    591 -------------------------------------------------- 590

  chr20_29302950_   1047 AAGGAAAGATTTTTTGGCTATGACTCTACAAGCATAGGCAACAAAAGCAA 1096
                         ------    ---------     v i v     i i          v  
  L1M4_orf2#LINE/    591 ------AGAT---------ATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr20_29302950_   1097 AAATAGACAAATGGGATTAAATCAAA-CTAAAAACTCT---ACAGCAAAG 1142
                                i    v   i vv      -i        i ---i vv     
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr20_29302950_   1143 GAAAC-ATTCAGA--GTGAACAGACAGCT-ACAGAATGGGAGAAA-TATT 1187
                           v  -  iv   --     v     i i-               -    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr20_29302950_   1188 TGCAAACTATATATATGACAAGTGGTTAATATCCAGAATATATAAGAAAC 1237
                               ii      v   i   v ii vi                ii   
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr20_29302950_   1238 TGAAACAACTCAAGAGAAAAAATAAAAAGACCACCAAATAACCTGATTTA 1287
                          vvv         v ------          ----        ii   ? 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATA------ATAAAAAGAC----AAATAACCCAATTWA 815

  chr20_29302950_   1288 AAAATTGGCAAATGATCTGAAGAGACACTCCTCAAAATAAGA----CAAA 1333
                              v      v   i    v     i i   v   v    ----    
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr20_29302950_   1334 TAGCCAA-AAGTTATATGAAGAAATGCTCAACAGCACTAATAAT 1376
                          i     -   i- i     i i          v  ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGC-ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (120 / 75)
Gap_init rate = 0.02 (18 / 815), avg. gap size = 5.39 (97 / 18)  


3178 27.34 0.66 0.55  chr20_29314759_29320551.rev     4394  5300 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_29314759_   4394 TGGAAGAACATTCCATGCTCATGGACAGGAAGAATCAATATCGTGAAAAT 4443
                              ii i  i     i       iv      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_29314759_   4444 GGCCATACTGCCCAAGGTAATTTATAGATCCAGTGCCATCCCCATCAAGC 4493
                            v     v     iv i  i  i    i  ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_29314759_   4494 TACCAATGACTGTCTTCACAGAATTGGAAAAAAGTACTTTAAAGTTCATA 4543
                          v   iivi iv i  ii     v v  v  ivvv iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_29314759_   4544 TGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAGAA 4593
                              viiv  ii  v  viv  v     i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_29314759_   4594 CAAAACTGGAGGCATCATGCTACTTGACTTCAAACTATACTACAAGGCTA 4643
                             ii      vv   ii  v iii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_29314759_   4644 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGACATAGACCAA 4693
                               i   i    ii         i iv ii i   v i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_29314759_   4694 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTGCAACCAT 4741
                              i    i--    i  --        vv   i    i iiiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr20_29314759_   4742 CTGATCTTTGACAAACCTGACAAAAACAGGAAATGGGGAAAGGATTCCCT 4791
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_29314759_   4792 ATTTAATAAATGGTGCCGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 4841
                         v  i  i         i    v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_29314759_   4842 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 4891
                          ii    i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_29314759_   4892 AAAGACTTAAATGTTAGATCTAAAACCATAAAAACCATAGAAGAAAACCT 4941
                          ?    i       v   v       i      vi v           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_29314759_   4942 AGGCA-ATACCATTCAGGACAT--AGTCATGGGCAAGGACTTCATGGCTA 4988
                            ?i- v i -   iv   v --i  i --     v ii   v i v  
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTA--GGCAATGGTTTCTTAGATA 595

  chr20_29314759_   4989 AAACACCGAAAACAATGGCAACAGAAGCCAAAATAGACAAATGGGATCTA 5038
                         vi     i   i  vvi      i   vv        i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_29314759_   5039 ATTAAA-CTAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5087
                           i   -i   i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_29314759_   5088 CAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5137
                         v  i     i                 v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_29314759_   5138 AAGGGCTAATATCTAGAATCTACAAAGAACTTAAACAAATGTACAAGAAA 5187
                          i  i  vi    i     v  i        ivv    v vv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_29314759_   5188 AAATCAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5237
                           iv    i     v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_29314759_   5238 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAAGGCTCAT 5287
                            v        i  vi viii     v  i          i v     v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_29314759_   5288 CATCACTGGCCAT 5300
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (150 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.57 (11 / 7)  


3286 24.22 0.76 2.59  chr20_29347288_29351058     2355  3279 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_29347288_   2355 TGGAAAGATATTCCATGTTCATGGTTTGGAAGAATCAATATTGTTAAAAT 2404
                                    i            v        v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_29347288_   2405 GTCCATCCTACCCAAAGCAATCTACAGATTCAATGCATTCCCTATCAAAA 2454
                          v v  v  v      vii              i   v            
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_29347288_   2455 TACCAAGGACATTCTTCACAGAAATAGAAAAAAACC-ATTCTAAAATTTA 2503
                          v   ivvi v  i  ii       v  v  --i i-  i        i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAA--GCTGATCCTAAAATTCA 148

  chr20_29347288_   2504 CATAGAACCACAAAAGACCCAGAATAGCGAAAGCTATCCTAAGCAAAAAG 2553
                         i  i   vii   ii             v   i v   i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_29347288_   2554 AACAAAACTGGAGGAACCACATTACCTGACTTCAAATTATACTACAGTGC 2603
                               ii       vi    i v  ii i      viv       iv  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_29347288_   2604 TATAGTAACCAAAACAGCATGGTATTGGTAAAAAAAAAAAAAAAAAAAAA 2653
                           i     i   i    ii     i   i v  ii --------------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA-------------- 284

  chr20_29347288_   2654 AAAAAACAGACATATAGACCTATGGAATAGAATAGAGAACACAGAAACAA 2703
                         ------i           i v            v    iiv      i  
  L1M4_orf2#LINE/    285 ------TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr20_29347288_   2704 ACC-AGACACCTTCAACGAACTCATTTTCAACAAATGTGCCAAAAACATA 2752
                            - v   ii viiiiv  i v      i    iv       i v   v
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr20_29347288_   2753 CACTGGGGAAAAGACAGTCTTTTCAATAAATAGTGCTCAGA-AACTGGAT 2801
                           v        ii i           i    i     vi  -        
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr20_29347288_   2802 ATCCATACTCAGAAGAATGAAGCTAGACCCC-ATCTCTCACCATATACAA 2850
                          ?   i iv  i          i i      - i   v            
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr20_29347288_   2851 AAATAAAATTGAAATAGATCAAAGACTTAAATCTAAGACCTCAAACTATG 2900
                             v  v ii    i     ?    i     v     v  v       i
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr20_29347288_   2901 GAACGACTACAAAAAAATACTGGAAAAATTCTTCAGGACCTCAGTCTGGT 2950
                         i   vvi  v  i    i iv  ?iv  v     iv     ii vi i v
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr20_29347288_   2951 CAAAAATGTATTGAGCAATATTCCACAGGCACAGGCAACCAAAGCAAAA- 2999
                            vii v v  iiii vv iv   v i     i     v    v    -
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr20_29347288_   3000 TGTACAAATGGGGTCACATCAA-GTTAAAAAGCTTCTGCACAGGAAAGGA 3048
                          iv i    v  iiiv      -i       -   i  ii vvv      
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

  chr20_29347288_   3049 AATAATCAACAAAGTAAAAAAACAACCCACAGAATGGAAGAAAATATTTG 3098
                         v iv     v     i    i                i            
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr20_29347288_   3099 CAAATTACCCATCTAACAAGAGATTAATAAGCAGAATATATAAGGACCTC 3148
                              i ivi    i i   i  i vi  vv            i  v   
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr20_29347288_   3149 AAACATCTTTATAGAAAAAAAATCTAATAATCCAATC-AAAGATGGACAA 3197
                         vv   v  iv   iv     i - v     i     i-   i    i   
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGA-CAAATAACCCAATTWAAAAATGGGCAA 826

  chr20_29347288_   3198 GAGAGTTGAATAGACATCCCTCAAAAGAAGATATATAAAAGACAAACAGG 3247
                         ii  v            ii   v            i   v i v  i i 
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr20_29347288_   3248 CATGTGAAAAGGTGCTCAACATCATTGATCAT 3279
                           ii       i            ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (136 / 85)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.82 (31 / 11)  


3199 27.53 0.55 0.55  chr20_29383680_29390078     5000  5907 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_29383680_   5000 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 5049
                              ii i  i     i      i v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_29383680_   5050 GGCCATACTGTCCGAGGTAATTTATAGATTCAATGCCATCCCCATCAAAC 5099
                            v     vi  i iv i  i  i        i  v     i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_29383680_   5100 TACCAATGACTTTCATCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5147
                          v   iivi i  iv ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_29383680_   5148 TATGGAACCAATAAAGAGCCC-GCATCGCCAAGTCAATCCTAAGCCAAAA 5196
                                vii-i  i ii   - v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    149 TATGGAAATG-CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_29383680_   5197 GAACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGG 5246
                                 i      vv   ii  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_29383680_   5247 CTACAGTAACCAAAACAGCATGGTACTGGTATCAAAACAGAGATATAGAT 5296
                                  i   i    ii         i  v ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_29383680_   5297 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCGTATCTACAAC 5344
                                 i    i--    i  --        vv iiiii  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr20_29383680_   5345 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5394
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_29383680_   5395 CCTATCTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5444
                         i  v ii  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_29383680_   5445 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGACGG 5494
                             ii    i    v   i     v              i    i i  
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_29383680_   5495 ATTAAAGACTTAAACGTTAGATCTAAAACCATAAAAACCCTAGAAGAAAA 5544
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_29383680_   5545 CCTAGGAATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5594
                          v    ?i v viv   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_29383680_   5595 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5644
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_29383680_   5645 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5694
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_29383680_   5695 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTTATCTGACA 5744
                         v  i     i   i             v  ii   vii iv       i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_29383680_   5745 AAGGGCTAATATCCAGAATCTACAATGAACACAAACAAATTTACAAGGAA 5794
                          i  i  vi          v  i  v    v vv    v iv i  vi  
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_29383680_   5795 AAAACGAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5844
                           i  i  i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_29383680_   5845 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAACATGCTCAC 5894
                            v        i  vi viii     v  i          v       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_29383680_   5895 CATCACTGGCCAT 5907
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.65 (153 / 93)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


1192 26.07 0.00 0.00  chr20_29812973_29815147.rev      499   778 (1397)    L1M4_orf2#LINE/L1      138   417 (491)  

  chr20_29812973_    499 CCTAAAATTCACATGGAACCACAAAAGACCCCATATAGCCAAACCAATCC 548
                                    i      vii   ii     viv         v     i
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr20_29812973_    549 TATGCAAAGAGAACAAAGCTGAAGGCATCAAATTACCAGCCTTCAAAATA 598
                          iviv  ii         i  i   vv   v i v  vivi       iv
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr20_29812973_    599 CATTACAAAGCTATAGTAACCATAACAGCATGGTACTGGCATAAAAACAG 648
                         i i          i     i  vi    ii              ii i  
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr20_29812973_    649 ACACACAGACAAATGGAATAGGATAGAGAACCCAGGAAAAAATCCACGTA 698
                            i i   iv          i  v    ii    i  v   i   iii 
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACA 337

  chr20_29812973_    699 TTTATAGCCAACTGATTTTTGACAACAGCACCAAGAACATTCCTTGGTGG 748
                              i i   i       i     vi ii      v     vv   v i
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGA 387

  chr20_29812973_    749 AGGGACAGTCTTTTCAATAAATGGTGCTAG 778
                          i i i           i          i 
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTTCAACAAATGGTGCTGG 417

Transitions / transversions = 2.32 (51 / 22)
Gap_init rate = 0.00 (0 / 280), avg. gap size = 0.00 (0 / 0)  

 613 22.82 2.68 0.00  chr20_29812973_29815147.rev      885  1033 (1142)    L1M4_orf2#LINE/L1      401   553 (355)  

  chr20_29812973_    885 TCAAAAAATGGTGCTGATCAAACTAGATATTTAAATGCAGAAAAATGAAA 934
                             v           ivvv    i    ?ii v     i  i      i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_29812973_    935 CTAGACATCTATTTCTTACCATATACAAAAATCAACTCAAAATGGATTAA 984
                         i i   vi   ii  vi               i              i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_29812973_    985 AGACTAATATGTAAGACCTTAAACTATGAAACAACTA----AAAACATAG 1030
                             iv v        v  v       i    vvi  ----         
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_29812973_   1031 GGG 1033
                          ? 
  L1M4_orf2#LINE/    551 GNG 553

Transitions / transversions = 1.38 (18 / 13)
Gap_init rate = 0.01 (1 / 153), avg. gap size = 4.00 (4 / 1)  

1060 24.28 8.96 1.16  chr20_29812973_29815147.rev     1338  1683 (492)    L1M4_orf2#LINE/L1      536   908 (0)  

  chr20_29812973_   1338 TAAAATAAAAACATAGGTG-AAATACTTTAGGACAC--GGTTCTGGGCAA 1384
                           i  -i          ? -    -   iiv   vi--    --i     
  L1M4_orf2#LINE/    536 TAGAA-GAAAACATAGGNGTAAAT-CTTCGTGACCTTGGGTT--AGGCAA 581

  chr20_29812973_   1385 AGATCCTATGAACATGACCTCAAAAGTATAGGCAACAAAAGCAAAAGTAG 1434
                         v i iiiv ii i     vi      i i i          v    i   
  L1M4_orf2#LINE/    582 TGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAG 631

  chr20_29812973_   1435 ACAAATGGGATTATATTAAATTTAAAACTTTCTGCACAGCAGAGGAAACA 1484
                          i    v   i vi  i   v      vi  i  ii vv  i    v  v
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr20_29812973_   1485 ATCAACAGAGTGAAGAGACAACTAA-AGAATGGGAGAAAATACGTGCTAA 1533
                              v i      i       iv -                iv   v  
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr20_29812973_   1534 CTATTCATTCAAGAAGGGACTAATATCCAGAATACACAAGGAACTC---- 1579
                         ii  vi  iii v        vi           i i  i      ----
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTAC 781

  chr20_29812973_   1580 -------------------AAATAACTCAAC----AGCCGGACAAATGAG 1606
                         -------------------       i   i---- ivi  i    v  v
  L1M4_orf2#LINE/    782 AACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr20_29812973_   1607 CTGAACAGACATCTCTCAAAAGAACACATACAAATGGCAAACAGGTATGT 1656
                         i    i      i    v      v i           v  i i i ii 
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr20_29812973_   1657 GAAAAAATGCTCAACATCACTAATCAT 1683
                              i             ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.07 (56 / 27)
Gap_init rate = 0.02 (8 / 373), avg. gap size = 4.38 (35 / 8)  


3632 19.91 5.82 0.70  chr20_30170399_30173083.rev     1335  2193 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr20_30170399_   1335 AGATATTCCATGTTCATGGACTAGAAGACTCAATATTGTCAGGATGTCAG 1384
                               i             i i       i        i i    v  i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr20_30170399_   1385 TTCTCTCCAAATTGATCTATAGATTCAATGCAATCCTTATCAAAATTCCA 1434
                          v   i             i        i       i         i   
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr20_30170399_   1435 GCAGGTTTTTCTGTAGAAACTGACAAGCTGATTCTAGCATTTATATGGAA 1484
                           v vi    i  i     i            i   iv   i        
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr20_30170399_   1485 ATACAAAGGACCCAGAACATCTAAGACAACCTTAAAAA-------CGTAA 1527
                           i   i          i v i  i    i   i    ------- iv i
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr20_30170399_   1528 TTGGAGGACTTATACTACATAATTTCTAAACATATTATAAAGCTACAATA 1577
                                   i i   v vi      v    v  i  i         i  
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr20_30170399_   1578 -TCAAGACAGTGTGGTA--------AGAATATGCATAAAGATCAGTGGAA 1618
                         -                --------  i   vi    v      i     
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr20_30170399_   1619 AATAATTAAAAGTCTATAAATAAATCTTTACATTTATACTAAATTGATTT 1668
                         v v    i i    i v       i iv         iv v         
  L1M4_orf2#LINE/    306 TAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTT 355

  chr20_30170399_   1669 TCAACAAAGCTGACAAGGCAAATTCAATAGAGAAACATAAGTCTTTTCAA 1718
                           i    i v  v    i v -      i i    v vv           
  L1M4_orf2#LINE/    356 TCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr20_30170399_   1719 AACATAGTGCTTGGACCACTGGGTAGCCATATGCACA----------TGG 1758
                         v v  i     v    v     i  ?   i     v ----------   
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr20_30170399_   1759 A-----ACCTCAGAACATACACACAAAAATTAAGTCAAAATGGATCACAG 1803
                          -----      v v    i   --        v             ?  
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACA--AAAATTAACTCAAAATGGATCAWAG 502

  chr20_30170399_   1804 AACTAAACAAAAAAGCTAAAACTCAAAAACCTCTATACGGAAAAAATAAG 1853
                          v     iiv  i          vv     iii  v -i     v   i 
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA-AGAAAACATAGG 551

  chr20_30170399_   1854 ---AAATCATTGTGATCTTGGGTTAGGCAAAAATGTCTTAGATACAACAC 1900
                         ---     v i    i              vii v         ii    
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_30170399_   1901 CAAAACCAGAATCCATTAAAAAAATTATA-ATAAATTAAATTTCATAAAA 1949
                              v  v  v v iv   i   vv   -       ii i     v   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_30170399_   1950 ATTTAAAAACTTTTACACTTCCAAAGATACCACTAAGAAAATGAAAAGAT 1999
                            -          iii    v  i  i  i ii      i        i
  L1M4_orf2#LINE/    652 ATT-AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_30170399_   2000 GGGCCAAAGACTAGTGGAAAATTCTTTGCAAATCACATACCTGATAAGGA 2049
                         iiv   v   v i vi      -v           i   i         i
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAAT-ATTTGCAAATCATATATCTGATAAGGG 749

  chr20_30170399_   2050 ACTTATATCCAGAATATACAAAGAAC-------ACTTAATAAGAAAATGA 2092
                             i             i       -------   i     v    v  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_30170399_   2093 CAA----TCCGATTTAAAAATGGACAAGAGATTTGTACAGAAATT-CACC 2137
                            ----i  i   ?        i   ii      v i   v   - v  
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr20_30170399_   2138 AAAGAAGATATATGAATGACTAATAAGCATA---AAATATATTTAATATC 2184
                                     ii    i i        i ---   v  ii i  i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr20_30170399_   2185 ATTTGTCAA 2193
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.71 (106 / 62)
Gap_init rate = 0.02 (16 / 903), avg. gap size = 3.50 (56 / 16)  


 268 17.05 5.68 1.14  chr20_30453672_30456870.rev      392   479 (2720)    L1M4_orf2#LINE/L1      817   908 (0)  

  chr20_30453672_    392 AAATGGGCAAA--ACT--AATAGAAAATTCACGCAGGAAGATGATA-AAA 436
                                    -- i --      v v   v vv i      -   -   
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT-ATACAAA 865

  chr20_30453672_    437 TGGTCAGTAAGCATATGAAAAGGAATTCATCATCAAGGAAATG 479
                            i  i      i        ivii   v     ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.14 (8 / 7)
Gap_init rate = 0.04 (4 / 92), avg. gap size = 1.50 (6 / 4)  

 415 29.37 5.59 0.70  chr20_30453672_30456870.rev     1547  1689 (1510)    L1M4_orf2#LINE/L1        1   150 (758)  

  chr20_30453672_   1547 TAAAAAAACATACTATATCCATGAACTGGAAGAC--AACATGGCCAAGAT 1594
                          ii   i i  v i  i i    i i        --  i  v ii     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_30453672_   1595 GTCACTTCTCCCCAAACTAACCAATGGGTTTAATGCATTTACTATTGAAA 1644
                          v  v v         i i i v ii i  i  i   v iv    ii   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_30453672_   1645 CTCCACCAAAACTTTATTGTAGA---TAATA---TGATTCTAAAATTCAT 1688
                         ii   v viv-    v   i   --- i i ---    i           
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_30453672_   1689 A 1689
                          
  L1M4_orf2#LINE/    150 A 150

Transitions / transversions = 2.50 (30 / 12)
Gap_init rate = 0.03 (4 / 150), avg. gap size = 2.25 (9 / 4)  

1977 24.40 10.38 2.52  chr20_30453672_30456870.rev     1995  2707 (492)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr20_30453672_   1995 TAAAATTTCCATGTAAAGACAAAGAAACCAGAATAGCTGAAACAACTCTG 2044
                                ivi   v   vi   i i v          ii      iii  
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr20_30453672_   2045 AAAAAGAAAAACGAAGGTGGAGGAATAACACTACCTGATTTTAGGACTTA 2094
                                 i   i   v       v v     v  ii    i ii     
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_30453672_   2095 CTATACAGCTACATTACAGTAATCAAGACAGTACGGTATTGACAGAGGAA 2144
                            i v       -----              ii    i  i  v i i 
  L1M4_orf2#LINE/    240 CTACAAAGCTACA-----GTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr20_30453672_   2145 CAGATGCGTAGGTCAATGAGCCAGAACAGTGTGCGTAGGAATAGAACTTT 2194
                         i   iiii   i      iivi    iv v v ivi  i    -   i--
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA-AACC-- 331

  chr20_30453672_   2195 TCACAAAAT-ATGGCCAACTGACTTTTGCTAGAGGTGAGAAAGCAATTCA 2243
                         -  i v v -    i   i   i   i vi ii    vv  ii v     
  L1M4_orf2#LINE/    332 -CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr20_30453672_   2244 ATAAATAAAGAATAATCATTTTAAGCAAATGGTTTTGGAATAATTGGTCC 2293
                           iiiv        i  v   i  -        vi   i i  i   viv
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAA-CAAATGGTGCTGGGACAACTGGATA 429

  chr20_30453672_   2294 CCCA-----AAAAGGAAAATGAACATTGA--TGTAACCTTATGCTTAATT 2336
                         ?   -----     ---      -i   i--iviv    i ii ivv  v
  L1M4_orf2#LINE/    430 KCCACATGCAAAAG---AATGAA-GTTGGACCCCTACCTCACACCATATA 475

  chr20_30453672_   2337 TAAAAATTAATTCAAA-TGCAATCACAGACTTAAATGTAA-AGC------ 2378
                         i         i     -  -i    ?    i         -   ------
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATG-GATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr20_30453672_   2379 -ATACAACTTTTAGAAAAAAA-----GAGAAAATTTT-----------GT 2411
                         -   v    i      i    ----- ? v    i  -----------  
  L1M4_orf2#LINE/    525 TATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr20_30453672_   2412 TAGCCAAAGAGTGCTTAGATATGACACCAAAAA---AAACTATAAAATTT 2458
                            v   v iv v                   i---  i v i    vv-
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA- 623

  chr20_30453672_   2459 AAAAATAGATAAATTAGACTTCATAAGAATTCAAACCTTTTGCTCTATGA 2508
                                        i        v i    v   v      iv  vii 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr20_30453672_   2509 AGCACACTCTTAGGCAAATTAAAAGAT-----------TAGGAGAAAATA 2547
                           v     v i i v  i v      i----------- i          
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr20_30453672_   2548 TTTGCAAATCACGTATCCAACAAATAACTTGTGTCTAGAACA-------- 2589
                                    ii    ii i  ivi      i  i    i --------
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr20_30453672_   2590 ----------CTCAACAGTAAGAAAA-----AATCCAATTTGAAAATAG- 2623
                         ----------     i i   i  i -----  i      ?i     i -
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr20_30453672_   2624 -AAAAGTCTTGAACATAAACTACACCAAAGAGAATATTCAAATGGAACC- 2671
                         -   i vi     i v v i v v       ii    v       --  -
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG--CCA 871

  chr20_30453672_   2672 -TAAGGAGATGAAAAGATATTCAACATCATTAGCCAC 2707
                         -    v v          ii         ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.93 (112 / 58)
Gap_init rate = 0.03 (23 / 769), avg. gap size = 4.00 (92 / 23)  


1153 15.58 0.50 0.00  chr20_30704554_30708266     1267  1465 (2248)    L1M4_orf2#LINE/L1        1   200 (708)  

  chr20_30704554_   1267 TGGAAAAATA-CCAATGTTCATAGATCTAAAGACCCAATACCATTAAGAT 1315
                               i   -  v        i   ivi     ii    iii       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_30704554_   1316 GGCAAGACTCCCCAAATTGATCTTCAGATTCAACACAATCTCCATCAAAA 1365
                              v                 v          i     i i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_30704554_   1366 TTCCAACTTGGTTCTTTACAGAAATTGACAAGCTGATCCTAAAATTCATA 1415
                          i   i  vvv  i   i                                
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_30704554_   1416 TGGAAATTTAAGGGACTCAGAAAAGCTAAAACAGTCCTGAAAAAGAATAA 1465
                                vi       i     v   i      i  i          v  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

Transitions / transversions = 2.10 (21 / 10)
Gap_init rate = 0.01 (1 / 200), avg. gap size = 1.00 (1 / 1)  

2419 12.28 8.83 11.68  chr20_30704554_30708266     1752  2419 (1294)    L1M4_orf2#LINE/L1      176   824 (84)  

  chr20_30704554_   1752 CCAAAAAAA----GAAGAAGAAAAAATGAACAATGTTGGAGTGCACACAC 1797
                               v  ----   i     -----      v       vi v     
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAA-----GAACAAAGTTGGAGGACTCACAC 220

  chr20_30704554_   1798 TTCC-AATTTCAAAAATTACTATAATAAACTACAGTAATCAGGACAATGT 1846
                             -          v      i  -- i            i    i   
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACAA--AGCTACAGTAATCAAGACAGTGT 268

  chr20_30704554_   1847 GGTACTGGCATAAGGACAGACATAGAGATCAATGAAATATAAATAAGAGT 1896
                                         i       v         i    -i   ------
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATA-GAAT------ 311

  chr20_30704554_   1897 CCTGAGAGTCCAGAAATAAACCCTCACATTTG-GTTCAGCCG-------- 1937
                         --                     vi      i- v   iii --------
  L1M4_orf2#LINE/    312 --TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGA 359

  chr20_30704554_   1938 CAAGAG--CCGAACATATTTAATGGTGGAG----------TTCAA----T 1971
                             i --  i ivvi   i     v i i----------     ---- 
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr20_30704554_   1972 GG-----GGAAAACAGAGT-----CTTGCAAAAGAAAGAGGTCAGACCCC 2011
                           -----   v   v ii ----- v          v  i  ii      
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC 459

  chr20_30704554_   2012 TGCCTCACACCATACACAAAAATTAA-----AGTGGATGA-AAAC--AAA 2053
                          i            i           ----- i     v - i  --   
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr20_30704554_   2054 TGTAGGAGCTAAAACTATAAAACTCT-----GAGAACATAGACATAAATC 2098
                             i                     -----  i       i?i      
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr20_30704554_   2099 TTCATGACCTTGGATTAGGCAATAGTTTCATAAATATGATACCAAAAGCA 2148
                            i         i         i     v  i      i          
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr20_30704554_   2149 CAAGCAACCAAAGAAAAAATAGAC----TAGGCTTCATCAGAATTTAAAA 2194
                                 v              i---- i i        i    v    
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr20_30704554_   2195 TTTTGCATCAGGCATGGTGGCTCACACCTGAAATCCCAGCACTTTGGGAG 2244
                         i   ----------------------------------------------
  L1M4_orf2#LINE/    660 CTTT---------------------------------------------- 663

  chr20_30704554_   2245 GCTGTGGCAGGAGGATCGCTTGAGACTGGACACTATCAAAAAAGTGAAAA 2294
                         --    ------------   v i --            i          
  L1M4_orf2#LINE/    664 --TGTG------------CTTCAAA--GGACACTATCAAGAAAGTGAAAA 697

  chr20_30704554_   2295 GACAACCCACAGGATAGGAGAAAATAACTGACAATCATATATCTGATAAC 2344
                                     i  i          vi  vv                 v
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_30704554_   2345 AGA-TTCTAACCAGCATATATAAAGAACCCTTACAACTCAATAATAAAA- 2392
                         i  -  v  v    v             i                    -
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_30704554_   2393 GACAAATAGCCCAGTTTAAAAATGGGC 2419
                                 i    i  ?          
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGC 824

Transitions / transversions = 1.96 (53 / 27)
Gap_init rate = 0.04 (23 / 649), avg. gap size = 5.96 (137 / 23)  

 624  5.56 0.00 0.00  chr20_30704554_30708266     3132  3221 (492)    L1M4_orf2#LINE/L1      819   908 (0)  

  chr20_30704554_   3132 ATGGGCATAGGATGTAAATAGACATTTCTCCAAAGAAGACATACAAATGG 3181
                                v     v i                       i          
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr20_30704554_   3182 CCAATAAGCACATGAAAAGATACTCAACATCATTAGTCAT 3221
                                              i          ????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (3 / 2)
Gap_init rate = 0.00 (0 / 90), avg. gap size = 0.00 (0 / 0)  


3597 15.80 3.35 1.87  chr20_30991057_30992795      501  1247 (492)    L1M4_orf2#LINE/L1      151   908 (0)  

  chr20_30991057_    501 TGGAGATACAAGGGATATAGA-TAGTAAGAAAAAAATCTTGAGAAAGAA- 548
                             i  i       ivi   -   iv --   v        i      -
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCA--AAACAATCTTGAAAAAGAAG 198

  chr20_30991057_    549 --CAGAGTTGAAGGACTCACAATTCCCAAGTTCAAAACTGAATATGAAGT 596
                         --  i     i          v       v         v v  ii   i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_30991057_    597 TA-AGTAATCAAGACAATGTGATACTGGCATAAAGAAAGACATGTAAATC 645
                           -             i    i           i  v      i  i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_30991057_    646 AATGGAATAGAATTTAGAGTTAAAAAATAAATTCTCACATT-ATGATCAA 694
                                       v     iv i       ii vi     -   i    
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_30991057_    695 TTGATTTTTGACAAGAATGCTGAGACAATCAAATGGGGAGA-AATAATAT 743
                                 i      ii   ii    v  iv        i -    i --
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT-- 396

  chr20_30991057_    744 ATTTTTTAAAACATGTCCTGCTGGGACAATAGGGATAACTTTATCTGTAT 793
                         -i    i  v v   v--           i-v     ? i-- iv  i -
  L1M4_orf2#LINE/    397 -CTTTTCAACAAATGG--TGCTGGGACAAC-TGGATAKCC--ACATGCA- 439

  chr20_30991057_    794 TAGAAGAATGAAGTTAGACTCCTACCTCATAACACATACAAAAATTAACT 843
                         --i            i   i         i v  i               
  L1M4_orf2#LINE/    440 --AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr20_30991057_    844 CCAAATGGATCATAGACCTAAATGTAAGAGCCAAAATTATAAGACTTTTA 893
                          v          ?                  i    i     i   i   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr20_30991057_    894 GAAGAAAATAAATGGA-AAATACTTGTGACCTT-----AGACAGTG-TGT 936
                                 i v v ?i-    vi i        -----  i  i  - v 
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_30991057_    937 CTTAGATATGACACCAAAA--ACAAGCTACAAAAGAAAAAAACAGATAAA 984
                                            --      v             -i       
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAA 636

  chr20_30991057_    985 TTGGACTTTGTCAAAATTAAAAACTTTTGGGCTGCAAAGGATACCGTCAA 1034
                                 ii                   v   v       i  ii    
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr20_30991057_   1035 GAAAGTGAAAGGGTAACC-------TGAAAGAAAATACTTGCAAATCATA 1077
                                   i ii    -------  ii        i            
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr20_30991057_   1078 TATCTGATAAGGGACTAGTATCCAGAATATATAAAGCACTCTTGCAACTT 1127
                                         v                   v      i     i
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr20_30991057_   1128 GATAA--AAATGATAAATAACCAAATTAAGATACGGGTAAAGGATCTAAA 1175
                         i    --   v  i        v    ? i v i   i       i i  
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_30991057_   1176 TAAACATTTCTTCAAAGAAGATGTACAAATGGCTAATAAGTATATTAAAT 1225
                           i        i          i          i      i i  v   v
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_30991057_   1226 GATGGTGAACATCATTAGCTAT 1247
                             v v       ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (78 / 36)
Gap_init rate = 0.02 (18 / 758), avg. gap size = 2.17 (39 / 18)  


1345 17.51 3.52 25.92  chr20_30998223_31002363     2536  3700 (441)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr20_30998223_   2536 AAGATTTAC--TGTTAATGGGT-AGAAGACTC--TCTGATTAAGAATAAA 2580
                              v v --    v    i -i       i-- v vi      vviv 
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr20_30998223_   2581 ATTATCTCCAAATTGATTTATAGGTTAACTGAAATACCAATCAATATCCC 2630
                           vv  i          i  i  i  v vi v   v  v     v     
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr20_30998223_   2631 AGAAGAATTTTT-GTAGAAATTGACACACTGATTCTAAAATTTATTT--- 2676
                           vv vv     - i           vi     i        i  v ---
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr20_30998223_   2677 ------AGG---CCAG-----TCAAAATAGCTTTGGCAAAGGA-AACTAA 2711
                         ------   ---    -----i     i iii   iv    i -   v  
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr20_30998223_   2712 GATGAAGGGCTAACATTGCCTGATTTCAAGACTTATTGTGAAGCCATGGT 2761
                          v  i   i  v   i v  ii       i     i iii    i ii  
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr20_30998223_   2762 AATCAAGACAGTGTGGTAATGGCATAGAGACAGACAGACAGATCAATGGA 2811
                                           v       ii  i     v i           
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr20_30998223_   2812 ATGGCACAGAAAGTCCAGAGATATATCCATACATATATGGACATCTG-TT 2860
                           i v iv  i        i   v i        v     v  vi  -  
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr20_30998223_   2861 TCTGACAAAAGTGCAAAGGCAATTCAGTGGAGAAAAGACAGTCTTAAAGC 2910
                          ii     ii    v   i v     i   i    ii i      -----
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT----- 399

  chr20_30998223_   2911 AATGAACTTGGATCCACACCTCACACCACATACAAAAAGCAATTCAAAAT 2960
                         -------  ------------------------------   i---    
  L1M4_orf2#LINE/    400 -------TT------------------------------CAAC---AAAT 409

  chr20_30998223_   2961 GGGCCATGCATGATGGTTCACACCCGTAATCCAAGCACTTTGGGAGGATG 3010
                           ----   -----------------------------------------
  L1M4_orf2#LINE/    410 GG----TGC----------------------------------------- 414

  chr20_30998223_   3011 AGGTGGGAAGATCACTTGAGGCCAGAAGTTCGAGACCAGCCTGGCCAACA 3060
                         ---     -------------------------------------    -
  L1M4_orf2#LINE/    415 ---TGGGA-------------------------------------CAAC- 423

  chr20_30998223_   3061 TGGCAAAACCCCATCTCTGCTAAACATACAAAAAATTAGCCAGGCATGGC 3110
                            -- v ?  ------------    i     i ----------   --
  L1M4_orf2#LINE/    424 TGG--ATAKCC------------ACATGCAAAAGA----------ATG-- 447

  chr20_30998223_   3111 GGTGCCTGCCTGCAATCCCAGCTACTCGGGAGGCTGAGGCACAAGAATCG 3160
                         ------------------------------------------   -----
  L1M4_orf2#LINE/    448 ------------------------------------------AAG----- 450

  chr20_30998223_   3161 CTTGAACCTGGGAGGCGGAGGCTGCAGTGAGCCAAGATCGCACCACTGCA 3210
                         -   i   i------------  i ------- ----  i     - ii 
  L1M4_orf2#LINE/    451 -TTGGACCC------------CTAC-------C----TCACACCA-TATA 475

  chr20_30998223_   3211 CTGCAGCCTGGGCAACAGAGCAAGACTCTGTCTCAAAAACAAACAAAACA 3260
                          ---------------------------------     iv   ------
  L1M4_orf2#LINE/    476 C---------------------------------AAAAATTAAC------ 486

  chr20_30998223_   3261 ACAAAACAACAACAACAACAACAAAAATGGAACATAGAACTAAAGGCAAA 3310
                         ---------------------iv        v  ?   v     v i  i
  L1M4_orf2#LINE/    487 ---------------------TCAAAATGGATCAWAGACCTAAATGTAAG 515

  chr20_30998223_   3311 AGTTAAAACTA--AAACTTCCAGAAGAAATCGTAGGAGAAAACCTTTGTG 3358
                           i        --     iii        v i    ? v   i   i   
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr20_30998223_   3359 ACCTTGGTTTAGGCAAAGATTGTTTGCATGCAACACCGATAGAGCATGAT 3408
                                v        v i  vi  iv  iii     i --i    ii v
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA--AAGCACAAG 613

  chr20_30998223_   3409 TCATAAAATATCAAGTTAATAA--CAG--TTTATCAAACTTAAAAACTTC 3454
                         iv i    v vv  i vi    --ii --  i      v          i
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr20_30998223_   3455 TGCTCTTCAAAAGACACTGTTAAGAGAAC--AAAGATAAACCACAGACTG 3502
                           iv       i      i i    i ii--     i  v       v  
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr20_30998223_   3503 GGAGAAGATATTTGCAAATCCTATATCTGATAAAG--CTCCTATTTAGAA 3550
                               i             v            i --  iv   ii    
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr20_30998223_   3551 TATATAAA---CTCTCAGAACTCAACAAGGAAA---CAAGTAATACAATA 3594
                                 ---    i v       i  vi   ---   i   iv    v
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr20_30998223_   3595 AAAACATTAGAAAGAGGTTTGAATAGACACTTCACCAAATTTGAAGAGAC 3644
                         ?   v  vi v  ii i            i   v     ---     v -
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA---GAAGATA- 859

  chr20_30998223_   3645 TTCACTGTAAGAATTAAAGAGGAAACACGAAGGACAGCTCAACAGTCAAC 3694
                          v  ----  viiii  vi  v --  i   iiivv        -   ??
  L1M4_orf2#LINE/    860 TACA----AATGGCCAATAAGCA--CATGAAAAGATGCTCAACA-TCAZZ 902

  chr20_30998223_   3695 AGGGAC 3700
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.63 (124 / 76)
Gap_init rate = 0.04 (40 / 904), avg. gap size = 8.57 (343 / 40)  


 341 29.17 2.50 0.83  chr20_31004543_31006521.rev      362   481 (1498)    L1M4_orf2#LINE/L1      472   593 (315)  

  chr20_31004543_    362 TACACAACAATTAATTGAAGATGGATCATAGAGCTAAAT-TAAAAGCCAA 410
                           i    v      i v  i        ?   v      -   i   i  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAA 521

  chr20_31004543_    411 AATCTCTAG--TTTCTAGAGGGAAATCTAAGAGAATATCTTTGTAATTTT 458
                           -  v  i--i ii    i i   iv  i ? v v     i  i ii  
  L1M4_orf2#LINE/    522 AA-CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr20_31004543_    459 AATGTAAGCAAAAATTTATTAGA 481
                         iivv  i    vii   v     
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGA 593

Transitions / transversions = 2.00 (22 / 11)
Gap_init rate = 0.02 (3 / 122), avg. gap size = 1.33 (4 / 3)  

2059 20.26 3.52 0.66  chr20_31004543_31006521.rev      496   949 (1030)    L1M4_orf2#LINE/L1      219   685 (223)  

  chr20_31004543_    496 ACTTGCTGATTTCAAAACATATTACAAAGCTACAGGAATCAAGACAGTGT 545
                             v ii          v  i             v              
  L1M4_orf2#LINE/    219 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 268

  chr20_31004543_    546 GGTACAGGCATAAAAACAGACATATAAACCAATGGAATAGAA--GAGAGT 593
                              v       ii i         i i             --      
  L1M4_orf2#LINE/    269 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 318

  chr20_31004543_    594 ATCCAAAAATAAAGCCTCACATATATAGCCAAATGATATTCAACAAAAGT 643
                         --   i       v  vi    v   i i   v    v   i    ii  
  L1M4_orf2#LINE/    319 --CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr20_31004543_    644 GCCAAGACCACTCAATTGGGAAAGA-TAGTCTCTACAACAAATGGTTTTG 692
                                   i     v        -      i v           vi  
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr20_31004543_    693 GGAAAACCGAATTGCCACATGCAAAAGAGTAAAACTGGACTGTTATTTTA 742
                            v   i i  v?              i i  ii     ivi  ii i 
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr20_31004543_    743 TGCCATATACAAAAATGAACTCAAAATGAATTAAATACCTAAAGATAATA 792
                         ii              v           i  i ? v       vi   v 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr20_31004543_    793 CCCAAAACTGTAAAAACTCCTAGAA-AAAATATGGAGGAAAAGCTTCATA 841
                         v i      i     -   i     -    i  i i? v   v    i i
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATCTTCGTG 565

  chr20_31004543_    842 ACATTGGATTAGGCCATTATTTCTTGGATATGACACTAAAAAAACAGGCA 891
                           v    i      v  vi      i          i    iv   i   
  L1M4_orf2#LINE/    566 ACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr20_31004543_    892 ATGAAAGCAAAAATAGA------------CATTAAACTTGAAAACCTCTG 929
                          ii    v         ------------   i   v  i     i i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr20_31004543_    930 TGTATCAAAAAACGTAATCA 949
                           iv     ii  iiv    
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCA 685

Transitions / transversions = 1.97 (59 / 30)
Gap_init rate = 0.01 (6 / 467), avg. gap size = 3.17 (19 / 6)  

 984 13.52 3.69 6.15  chr20_31004543_31006521.rev     1244  1487 (492)    L1M4_orf2#LINE/L1      671   908 (0)  

  chr20_31004543_   1244 CAAAAACCACAATCAACAATCAACCCAATGAAAACGA-AGCCTACAGAAT 1292
                             iiv   v     v  ------- i      -  - i  i       
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAA-------AGTGAAAA-GACAACCCACAGAAT 712

  chr20_31004543_   1293 GGGAGAAAGTATCTGAAAATCATATCCCTGATAAGAGGTTAATATCCATA 1342
                                 i   i  v         vi        i ii vi      v 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr20_31004543_   1343 ATATATAAAGAACTCCTACAACTTAA-----AAACAACAAC--ACCCAAT 1385
                                        i       i  -----   vi    v--       
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr20_31004543_   1386 TTGAAAATGGGCAAAAGACTTGAATAGATATTTATTTCTCCAAAGATGAT 1435
                          ?i            i  i         i    ----         v   
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTT----CTCCAAAGAAGAT 858

  chr20_31004543_   1436 ATACAA-TGGCCAACAAGCACATGAAAAGATGATTGCCAACCTCATGAAT 1484
                               -       i                 v ---    v   ?????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCT---CAACATCAZZZZZ 905

  chr20_31004543_   1485 CAT 1487
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.67 (20 / 12)
Gap_init rate = 0.03 (8 / 238), avg. gap size = 3.00 (24 / 8)  


 566 19.81 0.00 0.00  chr20_32258269_32262787.rev     2555  2660 (1859)    L1M4_orf2#LINE/L1        1   106 (802)  

  chr20_32258269_   2555 TGGAAAGCCATCTCATGTTCATAGATTGGAAGAATCAATATTGTTAAAAT 2604
                                vi   i         i          v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_32258269_   2605 GTCCATACTACTTAAAGTGATTTACAGATTCAATGCAGTCCTTATCTACA 2654
                          v v     v ii   v    i           i   i   i    v v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_32258269_   2655 CACCAG 2660
                         iv    
  L1M4_orf2#LINE/    101 TCCCAG 106

Transitions / transversions = 1.33 (12 / 9)
Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.00 (0 / 0)  

 938 25.28 2.97 1.86  chr20_32258269_32262787.rev     2972  3240 (1279)    L1M4_orf2#LINE/L1       97   368 (540)  

  chr20_32258269_   2972 AAAATACCAATGACATTCTTCACAAAAATATTTTTAAAAG----TCCTAA 3017
                              v   iivi v  i  ii  i    ---- v v   ----      
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAAT----TGACAAGCTGATCCTAA 142

  chr20_32258269_   3018 AATTTATATGGAACAGCAAAAGACCCAGAATAGCCAAAGCTATCCTGATC 3067
                             i        vv    ii                 i v   i   vv
  L1M4_orf2#LINE/    143 AATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr20_32258269_   3068 AAACAGAAAAAAGCCGTAGGCATCACA-TACCTGATTTCAAGTTATACTA 3116
                           iv    v    ii v   vv     - v  ii       iviv     
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTA 242

  chr20_32258269_   3117 CAAAGCTATAGTAACCCAAACAGCATGGCACTAGCATAAAAACAGATACA 3166
                                 i     i v i    ii   i   i      ii i   i i 
  L1M4_orf2#LINE/    243 CAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA 292

  chr20_32258269_   3167 TAGACCAATGGAACAGAATAGAAAACCCGGAAACAAATCTATACATTTAC 3216
                             i        i     v  i ii  i    i   i i         i
  L1M4_orf2#LINE/    293 TAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr20_32258269_   3217 AGTCAACT---CTTTAATAAATGGTGC 3240
                         i     i ---i  ii i  i-     
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAG-GGTGC 368

Transitions / transversions = 2.40 (48 / 20)
Gap_init rate = 0.02 (5 / 272), avg. gap size = 2.60 (13 / 5)  

1714 22.45 6.24 1.04  chr20_32258269_32262787.rev     3547  4027 (492)    L1M4_orf2#LINE/L1      403   908 (0)  

  chr20_32258269_   3547 AATAAATGGTGCTGGAAAAACTGGATATCCATATGAAGAAGAATTAAACT 3596
                           i            i v         ?   i   v i      v  ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr20_32258269_   3597 ATACCCCCATTTCTCACCATATACAAAAATCAAATCAAAATGGATTAAAG 3646
                         iv     i ii  v                i  v           i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr20_32258269_   3647 ACTTAAGTGTAAGAACTGAAACTATGAAACCACTAGAAGAAAACAT-TGT 3695
                           i   i       i  i       i    ivi             -v ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr20_32258269_   3696 GGAAATGCTTGAGGATGTTGGTCCTGGCAAAGATTTCTTGAGTAAGACCT 3745
                          v    -   viv  iv    viiv     v i      iii  v   vi
  L1M4_orf2#LINE/    553 GTAAAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_32258269_   3746 CAAAAGCACAAGCAACCAAAGCAAAAATGGACAAATGCGATAATATCAAG 3795
                                         v    v      i  i    vv  ivvi     i
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_32258269_   3796 GC-AAAAACCT--GCACAGCAAAGGAAACAATCCATAAAGTGAAGAGATA 3842
                         ii-      i -- ii vv       v  v   v v        i   i 
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACA 701

  chr20_32258269_   3843 ACCTACAGAATGGGA--AAATATTAATACACACTAGTCAACTGACAAGGG 3890
                            i           --       -- i  v ii vvi v    i     
  L1M4_orf2#LINE/    702 ACCCACAGAATGGGAGAAAATATT--TGCAAATCATATATCTGATAAGGG 749

  chr20_32258269_   3891 ATTAATAACCAGAATATGTAAGGAACTC----AACTCACTGGTTTAAAAA 3936
                          i vi  v         i   i      ----      v ii --     
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT--AAAAA 797

  chr20_32258269_   3937 -------AATCCAATTTAAAAATG-------------AACAGGCATTTCT 3966
                         -------  i      ?       -------------  i  i       
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_32258269_   3967 CAAAAGAAGGCATACAAAGGGCCAACAGGCATATGAGTAAATAGTCAATA 4016
                          v       ii       v      i i   i    iv i  iv    i 
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_32258269_   4017 TCACTAATCAT 4027
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.60 (64 / 40)
Gap_init rate = 0.02 (10 / 506), avg. gap size = 3.50 (35 / 10)  


2268 15.51 4.28 8.91  chr20_32514671_32518348.rev     1314  1874 (1804)    L1M4_orf2#LINE/L1        4   538 (370)  

  chr20_32514671_   1314 AAAGATATCC-ACATTCATGGATTGGAAGACTTAATATTGTTAAGATGAC 1362
                                   - ii                                  i 
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr20_32514671_   1363 CACACTACCCCAGATTGATACAGATATTGAATCTGTATTGATCAATATGG 1412
                         v i   -     i      -------------------------------
  L1M4_orf2#LINE/     54 AATACT-CCCCAAATTGAT------------------------------- 71

  chr20_32514671_   1413 ATTTTATTGATTCTGTACATTCAATAAAATCCCCTATCAAAATCCAAATG 1462
                         ------------  ii v      iiv      -           v iiv
  L1M4_orf2#LINE/     72 ------------CTACAGATTCAACGCAATCCC-TATCAAAATCCCAGCT 108

  chr20_32514671_   1463 ACTTCTTTTTTTCAGAAATAAAAAAATCCATCCTAAAATTCATATGGAAT 1512
                         i --       v       vi v  iiiv                    v
  L1M4_orf2#LINE/    109 GC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAA 156

  chr20_32514671_   1513 CTCAAAGGACCCTGAATAGTCAAAAGCAGCTTGAAAAA-AAGAACAAAGT 1561
                         iv   i      v      i     vv v         -           
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr20_32514671_   1562 TGGAGGACACATACCTTCCTGATTTGAAAACTTGCTACAAAGCTATAGC- 1610
                                 v  i  -    ii    v       i           i  i-
  L1M4_orf2#LINE/    207 TGGAGGACTCACAC-TTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr20_32514671_   1611 -----------GTGGTATTGGCA----AATCAGACATACAGACCAACAGA 1645
                         -----------      i     ----i  -       i   i   ii  
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGAT-AGACATATAGATCAATGGA 304

  chr20_32514671_   1646 ATAAAC-----AGCCCAGAAATAATCCCTTGCATATATGGTAAAATGCTA 1690
                            i v-----  i          v   v i   v      v  v  v v
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr20_32514671_   1691 TT-GACAATGGTGCCACAGTCATGCAATGGGGAAAGGACAGTCTTTTCAA 1739
                           -     v       viii   v            i i           
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr20_32514671_   1740 CAAATGGTGCTTGGGAAAATTGGACATTCACATTCAAAAAGATGAAGTTG 1789
                                    -    v  i    i ?i     v     ii         
  L1M4_orf2#LINE/    405 CAAATGGTGCT-GGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr20_32514671_   1790 GACCCTTACCCAACACCATATACAAAATTTAACTTAAAATGGATAAAAGA 1839
                              i    iv               v      i         v ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr20_32514671_   1840 TCTAAATGTAAGAGCTAAAATTAAAGAACTCTCAG 1874
                         i                   i  v i      i  
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

Transitions / transversions = 1.50 (51 / 34)
Gap_init rate = 0.02 (13 / 535), avg. gap size = 5.69 (74 / 13)  

 406 25.96 1.92 0.00  chr20_32514671_32518348.rev     2161  2264 (1414)    L1M4_orf2#LINE/L1      537   642 (266)  

  chr20_32514671_   2161 AAAAAAGAACTTAGG-GCAAAGCTTTATGACACTGGATTTGGAAATGATT 2209
                          i  i i   v    - i   v   ii    vi   i  v  v    i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_32514671_   2210 TCTTGGATATGACACCAAAGGTACAGGTGACAAA-GAAAAAACTGACAGG 2258
                             i              i i   i ii     -       iv  i ii
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr20_32514671_   2259 CTGGGC 2264
                         i   i 
  L1M4_orf2#LINE/    637 TTGGAC 642

Transitions / transversions = 3.50 (21 / 6)
Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.00 (2 / 2)  

1219 16.03 2.79 0.35  chr20_32514671_32518348.rev     2900  3186 (492)    L1M4_orf2#LINE/L1      615   908 (0)  

  chr20_32514671_   2900 AAGAAAAGAAAAAATTGACAAATCAGAC---ATCAAAATCTAAAATGTTT 2946
                           v            v  i    ii   ---        -     vv   
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT-TAAAAACTTT 663

  chr20_32514671_   2947 TATACATCAAAGGGCACTATC--TACAGTAAAAAGGAAACC-ACAGAATG 2993
                          i i v       i       --v v   i     iv    -        
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr20_32514671_   2994 GGAGAAAATAATTGCAAATCATGTATTTGATAAGGGATTAACACCCAGAA 3043
                                   v           i   i          i vii i      
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr20_32514671_   3044 TATATAGAGAACACCTAAAACTCAATCGCAAAA-GAAAAAAAAAACAAC- 3091
                               i     v i  v        vii    -  v   v  vv   i-
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr20_32514671_   3092 AACAAATGGGCAAAGGACTTGAAGAGACATTTTTCCAAAGAAGATACACA 3141
                         ? v              i     v        i             i   
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr20_32514671_   3142 AATAGCCAAGAAGCATATGAAAAGATACTCAACATCACAAACCAT 3186
                            i     v     i          i          ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.25 (25 / 20)
Gap_init rate = 0.02 (6 / 294), avg. gap size = 1.50 (9 / 6)  


 367 20.39 4.85 2.91  chr20_32547220_32552657.rev     3207  3309 (2129)    L1M4_orf2#LINE/L1        1   105 (803)  

  chr20_32547220_   3207 TGTAAAGACATCCCATGTTCATGGGTTGAAAAA-TTAATACTCCACTAA- 3254
                           v     i               i   i  i -      i --ii   -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATT--GTTAAG 48

  chr20_32547220_   3255 -TAACCGTACTATTAAAAATT--TCTACAGATTCAATGCAATCCCTACAG 3301
                         - ii vi    viiv   -  --             i          ivi
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAA-TTGATCTACAGATTCAACGCAATCCCTATCA 97

  chr20_32547220_   3302 AAATACCA 3309
                             v   
  L1M4_orf2#LINE/     98 AAATCCCA 105

Transitions / transversions = 2.50 (15 / 6)
Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.60 (8 / 5)  

1015 26.41 2.46 0.70  chr20_32547220_32552657.rev     3616  3899 (1539)    L1M4_orf2#LINE/L1       96   384 (524)  

  chr20_32547220_   3616 CAAAAACAACCAATGACATTCTTCACAGAAATAGAAAAAACAATCCTAAA 3665
                              v --   iivi v  i  ii       v  v  ivii        
  L1M4_orf2#LINE/     96 CAAAATC--CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr20_32547220_   3666 ACTCATACTGAACTACAAAGGATCCTGAATAGCCAAAGCCATTCTGAACA 3715
                          i     iv   v i   i   i  v           i v  ii    v 
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAA 193

  chr20_32547220_   3716 A-------AAAGCTGGAGGCATCACACTACTGGACTTCAAGATATACAAC 3758
                          -------    i      vv       v ivi i     i iv   v  
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC 243

  chr20_32547220_   3759 AAAGCTATAGTAACCAATACAGCATGGTACTGGCATAATAGCAGACACAT 3808
                                i     i   v    ii              viii     i  
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr20_32547220_   3809 AGACCAGTGGAACAGAAGAGAGAACCCAGAAACAAACCCACATATTTACA 3858
                            i  i     i    vv    ii       i       i i     ii
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATG 343

  chr20_32547220_   3859 TCCAACTGATTTTCAATAAAGACACTAAGAACAATCATTGG 3899
                         vi   i        i i  i iii i    v  v   v   
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

Transitions / transversions = 2.00 (50 / 25)
Gap_init rate = 0.01 (2 / 289), avg. gap size = 4.50 (9 / 2)  

 536 22.90 1.53 0.76  chr20_32547220_32552657.rev     4185  4315 (1123)    L1M4_orf2#LINE/L1      370   501 (407)  

  chr20_32547220_   4185 AAGAACAATCATTGGGGGAAAGGACACTCTCTTCAATAAATGGTACTGGA 4234
                             v  v   v -        i i v   i     i       i    i
  L1M4_orf2#LINE/    370 AAGACCATTCAAT-GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 418

  chr20_32547220_   4235 ATAACAGAA-ATCTATATGCTAAA-AATGAAAGTAGACCCCTTTCTCTCA 4282
                          i   v i - ? i i    v   -      iv i       vi   v  
  L1M4_orf2#LINE/    419 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 468

  chr20_32547220_   4283 TAACGTACAAAAATCAACTCAAAATGGATTAAA 4315
                         iv ii         i              i ? 
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWA 501

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.02 (3 / 132), avg. gap size = 1.00 (3 / 3)  

 732 24.62 6.69 1.82  chr20_32547220_32552657.rev     4664  4992 (446)    L1M4_orf2#LINE/L1      564   908 (0)  

  chr20_32547220_   4664 TGGCCCTG----AGCCAA-GATTTTATAAAGAGGACATAAAAAGCACAGG 4708
                           i  i  ----  v   - i   iv  i v v    iv         i 
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr20_32547220_   4709 CAACAAAAATAAAAATAGACAAATTGGGTTATATGAAACTAAAAAGCTTT 4758
                                 iv         i       ii vi  v   v v    i    
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr20_32547220_   4759 GGCATAGCAAAGGAAACAATCAACACAGTGTAGAGACAATCTGCAGAATG 4808
                         v iiivv       v  v     v v    v i      i ii       
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr20_32547220_   4809 GGAGAAAGTATATGCAAACAATTCATCCAACAAAGAA----TATCCAGAA 4854
                                i   v      iv  vi   ii i  i i ----         
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr20_32547220_   4855 TATACAA-GAACTC----AAC--AGCAAAAAAGAAGAAAAACAATGCA-T 4896
                             i  -      ----   -- ii  v   -    v   i  iv  - 
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAA-AAGACAAATAACCCAAT 812

  chr20_32547220_   4897 TAAAAAATGGG-ATATGAGCTAAATAGATATCTCTCAAAATAACAATGTT 4945
                          ?         - v v  vi i      i  i    v   v  -i  i -
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-GATAT- 860

  chr20_32547220_   4946 AAACATAACTAATCATCA----GGGAGATGCAAATCAAAACCACAATGAA 4991
                          v v  ii i   v v  ----iii      ---    v i  ???????
  L1M4_orf2#LINE/    861 ACAAATGGCCAATAAGCACATGAAAAGATGC---TCAACATCAZZZZZZZ 907

  chr20_32547220_   4992 C 4992
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.35 (46 / 34)
Gap_init rate = 0.04 (13 / 345), avg. gap size = 2.15 (28 / 13)  


 818 20.20 0.49 6.40  chr20_33076474_33080170.rev     1986  2188 (1509)    L1M4_orf2#LINE/L1        1   191 (717)  

  chr20_33076474_   1986 TGTAAAGACATCCCATGTCTTTGAATCAGAAAA-TTAATATTGTTAAGAT 2034
                           v     i         iiv  i  ii   i -                
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_33076474_   2035 AATGATAGTCCCATTCTGATCTATAGATCAGCCTTACAGATTCAACACAA 2084
                         iiii   v    ----ii ---  v    -----            i   
  L1M4_orf2#LINE/     51 GGCAATACTCCC----CAA---ATTGATC-----TACAGATTCAACGCAA 88

  chr20_33076474_   2085 TTTCTGTCATAACTCTCAGCTGACTACTTTGCACAAATGGAGTAGCTGAT 2134
                          ii  i   -  v  i      v  vi      v    v  vv       
  L1M4_orf2#LINE/     89 TCCCTATCA-AAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGAT 137

  chr20_33076474_   2135 CCTAAAGTTCATGTGGAAATGCAGGAGACTTGGATTAACAAAAACAGTCT 2184
                               i     i          i i   iii  v  i v      i   
  L1M4_orf2#LINE/    138 CCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr20_33076474_   2185 TGAA 2188
                             
  L1M4_orf2#LINE/    188 TGAA 191

Transitions / transversions = 2.15 (28 / 13)
Gap_init rate = 0.03 (5 / 191), avg. gap size = 2.80 (14 / 5)  

3299 15.20 3.80 5.56  chr20_33076474_33080170.rev     2469  3205 (492)    L1M4_orf2#LINE/L1      185   908 (0)  

  chr20_33076474_   2469 TCTCAAAAAAAAAAAACAACCTAAGACAACTCACA--TCCTGACTTGAAA 2516
                            ii     i  i     vv vi  vi       --   ii i  v   
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr20_33076474_   2517 ACTTACTACAAAGCTGCA---ATCGAGACACTATGCTGCTGGCCTGAGGA 2563
                                        i  ---   i     v i  v i     v i    
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr20_33076474_   2564 TAGACATATTGATCAATGGAATATTGTTGAGAGTTCAGAAATAAACCCTC 2613
                                  v             vvi        i             --
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC-- 332

  chr20_33076474_   2614 ATGCTTATTATGATCAATTGATTTTCAGT--GGGTACCAAGACCATTCAT 2661
                           i v -     i             iii--    i             v
  L1M4_orf2#LINE/    333 ATACAT-TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr20_33076474_   2662 TGGTGGAAACAGTAGTAGTCTTTTCAACAAATGGTATTGGGACCATTTGA 2711
                            -     -- - i                    ii      v i v  
  L1M4_orf2#LINE/    382 TGG-GGAAA--G-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGA 427

  chr20_33076474_   2712 TGTCCACATGCGAAAGAATGAAGTTAGATCCCCTGCCTTATGTCATATAC 2761
                          i?        i             i  -     i   i iii       
  L1M4_orf2#LINE/    428 TAKCCACATGCAAAAGAATGAAGTTGGA-CCCCTACCTCACACCATATAC 476

  chr20_33076474_   2762 AAAA------TTAAAA-GGGTCAAAGACCTAAATGTAAGAGCTAAACCTG 2804
                             ------ i    -  i   ?                      v  i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr20_33076474_   2805 TGAAACCCTTAGAAGAAAACATAAGGATAAAGCTTCATGACCTTGGATTT 2854
                          i    i                i ?i    v    i         i  v
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr20_33076474_   2855 AACAATTTAGCTGTCATACACAATGACATCTGAAGCACAAGCAACCAGAT 2904
                         ii    --- v v  v  v i -     i vi             v i v
  L1M4_orf2#LINE/    577 GGCAAT---GGTTTCTTAGATA-TGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_33076474_   2905 AAA---TA-ATAAATTGGACTTCATCAAAATTAAAACTTTTTGTTCTTCA 2950
                            ---  -                           vi      v     
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_33076474_   2951 GAAAACACAATGAGGAAAGTGAAAAGAGAACCCACAGAATGGAAGAACGT 3000
                         i ii    v  v i             v              i    ---
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA--- 719

  chr20_33076474_   3001 TTTTTGTGGGTAAGGCAGGGTGGGACATCTTTGCAAATAATATATCTAAT 3050
                         -----------  -------------- v         v        i  
  L1M4_orf2#LINE/    720 -----------AA--------------TATTTGCAAATCATATATCTGAT 744

  chr20_33076474_   3051 AAGGGATTTGTATCTAGAATGTATAAAGAACTCTCATAAC--AATAATAA 3098
                               i       i     i             i i   --        
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_33076474_   3099 AAA-------AACCCATTTCAAAATATAGACAAAGGATCTGAATAGATGT 3141
                            -------      v  ?    -  i i        i        ii 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAA-ATGGGCAAAGGATTTGAATAGACAT 843

  chr20_33076474_   3142 TTCTCCAAAGAAGATATATAAATAATTATTAAGCACGTGAAAA-ATGTTC 3190
                                           i    iiii v       i      -   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_33076474_   3191 ACCATCATTAGCCGT 3205
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (73 / 35)
Gap_init rate = 0.03 (21 / 724), avg. gap size = 3.29 (69 / 21)  


3154 14.40 24.69 0.14  chr20_33110994_33114029     1816  2544 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_33110994_   1816 TGGAAAGCTATCTTGTAGTTCATGGATCAGAAGATTTAATATTGTTAAGA 1865
                                v    iii -          ii     i               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCAT-GTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr20_33110994_   1866 TGATAATACTCCCTAAATTGACCTACAAATTCAATGCAATCACTATCAAA 1915
                           ii         i       i     i      i      v        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_33110994_   1916 ATCTCAGCTGGCTTCTTTGCAGAAATTGGCAAGCTGATCCTGAAATTCAC 1965
                            i      v   i             i            i       i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_33110994_   1966 ATGCAAATATAAGGGATGCATAACAGCCAAAACAATCTTGA--------- 2006
                            v    ii      iv  v  i                 ---------
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_33110994_   2007 ----------------------TCT------------------------- 2009
                         ----------------------  i-------------------------
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_33110994_   2010 ---GTAA---------------------ATA------------------- 2016
                         ---    ---------------------   -------------------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_33110994_   2017 --------------------CAAAAATAAACCCGTG--TCTATGATCAGT 2044
                         --------------------  i          i i-- i    i   i 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_33110994_   2045 TGATTTTTGACAAGGTTGCCAAGACAATTCAATGATGAAAGAGTAGTTTT 2094
                                i       v         v        iv      i    i  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_33110994_   2095 TTCAATAAGTGGTGCTGTGACAACTGGATAGTCACATGCAAAAGAATGAA 2144
                              i  i        v            ?i                  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_33110994_   2145 ACTGGACCCCTGCCTCACATGATAAACAAAG-TCAATGCAAA-TGGATCA 2192
                         ii         i       iv   v     i- i  iv    -       
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_33110994_   2193 AAGATCTAAATGTAAGATACAAAA-TATAAAATTCTCAGAAGAATACATA 2241
                         ?   i            vvi    -       i   i       v     
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_33110994_   2242 GG--TAAATCTTTGTGACCTTGGATTAGGAAATGGTTTCTTAGATGC-AC 2288
                           --        i          i     v               ii-  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_33110994_   2289 ACCAATACC-CAAGTAACAAAAGATAAAAT---------GAACTTCATCA 2328
                              v v -    i         v     --------- i         
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_33110994_   2329 AAATTAAAGACTTT-GTGTTTCAAAGGACACCATCAAGAGAGTGAAAAGA 2377
                                 i     -   i            i       i          
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_33110994_   2378 CAGCT-ACTTAATGGGGGAAAATATTTGCAAATTACA---------AGGA 2417
                           i i-  vv      i                i i ---------   i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_33110994_   2418 ATTAGTATCCAGAA----------ACTAATACAACTCAATAATAAAAAGA 2457
                          i v          ----------   vv                     
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_33110994_   2458 CAA----CCCAATCAAGAAATGGAGAAAGCAGATGAACAGACATTTCTCC 2503
                            ----      i? i      iv    v vv    i            
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr20_33110994_   2504 AAAA-------------GTCCAATAA-----TAAACAGATGATCAACATT 2535
                            i------------- v       ----- i  v     v       i
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr20_33110994_   2536 AGTCATCAG 2544
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.19 (70 / 32)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 9.05 (181 / 20)  


3090 28.07 0.99 0.66  chr20_33123000_33129353.rev     4958  5862 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_33123000_   4958 TGGAAGAACATCCCATGCTCATGAATAGGAAGAATCAATATTGTGAAAAT 5007
                              ii i        i     i  v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_33123000_   5008 GGCCATATTGCCCGAGGTAATTGATAGATTCAATGCCATCCCCATCAAGC 5057
                            v   i v   i iv i  iv i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_33123000_   5058 TACCAATTACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5105
                          v   ii i i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_33123000_   5106 TATGGAACCAAAAAAGAGCCCACATTGCCAAGACAATCCTAAGCCAAAAG 5155
                                viiv  ii  v  viv  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_33123000_   5156 AACCAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5205
                            -    i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    199 AAC-AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_33123000_   5206 CTACTGTAACCAAAACAGCATGGTACTATTACCAAAACAGAGATATAGAC 5255
                             v    i   i    ii       ivi iv ii i   v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_33123000_   5256 CAGTGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5303
                           i     i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr20_33123000_   5304 TGTCCGATCTTTGACAAACCTGACAAAAGCAAGAAATGGGGAAAGGATTC 5353
                         iivii   i  i     ivv  v   i v  vvv           i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_33123000_   5354 CCTATTTAATAAATAGTGCTGGGAAAACTGGCTAGCCACATGTAGAAAGC 5403
                         i  v  i  i    i         v      v  ?       i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_33123000_   5404 TGAAACTGGATCCTTTCCTTACACTTTATACAAAAATTAATTCAAGATTG 5453
                             ii    i  i v   i    iv              i    i  v 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_33123000_   5454 ATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5503
                           i ?    i       v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_33123000_   5504 TCTAGGCAATACTATTCA-GGCCATAGGCACGGGCAAGGACTTCATGACT 5552
                         iv    ?ivv v v   i- i  v i  i-ii     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGAT 594

  chr20_33123000_   5553 AAAACACCAAAAGCAATGGCAACAAAAGCCAGAATTGGCAAATGGGATCT 5602
                          vi            vvi          vv i   v ii    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_33123000_   5603 AATTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGAGTGA 5652
                         v  i   v v  i i   i  iiivv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_33123000_   5653 ACAGGCAACCTACGGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5702
                          v  i     i  i              v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_33123000_   5703 AAAGGGCTAATATCCAGAATCTACAAAGAACT--TA-AATTTA-CAAGAA 5748
                           i  i  vi          v  i        --  -  i i -i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_33123000_   5749 AAAAGCAAACAGCCCCATCAAAAACTGGGCGAAGGATATGAACAGACACT 5798
                            ii    i i   v  i?    v     i      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_33123000_   5799 TTTCAAAAGAAGACGTTTATGCAGCCAACAGACACAGGAAAAAATGCTCA 5848
                          i  v        ii vi viii     i ii    v     i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_33123000_   5849 TCATCACTGGCCAT 5862
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (161 / 89)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.36 (15 / 11)  


 416 12.61 3.36 9.24  chr20_33234904_33237110      319   437 (1770)    L1M4_orf2#LINE/L1      797   908 (0)  

  chr20_33234904_    319 AGACAGAACAGATTCAATAATGAAAATAGGAAAAAGCAGAGTAAATTT-- 366
                              -  i - ii    v?-i     i  v   i --------    --
  L1M4_orf2#LINE/    797 AGACA-AATA-ACCCAATTW-AAAAATGGGCAAAGG--------ATTTGA 835

  chr20_33234904_    367 -TAGACATTTCTT-AAAGAAGATACACCAGTGGCCAATAAGCACATGAAA 414
                         -           i-          i  v i                    
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr20_33234904_    415 AGATGCCCAACATCGTTATAGTC 437
                               i       i????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.05 (6 / 112), avg. gap size = 2.50 (15 / 6)  

1896 26.65 0.21 0.21  chr20_33234904_33237110      501   984 (1223)    L1M4_orf2#LINE/L1       23   506 (402)  

  chr20_33234904_    501 GGATGGATAGAATCAATATTGTGAAAATGACCATACTGCCAAAAGCAATC 550
                             v iv   v i        v  i   i v     v  v   vii   
  L1M4_orf2#LINE/     23 GGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATC 72

  chr20_33234904_    551 TACAAATTC-ACGCAGTCCCCATCAAAATACCACCATCATTCTTCACAGA 599
                             i    -     i    i        v   v vv v  i  ii    
  L1M4_orf2#LINE/     73 TACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chr20_33234904_    600 GTTAGAAAAAACAATTCTAAAATTCATATGGAATCAAAAAAGAGCCCACA 649
                         iv v  v  ivii  i                 viiv  ii  v  viv 
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAA 172

  chr20_33234904_    650 TGGCCAAAGCAAGAGTAAGCAAAAAGAACAAATCTGGAGGCATCACACTA 699
                          i      i   vvv i iv  i         vi      vv       v
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT 222

  chr20_33234904_    700 CCTGATTTCAAATTATACTATAAGGCCATAGTCACCAAAACAGCATGATA 749
                           ii        viv     i  i  i i   v i   i    ii  i  
  L1M4_orf2#LINE/    223 CCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTA 272

  chr20_33234904_    750 CTGGTATAAAAATAGGCACATAGACCAATGGAACAGAATAGAGAACCCAG 799
                             i    ii    i  i     i        i     v    ii    
  L1M4_orf2#LINE/    273 CTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAG 322

  chr20_33234904_    800 AAATAAACCCAAATACTTATAGCCAACTGATCTTTGACAAAGCAAACAAA 849
                                    v i i    i i   i    i  i     i vviv   i
  L1M4_orf2#LINE/    323 AAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAG 372

  chr20_33234904_    850 AACATAAAAGTGGGGAAAGGACACCCTTTTCAACAAATGGTGCTGGGATA 899
                          v   vv  -         i i vi                       i 
  L1M4_orf2#LINE/    373 ACCATTCAA-TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr20_33234904_    900 ATTGGTTAGCCACAGGTAGAAGAACGAAACTGGATCCTCATCTTTTACCT 949
                          i   v  ?     v i i     i   ii    i  ii i  ivi   v
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCA 471

  chr20_33234904_    950 TATACAAAAATCAACTCAAGATGGATTGAGGAGCT 984
                                    i       i      ii?i  v  
  L1M4_orf2#LINE/    472 TATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

Transitions / transversions = 1.70 (80 / 47)
Gap_init rate = 0.00 (2 / 484), avg. gap size = 1.00 (2 / 2)  

1291 23.86 1.36 3.18  chr20_33234904_33237110     1276  1715 (492)    L1M4_orf2#LINE/L1      477   908 (0)  

  chr20_33234904_   1276 AAAAA--AACACAAGATGGATTAAGGACCTAAACCCAAGACCTGAAACTG 1323
                              --   v   i      i ?i        ivi    v  i     i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr20_33234904_   1324 TAAAATTTCTAGAAGATAACATTGGAAAAACCCTTCTAGACATTGGCTTA 1373
                              i ii       v     v  ?iv  vi    vv   v    v   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr20_33234904_   1374 GCCAAAGATTTCA-AGACAAAAAAACCAAAAGCAGTTGCAATATAAATAA 1422
                          v   v i    v-   i vi v -         vvv    i v  iv  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACA-CCAAAAGCACAAGCAACAAAAGAAA 625

  chr20_33234904_   1423 AGGTAAATAGCTGGGACCTAATTAAACCAAAGAGCTTTTGCACGGCAAAA 1472
                          ii  i   iv v    i v  i   viv  i i      ii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr20_33234904_   1473 GGAACAGTCAGCAGAGTAAACAGACAACTCACAGAGTGGGAGAAAATCTT 1522
                          iv  vi   iv i   i  v       i      i           v  
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr20_33234904_   1523 CACAATCTATACATCTGACAAAGGACTAATATCCAGAATCTACAATGAAC 1572
                         ii   vii   i      i  i     vi          v  i  v    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr20_33234904_   1573 TCAAACGAATCAGTAAGACAAAAAAAAAAAAAAAAAAAATCAATCCCAAC 1622
                           vv  i v   i   --i     i v   v  -----------     i
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAA--TAAAAAGACAAATAA-----------CCCAAT 812

  chr20_33234904_   1623 -AAAAAGTGGGCTAAGGAGATGAATAGACAATTCTCAAAAGAAGATATAC 1671
                         -?    i     v     vv          v     v             
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr20_33234904_   1672 AAATAGCCAACAA--ACATGAAAAAATGCTCAACATTACTAATGAT 1715
                             i     i  --         i           i ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.17 (55 / 47)
Gap_init rate = 0.02 (7 / 432), avg. gap size = 2.86 (20 / 7)  


2867 18.35 6.80 0.00  chr20_33618144_33619767      501  1132 (492)    L1M4_orf2#LINE/L1      234   908 (0)  

  chr20_33618144_    501 AATTTACTGCAGAG--ACAGTAATAAAGG-AGTATGGTAGTGGCATAA-- 545
                           i     i  i  --        v   i-   i     v        --
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr20_33618144_    546 ------ACATAGATCAGTAGAATAGAACTGAGAGTCCAGAAAGAAATCCA 589
                         ------ i        i i        i              v   i   
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr20_33618144_    590 CATATCTATGGTCAATTGATCTTCAACAAGGGTACCTAGACCATTCAATG 639
                         i i  i              i   i        i  v             
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr20_33618144_    640 GGAAAAGAACCATCTCTCCAACAGATGGAGCTGAGACAACTGGACAGTCA 689
                           i      ivi   i i     i    v    i          i ?i  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr20_33618144_    690 CATACAAAAGTATGAGGTCAGACCCTCACCTCACACTAGATACAAAAACT 739
                            i      v    i  ii     ii         i v         i 
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr20_33618144_    740 AACCCCAAATGGATCACAGACTTAAACATGAGAGTCAAAACTC--AAACT 787
                            i v          ?    i    ii i    ii      v--     
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr20_33618144_    788 CACAGCAGAAAACA--GGCAAAAGTCTTCATGACCTTGGATTTTGCAAAG 835
                          vi  v        --  ?iv  i     i         i  vv    v 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr20_33618144_    836 GTTTCTTAGCTATAAC-CAAAAAGCACAGTCAATAAAAGAAATAA-AAAT 883
                                  v   i  - v         iv   i        v  - i  
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT 633

  chr20_33618144_    884 A-----GACTTCATCAAAATTAAAATCTCTTTTGCTTTAAAGGACACTAT 928
                          -----                   v  i  v     i            
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr20_33618144_    929 CAATAGAGTGAAAAGACAAC--GTAGAAAGTGAGAAAATATTTGCAAGCC 976
                            v i              --ii    v v                ii 
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr20_33618144_    977 ATATA-------AAAATCTAGTAGCCAGAATATACAAAGAACTCCTACAA 1019
                              ------- iiiv  v   v          i         i     
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAA 783

  chr20_33618144_   1020 CTCAACAACAAAACAACAA----TCTAATTTTAAAACGGACAAAGGACTT 1065
                              i  i    vi    ----i i    ?v    i  i       i  
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr20_33618144_   1066 ---TAGACATGTCTCCAA----GATATACAAAGTTCTAAAAACCACATGA 1108
                         ---       v       ----          vvv i  v  v       
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr20_33618144_   1109 AGAC-TGTTCAGTGTCATTAGGAAA 1132
                          i v-  i   iii   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.03 (75 / 37)
Gap_init rate = 0.02 (14 / 675), avg. gap size = 3.07 (43 / 14)  


1200 26.85 6.64 4.32  chr20_34448582_34450220.rev      501  1148 (491)    L1M4_orf2#LINE/L1      246   908 (0)  

  chr20_34448582_    501 AGATACAGTGATTA-----GTGTAGAACCGAAATAGACAAAGAGATAGAC 545
                           v      i  i -----    i v  i iv   -----  -       
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATA-----AG-GATAGAC 289

  chr20_34448582_    546 AAAGAGATCAATGAAACAGAAC--AGAGTTCCCAGAAACAGATCCATAAA 593
                          v v         i  i    i--     --       i i i     v 
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGT--CCAGAAATAAACCCATACA 337

  chr20_34448582_    594 TACATGGGCGCTTAAACATAAAACAGAGATGGTATTTCAAATCAGTGAGA 643
                          vi    v iv  i viv vi -  ii i  vi vvv v v   i  i i
  L1M4_orf2#LINE/    338 TTTATGGTCAATTGATTTTCGA-CAAGGGTGCCAAGACCATTCAATGGGG 386

  chr20_34448582_    644 AAAGGACAGGGTGTTCAATTAATGCTGCTGGGACAATAGGCTAGCTATA- 692
                             i i  vv v     iv    v           iv  v  ? i i -
  L1M4_orf2#LINE/    387 AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr20_34448582_    693 ---GAAAAATGAAATCAGATCCCTATTTCACACCGCATGCAAAGATAAAA 739
                         ---i  i      i ii  i     ii       ii  i    i  v  -
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA- 485

  chr20_34448582_    740 GACCTAAACTTGATTAAATATCTCAATATGAAACAAAAGGAAATAAAATG 789
                         -- ii   v v   i ? v i  v   i i --------  iv     iv
  L1M4_orf2#LINE/    486 --CTCAAAATGGATCAWAGACCTAAATGTAA--------GAGCTAAAACT 525

  chr20_34448582_    790 A--AAATACTTAGAAGAGATC-TAGAATTA--TCTTTATGACCTTGGGTG 834
                          --   iv         i v -   i?v  --    ii           v
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr20_34448582_    835 GGG-AAGGCCTTCTTAAAGAAGTTGCAAAGAAATAAAAGCAAGTGAAGGG 883
                         i  -  v vi      i v v vii v  -  ii v      vvi   ii
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAA-AAGCACAAGCAACAAAAGAA 624

  chr20_34448582_    884 GAAA---ATAAATTTTACTACCCCCAAAGTTTAAA-CTTCTG-AATGTAG 928
                         i   ---       vv   -i vi    i  v   -   i  -iv vi i
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACT-TCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr20_34448582_    929 AAGACAC-------AAAGTTAACAGACAAGCAACACAACTTGGAGAAAAT 971
                          i     -------     v  v      v v   v  - v         
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA-TGGGAGAAAAT 722

  chr20_34448582_    972 ATTTGCGA--CAAA-----GATAACAAGGATTAATATTCACA-TATATAA 1013
                               i --  v -----     --i   i vi   i  v -       
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAA--GGGACTTGTATCCAGAATATATAA 770

  chr20_34448582_   1014 AC--CTCTTTACAAATTAATAAGAAAAAGATG--TGACGCA--TAAAAAA 1057
                          v--     -    v i     v       ii-- i  v  -- ?     
  L1M4_orf2#LINE/    771 AGAACTCTT-ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_34448582_   1058 CTGGGCAAAGTATATGAACAGGCATTTTGCAGAAGAGAAAAATTCAGATG 1107
                         -         v  v    i  i     iv vi    - i v  v  i   
  L1M4_orf2#LINE/    820 -TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA-AGATATACAAATG 867

  chr20_34448582_   1108 ACCGCTAAACACATCATGAGACACTCAGCTTCTCTAATAGT 1148
                         i  iv   i     v vi   ii    i v  v????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (95 / 75)
Gap_init rate = 0.05 (30 / 663), avg. gap size = 2.37 (71 / 30)  


 968 12.82 0.00 1.28  chr20_34595772_34599110      492   647 (2692)    L1M4_orf2#LINE/L1        8   161 (747)  

  chr20_34595772_    492 ATTTTCCACTGTTCACGGATTGGAAGACTTAGTTTTGGTAAGATGGCAAT 541
                           v i   -      i               i v   v            
  L1M4_orf2#LINE/      8 ATATCCCA-TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr20_34595772_    542 ACTCCCCCAAATTAATCTACAGGTTTGACACAACCCTTATCAAAATCCCA 591
                                -     i        i  ii  i   i  i             
  L1M4_orf2#LINE/     57 ACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr20_34595772_    592 GCTCCCTTTTCTGCAGAAATTGAGACACTGACCCTAAAATTCATATGGAA 641
                            v      i            v vi    i                  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr20_34595772_    642 ATGTAA 647
                            i  
  L1M4_orf2#LINE/    156 ATGCAA 161

Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.01 (2 / 154), avg. gap size = 1.00 (2 / 2)  

1316 15.14 3.59 0.80  chr20_34595772_34599110      980  1230 (2109)    L1M4_orf2#LINE/L1      252   509 (399)  

  chr20_34595772_    980 AATAATCAAGATTGTGTAGTACTGGCAAAAGGGTAGACATATATATCAAT 1029
                          i         iv    i         v    i          v      
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_34595772_   1030 GAAACAGAATTAAGAGTCCA-AAATAAACCCATACATTAATGGACAACTG 1078
                          i  i      i        -                 v    v   i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_34595772_   1079 ACTTTAGACAACAGTGCCAAGGT-ATTCAATGGGGAAAGAAGTA------ 1121
                          i   v     vi        ii-                 -  ------
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-TAGTCTTT 400

  chr20_34595772_   1122 TCAACAAATGGTGCTAATGTAACTGGATATCCAAATGCAAAAAAAAGGAA 1171
                                        iivii         ?   v        i  -v   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-TGAA 449

  chr20_34595772_   1172 GCTGGACCCTTACCTTGCAACATATACAAAA-TTAACTCAGTATGGATTA 1220
                          i       i     ii  v           -        iv      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_34595772_   1221 AAGACCTGAA 1230
                         ?      i  
  L1M4_orf2#LINE/    500 WAGACCTAAA 509

Transitions / transversions = 2.00 (24 / 12)
Gap_init rate = 0.02 (6 / 258), avg. gap size = 1.83 (11 / 6)  

 649 17.56 3.05 0.00  chr20_34595772_34599110     1830  1960 (1379)    L1M4_orf2#LINE/L1      537   671 (237)  

  chr20_34595772_   1830 AAAAGAAAACACAAGTGTAAACATTCATAACCTTGGATCAGGCAATGACT 1879
                          i         i i ?     iv   i i       i i        ii 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_34595772_   1880 TCTTGGGTATGACACCAAA-GCACAAGCAACCAAAGAAAACACAGATAAA 1928
                             i i            -           v        v i       
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr20_34595772_   1929 CTAAACTT-A--AAAGTTAAAAACACTTGTGCTTC 1960
                         i ii    - --   i        vi         
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

Transitions / transversions = 4.50 (18 / 4)
Gap_init rate = 0.02 (3 / 135), avg. gap size = 1.33 (4 / 3)  

 743 15.98 11.42 2.74  chr20_34595772_34599110     2241  2459 (880)    L1M4_orf2#LINE/L1      610   847 (61)  

  chr20_34595772_   2241 CAAAAAACAAAA-AAAAAATAAA-AAAT--AA-------AAAAT---AAA 2276
                            iv       -        i -    --i -------     ---   
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr20_34595772_   2277 CTT--GTGTTTCAAAGAACACATGTTTATCAAGAAAGTGAAAGGATAACT 2324
                            --   i       i    -----                i  i   i
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACAC-----TATCAAGAAAGTGAAAAGACAACC 704

  chr20_34595772_   2325 CACATAATAAGAGAAAATATTTGCAACTCATTTATCTGATAAGGGTGCAA 2374
                             v   ii                v    v             vvivi
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr20_34595772_   2375 TAGCCGGAATATGTAAAGAACTTCTACAGCTCAA-AACCAAAAGACAAAT 2423
                           v  i      i         ii    i     -  iv           
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr20_34595772_   2424 T------TTTAAA--TAGGTAAAAGGATCTAAATAGACACTTTT 2459
                         v------  ?   -- i  i   -    i i        i  i 
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAA-GGATTTGAATAGACATTTCT 847

Transitions / transversions = 2.40 (24 / 10)
Gap_init rate = 0.05 (11 / 238), avg. gap size = 2.82 (31 / 11)  

 359 12.82 1.28 3.85  chr20_34595772_34599110     2771  2848 (491)    L1M4_orf2#LINE/L1      833   908 (0)  

  chr20_34595772_   2771 TAAATAGATAATTCTCTGAAGAAGATACACAAATGTCCAATAATAAGCAT 2820
                          i      i v     ii         i       v       ---   i
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA---GCAC 879

  chr20_34595772_   2821 GTGAAAA-ATGCTCAACATCTTCAGTCAC 2848
                         i      -            v????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.03 (2 / 76), avg. gap size = 2.00 (4 / 2)  


2342 19.29 1.45 0.83  chr20_35090165_35093773     1605  2086 (1523)    L1M4_orf2#LINE/L1        1   485 (423)  

  chr20_35090165_   1605 TGAAAAGACATCCTATGATCATGGACTGGAAGACTTGACATTCTTAAGAT 1654
                           i     i    i   v       i          i i   v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_35090165_   1655 GTCAACACTAGCCAATGCGATCTCCATATTCAATGCAATCTCTGTCAAAA 1704
                          v   i   vv    vvi     v  v      i      i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_35090165_   1705 TTCCACAATG---TTTTTGCAGAAAGAGAAAAATCCATCCTAAAACTCAT 1751
                          i   -iv  ---            vv  v  iiiv         i    
  L1M4_orf2#LINE/    101 TCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_35090165_   1752 ACAGACTCTCAAGAAATCTTAAATAGCTAAAACAATCTTAAGAAAGAAAA 1801
                          ii  vviv    ii i ivi      i           i i      i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_35090165_   1802 ACAAAGTTGGAGGTCTCACACCTCCTGATTTTAAAACTTATGACACAAAG 1851
                                      v       i   ii    i        i--i      
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC--TACAAAG 247

  chr20_35090165_   1852 CTATGGTTATCAAAACAGTGTGGTACTGA-ATACAGATAGACATATAGTC 1900
                            ii  v     i              i-   vi             vi
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_35090165_   1901 CAATG-AATAGAATAGAGAGCCCAGAATTAAACCCCCATATCTATGCTCA 1949
                              -        v     i      v       vi i  i    v   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_35090165_   1950 AGTGACTTTTCAACAAGGATTCTAAGCTCATTCAATGGG-AAAGGGCAGT 1998
                          v   -     i      i v i   vi           -    iii   
  L1M4_orf2#LINE/    348 ATTGA-TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_35090165_   1999 CTTT-CAACAAATCGTGCTGGGAAAAATGGATATCCATGTGCAAAAGAAT 2047
                             -        v         v  v      ?   ii           
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_35090165_   2048 GACTTTAGACCCTTATCTAACACCATATACAAAAATTAA 2086
                           vv  i     i  i  v                    
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA 485

Transitions / transversions = 1.63 (57 / 35)
Gap_init rate = 0.02 (8 / 485), avg. gap size = 1.38 (11 / 8)  

1827 18.36 2.42 0.97  chr20_35090165_35093773     2704  3117 (492)    L1M4_orf2#LINE/L1      489   908 (0)  

  chr20_35090165_   2704 AAAATAGA-CATAA---TAAATATAAGAGCTAAAAACTATAAAACTCTTA 2749
                              i  -  ? i---     i            -              
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA-CTATAAAACTCTTA 537

  chr20_35090165_   2750 GACGAAAACATAGGGGAAAAGTTTTATAATACTGGATTTGGCAATGATTT 2799
                           v           ? v   vi  ii i ivi   i  v       i   
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_35090165_   2800 CTTGTGTATGACACCAAAAGCACAGACAAAAAATGAAAAGA---ATAAAT 2846
                            ivi                  ii   v   v     i ---      
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr20_35090165_   2847 TG-ACTTTATTAAGATTAAAAACTTTCATGTGTCAA-GAACACTATCAAC 2894
                           -    i  i  i            ii  iv    - i          v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_35090165_   2895 GGAATGAAAAGGCAACCCACAGAATGGGAGAAAATACTTGTAAATAGTAT 2944
                         ii i       i                        i   i    vi   
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_35090165_   2945 ATTTTATAGGAGATTAATATCTAGAATACATAAAGAACTCCTACAATTTA 2994
                           i v   i i  i vi    i      i           i     i i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_35090165_   2995 ACAAAAACAAAACCCAAAACTCATAATTAAAAAAATGGGCAAAAGACTCG 3044
                          i  v  v  i  vv v   i  --   ?     -        i  i i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCA--ATTWAAAAA-TGGGCAAAGGATTTG 834

  chr20_35090165_   3045 AATAGACATTTCTATAATGAAGATATATAGATGGGCAA-AAGCACATGAA 3093
                                      vi  v         i i    v   -           
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr20_35090165_   3094 AAGATACTCAATATTACTAATCAT 3117
                              i     i  i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.48 (52 / 21)
Gap_init rate = 0.02 (9 / 420), avg. gap size = 1.56 (14 / 9)  


2852 14.10 4.32 9.06  chr20_35280589_35282275.rev      501  1195 (492)    L1M4_orf2#LINE/L1      247   908 (0)  

  chr20_35280589_    501 GTTACAGTAATCAAGACAGCGTGGCACTGGCATAAGGACA---ATACAGA 547
                          i                 i    i             i ---   i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_35280589_    548 TTAATGAAATAGAATTATGAGTCCAGAAATCAACCCTTACATTTATTGTC 597
                          i    i         iv            v     v         v   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_35280589_    598 AAGTGATTC-CTACAAGGATGTATGTGCCAAGGCAATTCGTTAGGGAAAG 646
                           v     i- v      ------        i v    iv i       
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGG------GTGCCAAGACCATTCAATGGGGAAAG 390

  chr20_35280589_    647 AACAGCCTTTTCAACAAATGGGTCTAGGACAACTG------------CAA 684
                           i  i               vv  i         ------------   
  L1M4_orf2#LINE/    391 AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr20_35280589_    685 AAGAA-GA--CTGGACCCCCTACATCACACCATACACAAAAATTAACTCA 731
                              -  --i        -   v          i               
  L1M4_orf2#LINE/    441 AAGAATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACTCA 489

  chr20_35280589_    732 CAATGAATCAGAAACCTAAGGGTAGGAGCCAAAAGTATAAAATTCTTTTA 781
                         v    i    ? i      iv   i    i    v       i    vv 
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_35280589_    782 AGAAAACATAGTAGTAAATCTTCTTAACCTTGGATTACATAATGGCATCT 831
                                    v?          v i       i   vii     iv   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr20_35280589_    832 TAGACATGACACCTAAAGCACAAACAACAACAACAAAACATTTTAAAACT 881
                             i        v         i      -  v    v  vvvv   i 
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAA-AAGAAAAAATAGATAAATT 638

  chr20_35280589_    882 GGACTTCATCAAAATTAAGATTTTTTGTGCCTCAAAAGACAACATCATGA 931
                                           i vi        i     i    vi    v  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGA 688

  chr20_35280589_    932 AAGTGAAAATACAACCTTCAGACTGTGAGAAAATATTTGCAAATCATGTA 981
                                  v      iv    v  v                     i  
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_35280589_    982 TTTAATAAGGAACCTCTAACCAGAG--------AAACCCTTACAACTCAA 1023
                          i i      i  i v  v     i--------i   i            
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_35280589_   1024 TAATATAAAAAGATAAATAAAAGGAAATAAGAGGTGTATAGATTGTAGAA 1073
                              --      i      v-----------------------------
  L1M4_orf2#LINE/    789 TAATA--AAAAGACAAATAAC----------------------------- 807

  chr20_35280589_   1074 GGAAGAAAAAAAGACCAA---AAACATTTTTTTCAATGGACAATGGATTT 1120
                         --------------    ---   ----------     i   v      
  L1M4_orf2#LINE/    808 --------------CCAATTWAAA----------AATGGGCAAAGGATTT 833

  chr20_35280589_   1121 GAATAGACATTCTTCTAAAGAAGATATGCAAGAGACCAATAAGCACATAA 1170
                                    ii  i           i   iv i             i 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr20_35280589_   1171 AGAGATACTCAACATTATTACCTAT 1195
                          i    i        i ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (57 / 39)
Gap_init rate = 0.02 (13 / 662), avg. gap size = 7.15 (93 / 13)  


1753 23.17 2.20 0.73  chr20_35382747_35385159.rev      528   937 (1476)    L1M4_orf2#LINE/L1        3   418 (490)  

  chr20_35382747_    528 GAAAGATATTCCAATGTGTTCATGGATTGGAAGAATTAATATTTCTAAAA 577
                                  i   ---                  v        vi   i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCA---TGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr20_35382747_    578 TGTCCATATTACCCAAAGCAACCTACAGATGAAATGTAATCCCTATCAAA 627
                           v v   i v      vii i        vv  i i             
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_35382747_    628 ATTCCAATGGTATTTTTCACAGAAATAAAAAAGAAAATCCCAAAATTCAT 677
                           i   iiv iv     ii       vi v   vvi    i         
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_35382747_    678 ATG-ACCCACAAGAGACCTCACATAACCAGAGCAATCTTGAGAAAGAA-- 724
                            - vvii    i    iviv   i   i i         i      --
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_35382747_    725 -CAAAGCTGGAGGCATCACACTTCCTGATTTCAAATTATATTACAAAGCT 773
                         -     i      vv          ii        viv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_35382747_    774 CTAGTAATCAAAACAATATGGTACTGACATAA----AAACA-ATAGTTCA 818
                         vi         i   i i        i     ---- i   -    v   
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_35382747_    819 ATTGAAAAGAACAAAGAGCCTGGAAATAGACCCAAGCATATATGGTCAAC 868
                           v   v    ivi    i ii      i     vi   v         i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_35382747_    869 TAATCTTTGACAAGGGCACTAAGAATACACAAAAGGGGAAAGATAACCTC 918
                          i  i  i        ii i    vi iv   vi   i  ii   ii  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_35382747_    919 TTCAATAAATGGTGTTGGG 937
                              i        i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGG 418

Transitions / transversions = 1.97 (63 / 32)
Gap_init rate = 0.01 (5 / 416), avg. gap size = 2.40 (12 / 5)  

 656 20.39 4.61 0.00  chr20_35382747_35385159.rev     1221  1372 (1041)    L1M4_orf2#LINE/L1      403   561 (347)  

  chr20_35382747_   1221 AATAAATGGTGCTTGGAAAACTAGATAGCCACTTACAAAATAATGAAATT 1270
                           i          v   v    i    ?    v i     v      i  
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr20_35382747_   1271 GAACCCTTA-----TACTATATACAAAAATCATCTCAAAATAGATTAAAC 1315
                          i    i  -----i  i            i v        i   i ? v
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr20_35382747_   1316 ACTTAAATATAAAATCTGAAATTTTAAAACTCCTAGAAGAAAACA--GGG 1363
                           i     i   i v  i   i v        i            --  ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr20_35382747_   1364 AAAAAGCTT 1372
                         iv   v   
  L1M4_orf2#LINE/    553 GTAAATCTT 561

Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.01 (2 / 159), avg. gap size = 3.50 (7 / 2)  

1350 23.22 0.00 1.91  chr20_35382747_35385159.rev     1556  1921 (492)    L1M4_orf2#LINE/L1      550   908 (0)  

  chr20_35382747_   1556 GGGAAAAAGCATTTTGACATTGGCCTTGGCAACAATTTTTTGGATATGGC 1605
                           ?iv   v v iv    v    vi v     iii   i  i      i 
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_35382747_   1606 AACTAAAGCACAGGCAACAAACACAAAAATAAAAAAAATAGGACTGCATC 1655
                          v v        i        viv      - i v    v     v    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGATAAATTGGACTTCATC 648

  chr20_35382747_   1656 AAACTAAAAAGTTTCTGCACAGCAAAGGAAACAATCAACAAAATGAAAAG 1705
                            v v    ii  i  ii vv       v  v     v   i       
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_35382747_   1706 GCCATCTACAGAATGGAAGAAAATGTTTGCAAATCATATATATGATAGGG 1755
                         i v i i         i       i                v     i  
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_35382747_   1756 TATTAATATCCAAAATATATAAGAAACTCATACAACTCCATAGCAAAAAA 1805
                         v i vi      i         ii     v        v   ii     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_35382747_   1806 ACAACCCAACGAACCCAATTTTTTAAATGGTCAAAGGACCTAAATAGACA 1855
                             ---- i-         -?vv      v       ii i        
  L1M4_orf2#LINE/    799 ACAA----AT-AACCCAATT-WAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_35382747_   1856 GTTTTCCAAAGAAAACATACTAATGGTCAGCAGGTCTATGGAAGGGTTAT 1905
                         v  i         i i    v     i  ii i ivi   i  i i vv 
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_35382747_   1906 CAACATCACTAAATAT 1921
                                 ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.37 (48 / 35)
Gap_init rate = 0.01 (4 / 359), avg. gap size = 1.75 (7 / 4)  


 253 29.15 18.50 1.88  chr20_35428726_35434981.rev      156   474 (5782)    L1M4_orf2#LINE/L1      537   908 (0)  

  chr20_35428726_    156 AGGGGAAAAGATAA---TGAATTTTCATATCTCTGAATGGGGAAA-GCAT 201
                           ii     v   i--- i   i   i iv ii  ii vi  v  - vv 
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_35428726_    202 TCCTAAACATGACAT---AAGACCTAGAAACCATTTTTTAAAT-GATAAA 247
                           i  i i      i---   vv v  v   v vvvvvv    -      
  L1M4_orf2#LINE/    587 TCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr20_35428726_    248 TCAATCTACATAAAAAT------CTGATATGGCTCAATAGACATCATAAA 291
                          iiiv  v   v     ------  vv i  vi    vi    ii  v  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr20_35428726_    292 CAAGTTCAAAGGACAA---ACAAA----GA-AAAATAATTGCAACTCATA 333
                         v  iv v   i     ---   i ----  -      v      v     
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr20_35428726_    334 TGATAGGTAAGGGTGTTTTTTTTTCTTAGCATGTATATAATAAGCTCCCA 383
                          iviv i      v---i  v v  i-  v  --      vi i   ii 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGA---CTTGTATCC-AGAAT--ATATAAAGAACTCTTA 780

  chr20_35428726_    384 TAA------AATAAGAA---AAATGAC--------AACAT---------- 406
                         i  ------     i  ---    i  --------  v  ----------
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr20_35428726_    407 -----ATAG-----TTTACAGAAAAAGCAAACAAATGGCTCGCAAACATA 446
                         -----    ----- i v  i i  iii v         ivii  i  i 
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr20_35428726_    447 TGACAAGATGCTCAACCTCACTCATAAG 474
                            v            v   ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.16 (50 / 43)
Gap_init rate = 0.04 (16 / 372), avg. gap size = 4.06 (65 / 16)  

2014 17.91 18.34 0.00  chr20_35428726_35434981.rev     3847  4315 (1941)    L1M4_orf2#LINE/L1        1   555 (353)  

  chr20_35428726_   3847 TGGAAAGACATCCCGTGTTCATGGCTCAGAAGCCTAAATATTATTAAGAT 3896
                                 i     i         v ii    v  v      i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_35428726_   3897 GGCAATACTCCCCAA-TTGGTCTGC-------------TCCCTATCAAAG 3932
                                        -   i   i -------------           i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_35428726_   3933 TCCCAGCTAGTTTCTTTGCCAAAATTGACAAACTGATCTTAAAATTCATA 3982
                                 ivi  i     vi          i      i           
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_35428726_   3983 TGGAAAGTCATGGGACCCAGAATAGCCAAA-CAGTCTTTAA---GAAAAA 4028
                               vv  v                   -  i    v  ---   i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_35428726_   4029 CAAAGTTTGAGGACTCACACTTTTCAATTTCAAAACT----GTAAAACAA 4074
                                v              ii             ----ii   i v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_35428726_   4075 CAGTAA------CAGCATGGTACTGGTATAAGTGTAGACTTATAAACCAG 4118
                               ------   ii         i     vi     v    i i  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_35428726_   4119 TGGAGGGGAATTCAGAGTCCAAAAGGAAACAATCACATTGACAGTCAATT 4168
                             ivi     v        i  iv    vvvi     v ii       
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_35428726_   4169 GATTTTATGCAAGGGTGCCAAGACAATTCAAGGGAGAA------------ 4206
                               vvi               v      v  i   ------------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_35428726_   4207 ----------------------------------------------GAAG 4210
                         ----------------------------------------------    
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_35428726_   4211 CTGGACACCTTCCTCAAATCCTGCATAAAAATCAACACAAATTGGATCAC 4260
                         i     v   v     v i v ii i      i   v    v       ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_35428726_   4261 AAACCTAAATGAAAGAGGTAAAAATAAAAAACTCTCATAAGAAAATATAG 4310
                          i         v     v     v  v        i v       i    
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_35428726_   4311 GCATA 4315
                          ?i  
  L1M4_orf2#LINE/    551 GNGTA 555

Transitions / transversions = 1.34 (47 / 35)
Gap_init rate = 0.01 (7 / 555), avg. gap size = 12.29 (86 / 7)  

 217 16.67 12.50 0.00  chr20_35428726_35434981.rev     4643  4690 (1566)    L1M4_orf2#LINE/L1      537   590 (318)  

  chr20_35428726_   4643 AAAAGAAAATATAGGCATAAATGTT-ATGACCTTGGATTA-----TGATT 4686
                          i       i     ?i     v  -i         i   -----  i  
  L1M4_orf2#LINE/    537 AGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT 586

  chr20_35428726_   4687 TCTT 4690
                             
  L1M4_orf2#LINE/    587 TCTT 590

Transitions / transversions = 6.00 (6 / 1)
Gap_init rate = 0.04 (2 / 54), avg. gap size = 3.00 (6 / 2)  

1148 17.90 3.06 0.00  chr20_35428726_35434981.rev     5004  5232 (1024)    L1M4_orf2#LINE/L1      547   782 (126)  

  chr20_35428726_   5004 ACAGGTGTGAGCCACCGC-ACCT--GGCCAGATTATGATTTCTTAAATAC 5050
                          i   ?  i ii vi  i-    --  ii  iiv   i       i   i
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_35428726_   5051 AACACCTAGAGCACAAGCAACAAAAGGAAAAATA----AACTGCACTTCA 5096
                         i     v i                 i       ----  i  v      
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_35428726_   5097 TCACAATTAAAAACTTCTGTTTTCCAAAGAACAACATCAAGAAAATAAAA 5146
                            v            i   vi i     i   vi         i i   
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_35428726_   5147 GTACAACCCACAGAATAGGAGAAAATATTTGCAAATCATATATCTGACAA 5196
                         iv              i                              i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_35428726_   5197 GAGACTTGTATCTACAATATATAAAAATCTCTTACA 5232
                          i          i v          i v        
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

Transitions / transversions = 3.00 (30 / 10)
Gap_init rate = 0.01 (3 / 236), avg. gap size = 2.33 (7 / 3)  

 602 13.56 0.00 1.69  chr20_35428726_35434981.rev     5647  5764 (492)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr20_35428726_   5647 AAAAAAATAGATTACATTAATCATAAAAATAGGCAAAGAACTTGAATAGA 5696
                              i i i  v  -ii   i?-      i       i i         
  L1M4_orf2#LINE/    793 AAAAAGACAAATAAC-CCAATTW-AAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_35428726_   5697 CATTCCTCCAAAGAAGATATACAAATTGCCAATAAGCACATGAAAAGATG 5746
                             i                     v                       
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr20_35428726_   5747 CTTAATGTCACTAGTAAT 5764
                           i  ii   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 6.50 (13 / 2)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.00 (2 / 2)  


2096 16.17 15.47 0.69  chr20_35724696_35729062.rev     1815  2247 (2120)    L1M4_orf2#LINE/L1        1   497 (411)  

  chr20_35724696_   1815 TGGAAACATATCCCATGTTCATGGATCAAAAGACTTAATATTGTTAAGAT 1864
                               v                   iii                     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_35724696_   1865 GGTAATATTCCCCAAATGGATCTACAGATTCAATACAATTTCTATCAAAA 1914
                           i    i         v               ii    ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_35724696_   1915 TTCCAGCTGGATTTTTTTTTCCAGAAAATGACAAGCTGATCCTAAAATTC 1964
                          i       ---ii      v      v                      
  L1M4_orf2#LINE/    101 TCCCAGCTG---CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr20_35724696_   1965 ATATGGAATTGCAAATTGTCCCAAATCACCAAAAGAATTTTGAAAAAGAA 2014
                                 v     ivvii  vi   vi      v   i           
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_35724696_   2015 GAACAAAATTAGAGAACTCACACCTTCTGATTTCAAA------------- 2051
                                i  i   i        i i ii        -------------
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_35724696_   2052 ------TAAT------------------------------------AGAT 2059
                         ------    ------------------------------------    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_35724696_   2060 TAACAGAACAGAATCAATAGTCCAGAAATAAACTCTTACTTTTATGATCA 2109
                         i  ii   i     ii v               i v   v      i   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_35724696_   2110 ATTGATTTTCAACAAAAGTGCCAG----------TGAAGATATAATCACC 2149
                                   i    ii      i----------  ii  v v   vii 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_35724696_   2150 TTTTTCACAAAGGGTGCTGGAACAACTGGATATGCACAT-CTAAAGAATG 2198
                             iv     v        i           ?v     - v        
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_35724696_   2199 AAATTGGACCCCTAACTCATACCATATGCAAAA-TTAACTCAAAGTGAAT 2247
                           i           v    i       i     -          i  i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

Transitions / transversions = 2.29 (48 / 21)
Gap_init rate = 0.01 (6 / 497), avg. gap size = 11.67 (70 / 6)  

 991 16.89 1.83 1.83  chr20_35724696_35729062.rev     2593  2811 (1556)    L1M4_orf2#LINE/L1      491   709 (199)  

  chr20_35724696_   2593 AATGGATCATAGCCATAAGTGTAAAAGCTAAAACTATAAAAACTCTTAGA 2642
                                  ?  v v   i     i                -        
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGA 539

  chr20_35724696_   2643 AAAAAATCACAGGAGTAAATCTTTATCACTTTGGGTTAAGCAATGGGCCC 2692
                          i    -  i   ?         ii v  i        i       vii 
  L1M4_orf2#LINE/    540 AGAAAA-CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_35724696_   2693 ATAGATAC----CTAAAAGCACAAATGACAAAAGAAAAAATAGATACATT 2738
                         v      i---- i          iii                   v   
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_35724696_   2739 TAACTTCCTCAAAACTAAAAAACATTTGTAATACAAATGACATTATCAAG 2788
                         vi     v      i      - v     iv v    v    i       
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_35724696_   2789 AAAGTGAAAAAGGCCAGGCACAG 2811
                                   - i v vv     
  L1M4_orf2#LINE/    688 AAAGTGAAAA-GACAACCCACAG 709

Transitions / transversions = 1.33 (20 / 15)
Gap_init rate = 0.02 (5 / 219), avg. gap size = 1.60 (8 / 5)  

 511  8.54 0.00 3.66  chr20_35724696_35729062.rev     3102  3183 (1184)    L1M4_orf2#LINE/L1      685   763 (145)  

  chr20_35724696_   3102 AAGAAAGTGAAAAGACACCCCATAGAACGGGGGAAAATATTTGCAACTCA 3151
                                          v    i    i   i              v   
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr20_35724696_   3152 TACATCTGATAAGGAACTTGTATCTGTCAGAA 3183
                           i           i         ---     
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATC---CAGAA 763

Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.01 (1 / 79), avg. gap size = 3.00 (3 / 1)  

 790 12.75 4.03 0.67  chr20_35724696_35729062.rev     3728  3876 (491)    L1M4_orf2#LINE/L1      755   908 (0)  

  chr20_35724696_   3728 TATCCAGAATATATGAAGAATTCTTACAACTCAATAATAAAATAAC---C 3774
                                       i     i                     vi  ---i
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAAT 804

  chr20_35724696_   3775 AACTCAGTTTTTTAAATGGGTAAGGGATCTGAATAGGCAGTTCTCCAAAG 3824
                            i  i  ?vv-       i  i    i       i  v          
  L1M4_orf2#LINE/    805 AACCCAATTWAA-AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr20_35724696_   3825 AAGATATGCAAATGAC---TAAGCACATGAAAAGATGCTCAACTTCCTTA 3871
                                i      i ---                        v  v???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr20_35724696_   3872 ATCAT 3876
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.02 (3 / 154), avg. gap size = 2.33 (7 / 3)  


1889 27.56 5.32 2.35  chr20_36081275_36083076      502  1310 (492)    L1M4_orf2#LINE/L1       76   908 (0)  

  chr20_36081275_    502 AGAGTCAGCATAATCCTAATCAAAATCCCAGTAGGATTTCT-GCAGAAAT 550
                            v   i ii     iv             iv vv   i -        
  L1M4_orf2#LINE/     76 AGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAAT 125

  chr20_36081275_    551 ATGA-----TGAGTCTAAAACTGATAGAGAAATGCAAAGGACCCAAAATA 595
                         -   -----   vi      i v   vi         i       i    
  L1M4_orf2#LINE/    126 -TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATA 174

  chr20_36081275_    596 GAAAAGACAATCTTCAAAAATAAGAATGCAGTTACAGAACTTACACTAAC 645
                          vv  i        v     v     iiv    iv  i   i     vv 
  L1M4_orf2#LINE/    175 GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCC 224

  chr20_36081275_    646 TGATTTCAAGGTTTACTATAAAGATACAATAATTAAAGGACAGTGTA-TA 694
                         ii       iii      i    v    i    i  --        i-  
  L1M4_orf2#LINE/    225 CAATTTCAAAACTTACTACAAAGCTACAGTAATCAA--GACAGTGTGGTA 272

  chr20_36081275_    695 CTTGGCATAAAGAAA------------AATG-AACAGAAC--AGAGTTCA 729
                           -       i  v ------------    -  i    i--     i  
  L1M4_orf2#LINE/    273 CT-GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCA 321

  chr20_36081275_    730 GAAATAGACCACACATAGAATAGAGAGTCCAGCTACACACCTGACAAATA 779
                               i   ---    v v -v vi   - ii i- iviii     ivi
  L1M4_orf2#LINE/    322 GAAATAAACC---CATACATT-TATGGTC-AATTG-ATTTTCGACAAGGG 365

  chr20_36081275_    780 TGACAGTAAAATGAAGGGGTGAAAAGAATGGCCTTTTCAATTAAAGGTGC 829
                           v  iv vv  vv iv  - i       i i        iv  v     
  L1M4_orf2#LINE/    366 TGCCAAGACCATTCAATGG-GGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr20_36081275_    830 TATGTCACTTGGCTACTCATATGAAAAAAAAAAAAAATATATATATATAT 879
                          iv v  vi   v  ?i  i   v    i  vi  iv iv iviv  iv 
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr20_36081275_    880 ATATATATATATATATGTATGTATCTTGAT-TCCATCACATCCTATTTAA 928
                         -i i i-i     i viv  -  v  ii v- vv    ? v--- ii   
  L1M4_orf2#LINE/    465 -CACAC-CATATACAAAAAT-TAACTCAAAATGGATCAWAG---ACCTAA 508

  chr20_36081275_    929 ATGTGAAATGTAAAACAATAAAGCTTTCCAAAGGAAACAGACAAGAACAT 978
                             i i vv      v     i  i ivi   i     v vi? v v  
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr20_36081275_    979 CTCTGTGATCCTGGAGTAGGCAAAGATTTCTTAAATAGGACACAAAAAG- 1027
                           ii    i i   iv       v i       i   v     v     -
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGC 608

  chr20_36081275_   1028 -------------AAAAAAACTGATAAATTGGACTACCTTAAAATTTAAG 1064
                         -------------i      iv             v v i      -  i
  L1M4_orf2#LINE/    609 ACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT-AAA 657

  chr20_36081275_   1065 AACTTCTCTTCATCAGAAGACACTATTAC-AGAGTGAAAAGGCAATTCAA 1113
                              i v v v   i i        i v- i         i   ii  v
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr20_36081275_   1114 AAAGTGACAGAAGATACTTGC----TATATATCTGACAAAACACTCATAT 1159
                          i i  iv    i   i    ----i          i  iiv   ii   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr20_36081275_   1160 CTATAATATACAAAAGATTTTTAAAAAATCATTTAAAAAAGGAAAGACAA 1209
                          i v      i   ii i i   v  v-   v v v    i  v i i  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAAC-TCAATAATAAAAAGACAAATAA 806

  chr20_36081275_   1210 CCTAACAGAAACATGAA-AAAGGACCTGAATAGACATATCACAAAAAAGG 1258
                           i  iv?   v   ii-      ii           v  v v   i i 
  L1M4_orf2#LINE/    807 CCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

  chr20_36081275_   1259 ATAGCCAAATAGCCAATAAACATATGACAAGACTTTAAATATCATTAGTC 1308
                            vv     i        i  i    v    ivi v  i    ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr20_36081275_   1309 AG 1310
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.43 (129 / 90)
Gap_init rate = 0.03 (25 / 833), avg. gap size = 2.48 (62 / 25)  


4365 17.69 3.17 0.68  chr20_36133100_36134998.rev      527  1408 (491)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr20_36133100_    527 AAGACATCCCCTGTTCATGAGCTGAAACACTTAAGACTGCTAAAATCGCA 576
                             i     v        iii  i  v      v i  i   i  v   
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr20_36133100_    577 ATACTCCCCAAAGTGACCCGCAGACTCAATGCATTCCCTAGTAAAACTTC 626
                                     v   i ii    i    i   v      vi    iii 
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr20_36133100_    627 AATTACCTTTTTTGCAGAAATGGAAAAGGTGATTGTTAAATTCATAGGGA 676
                          ii i                v  v   v    iv v         v   
  L1M4_orf2#LINE/    105 AGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA 154

  chr20_36133100_    677 ATTGCAAGCGATCCTAAATAGCCAAAACAATACTGAAAAAGAA---C--- 720
                          v      v  i  vi               vi          --- ---
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr20_36133100_    721 -TCTGAGGACTCATACTTACTGATTTTAAAACTTACTACAAAACTACAGT 769
                         - iv         i    v ii    i               i       
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr20_36133100_    770 GATGGAGATAGTGTGGTATGAGCATA-GGATAGACATATACATTAATGGA 818
                         i  vi   i         ivi     -             v  i      
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr20_36133100_    819 ATAGAATTGAGAATCCAGAAATAAACCAATACATCTGTGGCCAATTGATT 868
                                     i              v      i i   i         
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr20_36133100_    869 TTTGACAAGGGTGCTGGG--CATTCAGGTGGAGGAAAAGAGTAGTCTCTT 916
                           i           iii --      i-   i --     i      i  
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAA-TGGGG--AAAGAATAGTCTTTT 401

  chr20_36133100_    917 CAACAAATGGTGCTGGGACAAATGGATATCTACAGGCAAAAGAATGAAGT 966
                                              v      ? i   v               
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_36133100_    967 TGGTCCCCCCCTACATCACACCACATACAAAAACTAACTCAAAACAGATT 1016
                            ---v       v        i         i          ii   i
  L1M4_orf2#LINE/    452 TGG---ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_36133100_   1017 AAGAACGTAAATTTAAGACATAAAATTATAAAACTTCTAGAAGAAAACAC 1066
                          ?ii  v     v     vv     i         ii            i
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_36133100_   1067 AGAAAAAAATTGTCATGACCTGGGATT-GGCAACAGATTATTACATGTGA 1115
                           i?iv    iv  i      v  i  -     ii v  v   v  i   
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_36133100_   1116 CACCAAAAGCATGAGCAACAACCACAAAAATAGATAAATTGGAACTCATA 1165
                                    ii        vviv                  vi    v
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_36133100_   1166 AAAATAAAAAACTTTTGCACATCAAAGGATATTACCTAGAAAGTGAAAAG 1215
                              v           ii v        i i  i v             
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_36133100_   1216 ACAACTTATAG-----GAGAAAATAGTTGCAAATCATTTATGTGATAAAG 1260
                              ii i  -----         v           v   v      i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_36133100_   1261 GTATATTATCCACAATATATAAAGAACTTTTACAACTCAA----AAAAAG 1306
                          vv vv      v               i           ----      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_36133100_   1307 -CAAATAACCCAATTTGAAAATGGGCAAAGGAATTGAACACACATTTCTC 1355
                         -              ?i               v     i v         
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_36133100_   1356 CAAAGA-------TAAACAGCCGACAAGCATACTGAAAGATGATCAGTAT 1398
                               -------i   ii   i i     i ivi       v   ii  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_36133100_   1399 CGTTAGTAAT 1408
                          i????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.67 (95 / 57)
Gap_init rate = 0.01 (12 / 904), avg. gap size = 2.83 (34 / 12)  


 895 22.82 1.28 14.36  chr20_36141289_36144669.rev     1640  2029 (1352)    L1M4_orf2#LINE/L1        1   339 (569)  

  chr20_36141289_   1640 TGGAAAAAC-TTCTATGCTCATGGATAGGAAAAATCAATATTGTTGAAAT 1688
                               i i- i i   i        v    i v i         i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_36141289_   1689 GGCCATACTACCCAAAGCAATGTACAGATTCAATGCTATTCCTATCAAAC 1738
                            v     v      vii  v           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_36141289_   1739 TACCAAAGACATTCTTCACAGAA-TTAGGAAAAACTATTTTTGCATGCAC 1787
                          v   ivvi v  i  ii     -  --  v  i  i-------------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTG------------- 135

  chr20_36141289_   1788 AGCATCTACTAACAAAAACAAAACAAAGAGAAAACAATATTCTAAAATTG 1837
                         --------------------------------------  i        v
  L1M4_orf2#LINE/    136 --------------------------------------ATCCTAAAATTC 147

  chr20_36141289_   1838 ATTCTGAGCCAATAAAAAG--CCCA-AATAGCCAAAGCAATCCTAAGCAA 1884
                           viv  ---   iv  i --    -          i     i i iv  
  L1M4_orf2#LINE/    148 ATATGGA---AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_36141289_   1885 AAAGAACAAAGCCCAGGGCATCACATTACCCAACTTCAAACTATACTATA 1934
                         i          iivii  vv     i v     i      viv     i 
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_36141289_   1935 AGGCTACAGTAACTAAAACAGCATGGAAATGGTACAAAAACAGATACAAA 1984
                          i          ii  i    ii   v v   i i  ii i   i i v 
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_36141289_   1985 GACCAATGGAACAGGGTAGAGAACTCAGAAATAAAGCTGTACACT 2029
                           i        i  ii v    iii          v ii    i 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

Transitions / transversions = 2.07 (60 / 29)
Gap_init rate = 0.02 (7 / 339), avg. gap size = 8.71 (61 / 7)  

1561 27.55 5.68 0.33  chr20_36141289_36144669.rev     2291  2889 (492)    L1M4_orf2#LINE/L1      278   908 (0)  

  chr20_36141289_   2291 ACAAAGAGAGACTCA-AGACTCAAAAAAATA-AAT---AAAT----AAAT 2331
                          i  i  v    vi -   -    vii    -   ---i i ----    
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGA-TCAATGGAATAGAATTGAGAGTCCAGAAAT 326

  chr20_36141289_   2332 AAAGCTGTACACCTACAAG-AATCTGATCTTTGACAAAGCTGATGATAAC 2380
                            v ii    ii  iiiv-   -    i  i     i v  vii v v 
  L1M4_orf2#LINE/    327 AAACCCATACATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACC 375

  chr20_36141289_   2381 AAGCAATGGGGAAAGTATTCTCTATTCAATAAATGGTGCTGGGATAGCTG 2430
                          vv            v  vv   v     i              i i   
  L1M4_orf2#LINE/    376 ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

  chr20_36141289_   2431 GCTATCCATATGCAGAAGATTAAAACTGGACCCATTCCTTTTACCATATA 2480
                          v  ?   i     i    v i  ii       v v   ivi        
  L1M4_orf2#LINE/    426 GATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATA 475

  chr20_36141289_   2481 TAAAAACCAACTCAAAGTGGATCA-AGACTTAA-TGTAAAACCTCCAACT 2528
                         i     ii        i       -    i   -     i v  vv    
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr20_36141289_   2529 ACAAAGACCCTAGGAGAAAACCTAGG---AAAT-------ACCATG--CC 2566
                          i   ivi i   i       v    ---    -------   v  --ii
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr20_36141289_   2567 GGACACCGGC--CCTGGCAAAGACTCCAAAAGTAACTGCAACAAAA--AC 2612
                         i i  vi  i-- i i vv v   v       i vvv         -- v
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr20_36141289_   2613 AAACTGAAAAGTAAAATCTAATTAAACTAAAGAGCTTCTACACAGCAAAA 2662
                            iv  v  i vii ii v  i   v v  i i   i iii vv    i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr20_36141289_   2663 GAAACTATCAACAGAGCAAAAAGACAACTTACAGAATGGGAGAAAATATT 2712
                           v        v i  ii          ii                    
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr20_36141289_   2713 TGCAAACTATGCCACCATCAAAGGCCTAATATCTACAATCTATGAGGAAC 2762
                               ii  iivv iivi  i  v  vi    i v   v   i i    
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr20_36141289_   2763 TT----AAGTCAATAAGCAAGTAACAAAAAACCCCATT-AAAAATAGGTA 2807
                          i----  v       vv  ivi     v     v   -      i  i 
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCA 825

  chr20_36141289_   2808 AAGGACACAAACTGACACTTTTCAAAAGAAGACATACATGCAGCCAACAA 2857
                              ivii  iv    i  i  v        i     viii     i  
  L1M4_orf2#LINE/    826 AAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr20_36141289_   2858 GCATATTTAAAAA-GCTCAGTATCACTAATCAT 2889
                            i  vv   i -     ii    ????????
  L1M4_orf2#LINE/    876 GCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (100 / 64)
Gap_init rate = 0.03 (17 / 631), avg. gap size = 2.12 (36 / 17)  


3102 16.12 13.52 4.78  chr20_36246513_36249161.rev     1015  1746 (903)    L1M4_orf2#LINE/L1        1   796 (112)  

  chr20_36246513_   1015 TGGAGGCAGACTCCATGTTCATGGATCAAAGGACTTAATATTATTAAGAT 1064
                             iiv v ii              iii i           i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_36246513_   1065 GGCAATACTCTTGGAATTCGTCTAAAGGTTCAATGCAATCTCTGTCAAAA 1114
                                   iivi    vi    v  i     i      i  i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_36246513_   1115 TTCCAGCTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCAGAAATTGAC 1164
                          i       ---------------------ii                  
  L1M4_orf2#LINE/    101 TCCCAGCTG---------------------CCTTTTTTGCAGAAATTGAC 129

  chr20_36246513_   1165 AAGATGATCCTAAAATTCATATGGAATTGCAAGAGACCCCAAATA----- 1209
                            v                      v      i     vi    -----
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAA 179

  chr20_36246513_   1210 -------------------------------------------------- 1209
                         --------------------------------------------------
  L1M4_orf2#LINE/    180 AACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATT 229

  chr20_36246513_   1210 ----AACTAACTACAATGCT-CAGGTAATCAAGACAGTTTGGTACCAGCC 1254
                         ----    v       v   -   -             v      ii  v
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAG-TAATCAAGACAGTGTGGTACTGGCA 278

  chr20_36246513_   1255 TAAGGATAGACATATAGATTAAGGGAATAAAATTGAGCATCCAGAGATAA 1304
                                            i  v      i       vi      i    
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr20_36246513_   1305 ACCTTTATGCTTATGGCCAATTGCCTTTCAACAATGGTACCAAGACCATT 1354
                            iv  iii      i      vi    i    v   i           
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr20_36246513_   1355 CATTCAACAGGGGAAAGAAGAGTCTTT-CAACAAATGGTGCTAGGACAAC 1403
                           v -----          v       -              i       
  L1M4_orf2#LINE/    379 CAAT-----GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr20_36246513_   1404 TAGATATTCACAT---------------------------CCACACCATA 1426
                          i    ?i     ---------------------------i         
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr20_36246513_   1427 CACAAAAATCAACTCAAAATGGATCATAGACCTAAATGTAAG--TTAAAA 1474
                         i        i                ?               --i     
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr20_36246513_   1475 GTATAAAACTCTTAGAAAAAAACACAGGATTAAACTTTCATGACCTTGGG 1524
                         v                i      i   ?v    ii   i          
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr20_36246513_   1525 TTAATCTAAGTCTTCTTATATATAACATTAAAGGCACAAATGGCTAAAGA 1574
                            iv v v vi      v    i   ii   i      iiii v     
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr20_36246513_   1575 AAAAA-----AGACTGAACTTCATTACAATTAAAAAGTTTTCTGCTGCAA 1619
                              ----- i i  i       i v         v    v    v   
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr20_36246513_   1620 ACAATATCATCAAGAAAGTGGAAAGACAACCCACATAAACTAAAAAAAAA 1669
                          vi i ii            i              v  -- iii i    
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAA--TGGGAGAAAA 721

  chr20_36246513_   1670 G----GAAAATCACATATCTTATTAAGGGATTTGTATCCAGAGTATATAA 1715
                         v---- v      i      v  -      i           i       
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGAT-AAGGGACTTGTATCCAGAATATATAA 770

  chr20_36246513_   1716 GGAAGCTTTGCAACTCATATACATAATAAAA 1746
                         i   vii  i       -----         
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCA-----ATAATAAAA 796

Transitions / transversions = 2.11 (78 / 37)
Gap_init rate = 0.02 (13 / 796), avg. gap size = 10.31 (134 / 13)  

 666 10.26 4.27 0.00  chr20_36246513_36249161.rev     2042  2158 (491)    L1M4_orf2#LINE/L1      787   908 (0)  

  chr20_36246513_   2042 AATAAATAAAAGTCAAATAACCTAA-----AAATGGGCAAAGGATTTGAA 2086
                              vv     v         i  -----                    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_36246513_   2087 GAGATATTTCTCCAAAGAAGACATGCAAATGGCCAGTAAGCACATGAAAA 2136
                         v   i                i  i          i              
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_36246513_   2137 GATGTTCAGCATCTTCAGTCAT 2158
                             i   i    v????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (7 / 5)
Gap_init rate = 0.01 (1 / 122), avg. gap size = 5.00 (5 / 1)  


 560 12.90 0.00 0.00  chr20_36266759_36269869.rev        3    95 (3016)    L1M4_orf2#LINE/L1      816   908 (0)  

  chr20_36266759_      3 AAACTGGACAAAGGACCTGAATAGGCTTTTCTCCAAAGAAGATGTACAGA 52
                            v   i       ii       i v                i    i 
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr20_36266759_     53 TGGCCAATAAGCACATGACAAGATATTCAACATTACTGGCCAT 95
                                           v     ii       i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.00 (0 / 0)  

2617 13.08 1.88 27.64  chr20_36266759_36269869.rev     1401  2623 (488)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_36266759_   1401 TGGAAAGACACACTATATTCATGGATAGGA----------TTGTTAAGAC 1440
                                 i iv i  i         v   ----------         i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_36266759_   1441 GTCAATACCACCCAAAGCAATATATAGGTTCAATGTAATCC-TATCAAAA 1489
                          v      iv      vii  v  i  i     i i     -        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_36266759_   1490 TTCCAACTGCTTTTTTGTCCAGAAAT-AAAAAGCCACTTCTCAAATTTAA 1538
                          i   i    i     - v       -i v    iiv i  v     i v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTT-TGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_36266759_   1539 AACAGATTGCAATAGGCCCCAAATGGCCAAAACA-TCTTGGAAA-GAAGG 1586
                          vvii v     vi i   vi   i         -     i   -    i
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_36266759_   1587 CCAAAGTTGGAGGACCCAGAGTTTTCAATTTCAAAACTTACTGCAAAGGT 1636
                         v              i  v v  ii                 i     v 
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_36266759_   1637 ATAGTAATCAAAACAGTGTGGTACTTCCATAAAGATAAATGTATGGA-CA 1685
                          i         i             vv     i    i ii   i  -  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_36266759_   1686 AAGGAATAGAATTTTGAATCCCAAAATAATCCCATGCATCTATGGCCAAT 1735
                          v           vv  i   vi      v     i   i     i    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_36266759_   1736 -GATTTTTGACAAGGGTCCCAAGTCCATTCAATGGAGAAAGAATAGTCTC 1784
                         -      i         v     v           i             i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_36266759_   1785 TTCAACAAATTATGCTGAGACAATTGGATTTCCAAACATAAAAGAATAAA 1834
                                   vi     i     i     v?   v iii        i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_36266759_   1835 GTTGGACCCCTGCTTCACACCATATTAAAAAATTTACTAAAAATAGATCA 1884
                                    i i           vv       v   v     i     
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_36266759_   1885 ACAACCTAAATATAAGAGCTAAAACTATAAAACTCACAGAAAAAGCCAGG 1934
                         ?vi        i                       ---------------
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTC--------------- 534

  chr20_36266759_   1935 TGCATTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGT 1984
                         --------------------------------------------------
  L1M4_orf2#LINE/    535 -------------------------------------------------- 534

  chr20_36266759_   1985 GGATCACGAGGTCAGGAGATCGAGATCATCCTGGCTAACACGGCGAAACC 2034
                         ----------- i  i   -------------------------------
  L1M4_orf2#LINE/    535 -----------TTAGAAGA------------------------------- 542

  chr20_36266759_   2035 CAATCTCTACTAAAAATACAAAACAAAACAAAACAAAAAAAATAGATGGC 2084
                         --------------------------------------------------
  L1M4_orf2#LINE/    543 -------------------------------------------------- 542

  chr20_36266759_   2085 CGTGGTGGCGGGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAAGA 2134
                         --------------------------------------------------
  L1M4_orf2#LINE/    543 -------------------------------------------------- 542

  chr20_36266759_   2135 GAATGGAATGAACCTGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCC 2184
                         --------------------------------------------------
  L1M4_orf2#LINE/    543 -------------------------------------------------- 542

  chr20_36266759_   2185 ACTGCACTCCAGCCTGGGCAACAGAGCGAGACTCCATCTCAAAACAACAA 2234
                         -----------------------------------------     ----
  L1M4_orf2#LINE/    543 -----------------------------------------AAACA---- 547

  chr20_36266759_   2235 CAACAACAACAAAAATCATAGAAAAAAAGTAGGGGTAAATCTTAATGAGC 2284
                         -----------------------------    ?         vi   v 
  L1M4_orf2#LINE/    548 -----------------------------TAGGNGTAAATCTTCGTGACC 568

  chr20_36266759_   2285 TTGGATTTGCCAATAGATACTTCTCAGATATGACACCAAAAATACAATCA 2334
                             i  v v    i ---i    i                ii    v  
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGG---TTTCTTAGATATGACACCAAAAGCACAAGCA 615

  chr20_36266759_   2335 ACGTAAATAAAAATGGATAAATTAGACTTCATCAAAATTAAAATCTTTAG 2384
                           iv  iv      i        i                   v    v 
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

  chr20_36266759_   2385 TGCATCAAAGGAAATTATCAAGAAAGTGAAAAGGCAACATATAGAATGGG 2434
                            v        v i                  i    vi i        
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr20_36266759_   2435 AGAAAATATTTGCAAATTGTATATTTGATGAG---TTTAATATACAGAAT 2481
                                          ii     i    i  ---i  i-   v      
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG-TATCCAGAAT 764

  chr20_36266759_   2482 ATGTAAAGAATTTATACTAC--AACAACAAAAAAATA--CAACCCAATTA 2527
                           i       i iv   v  --  i  i     i i --i         ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr20_36266759_   2528 CCAACTAGGTAAAGAACTTGAATAGTTATTTCTCCAAAGAAGATGTACAG 2577
                         vv  v i  i    i i        vi                 i    i
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr20_36266759_   2578 ATGGCCAACAAGCACATGAAAAGATACATCACCAGTCAATAGGGAA 2623
                                 i                i -   v  -   ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGC-TCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.74 (99 / 57)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 20.06 (361 / 18)  


2709 25.93 2.31 3.59  chr20_36458568_36460622.rev      692  1555 (500)    L1M4_orf2#LINE/L1        2   854 (54)  

  chr20_36458568_    692 GGAGAGACAACCTGCATTCACAGATTGGATGACTCAACACAGCAAAGATG 741
                            i   i v  iiii    ii       v    i  i iv iv      
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_36458568_    742 ACAGTCCTCTCCAAATTTATTTATATGTTTAATATAATTCCGATCAAAGT 791
                         i  i v   i       v  i  i vi  i  iii   i  v      i 
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_36458568_    792 TCCAGCAGGAGTTTTTGTAAATATAGATGAGCTGATTCGAAAGTGTACTC 841
                         i     v vvv      i i v  v  ii       i v   i vi ivi
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr20_36458568_    842 TTAAAGGGAAAAGAGCTAGAAATGTTAAAAGAATTTTGGAAATGAAGAAT 891
                         vv   v v  ii  v i    vv ii    v   i   i   v      i
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_36458568_    892 AAAGTTGGAGAAATCACACTACCTGTTTTTAAGACTTACTGTGTAATAAC 941
                                   i v       v  iiv   i  i       ii--  - i 
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTAC--AA-AGC 248

  chr20_36458568_    942 AACAGCAATGAAGACAGTG--GTATTGG---AGGAACAGACTCACAGACC 986
                         v    i   v         --   i   --- i i i    vi i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_36458568_    987 CAGGGAACAGAGTAGAGAGTCCAGAAATAGATCCAGGCAAGTATGGGCAA 1036
                         v v    i   i v               i i   vi  vv     v   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_36458568_   1037 CTGATTCTTGAAAAAGTTTCAAAAGCAACTCCATGGAGAAAGAATAGTGC 1086
                         i     i i  v  i v v v  ii v i  v    i           - 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT-C 397

  chr20_36458568_   1087 TCCCCCA-AAATATTGGTGGCATAATTGGACATCCACAGGCCAAAAAATA 1135
                          iii v -    iv  v   v i  i    i ?     v  v   i   i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_36458568_   1136 AACCTTCACCCAAACTGTACACTGTATGCAAAAATTAACTCAAAATGAAT 1185
                           vi vv    vv  ivi    ii   i                   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_36458568_   1186 CATAGATCTAAATATAAAATGC-AAAACTATAAAACTTTTAGAAGAAAAC 1234
                           ?   i      i   i -  -              i            
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_36458568_   1235 ACAAAAG-AAA--------ACCTAGGTCTTGGTAAAGATTTCTTAGATAT 1275
                          i ii? -   --------    v  vi v  i  v i            
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_36458568_   1276 TACACCAAAAGCACAGGCCATGAAAGAAAAA-TA-ATAAGTTGGACTTCA 1323
                         v              i  v ii         -  -    i          
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_36458568_   1324 TCAAAATTAAAAACTTGTAATCTGTGAACAGCCTTGTTAAGAGAATGAAA 1373
                                         v ivv  vii  vii vi i i    i i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_36458568_   1374 TGGCAGGCCACAAACTGGGAGAAAACGT--GCCAATTAAAGTATCTGACA 1421
                         v i  iv     i v          ii --  v   i v -       i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA-TATCTGATA 745

  chr20_36458568_   1422 AAAGACTTGTATCTAGAATATATATATATGTATATGTACACATACACACA 1471
                          ii          i          v v ---------  v v    ----
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGA---------ACTCTTACA---- 782

  chr20_36458568_   1472 TAACCTCTTTAGACTCAACCTTAAGATAATAAATAATCCAATGAGAAAAT 1521
                         ------------      ivv   i vi i      i     v?i     
  L1M4_orf2#LINE/    783 ------------ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr20_36458568_   1522 CTGTAAAAGACTTGATTAGGTAACTCACCAAAGA 1555
                         vv i   i  i    v   ii vi  v       
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

Transitions / transversions = 1.53 (133 / 87)
Gap_init rate = 0.02 (16 / 853), avg. gap size = 3.19 (51 / 16)  


2561 14.90 8.42 0.00  chr20_36863721_36866656.rev      501   963 (1973)    L1M4_orf2#LINE/L1      197   698 (210)  

  chr20_36863721_    501 AGAATAA-GTTGGGGGACTCACAAGTCCTGATTTCAAAACTTACTAGGAA 549
                             i  -     i         vv   ii                vi  
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_36863721_    550 ACTTCAGTCATCAAGGCAGGGTGGTACGGGTATAAGGATGGGCATACAGA 599
                         i  v    v      i   v       v  i        i i    i   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_36863721_    600 CCAATGGAATAAAACTGAGAGTCCAGACAGAAGCCCTTACACTTACTGCC 649
                         i          i  i            v v  i   v    i   iv i 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_36863721_    650 AATTGATTTTCAACAAGAGTGCCAAGACAATTTAATGGGGAAAGAATAGT 699
                                    i     i          v   i                 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_36863721_    700 GTTTTCAAAAAATGGTGCTGGGACAACTGGATATCCACATGCAAAAGAAT 749
                         v       v                        ?                
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_36863721_    750 GAATTTGGATCCCTGCTTCATACTATATGCAA---------CA------- 783
                            v     i    i i   i  i    i   ---------  -------
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_36863721_    784 -TATAGATCTAAATGTAAGAGCTAAAACTATAAAACTCTCTGAAGAAAAC 832
                         -i ?   i                               iv         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_36863721_    833 ATAAGCCTAAATCTTCATGACTTTGGATTAAACAGTAGTTGCTTAGATAT 882
                            i ?v         i    i    i   ii  i i   v         
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_36863721_    883 TA--------GCACAAGCAACAAAAGAAAAAA-AAATAGAT--------- 914
                         v --------                      - i   i  ---------
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_36863721_    915 ---AAATTAAAAACTTTTGTGCTTTCAGGGGTATCATCAAGAAAGTGAAA 961
                         ---                     iv i  ii ii               
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_36863721_    962 AG 963
                           
  L1M4_orf2#LINE/    697 AG 698

Transitions / transversions = 2.30 (46 / 20)
Gap_init rate = 0.01 (6 / 502), avg. gap size = 6.50 (39 / 6)  

 748 14.07 4.44 0.00  chr20_36863721_36866656.rev     2002  2136 (800)    L1M4_orf2#LINE/L1      688   828 (80)  

  chr20_36863721_   2002 AAAATAATACAATATCCCACAGAACGGGAGGAAATATTTGCAAATCATAT 2051
                            i i v vi i v         i     i                   
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_36863721_   2052 TCCTGGTAAGGGACTTATATCTAGAATATATAAGGAACTCTTACAACTCT 2101
                         vi   i          i    i           i               v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_36863721_   2102 ATAATAAAGAGACAAATAA------TAAAAAATGGGCAAGG 2136
                                 i          ------ ?            i 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAG 828

Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.01 (1 / 141), avg. gap size = 6.00 (6 / 1)  

 297 14.91 13.16 3.51  chr20_36863721_36866656.rev     2331  2444 (492)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr20_36863721_   2331 CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-GGCCAAGGGATCT 2379
                              v  v     i v   v  vvv  vv?     -  v   i    i 
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr20_36863721_   2380 GGATAGACATTTCTTCAAAGAAGATAGATATACACATGGCCAA------- 2422
                          i            i           ----    v        -------
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATA----TACAAATGGCCAATAAGCAC 879

  chr20_36863721_   2423 -------GATGCTCAACATCATTAGCAAT 2444
                         -------              ????????
  L1M4_orf2#LINE/    880 ATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 0.45 (5 / 11)
Gap_init rate = 0.02 (3 / 125), avg. gap size = 6.33 (19 / 3)  


2773 18.90 17.95 1.37  chr20_36959409_36961086.rev      457  1186 (492)    L1M4_orf2#LINE/L1       58   908 (0)  

  chr20_36959409_    457 CCTCCCAAAGTGCTGGGATTACAGGTGTCAGC-CA---CCTGT---AATC 499
                          ii      v  v ----i     i -   i -  ---   i ---    
  L1M4_orf2#LINE/     58 CTCCCCAAATTGAT----CTACAGAT-TCAACGCAATCCCTATCAAAATC 102

  chr20_36959409_    500 TCCAATGATGTTTTTTGCAGAC-TAGAATAGCTTACTCTAAAATTCATAG 548
                         -   iiviiv           v- v  vv    v ii            v
  L1M4_orf2#LINE/    103 -CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATAT 151

  chr20_36959409_    549 GGAATCTCAAGGAACCT-GAATAGCCAACACAACCCTGAAAAAGAAGAAC 597
                             viv     i   i-          v    i i              
  L1M4_orf2#LINE/    152 GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAAC 201

  chr20_36959409_    598 AAAGCTGGCGGATTCACACTTCCTGATTTCAAAACGAACTCCAAAACTCT 647
                             i   v   i          ii          vv   v    i  vi
  L1M4_orf2#LINE/    202 AAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTAC 251

  chr20_36959409_    648 AGCA-TCAA-ACAGTGTGGGGCTGGCATAAAGACAAACATATAGACCAAT 695
                           i -    -         vi         i  i i         i    
  L1M4_orf2#LINE/    252 AGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_36959409_    696 AAAATAGAAT--AGAGTCCAGAAACAAACCCTCACATACACGGTTAAATG 743
                         ii        --            i      vi    vi i   i  v  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_36959409_    744 ATTTTAGACA-GGGTACCAAGGCCATTCAATGGAGAAAAGACCAACCATC 792
                              v    -    i     i           i    i----  ivi  
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAG----AATAGTC 397

  chr20_36959409_    793 TTTCCAACAGATAGTG-TAGGAAAATTGGATATCCGCATGCAAAAGAATG 841
                            i     i  i   - i   v  i      ?  i              
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_36959409_    842 AAGTTAGATCCTTACCCAATACCATATATAAGATTTAATTCAAACTGGAC 891
                              i  i  i    iv i        i  i v    i     v    i
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_36959409_    892 CCATGACCTAAATGAAAGACCTAAAACTATAAAACTCTTAGGAGAAAACA 941
                          v?v          v    v                     i        
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_36959409_    942 TAGAACAAAACCTCCATGATAGTGGATTTGGCAGTGATTTC--------- 982
                            i?vv   i  i i   ivv   i  v    i  i    ---------
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_36959409_    983 -------------------------------------------------- 982
                         --------------------------------------------------
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_36959409_    983 -----------------------------------------------AAA 985
                         -----------------------------------------------   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_36959409_    986 GACATCCTATAGAATGGGAGAAAATA---GTACGTC---TATCTGATAAG 1029
                             v  i i                --- i vi  ---           
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_36959409_   1030 GGATTCATCTCCAGAATACATAGAGAAATCCTAAAATTCAATGACAAAAA 1079
                            i ii v         i   i    v  i  v  i     i i     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_36959409_   1080 CCCAA----CCCAGTTCAAACATGGACAAAGGACTTGAATAGACATTTCT 1125
                         vv   ----    i  ?   v    i       i                
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_36959409_   1126 CCAAAGAAGACATACAGATGGACAACGGGCACATGAAAAGATGCTCAACG 1175
                                   i     i    v   iii                     i
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_36959409_   1176 TCACTCATCAC 1186
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.91 (88 / 46)
Gap_init rate = 0.02 (18 / 851), avg. gap size = 7.83 (141 / 18)  


2560 23.01 4.95 8.17  chr20_37302942_37305276      914  1843 (492)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr20_37302942_    914 TATGTCTTGCTCATGGGTCTGAA---TCAGTATT---AAGAAGTCATTTC 957
                            vi v  i      i iv   --- i i    ---    v v  v v 
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr20_37302942_    958 TCTCCAAAATGGCATATGAATTTAATATAAT-----------TCCAAGC- 995
                           i     v  iiv  iii   i  iii   -----------   v   -
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr20_37302942_    996 -------------AAATGGACACACTAATTCTAAAATTCATTTGGAAATG 1032
                         -------------    v    vi  i  i           v        
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATG 158

  chr20_37302942_   1033 CTAAGAACCTGGCATATTCAAAATAACTGTGAAAA-GAAGAAAAAAGCTT 1081
                          v i i   ii v   vi     i  iiv      -      v    i v
  L1M4_orf2#LINE/    159 CAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr20_37302942_   1082 GAAGTCTTATGCTACCTGATTTCAAGATTTGTTGTAAAGTTACATTAATC 1131
                           i v  i ii  v  ii       i i  ii ii    i    v     
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr20_37302942_   1132 AA-ACTGTA-AGTTTTGTCATCAAAATAGACAAATAGATGAAGGTAACAG 1179
                           -  v  i-i  vi  v   v ii       v      v  v v  i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr20_37302942_   1180 AATTAGAGAGTCCAGAAATATATAACAGAATAGAATTCCGCATATATAGG 1229
                             -               ---   -----------  ii i  v  v 
  L1M4_orf2#LINE/    309 AATT-GAGAGTCCAGAAATA---AAC-----------CCATACATTTATG 343

  chr20_37302942_   1230 GGCAGCTGATTTTCAATAAAG-TGCAAAAGACAATTCAATGAGGACAGGG 1278
                          v  ii        i i  i -   v  -   v        i   v  ii
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAA-GACCATTCAATGGGGAAAGAA 392

  chr20_37302942_   1279 TAGCCTTTTAAACAAATAGTGCTTGAAGCATTTGGATATCCATATGCAAA 1328
                            i     v       i     v i -  vi      ?   i       
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGA-CAACTGGATAKCCACATGCAAA 441

  chr20_37302942_   1329 AATATCTAAACTTTGATCTGTACCTTCTACCATATATAAAAATTTAAA-- 1376
                          iv  --i  v  v  i iv     ivi        i       --  --
  L1M4_orf2#LINE/    442 AGAAT--GAAGTTGGACCCCTACCTCACACCATATACAAAAATT--AACT 487

  chr20_37302942_   1377 -AAAATGGATCATGGATCCAAATATAAAACATAAACTATAAACTATGAAT 1425
                         -           ?i  i i    i   i -----i   -       ----
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGA-----GCTA-AAACTAT---- 527

  chr20_37302942_   1426 ATATACATATAAGTATAAATCCAAATATAAAACATAAACCTATAAAACTT 1475
                         -------------------------------------------      i
  L1M4_orf2#LINE/    528 -------------------------------------------AAAACTC 534

  chr20_37302942_   1476 CTAGAAGAGA---CAGGAGAGAATCTTTGTGACTTTGGATTAGGCAAAGA 1522
                         i       i ---i   ? vi      i     i    i        v i
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG 584

  chr20_37302942_   1523 GTTCTTAGATAAGACAACAAAAGCATAAGT--CAAA-GAAGACATGGACC 1569
                         v          v    v        i   i--    -   i v  i  iv
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATA 634

  chr20_37302942_   1570 AACTGCCTTTCATCAACATTAAAAACATTTGGTCTTCAAAAGATACTGTC 1619
                           i  vvi        v         v    vv       i  i   i  
  L1M4_orf2#LINE/    635 AATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC 684

  chr20_37302942_   1620 AAGAGAGAACACAAAGATAAGCCACAGGCTGAGAGGAAAGCTTTGTAGAA 1669
                             i  --iiv     i  v      iv  i   i   vv    i i v
  L1M4_orf2#LINE/    685 AAGAAAG--TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr20_37302942_   1670 CAAATATCCGCTAAAGGACTTATATCCAGTATATTTAAGGAGCTCTTAAA 1719
                           v     i v   i      i       v    v   i  i      v 
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr20_37302942_   1720 ATTTTATATTAAGAATACAAAGACCCC--CCAAAAATTGAACAGAATATG 1767
                          i iv   v   i  v     v v   --ii?    v  ii  i iv  v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_37302942_   1768 TAAACAGAGACTTTATCAAAAAAGATAAATAGATGGTGAATAGGTACATG 1817
                          i  i   v i  ivi    i      v i i    iv    i i     
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_37302942_   1818 AAAAGATGTTCAACATCATGAGCCAT 1843
                                 i         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (130 / 80)
Gap_init rate = 0.03 (24 / 900), avg. gap size = 5.08 (122 / 24)  


1594 23.75 3.09 1.43  chr20_37412039_37418698     3305  3725 (2935)    L1M4_orf2#LINE/L1        1   428 (480)  

  chr20_37412039_   3305 TGGCAATATGTCCCACATTCATGGTTTGAAAAAAGTAATATCATTAAAAT 3354
                            v  v  i     ii       v   i  i vv      ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_37412039_   3355 GTTCGTACTACACAAAACTATCTACAGATTCAATGTAATCCCTATCAAAA 3404
                          vivi    v v    viv              i i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_37412039_   3405 TTACAA-TGACATTTTCACAAACATTAGAAAAA--AATCCTAAAATTCAT 3451
                          iv  i-  v v    ii  i v   -  v  i--i              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT-GACAAGCTGATCCTAAAATTCAT 149

  chr20_37412039_   3452 ATAGAACTACAAAAGACCCTGAGTAGCCAAAGCAATCTTGAATAAAAATA 3501
                           i   v i   ii     v  i        i          v  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_37412039_   3502 ACAAAGGTGGAGG---CATCACTACCTGATTTCAAAATCTACTATGAAGT 3548
                               v      ---  -    v  ii         ii     ii   i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCA-CACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_37412039_   3549 TATAGCAATATAAAA------AGCACTGACAAAAAAAACAAACATGTGGA 3592
                           i  i   -i  i ------i i    i  v  ii -i i    i i  
  L1M4_orf2#LINE/    249 TACAGTAAT-CAAGACAGTGTGGTACTGGCATAAGGA-TAGACATATAGA 296

  chr20_37412039_   3593 CCAACGGAAGAGAACAGAGAGCCCAGAAATAAATCCAGACATTTACAGTC 3642
                         i   i    v    iv     i           i   v       ii   
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_37412039_   3643 AATTGGTCTTTTACAAAGATGCTGAAAACCAC-CAATGGGAGAAATGACA 3691
                              i i  iv    i i   i-  i    i-       -    vi i 
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCC-AAGACCATTCAATGGG-GAAAGAATA 394

  chr20_37412039_   3692 GCCTCTTCAATAAATAGTGTTGGCAAAACTAGAT 3725
                          i  i     i    i   i   v v    i   
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

Transitions / transversions = 2.33 (70 / 30)
Gap_init rate = 0.03 (11 / 428), avg. gap size = 1.73 (19 / 11)  

1852 23.37 2.74 0.42  chr20_37412039_37418698     4120  4594 (2066)    L1M4_orf2#LINE/L1      423   908 (0)  

  chr20_37412039_   4120 CTAGATATCCACATGCAAGAGAATGGAATTGAACCCTTATCTTAAACCAT 4169
                           i    ?          i      i i   i    i  i  i v     
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr20_37412039_   4170 ATA--AAAATCAACTCAAAATGGATGAAAGGCTTAAATAAAAGACCTGAA 4217
                            --     i              v ?  i i     iv    v  i  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr20_37412039_   4218 ACTGTAAAACTACACATAGAAAACACAGGTA-AAAGCATTTTGATATTGG 4266
                            i       vivviv        i   ?i-   v v iv   iv    
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr20_37412039_   4267 ACTGGGCAATGATTTTTTGGATATGATCACAAAAGCACAGGCAATGAAAG 4316
                         ii i       i   i  i       ivv          i    ii    
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_37412039_   4317 CAAAAATAGGCA--TTG-----CATCAAACT--AAAATTTTTCTGCACAA 4357
                         v        ii --   -----       v --    i    v   vi--
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT-- 670

  chr20_37412039_   4358 CAAAGGAAACAATCAGCAGAGTGAAGAGATAACCTACAGAATTGGA-AAA 4406
                                v  v    iv i      i   i    i       v   -   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr20_37412039_   4407 ATATCTGCAAACCATACATCTGATCAGGGGATCATATCCAAGATATGTAA 4456
                             i      i    i       v    iv ii      ii    i   
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr20_37412039_   4457 GAAACTACAACAACTTAACAGAAAGGAAACAAAGAACCCAATTTAAGTGT 4506
                         ii    viv      i  i iv  ii i     v         ?  ivi 
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr20_37412039_   4507 GGGTGAAGGACCCAAATAGACATTTTTCAAAAAAAGAAATACAAATGGCC 4556
                            ii     iiii           i  v   i    v            
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr20_37412039_   4557 AAAATGTTCATGAAAAAAAGTCCAGCATCACTAATCTT 4594
                           v v iv        i v ii  i     ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (72 / 35)
Gap_init rate = 0.01 (7 / 486), avg. gap size = 2.14 (15 / 7)  

1315 29.03 6.91 2.92  chr20_37412039_37418698     5518  6168 (492)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr20_37412039_   5518 AATATTTATTTCAAAGTTGTAATAATTAATACAGTATGATATTGGCACAA 5567
                           v i   i v     i ii i    i  v     i  i  i     i  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr20_37412039_   5568 G-ACAAA-ATATG---CA-TGGAACA-AATAGAGAA-CCAGAAATAGATC 5609
                          - i i -    i---  -     i -   v    i-         i i 
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr20_37412039_   5610 CAAACGTGTGTATCCACTTGGCTTGTGACAATGGTGACA---CCGCATTG 5656
                           v  i v i ivi  v   ii  vi     v    v  ---  --   -
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACC--ATT- 378

  chr20_37412039_   5657 CAGTGCAGAGAGG-TCATTCCTTCAATAAGAGGAAGTCATATTGGGTCGA 5705
                           i  vi  i  i- vi iii     i  iv  ------ ii    v i 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGG------TGCTGGGACAA 422

  chr20_37412039_   5706 TTGGATAGTCACATGGAAAAAAACGAATCTGGAGCTGTATCACACATCCT 5755
                         i      ?i      v    i  i   vi    v iv  i v    i v 
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr20_37412039_   5756 ACACAAAAATAAATTCCAGATACATTATAGTTTTAAATGTAAACAGTAAA 5805
                          i        v  i  v i  iv  i ?  vii         i-  iv  
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAG-AGCTAA 521

  chr20_37412039_   5806 AACAACAAAATGTTGTAAAGATAAATTTGGGAATA--TTTTCATTACTTT 5853
                            v i    ivi vvi    -   iv i  ?i  -- i   i v  i  
  L1M4_orf2#LINE/    522 AACTATAAAACTCTTAGAAGA-AAACATAGGNGTAAATCTTCGTGACCTT 570

  chr20_37412039_   5854 AGAGTAGTTTAATA-TTTCCCAGGAAAGATAC----AATACTGCCCATAA 5898
                         i iv   vi-   i-    ii  iv v  i  ---- ii  viv v i  
  L1M4_orf2#LINE/    571 GGGTTAGGC-AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr20_37412039_   5899 AA----AGATTGTTAAGTTGATCTTAATTAAAATTAAGAA--TTTGTATT 5942
                           ---- i  v v   i   iv   v  i        i  --     ii 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr20_37412039_   5943 TATCAAAATACACCATTAGGAGAATAAAAATGCAAGCAACAGAGTGGGAG 5992
                          --    iv    i  i i  i i i    vi   v v     i      
  L1M4_orf2#LINE/    670 T--CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr20_37412039_   5993 G---TATTTA-AGATACATTTATTCAACAAGGGGATATTATCCACAAAAT 6038
                         i---     i- i  -   v   iii i     iv vv      --i   
  L1M4_orf2#LINE/    718 AAAATATTTGCAAAT-CATATATCTGATAAGGGACTTGTATCCA--GAAT 764

  chr20_37412039_   6039 ATTTAGGAAGTGTTTCTACAAATCTGTAACAA------------CCCAAT 6076
                           v  --   vii ii     v  vi   i  ------------      
  L1M4_orf2#LINE/    765 ATATA--AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT 812

  chr20_37412039_   6077 T-GGAGATGGGCTTAAAACCTGAATAGGCTCTTCACAAAAGAGGATA-A- 6123
                          -ii i      vv ii ii       i vi   v v     i    - -
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr20_37412039_   6124 AAATAGCCGATAAGCATATGAAACAAT-TTTAACCTCATTAGTAAT 6168
                             i   i       i      vi  -i i   v   ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (124 / 62)
Gap_init rate = 0.04 (30 / 677), avg. gap size = 2.13 (64 / 30)  


3232 26.39 1.22 0.55  chr20_37429796_37435293     4105  5006 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_37429796_   4105 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4154
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_37429796_   4155 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4204
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_37429796_   4205 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 4252
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_37429796_   4253 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTCAGCCAAAAG 4302
                                viiv  ii  v  v v  v     iv     i v ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_37429796_   4303 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 4352
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_37429796_   4353 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGATAGATC 4402
                                 i   i    ii         i iv ii i   v v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_37429796_   4403 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCTGCATATCTACAACT 4450
                                i    i--    i  --        vv iii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_37429796_   4451 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGCATTCC 4500
                          vi    i  i     ivv  vv  i v  vv            v  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_37429796_   4501 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 4550
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_37429796_   4551 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 4600
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_37429796_   4601 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 4650
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_37429796_   4651 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 4700
                         v    ?i v viv   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_37429796_   4701 AACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAA 4750
                         i            vvi           v     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_37429796_   4751 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 4800
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_37429796_   4801 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 4850
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_37429796_   4851 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 4900
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_37429796_   4901 AAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACA---C 4943
                          i    ----   v  i?    i     i     iv    i     --- 
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_37429796_   4944 TTCAGAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 4993
                          i  -       i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    847 TCCA-AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_37429796_   4994 CATCACTGGCCAT 5006
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (139 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 2.00 (16 / 8)  


1521 28.62 2.83 1.16  chr20_37470939_37472531      501  1101 (492)    L1M4_orf2#LINE/L1      298   908 (0)  

  chr20_37470939_    501 CAATGGAACAGAATAGGAAACGCAAAAATAAAGCTGCACACCTATAGCTA 550
                                 i     v ii iiv  i       v iii   ii   i ii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_37470939_    551 TCTGATCCTTGACAAGGCTGAAAAAAAAAAAAAGCAATGGGAAAGGGCTC 600
                         vi    ii i       v  vv  i vv v---v       i  i iv v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCAT---TCAATGGGGAAAGAATA 394

  chr20_37470939_    601 -CCTATTCAATTAATGGTG-TGTGATAACCTGCCTAGCCATATGTA---G 645
                         -i  v     iv       -  v  i   -  vv  ?   i   i --- 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAAC-TGGATAKCCACATGCAAAAG 443

  chr20_37470939_    646 GATGAAACTGGATGCCCAACTTTCACCATATACAAAAATTAACTCACAAT 695
                         i     ii    iv  i v  iv                       v   
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_37470939_    696 ----TAAATATTTTAATGTAAGACCTCAAACAGTAAGAATCCTAGAAGAA 741
                         ----i ? v ii v         v  v    vi   i v  i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_37470939_    742 AACCTAGGAAATGGTATTCTGGACATCAACCTTGGGAAAGAATTTATGAG 791
                            v    ?ivvii v   vv   v iiiv-  i  v  vii   v v  
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGG-TTAGGCAATGGTTTCTTAG 592

  chr20_37470939_    792 -TAAGTCCTCAAAAGCAATTGCAACAAAAAACAGACTTGACAAGTGGAA- 839
                         -  v v vi        vvv         i v i v v  i  i v i -
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr20_37470939_    840 ---ACTAAACCAAAGAGCTTCTATACAGTAAAAGAAACTATCAACAGGGT 886
                         --- ii   viv  i i   i i i vvi   i  v        v ii  
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr20_37470939_    887 AAACAGATATGCTACAGAATAGGAGAAAAGATTCACAAACGATGCAGCTG 936
                         i  v   i vv i       i        v   ii    iv  ii v   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_37470939_    937 GAAAAGGTCTAATATCCAGAATGTATAAGAGAAA-CAAACAATTCAATAA 985
                         iv  i  v  vi          i     -    v- vv    i       
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAA-AGAACTCTTACAACTCAATAA 791

  chr20_37470939_    986 ACGAAAAGCAAATAACCCCATTAAAAACTGAGCAAAAGATATGAACAGAC 1035
                         vvi   ii          v   ?    v  i     i   v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_37470939_   1036 ACTTCTCAAAAGAAGGTATACAAGCAGCCAACAA--ACATGAAAAAAATG 1083
                          i     v       i       iii     i  --         i -  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chr20_37470939_   1084 CTCCACATCATTAATCAT 1101
                            v      ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.24 (93 / 75)
Gap_init rate = 0.02 (13 / 611), avg. gap size = 1.85 (24 / 13)  


2088 23.62 7.22 3.28  chr20_37498692_37500433.rev      493  1254 (488)    L1M4_orf2#LINE/L1      117   908 (0)  

  chr20_37498692_    493 TACAGTAA--GGCAAGTTTATCCTAAAATTTATATGGAAAGGCACAAGCC 540
                          i   v  -- i    i v           i         v   vii v 
  L1M4_orf2#LINE/    117 TGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGAC 166

  chr20_37498692_    541 CTATAATAGCTAAAACAATCTTGAACAAAGAAGAATAAA-TTG------T 583
                          i v      i              -         i   -   ------ 
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAA-AAAGAAGAACAAAGTTGGAGGACT 215

  chr20_37498692_    584 TTCATTTC---ATTTTA----TTATT------CTACCAATA-TTAAG--- 616
                         iv  i   ---    i ----   i ------    - i  - i   ---
  L1M4_orf2#LINE/    216 CACACTTCCCAATTTCAAAACTTACTACAAAGCTAC-AGTAATCAAGACA 264

  chr20_37498692_    617 GTTT----CCTGTATAGCTATAGTAATTTATTCTGACCAATGGGAAAGAA 662
                           v ---- iv i   ivv    vv  v  ----  i      i v    
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATA----GATCAATGGAATAGAA 310

  chr20_37498692_    663 CAGAAAACCCAGAAATAGACCTGCATGAATGTAC--CCAATTAATTTTTG 710
                         iv  i ii         i   --   iv  v  i--i     i     i 
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACC--CATACATTTATGGTCAATTGATTTTCG 358

  chr20_37498692_    711 ACAAAGGTGTAAAAGCAATTAAAT----AAAGGATAGCCTTTTAAACAAA 756
                             i    iv  ii v   v   ----    i    i     v      
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr20_37498692_    757 TTATACTGAAGCAGTTGGATATTAGTAGACAAACGAAAATGATCATCAAC 806
                          vi i   iii  ii      ?ivii vi    -- i     vvv vi  
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAA--AGAATGAAGTTGGAC 456

  chr20_37498692_    807 CTGAACCTCATACCTTATCTAAAAATTAACTCAAAATTGTTCACAAACAT 856
                          ivv      i   v   vi                 v v   ? i  v 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr20_37498692_    857 AAATGTAAAACATAAAATTATAATGCTTTTGGGGGGAAA-ATAGAA--AA 903
                                 i vv     i     vi  i  i ii i   -    i?--  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_37498692_    904 ACTTTTAAGGCATTTGGGGTTAGGGAAAGTGTTCTTAGGTAGAGTTCTTA 953
                          ii  iiv i v  --        v  --  -------  ----      
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTT--GGGTTAGGCAA--TG-------GT----TTCTTA 591

  chr20_37498692_    954 GGTTTGACACCAAAAGCATGATC--CAGAAAAGAAAATA-ATAAATTGGA 1000
                          i v              ii v --  i  i i      -          
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_37498692_   1001 CCTCATCAAAATTAAAAACTTTTGCTCTGTGAAATATTCTATTGAGAG-- 1048
                          i                      iv  vii  iv iv    ii   i--
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_37498692_   1049 -GAAAA--CAAGGTACTGACTGAAAGAATGTATTTGCAAATCACGTATCT 1095
                         -     --   vvi  v  v  ii    vi             ii     
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_37498692_   1096 GACAAAGGATTAGTATCTAGAATATACAAAGAGTTAT--CAA---AAGAG 1140
                           i  i   i v     i        i     ii v --   ---  v i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_37498692_   1141 TAAAAA-ACAAC--ACTCAATTCAAAAATTGGCAAAAGACATGAACAGAC 1187
                               -    v--  i     ?      v      i  iv    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_37498692_   1188 ATTTCACTGAAGAGGGTATACAAATGATATATAAGCACAATTAAAGATAT 1237
                              v ii    i i          iivv         vvv      ii
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_37498692_   1238 GCAACTTTATTAGCCAT 1254
                         v    v i ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (109 / 67)
Gap_init rate = 0.04 (30 / 792), avg. gap size = 2.67 (80 / 30)  


2345 24.05 6.04 5.03  chr20_37747594_37751727     2749  3642 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr20_37747594_   2749 AGACATACCATATTCATGAATTGGATGACTTAACATATTAAAAATGAAAA 2798
                            i  v    i      i      v       i  vv v  i   iv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr20_37747594_   2799 TTCTATACAAATTGA----CAGGTTTAATGTAATTTCTATCAAAACCCCA 2844
                          v  viv        ----   i  i  i i   ii         i    
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr20_37747594_   2845 GCCAGGCATTTTGTAGATACAGATAATATTATTCTAAAATTCATATGGAA 2894
                           iivviv     i   v iv  i  vv v  i                 
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAA 155

  chr20_37747594_   2895 AGGCAAAAAAAAAACAGTATAGCTAAAACA--CTTGAAA--GAAAAATAA 2940
                          v    iii vv--   v     i      --       --   i  i  
  L1M4_orf2#LINE/    156 ATGCAAGGGACC--CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr20_37747594_   2941 AGTGAAAGAAAACACTCTAACCAATTTCAAGATGTATCATGTAGCTA-AG 2989
                            vii  i vv   v  vv          i iv  ii iiv     -  
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr20_37747594_   2990 TAATTAAGACTATGTGGTATTGGTA-GTGGGTAGGCAT------CGATGG 3032
                             i     vi       i   i -iv  i   i   ------ i    
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr20_37747594_   3033 AACAGAATAAAAAA--CAAAAAAAGTCCCATATAAGTTTTGTG---AACT 3077
                           i     vi i i--  i   v iv      i ---   i  ---  i 
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACA---TTTATGGTCAATT 350

  chr20_37747594_   3078 GATTTTAGACAAAAATGCACAAGAA-ATTCAATGGAGGAAGGGCAGTCTT 3126
                               v     iii   -     v-         i i   iii      
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGC-CAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_37747594_   3127 TTCAACAAATGGTGCTGGAGCAATTAGATAATCATATGCAAAAGA-TAAA 3175
                                           ii   i i    ?i  i          - i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_37747594_   3176 TCTCAACTTAAACCTCATACCTTATGTAAAATTTAACTCAAA-----TCA 3220
                         vi vi  iivv      i   v   ii    v          -----   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_37747594_   3221 TATATTTAAAAGTAAAATATAAAACTATAAAACTTTTAGAAGGAAACACA 3270
                         ? v ii    v    i vv               i       i     i 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_37747594_   3271 GGAGAAGATCTTCAAGACTGAGTGGTTAG-TGAGGACATTTTAGACATGA 3319
                           ? v i      iv   ivv -      -ii v iiv i     i    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTG-GGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_37747594_   3320 CACCGAAAGCACAAACAATTTTTAAAACCGGTTAAAAAAGGTA-ATAAAT 3368
                             i         i   i----    --- --      --  -      
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAAC----AAAA---G--AAAAAA--TAGATAAAT 637

  chr20_37747594_   3369 GCAACTTCATTAAAATTAGCCCAATGAAACAGACCAAAATTAGTCTGTG- 3417
                         vvi       i       -----------------    i -- i    -
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTA-----------------AAAACT--TTTGTGC 668

  chr20_37747594_   3418 ---AAAGGTC-CTTTTAGGAGGATAAAAAGACAAGCTATAGACTGGGAGA 3463
                         ---     v -  v i i  iii i         v i i   v       
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr20_37747594_   3464 GAACAGTATTTGCAAACCAC----TTAATAAAGAACTCATGTGAAAAATA 3509
                         i  ---          i  i----i i    i i   ii i vv i    
  L1M4_orf2#LINE/    719 AAA---TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr20_37747594_   3510 TTTGAAGAATTCTAATAACTAAATATTAAAAA-----ACAATCTAATTAG 3554
                          v i     i   v i    v    v      ----- i  i i    ?i
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr20_37747594_   3555 AAAATGTACAAACAACAGGAAGAATTATTTCACTGAA----------AAG 3594
                               vi    vi ivv   v ivi     v ii  ----------  i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr20_37747594_   3595 TGAATAACAAGCATCTCATAACGAAAGATGGTTAACGTTATTAGCCAT 3642
                           ivi  i     ---   i --       v i   i i ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCA---CATGA--AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (138 / 73)
Gap_init rate = 0.03 (31 / 903), avg. gap size = 3.19 (99 / 31)  


2416 26.60 5.23 1.39  chr20_37791816_37794105.rev      938  1798 (492)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr20_37791816_    938 ATGTTAATAGACTGGATGACTCAGTGGTATTAAGATGTCAAT--TGCCCA 985
                              v  i  i    v    i i iv i        v    -- v    
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr20_37791816_    986 TCTCACAATCTTTATATTCAGTACAATCTCAATCAAAATCACAGCAAGGT 1035
                         vv ii--    vi v     iii     i v         v    vivv 
  L1M4_orf2#LINE/     65 AATTG--ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr20_37791816_   1036 ATTTTGTAAAAATTGACAAGATGATTCTAAAATTTACATGGTAATGCAAA 1085
                         v     i i           v    i        i i    v       i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr20_37791816_   1086 GAGAATATAATAACCAAAATAATTTTAGAAAA-AAGGTCAAAATTGCAGT 1134
                          iivvi v    i      i   i  ii    -   iv    i   v  v
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr20_37791816_   1135 ACTCATACAGGCTAATTTTAAGACTTACTATAAAGCTACAATAACCAGGA 1184
                              i  vvv i     i  i        i         i   i  i  
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr20_37791816_   1185 CATTGTATTATCAATGAAATAATATACTCATAAATTAATGGATCACAAGT 1234
                           v   iv  iiiiiiv  vi   v  vi   i  i      vi v  v 
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr20_37791816_   1235 AAG---TCAGACCAAGACCCATACATATATTGACAATTGATGTTTTTAAA 1281
                         i  ---i    vvv i          v   v v        ---   vi 
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT---TTTCGA 359

  chr20_37791816_   1282 CAAAGGTAC-AAAACTAA-CAAAATGAAAAAGGTAACG----CACCCA-- 1323
                            i   i -  i  i v-   viv i   iii  iiv----  v v --
  L1M4_orf2#LINE/    360 CAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAAT 409

  chr20_37791816_   1324 -----TGGAAAAATTGCAT---CATATCCAAAAATATATAAATTGTAATC 1365
                         -----   i v  i  v  ---  i  v     iv  i-  i   -i i 
  L1M4_orf2#LINE/    410 GGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG-AAGTTG-GACC 457

  chr20_37791816_   1366 CATACTTTGCACCACCGGCAAAAAATTAATTGAGAATATATTATAGATGT 1415
                          v   i ii     ivvi      -    i v i   iv  i ?   iv 
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAA-TTAACTCAAAATGGATCAWAGACCT 506

  chr20_37791816_   1416 AAACCTAAAACCTCTACTCATAGAACTTCTAGGAAAAAA-ATAGGAGATA 1464
                            iv   i v  vv vii   i    ii   i i    -     ? vv 
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_37791816_   1465 ATCTTTGTGATATTGAGTTAGGCAAAGACATTTTAGATACAACACTAAAA 1514
                              i    iv   i         v iiv i       ii    i    
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr20_37791816_   1515 GCACAGCCATTAAAAGGAAAAAAT-GATAAATAGGACTTTAATTAAAAAT 1563
                              iv  vi     -       -       v      i - i    v 
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCA-TCAAAATT 654

  chr20_37791816_   1564 AAGAACTTCTGCTCTTCATAAGACCCTGTTACAATAATGAAAA-ACAAGC 1612
                           i     i  iv     v i   v  i i vi v i      -    v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr20_37791816_   1613 CACAAAATAGGAGAAGATACTTTCAAA-CACATTAATCTAATAAGGTACT 1661
                             i   i      i   i  v    -  i  --    i      v   
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGATAAGGGACT 752

  chr20_37791816_   1662 TGTATCCAGAATATATAAAGAACTCTT------------TAAAAAGATAA 1699
                                                    ------------        i  
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr20_37791816_   1700 -----CAAATTTTTAAGTGAGCAAAAGATTTAGGCTGATATTTAACCAAC 1744
                         ----- v    ?vv  i  i     i     iiiiv  i    vv    v
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr20_37791816_   1745 GATGATATGCAAATGGCAAGTAAGTG--TGCAATGATGCTCTATATTATT 1792
                           v     i        v i    ii--  v  v       v i  i ??
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZ 902

  chr20_37791816_   1793 AATCAT 1798
                         ??????
  L1M4_orf2#LINE/    903 ZZZZZZ 908

Transitions / transversions = 1.46 (134 / 92)
Gap_init rate = 0.03 (23 / 894), avg. gap size = 2.48 (57 / 23)  


2880 27.38 2.94 0.23  chr20_38031476_38037203.rev     4355  5238 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_38031476_   4355 TGGAAAAACATTCCATCCTCATAACTAGGAAGAAGCAATATCATGAAAAT 4404
                               i i  i    vi    iiv v      vvi     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_38031476_   4405 GGCCATACTGGCCAAAGTAATTTATAGATTCAATGCTATTCCCATCAAAC 4454
                            v     vv     v i  i  i        i  v  i  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_38031476_   4455 TACCATTGACAGTCTTCACAGAATTATAAAAAACT-ACTTTAAATTTCAC 4503
                          v   vivi vv i  ii     v - i v  i  - iii    v    i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAAT-TGACAAGCTGATCCTAAAATTCAT 149

  chr20_38031476_   4504 AGGGGACCAAAAAAGAGCATGTATAGCCAAGACAATTCTAAGCAAAAAGA 4553
                          v  i viiv  ii  v vv v        i     ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_38031476_   4554 ACAAAGCTGGAGGCATCAAGCTACCTGACTTCAAACTATGCCACAAGACT 4603
                               i      vv   vi  v  ii i      viv i i    ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_38031476_   4604 ACAATAACCAAAACAGCATGGTACTGATACCAAAACAGGCATATAGACCA 4653
                            i   i   i    ii        ii iv ii i  i        i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_38031476_   4654 ATGTAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCATC 4703
                            v  i    iv    vii         vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_38031476_   4704 TGATCTTTGGTAAA-----CAAG------CAATGGGGAAAAAATTCCCTA 4742
                             i  i ii  i-----    ------           i   vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_38031476_   4743 TTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATTCAGAAAACTGAA 4792
                           i  i              v      v  ?   i  v  i  i v    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_38031476_   4793 ACTGGACCCCTTCCTCACACCTTATACAAAAATTAACTCAAGATGGATTA 4842
                         ii         v         v                   i      i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_38031476_   4843 GAGACATAAATGTAAAAACCAAAGCCATAAAAACCCTAGAAGAAAACCTA 4892
                         ?    v         i i i   i i      vi i           v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_38031476_   4893 GGCA-ATACCATTCAGGACATAGGCATGGGCAAAGATTTCATGACGAAGA 4941
                           ?i- v i -   iv   v v  vv i     v i    v iivv v  
  L1M4_orf2#LINE/    550 GGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_38031476_   4942 TGCCAAAAGCAATTGCAACAAAAGCGAAAATTGACAAATGGGATCTAATT 4991
                         ii         vvv          vi     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_38031476_   4992 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCATCAGAGTGAACAT 5041
                            v v  i i   i  ii vv    i  v    v  vv i      v v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_38031476_   5042 GCAACCTACAGAATGGGAGAAAAATTTTGCAATCTACCCCTCTGACAAAG 5091
                         i     i                vv       vii iviv     i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_38031476_   5092 GTCTAGTATCCAGAAT---CAAACAAAT-TTACGA---------GAAAAA 5128
                          v  v           ---i   v  v -    i ---------i    i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_38031476_   5129 ACAAACAACCCCATCAAAAAATGGGCAAAGGATATGAACAGACATTTCTC 5178
                              i     v  i?                 v    i           
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_38031476_   5179 AAAAGAAGACATTTATGCAGCCGACAAACATATGAAAAAAAGCTCAACAT 5228
                         v        i  vi viii   i i  i  i       i v         
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_38031476_   5229 AACTGATATT 5238
                         v ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 3.11 (28 / 9)  


2945 26.76 1.45 0.67  chr20_38058823_38060709      501  1397 (490)    L1M4_orf2#LINE/L1        5   908 (0)  

  chr20_38058823_    501 AAAATATTACATCCTCATGGATAGGAAGAATCAATATGGTGAAAATGGCC 550
                           i    iv   vi        v      v i     v  v  i     v
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr20_38058823_    551 ATACTGCCTAAAGTAATTTATAGATTCAACGCTATTCCCATCAAACTACC 600
                              v  i   v i  i  i           v  i  i      v v  
  L1M4_orf2#LINE/     55 ATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCC 104

  chr20_38058823_    601 A-CTGACATTCTTCACAGAATTAGAAAATACTGCTT-TAAATTTCATATG 648
                          -   v -  i  ii     v v  v  -i   v i-    v        
  L1M4_orf2#LINE/    105 AGCTGCC-TTTTTTGCAGAAATTGACAA-GCTGATCCTAAAATTCATATG 152

  chr20_38058823_    649 GAATGAAAAAAGAGCCAATATAGCCAAGACAATCCTAAGCAAAAAGAACA 698
                            vviv  ii  v   iv        i      i i iv  i       
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_38058823_    699 AAGCTGGAGGCATCATGCTACCTGACTTTAAACTACACTGCAAGGCTACA 748
                            i      vv   ii  v  ii i  i   vivi   i   i      
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_38058823_    749 GTAACCAAAACAGCATGATACTGGTATCAAAACAGATATATAGACCAAGG 798
                             i   i    ii  i      i  v ii i   i       i   v 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATG 302

  chr20_38058823_    799 AAACAGAACAGAGACCTCAGAAATAACACCACACATCTACAACCATCTGA 848
                         i  i    iv    vii         vv   i    i  iiii  vi   
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_38058823_    849 TCTTTGACAAACCTGACAAAAACAAGGAATGGGGAAAGAATTCCCTATTT 898
                          i  i     ivv  v   i v  vvv              vvi  v  i
  L1M4_orf2#LINE/    353 TTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTC 402

  chr20_38058823_    899 AATCAATGGTACTGGGAAAACTGGCTAGCCATATGCAGAAAACTGAAACT 948
                           iv      i      v      v  ?   i     i  i v    ii 
  L1M4_orf2#LINE/    403 AACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTT 452

  chr20_38058823_    949 GGAGGGCTTCCTTACACCTTTTACAAAAATTAACCCAAGATGGATTAAAG 998
                            vvv  v   i     v v             i   i      i ?  
  L1M4_orf2#LINE/    453 GGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAG 502

  chr20_38058823_    999 ACTTAAATGTAAAACCCAAAACCATACAAACCCT-AGAAGAAAACCTAGG 1047
                           i         i v i     i   -    i  -          v    
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATA-AAACTCTTAGAAGAAAACATAGG 551

  chr20_38058823_   1048 CA-ATACCATTCAGGACATAGGCATGGGCAAAGACTACATGACAAAAACA 1096
                         ?i- v i -   iv   v v  vv i     v ii v v iivv vi   
  L1M4_orf2#LINE/    552 NGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_38058823_   1097 CCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGGGATCT------ 1140
                                  vvv          vv     v  i    v   ii ------
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_38058823_   1141 AATTAAAGAGCTTCTGCACAGCAAAATAAACTAGCATCAGAGTGAACAGG 1190
                                i -   i  ii vv    iv v    v  vv i      v  i
  L1M4_orf2#LINE/    651 AATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_38058823_   1191 CAGCCTACAGAATGGGAGAAAATGTTTGCAATCTACCCGTCTAACAAAGG 1240
                           i  i                 i       vii ivii   i i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_38058823_   1241 TCTAATATCCAGAATCTACAAGGAACTTACACAAATTTATAAGAAAAAAA 1290
                         v  vi          v  i  i     ivi    v iv    v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_38058823_   1291 ACAAACAATCCCATTTAAAAGTGGGCAGAAGGTATGGACAGACACTTCTC 1340
                         -    i  i  v   ?    i      i i i v  i i     i     
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_38058823_   1341 AAAAGAAGACATTTATTCAGTCGATGA--ACATGAAAAAA-GCTCAACAT 1387
                         v        i  vi vvii i i  i --         i -         
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_38058823_   1388 AACGGATCAT 1397
                         v ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.34 (135 / 101)
Gap_init rate = 0.01 (13 / 904), avg. gap size = 1.46 (19 / 13)  


3160 23.61 0.67 3.12  chr20_38129795_38134598     3415  4312 (492)    L1M4_orf2#LINE/L1       33   908 (0)  

  chr20_38129795_   3415 ACTCAATATTGTTAAAATGTCCATGCTACCCAAGGCAATCTACAGATTTG 3464
                            i           i   v v  i  v     ivii           ii
  L1M4_orf2#LINE/     33 ACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCA 82

  chr20_38129795_   3465 AGGCAATCCCTATCAAAATGTTAATGACATTCTACACAGAAATAGAAAAA 3514
                          v                 vii iivi v  i vii       v  v  i
  L1M4_orf2#LINE/     83 ACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG 132

  chr20_38129795_   3515 AAAAATCCTAAAATTTATATGGAACCACAAAG-ACCCAGAATAGACAAAG 3563
                         vvi -          i        vii   i -           v    i
  L1M4_orf2#LINE/    133 CTGA-TCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA 181

  chr20_38129795_   3564 CTATCTTAAGGAAAAAGAACAAAGCCAGAGAAATAACAGTACCTGACTTC 3613
                          v     i ii  i          iii   i v v   v v  ii i   
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr20_38129795_   3614 AAGTTATACTTCAGAGCTATAGTAACAAAAACAGCATGGTACTGGCATTA 3663
                           iviv    v  i     i     iv  i    ii            - 
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT-A 280

  chr20_38129795_   3664 AAAACAGACACATAGACCAATAAAACAGAATAGAGCACCCAGAAGCAAAT 3713
                          ii i     i     i    ii  i     v   vii      ii   i
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr20_38129795_   3714 CCACACATCTACAGTGAACTCATTTTTGACAACGGTGCCAAGAATGTACA 3763
                            i    i  ii  v  i v     i     v          vii v  
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr20_38129795_   3764 CTAGGAAAA-AGT-GTCTCTTCAATAAATGGTGCTGTGAAAACTGGTTAT 3811
                         v i  i   - i -    i     i           v  v      v  ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr20_38129795_   3812 ACATATGCAGAAGAATAAAACTAGACCCCTATCTCTTGCCATATAAAAAA 3861
                         v  i     i      i  ii i        i   vii       v    
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr20_38129795_   3862 ATCAAATAAAAATGGATTAAAGACTTAAATTTTAGACCCCAAACTATGAA 3911
                           i  v v         i ?    i     v v   v iv       i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr20_38129795_   3912 ACTACTGTAAGAAAACGTTGGGGAAACTTTTTAGGACATTAGCCTGAGCT 3961
                            vi iv        i v  ? v  v i  iiv   v  i vi ii  -
  L1M4_orf2#LINE/    531 ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC- 579

  chr20_38129795_   3962 AAAATTTTTTTAGTAATACCCTGTGGGTAATAGTAATACCCTATTAAGTT 4011
                           viv   i    ----------------   - i i   -- --  i--
  L1M4_orf2#LINE/    580 AATGGTTTCTTAG----------------ATA-TGACACC--A--AAA-- 606

  chr20_38129795_   4012 GCACAGGAAACTTAAGCAAAAAT-GACAAATGGAATCACATCAAG-TTAA 4059
                              i v   vv   v      -  i    v i iiv      i-    
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAA 656

  chr20_38129795_   4060 AAAGCTTCTGCACAGCAAAGGATACAATCCACAAAGTGAAGAGATGACCC 4109
                            -   i  ii vv       i  v   v v        i   ii    
  L1M4_orf2#LINE/    657 AAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr20_38129795_   4110 ACAGAATGGGAGAAAATATTTGCAAACTATCCATCTGACAAGGGATTAAT 4159
                                                   ii  vi      i      i vi 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr20_38129795_   4160 AAATAGAATATATAAGGAGCTCAAACAACTCTATAGAAAAAAAATCTAAT 4209
                          vvi           i  i   vv       v   iv     i - v   
  L1M4_orf2#LINE/    756 ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA-CAAAT 804

  chr20_38129795_   4210 AATCTTATC-AAAAATGGGCAAAAGATTTGAATAGACATTTCTCAAAAGA 4258
                           i iv  i-             i                    v     
  L1M4_orf2#LINE/    805 AACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr20_38129795_   4259 AGATACACAAATGGAAAACCAGCCTATGAAAAGGTGCTCAACATCATTGA 4308
                              i        vv  iv   vi        i            ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr20_38129795_   4309 TCGT 4312
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.61 (129 / 80)
Gap_init rate = 0.02 (16 / 876), avg. gap size = 2.12 (34 / 16)  


2209 24.43 2.15 4.83  chr20_38270237_38271929      457  1201 (492)    L1M4_orf2#LINE/L1      184   908 (0)  

  chr20_38270237_    457 ATATTGAAAAGAAAAAGCACATACCTGAAAAAAAAAATTTAACCCATTGC 506
                           v       -- i   v   v vi  i ii -----i i ---  i v 
  L1M4_orf2#LINE/    184 ATCTTGAAAA--AGAAGAACAAAGTTGGAGGA-----CTCA---CACTTC 223

  chr20_38270237_    507 CTGACTTTAAATTATACTGCAAGGCTATAGTAACGAAAACAGCATGATGG 556
                          ii i  i   viv    i   i    i     iv  i    ii  i iv
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr20_38270237_    557 TGGTACAAAAATAGATACATTGATCAATGAAACAGAATAGAGAATCCAGA 606
                            i i  ii     i i  v        i  i     v    i      
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr20_38270237_    607 AATAAACCCACATACCTAGAACCAACCAATCTTCAATAAAG---TCAACA 653
                                   i i ii  viii   iii  i   i i  i ---i   v 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr20_38270237_    654 CAAATAAACAATGGGGAGAGGACACATTATTCAATACATGATGCTTGGAA 703
                          v v ---         i  i i vvi v     i v   i    v   v
  L1M4_orf2#LINE/    374 CCATT---CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

  chr20_38270237_    704 AACTCACTAGCCATATGCAGAAGAATGAAACTGGATCCCTATCTCTCACC 753
                             viv  ?   i     i         ii    i     i   v    
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr20_38270237_    754 ATATACAAAAATTAACTCAAGATGGATTAAAGACCTAAATATAAGATCTG 803
                                             i      i ?          i     v  i
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr20_38270237_    804 AAGCTATAAAAATCCTAGAAGACAACCTAGAAAAAACTCTTCTGAATATT 853
                           i        v  i       v   v   i?iv  v     vvi iv  
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr20_38270237_    854 GGCCTAGGCAAAAAATTTATGAGGAA-GACCCCAAAAGTAATTGCAACAG 902
                           vi       vii-   v v  iv -   v       i vvv      i
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr20_38270237_    903 AAACAAAAATAGACTTGGGACTTAATCAAATGGGACTTCATCAAACTAAA 952
                           iv         i-------------    v             v v  
  L1M4_orf2#LINE/    620 AAGAAAAAATAGAT-------------AAATTGGACTTCATCAAAATTAA 656

  chr20_38270237_    953 AAGCTTCTG--CTTAGCAAAAGAAGTAACCAACA----GAACAAACAATC 996
                           i   i  --   --    i  viiv i   v ----   v i    i 
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTT--CAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr20_38270237_    997 TACAGAATGGGAGAAAATATTTATATTAATAAATTATAGTTACAACAAAG 1046
                         i                     ii ------   i   vv vii i  i 
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCA------AATCATATATCTGATAAGG 748

  chr20_38270237_   1047 AATTAACATCCCAAATCTATAAGGGACTCAAAACAACTCAACAAGAAAAA 1096
                         i i vii    vi   v     i i    vv -        i  v     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTA-CAACTCAATAATAAAAA 797

  chr20_38270237_   1097 -----ATAACCCCACTAAAAACTGGGCATGAGACATGAACAG-TATTTCT 1140
                         -----       v i ?    v      vii  iv    i  -i      
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_38270237_   1141 GAAAAGAAGAAACACAAGTGGCCAATAAACACATGAAAAAATGTTCAACA 1190
                         vv        v i    i          i          i   i      
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_38270237_   1191 TCACTAATCAT 1201
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.70 (112 / 66)
Gap_init rate = 0.02 (15 / 725), avg. gap size = 3.47 (52 / 15)  


3357 25.06 1.77 1.55  chr20_38410004_38414274     2874  3779 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_38410004_   2874 TGGAAAGATAGTCCATGTTCCTGGATTAGAAGAATCAATATTGTTAAAAT 2923
                                   vi        v      i     v i           i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_38410004_   2924 GTCTATACTTCTCAAAGCAATCTACAGATTTAATGCAATCCCTATCAAAA 2973
                          v v     i i    vii           i  i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_38410004_   2974 TATCAATGATCTTCTTCACAGAAATAGAAAAAAAAGTTT---AATTTATA 3020
                          vi  iivii   i  ii       v  v  ivvii ii---    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_38410004_   3021 TGAAACCACAGAAGACCCAGAATAACCAAAGCTATCCTAAGCAAAAAGAG 3070
                           i  vii  iii           i     i v   i i iv  i    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_38410004_   3071 CAAAACTGAAGTAATAACATTAATAACATTATCTGACTTCAAATTATGTT 3120
                             ii  i  ----i  ----- v   i vi ii i      viv ii 
  L1M4_orf2#LINE/    201 CAAAGTTGGAG----GAC-----TCACACTTCCCAATTTCAAAACTTACT 241

  chr20_38410004_   3121 GCAGAGCTATAGTATCCAAATTGGCACGGTAGTAGTATAAAAACAGGCAC 3170
                         i  i     i    vi   ivii iii    v i i    ii i  i  i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_38410004_   3171 ATAGGCCAGTTTAACAGAATAGAGAACCCAGAAATAAATCCATACATCTA 3220
                             ii  i vv  i     v    ii           i        i  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_38410004_   3221 CAGTGAGCACATTTTCAACAAAATTTTTGAGAGCACACATTGGGGAAAGG 3270
                         ii  v iivv      i    iiv viii   v  iv  v         i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_38410004_   3271 ACAGTCTCTTCAATAAATGTTGCTGGGAAAACTGGATATCCATATGCAGA 3320
                          i     i     i     v        v         ?   i     i 
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_38410004_   3321 AGAATGAAACTAGACTCCTATCTCTCACCATATA-AAAAAT-AA----AA 3364
                                 ii i   i    i   v         -      -  ----  
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_38410004_   3365 ATGGATTCAAGACTTAAATTCAAGGCCTCAACATATAAAACTACTAAAAG 3414
                               iv?    i     vi   iv  v  vv         vi  i   
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_38410004_   3415 AAAGCATTGGGG-AAA-CTCCA-GGTATTGGAGTGGGCAAAGAAGACTTC 3461
                            i   v  ? -   -  i i- iiv    iv i     v i---i   
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG---TTTC 588

  chr20_38410004_   3462 TTGAATAATAAC-CCACAGGCACACGCAACCAAAGCAAAAATGGACAAAT 3510
                           ii   - i  -   v i     v     v    v      i  i    
  L1M4_orf2#LINE/    589 TTAGATA-TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr20_38410004_   3511 GGGATCACATCAAG-TTAAAAAGTTTCTGCCCAGCAAAGGATGCAATCAA 3559
                         v   iiv      i-       v   -  iv vv       ii v     
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAA 686

  chr20_38410004_   3560 CAAAGTGAAGAGATGACCCACAGAATGGGAGAAAATATTTGCAAACTACC 3609
                         v        i   ii                              ii iv
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

  chr20_38410004_   3610 CATATGACAAGGGATTAATAACTAGAATATATAAGGAGCTCAAACAACTC 3659
                         i  v   i      i vi  v i           i  i   vv       
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr20_38410004_   3660 --TAGAAAAAAAATTAATCATGTAATTAAAAAATGGACAAAAGATTTGAA 3707
                         --  iv     i iv   v ivi    ?        i    i        
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_38410004_   3708 TAGATATTTCTCAAAAGAAGACATACAAATGGCAAACAGGTATATGAAAA 3757
                             i       v        i           v  i i i i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_38410004_   3758 GGCACTCAACATCATTAATCAT 3779
                          iii          ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.14 (152 / 71)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.00 (30 / 15)  


3810 15.26 3.66 11.29  chr20_38634938_38637450     1039  2021 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_38634938_   1039 TGGATAGACATCTCTTGCTCATGGATTAGAAGACTTAATATTGTCCAAAT 1088
                             v   i   i v  i         i                iv i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_38634938_   1089 GTCAATACTACTCAAAGCAATCTACAGATTCAATGAAATCGCTATCAAAA 1138
                          v       v i    vii              i v    v         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_38634938_   1139 TCCTAATGGCATTTTTTTGGCAGAAATGAAAAAACTCATCTTAAAATTCA 1188
                            i iiv  v      --        vi v  i  v   i         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT--GCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_38634938_   1189 TAGGGAATCTCAAGGGACCCTGAACAGTCAAAACAACCTTATAACAGAAA 1238
                           v    viv          v   i  i        i   iv  v    i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_38634938_   1239 AACAAAGTTGGAGG----------TCTGATTTCAAAACATATTACAAAGC 1278
                                       ----------i ii          v  i        
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_38634938_   1279 TACAGTAATCAAAACAGTGTTGTACTGACATAAAGACAAGACACATAGAC 1328
                                     i       v      i     i  i -    i     i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGAT 297

  chr20_38634938_   1329 AAATGGAATAAAATAAAGAG-CCAGAAATAAATCCTCTCATGTG-GGTCA 1376
                         v         i   vi    -           i  viv   v i-     
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_38634938_   1377 AGTGATCTTCAACAAGCGTGCCAAGAGCATTCAGTGAGGAAAGAGCAATC 1426
                          v    i   i     v         v      i  i       ii i  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_38634938_   1427 TCTTCAGTAAATGGTGCTGGGGAATCTGGATATTCAAATGCAAAAGAATG 1476
                          i    ii             iv v       ?i  v             
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_38634938_   1477 AAGTTGTACCGTTACCTTATACCATATATAAAAATTAACTCAAAAT---- 1522
                               v   vi     i i        i                 ----
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_38634938_   1523 -AAAGACCTAAACATAGGCTCTGAAACTCTAAAACTCTCAGAAGAAAACA 1571
                         - ?         ii  i vv  i     v         i           
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_38634938_   1572 -GGGAGAAAAGCTTCATGACATTGAGTTTGGCAAGGATTCCCAAGATACA 1620
                         -i  ? v   v    i    v   i   v     v i  -----------
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTT----------- 586

  chr20_38634938_   1621 ACTGAAACTCAATATGTTTGAAACTCTAAACTCTAAAACTCGTAGATGAA 1670
                         -------------------------------   --------     ---
  L1M4_orf2#LINE/    587 -------------------------------TCT--------TAGAT--- 594

  chr20_38634938_   1671 AACAGGGAGAAAAGTTCATGACATTGGGATTGGCAAGGATTCCCAGGATA 1720
                         ------------------------------------------------- 
  L1M4_orf2#LINE/    595 -------------------------------------------------A 595

  chr20_38634938_   1721 TGACACCAAAAGCACAGGCAACAAAAGCAAAAATAAATGAATGGGACTAT 1770
                                         i          v       i  i   v     vi
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_38634938_   1771 ATCAAATTTCAAAACTTTTGTGCATCAAAAGACACAATCGACAGAGTGAA 1820
                               v  v             v     i     v   i v i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_38634938_   1821 AAGGCAACCCACAGAATGGGAGGAAATACTTGCAAATCATATATCTGTTA 1870
                            i                  i     i                  v  
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_38634938_   1871 TGGGGTTTATATCCAGAATATATACAGAACTCCTACAACTCAACAAAAAA 1920
                         v   ii  i               v       i          i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_38634938_   1921 CAAAGCAAAACAAGAAACCTGATTTAAAA-TGGGCAAAAAATTTAATTTA 1969
                         ------  i    iv    ii   ?    -        ii    i v vi
  L1M4_orf2#LINE/    796 ------AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr20_38634938_   1970 ACGTTTCTCCAAAGAAAA-----------------AGCATATAAAAAGAT 2002
                           i             i -----------------    i  i       
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_38634938_   2003 GCTCAACATCACTAATTAT 2021
                                    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (89 / 57)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 11.31 (147 / 13)  


1990 20.37 4.85 16.97  chr20_38659477_38661765      779  1809 (480)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_38659477_    779 GAAAGTATATACTGTATTCATGGGTTGGAAGACTCAAGATTGTTAAAATA 828
                              -    v ii i       i          i  v        i  i
  L1M4_orf2#LINE/      3 GAAAG-ATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_38659477_    829 TAAATTTATTCCT--AACTAACCTATAATTTTAGGGTAATCCCAATCAAA 876
                         vv   -- i   i--  i i i   i iv  i iv i      v      
  L1M4_orf2#LINE/     52 GCAAT--ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_38659477_    877 ACTCCAGCAGACTTTTA-AAAGTAAATTGAAAAATTGATTCTAAAATGTG 925
                          ii     v v     v-iv  -       v  ii    i       vii
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAG-AAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_38659477_    926 TGTAAAAAAACAAAGGCCCTAGAAGAGCCAAAACAATTTTGCAAAAGAAG 975
                          i ii   vi   i  v  i    v            i   v        
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_38659477_    976 AACA--TTTTGAGGACTTTCAACACCTGGTTTCAAGACTTCCAGTAAAGC 1023
                             --v  v       iv  viv  iii      i    v vii     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_38659477_   1024 TACTGGAATCTAGGCAGTG--GTATTGGCATAAGAATAGAAAAGCTGGGT 1071
                            v v    v  i     --   i         i     ----------
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGA---------- 288

  chr20_38659477_   1072 GCAGTAGCACAGGTCTGTAATCCCAGCTACTCAAGAGGCTGAAGTGGAAG 1121
                         --------------------------------------------------
  L1M4_orf2#LINE/    289 -------------------------------------------------- 288

  chr20_38659477_   1122 CGTCACTTGAGCCCAGGAGTTTGCGACCAGCCTGGGCAACATAGCAAGAC 1171
                         --------------------------------------------------
  L1M4_orf2#LINE/    289 -------------------------------------------------- 288

  chr20_38659477_   1172 TCCATCTTGCTAAGAAAAAAAAAGAATAGGCATACAGATCAATGAAACAC 1221
                         ------------------------------    i         i  i v
  L1M4_orf2#LINE/    289 ------------------------------CATATAGATCAATGGAATAG 308

  chr20_38659477_   1222 AACAGAGAGTACAGAAATAAACTCACACATATACGGTCCCTTTGGTTTTA 1271
                           iv      v           i  i    v  i    vv  - i    v
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT-GATTTTC 357

  chr20_38659477_   1272 GACAAATATGCCAAG-TCATCCAATGGGACAGGGATAACTGTTTCTACAA 1320
                              ivi       -i   i       iv i i   iiiv    v    
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr20_38659477_   1321 ATGGTGTTGGAATAACTGAACATACATATGCATAAAGAATAAGTAAATAT 1370
                               i   i i     i i ?v  i     -       ----------
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCA-AAAGAAT---------- 446

  chr20_38659477_   1371 AAAAAAGAAGAATCTTGTCCTCTACCTCATGCAACAGATAATAATTAATT 1420
                         ------    ---i v v  i        ii v i v i  v      i 
  L1M4_orf2#LINE/    447 ------GAAG---TTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr20_38659477_   1421 CAAATAATTGATCACAGACTTAACTTTAAGAGTTAAGACTGTAAATGTTC 1470
                             --  v     ?    i   v v      i   i   i    vv ii
  L1M4_orf2#LINE/    488 CAAA--ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCT 535

  chr20_38659477_   1471 TAAAAGTAA-CAGAAG-----ATCTTTACAAGATTGGGATAGGCAAATAT 1514
                           i   v  -  v i -----     iiii vv     v       vvi 
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGT 585

  chr20_38659477_   1515 TTCTTATATAGAACCTGAAAA----AAGGACCCATTGTAAAAAAAT-GAT 1559
                               v   vi  viv    ----   v v v vv --       -   
  L1M4_orf2#LINE/    586 TTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG--AAAAAATAGAT 633

  chr20_38659477_   1560 AAATTGGTCTTCATCAAAATGCAAAAATGTCTTCTCTTTAAAAGGCACCA 1609
                                v            -i     iv i viv   i   i i   i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr20_38659477_   1610 TTAACATA--------ACAGGCTACATA-TGGGAAAAAATATTTACAACA 1650
                          i  v v --------   iv i   v -     i         i   vv
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr20_38659477_   1651 CATATGCTTGACAAGAGACTTATATCCAGAGTATTTAAAGAACTCTTCCA 1700
                              iii   i   i     i        i   v            v  
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr20_38659477_   1701 ACTCAATAGTAAAAAGA---ACAGCCTAAATTTTGTAAGTAGGCAAA--- 1744
                                 i        --- i i  i  --  ?iv  i i      ---
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAA--TTWAAAAATGGGCAAAGGA 830

  chr20_38659477_   1745 ---------ATGTTTCTC-----AAGATACACAAACTGTCAA--AGTTCA 1778
                         --------- ii      -----      i     iv i   --  --  
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG--CA 878

  chr20_38659477_   1779 CATTAAAAAATCATTAGTAATCAGGGATTGG 1809
                            v    i  vv i ii -   ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACA-TCAZZZZZZZZ 908

Transitions / transversions = 1.52 (125 / 82)
Gap_init rate = 0.03 (29 / 906), avg. gap size = 7.76 (225 / 29)  


1631 22.10 10.37 8.34  chr20_38670142_38673294     1780  2666 (487)    L1M4_orf2#LINE/L1        4   908 (0)  

  chr20_38670142_   1780 AAAAACATTCGAGGTTCATGGATTGGGAAACTTAATATTGTTAAGATGGC 1829
                            i i  i v v             i i                     
  L1M4_orf2#LINE/      4 AAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGC 53

  chr20_38670142_   1830 AATATTCCTCAAATTGATCTACAAATTTAACACAATCCCTATCAGAATCC 1879
                             i   i              i   i   i            i     
  L1M4_orf2#LINE/     54 AATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCC 103

  chr20_38670142_   1880 CAGCTTGCTTCTTTGTAGAAATTGA--AACTGATTATAAAATTCATATGT 1927
                              vv   i    i         -- i     iv             v
  L1M4_orf2#LINE/    104 CAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGG 153

  chr20_38670142_   1928 AATTTCAAAGGTCTCAGAATAGTCAAAATCATCTTGAAGAA----AACAA 1973
                           v v   i  v i        i     iv        i  ----     
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr20_38670142_   1974 AGTT------TTCCCAAATGCCCA---TCAA------TTATAGA-CTG-- 2005
                             ------i  v  v- v    ---    ------i  i i -  i--
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACAC-TTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_38670142_   2006 --GATAAAGAAAATGTGGTAC--ATATACACCATGGA-ATACTACATTGC 2050
                         --i  v    v i        --ii   - vv  i  -   -  v  -- 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATA-AGGATAGACATA-TAGAT--C 298

  chr20_38670142_   2051 CATAAAAAGGAAT-GAGATCATGTCCTTTGCAGGGATGTAGATGAAGCTG 2099
                         v  ii  vi    -    ----    -----  ------ i  i  v ii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGA----GTCC-----AG------AAATAAACCCA 333

  chr20_38670142_   2100 GA-------AGCCA--TCATCCTCAGCAAA----CTAACACAGG--AACA 2134
                         v -------i i  -- v  ii  ii   i---- i  v  viv--  ii
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr20_38670142_   2135 GAAAACCAAACACCGCATGTTCTCACTCATAAATGGGAGTTGAACAATGA 2184
                          ii  v-i  i ----i v  i   --- i      viv v i    ivi
  L1M4_orf2#LINE/    384 GGGAAA-GAATA----GTCTTTTCA---ACAAATGGTGCTGGGACAACTG 425

  chr20_38670142_   2185 GA-A--CACATGGACACAAG---GAGG--GGAAC---AGCACACACCAGG 2223
                           - --      --  v   ---  i --   v --- v v       --
  L1M4_orf2#LINE/    426 GATAKCCACATG--CAAAAGAATGAAGTTGGACCCCTACCTCACACCA-- 471

  chr20_38670142_   2224 GCCTATTAGGGGGTGGGAGATAAGGGGAGGGAACTTAGAGGATGGGTCAA 2273
                         ---   ------------- i  i--- ivv    i i --    i   ?
  L1M4_orf2#LINE/    472 ---TAT-------------ACAAA---AATTAACTCAAA--ATGGATCAW 500

  chr20_38670142_   2274 -----TAGGTGCAACAAACCA---CCATGGCACACGTATA------CCTA 2309
                         -----  ii  i  -i i i --- i  iiv  v v  v ------ v  
  L1M4_orf2#LINE/    501 AGACCTAAATGTAA-GAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_38670142_   2310 CGTAACAAACCTCCACGTTCT--------GCACACGTATCCCAGA----- 2346
                         v ?i-i   i  i ii vi  --------   vvv  v  ii   -----
  L1M4_orf2#LINE/    550 GGNG-TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_38670142_   2347 -ACTTAAAGTAAAATTTAAAACAAAACTGCATGTTCTGCACATGTACCCC 2395
                         -  iv    i v  vi---       ----------- v v vi  v---
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGC---AACAAAA-----------GAAAAAATAG--- 631

  chr20_38670142_   2396 AGAACTTAAAGTATAATAAAAAATAAAA---TTTAAGA--AAAAGAAAAG 2440
                          v  v  ii v - v  v    v     ---   iv v--v    i v v
  L1M4_orf2#LINE/    632 ATAAATTGGACT-TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACAC 680

  chr20_38670142_   2441 AAACAAAAA--TGAAAAGGCAACCCACAGAATGAAAGAAGATATATTCAA 2488
                         v v   i  --       i              ii    i    v v   
  L1M4_orf2#LINE/    681 TATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA 730

  chr20_38670142_   2489 ATGCTGTCTCTGATGAGAGACTTGT-TCTAGAACATGTAAAGAGCTCTTA 2537
                           vv i v      i  i       -  i    i  i      i      
  L1M4_orf2#LINE/    731 ATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTA 780

  chr20_38670142_   2538 AAACTGGGTAATAAAAAGACAAATAACCCAATTTAAAGATAGGCAAAGGA 2587
                         v    vii                         ?   i  i         
  L1M4_orf2#LINE/    781 CAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGA 830

  chr20_38670142_   2588 TTTGGATTGGCCTTTATCCAAAGAAGATATACAAATAGCCAATAAACACA 2637
                             i  v i v   v                    i        i    
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr20_38670142_   2638 TAAAAAGATGCTCAACCATTAAGCAGGGA 2666
                          i              -  i ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAAC-ATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (114 / 79)
Gap_init rate = 0.06 (50 / 905), avg. gap size = 3.32 (166 / 50)  


1793 26.34 13.05 4.15  chr20_38675875_38678727.rev     1542  2361 (492)    L1M4_orf2#LINE/L1       16   908 (0)  

  chr20_38675875_   1542 TGGTTATGGATACGAAGATATAATGTTGTCAAGATGTTAATCCTCTCCCA 1591
                           v i      vv     iv    i    i      vi   v   i  v 
  L1M4_orf2#LINE/     16 TGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAA 65

  chr20_38675875_   1592 ACCGACCAATAGATTCAACATAATCACAATAGAAA--------GACTTTT 1633
                          ii  i v i         ii    v v  vi   -------- v     
  L1M4_orf2#LINE/     66 ATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTT 115

  chr20_38675875_   1634 --GCAGAAACTGAAAAAAATGACTCTACTATTTATATATAAATGCAAGC- 1680
                         --       i   v  iv-   ii   vv   i    iv         v-
  L1M4_orf2#LINE/    116 TTGCAGAAATTGACAAGC-TGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr20_38675875_   1681 ACATAGAATACTTTGATAAAACAATCTTGATAAAGAAGAACA--GTTAGT 1728
                           vi      ---- vi             v           --   i v
  L1M4_orf2#LINE/    165 ACCCAGAATA----GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

  chr20_38675875_   1729 CAACTTATACTATCTGATTTCAAGACTCATTTTAAAGCTAAAGCAATTAA 1778
                         vi   i i   vi ii       i   i i vi       v  i   i  
  L1M4_orf2#LINE/    211 GGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAA 260

  chr20_38675875_   1779 GACAATGTGGTACTGGCATAACCATCAACAAAT-GATTAGTGGAACAGAA 1827
                             i                vv  vi   v  -   i i     i    
  L1M4_orf2#LINE/    261 GACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAA 310

  chr20_38675875_   1828 CAGAAAGCTCATAAACACACTC---CACT---GGCCAACTAATTTTTGAT 1871
                         iv  i  ii  v   i v  i ---  i ---  i   i i     i  i
  L1M4_orf2#LINE/    311 TTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGAC 360

  chr20_38675875_   1872 AGAATCATCAAAGCAATTCAATACAGAAAGAAAAGTCTTCT-AACTAAGG 1920
                          iiiviii   ii v       ivi       v      i -   v  v 
  L1M4_orf2#LINE/    361 AAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATG 410

  chr20_38675875_   1921 ATGCTGCAATAGCCAGTTATTCTCGTG-AGAAAAA-GGACTTTAACTGCC 1968
                         i     vi i i ii v  ?i v i  - i  i  - i v  vi  iv i
  L1M4_orf2#LINE/    411 GTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCT 460

  chr20_38675875_   1969 ACTTTATACAATATACAAA------------------------------- 1987
                           i i i  v         -------------------------------
  L1M4_orf2#LINE/    461 ACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAAT 510

  chr20_38675875_   1988 -------------CCACACAGTTTTCAATAGAAA-TATAGGA-TAGTATC 2022
                         ------------- i i v ii i i iv     -i     ?-  i-   
  L1M4_orf2#LINE/    511 GTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA-ATC 559

  chr20_38675875_   2023 TTTATGACTTAGGGATAGACTAAGTTTTCTTTGACAAGACTC-------- 2064
                           ii    i v   v   i v v v      v  i v   v --------
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr20_38675875_   2065 -----------AGAAAAACT-GATAAATTAGACTTCATCAAAGCTTGAAA 2102
                         -----------       v -        i            ii vi   
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr20_38675875_   2103 CTTCTGCTCATAAATAGACGTTATTAAGAAAACTTCTGCTCATAGATAGA 2152
                            i  iv v v  vi   ii   i      i----  --------- i 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAG----TG---------AAA 696

  chr20_38675875_   2153 CACTGTTAGGTAGGCAATCTACAAACTGGATAAAATTATAAGTAAAACAG 2202
                         -----------  i   i i   i v   ivi   v   vv i   v  v
  L1M4_orf2#LINE/    697 -----------AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr20_38675875_   2203 ATGTTATCTGACAATAGACTGGTATCCAGGATGTATAAAGAACTCCTGCA 2252
                           ---      i  vi    v        i  i            i i  
  L1M4_orf2#LINE/    736 AT---ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr20_38675875_   2253 ATTTAATAATAAAGGAG---------------TAAAAATGAGCAAATTAA 2287
                          i i         i-  ---------------?       i     vv v
  L1M4_orf2#LINE/    783 ACTCAATAATAAAA-AGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr20_38675875_   2288 CTGGACAGGCATTTCAC---AAAATATATACACCTGGCCAATGACCAGAT 2334
                         i  i i  i      v --- i  v       vv        i v  v  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr20_38675875_   2335 ATAAAAATACTCAATATCATTACTTAT 2361
                         iv   i  i     i    ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (132 / 81)
Gap_init rate = 0.03 (25 / 893), avg. gap size = 5.64 (141 / 25)  


3305 25.77 1.11 0.66  chr20_38680877_38687158     4887  5790 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_38680877_   4887 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4936
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_38680877_   4937 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCGAGC 4986
                            v     v     iv i  i           i  v     i   i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_38680877_   4987 TACCAA-TGCCTTTCTT-CACAGATTTGGAAAAAACT-ACTTTAAAGTTC 5033
                          v   i-       i  -  v i   ---i v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATT---GACAAGCTGATCCTAAAATTC 147

  chr20_38680877_   5034 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAA 5083
                                 viiv  ii  v  v v  v     iv     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_38680877_   5084 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5133
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_38680877_   5134 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5183
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_38680877_   5184 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAAC 5231
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr20_38680877_   5232 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTA 5281
                         i vi    i  i     ivv  vv  i v  vv            i  vi
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_38680877_   5282 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5331
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_38680877_   5332 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5381
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_38680877_   5382 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5431
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_38680877_   5432 CCTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5480
                          v    ?i- v i -   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_38680877_   5481 AAAACACCAAAAGCAATGGCAACATAAGACAAAATTGACAAATGGGATCT 5530
                          vi            vvi      v    v     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_38680877_   5531 AATTAAACTAAAGAGCTTCTGTACAGCAAAAGAAACTACCATCAGAGTGA 5580
                         v  i   v v  i i   i   i vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_38680877_   5581 ACAGGCAACCTACAAAATGGGAGAAAATTTTTGCCACCTACTCATCTGAC 5630
                          v  i     i   i             v     v vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_38680877_   5631 AAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA 5680
                           i  i  vi          v  i  v      vv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_38680877_   5681 AAAAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5726
                            i    ----   v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_38680877_   5727 TCTCAAAAGAAGATATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5776
                             v           vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_38680877_   5777 CCATCACTGGCCAT 5790
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (136 / 93)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.78 (16 / 9)  


 227 22.41 1.72 0.00  chr20_38982297_38985586      447   504 (2786)    L1M4_orf2#LINE/L1      745   803 (105)  

  chr20_38982297_    447 AAAGGACTAGTGTCTGAAGTATATAAAGGACTCTCAAAATTCAACCATAA 496
                           i     v  i  iii i         i     i v  i    iv    
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_38982297_    497 AAA-ACAAA 504
                            -     
  L1M4_orf2#LINE/    795 AAAGACAAA 803

Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1)  

3349 15.79 3.72 0.77  chr20_38982297_38985586     1608  2253 (1037)    L1M4_orf2#LINE/L1        1   665 (243)  

  chr20_38982297_   1608 TGGAAAGATACCTGACATTCATGTATTATAAGAAGTAATATTGTTAAGAT 1657
                                   i iv ii      v   iv    vv               
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_38982297_   1658 GACAATACTCCTCATATTGATCTCTGGAATCAATGTAATTTCTATCAAAG 1707
                          i         i  v        vii  v    i i   ii        i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_38982297_   1708 TCTCAGTTGTCTTTTT-GCAGAACTTGACAAGATGATTCTAAAAAAATAA 1756
                           i   i  i      -      v        v    i      --- vv
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA---TTC 147

  chr20_38982297_   1757 ACATGGAAATGCAAG--------AATAGGCAAAACAATCTTGAAAAAGAA 1798
                          i             --------     v                     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_38982297_   1799 GAACAAAACTGGAGGACTCACA--TCTCAATTTCAAAACTTACTATACAG 1846
                                ii             --  i                  i v  
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_38982297_   1847 TTACAATAATCAGGACATTATGGATCTAACATAAGGATAGAAATATAGAC 1896
                         i    i      i    v i   vv  ii            v       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_38982297_   1897 CAATGAAATGGATTCTGAAA-TTAAGAAATAAACTCTCACATT-ATGGTC 1944
                              i   i  v -   i - iv          i vi     -      
  L1M4_orf2#LINE/    298 CAATGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_38982297_   1945 AACTCATTTTCCTGAAGGGTACCATGACAATTCAATGGGAAAAGAATAGC 1994
                           i v      vvv      i   v   v          i         i
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_38982297_   1995 CTTTTCCAAAAATGGTGCTGGGATAACTGGATATCCACATGCAAAAGAAT 2044
                               v v              i         ?                
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_38982297_   2045 GAAATTGGGCCCCTACCTCACACCACGTG--AAAATTAATTCAAAATCAA 2092
                            i    i                ii i--        i       vi 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_38982297_   2093 TTAGAGACCTAAATGTAAAAGCTAAATTCATAAGAGTCTTATA-GAAAAC 2141
                          i ?              i       vii    i v     v -      
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_38982297_   2142 ATAAGGAACAAATT---GTGTCCTTGGATTAGGCAATGGTTTCTTAAATA 2188
                            -  ?ii    i---   v      i                  i   
  L1M4_orf2#LINE/    547 ATA-GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_38982297_   2189 TAACACCAAAAACCCAAACAACAAAAGAAAAA-----TAAATTGGAGTTC 2233
                          i         i v   i              -----         v   
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_38982297_   2234 ATCAAAATTTTAAACTTTTG 2253
                                  vv         
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.61 (61 / 38)
Gap_init rate = 0.02 (12 / 665), avg. gap size = 2.42 (29 / 12)  

1215 17.32 2.76 0.39  chr20_38982297_38985586     2545  2798 (492)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr20_38982297_   2545 AAAAT--AAAACTTTTGCACATCAAAGGACACTATAATTAAAGCAAAAAA 2592
                              --          ii v              v vv    ii    i
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_38982297_   2593 ATC-CCCATAAGATGGGAGAAAATGTTTGCAAATCATGTATCTGACAAGG 2641
                          iv-    i ii            i            i       i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_38982297_   2642 AGCTTGTATTTAGAATGTATAAAGAACACTTACAAATTGAACCCCCAAAA 2691
                         ii       ii     i          v       v i-  ivviv    
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTC-AATAATAAAAA 797

  chr20_38982297_   2692 GCCAAATAAGCCAATCTAAAACCAGGCAACGAATTTGAATAGACATTTCT 2741
                          v       v     i?    vii     v i                  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_38982297_   2742 CTAA----TATATGCAAATGGCCAATAAGCACATGAGAAGATGCTCAGCA 2787
                          i  ----v    i                      i          i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_38982297_   2788 TCATTAGTCAT 2798
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.87 (28 / 15)
Gap_init rate = 0.02 (4 / 260), avg. gap size = 2.00 (8 / 4)  


1403 24.12 0.29 1.18  chr20_39060727_39062662      501   840 (1096)    L1M4_orf2#LINE/L1      279   615 (293)  

  chr20_39060727_    501 TAGAAACAGATGTATAGACCAATGAAACAGAATAGAGAGAACAGAAATAA 550
                           iii i   ii      i     i  i     v     vv         
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr20_39060727_    551 ATCCCTACAACTACAGCCAACTCATTTTTCAACAAAGGTGCAAACAACAC 600
                          i  v    vi  ii i   i v     - i    i     v  v v  i
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTT-CGACAAGGGTGCCAAGACCAT 377

  chr20_39060727_    601 ACATCGGGGGAAAGGACAGTGTCATCAATACATGGTGCCAGGAAAATTGG 650
                         v  vi    -    i i   v iv    i v       ii   v  i   
  L1M4_orf2#LINE/    378 TCAATGGGG-AAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr20_39060727_    651 GTATTTATATGCAAAAAAATTAAACTAGACCCCTACCTTTCACCATATAC 700
                         i  ?ii i        i   v  ii i           iv          
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr20_39060727_    701 AAAAATCAACTCAAAATGGATTAAACACTTAGATCTAAGATCCAAAACTA 750
                               i              i ? v  i  i  v     v i       
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr20_39060727_    751 TGAAACTCTACTAGAAGAAAACATGGGGACACATTTTT-TGACATTGTTT 799
                          i       --             i  ?ii v  i  i-    v   vv 
  L1M4_orf2#LINE/    527 TAAAACTCT--TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGT 574

  chr20_39060727_    800 TGGACAAGGGTTTTTTAGATAAGCCCTCAAAAGCACAGGCA 840
                          i i   v     i       v v vi          i   
  L1M4_orf2#LINE/    575 TAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCA 615

Transitions / transversions = 1.82 (51 / 28)
Gap_init rate = 0.01 (4 / 337), avg. gap size = 1.25 (5 / 4)  

 962 18.27 5.13 7.37  chr20_39060727_39062662     1133  1444 (492)    L1M4_orf2#LINE/L1      604   908 (0)  

  chr20_39060727_   1133 AAAGTACAGGCATCAAAAGCAAACATAGACAAATGGAATTACATCAAACT 1182
                             i   i   v      v   v     i    v i i v       v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAAT 653

  chr20_39060727_   1183 GAAAAGCTTCTGCAC--AAAAAAACA-----ACGCA--TGAAGAGATAAC 1223
                         v    i   i  ii --v   ii   ----- v v --    i   i   
  L1M4_orf2#LINE/    654 TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr20_39060727_   1224 ACACAGAGTGGGAGAAAATATTTGCAAACTATACATCTGGTTAA------ 1267
                         v      i                    ii   i     i v i------
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTT 753

  chr20_39060727_   1268 -TATCCAGAATATATAAGTAACTCAGACAACTCAATAGCAATAAACAAAA 1316
                         -                iv     vv           ---     -----
  L1M4_orf2#LINE/    754 GTATCCAGAATATATAAAGAACTCTTACAACTCAATA---ATAAA----- 795

  chr20_39060727_   1317 ACAAAAACAAAAAACAAACCAAATAGTCCAATTTTAAAGTGGAAAAAAGA 1366
                         ---  i     v   ------------      ?v   i   iv   i  
  L1M4_orf2#LINE/    796 ---AAGACAAATAAC------------CCAATTWAAAAATGGGCAAAGGA 830

  chr20_39060727_   1367 CCTGAATAGACATTTCTCAAAATAAGAGTTACAAATGGCCAACAGATATT 1416
                         ii                v   v    vv             i iii iv
  L1M4_orf2#LINE/    831 TTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACA 880

  chr20_39060727_   1417 TGAAAGAATGCTCAACATCACTAGTCAT 1444
                              ii             ????????
  L1M4_orf2#LINE/    881 TGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (33 / 23)
Gap_init rate = 0.02 (7 / 305), avg. gap size = 5.57 (39 / 7)  


2753 25.63 6.09 0.63  chr20_39248301_39252701.rev     1162  1949 (2451)    L1M4_orf2#LINE/L1        1   831 (77)  

  chr20_39248301_   1162 TGGAAAGACATCCCAAGCTTATGGATTGGAAAAATTAATATT---AAAAT 1208
                                 i      v i i           i v        ---  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_39248301_   1209 GGCCACACTGTCCAAAGCAATCTACAGATTCAATGCAATTGCTATCAAAA 1258
                            v i   vi     vii              i     iv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_39248301_   1259 TACCAATGTGATTTTTTCACAGGAGTAGAAAAA--AACCCTAAAATTTGT 1306
                          v   ii-  vi     ii   i i v  v  i--i i         ii 
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_39248301_   1307 ACAGAACCACGAAAGAGCTAAAATAGTCAAAGCAATCCTAAGCAAAAAGA 1356
                          ii   vii i ii  v i i     i    i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_39248301_   1357 ACAAAGCTGTAGGCATCACATTACCTGACTTCAAAATATATCACAAGGCT 1406
                               i  v   vv     i v  ii i       iv  ii    i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_39248301_   1407 ATAGTAACCAAAACAACATGGTATTGGTATAAAAATAGACCCACAGACCA 1456
                          i     i   i   iii     i   i    ii      vi i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_39248301_   1457 AAGGAAAAGAAAATAGAACCCAGAAATAAAGCCACATATTTACAGCCAGC 1506
                          v    v    vvv   ii           v   i i     ii i  ii
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_39248301_   1507 TGATTTTCAACAAAGGTGCCAAGAACATGCAATGAGGAAAGGACACCCTC 1556
                                 i    i          v   v     i      i i vi  i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_39248301_   1557 TTCAATAAATGATGCTGGGAAAATTAGATATCCATAAGCAAAAGAATAAA 1606
                              i     i        v  i i    ?   i v          i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_39248301_   1607 ACTGGACCTGTATCTCTCACCATATACAAAAGTTAA-----GACAGATTA 1651
                         ii      iv  i   v              i    -----i ii   i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_39248301_   1652 AAGATTTAAATATAAGACCTTGAATTATGAAACTACTAGAAGAAAACA-- 1699
                         ?   ii     i     v  vi  i   i     vi            --
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_39248301_   1700 -GTGCAGAACACTTCAGGACATTGGTCTGAGCAACGATTTTATGGCTAAG 1748
                         - ? i -  i-    iv   v    vi ii    i i   iv i v  v 
  L1M4_orf2#LINE/    550 GGNGTA-AAT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_39248301_   1749 ACCTCAAAAACACAA----CTAAAACAAAAATAGACAAAGGGAACT--AT 1792
                           vi     i     ---- v   iv         i   vv i   --  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_39248301_   1793 ----ATTAAAAATCTTCTGCATAGCAAAGGAAATAATCAGCACAG----- 1833
                         ----        -   i  iiivv       v iv    iv v  -----
  L1M4_orf2#LINE/    648 CAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_39248301_   1834 AGACAATATGTTGAGTGGGAGAAAATATTTGCAAAACTATTCATCCAACA 1883
                               iviiiv  i                    v -  vi   ii i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATC-ATATATCTGATA 745

  chr20_39248301_   1884 AAGGACTAATATCTAGAATATATAAGGAATTC------------------ 1915
                          i     vi    i           i   i  ------------------
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_39248301_   1916 --AACAAAAAATCATATTAAAAAGTGGGCAAAAGGT 1949
                         --i     v  i vv   ?    i        i i 
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGAT 831

Transitions / transversions = 2.30 (138 / 60)
Gap_init rate = 0.02 (14 / 831), avg. gap size = 3.79 (53 / 14)  

 362 19.32 0.00 0.00  chr20_39248301_39252701.rev     2256  2343 (2057)    L1M4_orf2#LINE/L1      821   908 (0)  

  chr20_39248301_   2256 GGACAAAAGACATGAATAGACAATTCACAAAAGAAGACATACACATGGCC 2305
                           i    i  iv          v   v v        i     v      
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr20_39248301_   2306 AATAGGTATATTAAAGAACACTCAACATCACAAATCAA 2343
                             i i i  v   ii ii          ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.83 (11 / 6)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.00 (0 / 0)  

1966 11.68 3.80 30.39  chr20_39248301_39252701.rev     2870  3922 (478)    L1M4_orf2#LINE/L1      136   908 (0)  

  chr20_39248301_   2870 ATCCTAAAGTTTATATAGAATCTCAGGGGACCCCAAATAGACAAA----- 2914
                                 i  i    i   viv  i       vi     v    -----
  L1M4_orf2#LINE/    136 ATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAAT 185

  chr20_39248301_   2915 -CTGAGAAAAAA---CAAAGTTGAAGGAGTCACACTCACTTGATTTCAAA 2960
                         -i   i   i  ---        i    v       i- iii        
  L1M4_orf2#LINE/    186 CTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT-CCCAATTTCAAA 234

  chr20_39248301_   2961 TTGTACTACAAAGCTACAGTAATCAAAACAGTGTGGTACTGGCATAAGGA 3010
                         viv                       i                       
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr20_39248301_   3011 GAGACATACAAAACCAATGGAATAAAATAAAAAGCCCAGAAATC--CCCA 3058
                         v       i i -i          i   vi i  i        v--    
  L1M4_orf2#LINE/    285 TAGACATATAGA-TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr20_39248301_   3059 CGTA---ATGGTCAATTGATTTTTGACAGGGGTGCAAAGACCATTCAATG 3105
                         iii ---                i    i      v              
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr20_39248301_   3106 GGAAAAGA-CAGTCTTTTCACCAAAAGGTGCTGGGA-AACTGGATATATA 3153
                           i     -i          v    v          -         ?vi 
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr20_39248301_   3154 CATGCAAAAGTATGAAATTATACTCTTACCTTGTACTATATACAGAAATT 3203
                                   v     i  iv  i i     iii  i       i     
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr20_39248301_   3204 TACTTAAAATAGATCAAAGAACTAAA---AAAAGCTAAAGCTATAAAATA 3250
                         v   i     i     ?   v     ---  i       i        iv
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr20_39248301_   3251 CTTAGAAGAAAATAGAATCCTTCCAGATTTTTGATTAGGCAATTATTACT 3300
                                     i ---------------------    ?----------
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACA---------------------TAGGN---------- 552

  chr20_39248301_   3301 TTTTTTTTTTTTTTTTTTTTTTTGAGACAGGTTCTTGCTCTGTTGCTGGA 3350
                         --------------------------------------------------
  L1M4_orf2#LINE/    553 -------------------------------------------------- 552

  chr20_39248301_   3351 GTGCAGTGGTACAATCAAACCTACTGCAGTTTCAAACTCCTGGGCTCAAG 3400
                         --------   -    ----------------------------------
  L1M4_orf2#LINE/    553 --------GTA-AATC---------------------------------- 559

  chr20_39248301_   3401 CAGTCATCCCACCTTAGCCTCCTGAGTAGCTAGGATTACAAGTGTGCACA 3450
                         --------------------------------------------------
  L1M4_orf2#LINE/    560 -------------------------------------------------- 559

  chr20_39248301_   3451 CCTGGCTAATTTTATTATTACTATTTTGTGTGTGGGTGTGTGTGTAGACA 3500
                         ------------------------  i   --------------------
  L1M4_orf2#LINE/    560 ------------------------TTCGTG-------------------- 565

  chr20_39248301_   3501 GGATCTTGCTATGTTGCCCAGGCTGGTCTTGAACTCCTGACTTCAAGCAT 3550
                         -- i    ------------------------------------------
  L1M4_orf2#LINE/    566 --ACCTTG------------------------------------------ 571

  chr20_39248301_   3551 TCCTCCCCAACCTCCCAAAGTGCTGAGATTACAGGTGCAAGCCACCCCAT 3600
                         --------------------------------------------------
  L1M4_orf2#LINE/    572 -------------------------------------------------- 571

  chr20_39248301_   3601 CTGGCCAGGCAATGATTTCTTATGTATGACACTCAAAGCATAGGCAACAA 3650
                         --  ii        i       vi        iv      i i       
  L1M4_orf2#LINE/    572 --GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAA 619

  chr20_39248301_   3651 AAGAAAA--TA-ATAATTTGGATTACGTCAAAATCTAAAACTTTTGTGTT 3697
                                --  -    v     i v i       iv            i 
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr20_39248301_   3698 TCAAAGAACACTGTTAAAAGAATGAAAG---AACCCACAGAATGGGAGAA 3744
                               i     i i  i i i     i---                   
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAA 719

  chr20_39248301_   3745 AAGAGCTGAAAATCATACATCTGATAAGAGATTTATATTCAGAATATGTA 3794
                           v vi  v        i          i  i  i   i        i  
  L1M4_orf2#LINE/    720 AATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATA 769

  chr20_39248301_   3795 TAGAACTCCTAAAACTGAACAACAAAA-----------CCAATTCAAAAA 3833
                         v       i  v    v  i  i    -----------      ?     
  L1M4_orf2#LINE/    770 AAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAA 819

  chr20_39248301_   3834 CGGGCAAATGATTT----AGACATTTCTCATAGGAAAATATACAAATGGC 3879
                         i       v     ----           vv i   i             
  L1M4_orf2#LINE/    820 TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGC 869

  chr20_39248301_   3880 CAATAAGTACATGAAAAGACGAACCTTTGGCATTAGGGAAATG 3922
                                i           i ----i iii   i ????????
  L1M4_orf2#LINE/    870 CAATAAGCACATGAAAAGATG----CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.61 (86 / 33)
Gap_init rate = 0.03 (21 / 773), avg. gap size = 17.14 (360 / 21)  


1415 17.46 31.22 3.88  chr20_39291211_39292673.rev      405   971 (492)    L1M4_orf2#LINE/L1      187   908 (0)  

  chr20_39291211_    405 TTGAAACAGTAAAAAAAAAAAATCTAAGAAT--ATATTTAACCCAATATA 452
                               v  ---  i  v   i ivi  i i-- i i  --      ---
  L1M4_orf2#LINE/    187 TTGAAAAAG---AAGAACAAAGTTGGAGGACTCACACTT--CCCAAT--- 228

  chr20_39291211_    453 TGCAAAATATTATTTCAACATCTATTTAATA-TTAAAA-ATTGT------ 494
                          v     i-   i v   - v   i-- i  - i  i - v   ------
  L1M4_orf2#LINE/    229 TTCAAAAC-TTACTACAA-AGCTAC--AGTAATCAAGACAGTGTGGTACT 274

  chr20_39291211_    495 ----TAATGA-AGGCATATAGACCAATGGAGTAGAATGGAGAGACCAGAA 539
                         ----   v  -  i        i       i      v     v      
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr20_39291211_    540 ACAAATCCTCACACATAAGGTCAAATGATTTTTTACAAGGATGCCAAGAC 589
                          i   i  vi   iv  v      v       iv      i         
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr20_39291211_    590 CTTTCAATGGGAATAGGACAGTCTTTTCAACAAATGGTGCTGAGAAAACT 639
                          v         i v  i i                       i  v    
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr20_39291211_    640 GGCTATCTA-ATGGAAAATAATAGAGTTGGATCCTTACCTTACACCATAT 688
                           v  ? i -   v    v   ii       i  i     i         
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr20_39291211_    689 ATATAAAAGTTAACTCAAAATGAATCGAAGACCTAAACAAAAGATCTAAA 738
                          i --   i             i   i?         iiv    v     
  L1M4_orf2#LINE/    475 ACA--AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr20_39291211_    739 ACTATAAAATGCTTAGAAGAAGACAGAGGAG------------------- 769
                                  iv          i   v   ? -------------------
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr20_39291211_    770 ------------------------------AAAAGC-------------- 775
                         ------------------------------      --------------
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_39291211_    776 --------------------TTCAT------------------------- 780
                         --------------------     -------------------------
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_39291211_    781 ---GACACT----------------------------------------- 786
                         ---      -----------------------------------------
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_39291211_    787 ---TGCAAACCATATATCTAATAAAGGGGTAATATCTAGAACATATAGAG 833
                         ---      i         i    i  iv vi    i    i     i  
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_39291211_    834 AATTTCTACAACCCAACAAAAACAGCAAAAAACCCCAGACAACCTGATT- 882
                           i ii      i   i  v  -----   i  --- i i    ii   -
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAA-----AAAGAC---AAATAACCCAATTW 814

  chr20_39291211_    883 -AAAATGGTCAAAGGACTTGAATAGACATTTATTCAAAGAAGATACACAA 931
                         -       v       i              v i           i    
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr20_39291211_    932 ATG---AATAAGCACATTAAAA-ATACTCAACGTTAATATAATT 971
                            ---           v    -  i      i i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (65 / 31)
Gap_init rate = 0.03 (22 / 722), avg. gap size = 9.05 (199 / 22)  


4147 15.26 7.33 0.48  chr20_39334699_39336532.rev      503  1334 (500)    L1M4_orf2#LINE/L1        1   889 (19)  

  chr20_39334699_    503 TGGAAAGACATCC-------ATGGATTAGAATACTTAA--------AGAT 537
                                 i    -------       i   v      --------    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_39334699_    538 GGCAATACTACTCAAAGTGATGTAAAGATTCAGTGCAATCTTGACCAAAA 587
                                  v i    v    v  v       ii      iiv i     
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_39334699_    588 TTCCAG-TACCTATTTTTGCAGAAATAGGAAAGCTGATCCTAAAATTCAT 636
                          i    - i   -             v iv                    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_39334699_    637 ATAGAATTGCAAGGGACCCTGAATAGTCAAAACAATCTTGAAAAAGAAAA 686
                           i   v            v      i                     i 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_39334699_    687 ACAAAGTTGGAGTATTCATGCTTCCCAATTTCAAAAGATACTACAAAGCT 736
                                     v i   ii                vv            
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_39334699_    737 ACAATAATCAAAATAG----GTATAAGCATAAGAATAGACATATAGATCA 782
                            i       i i  ----   ivi       i                
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_39334699_    783 GTGGAATAAAACTGAGAGTCCAGAAATAAACCTGTACATCTGTGACC--- 829
                         i       i  i                    ii     i i  ii ---
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_39334699_    830 -----TTTGAGAACAGTGCCAAGATGATTCACTGGGGAAAGGACAATCTC 874
                         -----  i  v  vi         iv     v         i i i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_39334699_    875 TTTAACAAATGGTGCAGGTACAACTGGTTATCTACATGCAAAAGAATGAA 924
                           i            v  v        v  ? i                 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_39334699_    925 GTTGGACCCC------ACAC---ATATTAAAATTAACTCAAAATGGACCA 965
                                   ------    ---   iv                   i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_39334699_    966 AATAACTAATTATAAGAGTTAAGACTATAAA-CTCTTAGAAGAAAACATA 1014
                         ? v v    v i      i   i        -                  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_39334699_   1015 AGGGTAAATCTTCATGACCTTGGATTTGGTAATGGATTCTTAGAAAC-AC 1063
                         i ?          i         i  v  i     v        v i-  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_39334699_   1064 ACCAAAAGCACAAGCAACGAAAGAAAAAATAGACAAATTGGATGGCATCA 1113
                                           i              i        ivv     
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_39334699_   1114 AATGTTAAAA--TTTTG--CAGCAAAGGATGCTATCAAGTAAGTGGAAAG 1159
                           -i      --     -- vv       ii        v     i    
  L1M4_orf2#LINE/    650 AA-ATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_39334699_   1160 GCAACCTGCAGAATGGGAGGAGATATCTGCAAATC-------TGTTAAAA 1202
                         i     ii           i i    i        -------  v   ii
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_39334699_   1203 AAC----AAACAAAACAAAACGAAAAACTCTTAACAACTGAACAACAGAA 1248
                         i  ---- vv  i  i v -ii  i        -     v  i  i i  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATA-TAAAGAACTCTTA-CAACTCAATAATAAAA 796

  chr20_39334699_   1249 A---AGATAACCCAATTAAAATATGGGCAAGGGACTTGAATAGACATTT- 1294
                          --- i           ?   v        i   i              -
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_39334699_   1295 TGTAAAGA---TATGCAAATGGCCAAGAAACATATGAAAAGAT 1334
                          vi     ---   i           v  i  i          
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

Transitions / transversions = 2.00 (82 / 41)
Gap_init rate = 0.02 (20 / 889), avg. gap size = 3.25 (65 / 20)  


 350 27.93 13.97 1.68  chr20_39739258_39742152     1175  1353 (1542)    L1M4_orf2#LINE/L1       79   279 (629)  

  chr20_39739258_   1175 TTTACTGCAGTTCTAATCAACATTCTAAC--ATTTCTTTG--GAACTT-- 1218
                           i vi   i i iv     v  i i i --vi  i    --   v  --
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGA 128

  chr20_39739258_   1219 -AAGCTGATTCTAAAATGTAAATAGAAATGTA------TAAGAACAGATA 1261
                         -        i       vi v  i      i ------iv    i  vi 
  L1M4_orf2#LINE/    129 CAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA 178

  chr20_39739258_   1262 AGACA--C---AGTGAGAAGTAGAAAATGGGTGGACTCACCCTAGGATAC 1306
                          i   -- --- ivi     v v   i v  v        v  v---iv 
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT---CCC 225

  chr20_39739258_   1307 AA---CAAGACATAT--CAAG--TATGGTAATTAAGGCAGTATGGGCCTG 1349
                           ---   i  v  i--   i--  ii     i   i    i   vv   
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr20_39739258_   1350 GCAT 1353
                             
  L1M4_orf2#LINE/    276 GCAT 279

Transitions / transversions = 1.50 (30 / 20)
Gap_init rate = 0.05 (10 / 201), avg. gap size = 2.80 (28 / 10)  

 431 30.95 14.83 3.58  chr20_39739258_39742152     1669  2059 (836)    L1M4_orf2#LINE/L1      264   698 (210)  

  chr20_39739258_   1669 AGGGTGCCATTGAAACAAAGATATGTAACTGGACCATCAGAACAGAATAC 1718
                           v   vi i  iv i  i    vii vv i  i  vii   i     vv
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr20_39739258_   1719 AGAGCCCAAAAACACACCCATA-----------GATTGATATCTGATATA 1757
                             i   i   i v       -----------i      v ii  i vi
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr20_39739258_   1758 AATGACACAGCAACATTGCAGGTAAGTGGAGAAAAGATAGGCTTTTCAA- 1806
                         ii  v  -  - v    -----i  -   i    ii    v        -
  L1M4_orf2#LINE/    364 GGTGCCA-AG-ACCATT-----CAA-TGGGGAAAGAATAGTCTTTTCAAC 405

  chr20_39739258_   1807 AAA--GTGATGAG-TAATTAGTTACTCATATAGAAAAAATAAAACAAAAT 1853
                            --   v  i -i  i i v  ?i  i  iv    i ---- ii  i 
  L1M4_orf2#LINE/    406 AAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA----ATGAAGT 451

  chr20_39739258_   1854 TGGAATTCT----CAGACCAAATA---AAATT----CCAAGTGGAATTCA 1892
                             vii  ----  v    v   ---     ---- v  i    --   
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA--TCA 499

  chr20_39739258_   1893 GGAACCTA---GTTAGA------------AAACTTTTAGAA-----TGTG 1922
                         ?ii     ---  v   ------------     i      -----ii i
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_39739258_   1923 GGAATATATCTACGC--TCTTAGGTTAAA----GATTTACTAAA----AT 1962
                           ?i  v    v  i--i   i     ii---- i   vi  i ---- i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_39739258_   1963 ACAAAAAACACAACTCATAAAGAAAAAGGTTGATAG-TTA-ACATCAATG 2010
                           v    i     viv i   ii    ii v    i-  i-  v   vii
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_39739258_   2011 AAATTAGAAACACCTGAGTTCTGAAAACCATCATTAACGTGGTGAAAAG 2059
                               i    vii  v i iii  iiv  ii  i  vivi        
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

Transitions / transversions = 2.19 (81 / 37)
Gap_init rate = 0.05 (21 / 435), avg. gap size = 3.43 (72 / 21)  

 432 24.88 10.24 0.98  chr20_39739258_39742152     2206  2410 (485)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr20_39739258_   2206 AAGAAAG-AAATATCTAACTC-CAGATTGGGGGAAAATGTTTGCAATATA 2253
                                -i  v vvi   i -    v    i      i       vvi 
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr20_39739258_   2254 CATAATTGACAAAGGATTTGAATCCAGAACATATAAATAACTC--ATAAA 2301
                         i   vi   i  i   i   v        i       v     -- i  v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr20_39739258_   2302 TCGATAATTTAAAAAAA-----------ACTGGAAAATGGGTAAAAG--T 2338
                           i     --     i ----------- i ?i        i   i -- 
  L1M4_orf2#LINE/    785 TCAATAAT--AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_39739258_   2339 CAAACAGGTAAATCTTAGAATAAGAAACCAAAATGGACAATAAATATATG 2388
                         ii  i  ii vv   ivi  v    v ivv      v      ii i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_39739258_   2389 AAAAGATAATC----TCATGAAGAAT 2410
                                iv  ----   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (31 / 19)
Gap_init rate = 0.03 (7 / 224), avg. gap size = 3.29 (23 / 7)  


3091 27.17 0.66 0.77  chr20_39743249_39745639.rev      991  1899 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_39743249_    991 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 1040
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_39743249_   1041 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 1090
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_39743249_   1091 TACCAATGACTTTCCTCACAGAC-TTGGAAAAAAAACT-ACTTTAAAGTT 1138
                          v   iivi i  ii ii    v-   ---- v  i  - iii    i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG----ACAAGCTGATCCTAAAATT 146

  chr20_39743249_   1139 CATATGGAACCAAAAAAGAGTCCGCATTGCCAAGTCAATCCTAAGCCAAA 1188
                                  viiv  ii  vi v v  v     iv     i i ivv i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_39743249_   1189 AGAACAAAGCTGGAGGCATCACGCTACCTGACTGCAAACTATACTACAAG 1238
                                  i      vv    i  v  ii i v    viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_39743249_   1239 CCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGA 1288
                         v         i   i    ii         i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_39743249_   1289 CCAATGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAA 1336
                         i        i    i--    i  --        vv   i    i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr20_39743249_   1337 CTATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATT 1386
                         ii vi    i  i     ivv  v   i v  vvv           i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_39743249_   1387 CCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAG 1436
                         vi  v  i  i              v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_39743249_   1437 CTGAAACTGGATCCTTTCTTTACACCTTATACAAAAATTAATTCAAGAAG 1486
                         v    ii    i  i v i i     v              i    i v 
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_39743249_   1487 GATTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAA 1536
                            i ?    i       v   v       i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_39743249_   1537 ATCTAGGCA-ATACCATGCAGGACATAGGCATGGGCAAGAACTTCATGTC 1585
                          iv    ?i- v i - v iv   v v  vv i     viii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_39743249_   1586 TAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGAAG 1635
                           vi            vvi          vv     v  i    v   vv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_39743249_   1636 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACAACCATCACAGTG 1685
                          v  i   v v  i i   i  ii vv    i  v  v i  vv v    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_39743249_   1686 AACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGA 1735
                           v  i     i                 v       vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_39743249_   1736 CAAAGGGCTAATATCCAGAATCTACAAAGAACTCAAACCAATTTACAAGA 1785
                         i  i  i  vi          v  i         vv  v v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_39743249_   1786 AAAAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAACAGACAC 1835
                             i     i     v  i? v  i            v    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_39743249_   1836 TT-TCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGTTC 1884
                           -  v        i  vi viii     v ii          i   i  
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_39743249_   1885 ATCATCACTGGCCAT 1899
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (140 / 103)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2597 26.26 4.57 0.91  chr20_39802849_39808031.rev     3816  4691 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_39802849_   3816 TGGAAAAACATTCCATGTTCACGGATTGGAAGAATCACTATTATTAA--- 3862
                               i i  i         i           v i v    i    ---
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_39802849_   3863 ---AATACTGCCCAAAGCAATCTACAGATTCAACACTATTCCTAACAAAC 3909
                         ---      v      vii               i v  i    v    v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_39802849_   3910 CACCAACATAATGTTTCACAGAAA--GAAAA---------AAAACTACTC 3948
                         iv   i vvvv v   ii      --  v  ---------    i vv v
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_39802849_   3949 TTTAAA---AAG---CCCA-ATTAGCCAAAGCAATCCTACCCAAAAAGAA 3991
                          vv   ---   ---    - v        i     i ivvv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_39802849_   3992 CAAAGTCAGAGACATCACATTATGTGACTTCAAACTGTATTATAAGGCTA 4041
                               ii   ivv     i vivii i      viv  i  i  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_39802849_   4042 CAGTAACCAAAACAGCATGGTACTTGTACAAAAACAGACACATAGACCCA 4091
                               i   i    ii       v i i  ii i     i     i v 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_39802849_   4092 AGGAACAGAACAGAGAACTCAGAAATAAAGCCACACACCTGCAACCATCT 4141
                         v    i    iv    iii          v   i   ii iiiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_39802849_   4142 GATCTTCGATGAAGTCAACAAAAACAAGCAATGGAGAAAGGACTCTATAT 4191
                            i     ii i viiv   i v  vv      i     i ivv v v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_39802849_   4192 TCAATAAATGCTGCTGGGATAACTGGCTAATCATATGCAGAAGAATGAAA 4241
                             i     v        i      v  ?i  i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_39802849_   4242 CTGGACCCCTACTTTTTACCATATACAAAAATTAATTCAAGATGGATCAA 4291
                         i           i ivi                  i    i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_39802849_   4292 AGATTTAAATATAAGACCTCAAGCTATAAAAATCCTATAAGAAAACCTGA 4341
                            ii     i     v  v  i        v  i  v        v ii
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_39802849_   4342 G---AAATACCATTCTGGACATCGC-TCATGGCAAAGAATTTATAGCTAA 4387
                          ---    -- -   vv   v i v- i -     v iv  iv   v  v
  L1M4_orf2#LINE/    551 GNGTAAAT--C-TTCGTGACCTTGGGTTA-GGCAATGGTTTCTTAGATAT 596

  chr20_39802849_   4388 GACCTCAAAAAT-CAATCTCAACAAAACAAAAACT-GACAAGT-GGGCCC 4434
                            vi     ii-   v --       v     v -  i  i -  i ii
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGC--AACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_39802849_   4435 TAT-GAAGCTAAACAGCATCTGCACAGCAAAAGAAACTACCAACAAGGTA 4483
                         i  -i  ii    - i v i  ii vv    i  v    i   v  i  i
  L1M4_orf2#LINE/    645 CATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_39802849_   4484 AACAGACAACCTATAGAATGAGAGAAAATAGCCACAAACTATGCATCTGA 4533
                           v        i i      i         viii    ii  ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_39802849_   4534 CAAAGATCTAATATTGAGACTCTGTAAGAAAC-CT---AAATCAGCAAGC 4579
                         i  i iv  vi   iv   v v i   ii   -  ---  v   ii  vv
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_39802849_   4580 AAAAAACAA----CCCCATCAAAAAATAGGCAAAGGACATGAACAGACAC 4625
                             i    ----   v  i?      i         iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_39802849_   4626 TTTTGAAAAGAAGACATACAAATGGCCAACAAACATATGAAAAAAATGCT 4675
                           i vv        i              i  i  i       i -    
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TGCT 892

  chr20_39802849_   4676 CCACATTACTAATCAC 4691
                          v    i ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (142 / 85)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.29 (48 / 21)  


3169 26.53 1.44 0.67  chr20_39863603_39869951.rev     4956  5856 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_39863603_   4956 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTGAAAAT 5005
                              ii i  i     i        v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_39863603_   5006 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5055
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_39863603_   5056 TACCAATGACTTTCCTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5103
                          v   iivi i  ii ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_39863603_   5104 TATGGAACCAAAACAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5153
                                viiv  vi  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_39863603_   5154 AACAAAGTTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGTC 5203
                                       vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_39863603_   5204 TACAGTAACCAAAACAGCACGGTACTGGTACCAAAACAGAGATATAGACC 5253
                                 i   i    iii        i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_39863603_   5254 AATGGAACAGAACAGAGACCTCAGAAATAA---TAGCCATCTACAACTAT 5300
                                i    iv    vii         ---i vv   i  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_39863603_   5301 CTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTTCCT 5350
                         i    i  i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_39863603_   5351 ATTCAACAAATGGTGCTGGGAAAACAGGCTAGCCATAAGTAGAAAGCTGA 5400
                         v                    v   v  v  ?   i v i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_39863603_   5401 AACTAGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATT 5450
                          ii i  i    v   i     v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_39863603_   5451 AAAGACTTACACGTTAGACCTAAAACCATAAGAACCCTAGAAGAAAACCT 5500
                          ?    i  v i  v   v       i    i vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_39863603_   5501 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATCTCAAA- 5548
                            ?i- v i -   iv   v v  vv i     v ii   --- i i -
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTC---TTAGAT 594

  chr20_39863603_   5549 --AACACCAAAAGCAATGGCAACAAAAGCCAACATTGACAAATGGGATCT 5596
                         --i            vvi          vv  v  v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_39863603_   5597 AATTAAACTTAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5646
                         v  i   v    i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_39863603_   5647 ACAGGCAACCTACAGAATGGGAGAAAATTTTTACAATCTACTCATCTGAC 5696
                          v  i     i                 v   i   vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_39863603_   5697 AAAGGGCTAATATCCAGAATCTACAAAGAACTCTAACAAATTTACAAGAA 5746
                           i  i  vi          v  i          v    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_39863603_   5747 AAAAACAA----CCCCATCAAAAAGTGGGTGAAGGATATGAACAGACACT 5792
                            i    ----   v  i?    i    ii      v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_39863603_   5793 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5842
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_39863603_   5843 TCATCACTGGCCAT 5856
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (141 / 94)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


3259 26.54 0.77 0.77  chr20_40267824_40274112     4890  5797 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_40267824_   4890 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4939
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_40267824_   4940 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGT 4989
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_40267824_   4990 TACCAATGACTTTCTTCATAGAA-TTGGAAAAAACT-ACTTTAAAATTCA 5037
                          v   iivi i  i  iii    -   -- v  i  - iii         
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_40267824_   5038 TATGGAAC--CAAAGAAGAGCCCACA-TCGCCAAGTCAATCCTAACCCAA 5084
                                v--   i i ---    v - v     iv     i i vvv i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGA---CCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_40267824_   5085 AAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAA 5134
                                   i      vv       v  ii i      viv        
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_40267824_   5135 GGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAG 5184
                         i          i   i    ii         i iv ii i   v      
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_40267824_   5185 ATCAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACA 5232
                                   i    i--    i  --        vv  ii i  i  ii
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATG 343

  chr20_40267824_   5233 ACTGTCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAT 5282
                         iiiivi    i  i     ivv  vv  i v  vv            i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_40267824_   5283 TCCCTCTCTAATAAATGGTGCTGGGTAAACTGGCTAGCCATATGTAGAAA 5332
                         vvi  i ii  i             vv      v  ?   i   i i  i
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_40267824_   5333 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAGTTCAAGAT 5382
                         iv    ii    i    v   i     v           i ii    i  
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_40267824_   5383 GGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGGA 5432
                             i ?    i    i  v   v       i      vi i      i 
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_40267824_   5433 AACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTC 5482
                            v    ?i v viv   iv   v v  vv i     v ii   v ivv
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_40267824_   5483 TAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATC 5532
                           vi            vvi           v     v  i    v   ii
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_40267824_   5533 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTG 5582
                          v  i   v v  i i   i  ii vv    i  v    i  vv i    
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_40267824_   5583 AACGGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGA 5632
                           vi i     i   i             v  i    vii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_40267824_   5633 CAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5682
                         i  i  i  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_40267824_   5683 AAAAAACAAACAACCCCGTCAAAAAGTGGGCGAAGGACATGAACAGACAC 5732
                             i     i     vi i?    i     i     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_40267824_   5733 TTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5782
                              v        i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_40267824_   5783 ACCATCACTGGCCAT 5797
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (145 / 92)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


1176 27.40 9.02 4.05  chr20_40358852_40360804      607  1471 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_40358852_    607 TAGAAAGACATCCCTTATCTCA--GGTAAGATAATTCAACATCTTAAAGA 654
                          i      i     v i -   -- i vi  vi i i  i  iv v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGT-TCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr20_40358852_    655 TGTCATTTCACTCTAA-TTAATGTATAAATTTAATGCAATCCC----AGA 699
                           v  v v v i i  -  i  v  i i   i  i        ---- i 
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_40358852_    700 ATTACTAATAGACTTTTT---ATGAATCTGGACAAGTGGACACTAAAATT 746
                           i- i iiv v      --- vi   i--      iv  iv        
  L1M4_orf2#LINE/    100 ATC-CCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATT 146

  chr20_40358852_    747 TATAGGGAACATGCAAG--------AAGAGCTAGAA-ACTCACTGAAAAA 787
                         i   v    -       --------  v   i i  - v  -i       
  L1M4_orf2#LINE/    147 CATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATC-TTGAAAAA 194

  chr20_40358852_    788 GGAAATCTC-GATGGGGAACTTTC-CCTCGCAGACATTAAAGTTTA---- 831
                          i i v vv- v   i i   iv - i  v  - iv i   ii   ----
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCA-ATTTCAAAACTTACTAC 243

  chr20_40358852_    832 ---GATCCCATAATTATAACAGTGTGGGGCTGCTGCGTAA--ATAGCCAC 876
                         --- v v vi    i vi         vi   --  i   --    v  i
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTG--GCATAAGGATAGACAT 291

  chr20_40358852_    877 ATAGACTGGTGGGATAGAATACGACA-TCCAGAAAAACACCCAAGAACAT 925
                              iiii   i       -i  v -        v v     viv iv 
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAAT-TGAGAGTCCAGAAATAAACCCATACATTT 340

  chr20_40358852_    926 ATGAAAATTTAAAATATGAGAAAAG---CAGCATC--TCAAATTATCGGG 970
                            ivv v  i vv vi  v  ii ---  iv i --    ---- v   
  L1M4_orf2#LINE/    341 ATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA----TGGGG 386

  chr20_40358852_    971 ACAAAAATGGACTTTTAAATACATGTTGCTAAGACAACTAGACAGACATT 1020
                          -  i   i v     v  i v   v    ii       i  i ?v  iv
  L1M4_orf2#LINE/    387 A-AAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr20_40358852_   1021 TGGGAAAACAGATAAAAATTAGATCCATAATTTACATCACACACAAAAAC 1070
                           vi   i--i  i  i-  i  i  v  vi i   i  i i       i
  L1M4_orf2#LINE/    436 TGCAAAAG--AATGAAG-TTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr20_40358852_   1071 AAAGACCAAAC--ATCAGAAAACTAAATATAAAAATACTAAAATACATAA 1118
                         v  vv v   i--    ? i v      i   i i--      i-i    
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAG--CTAAAAC-TATAA 529

  chr20_40358852_   1119 GACT--TAGAAGCAAACAT--GGGTAAATTCCTTTATAGCCT-GAGTGTA 1163
                         i   --      v      -- ?      --   ii ii   - i  -  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGT-TA 576

  chr20_40358852_   1164 AGAAAAAACTTTTTAACTGTGATTC--AAAGTTTAAATGTAATAAAAGAA 1211
                         i v  viii  i   iv i   iv --    ivi  -- i  i       
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAA--GCAACAAAAGAA 624

  chr20_40358852_   1212 AAAA------AAT--GA-TTCATC-----TGACAACATTTTATTTGCTGT 1247
                             ------   --  -      ----- i v   -    i --   - 
  L1M4_orf2#LINE/    625 AAAATAGATAAATTGGACTTCATCAAAATTAAAAAC-TTTTGT--GCT-T 670

  chr20_40358852_   1248 GGCAAAAA----TAT-AAGCAAAGTCAACAGATAAATCACAAACTGGAAA 1292
                         --    ii----   -   -     v  v   i  vi    i v   i i
  L1M4_orf2#LINE/    671 --CAAAGGACACTATCAAG-AAAGTGAAAAGACAACCCACAGAATGGGAG 717

  chr20_40358852_   1293 AAA----CTGCAA--CATATATCACAGATAAAGTACTGATATCTCTGATA 1336
                            ----i     --        v--     i v   vi    ivvi   
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCT--GATAAGGGACTTGTATCCAGAATA 765

  chr20_40358852_   1337 TATAAATAACT-TTAAAAATTGATAG-AAAAAG-TAAA-AAACAAACTGA 1382
                               v    -   v  v ii   i-      -i   -  v v  i ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr20_40358852_   1383 AAATTGAGCAAAAGACATAAACAGGTAATTC---AAAAATTACATAAAAA 1429
                            v  i     i  iv i  i  ii v   ---   i vv i   v   
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 865

  chr20_40358852_   1430 TGGCTATTAAGTATAGGAGAATATAG-CAATTTCACTTATAAG 1471
                             i v    i i v  i  v  iv-   iv   ????????
  L1M4_orf2#LINE/    866 TGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.06 (55 / 908), avg. gap size = 2.05 (113 / 55)  


1086 27.17 12.47 3.02  chr20_40497196_40498994      538  1299 (500)    L1M4_orf2#LINE/L1       31   864 (44)  

  chr20_40497196_    538 AGATTGAATATCAT-AAAATGTCAATTAC-CCACATATTGTTCTATACAT 585
                            i v     ii -  i   v    -  -  v  v    v    i v  
  L1M4_orf2#LINE/     31 AGACTTAATATTGTTAAGATGGCAAT-ACTCCCCAAATTGATCTACAGAT 79

  chr20_40497196_    586 TCAAGGCAATTCTAATAAAAACAACAGATGTTTTCATTA---AACTTGAT 632
                             v     i iv  v    ivv   v  ii  iv  i---  v    i
  L1M4_orf2#LINE/     80 TCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGAC 129

  chr20_40497196_    633 AAGTAGATACTAAAAT------GAAAGAGCCAAGGG--CAAGAATAACCA 674
                            iv   v       ------ i  iv  -     -- v      i   
  L1M4_orf2#LINE/    130 AAGCTGATCCTAAAATTCATATGGAAATGC-AAGGGACCCAGAATAGCCA 178

  chr20_40497196_    675 AGATATTGCTGAACAAGTATGAGGA----GGAGGAATCTTCTCTACCAGA 720
                          i i v vi    v   v vi vi ----      v  vivii v   - 
  L1M4_orf2#LINE/    179 AAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCA-A 227

  chr20_40497196_    721 GATCAGGAC--ACTGTGAAGCTGTAATAAATATGACTATGCATGGTTACA 768
                         vv   ii  --   iii     ii i   vi v   vi  --    -  v
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTG--TGGT-ACT 274

  chr20_40497196_    769 GTGCAT--GGA----------GGCCAGTGGAATAGA-----GAGCTCAGA 801
                          -    --   ---------- ii  i         -----   ii    
  L1M4_orf2#LINE/    275 G-GCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr20_40497196_    802 AAAAAATTCATGCATATAAG---AA---ATTTT-GGCATAAGTCAGATAT 844
                           v   ii   i   v  v ---  ---     - i  vii  -- vi v
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT--GCCAA 371

  chr20_40497196_    845 GGCCTGGTAGAGCAGGGAAGGAG-AGACTGT-----AAAAAGGACTTGGA 888
                          i  --i vv iii     i  i-  v  v -----   vi vi  v   
  L1M4_orf2#LINE/    372 GACC--ATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGA 419

  chr20_40497196_    889 TAAAGTGTTTATCAATGTAATAAAAAAATAAAATTTTCACTCC-ATCTCT 937
                         i  v-  vv  ? v ii i-i    i   i  i  vv-  i  - i   v
  L1M4_orf2#LINE/    420 CAAC-TGGATAKCCACATG-CAAAAGAATGAAGTTGG-ACCCCTACCTCA 466

  chr20_40497196_    938 CACCCTATGCAAAAATTAATTGCAGATAGATCAAAAACTTAAATTTCAGG 987
                             v   i          i vv i  i     ? i  i     v - i 
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT-AAG 515

  chr20_40497196_    988 AGC-AAAACTATGCAACTTTTAGCAGAAA-TATAGGC--AATCATCTTTC 1033
                            -        iv    i    v     -i     ?--  --     iv
  L1M4_orf2#LINE/    516 AGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA--ATCTTCG 563

  chr20_40497196_   1034 TCACCTTGGTTTAGGGAAGAATTTCTTA---AGGACACAAAATGTGTTAA 1080
                          v       v     v  vii       --- v     v   v iiiv i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAG 613

  chr20_40497196_   1081 CTATATAA-ACAAAGT-GATAAAATTGG-CT--AT---AATTAAGGACTT 1122
                          v i v  - v   i -      -    -  --  ---      ii    
  L1M4_orf2#LINE/    614 CAACAAAAGAAAAAATAGATAAA-TTGGACTTCATCAAAATTAAAAACTT 662

  chr20_40497196_   1123 TTGTTTTTCAAAG-ATACCTTAGAAGAAGTAAAAA--CAGC-----AAAT 1164
                             vi       - i  iv vi ii    i    --  i -----i   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr20_40497196_   1165 T-------ACATTTGTAA---------CTGGCAAAATATT---ATCAAAA 1195
                         v------- i     i  ---------   ii  iiv i ---   v i 
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr20_40497196_   1196 GTATATTATAAAACTATTACATATCAATAAAGAAAAGAGCATATAACCCA 1245
                         i     v - i    v     vv       vi      -  v        
  L1M4_orf2#LINE/    763 ATATATAA-AGAACTCTTACAACTCAATAATAAAAAGA-CAAATAACCCA 810

  chr20_40497196_   1246 GTAGAAAAGTAGGCAAAAGACATGAACAGATATC---CCACAGAAAATGA 1292
                         i v?    i i      i  iv    i   i  i---   v    i  --
  L1M4_orf2#LINE/    811 ATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT-- 858

  chr20_40497196_   1293 AATACAA 1299
                         -      
  L1M4_orf2#LINE/    859 -ATACAA 864

Transitions / transversions = 1.33 (116 / 87)
Gap_init rate = 0.06 (49 / 834), avg. gap size = 2.41 (118 / 49)  


 294 31.39 17.22 2.91  chr20_40609288_40611382      859  1648 (447)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr20_40609288_    859 AGGCATTCTATGATCTTGGATAGGA-TAC--AATGATATAACAAATGTGC 905
                           ii  i i   v  v     v   -v  --   iv i v - i   -  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTA-AGATG-GC 53

  chr20_40609288_    906 TATATTATTATTAAATTAATTTACAAACTCAATGCAATCT-TGTAAAAAT 954
                         v   i vii--i     i  i    i i    i      i- i v     
  L1M4_orf2#LINE/     54 AATACTCCC--CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_40609288_    955 TCTAATTGGACTCCTATA-AGAACTAGATAAACTTAGCTTAAAATTTATA 1003
                         i i ii  v-  ii v i-    v v  i  i  v v i       i   
  L1M4_orf2#LINE/    102 CCCAGCTGC-CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_40609288_   1004 AGAAAGAATAACA-ATCCATGACTAGCTAAGAT------------GAAGG 1040
                         v i  ivii  vi- i   -  v    i  i i------------    i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_40609288_   1041 A------TGG-TGACTTGCCCAATCCAATACTGAAACAGAACAAAAGGC- 1082
                          ------   -v    ii v vvi     viii    vv vi v  i  -
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_40609288_   1083 ACAGTAAT------AGTG--GAATTGA-ATAATGA----------GCTC- 1112
                                 ------    -- v i  i-    v  ---------- v  -
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_40609288_   1113 -TGAGAAAGGCCAATGAAAATATAAAAATATATC-ATGTAATAAATGTTA 1160
                         -  ii v  i-- v   i i vi i     v i -  ii v v -  v v
  L1M4_orf2#LINE/    300 ATGGAATAGA--ATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTC 346

  chr20_40609288_   1161 AATTGCACATCAATAAAA-----AAG------TGATGG--ACAGATTTGT 1197
                              vviv  i i  ii-----   ------ii    -- v   v v  
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_40609288_   1198 ---------AGATA-TGTTGGAAATACTGGATCACCCTATGGAAAAAAAT 1237
                         --------- i  i-  i   i vv       v?  vi   v    i   
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_40609288_   1238 AAA---------------------ACATGCAAAGATAGATTTCAAATGGA 1266
                         i  --------------------- i  i    i  vi i iv       
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_40609288_   1267 TCAAATAACAAAACATAAAAACTGAAACTATAAAGTTATTAAGAGAAAAT 1316
                            ? v v v   ii   i i  i          ii v   ii      i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_40609288_   1317 ATAGAAGACTATACTTGTGACTTAAGGGTGGAGGA------CTTAA---- 1356
                             i? vvv  vi i     i vi  v i ivi ------    i----
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_40609288_   1357 GACTTGAAAGACACACATCATAAATCAAAGCACTGAGGAATTTTATT--A 1404
                            viv   ii    viiv i   vv   iv iv  vi    vv i -- 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_40609288_   1405 TC-----TAAAAA---TTATG----GATGTATATT--CAGTAAAATAAGC 1440
                           -----      ---  i  ----i v v i i --  iv   i i iv
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_40609288_   1441 AGA--AC--ACAGATTGGGAAAAGATACTTGTGATGTCTTAAATC-GACA 1485
                            --  --     v     i  i   i   ii -i  v  v   -  i 
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATA 745

  chr20_40609288_   1486 ACCAAATAATATCCAGGATATA-AATGCAACTCGTGAAAATTTAATAG-- 1532
                          vvi v vi       i     -  v -     v - v  i i    i--
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAG-AACTCTT-ACAACTCAATAATA 793

  chr20_40609288_   1533 AAAACACAGG-AACCC--TTTCTCCAAGAAACGCGCAGGTGTTATGTGAA 1579
                             v   ii-     --  ?----- i   i v   iiv --  v    
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTW-----AAAAATGGGCAAAGG--ATTTGAA 836

  chr20_40609288_   1580 CAGTCAAT-----AAAGAAGAGGGAAGGCAAAATATTAAGGAGCAT-TGG 1623
                         i  v  v -----        viv ---    vviii  vi    i-  i
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATA---CAAATGGCCAATAAGCACATGA 883

  chr20_40609288_   1624 ACTGATGCTCCAAC-TCATTAGTTAT 1648
                          vv       -   -   ????????
  L1M4_orf2#LINE/    884 AAAGATGCTC-AACATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (143 / 101)
Gap_init rate = 0.06 (52 / 903), avg. gap size = 3.06 (159 / 52)  


3289 26.54 0.55 0.55  chr20_40677242_40683521.rev     4881  5788 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_40677242_   4881 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 4930
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_40677242_   4931 GGCCATACTGCCCAAGGTAATTTACAGTTTCAATGCCATCCCCATCAAGC 4980
                            v     v     iv i  i     v     i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_40677242_   4981 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5027
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_40677242_   5028 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAACCCAAAA 5077
                                 viiv  ii  v  v v  v     iv     i i vvv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_40677242_   5078 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5127
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_40677242_   5128 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5177
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_40677242_   5178 CAATGGAACAGAAC--AGAGCCCTCAGAAATAACGCTGCATATCTACAAC 5225
                                 i    i--    i  --        vv iii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr20_40677242_   5226 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5275
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_40677242_   5276 CCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5325
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_40677242_   5326 TGAAACTGGATCCCTTCCTTATGCCTTATACAAAAATCAATTCAAGATGG 5375
                             ii    i    v   i ii  v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_40677242_   5376 ATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGGAGAAAA 5425
                           i ?   ii    i  v   v       i      vi i   i      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_40677242_   5426 CCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCA 5475
                          v    ?i v viv   iv   v v  vv i     v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_40677242_   5476 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTCACAAATGGGATCTC 5525
                         vi            vvi          vv     vv i    v   ii  
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_40677242_   5526 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5575
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_40677242_   5576 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5625
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_40677242_   5626 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5675
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_40677242_   5676 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5725
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_40677242_   5726 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5775
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_40677242_   5776 CATCACTGGCCAT 5788
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (141 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


2676 26.82 2.92 1.01  chr20_40880000_40885359     3978  4868 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_40880000_   3978 TGGAAAAACATTCCATCCTCATGGATAGGAAGAATCAATACTGTGAAAAT 4027
                               i i  i    vi        v      v i    i   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_40880000_   4028 GGCCATAATGCCCAAAGTAATTTACAGATTCAACACTGCTCCCATCAAAC 4077
                            v   v v      v i  i            i viii  i      v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_40880000_   4078 TACCATTGACATTACTCACAGAATTAGAAAAAATAGTTTTAAATTTCATA 4127
                          v   vivi v  vi ii     v v  v  iv ii ii    v      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_40880000_   4128 TGGAA-T-CAAAGAAGACCC--------CAAGACAATCCTAAGCAAACAA 4167
                              - -   i --     --------   i      i i iv  iv i
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_40880000_   4168 AACAAAGCTGGAGGCATCAAACTACTTGACTTTAAACTATACTACAAGGA 4217
                                i      vv   v   v iii i  i   viv        i v
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_40880000_   4218 TACAGCAACCAAAACAGCATGGTACCTGTACCAAAACAGATATACAGACC 4267
                              i  i   i    ii      iv i iv ii i   i   i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_40880000_   4268 AATGGAACAGAATAGAGACCTCAGAAATAACACCACACATCTACAACCAT 4317
                                i     v    vii         vv   i    i  iiii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_40880000_   4318 CTGATCTTCAACAAACCTGACAAAAACAAGCAATGGGGAAAGGACATCCT 4367
                         i    i   i    ivv  v   i v  vv            i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_40880000_   4368 ATTAAGTAAATGGTGCTGGGATAACTGCCTAGCCAAATGCAAAAACAGAA 4417
                         v  v ii              i     vv  ?   v        iv vi 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_40880000_   4418 AGT-GGACCACTTCCTTATACCTTATAGAAAAATTATCTCAAGATAGATT 4466
                            -     v  v   i i   v    v        v     i  i   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_40880000_   4467 AAAGACTTAAATGTAAAACCCAAAACCATAAAAATCTCAGAAGAAAACCT 4516
                          ?    i         i v i     i      v   i          v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_40880000_   4517 AGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTC------ATG 4559
                            ?i- v i -   iv   v v  vv i     v ii   ------   
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_40880000_   4560 ACAAAAATGCCAAAAGCAATTGCAACAAAGGCCAAAATTGACCAATGAGA 4609
                            ------         vvv        i vv     v  iv   vi  
  L1M4_orf2#LINE/    598 ACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_40880000_   4610 TCTAACTAAACTAAAGAGCTCCTGCACAGCAAAAGAAACTAGCATCAGAG 4659
                         ii v ii   v v  i i  ii  ii vv    i  v    v  vv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_40880000_   4660 TGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCT 4709
                             v  i     i                 v       vii ivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_40880000_   4710 GACAAAAATCTAATATCCACAAGTTACAAGGAACT--TA-AACATATTTA 4756
                           i  iiiv  vi      v  vv  i  i     --  -   vi v v 
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_40880000_   4757 CAAGAAAA-AAACAACCCA-TCAAAAAGTGG-CAAAGGATATGAACAGAC 4803
                         i  i  i -   i      - i?    i   -        v    i    
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_40880000_   4804 ACTTCTCAAACGAAGACATTTACGCAGCCAACAA--ACATGAAAAAAAGC 4851
                          i     v  v     i  vi viii     i  --         i v  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_40880000_   4852 TCAACATCACTGATCAT 4868
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (135 / 100)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.33 (35 / 15)  


2178 27.70 2.96 0.74  chr20_41471422_41474558     1471  2145 (992)    L1M4_orf2#LINE/L1        2   691 (217)  

  chr20_41471422_   1471 GAAAAAATAGCCCATGCTCATGGATTGGAAGAATCAGTATCATTAAAATT 1520
                          i   i   v      i               v i i   ii    i  v
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_41471422_   1521 ACCATACTGCTCGAAGCAATCAACAGACTTAATGCAATTCCTATCAAAAT 1570
                         i v     v i i  vii   v     i i  i     i           
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_41471422_   1571 ACCAAGGTCATTTTTCACAGAATTAGAATAAAC-AATGTTAAAATTCATA 1619
                         v   ivvv v     ii     v v  -i  i -i  vi           
  L1M4_orf2#LINE/    102 CCCAGCTGCCTTTTTTGCAGAAATTGA-CAAGCTGATCCTAAAATTCATA 150

  chr20_41471422_   1620 TGAACCCAAAAAAGAGTCCAAATAGCCAAAGCAATCCT-------AAGCA 1662
                           i vviiv  ii  vi vi          i     i -------   - 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG-A 199

  chr20_41471422_   1663 ACAAA----------TAACACTGTCTGACTTTAAATTATACAACCAGGCT 1702
                              ---------- v     vi ii i  i   viv   v  v i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_41471422_   1703 ACAGCAACCAAAACAGCATGGTACTGGCATAAAAATAGATACATAGACCA 1752
                             i  i   i    ii              ii     i i     i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_41471422_   1753 GTGGAACAGAAAAGAGAACCCAGAAATAAAGCCACATACCTAATGAT-AA 1801
                         i     i    vv    ii           v   i i ii  -  i -  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA-TGGTCAA 348

  chr20_41471422_   1802 TTGATCTTCAACAGAGTCAACAAAAACGTACACTGAGGAAAGGACACCTT 1851
                              i   i   ii viiv   i v i v  v  i      i i vii 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_41471422_   1852 ATTCCGAAAATGGTGCTGGAAAAATTAGATAGCCATAAGCAGGAGAATGA 1901
                         v   viv            i v  i i    ?   i v   ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_41471422_   1902 AATTGGTCCCATATCTCTCACCATAGACAAAAATTAACTCAAGACAGATT 1951
                          i    v   v  i   v       v                i ii   i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_41471422_   1952 AAAGGCTTAAATGTAAGACCCGAAACTATAAAAATTCTAGAAGGAAACCT 2001
                          ?  i i           v ii           v ii      i    v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_41471422_   2002 AGAAAAAAATTATTCTGGATATTGGCCTAGGCAAAGAATTTATAACCAAG 2051
                           i?iv    i-   vv  iv    vi       v iv  iv  ivi v 
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_41471422_   2052 ACCTCAAAAGCATATGCGACAGAAACAAAAATAGACAAATGGAATTATAT 2101
                           vi        i v  i   i  iv         i    v i i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_41471422_   2102 CAAG-CTAAAAATATTCTGCACATCAAAAGAAACAATCAACAGAG 2145
                            i-i      i-  i  ii v     i  v  v     v i  
  L1M4_orf2#LINE/    648 CAAAATTAAAAAC-TTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

Transitions / transversions = 1.79 (118 / 66)
Gap_init rate = 0.01 (10 / 690), avg. gap size = 2.50 (25 / 10)  

 600 26.67 7.18 0.00  chr20_41471422_41474558     2454  2648 (489)    L1M4_orf2#LINE/L1      672   880 (28)  

  chr20_41471422_   2454 AAAAGAAACAACCAACAGAATG----GTCAAACTATGGAATGGGAGAAGT 2499
                            i  v  v i   v i i  ---- v   v i ii           iv
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 721

  chr20_41471422_   2500 TATTTGCAAACTATGCATCCAACAAAGGACTAATATCCAGAATCTACAAG 2549
                                   ii  ii   ii i  i     vi          v  i  i
  L1M4_orf2#LINE/    722 TATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAA 771

  chr20_41471422_   2550 GACCTCAAATAACTCAACAGCAACAA----AATAACCCCATTAAAAAGTG 2595
                           v   vv i       i ii  v  ----        v   ?    i  
  L1M4_orf2#LINE/    772 GAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATG 821

  chr20_41471422_   2596 TGTGAAAGATATGAACAGATACTTTTTAAAAGAAGACATACA---GGT-- 2640
                         v ii  i   v    i   i i  i iv        i     ---  i--
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr20_41471422_   2641 -TGAGCACA 2648
                         - i      
  L1M4_orf2#LINE/    872 ATAAGCACA 880

Transitions / transversions = 2.19 (35 / 16)
Gap_init rate = 0.02 (4 / 209), avg. gap size = 3.50 (14 / 4)  


1288 16.79 1.44 16.07  chr20_41614195_41616861      607  1023 (1644)    L1M4_orf2#LINE/L1        1   356 (552)  

  chr20_41614195_    607 TGGAAAGAGATCT-GTGTTCATGGCTAGGAAGACTTAATATTGTTAAGAT 655
                                 v   i-i         v v                       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_41614195_    656 GTCAATATTACCCAAAGATATTTACATATTCAATGCAATCCCTATCAAAA 705
                          v     i v      vvv  i    v      i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_41614195_    706 TCTCAGCTGATTATTTTTTTCTTGCAGAAATGGAAAGACAGATCCTTAAA 755
                           i      ------ii   i          v  v ii v      v   
  L1M4_orf2#LINE/    101 TCCCAGCTG------CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA 144

  chr20_41614195_    756 TTCCTATGGAATTGCATGAGGCCTCAGA-TAGCCCAAACAATCTTAATAA 804
                            v       v    v i i  -    -     v          i v  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACC-CAGAATAGCCAAAACAATCTTGAAAA 193

  chr20_41614195_    805 AGTATAACAAAGTTGAAGAACAAACCGATTTCTTTCTTTCTTTCTTTTCT 854
                           v v          i  i  vv  -- i   iivv    ----------
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAGGACTCAC--ACTTCCCAATTTC---------- 231

  chr20_41614195_    855 TTTTCTTTTTCTTTTTTTTTTTTACAGAGTTTTGCTCTCGTTGCCCAGGC 904
                         ------------------------- i ii  ------------------
  L1M4_orf2#LINE/    232 -------------------------AAAACTT------------------ 238

  chr20_41614195_    905 TGGAATGCAAAGCCACAATAATCAAAACAGTGTGTTACTGGCATAAGGA- 953
                         --- v i      i   i       i        v              -
  L1M4_orf2#LINE/    239 ---ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr20_41614195_    954 ---CAAATAGACCAATAGGATGGAATTCAGAGTCTAAAAACAAGTCCATA 1000
                         ---  v     i    i i  i     v      i i   i  ii     
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr20_41614195_   1001 TGTCCATAACCAATTGAAATTTT 1023
                         ii ii  iii       --    
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGA--TTTT 356

Transitions / transversions = 1.50 (42 / 28)
Gap_init rate = 0.03 (9 / 356), avg. gap size = 8.11 (73 / 9)  

1750 16.56 0.00 0.00  chr20_41614195_41616861     1324  1625 (1042)    L1M4_orf2#LINE/L1      346   647 (261)  

  chr20_41614195_   1324 CAATTGATTTTCAGTAAGAATGCCAAGTCCATTAAATGGGGAAAGTACAG 1373
                                     iii   ii       v     v           v i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_41614195_   1374 TTTCTTCAACAAATGGGTCTGGGGTAACTGGATTTATACTTGTAAAAGAA 1423
                          i i            vv     ii        v?vi  v  i       
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_41614195_   1424 TGAAATTGGATACCTACCTCACCCCATATTCAAGAATTAACTCAAAATGG 1473
                             i     iv          v      v   i                
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_41614195_   1474 ATTGATGACCTAAATATAAGAACTAAAACTATAAAACCCTAAGAAGAAAA 1523
                           ii?v         i     i               i  v         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_41614195_   1524 CATAAAGGTATATCTTCATGACCTTGGAATTGGCAATGAATTCTTAGCTA 1573
                             ii?   v      i         iv v       iv       v  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_41614195_   1574 TGGCACCAAAAGCATAAGCAACAAAAGAGAAAATAGATAAATTGAACTTC 1623
                           i           i             i               i     
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_41614195_   1624 AT 1625
                           
  L1M4_orf2#LINE/    646 AT 647

Transitions / transversions = 1.61 (29 / 18)
Gap_init rate = 0.00 (0 / 302), avg. gap size = 0.00 (0 / 0)  

1178 16.18 8.09 0.74  chr20_41614195_41616861     1904  2175 (492)    L1M4_orf2#LINE/L1      617   908 (0)  

  chr20_41614195_   1904 CAAAAAAAAAAA-----AAATTGAATTTCATAAAAATTTAAAGACTTTTG 1948
                              i      -----      i i     v      -   i       
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT-AAAAACTTTTG 665

  chr20_41614195_   1949 TGCATCAAAGGACATTATCAAAAAAGTGAAAAG-CA-CCTACAGGATGGA 1996
                            v          i      i           -  -  i    i    i
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

  chr20_41614195_   1997 AGAAAACATTTGCAAAT------TTT-ACAAGGGTTTAACATGTGGAATA 2039
                               i          ------ i - i     vi vii  vii     
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

  chr20_41614195_   2040 TATAAAGAACTCCTAAAACTAAGCAACAAAAAG--------CCCAGTTAA 2081
                                     i  v    v ii  i      --------    i  ? 
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWA 815

  chr20_41614195_   2082 AAGATGGGCAAACAACTTAAATAGATATTTCTCCAAAAAAATACATACAA 2131
                           i         vi i  i      i           i  i- i      
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG-ATATACAA 864

  chr20_41614195_   2132 ATGGCCAGTGAGCCCATGAAGAGTTGCTCAACATCATTAGACAT 2175
                                i i   v      i  v            ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 3.30 (33 / 10)
Gap_init rate = 0.03 (8 / 292), avg. gap size = 3.00 (24 / 8)  


3236 18.11 1.35 1.80  chr20_41865379_41870022.rev     2938  3605 (1039)    L1M4_orf2#LINE/L1        1   665 (243)  

  chr20_41865379_   2938 TGGGAAAACGTCC-ACGTTTATGGATTGCAAGATTTAAT-TTGCTAAGAT 2985
                            i  i ii   - i   i        v    i     -   i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_41865379_   2986 GGCAAAATTCTTTGA-TTGCTCTACAGATTCAAAGCAATCTCAATCTAA- 3033
                              v i  iiii -   v             v      i v   v  -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_41865379_   3034 TCCGAGCAGACTTTTCTGCAAAAAGTGTCAAACTGATCCTAAGATTAACA 3083
                            v   v v     i    i   v  v   i          i   v i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_41865379_   3084 TATAAATACAAGAGACCTTTAATAAGCAGAGTAACCTTGAAAAAGAAGAA 3133
                          iv    i    i    ivv    iv  i ii  i               
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_41865379_   3134 CACAGTACGAAGACTGAAACGTCCCAATTTTAAAACATATTACAAAGCTA 3183
                           v   vv  i    v v  v         i     v  i          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_41865379_   3184 CAGTAATCAAAACAGTGTGAGACTTTCATAAAGATAGACATATAGACCAA 3233
                                   i        iv   vv     i              i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_41865379_   3234 AAGAATAGAATTGAGAGATCAGAAATAAACCCTTACATTTATGATCAATT 3283
                         vi               vi             v          i      
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_41865379_   3284 AATTTTTGACAAAAGTGTCAAAACAATTTCAGAGGGGGTAAAATTGTCTT 3333
                         i     i     ii   i   i  v   -  iv    iv i   v     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATT-CAATGGGGAAAGAATAGTCTT 399

  chr20_41865379_   3334 TTTAACAAATGGTGCTAGGATAATTAGCCAAAAAAATTTCTTTACA---A 3380
                           i             i   i  i i --------  v? i--   --- 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGG--------ATAKCC--ACATGCA 439

  chr20_41865379_   3381 AAAGAATTAA-TCGAACCCCTACCTCACTCTATATATAAAAATTAACTCA 3429
                                v  - i i             v i     i             
  L1M4_orf2#LINE/    440 AAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCA 489

  chr20_41865379_   3430 CAGTGGATGCAAGATCTAAATGCAAGAGCTAAAATTATAAAATTCTTAGA 3479
                         v i     vv?   i       i           i       i       
  L1M4_orf2#LINE/    490 AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_41865379_   3480 AGAAAGT-TAGGTAGAAATCTTTGTGACCTAGGATTAGACAAGAATCTCT 3528
                              ii-    ?iv       i       v  i    i   vii i   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCT 589

  chr20_41865379_   3529 TAGATATGACACCAAAAGCACTAGCAACAAAAGAAAAAAATAGATAAATT 3578
                                              v                 -          
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATT 638

  chr20_41865379_   3579 AGACTTCATCAAAATTTAGGACTTTTG 3605
                         i               v ii       
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.68 (74 / 44)
Gap_init rate = 0.02 (11 / 665), avg. gap size = 1.91 (21 / 11)  

1141 16.98 7.92 0.00  chr20_41865379_41870022.rev     3888  4152 (492)    L1M4_orf2#LINE/L1      623   908 (0)  

  chr20_41865379_   3888 AAAAAATA-ATAA--------TAATAATAATTAGGA-CTTTTGTGCTCCA 3927
                                 -    -------- v  v v     ii -          i  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_41865379_   3928 AAGAATACTATCAAGAAAGTGAAAAGACAACTCACAGAATGAGAGAAAGT 3977
                            i i                         i         i      i 
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_41865379_   3978 ATTTGCAAATCATGTATCTTATAAGGGAAGAGTATTTGGAATATATCAAA 4027
                                      i     v        vvv    iii        v  i
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_41865379_   4028 TATGTTTAAAACTCAACAATAATAAGACACATAATCCAATTTTATAATGA 4077
                         v ivi   v       i     v      v    i      ?v v    i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_41865379_   4078 GTGAAAGGCTT----AGACAT----CCAAAGA---TATACAAGTGGCCAA 4116
                          ii  i ii  ----      ----       ---       i       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_41865379_   4117 GAAACACATGAGAAAATGCTCAATATCATTCGTTAT 4152
                         v  i       i  i        i    ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (28 / 16)
Gap_init rate = 0.02 (6 / 286), avg. gap size = 3.50 (21 / 6)  


3182 27.14 0.33 0.55  chr20_41880000_41882296      896  1805 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_41880000_    896 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 945
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_41880000_    946 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 995
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_41880000_    996 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1043
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_41880000_   1044 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTGAGCCAAAAG 1093
                                viiv  ii  v  viv  v     iv     i   ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_41880000_   1094 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 1143
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_41880000_   1144 TACAGTAACCAAAACAGCATGGTACTGGTACCACAACAGAGATATAGATC 1193
                                 i   i    ii         i iv vi i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_41880000_   1194 AATGGAACAGAACAGAGCCCCCAGAAATAACGCCGCATACCTACAACTAT 1243
                                i    iv   vvi          vv  ii i ii  iiiii v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_41880000_   1244 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCT 1293
                         i    i  i     ivv  vv  i v  vv            i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_41880000_   1294 ATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 1343
                         v  i  i              v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_41880000_   1344 AACTGGATCCCTTCCTTACACCTTATACAAAAAACAATTCAAGATGGATT 1393
                          ii    i    v   i     v          vi  i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_41880000_   1394 AAAGATGTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 1443
                          ?   iv    i  v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_41880000_   1444 AGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAA 1493
                            ?i v viv   iv   v v  vv i     v ii   v ivvi vi 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_41880000_   1494 CACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATT 1543
                                    vvi          vv     v  i    v   ii v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_41880000_   1544 AAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAG 1593
                            v v  i i   i  ii vv    i  v    i  vv i      v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_41880000_   1594 GCAACCTACAACATGGGAGAAAATTTTCACAACCTACTCATCTGACAAAG 1643
                         i     i   iv            v  ii   vii ivi      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_41880000_   1644 GGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAA-AAA 1692
                          i  vi          v  i  v      vv    v ---   v  -   
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACT---CAATAATAAA 795

  chr20_41880000_   1693 AAAAAAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 1742
                           i v   i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_41880000_   1743 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 1792
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_41880000_   1793 CATCACTGGTCAT 1805
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (141 / 102)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


3089 27.06 1.67 0.56  chr20_41933453_41939824.rev     4983  5880 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_41933453_   4983 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATAACGTGAAAAT 5032
                              ii i  i     i        v      v i    vi  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_41933453_   5033 GGCCATACTGCCCAAGGTAAATTATAGATTCAATGCCATCCCCATCAAGC 5082
                            v     v     iv i vi  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_41933453_   5083 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5130
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_41933453_   5131 TATGGAAGCAAAAAAGAGCCCACATTGCCAAGTCAATCCTAAGCCAAAAG 5180
                                iiiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_41933453_   5181 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5230
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_41933453_   5231 TA-----ACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5275
                           ----- i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_41933453_   5276 AATGGA-CGGAAC--AGAGCCCTCAGAAATAATACCACACATCTACAACC 5322
                               -ii   i--    i  --        vv   i    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_41933453_   5323 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5372
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_41933453_   5373 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5422
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_41933453_   5423 GAAACTGGATCCCTTCCTTACACCTTGTACAAAAATTAATTCAAGATGGA 5472
                            ii    i    v   i     v i            i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_41933453_   5473 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGGAAAC 5522
                          i ?    i       v   v       i      vi i      i    
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_41933453_   5523 ATAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5571
                              ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_41933453_   5572 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5621
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_41933453_   5622 ATTAAGCTGAAGAGCTTCTGCACAGCAAAAGAAATGACCATCAGAGTGAA 5671
                           i  iv v  i i   i  ii vv    i  v iv i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_41933453_   5672 CAGGCAACCTACAGAATGGAAGAAAATTTTCACAATCTACCCATCTGACA 5721
                         v  i     i         i       v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_41933453_   5722 AAGGGCTAATATCCAGAATCTACAAAGAACCTAAACAAATTTACAAGAAA 5771
                          i  i  vi          v  i       iivv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_41933453_   5772 AAAACAA----CCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTT 5817
                           i    ----   v  i?    i     i      v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_41933453_   5818 CTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTCAT 5867
                            v        i  vi viii     i ii          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_41933453_   5868 CATCACTGGTCAT 5880
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (147 / 92)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 2.00 (20 / 10)  


2961 26.40 2.36 0.34  chr20_42120870_42125944     3694  4583 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_42120870_   3694 TGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATAGTGTGAAAAT 3743
                               v i        i        v  v   v i    v   v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_42120870_   3744 GACCATACTGCCAAAAGCAATCTATAAATTAAATGCAATTCCCATCAAAA 3793
                          i v     v  v   vii     i i   v  i     i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_42120870_   3794 CACCACCAACATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCATG 3843
                         iv   v vi v  i  ii     v v  v  ivii              i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_42120870_   3844 TGGAATCAAAAAAGAGCCCTCATAGCCAAAGCATGACTAAGCAAAAAGAA 3893
                              viiv  ii  v  vvv         i  vvvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_42120870_   3894 CAAATCTGGAGGCATCACATTACCCGACTTCAAA-----CTATATGGCCA 3938
                             vi      vv     i v   i i      -----   i vi  i 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_42120870_   3939 TAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCATATAGACCA- 3987
                         i   v i   i    ii         i    ii    i        i  -
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_42120870_   3988 TGGAAAAGATTAGAGAACCCAGATATAAAGCCAAATCCTTACAACCAACT 4037
                              v   v v    ii     v     v   v ivi   iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_42120870_   4038 GATCTTTAACAAAGCAAACAATAACATGAAGTGGGGAAAGGACACCTTAT 4087
                            i  ii    i vviv   v v   vv i         i i vii v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_42120870_   4088 TCAACAAATGGTGCTTGGATAATTGGCAAGCCACATGTAGAAGAGTGAAA 4137
                                        v   i  i   vv ?       i i    i    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_42120870_   4138 CTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAAATGGATGGA 4187
                         i    i  ii i   v    v           i              vi?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_42120870_   4188 AGACTTAAATCTAAGACCTGAAACCCTAAAAATTCTAGAAGATAACACTG 4237
                             i     v     v  i    iv     v ii       v    iv 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_42120870_   4238 GAAAAACCCTTCCACAGACATTGGCTTAGGCAAAGACTTCATGACCAAGA 4287
                          ?iv  vi    --vv   v    v        v ii   v iivi v  
  L1M4_orf2#LINE/    551 GNGTAAATCTTC--GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_42120870_   4288 ACCCAAAAGCAAATGCAACAAAAACAAAGGTAAATAGATGGGACTTAATT 4337
                         vv         v v         iv   ii  i   i  v      v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_42120870_   4338 AAACTAAAAAGCT---GCACAGCAAAAGA-ACCAGCAGG---GTAAACAG 4380
                            v v    i  --- ii vv    i  -  i v  i ---  i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_42120870_   4381 ACAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACTTTCGACAAAG 4430
                                     i           v  ii   vii   iv ii  i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_42120870_   4431 GACTAATATCCAGAATCTACAAAGGAACTC----AAATCAGCAAGAAAAA 4476
                             vi          v  i    -     ----  v   ii  v     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAG-AACTCTTACAACTCAATAATAAAAA 797

  chr20_42120870_   4477 AACAA----TCCCATCAAAAATTGGGCTAAGGAGATGAATAGAGAATTCT 4522
                         i    ----i  v  i?    v     v     vv        v v    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_42120870_   4523 CAAAAGAAAATATACAAATGGCCAACAAACATATTAAAAAATACTTAACA 4572
                          v      i                i  i  i  v    i  i  i    
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_42120870_   4573 TCATTATGATC 4583
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.26 (129 / 102)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.67 (24 / 9)  


2191 23.80 6.22 0.00  chr20_42937112_42942470     3221  3783 (1576)    L1M4_orf2#LINE/L1        1   598 (310)  

  chr20_42937112_   3221 TGGATAGATATTCCATGTTCATGGAT-AAAAGACTCAATACTGTTAATAT 3269
                             v      i              -ii      i    i      v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_42937112_   3270 ATCAGTTCTTCCCTATTTAATCTATAGATTCAACACGATCCCAATAAAAA 3319
                         iv  i v  i   v v  i     i         i i     v  v    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_42937112_   3320 TCCCAATGAGTAATTTTGTGGATGTCGACACATTTATTCTAAAATGTATA 3369
                              iivivivv     ii  vi i    vii v  i       vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_42937112_   3370 CAGAAATGCAAAAGAACCAGAACAACCAACAAAATGCTGAG---GAAGAA 3416
                         ii         ii  v      i i    v v   vi   i---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_42937112_   3417 CAAAGTTGGAGGACTGACACTACCTCACTTCAAGACTTACAACAAAACTA 3466
                                        v     v  iv i     i      v     i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_42937112_   3467 TAGTAATCAAGGCAGTGTGGTCTTGGCAAAAGAACAGACAAATAAATCAA 3516
                         i          i         vi     v   i i     v   i     
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_42937112_   3517 TGGAACAGAATAGAGAATTTAGAAATAGACCCACACAA--ATAGTGAACT 3564
                              i     v    i ii       i     i   v--  i  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_42937112_   3565 GATCTTTAAAAAGAA-GCAAAAGCAATGCAATGGAGAAAGGATAGCCTTT 3613
                            i  ii v   ii-  v  ii v  v      i     i    i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_42937112_   3614 TCAACAAATGGTGGTGGAACAACAGGACGTCCGCACACACAAAAATGAAT 3663
                                      v   i     v   ii?  i  ii  v  i      v
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_42937112_   3664 GTAGA----TAC-TGATAACTTTCACAAAATTTAACTCAAAA-------- 3700
                         v i  ----   - v i v v vi      v           --------
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_42937112_   3701 AGGC---------------AAAACTACAAAACTTCTAAATGATAACATAG 3735
                           i ---------------       i      ii  i v  v       
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_42937112_   3736 AAGAAAATTTAGGGGACCTTGGGTTTGGCAATGAATGTTTAGATATGA 3783
                         i? v    i vv v           v       iv vi          
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

Transitions / transversions = 1.49 (79 / 53)
Gap_init rate = 0.01 (8 / 598), avg. gap size = 4.38 (35 / 8)  

1080 21.71 5.59 0.99  chr20_42937112_42942470     4566  4869 (490)    L1M4_orf2#LINE/L1      591   908 (0)  

  chr20_42937112_   4566 AGGTATAACATAAAAAACATGATCCATGAAAGAAAAATTGG-TAAGTTAG 4614
                           i   i   iv    i  ii v v ii         v i -   i  i 
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_42937112_   4615 ACTTCATCAAAATTA---------GTGC----AAAGTCACTGTCGAGAGG 4651
                                        ---------    ----  i v    i  i   ii
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_42937112_   4652 AT-AAAAGACAAGCTACAGACAAGAAGAAAAAATCTTTGCAAAGCACATA 4700
                         i -         v i     -- vii  i     v        v  i   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGA--ATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_42937112_   4701 TCACCTAAAGGACGAGTATGCAAAATATACAAAGAATTCTTAAAATTCAG 4750
                           vvv   i    vv    v  i      i      i     v  i   i
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_42937112_   4751 TGATAAAAAAGCAAATAATCCAATT--AAAATGAGTGAAAAAATCTGAAC 4798
                          i       ii       i      --      i i-   ii  i    i
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGC-AAAGGATTTGAAT 837

  chr20_42937112_   4799 ATACACCTAACCAAGGAAAATATACAGGTGGCAAATAAGCACATGAAAAG 4848
                          v   ii vv    i   i       ii    v                 
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_42937112_   4849 ATGCTCAACATTGTATGTCAT 4869
                                    ii????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.30 (46 / 20)
Gap_init rate = 0.02 (7 / 318), avg. gap size = 2.86 (20 / 7)  


1510 27.14 1.50 2.56  chr20_43124897_43128507.rev     1875  2342 (1269)    L1M4_orf2#LINE/L1        1   463 (445)  

  chr20_43124897_   1875 TGAAAAAACATTCCATGTTCATAGATGGGAAGAATCA---TTGTTAACAT 1921
                           i   i i  i          i   v      v i ---       v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_43124897_   1922 GGCTATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAT 1971
                            v     v      vii  i           i  v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_43124897_   1972 TACTAATGACATTCTTCACAGAATTAGAAAAAAACAG-TTTAAAAATTCA 2020
                          v i iivi v  i  ii     v v  v  i-- v - iiv        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCA 148

  chr20_43124897_   2021 TACAGAATTTTTTAAAAG-CCCAAAACA-CCAAGGCAATGCTAAGCAAAA 2068
                           ii   v vi--  ii -    i  i -    ii    vi i --    
  L1M4_orf2#LINE/    149 TATGGAAATGC--AAGGGACCCAGAATAGCCAAAACAATCTTGA--AAAA 194

  chr20_43124897_   2069 AAAAAACAAAGCTGCAGGTTTGAAGTTGGTTTAACCAAATTCAAACTAGG 2118
                         i  i       i  v   vi v vii --- i--    v      vivvi
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACT---TC--CCAATTTCAAAACTTA 239

  chr20_43124897_   2119 CTACAAGGCTACAGTAACCAAACCAGCATGGCACTGGTACAAAAACAGAC 2168
                               i          i   iv   ii   i     i i  ii i    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr20_43124897_   2169 ATACAGATCAGTGGGACAGAACAGAAAGCCTAGAAATAAGGCTGTATACC 2218
                            i      i   i i    iv  i  i i        iv ii  i ii
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT 339

  chr20_43124897_   2219 TACAACCAAGTGATCGTCGACAAAGCTGACAAAAACAAGCAATGGGGAAA 2268
                           iiii   v    iv       i v  v   i v  vv           
  L1M4_orf2#LINE/    340 TATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAA 389

  chr20_43124897_   2269 GGAATC-CCTATTCAATAAATGGTCCTGGGATAATTGGCTAGCCATATGC 2317
                          -   v-i  v     i       v      i  i   v  ?   i    
  L1M4_orf2#LINE/    390 G-AATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr20_43124897_   2318 AGAAGATTAAAACTGGACCCCCCCC 2342
                          i    v i  ii        iv  
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACC 463

Transitions / transversions = 1.93 (83 / 43)
Gap_init rate = 0.02 (11 / 463), avg. gap size = 1.73 (19 / 11)  

1400 26.65 1.10 1.32  chr20_43124897_43128507.rev     2666  3119 (492)    L1M4_orf2#LINE/L1      456   908 (0)  

  chr20_43124897_   2666 CCCCTTCCTTATATCATACACAAAAATCAAGTTGAGATAAATTAAAGACT 2715
                              v   i i i    i        i  v ii i  ii  i ?    i
  L1M4_orf2#LINE/    456 CCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACC 505

  chr20_43124897_   2716 TAAAAGTAAAATCTAAAACTATAAAAACCATGGAAGATAACCTAGG---A 2762
                             v    i v              vi v i     v   v    --- 
  L1M4_orf2#LINE/    506 TAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTA 555

  chr20_43124897_   2763 AATACCACTCTG-GACATAGGACCTGGCAAAGATTTCATGACGAAGACAC 2811
                            ----  ii -   v v  iiiv     v i    v iivv v     
  L1M4_orf2#LINE/    556 AAT----CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_43124897_   2812 CAAAAGCAACTGCAACAAAAACAAAAATCAACAAATGAAACCAAATTAAA 2861
                                 vvv         iv      vi i    vii  ivv  i   
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_43124897_   2862 CTAAAGAGCTTCTGCACAGCAAGAGGTAAACTATCAAGGGAGTAAACAGA 2911
                         v v  i i   i  ii vv   -   - v         ii   i  v   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGTGCTTCAA-AGG-ACACTATCAAGAAAGTGAAAAGA 699

  chr20_43124897_   2912 CAACTTACAGAATGGGAGGAAATATTTGCAAACTATGCATCCAACAAAGA 2961
                             ii            i             ii  ii   ii i  i i
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_43124897_   2962 TCTAATATCCAGAATCCACAAGGAACTTAAACGAATTTATAAGCAAAAAA 3011
                         v  vi          vi i  i     ivv  i v iv    vv    i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_43124897_   3012 CAAACCTTCCTGTTAAAAAGTGGGCAGAGGACATGAACAGACACTTTTCA 3061
                             ivvi  vi  ?    i      i    iv    i     i  i  v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr20_43124897_   3062 AAAGAAAATGTACATGTGGCCAACAAGCATATTCAAAG-TGCTCAACATC 3110
                               i  i    vi       i     i  vv    -           
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr20_43124897_   3111 ATTAATCAT 3119
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.53 (72 / 47)
Gap_init rate = 0.01 (6 / 453), avg. gap size = 1.83 (11 / 6)  


3093 25.61 2.21 2.87  chr20_43194415_43196340.rev      529  1434 (492)    L1M4_orf2#LINE/L1        9   908 (0)  

  chr20_43194415_    529 TATTTTATGTTTATGGATTA-AAGAATTTATATTGTTAAAATGTCCATAC 577
                            iii     i       i-    v  v          i   v v    
  L1M4_orf2#LINE/      9 TATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATAC 58

  chr20_43194415_    578 TACTCAAAGCAATCTACAGATTCAATGAAATGCCTATCAAAATTCCAAG- 626
                          v i    vii              i v   v           i   iv-
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCT 108

  chr20_43194415_    627 GATATTTTCATAGAACTAGAAATAAAAGGCCCTAAAATTTACAGGGAACC 676
                          viv    iii    v v  v - ivv ii         i i v    vi
  L1M4_orf2#LINE/    109 GCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCATATGGAAAT 157

  chr20_43194415_    677 ACAAAAGACCTTTCGTTAAAGACT-GCTTTAACAAAGCAATCTTGAGCAA 725
                         i   ii    i--------   v -  -----    i         iv  
  L1M4_orf2#LINE/    158 GCAAGGGACCC--------AGAATAGC-----CAAAACAATCTTGAAAAA 194

  chr20_43194415_    726 AAGTGACAATTTTTTTTGTCAGGAGGCATCACACTACCTGATTTCAAAAT 775
                         i ivi    vv  --------     vv       v  ii         i
  L1M4_orf2#LINE/    195 GAAGAACAAAGTT--------GGAGGACTCACACTTCCCAATTTCAAAAC 236

  chr20_43194415_    776 ACACTACAAAGCCATAGTAATCAAAATAAGATGGTACTGGCATAAAAATA 825
                         vi          i i         i i ivi              ii   
  L1M4_orf2#LINE/    237 TTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA 286

  chr20_43194415_    826 GACACATAGGCCAATAGAACAAACAAAATAGACATCCCAGAAATAAATCC 875
                             i    ii    i   i i ----  v  v vi           i  
  L1M4_orf2#LINE/    287 GACATATAGATCAATGGAATAGA----ATTGAGAGTCCAGAAATAAACCC 332

  chr20_43194415_    876 ATGCATTTACAGTCAACTGAGTTTTGACAAAGATGCCAAAAATACACAAT 925
                           i      ii     i   v   i     i i      i vi iv    
  L1M4_orf2#LINE/    333 ATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAAT 382

  chr20_43194415_    926 GGGGAAGAGACAGTCTCTTCAGTAA-TAATGTTGGCAAAGCTGGATATCC 974
                               iii i     i    ii  - ii  i   v v i       ?  
  L1M4_orf2#LINE/    383 GGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCC 432

  chr20_43194415_    975 ATATGCAGAAGACTAAAATTGGACCCTTATCACACACCACATGTAAAAAT 1024
                          i     i    v i  i        i  i v       i  ii      
  L1M4_orf2#LINE/    433 ACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAAT 482

  chr20_43194415_   1025 CAAC--AAAGTGGGTTAAAGACTTAAA-----GACTTGAAACTGTAAAGC 1067
                         i   --   i   i i ?    i    -----  vi i     i    i 
  L1M4_orf2#LINE/    483 TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAAC 532

  chr20_43194415_   1068 TACTAGAAAAAAATATAGTGGGAAAGGTCCACAGCATTGGTCTGGGCAAT 1117
                          vi     i    i    v? v   vv i iiii v    vi i      
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr20_43194415_   1118 TATATTTTGGATATGGCCCCAAAAATATAGGCAATAAGAGCAAAAATAGA 1167
                         vi v i  i      i v      ii i i    i  i  v         
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr20_43194415_   1168 CAAATGAAATTACATCAAACTAACAAGCTTCTGCACAAAAAAGGAAAC-- 1215
                         i    vii i v       v v v  i   i  ii vvv      v  --
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr20_43194415_   1216 --AACAGATTGAAGAGACAACTTATGAAGTGGGAGAAATTATTTGCAAAC 1263
                         --  v i v    i       ii iii i         v          i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr20_43194415_   1264 CATGCATCTGATAGGGGATTAATATCTAAAATATATAAGAAACTCAGACA 1313
                            ii        i    i vi    i i         ii     vv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr20_43194415_   1314 ACTCAATAG--AAAAAATA--TAACCCAATTAAGGAGTGAATAAAGAATC 1359
                                 i--    i i --          ? ii i  iii    i  i
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_43194415_   1360 TGAATAGATATTT-TCAATAGAATACATACAAATAACCCATAAGTATATT 1408
                                 i    -  v v    v i        ii  v     i i  v
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_43194415_   1409 TGAAAACGATCAACATCACTGATCAT 1434
                         vi  i i v         ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.17 (156 / 72)
Gap_init rate = 0.02 (15 / 900), avg. gap size = 3.07 (46 / 15)  


3009 24.82 1.65 1.65  chr20_43275709_43277932      501  1350 (874)    L1M4_orf2#LINE/L1       14   863 (45)  

  chr20_43275709_    501 CATGCTCATGGATGAGTAGAATCAATATTGTGAGAATGACCATACTGCCA 550
                             i        vi v   v i        v ii   i v     v  v
  L1M4_orf2#LINE/     14 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 63

  chr20_43275709_    551 AAAGCAATCTACAAATTCAAGGCAATCCGCATCAAAATACCACCATCATT 600
                            vii       i      v       vi        v   v vv v  
  L1M4_orf2#LINE/     64 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT 113

  chr20_43275709_    601 CTTCACAGA--TTTAGGAAAAGC-AATTCTAAAATTCATATGGAAC--CA 645
                         i  ii    --  ---  v    -i  i                 v--  
  L1M4_orf2#LINE/    114 TTTTGCAGAAATT---GACAAGCTGATCCTAAAATTCATATGGAAATGCA 160

  chr20_43275709_    646 AAAAACAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAACAAATCTG 695
                          iii  --  viv         i   vvi i iv  i         vi  
  L1M4_orf2#LINE/    161 AGGGAC--CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTG 208

  chr20_43275709_    696 GAGGCATCACACTACCTGATTTCAAACTATACTATAAGGCCATAGTCACC 745
                             vv       v  ii        viv     i  i  i i   v i 
  L1M4_orf2#LINE/    209 GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATC 258

  chr20_43275709_    746 AAAATAGCGTGGCACTGGTATAAAAATAGGCACATAGACCAATGGAACAG 795
                           i i  i    i     i    ii    i  i     i        i  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr20_43275709_    796 AATAGAGAACCCAGAAATAAACCCAAATACTTATAGCCAAATGATCTTTG 845
                            v    ii               v i i    i i   v    i  i 
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr20_43275709_    846 GCAAAGCAAACAAAAACATAAAGTGGGGAAAAGGATTCCCTTTTCAACAA 895
                         i   i vviv   i v   vv i        - i  vvi           
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAA-GAATAGTCTTTTCAACAA 407

  chr20_43275709_    896 ATGGTGCTGGGATAATTGGCTACCCACATGTGGGAGAATGAAACTGGATC 945
                                     i  i   v  ?       iiii        ii    i 
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr20_43275709_    946 CTCATCTCACACTTTATACAAAAATCAACTCAAGATAGATTAAAGACTTA 995
                          ii i       iv           i       i  i   i ?    i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr20_43275709_    996 AAACTAATACCTGAAACTATAAAAATTCTAGAAGATAACATTGGAA-AAA 1044
                           vv   v v  i           v ii       v     v  ?i-   
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAA 557

  chr20_43275709_   1045 TCCTTCTAGACATTGGCTTAGGCAAGGATTTC------ATGAC-CAAAAG 1087
                           -   vv   v    v        v i    ------     - v   i
  L1M4_orf2#LINE/    558 TC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr20_43275709_   1088 GCAAAAAGCAATTGCAATTAAAACAAAGATAAATAGCTGGGACCTAATTA 1137
                            -----   --    iv   iv   i   i   iv v    i v  i 
  L1M4_orf2#LINE/    607 GCA-----CAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_43275709_   1138 AACTAAAGGGCTTTTGCACAGCAAAAGGAACAGTCAGTAGAGTAAATGGA 1187
                           v v  iii      ii vv    i iv  vi   iv i   i  vi  
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_43275709_   1188 CAACCCACAGAGTGGGAGAAAATCTTCACATTCTATACATCTGACAAAGG 1237
                                    i           v  ii  vvii   i      i  i  
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_43275709_   1238 ACTAATATCCAGAATTTACAACGAACTCAAACAAATCAGTAAGAAAAA-A 1286
                            vi          v  i  v      vv    v   i   v     - 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_43275709_   1287 CGATCAATCCCACCAAAAAGTGGGCTAAGGACATGAACAGACAATCCTTA 1336
                          i vi  i  v ii?    i     v     iv    i     v i  iv
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr20_43275709_   1337 AAAGAAGATATACA 1350
                                       
  L1M4_orf2#LINE/    850 AAAGAAGATATACA 863

Transitions / transversions = 1.46 (123 / 84)
Gap_init rate = 0.02 (13 / 850), avg. gap size = 2.15 (28 / 13)  

 355  6.90 0.00 0.00  chr20_43275709_43277932     1675  1732 (492)    L1M4_orf2#LINE/L1      851   908 (0)  

  chr20_43275709_   1675 AAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCA 1724
                                               i  i  i       i             
  L1M4_orf2#LINE/    851 AAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 900

  chr20_43275709_   1725 CTAATGAT 1732
                         ????????
  L1M4_orf2#LINE/    901 ZZZZZZZZ 908

Transitions / transversions = 1.00 (4 / 0)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.00 (0 / 0)  


3956 19.64 2.22 1.44  chr20_43304969_43307097.rev      737  1637 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_43304969_    737 TAGAAAGCTATACTGTGTTCATGGATTGGAAAACTCGATGTTGCCAAGCT 786
                          i     v   v ii                i   ii  i   ii   v 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_43304969_    787 GGTAATTCTTCACAAATTGATCTATAAATTCAATGCAATCCCTAG-AAAA 835
                           i   v  i v            i i      i          v-    
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_43304969_    836 CTTCAGGTGAATTTTT-GTTGAAATAGATCAGTGAATCCCAAAATTTGTA 884
                         iii   v  vv     - iv     v  iv  ivi    i      ii  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_43304969_    885 TACAAATGCAAGGGACCCAGAATAGCCAAAACAGTCTTAAAAAAAAAGGG 934
                          iv                              i    i     i   ii
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_43304969_    935 CAGAATTGGAGGACTCACATTTTTTTATTTCAACGTGTACTACAAATCTA 984
                           i i              i  iiiv       viiv         v   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_43304969_    985 CAATT-TCAAGATGTTGTGTTACTAGCATAAGGATAAACACAATATATCA 1033
                           i v-      iiv    v    i           i   i -  v    
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATA-TAGATCA 299

  chr20_43304969_   1034 AAGGAATAGAATTGAGAATCCATAAATAAGCCATTACATTT----TAAAT 1079
                          v               i    v      i  vv       ---- v   
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_43304969_   1080 TGTCTTATTTTCAACAAAGGTACAAAAACTATCCAGTGGGGATAGAGTAG 1129
                           ----      i    i   i v  i  i  i  i      v   i   
  L1M4_orf2#LINE/    350 TG----ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_43304969_   1130 TCTTTTCAACAAATAATGG-GGAAAAACTGGATATGCACCTGCAAAAAAA 1178
                                       ii  v-  i v         ?v   v       i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_43304969_   1179 TATACATGGACTGTTACATCATATCAAGTACAAAAATGGGCTCCAAATAA 1228
                          iv vv     ivi   v   i i  vi         vii   v    ii
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_43304969_   1229 AACA-AGACCTAAATATATGAACTAAAATTACAAAACTCTTTGAGGAAAA 1277
                          v  -          i  v  i      i  i         v  i     
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_43304969_   1278 CATAAATGTATATCTTCATGATCT--GGTAATCAGCATCAATTTCTTAGA 1325
                             ii?   v      i   i  --   -- vi   viii         
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGT--TAGGCAATGGTTTCTTAGA 593

  chr20_43304969_   1326 TATGCTACCAAAAGCACAAGCAACAAAAGGAATAATAGATCCAAAAATAG 1375
                             vi                       i  v       ---   v i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGAT---AAATTGG 640

  chr20_43304969_   1376 ATT-----AAAGTTAAAAACTTTGGTGAGTCAAAGGGCACTAATAAGAAA 1420
                          i -----   i           v   vv       i     vi      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_43304969_   1421 -TGAAAAGATAACCCACAGACATGGGAGAAAATATTTGCAAATTTTATAT 1469
                         -        i          -                      iv     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGA-ATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_43304969_   1470 CTGATAAGGGCCTAGTATTCAAAATACAAAAAGAACTCCTAAAA-TCAAC 1518
                                   v  v    i  i    i v         i  v  -    i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_43304969_   1519 CATAAAA-GACAAA-AACCATGATTAAAAACTGGGCATCAGATTTTAACA 1566
                         v      -      -    -ii   ?    v      vvi     v  i 
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACC-CAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr20_43304969_   1567 GACATTTCTCCAAAAGAAAATGTACAAATGGCCAATAAGCATGTAAAATG 1616
                                       -   i  i                   ii i   v 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_43304969_   1617 ATGGGTGATATCATTAGACCT 1637
                            vvii i    ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.60 (107 / 67)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 1.74 (33 / 19)  


3170 25.95 1.67 0.56  chr20_43534497_43541168.rev     5283  6180 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_43534497_   5283 TGGAAAAACAATCCATGCTCATGGATAAGAAGAATCAATATCGTGAAAAT 5332
                               i i vi     i        vi     v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_43534497_   5333 GGCTATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGC 5382
                            v     v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_43534497_   5383 TATCA-CTGACTTTCTTCACAGAATTAGAAAAAACGACTTTAAATTTCAT 5431
                          vi  -   v    i  -i     v v  v  ivi  iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_43534497_   5432 ATGGAACCAAATAAAAG-CCCACA-TAGCCAAGACAATCCTAAGCAAAAA 5479
                               -- vii  ii -    v -       i      i i iv  i  
  L1M4_orf2#LINE/    150 ATGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_43534497_   5480 GAACAAAGCTGGAAGCATCACGCTAACTGACTTCAAGCTATACTACAAGG 5529
                                 i    i vv    i  vv ii i     iviv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_43534497_   5530 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGAC 5579
                                  i   i    ii         i iv ii i   i       i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_43534497_   5580 CAACAGAACAGAACAGAGGCCTCAGAAATAACACTACACATCTACAGCCA 5629
                            ii   i    iv   ivii         vv i i    i  ii i  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_43534497_   5630 CCTGATCTTTGACAAACATGGCAAAAACAAGCAATGGGGAAAGGATTCCC 5679
                         vi    i  i     ivi  v   i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_43534497_   5680 TATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATGCAGAAAACTG 5729
                          v  i  i        i     v      v  ?   i     i  i v  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_43534497_   5730 AAACTGGACCCCTTTCCTTACACCTTATGCAAAAATTAACTCAAGATGGA 5779
                           ii         v-   i     v   i               i     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTA-CCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_43534497_   5780 TTAAAGACTTAAATGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5829
                          i ?    i           v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_43534497_   5830 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTA 5878
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_43534497_   5879 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCCA 5928
                         vi            vvi          vv     v  i    v   iiiv
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_43534497_   5929 ATTAAACTACAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGAA 5978
                           i   v vv i i   i  ii vv    i  v       vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_43534497_   5979 CAGGCAGCCTACAGAATGGGAGAAAATTTTTGCACTCTATCCATCTGACA 6028
                         v  i  i  i                 v      vvii  vi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_43534497_   6029 AAGGGCTAATATACAGAATCTACAA-GAACTCAAACAAATTTACGAGAAA 6077
                          i  i  vi   v      v  i  -      vv    v iv ii v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_43534497_   6078 AA-------AACCCCATTAGAACGTGGGCGAAGGATATGAACAGATGCTT 6120
                           -------     v   ?i  vi     i      v    i   iii  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_43534497_   6121 CTCAAAAGAAGACATTTATGCAGCCAACAA--ACATGAAAA-ATGCTCAT 6167
                            v        i  vi viii     i  --         -       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_43534497_   6168 CATCACTGGTCAT 6180
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (137 / 92)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 1.67 (20 / 12)  


2554 23.02 12.55 1.95  chr20_43664404_43668740.rev     3025  3845 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_43664404_   3025 TGGAAAGATATCTTGTGTTCAAGGATTGGTAGACTTAATATTGTTAAAAA 3074
                                     iii      v       v                 i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr20_43664404_   3075 TATTTACACTACCCGAAATAATGTACGAACTTAATGCAAACCCTATCAAA 3124
                          iviv i   v   i  v i  v   ii i i  i    v          
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_43664404_   3125 ATCCAAATGGCATTTATTGTAGAAATAGGAAAAA-AATTCTAAAGTTCAT 3173
                             v iiv  v   v   i      v iv  iv-i  i     i     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_43664404_   3174 GTGAAATCTTAAAAGACTCCAAATAGCCAAAACAATCTTGAGAAAGAAGA 3223
                         i  i  vivi  ii   i vi                    i        
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_43664404_   3224 ATAAAGCTAGAGGCATCACACTTCTTGATTTCAAAACATATTTCCAAAGT 3273
                          i    i i    vv         iii          v  i -v     i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT-ACAAAGC 248

  chr20_43664404_   3274 CACAGTAATCAAAACAGTATAACACTGACATAAAAACAGATACGTAGACT 3323
                         i           i     i iii    i     ii i   i ii    ii
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_43664404_   3324 GATAGAACAGAATATAGAGTCCAGAAATAAGCCCTCATATACAAGGTCTA 3373
                         i  i   i     vv               i   vi i  vi v    v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_43664404_   3374 ATGATCTTTAATAAGAGTTTCAAAACTGTACATTGGGGAAAGGGTAGTTT 3423
                         v    i  ii i   i  vi   i  ii v  v         ii    i 
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_43664404_   3424 CTTCAATAAATGTTGTTAG----------TA------------------- 3444
                         i     i     v  i i ----------  -------------------
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_43664404_   3445 ---TGGACCCTTAT-----ACCATACACAAAAATTAACTCAAAAAGAAGT 3486
                         ---       i  i-----      i                  v i - 
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA-T 497

  chr20_43664404_   3487 TA---ATTT---TTTATAAAC---ATCTATAAAACTCCCAGAAGAAAGCA 3527
                         i --- ii --- v  vi i --- v           ii        i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_43664404_   3528 ATTAAA---AAATC---ATGACATTGAAAAGGGAAATGGCTTTTTAGATA 3571
                         --  ii---     ---i    v   iivvi  v     i  i       
  L1M4_orf2#LINE/    548 --TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_43664404_   3572 TGATACCAAA-GCACAGGCAACAAAAGCAGAAATAGAGAAATAGGGTGAC 3620
                            i      -     i          v i       v    v  iivv 
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_43664404_   3621 GTCAAACTAAAAAACTT----------------------------ATGAA 3642
                         i     v v        ----------------------------i    
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_43664404_   3643 A---------------TTGGAGAAAATATTTGCAAGAGAGATATTAGATA 3677
                          --------------- v                 ivv v    iv    
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_43664404_   3678 AGAGGTTAATATCTAGAATATATTTTAAA--ACTCCTTTAACTCAATAAC 3725
                           i ii vi    i         ---   --    i vi          i
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATAT---AAAGAACTCTTACAACTCAATAAT 792

  chr20_43664404_   3726 AGCCCCCTGAATAATAAATAATCAAATTTTAAAAATGAGCAAAGGATT-A 3774
                          i-------  vi i      i v    ?-       i          -i
  L1M4_orf2#LINE/    793 AA-------AAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTTG 834

  chr20_43664404_   3775 AACAGACATTTCTCCAAAGAAGATACACAAATGGCCATT---TATTTGGA 3821
                           i                      i           v ---i iv  i 
  L1M4_orf2#LINE/    835 AATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAA 884

  chr20_43664404_   3822 AAAATGCTTAAAATTATTAATCAT 3845
                           i     i  v  i ????????
  L1M4_orf2#LINE/    885 AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.13 (128 / 60)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 5.41 (119 / 22)  


2693 23.39 9.43 1.67  chr20_43699639_43702992.rev     2025  2862 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr20_43699639_   2025 AGACATTCTGTTTTCACAGATTGGAAGAATTAATAATATTGTTAAAATGT 2074
                            i  i ii v    ii          v      ---       i   v
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATA---TTGTTAAGATGG 52

  chr20_43699639_   2075 CCATACTACCCAAAGTGTTCTACAGATGCAATGCAATCA-TATCAAAATT 2123
                          v     v      v  v         v   i      v-         i
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_43699639_   2124 CCAATGACATTTTTCACAGAAATAGAAAAA--AACCTTAAAATTTATATG 2171
                            iivi v     ii       v  v  i--i i i       i     
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATG 152

  chr20_43699639_   2172 GAA-TCCCAAAGACCCCAAATTGCTAGAACTATCTTGGGCAAAAACAAGA 2220
                            - v v ii     vi   v  i i   v      iiv  i  v  v 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_43699639_   2221 AAGCTGAACATATCACACTACCTGGTTTTAAAGTATATTACAAAGTTATA 2270
                            i  i vivv       v  iii   i   iiv  i       i  i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_43699639_   2271 AAAATCAAAACAGTATAATGCTGGCATTTAAAG-CAGAAACATAGATCAA 2319
                         iv      i     i ii i       --  i -i   v i         
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCAT--AAGGATAGACATATAGATCAA 300

  chr20_43699639_   2320 AGGAATATGACAGAGAACCTAGAAACAAACAGAATCATTTATGGTCAACT 2369
                         v      vi iv    ii i     i    vv vv             i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_43699639_   2370 GATTTT-GACAAAGATACCAATAAAACTCAACTGGCAAAGAACAGCCTCT 2418
                               -     i i i    v vv i    iv  v      i  i  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_43699639_   2419 TCAATAAAAGTTCCTGGCAAAACTGGATGCTCACATGCAGAAGAATGAAA 2468
                             i   v v v    v v        i?i        i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_43699639_   2469 TTGGACCCTAATTTCACATCATATACAAAAATCAATTCTAAATGGATTAA 2518
                                 iv ii     i             i  i  v        i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_43699639_   2519 ATAATTAAATGTAAAACCTAAAACCTAAAACTGTAAAAGTACTAGAAGAA 2568
                          v vi         i v       ------- i     v vi        
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAAC-------TATAAAACTCTTAGAAGAA 543

  chr20_43699639_   2569 AACATAGAAGGGAAGCTCCATTACATTGGTCTAGGCAATG-------AGA 2611
                                i? vi  v  i i v  v    vi         -------   
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_43699639_   2612 ------ACCAAAA-C--------------------TAGACAAGTGGGATA 2634
                         ------       - --------------------    i  i v   iv
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_43699639_   2635 ATATCAAA----------------CCACAAAGAAAACAACTAACAGAGTT 2668
                         vi      ---------------- iv     i v  v ii  v i   v
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_43699639_   2669 AAGAGACAACCTATGGAATGGGAGAAAATACTTAGAAACCATGCATCTGA 2718
                           i        i ii               i  iv   i   ii      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_43699639_   2719 TAAGGG-CTAATATCCAAAATATGTAAGGAACTCAAACAACTCACCAGCA 2767
                               -  vi      i     i   i      vv        vi ii 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_43699639_   2768 AG----CAAACAACCTGATTAAAAAATTGGCAAAGGAC---------CA- 2803
                          i----    i    ii   ?      v         i---------  -
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_43699639_   2804 ------AAAGAAGACATGCA--TAGCCAATAGGTAGATGAAAAAAAATGC 2845
                         ------        i  i  -- i       i i v       i --   
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA--TGC 891

  chr20_43699639_   2846 TCAACATCACTAATCAT 2862
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (120 / 72)
Gap_init rate = 0.02 (19 / 903), avg. gap size = 4.89 (93 / 19)  


3117 27.15 0.77 0.55  chr20_43713035_43719397     4966  5871 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_43713035_   4966 TGGAATAACATTCCATGCTCATGGCTAGGAAGAATCAATATCGAGAAAAT 5015
                              vi i  i     i      v v      v i     i vv  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_43713035_   5016 GGCCATACTGCCCAAGGTAAATTATAGATTCAATGCCATCCACATCAAGC 5065
                            v     v     iv i vi  i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_43713035_   5066 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTCA 5113
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_43713035_   5114 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAACCAAAAG 5163
                                viiv  ii  v  viv  v     iv     i i  vv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_43713035_   5164 AACAAAGCTGGAGGCATCACGTTACCTGACTTCAAATTATACTACAAGCC 5213
                                i      vv    ii v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_43713035_   5214 TACAGTAACCAAAACAGCATAGTACTGGTAAAAAAAAACAGAGATATAGA 5263
                                 i   i    ii i       i v  ii --i   v       
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA--TAGACATATAGA 296

  chr20_43713035_   5264 CGAATGGAACAGAACAGAGGGCTCAGAAATAACACCACACATCTACAACC 5313
                         iv       i    iv   i ii         vv   i    i  iiii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTC 346

  chr20_43713035_   5314 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5363
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_43713035_   5364 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATGTGCAGAAAGCT 5413
                           v  i  i              v      v  ?   ii    i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_43713035_   5414 GAAACTAGATCCTTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5463
                            ii i  i  i v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_43713035_   5464 TTAAAGACTTAAATGTTAGATGTAAAACCATAAAAACCCTGGAAGAAAAC 5513
                          i ?    i       v   vv      i      vi i i         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_43713035_   5514 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTA 5562
                         v    ?i- v i -   iv   v v  vv i     v ii   v iiv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_43713035_   5563 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAGTGGGATCTA 5612
                         vi            vvi          vv        i  i v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_43713035_   5613 ATTAATCTAAAGAGCTTCTGCACAGCAAAGGAAACTACCATCAGAGTGAA 5662
                           i  vv v  i i   i  ii vv       v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_43713035_   5663 CAGGCAACCTACAGAACGGGAGAAAATTTTTGCAATCTACCCATCTGACA 5712
                         v  i     i      i          v       vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_43713035_   5713 AAGGGCTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAA 5762
                          i  i  vi          v  i         vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_43713035_   5763 AAACCAAA---CCCA-TCAAAGAGTGGGCAAAGGATATGAACAGACACTT 5808
                           iv    ---    - i?  i i            v    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_43713035_   5809 CTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAGATGCTCAT 5858
                            v        i  vi viii     v ii                  v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_43713035_   5859 CACCACTGGCCAT 5871
                           i  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (142 / 100)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.50 (12 / 8)  


3256 27.20 0.44 0.44  chr20_43722721_43729122.rev     5003  5910 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_43722721_   5003 TGGAAGAACATTCCATGCTCATGGCTAGGAAGAATCAATATCATGAAAAT 5052
                              ii i  i     i      v v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_43722721_   5053 GGCCATACTGTCCAAGGTAATTTATAGATTCAATGCCATCCACATCAAGC 5102
                            v     vi    iv i  i  i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_43722721_   5103 TACCAATGACTTTCTTCACAGAA-TTGGGAAAAACT-ACTTTAAAGTTCA 5150
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_43722721_   5151 TATGGAACCAAAAAAGAGCCCGCATCACCAAGACAATCCTAAGCCAAAAG 5200
                                viiv  ii  v  v v  vi    i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_43722721_   5201 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5250
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_43722721_   5251 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACGGAGATATAGATC 5300
                                 i   i    ii         i iv ii ii  v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_43722721_   5301 AATGGAACAGAAC--AGAGCCCTCAGTAATAACGCCGCATATCTACAACT 5348
                                i    i--    i  --  v     vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_43722721_   5349 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5398
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_43722721_   5399 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5448
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_43722721_   5449 GAAACTGGATCCCTTCCTTACACCGTATACAAAAATTAATTCAAGATGGA 5498
                            ii    i    v   i     i              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_43722721_   5499 TTAAAGACTTAAACGTTATACCTAAAACCATAAAAACCCTAGAAGAAAAC 5548
                          i ?    i    i  v v v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_43722721_   5549 CTAGGCATTGCCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCTAA 5598
                         v    ?i viviv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_43722721_   5599 AACGCCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 5648
                         i  i         vvi          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_43722721_   5649 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5698
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_43722721_   5699 AGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5748
                           i     i   i             v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_43722721_   5749 AGGGCTAATATCCAGAATCTATAAAGAACTCAAACAAATTTACAAGAAAA 5798
                         i  i  vi          v            vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_43722721_   5799 AAACAAACAACCCCATAAAAAAGTGGGTGAAGGACATGAACAGACACTTC 5848
                          i     i     v  v?    i    ii     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_43722721_   5849 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACC 5898
                           v        i  vi viii     v  i          i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_43722721_   5899 ATCACTGGCCAT 5910
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (146 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2945 26.34 2.12 1.00  chr20_43731112_43734699     2201  3096 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_43731112_   2201 GAAAAACATTCTATGCTCATGGATAGGAAGGGTCAATATTGTTAAAATAG 2250
                             i i  i i   i        v     iv i           i  i 
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_43731112_   2251 TCATACTGCCCAAAACAATTTACGGATTCAATGTTATTCCTATATACAAA 2300
                         iv     v      vii  i   i       i iv  i     ---    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTAT---CAAA 99

  chr20_43731112_   2301 CTACCAAC---ATTTTTCACAGAATCAGAAAAAGCCATTTGAAAATGCAT 2347
                         v v   i ---v     ii     viv  v  iviv  iiv     v   
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_43731112_   2348 TTGGAAGCAAAAAGGGCCTGGA-TAGCCAAAACAATTCTAAGCAAAAAGA 2396
                         v     iiiv  i  i  ii  -             ii i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_43731112_   2397 CCAAAGCTGGAGGCATTATACTTCCAGACTTCAAACTATACTACAAGCCT 2446
                         v     i      vv i i      vi i      viv        iv  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_43731112_   2447 ACAGTAACCAAAACAGCATGGTACTGGTACAAAATGAGA-ATCATTAACA 2495
                                i   i    ii         i i  iivv   -  -  vi iv
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT-ATAGATC 298

  chr20_43731112_   2496 AATGAAACAGAATAGAGAACCCAGAAATAAAGCTACACACCTACAACTGT 2545
                             i  i     v    ii           v i i   ii  iiiiiiv
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_43731112_   2546 CTGATCTTCAATGAAGCTGACAAAAACAATCAATGGGAAAAGGACTTCCT 2595
                         i    i   i ii i v  v   i v  v        i    i ivvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_43731112_   2596 ATTCAATAAATGCTACTGGCATAACTGGCTAACCATATGCAGAAGAATGA 2645
                         v     i     v i    v i      v  ?   i     i        
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_43731112_   2646 AACTGGACCCCCACTTTTTACCACATACAAAAATCAATACAAGATGGATT 2695
                          ii        i  i ivi    i          i  iv   i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_43731112_   2696 AAAGACTTAAATGTAAAATCTAAAGCTATAAAGACCCTAGAAGAAAATCT 2745
                          ?    i         i v     i       ivi i          iv 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_43731112_   2746 AGA---AAATACCATTCTGGACATTGGCCCAGGCAAAGACTTCAT-GATA 2791
                           i---    -- -   vv   v    vii      v ii   v -    
  L1M4_orf2#LINE/    549 AGGNGTAAAT--C-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_43731112_   2792 AAAACTCTACAAGCAATTGCAACCAAAACAAAAATTGACAAGTGGGACCT 2841
                         vi - v i v     vvv     v   iv      v  i  i v    i 
  L1M4_orf2#LINE/    596 TGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_43731112_   2842 AATTAAACTAAAGAGCTTCTACACTGGAAAAGAAACTATCAACAGAGT-A 2890
                         v  i   v v  i i   i iii  vv   i  v        v i   - 
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_43731112_   2891 AAAGACAACCTACAGAATGGGAACAAATATTTGCAAACTATGCATCCAAC 2940
                                   i           iv             ii  ii   ii i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_43731112_   2941 AAAGATCTAATATCCAGAATCTATAAAGAACTT----AAATCAACAAGCA 2986
                           i iv  vi          v           i----  v    i  vv 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_43731112_   2987 AAAAACAAAAAAA--AATTTTAA--TGGGTAAAGGACATGAACAGACCCT 3032
                            i     v  v--    ?v  --    i      iv    i    vi 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_43731112_   3033 TCTCAAAAGAAGACATA-ATGTGGCCAAAAAGCATATGATAAAAATGCTC 3081
                             v        i   - vi       v     i    -   i      
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA-AAAGATGCTC 893

  chr20_43731112_   3082 AGTATCACTAATCAT 3096
                          ii    ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (147 / 86)
Gap_init rate = 0.02 (16 / 906), avg. gap size = 1.75 (28 / 16)  


1180 25.41 2.16 0.81  chr20_43750146_43756534.rev      131   500 (5889)    L1M4_orf2#LINE/L1      431   805 (103)  

  chr20_43750146_    131 CCATATGCAGAAAATTGAAACTGGGCCTCTTCCTTATGCCTTATACAAAA 180
                            i     i  i v    ii   i  i  v   i ii  v         
  L1M4_orf2#LINE/    431 CCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA 480

  chr20_43750146_    181 ATTAACTCAAGATGGATTAAAGGCTTAACTGTAAAACTCCAGACTATAAA 230
                                   i      i ?  i i   v     i viiv i        
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr20_43750146_    231 AACTCT-AGAAGAAAATCTGGGCA-ATACCATTCAGGACATAGGCATTGG 278
                          -    -         iv i  ?i- v i -   iv   v v  vv v  
  L1M4_orf2#LINE/    531 A-CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGG 578

  chr20_43750146_    279 CAAAGATTTCAT-GACAAAATCACCAAAAGCAATTGCAACAAAAGCAAAA 327
                            v i    v -  i vi -           vvv          v    
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAA 627

  chr20_43750146_    328 ATTGACAAATGGCATCTAATTAAACTAAAGAGCTTCTGTACAGCAAAATA 377
                           v  i    v v ii v  i   v v  i i   i   i vv    iv 
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr20_43750146_    378 GACTATCATCAGAGTGAACAGACAACCTACAAAATGGGAGAAAATGTTTG 427
                         v       vv i      v        i   i             i    
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr20_43750146_    428 CAATCTATCCACCTGACAAACGTCTAGTATCCAGAGTCTACAAGGAACT- 476
                            vii  vi i    i  iv v  v         i v  i  i     -
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr20_43750146_    477 -TA-AATTTA-TAAGAAAAA-ACAAACA 500
                         -  -  i i -   v     -     i 
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATA 805

Transitions / transversions = 1.24 (51 / 41)
Gap_init rate = 0.03 (10 / 375), avg. gap size = 1.10 (11 / 10)  

3205 26.82 0.88 0.66  chr20_43750146_43756534.rev     4992  5897 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_43750146_   4992 TGGAAGAACATTCCATGCTCATGGCTAGGAAGAATCAATATCATGAAAAT 5041
                              ii i  i     i      v v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_43750146_   5042 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5091
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_43750146_   5092 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5139
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_43750146_   5140 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5189
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_43750146_   5190 AACAAAGCTGGAGGCATCACACTACCTGACTTCAGACTATACTCCAAGGC 5239
                                i      vv       v  ii i    i viv    v   i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_43750146_   5240 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5289
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_43750146_   5290 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5337
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_43750146_   5338 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5387
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_43750146_   5388 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5437
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_43750146_   5438 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5487
                            ii    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_43750146_   5488 TTAAAGACTTAAACGTTATACCTAAAACCATAAAAACCCTAGAAGAAAAC 5537
                          i ?    i    i  v v v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_43750146_   5538 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 5587
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_43750146_   5588 AACACCAAAAGCAATGGAAACAAAAGCCAAAATTGACAAATGGGATCTAA 5637
                         i            vvi v        vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_43750146_   5638 TTAAACTAAAGAGCTTCTGCATAGCAAAAGAAACTACCATCAGA----GA 5683
                          i   v v  i i   i  iiivv    i  v    i  --   ----  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA--AGAAAGTGA 694

  chr20_43750146_   5684 ACAGGCAACCCATAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGAC 5733
                          v  i       i i             v  i    vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_43750146_   5734 AAAGGGCTAATATCCAGAATCTACAATGAACTCTAACAAATTTACAAGGA 5783
                           i  i  vi          v  i  v       v    v iv i  vi 
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_43750146_   5784 AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACT 5833
                            i     i     v  i?    i     i     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_43750146_   5834 TCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCA 5883
                             v        i  vi viii     v  i          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_43750146_   5884 CCATCACTGGCCAT 5897
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (143 / 96)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 2.00 (14 / 7)  


3198 26.59 0.44 0.66  chr20_43776235_43782628     4994  5903 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_43776235_   4994 TGGAAAAACATTCCACACTCATGGATAGGAAGAATCAATGTTGTGAAAAT 5043
                               i i  i   iii        v      v i   i    v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_43776235_   5044 GGCCATACTACCCAAAGTAATTTATAGATTCAATGCTATTCCCATTAAAC 5093
                            v     v      v i  i  i        i  v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_43776235_   5094 TACTA-TTGACATTCTTGACAGAATTAGAAAAATCTATTTTAAAATTCAT 5142
                          v i -i  v v  i   -     v v  v  iiiv  ii          
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTG-CAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_43776235_   5143 ATGGAACCAAAAAAAGAGCCTGAACAGCCAAGACAATCCTAAGCAAAAAG 5192
                               viiv  ii-  v  v   i      i      i i iv  i   
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_43776235_   5193 AACAAAGCCAGAGGCATCATGTTATCCAACTTCAAACTATACTACAACGC 5242
                                iii    vv   iii vi    i      viv        v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_43776235_   5243 TACAATAACCAAAGCAGCATGGTACTGGTACAAGAACAGACACATAGAAA 5292
                             i   i   ii   ii         i i   i i     i     vv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_43776235_   5293 AATGGAACTGAATAGAGGGAACTAAGAAATAAGGCTGCACATCTACAACC 5342
                                iv    v   i vv --        iv iii    i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_43776235_   5343 ATCTGATATTCAGCAAACCTGACAAAAACAAGCAATGAGAAAAGGATTCC 5392
                          vi    v   ii   ivv  v   i v  vv     i i    i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_43776235_   5393 CTATTTAATAAATGGTGCTGAAAAAAGTGGCTAGCCACATGCAGAAAATT 5442
                           v  i  i           ii v  v   v  ?         i  i v 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_43776235_   5443 GAAACTGGACTCCTTCCTTATACCACATACAAGAATTAACTCAAGATGGA 5492
                            ii     i   v   i i    i      i           i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_43776235_   5493 TTAAAGACTTAAATGTAAAACCCAAAACTACAAAACCCCTAGAAGAAAAT 5542
                          i ?    i         i v i       i     i i          i
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_43776235_   5543 CTAGGCA-ATACCATTCAGGACGTAGGCATGGGCAAAGATTTCAT-GATG 5590
                         v    ?i- v i -   iv   v v  vv i     v i    v -   -
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT- 594

  chr20_43776235_   5591 AAAACACCAAA-GCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCT 5639
                          vi        -   vvv          v      v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_43776235_   5640 AATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAGAGTGA 5689
                         v  i   v v  i i   i  ii vv    i  v       vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_43776235_   5690 ACAGACAACCTACAGAAATGGAGTATATTTTTGCAATCTATCCGTCTGAC 5739
                          v        i      vv    v v  v       vii  vii     i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_43776235_   5740 AAAGTTCTAGTATCCAGAGTCTACAAGAAACTTAAACAAATTTATAAGAA 5789
                           i vv  v         i v  i  ii    ivv    v iv    v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_43776235_   5790 AAAAACAAACAATCCCATTAAAAAGTGGGCAAAGGACTTGAACAGGCACT 5839
                            i     i  i  v   ?    i           i     i  i  i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_43776235_   5840 TCTCAAAAGAAGACATATATGTGGCCAACAAACATATGAAACAAGGCTCA 5889
                             v        i   i vi       i  i  i      vi v     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_43776235_   5890 ACATCGCTGATCAT 5903
                              i????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.48 (142 / 96)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 1.11 (10 / 9)  


2617 25.97 1.05 5.97  chr20_43789282_43791266      539  1493 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_43789282_    539 TGGACAAACATTCCATGCTCATGGATAGAAAAAAATCAATATTGTGAAAA 588
                             v i i  i     i        v i  i v- i        v  i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGAC-TTAATATTGTTAAGA 49

  chr20_43789282_    589 TGGCCATACTGCCCAGAGTAATTTATAGATTCAATGCTATTCCCATTAAA 638
                             v     v    i v i  i  i        i  v  i  i  i   
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_43789282_    639 CTACCA-TTGATATTCTT-CATTAAATTAGAAGA-AAACT-ATTTTAAAA 684
                         v v   -i  viv  i  -  v-     ----  -  i  -  ii     
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAG-AAATT----GACAAGCTGATCCTAAAA 144

  chr20_43789282_    685 TTCATATGGAACCAAAGAAGAGTCTGAATAGCCAAGGAAATCCTATGCAA 734
                                    viiv iii  vi v          iiv    i iviv  
  L1M4_orf2#LINE/    145 TTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAA 194

  chr20_43789282_    735 AAAGAACAAAGCTGAAGGCATCATGTTACCAGATTTCAAACTGTGCTACA 784
                         i          i  i   vv   iii v  vi        viv i     
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_43789282_    785 AGGCTGCAATAACCAAAACAGCATGGCACTAGTACAAGAACAGACACATA 834
                          i   i  i   i   i    ii   i   i i i   i i     i   
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_43789282_    835 GAACAATGGAACAGAATAGAGAACTCAGAAATAAGACCACACAGCTACAA 884
                           v        i     v    iii         iv   i   vi  iii
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_43789282_    885 CCATCTGATCTTTGACAAACCTGACAAAAAAAAAAGCAATGGGAAAAGGA 934
                         i  vi    i  i     ivv  v   i vv v--v       i    i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCAT--TCAATGGGGAAAGAA 392

  chr20_43789282_    935 TTCCCTATTTAGTAAATGGTGCTGGGAGAATTGGCTAGCCATGTGCAGAA 984
                          vvi  v  i ii              v  i   v  ?   ii    i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_43789282_    985 AATTGACACTGGACTCTTTCCCTATACCTCATACAAGAATTAACTCAAGA 1034
                         i v   vii     i i v  ii i   vi      i           i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_43789282_   1035 TGTATTAAAGATTTAAATGTAAAACCCAAAACTATAAAAACCCTAGAAGA 1084
                           v  i ?   ii         i v i            vi i       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_43789282_   1085 AAATCTAGGCA-ATACCATTCAGGATTTAGGCATGGACAAAGATCTCATG 1133
                            iv    ?i- v i -   iv  ii v  vv i i   v i i  v i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_43789282_   1134 G---TGAAATTGCCAAAAGCAATTGCTACAAAAATAAATAAATAGCAAAA 1180
                          ---   v ---         -----------------------------
  L1M4_orf2#LINE/    592 GATATGACA---CCAAAAGCA----------------------------- 609

  chr20_43789282_   1181 TTAAAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGAGATCTAATT 1230
                         ---------   --          v      v  i    vi  ii v  i
  L1M4_orf2#LINE/    610 ---------CAA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_43789282_   1231 AAACTAAAGAGCTTCTGCACAGCAAAAAAAAAACTATCATCAGACTGAAC 1280
                            v v  i i   i  ii vv    ii v --      vv i v    v
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACA--CTATCAAGAAAGTGAAA 696

  chr20_43789282_   1281 AGGCAACTTACAAAAATGGAGTAAATTTTTGCAATCTATCCATCTGACAA 1330
                           i    ii   i  vv    v    v       vii  vi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_43789282_   1331 AGTCCTAATATCAAGAATCTACAAAGAATTTAAACAAACTTA-CAAGAAA 1379
                         i vv  vi    v     v  i      i ivv    -  i -i  v   
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAA-CTCAATAATAAA 795

  chr20_43789282_   1380 AAAACAAACAATCCCATTAAAAAGTGGGCAAAGGACATGAACAGATACTT 1429
                           i     i  i  v   ?    i           iv    i   i i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_43789282_   1430 CTCAAAAGAAGATA-AAATATGCAGCCAACAAACATATGTAAAAAAGCTC 1478
                            v          - v v   --     i  i  i   v   i v    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG--GCCAATAAGCACATGAAAAGATGCTC 893

  chr20_43789282_   1479 AACATCACTGATCAT 1493
                                ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.62 (151 / 93)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 3.53 (67 / 19)  


2600 21.66 3.44 11.54  chr20_43795666_43798217     1079  2066 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_43795666_   1079 TGGAAAGATATCCCATGTTTATGGGATGGAAGAATTAATATCGTGGAAAT 1128
                                            i    iv       v       i  vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_43795666_   1129 ATTCAT-CTACCCAAAGCAATTTACATAGTCATTGCCATCTCTATCAAAA 1177
                         iviv  -  v      vii  i    v v   vi  v   i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_43795666_   1178 TCCCAA-TGTCATTCTTCACATAAAT-AAGAAAAAAATCCCAAA-TTCAT 1224
                              i-  i -  i  ii  v    -i v  ivvi    i   -     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_43795666_   1225 ATGGAACCACAAAAAA-----AATAGCCAAGGCAATCATGAGGGAAAAAA 1269
                               vii   iii -----         ii     v   -----    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-----AAAA 194

  chr20_43795666_   1270 AAAAAAAAAACGTAGAGGCATCATACT-ACTAATTTCAAACTATACTACA 1318
                         i  i  v   vv i    vv   i   -v i         viv       
  L1M4_orf2#LINE/    195 GAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACA 244

  chr20_43795666_   1319 AAG------TGATAAAAA-----TGGCACTGACATAAAAATAGACACATT 1357
                            ------ i  v  i -----   i    i     ii       i  v
  L1M4_orf2#LINE/    245 AAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATA 294

  chr20_43795666_   1358 GACCAATAGAATAAA-----GAGTGCAGAAATGAACTCATACATATACAG 1402
                           i    i     i -----    v       i   i       v  ii 
  L1M4_orf2#LINE/    295 GATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_43795666_   1403 TCATTTGACATTCAACAAAGGTGCCAAAAATACACAATAGGAAAAGGAAA 1452
                            v    iv   i    i        i vi iv    i  i    i v 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_43795666_   1453 GTCTCTCCAATAAATGGTGTTGGGAAAATTGGATATCCAAATGTAGAAGA 1502
                             i i   i        i     v  i      ?   v   i i    
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_43795666_   1503 ATGAAATTGGACCCTTATCTCACACCATATACAAAAATGAACT-AAAATG 1551
                              i        i  i                    v    -      
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_43795666_   1552 GGTTAAAGACTTATACACATAATGGGAGGCAGAGGTTGCAGTGAGCTGAG 1601
                          i i ?    i  -------    --------------------------
  L1M4_orf2#LINE/    495 GATCAWAGACCTA-------AATG-------------------------- 511

  chr20_43795666_   1602 ATCATGCCACTGCACTCTGGCCTGGGCAACAAAAGCAAAACTCTGTCTCA 1651
                         --------------------------------------------------
  L1M4_orf2#LINE/    512 -------------------------------------------------- 511

  chr20_43795666_   1652 AAAAAAAAAAAAGACTTACACAGAAGACCTGAAACTGTAAAACTACTACA 1701
                         ----------------  ------   v  i     i       vi  v 
  L1M4_orf2#LINE/    512 ----------------TA------AGAGCTAAAACTATAAAACTCTTAGA 539

  chr20_43795666_   1702 AGAAAACAGAGGGGAAAAAAACTACAGGACATTGGTCTGGGCAATGATTT 1751
                                 v   ? v   v--  v iv   v    vi i       i   
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAAT--CTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_43795666_   1752 TTCAGATTTGGCCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAAT 1801
                         i i    v  i vi          i          v         i    
  L1M4_orf2#LINE/    588 CTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAAT 637

  chr20_43795666_   1802 GGGATTACATTAAACTAAGAAGCTTCTGCACAATAAAGGAAACAACTAAC 1851
                         v   i v   i   v v i  i   i  ii vvi      v  v ii  v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_43795666_   1852 AGAGTGAACAGATGCTCTACAGTTTCGGAGAAAATACCTGCAAGCCATGT 1901
                          i      v   iivi i    vv v          ii     ii   i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_43795666_   1902 ATTTCATAGGGGGCTAATATTCAAAATACATAAGGAATTCAAACAACTCT 1951
                           i v   i   i  vi   i  i    i    i   i  vv       v
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_43795666_   1952 TTAGCAAGAAAACAAC---CCCATTTAAAAAATGGACAAGGGACCTGAAT 1998
                         v  ii  i  i    v---    v  ?        i   i   ii     
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_43795666_   1999 G----TTTCTCAAAAGAAGACACACACATGGCCAACAGATATACAAAAAA 2044
                         i----      v        i i   v        i iii i ii    i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_43795666_   2045 AAAGCTCAATGTTCCTAACCAT 2066
                          v-      ii iv????????
  L1M4_orf2#LINE/    888 AT-GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (134 / 76)
Gap_init rate = 0.02 (19 / 908), avg. gap size = 7.79 (148 / 19)  


1990 19.29 8.59 12.47  chr20_44504273_44506111.rev      499  1348 (491)    L1M4_orf2#LINE/L1       92   908 (0)  

  chr20_44504273_    499 CTATCAAAATCTCAGCAGGATTTTTTGTAGATACAGGCAACATCATCTGA 548
                                    i    v vv       i   v iv i   vv v   iv 
  L1M4_orf2#LINE/     92 CTATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTA 141

  chr20_44504273_    549 AAGTTTGTATGGAAAGGCAAAGGCACTGGAATAGCTAACATAATTTTGAA 598
                           i  ii        v    i  vv ii       i  v i   i     
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAA 191

  chr20_44504273_    599 AAAGAATAATAAAATGGGAGGAATCG---------GTTTC---------- 629
                               v  i   i v      v  i---------i    ----------
  L1M4_orf2#LINE/    192 AAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT 241

  chr20_44504273_    630 ---------CAGTAATCAAGACTATGTGGTATTGGAGGATGGATAGACAC 670
                         ---------             vi       i   viv v         i
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_44504273_    671 ATAGATCAATGGAATATAACAAAGAATCCAGAAATAGACCCACACAAATA 720
                                         v  ivi   i          i     i   vv  
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_44504273_    721 TGTCCAACTGACATTTTACAAAAGTGCAAAAGCAATTCAGTGGACAAAGG 770
                           vi   i   iv  iv    ii    v  ii v     i   iv    i
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_44504273_    771 ATAGTCTTTTCAACAAAAAAGGTGGTGCTGGAACAGTAAGACATCTATGA 820
                                          -----         i   iivi  i ? i iiv
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAA-----TGGTGCTGGGACAACTGGATAKCCACAT 436

  chr20_44504273_    821 GCAAAAAAAGAAAAAAGAAGGAAGAAGAAGAAAGAAAAGAAAGAGAGAAA 870
                               ----------   v    --------------------------
  L1M4_orf2#LINE/    437 GCAAAA----------GAATGAAG-------------------------- 450

  chr20_44504273_    871 GAACAGAACTTCACCCTAGGTCTCACACCTTACATTAAAATTAACTTGAA 920
                         ---iv i  ----     --i        v  i iv          ii  
  L1M4_orf2#LINE/    451 ---TTGGAC----CCCTA--CCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_44504273_    921 ATCAATCTCAGATTTAAATTATAAGAG--------ATAAAACTTTCAAAA 962
                           vi   v?   ii     -i      --------        i i i  
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAAT-GTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr20_44504273_    963 AAAA---TAAGAGAAAATATTTGGGATCTAGATAGTGAGGCAA------- 1002
                         i   ---  i ? v    v  i v  i  v i--  v      -------
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGG--GTTAGGCAATGGTTTC 588

  chr20_44504273_   1003 --AGAATTGACAACAAAAGCACAATCCATAAAAGGAAACAT--------T 1042
                         --   vv     v           v v i     i   v  -------- 
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_44504273_   1043 GAACTTCATCAAA-TTAAAA-TTTTTGTGCTTCAGAAGACCTTGCTA-CA 1089
                          i           -      -i            i i   ---i   -  
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGAC---ACTATCA 685

  chr20_44504273_   1090 AGGA--TGAAAAGACAAGCTACACACTGGGAGAAAATATTTGCAAACCAT 1137
                           i --           v i   v v                    i   
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr20_44504273_   1138 TCATATAACAAAGAACTAGTACCTAAAATGTACCAGTACTTTGTTGTATA 1187
                         vi  v i i  i i   v   i i i   i  ----------------  
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATA----------------TA 769

  chr20_44504273_   1188 AATGGTTTGCAAATATTATTATATATCCTCTGATATAAGGAATTCTCAAA 1237
                           --------i  --------------    --  i  ------     -
  L1M4_orf2#LINE/    770 AA--------GAA--------------CTCT--TACAA------CTCAA- 788

  chr20_44504273_   1238 CCTTAACAGAAAAA-AAA-AATCAAATTAGAAAATGGGCAAA-------- 1277
                         ---   i i   i -   -  i v    ?i            --------
  L1M4_orf2#LINE/    789 ---TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr20_44504273_   1278 --AGACATTTTATCAAAAAAGATATATAGATAGTAAGTAAGCACATGAAA 1325
                         --        ivi    i        i i  i iv i             
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

  chr20_44504273_   1326 AGATGTTTAACATCCATTAGAGA 1348
                              i i      v????????
  L1M4_orf2#LINE/    886 AGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (101 / 59)
Gap_init rate = 0.03 (27 / 817), avg. gap size = 6.63 (179 / 27)  


2391 28.44 5.99 0.71  chr20_44532760_44534628.rev      527  1377 (492)    L1M4_orf2#LINE/L1       13   908 (0)  

  chr20_44532760_    527 CTATGTCCATGAATTAGAAAACTAAATATTGTAAAGATGTCAAGATTTGA 576
                          i    i    i   i   i   v        v      v   v i ivv
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr20_44532760_    577 CAAGTTAATTGATAAATTCAATGCAATCCCTGTCAAAATCCTAGCAAGCT 626
                            i  i  iv i i      i         i         i   viv  
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr20_44532760_    627 TTTTTGTGGAAATTGAT--GTTAACATTACAATGTACCTAGAAATGCAAA 674
                               ii        i-- i i ivi  v   vi iv i         i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr20_44532760_    675 TGGCCAAGAATAGCCCAGCCAATCTTGAA------GAACAAAGTTAAGAG 718
                         v i  v         v iv          ------          iiii 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr20_44532760_    719 ACTTATACTACCAGATATTAAGACTTATTTTAAAATTACAGTAATTAAG- 767
                            i i   v  vi  v i  i     i vi   ii         i   -
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr20_44532760_    768 ---TATGGTGTTGGCATAAGAACAGATAATTAAAGGAAAGAAACAAAATA 814
                         --- i    ii         i i   i vv  i vv  v i  i i   v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr20_44532760_    815 TAGAACCCAGAAATAAACCTATATAGCTTATGAAAAA---------AGCC 855
                         v   ii             i   i -i     ivv  ---------ii v
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACA-TTTATGGTCAATTGATTTTCGACA 361

  chr20_44532760_    856 ATACTGCAGAG------CAGTGGGGAAGGAATGATCTTTTCAATAGATGG 899
                          viv   vi  ------  i       i    ii         i i    
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr20_44532760_    900 TGTTGAGTCATGTGGGAAATTATATGAGAAAGAAAGAAAT-------CTA 942
                           i  i v  vv   iv ?ii i   vi      v   i -------   
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr20_44532760_    943 CCTTTCACCGTATACTTAAATAAATCCCATGTGAATT-TATCTCTAATTG 991
                            iv    i     vv    v  ii v vi  i  i-? vvi    v  
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr20_44532760_    992 TGAAAAGTAAAAC---AAAGC-ATTAGGTGATATAATAGGACAATATTTT 1037
                          i i iv      ---   i -v    iv  v vv     ?vv v  i  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTT 561

  chr20_44532760_   1038 CATGAATTTGAAGTAGGAAAAGGTGTCTTAAATAGGACA---AAACCACA 1084
                          i   vi   iiv    v  v   v     i   v    ---   v    
  L1M4_orf2#LINE/    562 CGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr20_44532760_   1085 TTAACCAGAAAGGAAAAGATTGATAAATTTGACTACATTAAAATTAAGAA 1134
                         -- i v v   i     i  v        v    v   i        i  
  L1M4_orf2#LINE/    612 --AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr20_44532760_   1135 CTCCTGTTCCTCAAAAGACACCATTAAAAGAGTGAAAGAGGCAAGCCAAA 1184
                           ii   v i     i     i  i  i i       -  i   v   v 
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA-AGACAACCCACA 708

  chr20_44532760_   1185 GAATGGAAGAAGGTATTGGTAATAAATATACCTGACACAGTATTCTTATA 1234
                               i    ii    v i  vvv     i    i vi v i iv   v
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr20_44532760_   1235 CTGTATATACACAAAACCTTTTTGAATTGATAG--------CAGACAACC 1276
                          v v     i v i   ii  vii v ii   i--------  i i    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr20_44532760_   1277 CAATTTTAAAAATGGGCAAAATACTTGAACAGGCACGTCACACACACCCA 1326
                              ?-             iv i     i  i  iv  v -  v vvvi
  L1M4_orf2#LINE/    809 CAATTW-AAAAATGGGCAAAGGATTTGAATAGACATTTCTC-CAAAGAAG 856

  chr20_44532760_   1327 ATATCAAAATGGACAATAGGTATA-GAAAAGGTGCTCAGCCTCATCAGTA 1375
                             vv      v     i i i -      i      i v   ??????
  L1M4_orf2#LINE/    857 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZ 906

  chr20_44532760_   1376 AT 1377
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.45 (141 / 97)
Gap_init rate = 0.02 (17 / 896), avg. gap size = 3.35 (57 / 17)  


 274 31.00 17.81 3.37  chr20_44544759_44546482.rev      512  1224 (500)    L1M4_orf2#LINE/L1       61   876 (32)  

  chr20_44544759_    512 CCCAAGTATATACATAAATTCAATAGTATCTCCATTTAAAAAATCC--AT 559
                              i vv  vi i i      iivv   i i  i---       --ii
  L1M4_orf2#LINE/     61 CCCAAATTGATCTACAGATTCAACGCAATCCCTATC---AAAATCCCAGC 107

  chr20_44544759_    560 TAAGATTATTTTATAAACTGTGATAAACAGATACATGATTTTCACA---- 605
                          -- vi v    ii i vvv   i  i v   v - i vv    i ----
  L1M4_orf2#LINE/    108 T--GCCTTTTTTGCAGAAATTGACAAGCTGATCC-TAAAATTCATATGGA 154

  chr20_44544759_    606 ----CAAGGGA---AAAATGTGACAGACTAGTTTTTTACATGAAAAGTTA 648
                         ----       --- i   i- v  i vi i i  vv v v   i iiv 
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATA-GCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr20_44544759_    649 A--TGAAGGTCTTGTTCTTGCCAGGGTGCAGAGTC-------AAGTTGTA 689
                          --  i   v  iiiv   v   ivv -  i iii-------   i ii 
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTT-CAAAACTTACTACAAAGCTACA 252

  chr20_44544759_    690 GTAATTCAAGTGGGT-TAGGAATGTCATCAGCACAGATGAAGAGATCAAA 738
                              -    vvi  - i v v  v   v  v i   iiv v       v
  L1M4_orf2#LINE/    253 GTAAT-CAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAAT 301

  chr20_44544759_    739 GAAA-------GAGAGCCCAGAAACAGATGCAAA----TATGGGAATGTT 777
                          i  -------     i       i i iv  v ----     vv -i  
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA-ATT 350

  chr20_44544759_    778 TACTGCCTAAAAAAGATGACCTGCAAGTCTGTT-----GGGAAACAAT-- 820
                         v i vi -i v  i i  -  ---   v ii  -----      v   --
  L1M4_orf2#LINE/    351 GATTTTC-GACAAGGGTG-CC---AAGACCATTCAATGGGGAAAGAATAG 395

  chr20_44544759_    821 -----TCAATGAATACTGAGGCAATAACTGAATATCCCTTAGTAGGGGGA 865
                         -----    ii   iv  vv vi i     i   ?  vivv i iii i 
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_44544759_    866 --GAGCAAGATCCCTCCCTGAC----TATG---AGACTATGTTCCAGATG 906
                         --i  ivi  i    v   v  ----   i--- i i  -ii  v i   
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA-ACTCAAAATG 494

  chr20_44544759_    907 AAATAAAAGA--TAATTAT------TAAAACTATTAAAATGTTAGAA--- 945
                         i - v ?   --   v i ------         v   v v      ---
  L1M4_orf2#LINE/    495 GA-TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_44544759_    946 AATG-AGG-----ATTTTCA-GAC-TTACAATAGAAAA--ATGTCTTAAA 985
                           ii-   -----  i   i-   -  iviv   iv  --i v     i 
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_44544759_    986 ---GACTC---AAGTGCCAG--ATAAAAGAAAA--TA-ATAAAATCGACC 1024
                         ---   v ---   ii v  -- i         --  -     v v   i
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_44544759_   1025 TTATAAAGGAGAAAAATCTCTGTG----AAAAAATA--------AAAGGG 1062
                          i  v  iivv     ii i    ----   ii i --------    v 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_44544759_   1063 A----------CACAGAA----AAAACTTAA-ATTAGTATGTTGTATAAC 1097
                          ----------       ---- i  ---  -   v i vi ii    v 
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAA---AATATTTGCAAATCATATATC 740

  chr20_44544759_   1098 CAACAAGGAACTC--ATTCAGAATTTATACAGA-----------TCAATA 1134
                         ii i    i   i--  i      v    v   -----------      
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_44544759_   1135 AGAAAAAAAAATAGAAGCTGCAGACTAGACAAATGCCTAAAGTATATGAA 1184
                          v     i v v v  v --  - i ?i -     vvi    v  v    
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACC--CA-ATTWAA-AAATGGGCAAAGGATTTGAA 836

  chr20_44544759_   1185 TGAAAAGTTCACTGAAGAAAGCATACAAATGATCAATAAG 1224
                          ii v v   v ii     iii         ii       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

Transitions / transversions = 1.42 (128 / 90)
Gap_init rate = 0.06 (49 / 816), avg. gap size = 3.08 (151 / 49)  


 327 32.33 12.37 3.18  chr20_44548475_44550040.rev      501  1066 (500)    L1M4_orf2#LINE/L1      239   856 (52)  

  chr20_44548475_    501 ACCACACTGCTATAATAA--AAAAGAATATTATACT--CATCCAGAACAG 546
                           i   vv    i i   --  i v i i vi    --   v-  i i  
  L1M4_orf2#LINE/    239 ACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA-AGGATAG 287

  chr20_44548475_    547 ACAAATACACGAATGGAATAAAA--GAAATTTCAGAAGATGATTTCTATA 594
                            v   v iv         i  --  i v i     -  i vii -   
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA-ATAAACCC-ATA 335

  chr20_44548475_    595 GATGTATAGT--ACTGATGGCTTGTGTGTAAGGATGGCATCATAAGTCAG 642
                         v  v   i  -- i    ---  vi -ii    i  v  vv iv v   i
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGAT---TTTCG-ACAAGGGTGCCAAGACCATTCAA 381

  chr20_44548475_    643 TGAGGACAGGATGGATGCTTTGGTGGGTGGTATTGTAAAAACTG---ACT 689
                           i   v  i  i vivi  iiiiiii    ii  vi v     --- ?i
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKC 431

  chr20_44548475_    690 CATTGTTCAGAGAAAATGGGGCTGGTTGTCCA--TTATGCCATATACAAA 737
                           i-i v  i - i    ii i   vivi i -- i ii           
  L1M4_orf2#LINE/    432 CAC-ATGCAAA-AGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr20_44548475_    738 TAT-------AGACAGATTA-------AAATGTGAATTTTAAACCCGTAA 773
                         v  ------- i ii   i -------      i ivvi    v ii   
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr20_44548475_    774 TGCTGATAGGAGAA--------TGT----CTTTGTGGTCTAGGAT---GC 808
                         vi  vv   i    --------?  ----   i   ii  v  i ---  
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr20_44548475_    809 AGTGGGCTTCTTAAACA--ACAACAAAAAGACAATAAGCAAATGCTGTAA 856
                          i   -i      i i --   v     iv    vv i    v ----  
  L1M4_orf2#LINE/    580 AATGG-TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG----AA 624

  chr20_44548475_    857 GTCAAACATGCTA---TGGATGTGATAAAAAACGAAGGATTTCTGA---T 900
                         i--   i - v  ---    iv v  v    -iv  ii i  i  v--- 
  L1M4_orf2#LINE/    625 A--AAATA-GATAAATTGGACTTCATCAAAA-TTAAAAACTTTTGTGCTT 670

  chr20_44548475_    901 CAAGAGAAGCC--CCAGA--GTCAACAGGCAAATGACAGATTGACAGGAG 946
                            ii  vi i-- v   --  v  v  i   viv     v  iv  i i
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAA 720

  chr20_44548475_    947 -TAACCGTACATTTTAAACCAAA-AAATACCTTATAT--ATAACATG-AA 991
                         -  vii i v  iv  v i vi -  iviv   i   -- v  i  i-  
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAA 770

  chr20_44548475_    992 ATA--TATT-CAATTCCACAAAGAAAAGA-AAA-AA---AATTAGAAAAT 1033
                          v -- v  -   i  v i  vi      -   -  ---    ?i     
  L1M4_orf2#LINE/    771 AGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAAT 820

  chr20_44548475_   1034 GAGCAAAGAACATGAAGAAGCAATTC---AAAAAAG 1066
                          i      i iv    v ii  v   ---   i   
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 856

Transitions / transversions = 1.65 (112 / 68)
Gap_init rate = 0.06 (38 / 618), avg. gap size = 2.32 (88 / 38)  


1523 17.55 4.08 20.89  chr20_44596676_44598471      501  1309 (487)    L1M4_orf2#LINE/L1      236   908 (0)  

  chr20_44596676_    501 CTTAAAATAAAGCTATAGCAATCATCACAGTGTGATATTGACTTAAGGAT 550
                             vv i       i  i     vv        i  i  i v       
  L1M4_orf2#LINE/    236 CTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGAT 285

  chr20_44596676_    551 AGAGAATTTGATCAATGGAACAGAATAGAGATTCCAGAAATAAATCTCTA 600
                            v vv v           i     v    v            i iv  
  L1M4_orf2#LINE/    286 AGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATA 335

  chr20_44596676_    601 CATTTATGGTTACTTTATTTGTGACAAATATGTAAAGGCAATTTAATGAG 650
                                   i v  v    vi     ivi  iv   i v   i    i 
  L1M4_orf2#LINE/    336 CATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG 385

  chr20_44596676_    651 G------T--TTTTCTCAACAAACTGTGTTTGATGAATCAGGTATCCATA 692
                          ------ -- i  i        iv   i v ivv  iii i  ?   i 
  L1M4_orf2#LINE/    386 GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr20_44596676_    693 TATAAAAAACAAACAAAAACTTAGACTCTTATTT-ATATCATATACAACA 741
                          ii    i --- ii  i--  i   i i  ii - i i         v 
  L1M4_orf2#LINE/    436 TGCAAAAGA---ATGAAG--TTGGACCCCTACCTCACACCATATACAAAA 480

  chr20_44596676_    742 ATTAACTCAAAATGGAGCCTGGACAGAAAATTAAGAGCTAAAACTGTGAA 791
                                         v v?i   vv   vv              i i  
  L1M4_orf2#LINE/    481 ATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAA 530

  chr20_44596676_    792 ACTTAAATAGCTGGGTGTGGTGCCACATGTCTGTAGTCCCAGCTACTGGG 841
                            -----------------------------------------------
  L1M4_orf2#LINE/    531 ACT----------------------------------------------- 533

  chr20_44596676_    842 GAGGCTGAGTCAGGAGAATCACTTGAGGCTGGGAGTTCAAGGCTGTAGTG 891
                         --------------------------------------------------
  L1M4_orf2#LINE/    534 -------------------------------------------------- 533

  chr20_44596676_    892 TGCTATGATCATGCCTGTGAATAGCCATTGAACTCCAGCCTGTGCAACAT 941
                         --------------------------------------------------
  L1M4_orf2#LINE/    534 -------------------------------------------------- 533

  chr20_44596676_    942 GGTGAGACTGTCTTTAAAAAAAAAAACTTATAAAAGAAAAATCTTCAAGA 991
                         -----------   --- i  i     --   ii? v   -     iv  
  L1M4_orf2#LINE/    534 -----------CTT---AGAAGAAAAC--ATAGGNGTAAA-TCTTCGTGA 566

  chr20_44596676_    992 CCTTAGGTTAGGCAAAGATTTCTTAGATGAG-CAGCAATAGAACAATCTA 1040
                             i          v i          iv -  v   v  v    v v 
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr20_44596676_   1041 CAAGAGAAAAAA---ATAA--TAGAGTTTATCAAAATTAACA-CTTCTGT 1084
                            i        ---    -- i  v  i           v -   i   
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr20_44596676_   1085 TCTTTGAAAGACACCACCAAGAAAACCAAATGACAAGCCACAGACTAGGA 1134
                         v   ii  i     i i       iiv   v     v       v i   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr20_44596676_   1135 GAAAATATTTGCAAATAATGTATTTGTTGAAGGATTCATATCCAGAATAT 1184
                                         v  i   i  v i i   i ii            
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr20_44596676_   1185 GTAAAGAACACTTAAAACTCAAAAATAAG----CAAACAACCTAATTGAA 1230
                         i        v    v       v     i----    i    i    ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr20_44596676_   1231 AATTGGGTAA-GTATTTGGGTAGATATTTCACCAAAGAATAGATAT---- 1275
                           v    i  - v     ii    i     v        v v   i----
  L1M4_orf2#LINE/    817 AAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAAT 866

  chr20_44596676_   1276 ------TAAGCACAT-AAAAGTTGTTCA-TATTATTAGTCAT 1309
                         ------         -     v  i   -i  i ????????
  L1M4_orf2#LINE/    867 GGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (82 / 56)
Gap_init rate = 0.03 (18 / 673), avg. gap size = 11.22 (202 / 18)  


 490 21.13 22.54 0.00  chr20_45130616_45132856      501   642 (1599)    L1M4_orf2#LINE/L1       71   244 (664)  

  chr20_45130616_    501 TCTGTTGATTCAGTCCAATTCCTACCAAAATCCCAGATGG-TGTTTAGTA 549
                            iiv      iiv    i    i           v  v- v   v i 
  L1M4_orf2#LINE/     71 TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGCA 120

  chr20_45130616_    550 GAAACTGACA--------------------------TGCAAAGTAACTAA 573
                             i     --------------------------     i v v i i
  L1M4_orf2#LINE/    121 GAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAG 170

  chr20_45130616_    574 AA--GCCAAAACAAACTTGAAAAAGAA---CAAAGTTGGAGAACTTATAC 618
                           --          v            ---           i   i i  
  L1M4_orf2#LINE/    171 AATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACAC 220

  chr20_45130616_    619 TACCTGGTTTCAAAACTCACCATA 642
                          v  iii          i  i i 
  L1M4_orf2#LINE/    221 TTCCCAATTTCAAAACTTACTACA 244

Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.02 (4 / 174), avg. gap size = 8.00 (32 / 4)  

 632 22.22 5.23 0.00  chr20_45130616_45132856      926  1078 (1163)    L1M4_orf2#LINE/L1      232   392 (516)  

  chr20_45130616_    926 AAAAATCACCATAAAGCTTCAGTAATAAGGATAGGATGGAATTGGTATA- 974
                             v i  i i      v       v i  i  vi   v i   i   -
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr20_45130616_    975 GGATAGA----TAAATCAGTGAAACAGAAT--AAAGTCCAGAAATAAACC 1018
                                ----  i    i  i  i     -- i                
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr20_45130616_   1019 TTCTCATTTATGGTCAGTTTATCTTTGGCAAATGTACCAAG-TAATTCAG 1067
                         iviv            i  v  i  i i   iv  i     -iv     i
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr20_45130616_   1068 TGGGGGAAGAA 1078
                              i     
  L1M4_orf2#LINE/    382 TGGGGAAAGAA 392

Transitions / transversions = 2.40 (24 / 10)
Gap_init rate = 0.02 (4 / 161), avg. gap size = 2.00 (8 / 4)  

 203 17.02 4.26 2.13  chr20_45130616_45132856     1201  1247 (994)    L1M4_orf2#LINE/L1      378   425 (483)  

  chr20_45130616_   1201 TCAGTGGGAGAAAGGATAGACTTTTTA--TAGTGGTCCTGGAACAACTG 1247
                            i    -     i    v     i --v i    v    i       
  L1M4_orf2#LINE/    378 TCAATGGG-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTG 425

Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.50 (3 / 2)  

1595 19.43 11.26 4.86  chr20_45130616_45132856     1297  1749 (492)    L1M4_orf2#LINE/L1      427   908 (0)  

  chr20_45130616_   1297 ATATATATATATGAAAAGATGAATTTAAGTCCTTAATCCACACTGTATAC 1346
                            ?vi i  iii   ii     v  iiii  i  vii     ii     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATAC 476

  chr20_45130616_   1347 AAAGATTAACTTAAATTGGATCATAGACCTAAATACAAGAAT----ACTG 1392
                            i       i   v       ?          ii    ii----   i
  L1M4_orf2#LINE/    477 AAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTA 526

  chr20_45130616_   1393 TGAAATTTCTAGAAGAAAACACAAGAGCAGTTCTTTGTGACCTTGAATTA 1442
                          i   i ii            i i ? i iv    i         ii   
  L1M4_orf2#LINE/    527 TAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA 576

  chr20_45130616_   1443 GGCAA--------------------CAAAAGCAAAATGCATCAAAGAAAA 1472
                              --------------------        v  -   v    ii   
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAA-GCAACAAAAGAAA 625

  chr20_45130616_   1473 AAATCAACAACCT--AC--------AAT------CTTTTGCTCTTCAAAA 1506
                             vi i  vi --  --------   ------      iv       i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr20_45130616_   1507 GACACCATTAAGAAA-----AAGACAAGCCACAAACTGGGAGATAATATT 1551
                              i  i      -----       v     i v       v      
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr20_45130616_   1552 CACAAATCATGTATCTGATCAAGGACTTGTGTCCAAGATATATAAAGAAC 1601
                         ii        i        v i        i    ii             
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr20_45130616_   1602 TCTTATAAC--AGTAATAAGAGGCCAAA---CCTAATTTTTTAAAAAGAT 1646
                              i   -- i      i i v    ---  i    ?---     ---
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW---AAAAA--- 819

  chr20_45130616_   1647 TTGACTAGGGTTTGATGGGAAAAAGATTTGAGTAGATATTTCATCAAAGA 1696
                         ---------------    v   i       i    i     vi      
  L1M4_orf2#LINE/    820 ---------------TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGA 854

  chr20_45130616_   1697 AGATATGTGAATGGCTAAAAAGCACATGAAAA-ATGCCCAACACCATTAG 1745
                               iii      i  v             -    i     i  ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr20_45130616_   1746 TCAT 1749
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 3.67 (66 / 18)
Gap_init rate = 0.02 (12 / 482), avg. gap size = 6.08 (73 / 12)  


1509 22.53 1.23 0.31  chr20_45143826_45147198      809  1132 (2241)    L1M4_orf2#LINE/L1        1   327 (581)  

  chr20_45143826_    809 TGGAGATATATACCTGGTTCGTGAATCAGAAGACTTAATATTGTTAAAAT 858
                             i v    v  vv    i  i  ii                   i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_45143826_    859 GCCAGCTCTTCCCAAATTGAGCTATAAGATT-AATACAATCTCTATCAAC 907
                          v  iiv  i          v   i -    -  ii     i       v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACA-GATTCAACGCAATCCCTATCAAA 99

  chr20_45143826_    908 ATCTCAG--GCTTTTTTTA-AGAAACTGTCAAGCTGTTTCTGAACTTTAA 954
                            i   --  i      i-     i  v       v i  i  v  i v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_45143826_    955 ATGGAAATGCAGAGGACCAAGAAGGGCCACAATGACTTTTGTAGAGAAGA 1004
                                    ii     v    vi    v  ii ii  viv i      
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_45143826_   1005 ACAAAGTTAGAGGGCTAAGACTACCTGATTTTAAAATCCATTTTAAAGCC 1054
                                 i    i  v v   v  ii    i    iii i vi     i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_45143826_   1055 ACAGTACTTAAGACAATGCAGCACTGGCATAAAAATAGACAAATAAATCA 1104
                               v i      i  ii i          ii       v   i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_45143826_   1105 ATGGAACAGAATTGAGAGTTCAGAAATA 1132
                               i            i        
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATA 327

Transitions / transversions = 2.17 (50 / 23)
Gap_init rate = 0.01 (4 / 327), avg. gap size = 1.25 (5 / 4)  

 489 17.89 7.37 0.00  chr20_45143826_45147198     1426  1520 (1853)    L1M4_orf2#LINE/L1      324   425 (483)  

  chr20_45143826_   1426 AATTAACCCACATGTATATGGTCACCTGATTTTTGACAA-------AAGA 1468
                            v      i ii v        vi       i     -------    
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr20_45143826_   1469 CAATTCAATGGAGAAAGGACAGTCTTTTCAACAAAAGATGCTGGAACAGC 1518
                          v         i     i i               v i      i   i 
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr20_45143826_   1519 CG 1520
                         i 
  L1M4_orf2#LINE/    424 TG 425

Transitions / transversions = 2.40 (12 / 5)
Gap_init rate = 0.01 (1 / 102), avg. gap size = 7.00 (7 / 1)  

 936 23.89 9.73 1.77  chr20_45143826_45147198     1845  2183 (1190)    L1M4_orf2#LINE/L1      460   825 (83)  

  chr20_45143826_   1845 TACCTCACATGACACACAAAAAA-AATGCAAAATAGATCATAGACTTAAA 1893
                                  iv i i       v-  iv      i     ?    i    
  L1M4_orf2#LINE/    460 TACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAA 509

  chr20_45143826_   1894 TATAA-------AACTGTAAT-CTTCTACAAGAAAACATAGGAG-ACAGT 1934
                          i   -------    i   v-  ii  v             ? - v vi
  L1M4_orf2#LINE/    510 TGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC 559

  chr20_45143826_   1935 TTTGTGACTTTGATTTAGGCAAAGATTTCTCATATGTAACACCAAAAATA 1984
                           i     i   iv        v i     i v  i i         ii 
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr20_45143826_   1985 TGATCCA-AAAAGAAAAAA-AGAATATAAACTGGACTTCATACAAATTTA 2032
                         ii v v -           -   ---    i          vv     v 
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGA---TAAATTGGACTTCATCAAAATTAA 656

  chr20_45143826_   2033 AAACT---GT---TCAGAGAA--------------TGAAAAGA-AATCCA 2061
                              ---  ---   i  i --------------        -  i   
  L1M4_orf2#LINE/    657 AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCA 706

  chr20_45143826_   2062 TGGTCCAGGAGAAAAATAATTGCAAGGCATATCTCGAATAAAGCATGTGT 2111
                         ii vvii        -  v      iv     v  vi    i v iv   
  L1M4_orf2#LINE/    707 CAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr20_45143826_   2112 TTATATAGAATATAGAAGGAGTGTTCAAAATCCAATAATAAGAAAGCAAA 2161
                         --  vi        v  i  iivi i v  ii         i  ii    
  L1M4_orf2#LINE/    756 --ATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA 803

  chr20_45143826_   2162 CAATCTGATAAAGAAATGGGCA 2183
                         i  i ii  v? i         
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCA 825

Transitions / transversions = 1.79 (50 / 28)
Gap_init rate = 0.04 (13 / 366), avg. gap size = 3.00 (39 / 13)  

 349 17.32 5.51 7.09  chr20_45143826_45147198     2755  2881 (492)    L1M4_orf2#LINE/L1      784   908 (0)  

  chr20_45143826_   2755 CTCAAAAAATAAAGAAATAAA------AATAAAGAAATGGGCAAAATATT 2798
                              v  -    i i i   ------   v? i           iv   
  L1M4_orf2#LINE/    784 CTCAATAA-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_45143826_   2799 TGAACAGATGATAGATGCCTCACCAAAGAAGATATAGGGATGGCCAA-AA 2847
                             -------    iiii  v              vii        -  
  L1M4_orf2#LINE/    833 TGAA-------TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAA 875

  chr20_45143826_   2848 GCACATGATTAAGATGCCAAATGTCATTAATCAT 2881
                                 v-       iv  ii   ????????
  L1M4_orf2#LINE/    876 GCACATGAA-AAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.04 (5 / 125), avg. gap size = 3.20 (16 / 5)  


 975 12.74 2.55 0.00  chr20_45165750_45167737.rev      501   657 (1331)    L1M4_orf2#LINE/L1      196   356 (552)  

  chr20_45165750_    501 AAGAACAAAGGTGGAGGACTCCTACTTTCCATTTTTGAAACTTACTACAA 550
                                   v          vi    i   v   ii             
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_45165750_    551 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGGCATACATACAG 600
                                                               ii v     i  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_45165750_    601 ATCTATGGGATAAAATGAAGAGTCAAGAAATAAAC----ATATTTACGGC 646
                            v    i   i   vi      v          ---- i     i  i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_45165750_    647 CAATTGATTTT 657
                                    
  L1M4_orf2#LINE/    346 CAATTGATTTT 356

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.01 (1 / 161), avg. gap size = 4.00 (4 / 1)  

2876 13.81 2.65 2.65  chr20_45165750_45167737.rev      954  1518 (470)    L1M4_orf2#LINE/L1      344   908 (0)  

  chr20_45165750_    954 GCCAATTGATTTTCTGACA-GGATGTTGAGACAATTCAGTAGGGGAAAGA 1002
                          i            -    -  i  iii    v     i -         
  L1M4_orf2#LINE/    344 GTCAATTGATTTTC-GACAAGGGTGCCAAGACCATTCAAT-GGGGAAAGA 391

  chr20_45165750_   1003 AGAGTCTTTTCAACAAATGCTACTGGGACGACTTGATAGTCATAGGTAAA 1052
                          v                 v i       i   v    ?i  i v i   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_45165750_   1053 ACAATGAGGTTGCACCCCTGCCTCACATCATACACACAAATTAACTCAAA 1102
                          v     i    v      i       i    i   v             
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAA 491

  chr20_45165750_   1103 ATGGATCACAGACCTAAATGTAAGAGCTAAAATGAGAAAATTCTTAGAAA 1152
                                 ?                       iv v    i        i
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_45165750_   1153 AAAGTGCAGGAGTAAATCTCTGTGACCT-AGGTTAGGCAATAGGGTCTCA 1201
                            iiii   ?        ii       -i           i vv   i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_45165750_   1202 GATATGACACCAAAAGCAAAAGTAACCAAAGAAAATATACATAAATTGCA 1251
                                           v   i   v        v   v        v 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_45165750_   1252 CTTCATAAAAATAAAAAGCTTG-GTATTTCAAAGGATACCACAAAGAAAA 1300
                               v     v    i   v-  ii         i  i iv      i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_45165750_   1301 TGGAAAGACAACTCACAGAATGAGAGAGAAAATATTTGCAAATCACATAT 1350
                           i         i         i    --                i    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGA--AAATATTTGCAAATCATATAT 739

  chr20_45165750_   1351 CTGATAATAGACTGGTATCCAGA-TATATAAA-AACTCTTATAA-----T 1393
                                vi    v         -        -        i  ----- 
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_45165750_   1394 GATATAAAGACAAA----CCAATT-AAAAATGAGCAAAAGATTTGAATAA 1438
                         i   v         ----      -       i     i          i
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr20_45165750_   1439 ATATTTTTCCAAAGAAGATATACAAATGGCCAATAAGCACATAAAAACAT 1488
                          i    i                                   i    v  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_45165750_   1489 CACTAGTCACTTGTCAACATTATTAGGGAA 1518
                         --------i  ---      i ????????
  L1M4_orf2#LINE/    890 --------GCT---CAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (50 / 25)
Gap_init rate = 0.02 (13 / 565), avg. gap size = 2.31 (30 / 13)  


3908 19.72 4.67 0.35  chr20_45873772_45876019      900  1756 (492)    L1M4_orf2#LINE/L1       15   908 (0)  

  chr20_45873772_    900 ATGCTCATGAATCAGAGGACTTAATACTGGTAAAATGCCCTTACCTTCCA 949
                            i     i  ii  i         i  v   i   v vv   iii   
  L1M4_orf2#LINE/     15 ATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCA 64

  chr20_45873772_    950 AAGCGATCTATAGATTCAATGCAACCCCTATCAAAATTCTAATT----TT 995
                           vi      i        i    i            i i ii ----  
  L1M4_orf2#LINE/     65 AATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTT 114

  chr20_45873772_    996 TTTGTGGAAATAGAAAAATTTATACTAAAATTCATATGGAACCTCAAGGC 1045
                             ii     v  v  ii v  v                 viv     v
  L1M4_orf2#LINE/    115 TTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr20_45873772_   1046 ACCTCAAATAGCCAAAACAATCTTGAAAAAGAAGAATG--GTTAGAGACA 1093
                            ivi                              ii--   i   ivv
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGAC 214

  chr20_45873772_   1094 TCACACTTCCTGATTTCAAAACTTACTGCAAAGCTACAGTAATCAAAACA 1143
                                   ii               i                  i   
  L1M4_orf2#LINE/    215 TCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACA 264

  chr20_45873772_   1144 GTATCATACTGACATAAAGATAGGTGTGTAGACCAAGGGAACAGTACAGA 1193
                           i vi     i     i     iii i    i   v    i  v iv  
  L1M4_orf2#LINE/    265 GTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGA 314

  chr20_45873772_   1194 CAGCCCAGAATTAAACCCTCACATGTAGGG-CAGATGATCTTCGACAAAG 1242
                         v  i      v       vi    v  v  -  iv    i        i 
  L1M4_orf2#LINE/    315 GAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGG 364

  chr20_45873772_   1243 ATGCTAAGACCGCTCAATGGAGAAAGAACAGTCCCTTCAACAAATGGTGT 1292
                         i   i      ii       i       i    ii              i
  L1M4_orf2#LINE/    365 GTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGC 414

  chr20_45873772_   1293 TGCAAAAACTGTATATCTACATACAAAAGAA----------------CCT 1326
                           vi v     v   ? i    i        ----------------   
  L1M4_orf2#LINE/    415 TGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCT 464

  chr20_45873772_   1327 TTTATCATATATAAAAATTAACTCAAAATGGATAAAAAACCTAAACACAA 1376
                         ivi i      i                     v ? i       iii  
  L1M4_orf2#LINE/    465 CACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAA 514

  chr20_45873772_   1377 -ACCTAAAACTGTAAAACTCCTAGAATAAAACATAAGAGAGAAGCTTCAT 1425
                         - v        i        i     v        i ? vi  v    i 
  L1M4_orf2#LINE/    515 GAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGT 564

  chr20_45873772_   1426 GACATTGGATTTGGCAACGATTTATTGAATGTGAAACTAAAAGTGTAGAC 1475
                            v    i  v     i i   v  ii  i   v  i     iii ii 
  L1M4_orf2#LINE/    565 GACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGC 614

  chr20_45873772_   1476 AGCAAAAGAAAAAATAGATACATTGGACTACAGCAATATTAAACACTTT- 1524
                          i                  v        v  v   v      v     -
  L1M4_orf2#LINE/    615 AACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTT 664

  chr20_45873772_   1525 --GCATCTAAAGACAC----AGCAGAGTGAAAGG-TAACCTATGAAATGG 1567
                         --  v  v  i     ---- iv i       i -i    i iii     
  L1M4_orf2#LINE/    665 GTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGG 714

  chr20_45873772_   1568 GAGAAAATGTTTG-AAAT-ATATAT-----AAGGGGCTAATATCCAGGAT 1610
                                 i    -    -      -----     i  vi       i  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAAT 764

  chr20_45873772_   1611 AT-TAAAAACAAACTCCTACAACTCAACAACAAAAAAAGAAATAACCCTA 1659
                           -    i ---    i          i  i     i v         v 
  L1M4_orf2#LINE/    765 ATATAAAGA---ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA 811

  chr20_45873772_   1660 TTATAAAATGAGCAAAGGACTTGAATAAAGATTTCTCCAAAGAAGATATA 1709
                           ?v      i        i       i v                    
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr20_45873772_   1710 CAGATGGCCCATAAACACAAGAAAAGATGCTCAGCACCACTAATCAT 1756
                           i      v    i    v             i  i  ????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.11 (112 / 53)
Gap_init rate = 0.01 (13 / 894), avg. gap size = 3.31 (43 / 13)  


 853 23.03 0.00 0.00  chr20_46057569_46060443.rev     1164  1341 (1534)    L1M4_orf2#LINE/L1        1   178 (730)  

  chr20_46057569_   1164 TGGAGAGATAGTCCAGGTTCATAAATAGGAAGACTCAGTATTGTCAAGAT 1213
                             i     vi   v      ii  v        i i      i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_46057569_   1214 GTCAGCTCTTCCCAACTTGATCAACAGATTCAATGCAATCCCAATCAAAA 1263
                          v  iiv  i     v      v          i        v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_46057569_   1264 TTCCTGCAAGTTATATTGAGGATATTGACAAACCGATTCTAAAGTTTTTA 1313
                          i  v  vivi v v   vi  v        i i   i     i  iv  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_46057569_   1314 TGGAGAAGTAAAAGACCCAGAATAGCCA 1341
                             i v i  ii               
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCA 178

Transitions / transversions = 1.41 (24 / 17)
Gap_init rate = 0.00 (0 / 178), avg. gap size = 0.00 (0 / 0)  

2650 21.02 4.43 2.90  chr20_46057569_46060443.rev     1653  2375 (500)    L1M4_orf2#LINE/L1      160   893 (15)  

  chr20_46057569_   1653 AAGAGACACAGAATAGCCAACACA---TAGTAAAAGA-GAACAAAATTGG 1698
                            i   v            v   --- v v      -       i    
  L1M4_orf2#LINE/    160 AAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr20_46057569_   1699 AGGACTCACACTACCTGACCTCAAGACTTACTGTAAAGCTACAGTAATCA 1748
                                     v  ii ii    i       ii                
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCA 259

  chr20_46057569_   1749 AGACACTATGGTACTGGTC---------ACATTGATAGATCAATGAAACA 1789
                              v i         iv---------    --           i  i 
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACAT--ATAGATCAATGGAATA 307

  chr20_46057569_   1790 GAATAGAGAGCCCAGAAATAGACCCACATAAATAGAGTCAACTAATCTTT 1839
                             v     i         i     i i vv  vi     i i  i  i
  L1M4_orf2#LINE/    308 GAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTC 357

  chr20_46057569_   1840 GACAAAGGAGC-AAAACCAGTACAAATGAGGCAAAGA-----CCTCTCAA 1883
                              i  v  -  i    v -   -  i  -     ----- i i    
  L1M4_orf2#LINE/    358 GACAAGGGTGCCAAGACCATT-CAA-TGGGG-AAAGAATAGTCTTTTCAA 404

  chr20_46057569_   1884 CAAATGGTGCTCCAACAACTGGACATTTACCTGAAAAAAAACAAAACAAA 1933
                                    vvi         i ?ii  v  v    i  ii  ii---
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT--- 451

  chr20_46057569_   1934 ACAATGAACCTAGTCGCACAGTTTACATCCTTTACAAAAGT-AACTCAAA 1982
                         ----  i   ---- vi  --i i   i v v       i -        
  L1M4_orf2#LINE/    452 ----TGGACC----CCTAC--CTCACACCATATACAAAAATTAACTCAAA 491

  chr20_46057569_   1983 ATGGAACACAGACCTAAACATAAAATGC--AGACTATAAAATTCCTAGAA 2030
                              v  ?         ii   i -  -- i         i  i     
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCTTAGAA 540

  chr20_46057569_   2031 GATAACATAGGAGAAAATCAAGATGACCTTGGGTTTGGTGATGACTTTAT 2080
                           v        ? v     vvvi            v  ii   ii  iv 
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_46057569_   2081 AGATG---CACCAAAGGTATAATTCATGAAAGAAAGAATTGATGAGCTGA 2127
                             i---       i i i  viv ii       i   v   i ii  i
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_46057569_   2128 ACTCCATTACAATTGAAA--TGTAATGCTCTGCAAAAGATACTGTCAAGA 2175
                            i   i v    i   -- v vi    i--    i  i   i      
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAGA 688

  chr20_46057569_   2176 GAATGAAAAGGCAAGCCCCAGACTGGGAGAAAATATTTGCAAAAGACACA 2225
                         i i       i   v  v    v                    vv i i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_46057569_   2226 TCTGATAAAGGACTGTTACCCAAAATATAAAAAGAACTCTTAAAACTAAA 2275
                                 i     vv  i   i      v            v    v  
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_46057569_   2276 CAATAAGAAAACAA----TCCAACT-AAAAATGGGTCAAAGATCTTAAAC 2320
                         i     i  i    ----i    i -         iv  i   i v  vv
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr20_46057569_   2321 TACACCTCACCAAAGAAGACGTACAGATGGCAAATAAGCATATAAAAAGA 2370
                         v   ii  v          ii    i     v        i  i      
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA 888

  chr20_46057569_   2371 TGCCC 2375
                            i 
  L1M4_orf2#LINE/    889 TGCTC 893

Transitions / transversions = 1.92 (98 / 51)
Gap_init rate = 0.03 (20 / 734), avg. gap size = 2.65 (53 / 20)  


3778 20.70 1.28 1.74  chr20_46194095_46196603.rev     1150  2009 (500)    L1M4_orf2#LINE/L1        1   856 (52)  

  chr20_46194095_   1150 TGGAGAGATGTCTCATGTTCATGGATTGGAAGACTTAATTCTGTTAAAGT 1199
                             i    i  i                          vi      ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_46194095_   1200 GTCCCTACTACCCTAAGCATTCTACAGATTCAAAGTAATCCCTATCAAAA 1249
                          v vv    v   v  viiv             v i              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_46194095_   1250 TCACATGGAATTTTATTTTTACAGAAAT--ACAAAAAAATTCAGAAATTT 1297
                           v  - vviii  --    i       --    ivvi  i vi     i
  L1M4_orf2#LINE/    101 TCCCA-GCTGCCTT--TTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr20_46194095_   1298 ATATGGAACCACAAAAGACCCAGAATACCCAAAATAATCTTGAAAAACAA 1347
                                 vii   ii           v      i            v  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_46194095_   1348 GAACAAAACCAGAGGCATAACATTTCCTGATCACAAAATATATTACAAAG 1397
                                iiii    vv v   i    ii  iv     iv  i       
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_46194095_   1398 TTATAGTCATTAAAACAGTATGGTACTGGCATAAAGACAGACCTATAGAT 1447
                         i  i   v  i  i     i              i  i    v       
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_46194095_   1448 GAATGGAATTATAATAGAGGGCCCAGAAATAAATACCCAAATAT--ATGG 1495
                         v        - v   v   i i           --    v i  --    
  L1M4_orf2#LINE/    298 CAATGGAAT-AGAATTGAGAGTCCAGAAATAAA--CCCATACATTTATGG 344

  chr20_46194095_   1496 TAGGATGATTTTCAACATGGGTGCCAAGAATACACAATAGGGAAAGGATA 1545
                          viiv        i   v           vi iv    i       i   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_46194095_   1546 GCCTCTTCAATAAATAGTGGTGGGAAAATTGGATATACATATGCAAAAGA 1595
                          i  i     i    i   v     v  i      ?v  i          
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_46194095_   1596 ATGAAATTAGATCCTTATCTTTGTCTTACACCATTTACAAACATCACCTA 1645
                              i  i  i  i  i  i------       v      v  i v  v
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTC------ACACCATATACAAAAATTAACTC 488

  chr20_46194095_   1646 AAAATGGATTAAAGCCTTAAATGTAAGATCTAAAACTATAAAGCTCCTAG 1695
                                  i ?  v i           v             i   i   
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr20_46194095_   1696 AGGAAAGCATAGGGGAAAAT-TTCATGACATTGGTCTTGGCAGTGATTTC 1744
                          i    i      ? v    -   i    v    vi v    i  i    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_46194095_   1745 ATGGATACAACACCAAAAGCATGGGCAACTAAAGCAAAAATAGACAAGTA 1794
                         v i    ii            iii     v    v         i  i v
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATT 638

  chr20_46194095_   1795 CGATGCCA----AACTAAACAGCTTCCGCACAGCGAAGGAAACAATCAGT 1840
                         v  ivi  ----  i    - i   ii ii vv i     v  v    iv
  L1M4_orf2#LINE/    639 GGACTTCATCAAAATTAAA-AACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_46194095_   1841 AGAGTAAAAAGGTAGCCTACAGAATGAGAGAAAATATTTGCAAACTATGT 1890
                          i   i     ii i  i        i                 ii  i 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_46194095_   1891 ATCTGATAAGGGA-TAATTTCCAAAATATATAAGGAACTCCTACAACTTT 1939
                                      - vi v    i         i      i       iv
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_46194095_   1940 ATAGCAAAAAATCCCTAATAACCCAATTAAAAAATGG-CTAAGGATTTCA 1988
                            ii     iv v--            ?        - v        v 
  L1M4_orf2#LINE/    788 ATAATAAAAAGACA--AATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr20_46194095_   1989 ATAGACATTTCTCCAAAGAAG 2009
                                              
  L1M4_orf2#LINE/    836 ATAGACATTTCTCCAAAGAAG 856

Transitions / transversions = 1.68 (109 / 65)
Gap_init rate = 0.02 (13 / 856), avg. gap size = 2.00 (26 / 13)  


 240 20.75 1.89 0.00  chr20_46763334_46764972       72   124 (1515)    L1M4_orf2#LINE/L1      260   313 (595)  

  chr20_46763334_     72 AGGCAACATAGTACT-GTATAAAGATAGGCCTAGAGATCAATGGAAAAGA 120
                           i  iii i     - i    i     i v  v            v   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr20_46763334_    121 ATTG 124
                             
  L1M4_orf2#LINE/    310 ATTG 313

Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1)  

2888 15.46 2.01 6.49  chr20_46763334_46764972      501  1147 (492)    L1M4_orf2#LINE/L1      291   908 (0)  

  chr20_46763334_    501 TAAAAATCAATGCATATCAAAAAAAATTGAGAGTCCAGAAATAAATCCTT 550
                           v i       ------i  v i                     i  v 
  L1M4_orf2#LINE/    291 TATAGATCAATG------GAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr20_46763334_    551 ACATTTATGGTCAGTTAATTTTCCACAAGGATGCCAAGGCAATTAAATGG 600
                                      i  i      v      i       i v   v     
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr20_46763334_    601 ACAAAAGAACTGTCTTTTCAACAAATGATGC------AACTGAATATCCA 644
                         i-i      iv                i   ------     i   ?   
  L1M4_orf2#LINE/    385 G-GAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr20_46763334_    645 TGTGCAACAAAATGAGGCTGG-CCCCTTCCTCATGCCACACACAAAAATG 693
                         ii     v i     i i   -     v     ii   i i        v
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr20_46763334_    694 GACTCAAAATGGATCACAGACCTAAATGTAAGAACTAAAACTATAAAACT 743
                         i               ?                i                
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr20_46763334_    744 GTCAGA-GAAAACACAGGAGTAAACCCCTTGTGACCTTAAGTTAGGCGAA 792
                         v i   -       i   ?     i i- i        ii       i v
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATCT-TCGTGACCTTGGGTTAGGCAAT 582

  chr20_46763334_    793 GTGCTCTTAGATATGAC--CAAATGCACAAGCAACTTAA-AAAAAATAGA 839
                          vvi             --    v           vv  -          
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr20_46763334_    840 TAACGTGAATTTCACCACAATTTAAAACTTCTGTGCTTCAAATGACACTA 889
                            vv  i i    i  v    v       i           v       
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr20_46763334_    890 CCCCAACGTGAAAGCCAAAAAATAAATAAAATTTAAAAGGAAGGGAAAAG 939
                         i ----------------------------------   i   v      
  L1M4_orf2#LINE/    683 TC----------------------------------AAGAAAGTGAAAAG 698

  chr20_46763334_    940 ACAATCTGCCTAATGAG-GAAAATAGT-ATCAATTACACATCTGATGAGG 987
                             i ii vv    i -       v -iiv   i i i       i   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_46763334_    988 AACTTGTACCCAGAATATGTAAAGAACCCTTACAACTTAACAACAAAAAG 1037
                         i       i         i        i         i  i  i      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_46763334_   1038 ATAAATAATACAAGTAAAAAACAGGCATAGGACTTGAACAGACATTTCTC 1087
                          i      iv   v ?     ii    v    i     i           
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_46763334_   1088 CAAAGAAGATACACAAATGTCCAATAAGCAGATGAAAAGATGTTCAACAT 1137
                                    i       v          v           i       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_46763334_   1138 CATGTGGGAA 1147
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.00 (64 / 32)
Gap_init rate = 0.02 (11 / 618), avg. gap size = 5.00 (55 / 11)  


 427 24.17 3.33 2.50  chr20_46827645_46829698      485   604 (1450)    L1M4_orf2#LINE/L1      134   254 (654)  

  chr20_46827645_    485 TAATTCTAATATGTTCATGGTAAGGCAAAGAAACTAGAATAGCCAAAACA 534
                          i  i    v  vivi    v  v    i i v i               
  L1M4_orf2#LINE/    134 TGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACA 183

  chr20_46827645_    535 ATTCTGTAAAAGAA---CAGTGTTGGAGGATTCACATTATCCAGTTTTAA 581
                           ii  v       ---  iv         i     i vi   i   i  
  L1M4_orf2#LINE/    184 ATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAA 233

  chr20_46827645_    582 GAATTATTATGGCCAGGC-ACAGT 604
                         i v   i  --- v i  -     
  L1M4_orf2#LINE/    234 AACTTACTA---CAAAGCTACAGT 254

Transitions / transversions = 1.64 (18 / 11)
Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.33 (7 / 3)  

1971 21.85 6.68 4.25  chr20_46827645_46829698      904  1562 (492)    L1M4_orf2#LINE/L1      234   908 (0)  

  chr20_46827645_    904 AACT-ATTATAAAGTTACAATAATTATGATGATATGGTACTGGTGAAAGG 952
                             - i  i    i    i    i v  iii i         iiv    
  L1M4_orf2#LINE/    234 AACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGG 283

  chr20_46827645_    953 GGAGACACACAGATCAATGGAACAGAAAAGAGAGTACAGGAATTGACCCA 1002
                         iv     i i            i    vv      v   i   vi     
  L1M4_orf2#LINE/    284 ATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCA 333

  chr20_46827645_   1003 CACAAATATGGCCGTTTGACTTTTCATAAGGATGCAAAGGCAATTCCGTA 1052
                         i   vv     i iv    i   iv i    i   v   i v    vi i
  L1M4_orf2#LINE/    334 TACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr20_46827645_   1053 GAGAAAGGACAGTCTTTTAAACTGTTGCTTTAAACCAATGATCTTGGAAC 1102
                          i     i i        --------- ----   v    i vi   i  
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTT---------C----AACAAATGGTGCTGGGAC 420

  chr20_46827645_   1103 AACCACACA-CGATATGCAAATTAATGAACCTCAACCTAAACTACACACT 1151
                            iiv i - v i       vv      vi vi   ivv  iv     i
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACC 470

  chr20_46827645_   1152 TCATACAAAAGTAAACTCAAAATGGATCACAGATCTAAAT-------TCA 1194
                         vi        i v                ?   i      -------ii 
  L1M4_orf2#LINE/    471 ATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTA 520

  chr20_46827645_   1195 AAAC-ATAAAACT-TTAGAAGAAAACA--GGAGAAAATCCTTGTGACCTG 1240
                             -        -             --  ? v     i i       v
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT 570

  chr20_46827645_   1241 AGATTAAGAAAAGAGTTCTTAGATGTGACATTAAAAA---AAGCAAGATC 1287
                         i i   i v  v iv         i     ii    i---      ----
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA---- 616

  chr20_46827645_   1288 CGTAAAAGAAGAAAAGGGATAAATTAGA----A-CAAAAATGAAAACTTT 1332
                         --i       -    vi        i  ---- -     v i        
  L1M4_orf2#LINE/    617 --CAAAAGAA-AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr20_46827645_   1333 TGCCATGCAAAATACACTGTCAAGAGAAC-AAAAGACAAGCTACAGATGG 1381
                           ivv v    iv     i      i ii-         v i     vv 
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr20_46827645_   1382 GGAGAAAATATTTACAAATGACATATCTGACAAAGGATTTATATTCAGAA 1431
                                      i     v i        i  i   i  i   i     
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr20_46827645_   1432 TACA------ACCCT---AAATTAACAA----AGGA--AACAAGCCAAAA 1466
                           i ------  i  ---  v i  i  ---- i  --  i  v    --
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAA-- 811

  chr20_46827645_   1467 TTTTTAA---TGGATTAAAAAACTTGAACAT---TTTCTTCACCCAAGAA 1510
                         --  ?  ---   ii-   ii i     i v---     i  ---     
  L1M4_orf2#LINE/    812 --TTWAAAAATGGGC-AAAGGATTTGAATAGACATTTCTCCA---AAGAA 855

  chr20_46827645_   1511 G-TATATAAATGGTAAATATGCACATGAAAAGATAGGCAGCATCATTAGC 1559
                          -    i      iv    v              ivv  i     ?????
  L1M4_orf2#LINE/    856 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZ 905

  chr20_46827645_   1560 GAT 1562
                         ???
  L1M4_orf2#LINE/    906 ZZZ 908

Transitions / transversions = 1.88 (92 / 49)
Gap_init rate = 0.04 (24 / 675), avg. gap size = 3.00 (72 / 24)  


3219 26.00 1.56 0.67  chr20_47027172_47033571.rev     5009  5908 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_47027172_   5009 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 5058
                              ii i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_47027172_   5059 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5108
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_47027172_   5109 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5156
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_47027172_   5157 TATGGAACCGAAAAAGAGCGCACATTGCCAAGACAATCCTAAGCAAAAAG 5206
                                vi v  ii  v vviv  v     i      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_47027172_   5207 AACAAATCTAGAGGCATCACACTACCTGACTTCAAACTATACTACAACGC 5256
                               vi i    vv       v  ii i      viv        v  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_47027172_   5257 TA-----ACCAAAACAGCATGGTACTGGTACCAAAACAGAGAGACAGACC 5301
                           ----- i   i    ii         i iv ii i   v v i   i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_47027172_   5302 AATGGAACAGCAC--AGAGTCCTCAGAAATA---CCATGCATCTACAACC 5346
                                i  v i--       --       ---    i   i  iiii 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_47027172_   5347 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTTC 5396
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_47027172_   5397 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5446
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_47027172_   5447 GAAACTGGATCCCTTCCTTATACCTTAGACAAAAATTAATTCAAGATGGA 5496
                            ii    i    v   i i   v  v           i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_47027172_   5497 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACTCT-AGAAGAAAA 5545
                          i ?    i       v   v       i      -    -         
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAA 545

  chr20_47027172_   5546 CCTAGGCA-ATACCATTCAGGAACTAGGCGTGGGCAAGGACTTCATGACT 5594
                          v    ?i- v i -   iv  v  v  vv i     v ii   v iiv 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_47027172_   5595 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATAGACAAATGGGATCT 5644
                          vi            vvi          vv        i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_47027172_   5645 AATTAAACGAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGA 5694
                         v  i   vvv  i i   i  ii vv    i  v    i  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_47027172_   5695 ACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTACCCATCTGAC 5744
                          v  i     i                 v       vii ivi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_47027172_   5745 AAAGGGCTAATATCCAGAATCTACAAAGAACTTAAACAAATTTACAAGAA 5794
                           i  i  vi          v  i        ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_47027172_   5795 AAAAACAAGCAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACT 5844
                            i    ii     v  i?    i            v    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_47027172_   5845 GCTCAAAAGAAGACATTTATGTAGCCAACGGACACATGAAAAAATGCTCA 5894
                         v   v        i  vi vi i     iiii          i       
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_47027172_   5895 TCATCACTGGTCGT 5908
                         v     ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (138 / 92)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 1.82 (20 / 11)  


 682 20.71 8.88 0.59  chr20_47157150_47159557      501   669 (1739)    L1M4_orf2#LINE/L1      113   295 (613)  

  chr20_47157150_    501 TTTTTGTGGACATAGAAAAGCCCATCCTAAAATTTATAAGGAATCCTAAG 550
                               ii  v  v  v    iv           i   v    vivi   
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr20_47157150_    551 GGACCCTGAATAACCAAAAACAATCTTGAAAA-------CTTAGCTGAAG 593
                               v     i      -            ------- vv  i  i  
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAA-CAATCTTGAAAAAGAAGAACAAAGTTGGAG 211

  chr20_47157150_    594 GACTCATAGGTTAAGATTTCAAAATTTACTACA--------GTAATCAAA 635
                               i vv ivvi         i        --------        i
  L1M4_orf2#LINE/    212 GACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAG 261

  chr20_47157150_    636 TCAGTGTGGTACCAGCACAACAACAGACATATAG 669
                         v           ii   i  vi i          
  L1M4_orf2#LINE/    262 ACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

Transitions / transversions = 1.19 (19 / 16)
Gap_init rate = 0.02 (3 / 183), avg. gap size = 5.33 (16 / 3)  

2286 17.46 7.58 2.47  chr20_47157150_47159557     1351  1917 (491)    L1M4_orf2#LINE/L1      313   908 (0)  

  chr20_47157150_   1351 GAGAATCCAGAAGT----CCTTCCATGTA----------ATTTTTGACAA 1386
                             i       i ----  v v   v  ----------     i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr20_47157150_   1387 GGGTGCCAAGACCATTCAATGGGGGAGGGACAGTCTTTTCA-CAAATACT 1435
                                                 i i i i          -     iv 
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr20_47157150_   1436 GTTGGGAAAACAG--TGTGCACTTGCCAAGGAATGAAGCTGGACCCTTAC 1483
                          i     v   v -- i?v   v   v  i        i       i   
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr20_47157150_   1484 CTAACACCATACACAAAA-TTAGCTTAAAATGGATGAAAGACCTAAATCT 1532
                           v        i      -   i  i         v ?          v 
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr20_47157150_   1533 AAGA-CTAAAACTA--AAACAT---GAGGCAAATC----CGCAAATCTTC 1572
                             -         --    vi---  i v   iv----? i        
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTC 562

  chr20_47157150_   1573 ATGAG-TTGGACTTAGCAATGTTTTCTTAAGTATGACACCAGAA--ACAG 1619
                         i   v-    ii vi      v       ii          i  --   i
  L1M4_orf2#LINE/    563 GTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr20_47157150_   1620 GCAACAAAAGAAAGTAATAGACAAACTAGACTTCATCAAAATTAAAACCT 1669
                                      i-      i   i i                   v  
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAA-AATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr20_47157150_   1670 TTTTTGCATCAAAAGCTTTTCTGCAAAAAGCTTTTGCAGAATGAAAAAAC 1719
                            v   v     i vivi v -   i  ---------- i      i  
  L1M4_orf2#LINE/    662 TTTGTGCTTCAAAGGACACTAT-CAAGAA----------AGTGAAAAGAC 700

  chr20_47157150_   1720 AACTCACAGAATGGGAAGAAAAAAACTGCAAGTCACAT--CTGTTAAGGG 1767
                            i            -     v vi     i   i  --   v      
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGA-GAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_47157150_   1768 ATTAATATCCAGAATACACACAATACTCCTAAAATTCAACAACAAG---- 1813
                          i vi           i i v iv    i  v  i    i  i  i----
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_47157150_   1814 CAACATGATTCAA--AAAAAATGGGCAA--GACTTGGACAGACATTTATC 1859
                            -  i ii   --?            --  i   i i        v  
  L1M4_orf2#LINE/    800 CAA-ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_47157150_   1860 CAAAGAAGATAGACAAATGGCCAATAAATAC--GAAAAGATGTTCAACAT 1907
                                    v               ii  --         i       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_47157150_   1908 CGTTAGGGAA 1917
                          i????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.88 (62 / 33)
Gap_init rate = 0.04 (21 / 596), avg. gap size = 2.71 (57 / 21)  


 817 28.03 11.46 5.93  chr20_47537292_47539019.rev      501  1242 (486)    L1M4_orf2#LINE/L1      126   908 (0)  

  chr20_47537292_    501 TAACAAACTTA--CTAAAAAGTTTGTAGAGAGGAT-TAAAGGTCCACAAA 547
                          i    i  v --      --  ii  vi  i-  -i  i  v  vvi  
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAA--TTCATATGGAA-ATGCAAGGGACCCAGAA 172

  chr20_47537292_    548 TAGCCAAGTGTGCCCTAAAAAAGAACAAAGAAGAGAGACAAGGGCTACAG 597
                                ivvvii i i        v  vi   vvi  ---  i  -  -
  L1M4_orf2#LINE/    173 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA---GGACT-CA- 217

  chr20_47537292_    598 GCACT----------AAAGCTCACTATAAAGCCATGCTAATAAAAACAGG 637
                         -    ----------   i  i    i     i iiv    v  i    v
  L1M4_orf2#LINE/    218 -CACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr20_47537292_    638 ACCACAGTGACATAAGCACAAGA-----AGCCCAATGGAGCAGAGTGGGG 682
                         iivii v  i      v i -  -----  vi       ii   i v i 
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATA-GACATATAGATCAATGGAATAGAATTGAG 315

  chr20_47537292_    683 AGTGCAAGA------------------GGC---TTCATAT--GACAAAGG 709
                            v  ii ------------------  i---  v  v --     i  
  L1M4_orf2#LINE/    316 AGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

  chr20_47537292_    710 TGGCCCACAGATCAGC---TGGGGAAAGGACAAGTTATTTCA-TAGGTAG 755
                           --   -   i  vi---         i i -  iv     -i ii i 
  L1M4_orf2#LINE/    366 TG--CCA-AGACCATTCAATGGGGAAAGAATA-GTCTTTTCAACAAATGG 411

  chr20_47537292_    756 TTTTCAGAAAACTAGCCAGCTATAGG-GAATGAATGAAGTTGGCTCCCTA 804
                          vi vi  v    i vi ? i i v -i  v            vi     
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr20_47537292_    805 CCAAATCACACACACACACACACACACACACACACACACACACACACACA 854
                           ---      -----------------  i i   v v ivv  v  v 
  L1M4_orf2#LINE/    462 CC---TCACAC-----------------CATATACAAAAATTAACTCAAA 491

  chr20_47537292_    855 ATTGGTTAAAGACCTAAA-GTAAAAAATAAAAATATAAAATTAATA-AAC 902
                           v i i ?         -    i iv     v       i vv  -  v
  L1M4_orf2#LINE/    492 ATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAG 541

  chr20_47537292_    903 AAAAC-----------TGTTTGCAACTTAGGGGCAGGGGAGGA---CTCA 938
                              ----------- v  i ii  i v   vi   vi v i---  i 
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_47537292_    939 AACAAAAACTTTAAAAGCACAAACTATACAGCCAAAAATAGATTATCTTG 988
                         i i vi - vii          i v i v ivv          v vi v 
  L1M4_orf2#LINE/    592 GATATGA-CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_47537292_    989 A--TCACT----TTAAAAAGATTTCTGCTTAATAAAGGACACCAT-AGGC 1031
                          --   ii----       vv   v     --i         i  - i -
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTT--CAAAGGACACTATCAAG- 687

  chr20_47537292_   1032 AAAGTTAACAGGTAGGTGACAAAGCAGAAGAAGATATTTGCAATGTCTAA 1081
                              v  v  ii iviv   i iii i    i          -i  vv 
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAA-ATCATA 736

  chr20_47537292_   1082 AATCC-ACAAGGGACTTAAAATCTGCATTATACAAAGGAATCCTGCAAAT 1130
                         v   i- i         iv -  iiv v    i    i v  i i   v 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTA-TCCAGAATATATAAAGAACTCTTACAACT 785

  chr20_47537292_   1131 CATCAAGAAAAAAACAGGAATCCTGATAGAAAAATGGGCCACT-ATGTGC 1179
                           vi  v     i   iiv v  ii  v?          v vv-  v  v
  L1M4_orf2#LINE/    786 CAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGA 835

  chr20_47537292_   1180 ACAGGTGATATTT-------------ATACAAGAGAACAATAAGCATATG 1216
                          i  --- i    -------------      iv iv         i   
  L1M4_orf2#LINE/    836 ATAG---ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_47537292_   1217 AAGAGAGTCTCAGAC-TCATTAGTAAT 1242
                           i   vv    -  -   ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCA-ACATCAZZZZZZZZ 908

Transitions / transversions = 1.36 (118 / 87)
Gap_init rate = 0.05 (39 / 783), avg. gap size = 3.31 (129 / 39)  


2200 26.59 1.11 3.32  chr20_48385432_48387145      501  1222 (492)    L1M4_orf2#LINE/L1      203   908 (0)  

  chr20_48385432_    501 AGGTGGGAGGGCTCAT--TTGATGCAATGCTAAGGTTTACTGTTCAGCTG 548
                          i  v     i    i--  --iv    vii  iii     iivv    i
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTT--CCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_48385432_    549 TGGTAATCAAGACAGTCTGGT--TGGCAGAGGGACAGATGCATGCAACAG 596
                         ii              v    --     v i   i   iii  iv v  i
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_48385432_    597 TGGAACAGAGTAGAGAACCCAAGAATAGACACGCACAAATGTGCCCAAAA 646
                              i   i v    ii   ii    i  v ii   vv i  vi   vv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_48385432_    647 GATTTTTGACAAAGATGCAAAAGCAGTTCAATGGAAGATAAAAAGCCTTT 696
                               i     i i   v  ii vi        iii vi  v  i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_48385432_    697 TCAACAGATCGTGCTGGGGCAATTTGACATCCACACGCAAGA-AACAAAG 745
                               i  v        i   i v  i ?     i    i -  ii   
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_48385432_    746 CACATTGACCTAAACCTCACACGTTATACAAAACTTCACTCAAAATGGAT 795
                         i--- v    ivv         vv         v  v             
  L1M4_orf2#LINE/    451 T---TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_48385432_    796 CATAGACTTAAAGATAAAACATAAAGCTATAAAACATTTAGAAAAAAGCA 845
                           ?    i    vi   i vv    i         vi      i   i  
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_48385432_    846 --GGAGAAAATCAGTCTTCAGAATCTAAGGCTAGGCAAAGAATTACTAGA 893
                         --  ? v     ----   ivi i  vi  i       v iv  vi    
  L1M4_orf2#LINE/    548 TAGGNGTAAATC----TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_48385432_    894 TGTGAAAACCAAAAGCACAATTCATAAAAGGAAAAAAATTGATAAATCGG 943
                          i   v -            viv i     --       v       i  
  L1M4_orf2#LINE/    594 TATGACA-CCAAAAGCACAAGCAACAAAAG--AAAAAATAGATAAATTGG 640

  chr20_48385432_    944 ACCTCATCAAAGTTGAAAACTTTTAACCCATGAGAGGCCCAATTAAGAGG 993
                           i        i  i         ivv ivii ii i v v  i    ii
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_48385432_    994 AGGAAAAGACAAGCTACAGATTAGGAGAATATATTTGCAAACTGCATATC 1043
                         iv          v i     v i      v           iiii     
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_48385432_   1044 TGACAAAGAACTAGTACCTAGAATTCTTAAAACTTGACGGAATTCTCGAG 1093
                            i  i i   v   i i     viv    --------   i   i- v
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAA--------GAACTCTT-AC 781

  chr20_48385432_   1094 AACTCTCAAAAGTCAGCAGTTAAAAAAATCCAAATAGAAAATGAGCAAAA 1143
                              --  v i v iv  vi   v  -i    v ?i      i     i
  L1M4_orf2#LINE/    782 AACTC--AATAATAAAAAGACAAATAA-CCCAATTWAAAAATGGGCAAAG 828

  chr20_48385432_   1144 GACACAAACAAATATTTCACTGAAAAGAACATGCAGATGGA-AATAAACA 1192
                           ivii  i i i     v ii  i ii i  i  i    v-     i  
  L1M4_orf2#LINE/    829 GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCA 878

  chr20_48385432_   1193 CATGAAAAAATGTTCAACATCATTAGCCAT 1222
                                 i   i         ????????
  L1M4_orf2#LINE/    879 CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (123 / 65)
Gap_init rate = 0.02 (14 / 706), avg. gap size = 2.29 (32 / 14)  


 875 27.13 0.00 0.00  chr20_48858053_48860586.rev      889  1135 (1399)    L1M4_orf2#LINE/L1        1   247 (661)  

  chr20_48858053_    889 TGGAAACATATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAAT 938
                               v          i        v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_48858053_    939 GACCATACTGCCAAAAGCAATCTACAAATTCAATGTAATTCCCATCAAAA 988
                          i v     v  v   vii       i      i i   i  i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_48858053_    989 TACCACCATCGTTCTTCATGGAACTAGAAAAAAAAATCCTAAAATTCATA 1038
                          v   v vv v  i  iiii   v v  v  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_48858053_   1039 TGGAACCAAAAAAGAGCCCTCACAGCCAAAGCAAAACTAAGCAAAAAGAA 1088
                              viiv  ii  v  vvv i       i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_48858053_   1089 CAAATCTGGAGGCATCACATTACCTGATTTCAAAATATACTATAAAG 1135
                             vi      vv     i v  ii         iv     i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

Transitions / transversions = 1.03 (34 / 33)
Gap_init rate = 0.00 (0 / 247), avg. gap size = 0.00 (0 / 0)  

2108 23.92 4.82 0.33  chr20_48858053_48860586.rev     1441  2042 (492)    L1M4_orf2#LINE/L1      280   908 (0)  

  chr20_48858053_   1441 AAAAATAGGCACATAGACCAATGGAACAGAACAGAGA-CCCAGAAATAAA 1489
                           ii    i  i     i        i    iv    -i           
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr20_48858053_   1490 CCCAAATACTTACAGCCAACTGATCTTTGACAAAGTAAACAAAAACCAG- 1538
                             v i i   ii i   i    i  i     i -ivi v  i    v-
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTTTCGACAAGG-GTGCCAAGACCATT 378

  chr20_48858053_   1539 AAGTGGAGAAAGGACACCCTATTCAACAAATGCTGCTGGGATAATTGGCT 1588
                         v i   i     i i vi  v           v        i  i   v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr20_48858053_   1589 AGCCACATGTAGAAGAATGAAACTGGATCCTCATCTCTCACCTTATACAA 1638
                          ?       i i         ii    i  ii i   v    v       
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr20_48858053_   1639 AAATCAACTCAAGATGCATCAAACACTTAAATCTAAGACCTGAAACCATA 1688
                             i       i   v    ? v  i     v     v  i    i   
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr20_48858053_   1689 AAAATTCTAGAAGATAACATTGGAAAAACGCTTCTAGAGATTGGCTTAGG 1738
                            v ii       v     v  ?iv  vv    vv  vv    v     
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr20_48858053_   1739 CAAAGACTTTATGACCAAGAACCCAAAAGCAAATGCAATAAAAACAAAGA 1788
                            v ii  iv iivi v  vv         v v    i    iv   i 
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

  chr20_48858053_   1789 TAAATAGGTGGGACTT-----AAACTAAAAAGCTTCTGCACAGCAAAAGA 1833
                           i   ii v      -----   i      -   i  ii vv    i  
  L1M4_orf2#LINE/    629 TAGATAAATTGGACTTCATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGA 677

  chr20_48858053_   1834 AATAATCAGCAGAGTAAACAGACAACCCACAGAGTGGGAGAAAATCTTCA 1883
                         v iv    iv i   i  v              i           v  ii
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr20_48858053_   1884 CAATCTATGCATCTGACAAGGGATTAATATCCAGAATA------------ 1921
                            vii  ii      i      i vi           ------------
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr20_48858053_   1922 ------CTAAGCAAGAAAAAAA-AAAT--CCCA-TCAAAAAGTGAGCAAA 1961
                         ------  v ii  v     i -    --    - i?    i  i     
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr20_48858053_   1962 GGACATGAATAGACAGTTCTCAAAACAAGATATACAAGTGGCCAACAAAC 2011
                            iv          v     v   v           i       i  i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr20_48858053_   2012 ATATGAAAAACTGATCAACATCACTAATGAT 2042
                          i       iv  v         ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (86 / 54)
Gap_init rate = 0.01 (9 / 629), avg. gap size = 3.44 (31 / 9)  


1184 27.85 8.22 3.20  chr20_49199518_49203136     2019  2456 (1163)    L1M4_orf2#LINE/L1        3   462 (446)  

  chr20_49199518_   2019 GAGAGATA--CTATATTCATGAATTGGAAGGTTCGATATTGTAAAGCTAT 2066
                           i     -- i  i      i        ii ii       v   v iv
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_49199518_   2067 CAGTTCTCACGAAAT----CTACAGGTACGGTGCAATCC---TCACAATC 2109
                           i v   v v    ----      i v iii       ---   v    
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_49199518_   2110 TCAACAGGTTTCTTTTTTGTGTTTGGAAATTGATAAACTGATTCTTAAAT 2159
                         i  i v ---i        ii----        i  i     i  v    
  L1M4_orf2#LINE/    103 CCAGCTG---CCTTTTTTGCA----GAAATTGACAAGCTGATCCTAAAAT 145

  chr20_49199518_   2160 TTATACAAAAATGTAAAAGTCCAGGGACAACCAAGACAACC----ACAGA 2205
                          i   iii     i  ii v  vi i i i    i    i ---- v ii
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_49199518_   2206 AAGGACAAAGTTGGAGGA------------------AAGACTTAGTAACA 2237
                            i              ------------------  i     v  vv 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_49199518_   2238 GATGACAATAACGAGGAGAGTGTAATATTTGTGCAAGGATACACAAGCAG 2287
                         iiiv   i   iv i  v     ii  i v iii       v   vii  
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_49199518_   2288 ACCAGCAAAAAAGAATAGCAGTTTCTAGAAACAGACCCACAAATATAAAG 2337
                          i  iiii  v     v -  vv  i     i i     i v  v  vi 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTG-AGAGTCCAGAAATAAACCCATACATTTATGG 344

  chr20_49199518_   2338 TAACATGATTTATGACAAAGGTG-----GCCTTTCTGAGTAATGGGGAAA 2382
                          v vv      vi     i    -----i  v   -----          
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTC-----AATGGGGAAA 389

  chr20_49199518_   2383 GAGTGGTCCTTTCAACAGATATAGCTGGGTCAATCAGCTATCCATAAGGA 2432
                           i i   i        i  ivv      v   iii v  ?   i v v 
  L1M4_orf2#LINE/    390 GAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCA 439

  chr20_49199518_   2433 AAAGTGGTGAAACTTGACTCCTAC 2456
                             -ii    ii v   i     
  L1M4_orf2#LINE/    440 AAAG-AATGAAGTTGGACCCCTAC 462

Transitions / transversions = 1.95 (80 / 41)
Gap_init rate = 0.02 (11 / 460), avg. gap size = 4.55 (50 / 11)  

 719 28.53 11.71 0.00  chr20_49199518_49203136     2787  3119 (500)    L1M4_orf2#LINE/L1      493   864 (44)  

  chr20_49199518_   2787 TGGATTTTAAATCTAAATATGAAAGGTAAAACAATAAAGCCACTGGAGGA 2836
                              iv? i i      i i i  v      v     i ivi i  i  
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_49199518_   2837 -----TAGGAGAATATCTTTACGACTTTGGGGCAAGAAAAGATTTCTTAA 2881
                         -----    ? v v     iii   i     vi i v  v i       i
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr20_49199518_   2882 GTAAGGCACGAATAGCACTTACCATAAATGAAAGACC-TATACATTGGAT 2930
                         i  v i   v  v     vvi v i   v    i vi-v   v      i
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGAC 642

  chr20_49199518_   2931 TACATTAAAATTAAGAACTTTTGTTCATCAA--GTCAC-GTTAAGAAAAT 2977
                          v   i        i         v v    -- v   -i i      i 
  L1M4_orf2#LINE/    643 TTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGT 692

  chr20_49199518_   2978 GA-----CAATC---AGAATGAGTGAGG-TGTTTGCAATACAAATTACTG 3018
                           -----   i ---      i v  ii- i       vv  v  vv   
  L1M4_orf2#LINE/    693 GAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG 742

  chr20_49199518_   3019 AAAAAAGGGTCATATTCACAATATGTCATGAATTTTTACAAAGCAATAAG 3068
                          v  ii iv ii   i  v     i v v   i i      vv      v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_49199518_   3069 AAAAGGA-------------------ATAGGAAAAAAATATAAATAAAC- 3098
                             i  -------------------  i  v   ii  v i    i  -
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_49199518_   3099 -TTCACGAAAGAAGATATTCAA 3119
                         -   v v           v   
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAA 864

Transitions / transversions = 1.21 (51 / 42)
Gap_init rate = 0.02 (9 / 372), avg. gap size = 4.33 (39 / 9)  


3559 24.50 0.99 0.77  chr20_50555213_50559429     2821  3726 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_50555213_   2821 TGGAAATATACTTCATGTTTTCATAGATTGGCAGAATCAATATTGTTAAA 2870
                               v   iii      --   i      v   v i           i
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTT--CATGGATTGGAAGACTTAATATTGTTAAG 48

  chr20_50555213_   2871 ATGTCCACACTACCCAAAGCAATCTACAGATTAAATGCAATCTCTATCAA 2920
                            v v i   v      vii           v  i      i       
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr20_50555213_   2921 AATACCAATGACTTTCTTCACAGAAATAGAAAAAAAAATCCTAAAATTTA 2970
                            v   iivi i  i  ii       v  v  ivvi           i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_50555213_   2971 TTGAGAACTACAAAAGACCCATAATAGTCAAATATATCCTGAGAAAAAAA 3020
                          vvi   v i   ii      v     i    vvv   i   -    i  
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGA-AAAAGAA 197

  chr20_50555213_   3021 GAACAAAACTGAAGTAATCACATTACCTGACTTCCAG--TTATCCTATGG 3068
                                ii  i  v v     i v  ii i   v i--   --   iii
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA--CTACAA 245

  chr20_50555213_   3069 AGCTATAGTAACAAAAGCAGCATGGTACTGACATAA----AGACACATAG 3114
                              i     iv  ii   ii        i     ----     i    
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_50555213_   3115 ACCAATAGAACAGAATAGAAAACCCAGAAATAAATCCATGCGTCTTCAGT 3164
                          i    i   i     v  i ii           i    i i i vii  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_50555213_   3165 GAACTCATTTTTGACAGAGGTGCCAAGAATATACACTGGGGTGAGGACAG 3214
                         v  i v     i    ii          vi  v  v     vi  i i  
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_50555213_   3215 TCTCTTCAATAAGTGGTGCTGTGAAAACTGGATATCCATATGCAGCAGAA 3264
                            i     i  i        v  v         ?   i     iv    
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_50555213_   3265 TGAAACTATACCCCTATCTCTTGCCATATACAAAAACCAAAT-AAAATGA 3313
                             ii iv       i   vii             ii  v -      i
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_50555213_   3314 ATTAAAGACTTAAATCTAAAACCTCAAACTATGAAACTACTTA-AAGAAA 3362
                           i ?    i     v   i v  v       i     -    -      
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT-CTTAGAAGAAA 544

  chr20_50555213_   3363 ACATTGAGGAAACTCTCCAGGATGTTGGACTGGGCAAAGATTTCTTGAGT 3412
                             v i? v  v   i iv  iv    ii i     v i      iii 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_50555213_   3413 AATACCCCACAAGCACAGACAACCAAAGCAAAAATAGACAAATGGGATAA 3462
                          vv  v   v       ii    v    v         i    v   ivv
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_50555213_   3463 CATCAAG-TTAAAAAGCTTCTGCACAGCAAAGGAAATCATCAACAAAGTG 3511
                               i-       -   i  ii vv       v ii     v      
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_50555213_   3512 AAAAGGCAACCCACAGAATGGAAGAAAATATTTGCAAACTACCCATCTGA 3561
                              i               i                ii ivi      
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_50555213_   3562 CGAGGGATTAATAACCAGAATACATAAATAGCTCAAACAACTCTGTTGGA 3611
                         ii     i vi  v        i     v i   vv       vi viv 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_50555213_   3612 AAAAATCCAACGACCTGATTTAAAAATGAGTAAAAGGTCTGAATAGAGAT 3661
                             iv v  ii   ii   ?       i i   i i i        v  
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_50555213_   3662 TTCTCAAAAGAAGTCATACAAAGGATAAACAGGTATATGAAAAGGTGCTC 3711
                              v       vi       v iiv  i i i i        i     
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_50555213_   3712 AATATCCTTGATCAT 3726
                           i   v????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.76 (139 / 79)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.60 (16 / 10)  


3072 26.45 0.65 3.01  chr20_50592398_50599128     5310  6239 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_50592398_   5310 TGGAAGAACATTCCATGCTCGTGGATAGGAAGAATCAATATCGTGAAAAT 5359
                              ii i  i     i  i     v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_50592398_   5360 GACCATACTGCCCAAGGTAATTTATAGATTCAGTGCCATCCCCATCAAGC 5409
                          i v     v     iv i  i  i       ii  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_50592398_   5410 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAAACT-ACTTTAAAGTTC 5457
                          v   iivi i  i  ii     -   --- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG---ACAAGCTGATCCTAAAATTC 147

  chr20_50592398_   5458 ATGTGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAA 5507
                           i     viiv  ii  v  v v  v     i      i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_50592398_   5508 GAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGG 5557
                                 i      vv    i  v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_50592398_   5558 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGCATGGTACTG 5607
                                  i   i    ii         i -------------------
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCA------------------- 278

  chr20_50592398_   5608 GTACCAAAACAGAGATGTAGACCAATGGAACAGAAC--AGAGCCCTCAGA 5655
                         -  -- ii i   v  i    i        i    i--    i  --   
  L1M4_orf2#LINE/    279 -TA--AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC--AGA 323

  chr20_50592398_   5656 AATAATACCACACGTCTACAACCATCTGATCTTTGACAAACCTGACAAAA 5705
                              vv   i  i i  iiii  vi    i  i     ivv  v   i 
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGA 373

  chr20_50592398_   5706 GCAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAAC 5755
                         v  vvv           i  vvi  v  i  i              v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr20_50592398_   5756 TGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCTTTACACCTTA 5805
                            v  ?   i   i i  iiv    ii    i    v i i     v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr20_50592398_   5806 TACAAAAATTAATTCAAGACGGATTAGAGACTTAAATGTTAGACCTAAAA 5855
                                     i    i i    i ?    i       v   v      
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr20_50592398_   5856 CCATAAAAACCCTAGAA-AAATCCTAGGCA-ATACCATTCAGGATGTAGG 5903
                          i      vi i     -   v v    ?i- v i -   iv  iv v  
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGG 572

  chr20_50592398_   5904 CATGGGCAAGGACTTCATGTCTGAAACACCAAAAGCAATGGCAACAAAAG 5953
                         vv i     v ii   v ivv ivi            vvi          
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_50592398_   5954 CCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA 6003
                         vv     v  i    v   ii v  i   v v  i i   i  ii vv  
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_50592398_   6004 AAAGAAACTACCATCAGAGTGAACAAGCAATCTACAGAATGGGAGAACAT 6053
                           i  v    i  vv i      v ii   i i              v  
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_50592398_   6054 TTTTGCAATCTACCCATCTGACAAAGGGCTAATATCCAGAATCTACAAAG 6103
                         v       vii ivi      i  i  i  vi          v  i    
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_50592398_   6104 AACTTAAACAAATTTACAAGAAAAAATCAAACAACCCCATCAACAAGTGG 6153
                             ivv    v iv i  v     iv    i     v  i? v  i   
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_50592398_   6154 GTGAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAA 6203
                          ii      v    i     i     v        i  vi viii     
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_50592398_   6204 AAAACACATGAAAAAATGCTCATCATCACTGGCCAT 6239
                         v  i          i       v     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.57 (148 / 94)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 3.40 (34 / 10)  


2794 26.16 3.95 1.58  chr20_50605142_50609274.rev     2755  3641 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_50605142_   2755 TGGAAGAATATTCCATGCTCATTTATCAAAAGAGTTAATATTGTTAAAAT 2804
                              ii    i     i    vv  iii    v             i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_50605142_   2805 GAC--------CCAAAGCAATCTATAGATTCAATGTAATCTCTATCAAAA 2846
                          i --------     vii     i        i i    i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_50605142_   2847 TACCAATGATATTCTTCACTGAAATAGAAAAAAAAATC-TAAAATTTGGA 2895
                          v   iiviiv  i  ii v     v  v  ivvi   -       iiv 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_50605142_   2896 TGTAACCACAGAATATCCTGAATATCCAAAGGAATCCTGAGCAAAAAGAA 2945
                           v  vii  iiiv i  v     v     iv    i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_50605142_   2946 CAAAGCTGGAGGTATCACACTACC--------AGACCTA-----AAGATA 2982
                              i      vv       v  -------- i  i  -----   v  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_50605142_   2983 TATTA--CAAAATAGCATGGTACTGACATAAAAATAGATCCATAGGCTAA 3030
                         i v  --   i i  ii        i     ii     ivi    iii  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_50605142_   3031 TGGGACAGAACAGAGAACCCAGAAATTAATCCACATATCTACAGCCAACT 3080
                            i i    iv    ii        v  i   i i  i  ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_50605142_   3081 GATTTTTTACAAAAGTACCGAAAC-ACTCATTTGGGGGAAAGGACAGTCT 3129
                               iv    ii  i  i i  - i   v --        i i     
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAAT--GGGGAAAGAATAGTCT 398

  chr20_50605142_   3130 CTTCAATAAGTGGTGCTGGGAAAACCAGAGATCCATGTGCAAAAGAATAA 3179
                         i     i  i           v   ii  v ?   ii           i 
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_50605142_   3180 AACTAGACCCCCATCTCTCACTCTATACAAAAATGGACTCAAAATGGATC 3229
                          ii i      i i   v   iv           vi              
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_50605142_   3230 AACGTCCTAAATATAA-AGTTCAAAACAATAAAACTACTGAAAGAAAACA 3278
                          ?v v       i   -  i -     v        vi ii         
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCT-AAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_50605142_   3279 ACAGGGGAAACACTTCAAGACATTGG-TCAGAAAAAATATTTTATGAATT 3327
                         -i   ? v  vv    iv   v    - i  iv  -- iv   v v iv 
  L1M4_orf2#LINE/    548 -TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA--TGGTTTCTTAGAT 594

  chr20_50605142_   3328 AAGACCTCAAAAGCACAGAGAGCAAAAGCAAAAATAAACAAAAGGGATTA 3377
                          v   vi          iiv i      v       i i   vv   i v
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_50605142_   3378 TATCAAG-CTAAAAA-------GCTTCCAAAAGAAGAGAAAACAACATAG 3419
                         i     i-i      -------     --    i v vv v-   v v  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTC--AAAGGACACTAT-CAAGAAAG 691

  chr20_50605142_   3420 TGAAAAAACAACTTCTAAAATAGGAGAAAATATTTGCAAACTTCTCATCT 3469
                               i     iivi i   i                  iivivi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_50605142_   3470 CACAGCGAATTAATGTCCAGAATTTACAAGGGATCCAAACATCTCAACAG 3519
                         v i iv i i vi i        v  i  i i ii vv   v     i -
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA- 790

  chr20_50605142_   3520 CAAAAAAAAAAAACAAACAATCCAATTTAAAAATGAGCAAATGATCCGAA 3569
                         ---- v     i     i  i      ?       i     v   ii   
  L1M4_orf2#LINE/    791 ----ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_50605142_   3570 CAGACATTTCTCAAAAGAAAATACACAGATGACCAACAAATGTATTTTAA 3619
                         i           v      i   i   i   i    i  iiii  vvv  
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_50605142_   3620 AATGCTCAACATCATTAATTAT 3641
                         i             ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.92 (150 / 78)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.88 (49 / 17)  


3319 25.88 1.00 0.55  chr20_51505758_51512012.rev     4860  5763 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_51505758_   4860 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4909
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_51505758_   4910 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4959
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_51505758_   4960 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5006
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_51505758_   5007 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAA 5056
                                 viiv  ii  v  v v  v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_51505758_   5057 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5106
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_51505758_   5107 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5156
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_51505758_   5157 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5204
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr20_51505758_   5205 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5254
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_51505758_   5255 CCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5304
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_51505758_   5305 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5354
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_51505758_   5355 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5404
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_51505758_   5405 CCTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5454
                          v    ?v v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_51505758_   5455 AAACACCAAAAGCAAAGGCAACAAAAGACAAAATTTACAAATGGGATCTA 5504
                         vi            v i           v     vv i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_51505758_   5505 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5554
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_51505758_   5555 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5604
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_51505758_   5605 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5654
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_51505758_   5655 AAAACAA----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5700
                           i    ----   v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_51505758_   5701 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5750
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_51505758_   5751 CATCACTGGCCAT 5763
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (137 / 93)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


3338 26.21 0.55 0.55  chr20_51522091_51528369     4880  5787 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_51522091_   4880 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4929
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_51522091_   4930 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4979
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_51522091_   4980 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5026
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_51522091_   5027 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAA 5076
                                 viiv  ii  v  v v  v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_51522091_   5077 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5126
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_51522091_   5127 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5176
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_51522091_   5177 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5224
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr20_51522091_   5225 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5274
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_51522091_   5275 CCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5324
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_51522091_   5325 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5374
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_51522091_   5375 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5424
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_51522091_   5425 CCTAGGCTTTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTA 5474
                          v    ?v v viv   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_51522091_   5475 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAATTGGGATCTA 5524
                         vi            vvi           v     v  i  v v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_51522091_   5525 ATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5574
                           i   v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_51522091_   5575 CAGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACA 5624
                         v  i     i   i             v  ii   vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_51522091_   5625 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5674
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_51522091_   5675 AAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTT 5724
                           i     i     v  i?    i     i     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_51522091_   5725 CTCAAAAGAAGACATTTATGCAGCCAACAGACACCTGAAAAAATGCTCAT 5774
                            v        i  vi viii     i ii   v      i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_51522091_   5775 CATCACTGGCCAT 5787
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.49 (140 / 94)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.43 (10 / 7)  


3333 26.11 1.00 0.55  chr20_51553298_51559570     4878  5781 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_51553298_   4878 TGGAAGAACATTCCATGCTCATGGGTAGGAGGAATCAATATCGTGAAAAT 4927
                              ii i  i     i      i v   i  v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_51553298_   4928 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGTCATCCCCATCAAGC 4977
                            v     v     iv i  i           i iv     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_51553298_   4978 TACCAA-TGCCTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTC 5024
                          v   i-       i  -i     -   -- v  i  - iii    i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-GCAGAAATTG--ACAAGCTGATCCTAAAATTC 147

  chr20_51553298_   5025 ATATGGAACCAAAAAAGAGCCCGCATCGCCAAGGCAATCCTAAGCCAAAA 5074
                                 viiv  ii  v  v v  v     ii     i i ivv i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_51553298_   5075 GAACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGG 5124
                                 i      vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_51553298_   5125 CTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAT 5174
                                  i   i    ii         i iv ii i   v        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_51553298_   5175 CAATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAAC 5222
                                 i    i--    i  --        vv  ii i  i  iiii
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGT 345

  chr20_51553298_   5223 TATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTC 5272
                         i vi    i  i     ivv  vv  i v  vv            i  vv
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_51553298_   5273 CCTGTTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGC 5322
                         i  v  i  i              v      v  ?   i   i i  iiv
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_51553298_   5323 TGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGG 5372
                             ii    i    v   i     v           i  i    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_51553298_   5373 ATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAA 5422
                           i ?    i    i  v   v       i      vi i          
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_51553298_   5423 CCTAGGCATTACCATTCAGGACATAGGCATGAGCAAGGACTTCATGTCCA 5472
                          v    ?i v viv   iv   v v  vv ii    v ii   v ivvi 
  L1M4_orf2#LINE/    546 CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

  chr20_51553298_   5473 AAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTA 5522
                         vi            vvi           v     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_51553298_   5523 ATCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5572
                               v v  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_51553298_   5573 CAGGCAACCTACAAAATGGGAGAAAATTTTCGCAACCTACTCATCTGACA 5622
                         v  i     i   i             v  i    vii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_51553298_   5623 AAGGGCTCATATCCAGAATCTACAATGAACTC----AAATTTACAAGAAA 5668
                          i  i  ii          v  i  v      ----  v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_51553298_   5669 AAAACAAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTT 5718
                           i     i     v  i?    i    ii     iv    i     i  
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_51553298_   5719 CTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCAT 5768
                            v        i  vi viii     v  i          i       v
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_51553298_   5769 CATCACTGGCCAT 5781
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (143 / 89)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.75 (14 / 8)  


2900 24.45 3.76 3.32  chr20_52058870_52061946     1682  2585 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_52058870_   1682 TGGAGAGACACACAATGTTCATGGATTGGAAGACTCA-CATAGTAAAGAT 1730
                             i   i iv v                     i -i  v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_52058870_   1731 GTCAATCTGCCCCAAATTGATATACAGGTTTAATGCAATTCCTGTCAAAA 1780
                          v    viv            v     i  i  i     i   i      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_52058870_   1781 TTCCAGC--ACTTGTAGCAAGACATTTTGTAGAGATAGATGAGGTTATTC 1828
                          i     --v   -----------     i   i  v  ii  v v  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTT-----------TTTTGCAGAAATTGACAAGCTGATCC 139

  chr20_52058870_   1829 TAACATTTATATGGAAAGACAAAGGATTTAGAATAATT-------TTTTA 1871
                            v   i         vi   i   iii      iii------- i  i
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTG 189

  chr20_52058870_   1872 AAATA------TAAA-TTG-ATGAATCAGTCTATCTGATCACAAGCCTTG 1913
                            v ------i   -   - v  v   vv  vi ii  iv   iv   i
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_52058870_   1914 TTATATAGCTACAGTAAGCAAGGCTGTATGGTATTGGTGGAGACATAGAC 1963
                         i  i v           v    i v  i     i   iiv iiv      
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr20_52058870_   1964 ATATAGAACCAATGGAATAGA-----GAAGCCAGAAA-AGACCCACACAA 2007
                                -i            -----  iv       - i     i   v
  L1M4_orf2#LINE/    290 ATATAGA-TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACAT 338

  chr20_52058870_   2008 GTATGCCCAGACGACTTTTGACAAAGGTGTAAAAGCAATTCTACAGAATA 2057
                         v    vi  ivi  i   i     i    iv  ii v    v ii iiv 
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr20_52058870_   2058 AAGATAGTCTTTTCAACAAATTGTGCTAGAGCAATTTGACATCTATAGAG 2107
                          ii                  v     i ii   i v  i ? i i v- 
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACAT-G 437

  chr20_52058870_   2108 GAAAAGAAAGAACCTCAATTTAAGTCTCACATCTTATATAAAAATTATCT 2157
                         v       v   vi vi iiivvii      i v    i        v  
  L1M4_orf2#LINE/    438 CAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACT 487

  chr20_52058870_   2158 CAAAAGAGATCGTGGACTTAAACATAAAACCTCAAA-TATAAAACTTTTA 2206
                              vi    i?i   i    ii   i v  v   -         i   
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr20_52058870_   2207 GGAAAAAA-ATAAGAGAAAATTTCTGAGACCTATGGTTAAAAAAA---TC 2252
                          i i    -   i ? v    i ii v     vv     iiv  v--- i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTT 587

  chr20_52058870_   2253 CATAAA-A-GACCAAAGACCAAAAGCAAAATCCATAAAAAGAAAACATA- 2299
                          v  i - -   -----          v  v v i    -     v   -
  L1M4_orf2#LINE/    588 CTTAGATATGAC-----ACCAAAAGCACAAGCAACAAAA-GAAAAAATAG 631

  chr20_52058870_   2300 ATAAATTGGAATTCATCAAAACTAAAAAATTTTGCCCTGTAAAAGATCCT 2349
                                   v          i      v     iv  vi   i  iv  
  L1M4_orf2#LINE/    632 ATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACT 681

  chr20_52058870_   2350 GTTAAAAAGATGAAAAGAGAAACTAGAGAGTGGGAGAAAATATTTGCAAA 2399
                         i i  i  ii        v  v i v   i                    
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr20_52058870_   2400 CCACGTATCTGACGAGAGACTAGTATTTAGAATACATTTAAAAGAAAAAA 2449
                         i  ii       ii  i    v    ii      i  --------   i 
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGACTTGTATCCAGAATATAT--------AAAGA 773

  chr20_52058870_   2450 ATTCTTAAAACTCAACATTAAAAACAAACAAAACAATCCAATTAGAAAAT 2499
                          i     v       i v      --i     -i  i      ?i     
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAA--GACAAA-TAACCCAATTWAAAAAT 820

  chr20_52058870_   2500 GGGCAAAAGACGTGAGGGGGCATTTCATTGCAGAGGATATGCAGATGGCA 2549
                                i  iv   ivi i      viiiv   i     i  i     v
  L1M4_orf2#LINE/    821 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 870

  chr20_52058870_   2550 AATAAGCACAT--AAAGATGTTCAATCTCATTAACCAT 2585
                                    --       i    iv   ????????
  L1M4_orf2#LINE/    871 AATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (139 / 78)
Gap_init rate = 0.03 (23 / 908), avg. gap size = 2.78 (64 / 23)  


2902 27.20 2.82 0.34  chr20_52289489_52293849     2984  3869 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_52289489_   2984 TGGAAGGATATTCCATGCTCATGGATAGGAAGAATCAATATCCTGAAAGT 3033
                              i     i     i        v      v i     iv v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_52289489_   3034 GGCCATA-TGCCCAAAGTAATTTATAGATTCAATGCCATCCCCATCAAGC 3082
                            v   - v      v i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_52289489_   3083 TACCAATGACTTTCTTCACAGAATTGGAAAAA---A--CTAAAGTTCATA 3127
                          v   iivi i  i  ii     v v  v  i--- --     i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_52289489_   3128 TGGAACCAAAAAAGAGCCTGCATTGCCAAGTCAA-----------AAGAA 3166
                              viiv  ii  v  v v  v     iv   -----------     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_52289489_   3167 CAAAGCTGGAGGCATCATGCTACCCGACTTCAAACTATACTACAAGGCTA 3216
                              i      vv   ii  v   i i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_52289489_   3217 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGGCCAA 3266
                               i   i    ii         i iv ii i   v      ii   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_52289489_   3267 TGGAACAGAAC--AGAGCCCTCAGAAATAATACCACACATCGACAACTAT 3314
                              i    i--    i  --        vv   i    iv iiiii v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr20_52289489_   3315 CTGATCTTTGACAAACCAGACAAAAACAAGATATTGGGAAAGGATTCCCT 3364
                         i    i  i     ivvv v   i v  vvvv  v       i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_52289489_   3365 ATTTAACAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3414
                         v  i                 v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_52289489_   3415 AACTGGATCCCTTCCTTATTCCTTATACAAAAATTAATTCAAGATGGATT 3464
                          ii    i    v   i iv  v              i    i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_52289489_   3465 AAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCT 3514
                          ?    i       v   v       i      vi i           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_52289489_   3515 AGGCA-ATACCATTCAGGACATAGGCATGGGTAAGGACTTCATGTCCAAA 3563
                            ?i- v i -   iv   v v  vv i  i  v ii   v ivvi vi
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_52289489_   3564 ACACCAAAAGCAAGGGCAACAAAAACCAAAATTGACAAATGGGATCTAAT 3613
                                     vii         ivv     v  i    v   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_52289489_   3614 TAAACTAAAGCGCTTCTGCACAGCACAAGAAACTACCATCAGAGTGAACA 3663
                         i   v v  ivi   i  ii vv  v i  v    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_52289489_   3664 GGCAACCTACAGAATGGGAGGGAATTTTTGCAATCTACTCATCTGACAAA 3713
                          i     i            ii   v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_52289489_   3714 GGGCTAACATACAGAATCTACAAAGAACACAAACAAAT---TTACAAGAA 3760
                           i  vii  v      v  i       v vv    v --- v i  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_52289489_   3761 AACAA-CAACCCCATCAAAAAGCGGGCAAAGGGTATGAACAGACATT-CT 3808
                         i    -i     v  i?    ii         i v    i       -  
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_52289489_   3809 CAAAAGAAGACATTTATGCAGCCAACAGACACCTGAAAAAATGCTCATCA 3858
                          v        i  vi viii     i ii   v      i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_52289489_   3859 TCACTGGCCAT 3869
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.37 (137 / 100)
Gap_init rate = 0.01 (11 / 908), avg. gap size = 2.55 (28 / 11)  


 402 25.86 2.59 1.72  chr20_52385325_52387769      924  1039 (1406)    L1M4_orf2#LINE/L1        1   117 (791)  

  chr20_52385325_    924 TGAAAAAACATTCCATGCTTATAGGTTGGAAGAATTTATATTGTTAAAAT 973
                           i   i i  i     i i  i i        v  v          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_52385325_    974 GGCCATACTATCCAAGGCAATCCTATTTAATTTAATGCTATTCCTATCAA 1023
                            v     vi    ivii   -  iv-i   i  i  v  i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATC-TACA-GATTCAACGCAATCCCTATCAA 98

  chr20_52385325_   1024 A---CTAGCAACATTATTT 1039
                          --- i   vi v  v   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTT 117

Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.03 (3 / 117), avg. gap size = 1.67 (5 / 3)  

2372 27.40 2.28 2.40  chr20_52385325_52387769     1122  1953 (492)    L1M4_orf2#LINE/L1       78   908 (0)  

  chr20_52385325_   1122 ATTTAATGCTATTCCTATCAAA---CTAGCAATATTATTTTTCACAGACA 1168
                            i  i  v  i         --- i   -- iii-     ii    v 
  L1M4_orf2#LINE/     78 ATTCAACGCAATCCCTATCAAAATCCCAGC--TGCC-TTTTTTGCAGAAA 124

  chr20_52385325_   1169 TTAGAAAATTATTTAGAATTTATTCTAAAATTCATATAGAACCAGAAAGG 1218
                           iiv  ii i----------  i             i   viiv  i  
  L1M4_orf2#LINE/    125 TTGACAAGCTG----------ATCCTAAAATTCATATGGAAATGCAAGGG 164

  chr20_52385325_   1219 AGCCCAAATACCCAAAGCAATCCTAAGCAAAAACAACAACACACCAGAGG 1268
                          v  vi    v     i     i i iv  i  v     - -iiii    
  L1M4_orf2#LINE/    165 ACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA-A-GTTGGAGG 212

  chr20_52385325_   1269 CATCGGATTACCTGACATCAAACTATACTATAAGTCTACAGTAACCAAAA 1318
                         vv  iv i v  ii iv     viv     i  iv         i   i 
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr20_52385325_   1319 CAGTATGGTACTGGTACAA----AAACATA--GATCAATGGAACAGAATA 1362
                             i         i i  ---- i     --           i     v
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATT 312

  chr20_52385325_   1363 GAGAACTCAGAAATAAAGCCACACACCTACAGCCATCTGATCTTTGACAA 1412
                             iii          v   i   ii  ii i  vi    i  i     
  L1M4_orf2#LINE/    313 GAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAA 362

  chr20_52385325_   1413 A--TGAAAAAAATAAGCAACAAGGAAAGGACTTCCTATTCAA-AAATTGT 1459
                         i--  vv  i vi vv   iii      i ivvi  v     -    v  
  L1M4_orf2#LINE/    363 GGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGT 412

  chr20_52385325_   1460 GCTAGCACAGCTGGCTAGCCATATGCAGAAGAACAAAACTGGACTCCTAC 1509
                            i v   i    v  ?   i     i     ii  ii     i     
  L1M4_orf2#LINE/    413 GCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTAC 462

  chr20_52385325_   1510 ATTTTACCATATACAAAAATTAACTCAAGATGGATTA-AAATTTAAATGT 1558
                         v ivi                       i      i - i ii       
  L1M4_orf2#LINE/    463 CTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT 512

  chr20_52385325_   1559 AAAACTTCAAATTATAAGAATCCTGGAAGGAAACCTAGGAA-ACACCATT 1607
                           i vi v   i     i v  i i    i    v    ?i- v i -  
  L1M4_orf2#LINE/    513 AAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TT 561

  chr20_52385325_   1608 CTGGACATCAACCTTAGGAAAGAACTTAT--GAC-TGTCCTCAAAAGT-T 1653
                          vv   v iiiv-     v  viii  v --  i-  v vi      i-i
  L1M4_orf2#LINE/    562 CGTGACCTTGGG-TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCAC 610

  chr20_52385325_   1654 AATTGCAACAAGAACAAAAATTGACAAGTGGGATCTAATTAAA-TTAAAG 1702
                           --       i iv      v  i  i v   ii v  i   -     i
  L1M4_orf2#LINE/    611 AA--GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAA 658

  chr20_52385325_   1703 AGCTTCTGTACAGCAAAACAAGCTATCAACAGAGTAAACAGACAACCTCC 1752
                          -   i   i vv    iv vi       v i   i  v        iv 
  L1M4_orf2#LINE/    659 A-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr20_52385325_   1753 AGAATAGGAGAAAGTATTAACAAATTATGCATCCAACAAAGGTCTAATAT 1802
                              i       i    vi     i  ii   ii i  i  v  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr20_52385325_   1803 CCAGAATCAATAAGGAACTTAAACAATTAAACAAGCACAAAACAAACAAC 1852
                                vv    i     ivv    i v  i  vv v  i     i   
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr20_52385325_   1853 CCCATTAAAAAGTGGGCAGAAGACATGAACAGTCACTTCTCAAAAGAAGA 1902
                           v   ?    i      i i  iv    i  v  i     v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr20_52385325_   1903 CACACAAGTGGTCAATTAAAGTATGAAACAATGTTCCACATCACTAATAA 1952
                         i i    i   i    v ivii      vi   i  v      ???????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr20_52385325_   1953 T 1953
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.88 (147 / 78)
Gap_init rate = 0.02 (20 / 831), avg. gap size = 1.95 (39 / 20)  


2515 26.48 0.30 0.00  chr20_52419487_52421541.rev      501  1161 (894)    L1M4_orf2#LINE/L1      167   829 (79)  

  chr20_52419487_    501 CCAAAATAGCCAAAGCAATCCTGAGCAAAAAGAACAAAGCTGTATGCATC 550
                            i          i     i   iv  i          i  v v vv  
  L1M4_orf2#LINE/    167 CCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTC 216

  chr20_52419487_    551 ACACTATCTGACTTCAAAATATACTACAGTGCTATAGAAAGGAAAACTGC 600
                              vi ii i       iv       iv    i  v  vv  i  v i
  L1M4_orf2#LINE/    217 ACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGT 266

  chr20_52419487_    601 ATGGTATAGGTATGAAAACAGACACACAGACCAATGAAACAGAATAGAGA 650
                         i     iv  i  i ii i     i i   i     i  i     v    
  L1M4_orf2#LINE/    267 GTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGA 316

  chr20_52419487_    651 AACCAGAAATAAATCCACATATTTATAGCCAACTGATTTTTGACAAAGGC 700
                         iv           i   i i      i i   i       i     i  i
  L1M4_orf2#LINE/    317 GTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGT 366

  chr20_52419487_    701 AACAAGAACATACATTTGAGAAGTGACATTCTCTTAAATAAGTGGTGCTG 750
                         iv     v   v  v v i   ivi i v   i  v  i  i        
  L1M4_orf2#LINE/    367 GCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTG 416

  chr20_52419487_    751 GGAAAACTGGATAGCCATGTGCAGAAGAATGAAAC--AACCCCTATCTCT 798
                            v         ?   ii    i         ii--i       i   v
  L1M4_orf2#LINE/    417 GGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCA 466

  chr20_52419487_    799 TACCACATAGAAAAATTAACTAAAAATGGATTAAAGACTTAAATGTAAGA 848
                         i    i   v           v         i ?    i           
  L1M4_orf2#LINE/    467 CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGA 516

  chr20_52419487_    849 CCCAGAACTATAAAACTACTAGAAGAAAACATAGGGAAAACACTTTAAGA 898
                         v i i            vi                ?iv  vv   iiv  
  L1M4_orf2#LINE/    517 GCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGA 566

  chr20_52419487_    899 CATTGGTCTTGGCAAATATTTTATGGCTAAAACATCAAAAGCACAGACAA 948
                          v    vi v     vvi   iv i v  vi   i          ii   
  L1M4_orf2#LINE/    567 CCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAA 616

  chr20_52419487_    949 CGAAAACAAAAATAGACAAATGGAACTATGTTAAACTAAAAATCTTCTGC 998
                          i   iv         i    v i   vii i   v v    v   i  i
  L1M4_orf2#LINE/    617 CAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr20_52419487_    999 ACAATGAAGGAAACAATCAACACATTGAAGATACAACCCATAGAATGGGA 1048
                         i vvii     v  v     v v v    i v        i         
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr20_52419487_   1049 GGACATACCTACAAAATATTTATTTGATAAGAAACTAATATCCAGAATAC 1098
                          i v   ii i    vi  v   i       ii   vi           i
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr20_52419487_   1099 ACAAGGGGCTCAAACAACTCAACAGCAAGATAATGAATAACCCCATTAAA 1148
                          i  i ii   vv         i ii  i vi ii        v   ?  
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAA 816

  chr20_52419487_   1149 AAGTGGGCTAGGG 1161
                           i     v i  
  L1M4_orf2#LINE/    817 AAATGGGCAAAGG 829

Transitions / transversions = 1.67 (107 / 64)
Gap_init rate = 0.00 (1 / 663), avg. gap size = 2.00 (2 / 1)  

 384  9.57 6.96 6.09  chr20_52419487_52421541.rev     1449  1563 (492)    L1M4_orf2#LINE/L1      793   908 (0)  

  chr20_52419487_   1449 AAAAAGAAAAAAAA---AA---AAAAGTGGGCTA-GAATTCTGAATAGAC 1491
                                v   v  ---  ---    i     v - i   -         
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT-TGAATAGAC 841

  chr20_52419487_   1492 ATTTCTCAAAAGAAGACATA-AAATGGCCAATAAATACATGAAAAGAAGA 1540
                                v        i   -             ii           v -
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG- 890

  chr20_52419487_   1541 AAAAGCTCAACACCACTAGTCAT 1563
                         -----       i  ????????
  L1M4_orf2#LINE/    891 -----CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.20 (6 / 5)
Gap_init rate = 0.05 (6 / 116), avg. gap size = 2.50 (15 / 6)  


1038 25.47 24.93 4.00  chr20_52441350_52445492.rev     2902  3651 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr20_52441350_   2902 GGAGAAGCATACCATGTTCATGGATAGAAATAAGCAATCTAGTTAA-ATG 2950
                            i iii  v              v i  v vvi   v v     -   
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_52441350_   2951 --AACA-TCTTCAAAATGTATCTATGAATTCAATGCAATCCCAGTCAAAA 2997
                         --  i -  ii    v  -     iii      i        vi      
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTG-ATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_52441350_   2998 TCTCAGCAGAATTTTTTTGGTAAAACCTGACAATCTGAT----------- 3036
                           i    v --ii     v i i  vi      v     -----------
  L1M4_orf2#LINE/    101 TCCCAGCTG--CCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_52441350_   3037 --TAGAAA------------------ACCAAAATAGTTTTGAAAA----G 3062
                         -- i    ------------------i      i i i       ---- 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_52441350_   3063 AATAAAATTAAAAGATCAACACTTCTGTATT--------------AAAGT 3098
                           i   i  ii i  iiv       ivv   --------------    i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_52441350_   3099 TAGATTAA--------GTATGGTATTTGCATAAGAATAGACA----GATT 3136
                           v v   --------  i     i v       i       ----   i
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_52441350_   3137 ATTAAAACAGAATAGAAACTC-AGAAATAGACTCCATACAT--------- 3176
                          v ii  i     v  i v  -       i  -        ---------
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACATTTATGGTCA 347

  chr20_52441350_   3177 ---AATTTTCATTAAGA-CGTCAAAGCAATATACCAAGAAAAGAAATGT- 3221
                         ---i      ivi   i-i i   ii v  vi viii i      vv  -
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_52441350_   3222 ---------AATGGTGATAGGA-------------ACAAGCA-------- 3241
                         ---------       v i   -------------   v   --------
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_52441350_   3242 -----------------------------------------------GAT 3244
                         -----------------------------------------------   
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_52441350_   3245 ----------AATGTGAAAACTAAAGCTATCAACCTTCTAGAAAAAAACC 3284
                         ----------     i i i     i    v  v  ii     i     -
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC- 546

  chr20_52441350_   3285 AT-----TAAAACATTATTTGGAACC--AGGTGGTAGGCAACGATTTCTT 3327
                           -----    v ----  i vi   --i   --       i i      
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC----TTCGTGACCTTGGGT--TAGGCAATGGTTTCTT 590

  chr20_52441350_   3328 AGTTAGAACACTGAAAGCAACCTGGAGTATGCAAAAATTTCTAAGGATAT 3377
                           v  vi    ii      --------i v    v  -----   i ---
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCA--------CAAGCAACAA-----AAGAA--- 624

  chr20_52441350_   3378 AAAAAT---TATGTTAGGCTTCACCAAAATGAAAGACTTCTGCTCACTAA 3424
                         -     ---  vi  i i     i      v   i    i  iv vii  
  L1M4_orf2#LINE/    625 -AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr20_52441350_   3425 AAACTATTATAAAGAAAATAAATAGTTTAGGCCCAGACTGAAAGAAAATA 3474
                          iivi i   v      i i  v  viv vv v    v  ii        
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr20_52441350_   3475 ATTGTAAAGCTTACGTATAACAGTAGGCTTGTATCCAG--TGTCCAGCTA 3522
                         v   i   v v  ii v i i ivi i           -- i vi ivv 
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr20_52441350_   3523 TATTCGTACAAGTCAATAA---AAGGACAATCACTCCAACTAAAAATTGA 3569
                         - i  v     v       ---  i     vi vi    i ?    v  i
  L1M4_orf2#LINE/    774 -ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_52441350_   3570 GGAAAT-ACTTCAATATA----TCTTGAAAGAAAAGTATACAAATGGCCA 3614
                          v   v- i  v    v ----   iv      i -              
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA-TATACAAATGGCCA 871

  chr20_52441350_   3615 ATAAATGTGTGAAAAATTGCTCATTATCAATAGTCAT 3651
                             iiiii      iv      vi    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (119 / 71)
Gap_init rate = 0.04 (34 / 907), avg. gap size = 6.38 (217 / 34)  


 765 30.01 9.48 4.92  chr20_52464978_52467716.rev     1407  2239 (500)    L1M4_orf2#LINE/L1       25   895 (13)  

  chr20_52464978_   1407 ATTTGAAGAAATGGTATTATAAAAATGTCAATTCTCTGTAACTCGATTTA 1456
                            v     vv ii    i v  i   v    v   ivi  v i   i  
  L1M4_orf2#LINE/     25 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 74

  chr20_52464978_   1457 TAAATTCAAC--AATCATTCCAGTAAAAATACAAAAACATTTTTTG--GA 1502
                         i i       --    --i i vi    viv  ivvi v       --  
  L1M4_orf2#LINE/     75 CAGATTCAACGCAATC--CCTATCAAAATCCCAGCTGCCTTTTTTGCAGA 122

  chr20_52464978_   1503 GCTAGACAAGTTTATTATAAAGCTTATTTGGCCAAT-CAAAGAAGCAAAA 1551
                         iv v      i v  iv    ii i  v   v-   -   i i v v i 
  L1M4_orf2#LINE/    123 AATTGACAAGCTGATCCTAAAATTCATATGGA-AATGCAAGGGACCCAGA 171

  chr20_52464978_   1552 ACCATCAGGAAAACCCTTAAAAAAAAAGAATAATGGTGGAATGGGAAATA 1601
                          ivii  ii v  i -  i     i     i  v v    ---   vvi 
  L1M4_orf2#LINE/    172 ATAGCCAAAACAATC-TTGAAAAAGAAGAACAAAGTTGGA---GGACTCA 217

  chr20_52464978_   1602 GCCAGTCCTACCAGATATTAAAACATA-TATAAAGCCTTTCCAATAA--- 1647
                         --  v i --   -  v i     v  -  i     --- v  i   ---
  L1M4_orf2#LINE/    218 --CACTTC--CCA-ATTTCAAAACTTACTACAAAGC---TACAGTAATCA 259

  chr20_52464978_   1648 -AACAATGTGATATTGGTGCATGGGTGGATATAGAGAACAATGAATCAGA 1696
                         -i   i    i  i   iii v  i i  i   v   v     i vi   
  L1M4_orf2#LINE/    260 AGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGA 309

  chr20_52464978_   1697 A--GAGAAATCCAGAAATTAATCCA---ATT---GGATAAACAAATTTAG 1738
                          --    i-         v  i   ---   ---  vi  vii v   v 
  L1M4_orf2#LINE/    310 ATTGAGAG-TCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr20_52464978_   1739 TACACACAAAAAAATCAGTATTTTAACTCAATTGGGTAAAAAGGGATGTT 1788
                         -----    iiivii  iv ii--- i     v   v  i  vi - v  
  L1M4_orf2#LINE/    359 -----ACAAGGGTGCCAAGACC---ATTCAATGGGGAAAGAATAG-TCTT 399

  chr20_52464978_   1789 TTCA-TAAGTGATGTTCAAATAATTGGATTACTCTATGGAAAAATATAAA 1837
                             -i  i  i  i vii i  i     v? ivi   v    iv  i  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_52464978_   1838 GTTAGATA--TAATTCTCAAACTGTGTGCAATGATGATTTCCAAATGG-T 1884
                            i  iv--  --i    v  ii i i   vi  v vi  v      - 
  L1M4_orf2#LINE/    450 GTTGGACCCCTA--CCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_52464978_   1885 CAAAGATTTACATGTAATGAAAAAAATGAAACAATACAAATATTAATATA 1934
                           ?   ii  v      -----i iv i    v   v  v v   i--- 
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAA-----GAGCTAAAACTATAAAACTCTTAG---A 539

  chr20_52464978_   1935 AGGAAACATTGATG--AATCTCTCTA----TAAATTATGATAAAGGTTTC 1978
                           i      v i? --     iiv i---- iii   - ii  v      
  L1M4_orf2#LINE/    540 AGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTA-GGCAATGGTTTC 588

  chr20_52464978_   1979 CTAATAATAATTC--AAAGTCCGCATGCAAAAAAGGAAAGGAC-TCTGAA 2025
                         i  ivv  i iv --    -- i  v    v   i    ii i-vv i  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAG--CACAAGCAACAAAAGAAAAAATAGATAAA 636

  chr20_52464978_   2026 TTTAGTTACTTAAAAAT---AAACTTTTG------------CACTAT-AA 2059
                           viii v v v     ---         ------------      -  
  L1M4_orf2#LINE/    637 TTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

  chr20_52464978_   2060 GCAAACTAAAAATGTAAATTACAAAACAGGAAAAAAATATGTGCAATTTA 2109
                          -   v i    vii  vii   i  ii   i    -   v     v i 
  L1M4_orf2#LINE/    687 G-AAAGTGAAAAGACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCA 734

  chr20_52464978_   2110 TATACCCT-TAAGA----------CAGAA-----AAAGA-CTCT------ 2136
                             i iv-    i----------     -----     -    ------
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC 784

  chr20_52464978_   2137 -----AAAAAAAAGTTCAACAATTCTATGAGAAAAACAAGCAATGGATAT 2181
                         -----  v      viv  i  ii v  v?-     iii    v    v 
  L1M4_orf2#LINE/    785 TCAATAATAAAAAGACAAATAACCCAATTW-AAAAATGGGCAAAGGATTT 833

  chr20_52464978_   2182 GAACAGATGGTTCAC---AGTAAAAATACAAATATACTTTAA-CATAATA 2227
                            i   iiv   v ---  v i v        ivv vv   -  i vv 
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr20_52464978_   2228 TAAGGTGCTCAA 2239
                         v   i       
  L1M4_orf2#LINE/    884 AAAGATGCTCAA 895

Transitions / transversions = 1.41 (144 / 102)
Gap_init rate = 0.05 (45 / 871), avg. gap size = 2.67 (120 / 45)  


2131 25.73 6.36 1.52  chr20_52474415_52476129      501  1223 (492)    L1M4_orf2#LINE/L1      151   908 (0)  

  chr20_52474415_    501 TGGAACCAAAAAGAGCCCACA-TGGCCAAAGCAAGACTAAGCAAAAAGAA 549
                              viiv  i ii    v - i      i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_52474415_    550 CAAATCTGGAGGTGTCACATTACCTGACTTCAAACTATAATATAAAGCTA 599
                             vi      vv     i v  ii i      viv  v  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_52474415_    600 CAGTCACCAAACCAGCATGGCACTGGTATAAAAATAGGCACATGGACCAA 649
                             v i   iv   ii   i     i    ii    i  i  i  i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_52474415_    650 TGTGACAGAACAGAGAAACAGAGAACCCAGAAATAAAGACAAATACTCAC 699
                           -----   i   --- iv    ii           vv  v i i i i
  L1M4_orf2#LINE/    301 TG-----GAATAGA---ATTGAGAGTCCAGAAATAAACCCATACATTTAT 342

  chr20_52474415_    700 AGCCAACTGATGTTTGACAAAGCAAACAATAACATAAAGTGGAGAAAGGA 749
                         i i   i    v  i     i vviv   v v   vv i   i     i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr20_52474415_    750 CACACTATTCAACAA-TGGTGCTGAGATAATTGACAAGCCACATGCAGAA 798
                         i vv  v        -        i  i  i  ivv ?         i  
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_52474415_    799 GAATGAAACTGGATTCACATCTCTCACCTCATACAAAAATCAACTCAAGA 848
                                ii    ii vi i   v    vi          i       i 
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_52474415_    849 TGGATCAAAGACTTAAATCTAAGACC-------------CTTTTAGA--- 882
                                ?    i     v     v -------------  i     ---
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_52474415_    883 ---CAT---------------------TGGCTTAGGCAAAGACTTCATGG 908
                         ---   ---------------------   v        v ii   v i 
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr20_52474415_    909 CCA--ACAACCCAAAACCAAATGCAACAAAA-ACAAAGGAAATAGATGGG 955
                         vi --   --      v  v v         - v   iv i   i  v  
  L1M4_orf2#LINE/    593 ATATGACA--CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_52474415_    956 ACTTAATTTAACTAAAATGCTTCTGCATAGCAAAAGAAATAATCAGCAGA 1005
                             v  iv  v v   vi   i  iiivv    i  v iv    iv i 
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAA 690

  chr20_52474415_   1006 GTAAACGGACAACTCACAAAGTGGGAGAAAATATTAGCAAACTATGCATC 1055
                           i  vi      i    i i              v     ii  ii   
  L1M4_orf2#LINE/    691 GTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATC 740

  chr20_52474415_   1056 CAACAAAGGACTCATGTTCAGAATCTACAAGGAACTCAAAGAAATCAGCA 1105
                         ii i  i     ii i i      v  i  i      vv v  v   ii 
  L1M4_orf2#LINE/    741 TGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATA 790

  chr20_52474415_   1106 AGTAAAAAGCCAAATAATCCCATCAAAAAGTGGGCTAAGGATATGAAAAG 1155
                          -       v       i  v  i?    i     v      v    v  
  L1M4_orf2#LINE/    791 A-TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr20_52474415_   1156 ACAGTTATCAAAAGAAGACATACAAATGGCCAA-AAACATATGAAAAAAT 1204
                            v  v  v        i              -  i  i       i  
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_52474415_   1205 GCTAAATATCACTAATTAT 1223
                            v  i    ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.51 (110 / 73)
Gap_init rate = 0.02 (12 / 758), avg. gap size = 4.75 (57 / 12)  


2439 25.57 5.91 2.73  chr20_52616418_52618370.rev      600  1479 (474)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_52616418_    600 TGGAGAATCATACCATGTTCATGAAT----GGACTTAACATAGAAAAGAT 645
                             i ivi  v           i  ----i       i  v vv     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_52616418_    646 ATCGGTTCTCCCACAATTTGCTCTATAGGCTTAACATAA---CTCTCAAA 692
                         iv ii v     -   v   v    i  ii i   ii  ---  v     
  L1M4_orf2#LINE/     51 GGCAATACTCCC-CAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_52616418_    693 ATCCCAACAAGGATTTTCTGTAGATATAGACAGGCTTATTTTTAAGTTT- 741
                               i v- vv    i  i   v  v    i   v  ii v  i  i-
  L1M4_orf2#LINE/    100 ATCCCAGCT-GCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_52616418_    742 TATGGAAAGGCACAGCCACTAGATTAGCTAAAATAACTTTGAAAAAGA-G 790
                                 v   vi vvv i   v    i    i  ii          - 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_52616418_    791 AATAAAGTGAAATGAATCACTCTACCCAATATTAAAGATTACTATATAGC 840
                           i     vii v  v    v  v      v i   iv      i v   
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_52616418_    841 TACAGTAATCAAGAGAGTATGATATTGGCAGAGAAACAGATATACAGATC 890
                                       v   i  i  i     v iii i   i   i     
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_52616418_    891 AATGGAAAAGAATAGAGAATCTAGGAACAGACTCACATAAATATGCCCAA 940
                                v     v    i  i  i  i i  i  i i vv    vi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_52616418_    941 ATAATTTTTGACAAAGGTAAAAAAATCAATTCAATAAGGAAAGAATAATT 990
                         v i     i     i   ivv  i i  -      ii          i i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTC 397

  chr20_52616418_    991 TTTTTCAACAAATGATAGTGGAATAATTGGACAATCACAGGGAAAAGAAT 1040
                             -         i iv   i i  i    i ?i    v v        
  L1M4_orf2#LINE/    398 TTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_52616418_   1041 TAAATTCAATCCACATTTCACTCCTAATACAAAAATTAAACTCAAAATGA 1090
                         v  i  vi i  vi ii    v  vv             -         i
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAA-CTCAAAATGG 495

  chr20_52616418_   1091 ATCATA--TTTAAATGTAAAACTTAAAACTATACCTTTTTTCTTAAGAAA 1138
                             ? --ii         i vi          vvvi i  ----    i
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTT----AGAAG 541

  chr20_52616418_   1139 AAAACA-AGA---AAATCTTTAGGA--TTGAACTTCAGGCAAGGAGTTCT 1182
                               -  i---       iiv  --   iii --      v iv    
  L1M4_orf2#LINE/    542 AAAACATAGGNGTAAATCTTCGTGACCTTGGGTT--AGGCAATGGTTTCT 589

  chr20_52616418_   1183 TAGACTTTACACCAAAAGCATGAACAATAAAGGTAAAAATTCAGAAATTG 1232
                             iv v            ii i   i   i v      vv v      
  L1M4_orf2#LINE/    590 TAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_52616418_   1233 GGTCTCATCAAAATTAATA-CTTTTCTTCTGGAAAAGATCCTGTTAAGAG 1281
                          iii             v -     v v  vv   i  iv  i i    i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_52616418_   1282 GGTGAAAGAAAAATCTATGCACTGGGAGAACATATTTTCCAG-CACA-AT 1329
                         i      ii v  i i iiv v        v      v v i-  i -  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_52616418_   1330 CTGACACATATATATACACACATACACGCACACACACAAACGCACACACT 1379
                             i ----- viv  viii  v  - v i i i v i -------   
  L1M4_orf2#LINE/    740 CTGATA-----AGGGACTTGTATCCA-GAATATATAAAGA-------ACT 776

  chr20_52616418_   1380 CCCAATACTCAATAGTAAAAAAA-AAATAG---------AAAATAGGTCA 1419
                          ii vv        i      i -     i---------     i  iv 
  L1M4_orf2#LINE/    777 CTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAA 826

  chr20_52616418_   1420 AATACATAAAGAGACATTTC---ATAGAAGATATACAGA---------AG 1457
                          iv iv i  v         --- v            i ---------  
  L1M4_orf2#LINE/    827 AGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr20_52616418_   1458 CA----------TGTTCAACATCATTAGCCAC 1479
                           ----------  i         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (135 / 88)
Gap_init rate = 0.03 (26 / 908), avg. gap size = 2.92 (76 / 26)  


3228 21.18 2.58 5.16  chr20_52630058_52634260.rev     2782  3711 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_52630058_   2782 GAAAGGCATCCTGTTTTCATAGATTGAAAGACTTAACATTGTTAAAATTA 2831
                              ii    ii v     i     i         i        i  -i
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT-G 51

  chr20_52630058_   2832 ACATTGTTAAAAAAAAGACTTAACATACAATCTAAAATGATCTACAGATT 2881
                         i  ---------------------    vvi i   v             
  L1M4_orf2#LINE/     52 GCA---------------------ATACTCCCCAAATTGATCTACAGATT 80

  chr20_52630058_   2882 CAATGTAATCTCTATCAAAATCCCAGGAGCTTTTTTTTTTTTCAGAAATA 2931
                            i i    i               vv  i      v----       -
  L1M4_orf2#LINE/     81 CAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTG----CAGAAAT- 125

  chr20_52630058_   2932 GGAAAAGCAAAGC-TAAAATTCATATGAAAACACAAAGAACCTTATATAG 2980
                         v  v    vi v -             i   ii   i i   iviv    
  L1M4_orf2#LINE/    126 TGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAG 175

  chr20_52630058_   2981 TCAAAACAATC--AACATAAAAGAACAAAGCCAGAG---------TTGC- 3018
                         i          --i v v i          iii   ---------  v -
  L1M4_orf2#LINE/    176 CCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCC 225

  chr20_52630058_   3019 ---TTCAAAATATACTACAAAGCTACAATAATCTAAATAATATGGTACTG 3065
                         ---       iv               i     v i i i i        
  L1M4_orf2#LINE/    226 AATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTG 275

  chr20_52630058_   3066 GCACATAGGCAAACATACAGA-CACATGGAACAGAAA-GAGAACCTGGAA 3113
                            i vi ii i     i   -  -      i    v-    ii ii   
  L1M4_orf2#LINE/    276 GCATAAGGATAGACATATAGATCA-ATGGAATAGAATTGAGAGTCCAGAA 324

  chr20_52630058_   3114 ATAAATTGATGCTTATACAATAAAATGGTCTTTCACAAGGGTGCCAAGTT 3163
                              iiv  i v v  iii v  v  i i  iv              vi
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGAC 374

  chr20_52630058_   3164 TATACAACAGGAAAATGATAGGCTTTTCAACAAATGATGCTACAAAATCT 3213
                         i  v   ii  i   vi    v              i    ivi v v  
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr20_52630058_   3214 GTATATCCATATGAAAAATAATGAAATTGTACCCTTACTTCAC--CATAA 3261
                          v   ?   i   v    v      i   v    i   i    --    v
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr20_52630058_   3262 ACAAAAAATCAATTCAAAATGGATTAGAGACTTAAATGTAAGACCTGAAA 3311
                                - i  i           i ?    i           v  i   
  L1M4_orf2#LINE/    475 ACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr20_52630058_   3312 CTATAAAACTCCTAGAATAAAACAGAGGGAAAAGGCTTTATGACAGTGGT 3361
                                    i     v      v   ?iv  iv   ii    vv   v
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr20_52630058_   3362 CTTGACAGTGATTTCTTGGATATGAGACCAAAAACACAGGCAATGAAAGC 3411
                         i v i  i  i      i       v       i    i    ii    v
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr20_52630058_   3412 AAAAATAGACAAGTAGGACTACATCAAA-CTAAAAAGTTT-ATACATAGA 3459
                                  i  i v     v       -i      v   -i i v v- 
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC-A 672

  chr20_52630058_   3460 AAAGAAACAATCAACAGAGTGAAAAGGCAACCTATAGCATGAGA-AAAAT 3508
                           i  v  v     v i         i     i i  v   i  -     
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_52630058_   3509 ATCTGCAAACCATATCCTTGATAAAGGGTTAATAGCCAAAATATATAAGA 3558
                           i      i     vii      i  ii vi  v   i         ii
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_52630058_   3559 AATTCGTATAACTCAATAGCAAAAATAATAAAAGTAAAAATAAATAAGCC 3608
                           i  v  i         ---------      ---- i i      v  
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATA---------ATAAAA----AGACAAATAACCC 809

  chr20_52630058_   3609 AATTTTAAAATGGGCAAATGTCTATTCAAAGATAGACATTTCTCCACAGA 3658
                             ?v            v ---   ii  --              v   
  L1M4_orf2#LINE/    810 AATTWAAAAATGGGCAAAGG---ATTTGAA--TAGACATTTCTCCAAAGA 854

  chr20_52630058_   3659 AGACATACAC-TGACCAATGGATATATCAGAAGATTCTCAACATCACTAA 3707
                            i     v-  i     iiii i  v i     v          ????
  L1M4_orf2#LINE/    855 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZ 904

  chr20_52630058_   3708 TCAT 3711
                         ????
  L1M4_orf2#LINE/    905 ZZZZ 908

Transitions / transversions = 1.80 (124 / 69)
Gap_init rate = 0.02 (22 / 906), avg. gap size = 3.27 (72 / 22)  

 229 22.22 0.00 0.00  chr20_52630058_52634260.rev     4094  4156 (47)  C L1M4_orf2#LINE/L1   (66)   842   780  

C chr20_52630058_   4156 ACAACTTTACAAGAAAAAAACAAGCAACCCCATCAAAAAGTGGGCAAAGA 4107
                               iv i  v     i    ii     v  i?    i         i
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGG 829

C chr20_52630058_   4106 ATATGAAGAGACA 4094
                           v    v     
  L1M4_orf2#LINE/    830 ATTTGAATAGACA 842

Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.00 (0 / 0)  


1586 29.21 2.73 1.93  chr20_52834550_52843281.rev     3715  4337 (4395)    L1M4_orf2#LINE/L1        1   628 (280)  

  chr20_52834550_   3715 TGAAAAAAAATTCCATGCTCATGGATAGGAAGAATTAATATTATAAAAAT 3764
                           i   i v  i     i        v      v        i v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_52834550_   3765 GGCCATACTGCCCCAAAGCAATTTATAGATTCAATGCTATTCCTATCAAA 3814
                            v     -       vii  i  i        i  v  i         
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_52834550_   3815 TTATTAATGACATTCTTCACAGAA-TTGAAATAAAACT-ATTTTAAAATG 3862
                         v vii iivi v  i  ii     -    v --- i  -  ii      v
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACA---AGCTGATCCTAAAATT 146

  chr20_52834550_   3863 CATATGGAACCAAAAAGAGCCCA-AATAACCAAGGCAATCCTAAGTAAAA 3911
                                  viiv  i ii    -    i    ii     i i iv  i 
  L1M4_orf2#LINE/    147 CATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGA 196

  chr20_52834550_   3912 AGAACGAAGCCAGAAGCATCATATTACCTGACTCCAAACTATACTACAAG 3961
                              i   iii  i vv   i i v  ii i i    viv        i
  L1M4_orf2#LINE/    197 AGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_52834550_   3962 TCTACAGTATCCAAAACGACATGATACTGGTACAAAAACAGACCCAAAGA 4011
                         v        vi   i  iiii  i      i i  ii i    vi v   
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_52834550_   4012 ACAATGGAACAGAATACAGAGCCCAGAAATAATGGTGCACACCTTCA--A 4059
                         v        i     vv    i          --iiv  i  v  i --i
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAA--ACCCATACATTTATGG 344

  chr20_52834550_   4060 CCATCTGATCTTCAATAGCATCAACAAAAACAACCAATGAAGAAA--ATA 4107
                         i  vi    i   i i iviviiv   i v  vi     ii    --   
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_52834550_   4108 CTTCCTATTCAATAAATTGTGCCAAAGTAACTGGTTAGGCATATGCAAAA 4157
                         v --  v     i    v    iiiiii      v  ?v  i        
  L1M4_orf2#LINE/    395 GT--CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_52834550_   4158 GATTGAAACTCGACCCCTTCCTTACACCAAATACTAAAATCCACTCGA-- 4205
                           v    ii v       v   i      v    v     iv    i --
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_52834550_   4206 CCGATTAGA----TAAATGTGCAACCTAAAAGTATAAAAACCATAGAAGA 4251
                         iv   i ? ----       ivi v      v       vi v       
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_52834550_   4252 TAAGCTTAAAAATA--CCATTCTGAACATAGCAACT-GGCAAAGATTTCA 4298
                         -  i v  ii?i  --i v iv   v v i --ii -     v i    v
  L1M4_orf2#LINE/    543 -AAACATAGGNGTAAATCTTCGTGACCTTGG--GTTAGGCAATGGTTTCT 589

  chr20_52834550_   4299 T-GATGAAGATGCCAAAAGCAATTGCAATAAAAACAAGAA 4337
                          -   - v  ii         vvv    i    iv  i  
  L1M4_orf2#LINE/    590 TAGAT-ATGACACCAAAAGCACAAGCAACAAAAGAAAAAA 628

Transitions / transversions = 1.75 (114 / 65)
Gap_init rate = 0.03 (17 / 628), avg. gap size = 1.71 (29 / 17)  

 868 25.52 3.15 0.35  chr20_52834550_52843281.rev     4627  4912 (3820)    L1M4_orf2#LINE/L1      615   908 (0)  

  chr20_52834550_   4627 AACAAACAAAAAAAAGTGACAAATGGGACCTGATTAAACGAAAGACCTTC 4676
                               - i      vv  i    v    i v  i   vvv  i v   i
  L1M4_orf2#LINE/    615 AACAAA-AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTT 663

  chr20_52834550_   4677 TGCACAGCAAAAGAAACTATCCACAGAATAAACAGACAAACTACAAAATG 4726
                           ii vv    i  v      v v i i i  v      v i   i    
  L1M4_orf2#LINE/    664 TGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATG 713

  chr20_52834550_   4727 GGAGAAAATATTTGCAAACAATGCATCTGACAAAGGTCTAATATCCAGCA 4776
                                           iv  ii      i  i  v  vi       v 
  L1M4_orf2#LINE/    714 GGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

  chr20_52834550_   4777 TCTATAAGGAACTT----AAATC-----TACAAGCAAAAACAACCCCATT 4817
                          v     i     i----  v  -----  v  iv v   i     v   
  L1M4_orf2#LINE/    764 TATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATT 813

  chr20_52834550_   4818 AAAAAGTGGGCAAAGGACATAAACAGACACTTTTTAAAAGACAACATACA 4867
                         ?    i           iv i  i     i  i iv     vi i     
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 863

  chr20_52834550_   4868 CGCAGCCAACGAGCATATGAAAAACTACTCAACGTCACTAATCAT 4912
                         viii     ii    i       iv i      i   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.40 (42 / 30)
Gap_init rate = 0.01 (3 / 294), avg. gap size = 3.33 (10 / 3)  

3207 26.97 1.11 0.33  chr20_52834550_52843281.rev     5553  6453 (2279)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr20_52834550_   6453 TGGAAGAACATTCCATGCTCATGGATAGGAAGAATCAATATTGTGAAAAT 6404
                              ii i  i     i        v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr20_52834550_   6403 GGCCATACTGCCCAAGGTGATTTACAGATTCAATGCCATCCCCATCAAGC 6354
                            v     v     iv    i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr20_52834550_   6353 TACCAATGACTTTCTTCACAGAATAGGAAAAAACT-ACTTTAAAGTTCAT 6305
                          v   iivi i  i  ii     - vvi v  i  - iii    i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAATTCAT 149

C chr20_52834550_   6304 ATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGA 6255
                               viiv  ii  v  v v  v     iv     i i ivv i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

C chr20_52834550_   6254 ACAAAGCTGGAGGCATCACACTATCTGACTTCAAACTATACTACAAGGCT 6205
                               i      vv       vi ii i      viv        i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

C chr20_52834550_   6204 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAGCAGAGATATAGATCA 6155
                                i   i    ii         i iv iiii   v          
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

C chr20_52834550_   6154 ATGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAACTA 6107
                               i    i--    i  --        vv  ii i  i  iiiii 
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

C chr20_52834550_   6106 TCTGATCTTTGTCAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCC 6057
                         vi    i  i v   ivv  vv  i v  vv            i  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chr20_52834550_   6056 TATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTG 6007
                          v  i  i              v      v  ?   i   i i  iiv  
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

C chr20_52834550_   6006 AAACTGGATCCCTTCCTTACACCTTATATAAAAATCAATTTAAGATGGAT 5957
                           ii    i    v   i     v    i      i  i i  i      
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

C chr20_52834550_   5956 TAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACC 5907
                         i ?    i    i  v   v       i      vi i           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

C chr20_52834550_   5906 TAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAA 5857
                             ?i v viv   iv   v v  vv i     v ii   v ivv  vi
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

C chr20_52834550_   5856 ACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAT-GGATCTAAT 5808
                                     vvi          vv     v  i    -   ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

C chr20_52834550_   5807 TAAACTCAAGAGCTTCTGCACAGCAAAAGA-ACTACCATCAGAGTGAACA 5759
                         i   v i  i i   i  ii vv    i  -    i  vv i      v 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

C chr20_52834550_   5758 GGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAA 5709
                          i     i   i             v       vii ivi      i  i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

C chr20_52834550_   5708 GGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAA 5659
                           i  vi          v  i  v      vv    v iv i  v     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

C chr20_52834550_   5658 AACAG----CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCT 5613
                         i   i----   v  i?    i     i     iv    i     i    
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

C chr20_52834550_   5612 CAAAAGAAGACATTTATGCAGCCAAAAAACACG-GAAAAAATGCTCACCA 5564
                          v        i  vi viii     v  i   i-     i       v  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

C chr20_52834550_   5563 TCACTGGCCAT 5553
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.52 (144 / 95)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2942 28.84 0.77 0.44  chr20_52932365_52937016.rev     3256  4160 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_52932365_   3256 TGGAAGAACATTCCATGCTCATGGATAGGAAGAAATGATATCATGAAAGT 3305
                              ii i  i     i        v      vv i    ii v  ii 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_52932365_   3306 GGCCATTCTGCCTAAGGTAATTTATAGATTCAATGCCATCCGCATCAAGC 3355
                            v  v  v  i  iv i  i  i        i  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_52932365_   3356 TACCAATGACTTTCTTCACAGAATTGGAAAAAATTACTTTAAAGTTCATA 3405
                          v   iivi i  i  ii     v v  v  iv v iii    i      
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_52932365_   3406 TGGAACCAAAAAAGAGCCCACATTTCCAAGACAATCCTAAGCCAAAAGAA 3455
                              viiv  ii  v  viv  vv    i      i i ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_52932365_   3456 CAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTA 3505
                              i      vv    i  v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_52932365_   3506 CAGCAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGAGCAA 3555
                            i  i   i    ii         i iv ii i   v       v   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_52932365_   3556 TGGAACAGAAC--ACAGCCCTCAGAAATAATACCACACATCTACAACCAT 3603
                              i    i-- v  i  --        vv   i    i  iiii  v
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCAA 348

  chr20_52932365_   3604 CTGATCGTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCT 3653
                         i    iv i     ivv  v   i v  vvv           i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_52932365_   3654 AGTTAATAAATGGTCCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGA 3703
                         vv i  i       v      v      v  ?   i   i i  iiv   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_52932365_   3704 AACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCGAGATGGATT 3753
                          ii    i    v   i     v              i  i i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_52932365_   3754 AAAGACTTAAATGTTAGGCCTAAAACCATAAAAACCCCAGAAGACAACCT 3803
                          ?    i       v  iv       i      vi ii      v   v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_52932365_   3804 AGGCAGTA--CCATTCAGGACATAGGCATGGGCAAGGACTTCATGACTAA 3851
                            ?-   --i -   iv   v v  vv i     v ii   v iiv  v
  L1M4_orf2#LINE/    549 AGGN-GTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_52932365_   3852 ATCACCAAAAGCAAGGGCAACAAAAGCCAAAATTGACAAATGGGATCTAA 3901
                         iv           vii          vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_52932365_   3902 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 3951
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_52932365_   3952 AGGCAACCTACAGAATGGAAGAAAATTTTTGCAATCTACCCATCTGACAA 4001
                           i     i         i       v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_52932365_   4002 AGGGCTAATATCCAGAATCTACAAAAAACTTAAACAAATTTCCAAGAAAA 4051
                         i  i  vi          v  i   i    ivv    v ivvi  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_52932365_   4052 AAAT---CAACCCCATAAAAAAGTAGGTTAAGGACATGAACAGACACTTC 4098
                          i i---i     v  v?    i i  iv     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_52932365_   4099 TTAAAAGAAGACATTTATGCAGCCAACAGACACATTAAAAAATGCTCATC 4148
                          iv        i  vi viii     i ii     v    i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_52932365_   4149 ATCACTGGCCAT 4160
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.42 (151 / 106)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.83 (11 / 6)  


1728 30.21 0.19 0.39  chr20_53111415_53117484.rev     4373  4885 (1185)    L1M4_orf2#LINE/L1        1   512 (396)  

  chr20_53111415_   4373 TGGAAAAACATTCCATGCTCATAAATAGGAATAATCAATATTGTGAAAAT 4422
                               i i  i     i    ii  v    v v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53111415_   4423 GGCGATACTGGCCAAAGCAATTTATAGATTCAATACTATTCCCATTAAAC 4472
                            i     vv     vii  i  i        ii v  i  i  i   v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53111415_   4473 TACCATTGACATTCTTCACAGAATTAGAGAAAACTATTTTAAAATATATA 4522
                          v   vivi v  i  ii     v v  v  iviv  ii      vi   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_53111415_   4523 TGGAACCAAAAATGAGCTTGTATGGCCAAGCTGATTCTAAGCAAAAAGAA 4572
                              viiv  iv  v iv v  i     ivii  ii i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_53111415_   4573 TAAAACTAGAGGTATCACACTACCCAACTTTAAGCTATATTTCAAGGCTA 4622
                         i   ii i    vv       v     i  i  iviv  i v   i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_53111415_   4623 CACTAACCAAAACAGCATGGTACTGGAAAAAAAAACAGACACAGAGACTA 4672
                           v   i   i    ii         -v v  ii i     i v   ii 
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGG-CATAAGGATAGACATATAGATCA 299

  chr20_53111415_   4673 ATGGAACAGAATGGAAAACTCAGAAATAAGACTAGACATCTACAACCATC 4722
                               i     v  i iii         iv i v    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_53111415_   4723 TGAACTTTAACAAACCTGACCAAAACAA-GCAATGGAGAAAGGATTTCCT 4771
                            vi  ii    ivv  -    i  v -v      i     i  vvi  
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTG-CCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_53111415_   4772 ATTTAATAAATGGTGCTGGGAGAACTGACTAGCCATATGCAGAAAATTGA 4821
                         v  i  i              v     iv  ?   i     i  i v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_53111415_   4822 AACTGGGCCCCTTCCTTACAGTTTATACAAAAATTAACTCAAGATGGATG 4871
                          ii   i     v   i   viv                   i      v
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_53111415_   4872 AAAGGTTTAAATGT 4885
                          ?  iii       
  L1M4_orf2#LINE/    499 AWAGACCTAAATGT 512

Transitions / transversions = 1.73 (97 / 56)
Gap_init rate = 0.01 (3 / 512), avg. gap size = 1.00 (3 / 3)  

1034 26.00 4.02 1.65  chr20_53111415_53117484.rev     5157  5579 (491)    L1M4_orf2#LINE/L1      476   908 (0)  

  chr20_53111415_   5157 CAAAACTCCATCTAAAAAAAATTAAATAAATAAATGTAAAACTCAAAACT 5206
                              v iv iii    vii  i ? v vv         i vii      
  L1M4_orf2#LINE/    476 CAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr20_53111415_   5207 ATAAAAACCCTT----GAAAATCTAGGCA-ATACCATTCAGGACATAAAC 5251
                               - i   ----     iv    ?i- v i -   iv   v viiv
  L1M4_orf2#LINE/    526 ATAAAA-CTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACCTTGGG 573

  chr20_53111415_   5252 ATGGGCAAAGATTTCATG---ATGACAATGCCAAAAGCAAATTCAACAAA 5298
                         v i     v i    v i---      ---         v vv       
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACA---CCAAAAGCACAAGCAACAAA 620

  chr20_53111415_   5299 AGCAAAAATTGACAAATGATATCTAAATAAACTAAAGAGCTTCTGCACAG 5348
                           v      v  i    viv ii v vi   v v  i i   i  ii vv
  L1M4_orf2#LINE/    621 AGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr20_53111415_   5349 CAAAAGAAACTATCATCAGAAAG--AAGAGACAACCTACAGAATGGGAGA 5396
                             i  v       --      --  i        i             
  L1M4_orf2#LINE/    671 CAAAGGACACTATCA--AGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr20_53111415_   5397 AAATTTTTGCAATCTATCCATCTGATAAAGGTCTAATATCCAGAGTCTAC 5446
                             v       vii  vi         i  v  vi        i v  i
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATAT 768

  chr20_53111415_   5447 AAATAACTTAAACAAATTTACAAGAAAAAAA-----AACCCA-TTAAAAA 5490
                            v    ivv    v iv i  v     i -----      -  ?    
  L1M4_orf2#LINE/    769 AAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAA 818

  chr20_53111415_   5491 TTGGGCAAAGGACATGAGCAGACATTTCTCAAAAGAAGACACTTATGCAG 5540
                         v           iv   ii           v        i ivi viii 
  L1M4_orf2#LINE/    819 ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGG 868

  chr20_53111415_   5541 CCA-CAAACATATGAACAAAAGCTCAACATCTTTGTTCAT 5579
                            -i  i  i     v i v          v????????
  L1M4_orf2#LINE/    869 CCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.14 (57 / 50)
Gap_init rate = 0.03 (11 / 433), avg. gap size = 2.18 (24 / 11)  


3192 26.40 0.66 0.77  chr20_53270503_53276919.rev     5017  5925 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53270503_   5017 TGGAAGAACATTCCATGCTCATGGGTAGGAAGCATCAATATTGTGAAAAT 5066
                              ii i  i     i      i v     vv i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53270503_   5067 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGC 5116
                            v     v     iv i  i  i        i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53270503_   5117 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5164
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_53270503_   5165 TATGGAACCAAAAAAGAGCCCGCATCACCAAGTCAATCGTAAGCCAAAAG 5214
                                viiv  ii  v  v v  vi    iv     v i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_53270503_   5215 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5264
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_53270503_   5265 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5314
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_53270503_   5315 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCACATATCTACAACT 5362
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_53270503_   5363 CTCTGATATTTGACAAACCTGAGAAAAACGAGAAATGGGGAAAGGATTCC 5412
                         vvi    v  i     ivv  vv  i v ivvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_53270503_   5413 CTAGTTAATAAATGGTCCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5462
                           vv i  i       v      v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_53270503_   5463 GAAAATGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5512
                            iv    i    v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_53270503_   5513 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5562
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_53270503_   5563 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCGTGTCTAA 5612
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_53270503_   5613 AACACCAAAAGCAATGGCAACATAAAGCCAAAATTGACAAATGGGATCTA 5662
                         i            vvi      -    vv     v  i    v   ii v
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACA-AAAGAAAAAATAGATAAATTGGACTTC 645

  chr20_53270503_   5663 ATTAAACTGAAGACCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5712
                           i   v v  i v   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

  chr20_53270503_   5713 CAGGCAACCTACAGAATGGGAGAAAATTTTCGCAA--CATACTCATCTGA 5760
                         v  i     i                 v  i    --    i--      
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTGA 743

  chr20_53270503_   5761 CAAAGGCCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGA 5810
                         i  i  v  vi          v  i  v      vv    v iv i  v 
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_53270503_   5811 AAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACAC 5860
                             i     i     v  i?    i     i     iv    i     i
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACAT 843

  chr20_53270503_   5861 TTCTCAAAATAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTC 5910
                              v   v    i  vi viii     v  i          i      
  L1M4_orf2#LINE/    844 TTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_53270503_   5911 ACCATCACTGGCCAT 5925
                          v     ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.27 (132 / 104)
Gap_init rate = 0.01 (8 / 908), avg. gap size = 1.62 (13 / 8)  


2827 26.36 3.75 0.57  chr20_53284791_53287503.rev     1342  2221 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53284791_   1342 TGGGAAGAAATTCTATGTTCATGGATTGGAAGAATTAATATTGTAAAAAT 1391
                            i    v  i i                   v          v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53284791_   1392 ACTCATATTATCCAAAGATATCTATAGATTCAACAAAATCCCTATCAAAA 1441
                         iviv   i vi     vvv     i         iv              
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53284791_   1442 TTCCAATGGCACTTTTATTACAGAAATAGGCAAAAAAAAA--AAAAATTG 1489
                          i   iiv  -     -  i       v i   ivvi vv--    v ii
  L1M4_orf2#LINE/    101 TCCCAGCTGC-CTTTT-TTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_53284791_   1490 TACAAAGCCAGAAATGAATCATGAATAGCCAAAGCAAT-TTGAGGAAGAA 1538
                           iii iviiv  iv  vi  -           i    -    ii     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_53284791_   1539 GAACAA-TTTGGAGGTTTTGCACATCCTAATTTCAAATTATATTACATAT 1587
                               -v       vi ii   v   i         viv  i    v v
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_53284791_   1588 GTATAATAATCTAAACATTATGGTACTGGAATGAAAACAGATATATAGAT 1637
                         v  i i     v i   v i         v  i ii i   i        
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_53284791_   1638 CAACGGAGCAAAGTCAAGAGCTCAGAAATAAACCCTGGCAGACATAGTCA 1687
                            i   ii i i ii    ii             vvi  vvi  i    
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_53284791_   1688 ACTAATTTTTGACAAGAGCATCCAAAATACGTGATGGGGAAAGGATAGGC 1737
                          i i     i      i iii v i vi ivii          i    v 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_53284791_   1738 TCTTCAATCA----------GAAAACTGGGTGTTCACATGCAAAAGAATA 1777
                          i     iv ----------  v      i i?i               i
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_53284791_   1778 AAATTGGACCACTGTATTACACCATACACGAAAATAAGCTGGAAATGGAT 1827
                           i       v  iiv i        i  i     v i  vi        
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_53284791_   1828 TACAGCATTACAC-------CTAAAACCATAAAACTCTTAGAAGAACACA 1870
                         i ?  vvi  v i-------       i                  v   
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_53284791_   1871 CAGAGGAAAAGCTTCATGACATTGGTATTGACAATGATTTATT-GATATG 1919
                         i  i? v   v    i    v    vv v i     i   v  -      
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_53284791_   1920 ACACCAAAAGCTTAAGGCAACAAAAGCAAAAACAAATATGTGGGACTGCA 1969
                                    vi   -         v     i i   vi v     v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAG-CAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_53284791_   1970 CTGGACTAAAAAACTTTAGCATAGCAAAGGAAACGATCAACAAAATGAAA 2019
                         iiii v v         v iiivv       v  v     v   i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_53284791_   2020 -GATATCCTAAGGAGTCTGAAAACAAATTCTCAAATTATATATGTAATAA 2068
                         -  i v  i vi  i vv  i  v v   iv     i      v i    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_53284791_   2069 AAAGTTGATATTCTAATTATATAAGAAACCCATGCCACTCATTAGCAAAA 2118
                         iiiii vi   i vi v       ii   i v i v     v  ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_53284791_   2119 AAA-ATATAACCCTATT-AAAAATGAGCAAAGAACCTAAAAAGACGATTT 2166
                          i - v       v   -       i      i ii i  v    -    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC-ATTT 845

  chr20_53284791_   2167 CCC--AAGAAGACATACAAATAACCAATATGCAAATG------TACTGAA 2208
                          i --       i        ii      v   v   ------ i  v  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_53284791_   2209 CAACACTAATTAT 2221
                           v  ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (138 / 91)
Gap_init rate = 0.02 (16 / 908), avg. gap size = 2.38 (38 / 16)  


2484 29.13 2.34 1.00  chr20_53294116_53298798     3296  4191 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53294116_   3296 TGGAAAAGTAATCTATGCTCATGGATAGGAAGAATCAATATTGTGAATAT 3345
                               ii  vi i   i        v      v i        v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53294116_   3346 GGCCATACTGCCCAAAGTAATTTATAGATCCAATGATATTCCCATCAAGC 3395
                            v     v      v i  i  i    i   i vv  i  i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53294116_   3396 TCCCATTGACTTTCTTTG--GATAATTAGGACAAACT-ACTTTAACTTTC 3442
                              vivi i  i    --  -    --     i  - iii   vv   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGA-AATT--GACAAGCTGATCCTAAAATTC 147

  chr20_53294116_   3443 ATATGGAACTCAAAAAGAGCCCGTATAGCCAAGGCAATTCTAAGCAAAAA 3492
                                 v vv  ii  v  v v        ii    ii i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_53294116_   3493 CAACAAAGATGAAGGCATTATGCTACCTAACTTCAAACTATACTACAAGG 3542
                         v       v  i   vv i ii  v  i  i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_53294116_   3543 CTACAGTAACCAAAACAGCATGATATTAGTACCAAAACAGATATGCAGAC 3592
                                  i   i    ii  i  i i i iv ii i   i  ii   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_53294116_   3593 CAATGGAACAGAATAGAGACATTAGAAATAACACCACACATCTACAACTA 3642
                                 i     v    vvii        vv   i    i  iiiii 
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_53294116_   3643 TCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGAC--TC 3690
                         vi    i  i     ivv  vv  i v  vv            i i--  
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_53294116_   3691 TTTATTTAATAAATGGTTTGGGGAAAACTGGCTAGCCATA-ACAGAAAAC 3739
                            -- i  i       viv    v      v  ?   i -i  i  i v
  L1M4_orf2#LINE/    398 TTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_53294116_   3740 TGAAACTGGAAAACTTCCCTACACCTTATATGAAAATTAAGTCAAGATGG 3789
                             ii    vvv  v  ii     v    ii        v    i    
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGG 495

  chr20_53294116_   3790 GTTAAAGTCTTAAATGTAAAAACCAAAACCATAAAACCCT-AGAAGAAAA 3838
                         i i ?  v i         i i i     i       i  -         
  L1M4_orf2#LINE/    496 ATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA 545

  chr20_53294116_   3839 CCTAGGCA-ATACCATTCAGGACAGAGGCATGGGCCAAGATTTCATGACC 3887
                          v    ?i- v i -   iv   vvv  vv i   v v i    v iivi
  L1M4_orf2#LINE/    546 CATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_53294116_   3888 AAAACACCAAAAGCAATTGCAACAAAAGCCAAAACCGACAAATGGGAGCT 3937
                          vi            vvv          vv    iv  i    v   vi 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_53294116_   3938 AACTAAACTAAAGAGCTTCTGCACAGCAAAATAAACTAGCATCAGAGTGA 3987
                         v ii   v v  i i   i  ii vv    iv v    v  vv i     
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_53294116_   3988 ACAGGCATCCTACAGAATGGGGGAAAATTTTTGCAGTCTCTCCATCTGAC 4037
                          v  i  v  i          i      v      iviiv vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_53294116_   4038 AAAGGTCAAATATCCAGAATCTACAAGGAATGTAAACAA---AGTCACAA 4084
                           i  v vvi          v  i  i   ivivv    --- i v i  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_53294116_   4085 GA-GAAACACAACCCCATCAAAAA---------GGATATGTACAGACACT 4124
                         i -  v v i     v  i?    ---------    v  v i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_53294116_   4125 TCGCAAAAGAACATATTTATCCATCCAAAAAACATAGGAAAAAAAAAAGC 4174
                           v v      v    vi vviiv    v  i  i v     i v---  
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT---GC 891

  chr20_53294116_   4175 TCAACATCACTGGTCAT 4191
                                  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.23 (142 / 115)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 2.14 (30 / 14)  


3417 17.82 8.62 4.25  chr20_53347391_53349720      969  1838 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53347391_    969 TGAAACGTCATTCAATGTACACGGATAGGAAAACTTAA---------GAT 1009
                           i  v vi  i v    v  i    v    i      ---------   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53347391_   1010 AGCGATACACGCCTAATTC-TCAACAGATGTACCGCAATCCTTATCAAAA 1058
                         i  i    v v  v    v-  v      vi v        i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53347391_   1059 TCTCCCATGCCTTTTT-GCATAAATTAACAAGTAGATC-TAGAATTCATA 1106
                           i vvv         -   v     i     iv    -  i        
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_53347391_   1107 T---------AGGGACCCAGAATAGTCAAATCAATCTTGAT---GAAGAA 1144
                          ---------               i    v         v---      
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_53347391_   1145 CAAGACTGGGGGACTTTCACTTTTCAATTTCAAAGCTTACTACAAAGCAA 1194
                            iii   i     iv     ii          i             v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_53347391_   1195 CAATAATCAAGATCATGTGATACTAGCCTAAGGACAGCC-TGTTGATCAA 1243
                           i         ivi    i    i  v      i  v - i v      
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_53347391_   1244 TAGAATGAAATTGAGAGTCCAGAAATAAAGTCCTACATTTATGGCTAATT 1293
                          i    ii                     vi v           ii    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_53347391_   1294 GATTTTCAACAAGGATGCCAAAACAATTCAGTGAGAAAAAAAAAAAAAAA 1343
                                i      i      i  v     i  i i   i  --------
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA-------- 392

  chr20_53347391_   1344 AAGAGTCTTTTCAACAAATGGTGCCCAGACAATTGGATATCCACATGCAA 1393
                         --v                     ivi     i      ?          
  L1M4_orf2#LINE/    393 --TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAA 440

  chr20_53347391_   1394 AAAAAAAAAAAAAAAAAAAAATTAAGTTGGACCCCAACCACATACCATAT 1443
                           i  ---------------- v            v   v  i       
  L1M4_orf2#LINE/    441 AAGAA----------------TGAAGTTGGACCCCTACCTCACACCATAT 474

  chr20_53347391_   1444 ATAAAAAACTAATTTAAAATATATGACAAACCTATATGTAAGAGTCAAAA 1493
                          i     -i   i i     iv  v ? i     v         ii    
  L1M4_orf2#LINE/    475 ACAAAAA-TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr20_53347391_   1494 ATACAAAACTCTTAGAAGAAAACATGAGAATACATCTTCATAA------- 1536
                         v  i                     ii ?i  v      i i -------
  L1M4_orf2#LINE/    524 CTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGG 573

  chr20_53347391_   1537 ------AAT---TTATCAGATACTATACTAAAAGCAAAAGCAATAAAAGA 1577
                         ------   ---  v i     iv i  i       v      i      
  L1M4_orf2#LINE/    574 TTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGA 623

  chr20_53347391_   1578 AAAAA---ATAAATTGGAGTTCACGGAAATTAAAATATTTTTGCACTACA 1624
                              ---          v    ivi         - i     ii  v  
  L1M4_orf2#LINE/    624 AAAAATAGATAAATTGGACTTCATCAAAATTAAAA-ACTTTTGTGCTTCA 672

  chr20_53347391_   1625 AA--ACATGATT-------------------TTACTGACTGGGAGAAAAT 1653
                           --   iv  i-------------------ii  v  v           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_53347391_   1654 GTTGGCAAATCATATAACTGATGAGGGACCTGTATCTAGAATACATCAAA 1703
                         i  v            v     i      i      i      i  v  i
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_53347391_   1704 AATTCTTTTAACTCAATAA------GACAAATAGCT--ATTTTTTTTAAA 1745
                           i    vi          ------        i i--   ?------- 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW-------A 815

  chr20_53347391_   1746 AAAATGAGCAAATAAATCTGCCTAGATATATCTCTAAAGAAGATATATTG 1795
                               i     -ii  i  vv    i  v    i            i-i
  L1M4_orf2#LINE/    816 AAAATGGGCAAA-GGATTTGAATAGACATTTCTCCAAAGAAGATATAC-A 863

  chr20_53347391_   1796 AATTGC--ATAAGCATGAGAAAAGATGCTCAACATCATTAGCTAT 1838
                            v  --       iiv                   ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (95 / 56)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 5.09 (112 / 22)  


2869 26.00 2.33 1.44  chr20_53355318_53361074     4366  5265 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53355318_   4366 TGGAACATACATTCCATCCTCATGGATAGGAAGAATCAATATCGTGAAAA 4415
                              - v i  i    vi        v      v i     i  v  i 
  L1M4_orf2#LINE/      1 TGGAA-AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr20_53355318_   4416 TGGCCATACTGCCCAGAGTAATCTACAGATTCAATGCTAT-----TCAAA 4460
                             v     v    i v i              i  v  -----     
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_53355318_   4461 CTACCA-TTGAATTCTTCACAGAATTAGAAAAAACT-ACTTTAAATTTCA 4508
                         v v   -i  vv  i  ii     v v  v  i-  - iii    v    
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCA 148

  chr20_53355318_   4509 TATGGAACCAGAGAAGACCCCCTATAGTCAACACAATCCTAAGCAAAAAG 4558
                                viiv iii     vvv    i   v      i i iv  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_53355318_   4559 AACAAAGCTGGAAGCATCATGCAACCTGACTTCGAACTATACTACAAGGC 4608
                                i    i vv   ii vv  ii i   i  viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_53355318_   4609 TACAGTAAGCAAAACAGCATAGTACTGGTACCAAAACAAATATGTACACC 4658
                                 v   i    ii i       i iv ii i i i  i  v i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_53355318_   4659 AATGGAACAGAACAGAGACCTCAGAAATAACACCACACATCTATAACCA- 4707
                                i    iv    vii         vv   i    i   iii  -
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_53355318_   4708 ----TCTTCGACAAACCTGACAAAAACAATCAATGGGGAAGGGATTTCCT 4753
                         ---- i        ivv  v   i v  v           i i  vvi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_53355318_   4754 ATTCAATAAATGGTGCTAGGAAAACTGACTACCTATATGCAGAAAACCGT 4803
                         v     i          i   v     iv  ? i i     i  i vi v
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_53355318_   4804 AACTGGACCCCTTCCTTACACCTTATTCAAAAATTAACTTAAGATGGATT 4853
                          ii         v   i     v   v            i  i      i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_53355318_   4854 AAAGATGTAAATGTAAAACCTAAAACCATAAAAACTCT-AGAAGAAAACC 4902
                          ?   iv         i v       i      -    -          v
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACA 547

  chr20_53355318_   4903 TAGGCA-ATATCACTCA-GGTCATAGGCATGGACAAAGACTTC------A 4944
                             ?i- v   -i  i- ii v i  i- i i   v ii   ------ 
  L1M4_orf2#LINE/    548 TAGGNGTAAATC-TTCGTGACCTTGGGT-TAGGCAATGGTTTCTTAGATA 595

  chr20_53355318_   4945 TGACAAAAATGCCAAAAGCAATTGCAACAAAAGCCAAAATTGACAAATGG 4994
                              ------         vvv          vv     v  i    v 
  L1M4_orf2#LINE/    596 TGACA------CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTG 639

  chr20_53355318_   4995 GATCTAACTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCATCAG 5044
                           ii v ii   v v  i i   i  ii vv    i  v       vv i
  L1M4_orf2#LINE/    640 GACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_53355318_   5045 AGTGAACAGGCAACCTACAGAATGGGAGAAATTTTTTGCAATCTACCTAT 5094
                               v  i     i               v v       vii iv   
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_53355318_   5095 CTGACAAAGGTCTAATACCCAGAATCTACCAGGAACTTAAACAAATTTAC 5144
                             i  i  v  vi  i       v  iv i     ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_53355318_   5145 AAGAAAAAAAATCAAACAACCCCATCAAAAAGCGGCCAAAGGAAATGAAC 5194
                           v     i --    i     v  i?    ii  v       vv    i
  L1M4_orf2#LINE/    790 AATAAAAAGA--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_53355318_   5195 AGACACGTCTCAACAGAAGACATTTACATGGCCAAAAACCATATGAAGAA 5244
                              iv    v v      i  vi v        v  v  i     i i
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_53355318_   5245 AAGCTCAACATCACTGATCAT 5265
                          v           ????????
  L1M4_orf2#LINE/    888 ATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.32 (131 / 99)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.27 (34 / 15)  


2408 27.31 6.71 1.62  chr20_53385342_53387269.rev      583  1446 (482)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53385342_    583 TGGAAAGATTTTCTGTGTTTCCAGAATGGAATACTCTACCTAGTAAAGAT 632
                                  v i ii    ivii  v     v   iv iv v  v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53385342_    633 GCCAATTCTTCCTAAATTGAGGTATAGGTTTAAC---ATGTTTAC----- 674
                          v    v  i  i       vv  i  i  i   ---  vii  i-----
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53385342_    675 ---------------TTGTAGATACAGATAAGCTGATTCTAAAGATCAC- 708
                         ---------------   i   v iv  i        i     iv   i-
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_53385342_    709 -GGAAAGGCAAAGGAATTAGACTAGCAACAGCAATTGTGTAAAGTAAGAA 757
                         -     v    i   vii   v    v v i    iv  v   iv     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_53385342_    758 TTAAGTAGGAGAA-TCACATTACTTGATTTTGAAGACTTCCTTTATAGGT 806
                         iv    v    i -     i v iii    ii  -    v  vi v  v 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAA-ACTTACTACAAAGCT 249

  chr20_53385342_    807 TCAGTAATCAGGA--ATATTGTATTAGTAAAAGAATAAATATATAAATCA 854
                         v         i  --i i v   i i i v   i   i i     i    
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_53385342_    855 ATGGAACAGAATGGAGAACTCAGAAACAGTTCCACACA---AGGAT---- 897
                               i     v    iii      i ivi   i   --- v i ----
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_53385342_    898 -GAGTCTTGACAAAGGTGCAAAAGCAATTCAATAGAGGAAGGATAGTCTT 946
                         -  v i i     i     v  ii v       i i i   i        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_53385342_    947 TTCAACAAATGATGCTTGAATAATTGGACATTTATAGGCATAAAAAT-AA 995
                                    i    v i i  i    i ?ii i v   v  i   -  
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_53385342_    996 TCTAAA-----ACT---CATC-TATGAAATAATTGACTTGAA-TGGCTCA 1035
                         vi ii -----  i---  i -   iv  v    i   ii  -   v   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_53385342_   1036 TAGATCTAAATATAAACGATAAAATTATCAAACTTTTAGAGAAAAACATA 1085
                         ?   i      i   iv v     i   v     i     ii        
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_53385342_   1086 GGAAAAAGTTCTCATGACCTAGGATTAGGCAAAGAGTTCTTATATAAGAA 1135
                           ?iv  i ii  i      v  i        v iv      v   v  v
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_53385342_   1136 ACTAATGTCATGATCCATGAAAGGGAAAATTAATATATTGGAC---ATCA 1182
                           i  viv  ii v v ii    ii     vi   v       ---    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_53385342_   1183 AAATGTAAAACTTCT-TCCATACAAAAGACCTTCTTACAAGCATGAAAAT 1231
                             vv       i - v v -    i   vi v i vi ivi      v
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTT-CAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_53385342_   1232 AAAAGCCAAATACTGGGAGAAAATACTCGCAAATCACATATTTGCAAATA 1281
                          v  v   v v v            i i        i    i  ---   
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTG---ATA 745

  chr20_53385342_   1282 TCAGATACACATGACTCACATGCCTAATATAAAAAGAACTCT-----CTA 1326
                         --  i-------    iii  v vv      v          -----  v
  L1M4_orf2#LINE/    746 --AGG-------GACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

  chr20_53385342_   1327 AACAGTAAGAAAACAAGCAATCCAATTAGAGAATGGGCAACAAACTTGAG 1376
                           i i   i  i    ii  i      ?i i         vii i    i
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

  chr20_53385342_   1377 CAGACACTTCACCAAAGATGATATATGAGTAGCACATAAGCACAAGAAAA 1426
                         i     i   v       v      ii i i  vv         v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_53385342_   1427 AA--ATCCACATTATTAGTTAT 1446
                         i --v  v    i ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.58 (142 / 90)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.43 (72 / 21)  


1569 25.98 12.73 4.86  chr20_53415010_53417434     1171  1932 (493)    L1M4_orf2#LINE/L1       59   880 (28)  

  chr20_53415010_   1171 TCTCTAAATTCATCTATAGATTCACCAAAATCTTAATTATAATTCCAGCA 1220
                           i i     v     i       v iv    iiv  i v   i     -
  L1M4_orf2#LINE/     59 TCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGC- 107

  chr20_53415010_   1221 AATGTTTGTTGTTGTTGTTGTTTCTGTTAATTTGACAAATGGATTCCAAA 1270
                         --  ii v  ----   iv --------  v       iiv   i i   
  L1M4_orf2#LINE/    108 --TGCCTTTT----TTGCAG--------AAATTGACAAGCTGATCCTAAA 143

  chr20_53415010_   1271 ATTTACATAGAAATTCAAAATACCTAGACCTTAACCTAGACCTGAACTAC 1320
                            i i  i     v   iiv   i   ----- --   -- ii  ----
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGA-----A--TAG--CCAAA---- 180

  chr20_53415010_   1321 ACAATCTTTTAAAAAGATAGCAAAG-------ACTTTTCCTTACCTGATT 1363
                                 vv    ii v i     -------   iviv   -  ii   
  L1M4_orf2#LINE/    181 ACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTT-CCCAATT 229

  chr20_53415010_   1364 TCAAGACTCACCATAATGCTACATTAGTCAAGCTAGTGCAGTTGTGGCAC 1413
                             i   i  i i  v      v  i     vi    ii  vv     i
  L1M4_orf2#LINE/    230 TCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCAT 279

  chr20_53415010_   1414 AAAGCTGGACAAATGAATTCATAGCTCTGAATAGAGAGTCCAGAAATAGA 1463
                           i v i    v  ii  iv  i vviv    v               i 
  L1M4_orf2#LINE/    280 AAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAA 329

  chr20_53415010_   1464 CACATATGCATATGGTCAATTGATTTGTTGGCAAAGATGCCAAAACATTT 1513
                          v    iiiv                - i i   i i      i  vv  
  L1M4_orf2#LINE/    330 CCCATACATTTATGGTCAATTGATTT-TCGACAAGGGTGCCAAGACCATT 378

  chr20_53415010_   1514 CAATAAAGAAAAGAAAGTTTATTCA-CAAGAGAATGCTGGAACAATTGGA 1562
                             iii    ii v   i v    -   - vii      i    i    
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAA-ATGGTGCTGGGACAACTGGA 427

  chr20_53415010_   1563 TAACCGCATAGAACAAAAGA-TGAAACTCAATGCCTACCTAACTTTCAAT 1611
                           ?  i   i---       -    ii vi iv       v  viivv  
  L1M4_orf2#LINE/    428 TAKCCACATG---CAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr20_53415010_   1612 GCAAAAATCTAAGCCAAGATAAAT-ATATACCTAAATGTAGGAGCTAAAA 1660
                         i       -   vi   i  ii  - ? v           i         
  L1M4_orf2#LINE/    475 ACAAAAAT-TAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr20_53415010_   1661 CTGTAAAGCTTTCTAAACTAATGCATAAGAAAATATCCTTATGGCTATAA 1710
                           i    i  i -  i vv  vi    i ?iv v   i ii  i iv ii
  L1M4_orf2#LINE/    524 CTATAAAACTCT-TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr20_53415010_   1711 GTTAGGCAAAGATTTCTTA----TAAC-TCAGGAACATTGATCATACAAG 1755
                                  v i       ---- i  -i  ii i  iviiiv i v   
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_53415010_   1756 AAACAATA----AATTTGACTTC------------------TGTTCATTA 1783
                            v    ----    v      ------------------   v v i 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_53415010_   1784 ---GATATTATCAAGAAAATTAATATGTA---TGCA---TGGAGAAAAA- 1823
                         ---  i i          i v  v vii ---ii  ---   iii    -
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_53415010_   1824 ---------------------------------ATCCAGAATACATAAAG 1840
                         ---------------------------------          i      
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_53415010_   1841 AAATCTTATGAT--GGTAATAAAAAGATAAA----CTAAT-AATAAATG- 1882
                           v     ii i--ii           i   ---- i   -? v     -
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_53415010_   1883 -CAA----T---AATCCATATTTC-ACAAGGAAGATAAGCAGAATGGCCA 1923
                         -   ---- ---   vv i     -v   i       vi  -        
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA-AATGGCCA 871

  chr20_53415010_   1924 ATACACACA 1932
                            vi    
  L1M4_orf2#LINE/    872 ATAAGCACA 880

Transitions / transversions = 1.90 (127 / 67)
Gap_init rate = 0.04 (33 / 822), avg. gap size = 4.06 (134 / 33)  


3562 25.69 0.22 0.11  chr20_53452229_53455890.rev     2264  3170 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53452229_   2264 TGGAAAGATATTCTATCTTCATAGATTAGAAGAATCAAAATTGTTAAAAT 2313
                                    i i  v     i    i     v i  v        i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53452229_   2314 GTTCATACTACCCAAAGAAATCTGGAGATTCAATATAATCTACATCAAAA 2363
                          viv     v      vvi    iv        iii    ivi       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53452229_   2364 TATCAGTGACATTCTTCACAGAAAAAGAAAAAA-AATCCTAAAATTTATA 2412
                          vi   ivi v  i  ii      vv  v  iv-i           i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_53452229_   2413 TTGAACCATAGAAGACCTTGAATAGCCAAAGCTATCCTGAGCAAAAAGAA 2462
                          v   viii iii    iv           i v   i   iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_53452229_   2463 CAAAACAGGAGGAATCACATTATCTGACTTCAAATTATGCTGCAGAGCTA 2512
                             iiv      v     i vi ii i      viv i  i  i     
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_53452229_   2513 TAGTAACCAAAACAGCATGGTACTGGCATAAAAATAGACACATAGACCAA 2562
                         i     i   i    ii              ii       i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_53452229_   2563 TGGAACAGAATGGTGAACCTACTAAAAAATCCATACATCTAGAGTAAACT 2612
                              i     v v  ii i vv  v   i        i  vi  v  i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_53452229_   2613 TATTTTCAATAAAGGTGTCAAGAACATACAATGGGGAAAGAATAGTCTCT 2662
                         v      i i  i    i     v   v                    i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_53452229_   2663 TCAATAAATGGTGCTGGGAAAACTAGACACGCATATGCAGAAGGATGAAA 2712
                             i              v    i  i ?v  i     i   i     i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_53452229_   2713 CCATACTCCTATCTCTCACTATACA-AAAAATTCAAATTGAAATGGATAA 2761
                         iiiv  i    i   v   i   i -       -  v ii        v 
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATT-AACTCAAAATGGATCA 499

  chr20_53452229_   2762 AATACATAAATCTAAGACCTCGAGCTATAAAACTTCTAAAAGAAAACATT 2811
                         ? v  v     v     v  vi i          ii  i          v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_53452229_   2812 TGGAAAATTCTCTAAGACATTGATCTGAGCAAAGATTTTTTGAGTAATAC 2861
                         v ?iv  v   iiiv   v   ivi ii    v i   i  iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_53452229_   2862 GCCCAAAGCACAGGCAACCAATGTAAAAATGGACACATGGGATCACATTA 2911
                         i  v        i     v  v v      i  i v  v   iiv   i 
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_53452229_   2912 AGTTGAAATGATTTTGAGCAGCAAAGCAAACAATCAACAAAGTGAAGAGA 2961
                          iv v   viv     v  vv     v v  v     v        i   
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_53452229_   2962 CAACCCACAGAATGAGAGAAAATATTTGCAAAATGTCCATTTGACAAGGG 3011
                                       i                 vii vi  i   i     
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_53452229_   3012 ATTAATGACCAGAATATGTAAGGAACTCAAACAGTTCTATAGGAAAAAAT 3061
                          i vi iv         i   i      vv   ii  v   iv     iv
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_53452229_   3062 CTAATAATCTGATTAAAAAGTGGGCAAAAGGTCTGAATAGACATTTCTCA 3111
                          v     i ii   ?    i        i i i                v
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr20_53452229_   3112 AAAGAAGACATACAAATGGTAAACAGGTATATGAAAAGGTGCTCAATATC 3161
                                 i          iv  i i i i        i       i   
  L1M4_orf2#LINE/    850 AAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATC 899

  chr20_53452229_   3162 ATTGGTCAT 3170
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 1.60 (141 / 88)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.00 (3 / 3)  


 648 25.00 20.71 0.36  chr20_53459255_53463715     2751  3030 (1431)    L1M4_orf2#LINE/L1       29   365 (543)  

  chr20_53459255_   2751 GAATAC--AATA--GTAAAGATGTCAGTATCATCCATATTCATATACAGA 2796
                            v  --    --  v      v  i  iivi   v   v  v      
  L1M4_orf2#LINE/     29 GAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chr20_53459255_   2797 TTTAATGCAATTTCTACCAAAATCCCTGCAAGAATTTTTTGTAGATTTAG 2846
                           i  i     ii   i         v  v- vv       i   vv v 
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAGCT-GCCTTTTTTGCAGAAATTG 127

  chr20_53459255_   2847 ACAA-----------------TAT-----TG------------------- 2855
                             -----------------   -----  -------------------
  L1M4_orf2#LINE/    128 ACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCAGAATAGCC 177

  chr20_53459255_   2856 --AATAATCTTGAAAACAAAAAATAAGGTGAGATGAATTAGTCTACTCAA 2903
                         --  i           vi  i  i  i  vi  v  v i vv  v i   
  L1M4_orf2#LINE/    178 AAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAA 227

  chr20_53459255_   2904 TTTTAAGA---ATTACATAG----AGTAATCAAGACTGTATGATATTGGC 2946
                            i  i --- i    v  ----            v  i  i  i    
  L1M4_orf2#LINE/    228 TTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGC 277

  chr20_53459255_   2947 A-GAGAATGGACACACAGATCAATGAAATGGAAT--AGAGTCTAGTCATG 2993
                          -i  i  i    i i         i   i    --      i  vv  i
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr20_53459255_   2994 GACCCACATACATATG-TGAAACAATTTTGGACAAAAG 3030
                         i     i i iv    - v  vii     v     ii 
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGACAAGGG 365

Transitions / transversions = 1.41 (41 / 29)
Gap_init rate = 0.03 (11 / 337), avg. gap size = 5.36 (59 / 11)  

1039 26.18 7.87 4.13  chr20_53459255_53463715     3454  3961 (500)    L1M4_orf2#LINE/L1      359   885 (23)  

  chr20_53459255_   3454 ACAAAAGT-TCAAAACCAATTCAATGGAAGAAGGAGAGCCTTTTCAATAT 3502
                             ii  -i   i    -        iii   i v  i        i v
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCA-TTCAATGGGGAAAGAATAGTCTTTTCAACAA 407

  chr20_53459255_   3503 ATGATGCTGAGCTAATTGGATATCAACAAGTGAAA-AATGAGCTCAGACT 3551
                            i     i vi  i      ? v   v ii   -     iv ii   i
  L1M4_orf2#LINE/    408 ATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACC 457

  chr20_53459255_   3552 --TAAGTCACATACTTTACAAAAATTAA---------AATCACAGGCTTA 3590
                         --  vv     ivv v            ---------i    ?  i i  
  L1M4_orf2#LINE/    458 CCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTA 507

  chr20_53459255_   3591 AATGTACAACCTGAAACTATACAGTTTGTAGAAAAATAGAACATTTTCAA 3640
                               vi v  i        v ii iv     i  ---     ----- 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA---AACAT-----A 549

  chr20_53459255_   3641 CATCTAGAGTTTTCAACATCTAGAGTTAGGCAAAAAGGCTATATAGACTT 3690
                         vi?v  i - i   ivv i  v i         v--  i viv    iv 
  L1M4_orf2#LINE/    550 GGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAAT--GGTTTCTTAGATAT 596

  chr20_53459255_   3691 GATACTAAAAGCAGTTTATG----AAAGGAAAAAATTGATAA-TAGGACC 3735
                           i  i       ---i v ----   i        v     - v    i
  L1M4_orf2#LINE/    597 GACACCAAAAGCA---CAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_53459255_   3736 TCAACAAAATTAAATACTCTTGTTCTGCAAA--ATTCTATCCTAAGAGAA 3783
                            v          v   i    v  v    -- iv     --    i i
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATC--AAGAAAG 691

  chr20_53459255_   3784 TGGAAAGACAAGCTAAAGACCACGATAAAATATCTGCAAGTCACAT--CT 3831
                           i        v i v   viiv  v       i     i   i  --  
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_53459255_   3832 GACAAATGA--TG-----GGGATGTTCAAAACTGAATGTTCAAAACTTAG 3874
                           i  iv  --  -----i i  i vi   ---   ivi i v    i i
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAA---GAACTCTTACAACTCAA 788

  chr20_53459255_   3875 CATTAAAAA---AAAT--C----TTAGAAAATGGACCAAAAACCACAGTG 3915
                         i v      ---    -- ----  ?i       i v  ii iivv i -
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT- 837

  chr20_53459255_   3916 ATGCATTTTACCAGAGAA--TATACAAATGAGAAATAAACACATAAAA 3961
                          vi     iv   i    --          ivv     i     i   
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAA 885

Transitions / transversions = 1.63 (80 / 49)
Gap_init rate = 0.04 (23 / 527), avg. gap size = 2.65 (61 / 23)  


1920 24.84 5.97 1.94  chr20_53513513_53515124.rev      501  1120 (492)    L1M4_orf2#LINE/L1      264   908 (0)  

  chr20_53513513_    501 AGTATGATAGTAGAGAAAGGATAAACATATAGATCAATAGAAGAGATTAG 550
                            i  i  v i viv       i              i   v   v v 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr20_53513513_    551 AAAAGTCAGAAATAGACTCACAAATT-ATAGTTGATTGACTCTT---AAA 596
                          i ivi        i  i  i v   -  i  ii     i i i---  i
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr20_53513513_    597 GATGCAAAAGCAATT----AGGGACAAGATAGTTTTTTCAAAAAATTATG 642
                          i   v  ii v   ----i    v ii     i       v    vi  
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr20_53513513_    643 CTGAAATA--TGGG------------AAAAAATGAGTTTTTACCAATATT 678
                            ii i --   i------------   i     iv  vv   vv  ii
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr20_53513513_    679 TTGCACCCTATACAAAAGT-AACTCAGAATAGATCATAAACTTGAATATG 727
                          ii    v         i -      i   i     ? i  i i   i i
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr20_53513513_    728 AAACCTAAAAGCACAGCATTCCTTAAAAAAAAAAAAAAAGAAAGAAAATC 777
                          i v      vi i iv i  -   i  i    v v ii?--- v     
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTC-TTAGAAGAAAACATAGGN---GTAAATC 559

  chr20_53513513_    778 TCTGTGACCTTGAGTTTGGCAAAGATTTATTAGGTATGACACCAAAGACA 827
                          ii         i   v     v i   v    i            ii  
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr20_53513513_    828 TGATTCATAGACTAATTTAAAAATAGGTAAATTGAACTTCACCAAAATTA 877
                         ii viv i i vv  ----       i       i      i        
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAA----AAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr20_53513513_    878 ACTGGATTTTT---CTTCAAAAGAAAC----AAGAA--TGAGAAGGCAAG 918
                          --ii i    ---       i  v  ----     --   i   i   v
  L1M4_orf2#LINE/    656 A--AAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAAC 703

  chr20_53513513_    919 GCACAGATTAGGAGAAAATATTCACAAAACTCA---ATCTGATGAAAGAC 965
                         v      v i            ii    --   ---       i ii   
  L1M4_orf2#LINE/    704 CCACAGAATGGGAGAAAATATTTGCAAA--TCATATATCTGATAAGGGAC 751

  chr20_53513513_    966 TTTTATGCAAAAGGTATAAAGAACTCTCA-AACCCAATAATCAGAAAGCA 1014
                           v   v  i  vi             i -   i       v i  ii  
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACA 801

  chr20_53513513_   1015 AATAATTCAGTTAGGAAATGGGCAAAATACTTGAACAGACATTTCACTAA 1064
                              ii  i  ?ii           iv i     i         v i  
  L1M4_orf2#LINE/    802 AATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 851

  chr20_53513513_   1065 -GAAAATATAAGGATGACAAATAAGCAGATGGAAAGCTACTTAGCATCAC 1113
                         -   i     vii   i v        v   i    v i  i i     ?
  L1M4_orf2#LINE/    852 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZ 901

  chr20_53513513_   1114 TAGTGAC 1120
                         ???????
  L1M4_orf2#LINE/    902 ZZZZZZZ 908

Transitions / transversions = 2.28 (105 / 46)
Gap_init rate = 0.03 (17 / 645), avg. gap size = 2.88 (49 / 17)  


2911 26.59 1.32 1.54  chr20_53542688_53552861      493  1402 (8772)  C L1M4_orf2#LINE/L1   (0)   908     1  

C chr20_53542688_   1402 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCATGAAAAT 1353
                               i i  i     i        v      v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr20_53542688_   1352 GGACATACTGCCCAAAGCAATTTATAGATTCAATATTACCCCCATCAAGC 1303
                           vv     v      vii  i  i        iiiv i   i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr20_53542688_   1302 TACCATTGACTTTTTTCACAGAATTAGAAACAACT-ACTTTAAACTTCAT 1254
                          v   vivi i     ii     v v  v - i  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACA-AGCTGATCCTAAAATTCAT 149

C chr20_53542688_   1253 ATGGAATCAAAAAAGAGCCTGCATAGCCAAGACAATCCTAAGCAAAAAGA 1204
                               viiv  ii  v  v v        i      i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

C chr20_53542688_   1203 ACAAAGCTGGAGGCATCATGCTGCCTGACTTCAAACTATACTACAAGACT 1154
                               i      vv   ii  v  ii i      viv        ii  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

C chr20_53542688_   1153 ACAGTAACAAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACCA 1104
                                iv  i    ii         i iv ii i   v       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

C chr20_53542688_   1103 ATGGAACAGAAC--AGAGTCCTCAGAAATAACACCACACATCTACAACCA 1056
                               i    i--       --        vv   i    i  iiii  
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTCA 347

C chr20_53542688_   1055 TCTGATCTTTGACAAACCTGACA----CAAGCAATGGGGAAAAGATTCCC 1010
                         vi    i  i     ivv  v  ----  vv           ii  vvi 
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

C chr20_53542688_   1009 TATTTAATAAATGCTGTTGGGAAAACTAGCTAGCCACATGCAAAAAAAAA 960
                          v  i  i     v  i     v    i v  ?            i  --
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA-- 445

C chr20_53542688_    959 TTGAAATTGGACCCCTTCCTTATACCTTATACAAAAATCCACTCAAGATG 910
                         -    i          v   i i   v           iv      i   
  L1M4_orf2#LINE/    446 -TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

C chr20_53542688_    909 GATTAAAGACTGAAACCTAAGACCTAAAACCATAAAAATCCTA-AAGAAA 861
                            i ?    iv   iv     v       i      v  i  -      
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

C chr20_53542688_    860 ACCTTGGCA-ATACCACTCAGGACATAGACATGGGCAAAGACTTCATGTC 812
                           v v  ?i- v i -i  iv   v v ivv i     v ii   v ivv
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

C chr20_53542688_    811 TAAAACACCAAAAGCAATGGCAACACAAGCCAAAATTGACAAATGGGAAC 762
                           vi            vvi      v   vv     v  i    v   vi
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

C chr20_53542688_    761 CAGCAGCACATCAAAACAAAGAGCTTCTGCACAGCAAAAGAAACTGTCAT 712
                         i-------        iv  i i   i  ii vv    i  v   i   v
  L1M4_orf2#LINE/    644 T-------CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAA 686

C chr20_53542688_    711 CAGCATGAACAGACAACCTACAGAATGGGAGAAAATTTTTGCCATCTATC 662
                         v ivi    v        i                 v     v vii  v
  L1M4_orf2#LINE/    687 GAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATA 736

C chr20_53542688_    661 CATCTGACAAAGGGCTAATATCCAGAAACGACAAATAACT--TA-AACAC 615
                         i      i  i  i  vi         vvv i   v    --  -   v 
  L1M4_orf2#LINE/    737 TATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTC 786

C chr20_53542688_    614 GTTTGTAAGAAAAAAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAA 565
                         iv vi   i  i v   i     v  i?    i            v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

C chr20_53542688_    564 CAGCAACTTCTCAAAAGATGACATTTATGCAGCCAACAAACATATGAAAA 515
                         i  vv i     v     v  i  vi viii     i  i  i       
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

C chr20_53542688_    514 AATGCTCATCATCACTGGTCAT 493
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (136 / 102)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 2.17 (26 / 12)  

 458 20.49 0.00 0.00  chr20_53542688_53552861     4777  4898 (5276)  C L1M4_orf2#LINE/L1   (0)   908   787  

C chr20_53542688_   4898 AAAAAAAAAAAAACAAACAACCCCATCAACAAGTGGGCAAAGGATATGAA 4849
                           v  v     i     i     v  i? v  i            v    
  L1M4_orf2#LINE/    787 AATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA 836

C chr20_53542688_   4848 CAGACACTTCTCAAAAGAAGATATTTATGCAGCCAAAAGACACAAGAAAA 4799
                         i     i     v           vi viii     v ii    v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

C chr20_53542688_   4798 AATGCTCATCATCACTGGCCAT 4777
                         i       v     ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (13 / 11)
Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.00 (0 / 0)  

2859 27.47 0.62 0.62  chr20_53542688_53552861     5204  6004 (4170)  C L1M4_orf2#LINE/L1   (107)   801     1  

C chr20_53542688_   6004 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 5955
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

C chr20_53542688_   5954 GGCCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCATTAAGC 5905
                            v     v     iv i  i  i        i iv     i  i  iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

C chr20_53542688_   5904 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5857
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

C chr20_53542688_   5856 TATGGAACCAAAAAAGAGCCCGCATTGCCAAGACAATCCTAAGCCAAAAG 5807
                                viiv  ii  v  v v  v     i      i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

C chr20_53542688_   5806 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGC 5757
                                i      vv    i  v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

C chr20_53542688_   5756 TACAGTAACCAGAACAGCATGATACTGGTACCAAAACAGAGATATAGACA 5707
                                 i  ii    ii  i      i iv ii i   v       iv
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

C chr20_53542688_   5706 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCACATATCTACAACT 5659
                                i    i--    i  --        vv   i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

C chr20_53542688_   5658 ATCTGATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCC 5609
                          vi    i  i     ivv  v   i v  vvv           i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

C chr20_53542688_   5608 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5559
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

C chr20_53542688_   5558 GAAACTGGATGCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGA 5509
                            ii    iv   v   i     v              i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

C chr20_53542688_   5508 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5459
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

C chr20_53542688_   5458 CTAGGCA-ATACCATTCAGGACATAGGCATGGGCAAGGACTTCGTGTCTA 5410
                         v    ?i- v i -   iv   v v  vv i     v ii   v ivv  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATA 595

C chr20_53542688_   5409 AAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTA 5360
                         vi            vvi          vv     v  i    v   ii v
  L1M4_orf2#LINE/    596 TGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTC 645

C chr20_53542688_   5359 ATTAAACTCAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAA 5310
                           i   v i  i i   i  ii vv    i  v    i  vv i      
  L1M4_orf2#LINE/    646 ATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAA 695

C chr20_53542688_   5309 CAGGCAACCTATGGAATGGGAGAAAATTTTTGCAAGCTACTCATCTGACA 5260
                         v  i     i ii              v       iii ivi      i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

C chr20_53542688_   5259 AAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAA 5210
                          i  i  vi          v  i  v      vv    v iv i  v   
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

C chr20_53542688_   5209 AAAACA 5204
                           i   
  L1M4_orf2#LINE/    796 AAGACA 801

Transitions / transversions = 1.55 (132 / 85)
Gap_init rate = 0.01 (7 / 801), avg. gap size = 1.43 (10 / 7)  

1929 27.24 2.72 0.48  chr20_53542688_53552861     8356  8979 (1195)  C L1M4_orf2#LINE/L1   (0)   908   271  

C chr20_53542688_   8979 TGCTGGTACCAAAACAGAGATATAGACCTATGGAACAGAACACAGGCCTC 8930
                          i    i iv ii i   v       i v      i    ivv  ivii 
  L1M4_orf2#LINE/    271 TACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCC 320

C chr20_53542688_   8929 AGAAATACCACCACATATCTACAGCCATCTGATCTTTGACAAACCTCACA 8880
                                vvv   i i  i  ii i  vi    i  i     ivv vv  
  L1M4_orf2#LINE/    321 AGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCA 370

C chr20_53542688_   8879 AAAACAAGCAATGAGGGAAGGATTCCCTATTTAATAAATG---TTGGGAA 8833
                          i v  vv     i  i   i  vvi  v  i  i     ---i     v
  L1M4_orf2#LINE/    371 AGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGAC 420

C chr20_53542688_   8832 AACTGGCTTGCCATATGTAAAAAAACTGAAACTGGACCCCTTCCTTATAC 8783
                               v v?   i   i    i  -    ii         v   i i  
  L1M4_orf2#LINE/    421 AACTGGATAKCCACATGCAAAAGAA-TGAAGTTGGACCCCTACCTCACAC 469

C chr20_53542688_   8782 CTTATACAAAAATCAACTCAAGAAGGATTAAAGATTTAAACATAAGTCCT 8733
                          v           i       i v    i ?   ii    ii    vv  
  L1M4_orf2#LINE/    470 CATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCT 519

C chr20_53542688_   8732 AAAATCATAAAAATCCTAGAAGAAAACCTGGGCA-ATACCATTCAGGACA 8684
                             ii      v  i           v i  ?i- v i -   iv   v
  L1M4_orf2#LINE/    520 AAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATC-TTCGTGACC 568

C chr20_53542688_   8683 TAGGCATGGGCAAAGACTTCGTGCCTACAACACCAGAAGCAATGGCAACA 8634
                          v  vv i     v ii   v ivv  ii      i     vvi      
  L1M4_orf2#LINE/    569 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 618

C chr20_53542688_   8633 AAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCA 8584
                            - vv     v  i    v   ii v  i   v v  i i   i  ii
  L1M4_orf2#LINE/    619 AAA-GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTG 667

C chr20_53542688_   8583 CAGCAAAAGAAACTATCAG---AGTGAAAAGGCAACCTACAGAATGGGAG 8537
                          vv    i  v       i---         i     i            
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAG 717

C chr20_53542688_   8536 AAAATTTTTGCAATCTATCCATCTGACAAAGGGCTGATATCTAGAAACTA 8487
                              v       vii  vi      i  i  i  vi    i    vv  
  L1M4_orf2#LINE/    718 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 767

C chr20_53542688_   8486 CAAAGAACT--TA-AATTTA-CAAGAAAAAACCAA----CCCCATCAAAA 8445
                         i        --  -  i i -i  v     iv   ----   v  i?   
  L1M4_orf2#LINE/    768 TAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAA 817

C chr20_53542688_   8444 AGTGGGCAAAGGATATGAACAGATACTCCTCAAAAGAAGACATTTATGCA 8395
                          i            v    i   i i i   v        i  vi viii
  L1M4_orf2#LINE/    818 AATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATG 867

C chr20_53542688_   8394 GCCAACAA--ACATGAAAAAAAGCTCATCATCCCTGGCCAA 8356
                              i  --         i v     v    v????????
  L1M4_orf2#LINE/    868 GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (98 / 68)
Gap_init rate = 0.02 (11 / 638), avg. gap size = 1.82 (20 / 11)  

1901 24.26 8.27 3.51  chr20_53542688_53552861     8970  9682 (492)    L1M4_orf2#LINE/L1      162   908 (0) *

  chr20_53542688_   8970 GGTACCAGCAGAATAGCTAAAACAATCTTGAGAAAGTAGAGCAAAACTGA 9019
                           v   --         i             i    v   i    ii  i
  L1M4_orf2#LINE/    162 GGGACC--CAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG 209

  chr20_53542688_   9020 AATCATCACACTTACTGGTTTTTATTTAGAA---ATTACACATCTACACT 9066
                          ivvv        v iii   i----- i  --- i    v v     v 
  L1M4_orf2#LINE/    210 AGGACTCACACTTCCCAATTTC-----AAAACTTACTACAAAGCTACAGT 254

  chr20_53542688_   9067 AATTAAAATAGTATAGTACTGGCATAA----AAACAAATAGACCATTGGA 9112
                            i  i i   i i            ---- i   v     i  v    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr20_53542688_   9113 ATAGACTTTATAGGC-------ACACTTACACATACAGAGT-AACTTATT 9154
                              v  v v  v ------- v  ii i    vi vi  -  i v   
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr20_53542688_   9155 TTAAACAAGAG--ACACGA--ATACA-TCAGAAAAGGATAATCTTTTCAA 9199
                           vi     i --v  v  --  v  - vi i    i   i         
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAA 404

  chr20_53542688_   9200 CAAAGGGTTTTGGAA-AACTGGAAATACACACACATAA--ATAGAATTGG 9246
                             v   vi   i -       v ?v    ii  v  --  ii i    
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr20_53542688_   9247 AATTTTATGTTACACTATACAAAAAAAAAATCACTTCAAAATTGGT---- 9292
                          viii  iv i    i   i v     --- i vi       v i ----
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAA---TTAACTCAAAATGGATCAWA 501

  chr20_53542688_   9293 ----------TAAAACCTAAGACCATAAATCCCCTAGAAGAAAACATAGG 9332
                         ----------   i v    i  i     v i i                
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGG 551

  chr20_53542688_   9333 AGGATAGCTTCATGACATTGGTCTTGGCAATTAATTGATGGGTATGACAG 9382
                         ? v v v    i    v    vi v      viv  vv i i       v
  L1M4_orf2#LINE/    552 NGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_53542688_   9383 TAAAAGCACAGGCAATTAGAGCAAATATAGACAAGTGGGACCACATCAAA 9432
                         i         i    iv i  v   v     i  i v    iv       
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAA 651

  chr20_53542688_   9433 CTTAAAAAGCTTCTATATGGCAAAGAAAAT----AGTAGAGTGAAAAAAG 9478
                         v       -   i i iivv     i v i---- iv i        i -
  L1M4_orf2#LINE/    652 ATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA- 699

  chr20_53542688_   9479 CAATCTACAGAATGGGAGA---TATTTTCAACTTACATCTCCAA--AGGG 9523
                            i i             ---     v   v i i  v  ii --    
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_53542688_   9524 ATTAATTTCCAAAATTTTTAAGGAACTCCTACAA-TCAATTTGATAGCAA 9572
                          i vi v    i   v v   i      i     -     --------  
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT--------AA 791

  chr20_53542688_   9573 CAACCCAACAACCAAACAACCTGGTTGAAAAAAAGGAGAAAGGACTTGAA 9622
                         i  ---  vi  -   i    iii  -?     v  iv      i     
  L1M4_orf2#LINE/    792 TAA---AAAGAC-AAATAACCCAATT-WAAAAATGGGCAAAGGATTTGAA 836

  chr20_53542688_   9623 TAGGCATTTCTCCAAA------------ATGGCCAATAGGTATAGGAAAA 9660
                            i            ------------          i i i v     
  L1M4_orf2#LINE/    837 TAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAA 886

  chr20_53542688_   9661 AGTGGCCAACATCACATCATCA 9682
                         ii  vi        ????????
  L1M4_orf2#LINE/    887 GATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (101 / 69)
Gap_init rate = 0.03 (24 / 747), avg. gap size = 3.50 (84 / 24)  


2729 25.11 4.00 3.11  chr20_53569497_53573323.rev     2436  3335 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53569497_   2436 TGGTAGAATATTCTATTCTCATGGACTATAAGA----ATAACATTAAAAT 2481
                            v ii    i i  vi       i iv    ----   vii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53569497_   2482 GGCCATGCTTCACACAGAAATCTACAGATTCAACATTATTCCTATCAAAC 2531
                            v  i  i v  v vvi               iiv  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53569497_   2532 TAACAA-TGTCTTTTTTTTTTTTTTTTTACAGAATTAGAAAAAAATATGC 2580
                          vv  i-  i       -----------i     v v  v  ivvv  v 
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTT-----------GCAGAAATTGACAAGCTGATCC 139

  chr20_53569497_   2581 TAAAATTCAAATGGGATAACAACAAAAAGAGTCCA-AATAGCCAAAGCAA 2629
                                  v    i ----- iiv  i iii   -          i   
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAA-----ATGCAAGGGACCCAGAATAGCCAAAACAA 184

  chr20_53569497_   2630 TTCT---AAGGAAAAAGAAAGCCAGAGGCATCACATTACCCAACTTCAAA 2676
                          ii ---  i   i  v    iii    vv     i v     i      
  L1M4_orf2#LINE/    185 TCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA 234

  chr20_53569497_   2677 CTATACTATCAGGCTACACTAACCAAAACAGCATGGTACTGGTACAAAAA 2726
                         viv     iv i      v   i   i    ii         i i  ii 
  L1M4_orf2#LINE/    235 ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA 284

  chr20_53569497_   2727 CAGACACATAGACCAATGAAACAGA-----GAATCCAGAAATAAAGCCAT 2771
                         i     i     i     i  i   -----  i            v    
  L1M4_orf2#LINE/    285 TAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCAT 334

  chr20_53569497_   2772 ACTTCTACAG-CAATCTGATCTTCAACAAAGTCTACAAAAGTAAGCAGTG 2820
                           v i  ii -    -    i   i    i vivv   i vi vv  i  
  L1M4_orf2#LINE/    335 ACATTTATGGTCAAT-TGATTTTCGACAAGGGTGCCAAGACCATTCAATG 383

  chr20_53569497_   2821 TGGAAATAACTCCCTATTCACTAAATGGTGCTGGAATAGCTGGCTAGCCA 2870
                         v     v  ivvi  v    vi            i i i    v  ?   
  L1M4_orf2#LINE/    384 GGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCA 433

  chr20_53569497_   2871 TATACAGAAGAATGAAACTGGACCCCTACCTTTCATCATATATAAAAATT 2920
                         i  i  i         ii             iv  i      i       
  L1M4_orf2#LINE/    434 CATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATT 483

  chr20_53569497_   2921 AACTCAAGGTGGATTAAATATTTAAATATAAGACCTCTAACTATAGAAAT 2970
                                ii     i ? v ii     i     v  vv       i  v 
  L1M4_orf2#LINE/    484 AACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACT 533

  chr20_53569497_   2971 CCTAGAAGAAAACCTAGGAA-ACACCATTCCGGACACTGACCTTGGG--A 3017
                          i           v    ?i- v i -- i  -----          -- 
  L1M4_orf2#LINE/    534 CTTAGAAGAAAACATAGGNGTAAATC--TTCG-----TGACCTTGGGTTA 576

  chr20_53569497_   3018 AATA----TTTAT--GACTAAGTCCCCAAAAGCAATTGCAACAAAACCAA 3061
                         iii ----   v --  -  v v v         vvv         vv  
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr20_53569497_   3062 AAATTGACATGTAGGACCTAATTAAACTAAAGAGCTTCTGCACTTTTTCT 3111
                             v  i vi v    i v  i   v v  i i   i  ii   --- v
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT---CA 672

  chr20_53569497_   3112 GTGAAC--TATTACCAGAGTAAATGGACAATCTACAGAATAAGAGAAAAT 3159
                         iv i  --   i vv i   i  vi     i i       ii        
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_53569497_   3160 GTTTGCAAACTATGTATCTGACAAAAGTCCAATATCCAGAATCTATAAGG 3209
                         i        ii  i       i  ii v ivi          v     i 
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_53569497_   3210 AACTT----AAAGCAATAAGAAAAAAA-----AACGCA-TTAAAAAATAG 3249
                             i----  vv      v     i -----   v  -  ?      i 
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_53569497_   3250 GGACACGACATGAACAGATACTTCTCAAAAGAAGAAATACAAGTGGCCAA 3299
                          v v v  iv    i   i i     v        v      i       
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_53569497_   3300 CAGACATATAAAAAAATGCTCCACATCACTAGTCAT 3335
                         i ii  i  i    i      v      ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (135 / 87)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 3.05 (64 / 21)  


3129 27.42 0.44 0.44  chr20_53856461_53859419     1560  2467 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53856461_   1560 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATTGTGAAAAT 1609
                              ii i  i     i      i v      v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53856461_   1610 AGCCATACTGCCCAAGATAATTTACAGATTAAATGCCATCCCCATCAAGC 1659
                         i  v     v     iv i  i        v  i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53856461_   1660 TACTAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 1707
                          v i iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_53856461_   1708 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 1757
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_53856461_   1758 AACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGCC 1807
                                i      vv    i  v  ii i      viv        iv 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_53856461_   1808 TACAGTAACCAAAACAGCATGGTACTGGCACCAAAACAGAGCTATAGAGC 1857
                                 i   i    ii           iv ii i   vv      v 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_53856461_   1858 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGACACATATCTACAACT 1905
                                i    i--    i  --        vvv  i i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_53856461_   1906 ATCTGACCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 1955
                          vi   ii  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_53856461_   1956 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 2005
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_53856461_   2006 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAGTTCAAAATGGA 2055
                            ii    i    v   i     v           i ii          
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_53856461_   2056 TTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCAAGAAGAAAAC 2105
                          i ?    i    i  v   v       i      vi iv          
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_53856461_   2106 CTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAA 2155
                         v    ?i v viv   iv   v v  vv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_53856461_   2156 AACACAAAAAGCAATGGCAACAAAAGCCAAAATTGACAAAGGGGATCTAA 2205
                         i    v       vvi          vv     v  i   vv   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_53856461_   2206 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAGCAGCAGTGTGAAC 2255
                          i   v v  i i   i  ii vv    i  v    v  iv iv     v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_53856461_   2256 AGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAA 2305
                           i     i   i             v       vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_53856461_   2306 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTCACAAGAAAA 2355
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_53856461_   2356 AAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTC 2405
                          i     i     v  i?    i            v    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_53856461_   2406 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAACTGTTCACC 2455
                           v        i  vi viii     v  i          iv  i   v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_53856461_   2456 ATCACTGGCCAT 2467
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.33 (140 / 105)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2777 25.81 9.48 0.48  chr20_53867530_53873732     4879  5711 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53867530_   4879 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4928
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53867530_   4929 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 4978
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53867530_   4979 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5026
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_53867530_   5027 TATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5076
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_53867530_   5077 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5126
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_53867530_   5127 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATC 5176
                                 i   i    ii         i iv ii i   v         
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_53867530_   5177 AATGGAACAGAAC--AGAGCCCTCAGAAATAATGCCGCATATCTACAACT 5224
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_53867530_   5225 ATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCC 5274
                          vi    i  i     ivv  vv  i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_53867530_   5275 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5324
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_53867530_   5325 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5374
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_53867530_   5375 TTAAAGATTTAAACATTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5424
                          i ?   ii    ii v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_53867530_   5425 CTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTC------AT 5468
                         v    ?i v viv   iv   v v  vv i     v ii   ------  
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_53867530_   5469 GACAGCAAAAG--------------------------------------- 5479
                             v      ---------------------------------------
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_53867530_   5480 ----------AAACT-----------------ACCATCAG---AGTGAAC 5499
                         ----------     -----------------  i    i---      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_53867530_   5500 AGGCAACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAA 5549
                           i     i   iv            v  i    vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_53867530_   5550 AGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAA 5599
                         i  i  vi          v  i  v      vv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_53867530_   5600 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5649
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_53867530_   5650 TCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATC 5699
                           v        i  vi viii     v  i        i i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_53867530_   5700 CTCACTGGCCAT 5711
                         v   ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.64 (131 / 80)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 9.22 (83 / 9)  


2255 27.14 2.59 4.43  chr20_53874779_53880078     3890  4814 (486)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53874779_   3890 TAGACAAACATTCCATGCTCATCAATTGGAAGAATCAATACCATTAAAAT 3939
                          i  v i i  i     i    vi         v i    iii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53874779_   3940 GGCCATACTGTCCCAAAC-AATCTACCAATTTGAT---ATTTACATCAAA 3985
                            v     -i      i-i      vi   ii i---  iivi      
  L1M4_orf2#LINE/     51 GGCAATACT-CCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_53874779_   3986 GTGGCAACATCATCTTTCACA-AAACTAGGAAAAACT-ATTCTGAAATTT 4033
                         i vv  i vv v i   ii  -   i --  v  i  -  i  i     i
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATT--GACAAGCTGATCCTAAAATTC 147

  chr20_53874779_   4034 ATATCTAACCAAAAAAGATCCCAAATGGCCAAAGCAATCCTAAGCAAAAA 4083
                             vv  viiv  ii  i  vi   i      i     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_53874779_   4084 GAATAAACTCAGAGGCATTACATTACCTGACTTCAAACTATAGTATAAGG 4133
                            i   v ii    vv i   i v  ii i      viv  v  i  i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_53874779_   4134 CTACAGTAACCATAACAGCATGGTACTGGTACAAGAACAGATACCAATAG 4183
                                  i  vi    ii         i i   i i   i i--    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT--ATAG 295

  chr20_53874779_   4184 AACAGAATTTTAAAACCAATAGAACAGAATTTTAAAAAACACAAATAAAG 4233
                          --------------i    i   i      v- i ivv  v       v
  L1M4_orf2#LINE/    296 A--------------TCAATGGAATAGAATTG-AGAGTCCAGAAATAAAC 330

  chr20_53874779_   4234 CTGCATACCTCCA--GCTATCTGATCTTCAGCAAAGTCAACAAAAATAAG 4281
                          --     v ii -- ii vi    i   ii   i viiv   i vi vv
  L1M4_orf2#LINE/    331 C--CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr20_53874779_   4282 CAATGAGGAAAAGACTCCCTATTCAATAAATCGTACTGAGATAGCTGACT 4331
                              i     ii ivvi  v     i    v  i   i  i i   iv 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr20_53874779_   4332 AACCATATGCAGAAGAATGTAACTGGACCTCTACCATTTGCCATATACCA 4381
                          ?   i     i       v ii      i     vivii        v 
  L1M4_orf2#LINE/    429 AKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAA 478

  chr20_53874779_   4382 AAATTAACTAAATGTGGATTATAGATTTAAATGTCAGACCTCAAGCTTAT 4431
                                  v  vi     i ?   ii       v   v  v  i  -  
  L1M4_orf2#LINE/    479 AAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACT-AT 527

  chr20_53874779_   4432 AAAAATCCTAGAAGAACACCCAGGGG-ACATCACACTGCACACTAACCTT 4480
                             v  i        v  vi   ? - v   ---- v i--- i     
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATC----TTCG---TGACCTT 570

  chr20_53874779_   4481 GGG--AAAGAAT------TTATGAC-TAACTCCTTGAAAGCAATTGCAAC 4521
                            -- iiv   ------   -  i- i  v  --i      vvv     
  L1M4_orf2#LINE/    571 GGGTTAGGCAATGGTTTCTTA-GATATGACACC--AAAAGCACAAGCAAC 617

  chr20_53874779_   4522 AAAAACAAAAAATTGATAAGTAGAACATAATTAAATTTTG---CTTCTGT 4568
                             i-       v     i v i  v v  i   v  vi---   i   
  L1M4_orf2#LINE/    618 AAAAG-AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGT 666

  chr20_53874779_   4569 TCAGCAAAAGAAATAATCAACAGGGTAATCAGACGACCTACAGAATAGGA 4618
                         v vv    i  v iv     v ii  i vv    i   i       i   
  L1M4_orf2#LINE/    667 GCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGA 716

  chr20_53874779_   4619 GAAAATATTTCCAAACTATGCATATGACAAAGG--TTAAATACCCAGAAT 4666
                                   v    ii  ii  v   i  i  --  i--  i       
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTG--TATCCAGAAT 764

  chr20_53874779_   4667 CTACAAGGAATTTAAAGAACTGAACAAGCAAAAC-CAAATAATCCCATTT 4715
                         v  i  i   i ivv v    v  i  vv    v-       i  v   ?
  L1M4_orf2#LINE/    765 ATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTW 814

  chr20_53874779_   4716 AAAAAACTGGGCAAAACACAGAAACAGACACTTCTCAAAAGAAGACATAC 4765
                              --        iv ivvi  i     i     v        i    
  L1M4_orf2#LINE/    815 AAAAA--TGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr20_53874779_   4766 AAATGGCCAACAAACATATGAGAAAATGCAAATCAAAACCACAGGGAAA 4814
                                   i  i  i    i  i    ---    v i  ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.68 (155 / 92)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 2.41 (65 / 27)  


3036 27.37 1.10 0.88  chr20_53908944_53915362.rev     5024  5929 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_53908944_   5024 TGGAAGAACATTCCCTGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 5073
                              ii i  i  v  i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_53908944_   5074 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 5123
                            v     v     iv i  i           i  v     i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_53908944_   5124 TATCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5171
                          vi  iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_53908944_   5172 TATGGAATCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAG 5221
                                viiv  ii  v  v v  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_53908944_   5222 AACAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATATACTACAAG 5271
                                i      vv   ii  v  ii i      -- iv        i
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAA--ACTTACTACAAA 246

  chr20_53908944_   5272 GCTACAGTAACCAAAACAGCATGGTATTGGTACCAAAACAGAGATATAGA 5321
                                   i   i    ii     i   i iv ii i   v       
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_53908944_   5322 TCACTGGAACAGAAC--AGAGCCCTCAGAAATAACACCGCATATCTACAA 5369
                            v     i    i--    i  --        vv  ii i  i  iii
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGG 344

  chr20_53908944_   5370 CTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATT 5419
                         ii vi    i  i     ivv  vv  i v  vv            i  v
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_53908944_   5420 CCCTATTTAATAAATGGTGCTTGGAAAACTGGCTAGCCATATGTAGAAAG 5469
                         vi  v  i  i          v   v      v  ?   i   i i  ii
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_53908944_   5470 CTGAAACTGGATCCTTTCCTTACATCTTATGCAAAAATTAATTCAAGATG 5519
                         v    ii    i  i v   i   i v   i          i    i   
  L1M4_orf2#LINE/    445 ATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_53908944_   5520 GATTAAAGACTTAAAC---AGA-CTTAAACCATAAAAACCCTAGAAGAAA 5565
                            i ?    i    i---   -  v    i      vi i         
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_53908944_   5566 ACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCT 5615
                           v    ?i v viv   iv   v v  vv i     v ii   v ivv 
  L1M4_orf2#LINE/    545 ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGAT 594

  chr20_53908944_   5616 AAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCT 5665
                          vi            vvi          vv     v  i    v   ii 
  L1M4_orf2#LINE/    595 ATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT 644

  chr20_53908944_   5666 ACTTAAACTAAAGAGCTTCTGAACAGCAAAAGAAACTACCATCAGAGCGA 5715
                         vv i   v v  i i   i  vi vv    i  v    i  vv i  i  
  L1M4_orf2#LINE/    645 CATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_53908944_   5716 ACAGGCAACCTAAAAAATGGAAGAAAATTTTCGCAA--CGTACTCATCTG 5763
                          v  i     i v i     i       v  i    -- i  i--     
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT--ATCTG 742

  chr20_53908944_   5764 ACAAAGGGCTAATATCCAGCATCTACAATGAACTCAAACAAATTTACAAG 5813
                          i  i  i  vi       v  v  i  v      vv    v iv i  v
  L1M4_orf2#LINE/    743 ATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAAT 792

  chr20_53908944_   5814 AAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACA 5863
                              i     i     v  i?    i            v    i     
  L1M4_orf2#LINE/    793 AAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACA 842

  chr20_53908944_   5864 CTTCTCAAAAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCT 5913
                         i     v        i  vi viii     v ii          i     
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_53908944_   5914 CATCATGACTGGCCAT 5929
                           v   v ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (145 / 99)
Gap_init rate = 0.01 (10 / 908), avg. gap size = 1.80 (18 / 10)  


3085 27.33 0.88 1.21  chr20_54061820_54064263     1042  1952 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_54061820_   1042 TGGAAAAACATTTGATGCTCATGGATAGGAAGAATCAATATCATCAAAAT 1091
                               i i  iiv   i        v      v i     ii i  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_54061820_   1092 GGCCATACTGCCCAAAGTAATTTATAGATTCAGTGCTATCCACATCAAGC 1141
                            v     v      v i  i  i       ii  v    vi     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_54061820_   1142 TACCATTGACTTTCTTCACAGAATTAGAAACGACT-ACTTTAAATTTCAT 1190
                          v   vivi i  i  ii     v v  v v -  - iii    v     
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCAT 149

  chr20_54061820_   1191 AGGGAATTTTAAAAGATCCTGTATAGCCAAGGCAGTCCTAAGCAAAAAGA 1240
                          v    v vi  ii  i  v v        ii  i  i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_54061820_   1241 ACAAAGCTGGAGTCATCACACTACCTGACTTCAAACTATGCTACAAGGCT 1290
                               i     vvv       v  ii i      viv i      i   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_54061820_   1291 ACAGTCACCAAAACAGCATGGTACTGGTACAAAAACAGATATATAGACCA 1340
                              v i   i    ii         i i  ii i   i       i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_54061820_   1341 ATGGAACAGAACAGAGGCCTCATAAATAATGCCACACATCTACAACCATC 1390
                               i    iv   ivii  v      vv   i    i  iiii  vi
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_54061820_   1391 TGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTTCCTA 1440
                             i  i     ivv  v   i v  vv            i  vvi  v
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_54061820_   1441 TTTAATAAATGGTGTTTGGAAAACTGGCTAGCCATATGTAGAAAAGTGAA 1490
                           i  i        i v   v      v  ?   i   i i  i i    
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_54061820_   1491 ACTGGACCCCTTCCTTACTCCTTATACAAAAATTAACTCAAGGTGGATTG 1540
                         ii         v   i  v  v                   ii     ii
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_54061820_   1541 AAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTT-GAAGAAAACCT 1589
                         ?    i    i      v       i      - i   -         v 
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAA-CTCTTAGAAGAAAACAT 548

  chr20_54061820_   1590 AGGCA-ATACCATTCAGGACATAGGCATAGGCAAAGACT-CATGACTAAC 1637
                            ?i- v i -   iv   v v  vv       v ii - v iiv  vv
  L1M4_orf2#LINE/    549 AGGNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_54061820_   1638 ACACCAGAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGAATCTAAT 1687
                               i     vvi          vv     v  i    v i ii v  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_54061820_   1688 TAAACTAAAGAGCTTCTGCACAGCAAAAAAAAAAAAAAAACTATCATCAG 1737
                         i   v v  i i   i  ii vv    ii v --------      vv i
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACA--------CTATCAAGAA 689

  chr20_54061820_   1738 AGTGAACAGGCAACCTATAGAATGGGAGAAAATGTTTGCAATCTATCCAT 1787
                               v  i     i i               i       vii  vi  
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_54061820_   1788 CTGACAAAGGGCTAATATCTAGAATCTACAAGGAAGTTAAACAAATTTAC 1837
                             i  i  i  vi    i     v  i  i   v ivv    v iv i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_54061820_   1838 AAGAAAAAAACAA----CCCCATCAATAAGTGGGTGTAGGATATGAACAG 1883
                           v     i    ----   v  i? v  i    iiv     v    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr20_54061820_   1884 ACACTTCACAAAAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAA 1933
                            i   v v        i  vi vii      i  i  i       i v
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_54061820_   1934 GCTCATCATCACTGGTCAT 1952
                              v     ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (146 / 99)
Gap_init rate = 0.01 (9 / 908), avg. gap size = 2.11 (19 / 9)  


2501 26.54 4.37 2.91  chr20_54072839_54075249     1027  1919 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_54072839_   1027 GAAGGATACACCATAAATGCTCATGGATTGGAAGATTCCATGTTGCTAAG 1076
                            i    iv    ---- i               i iv  i   i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCAT----GTTCATGGATTGGAAGACTTAATATTGTTAAG 48

  chr20_54072839_   1077 ATGTCAGTTATCCCCATACTGATCTATATATTCAATGCATTTCCAATCAC 1126
                            v  i vv      v i       i v      i   v i  v    v
  L1M4_orf2#LINE/     49 ATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr20_54072839_   1127 ATTTCTAGCAGGAGTTGTTATGCAAATGAATGAGCTGATTCTAAAATTTA 1176
                          v i i   v vvv  v  iiiv    vi ii       i        i 
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_54072839_   1177 TATGGAAATGCAAAGGACCTGAAATAGTCAAAATAATTTGTAAAAATAAA 1226
                                      i     iii     i     i   i vv     v  i
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_54072839_   1227 AAT---GTTAGGGAATTTACA-------------AAACGCACTATAGAAT 1260
                           i---   i i i i i   -------------    vi    i i ii
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_54072839_   1261 TA-AATAATCAAAATAGTGTGGCATCACTTTAATAATAGACATAAAAGCC 1309
                           - i       i i       i iiiviv   vi         v iii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_54072839_   1310 AATGAAGGAGAATAAATATTCCAGGAATAGACTCACACATATAAAGCCAA 1359
                             i iv     vi v v     i    i  i  i    v  vi i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_54072839_   1360 TTGATTATCAGCAAATGT------ACAATTCAATAGAAAAAGA-TAAT-- 1400
                               v  ii   iv  ------  v       i ii     -  i --
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_54072839_   1401 TCTCAACTATCTTTTCTTGAAGATGGTACTGTAACAATCAGTTACCTATA 1450
                          i     ------------- i     i   vi    iii v  ? i i 
  L1M4_orf2#LINE/    399 TTTCAAC-------------AAATGGTGCTGGGACAACTGGATAKCCACA 435

  chr20_54072839_   1451 TTTTTTTAAAAAAACCTCATT----CATTACCTCACAATACACCCAAAAA 1496
                          vi----    i  ivvvi  ---- vi         vi i iv      
  L1M4_orf2#LINE/    436 TGC----AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAA 481

  chr20_54072839_   1497 ATAATTCAAAGTGGACCACAGACCTAAATGTAAGAGGAAAAATGATAAAA 1546
                         v   i     i    i  ?                 vv    iv      
  L1M4_orf2#LINE/    482 TTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAA 531

  chr20_54072839_   1547 TTTCAAGTAGAAAAACACAAGAAATAATTTTTATGATATTGAGTTAGGAA 1596
                         i iiv  v      -  i i ?ivv   i  ii   iv   i      v 
  L1M4_orf2#LINE/    532 CTCTTAGAAGAAAA-CATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCA 580

  chr20_54072839_   1597 AAGATTTCTTAGATGGGACA---AAAGCATGAACTGGAAATGAAAAATAT 1643
                          v i          iv    ---      ii i viv   v      -  
  L1M4_orf2#LINE/    581 ATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA-AT 629

  chr20_54072839_   1644 TGATAAATTGAA-TTCATCAAAATTAAAA-CCTTTGTCCTGCATAAGATA 1691
                         v         i -                - i     v  v  v i  i 
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr20_54072839_   1692 TTATTAATAAAATGAAAAAGCAAACCACAAATTAAGAGAAAATACTTTCA 1741
                         i   i  v   i      ii   v     i v ii         i  v  
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr20_54072839_   1742 AAACGTATAT--GATAAAGGAATTACATCTAAAATATATTTTAAAAACTC 1789
                           v i     --     i   v  ii   i i       v--  i     
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATA--AAGAACTC 777

  chr20_54072839_   1790 TTACAACTCCACAATAAGAAGATCAAAAAC--AGATTAAAAATGGGCCCA 1837
                                  v i     i    iv  v   -- iv ?          vv 
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr20_54072839_   1838 AAATTTGAATAGTTACCCACACTAAAAACAACATATGAATAAAAAATTAG 1887
                         ii          vi iii- v i   i vi i   ii   iivv   v  
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTT-CTCCAAAGAAGATATACAAATGGCCAATAAG 876

  chr20_54072839_   1888 AATATAAAAAGACATTCAACATCATTACTCAT 1919
                         v i  i      iii         ????????
  L1M4_orf2#LINE/    877 CACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.81 (150 / 83)
Gap_init rate = 0.02 (19 / 906), avg. gap size = 3.42 (65 / 19)  


 327 21.79 0.00 1.28  chr20_54088016_54091018.rev      499   576 (2427)    L1M4_orf2#LINE/L1       30   106 (802)  

  chr20_54088016_    499 AAGATTCACTTTTGTATAAGATGTGAATTCTCCCCAAATTGATCTATATA 548
                             i i v v    -       vv   v                 i v 
  L1M4_orf2#LINE/     30 AAGACTTAATATTGT-TAAGATGGCAATACTCCCCAAATTGATCTACAGA 78

  chr20_54088016_    549 TCCAATCTGATCTCAATTAAAATCCCAG 576
                          i   ivii   i v  i          
  L1M4_orf2#LINE/     79 TTCAACGCAATCCCTATCAAAATCCCAG 106

Transitions / transversions = 1.12 (9 / 8)
Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1)  

 994 25.84 2.33 2.07  chr20_54088016_54091018.rev     1327  1713 (1290)  C L1M4_orf2#LINE/L1   (0)   908   521  

C chr20_54088016_   1713 AAACTGTAAAAATCCTAGAAGAAAACCTAGG---AAATGCCATTCTGGAT 1667
                              i     v  i           v    ---    -- v iv  ivi
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT--CTTCGTGACC 568

C chr20_54088016_   1666 ATGGCCCTTAGGGAAGAATTTAT--GACTAAGTCCTCAAAAGCAATTGCA 1619
                         v   v--     v  vii   v --  -  v v vi        vvv   
  L1M4_orf2#LINE/    569 TTGGG--TTAGGCAATGGTTTCTTAGA-TATGACACCAAAAGCACAAGCA 615

C chr20_54088016_   1618 ACAAAAACAAAAATTCACAAGTGGGACCTAATCAAACTAAAGGACTTCTG 1569
                               iv      vv i  i v    i v      v v  ii    i  
  L1M4_orf2#LINE/    616 ACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTG 665

C chr20_54088016_   1568 CACAGCAAAAGAAACTGTAAACAGAGTAAACAGACAACATACAGAATGGG 1519
                         ii vv    i  v   i v  v i   i  v       vi          
  L1M4_orf2#LINE/    666 TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG 715

C chr20_54088016_   1518 AGAAAATATTCACAAACTCTGTATCTGACAAAGTTCTAATACCCAGAATC 1469
                                   ii    iiv i       i  i vv  vi  i       v
  L1M4_orf2#LINE/    716 AGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATA 765

C chr20_54088016_   1468 TATAAGAAACTTAAACAACAGAACAAGAAAAAAACAG----CCCCATGTT 1423
                              ii    ivv     vv  i  v     i   i----   v  ---
  L1M4_orf2#LINE/    766 TATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCAAT--- 812

C chr20_54088016_   1422 TAAAAAATGGGCAAAAGTCATGAACAGAGACTTCTCAAAAGAAGACATAC 1373
                          ?             i viv    i   v i     v        i    
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

C chr20_54088016_   1372 AAAAATCCAACAAACATATGAAGAAATTTTTATCATCACTAATCAT 1327
                            viv    i  i  i     i i  vi i v     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.02 (50 / 49)
Gap_init rate = 0.02 (7 / 388), avg. gap size = 2.43 (17 / 7)  

3040 23.48 1.52 0.76  chr20_54088016_54091018.rev     1724  2511 (492)    L1M4_orf2#LINE/L1      115   908 (0)  

  chr20_54088016_   1724 TTTGGATAGAAATCAATAAGCTGATTCTAAAATTCATATGGAAGGACAAA 1773
                             --i      ii i        i                 ivi   i
  L1M4_orf2#LINE/    115 TTTG--CAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr20_54088016_   1774 GGATCTAGAATAGCCAAAACTACTTTGAAAAAGAAGAAAAAAATTGGTAG 1823
                            i i              v ii              v   i    vi 
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGG 212

  chr20_54088016_   1824 ATGAATTTTACTTGATTTTAACACTCATTACAGACCTATAATAATCAAGA 1873
                          ivv ivi v iii    i  v   i i    i v   i i         
  L1M4_orf2#LINE/    213 ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGA 262

  chr20_54088016_   1874 CAGTGTGGTACTGGCTTAAAAGATAGATAAATATGTAAATGGAACAGAAT 1923
                                        v   i-      i v   vi v       i     
  L1M4_orf2#LINE/    263 CAGTGTGGTACTGGCATAAG-GATAGACATATAGATCAATGGAATAGAAT 311

  chr20_54088016_   1924 AGAGAGTCCAGAAATTGACCCTTACATATATAGACAACTGCTTTT-GACA 1972
                         v              vi    v     v   i v   i  v    -    
  L1M4_orf2#LINE/    312 TGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACA 361

  chr20_54088016_   1973 AAGGTGC-AAGACAATTCAGCATAGAAAGGATATTCTTTTCAACAAATGG 2021
                          i     -     v     iiivi     i   v                
  L1M4_orf2#LINE/    362 AGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGG 411

  chr20_54088016_   2022 TGCTGAAACCATCGGCTATCCACATGTAAAGAAATGAACTTTGGTTCATA 2071
                              ii  v ii  v  ?       i   ii      v  v iii v  
  L1M4_orf2#LINE/    412 TGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTA 461

  chr20_54088016_   2072 TCCCTAATCATATA-AAAAATTACCTCAAACAGAATCTTAGACCTAAATA 2120
                         i i vv i      -        v      vv i   v?          i
  L1M4_orf2#LINE/    462 CCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATG 511

  chr20_54088016_   2121 TAAAGCCTAAAACCATAAAAAGTCTAGGAAAAAAGCCATAGGAGAAATTC 2170
                            iiv       i      vvii   i i    --      ? v  v  
  L1M4_orf2#LINE/    512 TAAGAGCTAAAACTATAAAACTCTTAGAAGAAAA--CATAGGNGTAAATC 559

  chr20_54088016_   2171 TTTGAGACCT-GATTTGGGTAAAGATTTGTTAGACACTAAATCAAAAGCA 2219
                           i v     - iv  i  i  v i   v     i iv v i        
  L1M4_orf2#LINE/    560 TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCA 609

  chr20_54088016_   2220 TGATCCATAACAAAACAAATTGATAAA-----CTTCATCAAAATTAAAAA 2264
                         ii v v i  v i  v    v      -----                  
  L1M4_orf2#LINE/    610 CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAA 659

  chr20_54088016_   2265 TATCTCCTTTTTAAAAGACACTGT--AGAAGAATAAACAGACAAGAAGCA 2312
                         iv i vivi  i   i      i --    - i i  v      vvvi  
  L1M4_orf2#LINE/    660 CTTTTGTGCTTCAAAGGACACTATCAAGAA-AGTGAAAAGACAACCCACA 708

  chr20_54088016_   2313 CACTCGAAGAAAATATTTGCATATCGTATATCTGATAAAGAACTTATATC 2362
                         v v v i              v   i            i i    i    
  L1M4_orf2#LINE/    709 GAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATC 758

  chr20_54088016_   2363 CAGATTATATCAAAAACCCTCAAAACTCACTAATGAGAAATCAAGCAACC 2412
                             v     v  i   i  i v      v    i i  iv   ii    
  L1M4_orf2#LINE/    759 CAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACC 808

  chr20_54088016_   2413 CAACT-AAAAATAGGCAAAAGATTTGAAAAGAGGCTTCATCAGATAAAAA 2461
                            i -      i      i        v   vii   vi  i v  i v
  L1M4_orf2#LINE/    809 CAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr20_54088016_   2462 ATATATATGACAAATAAGCATCTGAAAAGATGCTCAGCATCATTATTTGT 2511
                            i v   i v        iv              i     ????????
  L1M4_orf2#LINE/    859 ATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.46 (108 / 74)
Gap_init rate = 0.01 (11 / 794), avg. gap size = 1.64 (18 / 11)  


2410 21.77 2.54 8.10  chr20_54290752_54292556      488  1314 (491)    L1M4_orf2#LINE/L1      128   908 (0)  

  chr20_54290752_    488 ATAAGCATGTTATTAAAAATAACTTTCTATATGGAACTATAAACGATCTT 537
                          i    -  v vi     ------   -        v ii  iv  i iv
  L1M4_orf2#LINE/    128 ACAAGC-TGATCCTAAAA------TTC-ATATGGAAATGCAAGGGACCCA 169

  chr20_54290752_    538 GAATAGTCAAAGCACCCTTGACCAAAAAAAAAA-AAAGTTGAAGGCAGTT 586
                               i    i  vi     --    i  i  -       i   -----
  L1M4_orf2#LINE/    170 GAATAGCCAAAACAATCTTGA--AAAAGAAGAACAAAGTTGGAGG----- 212

  chr20_54290752_    587 GGAAGCACT-ATACTACCTGACTTCAAAATATACTACAAAGCTATAGTAA 635
                         ------   - i   v  ii i       iv             i     
  L1M4_orf2#LINE/    213 ------ACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr20_54290752_    636 CCAAAATAGCATGGTATTGGCATAAAAACAGGCACATGGACCATCGGAGC 685
                         i   i i  ii     i        ii i  i  i  i  i  vi   ii
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr20_54290752_    686 AGAAGAGAGAACCCAGAAATAAATCCATGCATCTACAGCCAACTAATTTT 735
                             vv    ii           i    i   i  ii i   i i     
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr20_54290752_    736 TGACAAAGGTGCCAAGAAAACACATTGGGAAAAGGATAGTCTATTCAATA 785
                         i     i          vv iv  v    i    i       v     i 
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr20_54290752_    786 AATGGTGCCGGGAAAATTGGATACCCACATGCAGAAGAATGAAACCTGAC 835
                                 i    v  i      ?         i         iiiv   
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr20_54290752_    836 ACTTATCTTTCACCAAATACAAGAATCAACTCAAAGTGGATTAAAGACTT 885
                         v i  i  iv     v      i   i        i     i ?    i 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr20_54290752_    886 AAGTGTGAAACTCAAAACTATAAAATTACCAGAAGAAAACATAGAGG-AA 934
                           i   i i vii            i vii              i? -  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_54290752_    935 ATGCTTCATGACAT-GAATTGGACAAGGGTTTTCTGCATAAGACCTCAAA 983
                           -    i    v - ii  i i   v     ii iv   v   vi    
  L1M4_orf2#LINE/    557 AT-CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAA 605

  chr20_54290752_    984 AGCACAGGCAATCAAAGCAAAAATGAACAAATGGGATTACATCAAACTAA 1033
                               i    iv    v      ii i    v   i v       v v 
  L1M4_orf2#LINE/    606 AGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr20_54290752_   1034 AAAGCTTCTGAACAGCAAAGGAAACAATCAACAAAG-----AGATAATCT 1078
                            i   i  vi vv       v  v     v    -----   i  i i
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr20_54290752_   1079 AC-----GGGA---AATATTTGCAAACCATACATCTGACATTCTTGTGAT 1120
                           -----    ---            i    i      i ----------
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA---------- 745

  chr20_54290752_   1121 ATAGTCATGGTATATTCCTGAATCGGTGGCTCACATGATATATTCTTGTA 1170
                          vi v - v    ---  v    --------- i  i viv i    ---
  L1M4_orf2#LINE/    746 AGGGAC-TTGTAT---CCAGAAT---------ATATAAAGAACTCTT--- 779

  chr20_54290752_   1171 ACATACTCATGACATGTAAAAAACTCAACTCAATAGGAAAAATA-CCTAA 1219
                            -     -- i -i      --------------  v     -  i  
  L1M4_orf2#LINE/    780 ACA-ACTCA--ATA-ATAAAAA--------------GACAAATAACCCAA 811

  chr20_54290752_   1220 TTTTAAAATGGGAAAAAGACTTTAATAGACATT---AGAAATAAGACATA 1266
                           ?v        v   i  i  v          ---vv   v    i   
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATA 861

  chr20_54290752_   1267 TAATGAGCCAACAGTTATCTTTAAAAAATGTCCAACATCTCTAATCAT 1314
                         i  vvi     i ivi - v v    i   ii       v????????
  L1M4_orf2#LINE/    862 CAAATGGCCAATAAGCA-CATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.98 (117 / 59)
Gap_init rate = 0.03 (25 / 781), avg. gap size = 3.52 (88 / 25)  


3359 26.10 0.22 0.22  chr20_54328008_54330080      674  1581 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_54328008_    674 TGGAAACACATCCCATGCTTATGGATGGGTAGAATCAATATTGTGAAAAT 723
                               v i        i i      v  v   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_54328008_    724 GACCACAATGCCAAAAGCAATCTACAAGTTCAACACAATCCCCATCAAAA 773
                          i v i v v  v   vii       ii      i       i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_54328008_    774 TACCACCATCATTCTTCACAGAATTAGAAAAAACAATTCTAAAATTTATA 823
                          v   v vv v  i  ii     v v  v  ivii  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_54328008_    824 TGGAACCAAAAAAAGAGCCC-GCATAGCCAAAGCAAGACTAAGCAAAAAG 872
                              -- viv  i ii   - v         i   vvi i iv  i   
  L1M4_orf2#LINE/    151 TGGAA--ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_54328008_    873 AATAAATCTGGAGGCATCACACTATCTGATTTCAAACTATACTATGAGGC 922
                           i   vi      vv       vi ii        viv     ii i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_54328008_    923 CATAGTCACCAAAATAGCGTGATACTGGTATAAAAATAGGCACATAGACC 972
                         i i   v i   i i  i   i      i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_54328008_    973 AATGGAACAGAATAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAA 1022
                                i     v    ii               v i i   ii i   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_54328008_   1023 CTGATCTTCAACAAAGCAAACAAAAATATAAAGTGAGGAAAGGACACCCT 1072
                         i    i   i    i vviv   i vi  vv i  i      i i vi  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_54328008_   1073 TTTCAACAAACGGTGCTGGGATAATTGGCAAGCCACATGTAGGAGAATGA 1122
                                   i          i  i   vv ?       i ii       
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_54328008_   1123 AACTGGACCCTCATCTCTCATCATATACAAAAATTAACTCAAGGTGGATT 1172
                          ii       ii i   v  i                     ii     i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_54328008_   1173 AAGGGCTTAAACCTAAGACCTGTAACTATAAAAATTCTAGAAGACAACAT 1222
                          ?i i i    iv     v  iv          v ii       v     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_54328008_   1223 TGGAAAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAGGA 1272
                         v  ?iv  vi    vv   v    v        v i    v iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_54328008_   1273 ACCCAAAATCAAATGCAATAAAAACAAAGATAAATAGCTGGGACCTAATT 1322
                         vv      v  v v    i    iv   i   i   iv v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_54328008_   1323 AAACTAAAGAGCTTTTGCACAGCAAAAGGAACAGTCAGCAAAGTAAACAG 1372
                            v v  i i      ii vv    i iv  vi   iv     i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_54328008_   1373 ACAACCCACACAGTAGAAGAAAATCTTCAGAATCTGTACATCTGACAAAG 1422
                                   v i i i       v  iiv  viii  i      i  i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_54328008_   1423 GACTAATATCCAGAATCTACAACAAACTCAAACAAATCAATAA-AAAAAA 1471
                             vi          v  i  vi     vv    v       -     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_54328008_   1472 ACAAATAATCCCATCAAAAAGTGTGCTAAGGACGTGAATAGACAATTCTC 1521
                                 i  v  i?    i  v  v     iv          v     
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_54328008_   1522 AAAAGAAGATATACAAATGGCAAACAAACATATGAAAAAATGCTCAACAT 1571
                         v                    v  i  i  i       i           
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_54328008_   1572 CACTAACTAT 1581
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (139 / 94)
Gap_init rate = 0.00 (3 / 908), avg. gap size = 1.33 (4 / 3)  


2660 20.61 6.71 1.12  chr20_54516596_54518212      501  1126 (491)    L1M4_orf2#LINE/L1      248   908 (0)  

  chr20_54516596_    501 CTACACTAATCAAGATAGTGTGGTGCTGGCATGAGAACGGGCATATACAT 550
                              v         i        i       i  i ii i      v  
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_54516596_    551 CAATGGAATAAAATAGGGAGTCCGGAAATAAACCCTCACATGTATGGTCA 600
                                   i   v i      i           vi    v        
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_54516596_    601 -TTGATTTTTGACAAAAGGGCCAAGTCAATTCGATGGGGGAAAGAATAGT 649
                         -        i     ii v      v v    i      -          
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGT 396

  chr20_54516596_    650 TTTTTCAACAAATAGTG-TGGGGTAACTGGATATCCACATGCAGAAGAAT 698
                         i            i   -    ii         ?         i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_54516596_    699 GAATTTGGACCCTTACCTTACATTGAATGTAAAAATAAACTCAAAGTG-A 747
                            v        i     i   iiiv  ii      v        i  - 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_54516596_    748 TCACAGACCTAAATCTGTAAGTTTTAGTTACAAACCACTTAGGAGAAA-C 796
                            ?          v ivi  i vv ii  i   v v     i     - 
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_54516596_    797 GCAGGAGTAAATC---ACAATCTTGGGTTAGGCGATGACTTACTAAATAT 843
                         ii   ?       ---iii i            i   ii  vi  i    
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_54516596_    844 GACACCAAAAACGTA-GCAGTAAGAGAGAAAATTGCTAAGTCCAATTTCA 892
                                   i ii -   ii  i   i     v v   i ivi i    
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_54516596_    893 TCAAAATAAAAAACTTTTGTA-----------ATTATCCAG----TGTAA 927
                                v            i----------- i    v  ----  v  
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_54516596_    928 -GATATTTTGTCATAACAG-------T-CTTGGA----------CTAAGA 958
                         -  i viiii-  v  ii ------- -i   v ----------  i v 
  L1M4_orf2#LINE/    697 AGACAACCCA-CAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_54516596_    959 CAGAACTTATATCCAGAATATGCTGTATAAAGACCTCTTAGAACGCAACA 1008
                         vi i    i            -----       v      v   v   i 
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATAT-----ATAAAGAACTCTTACAACTCAATA 790

  chr20_54516596_   1009 TCAAAGAGACAAATAATACAATTAAGAAATGGACCAGGGATTTAAGCAGA 1058
                         vi   i          iv     ? i      i v i      i ii   
  L1M4_orf2#LINE/    791 ATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGA 840

  chr20_54516596_   1059 CATTTCTCCAGAGAAGGTATACAGATGGTCAGTTAGCACGTGAAAAGATG 1108
                                   i     i      i    i  i v     i          
  L1M4_orf2#LINE/    841 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 890

  chr20_54516596_   1109 CTTAACATCTCTGGTCAT 1126
                           i      v????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.38 (88 / 37)
Gap_init rate = 0.02 (15 / 661), avg. gap size = 3.27 (49 / 15)  


1090 23.14 3.92 0.00  chr20_54778429_54780800.rev      501   755 (1617)    L1M4_orf2#LINE/L1      264   528 (380)  

  chr20_54778429_    501 AGTGTGGTATTGACAAAAGCAAGGACACATGGATCAGTGGAACAGAACAG 550
                                  i  i  v   v vi    i  i     i     i    iv 
  L1M4_orf2#LINE/    264 AGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTG 313

  chr20_54778429_    551 AGAGTTCAGAAAGAGACCCATACATTTAATGCCAGGTGATTTTCAATAAT 600
                              i      v i             vv i  iv        i i  v
  L1M4_orf2#LINE/    314 AGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAG 363

  chr20_54778429_    601 AGTGTCAAAGCAATTCAATGCAGAAAGGAAAGTCTTT-CAACAAATGGTG 649
                         i   i   ii v        vi     i v       -            
  L1M4_orf2#LINE/    364 GGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTG 413

  chr20_54778429_    650 CTGGAACAGTTGGACACCCATACACAAAA-AATGAACTTCAACCCATATT 698
                             i   ii    i ?   i ii     -      v  vi    v  ii
  L1M4_orf2#LINE/    414 CTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACC 463

  chr20_54778429_    699 TCA-ATTTTTT-------TTAAGTTAAAATCGATCATAGACCTCAGTGTA 740
                            - iiv v -------    v i     v     ?      v i    
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr20_54778429_    741 AAAGTTAAAACTACA 755
                          i  i        i 
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATA 528

Transitions / transversions = 1.85 (37 / 20)
Gap_init rate = 0.02 (4 / 265), avg. gap size = 2.50 (10 / 4)  

1280 22.16 3.24 1.35  chr20_54778429_54780800.rev     1035  1404 (968)    L1M4_orf2#LINE/L1      503   879 (29)  

  chr20_54778429_   1035 ACCTCAATA-AATAAATAAATAAATAAAACTTCTAGAAGAAAACATAGGA 1083
                             v   i-  v iv    vvv        ii                ?
  L1M4_orf2#LINE/    503 ACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGN 552

  chr20_54778429_   1084 GAAAATCTTCATAACTTTGGATTAGGCACAGGTTTTTTTAAGATAGAACA 1133
                          v        i i  i    i       vv     i  --     vi   
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT--AGATATGACA 600

  chr20_54778429_   1134 CAAAAAGCATAAATTGTAAA-GAACAAATTGATAAATTGGACTT----AA 1178
                          v       i  iivii   -   v    v              ----  
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAA 650

  chr20_54778429_   1179 AACGAAAAACTTCTAT-CTTCGAGAGACACTGTTACAAAAATGAAAAGAC 1227
                           iv        i i -    i ii      i i vi   i         
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_54778429_   1228 AAGCCACAGACTGTGAAAATATATTTGCAAAACGCATATCTGATAGAGGA 1277
                           v       v  v  i  v           v ii          ii   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_54778429_   1278 CTGGAATGGAGAATATATAAATAACCCTCACAAGACAGTAATAAGAAAAC 1327
                           v v  vv            v   i  i    vv  i      i  i  
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGAC 800

  chr20_54778429_   1328 AAATAACTCAATT-AAAAATTGGCAAAATATTTGAACCAATACCTTGTTA 1376
                                i     -      v      iv       ivi i ii ivii 
  L1M4_orf2#LINE/    801 AAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCA 850

  chr20_54778429_   1377 AAGGGAACGAAATACA----GCCGAGAAGGAC 1404
                            --  -  v     ----   i v   v  
  L1M4_orf2#LINE/    851 AAG--AA-GATATACAAATGGCCAATAAGCAC 879

Transitions / transversions = 1.31 (46 / 35)
Gap_init rate = 0.02 (9 / 377), avg. gap size = 1.89 (17 / 9)  

 305 16.39 0.00 0.00  chr20_54778429_54780800.rev     1820  1880 (492)    L1M4_orf2#LINE/L1      848   908 (0)  

  chr20_54778429_   1820 CTAAAGAATATATATGGATGGCCAATAGACTAATGAAAAGATGCTCAACA 1869
                          i      v     iii          ii vv                  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_54778429_   1870 TTATTAGTCAT 1880
                          i ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.00 (0 / 0)  


3523 20.48 4.89 1.59  chr20_55085623_55088595.rev     1603  2481 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_55085623_   1603 TGGTATAACATCCCATGCTCATGTATTGGAAGACTTAA-ATTCTTAAGAT 1651
                            v vi i        i     v              -   v       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_55085623_   1652 G-------TC---------ACCTACAGATTCAGTGCCATCCTTATCAAAA 1685
                          -------  --------- i           ii  v    i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_55085623_   1686 TGCCCCATGGCATGTTTTGCA-AAACTAAAAAAAACACCCTAAAATTCCT 1734
                          -   viiv  v v       -   i i v  ivvv i          v 
  L1M4_orf2#LINE/    101 T-CCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_55085623_   1735 GTGGAATCTCAAAGGAATCTGAATAGCCAAAA-AGCTTTGAAGAAAAATA 1783
                         i     viv   i   vi v            - iii     i  i  v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_55085623_   1784 ACAGAGTTGGATGACTCACACTTCCCGATTTCATAACATATTACAAAGCC 1833
                            i       v              i      v   v  i        i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_55085623_   1834 ACAGTAATCAAAACAGTGTGGTACTGGCATAAAGACAGTTACATAAACAA 1883
                                    i                    i  i  vi i   i iv 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_55085623_   1884 ATGGAATGGAATAAACAGTCTAGAAATAAACCTTTATATGTATACTCAAC 1933
                                i    vi v    i           iv  i  v   iv    i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_55085623_   1934 TGATCTTCAACA-GGATGCTAAGCCCATTCAATGGGAAAAGGACAGTCTC 1982
                             i   i   -  i   i   v            i    i i     i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_55085623_   1983 TTCAACAAATTGTGTTGGGAAAACTGGATATCCAAGTGCAAAAGAATGAA 2032
                                   v   i     v         ?   vi              
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_55085623_   2033 GTTGGGTCTTTATCTTAGACTGTGTATAAAAATTAA------AGGGATTA 2076
                              ii ii  i  i v  ii i  i         ------ v    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_55085623_   2077 TATATCTAAACAAAAAACCCAAATGTTTAAAACTCCTAGAA-AAAACTTA 2125
                         ? v i     iiv  i v i   vv v        i     -     v  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_55085623_   2126 GGGGGGCAATCCTCATGACAC-GAATT------TGGT--CTTGGATATGA 2166
                           ? vi-    i  i    vi- ii  ------    --   i       
  L1M4_orf2#LINE/    550 GGNGTA-AATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_55085623_   2167 CACTACAAGCACAGACAAAAAAAGCAAAAATACACAAATGAGACTAATTT 2216
                            i v       ii   v     v       v i    vi    vvv i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_55085623_   2217 AAAGTTAAAAACTTTT-T-CCTCAAAGGACACAATCAGAAAAGGTAATAA 2264
                            i            - - i           v    ii    ---- --
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG----T-- 692

  chr20_55085623_   2265 GAGAAAAGGTAATAAGAGGCAGAATAAGAGAATATATTTGTAAACCATAT 2314
                         --      --- i  vvvi      ii     v       i   i     
  L1M4_orf2#LINE/    693 --GAAAAG---ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_55085623_   2315 ATCTGATAAGACGTTAGTATCTA-AATATAAAAAGAACT---ACAACTCA 2360
                                   ivii v     i -      v        ---        
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_55085623_   2361 GCAACAAAAAT-CATGTAACCTGATTTTAAAGTGGGCAAAAGACTTGAAT 2409
                         ii  i     v-  vi     ii   ?v   i        i  i      
  L1M4_orf2#LINE/    788 ATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAAT 837

  chr20_55085623_   2410 AGACATTTCCGTAAACATAATATACAAATGACCAAGAAATACATGAAAAG 2459
                                  ivi   v vi           i    v  ii          
  L1M4_orf2#LINE/    838 AGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAG 887

  chr20_55085623_   2460 ATGCTTCAACATCACTACTCAT 2481
                              -        ????????
  L1M4_orf2#LINE/    888 ATGCT-CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.63 (109 / 67)
Gap_init rate = 0.02 (22 / 908), avg. gap size = 2.59 (57 / 22)  


1017 23.01 10.12 3.07  chr20_55497093_55499708      636   961 (1655)    L1M4_orf2#LINE/L1        1   349 (559)  

  chr20_55497093_    636 TGGAGGGATACACTCTTCTGTTCACGGATTGGGAGACTCAGTATTGTTAA 685
                             ii    ---  iiv      i       i     i i         
  L1M4_orf2#LINE/      1 TGGAAAGATA---TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA 47

  chr20_55497093_    686 AGTGTAAAATTCTTTCCAAATTGATCTATACATTCAT-----TCCCC--C 728
                         ii  -iv   v  ii             i v     v-----    i-- 
  L1M4_orf2#LINE/     48 GATG-GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr20_55497093_    729 AAAGATCTCAGCAACATTTTCTTTTTGCATAAATTCACAAGTGGATTTGA 778
                            -   i    vi v    ----     v     v     iv   iiv 
  L1M4_orf2#LINE/     97 AAA-ATCCCAGCTGCCTTTT----TTGCAGAAATTGACAAGCTGATCCTA 141

  chr20_55497093_    779 AAATTTAGATGGAAAGGCAAAGGATTCAGAATCACCAAAAACAACTTTAG 828
                              i v       v    i   ii      vi      -   ii  ii
  L1M4_orf2#LINE/    142 AAATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA-CAATCTTGA 190

  chr20_55497093_    829 AAAAGAAGAACAAAGCTGGAGGACTTGCATTATCTGAGTTTGAGGCTGAC 878
                                        i         ii  i vi ii v  ii ii  v  
  L1M4_orf2#LINE/    191 AAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTAC 240

  chr20_55497093_    879 TATAC-GCTG------TCAAGACAGCCTGGTTCTG--ATGAAG---GAC- 915
                           i v-   i------         iv    v   --  i i ---   -
  L1M4_orf2#LINE/    241 TACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACA 290

  chr20_55497093_    916 --TAGCT---TGGGAAAGAATGGAG---CTACAAC---ACCCACACAT-- 952
                         --   v ---   i v     v   --- i v  v---     i    --
  L1M4_orf2#LINE/    291 TATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTT 340

  chr20_55497093_    953 GTGGCCAAT 961
                         i   i    
  L1M4_orf2#LINE/    341 ATGGTCAAT 349

Transitions / transversions = 2.00 (50 / 25)
Gap_init rate = 0.05 (16 / 349), avg. gap size = 2.69 (43 / 16)  

 792 30.19 0.75 1.13  chr20_55497093_55499708     1255  1519 (1097)    L1M4_orf2#LINE/L1      344   607 (301)  

  chr20_55497093_   1255 GTCAATACATTTT-AATACAGCTGCGAAGAGAAGTCAAGGGACAAGGGAT 1303
                               vv     -i i vi v   v    vv v    v  iv  i i  
  L1M4_orf2#LINE/    344 GTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAAT 393

  chr20_55497093_   1304 AGTTTTTAAAATAGATGGTGCTAAAACAA-TACATCAACCATGTGTGGAA 1352
                            i   vv  i i        iii    - iv  - ?   ii  iii  
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT-AKCCACATGCAAAA 442

  chr20_55497093_   1353 AAGCGAACCTTGATCCACACCTTGGGTCATAAGCGCTATTTGGCTCAAAA 1402
                         i ii   vi v  i  vi    iivii    vi ivv v  ii       
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_55497093_   1403 GGAATCACAGACTTAAATGTAAAACATAACATTATAAAACTTCCAGAAGT 1452
                         v i    ?    i         i vv   v i         iii     v
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_55497093_   1453 AAACCTGGGAAAAGACCTTCGCGACCTTGAGTTATGCAAAAGATTTCTTA 1502
                             v i  ?iv i i     i       i    v    -v i       
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAA-TGGTTTCTTA 591

  chr20_55497093_   1503 GATAATGACATCAAAAG 1519
                             -     i      
  L1M4_orf2#LINE/    592 GATA-TGACACCAAAAG 607

Transitions / transversions = 1.57 (47 / 30)
Gap_init rate = 0.02 (5 / 264), avg. gap size = 1.00 (5 / 5)  

 876 19.05 9.52 3.30  chr20_55497093_55499708     1852  2124 (492)    L1M4_orf2#LINE/L1      619   908 (0)  

  chr20_55497093_   1852 AAAGAAAACCGGCAGATAAATTAGACTTCATCAAAATTGAAAAAAAAATT 1901
                                 --iii         i               ---     vv  
  L1M4_orf2#LINE/    619 AAAGAAAA--AATAGATAAATTGGACTTCATCAAAATT---AAAAACTTT 663

  chr20_55497093_   1902 TGCTGTTTGAAAG-ACACCATTACATGAATGAAAAGACAAGACACAGACT 1950
                           -  i  v    -    i  i vivi i           vv      v 
  L1M4_orf2#LINE/    664 TG-TGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr20_55497093_   1951 GGAAGAAAATATTTACAAAACATATGTCTGATAAAGAACTTGTGTCCAGA 2000
                           i           i    v     i        i i      i      
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr20_55497093_   2001 ATACATGAATAACTCT---------------------CAAACAACCCAGA 2029
                            i  i  v      ---------------------    i      - 
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAACCCA-A 811

  chr20_55497093_   2030 GTACAAAATGT-CAAAAGCTATGAACAGGCA---CCTCACAGAAACCATC 2075
                         v ?v      v-    i v v    i  i  --- ii  v    i--  v
  L1M4_orf2#LINE/    812 TTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG--ATA 859

  chr20_55497093_   2076 TGCAGATGGCAAATAAGCATGTGAAAAGATTTTCCAAATCATTGGCTAT 2124
                          i  i     v        ii         vi  v v    ????????
  L1M4_orf2#LINE/    860 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.43 (30 / 21)
Gap_init rate = 0.03 (9 / 290), avg. gap size = 3.89 (35 / 9)  


3187 23.78 1.52 3.58  chr20_55649310_55651768     1047  1967 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr20_55649310_   1047 GATAGTCTGTGCTCATGAATTGGAAGATTCAATATTATTAATGA-GTCAA 1095
                             vi ii  i     i         i i      i    -  - v   
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAA-GATGGCAA 55

  chr20_55649310_   1096 TTTTTCCCAACCTGATTCATAGAGTCAATACAATCCCAATAAAAATCCTA 1145
                          vi i     vi    ii i   v    ii       v  v       i 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr20_55649310_   1146 GCAAACTATTTTGTAGATATTGACAAACTGATTC-AAAATTGTATATTGA 1194
                           viv  v     i   v        i     i -      -i    v  
  L1M4_orf2#LINE/    106 GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT-CATATGGA 154

  chr20_55649310_   1195 AAGGCAAAATATCTAAAATAGCCAAGACAATAATGAAGAA-AAGAAAAAA 1243
                           v    iiv i i i         i     vv    i  -     v   
  L1M4_orf2#LINE/    155 AATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA 204

  chr20_55649310_   1244 GTCGGAGGGCTCACACTAACTTATCTGAAGACTTACTATAAAGCTGTATC 1293
                           i     i        vv iv  i v  i        i      ii vi
  L1M4_orf2#LINE/    205 GTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGT 254

  chr20_55649310_   1294 CATCAAGATAGCATGGTATTGGCAAAAAAGTGGACAAATTGATTAGTGGA 1343
                         v       i  ii     i     v  iii i    v  v   i i    
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGA 304

  chr20_55649310_   1344 ACAGAATAGAG-GTCCAGAAAGAGACT-ACACAAATATAGTCAATTGATC 1391
                          i     v   -         v i  i- i   vv   i          i
  L1M4_orf2#LINE/    305 ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATT 354

  chr20_55649310_   1392 TTTGATGAAGGAGCAAAGGAAATTCAATGTAGAGAGGAAAGTCCTTTTTA 1441
                           i  ii i  v  v   ivv        vi  i  i v    -    i 
  L1M4_orf2#LINE/    355 TTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC-TTTTCA 403

  chr20_55649310_   1442 ACAATTGGTCCTTTTAACAATTTTAACAATTGGAACACTTGAATATC-AT 1490
                             v    v  -------------------  i   vi  i   ? - i
  L1M4_orf2#LINE/    404 ACAAATGGTGCT-------------------GGGACAACTGGATAKCCAC 434

  chr20_55649310_   1491 GTGCAAAAACATCAACCTAGACGCAATGCTTACGCTTTCC-CAAAAATTC 1539
                         i       iv  v  vi i   v vvvv  i  i iv vi-        v
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr20_55649310_   1540 ACTCAAAATGGATCCTGGACCTAAA----ACA--CAAAACCATAAAACCT 1583
                                       v?i        ---- v --i     i       ii
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTC 534

  chr20_55649310_   1584 TGAGAAAGAAATATGGGTAGAAAATCTAGGTGACCTTTGGCTTGGTGGTG 1633
                          v    ii   i  i  ?- v      vv        v  i v  iii  
  L1M4_orf2#LINE/    535 TTAGAAGAAAACATAGGN-GTAAATCTTCGTGACCTTGGGTTAGGCAATG 583

  chr20_55649310_   1634 AGCTATCAGATATAACCCGAAAAGCATGATCCATGAAAGAAAAAATTGAT 1683
                         ivi v i      i  v v       ii v v ii           ----
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT---- 629

  chr20_55649310_   1684 AATTATTGATAAATTGGACTTTATTAGGAT-AAAAAATCCTGATCGGTGA 1732
                         ---- --              i  i ii  -     v ii  vv vvii 
  L1M4_orf2#LINE/    630 ----A--GATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAA 673

  chr20_55649310_   1733 AAGACAATGTTAAGAGAATAAAAAGACAAGCCACAGATTGGGAGAAAATA 1782
                          i    v i i    i i i         v       v            
  L1M4_orf2#LINE/    674 AGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 723

  chr20_55649310_   1783 TTTACAAAACACACATCAGATAAAGGACTTGTATCAAAAATATACAAAGA 1832
                            i    v  i i   v     i           v i      i     
  L1M4_orf2#LINE/    724 TTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr20_55649310_   1833 ACTTGTGAAACTCAACAATAAGGAAACAAACAACCCCATTTAAAAATGGG 1882
                            iv iv       i     ii i     i     v   ?         
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr20_55649310_   1883 CCAAAGATCTGAACAGATACCTCAACACAGAAGATATACAGATGGCAAAT 1932
                          v  i   i    i   i ii  vv  v            i     v   
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr20_55649310_   1933 AAGCATATGAAAAGATGCTCAAAATCATTTGCCAC 1967
                              i                v    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.56 (131 / 84)
Gap_init rate = 0.02 (17 / 902), avg. gap size = 2.76 (47 / 17)  


 692 28.84 7.80 8.27  chr20_55783955_55785772.rev      497  1342 (476)    L1M4_orf2#LINE/L1       67   908 (0)  

  chr20_55783955_    497 TTGAACCTATAAATTCAGTACAACTTTAATCAAA--CTGATCAAGTTTGA 544
                             -i   i i     iii   iiiiv      -- iv v vivi  --
  L1M4_orf2#LINE/     67 TTGA-TCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTT-- 113

  chr20_55783955_    545 TTTTGATGAAACTAACA------TTC----ATTTAGATGGAGGAAT---A 581
                              vv    i i   ------ i ----   i v     --   --- 
  L1M4_orf2#LINE/    114 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGA--AATGCAA 161

  chr20_55783955_    582 ATAATCCATGAAGAAGAGCTAAACCCACTTTGCAAAAGGAGAGTAAAAAG 631
                         ivi i   ----   v   i   v v ii   v     i   ii   i--
  L1M4_orf2#LINE/    162 GGGACCCA----GAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG-- 205

  chr20_55783955_    632 GAGTCTTCCCCAGGGCCAGGACTAGGGTACCCCAAGTGCCTCTTGCCTCA 681
                         -----  ------  --      viviivi     -------  ---   
  L1M4_orf2#LINE/    206 -----TT------GG--AGGACTCACACTTCCCAA-------TT---TCA 232

  chr20_55783955_    682 TAACACCCACTACAAAGACACAGTCATAAAAACCATGCAGTACTAATACA 731
                         -  -  ii         vi     v  v  i  vi  ii     iii i 
  L1M4_orf2#LINE/    233 -AA-ACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATA 280

  chr20_55783955_    732 AGGACAGACACATAGACCAA-------------AGCAGCCCGGCAGAGAA 768
                             i     i     i   -------------  -  i  i - i v  
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAG-AGTCCAG-AAATAA 328

  chr20_55783955_    769 AGTCCCATGTACCGACAGGGACTCAA--GATGTGGTGATGCAGGGGCCG- 815
                          --     ii iiv ii ----    --   v v-i  iivi  v   i-
  L1M4_orf2#LINE/    329 A--CCCATACATTTATGG----TCAATTGATTTT-CGACAAGGGTGCCAA 371

  chr20_55783955_    816 GA--AATCTATGGGG---------TCATTTTA-TA---GATGTTGGAATA 850
                           -- v  v      ---------  v   i -i --- i  i   i i 
  L1M4_orf2#LINE/    372 GACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACA 421

  chr20_55783955_    851 A-TGGAC-TTGAGA-GCTAAAGAA--AAATAGGCATTGACCTGCCTAATA 895
                          -    i-?iv v -  v      --  i v  - ii--   i   v i 
  L1M4_orf2#LINE/    422 ACTGGATAKCCACATGCAAAAGAATGAAGTTGG-ACC--CCTACCTCACA 468

  chr20_55783955_    896 CAACACATAAAG-TGGACTCCATAGAAATCAAAGACCTTACT-TAAAAGG 943
                          v i i i   i- vi    v v vii    ?      v v -   i  v
  L1M4_orf2#LINE/    469 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 518

  chr20_55783955_    944 AAAAACCA-AA---TGTTAGCGTGCAAGAAAA--TGGGGATAATAGCTTT 987
                         v     i -  --- v    -----       -- i  ?i   - v   i
  L1M4_orf2#LINE/    519 TAAAACTATAAAACTCTTAG-----AAGAAAACATAGGNGTAA-ATCTTC 562

  chr20_55783955_    988 GTGACCTAGACATTGCG-AATGGTTTATGAAACAAAATTTCAAGAGCACA 1036
                                v i-i  iv -        v v i i vi ivi   i      
  L1M4_orf2#LINE/    563 GTGACCTTGG-GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACA 611

  chr20_55783955_   1037 AACCATAAAGCCAAAACCTGATTCATTTAATTACATCAAAACTGAGAA-- 1084
                          i v i   ivv    viv   vv   vi i v        i i i  --
  L1M4_orf2#LINE/    612 AGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACT 661

  chr20_55783955_   1085 TTTCTGCTTCATCAGCTGACAAAAGATACCTTCGACAAAATTAACAGAAC 1134
                            v       ----------  i  i  iv  i v   i v  v   - 
  L1M4_orf2#LINE/    662 TTTGTGCTTCA----------AAGGACACTATCAAGAAAGTGAAAAGA-C 700

  chr20_55783955_   1135 AATG-ATAACTTGAGAAAAGATATTTATAATATCTAAAATC-AACAGGGG 1182
                           iv- i ivv  i  i  i      ii  -   vv v   -i i i   
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAA-ATCATATATCTGATAAGGG 749

  chr20_55783955_   1183 AGTAATATGTGGATTTTATCAAGAAC-CTGGCACATAAACAAAAAAAAGA 1231
                          v vi   vii  v v   v      -  vi  vv v  i  v       
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_55783955_   1232 GAGGAACCCCAATGGGAAAATGGATGAAAGATACGAACAGGCAAATTTAC 1281
                         v iiv v      v?i       iii  i   vi   i  i  vv i v 
  L1M4_orf2#LINE/    800 CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCC 849

  chr20_55783955_   1282 AGACAAGGAAACCTAAAGAGCTGATAAACATATGAAA-GTTGTTAAATTC 1330
                          i v   - v ivi   vi  ii    i  i      - v  i v  -- 
  L1M4_orf2#LINE/    850 AAAGAAG-ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA--C 896

  chr20_55783955_   1331 ATTAGTAGTCAG 1342
                           i ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.50 (144 / 96)
Gap_init rate = 0.06 (52 / 842), avg. gap size = 2.62 (136 / 52)  


4187 17.06 7.06 0.24  chr20_55866500_55868693.rev      853  1702 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_55866500_    853 TGGAAAGACAACCCATGTTCATGAGTTG-AAGCATTAATATTATTAAGAT 901
                                 i v            ii   -   vv        i       
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_55866500_    902 GGCAATACTCCTCAAATTGATCTACAGATTCAATGCAATTACTATCAAAA 951
                                    i                     i     iv         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_55866500_    952 TCCCAGCTTCCCGTTTTGCAGAAATTGATAAGGTGATCCTAACATTCACG 1001
                                 v  iv               i   v         v     ii
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_55866500_   1002 TGGAAATGCAAGGAACCTAGAATGGATGAAATAATTTTGAAAAAGGAAAA 1051
                                      i   i     i vii   i   i         i i  
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_55866500_   1052 TA---TTGGAGGACTCATACTTCCCAATTGCAAAATTTAGTACAAAGCTA 1098
                         i ---            i           v     i   v          
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_55866500_   1099 AAGTAATCAAGAAATTGTGA-------ATAAAGATAGACATATAGAT--- 1138
                         v           v v    i-------    i               ---
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_55866500_   1139 -GTACATATATTTGAGATTCCAGAAGTAAGCCCTTACAATTGTAATCAAT 1187
                         - v -   v v      v       i   i   v    v  i ii     
  L1M4_orf2#LINE/    301 TGGA-ATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_55866500_   1188 TTATTTTTGG----------------------TGGGGCAAAAATAGTCTT 1215
                          v     i i----------------------     v  i         
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_55866500_   1216 TTTAACAAATTGTGCTGGGATGACTGGACACCCACATGGAAAAAAA-GAA 1264
                           i       v         ii      i ?       v    i  -   
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_55866500_   1265 GCTGGACCCTTATCT----------ACAAAAAATAACTCAAAATGGACCA 1304
                          i       i  i  ----------       v              i  
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_55866500_   1305 TAAACCTAAACATAAGCACTAAAACTACAAAACTCTTAGAATAAAA---- 1350
                         ? i       ii    vi         i             v    ----
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_55866500_   1351 ----TAAATCTTAGTGTCCTTGAAATAGGCAGTACTTTCCTAGATACAAT 1396
                         ----        v   v     iiv      i iv    i      ii i
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_55866500_   1397 GCTAAAAGCACAAATGATAAGACAAAGAATCAGTAAATTGGGTTTAATCA 1446
                         i i          iii i  i v   i   vii        ii  v    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_55866500_   1447 TAATTTAAAATGTTTGTGCTTCAAAGGACACCATCAAAAAGGTGAAAGAA 1496
                         v    v    iv                   i     i  i      - i
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA-AG 698

  chr20_55866500_   1497 ACA--CCACAGAAGGAGAGAAAATATTTGCAAATCAAATGTCTGTTAAGA 1544
                            --        v i                    v  i    v    i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_55866500_   1545 GATTTGTACCCAAAATATGCAAAGAACT--TACAACTCAACAACTAAAAG 1592
                           i     i   i     ii        --          i  iv     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_55866500_   1593 GCAAATATCTGATTTCGAAAATGGACAAAAGATTTGAGTGGACATTTCTC 1642
                         i      v iv v  ?i       i    i       i i          
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_55866500_   1643 CAAAACATATATCTAAATGCCTAATAAGCACATGAAAAGATGCCCAATAT 1692
                             iv v    vi     v i                     i   i  
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_55866500_   1693 CATTATTTAT 1702
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.96 (94 / 48)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 5.17 (62 / 12)  


2957 27.62 0.55 0.22  chr20_55894784_55897069.rev      890  1794 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_55894784_    890 TGGAAACAGATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAGAAT 939
                               v v        i        v  v   v i        v ii  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_55894784_    940 GACCATACTGGCAAAGGCAATCTACAAATTCAATGCAATTGCCATCAAAA 989
                          i v     vv v  ivii       i      i     iv i       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_55894784_    990 TACCATCATCATTCTTCACAGAACTAGAAAAA--AATCCTAAAATTCATA 1037
                          v   v vv v  i  ii     v v  v  i--i               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_55894784_   1038 TGGAACCAAAAAAGTCCCCACATTGCAAAAGCAAGACTAAGCAAAAAGAA 1087
                              viiv  ii v   viv  v  v   i   vvi i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_55894784_   1088 CAAATCTGGAGGCATTACATTACCTGACTTCAAACTATACTACAAGGCTA 1137
                             vi      vv i   i v  ii i      viv        i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_55894784_   1138 TAGTTACTAAAACAGCATGGTACTAGTATAAAAATAGGCACATAGACCAA 1187
                         i   v ii  i    ii       i i    ii    i  i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_55894784_   1188 TGGAACAGAATAAAGAACCCAGAAATACAGCAGAATATTTACAGCCAACT 1237
                              i     vi   ii         v v viv i     ii i   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_55894784_   1238 GATCT---ACAAAGCAAATAAAAACATAAAGTGGGTAAAGGGCATCCTAT 1284
                            i ---    i vvivi  i v   vv i    v    iii vi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_55894784_   1285 TCAACAAATGGTGCTGGGATAATTGGCAAGGCACATGTAGAAGAATGAAA 1334
                                            i  i   vv ?v      i i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_55894784_   1335 CTGGATCCTCATCTCTCACCTTATACAAAAGTCAACTCAAGATGGATCAA 1384
                         i    i  ii i   v    v         i i       i        ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_55894784_   1385 AGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAGATAACATCA 1434
                             i     v     v  i    i      v ii       v     vi
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_55894784_   1435 GAAAAACTCTTCTAGACATTGGCTTAGGCAAGGAGTTCATGACCAAGAAT 1484
                          ?iv  v     vv   v    v        v iv   v iivi v  vv
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_55894784_   1485 CCAAAAGGAACTGCAACAAAAACAAAGATAAATATAATGGGACCTAATTA 1534
                                v vvv         iv   i   i   -   v    i v  i 
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATA-AATTGGACTTCATCA 649

  chr20_55894784_   1535 AAAGAAAAAGCTTCAGCAAAGCAAAAGAAATAATCAGCTGAGGAAACAAA 1584
                            vv    i   iv iivvv    i  v iv    ivvi  vi  v i 
  L1M4_orf2#LINE/    650 AAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGA 699

  chr20_55894784_   1585 CAACCTACAGAGTGGGAGAAAATATTAACAAACTACACATCTGACTAACT 1634
                              i     i              vi    ii i i      iv ivv
  L1M4_orf2#LINE/    700 CAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGG 749

  chr20_55894784_   1635 ACTAATATCCCGAATCTACAAGGAACTCAAACAAATAAGCAAGAAAAAAA 1684
                            vi     v    v  i  i      vv    v v ii  v     i 
  L1M4_orf2#LINE/    750 ACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGA 799

  chr20_55894784_   1685 ACAAATGATCCCATCAAAAAGTGGGCTAAGGACACGAATGTAGAATTCTC 1734
                         -     i i  v  i?    i     v     ivi    iv v v     
  L1M4_orf2#LINE/    800 -CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_55894784_   1735 AAAAGAAGATATACAAATGGCCAATGAACATATGAAAAAATGCTCAACGT 1784
                         v                        i i  i       i         i 
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_55894784_   1785 CACTAATGAT 1794
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.20 (134 / 112)
Gap_init rate = 0.00 (4 / 908), avg. gap size = 1.75 (7 / 4)  


2115 23.80 5.59 2.88  chr20_56130152_56132430      634  1259 (1020)    L1M4_orf2#LINE/L1        1   643 (265)  

  chr20_56130152_    634 TGGACAGATAGTCCATATTCATGGATTGAAAGACTCAATATTGTTAAGAT 683
                             v     vi    i           i      i              
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_56130152_    684 GTCAAT-TTTTCTGAATTTTTTCCTACAGATTCATTGTAA-CACTAATTT 731
                          v    -i ii ii    vv --           vi i  - v   -- i
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGAT--CTACAGATTCAACGCAATCCCTA--TC 96

  chr20_56130152_    732 AAAAATCAGGAAGCTATTTT--CTGAATATCAAGAAACTGACTCTAAAGT 779
                             vi vi vv  iv    -- v   -  ii v  i    ii     i 
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAA-ATTGACAAGCTGATCCTAAAAT 145

  chr20_56130152_    780 TTATGTAGAAGCACAAAAGATCCAAAATAGCCAACATGACACTAAAGAAG 829
                          i  i i   iii   ii  i   i         v ii ivi i  i   
  L1M4_orf2#LINE/    146 TCATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAG 195

  chr20_56130152_    830 AAGAGCA---------GACT--------------TCAAGACTTA-----A 851
                             i  ---------    --------------    i     ----- 
  L1M4_orf2#LINE/    196 AAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAA 245

  chr20_56130152_    852 AGCTACAGTAATCAAGACAGAATGATATTGGCAAAAGAATAGGGACATAA 901
                                             vi  i  i     v   i    iv i   i
  L1M4_orf2#LINE/    246 AGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAG 295

  chr20_56130152_    902 CTCATTCGAACAGAATAGAGAGACCAAAAATAGAGTCACACAAATATAGT 951
                         v   v v   i     v     v   i     i vi  i   vv   i  
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_56130152_    952 CAACTGATCTTCAGCAAAGAAACAAAGGCACTTCTAAGGAGAAAGTATAG 1001
                            i    i   ii   i ivi v   i vv   v v  i     v    
  L1M4_orf2#LINE/    346 CAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAG 395

  chr20_56130152_   1002 TCTCTTCAACAAATGGTGCTGGAACAATTGGACATCCATATGCAAAAAAA 1051
                            i                  i    i    i ?   i        i  
  L1M4_orf2#LINE/    396 TCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA 445

  chr20_56130152_   1052 AAAAAAAAAAAAAAATCCAGACACGAACCTTACATCCTTCAGAAAAATTA 1101
                         vi  i-----------iii   v vv    i   i v vi v        
  L1M4_orf2#LINE/    446 TGAAG-----------TTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr20_56130152_   1102 ACTCAAAATGAATCACAGACCTAACTATAAAA--TGGACCACTATAAAAC 1149
                                   i    ?        v i   i -- ii --          
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA--ACTATAAAAC 532

  chr20_56130152_   1150 TTCTAGAAGATAACATGGAAGAAAATCTAAGTGACATTGGGTTTAGCAAT 1199
                          ii       v     i i? v      vv     v       vi     
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr20_56130152_   1200 GAGTTTTTAGATAAAATACCAAAAGCATAATTCATGAAAGAAAAAATA-A 1248
                          iv  i       vi i          i  viv ii            - 
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr20_56130152_   1249 TAAATTAGACT 1259
                               i    
  L1M4_orf2#LINE/    633 TAAATTGGACT 643

Transitions / transversions = 1.81 (94 / 52)
Gap_init rate = 0.02 (13 / 643), avg. gap size = 4.08 (53 / 13)  

 805 22.69 9.24 0.00  chr20_56130152_56132430     1550  1787 (492)    L1M4_orf2#LINE/L1      649   908 (0)  

  chr20_56130152_   1550 AAAATTAAAAACCTCTGCTCAGTGAAAGACATTGTTAAAACAATCAAAGG 1599
                                     i i  iv vvii  i    i i i  i v i v   i 
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_56130152_   1600 -CAAGCCACAGACAGGGGGAAGATACT-ATAAAACACTTACCTGATAAAC 1647
                         -   v       vv   i   i   i -ii   v  iv  i       iv
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_56130152_   1648 GACTTGTATCCAAAACATA----GAGTTCTTAAAAC-----AATAAGGAG 1688
                                     i  i   ----  ii     v   -----     ii  
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_56130152_   1689 ACAAA----CCAA-------ATGGGTGAAAGATCTGAAAAGACATCTCAT 1727
                              ----    -------     ii  i   i    v      i  vi
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_56130152_   1728 TAACAAAGATACACAGATGGCAAATAAGTATATGAAAAGATGCTCAACAT 1777
                         i  vi      i   i     v      i i                   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_56130152_   1778 CATATGTCAA 1787
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.38 (38 / 16)
Gap_init rate = 0.02 (6 / 260), avg. gap size = 3.67 (22 / 6)  


2902 25.45 3.75 0.57  chr20_56260434_56262658      854  1733 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_56260434_    854 TGTAAATACATCCCATGTTCATGGATTAGAAGAATCAATATCATAAAAAT 903
                           v   v i                  i     v i     ii v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_56260434_    904 GACCACATTGCCCAAAGTAATCTACAGATTTAATGCAATTCTTATCAAAA 953
                          i v i i v      v i           i  i     i i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_56260434_    954 TATCAATT-CATTATTCACAGAATTAGGAAAAAAAATCCTAAAATTCATA 1002
                          vi  ii - v  v  ii     v v iv  ivvi               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_56260434_   1003 TAGAATTAAAAAAG--TCAGAATAGCCACAGCAACACCAAGCTAAAAGAA 1050
                          i   v iv  ii --i           v i   iviii ivv i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_56260434_   1051 CAAATCTGGAGGCATCACATTACCCAACTTCAAATTATAGTACAAGGCTA 1100
                             vi      vv     i v     i      viv  v     i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_56260434_   1101 TAGTAACCAAAACACCACGGTAATAGTATAAAAGCAAAC--------CAC 1142
                         i     i   i   viii    v i i    iiii i  --------  v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_56260434_   1143 TGCAACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTACAACCAACT 1192
                           v  i     v    ii           v   v i i   iiii   i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_56260434_   1193 GATCTTTCACAA---TGCATACAAAAC-ATACACTGGAGAAAGGATATTC 1238
                            i  iv    ---   ---   i  -  v  v   i     i   v  
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGC---CAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_56260434_   1239 TATTCAATAAATGGTGCTGGGAAAACTGGCTAGCTACATGGAGAAGAACG 1288
                          v     i              v      v  ? i     v i     i 
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_56260434_   1289 AAACTGGATCCTTATCTCTCCCTTTATACAAAAATCTACTCAAGAT---- 1334
                           ii    i  i  i   v v iv           iv      i  ----
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_56260434_   1335 ------TTTAAATCTAAGACCTGAAACCATAAACATTATAGAAGAAAATC 1378
                         ------ii     v     v  i    i     vv iv          iv
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_56260434_   1379 TAGGAAAAACTCTTTCTGGACACTGGTGTAGGCAAAGAATTTATGACTAA 1428
                             ?iv  v    iv  -  vi   vv       v iv  iv iiv  v
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTG-ACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_56260434_   1429 GACCCCAAAAGCAAATTTAACAAAAACCAATATAAATAAATGCGATCTAA 1478
                            v         v vvi       ivv  v   i      vv  ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_56260434_   1479 TTAAACTAAAAAGCTTCTGCACAGCAAAAGAAATAGTCATCAAAG----- 1523
                          i   v v    i   i  ii vv    i  v ivi   vv    -----
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_56260434_   1524 AGACAACTCACAGAATGGGAGAAAATATTTGCGAACCATGCATCCAACAA 1573
                                i                        i  i   ii   ii i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_56260434_   1574 AGAACTAATATCCAGAATCTACAAGGAACTCAAACAAATCAA--AGAAAA 1621
                         i i   vi          v  i  i      vv    v    -- v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_56260434_   1622 AAACAAATAATCCCACTGAAAAGTGGGCCAATGATATGAATAGGACATTT 1671
                          i        i  v i ?    i     v  v   v       -      
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG-ACATTT 845

  chr20_56260434_   1672 CTCAAAAGAAGATATACAAATGGCCAAGAAGCATATAAAAAAA-ATTCAA 1720
                            v                       v     i  i    i -ii    
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_56260434_   1721 CATCACTAATTAT 1733
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.35 (127 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.17 (38 / 12)  


 368 20.21 9.57 0.00  chr20_56534763_56537384.rev      245   338 (2284)    L1M4_orf2#LINE/L1        1   103 (805)  

  chr20_56534763_    245 TGGAAAGACATGCCATGTT----GAC--AAAGAC--AATATTGTGAAGAT 286
                                 i  v       ----  i--i     --        v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_56534763_    287 GTCAATTCTTCC-AAACTGATTTACACAGTCAGCATAATTCTAATCAAAA 335
                          v    v  i  -   i    i    v v   i ii   i iv       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_56534763_    336 CCC 338
                         i  
  L1M4_orf2#LINE/    101 TCC 103

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.04 (4 / 103), avg. gap size = 2.25 (9 / 4)  

 379 21.88 3.12 0.00  chr20_56534763_56537384.rev      501   596 (2026)    L1M4_orf2#LINE/L1      112   210 (698)  

  chr20_56534763_    501 TTTTTTGTAGAAATCAACAAGCAGATTCTAAAATTTTTATGAAAAGATAA 550
                                i      ii      v   i        iv    i   vii  
  L1M4_orf2#LINE/    112 TTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAA 161

  chr20_56534763_    551 AGAA---AAAATAACAAAAGTGATCTTGAAAAAGAAGAATAAAGTTAGA 596
                         i i --- i    i v   iii                 i      i  
  L1M4_orf2#LINE/    162 GGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 210

Transitions / transversions = 4.25 (17 / 4)
Gap_init rate = 0.01 (1 / 99), avg. gap size = 3.00 (3 / 1)  

1539 27.00 2.59 0.65  chr20_56534763_56537384.rev     1050  1512 (1110)    L1M4_orf2#LINE/L1      194   665 (243)  

  chr20_56534763_   1050 AGAAGAATATATTTTAAATAAAGTCACCCTACCTGATTT--------AGT 1091
                                i v v  vi i--i v    v  v  ii    -------- v 
  L1M4_orf2#LINE/    194 AGAAGAACAAAGTTGGAG--GACTCACACTTCCCAATTTCAAAACTTACT 241

  chr20_56534763_   1092 ACAAAGGTAAGATATTCAAGAGAATGTGGAATTAGAGAAAGGGCAGACAT 1141
                               v  vii  v      v i     v i i viv    ii      
  L1M4_orf2#LINE/    242 ACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACAT 291

  chr20_56534763_   1142 ATAGACCAACGCAATAGACTATAAAGTCCAGATATAGGCCTATACAGAGT 1191
                              i   i v      v vv i        v   ii  i     vvvv
  L1M4_orf2#LINE/    292 ATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTA 341

  chr20_56534763_   1192 GGGTCAGTTGATTTAGGACACAGTTGCAAAGGCAATTAAGTAGAGAAAAA 1241
                         v     i       vv    vi v   v   i v   v i i i    i 
  L1M4_orf2#LINE/    342 TGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGA 391

  chr20_56534763_   1242 GTAGTCTTCTCAACCAATGGGGTTGGAATAATTGGATATTTATTTTTAAA 1291
                         i       i     v     v i   i i  i      ?ii iv vi   
  L1M4_orf2#LINE/    392 ATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAA 441

  chr20_56534763_   1292 A---TGAACCTCCATTCATATATCACACTATAT-CAAAATATTCACTCAA 1337
                          ---    vi vv ii v  iv      i    -     -   v      
  L1M4_orf2#LINE/    442 AGAATGAAGTTGGACCCCTACCTCACACCATATACAAAA-ATTAACTCAA 490

  chr20_56534763_   1338 AATAGATAATAGACTTCAATGTAAAACTTTAAACTATAAAACCTTCAGGA 1387
                            i   v ?    i v       i vi v            ii i  i 
  L1M4_orf2#LINE/    491 AATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAA 540

  chr20_56534763_   1388 GAAAACATAGAAGATAATCTTTGTGACCCTAGATTAAGTAAATATTTCTC 1437
                                   i? vv      i      i i i   i i  vvi     i
  L1M4_orf2#LINE/    541 GAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTT 590

  chr20_56534763_   1438 AGATATGGCCCCAAAAATATAATCCACAAAAGAAAAAATTGATAAATTAT 1487
                                i v      ii i  v v              v        iv
  L1M4_orf2#LINE/    591 AGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGG 640

  chr20_56534763_   1488 ACTTGATCAAAATTAACAACCTATG 1512
                             v           v   i v  
  L1M4_orf2#LINE/    641 ACTTCATCAAAATTAAAAACTTTTG 665

Transitions / transversions = 1.14 (65 / 57)
Gap_init rate = 0.01 (5 / 472), avg. gap size = 3.00 (15 / 5)  

 647 21.49 7.46 1.75  chr20_56534763_56537384.rev     1903  2130 (492)    L1M4_orf2#LINE/L1      668   908 (0)  

  chr20_56534763_   1903 CTCCAAGAGACATCATTAAGAAAATTAATAAGAAAGCTAGCAGAATA--- 1949
                           i   ii    ii  i      i v  -    v i ivi      i---
  L1M4_orf2#LINE/    668 CTTCAAAGGACACTATCAAGAAAGTGAA-AAGACAACCCACAGAATGGGA 716

  chr20_56534763_   1950 ------ATTTGCTAATAACATATCTAGAAAAGAACTTGTATCCAGAATAT 1993
                         ------      v   v i      iiv  i i                 
  L1M4_orf2#LINE/    717 GAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr20_56534763_   1994 GTAAATA-CTCA-ATAAGTTCAATAATAAAAC-ACAAACAATTCGAATTT 2040
                         i    v -   v- i  -i            v-     i  ii -    ?
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAA-CTCAATAATAAAAAGACAAATAACCC-AATTW 814

  chr20_56534763_   2041 TAAAATGGGCAAAAGGTTTGAA-----ATCTTCACCAAAGAAAATATAGT 2085
                         v            i i      -----  -   v        i     vv
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACAT-TTCTCCAAAGAAGATATACA 863

  chr20_56534763_   2086 GATTTTAAATAAGCCCATAAAAAGGTGTTAAACATCATTAGTCAT 2130
                         i  vviv       v   i     i  i v       ????????
  L1M4_orf2#LINE/    864 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.67 (30 / 18)
Gap_init rate = 0.04 (9 / 241), avg. gap size = 2.33 (21 / 9)  


 486 28.67 2.00 0.00  chr20_56739649_56744387     3079  3228 (1511)    L1M4_orf2#LINE/L1        1   153 (755)  

  chr20_56739649_   3079 TGGCGAGACATATCATATTCATGGATTGGAAAATTCAATATAATAAAGAT 3128
                            vi   i  vi   i              i i i     vi v     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_56739649_   3129 GCAAATTCACCTCAAATAGGTCTTTAGGTTTAATATAATTTCTATCAAAA 3178
                          vv   v v  i     v i   vi  i  i  iii   ii         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_56739649_   3179 TTCTAAGT---TTTAAAATACACATAGACAAGCTTATTCTAAAATTTATA 3225
                          i i iv ---   vvvii v v  v        v  i        i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_56739649_   3226 TGG 3228
                            
  L1M4_orf2#LINE/    151 TGG 153

Transitions / transversions = 1.39 (25 / 18)
Gap_init rate = 0.01 (1 / 153), avg. gap size = 3.00 (3 / 1)  

2380 25.84 4.55 1.61  chr20_56739649_56744387     3501  4247 (492)    L1M4_orf2#LINE/L1      140   908 (0)  

  chr20_56739649_   3501 TAAAATATATATGGAAAGACACC--ACCCAAGGATAGCTAAAACAAC--- 3545
                               vi         vi  vv--     - i     i       i---
  L1M4_orf2#LINE/    140 TAAAATTCATATGGAAATGCAAGGGACCCA-GAATAGCCAAAACAATCTT 188

  chr20_56739649_   3546 ---AAAGACCAATAAAATGAGAGGAC--ACACT--CTGATATTTAAGGTT 3588
                         ---     vv  i   i vi      --     -- ii  -  i  iii 
  L1M4_orf2#LINE/    189 GAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAAT-TTCAAAACT 237

  chr20_56739649_   3589 TACACTTTAGCTACAGTAATCAAGACAGTACGGTACTGGTGGAGGGA--A 3636
                            vvivv                     ii        iiv i   --i
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr20_56739649_   3637 CCACATCAATGAATGGAATAGATTAGAGAACCCAGAAACAGACCCCACAC 3686
                         v  i  vi  v           v v    ii       i i    - i  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCC-ATAC 336

  chr20_56739649_   3687 AAATATGCTCAAAACTGATATTTAACAAAGGTACAAAGGCTATTCAACAG 3736
                          vv    v    --i    v  ii    i   i v   i i      ii 
  L1M4_orf2#LINE/    337 ATTTATGGTCAA--TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr20_56739649_   3737 AAGAAGGATCATCTTTTCAACAAATGGTATTGGAGTAACTGGATATCCAT 3786
                         iii   i  vi                 ii   iii         ?   i
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr20_56739649_   3787 AGGCAAGAAAATGAATATCTACCTAAATCCCACACTTTACACAACA-CTA 3835
                          v    i i      vv vv   ivv i i     iv  i    v -i  
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr20_56739649_   3836 ACTCAAAATG-ATTATGGAGTTATTATTG----------AACTATAAA-C 3873
                                   -  i ?i  vi  -- v  ----------         - 
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTA--AATGTAAGAGCTAAAACTATAAAAC 532

  chr20_56739649_   3874 TTTTAGAAAAAGACATGGGAGAGAATCTTCAGGATCTAGGGCTAGACAAA 3923
                          i      i  i    i  ? vi       iv  i  v   i   i   v
  L1M4_orf2#LINE/    533 TCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAAT 582

  chr20_56739649_   3924 GAATTCTTAAACTTAATACCAAAAGCATGATCCATAAAAAGAAAAATGGA 3973
                          iv      i iv i i          ii v v i    ii      i  
  L1M4_orf2#LINE/    583 GGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGA 632

  chr20_56739649_   3974 TAAATTGAACCTCATCAAAATTTAAAATCTTTGTTTTACCAAAGGCCA-T 4022
                                i  i           v    ii     vi -i      v  - 
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT-TCAAAGGACACT 681

  chr20_56739649_   4023 GCTAAGAGAATGAAAAGATA-----TGGACTGTAAAAAAATATTTGCAAG 4067
                         iii    i i        i -----ii  v  vi i             i
  L1M4_orf2#LINE/    682 ATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAA 731

  chr20_56739649_   4068 CCATATGTTCAACAAAAAATAAACTAGTATCTGAAATACATAAAGAATTC 4117
                         i     i iii i  iii ----  v     iii    i        i  
  L1M4_orf2#LINE/    732 TCATATATCTGATAAGGGA----CTTGTATCCAGAATATATAAAGAACTC 777

  chr20_56739649_   4118 TCAAAACTAAACAGCAAAAAG-CAAACAACCGAATTGAAATCTGGGCCAA 4166
                          i v    v  i ii      -    i    v    ?   vv     v  
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAA 827

  chr20_56739649_   4167 AGACATGCACAGAGATTTCACTGAAGAGGATATACAGAGAACAAATAAAC 4216
                         i  iv  v i   v     v ii    i        i vii v     i 
  L1M4_orf2#LINE/    828 GGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGC 877

  chr20_56739649_   4217 ACATGGAAAGTTGTTTAACATCATTAGCCAT 4247
                              i    v  i i       ????????
  L1M4_orf2#LINE/    878 ACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.10 (128 / 61)
Gap_init rate = 0.02 (19 / 769), avg. gap size = 2.42 (46 / 19)  

 284 19.30 0.00 0.00  chr20_56739649_56744387     4683  4739 (0)    L1M4_orf2#LINE/L1      638   694 (214)  

  chr20_56739649_   4683 TGGATTTCATCAAAATTAAAGAGTTTTGTTCTTCAAAAGAAACTGTTAAG 4732
                             i               i v      v       i  v   i i   
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_56739649_   4733 AGAAGGA 4739
                          i iv  
  L1M4_orf2#LINE/    688 AAAGTGA 694

Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.00 (0 / 0)  


2788 25.64 3.31 2.98  chr20_56745440_56748546     1711  2615 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_56745440_   1711 TGGATAAAAACCACATGT--ATGCCTTAGA-GACTCAATATTGTTTAGAT 1757
                             v i v i v     --   vv  i  -    i         v    
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_56745440_   1758 GCAAATTCTTCCCAGACTGAACAGATTTCTCTAGCTTCAACACAATTCTA 1807
                          vv   v  i    i i   -------   vi  v      i    i iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGA-------TCTACAGATTCAACGCAATCCCT 93

  chr20_56745440_   1808 ATCCAAATATGAATAGAATTTTTAAATAAAATTGACAAATTGTTTCTAAG 1857
                            v    viv iiv vv     vivvi          ii  v i    i
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr20_56745440_   1858 ATTTAAATGGAAATGCAAAAGGCTTAGAATAGTTAAAAAGAAAAAATACT 1907
                            i v            ii i ii       ii    ------------
  L1M4_orf2#LINE/    144 ATTCATATGGAAATGCAAGGGACCCAGAATAGCCAAAA------------ 181

  chr20_56745440_   1908 CAACCTTTAAAATAAACAACCAAGTTGGAGAACTTGAACTTACTGGTTTA 1957
                            i   v    vi  v   v         i   iiv    v iii   v
  L1M4_orf2#LINE/    182 CAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTC 231

  chr20_56745440_   1958 AAAATATATCA-GAAGCTACAGTAATCAAGGTGGCGTGGAACTGATGGAA 2006
                             iv  ii -i                 iii i    v    iiiv  
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr20_56745440_   2007 TCATAGACA----GATCAATGGATCATAATAGATAATCCAAATATAGACT 2052
                         vv       ----          vi v   v  v i    i v   i  i
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAACC 331

  chr20_56745440_   2053 TAGACATACTCAGTTAACTGATTTTTTACAGAAGTATCACG-CCA---AG 2098
                         i v    vivii  i  i       iv   iii  ii  v -   --- i
  L1M4_orf2#LINE/    332 CATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAA 381

  chr20_56745440_   2099 TGAGGAAAAAA-AGCATCTTTTCAGCAAATGG-GCTAGAAAAACTAGGAA 2146
                           i     i  -  --        i       -   i i v    i iv 
  L1M4_orf2#LINE/    382 TGGGGAAAGAATAG--TCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr20_56745440_   2147 --CATATATAGAGGAAAGAGTCTTGACTCCTACTTCACATTACACAGAAA 2194
                         --  i  ii i i   v  ivi v   i     i     ii i i v   
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr20_56745440_   2195 AATTAATTTGAGATGGATGGATCATAGACCTAA-CATAAGAGCTAGAACT 2243
                               i ii i      ----  ?        -ii         i    
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGAT----CAWAGACCTAAATGTAAGAGCTAAAACT 525

  chr20_56745440_   2244 CTAAAGCTCCTTGCAGAATACATGGGAAAATATCTTCATGGACGTGAGGT 2293
                         v    i   i v v    v    i  ?iv v      i  iv v  i v 
  L1M4_orf2#LINE/    526 ATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTT 575

  chr20_56745440_   2294 AAGCAAAGATTTCTTAGA-----CCCCAAAAGCACTGATCACAAAAAGAA 2338
                          i    v i         ----- v          viiiv      ii  
  L1M4_orf2#LINE/    576 AGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAA 625

  chr20_56745440_   2339 ATACTAACAAATTGG-CCTCATCAAAATAAAAAACTTCTGCTTATCAAAA 2387
                          v ivi i       - i          v        i  iviv     i
  L1M4_orf2#LINE/    626 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 675

  chr20_56745440_   2388 GTCAACATTAAGAATATGAAAAGGCAAGCCACAGATTGGGAGAAAATATT 2437
                          v  vi  i     vi       i   v       v              
  L1M4_orf2#LINE/    676 GACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATT 725

  chr20_56745440_   2438 TGCAATACATATGTCTGACAAAGAATTTATACCCAGAATATTTAAAGAGC 2487
                              vv     i     i  i i i  i  i         v      i 
  L1M4_orf2#LINE/    726 TGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAAC 775

  chr20_56745440_   2488 CCCTACAGTTCAATAATAAAACAACATAAACAAC--AAC-AACAAACAGA 2534
                         i i    ii            vi   --  i   --  i-? v   ii i
  L1M4_orf2#LINE/    776 TCTTACAACTCAATAATAAAAAGACA--AATAACCCAATTWAAAAATGGG 823

  chr20_56745440_   2535 -AAAAGACTTGGATAGATATTTCAGAAAAGAAGATATACAAATGG---AT 2580
                         -   i  i   i     i     vvv                   ---  
  L1M4_orf2#LINE/    824 CAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAAT 873

  chr20_56745440_   2581 AAAAACATGTAAAGTTACTCGATATCATTAGTTAT 2615
                           iv     v    v i   i i    ????????
  L1M4_orf2#LINE/    874 AAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.69 (144 / 85)
Gap_init rate = 0.02 (21 / 908), avg. gap size = 2.71 (57 / 21)  


3400 22.53 1.87 2.09  chr20_56976940_56979226      886  1795 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_56976940_    886 TGAAAAGATATTCCATCCTCATGGATTGAAAGAATTAATAGTATTGAAAT 935
                           i        i    vi          i    v      v i  i i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_56976940_    936 GACAATACTATCCAAAGCAATTTACAGATTCAATGCAATCGCTATCAGAA 985
                          i       vi     vii  i           i      v      -  
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCA-AA 99

  chr20_56976940_    986 ATACCAATGACATTC---ACAGAAATAGAAAAAAAAATCCTAAAATTTAT 1032
                           v   iivi v  i---i       v  v  ivvi           i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_56976940_   1033 ATAGAACCACAAAAGACTCTGTATTGCCAAAGCAATCCTAAGCAAAAAGA 1082
                           i   vii   ii   i v v  v      i     i i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_56976940_   1083 ACAAAGTTGGAGGCATCACACT-ACAAACTTCAAAATATATTACAAAGCT 1131
                                      vv       -v v  i       iv  i         
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_56976940_   1132 ATAGTAACCCAAACAGCATGGCACTGGCATAAAAACAGACAAATATACCA 1181
                          i     i v i    ii   i          ii i     v   v i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_56976940_   1182 ATAGAACAGAATAGAGGACCCAGATATAAATCCACACATTCATATCCAAT 1231
                           i   i     v   iii     v     i   i     i  ivi    
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_56976940_   1232 TCATCTTTGACAAAGGTACAAAGAACGTACAATGGAAAAAGGATAGTCTT 1281
                          v  i  i     i   i v    v i v      ii    i        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_56976940_   1282 TTCAACAAATGCTGCTGGAAAAACTGGATAAACTATATGCAGAAGAATGA 1331
                                    v      i v         ?- i i     i        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAK-CCACATGCAAAAGAATGA 448

  chr20_56976940_   1332 AACTAAACCCCTATCACTCAGCATACACAAAAATCAAATCAAAATGGATT 1381
                          ii ii       i v v  v    i        i  v           i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_56976940_   1382 A-AGATTTGAATGTAACACCTGAAATTATGAAACTACTAAAAGAGAACAT 1430
                          -   ii i       v v  i   i   i     vi  i    i     
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_56976940_   1431 TTGGA-AAATGCTCCAAGACATTGGTCTCGGGCAAGCAAAGATTTTTTTG 1479
                         vv ?i-    -  i iv   v    ----- vi i    v i   i  v 
  L1M4_orf2#LINE/    549 AGGNGTAAAT-CTTCGTGACCTTGG-----GTTAGGCAATGGTTTCTTAG 592

  chr20_56976940_   1480 TGTAAGACCTCACAAGTACAAACAACAAAAGCAAGTGAAAATAGACAGAT 1529
                         -i  v   vi  v   i    i         -  ---        i i  
  L1M4_orf2#LINE/    593 -ATATGACACCAAAAGCACAAGCAACAAAAG-AA---AAAATAGATAAAT 637

  chr20_56976940_   1530 GGGATTACATCAAG-CTAAACA-------GC---AAAGGAAACAATCAAC 1568
                         v   i v      i-i    v -------  ---      v  v     v
  L1M4_orf2#LINE/    638 TGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAG 687

  chr20_56976940_   1569 AAAATGAAGAGACAACTCACAGAATGGCAGGAAATATTTGCAAACTACCC 1618
                            i    i       i          v  i             ii ivi
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_56976940_   1619 ATTTGACAAGGGATTCATAATCAGAATATATAAGAAGCTCAAACAACAGC 1668
                           i   i      i ii  vi            ii i   vv     -v 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAAC-TC 786

  chr20_56976940_   1669 AAAAACAAAACAAAACAAAATACAATCTGATTTTTAAATGGGCAAAAGAT 1718
                           v  i    -- i     ---i  i ii   ?vv           i   
  L1M4_orf2#LINE/    787 AATAATAAAA--AGACAAA---TAACCCAATTWAAAAATGGGCAAAGGAT 831

  chr20_56976940_   1719 TGGAATAGACATTTCTCAAAAGAAGCCATACAAATGGCTAACAGGTATAT 1768
                          v               v       vi           i  i i i i  
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr20_56976940_   1769 GAAAAAATGTTCAACATCACTAATCAC 1795
                              i   i         ????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.89 (132 / 70)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.12 (36 / 17)  


2554 26.19 2.59 4.74  chr20_57169967_57172290.rev      906  1833 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_57169967_    906 TGATAAAACACTCCATGCTCATGGATTATAAGACTCAATATCATTAAAAT 955
                           iv  i i ii     i         iv      i     ii    i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_57169967_    956 GTCCATACTGCTCAAA-------GCA-ATTCAACACTATTCCTATCAAAT 997
                          v v     v i    -------i  -       i v  i         v
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_57169967_    998 TACCAA-TGTCATTTTTCACAGAATTAGAAAAAAACT-ATTCCAGAATTC 1045
                          v   i-  i -     ii     v v  v  i--  -  i i i     
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr20_57169967_   1046 ATATGGAACCAAAAAGGAGCCCGAATAGCCAAAGCAATCCTAAGCAAAAA 1095
                                 viiv  i   v  v           i     i i iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_57169967_   1096 TAACAAAGCCAGAGGCATCACATTATCTGACTTCAAACTATACTACAAGG 1145
                         v       iii    vv     i vi ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_57169967_   1146 CCACAATAACCAACACAGCATGGTATTGGTATAAAAATAGACACACAGAC 1195
                          i   i   i   v    ii     i   i    ii       i i   i
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_57169967_   1196 CAATGGAACAGAATAGAGAACCCAGAAATAAAGCTGCACACCTAAAACCA 1245
                                 i     v    ii           v iii   ii  viii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_57169967_   1246 ACTGATTTTCAACAAAGTCAACAAAAATAAACAGTGAAAGAAAGGACCCC 1295
                          i        i    i viiv   i vi vv  i  ii-     i ivvi
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGG-GAAAGAATAGT 396

  chr20_57169967_   1296 CTATTCAATAAATGGTGCTGGGGAAACTAGCTAACCATATGCAGAAGAAT 1345
                           v     i             iv    i v  ?   i     i      
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_57169967_   1346 GTTGAATAGAGTGATTAGTGCCACTCTAATTCCAGAATGAAACTGGACTC 1395
                          --------------------------------------  ii     i 
  L1M4_orf2#LINE/    447 G--------------------------------------AAGTTGGACCC 458

  chr20_57169967_   1396 TTACCTCTCAATATATACAAAAATTAACCCAAAATGAATTAAATACTTAA 1445
                         i      v  vi                i       i  i ? v  i   
  L1M4_orf2#LINE/    459 CTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAA 508

  chr20_57169967_   1446 ATGTAAGACTTCAAACTATAAAAATCCTACAAGAAAACCAAGGAAATACT 1495
                                 vi v           v  i  v        vv   ?ivv v 
  L1M4_orf2#LINE/    509 ATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT 558

  chr20_57169967_   1496 CTTCTGAATGTCAGCCTAGACAAAGAATT-TAAGACTAAGTCCTCAAAAG 1544
                             vvi iv ii vi   i   v iv  - v   -  v v vi      
  L1M4_orf2#LINE/    559 CTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA-TATGACACCAAAAG 607

  chr20_57169967_   1545 CAAATGCAACAAAAATAAATATTGACAACTGGTACCTAATTAAACCAAAG 1594
                           v v         iv   v  v  i  v v v  i v  i   viv  i
  L1M4_orf2#LINE/    608 CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAA 657

  chr20_57169967_   1595 TGTTTCTATGTAGCAAAAGAAATAATCAACAATGTAAACAGACAACCTAT 1644
                         vii  i i  ivv    i  v iv     v  v  i  v        i i
  L1M4_orf2#LINE/    658 AACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCAC 707

  chr20_57169967_   1645 GGAATGGGAGAAACGATTTGCAAACTATGCAGCCAACAGAGGTCTAATAT 1694
                         i            vv         ii  ii v ii i ii  v  vi   
  L1M4_orf2#LINE/    708 AGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTAT 757

  chr20_57169967_   1695 TCAGAATCTATAAGGAACTTAAACAA----ACAACAA-----CAAA--AC 1733
                         i      v     i     ivv    ---- i  i  -----    --  
  L1M4_orf2#LINE/    758 CCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAAC 807

  chr20_57169967_   1734 C--ATTAAAAAGTGAGCAAAGGTCATGAAGAGACACTTCTCAAAAGAAGA 1781
                          --   ?    i  i       viv    v     i     v        
  L1M4_orf2#LINE/    808 CCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGA 857

  chr20_57169967_   1782 CATGCAAGCAGCCAACAAGCATATTTTAAAAATGCTCATCATCTCTGATT 1831
                         i  i   iii     i     i  vv-   i       v    v??????
  L1M4_orf2#LINE/    858 TATACAAATGGCCAATAAGCACATGA-AAAGATGCTCAACATCAZZZZZZ 906

  chr20_57169967_   1832 AT 1833
                         ??
  L1M4_orf2#LINE/    907 ZZ 908

Transitions / transversions = 1.57 (146 / 93)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 4.53 (68 / 15)  


1785 22.91 1.13 15.87  chr20_57175134_57178406.rev     1718  2782 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_57175134_   1718 TAAAGAGGCATATTGTGTTCATGCATTGGAAGATTCAACATAGTAAAAAT 1767
                          ii i  ii  viii        v         i i  i  v  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_57175134_   1768 GTCAATTCTCCCTAAATTGATATACAGGTTTAATGCAATTCCTATCAAAA 1817
                          v    v     i        v     i  i  i     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_57175134_   1818 CCCTAGTAAGATATTTTTGTGGGCATAGACAAGATTATTCTAAAATTTAT 1867
                         i  i  ivivv -      ii iv  v      v v  i        i  
  L1M4_orf2#LINE/    101 TCCCAGCTGCCT-TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_57175134_   1868 ATAGAAAGGCAAAAGAACTGGAATAACTCAAACAAGTTTGAAGAAAGATA 1917
                           i    v    ii  v ii     i iv      vi     i  ii v 
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_57175134_   1918 ATAAAGTGTAAAGAATCAGTCTACCTAACTTGATAACTTATTATATAGCC 1967
                          i     vvi i  v   vv  v  i  i  v v      i  i v   i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_57175134_   1968 AAAGTAATCAAGACTGTATTGTCAGAATAGACACAGACATGAGTAGAACA 2017
                          v            v  i v  ----------  v i   i  -------
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGT----------ACTGGCATAAG------- 282

  chr20_57175134_   2018 AAATAATTAAAAAAAAAAACATAAATCAATCTGCACAAATATACCCAACT 2067
                         -i   i---------- v i   i      -- ---i    v ---- i 
  L1M4_orf2#LINE/    283 -GATAG----------ACATATAGATCAAT--G---GAATAGA----ATT 312

  chr20_57175134_   2068 GATTTTTTTTTCTTTTGAGATGGAGTCTTGCTCTGTCACCCAGGCTGGAG 2117
                           --------------------     -------------   i------
  L1M4_orf2#LINE/    313 GA--------------------GAGTC-------------CAGA------ 323

  chr20_57175134_   2118 TGCAGTGGCACGATCTCAGCTCAGTGCAACCTCTGCCTCCTGGGTTCAAG 2167
                         ---------------------- i i-    ---------------  vi
  L1M4_orf2#LINE/    324 ----------------------AATA-AACC---------------CATA 335

  chr20_57175134_   2168 CAATTCTCCTGCCTCAGCCAACTGATTTTTTGACAAAGGT-TGAAAGCAG 2216
                           v  v --------i i   i       i-     i   -iv  ii vi
  L1M4_orf2#LINE/    336 CATTTAT--------GGTCAATTGATTTTC-GACAAGGGTGCCAAGACCA 376

  chr20_57175134_   2217 TTCTGTAGAGAGAGTGTAGATGTTTCAACAAATGATGCTGAAACAATTGA 2266
                            vi i i  i  vi   viv            i     ii    i  i
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGG 426

  chr20_57175134_   2267 CT-TCCGCAGGCAAAAGAAAAAAGAAAAAAAAAACCTTGACCTAAACCTC 2315
                         v -?  i  v         vi   -----------i v    ivv     
  L1M4_orf2#LINE/    427 ATAKCCACATGCAAAAGAATGAAG-----------TTGGACCCCTACCTC 465

  chr20_57175134_   2316 ACATCTTACTTATATAGAAATTAACTCAAAAT--ATTTAAAACAGTCTTA 2363
                            i -- --    i i               --  i---- ?  v i  
  L1M4_orf2#LINE/    466 ACACC--A--TATACAAAAATTAACTCAAAATGGATC----AWAGACCTA 507

  chr20_57175134_   2364 AATGTGAAATATAAAACTGTAAAAG-CTTAGGGGAAAAAAAGCACAGGAG 2412
                              i i vv       i     v-     ----  i   i  i   ? 
  L1M4_orf2#LINE/    508 AATGTAAGAGCTAAAACTATAAAACTCTTAG----AAGAAAACATAGGNG 553

  chr20_57175134_   2413 AAAATCTTTAGGACTTCTAAAGTGGGAAAGAGTTCCT-AGACTTGAAACA 2461
                         v       iiv   i - iiiv i  v  vi   i  -   iv   v  v
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGATATGACACC 602

  chr20_57175134_   2462 AAAAGTATGAGCCATAAAAGGAAAATATA-ATAAAATGGACCTCATCGAA 2510
                              i ii   v i     i    -   -     v     i     i  
  L1M4_orf2#LINE/    603 AAAAGCACAAGCAACAAAAGAAAAA-ATAGATAAATTGGACTTCATCAAA 651

  chr20_57175134_   2511 GTTAATTTTTTTTTTTTTGCTCTGTGCAAA---CCCCTGCTTATAATAAG 2557
                         i    vvvi    v ---   i----    --- v -----   --i   
  L1M4_orf2#LINE/    652 ATTAAAAACTTTTGT---GCTT----CAAAGGACAC-----TAT--CAAG 687

  chr20_57175134_   2558 AGAATAAAAA-ACTAGCTACAGATCTGGAGAAAGTATTCACAAACAACAT 2606
                          i i i    -  v v i     viv       i    ii    iv i  
  L1M4_orf2#LINE/    688 AAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATAT 737

  chr20_57175134_   2607 ATCTGACAAGGGACTTATATTTAAAATCTATACAGAACTATGAAAATTTA 2656
                               i         i   ii i   v    v      v v v  i i 
  L1M4_orf2#LINE/    738 ATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCA 787

  chr20_57175134_   2657 ACAGTTAAAAAAAAACCAACAACAATCCAATTAGAAAGTGTGCAAAC-AC 2705
                          i i ---     i  v  i   ---      ?i   i  v     v- i
  L1M4_orf2#LINE/    788 ATAAT---AAAAAGACAAATAAC---CCAATTWAAAAATGGGCAAAGGAT 831

  chr20_57175134_   2706 ATGAAGCAAGTTATCACCAAAAACGGTATACAGCCAGCAGATAAGCACAC 2755
                         v    vvi vv v  v     i v i      ivii  vi         i
  L1M4_orf2#LINE/    832 TTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr20_57175134_   2756 GAAAAGGTGTTCAACATCTTTAGCCAC 2782
                               i  i        v????????
  L1M4_orf2#LINE/    882 GAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.61 (148 / 92)
Gap_init rate = 0.04 (36 / 908), avg. gap size = 5.03 (181 / 36)  


 226 27.22 3.80 4.43  chr20_57536700_57539543      233   390 (2454)    L1M4_orf2#LINE/L1      752   908 (0)  

  chr20_57536700_    233 TTATGTCTGTAATATATAGAAAATGGCTATAATCAAAGAAGAATTCAAG- 281
                           i i  iiv        i i  ivvi  i  iiv  v  v  --v   -
  L1M4_orf2#LINE/    752 TTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA--AAAGA 799

  chr20_57536700_    282 CAAA-AACCAAATTTTTCAAATCAAGTAAAAGATATAAACAAAGAATTC- 329
                             -    v    ?--v   viii i   i   v i  i i v v   -
  L1M4_orf2#LINE/    800 CAAATAACCCAATTW--AAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_57536700_    330 --AGAGAAAATGAAATGCGAATGGCCCATAATCATAT-AAAAGAGGCTCA 376
                         -- i    i  ---  i i       v    v  i  -      v     
  L1M4_orf2#LINE/    848 CCAAAGAAGAT---ATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_57536700_    377 GCTTCAAAGAACTA 390
                         i v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (25 / 17)
Gap_init rate = 0.04 (7 / 157), avg. gap size = 1.86 (13 / 7)  

1172 25.66 7.14 1.06  chr20_57536700_57539543     1179  1556 (1288)    L1M4_orf2#LINE/L1        1   401 (507)  

  chr20_57536700_   1179 TGGAGAGATATTTCCTGTTTATGAATAGGAAGACTCGATAGTGTCAGGAT 1228
                             i      ii v    i   i  v        ii   v   i i   
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_57536700_   1229 GTGAGTTTTTCCTAAGTTGGTCTATAGATTCAATGCAATGGCAGTCAAAA 1278
                          vv i vi i  i  i   i    i        i     vv vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_57536700_   1279 GCACAGCCAGTTATTTTGAAGACAATGGCCAATTGATTCTAAA------- 1321
                         v v    iivi v     v   v v  i v ii    i     -------
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_57536700_   1322 --GAG--GCAAAGGACT-ACAATACCTAACACAATATTTTA---GAAGGA 1363
                         --  i--    i    i- v    v i  v     v  vv ---    i 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_57536700_   1364 CAAAGGTG-ACAACTGATACTACCTAACTTCAAGATAAGATATAAAGCTA 1412
                              v  - vi   v i   v  i  i     i ivviv  i       
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_57536700_   1413 CAGTAACCAAGACAGTGTGGTAGTGGCAAAAGAATAAGCAGATAGACAAA 1462
                               i               v     v   i   ii  v     iv  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_57536700_   1463 TGGAGCAGAATAGAGAGCCCAGAAATGTGTAAAC--ATAAAT--ATTGTC 1508
                             ii     v     i        ----    --   v  --  v   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAAT----AAACCCATACATTTATGGTC 346

  chr20_57536700_   1509 AACTGATCTTTGATGAAGGAGAAAAGGCAATAAAATAG-------ATAGT 1551
                           i    i  i  ii i  v vv   i v  vv   i -------     
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_57536700_   1552 CTTTT 1556
                              
  L1M4_orf2#LINE/    397 CTTTT 401

Transitions / transversions = 1.26 (54 / 43)
Gap_init rate = 0.02 (9 / 401), avg. gap size = 3.44 (31 / 9)  

1558 22.53 5.93 2.96  chr20_57536700_57539543     1847  2352 (492)    L1M4_orf2#LINE/L1      388   908 (0)  

  chr20_57536700_   1847 AAGA-TAGTCTTTTTCAACAA--GGTGCTGGAACAACTGGACATCCACAT 1893
                             -         -      --        i         i ?      
  L1M4_orf2#LINE/    388 AAGAATAGTCTTTT-CAACAAATGGTGCTGGGACAACTGGATAKCCACAT 436

  chr20_57536700_   1894 ACGAAA-AATAAATTTACACACAGACCTTTCAC-------AAAAATTAAC 1935
                         i i   -   i  v  iv  v vv    iv   -------          
  L1M4_orf2#LINE/    437 GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAAC 486

  chr20_57536700_   1936 TCAAAATGCATTACAGACTTAAATGTAAAATGC-AAAACTGTGAAACTCC 1984
                                 v  i ?    i         i -  -      i i      i
  L1M4_orf2#LINE/    487 TCAAAATGGATCAWAGACCTAAATGTAAGA-GCTAAAACTATAAAACTCT 535

  chr20_57536700_   1985 TAGATGATGATATTGGCAAAAATCTAGATTATCTTGAGTTTGGCAAGAAC 2034
                             v  vi i  v  ?iv      vvi v i    i   v     vii-
  L1M4_orf2#LINE/    536 TAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGG- 584

  chr20_57536700_   2035 TTTTTTAGCTATAACACCATAGGCATGATCTATGCAAGAAAAATTGAGAT 2084
                            i    v   i      v i   ii v v iiv        v -    
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT-AGAT 633

  chr20_57536700_   2085 T--CTGGACTTTATTAAAATTAAAAACTTCTGTG-----AAACACATTGT 2127
                         v--i       i  i              i    -----  iv   i i 
  L1M4_orf2#LINE/    634 AAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTAT 683

  chr20_57536700_   2128 CAAGAGAATGAAAAGACAAGCTACAGTCTGGGGCAAAATAGTTGCAAA-- 2175
                              i i           v i    vv    iv      v       --
  L1M4_orf2#LINE/    684 CAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATC 733

  chr20_57536700_   2176 AGACAT---ATAAAGGACCATCAACCAAAATACACAAAAAGATTCTTAAA 2222
                          v i  ---    i    ivvi v   i    i i   i - i     v 
  L1M4_orf2#LINE/    734 ATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGA-ACTCTTACA 782

  chr20_57536700_   2223 ACTCAACAATAAGGAAACAAACAACCTTATTTTTTTTCTTTTAAA----- 2267
                               i     ii i     i    iv   ?----------   -----
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTW----------AAAAATGG 822

  chr20_57536700_   2268 GCCAAGACCTT-AACAGACACCTCACCAAAGAAGATCTACAGATCGCAGA 2316
                           v   ivi  -  i     ii  v           v    i  v  vi 
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_57536700_   2317 TAAGGATTTGAAAAAGTCCTCCGCATCATATGTCAT 2352
                             v iv      ii v   vi     ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.44 (65 / 45)
Gap_init rate = 0.03 (17 / 521), avg. gap size = 2.65 (45 / 17)  


3237 27.31 0.44 0.44  chr20_57540478_57546753.rev     4877  5784 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_57540478_   4877 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 4926
                              ii i  i     i      i v      v i     i  v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_57540478_   4927 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGTCCTCCCCATCAAGC 4976
                            v     v     iv i  i           i ivv    i     iv
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_57540478_   4977 TACCAATGACTTTCTTCACAGAA-TTGGAAAAAACT-ACTTTAAAGTTCA 5024
                          v   iivi i  i  ii     -   -- v  i  - iii    i    
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTG--ACAAGCTGATCCTAAAATTCA 148

  chr20_57540478_   5025 TATGGAACCAAAAAAGAGCCCACATCGCCAAGTCAATCCTAAGCCAAAAG 5074
                                viiv  ii  v  viv  v     iv     i i ivv i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_57540478_   5075 AACAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGC 5124
                                i      vv       v  ii i      viv        i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_57540478_   5125 TACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGACC 5174
                                 i   i    ii         i iv ii i   v       i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_57540478_   5175 AATGGAACAGAAC--AGAGCCCTCAGAAATAACGCCGCATATCTACAACT 5222
                                i    i--    i  --        vv  ii i  i  iiiii
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCC--AGAAATAAACCCATACATTTATGGTC 346

  chr20_57540478_   5223 ATCTGATCTTTGACAAACCTGAGGAAAACAAGCAATGGGGAAAGGATTCC 5272
                          vi    i  i     ivv  vvi i v  vv            i  vvi
  L1M4_orf2#LINE/    347 AATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGT 396

  chr20_57540478_   5273 CTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCT 5322
                           v  i  i              v      v  ?   i   i i  iiv 
  L1M4_orf2#LINE/    397 CTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_57540478_   5323 GAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGA 5372
                            ii    i    v   i     v           i  i    i     
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_57540478_   5373 TTAAAGACTTAAATGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAAC 5422
                          i ?    i       v   v       i      vi i           
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAAC 546

  chr20_57540478_   5423 CTAGGCTTTACCATTCAGGACATAGACATGGGCAAGGACTTCATGTCTAA 5472
                         v    ?v v viv   iv   v v ivv i     v ii   v ivv  v
  L1M4_orf2#LINE/    547 ATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATAT 596

  chr20_57540478_   5473 AACACCAAAAGCAATGGCAACCAAAGCCAAAATTGACAAATGGGATCTAA 5522
                         i            vvi     v    vv     v  i    v   ii v 
  L1M4_orf2#LINE/    597 GACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_57540478_   5523 TTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC 5572
                          i   v v  i i   i  ii vv    i  v    i  vv i      v
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_57540478_   5573 AGGCAACCTACAAAATGGGAGAAAATTTTCACAACCTACTCATCTGACAA 5622
                           i     i   i             v  ii   vii ivi      i  
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_57540478_   5623 AGGGCTAATATCCAGAATCTACAATGAACTCCAACAAATTTACAAGAAAA 5672
                         i  i  vi          v  i  v      iv    v iv i  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_57540478_   5673 AAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 5722
                          i     i     v  i?    i     i     iv    i     i   
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_57540478_   5723 TCAAAAGAAGACATTTATGCAGCCAAAAAATACATGAAAAAATGCTCACC 5772
                           v        i  vi viii     v  ii         i       v 
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_57540478_   5773 ATCACTGGCCAT 5784
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (147 / 97)
Gap_init rate = 0.01 (5 / 908), avg. gap size = 1.60 (8 / 5)  


2941 26.26 1.76 1.98  chr20_57555996_57559488     2092  3001 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_57555996_   2092 TGGAAAAATATTCCATGGCTCATGGACTGGAAGAATTAATATTGTTAAAA 2141
                               i    i     -i       i       v             i 
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATG-TTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr20_57555996_   2142 TGGTCATGAGGCCCAAAGCAATTTACAGATTCAGTGCTAGTTCTATCAAA 2191
                            iv  ivvv      vii  i          ii  v vii        
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_57555996_   2192 CTACTGATGACATTTTTTACAGAATTAGAAAAAAACT-ATCCTCAAATTC 2240
                         v v iiiivi v      i     v v  v  i--  -     v      
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTC 147

  chr20_57555996_   2241 ACATGGAACCAAAATGAGCCCA-AATAAGCAATAAAATCTTAAGCAAGAA 2289
                          i      viiv  v ii    -    iv   v v      i iv     
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_57555996_   2290 GAACAAAGCTAGAGGTGTCACACTACCTGACTTCAAATTATACTACAAGG 2339
                                 i i    vv       v  ii i      viv        i 
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_57555996_   2340 CTACAGTAACTGAAACGGCATGGTAGTGGTACAAAAACAGACATGTAGAG 2389
                                  iii i  i ii     v   i i  ii i      i    v
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_57555996_   2390 CAATGGATCAGGTTATATAACCCAGAAATAAAGCTGCATATCCACAACCA 2439
                                vi  iv vv v ii           v iii i  ii iiii  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_57555996_   2440 TCTGATCTTTGACAAAGCTGACCAAAAAAAAAAAAAAGTAATGGAGAAAG 2489
                         vi    i  i     i v  -    i vv v------vi     i     
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTG-CCAAGACCAT------TCAATGGGGAAAG 390

  chr20_57555996_   2490 GGC--TCCTTATTCAATAAAAGGTGCTGGGATAACTGGTTGGCCACATGC 2537
                         iii--  i  --    i   v          i      v i?        
  L1M4_orf2#LINE/    391 AATAGTCTTT--TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr20_57555996_   2538 TGAAGATTAAAACTGGACTCCTTCCTTACACCATATACAAAAATCAACTC 2587
                         vi    v i  ii     i   v   i                 i     
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTC 488

  chr20_57555996_   2588 AAGATGCATTAAAGACTTAAATGTAAAACCGAAAATGATAAAAACCTTAG 2637
                           i   v  i ?    i         i v v    iv      vi     
  L1M4_orf2#LINE/    489 AAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAG 538

  chr20_57555996_   2638 AAGAAAACTTAGGAGATATTGTTCTGGACTTAGACCCTGGCAAAGCTTTC 2687
                                 v    ? vv v v   vv   i v iviiv     v v    
  L1M4_orf2#LINE/    539 AAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTC 588

  chr20_57555996_   2688 A-AGACA-GAC-TCAAA--CATCAATTGCAACAAAACCAAAAACTGACAA 2732
                         v-   i -   -i    --  -   --         vv     iv  i  
  L1M4_orf2#LINE/    589 TTAGATATGACACCAAAAGCA-CAA--GCAACAAAAGAAAAAATAGATAA 635

  chr20_57555996_   2733 GTGGGACCTAAATAGACTAAGGAGCTTCTGCACAGGAAAAGAAACTATCA 2782
                         i v    i v vi i v v ii i   i  ii vvv   i  v       
  L1M4_orf2#LINE/    636 ATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCA 685

  chr20_57555996_   2783 ACAGAATAAACAGAGAACCTGCAGAATGGGAGAAAATATTTGCAAACTGT 2832
                          v i i i  v   v    ii                         iii 
  L1M4_orf2#LINE/    686 AGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCAT 735

  chr20_57555996_   2833 GCATCCGACACAAATCTAATACCCAGAATCTGTAAGAAACTT----AAAT 2878
                         ii   i  i viiiv  vi  i       v i   ii    i----  v 
  L1M4_orf2#LINE/    736 ATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACT 785

  chr20_57555996_   2879 CAACAAGCCTAAAA---CAAATGGCCCCATTAAAAAATGGTCAAAGGACA 2925
                            i  ---     ---     ii   v   ?        v       iv
  L1M4_orf2#LINE/    786 CAATAA---TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_57555996_   2926 TGAACAGATAATTCTCAAAAGAAAACATACATATGGCCATCAGGCATATG 2975
                             i   i v     v      i i     v       vi i   i   
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 882

  chr20_57555996_   2976 AAAAAATGCTCAACATTAGTAATTAT 3001
                             i           i ????????
  L1M4_orf2#LINE/    883 AAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (143 / 92)
Gap_init rate = 0.02 (17 / 908), avg. gap size = 2.00 (34 / 17)  


3072 24.40 4.99 1.93  chr20_57601204_57603446.rev      871  1751 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_57601204_    871 TGGAGAGAGAATCCATGTTCATGGAT-------------ATTGTCAAGAT 907
                             i   v vi              -------------     i     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_57601204_    908 GTCAGTTCTTCTCTATTTGACCCGTAAATTCAATGCAATCTCAGTCAAAA 957
                          v  i v  i i v v    i iii i      i      i vi      
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_57601204_    958 TC--AGTTGTGACT-----------ATTCACAAACTGAATCTAAGGTTTA 994
                           --  i  i--  -----------   v    i    vi    ii  i 
  L1M4_orf2#LINE/    101 TCCCAGCTGC--CTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_57601204_    995 TATGGAGAGGCAAAAGGCCTAGCATCCCCAACACGCTGTTGAAGGAGAAG 1044
                               i v    ii i  i  v  vv    v  iv v     ii     
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_57601204_   1045 AACAAAGTTGGAAGACTGGCA-TTCCCGACTTTAAGACTTACTATAAAGC 1093
                                     i    vi  -     i i  i  i        i     
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_57601204_   1094 TACATTAATCAAGACAGTGTGATACTGGCAGAAAAACAGCCAAATAAATC 1143
                             v                i        v  ii i  v  v   i   
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_57601204_   1144 AGTGGAATTGAATAGGGAGCTCAGGAATTGATCCACATAAATATAGTCAA 1193
                          i      v    v i   ii   i   vi i   i i vv   i     
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_57601204_   1194 CTGATTTTTGACAAAGGATCCAAGACAATATAATGGAGAAAAGAAAGTCT 1243
                         i       i     i  vv       v  vi     i    ii v     
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_57601204_   1244 TTTCAACAAATGTT-CTCAAACAAGTGGATATCCACATGCAAAAAAGCAA 1292
                                     v -  vii    v      ?            i i---
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--- 445

  chr20_57601204_   1293 CTGAATCTAGACATAAGCCTTACACCCTTCACAAAAATTAATTCAAAATA 1342
                         -    vi i   vivvi   i     v vi           i       i
  L1M4_orf2#LINE/    446 -TGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG 494

  chr20_57601204_   1343 TATCATAGAACTAAATGTAAAATATAAAACTGTAAAACTCCTAGAAGATA 1392
                         v    ?   v          i vv       i        i       v 
  L1M4_orf2#LINE/    495 GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA 544

  chr20_57601204_   1393 ACACAGGAGAAAAGTCTAGAAAACCTTAGGTTTTGTGAGGACATTTTAGA 1442
                            i   ? v   -   vvivi     i    vv ii v iiv i     
  L1M4_orf2#LINE/    545 ACATAGGNGTAAA-TCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_57601204_   1443 TGCAATATTATG-GCATCATCCTTGAAAGAAATAATTGATATACTGGACT 1491
                          iii i ii vi-   iv v vvii       v   v    v i      
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_57601204_   1492 TCATTAAAA--AAAAAAGTCTACTTTGTAC------AGACACTGTCAAGA 1533
                             i    --     ---  --     i ------i      i      
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAA---CT--TTTGTGCTTCAAAGGACACTATCAAGA 688

  chr20_57601204_   1534 GATTGAAAAGAGAAGCTGAAGACTGGGAGAAAATATTTGTAAA--AGACA 1581
                         i v        v  v iiv   v                i   -- v i 
  L1M4_orf2#LINE/    689 AAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATA 738

  chr20_57601204_   1582 CCTAAAAAAGGACTGTTATCCAAAATATACAGAGAACTCTTGAAACTCAA 1631
                         i  i v  i     vv      i      i i         iv       
  L1M4_orf2#LINE/    739 TCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAA 788

  chr20_57601204_   1632 CAACAAGAGAATGAACAATTTGATTTGAAAATGGGCCAAAAGCCTGAATA 1681
                         i  i  i ii ii  i  iiii   ?i         v  iiiii      
  L1M4_orf2#LINE/    789 TAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATA 838

  chr20_57601204_   1682 GA----TCACCCATCAAAATAACCTACAGATG-CTAAGTAGTACATGAGA 1726
                           ----  v  v vv  i   ---    i   - i  vv  i      i 
  L1M4_orf2#LINE/    839 GACATTTCTCCAAAGAAGATA---TACAAATGGCCAATAAGCACATGAAA 885

  chr20_57601204_   1727 AGATGCTCCAAACATTATGCCATTA 1751
                                 --     i ????????
  L1M4_orf2#LINE/    886 AGATGCTC--AACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (133 / 78)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 3.39 (61 / 18)  


1643 29.49 10.92 1.46  chr20_57721957_57724681.rev     1410  2233 (492)    L1M4_orf2#LINE/L1        7   908 (0)  

  chr20_57721957_   1410 GATATACCATGTTCACAGACCAAATTACTGAATGTTTTAAAGATTTTATT 1459
                              v         ii  iiii vv   v   i  v v     vvi v 
  L1M4_orf2#LINE/      7 GATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAAT 56

  chr20_57721957_   1460 TGTTCCTAAATTGACCCACAAGTTCAATGTAATTCCAATCCAACTTACAA 1509
                         vv i  i       i i   ii     i i   i  v   v  v iv  i
  L1M4_orf2#LINE/     57 ACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAG 106

  chr20_57721957_   1510 AAGGTTTATGTGTATG---TGTGTAAATTAATTCAAATTTTTATATAGAA 1556
                         vv vi  v v  i vi---  -ii  ii i  i v  vv  i    i   
  L1M4_orf2#LINE/    107 CTGCCTTTTTTGCAGAAATTG-ACAAGCTGATCCTAAAATTCATATGGAA 155

  chr20_57721957_   1557 ATGTCTAGAACCAAGAATGACTAAGATGATCTTGAAGAAAAAAAACAAAG 1606
                            ivvi i   v     ii i  i ii        i  i  i       
  L1M4_orf2#LINE/    156 ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAG 205

  chr20_57721957_   1607 TGGTAGGATTTCCACTATCAGATATCATGACTGATTTTAAATCTCCAACA 1656
                          v v    i iv    vi vi  v   vi   v i vi   v  v  ii 
  L1M4_orf2#LINE/    206 TTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTA 255

  chr20_57721957_   1657 ATTATGATGATGTGCTATTGGAACAAGTTCAGACA----GGCCAATGGAA 1702
                           i v  iii    v  i   v i   vvi     ---- ii        
  L1M4_orf2#LINE/    256 ATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAA 305

  chr20_57721957_   1703 CAGAACATG-GAGCCCAGAAATAGACCCACGCAGTGTACTG---ACTGAT 1748
                         i    i-  -   i         i     ii  v -  iv --- i    
  L1M4_orf2#LINE/    306 TAGAAT-TGAGAGTCCAGAAATAAACCCATACATT-TATGGTCAATTGAT 353

  chr20_57721957_   1749 TTATGAGAAAAGAACACAG-CTGTGCAGTAGGAAAAGAATGGTCCTTTCA 1797
                           vi  v  ii vi vv  - ii v  i i  i       i   i     
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr20_57721957_   1798 CCAAATGGTGGAGGATCAATGGGATATCCATATGGGAAA-ATTGATTCCT 1846
                         v         vv  iv   iv     ?   i   vi   - v   vviiv
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr20_57721957_   1847 GATCCCTCCCTCATACCATACATAAAA-TTAATTC----TG-ATT----- 1885
                           i    v     i      i i    -    i  ----  -  i-----
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr20_57721957_   1886 -CCAAATTTCAGAGC-AAAACAAATAACACTTCTAGAAGAAAACA--GGA 1931
                         - i    v v     -     v -   v   ii            --  ?
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTA-TAAAACTCTTAGAAGAAAACATAGGN 552

  chr20_57721957_   1932 GAAAAGCTTTATGGTTTGTGGGT-AGGCAAATACTCCTTACATAAGATAC 1980
                          v   v   ii  iii -     -      vvii i    v   v  i  
  L1M4_orf2#LINE/    553 GTAAATCTTCGTGACCT-TGGGTTAGGCAATGGTTTCTTAGATATGACAC 601

  chr20_57721957_   1981 AAAAAG------------GAAAAAAGATTGCTAAAT-GGACCTACATTAA 2017
                         v     ------------i i    i  v v     -    i -   i  
  L1M4_orf2#LINE/    602 CAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATCAA 650

  chr20_57721957_   2018 AATTAAATATTTCTTTTCCTGAAAATATATAATTAAGTGAATGTAAAGGC 2067
                                v i  i v v i v   iv i iv  i   vi i  v    i 
  L1M4_orf2#LINE/    651 AATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGAC 700

  chr20_57721957_   2068 AAAGCACAT--TG--AGGAACT---------TCA---ACC-----AAAGA 2096
                           vv    v--  --  i  v ---------   --- i ----- ii  
  L1M4_orf2#LINE/    701 AACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGA 750

  chr20_57721957_   2097 CTCATATCCAGAATATATATTTTTTAA--ATTCCTAGAATTCAAT----- 2139
                           ii               ------  -- i  i  v  i     -----
  L1M4_orf2#LINE/    751 CTTGTATCCAGAATATATA------AAGAACTCTTACAACTCAATAATAA 794

  chr20_57721957_   2140 -----------------TTTTAAAACTTTCAAAAAACTC-AACAGGTACT 2171
                         -----------------  ?v    ivvv    ii i i-  i  ii i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_57721957_   2172 TC-ATAAAGAAGACATACAAATAGCCA-TGAAAAAATAAAAAGGAGCTCA 2219
                           -vi        i        i    - i iv v  i     iv     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_57721957_   2220 ACCTCATTCGTTTT 2233
                           v   ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.04 (32 / 902), avg. gap size = 3.19 (102 / 32)  


4073 18.88 4.23 0.34  chr20_57866871_57870519.rev     2286  3159 (490)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_57866871_   2286 TGGAAAGGTAATCCCATGGTCATGGATTGGAAGATTTGATAT-GTTAAAA 2334
                                i  -       v               i  i    -     i 
  L1M4_orf2#LINE/      1 TGGAAAGATA-TCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA 49

  chr20_57866871_   2335 TGGCAATACTCCCTGAAATAGA-CTACAGATACAATACAATCCATATCAA 2383
                                      i-    v  -        v   ii      v      
  L1M4_orf2#LINE/     50 TGGCAATACTCCCC-AAATTGATCTACAGATTCAACGCAATCCCTATCAA 98

  chr20_57866871_   2384 AATCCTAATGGTCTTCTT-GCAGAAATGGAAAAGCTAACCCTAAAAATCA 2432
                              i iiv i   i  -        v  v     i i       v   
  L1M4_orf2#LINE/     99 AATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCA 148

  chr20_57866871_   2433 TATGAAAATGGAAGAGACCCAGCATAACCAAAAAACTCT-------AATG 2475
                             i     v   i       v   i      v v   -------i v 
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_57866871_   2476 AATAAAGTTGGAGAACTCATACTTCCCAAATTCAAAATTTACGACAAACC 2525
                           i          i     i         v       i    v     v 
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_57866871_   2526 TACATTA-TTGAAATTATGTGGTACTAGCATAATGATAGACCTCTAGACC 2574
                             v  - ii i ivi         i      v       v v    i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_57866871_   2575 AATAGAATGTAATTGTGTGTCTAGAAATAAATCCACCCATCTATGGTCAC 2624
                            i    iv     v v   i         i   iv   i        v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_57866871_   2625 CTGAGTTTCATCAAGGGTAT-AAGACCATTCCATGGGGGAAAGTATAGTT 2673
                         i   v    iv       ii-          v      -    v     i
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGG-AAAGAATAGTC 397

  chr20_57866871_   2674 TCTT----AAATTGTTCTGGGACAATTGGACAAACACATGCAATATAATG 2719
                          i  ----    v  v         i    i ?v         v v    
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_57866871_   2720 AGGATGGAACCTTACTTCAGATCATGTACAGAAATTAA-------TGGAT 2762
                          i v    v  i   i   v i   i    i       -------     
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_57866871_   2763 TAGAGACCTAAATGTAAGAGCCAAAACTCTGAAACGCA-GGAAAAAAATG 2811
                         i ?                  i      v i    v v-i   i    ii
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_57866871_   2812 CAGGAGTCAATCTTTATGACCTTGGATCTGGCAGTGGATTCTTAAATATG 2861
                         i   ?  v      ii         i iv    i   v      i     
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_57866871_   2862 ATAC---AGATACAAGCAATGGAAGAAACATTAGATAAATCGGACTGTAG 2908
                          i  --- iii        iii      v v         i     vi v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_57866871_   2909 CACAATTCAAAACTTTTGTGCATCAAAGGACACTCCCAA-AAAGTGGAAA 2957
                           v    v             v            vi   -      i   
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_57866871_   2958 GACACCCTACAGAATGGGAGAAAATATTTGCAAATTGTATCTCTGA---G 3004
                             v  i                           ii   v     --- 
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_57866871_   3005 AGTCTAGTATTCAAAATATATAAAGAAGTGTTACAACCAAACAACAAAA- 3053
                         i v  v    i  i             v v       iv  i  i    -
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_57866871_   3054 --CA--CAACCCAAAT-ACAAATGGCCAAAGGACTTGAATAAGCATTTCT 3098
                         --  --i       v - v      v       i       ii       
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_57866871_   3099 TCAGAGAAGACCTACAGATGGCCAGTAAGCACACAGAAAGATATTCAGCA 3148
                         i  i      iv    i       i        iii      ii   i  
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_57866871_   3149 TGATTAGTCAT 3159
                          v ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.53 (98 / 64)
Gap_init rate = 0.02 (18 / 908), avg. gap size = 2.22 (40 / 18)  


2001 27.05 10.63 0.97  chr20_57913958_57915860      584  1411 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_57913958_    584 TGGAGAGATACACCATGTTTATAAACTAG-----TTATGACTGTTAACAT 628
                             i     iv       i  ii i i -----   vv i      v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_57913958_    629 GTTATTTCTCCCCATATTGATCTA------------AAACCTGAGTCATA 666
                          vi v v       v         ------------  v  iv -   v 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTA-TCAAA 99

  chr20_57913958_    667 ATTCCAGC-----------AAGCAATTGATAAACCAATTCTAAAATTTAT 705
                           i     -----------v  v      i  i ii  i        i  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_57913958_    706 ATAGAAGCTCAAAAGGCCTATAATTTCCAAAACAATATTTTAAAA-AACC 754
                           i   iiv   ii i  i v   vv          v  vv    -  vv
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_57913958_    755 ACAATGTTGGAAGACTTATACTGACTGACTTCAAGACTAACCACAAATCT 804
                             v      i    i i   vv ii i     i   v  i     v  
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_57913958_    805 ACCATAATCAAAACAGTGTGGTACTGACATAAAGAAAAGTAGACCTAT-G 853
                           vi       i              i     i  ----     v   - 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGA----TAGACATATAG 295

  chr20_57913958_    854 ATAAATAGAACAGATTGGAGGACCAAGAAATAGACACAC-TATTACAGAG 902
                           v   i   i   v v   iii v       i  v  i-i   -i vi 
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT-TATGG 344

  chr20_57913958_    903 TCA--TGATTTTCAACAAAGAAACCAAAGAAATCCAATGGA-AAAGAAAA 949
                            --        i    i ivi    iivv  i      i-      v 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATA 394

  chr20_57913958_    950 GCCTTTACAGCAAATAATCCCGTAATAACTGCATATCTATATG--AAAAA 997
                          i    v  i     ii v i vi i     v   ? i i   --   i 
  L1M4_orf2#LINE/    395 GTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGA 444

  chr20_57913958_    998 ATGAACCTCCAATCTCTGCATCATACCTTAATCAAATATTAATTTGAGAT 1047
                              vi v-i i i  i v   i   v  vv    v     i ii i  
  L1M4_orf2#LINE/    445 ATGAAGTTG-GACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_57913958_   1048 T-ATAATACTCCTAAACATAAAAGCTAAAACTATAAAATTTTT-GTGGAA 1095
                         v-  v ? vv      ii   i                i i  - vi   
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_57913958_   1096 AA-ATAATAGAACATCTTAGTGATTTAAGAGTCGACAAAAATTTTTTGGG 1144
                           -   iv? v v     v    ii vi iv v i   vii   i  i i
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_57913958_   1145 T----CACGGAAAGCA---ATAACCATA---AAAATAGATCAAGTAGATT 1184
                          ----   vi      ---ii   v v ---         v  v i  i 
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_57913958_   1185 TCA---AAATTTAAAACT-----GCT-CACCAGATATCATTAAGAAAATG 1225
                            ---     v      -----   -  vvi  i ii  i      i  
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_57913958_   1226 AATAAGCAAGATACAATTTTGGAGAAAACAT----AGAACATATATATGT 1271
                           v ii   vvi   ivv v        i  ---- i v       v  v
  L1M4_orf2#LINE/    694 AAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGA 743

  chr20_57913958_   1272 CAAAGGAGTGGAATCTAGGATACCTAA-GAACT----------------- 1303
                         i  i   v v v   i  i   iv   -     -----------------
  L1M4_orf2#LINE/    744 TAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATA 793

  chr20_57913958_   1304 -------AGATAGTCCAAT-AAAAAATGAACAAAATATTTAAAATATATA 1345
                         ------- i   ii     -?       ii    iv    i  -  v i 
  L1M4_orf2#LINE/    794 AAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAA-TAGACA 842

  chr20_57913958_   1346 CTTTACAAAGGAAAATATATGAATGGCCAGAAAGCACATGAAAAAGTGCT 1395
                         i  iv v  i   i     ii        iv             ii    
  L1M4_orf2#LINE/    843 TTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT 892

  chr20_57913958_   1396 CAGCATCACTAGTCAT 1411
                           i     ????????
  L1M4_orf2#LINE/    893 CAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (131 / 89)
Gap_init rate = 0.03 (27 / 908), avg. gap size = 3.56 (96 / 27)  


 366 29.49 12.84 5.47  chr20_57936256_57938113      532  1372 (486)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr20_57936256_    532 AGTTGTTCC-TATTCATTAATGGAAGGACTTAACATTATAAAACCATCAA 580
                           v i i  - i     vi  v i i       i   i v  iviiv   
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr20_57936256_    581 TGCTTCACTAAAATAAACATCTGAATTTCTA-AACTCCAAAGCAATTCCA 629
                          i  i v --    -------   ---    - iv i   v     i  v
  L1M4_orf2#LINE/     56 TACTCCCC--AAAT-------TGA---TCTACAGATTCAACGCAATCCCT 93

  chr20_57936256_    630 GTAAAAATCACAAAATAATAATTTG-AGAGATTTG---GCTAATTCTTTT 675
                         i v      v  ivvvvv vv    -   i   vi---   i  i  ---
  L1M4_orf2#LINE/     94 ATCAAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT--- 140

  chr20_57936256_    676 AAAACATGTATGGAGGAATAATGCTGCTCTA--ATA-CTAAAATAACTTT 722
                             ivii      iivii  v -- vi i --   - i    i  ii  
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGG--GACCCAGAATAGCCAAAACAATCTT 188

  chr20_57936256_    723 TAAAATATTAGAGAAGAA-AAA----------TCACCTTATTTGATATTA 761
                         v    ------       -   ----------    vi viiii  v i 
  L1M4_orf2#LINE/    189 GAAAA------AGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCA 232

  chr20_57936256_    762 AAACATATTACAAAGTCACAAGAAATAACTATAAACAGTGAAGTATTAAG 811
                             v  i       ii   i----   ii - i      vi   i iiv
  L1M4_orf2#LINE/    233 AAACTTACTACAAAGCTACAG----TAATCA-AGACAGTGTGGTACTGGC 277

  chr20_57936256_    812 A-ATGGA-AAACAAATGGATCAATAAAACAAAAC--AGAATTCAAACACA 857
                          - v   - i   v  i       ii  i i  i--   i i  i v i 
  L1M4_orf2#LINE/    278 ATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATA 327

  chr20_57936256_    858 TAAGCATATATT---GG-AAGTTCATATTTGAGTCAGATGGTTTCG---- 899
                         v vv    i   ---  -v i  v  v  i  --  - v   vi i----
  L1M4_orf2#LINE/    328 AACCCATACATTTATGGTCAATTGATTTTCGA--CA-AGGGTGCCAAGAC 374

  chr20_57936256_    900 CA---AATCGGGAAAGG-TAAACTGGTCAATAAATGGT-CTGGGAAAAGT 944
                           ---   v       i-  iv  vv    i       -      v  v 
  L1M4_orf2#LINE/    375 CATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr20_57936256_    945 GACTTGGCATGTGGAAAA-AATAACATTAGAAATCTATTTTGC----CAT 989
                          iv v?v  ii  v    -   i vi  i  vvi   ii ii ----i  
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATAT 474

  chr20_57936256_    990 AAAAAAATAAGGTCTAGATAAATTAACTACATGAATGTAAAAAGTAAATG 1039
                          v      v iv  v i  ii  i ?vv  v i       i iv    vv
  L1M4_orf2#LINE/    475 ACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC 524

  chr20_57936256_   1040 TTTATAAACTATTAGCAGAAAATTCAGGAGGCTATCACTAAGATGTTCCA 1089
                          v  -     v    v      ivi   ? vvv   viiiv  iv  --i
  L1M4_orf2#LINE/    525 TATA-AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT--G 571

  chr20_57936256_   1090 AG--AGGAAAGAATTT----------AAAACAAATGCACAA--AACATAC 1125
                         i --   v  vii   ---------- v v    v      --    v v
  L1M4_orf2#LINE/    572 GGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAA 621

  chr20_57936256_   1126 AAAGTAATAGAT---TTTAACTT-----------------TTTGTGCATC 1155
                         i  iv       ---  vi    -----------------       v  
  L1M4_orf2#LINE/    622 GAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTC 671

  chr20_57936256_   1156 A-------CTGTT-------TGTAAAAGAGAGGCAGCATACTAGGA--AG 1189
                          -------  i i-------  -      v iv vi  v v i   -- i
  L1M4_orf2#LINE/    672 AAAGGACACTATCAAGAAAGTG-AAAAGACAACCCACAGAATGGGAGAAA 720

  chr20_57936256_   1190 ACATTTGCAA-TGGAATAAGAGACTAAGGATTAACATAAAAAGTATTATT 1238
                          i        - viv   vvv  iv i   i vii  vv i i   ----
  L1M4_orf2#LINE/    721 ATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT---- 766

  chr20_57936256_   1239 ATGAAGAACT-TAACAAATCAAGGAGGAAAAAAAAGCAATAACCCAACAG 1287
                           i       - v    v    vi vi    i v --          i-v
  L1M4_orf2#LINE/    767 ATAAAGAACTCTTACAACTCAATAATAAAAAGACA--AATAACCCAAT-T 813

  chr20_57936256_   1288 CAAAAATGGA-AAAGAA---GAAGAGGTCATTC------AGAAAGTAAAA 1327
                         ?        i-    i ---   v  i-    i------    ii  v -
  L1M4_orf2#LINE/    814 WAAAAATGGGCAAAGGATTTGAATAGA-CATTTCTCCAAAGAAGATATA- 861

  chr20_57936256_   1328 CTCAACTGGCTAATAAAGAAATGAAAA--TGCT--ACCTCCATGGTAAT 1372
                         --   v    i     iv v       --    --  v  v????????
  L1M4_orf2#LINE/    862 --CAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.18 (132 / 112)
Gap_init rate = 0.06 (52 / 903), avg. gap size = 2.96 (154 / 52)  


2433 23.98 5.27 4.74  chr20_57988169_57990526.rev      696  1454 (904)    L1M4_orf2#LINE/L1        1   763 (145)  

  chr20_57988169_    696 TGAAAAGATATACTGTGTTTACAGACTGAAAGACTCAGTATTGCCAAGAT 745
                           i        v ii    i ii  i  i      i i     ii     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_57988169_    746 GACAGTTCTTTCCAAATTGACCTATAAAGTCAGCATGATCCCAATCAAAA 795
                          i  i v  ii         i   i i v   i iii     v       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_57988169_    796 GACTAGCAGAATATTTTAGAGATATCAACAAGCTGATCTGAAAATT-ATA 844
                         vv i   v vv v    iv   v  ii           iv      -   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_57988169_    845 TAGAAAGGCAAAGAAATTTGAATACGCAAAATCATTTTGAAAAAGAAACA 894
                          i    v    i i viiv     vv     iv  i           iv 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_57988169_    895 CAAAGTTAGAGGACTCACACTATATAATTTCAAGATTTATTATAAAAATA 944
                                i             vivi        i i   i  i   iv  
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_57988169_    945 CAGTAATCCAGAGAGTATAGTATTGATGAAAAGATAAATATATACATCAC 994
                                 v   v   i i   i  iiiv  i    i i     v    v
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_57988169_    995 TGAAACAGAATAGAGAGTTTAGAAATAGGCCCACACAAGTATGGTTGATT 1044
                           i  i     v      ii       ii    i   vv      ii   
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_57988169_   1045 GATTTTTGAGAATAATACAAAGGC------------------TAGCCTTT 1076
                               i  v  vii i v   i ------------------   i    
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_57988169_   1077 TCAACACATGATTCTGAAACAATTAGATGTTCATAAGCAAAAAAAAATAA 1126
                               v   i v   ii    i i   i?i  i v      i  -- i 
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAA--TGA 448

  chr20_57988169_   1127 ACCTGGGTCTATATCTCACACTTTAGACAAAAATTAATTCAAAATGGATC 1176
                          vi   ii iv  i       iv  v           i            
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_57988169_   1177 ACAGACATACATGTAAAACATAAAACTATAAAACTTTTAGTAAAAAA--- 1223
                          ?    v  v      i vv               i    v i    ---
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_57988169_   1224 AGGAGAAAATCTTGATGAC------------AATG---TGTTAGATAACA 1258
                            ? v       vi    ------------    --- v       vv 
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_57988169_   1259 CCACCAAAAACATGATC--CAGAAGAGAAAATATTGATGAATTGGATTTT 1306
                          -       i  ii v --  i    i      --   i       i  i
  L1M4_orf2#LINE/    599 C-ACCAAAAGCACAAGCAACAAAAGAAAAAATA--GATAAATTGGACTTC 645

  chr20_57988169_   1307 ATCAAAATGTAATAACTTTTGCTCTGTAAGAAATGCTGTTAAAAGAATGA 1356
                                 -   v        iv  vi  iii ii  i i  i i i   
  L1M4_orf2#LINE/    646 ATCAAAAT-TAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGA 694

  chr20_57988169_   1357 AAAGACAAAGGTAAGAATGAGAAGACAAAAATGAAAAGACAATTGCCTGA 1406
                                 vvv-------------   i  -----------------  i
  L1M4_orf2#LINE/    695 AAAGACAACCC-------------ACAGAA-----------------TGG 714

  chr20_57988169_   1407 GAGAAAATACTTCCATTTCATATG-CTGACAAAGGATTTGTATTCAAAA 1454
                                  i  v  vv      i-    i  i   i      i  i  
  L1M4_orf2#LINE/    715 GAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAA 763

Transitions / transversions = 1.93 (118 / 61)
Gap_init rate = 0.02 (13 / 763), avg. gap size = 5.85 (76 / 13)  

 385 16.51 2.75 3.67  chr20_57988169_57990526.rev     1750  1858 (500)    L1M4_orf2#LINE/L1      769   876 (32)  

  chr20_57988169_   1750 AAAGAAACTC---CATCTCAAAAAAAAAAAGACAAAAACAATACAATTTT 1796
                               -   ---  v     v  v           --i  iv     ?v
  L1M4_orf2#LINE/    769 AAAGAA-CTCTTACAACTCAATAATAAAAAGACAAA--TAACCCAATTWA 815

  chr20_57988169_   1797 AAAATGGGCAAAGGGTTTGAACAGACACCTCTCCAAAAAAAGAGATACAG 1846
                                       i      i     ii        i  -  v     i
  L1M4_orf2#LINE/    816 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAA-GATATACAA 864

  chr20_57988169_   1847 ATAGTAAATAAG 1858
                           i iv      
  L1M4_orf2#LINE/    865 ATGGCCAATAAG 876

Transitions / transversions = 1.43 (10 / 7)
Gap_init rate = 0.04 (4 / 108), avg. gap size = 1.75 (7 / 4)  


3141 26.70 1.90 0.45  chr20_58023333_58027567.rev     2849  3743 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_58023333_   2849 TGTAAAGACATTTCATGCCCATGGATCAGAAGAATTAATGTTGT-AAAAT 2897
                           v     i  ii    ii       ii     v     i    -  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_58023333_   2898 TATCACACTATGCAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAA 2947
                         viiv i   viv    vii              i                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_58023333_   2948 CACCAATGACATTCTTCACAGAAATAGAAAAAAAAATCTTAAAATTTGTG 2997
                         iv   iivi v  i  ii       v  v  ivvi   i       ii i
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_58023333_   2998 TGGAACCACAGAAGGTCCTGAAGAGCCAAAACAATTCTGAGCACAAAAGA 3047
                              vii  iii ii  v   v            ii   iv vi  ii 
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_58023333_   3048 CAAAGTTACAAGGA-TCACACTATCAGACTTCAAAATATACTACAAAACT 3096
                                i-i    -       vi vi i       iv         i  
  L1M4_orf2#LINE/    201 CAAAGTTG-GAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_58023333_   3097 ATAATAACTGAAACAGCATGGTACT---ATAAAAACAGACACATCAATAA 3143
                          i i   iii i    ii       ---    ii i     i  vi  v 
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_58023333_   3144 ATGAAACAGAATACAGACTCAAGCAATTAATACACATATCTTTAGCCAAC 3193
                            i  i     vv   v  v  v   v  iv  i i  i v i i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_58023333_   3194 TGATTTTTGACAAAAAGACTACGAACATTCATTGAGGAAAAGATAGTCTT 3243
                                i     iiivi i v  v      v  i     ii        
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_58023333_   3244 TCCAACAAATGGTGCTGGGGAAAGTAGGTATCTATATGCAGAAGAATGAA 3293
                          i                 iv  v i i  ? i i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_58023333_   3294 ACTAGACTCCCCTCTCTCACCCTATACAGAAATCAACTCAAAGTGGATCA 3343
                         ii i   i  ivi   v    v      i    i        i       
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_58023333_   3344 AAGACCTAAATGTGAGACCCAAAACTATAAGACTATTGGAAGAAAATCTA 3393
                         ?            i   v i          i   v  i        iv  
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_58023333_   3394 GGGA-AAATGCTTCAGGAAATTGGTCTTGTAAAAAAACTTATGAG-TAAG 3441
                           ?i-    -    iv  vv    vi v -iv  viii  v v  -  v 
  L1M4_orf2#LINE/    550 GGNGTAAAT-CTTCGTGACCTTGGGTTAG-GCAATGGTTTCTTAGATATG 597

  chr20_58023333_   3442 ACCTCGAAAGCATAGACAACAAAAGCAAAAATAATCAAATAGGATTATAT 3491
                           vi i      i ii         v       ivi    v   i vi  
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_58023333_   3492 CAAA-CGAAAAATTTTCTGCACAGCAAAGGAAACTAC----AGAGTGAAA 3536
                             -iv     i   -  ii vv       v    i---- i       
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTT-TGTGCTTCAAAGGACACTATCAAGAAAGTGAAA 696

  chr20_58023333_   3537 AGTTAACGTACAAAATGGGAGAAAATATCTGCAAACTATTTATCCAATAA 3586
                           vi   vi   i               i      ii  v    ii    
  L1M4_orf2#LINE/    697 AGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_58023333_   3587 GGGGTTATTATCTGGAATACACGAGGAGCTCAAATATCTCAACAGCAAAA 3636
                            ii vv    ii     i ii i  i   vv i v     i ii    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_58023333_   3637 TAA-AAAGAATCCAATTTTAAAATGGGTAAATGATCTGAACAGATGTTTC 3685
                         vi -   v  i      ?v        i   v   i    i   ii    
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_58023333_   3686 TC---AAAAGACATA-AAATGGCCAAAAAATATATGAAAAACTGCTTAAC 3731
                           --- i    i   -          v  ii i       iv    i   
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_58023333_   3732 ATCATGAATGGT 3743
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 2.05 (158 / 77)
Gap_init rate = 0.02 (14 / 908), avg. gap size = 1.50 (21 / 14)  


1986 26.51 1.59 4.03  chr20_58136276_58137961      501  1194 (492)    L1M4_orf2#LINE/L1      232   908 (0)  

  chr20_58136276_    501 AAGACTTACAGTGTAGCTGCCATAATCAAGTCAGTGTGACACTGGCAGAG 550
                           i      viiiv    i vi        v       ii       v i
  L1M4_orf2#LINE/    232 AAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAA 281

  chr20_58136276_    551 AGATAGACACGTGGATCAATGGAAAATAACAGAGAACTCAGTGGTTAGGT 600
                         i        ii i           v v  iv    iii   vii - iii
  L1M4_orf2#LINE/    282 GGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAAT-AAAC 330

  chr20_58136276_    601 CCACATAAATACGCCCAACTGATTTTTGGCGAAGATGCAAAAGCAGCTCA 650
                            i i vv  i vi   i       i i i i i   v  ii vii   
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr20_58136276_    651 TAGTAGGAAGAAGAGACTTT-CAAGAAAAGGTGTGAGAGCCATTGGACAT 699
                         vv vi i     v  v    -   v   v    ivi ii v i    i ?
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAK 430

  chr20_58136276_    700 CCATAGGCAAGAAGAAAACAAAGAA-AAAGATAAAAAGAGAACCTCTACC 748
                            i v    ----------     -i   v ------- i   i     
  L1M4_orf2#LINE/    431 CCACATGCAA----------AAGAATGAAGTT-------GGACCCCTACC 463

  chr20_58136276_    749 TAAACCTCATCACCTTATGCAAAAATTAACTCAAAATGGATCATGGACT- 797
                          ------  -    v   i                        ?i   i-
  L1M4_orf2#LINE/    464 T------CA-CACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr20_58136276_    798 -AATGTAAAA-CTAAAGCCATAAAACTTCTAAAA-AAAACATAAAATAAA 844
                         -       i -     i i        ii  i  -        ii?vv  
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_58136276_    845 ATCTTTG-GAGTTGAGGGCTAGGTGAACA--TTCTTAGACATGACACACA 891
                              i -  vi v-   i    i-  ii--        i       vv 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTT-GGGTTAGGC-AATGGTTTCTTAGATATGACACCAA 604

  chr20_58136276_    892 AAGCACAACCCATAAAAGAAAGAATGGATACATTGAAGCCCATCAAAATA 941
                                 v v i        i   i    v    i vii         v
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr20_58136276_    942 CAAAACTTTTGTTCTGTGAAAACCCATATGAAGAGGATGAAAAGAGAAGC 991
                         v           v  vii  iiv vv   v    iii        v  v 
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

  chr20_58136276_    992 TACAGGCTA--AGAAAATACTCAATAACTATATATCCAATAAAAGATTTA 1039
                         i    iv i--        i iivv  ii       ii    ii  i  i
  L1M4_orf2#LINE/    705 CACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTG 754

  chr20_58136276_   1040 TACTAAGAATATTTAAGGACTTCTCAAAACTCAAATGTAAAAAAATAAAA 1089
                           iiv       v   i  vi   i v       vvi      i i   -
  L1M4_orf2#LINE/    755 TATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAA- 803

  chr20_58136276_   1090 GAATCCAATTAGAAAATAGGCAAAATACATGAAGACACATTTTACTGAAG 1139
                         v  i      ?i     i      iv iv    v v      iv ii   
  L1M4_orf2#LINE/    804 TAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAG 853

  chr20_58136276_   1140 AGAATATACAGATGGCAAATAAGTATATGAGAAGATATTTAACATCATTA 1189
                          ii       i     v      i i    i     ii i       ???
  L1M4_orf2#LINE/    854 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZ 903

  chr20_58136276_   1190 ACCAT 1194
                         ?????
  L1M4_orf2#LINE/    904 ZZZZZ 908

Transitions / transversions = 1.90 (118 / 62)
Gap_init rate = 0.02 (16 / 677), avg. gap size = 2.44 (39 / 16)  


2802 26.42 4.10 0.91  chr20_58204145_58208504.rev     2991  3868 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_58204145_   2991 GAAAAACATTCCATGCTTATGGATAGGAAGAATCAATATTGTGAAAATGG 3040
                             i i  i     i i      v      v i        v  i    
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_58204145_   3041 CCATAATGCCCAAAGTAATTTATAGATTCAATGCTATTCCCATTAAACTA 3090
                          v   v v      v i  i  i        i  v  i  i  i   v v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_58204145_   3091 CCATTGACATTCTTCACAGAATTAGAAAAAAACT-ACATTAAAATGCATA 3139
                            vivi v  i  ii     v v  v  i--  - ivi      v    
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAG--CTGATCCTAAAATTCATA 150

  chr20_58204145_   3140 TGGAATCAAAAAAGAGCCTGTACATCCAAGACAATCCTAAGCAAAAAGAA 3189
                              viiv  ii  v  v v i v    i      i i iv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_58204145_   3190 CAAAGCTGGAGGCATCATGCC-ACTAACTTCAAATTATACTACAAGTCTA 3238
                              i      vv   ii i-v i  i      viv        iv   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_58204145_   3239 TAGTAACCAAAACAGCATGGTACCAGTACAGAAACAGACACATAGACCAA 3288
                         i     i   i    ii      ii i i iii i     i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_58204145_   3289 TGGAACAGAAT----AACTCAGAAATAAGACTGCACATCTACAACCATCT 3334
                              i     ---- iii         iv iii    i  iiii  vi 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_58204145_   3335 GATCTTTGACAAACCTGACAAAAACAAGAAATGGGGAAAGGATTCCCTAT 3384
                            i  i     ivv  v   i v  vvv           i  vvi  v 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_58204145_   3385 TTAATTAGTGGTGCTGGGAAAACTGGCAAGCCATATGAGGGAAACTGAAA 3434
                          i  iv i           v      vv ?   i   viii i v    i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_58204145_   3435 CTGGACCCCTTCCTTACACCTTATGCAAAAATTAACTCAAGATGGATTAA 3484
                         i         v   i     v   i               i      i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_58204145_   3485 AGACTTAAACGTAAAACCCAAAACTATAAAAACCCTAGAAGAAAATCTAG 3534
                             i    i    i v i            vi i          iv   
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_58204145_   3535 GCA-ATACCATTCAGGACCTAGGCACAGGCAAAGCTTTCATAATGAAAAC 3583
                          ?i- v i -   iv     v  vvi      v v    v  ivv vi  
  L1M4_orf2#LINE/    551 GNGTAAATC-TTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_58204145_   3584 CTCAAAAGCA--ATTTGTAACAGAAGCAAAAATTGACAAATGGGATTT-- 3629
                         vi        -- --- i    i   v      v  i    v   i  --
  L1M4_orf2#LINE/    600 ACCAAAAGCACAA---GCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_58204145_   3630 ----AATTAAAGAGCTTCTGCACAGCAAAAGAAACTA-CAATCAGAGTGA 3674
                         ----       i -   i  ii vv    i  v    -   v- i     
  L1M4_orf2#LINE/    647 TCAAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAG-AAAGTGA 694

  chr20_58204145_   3675 ACAGACAACCTATAGAATGGGAGAAAATTTTCACAATCTATCCATCTGAC 3724
                          v        i i               v  ii   vii  vi      i
  L1M4_orf2#LINE/    695 AAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGAT 744

  chr20_58204145_   3725 AAAGGGCTAATATACAGAATCTACAAGGAACTTAAACAAATTTACAAGAA 3774
                           i  i  vi   v      v  i  i     ivv    v iv i  v  
  L1M4_orf2#LINE/    745 AAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAA 794

  chr20_58204145_   3775 AAAAACAA----CCCCATTAAAAAGTGGGTGAAGGACATGAACAGACACT 3820
                            i    ----   v   ?    i    ii     iv    i     i 
  L1M4_orf2#LINE/    795 AAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_58204145_   3821 TCTC-AAAGA---------------CAATAAACATATGAAAAAGAGCTCA 3854
                             -     ---------------      i  i       iiv     
  L1M4_orf2#LINE/    845 TCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCA 894

  chr20_58204145_   3855 ACATCACTGATCAC 3868
                               ????????
  L1M4_orf2#LINE/    895 ACATCAZZZZZZZZ 908

Transitions / transversions = 1.59 (140 / 88)
Gap_init rate = 0.02 (15 / 906), avg. gap size = 2.93 (44 / 15)  


2029 25.99 2.38 1.90  chr20_58226512_58228130.rev      497  1127 (492)    L1M4_orf2#LINE/L1      275   908 (0)  

  chr20_58226512_    497 GGAGTAAAAACACACACATACACCGGTGGAACAGGGCAGAGAACACAGAA 546
                           vi   ii i v   i   v i ii     i  iiiv    iiv     
  L1M4_orf2#LINE/    275 GGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAA 324

  chr20_58226512_    547 ATAACTCCATGCGCTCAGAGCTAAGTGGCCTTTCAA-AAAGGTACTGAGA 595
                             vi    i ii i vi ii  v  ii-    i -  i   i ii   
  L1M4_orf2#LINE/    325 ATAAACCCATACATTTATGGTCAATTGAT-TTTCGACAAGGGTGCCAAGA 373

  chr20_58226512_    596 ACACCCACTGGGGAAAGAACAGTCTCTTTAATACACGGTACCAGAAAAAC 645
                         v  ii  v           i     i  i  i v i   i ii i v   
  L1M4_orf2#LINE/    374 CCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAAC 423

  chr20_58226512_    646 TGGCTAGTCACATGCA---GCATGAAATTGGACCCCTATCTGTCACCCTA 692
                            v  ?i        --- v     i           i  vv    v  
  L1M4_orf2#LINE/    424 TGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr20_58226512_    693 TACAAAAATCA-CCCAAAATGGATTAAAGATTTAGGTGTTGTAAGACCCA 741
                                  i - i          i ?   ii  ii   ---    v i 
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGT---AAGAGCTA 520

  chr20_58226512_    742 AAACCATAGA-CTACTAGAAGAAAACATCCACG-AAATGCTTGATGACAT 789
                             i   i -  vi             vvi? -    -   vi    v 
  L1M4_orf2#LINE/    521 AAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAAT-CTTCGTGACCT 569

  chr20_58226512_    790 TGGCCTGAGCAAGGATTTTTTTGGATTAGA-GCTCACAGCACAGGAAACA 838
                            vi ii    v i   i  -i   vv  -i iv v      i v    
  L1M4_orf2#LINE/    570 TGGGTTAGGCAATGGTTTCTT-AGATATGACACCAAAAGCACAAGCAACA 618

  chr20_58226512_    839 AAACCAAAGGCAGGCAAATGGGATTACATCCAA-CTAAAAAGCTCTGTAC 887
                            vv   iii  ii    v   i v    v  -i      vi i   i 
  L1M4_orf2#LINE/    619 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 668

  chr20_58226512_    888 AACAAAAGAAACGATCAACAGAATGGAGAGACAGCCTAT-GCATGTGAGA 936
                         vv    i  v  v     v i i  i i     i  i i- v   v    
  L1M4_orf2#LINE/    669 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr20_58226512_    937 AAATATTTGCAAACTATGTATCTGATAAGAAGCTAATATCCAAAATATCT 986
                                      ii  i           iii  vi      i     --
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATAT-- 766

  chr20_58226512_    987 AATAAGGAAGTC----AACTCAATAGCAAAAAAAAAAAAAAAAGTCCAAT 1032
                         -    i   v  ----         ii     i v   v  ---i     
  L1M4_orf2#LINE/    767 -ATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA---CCCAAT 812

  chr20_58226512_   1033 TTAAAA-TGGACAAAAATTCTGAATAGACATTTCTCAAAAGAAGACATTC 1081
                          ?    -   i    iiv i                v        i  v 
  L1M4_orf2#LINE/    813 TWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATAC 862

  chr20_58226512_   1082 AAATGTCCAACTGGCATATTAAAAAATGTTCAGCATCATCATTATG 1127
                              v    ivi   i  v    i   i   i     ????????
  L1M4_orf2#LINE/    863 AAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.02 (107 / 53)
Gap_init rate = 0.03 (16 / 634), avg. gap size = 1.69 (27 / 16)  


3704 20.98 3.88 0.46  chr20_58390272_58393723     2084  2960 (492)    L1M4_orf2#LINE/L1        2   908 (0)  

  chr20_58390272_   2084 GAAAAAATGT---ATGTTCATGGACAGGAAGAAGTGGTATTGTTATGACG 2130
                          i   i  i ---           iv      vv ii        v  i 
  L1M4_orf2#LINE/      2 GGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATG 51

  chr20_58390272_   2131 GCAATACAGCCCAAATTGATTTATAGGTTAAAAGCAATCCCAATCAGTAT 2180
                                vv           i  i  i  v  v        v    iv  
  L1M4_orf2#LINE/     52 GCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 101

  chr20_58390272_   2181 ----GCATACCTTTT-----------AACAAGCTGTTTCTAAACTTTATA 2215
                         ----  - i      -----------i        v i     v  i   
  L1M4_orf2#LINE/    102 CCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_58390272_   2216 TGGAATTGTGATGAACCATAAATATCGAAAACAGTTTTGAAGAAGAAGAA 2265
                              v  ii v i   vvi    v v      i i     i        
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_58390272_   2266 TCAAATAGGCAGACTCAC--TTCTTGACTTCAAAACTTACTACAATGAAA 2313
                         iv  i v  vi       --   iii i                 v vv 
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_58390272_   2314 TGGTCATCAAGAAAGTATGGTCCTGGCATAAGGATAGACGTATAGATAAA 2363
                         ii  v       v   i    v                 i       v  
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_58390272_   2364 TGGAGTAAAAGTGAGAGTCCAGAAATAAAACCTTGTGTCTATGGTCAACT 2413
                             i  i  v                  v  v iii i         i 
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_58390272_   2414 GAATTTTGACAAGGATGTCAAAACTATTCAATAGAGAAAAAAGAGTCTTA 2463
                           v   i       i  i   i  i       i i    i  v      v
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_58390272_   2464 CCAACAAATGGTTTAGGGACA--------GCCATATGCCAAAGAATGAAA 2505
                         i           viv      --------?   i    v          i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_58390272_   2506 TGGGACTCTTCCCTCTCACCGAACACAAATAGGAACTCAAAGTAGTTTAA 2555
                          v    i i v    v    iv i     v vv        i i v i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_58390272_   2556 AGGCCTAAATGTAAGAACTAAAATTATAAATCTTTTAGAATAAGTCATAG 2605
                           i             i      i      v  i      v  iv     
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_58390272_   2606 GGGAAAATCTTCCCAATCTCAGATATGATAAAATACTCTTAGATATGACA 2655
                          ? v        vii i  ii i vv ii  vivvi              
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_58390272_   2656 ATAAAAGTATGAACAGCAAAATAAAAAAATCAATAATTTGGACTT-ATCA 2704
                         vi     i ii i  i     -i       vi    v        -    
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAA-GAAAAAATAGATAAATTGGACTTCATCA 649

  chr20_58390272_   2705 AAATTCTAAAAGTTTTTG--CATCAAAAGATACTATCAAGAAAGTGAAAA 2752
                              --    ii     -- v     i  i                   
  L1M4_orf2#LINE/    650 AAATT--AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_58390272_   2753 GTCAATAAACGGTATGGGAGAAAATATTTGCAAATACTATATCTCATAAA 2802
                          v   ivv  i v                      vv       v    i
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_58390272_   2803 GGACTTATATCTAGAATATATAA-GAACACTTATAA-TCAAGAACAAGAA 2850
                               i    i           -    v    i  -    v  i  i  
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_58390272_   2851 TATAAATAACCCAATTTAAAAATGAGCAAAGTATGTAAATGCACGTTTTT 2900
                         v i             ?       i      v  v i   iv  i   i 
  L1M4_orf2#LINE/    798 GACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCT 847

  chr20_58390272_   2901 GCAAAGAAGATATAAAAATGTCCAATACGGACATGAAG-GATACTCGACA 2949
                         v             v     v      v v       i-   i   i   
  L1M4_orf2#LINE/    848 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 897

  chr20_58390272_   2950 TCATTAGTAAT 2960
                            ????????
  L1M4_orf2#LINE/    898 TCAZZZZZZZZ 908

Transitions / transversions = 1.34 (103 / 77)
Gap_init rate = 0.01 (13 / 907), avg. gap size = 2.92 (38 / 13)  


3193 26.10 0.44 0.44  chr20_58423047_58427294.rev     2849  3756 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_58423047_   2849 TGGAAATACATCCCATACTTATGGATTGAAAGAATCAATATTGTGAACAT 2898
                               v i       ii i        i    v i        v  v  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_58423047_   2899 GACCATAGTGCCCAGAGAAATTTACAGATTCATTGCAACGCCTATCGAAA 2948
                          i v   v v    i vvi  i          vi    iv      i   
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_58423047_   2949 CACAAACATCATTTTCCACAGAATTAGAAAAAACAATCCTAAAATTCATA 2998
                         iv v i vv v    iii     v v  v  ivii               
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_58423047_   2999 CGGAACCAAGAAAGAGCCTGAATAGCCAAGGCAATCCTAAACAAAAAGAA 3048
                         i    viivi ii  v  v          ii     i i  v  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_58423047_   3049 CAAATCTGGAAGCATCACATTAACTGACTTCAAACTGTACTAAAAGGCTA 3098
                             vi    i vv     i vv ii i      viv     v  i    
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_58423047_   3099 TCATAACCAAAACAGCATAGTACTGGTATAAAAGTAGATACATAGACCAA 3148
                         ivi   i   i    ii i       i    iii    i i     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_58423047_   3149 TGGAACAGAATAGAGAACCCAGAAATAAAGCCAAATAATTACAACCAACG 3198
                              i     v    ii           v   v i v   iiii   iv
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_58423047_   3199 GATCTTTGACAAAGCATACAAAAAT-AT-AAATTGGGGGAAAGGACACCC 3246
                            i  i     i -i i v  i i-  -v   --        i i vi 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGG-GTGCCAAGACCATTCAAT--GGGGAAAGAATAGTC 397

  chr20_58423047_   3247 TATTTAATAAATGATGCTATGAATATTGGATAGTCACATGTAGAAGAATG 3296
                          v  i  i     i    iv  vv i      ?i      i i       
  L1M4_orf2#LINE/    398 TTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_58423047_   3297 AAACTGGATCCCTATCTCTCACCATATACAAAAATTAACTCAAGGAGAAT 3346
                           ii    i     i   v                        iiv i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_58423047_   3347 TAAAGACTTAAATATAAGATCTGAAACCATAAAAATTCTAGAAGAAAACC 3396
                         i ?    i     i     v  i    i      v ii           v
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_58423047_   3397 TAGGAAAAATTATTCTAAACATTGGCCTAGGCAAAGAATTTATGACTAAG 3446
                             ?iv  v v   vvi  v    vi       v iv  iv iiv  v 
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_58423047_   3447 ACCCCAAAAGCAAATGCCACAAAAACAAAAATACATAAATGGGACCTAAA 3496
                           v         v v  v      iv       v      v    i v v
  L1M4_orf2#LINE/    598 ACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCAT 647

  chr20_58423047_   3497 TAAACTAAAAAGCTTCTTTACAGCAAAAGAAAGAGTCATCAGAGTAAAGA 3546
                         i   v v    i   i v i vv    i  v vvi   vv i   i  i 
  L1M4_orf2#LINE/    648 CAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_58423047_   3547 GATAACCTACAGAGTGAGAAAAAAATATTTGCAAATTATTCATCCAACAA 3596
                           i    i     i  i  i    -           i  vi   ii i  
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAA-TATTTGCAAATCATATATCTGATAA 746

  chr20_58423047_   3597 AGGACTAATATCCAGAATATACAAGGAACTCAAACAAATCAGCAAGAAAA 3646
                         i     vi             i  i      vv    v   ii  v    
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAA 796

  chr20_58423047_   3647 AGATAAACAACCCCATTAAAAAGTGGACAAATAACATAAATAGACATTTC 3696
                            i   i     v   ?    i   i    vi iv i            
  L1M4_orf2#LINE/    797 AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_58423047_   3697 TTAAAAGAAGATATACAAATGGCCAACAA--ACATGAAAAAATGCTTGAC 3744
                          iv                       i  --         i     ii  
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_58423047_   3745 ATCACTAATCAT 3756
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.53 (141 / 92)
Gap_init rate = 0.01 (6 / 908), avg. gap size = 1.33 (8 / 6)  


2194 28.39 7.36 1.87  chr20_58447397_58449507.rev      764  1619 (492)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr20_58447397_    764 AGACATCT-GTGTTCATGGGTTGGAAAAGTCAGTGTCGTAAAGGTATGAA 812
                            i   i-i         i      i v i i i i  v   i ivv  
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr20_58447397_    813 TTCTTTCCACATTGGTATGCAGGCTTAATATATAATTCCTGTCAGAATTC 862
                          v  ii   v    i v i   ii i  iii --  i   i   i   i 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCA--ATCCCTATCAAAATCC 103

  chr20_58447397_    863 CAGCAAGGTGG-----TGGTCATAATAGACAAGCTTATTAGAAACTTCAC 907
                             ----  v----- v iviv   v        v  ivv   v    i
  L1M4_orf2#LINE/    104 CAGC----TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_58447397_    908 ATAGAAAGATAAAGGCTCTAGAACAGCTAAAACAAAATTGAAAAAGAAGA 957
                           i    vii  i  vi i    i   i       vv             
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_58447397_    958 GTCAAGGGGGAGGTAC-CACCCTACCCTACGGTAAGTCTTCCTGTATAGC 1006
                         iiv   vv     -  -   v  v   v ivvi  iv   v  ii v   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGG-ACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_58447397_   1007 TACAGTGATAAATACAGTGTAACACTGGTGTAGGAGCAAGACAAACACAT 1056
                               i  v  v       iii     ii  i iii -    v i v  
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATA-GACATATAGAT 297

  chr20_58447397_   1057 CACT-----AGAACTGGGAATCCAGAAACAGACCAACACAATTATGCCCA 1101
                           v -----    i  i  i        i i   v i   v     vi  
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_58447397_   1102 ATTTATTTTTGGCAAAGGTGTGAAAGCTGTTCAATGAAGGCATTGTAGTA 1151
                            v     i i   i    iv  ii ii       ii iv vvi    v
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTC 397

  chr20_58447397_   1152 TTTTCAAAAAAATGGTGGTGGAAAAATTGGACACCCATA-ATAAAA-AAT 1199
                                v   -     v   i v  i    i ?   i -ii    -   
  L1M4_orf2#LINE/    398 TTTTCAACAAA-TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAAT 446

  chr20_58447397_   1200 ----CTGAACCTCAACCTAA-ACAATTTTTTAAAA---ACCCGAAATGAA 1241
                         ----i  i   i v    v -  v  v viv    ---  i i     i 
  L1M4_orf2#LINE/    447 GAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGA 496

  chr20_58447397_   1242 T---GGACATAAATGTGAAACAAAAAACTATAAA----TTAAAAAATATA 1284
                          ---i   v       i i vvv           ----   i  i v --
  L1M4_orf2#LINE/    497 TCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAA-- 544

  chr20_58447397_   1285 TATACATAGGTGAAAATCTTGGGGATCTAGGCTTAGGCAAAGAGTTTTTC 1334
                         ---       ? v       v v  i  v  v        v iv  i  v
  L1M4_orf2#LINE/    545 ---ACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTA 591

  chr20_58447397_   1335 CACTTTACACTAAAAGCACTTGC-----------------------TGAA 1361
                         v iv v    i        vv  -----------------------  i 
  L1M4_orf2#LINE/    592 GATATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_58447397_   1362 TGTCATTGAAATGAATCATTTTGCTATGC---AAAAGAGCCTGTCAAGAA 1408
                         iv    ii    v  vv i   -- i   ---   i  vv  i       
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTT--TGTGCTTCAAAGGACACTATCAAGAA 689

  chr20_58447397_   1409 AATAAAAAGACAAATTAGAGAACAGGA-AACATTTTTGCAAATTATATTT 1457
                          i i         vii v    ii   -  v  v         i    v 
  L1M4_orf2#LINE/    690 AGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATAT 739

  chr20_58447397_   1458 TCAAAAAAAGCCTCATTTTTTAAATGTATAAAGGATCTGTAAAACTCAAC 1507
                         iii v  ii v  ii v iivi   i       i iiiv  v       i
  L1M4_orf2#LINE/    740 CTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAAT 789

  chr20_58447397_   1508 ATTAAAAA-------AATCCAATTAAAAATTGGGCAAAAGGCATGAACAG 1550
                          v      -------  i      ?    v        i iiv    i  
  L1M4_orf2#LINE/    790 AATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAG 839

  chr20_58447397_   1551 ACATTTCACTGAAGAGGAGACATGGATGTCAAATAAGCATCTGGAAAGAT 1600
                                v ii    i  v i iii   v v        iv  i      
  L1M4_orf2#LINE/    840 ACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGAT 889

  chr20_58447397_   1601 GTTCAACATCATTAGCCAT 1619
                          i         ????????
  L1M4_orf2#LINE/    890 GCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.47 (143 / 97)
Gap_init rate = 0.02 (22 / 903), avg. gap size = 3.59 (79 / 22)  


3163 17.40 3.11 10.53  chr20_58467883_58471210     1906  2836 (492)    L1M4_orf2#LINE/L1       47   908 (0)  

  chr20_58467883_   1906 AAATGACAATACTCTCCAAATCAATCTATAGATTAATTGTAATCCCTATC 1955
                          i   i        i      ii     i     v vi i          
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr20_58467883_   1956 AAAATCCTGATGGC--TTTCTATAAAGATAGAAAAACTGAACCTACAATT 2003
                                iiiiv  --   i ii i i  v  v  i    v    v    
  L1M4_orf2#LINE/     97 AAAATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATT 146

  chr20_58467883_   2004 CTTATTAAAAAAAAAAAAATTCAAGGGACTCAGAATAGCCAAATCTGTCT 2053
                          v   ---------ii    v        i             v vi   
  L1M4_orf2#LINE/    147 CATAT---------GGAAATGCAAGGGACCCAGAATAGCCAAAACAATCT 187

  chr20_58467883_   2054 TGAAATGGAAGAACAAAGTTGGAGGACTCACACTTCCTGACTT-GAAACT 2102
                              vi                              ii i  -i     
  L1M4_orf2#LINE/    188 TGAAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACT 237

  chr20_58467883_   2103 GACTACAATCCTACCCTAATCAGGAT-GTATAACACTGGCATACATATAG 2151
                         v       vv    vv      i  i-  i iii         viv    
  L1M4_orf2#LINE/    238 TACTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAG 287

  chr20_58467883_   2152 CCAGA--GATCAAGGGAATAGAATTGAGAATAGAGGGGAAAAAAGC--AT 2197
                         v  v --      v               i vv  ---   v  i --  
  L1M4_orf2#LINE/    288 ACATATAGATCAATGGAATAGAATTGAGAGTCCAG---AAATAAACCCAT 334

  chr20_58467883_   2198 A-ATATATGGTCAATTGATTTGCAACAAGGGTTTCAACATAATTCAATGG 2246
                          -  v                v i        vi   v iv         
  L1M4_orf2#LINE/    335 ACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGG 384

  chr20_58467883_   2247 G-ATGGAATAATCTTTTCAACAAATGGTGCAGAGACAGCTGGATATC-GC 2294
                          - vi     i                   v i    i       ? -i 
  L1M4_orf2#LINE/    385 GGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCAC 434

  chr20_58467883_   2295 ATGCAAAAGAATGAAATTTGACC--TGTCTCATGTCACATACAAAAACTA 2342
                                        i  v    -- ii    iii  i         i  
  L1M4_orf2#LINE/    435 ATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTA 484

  chr20_58467883_   2343 AGTTAAATTGTATCAGAAACAGAAAT-TAAGTGCTAAAACACTGCTGAAT 2391
                          v i   v  v    ? i  vv    -    v        ----------
  L1M4_orf2#LINE/    485 ACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAAC---------- 524

  chr20_58467883_   2392 GAAAGCAAAGATCTAAATAAATCAAAAGATATCCTGTGTCCATGGGTTGA 2441
                         -----------------------------   ------------------
  L1M4_orf2#LINE/    525 -----------------------------TAT------------------ 527

  chr20_58467883_   2442 AAAACTTAATGTTGTTAAGACAAATTGTTAAGCTCTTAGAAAAAAAAAAT 2491
                               ----------------------------       i    v vv
  L1M4_orf2#LINE/    528 AAAACT----------------------------CTTAGAAGAAAACATA 549

  chr20_58467883_   2492 GGGGTCATTTTTTATGACCTTAGATTTGGCAATGGTTTCTCAGATGTGAC 2541
                           ?  v v i  ii       i i  v             i    i    
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_58467883_   2542 ATCAAAAGTATAAACAACAAAAACATAAAATAGATAATTTAGACTTCATC 2591
                          i      i i  i        iv -           v  i         
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAGAA-AAAATAGATAAATTGGACTTCATC 648

  chr20_58467883_   2592 AGTTTTAAAATCTTTTCTGTATCAAAGGATACTATCAAGA--GTAAAAAG 2639
                          ivv      v     v  iv        i          --  i     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_58467883_   2640 ATAATCCACAGAATG--AGAAAACATTCTCAAATCACATATCTGATAAGT 2687
                          i  i          --      i   iv       i            v
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_58467883_   2688 GTCTAACACCCAGAATACA--AAGAATTATTATAACTCAACAACAAA--G 2733
                          v  vii i        i --     i v   i       i  i   -- 
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_58467883_   2734 AC---TAACCTGATT-AAAAATGGGCAAAAGCGCTGAATAGACATTACTA 2779
                           ---     ii   -             i vvi            v  v
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_58467883_   2780 CAAAGACG---TACAAATGGTCAACAGGCATATGAACAAATGTTCACCAT 2826
                               v ---         i   i i   i     v i   i   v   
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_58467883_   2827 CAATATCATT 2836
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.48 (95 / 64)
Gap_init rate = 0.03 (23 / 862), avg. gap size = 5.52 (127 / 23)  


3336 25.17 1.56 0.67  chr20_58552450_58556981.rev     3143  4040 (492)    L1M4_orf2#LINE/L1        3   908 (0)  

  chr20_58552450_   3143 GAATAACAGTCTATGTTCCTGGATTGGAAGAATCAATATTGTGAAAATGT 3192
                            vi i vi i      v            v i        v  i   v
  L1M4_orf2#LINE/      3 GAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGG 52

  chr20_58552450_   3193 CCATACTACCTAAAACAATCTACAGATTCAATGCAATCCCTATTAAAATA 3242
                          v     v  i   vii              i           i     v
  L1M4_orf2#LINE/     53 CAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATC 102

  chr20_58552450_   3243 CCAATGACATTCTTCACAGAAATAGAAAAA--AATCATAATATATTTATG 3290
                            iivi v  i  ii       v  v  i--i   v   - -   i  i
  L1M4_orf2#LINE/    103 CCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAA-A-ATTCATA 150

  chr20_58552450_   3291 TGGAACCTCAAAAGACCCTGAATAGCCAAAGGTATCCTGACTAAAAAGAA 3340
                              viv   ii     v           ivv   i   vv  i     
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_58552450_   3341 CACAACTGGAGGAATCACATTACCTGACTTCAAGTTATGCTACAAAACTA 3390
                           v ii       v     i v  ii i     iviv i       i   
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTA 250

  chr20_58552450_   3391 TAGTAATTAAAACAGCATGGTACTGGCATAAAAACAGACTCATAGACCAA 3440
                         i      i  i    ii              ii i    vi     i   
  L1M4_orf2#LINE/    251 CAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAA 300

  chr20_58552450_   3441 TGGAACAGAATAAAAAACTTGGAAACAAATCCTTACATCCACAGTAAATT 3490
                              i     vi i iiiii    i   i  v     ii ii  v    
  L1M4_orf2#LINE/    301 TGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATT 350

  chr20_58552450_   3491 TATTTT-GACAAAGGTGCCAAGAACATATATTAGGGAAAGGACA--CTCT 3537
                         v     -     i          v   vi v i       i i --  i 
  L1M4_orf2#LINE/    351 GATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTT 400

  chr20_58552450_   3538 TCAATAAATGGTGCTGAGAAAACAGGAATTCCATATGCAGAAGAATGAAA 3587
                             i           i  v   v   vv?   i     i         i
  L1M4_orf2#LINE/    401 TCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAG 450

  chr20_58552450_   3588 CTAGACTCCTACCTCTCACCATATATGAAAATCAAAT-AAAATGGATTAA 3636
                         i i   i        v         ii     i  v -         i ?
  L1M4_orf2#LINE/    451 TTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAW 500

  chr20_58552450_   3637 AGACTTAAATCTAAGACCTCAAACTATGAAACTACTAAGAGAAAACTTTG 3686
                             i     v     v  v       i     vi  ii       v v 
  L1M4_orf2#LINE/    501 AGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAG 550

  chr20_58552450_   3687 GGGAAAACCTCCAGGCCATTGGACTGGGCATAGATTTATTGAGTAATACC 3736
                          ? v   i  i iv v v    ii i    vv i   v  iii  vv  v
  L1M4_orf2#LINE/    551 GNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACA 600

  chr20_58552450_   3737 CCACAAGCACAGGGAACCAAAGCAAAAATGGACAGAT-GGAGTCACAT-G 3784
                            v       i v   v    v      i  i i  -   v i-   -i
  L1M4_orf2#LINE/    601 CCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTT-CATCA 649

  chr20_58552450_   3785 AAGTTAAAAAGCTTTTGCACAGTAAAG------ATCAACAAAGTAAAGAG 3828
                           i       -      ii vvi    ------     v     i  i  
  L1M4_orf2#LINE/    650 AAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_58552450_   3829 CCAACCCATAAAATGTGAGAAAATGTTTGCAAACTACCTCTCTGACAAGG 3878
                         v       i i    v        i        ii iv v     i    
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_58552450_   3879 GATGAATAACTAGAATATATAAGGAGCTTAAACAACTCCATAGGAAAAAA 3928
                           ivvi  v i           i  i  ivv       v   iv     i
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_58552450_   3929 AATCTAATAATCTGACTAAAAAATAAGCAAAAGATCTGAACAGATGTTTC 3978
                          -- v     i ii i ?      ii     i   i    i   ii    
  L1M4_orf2#LINE/    799 A--CAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTC 846

  chr20_58552450_   3979 TCAAAAGACAACAAACAAATGGCAAACAGGTATATGAGAAGGTGCTCAAA 4028
                           v     vi i v         v  i i i i    i   i       v
  L1M4_orf2#LINE/    847 TCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 896

  chr20_58552450_   4029 ATCATTGATCAT 4040
                             ????????
  L1M4_orf2#LINE/    897 ATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (140 / 82)
Gap_init rate = 0.01 (12 / 906), avg. gap size = 1.67 (20 / 12)  


2196 26.36 1.67 3.21  chr20_58616490_58618198      501  1217 (492)    L1M4_orf2#LINE/L1      203   908 (0)  

  chr20_58616490_    501 AAGCTAGAGGCATCATGTTACCTGACTACAAACTATGCTACAAGGCTATA 550
                            i i    vv   iii v  ii i v    viv i      i    i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_58616490_    551 GTAACCAAAACAGTATGCATGGTACTGGTATAAAAACAGATACATAGACC 600
                             i   i     i  ----       i    ii i   i i     i 
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTG----GTACTGGCATAAGGATAGACATATAGATC 298

  chr20_58616490_    601 AATGGGACAGAAAAGAGAGCCCAGAAATAACACTGCATATCTATAACCAT 650
                              i i    vv     i          vv iii i  i   iii  v
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_58616490_    651 CTGCTCTTCAACAAG----TTAAAA--AAGCAATGAGGAAAGGACTCTCT 694
                         i  v i   i     ----ii  i -- vv     i      i ivv   
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_58616490_    695 ATTCAATAAATGGTGCTGGGACAGCTGGCTAGCCATATGCAGAAGATTGA 744
                         v     i                i    v  ?   i     i    v   
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_58616490_    745 AACAGGACCCCTTCCTTACACCATATAGAAAAATCACCTCAAGATGATTT 794
                          iiv        v   i          v      i v     i   ----
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATG---- 494

  chr20_58616490_    795 AATGATGGATTAAAGACTTAA-TGTAAAACCTGAAACTGTAAAAACCCTA 843
                         -------   i ?    i   -     i v  i     i     vi i  
  L1M4_orf2#LINE/    495 -------GATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTA 537

  chr20_58616490_    844 GAAGATAACCTAGG---AAATACCATCATGGACATAGGACCTGACAAAGA 890
                              v   v    ---    -- v  i  -  v v  iiiv i   v i
  L1M4_orf2#LINE/    538 GAAGAAAACATAGGNGTAAAT--CTTCGTG-ACCTTGGGTTAGGCAATGG 584

  chr20_58616490_    891 CTTCGCAACGAAGATGCCAAAAGCAATTGAG--ACAAAAATAAAAATTGA 938
                         i   vi ivv v  ii         --ii  --      iv      v  
  L1M4_orf2#LINE/    585 TTTCTTAGATATGACACCAAAAGCA--CAAGCAACAAAAGAAAAAATAGA 632

  chr20_58616490_    939 CAAATAGGACCTAACCAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA 988
                         i    v    i v i    v v  i i   i  ii vv    i  v    
  L1M4_orf2#LINE/    633 TAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA 682

  chr20_58616490_    989 TCAACAGAGTAAACAGTCAACCTGCAAAATGGAAGAAAATATTTGCAAAC 1038
                             v i   i  v  v     ii  i     i                i
  L1M4_orf2#LINE/    683 TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAAT 732

  chr20_58616490_   1039 TATGCATCCAACAAAACTCTAATATCCAGAATCTATAAGAGACTTAAACA 1088
                         i  ii   ii i  iivv  vi          v     iii   ivv   
  L1M4_orf2#LINE/    733 CATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACA 782

  chr20_58616490_   1089 AATCAACAAGTGAAAAATAAACAACCCCATTAAAAAGTGGGCAAAGGACA 1138
                          v    i  vvi   i i   i     v   ?    i           iv
  L1M4_orf2#LINE/    783 ACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATT 832

  chr20_58616490_   1139 TGATTACACACTTTTCAGAAAAAAGGCATATGTGTGTCAAACAAGCATAT 1188
                            v  v   i  i  v-   i   ii   iivi  v v  i     i  
  L1M4_orf2#LINE/    833 TGAATAGACATTTCTCC-AAAGAAGATATACAAATGGCCAATAAGCACAT 881

  chr20_58616490_   1189 GAAAAAAAATGCTTGACATCACTAATTGT 1217
                              i --    ii      ????????
  L1M4_orf2#LINE/    882 GAAAAGA--TGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (121 / 65)
Gap_init rate = 0.02 (12 / 706), avg. gap size = 2.92 (35 / 12)  


 202 29.41 0.00 0.00  chr20_58711416_58714097.rev     1488  1538 (1144)    L1M4_orf2#LINE/L1        5    55 (853)  

  chr20_58711416_   1488 AAAATACCCTATGTTCATAAATCAAAAGACCTAGTGTTTTTTAAATGACA 1537
                           i   i  i        ii  iii     i  i i  v  v i   i  
  L1M4_orf2#LINE/      5 AAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCA 54

  chr20_58711416_   1538 A 1538
                          
  L1M4_orf2#LINE/     55 A 55

Transitions / transversions = 6.50 (13 / 2)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.00 (0 / 0)  

2159 23.77 5.37 2.45  chr20_58711416_58714097.rev     1539  2190 (492)    L1M4_orf2#LINE/L1      238   908 (0)  

  chr20_58711416_   1539 TACTATCCAAATCTACAGATCCAAGGTTAAGACAGTGTGATATTGTTAAT 1588
                              --    v      ---i  -- i           i  i  vi vv
  L1M4_orf2#LINE/    238 TACTA--CAAAGCTACAG---TAA--TCAAGACAGTGTGGTACTGGCATA 280

  chr20_58711416_   1589 AGGACAGACGTATAGACCAGTGGGATAAAACTGAGAGCATGGAAAGAAAC 1638
                             i    i      i  i   i   i  i      ivii    v    
  L1M4_orf2#LINE/    281 AGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC 330

  chr20_58711416_   1639 GCATATATTTATAGTCCATCGTTTTTTGACAAGGGTGTCGAGACAGCTCA 1688
                         v    i      i   v  i v    i          i i    vii   
  L1M4_orf2#LINE/    331 CCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCA 380

  chr20_58711416_   1689 GTTAAACATAAATAGGTCTTTTGAACAAATGATGCTGGGACAACTAGATA 1738
                         i viiiv vi     -      v        i             i    
  L1M4_orf2#LINE/    381 ATGGGGAAAGAATAG-TCTTTTCAACAAATGGTGCTGGGACAACTGGATA 429

  chr20_58711416_   1739 TCCAGCTATAAAAGAAATAAATTAGAACCCTCCCTTCTACCATGAACAAA 1788
                         ?   vv ii       vv  i  i  v    v   ivi     iv     
  L1M4_orf2#LINE/    430 KCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACAAA 479

  chr20_58711416_   1789 AATTAACTCACAATGGATTAAACACCTAAGTGTAGGAAGTAAAACTATAA 1838
                                   v       i ? v      i    i  iv           
  L1M4_orf2#LINE/    480 AATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA 529

  chr20_58711416_   1839 AACTTTTAGAAGGAAGCACAGACGTCTATCATCATGACCTTGAATTAGTC 1888
                             i       i  i  i  i?  vv   v  i        ii    v 
  L1M4_orf2#LINE/    530 AACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGC 579

  chr20_58711416_   1889 AAAGTTCCCTTAAATGAGATACTGGAAGCACAA--------AG------- 1923
                           v v ii    i  iv  i  iii        --------  -------
  L1M4_orf2#LINE/    580 AATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAAAT 629

  chr20_58711416_   1924 -GATCAATTTGACTTTATGAAAATTAACG-TTTTTATGCTTCAAAGGGCA 1971
                         -   v    v     i  v        vi-i    i           i  
  L1M4_orf2#LINE/    630 AGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACA 679

  chr20_58711416_   1972 GCACCAAGAAAATAAAGACAAAAGCCACAGGGTGGAAGGAAAT-TTAAGA 2020
                         vi i       i i  i v v  v      ii   i  i    -  viv 
  L1M4_orf2#LINE/    680 CTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCA 729

  chr20_58711416_   2021 AAACA---ATTT-ACATAGCA---GCATC----ATATACAAATCATTCGT 2059
                           v  ---  i - i vi v --- i   ----     i   vv i  v 
  L1M4_orf2#LINE/    730 AATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTCTT 779

  chr20_58711416_   2060 -----TTGATAAGAAAAGAACCCTTAAAGAAAATGTCTCATTCTAAAATG 2104
                         ----- ii    v    ii  ----   v  ----i iv   ?v      
  L1M4_orf2#LINE/    780 ACAACTCAATAATAAAAAGAC----AAATAA----CCCAATTWAAAAATG 821

  chr20_58711416_   2105 AGCAAATTATATGAATAGAC-TTTCTTTAAAAAAGATTTAAAAATGGCCA 2153
                         i     vv  v         -     ii   i     v  v         
  L1M4_orf2#LINE/    822 GGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr20_58711416_   2154 ATAAACACATTAAACGGTGTTCAAAATCATTAGCCAT 2190
                             i     v   v i  i    v    ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.52 (91 / 60)
Gap_init rate = 0.02 (16 / 671), avg. gap size = 3.19 (51 / 16)  


 996 28.76 7.43 5.65  chr20_58730542_58732150      503  1121 (488)    L1M4_orf2#LINE/L1      279   908 (0)  

  chr20_58730542_    503 TAAAGATAGACAAGCAGGCCACTGGA-TACAATCTAGAGTCTGGAG-CAT 550
                            i        vii  ii  v    -  v   iv      ii  i-i v
  L1M4_orf2#LINE/    279 TAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA 328

  chr20_58730542_    551 GCCC-CACCTATGTGGACAGTGGACTTAAAATAAAGGTGGCATTAC---- 595
                         i   -i  v v i   v  i v  i  vvi i  i    v  vv  ----
  L1M4_orf2#LINE/    329 ACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATT 378

  chr20_58730542_    596 --------AGAGCTGAGTCTAGTCAAATACACAGTGGTGGATAAAGTGTA 637
                         -------- i  vvv     vv    -i v ii   v   ivv  v  v 
  L1M4_orf2#LINE/    379 CAATGGGGAAAGAATAGTCTTTTCAA-CAAATGGTGCTGGGACAACTGGA 427

  chr20_58730542_    638 TGTCCACGTAAGGCACAAAG---GAAGCATGATTTCTATATTATGCCACA 684
                          i?    i ---   -    ---    ivv  iii   iv i ii   i 
  L1M4_orf2#LINE/    428 TAKCCACAT---GCA-AAAGAATGAAGTTGGACCCCTACCTCACACCATA 473

  chr20_58730542_    685 C-TAAAAACCAGC-CGAAGTGGATCACAGACCTAAATGTCAAAGGTAGAA 732
                         i-i     ii i - i  i       ?            v i  v  i  
  L1M4_orf2#LINE/    474 TACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAA 523

  chr20_58730542_    733 CCATGGAGACCCTCA------AACA--GGAGAATATTTTCATTACCTCAG 774
                          i  ii -  i  i ------    --  ? v v  i   i v    ii 
  L1M4_orf2#LINE/    524 CTATAAA-ACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr20_58730542_    775 AAGTTAGGACATTGTTTTTCAAATCCCAGAGTAGTAAAACAAAAAAAAAA 824
                         --      vv  v    i i i  ---------i i v  v    i----
  L1M4_orf2#LINE/    573 --GTTAGGCAATGGTTTCTTAGAT---------ATGACACCAAAAG---- 607

  chr20_58730542_    825 AACACCAGTCATAAAGGAAAAGATTTCTAAATTTGATTATATTAAAATTA 874
                         --   v  iv i   i     i  vvv      v  i vi  i       
  L1M4_orf2#LINE/    608 --CACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTA 655

  chr20_58730542_    875 AGAATTTCATTCCTTCAAGAGACACACTGAAATAAGTGAAG------CCC 918
                          i  i  ivv v      ii     vv v  iv       i------   
  L1M4_orf2#LINE/    656 AAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCC 705

  chr20_58730542_    919 CTAGG-TTGAAAAATATATTTACATCTCACCTAT--GAAGAGGTACT-AT 964
                         vi  i- v i i  v      i  vv   iv   --  vi   v   -i 
  L1M4_orf2#LINE/    706 ACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGT 755

  chr20_58730542_    965 -TCTAGAAGAGTAGGAGATACATAAAGACCTCTTTCAAATCAATACTGAA 1013
                         -  i    ----------  i       v     v   v      v i  
  L1M4_orf2#LINE/    756 ATCCAGAA----------TATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_58730542_   1014 ATGGACAA----CCTAGCAGAAAAGCAGGCAGAAGACTTGAATCGGC--T 1057
                          -i     ----  i iiv?    iii    i i  i      v i -- 
  L1M4_orf2#LINE/    796 A-AGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATT 844

  chr20_58730542_   1058 CCTCCAAAAGAGGATAGTCAAATGGCTAATACATGTATGAAAATGT-CTC 1106
                         i       -  i    vv        i    viiii       vi -   
  L1M4_orf2#LINE/    845 TCTCCAAA-GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTC 893

  chr20_58730542_   1107 AACCTTATTAGCAGT 1121
                            v i ????????
  L1M4_orf2#LINE/    894 AACATCAZZZZZZZZ 908

Transitions / transversions = 1.45 (103 / 71)
Gap_init rate = 0.04 (27 / 630), avg. gap size = 3.00 (81 / 27)  


3280 18.58 4.78 1.37  chr20_58747178_58750215.rev      517  1248 (1790)    L1M4_orf2#LINE/L1      152   908 (0)  

  chr20_58747178_    517 GGAAATACAAGGAACCGACCTAGAATAGTCAAAGCAAACTTGAAAAAAAA 566
                               i     ----    i       i    i   v         i  
  L1M4_orf2#LINE/    152 GGAAATGCAAGG----GACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_58747178_    567 GAGCAAATTTGGGGTACTCACATTTCCCAATTTAAAAGCTTACTACAAAA 616
                           i    v    i v       i          v   i           i
  L1M4_orf2#LINE/    198 GAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAG 247

  chr20_58747178_    617 CTACAGTAATTAAGATATGATGGCAGTGATGTTGTGATAGACATACAGAT 666
                                   i    i vvi   i v  iii viv          i    
  L1M4_orf2#LINE/    248 CTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGAT 297

  chr20_58747178_    667 TAGTGGAAAAGAATGGAGAGTCCAAAAATAAATCT------------TCA 704
                         i i     v     v         i       i i------------   
  L1M4_orf2#LINE/    298 CAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCA 347

  chr20_58747178_    705 ACTGATTTTTGATGAGGGTGCCA-GAAAATAAAACCAATGAAGGAA-AAT 752
                          i       i  ii         -  vv  ----i     ii i  -   
  L1M4_orf2#LINE/    348 ATTGATTTTCGACAAGGGTGCCAAGACCAT----TCAATGGGGAAAGAAT 393

  chr20_58747178_    753 GGTCTTTTCAACCAGTGTTGCTGAGAAAAGTAGATATACATATGCAAAAG 802
                         i           v i  v     i  v  v i    ?v  i         
  L1M4_orf2#LINE/    394 AGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAG 443

  chr20_58747178_    803 AAAGCAGTTGT-TCCCTGCCTCACATTATGCA-AAAAATTATCTTGAAAT 850
                           v v     v-i    i       ii  ii -        v  ii    
  L1M4_orf2#LINE/    444 AATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAAT 493

  chr20_58747178_    851 GACTCATACAACTAAATGTAAGAGCTAAAATTATAGATCTCCTAGAAGAA 900
                          iv   ? v v                   i    i v   i        
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_58747178_    901 AATGTAGGAGTTTATCTTCATGATACTGGGTTAGGCAATGGTTTCTT--- 947
                           ii    ?  vv      i   ivi                     ---
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_58747178_    948 --TGGCATCAAA-GCACTAGTGACAAAAAACAAAAGCTGGATGAAGTGGA 994
                         --  i  i    -    v  ii      i v    -- i   i  v    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAA--TAGATAAATTGGA 641

  chr20_58747178_    995 CTTGATCAAAATGGAAG---TTTG--CCTCAA-GGACACCATCAAAGAAG 1038
                            v        vi  i---    -- i    -      i     ii   
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_58747178_   1039 TGAAAAGGCAGTCCACAGAATGGGAGAAAATATTTGCATTTTATATATTT 1088
                                i  ii                          vv i      i 
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_58747178_   1089 AATAATGAACTTGTATCTAGAATATACAAAGAACTCTTAAACCTCAAGAA 1138
                         i    v i         i        i            v v     v  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_58747178_   1139 TAAAAAG-CAAA-AATGCATCTTAAAAAGGGGCAAGGGGTTTGAATACTG 1186
                                -    -  iv  vi ?     v      i  i        vvv
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_58747178_   1187 ATTTTTCTAAAGAAGACATACAAATAGCCAA----CACCTGAAAAGATGC 1232
                             i  i        i        i     ----   v           
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_58747178_   1233 T-ACCATCATTAGTCAT 1248
                          - v     ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.75 (84 / 48)
Gap_init rate = 0.02 (17 / 757), avg. gap size = 2.65 (45 / 17)  

1474 23.97 11.07 3.64  chr20_58747178_58750215.rev     1983  2587 (451)    L1M4_orf2#LINE/L1      259   908 (0)  

  chr20_58747178_   1983 AAGTTATTGTGGTATTGACATAAGGTTAGACATATATATCAACAGGGCAG 2032
                            vi v       i  i       v          v     ii iii  
  L1M4_orf2#LINE/    259 AAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAATAG 308

  chr20_58747178_   2033 AAAT-AGAGTTCTTGAATAGAATCATA------TGGTCAACTGACTTTCA 2075
                           v -     i vvi    i vi    ------       i   i    i
  L1M4_orf2#LINE/    309 AATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCG 358

  chr20_58747178_   2076 ACAAAAGTACCAGTA--ATTCAATGGAGAAAGGATAGTGAAGGATTTCAA 2123
                             ii  i   iv --         i     i     vv----      
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT----TTTCAA 404

  chr20_58747178_   2124 CAAATGATGCTTGAACAATTGGA------CAT-CAAAA--------TT-- 2156
                               i    v i    i    ------   -     --------  --
  L1M4_orf2#LINE/    405 CAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGG 454

  chr20_58747178_   2157 ------------CAGCTTATATAAAAATTACCTTGAAATGGAACATAGGC 2194
                         ------------  v v    i        v  ii       v  ?  i 
  L1M4_orf2#LINE/    455 ACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGAC 504

  chr20_58747178_   2195 CTAAGTGTAAAACCTAAAAGCATAAAAATTCCCAAGTAAAATACAAGGGA 2244
                             i     i v      vi      v iiivi iv    i i i ? v
  L1M4_orf2#LINE/    505 CTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGT 554

  chr20_58747178_   2245 AACTATTTTTGA-----AATTTGGCA--GATTTCTTAG----GA-ATCA- 2281
                           v v  iv   -----ii  v    -- i        ----  - i  -
  L1M4_orf2#LINE/    555 AAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAA 604

  chr20_58747178_   2282 --GCCCGAACCATAAACAAAAACATTAATAGATTGAACTTCGCCAAAATT 2329
                         --  v i i v i   vi    v  vi   i    i     ii       
  L1M4_orf2#LINE/    605 AAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATT 654

  chr20_58747178_   2330 AAAAACTTCTGCTCTTCTCAAAACCCTGTTAAAAAAGTGAAAACTGAAAA 2379
                                 i  iv    vv ii  v  i i  i          --  v  
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA--GACAA 702

  chr20_58747178_   2380 TTTTCTACCACTGAAGGGTTGAAAATATTTGCAA--CACATATCTGATGA 2427
                         i------    v   v  vv              --  i         i 
  L1M4_orf2#LINE/    703 C------CCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAA 746

  chr20_58747178_   2428 AAGATATGTATCCAGAATATATAAATAACTGCCT-CAGCTT--TAAAAAT 2474
                         ii  iv                   v    - i -  i  i--   v  v
  L1M4_orf2#LINE/    747 GGGACTTGTATCCAGAATATATAAAGAACT-CTTACAACTCAATAATAAA 795

  chr20_58747178_   2475 AAAGCAAATGA--------AAAAATGTACAAAATATTTGAACAGATGCTG 2516
                           ii     i --------       vi    iv       i   iii v
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_58747178_   2517 TACCAAATAAAAGATATGGATGCTTGACATCATCAGT-CATTAGAGAAAT 2565
                         iv     v  i v   iii   --- v  --  v  i-   v i - i  
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATG---GCCA--ATAAGCACATGAAA-AGAT 889

  chr20_58747178_   2566 ATAAATTAACACCACAGTGAGA 2587
                         ii--- i    i  ????????
  L1M4_orf2#LINE/    890 GC---TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (90 / 53)
Gap_init rate = 0.04 (25 / 650), avg. gap size = 3.56 (89 / 25)  


3647 24.48 0.22 0.55  chr20_58987452_58989413      560  1470 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_58987452_    560 TGAAAAGATATTCCATGTTCATGGATTGAAAGATTTCATATTGTTAAAAA 609
                           i        i                i    i  v          i -
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGA- 49

  chr20_58987452_    610 TATCCATACCACCTAAAGCAATCTACAGATTCAATGCAATCCCTATCAAA 659
                          iv v    iv  i   vii              i               
  L1M4_orf2#LINE/     50 TGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA 99

  chr20_58987452_    660 ATACCCATGGGATTCTTCATATCAATAGAAAAAACAACCCTAAAATGTAT 709
                           v  viiv vv  i  iii vv   v  v  ivii i        vi  
  L1M4_orf2#LINE/    100 ATCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_58987452_    710 ATAGAACCGCAAAAGACCCAGGATAGCCAAAGCTATCTTGAGCAAAATGA 759
                           i   vi    ii       i         i v       iv  i v  
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_58987452_    760 ACAAAACTGAAATAATTACATTACCTGACTTCAAATTATACTACAGAGCT 809
                              ii  i iv v i   i v  ii i      viv       i    
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_58987452_    810 ATAGTAAACAAAACAGCATGGTACTGGCATAAAAACAAATATATAAACCA 859
                          i     v   i    ii              ii i i i     i i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_58987452_    860 ATGAAACAGAATAGAGAACCAAGAAACAAATCCATACATCTATGGTGAAC 909
                            i  i     v    ii v     i   i        i      v  i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_58987452_    910 TCATTTTCAACAAAAATGCCAAGAACATACACTGGGGAAAGGACAGTCCC 959
                          v      i    iii        v   v  v         i i    ii
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_58987452_    960 TTCAACAAATAATGCTGGGAAAACTGGATATCTATATGCAGAAGAATGAA 1009
                                   ii        v         ? i i     i         
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_58987452_   1010 ACTAGACTCC-ATCTCTCGCCATATACAAAATTCAAATAAAAACGGATTA 1058
                         ii i   i  - i   v i            v i  v v    i    i 
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_58987452_   1059 AAGACTTAAATCTAAAACCTCAAACTCTGAAACTACTAAAAGAAGATATC 1108
                         ?    i     v   i v  v     v i     vi  i     i i  v
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATA 549

  chr20_58987452_   1109 AAGGAACCTCTCTAGGATATCAGTCTGGGCAAGGGTTTCTTGAGTAATAC 1158
                         ii? v vv   iiiv  iv ii vi i     v        iii  vv  
  L1M4_orf2#LINE/    550 GGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGAC 599

  chr20_58987452_   1159 CCTACAAGTACAGACAACCAAAGCAAGAAGTAGACAAATGGAATCACATC 1208
                         v i v   i   ii    v    -  i  i    i    v i iiv    
  L1M4_orf2#LINE/    600 ACCAAAAGCACAAGCAACAAAAG-AAAAAATAGATAAATTGGACTTCATC 648

  chr20_58987452_   1209 AA-GTTAAAAAGCTTCTGTGCAGCAAAGGAAACAATCAACAAAGTGAAGA 1257
                           -i       -   i     vv       v  v     v        i 
  L1M4_orf2#LINE/    649 AAAATTAAAAA-CTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAA 697

  chr20_58987452_   1258 GACACCGCACAGAACGGGAGAAAATATTTGCAAACTATCCATGTGACAAG 1307
                             v v       i                   ii  vi  v   i   
  L1M4_orf2#LINE/    698 GACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAG 747

  chr20_58987452_   1308 AGATTAATAACCAGAATATATAAAGAGCTCAAACTACCCTATAGGAAAAA 1357
                         i  i vi  v                i   vv  v  i v   iv     
  L1M4_orf2#LINE/    748 GGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAA 797

  chr20_58987452_   1358 AATCTAATAATCTGTTTTAAAAATGGAAAAAATGATCTGAATAGATATTT 1407
                         i - v     i iiv  ?        iv   i-   i        i    
  L1M4_orf2#LINE/    798 GA-CAAATAACCCAATTWAAAAATGGGCAAAG-GATTTGAATAGACATTT 845

  chr20_58987452_   1408 CTCAAAAGAAGACATACAAATGGCAAATACGTACATTAAAAGGTGCTCAG 1457
                            v        i           v    v i    v     i      i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_58987452_   1458 CATCAGTGATCAT 1470
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 1.70 (138 / 81)
Gap_init rate = 0.01 (7 / 908), avg. gap size = 1.00 (7 / 7)  


2593 23.97 4.52 0.96  chr20_59025843_59027577      514  1243 (492)    L1M4_orf2#LINE/L1      153   908 (0)  

  chr20_59025843_    514 GAAATGCA--GAACCTAGAATAGCTAAAACAATCTCGAAAAAGAGGATTA 561
                                 -- i   i        i          i        i  vi 
  L1M4_orf2#LINE/    153 GAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACA 202

  chr20_59025843_    562 AAATGGGAGGAATCGTGCTACCCAATGTTAAGACTTATTATAAAGCCATA 611
                           i v      v  iii  v      v i  i     i  i     i i 
  L1M4_orf2#LINE/    203 AAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACA 252

  chr20_59025843_    612 GCAATTAAGACGGTGTGGTTCTGG-AGGAGCGATAGACATA--GATCAAT 658
                          i   i     i       v    - vi  -          --       
  L1M4_orf2#LINE/    253 GTAATCAAGACAGTGTGGTACTGGCATAAG-GATAGACATATAGATCAAT 301

  chr20_59025843_    659 GGAACAGAATAGAGAAGTTAGAAACAGATCCACCCAAATATGCCCGAGGG 708
                             i     v    ivii     i i i   iv  vv    vi i vv 
  L1M4_orf2#LINE/    302 GGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTG 351

  chr20_59025843_    709 GTTTT-GAAAAAGGTACAAAAATTATTCAATGGAGGAAGGACAGCCTTTT 757
                         i    -  v  i   i v  i ii         i i   i i  i     
  L1M4_orf2#LINE/    352 ATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_59025843_    758 TAACAAATGGTGCTAGGGCGATTG-AT-TCCGTATGCAAAAG--TGAGCC 803
                         i             i  i i i  -  -?  ii         --   ivi
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGT 451

  chr20_59025843_    804 TTAACCTAAACCTCATACCTTATACAAAAATCAACTCAAAATGGACCATT 853
                          vi   ivv      i   v           i             i  ?v
  L1M4_orf2#LINE/    452 TGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWA 501

  chr20_59025843_    854 AACTTAAA---AACATC--AAACTCTAAGACTTTTAGAAAAGAAAAAAAA 898
                         i  i    ---  v v --     v   i   i      i ---   v v
  L1M4_orf2#LINE/    502 GACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA---AAACAT 548

  chr20_59025843_    899 AGGAGAAAATCTTTAGGACCTATGCTCAGTGGAA-AATTT-TTAGACTTG 946
                            ? v       iiv     vv v i  - v  -ii   -     iv  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAG-GCAATGGTTTCTTAGATATG 597

  chr20_59025843_    947 ACACCAAGAGCAACACTCAG--------AAAAT-GATAAATTGGACCTCA 987
                                i    -  vv  i--------     -            i   
  L1M4_orf2#LINE/    598 ACACCAAAAGCA-CAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCA 646

  chr20_59025843_    988 ACAAAACGTAAAACTTTTGC-TTTCAGGAAGACCCTGTTAAGAGGATGAA 1036
                         v     ivv          i-i    i- i   v  i i    iii    
  L1M4_orf2#LINE/    647 TCAAAATTAAAAACTTTTGTGCTTCAA-AGGACACTATCAAGAAAGTGAA 695

  chr20_59025843_   1037 AAGACAAGCTATAGACTGGGAGGAAATGTTTGCAAACCATATATCTAACA 1086
                                v i i   v      i    i        i         i i 
  L1M4_orf2#LINE/    696 AAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATA 745

  chr20_59025843_   1087 AAGGACTCGAATCTAGAATATACAAATAACTC--AAAGCTCAAGCATAAA 1134
                          i     i v   i        i   v     -- v i     vv     
  L1M4_orf2#LINE/    746 AGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAA 795

  chr20_59025843_   1135 A---CAAAAAATCTG-TTAGAAAATAGCCAAAAGGCATAAAGGGACATTT 1180
                          ---    v  i ii-  ?i     i v    i iiv i  vi       
  L1M4_orf2#LINE/    796 AAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTT 845

  chr20_59025843_   1181 CACTGAGGGGGATATTCAGATGGCCAGTGAGCATCGGAAACAACGTTCAG 1230
                          v ii i ii     v  i       i i    ivv    vi i i   i
  L1M4_orf2#LINE/    846 CTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAA 895

  chr20_59025843_   1231 CATCATTAGCCAT 1243
                              ????????
  L1M4_orf2#LINE/    896 CATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (114 / 57)
Gap_init rate = 0.03 (22 / 756), avg. gap size = 1.82 (40 / 22)  


3029 22.47 1.44 7.84  chr20_59151900_59154078.rev      718  1687 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_59151900_    718 TGAAAAGACATCCCATGTTCATGGATTGAAAGAATTAATGCTGTGGAAAT 767
                           i     i                   i    v     ii   vi i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_59151900_    768 CACCATGCTACCAAAACTGATCTACAGATTCAATGCAATCCCTATCAAAT 817
                         vi v  i  v  v   i                i               -
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAA- 99

  chr20_59151900_    818 AACCAAGGACT-TTTTTTTCACAAAAACTGAAAAAGCAATCCTAAAATTC 866
                          v  v  --  -ii     ii  i   i   v  ivii            
  L1M4_orf2#LINE/    100 ATCCCAG--CTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTC 147

  chr20_59151900_    867 ATATGGAACCACAGAAGACCCTGAATGG----GACAATCCTGAGCAAAAA 912
                                 vii  iii     v    i ----i      i   iv  i  
  L1M4_orf2#LINE/    148 ATATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAA 197

  chr20_59151900_    913 CAGCAAAACCTTGAGGCATTACACTATCCAAGGCCAACATATACAACAAA 962
                         v i    ii- v    vv i     vi    vvi   v iv   v     
  L1M4_orf2#LINE/    198 GAACAAAGT-TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAA 246

  chr20_59151900_    963 GCTATAGTAACCAAAACAACATCATATTGGCATTAAAAACAGACACATAG 1012
                             i     i   i   iii vi  i      -  ii i     i    
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCAT-AAGGATAGACATATAG 295

  chr20_59151900_   1013 ATCAATGGAACAGAATAGAGAACCCAGAAATAAATCCATGTATTTACAGC 1062
                                   i     v    ii           i    ii     ii i
  L1M4_orf2#LINE/    296 ATCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGT 345

  chr20_59151900_   1063 CTACTGTGTATTTTCATGTATTTACAGCCCATCATGTATTTTCAATGAAG 1112
                          v i  ---      i-------   i------iv  iii-------   
  L1M4_orf2#LINE/    346 CAATTG---ATTTTCG-------ACAA------GGGTGCC-------AAG 372

  chr20_59151900_   1113 AACATTCAGTGAGGAAAGCACAATATTTTTAAGAAGTAATGCTGGAGAAA 1162
                          v      i  i      v i i v    i  v  i ii      iiv  
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr20_59151900_   1163 CTGGATATTCATATGCACATGAG---AGCT---CTCCATCTTAAGATGCT 1206
                                ?i  i     v v  i---  i --- i  --------- i i
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCC---------TACC 463

  chr20_59151900_   1207 TTAAACCATATACAAAAATCAAATCAAAATGGGTTAAAGACTTAAGTGAA 1256
                          i v               i  v         i i ?    i   i  v 
  L1M4_orf2#LINE/    464 TCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTA 513

  chr20_59151900_   1257 AGACCTGAAACTATAAGATTACTAGAAGAAAACACTGGAGAAACACTCTA 1306
                            v  i         i i vi            iv  ? v  vv  iii
  L1M4_orf2#LINE/    514 AGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCG 563

  chr20_59151900_   1307 GGACATTGG-TCATGGCGAAGATTTCCTGGGTGGGAAATCAAAAGCACAG 1355
                         v   v    - i -   i v i    i i i iv  v i          i
  L1M4_orf2#LINE/    564 TGACCTTGGGTTA-GGCAATGGTTTCTTAGATATGACACCAAAAGCACAA 612

  chr20_59151900_   1356 GCAACAAAAGCAAAAATAGACAAATGAGATTACATCAAACTAAAAGGCTT 1405
                                   v         i    vi  i v       v v   ii   
  L1M4_orf2#LINE/    613 GCAACAAAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTT 662

  chr20_59151900_   1406 CTGCCCAGCAAAAGAAACAAGCAATGGAGTGACAACGCAACCTACCAAAT 1455
                         i  iv vv    i  v  v v   vii     v  vi     i  vi   
  L1M4_orf2#LINE/    663 TTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAAT 712

  chr20_59151900_   1456 AGGAGAAAATATTTGCAAACTGT-CATCTGACAGGGGATTATTATCCAGA 1504
                         i                  iii -i      i i    i vv        
  L1M4_orf2#LINE/    713 GGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGA 762

  chr20_59151900_   1505 ATATATAAGGAACTCAAACAACTAAATAGCAAAACAAACAAACAAACAAA 1554
                                 i      vv      v    ii    ----- i     i  -
  L1M4_orf2#LINE/    763 ATATATAAAGAACTCTTACAACTCAATAATAAAA-----AGACAAATAA- 806

  chr20_59151900_   1555 AAGCCCACAAATAGTTTGATTAAAAATGGGCAAATGATTTAAAAATGGGC 1604
                         ---    -----------------------------   ?          
  L1M4_orf2#LINE/    807 ---CCCA-----------------------------ATTWAAAAATGGGC 824

  chr20_59151900_   1605 AAATGATCTGAATAGATATTTCTCAAAAGAAGACATACAAATGGCTAACA 1654
                            v   i        i       v        i           i  i 
  L1M4_orf2#LINE/    825 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 874

  chr20_59151900_   1655 GATATACAAAAA-ATGTTCAGCATCACTAATCAG 1687
                         iii i ii    -   i   i     ????????
  L1M4_orf2#LINE/    875 AGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.06 (144 / 70)
Gap_init rate = 0.02 (20 / 908), avg. gap size = 4.50 (90 / 20)  


3627 15.84 2.54 0.15  chr20_59559668_59561328      501  1169 (492)    L1M4_orf2#LINE/L1      224   908 (0)  

  chr20_59559668_    501 CTGATTCCAAAATTTACTAGAAAGCTAGTGTGATCAAGACAGCATGGTAC 550
                          ii   i     i      v       vv  i          ii      
  L1M4_orf2#LINE/    224 CCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGTGGTAC 273

  chr20_59559668_    551 TCACATAAGGATAGACATATAGACCAATAGAAGTGAATTAAGAGTCTAGA 600
                          vi                    i    i   vv     i      i   
  L1M4_orf2#LINE/    274 TGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGTCCAGA 323

  chr20_59559668_    601 AGTGAACCCATACTTCTATGGCCAGTTGATTTTTTGACAAAGGTGCCAAA 650
                          i i         v i     i  i        i-     i        i
  L1M4_orf2#LINE/    324 AATAAACCCATACATTTATGGTCAATTGATTTTC-GACAAGGGTGCCAAG 372

  chr20_59559668_    651 ACCATTCAATGGGGAAAAGACAGCCTTTTCAACAAATTGTGCTGGGACAG 700
                                          ii i  i             v           i
  L1M4_orf2#LINE/    373 ACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAA 422

  chr20_59559668_    701 CTGGACAGCTACATGCAAA-GAACGAAATTGGACCCCTACCTCACACCAT 749
                              i ? i         -   i   i                      
  L1M4_orf2#LINE/    423 CTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACACCAT 472

  chr20_59559668_    750 ATACAAAAGTTAACTCAAAATGGATCAAACACCAAAATGTAAGATCTAAA 799
                                 i                  ? v   v          v     
  L1M4_orf2#LINE/    473 ATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAA 522

  chr20_59559668_    800 ACTATAAAACTCTAAGAAGAAAACATAGGTGTAAGTCTTTGTGACCCTGG 849
                                      v               ?    i    i      i   
  L1M4_orf2#LINE/    523 ACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGG 572

  chr20_59559668_    850 ATTAGGCAGTGATTTCTTAGATATGACTCCTAAAGTGCAGGCAAGCAAAA 899
                         i       i  i               v  v    ii  i    vv   i
  L1M4_orf2#LINE/    573 GTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAG 622

  chr20_59559668_    900 AATAAATAAACAG--TGGACTTCCTCACAATTAAAAATGTCTGTGTTTTA 947
                           v     i i i--        v   v         iv i    i  i 
  L1M4_orf2#LINE/    623 AAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCA 672

  chr20_59559668_    948 AAGGATACCATCAAAAAAGTGAAAAGGC----CATAGCATGACAGAAAAT 993
                              i  i     i           i ----  i  v   iv       
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_59559668_    994 ATTTGTTAATTGTATAT---ATAAGAGTCTAGTATCAAGAATATATAAAG 1040
                              iv   ii     ---     i v  v     v             
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_59559668_   1041 AACTCTTACAACTTAATAA--AAAACACAAATAACTCAATTTCAAA-TGA 1087
                                      i     --    v         i     ?v   -  i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_59559668_   1088 GCAAAAGTTTTGAATAT---TTTTTCCAAAGAAGACATACGAATGTCCAA 1134
                              i v        v---   i           i    i    v    
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_59559668_   1135 TAAACACAT-AAAATCTGTGTAACGTCATTAGTAAG 1169
                            i     -    vv  ivi   i   ????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.00 (68 / 34)
Gap_init rate = 0.01 (9 / 685), avg. gap size = 2.00 (18 / 9)  


2989 25.46 3.88 0.23  chr20_59963032_59965259      861  1736 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_59963032_    861 TGGAAATATATCCCATGCTCACTTATTGGAAGAATCAATATTGTGAAAAT 910
                               v          i   ivv         v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_59963032_    911 GACCAAACTGCCCAAAGCAATCTACAGATTCAGTGCAATTCCTATCAAAA 960
                          i v v   v      vii             ii     i          
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_59963032_    961 TACCAACATTCCTTTTTCACAGAATTAGAAAAAC-AATGCTAAAATTCAT 1009
                          v   i - v       ii     v v  v  i -i  v           
  L1M4_orf2#LINE/    101 TCCCAGC-TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCAT 149

  chr20_59963032_   1010 TTGGAACCAAAAAAGAGCCTCAATAGGCAAAGCAATCTTAAGCAAAAAGA 1059
                         v     viiv  ii  v  vv     v    i       i iv  i    
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_59963032_   1060 ACAAATCTGGAGGCATCACATTACCTGACTTCCAACTATACTACAGGGCT 1109
                              vi      vv     i v  ii i   v  viv       ii   
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_59963032_   1110 ATAGTTACCAA-ACAGCATGATACTGGTGCAAAAGTAGATA-ACAGACCA 1157
                          i   v i   -    ii  i      iii  iii    i - i   i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_59963032_   1158 ATAGAACAGAATAGAGAATGAAGAAATAAAGCCAAATCCTTACGACCAAC 1207
                           i   i     v    i vv         v   v ivi   i ii   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_59963032_   1208 TGATCTTTGATAAAGCAAACAAAACCGT---AT----------------- 1237
                             i  i  i  i vviv   i   i ---  -----------------
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_59963032_   1238 -TCAATA---GATGCTAGGAAAAACTGGTGAGCCACGTGTAGAAGAATGA 1283
                         -    i --- i    i   v  -    vv ?    i  i i        
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAA-CTGGATAKCCACATGCAAAAGAATGA 448

  chr20_59963032_   1284 AACTGGATACCTATCTTTCAGCATATACAAAAATCAACTCAAA-TGAATT 1332
                          ii    iv    i  iv  v             i        -  i  i
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_59963032_   1333 AAAGACTTTAATCTAAGATCTGAAACCATAAAAATTCTAGAAGAAAACCT 1382
                          ?    i v   v     v  i    i      v ii           v 
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_59963032_   1383 AGGCAAAACTCTTCTGGACATCAGCCTTGGCAAAGAATTTATGACCAAGA 1432
                            ?iv  v     vv   v ii vi v     v iv  iv iivi v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_59963032_   1433 CCCCAAAAGCAAATGCAACAAAACCAAATATAAATAAGTGGGACCTAATT 1482
                          v         v v         vv   v   i    i v    i v  i
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_59963032_   1483 AAACTAAAAACCTTCTGCACTGCAAAAGAAAGAATCATTAGAGTAAACAG 1532
                            v v    v   i  ii  v    i  v vv    vv i   i  v  
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_59963032_   1533 AACACCCGCAGAATGGGAGAAAATGTTTGCAAACTATGCATTTGATAAAG 1582
                          vv    i                i        ii  ii  i      i 
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_59963032_   1583 AACTAATAATCAGAATCTGCAAGGAACTC----AAATCAGCAA-GAAAAG 1627
                         i   vi  vi      v ii  i      ----  v   ii  -i     
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_59963032_   1628 AAAAACAATCTCATTAAAAAGTGGGCAAATGACACGAATAGACATTTCTC 1677
                          v   i  i iv   ?    i        v  ivi               
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_59963032_   1678 AAAAGAAGATAAACAAATGGCCAAGAAACACATGAAAA-ATGCTTGACAT 1726
                         v          v            v  i          -     ii    
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_59963032_   1727 CACTAATCAT 1736
                           ????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 1.33 (125 / 94)
Gap_init rate = 0.01 (12 / 908), avg. gap size = 3.00 (36 / 12)  


 765 25.23 4.05 2.25  chr20_60030874_60033911      555   776 (2262)    L1M4_orf2#LINE/L1       13   238 (670)  

  chr20_60030874_    555 CTGTGTTCATGGGTCAGGAGACTCACAATAGTTAAGATGTCAACTCCTCC 604
                          ii         i ii i     i vv  v         v   iv ii  
  L1M4_orf2#LINE/     13 CCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCC 62

  chr20_60030874_    605 CAAACTGATCTGCAGAAGCAATGCA-TCCC----AAAGTCCCAGCAGCCT 649
                             i      i    vv   i   -    ----   i       v    
  L1M4_orf2#LINE/     63 CAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCT 112

  chr20_60030874_    650 CCTGTGTAGAAACTGACAAGGTGATTCTGAAATTCATACAGAAATGCAAA 699
                         ii v  i     i       v    i  i         ii         i
  L1M4_orf2#LINE/    113 TTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAG 162

  chr20_60030874_    700 AGTCTTAGATTAACCAACACAAC--TGTAAAAAAAGGTCAG-GCTGGCCG 746
                         i v ii   v  i    v    i--  v    i   iv  i- i   ---
  L1M4_orf2#LINE/    163 GGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGG--- 209

  chr20_60030874_    747 CAGTGGCTCACGCCTGTCA-TCCCAGCACTT 776
                         -  - i     i i vi  - ii  iv    
  L1M4_orf2#LINE/    210 -AG-GACTCACACTTCCCAATTTCAAAACTT 238

Transitions / transversions = 2.29 (39 / 17)
Gap_init rate = 0.03 (7 / 226), avg. gap size = 2.00 (14 / 7)  

1279 25.94 12.67 0.40  chr20_60030874_60033911     1660  2164 (874)    L1M4_orf2#LINE/L1      244   810 (98)  

  chr20_60030874_   1660 AAAGCTCCAGTAACCAGGACAGCACAGTGTTGGTGCAAAGTTAAACA--- 1706
                               v      i  i     iiii  ii   iii  i v  i   ---
  L1M4_orf2#LINE/    244 AAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATAT 293

  chr20_60030874_   1707 -GATCAAC---ACGGCCGTGCAGAGTCCACAAGCAGGCCCACACGCGGAT 1752
                         -      i--- ii vvv  -        v  ii ii    i  iivv  
  L1M4_orf2#LINE/    294 AGATCAATGGAATAGAATTG-AGAGTCCAGAAATAAACCCATACATTTAT 342

  chr20_60030874_   1753 GG--------------ACAAAGG---CAA-----TTCAGTGGTGA--GGA 1778
                           --------------    i  ---   -----    i   v  -- i 
  L1M4_orf2#LINE/    343 GGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAA 392

  chr20_60030874_   1779 CGGGCTTCTCA-CA-----TGCTGGAACAACTGGACAGACACAGGCAAAC 1822
                         ii v   i   -  -----      i         i ?v    v     v
  L1M4_orf2#LINE/    393 TAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAA 442

  chr20_60030874_   1823 CC------CTGGACCGACACCCCATAGTGTGTACCAACATCAACTCAAAA 1866
                         vv------i      vvi   i  i vii i   v  v  i         
  L1M4_orf2#LINE/    443 GAATGAAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAA 492

  chr20_60030874_   1867 TGGATC-CAGACCTAAATGTAAAACCTAAAACT-------TCC-AGAAGA 1907
                               -?              i v        -------  i-      
  L1M4_orf2#LINE/    493 TGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGA 542

  chr20_60030874_   1908 AAACA--GGAGAACATTTCTCTGACCCAGGGTTAGGCAAAGAAATTTTAG 1955
                              --  ? v v  i iiv     iv           v ivv i    
  L1M4_orf2#LINE/    543 AAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAG 592

  chr20_60030874_   1956 AAACAACATCAGAAACGAAATGCA-TAAAAGAACAAAAGGATAAACTGGA 2004
                          v ii   i  i  i iv  -   -i       v   vi      i    
  L1M4_orf2#LINE/    593 ATATGACACCAAAAGCACAA-GCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_60030874_   2005 CTTCATCAAAATGTTAAACTTCGGCTTTTCAGCAGACACTG-CTAGAGAA 2053
                                     vvv      iv ivi    ivi      i- v   i i
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_60030874_   2054 TGAGAAGACAAGGCACAGAACGG-ACAGACTCTTTAGAAAGCATCCATCT 2102
                            i       vv       i  - v i v v   iv   v   vi    
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_60030874_   2103 AATAAAGGGCTTGGATCCAGAATGTATGCAGAATCCTCAAAACTCAGTAA 2152
                         i    i  i    v         i   iv    ii  i v      i   
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_60030874_   2153 ------GA-AAATAACCCA 2164
                         ------  -          
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCA 810

Transitions / transversions = 1.56 (78 / 50)
Gap_init rate = 0.04 (20 / 567), avg. gap size = 3.30 (66 / 20)  

 289 21.59 6.82 0.00  chr20_60030874_60033911     2459  2546 (492)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr20_60030874_   2459 AAAAGTGGGCAA-----TTGAATAGACCCTTCGCCAAAGGTGGCAGACGG 2503
                             i       -----          vi   v      iv ii v  ii
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr20_60030874_   2504 ATG-CAAATGAGCACACGGAGAGAGCCCCAACATCATTAGTCAT 2546
                            - v   i      i i i   vv i        ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 3.00 (6 / 2)  


1261 30.26 5.32 3.43  chr20_60042213_60044893     1362  2207 (474)    L1M4_orf2#LINE/L1       47   908 (0)  

  chr20_60042213_   1362 AGATTTCAGTTCTCCCAAAATTGACCCACAGATT-GATACAACTTCAATT 1410
                             vv  i v     v       i i       -i ii   iii v  i
  L1M4_orf2#LINE/     47 AGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATC 96

  chr20_60042213_   1411 AAAATAACCTACAAGGACTTTTATG--GGCCCCGAAGAGTTGATTCTAAA 1458
                              --  i -ivv v     v  -- ivvii  vi  i    i     
  L1M4_orf2#LINE/     97 AAAAT--CCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAA 143

  chr20_60042213_   1459 ATTTATAAGGAAGAT-CAAAGTGCCAAGAGTTGCACAGACAATTCTCAAA 1507
                            i   v    -  -   i vi  v   i v  vv i     ii v   
  L1M4_orf2#LINE/    144 ATTCATATGGAA-ATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAA 192

  chr20_60042213_   1508 AGCAA---CAGAAT-GGAGTATT---ACCTCTAGTAGATATCAAGAATTA 1550
                          iv  ---  i i -    v i ---  i  i--i -  v    i v   
  L1M4_orf2#LINE/    193 AAGAAGAACAAAGTTGGAGGACTCACACTTCC--CA-ATTTCAAAACTTA 239

  chr20_60042213_   1551 GTATGGAGCTAAATTATTTAAGGACAGGATGCTACTGATGAAAGGACAGA 1600
                         v  iii     v v  v i   -    vi  v     iiiv     i   
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAG-ACAGTGTGGTACTGGCATAAGGATAGA 288

  chr20_60042213_   1601 CAGATAAACCAAGAGAAAACAACCGACAGGCTAGAAACGGATGCCACATA 1650
                           v   i i   vi   v v  ii  v  v i     iii i-   i i 
  L1M4_orf2#LINE/    289 CATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAAAC-CCATACA 337

  chr20_60042213_   1651 AT-ATAA--AACCTGAAATGTT--ACAGACGGGCCATGGAGACCA--CAG 1693
                         v -  ii--  i-   -- v  --   iiv v    ---      --  i
  L1M4_orf2#LINE/    338 TTTATGGTCAAT-TGA--TTTTCGACAAGGGTGCCA---AGACCATTCAA 381

  chr20_60042213_   1694 AGGTGAGGAAGGACCA----TTCAAATAAATAACACCAGGACAACTGTCA 1739
                         ---  i    i  vi ----  iv  i    iiii ii         vvv
  L1M4_orf2#LINE/    382 ---TGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGAT 428

  chr20_60042213_   1740 ATCCAAATAGGAGGCAAATGAAAATGGAGCTCTAACTCACACCACACACA 1789
                          ?   v  - v iivi      iv    v i   v         i i   
  L1M4_orf2#LINE/    429 AKCCACAT-GCAAAAGAATGAAGTTGGACCCCTACCTCACACCATATACA 477

  chr20_60042213_   1790 AACCCCATGCCAGGA-GGATTACATACTTAAAAGCAAAAGCAAAAGCTAT 1838
                           vvii vvi  ii -    i ? v  i    v i  i   v   i    
  L1M4_orf2#LINE/    478 AAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTAT 527

  chr20_60042213_   1839 CA---TTTTAGAAGAAAATACAGAAGACTATTCCTATTACCTTCGGGTTA 1885
                         v --- i           i i  i? vvv  iiiii v     -      
  L1M4_orf2#LINE/    528 AAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTT-GGGTTA 576

  chr20_60042213_   1886 GA-AAGGACTTCTTAAAGATGACTTGAAAAAGCTTACCAA-AAAGGAGAC 1933
                          i-  v ii      i v     viv    ivviv v   -   i  i v
  L1M4_orf2#LINE/    577 GGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAA 626

  chr20_60042213_   1934 AATAGATACATTCAACTACAGTAAAATCAAGGAGTCCTATTCGTCAGAAG 1983
                                 v   vi   v  vi     i  ii v ii i v v   i i 
  L1M4_orf2#LINE/    627 AATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGG 676

  chr20_60042213_   1984 ACACCATAAAGAAAGTGAAAAGATCAGATATAAACTGGAAGAAGATACTG 2033
                             i  v               iv vvi i i v   i    i   i v
  L1M4_orf2#LINE/    677 ACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTT 726

  chr20_60042213_   2034 GCCATATACAGATGACCT-ACAAAGGAACAGTAACCAGAATATGCACAGA 2082
                           v -  -  v  - i  - i  i   viv   v         ii v   
  L1M4_orf2#LINE/    727 GCAA-AT-CATAT-ATCTGATAAGGGACTTGTATCCAGAATATATAAAGA 773

  chr20_60042213_   2083 ACTCCTATAATT----AATACGAA-----ATAATTTAA--AGAAAACGGG 2121
                             i  i  i ----    vi  -----    iii  --?i    i   
  L1M4_orf2#LINE/    774 ACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGG 823

  chr20_60042213_   2122 GCAAAAAGACACAAACAGACATTTCAC---AGAAGGT-TACCCACAAACA 2167
                         -    i-  ivii  i         v ---     i -   vv iiiv  
  L1M4_orf2#LINE/    824 -CAAAG-GATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCA 871

  chr20_60042213_   2168 ATAAACATA-GAAAATTAATTTCCTCTATATTAAAGGAAAA 2207
                             i  i -     --i  v--   v i  i ????????
  L1M4_orf2#LINE/    872 ATAAGCACATGAAAA--GATG--CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.55 (153 / 99)
Gap_init rate = 0.05 (42 / 862), avg. gap size = 1.76 (74 / 42)  


 356 31.43 0.00 0.00  chr20_60046436_60048862      675   779 (1648)    L1M4_orf2#LINE/L1        1   105 (803)  

  chr20_60046436_    675 TGAAGAGGTACAACACGTTCGTGAATCAGAACACTCGATATTGCTAAGAT 724
                           i i  i  ivv  i    i  i  ii   v   ii      i      
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_60046436_    725 ATCAATGATCATAAAACCGATCTATAGACTCAATACAATCCCAAGCAAGA 774
                         iv    iv  viv   ii      i   i    ii       v v   i 
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_60046436_    775 TATCA 779
                          vi  
  L1M4_orf2#LINE/    101 TCCCA 105

Transitions / transversions = 2.30 (23 / 10)
Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.00 (0 / 0)  

1544 23.14 6.38 9.92  chr20_60046436_60048862     1089  1935 (492)    L1M4_orf2#LINE/L1       92   908 (0)  

  chr20_60046436_   1089 CTATCAAGGTATCAAGAGGCTTTTTTTGTAGAAGTTGACGAACTGATTCT 1138
                                ii vi  - vv  i       i    i     i i     i  
  L1M4_orf2#LINE/     92 CTATCAAAATCCCA-GCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCT 140

  chr20_60046436_   1139 GAAA--CACATG--AATGCAAACGACC-AGAACAGCCCTCAACGTTTTCG 1183
                         i   --  i   --       iv    -    i    v-v   iv i i 
  L1M4_orf2#LINE/    141 AAAATTCATATGGAAATGCAAGGGACCCAGAATAGCCA-AAACAATCTTG 189

  chr20_60046436_   1184 AAAAAGCAGCAC-----TGGAGGACTCCTGCCACCCA---TCAACACTCC 1225
                               v  v  -----          vii iv    ---    v   iv
  L1M4_orf2#LINE/    190 AAAAAGAAGAACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTA 239

  chr20_60046436_   1226 CT------CTA-AATGGGCTGGAAAGTGCTGAGCTG-CAGAAGGGAAGAC 1267
                           ------   - i iiv vi  v    iv vi   -  v    iv    
  L1M4_orf2#LINE/    240 CTACAAAGCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGAC 289

  chr20_60046436_   1268 AAGGACATGAGTGGA-CAGAAC--ACATCCCAGAAGTGACGTCCTCACAC 1314
                          viv v  v i    -i    i-- v vi      i i -ii  vi   i
  L1M4_orf2#LINE/    290 ATATAGATCAATGGAATAGAATTGAGAGTCCAGAAATAA-ACCCATACAT 338

  chr20_60046436_   1315 --GTGGCCGACTGAGTTTCAATAAAGGCAGCAGCATCGTTCAATAGAGAA 1362
                         --i   i i i   v    i i  i  iiv  iv i i      i i   
  L1M4_orf2#LINE/    339 TTATGGTCAATTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAA 388

  chr20_60046436_   1363 AGGAAGGTCTCCTCAACACATAAGGCTGGCATGATTGG-TAACCACA--- 1408
                           i vi    ii      v  iiv     v ii i   -  ?     ---
  L1M4_orf2#LINE/    389 AGAATAGTCTTTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGC 438

  chr20_60046436_   1409 GAAAAAATGAGTCTCAACCCCCTACCTTACAAC-TCTCCCAAAATTAACT 1457
                         i   i     ivi vi     -     i   v - v v v          
  L1M4_orf2#LINE/    439 AAAAGAATGAAGTTGGACCCC-TACCTCACACCATATACAAAAATTAACT 487

  chr20_60046436_   1458 TGAATTGGGTT---GA-------GTAAGAGCTAAAGCCATAAGCATTCTA 1497
                         ii  v   i i---  -------            i i    --------
  L1M4_orf2#LINE/    488 CAAAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATAA-------- 529

  chr20_60046436_   1498 GAAAACTCCTGTACCTTGGGTTAGGCAAAAATTTATTTAAGAAGGCACAA 1547
                         ---     ------------    --------------     ii  i i
  L1M4_orf2#LINE/    530 ---AACTC------------TTAG--------------AAGAAAACATAG 550

  chr20_60046436_   1548 GATGAATTCTTAAAATGACTCACTGGATTTATTTAAGAAGGCACAGGACG 1597
                          ?vv  v    vi--    ii--   i  ---------     ---- i 
  L1M4_orf2#LINE/    551 GNGTAAATCTTCG--TGACCT--TGGGTT---------AGGCA----ATG 583

  chr20_60046436_   1598 AATTCTTAAA-ATGATACACTGGATTTATTTAAGAAGGCACAAAATGAAT 1646
                         iv      i -    --   iii vvi i--   v ---      -   -
  L1M4_orf2#LINE/    584 GTTTCTTAGATATGA--CACCAAAAGCAC--AAGCA---ACAAAA-GAA- 624

  chr20_60046436_   1647 TCTTAAAAT-GATACATTGGGCTTCCTTAAAATTGAAAACTT--GCACTT 1693
                         ----     -    v     i    v i      i       -- ii   
  L1M4_orf2#LINE/    625 ----AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTT 670

  chr20_60046436_   1694 TAAA--ACGC-ATGCAGCTAAAA-GAAAAGGCAAAC-ACAGACCA--AGA 1736
                         i   --  i -  vv  --   i-      i   v -     vii--   
  L1M4_orf2#LINE/    671 CAAAGGACACTATCAAG--AAAGTGAAAAGACAACCCACAGAATGGGAGA 718

  chr20_60046436_   1737 AAATAGTTACAGAACAATTCTATCTGATAAATTACTTACATCTAGAAAAT 1786
                              v  i  i v  -- v          ivv    ii   i    v  
  L1M4_orf2#LINE/    719 AAATATTTGCAAATCA--TATATCTGATAAGGGACTTGTATCCAGAATAT 766

  chr20_60046436_   1787 ACATTTTAA--ACTCTTACTAAATCAATAATGACAAAACTAACAACCCAA 1834
                          i ----  --        -  v        i v  i  v  i       
  L1M4_orf2#LINE/    767 ATA----AAGAACTCTTAC-AACTCAATAATAAAAAGACAAATAACCCAA 811

  chr20_60046436_   1835 TTTAAAACACACAGACAAAAGATTTGAAAAGACACCTCCCGAAAGAAGAT 1884
                           ?    --- ii i    i        v     ii  i v         
  L1M4_orf2#LINE/    812 TTWAAAA---ATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGAT 858

  chr20_60046436_   1885 AGGCAAATGAGCAAATAAGCTGGTGGAAAGACGCTCAGCATTAGTCACTA 1934
                          vi      -  v       vvi  i     i     i   i ???????
  L1M4_orf2#LINE/    859 ATACAAATG-GCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZ 907

  chr20_60046436_   1935 G 1935
                         ?
  L1M4_orf2#LINE/    908 Z 908

Transitions / transversions = 1.76 (123 / 70)
Gap_init rate = 0.06 (47 / 817), avg. gap size = 2.94 (138 / 47)  


1458 22.22 4.44 1.67  chr20_60847825_60852002     2266  2625 (1553)    L1M4_orf2#LINE/L1        1   370 (538)  

  chr20_60847825_   2266 TGGAAAGATACCTCATGTTCATGCATTGCAAGAATTCATATTGTTAAAAT 2315
                                   i i          v    v    v  v          i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_60847825_   2316 TTTCATACTACCCAAAGTGATCTACAGATTCAGTGCAATCCCTATCAAAA 2365
                         vviv     v      v               ii                
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_60847825_   2366 TTTCAATGACATTTTACACAGAAATAGAAAAAAAAATCCTAGGATTCATA 2415
                          ii  iivi v    vii       v  v  ivvi      ii       
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_60847825_   2416 GTGAACCACAACAGACCTCAAATAGTCAAAGCAACATTAAGAAAGAGGAA 2465
                         vv   vii   vi    ivi     i    i   iv  i i     i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAA 200

  chr20_60847825_   2466 CAAAACTGGAGGCATCACACTTCCTAATTTC----CTTTTATATTACAAA 2511
                             ii      vv          i      ----   ---- i      
  L1M4_orf2#LINE/    201 CAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTT----ACTACAAA 246

  chr20_60847825_   2512 GCTATAGTAATCAAAACAGCATGGTACTAGTAC---------CACATAGA 2552
                             i         i    ii       i i i---------  i     
  L1M4_orf2#LINE/    247 GCTACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA 296

  chr20_60847825_   2553 CCCACGGAACAGAACAGAGAGCCCAGCAATAAACCCA--CTTTCGTACAG 2600
                         i v i    i    iv     i    v          -- v  --  ii 
  L1M4_orf2#LINE/    297 TCAATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATT--TATGG 344

  chr20_60847825_   2601 TCAAATCATCTTTGACAAGG-TGCTA 2625
                             v v  i  i       -   i 
  L1M4_orf2#LINE/    345 TCAATTGATTTTCGACAAGGGTGCCA 370

Transitions / transversions = 1.67 (50 / 30)
Gap_init rate = 0.02 (6 / 370), avg. gap size = 3.67 (22 / 6)  

 410 17.98 6.74 0.00  chr20_60847825_60852002     3042  3130 (1048)    L1M4_orf2#LINE/L1      359   453 (455)  

  chr20_60847825_   3042 ACAAGGGCACCAATAC-A--CAATGGGGAAAAAGCAGTCTCCTCAA---A 3085
                                ii    v  - --           i ii     ii    --- 
  L1M4_orf2#LINE/    359 ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAA 408

  chr20_60847825_   3086 CAGTGATGGGAAAACTGGATATCCCCATGCAAGAGAATGAAATTG 3130
                         ii   v     v         ?  v       i        i   
  L1M4_orf2#LINE/    409 TGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.03 (3 / 95), avg. gap size = 2.00 (6 / 3)  

1059 22.25 25.20 1.07  chr20_60847825_60852002     3314  3686 (492)    L1M4_orf2#LINE/L1      446   908 (0)  

  chr20_60847825_   3314 TGAAATTGTACCCTTATCTCACACCATGCAAAAAAAAATCAGCTTAAAGT 3363
                             i   v    i  i          -- v v      i i  i   i 
  L1M4_orf2#LINE/    446 TGAAGTTGGACCCCTACCTCACACCAT--ATACAAAAATTAACTCAAAAT 493

  chr20_60847825_   3364 GGATTAAAGATCTAAACATAAAACCTGAAACTATAACACTGCTAGGAGAA 3413
                             i ?   i     ii   i v  i         v   vi   i    
  L1M4_orf2#LINE/    494 GGATCAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAA 543

  chr20_60847825_   3414 AACATAGAAGAAAAGCTTCTTGACATTGGTCTTGGCAGTGATTTTTT--- 3460
                                i? v   v    v    v    vi v    i  i   i  ---
  L1M4_orf2#LINE/    544 AACATAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGA 593

  chr20_60847825_   3461 TATGACAGCAAAAACACAGGCAACAAAAGCAACA-----TAAATGAGACT 3505
                                v     i    i          v  v -----     vi    
  L1M4_orf2#LINE/    594 TATGACACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACT 643

  chr20_60847825_   3506 ACATTAAAATGAAAAGTCTCTGCACAGCAAAAGAAAC----AGCAAAACG 3551
                         v   i     v    iii i  ii vv    i  v  ---- iv   ii 
  L1M4_orf2#LINE/    644 TCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTG 693

  chr20_60847825_   3552 AAAAGGCAGTCTCTACAAAATGGGAGAAAA-------------------- 3581
                              i  ii i--   i            --------------------
  L1M4_orf2#LINE/    694 AAAAGACAACCC--ACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_60847825_   3582 -------------------------------------------------- 3581
                         --------------------------------------------------
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_60847825_   3582 -----------ATAACCCA-TTTAAAAATGGAAAAGGGGCCTGAGTAGAC 3619
                         -----------        -  ?        iv  i  iii   i     
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_60847825_   3620 ATTTTTCCAAAGAAGAGCTACATATGGCCAATGGGTTTCTGAAAAGGTGC 3669
                             i           vv    v         ii iviv       i   
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGC 891

  chr20_60847825_   3670 TCAACACCACTAGTCAT 3686
                               i  ????????
  L1M4_orf2#LINE/    892 TCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (52 / 28)
Gap_init rate = 0.02 (7 / 463), avg. gap size = 14.00 (98 / 7)  


3878 18.35 6.94 0.71  chr20_60858158_60859984.rev      501  1350 (477)    L1M4_orf2#LINE/L1        6   908 (0)  

  chr20_60858158_    501 AGACATCCCATGTTCATGGATTGGAAGATTTAATATTGTTAAGGTGTCAG 550
                            i                        i              i  v  i
  L1M4_orf2#LINE/      6 AGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAA 55

  chr20_60858158_    551 TACTACCCAAAGCACTCTACAGATTCAATGCAATCCGTATCAAATTTCAA 600
                             v      viiv             i       v       v i v 
  L1M4_orf2#LINE/     56 TACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCA 105

  chr20_60858158_    601 GAATGC--TTTTGGCAGAAATAGAAAAATCTG-TGCTAAAATTCATATGA 647
                          v-   --    v        v  v  i-   - v              i
  L1M4_orf2#LINE/    106 GC-TGCCTTTTTTGCAGAAATTGACAAG-CTGATCCTAAAATTCATATGG 153

  chr20_60858158_    648 AATCTCAAAGGATCCCGGACAGCCAAAACAATCTTGTAA--GAA-AATAA 694
                           viv   i   i  v i i                v  --   -  i  
  L1M4_orf2#LINE/    154 AAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 203

  chr20_60858158_    695 AGTTGGAGGTCTTACACTTCTTGATTTCAAAACTTACTACAAAGTTACAG 744
                                  v  i       iii                     i     
  L1M4_orf2#LINE/    204 AGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAG 253

  chr20_60858158_    745 T------------GTGGTGCTGGCATAAAGATAGACACGTAGACCAAGGG 782
                          ------------     i         i        ii    i   v  
  L1M4_orf2#LINE/    254 TAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGG 303

  chr20_60858158_    783 AATAGACTAGAAATCTCAGAAACGAACCCTTACCTTTATGGTCAAGTGAT 832
                               v v  i vii      ii     v   v           v    
  L1M4_orf2#LINE/    304 AATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGAT 353

  chr20_60858158_    833 CTTCA---------CCAAGACCATTCAGTGGGGAAAGGACAGTCTATTCA 873
                         i   i---------             i         i i     v    
  L1M4_orf2#LINE/    354 TTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCA 403

  chr20_60858158_    874 ACAAAGGGTGTTAGGAAAACGGGACATCCACTTGTA------TGAAGGTG 917
                              v    i i   v   v   i ?    v  i ------     v  
  L1M4_orf2#LINE/    404 ACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTG 453

  chr20_60858158_    918 GATCCTCCCCTCACACCATATACAAAAATGGACTTGAAGTGGATTAAAGA 967
                           i  iiv                     vi   ii  i     i ?   
  L1M4_orf2#LINE/    454 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGA 503

  chr20_60858158_    968 CCTGAACATAAGAACTAAAACCATAAAACTCCTAGGAGAAAACATAATTA 1017
                            i  ii     i       i         i   i          iv?i
  L1M4_orf2#LINE/    504 CCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNG 553

  chr20_60858158_   1018 -----CTTTACAACATTGATTTTGGCAATGATTTCTTGGGTATGACACCA 1062
                         -----   iiii  v   iv  v       i      i i          
  L1M4_orf2#LINE/    554 TAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCA 603

  chr20_60858158_   1063 AAAGCACAGGCCACAAAAGAAAAAAGTAGATAAATTGAACAACATAAACA 1112
                                 i  v             -           i  vv   v  v 
  L1M4_orf2#LINE/    604 AAAGCACAAGCAACAAAAGAAAAAA-TAGATAAATTGGACTTCATCAAAA 652

  chr20_60858158_   1113 CTGAA--TTTCTGTGTATCAAAGGATGCCATCAGGAGAGTGGAA-GTCAG 1159
                         i i  --i  i    iv        ii i    i  i    i  - v  i
  L1M4_orf2#LINE/    653 TTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAGACAA 702

  chr20_60858158_   1160 CTCACAAAAAAGGAGAAAATATTTGCAAATCACAT--CTGATAATGAGTT 1207
                          i    i  vi                     i  --       v iii 
  L1M4_orf2#LINE/    703 CCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGGGACT 752

  chr20_60858158_   1208 AACCTTGAGAGTATA------ACTCCTAAAACTCAACA-TGAAAA--CAA 1248
                         viiv iv   i    ------    i  v       i - i    --   
  L1M4_orf2#LINE/    753 TGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAA 802

  chr20_60858158_   1249 ACAATCCAATTCACAAATGGGCAAAGGACTC----AGACATTTCTCCAAA 1294
                          i  i      ? v              i i----               
  L1M4_orf2#LINE/    803 ATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAA 852

  chr20_60858158_   1295 GAAGATA--CAAATGGTCAACAAGCACATGAAA-GATGTTATTAATCATT 1341
                                --       i   i            -    i --i  -   i
  L1M4_orf2#LINE/    853 GAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCT--CAA-CATC 899

  chr20_60858158_   1342 AATCTTAAA 1350
                          ????????
  L1M4_orf2#LINE/    900 AZZZZZZZZ 908

Transitions / transversions = 2.04 (102 / 50)
Gap_init rate = 0.02 (22 / 903), avg. gap size = 2.95 (65 / 22)  


2896 20.62 2.27 0.32  chr20_61139944_61142941.rev      985  1600 (1398)    L1M4_orf2#LINE/L1        1   628 (280)  

  chr20_61139944_    985 TGGAAAGTCA-CCCGTGTTCACAGACTGGAGGACTTACTGTTGTTAAGAT 1033
                                vi -   i      ii  i    i      v i          
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_61139944_   1034 GAGAGTACTACTCAAAACAATCCACAGATTCAACGTCATCCTTATCAAAA 1083
                          iv i    v i    vii   i            iv    i        
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_61139944_   1084 TCCCAACAGCAATTTTTGCAAAAATTGAAAACCTTTATCCTAAAATTCAT 1133
                              i v  vv        i       v  v  -v              
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCT-GATCCTAAAATTCAT 149

  chr20_61139944_   1134 ATAGAACTTC-CGGAACCCTAAATAGCCCAAACGATCTTGAAAACGAAGA 1182
                           i   v v -v  i    vi       v    i          v     
  L1M4_orf2#LINE/    150 ATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_61139944_   1183 ACAAACTTGGAGAACTCACGTTTTCTGATTTCAAAACTTACTCATAAAGC 1232
                              v      i      ii  i ii               - i     
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACT-ACAAAGC 248

  chr20_61139944_   1233 TACAGTCATCAAGATAATGTGCTGCTGGTAAAAGGATGGATGTAGAGGCC 1282
                               v       i i    v i    i v      i  ii  v  ii 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_61139944_   1283 AATGGAGTAGAACAGAGAACCCCCATATGAACCCCCATATACATGGTCCA 1332
                               i     iv    ii  vv v  i     vi i  vi      v 
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_61139944_   1333 TTGACTTTCAATAAGGG-ACCAACACCA----GTGAGGAAAGGGCAGCCT 1377
                             i    i i     -i    v    ----i  i      iii  i  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_61139944_   1378 CCTCAACAAACGATGCTGGGAAAAAGGTATTTACACATGCAAAACAATGA 1427
                         ii        i i        v  vv v  v?v           v     
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGA 448

  chr20_61139944_   1428 AGTTGGACATTTATCTTACAACATATACAAAAATTAACATGAAATGGATC 1477
                                 vii  i  i   v                 vii         
  L1M4_orf2#LINE/    449 AGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATC 498

  chr20_61139944_   1478 AAAGACCTAAATGTAAGAGCTAAAACTATAAAACGCTTAGAAGAAAACAT 1527
                          ?                                v               
  L1M4_orf2#LINE/    499 AWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT 548

  chr20_61139944_   1528 AGGGGCAAATTATCACGACCTTCAACATGGCAATGGT-------AAATGG 1570
                            ? i    iv  ii      viiivv         ------- v   i
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_61139944_   1571 CACAGAAAGCATAGGCAACAAAAGAAAAAA 1600
                            vi      i i                
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAA 628

Transitions / transversions = 1.58 (76 / 48)
Gap_init rate = 0.01 (7 / 628), avg. gap size = 2.29 (16 / 7)  

 395 15.66 2.41 0.00  chr20_61139944_61142941.rev     1908  1990 (1008)    L1M4_orf2#LINE/L1      620   704 (204)  

  chr20_61139944_   1908 AACAGAAAACAGATAAATTGGA-TTCATCAAAATTAAA-GTTGTTCTGCA 1955
                           v i    i            -               -ii v  v   v
  L1M4_orf2#LINE/    620 AAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCT 669

  chr20_61139944_   1956 TTAAAAGACACTATCAAGAAAGTGAAACGTCAGCC 1990
                          i   i                     v v  i  
  L1M4_orf2#LINE/    670 TCAAAGGACACTATCAAGAAAGTGAAAAGACAACC 704

Transitions / transversions = 1.17 (7 / 6)
Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.00 (2 / 2)  

1182 12.04 4.17 0.46  chr20_61139944_61142941.rev     2291  2506 (492)    L1M4_orf2#LINE/L1      685   908 (0)  

  chr20_61139944_   2291 AAGAAAGTGAAACGTCAA-CCACAGAGTGGGAGAAAATATTTGCAAATCA 2339
                                     v v   -       i                       
  L1M4_orf2#LINE/    685 AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 734

  chr20_61139944_   2340 TATATCTGATAAGGGTTTTAATACCCAGGATTTATAAAGAACTGCTACAC 2389
                                        vi  -i  i    i  v           vi    v
  L1M4_orf2#LINE/    735 TATATCTGATAAGGGACTT-GTATCCAGAATATATAAAGAACTCTTACAA 783

  chr20_61139944_   2390 TTCAACAACAAAAA-------AATTCCATTTAAAAATAGGCAAAGGACTC 2432
                         i    i  i     -------  ii v   ?      i         i i
  L1M4_orf2#LINE/    784 CTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTT 833

  chr20_61139944_   2433 GAATAGATGTTTCTCCAAATAAGATATA-AAATGGCCAATAAGCACATGA 2481
                                ii          v        -                     
  L1M4_orf2#LINE/    834 GAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGA 883

  chr20_61139944_   2482 AAAGATGCTCAACAGCACTCACTGG 2506
                                       v  ????????
  L1M4_orf2#LINE/    884 AAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.78 (16 / 9)
Gap_init rate = 0.02 (4 / 224), avg. gap size = 2.50 (10 / 4)  


4381 18.33 2.94 0.23  chr20_61210015_61212965.rev     1577  2460 (491)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_61210015_   1577 TGGAAAGATATCTCATGTTCATGGATTGGGGGCCTTAATATT---AAGAT 1623
                                     i                ii v         ---     
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_61210015_   1624 GGCAATATTATCCGTAATGATCTACAGACTCAATGCAACCTCTATCAAAA 1673
                                i vi  iv v           i    i    i i         
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_61210015_   1674 TTCCAA--GGATCATTTGCAGAAAATGAAAACCCAATCCTCAAATTTATA 1721
                          i   i-- vv iv          v   v  v ii     v     i   
  L1M4_orf2#LINE/    101 TCCCAGCTGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATA 150

  chr20_61210015_   1722 TGAAATTTCAAGGAGATTCA-AGTGGCCAAAACAATCTTGAAAGAGGAGA 1770
                           i  v v     -  ii  - i i                  i  i   
  L1M4_orf2#LINE/    151 TGGAAATGCAAGG-GACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGA 199

  chr20_61210015_   1771 AAAAAAT-GGAGGACTGATATTTTCTAATTTCAAAACTTAGAACAAAGCC 1819
                          v   i -        v i i  i i              vv       i
  L1M4_orf2#LINE/    200 ACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCT 249

  chr20_61210015_   1820 ACAGTAGTCAAAATAGTATGATGCGGTCATCAAGATAGACATATAGACCA 1869
                               i    i i   i  i i v v   v i              i  
  L1M4_orf2#LINE/    250 ACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCA 299

  chr20_61210015_   1870 ATAGCATAGAATCTAT--TTCAGAGA-AAGCCTATATATCTATGGCCAAC 1916
                           i v       iv v-- i    i -  i  i   i  i     i   i
  L1M4_orf2#LINE/    300 ATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAAT 349

  chr20_61210015_   1917 TGATTTTCAACAAATGTGCCAAGACAATTCAATAGAGAAAGAATAATCTC 1966
                                 i    iv          v       i i         i   i
  L1M4_orf2#LINE/    350 TGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTT 399

  chr20_61210015_   1967 CTCAACAAATGGTGCTGAGACAACTATATATTCACAAGCAAAAAAA---A 2013
                         i                i       iv   ?i    v      i  --- 
  L1M4_orf2#LINE/    400 TTCAACAAATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAA 449

  chr20_61210015_   2014 AT----CATTTACCTCACACAATATACAAAAATAAACTCAAAATGTGTCA 2059
                         i ---- vii          v            v           vi   
  L1M4_orf2#LINE/    450 GTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCA 499

  chr20_61210015_   2060 AATATCTTAATGTAAGAGCTAAAACTATAAAACTC--AGAGTAAAATGTT 2107
                         ? v i  v                           --   iv    ii -
  L1M4_orf2#LINE/    500 WAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACAT- 548

  chr20_61210015_   2108 AGAGGTAAATCTTTATGACCTTGGATGTGGTAATGAACTCTTAGATAAGA 2157
                           i?         ii         i vv  i    ivi         v  
  L1M4_orf2#LINE/    549 AGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGA 598

  chr20_61210015_   2158 CACCAAAAGCACGAACAAGACAAGAAAAAA------AATTCAGTTTCATC 2201
                                     i i   v v         ------    viii      
  L1M4_orf2#LINE/    599 CACCAAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGACTTCATC 648

  chr20_61210015_   2202 AAAATTAAAAACTTTTGTGCATCAAGGGGTATTATCAAGAAAGTAAAAAG 2251
                                             v    i  ii i            i     
  L1M4_orf2#LINE/    649 AAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAGTGAAAAG 698

  chr20_61210015_   2252 ACAATCTATAGAATTGGAGAAAATATTTGTCAATCACATATTTGATAAGA 2301
                             i i i     v              iv     i    i       i
  L1M4_orf2#LINE/    699 ACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCTGATAAGG 748

  chr20_61210015_   2302 GACTCAGGTCTAGAATGTTTAAATAATTCTTATAACTCAACAACAAAAAG 2351
                             iivi  i     i v    v  i     i       i  i      
  L1M4_orf2#LINE/    749 GACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAG 798

  chr20_61210015_   2352 ACAGACAACCCAACT-ATAAATGAGCAAAGGACTTGAATAGACCTTTCTC 2400
                            i i       i - v     i        i          v      
  L1M4_orf2#LINE/    799 ACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGACATTTCTC 848

  chr20_61210015_   2401 CAAAGAAGATATACAAATGGCCAATAAGCCTGTGAGAAGATGTTCAACAT 2450
                                                      vii   i      i       
  L1M4_orf2#LINE/    849 CAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACAT 898

  chr20_61210015_   2451 CTTTAGTCAT 2460
                          v????????
  L1M4_orf2#LINE/    899 CAZZZZZZZZ 908

Transitions / transversions = 2.12 (108 / 51)
Gap_init rate = 0.01 (13 / 908), avg. gap size = 2.15 (28 / 13)  


 314 28.74 9.77 2.87  chr20_61611445_61613702.rev      493   666 (1592)    L1M4_orf2#LINE/L1      255   440 (468)  

  chr20_61611445_    493 AAACAAGACAGTGAGGTCTTGG--TGAGGAGACAGATACAGACATCAGTG 540
                           v          v   vi   -- i    v v v   i   --   i  
  L1M4_orf2#LINE/    255 AATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGA--TCAATG 302

  chr20_61611445_    541 TAACAGGAT--GGAGTCCAGAGACAGCCTCACACAAATGTGACCAAATG- 587
                         v  i  i  --i         i i iv i  i   vv i  ii   v  -
  L1M4_orf2#LINE/    303 GAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGA 352

  chr20_61611445_    588 TTCTCGGAGAAAGGCACTACAGTGATTTGACAGAGCAAGTATCATCTTTT 637
                           i   - v  i  ii i viiiv   ii ii i v   v  vi      
  L1M4_orf2#LINE/    353 TTTTCG-ACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTT 401

  chr20_61611445_    638 C---------TGCCGGGCACAG-TGGCT--CACGCATGCAA 666
                          ---------   i   -   i-   v -- - i       
  L1M4_orf2#LINE/    402 CAACAAATGGTGCTGGG-ACAACTGGATAKC-CACATGCAA 440

Transitions / transversions = 1.78 (32 / 18)
Gap_init rate = 0.05 (10 / 186), avg. gap size = 2.20 (22 / 10)  

1148 22.31 4.75 11.16  chr20_61611445_61613702.rev      909  1392 (866)    L1M4_orf2#LINE/L1      377   829 (79)  

  chr20_61611445_    909 TTCAA-AAAAAAAGAGTATAATCTTTTCAACAAATGGTGCTGGAAGAATT 957
                              -iiii     --   i                      i v  i 
  L1M4_orf2#LINE/    377 TTCAATGGGGAAAGA--ATAGTCTTTTCAACAAATGGTGCTGGGACAACT 424

  chr20_61611445_    958 TGACATTCACATGCAAAAAAAAAAAAAAAACAAAACAACAACAACAAAAA 1007
                         v  i ?i           i  vi  i------------------------
  L1M4_orf2#LINE/    425 GGATAKCCACATGCAAAAGAATGAAG------------------------ 450

  chr20_61611445_   1008 ACAACCAACCAAACAAAAACCTTGACCTAAATCTCACATATTATACAAAG 1057
                         --------------------i v    ivv i      ivv        i
  L1M4_orf2#LINE/    451 --------------------TTGGACCCCTACCTCACACCATATACAAAA 480

  chr20_61611445_   1058 ATTAACTATACAAATGGATAATGTATCTAAATATAAAATGTAAA-CTATA 1106
                                -i -        v ?iv i      i   i vv    -     
  L1M4_orf2#LINE/    481 ATTAACT-CA-AAATGGATCAWAGACCTAAATGTAAGAGCTAAAACTATA 528

  chr20_61611445_   1107 AAACATCTAGAAGAAAGTACAAGAGATAATCTTTGTGACCT-GAGC-AGC 1154
                             vii         ii i i ? vv      i       - i i-  v
  L1M4_orf2#LINE/    529 AAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACCTTGGGTTAGG 578

  chr20_61611445_   1155 CAAT-----------------ATTAAAAGCATGATCCACTTAAGAAAAAT 1187
                             ----------------- ii       ii v v  vv        -
  L1M4_orf2#LINE/    579 CAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACAAAAGAAAAA- 627

  chr20_61611445_   1188 ATGGATAAACTGGGCTTCACTGAAATAAAAAACTT--GTATTGTGAATGA 1235
                           i      i   i     iii    v        --  ii vii  v  
  L1M4_orf2#LINE/    628 ATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGA 677

  chr20_61611445_   1236 TCCTGTTAAGAGATTAGAAAGACAAGCCACAGACTTGGAGAAAATATGTG 1285
                         iv  i i    i v ii        v       v v           v  
  L1M4_orf2#LINE/    678 CACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATATTTG 727

  chr20_61611445_   1286 CAAGTCACAGAACTGACAAAGGACTTGTATCCACAATACATAGAAAACTC 1335
                            i   i v v    i  i             v    i   i i     
  L1M4_orf2#LINE/    728 CAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAGAACTC 777

  chr20_61611445_   1336 TCAAGACTCAACACCAAAAAATAAAAATAAACAATTCAATTGAAAACTTG 1385
                          i vi      i vi     i----- i   i  ii     ?    v v 
  L1M4_orf2#LINE/    778 TTACAACTCAATAATAAAAAG-----ACAAATAACCCAATTWAAAAATGG 822

  chr20_61611445_   1386 GCCAAGG 1392
                           v    
  L1M4_orf2#LINE/    823 GCAAAGG 829

Transitions / transversions = 1.81 (67 / 37)
Gap_init rate = 0.03 (12 / 453), avg. gap size = 6.42 (77 / 12)  

 392 21.28 0.00 0.00  chr20_61611445_61613702.rev     1684  1777 (481)    L1M4_orf2#LINE/L1      815   908 (0)  

  chr20_61611445_   1684 AAAAAAAAGTCAAGGATTTGAATAGACATTTCTGCAAAAAAGACATGCAA 1733
                              vii iv                      v    i    i  i   
  L1M4_orf2#LINE/    815 AAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAA 864

  chr20_61611445_   1734 ATGGCTAAAAGGTACATGAAAAGATCCATAGGGTTAGTCATTAG 1777
                              i  v i i            v vi ivi i ????????
  L1M4_orf2#LINE/    865 ATGGCCAATAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.00 (0 / 0)  


2389 20.51 6.23 0.55  chr20_62284904_62286961.rev      500  1045 (1013)    L1M4_orf2#LINE/L1      108   684 (224)  

  chr20_62284904_    500 TGTTCTGTTTGCAAAAACTGACAAACTCATTCTAAAAATTTGTATGGCAA 549
                           iii v      i   i      i  v  i      -  ii     v  
  L1M4_orf2#LINE/    108 TGCCTTTTTTGCAGAAATTGACAAGCTGATCCTAAAA-TTCATATGGAAA 156

  chr20_62284904_    550 TTCAAGGAATATAGACTAGTCAAAACAATTCTGAAAAAGAG---CAAAGT 596
                          v     i ivi   v   i         ii         i---      
  L1M4_orf2#LINE/    157 TGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGT 206

  chr20_62284904_    597 TGGACGAC--ACACTTCTCAGTTTCCAAACTTACTACAAAGCTGCAGTAA 644
                             v   --       i  i    v                 i      
  L1M4_orf2#LINE/    207 TGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAA 256

  chr20_62284904_    645 TCAAGGCAATGTGTTACTAGCATCAGGACGGGCATATGGATAAGTGGGAC 694
                              i  i    v    i    v    ii i     i   v i   i i
  L1M4_orf2#LINE/    257 TCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATCAATGGAAT 306

  chr20_62284904_    695 ATAATTGAGAGTCCAGAAGTAACCCCCTCTATTAATGATCAATTGATTTT 744
                          v                i   v   v vi   v   i            
  L1M4_orf2#LINE/    307 AGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAATTGATTTT 356

  chr20_62284904_    745 TGACAATGGCACAAAAACAATTTAATGGGAAAAAAACTGTCTTTTCAACA 794
                         i     v  ii v  i  v   i      i   i  iv            
  L1M4_orf2#LINE/    357 CGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACA 406

  chr20_62284904_    795 AACG-TGCCAGGACAACTAGATATCAAAA---AAAAAAATGAAGTTGGAC 840
                           i -   ii        i    ? v v ---    i             
  L1M4_orf2#LINE/    407 AATGGTGCTGGGACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGAC 456

  chr20_62284904_    841 CTCT--CTCA-----------AAAATTAGCTCGCACTGGATCACATATGT 877
                          i  --    -----------       i   iv v       ? v iv 
  L1M4_orf2#LINE/    457 CCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAWAGACCT 506

  chr20_62284904_    878 AAATGTAAGAACCAAAACT--------CCTAGAA---AACACCGCGGTAA 916
                                   i i      -------- i     ---    iv v?    
  L1M4_orf2#LINE/    507 AAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAA 556

  chr20_62284904_    917 ATCTTTCCGACTCTGGGTTCAGCAATGGTTTCTTAGCTATGACAACAACA 966
                              ivi   ii      vi               v       v   v 
  L1M4_orf2#LINE/    557 ATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAA 606

  chr20_62284904_    967 CTACAAGCCATTAAAGAAAAAA-AGTAATATATTGGACTTCAACAAGGTT 1015
                         vi      v iv          -  --   v           v   ii  
  L1M4_orf2#LINE/    607 GCACAAGCAACAAAAGAAAAAATAG--ATAAATTGGACTTCATCAAAATT 654

  chr20_62284904_   1016 TAAAACTTTCGGAGTTAAAATAACACTGTC 1045
                         v        i viv  v   vi     i  
  L1M4_orf2#LINE/    655 AAAAACTTTTGTGCTTCAAAGGACACTATC 684

Transitions / transversions = 1.53 (66 / 43)
Gap_init rate = 0.02 (11 / 577), avg. gap size = 3.36 (37 / 11)  

1157 15.35 3.51 0.00  chr20_62284904_62286961.rev     1342  1569 (489)    L1M4_orf2#LINE/L1      673   908 (0)  

  chr20_62284904_   1342 AATAACACTATCAATATGGTGAAAAGACAACCCAAAGACTGGGAGAAAAT 1391
                           vi          v vi                v   v           
  L1M4_orf2#LINE/    673 AAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAAT 722

  chr20_62284904_   1392 ATTTGCAAATCGTAAATCTGATAAAGAGCTTGTATTTGGAA---A-AAAG 1437
                                    i  v         i ii       iii   --- -    
  L1M4_orf2#LINE/    723 ATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATATAAAG 772

  chr20_62284904_   1438 AACTCTCATAACTCA-TAATAA---GACAAATAACCCAATTTTAGAATGA 1483
                               i i      -      ---                ?v i    i
  L1M4_orf2#LINE/    773 AACTCTTACAACTCAATAATAAAAAGACAAATAACCCAATTWAAAAATGG 822

  chr20_62284904_   1484 GCAGAGGACTTGAACAGACATTTCTCCAAAGATAACACGGGAATGGCCAA 1533
                            i    i     i                 vi i iivi         
  L1M4_orf2#LINE/    823 GCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAA 872

  chr20_62284904_   1534 TAAGCACATGAAGAGATGCCCAACAGCTAGTAATCC 1569
                                     i      i     v v????????
  L1M4_orf2#LINE/    873 TAAGCACATGAAAAGATGCTCAACATCAZZZZZZZZ 908

Transitions / transversions = 2.09 (23 / 11)
Gap_init rate = 0.02 (4 / 236), avg. gap size = 2.00 (8 / 4)  


2876 26.17 2.23 1.11  chr20_62433612_62435964.rev      964  1861 (492)    L1M4_orf2#LINE/L1        1   908 (0)  

  chr20_62433612_    964 TGGAAACATACCCCATGCTCATGAATGAATAGAATCAATATTGTGAAAAT 1013
                               v   i      i     i  viiv   v i        v  i  
  L1M4_orf2#LINE/      1 TGGAAAGATATCCCATGTTCATGGATTGGAAGACTTAATATTGTTAAGAT 50

  chr20_62433612_   1014 GACCATACTGCCAAAAGCAATCTATAAATTCAATGCAATTCTCATCAAAA 1063
                          i v     v  v   vii     i i      i     i ii       
  L1M4_orf2#LINE/     51 GGCAATACTCCCCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAA 100

  chr20_62433612_   1064 TATCA-TTATCATTCTTCACAGAACTAGAAAAAAAAAACCCTTAAATTTA 1112
                          vi  -i ii -  i  ii     v v  v  ivvi -i   v     i 
  L1M4_orf2#LINE/    101 TCCCAGCTGCC-TTTTTTGCAGAAATTGACAAGCTGA-TCCTAAAATTCA 148

  chr20_62433612_   1113 TATGGAA---CAAAAGAGCCCACATAGCCAAACCAAGAGTAAAGAAAAAG 1159
                                ---   ii  v  viv         v   vvv i  i  i   
  L1M4_orf2#LINE/    149 TATGGAAATGCAAGGGACCCAGAATAGCCAAAACAATCTTGAAAAAGAAG 198

  chr20_62433612_   1160 AACAAATCTGGAGGCATCACATTACCTGACTTCAAACTATACTACCAGGC 1209
                               vi      vv     i v  ii i      viv      v i  
  L1M4_orf2#LINE/    199 AACAAAGTTGGAGGACTCACACTTCCCAATTTCAAAACTTACTACAAAGC 248

  chr20_62433612_   1210 TATCATCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACC 1259
                           ivi v i   i    ii         i    ii    i  i     i 
  L1M4_orf2#LINE/    249 TACAGTAATCAAGACAGTGTGGTACTGGCATAAGGATAGACATATAGATC 298

  chr20_62433612_   1260 AATGGAAGAGACTAGCAATCCCAGAAATAAAGCCAAATATTTACACCCAA 1309
                                v   v v vi vi           v   v i     iivi   
  L1M4_orf2#LINE/    299 AATGGAATAGAATTGAGAGTCCAGAAATAAACCCATACATTTATGGTCAA 348

  chr20_62433612_   1310 CTGATCTTTGACAAAGCAAATGAGAACATAAAGTAGGGAAAGGACACACT 1359
                         i    i  i     i vvivii   v   vv i i       i i vv  
  L1M4_orf2#LINE/    349 TTGATTTTCGACAAGGGTGCCAAGACCATTCAATGGGGAAAGAATAGTCT 398

  chr20_62433612_   1360 ATTCAACAGGTGGTGCTGGGAATGATTGGCTAGCCACATGTAGAAGAATA 1409
                         v       ii           -ii i   v  ?       i i      i
  L1M4_orf2#LINE/    399 TTTCAACAAATGGTGCTGGGA-CAACTGGATAKCCACATGCAAAAGAATG 447

  chr20_62433612_   1410 AATCTGCATACTCATCTCTCACCTTATACAAAAATCAATTCAAGATGAAT 1459
                           vi  v iv ii i   v    v           i  i    i   i  
  L1M4_orf2#LINE/    448 AAGTTGGACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGAT 497

  chr20_62433612_   1460 CAAATACTTAAATCTAAGACCTGAAATCATAAAAATTCTAAAAGATAACA 1509
                           ? v  i     v     v  i   ii      v ii  i    v    
  L1M4_orf2#LINE/    498 CAWAGACCTAAATGTAAGAGCTAAAACTATAAAACTCTTAGAAGAAAACA 547

  chr20_62433612_   1510 TTGGAAAAACTCTTCTAGACATTGGCTT-GGCAAAGAGTTC------ATG 1552
                          v  ?iv  v     vv   v    v  -     v iv   ------   
  L1M4_orf2#LINE/    548 TAGGNGTAAATCTTCGTGACCTTGGGTTAGGCAATGGTTTCTTAGATATG 597

  chr20_62433612_   1553 ACCAACAACCTAAAAGCAAATGCAACAAAG--ATAAATAGA-A----GGA 1595
                           -----   -       v v        i-- v       - ----   
  L1M4_orf2#LINE/    598 AC-----ACC-AAAAGCACAAGCAACAAAAGAAAAAATAGATAAATTGGA 641

  chr20_62433612_   1596 CTTAATTAAACTAGAAAGCTTCTGCACAGCACAAGAAATAATCAGCAGAG 1645
                            v  i   v vi   i   i  ii vv  v i  v iv    iv i  
  L1M4_orf2#LINE/    642 CTTCATCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTATCAAGAAAG 691

  chr20_62433612_   1646 TAAACAGACAACCCACAGAGTGGGGGAAATT-TTCACAAACTATGCATCC 1694
                          i  v              i    i    v -  ii    ii  ii   i
  L1M4_orf2#LINE/    692 TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCATATATCT 741

  chr20_62433612_   1695 AACACAGGTCTAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAA 1744
                         i i vi  v  vi          v  i  i      vv    v   ii  
  L1M4_orf2#LINE/    742 GATAAGGGACTTGTATCCAGAATATATAAAGAACTCTTACAACTCAATAA 791

  chr20_62433612_   1745 GAAAAAAACAAATAATCCCATCAAAAAGTGGGCTAAGGACATAAATA-AC 1793
                         v     i        i  v  i?    i     v     iv i    -  
  L1M4_orf2#LINE/    792 TAAAAAGACAAATAACCCAATTWAAAAATGGGCAAAGGATTTGAATAGAC 841

  chr20_62433612_   1794 AATTCTCAAAAGAATATATACAAATGGCCAACAAACATATGAAAAAAATG 1843
                          v     v      v                i  i  i       i -  
  L1M4_orf2#LINE/    842 ATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGA-TG 890

  chr20_62433612_   1844 CTCAACATCACTAATGAT 1861
                                   ????????
  L1M4_orf2#LINE/    891 CTCAACATCAZZZZZZZZ 908

Transitions / transversions = 1.38 (134 / 97)
Gap_init rate = 0.02 (15 / 908), avg. gap size = 2.00 (30 / 15)  


10308 matching entries (first file).

Discrepancy summary:
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)

